Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011782.1 Corchorus capsularis cultivar CVL-1 contig11803, 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: 38258
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:6679 original size:90 final size:89
Alignment explanation
Indices: 6484--6750 Score: 491
Period size: 89 Copynumber: 3.0 Consensus size: 89
6474 CTTGTTCGAG
*
6484 TCAGATTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
1 TCAGGTTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
6549 AGTCGATATCCTATGTACCCAAAA
66 AGTCGATATCCTATGTACCCAAAA
*
6573 TCAGGTTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGTTTAGCTAACACT
1 TCAGGTTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
*
6638 AGTCGATATTCTATGTTACCCAAAA
66 AGTCGATATCCTATG-TACCCAAAA
6663 TCAGGTTGTTCAAGTCCCAAAGG-TTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
1 TCAGGTTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
6727 AGTCGATATCCTATGTACCCAAAA
66 AGTCGATATCCTATGTACCCAAAA
6751 AAAAAAAAAA
Statistics
Matches: 172, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
88 9 0.05
89 131 0.76
90 32 0.19
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (89 bp):
TCAGGTTGTTCAAGTCCCAAAGGTTTTTTTTTCCTTTCACAAGAAAGACGAGCTTAGCTAACACT
AGTCGATATCCTATGTACCCAAAA
Found at i:12048 original size:65 final size:66
Alignment explanation
Indices: 11914--12048 Score: 236
Period size: 65 Copynumber: 2.1 Consensus size: 66
11904 TCTTGTTGGG
* *
11914 ACTTGGGATTTAAAACGTTTTGAGAAACCCTAATTTGTGTTTTTATGCAAAATCTTTCGCTTTAT
1 ACTTGGGATTTAAAACGTTTTCAGAAACCCTAATTTGTGTTTTTATGAAAAATCTTTCGCTTTAT
11979 A
66 A
*
11980 ACTTGGGATTTAAAACGTTTTCAGAAACCCTAA-TTGTGTTTTTATGAAAAATCTTTGGCTTTAT
1 ACTTGGGATTTAAAACGTTTTCAGAAACCCTAATTTGTGTTTTTATGAAAAATCTTTCGCTTTAT
12044 A
66 A
12045 ACTT
1 ACTT
12049 TTGTGATGCT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 34 0.52
66 32 0.48
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (66 bp):
ACTTGGGATTTAAAACGTTTTCAGAAACCCTAATTTGTGTTTTTATGAAAAATCTTTCGCTTTAT
A
Found at i:13479 original size:83 final size:83
Alignment explanation
Indices: 13329--13752 Score: 187
Period size: 83 Copynumber: 4.8 Consensus size: 83
13319 TAGAAGGCAC
* * * * * * * * * *
13329 AAAAG-TGGCACTCCTATTATACATT-GAGGTATAATGGTGCCTCTAAATAAAAGCTGGTGACGG
1 AAAAGATGGCATTCCTATTATAC-TTAAAGGTATAGTGGTGCATCCAAATATAAGTTGGTAATGA
13392 GAATTTCTATTTGCAGCAA
65 GAATTTCTATTTGCAGCAA
* *
13411 AAGAGATGGCATTCCTATTATACTTAAAGGTATAGTGGTGCATCCAAATATAGGTTGGTAATGAG
1 AAAAGATGGCATTCCTATTATACTTAAAGGTATAGTGGTGCATCCAAATATAAGTTGGTAATGAG
* *
13476 AA-TTCTTATAATGCAGTTAA
66 AATTTC-TAT-TTGCAG-CAA
* * * *
13496 AGGCACAATCTGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCATTTCATGTAATAT-A
1 A---A-AA---GATGGCATTCCTATTATACTTAAAGGTATAGTGGTG-CA-TCCA---AATATAA
* * * * * * *
13560 CTTGGAACTCTTATTGTTCATCTAATATGCTA-TAGAAGGCAC
54 GTTGG------TAATG---A--GAAT-TTCTATTTGCA-GCAA
* * * * * * * * *
13602 AAAAG-TGGCACTCCTATTATACATT-GAGGTATAATGGTGCCTCTAAATAAAAGTTGGTGACGG
1 AAAAGATGGCATTCCTATTATAC-TTAAAGGTATAGTGGTGCATCCAAATATAAGTTGGTAATGA
13665 GAATTTCTATTTGCAGCAA
65 GAATTTCTATTTGCAGCAA
* * * *
13684 AAGAGATGGCATTCCTACTATACTTAAAGGTATAGTGGTGCATCCAAATATAGGTTGGTAATCAG
1 AAAAGATGGCATTCCTATTATACTTAAAGGTATAGTGGTGCATCCAAATATAAGTTGGTAATGAG
13749 AATT
66 AATT
13753 CTTATAATGC
Statistics
Matches: 245, Mismatches: 61, Indels: 71
0.65 0.16 0.19
Matches are distributed among these distances:
82 22 0.09
83 104 0.42
84 5 0.02
85 3 0.01
88 3 0.01
89 1 0.00
92 33 0.13
93 6 0.02
94 8 0.03
96 6 0.02
97 6 0.02
98 27 0.11
99 2 0.01
102 6 0.02
103 1 0.00
105 1 0.00
106 4 0.02
107 3 0.01
108 2 0.01
109 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (83 bp):
AAAAGATGGCATTCCTATTATACTTAAAGGTATAGTGGTGCATCCAAATATAAGTTGGTAATGAG
AATTTCTATTTGCAGCAA
Found at i:13806 original size:273 final size:268
Alignment explanation
Indices: 13313--13844 Score: 965
Period size: 273 Copynumber: 2.0 Consensus size: 268
13303 TTCTTATTGA
13313 ATGCTATAGAAGGCACAAAAGTGGCACTCCTATTATACATTGAGGTATAATGGTGCCTCTAAATA
1 ATGCTATAGAAGGCACAAAAGTGGCACTCCTATTATACATTGAGGTATAATGGTGCCTCTAAATA
*
13378 AAAGCTGGTGACGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACTTAAAGGTA
66 AAAGCTGGTGACGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTACTATACTTAAAGGTA
*
13443 TAGTGGTGCATCCAAATATAGGTTGGTAATGAGAATTCTTATAATGCAGTTAAAGGCACAATCTG
131 TAGTGGTGCATCCAAATATAGGTTGGTAATCAGAATTCTTATAATGCAGTTAAAGGCACAATCTG
*
13508 GTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCATTTCATGTAATATACTTGGAACTCTTA
196 GTGGCATTCCTACTATACATAAAGGTATAGTGGTG-C----CATGTAATATACCTGGAACTCTTA
13573 TTGTTCATCTAAT
256 TTGTTCATCTAAT
13586 ATGCTATAGAAGGCACAAAAGTGGCACTCCTATTATACATTGAGGTATAATGGTGCCTCTAAATA
1 ATGCTATAGAAGGCACAAAAGTGGCACTCCTATTATACATTGAGGTATAATGGTGCCTCTAAATA
*
13651 AAAGTTGGTGACGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTACTATACTTAAAGGTA
66 AAAGCTGGTGACGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTACTATACTTAAAGGTA
*
13716 TAGTGGTGCATCCAAATATAGGTTGGTAATCAGAATTCTTATAATGCAGTTAAAGGCACCATCTG
131 TAGTGGTGCATCCAAATATAGGTTGGTAATCAGAATTCTTATAATGCAGTTAAAGGCACAATCTG
*
13781 GTGGCATTCCTACTATACTTAAAGGTATAGTGGTGCCATGTAATATACCTGGAACTCTTATTGT
196 GTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCATGTAATATACCTGGAACTCTTATTGT
13845 GCAATGAATA
Statistics
Matches: 253, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
268 27 0.11
272 1 0.00
273 225 0.89
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (268 bp):
ATGCTATAGAAGGCACAAAAGTGGCACTCCTATTATACATTGAGGTATAATGGTGCCTCTAAATA
AAAGCTGGTGACGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTACTATACTTAAAGGTA
TAGTGGTGCATCCAAATATAGGTTGGTAATCAGAATTCTTATAATGCAGTTAAAGGCACAATCTG
GTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCATGTAATATACCTGGAACTCTTATTGTT
CATCTAAT
Found at i:14550 original size:371 final size:375
Alignment explanation
Indices: 13779--15301 Score: 2323
Period size: 371 Copynumber: 4.1 Consensus size: 375
13769 AGGCACCATC
* *
13779 TGGTGGCATTCCTACTATACTTAAAGGTATAGTGGTGCCA-----TGTAATATACCTGGAACTCT
1 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATTCCTGGAACTCT
* * *
13839 TATTGTGCAATG-AATATGAACAACCTTGAAGGCTCAATCTCCCTCGCCCACTCCATTTTTTCTG
66 TATTGTGCAATGAAATATGAACAATCTTGAAGGCTCAAGCTCCCTCGCCCACTCCATTTCTTCTG
* * **
13903 ATTCACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTCTGACTTTTTAGTATTCACT
131 ATACACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACCGTTTAGTATTCACT
13968 GCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCA
196 GCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCA
14033 AGTTCTTCTGTT--A---CATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATAC
261 AGTTCTTCTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATAC
*
14093 ATCAAGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTGTTG
326 ATCAAGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTGTGG
*
14143 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATTCCTGGAAGTCT
1 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATTCCTGGAACTCT
*
14208 TATTGTGCAATGAAATATGAACAATCTTGAAGGCTCACGCTCCCTCGCCCACTCCATTTCTTCTG
66 TATTGTGCAATGAAATATGAACAATCTTGAAGGCTCAAGCTCCCTCGCCCACTCCATTTCTTCTG
*
14273 ATACACCACCATGGGCAATTTAAG-TTT-TACTCAAAGTTGTTTTTTGACCGTTTAGTATTCACT
131 ATACACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACCGTTTAGTATTCACT
14336 GCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCA
196 GCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCA
*
14401 AGTAT-TTCTGTTACATGGAATTTTTTTTAA-GCTAAAAGGCA-AACTGTTGCATTCCTATTATA
261 AGT-TCTTCTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATA
* *
14463 CATCAAGGTATAATGGTGCATTGAATTAAGGTTGGTAAGAATTCTTTGTTG
325 CATCAAGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTGTGG
* ** *
14514 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCATGTAACGTTCCTGGAAGTCT
1 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATTCCTGGAACTCT
* *
14579 TATTGTGCAATGAAATATGAACAATCTTGAAGGATCAGGCTCCCTCGCCCACTCCATTTCTTCTG
66 TATTGTGCAATGAAATATGAACAATCTTGAAGGCTCAAGCTCCCTCGCCCACTCCATTTCTTCTG
*
14644 ATACACCACCATGAGCAATTTAAGTTTTATACTCAAAATTGTTTTTTGACTC-TTTAGTATTCAC
131 ATACACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGAC-CGTTTAGTATTCAC
* * * *
14708 TGCACACCCATCAAATGGCATCTATGCCTTGTTTAGATTTTGTTCTATCTATTTTTAAACGATGC
195 TGCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGC
*
14773 AAGTTCTTTTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATA
260 AAGTTCTTCTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATA
14838 CATCAAGGTATAATGGTGCA-CTGAATTAAGGTTGGTAAGATAAGAATTCTTTGTGG
325 CATCAAGGTATAATGGTGCATC-GAATTAAGGTT-G---G-TAAGAATTCTTTGTGG
* *
14894 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAA-ATCTACATCGAACT
1 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATAT-T-CCTGGAACT
* * * * * *
14958 CTAACTGTGCAATGAAATATGAA-AA--AT--A--TTCATGCTCCCTCGCCCACTCCATCTCTTC
64 CTTATTGTGCAATGAAATATGAACAATCTTGAAGGCTCAAGCTCCCTCGCCCACTCCATTTCTTC
* * *
15016 TGATACACCACCATGAGCAATCTAAGTTTTATACTCAAGGTTGTTTTTTGACTGTTTAGTATTCA
129 TGATACACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACCGTTTAGTATTCA
*
15081 CTGCACATCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATG
194 CTGCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATG
* * * * *
15146 CAAATTCTTTTG-T--ATGGCATTTTTCTTAATGCTAAAAGGCACAACTTTTGTATTCCTATTAT
259 CAAGTTCTTCTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTAT
* *
15208 ACATCATGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTCTGG
324 ACATCAAGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTGTGG
15260 TGGTGGCATTCCTACTATACA-AAAGGTATAGTGGTGCCAGTT
1 TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTT
15302 GGATTTTTCT
Statistics
Matches: 1076, Mismatches: 55, Indels: 55
0.91 0.05 0.05
Matches are distributed among these distances:
364 39 0.04
365 21 0.02
366 36 0.03
367 1 0.00
368 108 0.10
369 34 0.03
370 72 0.07
371 296 0.28
372 16 0.01
373 132 0.12
374 170 0.16
375 52 0.05
376 2 0.00
378 1 0.00
379 2 0.00
380 67 0.06
381 27 0.03
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (375 bp):
TGGTGGCATTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATTCCTGGAACTCT
TATTGTGCAATGAAATATGAACAATCTTGAAGGCTCAAGCTCCCTCGCCCACTCCATTTCTTCTG
ATACACCACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACCGTTTAGTATTCACT
GCACACCCATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCA
AGTTCTTCTGTTACATGGCATTTTTTTTAATGCTAAAAGGCACAACTGTTGCATTCCTATTATAC
ATCAAGGTATAATGGTGCATCGAATTAAGGTTGGTAAGAATTCTTTGTGG
Found at i:31800 original size:2 final size:2
Alignment explanation
Indices: 31793--31822 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31783 TAAATTCTTG
31793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31823 TCTTGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34623 original size:9 final size:9
Alignment explanation
Indices: 34606--34640 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
34596 ACTCGCTGCA
34606 TCTTCGTCT
1 TCTTCGTCT
*
34615 TCGTCGTCT
1 TCTTCGTCT
*
34624 TCTTCTTCT
1 TCTTCGTCT
34633 TCTTCGTC
1 TCTTCGTC
34641 GCTAAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.11, T:0.54
Consensus pattern (9 bp):
TCTTCGTCT
Found at i:36808 original size:12 final size:13
Alignment explanation
Indices: 36791--36827 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
36781 TTAGCTTTTT
36791 TTTTTTTATTT-C
1 TTTTTTTATTTAC
36803 TTTTTTTATTTAGC
1 TTTTTTTATTTA-C
36817 TTTTTTT-TTTA
1 TTTTTTTATTTA
36828 TTTCTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.48
13 4 0.17
14 8 0.35
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTTATTTAC
Found at i:36823 original size:17 final size:17
Alignment explanation
Indices: 36778--36830 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 17
36768 AGACTATAGG
36778 TATTTAGC-TTTTTTTT
1 TATTTAGCTTTTTTTTT
36794 T-TTTA--TTTCTTTTTT
1 TATTTAGCTTT-TTTTTT
36809 TATTTAGCTTTTTTTTT
1 TATTTAGCTTTTTTTTT
36826 TATTT
1 TATTT
36831 CTTTCTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 5 0.16
17 11 0.34
18 3 0.09
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (17 bp):
TATTTAGCTTTTTTTTT
Found at i:36845 original size:33 final size:30
Alignment explanation
Indices: 36778--36834 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
36768 AGACTATAGG
36778 TATTTAGCTTTTTTTTTTTTATTTCTTTTTT
1 TATTTAGC-TTTTTTTTTTTATTTCTTTTTT
36809 TATTTAGC-TTTTTTTTTTATTTCTTT
1 TATTTAGCTTTTTTTTTTTATTTCTTT
36835 CTAATGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.79
Consensus pattern (30 bp):
TATTTAGCTTTTTTTTTTTATTTCTTTTTT
Found at i:38208 original size:2 final size:2
Alignment explanation
Indices: 38203--38235 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38193 AGAGAATTTA
38203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38236 GCACTCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.