Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011271.1 Corchorus capsularis cultivar CVL-1 contig11292, 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: 25880
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1434 original size:22 final size:22
Alignment explanation
Indices: 1409--1598 Score: 75
Period size: 22 Copynumber: 8.6 Consensus size: 22
1399 TATGATCCCA
1409 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
* * * *
1431 TTATGATATTTTAATAACGATAC
1 TTATGAAATTTTGATAAC-CTTC
* ** * * *
1454 -TATGGAATTTCAAGAATCTTT
1 TTATGAAATTTTGATAACCTTC
* ** *
1475 TTAT-AATTTTTTTTAACTTTC
1 TTATGAAATTTTGATAACCTTC
* *
1496 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGATAACCTTC
* * *
1518 CTAAGGAATTTTGA-AGACC-TC
1 TTATGAAATTTTGATA-ACCTTC
* *
1539 AATATGGAATTTTGATAA-CTTCC
1 -TTATGAAATTTTGATAACCTT-C
**
1562 CAATGAAATTTTGATAAACCTTC
1 TTATGAAATTTTGAT-AACCTTC
* *
1585 CTATAAAATTTTGA
1 TTATGAAATTTTGA
1599 AAATTTTCAA
Statistics
Matches: 121, Mismatches: 37, Indels: 19
0.68 0.21 0.11
Matches are distributed among these distances:
21 16 0.13
22 83 0.69
23 19 0.16
24 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTTC
Found at i:1594 original size:23 final size:22
Alignment explanation
Indices: 1546--1598 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1536 CTCAATATGG
*
1546 AATTTTGATAACTTCCCAATGA
1 AATTTTGATAACTTCCCAATAA
*
1568 AATTTTGATAAACCTT-CCTATAA
1 AATTTTGAT-AA-CTTCCCAATAA
1591 AATTTTGA
1 AATTTTGA
1599 AAATTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 15 0.56
24 3 0.11
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTTTGATAACTTCCCAATAA
Found at i:1670 original size:27 final size:28
Alignment explanation
Indices: 1640--1693 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1630 TTATCACTCC
1640 CCTCGGTT-TTCTCCTT-CACATCTCTTT
1 CCTC-GTTCTTCTCCTTCCACATCTCTTT
*
1667 CCTCTTTCTTCTCCTTCCACATCTCTT
1 CCTCGTTCTTCTCCTTCCACATCTCTT
1694 CACCATGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 12 0.50
28 10 0.42
ACGTcount: A:0.07, C:0.41, G:0.04, T:0.48
Consensus pattern (28 bp):
CCTCGTTCTTCTCCTTCCACATCTCTTT
Found at i:4422 original size:166 final size:165
Alignment explanation
Indices: 4048--4455 Score: 552
Period size: 166 Copynumber: 2.5 Consensus size: 165
4038 TGAATCATTT
* * *
4048 GTCAATTGAGAAATGACCAAAAAGTTTAGTTCTTTAATCCCCTCAAGAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** * ** * * *
4113 TTAAGTAATCTACTAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTGGCTCATCATCAATTATTT
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAACTTCTCTAACTCATAAGCAATTATGT
* *
4178 ATGGGATCTTTTATTAATTCCACTACTCTATTCAA
131 ATGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * *
4213 GTCCATTGAGAAATGACAAAAAAGATTACTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACGT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
4278 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA-AAAACTTCTCTAACTTCATAAGCAAGCTT-
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAACTTCTCTAAC-TCATAAGCAA--TTA
4341 TGGTA-GGGATCTTTTAGTAATTCCACTACTCTATTAAA
128 T-GTATGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
4379 GTCAATTGACAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAAAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
4444 TTAAGTAATCTG
66 TTAAGTAATCTG
4456 TTAAGTGGGA
Statistics
Matches: 211, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
164 9 0.04
165 96 0.45
166 102 0.48
167 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAACTTCTCTAACTCATAAGCAATTATGT
ATGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:4520 original size:166 final size:165
Alignment explanation
Indices: 4048--4533 Score: 550
Period size: 166 Copynumber: 2.9 Consensus size: 165
4038 TGAATCATTT
* * *
4048 GTCAATTGAGAAATGACCAAAAAGTTTAGTTCTTTAATCCCCTCAAGAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * * **
4113 TTAAGTAATCTACTAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTGGCTCATCATCAATTATTT
66 TTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTC-TCATTAATCAGCT
* * *
4178 ATG-GGATCTTTTATTAATTCCACTACTCTATTCAA
130 ATGTAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * *
4213 GTCCATTGAGAAATGACAAAAAAGATTACTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACGT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
* * * * *
4278 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-AACTTCTCTAACT-TCA-TAAGCAAGCT
66 TTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCTCATTAATC-AGCT
*
4340 TTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
130 AT-GTA--GATCTTTTAGTAATTCCACTACTCTATTAAA
* *
4379 GTCAATTGACAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAAAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * *
4444 TTAAGTAATCTGTTAAGTGGGAAAAAAC-AAAAACAATTAGTTCTCTCGCTCCTCATTAATCCGG
66 TTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAA-AATTAGTTCTCTAGCT-CTCATTAATCAGC
* *
4508 GATGTAGATCTTTTAGGAATTTCCAC
129 TATGTAGATCTTTTAGTAA-TTCCAC
4534 ATGTTTATTC
Statistics
Matches: 264, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
161 2 0.01
162 6 0.02
163 1 0.00
164 9 0.03
165 94 0.36
166 125 0.47
167 15 0.06
168 3 0.01
169 5 0.02
170 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTGCTAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCTCATTAATCAGCTA
TGTAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:13878 original size:30 final size:30
Alignment explanation
Indices: 13844--13904 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
13834 TTCTAGTAAC
13844 ATTTATTGCATATTAAATAAAGA-TTCTAAT
1 ATTTATTGCATATT-AATAAAGATTTCTAAT
*
13874 ATTTATTGCATATTAATAAATATTTCTAAT
1 ATTTATTGCATATTAATAAAGATTTCTAAT
13904 A
1 A
13905 AAATCCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (30 bp):
ATTTATTGCATATTAATAAAGATTTCTAAT
Found at i:16410 original size:30 final size:31
Alignment explanation
Indices: 16376--16434 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
16366 GATACAGGTG
16376 TTTTTGATCTTT-TGATAACT-CTTTGTTCAC
1 TTTTTGATCTTTATGA-AACTCCTTTGTTCAC
*
16406 TTTTTTATCTTTAATGAAACTCCTTTGTT
1 TTTTTGATCTTT-ATGAAACTCCTTTGTT
16435 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 11 0.44
31 4 0.16
32 10 0.40
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTTGATCTTTATGAAACTCCTTTGTTCAC
Found at i:17227 original size:1 final size:1
Alignment explanation
Indices: 17221--17246 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
17211 CTTTGTAGAG
17221 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
17247 AAAGTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.