Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013494.1 Corchorus capsularis cultivar CVL-1 contig13515, 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: 13366
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:101 original size:47 final size:47
Alignment explanation
Indices: 1--192 Score: 289
Period size: 47 Copynumber: 4.0 Consensus size: 47
1 AAAAAGAGAATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGT
1 AAAAAGAG-ATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGT
*
49 AAAAAGAGATTAATCGGAGTTAAAGATGATGGTAATCAGTAAATCAGT
1 AAAAAGAGATTAATCGGAGTCAAAG-TGATGGTAATCAGTAAATCAGT
97 -AAAAGAGATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGT
1 AAAAAGAGATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGT
** * *
143 AAAAAGAGATTAATCAAAAGTC-AAGATAATAGTAATCAGTAAATCAGT
1 AAAAAGAGATTAATC-GGAGTCAAAG-TGATGGTAATCAGTAAATCAGT
191 AA
1 AA
193 TCAAGTAAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
46 22 0.16
47 56 0.42
48 56 0.42
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (47 bp):
AAAAAGAGATTAATCGGAGTCAAAGTGATGGTAATCAGTAAATCAGT
Found at i:289 original size:32 final size:31
Alignment explanation
Indices: 224--289 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
214 AGTAAATTGA
* *
224 TAATTACGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
255 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
287 TAA
1 TAA
290 ATCAGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 18 0.58
32 10 0.32
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.26
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:307 original size:71 final size:71
Alignment explanation
Indices: 153--308 Score: 158
Period size: 71 Copynumber: 2.2 Consensus size: 71
143 AAAAAGAGAT
* * *
153 TAATCAAAAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAACATAGTAATCAGTA
1 TAATTAAAAGTCAAGATAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
*
218 AATTGA
66 AATAGA
** * * *
224 TAATTACGAGTCAAGGTAAGAGATTAATCAGTAATTAAG-AGTCAAGGT-AAAA-ATAGTAATCA
1 TAATTAAAAGTCAAGATAAGAG--TAATCAGTAAATAAGTAATCAA-GTAAAAACATAGTAATCA
286 GTAAATCAG-
63 GTAAAT-AGA
*
295 TGATTAAAAGTCAA
1 TAATTAAAAGTCAA
309 TATTTTGATC
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
71 44 0.64
72 10 0.14
73 15 0.22
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (71 bp):
TAATTAAAAGTCAAGATAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAACATAGTAATCAGTA
AATAGA
Found at i:465 original size:14 final size:14
Alignment explanation
Indices: 428--467 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
418 AATGGTAAAG
*
428 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
442 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
456 AGTAAAGAGTAA
1 AGTAAAGAGTAA
468 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:521 original size:35 final size:34
Alignment explanation
Indices: 476--569 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 34
466 AAAATGATAA
476 AAAAGTAAAGAGTAATCAGCAAAAGAAGAATGGT
1 AAAAGTAAAGAGTAATCAGCAAAAGAAGAATGGT
* * *
510 AAAACGTAAAGAATAATCAGTAAAGGAAGAATGGT
1 AAAA-GTAAAGAGTAATCAGCAAAAGAAGAATGGT
*
545 AAAGAGTAAAGGGTAATCAGCAAAA
1 AAA-AGTAAAGAGTAATCAGCAAAA
570 AGTAAAAAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 4 0.08
35 46 0.90
36 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.15
Consensus pattern (34 bp):
AAAAGTAAAGAGTAATCAGCAAAAGAAGAATGGT
Found at i:687 original size:21 final size:21
Alignment explanation
Indices: 663--861 Score: 121
Period size: 21 Copynumber: 8.9 Consensus size: 21
653 ATCAGTAGAA
* *
663 AGTAATCATTAAGAGTAAAAC
1 AGTAATCAGTAAGAGTAAAAT
* * * *
684 AGTAACCAGTGAGAGCAAAGT
1 AGTAATCAGTAAGAGTAAAAT
* * *
705 GGTAATTAGTAAGAGTCAAAT
1 AGTAATCAGTAAGAGTAAAAT
*
726 AGTAATCAGTAAGAAGTAAAAG
1 AGTAATCAGTAAG-AGTAAAAT
*
748 AGTAATCAGTAAAAAAGGAGCAGAAAAT
1 AGTAATCAGT----AA-GAG--TAAAAT
776 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGT--AAGAGTAAAAT
* *
799 GGTAATCAGTAAAAAGTAAGAA-
1 AGTAATCAGT-AAGAGTAA-AAT
* **
821 GGTAATCAACAAGAGTAAAAT
1 AGTAATCAGTAAGAGTAAAAT
*
842 AGTAATCAGTACAAAGTAAA
1 AGTAATCAGTA-AGAGTAAA
862 GAATAATCGG
Statistics
Matches: 138, Mismatches: 29, Indels: 21
0.73 0.15 0.11
Matches are distributed among these distances:
20 2 0.01
21 55 0.40
22 39 0.28
23 16 0.12
25 3 0.02
26 8 0.06
27 1 0.01
28 14 0.10
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAATCAGTAAGAGTAAAAT
Found at i:758 original size:15 final size:15
Alignment explanation
Indices: 740--795 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
730 ATCAGTAAGA
740 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
755 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
769 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
783 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
796 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:868 original size:21 final size:22
Alignment explanation
Indices: 776--894 Score: 74
Period size: 21 Copynumber: 5.5 Consensus size: 22
766 AGCAGAAAAT
*
776 AGTAATCAGTAAAAGAGTAAA-A
1 AGTAATCAGTACAA-AGTAAAGA
* *
798 TGGTAATCAGTAAAAAGT-AAGA
1 -AGTAATCAGTACAAAGTAAAGA
820 AGGTAATCA--ACAAGAGTAAA-A
1 A-GTAATCAGTACAA-AGTAAAGA
841 TAGTAATCAGTACAAAGTAAAGA
1 -AGTAATCAGTACAAAGTAAAGA
* *
864 A-TAATCGGTA-AAA-TAATGA
1 AGTAATCAGTACAAAGTAAAGA
*
883 TGGTAATCAGTA
1 -AGTAATCAGTA
895 ATTCAGTAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
19 5 0.06
20 6 0.08
21 29 0.37
22 21 0.27
23 18 0.23
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (22 bp):
AGTAATCAGTACAAAGTAAAGA
Found at i:2231 original size:21 final size:21
Alignment explanation
Indices: 2198--2246 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2188 AAGAATTGTA
**
2198 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
2218 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
2239 GCATTCCT
1 GC-TTCCT
2247 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:6828 original size:28 final size:28
Alignment explanation
Indices: 6783--6836 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
6773 CATTTTTATT
*
6783 AAACTCAAAACAGTGAGTACAATTCTAA
1 AAACTCAAAACAGGGAGTACAATTCTAA
6811 AAAC-CAAAACCAGGGAGTACAATTCT
1 AAACTCAAAA-CAGGGAGTACAATTCT
6837 CACTTCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.19
Consensus pattern (28 bp):
AAACTCAAAACAGGGAGTACAATTCTAA
Found at i:12877 original size:2 final size:2
Alignment explanation
Indices: 12870--12906 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12860 AAAACTATGA
12870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12907 CTCTTGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.