Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019706.1 Corchorus olitorius cultivar O-4 contig19739, 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: 83953
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:13303 original size:135 final size:135
Alignment explanation
Indices: 13003--13289 Score: 348
Period size: 135 Copynumber: 2.1 Consensus size: 135
12993 ATCTTCTCAG
* ** *
13003 TGGGGCTAACTCTAGTAATTAGTGGGTTTTTAGAGTCACTCTCATTCAATGTTTTCTCGAGGACA
1 TGGGGCTAACTCTAGTAATTAGTGGGTTTTTAGAGTCACTCTCAGTCAATGCATCCTCGAGGACA
* * * * * *
13068 GAATTAGGTCTCTTCTTCCTGCAGCTACTACCATAAAAGGGTCTCTTATCCAAAGGAATCTTCTT
66 GAATTAGCTCTCTTCTTCCGGCAGCTACAACCATAAAAGGGTCTCTTATCCAAAGAAATCTCCTG
13133 AAGTC
131 AAGTC
* * * *
13138 TGGGGCTAGCTCTAGTAACTAGTGGGGTTTTT-GTGTCACTTTCAGTCAATGCATCCAT-GAGGA
1 TGGGGCTAACTCTAGTAATTAGT-GGGTTTTTAGAGTCACTCTCAGTCAATGCATCC-TCGAGGA
** *
13201 CAGAATTAGACTC-CTTCTTCCGGTTGCTACAACCATAAAAGGGTCTCTTCTCCAAAGAAATAC-
64 CAGAATTAG-CTCTCTTCTTCCGGCAGCTACAACCATAAAAGGGTCTCTTATCCAAAGAAAT-CT
*
13264 CCTGGAGTC
127 CCTGAAGTC
13273 TGGGGCTAACTCTAGTA
1 TGGGGCTAACTCTAGTA
13290 TTTACCGGCG
Statistics
Matches: 129, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
135 117 0.91
136 12 0.09
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (135 bp):
TGGGGCTAACTCTAGTAATTAGTGGGTTTTTAGAGTCACTCTCAGTCAATGCATCCTCGAGGACA
GAATTAGCTCTCTTCTTCCGGCAGCTACAACCATAAAAGGGTCTCTTATCCAAAGAAATCTCCTG
AAGTC
Found at i:13744 original size:18 final size:18
Alignment explanation
Indices: 13721--13758 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13711 ATCAAAAGGG
*
13721 GAAAAAGAAACGAAAAAA
1 GAAAAAGAAAAGAAAAAA
13739 GAAAAAGAAAAGAAAAAA
1 GAAAAAGAAAAGAAAAAA
13757 GA
1 GA
13759 TCGAAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAAAGAAAAAA
Found at i:28426 original size:2 final size:2
Alignment explanation
Indices: 28419--28449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28409 ATTCTAAGTG
28419 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 A
28450 ACTTATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49701 original size:27 final size:28
Alignment explanation
Indices: 49667--49720 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
49657 AAACTTTTCC
49667 TATGAGGTTTA-GGTTTTCCTTAGTCCT
1 TATGAGGTTTAGGGTTTTCCTTAGTCCT
*
49694 TATGAGGTTTAGGGTTTTCCTTTGTCC
1 TATGAGGTTTAGGGTTTTCCTTAGTCC
49721 CTCTTTCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (28 bp):
TATGAGGTTTAGGGTTTTCCTTAGTCCT
Found at i:49720 original size:28 final size:26
Alignment explanation
Indices: 49660--49720 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
49650 TGTAGTGAAA
49660 CTTT-TCCTATGAGGTTTAGGTTTTC
1 CTTTGTCCTATGAGGTTTAGGTTTTC
*
49685 CTTAGTCCTTATGAGGTTTAGGGTTTTC
1 CTTTGTCC-TATGAGGTTTA-GGTTTTC
49713 CTTTGTCC
1 CTTTGTCC
49721 CTCTTTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 3 0.10
26 3 0.10
27 11 0.35
28 14 0.45
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.49
Consensus pattern (26 bp):
CTTTGTCCTATGAGGTTTAGGTTTTC
Found at i:67267 original size:386 final size:387
Alignment explanation
Indices: 66525--67399 Score: 1411
Period size: 387 Copynumber: 2.3 Consensus size: 387
66515 AGCACTCTGG
* *
66525 GAGGACCTGACCCGAGGAGTGGACTGGAGACGCGTTTCCACGGACACGACGTTGGTGTTGCAACT
1 GAGGACCTGACCCGAAGAGTGGACTGGAGACGCGTTTCCACGGACACGACGTTGGTGTTGCAGCT
*
66590 GGAAAACAATAATGCAAAACTGCCTCAACCAGTTGCACTTCAAGGGTGATCGACAAGCGCAGAAG
66 GGAAAACAACAATGCAAAACT-CCTCAACCAGTTGCACTTCAAGGGTGATCGACAAGCGCAGAAG
* *
66655 ATGGATGAACGGATGACAAAGAGGGAAGAGGAACAAAGCAAACAAGCGCAGAACATGGGAGAACG
130 ATGGATGAACGGACGACAAAGAGGGAAGAGGAACAAAGCAAACAAGCACAGAACATGGGAGAACG
* *
66720 GATGACGAAGATGGAAGAGGAACTGAGAAAAAGAAAGGGTTTATTTTGTTAGTTAGGTAGGTTGT
195 GATGACAAAAATGGAAGAGGAACTGAGAAAAAGAAAGGGTTTATTTTGTTAGTTAGGTAGGTTGT
*
66785 TGCAAGATGAGATTTTGGGGCTGGGAGTTTAAAAAGATTCAATTTTTAAGGCTTTCTTGTGCTTA
260 TGCAAGATGAGATTTTGGGGCTAGGAGTTTAAAAAGATTCAATTTTTAAGGCTTTCTTGTGCTTA
*
66850 AATACGTAAAAGTAAGTTTTTTATGTTTTTTTTT-ATAGTTTAAGGTTTTTTTATGGGTTTAA
325 AATACGTAAAAGTAAGTTTTTTATGTTTTTTTTTAATAGTTTAAGGTTTTTTTATGGGTCTAA
* * *
66912 GAGGACCTGACCCGAAGAGTGGACTGGAGACACATTTCCACGGACACAACGTTGGTGTTGCAGCT
1 GAGGACCTGACCCGAAGAGTGGACTGGAGACGCGTTTCCACGGACACGACGTTGGTGTTGCAGCT
* * *
66977 GGAAAACAACAATGCAAATCTCCTCAACCAGTTGCACTTGAAGGTTGATCGACAAGCGCAGAAGA
66 GGAAAACAACAATGCAAAACTCCTCAACCAGTTGCACTTCAAGGGTGATCGACAAGCGCAGAAGA
* * * * *
67042 TGGATGGACGGACGACAAAGATGGAAGAGGAACAGAGCAAACAAGCACATAAGAT-GGAGGAACG
131 TGGATGAACGGACGACAAAGAGGGAAGAGGAACAAAGCAAACAAGCACAGAACATGGGA-GAACG
* *
67106 GATGACAAAAATGGATGAGGAACTGGGAAAAAGAAAGGGTTT-TTTT-TTAGTTAGGTAGGTTGT
195 GATGACAAAAATGGAAGAGGAACTGAGAAAAAGAAAGGGTTTATTTTGTTAGTTAGGTAGGTTGT
67169 TGCAAGATG-GAATTTTGGGGCTAGGAGTTTAAAAAGATTCAATTTTTAAGGCTTTCTTGTGCTT
260 TGCAAGATGAG-ATTTTGGGGCTAGGAGTTTAAAAAGATTCAATTTTTAAGGCTTTCTTGTGCTT
67233 AAAT-CGTAAAAAGTAAGGTTTTTTATGTTTTTTTTTTAATAGTTTAAGGTTTTTTTATGGGTCT
324 AAATACGT-AAAAGTAA-GTTTTTTATG-TTTTTTTTTAATAGTTTAAGGTTTTTTTATGGGTCT
*
67297 AG
386 AA
* * *
67299 GAGGACCTAACCCGAAGAGTGGACTGGAGACGCGTTTCCACGGACACGACATTGGTGTTGCAGTT
1 GAGGACCTGACCCGAAGAGTGGACTGGAGACGCGTTTCCACGGACACGACGTTGGTGTTGCAGCT
*
67364 GGAAAACAACAATGCAAACCTCCTCAACCAGTTGCA
66 GGAAAACAACAATGCAAAACTCCTCAACCAGTTGCA
67400 GCGTTAAAAC
Statistics
Matches: 452, Mismatches: 30, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
383 4 0.01
384 90 0.20
385 17 0.04
386 142 0.31
387 199 0.44
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (387 bp):
GAGGACCTGACCCGAAGAGTGGACTGGAGACGCGTTTCCACGGACACGACGTTGGTGTTGCAGCT
GGAAAACAACAATGCAAAACTCCTCAACCAGTTGCACTTCAAGGGTGATCGACAAGCGCAGAAGA
TGGATGAACGGACGACAAAGAGGGAAGAGGAACAAAGCAAACAAGCACAGAACATGGGAGAACGG
ATGACAAAAATGGAAGAGGAACTGAGAAAAAGAAAGGGTTTATTTTGTTAGTTAGGTAGGTTGTT
GCAAGATGAGATTTTGGGGCTAGGAGTTTAAAAAGATTCAATTTTTAAGGCTTTCTTGTGCTTAA
ATACGTAAAAGTAAGTTTTTTATGTTTTTTTTTAATAGTTTAAGGTTTTTTTATGGGTCTAA
Found at i:67707 original size:6 final size:6
Alignment explanation
Indices: 67696--67733 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
67686 TCCTCAAACC
*
67696 CCACCT CCACCT CCACCT CCACTT CCACCT CCACCT CC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CC
67734 CAACCAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.66, G:0.00, T:0.18
Consensus pattern (6 bp):
CCACCT
Found at i:76473 original size:33 final size:33
Alignment explanation
Indices: 76435--76503 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
76425 GGAGTAGTTC
*
76435 TTGTAATTTTTTGT-AAATTATATTCTGTTCTTA
1 TTGTAATTTTTT-TCAAATTATATTCGGTTCTTA
*
76468 TTGTAATTTTTTTCAAATTATATTGGGTTCTTA
1 TTGTAATTTTTTTCAAATTATATTCGGTTCTTA
76501 TTG
1 TTG
76504 ATTTTACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59
Consensus pattern (33 bp):
TTGTAATTTTTTTCAAATTATATTCGGTTCTTA
Found at i:76530 original size:23 final size:23
Alignment explanation
Indices: 76503--76551 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
76493 GGTTCTTATT
76503 GATTTTACTTTATTCTTGTTTTA
1 GATTTTACTTTATTCTTGTTTTA
76526 GATTTTACTTTATTCTTGTTTTA
1 GATTTTACTTTATTCTTGTTTTA
76549 GAT
1 GAT
76552 GGCTACACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.63
Consensus pattern (23 bp):
GATTTTACTTTATTCTTGTTTTA
Found at i:80146 original size:21 final size:21
Alignment explanation
Indices: 80113--80161 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
80103 AAACCAATCT
80113 TATGATT-ATTATATCTTTTA
1 TATGATTAATTATATCTTTTA
80133 TATGATTAATTATATCTTTTA
1 TATGATTAATTATATCTTTTA
80154 TATGATTA
1 TATGATTA
80162 TCATCATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (21 bp):
TATGATTAATTATATCTTTTA
Done.