Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012061.1 Corchorus capsularis cultivar CVL-1 contig12082, 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: 47547
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:344 original size:13 final size:13
Alignment explanation
Indices: 308--356 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
298 CTTAAATTTA
308 AAATTTATTAACC
1 AAATTTATTAACC
*
321 AAATTAATATTAGCC
1 AAATT--TATTAACC
336 AAATTTATTAACC
1 AAATTTATTAACC
349 AAATTTAT
1 AAATTTAT
357 AGTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 20 0.62
15 12 0.38
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATTTATTAACC
Found at i:596 original size:196 final size:197
Alignment explanation
Indices: 359--712 Score: 647
Period size: 196 Copynumber: 1.8 Consensus size: 197
349 AAATTTATAG
*
359 TAAAATTTATTTTACTATAATAATTCATACTTTAAACCGAAATATATCGGTGAATCGATCGAATT
1 TAAAATTTATTTTACTATAATAATTCATACTTTAAACCGAAATATATCGATGAATCGATCGAATT
* *
424 ATATTTTAACTTAAATTTA-AATTTATTAAACAAATTAATATTAGCCGAATGAACCAAATACTAT
66 ATATTTTAACTTAAATTCAGAATTTATTAAACAAATTAATATTAACCGAATGAACCAAATACTAT
488 GTTTGTAAAACATTAATCGAACCGAAATATTTCGGTTAATCGACCGAATTATATTTTAACTTAAA
131 GTTTGTAAAACATTAATCGAACCGAAATATTTCGGTTAATCGACCGAATTATATTTTAACTTAAA
553 TT
196 TT
555 TAAAATTTATTTTACTATAATAATTCATACTTTAAACCGAAATATATCGATGAATCGATCGAATT
1 TAAAATTTATTTTACTATAATAATTCATACTTTAAACCGAAATATATCGATGAATCGATCGAATT
* *
620 ATATTTTAACTTAAATTCAGAATTTATTAACCAAATTAATATTAACCGAATGAACCGAATACTAT
66 ATATTTTAACTTAAATTCAGAATTTATTAAACAAATTAATATTAACCGAATGAACCAAATACTAT
*
685 GTTTGTTAAACATTAATCGAACCGAAAT
131 GTTTGTAAAACATTAATCGAACCGAAAT
713 TTCCTATTCC
Statistics
Matches: 151, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
196 82 0.54
197 69 0.46
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (197 bp):
TAAAATTTATTTTACTATAATAATTCATACTTTAAACCGAAATATATCGATGAATCGATCGAATT
ATATTTTAACTTAAATTCAGAATTTATTAAACAAATTAATATTAACCGAATGAACCAAATACTAT
GTTTGTAAAACATTAATCGAACCGAAATATTTCGGTTAATCGACCGAATTATATTTTAACTTAAA
TT
Found at i:903 original size:97 final size:97
Alignment explanation
Indices: 737--916 Score: 342
Period size: 97 Copynumber: 1.9 Consensus size: 97
727 ATTAATCGAA
*
737 CCGAAATATATCGGTTAATCGACTGAATTATATTTTAACTTAAATTTAAAATTTATTTTACTATA
1 CCGAAATATATAGGTTAATCGACTGAATTATATTTTAACTTAAATTTAAAATTTATTTTACTATA
802 ATAATTCATACTTTAAACCGAAATATATCGGT
66 ATAATTCATACTTTAAACCGAAATATATCGGT
*
834 CCGAAATATTTAGGTTAATCGACTGAATTATATTTTAACTTAAATTTAAAATTTATTTTACTATA
1 CCGAAATATATAGGTTAATCGACTGAATTATATTTTAACTTAAATTTAAAATTTATTTTACTATA
899 ATAATTCATACTTTAAAC
66 ATAATTCATACTTTAAAC
917 ATCTTAATTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 81 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (97 bp):
CCGAAATATATAGGTTAATCGACTGAATTATATTTTAACTTAAATTTAAAATTTATTTTACTATA
ATAATTCATACTTTAAACCGAAATATATCGGT
Found at i:4931 original size:73 final size:74
Alignment explanation
Indices: 4812--4961 Score: 194
Period size: 73 Copynumber: 2.0 Consensus size: 74
4802 CAATACCCTC
* * * * * *
4812 TGGAAATTACTAAAGGCTCCCATCAACTTTTAATGTGGGAGAACCTTTTCG-CCCGTTTTGGTCT
1 TGGAAATTACTAAAGGCTCCCATCAACTTTCAATGAGGGACAACCTTTTAGCCCCCTTTTCGTCT
4876 TTTCTCGCT
66 TTTCTCGCT
* ** *
4885 TGGAATTTACTAAAGGCTCCTTTTAACTTTCAATGAGGGACAACCTTTTAGCCCCCTTTTCGTCT
1 TGGAAATTACTAAAGGCTCCCATCAACTTTCAATGAGGGACAACCTTTTAGCCCCCTTTTCGTCT
*
4950 TTTCTTGCT
66 TTTCTCGCT
4959 TGG
1 TGG
4962 TTAATTACCC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 43 0.66
74 22 0.34
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (74 bp):
TGGAAATTACTAAAGGCTCCCATCAACTTTCAATGAGGGACAACCTTTTAGCCCCCTTTTCGTCT
TTTCTCGCT
Found at i:5929 original size:72 final size:69
Alignment explanation
Indices: 5805--5936 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 69
5795 TGCACTATTT
* * * *
5805 TTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGTTCCTACCATTTTTTCCTTAGTGCATT
1 TTATATATAATTTTAGCATTTGGATGTAATTAATGATGCTCCCACCATTTTTTCCTTAGTGCATT
5870 TTAC
66 TTAC
* *
5874 TTATATATAATTTTAGCA-TTGAGATCATGTAATTAATGATGCTCCCACTATTTTTTCTTTAGT
1 TTATATATAATTTTAGCATTTG-G---ATGTAATTAATGATGCTCCCACCATTTTTTCCTTAGT
5937 TGTTAGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 3 0.06
69 18 0.34
72 32 0.60
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (69 bp):
TTATATATAATTTTAGCATTTGGATGTAATTAATGATGCTCCCACCATTTTTTCCTTAGTGCATT
TTAC
Found at i:6620 original size:2 final size:2
Alignment explanation
Indices: 6613--6647 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6603 TAATTACTGT
6613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6648 GCTTCGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10196 original size:31 final size:32
Alignment explanation
Indices: 10151--10211 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
10141 TCCAATTGGT
*
10151 CAACTTCTTGAAAGGTTTAGACTTAAATTGAG
1 CAACTTCTTGAAAGGTTTAGACTCAAATTGAG
10183 CAACTT-TTGAAAGGTTTAGACTCAAATTG
1 CAACTTCTTGAAAGGTTTAGACTCAAATTG
10212 GTGGCTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
CAACTTCTTGAAAGGTTTAGACTCAAATTGAG
Found at i:10466 original size:2 final size:2
Alignment explanation
Indices: 10459--10501 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
10449 AAGTTAGCTA
*
10459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10501 A
1 A
10502 AGAGTACGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10772 original size:124 final size:123
Alignment explanation
Indices: 10593--10906 Score: 524
Period size: 124 Copynumber: 2.6 Consensus size: 123
10583 ACTATTATAG
*
10593 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCTTTTTAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCTTTATAATTACTTTATTT
*
10658 TTATAATTTTACTATTTTTCAATAAAAATTTGGATATATTAAAATTTTTTAATATACAA
66 TTATAATTTTACTATTTTTCAATAAAAA-TTGGATATATTAAAATTTTTTAAAATACAA
* *
10717 TTTTATTCTACTAAAAACTATATTTTTATTCAATTAAATCTAATATCTCTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCTTTATAATTACTTTATTT
10782 TTATAATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTTAAAATACAA
66 TTATAATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTTAAAATACAA
* * * *
10840 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATAATTATTTTCTT
1 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCT-AATATCTTTATAATTACTTTATT
10903 TTTA
65 TTTA
10907 CCATTTTAAT
Statistics
Matches: 179, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
122 19 0.11
123 70 0.39
124 90 0.50
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.52
Consensus pattern (123 bp):
TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCTTTATAATTACTTTATTT
TTATAATTTTACTATTTTTCAATAAAAATTGGATATATTAAAATTTTTTAAAATACAA
Found at i:13842 original size:24 final size:23
Alignment explanation
Indices: 13815--13883 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
13805 CTTCAACATC
13815 CTTTTCTTTTTCCTGTTGCTCACG
1 CTTTTCTTTTT-CTGTTGCTCACG
* * *
13839 CTTTTTCTTCTGCTGTTGCTCACT
1 C-TTTTCTTTTTCTGTTGCTCACG
*
13863 CTTTTTCTTTTTCTGCTGCTC
1 C-TTTTCTTTTTCTGTTGCTC
13884 TTTGACTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 30 0.79
25 8 0.21
ACGTcount: A:0.03, C:0.29, G:0.12, T:0.57
Consensus pattern (23 bp):
CTTTTCTTTTTCTGTTGCTCACG
Found at i:16332 original size:10 final size:10
Alignment explanation
Indices: 16317--16341 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16307 GAGGACTCTA
16317 GAATTTTCTG
1 GAATTTTCTG
16327 GAATTTTCTG
1 GAATTTTCTG
16337 GAATT
1 GAATT
16342 GTGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:36119 original size:31 final size:31
Alignment explanation
Indices: 36081--36156 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
36071 AGAAGCAAAA
*
36081 TTGGGAGAATAAGTTTCGGCTAGCAGAATTT
1 TTGGGAGAATAAGTTTCGGCTAGAAGAATTT
36112 TTGGGAGAATAAGTTTCGGCTAGAAGAATTT
1 TTGGGAGAATAAGTTTCGGCTAGAAGAATTT
*
36143 TTGGGAGAAGAAGT
1 TTGGGAGAATAAGT
36157 CGACTAGAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.30
Consensus pattern (31 bp):
TTGGGAGAATAAGTTTCGGCTAGAAGAATTT
Found at i:36153 original size:15 final size:15
Alignment explanation
Indices: 36105--36154 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
36095 TTCGGCTAGC
36105 AGAATTTTTGGGAGA
1 AGAATTTTTGGGAGA
* * * *
36120 ATAAGTTTCGGCTAGA
1 AGAATTTTTGG-GAGA
36136 AGAATTTTTGGGAGA
1 AGAATTTTTGGGAGA
36151 AGAA
1 AGAA
36155 GTCGACTAGA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (15 bp):
AGAATTTTTGGGAGA
Found at i:36574 original size:59 final size:59
Alignment explanation
Indices: 36500--36621 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 59
36490 TTGAGTCATA
* * *
36500 TGATAGTTTTTGCATGAGTTGCATGAAAACCTAGGATTACAATTTGATTGTTGATGGAT
1 TGATAGTTTTTGCATGAGTTGCATGAAAACATAGGATAAAAATTTGATTGTTGATGGAT
* **
36559 TGATAGTTTTTGCATGAGTTGCATGAGAACATAGGATAAAAATTTGATTGTTTTTGGAT
1 TGATAGTTTTTGCATGAGTTGCATGAAAACATAGGATAAAAATTTGATTGTTGATGGAT
36618 TGAT
1 TGAT
36622 CTTTTATTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.40
Consensus pattern (59 bp):
TGATAGTTTTTGCATGAGTTGCATGAAAACATAGGATAAAAATTTGATTGTTGATGGAT
Done.