Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 383 of 427
Found at i:111433241 original size:152 final size:152
Alignment explanation
Indices: 111432965--111433322 Score: 635
Period size: 152 Copynumber: 2.4 Consensus size: 152
111432955 GGATTCATAT
*
111432965 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAA
1 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTACTAATGAAAAA
* * *
111433030 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAGCATATAGATATACCTCT
66 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCA
*
111433095 GTGCAACAAAACTTATAGTGAA
131 ATGCAACAAAACTTATAGTGAA
*
111433117 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTACTAATGAAAAT
1 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTACTAATGAAAAA
*
111433182 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACTTCA
66 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCA
111433247 ATGCAACAAAACTTATAGTGAA
131 ATGCAACAAAACTTATAGTGAA
* *
111433269 GAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATATCTA
1 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTA
111433323 TAGAGTACAT
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 197 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (152 bp):
AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTACTAATGAAAAA
AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCA
ATGCAACAAAACTTATAGTGAA
Found at i:111433372 original size:98 final size:98
Alignment explanation
Indices: 111433231--111433415 Score: 334
Period size: 98 Copynumber: 1.9 Consensus size: 98
111433221 GCAATAGAAC
* *
111433231 ACATAGATATACTTCAATGCAACAAAACTTATAGTGAAGAAAAGCATATGGTAAATGCTAATAGT
1 ACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCTAATAGT
*
111433296 ATTAGTTAAAATATTGCACGATATCTATAGAGT
66 ATTAGTTAAAATATTACACGATATCTATAGAGT
*
111433329 ACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCTAATAGT
1 ACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCTAATAGT
111433394 ATTAGTTAAAATATTACACGAT
66 ATTAGTTAAAATATTACACGAT
111433416 GTCTGCTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 83 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (98 bp):
ACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCTAATAGT
ATTAGTTAAAATATTACACGATATCTATAGAGT
Found at i:111433457 original size:152 final size:152
Alignment explanation
Indices: 111433322--111433781 Score: 791
Period size: 152 Copynumber: 3.0 Consensus size: 152
111433312 CACGATATCT
*
111433322 ATAGAGTACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
1 ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
*
111433387 TAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
66 TAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
111433452 TTTAAAGATCAGCTA-GCATGCA
131 TTTAAAGATCAGC-ACGCATGCA
* *
111433474 ATAGAGCACATAGATATACCTCAGAGCAACAAAACTTATAGTGAAAAAAAACATATGGTAAATGC
1 ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
111433539 TAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
66 TAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
111433604 TTTAAAGATCAGC-CAGCATGCA
131 TTTAAAGATCAGCAC-GCATGCA
* *
111433626 ATAGAGCACATAGATATACCTCTGTGCAATAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
1 ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
* * *
111433691 TAATAGTATTAGTTAAAATATTGCACAATGTTTGCTAATGAAATAAAGGATATCCTTAACATCAT
66 TAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
111433756 TTTAAAGATCAGC-CAGCATGCA
131 TTTAAAGATCAGCAC-GCATGCA
111433778 ATAG
1 ATAG
111433782 CACAAAACTT
Statistics
Matches: 295, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
152 295 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (152 bp):
ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
TAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
TTTAAAGATCAGCACGCATGCA
Found at i:111433531 original size:250 final size:250
Alignment explanation
Indices: 111433072--111433567 Score: 877
Period size: 250 Copynumber: 2.0 Consensus size: 250
111433062 CCAGCATGCA
* *
111433072 ATAGAGCATATAGATATACCTCTGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
1 ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
* *
111433137 TAATAGTATTAGTTAAAATATTGCACGATGTCTACTAATGAAAATAAGGATATCCTTAACATCAT
66 TAATAGTATTAGTTAAAATATTACACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCAT
*
111433202 TTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACTTCAATGCAACAAAACTTATAGTG
131 TTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCAATGCAACAAAACTTATAGTG
* *
111433267 AAGAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATATCT
196 AAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATATCT
*
111433322 ATAGAGTACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
1 ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
*
111433387 TAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCAT
66 TAATAGTATTAGTTAAAATATTACACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCAT
* *
111433452 TTTAAAGATCAGCTAGCATGCAATAGAGCACATAGATATACCTCAGA-GCAACAAAACTTATAGT
131 TTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCA-ATGCAACAAAACTTATAGT
111433516 GAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGAT
195 GAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGAT
111433568 GTCTGCTAAT
Statistics
Matches: 234, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
250 233 1.00
251 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (250 bp):
ATAGAGCACATAGATATACCTCAGTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGC
TAATAGTATTAGTTAAAATATTACACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCAT
TTTAAAGATCAGCCAGCATGCAATAGAACACATAGATATACCTCAATGCAACAAAACTTATAGTG
AAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATATCT
Found at i:111433709 original size:402 final size:402
Alignment explanation
Indices: 111432965--111433716 Score: 1378
Period size: 402 Copynumber: 1.9 Consensus size: 402
111432955 GGATTCATAT
*
111432965 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTGCACGATGTCTGCTAATGAAAAA
1 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAA
* *
111433030 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAGCATATAGATATACCTCT
66 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAGCACATAGATATACCTCA
* *
111433095 GTGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTG
131 GAGCAACAAAACTTATAGTGAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTG
*
111433160 CACGATGTCTACTAATGAAAATAAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAA
196 CACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAA
* *
111433225 TAGAACACATAGATATACTTCAATGCAACAAAACTTATAGTGAAGAAAAGCATATGGTAAATGCT
261 TAGAACACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCT
111433290 AATAGTATTAGTTAAAATATTGCACGATATCTATAGAGTACATAGATATACCTCAGTGCAACAAA
326 AATAGTATTAGTTAAAATATTGCACGATATCTATAGAGTACATAGATATACCTCAGTGCAACAAA
111433355 ACTTATAGTGAA
391 ACTTATAGTGAA
111433367 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAA
1 AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAA
*
111433432 AAGGATATCCTTAACATCATTTTAAAGATCAGCTAGCATGCAATAGAGCACATAGATATACCTCA
66 AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAGCACATAGATATACCTCA
111433497 GAGCAACAAAACTTATAGTGAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTG
131 GAGCAACAAAACTTATAGTGAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTG
*
111433562 CACGATGTCTGCTAATGAAAAAAAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAA
196 CACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAA
* ** *
111433627 TAGAGCACATAGATATACCTCTGTGCAATAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCT
261 TAGAACACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCT
111433692 AATAGTATTAGTTAAAATATTGCAC
326 AATAGTATTAGTTAAAATATTGCAC
111433717 AATGTTTGCT
Statistics
Matches: 336, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
402 336 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (402 bp):
AAAAAGCATATGGTAAATGCTAATAGTATTAGTTAAAATATTACACGATGTCTGCTAATGAAAAA
AAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAATAGAGCACATAGATATACCTCA
GAGCAACAAAACTTATAGTGAAAAAAAACATATGGTAAATGCTAATAGTATTAGTTAAAATATTG
CACGATGTCTACTAATGAAAAAAAGGATATCCTTAACATCATTTTAAAGATCAGCCAGCATGCAA
TAGAACACATAGATATACCTCAATGCAACAAAACTTATAGTGAAAAAAAGCATATGGTAAATGCT
AATAGTATTAGTTAAAATATTGCACGATATCTATAGAGTACATAGATATACCTCAGTGCAACAAA
ACTTATAGTGAA
Found at i:111436445 original size:154 final size:154
Alignment explanation
Indices: 111436160--111436467 Score: 571
Period size: 154 Copynumber: 2.0 Consensus size: 154
111436150 GAATCATCCC
*
111436160 CATTCTGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG
1 CATTATGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG
*
111436225 TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAATTTTTTCTTTGAAGAACGTAAAATT
66 TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATT
111436290 CAAGCCTAAAATCAGTGAAATCAA
131 CAAGCCTAAAATCAGTGAAATCAA
*
111436314 CATTATGCAGAATATAAGATAAAATAAAAACTATACACCACAGAATGCTATCAAAGGTATCAATG
1 CATTATGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG
*
111436379 TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACTTAAAATT
66 TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATT
*
111436444 CAAGCCTAAAATTAGTGAAATCAA
131 CAAGCCTAAAATCAGTGAAATCAA
111436468 TCTATCTTAC
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 149 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (154 bp):
CATTATGCAGAATATAAGATAAAATAAAAACTATACAACACAGAATGCTATCAAAGGTATCAATG
TCTGCTACCATATAAAATGACAGTTGATGAAGGAAGCAAACTTTTTCTTTGAAGAACGTAAAATT
CAAGCCTAAAATCAGTGAAATCAA
Found at i:111437567 original size:8 final size:8
Alignment explanation
Indices: 111437514--111437568 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
111437504 TAAATATTAC
111437514 ATTTTTAA
1 ATTTTTAA
*
111437522 GTTTTTAA
1 ATTTTTAA
*
111437530 TTTTTTAA
1 ATTTTTAA
*
111437538 TTTTTTGAA
1 ATTTTT-AA
111437547 GATTTTTATA
1 -ATTTTTA-A
111437557 ATTTTTAA
1 ATTTTTAA
111437565 ATTT
1 ATTT
111437569 ACATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 25 0.61
9 10 0.24
10 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (8 bp):
ATTTTTAA
Found at i:111437755 original size:28 final size:28
Alignment explanation
Indices: 111437718--111437777 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
111437708 ATTTTTAGAT
* * *
111437718 TTTAGGGTTTATGATTTATTAGT-TATAG
1 TTTAGAGTTTAGGATTTATGA-TCTATAG
*
111437746 TTTAGAGTTTGGGATTTATGATCTATAG
1 TTTAGAGTTTAGGATTTATGATCTATAG
111437774 TTTA
1 TTTA
111437778 TGGGTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.52
Consensus pattern (28 bp):
TTTAGAGTTTAGGATTTATGATCTATAG
Found at i:111437846 original size:14 final size:14
Alignment explanation
Indices: 111437793--111437861 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
111437783 TTAAAGGTTA
*
111437793 GTTTTAGGGTTTGGG
1 GTTTAAGGG-TTGGG
**
111437808 GTTTAAGAATTGGG
1 GTTTAAGGGTTGGG
*
111437822 ATTT-AGAGGTTGGG
1 GTTTAAG-GGTTGGG
*
111437836 GTTTAAGGGTTAGAG
1 GTTTAAGGGTT-GGG
*
111437851 TTTTAAGGGTT
1 GTTTAAGGGTT
111437862 TATGATTTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
13 2 0.05
14 20 0.48
15 20 0.48
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (14 bp):
GTTTAAGGGTTGGG
Found at i:111437880 original size:22 final size:22
Alignment explanation
Indices: 111437852--111437946 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 22
111437842 GGGTTAGAGT
111437852 TTTAAGGGTTTATGATTTGAGA
1 TTTAAGGGTTTATGATTTGAGA
** *
111437874 TTTAA-GGTTTCGGGTGTT-AGGA
1 TTTAAGGGTTTATGAT-TTGA-GA
* *
111437896 -TTAA-GGTTTATTG-TTTATAGT
1 TTTAAGGGTTTA-TGATTT-GAGA
111437917 TTTAAGGGTTTATGATTTGAGA
1 TTTAAGGGTTTATGATTTGAGA
111437939 TTT-AGGGT
1 TTTAAGGGT
111437947 CTGCTGTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
20 2 0.04
21 24 0.42
22 22 0.39
23 9 0.16
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.47
Consensus pattern (22 bp):
TTTAAGGGTTTATGATTTGAGA
Found at i:111438024 original size:66 final size:66
Alignment explanation
Indices: 111437907--111438032 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
111437897 TAAGGTTTAT
* * *
111437907 TGTTTATAGTTTTAAGGGTTTATGATTTGAGATTTAGGGTCTGC-TGTTTAAAGAGTTATTAATC
1 TGTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGCAGGTTAAAAG-GTTATTAATC
111437971 AG
65 AG
* *
111437973 TGTTTATAGTTTTAGGGGTTTATGATTAGAGATTTAGGGTCTGGAGGTTAAAAGGTTATT
1 TGTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGCAGGTTAAAAGGTTATT
111438033 GATTTAAGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 47 0.87
67 7 0.13
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.44
Consensus pattern (66 bp):
TGTTTATAGTTTTAAGGGTTTATGATTAGAGATTTAGGGTCTGCAGGTTAAAAGGTTATTAATCA
G
Found at i:111439000 original size:9 final size:9
Alignment explanation
Indices: 111438979--111439021 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
111438969 CCTTTACTAA
111438979 TTTAAAA-T
1 TTTAAAAGT
111438987 TTTAAAAGT
1 TTTAAAAGT
111438996 TTTAAAAGT
1 TTTAAAAGT
*
111439005 TTTAAAAAT
1 TTTAAAAGT
111439014 TTTAAAAG
1 TTTAAAAG
111439022 GCCTAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (9 bp):
TTTAAAAGT
Found at i:111443804 original size:33 final size:32
Alignment explanation
Indices: 111443767--111443837 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 32
111443757 CATGTTCATC
111443767 TCATATTCAAATCAAAAACCATTCATAATCAA
1 TCATATTCAAATCAAAAACCATTCATAATCAA
111443799 TTCATATTCAAATCAAAAACCATTCATAATCAA
1 -TCATATTCAAATCAAAAACCATTCATAATCAA
111443832 TCATAT
1 TCATAT
111443838 AGTCCCTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (32 bp):
TCATATTCAAATCAAAAACCATTCATAATCAA
Found at i:111450821 original size:22 final size:22
Alignment explanation
Indices: 111450775--111450821 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
111450765 TATTAGATAT
**
111450775 TAAATAGATATTTATTATTTTA
1 TAAATAGATATTTATTATTAAA
111450797 TAAA-AGATATTTATTAATTAAA
1 TAAATAGATATTTATT-ATTAAA
111450819 TAA
1 TAA
111450822 TTATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATAGATATTTATTATTAAA
Found at i:111452924 original size:23 final size:23
Alignment explanation
Indices: 111452892--111453019 Score: 80
Period size: 23 Copynumber: 5.4 Consensus size: 23
111452882 CGAAATACAA
*
111452892 CTCTTCGTGAGCTTCCCGATAGG
1 CTCTTTGTGAGCTTCCCGATAGG
* *
111452915 CTCTTTGTGAGCCTCCCGATAGTT
1 CTCTTTGTGAGCTTCCCGATAG-G
** *
111452939 CTCGCT-TGAACTTCCCGATATATGG
1 CTCTTTGTGAGCTTCCCG--ATA-GG
* **
111452964 CT-ATTCAGAGCTTCCCGATAGG
1 CTCTTTGTGAGCTTCCCGATAGG
** *
111452986 CTCTTCATGAGCTTCACGATATGG
1 CTCTTTGTGAGCTTCCCGATA-GG
*
111453010 TTCTTTGTGA
1 CTCTTTGTGA
111453020 ACTACCTGAT
Statistics
Matches: 78, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
22 4 0.05
23 45 0.58
24 14 0.18
25 14 0.18
26 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (23 bp):
CTCTTTGTGAGCTTCCCGATAGG
Found at i:111453449 original size:46 final size:46
Alignment explanation
Indices: 111453392--111453573 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
111453382 AATGTGCTCT
* *
111453392 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
111453438 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
111453484 GTCACATAAAATGAATAAGACCATGGTGGAAAGATACCATGGCAAT
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
111453530 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGATACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
111453574 TCATGTCGAA
Statistics
Matches: 119, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:111456733 original size:13 final size:13
Alignment explanation
Indices: 111456715--111456741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
111456705 GAAGTAATCG
111456715 CACACGGGCATGT
1 CACACGGGCATGT
111456728 CACACGGGCATGT
1 CACACGGGCATGT
111456741 C
1 C
111456742 CCTACCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (13 bp):
CACACGGGCATGT
Found at i:111459621 original size:23 final size:23
Alignment explanation
Indices: 111459591--111459645 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
111459581 ACATAATTCA
*
111459591 CCACAAGGGCCAAACAAAGTACG
1 CCACAAGGGCCAAACAAAATACG
111459614 CCACAAGGGCCAAACAAAATACG
1 CCACAAGGGCCAAACAAAATACG
*
111459637 CCACTAGGG
1 CCACAAGGG
111459646 AAACATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.31, G:0.22, T:0.05
Consensus pattern (23 bp):
CCACAAGGGCCAAACAAAATACG
Found at i:111461361 original size:3 final size:3
Alignment explanation
Indices: 111461347--111461402 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
111461337 AAACAAATAC
111461347 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
111461393 AAT AAT AAT A
1 AAT AAT AAT A
111461403 TAGTAACATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:111461753 original size:7 final size:7
Alignment explanation
Indices: 111461737--111461843 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
111461727 AATAAATGAA
*
111461737 ATAATTT
1 ATAATAT
111461744 ATAATAT
1 ATAATAT
111461751 ATAATAT
1 ATAATAT
*
111461758 A-AAAAT
1 ATAATAT
* *
111461764 GTAAGTTT
1 ATAA-TAT
*
111461772 TTAA-A-
1 ATAATAT
*
111461777 ATAATGT
1 ATAATAT
111461784 ATAATAT
1 ATAATAT
*
111461791 A-AATAA
1 ATAATAT
111461797 ATAAATAT
1 AT-AATAT
111461805 ATAAGATAT
1 AT-A-ATAT
111461814 ATAAGT-T
1 ATAA-TAT
111461821 A-AA-AT
1 ATAATAT
111461826 ATAATAT
1 ATAATAT
111461833 ATAATA-
1 ATAATAT
111461839 ATAAT
1 ATAAT
111461844 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:111461807 original size:21 final size:21
Alignment explanation
Indices: 111461775--111461839 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
111461765 TAAGTTTTTA
*
111461775 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
111461795 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
111461816 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
111461838 AA
1 AA
111461840 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:111461808 original size:28 final size:29
Alignment explanation
Indices: 111461777--111461837 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
111461767 AGTTTTTAAA
111461777 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
111461805 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
111461833 ATAAT
1 ATAAT
111461838 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:111461878 original size:12 final size:13
Alignment explanation
Indices: 111461859--111461889 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
111461849 AATTTTGAAA
111461859 ATATAAATAATAT
1 ATATAAATAATAT
111461872 A-ATAAATAATAT
1 ATATAAATAATAT
111461884 ATATAA
1 ATATAA
111461890 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:111461887 original size:16 final size:15
Alignment explanation
Indices: 111461864--111461894 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
111461854 TGAAAATATA
111461864 AATAATATAATAAAT
1 AATAATATAATAAAT
111461879 AATATATATAATAAAT
1 AATA-ATATAATAAAT
111461895 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:111462233 original size:18 final size:17
Alignment explanation
Indices: 111462197--111462329 Score: 167
Period size: 18 Copynumber: 7.5 Consensus size: 17
111462187 AATCATATCT
111462197 TCTAAGATTGTATATCATA
1 TCTAAGATTG-A-ATCATA
111462216 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
111462234 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
*
111462251 CCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
* *
111462269 TTTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
111462286 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
* *
111462304 TTTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
111462321 TCTAAGATT
1 TCTAAGATT
111462330 ACATATCATT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
17 44 0.44
18 45 0.45
19 11 0.11
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (17 bp):
TCTAAGATTGAATCATA
Found at i:111462256 original size:35 final size:35
Alignment explanation
Indices: 111462197--111462338 Score: 221
Period size: 35 Copynumber: 4.0 Consensus size: 35
111462187 AATCATATCT
111462197 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
*
111462234 TCTAAGATTGTATCATACCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
111462269 TTTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
111462304 TTTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
111462339 TGAAGATTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
35 85 0.85
36 5 0.05
37 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:111462704 original size:14 final size:14
Alignment explanation
Indices: 111462685--111462713 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
111462675 AACAACTTAG
111462685 TTTTTAATTAGGAC
1 TTTTTAATTAGGAC
111462699 TTTTTAATTAGGAC
1 TTTTTAATTAGGAC
111462713 T
1 T
111462714 CATGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTTTAATTAGGAC
Found at i:111468414 original size:34 final size:34
Alignment explanation
Indices: 111468371--111468436 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
111468361 CGTACTAACA
111468371 GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
1 GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
111468405 GAATCACGTACCGAGAGTTCTTACCGAATTGG
1 GAATCACGTACCGAGAGTTCTTACCGAATTGG
111468437 GCCCGTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (34 bp):
GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
Found at i:111469831 original size:26 final size:26
Alignment explanation
Indices: 111469795--111469930 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
111469785 GACATGATTC
111469795 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
111469821 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
111469847 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
111469873 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
111469899 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
111469925 TTATCA
1 TTATCA
111469931 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:111474159 original size:25 final size:27
Alignment explanation
Indices: 111474122--111474174 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
111474112 TCAAACATGC
111474122 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
111474148 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
111474174 A
1 A
111474175 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:111474308 original size:34 final size:34
Alignment explanation
Indices: 111474265--111474330 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
111474255 CGTACTAACA
111474265 GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
1 GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
111474299 GAATCACGTACCGAGAGTTCTTACCGAATTGG
1 GAATCACGTACCGAGAGTTCTTACCGAATTGG
111474331 GCCCGTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (34 bp):
GAATCACGTACCGAGAGTTCTTACCGAATTGGAT
Found at i:111475730 original size:26 final size:26
Alignment explanation
Indices: 111475694--111475827 Score: 232
Period size: 26 Copynumber: 5.2 Consensus size: 26
111475684 CATGATATTC
111475694 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
111475720 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
111475746 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
111475772 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
111475798 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
111475824 TTAT
1 TTAT
111475828 AAATTTGTAT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:111478275 original size:89 final size:88
Alignment explanation
Indices: 111478125--111478301 Score: 345
Period size: 89 Copynumber: 2.0 Consensus size: 88
111478115 AGGCTACTAC
111478125 TAACTCTTAGAACTTAAAAGGGTTGGAAATACATCAAATGGATGTGAAGTCAACTTTTCTAAATG
1 TAACTCTTAGAACTTAAAAGGGTTGGAAATACATCAAATGGATGTGAAGTCAACTTTTCTAAATG
111478190 ACTTCCCAAAGGAAGAAATCTAT
66 ACTTCCCAAAGGAAGAAATCTAT
111478213 TAACTCTTAGAACTTAAAAGGGTTGGAAAATACATCAAATGGATGTGAAGTCAACTTTTCTAAAT
1 TAACTCTTAGAACTTAAAAGGGTTGG-AAATACATCAAATGGATGTGAAGTCAACTTTTCTAAAT
111478278 GACTTCCCAAAGGAAGAAATCTAT
65 GACTTCCCAAAGGAAGAAATCTAT
111478302 GTCGAACTGC
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 26 0.30
89 62 0.70
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (88 bp):
TAACTCTTAGAACTTAAAAGGGTTGGAAATACATCAAATGGATGTGAAGTCAACTTTTCTAAATG
ACTTCCCAAAGGAAGAAATCTAT
Found at i:111482600 original size:30 final size:30
Alignment explanation
Indices: 111482566--111482655 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
111482556 GACACGGCCA
**
111482566 TGACACACGGGTGTGT-GGTCTACCCGTGTG
1 TGACACACGGGTGTGTAAATC-ACCCGTGTG
* *
111482596 TGACACACGAGCGTGTAAATCACCCGTGTG
1 TGACACACGGGTGTGTAAATCACCCGTGTG
* * * *
111482626 TGACACACTGGTGTATGAATCACCTGTGTG
1 TGACACACGGGTGTGTAAATCACCCGTGTG
111482656 GAAGTGCCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
30 47 0.96
31 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (30 bp):
TGACACACGGGTGTGTAAATCACCCGTGTG
Found at i:111484505 original size:6 final size:6
Alignment explanation
Indices: 111484494--111484519 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
111484484 AAAATTAAAT
111484494 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
111484520 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:111484960 original size:46 final size:46
Alignment explanation
Indices: 111484870--111484961 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
111484860 CGTGTTAGGC
**
111484870 CACACGGCCGTGTGGCTCGAGTTTAGCCCGTGTTAATCGTGAAAAT
1 CACACGGCCGTGTGGCTCGAGTTTAGCCCGTGTTAATCACGAAAAT
111484916 CACACGGCCGTGTGGCTCGAGTTTAGCCCGTGTTAATCACGAAAAT
1 CACACGGCCGTGTGGCTCGAGTTTAGCCCGTGTTAATCACGAAAAT
111484962 TGAATGCCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (46 bp):
CACACGGCCGTGTGGCTCGAGTTTAGCCCGTGTTAATCACGAAAAT
Found at i:111490182 original size:45 final size:45
Alignment explanation
Indices: 111490116--111490447 Score: 184
Period size: 45 Copynumber: 7.5 Consensus size: 45
111490106 ATCTGCTTCG
* * *
111490116 CTGCAACATCA-GGAAGTCAAGATTCGTCGTCTTCGATCTACTCCA
1 CTGCAACTTCAGGGAA-ACAAGATTCGTCGTCTTCAATCTACTCCA
** *
111490161 CTGCAACTTCAGGGAAACAAGA-TCTGTAAT-TTCAACCTACTCCA
1 CTGCAACTTCAGGGAAACAAGATTC-GTCGTCTTCAATCTACTCCA
* * * * * * * * * *
111490205 CTACAACTTTAGGG-AGCTAGGTTAGT-GACTTAAATCTGCTTCA
1 CTGCAACTTCAGGGAAACAAGATTCGTCGTCTTCAATCTACTCCA
* * *
111490248 CTGCAACTTCA-GGAAGTCAAGATTCATCGTCTTCGATCTACTCCA
1 CTGCAACTTCAGGGAA-ACAAGATTCGTCGTCTTCAATCTACTCCA
* * ** *
111490293 CCGCGACTTCAGGGAAACAAGA-TCTGTAAT-TTCAACCTACTCCA
1 CTGCAACTTCAGGGAAACAAGATTC-GTCGTCTTCAATCTACTCCA
* * * * * * * * * *
111490337 CTACAACTTTAGGG-AGCTAGGTTAGT-GACTTAAATCTGCTTCA
1 CTGCAACTTCAGGGAAACAAGATTCGTCGTCTTCAATCTACTCCA
* **
111490380 CTGCAACTTCA--TAAAGTCAAGATTCGTCGTCTTTGATCTACTCCA
1 CTGCAACTTCAGGGAAA--CAAGATTCGTCGTCTTCAATCTACTCCA
*
111490425 CTGCAACTTCAAGGAAACAAGAT
1 CTGCAACTTCAGGGAAACAAGAT
111490448 CTGTGGGATT
Statistics
Matches: 205, Mismatches: 65, Indels: 34
0.67 0.21 0.11
Matches are distributed among these distances:
42 3 0.01
43 51 0.25
44 65 0.32
45 75 0.37
46 8 0.04
47 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
CTGCAACTTCAGGGAAACAAGATTCGTCGTCTTCAATCTACTCCA
Found at i:111490212 original size:44 final size:45
Alignment explanation
Indices: 111490153--111490351 Score: 142
Period size: 44 Copynumber: 4.5 Consensus size: 45
111490143 CGTCTTCGAT
*
111490153 CTACTCCACTGCAACTTCAGGGAAACAAGATCT-GTAATTTCAAC
1 CTACTCCACTGCAACTTCAGGGAAACAAGATCTAGTAACTTCAAC
* * * * * * * *
111490197 CTACTCCACTACAACTTTAGGG-AGCTAGGT-TAGTGACTTAAAT
1 CTACTCCACTGCAACTTCAGGGAAACAAGATCTAGTAACTTCAAC
* * * * * *
111490240 CTGCTTCACTGCAACTTCA-GGAAGTCAAGATTCATCGT--CTTCGAT
1 CTACTCCACTGCAACTTCAGGGAA-ACAAGA-TC-TAGTAACTTCAAC
* * *
111490285 CTACTCCACCGCGACTTCAGGGAAACAAGATCT-GTAATTTCAAC
1 CTACTCCACTGCAACTTCAGGGAAACAAGATCTAGTAACTTCAAC
* *
111490329 CTACTCCACTACAACTTTAGGGA
1 CTACTCCACTGCAACTTCAGGGA
111490352 GCTAGGTTAG
Statistics
Matches: 115, Mismatches: 31, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
42 5 0.04
43 29 0.25
44 48 0.42
45 26 0.23
46 4 0.03
47 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (45 bp):
CTACTCCACTGCAACTTCAGGGAAACAAGATCTAGTAACTTCAAC
Found at i:111490263 original size:132 final size:133
Alignment explanation
Indices: 111489799--111490451 Score: 870
Period size: 132 Copynumber: 4.9 Consensus size: 133
111489789 AATCTTGGGT
* * * *
111489799 CTACTCTACTACAACTTCAGGGAGCTAGGATGGTGACTTAAATCTACTTCGCTGCAA-TATCAAG
1 CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACT-TCAGG
* * * * * * **
111489863 AA-ACTTAGATCCGCCATCTTCGATCTGCTCCACTGCAA-TCTCAGGGAAACAAGATCTACAATC
65 AAGTC-AAGATTCGTCGTCTTCGATCTACTCCACTGCAACT-TCAGGGAAACAAGATCTGTAATC
111489926 TTCAAC
128 TTCAAC
* *
111489932 CTACTCCACTACAACTTTAGGGAGCTAGGGTGGTGACTTAAATCTGCTTCGCTGCAACATCAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
** * * * * *
111489997 AACCTAGATCCGCCGTCTTCGATCTGA-TCCACTACAA-TCTCAGGGAAACAAGATCTGCAATCT
66 AGTCAAGATTCGTCGTCTTCGATCT-ACTCCACTGCAACT-TCAGGGAAACAAGATCTGTAATCT
*
111490060 TCAGC
129 TCAAC
* * *
111490065 CTACTCCACTACAACTTTAGGGCGCTAGGATGGTGGCTTAAATCTGCTTCGCTGCAACATCAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
111490130 AGTCAAGATTCGTCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTGTAAT-TTC
66 AGTCAAGATTCGTCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTGTAATCTTC
111490194 AAC
131 AAC
* * *
111490197 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
* * *
111490262 AGTCAAGATTCATCGTCTTCGATCTACTCCACCGCGACTTCAGGGAAACAAGATCTGTAAT-TTC
66 AGTCAAGATTCGTCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTGTAATCTTC
111490326 AAC
131 AAC
* * * **
111490329 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCATAA
1 CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
* *
111490394 AGTCAAGATTCGTCGTCTTTGATCTACTCCACTGCAACTTCAAGGAAACAAGATCTGT
66 AGTCAAGATTCGTCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTGT
111490452 GGGATTCGCC
Statistics
Matches: 476, Mismatches: 39, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
132 245 0.51
133 229 0.48
134 2 0.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (133 bp):
CTACTCCACTACAACTTTAGGGAGCTAGGATGGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
AGTCAAGATTCGTCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTGTAATCTTC
AAC
Found at i:111490388 original size:43 final size:43
Alignment explanation
Indices: 111490065--111490435 Score: 156
Period size: 45 Copynumber: 8.4 Consensus size: 43
111490055 AATCTTCAGC
* * * * * *
111490065 CTACTCCACTACAACTTTAGGGCGCTAGGA-TGGTGGCTTAAAT
1 CTACTCCACTGCAACTTCAGGGAGC-AAGATTAGTGACTTAAAT
* * * * * * * **
111490108 CTGCTTCGCTGCAACATCAGGAAGTCAAGATTCGTCGTCTTCGAT
1 CTACTCCACTGCAACTTCAGGGAG-CAAGATTAGT-GACTTAAAT
* * * * *
111490153 CTACTCCACTGCAACTTCAGGGAAACAAGATCT-GTAATTTCAAC
1 CTACTCCACTGCAACTTCAGGG-AGCAAGAT-TAGTGACTTAAAT
* * * *
111490197 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAAT
1 CTACTCCACTGCAACTTCAGGGAGCAAGATTAGTGACTTAAAT
* * * * **
111490240 CTGCTTCACTGCAACTTCAGGAAGTCAAGATTCA-TCGTCTTCGAT
1 CTACTCCACTGCAACTTCAGGGAG-CAAGATT-AGT-GACTTAAAT
* * * * * * *
111490285 CTACTCCACCGCGACTTCAGGGAAACAAGATCT-GTAATTTCAAC
1 CTACTCCACTGCAACTTCAGGG-AGCAAGAT-TAGTGACTTAAAT
* * * *
111490329 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAAT
1 CTACTCCACTGCAACTTCAGGGAGCAAGATTAGTGACTTAAAT
* * *** * * **
111490372 CTGCTTCACTGCAACTTCATAAAGTCAAGATTCGTCGTCTTTGAT
1 CTACTCCACTGCAACTTCAGGGAG-CAAGATTAGT-GACTTAAAT
111490417 CTACTCCACTGCAACTTCA
1 CTACTCCACTGCAACTTCA
111490436 AGGAAACAAG
Statistics
Matches: 233, Mismatches: 80, Indels: 28
0.68 0.23 0.08
Matches are distributed among these distances:
42 2 0.01
43 79 0.34
44 63 0.27
45 85 0.36
46 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (43 bp):
CTACTCCACTGCAACTTCAGGGAGCAAGATTAGTGACTTAAAT
Found at i:111507262 original size:30 final size:30
Alignment explanation
Indices: 111507228--111507285 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
111507218 CACTGCCATG
*
111507228 ACACACGGGCGTGTG-GTCTACCCGTGTGTC
1 ACACACGGGCGTGTGAATC-ACCCGTGTGTC
111507258 ACACACGGGCGTGTGAATCACCCGTGTG
1 ACACACGGGCGTGTGAATCACCCGTGTG
111507286 GAAGTGCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGAATCACCCGTGTGTC
Found at i:111510692 original size:3 final size:3
Alignment explanation
Indices: 111510684--111510718 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
111510674 AATGAGTCAA
111510684 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
111510719 AAAATGTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:111512682 original size:2 final size:2
Alignment explanation
Indices: 111512675--111512703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
111512665 TATCATTATC
111512675 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 A
111512704 AAATTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111519125 original size:22 final size:23
Alignment explanation
Indices: 111519077--111519141 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
111519067 ATTATATGAT
* * *
111519077 AAATATAAATTTAATCATTATAA
1 AAATAAAAATATAATAATTATAA
111519100 AAATAAAAATATAATAATT-TAA
1 AAATAAAAATATAATAATTATAA
* * *
111519122 AAATTAATATATAGTAATTA
1 AAATAAAAATATAATAATTA
111519142 AATAAATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATAAAAATATAATAATTATAA
Found at i:111522279 original size:18 final size:18
Alignment explanation
Indices: 111522256--111522290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
111522246 TTTTTTTTTG
111522256 AAATTATAAAAAAATATA
1 AAATTATAAAAAAATATA
*
111522274 AAATTATTAAAAAATAT
1 AAATTATAAAAAAATAT
111522291 GTCTAGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTATAAAAAAATATA
Found at i:111522405 original size:16 final size:18
Alignment explanation
Indices: 111522370--111522406 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
111522360 AATTATATAT
111522370 TTTTTATAATTTTCTCAA
1 TTTTTATAATTTTCTCAA
111522388 TTTTTAT-ATTTT-TCAA
1 TTTTTATAATTTTCTCAA
111522404 TTT
1 TTT
111522407 GTTTTGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATAATTTTCTCAA
Found at i:111523161 original size:20 final size:20
Alignment explanation
Indices: 111523136--111523178 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
111523126 TTAATTGCAT
111523136 ATCTCAATTAAGGAAAAACA
1 ATCTCAATTAAGGAAAAACA
111523156 ATCTCAATTAAGGAAAAACA
1 ATCTCAATTAAGGAAAAACA
111523176 ATC
1 ATC
111523179 GCAGTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.21
Consensus pattern (20 bp):
ATCTCAATTAAGGAAAAACA
Found at i:111528969 original size:18 final size:19
Alignment explanation
Indices: 111528946--111528985 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
111528936 TTCATTTACT
*
111528946 CTTATAGCATATTTCAT-A
1 CTTATAGCATATATCATCA
*
111528964 CTTATATCATATATCATCA
1 CTTATAGCATATATCATCA
111528983 CTT
1 CTT
111528986 GCACATGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
CTTATAGCATATATCATCA
Found at i:111529245 original size:42 final size:41
Alignment explanation
Indices: 111529145--111529298 Score: 155
Period size: 43 Copynumber: 3.6 Consensus size: 41
111529135 CAATGCCAAC
* *
111529145 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACATGAAATCAAATA-CGATGCCA-T
* *
111529188 GTCCCATACAAGGTCTTACATGAAATCAAATACGATGCCGAT
1 GTCCCAGACATGGTCTTACATGAAATCAAATACGATGCC-AT
* **
111529230 GTCCCAGACATGGTCTTACACGTAAATCATAAGCCGATGCCAAT
1 GTCCCAGACATGGTCTTACATG-AAATCA-AATACGATGCC-AT
* ** *
111529274 GTCCCAAATGTGGTCTTACAGGAAA
1 GTCCCAGACATGGTCTTACATGAAA
111529299 ACACATATCA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
42 27 0.29
43 38 0.40
44 29 0.31
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACATGAAATCAAATACGATGCCAT
Found at i:111530913 original size:38 final size:38
Alignment explanation
Indices: 111530830--111530981 Score: 182
Period size: 38 Copynumber: 3.9 Consensus size: 38
111530820 GAATCCAGCC
* * *
111530830 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT
1 ACCAGCACAAAGCCTGCGGGA-TTTAA-CCCGGATATAAT
* *
111530870 ACCAGCACTAAGCCTACGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
*
111530908 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
111530946 ACCAGCA-AGAAGCCTGC-GGACCTTTAAGCCCGGATA
1 ACCAGCACA-AAGCCTGCGGGA--TTTAA-CCCGGATA
111530982 CACATCAAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
37 3 0.03
38 61 0.61
39 10 0.10
40 26 0.26
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (38 bp):
ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:111537752 original size:11 final size:11
Alignment explanation
Indices: 111537738--111537763 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
111537728 AAGAAACGCA
111537738 AAAATAAAAAG
1 AAAATAAAAAG
111537749 AAAATAAAAAG
1 AAAATAAAAAG
111537760 AAAA
1 AAAA
111537764 ACAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:111546315 original size:4 final size:4
Alignment explanation
Indices: 111546306--111546348 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
111546296 ACATGCACAT
111546306 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
111546349 TATGAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:111547829 original size:21 final size:23
Alignment explanation
Indices: 111547805--111547851 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
111547795 TATTAAATAG
111547805 TTTTAT-ATATTTTTCATTTATTT
1 TTTTATAATATTTTTCATTTA-TT
111547828 TTTTATACATATTTTTCATTTATT
1 TTTTATA-ATATTTTTCATTTATT
111547852 AAATTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.27
24 2 0.09
25 14 0.64
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTATAATATTTTTCATTTATT
Found at i:111559444 original size:12 final size:12
Alignment explanation
Indices: 111559429--111559454 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
111559419 TCTCAAAGGA
111559429 TCTTCCTCATCC
1 TCTTCCTCATCC
111559441 TCTTCCTCATCC
1 TCTTCCTCATCC
111559453 TC
1 TC
111559455 ATCCAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.50, G:0.00, T:0.42
Consensus pattern (12 bp):
TCTTCCTCATCC
Found at i:111561632 original size:3 final size:3
Alignment explanation
Indices: 111561624--111561649 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
111561614 AGCAGGAAAT
111561624 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
111561650 AGTTACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:111563072 original size:21 final size:18
Alignment explanation
Indices: 111563033--111563089 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
111563023 TTTTTTTTTG
111563033 AATAAATATTTTATTAAT
1 AATAAATATTTTATTAAT
* *
111563051 AATAAATGTTATTATTCA-
1 AATAAATATT-TTATTAAT
*
111563069 AATAGATA-TTTATTAAAT
1 AATAAATATTTTATT-AAT
111563087 AAT
1 AAT
111563090 TATATTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 18 0.58
19 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
AATAAATATTTTATTAAT
Found at i:111568505 original size:49 final size:47
Alignment explanation
Indices: 111568418--111568512 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 47
111568408 AATCTATATG
** * * *
111568418 AAAGAATAATCTGGGAAAAATGTAATGGAATTACTAATTATAACAAT
1 AAAGAATAATCTGAAAAAAAAGTAATGAAATAACTAATTATAACAAT
111568465 AAAGAATAATCTGTAAAAAGAAAGTAATGAAATAACTAATTATAACAA
1 AAAGAATAATCTG-AAAAA-AAAGTAATGAAATAACTAATTATAACAA
111568513 CTACCATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 13 0.32
48 3 0.07
49 25 0.61
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.25
Consensus pattern (47 bp):
AAAGAATAATCTGAAAAAAAAGTAATGAAATAACTAATTATAACAAT
Found at i:111570767 original size:31 final size:33
Alignment explanation
Indices: 111570727--111570793 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
111570717 GTTCTGAAAA
* *
111570727 TATTCATTTCATTTGAAGAA-AA-TATAAATTT
1 TATTCATTTCATTTGAACAATAATTAAAAATTT
*
111570758 TATTTATTTCATTTGAACAATAATTAAAAATTT
1 TATTCATTTCATTTGAACAATAATTAAAAATTT
111570791 TAT
1 TAT
111570794 CATGCATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 18 0.58
32 2 0.06
33 11 0.35
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (33 bp):
TATTCATTTCATTTGAACAATAATTAAAAATTT
Found at i:111571366 original size:29 final size:29
Alignment explanation
Indices: 111571331--111571389 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
111571321 TACCTTAAAG
111571331 TTAGGTGCAAATATAATAAATATTAAGAT
1 TTAGGTGCAAATATAATAAATATTAAGAT
111571360 TTAGGTGCAAATATAATAAATATTAAGAT
1 TTAGGTGCAAATATAATAAATATTAAGAT
111571389 T
1 T
111571390 AAAATTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (29 bp):
TTAGGTGCAAATATAATAAATATTAAGAT
Found at i:111571583 original size:2 final size:2
Alignment explanation
Indices: 111571576--111571600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111571566 ACTTATAAAC
111571576 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 A
111571601 ATAGTGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111575344 original size:1 final size:1
Alignment explanation
Indices: 111575338--111575366 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
111575328 TGCTTCATTG
111575338 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
111575367 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:111580036 original size:24 final size:25
Alignment explanation
Indices: 111580009--111580063 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
111579999 AGACAAAATT
*
111580009 GTTTGAATAAAACTA-ATAATTAAA
1 GTTTGAATAAAAATATATAATTAAA
** * *
111580033 GTTTTTATAAAAATATTTAATTATA
1 GTTTGAATAAAAATATATAATTAAA
111580058 GTTTGA
1 GTTTGA
111580064 TTATTTTATT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (25 bp):
GTTTGAATAAAAATATATAATTAAA
Found at i:111585385 original size:22 final size:22
Alignment explanation
Indices: 111585344--111585402 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
111585334 ATAATAAATC
* *
111585344 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
111585364 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
111585386 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
111585403 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:111585479 original size:15 final size:16
Alignment explanation
Indices: 111585449--111585481 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
111585439 AAATAGTTAT
111585449 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
111585466 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
111585481 A
1 A
111585482 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:111585747 original size:19 final size:18
Alignment explanation
Indices: 111585719--111585754 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
111585709 TCCACCATTA
*
111585719 ATCATTTATATATATTTTT
1 ATCATATATAT-TATTTTT
111585738 ATCATATATATTATTTT
1 ATCATATATATTATTTT
111585755 CTAAGAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
ATCATATATATTATTTTT
Found at i:111586312 original size:26 final size:25
Alignment explanation
Indices: 111586257--111586318 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
111586247 TGAGCAATTC
*
111586257 AATTAATTAAATAAATTCTATAATA
1 AATTAATTAAATAAATTCTATAAAA
111586282 AATTAATGTAAATAAAATT-TA-AAAA
1 AATTAAT-TAAAT-AAATTCTATAAAA
111586307 AGATTAAATTAA
1 A-ATT-AATTAA
111586319 TCTTTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 11 0.34
26 13 0.41
27 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (25 bp):
AATTAATTAAATAAATTCTATAAAA
Found at i:111604403 original size:31 final size:31
Alignment explanation
Indices: 111604368--111604429 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
111604358 TGGTACATAG
111604368 AAGCTTAAACAAAATAAATGAAACATGGCAT
1 AAGCTTAAACAAAATAAATGAAACATGGCAT
111604399 AAGCTTAAACAAAATAAATGAAACATGGCAT
1 AAGCTTAAACAAAATAAATGAAACATGGCAT
111604430 CAGTTTCAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (31 bp):
AAGCTTAAACAAAATAAATGAAACATGGCAT
Found at i:111609465 original size:38 final size:40
Alignment explanation
Indices: 111609373--111609466 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
111609363 CGGCACCTTT
* * *
111609373 TGGTGTGTAGGGTT-GGATGGTTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTAGGATGGGTCGATTATATCCCCA-ACA
* *
111609413 TGGTGTGTAAGGTTAGG-TGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTAGGATGGGTCGATTATATCCCCAACA
*
111609451 TGGTGTGTTGGGTTAG
1 TGGTGTGTAGGGTTAG
111609467 TCGGAGATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 16 0.35
40 28 0.61
41 2 0.04
ACGTcount: A:0.16, C:0.13, G:0.34, T:0.37
Consensus pattern (40 bp):
TGGTGTGTAGGGTTAGGATGGGTCGATTATATCCCCAACA
Found at i:111612165 original size:3 final size:3
Alignment explanation
Indices: 111612157--111612206 Score: 55
Period size: 3 Copynumber: 15.3 Consensus size: 3
111612147 TAGTACTAAG
*
111612157 ATA ATA ATA ATA ATG ATA ATA ATA ATAA ATAA ATAA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A ATA ATA ATA
111612206 A
1 A
111612207 CGACAATACA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 29 0.66
4 15 0.34
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:111612902 original size:11 final size:11
Alignment explanation
Indices: 111612886--111612922 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
111612876 AAAAGTTATA
111612886 TTTTTTGTATT
1 TTTTTTGTATT
111612897 TTTTTTGTATT
1 TTTTTTGTATT
*
111612908 TTTTTACGTATT
1 TTTTT-TGTATT
111612920 TTT
1 TTT
111612923 AAAGAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTTTTGTATT
Found at i:111613678 original size:41 final size:41
Alignment explanation
Indices: 111613632--111613743 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
111613622 TTCAACTTCA
* * * *
111613632 ATCTGCTCCACTGCCACTTTAGGGAGATGAGATTTGTTTTG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTCTTTTG
*
111613673 ATCTGCTCTACTGCAACTTTAGGGAGATAAGACTTCTTTTG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTCTTTTG
* * * * *
111613714 ATTTGTTCTACTGCAACTTCAGAGAGATAA
1 ATCTGCTCCACTGCAACTTTAGGGAGATAA
111613744 AACCTATGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (41 bp):
ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTCTTTTG
Found at i:111613849 original size:34 final size:34
Alignment explanation
Indices: 111613805--111613871 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
111613795 AATGTGCTAT
* * *
111613805 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATA
1 CTTCAATCTACTCCACTGAAACTTCAAGGAGATA
*
111613839 CTTCAATCTACTCCGCTGAAACTTCAAGGAGAT
1 CTTCAATCTACTCCACTGAAACTTCAAGGAGAT
111613872 CTGCTGTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (34 bp):
CTTCAATCTACTCCACTGAAACTTCAAGGAGATA
Found at i:111614058 original size:68 final size:68
Alignment explanation
Indices: 111613850--111614057 Score: 326
Period size: 68 Copynumber: 3.1 Consensus size: 68
111613840 TTCAATCTAC
* *
111613850 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAATGCCATTTTAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
111613915 AGA
66 AGA
* *
111613918 TCTGCTGAAACTTTAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
111613983 AGA
66 AGA
* * * * * *
111613986 TCCGTTGAAACTTCAAGAAAATCTGTTATGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
111614051 AGA
66 AGA
111614054 TCCG
1 TCCG
111614058 TAATTCCCAG
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 128 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (68 bp):
TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
AGA
Found at i:111616511 original size:24 final size:24
Alignment explanation
Indices: 111616479--111616527 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
111616469 TCCCATTTAC
111616479 CTTTGAGTTGATAAATCACTAACG
1 CTTTGAGTTGATAAATCACTAACG
111616503 CTTTGAGTTGATAAATCACTAACG
1 CTTTGAGTTGATAAATCACTAACG
111616527 C
1 C
111616528 CGAATCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (24 bp):
CTTTGAGTTGATAAATCACTAACG
Found at i:111622235 original size:9 final size:9
Alignment explanation
Indices: 111622206--111622262 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
111622196 AATGCGTATG
111622206 ATGCAATACTA
1 ATGCAATA--A
*
111622217 ATGC-ATGA
1 ATGCAATAA
*
111622225 ATGCAATGA
1 ATGCAATAA
111622234 ATGCAATAA
1 ATGCAATAA
*
111622243 ATACAATAA
1 ATGCAATAA
111622252 ATGCAA-AA
1 ATGCAATAA
111622260 ATG
1 ATG
111622263 TGTTGATTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
8 10 0.24
9 25 0.61
10 2 0.05
11 4 0.10
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (9 bp):
ATGCAATAA
Found at i:111626353 original size:3 final size:3
Alignment explanation
Indices: 111626339--111626399 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
111626329 TAAAGAGTGT
* * *
111626339 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
111626387 TAA CAA TAA TAA T
1 TAA TAA TAA TAA T
111626400 GACACAACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:111626608 original size:3 final size:3
Alignment explanation
Indices: 111626600--111626743 Score: 62
Period size: 3 Copynumber: 47.0 Consensus size: 3
111626590 TAGTCCTAAG
*
111626600 ATA ATA ATA ATA ATG ATA ATA ATA ATAA ATAA ATAA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A ATA ATA ATA
** * * * * * *
111626649 ACG ATA ATA CATT A-A ATT ATA ATA GTA A-A GTA ATA ATA ATA GTG
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
111626693 ATA ATC CTA AT- ATA TTA GACA ATA ATA GTA A-A ATA ATA AGCA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA
111626738 ATA ATA
1 ATA ATA
111626744 TATTAAATTA
Statistics
Matches: 103, Mismatches: 30, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
2 6 0.06
3 77 0.75
4 20 0.19
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:111627867 original size:24 final size:25
Alignment explanation
Indices: 111627839--111627887 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
111627829 TGGGTTAGGA
*
111627839 TAGGTTGGGTTTTGGGC-TGTTGGG
1 TAGGTTGAGTTTTGGGCTTGTTGGG
*
111627863 TAGGTTTAGTTTTGGGCTTGTTGGG
1 TAGGTTGAGTTTTGGGCTTGTTGGG
111627888 GCCCAGGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.06, C:0.04, G:0.45, T:0.45
Consensus pattern (25 bp):
TAGGTTGAGTTTTGGGCTTGTTGGG
Found at i:111630366 original size:28 final size:27
Alignment explanation
Indices: 111630335--111630388 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
111630325 CTATATGTTT
*
111630335 AGTT-TTTGTTTTGTTTTTTTTTAATTTA
1 AGTTATTT-TTTTG-TTTTATTTAATTTA
111630363 AGTTATTTTTTTGTTTTATTTAATTT
1 AGTTATTTTTTTGTTTTATTTAATTT
111630389 TTCTCATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 9 0.38
29 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (27 bp):
AGTTATTTTTTTGTTTTATTTAATTTA
Found at i:111631178 original size:20 final size:20
Alignment explanation
Indices: 111631132--111631169 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
111631122 TATAATATTA
*
111631132 ATATTTAAT-ATTAAATAAG
1 ATATTTATTAATTAAATAAG
111631151 ATATTTATTAATTAAATAA
1 ATATTTATTAATTAAATAA
111631170 TTATATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATTTATTAATTAAATAAG
Found at i:111631198 original size:31 final size:32
Alignment explanation
Indices: 111631149--111631212 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
111631139 ATATTAAATA
*
111631149 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
111631180 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
111631212 A
1 A
111631213 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:111631328 original size:2 final size:2
Alignment explanation
Indices: 111631321--111631350 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
111631311 TTATTATTAT
111631321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111631351 GTAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:111632167 original size:15 final size:15
Alignment explanation
Indices: 111632144--111632191 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
111632134 TATCAAATTT
111632144 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
111632159 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
111632174 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
111632188 ATAT
1 ATAT
111632192 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:111632842 original size:18 final size:19
Alignment explanation
Indices: 111632821--111632861 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
111632811 AATGAAATGA
111632821 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
111632839 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
111632858 GAAA
1 GAAA
111632862 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:111634240 original size:13 final size:14
Alignment explanation
Indices: 111634222--111634262 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
111634212 CTCTCTTAAC
*
111634222 AAAAATTACAAA-A
1 AAAAATTAAAAATA
111634235 AAAAA-TAAAAATA
1 AAAAATTAAAAATA
*
111634248 AAAAATTTAAAATA
1 AAAAATTAAAAATA
111634262 A
1 A
111634263 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 11 0.46
14 8 0.33
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAATTAAAAATA
Found at i:111635724 original size:7 final size:7
Alignment explanation
Indices: 111635712--111635750 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
111635702 TGAGAAAGCC
111635712 AAAAAAG
1 AAAAAAG
111635719 AAAAAAG
1 AAAAAAG
111635726 AAAAAAG
1 AAAAAAG
111635733 AAAGAAAG
1 AAA-AAAG
111635741 AAATAAAG
1 AAA-AAAG
111635749 AA
1 AA
111635751 TTTTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:111635868 original size:38 final size:38
Alignment explanation
Indices: 111635796--111635867 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 38
111635786 TTATTGGGAA
* *
111635796 ATCCCTTATTTGCTGGAGAAAAGAAAAAAGAAAAAGAT
1 ATCCCTTATTTGATGGAAAAAAGAAAAAAGAAAAAGAT
*
111635834 ATCCCTTATTTGAT-TAAAAAAGAAAAAAGAAAAA
1 ATCCCTTATTTGATGGAAAAAAGAAAAAAGAAAAA
111635868 AAAATAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 18 0.58
38 13 0.42
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (38 bp):
ATCCCTTATTTGATGGAAAAAAGAAAAAAGAAAAAGAT
Found at i:111637214 original size:26 final size:25
Alignment explanation
Indices: 111637169--111637234 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
111637159 AATGGAACAT
* * *
111637169 AAATTTAAAGAACAATTTAGATAAAA
1 AAATTTAAATATCAAATTAGA-AAAA
111637195 AAATTTAAATATCAAATTAGAAAAA
1 AAATTTAAATATCAAATTAGAAAAA
* *
111637220 CAATTCAAAT-TCAAA
1 AAATTTAAATATCAAA
111637235 GAATACATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 5 0.14
25 12 0.34
26 18 0.51
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.27
Consensus pattern (25 bp):
AAATTTAAATATCAAATTAGAAAAA
Found at i:111637234 original size:24 final size:26
Alignment explanation
Indices: 111637185--111637234 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
111637175 AAAGAACAAT
*
111637185 TTAGATAAAAAAATTTAAATATCAAA
1 TTAGATAAAAAAATTCAAATATCAAA
*
111637211 TTAGA-AAAACAATTCAAAT-TCAAA
1 TTAGATAAAAAAATTCAAATATCAAA
111637235 GAATACATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (26 bp):
TTAGATAAAAAAATTCAAATATCAAA
Found at i:111637542 original size:21 final size:21
Alignment explanation
Indices: 111637516--111637567 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
111637506 ATGATGGTTG
* * *
111637516 TGAGATTAATTATTGTATTAA
1 TGAGATTAAATATTGCAATAA
*
111637537 TGAGATTAAATATTGCAATAG
1 TGAGATTAAATATTGCAATAA
111637558 TGAGATTAAA
1 TGAGATTAAA
111637568 ACCAATGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.38
Consensus pattern (21 bp):
TGAGATTAAATATTGCAATAA
Found at i:111638193 original size:12 final size:13
Alignment explanation
Indices: 111638169--111638193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111638159 ATATAATAGT
111638169 TAATTCAAAAAAA
1 TAATTCAAAAAAA
111638182 TAATTCAAAAAA
1 TAATTCAAAAAA
111638194 GTGCATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
TAATTCAAAAAAA
Found at i:111641883 original size:6 final size:6
Alignment explanation
Indices: 111641874--111641920 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
111641864 ACTGATTTGC
*
111641874 AAGGGG AA-GGG AAGGGG AAGGGG AAGGAG AAGGGG AATGGGAG AAGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AA-GGG-G AAGG
111641921 CGTTTTCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 5 0.14
6 23 0.64
7 5 0.14
8 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (6 bp):
AAGGGG
Found at i:111641890 original size:11 final size:11
Alignment explanation
Indices: 111641874--111641907 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
111641864 ACTGATTTGC
111641874 AAGGGGAAGGG
1 AAGGGGAAGGG
111641885 AAGGGGAAGGGG
1 AAGGGGAA-GGG
*
111641897 AAGGAGAAGGG
1 AAGGGGAAGGG
111641908 GAATGGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (11 bp):
AAGGGGAAGGG
Found at i:111641896 original size:17 final size:18
Alignment explanation
Indices: 111641874--111641920 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
111641864 ACTGATTTGC
111641874 AAGGGGAAGG-GAAGGGG
1 AAGGGGAAGGAGAAGGGG
111641891 AAGGGGAAGGAGAAGGGG
1 AAGGGGAAGGAGAAGGGG
111641909 AATGGGAGAAGG
1 AA-GGG-GAAGG
111641921 CGTTTTCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.37
18 9 0.33
19 3 0.11
20 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (18 bp):
AAGGGGAAGGAGAAGGGG
Found at i:111645693 original size:28 final size:28
Alignment explanation
Indices: 111645653--111645708 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
111645643 CTGTCAACAA
111645653 TTACAGCAGATGAAGTGTACATAGCTTT
1 TTACAGCAGATGAAGTGTACATAGCTTT
111645681 TTACAGCAGATGAAGTGTACATAGCTTT
1 TTACAGCAGATGAAGTGTACATAGCTTT
111645709 AAAAGGGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (28 bp):
TTACAGCAGATGAAGTGTACATAGCTTT
Found at i:111649052 original size:3 final size:3
Alignment explanation
Indices: 111648983--111649033 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
111648973 GGGACCACTC
111648983 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
111649031 TAT
1 TAT
111649034 ATTTTTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:111649065 original size:15 final size:14
Alignment explanation
Indices: 111648983--111649065 Score: 87
Period size: 15 Copynumber: 5.6 Consensus size: 14
111648973 GGGACCACTC
111648983 TATTATTATTATTAT
1 TATTA-TATTATTAT
111648998 TATTATTATTATTAT
1 TATTA-TATTATTAT
111649013 TATTATTATTATTAT
1 TATTA-TATTATTAT
*
111649028 TATTATATTTTTAAT
1 TATTATATTATT-AT
*
111649043 AATT-TATTATGTAT
1 TATTATATTAT-TAT
*
111649057 TAATATATT
1 TATTATATT
111649066 CATTTTAAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
14 15 0.25
15 45 0.75
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:111650638 original size:27 final size:28
Alignment explanation
Indices: 111650578--111650643 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
111650568 CGCTATATGT
*
111650578 AACGCCGCTAAAGAGCAGGACTTAAAAA
1 AACGCCGCTAAAGACCAGGACTTAAAAA
*
111650606 AGCGCCGCTAAAGACCAGGAC-TAAAAA
1 AACGCCGCTAAAGACCAGGACTTAAAAA
111650633 AACGCCGCTAA
1 AACGCCGCTAA
111650644 TTTGCCCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.09
Consensus pattern (28 bp):
AACGCCGCTAAAGACCAGGACTTAAAAA
Found at i:111656482 original size:9 final size:9
Alignment explanation
Indices: 111656468--111656543 Score: 71
Period size: 9 Copynumber: 8.1 Consensus size: 9
111656458 TTTAAGGAAA
*
111656468 TTATGTGAG
1 TTATGTAAG
111656477 TTATGTAAGTTG
1 TTATGTAA---G
*
111656489 TTATGTAAA
1 TTATGTAAG
111656498 TTATGTAAG
1 TTATGTAAG
* *
111656507 TTATATGAG
1 TTATGTAAG
111656516 TTATGTAAG
1 TTATGTAAG
*
111656525 TTATGTAAT
1 TTATGTAAG
*
111656534 TTATTTAAG
1 TTATGTAAG
111656543 T
1 T
111656544 AATATTCAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 45 0.83
12 9 0.17
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:111660105 original size:83 final size:83
Alignment explanation
Indices: 111659959--111660138 Score: 263
Period size: 83 Copynumber: 2.2 Consensus size: 83
111659949 GTGTTTTTAG
* * * *
111659959 GATAGTGCCACTAATTCCTAAATCGTGCCACATAAAATGACGTATTTTCATTCGGTTTCTCATAT
1 GATAGCGCCACTAATTCCTAAATCGCGCCACATAAAACGACGTATTTTCATTCGATTTCTCATAT
*
111660024 TCTTAGTGGCATTTATAA
66 TATTAGTGGCATTTATAA
* * *
111660042 GGTAGCGCCACTAATTCCTAAA-CGCGCCACATAAAACGATGTAGTTTTCATTCGATTTTTCATA
1 GATAGCGCCACTAATTCCTAAATCGCGCCACATAAAACGACGTA-TTTTCATTCGATTTCTCATA
*
111660106 TTATTAGTGGCGTTTATAA
65 TTATTAGTGGCATTTATAA
111660125 GATAGCGCCACTAA
1 GATAGCGCCACTAA
111660139 ATCCACTACC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 18 0.21
83 68 0.79
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (83 bp):
GATAGCGCCACTAATTCCTAAATCGCGCCACATAAAACGACGTATTTTCATTCGATTTCTCATAT
TATTAGTGGCATTTATAA
Found at i:111660159 original size:83 final size:82
Alignment explanation
Indices: 111659959--111660164 Score: 218
Period size: 83 Copynumber: 2.5 Consensus size: 82
111659949 GTGTTTTTAG
* * ** * * *
111659959 GATAGTGCCACTAATTCCTAAATCGTGCCACATAAAATGACGTATTTTCATTCGGTTTCTCATAT
1 GATAGCGCCACTAAATCCTAAA-CCCGCCAAATAAAACGACGTATTTTCATTCGATTTCTCATAT
*
111660024 TCTTAGTGGCATTTATAA
65 TATTAGTGGCATTTATAA
* * * * * *
111660042 GGTAGCGCCACTAATTCCTAAACGCGCCACATAAAACGATGTAGTTTTCATTCGATTTTTCATAT
1 GATAGCGCCACTAAATCCTAAACCCGCCAAATAAAACGACGTA-TTTTCATTCGATTTCTCATAT
*
111660107 TATTAGTGGCGTTTATAA
65 TATTAGTGGCATTTATAA
* *
111660125 GATAGCGCCACTAAATCC-ACTACCCGCGAAAT-AAACGACG
1 GATAGCGCCACTAAATCCTA-AACCCGCCAAATAAAACGACG
111660165 ACGTTTCAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
82 26 0.25
83 79 0.75
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (82 bp):
GATAGCGCCACTAAATCCTAAACCCGCCAAATAAAACGACGTATTTTCATTCGATTTCTCATATT
ATTAGTGGCATTTATAA
Found at i:111660489 original size:15 final size:14
Alignment explanation
Indices: 111660469--111660522 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
111660459 AATCCCAAAA
111660469 CCAATACACTAAACC
1 CCAATACACTAAA-C
*
111660484 CCAATACCCTAAAC
1 CCAATACACTAAAC
* *
111660498 CCTATAGACTAAAC
1 CCAATACACTAAAC
111660512 CCAATAC-CTAA
1 CCAATACACTAA
111660523 TCCTTAAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 4 0.12
14 17 0.52
15 12 0.36
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (14 bp):
CCAATACACTAAAC
Found at i:111660572 original size:21 final size:20
Alignment explanation
Indices: 111660507--111660572 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
111660497 CCCTATAGAC
*
111660507 TAAACCCAATACCTAATCCT
1 TAAACCCAATACCTAAACCT
** * *
111660527 TAAACCTTATAAACTAAA-TT
1 TAAACCCAAT-ACCTAAACCT
111660547 CTAAACCCAATACCCTAAACCT
1 -TAAACCCAATA-CCTAAACCT
111660569 TAAA
1 TAAA
111660573 TTTTAAACCT
Statistics
Matches: 33, Mismatches: 9, Indels: 7
0.67 0.18 0.14
Matches are distributed among these distances:
20 10 0.30
21 22 0.67
22 1 0.03
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACCCAATACCTAAACCT
Found at i:111661863 original size:39 final size:40
Alignment explanation
Indices: 111661820--111661904 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
111661810 GGATTAATAT
*
111661820 TTTAGCGGAGTTTG-AGAAAAACGCCCCTATAGGTCGACC
1 TTTAGCGGAGTTTGTAGAAAAACGCCCCTAAAGGTCGACC
* ** *
111661859 TTTAGCGGCGTTTGTTTAAAAACGCCGCTAAAGGTCGACC
1 TTTAGCGGAGTTTGTAGAAAAACGCCCCTAAAGGTCGACC
*
111661899 TATAGC
1 TTTAGC
111661905 AGCGTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (40 bp):
TTTAGCGGAGTTTGTAGAAAAACGCCCCTAAAGGTCGACC
Found at i:111661894 original size:40 final size:40
Alignment explanation
Indices: 111661836--111661929 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
111661826 GGAGTTTGAG
* * * *
111661836 AAAAACGCCCCTATAGGTCGACCTTTAGCGGCGTTTGTTT
1 AAAAACGCCACTAAAGGTCGACCTATAGCAGCGTTTGTTT
* *
111661876 AAAAACGCCGCTAAAGGTCGACCTATAGCAGCGTTTTTTT
1 AAAAACGCCACTAAAGGTCGACCTATAGCAGCGTTTGTTT
**
111661916 GTAAACGCCACTAA
1 AAAAACGCCACTAA
111661930 TACTCTATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (40 bp):
AAAAACGCCACTAAAGGTCGACCTATAGCAGCGTTTGTTT
Found at i:111662826 original size:25 final size:26
Alignment explanation
Indices: 111662792--111662842 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
111662782 AAGCCCTTTT
*
111662792 TTTTTTTCTTGC-TTTTAAAGAAAAC
1 TTTTGTTCTTGCTTTTTAAAGAAAAC
*
111662817 TTTTGTTCTTTCTTTTTAAAGAAAAC
1 TTTTGTTCTTGCTTTTTAAAGAAAAC
111662843 CCTTAATGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (26 bp):
TTTTGTTCTTGCTTTTTAAAGAAAAC
Found at i:111671964 original size:6 final size:6
Alignment explanation
Indices: 111671955--111671986 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
111671945 CTCTTGACCG
111671955 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GT
1 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GT
111671987 TGAGAGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTGGCT
Found at i:111681061 original size:5 final size:5
Alignment explanation
Indices: 111681053--111681080 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
111681043 ATTATTCCGC
111681053 CTTGG CTTGG CTTGG CTTGG CTTGG CTT
1 CTTGG CTTGG CTTGG CTTGG CTTGG CTT
111681081 ATGGTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.36, T:0.43
Consensus pattern (5 bp):
CTTGG
Found at i:111683739 original size:17 final size:19
Alignment explanation
Indices: 111683707--111683741 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
111683697 AACAAACCAT
111683707 TAATAATATAATTAAAATA
1 TAATAATATAATTAAAATA
111683726 TAATAA-AT-ATTAAAAT
1 TAATAATATAATTAAAAT
111683742 TTGTTCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAATATAATTAAAATA
Found at i:111686132 original size:27 final size:26
Alignment explanation
Indices: 111686101--111686185 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
111686091 TTAGTTTACC
* *
111686101 AAATTACTGAAATACCTTCGACTTGTA
1 AAATTACTCAAATACC-TCGATTTGTA
* *
111686128 AAATTAC-CAAAGTACCCCCGATTTATA
1 AAATTACTCAAA-TA-CCTCGATTTGTA
*
111686155 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTCAAATA-CCTCGATTTGTA
111686182 AAAT
1 AAAT
111686186 CATTGAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 3 0.06
27 39 0.81
28 6 0.12
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (26 bp):
AAATTACTCAAATACCTCGATTTGTA
Found at i:111686238 original size:27 final size:27
Alignment explanation
Indices: 111686200--111686482 Score: 332
Period size: 27 Copynumber: 10.3 Consensus size: 27
111686190 GAAATAAGAT
*
111686200 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* *
111686227 AGAATTACCATTTTACCCCCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* * *
111686254 AAAATTACTGTTTTACCCTCGATGTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* *
111686281 AGAATTATCGTTTTACCCTTGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* *
111686308 AGAATTACCGTTTTACCATCGATTTAT
1 AGAATTACCGTTTTACCCTCGATTTAC
**
111686335 AGAATTACTATTTTACCCTCGATTTACAGTTAC
1 AGAATTACCGTTTTACCCTCGA--T----TTAC
*
111686368 AGAATTACCGTTTTACCCTCGATTTAT
1 AGAATTACCGTTTTACCCTCGATTTAC
* * * *
111686395 AGAATTATCATTTTACCATCGATTTAT
1 AGAATTACCGTTTTACCCTCGATTTAC
111686422 AGAATTACCGTTTTACCCTCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* *
111686449 AGAATTACTGTTTTATCCTCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
*
111686476 AAAATTA
1 AGAATTA
111686483 TTGAAATACC
Statistics
Matches: 218, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
27 193 0.89
29 1 0.00
31 1 0.00
33 23 0.11
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (27 bp):
AGAATTACCGTTTTACCCTCGATTTAC
Found at i:111686307 original size:81 final size:81
Alignment explanation
Indices: 111686200--111686482 Score: 368
Period size: 81 Copynumber: 3.4 Consensus size: 81
111686190 GAAATAAGAT
* ** * *
111686200 AGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCCCGATTTACAAAATTACTGT
1 AGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCATCGATTTATAGAATTACTGT
111686265 TTTACCCTCGATGTAC
66 TTTACCCTCGATGTAC
* * * *
111686281 AGAATTATCGTTTTACCCTTGATTTACAGAATTACCGTTTTACCATCGATTTATAGAATTACTAT
1 AGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCATCGATTTATAGAATTACTGT
111686346 TTTACCCTCGATTTACAGTTAC
66 TTTACCCTCGA--T---G-TAC
* * *
111686368 AGAATTACCGTTTTACCCTCGATTTATAGAATTATCATTTTACCATCGATTTATAGAATTACCGT
1 AGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCATCGATTTATAGAATTACTGT
*
111686433 TTTACCCTCGATTTAC
66 TTTACCCTCGATGTAC
* * *
111686449 AGAATTACTGTTTTATCCTCGATTTACAAAATTA
1 AGAATTACCGTTTTACCCTCGATTTACAGAATTA
111686483 TTGAAATACC
Statistics
Matches: 175, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
81 100 0.57
83 1 0.01
85 1 0.01
86 1 0.01
87 72 0.41
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (81 bp):
AGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCATCGATTTATAGAATTACTGT
TTTACCCTCGATGTAC
Found at i:111686426 original size:114 final size:109
Alignment explanation
Indices: 111686198--111686479 Score: 386
Period size: 114 Copynumber: 2.6 Consensus size: 109
111686188 TTGAAATAAG
* * *
111686198 ATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCCCGATTTAC-AAAATTAC
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAAATTAC
* * * *
111686262 TGTTTTACCCTCGATGTACAGAATTATCGTTTTACCCTTGATTT
66 CGTTTTACCCTCGATGTACAGAATTATCATTTTACCATCGATTT
* * *
111686306 ACAGAATTACCGTTTTACCATCGATTTATAGAATTACTATTTTACCCTCGATTTACAGTTACAGA
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACA---A-A-A
* *
111686371 ATTACCGTTTTACCCTCGATTTATAGAATTATCATTTTACCATCGATTT
61 ATTACCGTTTTACCCTCGATGTACAGAATTATCATTTTACCATCGATTT
* *
111686420 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTATCCTCGATTTACAAAA
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAA
111686480 TTATTGAAAT
Statistics
Matches: 151, Mismatches: 17, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
108 50 0.33
109 1 0.01
110 1 0.01
111 1 0.01
112 1 0.01
113 1 0.01
114 96 0.64
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (109 bp):
ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAAATTAC
CGTTTTACCCTCGATGTACAGAATTATCATTTTACCATCGATTT
Found at i:111686494 original size:141 final size:141
Alignment explanation
Indices: 111686223--111686482 Score: 353
Period size: 141 Copynumber: 1.8 Consensus size: 141
111686213 TACCCTCGAT
* *
111686223 TTACAGAATTACCATTTTACCCCCGATTTACAAAATTACTGTTTTACCCTCGATGTACAGAATTA
1 TTACAGAATTACCATTTTACCCCCGATTTACAAAATTACTATTTTACCATCGATGTACAGAATTA
* * * * **
111686288 TCGTTTTACCCTTGATTTACAGAATTACCGTTTTACCATCGATTTATAGAATTACTATTTTACCC
66 CCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCATCGATTTACAAAATTACTATAATACCC
111686353 TCGATTTACAG
131 TCGATTTACAG
* * * * * *
111686364 TTACAGAATTACCGTTTTACCCTCGATTTATAGAATTA-TCATTTTACCATCGATTTATAGAATT
1 TTACAGAATTACCATTTTACCCCCGATTTACAAAATTACT-ATTTTACCATCGATGTACAGAATT
*
111686428 ACCGTTTTACCCTCGATTTACAGAATTACTGTTTTATCC-TCGATTTACAAAATTA
65 ACCGTTTTACCCTCGATTTACAGAATTACCGTTTTA-CCATCGATTTACAAAATTA
111686483 TTGAAATACC
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
140 1 0.01
141 101 0.97
142 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (141 bp):
TTACAGAATTACCATTTTACCCCCGATTTACAAAATTACTATTTTACCATCGATGTACAGAATTA
CCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCATCGATTTACAAAATTACTATAATACCC
TCGATTTACAG
Found at i:111686516 original size:27 final size:27
Alignment explanation
Indices: 111686486--111686628 Score: 103
Period size: 27 Copynumber: 5.3 Consensus size: 27
111686476 AAAATTATTG
*
111686486 AAATACCCTTAGTTTACAAAATTACCA
1 AAATACCCTTAGTTTATAAAATTACCA
* **
111686513 AAATACCCAT-GATCAATAAAATTACCA
1 AAATACCCTTAG-TTTATAAAATTACCA
* * * * *
111686540 AAATACCCCTGGTTTGTAAAACTACTA
1 AAATACCCTTAGTTTATAAAATTACCA
* * *
111686567 AAATA-CCTCTGGTTTGTAAAATTACTA
1 AAATACCCT-TAGTTTATAAAATTACCA
* * *
111686594 AAATACCCCT-GACTTGTAAAATTACCA
1 AAATACCCTTAG-TTTATAAAATTACCA
111686621 AAATACCC
1 AAATACCC
111686629 CTGATTTGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
26 4 0.04
27 89 0.93
28 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
AAATACCCTTAGTTTATAAAATTACCA
Found at i:111686629 original size:27 final size:27
Alignment explanation
Indices: 111686503--111686683 Score: 195
Period size: 27 Copynumber: 6.7 Consensus size: 27
111686493 CTTAGTTTAC
* ***
111686503 AAAATTACCAAAATACCCATGATCAAT
1 AAAATTACCAAAATACCCCTGATTTGT
*
111686530 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * * *
111686557 AAAACTACTAAAATACCTCTGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* *
111686584 AAAATTACTAAAATACCCCTGACTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
111686611 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * *
111686638 GAAATTATCAAAATA-CTCTCGATTTGT
1 AAAATTACCAAAATACCCCT-GATTTGT
* *
111686665 ATAA-TACCGAAATACCCCT
1 AAAATTACCAAAATACCCCT
111686684 ATAGGGTAGA
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.08
27 119 0.92
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGATTTGT
Found at i:111686713 original size:27 final size:27
Alignment explanation
Indices: 111686669--111686895 Score: 303
Period size: 27 Copynumber: 8.4 Consensus size: 27
111686659 ATTTGTATAA
111686669 TACCGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
* *
111686696 TATCGCAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
111686723 TACCGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
* * *
111686750 TATCGCAATA-CCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
* * * *
111686776 TACCGAAATACTCTTGTAAGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
* * *
111686803 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTATAGGGTAGAAT
* *
111686830 TACGGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
*
111686857 TACTGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAAT
*
111686884 TACCGAGATACC
1 TACCGAAATACC
111686896 TTGTGAGGTA
Statistics
Matches: 177, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 23 0.13
27 154 0.87
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
TACCGAAATACCCCTATAGGGTAGAAT
Found at i:111686751 original size:107 final size:107
Alignment explanation
Indices: 111686669--111686895 Score: 285
Period size: 107 Copynumber: 2.1 Consensus size: 107
111686659 ATTTGTATAA
* * * *
111686669 TACCGAAATACCCCTATAGGGTAGAATTATCGCAATACCCCTATAGGGTAGAATTACCGAAATAC
1 TACCGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATAC
**
111686734 CCCTATAGGGTAGAATTATCGCAATACCCTGTAGGGTAGAAT
66 CCCTATAGGGTAGAATTATCAAAATACCCTGTAGGGTAGAAT
* * * * * *
111686776 TACCGAAATACTCTTGTAAGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACGGAAATAC
1 TACCGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATAC
* * *
111686841 CCCTGTAGGGTAGAATTA-CTGAAATACCCCTATAGGGTAGAAT
66 CCCTATAGGGTAGAATTATC-AAAATA-CCCTGTAGGGTAGAAT
*
111686884 TACCGAGATACC
1 TACCGAAATACC
111686896 TTGTGAGGTA
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
106 1 0.01
107 77 0.75
108 25 0.24
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (107 bp):
TACCGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATAC
CCCTATAGGGTAGAATTATCAAAATACCCTGTAGGGTAGAAT
Found at i:111686895 original size:134 final size:134
Alignment explanation
Indices: 111686669--111686913 Score: 361
Period size: 134 Copynumber: 1.8 Consensus size: 134
111686659 ATTTGTATAA
* *
111686669 TACCGAAATACCCCTATAGGGTAGAATTATCGCAATACCCCTATAGGGTAGAATTACCGAAATAC
1 TACCGAAATACCCCTATAGGGTAGAAATATCGAAATACCCCTATAGGGTAGAATTACCGAAATAC
* *
111686734 CCCTATAGGGTAGAATTATCGCAATACCCTGT-AGGGTAGAATTACCGAAATACTCTTGTAAGGT
66 CCCTATAGGGTAGAATTACCGCAATACCCTGTGA-GGTAAAATTACCGAAATACTCTTGTAAGGT
111686798 AGAAT
130 AGAAT
* * * *
111686803 TACCGAAATACCCTTGTAGGGTAGAAATA-CGGAAATACCCCTGTAGGGTAGAATTACTGAAATA
1 TACCGAAATACCCCTATAGGGTAGAAATATC-GAAATACCCCTATAGGGTAGAATTACCGAAATA
*
111686867 CCCCTATAGGGTAGAATTACCG-AGATACCTTGTGAGGTAAAATTACC
65 CCCCTATAGGGTAGAATTACCGCA-ATACCCTGTGAGGTAAAATTACC
111686914 ATTTTTCCCC
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
133 2 0.02
134 96 0.97
135 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (134 bp):
TACCGAAATACCCCTATAGGGTAGAAATATCGAAATACCCCTATAGGGTAGAATTACCGAAATAC
CCCTATAGGGTAGAATTACCGCAATACCCTGTGAGGTAAAATTACCGAAATACTCTTGTAAGGTA
GAAT
Found at i:111687346 original size:6 final size:6
Alignment explanation
Indices: 111687315--111687402 Score: 74
Period size: 6 Copynumber: 14.3 Consensus size: 6
111687305 TTGCATTCAC
* *
111687315 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
111687364 -TCACCTA ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
111687403 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 4 0.06
6 54 0.82
7 6 0.09
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Done.