Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017198.1 Corchorus olitorius cultivar O-4 contig17231, 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: 22756
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1605 original size:49 final size:49
Alignment explanation
Indices: 1532--1627 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
1522 TGGCCGACTT
1532 ATTTGTATTTTCATTTCTCGTATATAACATTTATACATTTGTATTTGTG
1 ATTTGTATTTTCATTTCTCGTATATAACATTTATACATTTGTATTTGTG
*
1581 ATTTGTATTTTCATTTATTC-TATATAACATTTATACATTTGTATTTG
1 ATTTGTATTTTCATTT-CTCGTATATAACATTTATACATTTGTATTTG
1628 AAAAATGGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 43 0.96
50 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.56
Consensus pattern (49 bp):
ATTTGTATTTTCATTTCTCGTATATAACATTTATACATTTGTATTTGTG
Found at i:2381 original size:2 final size:2
Alignment explanation
Indices: 2376--2401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2366 ATCTGGACAG
2376 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2402 CACACGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3895 original size:144 final size:137
Alignment explanation
Indices: 3736--4263 Score: 495
Period size: 144 Copynumber: 3.8 Consensus size: 137
3726 TTGGCCACTA
*
3736 AAAAAAATAACTTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
* * * *
3801 GTCAATCAAAGTTATAGTTGATAGATGGTGATTTGATCATTTTGCTATAATTAAAAGAATCAATT
66 GCCAATCAAAGTTATAG-T-ATAGATGAT-A-TT-A--ATTTTGCCATAAATAAAAGAATCAATT
*
3866 AGAAATTATGTTAG
124 AGTAATTATGTTAG
* * * *
3880 AAAAAAATAAATTGATTGAACATACTAAATAAATAAATGAATCAAATTAGTCGTTAATTAACTTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
* * * *
3945 GCCAATCAAACTTATAACTAATTGATGATTATTAAATTTTGCCATAAATAAATGAATCAATTAGT
66 GCCAATCAAAGTTAT-AGT-ATAGATGA-TATT-AATTTTGCCATAAATAAAAGAATCAATTAGT
*
4010 AATTATGTCAG
127 AATTATGTTAG
* * * * * *
4021 -CAAAAATAAACTGATTCAACATGCTAAATAAACAAATGAACCAATTTAGTCC-TAAGTCAACTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAA-TCAACTT
* ** *
4084 T-CCAAATC--A---A-AGT-TA-CTCCTA-TAATTTTGCCATAAATAAACGAATCAATTAGTAA
65 TGCC-AATCAAAGTTATAGTATAGATGATATTAATTTTGCCATAAATAAAAGAATCAATTAGTAA
*
4139 TTACGTTAG
129 TTATGTTAG
* * * *
4148 CAAAAAAATAAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAATT
1 -AAAAAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACT
* * * *
4213 TTGCCAATCAAAGTTGTGATTGATTGATGATTATTTAATTTTACCATAAAT
64 TTGCCAATCAAAGTTAT-AGT-ATAGATGA-TA-TTAATTTTGCCATAAAT
4264 CGCTACCAAA
Statistics
Matches: 311, Mismatches: 51, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
127 39 0.13
128 1 0.00
129 8 0.03
130 50 0.16
131 5 0.02
132 1 0.00
133 2 0.01
135 1 0.00
137 2 0.01
138 1 0.00
139 6 0.02
140 56 0.18
141 38 0.12
143 18 0.06
144 81 0.26
145 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (137 bp):
AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTT
GCCAATCAAAGTTATAGTATAGATGATATTAATTTTGCCATAAATAAAAGAATCAATTAGTAATT
ATGTTAG
Found at i:4227 original size:130 final size:127
Alignment explanation
Indices: 3979--4227 Score: 347
Period size: 130 Copynumber: 1.9 Consensus size: 127
3969 ATGATTATTA
* *
3979 AATTTTGCCATAAATAAATGAATCAATTAGTAATTATGTCAGCAAAAATAAACTGATTCAACATG
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTCAGCAAAAATAAACTGATTCAACATG
*
4044 CTAAATAAACAAATGAACCAATTTAGTCCTAAGTCAACTTTCCAAATCAAAGTTACTCCTAT
66 CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTCCAAATCAAAGTTACTCCTAT
* * *
4106 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAAATAAAATTGATTGAAC
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTCAGC--AAAAAT-AAACTGATTCAAC
* * * * * *
4171 ATGCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCC-AATCAAAGTT
63 ATGCTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTT-CCAAATCAAAGTT
4228 GTGATTGATT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
127 40 0.38
129 6 0.06
130 58 0.55
131 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (127 bp):
AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTCAGCAAAAATAAACTGATTCAACATG
CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTCCAAATCAAAGTTACTCCTAT
Found at i:4403 original size:165 final size:164
Alignment explanation
Indices: 4113--4594 Score: 730
Period size: 165 Copynumber: 2.9 Consensus size: 164
4103 TATAATTTTG
** * *
4113 CCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAAAATAAAATTGATTGAACATGCTAA
1 CCATAAATAAATAAATCAATTAGTAATTATGTTA-C-CAAAAA-AAAATT-ATTGAACATGCTAA
* *
4178 ATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTGTGATTGATTGATGA
62 ATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGA
4243 TTATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
127 TTATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
* *
4281 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAACAATTATTGAACATGGTAAATAA
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAAATTATTGAACATGCTAAATAA
* * *
4346 ATAAATGAATCCAAGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTTTAATTGATTGATAATTA
66 ATAAATGAAT-CAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATTA
4411 TTTAATTTTACCATAAATCGCTACCAAAAAAATTA
130 TTTAATTTTACCATAAATCGCTACCAAAAAAATTA
*
4446 CCATAAATAAATAAATCAATTAGTGATTATGTTACCAAAAAAATTAATTATTGAACATGCTAAAT
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAA--AATTATTGAACATGCTAAAT
* * * * * * *
4511 AGACAAATGAATCAAGTTAGTCATTAGTTAAGTTAGCCAATCAATGTTATAACTGATTGATGATT
64 AAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATT
4576 ATTTAATTTTACCATAAAT
129 ATTTAATTTTACCATAAAT
4595 AAATCAATCA
Statistics
Matches: 288, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
164 27 0.09
165 131 0.45
166 69 0.24
167 30 0.10
168 31 0.11
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (164 bp):
CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAAATTATTGAACATGCTAAATAA
ATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATTAT
TTAATTTTACCATAAATCGCTACCAAAAAAATTA
Found at i:4687 original size:181 final size:181
Alignment explanation
Indices: 4498--4823 Score: 499
Period size: 181 Copynumber: 1.8 Consensus size: 181
4488 ATTAATTATT
* * * *
4498 GAACATGCTAAATAGACAAATGAATCAAGTTAGTCATTAGTTAAGTTAGCCAATCAATGTTATAA
1 GAACATGCTAAATAAACAAATCAATCAAGTTAGTCATTAGTTAACTTAGCCAATCAAAGTTATAA
* * *
4563 CTGATTGATGATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTATGTTAGCAAAAA
66 CTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTAGCAAAAA
**
4628 AATCGATTGATTGAACAATGAACATGCTAAATAAATTGATGCAAAAAAAAA
131 AATAAATTGATTGAACAATGAACATGCTAAATAAATTGATGCAAAAAAAAA
* * *
4679 GAACATGCTAAATAAATAAATCAATCAAGTTAGTCGTTAGTTAACTTTGCCAATCAAAGTTATAA
1 GAACATGCTAAATAAACAAATCAATCAAGTTAGTCATTAGTTAACTTAGCCAATCAAAGTTATAA
* * * *
4744 TTGATTCATAATTATTTAATTTTGCCATAAATAAATCAGTCAGTTAGTAATTACGTTAGCAAAAA
66 CTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTAGCAAAAA
*
4809 ACTAAATTGATTGAA
131 AATAAATTGATTGAA
4824 TATGCTAGCT
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
181 128 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (181 bp):
GAACATGCTAAATAAACAAATCAATCAAGTTAGTCATTAGTTAACTTAGCCAATCAAAGTTATAA
CTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTAGCAAAAA
AATAAATTGATTGAACAATGAACATGCTAAATAAATTGATGCAAAAAAAAA
Found at i:10438 original size:72 final size:72
Alignment explanation
Indices: 10310--10493 Score: 235
Period size: 72 Copynumber: 2.6 Consensus size: 72
10300 AGCCGGTGCA
* * * * * * * * * *
10310 GTGCTTGGTCGAGGTCA-GCTCTCAACCGCTTACCAGCCAGTCTCACTGGACGCTTAAGAGGGTT
1 GTGCTTGGTCAAGGT-AGGCTCTCCACCGCCTGCCAACCGGTATCTCTGGACCCTTAAGAGGGCT
10374 CTTCATCC
65 CTTCATCC
* *
10382 GTGCTTTGTCAAGGTTGGCTCTCCACCGCCTGCCAACCGGTATCTCTGGACCCTTAAGAGGGCTC
1 GTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAACCGGTATCTCTGGACCCTTAAGAGGGCTC
10447 TTCATCC
66 TTCATCC
*
10454 GTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAGCCGG
1 GTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAACCGG
10494 GACCGTGCTT
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
72 96 1.00
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (72 bp):
GTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAACCGGTATCTCTGGACCCTTAAGAGGGCTC
TTCATCC
Found at i:10518 original size:44 final size:44
Alignment explanation
Indices: 10452--10537 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
10442 GGCTCTTCAT
* *
10452 CCGTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAGCCGGGA
1 CCGTGCTTGGTCAAGGTAGGCTCTCCACCACCTACCAGCCGGGA
* *
10496 CCGTGCTTGGTCGAGGTCGGCTCTCCACCACCTACCAGCCGG
1 CCGTGCTTGGTCAAGGTAGGCTCTCCACCACCTACCAGCCGG
10538 TATCTCTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.13, C:0.38, G:0.30, T:0.19
Consensus pattern (44 bp):
CCGTGCTTGGTCAAGGTAGGCTCTCCACCACCTACCAGCCGGGA
Found at i:10669 original size:115 final size:116
Alignment explanation
Indices: 10380--10724 Score: 512
Period size: 115 Copynumber: 3.0 Consensus size: 116
10370 GGTTCTTCAT
* * * * *
10380 CCGTGCTTTGTCAAGGTTGGCTCTCCACCGCCTGCCAACCGGTATCTCTGGACCCTTAAGAGGGC
1 CCGTGCTTGGTCGAGGTTGGCTCTCCACCACCTGCCAGCCGGTATCTCTAGACCCTTAAGAGGGC
*
10445 TCTTCATCCGTGCTTGGTCAAGGTAGGCTCTCCACCGCCTGCCAGCCGGGA
66 TCTTCATCCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGGA
* *
10496 CCGTGCTTGGTCGAGGTCGGCTCTCCACCACCTACCAGCCGGTATCTCTAGACCCTTAAGAGGGC
1 CCGTGCTTGGTCGAGGTTGGCTCTCCACCACCTGCCAGCCGGTATCTCTAGACCCTTAAGAGGGC
** *
10561 TCTTCATTTGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTG-TAGCCGGGA
66 TCTTCATCCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGGA
* * * * * *
10611 CCGTGCTTGGTCGAGGTTGGCGCTCCATCATCTGCCAGCCGATATCTCTAGAACCTTAAGAGGGT
1 CCGTGCTTGGTCGAGGTTGGCTCTCCACCACCTGCCAGCCGGTATCTCTAGACCCTTAAGAGGGC
* *
10676 TGTTCATCCGTGCTTGGTCAAGGTCGGCTCTCCACCGCTTGCCAGCCGG
66 TCTTCATCCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGG
10725 TATCTCTGGA
Statistics
Matches: 204, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
115 102 0.50
116 102 0.50
ACGTcount: A:0.15, C:0.33, G:0.27, T:0.25
Consensus pattern (116 bp):
CCGTGCTTGGTCGAGGTTGGCTCTCCACCACCTGCCAGCCGGTATCTCTAGACCCTTAAGAGGGC
TCTTCATCCGTGCTTGGTCAAGGTCGGCTCTCCACCGCCTGCCAGCCGGGA
Found at i:10729 original size:72 final size:72
Alignment explanation
Indices: 10611--10746 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
10601 GTAGCCGGGA
* * *
10611 CCGTGCTTGGTCGAGGTTGGCGCTCCATCATCTGCCAGCCGATATCTCTAGAACC-TTAAGAGGG
1 CCGTGCTTGGTCAAGGTCGGCGCTCCACCATCTGCCAGCCGATATCTCT-GAACCTTTAAGAGGG
10675 TTGTTCAT
65 TTGTTCAT
* * * *
10683 CCGTGCTTGGTCAAGGTCGGCTCTCCACC-GCTTGCCAGCCGGTATCTCTGGACCTTTAAGAGGG
1 CCGTGCTTGGTCAAGGTCGGCGCTCCACCATC-TGCCAGCCGATATCTCTGAACCTTTAAGAGGG
10747 CTCTTCATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 5 0.09
72 50 0.91
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (72 bp):
CCGTGCTTGGTCAAGGTCGGCGCTCCACCATCTGCCAGCCGATATCTCTGAACCTTTAAGAGGGT
TGTTCAT
Done.