Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001834.1 Hibiscus syriacus cultivar Beakdansim tig00003708_pilon, whole genome shotgun sequence
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: 105026
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6883 original size:36 final size:35
Alignment explanation
Indices: 6832--6942 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
6822 TAAGATACTA
* *
6832 CCTA-AACATCACCATCTTCTATCACCGTTTTTACG
1 CCTATAACATCACCATCTTCTATCACC-ATTTCACG
* * *
6867 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
* * *
6902 CCTATATCCTTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
6937 CCTATA
1 CCTATA
6943 TAACCACCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 44 0.69
36 20 0.31
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCTATCACCATTTCACG
Found at i:15470 original size:2 final size:2
Alignment explanation
Indices: 15463--15489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15453 ACTACCAAAA
15463 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15490 CATACCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17943 original size:60 final size:60
Alignment explanation
Indices: 17862--17981 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
17852 GTCCTCCAAT
* *
17862 TATGACCCTCATTTTAAATTAGTCCTTAAACTTTTTAACA-TTCTAATTTCAACCCCAAAC
1 TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTC-AATTTCAACCCCAAAC
* * **
17922 TATGACTCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCATTCCCAAAC
1 TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCAACCCCAAAC
17982 CCTCATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 50 0.94
61 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (60 bp):
TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCAACCCCAAAC
Found at i:18312 original size:60 final size:59
Alignment explanation
Indices: 18167--18345 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 59
18157 ACATAGTTTG
* * * * **
18167 GGATGAAATTAAAATGTTCAAAAGTTTAGGTACTAATTTAGAATG-AGGTCATAGTTTGG
1 GGATGAAATTAAAATGTTTAAAAGTTTAGG-ACTAATTTAAAATGAAGATCATAATTTAA
* * * *
18226 GGATGGAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAAAATAATAATTTAA
1 GGATGAAATTAAAATGTTTAAAAGTTT-AGGACTAATTTAAAATGAAGATCATAATTTAA
* * * *
18286 GGATGAAATTTAAATTTTTAAAAGTTTGGGGACTAATTTAATATGAAGATCATAATTTAA
1 GGATGAAATTAAAATGTTTAAAAGTTT-AGGACTAATTTAAAATGAAGATCATAATTTAA
18346 AGACACATGA
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 37 0.37
60 63 0.63
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (59 bp):
GGATGAAATTAAAATGTTTAAAAGTTTAGGACTAATTTAAAATGAAGATCATAATTTAA
Found at i:23122 original size:20 final size:20
Alignment explanation
Indices: 23099--23145 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
23089 GTTTCCAAAT
23099 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
23119 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
23139 TCGCAAC
1 TCGCAAC
23146 ACTGAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:23182 original size:20 final size:20
Alignment explanation
Indices: 23152--23206 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
23142 CAACACTGAA
*
23152 TTTCAAATTCGCAACTCGA-
1 TTTCGAATTCGCAACTCGAT
23171 TTTCTGAATTCGCAACTCGAT
1 TTTC-GAATTCGCAACTCGAT
*
23192 TTTCGAATTCACAAC
1 TTTCGAATTCGCAAC
23207 ATGAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (20 bp):
TTTCGAATTCGCAACTCGAT
Found at i:23402 original size:14 final size:15
Alignment explanation
Indices: 23383--23421 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
23373 TCCCCATCTC
23383 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
23397 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
23413 TAATTTTTT
1 TAATTTTTT
23422 CAATTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:23767 original size:19 final size:19
Alignment explanation
Indices: 23743--23782 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
23733 GGATTTAGGA
23743 TATCTTATCAGAGAAAATG
1 TATCTTATCAGAGAAAATG
23762 TATCTTATCAGAGAAAATG
1 TATCTTATCAGAGAAAATG
23781 TA
1 TA
23783 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (19 bp):
TATCTTATCAGAGAAAATG
Found at i:24235 original size:24 final size:24
Alignment explanation
Indices: 24184--24235 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
24174 GTATTCGAAA
* *
24184 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATCTTGATCAATACCCGGAC
* *
24208 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
24232 TTTG
1 TTTG
24236 GTTATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:26181 original size:21 final size:21
Alignment explanation
Indices: 26155--26199 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26145 GATTTTTGGG
* *
26155 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
26176 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
26197 CAA
1 CAA
26200 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:26808 original size:18 final size:18
Alignment explanation
Indices: 26785--26819 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26775 CTAGGAGATT
26785 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
26803 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
26820 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:27071 original size:2 final size:2
Alignment explanation
Indices: 27064--27089 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27054 AATCTTGAGG
27064 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27090 GAAATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27578 original size:30 final size:32
Alignment explanation
Indices: 27523--27597 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
27513 CATGACATGT
*
27523 GTGAC-ATGTGAATTATATGGAAAAGAA-CTAC
1 GTGACTATGTG-ATAATATGGAAAAGAAGCTAC
27554 GTGACTATGTGATAATAT-GAAAAGAAGCTAC
1 GTGACTATGTGATAATATGGAAAAGAAGCTAC
*
27585 GTGA-TACGTGATA
1 GTGACTATGTGATA
27598 TGTGAAAGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 16 0.40
31 19 0.47
32 5 0.12
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (32 bp):
GTGACTATGTGATAATATGGAAAAGAAGCTAC
Found at i:27894 original size:149 final size:149
Alignment explanation
Indices: 27709--28161 Score: 906
Period size: 149 Copynumber: 3.0 Consensus size: 149
27699 GAGTCGAGGG
27709 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
27774 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
27839 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
27858 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
27923 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
27988 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28007 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
28072 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
28137 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28156 TCTACG
1 TCTACG
28162 GGGCACTTCG
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 304 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:31129 original size:21 final size:21
Alignment explanation
Indices: 31103--31147 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31093 GATTTCTGGG
* *
31103 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
31124 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
31145 CAA
1 CAA
31148 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:31734 original size:18 final size:18
Alignment explanation
Indices: 31711--31745 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31701 CTAGGAGATT
31711 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
31729 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
31746 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:32502 original size:31 final size:31
Alignment explanation
Indices: 32453--32527 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
32443 CATGACATGT
*
32453 GTGAC-ATGTGAATTATATGGAAAAGAA-CTAC
1 GTGACTATGTG-ATAATAT-GAAAAGAAGCTAC
*
32484 GTGACTATGTGATAATATGAAAATAAGCTAC
1 GTGACTATGTGATAATATGAAAAGAAGCTAC
*
32515 GTGA-TACGTGATA
1 GTGACTATGTGATA
32528 TGTGAAAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 15 0.38
31 19 0.49
32 5 0.13
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (31 bp):
GTGACTATGTGATAATATGAAAAGAAGCTAC
Found at i:32526 original size:30 final size:31
Alignment explanation
Indices: 32467--32527 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
32457 CATGTGAATT
*
32467 ATATGGAAAAGAACTACGTGACTATGTGATA
1 ATATGGAAAAGAACTACGTGACTACGTGATA
*
32498 ATAT-GAAAATAAGCTACGTGA-TACGTGATA
1 ATATGGAAAAGAA-CTACGTGACTACGTGATA
32528 TGTGAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (31 bp):
ATATGGAAAAGAACTACGTGACTACGTGATA
Found at i:32904 original size:144 final size:147
Alignment explanation
Indices: 32639--33086 Score: 821
Period size: 149 Copynumber: 3.0 Consensus size: 147
32629 GAGTCGAGAG
* *
32639 TCTACGTGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGA-ACA-
32704 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
64 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
32769 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
32788 TCTACGCGGTTCTTTAGGACATATGTATATCC-TTGGAACCTGTGTGAAGTCTTGAAAG-AC-AC
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGAACAAC
32850 TTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
66 TTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
32915 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
32932 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGA-ACA-
32997 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
64 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
33062 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
33081 TCTACG
1 TCTACG
33087 GGGCACTTCG
Statistics
Matches: 292, Mismatches: 2, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
144 116 0.40
145 26 0.09
146 2 0.01
147 2 0.01
148 25 0.09
149 121 0.41
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGAACAAC
TTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCAAT
Found at i:34779 original size:18 final size:18
Alignment explanation
Indices: 34756--34791 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34746 AAGCAAAAGG
34756 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
34774 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
34792 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:35224 original size:25 final size:25
Alignment explanation
Indices: 35186--35235 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35176 AAATCAATTA
*
35186 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
35211 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
35236 GAAATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:35664 original size:24 final size:24
Alignment explanation
Indices: 35612--35664 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
35602 TTTCATATGT
* *
35612 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
35636 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
35660 AATTT
1 AATTT
35665 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:36616 original size:6 final size:6
Alignment explanation
Indices: 36605--36639 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
36595 AAGCAAAAGG
* *
36605 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
36640 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:36629 original size:18 final size:18
Alignment explanation
Indices: 36606--36646 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
36596 AGCAAAAGGA
*
36606 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
36624 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
36642 AATCA
1 AATCA
36647 CAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:36901 original size:150 final size:150
Alignment explanation
Indices: 36631--37136 Score: 906
Period size: 150 Copynumber: 3.4 Consensus size: 150
36621 CGCAATCAAA
*
36631 ATCAAAATCCCAATCACAACCGGCTTTACCTTTTGGGACTTATTAACTTAGGT-ATTTTTAAATG
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
*
36695 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTGCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
36760 ACTTGAGTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
* *
36780 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTCTTAACTTAGGTGATTTTTAAATA
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
36845 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
*
36910 ACTTGATTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
**
36930 ATCAAAATATCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
* *
36995 CAAACGTTGTATTATGTGTATTTTATTTATGAATGCATACATTTTCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
37060 ACTTGAGTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
* *
37080 ATCAAAATCCCAATCAAAACTGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATT
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATT
37137 GTTGAGTTAA
Statistics
Matches: 340, Mismatches: 16, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
149 51 0.15
150 289 0.85
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (150 bp):
ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
ACTTGAGTTTGAACATTGCT
Found at i:45462 original size:20 final size:20
Alignment explanation
Indices: 45437--45485 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
45427 GTTAAACAGG
*
45437 GGGGAATCGATACCCCCTGA
1 GGGGAATCGATACCCACTGA
* *
45457 GGGGAATCTATACCCACTGG
1 GGGGAATCGATACCCACTGA
45477 GGGGAATCG
1 GGGGAATCG
45486 GTTCCTTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.16
Consensus pattern (20 bp):
GGGGAATCGATACCCACTGA
Found at i:46246 original size:20 final size:20
Alignment explanation
Indices: 46221--46259 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46211 GAGTTGCGAT
*
46221 AGTCAAATTCTCAACGTGAA
1 AGTCAAATTCGCAACGTGAA
46241 AGTCAAATTCGCAACGTGA
1 AGTCAAATTCGCAACGTGA
46260 TTCTCACGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (20 bp):
AGTCAAATTCGCAACGTGAA
Found at i:47918 original size:21 final size:21
Alignment explanation
Indices: 47894--48012 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
47884 GTGAAACGGG
* * * *
47894 CTCTTGAACGGTGGGACGGAC
1 CTCTTGAACGATGAGAGGGGC
*
47915 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
47936 CTCTTGAACGGTGGGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
*
47957 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
47978 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
47999 CTCTTGAACGATGA
1 CTCTTGAACGATGA
48013 CATGTGAATC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.01
21 79 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:47961 original size:42 final size:42
Alignment explanation
Indices: 47894--48014 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
47884 GTGAAACGGG
* *
47894 CTCTTGAACGGTGGGACGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* * *
47936 CTCTTGAACGGTGGGAGGGGTCTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* * *
47978 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACA
48015 TGTGAATCGG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
Found at i:48177 original size:4 final size:4
Alignment explanation
Indices: 48156--48201 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
48146 GGGCCGTTGA
* * *
48156 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
48202 TGTCGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:50200 original size:20 final size:21
Alignment explanation
Indices: 50171--50209 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
50161 TCGCGTTGCG
*
50171 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
50191 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
50210 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:50577 original size:22 final size:22
Alignment explanation
Indices: 50550--50600 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
50540 GATGGAGATA
50550 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
50572 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
50594 GACGGAT
1 GACGGAT
50601 GTTGCCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:50781 original size:20 final size:20
Alignment explanation
Indices: 50756--50821 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
50746 TAAACGTTCT
50756 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
50776 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
50796 TTGCGAAATTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
50816 TTGCGA
1 TTGCGA
50822 TTTACATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:50800 original size:40 final size:40
Alignment explanation
Indices: 50756--50846 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
50746 TAAACGTTCT
* *
50756 TTGCGAATTTGACTTATGTGTTGCGAATTTGACTTA-T-GTG
1 TTGCGAATTTGACTTATGTGTTGCG-ATTT-ACATATTCGCG
* *
50796 TTGCGAAATTGACTTCTGTGTTGCGATTTACATATTCGCG
1 TTGCGAATTTGACTTATGTGTTGCGATTTACATATTCGCG
50836 TTGCGAATTTG
1 TTGCGAATTTG
50847 GAAACTGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
38 4 0.09
39 5 0.11
40 35 0.80
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTTATGTGTTGCGATTTACATATTCGCG
Found at i:54051 original size:21 final size:21
Alignment explanation
Indices: 54000--54052 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
53990 ATTATTACTA
54000 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
54021 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
54042 TCGCAATGCGA
1 TCGCAATGCGA
54053 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:54084 original size:20 final size:20
Alignment explanation
Indices: 54062--54188 Score: 148
Period size: 20 Copynumber: 6.3 Consensus size: 20
54052 AATAAGTAAA
* *
54062 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
54082 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
* *
54103 TCGCAATGCGATACTGAATT
1 TCGCAACGCGATACTGACTT
*
54123 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
*
54143 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
54163 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
54183 TCGCAA
1 TCGCAA
54189 TGAGATTTTC
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.82
21 14 0.15
22 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:54104 original size:41 final size:41
Alignment explanation
Indices: 54059--54176 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
54049 GCGAATAAGT
*
54059 AAATCGCAATGCGATACTGACTATCGCAACGCGATA-ATAC
1 AAATCGCAATGCGATACTGACTTTCGCAACGCGATACATAC
* *
54099 AAAATCGCAATGCGATACTGAATTTCGCAACGCGATACTTAC
1 -AAATCGCAATGCGATACTGACTTTCGCAACGCGATACATAC
** * *
54141 -TTTCGCAACGCGATACTTACTTTCGCAACGCGATAC
1 AAATCGCAATGCGATACTGACTTTCGCAACGCGATAC
54177 TGACTTTCGC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 31 0.46
41 34 0.50
42 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
AAATCGCAATGCGATACTGACTTTCGCAACGCGATACATAC
Found at i:54714 original size:20 final size:20
Alignment explanation
Indices: 54665--54723 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
54655 TTTATTCTCT
* **
54665 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
54685 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
54705 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
54724 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:54914 original size:25 final size:24
Alignment explanation
Indices: 54860--54914 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
54850 TGTTTATTAT
* *
54860 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
54884 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
54910 TGTTT
1 TGTTT
54915 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:56062 original size:18 final size:18
Alignment explanation
Indices: 56041--56088 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
56031 TCCACTTCGG
*
56041 GAGCCATCACCTCTCCCA
1 GAGCCATCACCTCACCCA
*
56059 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
56077 GAGCCATCACCT
1 GAGCCATCACCT
56089 GATCAACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.46, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:56648 original size:20 final size:20
Alignment explanation
Indices: 56623--56668 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
56613 TAGTTTACTT
56623 TCGCAACACGAAAAT-GACTA
1 TCGCAACACGAAAATAG-CTA
* *
56643 TCGCAACGCGGAAATAGCTA
1 TCGCAACACGAAAATAGCTA
56663 TCGCAA
1 TCGCAA
56669 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAGCTA
Found at i:56684 original size:19 final size:19
Alignment explanation
Indices: 56662--56711 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
56652 GGAAATAGCT
*
56662 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
56681 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
56700 ATCGAAATGCGA
1 ATCGCAATGCGA
56712 TTTGTGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:56729 original size:19 final size:18
Alignment explanation
Indices: 56707--56797 Score: 81
Period size: 19 Copynumber: 5.3 Consensus size: 18
56697 AAAATCGAAA
56707 TGCGATTTGTGTTTCGCAT
1 TGCGATTT-TGTTTCGCAT
56726 TGCGATTTTG--TCG--T
1 TGCGATTTTGTTTCGCAT
*
56740 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCAT
56759 TGCGATTTTG--TCG--T
1 TGCGATTTTGTTTCGCAT
*
56773 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCAT
56792 TGCGAT
1 TGCGAT
56798 AGCCATTTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 20 0.34
16 6 0.10
17 6 0.10
18 2 0.03
19 25 0.42
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCAT
Found at i:56744 original size:14 final size:14
Alignment explanation
Indices: 56725--56781 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
56715 GTGTTTCGCA
56725 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
56739 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
56756 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
56772 TTGCGATTTT
1 TTGCGATTTT
56782 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:56755 original size:33 final size:33
Alignment explanation
Indices: 56718--56797 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
56708 GCGATTTGTG
56718 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
56751 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
56784 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
56798 AGCCATTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:56814 original size:20 final size:20
Alignment explanation
Indices: 56770--56856 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
56760 GCGATTTTGT
**
56770 CGTTGCGATTTTCATTTCGCA
1 CGTTGCGATAGTCATTTC-CA
* *
56791 --TTGCGATAGCCATTTTCA
1 CGTTGCGATAGTCATTTCCA
*
56809 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCA
**
56829 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCA
56849 CGTTGCGA
1 CGTTGCGA
56857 AAGTAAGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
18 2 0.04
19 12 0.21
20 42 0.75
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:56817 original size:39 final size:37
Alignment explanation
Indices: 56718--56856 Score: 125
Period size: 33 Copynumber: 3.8 Consensus size: 37
56708 GCGATTTGTG
56718 TTTCGCATTGCGAT----TTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATAGCATTTGTCGTTGCGATTTTCA
56751 TTTCGCATTGCGAT----TTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATAGCATTTGTCGTTGCGATTTTCA
**
56784 TTTCGCATTGCGATAGCCATTT-TCACGTTGCGATAGTCA
1 TTTCGCATTGCGATAG-CATTTGT--CGTTGCGATTTTCA
* *
56823 TTTCCGCGTTGCGATAGTCATTTCTGCGTTGCGA
1 TTT-CGCATTGCGATAG-CATTTGT-CGTTGCGA
56857 AAGTAAGTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 47 0.51
37 1 0.01
38 3 0.03
39 15 0.16
40 25 0.27
41 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.42
Consensus pattern (37 bp):
TTTCGCATTGCGATAGCATTTGTCGTTGCGATTTTCA
Found at i:56856 original size:40 final size:39
Alignment explanation
Indices: 56770--56845 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
56760 GCGATTTTGT
**
56770 CGTTGCGATTTTCATTTCGCATTGCGATAGCCATTTTCA
1 CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTTCA
* *
56809 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT-CGCATTGCGATAGCCATTT
56846 CTGCGTTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.47
40 17 0.53
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (39 bp):
CGTTGCGATAGTCATTTCGCATTGCGATAGCCATTTTCA
Found at i:56873 original size:20 final size:20
Alignment explanation
Indices: 56850--56902 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
56840 TCATTTCTGC
56850 GTTGCGAAAGTAAGTTTCGT
1 GTTGCGAAAGTAAGTTTCGT
*
56870 GTTGTGAAAGTAAGTTTCGT
1 GTTGCGAAAGTAAGTTTCGT
56890 GTTGCGAAAGTAA
1 GTTGCGAAAGTAA
56903 ACTATTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.08, G:0.30, T:0.34
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTTTCGT
Found at i:57235 original size:29 final size:29
Alignment explanation
Indices: 57191--57247 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
57181 CGTGCACGTG
*
57191 CTATTAAGTCTTCGTTCACCCCAATGGTT
1 CTATTAAGTCTCCGTTCACCCCAATGGTT
*
57220 CTATTACGTCTCCGTTCACCCCAATGGT
1 CTATTAAGTCTCCGTTCACCCCAATGGT
57248 GCGAAGACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.32, G:0.14, T:0.35
Consensus pattern (29 bp):
CTATTAAGTCTCCGTTCACCCCAATGGTT
Found at i:57316 original size:21 final size:21
Alignment explanation
Indices: 57290--57384 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
57280 CTGTCATCCC
57290 TCAAGAGTCCCCT-TCAATCGT
1 TCAAGAGTCCCCTATC-ATCGT
* **
57311 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTATCATCGT
* *
57332 TCAAGAGTCCCCT-CCACCGT
1 TCAAGAGTCCCCTATCATCGT
* * *
57352 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTATCATCGT
*
57373 TGAAGAGGTCCC
1 TCAAGA-GTCCC
57385 TCCCACCATT
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
20 14 0.25
21 37 0.66
22 5 0.09
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
TCAAGAGTCCCCTATCATCGT
Found at i:57370 original size:41 final size:42
Alignment explanation
Indices: 57280--57370 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
57270 CCCGACTCAC
* *
57280 CTGTCATCCCTCAAGAGTCCCCTTCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTTCAACCGTTCAAGAGGCCA
* *
57322 CTATCATCCCTCAAGAGTCCCC-TCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTTCAACCGTTCAAGAGGCCA
57363 CTGTCATC
1 CTGTCATC
57371 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTTCAACCGTTCAAGAGGCCA
Found at i:59008 original size:19 final size:19
Alignment explanation
Indices: 58956--59001 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
58946 GCAACGAGAG
58956 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58975 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58994 AATCGCAA
1 AATCGCAA
59002 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:59064 original size:20 final size:20
Alignment explanation
Indices: 59039--59134 Score: 174
Period size: 20 Copynumber: 4.8 Consensus size: 20
59029 TCGCATTGCG
*
59039 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
59059 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
59079 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
59099 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
59119 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
59135 TTCCCCGTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:59706 original size:20 final size:20
Alignment explanation
Indices: 59685--59793 Score: 112
Period size: 20 Copynumber: 5.4 Consensus size: 20
59675 TGTATTATCT
*
59685 CGTTGCGATAGTCAGAATCT
1 CGTTGCGATAGTCAGAATCG
* *
59705 CGTTGCGAAAGTTAGAATCG
1 CGTTGCGATAGTCAGAATCG
* *
59725 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGATAGTCAGAATCG
* **
59745 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAGAATCG
*
59766 CGTTGCGATAGTCATAATCG
1 CGTTGCGATAGTCAGAATCG
59786 CGTTGCGA
1 CGTTGCGA
59794 ATCTGGAAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:59779 original size:41 final size:41
Alignment explanation
Indices: 59660--59798 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
59650 AACTATGAAA
* * *
59660 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTCTGTATTATCGCGTTGCGATAGTCAGT
* *** ** *
59701 ATCTCGTTGCGAAAGT-TAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTCTGTATTATCGCGTTGCGATAGTCAGT
*
59741 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCA-T
1 ATCGCGTTGCGATTCTGTATTATCGCGTTGCGATAGTCAGT
*
59781 AATCGCGTTGCGAATCTG
1 -ATCGCGTTGCGATTCTG
59799 GAAACTGATT
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATTCTGTATTATCGCGTTGCGATAGTCAGT
Found at i:60717 original size:10 final size:10
Alignment explanation
Indices: 60704--60728 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60694 ATTTTATAAG
60704 TTTTTTTTAA
1 TTTTTTTTAA
60714 TTTTTTTTAA
1 TTTTTTTTAA
60724 TTTTT
1 TTTTT
60729 CATATCCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:62091 original size:2 final size:2
Alignment explanation
Indices: 62084--62109 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62074 TGTAATTCAA
62084 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
62110 TAATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62317 original size:2 final size:2
Alignment explanation
Indices: 62310--62348 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
62300 ATTACGTCGT
62310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62349 TGTAAAGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66876 original size:58 final size:58
Alignment explanation
Indices: 66806--66958 Score: 166
Period size: 58 Copynumber: 2.6 Consensus size: 58
66796 TGTCTTAATG
* * * *
66806 TATGACCCTCATTTTAAATTGGTCCTTAAGCTTTT-ACATGTTCCAATTTCATCCCTAAAC
1 TATGA-CCTCATTCTAAATTGGTCCTCAAACTTTTAACAT-TT-CAATTTCATCCCCAAAC
* * *
66866 TATGA-CTCATTCTAAATTAGTCCTCAAATTTTTGAACATTTCAATTTTATCCCCAAAC
1 TATGACCTCATTCTAAATTGGTCCTCAAACTTTT-AACATTTCAATTTCATCCCCAAAC
* *
66924 TATGACCTTCATTCTAAATTGGTCTTGAAACTTTT
1 TATGACC-TCATTCTAAATTGGTCCTCAAACTTTT
66959 TGCACATCCA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
58 43 0.55
59 3 0.04
60 32 0.41
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (58 bp):
TATGACCTCATTCTAAATTGGTCCTCAAACTTTTAACATTTCAATTTCATCCCCAAAC
Found at i:67702 original size:15 final size:15
Alignment explanation
Indices: 67684--67713 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
67674 TTACTTTATC
67684 TGTTATTATAATATA
1 TGTTATTATAATATA
67699 TGTTATTATAATATA
1 TGTTATTATAATATA
67714 AAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TGTTATTATAATATA
Found at i:75284 original size:3 final size:3
Alignment explanation
Indices: 75276--75367 Score: 50
Period size: 3 Copynumber: 31.7 Consensus size: 3
75266 CGTTTATATA
* * * *
75276 TAT TAT TA- TAT TAT TAT T-G TAT T-T ATAGA TAT TAT TAT TAT AAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TAT TAT
* * * * *
75320 TAT AAT AAA TAT TAT TAT AAT TA- TAT TA- TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
75366 TA
1 TA
75368 CAACCTTACA
Statistics
Matches: 66, Mismatches: 16, Indels: 14
0.69 0.17 0.15
Matches are distributed among these distances:
2 8 0.12
3 56 0.85
4 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:75323 original size:21 final size:20
Alignment explanation
Indices: 75272--75365 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 20
75262 GTGACGTTTA
*
75272 TATATATTATTATATTATTAT
1 TATA-ATTATAATATTATTAT
* *
75293 TGTATTTATAGATATTATTAT
1 TATAATTATA-ATATTATTAT
* *
75314 TATAAATATAATAAATATTAT
1 TATAATTATAAT-ATTATTAT
75335 TATAATTATATTATATTATTAT
1 TATAATTATA--ATATTATTAT
75357 TATAATTAT
1 TATAATTAT
75366 TACAACCTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.10
21 36 0.60
22 16 0.27
23 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATAATTATAATATTATTAT
Found at i:75806 original size:19 final size:19
Alignment explanation
Indices: 75782--75824 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
75772 GCACAACTCA
75782 CCACCATTAGGGTGAGTCG
1 CCACCATTAGGGTGAGTCG
*
75801 CCACCATTATGGTGAGTCG
1 CCACCATTAGGGTGAGTCG
75820 CCACC
1 CCACC
75825 GTAGCTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (19 bp):
CCACCATTAGGGTGAGTCG
Found at i:76813 original size:14 final size:14
Alignment explanation
Indices: 76794--76824 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
76784 CGAACCTACG
76794 AAGAGCAAACAACC
1 AAGAGCAAACAACC
*
76808 AAGAGCAAGCAACC
1 AAGAGCAAACAACC
76822 AAG
1 AAG
76825 CAAAAGCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.26, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAGCAAACAACC
Found at i:77762 original size:20 final size:20
Alignment explanation
Indices: 77725--77777 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
77715 AACCAACAAA
*
77725 TTCGCAACGCAAAACTCCAGT
1 TTCGCAACGC-GAACTCCAGT
77746 TTCGCAACGCGAACTCCAGT
1 TTCGCAACGCGAACTCCAGT
77766 TTCGCAACGCGA
1 TTCGCAACGCGA
77778 TTATCCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAGT
Found at i:84655 original size:75 final size:76
Alignment explanation
Indices: 84571--84720 Score: 259
Period size: 77 Copynumber: 2.0 Consensus size: 76
84561 TCATTTTGTC
84571 TCCATAATATATTTAAATCAATAA-TTT-TATTTTATTTTTTTAAATTATATTAATTTTATCTTC
1 TCCATAATATATTTAAATCAATAATTTTCTATTTTATTTTTTT-AATTATATTAATTTTATCTTC
84634 GAATTTATATCA
65 GAATTTATATCA
*
84646 TCCATAATATATTTAAATCAATAATTTTGCTTTTTTATTTTTTTAATTATATTAATTTTATCTTC
1 TCCATAATATATTTAAATCAATAATTTT-CTATTTTATTTTTTTAATTATATTAATTTTATCTTC
84711 GAATTTATAT
65 GAATTTATAT
84721 AATCGTGTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
75 24 0.34
76 3 0.04
77 31 0.44
78 13 0.18
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (76 bp):
TCCATAATATATTTAAATCAATAATTTTCTATTTTATTTTTTTAATTATATTAATTTTATCTTCG
AATTTATATCA
Found at i:85396 original size:23 final size:23
Alignment explanation
Indices: 85349--85397 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
85339 AATAACATAT
* **
85349 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
85372 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
85395 TAG
1 TAG
85398 ATATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:85459 original size:87 final size:87
Alignment explanation
Indices: 85313--85474 Score: 297
Period size: 87 Copynumber: 1.9 Consensus size: 87
85303 ATGTTATATC
*
85313 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
85378 ACGCTTATATAATAAAATAGAT
66 ACGCTTATATAATAAAATAGAT
*
85400 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
*
85465 ACGTTTATAT
66 ACGCTTATAT
85475 TGACCTATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
ACGCTTATATAATAAAATAGAT
Found at i:85869 original size:200 final size:198
Alignment explanation
Indices: 85469--86194 Score: 983
Period size: 200 Copynumber: 3.6 Consensus size: 198
85459 TAGGTAACGT
* *
85469 TTATATTGACCTATTTTCTAACTAAACCGGTATATTTATACC-GGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAACCGGTATATTTATACCGGGT-ACATTGTAAATTTACCTA
*
85533 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT--TAAATGTATCGACACT
64 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACT
* * * * *
85596 TTATGCGTGCACCTCATTGGGCATTCATTCTGGAAAAAAAGTATCGACACAAACTTAAAAAGTAT
128 TTATGCGTGCACCTCGTTTGGCATTCATTCTGG-ACAAAAGTATCGACACAAATTTAAAAAGTGT
*
85661 TGATACA
192 CGATACA
* * * *
85668 TTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGGTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAAT-AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* * *
85733 TACGTTGTAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
65 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* *
85798 ATGCGTACACCTCGTTTAGCATTCATTCTGGACAAAATGTATCGACACAAATTTAAAAAGTGTCG
130 ATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAA-GTATCGACACAAATTTAAAAAGTGTCG
85863 ATACA
194 ATACA
* * * **
85868 TTATGTTGACCTATTCTCTCATAAAACCGATATATTTATACCGATTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAAT-AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* *
85933 TACATTATAATTATCGGTTTCGATGTTATTGGGATTGATACTTTTAATAAATGTATCGACACTTT
65 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * ** *
85998 ATGCGTGCACCTCGTTTGGGTATTCATTCTAGACAATAAGTATCGACACAAATTCCACAAGTGTC
130 ATGCGTGCACCTCGTTT-GGCATTCATTCTGGACAA-AAGTATCGACACAAATTTAAAAAGTGTC
86063 GATACA
193 GATACA
* * * * * * *
86069 TTATGTTGACATGTTTTCTAATTAACCGGTATATTAATACAGGTTACATTGTTAATTTACCTATT
1 TTATGTTGACCTATTTTCTAATAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATT
* *
86134 ACATTATAATTATTGGTTTCGATGTTTTTGGGGTCGATACTTTTAGA-AAATGTATCGACAC
66 ACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
86195 ATATGTTTAT
Statistics
Matches: 468, Mismatches: 51, Indels: 15
0.88 0.10 0.03
Matches are distributed among these distances:
198 4 0.01
199 96 0.21
200 303 0.65
201 63 0.13
202 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (198 bp):
TTATGTTGACCTATTTTCTAATAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATT
ACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTA
TGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAATTTAAAAAGTGTCGAT
ACA
Found at i:88941 original size:19 final size:19
Alignment explanation
Indices: 88917--88964 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
88907 TTATATTCAC
88917 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
88936 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
88955 ATACAAAATT
1 ATACAAAATT
88965 TGTAAGGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:90769 original size:199 final size:201
Alignment explanation
Indices: 90414--91163 Score: 925
Period size: 199 Copynumber: 3.8 Consensus size: 201
90404 TTAAAACAAA
* * * * *
90414 TATCGATACAAATTT-AAAAGTGTCGCTACATTATATTA-ACCTATTTTCTAATTAAACTGGTAT
1 TATCGACACAAATTTAAAAAGTGTCGATACATTAT-GTAGACCTATTTTCTAATAAAACCGGTAT
* * * *
90477 ATTTATACCGGTTATATTACAAAATTACCTATTACATAATAATTATGAGTTTCGATGTTTTTGGG
65 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGG
* *
90542 ATC-A-AAAATTTAATAAATGTATCGACACTTTATCCGTGCA-CTCGTTTGGGCATTCATTCTGG
130 ATCGATACAATTT-ATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGG
90604 ACAAAAAG
194 ACAAAAAG
** *
90612 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCGCTCATAAAACCGGTATA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * ** *
90677 TTTATACCGCTTACATTGTAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTTTTGGAA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* * *
90742 TCGATACAATTT-TAAATGTATCGACACTTTATGTGTGCACCTCGTTT-GGCTTTCATTCTGGAT
131 TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGAC
90805 AAAAAG
196 AAAAAG
* * * * * * * *
90811 TATCGATA-TAATTTAAAAA-TATCGATACATCATGTTGACCTATTTTCTAAT-TAACCGATACA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * *
90873 TTTATACCGGTTATATTGTAAAGTTACATATTACATTATAATTATCAGTTTCGATGTTTTT-GGA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* * *
90937 TCAATACAATTT-TAAATGTATCGACACTTTATGCGTGGATCTCG-TTGGGCATTCATTCTGGAC
131 TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGAC
91000 AAAAAG
196 AAAAAG
* * * * *
91006 TATCGACACAAATTTAGAGAGTGTCGATACAATATGTATACCTATTTTCTCATAAAACCGGTATA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * * *
91071 TATCTATCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* *
91136 TTGATAC-TTTTAATAAATGTATCGACAC
131 TCGATACAATTT-ATAAATGTATCGACAC
91164 ATTTGTTTAC
Statistics
Matches: 470, Mismatches: 70, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
194 2 0.00
195 69 0.15
196 70 0.15
197 52 0.11
198 90 0.19
199 158 0.34
200 23 0.05
201 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (201 bp):
TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATTCATTCTGGAC
AAAAAG
Found at i:92704 original size:24 final size:24
Alignment explanation
Indices: 92685--92740 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
92675 CGAAATTTAT
92685 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
92709 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
92732 ATATGAAAT
1 AT-TGAAAT
92741 GAACATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:92708 original size:18 final size:18
Alignment explanation
Indices: 92685--92721 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
92675 CGAAATTTAT
92685 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
92703 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
92721 A
1 A
92722 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:97697 original size:23 final size:23
Alignment explanation
Indices: 97633--97686 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
97623 CGATTCCCAA
* * * *
97633 AAAGAGGGAATCGGTTTCCATTC
1 AAAGGGGGAATCAGTTCCCCTTC
97656 AAAGGGGGAATCAGTTCCCCTTC
1 AAAGGGGGAATCAGTTCCCCTTC
*
97679 AAGGGGGG
1 AAAGGGGG
97687 TATCGATTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAATCAGTTCCCCTTC
Found at i:101740 original size:117 final size:117
Alignment explanation
Indices: 101520--101741 Score: 279
Period size: 117 Copynumber: 1.9 Consensus size: 117
101510 CTTTCAAATC
* *
101520 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
101585 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
101637 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACT-CTTTTCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
101700 TTCATTTTGATTTTCCAAGTCTGTTTTAGTTT-TCAAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAGTTTCT-AAAAGAAG
101742 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 6 0.07
117 83 0.93
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:104576 original size:197 final size:197
Alignment explanation
Indices: 104240--105026 Score: 1187
Period size: 196 Copynumber: 4.0 Consensus size: 197
104230 AGTAATTTAA
* * * * *
104240 AAAAGTATCGACACAAATTTTAAAAGTGTCAATACATAATGTAGACATATTTTCTCATAAAATTG
1 AAAAGTATCGACACAAACTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTCATAAAATCG
104305 TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTCGATGTTTTT
66 TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* ** * *
104369 GGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCAATTAGTTTGGCATTCATTCTAG
131 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCTGG
104434 AC
196 AC
* * * *
104436 ACAAAGTATCGACACAAATTTTAAAAGTG-CGATAAATAATG-AGACCTATTCTCTCATAAAATC
1 A-AAAGTATCGACACAAACTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTCATAAAATC
*
104499 GATATATTTATACCTGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
65 G-TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
104564 TTAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCT
129 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCT
*
104629 GGAAA
194 GG-AC
* * *
104634 AAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAATCG
1 AAAAGTATCGACACAAACTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTCATAAAATCG
* *
104699 TATATTTATACCAGTTACATTGTAAATTTACCTATT-CATTATAATTATTGGTTTTGATGTTTTT
66 TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * *
104763 GGGAT-AATACAATTTTAAATGTATCGACACTTTATGCATGCACCTAGTTTGGCATTCATTCTGG
131 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCTGG
104827 AC
196 AC
* * *
104829 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACATATTCTCTTATAAAACC
1 AAAA-GTATCGACACAAACTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTCATAAAATC
*
104894 GGTATA-TTATACC-GTTACATTGTAAATTTA-CTATTACATTATAATTATGGGTTTCGATATTT
65 -GTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
104956 TTGGGATAGATACAATTTTAAATGTATCGACAC-TTATGTGTGCACCTAGTTTGACATTCATTCT
129 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCT
105020 GGAC
194 GGAC
105024 AAA
1 AAA
Statistics
Matches: 544, Mismatches: 37, Indels: 21
0.90 0.06 0.03
Matches are distributed among these distances:
194 5 0.01
195 107 0.20
196 202 0.37
197 161 0.30
198 47 0.09
199 22 0.04
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (197 bp):
AAAAGTATCGACACAAACTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTCATAAAATCG
TATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCTGG
AC
Done.