Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002505.1 Hibiscus syriacus cultivar Beakdansim tig00005103_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: 95662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1667 original size:16 final size:15
Alignment explanation
Indices: 1648--1710 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 15
1638 AATCTAACAA
1648 TAATAATTAATAATAT
1 TAATAATTAA-AATAT
* *
1664 TAATGATTAAATATAA
1 TAATAATTAAA-ATAT
1680 TAATAATTAAAAT-T
1 TAATAATTAAAATAT
1694 TAATAATATATAAATAT
1 TAATAAT-TA-AAATAT
1711 AGCAATGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.18
15 5 0.13
16 26 0.67
17 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TAATAATTAAAATAT
Found at i:1698 original size:22 final size:22
Alignment explanation
Indices: 1651--1698 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1641 CTAACAATAA
*
1651 TAAT-TAATAATATTAATGATT
1 TAATATAATAATATTAATAATT
*
1672 AAATATAATAATAATTAA-AATT
1 TAATATAATAAT-ATTAATAATT
1694 TAATA
1 TAATA
1699 ATATATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAATATAATAATATTAATAATT
Found at i:17600 original size:149 final size:150
Alignment explanation
Indices: 17325--17628 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 150
17315 TAAAAGTGCA
*
17325 TTTTTAAATGGTTTTATAAAAGAAGAAGTGTATGTGGAACAACCTCCAGGTTTTGAAGATTCAAA
1 TTTTTAAATGGTTTTATAAAAGAAGAAGCGTATGTGGAACAACCTCCAGGTTTTGAAGATTCAAA
*
17390 ATTTCCAGATTATGTTTTTAAATTGACAAAAGCTCTTTATGGTTTAAAACAAGCTCGTAGAGCTT
66 ATTTCCAGATTATGTTTTTAAATTGACAAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTT
17455 GGTATGAAAGATTGTC-AAT
131 GGTATGAAAGATTGTCAAAT
*
17474 TTTTTAAATGGTTTTATAAAAGAAGAAGCGTATGTGGAACAACCTCCAGTTTTTGAAGATTCAAA
1 TTTTTAAATGGTTTTATAAAAGAAGAAGCGTATGTGGAACAACCTCCAGGTTTTGAAGATTCAAA
17539 ATTTCCAGATTATGTTTTTAAATTGACAAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTT
66 ATTTCCAGATTATGTTTTTAAATTGACAAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTT
17604 GGTATGAAAGATTGTCAAAT
131 GGTATGAAAGATTGTCAAAT
17624 TTTTT
1 TTTTT
17629 TGAAAAAGGT
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
149 143 0.95
150 8 0.05
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (150 bp):
TTTTTAAATGGTTTTATAAAAGAAGAAGCGTATGTGGAACAACCTCCAGGTTTTGAAGATTCAAA
ATTTCCAGATTATGTTTTTAAATTGACAAAAGCTCTTTATGGTTTAAAACAAGCTCCTAGAGCTT
GGTATGAAAGATTGTCAAAT
Found at i:21563 original size:20 final size:20
Alignment explanation
Indices: 21538--21606 Score: 138
Period size: 20 Copynumber: 3.5 Consensus size: 20
21528 AGAGATGTAC
21538 CGATGCACTAGTCCATGCAT
1 CGATGCACTAGTCCATGCAT
21558 CGATGCACTAGTCCATGCAT
1 CGATGCACTAGTCCATGCAT
21578 CGATGCACTAGTCCATGCAT
1 CGATGCACTAGTCCATGCAT
21598 CGATGCACT
1 CGATGCACT
21607 CTCAATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
CGATGCACTAGTCCATGCAT
Found at i:33108 original size:31 final size:31
Alignment explanation
Indices: 33070--33137 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
33060 GAATTCTGGA
*
33070 CACCAGTTGATTGATACTAATAAACAAATCC
1 CACCAGTTGATCGATACTAATAAACAAATCC
*
33101 CACCAGTTGATCGATACTTATAAACAAATCC
1 CACCAGTTGATCGATACTAATAAACAAATCC
33132 CACCAG
1 CACCAG
33138 ATTCGAGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (31 bp):
CACCAGTTGATCGATACTAATAAACAAATCC
Found at i:33683 original size:95 final size:96
Alignment explanation
Indices: 33519--33691 Score: 312
Period size: 95 Copynumber: 1.8 Consensus size: 96
33509 ATGCTTTCAG
* *
33519 CCATGCAAGAGCTCTTAACTTTGTAATAAAAAACAAATCCTTCATACTTGCAGATTTTCCTTCGA
1 CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
33584 AAATTATATCATTTCTTATCAACTAGATACT
66 AAATTATATCATTTCTTATCAACTAGATACT
*
33615 CCATGCAAAAGCTCTTAACTTTTTAAT-AAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
1 CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
33679 AAATTATATCATT
66 AAATTATATCATT
33692 GATACTCCAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 49 0.66
96 25 0.34
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (96 bp):
CCATGCAAAAGCTCTTAACTTTGTAATAAAAAACAAACCCTTCATACTTGCAGATTTTCCTTCGA
AAATTATATCATTTCTTATCAACTAGATACT
Found at i:36026 original size:18 final size:19
Alignment explanation
Indices: 36002--36048 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
35992 GATTACGACT
36002 TCATTTTGAAAAAATTGGA
1 TCATTTTGAAAAAATTGGA
36021 -CATTTTGAAAAAATTGGA
1 TCATTTTGAAAAAATTGGA
*
36039 TGATTTTGAA
1 TCATTTTGAA
36049 TTGATTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (19 bp):
TCATTTTGAAAAAATTGGA
Found at i:38767 original size:3 final size:3
Alignment explanation
Indices: 38754--38809 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
38744 TATATGTAAC
*
38754 ATA ATTA ATA ATA ATA A-A CAAA ATA ATA ATA ATAA ATA ATA AT- ATA
1 ATA A-TA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA
38800 ATA ATA ATA A
1 ATA ATA ATA A
38810 AAAGACCCGG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
2 3 0.06
3 37 0.79
4 7 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:38782 original size:18 final size:19
Alignment explanation
Indices: 38754--38806 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
38744 TATATGTAAC
38754 ATAATTAATAATAATAAACA
1 ATAA-TAATAATAATAAACA
*
38774 A-AATAATAATAATAAATA
1 ATAATAATAATAATAAACA
38792 ATAAT-ATAATAATAA
1 ATAATAATAATAATAA
38807 TAAAAAGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 25 0.81
19 5 0.16
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATAATAATAATAAACA
Found at i:38785 original size:21 final size:21
Alignment explanation
Indices: 38754--38810 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
38744 TATATGTAAC
38754 ATAATTAATAAT-AATAAACAAA
1 ATAA-TAATAATAAAT-AACAAA
* *
38776 ATAATAATAATAAATAATAAT
1 ATAATAATAATAAATAACAAA
38797 ATAATAATAATAAA
1 ATAATAATAATAAA
38811 AAGACCCGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATAATAATAAATAACAAA
Found at i:39074 original size:40 final size:40
Alignment explanation
Indices: 38956--39077 Score: 113
Period size: 40 Copynumber: 3.0 Consensus size: 40
38946 TTGGTTGTTG
*
38956 GGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCGTCTAA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCT-G--GTC-AA
* ** * * **
39000 AGG-TGACAAGGTTTC-TACATGATGAGGAAATCTGGTCAA
1 GGGATGACACTG-CTCATACATGATGAAGAGTTCTGGTCAA
39039 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCA
39078 TCTTTAGGAG
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
39 6 0.10
40 29 0.48
42 1 0.02
43 20 0.33
44 4 0.07
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAA
Found at i:39241 original size:133 final size:134
Alignment explanation
Indices: 39014--39352 Score: 475
Period size: 133 Copynumber: 2.5 Consensus size: 134
39004 GACAAGGTTT
* * * *
39014 CTACATGATGAGGAAATCTGGTCAAGGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
*
39079 CTTTAGGAGGAGTGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTA-GGATGACACG
66 CTTTAGGAGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACACG
39143 GCTC
131 GCTC
* * *
39147 CTACGTGATGAGGAGGTCTGGTCAGGGGATGGCACTGCTCATACGTGATGAAGAGTTCTGGCCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
* * * *
39212 CTTTAGGTAGG-GAGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACAT
66 CTTTAGG-AGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACAC
39276 GGCTC
130 GGCTC
* * * * * * *
39281 CTACATGATGAGGAGATCTGGTCAGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCCAT
1 CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
*
39346 CTCTAGG
66 CTTTAGG
39353 GATAATGGTT
Statistics
Matches: 181, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
133 105 0.58
134 76 0.42
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
CTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCAT
CTTTAGGAGGAGAGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTATGGATGACACG
GCTC
Found at i:39712 original size:66 final size:61
Alignment explanation
Indices: 39531--39705 Score: 174
Period size: 66 Copynumber: 2.8 Consensus size: 61
39521 CAAAAGCAAC
* * * * **
39531 TGTCTCAAA-AGACAAAATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAGGGAAT
1 TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAGGGAAT
* ** * *
39590 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGTGTTTCATGGGAA
1 TGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGTGTTT-A-GGG-A
39655 AT
60 AT
39657 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
39706 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
59 8 0.09
61 8 0.09
62 13 0.14
63 8 0.09
64 5 0.05
65 2 0.02
66 28 0.30
67 20 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (61 bp):
TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAGGGAAT
Found at i:40036 original size:15 final size:15
Alignment explanation
Indices: 40018--40046 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40008 TTGTTTTAAG
40018 AGAAAATGTTTCAAT
1 AGAAAATGTTTCAAT
40033 AGAAAATGTTTCAA
1 AGAAAATGTTTCAA
40047 GTGAAACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (15 bp):
AGAAAATGTTTCAAT
Found at i:40052 original size:15 final size:15
Alignment explanation
Indices: 40009--40052 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
39999 AAGATGATCT
* *
40009 TGTTTTAAGAGAAAA
1 TGTTTCAAGTGAAAA
40024 TGTTTCAA-TAGAAAA
1 TGTTTCAAGT-GAAAA
40039 TGTTTCAAGTGAAA
1 TGTTTCAAGTGAAA
40053 CGACTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 24 0.96
16 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (15 bp):
TGTTTCAAGTGAAAA
Found at i:40287 original size:65 final size:63
Alignment explanation
Indices: 40173--40292 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 63
40163 GGGTAGTTTT
*
40173 AAAAGAAATTGTCTCGAGAGACAAAATTTTTTTCAAAGGAAACAAACTCAAAGATTTTTTCTC
1 AAAAGAAATTGTCTCGAGAGACAAAATTTTTTCCAAAGGAAACAAACTCAAAGATTTTTTCTC
* *
40236 AAAAG-AATTGTCTCAAGAGAGACAAAAATTTGTTTCCAAA-GAAATATACTCAAAGAT
1 AAAAGAAATTGTCTC--GAGAGAC-AAAATTT-TTTCCAAAGGAAACAAACTCAAAGAT
40293 GGATTACATC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
62 9 0.18
63 5 0.10
64 7 0.14
65 22 0.44
66 7 0.14
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (63 bp):
AAAAGAAATTGTCTCGAGAGACAAAATTTTTTCCAAAGGAAACAAACTCAAAGATTTTTTCTC
Found at i:40398 original size:117 final size:116
Alignment explanation
Indices: 40200--40410 Score: 291
Period size: 117 Copynumber: 1.8 Consensus size: 116
40190 GAGACAAAAT
*
40200 TTTTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAATTGTCTCAAGAGAGACAAAAAT
1 TTTTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAACTGTCTCAAGAGAGACAAAAAT
*
40265 TTGTTTCCAAAGAAATATACTCAAAGATGGATTACATCTTAAGTGAGACGA
66 TTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACGA
* * * ** *
40316 TTTTTTCAAAGGAGACAATCTCAAAGGTTGGTTTT-TCATTAGAAACTGTCTCAAGAGAGAC-AC
1 TTTTTTCAAAGGAAACAAACTCAAAGATT--TTTTCTCAAAAG-AACTGTCTCAAGAGAGACAAA
**
40379 AATTTGTTTTTAAAGAAATAAACTCAAAGATG
63 AATTTGTTTCCAAAGAAATAAACTCAAAGATG
40411 ATTTTGTTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
116 26 0.32
117 35 0.43
118 21 0.26
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (116 bp):
TTTTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAACTGTCTCAAGAGAGACAAAAAT
TTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACGA
Found at i:40453 original size:27 final size:28
Alignment explanation
Indices: 40391--40470 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 28
40381 TTTGTTTTTA
* * *
40391 AAGAAATAAACTCAAAGATGATTTTGTT
1 AAGAAACAGACTCAAAGATTATTTTGTT
* *
40419 AAGAAACAGACTCAAAGATTTTTTTTTT
1 AAGAAACAGACTCAAAGATTATTTTGTT
* * *
40447 ATG-AACAGACTCAAAAATTGTTTT
1 AAGAAACAGACTCAAAGATTATTTT
40471 AAGAGAGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (28 bp):
AAGAAACAGACTCAAAGATTATTTTGTT
Found at i:41043 original size:100 final size:103
Alignment explanation
Indices: 40870--41106 Score: 331
Period size: 100 Copynumber: 2.3 Consensus size: 103
40860 ATTATGAATG
*
40870 AAATGTCTCAAGCGAGATGAAATTTGTTTTGAAAGAAACAACAATCTCAATTGAGATTAATATTG
1 AAATGTCTCAAGCGAGATGAAATTTGTTTT-AAAG-AACAACAATCTCAAGTGAGATTAATATTG
* *
40935 TTTTAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGG-AA
64 TTTCAAGTGAAGCAAATTC-AAATTTGTATATCAAAGGAAA
* * *
40975 AAATGTCTAAAGCGAGATGAAGTTTGTTTT-AAG-A-AACAATCTCAAGTGAGATTAATTTTGTT
1 AAATGTCTCAAGCGAGATGAAATTTGTTTTAAAGAACAACAATCTCAAGTGAGATTAATATTGTT
*
41037 TCAAGTGAAGCAAATTCAAATTTGTATATGAAAGGAAA
66 TCAAGTGAAGCAAATTCAAATTTGTATATCAAAGGAAA
* *
41075 AAATGTCTCAAGCGAGACGCAA-TTGTTTTAAA
1 AAATGTCTCAAGCGAGATGAAATTTGTTTTAAA
41107 TTTCTCAAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
99 23 0.19
100 64 0.54
101 1 0.01
103 3 0.03
105 28 0.24
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (103 bp):
AAATGTCTCAAGCGAGATGAAATTTGTTTTAAAGAACAACAATCTCAAGTGAGATTAATATTGTT
TCAAGTGAAGCAAATTCAAATTTGTATATCAAAGGAAA
Found at i:41556 original size:4 final size:4
Alignment explanation
Indices: 41539--41603 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
41529 TTTCATGTGT
* *
41539 TATG TATA TATG TATG TATG TATGGG T-TG -ATG TATG TTTG TATG TATG
1 TATG TATG TATG TATG TATG TAT--G TATG TATG TATG TATG TATG TATG
41587 TATG TAT- TGATG TATG T
1 TATG TATG T-ATG TATG T
41604 TTTCTTGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 4 0.08
4 43 0.84
5 2 0.04
6 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:41580 original size:28 final size:28
Alignment explanation
Indices: 41540--41605 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
41530 TTCATGTGTT
* * *
41540 ATGTATATATGTATGTATGTATGGGTTG
1 ATGTATGTTTGTATGTATGTATGGATTG
*
41568 ATGTATGTTTGTATGTATGTATGTATTG
1 ATGTATGTTTGTATGTATGTATGGATTG
41596 ATGTATGTTT
1 ATGTATGTTT
41606 TCTTGATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (28 bp):
ATGTATGTTTGTATGTATGTATGGATTG
Found at i:42688 original size:42 final size:42
Alignment explanation
Indices: 42599--42697 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
42589 AGTCAGGAGA
42599 CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
1 CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
* * * * *
42641 TTCTTTGT-TGTTGTTTTTTTTCCTTTGTTTTTTTCTTTG-TTT
1 CTCTTTGTCTG-TGTTCTTTGTCCTCT-TTTTGTTCTTTGCTTT
* *
42683 CTCTTTTTCTTTGTT
1 CTCTTTGTCTGTGTT
42698 TTAATTGGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 32 0.70
43 12 0.26
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (42 bp):
CTCTTTGTCTGTGTTCTTTGTCCTCTTTTTGTTCTTTGCTTT
Found at i:42690 original size:32 final size:30
Alignment explanation
Indices: 42612--42690 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
42602 TTTGTCTGTG
*
42612 TTCTTTG-TCCTCTTTTTGTTCTTTGCTTT
1 TTCTTTGTTTCTCTTTTTGTTCTTTGCTTT
* * *
42641 TTCTTTGTTGT-TGTTTTTTTTCCTTTGTTTTT
1 TTCTTTGTT-TCTCTTTTTGTT-CTTTG-CTTT
42673 TTCTTTGTTTCTCTTTTT
1 TTCTTTGTTTCTCTTTTT
42691 CTTTGTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 6 0.15
32 18 0.45
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (30 bp):
TTCTTTGTTTCTCTTTTTGTTCTTTGCTTT
Found at i:43390 original size:45 final size:44
Alignment explanation
Indices: 43300--43391 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 44
43290 ATAAATGCAG
* * *
43300 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATGATTCAAGGCCTAAAGAGAGAGAA
* *
43344 TGTTTCAAGGTCGAAAAGAAT-ATTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATGATTCAAGGCCT-AAAGAGAGAGAA
43389 TGT
1 TGT
43392 CAAAATTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (44 bp):
TGTTTCAAGGTGAAAAGAATGATTCAAGGCCTAAAGAGAGAGAA
Found at i:48527 original size:3 final size:3
Alignment explanation
Indices: 48514--48567 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
48504 TATATGTAAC
*
48514 ATA ATTA ATA ATA ATA ATA A-A CAAA ATA ATA ATAA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A ATA ATA ATA ATA
48561 ATA ATA A
1 ATA ATA A
48568 AAAGACCCGG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
2 1 0.02
3 38 0.83
4 7 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:49520 original size:2 final size:2
Alignment explanation
Indices: 49513--49546 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49503 TGTAGTAAGA
49513 AT 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 AT
49547 GAAATTCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50243 original size:35 final size:35
Alignment explanation
Indices: 50197--50272 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
50187 CATAAACAAT
*
50197 TTCCTGGTTGGTCATGGGTGACTAGCGCCAGTATA
1 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
50232 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
1 TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
50267 TTCCTG
1 TTCCTG
50273 CAAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (35 bp):
TTCCTGGTTGGTCATGGGTGACTAGCCCCAGTATA
Found at i:52746 original size:13 final size:13
Alignment explanation
Indices: 52730--52756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52720 TATCTAGTTG
52730 ACATGTATATTAA
1 ACATGTATATTAA
52743 ACATGTATATTAA
1 ACATGTATATTAA
52756 A
1 A
52757 TATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ACATGTATATTAA
Found at i:53146 original size:16 final size:16
Alignment explanation
Indices: 53125--53155 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53115 TCTAGTTTTT
53125 CCGAGTACCCGGTTAC
1 CCGAGTACCCGGTTAC
53141 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
53156 GTTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:53380 original size:15 final size:15
Alignment explanation
Indices: 53360--53416 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
53350 AATCAGGTAT
53360 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
** *
53375 CGGGTACCCGCAAAATT
1 CGGGTACCCG-ATTA-C
53392 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
53407 CGGGTACCCG
1 CGGGTACCCG
53417 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:53428 original size:17 final size:16
Alignment explanation
Indices: 53360--53428 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
53350 AATCAGGTAT
**
53360 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
53375 CGGGTACCCGCAAAATT
1 CGGGTACCCG-AAAATC
**
53392 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
53407 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
53424 CGGGT
1 CGGGT
53429 CGGGACACAG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:53428 original size:32 final size:32
Alignment explanation
Indices: 53360--53428 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
53350 AATCAGGTAT
*
53360 CGGGTACCCGATTACCGGGTACCCGCAAAATT
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
53392 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
53424 CGGGT
1 CGGGT
53429 CGGGACACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:53486 original size:15 final size:16
Alignment explanation
Indices: 53454--53508 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
53444 GAAATCGTCG
*
53454 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
53471 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
53486 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
53502 ACCCGGA
1 ACCCGGA
53509 TTTGCACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 12 0.35
17 8 0.24
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:54110 original size:15 final size:15
Alignment explanation
Indices: 54090--54122 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54080 GGTGAATTAT
*
54090 TTTGAATTTAAATAA
1 TTTGAATTTAAACAA
54105 TTTGAATTTAAACAA
1 TTTGAATTTAAACAA
54120 TTT
1 TTT
54123 CAATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTGAATTTAAACAA
Found at i:54510 original size:77 final size:77
Alignment explanation
Indices: 54378--54638 Score: 321
Period size: 77 Copynumber: 3.4 Consensus size: 77
54368 TATTGTGAGT
* * * * *
54378 AACCTATTTTATTAATAAAAATATTAGCATTCTAGATCGTAATTTATTTATTAGTGAATCATGAT
1 AACCCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGAT
*
54443 ATTCTTAGGTGC
66 ATTCTTAGGCGC
* * * *
54455 AACCCATTTTATGAATAAATATATTAACATTCAAGATCGTAACTTATTTCTTAGTGAACCATGAC
1 AACCCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGAT
54520 ATTCTT-GAGCGC
66 ATTCTTAG-GCGC
* * * * * *
54532 TACCCATTTTGTTAATAAAAATATTAACATTCCAGATAGCAATTTATTTCTTACTGAACCATGAT
1 AACCCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGAT
* *
54597 ATTCTTAAGCAC
66 ATTCTTAGGCGC
*
54609 AATCCATTTTATT-A-AAAAATATTAACATTC
1 AACCCATTTTATTAATAAAAATATTAACATTC
54639 CAAATTACAA
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
75 16 0.10
76 2 0.01
77 139 0.89
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (77 bp):
AACCCATTTTATTAATAAAAATATTAACATTCAAGATCGTAATTTATTTCTTAGTGAACCATGAT
ATTCTTAGGCGC
Found at i:54674 original size:75 final size:75
Alignment explanation
Indices: 54421--54674 Score: 233
Period size: 77 Copynumber: 3.3 Consensus size: 75
54411 AGATCGTAAT
* * * * ** *
54421 TTATTTATTAGTGAATCATGATATTCTTAGGTGCAACCCATTTTATGAATAAATATATTAACATT
1 TTATTTCTTAATGAACCATGATATTCTTAAGCACAACCCATTTTATTAA-AAA-ATATTAACATT
***
54486 -CAAGATCGTAAC
64 CCAA-ATTACAAC
* * * * * *
54498 TTATTTCTTAGTGAACCATGACATTCTTGAGCGCTACCCATTTTGTTAATAAAAATATTAACATT
1 TTATTTCTTAATGAACCATGATATTCTTAAGCACAACCCATTTTATT-A-AAAAATATTAACATT
* *
54563 CCAGA-TAGCAAT
64 CCAAATTA-CAAC
* *
54575 TTATTTCTTACTGAACCATGATATTCTTAAGCACAATCCATTTTATTAAAAAATATTAACATTCC
1 TTATTTCTTAATGAACCATGATATTCTTAAGCACAACCCATTTTATTAAAAAATATTAACATTCC
54640 AAATTACAAC
66 AAATTACAAC
* * *
54650 TTATTTCCTAATGATCCATTATATT
1 TTATTTCTTAATGAACCATGATATT
54675 TTTAGACGCA
Statistics
Matches: 145, Mismatches: 27, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
75 43 0.30
76 3 0.02
77 92 0.63
78 6 0.04
79 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (75 bp):
TTATTTCTTAATGAACCATGATATTCTTAAGCACAACCCATTTTATTAAAAAATATTAACATTCC
AAATTACAAC
Found at i:54703 original size:2 final size:2
Alignment explanation
Indices: 54696--54726 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54686 CCGTATTTCT
54696 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 T
54727 TCATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54960 original size:78 final size:77
Alignment explanation
Indices: 54820--54973 Score: 184
Period size: 78 Copynumber: 2.0 Consensus size: 77
54810 GGTATAACTC
* * * * * *
54820 ATTTTATTATTAAAAATATTAAGATTCTAGATCGCAATCTATTTATTAGTGAACCACGACATTCT
1 ATTTTATTATAAAAAATATTAACATTCTAGATCACAACCTATTTATTAGTGAACCACAACATTAT
*
54885 TGGGCGCAACCT
66 TGGACGCAACCT
* ***
54897 ATTTTATTAATAAAAAATATTAACATTAC-ATATCACAACCTATTTATTAGTGAACTGTAACATT
1 ATTTTATT-ATAAAAAATATTAACATT-CTAGATCACAACCTATTTATTAGTGAACCACAACATT
54961 ATTGGACGCAACC
64 ATTGGACGCAACC
54974 GTAATTCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
77 8 0.12
78 55 0.86
79 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (77 bp):
ATTTTATTATAAAAAATATTAACATTCTAGATCACAACCTATTTATTAGTGAACCACAACATTAT
TGGACGCAACCT
Found at i:69221 original size:22 final size:22
Alignment explanation
Indices: 69195--69262 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
69185 TTAATTTTTA
69195 TTTAACTAGCAGCGATATTAAT
1 TTTAACTAGCAGCGATATTAAT
69217 TTTAACTAGCAGCGATATTAAT
1 TTTAACTAGCAGCGATATTAAT
* *
69239 TTTAATTAACAGCGATATTAAT
1 TTTAACTAGCAGCGATATTAAT
69261 TT
1 TT
69263 AACAGGCAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
TTTAACTAGCAGCGATATTAAT
Found at i:71069 original size:16 final size:16
Alignment explanation
Indices: 71048--71079 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
71038 ACTATTCACA
*
71048 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
71064 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
71080 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:74615 original size:16 final size:16
Alignment explanation
Indices: 74590--74623 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
74580 CAGGACCCTT
74590 CAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAA
* *
74606 CAAAACAAAACAAAAA
1 CAAAAAAAAAAAAAAA
74622 CA
1 CA
74624 TACACACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:82665 original size:19 final size:20
Alignment explanation
Indices: 82585--82677 Score: 98
Period size: 21 Copynumber: 4.6 Consensus size: 20
82575 TTCTAAACTT
**
82585 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
82605 AAAACCGCAACACGAAAAATG
1 AAAATCGCAACGCG-AAAATG
** *
82626 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGCGA-AAATG
82647 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
82666 AAAATCGCAACG
1 AAAATCGCAACG
82678 AGATAATCGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.28
20 13 0.21
21 31 0.51
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:82676 original size:40 final size:40
Alignment explanation
Indices: 82585--82680 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
82575 TTCTAAACTT
82585 AAAATCGCAAC-ATGAAAATGAAAACCGCAACACGAAAAATG
1 AAAATCGCAACGA-GAAAATGAAAACCGCAACACG-AAAATG
** * *
82626 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAACCGCAACACGAAAATG
82666 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
82681 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 18 0.38
41 11 0.23
42 18 0.38
ACGTcount: A:0.51, C:0.20, G:0.19, T:0.10
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAACCGCAACACGAAAATG
Found at i:82769 original size:39 final size:39
Alignment explanation
Indices: 82716--82800 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
82706 CATTGTGATT
82716 TCATTTCGCGTTGCGATTTTAATT-TCGCGTTGCGATAG
1 TCATTTCGCGTTGCGATTTTAATTCTCGCGTTGCGATAG
* * * **
82754 TCATTCTCTCGTTGCGATTTTCATTCTCTCGTTGCGATTT
1 TCATT-TCGCGTTGCGATTTTAATTCTCGCGTTGCGATAG
82794 TCATTTC
1 TCATTTC
82801 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
38 5 0.12
39 19 0.47
40 16 0.40
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (39 bp):
TCATTTCGCGTTGCGATTTTAATTCTCGCGTTGCGATAG
Found at i:82792 original size:20 final size:19
Alignment explanation
Indices: 82714--82800 Score: 111
Period size: 20 Copynumber: 4.5 Consensus size: 19
82704 CGCATTGTGA
82714 TTTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
*
82733 TTTAATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
** *
82752 AGTCATTCTCTCGTTGCGAT
1 TTTCATT-TCGCGTTGCGAT
*
82772 TTTCATTCTCTCGTTGCGAT
1 TTTCATT-TCGCGTTGCGAT
82792 TTTCATTTC
1 TTTCATTTC
82801 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 24 0.40
20 36 0.60
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCATTTCGCGTTGCGAT
Found at i:84626 original size:17 final size:17
Alignment explanation
Indices: 84596--84628 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
84586 GTTGCTGCCA
84596 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
84613 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
84629 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:84681 original size:92 final size:93
Alignment explanation
Indices: 84483--84855 Score: 562
Period size: 94 Copynumber: 4.1 Consensus size: 93
84473 TAGATTGCTT
* *
84483 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
84544 ATTTGTCTTT-TGTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGT-TTTGTCTTTTGGTTGA
* *
84572 AGTAAATTTATTTGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
84637 A-TTGTCTTTG-TTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
84664 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
84729 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
84758 AGTAAATTTGTTCGTTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
84823 AGTTGTCTTTGTTTTGTCATTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
84851 AGTAA
1 AGTAA
84856 TGCAATCCAT
Statistics
Matches: 263, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
89 33 0.13
91 18 0.07
92 74 0.28
93 35 0.13
94 103 0.39
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:84819 original size:186 final size:182
Alignment explanation
Indices: 84483--84855 Score: 563
Period size: 186 Copynumber: 2.0 Consensus size: 182
84473 TAGATTGCTT
84483 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
* * *
84548 GTCTTTTGTTTGTCTTTTGGTTGAAGTAAATTTATTTGGTTGCTGCCAATTCTGTTAAACTGTGT
66 GTCTTTTGTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGT
* *
84613 ATTCTTTAACACTGTGAAGTTAGTA-TTGTCTTTG-TTTGTCTTTTGGTTGAA
131 ATTCTTTAACACTCTGAAGTTAGTAGTTGTCTTTGTTTTGTCATTTGGTTG-A
* * *
84664 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
* *
84729 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGTTTGCTGCCAATTATGCTAAA
62 ATTTGTCTTTTG-TTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAA
*
84793 CTGTGTATTCTTTAATACTCTGAAGTTAGTAGTTGTCTTTGTTTTGTCATTTGGTTGA
125 CTGTGTATTCTTTAACACTCTGAAGTTAGTAGTTGTCTTTGTTTTGTCATTTGGTTGA
84851 AGTAA
1 AGTAA
84856 TGCAATCCAT
Statistics
Matches: 173, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
181 34 0.20
183 3 0.02
184 6 0.03
185 41 0.24
186 60 0.35
187 15 0.09
188 14 0.08
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.47
Consensus pattern (182 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTTGTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGT
ATTCTTTAACACTCTGAAGTTAGTAGTTGTCTTTGTTTTGTCATTTGGTTGA
Found at i:84972 original size:20 final size:20
Alignment explanation
Indices: 84947--85008 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
84937 TTTTGGTTGA
84947 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
84967 AATGAAAATCGCAATGCGA-
1 AATGAAAATCGCAACGAGAG
* *
84986 AACGAAAAGCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
85006 AAT
1 AAT
85009 CGCAACACGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.44
20 19 0.56
ACGTcount: A:0.50, C:0.16, G:0.24, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:85049 original size:19 final size:19
Alignment explanation
Indices: 84945--85039 Score: 76
Period size: 19 Copynumber: 5.2 Consensus size: 19
84935 TCTTTTGGTT
84945 GAAATGAAAATCGCAACGA-
1 GAAATGAAAATCGCAAC-AC
**
84964 GAGAATGAAAATCGCAATGC
1 GA-AATGAAAATCGCAACAC
* *
84984 GAAACGAAAAGCGC-A-AC
1 GAAATGAAAATCGCAACAC
*
85001 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACAC
*
85017 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACAC
85036 GAAA
1 GAAA
85040 CTATAATCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 7 0.12
15 2 0.03
16 3 0.05
17 2 0.03
18 2 0.03
19 28 0.47
20 16 0.27
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.08
Consensus pattern (19 bp):
GAAATGAAAATCGCAACAC
Found at i:85144 original size:20 final size:19
Alignment explanation
Indices: 85046--85165 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
85036 GAAACTATAA
85046 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
85065 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
85079 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
85098 TCGCGTTGCGA-TTTCGTT
1 TCGCGTTGCGATTTTCATT
85116 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
85135 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
*
85155 TCGTGTTGCGA
1 TCGCGTTGCGA
85166 CAGTCATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.10
16 3 0.04
17 3 0.04
18 17 0.20
19 34 0.41
20 18 0.22
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:85173 original size:39 final size:38
Alignment explanation
Indices: 85093--85190 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 38
85083 GTTACGATTT
* * ***
85093 TCATTTCGCGTTGCGA-TTTCGTTTCGCGTTGCGATTT
1 TCATTTCACGTTGCGATTTTCATTTCGCGTTGCGACAG
* *
85130 TCATTCTCTCGTTGCGATTTTCATTTCGTGTTGCGACAG
1 TCATT-TCACGTTGCGATTTTCATTTCGCGTTGCGACAG
85169 TCATTTTTCACGTTGCGATTTT
1 TCA--TTTCACGTTGCGATTTT
85191 AAGTTCAGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 5 0.10
38 10 0.20
39 19 0.38
40 14 0.28
41 2 0.04
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.47
Consensus pattern (38 bp):
TCATTTCACGTTGCGATTTTCATTTCGCGTTGCGACAG
Found at i:85666 original size:42 final size:42
Alignment explanation
Indices: 85590--85678 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
85580 GACTCGCCTG
* *
85590 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
* * * * *
85632 TCATTCCTCGAGAGTCCCCTCCTACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
85674 TCATC
1 TCATC
85679 GTTGAAGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
Found at i:87067 original size:13 final size:14
Alignment explanation
Indices: 87051--87085 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
87041 ATTGTTTAAT
87051 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
87064 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
87078 TGATTTGT
1 TGATTTGT
87086 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:87227 original size:14 final size:14
Alignment explanation
Indices: 87207--87245 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
87197 ATGCGAAATG
* *
87207 AAATCGCAACTAGA
1 AAATCGCAACGACA
*
87221 GAATCGCAACGACA
1 AAATCGCAACGACA
87235 AAATCGCAACG
1 AAATCGCAACG
87246 CGAAACTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:87258 original size:19 final size:19
Alignment explanation
Indices: 87234--87299 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
87224 TCGCAACGAC
87234 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
**
87253 AAAATCGCAATTCGAAACT
1 AAAATCGCAACGCGAAACT
*
87272 AAAAATTGCAACGCGAAACT
1 -AAAATCGCAACGCGAAACT
*
87292 AAATTCGC
1 AAAATCGC
87300 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.17
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:87282 original size:20 final size:20
Alignment explanation
Indices: 87234--87294 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
87224 TCGCAACGAC
87234 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAACTA
**
87253 AAAATCGCAATTCGAAACTA
1 AAAATCGCAACGCGAAACTA
*
87273 AAAATTGCAACGCGAAACTA
1 AAAATCGCAACGCGAAACTA
87293 AA
1 AA
87295 TTCGCGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACTA
Found at i:87317 original size:19 final size:19
Alignment explanation
Indices: 87295--87430 Score: 114
Period size: 19 Copynumber: 7.7 Consensus size: 19
87285 CGAAACTAAA
87295 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
87314 TTCGC-TTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
87328 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
87346 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
87361 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
87379 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** **
87398 TTCGTATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
87417 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
87431 AGACATTAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
13 2 0.02
14 15 0.16
16 9 0.10
17 3 0.03
18 6 0.07
19 47 0.52
20 9 0.10
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:87340 original size:32 final size:33
Alignment explanation
Indices: 87299--87392 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
87289 ACTAAATTCG
87299 CGTTGCGATTTTCATTTCGC-TTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
87331 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
87364 CGTTGCGATTTTCATTTCGCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
87393 TTCATTTCGT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 20 0.34
33 39 0.66
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:87476 original size:20 final size:19
Alignment explanation
Indices: 87365--87476 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 19
87355 CGATTCTCTC
** *
87365 GTTGCGATTTTCATTTCGC
1 GTTGCGATAGTCATTTCGT
**
87384 GTTGCGATTTTCATTTCGT
1 GTTGCGATAGTCATTTCGT
* *
87403 ATTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTT-CGT
* **
87423 GTTGCGATAGACATTAAGAT
1 GTTGCGATAGTCATTTCG-T
87443 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTT-CGT
87464 GTTGCGATAGTCA
1 GTTGCGATAGTCA
87477 AATAAATGCC
Statistics
Matches: 74, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 32 0.43
20 27 0.36
21 14 0.19
22 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:91574 original size:75 final size:72
Alignment explanation
Indices: 91485--91709 Score: 258
Period size: 75 Copynumber: 3.1 Consensus size: 72
91475 TAAACTCGAG
* * *
91485 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTGAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAAATATT-TATTTT-T-TTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
91550 TTAATTAAGT
63 TTAATTAAGA
*
91560 TTTAGGATATTATTTTATAT-TTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATATTATTTTAAATATTTAT-TTT-TTTT--GTATTTTAGTTTAAATAGGTTTTAGTAT
*
91624 TTTAATTAGGA
62 TTTAATTAAGA
* ** *
91635 TTTAGAATATTATTTTAAATA-TTATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTT
1 TTTAGGATATTATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAGGTTTT-AGTATTTT
*
91698 AATTAGGA
65 AATTAAGA
91706 TTTA
1 TTTA
91710 AGATGTTTTA
Statistics
Matches: 133, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
70 5 0.04
71 36 0.27
73 8 0.06
74 9 0.07
75 75 0.56
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (72 bp):
TTTAGGATATTATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTA
ATTAAGA
Found at i:91633 original size:19 final size:19
Alignment explanation
Indices: 91536--91639 Score: 54
Period size: 19 Copynumber: 5.5 Consensus size: 19
91526 TTAGTTTGAA
91536 TAGGTTTTAGTATTTTAAT
1 TAGGTTTTAGTATTTTAAT
* * * *
91555 TAAGTTTTAGGATATTATTT
1 TAGGTTTTAGTATTTTA-AT
** * *
91575 TATATTTTA-TCTTTGT-TT
1 TAGGTTTTAGTATTT-TAAT
* *
91593 TAGGTATTT--TAGTTTAAA
1 TAGGT-TTTAGTATTTTAAT
91611 TAGGTTTTAGTATTTTAAT
1 TAGGTTTTAGTATTTTAAT
*
91630 TAGGATTTAG
1 TAGGTTTTAG
91640 AATATTATTT
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
17 4 0.07
18 13 0.21
19 35 0.57
20 9 0.15
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (19 bp):
TAGGTTTTAGTATTTTAAT
Found at i:92408 original size:7 final size:7
Alignment explanation
Indices: 92359--92390 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
92349 TAAAAACCTT
92359 TTTATTTA
1 TTTA-TTA
92367 TTTATTA
1 TTTATTA
92374 TTTATTA
1 TTTATTA
92381 TTTATTA
1 TTTATTA
92388 TTT
1 TTT
92391 TCTCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:92420 original size:22 final size:22
Alignment explanation
Indices: 92374--92421 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
92364 TTATTTATTA
*
92374 TTTATTATTTATTATTTTCTCT
1 TTTATTATTTATTATTTTCTAT
92396 TTTATT-TATTATTATCTTT-TAT
1 TTTATTAT-TTATTAT-TTTCTAT
92418 TTTA
1 TTTA
92422 AATCTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATTATTTATTATTTTCTAT
Done.