Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008593.1 Corchorus capsularis cultivar CVL-1 contig08614, 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: 35947
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5551 original size:13 final size:13
Alignment explanation
Indices: 5533--5566 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5523 TAATTATTGT
5533 TTGCTTTATTAAA
1 TTGCTTTATTAAA
*
5546 TTGCTTTATTAAT
1 TTGCTTTATTAAA
5559 TTGCTTTA
1 TTGCTTTA
5567 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
TTGCTTTATTAAA
Found at i:5574 original size:6 final size:6
Alignment explanation
Indices: 5563--5589 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5553 ATTAATTTGC
5563 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
5590 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:8870 original size:23 final size:23
Alignment explanation
Indices: 8816--8873 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
8806 TCTTTTTACG
* *
8816 TTTTCTTTTCTTTTCTGCCCTAA
1 TTTTCTTTTCTTTTCTCCCCAAA
*
8839 TTTTTTTTTCTTTTC-CCCCAAA
1 TTTTCTTTTCTTTTCTCCCCAAA
8861 TTCTTCTTTTCTT
1 TT-TTCTTTTCTT
8874 CCCTGACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTCTTTTCTTTTCTCCCCAAA
Found at i:17495 original size:3 final size:3
Alignment explanation
Indices: 17487--17536 Score: 57
Period size: 3 Copynumber: 15.7 Consensus size: 3
17477 CACGAGTATA
17487 ATT ATT ATT ATT ATT ATT ATT A-T ATAT ATAT ATTT ATT ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T A-TT ATT AT-T ATT ATT
17535 AT
1 AT
17537 ATACGAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.05
3 29 0.67
4 11 0.26
5 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17547 original size:27 final size:27
Alignment explanation
Indices: 17494--17557 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
17484 ATAATTATTA
*
17494 TTATTAT-TATTATTATATATATATAT
1 TTATTATATATTATTATATAGATATAT
*
17520 TTATTATATATTATTATATACGA-GTAT
1 TTATTATATATTATTATATA-GATATAT
*
17547 TAATTATATAT
1 TTATTATATAT
17558 AATTTCACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.21
27 25 0.76
28 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TTATTATATATTATTATATAGATATAT
Found at i:19119 original size:84 final size:84
Alignment explanation
Indices: 18974--19139 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
18964 ACTAAGGTTG
* *
18974 CTTTGGGGAAACAAAATATCGCGTCACACACATAGGTTTCCAATGCCCTGCAATGAACTTCTTTA
1 CTTTGGGGAAACAAAATATCGCATCACACAAATAGGTTTCCAATGCCCTGCAATGAACTTCTTTA
19039 AGCCAGCACATTAATGCTA
66 AGCCAGCACATTAATGCTA
* *
19058 CTTTGGGGAAACAAAATATCGCATCACACAAATAGGTTTCCAGTGCCCTGCAATGAGCTTCTTTA
1 CTTTGGGGAAACAAAATATCGCATCACACAAATAGGTTTCCAATGCCCTGCAATGAACTTCTTTA
* *
19123 AGCTAGCACGTTAATGC
66 AGCCAGCACATTAATGC
19140 CCATGTGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (84 bp):
CTTTGGGGAAACAAAATATCGCATCACACAAATAGGTTTCCAATGCCCTGCAATGAACTTCTTTA
AGCCAGCACATTAATGCTA
Found at i:35054 original size:32 final size:32
Alignment explanation
Indices: 34994--35060 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
34984 ATACAAATCT
*
34994 AAACTCCATGTCATAGTTTGTGCCAAAAAAAA
1 AAACTCCATGTCATAGTTTATGCCAAAAAAAA
35026 AAACTCCATGTCATAG-TTAT-CACTAAAAAAAA
1 AAACTCCATGTCATAGTTTATGC-C-AAAAAAAA
35058 AAA
1 AAA
35061 AAAATCTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.03
31 4 0.12
32 27 0.84
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (32 bp):
AAACTCCATGTCATAGTTTATGCCAAAAAAAA
Found at i:35396 original size:17 final size:15
Alignment explanation
Indices: 35372--35475 Score: 77
Period size: 17 Copynumber: 6.6 Consensus size: 15
35362 TTTTATTTAG
*
35372 TATA-ATATATATTG
1 TATATATATATATTA
35386 TGATATTATATATATTA
1 T-ATA-TATATATATTA
*
35403 TATATATATATTTTGA
1 TATATATATATATT-A
* * *
35419 AATAATAAAGATATGTA
1 TAT-ATATATATAT-TA
*
35436 TTATATATAATATAATA
1 -TATATAT-ATATATTA
35453 TATATATATATATT-
1 TATATATATATATTA
35467 TATATATAT
1 TATATATAT
35476 GTTGAGGTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
14 10 0.14
15 18 0.25
16 13 0.18
17 23 0.32
18 7 0.10
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TATATATATATATTA
Found at i:35397 original size:2 final size:2
Alignment explanation
Indices: 35388--35475 Score: 64
Period size: 2 Copynumber: 47.0 Consensus size: 2
35378 ATATATTGTG
* * *
35388 AT AT -T AT AT AT AT -T AT AT AT AT AT AT -T TT GAA AT A- AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* *
35427 AG AT AT GT AT -T AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35466 TT AT AT AT AT
1 AT AT AT AT AT
35476 GTTGAGGTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
1 7 0.10
2 61 0.90
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35412 original size:30 final size:30
Alignment explanation
Indices: 35372--35475 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
35362 TTTTATTTAG
*
35372 TATA-ATATATATTGTGATAT-TATATATA
1 TATATATATATATTATGATATATATATATA
* * * *
35400 TTATATATATATATTTTGAAATAATAAAGATA
1 -TATATATATATATTATGATAT-ATATATATA
* * *
35432 TGTATTATATATAATATAATATATATATATA
1 TATA-TATATATATTATGATATATATATATA
*
35463 TATTTATATATAT
1 TATATATATATAT
35476 GTTGAGGTCA
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
29 4 0.07
30 22 0.39
31 12 0.21
32 19 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (30 bp):
TATATATATATATTATGATATATATATATA
Found at i:35884 original size:2 final size:2
Alignment explanation
Indices: 35877--35917 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
35867 TGGATCAACA
35877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35917 A
1 A
35918 GTAATACGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.