Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009002.1 Corchorus capsularis cultivar CVL-1 contig09023, 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: 59534
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:5286 original size:24 final size:24
Alignment explanation
Indices: 5251--5299 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5241 AAGAACAAGA
5251 AAAACAGATATTTTACAAAATTCT
1 AAAACAGATATTTTACAAAATTCT
*
5275 AAAACAGTTATTTTACAAAATTCT
1 AAAACAGATATTTTACAAAATTCT
5299 A
1 A
5300 TGTAATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAACAGATATTTTACAAAATTCT
Found at i:5376 original size:18 final size:19
Alignment explanation
Indices: 5353--5388 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5343 TTCCACTTTT
5353 TCTCTCTCCTTT-CTCTTC
1 TCTCTCTCCTTTACTCTTC
5371 TCTCTCTCCTTTACTCTT
1 TCTCTCTCCTTTACTCTT
5389 TCTACCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTCTCCTTTACTCTTC
Found at i:7484 original size:2 final size:2
Alignment explanation
Indices: 7477--7513 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7467 CTCTTCTTAT
7477 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 T
7514 TCAATAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7721 original size:27 final size:27
Alignment explanation
Indices: 7681--7755 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
7671 TTTTCACAAG
* *
7681 ATAATCACAATATTAATTAATTTATGA
1 ATAATCACATTATTAATTAATTCATGA
*
7708 ATAATCACATTATTAATTGATTCATGA
1 ATAATCACATTATTAATTAATTCATGA
*
7735 ATAATCACATTATTCATTAAT
1 ATAATCACATTATTAATTAAT
7756 GTCTTTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (27 bp):
ATAATCACATTATTAATTAATTCATGA
Found at i:13721 original size:15 final size:13
Alignment explanation
Indices: 13692--13717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13682 TTTATTTTGA
13692 TTATAAATATTAT
1 TTATAAATATTAT
13705 TTATAAATATTAT
1 TTATAAATATTAT
13718 ATTTGGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATAAATATTAT
Found at i:14443 original size:30 final size:30
Alignment explanation
Indices: 14398--14466 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
14388 TTTCTGCCTA
*
14398 TCTGATGTTATTTTTATG-ATGTTCATATTTG
1 TCTGAT-TTATTTTTA-GAATGTTCATATATG
*
14429 TCTGATTTTTTTTTAGAATGTTCATATATG
1 TCTGATTTATTTTTAGAATGTTCATATATG
14459 TCTAGATT
1 TCT-GATT
14467 GATAAGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 23 0.68
31 10 0.29
ACGTcount: A:0.22, C:0.07, G:0.14, T:0.57
Consensus pattern (30 bp):
TCTGATTTATTTTTAGAATGTTCATATATG
Found at i:17268 original size:17 final size:17
Alignment explanation
Indices: 17246--17284 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
17236 AGATTTTATA
17246 ACTTTGATAATTACTAT
1 ACTTTGATAATTACTAT
17263 ACTTTGATAATTACTAT
1 ACTTTGATAATTACTAT
*
17280 CCTTT
1 ACTTT
17285 TGTTTCTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (17 bp):
ACTTTGATAATTACTAT
Found at i:17767 original size:19 final size:18
Alignment explanation
Indices: 17737--17784 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 18
17727 GTCCCTCACC
17737 AATT-TTTTTTTTAAAAA
1 AATTATTTTTTTTAAAAA
17754 AAGTTATATTTTTTTAAAAA
1 AA-TTAT-TTTTTTTAAAAA
17774 AATTATTTTTT
1 AATTATTTTTT
17785 AATCAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 7 0.25
19 5 0.18
20 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTATTTTTTTTAAAAA
Found at i:19016 original size:2 final size:2
Alignment explanation
Indices: 19009--19045 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18999 TTTTGATGCA
19009 AT AT AT AT AT 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 AT AT AT AT AT A
19046 AGCATGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21536 original size:10 final size:11
Alignment explanation
Indices: 21519--21544 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21509 AAAGCAATGA
21519 CTTTTTTTTTT
1 CTTTTTTTTTT
21530 CTTTTTTTTTT
1 CTTTTTTTTTT
21541 CTTT
1 CTTT
21545 CTGGAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:23048 original size:17 final size:15
Alignment explanation
Indices: 23014--23070 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 15
23004 AGAAACCGAC
23014 TTATATATATAATAA
1 TTATATATATAATAA
23029 -T-TATATATAATAA
1 TTATATATATAATAA
* *
23042 TT-TAT-TATTATTA
1 TTATATATATAATAA
23055 TATATATATATAATAA
1 T-TATATATATAATAA
23071 AATATAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 19 0.56
14 6 0.18
15 3 0.09
16 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATATATAATAA
Found at i:36438 original size:5 final size:5
Alignment explanation
Indices: 36430--36466 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
36420 ATAAAAAGCA
*
36430 ATCTT ATCTC ATCTT ATCTT ATCTT ATCTT ATCTT AT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT AT
36467 ATATATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (5 bp):
ATCTT
Found at i:37725 original size:82 final size:85
Alignment explanation
Indices: 37624--37796 Score: 257
Period size: 82 Copynumber: 2.1 Consensus size: 85
37614 TATTAATGAA
*
37624 TATTAATGACACTATTTATTACCAAAATAG-TCAATTACCAAAATA-GAGCA-GGGG-AGAAAGT
1 TATTAATGACACCATTTATTACCAAAATAGAT-AATTACCAAAATAGGA-CAGGGGGAAGAAAGT
*
37685 GTAAGAAACTAATTGATAGAC-
64 GTAAGAAACTAATTGAGAGACT
*
37706 TATTAATGACACCATTTATTACCAAAATGGATAATTACCAAAATAGGACAGGGGGAAAGAAAGTG
1 TATTAATGACACCATTTATTACCAAAATAGATAATTACCAAAATAGGACAGGGGG-AAGAAAGTG
37771 TAAGAAACTAATTGAGAGACT
65 TAAGAAACTAATTGAGAGACT
37792 TATTA
1 TATTA
37797 GTAATCCGGC
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
82 43 0.52
83 7 0.09
85 27 0.33
86 5 0.06
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (85 bp):
TATTAATGACACCATTTATTACCAAAATAGATAATTACCAAAATAGGACAGGGGGAAGAAAGTGT
AAGAAACTAATTGAGAGACT
Found at i:40190 original size:46 final size:43
Alignment explanation
Indices: 40092--40208 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 43
40082 ACAATCAAAC
* * * * *
40092 CAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTTA
1 CAAAATTTCATACAGAGGTTATCAAAACTTCATAGTGTGGTTA
*
40135 CAAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTGTAGTTA
1 C-AAAATTTCATACAGAGGTTATCAAAACTTCATAGTGTG--GTTA
*
40181 TCAAAATTTCATACAGAGGTTACCAAAA
1 -CAAAATTTCATACAGAGGTTATCAAAA
40209 TGTCATAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 1 0.02
44 33 0.52
46 28 0.44
47 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (43 bp):
CAAAATTTCATACAGAGGTTATCAAAACTTCATAGTGTGGTTA
Found at i:40207 original size:22 final size:22
Alignment explanation
Indices: 40090--40282 Score: 116
Period size: 22 Copynumber: 8.5 Consensus size: 22
40080 TGACAATCAA
* * *
40090 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * *
40112 ATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
40134 ACAAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
40156 ATCAAAACTTCATAGTGTGTAGTT
1 ACCAAAATTTCATAGAGAG--GTT
* *
40180 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
40202 ACCAAAATGTCATAAAAAAAGTT
1 ACCAAAATTTCAT-AGAGAGGTT
* * *
40225 ACCAAAATTTCTTAGGGATGTT
1 ACCAAAATTTCATAGAGAGGTT
**
40247 AATAAAATTTCATAGGAAAGGAGGTT
1 ACCAAAATTTCATA-G--A-GAGGTT
40273 ACCAAAATTT
1 ACCAAAATTT
40283 GTGCTTATCA
Statistics
Matches: 125, Mismatches: 39, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
22 76 0.61
23 18 0.14
24 18 0.14
26 13 0.10
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:40215 original size:46 final size:43
Alignment explanation
Indices: 40114--40215 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 43
40104 GAAAGATTAT
* *
40114 CAAAATTTCATAGTGTGGTTACAAAAATTTCATATAGAGGTTAT
1 CAAAA-TTCATAGTGTGGTTACAAAAATTTCATACAGAGGTTAC
40158 CAAAACTTCATAGTGTGTAGTTATC-AAAATTTCATACAGAGGTTAC
1 CAAAA-TTCATAGTGTG--GTTA-CAAAAATTTCATACAGAGGTTAC
40204 CAAAATGTCATA
1 CAAAAT-TCATA
40216 AAAAAAGTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 16 0.31
45 1 0.02
46 33 0.65
47 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (43 bp):
CAAAATTCATAGTGTGGTTACAAAAATTTCATACAGAGGTTAC
Found at i:40339 original size:22 final size:22
Alignment explanation
Indices: 40287--40345 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
40277 AAATTTGTGC
** *
40287 TTATCAAAATTTCCTAGGGAGT
1 TTATCAAAATTTTATAGGGAGA
*
40309 TTAACAAAATTTTATAGGGAGA
1 TTATCAAAATTTTATAGGGAGA
*
40331 TTATGAAAATTTTAT
1 TTATCAAAATTTTAT
40346 GGAGAGGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGA
Found at i:40356 original size:22 final size:23
Alignment explanation
Indices: 40314--40363 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
40304 GGAGTTTAAC
40314 AAAATTTTATAGGGAGATTA-TG
1 AAAATTTTATAGGGAGATTATTG
*
40336 AAAATTTTAT-GGAGAGGTTATTG
1 AAAATTTTATAGG-GAGATTATTG
40359 AAAAT
1 AAAAT
40364 ACATAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (23 bp):
AAAATTTTATAGGGAGATTATTG
Found at i:40426 original size:22 final size:22
Alignment explanation
Indices: 40401--40633 Score: 154
Period size: 22 Copynumber: 10.6 Consensus size: 22
40391 CTCATAGGGA
40401 GGTTATCAAAATTTCATAATGT
1 GGTTATCAAAATTTCATAATGT
40423 GGTTATCAAAATTTTCATAATGT
1 GGTTATCAAAA-TTTCATAATGT
* * *
40446 GGTT-GC-AAATTTTATTTAGTGT
1 GGTTATCAAAATTTCA--TAATGT
* * * *
40468 GATTATTAAAATTTTAT-AGGTT
1 GGTTATCAAAATTTCATAATG-T
* * * *
40490 GATTATCAAAATTTCACACTGA
1 GGTTATCAAAATTTCATAATGT
* * *
40512 GATTATCGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAATGT
* * *
40534 GGTTACCAAAAGTTC--AGTGT
1 GGTTATCAAAATTTCATAATGT
* ** *
40554 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCATAATGT
40576 GGTTATCAAAATTTCATAATGAT
1 GGTTATCAAAATTTCATAATG-T
* *
40599 -GTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAATGT
* *
40620 AGTTATCAATATTT
1 GGTTATCAAAATTT
40634 TTACATTGGA
Statistics
Matches: 165, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
20 21 0.13
21 5 0.03
22 115 0.70
23 16 0.10
24 8 0.05
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAATGT
Found at i:40457 original size:21 final size:22
Alignment explanation
Indices: 40401--40458 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
40391 CTCATAGGGA
* *
40401 GGTTATCAAAATTTCATAATGT
1 GGTTAGCAAATTTTCATAATGT
*
40423 GGTTATCAAAATTTTCATAATGT
1 GGTTAGC-AAATTTTCATAATGT
40446 GGTT-GCAAATTTT
1 GGTTAGCAAATTTT
40459 ATTTAGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
23 18 0.55
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (22 bp):
GGTTAGCAAATTTTCATAATGT
Found at i:40569 original size:42 final size:43
Alignment explanation
Indices: 40509--40613 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 43
40499 AATTTCACAC
* * *
40509 TGAGATTATCGAAA-TTTCATAGTGTGGTTACCAAAAGTTCAGT-G
1 TGAG-TTATC-AAATTTTCATAGGGAGGTTACCAAAAGTTCA-TAA
* *
40553 TG-GTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAA
1 TGAGTTATCAAATTTTCATAGGGAGGTTACCAAAAGTTCATAA
40595 TGATGTTATCAAATTTTCA
1 TGA-GTTATCAAATTTTCA
40614 AAATGTAGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
41 4 0.08
42 30 0.58
43 1 0.02
44 17 0.33
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (43 bp):
TGAGTTATCAAATTTTCATAGGGAGGTTACCAAAAGTTCATAA
Found at i:44545 original size:18 final size:18
Alignment explanation
Indices: 44522--44557 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44512 CCTATGAAAT
*
44522 TCCAAAAAATTTTCAAAA
1 TCCAAAAAATCTTCAAAA
44540 TCCAAAAAATCTTCAAAA
1 TCCAAAAAATCTTCAAAA
44558 AACATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (18 bp):
TCCAAAAAATCTTCAAAA
Found at i:49012 original size:21 final size:22
Alignment explanation
Indices: 48981--49026 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
48971 GATTTAAAAA
48981 AAAAGGAAAAATAATGGTCTGC
1 AAAAGGAAAAATAATGGTCTGC
49003 AAAA-GAAAAATAATGGTCTGC
1 AAAAGGAAAAATAATGGTCTGC
49024 AAA
1 AAA
49027 GTTATCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (22 bp):
AAAAGGAAAAATAATGGTCTGC
Found at i:52602 original size:19 final size:18
Alignment explanation
Indices: 52578--52629 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
52568 GGGAGTAGAG
52578 AATAGAAGTATGGAGAGAC
1 AATAGAAGTATGGAGA-AC
*
52597 AATAGAA-TATGGAGAAG
1 AATAGAAGTATGGAGAAC
*
52614 AAGA-AAGTATGGAGAA
1 AATAGAAGTATGGAGAA
52630 GGGAGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.43
18 8 0.27
19 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.31, T:0.15
Consensus pattern (18 bp):
AATAGAAGTATGGAGAAC
Found at i:56192 original size:83 final size:83
Alignment explanation
Indices: 56053--56206 Score: 272
Period size: 83 Copynumber: 1.9 Consensus size: 83
56043 TTGAACCAGG
* *
56053 ATGGCCAAACTGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTGTGGTTTATAAAAG
1 ATGGCCAAACTGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGGTTTACAAAAG
56118 CATATGTTTATTATCGGT
66 CATATGTTTATTATCGGT
* *
56136 ATGGCCTAGCTGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGGTTTACAAAAG
1 ATGGCCAAACTGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGGTTTACAAAAG
56201 CATATG
66 CATATG
56207 CTTCAATCTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (83 bp):
ATGGCCAAACTGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGGTTTACAAAAG
CATATGTTTATTATCGGT
Found at i:56476 original size:23 final size:23
Alignment explanation
Indices: 56444--56489 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
56434 CAGATAAAGC
*
56444 AATACTAGCTCTTCCGGAGCCTT
1 AATACAAGCTCTTCCGGAGCCTT
56467 AATACAAGCTCTTCCGGAGCCTT
1 AATACAAGCTCTTCCGGAGCCTT
56490 CAATCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (23 bp):
AATACAAGCTCTTCCGGAGCCTT
Found at i:56518 original size:38 final size:38
Alignment explanation
Indices: 56467--56542 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
56457 CCGGAGCCTT
*
56467 AATACAAGCTCTTCCGGAGCCTTCAATCAAATTTGCAC
1 AATACAAGCTCTTCCGGAGCCATCAATCAAATTTGCAC
56505 AATACTAA-CTCTTCCGGAGCCATCAATCAAATTTGCAC
1 AATAC-AAGCTCTTCCGGAGCCATCAATCAAATTTGCAC
56543 TACTTGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 34 0.94
39 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (38 bp):
AATACAAGCTCTTCCGGAGCCATCAATCAAATTTGCAC
Found at i:57918 original size:54 final size:54
Alignment explanation
Indices: 57827--57929 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
57817 ATATAATTTA
*
57827 AAGTGGATAGTATGACAACTTCGGGTGTCAAACTTTGGCAACAATTAAAGTTTC
1 AAGTGGATAGTATGACAACTTCGGGTATCAAACTTTGGCAACAATTAAAGTTTC
* * *
57881 AAGTGGATAGTATGACAACTTCGGGTATCAGATTTTGGTAACAATTAAA
1 AAGTGGATAGTATGACAACTTCGGGTATCAAACTTTGGCAACAATTAAA
57930 CAAATATTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (54 bp):
AAGTGGATAGTATGACAACTTCGGGTATCAAACTTTGGCAACAATTAAAGTTTC
Found at i:57991 original size:29 final size:29
Alignment explanation
Indices: 57949--58067 Score: 193
Period size: 29 Copynumber: 4.1 Consensus size: 29
57939 CCATCCCTAA
*
57949 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
*
57978 TATGACAACTTCGGGTGTCAAAGTGATGC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
* *
58007 TATGACAACTTTGGGTGTCAAAGTGATGC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
*
58036 TATGACAACTTCGGGTGTCATAGTGATAC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
58065 TAT
1 TAT
58068 ATGTTTGATG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAGTGATAC
Found at i:58109 original size:33 final size:33
Alignment explanation
Indices: 58066--58167 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 33
58056 TAGTGATACT
* *
58066 ATATGTTTGATGTGACAACTTCAAGTGCCACTG
1 ATATGCTTGATGTGACAACTTCAAGTGCCACTA
* * * * *
58099 ATATGCTTGATATGACAACTTTAGGTGACGCTA
1 ATATGCTTGATGTGACAACTTCAAGTGCCACTA
* *
58132 ATATGCTCGAAGTGACAACTTCAAGTGCCACTA
1 ATATGCTTGATGTGACAACTTCAAGTGCCACTA
58165 ATA
1 ATA
58168 GATAAGGTAG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (33 bp):
ATATGCTTGATGTGACAACTTCAAGTGCCACTA
Found at i:58268 original size:32 final size:34
Alignment explanation
Indices: 58202--58276 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 34
58192 ATAAATTTTA
*
58202 ATGATAAAAGAAAGGTTAGAAAGAGGAGATTATGC
1 ATGAT-AAAGAAAGGTTAGAAAGAAGAGATTATGC
58237 ATGATAAAGAAAGG-TAG-AAGAAGAGATTATGC
1 ATGATAAAGAAAGGTTAGAAAGAAGAGATTATGC
*
58269 ATGTTAAA
1 ATGATAAA
58277 TAAACTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 21 0.55
33 3 0.08
34 9 0.24
35 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.27, T:0.21
Consensus pattern (34 bp):
ATGATAAAGAAAGGTTAGAAAGAAGAGATTATGC
Found at i:58339 original size:31 final size:31
Alignment explanation
Indices: 58301--58359 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
58291 TATCTAACCT
58301 TAGACTTGTATGATTCAACTTTCAATCTCTG
1 TAGACTTGTATGATTCAACTTTCAATCTCTG
*
58332 TAGACTTGTATGATTGAACTTTCAATCT
1 TAGACTTGTATGATTCAACTTTCAATCT
58360 TGATCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (31 bp):
TAGACTTGTATGATTCAACTTTCAATCTCTG
Found at i:58687 original size:12 final size:12
Alignment explanation
Indices: 58664--58693 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58654 GGTCCCCTTG
58664 TTATAT-ACTAA
1 TTATATAACTAA
58675 TTATATAACTAA
1 TTATATAACTAA
58687 TTATATA
1 TTATATA
58694 CCCTAAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATATAACTAA
Done.