Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012116.1 Corchorus olitorius cultivar O-4 contig12149, 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: 42546
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2567 original size:23 final size:23
Alignment explanation
Indices: 2541--2595 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2531 GAAATCAAAG
*
2541 AAAAGAGAAGATTA-AACAAAATA
1 AAAATAGAAGA-TAGAACAAAATA
* *
2564 AAAATAAAAGATAGAACAAATTA
1 AAAATAGAAGATAGAACAAAATA
2587 AAAATAGAA
1 AAAATAGAA
2596 ATTTAAGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAATAGAAGATAGAACAAAATA
Found at i:4100 original size:14 final size:13
Alignment explanation
Indices: 4081--4119 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4071 ACTCAACACT
4081 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
4095 AACTGACTCAACA
1 AACTGACTCAAAA
4108 AACTGACT-AAAA
1 AACTGACTCAAAA
4120 CCCGACAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:4112 original size:13 final size:13
Alignment explanation
Indices: 4070--4115 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
4060 GGCAGACTCA
4070 GACTCAACACTAACT
1 GACTCAACA--AACT
*
4085 GACTCGAAAAAACT
1 GACTC-AACAAACT
4099 GACTCAACAAACT
1 GACTCAACAAACT
4112 GACT
1 GACT
4116 AAAACCCGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:5077 original size:17 final size:17
Alignment explanation
Indices: 5055--5099 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
5045 CCCTTCTTCC
5055 CTATTTCCTTTCCCTTA
1 CTATTTCCTTTCCCTTA
* *
5072 CTATTTCCTCT-CCTTC
1 CTATTTCCTTTCCCTTA
5088 CTATTT-CTTTCC
1 CTATTTCCTTTCC
5100 TCTCTACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 10 0.42
ACGTcount: A:0.09, C:0.38, G:0.00, T:0.53
Consensus pattern (17 bp):
CTATTTCCTTTCCCTTA
Found at i:5091 original size:16 final size:16
Alignment explanation
Indices: 5041--5094 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
5031 ATATGACTTC
*
5041 ATTTCC-CTTCTTCCCT
1 ATTTCCTCTCCTT-CCT
* *
5057 ATTTCCTTTCCCTTACT
1 ATTTCCTCT-CCTTCCT
5074 ATTTCCTCTCCTTCCT
1 ATTTCCTCTCCTTCCT
5090 ATTTC
1 ATTTC
5095 TTTCCTCTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 17 0.55
17 11 0.35
18 3 0.10
ACGTcount: A:0.09, C:0.39, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTCCTCTCCTTCCT
Found at i:12848 original size:21 final size:21
Alignment explanation
Indices: 12822--12863 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12812 AAATTAAACA
12822 CCCAAGAACAAGAAAAGCAAG
1 CCCAAGAACAAGAAAAGCAAG
12843 CCCAAGAACAAGAAAAGCAAG
1 CCCAAGAACAAGAAAAGCAAG
12864 GAATATGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.24, G:0.19, T:0.00
Consensus pattern (21 bp):
CCCAAGAACAAGAAAAGCAAG
Found at i:16460 original size:13 final size:13
Alignment explanation
Indices: 16442--16467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16432 AGGTATCATT
16442 ATTATATGTGTTC
1 ATTATATGTGTTC
16455 ATTATATGTGTTC
1 ATTATATGTGTTC
16468 CACCAACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTATATGTGTTC
Found at i:23053 original size:120 final size:120
Alignment explanation
Indices: 22890--23268 Score: 568
Period size: 120 Copynumber: 3.2 Consensus size: 120
22880 ATCATGGGTC
* * * *
22890 GTCACCAAATATGAGGAAAATGCTT--AGTTATATGTGACGAAAA-TGTAAACGTCACATGTATA
1 GTCACAAAAAATGAGGAAAATG-TTCCA-TTATTTGTGACGAAAATTG-GAACGTCACATGTATA
** * * *
22952 GGTGACGCCCAT-TTTGTCATAAAATATTAAAATATAACGTCACTAACAATTGTTGATT
63 GGTGACG-GAATGTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
*
23010 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACAAAAATTGGAACGTCACATGTATAGGT
1 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATTGGAACGTCACATGTATAGGT
*
23075 GACGGAATGTGTGTCACAAAATACTACAATATAACGTCACTAACAATTGTTGATT
66 GACGGAATGTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
23130 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATTGGAACGTCACATGTATAGGT
1 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATTGGAACGTCACATGTATAGGT
* *
23195 GACGGAATGTGTGTCGCAAAATACTAAAATATAACGTCACTTACAATTGTTGATT
66 GACGGAATGTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
*
23250 GTCACAAAATATGAGGAAA
1 GTCACAAAAAATGAGGAAA
23269 TTTTTCATTA
Statistics
Matches: 239, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
119 4 0.02
120 232 0.97
121 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (120 bp):
GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATTGGAACGTCACATGTATAGGT
GACGGAATGTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
Found at i:23364 original size:119 final size:119
Alignment explanation
Indices: 22972--23317 Score: 453
Period size: 120 Copynumber: 2.9 Consensus size: 119
22962 ATTTTGTCAT
*
22972 AAAATATTAAAATATAACGTCACTAACAATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCA
1 AAAATACTAAAATATAACGTCACTAA-AATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCA
** * * * * * *
23037 TTATTTGTGACAAAAATTGGAACGTCACATGTATAGGTGACGGAATGTGTGTCAC
65 TTATTCCTGACGAAAATTAGAACGCCACAAGAATAGGTGACGGAATGTGTGTCGC
*
23092 AAAATACTACAATATAACGTCACTAACAATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCA
1 AAAATACTAAAATATAACGTCACTAA-AATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCA
** * * * *
23157 TTATTTGTGACGAAAATTGGAACGTCACATGTATAGGTGACGGAATGTGTGTCGC
65 TTATTCCTGACGAAAATTAGAACGCCACAAGAATAGGTGACGGAATGTGTGTCGC
* * * *
23212 AAAATACTAAAATATAACGTCACTTACAATTGTTGATTGTCACAAAATATGAGG-AAATTTTTCA
1 AAAATACTAAAATATAACGTCAC-TAAAATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCA
*
23276 TTATTCCTGACG-AATTTCAGAACGCCACAAGAATAGGTGACG
65 TTATTCCTGACGAAAATT-AGAACGCCACAAGAATAGGTGACG
23318 TAAGTTTCGT
Statistics
Matches: 208, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
118 4 0.02
119 38 0.18
120 164 0.79
121 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (119 bp):
AAAATACTAAAATATAACGTCACTAAAATTGTTGATTGTCACAAAAAATGAGGAAAATGTTCCAT
TATTCCTGACGAAAATTAGAACGCCACAAGAATAGGTGACGGAATGTGTGTCGC
Found at i:23381 original size:240 final size:239
Alignment explanation
Indices: 22888--23406 Score: 563
Period size: 240 Copynumber: 2.2 Consensus size: 239
22878 ATATCATGGG
* * *
22888 TCGTCACCAAATATGAGGAAAATGCTT-AGTTATATGTGACGAAAATGTAAACGTCACATGTATA
1 TCGTCACAAAAAATGAGGAAAATG-TTCA-TTATTTGTGACGAAAATGTAAACGTCACATGTATA
* * * *
22952 GGTGACGCCCATTTTGTCATAAAATATTAAAATATAACGTCACTAACAATTGTTGATTGTCACAA
64 GGTGACGCCAATTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCACAA
** * * * *
23017 AAAATGAGGAAAATGTTCCATTATTTGTGACAAAAATTGGAACGTCACATGTATAGGTGACGGAA
129 AAAATGAGGAAAATGTTCCATTATTCCTGACAAAAATTAGAACGCCACAAGAATAGGTGACGGAA
*
23082 TGTGTGTCACAAAATACTACAATATAACGTCACTAACAATTGTTGA
194 TGTGTGTCACAAAATACTACAATATAACGTCACTAACAATTGTTAA
* *
23128 TTGTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAAT-TGGAACGTCACATGTATA
1 TCGTCACAAAAAATGAGGAAAATGTT-CATTATTTGTGACGAAAATGT-AAACGTCACATGTATA
* * *
23192 GGTGACG-GAATGTGTGTCGCAAAATACTAAAATATAACGTCACTTACAATTGTTGATTGTCACA
64 GGTGACGCCAAT-TGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCACA
* * * * * *
23256 AAATATGAGG-AAATTTTTCATTATTCCTGAC-GAATTTCAGAACGCCACAAGAATAGGTGACGT
128 AAAAATGAGGAAAATGTTCCATTATTCCTGACAAAAATT-AGAACGCCACAAGAATAGGTGACGG
* * * **
23319 AA-GTTTCGTCATGCAATAT-GTA-TTTATAACGTCACTAA-AAGTTGTTAA
192 AATGTGT-GTCA--CAAAATACTACAATATAACGTCACTAACAA-TTGTTAA
* * *
23367 TCGTCACAAAAAAAT-AAGTAAATGTTCAATTATTCGTGAC
1 TCGTCAC-AAAAAATGAGGAAAATGTTC-ATTATTTGTGAC
23407 ACAATGAGTA
Statistics
Matches: 234, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
238 10 0.04
239 94 0.40
240 124 0.53
241 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (239 bp):
TCGTCACAAAAAATGAGGAAAATGTTCATTATTTGTGACGAAAATGTAAACGTCACATGTATAGG
TGACGCCAATTGTGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCACAAAA
AATGAGGAAAATGTTCCATTATTCCTGACAAAAATTAGAACGCCACAAGAATAGGTGACGGAATG
TGTGTCACAAAATACTACAATATAACGTCACTAACAATTGTTAA
Found at i:24894 original size:67 final size:67
Alignment explanation
Indices: 24786--24916 Score: 176
Period size: 67 Copynumber: 2.0 Consensus size: 67
24776 ATAAATTGAC
* *
24786 AAATTGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCTGATCTAAGTATTTAAGGAA
1 AAATTGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCAGATCTAAGTATATAAGGAA
24851 AA
66 AA
* * * *
24853 AAATTGACAGATTTGC-ATTTAATGTGGAGA-ATGACCGTTGGAGGCAGATCTGAGTATATAAGG
1 AAATTGAAAGACTTGCGA-TTAATGAGGA-ATATGACCGTTGGAGGCAGATCTAAGTATATAAGG
24916 A
64 A
24917 CCCAAAAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 1 0.02
67 54 0.96
68 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (67 bp):
AAATTGAAAGACTTGCGATTAATGAGGAATATGACCGTTGGAGGCAGATCTAAGTATATAAGGAA
AA
Found at i:25285 original size:28 final size:28
Alignment explanation
Indices: 25223--25278 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
25213 CACTTGTTCG
* *
25223 AGCTTGGGTTAAGCTCGGTGCTGTCACA
1 AGCTTGGGTGAAGCTCGGTGCTGTAACA
*
25251 AGCTTGGGTGAAGCTTGGTTGCTGTAAC
1 AGCTTGGGTGAAGCTCGG-TGCTGTAAC
25279 TACTTGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (28 bp):
AGCTTGGGTGAAGCTCGGTGCTGTAACA
Found at i:26725 original size:25 final size:25
Alignment explanation
Indices: 26687--26735 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
26677 AAAAATCTTT
*
26687 TTACCATTTGATTT-TTTCTAAAAC
1 TTACCATTTGATTTGTTTCCAAAAC
*
26711 TTACCAATTTTATTTGTTTCCAAAA
1 TTACC-ATTTGATTTGTTTCCAAAA
26736 TCTTCTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (25 bp):
TTACCATTTGATTTGTTTCCAAAAC
Found at i:31195 original size:28 final size:28
Alignment explanation
Indices: 31163--31232 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
31153 AGTGCATTTG
* *
31163 AAATGACCAAAATGCCCCTGGACTTGCA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
31191 AAATGACCAAAATGCCCCTGGTCATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
31219 AAATGACCAAAATG
1 AAATGACCAAAATG
31233 AGAAGCAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGAA
Found at i:31685 original size:19 final size:18
Alignment explanation
Indices: 31661--31696 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31651 TGAAGACCAT
31661 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
31680 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
31697 TTTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:34256 original size:20 final size:21
Alignment explanation
Indices: 34216--34259 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34206 CATAATTGAT
*
34216 AAAAAAAGTTGAATAATCTAA
1 AAAAAAAGTTAAATAATCTAA
*
34237 AAAAAAAGTTAAATGA-CTAA
1 AAAAAAAGTTAAATAATCTAA
34257 AAA
1 AAA
34260 GAATACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (21 bp):
AAAAAAAGTTAAATAATCTAA
Found at i:35230 original size:18 final size:19
Alignment explanation
Indices: 35207--35243 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35197 TAGATTTCGG
*
35207 AAAATTC-CAATCGAAAAC
1 AAAATTCGCAATCAAAAAC
35225 AAAATTCGCAATCAAAAAC
1 AAAATTCGCAATCAAAAAC
35244 TCCTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAATTCGCAATCAAAAAC
Found at i:41318 original size:16 final size:16
Alignment explanation
Indices: 41297--41328 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41287 CTTTGAAACC
41297 TAAAATGCTGAATACT
1 TAAAATGCTGAATACT
41313 TAAAATGCTGAATACT
1 TAAAATGCTGAATACT
41329 AAATAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
TAAAATGCTGAATACT
Done.