Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021090.1 Corchorus olitorius cultivar O-4 contig21123, 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: 30971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:58 original size:14 final size:15
Alignment explanation
Indices: 39--70 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29 GACCCCACTA
39 TTTCTG-GTTTTTTT
1 TTTCTGCGTTTTTTT
53 TTTCTGCGTTTTTTT
1 TTTCTGCGTTTTTTT
68 TTT
1 TTT
71 ATCTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (15 bp):
TTTCTGCGTTTTTTT
Found at i:1176 original size:97 final size:97
Alignment explanation
Indices: 1067--1261 Score: 372
Period size: 97 Copynumber: 2.0 Consensus size: 97
1057 TTTTACTTAT
1067 AATTAATTTCAATTATTATTTTAATTTTCTTTTAATTTAAAGACGATTGGTCATGTGAGTGAAAA
1 AATTAATTTCAATTATTATTTTAATTTTCTTTTAATTTAAAGACGATTGGTCATGTGAGTGAAAA
1132 CTAGTAATTATAAAAAGTTAAATAATTTTAAC
66 CTAGTAATTATAAAAAGTTAAATAATTTTAAC
*
1164 AATTAATTTCAATTATTATTTTAATTTTCTTTTAATTTAAAGACGATTGGTTATGTGAGTGAAAA
1 AATTAATTTCAATTATTATTTTAATTTTCTTTTAATTTAAAGACGATTGGTCATGTGAGTGAAAA
*
1229 TTAGTAATTATAAAAAGTTAAATAATTTTAAC
66 CTAGTAATTATAAAAAGTTAAATAATTTTAAC
1261 A
1 A
1262 CTAATTTGGT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (97 bp):
AATTAATTTCAATTATTATTTTAATTTTCTTTTAATTTAAAGACGATTGGTCATGTGAGTGAAAA
CTAGTAATTATAAAAAGTTAAATAATTTTAAC
Found at i:1277 original size:23 final size:22
Alignment explanation
Indices: 1251--1319 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 22
1241 AAAAGTTAAA
1251 TAATTTTAACACTAATTTGGTAG
1 TAATTTTAACAC-AATTTGGTAG
* * * *
1274 TAATTATAA-A-AAGTT--AAA
1 TAATTTTAACACAATTTGGTAG
1292 TAATTTTAACACCAATTTGGTAG
1 TAATTTTAACA-CAATTTGGTAG
1315 TAATT
1 TAATT
1320 ATAAAAAGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
18 9 0.27
19 1 0.03
20 4 0.12
21 4 0.12
22 1 0.03
23 14 0.42
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (22 bp):
TAATTTTAACACAATTTGGTAG
Found at i:1287 original size:41 final size:41
Alignment explanation
Indices: 1230--1354 Score: 241
Period size: 41 Copynumber: 3.0 Consensus size: 41
1220 GAGTGAAAAT
1230 TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
1 TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
*
1271 TAGTAATTATAAAAAGTTAAATAATTTTAACACCAATTTGG
1 TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
1312 TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
1 TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
1353 TA
1 TA
1355 CAGCACGTTG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (41 bp):
TAGTAATTATAAAAAGTTAAATAATTTTAACACTAATTTGG
Found at i:1300 original size:97 final size:97
Alignment explanation
Indices: 1099--1297 Score: 242
Period size: 97 Copynumber: 2.1 Consensus size: 97
1089 AATTTTCTTT
1099 TAATTTAAAGACGATTGGTCATGTGAGTGAAAACTAGTAATTATAAAAAGTTAAATAATTTTAAC
1 TAATTTAAAGACGATTGGTCATGTGAGTGAAAACTAGTAATTATAAAAAGTTAAATAATTTTAAC
* * ** ** ***
1164 AATTAATTTCAATTATTATTTTAATTTTCTTT
66 AACTAATTTCAATAATTATTAAAAAGTTCAAA
* *
1196 TAATTTAAAGACGATTGGTTATGTGAGTGAAAATTAGTAATTATAAAAAGTTAAATAATTTTAAC
1 TAATTTAAAGACGATTGGTCATGTGAGTGAAAACTAGTAATTATAAAAAGTTAAATAATTTTAAC
* *
1261 -ACTAATTTGGTAGTAATTA-TAAAAAGTT-AAA
66 AACTAATTT--CAATAATTATTAAAAAGTTCAAA
1292 TAATTT
1 TAATTT
1298 TAACACCAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
96 13 0.15
97 68 0.78
98 6 0.07
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.41
Consensus pattern (97 bp):
TAATTTAAAGACGATTGGTCATGTGAGTGAAAACTAGTAATTATAAAAAGTTAAATAATTTTAAC
AACTAATTTCAATAATTATTAAAAAGTTCAAA
Found at i:4497 original size:31 final size:31
Alignment explanation
Indices: 4459--4532 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
4449 GTTATCGATT
* *
4459 GGATTCAATTGACCCAATTTGGTAAGTAGAG
1 GGATTCAATTGACACAATTTGATAAGTAGAG
*
4490 GGATTCAATTGACACAATTTTATAAGTAGAG
1 GGATTCAATTGACACAATTTGATAAGTAGAG
*
4521 GGATTAAATTGA
1 GGATTCAATTGA
4533 TCATTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (31 bp):
GGATTCAATTGACACAATTTGATAAGTAGAG
Found at i:4578 original size:30 final size:29
Alignment explanation
Indices: 4506--4582 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
4496 AATTGACACA
**
4506 ATTTTATAAGTAGAGGGATTAAATTGATC
1 ATTTTATAAGTAGAGGGACCAAATTGATC
*
4535 ATTTTAT-AGTAGAGGGACCAAATTGATT
1 ATTTTATAAGTAGAGGGACCAAATTGATC
* *
4563 TTTTGTGTAAGTAGAGGGAC
1 ATTT-TATAAGTAGAGGGAC
4583 TTGTAGGGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 21 0.51
29 9 0.22
30 11 0.27
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
ATTTTATAAGTAGAGGGACCAAATTGATC
Found at i:5451 original size:35 final size:35
Alignment explanation
Indices: 5411--5481 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5401 AAGAGTTTGG
*
5411 GTATTAGTAGAATTTAAGAAGGAAGAGGAAATAAA
1 GTATTAGTAGAATTTAAGAAGAAAGAGGAAATAAA
5446 GTATTAGTAGAATTTAAGAAGAAAGAGGAAATAAA
1 GTATTAGTAGAATTTAAGAAGAAAGAGGAAATAAA
5481 G
1 G
5482 CAAAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (35 bp):
GTATTAGTAGAATTTAAGAAGAAAGAGGAAATAAA
Found at i:8562 original size:47 final size:47
Alignment explanation
Indices: 8493--8588 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
8483 TAATGTGTAT
*
8493 ATTGAATTCTTTGAACTTGAGTAAAGAGTTAATAGGTAGAAATATGG
1 ATTGAATTCTTTGAACTTGAGTAAAGAGTTAATAGGTAGAAATAAGG
8540 ATTGAATTCTTTGAACTTGAGTAAAGAGTTAATAGGTAGAAATAAGG
1 ATTGAATTCTTTGAACTTGAGTAAAGAGTTAATAGGTAGAAATAAGG
8587 AT
1 AT
8589 CGTTTTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (47 bp):
ATTGAATTCTTTGAACTTGAGTAAAGAGTTAATAGGTAGAAATAAGG
Found at i:10273 original size:32 final size:32
Alignment explanation
Indices: 10232--10292 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
10222 GCATTACTCG
*
10232 TCAGAAGCATAAAATCCATAAAAATCATCTCA
1 TCAGAAGCATAAAATACATAAAAATCATCTCA
10264 TCAGAAGCATAAAATACATAAAAATCATC
1 TCAGAAGCATAAAATACATAAAAATCATC
10293 AAATACACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.21
Consensus pattern (32 bp):
TCAGAAGCATAAAATACATAAAAATCATCTCA
Found at i:19569 original size:66 final size:66
Alignment explanation
Indices: 19495--19626 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
19485 CTACCTACCA
* * *
19495 AATACACAAATAAACAAATTACAAACTAAACTCACATCTCATGAAACTTGAAGCCTGGACCGTGA
1 AATACACAAATAAACAAATTACAAACTAAACTCACATCCCATGAAACTTGAACCCTGAACCGTGA
19560 G
66 G
* * * *
19561 AATACACAAATAAACAAATTACAAGCTAAACTCATATCCCGTGAAACTTGAACCCTTAACCGTGA
1 AATACACAAATAAACAAATTACAAACTAAACTCACATCCCATGAAACTTGAACCCTGAACCGTGA
19626 G
66 G
19627 GTACGGTGCA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.20
Consensus pattern (66 bp):
AATACACAAATAAACAAATTACAAACTAAACTCACATCCCATGAAACTTGAACCCTGAACCGTGA
G
Found at i:21595 original size:14 final size:14
Alignment explanation
Indices: 21568--21597 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21558 AAATTTAAAA
21568 GTAGAAACATTTTT
1 GTAGAAACATTTTT
21582 GTAGTAAACATTTTT
1 GTAG-AAACATTTTT
21597 G
1 G
21598 AAATTACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (14 bp):
GTAGAAACATTTTT
Found at i:30942 original size:17 final size:19
Alignment explanation
Indices: 30920--30964 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
30910 ACCAATACTT
30920 ATTAAAAG-A-TAAAAAGA
1 ATTAAAAGAACTAAAAAGA
30937 ATTAAAAGAAATCTAAAAAGA
1 ATTAAAAG-AA-CTAAAAAGA
30958 ATTAAAA
1 ATTAAAA
30965 AAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
19 1 0.04
21 15 0.62
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (19 bp):
ATTAAAAGAACTAAAAAGA
Done.