Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016737.1 Corchorus olitorius cultivar O-4 contig16770, 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: 25451
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:542 original size:206 final size:206
Alignment explanation
Indices: 187--597 Score: 779
Period size: 206 Copynumber: 2.0 Consensus size: 206
177 TTCATTATTA
187 ATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
1 ATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
252 ATACCAAAGGCTTTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACACG
66 ATACCAAAGGCTTTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACACG
*
317 TGTCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACAAAGTTATCATT
131 TGTCGAGATTTGAAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACAAAGTTATCATT
382 ATATATATATG
196 ATATATATATG
393 ATTTCTTTA-TTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
1 ATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
457 ATACCAAAGGCTTTTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACAC
66 ATACCAAAGGC-TTTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACAC
**
522 GTGTCGAGATTTGAAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACATTGTTATCAT
130 GTGTCGAGATTTGAAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACAAAGTTATCAT
587 TATATATATAT
195 TATATATATAT
598 ATATATATGA
Statistics
Matches: 201, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
205 66 0.33
206 135 0.67
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (206 bp):
ATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGTAAGAGAAATTATTGTTCTTTCTTAAAAT
ATACCAAAGGCTTTTTTCTAATCAATATATCAATATAATGAATATTAGAATTAATTAGAGACACG
TGTCGAGATTTGAAGGCCTCAACATTTAAAGAGTTTCCATATTTGTAGTGTACAAAGTTATCATT
ATATATATATG
Found at i:612 original size:7 final size:7
Alignment explanation
Indices: 588--623 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
578 TGTTATCATT
588 ATATAT-
1 ATATATG
594 ATATAT-
1 ATATATG
600 ATATATG
1 ATATATG
607 ATATATG
1 ATATATG
614 ATATATG
1 ATATATG
621 ATA
1 ATA
624 ATAAAAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (7 bp):
ATATATG
Found at i:1453 original size:15 final size:16
Alignment explanation
Indices: 1414--1455 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1404 AATAATATCC
1414 ATATGAATAACTCCAA
1 ATATGAATAACTCCAA
1430 ATATGAATAACTCCAA
1 ATATGAATAACTCCAA
*
1446 A-GTGAATAAC
1 ATATGAATAAC
1456 ATGATACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (16 bp):
ATATGAATAACTCCAA
Found at i:5654 original size:30 final size:30
Alignment explanation
Indices: 5620--5682 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
5610 ATCAACATTC
* * *
5620 AAAACGTTTTGCCTTTTTTTGAAAAACTCG
1 AAAACGCTTTGCCTTTATTTGAAAAACACG
*
5650 AAAACGCTTTGCCTTTATTTGTAAAACACG
1 AAAACGCTTTGCCTTTATTTGAAAAACACG
5680 AAA
1 AAA
5683 TTTATTGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (30 bp):
AAAACGCTTTGCCTTTATTTGAAAAACACG
Found at i:6439 original size:31 final size:30
Alignment explanation
Indices: 6404--6509 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
6394 TTGGACGGCT
*
6404 TGCCCCTAATTGACGCCAAATTGAAACGTTG
1 TGCCCCTAATT-AAGCCAAATTGAAACGTTG
*
6435 TGCCCC-AGA-TAAACCAAATTGAAACGTTG
1 TGCCCCTA-ATTAAGCCAAATTGAAACGTTG
* * * * * *
6464 TGTCCCAAATTAGGCCGAGATAGAAACGTTT
1 TGCCCCTAATTAAGCC-AAATTGAAACGTTG
*
6495 TGCCCTTAATTAAGC
1 TGCCCCTAATTAAGC
6510 AATTAGCCAG
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 23 0.39
30 7 0.12
31 29 0.49
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (30 bp):
TGCCCCTAATTAAGCCAAATTGAAACGTTG
Found at i:17370 original size:28 final size:26
Alignment explanation
Indices: 17306--17356 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
17296 AGCAAACAAA
17306 TTACAAACAAACTCACATTCCGTGAT
1 TTACAAACAAACTCACATTCCGTGAT
17332 TTACAAACAAACTCACATTCCGTGA
1 TTACAAACAAACTCACATTCCGTGA
17357 GATTTGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (26 bp):
TTACAAACAAACTCACATTCCGTGAT
Found at i:17548 original size:48 final size:51
Alignment explanation
Indices: 17482--17587 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 51
17472 AAGAAGGTTA
*
17482 CTTCATATACAAGATAGGTTAAATC-TTAACT-ATTTATTAATTGAATCAGC
1 CTTCATATA-AAGATAGGTTAAATCATTAACTAATTTATTAATTAAATCAGC
17532 CTTCATAT-AAGATAGGTTAAATCTTAATTAACTAATTTATTAATTAAATCAGC
1 CTTCATATAAAGATAGGTTAAATC---ATTAACTAATTTATTAATTAAATCAGC
17585 CTT
1 CTT
17588 AAAATCCTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
48 15 0.30
50 8 0.16
52 6 0.12
53 21 0.42
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (51 bp):
CTTCATATAAAGATAGGTTAAATCATTAACTAATTTATTAATTAAATCAGC
Found at i:18130 original size:68 final size:69
Alignment explanation
Indices: 18022--18205 Score: 291
Period size: 68 Copynumber: 2.6 Consensus size: 69
18012 TACGGTTGGC
* *
18022 AATAAAAGAAAAATTAATTTGTAAATACTGGATTAGTTTCTTAAGAG-A-TATATCTAAAAGGTA
1 AATAAAAGAAAAATTAATTTGTAATTATTGGATTAGTTTCTTAAGAGAATTATATCTAAAAGGTA
18085 AAAA
66 AAAA
18089 AATAAAAGAAAAAATTAATTTGTAATTATTGGATTAGTTTCTTAAGAGATATTATATCTAAAAGG
1 AATAAAAG-AAAAATTAATTTGTAATTATTGGATTAGTTTCTTAAGAGA-ATTATATCTAAAAGG
18154 TAAAAA
64 TAAAAA
18160 AATAAAAGAAAAATTAATTTGTAATTATTATTGGATTAGTTTCTTA
1 AATAAAAGAAAAATTAATTTGT-A--ATTATTGGATTAGTTTCTTA
18206 TGCGGATCTA
Statistics
Matches: 108, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
67 8 0.07
68 37 0.34
70 15 0.14
71 28 0.26
73 20 0.19
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (69 bp):
AATAAAAGAAAAATTAATTTGTAATTATTGGATTAGTTTCTTAAGAGAATTATATCTAAAAGGTA
AAAA
Found at i:19719 original size:36 final size:36
Alignment explanation
Indices: 19672--19743 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
19662 CCAACGTGAG
19672 CTGGCCACTTACAAACCCATCTCCATCAGTGATGCT
1 CTGGCCACTTACAAACCCATCTCCATCAGTGATGCT
19708 CTGGCCACTTACAAACCCATCTCCATCAGTGATGCT
1 CTGGCCACTTACAAACCCATCTCCATCAGTGATGCT
19744 GAAGGTTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (36 bp):
CTGGCCACTTACAAACCCATCTCCATCAGTGATGCT
Found at i:23769 original size:16 final size:16
Alignment explanation
Indices: 23742--23789 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
23732 TTTGGTTGAG
23742 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGGA
*
23757 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGGA
* *
23773 AGGGAAGGGAA-AGGA
1 AGGAAAGGAAATAGGA
23788 AG
1 AG
23790 TCATATTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.40, T:0.04
Consensus pattern (16 bp):
AGGAAAGGAAATAGGA
Found at i:24538 original size:27 final size:27
Alignment explanation
Indices: 24500--24564 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
24490 ACAAAATGTC
*
24500 ATCTAAATCAATTACAAAATATGACCA
1 ATCTAAATCAATTACAAAATATAACCA
24527 ATCTAAATCAATTACAAAATATAACCA
1 ATCTAAATCAATTACAAAATATAACCA
**
24554 AAATAAATCAA
1 ATCTAAATCAA
24565 GTAGATTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.25
Consensus pattern (27 bp):
ATCTAAATCAATTACAAAATATAACCA
Done.