Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008278.1 Corchorus capsularis cultivar CVL-1 contig08299, 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: 29537
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:279 original size:70 final size:70
Alignment explanation
Indices: 203--427 Score: 297
Period size: 70 Copynumber: 3.1 Consensus size: 70
193 TAATTAAAAT
*
203 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
268 AGTTGAG
66 AGTT--G
*
275 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAAAGA
1 ------AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
340 GTTTTTAGTTG
60 GTTTTTAGTTG
* * * * * * *
351 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAACAAAAATAGAGTTTTT
1 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
416 AGTTG
66 AGTTG
421 AGTAAAA
1 AGTAAAA
428 CTATAAAAAC
Statistics
Matches: 137, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
70 69 0.50
76 1 0.01
78 67 0.49
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.36
Consensus pattern (70 bp):
AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:280 original size:78 final size:78
Alignment explanation
Indices: 197--435 Score: 352
Period size: 78 Copynumber: 3.2 Consensus size: 78
187 TTTTTTTAAT
*
197 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
262 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
275 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAAAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
340 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * *
353 TAAAATAGTAAAA---T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAACAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
410 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
423 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
436 ACCTAAACAA
Statistics
Matches: 153, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
70 54 0.35
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
78 89 0.58
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:24444 original size:7 final size:7
Alignment explanation
Indices: 24433--24463 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
24423 TAAACAAAAT
*
24433 CACTTCT
1 CACTTCC
24440 CACTTCC
1 CACTTCC
24447 CACTTCC
1 CACTTCC
24454 CACTTCC
1 CACTTCC
24461 CAC
1 CAC
24464 CAAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.55, G:0.00, T:0.29
Consensus pattern (7 bp):
CACTTCC
Found at i:28150 original size:182 final size:178
Alignment explanation
Indices: 27798--28152 Score: 566
Period size: 182 Copynumber: 2.0 Consensus size: 178
27788 AAACAAATCA
27798 TTTTTTATTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCCTTAC
1 TTTTTTATTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCCTTAC
* * *
27863 AATTATATGTTGGACGATTGAATGTTTCGGTTTTAATTGTTTTTTTTCCCTATTTAACCGATCAT
66 AATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTCCCTATTTAACCGATCAA
* *
27928 GGTGATTTAGGTGTCTATTTAAAGGTAATTCCATGGTCTACAATCATT
131 GGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAATCATT
*
27976 TTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCACTTA
1 TTTTTTATTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATC-CTTA
* * ** *
28041 CAATTATGGGTTGGACGATTGAATGTTTCGGCTTTAATTCCTTTTTTTTTTTTCTATTTGACCGA
65 CAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAA-T--TGTTTTTTTTCCCTATTTAACCGA
*
28106 TCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTTCATGGTCTACAA
127 TCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAA
28153 CTTTCATGAA
Statistics
Matches: 161, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
178 59 0.37
179 38 0.24
180 1 0.01
182 63 0.39
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (178 bp):
TTTTTTATTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAATCCTTAC
AATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTCCCTATTTAACCGATCAA
GGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTACAATCATT
Found at i:28400 original size:14 final size:12
Alignment explanation
Indices: 28366--28397 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
28356 GAGTTTCGTG
28366 GAGAATTTAAGA
1 GAGAATTTAAGA
28378 GAGAATTTAAGA
1 GAGAATTTAAGA
28390 GAGAATTT
1 GAGAATTT
28398 TTATGTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (12 bp):
GAGAATTTAAGA
Found at i:28495 original size:60 final size:60
Alignment explanation
Indices: 28427--28549 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
28417 ACAAATATTT
28427 TTTTCCCTGTATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCTATTTAATCC
1 TTTTCCCTGTATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCTATTTAATCC
*
28487 TTTTCCCTGTATTATTTATCAAATGACTCTCATACTTTTATGCTTTATGCTATTTAATCC
1 TTTTCCCTGTATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCTATTTAATCC
28547 TTT
1 TTT
28550 ACAATTATGG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (60 bp):
TTTTCCCTGTATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCTATTTAATCC
Found at i:28948 original size:12 final size:12
Alignment explanation
Indices: 28931--28957 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28921 ACAAAATCCT
28931 TTGACATCTAGA
1 TTGACATCTAGA
28943 TTGACATCTAGA
1 TTGACATCTAGA
28955 TTG
1 TTG
28958 CTAAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (12 bp):
TTGACATCTAGA
Found at i:29348 original size:24 final size:26
Alignment explanation
Indices: 29316--29364 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
29306 CTTACAAAAA
*
29316 AATATTGATTGGCCC-AA-TAATAAC
1 AATATTGATTGACCCTAACTAATAAC
29340 AATATTGATTGACCCTAACTAATAA
1 AATATTGATTGACCCTAACTAATAA
29365 TAATTATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (26 bp):
AATATTGATTGACCCTAACTAATAAC
Found at i:29500 original size:33 final size:33
Alignment explanation
Indices: 29455--29536 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
29445 TATCCTCCAC
* *
29455 GGTGGTGGCATCCTCCGGGGACGGCACCCATCGT
1 GGTGG-GGCATCCTCCGGGGACGCCACCCACCGT
*
29489 GGTGGGGCATCCTCCGGGGACGCCTCCCACCGT
1 GGTGGGGCATCCTCCGGGGACGCCACCCACCGT
*
29522 GGTGGGGCGTCCTCC
1 GGTGGGGCATCCTCC
29537 A
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 39 0.89
34 5 0.11
ACGTcount: A:0.09, C:0.35, G:0.39, T:0.17
Consensus pattern (33 bp):
GGTGGGGCATCCTCCGGGGACGCCACCCACCGT
Done.