Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 125 of 310
Found at i:40197423 original size:3 final size:3
Alignment explanation
Indices: 40197415--40197440 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40197405 TTATCATTGT
40197415 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40197441 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40202604 original size:33 final size:33
Alignment explanation
Indices: 40202567--40202635 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
40202557 CTTCAGCCGC
40202567 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
1 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
* * *
40202600 CGCATGCCCCTCAGCCTTGGTCACCACGCTCCA
1 CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
40202633 CGC
1 CGC
40202636 GTCTGACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.52, G:0.17, T:0.14
Consensus pattern (33 bp):
CGCATACCCCTCAGCCTTGGCCACCACGCCCCA
Found at i:40203653 original size:215 final size:214
Alignment explanation
Indices: 40203265--40203694 Score: 726
Period size: 214 Copynumber: 2.0 Consensus size: 214
40203255 CGGAGGTGAA
*
40203265 AAACCCTCCTTTTCACTTGCCTTCAACCACCGTCCATGGTGGCCTTAATGGCGGTGGCGATGATG
1 AAACCCTCCTTTTCACTTGCCTTCAACCACCGTCCATGGTGGCCTTAATGGCGGCGGCGATGATG
*
40203330 GGTATGAAGCCCTAGCCAAAAAGAGAGAAATGGGGGAGAAAAGGGGAAGGAGAGAAAGAAAAAAG
66 GGTATGAAGCCCTAGCCAAAAAGAGAGAAATAGGGGAGAAAAGGGGAAGGAGAGAAAGAAAAAAG
40203395 CTTTCTATTTTCTTAAAAAAAAAGGGCTGGAAACAAAAAAAT-AAAAAAGGGGGTTTTAAGTTTT
131 CTTTCTATTTTCTTAAAAAAAAAGGGCTGGAAACAAAAAAATAAAAAAAGGGGGTTTTAAG-TTT
40203459 TTTTAAAAAAAAGAAGGCCTC
195 TTTT-AAAAAAAGAAGGCCTC
40203480 AAACCCTCCTTTTCACTTGCCTTCAACCACCGTCCATGGTGGCCTTAACT-GCGGCGGCGATGAT
1 AAACCCTCCTTTTCACTTGCCTTCAACCACCGTCCATGGTGGCCTTAA-TGGCGGCGGCGATGAT
40203544 -GGTATGAAGCCCTAGCCAAAAAGAGAGAAATAGGGGAGAAAAGGGGAAGGAGAGAAA-ACAAAA
65 GGGTATGAAGCCCTAGCCAAAAAGAGAGAAATAGGGGAGAAAAGGGGAAGGAGAGAAAGA-AAAA
*
40203607 AGCTTTCTGTTTTCTTAAAAAAAAGAGGGGCTGGAAACACAAAATAA-AAAAAAAGGGGGTTTTA
129 AGCTTTCTATTTTCTTAAAAAAAA-A-GGGCTGGAAACA-AAAA-AATAAAAAAAGGGGGTTTTA
40203671 AGTTTTTTTAAAAAAAGAAGGCCT
190 AGTTTTTTTAAAAAAAGAAGGCCT
40203695 GCTTTCTATT
Statistics
Matches: 205, Mismatches: 3, Indels: 13
0.93 0.01 0.06
Matches are distributed among these distances:
213 1 0.00
214 83 0.40
215 62 0.30
216 28 0.14
217 11 0.05
218 20 0.10
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (214 bp):
AAACCCTCCTTTTCACTTGCCTTCAACCACCGTCCATGGTGGCCTTAATGGCGGCGGCGATGATG
GGTATGAAGCCCTAGCCAAAAAGAGAGAAATAGGGGAGAAAAGGGGAAGGAGAGAAAGAAAAAAG
CTTTCTATTTTCTTAAAAAAAAAGGGCTGGAAACAAAAAAATAAAAAAAGGGGGTTTTAAGTTTT
TTTAAAAAAAGAAGGCCTC
Found at i:40203758 original size:83 final size:89
Alignment explanation
Indices: 40203608--40203779 Score: 284
Period size: 85 Copynumber: 2.0 Consensus size: 89
40203598 AAAACAAAAA
*
40203608 GCTTTCTGTTTTCTTAAAAAAAAGAGGGGCTGGAAACACAAAATAAAAAAAAAGGGGGTTTTAAG
1 GCTTTCTATTTTCTTAAAAAAAAGAGGGGCTGGAAACACAAAATAAAAAAAAAGGGGGTTTTAAG
40203673 -TTTTTTT-AAAAAAAGAAGGCCT
66 TTTTTTTTAAAAAAAAGAAGGCCT
*
40203695 GCTTTCTATTTTCTTAAAAAAAA-A-GGGCTGGAAACA-AAAA-AATAAAAAAGGGGGTTTTAAG
1 GCTTTCTATTTTCTTAAAAAAAAGAGGGGCTGGAAACACAAAATAAAAAAAAAGGGGGTTTTAAG
40203756 TTTTTTTTAAAAAAAAGAAGGCCT
66 TTTTTTTTAAAAAAAAGAAGGCCT
40203780 CCACTTTAAC
Statistics
Matches: 81, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
83 20 0.25
84 11 0.14
85 27 0.33
86 1 0.01
87 22 0.27
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (89 bp):
GCTTTCTATTTTCTTAAAAAAAAGAGGGGCTGGAAACACAAAATAAAAAAAAAGGGGGTTTTAAG
TTTTTTTTAAAAAAAAGAAGGCCT
Found at i:40204182 original size:3 final size:3
Alignment explanation
Indices: 40204160--40204235 Score: 89
Period size: 3 Copynumber: 24.3 Consensus size: 3
40204150 TTTTTATTTA
* * * *
40204160 TAT TAT TGT TAG TAT CAT TAT TAT TAT TAT TAT CTCCAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT
40204208 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40204236 CTCTTGTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
3 58 0.94
4 1 0.02
5 1 0.02
6 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:40204274 original size:20 final size:19
Alignment explanation
Indices: 40204237--40204288 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
40204227 ATTATTATTC
40204237 TCTTGTTATA-T-TACTAT
1 TCTTGTTATATTATACTAT
40204254 TCTTGTTATATTATCACTAT
1 TCTTGTTATATTAT-ACTAT
* *
40204274 TTTTCTTACTATTAT
1 TCTTGTTA-TATTAT
40204289 TATTACTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 1 0.03
19 1 0.03
20 11 0.38
21 6 0.21
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (19 bp):
TCTTGTTATATTATACTAT
Found at i:40204605 original size:15 final size:15
Alignment explanation
Indices: 40204585--40204615 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40204575 TATTATTTTC
40204585 TATTTATTACTATTA
1 TATTTATTACTATTA
40204600 TATTTATTACTATTA
1 TATTTATTACTATTA
40204615 T
1 T
40204616 TAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:40204717 original size:15 final size:15
Alignment explanation
Indices: 40204699--40204736 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40204689 CCCACTTAGC
40204699 TATTATTACTATTAT
1 TATTATTACTATTAT
*
40204714 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
40204729 AATTATTA
1 TATTATTA
40204737 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:40213225 original size:20 final size:18
Alignment explanation
Indices: 40213178--40213226 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40213168 CAAGATAAAC
40213178 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40213195 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
40213215 ATTAAATTAATA
1 ATTAAATTAATA
40213227 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40215244 original size:27 final size:27
Alignment explanation
Indices: 40215196--40215355 Score: 168
Period size: 27 Copynumber: 5.9 Consensus size: 27
40215186 GCGAGGCTGC
* *
40215196 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
40215223 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
40215249 CCGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
40215276 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
40215303 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
40215330 TAGATAAATTGTGGCATAGCCACCAG
1 CAGAT--ATTGTGGCAGAGCCACCAG
40215356 TACGCTTCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.08
27 84 0.74
28 19 0.17
29 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:40215286 original size:54 final size:54
Alignment explanation
Indices: 40215214--40215355 Score: 223
Period size: 54 Copynumber: 2.6 Consensus size: 54
40215204 GTGACGAAGT
* *
40215214 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACCGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
40215268 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
40215322 CACCAGATTAGATAAATTGTGGCATAGCCACCAG
1 CACCAGATCAGAT-AATTGTGGCATAGCCACCAG
40215356 TACGCTTCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
53 5 0.06
54 57 0.70
55 20 0.24
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:40215742 original size:8 final size:8
Alignment explanation
Indices: 40215726--40215755 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40215716 CTCAAAATAC
40215726 CGGCTTTT
1 CGGCTTTT
*
40215734 CGGCATTT
1 CGGCTTTT
40215742 CGGCTTTT
1 CGGCTTTT
40215750 CGGCTT
1 CGGCTT
40215756 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:40218437 original size:20 final size:20
Alignment explanation
Indices: 40218412--40218450 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40218402 AATGCTATAC
*
40218412 AGAGGCACTGAAGTGCAAAA
1 AGAGGCACTAAAGTGCAAAA
40218432 AGAGGCACTAAAGTGCAAA
1 AGAGGCACTAAAGTGCAAA
40218451 CAAAGTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.10
Consensus pattern (20 bp):
AGAGGCACTAAAGTGCAAAA
Found at i:40223831 original size:47 final size:48
Alignment explanation
Indices: 40223777--40223908 Score: 194
Period size: 47 Copynumber: 2.8 Consensus size: 48
40223767 TCACATCGAT
* *
40223777 AAGTACCTATACCATGGCTCATAGCCAAATCAAGGTAACTTATCTCAG
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
* * *
40223825 -AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
* *
40223872 AACTACCTATACCATTGCTCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTA
40223909 TAATTCGTAC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
47 42 0.56
48 33 0.44
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (48 bp):
AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCAG
Found at i:40226967 original size:51 final size:51
Alignment explanation
Indices: 40226903--40227000 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
40226893 TATAGGGATC
40226903 ATATAGATCGAGTTCGATTCGGAGGGATACATTTCCCTATGACCATGTCTT
1 ATATAGATCGAGTTCGATTCGGAGGGATACATTTCCCTATGACCATGTCTT
* * *
40226954 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATG
1 ATATAGATCGAGTTCGATTCGGAGGGATACATTTCCCTATGACCATG
40227001 CGGAAATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (51 bp):
ATATAGATCGAGTTCGATTCGGAGGGATACATTTCCCTATGACCATGTCTT
Found at i:40227675 original size:781 final size:773
Alignment explanation
Indices: 40226173--40228071 Score: 3584
Period size: 781 Copynumber: 2.4 Consensus size: 773
40226163 TTATAGGGTC
* * * *
40226173 ATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGAGCATGCGGAGATTAAAATCTCAC
1 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
40226238 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
66 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
40226303 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
131 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
40226368 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
196 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
40226433 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
261 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
40226498 GTGAAATCCTGCAGCTCCGATACATACCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCT
326 GTGAAATCCTGCAGCTCCGATACATACCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCT
* * *
40226563 CTCCGACCAAGCACGAACGGTCGCATTATCTTCGACTTTACTAAGAAATTCATTCTCCATGTCAA
391 CTCCGACAAAGCACGAACGGCCGCATTATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAA
40226628 ATTTTCTAACTTAGTAATTGAATACGGATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAA
456 ATTTTCTAACTTAGTAATTGAATACGGATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAA
* *
40226693 GATAATCAAAATGAAACACCGATTAGTGTCAAATAATAGCGATAAAATGCAAGCATATAAACAAT
521 GATAATCAAAACGAAACACCGATTAGTATCAAATAATAGCGATAAAATGCAAGCATATAAACAAT
40226758 AATTATAGCGCATATACGGGTAAGTACTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAA
586 AATTATAGCGCATATACGGGTAAGTACTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAA
40226823 GGTTCACTATATGTGGTTTAGTTCTAGAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCA
651 GGTTCACTATATGTGGTTTAGTTCTAGAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCA
40226888 CCCATTATAGGGATCATATAGATCGAGTTCGATTC-GGAGGGATACATTTCCCTATGACCATGTC
716 CCCATTATA-GGATCATATAGATCGAGTTCGATTCAGG-GGGATACATTTCCCTATG---A-G--
40226952 TT
773 -T
40226954 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
1 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
40227019 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
66 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
40227084 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
131 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
40227149 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
196 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
40227214 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
261 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
40227279 GTGAAATCCTGCAGCTCCGATACATACCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCT
326 GTGAAATCCTGCAGCTCCGATACATACCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCT
*
40227344 TTCCGACAAAGCACGAACGGCCGCATTATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAA
391 CTCCGACAAAGCACGAACGGCCGCATTATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAA
*
40227409 ATTTTCTAACTTAGTAATTGAATGCGGATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAA
456 ATTTTCTAACTTAGTAATTGAATACGGATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAA
*
40227474 GATAATCAAAACGAAACACCGGTTAGTATCAAATAATAGCGATAAAATGCAAGCATATAAACAAT
521 GATAATCAAAACGAAACACCGATTAGTATCAAATAATAGCGATAAAATGCAAGCATATAAACAAT
40227539 AATTATAGCGCATATACGGGTAAGTACTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAA
586 AATTATAGCGCATATACGGGTAAGTACTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAA
40227604 GGTTCACTATATGTGGTTTAGTTCTAGAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCA
651 GGTTCACTATATGTGGTTTAGTTCTAGAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCA
* *
40227669 CCCATTATAGGCTCATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGAGT
716 CCCATTATAGGATCATATAGATCGAGTTCGATTCAGGGGGATACATTTCCCTATGAGT
40227727 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
1 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
40227792 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
66 GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
40227857 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
131 GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
40227922 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
196 ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
40227987 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
261 CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
40228052 GTGAAATCCTGCAGCTCCGA
326 GTGAAATCCTGCAGCTCCGA
40228072 NNNNNNNNNN
Statistics
Matches: 1103, Mismatches: 14, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
773 346 0.31
776 1 0.00
777 1 0.00
780 41 0.04
781 714 0.65
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (773 bp):
ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGACCATGCGGAAATTAAAATCTCAC
GAAATCATAAGTACGGATGTACCCCGGAAGCAATCCACTAGCCCATGCGGAGGTGAAAACCTCAG
GAAAGTGTAGCTTCTTACTCCCACTTAGAATTCCAAAACTGCACCAAGGCTCGGAACAAATGCTT
ATCCACTCTAATATCTAGCAGGTAGGATATGTCACCATAGCTTTGGTAAAACAACTGCTTGATCC
CTTCATCCCAACTAGCCCAAATGTCTCTCAACTCTTGCAGCTCATTCTGTACTACATTGACGCGA
GTGAAATCCTGCAGCTCCGATACATACCCTTCTGCCAAGCTATCCCCCCTCTCAGATTGTAGCCT
CTCCGACAAAGCACGAACGGCCGCATTATCCTCGACTTTACTAAGAAATTCATTCTCCATGTCAA
ATTTTCTAACTTAGTAATTGAATACGGATTAACGCCTCCTTTAATATGCAATGTCATGCAAAAAA
GATAATCAAAACGAAACACCGATTAGTATCAAATAATAGCGATAAAATGCAAGCATATAAACAAT
AATTATAGCGCATATACGGGTAAGTACTAAGGCTCGACGCGGCTCCACCCAAGGATAGCTCCTAA
GGTTCACTATATGTGGTTTAGTTCTAGAGATAAGGTACCCGAACCAGCAGATTCCTCAATCCTCA
CCCATTATAGGATCATATAGATCGAGTTCGATTCAGGGGGATACATTTCCCTATGAGT
Found at i:40227746 original size:44 final size:44
Alignment explanation
Indices: 40227683--40227768 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
40227673 TTATAGGCTC
40227683 ATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGAGT
1 ATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGAGT
* *
40227727 ATATAGATTGAGTTCGGTTCGGGGGGATACATTTCCCTATGA
1 ATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGA
40227769 CCATGCGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (44 bp):
ATATAGATCGAGTTCGGTTCAGGGGGATACATTTCCCTATGAGT
Found at i:40229510 original size:16 final size:16
Alignment explanation
Indices: 40229479--40229508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40229469 TTGTCATGTG
40229479 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
40229495 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
40229509 TACTATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:40236019 original size:39 final size:40
Alignment explanation
Indices: 40235975--40236198 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 40
40235965 CTCCTCGTTT
* * * *
40235975 AAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
40236015 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
40236054 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
40236094 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 AAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
40236134 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 AAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
*
40236175 AAA-GCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGGACTTAACCCGGA
40236199 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 104 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:40236207 original size:41 final size:41
Alignment explanation
Indices: 40236130--40236207 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40236120 TTTGTATCTC
* * *
40236130 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40236171 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40236208 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40242604 original size:37 final size:37
Alignment explanation
Indices: 40242563--40242640 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
40242553 CTATTGTTCA
*
40242563 CTTAATGTCATTCATGATTTAACCTTAAAAGCAAATT
1 CTTAATGTCATTCATGATTTAACATTAAAAGCAAATT
40242600 CTTAATGTCATTCATGATTTAACATTAAAAGCAAATT
1 CTTAATGTCATTCATGATTTAACATTAAAAGCAAATT
40242637 CTTA
1 CTTA
40242641 GTAACTGTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (37 bp):
CTTAATGTCATTCATGATTTAACATTAAAAGCAAATT
Found at i:40245788 original size:24 final size:23
Alignment explanation
Indices: 40245754--40245799 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
40245744 ACAGTGTACA
* *
40245754 CTCATATAGAGCCATTTCGGGAAG
1 CTCATAAAGAGCC-TATCGGGAAG
40245778 CTCATAAAGAGCCTATCGGGAA
1 CTCATAAAGAGCCTATCGGGAA
40245800 TGTAACGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
CTCATAAAGAGCCTATCGGGAAG
Found at i:40253404 original size:249 final size:249
Alignment explanation
Indices: 40252961--40253458 Score: 987
Period size: 249 Copynumber: 2.0 Consensus size: 249
40252951 TGCTTAATCT
40252961 GTCAACAGGTAAAGGCCGAACATCAGGTACCTTCAGGTTTATTGCAGCCTGTGCTAATCCCTGAG
1 GTCAACAGGTAAAGGCCGAACATCAGGTACCTTCAGGTTTATTGCAGCCTGTGCTAATCCCTGAG
40253026 TGGAAATGGGATCAAGTTACTATGGATTTTGTGACAGGATTGCCACTTACACAGAAAAAGAAAGA
66 TGGAAATGGGATCAAGTTACTATGGATTTTGTGACAGGATTGCCACTTACACAGAAAAAGAAAGA
40253091 TGCAGTATGGGTTGTGATTGATAAGTTAACGAAGTCGGCTCATTTTATCCCAGTTCGCATGGATT
131 TGCAGTATGGGTTGTGATTGATAAGTTAACGAAGTCGGCTCATTTTATCCCAGTTCGCATGGATT
40253156 ATTCACTTGACAAGTTGGTCGAGTTGTATATTTCAGAGATAGTCAGACTACACG
196 ATTCACTTGACAAGTTGGTCGAGTTGTATATTTCAGAGATAGTCAGACTACACG
*
40253210 GTCAGCAGGTAAAGGCCGAACATCAGGTACCTTCAGGTTTATTGCAGCCTGTGCTAATCCCTGAG
1 GTCAACAGGTAAAGGCCGAACATCAGGTACCTTCAGGTTTATTGCAGCCTGTGCTAATCCCTGAG
40253275 TGGAAATGGGATCAAGTTACTATGGATTTTGTGACAGGATTGCCACTTACACAGAAAAAGAAAGA
66 TGGAAATGGGATCAAGTTACTATGGATTTTGTGACAGGATTGCCACTTACACAGAAAAAGAAAGA
40253340 TGCAGTATGGGTTGTGATTGATAAGTTAACGAAGTCGGCTCATTTTATCCCAGTTCGCATGGATT
131 TGCAGTATGGGTTGTGATTGATAAGTTAACGAAGTCGGCTCATTTTATCCCAGTTCGCATGGATT
40253405 ATTCACTTGACAAGTTGGTCGAGTTGTATATTTCAGAGATAGTCAGACTACACG
196 ATTCACTTGACAAGTTGGTCGAGTTGTATATTTCAGAGATAGTCAGACTACACG
40253459 TGGTACTGTT
Statistics
Matches: 248, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 248 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (249 bp):
GTCAACAGGTAAAGGCCGAACATCAGGTACCTTCAGGTTTATTGCAGCCTGTGCTAATCCCTGAG
TGGAAATGGGATCAAGTTACTATGGATTTTGTGACAGGATTGCCACTTACACAGAAAAAGAAAGA
TGCAGTATGGGTTGTGATTGATAAGTTAACGAAGTCGGCTCATTTTATCCCAGTTCGCATGGATT
ATTCACTTGACAAGTTGGTCGAGTTGTATATTTCAGAGATAGTCAGACTACACG
Found at i:40255237 original size:23 final size:22
Alignment explanation
Indices: 40255200--40255249 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
40255190 GGGAAAAAGT
**
40255200 GCAAATATGTGAAAGTTTAGGG
1 GCAAATATGCAAAAGTTTAGGG
40255222 GCNAAATATGCAAAAGTTTAGGG
1 GC-AAATATGCAAAAGTTTAGGG
40255245 GCAAA
1 GCAAA
40255250 AATGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.22
Consensus pattern (22 bp):
GCAAATATGCAAAAGTTTAGGG
Found at i:40256645 original size:22 final size:22
Alignment explanation
Indices: 40256620--40256665 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
40256610 AGTTTTAATA
40256620 GAAACAAACGGTATAGTCATAT
1 GAAACAAACGGTATAGTCATAT
*
40256642 GAAACAAATGGTATAGTCATAT
1 GAAACAAACGGTATAGTCATAT
40256664 GA
1 GA
40256666 TTGTTTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (22 bp):
GAAACAAACGGTATAGTCATAT
Found at i:40257090 original size:29 final size:29
Alignment explanation
Indices: 40257028--40257131 Score: 129
Period size: 29 Copynumber: 3.6 Consensus size: 29
40257018 GAATATAATG
*
40257028 TGATGGGCCATATAAATGAG-ATTGGGCC
1 TGATGGGCCATATAAATGTGAATTGGGCC
* *
40257056 TAATGGGCCATATGAATGTGAATTGGGCC
1 TGATGGGCCATATAAATGTGAATTGGGCC
* * * *
40257085 TGATGGGCCACATGAACGTGAGTTGGGCC
1 TGATGGGCCATATAAATGTGAATTGGGCC
*
40257114 GGATGGGCCATATAAATG
1 TGATGGGCCATATAAATG
40257132 AGATTAGGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
28 17 0.27
29 47 0.73
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.24
Consensus pattern (29 bp):
TGATGGGCCATATAAATGTGAATTGGGCC
Found at i:40262483 original size:17 final size:17
Alignment explanation
Indices: 40262458--40262491 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40262448 GAGTTGTAAC
*
40262458 ACCCTAAAAATCTCGAA
1 ACCCAAAAAATCTCGAA
40262475 ACCCAAAAAATCTCGAA
1 ACCCAAAAAATCTCGAA
40262492 TTTTTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.29, G:0.06, T:0.15
Consensus pattern (17 bp):
ACCCAAAAAATCTCGAA
Found at i:40263984 original size:29 final size:27
Alignment explanation
Indices: 40263943--40264088 Score: 116
Period size: 29 Copynumber: 5.1 Consensus size: 27
40263933 ATGAGCATGA
40263943 ATAT-AATGTGATTTGGGCTGGATGGGCC
1 ATATAAATGTGA-TTGGGCT-GATGGGCC
* *
40263971 ATATAAATGAGATTGGGCCTAATGGGCC
1 ATATAAATGTGATTGGG-CTGATGGGCC
* * *
40263999 ATATGAATGTGAATTAGGCCTGATAGGCC
1 ATATAAATGTG-ATT-GGGCTGATGGGCC
* * *
40264028 ATATGAATGTGAGTTGGGCCAGATGGGCT
1 ATATAAATGTGA-TTGGG-CTGATGGGCC
*
40264057 ATATAAATGAGATTGGGCCT-AGTGGGCC
1 ATATAAATGTGATTGGG-CTGA-TGGGCC
40264085 ATAT
1 ATAT
40264089 TCATGTATGT
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.01
28 44 0.46
29 49 0.51
30 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (27 bp):
ATATAAATGTGATTGGGCTGATGGGCC
Found at i:40264009 original size:57 final size:56
Alignment explanation
Indices: 40263943--40264088 Score: 138
Period size: 57 Copynumber: 2.6 Consensus size: 56
40263933 ATGAGCATGA
40263943 ATATAATGTGATTTGGGCTGGATGGGCCATATAAATGAGA-TTGGGCCTA-ATGGGCC
1 ATATAATGTGATTTGGGCT-GATGGGCCATATAAATGAGAGTTGGGCC-AGATGGGCC
* * * * * *
40263999 ATATGAATGTGAATTAGGCCTGATAGGCCATATGAATGTGAGTTGGGCCAGATGGGCT
1 ATAT-AATGTG-ATTTGGGCTGATGGGCCATATAAATGAGAGTTGGGCCAGATGGGCC
*
40264057 ATATAAATGAGA-TTGGGCCT-AGTGGGCCATAT
1 ATAT-AATGTGATTTGGG-CTGA-TGGGCCATAT
40264089 TCATGTATGT
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
56 8 0.11
57 36 0.49
58 29 0.40
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (56 bp):
ATATAATGTGATTTGGGCTGATGGGCCATATAAATGAGAGTTGGGCCAGATGGGCC
Found at i:40265314 original size:24 final size:24
Alignment explanation
Indices: 40265273--40265334 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
40265263 TGTAGCTTAT
* *
40265273 AAGAGCCATAATCAGGAAGTTCT-CA
1 AAGAACCAT-ATCGGGAAGTT-TACA
*
40265298 AAGAACCTTATCGGGAAGTTTACA
1 AAGAACCATATCGGGAAGTTTACA
40265322 AAGAACCATATCG
1 AAGAACCATATCG
40265335 AGAAACTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 24 0.75
25 7 0.22
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (24 bp):
AAGAACCATATCGGGAAGTTTACA
Found at i:40273901 original size:30 final size:30
Alignment explanation
Indices: 40273867--40273953 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
40273857 TGAACCCTCA
40273867 AGTGATAAAATGTCAATTTTTCCCTTATGT
1 AGTGATAAAATGTCAATTTTTCCCTTATGT
* *
40273897 AGTGATAAAATGTCGATTTTGCCCTTA--T
1 AGTGATAAAATGTCAATTTTTCCCTTATGT
* *
40273925 -GTGATAAAATGACAATTTTTCCCTCATGT
1 AGTGATAAAATGTCAATTTTTCCCTTATGT
40273954 GATAAAATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (30 bp):
AGTGATAAAATGTCAATTTTTCCCTTATGT
Found at i:40273942 original size:27 final size:27
Alignment explanation
Indices: 40273868--40274019 Score: 133
Period size: 27 Copynumber: 5.5 Consensus size: 27
40273858 GAACCCTCAA
* * *
40273868 GTGATAAAATGTCAATTTTTCCCTTATGT
1 GTGATAAAATGACGATTTTGCCCTTA--T
*
40273897 AGTGATAAAATGTCGATTTTGCCCTTAT
1 -GTGATAAAATGACGATTTTGCCCTTAT
* * *
40273925 GTGATAAAATGACAATTTTTCCCTCAT
1 GTGATAAAATGACGATTTTGCCCTTAT
* * *
40273952 GTGATAAAATGACGATTTTACCATTCT
1 GTGATAAAATGACGATTTTGCCCTTAT
** * * *
40273979 ACGATAAAATTATGATTTTGCCCTCAT
1 GTGATAAAATGACGATTTTGCCCTTAT
*
40274006 GTGGTAAAATGACG
1 GTGATAAAATGACG
40274020 GAAATACCCT
Statistics
Matches: 98, Mismatches: 24, Indels: 3
0.78 0.19 0.02
Matches are distributed among these distances:
27 73 0.74
28 1 0.01
30 24 0.24
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (27 bp):
GTGATAAAATGACGATTTTGCCCTTAT
Found at i:40273985 original size:54 final size:54
Alignment explanation
Indices: 40273870--40274019 Score: 156
Period size: 54 Copynumber: 2.7 Consensus size: 54
40273860 ACCCTCAAGT
* * * * * **
40273870 GATAAAATGTCAATTTTTCCCTTATGTAGTGATAAAATGTCGATTTTGCCCTTATGT
1 GATAAAATGACAATTTTTCCCTCA--T-GTGATAAAATGACGATTTTACCATTATAC
*
40273927 GATAAAATGACAATTTTTCCCTCATGTGATAAAATGACGATTTTACCATTCTAC
1 GATAAAATGACAATTTTTCCCTCATGTGATAAAATGACGATTTTACCATTATAC
* ** * *
40273981 GATAAAATTATGATTTTGCCCTCATGTGGTAAAATGACG
1 GATAAAATGACAATTTTTCCCTCATGTGATAAAATGACG
40274020 GAAATACCCT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 57 0.71
55 1 0.01
57 22 0.28
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (54 bp):
GATAAAATGACAATTTTTCCCTCATGTGATAAAATGACGATTTTACCATTATAC
Found at i:40274041 original size:54 final size:54
Alignment explanation
Indices: 40273939--40274042 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
40273929 TAAAATGACA
* ** *
40273939 ATTTTTCCCTCATGTGATAAAATGACGATTTTACCATTCTACGATAAAATTATG
1 ATTTTGCCCTCATGTGATAAAATGACGATAATACCATTATACGATAAAATTATG
* * * *
40273993 ATTTTGCCCTCATGTGGTAAAATGACGGA-AATACCCTTATAGGGTAAAAT
1 ATTTTGCCCTCATGTGATAAAATGAC-GATAATACCATTATACGATAAAAT
40274043 GACCGAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 39 0.95
55 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (54 bp):
ATTTTGCCCTCATGTGATAAAATGACGATAATACCATTATACGATAAAATTATG
Found at i:40274127 original size:27 final size:27
Alignment explanation
Indices: 40274008--40274127 Score: 100
Period size: 27 Copynumber: 4.4 Consensus size: 27
40273998 GCCCTCATGT
* * * *
40274008 GGTAAAATGACGGAAATACCCTTATAG
1 GGTAAAATGACTGAAATACCCCTGTAA
* **
40274035 GGTAAAATGACCGAAATACCCCCAT-A
1 GGTAAAATGACTGAAATACCCCTGTAA
* *
40274061 GGATAGAATGACTGAAATACCCCTGTAG
1 GG-TAAAATGACTGAAATACCCCTGTAA
* * *
40274089 GGTCAAATGACTGTAATA-CCTTAGTAA
1 GGTAAAATGACTGAAATACCCCT-GTAA
40274116 GGTAAAATGACT
1 GGTAAAATGACT
40274128 AATTTGCTCT
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.07
27 68 0.91
28 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCTGTAA
Found at i:40278807 original size:27 final size:27
Alignment explanation
Indices: 40278542--40278896 Score: 230
Period size: 27 Copynumber: 13.1 Consensus size: 27
40278532 TGTAGGGAAG
* * * *
40278542 AATTACTGAAATACCATTGGTTTATAA
1 AATTACCGAAATACCCTTGATTTGTAA
* * * *
40278569 AATTACCAAAATACCCTCGGTTCGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
* * *
40278596 AATTTCCAAAATACCCCT-AGTTTGTAA
1 AATTACCGAAATACCCTTGA-TTTGTAA
* * *
40278623 AATTACCAAAATACCCCTGATTTGTGA
1 AATTACCGAAATACCCTTGATTTGTAA
* **
40278650 AATTACTGAAATACTCC-TGATTTGTGC
1 AATTACCGAAATAC-CCTTGATTTGTAA
* * ** *
40278677 AATTACCGAAATATCCTCGACCTATAA
1 AATTACCGAAATACCCTTGATTTGTAA
* * *
40278704 AATTACTGAAATA-CCTTCAACTTGTAA
1 AATTACCGAAATACCCTT-GATTTGTAA
* * *
40278731 AATTACTGAAATACCCTCGACTTGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
* * *
40278758 AATTACAGAAATACCCCTGATTTGGAA
1 AATTACCGAAATACCCTTGATTTGTAA
* *
40278785 AATTACCGAAATACCCTTAATTTGGAA
1 AATTACCGAAATACCCTTGATTTGTAA
** * * **
40278812 AATTATAGAAATACCCCTAATTTACAA
1 AATTACCGAAATACCCTTGATTTGTAA
* **
40278839 AATTACAGAAATACCCTTGACTTTCAAA
1 AATTACCGAAATACCCTTGA-TTTGTAA
** * **
40278867 AATTACAAAAATACCATTGGCTTGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
40278894 AAT
1 AAT
40278897 ACCCTTGGTC
Statistics
Matches: 266, Mismatches: 55, Indels: 14
0.79 0.16 0.04
Matches are distributed among these distances:
26 5 0.02
27 233 0.88
28 28 0.11
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGATTTGTAA
Found at i:40279215 original size:41 final size:41
Alignment explanation
Indices: 40279168--40279290 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
40279158 GGAGGAAGAA
*
40279168 ATTGAGGATCACATGGTTGCTTGACAACTGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACTGTGGATCCACCG
* *
40279209 ATTGAGGATCGCATGGTTGCTTGATGA-TCGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACT-GTGGATCCACCG
* * *
40279250 ATTAAGGATCACATGGTTGCTTGACGACCGTGGATCTACCG
1 ATTGAGGATCACATGGTTGCTTGACGACTGTGGATCCACCG
40279291 GTCGCTTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 71 0.99
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCACATGGTTGCTTGACGACTGTGGATCCACCG
Found at i:40281785 original size:39 final size:39
Alignment explanation
Indices: 40281590--40281776 Score: 322
Period size: 39 Copynumber: 4.8 Consensus size: 39
40281580 ACTCAGTGAT
*
40281590 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
40281629 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
40281668 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
40281707 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
* * *
40281746 GAATTACGTCCGGGC-TAAAGTCCCGCAGGCT
1 GAATTATGTCCGGACTTAAGGT-CCGCAGGCT
40281777 TCGAGCTGGT
Statistics
Matches: 143, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
38 5 0.03
39 138 0.97
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (39 bp):
GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
Found at i:40281811 original size:117 final size:116
Alignment explanation
Indices: 40281590--40281823 Score: 296
Period size: 117 Copynumber: 2.0 Consensus size: 116
40281580 ACTCAGTGAT
* *
40281590 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTATGTCCGGACTTAAGGTCCGC
1 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGACTTAAAGTCCGC
* *
40281655 AGGCTATATGCTGGAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
66 AGGCTATATGCTGGAATTATGACCGGACTTAAAGTCCGCAGGCT-TATGCTG
* *
40281707 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGGC-TAAAGTCCCG
1 GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGACTTAAAGT-CCG
* ** * *
40281771 CAGGCT-TCGA-GCTGGTATTAT-ACCGGGTTTAAATTCCCGCAGGCTTGTGCTG
65 CAGGCTAT--ATGCTGGAATTATGACCGGACTTAAAGT-CCGCAGGCTTATGCTG
40281823 G
1 G
40281824 TATTGATTTC
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
116 22 0.22
117 79 0.77
118 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (116 bp):
GAATTATATCCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGACTTAAAGTCCGC
AGGCTATATGCTGGAATTATGACCGGACTTAAAGTCCGCAGGCTTATGCTG
Found at i:40282558 original size:22 final size:22
Alignment explanation
Indices: 40282530--40282590 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
40282520 TTATTCTAAT
*
40282530 TATGGCTTTGTGCCAACCT-ACA
1 TATGGCTCTGTGCCAACCTGA-A
*
40282552 TATGGCTCTGTGCCAACCTGAT
1 TATGGCTCTGTGCCAACCTGAA
*
40282574 TATGGCTGTGTGCCAAC
1 TATGGCTCTGTGCCAAC
40282591 TGCATTTGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (22 bp):
TATGGCTCTGTGCCAACCTGAA
Found at i:40286611 original size:40 final size:40
Alignment explanation
Indices: 40286554--40286640 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
40286544 TGAACTTTAA
40286554 TTTATTTAAACTAATCTTAGTTAATAATTGAGTTGCTGGAC
1 TTTA-TTAAACTAATCTTAGTTAATAATTGAGTTGCTGGAC
* * * *
40286595 TTTATTAAACTCATCTTAGTTAATTATTGATTTGTTGGAC
1 TTTATTAAACTAATCTTAGTTAATAATTGAGTTGCTGGAC
40286635 TTTATT
1 TTTATT
40286641 TTTATTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (40 bp):
TTTATTAAACTAATCTTAGTTAATAATTGAGTTGCTGGAC
Found at i:40289252 original size:50 final size:46
Alignment explanation
Indices: 40289176--40289297 Score: 127
Period size: 50 Copynumber: 2.6 Consensus size: 46
40289166 TGTCTTCGAC
** * * *
40289176 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--ATATA-A-ATAAT
* * *
40289226 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAAATAAT
*
40289272 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
40289298 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 27 0.44
47 1 0.02
48 5 0.08
50 29 0.47
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAAATAAT
Found at i:40291170 original size:21 final size:20
Alignment explanation
Indices: 40291146--40291184 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40291136 TTGTAAATCT
40291146 AGTAACATAATTGTTATTTTA
1 AGTAACATAA-TGTTATTTTA
**
40291167 AGTAATTTAATGTTATTT
1 AGTAACATAATGTTATTT
40291185 ATATGATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
AGTAACATAATGTTATTTTA
Found at i:40303056 original size:24 final size:23
Alignment explanation
Indices: 40303029--40303099 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
40303019 ATGTGGCTGT
*
40303029 TACATTACTTAAAGAAGAGCATTA
1 TACATCACTTAAAG-AGAGCATTA
40303053 TACATCACTTAAAG-GAGC-TGT-
1 TACATCACTTAAAGAGAGCAT-TA
*
40303074 TACATCATTTAAAGGAGAGCATTA
1 TACATCACTTAAA-GAGAGCATTA
40303098 TA
1 TA
40303100 TATCCTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 13 0.32
22 6 0.15
23 5 0.12
24 16 0.40
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (23 bp):
TACATCACTTAAAGAGAGCATTA
Found at i:40303079 original size:21 final size:21
Alignment explanation
Indices: 40303024--40303090 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 21
40303014 TGTTAATGTG
*
40303024 GCTGTTACATTACTTAAAGAAGA
1 GCTGTTACATCACTTAAAG--GA
40303047 GCAT-TATACATCACTTAAAGGA
1 GC-TGT-TACATCACTTAAAGGA
*
40303069 GCTGTTACATCATTTAAAGGA
1 GCTGTTACATCACTTAAAGGA
40303090 G
1 G
40303091 AGCATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 17 0.44
22 5 0.13
23 3 0.08
24 14 0.36
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (21 bp):
GCTGTTACATCACTTAAAGGA
Found at i:40303744 original size:24 final size:25
Alignment explanation
Indices: 40303711--40303762 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
40303701 ATTCTCAGTC
40303711 TTAGCCAAATTATCCTTTATTTATT
1 TTAGCCAAATTATCCTTTATTTATT
40303736 TTAG-CAAATTATCCTTTATTTATT
1 TTAGCCAAATTATCCTTTATTTATT
40303760 TTA
1 TTA
40303763 CCTATTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (25 bp):
TTAGCCAAATTATCCTTTATTTATT
Found at i:40305929 original size:24 final size:23
Alignment explanation
Indices: 40305902--40305958 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
40305892 GAAATAGTAC
*
40305902 AAGAAAAAAAGATGGAAAAAGAGA
1 AAGAAAAAAA-ATGGAAAAAAAGA
* *
40305926 AAGAATAGAAAATTGAAAAAAAGA
1 AAGAA-AAAAAATGGAAAAAAAGA
*
40305950 AAGGAAAAA
1 AAGAAAAAA
40305959 GTGAGGGAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.11
24 20 0.74
25 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (23 bp):
AAGAAAAAAAATGGAAAAAAAGA
Found at i:40311608 original size:40 final size:40
Alignment explanation
Indices: 40311548--40311634 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
40311538 TAAACTCTAA
* *
40311548 TTTATTTAAACTCATGTTAGTTAATAATTGAGTTGCTAGAC
1 TTTA-TTAAACTCATCTTAGTTAATAATTGAGTTGATAGAC
* * *
40311589 TTTATTAAACTCATCTTAGTTAATTATTGATTTGATGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGATAGAC
40311629 TTTATT
1 TTTATT
40311635 TCTTATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGATAGAC
Found at i:40321896 original size:40 final size:40
Alignment explanation
Indices: 40321817--40322073 Score: 315
Period size: 40 Copynumber: 6.5 Consensus size: 40
40321807 CGGATGATAG
* * * *
40321817 CCGGACTAAGATCCAAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
40321857 CCAGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
40321897 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
40321937 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
40321977 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
40322017 CCGGGCTAAGACCCGAGGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
40322057 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
40322074 ATACTTGGGT
Statistics
Matches: 184, Mismatches: 28, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 16 0.09
40 163 0.89
41 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:40321955 original size:80 final size:80
Alignment explanation
Indices: 40321817--40322073 Score: 394
Period size: 80 Copynumber: 3.2 Consensus size: 80
40321807 CGGATGATAG
* * * *
40321817 CCGGACTAAGATCCAAAGGCATTTGTGCGAGTTGCTATATCCAGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
40321882 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
40321897 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
40321962 TGCTAGTGATTATAT
66 TGCTAGTGATTATAT
* * * *
40321977 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAGGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
*
40322042 TGCGAGTTG-TTATAT
66 TGCTAG-TGATTATAT
40322057 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
40322074 ATACTTGGGT
Statistics
Matches: 166, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
78 1 0.01
79 13 0.08
80 150 0.90
81 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
TGCTAGTGATTATAT
Found at i:40335505 original size:40 final size:40
Alignment explanation
Indices: 40335434--40335586 Score: 204
Period size: 40 Copynumber: 3.9 Consensus size: 40
40335424 NNNNNNNNNN
* * *
40335434 GTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTT
1 GTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
* *
40335474 ATGCTAG-TGATTATATCCGGGCTAAGACCCGAAGGCATTT
1 GTGCGAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
* *
40335514 GTGCGAGTTGCTATATCCGGGCTAAGACCCGAGGGCATTT
1 GTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
40335554 GTGCGAGTTGTTATATCC-GGCTAA-ATCCCGAAG
1 GTGCGAGTTGTTATATCCGGGCTAAGA-CCCGAAG
40335587 ATACTTGGGT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 14 0.14
40 82 0.83
41 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
GTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTT
Found at i:40337202 original size:51 final size:51
Alignment explanation
Indices: 40337142--40337297 Score: 285
Period size: 51 Copynumber: 3.1 Consensus size: 51
40337132 ATTGATGTGT
*
40337142 TATATGTTCTGTAAAAGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
1 TATATGTTCTGTAAATGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
40337193 TATATGTTCTGTAAATGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
1 TATATGTTCTGTAAATGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
* *
40337244 TATGTGTTCTGTAAATTTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
1 TATATGTTCTGTAAATGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
40337295 TAT
1 TAT
40337298 GTGGTGAATG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 102 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (51 bp):
TATATGTTCTGTAAATGTTTTAAAATTGTTTGGATTATGTTTTATTTAAGC
Found at i:40358868 original size:33 final size:34
Alignment explanation
Indices: 40358808--40358874 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
40358798 CAGTTCAACC
* *
40358808 TCAGTTAGGGCCTTAGCCCAATACAGTAATAGTA
1 TCAGTGAGGGCCTTAGCCCAATACAGTAACAGTA
*
40358842 TCAGTGAGGG-CTTAGCCC-ATCTCAGTAACAGTA
1 TCAGTGAGGGCCTTAGCCCAAT-ACAGTAACAGTA
40358875 ATAGAAATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 2 0.07
33 18 0.62
34 9 0.31
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (34 bp):
TCAGTGAGGGCCTTAGCCCAATACAGTAACAGTA
Found at i:40359169 original size:26 final size:26
Alignment explanation
Indices: 40359138--40359198 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
40359128 AACATGCTCA
*
40359138 AACAGTCATACATCACATAGGGGTAT
1 AACAGTCATACACCACATAGGGGTAT
* ** *
40359164 ATCAGTCATTTACCTCATAGGGGTAT
1 AACAGTCATACACCACATAGGGGTAT
40359190 AACAGTCAT
1 AACAGTCAT
40359199 TTCATCAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (26 bp):
AACAGTCATACACCACATAGGGGTAT
Found at i:40360508 original size:14 final size:15
Alignment explanation
Indices: 40360481--40360515 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40360471 AGAAAGATAA
40360481 AAAAAGACCAAAAAC
1 AAAAAGACCAAAAAC
*
40360496 AAAACGACC-AAAAC
1 AAAAAGACCAAAAAC
40360510 AAAAAG
1 AAAAAG
40360516 GTTGCAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.71, C:0.20, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAGACCAAAAAC
Found at i:40367478 original size:13 final size:13
Alignment explanation
Indices: 40367425--40367483 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
40367415 TTTGGCAATT
*
40367425 CTTTTGAAAAATG
1 CTTTTGAGAAATG
* *
40367438 ATTTTGAGAAGTG
1 CTTTTGAGAAATG
*
40367451 C-TGTG-GCAAAGTG
1 CTTTTGAG-AAA-TG
40367464 CTTTTGAGAAATG
1 CTTTTGAGAAATG
40367477 CTTTTGA
1 CTTTTGA
40367484 AAAGTTTGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.03
12 5 0.14
13 22 0.63
14 6 0.17
15 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.37
Consensus pattern (13 bp):
CTTTTGAGAAATG
Found at i:40367487 original size:26 final size:26
Alignment explanation
Indices: 40367425--40367488 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
40367415 TTTGGCAATT
* *
40367425 CTTTTGAAAAATGATTTTGAGAAGTG
1 CTTTTGAAAAGTGATTTTGAGAAATG
* * * *
40367451 CTGTGGCAAAGTGCTTTTGAGAAATG
1 CTTTTGAAAAGTGATTTTGAGAAATG
40367477 CTTTTGAAAAGT
1 CTTTTGAAAAGT
40367489 TTGGCTTAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
CTTTTGAAAAGTGATTTTGAGAAATG
Found at i:40367711 original size:31 final size:29
Alignment explanation
Indices: 40367661--40367719 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
40367651 TAACTTGTTG
40367661 TAAATATTTTAATATATAAAATATAAATTT
1 TAAATATTTTAATATAT-AAATATAAATTT
*
40367691 TAAATATTTTTAAGTA-ATAAATATTAATT
1 TAAATA-TTTTAA-TATATAAATATAAATT
40367720 ACTTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 16 0.62
31 8 0.31
32 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAATATTTTAATATATAAATATAAATTT
Found at i:40370863 original size:15 final size:12
Alignment explanation
Indices: 40370826--40370854 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40370816 AGTGCATATA
40370826 TGCTTGGTTTGG
1 TGCTTGGTTTGG
40370838 TGCTTGGTTTGG
1 TGCTTGGTTTGG
40370850 TGCTT
1 TGCTT
40370855 ATAGGTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.38, T:0.52
Consensus pattern (12 bp):
TGCTTGGTTTGG
Found at i:40374882 original size:34 final size:34
Alignment explanation
Indices: 40374844--40374943 Score: 137
Period size: 34 Copynumber: 2.9 Consensus size: 34
40374834 GTCTCAATGA
* * *
40374844 GGGCCTTAGACCATTTCAGTAACAGTAGTAGTCT
1 GGGCCTAAGCCCATTTTAGTAACAGTAGTAGTCT
* *
40374878 GGGCCTAAGCCCATTTTAGTAATAGTAGCAGTCT
1 GGGCCTAAGCCCATTTTAGTAACAGTAGTAGTCT
* *
40374912 GGGCCTGAGCCCATTTTAGTAACAGTATTAGT
1 GGGCCTAAGCCCATTTTAGTAACAGTAGTAGT
40374944 ATAGTATGCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (34 bp):
GGGCCTAAGCCCATTTTAGTAACAGTAGTAGTCT
Found at i:40389277 original size:46 final size:46
Alignment explanation
Indices: 40389114--40389286 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
40389104 AACCTGCCCC
* * * *
40389114 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * *
40389160 TAAATGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-ATTTGCATC-CA
* *
40389211 -CA---AACTCGAACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
40389253 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40389287 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 2 0.02
46 56 0.54
47 25 0.24
49 2 0.02
50 7 0.07
51 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:40389279 original size:93 final size:93
Alignment explanation
Indices: 40389120--40389289 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
40389110 CCCCTAAGTG
* * *
40389120 AACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
40389185 GAGTTCAGATGCCTAGTTACATCTCACA
66 GAGTTCAGATGCCTAGTTACATCTCACA
* * *
40389213 AACTCGAACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
*
40389278 GAGTTCGGATGC
66 GAGTTCAGATGC
40389290 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (93 bp):
AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCAGATGCCTAGTTACATCTCACA
Found at i:40392643 original size:54 final size:53
Alignment explanation
Indices: 40392526--40392701 Score: 194
Period size: 54 Copynumber: 3.3 Consensus size: 53
40392516 GAATACTTTA
* * * *
40392526 GTTTACCAAATTACTGAAATATCCTC-AGTTGTAAAATTACCAAAGTACCCTC
1 GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
* * *
40392578 GGTTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTATCGAAA-TACCCTC
1 -GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATC-AAAGTACCCTC
* ** * *
40392632 AGTTTGCAAAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTC
1 -GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
40392686 GATTTACAAAATTACC
1 G-TTTACAAAATTACC
40392702 ATTTTACCCT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
53 26 0.26
54 72 0.71
55 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (53 bp):
GTTTACAAAATTACCGAAATATCCTCGACTTGTAAAATTATCAAAGTACCCTC
Found at i:40392669 original size:27 final size:27
Alignment explanation
Indices: 40392533--40392699 Score: 117
Period size: 27 Copynumber: 6.2 Consensus size: 27
40392523 TTAGTTTACC
* * *
40392533 AAATTACTGAAATATCCTC-AGTTGTA
1 AAATTATTGAAATACCCTCGATTTGTA
** * *
40392559 AAATTA-CCAAAGTACCCTCGGTTTATA
1 AAATTATTGAAA-TACCCTCGATTTGTA
*** *
40392586 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTATTGAAATACCCTCGATTTGTA
* *
40392613 AAATTATCGAAATACCCTC-AGTTTGCA
1 AAATTATTGAAATACCCTCGA-TTTGTA
**
40392640 AAATTATTGAAATACCCTCGACATGTA
1 AAATTATTGAAATACCCTCGATTTGTA
* **
40392667 AAATTA-TCAAAGTACCCTCGATTTACA
1 AAATTATTGAAA-TACCCTCGATTTGTA
40392694 AAATTA
1 AAATTA
40392700 CCATTTTACC
Statistics
Matches: 113, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.03
26 17 0.15
27 87 0.77
28 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTATTGAAATACCCTCGATTTGTA
Found at i:40392709 original size:27 final size:27
Alignment explanation
Indices: 40392679--40392851 Score: 256
Period size: 27 Copynumber: 6.4 Consensus size: 27
40392669 ATTATCAAAG
*
40392679 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
40392706 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTATTT
40392733 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
40392760 TACCCTCGATTTACAGAGTTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* *
40392787 TACCCTTGAATTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTATTT
* **
40392814 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTATTT
40392841 TACCCTCGATT
1 TACCCTCGATT
40392852 GTGAAATTAC
Statistics
Matches: 131, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 131 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTATTT
Found at i:40392737 original size:81 final size:81
Alignment explanation
Indices: 40392652--40392835 Score: 199
Period size: 81 Copynumber: 2.3 Consensus size: 81
40392642 ATTATTGAAA
** *
40392652 TACCCTCGACATGTAAAATTA-TCAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAT
1 TACCCTCGACATACAAAATTACT-AAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAA
* *
40392716 TTACAGAATTACTGTTT
65 TTACAAAATTACTATTT
** *** * * * *
40392733 TACCCTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAGTTACTATTTTACCCTTGAAT
1 TACCCTCGACATACAAAATTACTAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAAT
40392798 TACAAAATTACTATTT
66 TACAAAATTACTATTT
* **
40392814 TACCCTTGATTTACAAAATTAC
1 TACCCTCGACATACAAAATTAC
40392836 CGTTTTACCC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 86 0.99
82 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (81 bp):
TACCCTCGACATACAAAATTACTAAAGTACCCTCGATTTACAAAATTACCATTTTACCCTCGAAT
TACAAAATTACTATTT
Found at i:40392886 original size:27 final size:27
Alignment explanation
Indices: 40392856--40393237 Score: 441
Period size: 27 Copynumber: 14.2 Consensus size: 27
40392846 TCGATTGTGA
*
40392856 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** * ** *
40392883 AATTACCAAAACACCCCTAGT-TTGTAA
1 AATTACTGAAATACCCCT-GTAGGGTAG
** *
40392910 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
40392937 AATTACTAAAATA-CCCTAGTAAGGTAG
1 AATTACTGAAATACCCCT-GTAGGGTAG
* *
40392964 AATTACCG-AATACCTCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
40392990 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
40393017 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
40393044 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
40393071 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
40393098 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
40393125 AATTA-TCGCAATACCCCTATAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
40393152 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
40393179 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
40393206 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
40393232 AATTAC
1 AATTAC
40393238 CATTTTGCCC
Statistics
Matches: 304, Mismatches: 44, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
26 41 0.13
27 262 0.86
28 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:40393517 original size:27 final size:26
Alignment explanation
Indices: 40393479--40393530 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
40393469 CTCGCTGCAA
*
40393479 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
40393506 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACTTCGCCACAATATCTG
40393531 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:40393658 original size:6 final size:6
Alignment explanation
Indices: 40393649--40393801 Score: 143
Period size: 6 Copynumber: 24.8 Consensus size: 6
40393639 TTGCATTCAC
*
40393649 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
40393698 -TTACCTA ATTCTG ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ATACTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * *
40393748 ATTCTG ATTCTG GTTCTG ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
40393797 ATTCT
1 ATTCT
40393802 AGTTATGATA
Statistics
Matches: 121, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
5 7 0.06
6 98 0.81
7 11 0.09
8 5 0.04
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:40393684 original size:31 final size:31
Alignment explanation
Indices: 40393649--40393765 Score: 153
Period size: 31 Copynumber: 3.6 Consensus size: 31
40393639 TTGCATTCAC
40393649 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
40393680 ATTCTGATTCTGATTCTGTTACCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTA-C-----CTGATACTG
*
40393717 GTTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
40393748 ATTCTGATTCTGGTTCTG
1 ATTCTGATTCTGATTCTG
40393766 ATTTTGATTC
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
31 45 0.60
32 1 0.01
36 1 0.01
37 28 0.37
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:40393712 original size:37 final size:35
Alignment explanation
Indices: 40393649--40393801 Score: 154
Period size: 37 Copynumber: 4.3 Consensus size: 35
40393639 TTGCATTCAC
*
40393649 ATTCTGATTCTGATTCTGTTA-C---CTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTATCTGATTCTG
40393680 ATTCTGATTCTGATTCTGTTACCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCT-A-TCTGATTCTG
*
40393717 GTTCTGATTCTGATTCTGTTACCTGATACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCT-AT-CTGATTCTG
* * * *
40393754 ATTCTGGTTCTGATTTTGATT-CTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTG-TTAC-CT-ATCTGATTCTG
40393791 ATTCTGATTCT
1 ATTCTGATTCT
40393802 AGTTATGATA
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
31 21 0.20
32 1 0.01
36 1 0.01
37 76 0.74
38 4 0.04
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (35 bp):
ATTCTGATTCTGATTCTGTTACCTATCTGATTCTG
Found at i:40393724 original size:43 final size:42
Alignment explanation
Indices: 40393677--40393810 Score: 153
Period size: 43 Copynumber: 3.1 Consensus size: 42
40393667 TTACCTGATA
*
40393677 CTGATTCTGATTCTGATT-CTGTTACCTAATTCTGATTCTGGTT
1 CTGATTCTGATTCTG-TTACTGATA-CTAATTCTGATTCTGGTT
*
40393720 CTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGGTT
1 CTGATTCTGATTCTGTTA-CTGATACTAATTCTGATTCTGGTT
* * * * *
40393763 CTGATTTTGATTCTGTCACCTGATTCTGATTCTGATTCTAGTT
1 CTGATTCTGATTCTGTTA-CTGATACTAATTCTGATTCTGGTT
*
40393806 ATGAT
1 CTGAT
40393811 AATGTTTCTT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 2 0.02
43 75 0.91
44 5 0.06
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (42 bp):
CTGATTCTGATTCTGTTACTGATACTAATTCTGATTCTGGTT
Found at i:40399579 original size:93 final size:93
Alignment explanation
Indices: 40399468--40399638 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40399458 GCCCCTAAGT
* * *
40399468 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
40399533 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
40399561 GAACTCAGACTCAACTCAATGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
40399626 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40399639 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40399635 original size:46 final size:46
Alignment explanation
Indices: 40399463--40399635 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
40399453 AACCTGCCCC
* * *
40399463 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
40399509 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * * *
40399557 TCA-CGAACTCAGACTCAACTCAATGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
40399602 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40399636 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 58 0.56
47 27 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:40400092 original size:30 final size:30
Alignment explanation
Indices: 40400058--40400117 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
40400048 ATTTAATACG
40400058 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** * *
40400088 AACTTTTGCATAATTAGACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
40400118 GGCTCAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:40400475 original size:233 final size:233
Alignment explanation
Indices: 40400068--40400499 Score: 864
Period size: 233 Copynumber: 1.9 Consensus size: 233
40400058 AACTTTAAAA
40400068 AAATTACACTTTTGCCCCTAAACTTTTGCATAATTAGACTTTTGCCCCTAGGCTCAGGAATTAAA
1 AAATTACACTTTTGCCCCTAAACTTTTGCATAATTAGACTTTTGCCCCTAGGCTCAGGAATTAAA
40400133 CTTTATTCCTTATTCTTATGTTTTATAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAA
66 CTTTATTCCTTATTCTTATGTTTTATAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAA
40400198 TTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTGCCGATTAAGCCCTTTTACTCGTTT
131 TTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTGCCGATTAAGCCCTTTTACTCGTTT
40400263 TCACACACTTTTGCCCCTAAACTTTTGCATATTTAGAC
196 TCACACACTTTTGCCCCTAAACTTTTGCATATTTAGAC
40400301 AAATTACACTTTTGCCCCTAAACTTTTGCATAATTAGACTTTTGCCCCTAGGCTCAGGAATTAAA
1 AAATTACACTTTTGCCCCTAAACTTTTGCATAATTAGACTTTTGCCCCTAGGCTCAGGAATTAAA
40400366 CTTTATTCCTTATTCTTATGTTTTATAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAA
66 CTTTATTCCTTATTCTTATGTTTTATAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAA
40400431 TTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTGCCGATTAAGCCCTTTTACTCGTTT
131 TTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTGCCGATTAAGCCCTTTTACTCGTTT
40400496 TCAC
196 TCAC
40400500 TAAAAACCGA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 199 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.41
Consensus pattern (233 bp):
AAATTACACTTTTGCCCCTAAACTTTTGCATAATTAGACTTTTGCCCCTAGGCTCAGGAATTAAA
CTTTATTCCTTATTCTTATGTTTTATAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAA
TTCTCTCTCTAACATATACTTGTGACTATTAGGTATTTTTGCCGATTAAGCCCTTTTACTCGTTT
TCACACACTTTTGCCCCTAAACTTTTGCATATTTAGAC
Found at i:40403385 original size:31 final size:30
Alignment explanation
Indices: 40403343--40403406 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
40403333 CCTTTTCATA
*
40403343 TTTTATATTTCATAACACTGGGCCGAAGCC
1 TTTTATATTTCATAACACTAGGCCGAAGCC
**
40403373 TTTTCATATTTCATATTACTAGGCCGAAGCC
1 TTTT-ATATTTCATAACACTAGGCCGAAGCC
40403404 TTT
1 TTT
40403407 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTATATTTCATAACACTAGGCCGAAGCC
Found at i:40403642 original size:25 final size:24
Alignment explanation
Indices: 40403598--40403768 Score: 195
Period size: 25 Copynumber: 7.0 Consensus size: 24
40403588 TTGCTTTATC
*
40403598 ATATAACTGGAGGCCT-AGCCTCTTT
1 ATATAACTGG-GGCATAAGCC-CTTT
* *
40403623 -TAGTAACTTGGGCAAAAGCCCTTT
1 ATA-TAACTGGGGCATAAGCCCTTT
*
40403647 TTATAACTGGGGCATAAGCCCTTT
1 ATATAACTGGGGCATAAGCCCTTT
*
40403671 ATCGTAACTGGGGCATAAGCCCTTT
1 AT-ATAACTGGGGCATAAGCCCTTT
40403696 ATCATAACTGGGGCATAAGCCCTTT
1 AT-ATAACTGGGGCATAAGCCCTTT
*
40403721 ATCATAACTGGGGCATAAACCCTTT
1 AT-ATAACTGGGGCATAAGCCCTTT
* *
40403746 A-ATAACTAGGACATAAGCCCTTT
1 ATATAACTGGGGCATAAGCCCTTT
40403769 TGCACTTCCT
Statistics
Matches: 130, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
23 19 0.15
24 29 0.22
25 82 0.63
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
ATATAACTGGGGCATAAGCCCTTT
Found at i:40403840 original size:9 final size:9
Alignment explanation
Indices: 40403826--40403882 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40403816 ATCTCATGTG
40403826 CATATCATA
1 CATATCATA
*
40403835 CATATCATGTG
1 CATATCA--TA
40403846 CATATCATA
1 CATATCATA
* *
40403855 CATGTCATGTG
1 CATATCA--TA
40403866 CATATCATA
1 CATATCATA
40403875 CATATCAT
1 CATATCAT
40403883 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40403842 original size:20 final size:20
Alignment explanation
Indices: 40403814--40403884 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40403804 GCATTTATGA
*
40403814 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40403834 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40403854 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40403874 ACATATCATGT
1 ACATATCATGT
40403885 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40403849 original size:11 final size:11
Alignment explanation
Indices: 40403819--40403873 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40403809 TATGAACATC
40403819 TCATGTGCATA
1 TCATGTGCATA
*
40403830 TCA--TACATA
1 TCATGTGCATA
40403839 TCATGTGCATA
1 TCATGTGCATA
* *
40403850 TCA--TACATG
1 TCATGTGCATA
40403859 TCATGTGCATA
1 TCATGTGCATA
40403870 TCAT
1 TCAT
40403874 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40405226 original size:27 final size:27
Alignment explanation
Indices: 40405126--40405209 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
40405116 GGGCATATTC
* *
40405126 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
*
40405153 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40405180 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40405207 GTC
1 GTC
40405210 TTTTTACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:40405319 original size:27 final size:27
Alignment explanation
Indices: 40405271--40405322 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40405261 GTAAATCTAC
*
40405271 AAACCAAAGGTATTTTAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
*
40405298 AAACCAATGGTATTTCCA-TAATTTT
1 AAACCAAAGGTATTT-CAGTAATTTT
40405323 TAGAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:40405384 original size:27 final size:27
Alignment explanation
Indices: 40405354--40405516 Score: 154
Period size: 27 Copynumber: 6.0 Consensus size: 27
40405344 GTAACTTTGT
40405354 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
* * *
40405381 AAAT-TGAGGGTATTTCGGTAATTTCAC
1 AAATCAG-GGGTATTTTGGTAATTTTAC
* * *
40405408 AAACCAGTGGTAGTTTGGTAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
40405435 AAA-CTAGGGGTATTTTGGTAATTTTAC
1 AAATC-AGGGGTATTTTGGTAATTTTAC
*
40405462 AAAT-TGAGGGTATTTCT-GTAATTTTAC
1 AAATCAG-GGGTATTT-TGGTAATTTTAC
* * * * *
40405489 AAACCAAGGATATTTTAGCAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
40405516 A
1 A
40405517 GACTAGGGTA
Statistics
Matches: 111, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.04
27 105 0.95
28 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AAATCAGGGGTATTTTGGTAATTTTAC
Found at i:40405461 original size:81 final size:81
Alignment explanation
Indices: 40405359--40405553 Score: 259
Period size: 81 Copynumber: 2.4 Consensus size: 81
40405349 TTTGTAAATC
*
40405359 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTAGTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GATAGTT
* *
40405423 TGGTAATTTTACAAACT
65 TAGCAATTTTACAAACT
* * *
40405440 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGATATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGATAGTTT
*
40405505 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
* * ** *
40405521 A-GGGTATTCTAGTAATTTTGTAAATCGAGGGTA
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTA
40405554 AAACAGTAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
80 27 0.27
81 72 0.71
82 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGATAGTTT
AGCAATTTTACAAACT
Found at i:40405483 original size:54 final size:52
Alignment explanation
Indices: 40405361--40405539 Score: 155
Period size: 54 Copynumber: 3.3 Consensus size: 52
40405351 TGTAAATCAG
* * * * *
40405361 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACCA
1 GGGTATTTTAGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTTACAAA-TA
* *
40405414 GTGGTAGTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTGA
1 G-GGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAA-T-A
* * * * * *
40405469 GGGTATTTCT-GTAATTTTACAAACCAAGGATATTTTAGCAATTTTACAGACTA
1 GGGTATTT-TAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACA-AATA
*
40405522 GGGTATTCTAGTAATTTT
1 GGGTATTTTAGTAATTTT
40405540 GTAAATCGAG
Statistics
Matches: 106, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 1 0.01
53 17 0.16
54 82 0.77
55 6 0.06
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (52 bp):
GGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATA
Found at i:40405537 original size:26 final size:26
Alignment explanation
Indices: 40405361--40405539 Score: 130
Period size: 27 Copynumber: 6.7 Consensus size: 26
40405351 TGTAAATCAG
* * *
40405361 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTCTAGTAATTTTACAAACT-A
* * *
40405388 GGGTATT-TCGGTAATTTCACAAACCA
1 GGGTATTCT-AGTAATTTTACAAACTA
*
40405414 GTGGTAGTT-TGGTAATTTTACAAACTA
1 G-GGTA-TTCTAGTAATTTTACAAACTA
* * *
40405441 GGGGTATTTTGGTAATTTTACAAATTGA
1 -GGGTATTCTAGTAATTTTACAAACT-A
*
40405469 GGGTATTTCT-GTAATTTTACAAACCAA
1 GGGTA-TTCTAGTAATTTTACAAA-CTA
* * * *
40405496 GGATATTTTAGCAATTTTACAGACTA
1 GGGTATTCTAGTAATTTTACAAACTA
40405522 GGGTATTCTAGTAATTTT
1 GGGTATTCTAGTAATTTT
40405540 GTAAATCGAG
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
26 25 0.20
27 93 0.74
28 8 0.06
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (26 bp):
GGGTATTCTAGTAATTTTACAAACTA
Found at i:40405561 original size:27 final size:27
Alignment explanation
Indices: 40405532--40405715 Score: 235
Period size: 27 Copynumber: 6.8 Consensus size: 27
40405522 GGGTATTCTA
* *
40405532 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40405559 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40405586 GTACTTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40405613 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40405640 GTAATTATGTAAATCG-GGGTTAAAATG
1 GTAATTCTGTAAATCGAGGG-TAAAACG
* * *
40405667 GTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40405694 GTAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40405716 CTTTGGTAAT
Statistics
Matches: 140, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.02
27 134 0.96
28 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:40405577 original size:80 final size:81
Alignment explanation
Indices: 40405359--40405577 Score: 183
Period size: 81 Copynumber: 2.7 Consensus size: 81
40405349 TTTGTAAATC
* * * *** * * *
40405359 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATT-TCACAAACC-AGTGGTAGT
1 AGGGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCT-ACAAACCAAG-GATATT
* *
40405422 TTGGTAATTTTACAAACT
64 TTAGCAATTTTACAAACT
* * * *** * *
40405440 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGATATTTT
1 AGGGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGGATATTTT
*
40405505 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
** * *
40405521 A-GGGTATTCTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGG
1 AGGGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGG
40405578 GTAAAACGGT
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
80 44 0.37
81 71 0.60
82 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (81 bp):
AGGGGTATTCTAGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTACAAACCAAGGATATTTT
AGCAATTTTACAAACT
Found at i:40405742 original size:27 final size:27
Alignment explanation
Indices: 40405721--40405810 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
40405711 GGGTACTTTG
*
40405721 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
40405748 GTAATTTTACAAATCGATGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
40405775 GTATTTTTACAAA-CTAAGCGTATTTCG
1 GTAATTTTACAAATCGAAG-GTATTTCA
40405802 GTAATTTTA
1 GTAATTTTA
40405811 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.05
27 52 0.95
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:40405824 original size:27 final size:27
Alignment explanation
Indices: 40405721--40405825 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
40405711 GGGTACTTTG
* *
40405721 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
40405748 GTAATTTTACAAATCGATG-GTATTTCA
1 GTAATTTTACAAA-CTAAGAGTATTTCA
* * *
40405775 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
40405802 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
40405826 CTAAACAGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.05
27 56 0.85
28 7 0.11
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:40411552 original size:45 final size:46
Alignment explanation
Indices: 40411491--40411605 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 46
40411481 TGTGCCATGG
* *
40411491 TGTCTTTCAATAATGGTCTTATTTATTCTCT-TCTTAATGCCATAA
1 TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
* * * * * ** *
40411536 TGTCTTTCAACCATGGTTTTATTCATTTTTTGTCGTGTTGCCATAG
1 TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
*
40411582 TGTCTTTCAACTATGGTCTTATTT
1 TGTCTTTCAACAATGGTCTTATTT
40411606 CTTTGATTCA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
45 25 0.45
46 31 0.55
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.50
Consensus pattern (46 bp):
TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
Found at i:40411677 original size:45 final size:46
Alignment explanation
Indices: 40411640--40411741 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 46
40411630 CTTTCAGCTG
*
40411640 TGGTCTTACTCTG-TAGAATCGTGATGCCATAACGTCTTTCA-ATCA
1 TGGTCTTACTC-GATAGAATCATGATGCCATAACGTCTTTCAGATCA
*
40411685 TGGTCTTACTCGATAGAATCATGATGCCATAATGTCTTTCAG-TCA
1 TGGTCTTACTCGATAGAATCATGATGCCATAACGTCTTTCAGATCA
*
40411730 TGGTTTTACTCG
1 TGGTCTTACTCG
40411742 TTTCTGGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (46 bp):
TGGTCTTACTCGATAGAATCATGATGCCATAACGTCTTTCAGATCA
Found at i:40411807 original size:46 final size:47
Alignment explanation
Indices: 40411742--40411835 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 47
40411732 GTTTTACTCG
* * *
40411742 TTTCTGGTATGGTGCCATAGTGTTTTTCAACTATGGTCTTATTTATT
1 TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
*
40411789 TTTC-GGTATAGTGTCATAGTGTCTTTCAACTATGGTCTTAATTATT
1 TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
40411835 T
1 T
40411836 CTTTCAAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 39 0.91
47 4 0.09
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.50
Consensus pattern (47 bp):
TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
Found at i:40413570 original size:40 final size:42
Alignment explanation
Indices: 40413506--40413598 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
40413496 CTATGTTTGT
* *
40413506 CACTTAGTGTGCATATCGAGATAGCTTCAGCTATATA-A-AG
1 CACTTAGTGTGCAAATCGAGATAGCTTCAGATATATATATAG
*
40413546 CACTTAGTGTGCAAATC-AGAATAGCTTCGGATATATATATAG
1 CACTTAGTGTGCAAATCGAG-ATAGCTTCAGATATATATATAG
40413588 CACTTAGTGTG
1 CACTTAGTGTG
40413599 TGAGACTGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.04
40 31 0.66
41 1 0.02
42 13 0.28
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (42 bp):
CACTTAGTGTGCAAATCGAGATAGCTTCAGATATATATATAG
Found at i:40413640 original size:41 final size:41
Alignment explanation
Indices: 40413587--40413680 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
40413577 TATATATATA
*
40413587 GCACTTAGTGTGTGAGACTGTGATAGCTTCGTCTATGAAAG
1 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
40413628 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
1 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
*
40413669 CCACTTAGTGTG
1 GCACTTAGTGTG
40413681 CAAGATTACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (41 bp):
GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
Found at i:40413695 original size:41 final size:40
Alignment explanation
Indices: 40413526--40413705 Score: 139
Period size: 41 Copynumber: 4.4 Consensus size: 40
40413516 GCATATCGAG
* * *
40413526 ATAGCTTCAGCTATATAAAGCACTTAGTGTGCAA-A-TCAGA
1 ATAGCTTCGGCTAT-GAAAGCACTTAGTGTGCAAGACT-ATA
* * ** * *
40413566 ATAGCTTCGGATATATATATAGCACTTAGTGTGTGAGACTGTG
1 ATAGCTTCGGCTAT-GA-A-AGCACTTAGTGTGCAAGACTATA
* ** * *
40413609 ATAGCTTCGTCTATGAAAGGCACTTAGTGTGTGAGACTGTG
1 ATAGCTTCGGCTATGAAA-GCACTTAGTGTGCAAGACTATA
* *
40413650 ATAGCTTCGGCTATGAAAGCCACTTAGTGTGCAAGATTACA
1 ATAGCTTCGGCTATGAAAG-CACTTAGTGTGCAAGACTATA
40413691 ATAGCTTCGGCTATG
1 ATAGCTTCGGCTATG
40413706 CTTTGGCACT
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
40 17 0.15
41 71 0.61
42 15 0.13
43 13 0.11
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
ATAGCTTCGGCTATGAAAGCACTTAGTGTGCAAGACTATA
Found at i:40416967 original size:41 final size:41
Alignment explanation
Indices: 40416905--40416985 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
40416895 CATTATCACA
40416905 AGAGAAAACAAAATGGAACGAGGCTAATTACTCCATCCATT
1 AGAGAAAACAAAATGGAACGAGGCTAATTACTCCATCCATT
* *
40416946 AGAGGAAACAAAATGGAACGAGGCTAGTTACTCCATCCAT
1 AGAGAAAACAAAATGGAACGAGGCTAATTACTCCATCCAT
40416986 ACCGAACCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.19
Consensus pattern (41 bp):
AGAGAAAACAAAATGGAACGAGGCTAATTACTCCATCCATT
Found at i:40417395 original size:55 final size:55
Alignment explanation
Indices: 40417334--40417485 Score: 232
Period size: 55 Copynumber: 2.8 Consensus size: 55
40417324 ATATTAAGTC
* * *
40417334 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
40417389 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * *
40417444 CGCACACTTAGTGCTGCATATTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
40417486 GCACAATTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 89 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:40417488 original size:27 final size:27
Alignment explanation
Indices: 40417334--40417485 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
40417324 ATATTAAGTC
* *
40417334 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
40417361 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
40417389 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
40417416 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* * *
40417444 CGCACACTTAGTGCTGCATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
40417471 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40417486 GCACAATTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 66 0.56
28 51 0.44
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40417503 original size:27 final size:27
Alignment explanation
Indices: 40417363--40417504 Score: 78
Period size: 27 Copynumber: 5.2 Consensus size: 27
40417353 AATCAACTCG
*
40417363 CACACTTAGTGCTACATAA-TC-ATACTC
1 CACACTTAGTGCTGCA-AATTCAATAC-C
* * * *
40417390 GCACACTTAGTGCTACATAGTCAACT-CG
1 -CACACTTAGTGCTGCAAATTCAA-TACC
* * *
40417418 CACACTTAGTGCTACATAGTCAA-ACTC
1 CACACTTAGTGCTGCAAATTCAATAC-C
* * *
40417445 GCACACTTAGTGCTGCATATTCAATTCG
1 -CACACTTAGTGCTGCAAATTCAATACC
*
40417473 CACACTTAGTGCTGCACAATTTAA-ACC
1 CACACTTAGTGCTGCA-AATTCAATACC
40417500 CACAC
1 CACAC
40417505 AGTTAGCGCC
Statistics
Matches: 95, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
26 1 0.01
27 46 0.48
28 44 0.46
29 3 0.03
30 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.27
Consensus pattern (27 bp):
CACACTTAGTGCTGCAAATTCAATACC
Found at i:40420347 original size:31 final size:31
Alignment explanation
Indices: 40420309--40420372 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40420299 CCTTTTCATA
*
40420309 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
**
40420340 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
40420371 TT
1 TT
40420373 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:40420608 original size:25 final size:23
Alignment explanation
Indices: 40420565--40420710 Score: 177
Period size: 25 Copynumber: 6.0 Consensus size: 23
40420555 TGCTTTATCA
*
40420565 TATAACTGGAGGCCT-AGCCTCTTT
1 TATAACTGG-GGCATAAGCC-CTTT
*
40420589 TAGTAACTGGGGCAAAAGCCCTTTT
1 TA-TAACTGGGGCATAAGCCC-TTT
40420614 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
*
40420637 ATCGTAACTGGGGCATAAGCCCTTCAT
1 -T-ATAACTGGGGCATAAGCCCTT--T
40420664 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
*
40420687 AATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
40420710 T
1 T
40420711 GCACTTCCTC
Statistics
Matches: 108, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
23 26 0.24
24 24 0.22
25 56 0.52
26 1 0.01
27 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (23 bp):
TATAACTGGGGCATAAGCCCTTT
Found at i:40420644 original size:49 final size:48
Alignment explanation
Indices: 40420565--40420710 Score: 190
Period size: 49 Copynumber: 3.0 Consensus size: 48
40420555 TGCTTTATCA
* *
40420565 TATAACTGGAGGCCT-AGCCTCTTT-TAGTAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTAT-GTAACTGGGGCATAAGCCCTTTT
*
40420614 TATAACTGGGGCATAAGCCCTTTATCGTAACTGGGGCATAAGCCCTTCAT
1 TATAACTGGGGCATAAGCCCTTTAT-GTAACTGGGGCATAAGCCCTT-TT
*
40420664 TATAACTGGGGCATAAGCCCTTTA-ATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTATGTAACTGGGGCATAAGCCCTTTT
40420711 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
47 1 0.01
48 28 0.32
49 34 0.39
50 25 0.28
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTATGTAACTGGGGCATAAGCCCTTTT
Found at i:40420784 original size:20 final size:20
Alignment explanation
Indices: 40420756--40420826 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
40420746 GCATTTATGA
*
40420756 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40420776 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
* *
40420796 ACATGTCTTGTGCATATCAT
1 ACATATCATGTGCATATCAT
40420816 ACATATCATGT
1 ACATATCATGT
40420827 TTATCAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40422090 original size:25 final size:28
Alignment explanation
Indices: 40422053--40422140 Score: 98
Period size: 27 Copynumber: 3.3 Consensus size: 28
40422043 TCATACGGAA
*
40422053 CATA-AGGGCATATT-C-GTCATTTTAC
1 CATACAGGGCATATTACGGTCACTTTAC
40422078 CATACAGGG-ATATTACGGTCACTTTAC
1 CATACAGGGCATATTACGGTCACTTTAC
*
40422105 CCTACAAGGGC-T-TTACGGTCACTTTAC
1 CATAC-AGGGCATATTACGGTCACTTTAC
*
40422132 CCTACAGGG
1 CATACAGGG
40422141 GCTTTACGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.16
26 9 0.16
27 33 0.59
28 5 0.09
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (28 bp):
CATACAGGGCATATTACGGTCACTTTAC
Found at i:40422168 original size:27 final size:27
Alignment explanation
Indices: 40422068--40422151 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
40422058 GGGCATATTC
* * *
40422068 GTCATTTTACCATACA-GGGATATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
*
40422095 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40422122 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40422149 GTC
1 GTC
40422152 TTTTTACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 48 0.92
28 4 0.08
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:40422261 original size:27 final size:27
Alignment explanation
Indices: 40422213--40422264 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40422203 GTAAATCTAC
*
40422213 AAACCAAAGGTATTTTAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
*
40422240 AAACCAATGGTATTTCCA-TAATTTT
1 AAACCAAAGGTATTT-CAGTAATTTT
40422265 TAGAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:40422326 original size:27 final size:27
Alignment explanation
Indices: 40422296--40422539 Score: 239
Period size: 27 Copynumber: 9.0 Consensus size: 27
40422286 GAAACTTTGT
40422296 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
* ** *
40422323 AAAT-TGAGGGTATTTCAGTAATTTCAC
1 AAATCAG-GGGTATTTTGGTAATTTTAC
* *
40422350 AAACCAGTGGTATTTTGGTAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
40422377 AAA-CTAGGGGTATTTTGGTAATTTTAC
1 AAATC-AGGGGTATTTTGGTAATTTTAC
* ** *
40422404 AAAT-TGAGGGTATTTCAGTAATTTCAC
1 AAATCAG-GGGTATTTTGGTAATTTTAC
* *
40422431 AAACCAGTGGTATTTTGGTAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
40422458 AAA-CTAGGGGTATTTTGGTAATTTTAC
1 AAATC-AGGGGTATTTTGGTAATTTTAC
*
40422485 AAAT-TGAGGGTATTTCT-GTAATTTTAC
1 AAATCAG-GGGTATTT-TGGTAATTTTAC
* * * *
40422512 AAACCAAGGGTATTTTAGCAATTTTAC
1 AAATCAGGGGTATTTTGGTAATTTTAC
40422539 A
1 A
40422540 GACTATGGTA
Statistics
Matches: 178, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
26 6 0.03
27 169 0.95
28 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AAATCAGGGGTATTTTGGTAATTTTAC
Found at i:40422395 original size:81 final size:81
Alignment explanation
Indices: 40422301--40422576 Score: 430
Period size: 81 Copynumber: 3.4 Consensus size: 81
40422291 TTTGTAAATC
40422301 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
40422366 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
40422382 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
40422447 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
* *
40422463 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAG-GGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACC-AGTGGTATTT
* * *
40422527 TAGCAATTTTACAGACT
65 TGGTAATTTTACAAACT
* * * ** *
40422544 A-TGGTATTCTAGTAATTTTGTAAATCGAGGGTA
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTA
40422577 AAACAGTAAT
Statistics
Matches: 183, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
80 26 0.14
81 155 0.85
82 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTT
GGTAATTTTACAAACT
Found at i:40422584 original size:27 final size:27
Alignment explanation
Indices: 40422555--40422738 Score: 208
Period size: 27 Copynumber: 6.8 Consensus size: 27
40422545 TGGTATTCTA
* *
40422555 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40422582 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
40422609 ATACTTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40422636 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40422663 GTAATTATGTAAATCG-GGGTTAAAATG
1 GTAATTCTGTAAATCGAGGG-TAAAACG
* * *
40422690 GTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40422717 GTAATTTTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40422739 CTTTGGTAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
26 3 0.02
27 132 0.96
28 3 0.02
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:40422674 original size:54 final size:54
Alignment explanation
Indices: 40422555--40422738 Score: 235
Period size: 54 Copynumber: 3.4 Consensus size: 54
40422545 TGGTATTCTA
* * *
40422555 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
* * * *
40422609 ATACTTCTGTAAGTCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
* * * **
40422663 GTAATTATGTAAATCG-GGGTTAAAATGGTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTTTGTAAATCGAGGG-TAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
*
40422717 GTAATTTTGTAAATCGGGGGTA
1 GTAATTTTGTAAATCGAGGGTA
40422739 CTTTGGTAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 3 0.03
54 106 0.95
55 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (54 bp):
GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAATG
Found at i:40422765 original size:27 final size:27
Alignment explanation
Indices: 40422744--40422833 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
40422734 GGGTACTTTG
*
40422744 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
40422771 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
40422798 GTATTTTTACAAA-CTAAGCGTATTTCG
1 GTAATTTTACAAATCGAAG-GTATTTCA
40422825 GTAATTTTA
1 GTAATTTTA
40422834 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.05
27 52 0.95
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:40422775 original size:54 final size:54
Alignment explanation
Indices: 40422717--40422838 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 54
40422707 GGGTAAAATG
* * *
40422717 GTAATTTTGTAAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTGTAAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGCGTATTTCA
** * * *
40422771 GTAATTTTACAAATCGAGGGTATTTCAGTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTGTAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGCGTATTTCA
40422825 GTAATTTTAGTAAA
1 GTAATTTT-GTAAA
40422839 CTAAAGTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
53 7 0.13
54 45 0.82
55 3 0.05
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (54 bp):
GTAATTTTGTAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGCGTATTTCA
Found at i:40422847 original size:27 final size:27
Alignment explanation
Indices: 40422744--40422848 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
40422734 GGGTACTTTG
* *
40422744 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
40422771 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
40422798 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
40422825 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
40422849 CTAAACAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 54 0.84
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:40428537 original size:22 final size:21
Alignment explanation
Indices: 40428512--40428563 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
40428502 ACCTGAGAAG
40428512 AAAATCAAAAAAATAAAAATAA
1 AAAATCAAAAAAATAAAAA-AA
* ** *
40428534 AAAATTAATTAAATAAGAAAA
1 AAAATCAAAAAAATAAAAAAA
40428555 AAAA-CAAAA
1 AAAATCAAAA
40428564 TTGTAAGAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.09
21 6 0.26
22 15 0.65
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (21 bp):
AAAATCAAAAAAATAAAAAAA
Found at i:40428829 original size:18 final size:17
Alignment explanation
Indices: 40428804--40428837 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40428794 ATTAAACTAA
*
40428804 TTAACTAAATGCAAATT
1 TTAACTAAATGAAAATT
40428821 TTAACCTAAATGAAAAT
1 TTAA-CTAAATGAAAAT
40428838 AAGATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAACTAAATGAAAATT
Found at i:40434009 original size:25 final size:25
Alignment explanation
Indices: 40433981--40434030 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40433971 TCTTCTCATA
* *
40433981 TCTTCACTTCTCTCTCATTTTTCTT
1 TCTTCACTTCCCTCTCATTATTCTT
* *
40434006 TCTTCATTTCCCTTTCATTATTCTT
1 TCTTCACTTCCCTCTCATTATTCTT
40434031 CATTCCCTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (25 bp):
TCTTCACTTCCCTCTCATTATTCTT
Found at i:40436470 original size:19 final size:19
Alignment explanation
Indices: 40436446--40436483 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40436436 AGTATCGTCA
40436446 TTGGTATTCCAAGGAGAAT
1 TTGGTATTCCAAGGAGAAT
40436465 TTGGTATTCCAAGGAGAAT
1 TTGGTATTCCAAGGAGAAT
40436484 GGTAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
TTGGTATTCCAAGGAGAAT
Found at i:40436537 original size:34 final size:34
Alignment explanation
Indices: 40436489--40436563 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
40436479 AGAATGGTAA
*
40436489 AAGAGTATGAACGAGGAAAGTCCCATTGAACCTT
1 AAGAATATGAACGAGGAAAGTCCCATTGAACCTT
*
40436523 AAGAATATGAACGAGGAAAGTCCCGTTGAACCTT
1 AAGAATATGAACGAGGAAAGTCCCATTGAACCTT
*
40436557 AGGAATA
1 AAGAATA
40436564 GATTCAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (34 bp):
AAGAATATGAACGAGGAAAGTCCCATTGAACCTT
Done.