Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009479.1 Corchorus capsularis cultivar CVL-1 contig09500, 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: 25230
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3759 original size:144 final size:141
Alignment explanation
Indices: 3352--3952 Score: 564
Period size: 138 Copynumber: 4.3 Consensus size: 141
3342 TATGCTTGCT
* * * * *
3352 CCTTCGACTGTCAGAGTAA-TATTCATCAGAACTGGTATCATGGATTCCC--TCACTGTTTCGAT
1 CCTTTGACTGTCTGAGTAACCA-TCATCAGAACTTGTATCATGGA--CCCTATCACTGCTTCGAT
* * * **
3414 CCTGTTTGAAGCTT-GA--G-CTCCGTCTATCTGATCTTCCGCC-GAGTTTTTTTGTTCGCTTTC
63 CCCGTTTGAAGCTTGGAGTGCCTCCGTCTATCTGATCTT-CGCCTG-GATTTTTTGTTTGCCATC
* * **
3474 TGTCATTACGCTCAGT
126 TGTCATTATGCTTAAC
* * * ** * * ** *
3490 ACTTTGACCGTAC-AAGTAGTCTTCATCAGAACTAGTATCATGGATTCTCTCACTGCTTCGATCC
1 CCTTTGACTGT-CTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCC
* *
3554 CGTTGGAAGC-TGGAGTGCCTCCGTCTATCTGATCTTTCGCCTGAATTTTTTGTTTGCCATCTGT
65 CGTTTGAAGCTTGGAGTGCCTCCGTCTATCTGATC-TTCGCCTGGATTTTTTGTTTGCCATCTGT
*
3618 CATCATGCTTAAC
129 CATTATGCTTAAC
* * *
3631 CCTATGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGTTTCGATCCT
1 CCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCCC
3696 GTTTGAAGCTTGAGGAGTGCCTCCGTCTATCTGATCTATCGCCTGGATTTTTTGTTTGCCATCTG
66 GTTTGAAGCTT--GGAGTGCCTCCGTCTATCTGATCT-TCGCCTGGATTTTTTGTTTGCCATCTG
3761 TCATTATGCTTAAC
128 TCATTATGCTTAAC
*
3775 CTTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCCC
1 CCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCCC
* * * * ** * ** **
3840 GTTTGAAGCTTGCA----CTCTGTTTATCTGATCTTCCACCTAAATCTTTCCTTTGCTTTCTGTC
66 GTTTGAAGCTTGGAGTGCCTCCGTCTATCTGATCTT-CGCCTGGATTTTTTGTTTGCCATCTGTC
* *
3901 ATTACGCCTAAC
130 ATTATGCTTAAC
* * * * *
3913 CCTTTCACTGTCGGAGTAACCTTCATCGGAACTGGTATCA
1 CCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCA
3953 AAGATATTCT
Statistics
Matches: 385, Mismatches: 62, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
136 1 0.00
137 2 0.01
138 136 0.35
139 1 0.00
140 2 0.01
141 102 0.26
142 6 0.02
143 1 0.00
144 134 0.35
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (141 bp):
CCTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCCC
GTTTGAAGCTTGGAGTGCCTCCGTCTATCTGATCTTCGCCTGGATTTTTTGTTTGCCATCTGTCA
TTATGCTTAAC
Found at i:4011 original size:138 final size:138
Alignment explanation
Indices: 3512--4012 Score: 315
Period size: 144 Copynumber: 3.6 Consensus size: 138
3502 CAAGTAGTCT
* ** ** * * *
3512 TCATCAGAACTAGTATCATGGATTCTCTCACTGCTTCGATCCCGTTGGAAGCTGGAGTGC-CTCC
1 TCATCAGAACTGGTATCAAAGACACTATCACTGCTTCGATCCCGTTTGAAGCT----TGCACTCT
* * * * * ** ** * * * * *
3576 GTCTATCTGATCTTTCGCCTGAATTTTTTGTTTGCCATCTGTCATCATGCTTAACCCTATGACTG
62 GTCTATCTGACCTTCCACCTAAATCTTTCCTTTGCTTTCTGTCATTACGCCTAACCCTTTCACTG
*
3641 TCTGAGTAACCA
127 TCGGAGTAACCA
* ** * * * *
3653 TCATCAGAACTTGTATCATGGACCCTATCACTGTTTCGATCCTGTTTGAAGCTTGAGGAGTGCCT
1 TCATCAGAACTGGTATCAAAGACACTATCACTGCTTCGATCCCGTTTGAAGCTT--GCA----CT
* * * ** * ** ** * * * *
3718 CCGTCTATCTGATCTAT-CGCCTGGATTTTTTGTTTGCCATCTGTCATTATGCTTAACCTTTTGA
60 CTGTCTATCTGACCT-TCCACCTAAATCTTTCCTTTGCTTTCTGTCATTACGCCTAACCCTTTCA
*
3782 CTGTCTGAGTAACCA
124 CTGTCGGAGTAACCA
* ** * *
3797 TCATCAGAACTTGTATCATGGACCCTATCACTGCTTCGATCCCGTTTGAAGCTTGCACTCTGTTT
1 TCATCAGAACTGGTATCAAAGACACTATCACTGCTTCGATCCCGTTTGAAGCTTGCACTCTGTCT
*
3862 ATCTGATCTTCCACCTAAATCTTTCCTTTGCTTTCTGTCATTACGCCTAACCCTTTCACTGTCGG
66 ATCTGACCTTCCACCTAAATCTTTCCTTTGCTTTCTGTCATTACGCCTAACCCTTTCACTGTCGG
*
3927 AGTAACCT
131 AGTAACCA
* * * * * * **
3935 TCATCGGAACTGGTATCAAAGATATTCTCACTGTTTTGATCCCGTTTTGAA-CTTGTGCTCTGTC
1 TCATCAGAACTGGTATCAAAGACACTATCACTGCTTCGATCCCG-TTTGAAGCTTGCACTCTGTC
* *
3999 TCTTTGACCTTCCA
65 TATCTGACCTTCCA
4013 TCTATAGCAT
Statistics
Matches: 303, Mismatches: 47, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
137 2 0.01
138 118 0.39
139 7 0.02
141 46 0.15
142 2 0.01
144 127 0.42
145 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (138 bp):
TCATCAGAACTGGTATCAAAGACACTATCACTGCTTCGATCCCGTTTGAAGCTTGCACTCTGTCT
ATCTGACCTTCCACCTAAATCTTTCCTTTGCTTTCTGTCATTACGCCTAACCCTTTCACTGTCGG
AGTAACCA
Found at i:4330 original size:138 final size:138
Alignment explanation
Indices: 3757--4376 Score: 502
Period size: 138 Copynumber: 4.5 Consensus size: 138
3747 TTGTTTGCCA
* ** * * * *
3757 TCTGTCATTATGCTTAACCTTTTGACTGTCTGAGTAACCATCATCAGAACTTGTATCATGGACCC
1 TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACCTTCATCAGAACTGGTATCATGGACTC
* * * * ** * * * *
3822 TATCACTGCTTCGATCCCGTTTGAAGCTTGCACTCTGTTTATCTGATCTTCCACCTAAATC-TTT
66 TCTCACTGCTTCGATCCCGTTTTAAACTTGTACTCTGCCTCTCTGACCTTCCATCTAAAACTTTT
*
3886 CCTTTGCTT-
131 GC-TTG-TTC
** * ** * * * **
3895 TCTGTCATTACGCCTAACCCTTTCACTGTCGGAGTAACCTTCATCGGAACTGGTATCAAAGA-TA
1 TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACCTTCATCAGAACTGGTATCATGGACT-
* * * * * * * * * *
3959 TTCTCACTGTTTTGATCCCGTTTTGAACTTGTGCTCTGTCTCTTTGACCTTCCATCTATAGCATT
65 CTCTCACTGCTTCGATCCCGTTTTAAACTTGTACTCTGCCTCTCTGACCTTCCATCTAAAACTTT
*
4024 TGCTTGTTT
130 TGCTTGTTC
* * * * * * * *
4033 TCTGTCAATATTCTTGCTCCTCTGACTGTGTGAATAACCTTCAT-AGGAGCTGGTATAATGGATT
1 TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACCTTCATCA-GAACTGGTATCATGGACT
* * * * *
4097 CTCTTA-TGGCTTCGA-CCCTGTTTTAAGCTTGTAATCTGCCTCTCTGATCTTCCATCTAAAATT
65 CTCTCACT-GCTTCGATCCC-GTTTTAAACTTGTACTCTGCCTCTCTGACCTTCCATCTAAAACT
4160 TTTGCTTGTTC
128 TTTGCTTGTTC
* *
4171 TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACTTTCATCAGAACCGGTATCATGGACTC
1 TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACCTTCATCAGAACTGGTATCATGGACTC
* ** *
4236 TCTCACTCCTTCGATCCCGTTTTAAACTTGTGTTATGCCTGC-CTGACCTTCCATCTAAAACTTT
66 TCTCACTGCTTCGATCCCGTTTTAAACTTGTACTCTGCCT-CTCTGACCTTCCATCTAAAACTTT
*
4300 TGTTTGTTC
130 TGCTTGTTC
* ** * * * *
4309 TCTGTCATTGTTCTTGCCCCTTT--CGTAGTCCAAGTAATCTCCATCAGAACTCGTATCATGGAT
1 TCTGTCATTATTCTTGCCCCTTTGAC-T-GTCTGAGTAACCTTCATCAGAACTGGTATCATGGAC
4372 TCTCT
64 TCTCT
4377 GATCCCATTT
Statistics
Matches: 380, Mismatches: 89, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
136 1 0.00
137 7 0.02
138 361 0.95
139 11 0.03
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (138 bp):
TCTGTCATTATTCTTGCCCCTTTGACTGTCTGAGTAACCTTCATCAGAACTGGTATCATGGACTC
TCTCACTGCTTCGATCCCGTTTTAAACTTGTACTCTGCCTCTCTGACCTTCCATCTAAAACTTTT
GCTTGTTC
Found at i:7419 original size:23 final size:22
Alignment explanation
Indices: 7376--7419 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
7366 AGCAAACATA
*
7376 AAAGGAGGAAACAGGAAAGGAG
1 AAAGGAGGAAAAAGGAAAGGAG
7398 AAAGG-GGAAAAAGAGAGAAGGA
1 AAAGGAGGAAAAAG-GA-AAGGA
7420 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.57, C:0.02, G:0.41, T:0.00
Consensus pattern (22 bp):
AAAGGAGGAAAAAGGAAAGGAG
Found at i:11530 original size:20 final size:20
Alignment explanation
Indices: 11501--11539 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11491 ATTATTTGTT
11501 ATTTTAATTTAAAATTAATA
1 ATTTTAATTTAAAATTAATA
* *
11521 ATTTTTATTTTAAATTAAT
1 ATTTTAATTTAAAATTAAT
11540 TAAATGCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATTTAAAATTAATA
Found at i:14424 original size:14 final size:14
Alignment explanation
Indices: 14405--14432 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14395 CTTCGTAGTC
14405 AATAAGTTCTCTTT
1 AATAAGTTCTCTTT
14419 AATAAGTTCTCTTT
1 AATAAGTTCTCTTT
14433 CTTTGTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAAGTTCTCTTT
Found at i:15526 original size:17 final size:17
Alignment explanation
Indices: 15504--15567 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
15494 AACGATTGTG
15504 CATATGTACTTGAATCT
1 CATATGTACTTGAATCT
*
15521 CATATGTGACTGCTTTGAATGT
1 CATATGT-A---C-TTGAATCT
*
15543 GCATATGCACTTGAATCT
1 -CATATGTACTTGAATCT
15561 CATATGT
1 CATATGT
15568 GACTGCTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 13 0.35
18 8 0.22
19 1 0.03
21 1 0.03
22 8 0.22
23 6 0.16
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (17 bp):
CATATGTACTTGAATCT
Found at i:15555 original size:40 final size:40
Alignment explanation
Indices: 15500--15590 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
15490 AAGAAACGAT
*
15500 TGTGCATATGTACTTGAATCTCATATGTGACTGCTTTGAA
1 TGTGCATATGCACTTGAATCTCATATGTGACTGCTTTGAA
*
15540 TGTGCATATGCACTTGAATCTCATATGTGACTGCTTTGGA
1 TGTGCATATGCACTTGAATCTCATATGTGACTGCTTTGAA
15580 TGTGCATATGC
1 TGTGCATATGC
15591 CATGTGTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.38
Consensus pattern (40 bp):
TGTGCATATGCACTTGAATCTCATATGTGACTGCTTTGAA
Found at i:15588 original size:23 final size:23
Alignment explanation
Indices: 15513--15589 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 23
15503 GCATATGTAC
*
15513 TTGAATCT-CATATGTGACTGCT
1 TTGAATGTGCATATGTGACTGCT
*
15535 TTGAATGTGCATA--TG-C-AC-
1 TTGAATGTGCATATGTGACTGCT
*
15553 TTGAATCT-CATATGTGACTGCT
1 TTGAATGTGCATATGTGACTGCT
*
15575 TTGGATGTGCATATG
1 TTGAATGTGCATATG
15590 CCATGTGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
17 4 0.10
18 7 0.17
19 3 0.07
20 2 0.05
21 3 0.07
22 13 0.31
23 10 0.24
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (23 bp):
TTGAATGTGCATATGTGACTGCT
Found at i:19703 original size:42 final size:41
Alignment explanation
Indices: 19627--19744 Score: 177
Period size: 43 Copynumber: 2.9 Consensus size: 41
19617 TTAATCGAAA
*
19627 GATTTTTTCTTTAAATAAATAGATATAACCATCTATCAAATT
1 GATTTTTTCTTTAAATAAATAGATAT-ACTATCTATCAAATT
19669 GATTTTTTTCTTTAAATAAATAGATATACTATCTATCAAATT
1 GA-TTTTTTCTTTAAATAAATAGATATACTATCTATCAAATT
* *
19711 GATTTTTTGTTTAAAT-AA-AGAGATACTATCTATC
1 GATTTTTTCTTTAAATAAATAGATATACTATCTATC
19745 CAATAGGTGT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
39 15 0.21
40 2 0.03
41 13 0.18
42 18 0.25
43 24 0.33
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (41 bp):
GATTTTTTCTTTAAATAAATAGATATACTATCTATCAAATT
Found at i:21304 original size:15 final size:15
Alignment explanation
Indices: 21284--21313 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21274 GAAATATAGT
21284 TATATATAAGTACTA
1 TATATATAAGTACTA
*
21299 TATATATGAGTACTA
1 TATATATAAGTACTA
21314 CAAGTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (15 bp):
TATATATAAGTACTA
Found at i:22398 original size:13 final size:13
Alignment explanation
Indices: 22380--22404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22370 TAATAACACA
22380 ATATATATATATC
1 ATATATATATATC
22393 ATATATATATAT
1 ATATATATATAT
22405 ATTTAAAACA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATC
Done.