Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009322.1 Hibiscus syriacus cultivar Beakdansim tig00113081_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: 77956
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:343 original size:18 final size:18
Alignment explanation
Indices: 320--354 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
310 CTAGGAGATT
320 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
338 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
355 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:676 original size:2 final size:2
Alignment explanation
Indices: 669--700 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
659 GAACATGTGA
669 AT AT AT 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 AT AT AT
701 GTCTAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1474 original size:144 final size:147
Alignment explanation
Indices: 1210--1507 Score: 523
Period size: 144 Copynumber: 2.0 Consensus size: 147
1200 GAGTCGAGGG
1210 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTATGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATG-ATATTCTTTGGAACATGTGTGAAGTATGGAAAGACACAT
1275 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACA-TATTA
1340 TATGGCACTAC-GTGCAAT
129 TATGGCACTACGGTGCAAT
*
1358 TCTACGCGGTTCTTCGGGACATATG-TATTCTTTGGAACATGTGTGAA-TCTGGAAAGACA-ATA
1 TCTACGCGGTTCTTCGGGACATATGATATTCTTTGGAACATGTGTGAAGTATGGAAAGACACATA
*
1420 CTTGATCCTTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATATTATA
66 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATATTATA
*
1485 TGGCACTACGGTGTAAT
131 TGGCACTACGGTGCAAT
1502 TCTACG
1 TCTACG
1508 GGCACTTTGG
Statistics
Matches: 146, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
143 16 0.11
144 72 0.49
145 11 0.08
146 22 0.15
148 25 0.17
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTTCTTCGGGACATATGATATTCTTTGGAACATGTGTGAAGTATGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATATTATA
TGGCACTACGGTGCAAT
Found at i:3579 original size:19 final size:19
Alignment explanation
Indices: 3555--3609 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
3545 TATGAATAGT
3555 AATTACTATTTGAACAGTA
1 AATTACTATTTGAACAGTA
3574 AATTACTATTTGAACAGTA
1 AATTACTATTTGAACAGTA
* *
3593 AATCACTGTTTGAACAG
1 AATTACTATTTGAACAG
3610 CAACTCGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
AATTACTATTTGAACAGTA
Found at i:3741 original size:21 final size:21
Alignment explanation
Indices: 3715--3756 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3705 ATTTGAATAT
*
3715 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3736 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3757 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:6939 original size:29 final size:31
Alignment explanation
Indices: 6882--6941 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
6872 TAATTTAAGG
*
6882 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
6913 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
6942 TTACAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:7288 original size:40 final size:38
Alignment explanation
Indices: 7237--7327 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 38
7227 AAGGGGTACG
*
7237 AACAACAACTAAAGTTTTTAACGTC-ATGATACTAAAATGA
1 AACAA-AACTAAAGTTTTTAACGGCGA-GATACT-AAATGA
* *
7277 AACAAAGACTAAAGTTTTTACCGGCGAGGTACTAAATGA
1 AACAAA-ACTAAAGTTTTTAACGGCGAGATACTAAATGA
7316 AACAAAACTAAA
1 AACAAAACTAAA
7328 CTTTAGTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 6 0.13
39 13 0.28
40 26 0.57
41 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.23
Consensus pattern (38 bp):
AACAAAACTAAAGTTTTTAACGGCGAGATACTAAATGA
Found at i:14920 original size:6 final size:6
Alignment explanation
Indices: 14911--14938 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
14901 CTTCCACCCC
14911 TCGTAA TCGTAA TCGTAA TCGTAA TCGT
1 TCGTAA TCGTAA TCGTAA TCGTAA TCGT
14939 CTCTTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (6 bp):
TCGTAA
Found at i:17116 original size:114 final size:114
Alignment explanation
Indices: 16916--17149 Score: 407
Period size: 114 Copynumber: 2.1 Consensus size: 114
16906 GCGTGTTCAT
*
16916 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAGCAGAAATGAAAATCTTCCTGC
1 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAACAGAAATGAAAATCTTCCTGC
*
16981 TACAAGAATTAGTCTTCCTGTTCATCCCAAGGGACTGAAT-TCGGTATTA
66 TACAAGAATTAGTCTTACTGTTCATCCCAAGGGACTGAATCT-GGTATTA
* *
17030 AGTTCTGATAATTCTTTTGAGGAAAGGACCATTCAGGCATCTAACAGAAATGAAAATCTTCCTGC
1 AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAACAGAAATGAAAATCTTCCTGC
*
17095 TACAAGAATTAGTCTTACTGTTCCTCCCAAGGGACTGAATCTGGTATTA
66 TACAAGAATTAGTCTTACTGTTCATCCCAAGGGACTGAATCTGGTATTA
17144 AGTTCT
1 AGTTCT
17150 TTTGCTGGTG
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 113 0.99
115 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (114 bp):
AGTTCTGATAATTCATTTGAGGAAAGGACCATTCAAGCATCTAACAGAAATGAAAATCTTCCTGC
TACAAGAATTAGTCTTACTGTTCATCCCAAGGGACTGAATCTGGTATTA
Found at i:18294 original size:113 final size:114
Alignment explanation
Indices: 18089--18393 Score: 380
Period size: 113 Copynumber: 2.7 Consensus size: 114
18079 ATGCAATGCA
* *
18089 TCAACAACAACTAGCATTGCTAGCACATCAACAGTCCCTTCTGATGGCTGCTGCAGCTAAATCTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
* * ***** * *
18154 CTCCTGTAAATACTCGACATTCACCATCCAATGGTGCAATCATACCCTC
66 CTCCTGAAAATACTCGACATCCACCATCCAACACCACAAGCATACCCAC
* * * * * **
18203 TCAACAACAGCTAGCTTTGCTAGCACAGCAACAATCTCTT-TCATGGCTTCTGCAGCTAAAGGTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
* * * *
18267 CTCCTGGAAATACTC-AGCATCCTCCATCTACCACCACAAGCATACCCAC
66 CTCCTGAAAATACTCGA-CATCCACCATCCAACACCACAAGCATACCCAC
*
18316 TCAACAACAACTAGCTTTGTTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
18381 CTCCTGAAAATAC
66 CTCCTGAAAATAC
18394 GCAACAGCTT
Statistics
Matches: 159, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
112 1 0.01
113 90 0.57
114 68 0.43
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (114 bp):
TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
CTCCTGAAAATACTCGACATCCACCATCCAACACCACAAGCATACCCAC
Found at i:18407 original size:114 final size:113
Alignment explanation
Indices: 18089--18433 Score: 406
Period size: 114 Copynumber: 3.0 Consensus size: 113
18079 ATGCAATGCA
* *
18089 TCAACAACAACTAGCATTGCTAGCACATCAACAGTCCCTTCTGATGGCTGCTGCAGCTAAATCTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
* * ** ** * *
18154 CTCCTGTAAATACTCGACA-TTCACCATCCAATGGTGCAATCATACCCTC
66 CTCCTGAAAATACTCAACACTT--CCATCCACCGGCACAAGCATACCCAC
* * * * * **
18203 TCAACAACAGCTAGCTTTGCTAGCACAGCAACAATCTCTT-TCATGGCTTCTGCAGCTAAAGGTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
* * * * **
18267 CTCCTGGAAATACTCAGCATCCTCCATCTACCACCACAAGCATACCCAC
66 CTCCTGAAAATACTCAACA-CTTCCATCCACCGGCACAAGCATACCCAC
*
18316 TCAACAACAACTAGCTTTGTTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
1 TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
* *
18381 CTCCTGAAAATACGCAACAGCTTCCATCCACCGGCACAAGTATACCCAC
66 CTCCTGAAAATACTCAACA-CTTCCATCCACCGGCACAAGCATACCCAC
18430 TCAA
1 TCAA
18434 GCTTGGCCAA
Statistics
Matches: 189, Mismatches: 39, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
113 88 0.47
114 100 0.53
115 1 0.01
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.24
Consensus pattern (113 bp):
TCAACAACAACTAGCTTTGCTAGCACATCAACAGTCCCTTCTCATGGCTGCTGCAGCTAAATCTG
CTCCTGAAAATACTCAACACTTCCATCCACCGGCACAAGCATACCCAC
Found at i:31718 original size:33 final size:31
Alignment explanation
Indices: 31679--31776 Score: 108
Period size: 33 Copynumber: 3.1 Consensus size: 31
31669 CTATTCAATG
* *
31679 TCGACTAAGGAGGTGGAAAGTAGCTACTTAGCG
1 TCGACTAAGGA-G-GGAAAGTAGCTACTCAGCA
* *
31712 TTGACTAAGGAAGAGGCAAGTAGCTACTCAGCA
1 TCGACTAAGG-AG-GGAAAGTAGCTACTCAGCA
*
31745 TCGACTAATGA-GGAAAGTAGCTACTCAGCA
1 TCGACTAAGGAGGGAAAGTAGCTACTCAGCA
31775 TC
1 TC
31777 TAGTTCCCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 20 0.36
32 1 0.02
33 34 0.61
34 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (31 bp):
TCGACTAAGGAGGGAAAGTAGCTACTCAGCA
Found at i:32485 original size:60 final size:57
Alignment explanation
Indices: 32306--32565 Score: 313
Period size: 57 Copynumber: 4.5 Consensus size: 57
32296 CAACTATGGG
32306 GCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAGTACGAGGAAAAAAT
1 GCAAAAAGAACAGGAAAATG-C-CA-TACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * * * * * *
32366 GCAGAAGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATAT
1 GCAAAAAGAACAGGAAAATGCCATACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * * *
32423 GCAAAAAGAAGAGGAAAATGACACACTACGGGAACAATTACGACAGTACGAGGCAAAGAT
1 GCAAAAAGAACAGGAAAATG-C-CA-TACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * *
32483 GCAAAAAGAACCGGAAAATGCCATATGGGAACCATTACAACAGTACGAGGAAAAAAT
1 GCAAAAAGAACAGGAAAATGCCATACGGGAACAATTACAACAGTACGAGGAAAAAAT
* * *
32540 GCAGAAGGAACAGGAAAATGCAATAC
1 GCAAAAAGAACAGGAAAATGCCATAC
32566 CAAATGAGCA
Statistics
Matches: 168, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
57 96 0.57
58 5 0.03
59 4 0.02
60 63 0.38
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.11
Consensus pattern (57 bp):
GCAAAAAGAACAGGAAAATGCCATACGGGAACAATTACAACAGTACGAGGAAAAAAT
Found at i:32513 original size:117 final size:117
Alignment explanation
Indices: 32306--32559 Score: 355
Period size: 117 Copynumber: 2.2 Consensus size: 117
32296 CAACTATGGG
* * *
32306 GCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAGTACGAGGAAAAAATGCAGA
1 GCAAAAAGAACAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGAAAAAATGCAAA
* * * *
32371 AGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATAT
66 AAGAACAGGAAAATGCCATAGGGGAACAACTACAACAGTACGAGGAAAAAAT
* * * *
32423 GCAAAAAGAAGAGGAAAATGACACACTACGGGAACAATTACGACAGTACGAGGCAAAGATGCAAA
1 GCAAAAAGAACAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGAAAAAATGCAAA
* * * *
32488 AAGAACCGGAAAATGCCATATGGGAACCATTACAACAGTACGAGGAAAAAAT
66 AAGAACAGGAAAATGCCATAGGGGAACAACTACAACAGTACGAGGAAAAAAT
* *
32540 GCAGAAGGAACAGGAAAATG
1 GCAAAAAGAACAGGAAAATG
32560 CAATACCAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (117 bp):
GCAAAAAGAACAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGAAAAAATGCAAA
AAGAACAGGAAAATGCCATAGGGGAACAACTACAACAGTACGAGGAAAAAAT
Found at i:32829 original size:327 final size:327
Alignment explanation
Indices: 32235--32884 Score: 1102
Period size: 327 Copynumber: 2.0 Consensus size: 327
32225 TGACCAGGAC
* *
32235 ATACCAAATGAGCAGCCTTCTGCAATGGCAGAGCTTCAAAGAAGGATTCTCGACGTGGAAGCAAC
1 ATACCAAATGAGCAGCCTTCAGCAATGGCAGAGCTTCAAAGAAGGATTCTCGACATGGAAGCAAC
*
32300 TATGGGGCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAGTACGAGGAAAAAA
66 TATGGGGCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAATACGAGGAAAAAA
* *
32365 TGCAGAAGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATATGCAAAAA
131 TGAAAAAGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATATGCAAAAA
*
32430 GAAGAGGAAAATGACACACTACGGGAACAATTACGACAGTACGAGGCAAAGATGCAAAAAGAACC
196 GAAGAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGCAAAGATGCAAAAAGAACC
** * *
32495 GGAAAATGCCATATGGGAACCATTACAACAGTACGAGGAAAAAATGCAGAAGGAACAGGAAAATG
261 GGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAATGCAGAAGGAACAGGAAAATG
32560 CA
326 CA
*
32562 ATACCAAATGAGCAGCCTTCAGCAATGTCAGAGCTTCAAAGAAGGATTCTCGACATGGAAGCAAC
1 ATACCAAATGAGCAGCCTTCAGCAATGGCAGAGCTTCAAAGAAGGATTCTCGACATGGAAGCAAC
* * * *
32627 TTTGGGGCAAAAAGAACAGGAAAATGCCACATTATGGGAACAATTACGACAATATGAGGAAAAAA
66 TATGGGGCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAATACGAGGAAAAAA
* * * *
32692 TGAAAAAGGAACAGGAAAATGCTATAGGGGAACAATTACAATTGTACGCGGAAAATATGCGAAAA
131 TGAAAAAGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATATGCAAAAA
* *
32757 GAAGAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAAGATGCAAAAAGAACT
196 GAAGAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGCAAAGATGCAAAAAGAACC
*
32822 GGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAATGCATAAGGAACAGGAAAA
261 GGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAATGCAGAAGGAACAGGAAAA
32885 AGCACGGGAA
Statistics
Matches: 301, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
327 301 1.00
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (327 bp):
ATACCAAATGAGCAGCCTTCAGCAATGGCAGAGCTTCAAAGAAGGATTCTCGACATGGAAGCAAC
TATGGGGCAAAAAGAACAGGAAAATGCCACATTACGGGAACAATTACAACAATACGAGGAAAAAA
TGAAAAAGGAACAGGAAAATGCCATAGGGGAACAACTACAACTGTACGCGGAAAATATGCAAAAA
GAAGAGGAAAATGACACACTACGGGAACAATTACAACAGTACGAGGCAAAGATGCAAAAAGAACC
GGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAATGCAGAAGGAACAGGAAAATG
CA
Found at i:32923 original size:54 final size:56
Alignment explanation
Indices: 32633--33104 Score: 358
Period size: 60 Copynumber: 8.1 Consensus size: 56
32623 CAACTTTGGG
* * * * * *
32633 GCAAAAAGAACAGGAAAATGCCACATTATGGGAACAATTACGACAATATGAGGAAAAAAT
1 GCAAAAAGAACAGGAAAAAG-C-CA--ACGGGAACAATTACAACAGTACGAGGCAAAAAT
* * * ** *
32693 G-AAAAAGGAACAGGAAAATGCTATAGGGGAACAATTACAATTGTACGCGG-AAAATAT
1 GCAAAAA-GAACAGGAAAAAGCCA-ACGGGAACAATTACAACAGTACGAGGCAAAA-AT
* * * *
32750 GCGAAAAGAAGAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAAGAT
1 GCAAAAAGAACAGGAAAAAG-C-CA--ACGGGAACAATTACAACAGTACGAGGCAAAAAT
* * * * *
32810 GCAAAAAGAACTGGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAAT
1 GCAAAAAGAACAGGAAAAAGCCA-ACGGGAACAATTACAACAGTACGAGGCAAAAAT
* * * * *
32867 GCATAAGGAACAGGAAAAAG-C-ACGGGAACAATCACAACTGTACGAGGCAAATAT
1 GCAAAAAGAACAGGAAAAAGCCAACGGGAACAATTACAACAGTACGAGGCAAAAAT
* * * *
32921 GCAAAAAGAACAGGAAAATCGCACATTACGGGAACAGTTAAAACAGCACGAGGCAAAAAT
1 GCAAAAAGAACAGGAAAA-AGC-CA--ACGGGAACAATTACAACAGTACGAGGCAAAAAT
* * * * * *
32981 GCAAAAAGAACTGGAAAATGCCATACGGGAACAATTACAACAGTATGAAGCACATAT
1 GCAAAAAGAACAGGAAAAAGCCA-ACGGGAACAATTACAACAGTACGAGGCAAAAAT
** * *
33038 GCAAAAAGAACAGGAAAATGATACATTACGGGAACAATTAAAACAGTACGAGGCAAAGAT
1 GCAAAAAGAACAGGAAAA--AGCCA--ACGGGAACAATTACAACAGTACGAGGCAAAAAT
*
33098 GAAAAAA
1 GCAAAAA
33105 ATGGAGGAGA
Statistics
Matches: 335, Mismatches: 61, Indels: 32
0.78 0.14 0.07
Matches are distributed among these distances:
54 43 0.13
55 1 0.00
56 5 0.01
57 126 0.38
58 10 0.03
59 12 0.04
60 135 0.40
61 3 0.01
ACGTcount: A:0.50, C:0.15, G:0.22, T:0.13
Consensus pattern (56 bp):
GCAAAAAGAACAGGAAAAAGCCAACGGGAACAATTACAACAGTACGAGGCAAAAAT
Found at i:32948 original size:171 final size:172
Alignment explanation
Indices: 32633--33055 Score: 553
Period size: 171 Copynumber: 2.4 Consensus size: 172
32623 CAACTTTGGG
* * * * * *
32633 GCAAAAAGAACAGGAAAATGCCACATTATGGGAACAATTACGACAATATGAGGAAAAAATGAAAA
1 GCAAAAAGAACTGGAAAATG-C-CA-TACGGGAACAATTACAACAGTATGAAGAAAAAATGCAAA
* * * * * * *
32698 AGGAACAGGAAAATGCTATAGGGGAACAATTACAATTGTACGCGGAAAATATGCGAAAAGAAGAG
63 AGGAACAGGAAAAAGC--TACGGGAACAATCACAACTGTACGAGGAAAATATGCAAAAAGAACAG
* * *
32763 GAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAAGAT
126 GAAAATGACACATTACGGGAACAATTAAAACAGCACGAGGCAAAAAT
* * *
32810 GCAAAAAGAACTGGAAAATGCCATACAGGAACAATTACAACAGTACGAAGAAAAAATGCATAAGG
1 GCAAAAAGAACTGGAAAATGCCATACGGGAACAATTACAACAGTATGAAGAAAAAATGCAAAAGG
*
32875 AACAGGAAAAAGC-ACGGGAACAATCACAACTGTACGAGGCAAATATGCAAAAAGAACAGGAAAA
66 AACAGGAAAAAGCTACGGGAACAATCACAACTGTACGAGGAAAATATGCAAAAAGAACAGGAAAA
*
32939 TCG-CACATTACGGGAACAGTTAAAACAGCACGAGGCAAAAAT
131 T-GACACATTACGGGAACAATTAAAACAGCACGAGGCAAAAAT
* * * *
32981 GCAAAAAGAACTGGAAAATGCCATACGGGAACAATTACAACAGTATGAAGCACATATGCAAAAAG
1 GCAAAAAGAACTGGAAAATGCCATACGGGAACAATTACAACAGTATGAAGAAAAAATGCAAAAGG
33046 AACAGGAAAA
66 AACAGGAAAA
33056 TGATACATTA
Statistics
Matches: 217, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
171 148 0.68
172 1 0.00
174 46 0.21
175 2 0.01
176 1 0.00
177 19 0.09
ACGTcount: A:0.50, C:0.15, G:0.22, T:0.13
Consensus pattern (172 bp):
GCAAAAAGAACTGGAAAATGCCATACGGGAACAATTACAACAGTATGAAGAAAAAATGCAAAAGG
AACAGGAAAAAGCTACGGGAACAATCACAACTGTACGAGGAAAATATGCAAAAAGAACAGGAAAA
TGACACATTACGGGAACAATTAAAACAGCACGAGGCAAAAAT
Found at i:33094 original size:117 final size:118
Alignment explanation
Indices: 32633--33104 Score: 468
Period size: 117 Copynumber: 4.1 Consensus size: 118
32623 CAACTTTGGG
* * * * * * *
32633 GCAAAAAGAACAGGAAAATGCCACATTATGGGAACAATTACGACAATATGAGGAAAAAATG-AAA
1 GCAAAAAGAACAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAATATGCAAA
* * ** *
32697 AAGGAACAGGAAAATG--CTATAGGGGAACAATTACAATTGTACGCGG-AAAATAT
66 AA-GAACAGGAAAATGTAC-ATACGGGAACAATTAAAACAGTACGAGGCAAAA-AT
* * *
32750 GCGAAAAGAAGAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAAGATGCAAA
1 GCAAAAAGAACAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAATATGCAAA
* * * * * *
32815 AAGAACTGGAAAATG-CCATACAGGAACAATTACAACAGTACGAAGAAAAAAT
66 AAGAACAGGAAAATGTACATACGGGAACAATTAAAACAGTACGAGGCAAAAAT
* * * * *
32867 GCATAAGGAACAGGAAAA--A-GC---ACGGGAACAATCACAACTGTACGAGGCAAATATGCAAA
1 GCAAAAAGAACAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAATATGCAAA
* * *
32926 AAGAACAGGAAAATCGCACATTACGGGAACAGTTAAAACAGCACGAGGCAAAAAT
66 AAGAACAGGAAAAT-GTACA-TACGGGAACAATTAAAACAGTACGAGGCAAAAAT
* * * *
32981 GCAAAAAGAACTGGAAAATG-C-CA-TACGGGAACAATTACAACAGTATGAAGCACATATGCAAA
1 GCAAAAAGAACAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAATATGCAAA
*
33043 AAGAACAGGAAAATGATACATTACGGGAACAATTAAAACAGTACGAGGCAAAGAT
66 AAGAACAGGAAAATG-TACA-TACGGGAACAATTAAAACAGTACGAGGCAAAAAT
*
33098 GAAAAAA
1 GCAAAAA
33105 ATGGAGGAGA
Statistics
Matches: 298, Mismatches: 45, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
111 48 0.16
112 1 0.00
113 2 0.01
114 44 0.15
115 2 0.01
116 1 0.00
117 190 0.64
118 10 0.03
ACGTcount: A:0.50, C:0.15, G:0.22, T:0.13
Consensus pattern (118 bp):
GCAAAAAGAACAGGAAAATGACACATTACGGGAACAATTACAACAGTACGAGGCAAATATGCAAA
AAGAACAGGAAAATGTACATACGGGAACAATTAAAACAGTACGAGGCAAAAAT
Found at i:34249 original size:2 final size:2
Alignment explanation
Indices: 34242--34280 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
34232 GTTAATCTTT
34242 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
34281 GAATGGTATC
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:38687 original size:20 final size:21
Alignment explanation
Indices: 38638--38694 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
38628 AATATTTAAA
*
38638 ATAATAATAAATTTAATATGT
1 ATAAAAATAAATTTAATATGT
38659 ATAAAAATAAATTTAATAT-T
1 ATAAAAATAAATTTAATATGT
* *
38679 TTTAAAATAAATTTAA
1 ATAAAAATAAATTTAA
38695 AAATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAAAAATAAATTTAATATGT
Found at i:38784 original size:30 final size:27
Alignment explanation
Indices: 38729--38784 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
38719 TTAAGATTTT
* *
38729 AAATTATATTTATTTTTTTATATAATC
1 AAATTATATTTATTTTTTAACATAATC
38756 AAATTATAATTTAATTTTTTAAACATAAT
1 AAATTAT-ATTT-ATTTTTT-AACATAAT
38785 TAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 7 0.29
30 6 0.25
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATTATATTTATTTTTTAACATAATC
Found at i:38842 original size:18 final size:18
Alignment explanation
Indices: 38819--38865 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
38809 CTTATATATA
38819 TAATTATTAAATAA-AATT
1 TAATTATTAAA-AATAATT
38837 TAATTATATTAAAAATAATT
1 TAA-T-TATTAAAAATAATT
*
38857 TAATGATTA
1 TAATTATTA
38866 TATATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATTATTAAAAATAATT
Found at i:38848 original size:20 final size:20
Alignment explanation
Indices: 38823--38860 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38813 TATATATAAT
38823 TATTAAATAA-AATTTAATTA
1 TATTAAA-AATAATTTAATTA
38843 TATTAAAAATAATTTAAT
1 TATTAAAAATAATTTAAT
38861 GATTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAAAATAATTTAATTA
Found at i:39209 original size:18 final size:18
Alignment explanation
Indices: 39186--39220 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39176 CAGTTGAAAA
*
39186 TAAAATAAATTAAATAAT
1 TAAAATAAATAAAATAAT
*
39204 TAAAATTAATAAAATAA
1 TAAAATAAATAAAATAA
39221 CCCCCAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATAAATAAAATAAT
Found at i:42503 original size:32 final size:31
Alignment explanation
Indices: 42467--42542 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
42457 CGGGGCCGTG
*
42467 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
42499 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
42530 GAGCCTACCTAAG
1 GGGCCTACCTAAG
42543 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:42526 original size:63 final size:63
Alignment explanation
Indices: 42420--42542 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
42410 ACCTAAGGGA
* * ** *
42420 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
42483 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
42543 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:45371 original size:7 final size:7
Alignment explanation
Indices: 45359--45397 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
45349 GGTCAACAAT
45359 GGTCAAC
1 GGTCAAC
45366 GGTCAAC
1 GGTCAAC
45373 GGGTCAAC
1 -GGTCAAC
45381 GGTCAAC
1 GGTCAAC
45388 GGGTCAAC
1 -GGTCAAC
45396 GG
1 GG
45398 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:45379 original size:15 final size:15
Alignment explanation
Indices: 45359--45397 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
45349 GGTCAACAAT
45359 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
45374 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
45389 GGTCAACGG
1 GGTCAACGG
45398 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:45405 original size:13 final size:13
Alignment explanation
Indices: 45400--45448 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
45390 GTCAACGGGT
*
45400 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
45413 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
45426 CGGGTCAGGTAAA
1 CGGGTCGGGTAAA
45439 CGGGTCGGGT
1 CGGGTCGGGT
45449 CGGGTTATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:45410 original size:18 final size:18
Alignment explanation
Indices: 45387--45422 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45377 CAACGGTCAA
45387 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
45405 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
45423 AAACGGGTCA
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:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:45418 original size:8 final size:8
Alignment explanation
Indices: 45359--45400 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
45349 GGTCAACAAT
45359 GGTCAAC-
1 GGTCAACG
45366 GGTCAACG
1 GGTCAACG
45374 GGTCAAC-
1 GGTCAACG
45381 GGTCAACG
1 GGTCAACG
45389 GGTCAACG
1 GGTCAACG
45397 GGTC
1 GGTC
45401 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:47585 original size:32 final size:31
Alignment explanation
Indices: 47549--47624 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
47539 CGGGGCCGTG
*
47549 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
47581 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
47612 GAGCCTACCTAAG
1 GGGCCTACCTAAG
47625 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:47608 original size:63 final size:63
Alignment explanation
Indices: 47502--47624 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
47492 ACCTAAGGGA
* * ** *
47502 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
47565 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
47625 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:50453 original size:7 final size:7
Alignment explanation
Indices: 50441--50479 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
50431 GGTCAACAAT
50441 GGTCAAC
1 GGTCAAC
50448 GGTCAAC
1 GGTCAAC
50455 GGGTCAAC
1 -GGTCAAC
50463 GGTCAAC
1 GGTCAAC
50470 GGGTCAAC
1 -GGTCAAC
50478 GG
1 GG
50480 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:50461 original size:15 final size:15
Alignment explanation
Indices: 50441--50479 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
50431 GGTCAACAAT
50441 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
50456 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
50471 GGTCAACGG
1 GGTCAACGG
50480 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:50487 original size:13 final size:13
Alignment explanation
Indices: 50482--50530 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
50472 GTCAACGGGT
*
50482 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
50495 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
50508 CGGGTCAGGTAAA
1 CGGGTCGGGTAAA
50521 CGGGTCGGGT
1 CGGGTCGGGT
50531 CGGGTCGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:50492 original size:18 final size:18
Alignment explanation
Indices: 50469--50504 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
50459 CAACGGTCAA
50469 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
50487 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
50505 AAACGGGTCA
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:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:50500 original size:8 final size:8
Alignment explanation
Indices: 50441--50482 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
50431 GGTCAACAAT
50441 GGTCAAC-
1 GGTCAACG
50448 GGTCAACG
1 GGTCAACG
50456 GGTCAAC-
1 GGTCAACG
50463 GGTCAACG
1 GGTCAACG
50471 GGTCAACG
1 GGTCAACG
50479 GGTC
1 GGTC
50483 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:51812 original size:37 final size:37
Alignment explanation
Indices: 51762--51832 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
51752 TGTCAACTTA
* *
51762 CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
1 CCAAATTTGACAATTTCCAAGACAAACCTAACAATTG
*
51799 CCAAATTTGACAATTTCCAAGACAAATCTAACAA
1 CCAAATTTGACAATTTCCAAGACAAACCTAACAA
51833 ATCTTCACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (37 bp):
CCAAATTTGACAATTTCCAAGACAAACCTAACAATTG
Found at i:53721 original size:21 final size:21
Alignment explanation
Indices: 53683--53722 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53673 TCTGCTGAAA
**
53683 CTCCACCTGTTTTAGAGTATG
1 CTCCACCTGTTGCAGAGTATG
*
53704 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCAGAGTA
53723 CTACTTGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCAGAGTATG
Found at i:56363 original size:24 final size:24
Alignment explanation
Indices: 56336--56386 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
56326 TGAAATACTT
56336 AGGTCTATTTATAGTTAAGTTTTA
1 AGGTCTATTTATAGTTAAGTTTTA
56360 AGGTCTATTTATAGTTAAGTTTTA
1 AGGTCTATTTATAGTTAAGTTTTA
56384 AGG
1 AGG
56387 ACTAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (24 bp):
AGGTCTATTTATAGTTAAGTTTTA
Found at i:56563 original size:37 final size:37
Alignment explanation
Indices: 56522--56593 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
56512 TGTCAACTTA
*
56522 CCAAATTTGACAATTTGCAAGTCAAACCTAACAATTG
1 CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
* *
56559 CCAAATTTGATAATTTGCAAGCCAAATCTAACAAT
1 CCAAATTTGACAATTTGCAAGCCAAACCTAACAAT
56594 CACAACAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.28
Consensus pattern (37 bp):
CCAAATTTGACAATTTGCAAGCCAAACCTAACAATTG
Found at i:61890 original size:3 final size:3
Alignment explanation
Indices: 61882--61944 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
61872 GTTTTTATCT
*
61882 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
61927 TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
61945 CAAACTGGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63287 original size:3 final size:3
Alignment explanation
Indices: 63274--63328 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
63264 TTATTTGCAA
* *
63274 TAT TAT T-T TAT TAT TAT TAT TTT TAT ATAT AAAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT
63319 TAT TA- TAT TA
1 TAT TAT TAT TA
63329 GTCATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:63293 original size:14 final size:14
Alignment explanation
Indices: 63274--63324 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
63264 TTATTTGCAA
63274 TATTATTTTATTAT
1 TATTATTTTATTAT
63288 TATTATTTTTATATAT
1 TATTA-TTTTAT-TAT
*
63304 AAATTATTATT-TTAT
1 -TATTATT-TTATTAT
63319 TATTAT
1 TATTAT
63325 ATTAGTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 6 0.19
17 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:63325 original size:23 final size:23
Alignment explanation
Indices: 63283--63326 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
63273 ATATTATTTT
*
63283 ATTATTATTATTTTTATATATAA
1 ATTATTATTATTATTATATATAA
63306 ATTATTATT-TTATTATTATAT
1 ATTATTATTATTATTA-TATAT
63327 TAGTCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTATTATTATTATTATATATAA
Found at i:63336 original size:34 final size:34
Alignment explanation
Indices: 63274--63338 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
63264 TTATTTGCAA
* *
63274 TATTATTTTATTATTATTATTTTTATATATAAAT
1 TATTATTTTATTATTATTATTGTCATATATAAAT
63308 TATTATTTTATTATTA-TATTAGTCATATATA
1 TATTATTTTATTATTATTATT-GTCATATATA
63339 TATATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (34 bp):
TATTATTTTATTATTATTATTGTCATATATAAAT
Found at i:63475 original size:2 final size:2
Alignment explanation
Indices: 63470--63496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63460 TAAATGTGTG
63470 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 T
63497 TTAATATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64036 original size:17 final size:18
Alignment explanation
Indices: 64014--64048 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
64004 ATTTCTTTCA
64014 ATTATTTTT-TATCCTTT
1 ATTATTTTTATATCCTTT
64031 ATTATTTTTATATCCTTT
1 ATTATTTTTATATCCTTT
64049 TTTGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTTTATATCCTTT
Found at i:69329 original size:43 final size:43
Alignment explanation
Indices: 69281--69495 Score: 358
Period size: 43 Copynumber: 5.0 Consensus size: 43
69271 GCCAAATCTA
*
69281 CTCATCAATTGCTCCAACCGATCACCATTTAGTTCTTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* *
69324 CTCATCAATTTCTCCAACCGATCACCATTCAGTTCTTTCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
69367 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* *
69410 CTCATCAATTGCTCCAACCGATCACCATTAAGATCTTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* * *
69453 CTCATCAATTGCCCCAACAGATCATCATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
69496 TTACTTTCAA
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.31
Consensus pattern (43 bp):
CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
Found at i:70271 original size:75 final size:76
Alignment explanation
Indices: 70069--70323 Score: 347
Period size: 75 Copynumber: 3.4 Consensus size: 76
70059 ATTAGCAAGA
70069 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCA-AAATCAGGAATATTAACGCATTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATCAGGAATATTAACGCATTTTGA
70133 ACGTTTGTATC
66 ACGTTTGTATC
** * * * * *
70144 AGCAAAATGTTGTAGCAT-TTCAAAAACCCATTTCAATCAG-AATCAAGAATATTGACGCATTTT
1 AGC-AAATGTTGGGGCATGCT-GAAAGCCCATTTCAATCAGAAATCAGGAATATTAACGCATTTT
70207 GAACGTTTGTATC
64 GAACGTTTGTATC
* *
70220 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGGAATATTAACTCATTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATCAGGAATATTAACGCATTTTGA
**
70284 ACGTTCATATC
66 ACGTTTGTATC
* *
70295 AGCAAATGCTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
70324 CATCATCATG
Statistics
Matches: 155, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
75 86 0.55
76 69 0.45
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (76 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATCAGGAATATTAACGCATTTTGA
ACGTTTGTATC
Found at i:71660 original size:22 final size:22
Alignment explanation
Indices: 71634--71757 Score: 185
Period size: 22 Copynumber: 5.6 Consensus size: 22
71624 TATATTTACA
*
71634 CTCTTCAAAGATGATAGATTCA
1 CTCTTCAAAGATGATAGATTCT
*
71656 CTCTTCAAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
71678 CTCTTCAAAGATGGTAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
71700 CTCTTCAGAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
71722 CTCTTCAAAGATAATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
71744 TTTTTCAAAGATGA
1 CTCTTCAAAGATGA
71758 AAGCTTTATT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:72584 original size:3 final size:3
Alignment explanation
Indices: 72576--72649 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
72566 TTTTATCTTC
72576 ATT ATT ATT ATT -TT ATT -TGT -TT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* *
72618 ATTT ATT TTT ATT ATT AAT ATT ATT ATT ATT A
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
72650 CAAACATGCC
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:72621 original size:33 final size:33
Alignment explanation
Indices: 72576--72647 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
72566 TTTTATCTTC
*
72576 ATTATTATTATTTTATTTGT-TTATTATTATTATT
1 ATTA-TATTA-TTTATTTGTATTATTAATATTATT
*
72610 ATTATATTATTTATTTTTATTATTAATATTATT
1 ATTATATTATTTATTTGTATTATTAATATTATT
72643 ATTAT
1 ATTAT
72648 TACAAACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 8 0.23
33 23 0.66
34 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (33 bp):
ATTATATTATTTATTTGTATTATTAATATTATT
Found at i:73922 original size:21 final size:22
Alignment explanation
Indices: 73883--73923 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
73873 TAGTTTGATA
*
73883 ATTTTTATTTAATATATTTTGT
1 ATTTTAATTTAATATATTTTGT
*
73905 ATTTTAATTTTATA-ATTTT
1 ATTTTAATTTAATATATTTT
73924 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTTTAATTTAATATATTTTGT
Found at i:74016 original size:23 final size:21
Alignment explanation
Indices: 73958--74019 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
73948 TTATTTGCAA
73958 TATTATTTTATTATTACTTTT
1 TATTATTTTATTATTACTTTT
* *
73979 GATATATTTAAATTATTACTTTAAT
1 TAT-TATTT-TATTATTACTTT--T
74004 TATTATTTTATTATTA
1 TATTATTTTATTATTA
74020 TAATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.06
22 5 0.15
23 18 0.55
24 5 0.15
25 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTATTTTATTATTACTTTT
Done.