Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013647.1 Corchorus capsularis cultivar CVL-1 contig13668, 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: 43704
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:3821 original size:32 final size:32
Alignment explanation
Indices: 3780--3844 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3770 TCACTCGATT
3780 TCTAATTAAGGCCCTCCAATTTGATGCAACAA
1 TCTAATTAAGGCCCTCCAATTTGATGCAACAA
3812 TCTAATTAAGGCCCTCCAATTTGATGCAACAA
1 TCTAATTAAGGCCCTCCAATTTGATGCAACAA
3844 T
1 T
3845 AAAAAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (32 bp):
TCTAATTAAGGCCCTCCAATTTGATGCAACAA
Found at i:4295 original size:70 final size:71
Alignment explanation
Indices: 4203--4341 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 71
4193 GTAAGGTCTC
* *
4203 ATATTCGATTCTTTATTTCTTTTGAATGAGAAAGATTTTTTT-TAAAGGCAAATGAGATGAATTT
1 ATATTCGATTCTTTATTTCTTTTGAACGAGAAAAATTTTTTTGTAAAGGCAAATGAGATGAATTT
4267 TATTGA
66 TATTGA
*
4273 ATATTTGATTCTTTATTTCTTTTGAACGAGAAAAATTTTTTTGTAAAGGCAAATGAGATGAATTT
1 ATATTCGATTCTTTATTTCTTTTGAACGAGAAAAATTTTTTTGTAAAGGCAAATGAGATGAATTT
4338 TATT
66 TATT
4342 CAAAATGAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
70 39 0.60
71 26 0.40
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (71 bp):
ATATTCGATTCTTTATTTCTTTTGAACGAGAAAAATTTTTTTGTAAAGGCAAATGAGATGAATTT
TATTGA
Found at i:4618 original size:13 final size:13
Alignment explanation
Indices: 4593--4625 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4583 AAATCTCTGT
4593 ATATATACGAAAA
1 ATATATACGAAAA
4606 ATATACTAC-AAAA
1 ATATA-TACGAAAA
4619 ATATATA
1 ATATATA
4626 AATTGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 14 0.74
14 3 0.16
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (13 bp):
ATATATACGAAAA
Found at i:6657 original size:59 final size:60
Alignment explanation
Indices: 6538--6659 Score: 176
Period size: 60 Copynumber: 2.0 Consensus size: 60
6528 TTAAAGTTCG
* * *
6538 ATTCCTAACAGTCTCAAGTATATATAAAAAAAATATACAAAATCGATTCTCCAAAAACAC
1 ATTCCTAACAGTCTCAAGTATATAAAAAAAAAAGATACAAAATCAATTCTCCAAAAACAC
* *
6598 ATTCCTAACAGTTTCAAGTATA-AAAGAAAAAAAGA-ACGAAATCAATTCTCCAAAAACAC
1 ATTCCTAACAGTCTCAAGTATATAAA-AAAAAAAGATACAAAATCAATTCTCCAAAAACAC
6657 ATT
1 ATT
6660 TGTTAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
59 27 0.48
60 29 0.52
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.24
Consensus pattern (60 bp):
ATTCCTAACAGTCTCAAGTATATAAAAAAAAAAGATACAAAATCAATTCTCCAAAAACAC
Found at i:7739 original size:20 final size:21
Alignment explanation
Indices: 7706--7745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
7696 ATATACTATA
7706 ATAATAAATAT-AAATATTTT
1 ATAATAAATATAAAATATTTT
* *
7726 ATAATAATTTTAAAATATTT
1 ATAATAAATATAAAATATTT
7746 ATTTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATAAATATAAAATATTTT
Found at i:8481 original size:3 final size:3
Alignment explanation
Indices: 8473--8510 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
8463 ATAAATAAAT
8473 ATA ATA ATA ATA ATA ATA ATA ATAA ATA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT
8511 CTGTCTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13723 original size:23 final size:23
Alignment explanation
Indices: 13693--13743 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
13683 TATAGCTATG
13693 CTCCACCTTGATACTAGAGAAGC
1 CTCCACCTTGATACTAGAGAAGC
*
13716 CTCCACCTTGATACTGGAGAAGC
1 CTCCACCTTGATACTAGAGAAGC
*
13739 TTCCA
1 CTCCA
13744 ATTAGGGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (23 bp):
CTCCACCTTGATACTAGAGAAGC
Found at i:13891 original size:77 final size:77
Alignment explanation
Indices: 13764--13919 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
13754 TGCATTCATT
13764 TATGATAGTTGCCAAGTGATGATGTGGAGAAGAAATCTTAGTTAACTGAATTACACACTCATAGT
1 TATGATAGTTGCCAAGTGATGATGTGGAGAAGAAATCTTAGTTAACTGAATTACACACTCATAGT
13829 CTACACATATCA
66 CTACACATATCA
13841 TATGATAGTTGCCAAGTGATGATGTGGAGAAGAAATCTTAGTTAACTGAATTACACACTCATAGT
1 TATGATAGTTGCCAAGTGATGATGTGGAGAAGAAATCTTAGTTAACTGAATTACACACTCATAGT
13906 CTACACATATCA
66 CTACACATATCA
13918 TA
1 TA
13920 AGCTTAGTGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (77 bp):
TATGATAGTTGCCAAGTGATGATGTGGAGAAGAAATCTTAGTTAACTGAATTACACACTCATAGT
CTACACATATCA
Found at i:15371 original size:16 final size:16
Alignment explanation
Indices: 15350--15389 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
15340 CCTTTGTCTC
15350 AAAAAGAA-AAGAAAGA
1 AAAAAGAACAA-AAAGA
*
15366 AAAAAGAACCAAAAGA
1 AAAAAGAACAAAAAGA
15382 AAAAAGAA
1 AAAAAGAA
15390 TCTAAGTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAGAACAAAAAGA
Found at i:32187 original size:13 final size:13
Alignment explanation
Indices: 32169--32193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32159 TGTGAGATTT
32169 CTGAGAATTTTTG
1 CTGAGAATTTTTG
32182 CTGAGAATTTTT
1 CTGAGAATTTTT
32194 CCATGGAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
CTGAGAATTTTTG
Found at i:37062 original size:417 final size:418
Alignment explanation
Indices: 36274--37103 Score: 1500
Period size: 417 Copynumber: 2.0 Consensus size: 418
36264 TTTTGATTGT
* *
36274 CAAGTCTTTGCTCCTGGTCATTGTACCTTTTGATGGCATATTGTTTGATAAATGGACAATCAAAA
1 CAAGTCTTTGCTCCTGGTCACTGTACCTTTTGATGGCATATTGTTTGATAAAGGGACAATCAAAA
*
36339 GGTACAGGGATCAACTAAATGTGTACAAATGTATAGATATTGTATCTCATCTATATGAACGTATA
66 GGTACAGGGATCAACTAAATGTGTACAAATGTATAGATATTGTATCTCATCTATATGAACATATA
36404 GAAAATAAATTTAATCCACACTTCATAATATGTTTGTTTCATTTGTTTACTGAAATTATTTAATT
131 GAAAATAAATTTAATCCACACTTCATAATATGTTTGTTTCATTTGTTTACTGAAATTATTTAATT
* *
36469 GAAGTCAATGTTTTCAGTTATATATTATGGGTTTGGGTTATTTTATTCTGTTTAAATTGTATATG
196 GAAGTCAATGTTTTCAGTTATATATTATGGGTTTGGGTTATTTTATTCAGTTTAAATTGTATACG
* *
36534 ACCCTGAGGAAAGGCAGAAGAAGTTAGTGGATGAATTGACTTGACATGAAATTTGCCATTTCGTT
261 ACCCTGAGGAAAGGCACAAGAAGTTAGTGGATGAATTGACTTGACATGAAATTTGCCATTGCGTT
36599 ACTTCTATCAATTGTATGTTTTTAATTCTAATAGCCTAAAGCCAAGGATAGCAATATGCTTATCA
326 ACTTCTATCAATTGTATGTTTTTAATTCTAATAGCCTAAAGCCAAGGATAGCAATATGCTTATCA
* *
36664 TGTGCTTATGTGTCTTAGCCAAGGATAG
391 TGTGCTGACGTGTCTTAGCCAAGGATAG
*
36692 CAAGTCTTTGGTCCTGGTCACTGTACCTTTTGATGGCATATTGTTTGATAAAGGGACAATCAAAA
1 CAAGTCTTTGCTCCTGGTCACTGTACCTTTTGATGGCATATTGTTTGATAAAGGGACAATCAAAA
* * *
36757 GGTATAGTGATCAATTAAATGTGTACAAATGTATAGATATTGTATCTCATCTATATGAACATATA
66 GGTACAGGGATCAACTAAATGTGTACAAATGTATAGATATTGTATCTCATCTATATGAACATATA
* *
36822 GAGAATAAATTTAATCCACACTTCATAATATGTTTGTTTCATTTGTTTACTGAATTTATTT-ATT
131 GAAAATAAATTTAATCCACACTTCATAATATGTTTGTTTCATTTGTTTACTGAAATTATTTAATT
36886 GAAGTCAATGTTTTCAGTTATATATTATGGGTTTGGGTTATTTTATTCAGTTTAAATTGTATACG
196 GAAGTCAATGTTTTCAGTTATATATTATGGGTTTGGGTTATTTTATTCAGTTTAAATTGTATACG
* *
36951 ACCCTGAGGAAAGGCACAAGTAGTTAGTGGATGAATTGACTTGACATGAAATTTGCCGTTGCGTT
261 ACCCTGAGGAAAGGCACAAGAAGTTAGTGGATGAATTGACTTGACATGAAATTTGCCATTGCGTT
37016 ACTTCTATCAATTGTATGTTTTTAATTCTAATAGCCTAAAGCCAAGGATAGCAATATGCTTATCA
326 ACTTCTATCAATTGTATGTTTTTAATTCTAATAGCCTAAAGCCAAGGATAGCAATATGCTTATCA
37081 TGTGCTGACGTGTCTTAGCCAAG
391 TGTGCTGACGTGTCTTAGCCAAG
37104 ATTGCTATCC
Statistics
Matches: 395, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
417 213 0.54
418 182 0.46
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (418 bp):
CAAGTCTTTGCTCCTGGTCACTGTACCTTTTGATGGCATATTGTTTGATAAAGGGACAATCAAAA
GGTACAGGGATCAACTAAATGTGTACAAATGTATAGATATTGTATCTCATCTATATGAACATATA
GAAAATAAATTTAATCCACACTTCATAATATGTTTGTTTCATTTGTTTACTGAAATTATTTAATT
GAAGTCAATGTTTTCAGTTATATATTATGGGTTTGGGTTATTTTATTCAGTTTAAATTGTATACG
ACCCTGAGGAAAGGCACAAGAAGTTAGTGGATGAATTGACTTGACATGAAATTTGCCATTGCGTT
ACTTCTATCAATTGTATGTTTTTAATTCTAATAGCCTAAAGCCAAGGATAGCAATATGCTTATCA
TGTGCTGACGTGTCTTAGCCAAGGATAG
Found at i:41909 original size:32 final size:32
Alignment explanation
Indices: 41868--42019 Score: 288
Period size: 32 Copynumber: 4.8 Consensus size: 32
41858 TTGAGGGCCA
41868 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
41900 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
41932 ATGTG-ATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
41963 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
*
41995 ATGTGAGTTAAGGCAAGTTCAATGT
1 ATGTGAATTAAGGCAAGTTCAATGT
42020 CAATTGGGAA
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
31 31 0.26
32 87 0.74
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (32 bp):
ATGTGAATTAAGGCAAGTTCAATGTGATTTGG
Found at i:41946 original size:63 final size:63
Alignment explanation
Indices: 41868--42019 Score: 286
Period size: 63 Copynumber: 2.4 Consensus size: 63
41858 TTGAGGGCCA
41868 ATGTGAATTAAGGCAAGTTCAATGTGATTTGGATGTGAATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTG-ATTAAGGCAAGTTCAATGTGATTTGGATGTGAATTAAGGCAAGTTCAATGTGATTTGG
41932 ATGTGATTAAGGCAAGTTCAATGTGATTTGGATGTGAATTAAGGCAAGTTCAATGTGATTTGG
1 ATGTGATTAAGGCAAGTTCAATGTGATTTGGATGTGAATTAAGGCAAGTTCAATGTGATTTGG
41995 ATGTGAGTTAAGGCAAGTTCAATGT
1 ATGTGA-TTAAGGCAAGTTCAATGT
42020 CAATTGGGAA
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
63 64 0.74
64 23 0.26
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (63 bp):
ATGTGATTAAGGCAAGTTCAATGTGATTTGGATGTGAATTAAGGCAAGTTCAATGTGATTTGG
Found at i:43285 original size:227 final size:228
Alignment explanation
Indices: 42875--43299 Score: 588
Period size: 228 Copynumber: 1.9 Consensus size: 228
42865 TCACCAGTCC
* * *
42875 GATTTTAGATCTCTACTAATTGCAAGGGTAAATAACCTCCCTTTCGCTAGTATTTTCATATTACG
1 GATTTCAGATCTCGACTAATTGCAAGGGTAAATAACCTCCCTTTCGCTAGTATTCTCATATTACG
* * * *
42940 TAGCCCTAGACATTTTACAGGCTTCCGAGGCATTTTATATTTCAGATATTTTTTAAAAATTTGGA
66 TAGCCCTAAACATTTTACAAGCTTCCGAGGCATTTTATATTTCAGACATTTTTGAAAAATTTGGA
* * * *
43005 CATATATCACAAGTGATCTTTTTAAAATGGAAAATAAAATGTTAGTCGTTTTCTAATTTACTAAC
131 CATATATCACAAGCGACCTTTTTAAAATGAAAAATAAAATGTTAGTCGTTTTCTAATTTACCAAC
43070 CTTCTTTTATTCTTCTCAATCATTAACCAACCT
196 CTTCTTTTATTCTTCTCAATCATTAACCAACCT
* * * * * *
43103 GATTTCAGGTCTCGACTAATTGTAAGGGTAAATGACCTCCGTTTCTCTAGTATTCTCATTTTACG
1 GATTTCAGATCTCGACTAATTGCAAGGGTAAATAACCTCCCTTTCGCTAGTATTCTCATATTACG
** ** *
43168 T-GGTCTGAAACATTTTACAAGCTTTTGAGGCATTTTATATTTTAGACA-TTTTGAAAAATTTGG
66 TAGCCCT-AAACATTTTACAAGCTTCCGAGGCATTTTATATTTCAGACATTTTTGAAAAATTTGG
*
43231 ACATATATCA-TAGACGACCTTTTTAAAATGAAAAATAAAATG-TAGGTCGTTTTCTAATTTACC
130 ACATATATCACAAG-CGACCTTTTTAAAATGAAAAATAAAATGTTA-GTCGTTTTCTAATTTACC
43294 AACCTT
193 AACCTT
43300 TTATTCTTCT
Statistics
Matches: 171, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
226 4 0.02
227 75 0.44
228 92 0.54
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (228 bp):
GATTTCAGATCTCGACTAATTGCAAGGGTAAATAACCTCCCTTTCGCTAGTATTCTCATATTACG
TAGCCCTAAACATTTTACAAGCTTCCGAGGCATTTTATATTTCAGACATTTTTGAAAAATTTGGA
CATATATCACAAGCGACCTTTTTAAAATGAAAAATAAAATGTTAGTCGTTTTCTAATTTACCAAC
CTTCTTTTATTCTTCTCAATCATTAACCAACCT
Done.