Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007370.1 Corchorus capsularis cultivar CVL-1 contig07391, 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: 7369
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:226 original size:21 final size:22
Alignment explanation
Indices: 200--244 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
190 ATATAGGGGA
200 TTGCTAAAT-ACCGCCCCA-TTT
1 TTGCT-AATCACCGCCCCACTTT
*
221 TTGCTATTCACCGCCCCACTTT
1 TTGCTAATCACCGCCCCACTTT
243 TT
1 TT
245 ACACTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 14 0.67
22 5 0.24
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCACTTT
Found at i:419 original size:33 final size:33
Alignment explanation
Indices: 377--442 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
367 AAATAGCCGA
377 TTGAGCCATGGTAAGCCACCCTCCTAGGGCGGC
1 TTGAGCCATGGTAAGCCACCCTCCTAGGGCGGC
* *
410 TTGAGCCATGGTAAGCCGCCCTCCTGGGGCGGC
1 TTGAGCCATGGTAAGCCACCCTCCTAGGGCGGC
443 ACGGGTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.18
Consensus pattern (33 bp):
TTGAGCCATGGTAAGCCACCCTCCTAGGGCGGC
Found at i:525 original size:42 final size:42
Alignment explanation
Indices: 477--602 Score: 216
Period size: 42 Copynumber: 3.0 Consensus size: 42
467 TCAAAAATTA
477 CATTTTTCTTAAATCGTCATCAAAATACGGCATGTTATCGCT
1 CATTTTTCTTAAATCGTCATCAAAATACGGCATGTTATCGCT
*
519 CATTTTTCTTAAATCGTCATCAAAATACGACATGTTATCGCT
1 CATTTTTCTTAAATCGTCATCAAAATACGGCATGTTATCGCT
* * *
561 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAACGCT
1 CATTTTTCTTAAATCGTCATCAAAATACGGCATGTTATCGCT
603 ATTCTACATT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (42 bp):
CATTTTTCTTAAATCGTCATCAAAATACGGCATGTTATCGCT
Found at i:1047 original size:3 final size:3
Alignment explanation
Indices: 1039--1079 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1029 ATGTTTAATT
1039 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1080 GAACTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2872 original size:30 final size:29
Alignment explanation
Indices: 2796--2883 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
2786 CCCTTTGTGC
* * *
2796 CCCCTCAACTTGTAATGTTTGGACGTTTTG
1 CCCCTAAACTTTTAAT-TTTGGACATTTTG
*
2826 TCCCCTGAAC-TTTAATTTTGGACATTTTG
1 -CCCCTAAACTTTTAATTTTGGACATTTTG
*
2855 CCCCATAAACTTTTAATTTTGGACTTTTT
1 CCCC-TAAACTTTTAATTTTGGACATTTT
2884 TTTGCCCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.08
29 16 0.32
30 22 0.44
31 8 0.16
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (29 bp):
CCCCTAAACTTTTAATTTTGGACATTTTG
Found at i:5619 original size:28 final size:26
Alignment explanation
Indices: 5576--5739 Score: 134
Period size: 26 Copynumber: 6.1 Consensus size: 26
5566 TATTTCTTGA
*
5576 TTACTAATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* * *
5602 GTACTGATTACCATATTTTACCCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* *
5628 TTACTGATTACCTCTTTTCTTTCTAC-TT
1 TTACTGATTACC-ATTTT-TTACT-CTTT
* * *
5656 CTACTGAATACCACTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
*
5682 TTACTTAATTACCATTTTTTACTCCCCCTTT
1 TTAC-TGATTACCATTTTTTACT----CTTT
* *
5713 TTACTTAATACCA-TTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
5738 TT
1 TT
5740 TACCATTTTT
Statistics
Matches: 109, Mismatches: 20, Indels: 19
0.74 0.14 0.13
Matches are distributed among these distances:
25 7 0.06
26 42 0.39
27 21 0.19
28 15 0.14
29 9 0.08
30 7 0.06
31 8 0.07
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.53
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:5727 original size:30 final size:30
Alignment explanation
Indices: 5678--5734 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
5668 ACTTTTTACT
5678 CTTTTTACTTAATTACCATTTTTTACTCCCC
1 CTTTTTACTTAATTACCA-TTTTTACTCCCC
5709 CTTTTTACTTAA-TACCATTTTTACTC
1 CTTTTTACTTAATTACCATTTTTACTC
5735 TTTTTTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.35
30 5 0.19
31 12 0.46
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (30 bp):
CTTTTTACTTAATTACCATTTTTACTCCCC
Found at i:5748 original size:10 final size:9
Alignment explanation
Indices: 5721--5761 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
5711 TTTTACTTAA
5721 TACCATTTT
1 TACCATTTT
*
5730 TACTCTTTTT
1 TAC-CATTTT
5740 TACCATTTT
1 TACCATTTT
5749 TATCCATTTT
1 TA-CCATTTT
5759 TAC
1 TAC
5762 TGAATACCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (9 bp):
TACCATTTT
Found at i:5758 original size:19 final size:19
Alignment explanation
Indices: 5721--5761 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5711 TTTTACTTAA
*
5721 TACCATTTTTACTCTTTTT
1 TACCATTTTTACTCATTTT
5740 TACCATTTTTA-TCCATTTT
1 TACCATTTTTACT-CATTTT
5759 TAC
1 TAC
5762 TGAATACCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (19 bp):
TACCATTTTTACTCATTTT
Found at i:5784 original size:26 final size:25
Alignment explanation
Indices: 5576--5839 Score: 140
Period size: 27 Copynumber: 10.1 Consensus size: 25
5566 TATTTCTTGA
5576 TTACT-AATTACCATTTTTTACTCTTT
1 TTACTGAA-TACCA-TTTTTACTCTTT
* * *
5602 GTACTGATTACCATATTTTACCCTTT
1 TTACTGAATACCAT-TTTTACTCTTT
*
5628 TTACTGATTACC-TCTTTT-CTTTCTACTT
1 TTACTGAATACCAT-TTTTAC--TCT--TT
*
5656 CTACTGAATACCACTTTTTACTCTTT
1 TTACTGAATACCA-TTTTTACTCTTT
*
5682 TTACTTAATTACCATTTTTTACTCCCCCTTT
1 TTACTGAA-TACCA-TTTTTACT----CTTT
*
5713 TTACTTAATACCATTTTTACTC-TT
1 TTACTGAATACCATTTTTACTCTTT
5737 TT--T---TACCATTTTTA-TCCATTT
1 TTACTGAATACCATTTTTACT-C-TTT
*
5758 TTACTGAATACCACTTTTCACTCTTTT
1 TTACTGAATACCA-TTTTTACTC-TTT
5785 TTACTG-ATCACCATTTCTTACTCTTT
1 TTACTGAAT-ACCATTT-TTACTCTTT
5811 ATTACT-AATTACTC-TCTTTTACTCTTT
1 -TTACTGAA-TAC-CAT-TTTTACTCTTT
5838 TT
1 TT
5840 TATCTTACTT
Statistics
Matches: 193, Mismatches: 14, Indels: 62
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.01
19 12 0.06
21 4 0.02
22 1 0.01
23 1 0.01
24 5 0.03
25 7 0.04
26 55 0.28
27 56 0.29
28 20 0.10
29 12 0.06
30 7 0.04
31 12 0.06
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.53
Consensus pattern (25 bp):
TTACTGAATACCATTTTTACTCTTT
Found at i:6210 original size:34 final size:34
Alignment explanation
Indices: 6165--6286 Score: 122
Period size: 34 Copynumber: 3.5 Consensus size: 34
6155 CTTTATTATC
6165 AATTTACTGATTACTATCTTTTTACTTAATTACT
1 AATTTACTGATTACTATCTTTTTACTTAATTACT
* * **
6199 AATTTATTGATTATTAT-TATCTGGACTCTTAATTA-T
1 AATTTACTGATTACTATCT-T-TTTA--CTTAATTACT
* *
6235 CAATTTACTGATTACTATCTTTTTACATGATTACT
1 -AATTTACTGATTACTATCTTTTTACTTAATTACT
*
6270 GATTTACTGATTACTAT
1 AATTTACTGATTACTAT
6287 TACCTTGACT
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
33 1 0.01
34 38 0.54
35 3 0.04
36 3 0.04
37 24 0.34
38 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.51
Consensus pattern (34 bp):
AATTTACTGATTACTATCTTTTTACTTAATTACT
Found at i:6241 original size:71 final size:71
Alignment explanation
Indices: 6154--6298 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
6144 TCACTTTAAT
* * * * *
6154 TCTTTATTATCAATTTACTGATTACTATCTTTTTACTTAATTACTAATTTATTGATTATTATTAT
1 TCTTAATTATCAATTTACTGATTACTATCTTTTTACATAATTACTAATTTACTGATTACTATTAC
6219 CTGGAC
66 CTGGAC
* *
6225 TCTTAATTATCAATTTACTGATTACTATCTTTTTACATGATTACTGATTTACTGATTACTATTAC
1 TCTTAATTATCAATTTACTGATTACTATCTTTTTACATAATTACTAATTTACTGATTACTATTAC
*
6290 CTTGAC
66 CTGGAC
6296 TCT
1 TCT
6299 GATTAATCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (71 bp):
TCTTAATTATCAATTTACTGATTACTATCTTTTTACATAATTACTAATTTACTGATTACTATTAC
CTGGAC
Found at i:6303 original size:55 final size:55
Alignment explanation
Indices: 6242--6628 Score: 447
Period size: 55 Copynumber: 7.6 Consensus size: 55
6232 TATCAATTTA
* * * *
6242 CTGATTACTATCTTTTTACATGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* * *
6297 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATTATCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
6352 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTCATTACTATTGCCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
6407 CTGATTAATCT-ATTTTACTTAATTACTGATTTACTGATTACTATTA-C----CT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
6456 -TGATTAATCTC--TTT--TT----ACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
6502 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACT-TTA-----ACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
6551 CTGATTAATCTC----T--TT--TTACTGATTTACTGATTACTTTTTCCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
6598 CTGATTAATCTCTTTTTAC-TGATTACTGATT
1 CTGATTAATCTCTTTTTACTTAATTACTGATT
6629 GATCCCATTT
Statistics
Matches: 287, Mismatches: 16, Indels: 59
0.79 0.04 0.16
Matches are distributed among these distances:
41 42 0.15
42 3 0.01
43 2 0.01
45 3 0.01
46 2 0.01
47 29 0.10
48 10 0.03
49 20 0.07
51 3 0.01
52 1 0.00
53 1 0.00
54 44 0.15
55 127 0.44
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
Found at i:6371 original size:47 final size:48
Alignment explanation
Indices: 6320--6628 Score: 310
Period size: 47 Copynumber: 6.4 Consensus size: 48
6310 TTTTACTTAA
*
6320 TTACTGATTTACTGATTAC-CATTATCTTAACTCTGATTAATCTCTTT
1 TTACTGAATTACTGATTACTCATTATCTTAACTCTGATTAATCTCTTT
* * *
6367 TTACTTAATTACTGATTTACTCATTACTATTGCCTTGACTCTGATTAATCT-ATT
1 TTACTGAATTACTGA-TTACTCA-T--TA-T--CTTAACTCTGATTAATCTCTTT
* * * *
6421 TTACTTAATTACTGATTTACTGATTACTATTACCT-TGATTAATCTCTTT
1 TTACTGAATTACTGA-TTACTCATTA-TCTTAACTCTGATTAATCTCTTT
* * *
6470 TTACTGATTTACTGATTACT-ATTACCTTGACTCTGATTAATCTCTTT
1 TTACTGAATTACTGATTACTCATTATCTTAACTCTGATTAATCTCTTT
* *
6517 TTACTTAATTACTGATTTACTGATTA-CTTTAACTCTGATTAATCTCTTT
1 TTACTGAATTACTGA-TTACTCATTATC-TTAACTCTGATTAATCTCTTT
* * *
6566 TTACTGATTTACTGATTACT--TTTTCCTTGACTCTGATTAATCTCTTT
1 TTACTGAATTACTGATTACTCATTAT-CTTAACTCTGATTAATCTCTTT
6613 TTACTG-ATTACTGATT
1 TTACTGAATTACTGATT
6629 GATCCCATTT
Statistics
Matches: 223, Mismatches: 24, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
46 15 0.07
47 70 0.31
48 31 0.14
49 58 0.26
50 1 0.00
51 3 0.01
52 2 0.01
53 2 0.01
54 24 0.11
55 17 0.08
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (48 bp):
TTACTGAATTACTGATTACTCATTATCTTAACTCTGATTAATCTCTTT
Found at i:6512 original size:150 final size:143
Alignment explanation
Indices: 6265--6628 Score: 421
Period size: 150 Copynumber: 2.4 Consensus size: 143
6255 TTTTACATGA
*
6265 TTACTGATTTACTGATTACT-ATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
1 TTACTGAATTACTGATTACTGATTA-CTTGACTCTGATTAATCTC----T--TT--TTACTGATT
*
6329 TACTGATTACCATTATCTTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTCATTAC
57 TACTGATTACCATTACCTTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTCATTAC
*
6394 TATTGCCTTGACTCTGATTAATCT-ATT
122 ---T---TTAACTCTGATTAATCTCATT
* *
6421 TTACTTAATTACTGATTTACTGATTACTATTAC-CTTGATTAATCTCTTTTTACTGATTTACTGA
1 TTACTGAATTACTGA-TTACTGATTACT-TGACTC-TGATTAATCTCTTTTTACTGATTTACTGA
* * *
6485 TTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTTTAAC
63 TTACCATTACCTTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTCATTACTTTAAC
*
6550 TCTGATTAATCTCTTT
128 TCTGATTAATCTCATT
* ** *
6566 TTACTGATTTACTGATTACTTTTTCCTTGACTCTGATTAATCTCTTTTTACTGA-TTACTGATT
1 TTACTGAATTACTGATTACTGATTACTTGACTCTGATTAATCTCTTTTTACTGATTTACTGATT
6629 GATCCCATTT
Statistics
Matches: 187, Mismatches: 15, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
142 9 0.05
143 24 0.13
144 26 0.14
145 15 0.08
147 1 0.01
150 70 0.37
152 2 0.01
154 1 0.01
156 13 0.07
157 8 0.04
158 18 0.10
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (143 bp):
TTACTGAATTACTGATTACTGATTACTTGACTCTGATTAATCTCTTTTTACTGATTTACTGATTA
CCATTACCTTAACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTCATTACTTTAACTCT
GATTAATCTCATT
Found at i:6562 original size:96 final size:96
Alignment explanation
Indices: 6375--6628 Score: 415
Period size: 96 Copynumber: 2.7 Consensus size: 96
6365 TTTTACTTAA
* * *
6375 TTACTGATTTACTCATTACTATTGCCTTGACTCTGATTAATCT-ATTTTACTTAATTACTGATTT
1 TTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTT
*
6439 ACTGATTACTATTACCTTGATTAATCTCTTT
66 ACTGATTACTATTAACTTGATTAATCTCTTT
6470 TTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTT
1 TTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTT
6535 ACTGATTACT-TTAACTCTGATTAATCTCTTT
66 ACTGATTACTATTAACT-TGATTAATCTCTTT
* * *
6566 TTACTGATTTACTGATTACTTTTTCCTTGACTCTGATTAATCTCTTTTTAC-TGATTACTGATT
1 TTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
6629 GATCCCATTT
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
95 57 0.38
96 93 0.62
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (96 bp):
TTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTT
ACTGATTACTATTAACTTGATTAATCTCTTT
Done.