Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015884.1 Corchorus capsularis cultivar CVL-1 contig15905, 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: 32996
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5219 original size:21 final size:22
Alignment explanation
Indices: 5179--5222 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5169 AAGAAGAGTT
* *
5179 TAAAATTAAACTTAACGAACAA
1 TAAAATTAAACTAAAAGAACAA
5201 TAAAATT-AACTAAAAGAACAA
1 TAAAATTAAACTAAAAGAACAA
5222 T
1 T
5223 CAAGAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAATTAAACTAAAAGAACAA
Found at i:9537 original size:304 final size:304
Alignment explanation
Indices: 8968--9552 Score: 850
Period size: 304 Copynumber: 1.9 Consensus size: 304
8958 TGCTTCTCAA
* * *
8968 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGCGAAATGTCGATGACTGAGGCACATGTGTTCCACATTTTTATACTCTTCTT
* * * * *
9033 CACAATTGCTGACTCACTCAAATTTTTATATATAGGGTCTTCAAGAGTTTTCTTTACAAATGCAT
66 CACAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * * * * *
9098 CGTGACAAATTTTACCCAATACCTTGAGTTCACTGCAACACTTCTTAGTGACAGCTCCGATTTTG
131 CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGATGTAG
* * ** * * **
9163 AATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCATTTTTGTTTTGCAATTGTTTTTTTT
196 AATATACTTGTGAAAACTTCCCTCGAACAGGGCAGGCCCATTTTTGTCTTGCAATTGATTTTCCT
9228 TAATAATCAAGTC-GGGATTTTTCGCAGGTGAAATGACTCTGCTT
261 TAATAATCAAGTCTGGG-TTTTTCGCAGGTGAAATGACTCTGCTT
* * *
9272 GCAGAAGAGGATGGCGAAATGTCGATGACTGAGGCACATGTGTTCCATATTTTTATACTGTTCTT
1 GCAGAAGAAGATGGCGAAATGTCGATGACTGAGGCACATGTGTTCCACATTTTTATACTCTTCTT
* * * * *
9337 CGCAATTGTTGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
66 CACAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
*
9402 CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTGTAG
131 CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGATGTAG
*
9467 AATATATTTGTGAAAACTTCCCATCGAACAGGGCAGGCCCATTTTTGTCTTGCAATT-ATTTTCC
196 AATATACTTGTGAAAACTTCCC-TCGAACAGGGCAGGCCCATTTTTGTCTTGCAATTGATTTTCC
9531 TTAATAATCAAGTCTGGGTTTT
260 TTAATAATCAAGTCTGGGTTTT
9553 CTGCAGCTAA
Statistics
Matches: 247, Mismatches: 32, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
304 215 0.87
305 32 0.13
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (304 bp):
GCAGAAGAAGATGGCGAAATGTCGATGACTGAGGCACATGTGTTCCACATTTTTATACTCTTCTT
CACAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGATGTAG
AATATACTTGTGAAAACTTCCCTCGAACAGGGCAGGCCCATTTTTGTCTTGCAATTGATTTTCCT
TAATAATCAAGTCTGGGTTTTTCGCAGGTGAAATGACTCTGCTT
Found at i:11713 original size:303 final size:303
Alignment explanation
Indices: 11161--11749 Score: 845
Period size: 303 Copynumber: 1.9 Consensus size: 303
11151 AGAAGATTGT
* *
11161 GAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTTTGCAATTGTTAACTC
1 GAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTATACTCTTCTTCGCAATTGTTAACTC
* * * * *
11226 ACTCAAATTTTTATATATAGGGTCTTCAAGAGTCTTCTTTACAAATGCATCGTGACAAACTTTAC
66 ACTCAAATCTTTACATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGACAAACTTTAC
* * * * * *
11291 CCAATACCTTGAGTTCACTGCAACACTTCTTAGTGACAGCTCCGGTTTTGAATATACTTGTGAAA
131 CCAATACCATGAGTTCACCGCAACACTTCTTAATGACAGCTCCGGTGTAGAATATACTAGTGAAA
** * * ** * * **
11356 ACTTCCCTGGCACAGTGTAGTTCCATTTTCGTTTTGCAATTGTTTTTTTTAATAATCAAGTCGGG
196 ACTTCCCTGAAACAGGGCAGGCCCATTTTCGTCTTGCAATTATTTTCCTTAATAATCAAGTCGGG
* * *
11421 GTTTTCTATAGGTGAAATGACTCCGCTTGCAGAAGAGGATGGC
261 GTTTTCTACAGCTGAAACGACTCCGCTTGCAGAAGAGGATGGC
* * *
11464 GAAATGTCGATGATTGAGGCACATGTGTTCCATGTTTTTATACTCTTCTTCGCAATTGTTGACTC
1 GAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTATACTCTTCTTCGCAATTGTTAACTC
* * * *
11529 GCTTAAGTCTTTACATAAAGGATCTTTAAGAGTCTTCTTAACAAATGCATCGTGACAAACTTTAC
66 ACTCAAATCTTTACATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGACAAACTTTAC
*
11594 GCAATACCATGAGTTCACCGCAACACTTCTTAATGACAGCTCCGGTGTAGAATATACTAGTGAAA
131 CCAATACCATGAGTTCACCGCAACACTTCTTAATGACAGCTCCGGTGTAGAATATACTAGTGAAA
* *
11659 ACTTCCCTGAAACAGGGCAGGCCCATTTTTGTCTTGCAATTATTTTCCTTAATAATCAAGTCTGG
196 ACTTCCCTGAAACAGGGCAGGCCCATTTTCGTCTTGCAATTATTTTCCTTAATAATCAAGTCGGG
*
11724 GTTTTCTGCAGCTGAAACGACTCCGC
261 GTTTTCTACAGCTGAAACGACTCCGC
11750 CTGTTAAAAC
Statistics
Matches: 249, Mismatches: 37, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
303 249 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (303 bp):
GAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTATACTCTTCTTCGCAATTGTTAACTC
ACTCAAATCTTTACATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGACAAACTTTAC
CCAATACCATGAGTTCACCGCAACACTTCTTAATGACAGCTCCGGTGTAGAATATACTAGTGAAA
ACTTCCCTGAAACAGGGCAGGCCCATTTTCGTCTTGCAATTATTTTCCTTAATAATCAAGTCGGG
GTTTTCTACAGCTGAAACGACTCCGCTTGCAGAAGAGGATGGC
Found at i:12638 original size:35 final size:38
Alignment explanation
Indices: 12564--12642 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 38
12554 AAACATGTAA
12564 AATTAACTAAGAAAGCAGTCAAGAAAATTAGAGAAAAC
1 AATTAACTAAGAAAGCAGTCAAGAAAATTAGAGAAAAC
* * *
12602 AATTAACTAA-AAAGTAGTGAA-TAAATT-GAGAAAAC
1 AATTAACTAAGAAAGCAGTCAAGAAAATTAGAGAAAAC
12637 AATTAA
1 AATTAA
12643 AGAAAACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 14 0.37
36 5 0.13
37 9 0.24
38 10 0.26
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (38 bp):
AATTAACTAAGAAAGCAGTCAAGAAAATTAGAGAAAAC
Found at i:25396 original size:303 final size:303
Alignment explanation
Indices: 24835--25437 Score: 877
Period size: 303 Copynumber: 2.0 Consensus size: 303
24825 TGCTTCTCAA
* * *
24835 GCAGAAGAAGAGGGTGAAATGTCGATGACTGAGGCACATGTGTTCCAGGTTTTTGTACTCTTTTT
1 GCAGAAGAAGAGGGCGAAATGTCGATGACTGAGGCACATGTGTTCCAGGTTTTTATACTCTTCTT
* * * * * *
24900 TGCAATTGCTGACTCACTCAAATTTTTATATATAGGGTCTTCAAGAGTCTTCTTTACAAATGCAT
66 CGCAATCGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * * * * *
24965 CATGACAAACTTTACCCAATACCTTGAGTTCACTGCAACACTTCTTAGTGACAGCTCCGGTTTTG
131 CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTAAGTGACAGCTCCAGTATAG
* * * * *
25030 AATATACTTGTGAAAACTTCCCTAGCACAGGGCAGTTCCATTTTTGTTTTGCAATTTTTTTCCTT
196 AATATACTTGTGAAAACTTCCCTAGAACAGGGCAGTTCCATTTTTATCTGGCAATTATTTTCCTT
* *
25095 AATAATCAAGT-TGGGGTTTTCTGCAGGTGAAATGACTCCGGTT
261 AATAATCAAGTCT-GGGTTTTCTGCAGCTGAAACGACTCCGGTT
* * *
25138 GCAGAAGAGGATGGCGAAATGTCGATGACTGAGGCACATGTGTTCCATGTTTTTATACTCTTCTT
1 GCAGAAGAAGAGGGCGAAATGTCGATGACTGAGGCACATGTGTTCCAGGTTTTTATACTCTTCTT
* * * *
25203 CGCAATCGTTGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
66 CGCAATCGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
*
25268 CGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTAAGTGACAGCTCCAGTATAG
131 CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTAAGTGACAGCTCCAGTATAG
*
25333 AATATACTTGTGAAAACTTCCCTGGAACAGGGCA-TTCCCATTTTTATCTGGCAATTATTTTCCT
196 AATATACTTGTGAAAACTTCCCTAGAACAGGGCAGTT-CCATTTTTATCTGGCAATTATTTTCCT
* *
25397 TAATAATCAAGTCTTGGTTTTGTGCAGCTGAAACGACTCCG
260 TAATAATCAAGTCTGGGTTTTCTGCAGCTGAAACGACTCCG
25438 CCTGTTAAAA
Statistics
Matches: 265, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
302 2 0.01
303 262 0.99
304 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGAGGGCGAAATGTCGATGACTGAGGCACATGTGTTCCAGGTTTTTATACTCTTCTT
CGCAATCGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CATGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTAAGTGACAGCTCCAGTATAG
AATATACTTGTGAAAACTTCCCTAGAACAGGGCAGTTCCATTTTTATCTGGCAATTATTTTCCTT
AATAATCAAGTCTGGGTTTTCTGCAGCTGAAACGACTCCGGTT
Found at i:28794 original size:11 final size:11
Alignment explanation
Indices: 28778--28821 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
28768 TATACTATAT
*
28778 CTAATTAATAG
1 CTAATTAATAA
*
28789 CTAATTAATAT
1 CTAATTAATAA
28800 CTAATTAATAA
1 CTAATTAATAA
*
28811 TTAATTAATAA
1 CTAATTAATAA
28822 TGAATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:28799 original size:22 final size:22
Alignment explanation
Indices: 28774--28820 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28764 CCATTATACT
*
28774 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAACTAATTA
*
28796 ATATCTAATTAATAATTAATTA
1 ATATCTAATTAATAACTAATTA
28818 ATA
1 ATA
28821 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Found at i:31360 original size:17 final size:17
Alignment explanation
Indices: 31338--31370 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31328 ACTCACCTCA
31338 CAGCCATAACTGCTTTG
1 CAGCCATAACTGCTTTG
*
31355 CAGCCATAATTGCTTT
1 CAGCCATAACTGCTTT
31371 TCACCTCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (17 bp):
CAGCCATAACTGCTTTG
Found at i:31399 original size:37 final size:37
Alignment explanation
Indices: 31354--31459 Score: 212
Period size: 37 Copynumber: 2.9 Consensus size: 37
31344 TAACTGCTTT
31354 GCAGCCATAATTGCTTTTCACCTCACCACAGGCAAAA
1 GCAGCCATAATTGCTTTTCACCTCACCACAGGCAAAA
31391 GCAGCCATAATTGCTTTTCACCTCACCACAGGCAAAA
1 GCAGCCATAATTGCTTTTCACCTCACCACAGGCAAAA
31428 GCAGCCATAATTGCTTTTCACCTCACCACAGG
1 GCAGCCATAATTGCTTTTCACCTCACCACAGG
31460 TTACCAAAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (37 bp):
GCAGCCATAATTGCTTTTCACCTCACCACAGGCAAAA
Done.