Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014256.1 Corchorus olitorius cultivar O-4 contig14289, 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: 18347
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Found at i:2183 original size:93 final size:94
Alignment explanation
Indices: 2064--2247 Score: 289
Period size: 93 Copynumber: 2.0 Consensus size: 94
2054 AAAAAATTCT
* * * *
2064 GTCATTTGCCATTCCGTCTTGAAATACCGTTAACTAATTCTGCCCCAAAATACCGTTAAA-TTTT
1 GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCCCAAAATACCGTTAAACTTAT
2128 TCCAACCAAGAATACCGTTAACTTATACC
66 TCCAACCAAGAATACCGTTAACTTATACC
* * *
2157 GTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATACCGTTAAACTTAT
1 GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCCCAAAATACCGTTAAACTTAT
*
2222 TCCAATCAAGAATACCGTTAACTTAT
66 TCCAACCAAGAATACCGTTAACTTAT
2248 TCCGGTTAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 54 0.66
94 28 0.34
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (94 bp):
GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCCCAAAATACCGTTAAACTTAT
TCCAACCAAGAATACCGTTAACTTATACC
Found at i:2275 original size:210 final size:211
Alignment explanation
Indices: 2016--2459 Score: 723
Period size: 210 Copynumber: 2.1 Consensus size: 211
2006 CTTAATCCGC
*
2016 CCAAGAATACCGTTTACTTATTCCGGTTGAAAGGACGAAAAAAATTCTGTCATTTGCCATTCCGT
1 CCAAGAATACCGTTAACTTATTCCGGTTGAAAGGACGAAAAAAATTCTGTCATTTGCCATTCCGT
* * *
2081 CTTGAAATACCGTTAACTAATTCTGCCCCAA-AATACCGTTAAATTTTTCCAACCAAGAATACCG
66 CTTGAAATACCGTTAACTAATTCTG-CCAAAGAATACCGTTAAATTATTCCAACCAAGAATACCA
2145 TTAACTTATACCGTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATAC
130 TTAACTTATACCGTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATAC
*
2210 CGTTAAACTTATTCCAA
195 AGTTAAACTTATTCCAA
* * *
2227 TCAAGAATACCGTTAACTTATTCCGGTT-AACAGGAC-AAAAATATTCTGTCATTTGCCATTTCG
1 CCAAGAATACCGTTAACTTATTCCGGTTGAA-AGGACGAAAAAAATTCTGTCATTTGCCATTCCG
2290 TCTTGAAATACCGTTAACTAATTCTGCCAAAGAATACCGTTAAATTATTCCAACCAAGAATACCA
65 TCTTGAAATACCGTTAACTAATTCTGCCAAAGAATACCGTTAAATTATTCCAACCAAGAATACCA
* * * * *
2355 TTAACTTATTCCGTCATTTGTCATTCCGTCGTGGAATACCGTTAACTTATTCTGTCCGAGAATAC
130 TTAACTTATACCGTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATAC
2420 AGTTAAACTTATTCCAA
195 AGTTAAACTTATTCCAA
*
2437 CCAAGAATACCGTTAATTTATTC
1 CCAAGAATACCGTTAACTTATTC
2460 AGGTCAACTA
Statistics
Matches: 216, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
209 4 0.02
210 181 0.84
211 31 0.14
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (211 bp):
CCAAGAATACCGTTAACTTATTCCGGTTGAAAGGACGAAAAAAATTCTGTCATTTGCCATTCCGT
CTTGAAATACCGTTAACTAATTCTGCCAAAGAATACCGTTAAATTATTCCAACCAAGAATACCAT
TAACTTATACCGTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATACA
GTTAAACTTATTCCAA
Found at i:2307 original size:117 final size:116
Alignment explanation
Indices: 2157--2367 Score: 332
Period size: 117 Copynumber: 1.8 Consensus size: 116
2147 AACTTATACC
* **
2157 GTCATTTGACATTCCGTCGTGGAATACCGTTAACTAAATCTGCCCGAGAATACCGTTAAACTTAT
1 GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCAAAGAATACCGTTAAA-TTAT
* *
2222 TCCAATCAAGAATACCGTTAACTTATTCCGGTTAACAGGACAAAAATATTCT
65 TCCAACCAAGAATACCATTAACTTATTCCGGTTAACAGGACAAAAATATTCT
* * * *
2274 GTCATTTGCCATTTCGTCTTGAAATACCGTTAACTAATTCTGCCAAAGAATACCGTTAAATTATT
1 GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCAAAGAATACCGTTAAATTATT
2339 CCAACCAAGAATACCATTAACTTATTCCG
66 CCAACCAAGAATACCATTAACTTATTCCG
2368 TCATTTGTCA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
116 32 0.38
117 53 0.62
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (116 bp):
GTCATTTGACATTCCGTCGTGAAATACCGTTAACTAAATCTGCCAAAGAATACCGTTAAATTATT
CCAACCAAGAATACCATTAACTTATTCCGGTTAACAGGACAAAAATATTCT
Found at i:2339 original size:26 final size:25
Alignment explanation
Indices: 2296--2365 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
2286 TTCGTCTTGA
* **
2296 AATACCGTTAACTAATTCTGCCAAAG
1 AATACCGTTAACTTATTCAACC-AAG
*
2322 AATACCGTTAAATTATTCCAACCAAG
1 AATACCGTTAACTTATT-CAACCAAG
*
2348 AATACCATTAACTTATTC
1 AATACCGTTAACTTATTC
2366 CGTCATTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.03
26 33 0.89
27 3 0.08
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (25 bp):
AATACCGTTAACTTATTCAACCAAG
Found at i:2396 original size:93 final size:94
Alignment explanation
Indices: 2268--2459 Score: 271
Period size: 93 Copynumber: 2.1 Consensus size: 94
2258 AGGACAAAAA
* * * *
2268 TATTCTGTCATTTGCCATTTCGTCTTGAAATACCGTTAACTAATTCTG-CCAAAGAATACCGTTA
1 TATTCCGTCATTTGCCATTCCGTCGTGAAATACCGTTAACTAATTCTGTCC-AAGAATACAGTTA
2332 AA-TTATTCCAACCAAGAATACCATTAACT
65 AACTTATTCCAACCAAGAATACCATTAACT
* * * *
2361 TATTCCGTCATTTGTCATTCCGTCGTGGAATACCGTTAACTTATTCTGTCCGAGAATACAGTTAA
1 TATTCCGTCATTTGCCATTCCGTCGTGAAATACCGTTAACTAATTCTGTCCAAGAATACAGTTAA
* *
2426 ACTTATTCCAACCAAGAATACCGTTAATT
66 ACTTATTCCAACCAAGAATACCATTAACT
2455 TATTC
1 TATTC
2460 AGGTCAACTA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
93 55 0.63
94 32 0.37
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (94 bp):
TATTCCGTCATTTGCCATTCCGTCGTGAAATACCGTTAACTAATTCTGTCCAAGAATACAGTTAA
ACTTATTCCAACCAAGAATACCATTAACT
Found at i:2406 original size:26 final size:27
Alignment explanation
Indices: 2388--2452 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
2378 TTCCGTCGTG
* *
2388 GAATACCGTT-AACTTATTCTGTCCGA
1 GAATACAGTTAAACTTATTCCGTCCGA
** *
2414 GAATACAGTTAAACTTATTCCAACCAA
1 GAATACAGTTAAACTTATTCCGTCCGA
*
2441 GAATACCGTTAA
1 GAATACAGTTAA
2453 TTTATTCAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (27 bp):
GAATACAGTTAAACTTATTCCGTCCGA
Found at i:2654 original size:41 final size:41
Alignment explanation
Indices: 2597--2697 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 41
2587 CTATTCCCAT
* **
2597 GGGATACCGTTAACTTATTCCGTCTGTAACTTTTCCATCGA
1 GGGATACCGTTAACTTATTCCGTCTATAACTAATCCATCGA
* * * *
2638 GGGATACCATTAACTTATTCCTTCTATATCTAATGCATCGA
1 GGGATACCGTTAACTTATTCCGTCTATAACTAATCCATCGA
2679 GGGATACCGTTAACTTATT
1 GGGATACCGTTAACTTATT
2698 ACACCCAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (41 bp):
GGGATACCGTTAACTTATTCCGTCTATAACTAATCCATCGA
Found at i:5675 original size:12 final size:12
Alignment explanation
Indices: 5634--5674 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
5624 CAGATGATCT
5634 AAAATTTCTCAAAG
1 AAAATTT-T-AAAG
5648 AAAATTTTAAAG
1 AAAATTTTAAAG
5660 AAAATTTT-AAG
1 AAAATTTTAAAG
5671 AAAA
1 AAAA
5675 AAAAATCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.26
12 12 0.44
13 1 0.04
14 7 0.26
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (12 bp):
AAAATTTTAAAG
Done.