Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015728.1 Corchorus olitorius cultivar O-4 contig15761, 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: 74023
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:9509 original size:3 final size:3
Alignment explanation
Indices: 9501--9587 Score: 52
Period size: 3 Copynumber: 29.0 Consensus size: 3
9491 TAATTTAGAC
* * * * * *
9501 TTA TTA TTA TTA TTA TAA TAA TTA TTA -AA CTTA TTA TTA GTG GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
9546 TTA TAA TTA TTA -AA CTTA TTA TTA TAA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
9588 GTGGTATGTA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:9533 original size:30 final size:30
Alignment explanation
Indices: 9499--9570 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
9489 GTTAATTTAG
*
9499 ACTTATTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTAGTATAATAATTATTAA
* * *
9529 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTATTAGTATAATAATTATTAA
9559 ACTTATTATTAT
1 ACTTATTATTAT
9571 AATAATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (30 bp):
ACTTATTATTATTAGTATAATAATTATTAA
Found at i:9579 original size:30 final size:29
Alignment explanation
Indices: 9499--9587 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
9489 GTTAATTTAG
* *
9499 ACTTATTATTATTATTATAATAATTATTAA
1 ACTTATTATTA-TAATATTATAATTATTAA
**
9529 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-TAATATTATAATTATTAA
*
9559 ACTTATTATTATAATAATTATTATTATTA
1 ACTTATTATTATAAT-ATTATAATTATTA
9588 GTGGTATGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.04
30 49 0.96
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
ACTTATTATTATAATATTATAATTATTAA
Found at i:11474 original size:25 final size:27
Alignment explanation
Indices: 11440--11490 Score: 79
Period size: 25 Copynumber: 1.9 Consensus size: 27
11430 TGTGAGAACA
11440 AATATTAAAAA-TTAG-TTATGTAGCT
1 AATATTAAAAAGTTAGTTTATGTAGCT
11465 AATATTAAAAAGTTTAGTTTATGTAG
1 AATATTAAAAAG-TTAGTTTATGTAG
11491 TTTATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
27 4 0.17
28 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (27 bp):
AATATTAAAAAGTTAGTTTATGTAGCT
Found at i:13222 original size:272 final size:273
Alignment explanation
Indices: 12720--13264 Score: 993
Period size: 272 Copynumber: 2.0 Consensus size: 273
12710 TGGAACTAGC
12720 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
1 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
12785 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
66 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
*
12850 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATAGAAATGTAGATACA
131 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTAATGGAAGTAAAGATAGAAATGTAGATACA
* * * * *
12915 GACTTAATTATGCTCGATGGATGATTTGTCAAGACAATCATGTGAAAAACCAAAAAGAAAAAAGG
196 GACTTAATTATGCTCGATGAATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
12980 AGTTGCAAGAAAA
261 AGTTGCAAGAAAA
*
12993 ACTGATATCTACAAC-AAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTGA
1 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
13057 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
66 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
* *
13122 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTAATGGAAGTAAAGATGGAAATGTAGATGCA
131 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTAATGGAAGTAAAGATAGAAATGTAGATACA
*
13187 GATTTAATTATGCTCGATGAATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
196 GACTTAATTATGCTCGATGAATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
13252 AGTTGCAAGAAAA
261 AGTTGCAAGAAAA
13265 GTCAAGTTAG
Statistics
Matches: 262, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
272 247 0.94
273 15 0.06
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (273 bp):
ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTAATGGAAGTAAAGATAGAAATGTAGATACA
GACTTAATTATGCTCGATGAATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
AGTTGCAAGAAAA
Found at i:16940 original size:2 final size:2
Alignment explanation
Indices: 16933--16964 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16923 TATGCTCGTG
16933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16965 AATTTCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17542 original size:53 final size:53
Alignment explanation
Indices: 17484--17593 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
17474 TCTTTAAATC
* *
17484 CAATAGTTCATTACATTTTGTATTATTTGGTATGTGTGCTTATTTATTAGGTT
1 CAATAGTTCATTACATTTTATATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
17537 CAATAGTTCATTGCATTTTATATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTACATTTTATATTATTTGGTATGTGTGCTTATTTAATAGGTT
17590 CAAT
1 CAAT
17594 TGAATAAACA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (53 bp):
CAATAGTTCATTACATTTTATATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:28465 original size:2 final size:2
Alignment explanation
Indices: 28460--28484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28450 TATATAATGT
28460 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28485 AATAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30324 original size:27 final size:27
Alignment explanation
Indices: 30294--30346 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
30284 TAAACCTAAA
30294 TTTCATACTACCTCAAAGTTAAAATCC
1 TTTCATACTACCTCAAAGTTAAAATCC
*
30321 TTTCATACTGCCTCAAAGTTAAAATC
1 TTTCATACTACCTCAAAGTTAAAATC
30347 TGGGGAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (27 bp):
TTTCATACTACCTCAAAGTTAAAATCC
Found at i:33187 original size:23 final size:23
Alignment explanation
Indices: 33157--33200 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
33147 GTTACAAATC
33157 AATAGTGTTTAGCCCCAAATAAT
1 AATAGTGTTTAGCCCCAAATAAT
33180 AATAGTGTTTAGCCCCAAATA
1 AATAGTGTTTAGCCCCAAATA
33201 TATATACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
AATAGTGTTTAGCCCCAAATAAT
Found at i:35086 original size:19 final size:20
Alignment explanation
Indices: 35047--35086 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
35037 TATTCATCAC
*
35047 AATAATTTTCTGATCTAAAAA
1 AATAATTTTC-GATATAAAAA
35068 AATAATTTTC-ATATAAAAA
1 AATAATTTTCGATATAAAAA
35087 TCGATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (20 bp):
AATAATTTTCGATATAAAAA
Found at i:49270 original size:12 final size:12
Alignment explanation
Indices: 49253--49284 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
49243 GGACGATGAG
*
49253 GAAGAAGAATCT
1 GAAGAAGAATCA
49265 GAAGAAGAATCA
1 GAAGAAGAATCA
49277 GAAGAAGA
1 GAAGAAGA
49285 GAAGGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (12 bp):
GAAGAAGAATCA
Found at i:50273 original size:32 final size:32
Alignment explanation
Indices: 50232--50296 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
50222 CATTCAGCAT
*
50232 TTTGAGCTTTTACAA-AAGGCCTCCGTTCCTGA
1 TTTGAGCTTTTACAACAA-GCCTCCATTCCTGA
*
50264 TTTGAGCTTTTACAACAAGCCTCCATTCTTGA
1 TTTGAGCTTTTACAACAAGCCTCCATTCCTGA
50296 T
1 T
50297 CACATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (32 bp):
TTTGAGCTTTTACAACAAGCCTCCATTCCTGA
Found at i:61581 original size:21 final size:21
Alignment explanation
Indices: 61557--61596 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
61547 TCCGTTTAAG
61557 ACATGTCCCATATTTTCAAAT
1 ACATGTCCCATATTTTCAAAT
61578 ACATGTCCCATATTTTCAA
1 ACATGTCCCATATTTTCAA
61597 GACCCGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (21 bp):
ACATGTCCCATATTTTCAAAT
Found at i:65503 original size:16 final size:16
Alignment explanation
Indices: 65482--65512 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65472 TTAAATAAAT
*
65482 AATAATTATTTTTTAG
1 AATAATTATTATTTAG
65498 AATAATTATTATTTA
1 AATAATTATTATTTA
65513 AAATTTCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATAATTATTATTTAG
Done.