Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009761.1 Corchorus capsularis cultivar CVL-1 contig09782, 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: 60516
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3369 original size:22 final size:22
Alignment explanation
Indices: 3341--3384 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3331 CCCAAAATAC
3341 GTGTTATAACATGTAGTATCAA
1 GTGTTATAACATGTAGTATCAA
**
3363 GTGTTATAGTATGTAGTATCAA
1 GTGTTATAACATGTAGTATCAA
3385 ATAGTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGTTATAACATGTAGTATCAA
Found at i:12671 original size:1 final size:1
Alignment explanation
Indices: 12665--12693 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
12655 TGCTTTCCTC
12665 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12694 AACACAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17071 original size:30 final size:30
Alignment explanation
Indices: 17029--17106 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 30
17019 TGGTTAATTA
*
17029 AGTTCCTAACGTTGCAAAATCGGTTCAAATC
1 AGTTCC-AACGTTGCAAAATCGGCTCAAATC
17060 AGTTCCAACGTTGCAAAATCGGCTCAAATC
1 AGTTCCAACGTTGCAAAATCGGCTCAAATC
*
17090 AGTCCCCAACGTTGCAA
1 AGT-TCCAACGTTGCAA
17107 TCCCTGAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 26 0.59
31 18 0.41
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (30 bp):
AGTTCCAACGTTGCAAAATCGGCTCAAATC
Found at i:18940 original size:2 final size:2
Alignment explanation
Indices: 18933--18962 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18923 ACGATTTTGT
18933 TA TA TA TA TA TA T- 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 T
18963 TTATTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22145 original size:10 final size:10
Alignment explanation
Indices: 22130--22154 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22120 ACAAGGAGAA
22130 TTTTTTTTAT
1 TTTTTTTTAT
22140 TTTTTTTTAT
1 TTTTTTTTAT
22150 TTTTT
1 TTTTT
22155 ACCTATCTCA
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:32940 original size:12 final size:12
Alignment explanation
Indices: 32923--32953 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
32913 TACTAAACCA
32923 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
32935 ATCCTCTTCAAT
1 ATCCTCCTCAAT
32947 ATCCTCC
1 ATCCTCC
32954 AAAACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:36732 original size:14 final size:15
Alignment explanation
Indices: 36713--36742 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36703 TGGCCCGTCC
36713 AAAAAC-AAAAACAA
1 AAAAACAAAAAACAA
36727 AAAAACAAAAAACAA
1 AAAAACAAAAAACAA
36742 A
1 A
36743 CTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAACAA
Found at i:37984 original size:37 final size:37
Alignment explanation
Indices: 37943--38037 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
37933 CTCTAAGCCC
* *
37943 AAATAGGACGTAGGAGACAAAGATAAAAAG-CAAAATT
1 AAATAGGACGTTGGAAACAAAGA-AAAAAGCCAAAATT
** *
37980 AAATACAACGTTGGAAACAAAGACAAAAGCCAAAATT
1 AAATAGGACGTTGGAAACAAAGAAAAAAGCCAAAATT
38017 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
38038 AAGCAAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 5 0.10
37 45 0.90
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGAAAAAAGCCAAAATT
Found at i:38045 original size:31 final size:32
Alignment explanation
Indices: 37967--38047 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 32
37957 AGACAAAGAT
37967 AAAAAGCAAAATTAAATACAACGTTGGAAACAAA
1 AAAAAGCAAAATTAAATACAACGTTGGAAAC--A
**
38001 GACAAAAGCCAAAATTAAATAGGACGTTGGAAAC-
1 -A-AAAAG-CAAAATTAAATACAACGTTGGAAACA
38035 AAAAAGCAAAATT
1 AAAAAGCAAAATT
38048 GACTTTCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 7 0.17
32 5 0.12
33 1 0.02
35 1 0.02
36 5 0.12
37 23 0.55
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (32 bp):
AAAAAGCAAAATTAAATACAACGTTGGAAACA
Found at i:38255 original size:32 final size:32
Alignment explanation
Indices: 38187--38256 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
38177 GGCAATTTAG
*** * *
38187 AAATATGTTTTTTTAAAATGGGATACAATCGG
1 AAATATGTTTTAACAAAAAGGGATACAATCGA
38219 AAATATGTTTTAACAAAAAGGG-TACAATCAGA
1 AAATATGTTTTAACAAAAAGGGATACAATC-GA
38251 AAATAT
1 AAATAT
38257 AAAGTTTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (32 bp):
AAATATGTTTTAACAAAAAGGGATACAATCGA
Found at i:49805 original size:3 final size:3
Alignment explanation
Indices: 49797--49826 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
49787 AAGCAGATAG
*
49797 AGA AGA AGA AGA AGA GGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
49827 TACATGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:57453 original size:21 final size:21
Alignment explanation
Indices: 57427--57491 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
57417 TTGGTTTCAC
57427 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
57448 TTGTTTGATGAAATTGTGTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
57474 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
57492 TATCATCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:58666 original size:532 final size:522
Alignment explanation
Indices: 57670--58743 Score: 1774
Period size: 532 Copynumber: 2.0 Consensus size: 522
57660 ATGTTGATTC
*
57670 TTAGACATGAATTCTATATTTGCCACGGTTTTTGAAACGGTTTTCTTAAAACCGTGGGAAAATTC
1 TTAGACATGAATTCTATATTTACCACGGTTTTTGAAACGGTTTTCTTAAAACCGTGGGAAAATTC
* * * * *
57735 GTGGCTATTTGGCACGGCCTTTGCGACGACTTTTCAATTTGCCACGGGTTTTGCAGCGGGTTTAC
66 GTGGCTATTTGGCACGGCATTTGCCACAACTTTTCAATTTCCCACGGGTTTTGCAGAGGGTTTAC
* *
57800 AGAATCCCGTGGCAAAAGCCGTGGAAAATTGAGAGATGATTGACCTCAAACTCTACACTTATATA
131 AGAATCCCATGGCAAAAGCCGTGGAAAATTGAGAGATGATTGACCTCAAACCCTACACTTATATA
* *
57865 AGTTGATATTGGCTAATGGTCTGCATTTATATCATCTCAAAATTCTATATTGTCTCCAAAAATTG
196 AGTTGATATTGGCTAATGATCTGCATTTATATCATCTCAAAATTCTATATTGTCCCCAAAAATTG
*
57930 TGTAATTTCTAATTTCATAAAAAAATTTAATTGAATCTTTACACAATGTCATAATATACAAATGC
261 TGTAATTTCTAATTACATAAAAAAATTTAATTGAATCTTTACACAATGTCATAATATACAAATGC
*
57995 CTTAGTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAGTCTAGTTACAATTTT
326 CTTAGTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAATCTAGTTACAATTTT
58060 GATTTTTTTTCCACTCCCCAAACTATTTTACATTAAATTCTACATCAAATACTCGAGCTAAACAC
391 GATTTTTTTTCCACTCCCCAAACTATTTTACATTAAATTCTACATCAAATACTCGAGCTAAACAC
* *
58125 AATAGGGTACCATATAAACCTTTAATTTTATGGGAACTTCAAATTATCTTTGTTTAGAGTAAAAT
456 AATAGGGTACCATAAAAACCTTTAATTTTATGGAAACTTCAAATTATCTTTGTTTAGAGTAAAAT
58190 TT
521 TT
* *
58192 TTAGACATAAATTTTATATTTACCACGGTTTTTGAAACGGTTTTCTTAAAACCGTGGGAAAATTC
1 TTAGACATGAATTCTATATTTACCACGGTTTTTGAAACGGTTTTCTTAAAACCGTGGGAAAATTC
*
58257 GTGGCTATTTGGCACGGCATTTGCCACAACTTTTCAATTTCCCACGGTTTTTGCAGAGGGTTTAC
66 GTGGCTATTTGGCACGGCATTTGCCACAACTTTTCAATTTCCCACGGGTTTTGCAGAGGGTTTAC
* * * *
58322 AGAATCCTATGGGAAAAGCTGTGGCAAATTGAGAGATGATTGACCTCAAACCCTACACTTATATA
131 AGAATCCCATGGCAAAAGCCGTGGAAAATTGAGAGATGATTGACCTCAAACCCTACACTTATATA
58387 AGTT-AGTAATTGGCTAATGATCACATAATTGCATTTATATCATCTCAAAATTCTATATTGTCCC
196 AGTTGA-T-ATTGGCTAATGAT--C-----TGCATTTATATCATCTCAAAATTCTATATTGTCCC
* *
58451 CAAAAATTGTGTAATTTCTAATTAC-TTAAAAAATTTAATTGAATGTTTACACAGTATTGTCATA
252 CAAAAATTGTGTAATTTCTAATTACATAAAAAAATTTAATTGAATCTTTACACA--A-TGTCATA
**
58515 ATATACAAATGTGTTAGTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAATCT
314 ATATACAAATGCCTTAGTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAATCT
*
58580 AGTTACAATTTTGATTTTTTTTCCACTCCCCGAACTATTTTACATTAAATTCTACATCAAATACT
379 AGTTACAATTTTGATTTTTTTTCCACTCCCCAAACTATTTTACATTAAATTCTACATCAAATACT
*
58645 CGAGTTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGAAACTTCAAATTATCTTTGT
444 CGAGCTAAACACAATAGGGTACCATAAAAACCTTTAATTTTATGGAAACTTCAAATTATCTTTGT
*
58710 TTAGGGTAAAATTT
509 TTAGAGTAAAATTT
58724 TTAGACATGAATTCTATATT
1 TTAGACATGAATTCTATATT
58744 ATGAACCCCA
Statistics
Matches: 510, Mismatches: 30, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
521 1 0.00
522 185 0.36
523 12 0.02
525 1 0.00
529 26 0.05
530 58 0.11
531 1 0.00
532 226 0.44
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (522 bp):
TTAGACATGAATTCTATATTTACCACGGTTTTTGAAACGGTTTTCTTAAAACCGTGGGAAAATTC
GTGGCTATTTGGCACGGCATTTGCCACAACTTTTCAATTTCCCACGGGTTTTGCAGAGGGTTTAC
AGAATCCCATGGCAAAAGCCGTGGAAAATTGAGAGATGATTGACCTCAAACCCTACACTTATATA
AGTTGATATTGGCTAATGATCTGCATTTATATCATCTCAAAATTCTATATTGTCCCCAAAAATTG
TGTAATTTCTAATTACATAAAAAAATTTAATTGAATCTTTACACAATGTCATAATATACAAATGC
CTTAGTAGTGTGTTCATAGATAGTATTACAAATACATTTAGCCAATTAAATCTAGTTACAATTTT
GATTTTTTTTCCACTCCCCAAACTATTTTACATTAAATTCTACATCAAATACTCGAGCTAAACAC
AATAGGGTACCATAAAAACCTTTAATTTTATGGAAACTTCAAATTATCTTTGTTTAGAGTAAAAT
TT
Done.