Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007361.1 Corchorus capsularis cultivar CVL-1 contig07382, 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: 50894
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5352 original size:16 final size:16
Alignment explanation
Indices: 5333--5386 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5323 AACCTAAACT
5333 CGAAAAAACCCGAACC
1 CGAAAAAACCCGAACC
* * *
5349 CGAAAAAGCTCAAACC
1 CGAAAAAACCCGAACC
* *
5365 CAAAAAAACCCGAATC
1 CGAAAAAACCCGAACC
5381 CGAAAA
1 CGAAAA
5387 TTTATGAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.54, C:0.31, G:0.11, T:0.04
Consensus pattern (16 bp):
CGAAAAAACCCGAACC
Found at i:10392 original size:28 final size:30
Alignment explanation
Indices: 10322--10400 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
10312 AGCTTTGACA
* **
10322 CCAAGTGGAAACCCACACTCAAATACAATC
1 CCAAGTGCAAACCCACACTTGAATACAATC
10352 CCAAGTGCAAACCCACACTTGAAT-CAA-C
1 CCAAGTGCAAACCCACACTTGAATACAATC
*
10380 CCAAG-GCACAACCCGCACTTG
1 CCAAGTGCA-AACCCACACTTG
10401 TAAAAACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 3 0.07
28 17 0.39
29 3 0.07
30 21 0.48
ACGTcount: A:0.38, C:0.37, G:0.13, T:0.13
Consensus pattern (30 bp):
CCAAGTGCAAACCCACACTTGAATACAATC
Found at i:14827 original size:6 final size:6
Alignment explanation
Indices: 14816--14848 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
14806 TTAGTGATTC
*
14816 GGTTTA GGTTTA GGTTTA GGTTTA TGTTT- GGTT
1 GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTT
14849 GAAAGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 3 0.12
6 22 0.88
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (6 bp):
GGTTTA
Found at i:17950 original size:44 final size:44
Alignment explanation
Indices: 17887--18013 Score: 182
Period size: 44 Copynumber: 2.9 Consensus size: 44
17877 GGGCTCTACT
*
17887 AACCTCAAAAATGGCTTCAATCTCCTTCAAAATAGCTTCGTTTC
1 AACCTCAAAAATGGCTTCAACCTCCTTCAAAATAGCTTCGTTTC
* * *
17931 AACCTCAAAAGTGGCTTCAACCTCTTTCAAAATAGTTTCGTTTC
1 AACCTCAAAAATGGCTTCAACCTCCTTCAAAATAGCTTCGTTTC
* * * *
17975 AGCCTCAAAATTGGCTTTAGCCTCCTTCAAAATAGCTTC
1 AACCTCAAAAATGGCTTCAACCTCCTTCAAAATAGCTTC
18014 TACATCAAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (44 bp):
AACCTCAAAAATGGCTTCAACCTCCTTCAAAATAGCTTCGTTTC
Found at i:23607 original size:62 final size:62
Alignment explanation
Indices: 23504--23666 Score: 193
Period size: 62 Copynumber: 2.6 Consensus size: 62
23494 GACGTGGCAT
* * * * * *
23504 GCCACGTATACCAAAAAGTTACATGTGGCACGTCACGTGTACCAAAAAGTGACACAT-ATCAC
1 GCCACGTGTTCCAAAAAGTGACATGTGGCATGACACATGTACCAAAAAGTGACACATGA-CAC
* * * *
23566 GCCACGTGTTCCAAAAAGTGACACGCGGCATGACACATGTACCAAAAAGTGACACGTGACAT
1 GCCACGTGTTCCAAAAAGTGACATGTGGCATGACACATGTACCAAAAAGTGACACATGACAC
* * *
23628 GCCACATGTTTCAAAAAGTGACATGTGGCATGCCACATG
1 GCCACGTGTTCCAAAAAGTGACATGTGGCATGACACATG
23667 CAAAAAAGGA
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
62 84 0.99
63 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (62 bp):
GCCACGTGTTCCAAAAAGTGACATGTGGCATGACACATGTACCAAAAAGTGACACATGACAC
Found at i:23621 original size:31 final size:31
Alignment explanation
Indices: 23495--23666 Score: 173
Period size: 31 Copynumber: 5.5 Consensus size: 31
23485 AGGGTGTCCG
* * *
23495 ACGTGGCATGCCACGTATACCAAAAAGTTAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* * * *
23526 ATGTGGCACGTCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* ** * * *
23557 ACATATCACGCCACGTGTTCCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* *
23588 ACGCGGCATGACACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* **
23619 ACGTGACATGCCACATGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
*
23650 ATGTGGCATGCCACATG
1 ACGTGGCATGCCACATG
23667 CAAAAAAGGA
Statistics
Matches: 115, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGAC
Found at i:25143 original size:13 final size:13
Alignment explanation
Indices: 25125--25149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25115 AATATAATTA
25125 AATTATTATTTTT
1 AATTATTATTTTT
25138 AATTATTATTTT
1 AATTATTATTTT
25150 AATGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTATTATTTTT
Found at i:29219 original size:10 final size:8
Alignment explanation
Indices: 29197--29258 Score: 61
Period size: 9 Copynumber: 7.0 Consensus size: 8
29187 CCCCTTATCA
29197 ATATCATAT
1 ATAT-ATAT
29206 ATCATATCAT
1 AT-ATAT-AT
29216 ATCATATAT
1 AT-ATATAT
29225 ATCATATAT
1 AT-ATATAT
*
29234 CATATATAC
1 -ATATATAT
29243 ATATATAT
1 ATATATAT
29251 ATATATAT
1 ATATATAT
29259 TTAAAACAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
8 15 0.31
9 20 0.42
10 13 0.27
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATATAT
Found at i:29224 original size:2 final size:2
Alignment explanation
Indices: 29197--29258 Score: 61
Period size: 2 Copynumber: 28.0 Consensus size: 2
29187 CCCCTTATCA
29197 AT AT CAT AT AT CAT AT CAT AT CAT AT AT AT CAT AT AT CAT AT AT
1 AT AT -AT AT AT -AT AT -AT AT -AT AT AT AT -AT AT AT -AT AT AT
*
29241 AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
29259 TTAAAACAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 40 0.77
3 12 0.23
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29227 original size:26 final size:24
Alignment explanation
Indices: 29197--29256 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 24
29187 CCCCTTATCA
29197 ATATCATATATCATATCATATCATAT
1 ATATCATATATCATAT-ATA-CATAT
29223 ATATCATATATCATATATACATAT
1 ATATCATATATCATATATACATAT
29247 ATAT-ATATAT
1 ATATCATATAT
29257 ATTTAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.18
24 9 0.26
25 3 0.09
26 16 0.47
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATCATATATCATATATACATAT
Found at i:31962 original size:28 final size:28
Alignment explanation
Indices: 31909--31965 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
31899 GACTATTTAA
*
31909 ATTTATATACTCAATTGATGCCAAAAAT
1 ATTTATATACTCAATTGATACCAAAAAT
* *
31937 ATTTATCTACTCAATT-ATTACTAAAAAT
1 ATTTATATACTCAATTGA-TACCAAAAAT
31965 A
1 A
31966 GAAAAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTTATATACTCAATTGATACCAAAAAT
Found at i:39206 original size:30 final size:30
Alignment explanation
Indices: 39170--39232 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
39160 TTTCTTAAGA
*
39170 AAAAACTTTCTA-GTTTTAAACTTTCTATAG
1 AAAAACTTTCTACCTTTT-AACTTTCTATAG
*
39200 AAAAACTTTCTACCTTTTTACTTTCTATAG
1 AAAAACTTTCTACCTTTTAACTTTCTATAG
39230 AAA
1 AAA
39233 CTTCCAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAAACTTTCTACCTTTTAACTTTCTATAG
Found at i:40196 original size:21 final size:21
Alignment explanation
Indices: 40171--40222 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40161 AAATTAACCA
*
40171 TTAATAAGGTTACTGAAA-TGC
1 TTAATAAGGTTACT-AAAGAGC
*
40192 TTAATAAGCTTACTAAAGAGC
1 TTAATAAGGTTACTAAAGAGC
*
40213 TAAATAAGGT
1 TTAATAAGGT
40223 GATTTACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (21 bp):
TTAATAAGGTTACTAAAGAGC
Found at i:41792 original size:40 final size:41
Alignment explanation
Indices: 41708--41793 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 41
41698 GATGATAAAA
* *
41708 AAAACTTATCCAAGTTACCAAAAAGTTTAACAGGAGTATAT
1 AAAACTTATCCAAGTTACCAAAAAGCTTAACAGAAGTATAT
*
41749 AAAACTT-TCCAAGGTTACTAAAAAGCTTAACA-AAGT-TACT
1 AAAACTTATCCAA-GTTACCAAAAAGCTTAACAGAAGTATA-T
41789 AAAAC
1 AAAAC
41794 GTATATATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
39 2 0.05
40 14 0.35
41 24 0.60
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (41 bp):
AAAACTTATCCAAGTTACCAAAAAGCTTAACAGAAGTATAT
Found at i:42087 original size:22 final size:22
Alignment explanation
Indices: 42060--42129 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
42050 CACGATTATG
42060 AAAATTTTAGTAAAGGTTACTA
1 AAAATTTTAGTAAAGGTTACTA
* * * *
42082 AAAATTGTAATAAGGGATACTA
1 AAAATTTTAGTAAAGGTTACTA
**
42104 AAACGTTTAGT-AAGGTTACTTA
1 AAAATTTTAGTAAAGGTTAC-TA
42126 AAAA
1 AAAA
42130 CTTATTAAGT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (22 bp):
AAAATTTTAGTAAAGGTTACTA
Found at i:42096 original size:21 final size:20
Alignment explanation
Indices: 42072--42145 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 20
42062 AATTTTAGTA
42072 AAGGTTACTAAAAATTGTAAT
1 AAGGTTACTAAAAATT-TAAT
* * *
42093 AAGGGATACTAAAACGTTTAGT
1 AA-GGTTACTAAAA-ATTTAAT
* *
42115 AAGGTTACTTAAAAACTTATT
1 AAGGTTAC-TAAAAATTTAAT
42136 AA-GTTACTAA
1 AAGGTTACTAA
42146 CAATGTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.07
20 5 0.12
21 13 0.30
22 20 0.47
23 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (20 bp):
AAGGTTACTAAAAATTTAAT
Found at i:42451 original size:19 final size:20
Alignment explanation
Indices: 42412--42450 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42402 AAAAAAATAC
42412 TTCATAAGGTTACTATAAAA
1 TTCATAAGGTTACTATAAAA
42432 TTCATAA-GTTAACTATAAA
1 TTCATAAGGTT-ACTATAAA
42451 TCTTACAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCATAAGGTTACTATAAAA
Found at i:42610 original size:87 final size:87
Alignment explanation
Indices: 42513--42692 Score: 326
Period size: 87 Copynumber: 2.1 Consensus size: 87
42503 TAAGATCATT
42513 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTTAAAAA-CTTTTAAGTTTAA
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTA-TTTAAAAAGCTTTTAAGTTTAA
42577 TGAAAAATTTATAAGCTTACCAA
65 TGAAAAATTTATAAGCTTACCAA
42600 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
*
42665 GAAAATTTTATAAGCTTACCAA
66 GAAAAATTTATAAGCTTACCAA
*
42687 GAAAAT
1 AAAAAT
42693 TTACAAGGTT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
86 8 0.09
87 82 0.91
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (87 bp):
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
GAAAAATTTATAAGCTTACCAA
Found at i:42751 original size:19 final size:21
Alignment explanation
Indices: 42727--42774 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
42717 CCAATTACAA
*
42727 TAAAAGTTAAAT-AGTTTA-C
1 TAAAAGTTAAATAAGATTACC
*
42746 TAAAAGCTAAATAAGATTACC
1 TAAAAGTTAAATAAGATTACC
42767 TAAAAGTT
1 TAAAAGTT
42775 TTTCAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (21 bp):
TAAAAGTTAAATAAGATTACC
Found at i:43175 original size:27 final size:27
Alignment explanation
Indices: 43135--43186 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
43125 TAAGGTGACT
*
43135 AAAAAACTTTATAAGG-CCAAAAAAGG
1 AAAAAAATTTATAAGGTCCAAAAAAGG
43161 AAAAAAATTTAATAAGGTCCAAAAAA
1 AAAAAAATTT-ATAAGGTCCAAAAAA
43187 AACTCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.17
Consensus pattern (27 bp):
AAAAAAATTTATAAGGTCCAAAAAAGG
Found at i:47481 original size:111 final size:111
Alignment explanation
Indices: 47337--47559 Score: 419
Period size: 111 Copynumber: 2.0 Consensus size: 111
47327 AACAATCTAT
* *
47337 ATTATAATAGGGTAAATAACTATAGACATCATTGTTTGGTTATGTATACAGTATATTGTGTCTTT
1 ATTATAATAGGGTAAATAACTATAGAAACCATTGTTTGGTTATGTATACAGTATATTGTGTCTTT
*
47402 CAACTTTAAATCCATCTAAATGCATTCAACAAATCAATCTATACCA
66 CAACTTTAAATCCATCTAAATGCATTCAACAAACCAATCTATACCA
47448 ATTATAATAGGGTAAATAACTATAGAAACCATTGTTTGGTTATGTATACAGTATATTGTGTCTTT
1 ATTATAATAGGGTAAATAACTATAGAAACCATTGTTTGGTTATGTATACAGTATATTGTGTCTTT
47513 CAACTTTAAATCCATCTAAATGCATTCAACAAACCAATCTATACCA
66 CAACTTTAAATCCATCTAAATGCATTCAACAAACCAATCTATACCA
47559 A
1 A
47560 CGAGGGGTAG
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (111 bp):
ATTATAATAGGGTAAATAACTATAGAAACCATTGTTTGGTTATGTATACAGTATATTGTGTCTTT
CAACTTTAAATCCATCTAAATGCATTCAACAAACCAATCTATACCA
Found at i:47890 original size:11 final size:12
Alignment explanation
Indices: 47875--47931 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
47865 TTCAAAAATA
47875 CCCGAACCCGA-
1 CCCGAACCCGAT
*
47886 CCCGAGA-CCGAG
1 CCCGA-ACCCGAT
*
47898 ACC-AAGCCCGAT
1 CCCGAA-CCCGAT
47910 CCCG-ACCCGAT
1 CCCGAACCCGAT
47921 CCCGAACCCGA
1 CCCGAACCCGA
47932 AATATAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
10 1 0.03
11 20 0.54
12 16 0.43
ACGTcount: A:0.26, C:0.49, G:0.21, T:0.04
Consensus pattern (12 bp):
CCCGAACCCGAT
Done.