Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012574.1 Corchorus olitorius cultivar O-4 contig12607, 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: 32637
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:569 original size:25 final size:26
Alignment explanation
Indices: 538--588 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
528 TAGTAGAATA
538 ATTGTAA-AAAAT-TATTTCTAAAAAT
1 ATTGTAAGAAAATATATTT-TAAAAAT
*
563 ATTGTAAGAGAATATATTTTAAAAAT
1 ATTGTAAGAAAATATATTTTAAAAAT
589 TCTAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (26 bp):
ATTGTAAGAAAATATATTTTAAAAAT
Found at i:3384 original size:42 final size:42
Alignment explanation
Indices: 3338--3428 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
3328 AGCAACAATT
* *
3338 AATATTAGTTTTATTTTGATGAATAATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATAACCTAGAGATGGAGTAG
* *
3380 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAT
1 AATATTAGCTTTATTTTGATGAATAACCTAGAGATGGAGTAG
3422 AAT-TTAG
1 AATATTAG
3429 GTAATGCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATAACCTAGAGATGGAGTAG
Found at i:5053 original size:31 final size:30
Alignment explanation
Indices: 4986--5054 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
4976 AAAATGCAAT
** * *
4986 TCAGGATATAACGTTACGACTTGTGTCAAT
1 TCAGGATATAACGTTACGACACGGGTCAAA
* *
5016 TTAGGATATAACGTTATCGAGACGGGTCAAA
1 TCAGGATATAACGTTA-CGACACGGGTCAAA
5047 TCAGGATA
1 TCAGGATA
5055 AAATCAGACG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (30 bp):
TCAGGATATAACGTTACGACACGGGTCAAA
Found at i:6380 original size:36 final size:36
Alignment explanation
Indices: 6333--6407 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
6323 AAATATCCTG
6333 CAGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTC
1 CAGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTC
6369 CAGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTC
1 CAGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTC
6405 CAG
1 CAG
6408 CACAGTGGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (36 bp):
CAGTTTGGAAAGCCATTTTTGCTAAGTTGAGAATTC
Found at i:6714 original size:30 final size:31
Alignment explanation
Indices: 6655--6719 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
6645 AGGGTAATTT
*
6655 TATCCTAAATTGATACAATCCGATAACGTTA
1 TATCCTAAATTGACACAATCCGATAACGTTA
6686 TATCCTAAATTGACACAAAT-CG-TAACGTTA
1 TATCCTAAATTGACAC-AATCCGATAACGTTA
6716 TATC
1 TATC
6720 TTGGATTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 12 0.38
31 17 0.53
32 3 0.09
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (31 bp):
TATCCTAAATTGACACAATCCGATAACGTTA
Found at i:13620 original size:18 final size:18
Alignment explanation
Indices: 13599--13638 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
13589 TGCTGGATAA
13599 CATATAATTTGAACAGGG
1 CATATAATTTGAACAGGG
13617 CATATAATTTGAACAGGG
1 CATATAATTTGAACAGGG
13635 CATA
1 CATA
13639 CAATACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (18 bp):
CATATAATTTGAACAGGG
Found at i:13959 original size:22 final size:23
Alignment explanation
Indices: 13922--13965 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
13912 AAAAAGCTTT
13922 TTTCCATAATAAAAAA-GGAACA
1 TTTCCATAATAAAAAATGGAACA
**
13944 TTTCCATAATCTAAAATGGAAC
1 TTTCCATAATAAAAAATGGAAC
13966 TAAAAGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (23 bp):
TTTCCATAATAAAAAATGGAACA
Found at i:15531 original size:176 final size:175
Alignment explanation
Indices: 15237--15587 Score: 573
Period size: 176 Copynumber: 2.0 Consensus size: 175
15227 ATTATAAGTC
*
15237 AAATAAAATAATTGCAAGTTAAGGAAATAATAAATTTTAATCATAATACATTATATTATCAAATA
1 AAATAAAATAATTGCAAGTTAAGGAAATAATAAATTTTAATCATAATACATTAAATTATCAAATA
*
15302 GAAAGATGTCAATCACAAAAACCTTTTTAATTAAAAAATGGTAAAAATAAAATAATTATAAAATA
66 GAAAGATGTCAATCACAAAAACCTTTTTAATTAAAAAATGATAAAAATAAAATAATTATAAAATA
*
15367 TTGAATTTAATTGAATGAAAATAGAGTTTTTAATAGAATAAAACTG
131 TTG-ATTTAATTAAATGAAAATAGAGTTTTTAATAGAATAAAACTG
*
15413 AAATAAAATAATTGCACA-TTAAGGAAATAA-AATTTTTTAATCATAATACATTAAATTATCAAA
1 AAATAAAATAATTGCA-AGTTAAGGAAATAATAA-ATTTTAATCATAATACATTAAATTATCAAA
* *
15476 TAGAAAGATGTCAATCATAATAA-CTTTTTAAATTAAAAAATGATAAAAATAAAATAATTATAAA
64 TAGAAAGATGTCAATCACAAAAACCTTTTT-AATTAAAAAATGATAAAAATAAAATAATTATAAA
* *
15540 ATATTGATTTAATTAAATGATAATAGAGTTTTTAGTAGAATAAAACTG
128 ATATTGATTTAATTAAATGAAAATAGAGTTTTTAATAGAATAAAACTG
15588 TATATTAAAA
Statistics
Matches: 164, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
175 47 0.29
176 116 0.71
177 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (175 bp):
AAATAAAATAATTGCAAGTTAAGGAAATAATAAATTTTAATCATAATACATTAAATTATCAAATA
GAAAGATGTCAATCACAAAAACCTTTTTAATTAAAAAATGATAAAAATAAAATAATTATAAAATA
TTGATTTAATTAAATGAAAATAGAGTTTTTAATAGAATAAAACTG
Found at i:15762 original size:122 final size:121
Alignment explanation
Indices: 15512--15754 Score: 289
Period size: 122 Copynumber: 2.0 Consensus size: 121
15502 TTTAAATTAA
*
15512 AAAATGATAAAAATAAAATAATTATAAAATATTGATTTAATTAAATGATAATAGAGTTTTTAGTA
1 AAAATAATAAAAATAAAATAATTATAAAATATTGATTTAATTAAATGATAATAGAGTTTTTAGTA
* * * * *
15577 GAATAAAACTGTATATTAAAAAATTTAATATATCCAAATATTTATTGAAAAATAGT
66 GAATAAAACTATATATTAAAAAATTGAATATATACAAATATGTATTGAAAAATAAT
* *
15633 AAAATAATAAAAATAAAGTAATTATAAAGATATTAGATTT-ATTTAAT-ATAAATAGAGTTTTTA
1 AAAATAATAAAAATAAAATAATTATAAA-ATATT-GATTTAATTAAATGAT-AATAGAGTTTTTA
** * *
15696 GTAGAATAAAACTATAATAGTTAATCAA-TGACATTTA-AGAAATATGT-TTGAAAAATAAT
63 GTAGAATAAAACTAT-ATA-TTAAAAAATTGA-ATATATACAAATATGTATTGAAAAATAAT
15755 GGTATAATGG
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
121 28 0.27
122 49 0.47
123 17 0.16
124 10 0.10
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (121 bp):
AAAATAATAAAAATAAAATAATTATAAAATATTGATTTAATTAAATGATAATAGAGTTTTTAGTA
GAATAAAACTATATATTAAAAAATTGAATATATACAAATATGTATTGAAAAATAAT
Found at i:21402 original size:234 final size:234
Alignment explanation
Indices: 20986--21447 Score: 827
Period size: 234 Copynumber: 2.0 Consensus size: 234
20976 GTTCAACATA
20986 ATGTCGCTCGGCGTAGACATGACAATGTCGTTCCAACAGACGGCGCCAAATTGTTGAGGGATAAA
1 ATGTCGCTCGGCGTAGACATGACAATGTCGTTCCAACAGACGGCGCCAAATTGTTGAGGGATAAA
*
21051 TAACCAACAAGTTCGATCTTAGGAGATCGTCTCCTGAGCCTCTGAAACCCGTAAGGTTGAGGACA
66 TAACCAACAAGTACGATCTTAGGAGATCGTCTCCTGAGCCTCTGAAACCCGTAAGGTTGAGGACA
* *
21116 TGCAGACAGAGGAACACCTCAAGTAATTTGGAGGATATTAAAGTAGTCTTCTTAGGTCAGAAGCT
131 TGCAGACAGAGGAACACCTCAAGTAATTGGGAGGATATCAAAGTAGTCTTCTTAGGTCAGAAGCT
*
21181 ATGAGTTTTCATAATGAGTTATAAATGAGGGGTTAGTCT
196 ATGAGTTTTCATAATGAGTCATAAATGAGGGGTTAGTCT
21220 ATGTCGCTCGGCGTAGACATGACAATGTCGTTCCAACAGACGGCGCCAAATTGTTGAGGGATAAA
1 ATGTCGCTCGGCGTAGACATGACAATGTCGTTCCAACAGACGGCGCCAAATTGTTGAGGGATAAA
** *
21285 TAACCAACAAGTACGAT-TCTAGGAGATCGTCTTTTGAGCCTCTGAAACCCGTAAGGTTGGGGAC
66 TAACCAACAAGTACGATCT-TAGGAGATCGTCTCCTGAGCCTCTGAAACCCGTAAGGTTGAGGAC
*
21349 ATGCAGACAGAGGAACACCTCAAGTAATTGGGAGGATATCAAAGTATTCTTCTTAGGTCAGAAGC
130 ATGCAGACAGAGGAACACCTCAAGTAATTGGGAGGATATCAAAGTAGTCTTCTTAGGTCAGAAGC
*
21414 TATGAGTTTTCATAATGAGTCATAGATGAGGGGT
195 TATGAGTTTTCATAATGAGTCATAAATGAGGGGT
21448 ATGTCTCTCT
Statistics
Matches: 218, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
233 1 0.00
234 217 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (234 bp):
ATGTCGCTCGGCGTAGACATGACAATGTCGTTCCAACAGACGGCGCCAAATTGTTGAGGGATAAA
TAACCAACAAGTACGATCTTAGGAGATCGTCTCCTGAGCCTCTGAAACCCGTAAGGTTGAGGACA
TGCAGACAGAGGAACACCTCAAGTAATTGGGAGGATATCAAAGTAGTCTTCTTAGGTCAGAAGCT
ATGAGTTTTCATAATGAGTCATAAATGAGGGGTTAGTCT
Found at i:24230 original size:12 final size:12
Alignment explanation
Indices: 24213--24250 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24203 ATCGCTTTTT
24213 GAGAAGAAAAAG
1 GAGAAGAAAAAG
*
24225 GAGAAGAACAAG
1 GAGAAGAAAAAG
24237 G-GAGAGAAAAAG
1 GAGA-AGAAAAAG
24249 GA
1 GA
24251 TCGGGTACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.61, C:0.03, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGAAGAAAAAG
Found at i:26696 original size:30 final size:30
Alignment explanation
Indices: 26662--26752 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
26652 AACGTTTCGA
26662 CATAGGATGTCAGAAACAAATATCGAATGG
1 CATAGGATGTCAGAAACAAATATCGAATGG
* ** * * *
26692 CATAGGATGTTA-AATTACAT-GC-ATTCGG
1 CATAGGATGTCAGAAACAAATATCGAAT-GG
*
26720 GATAGGATGTCAGAAACAAATATCGAATGG
1 CATAGGATGTCAGAAACAAATATCGAATGG
26750 CAT
1 CAT
26753 GCCTATATCT
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
27 2 0.05
28 13 0.30
29 10 0.23
30 16 0.37
31 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (30 bp):
CATAGGATGTCAGAAACAAATATCGAATGG
Found at i:27495 original size:19 final size:19
Alignment explanation
Indices: 27468--27509 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
27458 AAACGAATCA
27468 ATCACGCAAAACGCCTATT
1 ATCACGCAAAACGCCTATT
* *
27487 ATCATGCAAAGCGCCTATT
1 ATCACGCAAAACGCCTATT
27506 ATCA
1 ATCA
27510 ATATACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (19 bp):
ATCACGCAAAACGCCTATT
Done.