Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017099.1 Corchorus olitorius cultivar O-4 contig17132, 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: 11267
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Found at i:45 original size:20 final size:20
Alignment explanation
Indices: 2--47 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1 T
*
2 TGTTTTCAATATATTACTCC
1 TGTTTTCAATATATTACTCA
*
22 TGTTTTCAATAT-TTCATTCA
1 TGTTTTCAATATATT-ACTCA
42 TGTTTT
1 TGTTTT
48 GCCCTTCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.57
Consensus pattern (20 bp):
TGTTTTCAATATATTACTCA
Found at i:98 original size:47 final size:47
Alignment explanation
Indices: 22--142 Score: 197
Period size: 47 Copynumber: 2.5 Consensus size: 47
12 ATATTACTCC
*
22 TGTTTTCAATATTTCATTCATGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCAATATTT-ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
* *
70 TGTTTTCAATCTTTATTCCTGTTTTGCCCTTCCCGGTCGGATGGTGT
1 TGTTTTCAATATTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
117 TGTTTTCAATATCTTATTCCTGTTTT
1 TGTTTTCAATAT-TTATTCCTGTTTT
143 CAATGTTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 42 0.62
48 26 0.38
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (47 bp):
TGTTTTCAATATTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
Found at i:142 original size:20 final size:20
Alignment explanation
Indices: 117--162 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
107 CGGATGGTGT
*
117 TGTTTTCAATATCTTATTCC
1 TGTTTTCAATATCTTATTCA
* *
137 TGTTTTCAATGTTTTATTCA
1 TGTTTTCAATATCTTATTCA
157 TGTTTT
1 TGTTTT
163 GCCCTTCCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATCTTATTCA
Found at i:210 original size:20 final size:20
Alignment explanation
Indices: 185--230 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
175 CGGAAGGTGT
*
185 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAAAGTTTTATTCC
205 TGTTTTCAAAGTTTTATTCC
1 TGTTTTCAAAGTTTTATTCC
*
225 CGTTTT
1 TGTTTT
231 GCCCTTTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (20 bp):
TGTTTTCAAAGTTTTATTCC
Found at i:276 original size:20 final size:20
Alignment explanation
Indices: 253--298 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
243 CGAGATGTGT
*
253 TGTTTTTAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
273 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
*
293 CGTTTT
1 TGTTTT
299 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:346 original size:20 final size:20
Alignment explanation
Indices: 321--366 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
311 CGGAAGGTGT
321 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
341 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
361 TGTTTT
1 TGTTTT
367 GCCGTTCCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:414 original size:68 final size:68
Alignment explanation
Indices: 70--397 Score: 516
Period size: 68 Copynumber: 4.8 Consensus size: 68
60 CGGAAGGTGT
* * * *
70 TGTTTTCAAT-CTTTATTCCTGTTTTGCCCTTCCCGGTCGGATGGTGTTGTTTTCAATATCTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
134 TCC
66 TCC
*
137 TGTTTTCAATGTTTTATTCATGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
202 TCC
66 TCC
* * ** * *
205 TGTTTTCAAAGTTTTATTCCCGTTTTGCCCTTTTCGGTC-GAGATGTGTTGTTTTTAATGTTTTA
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGA-AGGTGTTGTTTTCAATGTTTTA
269 TTCC
65 TTCC
*
273 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
338 TCC
66 TCC
*
341 TGTTTTCAATGTTTTATTCCTGTTTTGCCGTTCCCGGTCGGAAGGTGTTGTTTTCAA
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAA
398 CATTCTATTC
Statistics
Matches: 239, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
67 12 0.05
68 225 0.94
69 2 0.01
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
TCC
Found at i:510 original size:48 final size:48
Alignment explanation
Indices: 342--503 Score: 234
Period size: 48 Copynumber: 3.4 Consensus size: 48
332 TTTTATTCCT
* * * *
342 GTTTTCAATGTTTTATTCCTGTTTTGCCGTTCCCGGTCGGAAGGTGTT
1 GTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTC
* * * *
390 GTTTTCAACATTCTATTCCAGTTTTGCCCTTCCTGGTCGGAAGGTGTG
1 GTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTC
*
438 GTTTTCAATATCTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTC
1 GTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTC
*
486 GTTCTCAATATTTTATTC
1 GTTTTCAATATTTTATTC
504 TTGTTTTCAA
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (48 bp):
GTTTTCAATATTTTATTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGTC
Found at i:2050 original size:16 final size:16
Alignment explanation
Indices: 2008--2051 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
1998 GATAACAACC
2008 AAATCATGACTCCACT
1 AAATCATGACTCCACT
* *
2024 -AA-CAAGACTCCAGT
1 AAATCATGACTCCACT
2038 AAATCATGACTCCA
1 AAATCATGACTCCA
2052 ATATATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (16 bp):
AAATCATGACTCCACT
Found at i:2180 original size:15 final size:17
Alignment explanation
Indices: 2140--2184 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
2130 TTTGCTAAAC
2140 TTCATTATATGAACAAT
1 TTCATTATATGAACAAT
2157 TTCATTATATGAACAA-
1 TTCATTATATGAACAAT
2173 TT-ATTATATGAA
1 TTCATTATATGAA
2185 TAAATACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 16 0.57
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (17 bp):
TTCATTATATGAACAAT
Found at i:2514 original size:130 final size:130
Alignment explanation
Indices: 2355--2597 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 130
2345 AACAATATTA
* * *
2355 ATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATAATAAAAA-TAAAT
1 ATATTTTAAAAATACTAATATATATAAG-TTTTTAATTAAAATAGTAAAATAATAAAAATTAAAT
*
2419 TG-TATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAA
65 AGTTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAA
2483 GT
129 GT
* **
2485 ATATTTTAAAAATACTAATATATATAAGTTTTTATTTAAAATAGTAAAATGGTAAAAATTAAATA
1 ATATTTTAAAAATACTAATATATATAAGTTTTTAATTAAAATAGTAAAATAATAAAAATTAAATA
*
2550 GTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTG
66 GTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG
2598 GATAAAATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
129 26 0.25
130 52 0.50
131 25 0.24
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (130 bp):
ATATTTTAAAAATACTAATATATATAAGTTTTTAATTAAAATAGTAAAATAATAAAAATTAAATA
GTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
Found at i:5459 original size:29 final size:28
Alignment explanation
Indices: 5427--5498 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
5417 ACTTGTAGCG
*
5427 TTTGGACGTTTTGTCCCTTGAATTTCAAT
1 TTTGGACGTTTTGTCCC-TGAACTTCAAT
* * *
5456 TTTGGACACTTTGGTCTCTGAACTTCAAT
1 TTTGGAC-GTTTTGTCCCTGAACTTCAAT
*
5485 TTTGGGATGTTTTG
1 TTT-GGACGTTTTG
5499 CCCCCTCAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (28 bp):
TTTGGACGTTTTGTCCCTGAACTTCAAT
Found at i:7141 original size:15 final size:14
Alignment explanation
Indices: 7104--7142 Score: 69
Period size: 14 Copynumber: 2.7 Consensus size: 14
7094 TTTTCACATA
7104 TATTATCTAATGTT
1 TATTATCTAATGTT
7118 TATTATCTAATGTT
1 TATTATCTAATGTT
7132 TATGTATCTAA
1 TAT-TATCTAA
7143 AATGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (14 bp):
TATTATCTAATGTT
Found at i:7583 original size:39 final size:40
Alignment explanation
Indices: 7527--7607 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
7517 TTTAATTCCT
7527 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
7567 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
7606 AT
1 AT
7608 TCTTAGGTAT
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:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:7932 original size:51 final size:51
Alignment explanation
Indices: 7872--7974 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
7862 TCACTACAAC
7872 TTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
1 TTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
7923 TTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
1 TTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
7974 T
1 T
7975 AAATCGGATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.38
Consensus pattern (51 bp):
TTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAA
Found at i:8015 original size:254 final size:249
Alignment explanation
Indices: 7717--8173 Score: 851
Period size: 251 Copynumber: 1.8 Consensus size: 249
7707 TTCCTTAATA
7717 ATAAATAAATCGGATCTTAATATCTTTTTAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
1 ATAAATAAATCGGATCTTAATATCTTTTTAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
*
7782 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTAA
66 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTT-GTATAGTT-T-TATATATAATAATAA
7847 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
128 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
7912 CCATTGATAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG
193 CCATTGATAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG
7969 ATAAATAAATCGGATCTTTAATATCTTTTTTAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATC-TTTTTAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
8034 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGTATAGTTTTATATATAATAATAAT
64 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGTATAGTTTTATATATAATAATAAT
8099 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
129 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
8164 CATTGATAAA
194 CATTGATAAA
8174 GCTATTAAGC
Statistics
Matches: 201, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
251 90 0.45
252 17 0.08
253 16 0.08
254 78 0.39
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (249 bp):
ATAAATAAATCGGATCTTAATATCTTTTTAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGTATAGTTTTATATATAATAATAATGT
GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
TTGATAAATTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTG
Found at i:8735 original size:36 final size:36
Alignment explanation
Indices: 8688--8757 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
8678 GAGATTTTGG
* *
8688 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
8724 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
8758 GGTTATTGAA
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:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:10678 original size:2 final size:2
Alignment explanation
Indices: 10673--10712 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
10663 TCGTCTCTCA
*
10673 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
10713 AGTCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10977 original size:39 final size:40
Alignment explanation
Indices: 10921--11001 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
10911 TTTAATTCCT
10921 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
10961 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
11000 AT
1 AT
11002 TTTTAGGTAT
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:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.