Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015487.1 Corchorus olitorius cultivar O-4 contig15520, 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: 17743
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1320 original size:22 final size:22
Alignment explanation
Indices: 1147--1376 Score: 168
Period size: 22 Copynumber: 10.6 Consensus size: 22
1137 CTCCAATGTA
*
1147 GAAATATTGATAACCACAC--T
1 GAAATTTTGATAACCACACTAT
* * *
1167 GAAAATTTGATAACCTCATTAT
1 GAAATTTTGATAACCACACTAT
* * *
1189 -AGAATTTCGATAACCTCCCTAT
1 GA-AATTTTGATAACCACACTAT
* *
1211 GAAAGTTTGATAACCACACTGT
1 GAAATTTTGATAACCACACTAT
*
1233 GAAGTTTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
1255 GAAATTTTGATAACCTCAGTGT
1 GAAATTTTGATAACCACACTAT
* * *
1277 GAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* *
1299 GAAATTTTGATAATCAAACTAT
1 GAAATTTTGATAACCACACTAT
* ***
1321 -AAA-ATTG-TAACCGTGCTAT
1 GAAATTTTGATAACCACACTAT
*
1340 GAAAATTTTGATAAACACAAC-AT
1 G-AAATTTTGATAACCAC-ACTAT
*
1363 GAAATTTCGATAAC
1 GAAATTTTGATAAC
1377 GTCTCTATGA
Statistics
Matches: 162, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
19 8 0.05
20 18 0.11
21 7 0.04
22 120 0.74
23 8 0.05
24 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:1430 original size:22 final size:22
Alignment explanation
Indices: 1400--1496 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 22
1390 TGAAATTGTG
* * *
1400 AATTGTGATATCCTCTCTATGT
1 AATTTTGATAACCTCTCTATGA
* *
1422 AATTTTGATAACTTCTCCATGA
1 AATTTTGATAACCTCTCTATGA
* *
1444 AATTTTCATAACCTCCCTATGA
1 AATTTTGATAACCTCTCTATGA
* *
1466 AATTTTGTTAACCTC-C-AGGA
1 AATTTTGATAACCTCTCTATGA
1486 AATTTTGATAA
1 AATTTTGATAA
1497 GCACGAATAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 13 0.21
21 1 0.02
22 48 0.77
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (22 bp):
AATTTTGATAACCTCTCTATGA
Found at i:1490 original size:42 final size:43
Alignment explanation
Indices: 1411--1496 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
1401 ATTGTGATAT
* * *
1411 CCTCTCTATGTAATTTTGATAACTTCTCCATGAAATTTTCATAA
1 CCTCCCTATGAAATTTTGATAAC-TCTCCAGGAAATTTTCATAA
* *
1455 CCTCCCTATGAAATTTTGTTAAC-CTCCAGGAAATTTTGATAA
1 CCTCCCTATGAAATTTTGATAACTCTCCAGGAAATTTTCATAA
1497 GCACGAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 17 0.46
44 20 0.54
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (43 bp):
CCTCCCTATGAAATTTTGATAACTCTCCAGGAAATTTTCATAA
Found at i:1554 original size:22 final size:21
Alignment explanation
Indices: 1524--1605 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
1514 CTCCCTCCCA
* * *
1524 ATGATATTTTGTTAACATTCTT
1 ATGAAATTTTGATAAC-TTCCT
*
1546 ATGAAATTTTGATAACTACACT
1 ATGAAATTTTGATAACTTC-CT
*
1568 AT-AAAGTTTTGATAACCTTCGT
1 ATGAAA-TTTTGATAA-CTTCCT
* *
1590 ACGAAATTTTGTTAAC
1 ATGAAATTTTGATAAC
1606 CTCCCTAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 6 0.12
22 36 0.75
23 6 0.12
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (21 bp):
ATGAAATTTTGATAACTTCCT
Found at i:1933 original size:22 final size:22
Alignment explanation
Indices: 1818--1936 Score: 102
Period size: 22 Copynumber: 5.4 Consensus size: 22
1808 GGGAGTCTAA
**
1818 GAAATTTTGATAACCTTTTTAT
1 GAAATTTTGATAACCTTCCTAT
* *
1840 AAAATTTTGATAA-CTATACTAT
1 GAAATTTTGATAACCT-TCCTAT
*
1862 GAAGTTTTGATAACC-TCCATAT
1 GAAATTTTGATAACCTTCC-TAT
* *
1884 GAAATTTTGGTAACC-ACACTACT
1 GAAATTTTGATAACCTTC-CTA-T
1907 -AAATTTTGATAACCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
*
1928 GTAATTTTG
1 GAAATTTTG
1937 GTTTGATTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
21 5 0.06
22 69 0.88
23 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCCTAT
Found at i:1937 original size:44 final size:44
Alignment explanation
Indices: 1818--1938 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
1808 GGGAGTCTAA
** * * * *
1818 GAAATTTTGATAACCTTTTTATAAAATTTTGATAACTATACTAT
1 GAAATTTTGATAACCTTCCTATGAAATTTTGGTAACCACACTAT
*
1862 GAAGTTTTGATAACC-TCCATATGAAATTTTGGTAACCACACTACT
1 GAAATTTTGATAACCTTCC-TATGAAATTTTGGTAACCACACTA-T
*
1907 -AAATTTTGATAACCTTCCTATGTAATTTTGGT
1 GAAATTTTGATAACCTTCCTATGAAATTTTGGT
1939 TTGATTGTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 1 0.02
44 60 0.92
45 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (44 bp):
GAAATTTTGATAACCTTCCTATGAAATTTTGGTAACCACACTAT
Found at i:2579 original size:31 final size:30
Alignment explanation
Indices: 2544--2602 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
2534 ATTGACTCCA
2544 CTAAAATTG-AAGTTTTACAATATTAACCCTT
1 CTAAAA-TGAAAGTTTTA-AATATTAACCCTT
*
2575 CTAAAATGAAAGTTTTATATATTAACCC
1 CTAAAATGAAAGTTTTAAATATTAACCC
2603 CATTAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (30 bp):
CTAAAATGAAAGTTTTAAATATTAACCCTT
Found at i:2599 original size:30 final size:30
Alignment explanation
Indices: 2544--2641 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
2534 ATTGACTCCA
*
2544 CTAAAATTG-AAGTTTTACAATATTAACCCTT
1 CTAAAA-TGAAAGTTTTA-TATATTAACCCTT
*
2575 CTAAAATGAAAGTTTTATATATTAACCCCAT
1 CTAAAATGAAAGTTTTATATATTAA-CCCTT
* * * *
2606 -TAAAATCAAAATTTTATAGTATTGACCCTA
1 CTAAAATGAAAGTTTTATA-TATTAACCCTT
2636 CTAAAA
1 CTAAAA
2642 ATGTTGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 28 0.50
31 28 0.50
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (30 bp):
CTAAAATGAAAGTTTTATATATTAACCCTT
Found at i:3678 original size:21 final size:20
Alignment explanation
Indices: 3619--3678 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
3609 CATTTTTTAA
*
3619 TATAATGTTATTAAAGAAGT
1 TATAATGTTATTAAAAAAGT
*
3639 TATAATGATTATCAAAAAAGT
1 TATAATG-TTATTAAAAAAGT
*
3660 TATAATGGTATTAACAAAA
1 TATAATGTTATTAA-AAAA
3679 TTCAGCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.35
21 22 0.65
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (20 bp):
TATAATGTTATTAAAAAAGT
Found at i:5053 original size:13 final size:13
Alignment explanation
Indices: 5035--5061 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5025 AAACGGAAAA
5035 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
5048 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
5061 T
1 T
5062 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:6768 original size:25 final size:25
Alignment explanation
Indices: 6729--6801 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
6719 TTGTTGCAGG
*
6729 AAGTGGCACAGGGCCTGATAGAAGA
1 AAGTGGCGCAGGGCCTGATAGAAGA
* * *
6754 AAGTGGCGCAAGGCCTGAGAAAAGA
1 AAGTGGCGCAGGGCCTGATAGAAGA
*
6779 AAGTGGCGTAGGGCCTGATAGAA
1 AAGTGGCGCAGGGCCTGATAGAA
6802 AATAAGCACA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.36, C:0.15, G:0.37, T:0.12
Consensus pattern (25 bp):
AAGTGGCGCAGGGCCTGATAGAAGA
Found at i:6981 original size:32 final size:32
Alignment explanation
Indices: 6945--7032 Score: 149
Period size: 32 Copynumber: 2.8 Consensus size: 32
6935 TGTCTTCCTA
* *
6945 TTAATTGCTTCTTCAATCTGATCTGTTCTGCT
1 TTAATTACTTCTTCAATCTGATCTGTTCTACT
6977 TTAATTACTTCTTCAATCTGATCTGTTCTACT
1 TTAATTACTTCTTCAATCTGATCTGTTCTACT
*
7009 TTAATTACTTCTTCAGTCTGATCT
1 TTAATTACTTCTTCAATCTGATCT
7033 CTCAGAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.50
Consensus pattern (32 bp):
TTAATTACTTCTTCAATCTGATCTGTTCTACT
Found at i:10506 original size:178 final size:178
Alignment explanation
Indices: 10209--10553 Score: 484
Period size: 178 Copynumber: 1.9 Consensus size: 178
10199 CGGTTATCTG
* *
10209 ATTGAGGTGATTTAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
1 ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
* *
10274 AAAACTAAATATAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACGG
66 AAAACTAAATATAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAAAGG
* *
10339 GAATAGACGGTCCACTTAATATTATATAACTTT-TGCTCTAGATGTCTA
131 AAATAGACGGTCCACTTAATATTACATAA-TTTGTGCTCTAGATGTCTA
* * * *
10387 ATTGAGATGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAA-GAGCTC
1 ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGA-CTC
* * *
10451 GAAAACTAAATTTAATG-TTCGAGGTAT-AAAAATTGCTTTC-AAAGAATTAGTTGTTTCGGTTA
65 GAAAACTAAATATAATGTTTC-AAGTATCAAAAA-TGCTTCCGAAA-AATTAGTTGTTTCGGTTA
*
10513 AAGGAAATAGACGGTCTACTTAATATTACATAATTTGTGCT
127 AAGGAAATAGACGGTCCACTTAATATTACATAATTTGTGCT
10554 TATGGTGGAA
Statistics
Matches: 148, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
177 16 0.11
178 132 0.89
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (178 bp):
ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
AAAACTAAATATAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAAAGG
AAATAGACGGTCCACTTAATATTACATAATTTGTGCTCTAGATGTCTA
Found at i:16313 original size:5 final size:5
Alignment explanation
Indices: 16305--16343 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
16295 AAAAGCCATA
16305 TATCT TATCT TA-C- TATCT TA-C- TATCT TATCT TATCT TAT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TAT
16344 TACTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 4 0.13
4 4 0.13
5 22 0.73
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (5 bp):
TATCT
Found at i:16346 original size:21 final size:21
Alignment explanation
Indices: 16305--16349 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
16295 AAAAGCCATA
*
16305 TATCTTATCTTACTATCTTAC
1 TATCTTATCTTACTATATTAC
16326 TATCTTATCTTATCT-TATTAC
1 TATCTTATCTTA-CTATATTAC
16347 TAT
1 TAT
16350 ATAAAATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (21 bp):
TATCTTATCTTACTATATTAC
Found at i:17571 original size:14 final size:14
Alignment explanation
Indices: 17552--17585 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17542 TTTTATAATT
17552 ATTTTACTTTTACC
1 ATTTTACTTTTACC
* *
17566 ATTTTATTTTTACT
1 ATTTTACTTTTACC
17580 ATTTTA
1 ATTTTA
17586 ATTTAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTACTTTTACC
Found at i:17633 original size:15 final size:15
Alignment explanation
Indices: 17613--17643 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17603 GATTAACCTG
17613 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
17628 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
17643 T
1 T
17644 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Done.