Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012507.1 Corchorus olitorius cultivar O-4 contig12540, 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: 31958
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11 original size:3 final size:3
Alignment explanation
Indices: 4--251 Score: 246
Period size: 3 Copynumber: 83.7 Consensus size: 3
1 GTC
4 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98 TTA -TA TTA -TA TTA TTA -TA TTA -TA TTA -TA TTA -TA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * ** * ** *
138 GTAA GTA CTA TAAA TCA CCCAA TTT TGTA CAA TTT TTA TTA TTA TTA
1 -TTA TTA TTA T-TA TTA --TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
185 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
232 TTA TTA TTA -TA TTAA TTA TT
1 TTA TTA TTA TTA TT-A TTA TT
252 GGCCTATGAA
Statistics
Matches: 205, Mismatches: 23, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
2 19 0.09
3 175 0.85
4 9 0.04
5 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2118 original size:5 final size:5
Alignment explanation
Indices: 2110--2136 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2100 AAAAAAAAAG
2110 CTAAA CTAAA CTAAA CTAAA CTAAA CT
1 CTAAA CTAAA CTAAA CTAAA CTAAA CT
2137 TTAACTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (5 bp):
CTAAA
Found at i:2187 original size:2 final size:2
Alignment explanation
Indices: 2180--2206 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2170 AAAATTATGT
2180 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2207 TCAGAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14186 original size:44 final size:44
Alignment explanation
Indices: 14123--14212 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
14113 TGTGGAAGTC
14123 ATGTTGTCTTCACTAGTGGGTGTAGGAATTGAAACCGGGGTGGG
1 ATGTTGTCTTCACTAGTGGGTGTAGGAATTGAAACCGGGGTGGG
14167 ATGTTGTCTTCACTAGTGGGTGTAGGAATTGAAACCGGGGTGGG
1 ATGTTGTCTTCACTAGTGGGTGTAGGAATTGAAACCGGGGTGGG
14211 AT
1 AT
14213 TTAGAGGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.21, C:0.11, G:0.38, T:0.30
Consensus pattern (44 bp):
ATGTTGTCTTCACTAGTGGGTGTAGGAATTGAAACCGGGGTGGG
Found at i:16533 original size:7 final size:7
Alignment explanation
Indices: 16521--16553 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
16511 CACGGGCCAC
16521 TTTTTCT
1 TTTTTCT
16528 TTTTTCT
1 TTTTTCT
16535 TTTTTCT
1 TTTTTCT
16542 TTTTTCT
1 TTTTTCT
16549 TTTTT
1 TTTTT
16554 TTTCGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:23225 original size:26 final size:26
Alignment explanation
Indices: 23174--23222 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
23164 CCCACTTTGT
* *
23174 CTTTTATTTTCCTAGTCTTTATTTAG
1 CTTTTAATTTCCTAGTCTGTATTTAG
23200 CTTTTAATTTCCTAGT-TGTATTT
1 CTTTTAATTTCCTAGTCTGTATTT
23223 TAGGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.61
Consensus pattern (26 bp):
CTTTTAATTTCCTAGTCTGTATTTAG
Found at i:23753 original size:30 final size:32
Alignment explanation
Indices: 23717--23782 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
23707 ACAGCGTTCA
*
23717 ACGTGTC-CTTTTTT-GTACACGTGGCGTGCC
1 ACGTGTCACTTTTTTGGTACACGTGGCATGCC
* *
23747 ACGTGTCATTTTTTTGGTAGACGTGGCATGCC
1 ACGTGTCACTTTTTTGGTACACGTGGCATGCC
23779 ACGT
1 ACGT
23783 CGGATGTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.23
31 6 0.19
32 18 0.58
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (32 bp):
ACGTGTCACTTTTTTGGTACACGTGGCATGCC
Found at i:31325 original size:33 final size:33
Alignment explanation
Indices: 31281--31344 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
31271 AATTAAGCAT
*
31281 GTAATTTTAATGGATTCAAACCAAATACTAAGA
1 GTAACTTTAATGGATTCAAACCAAATACTAAGA
31314 GTAACTTTAATGGATTCAAACCAAATACTAA
1 GTAACTTTAATGGATTCAAACCAAATACTAA
31345 CTTTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (33 bp):
GTAACTTTAATGGATTCAAACCAAATACTAAGA
Done.