Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016596.1 Corchorus olitorius cultivar O-4 contig16629, 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: 35617
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4217 original size:30 final size:31
Alignment explanation
Indices: 4183--4255 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 31
4173 TATTATCAAG
*
4183 TTTAAAACTAATCATTAATTATTCATTA-TT
1 TTTAAAACTAATCATTAATTATTCATCATTT
4213 TTTAAAACTAATCATTAATTATTCATCATTT
1 TTTAAAACTAATCATTAATTATTCATCATTT
4244 TTTAAAACTAAT
1 TTTAAAACTAAT
4256 AAAGTTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 27 0.66
31 14 0.34
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTAAAACTAATCATTAATTATTCATCATTT
Found at i:18321 original size:40 final size:40
Alignment explanation
Indices: 18246--18322 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
18236 TCCGGTGTTG
**
18246 AGAAATTCCCAAGTAAGAAATTTGGAAGTTTAAACTCAAA
1 AGAAATTCCCAAGTAAGAAATTTGGAAGTAAAAACTCAAA
**
18286 AGAAATTTTCAAGTACA-AAATTTGGAAGTAAAAACTC
1 AGAAATTCCCAAGTA-AGAAATTTGGAAGTAAAAACTC
18323 TCACTCGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (40 bp):
AGAAATTCCCAAGTAAGAAATTTGGAAGTAAAAACTCAAA
Found at i:19114 original size:76 final size:76
Alignment explanation
Indices: 18454--19113 Score: 891
Period size: 76 Copynumber: 8.8 Consensus size: 76
18444 ATTTCCAAGC
* ** * * *
18454 ATGAAATTTGGAAGTACAAAATTTCCAAGTGTAAGTGGTTACCCTATGTGCGGATGAGAGACATA
1 ATGAAATTTGGAAGTAC-AAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATA
* *
18519 GGGGGGAAGTAA
65 GGGAGGAAGTAG
* * * * *
18531 AAGAAATTTGGAAGTAAAAATTTCCAAGTGTAAGTTGTCACCCTATGTGCGGATGAGACACATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
* *
18596 GGAGAAAGTAA
66 GGAGGAAGTAG
* * * * * * * * *
18607 AAGAAATTTGGAAGAAAAAACTTCCAAGTGTAAGTTGT------ATGCGCGGATGAGTCTCATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
*
18666 GGAGGAAGCAG
66 GGAGGAAGTAG
* *
18677 ATAAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCAGATGAGACACATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
18742 GGAGGAAGTAG
66 GGAGGAAGTAG
* * * *
18753 ATAAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATTACCCAATGTGCAGATGAAACACATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
18818 GGAGGAAGTAG
66 GGAGGAAGTAG
* * *
18829 AAGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGTCTCATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
18894 GGAGGAAGTAG
66 GGAGGAAGTAG
*
18905 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAAACACATAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
*
18970 GGAGAAAGTAG
66 GGAGGAAGTAG
* * *
18981 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGTCTCATTG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
19046 GGAGGAAGTAG
66 GGAGGAAGTAG
* * *
19057 ATGAAATTTGGAAGTACAAGTTTCCAAGTGTAAATTGTCACCCAATGTGCAGATGAG
1 ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAG
19114 TGACATAAGA
Statistics
Matches: 528, Mismatches: 49, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
70 57 0.11
76 456 0.86
77 15 0.03
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (76 bp):
ATGAAATTTGGAAGTACAAATTTCCAAGTGTAAATTATCACCCAATGTGCGGATGAGACACATAG
GGAGGAAGTAG
Found at i:19347 original size:69 final size:69
Alignment explanation
Indices: 19264--19401 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
19254 AGCATCCATG
* *
19264 TAGACAAAGGCAACTTAAACTCAAAAAGGACAACAATGGGCAAACAAACACAAGTCATAGTCTAC
1 TAGACAAAGACAACTTAAACTCAAAAAGGACAACAATGGGCAAACAAACACAAGTCATAGCCTAC
19329 CCAA
66 CCAA
* *
19333 TAGACAAAGACAACTTAAACTCAAAAAGGACGACAATGTGCAAACAAACACAAGTCATAGCCTAC
1 TAGACAAAGACAACTTAAACTCAAAAAGGACAACAATGGGCAAACAAACACAAGTCATAGCCTAC
19398 CCAA
66 CCAA
19402 AACACTACCA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.13
Consensus pattern (69 bp):
TAGACAAAGACAACTTAAACTCAAAAAGGACAACAATGGGCAAACAAACACAAGTCATAGCCTAC
CCAA
Found at i:22021 original size:92 final size:93
Alignment explanation
Indices: 21864--22054 Score: 330
Period size: 92 Copynumber: 2.1 Consensus size: 93
21854 TATAAGAGAG
* * *
21864 TAAAGAACTAATCCAACGGCCCATGTATGTTTGAATCAAGGGCTCAGATTAAAAACCTCATGACA
1 TAAAGAACTAATCCAACGACCCATGAATGCTTGAATCAAGGGCTCAGATTAAAAACCTCATGACA
*
21929 TTGAAAAGTCACATTAATGAGGGTAC-T
66 TTCAAAAGTCACATTAATGAGGGTACAT
*
21956 TAAAGAACTAATCCAACGACCCATGAATGCTTGAATCAAGGGCTCAGATTAAAATCCTCATGACA
1 TAAAGAACTAATCCAACGACCCATGAATGCTTGAATCAAGGGCTCAGATTAAAAACCTCATGACA
22021 TTCAAAAGTCACATTAATGAGGGTACAT
66 TTCAAAAGTCACATTAATGAGGGTACAT
22049 TAAAGA
1 TAAAGA
22055 TGACTTTAAG
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 86 0.92
93 7 0.08
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (93 bp):
TAAAGAACTAATCCAACGACCCATGAATGCTTGAATCAAGGGCTCAGATTAAAAACCTCATGACA
TTCAAAAGTCACATTAATGAGGGTACAT
Found at i:22193 original size:2 final size:2
Alignment explanation
Indices: 22186--22214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22176 AAGAAAAATA
22186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22215 AAAGAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24283 original size:14 final size:14
Alignment explanation
Indices: 24264--24302 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
24254 TATCCTTATA
*
24264 ACTATTTTATTTTT
1 ACTATTTTACTTTT
24278 ACTATTTTACTTTT
1 ACTATTTTACTTTT
24292 A-TAGTTTTACT
1 ACTA-TTTTACT
24303 CAACTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (14 bp):
ACTATTTTACTTTT
Found at i:24310 original size:85 final size:85
Alignment explanation
Indices: 24203--24373 Score: 288
Period size: 85 Copynumber: 2.0 Consensus size: 85
24193 TTGTTTAAAT
*
24203 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
24268 TTTTATTTTTACTATTTTAC
66 TTTTATTTTTACGATATTAC
* * *
24288 TTTTATAGTTTTACTCAACTAAAAGCTTTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
24353 TTTTATTTTTACGATATTAC
66 TTTTATTTTTACGATATTAC
24373 T
1 T
24374 AATTTAATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACGATATTAC
Found at i:26397 original size:25 final size:25
Alignment explanation
Indices: 26360--26409 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
26350 CCAACCAATC
*
26360 TTTGAGCATTCTCGCCCGGTCTCTA
1 TTTGAGCACTCTCGCCCGGTCTCTA
*
26385 TTTGAGCACTCTCGCTCGGTCTCTA
1 TTTGAGCACTCTCGCCCGGTCTCTA
26410 CAAACCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.32, G:0.20, T:0.36
Consensus pattern (25 bp):
TTTGAGCACTCTCGCCCGGTCTCTA
Found at i:26434 original size:21 final size:21
Alignment explanation
Indices: 26406--26447 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26396 TCGCTCGGTC
*
26406 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
26426 TCTATCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
26448 CACATACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Done.