Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022760.1 Corchorus olitorius cultivar O-4 contig22793, 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: 108851
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:614 original size:12 final size:11
Alignment explanation
Indices: 599--642 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
589 AATGATTTTT
599 AAAAAAAAACAG
1 AAAAAAAAA-AG
*
611 AAAAAAAGAAG
1 AAAAAAAAAAG
622 AAAAAAAAGAAG
1 AAAAAAAA-AAG
634 AAGAAAAAA
1 AA-AAAAAA
643 TGAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.32
12 13 0.46
13 6 0.21
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:629 original size:15 final size:15
Alignment explanation
Indices: 611--642 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
601 AAAAAAACAG
611 AAAAAAAGAAGAAAA
1 AAAAAAAGAAGAAAA
*
626 AAAAGAAGAAGAAAA
1 AAAAAAAGAAGAAAA
641 AA
1 AA
643 TGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAGAAAA
Found at i:799 original size:15 final size:16
Alignment explanation
Indices: 771--807 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
761 GGTCCCTGAC
771 TATTTTTTAAAAAATA
1 TATTTTTTAAAAAATA
*
787 TATTTTTT-TAAAATA
1 TATTTTTTAAAAAATA
802 T-TTTTT
1 TATTTTT
808 AATCAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTTTAAAAAATA
Found at i:1588 original size:11 final size:10
Alignment explanation
Indices: 1560--1587 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1550 ATTATCATTT
1560 AAAAAAAATA
1 AAAAAAAATA
1570 AAAAAAAATA
1 AAAAAAAATA
1580 AAAAAAAA
1 AAAAAAAA
1588 AACCAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:2093 original size:42 final size:43
Alignment explanation
Indices: 2042--2135 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
2032 AGTGCATTAC
*
2042 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCACTAGGTAATTCATCAAAATAAAG
2083 CTAATATTCTACTCCTCCATCACTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCACTAGGTAATTCATCAAAATAAAG
2128 CTAATATT
1 CTAATATT
2136 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCACTAGGTAATTCATCAAAATAAAG
Found at i:3956 original size:4 final size:4
Alignment explanation
Indices: 3947--3972 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3937 GTACTTTGGT
3947 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
3973 ACTCTTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4166 original size:17 final size:16
Alignment explanation
Indices: 4126--4176 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
4116 CATGTAATCT
*
4126 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
4142 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
4159 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
4176 T
1 T
4177 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:6402 original size:24 final size:24
Alignment explanation
Indices: 6375--6422 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6365 TCTCTTTTTT
*
6375 TTTTCAGTAAAATATATTCCTTTC
1 TTTTCAATAAAATATATTCCTTTC
*
6399 TTTTCAATAGAATATATTCCTTTC
1 TTTTCAATAAAATATATTCCTTTC
6423 CTTTAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTCAATAAAATATATTCCTTTC
Found at i:14277 original size:17 final size:17
Alignment explanation
Indices: 14252--14298 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
14242 CATCATTACC
14252 TTAAAAATATTAA-TTAA
1 TTAAAAATA-TAATTTAA
*
14269 TTAATAATATAATTTAA
1 TTAAAAATATAATTTAA
**
14286 TTACCAATATAAT
1 TTAAAAATATAAT
14299 AAGAAAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAATATAATTTAA
Found at i:16613 original size:12 final size:13
Alignment explanation
Indices: 16591--16619 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16581 GGAGACTTGA
16591 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
16604 AAAAAG-AAAAGG
1 AAAAAGAAAAAGG
16616 AAAA
1 AAAA
16620 TCACATCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGG
Found at i:21477 original size:128 final size:129
Alignment explanation
Indices: 21156--21530 Score: 628
Period size: 128 Copynumber: 2.9 Consensus size: 129
21146 CATATTCAAA
21156 AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTG-AAGACACACCACCCGGA
1 AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAAG-CACACCACCCGGA
21220 TAAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGAGGAGGGTGAAG
65 TAAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGAGGAGGGTGAAG
* * * ** *
21285 AGAGTTGCTTAAGGAAGGCAAGGAAACCATTAAAGACAAAGTTGTTGAAGGCACACCACCCGGAT
1 AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAAGCACACCACCCGGAT
* * *
21350 AAACACTAAATGGACCAGGGAGGTCACCAGGATAAAATCCAAACATGGGGTGAGG-GGGTGAAG
66 AAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGAGGAGGGTGAAG
* *
21413 AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAAGCACACTACTCGGAT
1 AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAAGCACACCACCCGGAT
21478 AAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGA
66 AAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGA
21531 AGGCTTGATA
Statistics
Matches: 225, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
128 115 0.51
129 108 0.48
130 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (129 bp):
AGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAAGCACACCACCCGGAT
AAACACTAGATGGACCAGGGAGGTCACCAGGATAAAATTCAAACATGGGGGGAGGAGGGTGAAG
Found at i:21939 original size:48 final size:48
Alignment explanation
Indices: 21866--21961 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
21856 AAAAGTTATC
* **
21866 ATGTTAAGGGTTTTAAGCAAATTACCTAGAAATCATTTTTGCTTGCGT
1 ATGTTAAGGGTTTTAAGCAAATTACCCAGAAATCATTTGGGCTTGCGT
*
21914 ATGTTAAGGGTTTTAAGCAACTTACCCAGAAATCATTTGGGCTTGCGT
1 ATGTTAAGGGTTTTAAGCAAATTACCCAGAAATCATTTGGGCTTGCGT
21962 TGCTGGGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (48 bp):
ATGTTAAGGGTTTTAAGCAAATTACCCAGAAATCATTTGGGCTTGCGT
Found at i:28749 original size:6 final size:6
Alignment explanation
Indices: 28738--28775 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28728 GCATGGAATC
*
28738 GAACCA GAACCA GAACCA GCAACCA GAA-CA AAACCA GA
1 GAACCA GAACCA GAACCA G-AACCA GAACCA GAACCA GA
28776 TCAACCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.53, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
GAACCA
Found at i:29593 original size:12 final size:12
Alignment explanation
Indices: 29576--29609 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
29566 ACAAAAATTA
29576 GAAGCATTTTCT
1 GAAGCATTTTCT
29588 GAAGCATTTTCT
1 GAAGCATTTTCT
29600 GAAGCATTTT
1 GAAGCATTTT
29610 GTAGGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (12 bp):
GAAGCATTTTCT
Found at i:30423 original size:19 final size:20
Alignment explanation
Indices: 30399--30436 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30389 ATTTATCCTG
*
30399 AAATGGGTAG-TTTTATTTA
1 AAATGGATAGTTTTTATTTA
30418 AAATGGATAGTTTTTATTT
1 AAATGGATAGTTTTTATTT
30437 TGTTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AAATGGATAGTTTTTATTTA
Found at i:38621 original size:30 final size:30
Alignment explanation
Indices: 38587--38643 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
38577 TTGTGTTCCC
38587 TTTCTCTTTGCTATTTGAAATTTTGTTAGG
1 TTTCTCTTTGCTATTTGAAATTTTGTTAGG
*
38617 TTTCTCTTTGGTATTTGAAATTTTGTT
1 TTTCTCTTTGCTATTTGAAATTTTGTT
38644 TCGCCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.60
Consensus pattern (30 bp):
TTTCTCTTTGCTATTTGAAATTTTGTTAGG
Found at i:41482 original size:2 final size:2
Alignment explanation
Indices: 41475--41501 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41465 TCCTCCTTCA
41475 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
41502 GTGAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:50809 original size:19 final size:19
Alignment explanation
Indices: 50765--50808 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
50755 GGGGAGGGTA
50765 TTTTTTTCTCAAATAAAAT
1 TTTTTTTCTCAAATAAAAT
*
50784 TATTTTTT-TCAAAT-AACT
1 T-TTTTTTCTCAAATAAAAT
50802 TTTTTTT
1 TTTTTTT
50809 TAGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 7 0.30
20 6 0.26
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTTCTCAAATAAAAT
Found at i:51473 original size:16 final size:16
Alignment explanation
Indices: 51452--51483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51442 ATTCTAGGCT
*
51452 TTTTTTTTTTTTTTTC
1 TTTTTTCTTTTTTTTC
51468 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
51484 ATCACGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:64441 original size:162 final size:162
Alignment explanation
Indices: 64167--64492 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 162
64157 TACTTTACCT
64167 TTCCAATTAGCCAATTTACCAAGAACTCTATCAATAACATGCTGGTACGTATTCTTTGTAACTCT
1 TTCCAATTAGCCAATTTACCAAGAACTCTATCAATAACATGCTGGTACGTATTCTTTGTAACTCT
64232 ACCATGAATAATTGGTACTCCCAAATACGTACCAAGCTCCAAAGCTAATGGAATTTCACATAAAT
66 ACCATGAATAATTGGTACTCCCAAATACGTACCAAGCTCCAAAGCTAATGGAATTTCACATAAAT
64297 GACTTAAACACCGAGCCTTTTCACCAGGTACA
131 GACTTAAACACCGAGCCTTTTCACCAGGTACA
64329 TTCCAATTAGCCAATTTACCAAGAACTCTATCAATAACATGCTGGTACGTATTCTTTGTAACTCT
1 TTCCAATTAGCCAATTTACCAAGAACTCTATCAATAACATGCTGGTACGTATTCTTTGTAACTCT
*
64394 ACCATGAATAATTGGTACTCCCAAATACGTACCAAGCTCCGAAGCTAATGGAATTTCACATAAAT
66 ACCATGAATAATTGGTACTCCCAAATACGTACCAAGCTCCAAAGCTAATGGAATTTCACATAAAT
64459 GACTTAAACACCGAGCCTTTTCACCAGGTACA
131 GACTTAAACACCGAGCCTTTTCACCAGGTACA
64491 TT
1 TT
64493 TGGAGAAATC
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 163 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (162 bp):
TTCCAATTAGCCAATTTACCAAGAACTCTATCAATAACATGCTGGTACGTATTCTTTGTAACTCT
ACCATGAATAATTGGTACTCCCAAATACGTACCAAGCTCCAAAGCTAATGGAATTTCACATAAAT
GACTTAAACACCGAGCCTTTTCACCAGGTACA
Found at i:78888 original size:22 final size:21
Alignment explanation
Indices: 78863--78939 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 21
78853 TATTTTTATG
*
78863 AAATTTTGATAATTATCCTATT
1 AAATTTTGATAATTA-CCTATA
**
78885 AAATTTTGATAACCACCATATGA
1 AAATTTTGATAATTACC-TAT-A
78908 AAA-TTTGATAATTACCTATA
1 AAATTTTGATAATTACCTATA
*
78928 AAATTGTGATAA
1 AAATTTTGATAA
78940 ACTCCATAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 27 0.59
23 3 0.07
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATA
Found at i:78947 original size:43 final size:44
Alignment explanation
Indices: 78859--78961 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 44
78849 TGAATATTTT
* * * *
78859 TATGAAATTTTGATAATTATCCTATTAAATTTTGATAACCACCA
1 TATGAAAATTTGATAATTATCCTATAAAATTGTGATAAACACCA
*
78903 TATGAAAATTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATGAAAATTTGATAATTATCCTATAAAATTGTGATAAACACCA
* *
78946 TAAGAAACTTTGATAA
1 TATGAAAATTTGATAA
78962 CCTAACTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 34 0.65
44 18 0.35
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (44 bp):
TATGAAAATTTGATAATTATCCTATAAAATTGTGATAAACACCA
Found at i:79012 original size:20 final size:21
Alignment explanation
Indices: 78967--79029 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
78957 GATAACCTAA
* *
78967 CTATGAAATTTTAATAAACTTTC
1 CTATG-AATTTTGATAATC-TTC
78990 CTATGAATTTTG-TAATCTTC
1 CTATGAATTTTGATAATCTTC
*
79010 CTATGATTTTTGATAATCTT
1 CTATGAATTTTGATAATCTT
79030 TGTGTGAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 14 0.39
21 11 0.31
22 6 0.17
23 5 0.14
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (21 bp):
CTATGAATTTTGATAATCTTC
Found at i:80988 original size:3 final size:3
Alignment explanation
Indices: 80980--81010 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
80970 TTAAATCATA
80980 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
81011 TATAGTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:88350 original size:5 final size:5
Alignment explanation
Indices: 88340--88380 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
88330 TCTTTACATT
* * *
88340 TTTTC TTTTC TTTTC TTTCC TTTTC TTTTA TTTAC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
88381 AAGTTCTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Done.