Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007282.1 Corchorus capsularis cultivar CVL-1 contig07303, 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: 35495
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:9517 original size:30 final size:30
Alignment explanation
Indices: 9477--9539 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9467 TGTCTTCAAG
9477 TCCATAATAAGTCCTT-GGCGCATCATTCCC
1 TCCATAATAAG-CCTTGGGCGCATCATTCCC
*
9507 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATAATAAGCCTTGGGCGCATCATTCCC
9537 TCC
1 TCC
9540 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCC
Found at i:9827 original size:31 final size:31
Alignment explanation
Indices: 9767--9904 Score: 132
Period size: 31 Copynumber: 4.5 Consensus size: 31
9757 ACGGTGTCCG
* * * *
9767 ACGTGGCATGGCACGTGTACCAAAGAGTGAC
1 ACGTGGCATGCCACATGTATCAAAAAGTGAC
* * *
9798 ATGTGGCACGCCACATGTATAAAAAAGTGAC
1 ACGTGGCATGCCACATGTATCAAAAAGTGAC
* * * * *
9829 ACATGTCATGTCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTATCAAAAAGTGAC
* *
9860 ACGTGGCATGCCACATGTTTCAAAAAGTGGC
1 ACGTGGCATGCCACATGTATCAAAAAGTGAC
* *
9891 ACATGTCATGCCAC
1 ACGTGGCATGCCAC
9905 GTGCACAAAT
Statistics
Matches: 83, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTATCAAAAAGTGAC
Found at i:9875 original size:62 final size:62
Alignment explanation
Indices: 9773--9907 Score: 198
Period size: 62 Copynumber: 2.2 Consensus size: 62
9763 TCCGACGTGG
* * *
9773 CATGGCACGTGTACCAAAGAGTGACATGTGGCACGCCACATGTATAAAAAAGTGACACATGT
1 CATGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTATAAAAAAGTGACACATGT
* * * * *
9835 CATGTCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTTTCAAAAAGTGGCACATGT
1 CATGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTATAAAAAAGTGACACATGT
9897 CATGCCACGTG
1 CATGCCACGTG
9908 CACAAATGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.21
Consensus pattern (62 bp):
CATGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATGTATAAAAAAGTGACACATGT
Found at i:19441 original size:21 final size:21
Alignment explanation
Indices: 19415--19454 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19405 CCGCGGGCTA
*
19415 CCCACTATCGGGTGACCCCTG
1 CCCACTACCGGGTGACCCCTG
*
19436 CCCACTCCCGGGTGACCCC
1 CCCACTACCGGGTGACCCC
19455 AGAAACTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.50, G:0.23, T:0.15
Consensus pattern (21 bp):
CCCACTACCGGGTGACCCCTG
Found at i:20397 original size:49 final size:49
Alignment explanation
Indices: 20224--20703 Score: 587
Period size: 49 Copynumber: 9.9 Consensus size: 49
20214 GAAATTAGTA
* *
20224 CCTTCCATCCGGGAAGGGCATTTTGGGAAA-AGTAGGTAAAAAA-AGTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
* * * * *
20271 CTTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAG-GTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
* * * *
20319 CTTTCTGTCCAGGAAGGGCATTTTGGGAAATAGTAGGTAAAAAAGAGTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
* * *
20368 TCTTCCGTCCGGGAAGGGCATTTTAGGAAATAGCAGGTAAAAATA-AATG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAA-AGAGTG
* * *
20417 CCTTCCGTCTGGGAAGGGCATTTTAGGAAATAGAAGGTAAAAAAGAGTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
*
20466 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAATG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
** * *
20515 CCTTCCGTCCTAGAATGGCATTTTGGGAAATAGCAGGTTAAAAAGAGTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
* *
20564 CCTTCCGTGCGGGAAGGGCGTTTTGGGAAATA-CTAGGTAAAGATAA-A-TG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGC-AGGTAAA-A-AAGAGTG
* * *
20613 CCTTCCATTCGGGAAGGGCATTTTGGGAAATAGCAAGTAAAAAAGAGTG
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
* * * * *
20662 TCTTCCGCCCGGGAAGGGCGTTTTAGGAAAAAGCAGGTAAAA
1 CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAA
20704 CTGAAAAATT
Statistics
Matches: 371, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
47 29 0.08
48 55 0.15
49 281 0.76
50 4 0.01
51 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (49 bp):
CCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTG
Found at i:23710 original size:40 final size:40
Alignment explanation
Indices: 23655--23739 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
23645 GTTACACTAC
23655 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
23695 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
*
23735 AAACA
1 GAACA
23740 AATTAAAACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (40 bp):
GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
Found at i:24403 original size:61 final size:62
Alignment explanation
Indices: 24277--24899 Score: 411
Period size: 61 Copynumber: 9.9 Consensus size: 62
24267 GTAACCAAGG
* * * * * * *
24277 AAGACCTGTCCGAGGTTTGAAACTTG-AGAAGACCAGTCCGTGGTGGACT-TTAAAAATAAGG
1 AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTCGA-TATTGAAAATGAGA
* * *
24338 AAGACTTGTCTAAGGTCTGAAACTT-AAGAAGACCAGTCTGTGGTCGATATTGAAAACGAGA
1 AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTCGATATTGAAAATGAGA
* * * * *
24399 AAGACCTGTCTGAGGTCTGGAA-TTGAAGAAGACTAGTCTATGGTCGATATTGAAATTGAGG
1 AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTCGATATTGAAAATGAGA
* * * * *
24460 AAGACCTGTCTAAGGTCTAAAATTGAAAATCTGAGATAGAGACTAGTCTGTGGTCGATATTGAAG
1 AAGACCTGTCTGAGGTC------TGAAACT-TGA-AGA-AGACCAGTCTGTGGTCGATATTGAAA
* *
24525 TTGAGG
57 ATGAGA
* * ** * *
24531 AAGACCTGCCTGAGGTC-GAGAA-TTGAAGAGGACCAAACCGTGGTCGACT-TTGAAAATTAAGA
1 AAGACCTGTCTGAGGTCTGA-AACTTGAAGAAGACCAGTCTGTGGTCGA-TATTGAAAA-TGAGA
* * * *
24593 AAGACCTGTTTGAGGTCTGAAAC-TGCAA-AAGACAAGTCCGTGGTCGA-ATTTGAAAACTGATA
1 AAGACCTGTCTGAGGTCTGAAACTTG-AAGAAGACCAGTCTGTGGTCGATA-TTGAAAA-TGAGA
* * * *
24655 AAGACCTGTCTGAGGTCTG-AAGTTGAAGAAGACTAATCTGTGGTC--TACTTGAAAAACTAAGA
1 AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTCGATA-TTG-AAAA-TGAGA
* * * *
24717 AAGACTTGTCTGAAGTC---AACTTTGAAGAAGACCAGTCTGTGGTCGATATTGAAATTGAGG
1 AAGACCTGTCTGAGGTCTGAAAC-TTGAAGAAGACCAGTCTGTGGTCGATATTGAAAATGAGA
* * * *
24777 AAGACCTATCTGAGGTCAACTTTGAAGA-TCTGAGAAAGAGACCAGTCTGTGGTCGCTTTTGAAA
1 AAGACCTGTCTGAGGT---C--TGAA-ACT-TGA-AGA-AGACCAGTCTGTGGTCGATATTGAAA
* * *
24841 TTAAGG
57 ATGAGA
*
24847 AAGACCTGTCTGAGGTCTGAAAC-TGAAGAAGACCAGTCCGTGGTCTG-TATTGA
1 AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTC-GATATTGA
24900 TACTTGAGAT
Statistics
Matches: 449, Mismatches: 71, Indels: 84
0.74 0.12 0.14
Matches are distributed among these distances:
60 21 0.05
61 184 0.41
62 113 0.25
63 13 0.03
64 4 0.01
65 6 0.01
67 6 0.01
68 5 0.01
69 6 0.01
70 46 0.10
71 45 0.10
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (62 bp):
AAGACCTGTCTGAGGTCTGAAACTTGAAGAAGACCAGTCTGTGGTCGATATTGAAAATGAGA
Found at i:24549 original size:33 final size:33
Alignment explanation
Indices: 24365--24557 Score: 105
Period size: 33 Copynumber: 5.8 Consensus size: 33
24355 TGAAACTTAA
* * * **
24365 GAAGACCAGTCTGTGGTCGATATTGAAAACGAG
1 GAAGACCTGTCTGAGGTCGAAATTGAAATTGAG
* * *
24398 AAAGACCTGTCTGAGGTC-----TGGAATTGAA
1 GAAGACCTGTCTGAGGTCGAAATTGAAATTGAG
*
24426 GAAGA-CTAGTCT-ATGGTCGATATTGAAATTGAG
1 GAAGACCT-GTCTGA-GGTCGAAATTGAAATTGAG
* *
24459 GAAGACCTGTCTAAGGTCTAAAATTGAAAATCTGA-
1 GAAGACCTGTCTGAGGTC-GAAATTG-AAAT-TGAG
* * * *
24494 GATAGAGACTAGTCTGTGGTCGATATTGAAGTTGAG
1 GA-AGA-CCT-GTCTGAGGTCGAAATTGAAATTGAG
*
24530 GAAGACCTGCCTGAGGTCGAGAATTGAA
1 GAAGACCTGTCTGAGGTCGA-AATTGAA
24558 GAGGACCAAA
Statistics
Matches: 121, Mismatches: 22, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
27 3 0.02
28 18 0.15
33 46 0.38
34 16 0.13
35 12 0.10
36 11 0.09
37 7 0.06
38 8 0.07
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (33 bp):
GAAGACCTGTCTGAGGTCGAAATTGAAATTGAG
Found at i:24607 original size:62 final size:62
Alignment explanation
Indices: 24531--24891 Score: 247
Period size: 62 Copynumber: 5.7 Consensus size: 62
24521 GAAGTTGAGG
* * * *
24531 AAGACCTGCCTGAGGTC-GAGAATTGAAGAGGACCAAACCGTGGTCGACTTTGAAAATTAAGA
1 AAGACCTGTCTGAGGTCTGA-AATTGAAGAAGACCAATCCGTGGTCGACTTTGAAAACTAAGA
* * * * *
24593 AAGACCTGTTTGAGGTCTGAAACTGCAA-AAGA-CAAGTCCGTGGTCGAATTTGAAAACTGATA
1 AAGACCTGTCTGAGGTCTGAAATTG-AAGAAGACCAA-TCCGTGGTCGACTTTGAAAACTAAGA
* * * *
24655 AAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACTAATCTGTGGTCTAC-TTGAAAAACTAAGA
1 AAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAATCCGTGGTCGACTTTG-AAAACTAAGA
* * * * * * * *
24717 AAGACTTGTCTGAAGTC--AACTTTGAAGAAGACCAGTCTGTGGTCGA-TATTG-AAATTGAGG
1 AAGACCTGTCTGAGGTCTGAA-ATTGAAGAAGACCAATCCGTGGTCGACT-TTGAAAACTAAGA
* * * *
24777 AAGACCTATCTGAGGTCAACTTTGAAGATCTGAGAAAGAGACCAGTCTGTGGTCG-CTTTTG-AA
1 AAGACCTGTCTGAGGT---C--TGAA-AT-TGA-AGA-AGACCAATCCGTGGTCGAC-TTTGAAA
* *
24840 ATTAAGG
56 ACTAAGA
* *
24847 AAGACCTGTCTGAGGTCTGAAACTGAAGAAGACCAGTCCGTGGTC
1 AAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAATCCGTGGTC
24892 TGTATTGATA
Statistics
Matches: 240, Mismatches: 38, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
60 21 0.09
61 45 0.19
62 106 0.44
63 10 0.04
64 1 0.00
65 4 0.02
67 4 0.02
68 3 0.01
69 2 0.01
70 43 0.18
71 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.24
Consensus pattern (62 bp):
AAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAATCCGTGGTCGACTTTGAAAACTAAGA
Found at i:24614 original size:255 final size:256
Alignment explanation
Indices: 24197--24699 Score: 646
Period size: 255 Copynumber: 2.0 Consensus size: 256
24187 CTGATTAAAG
* *
24197 AATTGAGAAAGACCTGTCTGAGGTCTAAAATTGAAAATCTGAGATTGAGACTAATCTCTGGTCGA
1 AATTGAGAAAGACCTGTCTAAGGTCTAAAATTGAAAATCTGAGATAGAGACTAATCTCTGGTCGA
* * ** *
24262 CTTTTGTAACCAAGGAAGACCTGTCCGAGGTTTGAAACTTGAGAAGACCAGTCCGTGGTGGACTT
66 CTATTGTAACCAAGGAAGACCTGTCCGAGGTTCGAAACTTGAGAAGACCAAACCGTGGTCGACTT
* * * * *
24327 TAAAAATAAGGAAGACTTGTCTAAGGTCTGAAACT-TAAGAAGACCAGTCTGTGGTCG-ATATTG
131 TAAAAATAAGAAAGACCTGTCTAAGGTCTGAAACTGCAA-AAGACAAGTCCGTGGTCGAAT-TTG
*
24390 AAAAC-GAGAAAGACCTGTCTGAGGTCTGGAA-TTGAAGAAGACTAGTCTATGGTCGATATTGA
194 AAAACTGAGAAAGACCTGTCTGAGGTCT-GAAGTTGAAGAAGACTAATCTATGGTCGATATTGA
* * *
24452 AATTGAGGAAGACCTGTCTAAGGTCTAAAATTGAAAATCTGAGATAGAGACTAGTCTGTGGTCGA
1 AATTGAGAAAGACCTGTCTAAGGTCTAAAATTGAAAATCTGAGATAGAGACTAATCTCTGGTCGA
*** *
24517 -TATTG-AAGTTGAGGAAGACCTG-CCTGAGG-TCGAGAA-TTGAAGAGGACCAAACCGTGGTCG
66 CTATTGTAA-CCAAGGAAGACCTGTCC-GAGGTTCGA-AACTTG-AGAAGACCAAACCGTGGTCG
* * *
24577 ACTTTGAAAATTAAGAAAGACCTGTTTGAGGTCTGAAACTGCAAAAGACAAGTCCGTGGTCGAAT
127 ACTTT-AAAAATAAGAAAGACCTGTCTAAGGTCTGAAACTGCAAAAGACAAGTCCGTGGTCGAAT
* *
24642 TTGAAAACTGATAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACTAATCTGTGGTC
191 TTGAAAACTGAGAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACTAATCTATGGTC
24700 TACTTGAAAA
Statistics
Matches: 214, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
253 10 0.05
254 42 0.20
255 116 0.54
256 46 0.21
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (256 bp):
AATTGAGAAAGACCTGTCTAAGGTCTAAAATTGAAAATCTGAGATAGAGACTAATCTCTGGTCGA
CTATTGTAACCAAGGAAGACCTGTCCGAGGTTCGAAACTTGAGAAGACCAAACCGTGGTCGACTT
TAAAAATAAGAAAGACCTGTCTAAGGTCTGAAACTGCAAAAGACAAGTCCGTGGTCGAATTTGAA
AACTGAGAAAGACCTGTCTGAGGTCTGAAGTTGAAGAAGACTAATCTATGGTCGATATTGA
Found at i:24802 original size:33 final size:33
Alignment explanation
Indices: 24765--24863 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 33
24755 GTGGTCGATA
24765 TTGAAATTGAGGAAGACCTATCTGAGGTCAAC-T
1 TTGAAATTGAGGAAGACCTATCTGAGGTC-ACTT
* * *
24798 TTGAAGATCTGAGAAAGAGACC-AGTCTGTGGTCGCTT
1 TTGAA-AT-TGAG-GA-AGACCTA-TCTGAGGTCACTT
* *
24835 TTGAAATTAAGGAAGACCTGTCTGAGGTC
1 TTGAAATTGAGGAAGACCTATCTGAGGTC
24864 TGAAACTGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
33 18 0.35
34 3 0.06
35 7 0.13
36 5 0.10
37 19 0.37
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (33 bp):
TTGAAATTGAGGAAGACCTATCTGAGGTCACTT
Found at i:25319 original size:17 final size:18
Alignment explanation
Indices: 25285--25320 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
25275 TATCAATCTA
25285 CTTTTGATAACTTTGCCCC
1 CTTTTGATAAC-TTGCCCC
25304 CTTTTGATAA-TTGCCCC
1 CTTTTGATAACTTGCCCC
25321 ATTACTGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (18 bp):
CTTTTGATAACTTGCCCC
Found at i:25536 original size:13 final size:13
Alignment explanation
Indices: 25518--25543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25508 AAGATATGGA
25518 TAGATAACAAAGG
1 TAGATAACAAAGG
25531 TAGATAACAAAGG
1 TAGATAACAAAGG
25544 AACATCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
TAGATAACAAAGG
Found at i:30293 original size:33 final size:32
Alignment explanation
Indices: 30229--30305 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
30219 AAGCCGCGCA
* *
30229 ACACCGGCCACGCGACTTGGAGATGCCCGGCC
1 ACACCGGCCACGCGACATGGACATGCCCGGCC
*
30261 ATCACCGGCCACGCGACAT-GACCATGCTCGGCC
1 A-CACCGGCCACGCGACATGGA-CATGCCCGGCC
30294 ACAACCGGCCAC
1 AC-ACCGGCCAC
30306 ATGACTCAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (32 bp):
ACACCGGCCACGCGACATGGACATGCCCGGCC
Done.