Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000991.1 Corchorus capsularis cultivar CVL-1 contig00991, 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: 7324
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Found at i:1224 original size:22 final size:21
Alignment explanation
Indices: 1169--1405 Score: 97
Period size: 22 Copynumber: 11.0 Consensus size: 21
1159 CACATTTTGC
*
1169 AAATTTGATAACCTCATTATA
1 AAATTTGATAACCTCACTATA
* *
1190 AAATTTCGTTAACCTCCCTATGA
1 AAATTT-GATAACCTCACTAT-A
* *
1213 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCTCACTAT-A
* * * * *
1235 AATTTTGGTTACCACACTATG
1 AAATTTGATAACCTCACTATA
* * *
1256 AAATTTCGACAACCTCAGTGTGA
1 AAATTT-GATAACCTCACTAT-A
* * *
1279 AATTTTGATAATCCGC-CTACA
1 AAATTTGATAA-CCTCACTATA
* * *
1300 AAATTTTAATAATCACACTAAATA
1 AAA-TTTGATAACCTCACT--ATA
* *
1324 AAA-TTGGTAACCGCACTATGA
1 AAATTTGATAACCTCACTAT-A
*
1345 AATTTTGATAACCT---TATA
1 AAATTTGATAACCTCACTATA
* *
1363 AAATTTTGATAACCACACCATA
1 AAA-TTTGATAACCTCACTATA
* *
1385 AAATTTCAATAACCTCCCTAT
1 AAATTT-GATAACCTCACTAT
1406 GAGAATGAAA
Statistics
Matches: 155, Mismatches: 45, Indels: 31
0.67 0.19 0.13
Matches are distributed among these distances:
18 3 0.02
19 13 0.08
20 2 0.01
21 22 0.14
22 95 0.61
23 15 0.10
24 5 0.03
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (21 bp):
AAATTTGATAACCTCACTATA
Found at i:1238 original size:44 final size:42
Alignment explanation
Indices: 1169--1283 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 42
1159 CACATTTTGC
* * * * *
1169 AAATTTGATAACCTCATTATAAAATTTCGTTAACCTCCCTATG
1 AAATTTGATAACCTCACTGTGAAATTTCGTT-ACCACACTATG
* *
1212 AAAATTTGATAACCACACTGTGAAATTTTGGTTACCACACTATG
1 -AAATTTGATAACCTCACTGTGAAA-TTTCGTTACCACACTATG
* *
1256 AAATTTCGACAACCTCAGTGTGAAATTT
1 AAATTT-GATAACCTCACTGTGAAATTT
1284 TGATAATCCG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
43 9 0.15
44 44 0.75
45 6 0.10
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (42 bp):
AAATTTGATAACCTCACTGTGAAATTTCGTTACCACACTATG
Found at i:1270 original size:66 final size:66
Alignment explanation
Indices: 1145--1289 Score: 148
Period size: 66 Copynumber: 2.2 Consensus size: 66
1135 CTCCATTGTA
* * * * ** *
1145 AAAATATTGATAACCACATTTTGCAAATTTGATAACCTCATTATAAAATTTCGTTAACCTCCCTA
1 AAAAT-TTGATAACCACACTGTGCAAATTTGATAACCACACTATAAAATTTCGACAACCTCACTA
1210 TG
65 TG
* * * * *
1212 AAAATTTGATAACCACACTGTG-AAATTTTGGTTACCACACTATGAAATTTCGACAACCTCAGTG
1 AAAATTTGATAACCACACTGTGCAAA-TTTGATAACCACACTATAAAATTTCGACAACCTCACTA
1276 TG
65 TG
*
1278 AAATTTTGATAA
1 AAAATTTGATAA
1290 TCCGCCTACA
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
65 3 0.05
66 56 0.88
67 5 0.08
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (66 bp):
AAAATTTGATAACCACACTGTGCAAATTTGATAACCACACTATAAAATTTCGACAACCTCACTAT
G
Found at i:1479 original size:22 final size:22
Alignment explanation
Indices: 1436--1496 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1426 TTGTCTATGT
**
1436 ATTTTCGATAACCTCTAAATAAA
1 ATTTTC-ATAACCTCCCAATAAA
*
1459 ATTTTCATAACCTCCCCATAAA
1 ATTTTCATAACCTCCCAATAAA
**
1481 ATTTTGTTAACCTCCC
1 ATTTTCATAACCTCCC
1497 TAGAATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (22 bp):
ATTTTCATAACCTCCCAATAAA
Found at i:1506 original size:22 final size:22
Alignment explanation
Indices: 1456--1508 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1446 ACCTCTAAAT
** *
1456 AAAATTTTCATAACCTCCCCAT
1 AAAATTTTGTTAACCTCCCCAG
*
1478 AAAATTTTGTTAACCTCCCTAG
1 AAAATTTTGTTAACCTCCCCAG
*
1500 AATATTTTG
1 AAAATTTTG
1509 ATAAGCACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAATTTTGTTAACCTCCCCAG
Found at i:1628 original size:66 final size:65
Alignment explanation
Indices: 1537--1701 Score: 154
Period size: 66 Copynumber: 2.5 Consensus size: 65
1527 AGCCTCCCTC
* * * * * *
1537 ATGAAATTTTGTTAACTTTCA-TATGAAATTTTATTAACATCCCTAAGAAATTTTGGTAAACTCT
1 ATGAAATTTTGATAAC-TACACTATGAAATTTTA-CAACATCCATAAGAAATTTTGGTAAACACA
*
1601 GT
64 CT
* * * * *
1603 ATGAAATTTTGATAACTACACTATGAAGTTTTGACAACTTCTATATGAAATTTTGGTAACCACAC
1 ATGAAATTTTGATAACTACACTATGAAATTTT-ACAACATCCATAAGAAATTTTGGTAAACACAC
1668 T
65 T
* *
1669 ATGAAATTTTGATAA-TCCATCTATGTAATTTTA
1 ATGAAATTTTGATAACTACA-CTATGAAATTTTA
1702 GTTTGATTGT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
65 7 0.09
66 73 0.90
67 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (65 bp):
ATGAAATTTTGATAACTACACTATGAAATTTTACAACATCCATAAGAAATTTTGGTAAACACACT
Found at i:1680 original size:44 final size:43
Alignment explanation
Indices: 1537--1680 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 43
1527 AGCCTCCCTC
* *
1537 ATGAAATTTTGTTAACTT-TCATATGAAATTTT-ATTAA-CATCCCT
1 ATGAAATTTTG-AAACTTCT-ATATGAAATTTTGA-TAACCA-CACT
* * *
1581 AAGAAATTTTGGTAAAC-TCTGTATGAAATTTTGATAACTACACT
1 ATGAAATTTT-G-AAACTTCTATATGAAATTTTGATAACCACACT
* *
1625 ATGAAGTTTTGACAACTTCTATATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGA-AACTTCTATATGAAATTTTGATAACCACACT
1669 ATGAAATTTTGA
1 ATGAAATTTTGA
1681 TAATCCATCT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 70 0.84
45 8 0.10
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (43 bp):
ATGAAATTTTGAAACTTCTATATGAAATTTTGATAACCACACT
Found at i:1692 original size:22 final size:23
Alignment explanation
Indices: 1537--1700 Score: 91
Period size: 22 Copynumber: 7.4 Consensus size: 23
1527 AGCCTCCCTC
* *
1537 ATGAAATTTTGTTAACT--TTCAT
1 ATGAAATTTTGATAACTCCATC-T
1559 ATGAAATTTT-ATTAACATCC--CT
1 ATGAAATTTTGA-TAAC-TCCATCT
* * *
1581 AAGAAATTTTGGTAAACT-C-TGT
1 ATGAAATTTTGAT-AACTCCATCT
*
1603 ATGAAATTTTGATAACTACA-CT
1 ATGAAATTTTGATAACTCCATCT
* * * *
1625 ATGAAGTTTTGACAACTTC-TAT
1 ATGAAATTTTGATAACTCCATCT
*
1647 ATGAAATTTTGGTAAC-CACA-CT
1 ATGAAATTTTGATAACTC-CATCT
1669 ATGAAATTTTGATAA-TCCATCT
1 ATGAAATTTTGATAACTCCATCT
*
1691 ATGTAATTTT
1 ATGAAATTTT
1701 AGTTTGATTG
Statistics
Matches: 110, Mismatches: 18, Indels: 28
0.71 0.12 0.18
Matches are distributed among these distances:
21 7 0.06
22 98 0.89
23 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (23 bp):
ATGAAATTTTGATAACTCCATCT
Found at i:2184 original size:31 final size:30
Alignment explanation
Indices: 2149--2246 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
2139 GTTATCAAAT
2149 CTTTAATAGTAGTTAGGTGTCAAATTTTAAA
1 CTTTAATAGTAGTTA-GTGTCAAATTTTAAA
* * * ** *
2180 CTTT-A-AGGATCTTAGTTTC-CGTTATCAAA
1 CTTTAATAGTA-GTTAGTGTCAAATT-TTAAA
2209 TCTTTAATAGTAGTTAAGTGTCAAATTTTAAA
1 -CTTTAATAGTAGTT-AGTGTCAAATTTTAAA
2241 CTTTAA
1 CTTTAA
2247 GGATCAAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
28 2 0.04
29 11 0.23
30 8 0.17
31 13 0.27
32 12 0.25
33 2 0.04
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
CTTTAATAGTAGTTAGTGTCAAATTTTAAA
Found at i:2197 original size:61 final size:61
Alignment explanation
Indices: 2130--2251 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
2120 GAGATTGAGT
*
2130 TTAGTTTCCGTTATCAAATCTTTAATAGTAGTTAGGTGTCAAATTTTAAACTTTAAGGATC
1 TTAGTTTCCGTTATCAAATCTTTAATAGTAGTTAAGTGTCAAATTTTAAACTTTAAGGATC
2191 TTAGTTTCCGTTATCAAATCTTTAATAGTAGTTAAGTGTCAAATTTTAAACTTTAAGGATC
1 TTAGTTTCCGTTATCAAATCTTTAATAGTAGTTAAGTGTCAAATTTTAAACTTTAAGGATC
2252 AAAATTTACC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (61 bp):
TTAGTTTCCGTTATCAAATCTTTAATAGTAGTTAAGTGTCAAATTTTAAACTTTAAGGATC
Found at i:5473 original size:31 final size:31
Alignment explanation
Indices: 5438--5503 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
5428 AACTTTATGT
5438 TTTCCGATTGTACCCCTTTTCTTTAAACATA
1 TTTCCGATTGTACCCCTTTTCTTTAAACATA
* * *
5469 TTTCCGATTGTACCTCTTTTTTTTAAATATA
1 TTTCCGATTGTACCCCTTTTCTTTAAACATA
5500 TTTC
1 TTTC
5504 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (31 bp):
TTTCCGATTGTACCCCTTTTCTTTAAACATA
Found at i:5534 original size:25 final size:27
Alignment explanation
Indices: 5493--5551 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
5483 TCTTTTTTTT
* *
5493 AAATATATTTCTAAATTGCCATTATTA
1 AAATATATTTCTAAATTACAATTATTA
5520 AAATATATTT-T-AATTACAATTATTA
1 AAATATATTTCTAAATTACAATTATTA
*
5545 AATTATA
1 AAATATA
5552 ATACGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 18 0.62
26 1 0.03
27 10 0.34
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (27 bp):
AAATATATTTCTAAATTACAATTATTA
Found at i:6857 original size:2 final size:2
Alignment explanation
Indices: 6850--6884 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6840 TTAAAACTAG
*
6850 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6885 TATTTTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7036 original size:18 final size:18
Alignment explanation
Indices: 7013--7049 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7003 ATTTCAAATC
7013 ATTATGGGAGAATTACAA
1 ATTATGGGAGAATTACAA
* *
7031 ATTATGGTAGATTTACAA
1 ATTATGGGAGAATTACAA
7049 A
1 A
7050 ATCTTTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (18 bp):
ATTATGGGAGAATTACAA
Done.