Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013594.1 Corchorus capsularis cultivar CVL-1 contig13615, 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: 48835
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1469 original size:13 final size:13
Alignment explanation
Indices: 1447--1479 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1437 AATTACCAAC
1447 CAAG-GGTTTGAT
1 CAAGTGGTTTGAT
1459 CAAGTGGTTTGAT
1 CAAGTGGTTTGAT
1472 CAAGTGGT
1 CAAGTGGT
1480 AAACGGCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (13 bp):
CAAGTGGTTTGAT
Found at i:2831 original size:33 final size:33
Alignment explanation
Indices: 2784--2868 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
2774 GGCGCGAGTG
*
2784 ACCGGCCATGCGACTTGGAGAAGACC-GGCCAAC
1 ACCGGCCACGCGACTTGGAGAAG-CCGGGCCAAC
* * * *
2817 ACCGACCACGCGACTCGGAGATGCCGGGCCATC
1 ACCGGCCACGCGACTTGGAGAAGCCGGGCCAAC
*
2850 ACCGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
2869 CATGTCCGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 2 0.05
33 41 0.95
ACGTcount: A:0.25, C:0.36, G:0.31, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCGGGCCAAC
Found at i:2880 original size:33 final size:30
Alignment explanation
Indices: 2784--2890 Score: 97
Period size: 33 Copynumber: 3.3 Consensus size: 30
2774 GGCGCGAGTG
* *
2784 ACCGGCCATGCGACTTGGAGAAGACCGGCCAAC
1 ACCGGCCACGCGAC-TGGAGATG-CCGGCC-AC
*
2817 ACCGACCACGCGACTCGGAGATGCCGGGCCATC
1 ACCGGCCACGCGACT-GGAGATGCC-GGCCA-C
*
2850 ACCGGCCACGCGACATGGACATGTCCGGCCAC
1 ACCGGCCACGCGAC-TGGAGATG-CCGGCCAC
2882 AACCGGCCA
1 -ACCGGCCA
2891 TCGCTTGGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
32 5 0.08
33 55 0.87
34 3 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.08
Consensus pattern (30 bp):
ACCGGCCACGCGACTGGAGATGCCGGCCAC
Found at i:6204 original size:2 final size:2
Alignment explanation
Indices: 6197--6226 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6187 TCCATGCTTT
6197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6227 GATAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6264 original size:21 final size:21
Alignment explanation
Indices: 6240--6294 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 21
6230 AATAATGTAC
6240 ATTTATGAGTACAATGCATAA
1 ATTTATGAGTACAATGCATAA
*
6261 ATTTAT--G--CATTG-A-AA
1 ATTTATGAGTACAATGCATAA
6276 ATTTATGAGTACAATGCAT
1 ATTTATGAGTACAATGCAT
6295 TAGTTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
15 8 0.31
16 1 0.04
17 5 0.19
19 5 0.19
20 1 0.04
21 6 0.23
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
ATTTATGAGTACAATGCATAA
Found at i:7475 original size:13 final size:13
Alignment explanation
Indices: 7457--7504 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
7447 TCATGCACCC
7457 AAAACAATTTATT
1 AAAACAATTTATT
7470 AAAACAATTTATAAAT
1 AAAACAATTTAT---T
* *
7486 AAGACAATTTAAT
1 AAAACAATTTATT
7499 AAAACA
1 AAAACA
7505 GTAATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 18 0.62
16 11 0.38
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAACAATTTATT
Found at i:8531 original size:18 final size:18
Alignment explanation
Indices: 8508--8543 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
8498 TCCTTTAAGT
8508 TTGTCCATGCTTCCTTGC
1 TTGTCCATGCTTCCTTGC
8526 TTGTCCATGCTTCCTTGC
1 TTGTCCATGCTTCCTTGC
8544 ACTCCTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.33, G:0.17, T:0.44
Consensus pattern (18 bp):
TTGTCCATGCTTCCTTGC
Found at i:15230 original size:14 final size:15
Alignment explanation
Indices: 15211--15243 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
15201 AACAACTTCA
15211 TTTCTTTTT-TTCTT
1 TTTCTTTTTCTTCTT
15225 TTTCTTTTTCCTTCTT
1 TTTCTTTTT-CTTCTT
15241 TTT
1 TTT
15244 GCTCATTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTCTTCTT
Found at i:20499 original size:13 final size:12
Alignment explanation
Indices: 20469--20511 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
20459 CATCGATACC
20469 TCGATATATCCG
1 TCGATATATCCG
20481 TCGATATATCCG
1 TCGATATATCCG
*
20493 TTCGATATATCCA
1 -TCGATATATCCG
20506 TCGATA
1 TCGATA
20512 CCTGTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:20889 original size:20 final size:21
Alignment explanation
Indices: 20864--20902 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20854 GGATTTGCTA
*
20864 ATTGATTTAGTAAA-ATTGGG
1 ATTGATATAGTAAATATTGGG
20884 ATTGATATAGTAAATATTG
1 ATTGATATAGTAAATATTG
20903 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (21 bp):
ATTGATATAGTAAATATTGGG
Found at i:27890 original size:17 final size:16
Alignment explanation
Indices: 27868--27908 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
27858 TGGGTGTACT
27868 ATTTTTCCTTCACTAGG
1 ATTTTTCCTTCAC-AGG
27885 ATTTTTCC--CACAGG
1 ATTTTTCCTTCACAGG
*
27899 GTTTTTCCTT
1 ATTTTTCCTT
27909 TTGAAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 10 0.48
15 3 0.14
17 8 0.38
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (16 bp):
ATTTTTCCTTCACAGG
Found at i:28153 original size:28 final size:28
Alignment explanation
Indices: 28112--28165 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28102 TCCCAAATTT
* * *
28112 AAAAATTAAGGGGGTAAAGTGTCCCCGA
1 AAAAAGTAAAGGGGTAAAATGTCCCCGA
28140 AAAAAGTAAAGGGGTAAAATGTCCCC
1 AAAAAGTAAAGGGGTAAAATGTCCCC
28166 TCTGAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.17
Consensus pattern (28 bp):
AAAAAGTAAAGGGGTAAAATGTCCCCGA
Found at i:28943 original size:28 final size:28
Alignment explanation
Indices: 28906--28989 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
28896 AAAATTTAAC
* *
28906 TTTTATTATAATAGAGTTTTAGTAGTTT
1 TTTTTTTATAAAAGAGTTTTAGTAGTTT
* *
28934 TTTTTTTATAACAGAGTTTTAGTATTTT
1 TTTTTTTATAAAAGAGTTTTAGTAGTTT
*
28962 TTTTTTTGTAAAAAGAGTTTTAGTAGTT
1 TTTTTTTAT-AAAAGAGTTTTAGTAGTT
28990 ATAGCATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 33 0.67
29 16 0.33
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.57
Consensus pattern (28 bp):
TTTTTTTATAAAAGAGTTTTAGTAGTTT
Found at i:31516 original size:46 final size:46
Alignment explanation
Indices: 31449--31541 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
31439 AAATGCGCAT
*
31449 TTCAAAAGTTTGACAATCACTTCTCTTATTCAACAATCATCAATCA
1 TTCAAAAGTTTCACAATCACTTCTCTTATTCAACAATCATCAATCA
* *
31495 TTCAAAATTTTCATAATCACTTCTCTTATTCAACAATCATCAATCA
1 TTCAAAAGTTTCACAATCACTTCTCTTATTCAACAATCATCAATCA
31541 T
1 T
31542 CGTGGAGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (46 bp):
TTCAAAAGTTTCACAATCACTTCTCTTATTCAACAATCATCAATCA
Found at i:33048 original size:19 final size:19
Alignment explanation
Indices: 33021--33057 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33011 GCATTTGAAT
* *
33021 AAGATTTCAAATTCAACAG
1 AAGAATTCAAATCCAACAG
33040 AAGAATTCAAATCCAACA
1 AAGAATTCAAATCCAACA
33058 ATAGATAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (19 bp):
AAGAATTCAAATCCAACAG
Found at i:35864 original size:33 final size:33
Alignment explanation
Indices: 35766--35864 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
35756 TTTGAATTCT
* * *
35766 ATTGTTCCCACTAATATTATGCCTCAGAATGAA
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
* * * *
35799 ATTGCTGCCACTGATGTTGTGCTTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
35832 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
35865 TGATACGAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
Found at i:42419 original size:16 final size:16
Alignment explanation
Indices: 42398--42429 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42388 GTTATATCGA
*
42398 AAAATATAAAAAAAAT
1 AAAATAAAAAAAAAAT
42414 AAAATAAAAAAAAAAT
1 AAAATAAAAAAAAAAT
42430 TTCGACCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAAAAAAT
Found at i:47827 original size:30 final size:33
Alignment explanation
Indices: 47791--47860 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
47781 CATCGCATGC
* *
47791 GACATCGCATGG-G-A-CAACCGTCCAGAACCG
1 GACATCGCATGGCGCACCAACCGGCCACAACCG
* *
47821 GCCATCGCTTGGCGCACCAACCGGCCACAACCG
1 GACATCGCATGGCGCACCAACCGGCCACAACCG
47854 GACATCG
1 GACATCG
47861 ATTGGGTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
32 1 0.03
33 20 0.62
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.10
Consensus pattern (33 bp):
GACATCGCATGGCGCACCAACCGGCCACAACCG
Done.