Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013033.1 Corchorus capsularis cultivar CVL-1 contig13054, 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: 2143
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:304 original size:14 final size:14
Alignment explanation
Indices: 285--323 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
275 ACTCAAAACC
285 TTTTTGAAAACCCA
1 TTTTTGAAAACCCA
*
299 TTTTTGAAAA-CCT
1 TTTTTGAAAACCCA
312 TTTATTGAAAAC
1 TTT-TTGAAAAC
324 AATTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (14 bp):
TTTTTGAAAACCCA
Found at i:329 original size:26 final size:25
Alignment explanation
Indices: 279--329 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
269 AAAAAGACTC
*
279 AAAACCTTTTTGAAAACCCATTTTTG
1 AAAACCTTTTTGAAAA-CCAATTTTG
305 AAAACCTTTTATTGAAAA-CAATTTT
1 AAAACC-TTT-TTGAAAACCAATTTT
330 TTTGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (25 bp):
AAAACCTTTTTGAAAACCAATTTTG
Found at i:334 original size:15 final size:14
Alignment explanation
Indices: 285--337 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
275 ACTCAAAACC
***
285 TTTTTGAAAACCCA
1 TTTTTGAAAACATT
*
299 TTTTTGAAAACCTT
1 TTTTTGAAAACATT
*
313 TTATTGAAAACAATT
1 TTTTTGAAAAC-ATT
328 TTTTTGAAAA
1 TTTTTGAAAA
338 ATGTATCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (14 bp):
TTTTTGAAAACATT
Found at i:427 original size:23 final size:23
Alignment explanation
Indices: 400--467 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
390 AACTTGATTT
400 TTCTTTTCTTTTTCTTTTTA-TTC
1 TTCTTTTCTTTTT-TTTTTACTTC
*
423 TTCTTTTTTTCTCTTTTTTTATCTTC
1 TTCTTTTCTT-T-TTTTTTTA-CTTC
*
449 CTCTTTTCTTTTTTTTTTA
1 TTCTTTTCTTTTTTTTTTA
468 ATGGGAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 9 0.24
24 15 0.39
25 3 0.08
26 11 0.29
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTCTTTTCTTTTTTTTTTACTTC
Found at i:441 original size:24 final size:23
Alignment explanation
Indices: 406--465 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
396 ATTTTTCTTT
* *
406 TCTTTT-TCTTTTTAT-TCTTCT
1 TCTTTTCTCTTTTTTTATCTTCC
*
427 TTTTTTCTCTTTTTTTATCTTCC
1 TCTTTTCTCTTTTTTTATCTTCC
*
450 TCTTTTCTTTTTTTTT
1 TCTTTTCTCTTTTTTT
466 TAATGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 5 0.16
22 8 0.25
23 19 0.59
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TCTTTTCTCTTTTTTTATCTTCC
Found at i:447 original size:20 final size:20
Alignment explanation
Indices: 397--464 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
387 TGGAACTTGA
*
397 TTTTTCTTTTCTTTTTCTTTT
1 TTTTTCTTTTCTTTCTC-TTT
418 TATTCTTCTTTT-TTTCTCTTT
1 T-TT-TTCTTTTCTTTCTCTTT
*
439 TTTTATCTTCCTCTTT-TCTTT
1 TTTT-TCTT-TTCTTTCTCTTT
460 TTTTT
1 TTTTT
465 TTAATGGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 1 0.03
20 7 0.17
21 15 0.38
22 10 0.25
23 7 0.17
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTCTTTCTCTTT
Found at i:691 original size:5 final size:5
Alignment explanation
Indices: 681--750 Score: 81
Period size: 5 Copynumber: 13.8 Consensus size: 5
671 AACTTGGCTT
* *
681 TTTTG TTTTG TTTTG TTTTTT TTTTG TTTTG TTTTTTG TTTTG TTTTT
1 TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG --TTTTG TTTTG TTTTG
729 TTTTG -TTTG TTTTG TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTT
751 TTGAGCAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
4 8 0.14
5 40 0.70
6 4 0.07
7 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (5 bp):
TTTTG
Found at i:700 original size:1 final size:1
Alignment explanation
Indices: 679--752 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
669 GGAACTTGGC
* * * * * * * * * *
679 TTTTTTGTTTTGTTTTGTTTTTTTTTTGTTTTGTTTTTTGTTTTGTTTTTTTTTGTTTGTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
744 TTTTTTTTT
1 TTTTTTTTT
753 GAGCAATTTG
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (1 bp):
T
Found at i:705 original size:16 final size:16
Alignment explanation
Indices: 679--753 Score: 109
Period size: 16 Copynumber: 4.7 Consensus size: 16
669 GGAACTTGGC
679 TTTTTTGTTTTGTTTTG
1 TTTTTT-TTTTGTTTTG
696 TTTTTTTTTTGTTTTG
1 TTTTTTTTTTGTTTTG
712 TTTTTTGTTTTG-TTT-
1 TTTTTT-TTTTGTTTTG
*
727 TTTTTTGTTTGTTTTG
1 TTTTTTTTTTGTTTTG
743 TTTTTTTTTTG
1 TTTTTTTTTTG
754 AGCAATTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 4 0.08
15 9 0.17
16 29 0.55
17 11 0.21
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTGTTTTG
Found at i:1659 original size:42 final size:42
Alignment explanation
Indices: 1569--1669 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1559 CATACAAGTG
* * ** *
1569 AATGCATGATGGATGCATGAGCATATATACTAATTAATGGGT
1 AATGCATGATGGATGCATGAACATATATACAAAAGAATGGGC
* *
1611 AGTGCATGATCGATGCATGAACATATATACAAAAGAA-GGGAC
1 AATGCATGATGGATGCATGAACATATATACAAAAGAATGGG-C
1653 AATGCATGATGGATGCA
1 AATGCATGATGGATGCA
1670 GGCATATACA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (42 bp):
AATGCATGATGGATGCATGAACATATATACAAAAGAATGGGC
Done.