Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015568.1 Corchorus olitorius cultivar O-4 contig15601, 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: 65066
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3608 original size:30 final size:30
Alignment explanation
Indices: 3574--3681 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
3564 GATAGGTCCT
*
3574 AAATTGCAGCAATTGAAAGAAAAAAGGGCG
1 AAATTGCAACAATTGAAAGAAAAAAGGGCG
** * *
3604 AAATTGCAGTAATTGAATGTAAAAAA-GGCA
1 AAATTGCAACAATTGAAAG-AAAAAAGGGCG
**
3634 AAATTGCAACAATTGAAAGGGAAAAGGGCG
1 AAATTGCAACAATTGAAAGAAAAAAGGGCG
* *
3664 AAATCGCAACAAATGAAA
1 AAATTGCAACAATTGAAA
3682 ACATGAAGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.06
30 55 0.85
31 6 0.09
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.16
Consensus pattern (30 bp):
AAATTGCAACAATTGAAAGAAAAAAGGGCG
Found at i:7965 original size:33 final size:33
Alignment explanation
Indices: 7920--8000 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
7910 GTATTTTAGA
* *
7920 TGTTGTTAGTGATGATACTAAACCTAATTTAAG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
* ** *
7953 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
7986 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
8001 AACAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTAATTTAAG
Found at i:8014 original size:33 final size:33
Alignment explanation
Indices: 7947--8048 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
7937 CTAAACCTAA
* *
7947 TTTAAGTGTTGTTTGTGATGACACTAAA-TCTGT
1 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGT
*
7980 TTTAGGTGTTGTTTGTGATGAAACAAATTTTGT
1 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
**
8013 TTT-GGATGTTAATTGTGATGAAAACAAA-TCTGT
1 TTTAGG-TGTTGTTTGTGATG-AAACAAATTCTGT
8046 TTT
1 TTT
8049 GGTTGATCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
32 5 0.08
33 48 0.80
34 7 0.12
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
Found at i:11519 original size:32 final size:32
Alignment explanation
Indices: 11483--11582 Score: 78
Period size: 32 Copynumber: 3.1 Consensus size: 32
11473 TTCGGGTTCG
11483 GGTTTGAGTCAGG-TCGGGTTAAATTTGGGTAA
1 GGTTT-AGTCAGGTTCGGGTTAAATTTGGGTAA
* * * * *
11515 GGTTTATTCGGGTTTGGGTTAAATTTGTGTCA
1 GGTTTAGTCAGGTTCGGGTTAAATTTGGGTAA
* * * * *
11547 GGTTGATTC-GTGTTCGGGTCAATTTTGGGTTA
1 GGTTTAGTCAG-GTTCGGGTTAAATTTGGGTAA
11579 GGTT
1 GGTT
11583 AATTCGGATT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
31 6 0.11
32 49 0.89
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (32 bp):
GGTTTAGTCAGGTTCGGGTTAAATTTGGGTAA
Found at i:11588 original size:32 final size:32
Alignment explanation
Indices: 11496--11594 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
11486 TTGAGTCAGG
*
11496 TCGGGTTAAATTTGGGTAAGGTTTATTCGGGT
1 TCGGGTTAAATTTGGGTAAGGTTAATTCGGGT
* * * * *
11528 TTGGGTTAAATTTGTGTCAGGTTGATTCGTGT
1 TCGGGTTAAATTTGGGTAAGGTTAATTCGGGT
* * * *
11560 TCGGGTCAATTTTGGGTTAGGTTAATTCGGAT
1 TCGGGTTAAATTTGGGTAAGGTTAATTCGGGT
11592 TCG
1 TCG
11595 AGTTCGGACT
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.17, C:0.08, G:0.32, T:0.42
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTAAGGTTAATTCGGGT
Found at i:11770 original size:20 final size:20
Alignment explanation
Indices: 11737--11775 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11727 CATAGATGAA
*
11737 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
11757 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
11776 GAATTCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:11852 original size:15 final size:15
Alignment explanation
Indices: 11804--11865 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
11794 GTTCGGATTC
11804 GAGTTCTTTCGGGTTT
1 GAGTT-TTTCGGGTTT
* *
11820 CAAATTTTTCGGGTTTT
1 -GAGTTTTTCGGG-TTT
11837 G-GTTTTTTCGGGTTT
1 GAG-TTTTTCGGGTTT
*
11852 GAGCTTTTCGGGTT
1 GAGTTTTTCGGGTT
11866 CAGGTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 14 0.38
16 17 0.46
17 6 0.16
ACGTcount: A:0.08, C:0.11, G:0.29, T:0.52
Consensus pattern (15 bp):
GAGTTTTTCGGGTTT
Found at i:12744 original size:106 final size:104
Alignment explanation
Indices: 12524--12781 Score: 392
Period size: 106 Copynumber: 2.5 Consensus size: 104
12514 TTTTCTAAAT
* **
12524 CTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTC
1 CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTC
* * *
12588 TAAAACCCTATGACAATATTATTAATTATGGAATTTACC
66 TAAAACCCTATAAAAATATTATTAATTATGAAATTTACC
* *
12627 CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTC
1 CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTC
*
12692 TAAAACCCTATAAAAATAAATTATTAATTTTGAAATTTACC
66 TAAAACCCTATAAAAAT--ATTATTAATTATGAAATTTACC
*
12733 CTTAAAATAAAAATAAAATTTTAATCTGGGGCTAAACTTAGTGAAATTA
1 CTTAAAATAAAAATAAAATTTTAAT-TTGGGCTAAACTTAGTGAAATTA
12782 AGGCTAAACT
Statistics
Matches: 141, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 39 0.28
104 35 0.25
106 45 0.32
107 22 0.16
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (104 bp):
CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTC
TAAAACCCTATAAAAATATTATTAATTATGAAATTTACC
Found at i:15319 original size:21 final size:19
Alignment explanation
Indices: 15267--15321 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
15257 TTTATTTTCC
*
15267 TTTTTTCTTCCCTTCCTTT
1 TTTTTTCTTCTCTTCCTTT
*
15286 TTCTTTTCTTTCTTTTCCTTT
1 TT-TTTTC-TTCTCTTCCTTT
15307 CTATTTTTCTTCTCT
1 -T-TTTTTCTTCTCT
15322 ATTTTTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 5 0.17
21 15 0.52
22 6 0.21
23 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTCTTCTCTTCCTTT
Found at i:15322 original size:13 final size:12
Alignment explanation
Indices: 15289--15334 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
15279 TTCCTTTTTC
15289 TTTTCTTTC--T
1 TTTTCTTTCTAT
*
15299 TTTCCTTTCTAT
1 TTTTCTTTCTAT
15311 TTTTCTTCTCTAT
1 TTTTCTT-TCTAT
15324 TTTTCTCTTCT
1 TTTTCT-TTCT
15335 TCTTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 8 0.27
12 7 0.23
13 14 0.47
14 1 0.03
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTCTTTCTAT
Found at i:15334 original size:18 final size:16
Alignment explanation
Indices: 15310--15346 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15300 TTCCTTTCTA
*
15310 TTTT-TCTTC-TCTAT
1 TTTTCTCTTCTTCTTT
15324 TTTTCTCTTCTTCTTT
1 TTTTCTCTTCTTCTTT
15340 TTTTCTC
1 TTTTCTC
15347 CCTCTTTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 5 0.25
16 11 0.55
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTCTTCTTCTTT
Found at i:15541 original size:46 final size:46
Alignment explanation
Indices: 15453--15541 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
15443 CTAGGACCCA
* *
15453 ACGCTGCCCATTGGCAGCAGTGTGGCCCAGCACTGGCTAGGCCCGC
1 ACGCTGCCCATTGGCAGCAGTGCGGCCCAGCACTGGCCAGGCCCGC
**
15499 ACGCTGCCCATTGGCAGCAGTGCGGCCCAGCGTTGGCCAGGCC
1 ACGCTGCCCATTGGCAGCAGTGCGGCCCAGCACTGGCCAGGCC
15542 TGCTTAGCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.15, C:0.37, G:0.34, T:0.15
Consensus pattern (46 bp):
ACGCTGCCCATTGGCAGCAGTGCGGCCCAGCACTGGCCAGGCCCGC
Found at i:16405 original size:18 final size:18
Alignment explanation
Indices: 16368--16403 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
16358 TTTAGACTTC
16368 ACAATATCATTTAAAAAA
1 ACAATATCATTTAAAAAA
16386 ACAAT-TCATTTAAAAAA
1 ACAATATCATTTAAAAAA
16403 A
1 A
16404 ACTGCCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
ACAATATCATTTAAAAAA
Found at i:19714 original size:13 final size:13
Alignment explanation
Indices: 19696--19720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19686 TTAGAATTCC
19696 AAATAATATTTAT
1 AAATAATATTTAT
19709 AAATAATATTTA
1 AAATAATATTTA
19721 GGAAATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:21665 original size:21 final size:20
Alignment explanation
Indices: 21648--21706 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
21638 TGAAATGTTG
21648 TCACTATTTGGTGTAATGAT
1 TCACTATTTGGTGTAATGAT
*
21668 TC-CT-TTTAGGTGTAATGGT
1 TCACTATTT-GGTGTAATGAT
* *
21687 ATCACTAATAGGTGTAATGA
1 -TCACTATTTGGTGTAATGA
21707 AGTTTCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.10
19 12 0.39
20 4 0.13
21 11 0.35
22 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (20 bp):
TCACTATTTGGTGTAATGAT
Found at i:22109 original size:11 final size:11
Alignment explanation
Indices: 22092--22144 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
22082 AATCTATGCC
22092 AAGAAAAAGGA
1 AAGAAAAAGGA
* * *
22103 AATAAAATGGC
1 AAGAAAAAGGA
*
22114 AAGAAAAAGGT
1 AAGAAAAAGGA
*
22125 AAGAAAAATGGC
1 AAGAAAAA-GGA
22137 AAGAAAAA
1 AAGAAAAA
22145 TGCTTTGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.66, C:0.04, G:0.23, T:0.08
Consensus pattern (11 bp):
AAGAAAAAGGA
Found at i:22116 original size:22 final size:23
Alignment explanation
Indices: 22091--22144 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
22081 AAATCTATGC
22091 CAAGAAAAAGG-AA-ATAAAATGG
1 CAAGAAAAAGGTAAGA-AAAATGG
22113 CAAGAAAAAGGTAAGAAAAATGG
1 CAAGAAAAAGGTAAGAAAAATGG
22136 CAAGAAAAA
1 CAAGAAAAA
22145 TGCTTTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.37
23 18 0.60
24 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.22, T:0.07
Consensus pattern (23 bp):
CAAGAAAAAGGTAAGAAAAATGG
Found at i:22145 original size:12 final size:12
Alignment explanation
Indices: 22106--22146 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
22096 AAAAGGAAAT
22106 AAAATGGCAAGA
1 AAAATGGCAAGA
*
22118 AAAA-GGTAAGA
1 AAAATGGCAAGA
22129 AAAATGGCAAGA
1 AAAATGGCAAGA
22141 AAAATG
1 AAAATG
22147 CTTTGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.61, C:0.05, G:0.24, T:0.10
Consensus pattern (12 bp):
AAAATGGCAAGA
Found at i:31864 original size:2 final size:2
Alignment explanation
Indices: 31851--31881 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31841 TTTTTAGTAC
*
31851 AT AT AA 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 A
31882 AAAGAGTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:32171 original size:4 final size:4
Alignment explanation
Indices: 32162--32197 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
32152 TATCTTACCT
32162 ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
32198 TTTATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:32818 original size:21 final size:21
Alignment explanation
Indices: 32770--32818 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
32760 AGTAACAATC
*
32770 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
32790 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
32811 AAATAAAT
1 AAATAAAT
32819 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:33693 original size:22 final size:22
Alignment explanation
Indices: 33665--33718 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
33655 CCTGTCAAGA
*
33665 ACCTCCCCGTTCGCGGTAAGGG
1 ACCTCCCCGTTCGCGGCAAGGG
33687 ACCTCCCCGTTCGCGGCAAGGG
1 ACCTCCCCGTTCGCGGCAAGGG
33709 ACCTCCCCGT
1 ACCTCCCCGT
33719 GCCCGGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.13, C:0.43, G:0.28, T:0.17
Consensus pattern (22 bp):
ACCTCCCCGTTCGCGGCAAGGG
Found at i:35495 original size:3 final size:3
Alignment explanation
Indices: 35489--35525 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
35479 AAAAAAAAAG
*
35489 TTA TTA TTA TTA TT- TT- TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35526 CTATGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:36708 original size:15 final size:15
Alignment explanation
Indices: 36688--36716 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36678 ACCGTTTCTC
36688 TCTTCTTCTTCTTTT
1 TCTTCTTCTTCTTTT
36703 TCTTCTTCTTCTTT
1 TCTTCTTCTTCTTT
36717 ACTTGTACTC
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TCTTCTTCTTCTTTT
Found at i:41883 original size:6 final size:7
Alignment explanation
Indices: 41847--41885 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
41837 TAATTCTTAA
41847 ATTTTAT
1 ATTTTAT
41854 ATTTTAT
1 ATTTTAT
41861 ATTTTAT
1 ATTTTAT
*
41868 ATTTTGT
1 ATTTTAT
41875 -TTTTAT
1 ATTTTAT
41881 -TTTTA
1 ATTTTA
41886 CTCATCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (7 bp):
ATTTTAT
Found at i:46364 original size:14 final size:14
Alignment explanation
Indices: 46345--46374 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
46335 TAAAATCATC
46345 TACAGATTAATATA
1 TACAGATTAATATA
46359 TACAGATTAATATA
1 TACAGATTAATATA
46373 TA
1 TA
46375 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
TACAGATTAATATA
Found at i:46373 original size:2 final size:2
Alignment explanation
Indices: 46368--46393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46358 ATACAGATTA
46368 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
46394 GACATCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47502 original size:1 final size:1
Alignment explanation
Indices: 47496--47520 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
47486 GCCACCCCAA
47496 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
47521 GTTTTCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:50252 original size:32 final size:32
Alignment explanation
Indices: 50206--50285 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
50196 GATAGCCCTT
*
50206 TTGCCCCCTGAACTTTGCAAATTTAGACCAGA
1 TTGCTCCCTGAACTTTGCAAATTTAGACCAGA
* *
50238 TTGTTCCCTGAACTTTGCAAATTTAGGCCAGA
1 TTGCTCCCTGAACTTTGCAAATTTAGACCAGA
50270 TTGCTCCCTGAACTTT
1 TTGCTCCCTGAACTTT
50286 AAATTTTGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGCTCCCTGAACTTTGCAAATTTAGACCAGA
Found at i:54411 original size:26 final size:27
Alignment explanation
Indices: 54382--54448 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 27
54372 TCTTTCGACT
54382 TTGCATTTGGGCA-TTTTAG-TTTGAGA
1 TTGCATTTGGGCATTTTTAGTTTTG-GA
54408 TTGCATTTGGGCATTTTTAGTTTTTGGA
1 TTGCATTTGGGCATTTTTAG-TTTTGGA
54436 TTGCATTTGGGCA
1 TTGCATTTGGGCA
54449 CATTGCCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 13 0.34
27 6 0.16
28 15 0.39
29 4 0.11
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.48
Consensus pattern (27 bp):
TTGCATTTGGGCATTTTTAGTTTTGGA
Found at i:55059 original size:29 final size:29
Alignment explanation
Indices: 55022--55083 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
55012 GCATTTTTCA
*
55022 TACATCATTATCATTGTCATTCAGCATAC
1 TACATCATTAGCATTGTCATTCAGCATAC
55051 TACATCATTAGCATTGTCATTCAGCATAC
1 TACATCATTAGCATTGTCATTCAGCATAC
55080 -ACAT
1 TACAT
55084 GGCACCAGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.35
Consensus pattern (29 bp):
TACATCATTAGCATTGTCATTCAGCATAC
Found at i:56931 original size:41 final size:41
Alignment explanation
Indices: 56837--57104 Score: 396
Period size: 41 Copynumber: 6.6 Consensus size: 41
56827 TTTTATTTCG
* *
56837 AGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT--TTATCCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTT-TTCCC
* * *
56877 AGTTTGCCCTTCCCCACCGAAAGGTATTCTTTACTTTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
*
56918 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
* * * *
56959 AGTTTACCCTTCCCCACCGGAAGGTATTCTTTACATTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
*
57000 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
*
57041 AGTTTACCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
*
57082 AGTTTGCCCTTCCCGACCGGAAG
1 AGTTTGCCCTTCCCCACCGGAAG
57105 TGATGCGCCA
Statistics
Matches: 203, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
40 28 0.14
41 173 0.85
42 2 0.01
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (41 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
Found at i:56986 original size:82 final size:82
Alignment explanation
Indices: 56837--57104 Score: 441
Period size: 82 Copynumber: 3.3 Consensus size: 82
56827 TTTTATTTCG
* * * * *
56837 AGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT--TTATCCCCAGTTTGCCCTTCCCCACCGAAAG
1 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTT-TTCCCAGTTTACCCTTCCCCACCGGAAG
56900 GTATTCTTTACTTTTCCC
65 GTATTCTTTACTTTTCCC
56918 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGG
1 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGG
*
56983 TATTCTTTACATTTCCC
66 TATTCTTTACTTTTCCC
57000 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGG
1 AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGG
* *
57065 TGTTGTTTACTTTTCCC
66 TATTCTTTACTTTTCCC
57082 AGTTTGCCCTTCCCGACCGGAAG
1 AGTTTGCCCTTCCCGACCGGAAG
57105 TGATGCGCCA
Statistics
Matches: 176, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
81 30 0.17
82 144 0.82
83 2 0.01
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (82 bp):
AGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGG
TATTCTTTACTTTTCCC
Found at i:57044 original size:123 final size:122
Alignment explanation
Indices: 56793--57104 Score: 408
Period size: 123 Copynumber: 2.5 Consensus size: 122
56783 TATTCCCAAA
* * * *
56793 TTGCCCTTCCCGGCCGGAAGGTGTTGTTTACTTATTTTATTTCGAGTTTGCCCTTCCCCATCGGA
1 TTGCCCTTCCCGACCGGAAGGTGTTGTTTAC-----TT-TTCCCAGTTTGCCCTTCCCCACCGGA
* * **
56858 AGGTGTTGTTTTTATCCCCAGTTTGCCCTTCCCCACCGAAAGGTATTCTTTACTTTTCCCAGT
60 AGGTATTCTTTACATCCCCAGTTTGCCCTTCCCCACCGAAAGGTATTCTTTACTTTTCCCAGT
*
56921 TTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTACCCTTCCCCACCGGAAGGTAT
1 TTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTAT
* * * * *
56986 TCTTTACATTTCCCAGTTTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGT
66 TCTTTACA-TCCCCAGTTTGCCCTTCCCCACCGAAAGGTATTCTTTACTTTTCCCAGT
* * *
57044 TTACCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCGACCGGAAG
1 TTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAG
57105 TGATGCGCCA
Statistics
Matches: 165, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
122 32 0.19
123 103 0.62
128 30 0.18
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.36
Consensus pattern (122 bp):
TTGCCCTTCCCGACCGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTAT
TCTTTACATCCCCAGTTTGCCCTTCCCCACCGAAAGGTATTCTTTACTTTTCCCAGT
Found at i:58122 original size:25 final size:24
Alignment explanation
Indices: 58086--58132 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
58076 TCCTTCTATT
58086 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
58109 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
58133 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:63188 original size:29 final size:29
Alignment explanation
Indices: 63146--63205 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
63136 GATGGGCAAC
63146 GCAAGGCAGATTTTGTTAGGGATCTTCAT
1 GCAAGGCAGATTTTGTTAGGGATCTTCAT
63175 GCAAGGCAGATTTTGTTAGGGATCTTCAT
1 GCAAGGCAGATTTTGTTAGGGATCTTCAT
63204 GC
1 GC
63206 TAACAAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (29 bp):
GCAAGGCAGATTTTGTTAGGGATCTTCAT
Found at i:64455 original size:40 final size:40
Alignment explanation
Indices: 64402--65066 Score: 628
Period size: 41 Copynumber: 16.8 Consensus size: 40
64392 CAGGAAGATA
*
64402 TTGTTTACTTTTCCAGTTTGCCCTTCCCTACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * ** * *
64442 TTGTTTGCCTTTCCCAGTTTGCCCTTCCGGATCGGAAGTTG
1 TTGTTT-ACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
64483 TTGTTTAC-TTTCCTGTTTTGTCCTTCCCCAGCGGAAGGTG
1 TTGTTTACTTTTCCAG-TTTGCCCTTCCCCACCGGAAGGTG
* **
64523 TTGTTT--TTATCCCTAGTTTGCCCTTCCCCACTAGAAGGTG
1 TTGTTTACTT-TTCC-AGTTTGCCCTTCCCCACCGGAAGGTG
* * **
64563 TTGTTTACTTTTCCCAGTTTGCCTTTCCCGACCAAAAGGTG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * *
64604 TTATTTACTTTTCCTAGTTTGTCCTTCCCTACCGAAAGGTG
1 TTGTTTACTTTTCC-AGTTTGCCCTTCCCCACCGGAAGGTG
* *
64645 TTGTTTACTTTTCCCAGTTTGCCCTTCCCGACCGGAAGATG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * * *
64686 TTGTTTACCTTT---GTTTGCGCTTCTCGACCGGAAGGCG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
64723 TTGTTTACTTTTCCAGTTTGTCATTCCCTACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
64763 TTGTTTA-TTTTCCTGTTTTGTCTTTCCCCACCGGAAGGTG
1 TTGTTTACTTTTCCAG-TTTGCCCTTCCCCACCGGAAGGTG
* * ** *
64803 TTCTTTTC-AATCTC-GTATTGCCCTTCCCCATCGGAAGGTG
1 TTGTTTACTTTTC-CAGT-TTGCCCTTCCCCACCGGAAGGTG
64843 TTGTTTACTTTTCCAGTTTG-------CCACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* **
64876 TTGTTTACTTTTCCAGTTTGCCTTTCCCCAATGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
*
64916 TTGTTTACTTTTCCCAGTTTGCCCTTCCCCGCCGGAAGGTG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
64957 TTGTTTACTTTTTCCAGTTTACCCTTCCCCACGGGAAGATG
1 TTGTTTAC-TTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * *
64998 TTGTTT--TATTCCTGTTTGCCCTTCCCAAACGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
*
65036 TTTTTTACTTTTCCCAGTTTGCCCTTCCCCA
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCA
Statistics
Matches: 511, Mismatches: 83, Indels: 61
0.78 0.13 0.09
Matches are distributed among these distances:
33 32 0.06
37 32 0.06
38 30 0.06
39 14 0.03
40 175 0.34
41 218 0.43
42 10 0.02
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (40 bp):
TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
Found at i:64876 original size:33 final size:33
Alignment explanation
Indices: 64834--64938 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
64824 CCTTCCCCAT
64834 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
1 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
*
64867 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCTTTCCC
1 CGGAAGGTGTTGTTTACTTTTCCAGTTTG-C---CAC
64904 CAATGGAAGGTGTTGTTTACTTTTCCCAGTTTGCC
1 C---GGAAGGTGTTGTTTACTTTT-CCAGTTTGCC
64939 CTTCCCCGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
33 29 0.46
34 1 0.02
37 4 0.06
40 21 0.33
41 8 0.13
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (33 bp):
CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
Found at i:64886 original size:153 final size:157
Alignment explanation
Indices: 64402--65066 Score: 548
Period size: 153 Copynumber: 4.2 Consensus size: 157
64392 CAGGAAGATA
* * * * * *
64402 TTGTTTACTTTTCCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTGCCTTTCCCAGTTTGCCCT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTT-ACTTTTCCTGTTTGTCCT
** * * * * * * * *
64467 TCCGGATCGGAAGTTGTTGTTTACT--TTCCTGTTTTGTCCTTCCCCAGCGGAAGGTGTTGTTTT
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAG-TTTGCCCTTCCCCACCGGAAGATGTTG--TT
* * **
64530 TATCCCTAGTTTGCC-CTTCCCCACTAGAAGGTG
127 TA--CCTTGTTT-CCGCTTCTCCACCGGAAGGTG
* ** *
64563 TTGTTTACTTTTCCCAGTTTGCCTTTCCCGACCAAAAGGTGTTATTTACTTTTCCTAGTTTGTCC
1 TTGTTTACTTTT-CCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCT-GTTTGTCC
* * * ** *
64628 TTCCCTACCGAAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCGACCGGAAGATGTTGTTTA
64 TTCCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTGTTTA
* * *
64693 CCTTTGTTTGCGCTTCTCGACCGGAAGGCG
129 CC-TTGTTTCCGCTTCTCCACCGGAAGGTG
* * * *
64723 TTGTTTACTTTTCCAGTTTGTCATTCCCTACCGGAAGGTGTTGTTTA-TTTTCCTGTTTTGTCTT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTG-TTTGTCCT
* * * *
64787 TCCCCACCGGAAGGTGTTCTTTTC-AATCTC-GTATTGCCCTTCCCCATCGGAAGGTGTTGTTTA
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAGT-TTGCCCTTCCCCACCGGAAGATGTTGTTTA
64850 -C-T-TTTCCAG-TT-TGCCACCGGAAGGTG
129 CCTTGTTTCC-GCTTCT-CCACCGGAAGGTG
** * *
64876 TTGTTTACTTTTCCAGTTTGCCTTTCCCCAATGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTT-CCTGTTTGTCCT
* * ** * * *
64941 TCCCCGCCGGAAGGTGTTGTTTACTTTTTCCAGTTTACCCTTCCCCACGGGAAGATGTTGTTTTA
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTG-TTTA
*
65006 TTCC-TGTTTGCC-CTTC-CCAAACGGAAGGTG
129 --CCTTGTTT-CCGCTTCTCC-ACCGGAAGGTG
* *
65036 TTTTTTACTTTTCCCAGTTTGCCCTTCCCCA
1 TTGTTTACTTTT-CCAGTTTGCCTTTCCCCA
Statistics
Matches: 411, Mismatches: 69, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
152 1 0.00
153 59 0.14
154 33 0.08
155 27 0.07
156 9 0.02
157 31 0.08
158 34 0.08
159 36 0.09
160 56 0.14
161 41 0.10
162 57 0.14
163 23 0.06
164 4 0.01
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (157 bp):
TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTGTTTGTCCTT
CCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTGTTTACC
TTGTTTCCGCTTCTCCACCGGAAGGTG
Done.