Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014960.1 Corchorus olitorius cultivar O-4 contig14993, 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: 33599
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:8117 original size:25 final size:25
Alignment explanation
Indices: 8083--8133 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
8073 CATCATCATG
8083 TTATGTGATTGAGTAACCAAAATAT
1 TTATGTGATTGAGTAACCAAAATAT
8108 TTATGTGATTGAGTAACCAAAATAT
1 TTATGTGATTGAGTAACCAAAATAT
8133 T
1 T
8134 CAATATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (25 bp):
TTATGTGATTGAGTAACCAAAATAT
Found at i:13370 original size:19 final size:18
Alignment explanation
Indices: 13346--13381 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13336 TGAAGACTTA
13346 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
13365 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
13382 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:13388 original size:30 final size:30
Alignment explanation
Indices: 13334--13393 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
13324 GAAGTTCGTG
* *
13334 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
13364 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
13394 ACAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:29359 original size:19 final size:18
Alignment explanation
Indices: 29314--29361 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
29304 TAGGAGTAAT
*
29314 TTTAAAGTAAAAATATAA
1 TTTAAAATAAAAATATAA
*
29332 TTTATAAATAAAAATTTAA
1 TTTA-AAATAAAAATATAA
29351 TATTAAAATAA
1 T-TTAAAATAA
29362 TTAATTAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 19 0.73
20 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTTAAAATAAAAATATAA
Found at i:29870 original size:95 final size:96
Alignment explanation
Indices: 29754--29938 Score: 302
Period size: 95 Copynumber: 1.9 Consensus size: 96
29744 TCCTTGGGTT
*
29754 GGCTGGTTACTATTGGAGGTTTG-TGGAGGGATTTTCTAGCATTGCAATGCAGATGACTAAATTG
1 GGCTGGTTACTATCGGAGGTTTGTTGG-GGGATTTTCTAGCATTGCAATGCAGATGACTAAATTG
*
29818 ACCCG-AAAGGTGCTAAGTTCAAATGAACTAA
65 ACCCGAAAAGGTACTAAGTTCAAATGAACTAA
*
29849 GGCTGGTTACTATCGGAGGTTTGTTGGGGGATTTTCTAGCATTGCAATGCGGATGACTAAATTGA
1 GGCTGGTTACTATCGGAGGTTTGTTGGGGGATTTTCTAGCATTGCAATGCAGATGACTAAATTGA
* *
29914 CTCGAAAAGGTACTAAGTTCGAATG
66 CCCGAAAAGGTACTAAGTTCAAATG
29939 GATTGATGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
95 62 0.75
96 21 0.25
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (96 bp):
GGCTGGTTACTATCGGAGGTTTGTTGGGGGATTTTCTAGCATTGCAATGCAGATGACTAAATTGA
CCCGAAAAGGTACTAAGTTCAAATGAACTAA
Found at i:32224 original size:24 final size:24
Alignment explanation
Indices: 32197--32247 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
32187 TTTTGAGAGC
*
32197 TTTAGTCTTGGCCTAGTGCAACTT
1 TTTAGTCTTGCCCTAGTGCAACTT
* *
32221 TTTAGTCTTGCCCTAGTGTAATTT
1 TTTAGTCTTGCCCTAGTGCAACTT
32245 TTT
1 TTT
32248 TCTCTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (24 bp):
TTTAGTCTTGCCCTAGTGCAACTT
Found at i:32253 original size:24 final size:24
Alignment explanation
Indices: 32197--32253 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
32187 TTTTGAGAGC
* *
32197 TTTAGTCTTGGCCTAGTGCAACTT
1 TTTACTCTTGCCCTAGTGCAACTT
* * *
32221 TTTAGTCTTGCCCTAGTGTAATTT
1 TTTACTCTTGCCCTAGTGCAACTT
*
32245 TTTTCTCTT
1 TTTACTCTT
32254 CCTACGGCGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (24 bp):
TTTACTCTTGCCCTAGTGCAACTT
Found at i:33252 original size:31 final size:31
Alignment explanation
Indices: 33181--33252 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
33171 GAACAAAGAA
* *
33181 CAGATTCAACCAAGAAAAAGAATTACAATAT
1 CAGATTCAACCAAGAAAAAGAATTACAACAC
*
33212 CAGACTCAACCAAGAAAACA-AATTACAACAC
1 CAGATTCAACCAAGAAAA-AGAATTACAACAC
33243 CAGATTCAAC
1 CAGATTCAAC
33253 TAGACCCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.53, C:0.24, G:0.08, T:0.15
Consensus pattern (31 bp):
CAGATTCAACCAAGAAAAAGAATTACAACAC
Found at i:33283 original size:12 final size:12
Alignment explanation
Indices: 33266--33295 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33256 ACCCGACAAT
33266 TCGTGTATCGTG
1 TCGTGTATCGTG
*
33278 TCGTGTCTCGTG
1 TCGTGTATCGTG
33290 TCGTGT
1 TCGTGT
33296 TTACATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.33, T:0.43
Consensus pattern (12 bp):
TCGTGTATCGTG
Done.