Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013611.1 Corchorus olitorius cultivar O-4 contig13644, 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: 38090
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--65 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
43 CA CA CA CA CA -A AA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA
66 AAAGAGGTGT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:404 original size:63 final size:66
Alignment explanation
Indices: 308--447 Score: 205
Period size: 63 Copynumber: 2.2 Consensus size: 66
298 TACATCTAAT
* * *
308 TTACTTTCATTCATATTAATCATATTAAGCATATTCATGTTGA-TT-TC-TTAAGCATGCTCATA
1 TTACTTTCATTCATATTAATCACATTAAGCATATTCATATTCATTTCTCATTAAGCATGCTCATA
*
370 C
66 A
* *
371 TTACTTTCATTCATATTAATCACATTAAGCATATTCCTATTCATTTCTCATTAAGCATGTTCATA
1 TTACTTTCATTCATATTAATCACATTAAGCATATTCATATTCATTTCTCATTAAGCATGCTCATA
436 A
66 A
437 TTACTTTCATT
1 TTACTTTCATT
448 TATCCATTAG
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 39 0.57
64 2 0.03
65 2 0.03
66 25 0.37
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (66 bp):
TTACTTTCATTCATATTAATCACATTAAGCATATTCATATTCATTTCTCATTAAGCATGCTCATA
A
Found at i:3049 original size:13 final size:13
Alignment explanation
Indices: 3031--3056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3021 AATGATTTAA
3031 AAATCAATTCTTT
1 AAATCAATTCTTT
3044 AAATCAATTCTTT
1 AAATCAATTCTTT
3057 GAAAGTTGAT
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATCAATTCTTT
Found at i:3252 original size:91 final size:92
Alignment explanation
Indices: 3136--3336 Score: 255
Period size: 91 Copynumber: 2.2 Consensus size: 92
3126 GTCTTTGGGT
* * * * *
3136 TAAACTTAACTT-AAAGATTGGTTCTTTGATCCTTTTAAGTTAAGGTTAACTTAAAAATTAATTC
1 TAAAATTAACTTGAAA-ATTGATTCTTTGATACTTTTAAGTTAAGATTAACTTAAAAACTAATTC
*
3200 TTTAAACCAAAGCTTAAATTTTTAAG-C
65 TTTAAACCAAAGCTTAAACTTTTAAGAC
* * *
3227 TAAAATTAACTTGAAAATTGATTCTTTGATACTTTTGAGTTAAGATTAATTTGAAAACTAATTCT
1 TAAAATTAACTTGAAAATTGATTCTTTGATACTTTTAAGTTAAGATTAACTTAAAAACTAATTCT
* * * *
3292 TTAAGCTAAAGTTTAGACTTTTAAGAC
66 TTAAACCAAAGCTTAAACTTTTAAGAC
3319 -AAAATTAACTTGAAAATT
1 TAAAATTAACTTGAAAATT
3337 TATTATTGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
91 91 0.96
92 4 0.04
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (92 bp):
TAAAATTAACTTGAAAATTGATTCTTTGATACTTTTAAGTTAAGATTAACTTAAAAACTAATTCT
TTAAACCAAAGCTTAAACTTTTAAGAC
Found at i:3371 original size:91 final size:90
Alignment explanation
Indices: 3189--3518 Score: 267
Period size: 91 Copynumber: 3.6 Consensus size: 90
3179 GGTTAACTTA
* * * *
3189 AAAATTAATTCTTTAAACCAAAGCTTAAATTTTTAAG-CTAAAATTAACTTGAAAATTGATTCTT
1 AAAATTAATTCTTTAAACTAAAGTTTAGA-TTTTAAGAC-AAAATTAACTTGAAAATTGATT-AT
**
3253 TG-ATAC-TTTTGAGTTAAGATTAATTTG
63 TGAAT-CTTTTTGAGTTAATCTTAATTTG
* * *
3280 AAAACTAATTCTTTAAGCTAAAGTTTAGACTTTTAAGACAAAATTAACTTGAAAATTTATTATTG
1 AAAATTAATTCTTTAAACTAAAGTTTAGA-TTTTAAGACAAAATTAACTTGAAAATTGATTATTG
* * *
3345 AATCTTTTTAAGCTAATCTTAGTTTG
65 AATCTTTTTGAGTTAATCTTAATTTG
* * ** ** * *
3371 AAAATTAAAAT-TTTGATTTAAAGGTTT-GATTTTTGGATTAAAATTAACTTGGAAATTGATTAT
1 AAAATT-AATTCTTTAAACTAAA-GTTTAGATTTTAAGA-CAAAATTAACTTGAAAATTGATTAT
3434 TGAATCTTTTTGAGTTAATCTTAATTTG
63 TGAATCTTTTTGAGTTAATCTTAATTTG
* ** ** * * **
3462 AAAGTTAAAACTTTGCATTAAAGGTTT-GATTTTTAGGTTAAAATTAACTTGAAAATT
1 AAAATTAATTCTTTAAACTAAA-GTTTAGA-TTTTAAGACAAAATTAACTTGAAAATT
3519 TAGCCTTTAA
Statistics
Matches: 198, Mismatches: 33, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
90 13 0.07
91 171 0.86
92 14 0.07
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (90 bp):
AAAATTAATTCTTTAAACTAAAGTTTAGATTTTAAGACAAAATTAACTTGAAAATTGATTATTGA
ATCTTTTTGAGTTAATCTTAATTTG
Found at i:10605 original size:17 final size:17
Alignment explanation
Indices: 10583--10619 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10573 TGCAAAGATC
* *
10583 TTTCTTTTTTTTATTTA
1 TTTCTTTTTCTAATTTA
10600 TTTCTTTTTCTAATTTA
1 TTTCTTTTTCTAATTTA
10617 TTT
1 TTT
10620 TTATTCGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTCTAATTTA
Found at i:23864 original size:24 final size:24
Alignment explanation
Indices: 23837--23882 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
23827 TCTTTTATTC
23837 TATGCTTGAGCCTTTAATTTTGTT
1 TATGCTTGAGCCTTTAATTTTGTT
* * * *
23861 TATGTTTGGGCTTTTTATTTTG
1 TATGCTTGAGCCTTTAATTTTG
23883 GGCTTTTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.59
Consensus pattern (24 bp):
TATGCTTGAGCCTTTAATTTTGTT
Found at i:23884 original size:14 final size:15
Alignment explanation
Indices: 23859--23889 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
23849 TTTAATTTTG
23859 TTTATGTTTGGGCTT
1 TTTATGTTTGGGCTT
23874 TTTAT-TTTGGGCTT
1 TTTATGTTTGGGCTT
23888 TT
1 TT
23890 AAATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.06, C:0.06, G:0.23, T:0.65
Consensus pattern (15 bp):
TTTATGTTTGGGCTT
Found at i:24333 original size:35 final size:34
Alignment explanation
Indices: 24289--24556 Score: 290
Period size: 35 Copynumber: 7.7 Consensus size: 34
24279 AGTGAGTAAA
* *
24289 TAACTTAATTCATGGTAATTAAATAAGTCGATAAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTC-ATAAG
* *
24324 TAACTTAATTCAGGGTAATTAAGTAGGTCAGTGAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCA-TAAG
*
24359 TAACTTAATTCAGAGTAATTAAGTAAGTCAGT-AG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCA-TAAG
*
24393 TAACTTAATTCTGGGTAATTAAGTAAGTCAATAAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTC-ATAAG
*
24428 TAACTTAATTCAGGGTGATTAAGTAAGTCAATAAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTC-ATAAG
* * *
24463 TAACTTAATTCAAGATAATTAAGTAAGTCAGCAA-
1 TAACTTAATTCAGGGTAATTAAGTAAGTCA-TAAG
* * * * *
24497 TCATCTTAGTTCAGGATAATTAAGAAAATCAATAAG
1 T-AACTTAATTCAGGGTAATTAAGTAAGTC-ATAAG
*
24533 TAACTTAA-TCAGGGGTCATTAAGT
1 TAACTTAATTCA-GGGTAATTAAGT
24557 TTATTAAGAG
Statistics
Matches: 200, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
34 36 0.18
35 162 0.81
36 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (34 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCATAAG
Found at i:24469 original size:104 final size:104
Alignment explanation
Indices: 24287--24556 Score: 348
Period size: 104 Copynumber: 2.6 Consensus size: 104
24277 ATAGTGAGTA
* * *
24287 AATAACTTAATTCAT-GGTAATTAAATAAGTCGATAAGTAACTTAATTCAGGGTAATTAAGTAGG
1 AATAACTTAATTC-TGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGTAAG
* * *
24351 TCAGTGAGTAACTTAATTC-AGAGTAATTAAGTAAGTCAGT
65 TCAATAAGTAACTTAATTCAAGA-TAATTAAGTAAGTCAGC
* *
24391 AGTAACTTAATTCTGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTGATTAAGTAAGT
1 AATAACTTAATTCTGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGTAAGT
24456 CAATAAGTAACTTAATTCAAGATAATTAAGTAAGTCAGC
66 CAATAAGTAACTTAATTCAAGATAATTAAGTAAGTCAGC
* * * * * * *
24495 AATCATCTTAGTTCAGGATAATTAAGAAAATCAATAAGTAACTTAA-TCAGGGGTCATTAAGT
1 AAT-AACTTAATTCTGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCA-GGGTAATTAAGT
24557 TTATTAAGAG
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
103 1 0.01
104 95 0.65
105 50 0.34
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (104 bp):
AATAACTTAATTCTGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGTAAGT
CAATAAGTAACTTAATTCAAGATAATTAAGTAAGTCAGC
Found at i:24492 original size:70 final size:70
Alignment explanation
Indices: 24283--24556 Score: 329
Period size: 70 Copynumber: 3.9 Consensus size: 70
24273 GCATATAGTG
* * * *
24283 AGTAAATAACTTAATTCATGGTAATTAAATAAGTCGATAAGTAACTTAATTCAGGGTAATTAAGT
1 AGTAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGT
*
24348 AGGTC
66 AAGTC
* * * *
24353 AGTGAGTAACTTAATTCAGAGTAATTAAGTAAGTCAGT-AGTAACTTAATTCTGGGTAATTAAGT
1 AGTAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGT
24417 AAGTC
66 AAGTC
* * * *
24422 AATAAGTAACTTAATTCAGGGTGATTAAGTAAGTCAATAAGTAACTTAATTCAAGATAATTAAGT
1 AGTAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGT
24487 AAGTC
66 AAGTC
* * * * * * *
24492 AGCAA-TCATCTTAGTTCAGGATAATTAAGAAAATCAATAAGTAACTTAA-TCAGGGGTCATTAA
1 AGTAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCA-GGGTAATTAA
24555 GT
64 GT
24557 TTATTAAGAG
Statistics
Matches: 173, Mismatches: 28, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
69 66 0.38
70 107 0.62
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (70 bp):
AGTAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTAAGT
AAGTC
Found at i:26813 original size:18 final size:20
Alignment explanation
Indices: 26777--26814 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
26767 AGGGTTTGAC
*
26777 CCCACTAAAAATAATATTGT
1 CCCACTAAAAAGAATATTGT
26797 CCCA-TAAAAAGAA-ATTGT
1 CCCACTAAAAAGAATATTGT
26815 GAGGACTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (20 bp):
CCCACTAAAAAGAATATTGT
Found at i:35959 original size:6 final size:6
Alignment explanation
Indices: 35948--35972 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35938 TTAAAAAAAG
35948 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
35973 GATATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:37530 original size:20 final size:19
Alignment explanation
Indices: 37492--37530 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
37482 ATTTACTTTC
*
37492 TATATAATATATGCAAGTA
1 TATATAATATATACAAGTA
*
37511 TATATATATATATACTAGTA
1 TATATA-ATATATACAAGTA
37531 AAGACACGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
TATATAATATATACAAGTA
Done.