Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012873.1 Corchorus capsularis cultivar CVL-1 contig12894, 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: 84959
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3222 original size:41 final size:41
Alignment explanation
Indices: 3164--3241 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
3154 TTGAAATTAG
*
3164 TCAGTTCCAATCGTAAACCGAAAAACCCAACACGAATTTAC
1 TCAGTTCCAATCATAAACCGAAAAACCCAACACGAATTTAC
* * *
3205 TCAGTTTCAATCATAAACCGAAGAACCCGACACGAAT
1 TCAGTTCCAATCATAAACCGAAAAACCCAACACGAAT
3242 GCGCGGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (41 bp):
TCAGTTCCAATCATAAACCGAAAAACCCAACACGAATTTAC
Found at i:9120 original size:3 final size:3
Alignment explanation
Indices: 9112--9146 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
9102 TGGAGCTTAA
9112 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9147 ATGTTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:24971 original size:13 final size:13
Alignment explanation
Indices: 24953--24983 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
24943 CATTCTATGA
24953 TAAATATAATATT
1 TAAATATAATATT
24966 TAAATATAATATT
1 TAAATATAATATT
24979 TAAAT
1 TAAAT
24984 TTATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATATAATATT
Found at i:35445 original size:2 final size:2
Alignment explanation
Indices: 35432--35474 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
35422 TTGCATGTTC
*
35432 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
35474 A
1 A
35475 GAAATTAGTC
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:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:37070 original size:17 final size:17
Alignment explanation
Indices: 37045--37079 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
37035 TGAAGAGAAA
37045 TTTCATCCTTTCAGGAT
1 TTTCATCCTTTCAGGAT
*
37062 TTTCGTCCTTTCAGGAT
1 TTTCATCCTTTCAGGAT
37079 T
1 T
37080 GCTTGATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (17 bp):
TTTCATCCTTTCAGGAT
Found at i:63892 original size:17 final size:17
Alignment explanation
Indices: 63867--63902 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
63857 GCACCCTCAA
*
63867 ATGTAAAATGTTTTCAC
1 ATGTAAAATGTTTCCAC
*
63884 ATGTGAAATGTTTCCAC
1 ATGTAAAATGTTTCCAC
63901 AT
1 AT
63903 ATTTAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (17 bp):
ATGTAAAATGTTTCCAC
Found at i:65985 original size:22 final size:21
Alignment explanation
Indices: 65960--66002 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
65950 TTCCATTAAT
65960 TCATAATCTTTA-CCTTTATTTA
1 TCAT-ATCTTTATCCTTT-TTTA
*
65982 TCATCTCTTTATCCTTTTTTA
1 TCATATCTTTATCCTTTTTTA
66003 ATCTCTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATATCTTTATCCTTTTTTA
Found at i:66006 original size:19 final size:20
Alignment explanation
Indices: 65966--66008 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
65956 TAATTCATAA
65966 TCTTTACCTTTATTTATCATC
1 TCTTTACCTTTATTTA-CATC
65987 TCTTTATCCTTT-TTTA-ATC
1 TCTTTA-CCTTTATTTACATC
66006 TCT
1 TCT
66009 AAGAAGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (20 bp):
TCTTTACCTTTATTTACATC
Found at i:66279 original size:118 final size:118
Alignment explanation
Indices: 66063--66288 Score: 330
Period size: 118 Copynumber: 1.9 Consensus size: 118
66053 TTTACTCACG
66063 TTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTCATTATAGCATTTGATATACAAAAAACGG
1 TTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTCATTATAGCATTTGATATACAAAAAACGG
66128 TTGCTTCCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGCTGCTACTACA
66 TTGCTTCCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGCTGCTACTACA
* * * * * * *
66181 TTTCCTACTTCTCATAAAACTGAATTTCCTATTTCTGATTATAGCATTTGATTTATAAAAAA-GG
1 TTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTCATTATAGCATTTGATATACAAAAAACGG
* * * *
66245 TTGGC-TGCATAATTCCTAAAATTTAAGAAGGAAAACAGCTTGCT
66 TT-GCTTCCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGCT
66289 ACAATAAGAT
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
117 39 0.41
118 57 0.59
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (118 bp):
TTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTCATTATAGCATTTGATATACAAAAAACGG
TTGCTTCCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGCTGCTACTACA
Found at i:68409 original size:21 final size:21
Alignment explanation
Indices: 68383--68426 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
68373 AATAATTGGA
68383 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
* *
68404 TTGCTAAATACCGCCCCCGTT
1 TTGCTAAACACCGCCCCCCTT
68425 TT
1 TT
68427 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.41, G:0.11, T:0.30
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:70159 original size:121 final size:121
Alignment explanation
Indices: 69940--70180 Score: 473
Period size: 121 Copynumber: 2.0 Consensus size: 121
69930 GCTCATCTCT
69940 AGGGATATTGGATTTTCCATTGGAGTCTATGAAGAAGTTGCTTCCCTCTATAAATGACACAGATG
1 AGGGATATTGGATTTTCCATTGGAGTCTATGAAGAAGTTGCTTCCCTCTATAAATGACACAGATG
70005 CCCAACTCCTGATAGCCCCTATCACAAAAGAGGAGATAAGGTCAGTTATGTTTTCC
66 CCCAACTCCTGATAGCCCCTATCACAAAAGAGGAGATAAGGTCAGTTATGTTTTCC
70061 AGGGATATTGGATTTTCCATTGGAGTCTATGAAGAAGTTGCTTCCCTCTATAAATGACACAGATG
1 AGGGATATTGGATTTTCCATTGGAGTCTATGAAGAAGTTGCTTCCCTCTATAAATGACACAGATG
*
70126 CCCAACTCCTGATAGCCCCTATCACAAATGAGGAGATAAGGTCAGTTATGTTTTC
66 CCCAACTCCTGATAGCCCCTATCACAAAAGAGGAGATAAGGTCAGTTATGTTTTC
70181 TATAACCAGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (121 bp):
AGGGATATTGGATTTTCCATTGGAGTCTATGAAGAAGTTGCTTCCCTCTATAAATGACACAGATG
CCCAACTCCTGATAGCCCCTATCACAAAAGAGGAGATAAGGTCAGTTATGTTTTCC
Found at i:72705 original size:21 final size:21
Alignment explanation
Indices: 72679--72727 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
72669 GCACTGGAGT
* * *
72679 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
72700 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
72721 ACATGGG
1 ACATGGG
72728 CCCCCAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:73683 original size:25 final size:25
Alignment explanation
Indices: 73621--73679 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
73611 TTCAAACCCT
*
73621 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
73646 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
73670 AAA-TTCATTT
1 AAACTTCATTT
73680 TTCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:73718 original size:26 final size:26
Alignment explanation
Indices: 73689--73760 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
73679 TTTCTTCATT
*
73689 TTAATCATAAACTGATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
73715 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
73741 TTAAACATAAACTAA-TAAAT
1 TTAATCATAAACTAATTAAAT
73761 TAAGTAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 4 0.10
26 38 0.90
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:82586 original size:12 final size:12
Alignment explanation
Indices: 82566--82604 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
82556 GGAAGAAACT
82566 CAAGTTCTTCAC
1 CAAGTTCTTCAC
* *
82578 CAAGCTCTTCAT
1 CAAGTTCTTCAC
82590 CAAGTTCTTCAC
1 CAAGTTCTTCAC
82602 CAA
1 CAA
82605 TCTACAATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.33, G:0.08, T:0.31
Consensus pattern (12 bp):
CAAGTTCTTCAC
Found at i:84180 original size:329 final size:329
Alignment explanation
Indices: 83645--84956 Score: 903
Period size: 329 Copynumber: 4.0 Consensus size: 329
83635 CCAGCAATTA
* * * * *
83645 TTTTTA-AAACATCTGAATGATTGTTTCGTTTTGATTAGAAATTAATTCGGAAAAAAAATAGGAA
1 TTTTTACAAGCATCTGAAT-CTTGTTTCGATTT-ATTAGAAATTAATTC---AGAAAAATATGAA
* * * * * * * *
83709 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATTTTTTTATGAG
61 AAACGATATTAAAAACGTGAAAAGCACTTCAATATTTTTGGCATTAAATTATATTATATTATGAG
* * * *
83774 TATTCTGGCTAAAAATTAAGGAAAAAATTTTCTGGTCATTTTTTGCAAAATTTTAGCCGAAATCG
126 TATTCTAGCCAAAAATTAAGGAAAAAATTTTCTGGTCATTTTCTGCAAAATTTTAGCCAAAATCG
* * * * *
83839 TGTACTAATCATCACGGTTTTTTGCTAAAAATGCTTTTCGGGGTCCCGACTCAGTTTTGCATGAT
191 GGAACTAATCATCACGGTTTTTTGCGAAAAATGCGTTTCGGGGTCCCGACTCAATTTTGCATGAT
*** * *
83904 TTTTGACGTTGAGAGTCCTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATAACATTT
256 TTTTGACACCGACAGTCCTTGAAATATCTATATTCATCTAATAAAATCTCAACCACATAACATTT
*
83969 AATAATTTG
321 AAGAATTTG
*
83978 TTTTTACAAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATGAAAAAC
1 TTTTTACAAGCATCTGAATCTTGTTTCGATTT-ATTAGAAATTAATTCAGAAAAATATGAAAAAC
* *
84043 GATATTAAAAACGTGAAATGTAC-TCAAATATTTTTGGCATTAAATTATA-TATATTATGAGTAT
65 GATATTAAAAACGTGAAAAGCACTTC-AATATTTTTGGCATTAAATTATATTATATTATGAGTAT
* * ** ** * *
84106 TTTATCCAAAAATTGGGGAAAATTTTTTC-GGTTCATTTTCTGCTAAATTTTAGGCAAAATCGGG
129 TCTAGCCAAAAATTAAGGAAAAAATTTTCTGG-TCATTTTCTGCAAAATTTTAGCCAAAATCGGG
* * *
84170 AACTAATCATCACTGTTTTTTGCGAAAAATGCGTTTCGGGGTCCCGGCTCAATTTTGCATGGTTT
193 AACTAATCATCACGGTTTTTTGCGAAAAATGCGTTTCGGGGTCCCGACTCAATTTTGCATGATTT
* * * ** **
84235 TTGGCACCGACAGTCCTTGAAATCTCTATATTCATCTAATAAAATCTTAGTCACATTGCATTTAA
258 TTGACACCGACAGTCCTTGAAATATCTATATTCATCTAATAAAATCTCAACCACATAACATTTAA
*
84300 GGATTTG
323 GAATTTG
* * *
84307 TTTTTACGAGCATCTAAATCTTGTTTTGATTGTATTAGAAATTAATTCAGAAAAATATGAAAAAC
1 TTTTTACAAGCATCTGAATCTTGTTTCGATT-TATTAGAAATTAATTCAGAAAAATATGAAAAAC
* * * * * * * * * * *
84372 GATATTAAAAGCATGAAAAACCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTTATAAGTA
65 GATATTAAAAACGTGAAAAGCACTTCAATATTTTTGGCATT-AAAT-TATATTATATTATGAGTA
* * * * * * * *
84437 TTATGGCTAAAAATTGAGGGAAAAATCTTTC-GAGTAAATTTT-TGCAAAATTTAACCCGAAAA-
128 TTCTAGCCAAAAATTAAGGAAAAAAT-TTTCTG-GT-CATTTTCTGCAAAATTTTAGCC-AAAAT
* * * ** * ** * *
84499 CGTGCAATAATCTATAATCAATCACGGTTTTTGGCTAAAAAAACG-TTCCGGGAACTG-GTACAA
189 CG-G---GAA-C--TAATC-ATCACGGTTTTTTGCGAAAAATGCGTTTCGGGGTCCCGACT-CAA
* * * * * * * * **
84562 TTTTGAATGATTATT-AGCGCCAAAACTCCTTGTAATATCCATATTCATCTAACCAAA--TC--C
245 TTTTGCATGATTTTTGA-CACCGACAGTCCTTGAAATATCTATATTCATCTAATAAAATCTCAAC
84622 CAGC----C--------A-TTG
309 CA-CATAACATTTAAGAATTTG
* * * * * *
84631 TTTTTACAAACATCTGAATCATGTTTCGTTTTAATAAGAAATTAATTCGGAAAAAATAGGAAAAA
1 TTTTTACAAGCATCTGAATCTTGTTTCGATTT-ATTAGAAATTAATTCAG-AAAAATATGAAAAA
* * * * * * * *
84696 TGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGG-AGTTGAATTATA-TATTTTTATGACT
64 CGATATTAAAAACGTGAAAAGCACTTCAATATTTTTGGCA-TTAAATTATATTA-TATTATGAGT
* * *
84759 ATTGT-GACTAAAAATTAAGGAAAAAAATTTTCTGGTCATTTT-TGGCAAAATTTTAGCCGAAAT
127 ATTCTAG-CCAAAAATTAAGG-AAAAAATTTTCTGGTCATTTTCT-GCAAAATTTTAGCCAAAAT
* * * * * * ** *
84822 TGTGTACTAACCACCACGGTTTTTTTGCTAAAAGCGCTTTTC-GGG-CCCTGACT-AAGTTTTGC
189 CGGGAACTAATCATCACGG-TTTTTTGCGAAAAATGCGTTTCGGGGTCCC-GACTCAA-TTTTGC
* ** * * * * **
84884 ATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCTTCTAATCAAATCTCGGCCACATAG
251 ATGATTTTTGACACCGACAGTCCTTGAAATATCTATATTCATCTAATAAAATCTCAACCACATA-
84949 A-ATTTAAG
315 ACATTTAAG
84957 GAT
Statistics
Matches: 767, Mismatches: 158, Indels: 111
0.74 0.15 0.11
Matches are distributed among these distances:
315 9 0.01
316 67 0.09
317 4 0.01
318 3 0.00
319 2 0.00
320 3 0.00
322 11 0.01
323 48 0.06
324 52 0.07
325 49 0.06
328 2 0.00
329 266 0.35
330 59 0.08
331 4 0.01
332 28 0.04
333 51 0.07
334 22 0.03
336 2 0.00
337 3 0.00
338 2 0.00
339 1 0.00
340 59 0.08
341 20 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (329 bp):
TTTTTACAAGCATCTGAATCTTGTTTCGATTTATTAGAAATTAATTCAGAAAAATATGAAAAACG
ATATTAAAAACGTGAAAAGCACTTCAATATTTTTGGCATTAAATTATATTATATTATGAGTATTC
TAGCCAAAAATTAAGGAAAAAATTTTCTGGTCATTTTCTGCAAAATTTTAGCCAAAATCGGGAAC
TAATCATCACGGTTTTTTGCGAAAAATGCGTTTCGGGGTCCCGACTCAATTTTGCATGATTTTTG
ACACCGACAGTCCTTGAAATATCTATATTCATCTAATAAAATCTCAACCACATAACATTTAAGAA
TTTG
Done.