Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010632.1 Corchorus capsularis cultivar CVL-1 contig10653, 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: 10514
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Found at i:797 original size:28 final size:28
Alignment explanation
Indices: 727--799 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
717 CATTTTACTC
*
727 TTTTACTGATTACTATTTTCTGCTCCTT
1 TTTTACTGATTACTCTTTTCTGCTCCTT
755 TTTTACTGATTACTCTTTTCTGCTCCTT
1 TTTTACTGATTACTCTTTTCTGCTCCTT
783 TTTTACTGATTACTCTT
1 TTTTACTGATTACTCTT
800 GCTTTTTACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.58
Consensus pattern (28 bp):
TTTTACTGATTACTCTTTTCTGCTCCTT
Found at i:852 original size:21 final size:21
Alignment explanation
Indices: 805--951 Score: 120
Period size: 21 Copynumber: 6.9 Consensus size: 21
795 CTCTTGCTTT
805 TTACTGATTACCT-TTTTACTTC
1 TTACTGATTA-CTATTTTAC-TC
*
827 TTACTGATTACTATTTTACCC
1 TTACTGATTACTATTTTACTC
* * *
848 TTACTGATCACTA-TTTATTTT
1 TTACTGATTACTATTTTA-CTC
**
869 TTACTGGCTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
** * *
890 TTGTTGATTACCT-TCTTACTTT
1 TTACTGATTA-CTATTTTAC-TC
912 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
* *
933 TTACTAATTACCATTTTAC
1 TTACTGATTACTATTTTAC
952 CCTTTCAGAT
Statistics
Matches: 97, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.04
21 57 0.59
22 36 0.37
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.52
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:944 original size:43 final size:42
Alignment explanation
Indices: 655--739 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
645 CTGACTATTC
* **
655 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
*
697 TCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTAC
1 T-TTACTTTTTACTGATTACTATTTTACTC--TTACTGATTAC
740 TATTTTCTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.03
43 26 0.72
45 9 0.25
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCT
Found at i:983 original size:85 final size:86
Alignment explanation
Indices: 801--983 Score: 196
Period size: 85 Copynumber: 2.2 Consensus size: 86
791 ATTACTCTTG
* * * *
801 CTTTTTACTGATTACCTTTTTACTTCTTACTGATTACTATTTTACCCTTACTGATCACTATTTAT
1 CTTTTTACTGATTACCTTCTTACTTCTTACTGATTACTATTTTACCCTTACTAATCACCATTTAC
** * *
866 TTTTTACTGGCTACTATTTTA
66 CCTTTACTAGATACTATTTTA
* * * *
887 CTCTTGT--TGATTACCTTCTTACTTTTTACTGATTACTATTTTACTCTTACTAATTACCATTTT
1 CT-TTTTACTGATTACCTTCTTACTTCTTACTGATTACTATTTTACCCTTACTAATCACCA-TTT
950 ACCCTTT-C-AGATACCT-TTTTA
64 ACCCTTTACTAGATA-CTATTTTA
971 CTTTTTACTGATT
1 CTTTTTACTGATT
984 GCATGCTATT
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
83 3 0.04
84 10 0.13
85 54 0.68
86 9 0.11
87 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (86 bp):
CTTTTTACTGATTACCTTCTTACTTCTTACTGATTACTATTTTACCCTTACTAATCACCATTTAC
CCTTTACTAGATACTATTTTA
Found at i:1215 original size:33 final size:31
Alignment explanation
Indices: 1173--1241 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1163 TTAATTATCG
* *
1173 AATTACTGATTACTAT-TTTTACCTTGACTCTTT
1 AATTACTGATTA--ATCTCTTACATTGACTC-TT
1206 AATTACTGATTAATCTCTTACATTGACTCTT
1 AATTACTGATTAATCTCTTACATTGACTCTT
1237 AATTA
1 AATTA
1242 TCAATTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.27
32 12 0.36
33 12 0.36
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (31 bp):
AATTACTGATTAATCTCTTACATTGACTCTT
Found at i:1311 original size:55 final size:55
Alignment explanation
Indices: 1250--1510 Score: 411
Period size: 55 Copynumber: 4.8 Consensus size: 55
1240 TATCAATTTA
* * * * *
1250 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
**
1305 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1360 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
* *
1415 CTGATTAATCTCTTTTCACTTTATTACTGATTTACTGATTAC---TACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
*
1467 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTA
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTA
1511 CCTCTTACTT
Statistics
Matches: 194, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
52 51 0.26
55 143 0.74
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
Found at i:2466 original size:101 final size:101
Alignment explanation
Indices: 2327--2685 Score: 643
Period size: 101 Copynumber: 3.6 Consensus size: 101
2317 ATTCAAAGGC
* *
2327 GACA-TTTTATTTACTAA--ACTTAAAAATTCTATCTTTTATTCAAAGGTTAAATCTTTATTTAC
1 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
2389 TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
66 TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
* *
2425 GACATTTTTATTTACCAATTACTTAACAATTCAATCTTTTATTCAAAGGTTAAATCTCTATTTAC
1 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
2490 TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
66 TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
2526 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
1 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
*
2591 TAATTACTCTAAAAATTCAATCTTTTACCCTAAGAT
66 TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
*
2627 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCTTT
1 GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
2686 TAGCCAATTA
Statistics
Matches: 250, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
98 4 0.02
99 12 0.05
101 234 0.94
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.43
Consensus pattern (101 bp):
GACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTAC
TAATTACTCTAAAAATTCAATCTTTTACCCAAAGAT
Found at i:2687 original size:51 final size:51
Alignment explanation
Indices: 2282--2687 Score: 436
Period size: 51 Copynumber: 8.1 Consensus size: 51
2272 AACTAATCAA
** * * * * **
2282 TTTATTTACTAATGGCCTAAAAGTTCAAACTTCTAATTCAAAGGCGACA--T
1 TTTATTTACTAATTACTTAAAAATTCAATCTT-TTATTCAAAGGTTACATCT
* *
2332 TTTATTTACTAA--ACTTAAAAATTCTATCTTTTATTCAAAGGTTAAATC-
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
** * *
2380 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT-T
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTACATCT
* * *
2431 TTTATTTACCAATTACTTAACAATTCAATCTTTTATTCAAAGGTTAAATC-
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
* ** * *
2481 TCTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT-T
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTACATCT
* *
2532 TTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC-
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
** * * *
2582 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCTAAGATGACAT-T
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTACATCT
*
2633 TTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
2684 TTTA
1 TTTA
2688 GCCAATTATC
Statistics
Matches: 293, Mismatches: 50, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
47 12 0.04
48 25 0.09
50 126 0.43
51 130 0.44
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (51 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
Found at i:3541 original size:26 final size:26
Alignment explanation
Indices: 3512--3564 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3502 TAAATCAACT
*
3512 ATGAGCAATATGAAAGTTGAAGAACA
1 ATGAACAATATGAAAGTTGAAGAACA
3538 ATGAACAATATGAAAGTTGAAGAACA
1 ATGAACAATATGAAAGTTGAAGAACA
3564 A
1 A
3565 ATACAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.19
Consensus pattern (26 bp):
ATGAACAATATGAAAGTTGAAGAACA
Found at i:7011 original size:27 final size:27
Alignment explanation
Indices: 6981--7056 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
6971 AGGTGAACTT
**
6981 AAAAATGAGTAAAATGTCCC-TGAGTGC
1 AAAAATGACCAAAATG-CCCTTGAGTGC
*
7008 AAAAATGACCAAAATGCCCTTGGGTGC
1 AAAAATGACCAAAATGCCCTTGAGTGC
* *
7035 AAAATTGACCAAAATACCCTTG
1 AAAAATGACCAAAATGCCCTTG
7057 GGCGGCCCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCTTGAGTGC
Found at i:7057 original size:27 final size:27
Alignment explanation
Indices: 7004--7058 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6994 ATGTCCCTGA
*
7004 GTGCAAAAATGACCAAAATGCCCTTGG
1 GTGCAAAAATGACCAAAATACCCTTGG
*
7031 GTGCAAAATTGACCAAAATACCCTTGG
1 GTGCAAAAATGACCAAAATACCCTTGG
7058 G
1 G
7059 CGGCCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (27 bp):
GTGCAAAAATGACCAAAATACCCTTGG
Done.