Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 130 of 182
Found at i:41130539 original size:11 final size:11
Alignment explanation
Indices: 41130458--41130539 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
41130448 TACTTTTGTC
*
41130458 TTTTCTTTTTC
1 TTTTCTTTTTT
41130469 TTTTCTTTTTT
1 TTTTCTTTTTT
**
41130480 TTTTCTCAATTT
1 TTTTCT-TTTTT
41130492 TTTTCAATTCTTTT
1 TTTTC--TT-TTTT
**
41130506 TTTTC-AATTT
1 TTTTCTTTTTT
**
41130516 TTTTC-GATTT
1 TTTTCTTTTTT
41130526 TTTTCTTTTTT
1 TTTTCTTTTTT
41130537 TTT
1 TTT
41130540 AAAATAATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
10 17 0.30
11 22 0.39
12 8 0.14
14 9 0.16
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:41131469 original size:6 final size:6
Alignment explanation
Indices: 41131458--41131495 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
41131448 ATAATTAAAA
41131458 AAAACT AAAACT AAAA-T AAAA-T AAAACT AAAACT AAAA
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAA
41131496 ATGAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAACT
Found at i:41131472 original size:16 final size:16
Alignment explanation
Indices: 41131453--41131495 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
41131443 GGTGCATAAT
41131453 TAAAA-AAAACTAAAAC
1 TAAAATAAAA-TAAAAC
41131469 TAAAATAAAATAAAAC
1 TAAAATAAAATAAAAC
41131485 TAAAACTAAAA
1 TAAAA-TAAAA
41131496 ATGAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAATAAAATAAAAC
Found at i:41131486 original size:22 final size:23
Alignment explanation
Indices: 41131453--41131517 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
41131443 GGTGCATAAT
41131453 TAAAA-AAAACTAAAACT-AAAA
1 TAAAATAAAACTAAAACTAAAAA
41131474 TAAAATAAAACTAAAACTAAAAA
1 TAAAATAAAACTAAAACTAAAAA
*
41131497 TGAAAT-AAA-T-AAACTAAAAA
1 TAAAATAAAACTAAAACTAAAAA
41131517 T
1 T
41131518 TTTTTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 11 0.27
21 6 0.15
22 15 0.37
23 9 0.22
ACGTcount: A:0.72, C:0.08, G:0.02, T:0.18
Consensus pattern (23 bp):
TAAAATAAAACTAAAACTAAAAA
Found at i:41135289 original size:31 final size:31
Alignment explanation
Indices: 41135254--41135312 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
41135244 GCACTCCCCA
41135254 TTAAGCTCCACAGTGGACAACTCCTCTACCC
1 TTAAGCTCCACAGTGGACAACTCCTCTACCC
41135285 TTAAGCTCCACAGTGGACAACTCCTCTA
1 TTAAGCTCCACAGTGGACAACTCCTCTA
41135313 ACTTCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.24
Consensus pattern (31 bp):
TTAAGCTCCACAGTGGACAACTCCTCTACCC
Found at i:41138298 original size:13 final size:13
Alignment explanation
Indices: 41138282--41138314 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41138272 AACATATAAT
41138282 AATAATAATCCTA
1 AATAATAATCCTA
*
41138295 AATATTAATCCTA
1 AATAATAATCCTA
41138308 AA-AATAA
1 AATAATAA
41138315 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:41143592 original size:289 final size:289
Alignment explanation
Indices: 41143073--41143654 Score: 1103
Period size: 289 Copynumber: 2.0 Consensus size: 289
41143063 AATTAACTTG
41143073 CAATTGTCCACTCAGAACTCTATCATGCACAAAGTGCATATCAATTTCAATATGTTTTGCTCGAG
1 CAATTGTCCACTCAGAACTCTATCATGCACAAAGTGCATATCAATTTCAATATGTTTTGCTCGAG
*
41143138 CATGCATAACAGGATTTGCAACAAGTGAGACAGCACTTACATTGTCACACCAAACCATTAGTATT
66 CATGCATAACAGGATTTGCAACAAGTGAGACAGCACTCACATTGTCACACCAAACCATTAGTATT
*
41143203 CCCATGGGAGCAACTCCAACCTCTGTAAGTAAAGACTGAAACCAGACAAATTTAGATGTAGCATT
131 CCCATGGGAGCAACTCCAACCTCTGTAAGTAAAGACTGAAACCAAACAAATTTAGATGTAGCATT
*
41143268 TGCCAAGCTCTTGTATTCTACCTCAGTGGTAGATCTCGATACAGTACTTTGTTTCTTTGATGACC
196 TGCCAAGCTCTTGTATTCTACCTCAGTGGTAGATCTCAATACAGTACTTTGTTTCTTTGATGACC
41143333 ATCCAACCAAATTGTCTCCTAGATACATA
261 ATCCAACCAAATTGTCTCCTAGATACATA
41143362 CAATTGTCCACTCAGAACTCTATCATGCACAAAGTGCATATCAATTTCAATATGTTTTGCTC-AG
1 CAATTGTCCACTCAGAACTCTATCATGCACAAAGTGCATATCAATTTCAATATGTTTTGCTCGA-
*
41143426 GCATGCATAACAGGATTTGCTACAAGTGAGACAGCACTCACATTGTCACACCAAACCATTAGTAT
65 GCATGCATAACAGGATTTGCAACAAGTGAGACAGCACTCACATTGTCACACCAAACCATTAGTAT
*
41143491 TCCCATGGGAGCAACTCCAACCTCTGTAAGTAAAGACTGAAACCAAACAAGTTTAGATGTAGCAT
130 TCCCATGGGAGCAACTCCAACCTCTGTAAGTAAAGACTGAAACCAAACAAATTTAGATGTAGCAT
41143556 TTGCCAAGCTCTTGTATTCTACCTCAGTGGTAGATCTCAATACAGTACTTTGTTTCTTTGATGAC
195 TTGCCAAGCTCTTGTATTCTACCTCAGTGGTAGATCTCAATACAGTACTTTGTTTCTTTGATGAC
41143621 CATCCAACCAAATTGTCTCCTAGATACATA
260 CATCCAACCAAATTGTCTCCTAGATACATA
41143651 CAAT
1 CAAT
41143655 AGCCAGATGT
Statistics
Matches: 287, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
288 1 0.00
289 286 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (289 bp):
CAATTGTCCACTCAGAACTCTATCATGCACAAAGTGCATATCAATTTCAATATGTTTTGCTCGAG
CATGCATAACAGGATTTGCAACAAGTGAGACAGCACTCACATTGTCACACCAAACCATTAGTATT
CCCATGGGAGCAACTCCAACCTCTGTAAGTAAAGACTGAAACCAAACAAATTTAGATGTAGCATT
TGCCAAGCTCTTGTATTCTACCTCAGTGGTAGATCTCAATACAGTACTTTGTTTCTTTGATGACC
ATCCAACCAAATTGTCTCCTAGATACATA
Found at i:41149231 original size:6 final size:6
Alignment explanation
Indices: 41149222--41149343 Score: 76
Period size: 6 Copynumber: 21.0 Consensus size: 6
41149212 TAAAATAATT
* * *
41149222 TTTAAA TTT-AT TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** ** * *
41149269 TGCATT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
41149315 TTTGAAA --TAAT TTTAAA ATTAAA ATTAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
41149344 AAGCCCAAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
4 2 0.02
5 16 0.18
6 64 0.74
7 5 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:41149231 original size:24 final size:25
Alignment explanation
Indices: 41149198--41149290 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 25
41149188 TTTGGGTCAA
*
41149198 TTTT-AATTTAAGTTTAAAAT-AAT
1 TTTTAAATTTAAATTTAAAATAAAT
*
41149221 TTTTAAATTT-ATTTCTAAAATTAAATT
1 TTTTAAATTTAAATT-TAAAA-TAAA-T
**
41149248 TACTTTAAATTTAAATTT-AAATGCAT
1 T--TTTAAATTTAAATTTAAAATAAAT
41149274 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
41149291 TTTTAAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
23 7 0.12
24 25 0.44
25 1 0.02
26 4 0.07
27 4 0.07
28 3 0.05
29 10 0.18
30 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTAAATTTAAATTTAAAATAAAT
Found at i:41149255 original size:41 final size:41
Alignment explanation
Indices: 41149222--41149307 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
41149212 TAAAATAATT
** *
41149222 TTTAAATTTATTTCTAAAATTAAATTTACTTTAAATTTAAA
1 TTTAAATGCATTTCTAAAATTAAATTTACTTTAAATATAAA
* * * *
41149263 TTTAAATGCATTTTTAAATTTAAATTTATTTTAAATTTAAA
1 TTTAAATGCATTTCTAAAATTAAATTTACTTTAAATATAAA
41149304 TTTA
1 TTTA
41149308 GTTTAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (41 bp):
TTTAAATGCATTTCTAAAATTAAATTTACTTTAAATATAAA
Found at i:41149329 original size:17 final size:17
Alignment explanation
Indices: 41149222--41149337 Score: 99
Period size: 17 Copynumber: 6.4 Consensus size: 17
41149212 TAAAATAATT
41149222 TTTAAATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
* *
41149240 ATTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
41149257 TTTAAATTTAAATGCATTTTTAAA
1 TTTAAA-TT---T--A-TTTTAAA
41149281 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
41149298 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
41149315 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
41149332 ATTAAA
1 TTTAAA
41149338 ATTAAAAAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.04
17 45 0.55
18 17 0.21
20 1 0.01
21 1 0.01
23 3 0.04
24 12 0.15
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41151218 original size:29 final size:28
Alignment explanation
Indices: 41151155--41151464 Score: 125
Period size: 29 Copynumber: 10.5 Consensus size: 28
41151145 CTGAACTGTC
* *
41151155 CAAAAATTACCATTTTACCCCTAAACTTTC-
1 CAAAAATT-CCATTTTA-ACCTCAA-TTTCA
*
41151185 C-AAAATTCCGTTTTAACCTCAATTTCA
1 CAAAAATTCCATTTTAACCTCAATTTCA
* *
41151212 TCAAAAATTACCATTTTACCCTCGAACTTC-
1 -CAAAAATT-CCATTTTAACCTC-AATTTCA
* * *
41151242 CCAAAATTCCATTTTTAACCCCGATTTCA
1 CAAAAATTCCA-TTTTAACCTCAATTTCA
*
41151271 TCAAAAATTACCATTTTACCCTCGAACTTTC-
1 -CAAAAATT-CCATTTTAACCTC-AA-TTTCA
**
41151302 C-AAAATTCCATTTTTAACCTCGGTTTCA
1 CAAAAATTCCA-TTTTAACCTCAATTTCA
* * * *
41151330 CCAAAAATTACCAATATACCCCTAAACTTTC-
1 -CAAAAATT-CCATTTTA-ACCTCAA-TTTCA
* *
41151361 C-AAAATTCCATTTTTAACCCCAGTTTCA
1 CAAAAATTCCA-TTTTAACCTCAATTTCA
* * *
41151389 TCAAAAATTACCAGTTTACCCCCAAACTTTC-
1 -CAAAAATT-CCATTTTAACCTC-AA-TTTCA
* * * *
41151420 C-AAGATTCCATTTTTAACCCCGATCTCA
1 CAAAAATTCCA-TTTTAACCTCAATTTCA
41151448 CCAAAAATTACCATTTT
1 -CAAAAATT-CCATTTT
41151465 GCCCCCTCGC
Statistics
Matches: 211, Mismatches: 39, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
26 4 0.02
27 16 0.08
28 28 0.13
29 67 0.32
30 62 0.29
31 22 0.10
32 12 0.06
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (28 bp):
CAAAAATTCCATTTTAACCTCAATTTCA
Found at i:41151469 original size:29 final size:28
Alignment explanation
Indices: 41151437--41151497 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
41151427 CCATTTTTAA
*
41151437 CCCCGATCTCACCAAAAATTACCATTTTG
1 CCCC-ATCGCACCAAAAATTACCATTTTG
* ** *
41151466 CCCCCTCGCGTCTAAAATTACCATTTTG
1 CCCCATCGCACCAAAAATTACCATTTTG
41151494 CCCC
1 CCCC
41151498 CGGGTATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.28
Consensus pattern (28 bp):
CCCCATCGCACCAAAAATTACCATTTTG
Found at i:41151470 original size:59 final size:59
Alignment explanation
Indices: 41151154--41151470 Score: 422
Period size: 59 Copynumber: 5.4 Consensus size: 59
41151144 CCTGAACTGT
* * * *
41151154 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-GTTTTAACCTCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
41151212 TCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
41151271 TCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
41151330 CCAAAAATTACCAATATACCCCTAAACTTTCCAAAATTCCATTTTTAACCCC-AGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
* * * *
41151389 TCAAAAATTACCAGTTTACCCCCAAACTTTCCAAGATTCCATTTTTAACCCCGATCTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
41151448 CCAAAAATTACCATTTTGCCCCC
1 CCAAAAATTACCATTTTACCCCC
41151471 TCGCGTCTAA
Statistics
Matches: 228, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
58 35 0.15
59 192 0.84
60 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:41151510 original size:28 final size:28
Alignment explanation
Indices: 41151451--41151510 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
41151441 GATCTCACCA
* * *
41151451 AAAATTACCATTTTGCCCCCTCGCGTCT
1 AAAATTACCATTTTGCCCCCGCGCATCC
* *
41151479 AAAATTACCATTTTGCCCCCGGGTATCC
1 AAAATTACCATTTTGCCCCCGCGCATCC
41151507 AAAA
1 AAAA
41151511 GTCCCGTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGCGCATCC
Found at i:41163601 original size:77 final size:76
Alignment explanation
Indices: 41163399--41163631 Score: 351
Period size: 75 Copynumber: 3.0 Consensus size: 76
41163389 TAGGAAGAAG
41163399 GAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTG-
1 GAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
41163463 AATTGAAGTAA
66 AATTGAAGTAA
* * *
41163474 GAGCAAGATCCTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGA
1 GAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
41163539 AATTGAAGTAA
66 AATTGAAGTAA
* * * **
41163550 GAGCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTC
1 GAGCAACATCA-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTT--TATCTC
*
41163615 AGAAATTGAAGTAA
63 TGAAATTGAAGTAA
41163629 GAG
1 GAG
41163632 TAAAATGAAG
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
75 61 0.43
76 20 0.14
77 41 0.29
79 20 0.14
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (76 bp):
GAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
AATTGAAGTAA
Found at i:41163633 original size:243 final size:244
Alignment explanation
Indices: 41163059--41163822 Score: 1187
Period size: 245 Copynumber: 3.1 Consensus size: 244
41163049 AATCCAACAT
*
41163059 CATCTTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
1 CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
*
41163124 TGAAGAGTAAGAGTAGGAAGAAGAAGCAACATCATTTCCTATCCTAATTGAGTAGATTGAAGTAG
66 TG-A-AGTAAGAGTAGGAAGAAGAAGCAACATCATTTCCTATCCT-CTTGA--A-ATTGAAGTAG
** * *
41163189 A-TAAAGTTATA-AAGTCTTAATATCTCTGAAATTGAAGTAAAAGCAAGATCCTTTCCTATCCTC
125 AGT-TGGATA-ACAAGTCTT--TATCTCTGAAATTGAAGTAAGAGCAAGATCCTTTCCTATCCTC
*
41163252 TTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGAGTAAGAGCAA
186 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTG-A-AGTAAGAGCAA
41163313 CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
1 CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
*
41163378 TGAAGTAAGAGTAGGAAGAAGGAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
66 TGAAGTAAGAGTAGGAAGAAGAAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
41163443 ATAACAAGTCTTTATCTCTG-AATTGAAGTAAGAGCAAGATCCTTTCCTATCCTCTTGAAATTGA
131 ATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCCTTTCCTATCCTCTTGAAATTGA
*
41163507 AGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAGCAA
196 AGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
* * *
41163556 CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCAGAAAT
1 CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
* * * *
41163621 TGAAGTAAGAGTA-AAATGAAGCACCAACATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGGTT
66 TGAAGTAAGAGTAGGAA-GAAGAAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGA-GTT
* * *
41163685 GGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAACATCATTTCCTATCCTCTTGAAATT
129 GGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCCTTTCCTATCCTCTTGAAATT
*
41163750 AAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
194 GAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
41163801 CATCA-TTTCCTATCCTCTTGAA
1 CATCATTTTCCTATCCTCTTGAA
41163823 TGAAGTTTGA
Statistics
Matches: 484, Mismatches: 21, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
242 2 0.00
243 126 0.26
244 43 0.09
245 171 0.35
246 8 0.02
247 1 0.00
248 21 0.04
249 2 0.00
251 4 0.01
252 39 0.08
253 1 0.00
254 66 0.14
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (244 bp):
CATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGACAACAAACCTTCGTCCCTCTGAAAT
TGAAGTAAGAGTAGGAAGAAGAAGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
ATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCCTTTCCTATCCTCTTGAAATTGA
AGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
Found at i:41163678 original size:168 final size:166
Alignment explanation
Indices: 41163485--41163797 Score: 511
Period size: 168 Copynumber: 1.9 Consensus size: 166
41163475 AGCAAGATCC
*
41163485 TTTCCTATCCTCTTGAAATTGAAGTAGA-GTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
* *
41163549 AGAGCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCT
66 AGAGCAACATCA-TTTCCTATCCTCTTGAAATTAAAGTAAAGCTGGATAACAAGCCTT--TACCT
41163614 CAGAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCG
128 CAGAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCG
41163653 TTTCCTATCCTCTTGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
1 TTTCCTATCCTCTTGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
* * * * * *
41163718 AGAGTAACATCATTTCCTATCCTCTTGAAATTAAAGTAGAGTTGGATAACAAGTCTTTATCTCTG
66 AGAGCAACATCATTTCCTATCCTCTTGAAATTAAAGTAAAGCTGGATAACAAGCCTTTACCTCAG
41163783 AAATTGAAGTAAGAG
131 AAATTGAAGTAAGAG
41163798 CAACATCATT
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
166 20 0.15
168 69 0.51
169 46 0.34
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (166 bp):
TTTCCTATCCTCTTGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
AGAGCAACATCATTTCCTATCCTCTTGAAATTAAAGTAAAGCTGGATAACAAGCCTTTACCTCAG
AAATTGAAGTAAGAGTAAAATGAAGCACCAACATCG
Found at i:41163709 original size:39 final size:39
Alignment explanation
Indices: 41163666--41163793 Score: 131
Period size: 38 Copynumber: 3.3 Consensus size: 39
41163656 CCTATCCTCT
41163666 TGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTC
* * * ** *
41163705 TGAAATTGAAGTA-AGAG-T-AACATCATTTC-CTATCCTC
1 TGAAATTGAAGTAGAG-GTTGGATAACAAGTCTTTAT-CTC
*
41163742 TTGAAATTAAAGTAGA-GTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTC
41163781 TGAAATTGAAGTA
1 TGAAATTGAAGTA
41163794 AGAGCAACAT
Statistics
Matches: 68, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
36 3 0.04
37 10 0.15
38 28 0.41
39 24 0.35
40 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (39 bp):
TGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTC
Found at i:41163759 original size:37 final size:38
Alignment explanation
Indices: 41163705--41163822 Score: 116
Period size: 38 Copynumber: 3.1 Consensus size: 38
41163695 TCTTTATCTC
41163705 TGAAATTGAAGTAAGAGTAACATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGTAACATCATTTCCTATCCTCT
* * * * ** *
41163743 TGAAATTAAAGT-AGAGTTGGATAACAAGTCTTTAT-CTC-
1 TGAAATTGAAGTAAGAG-T-AACATCATTTC-CTATCCTCT
*
41163781 TGAAATTGAAGTAAGAGCAACATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGTAACATCATTTCCTATCCTCT
41163819 TGAA
1 TGAA
41163823 TGAAGTTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
36 3 0.05
37 13 0.22
38 27 0.46
39 13 0.22
40 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (38 bp):
TGAAATTGAAGTAAGAGTAACATCATTTCCTATCCTCT
Found at i:41163791 original size:76 final size:77
Alignment explanation
Indices: 41163645--41163822 Score: 322
Period size: 76 Copynumber: 2.3 Consensus size: 77
41163635 AATGAAGCAC
* *
41163645 CAACATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAA
1 CAACATCATTTCCTATCCTCTTGAAATTAAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAA
41163710 TTGAAGTAAGAG
66 TTGAAGTAAGAG
*
41163722 TAACATCATTTCCTATCCTCTTGAAATTAAAGTAGA-GTTGGATAACAAGTCTTTATCTCTGAAA
1 CAACATCATTTCCTATCCTCTTGAAATTAAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAA
41163786 TTGAAGTAAGAG
66 TTGAAGTAAGAG
41163798 CAACATCATTTCCTATCCTCTTGAA
1 CAACATCATTTCCTATCCTCTTGAA
41163823 TGAAGTTTGA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 64 0.66
77 33 0.34
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (77 bp):
CAACATCATTTCCTATCCTCTTGAAATTAAAGTAGAGGTTGGATAACAAGTCTTTATCTCTGAAA
TTGAAGTAAGAG
Found at i:41164259 original size:41 final size:41
Alignment explanation
Indices: 41164214--41164301 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
41164204 GGTCAATTTT
** *
41164214 AATTTAAGTTAAAATGATTTTTAAATTTATTTCTAAAATTA
1 AATTTAAGTTAAAATGAAATTTAAATTCATTTCTAAAATTA
** * * * *
41164255 AATTTACTTTAAATTTAAATTTAAATTCATTTTTAAATTTA
1 AATTTAAGTTAAAATGAAATTTAAATTCATTTCTAAAATTA
41164296 AATTTA
1 AATTTA
41164302 TTTTAAATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (41 bp):
AATTTAAGTTAAAATGAAATTTAAATTCATTTCTAAAATTA
Found at i:41164271 original size:6 final size:6
Alignment explanation
Indices: 41164233--41164333 Score: 84
Period size: 6 Copynumber: 17.2 Consensus size: 6
41164223 TAAAATGATT
* * *
41164233 TTTAAA TTT-AT TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
41164280 TTCATT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41164326 TTTGAAA T
1 TTT-AAA T
41164334 AATTTTTAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
5 15 0.21
6 52 0.71
7 6 0.08
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:41164272 original size:17 final size:17
Alignment explanation
Indices: 41164233--41164333 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 17
41164223 TAAAATGATT
*
41164233 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
*
41164251 ATTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
41164268 TTTAAATTTAAATTCATTTTTAAA
1 TTTAAATTT--A--C---TTTAAA
*
41164292 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
41164309 TTTAAATTTAGTTTAAA
1 TTTAAATTTACTTTAAA
41164326 TTTGAAAT
1 TTT-AAAT
41164334 AATTTTTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
17 37 0.53
18 15 0.21
19 1 0.01
21 1 0.01
22 1 0.01
24 15 0.21
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:41164307 original size:41 final size:41
Alignment explanation
Indices: 41164233--41164318 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
41164223 TAAAATGATT
*
41164233 TTTAAATTTATTTCTAAAATTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
* * *
41164274 TTTAAATTCATTTTTAAATTTAAATTTATTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
41164315 TTTA
1 TTTA
41164319 GTTTAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
Found at i:41164341 original size:18 final size:16
Alignment explanation
Indices: 41164268--41164350 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 16
41164258 TTACTTTAAA
41164268 TTTAAATTTAAATTCATT
1 TTTAAATTTAAA-T-ATT
*
41164286 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATAT-T
41164303 TTTAAATTTAAAT-TT
1 TTTAAATTTAAATATT
41164318 AGTTTAAATTTGAAATAATT
1 --TTTAAATTT-AAAT-ATT
*
41164338 TTTAAATTAAAAT
1 TTTAAATTTAAAT
41164351 TAAAAAGCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 28 0.49
18 24 0.42
20 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTAAATTTAAATATT
Found at i:41164341 original size:35 final size:35
Alignment explanation
Indices: 41164268--41164351 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
41164258 TTACTTTAAA
* *
41164268 TTTAAATTTAAATTCATTTTTAAATTTAAATTTAT
1 TTTAAATTTAAATTCATGTTTAAATTTAAATATAT
*
41164303 TTTAAATTTAAATTTA-GTTTAAATTTGAAATA-ATT
1 TTTAAATTTAAATTCATGTTTAAATTT-AAATATA-T
*
41164338 TTTAAATTAAAATT
1 TTTAAATTTAAATT
41164352 AAAAAGCCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 10 0.23
35 33 0.77
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTAAATTTAAATTCATGTTTAAATTTAAATATAT
Found at i:41166229 original size:29 final size:28
Alignment explanation
Indices: 41166139--41166385 Score: 132
Period size: 29 Copynumber: 8.5 Consensus size: 28
41166129 GAACTGTCTG
*
41166139 AAAATTACCATTTT-ACCCCTAAACTTTCC
1 AAAATTACCATTTTAACCCC--AACTTACC
* * * *
41166168 AAAATT-CCGTTTTAACCTCAATTTCATCA
1 AAAATTACCATTTTAACCCCAACTT-A-CC
41166197 AAAATTACCATTTT-ACCTCCAAACTTACC
1 AAAATTACCATTTTAACC-CC-AACTTACC
***
41166226 AAAATT-CCATTTTTAACCCCGGTTTCACC
1 AAAATTACCA-TTTTAACCCCAACTT-ACC
* *
41166255 AAAAATTACCATTTT-ACCCCTAAACTTTCT
1 -AAAATTACCATTTTAACCCC--AACTTACC
* * *
41166285 AAAATT-CCATTTTAACCCCGATTTAATCA
1 AAAATTACCATTTTAACCCCAACTT-A-CC
*
41166314 AAAATTACCATTTT-ACCCCGAACTTTCC
1 AAAATTACCATTTTAACCCC-AACTTACC
* * *
41166342 AAGATT-CCATTTTTAACCCCGATCTCACC
1 AAAATTACCA-TTTTAACCCC-AACTTACC
41166371 AAAAATTACCATTTT
1 -AAAATTACCATTTT
41166386 GCCCCTACGC
Statistics
Matches: 166, Mismatches: 30, Indels: 43
0.69 0.13 0.18
Matches are distributed among these distances:
27 10 0.06
28 28 0.17
29 75 0.45
30 41 0.25
31 12 0.07
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTACCATTTTAACCCCAACTTACC
Found at i:41166229 original size:58 final size:59
Alignment explanation
Indices: 41166139--41166392 Score: 354
Period size: 58 Copynumber: 4.4 Consensus size: 59
41166129 GAACTGTCTG
* * * *
41166139 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-GTTTTAACCTCAATTTCATCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
41166197 AAAATTACCATTTTACCTCC-AAACTTACCAAAATTCCATTTTTAACCCCGGTTTCACCA
1 AAAATTACCATTTTACC-CCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
41166256 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCA-TTTTAACCCCGATTTAATCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
41166314 AAAATTACCATTTTACCCC-GAACTTTCCAAGATTCCATTTTTAACCCCGATCTCACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
41166372 AAAATTACCATTTTGCCCCTA
1 AAAATTACCATTTTACCCCTA
41166393 CGCATCCAAA
Statistics
Matches: 172, Mismatches: 19, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
57 15 0.09
58 106 0.62
59 51 0.30
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:41167664 original size:26 final size:26
Alignment explanation
Indices: 41167634--41167685 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
41167624 AAATAAAAAG
* *
41167634 TTAATAAAATCAGTTGGTCAAATCAA
1 TTAATAAAATCAATTGATCAAATCAA
*
41167660 TTAATAGAATCAATTGATCAAATCAA
1 TTAATAAAATCAATTGATCAAATCAA
41167686 CCACTGCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (26 bp):
TTAATAAAATCAATTGATCAAATCAA
Found at i:41172684 original size:22 final size:21
Alignment explanation
Indices: 41172652--41172692 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
41172642 CAATAAAATC
*
41172652 TGTTTTTTTTTGTTGTTTTAA
1 TGTTTTTTTTTATTGTTTTAA
41172673 TGTTATTTTTTTATTGTTTT
1 TGTT-TTTTTTTATTGTTTT
41172693 CTTCTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (21 bp):
TGTTTTTTTTTATTGTTTTAA
Found at i:41172700 original size:22 final size:22
Alignment explanation
Indices: 41172656--41172703 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
41172646 AAAATCTGTT
* *
41172656 TTTTTTTGTTGTTTTAATGTTA
1 TTTTTTTATTGTTTTAATCTTA
**
41172678 TTTTTTTATTGTTTTCTTCTTA
1 TTTTTTTATTGTTTTAATCTTA
41172700 TTTT
1 TTTT
41172704 CCTACCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTTTATTGTTTTAATCTTA
Found at i:41172855 original size:9 final size:9
Alignment explanation
Indices: 41172841--41172865 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41172831 AAAATATTTA
41172841 TTTTAATAT
1 TTTTAATAT
41172850 TTTTAATAT
1 TTTTAATAT
41172859 TTTTAAT
1 TTTTAAT
41172866 GTATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:41178117 original size:17 final size:16
Alignment explanation
Indices: 41178088--41178121 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41178078 AACTAATTTA
41178088 TTTTAATTTATTTGAT
1 TTTTAATTTATTTGAT
*
41178104 TTTTTATTTAATTTGAT
1 TTTTAATTT-ATTTGAT
41178121 T
1 T
41178122 CTCAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTAATTTATTTGAT
Found at i:41179010 original size:16 final size:16
Alignment explanation
Indices: 41178989--41179043 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
41178979 TTAATCATTT
41178989 TAATATTAAATTAATA
1 TAATATTAAATTAATA
* * *
41179005 TAATATT-TATCAAAA
1 TAATATTAAATTAATA
41179020 TAAATATTAAATTAATA
1 T-AATATTAAATTAATA
*
41179037 GAATATT
1 TAATATT
41179044 TACCTACAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 6 0.20
16 19 0.63
17 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:41179027 original size:32 final size:34
Alignment explanation
Indices: 41178990--41179079 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 34
41178980 TAATCATTTT
41178990 AATATTAAATTAATATAATATTTA-T-CAAAATA
1 AATATTAAATTAATATAATATTTACTACAAAATA
* *
41179022 AATATTAAATTAATAGAATATTTACCTACAAGATA
1 AATATTAAATTAATATAATATTTA-CTACAAAATA
* *
41179057 AACATTAAATTAAATTTAATATT
1 AATATTAAATT-AATATAATATT
41179080 AAGATAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 23 0.47
34 1 0.02
35 16 0.33
36 9 0.18
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (34 bp):
AATATTAAATTAATATAATATTTACTACAAAATA
Found at i:41179107 original size:20 final size:18
Alignment explanation
Indices: 41179060--41179108 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
41179050 CAAGATAAAC
41179060 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41179077 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
41179097 ATTAAATTAATA
1 ATTAAATTAATA
41179109 AAATACTATT
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:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41180729 original size:6 final size:6
Alignment explanation
Indices: 41180718--41180744 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41180708 AGAAGCTAAA
41180718 CCATCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCA
41180745 ACCGCTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATCT
Found at i:41183637 original size:17 final size:17
Alignment explanation
Indices: 41183611--41183643 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41183601 TAGCTGACGG
41183611 GAATAGGTAAAGAAATT
1 GAATAGGTAAAGAAATT
*
41183628 GAATATGTAAAGAAAT
1 GAATAGGTAAAGAAAT
41183644 AGGTTGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (17 bp):
GAATAGGTAAAGAAATT
Found at i:41187719 original size:3 final size:3
Alignment explanation
Indices: 41187663--41187700 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41187653 GGCTTTAGGG
41187663 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41187701 ATACTCGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41188552 original size:26 final size:25
Alignment explanation
Indices: 41188523--41188583 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
41188513 ATTTGGAGGA
**
41188523 TTACATTATCATCAAATTTCTAAAAT
1 TTACATTATCAAAAAATTTCT-AAAT
41188549 TTAC-TTAATTCAAAAAATTTCTAAAT
1 TTACATT-A-TCAAAAAATTTCTAAAT
*
41188575 TTTCATTAT
1 TTACATTAT
41188584 TTAAAACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.10
26 13 0.45
27 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (25 bp):
TTACATTATCAAAAAATTTCTAAAT
Found at i:41188589 original size:26 final size:28
Alignment explanation
Indices: 41188536--41188606 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
41188526 CATTATCATC
*
41188536 AAATTTCTAAAATTT-ACTTAATTCAAA
1 AAATTTCTAAATTTTCACTTAATTCAAA
*
41188563 AAATTTCTAAATTTTCA-TT-ATTTAAA
1 AAATTTCTAAATTTTCACTTAATTCAAA
* *
41188589 ACATTTTTAAATATTTCA
1 AAATTTCTAAAT-TTTCA
41188607 ATCTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.42
27 21 0.55
28 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATTTCTAAATTTTCACTTAATTCAAA
Found at i:41193017 original size:59 final size:57
Alignment explanation
Indices: 41192886--41193070 Score: 187
Period size: 59 Copynumber: 3.2 Consensus size: 57
41192876 TTAATATAAT
* * *
41192886 ATTTGGTACCTGTATTTGATATTTTT-TTAATTTGATACCTAAAC-TTTTTGACCCA
1 ATTTGGTACCTGAACTTGATATTTTTCTTAATTTGGTACCTAAACTTTTTTGACCCA
* *
41192941 ATTTGGTACTTGAACTTGATATTTTTTCTTATTTTGGTACCTAAACTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGATA-TTTTTCTTAATTTGGTACCTAAACTTTTTT-GACCCA
* * * * * **
41193000 ATTTGATACCTGCACTTGGCA-ATTTTTCCTAATTTGGTACTTAAGCTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTT-G-ATATTTTTCTTAATTTGGTACCTAAAC-TTTTTT-GACCCA
41193060 ATTTGGTACCT
1 ATTTGGTACCT
41193071 AAAATTATTA
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
55 18 0.17
56 5 0.05
57 16 0.15
58 5 0.05
59 40 0.37
60 22 0.21
61 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (57 bp):
ATTTGGTACCTGAACTTGATATTTTTCTTAATTTGGTACCTAAACTTTTTTGACCCA
Found at i:41193311 original size:30 final size:31
Alignment explanation
Indices: 41193275--41193408 Score: 104
Period size: 31 Copynumber: 4.5 Consensus size: 31
41193265 GGACCCCAAA
* * * *
41193275 AAGTTTAAGTGCCAACTTA-AAAAACGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGAC
*
41193305 AAGTTTAGGTACCAAATTAGAAAAAAGTGAC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGAC
* * **
41193336 AAGTTTGAGTATCAAATTAGATCAAA---A-
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGAC
*
41193363 AA-TATTAAGTACCAAATTA-AAAAAA-TGTC
1 AAGT-TTAAGTACCAAATTAGAAAAAAGTGAC
*
41193392 AAGTCTAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
41193409 ATTATATTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
26 5 0.06
27 15 0.18
28 1 0.01
29 14 0.17
30 17 0.21
31 30 0.37
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGAC
Found at i:41193816 original size:17 final size:18
Alignment explanation
Indices: 41193780--41193826 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
41193770 TTAAGTCTTT
*
41193780 TTAAAATTA-AAAAATCA
1 TTAAAATTATAAAAATAA
41193797 TTAAAATTATAAAAA-AA
1 TTAAAATTATAAAAATAA
41193814 TTATAATATTATA
1 TTA-AA-ATTATA
41193827 TCAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 13 0.50
18 7 0.27
19 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAATTATAAAAATAA
Found at i:41202636 original size:35 final size:35
Alignment explanation
Indices: 41202592--41202660 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
41202582 GTACTATGAG
* *
41202592 AAAAGTTATAGATTTAGTCCATATTCTTTAACTAA
1 AAAAGTTATAGATTTAGTCAATATTCTTCAACTAA
*
41202627 AAAATTTATAGATTTAGTCAATATTCTTCAACTA
1 AAAAGTTATAGATTTAGTCAATATTCTTCAACTA
41202661 GTCCACCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (35 bp):
AAAAGTTATAGATTTAGTCAATATTCTTCAACTAA
Found at i:41203255 original size:58 final size:57
Alignment explanation
Indices: 41203154--41203320 Score: 187
Period size: 59 Copynumber: 2.9 Consensus size: 57
41203144 TTAATATAAT
* * *
41203154 ATTTGGTACCTGTATTTGATATTTTT-TTAATTTGATACCTAAACTTTTTT-GACCCA
1 ATTTGGTACCTGAACTTGATATTTTTCTTAATTTGGTACCTAAACTTTTTTGGA-CCA
* *
41203210 ATTTGTTACTTGAACTTGATATTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCA
1 ATTTGGTACCTGAACTTGATA-TTTTTCTTAATTTGGTACCTAAAC-TTTTTTGGACCA
* * * *
41203269 ATTTGGTACCTGCACTTGGCA-ATTTTTCCTAATTTGGTACTTAAGCTTTTTT
1 ATTTGGTACCTGAACTT-G-ATATTTTTCTTAATTTGGTACCTAAACTTTTTT
41203321 TTAGATTCAA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
56 17 0.18
57 5 0.05
58 23 0.24
59 44 0.47
60 4 0.04
61 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.50
Consensus pattern (57 bp):
ATTTGGTACCTGAACTTGATATTTTTCTTAATTTGGTACCTAAACTTTTTTGGACCA
Found at i:41203578 original size:29 final size:30
Alignment explanation
Indices: 41203545--41203622 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
41203535 GAACCCCAAA
* *
41203545 AAGTTTAAGTACCAACTT-AAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAGTGAC
*
41203574 AAGTTTAGGTACCAAATTAAAAAAAGTGAC
1 AAGTTTAAGTACCAAATTAAAAAAAGTGAC
* *
41203604 AAGTTTGAGTATCAAATTA
1 AAGTTTAAGTACCAAATTA
41203623 GATCAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAAAAAAAGTGAC
Found at i:41203621 original size:87 final size:88
Alignment explanation
Indices: 41203490--41203677 Score: 192
Period size: 87 Copynumber: 2.1 Consensus size: 88
41203480 TAAAAAATAA
*
41203490 TTAGGTACCAAATTAAGAAAAAGAAGCAAGTTCATGTACTAAATT-GAACCCCAAAAAGT-TTAA
1 TTAGGTACCAAATTAAGAAAAAGAAGCAAGTTCATGTACTAAATTAG-A--CCAAAAAATATTAA
* * *
41203553 GTACCAACTT-AAAAAAGTGTCAAGT
63 GTACCAAATTAAAAAAAATATCAAGT
* * *
41203578 TTAGGTACCAAATTAA-AAAAAG-TGACAAGTTTGA-GTA-TCAAATTAGATCAAAAAATATTAA
1 TTAGGTACCAAATTAAGAAAAAGAAG-CAAG-TTCATGTACT-AAATTAGACCAAAAAATATTAA
41203639 GTACCAAATTAAAAAAAATATCAAGT
63 GTACCAAATTAAAAAAAATATCAAGT
* *
41203665 CTAGATACCAAAT
1 TTAGGTACCAAAT
41203678 ATTATATTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
85 7 0.08
86 15 0.18
87 43 0.51
88 20 0.24
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (88 bp):
TTAGGTACCAAATTAAGAAAAAGAAGCAAGTTCATGTACTAAATTAGACCAAAAAATATTAAGTA
CCAAATTAAAAAAAATATCAAGT
Found at i:41205132 original size:18 final size:18
Alignment explanation
Indices: 41205109--41205148 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41205099 ATTATATAAT
41205109 ATTTAAATATATAATTTA
1 ATTTAAATATATAATTTA
* *
41205127 ATTTAAATGTATATTTTA
1 ATTTAAATATATAATTTA
41205145 ATTT
1 ATTT
41205149 TAACTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTTAAATATATAATTTA
Found at i:41206114 original size:60 final size:58
Alignment explanation
Indices: 41205974--41206141 Score: 205
Period size: 60 Copynumber: 2.9 Consensus size: 58
41205964 ATATAATATA
** * *
41205974 TTGGTACCTGAACTTGATATTTTTTTTAATTCGGTACCTAAA--TTTTTTGACATAAT
1 TTGGTACCTGAACTTGGCAATTTTTTTAATTTGGTACCTAAACTTTTTTTGACATAAT
* * * *
41206030 TTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCTAAT
1 TTGGTACCTGAACTTGGCAATTTTT-TTAATTTGGTACCTAAACTTTTTTT-GACATAAT
*
41206090 TTGGTACCTGTACTTGGCAATTTTTTCTAATTTGGTACCTAAAACTTTTTTT
1 TTGGTACCTGAACTTGGCAATTTTTT-TAATTTGGTACCT-AAACTTTTTTT
41206142 AGATTCAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
56 22 0.23
57 16 0.16
59 7 0.07
60 41 0.42
61 11 0.11
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (58 bp):
TTGGTACCTGAACTTGGCAATTTTTTTAATTTGGTACCTAAACTTTTTTTGACATAAT
Found at i:41206398 original size:30 final size:31
Alignment explanation
Indices: 41206362--41206440 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
41206352 TGGACCCAAA
* *
41206362 AAGTTTAAGTATCAACTTA-AAAAAAGTGTC
1 AAGTTTAAGTATCAAATTAGAAAAAAATGTC
* *
41206392 AAGTTTAGGAATCAAATTAGGAAAAAAATGTC
1 AAGTTTAAGTATCAAATTA-GAAAAAAATGTC
* *
41206424 AAGTTCAAGTACCAAAT
1 AAGTTTAAGTATCAAAT
41206441 ATTATATTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 16 0.41
32 23 0.59
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAGAAAAAAATGTC
Found at i:41206440 original size:32 final size:31
Alignment explanation
Indices: 41206312--41206440 Score: 81
Period size: 32 Copynumber: 4.3 Consensus size: 31
41206302 AAAAAATTAG
* *
41206312 GTACCAAATTAGGAAAAATAGTCAAGTTCAT
1 GTACCAAATTAGGAAAAAAAGTCAAGTTCAA
*** *
41206343 GTACCAAATT-GGACCCAAA---AAGTTTAA
1 GTACCAAATTAGGAAAAAAAGTCAAGTTCAA
* * * * *
41206370 GTATCAACTTA--AAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAGGAAAAAA-AGTCAAGTTCAA
* *
41206400 GAATCAAATTAGGAAAAAAATGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAAA-GTCAAGTTCAA
41206432 GTACCAAAT
1 GTACCAAAT
41206441 ATTATATTAA
Statistics
Matches: 70, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
26 3 0.04
27 14 0.20
30 21 0.30
31 10 0.14
32 22 0.31
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.25
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAAAGTCAAGTTCAA
Found at i:41206656 original size:17 final size:17
Alignment explanation
Indices: 41206634--41206668 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41206624 CCTTTAAATG
41206634 TTTGTTTTAGTGTTATA
1 TTTGTTTTAGTGTTATA
41206651 TTTGTTTTAGTGTTATA
1 TTTGTTTTAGTGTTATA
41206668 T
1 T
41206669 ATAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (17 bp):
TTTGTTTTAGTGTTATA
Found at i:41211226 original size:26 final size:25
Alignment explanation
Indices: 41211197--41211249 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
41211187 TTTTAATTTT
41211197 TTTATAAAA-TTTATATTATTTTAATA
1 TTTA-AAAATTTTATA-TATTTTAATA
* *
41211223 TTTAATAATTTTATATATTTTTATA
1 TTTAAAAATTTTATATATTTTAATA
41211248 TT
1 TT
41211250 GTTGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAAAATTTTATATATTTTAATA
Found at i:41211247 original size:8 final size:9
Alignment explanation
Indices: 41211196--41211249 Score: 51
Period size: 8 Copynumber: 6.2 Consensus size: 9
41211186 TTTTTAATTT
*
41211196 TTTTATAAA
1 TTTTATATA
*
41211205 ATTTATATTA
1 TTTTATA-TA
41211215 TTTTA-ATA
1 TTTTATATA
*
41211223 TTTAATA-A
1 TTTTATATA
41211231 TTTTATATA
1 TTTTATATA
41211240 TTTT-TATA
1 TTTTATATA
41211248 TT
1 TT
41211250 GTTGAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 19 0.51
9 13 0.35
10 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTATATA
Found at i:41213440 original size:51 final size:49
Alignment explanation
Indices: 41213335--41213451 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 49
41213325 ATGTGTTTTT
* * * * * *
41213335 TTTTAAATAT-T-ATAAAAATGTAATAATATTAACAATTAAATTTTAAT
1 TTTTAAATATATAATAAAAATCTAAAAATATTAAAAATAAAATTCTAAA
*
41213382 TTTTAAATATATAATAAAAATCTAAAAATTCTTAAAAATAAAATTACTAAA
1 TTTTAAATATATAATAAAAATCTAAAAA-TATTAAAAATAAAATT-CTAAA
*
41213433 TTTTAAATTTATAA-AAAAA
1 TTTTAAATATATAATAAAAA
41213452 GTAAAAAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
47 10 0.17
48 1 0.02
49 13 0.22
50 18 0.31
51 16 0.28
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (49 bp):
TTTTAAATATATAATAAAAATCTAAAAATATTAAAAATAAAATTCTAAA
Found at i:41213450 original size:49 final size:47
Alignment explanation
Indices: 41213335--41213450 Score: 108
Period size: 49 Copynumber: 2.4 Consensus size: 47
41213325 ATGTGTTTTT
* * * * * *
41213335 TTTTAAATATTAT-AAAAATGTAATAATATTAACAATTAAATTTTAAT
1 TTTTAAAT-TTATAAAAAATCTAAAAATATTAAAAATAAAATTCTAAA
* *
41213382 TTTTAAATATATAATAAAAATCTAAAAATTCTTAAAAATAAAATTACTAAA
1 TTTTAAATTTAT-A-AAAAATCTAAAAA-TATTAAAAATAAAATT-CTAAA
41213433 TTTTAAATTTATAAAAAA
1 TTTTAAATTTATAAAAAA
41213451 AGTAAAAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
46 3 0.05
47 8 0.15
49 16 0.29
50 14 0.25
51 14 0.25
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (47 bp):
TTTTAAATTTATAAAAAATCTAAAAATATTAAAAATAAAATTCTAAA
Found at i:41215254 original size:22 final size:22
Alignment explanation
Indices: 41215204--41215255 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
41215194 AAAATTTAAA
41215204 AATATTAATTTTAATAAATAAT
1 AATATTAATTTTAATAAATAAT
*
41215226 AA-A-TAATTTT-TTAAATAAT
1 AATATTAATTTTAATAAATAAT
41215245 AATATCTAATT
1 AATAT-TAATT
41215256 CTATTTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.38
20 8 0.31
21 1 0.04
22 7 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATTAATTTTAATAAATAAT
Found at i:41216635 original size:3 final size:3
Alignment explanation
Indices: 41216627--41216673 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
41216617 AATCCAAAAC
41216627 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41216674 CCTTTAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41216994 original size:16 final size:17
Alignment explanation
Indices: 41216959--41216993 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41216949 TGCATAATAT
41216959 AATAAACATATTTAAAA
1 AATAAACATATTTAAAA
41216976 AATAAACAT-TTATAAAA
1 AATAAACATATT-TAAAA
41216993 A
1 A
41216994 TTTAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAACATATTTAAAA
Found at i:41217471 original size:17 final size:17
Alignment explanation
Indices: 41217433--41217473 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
41217423 TTAAATTGAA
**
41217433 ATTAAAAAAATTACAAT
1 ATTAAAAAAACAACAAT
41217450 A-TAAAAAAACAACAAT
1 ATTAAAAAAACAACAAT
41217466 ATTAAAAA
1 ATTAAAAA
41217474 TAAAATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (17 bp):
ATTAAAAAAACAACAAT
Found at i:41218016 original size:69 final size:69
Alignment explanation
Indices: 41217905--41218035 Score: 244
Period size: 69 Copynumber: 1.9 Consensus size: 69
41217895 AATTTTTTTA
*
41217905 AAAATATACACGTCATCTTTTAAAGGGTGGGTGGGTTCAACCTCTACTTGCACTTCCCAGTTCGT
1 AAAATATACACGTCATCTTTTAAAGGGAGGGTGGGTTCAACCTCTACTTGCACTTCCCAGTTCGT
41217970 TTGG
66 TTGG
*
41217974 AAAATGTACACGTCATCTTTTAAAGGGAGGGTGGGTTCAACCTCTACTTGCACTTCCCAGTT
1 AAAATATACACGTCATCTTTTAAAGGGAGGGTGGGTTCAACCTCTACTTGCACTTCCCAGTT
41218036 AAGAATCTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (69 bp):
AAAATATACACGTCATCTTTTAAAGGGAGGGTGGGTTCAACCTCTACTTGCACTTCCCAGTTCGT
TTGG
Found at i:41222493 original size:24 final size:23
Alignment explanation
Indices: 41222466--41222528 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
41222456 TGATTAATAT
41222466 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
**
41222490 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
41222513 TGTTTGTAAACATGTT
1 TGTTCGTGAACATGTT
41222529 TGATTAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:41222535 original size:23 final size:23
Alignment explanation
Indices: 41222466--41222535 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
41222456 TGATTAATAT
* *
41222466 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTAAACATGTTCGATTA-A
* *
41222490 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTAAACATGTTCGATTAA
* *
41222513 TGTTTGTAAACATGTTTGATTAA
1 TGTTCGTAAACATGTTCGATTAA
41222536 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTTCGTAAACATGTTCGATTAA
Found at i:41224938 original size:30 final size:29
Alignment explanation
Indices: 41224908--41224985 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
41224898 TCCTCGAACT
* *
41224908 TTCTAAAAATCACA-TTTGTACCCCTAAAC
1 TTCTAAAAATTACATTTTG-ACCCCCAAAC
41224937 TTCATAAAAATTACATTTTGACCCCCAAAC
1 TTC-TAAAAATTACATTTTGACCCCCAAAC
41224967 TTCTCAAAAATTACATTTT
1 TTCT-AAAAATTACATTTT
41224986 ATTACAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 4 0.09
30 36 0.82
31 4 0.09
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCTAAAAATTACATTTTGACCCCCAAAC
Found at i:41225089 original size:60 final size:59
Alignment explanation
Indices: 41224991--41225220 Score: 211
Period size: 60 Copynumber: 3.8 Consensus size: 59
41224981 ATTTTATTAC
* * * * *
41224991 AATTACATTTTGACTCTCGAACTTCTTAAAAATTACATTTTGACCTTCGAACTTCTT-AAA
1 AATTACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTGACC-CCAAACTT-TTCAAA
* *
41225051 AATTACATTTTGACCCTCAAACTTCTCAAAAATCACATTTTGACCCCAAACTTTTCCAA
1 AATTACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTGACCCCAAACTTTTCAAA
** * * * *
41225110 AATTGTATTTTTGACCATCAAACTTTCTC-AAAATTACATTTTGACTCCAAACTCATCCAAA
1 AATTACA-TTTTGACCCTCAAAC-TTCTCAAAAATTACATTTTGACCCCAAACT-TTTCAAA
*
41225171 AATTACCATTTT-A-CCTCTAAACATCT-AAAAATTACCATTTT-ACCCTCAAA
1 AATTA-CATTTTGACCCTC-AAACTTCTCAAAAATTA-CATTTTGACCC-CAAA
41225221 TGTCCAAAAG
Statistics
Matches: 141, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
58 2 0.01
59 29 0.21
60 92 0.65
61 17 0.12
62 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (59 bp):
AATTACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTGACCCCAAACTTTTCAAA
Found at i:41225173 original size:30 final size:29
Alignment explanation
Indices: 41224991--41225211 Score: 173
Period size: 30 Copynumber: 7.4 Consensus size: 29
41224981 ATTTTATTAC
* *
41224991 AATTACATTTTGACTCTCGAACTTCTTAAA
1 AATTACATTTTGACTC-CAAACTTCTCAAA
* * *
41225021 AATTACATTTTGACCTTCGAACTTCTTAAA
1 AATTACATTTTGA-CTCCAAACTTCTCAAA
*
41225051 AATTACATTTTGACCCTCAAACTTCTCAAA
1 AATTACATTTTGACTC-CAAACTTCTCAAA
* * * *
41225081 AATCACATTTTGACCCCAAACTTTTCCAA
1 AATTACATTTTGACTCCAAACTTCTCAAA
**
41225110 AATTGTATTTTTGAC-CATCAAACTTTCTC-AA
1 AATTACA-TTTTGACTC--CAAAC-TTCTCAAA
41225141 AATTACATTTTGACTCCAAAC-TCATCCAAA
1 AATTACATTTTGACTCCAAACTTC-T-CAAA
* *
41225171 AATTACCATTTT-ACCTCTAAACATCT-AAA
1 AATTA-CATTTTGA-CTCCAAACTTCTCAAA
41225200 AATTACCATTTT
1 AATTA-CATTTT
41225212 ACCCTCAAAT
Statistics
Matches: 163, Mismatches: 15, Indels: 27
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.01
28 1 0.01
29 38 0.23
30 87 0.53
31 29 0.18
32 6 0.04
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
AATTACATTTTGACTCCAAACTTCTCAAA
Found at i:41234400 original size:49 final size:49
Alignment explanation
Indices: 41234234--41234408 Score: 165
Period size: 49 Copynumber: 3.6 Consensus size: 49
41234224 CCGAGGAAAT
* * * * * * *
41234234 ATGAAGATATGAAGGAAAAAGTTGAGGCCGCAATGATGAACCCGGTTCC
1 ATGAAGATGTGAAGGGAAAAGTTGAGGCCGCAACGGTAAACCCGATACC
* * * *
41234283 TTAAAAGATGTGATA-GG-AAGGATTGAGGCCGCAACGGTAAATCCGATACC
1 AT-GAAGATGTGA-AGGGAAAAG-TTGAGGCCGCAACGGTAAACCCGATACC
* **
41234333 ATGAAGATGCGATTGGAAAAGTTGAGGCCGCAACGGTAAACCCGATACC
1 ATGAAGATGTGAAGGGAAAAGTTGAGGCCGCAACGGTAAACCCGATACC
* *
41234382 ATGAAGATTTGAAGGGAAAGGTTGAGG
1 ATGAAGATGTGAAGGGAAAAGTTGAGG
41234409 TTGCTATGGC
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
49 63 0.64
50 35 0.35
51 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (49 bp):
ATGAAGATGTGAAGGGAAAAGTTGAGGCCGCAACGGTAAACCCGATACC
Found at i:41234911 original size:78 final size:78
Alignment explanation
Indices: 41234762--41236131 Score: 545
Period size: 78 Copynumber: 17.6 Consensus size: 78
41234752 AAAGATTTCG
* * * * * *
41234762 ATCTCTTACCCCGATCATAGGGCAGATCACAGTCATCCGATCTTTTACTCC-GAGCTTAAGG-CA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTAC-CCTGAGCTT-GGGACA
* * *
41234825 TATTACCATCAACCA
64 GATCACCATCAGCCA
* * * ** * * *
41234840 ATCCCTTACCCTGAGCATAGGGCAGATTGCAGGTATTCGATCTTTTACCCTGACCTTGGGACAGG
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAGA
*
41234905 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * *
41234918 ATCTCTTA-CCTCGAGCCTAGGACAGATTACAACCATCCGAT-TTTTACCCCGAGCTTGGGGCAG
1 ATCTCTTACCCT-GAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAG
*
41234981 ATCACCATTAGCCA
65 ATCACCATCAGCCA
* * * ** * * * * *
41234995 ATCTCTTACCCCGAG-CTTGAGGCAGATTGCAGTTATCCAATATTTTA-CCTCAAGCCTGAGACA
1 ATCTCTTACCCTGAGCCTAG-GGCAGATTACAGCCATCCGATCTTTTACCCT-GAGCTTGGGACA
*
41235058 GATCACCATTAGCCA
64 GATCACCATCAGCCA
* * * * * * * *
41235073 ATATCTTACCCCGAGCCT-GTGGAAAATTACAACCATTCTATCTTTTACCCTGAGCTTGGTACAG
1 ATCTCTTACCCTGAGCCTAG-GGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAG
41235137 ATC-CACATCAGCCA
65 ATCAC-CATCAGCCA
* * *
41235151 ATCTCTTACCCCGAGCCTA-GGTAGATTACAGCCATCCGATCTTTTATCCC-GAGCTTGGGGCAG
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTA-CCCTGAGCTTGGGACAG
*
41235214 ATCACCATTAG-CA
65 ATCACCATCAGCCA
* * * * ** * *
41235227 ATCTCTTACCTTGAGCTTGGGGCAGATTATAGTTATCCAATTTTTTTACCCTGAGCTTGGGGA-A
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGA-TCTTTTACCCTGAGCTT-GGGACA
41235291 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * * * *
41235306 ATCTCTTA-CCTCCAGCCTAGGCCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCT-AGACAG
1 ATCTCTTACCCT-GAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAG
* *
41235369 ATTAACATCAGCCA
65 ATCACCATCAGCCA
* ** * * * ** * * * * * *
41235383 ATCTTTTACCCCAAGCCTGGGGTAGATTGCAGGTATCTGATC-TTT-GCCTCAAGCCT-AGAGTA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCT-GAGCTTGGGA-CA
*
41235445 GATCACCAT-TGACCA
64 GATCACCATCAG-CCA
* * ** * * * *
41235460 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCTATTCGATCTTTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAGA
*
41235525 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * * * * *
41235538 ATCTTTTA-CCTCGAGCTTGGGGCAGA-T-CA-CCATCAGTCAATCTCTTACCCCGAGCATAGGG
1 ATCTCTTACCCT-GAGCCTAGGGCAGATTACAGCCATC---CGATCTTTTACCCTGAGC-TTGGG
* *** * *
41235599 -TAGAT-TGTAGTCATCTA
61 ACAGATCACCA-TCAGCCA
* * * * * ** * *
41235616 ATCTTTTACCC-GAGCTTGGGGCAGATTACCA-TCAGCTAATCTCTTA-CCTAGAGCCTAGGG-C
1 ATCTCTTACCCTGAGCCTAGGGCAGATTA-CAGCCATCCGATCTTTTACCCT-GAG-CTTGGGAC
*
41235677 AGATTGCAGCCATC--CGA
63 AGA-T-CA-CCATCAGCCA
* * * * * * * * ** * **
41235694 A-CTTTTATCCC-GAGCCTCGAGCAGATCACCA-TCAACCAATCTCTTACCCAAAGCCTGGGGTA
1 ATCTCTTA-CCCTGAGCCTAGGGCAGATTA-CAGCCATCCGATCTTTTACCCTGAGCTTGGGACA
* *
41235756 GATTGTAGCCAT---CCG
64 GA-T-CA-CCATCAGCCA
* * * * ** ** * * **
41235771 ATCTCTTGCCTTGAGCTTGGGGCAGATTGTAATCATTCGATCTTTTACCCCGAGCTTGGGGTAGA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAGA
*
41235836 TCACTATCAGCCA
66 TCACCATCAGCCA
** * * * * * *
41235849 ATCTCTTACCCCAAGCCTTGGGCAGATTGA-AACCATTCGATCTTGTACCCTAAGCTTGGG-CAA
1 ATCTCTTACCCTGAGCCTAGGGCAGATT-ACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAG
* *
41235912 ATCACCATAAGTCA
65 ATCACCATCAGCCA
* ** * * ** * * * *
41235926 ATCTCTTACCCCGAGTTTAAGGCAAATTGTAGTCATTCGATCTTTTACCCTGAGCCTAGGGA-AA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAG-CTTGGGACAG
* *
41235990 ATCACAATCAACCA
65 ATCACCATCAGCCA
* * * ** * * * * *
41236004 ATCTCTTACCCCGAGCTTGGGGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGG-CAA
1 ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAG-CTTGGGACAG
*
41236068 ATCACCATCAACCA
65 ATCACCATCAGCCA
* * * * *
41236082 ATCTCTTACCCCGAACCT-GAGACAGATTACAACCATCTGATCTTTTACCC
1 ATCTCTTACCCTGAGCCTAG-GGCAGATTACAGCCATCCGATCTTTTACCC
41236132 CGATCATGGG
Statistics
Matches: 1001, Mismatches: 232, Indels: 118
0.74 0.17 0.09
Matches are distributed among these distances:
75 8 0.01
76 37 0.04
77 324 0.32
78 575 0.57
79 49 0.05
80 7 0.01
81 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCTGAGCCTAGGGCAGATTACAGCCATCCGATCTTTTACCCTGAGCTTGGGACAGA
TCACCATCAGCCA
Found at i:41235252 original size:38 final size:38
Alignment explanation
Indices: 41235201--41235316 Score: 117
Period size: 40 Copynumber: 3.0 Consensus size: 38
41235191 CTTTTATCCC
41235201 GAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCTT
1 GAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCTT
* * * * * *
41235239 GAGCTTGGGGCAGATTA-TAGTTATCCAATTTTTTTACCCT
1 GAGCTTGGGGCAGATCACCA-TTA-GCAA-TCTCTTACCTT
* *
41235279 GAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCT
1 GAGCTTGGGGCAGATCACCATTAG-CAATCTCTTACCT
41235317 CCAGCCTAGG
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
37 1 0.02
38 19 0.32
39 10 0.17
40 28 0.47
41 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (38 bp):
GAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCTT
Found at i:41235392 original size:38 final size:37
Alignment explanation
Indices: 41235297--41235400 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 37
41235287 GGAAGATCAC
* *
41235297 CATCAGCCAATCTCTTACCTCCAGCCTAGGCCAGATTG
1 CATCAGCCAATCTCTTACC-CCAGCCTAGGACAGATTA
* * *
41235335 CAGCCATCCGATCTCTTACCCCGAGCCTA-GACAGATTAA
1 CA-TCAGCCAATCTCTTACCCC-AGCCTAGGACAGATT-A
*
41235374 CATCAGCCAATCTTTTACCCCAAGCCT
1 CATCAGCCAATCTCTTACCCC-AGCCT
41235401 GGGGTAGATT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
38 31 0.58
39 22 0.42
ACGTcount: A:0.26, C:0.38, G:0.13, T:0.23
Consensus pattern (37 bp):
CATCAGCCAATCTCTTACCCCAGCCTAGGACAGATTA
Found at i:41235427 original size:233 final size:233
Alignment explanation
Indices: 41234900--41235553 Score: 669
Period size: 233 Copynumber: 2.8 Consensus size: 233
41234890 TGACCTTGGG
* * * * * * *
41234900 ACAGGTCACCATCAGCTAATCTCTTACCTCGAGCCTAGGACAGATTACAACCATCCGAT-TTTTA
1 ACAGATCAACATCAGCCAATCTCTTACCCCAAGCCTAGG-TAGATTACAGCCATCCGATCTTTTA
* *
41234964 CCCCGAGCTTGGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTTGAGGCAGATTGCAGTT
65 CCCCGAGCTTGGGGCAGATCACCATTAG-CAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTT
* * * * *
41235029 ATCCAATATTTTA-CCTCAAGCCT-GAGACAGATCACCATTAGCCAATATCTTACC-CCGAGCCT
129 ATCCAATATTTTACCCT-GAGCTTGGGGA-AGATCACCATCAGCCAATCTCTTACCTCCGAGCCT
* * * * * * *
41235091 GTGGAAAATTACAACCATTCTATCTTTTACCCTGAGCTTGGT
192 GTGCAAAATTACAACCATCCGATCTCTTACCCCGAGCCTAGT
* * *
41235133 ACAGATCCACATCAGCCAATCTCTTACCCCGAGCCTAGGTAGATTACAGCCATCCGATCTTTTAT
1 ACAGATCAACATCAGCCAATCTCTTACCCCAAGCCTAGGTAGATTACAGCCATCCGATCTTTTAC
** *
41235198 CCCGAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCTTGAGCTTGGGGCAGATTATAGTTAT
66 CCCGAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTTAT
*
41235263 CCAATTTTTTTACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCC-AGCCTAG-
131 CCAA-TATTTTACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCCGAGCCT-GT
* * * *
41235326 GCCAGATTGCAGCCATCCGATCTCTTACCCCGAGCCTAG-
194 GCAAAATTACAACCATCCGATCTCTTACCCCGAGCCTAGT
* * * * ** * *
41235365 ACAGATTAACATCAGCCAATCTTTTACCCCAAGCCTGGGGTAGATTGCAGGTATCTGATC-TTTG
1 ACAGATCAACATCAGCCAATCTCTTACCCCAAGCCT-AGGTAGATTACAGCCATCCGATCTTTTA
* * * * * * * * *
41235429 CCTCAAGCCTAGAGTAGATCACCATTGACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCT
65 CCCCGAGCTTGGGGCAGATCACCATT-AGCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTT
* * * * * * *
41235494 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTTTTACCT-CGAGC
129 ATCCAATATTTTACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCCGAGC
41235554 TTGGGGCAGA
Statistics
Matches: 352, Mismatches: 60, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
231 1 0.00
232 155 0.44
233 187 0.53
234 9 0.03
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (233 bp):
ACAGATCAACATCAGCCAATCTCTTACCCCAAGCCTAGGTAGATTACAGCCATCCGATCTTTTAC
CCCGAGCTTGGGGCAGATCACCATTAGCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTTAT
CCAATATTTTACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCCGAGCCTGTGC
AAAATTACAACCATCCGATCTCTTACCCCGAGCCTAGT
Found at i:41235708 original size:116 final size:116
Alignment explanation
Indices: 41235208--41235680 Score: 356
Period size: 116 Copynumber: 4.1 Consensus size: 116
41235198 CCCGAGCTTG
* ** * * * * * * *
41235208 GGGCAGATCACCATTAGCAATCTCTTACCTTGAGCTTGGGGCAGATTATAGTTATCCAATTTTTT
1 GGGCAGATCACCATCAGCAATCTCTTACCCCGAGCATAGGGTAGATTGTAGTCATCTAA-TCTTT
* * * **
41235273 TACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCCAGCCTA
65 TACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
* * * ** * * * *
41235325 GGCCAGATTGCAGCCATC--CGATCTCTTACCCCGAGCCTA-GACAGATT-AACATCAGCCAATC
1 GGGCAGA-T-CA-CCATCAGCAATCTCTTACCCCGAGCATAGGGTAGATTGTA-GTCATCTAATC
* * * ** * * *
41235386 TTTTACCCCAAGCCTGGGGTAGATTGCA-GGT-ATCTGATCT-TTGCCTCA-AGCCTA
62 TTTTACCCCGAGCTTGGGGCAGA-T-CACCATCAGCTAATCTCTTACCT-AGAGCCTA
* * * * * * * *
41235440 GAGTAGATCACCATTGACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAG-CTAT-TCGATCT
1 GGGCAGATCACCA-TCAGCAATCTCTTACCCCGAGCATAGGGTAGATTGTAGTC-ATCT-AATCT
* * * *
41235503 TTTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTTTTACCTCGAGCTTG
63 TTTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
41235557 GGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCATAGGGTAGATTGTAGTCATCTAATCTTT
1 GGGCAGATCACCATCAG-CAATCTCTTACCCCGAGCATAGGGTAGATTGTAGTCATCTAATCTTT
*
41235622 TA-CCCGAGCTTGGGGCAGATTACCATCAGCTAATCTCTTACCTAGAGCCTA
65 TACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
41235673 GGGCAGAT
1 GGGCAGAT
41235681 TGCAGCCATC
Statistics
Matches: 275, Mismatches: 60, Indels: 43
0.73 0.16 0.11
Matches are distributed among these distances:
112 3 0.01
113 3 0.01
114 3 0.01
115 37 0.13
116 119 0.43
117 83 0.30
118 21 0.08
119 2 0.01
120 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (116 bp):
GGGCAGATCACCATCAGCAATCTCTTACCCCGAGCATAGGGTAGATTGTAGTCATCTAATCTTTT
ACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
Found at i:41235735 original size:116 final size:114
Alignment explanation
Indices: 41235208--41235742 Score: 338
Period size: 116 Copynumber: 4.6 Consensus size: 114
41235198 CCCGAGCTTG
** ** * * * * * *
41235208 GGGCAGATCACCATTAGCAATCTCTTACCTTGAGCTTGGGGCAGATTA-TAGTTATCCAATTTTT
1 GGGCAGATCACCATCCG-AATCTCTTACCCCGAGCCTAGAGCAGATTAGCA-TCATCCAA-TCTT
* * **
41235272 TTACCCTGAGCTTGGGGAAGATCACCATCAGCCAATCTCTTACCTCCAGCCTA
63 TTACCC-GAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
* * *
41235325 GGCCAGATTGCAGCCATCCG-ATCTCTTACCCCGAGCCTAGA-CAGATTAACATCAGCCAATCTT
1 GGGCAGA-T-CA-CCATCCGAATCTCTTACCCCGAGCCTAGAGCAGATTAGCATCATCCAATCTT
* * * ** * * *
41235388 TTACCCCAAGCCTGGGGTAGATTGCA-GGT-ATCTGATCT-TTGCCTCA-AGCCTA
63 TTA-CCCGAGCTTGGGGCAGA-T-CACCATCAGCTAATCTCTTACCT-AGAGCCTA
* * * * * *
41235440 GAGTAGATCACCATTGACC-AATCTCTTACCCCGAGCCTGGGGCAGATTGTAGC-T-ATTCGATC
1 GGGCAGATCACCA-T--CCGAATCTCTTACCCCGAGCCTAGAGCAGA-T-TAGCATCATCCAATC
* * * *
41235502 TTTTACCCCGAGCTTGGGGCAGATCACCATCAGCTAATCTTTTACCTCGAGCTTG
61 TTTTA-CCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
* * * * * *
41235557 GGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCATAGGGTAGATT-GTAGTCATCTAATCTT
1 GGGCAGATCACCATCCG--AATCTCTTACCCCGAGCCTAGAGCAGATTAGCA-TCATCCAATCTT
*
41235621 TTACCCGAGCTTGGGGCAGATTACCATCAGCTAATCTCTTACCTAGAGCCTA
63 TTACCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
* * * * * * *
41235673 GGGCAGATTGCAGCCATCCGAA-CTTTTATCCCGAGCCTCGAGCAGATCACCATCAACCAATCTC
1 GGGCAGA-T-CA-CCATCCGAATCTCTTACCCCGAGCCTAGAGCAGATTAGCATCATCCAATCTT
41235737 TTACCC
63 TTACCC
41235743 AAAGCCTGGG
Statistics
Matches: 319, Mismatches: 70, Indels: 59
0.71 0.16 0.13
Matches are distributed among these distances:
112 3 0.01
113 3 0.01
114 5 0.02
115 39 0.12
116 147 0.46
117 84 0.26
118 25 0.08
119 8 0.03
120 5 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (114 bp):
GGGCAGATCACCATCCGAATCTCTTACCCCGAGCCTAGAGCAGATTAGCATCATCCAATCTTTTA
CCCGAGCTTGGGGCAGATCACCATCAGCTAATCTCTTACCTAGAGCCTA
Found at i:41235858 original size:39 final size:39
Alignment explanation
Indices: 41234879--41236095 Score: 320
Period size: 39 Copynumber: 31.4 Consensus size: 39
41234869 CAGGTATTCG
* * * * * *
41234879 ATCTTTTACCCTGACCTTGGGACAGGTCACCATCAGCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * * * * * *
41234918 ATCTCTTACCTCGAGCCTAGGACAGATTACAACCATCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* *
41234957 AT-TTTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* ** * *
41234995 ATCTCTTACCCCGAGCTTGAGGCAGAT-TGCAGTTATCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCA
* * * * * * * *
41235034 ATATTTTACCTCAAGCCTGAGACAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * * * * * ** *
41235073 ATATCTTACCCCGAGCCTGTGGAAAATTACAACCATTCT
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * **
41235112 ATCTTTTACCCTGAGCTTGGTACAGATC-CACATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAC-CATCAGCCA
* * * * * * *
41235151 ATCTCTTACCCCGAGCCT-AGGTAGATTA-CAGCCATCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCA
* * *
41235189 ATCTTTTATCCCGAGCTTGGGGCAGATCACCATTAG-CA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
** * * * *
41235227 ATCTCTTACCTTGAGCTTGGGGCAGATTA-TAGTTATCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCA
* * * *
41235266 ATTTTTTTACCCTGAGCTTGGGGAAGATCACCATCAGCCA
1 A-TCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * *
41235306 ATCTCTTACCTCC-AGCCTAGGCCAGATTGCAGCCAT---CCG
1 ATCTCTTACC-CCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* * * * *
41235345 ATCTCTTACCCCGAGCCT-AGACAGATTAACATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * ** *
41235383 ATCTTTTACCCCAAGCCTGGGGTAGATTGCAGGTATCTG---
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* * * * * * * *
41235422 ATCT-TTGCCTCAAGCCTAGAGTAGATCACCAT-TGACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG-CCA
* * * ** *
41235460 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGC-T-ATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CACCATCAGCCA
* *
41235499 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
41235538 ATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * *** * *
41235577 ATCTCTTACCCCGAGCATAGGGTAGAT-TGTAGTCATCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCA
* * *
41235616 ATCTTTTA-CCCGAGCTTGGGGCAGATTACCATCAGCTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
** * * *
41235654 ATCTCTTACCTAGAGCCTAGGGCAGATTGCAGCCATC--CGA
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* * * * * *
41235694 A-CTTTTATCCCGAGCCTCGAGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
** * * * *
41235732 ATCTCTTACCCAAAGCCTGGGGTAGATTGTAGCCAT---CCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* ** **** ** *
41235771 ATCTCTTGCCTTGAGCTTGGGGCAGATTGTAATCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
41235810 ATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * ** *
41235849 ATCTCTTACCCCAAGCCTT-GGGCAGATTGA-AACCATTCG
1 ATCTCTTACCCCGAG-CTTGGGGCAGA-TCACCATCAGCCA
** * * *
41235888 ATCT-TGTACCCTAAGCTT-GGGCAAATCACCATAAGTCA
1 ATCTCT-TACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* ** * *** ** *
41235926 ATCTCTTACCCCGAGTTTAAGGCAAAT-TGTAGTCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCA
* * * * * * * *
41235965 ATCTTTTACCCTGAGCCTAGGGAAAATCACAATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
**** * ** *
41236004 ATCTCTTACCCCGAGCTTGGGGCAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * *
41236043 ATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
41236082 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
41236096 ACCTGAGACA
Statistics
Matches: 839, Mismatches: 283, Indels: 112
0.68 0.23 0.09
Matches are distributed among these distances:
34 2 0.00
35 5 0.01
36 10 0.01
37 12 0.01
38 191 0.23
39 545 0.65
40 49 0.06
41 8 0.01
42 17 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
Found at i:41236005 original size:155 final size:156
Alignment explanation
Indices: 41235791--41236095 Score: 427
Period size: 155 Copynumber: 2.0 Consensus size: 156
41235781 TTGAGCTTGG
* * * * * * *
41235791 GGCAGATTGTAATCATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTT
1 GGCAAATTGTAATCATTCGATCTTTTACCCCGAGCCTAGGGAAAATCACAATCAACCAATCTCTT
* *
41235856 ACCCCAAGCCTT-GGGCAGATTGAAACCATTCGATCTTGTACCCTAAG-CTTGGGCAAATCACCA
66 ACCCCAAG-CTTGGGGCAGATTGAAACCATTCGATCTTGTACCCCAAGCCTAGGGCAAATCACCA
*
41235919 T-AAGTCAATCTCTTACCCCGAGTTTAA
130 TCAA-CCAATCTCTTACCCCGAGTTTAA
* *
41235946 GGCAAATTGTAGTCATTCGATCTTTTACCCTGAGCCTAGGGAAAATCACAATCAACCAATCTCTT
1 GGCAAATTGTAATCATTCGATCTTTTACCCCGAGCCTAGGGAAAATCACAATCAACCAATCTCTT
* * * *
41236011 ACCCCGAGCTTGGGGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGGCAAATCACCAT
66 ACCCCAAGCTTGGGGCAGATTGAAACCATTCGATCTTGTACCCCAAGCCTAGGGCAAATCACCAT
41236076 CAACCAATCTCTTACCCCGA
131 CAACCAATCTCTTACCCCGA
41236096 ACCTGAGACA
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
154 3 0.02
155 94 0.72
156 32 0.24
157 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (156 bp):
GGCAAATTGTAATCATTCGATCTTTTACCCCGAGCCTAGGGAAAATCACAATCAACCAATCTCTT
ACCCCAAGCTTGGGGCAGATTGAAACCATTCGATCTTGTACCCCAAGCCTAGGGCAAATCACCAT
CAACCAATCTCTTACCCCGAGTTTAA
Found at i:41236093 original size:272 final size:272
Alignment explanation
Indices: 41235456--41236095 Score: 712
Period size: 272 Copynumber: 2.4 Consensus size: 272
41235446 ATCACCATTG
*
41235456 ACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCTATTCGATCTTTTACCCCGAGCTTGGGG
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTTTTACCCCGAGCTTGGGG
* * * *
41235521 CAGATCACCATCAGCTAATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTAC
66 CAGATCACCATCAACCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTAC
* * * ** * * * * *
41235586 CCCGAGCATAGGGTAGATTGTAGTCATCTAATCTTTTACCCGAGCTTGGGGCAGATTACCATCAG
131 CCCAAGCATAGGGCAGATTGAAACCATCTAATCTTGTACCCAAGCTTGGGGCAAATCACCATAAG
* * * * *
41235651 CTAATCTCTTACCTAGAGCCTAGGGCAGATTGCAGCCATCCGAACTTTTATCCCGAGCCTCGAGC
196 CTAATCTCTTACCCAGAGCCTAAGGCAAATTGCAGCCATCCGAACTTTTATCCCGAGCCTAGAGA
* *
41235716 AGATCACCATCA
261 AAATCACAATCA
** * * * * **
41235728 ACCAATCTCTTACCCAAAGCCTGGGGTAGATTGTAGCCATCCGATCTCTTGCCTTGAGCTTGGGG
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTTTTACCCCGAGCTTGGGG
**** ** * * *
41235793 CAGATTGTAATCATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTTAC
66 CAGATCACCATCAACCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTAC
* * *
41235858 CCCAAGCCTTGGGCAGATTGAAACCAT-TCGATCTTGTACCCTAAGCTT-GGGCAAATCACCATA
131 CCCAAGCATAGGGCAGATTGAAACCATCT-AATCTTGTACCC-AAGCTTGGGGCAAATCACCATA
* ** * * * *
41235921 AG-TCAATCTCTTACCCCGAGTTTAAGGCAAATTGTAGTCATTCGATCTTTTA-CCCTGAGCCTA
194 AGCT-AATCTCTTACCCAGAGCCTAAGGCAAATTGCAGCCATCCGAACTTTTATCCC-GAGCCTA
*
41235984 GGGAAAATCACAATCA
257 GAGAAAATCACAATCA
* * * *
41236000 ACCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGG
1 ACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTTTTACCCCGAGCTTGGGG
* *
41236065 CAAATCACCATCAACCAATCTCTTACCCCGA
66 CAGATCACCATCAACCAATCTTTTACCCCGA
41236096 ACCTGAGACA
Statistics
Matches: 294, Mismatches: 70, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
271 5 0.02
272 284 0.97
273 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (272 bp):
ACCAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATTCGATCTTTTACCCCGAGCTTGGGG
CAGATCACCATCAACCAATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTAC
CCCAAGCATAGGGCAGATTGAAACCATCTAATCTTGTACCCAAGCTTGGGGCAAATCACCATAAG
CTAATCTCTTACCCAGAGCCTAAGGCAAATTGCAGCCATCCGAACTTTTATCCCGAGCCTAGAGA
AAATCACAATCA
Found at i:41236163 original size:156 final size:153
Alignment explanation
Indices: 41235804--41236167 Score: 383
Period size: 155 Copynumber: 2.3 Consensus size: 153
41235794 AGATTGTAAT
* *
41235804 CATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTTACCCCAAGCCTTG
1 CATTCGATCTTTTACCCCGAGCATGGGGTAGATCAC-ATCA-ACAATCTCTTACCCCAAGCCTTG
* * *
41235869 GGCAGATTGAAACCATTCGATCTTGTACCCTAAGCTTGGGCAAATCACCATAAGTCAATCTCTTA
64 GGCAGATTGAAACCATTCGATCTTGTACCCCAAGCTAGGGCAAATCACCATAAGCCAATCTCTTA
*** * ** **
41235934 CCCCGAGTTTAAGGCAAATTGTAGT
129 CCCCGAACCTAAGACAAATTACAAC
* * * * * *
41235959 CATTCGATCTTTTACCCTGAGCCTAGGGAAAATCACAATCAACCAATCTCTTACCCCGAG-CTTG
1 CATTCGATCTTTTACCCCGAGCATGGGGTAGATCAC-ATCAA-CAATCTCTTACCCCAAGCCTT-
* * *
41236023 GGGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAA-CCAATCTC
63 GGGCAGATTGAAACCATTCGATCTTGTACCCCAAG-CTAGGGCAAATCACCAT-AAGCCAATCTC
* *
41236087 TTACCCCGAACCTGAGACAGATTACAAC
126 TTACCCCGAACCTAAGACAAATTACAAC
* *
41236115 CA-TCTGATCTTTTACCCCGATCATGGGGTAGATCACAGTCATATAATCTCTTA
1 CATTC-GATCTTTTACCCCGAGCATGGGGTAGATCACA-TCA-ACAATCTCTTA
41236168 ACCTGATCAT
Statistics
Matches: 171, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
154 3 0.02
155 85 0.50
156 80 0.47
157 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (153 bp):
CATTCGATCTTTTACCCCGAGCATGGGGTAGATCACATCAACAATCTCTTACCCCAAGCCTTGGG
CAGATTGAAACCATTCGATCTTGTACCCCAAGCTAGGGCAAATCACCATAAGCCAATCTCTTACC
CCGAACCTAAGACAAATTACAAC
Found at i:41236181 original size:156 final size:153
Alignment explanation
Indices: 41235804--41236192 Score: 386
Period size: 156 Copynumber: 2.5 Consensus size: 153
41235794 AGATTGTAAT
* * * * *
41235804 CATTCGATCTTTTACCCCGAGCTTGGGGTAGATCACTATCAGCCAATCTCTTACCCCAAGCCTTG
1 CATTCGATCTTTTACCCCGAGCATGGGGTAGATCAC-ATCA-ACAATCTCTTACCCCGAGCATGG
* * *
41235869 GGCAGATTGAAACCATTCGATCTTGTACCCTAAGCTTGGGCAAATCACCATAAGTCAATCTCTTA
64 GGCAGATTGAAACCATTCGATCTTGTACCCCAAGCTAGGGCAAATCACCATAAGCCAATCTCTTA
*** * ** **
41235934 CCCCGAGTTTAAGGCAAATTGTAGT
129 CCCCGAACCTAAGACAAATTACAAC
* * * * * *
41235959 CATTCGATCTTTTACCCTGAGCCTAGGGAAAATCACAATCAACCAATCTCTTACCCCGAGCTTGG
1 CATTCGATCTTTTACCCCGAGCATGGGGTAGATCAC-ATCAA-CAATCTCTTACCCCGAGCATGG
* * *
41236024 GGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAA-CCAATCTCT
64 GGCAGATTGAAACCATTCGATCTTGTACCCCAAG-CTAGGGCAAATCACCAT-AAGCCAATCTCT
* *
41236088 TACCCCGAACCTGAGACAGATTACAAC
127 TACCCCGAACCTAAGACAAATTACAAC
* * * * *
41236115 CA-TCTGATCTTTTACCCCGATCATGGGGTAGATCACAGTCATATAATCTCTTAACCTGATCATG
1 CATTC-GATCTTTTACCCCGAGCATGGGGTAGATCACA-TCA-ACAATCTCTTACCCCGAGCATG
*
41236179 GGGTAGATTGAAAC
63 GGGCAGATTGAAAC
41236193 TATTTAATAT
Statistics
Matches: 189, Mismatches: 39, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
155 87 0.46
156 99 0.52
157 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (153 bp):
CATTCGATCTTTTACCCCGAGCATGGGGTAGATCACATCAACAATCTCTTACCCCGAGCATGGGG
CAGATTGAAACCATTCGATCTTGTACCCCAAGCTAGGGCAAATCACCATAAGCCAATCTCTTACC
CCGAACCTAAGACAAATTACAAC
Found at i:41236206 original size:39 final size:39
Alignment explanation
Indices: 41236159--41236309 Score: 194
Period size: 39 Copynumber: 3.9 Consensus size: 39
41236149 ACAGTCATAT
* * * * **
41236159 AATCTCTTAACCTGATCATGGGGTAGATTGAAACTATTT
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAACAATCC
* * * *
41236198 AATATCTTATCCCGATCATGGGGCAAATTGAAACCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAACAATCC
*
41236237 AATCTCTTACCCTGATCATGGGGCAGATTGAAACAATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAACAATCC
*
41236276 AATCTCTTACCCCAATCATGGGGCAGATTGAAAC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAAC
41236310 CATCATCTGA
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (39 bp):
AATCTCTTACCCCGATCATGGGGCAGATTGAAACAATCC
Found at i:41236212 original size:78 final size:77
Alignment explanation
Indices: 41236126--41236312 Score: 203
Period size: 78 Copynumber: 2.4 Consensus size: 77
41236116 ATCTGATCTT
* ** * *
41236126 TTACCCCGATCATGGGGTAGATCACAGTCATATAATCTCTTAACCTGATCATGGGGTAGATTGAA
1 TTACCCCGATCATGGGGCAGATCA-AACCATACAATCTCTTAACCTGATCATGGGGCAGATTGAA
* **
41236191 ACTATTTAATATC
65 ACAATCCAATATC
* * * * *
41236204 TTATCCCGATCATGGGGCAAATTGAAACCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAA
1 TTACCCCGATCATGGGGCAGA-TCAAACCATACAATCTCTTAACCTGATCATGGGGCAGATTGAA
*
41236269 ACAATCCAATCTC
65 ACAATCCAATATC
* *
41236282 TTACCCCAATCATGGGGCAGATTGAAACCAT
1 TTACCCCGATCATGGGGCAGA-TCAAACCAT
41236313 CATCTGATCT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 89 0.98
79 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (77 bp):
TTACCCCGATCATGGGGCAGATCAAACCATACAATCTCTTAACCTGATCATGGGGCAGATTGAAA
CAATCCAATATC
Found at i:41236313 original size:78 final size:78
Alignment explanation
Indices: 41236159--41236313 Score: 229
Period size: 78 Copynumber: 2.0 Consensus size: 78
41236149 ACAGTCATAT
* * ** * *
41236159 AATCTCTTAACCTGATCATGGGGTAGATTGAAACTATTTAATATCTTATCCCGATCATGGGGCAA
1 AATCTCTTAACCTGATCATGGGGCAGATTGAAACAATCCAATATCTTACCCCAATCATGGGGCAA
41236224 ATTGAAACCATCC
66 ATTGAAACCATCC
* * *
41236237 AATCTCTTACCCTGATCATGGGGCAGATTGAAACAATCCAATCTCTTACCCCAATCATGGGGCAG
1 AATCTCTTAACCTGATCATGGGGCAGATTGAAACAATCCAATATCTTACCCCAATCATGGGGCAA
41236302 ATTGAAACCATC
66 ATTGAAACCATC
41236314 ATCTGATCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (78 bp):
AATCTCTTAACCTGATCATGGGGCAGATTGAAACAATCCAATATCTTACCCCAATCATGGGGCAA
ATTGAAACCATCC
Found at i:41237539 original size:16 final size:15
Alignment explanation
Indices: 41237505--41237538 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41237495 TCGATCTATG
41237505 TTTTAAAAGAAAAAA
1 TTTTAAAAGAAAAAA
41237520 TTTTAAAA-AAAGAAA
1 TTTTAAAAGAAA-AAA
41237535 TTTT
1 TTTT
41237539 TTATACCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TTTTAAAAGAAAAAA
Found at i:41238255 original size:60 final size:59
Alignment explanation
Indices: 41238149--41238269 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 59
41238139 TTCTCGAACT
* * *
41238149 TTCTAAAAATCACATTTTTACCCTTAAACTTTGTAAAATGTACATTTTGACACCC-AAAC
1 TTCTAAAAATCACATTTTAACCCCTAAACTTTGTAAAATGTACATTTTAAC-CCCTAAAC
* *
41238208 TTCTCAAAAATTACATTTTAACCCCTAAACTTT-TCCAAAAT-TGCATTTTAACCCCTAAAC
1 TTCT-AAAAATCACATTTTAACCCCTAAACTTTGT--AAAATGTACATTTTAACCCCTAAAC
41238268 TT
1 TT
41238270 TCCCTAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
59 8 0.15
60 40 0.75
61 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
TTCTAAAAATCACATTTTAACCCCTAAACTTTGTAAAATGTACATTTTAACCCCTAAAC
Found at i:41238285 original size:29 final size:30
Alignment explanation
Indices: 41238214--41238297 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
41238204 AAACTTCTCA
* *
41238214 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTGCATTTTAACCCCTAAACTTTCCC
41238244 AAAATTGCATTTTAACCCCTAAACTTTCCC
1 AAAATTGCATTTTAACCCCTAAACTTTCCC
* * *
41238274 TAAATTGCTTTTTGACCCC-AAACT
1 AAAATTGCATTTTAACCCCTAAACT
41238298 CATCCAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 5 0.10
30 44 0.90
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTGCATTTTAACCCCTAAACTTTCCC
Found at i:41238309 original size:30 final size:30
Alignment explanation
Indices: 41238145--41238309 Score: 115
Period size: 30 Copynumber: 5.5 Consensus size: 30
41238135 GCTATTCTCG
* ** * *
41238145 AACTTTCTAAAAATCACATTTTTACCCTTA
1 AACTTTCCAAAAATTGCATTTTAACCCCTA
** * *
41238175 AACTTT-GTAAAATGTACATTTTGACACCC-A
1 AACTTTCCAAAAAT-TGCATTTTAAC-CCCTA
*
41238205 AAC-TTCTCAAAAATTACATTTTAACCCCTA
1 AACTTTC-CAAAAATTGCATTTTAACCCCTA
41238235 AACTTTTCC-AAAATTGCATTTTAACCCCTA
1 AAC-TTTCCAAAAATTGCATTTTAACCCCTA
** * *
41238265 AACTTTCCCTAAATTGCTTTTTGACCCC-A
1 AACTTTCCAAAAATTGCATTTTAACCCCTA
*
41238294 AACTCATCCAAAAATT
1 AACT-TTCCAAAAATT
41238310 ACCATTTTCC
Statistics
Matches: 111, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
29 20 0.18
30 80 0.72
31 8 0.07
32 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
AACTTTCCAAAAATTGCATTTTAACCCCTA
Found at i:41238321 original size:29 final size:28
Alignment explanation
Indices: 41238289--41238384 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 28
41238279 TGCTTTTTGA
41238289 CCCCAAACTCATCCAAAAATTACCATTTT
1 CCCCAAA-TCATCCAAAAATTACCATTTT
*
41238318 CCCCTCAATCATCC-AAAATTACCATTTT
1 CCCC-AAATCATCCAAAAATTACCATTTT
41238346 CCACTCAAA-CATCCAAAAATTACCATTTT
1 CC-C-CAAATCATCCAAAAATTACCATTTT
41238375 GCACCCAAAT
1 -C-CCCAAAT
41238385 GTCCGAAAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
28 21 0.36
29 31 0.53
30 5 0.09
31 1 0.02
ACGTcount: A:0.38, C:0.34, G:0.01, T:0.27
Consensus pattern (28 bp):
CCCCAAATCATCCAAAAATTACCATTTT
Found at i:41238344 original size:28 final size:29
Alignment explanation
Indices: 41238297--41238374 Score: 131
Period size: 28 Copynumber: 2.7 Consensus size: 29
41238287 GACCCCAAAC
*
41238297 TCATCCAAAAATTACCATTTTCCCCTCAA
1 TCATCCAAAAATTACCATTTTCCACTCAA
41238326 TCATCC-AAAATTACCATTTTCCACTCAA
1 TCATCCAAAAATTACCATTTTCCACTCAA
*
41238354 ACATCCAAAAATTACCATTTT
1 TCATCCAAAAATTACCATTTT
41238375 GCACCCAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 26 0.57
29 20 0.43
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.32
Consensus pattern (29 bp):
TCATCCAAAAATTACCATTTTCCACTCAA
Found at i:41238401 original size:57 final size:58
Alignment explanation
Indices: 41238298--41238412 Score: 130
Period size: 57 Copynumber: 2.0 Consensus size: 58
41238288 ACCCCAAACT
* * *
41238298 CATCCAAAAATTACCATTTTCCCCTCAATCATCCAAAATTACCATTTTCCA-CTCAAA
1 CATCCAAAAATTACCATTTTCCCCTAAATCATCCAAAATCACCATTTTCAACCTCAAA
* *
41238355 CATCCAAAAATTACCATTTTGCACCC-AAAT-GTCCGAAAGTCA-CATTTTCAACCTCAAA
1 CATCCAAAAATTACCATTTT-C-CCCTAAATCATCC-AAAATCACCATTTTCAACCTCAAA
41238413 TTTTCCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
57 31 0.63
58 15 0.31
59 3 0.06
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.28
Consensus pattern (58 bp):
CATCCAAAAATTACCATTTTCCCCTAAATCATCCAAAATCACCATTTTCAACCTCAAA
Found at i:41240296 original size:32 final size:32
Alignment explanation
Indices: 41240255--41240319 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41240245 CAAGCTAAGG
41240255 AGACGTTCACACCAGAGTAAGCCTCCACAAAA
1 AGACGTTCACACCAGAGTAAGCCTCCACAAAA
41240287 AGACGTTCACACCAGAGTAAGCCTCCACAAAA
1 AGACGTTCACACCAGAGTAAGCCTCCACAAAA
41240319 A
1 A
41240320 TTCTTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.31, G:0.15, T:0.12
Consensus pattern (32 bp):
AGACGTTCACACCAGAGTAAGCCTCCACAAAA
Found at i:41243129 original size:2 final size:2
Alignment explanation
Indices: 41243122--41243158 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41243112 ATTTTCACTC
41243122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41243159 CACTAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41243714 original size:23 final size:23
Alignment explanation
Indices: 41243667--41243717 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
41243657 TTAAGTTTAT
*
41243667 TTTAAATTTAAATTTGTATTTAA
1 TTTAAATTTAAATTTGTATTAAA
41243690 TTTAAATTTAAAATTAT-TA-TAAA
1 TTTAAATTT-AAATT-TGTATTAAA
41243713 TTTAA
1 TTTAA
41243718 TAAAATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 17 0.68
24 7 0.28
25 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATTTAAATTTGTATTAAA
Found at i:41244410 original size:19 final size:20
Alignment explanation
Indices: 41244386--41244429 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41244376 TGTTACATGC
*
41244386 TAATAAAT-ATTATTAGTAA
1 TAATAAATGATTATAAGTAA
*
41244405 TAAT-AATGATTATAATTAA
1 TAATAAATGATTATAAGTAA
41244424 TAATAA
1 TAATAA
41244430 TGACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 17 0.81
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAAATGATTATAAGTAA
Found at i:41245397 original size:22 final size:22
Alignment explanation
Indices: 41245372--41245414 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41245362 TCCTTCCCTT
41245372 TTTTTAAT-TTTTTAATTTAATC
1 TTTTTAATATTTTT-ATTTAATC
*
41245394 TTTTTCATATTTTTATTTAAT
1 TTTTTAATATTTTTATTTAAT
41245415 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTAATATTTTTATTTAATC
Found at i:41245742 original size:30 final size:29
Alignment explanation
Indices: 41245706--41245975 Score: 219
Period size: 30 Copynumber: 9.2 Consensus size: 29
41245696 CAGAAATGAA
* *
41245706 ATTTTAACCCCTAATCTTTTCCAAAATTAT
1 ATTTTAA-CCCTAAACTTTTCCAAAATTAC
* **
41245736 ATTTTAACCCTAAATTTTTTTATAAATTAC
1 ATTTTAACCCTAAACTTTTCCA-AAATTAC
*
41245766 ATTTTAACCCCTAAACTTTTCCAAAATTAT
1 ATTTTAA-CCCTAAACTTTTCCAAAATTAC
** *
41245796 ATTTTAACCCTAAAAATTTCTATAAATTAC
1 ATTTTAACCCTAAACTTTTCCA-AAATTAC
* * **
41245826 ATTTTGACCCAAAACTTTTCCAAAATTTT
1 ATTTTAACCCTAAACTTTTCCAAAATTAC
*
41245855 ATTTTAACCCTAAAACTTTT-TAGAAATTAC
1 ATTTTAACCCT-AAACTTTTCCA-AAATTAC
* * *
41245885 ATTTTTACCCCTAAA-TTTTCCATAATTCC
1 A-TTTTAACCCTAAACTTTTCCAAAATTAC
* *
41245914 ATTTTGACCCT-AA-TTTTACCAAAAATACC
1 ATTTTAACCCTAAACTTTT-CCAAAATTA-C
* *
41245943 ATTTT-ACCCTTAAAC-TTTCTAAAATTCC
1 ATTTTAACCC-TAAACTTTTCCAAAATTAC
41245971 ATTTT
1 ATTTT
41245976 TGCCCCCCAT
Statistics
Matches: 191, Mismatches: 37, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
27 6 0.03
28 24 0.13
29 61 0.32
30 79 0.41
31 21 0.11
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTTTCCAAAATTAC
Found at i:41245869 original size:59 final size:60
Alignment explanation
Indices: 41245706--41245926 Score: 302
Period size: 59 Copynumber: 3.7 Consensus size: 60
41245696 CAGAAATGAA
* **
41245706 ATTTTAACCCCTAATCTTTTCCAAAATTATATTTTAACCCTAAATTTTTTTATAAATTAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAATTTTTATAAATTAC
*
41245766 ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAATTTCTATAAATTAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAATTTTTATAAATTAC
* * * * *
41245826 ATTTTGA-CCCAAAACTTTTCCAAAATTTTATTTTAACCCTAAAACTTTTTAGAAATTAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAATTTTTATAAATTAC
* * ** *
41245885 ATTTTTACCCCTAAA-TTTTCCATAATTCCATTTTGACCCTAA
1 ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAA
41245927 TTTTACCAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 76 0.53
60 68 0.47
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAAATTTTTATAAATTAC
Found at i:41245969 original size:57 final size:56
Alignment explanation
Indices: 41245878--41246062 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 56
41245868 AACTTTTTAG
* * * *
41245878 AAATTA-CATTTTTACCCCTAAATTTTCCATAATTCCATTTTGACCCTAATTTTACCA
1 AAATTACCA-TTTTACCCTTAAACTTTCCAAAATTCCATTTTGACCC-AATTTCACCA
* * * * *
41245935 AAAATACCATTTTACCCTTAAACTTTCTAAAATTCCATTTTTGCCCCCCATTTCATCA
1 AAATTACCATTTTACCCTTAAACTTTCCAAAATTCCA-TTTTG-ACCCAATTTCACCA
* * *
41245993 AAATTTCCATTTTACCCTTGAACTTTCCAAAA-TCACATTTTGACCCAATTTCGACCT
1 AAATTACCATTTTACCCTTAAACTTTCCAAAATTC-CATTTTGACCCAATTTC-ACCA
41246050 AAATTACCATTTT
1 AAATTACCATTTT
41246063 TCCCCCGAGT
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
56 8 0.08
57 50 0.48
58 44 0.42
59 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.39
Consensus pattern (56 bp):
AAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTGACCCAATTTCACCA
Found at i:41246023 original size:29 final size:27
Alignment explanation
Indices: 41245714--41246038 Score: 125
Period size: 29 Copynumber: 11.1 Consensus size: 27
41245704 AAATTTTAAC
* **
41245714 CCCTAATCTTTTCCAAAATTATATTTTAA
1 CCCTAAAC-TTTCCAAAATTCCATTTT-A
* ** *
41245743 CCCTAAATTTTTTTATAAATTACATTTTAA
1 CCCTAAA-CTTTCCA-AAATTCCATTTT-A
**
41245773 CCCCTAAACTTTTCCAAAATTATATTTTAA
1 -CCCTAAAC-TTTCCAAAATTCCATTTT-A
* * *
41245803 CCCTAAAAATTTCTATAAATTACATTTTGA
1 CCCT-AAACTTTCCA-AAATTCCATTTT-A
* **
41245833 CCCAAAACTTTTCCAAAATTTTATTTTAA
1 CCCTAAAC-TTTCCAAAATTCCATTTT-A
** *
41245862 CCCTAAAACTTTTTAGAAATTACATTTTTA
1 CCCT-AAACTTTCCA-AAATTCCA-TTTTA
* *
41245892 CCCCTAAATTTTCCATAATTCCATTTTGA
1 -CCCTAAACTTTCCAAAATTCCATTTT-A
* *
41245921 CCCT-AATTTTACCAAAAATACCATTTTA
1 CCCTAAACTTT-CC-AAAATTCCATTTTA
* *
41245949 CCCTTAAACTTTCTAAAATTCCATTTTTG
1 CCC-TAAACTTTCCAAAATTCCA-TTTTA
***
41245978 CCCCCCA-TTTCATCAAAATTTCCATTTTA
1 CCCTAAACTTTC--CAAAA-TTCCATTTTA
*
41246007 CCCTTGAACTTTCCAAAA-TCACATTTTGA
1 CCC-TAAACTTTCCAAAATTC-CATTTT-A
41246036 CCC
1 CCC
41246039 AATTTCGACC
Statistics
Matches: 229, Mismatches: 43, Indels: 48
0.72 0.13 0.15
Matches are distributed among these distances:
27 12 0.05
28 29 0.13
29 87 0.38
30 78 0.34
31 23 0.10
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (27 bp):
CCCTAAACTTTCCAAAATTCCATTTTA
Found at i:41248848 original size:58 final size:58
Alignment explanation
Indices: 41248785--41249140 Score: 217
Period size: 58 Copynumber: 6.1 Consensus size: 58
41248775 AAAACGAAAA
* * *
41248785 TTTTGGATATCCGAGGGTAGAATGGAAATTTTGAAAGTTTCGGGGTCAAAAATAGAAT
1 TTTTGGATATTCGAGGGTAAAATGGAAATTTTGAAAATTTCGGGGTCAAAAATAGAAT
* * * *
41248843 TTTTGGA-ATTTTGAGGGTAAAATGGTAATTTTGAAAAAATTT-AGGGTTAAAAAT-GACA-
1 TTTTGGATA-TTCGAGGGTAAAATGGAAATTTTG--AAAATTTCGGGGTCAAAAATAGA-AT
* * * * ** * * *
41248901 TTTTAGATGTTCG-GGGTAAAACGGTAATTTTTGAAAAAATCGAGAT-AAAAATGGAAT
1 TTTTGGATATTCGAGGGTAAAATGG-AAATTTTGAAAATTTCGGGGTCAAAAATAGAAT
* * * * * * *
41248958 TTTTGGACATTCGAGGGTAGAATGGTAATTTTGAAAGTGTCGGTGTCAAAAATGGAAT
1 TTTTGGATATTCGAGGGTAAAATGGAAATTTTGAAAATTTCGGGGTCAAAAATAGAAT
* * * * ** *
41249016 TTTTGGA-ATTTTGAGGGTAAAAACGTAATTTTTTAGAAAAAATCGGGATCAAAAATAGAAT
1 TTTTGGATA-TTCGAGGGT-AAAATGGAA-ATTTT-GAAAATTTCGGGGTCAAAAATAGAAT
* * * * * * *
41249077 TTTTAGG-TATCCAAGGGTAAAATGGTAATTTTTAGAAGTTT-TGGGTCAAAAATATAAT
1 TTTT-GGATATTCGAGGGTAAAATGGAAATTTTGA-AAATTTCGGGGTCAAAAATAGAAT
41249135 TTTTGG
1 TTTTGG
41249141 GTAGTTTAGG
Statistics
Matches: 223, Mismatches: 57, Indels: 37
0.70 0.18 0.12
Matches are distributed among these distances:
56 12 0.05
57 41 0.18
58 98 0.44
59 23 0.10
60 16 0.07
61 30 0.13
62 3 0.01
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (58 bp):
TTTTGGATATTCGAGGGTAAAATGGAAATTTTGAAAATTTCGGGGTCAAAAATAGAAT
Found at i:41249008 original size:173 final size:174
Alignment explanation
Indices: 41248687--41249047 Score: 503
Period size: 173 Copynumber: 2.1 Consensus size: 174
41248677 TCGAGGGGCA
** * *
41248687 AAAATGGTAATTTTGGGAAAATTGGGGTTAAAATTGAAATTTTAGAAATTCGAGGGTAAAACGGT
1 AAAATGGTAATTTTGAAAAAATTAGGGTTAAAAATGAAATTTTAGAAATTCGAGGGTAAAACGGT
*
41248752 AATTTCTAGAAAAATCAAGATCAAAAACGAAAATTTTGGATATCCGAGGGTAGAATGGAAATTTT
66 AATTTCTAGAAAAATCAAGATCAAAAACGAAAATTTTGGACATCCGAGGGTAGAATGGAAATTTT
*
41248817 GAAAGTTTCGGGGTCAAAAATAGAATTTTTGGAATTTTGAGGGT
131 GAAAGTGTCGGGGTCAAAAATAGAATTTTTGGAATTTTGAGGGT
* **
41248861 AAAATGGTAATTTTGAAAAAATTTAGGGTTAAAAATGACATTTTAGATGTTCG-GGGTAAAACGG
1 AAAATGGTAATTTTGAAAAAA-TTAGGGTTAAAAATGAAATTTTAGAAATTCGAGGGTAAAACGG
* * * * * * *
41248925 TAATTT-TTGAAAAAATCGAGAT-AAAAATGGAATTTTTGGACATTCGAGGGTAGAATGGTAATT
65 TAATTTCTAG-AAAAATCAAGATCAAAAACGAAAATTTTGGACATCCGAGGGTAGAATGGAAATT
* *
41248988 TTGAAAGTGTCGGTGTCAAAAATGGAATTTTTGGAATTTTGAGGGT
129 TTGAAAGTGTCGGGGTCAAAAATAGAATTTTTGGAATTTTGAGGGT
**
41249034 AAAAACGTAATTTT
1 AAAATGGTAATTTT
41249048 TTAGAAAAAA
Statistics
Matches: 165, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
173 92 0.56
174 47 0.28
175 26 0.16
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (174 bp):
AAAATGGTAATTTTGAAAAAATTAGGGTTAAAAATGAAATTTTAGAAATTCGAGGGTAAAACGGT
AATTTCTAGAAAAATCAAGATCAAAAACGAAAATTTTGGACATCCGAGGGTAGAATGGAAATTTT
GAAAGTGTCGGGGTCAAAAATAGAATTTTTGGAATTTTGAGGGT
Found at i:41249037 original size:29 final size:29
Alignment explanation
Indices: 41248796--41249048 Score: 88
Period size: 29 Copynumber: 8.8 Consensus size: 29
41248786 TTTGGATATC
* * *
41248796 CGAGGGT-AGAATGGAAATTTTGAAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAA-TTT
*
41248825 CG-GGGTCAAAAATAGAATTTTTGGAATTT
1 CGAGGGT-AAAAATGGAATTTTTGGAATTT
* *
41248854 TGAGGGT-AAAATGGTAA-TTTTGAAAAAATTT
1 CGAGGGTAAAAATGG-AATTTTTG---GAATTT
*
41248885 --AGGGTTAAAAAT-GACA-TTTTAG-ATGTT
1 CGAGGG-TAAAAATGGA-ATTTTTGGAAT-TT
* * **
41248912 CG-GGGT-AAAACGGTAATTTTTGAAAAAAT
1 CGAGGGTAAAAATGG-AATTTTTG-GAATTT
*
41248941 CGA-GATAAAAATGGAATTTTTGGACA-TT
1 CGAGGGTAAAAATGGAATTTTTGGA-ATTT
* * *
41248969 CGAGGGT-AGAATGGTAA-TTTTGAAAGTGT
1 CGAGGGTAAAAATGG-AATTTTTGGAA-TTT
*
41248998 CG-GTGTCAAAAATGGAATTTTTGGAATTT
1 CGAGGGT-AAAAATGGAATTTTTGGAATTT
* * *
41249027 TGAGGGTAAAAACGTAATTTTT
1 CGAGGGTAAAAATGGAATTTTT
41249049 TAGAAAAAAT
Statistics
Matches: 165, Mismatches: 30, Indels: 58
0.65 0.12 0.23
Matches are distributed among these distances:
26 6 0.04
27 6 0.04
28 43 0.26
29 52 0.32
30 48 0.29
31 10 0.06
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
CGAGGGTAAAAATGGAATTTTTGGAATTT
Found at i:41249094 original size:119 final size:116
Alignment explanation
Indices: 41248832--41249140 Score: 283
Period size: 119 Copynumber: 2.6 Consensus size: 116
41248822 TTTCGGGGTC
*** * * * * *
41248832 AAAAATAGAATTTTTGGA-ATTTTGAGGGTAAAATGGTAATTTTGAAAAAATTTAGGGTTAAAAA
1 AAAAATAGAATTTTTGGACA-TCCAAGGGTAAAATGGTAATTTTG-AGAAGTGTCGGGTCAAAAA
* *
41248896 T-GACA-TTTTAG-ATGTTCG-GGGTAAAACGGTAATTTTTGAAAAAATCGAGAT
64 TAGA-ATTTTTGGAAT-TTTGAGGGTAAAACGGTAATTTTTGAAAAAATCGAGAT
* * * *
41248947 AAAAATGGAATTTTTGGACATTCGAGGGTAGAATGGTAATTTTGA-AAGTGTCGGTGTCAAAAAT
1 AAAAATAGAATTTTTGGACATCCAAGGGTAAAATGGTAATTTTGAGAAGTGTCGG-GTCAAAAAT
* *
41249011 GGAATTTTTGGAATTTTGAGGGTAAAAAC-GTAATTTTTTAGAAAAAATCGGGAT
65 AGAATTTTTGGAATTTTGAGGGT-AAAACGGTAA-TTTTT-GAAAAAATCGAGAT
* * * *
41249065 CAAAAATAGAATTTTTAGG-TATCCAAGGGTAAAATGGTAATTTTTAGAAGTTTTGGGTCAAAAA
1 -AAAAATAGAATTTTT-GGACATCCAAGGGTAAAATGGTAATTTTGAGAAGTGTCGGGTCAAAAA
*
41249129 TATAATTTTTGG
64 TAGAATTTTTGG
41249141 GTAGTTTAGG
Statistics
Matches: 162, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
113 6 0.04
114 10 0.06
115 49 0.30
116 11 0.07
117 10 0.06
118 13 0.08
119 54 0.33
120 9 0.06
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (116 bp):
AAAAATAGAATTTTTGGACATCCAAGGGTAAAATGGTAATTTTGAGAAGTGTCGGGTCAAAAATA
GAATTTTTGGAATTTTGAGGGTAAAACGGTAATTTTTGAAAAAATCGAGAT
Found at i:41250814 original size:26 final size:25
Alignment explanation
Indices: 41250749--41250819 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 25
41250739 TATTGATTTT
*
41250749 TTTCAAGAATAGGGTCTGTCTAATGA
1 TTTCAAGAAT-GGGTTTGTCTAATGA
*
41250775 TTTCAAGAATTGGGTTTGTCTATTGA
1 TTTCAAGAA-TGGGTTTGTCTAATGA
41250801 TTTCAAGAACTGGGTTTGT
1 TTTCAAGAA-TGGGTTTGT
41250820 GTTGATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (25 bp):
TTTCAAGAATGGGTTTGTCTAATGA
Found at i:41251240 original size:11 final size:11
Alignment explanation
Indices: 41251217--41251297 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
41251207 TTAATATTAT
*
41251217 TTTAAATTTAA
1 TTTAAATTAAA
41251228 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
41251239 TTTAAAGTAAA
1 TTTAAATTAAA
*
41251250 TTTAAA-TATA
1 TTTAAATTAAA
* *
41251260 CTT-ATTTAAA
1 TTTAAATTAAA
**
41251270 TTTACTTTAAA
1 TTTAAATTAAA
*
41251281 TTTAAAATAAA
1 TTTAAATTAAA
41251292 TTTAAA
1 TTTAAA
41251298 CTTTAATACA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
9 1 0.02
10 15 0.27
11 34 0.62
12 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:41251249 original size:17 final size:16
Alignment explanation
Indices: 41251217--41251256 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
41251207 TTAATATTAT
*
41251217 TTTAAATTTAATTAAA
1 TTTAAATTTAAGTAAA
41251233 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AAGTAAA
41251250 TTTAAAT
1 TTTAAAT
41251257 ATACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAGTAAA
Found at i:41251302 original size:7 final size:6
Alignment explanation
Indices: 41251217--41251303 Score: 67
Period size: 6 Copynumber: 14.8 Consensus size: 6
41251207 TTAATATTAT
* * *
41251217 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TATACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
* *
41251264 TTTAAA TTT-AC TTTAAA TTTAAA -ATAAA TTTAAA CTTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAA
41251304 TACAAAAGCC
Statistics
Matches: 63, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.03
5 16 0.25
6 36 0.57
7 5 0.08
8 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:41257163 original size:29 final size:29
Alignment explanation
Indices: 41257131--41257200 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
41257121 AGAGCGTTTT
* * *
41257131 AAAAAATCTGCCTATTCCTACAAATATTA
1 AAAAAATCTGCCTAATCCCACAAAAATTA
* * *
41257160 AAAAAAGCAGCCTAATCCCATAAAAATTA
1 AAAAAATCTGCCTAATCCCACAAAAATTA
41257189 AGAAAAATCTGC
1 A-AAAAATCTGC
41257201 ATTTTCTCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (29 bp):
AAAAAATCTGCCTAATCCCACAAAAATTA
Found at i:41260131 original size:27 final size:27
Alignment explanation
Indices: 41260067--41260131 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 27
41260057 AAATTTTATT
* *
41260067 AAAAATTAAAAAATATATGAATCGTAA
1 AAAAATTAAAATATATATGAATCATAA
41260094 AAAAA-TAAAATATATATAGAAT-ATAA
1 AAAAATTAAAATATATAT-GAATCATAA
41260120 AAAAATTAAAAT
1 AAAAATTAAAAT
41260132 TTTAAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (27 bp):
AAAAATTAAAATATATATGAATCATAA
Found at i:41260184 original size:19 final size:18
Alignment explanation
Indices: 41260149--41260199 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
41260139 AAGTCATAAG
41260149 AAAATTATAAAAATGTAA
1 AAAATTATAAAAATGTAA
* * *
41260167 AAAAATATAAAATTTGTAC
1 AAAATTATAAAA-ATGTAA
41260186 AAAATTATAAAAAT
1 AAAATTATAAAAAT
41260200 AATCATAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAATGTAA
Found at i:41260444 original size:23 final size:22
Alignment explanation
Indices: 41260379--41260455 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
41260369 TTTTATGCAC
*
41260379 TTTATAATTTTTTTTTTATAATT
1 TTTATAA-TTTTTTTTTACAATT
***
41260402 TTTATAA---AAGTTTACAATTT
1 TTTATAATTTTTTTTTACAA-TT
*
41260422 TTTATAATTTTTTTTTACGATT
1 TTTATAATTTTTTTTTACAATT
*
41260444 TTTATAGTTTTT
1 TTTATAATTTTT
41260456 AATAATTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
19 6 0.15
20 9 0.22
22 13 0.32
23 13 0.32
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTATAATTTTTTTTTACAATT
Found at i:41261392 original size:26 final size:27
Alignment explanation
Indices: 41261346--41261402 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
41261336 TTGAAGAAGA
*
41261346 AAAGAATGTATTTTGT-TTTTTAATGG
1 AAAGAATGTATTATGTCTTTTTAATGG
41261372 AAAGAATG-AGTTATGTCTTTTTTAATGG
1 AAAGAATGTA-TTATGTC-TTTTTAATGG
41261400 AAA
1 AAA
41261403 TAATCAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 13 0.48
28 13 0.48
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (27 bp):
AAAGAATGTATTATGTCTTTTTAATGG
Found at i:41261767 original size:31 final size:31
Alignment explanation
Indices: 41261710--41261792 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
41261700 GACCCTTAAA
* *
41261710 TTTTCTAAAAATTTAAAAATTTAACCCCCAAAT
1 TTTTC-AAAAA-TTCAAATTTTAACCCCCAAAT
**
41261743 TTTTCAAAAATTCAAATTTTAACCCTTAAAT
1 TTTTCAAAAATTCAAATTTTAACCCCCAAAT
41261774 TTTTCAAAAATTCAAATTT
1 TTTTCAAAAATTCAAATTT
41261793 GACCCCGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 36 0.78
32 5 0.11
33 5 0.11
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTTCAAAAATTCAAATTTTAACCCCCAAAT
Found at i:41273506 original size:50 final size:49
Alignment explanation
Indices: 41273380--41273506 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 49
41273370 TCTTTTACCT
* * * *
41273380 CTAAAGCTGTGGAGGTGCAGATTAAAACCGTAATCGCAAATCTCATACAC
1 CTAAAGCTGTAGAGG-GCAGATTGAAGCCGCAATCGCAAATCTCATACAC
* * *
41273430 CTAAAGCTGTAGAGGGACAGAATGAAGCCGCAATGGCAAATCTCATTCAC
1 CTAAAGCTGTAGAGGG-CAGATTGAAGCCGCAATCGCAAATCTCATACAC
41273480 CTAAAGCTGTAGAGGGCTAGATTGAAG
1 CTAAAGCTGTAGAGGGC-AGATTGAAG
41273507 TCACAATGAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.03
50 65 0.97
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (49 bp):
CTAAAGCTGTAGAGGGCAGATTGAAGCCGCAATCGCAAATCTCATACAC
Found at i:41273522 original size:50 final size:50
Alignment explanation
Indices: 41273416--41273527 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
41273406 ACCGTAATCG
* *
41273416 CAAATCTCATACACCTAAAGCTGTAGAGGGACAGAATGAAGCCGCAATGG
1 CAAATCTCATACACCTAAAGCTGTAGAGGGACAGAATGAAGCCACAATGA
* * *
41273466 CAAATCTCATTCACCTAAAGCTGTAGAGGG-CTAGATTGAAGTCACAATGA
1 CAAATCTCATACACCTAAAGCTGTAGAGGGAC-AGAATGAAGCCACAATGA
* *
41273516 CGAATCTTATAC
1 CAAATCTCATAC
41273528 TCTTGAAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 52 0.98
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (50 bp):
CAAATCTCATACACCTAAAGCTGTAGAGGGACAGAATGAAGCCACAATGA
Found at i:41273633 original size:40 final size:40
Alignment explanation
Indices: 41273589--41273732 Score: 143
Period size: 39 Copynumber: 3.6 Consensus size: 40
41273579 CAGAGGGAAA
* * *
41273589 ATTGAAGACCATCCGATCTTTTACCCCGATCAT-GAGGCAG
1 ATTGAAGACAATCCAATCTTTTACCCCGACCATAG-GGCAG
* ** *
41273629 ATTGAAGA-AATCTAATCTTTTACCCTAACCAAAGGGCAG
1 ATTGAAGACAATCCAATCTTTTACCCCGACCATAGGGCAG
* * * *
41273668 ATTGAAGACCAT-CAGATCTCTTACCTCGACCATAGGGCCG
1 ATTGAAGACAATCCA-ATCTTTTACCCCGACCATAGGGCAG
41273708 ATTGAA-ACAATCCAATCTTTTACCC
1 ATTGAAGACAATCCAATCTTTTACCC
41273733 TTAAAGTTAT
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 44 0.54
40 38 0.46
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
ATTGAAGACAATCCAATCTTTTACCCCGACCATAGGGCAG
Found at i:41273667 original size:39 final size:40
Alignment explanation
Indices: 41273624--41273733 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
41273614 CCGATCATGA
41273624 GGCAGATTGAAGA-AATCTAATCTTTTACCCT-AACCAAAG
1 GGCAGATTGAAGACAATC-AATCTTTTACCCTCAACCAAAG
* * * *
41273663 GGCAGATTGAAGACCATCAGATCTCTTA-CCTCGACCATAG
1 GGCAGATTGAAGACAATCA-ATCTTTTACCCTCAACCAAAG
*
41273703 GGCCGATTGAA-ACAATCCAATCTTTTACCCT
1 GGCAGATTGAAGACAAT-CAATCTTTTACCCT
41273734 TAAAGTTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 28 0.47
40 31 0.53
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
GGCAGATTGAAGACAATCAATCTTTTACCCTCAACCAAAG
Found at i:41273711 original size:79 final size:79
Alignment explanation
Indices: 41273560--41273733 Score: 217
Period size: 79 Copynumber: 2.2 Consensus size: 79
41273550 AGTTACAACC
* * * * * *
41273560 TCCAATCTCTTACTCTAACCAGAGGGAAAATTGAAGACCATCCGATCTTTTACCCCGATCATGAG
1 TCCAATCTTTTACCCTAACCAAAGGGAAAATTGAAGACCATCAGATCTCTTACCCCGACCATGAG
41273625 GCAGATTGAAGA-AA
66 GCAGATTGAA-ACAA
* * * *
41273639 TCTAATCTTTTACCCTAACCAAAGGGCAGATTGAAGACCATCAGATCTCTTACCTCGACCAT-AG
1 TCCAATCTTTTACCCTAACCAAAGGGAAAATTGAAGACCATCAGATCTCTTACCCCGACCATGA-
*
41273703 GGCCGATTGAAACAA
65 GGCAGATTGAAACAA
41273718 TCCAATCTTTTACCCT
1 TCCAATCTTTTACCCT
41273734 TAAAGTTATA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 2 0.02
79 79 0.98
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (79 bp):
TCCAATCTTTTACCCTAACCAAAGGGAAAATTGAAGACCATCAGATCTCTTACCCCGACCATGAG
GCAGATTGAAACAA
Found at i:41275050 original size:24 final size:26
Alignment explanation
Indices: 41274993--41275051 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
41274983 GAGTGGTTTG
*
41274993 TTTTTTAATGGAAAGAATGAGTTATATC
1 TTTTTTAATGGAAAGAATCAG-TATA-C
*
41275021 TTTTTTAATGGAAATAATCAG-ATA-
1 TTTTTTAATGGAAAGAATCAGTATAC
41275045 TTTTTTA
1 TTTTTTA
41275052 TTTGTTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.24
26 3 0.10
28 19 0.66
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (26 bp):
TTTTTTAATGGAAAGAATCAGTATAC
Found at i:41275364 original size:30 final size:30
Alignment explanation
Indices: 41275323--41275423 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
41275313 TTTATTTAAA
41275323 AAATTT-ACCCTCAAATTTTCTAAAAATTC
1 AAATTTGACCCTCAAATTTTCTAAAAATTC
* * *
41275352 AAATTTGACCCTCGAATTTT-TCATAAATTT
1 AAATTTGACCCTCAAATTTTCT-AAAAATTC
*
41275382 AAATTTAACCCTCAAAGTTTTC-AAAAATTC
1 AAATTTGACCCTCAAA-TTTTCTAAAAATTC
41275412 AAATTTGACCCT
1 AAATTTGACCCT
41275424 GTTTTAATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 7 0.12
30 49 0.82
31 4 0.07
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
AAATTTGACCCTCAAATTTTCTAAAAATTC
Done.