Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015448.1 Corchorus olitorius cultivar O-4 contig15481, 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: 109681
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1622 original size:5 final size:5
Alignment explanation
Indices: 1608--1653 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
1598 TTGTATTCAG
*
1608 ATAT- ATATA ATATA ATAGA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1654 TCCCTGTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:5342 original size:331 final size:324
Alignment explanation
Indices: 4246--5642 Score: 1247
Period size: 331 Copynumber: 4.3 Consensus size: 324
4236 CCAACCATTA
* * * * * * * * **
4246 TTTTTACAAACATTTGAATCATATTTCGTTTTAATTAGAAATTAGTTCGGGGAAA-A--AAAAAC
1 TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAAC
* * * * * * * **
4308 -ATATTAGAAGCGTAAAAAGCCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTACGAGTAT
66 GATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATATTTTATTAGTAT
** * * ** *
4372 AGTGGCTAAAAATTGAGAGAATATTTTTCTGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGT
131 TTTGG-AAAAAATTGAG-GAAAAACTTTC-GGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGT
* * * * * ** *
4437 ACTAACCATTACA-GTTTTTTGCTAAAAACGCGTTTC-GGCGCCCCAACTCAGTTTTGCATG-TT
192 AATAATCATCA-AGGTTTTTAGCTAAAAACGCG-TTCAGGGGCCCC-GGTTAGTTTTGCATGATT
* * * * * *
4499 TTTTGCGTCGAGACTCCTCGAAGTAT-T-TA-T-AT-T-A---AATCTCAGCCACAATGCATTTA
254 TTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATCTAATCTCAG-CACATTGGATTTA
*
4555 AGGATTT
318 AAGATTT
* * *
4562 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTTAGAATAATATGAAAAA
1 -TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAA
*
4627 CGATATTAAAAG--TGAGAACAGTCCTCCAATCTTTTTGGA-GTTGAATTATATATATTTTATGA
65 CGATATTAAAAGCATGA-AA-AGTCCTCCAATCTTTTT-GACGTTGAATTATATATATTTTATTA
* * * *
4689 GTATTTTAGACAAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAAATTAGGCGAAATCG
127 GTATTTTGGA-AAAAATTGAGGAAAAA-CTTTC-GGTCAATTTTTGCAAAATTTAGCCGAAATCG
* * * * *
4754 TGTATTTAGTCGAAATCAAGGTTTTTTGCTAAAAACGCGTTCTAGGGGCGCCGGTTCAGTGTTGC
189 TGTA-ATAATC---ATCAAGGTTTTTAGCTAAAAACGCGTTC-AGGGGCCCCGGTT-AGTTTTGC
* * **
4819 ATGATTTTTTTGCGCCAAGACTCCTTGAAATATCTGCATTCATCTAA-CTAAATCTCAGC-CATT
248 ATGA-TTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATCT-AATCTCAGCACATT
*
4882 GGATTTAAGGATTT
311 GGATTTAAAGATTT
* *** * * * * *
4896 GTAAAACAAGCATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAA
1 TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAG-AAA-AATATGAAAA
* ** * * *
4961 ACGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA-ATTTTTTTTAG
64 ACGATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATA-TTTTATTAG
* * ** *
5025 TATTATGGATAAAAATTGAGGAAATAACTTTCGATTCAATTTTTATAAAATTCTAGCCAAAATCG
128 TATTTTGGA-AAAAATTGAGGAAA-AACTTTCG-GTCAATTTTTGCAAAATT-TAGCCGAAATCG
* * * *
5090 TGTAATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTAGGTTTTGCATGAT
189 TGTAATAATCATCAAGGTTTTTAGCTAAAAACGCGTTCAGGGGCCCCGGTTA-GTTTTGCATGAT
* * * *
5155 TTTTGGCGTCAAGACTCTTTGAGATATCTATATTCATTTAATCTAATCTCAGCTACATTGGATTG
253 TTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATCTAATCTCAGC-ACATTGGATTT
*
5220 AAAAATTT
317 AAAGATTT
* *
5228 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAATA
1 -TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAA
* *
5293 CGATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTTACGTTAAATTATATATATTTTATTAGTA
65 CGATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATATTTTATTAGTA
* * *
5358 TTTTAGCAAAAATTTGATGGAAGAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
130 TTTT-GGAAAAAATTGA-GGAA-AAACTTTC-GGTCAATTTTTGCAAAA-TTTAGCCGAAATCGT
* * * * * * * * *
5423 GTACTAACCATCATGGTTTTCAGCTAAAAATGCATTCTGGGG-CCTGAATTAGTTTTGCATGATT
190 GTAATAATCATCAAGGTTTTTAGCTAAAAACGCGTTCAGGGGCCCCG-GTTAGTTTTGCATGATT
* * * * *
5487 TTTGGTGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGAATTTA
254 TTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATCTAATCTC-AGCACATTGGATTTA
*
5552 ATGATTT
318 AAGATTT
* *
5559 TTTTTACAAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAAC
1 TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAAC
* *
5624 GATATTAAAGGCGTGAAAA
66 GATATTAAAAGCATGAAAA
5643 AAAGGCTTTC
Statistics
Matches: 881, Mismatches: 149, Indels: 87
0.79 0.13 0.08
Matches are distributed among these distances:
317 42 0.05
318 1 0.00
319 2 0.00
320 28 0.03
321 85 0.10
322 1 0.00
323 4 0.00
324 23 0.03
325 16 0.02
327 24 0.03
328 1 0.00
329 1 0.00
330 124 0.14
331 173 0.20
332 121 0.14
333 86 0.10
334 21 0.02
335 99 0.11
336 26 0.03
337 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (324 bp):
TTTTTACAAGCATCTGAATCTTGTTTCGATTTAACTAGAAATTAATTCAGAAAAATATGAAAAAC
GATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGACGTTGAATTATATATATTTTATTAGTAT
TTTGGAAAAAATTGAGGAAAAACTTTCGGTCAATTTTTGCAAAATTTAGCCGAAATCGTGTAATA
ATCATCAAGGTTTTTAGCTAAAAACGCGTTCAGGGGCCCCGGTTAGTTTTGCATGATTTTTGGCG
TCAAGACTCCTTGAAATATCTATATTCATCTAATCTAATCTCAGCACATTGGATTTAAAGATTT
Found at i:5709 original size:29 final size:30
Alignment explanation
Indices: 5666--5723 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5656 TTTTTTGGTG
* * *
5666 TTGAAGTT-TAGGGGGCAAAATGTCCAAAA
1 TTGAAGTTCAAGGGGACAAAACGTCCAAAA
5695 TTGAAGTTCAAGGGGACAAAACGTCCAAA
1 TTGAAGTTCAAGGGGACAAAACGTCCAAA
5724 CGGCTACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (30 bp):
TTGAAGTTCAAGGGGACAAAACGTCCAAAA
Found at i:8551 original size:32 final size:32
Alignment explanation
Indices: 8505--8583 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 32
8495 AAGGAGCCCC
8505 AGACCGTTTACAGGCTTTTTTTTTGGTGAATT
1 AGACCGTTTACAGGCTTTTTTTTTGGTGAATT
*
8537 AGACTGTTTACAGGC-TTTTTTTTGGTGAATT
1 AGACCGTTTACAGGCTTTTTTTTTGGTGAATT
8568 AGACCGTTTACAGGCT
1 AGACCGTTTACAGGCT
8584 AGCCCACATG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 30 0.68
32 14 0.32
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (32 bp):
AGACCGTTTACAGGCTTTTTTTTTGGTGAATT
Found at i:23708 original size:31 final size:30
Alignment explanation
Indices: 23662--23799 Score: 114
Period size: 31 Copynumber: 4.5 Consensus size: 30
23652 TTTTGTGCAT
* *
23662 GTGGCATGCCACGTGTCACTTTTGGGTACAC
1 GTGGCGTGACACGTGTCACTTTT-GGTACAC
* * *
23693 ATGGCGTGATACGTGTCACCTTTTGGTACAT
1 GTGGCGTGACACGTGTCA-CTTTTGGTACAC
* * *
23724 GTGGCGTGCCACATGTCGCTTTTTGGTACAC
1 GTGGCGTGACACGTGTCAC-TTTTGGTACAC
* * * *
23755 GTGGCGTGCCACATGTCGCTTTTTTGTACAC
1 GTGGCGTGACACGTGTCAC-TTTTGGTACAC
* *
23786 GTGGCATGCCACGT
1 GTGGCGTGACACGT
23800 CGGACACCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.01
31 85 0.93
32 5 0.05
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (30 bp):
GTGGCGTGACACGTGTCACTTTTGGTACAC
Found at i:23727 original size:62 final size:61
Alignment explanation
Indices: 23650--23799 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 61
23640 TGGCACATAT
* * *
23650 CCTTTTGTGCATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGATACGTGTCA
1 CCTTTTGTACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGACACATGTCA
* * * * * * *
23711 CCTTTTGGTACATGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCG
1 CCTTTT-GTACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGACACATGTCA
* *
23773 CTTTTTTGTACACGTGGCATGCCACGT
1 C-CTTTTGTACATGTGGCATGCCACGT
23800 CGGACACCAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
61 6 0.08
62 63 0.86
63 4 0.05
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (61 bp):
CCTTTTGTACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGACACATGTCA
Found at i:24478 original size:44 final size:44
Alignment explanation
Indices: 24415--24500 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
24405 CAGTAACTCT
*
24415 TTTCCAAACATTAAGTAAAACCATGATCTTTACGATTTGCCTCC
1 TTTCCAAACATCAAGTAAAACCATGATCTTTACGATTTGCCTCC
24459 TTTCCAAACATCAAGTAAAACCATGATCTTTACGATTTGCCT
1 TTTCCAAACATCAAGTAAAACCATGATCTTTACGATTTGCCT
24501 TTTAAGGAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (44 bp):
TTTCCAAACATCAAGTAAAACCATGATCTTTACGATTTGCCTCC
Found at i:24641 original size:35 final size:35
Alignment explanation
Indices: 24590--24661 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
24580 TATCATATGA
*
24590 CTTTGGAGAGGGTTGAGCATAAGCAAAACAAATGC
1 CTTTGGAGAGGATTGAGCATAAGCAAAACAAATGC
24625 CTTTGGAGAGGATTGAGCATAAGCAAAACAAATGC
1 CTTTGGAGAGGATTGAGCATAAGCAAAACAAATGC
24660 CT
1 CT
24662 ATCTCATAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (35 bp):
CTTTGGAGAGGATTGAGCATAAGCAAAACAAATGC
Found at i:29897 original size:13 final size:13
Alignment explanation
Indices: 29879--29903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29869 ATTTGAAATC
29879 ATTTTTATTTATA
1 ATTTTTATTTATA
29892 ATTTTTATTTAT
1 ATTTTTATTTAT
29904 TTAATTTAAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:31586 original size:335 final size:330
Alignment explanation
Indices: 30900--31931 Score: 1329
Period size: 333 Copynumber: 3.1 Consensus size: 330
30890 GTACTAACAA
* * * * * * *
30900 AACCATCATGGTTTTTCGCTAAAAACGCATTCCAGGGACCCGACTCAATTTTGCATGATTTTTGG
1 AACCATCACGG-TTTTGGGTAAAAACGCGTTCC-GGGGCCCGGCTCAGTTTTGCATGATTTTTGG
* * * * ** *
30965 CTCCGAGACTACTTGAAATATCTATATTCATCTAATCAAATCTGTGTCACATTGGATTTAAGGAT
64 CGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTTAAGGAT
* * *
31030 TTGTTTTTACA-AGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGG
128 TTGTTTTTA-AGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGG
* ** *
31094 AAAAATGATATTAGAAATGTCAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAT
192 AAAAACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAT
*
31159 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTACAAAATTTTAGCCAAAA
257 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCAAAA
*
31224 TCATGTACT
322 TCGTGTACT
* *
31233 AACCATCACAGTTTTTGGGTAAAAACGCGTTCCGGGGCCCTGGGTCAGTTTTGCATGATTTTTGG
1 AACCATCAC-GGTTTTGGGTAAAAACGCGTTCCGGGGCCC-GGCTCAGTTTTGCATGATTTTTGG
* *
31298 CGCCAAGATTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGG
64 CGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTG-ATTTAAGG
* * * *
31363 ATTTGCTTTTAAGAGTC-TCTAAATCTTGTTTCGATTTAATCATAAACTAATTTGGAAACAAAAT
126 ATTTGTTTTTAAGAG-CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAA-AAAAT
*
31427 AGGAAAAACGATATTAGAAGCGTGAAAAATG-CTTTCAAT-TTTGTTGGCGTTGAATTATATATT
189 AGGAAAAACGATATTAGAAGCGT-AAAAA-GCCCTTCAATCTTT-TTGGCGTTGAATTATATATT
* * * * * * *
31490 TTTTATGAGTATTATCGCTAGAAATCGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAA-TTTAG
251 TTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAG
*
31554 CCAAAATCGTGTATT
316 CCAAAATCGTGTACT
* * *
31569 AACCATCACGGTTTTGGGCTAAAAACGCGTTTCGGGGCCCGGCTTAGTTTTGCATGATTTTTGGT
1 AACCATCACGGTTTTGGG-TAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGC
** * * *
31634 GTAAAGACTCGTTGAAATATCTATATTCATCTAACAAAATCTCAGCCACGTTAGATTTAAGGATT
65 GCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTTAAGGATT
* * *
31699 TGTTTTTATGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAA
129 TGTTTTTAAGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAA
* * ** * *
31764 AAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATAA
194 AAACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
* *
31829 GTATTTTAGCCAAAAATTGA-GAAATTATCTTTCGGGTCGATTTTTACAAAATTTTAGCCGAAAT
259 GTATTTTAGCCAAAAATTGAGGAAA-TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCAAAAT
31893 CGTGTACT
323 CGTGTACT
31901 AACCATCACGGTTTTTGGGTAAAAACGCGTT
1 AACCATCACGG-TTTTGGGTAAAAACGCGTT
31932 ACAGGGCCAT
Statistics
Matches: 604, Mismatches: 76, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
330 5 0.01
331 73 0.12
332 77 0.13
333 156 0.26
334 8 0.01
335 127 0.21
336 75 0.12
337 82 0.14
338 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
AACCATCACGGTTTTGGGTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCG
CCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGATTTAAGGATTTG
TTTTTAAGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAA
ACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
ATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCGT
GTACT
Found at i:35686 original size:26 final size:26
Alignment explanation
Indices: 35656--35712 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
35646 TGGACCCACA
*
35656 ATGGCTCAATTCCTTCTTACCCAAAC
1 ATGGCCCAATTCCTTCTTACCCAAAC
35682 ATGGCCCAATTCCTTCTTACCCAAAC
1 ATGGCCCAATTCCTTCTTACCCAAAC
35708 ATGGC
1 ATGGC
35713 GATCAATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.35, G:0.11, T:0.28
Consensus pattern (26 bp):
ATGGCCCAATTCCTTCTTACCCAAAC
Found at i:46147 original size:31 final size:32
Alignment explanation
Indices: 46094--46169 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
46084 GTGGTAATAC
*
46094 CACGTCGGACCAAAAATACCACATGGCAATGA
1 CACGTCGGACCAAAAATACCACAAGGCAATGA
* * * *
46126 CACGTTGGACC-AAAATGCCACAAGGCAAGGC
1 CACGTCGGACCAAAAATACCACAAGGCAATGA
*
46157 CACGTCAGACCAA
1 CACGTCGGACCAA
46170 GACGCTGACA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 25 0.69
32 11 0.31
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (32 bp):
CACGTCGGACCAAAAATACCACAAGGCAATGA
Found at i:53699 original size:78 final size:78
Alignment explanation
Indices: 53565--53725 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
53555 GTTTTCTACT
* *
53565 TAAAATAGTAAAATGGTAAACTGAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
53630 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* *
53643 TAAAATAGTAAAATGGTAAAATAAAATAGTTCTAAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
53708 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
53721 TAAAA
1 TAAAA
53726 CTATAAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:59565 original size:19 final size:20
Alignment explanation
Indices: 59535--59598 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
59525 TTGACACTGT
59535 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
* *
59556 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACAGATGAGA
*
59575 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTACAGATGAGA
59596 TTA
1 TTA
59599 TTAGAGCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
21 19 0.53
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:81145 original size:5 final size:5
Alignment explanation
Indices: 81119--81159 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
81109 GTGAAATTGT
*
81119 AAAGAA AAAGC AAAG- AAA-A AAAGA AAAGA AAAGA AAAGA AA
1 AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
81160 TCTCTTCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
4 6 0.19
5 22 0.69
6 4 0.12
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:81151 original size:18 final size:19
Alignment explanation
Indices: 81119--81155 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
81109 GTGAAATTGT
*
81119 AAAGAAAAAGCAAAGAAAA
1 AAAGAAAAAGAAAAGAAAA
81138 AAAG-AAAAGAAAAGAAAA
1 AAAGAAAAAGAAAAGAAAA
81156 GAAATCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAAGAAAA
Found at i:81286 original size:3 final size:3
Alignment explanation
Indices: 81278--81302 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
81268 TTTGAACACC
81278 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
81303 AAGCTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:84853 original size:77 final size:77
Alignment explanation
Indices: 84726--84877 Score: 277
Period size: 77 Copynumber: 2.0 Consensus size: 77
84716 AACGGATGTT
* *
84726 ATTAGGCCCTTGTTTGAACTAAAACGGTAACATTGAGCTCTAATTTGACCAAATTGAAAGGATAG
1 ATTAGGCCCTTATTTGAACTAAAACGGTAACATTGAGCTCTAATTCGACCAAATTGAAAGGATAG
*
84791 ACTCTAAATCAA
66 ACACTAAATCAA
84803 ATTAGGCCCTTATTTGAACTAAAACGGTAACATTGAGCTCTAATTCGACCAAATTGAAAGGATAG
1 ATTAGGCCCTTATTTGAACTAAAACGGTAACATTGAGCTCTAATTCGACCAAATTGAAAGGATAG
84868 ACACTAAATC
66 ACACTAAATC
84878 GAGCTTTTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (77 bp):
ATTAGGCCCTTATTTGAACTAAAACGGTAACATTGAGCTCTAATTCGACCAAATTGAAAGGATAG
ACACTAAATCAA
Found at i:90876 original size:37 final size:37
Alignment explanation
Indices: 90821--90901 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
90811 ATATTCTGAA
90821 AACGTAAGAGAATAATTAAAGACCCAATTAACTTTAGC
1 AACG-AAGAGAATAATTAAAGACCCAATTAACTTTAGC
90859 AACGAAGAGAATAATTAAAGACCCAATTAACTTTAGC
1 AACGAAGAGAATAATTAAAGACCCAATTAACTTTAGC
90896 AACGAA
1 AACGAA
90902 ATACTCGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 39 0.91
38 4 0.09
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (37 bp):
AACGAAGAGAATAATTAAAGACCCAATTAACTTTAGC
Found at i:90958 original size:35 final size:35
Alignment explanation
Indices: 90912--90987 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
90902 ATACTCGATT
* * **
90912 CCGAATTAGTCAGGATTTAATGTGGTTACCAGATA
1 CCGAATTAGTCAGGACTCAATGCAGTTACCAGATA
90947 CCGAATTAGTCAGGACTCAATGCAGTTACCAGATA
1 CCGAATTAGTCAGGACTCAATGCAGTTACCAGATA
90982 CCGAAT
1 CCGAAT
90988 GGTCCATACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (35 bp):
CCGAATTAGTCAGGACTCAATGCAGTTACCAGATA
Found at i:91050 original size:51 final size:51
Alignment explanation
Indices: 90994--91096 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
90984 GAATGGTCCA
* *
90994 TACCAAAAAGACATGGCTAAATGCATAATCGGAAGAGTTTAAGAAATGGGT
1 TACCAAAAAGACATGGCTAAACGCATAATCGGAAGAGTTTAAGAAAAGGGT
*
91045 TACCAAAAAGACATGGCTAAACGCATATTCGGAAGAGTTTAAGAAAAGGGT
1 TACCAAAAAGACATGGCTAAACGCATAATCGGAAGAGTTTAAGAAAAGGGT
91096 T
1 T
91097 TAAAAGTGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (51 bp):
TACCAAAAAGACATGGCTAAACGCATAATCGGAAGAGTTTAAGAAAAGGGT
Found at i:106581 original size:6 final size:6
Alignment explanation
Indices: 106542--106580 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
106532 TTCAAATGGA
106542 TTTTGT TTTTGT TATTT-T TTTTGT TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT T-TTTGT TTTTGT TTTTGT TTTTGT TTTT
106581 TACATTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.26
6 20 0.65
7 3 0.10
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:106581 original size:18 final size:18
Alignment explanation
Indices: 106542--106580 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
106532 TTCAAATGGA
106542 TTTTGTTTTTGTTATTTT
1 TTTTGTTTTTGTTATTTT
106560 TTTTGTTTTTGTT-TTTT
1 TTTTGTTTTTGTTATTTT
106577 TTTT
1 TTTT
106581 TACATTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (18 bp):
TTTTGTTTTTGTTATTTT
Found at i:109640 original size:1 final size:1
Alignment explanation
Indices: 109634--109681 Score: 87
Period size: 1 Copynumber: 48.0 Consensus size: 1
109624 TTCGTTTAAG
*
109634 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Done.