Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023704.1 Corchorus olitorius cultivar O-4 contig23737, 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: 32529
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:8248 original size:37 final size:36
Alignment explanation
Indices: 8193--8271 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
8183 AAACATTTCC
*
8193 TTCATAGTTTTCAAATTGGGAAAGTTCCTACCAAGTT
1 TTCA-AGTTTTCAAATTGGGAAAGTTCCCACCAAGTT
**
8230 TTCAAGTTTTCGAAATTGGGAAAGTTCCCGTCAAGTT
1 TTCAAGTTTTC-AAATTGGGAAAGTTCCCACCAAGTT
8267 TTCAA
1 TTCAA
8272 TTTAGGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 7 0.18
37 31 0.82
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (36 bp):
TTCAAGTTTTCAAATTGGGAAAGTTCCCACCAAGTT
Found at i:8263 original size:29 final size:29
Alignment explanation
Indices: 8231--8291 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
8221 TACCAAGTTT
8231 TCAAGTTTTCGAAATT-GGGAAAGTTCCCG
1 TCAAGTTTTC-AAATTAGGGAAAGTTCCCG
*
8260 TCAAGTTTTCAATTTAGGGAAAGTTCCCG
1 TCAAGTTTTCAAATTAGGGAAAGTTCCCG
8289 TCA
1 TCA
8292 TTTTCGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (29 bp):
TCAAGTTTTCAAATTAGGGAAAGTTCCCG
Found at i:15954 original size:25 final size:25
Alignment explanation
Indices: 15926--15993 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
15916 AATCTTGAGC
*
15926 ACTCTCGCTCGGTCTCTATTTGAAT
1 ACTCTTGCTCGGTCTCTATTTGAAT
15951 ACTCTTGCTCGGTCTCTATTTGAAT
1 ACTCTTGCTCGGTCTCTATTTGAAT
15976 ACTCTTGCTCGGTCTCTA
1 ACTCTTGCTCGGTCTCTA
15994 CAAACTAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (25 bp):
ACTCTTGCTCGGTCTCTATTTGAAT
Found at i:20056 original size:13 final size:14
Alignment explanation
Indices: 20025--20059 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
20015 TTTTCTTTTA
*
20025 TTTTTAAGTTATAT
1 TTTTTATGTTATAT
20039 TTTTTATGTTA-AT
1 TTTTTATGTTATAT
20052 TTTTTATG
1 TTTTTATG
20060 AATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (14 bp):
TTTTTATGTTATAT
Found at i:24115 original size:2 final size:2
Alignment explanation
Indices: 24108--24134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24098 CTAGGTATGT
24108 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
24135 GTGAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25383 original size:75 final size:75
Alignment explanation
Indices: 25294--25436 Score: 268
Period size: 75 Copynumber: 1.9 Consensus size: 75
25284 TACTCTAGTT
25294 TTTGAATCGATGGAGATTGAAGAGCAAAGAGCGAACTGGTTTGATGTATAGAAAATCGCTAACAA
1 TTTGAATCGATGGAGATTGAAGAGCAAAGAGCGAACTGGTTTGATGTATAGAAAATCGCTAACAA
25359 ATTCTTCTTG
66 ATTCTTCTTG
* *
25369 TTTGAATCGATGGAGATTGAAGAGCAATGAGCGAACTGGTTTGATGTATAGAAAATCGCTGACAA
1 TTTGAATCGATGGAGATTGAAGAGCAAAGAGCGAACTGGTTTGATGTATAGAAAATCGCTAACAA
25434 ATT
66 ATT
25437 TACAACGCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (75 bp):
TTTGAATCGATGGAGATTGAAGAGCAAAGAGCGAACTGGTTTGATGTATAGAAAATCGCTAACAA
ATTCTTCTTG
Found at i:26333 original size:73 final size:72
Alignment explanation
Indices: 26163--26439 Score: 269
Period size: 72 Copynumber: 3.8 Consensus size: 72
26153 ACAATATATA
* * * * * * * *
26163 TTCGTTGTTAAAAAAATTATCTTTTACACAACGACATTGTAGTCGTTAC--ATATATTTTGACAA
1 TTCGTTGTTAAAAGAATTATCTTTTACGCAA-TAC-TTTTTGACGTTACATATATATTTTGGCAG
26226 CGACATTTT
64 CGACATTTT
* *
26235 GTCGTTGTTAAAAGAATTATCTTTTACGCAATGACTTTTTTGACATTACATATATATTTTGGCAG
1 TTCGTTGTTAAAAGAATTATCTTTTACGCAAT-AC-TTTTTGACGTTACATATATATTTTGGCAG
*
26300 CTAC-TTTT
64 CGACATTTT
* * * * * *
26308 TTTGTTGTTAAAAGAATTATGTTTTACACAACAAC-TTTTAATCGTTAC--ATATATTTTGACAG
1 TTCGTTGTTAAAAGAATTATCTTTTACGCAA-TACTTTTTGA-CGTTACATATATATTTTGGCAG
26370 CGACATTTT
64 CGACATTTT
* * *
26379 TTCGTTGTTAAAATAATTATCTTTTACGTAACTACTTTTTGCCGTTACATATATATTTTGG
1 TTCGTTGTTAAAAGAATTATCTTTTACGCAA-TACTTTTTGACGTTACATATATATTTTGG
26440 TAATGACATT
Statistics
Matches: 166, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
70 16 0.10
71 44 0.27
72 48 0.29
73 43 0.26
74 15 0.09
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (72 bp):
TTCGTTGTTAAAAGAATTATCTTTTACGCAATACTTTTTGACGTTACATATATATTTTGGCAGCG
ACATTTT
Found at i:26353 original size:144 final size:144
Alignment explanation
Indices: 26166--26439 Score: 417
Period size: 144 Copynumber: 1.9 Consensus size: 144
26156 ATATATATTC
* *
26166 GTTGTTAAAAAAATTATCTTTTACACAACGACATTGTAGTCGTTACATATATTTTGACAACGACA
1 GTTGTTAAAAAAATTATCTTTTACACAACAACATTGTAATCGTTACATATATTTTGACAACGACA
26231 TTTTGTCGTTGTTAAAAGAATTATCTTTTACGCAA-TGACTTTTTTGACATTACATATATATTTT
66 TTTTGTCGTTGTTAAAAGAATTATCTTTTACGCAACT-AC-TTTTTGACATTACATATATATTTT
26295 GGCAGCTACTTTTTTT
129 GGCAGCTACTTTTTTT
* * * *
26311 GTTGTTAAAAGAATTATGTTTTACACAACAAC-TTTTAATCGTTACATATATTTTGACAGCGACA
1 GTTGTTAAAAAAATTATCTTTTACACAACAACATTGTAATCGTTACATATATTTTGACAACGACA
* * * * *
26375 TTTTTTCGTTGTTAAAATAATTATCTTTTACGTAACTACTTTTTGCCGTTACATATATATTTTGG
66 TTTTGTCGTTGTTAAAAGAATTATCTTTTACGCAACTACTTTTTGACATTACATATATATTTTGG
26440 TAATGACATT
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
143 24 0.21
144 63 0.54
145 30 0.26
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (144 bp):
GTTGTTAAAAAAATTATCTTTTACACAACAACATTGTAATCGTTACATATATTTTGACAACGACA
TTTTGTCGTTGTTAAAAGAATTATCTTTTACGCAACTACTTTTTGACATTACATATATATTTTGG
CAGCTACTTTTTTT
Found at i:26404 original size:71 final size:71
Alignment explanation
Indices: 26163--26432 Score: 308
Period size: 71 Copynumber: 3.8 Consensus size: 71
26153 ACAATATATA
* * *
26163 TTCGTTGTTAAAAAAATTATCTTTTACACAACGACATTGTAGTCGTTACATATATTTTGACAACG
1 TTCGTTGTTAAAAGAATTATCTTTTACACAACGAC-TTTTAGTCGTTACATATATTTTGACAGCG
26228 ACATTTT
65 ACATTTT
* * * * * * *
26235 GTCGTTGTTAAAAGAATTATCTTTTACGCAATGACTTTTTTGACATTACATATATATTTTGGCAG
1 TTCGTTGTTAAAAGAATTATCTTTTACACAACGAC-TTTTAGTCGTTAC--ATATATTTTGACAG
*
26300 CTAC-TTTT
63 CGACATTTT
* * * *
26308 TTTGTTGTTAAAAGAATTATGTTTTACACAACAACTTTTAATCGTTACATATATTTTGACAGCGA
1 TTCGTTGTTAAAAGAATTATCTTTTACACAACGACTTTTAGTCGTTACATATATTTTGACAGCGA
26373 CATTTT
66 CATTTT
* ** * * *
26379 TTCGTTGTTAAAATAATTATCTTTTACGTAACTACTTTTTGCCGTTACATATAT
1 TTCGTTGTTAAAAGAATTATCTTTTACACAACGACTTTTAGTCGTTACATATAT
26433 ATTTTGGTAA
Statistics
Matches: 162, Mismatches: 33, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
70 16 0.10
71 49 0.30
72 49 0.30
73 33 0.20
74 15 0.09
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (71 bp):
TTCGTTGTTAAAAGAATTATCTTTTACACAACGACTTTTAGTCGTTACATATATTTTGACAGCGA
CATTTT
Found at i:29725 original size:22 final size:22
Alignment explanation
Indices: 29700--29756 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
29690 ATTTCGACAG
* **
29700 CCTCCCTATGAAAATTTTATAA
1 CCTCACTATGAAAATTAGATAA
* *
29722 CCTCTCTATAAAAATTAGATAA
1 CCTCACTATGAAAATTAGATAA
*
29744 CCACACTATGAAA
1 CCTCACTATGAAA
29757 TGTTGATCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (22 bp):
CCTCACTATGAAAATTAGATAA
Found at i:30000 original size:131 final size:131
Alignment explanation
Indices: 29762--30431 Score: 826
Period size: 131 Copynumber: 5.1 Consensus size: 131
29752 TGAAATGTTG
* * * * *
29762 ATCACTTAGGCAACGGTATTATAAAGTTGTTACAAACAGTTTATGATTTTG-AAGCAACTTAAGA
1 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAA-CAACTTAAGA
* * *
29826 ATTTGTTGTTACGAATACTGTAAACATTGGCAACAACTAAAAAAATGTTGTGTGAAATACCATCA
65 ATTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCA
29891 AA
130 AA
29893 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCTGCAACAACTTAAGA
1 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTC-GCAACAACTTAAGA
* * * * * *
29958 AATTGTTCTAATGAATATTGTAAACATTGGCAACAACTAAAAACGTGTTGTGTAAACTACCATCA
65 ATTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCA
30023 AA
130 AA
* * *
30025 ATCACTTAGACAACGTTTTTATAAAGTTATTACGAAAAGTTTATGATTTCGCAACAACTTAAGAA
1 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAA
**
30090 TTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACTTTCAA
66 TTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAA
30155 A
131 A
* * * *
30156 ATCACTTAGACAACATTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGAA-TT-TGT
1 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAAC-AACTTAAGA
* * * * * * *
30219 TTTTATTGTTACGAAAATTGTAAGCATTAGCAACGACTAAAAAAGTGTTGTGTAAAATACCAACA
65 ATTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCA
30284 AA
130 AA
*** * ** * ** **
30286 ATCACTTAGGCAACAACTTTATAAAATTGTTACGAATAAATTATGATTTCGCAACGA-TTTTGTT
1 ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAA
* * ** * * * *
30350 TTTGTTGTTACGAAAACTGTAAGTATTGGCAACAATTAGAAAAGTTATTGGGTAAAATACCATCA
66 TTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAG-TGTTGTGTAAAATACCATCA
30415 AA
130 AA
*
30417 ATCACTAAGGCAACG
1 ATCACTTAGGCAACG
30432 ACTTTTAATT
Statistics
Matches: 476, Mismatches: 58, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
129 3 0.01
130 149 0.31
131 204 0.43
132 118 0.25
133 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (131 bp):
ATCACTTAGGCAACGTTTTTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACAACTTAAGAA
TTTGTTGTTACGAATATTGTAAACATTGGCAACAACTAAAAAAGTGTTGTGTAAAATACCATCAA
A
Found at i:32431 original size:2 final size:2
Alignment explanation
Indices: 32424--32448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32414 TCATAGAATA
32424 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 A
32449 ATTGTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.