Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006940.1 Corchorus capsularis cultivar CVL-1 contig06961, 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: 14688
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:179 original size:22 final size:22
Alignment explanation
Indices: 153--266 Score: 99
Period size: 22 Copynumber: 5.2 Consensus size: 22
143 TATAAGCTTC
* *
153 ATAACCACACTATAAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * *
175 ATAACCTCCCCATGAAATATT-
1 ATAACCTCACTATGAAATTTTG
196 AGTAACCTC-CTAATGAAATTTTG
1 A-TAACCTCACT-ATGAAATTTTG
* *
219 TTAACCACACTATGAAATTCTT-
1 ATAACCTCACTATGAAATT-TTG
* *
241 ATAACCTCGCTATGACATTTTG
1 ATAACCTCACTATGAAATTTTG
263 ATAA
1 ATAA
267 TCTCTTTGAT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
21 4 0.05
22 65 0.89
23 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (22 bp):
ATAACCTCACTATGAAATTTTG
Found at i:217 original size:44 final size:44
Alignment explanation
Indices: 153--266 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
143 TATAAGCTTC
* * * * *
153 ATAACCACACTATAAAATTTTGATAACCTCCCCATGAAA-TATT
1 ATAACCTCGCTATGAAATTTTGATAACCACACCATGAAATTATT
* * *
196 AGTAACCTC-CTAATGAAATTTTGTTAACCACACTATGAAATTCTT
1 A-TAACCTCGCT-ATGAAATTTTGATAACCACACCATGAAATTATT
*
241 ATAACCTCGCTATGACATTTTGATAA
1 ATAACCTCGCTATGAAATTTTGATAA
267 TCTCTTTGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
43 3 0.05
44 49 0.84
45 6 0.10
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (44 bp):
ATAACCTCGCTATGAAATTTTGATAACCACACCATGAAATTATT
Found at i:363 original size:24 final size:22
Alignment explanation
Indices: 302--485 Score: 108
Period size: 22 Copynumber: 8.3 Consensus size: 22
292 TTGTGATAAT
* *
302 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
324 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
346 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
*
370 TAACC-ACGCTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
** * *
392 TAA-CTTCCGTATGAGATTTTGA
1 TAACCAACC-TATGAAATTTTAA
* *
414 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
436 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
458 TAACTATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
480 TAACCA
1 TAACCA
486 CATAGAGACA
Statistics
Matches: 130, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
21 7 0.05
22 101 0.78
23 6 0.05
24 15 0.12
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:420 original size:44 final size:42
Alignment explanation
Indices: 309--483 Score: 161
Period size: 44 Copynumber: 4.0 Consensus size: 42
299 AATTAACCAC
** * *
309 CCTATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACATGAT
1 CCTATGAAATTTTGATAACC-ACCTATGAAATTTTGATAAC-T--T
*
355 CCTATGAAATTTTGGTAACCACGCTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACTT
* * *
398 CCGTATGAGATTTTGATAACCACACTATGGAATTTTGATAACCT
1 CC-TATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACTT
* * * *
442 CCTCATGAAATTATAATAACTATCTTATGAAATTTTGATAAC
1 CCT-ATGAAATTTTGATAACCA-CCTATGAAATTTTGATAAC
484 CACATAGAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.04
44 68 0.62
45 4 0.04
46 33 0.30
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (42 bp):
CCTATGAAATTTTGATAACCACCTATGAAATTTTGATAACTT
Found at i:461 original size:66 final size:66
Alignment explanation
Indices: 356--487 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
346 TAACATGATC
* * * *
356 CTATGAAATTTTGGTAACCACGCTATGAAATTTTGATAACT-TCCGTATGAGATTTTGATAACCA
1 CTATGAAATTTTGATAACCACGCTATGAAATTATAATAACTAT-CGTATGAAATTTTGATAACCA
420 CA
65 CA
* * *
422 CTATGGAATTTTGATAACCTC-CTCATGAAATTATAATAACTATCTTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCACGCT-ATGAAATTATAATAACTATCGTATGAAATTTTGATAACCA
486 CA
65 CA
488 TAGAGACAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 54 0.95
67 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACGCTATGAAATTATAATAACTATCGTATGAAATTTTGATAACCAC
A
Found at i:1103 original size:37 final size:38
Alignment explanation
Indices: 1032--1109 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
1022 AATCGAAGAA
1032 AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
* **
1070 AAAGACAAAAGGCAAAATTAAATAGGACG-TTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
1107 AAA
1 AAA
1110 AAGTCAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 11 0.30
38 26 0.70
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.13
Consensus pattern (38 bp):
AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
Found at i:1591 original size:31 final size:31
Alignment explanation
Indices: 1546--1624 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
1536 TTTAGTAATG
* *
1546 ACAATTTAGAAATATGTTTTAGAAAA-AAGGGT
1 ACAATTGA-AAATATATTTTA-AAAATAAGGGT
1578 ACAATTGAAAATATATTTTAAAAATAAGGGT
1 ACAATTGAAAATATATTTTAAAAATAAGGGT
* *
1609 ATAATCGGAAAATATA
1 ACAAT-TGAAAATATA
1625 AAGTTTCCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.10
31 21 0.51
32 16 0.39
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (31 bp):
ACAATTGAAAATATATTTTAAAAATAAGGGT
Found at i:10617 original size:1 final size:1
Alignment explanation
Indices: 10611--10667 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
10601 GTCATTGTAG
* * * * * *
10611 TTTTTTTGTTTTGTTTTGTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10668 GCAGATACAG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:10624 original size:5 final size:5
Alignment explanation
Indices: 10614--10668 Score: 67
Period size: 5 Copynumber: 11.0 Consensus size: 5
10604 ATTGTAGTTT
* * *
10614 TTTTG TTTTG TTTTG TTTTG TTTTT TTTTG TTTTTG TTTT- TTTTT TTTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG TTTTG
10664 TTTTG
1 TTTTG
10669 CAGATACAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
4 4 0.09
5 36 0.80
6 5 0.11
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:10645 original size:25 final size:25
Alignment explanation
Indices: 10611--10668 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
10601 GTCATTGTAG
10611 TTTTTTTG-TTTTGTTTTGTTTTGTT
1 TTTTTTTGTTTTTGTTTT-TTTTGTT
*
10636 TTTTTTTGTTTTTGTTTTTTTTTTT
1 TTTTTTTGTTTTTGTTTTTTTTGTT
10661 TTTTTTTG
1 TTTTTTTG
10669 CAGATACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (25 bp):
TTTTTTTGTTTTTGTTTTTTTTGTT
Done.