← return to the list of all guides

Micro-homology scoring of potential deletions

Guide: GCCGAGTCCTTAGGCCGCCA GGG

The following table lists possible deletions. Each sequence below represents the context around the guide's target, with deleted nucleotides shown as "-". They are ranked by the "micro-homology score". This score is correlated to the likelihood of finding a particular deletion, as predicted by the method of Bae et al. 2014.

Bae-Score Sequence Effect
GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGCCAGGGGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC (Wild-type sequence)
485.6 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGCC----------GGCGCGCGCCCAGATTGGGGACAAAGGAAGC 10 bp deleted → frameshift
417.6 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCG-------------GCGCGCGCCCAGATTGGGGACAAAGGAAGC 13 bp deleted → frameshift
346.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGC-----------GCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 11 bp deleted → frameshift
329.4 GCCCTGGCCACTTCCGGCGCGC----------------------------------GCCCAGATTGGGGACAAAGGAAGC 34 bp deleted → frameshift
327.6 GCCCTGGCCACTTCCGGCGCGCCG--------------------------GCGCGCGCCCAGATTGGGGACAAAGGAAGC 26 bp deleted → frameshift
294.4 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGCC--------------------CAGATTGGGGACAAAGGAAGC 20 bp deleted → frameshift
269.4 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGC----------------GCGCCCAGATTGGGGACAAAGGAAGC 16 bp deleted → frameshift
268.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGC--------GCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 8 bp deleted → frameshift
268.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG--------GGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 8 bp deleted → frameshift
256.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGC-----------------GCGCGCCCAGATTGGGGACAAAGGAAGC 17 bp deleted → frameshift
255.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG---------GGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 9 bp deleted → no frameshift
247.0 GCCCTGGCCACTTCCGGCGC----------------------------CGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 28 bp deleted → frameshift
244.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGC------------------GCCCAGATTGGGGACAAAGGAAGC 18 bp deleted → no frameshift
242.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG----------GCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 10 bp deleted → frameshift
231.0 GCCCTGGCCACTTCCGGCGCGCC------------------------------------CAGATTGGGGACAAAGGAAGC 36 bp deleted → no frameshift
198.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGC--------------GCGCGCCCAGATTGGGGACAAAGGAAGC 14 bp deleted → frameshift
190.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCC-----------------------CAGATTGGGGACAAAGGAAGC 23 bp deleted → frameshift
175.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGCCA---------------------GATTGGGGACAAAGGAAGC 21 bp deleted → no frameshift
161.6 GCCCTGGCCACTTCCGGCGCGC--------------------------------GCGCCCAGATTGGGGACAAAGGAAGC 32 bp deleted → frameshift
154.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGC-------------------GCGCCCAGATTGGGGACAAAGGAAGC 19 bp deleted → frameshift
147.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCC--------------------GGCGCGCGCCCAGATTGGGGACAAAGGAAGC 20 bp deleted → frameshift
140.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGC---------------------GCCCAGATTGGGGACAAAGGAAGC 21 bp deleted → no frameshift
126.8 GCCCTGGCCACTTCCGGCGCGCCG-----------------------CCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 23 bp deleted → frameshift
120.4 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCC------------------------AGATTGGGGACAAAGGAAGC 24 bp deleted → no frameshift
120.4 GCCCTGGCCACTTCCGGCGCGC------------------------GCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 24 bp deleted → no frameshift
120.0 GCCCTGGCCACTTCCGGCGC--------------------------------------CCAGATTGGGGACAAAGGAAGC 38 bp deleted → frameshift
114.8 GCCCTGGCCACTTCCGG-------------------------GGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 25 bp deleted → frameshift
109.2 GCCCTGGCCACTTCCGG--------------------------GGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 26 bp deleted → frameshift
103.6 GCCCTGGCCACTTCCGG---------------------------GCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 27 bp deleted → no frameshift
94.0 GCCCTGGCCACTTCCGGCGCGCCG-----------------------------CGCGCCCAGATTGGGGACAAAGGAAGC 29 bp deleted → frameshift
94.0 GCCCTGGCCACTTCCGGCGCG-----------------------------GCGCGCGCCCAGATTGGGGACAAAGGAAGC 29 bp deleted → frameshift
90.0 GCCCTGGC--------------------------------------GCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 38 bp deleted → frameshift
89.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCC------------------------------CAGATTGGGGACAAAGGAAGC 30 bp deleted → no frameshift
89.2 GCCCTGGCCACTTCCGGCGCGC------------------------------GCGCGCCCAGATTGGGGACAAAGGAAGC 30 bp deleted → no frameshift
89.2 GCCCTGGCCACTTCCGGC------------------------------CGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 30 bp deleted → no frameshift
84.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCC-------------------------------AGATTGGGGACAAAGGAAGC 31 bp deleted → frameshift
84.8 GCCCTGGCCACTTCCGGCGCGCCG-------------------------------CGCCCAGATTGGGGACAAAGGAAGC 31 bp deleted → frameshift
84.8 GCCCTGGCCACTTCCGGCG-------------------------------GCGCGCGCCCAGATTGGGGACAAAGGAAGC 31 bp deleted → frameshift
84.8 GCCCTGGCCACTTCCG-------------------------------CCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 31 bp deleted → frameshift
81.0 GCCCTGGCC----------------------------------------GGCGCGCGCCCAGATTGGGGACAAAGGAAGC 40 bp deleted → frameshift
76.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG---------------------------------GGACAAAGGAAGC 33 bp deleted → no frameshift
76.8 GCCCTGGCCACTTCCGGCGCGCCG---------------------------------CCCAGATTGGGGACAAAGGAAGC 33 bp deleted → no frameshift
73.2 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG----------------------------------GACAAAGGAAGC 34 bp deleted → frameshift
70.5 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAG-----------------------------ATTGGGGACAAAGGAAGC 29 bp deleted → frameshift
69.6 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG-----------------------------------ACAAAGGAAGC 35 bp deleted → frameshift
69.6 GCCCTGG-----------------------------------GGGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 35 bp deleted → frameshift
66.6 GCCCTGGC--------------------------------------------GCGCGCCCAGATTGGGGACAAAGGAAGC 44 bp deleted → frameshift
66.0 GCCCTGG------------------------------------GGCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 36 bp deleted → no frameshift
62.8 GCCCTGGCCACTTCCGGCGCGCC-------------------------------------AGATTGGGGACAAAGGAAGC 37 bp deleted → frameshift
62.8 GCCCTGGCCACTTCCG-------------------------------------CGCGCCCAGATTGGGGACAAAGGAAGC 37 bp deleted → frameshift
62.8 GCCCTGG-------------------------------------GCGCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 37 bp deleted → frameshift
61.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGG------------------------------------------AAGC 42 bp deleted → no frameshift
60.6 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGCCA--------------------------------AAGGAAGC 32 bp deleted → frameshift
60.0 GCC----------------------------------------------GGCGCGCGCCCAGATTGGGGACAAAGGAAGC 46 bp deleted → frameshift
56.8 GCCCTGGCCACTTCCG---------------------------------------CGCCCAGATTGGGGACAAAGGAAGC 39 bp deleted → no frameshift
54.0 GCCCTGGCCACTTCCGGC----------------------------------------CCAGATTGGGGACAAAGGAAGC 40 bp deleted → frameshift
51.6 GCCCTGGCCACTTCCG-----------------------------------------CCCAGATTGGGGACAAAGGAAGC 41 bp deleted → frameshift
49.5 GCCCTGGCCACTTCCGGCGCGCCGAG------------------------------------ATTGGGGACAAAGGAAGC 36 bp deleted → no frameshift
49.2 GCCCTGGCC--------------------------------------------------CAGATTGGGGACAAAGGAAGC 50 bp deleted → frameshift
48.8 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGCCGC------------------------------------------ 42 bp deleted → no frameshift
48.8 GCCC--------------------------------------------------------AGATTGGGGACAAAGGAAGC 56 bp deleted → frameshift
45.0 GCCCTGGCCACTTCCGGCGCGCCGA--------------------------------------TTGGGGACAAAGGAAGC 38 bp deleted → frameshift
44.4 GCCCTGGCCACTTCC--------------------------------------------CAGATTGGGGACAAAGGAAGC 44 bp deleted → frameshift
44.4 GC--------------------------------------------GCCGGCGCGCGCCCAGATTGGGGACAAAGGAAGC 44 bp deleted → frameshift
42.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAGGC--------------------------------------------- 45 bp deleted → no frameshift
42.0 GCCCTGGCCACTTCC---------------------------------------------AGATTGGGGACAAAGGAAGC 45 bp deleted → no frameshift
42.0 GCCC---------------------------------------------GGCGCGCGCCCAGATTGGGGACAAAGGAAGC 45 bp deleted → no frameshift
40.0 GCCCTGGC----------------------------------------------GCGCCCAGATTGGGGACAAAGGAAGC 46 bp deleted → frameshift
39.0 GCCCTGGCCA---------------------------------------------------GATTGGGGACAAAGGAAGC 51 bp deleted → no frameshift
36.6 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTT----------------------------------GGGGACAAAGGAAGC 34 bp deleted → frameshift
36.4 GCCCTGGC------------------------------------------------GCCCAGATTGGGGACAAAGGAAGC 48 bp deleted → no frameshift
32.8 GCCCTGGCCACTTCCGG--------------------------------------------------GGACAAAGGAAGC 50 bp deleted → frameshift
32.8 GC--------------------------------------------------GCGCGCCCAGATTGGGGACAAAGGAAGC 50 bp deleted → frameshift
31.5 GCCCTGGCCACTTCCGGCGCGCCGA---------------------------------------------CAAAGGAAGC 45 bp deleted → no frameshift
31.2 GCCCTGGCCACTTCCGG---------------------------------------------------GACAAAGGAAGC 51 bp deleted → no frameshift
30.0 GCCCTGGCCACTTCCGGCGCGCCGAGTCCTTAG----------------------------------------------C 46 bp deleted → frameshift
29.6 GCCCTGGCCACTTCCGG----------------------------------------------------ACAAAGGAAGC 52 bp deleted → frameshift
29.6 GC----------------------------------------------------GCGCCCAGATTGGGGACAAAGGAAGC 52 bp deleted → frameshift
26.8 GC------------------------------------------------------GCCCAGATTGGGGACAAAGGAAGC 54 bp deleted → no frameshift
25.8 GCCCTGGCCACTTCCGGCGCGCCGAG-------------------------------------------------GAAGC 49 bp deleted → frameshift
25.6 GCCC-------------------------------------------------------CAGATTGGGGACAAAGGAAGC 55 bp deleted → frameshift
25.0 GCCCTGG------------------------------------------------------------GGACAAAGGAAGC 60 bp deleted → no frameshift
23.2 GCC---------------------------------------------------------AGATTGGGGACAAAGGAAGC 57 bp deleted → no frameshift
22.2 GCCCTGGCCACTTCCGGCGCGCCGA----------------------------------------------------AGC 52 bp deleted → frameshift
22.0 GCCCTGGCCACTTCCGGCGCGC---------------------------------------------------------- 58 bp deleted → frameshift
21.3 GCCCTGGCCACTTCCGGCGCGCCGAG-----------------------------------------------------C 53 bp deleted → frameshift
20.8 GCCCTGGCCACTTCCGG-----------------------------------------------------------AAGC 59 bp deleted → frameshift
20.0 GCCCTGGCCACTTCCGGCGC------------------------------------------------------------ 60 bp deleted → no frameshift
18.8 GCCCTGG-------------------------------------------------------------GACAAAGGAAGC 61 bp deleted → frameshift
18.0 GCCCTGGCCACTTCCGGC-------------------------------------------------------------- 62 bp deleted → frameshift
18.0 GCCCTGG--------------------------------------------------------------ACAAAGGAAGC 62 bp deleted → frameshift
15.0 GCCCTGGCCAC------------------------------------------------------------AAAGGAAGC 60 bp deleted → no frameshift
14.8 GCCCTGGCCACTT----------------------------------------------------GGGGACAAAGGAAGC 52 bp deleted → frameshift
13.5 GCCCTGGCCA--------------------------------------------------------------AAGGAAGC 62 bp deleted → frameshift
12.8 GCCCTGG---------------------------------------------------------------------AAGC 69 bp deleted → no frameshift
10.8 GCCCTGGC------------------------------------------------------------------------ 72 bp deleted → no frameshift
8.0 GC------------------------------------------------------------------------------ 78 bp deleted → no frameshift
Version 4.7 - Documentation  - Contact us - Downloads/local installation - Paper - License
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.