Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009326.1 Corchorus capsularis cultivar CVL-1 contig09347, 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: 13058
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:32 original size:2 final size:2
Alignment explanation
Indices: 25--56 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15 GACTACTCGA
25 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
57 TCATCTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1646 original size:334 final size:329
Alignment explanation
Indices: 1015--1860 Score: 944
Period size: 334 Copynumber: 2.5 Consensus size: 329
1005 CTACATTGGA
* *
1015 TTTAAGAGCATCTAAAGCTTGTTTCG-TTTAATTAGAAATTAATTCA-AAAAATAATAGGAAAAA
1 TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAT-A-A-GAAAAA
* ** * * * **
1078 CAATTTTAGAAGAC-TGAAATGCCCTTTAATCTTTTGACGTTGAATTATATAATTTTTATGAGTA
63 CGACATTAGAA-ACGTCAAAAGTCCTCCAATCTTTTGACGTTGAATTATAT-ATTTTTATGAGTA
* *
1142 TTGTGGTTAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTG
126 TTGTAGTCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTG
* * * *
1207 TAATAATCATCACGGTTTTTTGGCTAAAAACGTGTTTTAGGGCCCCGACTAAGTTTTGCATGATT
191 T-ATAATCATCACGGTTTTTTGCCTAAAAACGCGTTTGAGGGACCCGACTAAGTTTTGCATGATT
* * * * *
1272 TTTGACGCCAAGACTCTTTGAGATATCCATATTTATCTAATCAAAAT-TCAACTTCATTGGATTT
255 TTTGACGCCAAGACTATTTGAAATATCCATATTCATCTAATC-AAATCTCAACTACATTGGAATT
1336 AAAAATTTGTT
319 AAAAATTTGTT
** * * *
1347 TTTACGAGCATCTAAATATTCTTGTTTCGATTTAATTAGACATTAATTTAGAAAAATATGAAAAA
1 TTTAAAAGCATCT-AA-A-TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAA
* *
1412 CGACATTA-AAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTA
63 CGACATTAGAAA-CGTCAAAAGTCCTCCAATC-TTTTGACGTTGAATTATATATTTTTATGAGTA
* * * *
1476 TTTTAG-CAAAAATTTGAGGGGAAAT-A-TTTTGTGTTAATTTTTGCAAAATTTTAGTCGAAATC
126 TTGTAGTCAAAAA-TTGA--GGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATC
*
1538 GTGT-TAATCATCATGG-TTTTTGCCTAAAAACGCGTTTCGA-GGACCCGACTCAA-TTTTGCAT
188 GTGTATAATCATCACGGTTTTTTGCCTAAAAACGCGTTT-GAGGGACCCGACT-AAGTTTTGCAT
** * * * *
1599 GATTTTTCTTTCCTCCGAGACTATTTGAAATATCTATATTCATCTAATCAAATCTCAGCTACATT
251 GA--TTT-TTGACGCCAAGACTATTTGAAATATCCATATTCATCTAATCAAATCTCAACTACATT
**
1664 GGAATTAAGGATTTGTT
313 GGAATTAAAAATTTGTT
* * *
1681 TTTAAAATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAATGA
1 TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAACGA
* * * * *
1746 TATTAGAAACGTCAAAAGTCCTTCAATATTTTGACATTGAATTATACAATTTTTATGAGTATTGT
66 CATTAGAAACGTCAAAAGTCCTCCAATCTTTTGACGTTGAATTATA-TATTTTTATGAGTATTGT
* *
1811 GGAT-AAAAATTGAGGAAATAACTTTCGAGGCAATTTTTGCAAAATTTTAG
130 AG-TCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAG
1861 CCAAAATGGT
Statistics
Matches: 433, Mismatches: 58, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
329 6 0.01
330 17 0.04
331 148 0.34
332 36 0.08
333 18 0.04
334 149 0.34
335 28 0.06
336 25 0.06
337 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (329 bp):
TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAACGA
CATTAGAAACGTCAAAAGTCCTCCAATCTTTTGACGTTGAATTATATATTTTTATGAGTATTGTA
GTCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTATAA
TCATCACGGTTTTTTGCCTAAAAACGCGTTTGAGGGACCCGACTAAGTTTTGCATGATTTTTGAC
GCCAAGACTATTTGAAATATCCATATTCATCTAATCAAATCTCAACTACATTGGAATTAAAAATT
TGTT
Found at i:1800 original size:331 final size:329
Alignment explanation
Indices: 1015--1860 Score: 962
Period size: 331 Copynumber: 2.5 Consensus size: 329
1005 CTACATTGGA
* *
1015 TTTAAGAGCATCTAAAGCTTGTTTCG-TTTAATTAGAAATTAATTCA-AAAAATAATAGGAAAAA
1 TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAT-A-A-GAAAAA
* * * * * *
1078 CAATTTTAGAAGAC-TGAAATGCCCTTTAATCTTTTGACGTTGAATTATATAATTTTTATGAGTA
63 CGATATTAGAA-ACGTGAAAAGTCCTTCAATATTTTGACGTTGAATTATA-AATTTTTATGAGTA
* *
1142 TTGTGGTTAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTG
126 TTGTAGTCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTG
* * * *
1207 TAATAATCATCACGGTTTTTTGGCTAAAAACGTGTTTTAGGGCCCCGACTAAGTTTTGCATGATT
191 T-ATAATCATCACGGTTTTTTGCCTAAAAACGCGTTTGAGGGACCCGACTAAGTTTTGCATGATT
* * * * *
1272 TTTGACGCCAAGACTCTTTGAGATATCCATATTTATCTAATCAAAATTCAACTTCATTGGATTTA
255 TTTGACGCCAAGACTATTTGAAATATCCATATTCATCTAATCAAAATTCAACTACATTGGAATTA
1337 AAAATTTGTT
320 AAAATTTGTT
** * * *
1347 TTTACGAGCATCTAAATATTCTTGTTTCGATTTAATTAGACATTAATTTAGAAAAATATGAAAAA
1 TTTAAAAGCATCT-AA-A-TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAA
* * * * *
1412 CGACATTA-AAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTA
63 CGATATTAGAAA-CGTGAAAAGTCCTTCAAT-ATTTTGACGTTGAATTATAAATTTTTATGAGTA
* * * *
1476 TTTTAG-CAAAAATTTGAGGGGAAAT-A-TTTTGTGTTAATTTTTGCAAAATTTTAGTCGAAATC
126 TTGTAGTCAAAAA-TTGA--GGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATC
*
1538 GTGT-TAATCATCATGG-TTTTTGCCTAAAAACGCGTTTCGA-GGACCCGACTCAA-TTTTGCAT
188 GTGTATAATCATCACGGTTTTTTGCCTAAAAACGCGTTT-GAGGGACCCGACT-AAGTTTTGCAT
** * * * *
1599 GATTTTTCTTTCCTCCGAGACTATTTGAAATATCTATATTCATCTAATC-AAATCTCAGCTACAT
251 GA--TTT-TTGACGCCAAGACTATTTGAAATATCCATATTCATCTAATCAAAAT-TCAACTACAT
**
1663 TGGAATTAAGGATTTGTT
312 TGGAATTAAAAATTTGTT
* * *
1681 TTTAAAATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAATGA
1 TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAACGA
* *
1746 TATTAGAAACGTCAAAAGTCCTTCAATATTTTGACATTGAATTATACAATTTTTATGAGTATTGT
66 TATTAGAAACGTGAAAAGTCCTTCAATATTTTGACGTTGAATTATA-AATTTTTATGAGTATTGT
* *
1811 GGAT-AAAAATTGAGGAAATAACTTTCGAGGCAATTTTTGCAAAATTTTAG
130 AG-TCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAG
1861 CCAAAATGGT
Statistics
Matches: 431, Mismatches: 60, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
329 6 0.01
330 17 0.04
331 148 0.34
332 36 0.08
333 18 0.04
334 148 0.34
335 27 0.06
336 25 0.06
337 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (329 bp):
TTTAAAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAACGA
TATTAGAAACGTGAAAAGTCCTTCAATATTTTGACGTTGAATTATAAATTTTTATGAGTATTGTA
GTCAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTATAA
TCATCACGGTTTTTTGCCTAAAAACGCGTTTGAGGGACCCGACTAAGTTTTGCATGATTTTTGAC
GCCAAGACTATTTGAAATATCCATATTCATCTAATCAAAATTCAACTACATTGGAATTAAAAATT
TGTT
Found at i:1975 original size:16 final size:15
Alignment explanation
Indices: 1954--1997 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1944 GTAGAATAAT
*
1954 TATAAAATTTAGGAAC
1 TATAAAATTT-GAAAC
1970 TATAAAA-TTGAAAC
1 TATAAAATTTGAAAC
1984 TATAAAA-TTGAAAC
1 TATAAAATTTGAAAC
1998 AGTTTAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 18 0.67
15 2 0.07
16 7 0.26
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (15 bp):
TATAAAATTTGAAAC
Found at i:1986 original size:14 final size:14
Alignment explanation
Indices: 1967--1997 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1957 AAAATTTAGG
1967 AACTATAAAATTGA
1 AACTATAAAATTGA
1981 AACTATAAAATTGA
1 AACTATAAAATTGA
1995 AAC
1 AAC
1998 AGTTTAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (14 bp):
AACTATAAAATTGA
Found at i:2285 original size:141 final size:140
Alignment explanation
Indices: 1981--2295 Score: 594
Period size: 140 Copynumber: 2.2 Consensus size: 140
1971 ATAAAATTGA
*
1981 AACTATAAAATTGAAACAGTTTAAGAGAATAATTTTAAAGTAAAGTTTGGATAAAAATTTGGAAA
1 AACTATAAAATTGAAACAGTTTGAGAGAATAATTTTAAAGTAAAGTTTGGATAAAAATTTGGAAA
2046 ATATAATTGGAAGAAAGTATGGAGATCTTTATTTCTTTGTCTTTGATCGGAAGTAGAATAATTAT
66 ATATAATTGGAAGAAAGTATGGAGATCTTTATTTCTTTGTCTTTGATCGGAAGTAGAATAATTAT
2111 AAAATTTAGG
131 AAAATTTAGG
* *
2121 AACTATAAAATTGAAACACTTTGAGAGAATAATTTTAAAGTAAAGTTTGGATAAAAATTTGGAGA
1 AACTATAAAATTGAAACAGTTTGAGAGAATAATTTTAAAGTAAAGTTTGGATAAAAATTTGGAAA
2186 ATATAATTGGAAGAAAGTATGGAGATCTTTTATTTCTTTGTCTTTGATCGGAAGTAGAATAATTA
66 ATATAATTGGAAGAAAGTATGGAGATC-TTTATTTCTTTGTCTTTGATCGGAAGTAGAATAATTA
2251 TAAAATTTAGG
130 TAAAATTTAGG
2262 AACTATAAAATTGAAACAGTTTGAGAGAATAATT
1 AACTATAAAATTGAAACAGTTTGAGAGAATAATT
2296 GATCGTGTCG
Statistics
Matches: 170, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
140 89 0.52
141 81 0.48
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.35
Consensus pattern (140 bp):
AACTATAAAATTGAAACAGTTTGAGAGAATAATTTTAAAGTAAAGTTTGGATAAAAATTTGGAAA
ATATAATTGGAAGAAAGTATGGAGATCTTTATTTCTTTGTCTTTGATCGGAAGTAGAATAATTAT
AAAATTTAGG
Done.