Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009016.1 Corchorus capsularis cultivar CVL-1 contig09037, 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: 4339
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:224 original size:109 final size:109
Alignment explanation
Indices: 92--366 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 109
82 AAAAAAATTA
92 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
155 AAAAAATTTTAATATATCCAAACTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAACTTTTTGGTAAAAATAAAGTAAT
200 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
265 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAACTTTTTGGTAAAAATAAAGTAAT
* *
309 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
367 CTATAATAGT
Statistics
Matches: 156, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 118 0.76
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAACTTTTTGGTAAAAATAAAGTAAT
Found at i:582 original size:173 final size:173
Alignment explanation
Indices: 293--626 Score: 641
Period size: 173 Copynumber: 1.9 Consensus size: 173
283 AAATTTTTTG
293 GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGT
1 GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGT
* *
358 AGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAATAAGGGTACAA
66 AGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATACATTTGAAAAATAAGGATACAA
423 TAGGTAATTCAAAAGTTTCTCAAAACTCGTATTTTTATATATA
131 TAGGTAATTCAAAAGTTTCTCAAAACTCGTATTTTTATATATA
466 GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGT
1 GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGT
*
531 AGAATAAAATTATAATAGTTAAGTAAGGGCATTTAAGACAATACATTTGAAAAATAAGGATACAA
66 AGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATACATTTGAAAAATAAGGATACAA
596 TAGGTAATTCAAAAGTTTCTCAAAACTCGTA
131 TAGGTAATTCAAAAGTTTCTCAAAACTCGTA
627 CTATATATAG
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 158 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (173 bp):
GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGT
AGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATACATTTGAAAAATAAGGATACAA
TAGGTAATTCAAAAGTTTCTCAAAACTCGTATTTTTATATATA
Found at i:828 original size:31 final size:30
Alignment explanation
Indices: 793--850 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
783 ATTTTAATAT
*
793 TGTGATTAATCAATAGCAATAAAATTAAAAC
1 TGTGATTAATCAATAACAAT-AAATTAAAAC
824 TGTGATTAATCAATAACAATAAATTAA
1 TGTGATTAATCAATAACAATAAATTAA
851 TTTTTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (30 bp):
TGTGATTAATCAATAACAATAAATTAAAAC
Found at i:2238 original size:3 final size:3
Alignment explanation
Indices: 2224--2300 Score: 93
Period size: 3 Copynumber: 25.7 Consensus size: 3
2214 ACATAATAGC
* *
2224 TCA TCT TCA TCA TCA TCA TCA TCA TCA TCA TCC TCA TCA TCA TCA TC-
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* * *
2271 TCCA TCA TCA TCT TCA TCT TCA TCT TCA TC
1 T-CA TCA TCA TCA TCA TCA TCA TCA TCA TC
2301 TTTACTGTGA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 1 0.02
3 60 0.97
4 1 0.02
ACGTcount: A:0.25, C:0.36, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Done.