Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012581.1 Corchorus olitorius cultivar O-4 contig12614, 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: 6811
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Found at i:1238 original size:16 final size:16
Alignment explanation
Indices: 1217--1289 Score: 94
Period size: 16 Copynumber: 4.6 Consensus size: 16
1207 GTCGGGTTGA
1217 TTGGGTTCGGGTCATT
1 TTGGGTTCGGGTCATT
*
1233 TTGGGTTTGGGTCATT
1 TTGGGTTCGGGTCATT
1249 TTCGGGTTCGGGTCA-T
1 TT-GGGTTCGGGTCATT
* *
1265 TTGGATTCGGGTAATT
1 TTGGGTTCGGGTCATT
*
1281 TCGGGTTCG
1 TTGGGTTCG
1290 CGTACCCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.20
16 28 0.57
17 11 0.22
ACGTcount: A:0.08, C:0.12, G:0.37, T:0.42
Consensus pattern (16 bp):
TTGGGTTCGGGTCATT
Found at i:1261 original size:33 final size:31
Alignment explanation
Indices: 1219--1289 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
1209 CGGGTTGATT
* * *
1219 GGGTTCGGGTCATTTTGGGTTTGGGTCATTTTC
1 GGGTTCGGGTCA-TTTGGATTCGGGT-AATTTC
1252 GGGTTCGGGTCATTTGGATTCGGGTAATTTC
1 GGGTTCGGGTCATTTGGATTCGGGTAATTTC
1283 GGGTTCG
1 GGGTTCG
1290 CGTACCCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 12 0.34
32 11 0.31
33 12 0.34
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (31 bp):
GGGTTCGGGTCATTTGGATTCGGGTAATTTC
Found at i:1341 original size:17 final size:17
Alignment explanation
Indices: 1301--1341 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1291 GTACCCAAAA
1301 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
1318 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
1334 TTTCGGGT
1 TTTCGGGT
1342 TGGCGGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:2374 original size:11 final size:11
Alignment explanation
Indices: 2355--2389 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2345 TTTTTCTGTT
*
2355 TTTTATTTTTG
1 TTTTGTTTTTG
*
2366 TTTTGTTTTCG
1 TTTTGTTTTTG
2377 TTTTGTTTTTG
1 TTTTGTTTTTG
2388 TT
1 TT
2390 GCGCCGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:3465 original size:24 final size:24
Alignment explanation
Indices: 3437--3483 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3427 TTTGGACTTT
3437 GGTGGGAATTTTCAATTTTGGGCC
1 GGTGGGAATTTTCAATTTTGGGCC
*
3461 GGTGGGAATTTTTAATTTTGGGC
1 GGTGGGAATTTTCAATTTTGGGC
3484 AAAGCCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (24 bp):
GGTGGGAATTTTCAATTTTGGGCC
Found at i:4672 original size:25 final size:25
Alignment explanation
Indices: 4636--4684 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
4626 TGTGGGTTTG
*
4636 TAGAGACTGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
4661 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
4685 GATTGTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:5517 original size:43 final size:43
Alignment explanation
Indices: 5452--5534 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
5442 TCATTATCAA
* *
5452 AATATTTTTTGATTATAGCATTATTAAAATATATAAAATTGTC
1 AATATATTTTAATTATAGCATTATTAAAATATATAAAATTGTC
5495 AATATATTTTAATTAT-GCCATTATTAAAATATATAAAATT
1 AATATATTTTAATTATAG-CATTATTAAAATATATAAAATT
5535 TCCATTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (43 bp):
AATATATTTTAATTATAGCATTATTAAAATATATAAAATTGTC
Found at i:6119 original size:16 final size:16
Alignment explanation
Indices: 6096--6136 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
6086 AGTCAACGTC
6096 CCGAACCTGCCTGAAT
1 CCGAACCTGCCTGAAT
*
6112 CGGAACCTGCCTGAAT
1 CCGAACCTGCCTGAAT
6128 CCGAACCTG
1 CCGAACCTG
6137 AAATTACCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (16 bp):
CCGAACCTGCCTGAAT
Found at i:6419 original size:34 final size:35
Alignment explanation
Indices: 6370--6445 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
6360 CTAAAAAGTC
* *
6370 TAAACAAATAAAGAGTCTA-GAAAGAGGTTTACTAA
1 TAAA-AAACAAAGAGTCTACAAAAGAGGTTTACTAA
*
6405 TAAAAAACAAAGAGTCTACAAAAGATGTTTACTAA
1 TAAAAAACAAAGAGTCTACAAAAGAGGTTTACTAA
6440 TAAAAA
1 TAAAAA
6446 CAATTACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 13 0.35
35 24 0.65
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.22
Consensus pattern (35 bp):
TAAAAAACAAAGAGTCTACAAAAGAGGTTTACTAA
Found at i:6596 original size:21 final size:21
Alignment explanation
Indices: 6570--6682 Score: 174
Period size: 21 Copynumber: 5.4 Consensus size: 21
6560 TGCTAGAAGT
6570 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
6591 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
6612 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
6633 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
6654 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
6675 TCATTGGA
1 TCATTGGA
6683 ATTGCCTAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 2 0.02
21 85 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.