Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006920.1 Corchorus capsularis cultivar CVL-1 contig06941, 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: 46644
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:498 original size:19 final size:18
Alignment explanation
Indices: 465--501 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
455 TTGAAATAAT
465 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
483 TCTTCATATTATCTTCAAG
1 TCTTCA-ATGATCTTCAAG
502 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:10317 original size:19 final size:18
Alignment explanation
Indices: 10284--10320 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10274 TTGAAATAAT
10284 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
10302 TCTTCATATTATCTTCAAG
1 TCTTCA-ATGATCTTCAAG
10321 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:16734 original size:16 final size:16
Alignment explanation
Indices: 16713--16757 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
16703 CTTCGATTTG
16713 ACCAAAAACCAAATTA
1 ACCAAAAACCAAATTA
*
16729 ACCAAAAACCGAATTA
1 ACCAAAAACCAAATTA
**
16745 AATAAAAACCAAA
1 ACCAAAAACCAAA
16758 ACTCTATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.64, C:0.22, G:0.02, T:0.11
Consensus pattern (16 bp):
ACCAAAAACCAAATTA
Found at i:21331 original size:389 final size:389
Alignment explanation
Indices: 20614--21389 Score: 1507
Period size: 389 Copynumber: 2.0 Consensus size: 389
20604 TCGTTTTAGC
20614 TCAGAAAGCTTTGAAATTTGAGCTTTAGACTTGTTTTAGTGTGATATTTCTGGGAAAAAATATTG
1 TCAGAAAGCTTTGAAATTTGAGCTTTAGACTTGTTTTAGTGTGATATTTCTGGGAAAAAATATTG
* *
20679 AAAAAAATCAATAAAATCTGTAGTGTAATCGGAATTTTTCAGGTTCATAGTTCTTATTGAGGTTA
66 AAAAAAATCAATAAAATCTGTAGTGTAATCGGAATTTTTCAGGTTCATAGTTCTTATCGAGCTTA
20744 TTTGGGAATTAGGGTTTTGATTGTGCAATTGATTCAATTGGTTGCAATTAACTCTAATTGATTGT
131 TTTGGGAATTAGGGTTTTGATTGTGCAATTGATTCAATTGGTTGCAATTAACTCTAATTGATTGT
*
20809 TTGTTTGACATTCTTGGGTTGCTTTTGCTGTGAATTGAGATTTAATTTGAAGAATTTCAGGTTGA
196 TTGTTTGACATTCTTGGGTTGCTTTTGCTGTGAATTGAGATTTAATTTAAAGAATTTCAGGTTGA
*
20874 AACCTTATTGGAGACAAGTGGTACAAAATTGGATCTAAGTGGTACTACGGTTTCTAATTGATTGA
261 AACCCTATTGGAGACAAGTGGTACAAAATTGGATCTAAGTGGTACTACGGTTTCTAATTGATTGA
20939 TTTGATTGAATTGTGTTTGATTGAGTTTTTGTGCAGCCTCTTTGAGAAGGAATTGAATTGAGCT
326 TTTGATTGAATTGTGTTTGATTGAGTTTTTGTGCAGCCTCTTTGAGAAGGAATTGAATTGAGCT
21003 TCAGAAAGCTTTGAAATTTGAGCTTTAGACTTGTTTTAGTGTGATATTTCTGGGAAAAAATATTG
1 TCAGAAAGCTTTGAAATTTGAGCTTTAGACTTGTTTTAGTGTGATATTTCTGGGAAAAAATATTG
21068 AAAAAAATCAATAAAATCTGTAGTGTAATCGGAATTTTTCAGGTTCATAGTTCTTATCGAGCTTA
66 AAAAAAATCAATAAAATCTGTAGTGTAATCGGAATTTTTCAGGTTCATAGTTCTTATCGAGCTTA
21133 TTTGGGAATTAGGGTTTTGATTGTGCAATTGATTCAATTGGTTGCAATTAACTCTAATTGATTGT
131 TTTGGGAATTAGGGTTTTGATTGTGCAATTGATTCAATTGGTTGCAATTAACTCTAATTGATTGT
*
21198 TTGTTTGAGATTCTTGGGTTGCTTTTGCTGTGAATTGAGATTTAATTTAAAGAATTTCAGGTTGA
196 TTGTTTGACATTCTTGGGTTGCTTTTGCTGTGAATTGAGATTTAATTTAAAGAATTTCAGGTTGA
21263 AACCCTATTGGAGACAAGTGGTACAAAATTGGATCTAAGTGGTACTACGGTTTCTAATTGATTGA
261 AACCCTATTGGAGACAAGTGGTACAAAATTGGATCTAAGTGGTACTACGGTTTCTAATTGATTGA
21328 TTTGATTGAATTGTGTTTGATTGAGTTTTTGTGCAGCCTCTTTGAGAAGGAATTGAATTGAG
326 TTTGATTGAATTGTGTTTGATTGAGTTTTTGTGCAGCCTCTTTGAGAAGGAATTGAATTGAG
21390 TTCGAGATCT
Statistics
Matches: 382, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
389 382 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (389 bp):
TCAGAAAGCTTTGAAATTTGAGCTTTAGACTTGTTTTAGTGTGATATTTCTGGGAAAAAATATTG
AAAAAAATCAATAAAATCTGTAGTGTAATCGGAATTTTTCAGGTTCATAGTTCTTATCGAGCTTA
TTTGGGAATTAGGGTTTTGATTGTGCAATTGATTCAATTGGTTGCAATTAACTCTAATTGATTGT
TTGTTTGACATTCTTGGGTTGCTTTTGCTGTGAATTGAGATTTAATTTAAAGAATTTCAGGTTGA
AACCCTATTGGAGACAAGTGGTACAAAATTGGATCTAAGTGGTACTACGGTTTCTAATTGATTGA
TTTGATTGAATTGTGTTTGATTGAGTTTTTGTGCAGCCTCTTTGAGAAGGAATTGAATTGAGCT
Found at i:27790 original size:6 final size:6
Alignment explanation
Indices: 27775--27841 Score: 93
Period size: 6 Copynumber: 11.5 Consensus size: 6
27765 TAAGTCTGTT
* *
27775 CTTTTC CTTTTT CTTTTC CTTTTC CTTTTC CTTTT- CTTTCC CTTTTC
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
*
27822 C-TTTC CTTCTC CTTTTC CTT
1 CTTTTC CTTTTC CTTTTC CTT
27842 CTGTCAGTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 9 0.17
6 44 0.83
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTTC
Found at i:27813 original size:17 final size:17
Alignment explanation
Indices: 27773--27841 Score: 93
Period size: 17 Copynumber: 4.0 Consensus size: 17
27763 CGTAAGTCTG
*
27773 TTCTTTTCCTTTTTCTT
1 TTCTTTTCCTTTTCCTT
27790 TTCCTTTTCCTTTTCCTT
1 TT-CTTTTCCTTTTCCTT
*
27808 TTCTTTCCCTTTTCCTT
1 TTCTTTTCCTTTTCCTT
* *
27825 TCCTTCTCCTTTTCCTT
1 TTCTTTTCCTTTTCCTT
27842 CTGTCAGTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 30 0.65
18 16 0.35
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTTTCCTTTTCCTT
Found at i:28703 original size:19 final size:20
Alignment explanation
Indices: 28667--28704 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28657 GCTGATAATA
*
28667 ATGCATTTGGTAATATAAGC
1 ATGCATTTGGTAAGATAAGC
*
28687 ATGC-TTTGGTTAGATAAG
1 ATGCATTTGGTAAGATAAG
28705 ATAATTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (20 bp):
ATGCATTTGGTAAGATAAGC
Found at i:29611 original size:24 final size:24
Alignment explanation
Indices: 29577--29631 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
29567 GGATTTCACA
29577 GCAAATGACGACCCAATTGAGGCT
1 GCAAATGACGACCCAATTGAGGCT
* *
29601 GGAAATGACGACCCCATTGAGGCT
1 GCAAATGACGACCCAATTGAGGCT
29625 GCAAATG
1 GCAAATG
29632 GAGAGGATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (24 bp):
GCAAATGACGACCCAATTGAGGCT
Found at i:29695 original size:27 final size:27
Alignment explanation
Indices: 29658--29774 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
29648 TCCGGCCCTC
* *
29658 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCAAGCAGTGGATCCT
* *
29685 CCCACTGCGACCCAAGCAGTTGATCCT
1 CCCACTTCGACCCAAGCAGTGGATCCT
* *
29712 CCCACTACGACCCAAGCAGTGGTTCCT
1 CCCACTTCGACCCAAGCAGTGGATCCT
* * *
29739 CCCACTTAGACCCCAGTAGTGGATCCT
1 CCCACTTCGACCCAAGCAGTGGATCCT
29766 CCCACTTCG
1 CCCACTTCG
29775 CCTCGGGTCG
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.21, C:0.41, G:0.18, T:0.20
Consensus pattern (27 bp):
CCCACTTCGACCCAAGCAGTGGATCCT
Found at i:31998 original size:2 final size:2
Alignment explanation
Indices: 31991--32024 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
31981 AACAATTTTC
31991 AT AT AT AT AT -T CAT 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
32025 GCTACTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 28 0.93
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32005 original size:12 final size:12
Alignment explanation
Indices: 31988--32024 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
31978 TAGAACAATT
31988 TTCATATATATA
1 TTCATATATATA
32000 TTCATATATATA
1 TTCATATATATA
32012 TAT-ATATATATA
1 T-TCATATATATA
32024 T
1 T
32025 GCTACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 23 0.96
13 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCATATATATA
Found at i:33766 original size:33 final size:33
Alignment explanation
Indices: 33668--33768 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 33
33658 TTGCAAAGAG
* * *
33668 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** **
33701 TAATTT-GAGTGTTGTTTGCGATGGCACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
* *
33734 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
33767 TG
1 TG
33769 GTTTGGATGC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
32 1 0.02
33 52 0.96
34 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.42
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:38267 original size:35 final size:35
Alignment explanation
Indices: 38228--38563 Score: 349
Period size: 35 Copynumber: 9.7 Consensus size: 35
38218 CAGTAATAAG
* * *
38228 TAACTTAATTCAGGGTAATTAAGTCAGTCGGTAAT
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* *
38263 TAACTTAATTAAGGGTAATTAAGTAATTCAGTTAT
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* * *
38298 TAACTTAATTCAGGGTAATTAAGTAATTTAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* * *
38333 CAACTTAATTCAGGGTAATTAAGTCAGT-AG---G
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* *
38364 TAGCTTAATTCAGGGTAATTAAGTAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* *
38399 TAACTTAATTTAGGGTAATTAAGTAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* * * *
38434 TAACTTAATTTAGGGTAATTAAGTGAGCCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* ** *
38469 TAACTTAATTCAGGGTAATTAATTGGGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
* * * * *
38504 CAACTTAAAATCTGGTTAATCAAGTAAGTCA-TTGAT
1 TAACTT-AATTCAGGGTAATTAAGTAAGTCAGTT-AT
**
38540 CGACTTAATTCAGGGTAATTAAGT
1 TAACTTAATTCAGGGTAATTAAGT
38564 TTAGTAAGAA
Statistics
Matches: 256, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
31 25 0.10
32 2 0.01
34 2 0.01
35 203 0.79
36 24 0.09
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (35 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAT
Found at i:38475 original size:136 final size:136
Alignment explanation
Indices: 38231--38490 Score: 387
Period size: 136 Copynumber: 1.9 Consensus size: 136
38221 TAATAAGTAA
* * * *
38231 CTTAATTCAGGGTAATTAAGTCAGTCGGTAATTAACTTAATTAAGGGTAATTAAGTAATTCAGTT
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTAAGGGTAATTAAGTAAGTCAGTT
* ***
38296 ATTAACTTAATTCAGGGTAATTAAGTAATTTAGTAATCAACTTAATTCAGGGTAATTAAGTCAGT
66 AGTAACTTAATTCAGGGTAATTAAGTAAGCCAGTAATCAACTTAATTCAGGGTAATTAAGTCAGT
38361 AGGTAG
131 AGGTAG
* *
38367 CTTAATTCAGGGTAATTAAGTAAGTCAGTTAGTAACTTAATTTAGGGTAATTAAGTAAGTCAGTT
1 CTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTAAGGGTAATTAAGTAAGTCAGTT
* * *
38432 AGTAACTTAATTTAGGGTAATTAAGTGAGCCAGTTAGT-AACTTAATTCAGGGTAATTAA
66 AGTAACTTAATTCAGGGTAATTAAGTAAGCCAG-TAATCAACTTAATTCAGGGTAATTAA
38491 TTGGGTCAGT
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
136 107 0.97
137 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (136 bp):
CTTAATTCAGGGTAATTAAGTAAGTCAGTAAGTAACTTAATTAAGGGTAATTAAGTAAGTCAGTT
AGTAACTTAATTCAGGGTAATTAAGTAAGCCAGTAATCAACTTAATTCAGGGTAATTAAGTCAGT
AGGTAG
Found at i:40154 original size:30 final size:30
Alignment explanation
Indices: 40118--40203 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
40108 CAAAGGATAA
*
40118 AATGGCATCTTTGGTGTGATTCCATCACCT
1 AATGGCATCTTTGGTGCGATTCCATCACCT
*
40148 AATGGCATCTTAGGTGCGATTCCATCACCT
1 AATGGCATCTTTGGTGCGATTCCATCACCT
*
40178 AATGGCAGCTTTGGTGCGATTCCATC
1 AATGGCATCTTTGGTGCGATTCCATC
40204 TCTTCCTTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (30 bp):
AATGGCATCTTTGGTGCGATTCCATCACCT
Found at i:40620 original size:33 final size:33
Alignment explanation
Indices: 40583--40699 Score: 112
Period size: 33 Copynumber: 3.5 Consensus size: 33
40573 CGACTTGGAG
40583 ATGCCCGGCCA-ACACCGGTCACGTGACATAACC
1 ATGCCCGGCCACA-ACCGGTCACGTGACATAACC
* ** * *
40616 ATGCCTGGCCACAACCGACCACGCGACATGACC
1 ATGCCCGGCCACAACCGGTCACGTGACATAACC
* * **
40649 ATGCCCTGCCACAACCGGTCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGTCACGTGACAT-AACC
*
40682 AAGCCCGGCCACAACCGG
1 ATGCCCGGCCACAACCGG
40700 CCACATGATC
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
32 1 0.01
33 66 0.97
34 1 0.01
ACGTcount: A:0.26, C:0.42, G:0.22, T:0.10
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGTCACGTGACATAACC
Done.