Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013846.1 Corchorus olitorius cultivar O-4 contig13879, 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: 71524
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:16248 original size:31 final size:31
Alignment explanation
Indices: 16170--16255 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
16160 ACTTTTTGAA
16170 ACACATGGTCACTTTTTTGGTACACATGGCGTG
1 ACACAT-GTCAC-TTTTTGGTACACATGGCGTG
* **
16203 ATATGTGTCACTTTTTGGTACACATGGCGTG
1 ACACATGTCACTTTTTGGTACACATGGCGTG
* *
16234 CCACATGTCGCTTTTTGGTACA
1 ACACATGTCACTTTTTGGTACA
16256 TGTGGCATGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
31 37 0.82
32 5 0.11
33 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (31 bp):
ACACATGTCACTTTTTGGTACACATGGCGTG
Found at i:16267 original size:31 final size:31
Alignment explanation
Indices: 16171--16267 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
16161 CTTTTTGAAA
* *
16171 CACATGGTCACTTTTTTGGTACACATGGCGTGA
1 CACAT-GTCAC-TTTTTGGTACACATGGCATGC
* ** *
16204 TATGTGTCACTTTTTGGTACACATGGCGTGC
1 CACATGTCACTTTTTGGTACACATGGCATGC
* **
16235 CACATGTCGCTTTTTGGTACATGTGGCATGC
1 CACATGTCACTTTTTGGTACACATGGCATGC
16266 CA
1 CA
16268 TCGTCGGACA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 46 0.87
32 5 0.09
33 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (31 bp):
CACATGTCACTTTTTGGTACACATGGCATGC
Found at i:21728 original size:2 final size:2
Alignment explanation
Indices: 21693--21718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21683 TTGTTATTAT
21693 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
21719 CGTGTATATA
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):
TA
Found at i:22353 original size:23 final size:23
Alignment explanation
Indices: 22327--22371 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
22317 CATTTATCTT
22327 TATACGAACATAATATTTTGTGA
1 TATACGAACATAATATTTTGTGA
*
22350 TATAGGAACATAATATTTTGTG
1 TATACGAACATAATATTTTGTG
22372 TTGTATGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (23 bp):
TATACGAACATAATATTTTGTGA
Found at i:23051 original size:16 final size:16
Alignment explanation
Indices: 23020--23063 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
23010 CTTTTTCAAG
23020 TTAAAA-TATA-ATTAT
1 TTAAAATTATATA-TAT
*
23035 TTAAATTTATATATAT
1 TTAAAATTATATATAT
23051 TTAAAATTATATA
1 TTAAAATTATATA
23064 AAAAATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 19 0.76
17 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATTATATATAT
Found at i:23551 original size:23 final size:23
Alignment explanation
Indices: 23525--23569 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
23515 CATTTATCTT
23525 TATACGAACATAATATTTTGTGA
1 TATACGAACATAATATTTTGTGA
23548 TATACGAACATAATATTTTGTG
1 TATACGAACATAATATTTTGTG
23570 TTAAATGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
TATACGAACATAATATTTTGTGA
Found at i:26618 original size:2 final size:2
Alignment explanation
Indices: 26611--26639 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
26601 GGCATAATGT
26611 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26640 GAAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26756 original size:116 final size:117
Alignment explanation
Indices: 26625--26858 Score: 420
Period size: 117 Copynumber: 2.0 Consensus size: 117
26615 TATATATATA
*
26625 TATATATATATTATAGAAAT-AAATTCTTG-ACAAAAAATAGAAAGAAATAAATTAAGAAAGAAG
1 TATATATATATTATAGAAATAAAATTCTTGCAAAAAAAAT-GAAAGAAATAAATTAAGAAAG-AG
26688 AAAG-AAAATTATATAGTAGTTAATCCCATACTCTGATATCAAATGTGTGATAG
64 AAAGAAAAATTATATAGTAGTTAATCCCATACTCTGATATCAAATGTGTGATAG
26741 TATATATATATTATAGAAATAAAATTCTTGCAAAAAAAATGAAAGAAATAAATTAAGAAAGAGAA
1 TATATATATATTATAGAAATAAAATTCTTGCAAAAAAAATGAAAGAAATAAATTAAGAAAGAGAA
26806 AGAAAAATTATATAGTAGTTAATCCCATACTCTGATATCAAATGTGTGATAG
66 AGAAAAATTATATAGTAGTTAATCCCATACTCTGATATCAAATGTGTGATAG
26858 T
1 T
26859 CTAATTTATT
Statistics
Matches: 114, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
116 26 0.23
117 80 0.70
118 8 0.07
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (117 bp):
TATATATATATTATAGAAATAAAATTCTTGCAAAAAAAATGAAAGAAATAAATTAAGAAAGAGAA
AGAAAAATTATATAGTAGTTAATCCCATACTCTGATATCAAATGTGTGATAG
Found at i:29163 original size:12 final size:12
Alignment explanation
Indices: 29146--29189 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
29136 TTTAATCCAG
29146 ATATCGACGGAT
1 ATATCGACGGAT
*
29158 ATATCGAAAGGAT
1 ATATCG-ACGGAT
*
29171 ATATCGACGGGT
1 ATATCGACGGAT
29183 ATATCGA
1 ATATCGA
29190 GGTATCGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:29661 original size:31 final size:31
Alignment explanation
Indices: 29622--29689 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
29612 TTTTGCCAAA
*
29622 TTAC-CAATTTGAGTCTAACCCTTTCAAAAG
1 TTACTCAATTTGAGCCTAACCCTTTCAAAAG
29652 TTACTCAATTTGAGCCTAACCCTTTCAAAAG
1 TTACTCAATTTGAGCCTAACCCTTTCAAAAG
*
29683 TTGCTCA
1 TTACTCA
29690 GTCTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (31 bp):
TTACTCAATTTGAGCCTAACCCTTTCAAAAG
Found at i:31593 original size:17 final size:16
Alignment explanation
Indices: 31553--31587 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
31543 ATCTAATATC
31553 TTTATAATTACTTTATT
1 TTTATAATTAC-TTATT
31570 TTTATAATTAC-TATT
1 TTTATAATTACTTATT
31585 TTT
1 TTT
31588 CAATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATAATTACTTATT
Found at i:35069 original size:2 final size:2
Alignment explanation
Indices: 35062--35086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35052 TAATGGAAGA
35062 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
35087 TGGGGTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:48863 original size:5 final size:5
Alignment explanation
Indices: 48855--48888 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
48845 TTTAAATCAA
* *
48855 TTATT TTATT TCATC TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTAT
48889 GTGAAATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:56074 original size:95 final size:95
Alignment explanation
Indices: 55911--56191 Score: 553
Period size: 95 Copynumber: 3.0 Consensus size: 95
55901 ATCAAAGTTT
55911 CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
1 CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
55976 AATGCAAATGGAGGAACTTCTTGTTTTGAA
66 AATGCAAATGGAGGAACTTCTTGTTTTGAA
56006 CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
1 CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
56071 AATGCAAATGGAGGAACTTCTTGTTTTGAA
66 AATGCAAATGGAGGAACTTCTTGTTTTGAA
*
56101 CAGATTGAAGTACTTATAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
1 CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
56166 AATGCAAATGGAGGAACTTCTTGTTT
66 AATGCAAATGGAGGAACTTCTTGTTT
56192 CTTCAAAATT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 185 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (95 bp):
CAGATTGAAGTACTTCTAACATGAAAAAAGGAAAAAGTAAAACAGAGCAACTCAACCACTTCTCC
AATGCAAATGGAGGAACTTCTTGTTTTGAA
Found at i:59460 original size:9 final size:9
Alignment explanation
Indices: 59446--59504 Score: 66
Period size: 9 Copynumber: 6.4 Consensus size: 9
59436 GAGTTAAAGG
59446 TTTTGTTTT
1 TTTTGTTTT
59455 TTTTG-TTT
1 TTTTGTTTT
* *
59463 TGTTGTTTG
1 TTTTGTTTT
59472 TTTTGTTTTGT
1 TTTTG-TTT-T
*
59483 TTTTTTTTT
1 TTTTGTTTT
59492 TTTTGTTTT
1 TTTTGTTTT
59501 TTTT
1 TTTT
59505 CTCAAAGACC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.17
9 24 0.59
10 6 0.15
11 4 0.10
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:59463 original size:5 final size:5
Alignment explanation
Indices: 59445--59504 Score: 70
Period size: 5 Copynumber: 12.0 Consensus size: 5
59435 TGAGTTAAAG
* *
59445 GTTTT GTTTT -TTTT GTTTT GTTGTTT GTTTT GTTTT GTTTT TTTTT TTTTT
1 GTTTT GTTTT GTTTT GTTTT G-T-TTT GTTTT GTTTT GTTTT GTTTT GTTTT
59496 GTTTT -TTTT
1 GTTTT GTTTT
59505 CTCAAAGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
4 8 0.16
5 36 0.72
6 2 0.04
7 4 0.08
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
GTTTT
Found at i:59470 original size:17 final size:16
Alignment explanation
Indices: 59451--59504 Score: 83
Period size: 17 Copynumber: 3.4 Consensus size: 16
59441 AAAGGTTTTG
59451 TTTTTTTTGTTTTGTT
1 TTTTTTTTGTTTTGTT
*
59467 GTTTGTTTTGTTTTGTT
1 -TTTTTTTTGTTTTGTT
59484 TTTTTTTT-TTTTGTT
1 TTTTTTTTGTTTTGTT
59499 TTTTTT
1 TTTTTT
59505 CTCAAAGACC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.37
16 7 0.20
17 15 0.43
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTTGTTTTGTT
Found at i:60470 original size:2 final size:2
Alignment explanation
Indices: 60463--60489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60453 ACAGCCTTCA
60463 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
60490 ATAAAATAAA
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:60566 original size:13 final size:13
Alignment explanation
Indices: 60548--60580 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
60538 TATCTTATAC
60548 ATCTTATCTTACT
1 ATCTTATCTTACT
*
60561 ATCTTATCTTATT
1 ATCTTATCTTACT
60574 ATCTTAT
1 ATCTTAT
60581 TATACTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (13 bp):
ATCTTATCTTACT
Found at i:63170 original size:22 final size:21
Alignment explanation
Indices: 63145--63229 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
63135 TACATAGGAA
63145 GGTTATCAATATTTCATATTGT
1 GGTTATCAA-ATTTCATATTGT
* * *
63167 GGTTACCAACATTTCATATGGA
1 GGTTATCAA-ATTTCATATTGT
* *
63189 GGTTATCGAAACTTCATAGTGT
1 GGTTATC-AAATTTCATATTGT
* *
63211 AGTTATCAAAATTTTATAT
1 GGTTATC-AAATTTCATAT
63230 AGAAATTACA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 46 0.96
23 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (21 bp):
GGTTATCAAATTTCATATTGT
Found at i:63205 original size:44 final size:44
Alignment explanation
Indices: 63144--63229 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
63134 ATACATAGGA
* * * *
63144 AGGTTATCAATATTTCATATTGTGGTTACCAACATTTCATATGG
1 AGGTTATCAATACTTCATAGTGTAGTTACCAAAATTTCATATGG
* *
63188 AGGTTATCGAA-ACTTCATAGTGTAGTTATCAAAATTTTATAT
1 AGGTTATC-AATACTTCATAGTGTAGTTACCAAAATTTCATAT
63230 AGAAATTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 33 0.94
45 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (44 bp):
AGGTTATCAATACTTCATAGTGTAGTTACCAAAATTTCATATGG
Found at i:63303 original size:22 final size:22
Alignment explanation
Indices: 63240--63303 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
63230 AGAAATTACA
* * *
63240 AAAATTTCATAAAAAGATTATC
1 AAAATTTCATAAGAAGGTTAAC
* *
63262 AAAATTTC-TTAGAGATGTTAAC
1 AAAATTTCATAAGA-AGGTTAAC
*
63284 TAAATTTCATAAGAAGGTTA
1 AAAATTTCATAAGAAGGTTA
63304 TCGATATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.09
22 25 0.78
23 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTAAC
Found at i:63599 original size:22 final size:22
Alignment explanation
Indices: 63503--63777 Score: 173
Period size: 22 Copynumber: 12.6 Consensus size: 22
63493 CATATGGAGG
* *
63503 TTATCGAAATTTCATGGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* * *
63525 TTA-CAAAATTTTATGAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGA
* *
63546 TTATCAAATTTTTCATAGTGTGG
1 TTATCAAA-ATTTCATAGTGTGA
* * *
63569 TTA-C-CAATTTTATAGCGTGA
1 TTATCAAAATTTCATAGTGTGA
* * *
63589 TTATCAAAATTTAATAGGGAGA
1 TTATCAAAATTTCATAGTGTGA
* * * ** *
63611 TTATCACAATTTCACACTAAGG
1 TTATCAAAATTTCATAGTGTGA
*
63633 TTATCAAAATTTCATAGTGTGC
1 TTATCAAAATTTCATAGTGTGA
*
63655 TTATCAAAATTTCATAGTGTGC
1 TTATCAAAATTTCATAGTGTGA
* * * *
63677 TTATCTAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGTGTGA
* *
63699 TTATCAAATTTTCATAAG-GTGG
1 TTATCAAAATTTCAT-AGTGTGA
* * * * *
63721 TTATCCAGATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGTGA
* *
63743 TTATCAAATTTTCACAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
63765 TTATCAATATTTC
1 TTATCAAAATTTC
63778 TACGTTGGAG
Statistics
Matches: 193, Mismatches: 52, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
20 13 0.07
21 17 0.09
22 151 0.78
23 12 0.06
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:63681 original size:44 final size:44
Alignment explanation
Indices: 63501--63777 Score: 195
Period size: 44 Copynumber: 6.3 Consensus size: 44
63491 CTCATATGGA
* * * * *
63501 GGTTATCGAAATTTCATGGTGTGATTA-CAAAATTTTATGAG-GA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAT-AGTGT
* * * *
63544 GGTTATCAAATTTTTCATAGTGTGGTTA-C-CAATTTTATAGCGT
1 GGTTATCAAA-ATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
* * * * * * * * **
63587 GATTATCAAAATTTAATAGGGAGATTATCACAATTTCACACTAA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
*
63631 GGTTATCAAAATTTCATAGTGTGCTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
* * * * *
63675 GCTTATCTAAATTTCACAATGTGGTTATCAAATTTTCATAAG-GT
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAT-AGTGT
* * * * * *
63719 GGTTATCCAGATTTCATAATGAGGTTATCAAATTTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
* *
63763 GATTATCAATATTTC
1 GGTTATCAAAATTTC
63778 TACGTTGGAG
Statistics
Matches: 185, Mismatches: 43, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
42 14 0.08
43 30 0.16
44 139 0.75
45 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
Found at i:63725 original size:66 final size:65
Alignment explanation
Indices: 63501--63776 Score: 213
Period size: 66 Copynumber: 4.2 Consensus size: 65
63491 CTCATATGGA
* * * * *
63501 GGTTATCGAAA-TTTCATGGTGTGATTA-CAAAATTTTATGAG-GAGGTTATCAAATTTTTCATA
1 GGTTATC-AAATTTTCATAGCGTGATTATCAAAATTTCAT-AGTGAGATTATCAAA--TTTCACA
*
63563 GTGT
62 ATGT
* * * * *
63567 GGTTA-CCAATTTT-ATAGCGTGATTATCAAAATTTAATAGGGAGATTATCACAATTTCACACTA
1 GGTTATCAAATTTTCATAGCGTGATTATCAAAATTTCATAGTGAGATTATCA-AATTTCACAATG
*
63630 A
65 T
* * * * *
63631 GGTTATCAAAATTTCATAGTGTGCTTATCAAAATTTCATAGTGTGCTTATCTAAATTTCACAATG
1 GGTTATCAAATTTTCATAGCGTGATTATCAAAATTTCATAGTGAGATTATC-AAATTTCACAATG
63696 T
65 T
* * * * * *
63697 GGTTATCAAATTTTCATAAG-GTGGTTATCCAGATTTCATAATGAGGTTATCAAATTTTCACAGT
1 GGTTATCAAATTTTCAT-AGCGTGATTATCAAAATTTCATAGTGAGATTATCAAA-TTTCACAAT
63761 GT
64 GT
*
63763 GATTATCAATATTT
1 GGTTATCAA-ATTT
63777 CTACGTTGGA
Statistics
Matches: 171, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
64 26 0.15
65 32 0.19
66 106 0.62
67 7 0.04
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (65 bp):
GGTTATCAAATTTTCATAGCGTGATTATCAAAATTTCATAGTGAGATTATCAAATTTCACAATGT
Found at i:65447 original size:30 final size:29
Alignment explanation
Indices: 65384--65447 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
65374 ACAAAACGGT
***
65384 CAAATAAGCCCCTGAACTCTAATTGCAGC
1 CAAATAAGCCCCTGAACTCTAATAAAAGC
65413 CAAATAAGCCCCTGAACTCTTAA-AAAATGC
1 CAAATAAGCCCCTGAACTC-TAATAAAA-GC
65443 CAAAT
1 CAAAT
65448 GCCCTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTAATAAAAGC
Found at i:66005 original size:27 final size:27
Alignment explanation
Indices: 65967--66023 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
65957 GCAATAAGCC
*
65967 TTAATTTTTTAAAAATATGGAAAGATA
1 TTAATTTTTTAAAAATATGAAAAGATA
***
65994 TTAATTTTTTAAGGTTATGAAAAGATA
1 TTAATTTTTTAAAAATATGAAAAGATA
66021 TTA
1 TTA
66024 TAATCTACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (27 bp):
TTAATTTTTTAAAAATATGAAAAGATA
Found at i:67550 original size:22 final size:22
Alignment explanation
Indices: 67517--67770 Score: 176
Period size: 22 Copynumber: 11.4 Consensus size: 22
67507 ACAATCAAAC
* *
67517 CAAAATTACATAGGATGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
67539 CACAATTTCATAGTG-TGGTTAA
1 CAAAATTTCATAG-GAAGGTTAT
*
67561 CAAAATTTCATATGG-ATGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
67583 CAAAACTTCACACAGG-A-GTTAT
1 CAAAA-TT-TCATAGGAAGGTTAT
** *
67605 CAAAATTTCATACAAAGGTTAC
1 CAAAATTTCATAGGAAGGTTAT
* **
67627 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
67649 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
**
67671 CAAAATTTCATACAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
67693 CGAAATTTTATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* *
67715 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
67737 CAAAATTTCATAGGCAGGGAGGTTAT
1 CAAAATTTCATAGG-A---AGGTTAT
67763 CAAAATTT
1 CAAAATTT
67771 GTGCTTATCA
Statistics
Matches: 180, Mismatches: 40, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.02
21 4 0.02
22 148 0.82
23 8 0.04
24 3 0.02
26 14 0.08
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:67625 original size:66 final size:65
Alignment explanation
Indices: 67555--67748 Score: 212
Period size: 66 Copynumber: 2.9 Consensus size: 65
67545 TTCATAGTGT
* * * *
67555 GGTTAACAAAATTTCATATGGATGTTATCAAAACTTCACACAGGA-GTTATCAAAATTTCATACA
1 GGTTAACAAAATTTTATA-GGATGTTATCAAAATTTCATA-AGGAGGTTAACAAAATTTCATACA
67619 AA
64 AA
* ** * * *
67621 GGTTACCAAAATTTTATAAAAAGGTTATCAAAATTTCTTAGGGAGGTTAACAAAATTTCATACAA
1 GGTTAACAAAATTTTAT-AGGATGTTATCAAAATTTCATAAGGAGGTTAACAAAATTTCATACAA
67686 A
65 A
* * *
67687 GGTTATCGAAATTTTATAGTG-TGGTTATCAAAATTTCATAAGAAGGTTAACAAAATTTCATA
1 GGTTAACAAAATTTTATAG-GAT-GTTATCAAAATTTCATAAGGAGGTTAACAAAATTTCATA
67749 GGCAGGGAGG
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
65 4 0.04
66 101 0.95
67 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (65 bp):
GGTTAACAAAATTTTATAGGATGTTATCAAAATTTCATAAGGAGGTTAACAAAATTTCATACAAA
Found at i:67844 original size:22 final size:22
Alignment explanation
Indices: 67793--67862 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
67783 GTTTCCTAGG
* *
67793 GAGGTTAAAAAAATTTAATAGG-
1 GAGGTTATAAAAATTTTAT-GGA
* *
67815 GAGCTTATGAAAATTTTATGGA
1 GAGGTTATAAAAATTTTATGGA
* * *
67837 GAGGTTATCAAAATTATATAGA
1 GAGGTTATAAAAATTTTATGGA
67859 GAGG
1 GAGG
67863 ATATCACGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (22 bp):
GAGGTTATAAAAATTTTATGGA
Found at i:67867 original size:22 final size:22
Alignment explanation
Indices: 67824--67868 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
67814 GGAGCTTATG
* * *
67824 AAAATTTTATGGAGAGGTTATC
1 AAAATTATATAGAGAGGATATC
67846 AAAATTATATAGAGAGGATATC
1 AAAATTATATAGAGAGGATATC
67868 A
1 A
67869 CGGTTTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (22 bp):
AAAATTATATAGAGAGGATATC
Found at i:67916 original size:22 final size:23
Alignment explanation
Indices: 67891--68117 Score: 99
Period size: 22 Copynumber: 10.5 Consensus size: 23
67881 CATAGGGAGT
* *
67891 TTATCGAAA-TTTCATGGTGTGG
1 TTATCAAAATTTTCATAGTGTGG
*
67913 TTATCAAAATTTTCATAGTGTGA
1 TTATCAAAATTTTCATAGTGTGG
** * *
67936 TTA-C-CGATTTT-ATAGTGCGA
1 TTATCAAAATTTTCATAGTGTGG
* * *
67956 TTATCAAAATTTT-ATAGGGAGA
1 TTATCAAAATTTTCATAGTGTGG
* * * *
67978 TTATCAAAA-TCTCACACTGAGG
1 TTATCAAAATTTTCATAGTGTGG
*
68000 TTTTC---A--TTCATAGTGTGG
1 TTATCAAAATTTTCATAGTGTGG
* **
68018 TTATTAAAA-TTTCACCGTGTGG
1 TTATCAAAATTTTCATAGTGTGG
*
68040 TTATC-AAATTTTCATAG-GAAGG
1 TTATCAAAATTTTCATAGTG-TGG
* * *
68062 TTATCGAAA-TTTCATAATGAGG
1 TTATCAAAATTTTCATAGTGTGG
* * *
68084 TTAAC-AAATTTTCACAGTGTAG
1 TTATCAAAATTTTCATAGTGTGG
*
68106 TTATCAATATTT
1 TTATCAAAATTT
68118 CAATGTTGGA
Statistics
Matches: 155, Mismatches: 36, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
18 11 0.07
19 1 0.01
20 11 0.07
21 16 0.10
22 93 0.60
23 23 0.15
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTCATAGTGTGG
Found at i:68056 original size:44 final size:44
Alignment explanation
Indices: 68006--68119 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 44
67996 GAGGTTTTCA
* ** * *
68006 TTCATAGTGTGGTTATTAAAATTTCACCGTGTGGTTATCAAATT
1 TTCATAGTGTGGTTATCAAAATTTCACAATGAGGTTAACAAATT
* * *
68050 TTCATAG-GAAGGTTATCGAAATTTCATAATGAGGTTAACAAATT
1 TTCATAGTG-TGGTTATCAAAATTTCACAATGAGGTTAACAAATT
* * *
68094 TTCACAGTGTAGTTATCAATATTTCA
1 TTCATAGTGTGGTTATCAAAATTTCA
68120 ATGTTGGAGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (44 bp):
TTCATAGTGTGGTTATCAAAATTTCACAATGAGGTTAACAAATT
Found at i:68949 original size:18 final size:18
Alignment explanation
Indices: 68926--68960 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
68916 TACCAATTCG
68926 CGTCAAT-TAGGGGCAGAC
1 CGTCAATGT-GGGGCAGAC
68944 CGTCAATGTGGGGCAGA
1 CGTCAATGTGGGGCAGA
68961 ATCTTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.26, C:0.20, G:0.37, T:0.17
Consensus pattern (18 bp):
CGTCAATGTGGGGCAGAC
Found at i:70321 original size:16 final size:16
Alignment explanation
Indices: 70300--70334 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
70290 TATGGTTAAA
*
70300 TTAAATGAATTTAATT
1 TTAAATAAATTTAATT
70316 TTAAATAAATTTAATT
1 TTAAATAAATTTAATT
70332 TTA
1 TTA
70335 TTTCAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATAAATTTAATT
Done.