Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 193 of 221
Found at i:56663397 original size:19 final size:20
Alignment explanation
Indices: 56663366--56663403 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56663356 TCATATTTTG
*
56663366 ATAATATAAAATATTTTAAT
1 ATAATATAAAATAATTTAAT
56663386 ATAATA-AAAATAATTTAA
1 ATAATATAAAATAATTTAA
56663404 ATTCAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATATAAAATAATTTAAT
Found at i:56682528 original size:26 final size:25
Alignment explanation
Indices: 56682499--56682595 Score: 86
Period size: 26 Copynumber: 3.7 Consensus size: 25
56682489 AAACGAAACA
* *
56682499 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATATA-AACAATTTAAAAT
** * *
56682525 AAATTGTATGTAAAACAAATTAAAAT
1 AAATAATATAT-AAACAATTTAAAAT
*
56682551 AAATAATACATAAAGCAATTTAAAAT
1 AAATAATATATAAA-CAATTTAAAAT
*
56682577 AAATAACATATAAGACAAT
1 AAATAATATATAA-ACAAT
56682596 AAAAAGTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
25 3 0.05
26 50 0.91
27 2 0.04
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (25 bp):
AAATAATATATAAACAATTTAAAAT
Found at i:56684532 original size:16 final size:16
Alignment explanation
Indices: 56684502--56684558 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
56684492 CATATTTTCA
56684502 TTAAAAACATAAAAATT
1 TTAAAAA-ATAAAAATT
*
56684519 TTAAAAAATGAAAATT
1 TTAAAAAATAAAAATT
*
56684535 TATGAAAAATAAAAATCT
1 T-TAAAAAATAAAAAT-T
56684553 TTAAAA
1 TTAAAA
56684559 TTCAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.26
17 23 0.68
18 2 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (16 bp):
TTAAAAAATAAAAATT
Found at i:56685699 original size:21 final size:21
Alignment explanation
Indices: 56685675--56685714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56685665 GAATGGAAAA
*
56685675 TAAAAAAAAATAAAGGAAAGT
1 TAAAAAAAAATAAAAGAAAGT
* *
56685696 TAAAATAATATAAAAGAAA
1 TAAAAAAAAATAAAAGAAA
56685715 AAATTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
TAAAAAAAAATAAAAGAAAGT
Found at i:56686000 original size:15 final size:15
Alignment explanation
Indices: 56685975--56686012 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
56685965 TTATACTACA
*
56685975 AAAACATTTATTATT
1 AAAATATTTATTATT
*
56685990 AATATATTTATTATT
1 AAAATATTTATTATT
56686005 AAAATATT
1 AAAATATT
56686013 AATATTGAAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:56688200 original size:53 final size:53
Alignment explanation
Indices: 56688133--56688239 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
56688123 TATTTAAGTA
* * *
56688133 ACAAATTGCGAATTGAGTTTTAACTCGATTGATATGTGTATTGTTGTTAATGT
1 ACAAATTACAAATTGAGTTTTAACTCGATTAATATGTGTATTGTTGTTAATGT
56688186 ACAAATTACAAATTGAGTTTTAACTCGATTAATATGTGTATTGTTGTTAATGT
1 ACAAATTACAAATTGAGTTTTAACTCGATTAATATGTGTATTGTTGTTAATGT
56688239 A
1 A
56688240 AGAAGTTCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (53 bp):
ACAAATTACAAATTGAGTTTTAACTCGATTAATATGTGTATTGTTGTTAATGT
Found at i:56689518 original size:13 final size:13
Alignment explanation
Indices: 56689497--56689547 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
56689487 AGTTCTTCAT
56689497 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
56689510 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
56689523 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
56689536 TACTTTTGAAAA
1 TGCTTTTGAAAA
56689548 ATTTGGTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:56697176 original size:5 final size:5
Alignment explanation
Indices: 56697168--56697220 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
56697158 TACCCTTTTC
*
56697168 TTTAT TTTAT TTTAT GTTAT TTTAT TTT-T CTTTA- TTTAT TTTAT TATTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT T-TTAT
56697218 TTT
1 TTT
56697221 TATATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 5 0.12
5 32 0.76
6 5 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:56697187 original size:10 final size:9
Alignment explanation
Indices: 56697168--56697269 Score: 57
Period size: 10 Copynumber: 10.8 Consensus size: 9
56697158 TACCCTTTTC
56697168 TTTATTTTAT
1 TTTA-TTTAT
56697178 TTTATGTTAT
1 TTTAT-TTAT
*
56697188 TTTATTTTT
1 TTTATTTAT
56697197 CTTTATTTAT
1 -TTTATTTAT
56697207 TTTATTATTAT
1 TTTA-T-TTAT
*
56697218 TTT-TATATT
1 TTTATTTA-T
*
56697227 TTTATATAT
1 TTTATTTAT
*
56697236 ATTATTTGA-
1 TTTATTT-AT
*
56697245 TCTATTT-T
1 TTTATTTAT
*
56697253 CTTATTTATT
1 TTTATTTA-T
56697263 TTTATTT
1 TTTATTT
56697270 TTATTTGTGC
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
8 7 0.10
9 24 0.33
10 34 0.47
11 7 0.10
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:56697197 original size:30 final size:30
Alignment explanation
Indices: 56697163--56697220 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
56697153 CCTTTTACCC
*
56697163 TTTTCTTTATTTTATTTTA-TGTTATTTTAT
1 TTTTCTTTA-TTTATTTTATTATTATTTTAT
56697193 TTTTCTTTATTTATTTTATTATTATTTT
1 TTTTCTTTATTTATTTTATTATTATTTT
56697221 TATATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (30 bp):
TTTTCTTTATTTATTTTATTATTATTTTAT
Found at i:56697202 original size:15 final size:15
Alignment explanation
Indices: 56697163--56697209 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
56697153 CCTTTTACCC
56697163 TTTTCTTTATTTTAT
1 TTTTCTTTATTTTAT
*
56697178 TTTAT-GTTATTTTAT
1 TTT-TCTTTATTTTAT
56697193 TTTTCTTTA-TTTAT
1 TTTTCTTTATTTTAT
56697207 TTT
1 TTT
56697210 ATTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 9 0.32
15 18 0.64
16 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTCTTTATTTTAT
Found at i:56697221 original size:12 final size:12
Alignment explanation
Indices: 56697172--56697344 Score: 57
Period size: 12 Copynumber: 14.9 Consensus size: 12
56697162 CTTTTCTTTA
56697172 TTTTATT-TTA-
1 TTTTATTATTAT
*
56697182 TGTTATT-TTAT
1 TTTTATTATTAT
*
56697193 TTTTCTTTATT-T
1 TTTT-ATTATTAT
56697205 ATTTTATTATTAT
1 -TTTTATTATTAT
56697218 TTTTA-TATT-T
1 TTTTATTATTAT
*
56697228 TTATATATATTA-
1 TTTTAT-TATTAT
*
56697240 TTTGATCTATT-T
1 TTTTAT-TATTAT
*
56697252 TCTTA-T-TTAT
1 TTTTATTATTAT
*
56697262 TTTTATTTTTAT
1 TTTTATTATTAT
** *
56697274 TTGTGCTTA-GAT
1 TT-TTATTATTAT
*
56697286 TTTAATT-TTAT
1 TTTTATTATTAT
*
56697297 TTTAATTATATTAT
1 TTTTA-T-TATTAT
*
56697311 TTTTAGTATT-T
1 TTTTATTATTAT
*
56697322 TTTTACTATTAT
1 TTTTATTATTAT
* *
56697334 TCTTACTATTA
1 TTTTATTATTA
56697345 CCTTTAATTT
Statistics
Matches: 123, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
9 2 0.02
10 20 0.16
11 28 0.23
12 54 0.44
13 11 0.09
14 8 0.07
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:56697230 original size:29 final size:30
Alignment explanation
Indices: 56697165--56697275 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 30
56697155 TTTTACCCTT
* *
56697165 TTCTTTATTTTATTTTA-TGTTATTTTATTT
1 TTCTTTA-TTTATTTTATTATTATTTTATTA
56697195 TTCTTTATTTATTTTATTATTATTTT-TATA
1 TTCTTTATTTATTTTATTATTATTTTAT-TA
* * * *
56697225 TT-TTTATATATATTATT-TGA-TCTATT-
1 TTCTTTATTTATTTTATTATTATTTTATTA
*
56697251 TTC-TTATTTATTTTTATTTTTATTT
1 TTCTTTATTTA-TTTTATTATTATTT
56697276 GTGCTTAGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
26 8 0.12
27 9 0.14
28 5 0.08
29 24 0.38
30 18 0.28
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (30 bp):
TTCTTTATTTATTTTATTATTATTTTATTA
Found at i:56697274 original size:24 final size:22
Alignment explanation
Indices: 56697177--56697275 Score: 72
Period size: 25 Copynumber: 4.0 Consensus size: 22
56697167 CTTTATTTTA
* *
56697177 TTTTATGTTATTTTATTTTTCTT
1 TTTTAT-TTATATTATTTTTATT
56697200 TATTTATTTTATTATTATTTTTATAT
1 T-TTTA-TTTA-TATTATTTTTAT-T
*
56697226 TTTTATATATATTATTTGATCTATT
1 TTTTATTTATATTATTT--T-TATT
*
56697251 TTCTTATTTATTTTTATTTTTATT
1 TT-TTATTTA-TATTATTTTTATT
56697275 T
1 T
56697276 GTGCTTAGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
23 9 0.15
24 15 0.24
25 20 0.32
26 11 0.18
27 7 0.11
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTATATTATTTTTATT
Found at i:56697392 original size:7 final size:6
Alignment explanation
Indices: 56697376--56697428 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
56697366 TTGAGTTTAT
* * * * * *
56697376 TTTTTC TTTTTC GTTTTC ATTTTC ATTTTC ATTTTC TTTTTG TTTTTA
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
56697424 TTTTT
1 TTTTT
56697429 GTTATTAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.08, C:0.11, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:56697398 original size:18 final size:18
Alignment explanation
Indices: 56697377--56697427 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
56697367 TGAGTTTATT
*
56697377 TTTTCTTTTTCGTTTTCA
1 TTTTCTTTTTCATTTTCA
* *
56697395 TTTTCATTTTCATTTTCT
1 TTTTCTTTTTCATTTTCA
*
56697413 TTTTGTTTTT-ATTTT
1 TTTTCTTTTTCATTTT
56697428 TGTTATTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTCATTTTCA
Found at i:56698437 original size:11 final size:10
Alignment explanation
Indices: 56698421--56698447 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56698411 ATTGTTCTAG
56698421 AAAAAAAAAT
1 AAAAAAAAAT
56698431 AAAAAAAAAT
1 AAAAAAAAAT
56698441 AAAAAAA
1 AAAAAAA
56698448 TTGATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:56699299 original size:30 final size:30
Alignment explanation
Indices: 56699285--56699346 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
56699275 TAGGCACATG
56699285 CCCGTGTGAGCCACACGGGCTGGACACTCA
1 CCCGTGTGAGCCACACGGGCTGGACACTCA
* *
56699315 CCCGTGTGAGCCACACGGGCTGAACACACA
1 CCCGTGTGAGCCACACGGGCTGGACACTCA
56699345 CC
1 CC
56699347 TATGTGCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (30 bp):
CCCGTGTGAGCCACACGGGCTGGACACTCA
Found at i:56702647 original size:43 final size:43
Alignment explanation
Indices: 56702599--56702891 Score: 286
Period size: 43 Copynumber: 6.8 Consensus size: 43
56702589 AAAAAAACAT
** * * *
56702599 CGCTAAAGGTCATGACCTTTAGCGGCGCTTCTCTAACAAACAC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATAACAAACGC
** * * * *
56702642 CGCTAAAGGTCATTG-TCTTTAGCGGCACTTTTCCT-ACAAATGC
1 CGCTAAAGACCA-TGACCTTTAGCGGCGCTTTT-ATAACAAACGC
* * *
56702685 CGCTAAAGACCATGACTTTTAGTGGCGCTTTTATATCAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATAACAAACGC
* * *
56702728 CGCTAAAGACCATGACTTTTAGCGGCACTTTTATATCAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATAACAAACGC
* * * *
56702771 CGCTAAAGACCATGACTTTTGGCGGCACTTTTATATCAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATAACAAACGC
* * **
56702814 CTCTAAAGACCAT-AGCCTTTAGCGGCGCTTCTACCACAAACGC
1 CGCTAAAGACCATGA-CCTTTAGCGGCGCTTTTATAACAAACGC
*
56702857 CGCTAAAGACCACGACCTTTTAGCGGCGCTCTTTA
1 CGCTAAAGACCATGACC-TTTAGCGGCGCT-TTTA
56702892 GTGGCGCTTT
Statistics
Matches: 214, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
42 4 0.02
43 190 0.89
44 17 0.08
45 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATAACAAACGC
Found at i:56702706 original size:86 final size:86
Alignment explanation
Indices: 56702599--56702891 Score: 331
Period size: 86 Copynumber: 3.4 Consensus size: 86
56702589 AAAAAAACAT
** * * * * * ** *
56702599 CGCTAAAGGTCATGACCTTTAGCGGCGCTTCTCTAACAAACACCGCTAAAGGTCATTGTCTTTAG
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTTTATATCAAACGCCGCTAAAGACCATTGACTTTAG
*
56702664 CGGCACTTTTCCTACAAATGC
66 CGGCACTTTTCCTACAAACGC
*
56702685 CGCTAAAGACCATGACTTTTAGTGGCGCTTTTATATCAAACGCCGCTAAAGACCA-TGACTTTTA
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTTTATATCAAACGCCGCTAAAGACCATTGAC-TTTA
*
56702749 GCGGCACTTTT-ATATCAAACGC
65 GCGGCACTTTTCCTA-CAAACGC
* * * * *
56702771 CGCTAAAGACCATGACTTTTGGCGGCACTTTTATATCAAACGCCTCTAAAGACCATAGCCTTTAG
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTTTATATCAAACGCCGCTAAAGACCATTGACTTTAG
* *
56702836 CGGCGCTTCTACC-ACAAACGC
66 CGGCACTT-TTCCTACAAACGC
*
56702857 CGCTAAAGACCACGACCTTTTAGCGGCGCTCTTTA
1 CGCTAAAGACCATGA-CTTTTAGCGGCGCT-TTTA
56702892 GTGGCGCTTT
Statistics
Matches: 175, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
85 5 0.03
86 150 0.86
87 16 0.09
88 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (86 bp):
CGCTAAAGACCATGACTTTTAGCGGCGCTTTTATATCAAACGCCGCTAAAGACCATTGACTTTAG
CGGCACTTTTCCTACAAACGC
Found at i:56702749 original size:129 final size:129
Alignment explanation
Indices: 56702599--56702886 Score: 323
Period size: 129 Copynumber: 2.2 Consensus size: 129
56702589 AAAAAAACAT
** * * ** *
56702599 CGCTAAAGGTCATGACCTTTAGCGGCGCTTCTCTAACAAACACCGCTAAAGGTCATTGTC-TTTA
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTCTATAACAAACACCGCTAAAGACCA-TGACTTTTA
* * * * * *
56702663 GCGGCACTTTTCCTA-CAAATGCCGCTAAAGACCAT-GACTTTTAGTGGCGCTTTTA-TATCAAA
65 GCGGCACTTTT-ATATCAAACGCCGCTAAAGACCATAG-CCTTTAGCGGCGCTTCTACCA-CAAA
56702725 CGC
127 CGC
* * * * *
56702728 CGCTAAAGACCATGACTTTTAGCGGCACTTTTATATCAAACGCCGCTAAAGACCATGACTTTTGG
1 CGCTAAAGACCATGACTTTTAGCGGCGCTTCTATAACAAACACCGCTAAAGACCATGACTTTTAG
*
56702793 CGGCACTTTTATATCAAACGCCTCTAAAGACCATAGCCTTTAGCGGCGCTTCTACCACAAACGC
66 CGGCACTTTTATATCAAACGCCGCTAAAGACCATAGCCTTTAGCGGCGCTTCTACCACAAACGC
*
56702857 CGCTAAAGACCACGACCTTTTAGCGGCGCT
1 CGCTAAAGACCATGA-CTTTTAGCGGCGCT
56702887 CTTTAGTGGC
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
128 5 0.04
129 113 0.85
130 15 0.11
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (129 bp):
CGCTAAAGACCATGACTTTTAGCGGCGCTTCTATAACAAACACCGCTAAAGACCATGACTTTTAG
CGGCACTTTTATATCAAACGCCGCTAAAGACCATAGCCTTTAGCGGCGCTTCTACCACAAACGC
Found at i:56703208 original size:19 final size:19
Alignment explanation
Indices: 56703184--56703221 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56703174 TACAAAAATG
*
56703184 TTAAAAGTTAAAATGATAA
1 TTAAAAGTCAAAATGATAA
56703203 TTAAAAGTCAAAATGATAA
1 TTAAAAGTCAAAATGATAA
56703222 AAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (19 bp):
TTAAAAGTCAAAATGATAA
Found at i:56703458 original size:66 final size:66
Alignment explanation
Indices: 56703350--56703513 Score: 206
Period size: 66 Copynumber: 2.5 Consensus size: 66
56703340 GCAGCCTCTA
* * * *
56703350 CTTCTCTCGCTGCCGCCTCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA-CTTCCGTTGAACCTT
1 CTTCTCTCGCAGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTT-CGTTGAACCTC
56703414 AG
65 AG
* * **
56703416 CTTCTCTCGCAGCCGCATCTGCTTTAAGTTGTAGCTGTAGTTCTTCATATCTTTTTTGAACCTCA
1 CTTCTCTCGCAGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTCGTTGAACCTCA
56703481 G
66 G
* *
56703482 CTTCTCTCG-ATGCTGCCTCCGCTTTAAGTTGT
1 CTTCTCTCGCA-GCCGCCTCTGCTTTAAGTTGT
56703514 GTAATTTGCT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.95
67 3 0.04
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.38
Consensus pattern (66 bp):
CTTCTCTCGCAGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTCGTTGAACCTCA
G
Found at i:56708898 original size:9 final size:9
Alignment explanation
Indices: 56708884--56709300 Score: 164
Period size: 9 Copynumber: 46.7 Consensus size: 9
56708874 AGTATATATG
56708884 AGTTATGTA
1 AGTTATGTA
56708893 AGTTATGTA
1 AGTTATGTA
*
56708902 AGTAATGTA
1 AGTTATGTA
*
56708911 AGTTAAGT-
1 AGTTATGTA
56708919 A-TTATGTA
1 AGTTATGTA
56708927 AGTTATGTA
1 AGTTATGTA
** *
56708936 AG-TCCGACA
1 AGTTATG-TA
*
56708945 AGTTAATATA
1 AGTT-ATGTA
*
56708955 TA-ATAT-TA
1 -AGTTATGTA
56708963 A-TTATGTA
1 AGTTATGTA
*
56708971 ACTTATGTATA
1 AGTTATG--TA
*
56708982 ATATTAATGTA
1 A-GTT-ATGTA
56708993 AGTTATGT-
1 AGTTATGTA
*
56709001 A-TTATATA
1 AGTTATGTA
* *
56709009 AGTTTTTTA
1 AGTTATGTA
*
56709018 AGTTATATA
1 AGTTATGTA
*
56709027 AGTTGTGT-
1 AGTTATGTA
56709035 A-TTATGTA
1 AGTTATGTA
56709043 AGTTATGTA
1 AGTTATGTA
*
56709052 AGTTGTGTA
1 AGTTATGTA
*
56709061 AGTTGTGT-
1 AGTTATGTA
56709069 A-TTATGTA
1 AGTTATGTA
56709077 AGTTATGTA
1 AGTTATGTA
* *
56709086 AG-TCTGACA
1 AGTTATG-TA
*
56709095 AGTTATGTTT
1 AGTTATG-TA
56709105 AG-TAT-TA
1 AGTTATGTA
56709112 A-TTAAT-TA
1 AGTT-ATGTA
56709120 AGTTATGTA
1 AGTTATGTA
56709129 AGTTATGTATA
1 AGTTATG--TA
*
56709140 ATATTAATGTA
1 A-GTT-ATGTA
56709151 AGTTATGT-
1 AGTTATGTA
56709159 A-TTATGTA
1 AGTTATGTA
* *
56709167 AGTTATTTT
1 AGTTATGTA
56709176 AGTTATGTA
1 AGTTATGTA
*
56709185 AGTTGTGT-
1 AGTTATGTA
*
56709193 A-TTATGTG
1 AGTTATGTA
*
56709201 AGTTATGCA
1 AGTTATGTA
*
56709210 ATTTATGTA
1 AGTTATGTA
*
56709219 GGCTATATAGT-
1 AG-T-TAT-GTA
* *
56709230 A-TTACGTT
1 AGTTATGTA
*
56709238 A-TTATGTT
1 AGTTATGTA
56709246 A-TTATGTA
1 AGTTATGTA
*
56709254 AGTTATGCA
1 AGTTATGTA
*
56709263 AGTTGTTATATA
1 A---GTTATGTA
*
56709275 AGTTCTATATA
1 AG-T-TATGTA
56709286 AGTTATGTA
1 AGTTATGTA
56709295 AGTTAT
1 AGTTAT
56709301 TATGTAAGTT
Statistics
Matches: 312, Mismatches: 54, Indels: 84
0.69 0.12 0.19
Matches are distributed among these distances:
7 40 0.13
8 46 0.15
9 168 0.54
10 15 0.05
11 24 0.08
12 13 0.04
13 6 0.02
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:56708998 original size:22 final size:22
Alignment explanation
Indices: 56708966--56709007 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56708956 AATATTAATT
56708966 ATGTAACTTATGTATAATATTA
1 ATGTAACTTATGTATAATATTA
* *
56708988 ATGTAAGTTATGTATTATAT
1 ATGTAACTTATGTATAATAT
56709008 AAGTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
ATGTAACTTATGTATAATATTA
Found at i:56709036 original size:34 final size:34
Alignment explanation
Indices: 56708991--56709088 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
56708981 AATATTAATG
* * * *
56708991 TAAGTTATGTATTATATAAGTTTTTTAAGTTATA
1 TAAGTTGTGTATTATGTAAGTTATGTAAGTTATA
* *
56709025 TAAGTTGTGTATTATGTAAGTTATGTAAGTTGTG
1 TAAGTTGTGTATTATGTAAGTTATGTAAGTTATA
56709059 TAAGTTGTGTATTATGTAAGTTATGTAAGT
1 TAAGTTGTGTATTATGTAAGTTATGTAAGT
56709089 CTGACAAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (34 bp):
TAAGTTGTGTATTATGTAAGTTATGTAAGTTATA
Found at i:56709073 original size:25 final size:27
Alignment explanation
Indices: 56708988--56709207 Score: 119
Period size: 25 Copynumber: 8.4 Consensus size: 27
56708978 TATAATATTA
* *
56708988 ATGTAAGTTATGT-A-TTATATAAGTT
1 ATGTAAGTTATGTAAGTTGTGTAAGTT
* * *
56709013 TTTTAAGTTATATAAGTTGTGTA--TT
1 ATGTAAGTTATGTAAGTTGTGTAAGTT
56709038 ATGTAAGTTATGTAAGTTGTGTAAGTT
1 ATGTAAGTTATGTAAGTTGTGTAAGTT
* *
56709065 GTGT-A-TTATGTAAGTTATGTAAG-T
1 ATGTAAGTTATGTAAGTTGTGTAAGTT
* * * *
56709089 CTGACAAGTTATGTTTAG-TAT-TAA-TT
1 ATG-TAAGTTATG-TAAGTTGTGTAAGTT
* *
56709115 AAT-TAAGTTATGTAAGTTATGTATAATATT
1 -ATGTAAGTTATGTAAG-T-TGTGTAA-GTT
*
56709145 AATGTAAGTTATGT-A-TTATGTAAGTT
1 -ATGTAAGTTATGTAAGTTGTGTAAGTT
* *
56709171 ATTTTAGTTATGTAAGTTGTGT-A-TT
1 ATGTAAGTTATGTAAGTTGTGTAAGTT
*
56709196 ATGTGAGTTATG
1 ATGTAAGTTATG
56709208 CAATTTATGT
Statistics
Matches: 151, Mismatches: 25, Indels: 38
0.71 0.12 0.18
Matches are distributed among these distances:
24 6 0.04
25 80 0.53
26 11 0.07
27 31 0.21
28 7 0.05
30 6 0.04
31 10 0.07
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (27 bp):
ATGTAAGTTATGTAAGTTGTGTAAGTT
Found at i:56709083 original size:43 final size:43
Alignment explanation
Indices: 56709036--56709193 Score: 128
Period size: 43 Copynumber: 3.6 Consensus size: 43
56709026 AAGTTGTGTA
*
56709036 TTATGTAAGTTATG-TAAGTTGTGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATGATAAGTTATGTAAGTT-TGTATTATGTAAG
* * * *
56709079 TTATGTAAG-TCTGACAAGTTATGTTTAGTATT-AATTAAT-TAAG
1 TTATGTAAGTTATGATAAGTTATG-TAAGT-TTGTATT-ATGTAAG
*
56709122 TTATGTAAGTTATGTATAATATTAATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATG-ATAA-GTT-ATGTAAGTT-TGTATTATGTAAG
* * *
56709169 TTATTTTAGTTATG-TAAGTTGTGTA
1 TTATGTAAGTTATGATAAGTTATGTA
56709194 TTATGTGAGT
Statistics
Matches: 90, Mismatches: 14, Indels: 22
0.71 0.11 0.17
Matches are distributed among these distances:
42 3 0.03
43 36 0.40
44 12 0.13
45 8 0.09
46 9 0.10
47 22 0.24
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (43 bp):
TTATGTAAGTTATGATAAGTTATGTAAGTTTGTATTATGTAAG
Found at i:56709132 original size:34 final size:37
Alignment explanation
Indices: 56709094--56709207 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 37
56709084 TAAGTCTGAC
56709094 AAGTTATGTTTAGTATTAAT-TAA-TTAAG-TTATGT
1 AAGTTATGTTTAGTATTAATGTAAGTTAAGATTATGT
* * *
56709128 AAGTTATGTATAATATTAATGTAAGTTATGTATTATGT
1 AAGTTATGTTTAGTATTAATGTAAGTTAAG-ATTATGT
**
56709166 AAGTTAT-TTTAG--TT-ATGTAAGTTGTGTATTATGT
1 AAGTTATGTTTAGTATTAATGTAAGTTAAG-ATTATGT
*
56709200 GAGTTATG
1 AAGTTATG
56709208 CAATTTATGT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
34 43 0.63
35 5 0.07
36 4 0.06
37 3 0.04
38 13 0.19
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.49
Consensus pattern (37 bp):
AAGTTATGTTTAGTATTAATGTAAGTTAAGATTATGT
Found at i:56709216 original size:34 final size:34
Alignment explanation
Indices: 56709146--56709218 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
56709136 TATAATATTA
***
56709146 ATGTAAGTTATGTATTATGTAAGTTATTTTAGTT
1 ATGTAAGTTATGTATTATGTAAGTTATGCAAGTT
* * *
56709180 ATGTAAGTTGTGTATTATGTGAGTTATGCAATTT
1 ATGTAAGTTATGTATTATGTAAGTTATGCAAGTT
56709214 ATGTA
1 ATGTA
56709219 GGCTATATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (34 bp):
ATGTAAGTTATGTATTATGTAAGTTATGCAAGTT
Found at i:56709288 original size:32 final size:33
Alignment explanation
Indices: 56709252--56709326 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
56709242 TGTTATTATG
*
56709252 TAAGTTATGCAAGTTGTTATATAAGTTC-TATA
1 TAAGTTATGCAAGTTATTATATAAGTTCATATA
* *
56709284 TAAGTTATGTAAGTTATTATGTAAGTTCTATATA
1 TAAGTTATGCAAGTTATTATATAAGTTC-ATATA
56709318 TAAGTTATG
1 TAAGTTATG
56709327 ATATGATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 25 0.66
34 13 0.34
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (33 bp):
TAAGTTATGCAAGTTATTATATAAGTTCATATA
Found at i:56709518 original size:33 final size:33
Alignment explanation
Indices: 56709481--56709575 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
56709471 ATAAAATTTG
56709481 AAATATATGTTACATATCCATACCATATATTAA
1 AAATATATGTTACATATCCATACCATATATTAA
*
56709514 AAATATA-G------AT---T-GCATATATTAA
1 AAATATATGTTACATATCCATACCATATATTAA
*
56709536 AAATATATGTTACATATCCATACCGTATATTAA
1 AAATATATGTTACATATCCATACCATATATTAA
56709569 AAATATA
1 AAATATA
56709576 GATTGCATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 22
0.66 0.04 0.30
Matches are distributed among these distances:
22 17 0.35
23 2 0.04
26 2 0.04
29 2 0.04
32 2 0.04
33 23 0.48
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (33 bp):
AAATATATGTTACATATCCATACCATATATTAA
Found at i:56709519 original size:22 final size:22
Alignment explanation
Indices: 56709494--56709542 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
56709484 TATATGTTAC
*
56709494 ATATCCATACCATATATTAAAA
1 ATATACATACCATATATTAAAA
* **
56709516 ATATAGATTGCATATATTAAAA
1 ATATACATACCATATATTAAAA
56709538 ATATA
1 ATATA
56709543 TGTTACATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATACATACCATATATTAAAA
Found at i:56709551 original size:22 final size:22
Alignment explanation
Indices: 56709504--56709552 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
56709494 ATATCCATAC
*
56709504 CATATATTAAAAATATAGATTG
1 CATATATTAAAAATATAGATTA
56709526 CATATATTAAAAATATATG-TTA
1 CATATATTAAAAATATA-GATTA
56709548 CATAT
1 CATAT
56709553 CCATACCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (22 bp):
CATATATTAAAAATATAGATTA
Found at i:56709565 original size:55 final size:55
Alignment explanation
Indices: 56709481--56709596 Score: 223
Period size: 55 Copynumber: 2.1 Consensus size: 55
56709471 ATAAAATTTG
56709481 AAATATATGTTACATATCCATACCATATATTAAAAATATAGATTGCATATATTAA
1 AAATATATGTTACATATCCATACCATATATTAAAAATATAGATTGCATATATTAA
*
56709536 AAATATATGTTACATATCCATACCGTATATTAAAAATATAGATTGCATATATTAA
1 AAATATATGTTACATATCCATACCATATATTAAAAATATAGATTGCATATATTAA
56709591 AAATAT
1 AAATAT
56709597 CTTATATTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (55 bp):
AAATATATGTTACATATCCATACCATATATTAAAAATATAGATTGCATATATTAA
Found at i:56709574 original size:22 final size:22
Alignment explanation
Indices: 56709549--56709597 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
56709539 TATATGTTAC
*
56709549 ATATCCATACCGTATATTAAAA
1 ATATCCATACCATATATTAAAA
** **
56709571 ATATAGATTGCATATATTAAAA
1 ATATCCATACCATATATTAAAA
56709593 ATATC
1 ATATC
56709598 TTATATTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATCCATACCATATATTAAAA
Found at i:56709630 original size:38 final size:39
Alignment explanation
Indices: 56709561--56709636 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
56709551 ATCCATACCG
56709561 TATATTAAAAATATAGATTGCATATATT-AAAAATATCT
1 TATATTAAAAATATAGATTGCATATATTAAAAAATATCT
*
56709599 TATATTAAAAAATATA-ATTG-ATATTTCTAAAAAATATC
1 TATATT-AAAAATATAGATTGCATATAT-TAAAAAATATC
56709637 CATTTTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 5 0.15
38 11 0.32
39 18 0.53
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.39
Consensus pattern (39 bp):
TATATTAAAAATATAGATTGCATATATTAAAAAATATCT
Found at i:56710120 original size:37 final size:38
Alignment explanation
Indices: 56710065--56710140 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
56710055 AACAGAACAA
* *
56710065 TTGATCAAATGGCTGTT-AACAATTGGCATTTGATACT
1 TTGATCAAATGGCGGTTAAACAATTGGCATTCGATACT
*
56710102 TTGATCAAATGGCGGTTAAAACAATTTGCATTCGATACT
1 TTGATCAAATGGCGGTT-AAACAATTGGCATTCGATACT
56710141 ACTTGCATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 16 0.47
39 18 0.53
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (38 bp):
TTGATCAAATGGCGGTTAAACAATTGGCATTCGATACT
Found at i:56710337 original size:14 final size:14
Alignment explanation
Indices: 56710318--56710347 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56710308 CTCGAACAGC
56710318 AAGATGATTAACTA
1 AAGATGATTAACTA
56710332 AAGATGATTAACTA
1 AAGATGATTAACTA
56710346 AA
1 AA
56710348 AAACCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:56711461 original size:42 final size:42
Alignment explanation
Indices: 56711414--56711498 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
56711404 TTTGCGAAGA
56711414 TTAACTCATTCAACATGGCTCTTTTTCTTTTTACCCAATTAG
1 TTAACTCATTCAACATGGCTCTTTTTCTTTTTACCCAATTAG
56711456 TTAACTCATTCAACATGGCTCTTTTTCTTTTTACCCAATTAG
1 TTAACTCATTCAACATGGCTCTTTTTCTTTTTACCCAATTAG
56711498 T
1 T
56711499 CGATCTAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (42 bp):
TTAACTCATTCAACATGGCTCTTTTTCTTTTTACCCAATTAG
Found at i:56711670 original size:16 final size:16
Alignment explanation
Indices: 56711626--56711671 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
56711616 CAGATTTTTT
*
56711626 CGATGGTAGAGGAGTG
1 CGATGGTAGACGAGTG
* **
56711642 CGACGGTCCACGAGTG
1 CGATGGTAGACGAGTG
56711658 CGATGGTAGACGAG
1 CGATGGTAGACGAG
56711672 CGCCGGCAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.43, T:0.15
Consensus pattern (16 bp):
CGATGGTAGACGAGTG
Found at i:56712255 original size:20 final size:20
Alignment explanation
Indices: 56712232--56712273 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56712222 TATTTTTAAA
56712232 TTTTAGTGTTTTTA-TTTCAT
1 TTTTA-TGTTTTTATTTTCAT
*
56712252 TTTTATTTTTTTATTTTCAT
1 TTTTATGTTTTTATTTTCAT
56712272 TT
1 TT
56712274 AATTCCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTATGTTTTTATTTTCAT
Found at i:56712255 original size:28 final size:28
Alignment explanation
Indices: 56712189--56712243 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
56712179 AATATATAGT
* *
56712189 ACTAATAATTATAAATTTTAGTGTTTTA
1 ACTAATATTTTTAAATTTTAGTGTTTTA
56712217 ACTAATATTTTTAAATTTTAGTGTTTT
1 ACTAATATTTTTAAATTTTAGTGTTTT
56712244 TATTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTAATATTTTTAAATTTTAGTGTTTTA
Found at i:56712936 original size:20 final size:20
Alignment explanation
Indices: 56712911--56712955 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
56712901 AATTTTTAGT
56712911 ATTTTAAC-TAAAATTTATAA
1 ATTTTAACATAAAA-TTATAA
56712931 ATTTT-ACATAAAATTATAA
1 ATTTTAACATAAAATTATAA
56712950 ATTTTA
1 ATTTTA
56712956 GCATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTAACATAAAATTATAA
Found at i:56714129 original size:375 final size:376
Alignment explanation
Indices: 56713248--56714298 Score: 1677
Period size: 375 Copynumber: 2.8 Consensus size: 376
56713238 AAAAAAATAT
* * *
56713248 AAAAGCATTAATTAATTGTATAAAATTCAAAACCT-AATATAAACCTTAATCTTATTAAACCCAC
1 AAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAGT-TAAACCTTAATCTTATTAAACCCGC
*
56713312 CTAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATA--TATCTCAA
65 CTAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATATCTCTCTCAA
56713375 GGCATAATTTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATAAA
130 GGCATAATTTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATAAA
* * *
56713440 TAAAAAAATTAATCTAAACCCAAAATTGTAACCCGACCCCTGAAACCCTAAGTC-CTAAATCTCT
195 T-AAAAAATTAATCTAAACCCAAAATCGTAACCCGACCCCTGAAACCCTAA-ACACAAAATC-C-
* ***
56713504 AGTCTTAA-TCATTAACATCTAACCCCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTA
256 ---C-TAAGTC-TTAACAACTAATATCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTA
56713568 AGCATAATCCATAATCTATAATCCCTAAATCCATATATATATATAGTACTCCCTAAACATTA
316 AGCATAATCCATAATCTATAATCCCTAAATCCA-ATATATATATAGTACTCCCTAAACATTA
56713630 AAAAGCATTAATTAAATATTGTATAAAATTCAAAATCTCAGTTAAACCTTAATCTTATTAAACCC
1 AAAAGCATTAATT--A-ATTGTATAAAATTCAAAATCTCAGTTAAACCTTAATCTTATTAAACCC
* *
56713695 GCCTAAATTAACCATTGACGGGATATAAATATTTAAGTATTCTATCTATTATATATATCTCTCTC
63 GCCTAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATATCTCTCTC
56713760 AAGGCATAATTTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATA
128 AAGGCATAATTTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATA
* * * * *
56713825 AATAAAAAATTAATCTAAACCCAAAATCATAACTCGGCCCTTGAAACCCTAAACAAAAAATCCCT
193 AATAAAAAATTAATCTAAACCCAAAATCGTAACCCGACCCCTGAAACCCTAAACACAAAATCCCT
56713890 AAGTCTTAACAACTAATATCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTAAGCATAA
258 AAGTCTTAACAACTAATATCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTAAGCATAA
56713955 TCCATAATCTATAATCCCTAAATCC-ATATATATATAGTACTCCCTAAACATTA
323 TCCATAATCTATAATCCCTAAATCCAATATATATATAGTACTCCCTAAACATTA
56714008 AAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAGTTAAACCTTAATCTTATTAAACCCGCC
1 AAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAGTTAAACCTTAATCTTATTAAACCCGCC
56714073 TAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATATCTCTCTCAAG
66 TAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATATCTCTCTCAAG
* *
56714138 GCATAATTAATTAAACCCTAAATTATACATATTTTACAATTACATAAGAACATATTTAAAATATA
131 GCATAA-T--TTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATA
* * *
56714203 AAT-AAAAATTATTCTAAA-CCAAAACCGTAACCCGACCCCTAAAACCCTAAACACAAAATCCCT
193 AATAAAAAATTAATCTAAACCCAAAATCGTAACCCGACCCCTGAAACCCTAAACACAAAATCCCT
*
56714266 AAGTCTTAACCACTAATATCTAACCCCTAAACC
258 AAGTCTTAACAACTAATATCTAACCCCTAAACC
56714299 ACTAACCCCT
Statistics
Matches: 627, Mismatches: 31, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
375 120 0.19
376 72 0.11
377 14 0.02
378 97 0.15
380 84 0.13
381 3 0.00
382 13 0.02
384 1 0.00
385 99 0.16
386 51 0.08
387 73 0.12
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (376 bp):
AAAAGCATTAATTAATTGTATAAAATTCAAAATCTCAGTTAAACCTTAATCTTATTAAACCCGCC
TAAATTAACCATTGAAGGGATATAAATATTTAAGTACTCTATCTATTATATATATCTCTCTCAAG
GCATAATTTAAACCCTAATTTATACATCTTTTACAATTACATAAGAACATATTTAAAATATAAAT
AAAAAATTAATCTAAACCCAAAATCGTAACCCGACCCCTGAAACCCTAAACACAAAATCCCTAAG
TCTTAACAACTAATATCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTAAGCATAATCC
ATAATCTATAATCCCTAAATCCAATATATATATAGTACTCCCTAAACATTA
Found at i:56714207 original size:23 final size:23
Alignment explanation
Indices: 56714164--56714207 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
56714154 CCTAAATTAT
* *
56714164 ACATATTTTACAATTACATAAGA
1 ACATATTTTAAAATTAAATAAGA
56714187 ACATA-TTTAAAATATAAATAA
1 ACATATTTTAAAAT-TAAATAA
56714208 AAATTATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ACATATTTTAAAATTAAATAAGA
Found at i:56714305 original size:15 final size:15
Alignment explanation
Indices: 56714285--56714313 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56714275 CCACTAATAT
56714285 CTAACCCCTAAACCA
1 CTAACCCCTAAACCA
56714300 CTAACCCCTAAACC
1 CTAACCCCTAAACC
56714314 TTAAATCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.14
Consensus pattern (15 bp):
CTAACCCCTAAACCA
Found at i:56715063 original size:41 final size:40
Alignment explanation
Indices: 56715008--56715095 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 40
56714998 CATACCGCTA
*
56715008 AAAACACAAACCATTAGCGGCGCTAA-AACAAAAATGCCACT
1 AAAAC-CAAACCATTAGCGGCGC-AATAACAAAAACGCCACT
*
56715049 AAAACCAATACCATTAGCGGCGCAATACCAAAAACGCCACT
1 AAAACCAA-ACCATTAGCGGCGCAATAACAAAAACGCCACT
56715090 AAAACC
1 AAAACC
56715096 CCGACAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 5 0.12
41 38 0.88
ACGTcount: A:0.48, C:0.30, G:0.11, T:0.11
Consensus pattern (40 bp):
AAAACCAAACCATTAGCGGCGCAATAACAAAAACGCCACT
Found at i:56715248 original size:124 final size:124
Alignment explanation
Indices: 56715006--56715251 Score: 264
Period size: 124 Copynumber: 2.0 Consensus size: 124
56714996 GCCATACCGC
*
56715006 TAAAAACACAAACCATTAGCGGCGCTAAAACAAAAATGCCACTAAAACCAATACCATTAGCGGCG
1 TAAAAACACAAACCATTAGCGGCGCTAAAACAAAAACGCCACTAAAACCAATACCATTAGCGGCG
* * *
56715071 CAATACCAAAAACGCCACTAAAACCCCGACAATTACCGGCGCTTCCTACAAAACGCCGT
66 CAATACCAAAAACGCCACTAAAACACCGACAATTACCGGCGCTACCCACAAAACGCCGT
* * ** * * * * *
56715130 TAAAAACACAGACCATTAGTGGCGCTTTAGCAGAAGCGCCACTAAAACCCATACCTTTAGCGGCG
1 TAAAAACACAAACCATTAGCGGCGCTAAAACAAAAACGCCACTAAAACCAATACCATTAGCGGCG
*** * * * *
56715195 TTTTATCGAAAAACGCCGA-TAAAA-ATCGAGAATTAGCGGCGCTACACCA-AAAACGCC
66 CAATA-CCAAAAACGCC-ACTAAAACACCGACAATTACCGGCGCTAC-CCACAAAACGCC
56715252 ACTAACGCCA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
124 81 0.82
125 17 0.17
126 1 0.01
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (124 bp):
TAAAAACACAAACCATTAGCGGCGCTAAAACAAAAACGCCACTAAAACCAATACCATTAGCGGCG
CAATACCAAAAACGCCACTAAAACACCGACAATTACCGGCGCTACCCACAAAACGCCGT
Found at i:56715351 original size:40 final size:39
Alignment explanation
Indices: 56715292--56715368 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
56715282 CCGTTATATT
* * * *
56715292 TTATTTTTTGCGGCGTTTTTCCTGAAAATGCCGCTAATAC
1 TTATTTCTTGCGGCATTTTT-CTAAAAATGCCACTAATAC
* *
56715332 TTATTTCTTGTGGCATTTTTTTAAAAATGCCACTAAT
1 TTATTTCTTGCGGCATTTTTCTAAAAATGCCACTAAT
56715369 GCTCAGTCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
39 14 0.45
40 17 0.55
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (39 bp):
TTATTTCTTGCGGCATTTTTCTAAAAATGCCACTAATAC
Found at i:56716395 original size:22 final size:21
Alignment explanation
Indices: 56716357--56716402 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
56716347 CGAAAATATA
*
56716357 TTAAATATATATATTTTATTT
1 TTAAATATATATATTTTAGTT
56716378 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TA-TTTTAGTT
56716400 TTA
1 TTA
56716403 TTTTAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
TTAAATATATATATTTTAGTT
Found at i:56716510 original size:53 final size:53
Alignment explanation
Indices: 56716430--56716610 Score: 185
Period size: 53 Copynumber: 3.7 Consensus size: 53
56716420 TTAGATTTTG
56716430 TTAC-AACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
* * * *
56716482 TTACTAACAATTAATACAATTAATAATTAATAATTT--TACTAA---CAAAATG
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATA-TAATTTGATAATT
* *
56716531 TTAGTAACAA-T--T--AA-T---AATTAATAATTTGATACAATTTGATAATT
1 TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
*
56716575 TTAGTAACAATTAATACAATTAACAATTAATAATTT
1 TTACTAACAATTAATACAATTAACAATTAATAATTT
56716611 TACTAACAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 31
0.72 0.06 0.22
Matches are distributed among these distances:
40 12 0.12
41 2 0.02
42 2 0.02
43 1 0.01
44 16 0.15
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 15 0.14
50 1 0.01
51 2 0.02
52 7 0.07
53 42 0.40
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (53 bp):
TTACTAACAATTAATACAATTAACAATTAATAATTTGATATAATTTGATAATT
Found at i:56716552 original size:93 final size:93
Alignment explanation
Indices: 56716444--56716627 Score: 332
Period size: 93 Copynumber: 2.0 Consensus size: 93
56716434 AACAATTAAT
* *
56716444 ACAATTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAATAAT
1 ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
56716509 TAATAATTTTACTAACAAAATGTTAGTA
66 TAATAATTTTACTAACAAAATGTTAGTA
* *
56716537 ACAATTAATAATTAATAATTTGATACAATTTGATAATTTTAGTAACAATTAATACAATTAACAAT
1 ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
56716602 TAATAATTTTACTAACAAAATGTTAG
66 TAATAATTTTACTAACAAAATGTTAG
56716628 ATTTTACAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (93 bp):
ACAATTAACAATTAATAATTTGATACAATTTGATAATTTTACTAACAATTAATACAATTAACAAT
TAATAATTTTACTAACAAAATGTTAGTA
Found at i:56716617 original size:19 final size:18
Alignment explanation
Indices: 56716546--56716619 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 18
56716536 AACAATTAAT
*
56716546 AATTAATAATTTGAT-AC
1 AATTAATAATTTTATAAC
*
56716563 AATTTGATAATTTTAGTAAC
1 AA-TTAATAATTTTA-TAAC
*
56716583 AATTAATACA--AT-TAAC
1 AATTAATA-ATTTTATAAC
56716599 AATTAATAATTTTACTAAC
1 AATTAATAATTTTA-TAAC
56716618 AA
1 AA
56716620 AATGTTAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
15 1 0.02
16 12 0.27
17 3 0.07
18 11 0.25
19 12 0.27
20 5 0.11
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (18 bp):
AATTAATAATTTTATAAC
Found at i:56716697 original size:22 final size:23
Alignment explanation
Indices: 56716672--56716731 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
56716662 AATTTGATAC
* *
56716672 AATTTTAATAACAAT-TAGCTTT
1 AATTTTAATAAAAATATAACTTT
*
56716694 AATTTTAATAAAAATATAATTTT
1 AATTTTAATAAAAATATAACTTT
56716717 AATTTTAATTAAAAA
1 AATTTTAA-TAAAAA
56716732 ATAGGCCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 14 0.42
23 13 0.39
24 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTTTAATAAAAATATAACTTT
Found at i:56718648 original size:75 final size:75
Alignment explanation
Indices: 56718528--56718666 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 75
56718518 TTACGGAAAA
* * * * * *
56718528 CGCCTCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGATGTATATTAGAATTAGTGGCGC
1 CGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGCGC
56718593 TTTATAGAAG
66 TTTATAGAAG
* * * *
56718603 CGCCGCAAAAAATGTTAACCAAAATGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG
1 CGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGCG
56718667 TTAGGGAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGCGC
TTTATAGAAG
Found at i:56718682 original size:75 final size:74
Alignment explanation
Indices: 56718508--56718682 Score: 172
Period size: 75 Copynumber: 2.3 Consensus size: 74
56718498 AAAACAAGTC
* * * * * *
56718508 TTAGCGGCGCTTACGGAAAACGCCTCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGATG
1 TTAGTGGCGCTTA-GAAAAACGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATG
* *
56718573 TATATTAGAA
65 TATAATACAA
* * * * * * *
56718583 TTAGTGGCGCTTTATAGAAGCGCCGCAAAAAATGTTAACCAAAATGCAGCGGTTTGGTCTCGATG
1 TTAGTGGCGC-TTAGAAAAACGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATG
56718648 TATAATACAA
65 TATAATACAA
56718658 TTAGTGGCG-TTAGGGAAAAACGCCG
1 TTAGTGGCGCTTA--GAAAAACGCCG
56718683 TTAAAGCATA
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
73 3 0.04
75 73 0.92
76 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (74 bp):
TTAGTGGCGCTTAGAAAAACGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGT
ATAATACAA
Found at i:56718813 original size:114 final size:114
Alignment explanation
Indices: 56718598--56719047 Score: 407
Period size: 114 Copynumber: 3.9 Consensus size: 114
56718588 GGCGCTTTAT
* * * * * * * * *
56718598 AGAAGCGCCGCAAAAAATGTTA-ACCAAAATGCAGCGGTTTGGTCTCGATGTATAATACAATTAG
1 AGAAGCGCCGCAAGATATG-CACACCAAAACGCAG-AGTTTGGTCTTGAGGTATATTAGAATTAG
* * *
56718662 TGGCG-TTA-GGGAAAAACGCCGTTAAAGCATAAC-ATTAGCGGCGATTTTCT
64 TGGCGCTTACTGG-AAAACGCCGCTAAAGCAT-ACTATTAGCGGCGATTTTCC
* * *
56718712 AGAATCGCCACAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTG
1 AGAAGCGCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
* * * *
56718777 GCGCTTACTGTAAAACGCCGCTAAAGCGTACTATTAGCGGCGCTTCTCC
66 GCGCTTACTGGAAAACGCCGCTAAAGCATACTATTAGCGGCGATTTTCC
* * * * * *
56718826 AGAAGCGCCGCTAA-AT-TTCTTA-ACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAATT
1 AGAAGCGCCGC-AAGATATGC--ACACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATT
* ** * **
56718888 AGTGGCGCTTAC-GAGAAAATGCCGCTAAATAATAGTATTAGCGGCGA--TTGG
62 AGTGGCGCTTACTG-GAAAACGCCGCTAAAGCATACTATTAGCGGCGATTTTCC
*
56718939 AGTTAAGCGCCGCAAGATATGCACGCCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAG
1 AG--AAGCGCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAG
* * * *
56719004 TGGCGCTGATTGGAAAACGCCGCTAAAGTACACTATTAGCGGCG
64 TGGCGCTTACTGGAAAACGCCGCTAAAGCATACTATTAGCGGCG
56719048 CGTTTTTAGA
Statistics
Matches: 269, Mismatches: 52, Indels: 30
0.77 0.15 0.09
Matches are distributed among these distances:
113 36 0.13
114 145 0.54
115 86 0.32
116 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (114 bp):
AGAAGCGCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
GCGCTTACTGGAAAACGCCGCTAAAGCATACTATTAGCGGCGATTTTCC
Found at i:56719177 original size:229 final size:229
Alignment explanation
Indices: 56718598--56719215 Score: 585
Period size: 229 Copynumber: 2.7 Consensus size: 229
56718588 GGCGCTTTAT
* * * ** * * *
56718598 AGAAGCGCCGCAAAAAATGTTAACCAAAA-TGCAGCGGTTT-GGTCTCGATGTATAATACAATTA
1 AGAAGCGCCGCTAAATATATTAACCAAAACT-CAGC-GTTTAAATCTTGATGTATACTAGAATTA
* * * * * * * *
56718661 GTGGCG-TTA-GGGAAAAACGCCGTTAAAGCATAACATTAGCGGCGATTTTCTAG-AATCGCCAC
64 GTGGCGCTTACGAG-AAAATGCAGCTAAAGCATAATATTAGCGGCGATTTT-TGGTAAGCGCCGC
* * *
56718723 AAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTGT
127 AAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGG
**
56718788 AAAACGCCGCTAAAGCGTACTATTAGCGGCGCTTCTCC
192 AAAACGCCGCTAAAGCACACTATTAGCGGCGCTTCTCC
* * *** *
56718826 AGAAGCGCCGCTAAATTTCTTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAATTAGT
1 AGAAGCGCCGCTAAATATATTAACCAAAACTCAGCGTTTAAATCTTGATGTATACTAGAATTAGT
* ** * *** *
56718891 GGCGCTTACGAGAAAATGCCGCTAAATAATAGTATTAGCGGCGATTGGAGTTAAGCGCCGCAAGA
66 GGCGCTTACGAGAAAATGCAGCTAAAGCATAATATTAGCGGCGATTTTTGGTAAGCGCCGCAAGA
* *
56718956 TATGCACGCCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTGGAAAA
131 TATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAA
* **
56719021 CGCCGCTAAAGTACACTATTAGCGGCGCGTT-TTT
196 CGCCGCTAAAGCACACTATTAGCGGCGC-TTCTCC
* * * * * *
56719055 AGATGCGCCG-TGGAATATATTAACCGAAA-TGCTGCGTTTAAATCTTGATGTGTACTGGAATTA
1 AGAAGCGCCGCT-AAATATATTAACCAAAACT-CAGCGTTTAAATCTTGATGTATACTAGAATTA
* * *
56719118 GTGGCG-TTCACGA-TAAATCGCAGCTAAAGCATATTATTAGCGGCGCTTTTTGGTAAGCGCCGC
64 GTGGCGCTT-ACGAGAAAAT-GCAGCTAAAGCATAATATTAGCGGCGATTTTTGGTAAGCGCCGC
* *
56719181 AAAATAT-CTTA-ACCAAAACGCACAGTTTTGGTCTT
127 AAGATATGC--ACACCAAAACGCAGAG-TTTGGTCTT
56719216 AACCATGCAT
Statistics
Matches: 321, Mismatches: 56, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
227 4 0.01
228 64 0.20
229 239 0.74
230 14 0.04
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (229 bp):
AGAAGCGCCGCTAAATATATTAACCAAAACTCAGCGTTTAAATCTTGATGTATACTAGAATTAGT
GGCGCTTACGAGAAAATGCAGCTAAAGCATAATATTAGCGGCGATTTTTGGTAAGCGCCGCAAGA
TATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAA
CGCCGCTAAAGCACACTATTAGCGGCGCTTCTCC
Found at i:56719539 original size:7 final size:7
Alignment explanation
Indices: 56719524--56719580 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
56719514 GGGTTATGGT
*
56719524 GTTTTGG
1 GTTTAGG
56719531 GTTTAGG
1 GTTTAGG
*
56719538 GTTTAGTA
1 GTTTAG-G
56719546 GTTTAGG
1 GTTTAGG
* *
56719553 ATTTAAG
1 GTTTAGG
*
56719560 ATTTAGG
1 GTTTAGG
*
56719567 GTTTGGG
1 GTTTAGG
56719574 GTTTAGG
1 GTTTAGG
56719581 CTACTTTAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:56720683 original size:44 final size:44
Alignment explanation
Indices: 56720628--56720726 Score: 162
Period size: 44 Copynumber: 2.2 Consensus size: 44
56720618 TCTGAAATTC
* * *
56720628 TCGCGTCCTTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAA
1 TCGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
*
56720672 TCGCCTCCTTCTTGCCGAATTTCTTGAAATCCCAAATCCCTAAA
1 TCGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
56720716 TCGCCTCCTTC
1 TCGCCTCCTTC
56720727 CTCCTTCCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.21, C:0.35, G:0.10, T:0.33
Consensus pattern (44 bp):
TCGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
Found at i:56722979 original size:3 final size:3
Alignment explanation
Indices: 56722964--56723025 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
56722954 CGTATGGAAG
* *
56722964 TAA TAA TAC TAA TAA TAA TATA TAA TAAA TAA TAGA TAA T-A CAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TA-A TAA TAA TAA TAA
*
56723011 T-A CAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
56723026 GCAATTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
2 2 0.04
3 37 0.77
4 9 0.19
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:56722990 original size:19 final size:20
Alignment explanation
Indices: 56722965--56723023 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
56722955 GTATGGAAGT
56722965 AATAATACTAATAATAATA-
1 AATAATACTAATAATAATAC
* *
56722984 TATAATAAATAATAGATAATAC
1 AATAAT-ACTAATA-ATAATAC
56723006 AATAATAC-AATAATAATA
1 AATAATACTAATAATAATA
56723024 ATGCAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.33
20 10 0.30
21 7 0.21
22 5 0.15
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAATACTAATAATAATAC
Found at i:56722996 original size:14 final size:13
Alignment explanation
Indices: 56722965--56723025 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 13
56722955 GTATGGAAGT
*
56722965 AATAATACTAAT-
1 AATAATAATAATA
56722977 AATAATATATAATA
1 AATAATA-ATAATA
56722991 AATAATAGATAATA
1 AATAATA-ATAATA
*
56723005 CAATAAT-ACAAT-
1 -AATAATAATAATA
56723017 AATAATAAT
1 AATAATAAT
56723026 GCAATTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.15
12 8 0.20
13 8 0.20
14 13 0.32
15 6 0.15
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:56723002 original size:11 final size:10
Alignment explanation
Indices: 56722964--56723024 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
56722954 CGTATGGAAG
*
56722964 TAATAAT-AC
1 TAATAATAAA
56722973 TAATAAT-AA
1 TAATAATAAA
56722982 TATATAATAAA
1 TA-ATAATAAA
56722993 TAATAGATAATA
1 TAATA-ATAA-A
*
56723005 CAATAATACAA
1 TAATAATA-AA
56723016 TAATAATAA
1 TAATAATAA
56723025 TGCAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 10 0.23
10 9 0.20
11 19 0.43
12 6 0.14
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (10 bp):
TAATAATAAA
Found at i:56725375 original size:44 final size:44
Alignment explanation
Indices: 56725317--56725403 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
56725307 CGTTCTATTT
* * **
56725317 TTTGTCTGTTTGTTTCTGGTTAATCTGGGTAACTTCATTTTCTG
1 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCTG
56725361 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCT
1 TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCT
56725404 TCTTCTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.14, C:0.15, G:0.18, T:0.53
Consensus pattern (44 bp):
TTTGGCTGTTTGTTTCTAGTTAATCCAGGTAACTTCATTTTCTG
Found at i:56726160 original size:3 final size:3
Alignment explanation
Indices: 56726152--56726178 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56726142 TAACTACATT
56726152 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
56726179 CATTTTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:56727082 original size:20 final size:19
Alignment explanation
Indices: 56727048--56727087 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
56727038 AGATGCTTCT
56727048 ATTTATGAATTTGGATTGG
1 ATTTATGAATTTGGATTGG
*
56727067 ATTTATGCAGTTTGGATTGG
1 ATTTATG-AATTTGGATTGG
56727087 A
1 A
56727088 AAATAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.45
Consensus pattern (19 bp):
ATTTATGAATTTGGATTGG
Found at i:56727439 original size:17 final size:17
Alignment explanation
Indices: 56727417--56727449 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56727407 ATTAATAAGA
56727417 TATTTAGCTTTAATGGG
1 TATTTAGCTTTAATGGG
56727434 TATTTAGCTTTAATGG
1 TATTTAGCTTTAATGG
56727450 ATAAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (17 bp):
TATTTAGCTTTAATGGG
Found at i:56734417 original size:50 final size:50
Alignment explanation
Indices: 56734300--56734542 Score: 342
Period size: 50 Copynumber: 4.8 Consensus size: 50
56734290 GATCATAACA
* ** * *
56734300 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
56734351 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
56734401 TGTCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
56734451 TGCCCATGCCATGTCCCAGACATGGTCTTACAAGGGACCTATCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56734501 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56734543 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 134 0.80
51 34 0.20
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56734914 original size:30 final size:29
Alignment explanation
Indices: 56734879--56734935 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
56734869 CCTCGACTCT
*
56734879 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTAC-ATTTTGCCCCTA
* *
56734909 AACTTTTGCATAATTACATTTTTCCCC
1 AACTTTTGCAAAATTACATTTTGCCCC
56734936 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (29 bp):
AACTTTTGCAAAATTACATTTTGCCCCTA
Found at i:56736853 original size:27 final size:27
Alignment explanation
Indices: 56736792--56736846 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56736782 GACACCGAGA
56736792 TAAACTTCGTCAACATCTCCTCAAGGT
1 TAAACTTCGTCAACATCTCCTCAAGGT
56736819 TAAACTTCGTCAACATCTCCTCAAGGT
1 TAAACTTCGTCAACATCTCCTCAAGGT
56736846 T
1 T
56736847 CGGCTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (27 bp):
TAAACTTCGTCAACATCTCCTCAAGGT
Found at i:56738126 original size:18 final size:18
Alignment explanation
Indices: 56738103--56738144 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
56738093 AATAGAAAGT
56738103 AAAAATTA-AACTAAAAAC
1 AAAAATTATAA-TAAAAAC
*
56738121 AAAAATTATAATAAAAAT
1 AAAAATTATAATAAAAAC
56738139 AAAAAT
1 AAAAAT
56738145 GGCTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAATTATAATAAAAAC
Found at i:56738139 original size:6 final size:6
Alignment explanation
Indices: 56738080--56738144 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
56738070 TGCCAGAAGC
* * * * *
56738080 AAATAA AAGA-AA AAATAGA AAGTAA AAATTA AACTAA AAACAA AAATTA
1 AAATAA AA-ATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAATAA
*
56738129 TAATAA AAATAA AAAT
1 AAATAA AAATAA AAAT
56738145 GGCTAAATTA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 1 0.02
6 37 0.84
7 6 0.14
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:56740315 original size:20 final size:21
Alignment explanation
Indices: 56740290--56740328 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
56740280 TTATTCTAGC
56740290 AATAAAGTAAA-TGAGCTGGA
1 AATAAAGTAAATTGAGCTGGA
*
56740310 AATAAATTAAATTGAGCTG
1 AATAAAGTAAATTGAGCTG
56740329 AAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (21 bp):
AATAAAGTAAATTGAGCTGGA
Found at i:56743527 original size:23 final size:24
Alignment explanation
Indices: 56743472--56743532 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
56743462 AAATTTTATT
* *
56743472 TTTATTTTTAAAATTATTAAAATA
1 TTTATTTTTAATATTATTAAAACA
56743496 TTATAATTTTTAATATTATT-AAACA
1 TT-T-ATTTTTAATATTATTAAAACA
56743521 TTTATTTTTAAT
1 TTTATTTTTAAT
56743533 CATATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 9 0.27
24 3 0.09
25 7 0.21
26 14 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATTTTTAATATTATTAAAACA
Found at i:56743564 original size:22 final size:22
Alignment explanation
Indices: 56743539--56743592 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
56743529 TAATCATATA
*
56743539 ATAAATTATTGATATAATTAAT
1 ATAATTTATTGATATAATTAAT
56743561 ATAATTTATTGATATAATTAAT
1 ATAATTTATTGATATAATTAAT
56743583 ATAATTTATT
1 ATAATTTATT
56743593 ATTTTAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATAATTTATTGATATAATTAAT
Found at i:56759216 original size:39 final size:36
Alignment explanation
Indices: 56759157--56759297 Score: 122
Period size: 39 Copynumber: 3.7 Consensus size: 36
56759147 TAACAGAATG
* *
56759157 TTAAATACATGACTTACTAAAATTTAAGTATATATTAC
1 TTAAATACATTACTTACTAAAATTTAA-T-TACATTAC
** *
56759195 ATTACTTACATTACTTACTAAAATAT-ATTACATTAC
1 -TTAAATACATTACTTACTAAAATTTAATTACATTAC
*
56759231 TTAAATATATTACTTACTAAAATTTATAACTTACATTAC
1 TTAAATACATTACTTACTAAAA-TT-TAA-TTACATTAC
* * *
56759270 ATAAACATATTACATTACTTAAAATTTA
1 TTAAATACATTAC-TTAC-TAAAATTTA
56759298 TATATATATT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
35 19 0.22
36 8 0.09
37 2 0.02
38 2 0.02
39 43 0.51
40 6 0.07
41 5 0.06
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAAATACATTACTTACTAAAATTTAATTACATTAC
Found at i:56759230 original size:18 final size:18
Alignment explanation
Indices: 56759204--56759294 Score: 89
Period size: 18 Copynumber: 4.9 Consensus size: 18
56759194 CATTACTTAC
56759204 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
56759221 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
56759239 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTAAAA--TAT
*
56759258 AACTTACATTAC-ATAAACAT
1 -A-TTACATTACTA-AAATAT
56759278 ATTACATTACTTAAAAT
1 ATTACATTAC-TAAAAT
56759295 TTATATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
17 13 0.21
18 25 0.41
19 7 0.11
20 4 0.07
21 5 0.08
22 7 0.11
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:56759244 original size:31 final size:31
Alignment explanation
Indices: 56759186--56759244 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
56759176 AAATTTAAGT
*
56759186 ATATATTACATTACTTACATTACTTACTAAA
1 ATATATTACATTACTTAAATTACTTACTAAA
56759217 ATATATTACATTACTTAAATATA-TTACT
1 ATATATTACATTACTTAAAT-TACTTACT
56759245 TACTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATTACATTACTTAAATTACTTACTAAA
Found at i:56759253 original size:17 final size:17
Alignment explanation
Indices: 56759204--56759264 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
56759194 CATTACTTAC
56759204 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
*
56759221 ATTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
*
56759239 ATTACTTACTAAAATTT
1 ATTACTTACTAAAATAT
*
56759256 ATAACTTAC
1 ATTACTTAC
56759265 ATTACATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:56760010 original size:153 final size:151
Alignment explanation
Indices: 56759630--56760067 Score: 603
Period size: 153 Copynumber: 3.0 Consensus size: 151
56759620 AAATATACTA
* * * *
56759630 TTTTTAAATTTATTTAAAAAAATATACTAAATTAATAAATTTCAAATATAATGTACTAAAATAAT
1 TTTTTAAATTTATTTAAAAACACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAAT
* * *
56759695 GTAAAAT----AAA--AAAAATAGTATATTTTTTAAAATTATTAAAATTCGAGAAAAAAATACGA
66 GTAAAATAAAAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAAATTAG-GAAAAAAATACGA
* *
56759754 ACATAAGGCTGAAATAAGGGTT
130 ACATAGGGCCGAAATAAGGGTT
* *
56759776 TTTTT--A---ATTT-AAAACACACGCTAAATTAATACATTTCAAATATAATGTACTAAAATAGT
1 TTTTTAAATTTATTTAAAAACACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAAT
* *
56759835 GTAAAATAAAAAAATTAAAAATAGTATATTTTATAAAAGTAATAAAATCTAGGAAAAAAATATGA
66 GTAAAATAAAAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAAAT-TAGGAAAAAAATACGA
56759900 ACATAGGGCCGAAATAAGGGTT
130 ACATAGGGCCGAAATAAGGGTT
*
56759922 TTTTTAAAATTTATTTAAAAACACACACTAAATTAATACAGTTCAAATATAATGTACTAAAATAA
1 TTTTT-AAATTTATTTAAAAACACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAA
* *
56759987 TGTAAAATAAAAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAAATTTGAAAAAAAATACGA
65 TGTAAAATAAAAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAAATTAGGAAAAAAATACGA
* *
56760052 ACAAAGGGCCAAAATA
130 ACATAGGGCCGAAATA
56760068 CGAACAATTG
Statistics
Matches: 256, Mismatches: 22, Indels: 22
0.85 0.07 0.07
Matches are distributed among these distances:
140 50 0.20
141 4 0.02
144 4 0.02
146 71 0.28
147 2 0.01
149 1 0.00
152 31 0.12
153 93 0.36
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.32
Consensus pattern (151 bp):
TTTTTAAATTTATTTAAAAACACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAAT
GTAAAATAAAAAAATTAAAAATAGTATATTTTTTAAAAGTAATAAAATTAGGAAAAAAATACGAA
CATAGGGCCGAAATAAGGGTT
Found at i:56760476 original size:12 final size:12
Alignment explanation
Indices: 56760459--56760487 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
56760449 ATACTTACAT
56760459 AACTTATATATA
1 AACTTATATATA
56760471 AACTTATATATA
1 AACTTATATATA
56760483 AACTT
1 AACTT
56760488 GCATAACTTA
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:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:56760501 original size:9 final size:9
Alignment explanation
Indices: 56760483--56760620 Score: 78
Period size: 9 Copynumber: 16.0 Consensus size: 9
56760473 CTTATATATA
*
56760483 AACTTGCAT
1 AACTTACAT
56760492 AACTTACAT
1 AACTTACAT
*
56760501 AA-TAACATAAT
1 AACTTAC---AT
56760512 AACTTACAT
1 AACTTACAT
*
56760521 AA--TACAC
1 AACTTACAT
56760528 AACTTACAT
1 AACTTACAT
* *
56760537 AAATTAAAT
1 AACTTACAT
56760546 AACTTACAT
1 AACTTACAT
56760555 AA--TACAT
1 AACTTACAT
**
56760562 AACTTTGAT
1 AACTTACAT
*
56760571 AACTAACAT
1 AACTTACAT
* *
56760580 TA--TACAC
1 AACTTACAT
56760587 AACTTACAT
1 AACTTACAT
56760596 AA--TACAT
1 AACTTACAT
**
56760603 TTCTTACAT
1 AACTTACAT
56760612 AACTTACAT
1 AACTTACAT
56760621 TATACACAAC
Statistics
Matches: 94, Mismatches: 23, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
7 22 0.23
8 3 0.03
9 62 0.66
11 4 0.04
12 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:56760515 original size:20 final size:18
Alignment explanation
Indices: 56760490--56760560 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 18
56760480 ATAAACTTGC
56760490 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACA-A
56760510 ATAACTTACATAATAC--
1 ATAACTTACATAATACAA
* *
56760526 ACAACTTACATAA-ATTAA
1 ATAACTTACATAATA-CAA
56760544 ATAACTTACATAATACA
1 ATAACTTACATAATACA
56760561 TAACTTTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.02
16 12 0.28
18 13 0.30
19 3 0.07
20 14 0.33
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAACTTACATAATACAA
Found at i:56760533 original size:16 final size:16
Alignment explanation
Indices: 56760489--56760566 Score: 84
Period size: 16 Copynumber: 4.5 Consensus size: 16
56760479 TATAAACTTG
56760489 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
56760506 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
*
56760525 CACAACTTACATAAATTA
1 CATAACTTACAT-AA-TA
*
56760543 AATAACTTACATAATA
1 CATAACTTACATAATA
56760559 CATAACTT
1 CATAACTT
56760567 TGATAACTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 19 0.37
17 5 0.10
18 12 0.23
19 2 0.04
20 14 0.27
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:56760591 original size:41 final size:41
Alignment explanation
Indices: 56760546--56760788 Score: 158
Period size: 41 Copynumber: 6.1 Consensus size: 41
56760536 TAAATTAAAT
**
56760546 AACTTACATAATACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAATACATAACTTACATAACTAACATTATACAC
** *
56760587 AACTTACATAATACATTTCTTACATAACTTACATTATACAC
1 AACTTACATAATACATAACTTACATAACTAACATTATACAC
* * *
56760628 AACTTAATTAATATTATACATAACATACATAA-T-ACATAATACAC
1 AACTT-A--CATA--ATACATAACTTACATAACTAACATTATACAC
* * *
56760672 AACTTA-AT--TA-ATAA-TATACATAA-TAGATATAATACAT
1 AACTTACATAATACATAACT-TACATAACTA-ACATTATACAC
* * *
56760709 AA--TACATAATACACAACTTA-AT---TAATATTATACAT
1 AACTTACATAATACATAACTTACATAACTAACATTATACAC
* * *
56760744 AACATACATAATACATAA--TACATAACTTACATAATACAC
1 AACTTACATAATACATAACTTACATAACTAACATTATACAC
56760783 AACTTA
1 AACTTA
56760789 ATTAATATTA
Statistics
Matches: 162, Mismatches: 21, Indels: 40
0.73 0.09 0.18
Matches are distributed among these distances:
35 28 0.17
36 8 0.05
37 24 0.15
38 4 0.02
39 19 0.12
40 3 0.02
41 41 0.25
42 1 0.01
43 1 0.01
44 18 0.11
45 1 0.01
46 14 0.09
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.33
Consensus pattern (41 bp):
AACTTACATAATACATAACTTACATAACTAACATTATACAC
Found at i:56760633 original size:25 final size:25
Alignment explanation
Indices: 56760483--56760633 Score: 95
Period size: 25 Copynumber: 6.2 Consensus size: 25
56760473 CTTATATATA
*
56760483 AACTTGCATAACTTACATAATA-AC
1 AACTTACATAACTTACATAATACAC
56760507 -A--TA-ATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
* * *
56760528 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAACTTACATAA--TACAC
**
56760555 AA--TACATAACTTTGATAACTA-AC
1 AACTTACATAACTTACATAA-TACAC
* * *
56760578 -ATTATACACAACTTACATAATACAT
1 AACT-TACATAACTTACATAATACAC
** *
56760603 TTCTTACATAACTTACATTATACAC
1 AACTTACATAACTTACATAATACAC
56760628 AACTTA
1 AACTTA
56760634 ATTAATATTA
Statistics
Matches: 95, Mismatches: 20, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
20 15 0.16
21 3 0.03
22 2 0.02
23 2 0.02
24 6 0.06
25 60 0.63
26 1 0.01
27 6 0.06
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:56760645 original size:21 final size:21
Alignment explanation
Indices: 56760619--56760691 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
56760609 CATAACTTAC
56760619 ATTATACACAACTTAATTAAT
1 ATTATACACAACTTAATTAAT
* *
56760640 ATTATACATAACATACA-TAAT
1 ATTATACACAACTTA-ATTAAT
*
56760661 ACATAATACACAACTTAATTAAT
1 --ATTATACACAACTTAATTAAT
*
56760684 AATATACA
1 ATTATACA
56760692 TAATAGATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
21 23 0.56
22 2 0.05
23 16 0.39
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTATACACAACTTAATTAAT
Found at i:56760664 original size:16 final size:16
Alignment explanation
Indices: 56760643--56760781 Score: 63
Period size: 16 Copynumber: 8.3 Consensus size: 16
56760633 AATTAATATT
56760643 ATACATAACATACATA
1 ATACATAACATACATA
* *
56760659 ATACATAATACACAACTTA
1 ATACAT-A-ACA-TACATA
*
56760678 ATTA-ATAATATACATA
1 A-TACATAACATACATA
*
56760694 ATAGATATA-ATACATA
1 ATACATA-ACATACATA
* *
56760710 ATACATAATACACAACTTA
1 ATACAT-A-ACA-TACATA
**
56760729 ATTA-ATATTATACATAA
1 A-TACATAACATACAT-A
56760746 CATACAT-A-ATACATA
1 -ATACATAACATACATA
*
56760761 ATACATAACTTACATA
1 ATACATAACATACATA
56760777 ATACA
1 ATACA
56760782 CAACTTAATT
Statistics
Matches: 94, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
14 6 0.06
15 4 0.04
16 46 0.49
17 11 0.12
18 9 0.10
19 14 0.15
20 4 0.04
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (16 bp):
ATACATAACATACATA
Found at i:56760674 original size:44 final size:44
Alignment explanation
Indices: 56760607--56760772 Score: 215
Period size: 44 Copynumber: 3.6 Consensus size: 44
56760597 ATACATTTCT
*
56760607 TACATAACTTACATTATACACAACTTAATTAATATTATACATAACA
1 TACATAA--TACATAATACACAACTTAATTAATATTATACATAACA
* *
56760653 TACATAATACATAATACACAACTTAATTAATAATATACATAATAGATATAA
1 TACATAATACATAATACACAACTTAATTAATATTATAC---AT--A-A-CA
56760704 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
1 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
*
56760748 TACATAATACATAATACATAACTTA
1 TACATAATACATAATACACAACTTA
56760773 CATAATACAC
Statistics
Matches: 107, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
44 54 0.50
45 1 0.01
46 8 0.07
47 2 0.02
48 2 0.02
49 1 0.01
50 1 0.01
51 38 0.36
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.33
Consensus pattern (44 bp):
TACATAATACATAATACACAACTTAATTAATATTATACATAACA
Found at i:56760709 original size:51 final size:51
Alignment explanation
Indices: 56760652--56760805 Score: 202
Period size: 51 Copynumber: 2.8 Consensus size: 51
56760642 TATACATAAC
56760652 ATACATAATACATAATACACAACTTAATTAATAATATACATAATAGAT-ATA
1 ATACATAATACATAATACACAACTTAATTAATAATATACATAATA-ATAATA
56760703 ATACATAATACATAATACACAACTTAATTAATATTATACATAACATACATAATACATA
1 ATACATAATACATAATACACAACTTAATTAATA--AT--AT-ACATA-ATAATA-ATA
*
56760761 ATACATAACTTACATAATACACAACTTAATTAATATTATACATAA
1 ATACATAA--TACATAATACACAACTTAATTAATAATATACATAA
56760806 CTTACATAAA
Statistics
Matches: 92, Mismatches: 1, Indels: 17
0.84 0.01 0.15
Matches are distributed among these distances:
51 33 0.36
53 2 0.02
54 1 0.01
55 7 0.08
56 9 0.10
57 3 0.03
58 12 0.13
60 25 0.27
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (51 bp):
ATACATAATACATAATACACAACTTAATTAATAATATACATAATAATAATA
Found at i:56760795 original size:16 final size:16
Alignment explanation
Indices: 56760755--56760788 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
56760745 ACATACATAA
*
56760755 TACATAATACATAACT
1 TACATAATACACAACT
56760771 TACATAATACACAACT
1 TACATAATACACAACT
56760787 TA
1 TA
56760789 ATTAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (16 bp):
TACATAATACACAACT
Found at i:56762857 original size:16 final size:16
Alignment explanation
Indices: 56762835--56762903 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
56762825 TTTGGTTCGC
56762835 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
56762851 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56762867 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
56762884 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56762900 TGTA
1 TGTA
56762904 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56762881 original size:33 final size:32
Alignment explanation
Indices: 56762835--56762903 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
56762825 TTTGGTTCGC
56762835 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
56762867 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
56762900 TGTA
1 TGTA
56762904 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:56762968 original size:44 final size:45
Alignment explanation
Indices: 56762884--56762974 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
56762874 GGATTAGAGG
* * *
56762884 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
56762929 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
56762973 TG
1 TG
56762975 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:56763160 original size:18 final size:17
Alignment explanation
Indices: 56763139--56763173 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56763129 TTATTATTAA
*
56763139 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56763157 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56763174 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56763335 original size:120 final size:120
Alignment explanation
Indices: 56763122--56763624 Score: 961
Period size: 120 Copynumber: 4.2 Consensus size: 120
56763112 ATCATATTTA
56763122 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
56763187 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
56763242 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTTTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
56763307 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
56763362 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
56763427 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
56763482 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
56763547 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
56763602 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
56763625 AACTTGAAAA
Statistics
Matches: 375, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 375 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:56763400 original size:18 final size:17
Alignment explanation
Indices: 56763379--56763413 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56763369 TTATTATTAA
*
56763379 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56763397 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56763414 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56763975 original size:18 final size:18
Alignment explanation
Indices: 56763952--56764011 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
56763942 TTAAAACAAG
56763952 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
56763970 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
56763987 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
56764005 TTACATT
1 TTACATT
56764012 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:56765567 original size:33 final size:33
Alignment explanation
Indices: 56765525--56765590 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
56765515 TTCTTCAAGA
56765525 AGCAGAACAAGGCGAAACATGTCAATCTAAGGG
1 AGCAGAACAAGGCGAAACATGTCAATCTAAGGG
56765558 AGCAGAACAAGGCGAAACATGTCAATCTAAGGG
1 AGCAGAACAAGGCGAAACATGTCAATCTAAGGG
56765591 CCTTGGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.12
Consensus pattern (33 bp):
AGCAGAACAAGGCGAAACATGTCAATCTAAGGG
Found at i:56765729 original size:33 final size:33
Alignment explanation
Indices: 56765690--56765765 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
56765680 ATTATAAAGC
*
56765690 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
56765723 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
56765756 ATGTATAATT
1 ATGTATAATT
56765766 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:56765863 original size:37 final size:37
Alignment explanation
Indices: 56765808--56765889 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
56765798 GTATAAATAT
* * *
56765808 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAGC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
56765845 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
56765882 ATTGATTA
1 ATTGATTA
56765890 ATAAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:56775628 original size:22 final size:22
Alignment explanation
Indices: 56775589--56775634 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
56775579 TTTATTTTGA
*
56775589 AATTAAAAAATATATTAAATAT
1 AATTAAAAAATATATTAAAGAT
** *
56775611 AATTAAAAGTTATTTTAAAGAT
1 AATTAAAAAATATATTAAAGAT
56775633 AA
1 AA
56775635 AATATGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
AATTAAAAAATATATTAAAGAT
Found at i:56775732 original size:18 final size:19
Alignment explanation
Indices: 56775695--56775734 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
56775685 GGGGGGCTTG
**
56775695 GGGGAAGTACAATTTTTTA
1 GGGGAAGTACAAAATTTTA
56775714 GGGGAAGTA-AAAATTTTA
1 GGGGAAGTACAAAATTTTA
56775732 GGG
1 GGG
56775735 ACAAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.35, C:0.03, G:0.33, T:0.30
Consensus pattern (19 bp):
GGGGAAGTACAAAATTTTA
Found at i:56782131 original size:19 final size:19
Alignment explanation
Indices: 56782090--56782131 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56782080 ATTGAACTTG
* *
56782090 AAAATTAGACCTGAGATCG
1 AAAATTAGACCTGAGACCC
56782109 AAAATTAGA-CTAGAGACCC
1 AAAATTAGACCT-GAGACCC
56782128 AAAA
1 AAAA
56782132 CTGAGGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAATTAGACCTGAGACCC
Found at i:56782487 original size:27 final size:27
Alignment explanation
Indices: 56782454--56782510 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
56782444 TTTGGTTAAA
56782454 AATTAACCAAATTACCCAAATTAACCG
1 AATTAACCAAATTACCCAAATTAACCG
* *
56782481 AATTAACTAAATTACCCGAATTAACCG
1 AATTAACCAAATTACCCAAATTAACCG
56782508 AAT
1 AAT
56782511 AGAATCACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (27 bp):
AATTAACCAAATTACCCAAATTAACCG
Found at i:56782492 original size:18 final size:18
Alignment explanation
Indices: 56782453--56782506 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
56782443 TTTTGGTTAA
* *
56782453 AAATTAACCAAATTACCC
1 AAATTAACCGAATTAACC
*
56782471 AAATTAACCGAATTAACT
1 AAATTAACCGAATTAACC
*
56782489 AAATTACCCGAATTAACC
1 AAATTAACCGAATTAACC
56782507 GAATAGAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:56782510 original size:9 final size:9
Alignment explanation
Indices: 56782453--56782506 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
56782443 TTTTGGTTAA
56782453 AAATTAACC
1 AAATTAACC
*
56782462 AAATTACCC
1 AAATTAACC
56782471 AAATTAACC
1 AAATTAACC
* *
56782480 GAATTAACT
1 AAATTAACC
*
56782489 AAATTACCC
1 AAATTAACC
*
56782498 GAATTAACC
1 AAATTAACC
56782507 GAATAGAATC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (9 bp):
AAATTAACC
Found at i:56782605 original size:6 final size:6
Alignment explanation
Indices: 56782594--56782622 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56782584 ACTTTTAGAC
56782594 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
56782623 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:56782646 original size:20 final size:20
Alignment explanation
Indices: 56782579--56782635 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
56782569 AAATTATTTG
* *
56782579 TTTAGACTTTTAGACTTTAGT
1 TTTAGAATTTTAG-TTTTAGT
56782600 TTTAG--TTTTAGTTTTAGT
1 TTTAGAATTTTAGTTTTAGT
*
56782618 TTTAGAATTTTATTTTTA
1 TTTAGAATTTTAGTTTTA
56782636 TTTATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 10 0.31
21 5 0.16
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.61
Consensus pattern (20 bp):
TTTAGAATTTTAGTTTTAGT
Found at i:56785600 original size:25 final size:26
Alignment explanation
Indices: 56785566--56785619 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
56785556 TCAATTCAAG
56785566 AGAAAGTTA-TAGAGAGAAATTTCTAA
1 AGAAAGTTATTAGAGA-AAATTTCTAA
**
56785592 AGAAA-TTATTTTAGAAAATTTCTAA
1 AGAAAGTTATTAGAGAAAATTTCTAA
56785617 AGA
1 AGA
56785620 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (26 bp):
AGAAAGTTATTAGAGAAAATTTCTAA
Found at i:56789035 original size:19 final size:20
Alignment explanation
Indices: 56788997--56789034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56788987 ATGGGGAGGG
* *
56788997 AAAATGAAAAATGTATTTTA
1 AAAATAAAAAATATATTTTA
56789017 AAAATAAAAAATATATTT
1 AAAATAAAAAATATATTT
56789035 ATTATATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATAAAAAATATATTTTA
Found at i:56796546 original size:11 final size:12
Alignment explanation
Indices: 56796530--56796559 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56796520 CAGAATTTGG
56796530 ACAAGAT-AAAA
1 ACAAGATAAAAA
56796541 ACAAGATAAAAA
1 ACAAGATAAAAA
56796553 ACAAGAT
1 ACAAGAT
56796560 TCTGCATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.10, G:0.10, T:0.10
Consensus pattern (12 bp):
ACAAGATAAAAA
Found at i:56800001 original size:19 final size:19
Alignment explanation
Indices: 56799966--56800021 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
56799956 TTTTTAAAAA
*
56799966 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
56799984 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
56800003 GA-AAATTATTTTG-ATTTT
1 TATAAA-TATTTTGAATTTT
56800021 T
1 T
56800022 TTTTGTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:56804114 original size:3 final size:3
Alignment explanation
Indices: 56804106--56804134 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56804096 TTGGTAATGT
56804106 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
56804135 TAAAAAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56804147 original size:3 final size:3
Alignment explanation
Indices: 56804141--56804222 Score: 137
Period size: 3 Copynumber: 27.3 Consensus size: 3
56804131 AGAATAAAAA
*
56804141 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
56804189 GAT GGT GAT GAT GAT GAT GAT GAT GAT GGT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
56804223 CAATAAGCAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:56804365 original size:42 final size:42
Alignment explanation
Indices: 56804310--56804400 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
56804300 ATGTGAACTT
56804310 AGCATAAAAACAAAGAAACTTGGCATGAACATTGGTAAGTGA
1 AGCATAAAAACAAAGAAACTTGGCATGAACATTGGTAAGTGA
56804352 AGCATAAAAACAAAGAAACTTGGCATGAACATTGGTAAGTGA
1 AGCATAAAAACAAAGAAACTTGGCATGAACATTGGTAAGTGA
56804394 AG-ATAAA
1 AGCATAAA
56804401 GAACTTAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 5 0.10
42 44 0.90
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (42 bp):
AGCATAAAAACAAAGAAACTTGGCATGAACATTGGTAAGTGA
Found at i:56807660 original size:51 final size:51
Alignment explanation
Indices: 56807599--56807701 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
56807589 AAATTAAAAG
56807599 ATTATACATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAACA
56807650 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
56807701 A
1 A
56807702 GTAATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (51 bp):
ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
Found at i:56807710 original size:33 final size:34
Alignment explanation
Indices: 56807647--56807757 Score: 106
Period size: 33 Copynumber: 3.4 Consensus size: 34
56807637 CATTAAACCA
* ***
56807647 ACAATTATACATACACCAACAATGTTTTTTAGGG
1 ACAATTATACATAAACCAACAATCAATTTTAGGG
56807681 ACAA-TA-ACATTAAACCAACAAGT-AATTTTA-GG
1 ACAATTATACA-TAAACCAACAA-TCAATTTTAGGG
* *
56807713 TCAATTATACATACACCAACAATCAATTTTA-GG
1 ACAATTATACATAAACCAACAATCAATTTTAGGG
*
56807746 TCAATTATACAT
1 ACAATTATACAT
56807758 GCTTTATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
32 9 0.13
33 50 0.75
34 8 0.12
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (34 bp):
ACAATTATACATAAACCAACAATCAATTTTAGGG
Done.