Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014325.1 Corchorus capsularis cultivar CVL-1 contig14346, 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: 15522
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:779 original size:26 final size:26
Alignment explanation
Indices: 750--832 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 26
740 ATTTTGAAAG
750 GAAACAAAACTTTAGATTTGAAACAA
1 GAAACAAAACTTTAGATTTGAAACAA
** * *
776 G-AA-AACCCTCGATTAGGATTTGGAA-AG
1 GAAACAAAACT---TTA-GATTTGAAACAA
803 GAAACAAAACTTTAGATTTGAAACAA
1 GAAACAAAACTTTAGATTTGAAACAA
829 GAAA
1 GAAA
833 ACCCTCGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 4 0.10
25 10 0.24
26 9 0.21
27 5 0.12
28 10 0.24
29 4 0.10
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (26 bp):
GAAACAAAACTTTAGATTTGAAACAA
Found at i:791 original size:27 final size:27
Alignment explanation
Indices: 761--845 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
751 AAACAAAACT
761 TTAGATTTGAAACAAGAAAACCCTCGA
1 TTAGATTTGAAACAAGAAAACCCTCGA
* *
788 TTAGGATTTGGAAAGGAA-ACAAA-ACT---
1 TTA-GATTT-GAAA-CAAGA-AAACCCTCGA
814 TTAGATTTGAAACAAGAAAACCCTCGA
1 TTAGATTTGAAACAAGAAAACCCTCGA
841 TTAGA
1 TTAGA
846 GACCTTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
23 5 0.11
24 7 0.16
25 5 0.11
26 3 0.07
27 8 0.18
28 5 0.11
29 7 0.16
30 5 0.11
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (27 bp):
TTAGATTTGAAACAAGAAAACCCTCGA
Found at i:791 original size:53 final size:53
Alignment explanation
Indices: 729--845 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
719 CGACTAGAGA
*
729 CCTCGATTAGAATTTTGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAAC
1 CCTCGATTAGAATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAAC
*
782 CCTCGATTAGGATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAAC
1 CCTCGATTAGAATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAAC
835 CCTCGATTAGA
1 CCTCGATTAGA
846 GACCTTAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (53 bp):
CCTCGATTAGAATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAAC
Found at i:1046 original size:130 final size:132
Alignment explanation
Indices: 782--1055 Score: 471
Period size: 130 Copynumber: 2.1 Consensus size: 132
772 ACAAGAAAAC
* *
782 CCTCGATTAGGATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAACCCTCGATTAGAG
1 CCTCGATTAGGAGTTGGAAAGGAAACAAAACTTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
*
847 ACCTTAATTAGGATTTGGAAAGGAAACAAAACTTAGAATTGAAACAAGAAAAACCCTCGATTAGA
66 ACCTCAATTAGGATTTGGAAAGGAAACAAAACTTAGAATTGAAACAAGAAAAACCCTCGATTAGA
912 GA
131 GA
* *
914 CCTCGATTAGG-GTTGGAAATGAAGCAAAA-TTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
1 CCTCGATTAGGAGTTGGAAAGGAAACAAAACTTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
* *
977 ACCTCAATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAAACCCTCGATTAGA
66 ACCTCAATTAGGATTTGGAAAGGAAACAAAACTTAGAATTGAAACAAGAAAAACCCTCGATTAGA
1042 GA
131 GA
1044 CCTCGATTAGGA
1 CCTCGATTAGGA
1056 TTTTAAACGA
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
130 108 0.81
131 15 0.11
132 11 0.08
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (132 bp):
CCTCGATTAGGAGTTGGAAAGGAAACAAAACTTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
ACCTCAATTAGGATTTGGAAAGGAAACAAAACTTAGAATTGAAACAAGAAAAACCCTCGATTAGA
GA
Found at i:1069 original size:65 final size:65
Alignment explanation
Indices: 782--1058 Score: 439
Period size: 66 Copynumber: 4.2 Consensus size: 65
772 ACAAGAAAAC
*
782 CCTCGATTAGGATTTGGAAAGGAAACAAAACTTTAGATTTGAAACAAGAAAACCCTCGATTAGAG
1 CCTCGATTAGGATTTGGAAAGGAAACAAAA-TTTAGAATTGAAACAAGAAAACCCTCGATTAGAG
847 A
65 A
** *
848 CCTTAATTAGGATTTGGAAAGGAAACAAAACTTAGAATTGAAACAAGAAAAACCCTCGATTAGAG
1 CCTCGATTAGGATTTGGAAAGGAAACAAAATTTAGAATTGAAACAAG-AAAACCCTCGATTAGAG
913 A
65 A
* * *
914 CCTCGATTAGG-GTTGGAAATGAAGCAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGA
1 CCTCGATTAGGATTTGGAAAGGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGA
* *
978 CCTCAATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAAACCCTCGATTAGAG
1 CCTCGATTAGGATTTGGAAAGGAAACAAAATTTAGAATTGAAACAAG-AAAACCCTCGATTAGAG
1043 A
65 A
1044 CCTCGATTAGGATTT
1 CCTCGATTAGGATTT
1059 TAAACGAAAC
Statistics
Matches: 194, Mismatches: 14, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
64 28 0.14
65 79 0.41
66 87 0.45
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (65 bp):
CCTCGATTAGGATTTGGAAAGGAAACAAAATTTAGAATTGAAACAAGAAAACCCTCGATTAGAGA
Found at i:2103 original size:41 final size:37
Alignment explanation
Indices: 2015--2119 Score: 156
Period size: 41 Copynumber: 2.7 Consensus size: 37
2005 TTTATTTATC
*
2015 TTTTTCCGACCTATTTCTATTTTAGGCCAAGTTTTTT
1 TTTTTCCGACCTCTTTCTATTTTAGGCCAAGTTTTTT
*
2052 TTTTCCCGACCTCTTTCTATTTTAGGCCAAGTATTTTTTTT
1 TTTTTCCGACCTCTTTCTATTTTAGGCCAAG----TTTTTT
2093 TTTTTCCGACCTCTTTCTATTTTAGGC
1 TTTTTCCGACCTCTTTCTATTTTAGGC
2120 TAAGGCTCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
37 29 0.48
41 32 0.52
ACGTcount: A:0.14, C:0.22, G:0.10, T:0.53
Consensus pattern (37 bp):
TTTTTCCGACCTCTTTCTATTTTAGGCCAAGTTTTTT
Found at i:2132 original size:41 final size:39
Alignment explanation
Indices: 2015--2134 Score: 154
Period size: 41 Copynumber: 3.1 Consensus size: 39
2005 TTTATTTATC
*
2015 TTTTTCCGACCTATTTCTATTTTAGGCCAA-G-TTTTTT
1 TTTTTCCGACCTCTTTCTATTTTAGGCCAAGGTTTTTTT
* *
2052 TTTTCCCGACCTCTTTCTATTTTAGGCCAAGTATTTTTTTT
1 TTTTTCCGACCTCTTTCTATTTTAGGCCAAG--GTTTTTTT
* * *
2093 TTTTTCCGACCTCTTTCTATTTTAGGCTAAGGCTCTTTT
1 TTTTTCCGACCTCTTTCTATTTTAGGCCAAGGTTTTTTT
2132 TTT
1 TTT
2135 CATTTTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
37 28 0.39
39 8 0.11
41 35 0.49
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (39 bp):
TTTTTCCGACCTCTTTCTATTTTAGGCCAAGGTTTTTTT
Found at i:5667 original size:4 final size:4
Alignment explanation
Indices: 5658--5684 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5648 GTAATAAAGT
5658 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
5685 TATGCAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:13371 original size:34 final size:34
Alignment explanation
Indices: 13328--13487 Score: 200
Period size: 34 Copynumber: 4.8 Consensus size: 34
13318 GAAATCTGAT
*
13328 GGGTACCAAAACATTGATATATTTTGTACATTTA
1 GGGTACCAAAACATTGATATATTTTGTATATTTA
* *
13362 GGGTACCAAAATATTGATATATTTTGTTTATTTA
1 GGGTACCAAAACATTGATATATTTTGTATATTTA
*
13396 GGGTACCAAAACCTTGATATATTTTG--T-TTTA
1 GGGTACCAAAACATTGATATATTTTGTATATTTA
* *
13427 GGGTACCAAAACAATGATATATTTTGTATATTCA
1 GGGTACCAAAACATTGATATATTTTGTATATTTA
* * **
13461 GGCTTCCAAAACAAAGGATATATTTTG
1 GGGTACCAAAAC-ATTGATATATTTTG
13488 ATTACTCGGT
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
31 28 0.25
32 1 0.01
33 1 0.01
34 68 0.61
35 13 0.12
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (34 bp):
GGGTACCAAAACATTGATATATTTTGTATATTTA
Found at i:13451 original size:65 final size:66
Alignment explanation
Indices: 13328--13487 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 66
13318 GAAATCTGAT
* * *
13328 GGGTACCAAAACATTGATATATTTTGTACATTTAGGGTACCAAAATATTGATATATTTTGTTTAT
1 GGGTACCAAAACATTGATATATTTTGT--ATTTAGGGTACCAAAACAATGATATATTTTGTATAT
*
13393 TTA
64 TCA
*
13396 GGGTACCAAAACCTTGATATATTTTGT-TTTAGGGTACCAAAACAATGATATATTTTGTATATTC
1 GGGTACCAAAACATTGATATATTTTGTATTTAGGGTACCAAAACAATGATATATTTTGTATATTC
13460 A
66 A
* * **
13461 GGCTTCCAAAACAAAGGATATATTTTG
1 GGGTACCAAAAC-ATTGATATATTTTG
13488 ATTACTCGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 44 0.54
66 11 0.14
68 26 0.32
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (66 bp):
GGGTACCAAAACATTGATATATTTTGTATTTAGGGTACCAAAACAATGATATATTTTGTATATTC
A
Found at i:13504 original size:34 final size:35
Alignment explanation
Indices: 13430--13504 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
13420 TGTTTTAGGG
* *
13430 TACCAAAACAATGATATATTTTGTATATTCAGGCT
1 TACCAAAACAAGGATATATTTTGTATACTCAGGCT
13465 T-CCAAAACAAAGGATATATTTTG-ATTACTC-GG-T
1 TACCAAAAC-AAGGATATATTTTGTA-TACTCAGGCT
13498 TACCAAA
1 TACCAAA
13505 TTCTCATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
33 2 0.06
34 15 0.43
35 18 0.51
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (35 bp):
TACCAAAACAAGGATATATTTTGTATACTCAGGCT
Found at i:13902 original size:18 final size:18
Alignment explanation
Indices: 13869--13911 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
13859 TTGTCTAAAA
*
13869 TTCTCTTCTTTTTCAATTT
1 TTCTC-TCTGTTTCAATTT
13888 TTCTCTCTGTTTCAATTT
1 TTCTCTCTGTTTCAATTT
*
13906 CTCTCT
1 TTCTCT
13912 TTTTCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTCTCTGTTTCAATTT
Found at i:14536 original size:38 final size:38
Alignment explanation
Indices: 14485--14608 Score: 176
Period size: 38 Copynumber: 3.1 Consensus size: 38
14475 ATGAATTAGC
*
14485 AAATATATATGTATGTAGTTCAATTTAGTATCTAATGG
1 AAATATATATGTATGTAGTTCAATTTAGTATATAATGG
14523 AAATATATATGTATGTAGTTCAATTTAGTATTTAATGGAAATGG
1 AAATATATATGTATGTAGTTCAATTTAGTA--T-AT---AATGG
*
14567 AAATATATATGTATGTAGTTCAATTTAGTATTTAATGG
1 AAATATATATGTATGTAGTTCAATTTAGTATATAATGG
14605 AAAT
1 AAAT
14609 GGGTTCGAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
38 39 0.50
40 1 0.01
41 2 0.03
42 1 0.01
44 35 0.45
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (38 bp):
AAATATATATGTATGTAGTTCAATTTAGTATATAATGG
Found at i:14567 original size:44 final size:44
Alignment explanation
Indices: 14518--14610 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
14508 TTTAGTATCT
14518 AATGGAAATATATATGTATGTAGTTCAATTTAGTATTTAATGGA
1 AATGGAAATATATATGTATGTAGTTCAATTTAGTATTTAATGGA
14562 AATGGAAATATATATGTATGTAGTTCAATTTAGTATTTAATGGA
1 AATGGAAATATATATGTATGTAGTTCAATTTAGTATTTAATGGA
14606 AATGG
1 AATGG
14611 GTTCGAATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (44 bp):
AATGGAAATATATATGTATGTAGTTCAATTTAGTATTTAATGGA
Found at i:14745 original size:34 final size:34
Alignment explanation
Indices: 14694--14856 Score: 245
Period size: 34 Copynumber: 4.8 Consensus size: 34
14684 ACCGAGTAAT
** *
14694 CAAAATATATCCTTTGTTTTGGAACCCTAAATATA
1 CAAAATATAT-CAATGTTTTGGTACCCTAAATATA
*
14729 CAAAATATATCATTGTTTTGGTACCCTAAATATA
1 CAAAATATATCAATGTTTTGGTACCCTAAATATA
* *
14763 CAAAATATATCAAGGTTTTGGTACCCTAAATAAA
1 CAAAATATATCAATGTTTTGGTACCCTAAATATA
* *
14797 CAAAATATATCAATATTTTGGTACCCTAAATGTA
1 CAAAATATATCAATGTTTTGGTACCCTAAATATA
14831 CAAAATATATCAATGTTTTGGTACCC
1 CAAAATATATCAATGTTTTGGTACCC
14857 ATCAGATTTC
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
34 108 0.92
35 10 0.08
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (34 bp):
CAAAATATATCAATGTTTTGGTACCCTAAATATA
Done.