Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010033.1 Corchorus capsularis cultivar CVL-1 contig10054, 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: 2302
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Found at i:1744 original size:78 final size:70
Alignment explanation
Indices: 1662--1816 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
1652 TAATTAAAAT
* * * * * *
1662 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
1727 AGTTG
66 AGTTG
*
1732 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
1797 AGTTG
66 AGTTG
1802 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
1817 ACCTAAACAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:2000 original size:73 final size:70
Alignment explanation
Indices: 1916--2071 Score: 181
Period size: 73 Copynumber: 2.2 Consensus size: 70
1906 ATAGTATAGA
* * * * * * *
1916 TAAAATGGTAAAATATAATAGTTATAAGGATATTAGCTTTAAATTTATATAAAAATTGCACG-TT
1 TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTT-AA-TTAAATAAAAATAG-A-GTTT
1980 TTAGTTGAG
62 TTAGTTGAG
*
1989 TAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAG
1 TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
2054 TTGAG
66 TTGAG
2059 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
2072 ACCTAAACAA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
69 1 0.01
70 22 0.30
71 14 0.19
72 2 0.03
73 34 0.47
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.37
Consensus pattern (70 bp):
TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
TTGAG
Found at i:2112 original size:255 final size:252
Alignment explanation
Indices: 1660--2191 Score: 951
Period size: 255 Copynumber: 2.1 Consensus size: 252
1650 TTTAATTAAA
1660 ATAG-TAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTT
1 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTT
1724 TTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATA
66 TTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATA
1789 GAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAA
131 GAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAA
*
1854 TAAGGGTATAATAGGCGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
196 TAAGGGTATAATAGACGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
*
1911 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAGCTTTAAATTTATATAAAAATTGCA
1 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTT-AA-TTATATAAAAATTG-A
1976 CG-TTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAA
63 -GTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAA
*
2040 AATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTGA
127 AATAGAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAA
2105 CAAATAAGGGTATAATAGACGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
192 CAAATAAGGGTATAATAGACGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
** *
2166 ATAGATAATAATAATAATATATAATA
1 ATAGATAA-AATGGTAAAATATAATA
2192 ATAATAATAA
Statistics
Matches: 269, Mismatches: 6, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
251 4 0.01
252 39 0.14
253 2 0.01
254 14 0.05
255 195 0.72
256 15 0.06
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (252 bp):
ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTT
TTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATA
GAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAA
TAAGGGTATAATAGACGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
Found at i:2178 original size:3 final size:3
Alignment explanation
Indices: 2170--2208 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2160 TATAGTATAG
2170 ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT
2209 TCAATAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2232 original size:23 final size:23
Alignment explanation
Indices: 2170--2216 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2160 TATAGTATAG
2170 ATAATAATAATAAT-ATAT-AATA
1 ATAATAATAATAATAAT-TCAATA
2192 ATAATAATAATAATAATTCAATA
1 ATAATAATAATAATAATTCAATA
2215 AT
1 AT
2217 CAATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
ATAATAATAATAATAATTCAATA
Done.