Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021238.1 Corchorus olitorius cultivar O-4 contig21271, 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: 18730
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:5993 original size:57 final size:57
Alignment explanation
Indices: 5885--5996 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 57
5875 ATTAATCAAA
*
5885 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCAT-AAAAAAGACGTTTTAGGACCGAGACT
* * *
5943 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAG
5997 GCATGATGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 21 0.43
58 13 0.27
59 15 0.31
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (57 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGACT
Found at i:7305 original size:36 final size:36
Alignment explanation
Indices: 7258--7327 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
7248 TTCAATAACC
* *
7258 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
7294 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
7328 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:8171 original size:205 final size:205
Alignment explanation
Indices: 7840--8448 Score: 1111
Period size: 205 Copynumber: 3.0 Consensus size: 205
7830 GCTTAATAAC
*
7840 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTA-ACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATA-AAAGTTGTAGTGAATA
*
7903 AGATACAACACA-T--TATTATTATATATAAAACTATACCAGAAAAAAATTAGTTGAACATTAGT
65 ATATACAACACACTACTATTA-TATATATAAAACTATACCAGAAAAAAATTAGTTGAACATTAGT
7965 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
129 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
8030 AGATCCGATTAA
194 AGATCCGATTAA
8042 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATAAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATAAAAGTTGTAGTGAATAA
8107 TATACAACACACTACTATTATATATATAAAACTATACCAGAAAAAAATTAGTTGAACATTAGTGG
66 TATACAACACACTACTATTATATATATAAAACTATACCAGAAAAAAATTAGTTGAACATTAGTGG
8172 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
131 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
8237 ATCCGATTAA
196 ATCCGATTAA
8247 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATAAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATAAAAGTTGTAGTGAATAA
* *
8312 TATACAACACACTACTATTATATATATAGAACTATACCAAAAAAAAAATTAGTTGAACATTAGTG
66 TATACAACACACTACTATTATATATATAAAACTATACC-AGAAAAAAATTAGTTGAACATTAGTG
8377 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
130 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
*
8442 TATCCGA
195 GATCCGA
8449 CTTGTTTATT
Statistics
Matches: 396, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
202 24 0.06
203 47 0.12
204 2 0.01
205 222 0.56
206 101 0.26
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (205 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATAAAAGTTGTAGTGAATAA
TATACAACACACTACTATTATATATATAAAACTATACCAGAAAAAAATTAGTTGAACATTAGTGG
TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
ATCCGATTAA
Found at i:8611 original size:39 final size:40
Alignment explanation
Indices: 8568--8648 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
8558 ATACCTAAGA
*
8568 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
8607 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
8647 AT
1 AT
8649 AGAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:9271 original size:6 final size:6
Alignment explanation
Indices: 9253--9282 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
9243 GTTTAGACTT
9253 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
9283 CTTCTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:13642 original size:60 final size:60
Alignment explanation
Indices: 13561--13738 Score: 315
Period size: 60 Copynumber: 3.0 Consensus size: 60
13551 CATGCTTATA
* *
13561 TTCTAAATGCAACT-A-AAAAACATTTTTGCAAATGATAACTAATGTCAAATTGATGGAG
1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAATTGATGGAG
*
13619 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAGTTGATGGAG
1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAATTGATGGAG
13679 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAATTGATGGAG
13739 GATAGCTAAA
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
58 14 0.12
59 1 0.01
60 99 0.87
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (60 bp):
TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAACTAATGTTAAATTGATGGAG
Found at i:17485 original size:107 final size:104
Alignment explanation
Indices: 17269--17529 Score: 364
Period size: 107 Copynumber: 2.5 Consensus size: 104
17259 AATATTTCTA
** ** * *
17269 ACCCTTAAAATAAAGTTTTAATTTTAATTT-AGGCTAAACTTAGTG-AATTAGTTATATATTTTG
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
17332 TTTCTAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAACCCTATAACAATATTATTAATTATGAAATTT
** * *
17371 ATTCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
17436 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCT-AAACCCTATAACAAT--ATTATTAATTATGAAATTT
*
17478 ACCCTTAAAATAAAAATAAAATCTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
17530 AGACTAAACT
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
102 24 0.17
103 14 0.10
104 20 0.14
105 15 0.11
107 66 0.47
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:18123 original size:6 final size:6
Alignment explanation
Indices: 18106--18135 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
18096 GACATCTTTT
18106 TATATAC TATATC TATATC TATATC TATAT
1 TATAT-C TATATC TATATC TATATC TATAT
18136 ATTATATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:18129 original size:12 final size:13
Alignment explanation
Indices: 18106--18142 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
18096 GACATCTTTT
18106 TATATACTATATC
1 TATATACTATATC
18119 TATAT-CTATATC
1 TATATACTATATC
*
18131 TATATATTATAT
1 TATATACTATAT
18143 AAGTCTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATACTATATC
Found at i:18462 original size:18 final size:20
Alignment explanation
Indices: 18419--18467 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
18409 CGTTAAACCT
18419 CTTATTATTATAATTATTAA
1 CTTATTATTATAATTATTAA
*
18439 GCTTATTATTATTA-TATTAA
1 -CTTATTATTATAATTATTAA
18459 -TTATTATTA
1 CTTATTATTA
18468 GTGGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
20 6 0.22
21 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
CTTATTATTATAATTATTAA
Done.