Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015149.1 Corchorus capsularis cultivar CVL-1 contig15170, 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: 56065
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:147 original size:14 final size:15
Alignment explanation
Indices: 119--149 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
109 AACACATATC
119 AACAATGGCAATCTT
1 AACAATGGCAATCTT
134 AACAATGG-AATCTT
1 AACAATGGCAATCTT
148 AA
1 AA
150 ATGTAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (15 bp):
AACAATGGCAATCTT
Found at i:471 original size:31 final size:30
Alignment explanation
Indices: 433--541 Score: 101
Period size: 31 Copynumber: 3.9 Consensus size: 30
423 TCCGACGTGG
*
433 CACGCCACGTGTACCAAAAAGTGACATATGA
1 CACGCCACGTGTACCAAAAAGTGACA-ATGT
* *
464 CACGCCACATGTAACAAAAAGT--C-ATGT
1 CACGCCACGTGTACCAAAAAGTGACAATGT
*
491 CA---CA--TGTACC-AAAGGTGACACATGT
1 CACGCCACGTGTACCAAAAAGTGACA-ATGT
516 CACGCCACGTGTACCAAAAAGTGACA
1 CACGCCACGTGTACCAAAAAGTGACA
542 CGTGGCATGC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
21 5 0.08
22 5 0.08
23 1 0.02
24 2 0.03
25 6 0.10
27 5 0.08
28 2 0.03
29 1 0.02
30 6 0.10
31 29 0.47
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.17
Consensus pattern (30 bp):
CACGCCACGTGTACCAAAAAGTGACAATGT
Found at i:554 original size:31 final size:31
Alignment explanation
Indices: 484--585 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
474 GTAACAAAAA
* * *
484 GTCATGTCACATGTACC-AAAGGTGACACAT
1 GTCATGCCACATGTACCAAAAAGTGACACGT
* *
514 GTCACGCCACGTGTACCAAAAAGTGACACGT
1 GTCATGCCACATGTACCAAAAAGTGACACGT
* ** * *
545 GGCATGCCACATGTTTCAAAAAATGGCACGT
1 GTCATGCCACATGTACCAAAAAGTGACACGT
576 GTCATGCCAC
1 GTCATGCCAC
586 GTGCACAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
30 14 0.24
31 44 0.76
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (31 bp):
GTCATGCCACATGTACCAAAAAGTGACACGT
Found at i:7776 original size:144 final size:144
Alignment explanation
Indices: 7516--7799 Score: 532
Period size: 144 Copynumber: 2.0 Consensus size: 144
7506 AATGGTTAGT
*
7516 ATTAAATCAAGCTTTTAGCCGACTTTTTACTGGACCTAGAGCTCAGGATTAGGCCCAAATTGACT
1 ATTAAATCAAGCTTTTAGCCGACTTTTTACTGGACCTAAAGCTCAGGATTAGGCCCAAATTGACT
7581 CAAATGCGGCAAAGGCCATCTGTCCAAATGGCCCAATTACAGACAACTTAATTGGACATGTTGCC
66 CAAATGCGGCAAAGGCCATCTGTCCAAATGGCCCAATTACAGACAACTTAATTGGACATGTTGCC
7646 CAGGAAGATGTCCA
131 CAGGAAGATGTCCA
* *
7660 ATTAAATCGAGCTTTTAGCCGACTTTTTACTGGATCTAAAGCTCAGGATTAGGCCCAAATTGACT
1 ATTAAATCAAGCTTTTAGCCGACTTTTTACTGGACCTAAAGCTCAGGATTAGGCCCAAATTGACT
*
7725 CAAATGCGGCAAAGGCTATCTGTCCAAATGGCCCAATTACAGACAACTTAATTGGACATGTTGCC
66 CAAATGCGGCAAAGGCCATCTGTCCAAATGGCCCAATTACAGACAACTTAATTGGACATGTTGCC
7790 CAGGAAGATG
131 CAGGAAGATG
7800 AGGCCCAAAT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (144 bp):
ATTAAATCAAGCTTTTAGCCGACTTTTTACTGGACCTAAAGCTCAGGATTAGGCCCAAATTGACT
CAAATGCGGCAAAGGCCATCTGTCCAAATGGCCCAATTACAGACAACTTAATTGGACATGTTGCC
CAGGAAGATGTCCA
Found at i:13275 original size:4 final size:4
Alignment explanation
Indices: 13266--13297 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
13256 CGCATGCAAG
*
13266 CATA CATA CATA CATA CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
13298 TACACATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:15356 original size:15 final size:14
Alignment explanation
Indices: 15336--15366 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
15326 CTTCAATTGA
15336 TTTTCTTTTTTCTTT
1 TTTTCTTTTTT-TTT
15351 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
15365 TT
1 TT
15367 ACAACCCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:18451 original size:2 final size:2
Alignment explanation
Indices: 18446--18479 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18436 CTCTCTCTCA
18446 AT AT AT AT 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 AT AT AT AT
18480 TACGTATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34407 original size:21 final size:22
Alignment explanation
Indices: 34378--34422 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
34368 TCATTTTGCT
34378 TAAGAAGGGTAATTA-ATCATA
1 TAAGAAGGGTAATTACATCATA
*
34399 TAAGCAGGGTAATTACATCATA
1 TAAGAAGGGTAATTACATCATA
34421 TA
1 TA
34423 TGCATCACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (22 bp):
TAAGAAGGGTAATTACATCATA
Found at i:34696 original size:8 final size:8
Alignment explanation
Indices: 34683--34710 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
34673 TGGGTATGAA
34683 ATGGGTAT
1 ATGGGTAT
34691 ATGGGTAT
1 ATGGGTAT
34699 ATGGGTAT
1 ATGGGTAT
34707 ATGG
1 ATGG
34711 ATATGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (8 bp):
ATGGGTAT
Found at i:37594 original size:27 final size:27
Alignment explanation
Indices: 37554--37608 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
37544 CCTCTCAAGT
37554 CCCTGCGAAAACATGACAAAGAAGGAG
1 CCCTGCGAAAACATGACAAAGAAGGAG
* *
37581 CCCTGCGAATACATGACAAAGGAGGAG
1 CCCTGCGAAAACATGACAAAGAAGGAG
37608 C
1 C
37609 ACTGACAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (27 bp):
CCCTGCGAAAACATGACAAAGAAGGAG
Found at i:45949 original size:24 final size:24
Alignment explanation
Indices: 45903--45953 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45893 GACAGATTTT
*
45903 AATAGTATCTTATTGTAGCAAAAA
1 AATAGTATCTTATTGAAGCAAAAA
**
45927 AATAGTATCTTATTGAATTAAAAA
1 AATAGTATCTTATTGAAGCAAAAA
45951 AAT
1 AAT
45954 CCAATTTCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (24 bp):
AATAGTATCTTATTGAAGCAAAAA
Found at i:52884 original size:32 final size:32
Alignment explanation
Indices: 52806--53121 Score: 577
Period size: 32 Copynumber: 10.0 Consensus size: 32
52796 TTGAGGGCCA
52806 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
52838 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
52869 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
52901 ATGTGAATTAAGGCAAGTTCAATTTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
52933 GTGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
52964 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
52996 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
53028 ATGTG-ATTAAGGCAAGTTCAATGTTATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
53059 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
53091 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
53122 GAAAGTTAAA
Statistics
Matches: 275, Mismatches: 6, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
31 116 0.42
32 159 0.58
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (32 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:52905 original size:63 final size:63
Alignment explanation
Indices: 52806--53121 Score: 580
Period size: 63 Copynumber: 5.0 Consensus size: 63
52796 TTGAGGGCCA
52806 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
*
52869 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATTTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
*
52933 GTGTG-ATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
*
52996 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTTATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
53059 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
53122 GAAAGTTAAA
Statistics
Matches: 245, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
63 185 0.76
64 60 0.24
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (63 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGG
Found at i:52969 original size:95 final size:95
Alignment explanation
Indices: 52806--53121 Score: 598
Period size: 95 Copynumber: 3.3 Consensus size: 95
52796 TTGAGGGCCA
52806 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGAT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGAT
52871 GTGAATTAAGGCAAGTTCAATGTCATTTGG
66 GTGAATTAAGGCAAGTTCAATGTCATTTGG
* *
52901 ATGTGAATTAAGGCAAGTTCAATTTCATTTGGGTGTGATTAAGGCAAGTTCAATGTCATTTGGAT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGAT
52966 GTGAATTAAGGCAAGTTCAATGTCATTTGG
66 GTGAATTAAGGCAAGTTCAATGTCATTTGG
*
52996 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTTATTTGGAT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGAT
53061 GTGAATTAAGGCAAGTTCAATGTCATTTGG
66 GTGAATTAAGGCAAGTTCAATGTCATTTGG
53091 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG
53122 GAAAGTTAAA
Statistics
Matches: 216, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
94 26 0.12
95 190 0.88
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (95 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGAT
GTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:55737 original size:332 final size:330
Alignment explanation
Indices: 54898--55958 Score: 1252
Period size: 332 Copynumber: 3.2 Consensus size: 330
54888 TTTGGCCCAC
** * * * *
54898 TTTTTCGGGTCAGTTAATGCCAAATTTTGGATGAAATCGTGCGCTTTA-CATCACGGTTTTTAGC
1 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGC-TAACCATCACGGTTTTTGGC
** *
54962 TGAAAATGCATTTCAGAG-TCCCGACC--AGTTTTGCATGATTTCTGGCGCCAAGAGTAATAGAA
65 TGAAAATGCACCT-AG-GCT-CCG-CCTGAGTTTTGCATGATTT-TGGCGCCAAGAGTAATTGAA
* *
55024 ATATCTATATTCATCTAACCAAATCTTAGTCACATTGAATTTAGGGATTTGTTTTTACGAGCATA
125 ATATCTATATTCATCTAACCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATA
* *
55089 TGTATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAGAACGATATTAGAAGCGT
190 TGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCGT
* ** ** * * *
55154 GAAAA--TGTAATTTTTTCTTTCTGGCGTTAAATTATATATGTTTTATGAGTATTGAGGCCAAAA
255 GAAAATCTTTTTTTTTTTCTTT-TGAAGTTGAATTATATATCTTTTATGAGTATTGTGGCCAAAA
*
55217 ATTGAGGAAAAA
319 TTTGAGGAAAAA
** * * *
55229 AATTTCGGGTCAATTTTTTCCAAATTTTGGACGAAAT--TGTG-T-ACCGATGACGGTTTTTGGC
1 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGCTAACC-ATCACGGTTTTTGGC
* ** * * *
55290 TGAAAATGCGTTCCGGGGC-CCTGGCTGAGTTTTTG-ATGATCTTTGGTGCCAAGAATAATTGAA
65 TGAAAATGC--ACCTAGGCTCC-GCCTGAG-TTTTGCATGAT-TTTGGCGCCAAGAGTAATTGAA
* * * * * * * *
55353 ATATCTATACTCATGTTAGCAAATCTTAGCCACATTGGATTTTAGAATTTGTTTTTACGAGCATC
125 ATATCTATATTCATCTAACCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATA
* * *
55418 TGAATCATGTTTCGATTTAATTAGAAGTTGATTTGGAAAAATAAGAAAAACGATATTAGAAGCGT
190 TGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCGT
*
55483 GAAAAATCTTTTTTTTTTTCTTTTGAAGTTGAATTATATATCTTTTATGAGCATTGTGGCCAAAA
255 G-AAAATCTTTTTTTTTTTCTTTTGAAGTTGAATTATATATCTTTTATGAGTATTGTGGCCAAAA
**
55548 TTTGAGGAAATTT
319 TTTGAGGAAA-AA
*
55561 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACTGTTTTTGGCT
1 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCT
* *
55626 GAAAATGCACCTAGGCTCCGCCTGAGTTTTGCATGATTTTTGCGCCAAGAGTAATTGAAAAATCT
66 GAAAATGCACCTAGGCTCCGCCTGAGTTTTGCATGATTTTGGCGCCAAGAGTAATTGAAATATCT
* * * * * * *
55691 GTTTTCATCTAACCAAATCTCAGTAAAATTGGATTGAAGGATTTGTTTTTACGAGCATTTGAATC
131 ATATTCATCTAACCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATC
* * *
55756 ATGTTTCGATTTAATTAGAAATTAATTCGG-AAAATAAGAAAAATGATATTAGATGCATGAAAAT
196 ATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAT
* * ** * * **
55820 CCTTTTTTTCTT-TTCGGCA-TTGAATTATATATCATTTAACAGTATTGTGGCCAAAATTTGAGG
261 CTTTTTTTTTTTCTTTTGAAGTTGAATTATATATCTTTTATGAGTATTGTGGCCAAAATTTGAGG
55883 AAAAA
326 AAAAA
* *
55888 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACAAAATCGTATGCTAACCATCACGGTTTTTGGCT
1 TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCT
55953 GAAAAT
66 GAAAAT
55959 ATGTTTCGGG
Statistics
Matches: 616, Mismatches: 94, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
326 1 0.00
327 73 0.12
328 67 0.11
329 148 0.24
330 26 0.04
331 101 0.16
332 152 0.25
333 16 0.03
334 6 0.01
335 23 0.04
336 3 0.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (330 bp):
TTTTTCGGGTCAGTTTTTGCCAAATTTTGGACGAAATCGTGTGCTAACCATCACGGTTTTTGGCT
GAAAATGCACCTAGGCTCCGCCTGAGTTTTGCATGATTTTGGCGCCAAGAGTAATTGAAATATCT
ATATTCATCTAACCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATC
ATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAT
CTTTTTTTTTTTCTTTTGAAGTTGAATTATATATCTTTTATGAGTATTGTGGCCAAAATTTGAGG
AAAAA
Done.