Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 29 of 37
Found at i:5070688 original size:13 final size:13
Alignment explanation
Indices: 5070670--5070694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5070660 ATAATGCATA
5070670 GTATCGATACATT
1 GTATCGATACATT
5070683 GTATCGATACAT
1 GTATCGATACAT
5070695 AACCACTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:5070801 original size:13 final size:13
Alignment explanation
Indices: 5070783--5070808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5070773 ACATACAAGA
5070783 TGTATCGATACAT
1 TGTATCGATACAT
5070796 TGTATCGATACAT
1 TGTATCGATACAT
5070809 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5070824 original size:33 final size:32
Alignment explanation
Indices: 5070763--5070830 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
5070753 CCTTAATTGT
5070763 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
5070795 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
5070828 TTG
1 TTG
5070831 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:5072287 original size:154 final size:153
Alignment explanation
Indices: 5072019--5072890 Score: 767
Period size: 154 Copynumber: 5.6 Consensus size: 153
5072009 TGGTGTATGA
* * * * * *
5072019 GTGATAACCTAGG-ATTCGATTCT-AGAAATTACAAAAATGCCCCTATGGGTATACCTTCGACAT
1 GTGACAACCTAGGAATT-GGTTCTAAAAAATTACGAAAATGCCCCTA-GGGGATACCTTCGACGT
* * * *
5072082 GAAAGTATCCTGATAACCCTAAAAGACTTCAAAAA-GATTATAGATAA--GATGAACCCATCCTA
64 AAAAGTAT-C-GAT-ACCCTAAAGGACTT-AAAAAGGATTTTA-A-AAGGGATGAACCTATCCTA
* * ***
5072144 AATACCCACCTTCGGTATAAAAATGAACCTG
123 AATACCCACCTTTGGCATAAAAGCAAACCTG
* * * *
5072175 GTGACAACTTAGGAATTTGTTCTAAAAAATTACGAAGATGCCCCTAGGGGATACTTTCGACGTAA
1 GTGACAACCTAGGAATTGGTTCTAAAAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAA
* *
5072240 AAGTATCGATACCTCTAAAGGACTTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATATCC
66 AAGTATCGATACC-CTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATACCC
* *
5072305 ACCTTTGGCATAAAAACAAACCTA
130 ACCTTTGGCATAAAAGCAAACCTG
* * * * *
5072329 GTGACGACCTAGGAGTTGGTTCCAAAAAATTACGAAAATG-CCCTGAGAGGATACCTTCGATGTA
1 GTGACAACCTAGGAATTGGTTCTAAAAAATTACGAAAATGCCCCT-AGGGGATACCTTCGACGTA
* * *
5072393 AAAGTA-CATGATACCCTTAAAGGACTTAAAAAGGATTTT-AAATGGATAAACCTACCCTAAATA
65 AAAGTATC--GATACCC-TAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATA
*** **
5072456 CCCACCTTCATCATAAAAGCAAACCAC
127 CCCACCTTTGGCATAAAAGCAAACCTG
* * * ** * *
5072483 GTGACAACCTAAGAGTTGGTTTTGGAAAATTA-TAAAGATGCCCAC-AGGGGATACCTTCGATGT
1 GTGACAACCTAGGAATTGGTTCTAAAAAATTACGAAA-ATGCCC-CTAGGGGATACCTTCGACGT
*
5072546 AAAAGTACCCGATACCCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATA
64 AAAAGTA-TCGATA-CCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATA
*
5072611 TCCACCTTTGGCATAAAAGCAAACCTG
127 CCCACCTTTGGCATAAAAGCAAACCTG
* ** * ** * * *
5072638 ATGATGACCTA-AAAGTTGGTTCTAAAAAATTACGAAAATGTTCTTGGGGGATAGCTTCGACGTA
1 GTGACAACCTAGGAA-TTGGTTCTAAAAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTA
* * * * *
5072702 GAAGTACTCAATACCCTTAAAGGACTTACAAAGGATTTTAAATGGGATGAACCTACCCTAAATAC
65 AAAGTA-TCGATACCC-TAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATAC
* * *
5072767 CCACATTTGGCATAAAAGCGAACCCG
128 CCACCTTTGGCATAAAAGCAAACCTG
* * ** * * * * * * *
5072793 GTGAGAACCTAGGACTCAGTTCTAGAGAAATTACAAAAAATGCCCTTAAGAGATACCTTTGACAT
1 GTGACAACCTAGGAATTGGTTCTA-AAAAATTAC-GAAAATGCCCCTAGGGGATACCTTCGACGT
* * *
5072858 AAAAGTATCCGGTACCCCTAAGGGATTTAAAAA
64 AAAAGTAT-CGATA-CCCTAAAGGACTTAAAAA
5072891 CATGAAGAAA
Statistics
Matches: 585, Mismatches: 105, Indels: 51
0.79 0.14 0.07
Matches are distributed among these distances:
152 2 0.00
153 17 0.03
154 239 0.41
155 209 0.36
156 51 0.09
157 64 0.11
158 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (153 bp):
GTGACAACCTAGGAATTGGTTCTAAAAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAA
AAGTATCGATACCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATACCCA
CCTTTGGCATAAAAGCAAACCTG
Found at i:5072718 original size:309 final size:309
Alignment explanation
Indices: 5072200--5072890 Score: 881
Period size: 309 Copynumber: 2.2 Consensus size: 309
5072190 TTTGTTCTAA
* * * *
5072200 AAAATTACGAAGATGCCCCTAGGGGATACTTTCGACGTAAAAGTATCGATACCTCTAAAGGACTT
1 AAAATTACAAAGATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCGATACCCCTAAAGGACTT
5072265 AAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAACAAACCTAG
66 AAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAACAAACCTAG
** *
5072330 TGACGACCTAGGAGTTGGTTCCAAAAAATTACGAAAATGCCCTGAGAGGATACCTTCGATGTAAA
131 TGACGACCTAAAAGTTGGTTCCAAAAAATTACGAAAATGCCCTGAGAGGATACCTTCGACGTAAA
*
5072395 AGTACATGATACCCTTAAAGGACTTAAAAAGGATTTTAAAT-GGATAAACCTACCCTAAATACCC
196 AGTACATAATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATAAACCTACCCTAAATACCC
5072459 ACCTTCATCATAAAAGCAAACCACGTGACAACCTAAGAGTTGGTTTTGG
261 ACCTTCATCATAAAAGCAAACCACGTGACAACCTAAGAGTTGGTTTTGG
* *
5072508 AAAATTATAAAGATGCCCAC-AGGGGATACCTTCGATGTAAAAGTACCCGATACCCCTAAAGGAC
1 AAAATTACAAAGATGCCC-CTAGGGGATACCTTCGACGTAAAAGTA-CCGATACCCCTAAAGGAC
* *
5072572 TTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAGCAAACCT
64 TTAAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAACAAACCT
* * * * * *
5072637 -GATGATGACCTAAAAGTTGGTTCTAAAAAATTACGAAAATGTTCTTG-GGGGATAGCTTCGACG
129 AG-TGACGACCTAAAAGTTGGTTCCAAAAAATTACGAAAATG-CCCTGAGAGGATACCTTCGACG
* * *
5072700 TAGAAGTAC-TCAATACCCTTAAAGGACTTACAAAGGATTTTAAATGGGATGAACCTACCCTAAA
192 TAAAAGTACAT-AATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATAAACCTACCCTAAA
* *** * * * * ** * *
5072764 TACCCACATTTGGCATAAAAGCGAACC-CGGTGAGAACCTAGGACTCAGTTCTAG
256 TACCCACCTTCATCATAAAAGCAAACCAC-GTGACAACCTAAGAGTTGGTTTTGG
* * * * * * * *
5072818 AGAAATTACAAAAAATGCCCTTAAGAGATACCTTTGACATAAAAGTATCCGGTACCCCTAAGGGA
1 A-AAATTAC-AAAGATGCCCCTAGGGGATACCTTCGACGTAAAAGTA-CCGATACCCCTAAAGGA
*
5072883 TTTAAAAA
63 CTTAAAAA
5072891 CATGAAGAAA
Statistics
Matches: 328, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
308 41 0.12
309 169 0.52
310 61 0.19
311 6 0.02
312 51 0.16
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (309 bp):
AAAATTACAAAGATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCGATACCCCTAAAGGACTT
AAAAAAGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAACAAACCTAG
TGACGACCTAAAAGTTGGTTCCAAAAAATTACGAAAATGCCCTGAGAGGATACCTTCGACGTAAA
AGTACATAATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATAAACCTACCCTAAATACCC
ACCTTCATCATAAAAGCAAACCACGTGACAACCTAAGAGTTGGTTTTGG
Found at i:5073460 original size:20 final size:20
Alignment explanation
Indices: 5073438--5073474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5073428 TTTATTCATT
5073438 TTTTA-TTTAATTTATTTAA
1 TTTTACTTTAATTTATTTAA
*
5073457 TTTTACTTTGATTTATTT
1 TTTTACTTTAATTTATTT
5073475 TCGAAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTACTTTAATTTATTTAA
Found at i:5080465 original size:155 final size:155
Alignment explanation
Indices: 5080076--5080490 Score: 396
Period size: 155 Copynumber: 2.7 Consensus size: 155
5080066 TTTGGACATG
* * * * *
5080076 AAAGTATCCCAGTAACCCTAAAGGACTCAAAAA-GATTATAGATGAGATGAACCTATCCTAAATA
1 AAAGTA-CCCAAT-ACCCTAAAGGACTTAAAAAGGATTTTAAATGGGATGAACCTATCCTAAATA
** * *
5080140 CCCACCTTCGGCAT-AAAAGCAGACTTGGTGACAACCTAGGAGTTGGTTCAGGAAAATTACGAAT
64 CCCACCTTCGGCATAAAAAGCAGACCCGGTGACAACCTAGGAGTTGGTTCAGAAAAATTACGAAA
* *
5080204 ATGCTTGTAGGGGATACCTTCGACTTA
129 ATGCTTGTAGGGGATAACTTCGACGTA
* * * *
5080231 AAAGTACCTAATACCCCT-AAGAGACTTAAAAGGGATTTTAAAAGGGATGAACCTATCCTATATA
1 AAAGTACCCAATA-CCCTAAAG-GACTTAAAAAGGATTTTAAATGGGATGAACCTATCCTAAATA
* * * ** * * *** * **
5080295 TCCGCGTTCAACATAAAAAG-GGGCCCGGTGATGGCCTAGTAGTTGGTTTTGAAAAATTACGAAA
64 CCCACCTTCGGCATAAAAAGCAGACCCGGTGACAACCTAGGAGTTGGTTCAGAAAAATTACGAAA
* * *
5080359 ATGCCTT-TGGGGGCTAACTTTGACGTA
129 ATG-CTTGTAGGGGATAACTTCGACGTA
*
5080386 AAAGTACCCGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGAACCTA-CCATAAATA
1 AAAGTACCCAATACCC-TAAAGGACTTAAAAAGGATTTTAAATGGGATGAACCTATCC-TAAATA
* *
5080450 CCCACCTTTGGCAT-AAAAGCTA-ACCCGATGACAACCTAGGA
64 CCCACCTTCGGCATAAAAAGC-AGACCCGGTGACAACCTAGGA
5080491 TTCGTTTCTA
Statistics
Matches: 201, Mismatches: 49, Indels: 20
0.74 0.18 0.07
Matches are distributed among these distances:
153 4 0.02
154 26 0.13
155 160 0.80
156 11 0.05
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (155 bp):
AAAGTACCCAATACCCTAAAGGACTTAAAAAGGATTTTAAATGGGATGAACCTATCCTAAATACC
CACCTTCGGCATAAAAAGCAGACCCGGTGACAACCTAGGAGTTGGTTCAGAAAAATTACGAAAAT
GCTTGTAGGGGATAACTTCGACGTA
Found at i:5085706 original size:22 final size:21
Alignment explanation
Indices: 5085681--5085736 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
5085671 TGTATTCTAA
5085681 TTTTCTCTCTATCTT-CTTCTCT
1 TTTTCTCTCT-T-TTCCTTCTCT
*
5085703 TTTTCTTTCTTTTCCTTCTCT
1 TTTTCTCTCTTTTCCTTCTCT
5085724 TTTT-TCTCTTTTC
1 TTTTCTCTCTTTTC
5085737 TTTTTCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.32
21 12 0.39
22 9 0.29
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTCTTTTCCTTCTCT
Found at i:5086443 original size:164 final size:161
Alignment explanation
Indices: 5086201--5086763 Score: 506
Period size: 154 Copynumber: 3.5 Consensus size: 161
5086191 CAATATATAC
* * * * *
5086201 AAAAATTGAAAATTCATG-AAATAATTTGAATTTTTCAAAATTGATTTAATGTGAAATT-AATAA
1 AAAAAATGAAAA-ACATGAAAATAA-ATGAATTTTTCAAAACTGATTTAATATG-AATTAAATAA
* * * * *
5086264 CAATA-TTAGATGAATTTCAAAAATTTTAAACTAAGAAAAATCCTCCCAAAAACATTTACGGAGT
63 TAATATTTA-ATGAATTTCAAAAATTATAAACTAAGAAAAATCCACCCGAAAATATTTACGGAGT
*
5086328 AGAAAACTCAGTTTTTTAGAAATAGGGAGATTTCAA
127 AGAAAACTCAGTTTTTTAGAAA-AGAGAGATTTCAA
* ** *
5086364 AAAAAATGAAAAACCCAGGAAAATAAATGAATTTTTTGAAACTGATTTAATATGAATTAAACAAT
1 AAAAAATGAAAAA--CATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAAT
* * * *
5086429 AATATTTAATGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCCCGAAAATATTTACAGAGTAA
64 AATATTTAATGAATTTCAAAAATTATAAACTAAGAAAAATCCACCCGAAAATATTTACGGAGT-A
* * * * *
5086494 AAAAATTCA-TTTTTCAAAAAAGAGAAATTT---
128 GAAAACTCAGTTTTTTAGAAAAGAGAGATTTCAA
* * * * *
5086524 ---TAAGGAAAAA-ATGAAAATGAATGAATTTTTGAAAAATGATTTAATATGAATTAAATAATAA
1 AAAAAATGAAAAACATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAA
* * * * * *
5086585 TATTTGATGAATTTCAAAAATTATAAACCAAAAAAAATGCACCCGAAAATATTTACGAAGCAGAA
66 TATTTAATGAATTTCAAAAATTATAAACTAAGAAAAATCCACCCGAAAATATTTACGGAGTAGAA
* * *
5086650 AACTCTGTTTTTT-GAAAACAAAAGAATTTCAA
131 AACTCAGTTTTTTAGAAAA-GAGAG-ATTTCAA
* * * * *
5086682 GAAAAAATGAAGAACATATAAAAATTAATGAATCTTTCAAAACTGATTTAATGGTG-ATTAAATA
1 -AAAAAATGAA-AA-ACATGAAAATAAATGAATTTTTCAAAACTGATTTAAT-ATGAATTAAATA
5086746 ATAATATTTGAA-GAATTT
62 ATAATATTT-AATGAATTT
5086764 TGGTGTTTGA
Statistics
Matches: 321, Mismatches: 58, Indels: 40
0.77 0.14 0.10
Matches are distributed among these distances:
153 11 0.03
154 103 0.32
155 4 0.01
157 8 0.02
162 5 0.02
163 25 0.08
164 92 0.29
165 70 0.22
166 3 0.01
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (161 bp):
AAAAAATGAAAAACATGAAAATAAATGAATTTTTCAAAACTGATTTAATATGAATTAAATAATAA
TATTTAATGAATTTCAAAAATTATAAACTAAGAAAAATCCACCCGAAAATATTTACGGAGTAGAA
AACTCAGTTTTTTAGAAAAGAGAGATTTCAA
Found at i:5087965 original size:20 final size:20
Alignment explanation
Indices: 5087940--5087993 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
5087930 CTACCACTAT
*
5087940 TTGTATCGATACATAGT-ACA
1 TTGTATCGATACATAATGA-A
*
5087960 TTGTATCGATACATAATGAG
1 TTGTATCGATACATAATGAA
5087980 TTGTATCGATACAT
1 TTGTATCGATACAT
5087994 TACTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATAATGAA
Found at i:5095918 original size:20 final size:20
Alignment explanation
Indices: 5095876--5095914 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5095866 CATGTAAATG
* *
5095876 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
5095896 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
5095915 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:5095983 original size:13 final size:13
Alignment explanation
Indices: 5095965--5095990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5095955 CAATTTTTTG
5095965 TGTATCGATACAT
1 TGTATCGATACAT
5095978 TGTATCGATACAT
1 TGTATCGATACAT
5095991 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5096729 original size:21 final size:21
Alignment explanation
Indices: 5096688--5096731 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5096678 CTCTCCTTTA
* *
5096688 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
5096709 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
5096730 TC
1 TC
5096732 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:5098553 original size:13 final size:13
Alignment explanation
Indices: 5098535--5098560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5098525 ATAATCACCC
5098535 TGTATCGATACAA
1 TGTATCGATACAA
5098548 TGTATCGATACAA
1 TGTATCGATACAA
5098561 AGAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5098572 original size:21 final size:21
Alignment explanation
Indices: 5098546--5098625 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
5098536 GTATCGATAC
5098546 AATGTATCGATACAAAGAAAA
1 AATGTATCGATACAAAGAAAA
** *
5098567 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA----AA
*
5098592 AATGTATCGATACACAG-AAA
1 AATGTATCGATACAAAGAAAA
*
5098612 CATGTATCGATACA
1 AATGTATCGATACA
5098626 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 14 0.29
21 17 0.35
24 1 0.02
25 16 0.33
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (21 bp):
AATGTATCGATACAAAGAAAA
Found at i:5100660 original size:15 final size:15
Alignment explanation
Indices: 5100640--5100670 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5100630 ATTTCGTTTG
*
5100640 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5100655 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5100670 G
1 G
5100671 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5101534 original size:13 final size:13
Alignment explanation
Indices: 5101516--5101540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5101506 CATAAAATGT
5101516 TGTATCGATACAA
1 TGTATCGATACAA
5101529 TGTATCGATACA
1 TGTATCGATACA
5101541 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5101538 original size:33 final size:33
Alignment explanation
Indices: 5101496--5101562 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5101486 TTCAACAATT
5101496 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5101529 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5101562 T
1 T
5101563 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5101621 original size:13 final size:13
Alignment explanation
Indices: 5101603--5101627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5101593 ATTACTCAAA
5101603 TGTATCGATACAT
1 TGTATCGATACAT
5101616 TGTATCGATACA
1 TGTATCGATACA
5101628 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5101729 original size:52 final size:52
Alignment explanation
Indices: 5101636--5101763 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
5101626 CACTGATCTT
*
5101636 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
5101687 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
5101739 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
5101764 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:5109990 original size:58 final size:60
Alignment explanation
Indices: 5109873--5110450 Score: 363
Period size: 71 Copynumber: 9.1 Consensus size: 60
5109863 GCATTTTTTC
5109873 TTTAAAGCCCACAACTCCGTGGCACCTTGT-TCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTT-TAT-CTTTTAAGTCCACAACTCCGTGGCACCCT
* *
5109934 TTTAAAGCCCACAATTCCGTGGCACC-TCATC-TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTATCTTTTAAGTCCACAACTCCGTGGCACCCT
* * * *
5109992 TTTAAAGCCCACAATTCTGTGGCACTTTTTTTATC-TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAAGCCCACAACTCCGTGGCAC---CTTTATCTTTTAAGTCCACAACTCCGTGGCACCCT
* *
5110054 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTATCT-TTT-AAGTCCACAACTCCGTGGCA--C----
5110118 TCTCT
58 -C-CT
* *
5110123 TTTCAAAGCCCACAACTCCGTGGCCCCTTCT-TCTTTTCAAAGCCCACAACTCCGTGGCACCTTC
1 TTT-AAAGCCCACAACTCCGTGGCACCTT-TATCTTTT--AAGTCCACAACTCCGTGGCA-C--C
5110187 TTCT
59 --CT
** * * *
5110191 TTTAAAGCCCACAACTTTGTGGCACTCTTTTTTTCCTTTTCAAAGCCCACAACTCTGTGGCACCT
1 TTTAAAGCCCACAACTCCGTGGCAC-C--TTTAT-CTTTT--AAGTCCACAACTCCGTGGCACC-
5110256 TTTTCT
59 ----CT
* ** * ** ** *
5110262 TTTAAAGCCCACAACTCTGTGGCACCTACAAC-TTT--GT-GGC-ACTCTC-TTTC-CCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTATCTTTTAAGTCCACAACTC-CGTGGCACCCT
* *
5110316 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTATCT-TTT-AAGTCCACAACTCCGTGGCA-------
5110381 TCCCT
57 -CCCT
* * * *
5110386 TTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTATCTTTT-AAGTCCACAACTCCGTGGCACCCT
5110448 TTT
1 TTT
5110451 TCCCTTTTAA
Statistics
Matches: 426, Mismatches: 43, Indels: 95
0.76 0.08 0.17
Matches are distributed among these distances:
54 28 0.07
56 3 0.01
58 56 0.13
59 4 0.01
60 13 0.03
61 70 0.16
62 40 0.09
63 1 0.00
66 3 0.01
67 23 0.05
68 10 0.02
69 5 0.01
70 39 0.09
71 130 0.31
72 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (60 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTATCTTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:5110100 original size:34 final size:33
Alignment explanation
Indices: 5109841--5110483 Score: 505
Period size: 34 Copynumber: 19.9 Consensus size: 33
5109831 TCAAATACCT
* * * *
5109841 TTTTAAAGTCCACGACTCAGTGGCA-TTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
5109873 -TTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
1 TTTTAAAGCCCACAACTCCGTGGCACCTT-TTTC
*
5109906 TTTT-AAGTCCACAACTCCGTGGCACC-----C
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* **
5109933 TTTTAAAGCCCACAATTCCGTGGCACC-TCATC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
5109965 -TTT-AAGTCCACAACTCCGTGGCACC-----C
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
5109991 TTTTAAAGCCCACAATTCTGTGGCA-CTTTTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
5110023 TATCTTTAAGTCCACAACTCCGTGGCACC-----C
1 T-T-TTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
5110053 GTTT-AAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
5110085 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 T-TTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TC
* *
5110122 TTTTCAAAGCCCACAACTCCGTGGCCCCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
*
5110156 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
**
5110190 TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-C--TTTTT-C
*
5110227 TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* ****
5110261 TTTTAAAGCCCACAACTCTGTGGCACCTACAAC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * **
5110294 TTTGT---G-GCAC-TCT-C-TTTC-CC---TT-
1 TTT-TAAAGCCCACAACTCCGTGGCACCTTTTTC
*
5110316 TTTA-AAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
5110348 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 T-TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C
*
5110385 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
5110419 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C
* *
5110455 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTT
5110484 CTCCCTTCCT
Statistics
Matches: 506, Mismatches: 50, Indels: 108
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.01
23 1 0.00
24 3 0.01
25 2 0.00
26 4 0.01
27 34 0.07
28 41 0.08
29 3 0.01
30 23 0.05
31 27 0.05
32 6 0.01
33 100 0.20
34 124 0.25
35 35 0.07
36 25 0.05
37 54 0.11
38 21 0.04
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:5110145 original size:71 final size:67
Alignment explanation
Indices: 5109839--5110288 Score: 387
Period size: 71 Copynumber: 6.9 Consensus size: 67
5109829 CTTCAAATAC
* * * * *
5109839 CTTTTTAAAGTCCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCACAACTCCGTGGCACCTTG
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTT-
*
5109902 TTC
65 TTT
* * *
5109905 CTTTT--AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCCGTGGCACC-TC
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
*
5109962 AT
66 TT
* * *
5109964 C-TTT--AAGTCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCTGTGGCA-CTTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
5110020 TT
66 TT
** * *
5110022 -TTATCTTTAAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAACTCCGTGGCACCT
1 CTT-T-TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCT
5110080 TTTT
64 TTTT
*
5110084 CTGTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACAACTCCGTGGCC
1 CT-TTTCAAAGCCCACAACTCCGTGGCAC-C-TTTT-TCTTTT-AAAGCCCACAACTCCGTGGCA
*
5110148 CCTTCTT
61 CCTTTTT
* **
5110155 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C--
5110220 TTTTT
63 TTTTT
* *
5110225 CCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCT
1 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCT
5110289 ACAACTTTGT
Statistics
Matches: 332, Mismatches: 26, Indels: 50
0.81 0.06 0.12
Matches are distributed among these distances:
57 1 0.00
58 53 0.16
59 2 0.01
60 3 0.01
61 63 0.19
62 34 0.10
63 2 0.01
64 19 0.06
66 5 0.02
67 19 0.06
68 8 0.02
69 7 0.02
70 9 0.03
71 107 0.32
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (67 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTT
TT
Found at i:5110223 original size:105 final size:100
Alignment explanation
Indices: 5109932--5110288 Score: 400
Period size: 105 Copynumber: 3.6 Consensus size: 100
5109922 CCGTGGCACC
* * *
5109932 CTTTTAAAGCCCACAATTCCGTGGCACCTCATC-TTTAAGTCCACAACTCCGTGGCA-C--C--C
1 CTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTTAAGCCCACAACTCCGTGGCACCTTCTTC
5109991 TTTTAAAGCCCACAA-TTCTGTGGCACT-TTTTTTAT
66 TTTTAAAGCCCACAACTT-TGTGGCACTCTTTTTT-T
* * *
5110026 C-TTT-AAGTCCACAACTCCGTGGCA-C-C--CGTTTAAGCCCACAACTCCGTGGCACCTTTTTC
1 CTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTTAAGCCCACAACTCCGTGGCACCTTCTTC
** *
5110085 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
66 T-TTTAAAGCCCACAACTTTGTGGCACTCTTTTTTT
*
5110121 CTTTTCAAAGCCCACAACTCCGTGGCCCCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTT
1 CTTTT-AAAGCCCACAACTCCGTGGCACC-TCTTCTTTT--AAGCCCACAACTCCGTGGCACCTT
5110186 CTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTT
62 CTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTT
* * *
5110225 CCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCT
1 -CTTTT-AAAGCCCACAACTCCGTGGCACC-TCTTCTTTT-AAGCCCACAACTCCGTGGCACCT
5110289 ACAACTTTGT
Statistics
Matches: 225, Mismatches: 18, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
88 1 0.00
89 22 0.10
90 2 0.01
91 1 0.00
92 18 0.08
93 3 0.01
94 3 0.01
95 24 0.11
96 9 0.04
98 18 0.08
99 1 0.00
101 1 0.00
103 4 0.02
104 54 0.24
105 64 0.28
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (100 bp):
CTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTTAAGCCCACAACTCCGTGGCACCTTCTTC
TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTT
Found at i:5110348 original size:87 final size:89
Alignment explanation
Indices: 5110201--5110374 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 89
5110191 TTTAAAGCCC
* * *
5110201 ACAACTTTGTGGCACTCTTTTTTTCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCT-TTT
1 ACAACTTTGTGGCACTCTTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
*
5110265 AAAGCCCACAACTCTGTGGCACCT
66 AAAGCCCACAACTCCGTGGCACCT
*
5110289 ACAACTTTGTGGCACTC-TCTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
1 ACAACTTTGTGGCACTCTTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
5110353 AAAGCCCACAACTCCGTGGCAC
66 AAAGCCCACAACTCCGTGGCAC
5110375 TCTTTTTCCC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 39 0.49
88 41 0.51
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (89 bp):
ACAACTTTGTGGCACTCTTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
AAAGCCCACAACTCCGTGGCACCT
Found at i:5110433 original size:104 final size:104
Alignment explanation
Indices: 5110315--5110503 Score: 292
Period size: 104 Copynumber: 1.8 Consensus size: 104
5110305 CTCTTTCCCT
**
5110315 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCA-TCTT
* *
5110379 TTTCCCTT-TTCAAAGCCCACAACTCCGTGGCACTTTTTTC
65 TCTCCCTTCCT-AAAGCCCACAACTCCGTGGCACTTTTTTC
* *
5110419 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCATCTTT
5110484 CTCCCTTCCTAAAGCCCACA
66 CTCCCTTCCTAAAGCCCACA
5110504 CAAGTCGGTG
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
104 47 0.61
105 30 0.39
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (104 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCATCTTT
CTCCCTTCCTAAAGCCCACAACTCCGTGGCACTTTTTTC
Found at i:5110443 original size:158 final size:158
Alignment explanation
Indices: 5110155--5110444 Score: 492
Period size: 158 Copynumber: 1.8 Consensus size: 158
5110145 GCCCCTTCTT
**
5110155 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
* * *
5110220 TTTTTCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
5110285 ACCTACAACTTTGTGGCACTCTCTTTCC
131 ACCTACAACTTTGTGGCACTCTCTTTCC
* *
5110313 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC-
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTAAAGCCCACAACTCCGTGGCACTCT
*
5110377 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGG
65 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
5110442 CAC
130 CAC
5110445 TCTTTTTCCC
Statistics
Matches: 123, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
158 98 0.80
159 25 0.20
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (158 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
ACCTACAACTTTGTGGCACTCTCTTTCC
Found at i:5110452 original size:70 final size:70
Alignment explanation
Indices: 5110297--5110483 Score: 306
Period size: 71 Copynumber: 2.7 Consensus size: 70
5110287 CTACAACTTT
* *
5110297 GTGGCACTCTCTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1 GTGGCACTCTTTTTCCC-TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCAC
5110362 AACTCC
65 AACTCC
5110368 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-TTTAAAGCCCAC
1 GTGGCACTCTTTTTCCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCAC
5110432 AACTCC
65 AACTCC
*
5110438 GTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTT
1 GTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCA-CTTT
5110484 CTCCCTTCCT
Statistics
Matches: 111, Mismatches: 3, Indels: 6
0.93 0.03 0.05
Matches are distributed among these distances:
68 19 0.17
69 4 0.04
70 43 0.39
71 45 0.41
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.35
Consensus pattern (70 bp):
GTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTGTTTAAAGCCCACA
ACTCC
Found at i:5110499 original size:229 final size:228
Alignment explanation
Indices: 5110087--5110503 Score: 619
Period size: 229 Copynumber: 1.8 Consensus size: 228
5110077 CCTTTTTCTG
*
5110087 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACAACTCCGTGGCCCCTT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCGTTTCAAAGCCCACAACTCCGTGGCCCCTT
**
5110152 CTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACT
66 CTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACT
* * * *
5110217 CTTTTTTTCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGT
131 CTTTTTTCCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTCCTTCTAAAGCCCACAACTCTGT
5110282 GGCACCTACAACTTTGTGGCACTCTCTTTCCCTT
195 GGCACCTACAACTTTGTGGCACTCTCTTTCCCTT
*
5110316 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCT-GTTT-AAAGCCCACAACTCCGTGGCACTCT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCGTTTCAAAGCCCACAACTCCGTGGC-CCCT
* * *
5110378 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGC
65 TCTT--CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGC
* *
5110443 ACTC-TTTTTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACA
128 ACTCTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTT-T-CCTT-CTAAAGCCCACA
5110504 CAAGTCGGTG
Statistics
Matches: 169, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
226 42 0.25
227 10 0.06
228 22 0.13
229 95 0.56
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.34
Consensus pattern (228 bp):
TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCGTTTCAAAGCCCACAACTCCGTGGCCCCTT
CTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACT
CTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCTTCTAAAGCCCACAACTCTGTG
GCACCTACAACTTTGTGGCACTCTCTTTCCCTT
Found at i:5110531 original size:33 final size:35
Alignment explanation
Indices: 5110488--5110557 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
5110478 ATCTTTCTCC
5110488 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
5110522 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
5110556 CT
1 CT
5110558 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:5110531 original size:104 final size:102
Alignment explanation
Indices: 5110319--5110536 Score: 253
Period size: 104 Copynumber: 2.1 Consensus size: 102
5110309 TTCCCTTTTT
** *
5110319 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCC
* * **
5110384 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
66 CTTCTCAAAGCCCACAACTCCGTGGCAC--TCTTCTTCC
* *
5110423 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTCTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTC
* *
5110487 CCTTC-CTAAAGCCCACACAAGTCGGTGGCAAC-CTTCTTCC
65 CCTTCTC-AAAG-CC-CACAACTCCGTGGC-ACTCTTCTTCC
5110527 AAAGCCCACA
1 AAAGCCCACA
5110537 CAAGTCGGTG
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
103 1 0.01
104 52 0.53
105 31 0.32
106 12 0.12
107 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.13, T:0.29
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCC
CTTCTCAAAGCCCACAACTCCGTGGCACTCTTCTTCC
Found at i:5110648 original size:52 final size:52
Alignment explanation
Indices: 5110557--5110793 Score: 282
Period size: 52 Copynumber: 4.5 Consensus size: 52
5110547 GCAACCCTTC
* *
5110557 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGGCACCTTTTCCATCTT
* * * *
5110609 TAAGTCCAATGTAGCTGGCCTTGACTCACCACATTGGCACC--TT-CATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGGCACCTTTTCCATCTT
*
5110658 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGGCACCTTTTCCATCTT
* * * *
5110710 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGGCA-CC-TTTTC--CATCTT
* * * *
5110766 TAAGCCCAATATCGTTGGCCATGAATCA
1 TAAGTCCAATATAGCTGGCCTTGAATCA
5110794 ACATATTGGC
Statistics
Matches: 156, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
49 42 0.27
50 2 0.01
51 2 0.01
52 75 0.48
53 2 0.01
54 5 0.03
56 28 0.18
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (52 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGGCACCTTTTCCATCTT
Found at i:5110686 original size:101 final size:101
Alignment explanation
Indices: 5110557--5110809 Score: 344
Period size: 101 Copynumber: 2.4 Consensus size: 101
5110547 GCAACCCTTC
5110557 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTA
*
5110622 GCTGGCCTTGACTCACCACATTGGCACCTTCATCTT
66 GCTGGCCTTGAATCACCACATTGGCACCTTCATCTT
* *
5110658 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTA
* *
5110723 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
66 GCTGGCCTTGAATCACCACATTGGCA-CC----T--TCATCTT
* * * * * *
5110766 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTT
5110810 ATCACTTTTC
Statistics
Matches: 133, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
101 86 0.65
102 2 0.02
106 1 0.01
108 44 0.33
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.33
Consensus pattern (101 bp):
TAAGCCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCACCACATTGGCACCTTCATCTT
Found at i:5110867 original size:67 final size:68
Alignment explanation
Indices: 5110759--5110885 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
5110749 TCCTTTTTCA
* * *
5110759 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
5110823 TCT
66 TCT
* * * *
5110826 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
5110886 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:5111650 original size:15 final size:15
Alignment explanation
Indices: 5111630--5111660 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5111620 ATTTCGTTTG
*
5111630 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5111645 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5111660 G
1 G
5111661 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5112523 original size:33 final size:33
Alignment explanation
Indices: 5112486--5112552 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5112476 TTCAACGATT
5112486 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5112519 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5112552 T
1 T
5112553 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5112524 original size:13 final size:13
Alignment explanation
Indices: 5112506--5112530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5112496 CATAAAATGT
5112506 TGTATCGATACAA
1 TGTATCGATACAA
5112519 TGTATCGATACA
1 TGTATCGATACA
5112531 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5112611 original size:13 final size:13
Alignment explanation
Indices: 5112593--5112617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5112583 ATTACTCAAA
5112593 TGTATCGATACAT
1 TGTATCGATACAT
5112606 TGTATCGATACA
1 TGTATCGATACA
5112618 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5112719 original size:52 final size:52
Alignment explanation
Indices: 5112626--5112753 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
5112616 CACTGATCTT
*
5112626 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
5112677 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
5112729 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
5112754 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:5119165 original size:20 final size:20
Alignment explanation
Indices: 5119123--5119161 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5119113 CGTGTAAATG
* *
5119123 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
5119143 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
5119162 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:5119230 original size:13 final size:13
Alignment explanation
Indices: 5119212--5119237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5119202 CAATTTTTTG
5119212 TGTATCGATACAT
1 TGTATCGATACAT
5119225 TGTATCGATACAT
1 TGTATCGATACAT
5119238 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5124899 original size:20 final size:20
Alignment explanation
Indices: 5124874--5124913 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5124864 AATATCACAG
**
5124874 TTTTTTAGAATTTTTTAAAA
1 TTTTTTAGAAAATTTTAAAA
*
5124894 TTTTTTTGAAAATTTTAAAA
1 TTTTTTAGAAAATTTTAAAA
5124914 AATTAGCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTTAGAAAATTTTAAAA
Found at i:5125629 original size:165 final size:164
Alignment explanation
Indices: 5125296--5125873 Score: 534
Period size: 165 Copynumber: 3.5 Consensus size: 164
5125286 TTCAGGCATC
* * * * * * *
5125296 AAAATTATTTAAATATTATCATTTAA-TCACTAGTAAATCAATTTTGAAAAATTCCTTTTATTTT
1 AAAATTA-TCAAATATTATTATTTAATTCA-TATTAAATTAGTTTTCAAAAATT-CATTTATTTT
* * * * * *
5125360 -ATGAGTTATTGATTTTCTT-TTGAAATTATCTTTATTTT-TAAAATACAAAGTTTTCTATTCCA
63 CATGAGTTTTTCATTTT-TTCTTAAAATTCTCTTT-TTTTGAAAAAT-C-GAGTTTTCTATTCCA
* *
5125422 TAAATG-TTTTCA-A-GGAGATTTTTCTTGGTTTTTAATTTTT
124 TAAA-GATTTT-AGAGGGGGATTTTTCTTAGTTTTTAATTTTT
* ** *
5125462 AAAATTAGTCAAATATTATTATTTAGTTCATATTAAATTAGTTTTCAAAAATTCATCCATTTTTA
1 AAAATTA-TCAAATATTATTATTTAATTCATATTAAATTAGTTTTCAAAAATTCATTTATTTTCA
* * * *
5125527 TGAGTTTTTCATTTTTTCTTAAAA-TCTCTATATTTTTGAAATATGGAGTTTTCTACTT-CGTAG
65 TGAGTTTTTCATTTTTTCTTAAAATTCTCT-T-TTTTTGAAAAATCGAGTTTTCTA-TTCCATAA
* *
5125590 ATATTTTAG-GGGGGATTTTTCTTAGTTTTTAACTTTT
127 AGATTTTAGAGGGGGATTTTTCTTAGTTTTTAATTTTT
* * * * *
5125627 AAAATTTATTATATATTATTATTTAATTCATATTAATTTAGCTTTCAAAAATTCATTTATTTTGA
1 AAAA-TTATCAAATATTATTATTTAATTCATATTAAATTAGTTTTCAAAAATTCATTTATTTTCA
5125692 TGAGTTTTTCATTTTTTCCTTAAAATTCTCTTTTTTTGAAAAATCGAGTTTTCTATTCCATAAAG
65 TGAGTTTTTCATTTTTT-CTTAAAATTCTCTTTTTTTGAAAAATCGAGTTTTCTATTCCATAAAG
* * ****
5125757 GTTTTTGAGGGGG-TTTTTC-TAGGTCCAAAATTTTT
129 ATTTTAGAGGGGGATTTTTCTTA-GTTTTTAATTTTT
* * * * *
5125792 AATATTCATCAAATATCATTATTTAAATCATATTAAATCAGTTTTGAAAAATTCATTTA-TTTCA
1 AAAATT-ATCAAATATTATTATTTAATTCATATTAAATTAGTTTTCAAAAATTCATTTATTTTCA
*
5125856 TGAGTTTTTAATTTTTTC
65 TGAGTTTTTCATTTTTTC
5125874 CTTGAAATGC
Statistics
Matches: 339, Mismatches: 56, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
163 1 0.00
164 27 0.08
165 215 0.63
166 83 0.24
167 13 0.04
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (164 bp):
AAAATTATCAAATATTATTATTTAATTCATATTAAATTAGTTTTCAAAAATTCATTTATTTTCAT
GAGTTTTTCATTTTTTCTTAAAATTCTCTTTTTTTGAAAAATCGAGTTTTCTATTCCATAAAGAT
TTTAGAGGGGGATTTTTCTTAGTTTTTAATTTTT
Found at i:5125941 original size:165 final size:165
Alignment explanation
Indices: 5125438--5126019 Score: 530
Period size: 165 Copynumber: 3.5 Consensus size: 165
5125428 TTTTCAAGGA
* ** * *
5125438 GATTTTTCTTGGTTTTTAATTTTTAAAATT-AGTCAAATATTATTATTTAGTTCATATTAAATTA
1 GATTTTTCTAGGTTTAAAATTTTTAAAATTCA-TCAAATATTATTATTTAATTCATATTAAATCA
** * *
5125502 GTTTTCAAAAATTCATCCATTTTTATGAGTTTTTCATTTTTT-CTTAAAATCTCTATATTTTTGA
65 GTTTTCAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATC-CCATATTTTTGA
* * * * *
5125566 AATATGGAGTTTTCTACT-TCGTAGATATTTTAGGGGG
129 AAAATCGAGTTTTCTACTCT-GTAAATATTTTTGGAGG
** * * * * * *
5125603 GATTTTTCTTA-GTTTTTAACTTTTAAAATTTATTATATATTATTATTTAATTCATATTAATTTA
1 GATTTTTC-TAGGTTTAAAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCA
* * * *
5125667 GCTTTCAAAAATTCATTTATTTTGATGAGTTTTTCATTTTTTCCTTAAAATTCTC-TTTTTTTGA
65 GTTTTCAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAA-TCCCATATTTTTGA
* ** **
5125731 AAAATCGAGTTTTCTATTCCATAAAGGTTTTT-GAGGG
129 AAAATCGAGTTTTCTACTCTGTAAATATTTTTGGA-GG
* ** * * *
5125768 GGTTTTTCTAGGTCCAAAATTTTTAATATTCATCAAATATCATTATTTAAATCATATTAAATCAG
1 GATTTTTCTAGGTTTAAAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCAG
* * * * *
5125833 TTTTGAAAAATTCATTTA-TTTCATGAGTTTTTAATTTTTTCCTTGAAATGCCCATGTTTTCGAA
66 TTTTCAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAAT-CCCATATTTTTGAA
** * *
5125897 AAATTAAGTTTTTTACTCTGTAAATATTTTTGGAGA
130 AAATCGAGTTTTCTACTCTGTAAATATTTTTGGAGG
* * ** * * * * *
5125933 GATTTTTCTCGATTTAAAATTTCAAAAATTCATCTAATATTTTTATTTAACTCTTATTAAATCAA
1 GATTTTTCTAGGTTTAAAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCAG
* *
5125998 TTTTAAAAAATTAAATTTATTT
66 TTTTCAAAAATT-CATTTATTT
5126020 CATAAAGTTT
Statistics
Matches: 335, Mismatches: 70, Indels: 22
0.78 0.16 0.05
Matches are distributed among these distances:
163 1 0.00
164 32 0.10
165 282 0.84
166 16 0.05
167 4 0.01
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (165 bp):
GATTTTTCTAGGTTTAAAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCAG
TTTTCAAAAATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATCCCATATTTTTGAAA
AATCGAGTTTTCTACTCTGTAAATATTTTTGGAGG
Found at i:5126009 original size:330 final size:331
Alignment explanation
Indices: 5125308--5126019 Score: 719
Period size: 330 Copynumber: 2.2 Consensus size: 331
5125298 AATTATTTAA
* * * * * *
5125308 ATATTATCATTTAA-TCACTAGTAAATCAATTTTGAAAAATTCCTTTTATTTTATGAGTTATTGA
1 ATATTATTATTTAACTCA-TATTAAATCAATTTTAAAAAATTACATTTATTTTATGAGTTATTCA
* * *
5125372 TTTTCTTTTGAAATTATCTTTATTTTTAAAATACAAAGTTTTCTATTCCATAAATGTTTTCAAGG
65 TTTTCTTTTAAAATTATCTTTATTTTAAAAATACAAAGTTTTCTATTCCATAAAGGTTTTCAAGG
* **** * ** *
5125437 AGATTTTTCTTGGTTTTTAATTTTTAAAATTAGTCAAATATTATTATTTAGTTCATATTAAATTA
130 AGATTTTTCTAGGTCCAAAATTTTTAAAATTAGTCAAATATCATTATTTAAATCATATTAAATCA
* * * *
5125502 GTTTTCAAAAATTCATCCATTTTTATGAGTTTTTCATTTTTTCTTAAAATCTCTATATTTTTGAA
195 GTTTTCAAAAATTCATCCATTTTCATGAGTTTTTAATTTTTTCTTAAAATCTCCATATTTTCGAA
* * * * * * * * *
5125567 ATATGGAGTTTTCTACTTCGTAGATATTTTAGGGGGGATTTTTCTTAGTTTTTAACTTTTAAAAT
260 AAATGAAGTTTTCTACTTCGTAAATATTTTAGGAGAGATTTTTCTTAGATTTAAAATTTAAAAAT
*
5125632 TTATTAT
325 TCATTAT
* * * ** * *
5125639 ATATTATTATTTAATTCATATTAATTTAGCTTTCAAAAATT-CATTTATTTTGATGAGTTTTTCA
1 ATATTATTATTTAACTCATATTAAATCAATTTTAAAAAATTACATTTATTTT-ATGAGTTATTCA
* * **
5125703 TTTT-TTCCTTAAAATTCTCTTT-TTTTGAAAAAT-C-GAGTTTTCTATTCCATAAAGGTTTTTG
65 TTTTCTT--TTAAAATTATCTTTATTTT-AAAAATACAAAGTTTTCTATTCCATAAAGGTTTTCA
* * *
5125764 AGGGGGTTTTTCTAGGTCCAAAATTTTTAATATTCA-TCAAATATCATTATTTAAATCATATTAA
127 AGGAGATTTTTCTAGGTCCAAAATTTTTAAAATT-AGTCAAATATCATTATTTAAATCATATTAA
* ** * *
5125828 ATCAGTTTTGAAAAATTCATTTA-TTTCATGAGTTTTTAATTTTTTCCTTGAAATGC-CCATGTT
191 ATCAGTTTTCAAAAATTCATCCATTTTCATGAGTTTTTAATTTTTT-CTTAAAAT-CTCCATATT
* * * *
5125891 TTCGAAAAATTAAGTTTTTTAC-TCTGTAAATATTTTTGGAGAGATTTTTC-TCGATTTAAAATT
254 TTCGAAAAATGAAGTTTTCTACTTC-GTAAATATTTTAGGAGAGATTTTTCTTAGATTTAAAATT
5125954 TCAAAAATTCATCTA-
318 T-AAAAATTCAT-TAT
* * *
5125969 ATATTTTTATTTAACTCTTATTAAATCAATTTTAAAAAATTAAATTTATTT
1 ATATTATTATTTAACTCATATTAAATCAATTTTAAAAAATTACATTTATTT
5126020 CATAAAGTTT
Statistics
Matches: 308, Mismatches: 61, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
329 32 0.10
330 195 0.63
331 61 0.20
332 20 0.06
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.50
Consensus pattern (331 bp):
ATATTATTATTTAACTCATATTAAATCAATTTTAAAAAATTACATTTATTTTATGAGTTATTCAT
TTTCTTTTAAAATTATCTTTATTTTAAAAATACAAAGTTTTCTATTCCATAAAGGTTTTCAAGGA
GATTTTTCTAGGTCCAAAATTTTTAAAATTAGTCAAATATCATTATTTAAATCATATTAAATCAG
TTTTCAAAAATTCATCCATTTTCATGAGTTTTTAATTTTTTCTTAAAATCTCCATATTTTCGAAA
AATGAAGTTTTCTACTTCGTAAATATTTTAGGAGAGATTTTTCTTAGATTTAAAATTTAAAAATT
CATTAT
Found at i:5126370 original size:10 final size:10
Alignment explanation
Indices: 5126351--5126410 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 10
5126341 CAACTAAAAA
5126351 AAAAAGGAGAG
1 AAAAA-GAGAG
5126362 AAAAAGAGAG
1 AAAAAGAGAG
*
5126372 AAAGAAAAGAAAG
1 --A-AAAAGAGAG
5126385 AAAAAGAGAAG
1 AAAAAGAG-AG
5126396 AAAATAGAGAG
1 AAAA-AGAGAG
5126407 AAAA
1 AAAA
5126411 TTAGAAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 11 0.26
11 18 0.43
12 5 0.12
13 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (10 bp):
AAAAAGAGAG
Found at i:5126396 original size:15 final size:17
Alignment explanation
Indices: 5126358--5126398 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
5126348 AAAAAAAAGG
5126358 AGAGAA-AAAGAGAGAA
1 AGAGAAGAAAGAGAGAA
*
5126374 AGAAAAGAAAGA-A-AA
1 AGAGAAGAAAGAGAGAA
5126389 AGAGAAGAAA
1 AGAGAAGAAA
5126399 ATAGAGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 6 0.27
17 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AGAGAAGAAAGAGAGAA
Found at i:5128321 original size:155 final size:155
Alignment explanation
Indices: 5128057--5128397 Score: 456
Period size: 155 Copynumber: 2.2 Consensus size: 155
5128047 TCTTCTAAAG
* *
5128057 GTATCGAGTACTTTTACGTTGAAGGTATCCTCTAGGGGTATTTTCATAATTTTCTAGAACCAACT
1 GTATCAAGTACTTTTACGTCGAAGGTATCCTCTAGGGGTATTTTCATAATTTTCTAGAACCAACT
5128122 CCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCTTTT
66 CCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCTTTT
*
5128187 TAAATCCTTTTTAAT-TCCTTTAAGA
131 AAAAT-CTTTTTAATGTCCTTTAAGA
*** * * *
5128212 GTATTTGGTACTTTTACGTCGAAGGTAT-CTCTTAGGGGTAATTTT-GTAATTTTTTAGAACTAA
1 GTATCAAGTACTTTTACGTCGAAGGTATCCTC-TAGGGGT-ATTTTCATAATTTTCTAGAACCAA
* * * *
5128275 CTCCTAGGTCATCACCGGGTCCATTTTTATGCTGGAA-GTGGATATTTAGGATATGTTCATCCCT
64 CTCCTAGGTCATCACCAGGTCCACTTTTATGC-CGAAGGTGGATATTTAGGATAGGTTCATCCCT
* * *
5128339 TTTAAAATCTTTTTTATGTCCTTTAGGG
128 TTTAAAATCTTTTTAATGTCCTTTAAGA
* *
5128367 GTATCAAGTACTTTTACATCGAAAGTATCCT
1 GTATCAAGTACTTTTACGTCGAAGGTATCCT
5128398 TTAAAGACAT
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
154 11 0.07
155 140 0.87
156 10 0.06
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (155 bp):
GTATCAAGTACTTTTACGTCGAAGGTATCCTCTAGGGGTATTTTCATAATTTTCTAGAACCAACT
CCTAGGTCATCACCAGGTCCACTTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCCTTTT
AAAATCTTTTTAATGTCCTTTAAGA
Found at i:5130263 original size:21 final size:21
Alignment explanation
Indices: 5130237--5130284 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5130227 TTCCAAATAC
*
5130237 AGAAAACAACAAAAGAGAAAAA
1 AGAAAACAAAAAAAG-GAAAAA
*
5130259 A-AAAAGAAAAAAAGGAAAAA
1 AGAAAACAAAAAAAGGAAAAA
5130279 AGAAAA
1 AGAAAA
5130285 AAAGTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 15 0.65
22 1 0.04
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (21 bp):
AGAAAACAAAAAAAGGAAAAA
Found at i:5130277 original size:16 final size:16
Alignment explanation
Indices: 5130258--5130288 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5130248 AAAGAGAAAA
5130258 AAAAAAGAAAAAAAGG
1 AAAAAAGAAAAAAAGG
5130274 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
5130289 TATGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Found at i:5130286 original size:8 final size:8
Alignment explanation
Indices: 5130257--5130288 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5130247 AAAAGAGAAA
5130257 AAAAAAAG
1 AAAAAAAG
5130265 AAAAAAAG
1 AAAAAAAG
*
5130273 GAAAAAAG
1 AAAAAAAG
5130281 AAAAAAAG
1 AAAAAAAG
5130289 TATGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5131527 original size:27 final size:27
Alignment explanation
Indices: 5131495--5131549 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
5131485 ATAATTGAAG
* *
5131495 ATAGATTGTATTTTCCTTATAATTATA
1 ATAGATTGTATTTTCCCTATAACTATA
*
5131522 ATAGATTGTGTTTTCCCTATAACTATA
1 ATAGATTGTATTTTCCCTATAACTATA
5131549 A
1 A
5131550 AGTTAAAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (27 bp):
ATAGATTGTATTTTCCCTATAACTATA
Found at i:5133115 original size:13 final size:13
Alignment explanation
Indices: 5133097--5133121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5133087 CATTTTATGG
5133097 TGTATCGATACAA
1 TGTATCGATACAA
5133110 TGTATCGATACA
1 TGTATCGATACA
5133122 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5133137 original size:32 final size:33
Alignment explanation
Indices: 5133074--5133141 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
5133064 CGTTACAAGC
**
5133074 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
5133107 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
5133139 CAA
1 CAA
5133142 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:5134558 original size:95 final size:95
Alignment explanation
Indices: 5134369--5134567 Score: 229
Period size: 95 Copynumber: 2.1 Consensus size: 95
5134359 AGCGGATTAT
* * *
5134369 AATAGTTAGCAAAGGCCCCACTAACAGGTTACAAAAATTAGCAAGGCCTCATTAATGAGTTACAA
1 AATAGTTAGCAAAGGCCCCACTAACAAGTTACAAAAACTAGCAAGGCCTCATTAATGAGTTAAAA
* ***
5134434 CAATTAGCATTAGCTCGGCTAATGGGTTAC
66 CAATTAGCATAAGCTCGGCTAACAAGTTAC
* * * *
5134464 AATAGTTAGCAAAGGCCCTACTAACAAGTTACAAAAGCTAGCAAGGCCTTATTAATGGGTTAAAA
1 AATAGTTAGCAAAGGCCCCACTAACAAGTTACAAAAACTAGCAAGGCCTCATTAATGAGTTAAAA
*** **
5134529 TGGTTAGTGTAAGCCTC-GCTAACAAGTTAC
66 CAATTAGCATAAG-CTCGGCTAACAAGTTAC
5134559 AATGAGTTA
1 AAT-AGTTA
5134568 CTTAGCATTA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
95 78 0.91
96 8 0.09
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (95 bp):
AATAGTTAGCAAAGGCCCCACTAACAAGTTACAAAAACTAGCAAGGCCTCATTAATGAGTTAAAA
CAATTAGCATAAGCTCGGCTAACAAGTTAC
Found at i:5134656 original size:32 final size:32
Alignment explanation
Indices: 5134582--5134667 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
5134572 GCATTAACCT
* *
5134582 ACTAATAGGTTATAATAGTTAACATCAGCTCC
1 ACTAATAGGTTAAAATAGTTAGCATCAGCTCC
** *
5134614 ACTAGCAGGTTAAAATAGTTAGCAT-AGGCTCT
1 ACTAATAGGTTAAAATAGTTAGCATCA-GCTCC
* *
5134646 AGTAATAGGTTACAATAGTTAG
1 ACTAATAGGTTAAAATAGTTAG
5134668 TTAGGCCTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (32 bp):
ACTAATAGGTTAAAATAGTTAGCATCAGCTCC
Found at i:5135467 original size:13 final size:13
Alignment explanation
Indices: 5135449--5135474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5135439 CAATTTTTTG
5135449 TGTATCGATACAT
1 TGTATCGATACAT
5135462 TGTATCGATACAT
1 TGTATCGATACAT
5135475 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5135910 original size:32 final size:32
Alignment explanation
Indices: 5135874--5135953 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
5135864 CTGCTAATGG
*
5135874 GTTACAATACTTAGCATAAACCTAGATAACGA
1 GTTACAATACTTAGCATAAACCTAGATAACAA
* * * * *
5135906 GTTACAATAGTTAGAATAAGCCTTGCTAACAA
1 GTTACAATACTTAGCATAAACCTAGATAACAA
*
5135938 CTTACAATACTTAGCA
1 GTTACAATACTTAGCA
5135954 AAGACCCCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (32 bp):
GTTACAATACTTAGCATAAACCTAGATAACAA
Found at i:5137124 original size:21 final size:21
Alignment explanation
Indices: 5137100--5137149 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5137090 AACAATTTTT
*
5137100 TATCAATACA-ATCGTATAATG
1 TATCAATACATATC-TAAAATG
* *
5137121 TATCGATACATGTCTAAAATG
1 TATCAATACATATCTAAAATG
5137142 TATCAATA
1 TATCAATA
5137150 TAGGATCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (21 bp):
TATCAATACATATCTAAAATG
Found at i:5144735 original size:79 final size:79
Alignment explanation
Indices: 5144652--5144953 Score: 272
Period size: 79 Copynumber: 3.8 Consensus size: 79
5144642 GAAAAATTTA
* * * * *
5144652 ATATTTTGTAGATAAAAACAGGGTTGGAGTATCCCCTCAG-AAATGATAGGGTTGGAGTATCCGC
1 ATATTTTGGAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAAATAACAGGGTTGGAGTATCCCC
*
5144716 GATTGTGAAAAACTG
66 GATTGTGGAAAA-TG
* ** * * * *
5144731 ATATTTTGGAAATAAAATC-GAGGTTGGAGTATTTCTTCA-AAAACACCAAGGTTGGAGTATCCC
1 ATATTTTGGAAATAAAAACAG-GGTTGGAGTATCCCCTCAGAAAATAACAGGGTTGGAGTATCCC
*
5144794 CGATTGTGGAAAATCA
65 CGATTGTGGAAAAT-G
* ** * * *
5144810 ATGTTTTGGAAAT-AAAACTAGGGTTGGAGTAT-CCCTTTGAAAATAACGGGGTTGGAATATCCT
1 ATATTTTGGAAATAAAAAC-AGGGTTGGAGTATCCCCTCAGAAAATAACAGGGTTGGAGTATCCC
*
5144873 CGATGGTGGAAAATTG
65 CGATTGTGGAAAA-TG
* * * * * **
5144889 ATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAAATAATGGGGTTGGAGTATCCCC
1 ATATTTTGGAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAAATAACAGGGTTGGAGTATCCCC
5144954 TTAGAAATAA
Statistics
Matches: 177, Mismatches: 37, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
78 8 0.05
79 136 0.77
80 33 0.19
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (79 bp):
ATATTTTGGAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAAATAACAGGGTTGGAGTATCCCC
GATTGTGGAAAATG
Found at i:5144962 original size:108 final size:107
Alignment explanation
Indices: 5144828--5145059 Score: 283
Period size: 108 Copynumber: 2.2 Consensus size: 107
5144818 GAAATAAAAC
* ** * *
5144828 TAGGGTTGGAGTAT-CCCTTTGAAAATAACGGGGTTGGAATATCCTCGATGGTGGAAAATTGATG
1 TAGGGTTGGAGTATCCCCTTAGAAAATAACAAGGTTGGAATATCCTCGATGGTAGAAAATTGATA
5144892 TTTT-AGAAATAAAATCGGGGTTAG-AGTATCCCCTCAGAAAATAA
66 TTTTGA-AAATAAAATCGGGGTT-GTAGTAT-CCCTC-GAAAATAA
* * * * *
5144936 TGGGGTTGGAGTATCCCCTTAG-AAATAACAAGTTTGGAGTATCCTCGATTGTATAAAATTGATA
1 TAGGGTTGGAGTATCCCCTTAGAAAATAACAAGGTTGGAATATCCTCGATGGTAGAAAATTGATA
* *
5145000 TTTTGAAAATAAAATTGGGGTTGTAGTATCCCTCGGAAATAA
66 TTTTGAAAATAAAATCGGGGTTGTAGTATCCCTCGAAAATAA
*
5145042 TAGGGTTGGAATATCCCC
1 TAGGGTTGGAGTATCCCC
5145060 GATGGTGGAA
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
106 23 0.21
107 6 0.06
108 71 0.66
109 7 0.07
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (107 bp):
TAGGGTTGGAGTATCCCCTTAGAAAATAACAAGGTTGGAATATCCTCGATGGTAGAAAATTGATA
TTTTGAAAATAAAATCGGGGTTGTAGTATCCCTCGAAAATAA
Found at i:5145057 original size:78 final size:79
Alignment explanation
Indices: 5144936--5145091 Score: 181
Period size: 78 Copynumber: 2.0 Consensus size: 79
5144926 CAGAAAATAA
* * * * * * *
5144936 TGGGGTTGGAGTATCCCCTTAGAAATAACAAGTTTGGAGTATCCTCGATTGTATAAAATTGATAT
1 TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAATATCCCCGATGGTAGAAAATCGATAT
5145001 TTT-GAAAATAAAAT
66 TTTAG-AAATAAAAT
* * * * *
5145015 TGGGGTTGTAGTAT-CCCTCGGAAATAATAGGGTTGGAATATCCCCGATGGTGGAAAATCGATAT
1 TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAATATCCCCGATGGTAGAAAATCGATAT
5145079 TTTAGAAATAAAA
66 TTTAGAAATAAAA
5145092 ACATCAATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
78 50 0.78
79 14 0.22
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (79 bp):
TGGGGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAATATCCCCGATGGTAGAAAATCGATAT
TTTAGAAATAAAAT
Found at i:5147496 original size:50 final size:49
Alignment explanation
Indices: 5147433--5147534 Score: 125
Period size: 50 Copynumber: 2.1 Consensus size: 49
5147423 AAAAATGCTT
* *
5147433 GAATGTTCGATACATTG-AGAAATATATTGATACATCTAGGTACAACCCA
1 GAATGTTCGATACAATGAAG-AATATATTGATACATCTAGGTAAAACCCA
* * * *
5147482 GAATGTATTGATACAATGAAGAATGTATTGATACATCTGGGTAAAACCTA
1 GAATGT-TCGATACAATGAAGAATATATTGATACATCTAGGTAAAACCCA
5147532 GAA
1 GAA
5147535 CCCAAAATGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 6 0.13
50 37 0.82
51 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (49 bp):
GAATGTTCGATACAATGAAGAATATATTGATACATCTAGGTAAAACCCA
Found at i:5150700 original size:20 final size:21
Alignment explanation
Indices: 5150663--5150712 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5150653 TTCTACAATT
5150663 TATATCGATATAATAAGTGAA
1 TATATCGATATAATAAGTGAA
* * *
5150684 TCTATCGATA-CATAAGTTAA
1 TATATCGATATAATAAGTGAA
5150704 TATATCGAT
1 TATATCGAT
5150713 GCATGCCTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
TATATCGATATAATAAGTGAA
Found at i:5151647 original size:13 final size:13
Alignment explanation
Indices: 5151615--5151652 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
5151605 TACACCAAGT
5151615 ATGTATCGATACA
1 ATGTATCGATACA
5151628 A-GTATCGATACA
1 ATGTATCGATACA
5151640 ATGTATCGATACA
1 ATGTATCGATACA
5151653 CAAAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5155234 original size:27 final size:27
Alignment explanation
Indices: 5155204--5155289 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
5155194 TTGGTGGCAT
5155204 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
5155231 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
5155259 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
5155286 TTTC
1 TTTC
5155290 AAAGCCCACA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:5155416 original size:171 final size:171
Alignment explanation
Indices: 5155098--5155829 Score: 1169
Period size: 171 Copynumber: 4.3 Consensus size: 171
5155088 TCGACAATTT
* * *
5155098 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCTAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
* * * *
5155163 AGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGA
66 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGA
5155221 GCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
130 GCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
5155263 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
*
5155328 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
66 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
*
5155393 CAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA-TTTC
131 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * * *
5155433 CAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
*
5155498 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCCCAAAGAG
66 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
5155563 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
131 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * *
5155604 CAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
5155669 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
66 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
*
5155734 CAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
131 CAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
** *
5155775 CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
5155830 TACTCCTCAA
Statistics
Matches: 534, Mismatches: 22, Indels: 15
0.94 0.04 0.03
Matches are distributed among these distances:
165 71 0.13
167 1 0.00
170 163 0.31
171 287 0.54
172 12 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (171 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG
CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:5155427 original size:116 final size:109
Alignment explanation
Indices: 5155098--5155848 Score: 936
Period size: 116 Copynumber: 6.7 Consensus size: 109
5155088 TCGACAATTT
* * *
5155098 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCTAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAA
5155163 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
*
5155208 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAA
5155273 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
5155318 CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CAGTCCTCAAAGAGCAGGA--C----ACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
*
5155383 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA-TTTC
59 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
5155433 CAATCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCA
1 CAGTCCTCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCA
* * * *
5155497 AAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTT-
64 AAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* *
5155549 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAA
* * *
5155614 AGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTT
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
5155659 CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CAGTCCTCAAAGAGCAGGA--C----ACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* *
5155724 CCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-
59 CCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
** * * * *
5155775 CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAA
1 CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAA
* *
5155840 TGAGAAGGA
65 AGAGCAGGA
5155849 TACACTTTAT
Statistics
Matches: 572, Mismatches: 40, Indels: 58
0.85 0.06 0.09
Matches are distributed among these distances:
109 47 0.08
110 220 0.38
111 2 0.00
112 2 0.00
113 1 0.00
114 1 0.00
115 56 0.10
116 229 0.40
117 14 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (109 bp):
CAGTCCTCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAA
GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:5155772 original size:29 final size:28
Alignment explanation
Indices: 5155692--5155774 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
5155682 TTTTCTTTTC
5155692 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
* * **
5155720 -CAGTCCC-CA-AAG-AGCAGGACACCTCTT
1 AAAG-CCCACACAAGTTGGTGG-CACCT-TT
5155747 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
5155775 CAGTCCTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
25 3 0.08
26 8 0.20
27 9 0.22
28 9 0.22
29 8 0.20
30 3 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (28 bp):
AAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:5155849 original size:55 final size:54
Alignment explanation
Indices: 5155095--5155848 Score: 961
Period size: 55 Copynumber: 13.4 Consensus size: 54
5155085 GATTCGACAA
* *
5155095 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
5155149 TTTCTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTC-AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
5155204 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
5155259 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
5155314 TTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
5155376 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
* * * *
5155430 TTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
* * * *
5155485 TTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
5155546 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
* *
5155600 TTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
* * *
5155656 TTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
* *
5155717 TTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-T
** *
5155772 TTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-T
* * * *
5155827 TTTTACTCCTCAATGAGAAGGA
1 TTTCAGTCCTCAAAGAGCAGGA
5155849 TACACTTTAT
Statistics
Matches: 627, Mismatches: 47, Indels: 51
0.86 0.06 0.07
Matches are distributed among these distances:
54 57 0.09
55 412 0.66
56 7 0.01
57 3 0.00
59 3 0.00
61 142 0.23
62 3 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:5156573 original size:16 final size:16
Alignment explanation
Indices: 5156552--5156583 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5156542 AGAGTGTTTG
5156552 AAAAAAAAAATTATTA
1 AAAAAAAAAATTATTA
5156568 AAAAAAAAAATTATTA
1 AAAAAAAAAATTATTA
5156584 TTATCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAAAAAATTATTA
Found at i:5156706 original size:19 final size:18
Alignment explanation
Indices: 5156682--5156812 Score: 103
Period size: 19 Copynumber: 7.9 Consensus size: 18
5156672 AATTCAACAA
5156682 TTTGTATCGATACATAGGT
1 TTTGTATCGATACATA-GT
5156701 TTTGTATCGATACA-A--
1 TTTGTATCGATACATAGT
5156716 --TGTATCGATACATAGGT
1 TTTGTATCGATACATA-GT
*
5156733 TTTGTATCGATAGA-A--
1 TTTGTATCGATACATAGT
5156748 --TGTATCGATACATAGGT
1 TTTGTATCGATACATA-GT
5156765 TTTGTATCGATACA-A--
1 TTTGTATCGATACATAGT
5156780 --TGTATCGATACATAAGT
1 TTTGTATCGATACAT-AGT
*
5156797 ATTGTATCGATACATA
1 TTTGTATCGATACATA
5156813 ATTAGCTACT
Statistics
Matches: 92, Mismatches: 2, Indels: 37
0.70 0.02 0.28
Matches are distributed among these distances:
13 35 0.38
14 2 0.02
15 1 0.01
18 4 0.04
19 50 0.54
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAGT
Found at i:5156721 original size:13 final size:13
Alignment explanation
Indices: 5156703--5156791 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 13
5156693 ACATAGGTTT
5156703 TGTATCGATACAA
1 TGTATCGATACAA
5156716 TGTATCGATACATA
1 TGTATCGATACA-A
*
5156730 GGTTTTGTATCGATAGAA
1 -----TGTATCGATACAA
5156748 TGTATCGATACATA
1 TGTATCGATACA-A
5156762 GGTTTTGTATCGATACAA
1 -----TGTATCGATACAA
5156780 TGTATCGATACA
1 TGTATCGATACA
5156792 TAAGTATTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 35 0.56
14 2 0.03
18 2 0.03
19 23 0.37
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5156725 original size:32 final size:32
Alignment explanation
Indices: 5156684--5156810 Score: 227
Period size: 32 Copynumber: 4.0 Consensus size: 32
5156674 TTCAACAATT
5156684 TGTATCGATACATAGGTTTTGTATCGATACAA
1 TGTATCGATACATAGGTTTTGTATCGATACAA
*
5156716 TGTATCGATACATAGGTTTTGTATCGATAGAA
1 TGTATCGATACATAGGTTTTGTATCGATACAA
5156748 TGTATCGATACATAGGTTTTGTATCGATACAA
1 TGTATCGATACATAGGTTTTGTATCGATACAA
* *
5156780 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAGGTTTTGTATCGATACA
5156811 TAATTAGCTA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 91 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAGGTTTTGTATCGATACAA
Found at i:5157168 original size:51 final size:53
Alignment explanation
Indices: 5157104--5157234 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
5157094 AGTTTATCAA
* * * *
5157104 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
5157155 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
5157209 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
5157235 CTCGTTGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
53 9 0.13
54 20 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:5157250 original size:28 final size:28
Alignment explanation
Indices: 5157218--5157293 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
5157208 TTTCTTCACA
* **
5157218 ATCGGGGATACTCCAACCTCGTTGTTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
5157246 ATCGGGG-TACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
5157273 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
5157294 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:5160761 original size:19 final size:20
Alignment explanation
Indices: 5160737--5160787 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5160727 GTATTGATAC
* *
5160737 ATTGTATCGATACAT-TTTT
1 ATTGTATCGATACATACTTA
5160756 ATTGTATCGATACATACTTA
1 ATTGTATCGATACATACTTA
5160776 ATTGTATCGATA
1 ATTGTATCGATA
5160788 TATAAAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTGTATCGATACATACTTA
Found at i:5162024 original size:20 final size:19
Alignment explanation
Indices: 5162001--5162074 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
5161991 CACACCCAAA
* *
5162001 TGTATCGATACTTGCTGCTT
1 TGTATCGATACATG-TGCAT
* *
5162021 TGTATCAATACATGTTCAT
1 TGTATCGATACATGTGCAT
5162040 TGTATCGATACATG-GCCAAAT
1 TGTATCGATACATGTG-C--AT
5162061 TGTATCGATACATG
1 TGTATCGATACATG
5162075 AAACTGGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 17 0.38
20 12 0.27
21 16 0.36
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:5162140 original size:13 final size:13
Alignment explanation
Indices: 5162119--5162149 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5162109 CGATACATGG
*
5162119 TACAATGTATCGA
1 TACATTGTATCGA
5162132 TACATTGTATCGA
1 TACATTGTATCGA
5162145 TACAT
1 TACAT
5162150 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5162145 original size:33 final size:32
Alignment explanation
Indices: 5162103--5162169 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
5162093 CTATCACTAT
5162103 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
5162136 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
5162169 T
1 T
5162170 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:5168335 original size:13 final size:13
Alignment explanation
Indices: 5168317--5168345 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5168307 ACAACATTCC
5168317 TTGTATCGATACA
1 TTGTATCGATACA
5168330 TTGTATCGATACA
1 TTGTATCGATACA
5168343 TTG
1 TTG
5168346 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5170224 original size:22 final size:22
Alignment explanation
Indices: 5170196--5170246 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 22
5170186 TTTTTACATG
*
5170196 AGGGGGAGAAGATAATTGTTTA
1 AGGGGGAGAAGATAATCGTTTA
5170218 A-GGGG-G-AGATAATCGTTTA
1 AGGGGGAGAAGATAATCGTTTA
5170237 AGGGGGAGAA
1 AGGGGGAGAA
5170247 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 13 0.52
20 5 0.20
21 5 0.20
22 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.41, T:0.22
Consensus pattern (22 bp):
AGGGGGAGAAGATAATCGTTTA
Found at i:5170229 original size:19 final size:19
Alignment explanation
Indices: 5170205--5170245 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5170195 GAGGGGGAGA
*
5170205 AGATAATTGTTTAAGGGGG
1 AGATAATCGTTTAAGGGGG
5170224 AGATAATCGTTTAAGGGGG
1 AGATAATCGTTTAAGGGGG
5170243 AGA
1 AGA
5170246 ATTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.37, T:0.27
Consensus pattern (19 bp):
AGATAATCGTTTAAGGGGG
Found at i:5171626 original size:9 final size:10
Alignment explanation
Indices: 5171596--5171626 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5171586 CAATTCTTTC
*
5171596 AAATTCAAAA
1 AAATTCGAAA
5171606 AAATTCGAAA
1 AAATTCGAAA
5171616 AAATTCGAAA
1 AAATTCGAAA
5171626 A
1 A
5171627 GAACCAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (10 bp):
AAATTCGAAA
Found at i:5172911 original size:15 final size:15
Alignment explanation
Indices: 5172891--5172928 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5172881 AAATAAATCA
5172891 AAAATTGTTG-AAAG
1 AAAATTGTTGAAAAG
*
5172905 TAAAATTCTTGAAAAG
1 -AAAATTGTTGAAAAG
5172921 AAAATTGT
1 AAAATTGT
5172929 CGAACTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.32
Consensus pattern (15 bp):
AAAATTGTTGAAAAG
Found at i:5179530 original size:13 final size:13
Alignment explanation
Indices: 5179512--5179538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5179502 ACACTATGCT
5179512 TTGTATTGATACA
1 TTGTATTGATACA
5179525 TTGTATTGATACA
1 TTGTATTGATACA
5179538 T
1 T
5179539 GTTCATTGTA
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:5179568 original size:20 final size:19
Alignment explanation
Indices: 5179523--5179577 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5179513 TGTATTGATA
* **
5179523 CATTGTATTGATACATGTT
1 CATTGTATCGATACATACT
5179542 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
*
5179561 CAATTGTATCGACACAT
1 C-ATTGTATCGATACAT
5179578 GAAAATGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:5182149 original size:65 final size:65
Alignment explanation
Indices: 5182047--5182174 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
5182037 TGCATTCATG
*
5182047 TTTTTCAAAAATTTGTTTACGAAAAAAAATCGTAAAAGTAATATTCTGTGTCAGTATCTCTCCTT
1 TTTTTCAAAAATTTGTTTACGAAAAAAAATCGTAAAAGTAATATTCTATGTCAGTATCTCTCCTT
5182112 TTTTTCAAAAATTTGTTTACGAAAAAAAATCGTAAAAGTAATATTCTATGTCAGTATCTCTCC
1 TTTTTCAAAAATTTGTTTACGAAAAAAAATCGTAAAAGTAATATTCTATGTCAGTATCTCTCC
5182175 AATGCTTGAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (65 bp):
TTTTTCAAAAATTTGTTTACGAAAAAAAATCGTAAAAGTAATATTCTATGTCAGTATCTCTCCTT
Found at i:5183019 original size:36 final size:36
Alignment explanation
Indices: 5182971--5183050 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
5182961 TTTCACGGAA
5182971 CTCTAAGAAGCAAGCTCAATCCTGAAGTTGAGTACGT
1 CTCT-AGAAGCAAGCTCAATCCTGAAGTTGAGTACGT
5183008 CTCTAGAAGCAAGCTCAATCCTGAAGTTGAGTACGT
1 CTCTAGAAGCAAGCTCAATCCTGAAGTTGAGTACGT
5183044 CTCTAGA
1 CTCTAGA
5183051 GCACCTGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 39 0.91
37 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (36 bp):
CTCTAGAAGCAAGCTCAATCCTGAAGTTGAGTACGT
Found at i:5190904 original size:29 final size:29
Alignment explanation
Indices: 5190862--5190924 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
5190852 TTAATTGCTT
5190862 CAAGCTGGTTATTATTTATTTTACACCTA
1 CAAGCTGGTTATTATTTATTTTACACCTA
5190891 CAAGCTGGTTATTATTTATTTTACACCTA
1 CAAGCTGGTTATTATTTATTTTACACCTA
5190920 CAAGC
1 CAAGC
5190925 AGCGTTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (29 bp):
CAAGCTGGTTATTATTTATTTTACACCTA
Found at i:5192104 original size:2 final size:2
Alignment explanation
Indices: 5192097--5192147 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
5192087 GCAAGTGCAC
* *
5192097 AG AG AG AG AG AG GG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5192139 AG AG AG AG A
1 AG AG AG AG A
5192148 ACCGGTTCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5204614 original size:25 final size:25
Alignment explanation
Indices: 5204585--5204634 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5204575 ACTCTTAAGG
5204585 ACCCATGAAAGGATACAAGACACAT
1 ACCCATGAAAGGATACAAGACACAT
5204610 ACCCATGAAAGGATACAAGACACAT
1 ACCCATGAAAGGATACAAGACACAT
5204635 GGCCAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (25 bp):
ACCCATGAAAGGATACAAGACACAT
Found at i:5207076 original size:44 final size:44
Alignment explanation
Indices: 5206992--5207082 Score: 148
Period size: 45 Copynumber: 2.1 Consensus size: 44
5206982 AGTTTCTTCA
*
5206992 TTACTTCTGTCAGCGCATGGTCATCCAACTGTGCAAGAAAAAAAT
1 TTACTTCTATCAGCGCATGGTCATCCAACTGTGCAAG-AAAAAAT
*
5207037 TTACTTCTATCAGTGCATGGTCA-CCAACTGTGCAAGAAAAAAT
1 TTACTTCTATCAGCGCATGGTCATCCAACTGTGCAAGAAAAAAT
5207080 TTA
1 TTA
5207083 GGCAGATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 10 0.23
44 13 0.30
45 21 0.48
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (44 bp):
TTACTTCTATCAGCGCATGGTCATCCAACTGTGCAAGAAAAAAT
Found at i:5209014 original size:39 final size:38
Alignment explanation
Indices: 5208952--5209030 Score: 131
Period size: 39 Copynumber: 2.1 Consensus size: 38
5208942 AATCATCTAG
* *
5208952 AATGATCTTTAGCTAAGTAGTTCACATAATCTTTGAGC
1 AATGATCTTCAACTAAGTAGTTCACATAATCTTTGAGC
5208990 AATGATCTTCAACTAGAGTAGTTCACATAATCTTTGAGC
1 AATGATCTTCAACTA-AGTAGTTCACATAATCTTTGAGC
5209029 AA
1 AA
5209031 ACGCTCTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (38 bp):
AATGATCTTCAACTAAGTAGTTCACATAATCTTTGAGC
Found at i:5219447 original size:15 final size:15
Alignment explanation
Indices: 5219427--5219457 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5219417 CAAACAACCG
5219427 ATACCATGATGTTCA
1 ATACCATGATGTTCA
5219442 ATACCATGATGTTCA
1 ATACCATGATGTTCA
5219457 A
1 A
5219458 CGTTGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ATACCATGATGTTCA
Found at i:5221901 original size:17 final size:18
Alignment explanation
Indices: 5221881--5221914 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5221871 TTTAAAAAAA
5221881 TTTATTTCA-TAAATATC
1 TTTATTTCATTAAATATC
*
5221898 TTTATTTTATTAAATAT
1 TTTATTTCATTAAATAT
5221915 AAATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATTTCATTAAATATC
Found at i:5222280 original size:16 final size:16
Alignment explanation
Indices: 5222259--5222313 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
5222249 AATAAAAATT
5222259 TAATATTATATTAAAA
1 TAATATTATATTAAAA
* *
5222275 TAATA-TAAATATAATA
1 TAATATTATAT-TAAAA
5222291 TAA-ATATATATTAAAA
1 TAATAT-TATATTAAAA
5222307 TTAATAT
1 -TAATAT
5222314 AATACAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 5 0.17
16 16 0.53
17 7 0.23
18 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATTATATTAAAA
Found at i:5222284 original size:27 final size:26
Alignment explanation
Indices: 5222237--5222291 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5222227 ACAAACAAAC
*
5222237 ATTATATAAAAAAATAAAAATTTAAT
1 ATTATATAAAAAAATAAAAATATAAT
* *
5222263 ATTATATTAAAATAATATAAATATAAT
1 ATTATA-TAAAAAAATAAAAATATAAT
5222290 AT
1 AT
5222292 AAATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTATATAAAAAAATAAAAATATAAT
Found at i:5222305 original size:22 final size:20
Alignment explanation
Indices: 5222272--5222315 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5222262 TATTATATTA
5222272 AAATAATAT-AAATATAATAT
1 AAATAATATAAAAT-TAATAT
5222292 AAATATATATTAAAATTAATAT
1 AAATA-ATA-TAAAATTAATAT
5222314 AA
1 AA
5222316 TACAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 9 0.43
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAATATAAAATTAATAT
Found at i:5222306 original size:32 final size:32
Alignment explanation
Indices: 5222260--5222355 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
5222250 ATAAAAATTT
5222260 AATATTATATTAAAATAATATAAATATAATATA
1 AATA-TATATTAAAATAATATAAATATAATATA
*
5222293 AATATATATTAAAATTAATAT-AATACAAATTATA
1 AATATATATTAAAA-TAATATAAATA-TAA-TATA
* *
5222327 AATAT-T-TTAAAAT-TTATAAAAAT-ATATA
1 AATATATATTAAAATAATATAAATATAATATA
5222355 A
1 A
5222356 TATTTTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
28 5 0.09
29 1 0.02
30 3 0.05
31 4 0.07
32 20 0.36
33 13 0.24
34 9 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
AATATATATTAAAATAATATAAATATAATATA
Found at i:5222961 original size:3 final size:3
Alignment explanation
Indices: 5222938--5222990 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
5222928 ATTACTTTAA
*
5222938 TAT TAT TA- AAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5222982 TAT TAT TAT
1 TAT TAT TAT
5222991 ATCAGATTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.07
3 39 0.87
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5223990 original size:67 final size:67
Alignment explanation
Indices: 5223882--5224009 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
5223872 GATTAATGCA
*
5223882 TAGATTGTTGATGGGAATCAGATTCATTTTGATATAAAAAAAATTGATAAGACTAATGCATAATA
1 TAGATTGTTGATGGGAATCAGATTCATTTTAATATAAAAAAAATTGATAAGACTAATGCATAATA
5223947 CG
66 CG
* * * * * *
5223949 TAGATTTTTTATGGGGATTAGATTC-TTCTTAATATGAAAAAAATTGATAAGAGTAATGCAT
1 TAGATTGTTGATGGGAATCAGATTCATT-TTAATATAAAAAAAATTGATAAGACTAATGCAT
5224010 GGATTGTAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 2 0.04
67 51 0.96
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (67 bp):
TAGATTGTTGATGGGAATCAGATTCATTTTAATATAAAAAAAATTGATAAGACTAATGCATAATA
CG
Found at i:5224216 original size:90 final size:88
Alignment explanation
Indices: 5224039--5224266 Score: 297
Period size: 90 Copynumber: 2.6 Consensus size: 88
5224029 AGAAGAATTG
*
5224039 GACTAATACATGAATTATATCTAAGAATCAGATT-TTTTTATAG---AAAAAAATTGATTGATTG
1 GACTAATACATGAATTATATCTGAGAATCAGATTCTTTTTATAGAAAAAAAAAATTGATTGATTG
5224100 TAAATGTCAAACTGCAAAGATTA
66 TAAATGTCAAACTGCAAAGATTA
* *
5224123 GACTAATGCATGAATTATATCTGAGAATC-GAATTCCTTTTTATAGAAAAAAGAAAAGTT-TTTG
1 GACTAATACATGAATTATATCTGAGAATCAG-ATT-CTTTTTATAGAAAAAA-AAAA-TTGATTG
* * *
5224186 ATTGTAAATGTCAGACTGTAAGGATTA
62 ATTGTAAATGTCAAACTGCAAAGATTA
* *
5224213 GACTAATCCATGAATTATATATGAGAATCAGATTCTTTTTTATAGAAAAAAAAA
1 GACTAATACATGAATTATATCTGAGAATCAGATTC-TTTTTATAGAAAAAAAAA
5224267 GAAAGACTGC
Statistics
Matches: 126, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
83 1 0.01
84 30 0.24
86 9 0.07
89 7 0.06
90 76 0.60
91 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (88 bp):
GACTAATACATGAATTATATCTGAGAATCAGATTCTTTTTATAGAAAAAAAAAATTGATTGATTG
TAAATGTCAAACTGCAAAGATTA
Found at i:5224318 original size:71 final size:71
Alignment explanation
Indices: 5224198--5224411 Score: 306
Period size: 71 Copynumber: 3.0 Consensus size: 71
5224188 TGTAAATGTC
* * * * *
5224198 AGACTGTAAGGATTAGACTAATCCATGAATTATATATGAGAATCAGATTCTTTTTTATAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTAAGAATCGGATTCTTTTTTATAG-AAAA
5224263 AAAAGAA
65 AAAAGAA
* * *
5224270 AGACTGCAAGGATTAGAC-AATGCATAAATTATATCTAAGAATCGGATTCCTTTTTGTAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTAAGAATCGGATTCTTTTTTATAGAAAAA
5224334 AAAGAA
66 AAAGAA
* *
5224340 AGACTACAAGGATTAGACTAATGCATGAATTGTATCTGAA-AATCGGATTCTTTTTTATAGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCT-AAGAATCGGATTCTTTTTTATAGAAAA
5224404 AAAAGAA
65 AAAAGAA
5224411 A
1 A
5224412 ACTTAATTGA
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
70 28 0.22
71 80 0.63
72 19 0.15
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (71 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATATCTAAGAATCGGATTCTTTTTTATAGAAAAA
AAAGAA
Found at i:5227728 original size:13 final size:13
Alignment explanation
Indices: 5227710--5227735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5227700 TACAAGCCAA
5227710 TGTATCGATACAT
1 TGTATCGATACAT
5227723 TGTATCGATACAT
1 TGTATCGATACAT
5227736 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5227800 original size:21 final size:21
Alignment explanation
Indices: 5227774--5227849 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
5227764 CTGCCAAGAA
*
5227774 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
5227795 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
5227815 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
5227836 ATGTATCGATACAT
1 ATGTATCGATACAT
5227850 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:5227820 original size:20 final size:20
Alignment explanation
Indices: 5227795--5227867 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5227785 CATCTTTTTT
5227795 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5227815 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
5227836 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5227856 ATGTATCGATAC
1 ATGTATCGATAC
5227868 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5227831 original size:41 final size:41
Alignment explanation
Indices: 5227774--5227867 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5227764 CTGCCAAGAA
*
5227774 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5227815 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5227856 ATGTATCGATAC
1 ATGTATCGATAC
5227868 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:5230921 original size:84 final size:84
Alignment explanation
Indices: 5230766--5230930 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
5230756 CATTTTCCAC
* * * *
5230766 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
5230831 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
5230850 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
5230912 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
5230931 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:5232982 original size:13 final size:13
Alignment explanation
Indices: 5232964--5232989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5232954 TACAAGCCAA
5232964 TGTATCGATACAT
1 TGTATCGATACAT
5232977 TGTATCGATACAT
1 TGTATCGATACAT
5232990 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5233054 original size:21 final size:21
Alignment explanation
Indices: 5233028--5233103 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
5233018 CTGCCAAGAA
*
5233028 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
5233049 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
5233069 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
5233090 ATGTATCGATACAT
1 ATGTATCGATACAT
5233104 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:5233074 original size:20 final size:20
Alignment explanation
Indices: 5233049--5233121 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5233039 CATCTTTTTT
5233049 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
5233069 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
5233090 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
5233110 ATGTATCGATAC
1 ATGTATCGATAC
5233122 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5233085 original size:41 final size:41
Alignment explanation
Indices: 5233028--5233121 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5233018 CTGCCAAGAA
*
5233028 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5233069 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
5233110 ATGTATCGATAC
1 ATGTATCGATAC
5233122 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:5237288 original size:164 final size:167
Alignment explanation
Indices: 5237106--5237505 Score: 466
Period size: 163 Copynumber: 2.4 Consensus size: 167
5237096 TTCAAACATC
* *
5237106 AAAATTAATCAAATATTATCACTT-ATTTCATATTAATTTAGTTTTTAAAAATTCATTCATTTTT
1 AAAATTCATCAAATATTATCACTTGA-TTCATATTAATTTAGTTTTCAAAAATTCATTCA-TTTT
* * * *
5237170 CATTCA-TTTTTGATTTTTTTCCTTGAAA-T-T-TTTTTTCGAAATACGGTATTTTCAACTCCGT
64 CA-TCAGTTTTTGA-TTTTGTCCTTAAAATTCTCTTTTTTAGAAATACGATATTTTCAACTCCGT
5237231 -AAATTTTTTTG-AGGAGA-TTTTTCTCAGTTTTCAATTTTT
127 AAAATTTTTTTGAAGG-GATTTTTTCTCAGTTTTCAATTTTT
**
5237270 AAAATTCATCAAATATTATCGTTTGATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATTATCACTTGATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCA
* * *
5237335 TGAGTTTTTGATTTTGTCCTTAAAATTCCTCTTTTTTATAAATACGATGTTTTCAACTCCGTAAA
66 TCAGTTTTTGATTTTGTCCTTAAAATT-CTCTTTTTTAGAAATACGATATTTTCAACTCCGTAAA
**
5237400 ATTTTTTTGAAGGGATTTTTTCTTGGTTTTCAATTTTT
130 ATTTTTTTGAAGGGATTTTTTCTCAGTTTTCAATTTTT
* * * * * * *
5237438 AAAATTCATC----A-GACCATTTGATTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCA
1 AAAATTCATCAAATATTATCACTTGATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCA
*
5237498 TGAGTTTT
66 TCAGTTTT
5237506 GAATTTTTCT
Statistics
Matches: 207, Mismatches: 20, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
162 14 0.07
163 64 0.31
164 54 0.26
165 2 0.01
166 27 0.13
167 13 0.06
168 33 0.16
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (167 bp):
AAAATTCATCAAATATTATCACTTGATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCA
TCAGTTTTTGATTTTGTCCTTAAAATTCTCTTTTTTAGAAATACGATATTTTCAACTCCGTAAAA
TTTTTTTGAAGGGATTTTTTCTCAGTTTTCAATTTTT
Found at i:5237560 original size:163 final size:163
Alignment explanation
Indices: 5237132--5237581 Score: 431
Period size: 163 Copynumber: 2.7 Consensus size: 163
5237122 TATCACTTAT
* * * * * * *
5237132 TTCATATTAATTTAGTTTTTAAAAATTCATTCATTTTTCATTCA-TTTTTGATTTTTTTCCTTGA
1 TTCATATTAATTCAATTTTAAAAAATTAATTCA-TTTTCA-TGAGTTTTTGA-TTTTGTCCTTAA
** * *
5237196 AA-T--T-TTTTTTCGAAATACGGTATTTTCAACTCCGTAAATTTTTTTGAGGAGA-TTTTTCTC
63 AATTCATCTTTTTTAAAAATACGATGTTTTCAACTCCGTAAATTTTTTTGAGG-GATTTTTTCTC
* * *
5237256 AGTTTTCAATTTTTAAAATTCATCAAATATTATCGTTTGA
127 AGTTTTCAATTTTTAAAATTCATC--A-ATGACCATTTGA
* * * *
5237296 TTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTTTGTCCTTAAAAT
1 TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTTTGTCCTTAAAAT
* * **
5237361 TCCTCTTTTTTATAAATACGATGTTTTCAACTCCGTAAAATTTTTTTGAAGGGATTTTTTCTTGG
66 TCATCTTTTTTAAAAATACGATGTTTTCAACTCCGT-AAATTTTTTTG-AGGGATTTTTTCTCAG
5237426 TTTTCAATTTTTAAAATTCATC-A-GACCATTTGA
129 TTTTCAATTTTTAAAATTCATCAATGACCATTTGA
*
5237459 TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCATGAG-TTTTGAATTTT-TCTTTGAAA
1 TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTG-ATTTTGTCCTT-AAA
* ***
5237522 A-TCTATTTTTTTTGAAAAA-ATCGA-GTTTTTTTCTCCGTAAATTTTTTTGGAGGGATTTTT
64 ATTC-ATCTTTTTT-AAAAATA-CGATGTTTTCAACTCCGTAAATTTTTTT-GAGGGATTTTT
5237582 CAATTTAAAA
Statistics
Matches: 248, Mismatches: 24, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
162 45 0.18
163 89 0.36
164 40 0.16
165 1 0.00
166 27 0.11
167 13 0.05
168 33 0.13
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (163 bp):
TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCATGAGTTTTTGATTTTGTCCTTAAAAT
TCATCTTTTTTAAAAATACGATGTTTTCAACTCCGTAAATTTTTTTGAGGGATTTTTTCTCAGTT
TTCAATTTTTAAAATTCATCAATGACCATTTGA
Found at i:5238180 original size:22 final size:23
Alignment explanation
Indices: 5238155--5238205 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5238145 AAAATAAAAA
*
5238155 AAAAAAGAGAAAGAAA-AGAG-AG
1 AAAAAAGAGAAACAAATAG-GTAG
*
5238177 AAAAAATAGAAACAAATAGGTAG
1 AAAAAAGAGAAACAAATAGGTAG
5238200 AAAAAA
1 AAAAAA
5238206 ATAAGACTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (23 bp):
AAAAAAGAGAAACAAATAGGTAG
Found at i:5239892 original size:24 final size:26
Alignment explanation
Indices: 5239864--5239915 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
5239854 AATCAAAATT
5239864 TTATTTATC-A-GGGATACTCCAACC
1 TTATTTATCGAGGGGATACTCCAACC
*
5239888 TTATTTCTCTGAGGGGATACTCCAACC
1 TTATTTATC-GAGGGGATACTCCAACC
5239915 T
1 T
5239916 CGCTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
26 1 0.04
27 15 0.62
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (26 bp):
TTATTTATCGAGGGGATACTCCAACC
Found at i:5240038 original size:97 final size:97
Alignment explanation
Indices: 5239918--5240096 Score: 315
Period size: 97 Copynumber: 1.8 Consensus size: 97
5239908 TCCAACCTCG
* *
5239918 CTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCATCATCGGGGGCACTCCAA
1 CTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCATCATCGAGGACACTCCAA
5239983 -CCCTATTCCTCCGAAGGAAAACTCGAACCCCA
66 TCCC-ATTCCTCCGAAGGAAAACTCGAACCCCA
*
5240015 CTTTTAAACACGTCAAAGTTTAAATCTTATTCTCACTTAAATTGTCATCATCGAGGACACTCCAA
1 CTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCATCATCGAGGACACTCCAA
5240080 TCCCATTCCTCCGAAGG
66 TCCCATTCCTCCGAAGG
5240097 GATACTCCAA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
97 75 0.96
98 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (97 bp):
CTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCATCATCGAGGACACTCCAA
TCCCATTCCTCCGAAGGAAAACTCGAACCCCA
Found at i:5240602 original size:17 final size:17
Alignment explanation
Indices: 5240580--5240612 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5240570 ATATTGAACT
5240580 AATATCAAGTCAAAACC
1 AATATCAAGTCAAAACC
5240597 AATATCAAGTCAAAAC
1 AATATCAAGTCAAAAC
5240613 ATAGCTAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (17 bp):
AATATCAAGTCAAAACC
Found at i:5242322 original size:21 final size:21
Alignment explanation
Indices: 5242289--5242329 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5242279 CTAAGTAAAA
5242289 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
5242310 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
5242330 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Done.