Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016074.1 Corchorus capsularis cultivar CVL-1 contig16095, 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: 7825
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:6014 original size:29 final size:27
Alignment explanation
Indices: 5960--6014 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5950 ATTTTTTTTT
*
5960 CTTACTCTTTTTACTAATTACTCTTTC
1 CTTACTCTTTTTACTAATTACACTTTC
* *
5987 CTTACTCTCTTTTATTGATTACCACTTT
1 CTTACTCT-TTTTACTAATTA-CACTTT
6015 TTACTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.35
28 10 0.43
29 5 0.22
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (27 bp):
CTTACTCTTTTTACTAATTACACTTTC
Found at i:6093 original size:22 final size:22
Alignment explanation
Indices: 6068--6416 Score: 182
Period size: 22 Copynumber: 15.6 Consensus size: 22
6058 ACTGATCACC
*
6068 TTTTACTCTTTACAGATTACTA
1 TTTTACTCTTTACTGATTACTA
* * *
6090 TTTTACTC-TTACTAATAACCA
1 TTTTACTCTTTACTGATTACTA
* *
6111 TTTTGCTC-TTACTAATTACTA
1 TTTTACTCTTTACTGATTACTA
* *
6132 TTTTAC-CTTTTATTGATTACTT
1 TTTTACTC-TTTACTGATTACTA
6154 TTTTACTATTTTACTCTTTACTGATTACCT-
1 TTTTAC-----T-C--TTTACTGATTA-CTA
* *
6184 TCTTACTTTTTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
*
6206 TTTTACTCTTTACTGATTACCA
1 TTTTACTCTTTACTGATTACTA
* *
6228 TTTTGCTC-TTACTGATTAC-C
1 TTTTACTCTTTACTGATTACTA
* *
6248 TTTTACTCTTTACAGATTACCA
1 TTTTACTCTTTACTGATTACTA
* * *
6270 TTTTGCTCTCGT--TGATTACCA
1 TTTTACTCT-TTACTGATTACTA
*
6291 TTTTGCTC-TTACTGATTACTA
1 TTTTACTCTTTACTGATTACTA
6312 TTTTAC-CTTTTACTGATTATCATTA
1 TTTTACTC-TTTACTGATTA-C--TA
* ** ***
6337 CTTTTTATTGATTACCTTTTACTA
1 --TTTTACTCTTTACTGATTACTA
* *
6361 TTTCATTCTTTACTGATTATCT-
1 TTTTACTCTTTACTGATTA-CTA
* *
6383 TTTTACTTTTTACTGATTAC-C
1 TTTTACTCTTTACTGATTACTA
*
6404 CTTTACTCTTTAC
1 TTTTACTCTTTAC
6417 CATTCTTCCT
Statistics
Matches: 254, Mismatches: 46, Indels: 55
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 96 0.38
22 108 0.43
23 4 0.02
24 2 0.01
25 3 0.01
26 1 0.00
27 12 0.05
29 1 0.00
30 15 0.06
31 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACTA
Found at i:6113 original size:21 final size:21
Alignment explanation
Indices: 6089--6137 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6079 ACAGATTACT
6089 ATTTTACTCTTACTAATAACC
1 ATTTTACTCTTACTAATAACC
* * *
6110 ATTTTGCTCTTACTAATTACT
1 ATTTTACTCTTACTAATAACC
6131 ATTTTAC
1 ATTTTAC
6138 CTTTTATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTACTCTTACTAATAACC
Found at i:6160 original size:30 final size:31
Alignment explanation
Indices: 6126--6196 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
6116 CTCTTACTAA
* * *
6126 TTACTATTTTACCT-TTTATTGATTACTTTT
1 TTACTATTTTACCTCTTTACTGATTACCTTC
6156 TTACTATTTTA-CTCTTTACTGATTACCTTC
1 TTACTATTTTACCTCTTTACTGATTACCTTC
6186 TTACT-TTTTAC
1 TTACTATTTTAC
6197 TGATTACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.59
Consensus pattern (31 bp):
TTACTATTTTACCTCTTTACTGATTACCTTC
Found at i:6181 original size:52 final size:51
Alignment explanation
Indices: 6110--6212 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 51
6100 ACTAATAACC
* * * *
6110 ATTTTGCTCTTACTAATTA-CTATTTTACCTTTTATTGATTACTTTTTTACT
1 ATTTTACTCTTACTAATTACCT-TCTTACCTTTTACTGATTACTATTTTACT
* *
6161 ATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTTACT
1 ATTTTACTC-TTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
6213 CTTTACTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 8 0.18
52 34 0.77
53 2 0.05
ACGTcount: A:0.21, C:0.17, G:0.04, T:0.57
Consensus pattern (51 bp):
ATTTTACTCTTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
Found at i:6359 original size:49 final size:50
Alignment explanation
Indices: 6306--6410 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 50
6296 CTCTTACTGA
* * *
6306 TTACTATTTTAC-CTTTTACTGATTATC-ATTACTTTTTATTGATTACCTT
1 TTACTATTTCACTC-TTTACTGATTATCTATTACTTTTTACTGATTACCCT
* *
6355 TTACTATTTCATTCTTTACTGATTATCTTTTTACTTTTTACTGATTACCCT
1 TTACTATTTCACTCTTTACTGATTATC-TATTACTTTTTACTGATTACCCT
6406 TTACT
1 TTACT
6411 CTTTACCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 23 0.48
50 1 0.02
51 24 0.50
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (50 bp):
TTACTATTTCACTCTTTACTGATTATCTATTACTTTTTACTGATTACCCT
Found at i:6387 original size:15 final size:14
Alignment explanation
Indices: 6333--6389 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
6323 ACTGATTATC
*
6333 ATTACTTTTTATTG
1 ATTACTTTTTACTG
*
6347 ATTACCTTTTACT-
1 ATTACTTTTTACTG
*
6360 ATTTCATTCTTTACTG
1 ATTAC-TT-TTTACTG
6376 ATTATCTTTTTACT
1 ATTA-CTTTTTACT
6390 TTTTACTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.12
14 12 0.35
15 12 0.35
16 5 0.15
17 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.60
Consensus pattern (14 bp):
ATTACTTTTTACTG
Found at i:6432 original size:35 final size:35
Alignment explanation
Indices: 6391--6484 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
6381 CTTTTTACTT
6391 TTTACTGATTACCCTTTACTCTTT-ACCATTCTTCC
1 TTTACTGATTACCCTTTACT-TTTGACCATTCTTCC
*
6426 TTTACTGATTACTCTTTACTTTTGACCATTCTTCC
1 TTTACTGATTACCCTTTACTTTTGACCATTCTTCC
*
6461 TTTACTGATTACTCATTTACTTTT
1 TTTACTGATTAC-CCTTTACTTTT
6485 TCTTTACTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 3 0.06
35 42 0.78
36 9 0.17
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.52
Consensus pattern (35 bp):
TTTACTGATTACCCTTTACTTTTGACCATTCTTCC
Found at i:6494 original size:26 final size:27
Alignment explanation
Indices: 6460--6510 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
6450 ACCATTCTTC
*
6460 CTTTACTGATTACTCA-TTTACTTTTT
1 CTTTACTGATTACTAATTTTACTTTTT
6486 CTTTACTGATTACTAATTTTACTTT
1 CTTTACTGATTACTAATTTTACTTT
6511 CTCCCTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.57
Consensus pattern (27 bp):
CTTTACTGATTACTAATTTTACTTTTT
Found at i:6669 original size:34 final size:35
Alignment explanation
Indices: 6553--6680 Score: 113
Period size: 34 Copynumber: 3.7 Consensus size: 35
6543 TTGACTTTTA
6553 ATTACTGATTTACTGATTACTA--TTTTTATCTTG
1 ATTACTGATTTACTGATTACTATCTTTTTATCTTG
* * * * * *
6586 ACT-CTTAATTACTGATTAATCTCTTATCTTGATTCTTA
1 ATTACTGATTTACTGATTACTATCTT-T-TT-A-TCTTG
*
6624 ATTA-TCAATTTACTGATTACTATCTTTTTA-CTTG
1 ATTACT-GATTTACTGATTACTATCTTTTTATCTTG
6658 ATTACTGATTTACTGATTACTAT
1 ATTACTGATTTACTGATTACTAT
6681 TACCTTGACT
Statistics
Matches: 73, Mismatches: 13, Indels: 17
0.71 0.13 0.17
Matches are distributed among these distances:
32 14 0.19
33 2 0.03
34 25 0.34
35 2 0.03
36 3 0.04
37 3 0.04
38 8 0.11
39 16 0.22
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (35 bp):
ATTACTGATTTACTGATTACTATCTTTTTATCTTG
Found at i:6688 original size:71 final size:71
Alignment explanation
Indices: 6543--6698 Score: 167
Period size: 71 Copynumber: 2.2 Consensus size: 71
6533 GACTAATCCA
* * *
6543 TTGACTTTTAATTA-CTGATTTACTGATTACTATTTTTATCTTGACTCTTAATTACTGATTAATC
1 TTGACTCTTAATTATC-AATTTACTGATTACTATTTTTATCTTGACTCTGAATTACTGATTAATC
* *
6607 TCTTATC
65 TATTACC
* * *
6614 TTGATTCTTAATTATCAATTTACTGATTACTATCTTTT-TACTTGATTACTGATTTACTGATT-A
1 TTGACTCTTAATTATCAATTTACTGATTACTAT-TTTTAT-CTTGACT-CTGAATTACTGATTAA
6677 -CTATTACC
63 TCTATTACC
*
6685 TTGACTCTTGATTA
1 TTGACTCTTAATTA
6699 ATCTCTTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
71 47 0.66
72 12 0.17
73 12 0.17
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (71 bp):
TTGACTCTTAATTATCAATTTACTGATTACTATTTTTATCTTGACTCTGAATTACTGATTAATCT
ATTACC
Found at i:6780 original size:55 final size:55
Alignment explanation
Indices: 6636--6831 Score: 302
Period size: 55 Copynumber: 3.5 Consensus size: 55
6626 TATCAATTTA
* * *
6636 CTGATTACTATCTTTTTACTTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACT
*
6691 CTTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACT
1 C-TGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACT
* *
6747 CTGATTAATCTCTTTTTACTTAATTACTCATTTACTGATTACTATTACTTTGACT
1 CTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACT
* * *
6802 CTGATTACTATATTTTTACTTGATTACTGA
1 CTGATTAATATCTTTTTACTTAATTACTGA
6832 CTGCCCCTTT
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
55 79 0.61
56 51 0.39
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.51
Consensus pattern (55 bp):
CTGATTAATATCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACT
Found at i:6805 original size:21 final size:20
Alignment explanation
Indices: 6781--6829 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
6771 TACTCATTTA
6781 CTGATTACTATTACTTTGACT
1 CTGATTACTA-TACTTTGACT
* *
6802 CTGATTACTATATTTTTACT
1 CTGATTACTATACTTTGACT
6822 -TGATTACT
1 CTGATTACT
6830 GACTGCCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 8 0.31
20 8 0.31
21 10 0.38
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (20 bp):
CTGATTACTATACTTTGACT
Found at i:7698 original size:50 final size:50
Alignment explanation
Indices: 7624--7792 Score: 205
Period size: 50 Copynumber: 3.4 Consensus size: 50
7614 ATTACTTTTT
* * * * * *
7624 TTAAAACTTCAATCTTTTATTCAAAGGTTACATCTCTATTTACTAATTAC
1 TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
* *
7674 TCTAAAAA-TCAATCTTTTGCTCAAAGGTGACATTTTTACTTATTAATTAC
1 T-TAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
* * * * *
7724 TAAAAAATTCAATTTTTTACCCAAAGATGACATTTTTACTTACTAATTAT
1 TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
7774 TTAAAAATTCAATCTTTTA
1 TTAAAAATTCAATCTTTTA
7793 TTTACAAATT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 5 0.05
50 90 0.90
51 5 0.05
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (50 bp):
TTAAAAATTCAATCTTTTACTCAAAGGTGACATTTTTACTTACTAATTAC
Done.