Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013626.1 Corchorus olitorius cultivar O-4 contig13659, 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: 63538
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2224 original size:16 final size:15
Alignment explanation
Indices: 2203--2249 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
2193 AGGAATAGGC
2203 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
*
2218 TAATCAATCAGAGCAA
1 -AATCAATCAAAGCAA
2234 AAT-AATGCAAAG-AA
1 AATCAAT-CAAAGCAA
2248 AA
1 AA
2250 AGTAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 7 0.25
15 7 0.25
16 14 0.50
ACGTcount: A:0.60, C:0.15, G:0.11, T:0.15
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:4134 original size:11 final size:11
Alignment explanation
Indices: 4118--4143 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4108 GTCCATAAAG
4118 CTCGCGCAAAT
1 CTCGCGCAAAT
4129 CTCGCGCAAAT
1 CTCGCGCAAAT
4140 CTCG
1 CTCG
4144 TTGTATCTTT
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:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (11 bp):
CTCGCGCAAAT
Found at i:4661 original size:35 final size:36
Alignment explanation
Indices: 4613--4681 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
4603 ACAAATTTAA
*
4613 AAAAAAACGGAAAAC-ACAAA-AATTTTTTTTTTCAG
1 AAAAAAACAGAAAACGA-AAAGAATTTTTTTTTTCAG
*
4648 AAAAACACAGAAAACGGAAAAGAATTTTTTTTTT
1 AAAAAAACAGAAAAC-GAAAAGAATTTTTTTTTT
4682 AGATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 13 0.45
36 3 0.10
37 13 0.45
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (36 bp):
AAAAAAACAGAAAACGAAAAGAATTTTTTTTTTCAG
Found at i:7519 original size:26 final size:26
Alignment explanation
Indices: 7477--7526 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
7467 ATGATTTAGG
*
7477 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTCTTTTGA
* *
7503 GGTTACTAACACTCTTTTTTTTTT
1 GGTTACTAACACCCTTTTTCTTTT
7527 TCAGAGGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (26 bp):
GGTTACTAACACCCTTTTTCTTTTGA
Found at i:10048 original size:27 final size:28
Alignment explanation
Indices: 10018--10089 Score: 110
Period size: 29 Copynumber: 2.6 Consensus size: 28
10008 TGCCAATGAG
*
10018 TGACCAAAATGCCCCTGGA-CGTGTAAA
1 TGACCAAAATGCCCCTGGATCGTGAAAA
*
10045 TGACCAAAATGCCCCTGGATTCTTGAAAA
1 TGACCAAAATGCCCCTGGA-TCGTGAAAA
10074 TGACCAAAATGCCCCT
1 TGACCAAAATGCCCCT
10090 AGGTGATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 19 0.46
29 22 0.54
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGATCGTGAAAA
Found at i:10716 original size:11 final size:10
Alignment explanation
Indices: 10700--10746 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
10690 AAACTCGTGT
10700 TTGAAGACTCA
1 TTGAAGA-TCA
*
10711 TTGAAGATAA
1 TTGAAGATCA
10721 TTTGAAGAT--
1 -TTGAAGATCA
10730 TTGAAGATCA
1 TTGAAGATCA
10740 TTGAAGA
1 TTGAAGA
10747 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:10735 original size:19 final size:18
Alignment explanation
Indices: 10711--10746 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10701 TGAAGACTCA
10711 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
10730 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
10747 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:11335 original size:11 final size:11
Alignment explanation
Indices: 11306--11337 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11296 AAATTGTATT
*
11306 TTGAAGAATTA
1 TTGAAGATTTA
11317 TTGAAGATTTA
1 TTGAAGATTTA
11328 TTGAAGATTT
1 TTGAAGATTT
11338 GGAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTGAAGATTTA
Found at i:16717 original size:27 final size:26
Alignment explanation
Indices: 16679--16768 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 26
16669 AACCTAAAGC
*
16679 ATGACCAAAATGCCCATGAGTGCACAA
1 ATGACCAAAATGCCCCTGAGTGCA-AA
16706 ATGACCAAAATGCCCCTGAGTGCATAA
1 ATGACCAAAATGCCCCTGAGTGCA-AA
*
16733 ATGACTAAAATGCCCCTGAGTGTGCAAA
1 ATGACCAAAATGCCCCTGA--GTGCAAA
16761 ATGACCAA
1 ATGACCAA
16769 TTAAGATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
27 43 0.75
28 9 0.16
29 5 0.09
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (26 bp):
ATGACCAAAATGCCCCTGAGTGCAAA
Found at i:17148 original size:59 final size:59
Alignment explanation
Indices: 17054--17611 Score: 857
Period size: 59 Copynumber: 9.4 Consensus size: 59
17044 TCTCCATCGA
* * * * * *
17054 AGACCTCGAACA-GATTTTACAAGCAAGATAGGATTTTGAACTGAAAACTCTCTACCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
* *
17112 AGACCTCGAACAGGATTTTAAAAAGAAGGCAAGATTTTGAATTGAAAACTCTCTATCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
*
17171 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAATTCTCTATCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
** *
17230 AGACCTCGAACAGGATTTTAAAAATTAGACAATATTTTGAATTGAAAACTCTCTATCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
*
17289 AGACCTCGAACAGGATTTTAAGAAAACAAGATAAGATTTTGAATTGAAAACTCTCTATCAG
1 AGACCTCGAACAGGATTTT-A-AAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
* *
17350 AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTACCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
* * *
17409 AGACCTCGATCAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAAATTCTCTATCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTG-AAAACTCTCTATCAG
* * *
17469 AGACCTCGATCAGGATTTTAAAAACTAGACAAGATTTTGAATTGAAAACTCTCTACCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
* * *
17528 AGACCTCGAACAGGATTTTAAAAGCAAGATAAGATTTTGAATTGAAAACTCTCTACCAG
1 AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
*
17587 AGACCTCGAACATGATTTTAAAAAC
1 AGACCTCGAACAGGATTTTAAAAAC
17612 CAGAGACCTC
Statistics
Matches: 461, Mismatches: 35, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
58 12 0.03
59 338 0.73
60 57 0.12
61 54 0.12
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (59 bp):
AGACCTCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAG
Found at i:17372 original size:179 final size:177
Alignment explanation
Indices: 17054--17611 Score: 875
Period size: 179 Copynumber: 3.1 Consensus size: 177
17044 TCTCCATCGA
* * * ** * *
17054 AGACCTCGAACA-GATTTTACAAGCAAGATAGGATTTTGAACTGAAAACTCTCTACCAGAGACCT
1 AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTATCAGAGACCT
* *
17118 CGAACAGGATTTTAAAAAGAAGGCAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACA
66 CGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACA
* *
17183 GGATTTTAAAAACAAGACAAGATTTTGAATTGAAAATTCTCTATCAG
131 GGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAG
**
17230 AGACCTCGAACAGGATTTTAAAAATTAGACAATATTTTGAATTGAAAACTCTCTATCAGAGACCT
1 AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTATCAGAGACCT
*
17295 CGAACAGGATTTTAAGAAAACAAGATAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAA
66 CGAACAGGATTTT-A-AAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAA
*
17360 CAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTACCAG
129 CAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAG
* *
17409 AGACCTCGATCAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAAATTCTCTATCAGAGACC
1 AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTG-AAAACTCTCTATCAGAGACC
* * *
17474 TCGATCAGGATTTTAAAAACTAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAAC
65 TCGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAAC
* *
17539 AGGATTTTAAAAGCAAGATAAGATTTTGAATTGAAAACTCTCTACCAG
130 AGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAG
*
17587 AGACCTCGAACATGATTTTAAAAAC
1 AGACCTCGAACAGGATTTTAAAAAC
17612 CAGAGACCTC
Statistics
Matches: 350, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
176 12 0.03
177 56 0.16
178 116 0.33
179 134 0.38
180 32 0.09
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (177 bp):
AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTATCAGAGACCT
CGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACA
GGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAG
Found at i:17606 original size:298 final size:296
Alignment explanation
Indices: 17054--17607 Score: 892
Period size: 298 Copynumber: 1.9 Consensus size: 296
17044 TCTCCATCGA
* * * *
17054 AGACCTCGAACAGATTTTACAAGCAAGATAGGATTTTGAACTGAAAACTCTCTACCAGAGACCTC
1 AGACCTCGAACAGATTTTAAAAACAAGACAAGATTTTGAACTGAAAACTCTCTACCAGAGACCTC
* *
17119 GAACAGGATTTTAAAAAGAAGGCAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACAG
66 GAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACAG
* *
17184 GATTTTAAAAACAAGACAAGATTTTGAATTGAAAATTCTCTATCAGAGACCTCGAACAGGATTTT
131 GATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATTTT
** * *
17249 AAAAATTAGACAATATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACAGGATTTTAAGAAA
196 AAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATTTTAAGAAA
17314 ACAAGATAAGATTTTGAATTGAAAACTCTCTATCAG
261 ACAAGATAAGATTTTGAATTGAAAACTCTCTATCAG
* *
17350 AGACCTCGAACAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAACTCTCTACCAGAGACCT
1 AGACCTCGAACA-GATTTTAAAAACAAGACAAGATTTTGAACTGAAAACTCTCTACCAGAGACCT
* * * *
17415 CGATCAGGATTTTAAAAACAAGACAATATTTTGAATTGAAAAATTCTCTATCAGAGACCTCGATC
65 CGAACAGGATTTTAAAAACAAGACAAGATTTTGAATTG-AAAACTCTCTATCAGAGACCTCGAAC
*
17480 AGGATTTTAAAAACTAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATT
129 AGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATT
* * *
17545 TTAAAAGCAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACATGATTTTAA
194 TTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATTTTAA
17608 AAACCAGAGA
Statistics
Matches: 234, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
296 12 0.05
297 80 0.34
298 142 0.61
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (296 bp):
AGACCTCGAACAGATTTTAAAAACAAGACAAGATTTTGAACTGAAAACTCTCTACCAGAGACCTC
GAACAGGATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTATCAGAGACCTCGAACAG
GATTTTAAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATTTT
AAAAACAAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGAACAGGATTTTAAGAAA
ACAAGATAAGATTTTGAATTGAAAACTCTCTATCAG
Found at i:17622 original size:28 final size:28
Alignment explanation
Indices: 17582--17643 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
17572 AAAACTCTCT
*
17582 ACCAGAGACCTCGAACATGATTTTAAAA
1 ACCAGAGACCTCGAACAGGATTTTAAAA
*
17610 ACCAGAGACCTCGAATAGGATTTTAAAA
1 ACCAGAGACCTCGAACAGGATTTTAAAA
17638 ACCAGA
1 ACCAGA
17644 TAAGATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (28 bp):
ACCAGAGACCTCGAACAGGATTTTAAAA
Found at i:17672 original size:87 final size:87
Alignment explanation
Indices: 17523--17698 Score: 307
Period size: 87 Copynumber: 2.0 Consensus size: 87
17513 AAAACTCTCT
*
17523 ACCAGAGACCTCGAACAGGATTTTAAAAGCAAGATAAGATTTTGAATTGAAAACTCTCTACCAGA
1 ACCAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGA
*
17588 GACCTCGAACATGATTTTAAAA
66 GACCTCGAACAGGATTTTAAAA
* * *
17610 ACCAGAGACCTCGAATAGGATTTTAAAAACCAGATAAGATTTTGAATTGAAAACTCTTTACCAGA
1 ACCAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGA
17675 GACCTCGAACAGGATTTTAAAA
66 GACCTCGAACAGGATTTTAAAA
17697 AC
1 AC
17699 AAGATATGAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (87 bp):
ACCAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGA
GACCTCGAACAGGATTTTAAAA
Found at i:17681 original size:59 final size:59
Alignment explanation
Indices: 17610--17762 Score: 263
Period size: 59 Copynumber: 2.6 Consensus size: 59
17600 GATTTTAAAA
* *
17610 ACCAGAGACCTCGAATAGGATTTTAAAAACCAGATAAGATTTTGAATTGAAAACTCTTT
1 ACCAGAGACCTCGAATAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCT
* *
17669 ACCAGAGACCTCGAACAGGATTTTAAAAACAAGATATGATTTTGAATTGAAAACTCTCT
1 ACCAGAGACCTCGAATAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCT
17728 ACCAGAGACCTCGAATAGGATTTT-AAAACAAGATA
1 ACCAGAGACCTCGAATAGGATTTTAAAAACAAGATA
17763 TGAGAGGGGA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 11 0.12
59 78 0.88
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (59 bp):
ACCAGAGACCTCGAATAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCT
Found at i:17730 original size:146 final size:146
Alignment explanation
Indices: 17466--17755 Score: 501
Period size: 146 Copynumber: 2.0 Consensus size: 146
17456 AATTCTCTAT
*
17466 CAGAGACCTCGATCAGGATTTTAAAAACTAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGA
1 CAGAGACCTCGATCAGGATTTTAAAAACCAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGA
*
17531 CCTCGAACAGGATTTTAAAAGCAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGA
66 CCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGA
*
17596 ACATGATTTTAAAAAC
131 ACAGGATTTTAAAAAC
* *
17612 CAGAGACCTCGAAT-AGGATTTTAAAAACCAGATAAGATTTTGAATTGAAAACTCTTTACCAGAG
1 CAGAGACCTCG-ATCAGGATTTTAAAAACCAGACAAGATTTTGAATTGAAAACTCTCTACCAGAG
*
17676 ACCTCGAACAGGATTTTAAAAACAAGATATGATTTTGAATTGAAAACTCTCTACCAGAGACCTCG
65 ACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCG
*
17741 AATAGGATTTTAAAA
130 AACAGGATTTTAAAA
17756 CAAGATATGA
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
146 134 0.99
147 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (146 bp):
CAGAGACCTCGATCAGGATTTTAAAAACCAGACAAGATTTTGAATTGAAAACTCTCTACCAGAGA
CCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTACCAGAGACCTCGA
ACAGGATTTTAAAAAC
Found at i:18157 original size:35 final size:36
Alignment explanation
Indices: 18103--18207 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 36
18093 TTTTTATTTA
*
18103 TTTCTTTTTTCCGACCTCTTTCTGTTTTAGG-CCAAGT
1 TTTC-TTTTT-CGACCTCTTTCTATTTTAGGTCCAAGT
*
18140 TTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAATT
1 TTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAAGT
* *
18176 TTTCCTTTTTCTACCTCTCTCTATTTTAGGTC
1 TTT-CTTTTTCGACCTCTTTCTATTTTAGGTC
18208 TTTTTTTTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
35 19 0.31
36 13 0.21
37 30 0.48
ACGTcount: A:0.11, C:0.25, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTCTTTTTCGACCTCTTTCTATTTTAGGTCCAAGT
Found at i:36878 original size:27 final size:26
Alignment explanation
Indices: 36840--36929 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 26
36830 AACCTAATGC
*
36840 ATGACCAAAATGCCCTTGAGTGCACAA
1 ATGACCAAAATGCCCCTGAGTGCA-AA
36867 ATGACCAAAATGCCCCTGAGTGCATAA
1 ATGACCAAAATGCCCCTGAGTGCA-AA
*
36894 ATGACTAAAATGCCCCTGAGTGTGCAAA
1 ATGACCAAAATGCCCCTGA--GTGCAAA
36922 ATGACCAA
1 ATGACCAA
36930 TTAAGAAACA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
27 43 0.75
28 9 0.16
29 5 0.09
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (26 bp):
ATGACCAAAATGCCCCTGAGTGCAAA
Found at i:40739 original size:16 final size:16
Alignment explanation
Indices: 40720--40763 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
40710 ACCCGCCCGA
* *
40720 ACCCAAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
40736 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
40752 ACCCGAACCCGA
1 ACCCGAACCCGA
40764 CTCGAGACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.41, G:0.14, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:41077 original size:15 final size:15
Alignment explanation
Indices: 41057--41085 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41047 AAAAGTACCT
41057 TATAACTAATTAAAG
1 TATAACTAATTAAAG
41072 TATAACTAATTAAA
1 TATAACTAATTAAA
41086 TACATGAAAT
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:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (15 bp):
TATAACTAATTAAAG
Found at i:41604 original size:13 final size:12
Alignment explanation
Indices: 41568--41614 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
41558 TCAATCTTTA
*
41568 TATATATTGATAA
1 TATATATT-ATAT
*
41581 TA-ATGTTATAT
1 TATATATTATAT
41592 TATATTATTATAT
1 TATA-TATTATAT
41605 TATATATTAT
1 TATATATTAT
41615 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:42436 original size:106 final size:105
Alignment explanation
Indices: 42299--42525 Score: 253
Period size: 105 Copynumber: 2.2 Consensus size: 105
42289 TTAGTCAAAT
*** **
42299 TTTCATAAA-TATTAGCCCCAATTAATAAAAAAATTTCATTTATAGAATTAGTACTCAAATTTAA
1 TTTCATAAAGT-TTAGCCCCAATTAATAAAAAAAAAGCA-TTATAGAATTAGTACAAAAATTTAA
* ** * * *
42363 GATTTATTAGTATAGGGTTTTAGTTTGAATATTTTA-ACATTA
64 AATTTAAAACTATAGGGTTTGAGTTTGAATA-TTTAGACATAA
* * **
42405 TTTCATAAAGTTTAGCCCCAAATTAA-GAAAAAAAAGGATTATAGCGTTAGTACAAAAATTTAAA
1 TTTCATAAAGTTTAGCCCC-AATTAATAAAAAAAAAGCATTATAGAATTAGTACAAAAATTTAAA
*
42469 ATTTAAAACTATAGGGTTTGAGTTTGAATATTTAGCCATAA
65 ATTTAAAACTATAGGGTTTGAGTTTGAATATTTAGACATAA
42510 TTTCATAAAGTTTAGC
1 TTTCATAAAGTTTAGC
42526 TAAATTTAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
104 4 0.04
105 67 0.66
106 24 0.24
107 7 0.07
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (105 bp):
TTTCATAAAGTTTAGCCCCAATTAATAAAAAAAAAGCATTATAGAATTAGTACAAAAATTTAAAA
TTTAAAACTATAGGGTTTGAGTTTGAATATTTAGACATAA
Found at i:42543 original size:105 final size:104
Alignment explanation
Indices: 42346--42551 Score: 254
Period size: 105 Copynumber: 2.0 Consensus size: 104
42336 ATTTATAGAA
** * ** * * *
42346 TTAGTACTCAAATTTAAGATTTATTAGTATAGGGTTTTAGTTTGAATATTTTAACATTATTTCAT
1 TTAGTACAAAAATTTAAAATTTAAAACTATAGGGTTTGAGTTTGAATATTTTAACATAATTTCAT
* *
42411 AAAGTTTAGCCCCAAATTAAGAAAAAAAAGGATTATAGCG
66 AAAGTTTAG-CCCAAATTAAAAAAAAAAAGAATTATAGCG
*
42451 TTAGTACAAAAATTTAAAATTTAAAACTATAGGGTTTGAGTTTGAATA-TTTAGCCATAATTTCA
1 TTAGTACAAAAATTTAAAATTTAAAACTATAGGGTTTGAGTTTGAATATTTTA-ACATAATTTCA
*
42515 TAAAGTTTAG-CTAAATTTAAAAATAAAAAAGAATTAT
65 TAAAGTTTAGCCCAAA-TTAAAAA-AAAAAAGAATTAT
42552 TATAGGGTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
103 4 0.05
104 10 0.12
105 72 0.84
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (104 bp):
TTAGTACAAAAATTTAAAATTTAAAACTATAGGGTTTGAGTTTGAATATTTTAACATAATTTCAT
AAAGTTTAGCCCAAATTAAAAAAAAAAAGAATTATAGCG
Found at i:44046 original size:29 final size:30
Alignment explanation
Indices: 44011--44068 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
44001 TGTCGCTCTG
* *
44011 CTCAATTTAGGGCCAAACAT-TTCAATTTA
1 CTCAATTAAGGGCCAAACATGCTCAATTTA
*
44040 CTCAATTAAGGTCCAAACATGCTCAATTT
1 CTCAATTAAGGGCCAAACATGCTCAATTT
44069 TGGACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (30 bp):
CTCAATTAAGGGCCAAACATGCTCAATTTA
Found at i:48362 original size:16 final size:16
Alignment explanation
Indices: 48337--48368 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48327 CCCACACTCG
48337 AGGACCCAAATTGCCT
1 AGGACCCAAATTGCCT
*
48353 AGGACGCAAATTGCCT
1 AGGACCCAAATTGCCT
48369 TTCCACTTGC
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:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (16 bp):
AGGACCCAAATTGCCT
Found at i:50494 original size:18 final size:18
Alignment explanation
Indices: 50439--50494 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
50429 ATGTCCCAAG
*
50439 TCTCGTACATCATCTGCAT
1 TCTC-TACATCATTTGCAT
* *
50458 TCTCTACAT-TTTCTCCAT
1 TCTCTACATCATT-TGCAT
*
50476 TCTCTCCATCATTTGCAT
1 TCTCTACATCATTTGCAT
50494 T
1 T
50495 AGCATCCCCT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 1 0.03
18 22 0.76
19 6 0.21
ACGTcount: A:0.18, C:0.32, G:0.05, T:0.45
Consensus pattern (18 bp):
TCTCTACATCATTTGCAT
Found at i:51138 original size:21 final size:21
Alignment explanation
Indices: 51112--51151 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51102 CAAACAACAA
*
51112 AAAGATGCCATTTGATCCATT
1 AAAGATGCCAATTGATCCATT
*
51133 AAAGATGCCAATTGGTCCA
1 AAAGATGCCAATTGATCCA
51152 ATGACTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCAATTGATCCATT
Found at i:54267 original size:11 final size:10
Alignment explanation
Indices: 54251--54298 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
54241 GAAGTTCATG
54251 ATTGAAGATTT
1 ATTGAAGA-TT
*
54262 ATTGAAGATA
1 ATTGAAGATT
54272 ATTTGAAGA-T
1 A-TTGAAGATT
54282 -TTGAAGATT
1 ATTGAAGATT
54291 ATTGAAGA
1 ATTGAAGA
54299 ATTTTCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 9 0.28
11 15 0.47
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.38
Consensus pattern (10 bp):
ATTGAAGATT
Found at i:54302 original size:19 final size:19
Alignment explanation
Indices: 54263--54298 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54253 TGAAGATTTA
54263 TTGAAGATAATTTGAAGAT
1 TTGAAGATAATTTGAAGAT
*
54282 TTGAAGATTA-TTGAAGA
1 TTGAAGATAATTTGAAGA
54299 ATTTTCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAT
Found at i:56168 original size:35 final size:34
Alignment explanation
Indices: 56117--56232 Score: 114
Period size: 35 Copynumber: 3.4 Consensus size: 34
56107 ACGTTTTCTA
* *
56117 AAAAAAAAATTCTTTGTTTCTGCATTTTCTTTTAATTT
1 AAAAAAAAA-T-TTTGTTTCTGCGTTTTCTTTT--TTG
* *
56155 AAAAAAAAA-TTTGTTT-TGTGTTTTGTGTTTTTG
1 AAAAAAAAATTTTGTTTCTGCGTTTTCT-TTTTTG
56188 AAAAAAAAATTTTGTTTCTGCGTTTT-TTTTTT-
1 AAAAAAAAATTTTGTTTCTGCGTTTTCTTTTTTG
*
56220 AAAAAAATATTTT
1 AAAAAAAAATTTT
56233 CTGTCTTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
32 12 0.17
33 16 0.23
34 15 0.22
35 17 0.25
38 9 0.13
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (34 bp):
AAAAAAAAATTTTGTTTCTGCGTTTTCTTTTTTG
Found at i:56197 original size:33 final size:31
Alignment explanation
Indices: 56129--56231 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 31
56119 AAAAAAATTC
*
56129 TTTGTTTCTGCATTTTCTTTTAATTTAAAAAAAAA
1 TTTGTTTCTGC-GTTT-TTTT--TTTAAAAAAAAA
*
56164 TTTGTTT-TGTGTTTTGTGTTTTTGAAAAAAAAA
1 TTTGTTTCTGCGTTTT-T-TTTTT-AAAAAAAAA
*
56197 TTTTGTTTCTGCGTTTTTTTTTTAAAAAAATA
1 -TTTGTTTCTGCGTTTTTTTTTTAAAAAAAAA
56229 TTT
1 TTT
56232 TCTGTCTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
31 3 0.05
32 12 0.20
33 18 0.31
34 12 0.20
35 14 0.24
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (31 bp):
TTTGTTTCTGCGTTTTTTTTTTAAAAAAAAA
Done.