Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018732.1 Corchorus olitorius cultivar O-4 contig18765, 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: 11855
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:14 original size:4 final size:4
Alignment explanation
Indices: 6--228 Score: 214
Period size: 4 Copynumber: 56.0 Consensus size: 4
1 GGGTG
* * * * * *
6 GTGT GTGT GTGT GTG- GTGT GTGT GTGC GTGC GTGC GTGC GTGC GTGC
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * *
53 GTGC GTGC GTGC GTGT GCGT GCGT GCGT GTGT GTGT GTGT GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * *
101 GTGT GTGT GTGT GTGC GTGC GTGC GTGC GTGC GTGT GTGC GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * *
149 GTGT ATGT GTGT GTGT GTGT GTGT GCGT GTGT GTGT GTGC GTGT GCGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
** *
197 GTGT GCAT GTGT GTGT GTGT GCGT GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
229 TTCTGAAGAC
Statistics
Matches: 196, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
3 3 0.02
4 193 0.98
ACGTcount: A:0.01, C:0.10, G:0.49, T:0.39
Consensus pattern (4 bp):
GTGT
Found at i:311 original size:2 final size:2
Alignment explanation
Indices: 304--349 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
294 CAGAGACAGA
* * *
304 GT GT GT GT GT GT GT GT GC GT GT GT GC GT GT GT GT GC GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
346 GT GT
1 GT GT
350 TTCTGAAGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (2 bp):
GT
Found at i:397 original size:121 final size:119
Alignment explanation
Indices: 189--424 Score: 427
Period size: 121 Copynumber: 2.0 Consensus size: 119
179 GTGTGTGTGC
189 GTGTGCGTGTGTGCATGTGTGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATT
1 GTGTGCGTGTGTGCATGTGTGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATT
254 GGTGTTCTTTAATGCAAAGTGAAAAGTTACCATGGTTTAGCAGAGACAGAGTGT
66 GGTGTTCTTTAATGCAAAGTGAAAAGTTACCATGGTTTAGCAGAGACAGAGTGT
* *
308 GTGTGTGTGTGTGCGTGTGTGCGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTA
1 GTGTGCGTGTGTGCATGTGT--GTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTA
*
373 TTGGTGTTCTTTAATGCAAAGTGAAAAGTTAGCATGGTTTAGCAGAGACAGA
64 TTGGTGTTCTTTAATGCAAAGTGAAAAGTTACCATGGTTTAGCAGAGACAGA
425 ATTGTATGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
119 18 0.16
121 94 0.84
ACGTcount: A:0.20, C:0.11, G:0.32, T:0.38
Consensus pattern (119 bp):
GTGTGCGTGTGTGCATGTGTGTGTGTGTGCGTGTGTGTGTTTCTGAAGACATTGTTACTCTTATT
GGTGTTCTTTAATGCAAAGTGAAAAGTTACCATGGTTTAGCAGAGACAGAGTGT
Found at i:2131 original size:31 final size:29
Alignment explanation
Indices: 2096--2201 Score: 70
Period size: 31 Copynumber: 3.5 Consensus size: 29
2086 GTCAAAAAAA
*
2096 GCCCCAAATTGAGCAGCCCTGAAAACGTTTG
1 GCCCCAAATTGAGCA-CACTG-AAACGTTTG
** * *
2127 GCCCCATTTTGTTGCA-ATTGAAACGTTTG
1 GCCCCAAATTG-AGCACACTGAAACGTTTG
* * * * *
2156 ACCCCAAATCGAGCATCGCAGCAAACATTTG
1 GCCCCAAATTGAGCA-CACTG-AAACGTTTG
2187 GCCCCAAATTGAGCA
1 GCCCCAAATTGAGCA
2202 TTTTGCCCAA
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
28 3 0.05
29 16 0.29
30 3 0.05
31 30 0.55
32 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (29 bp):
GCCCCAAATTGAGCACACTGAAACGTTTG
Found at i:4073 original size:3 final size:3
Alignment explanation
Indices: 4058--4104 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
4048 TATCCAAGTG
* *
4058 TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4105 AATAGTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4312 original size:26 final size:26
Alignment explanation
Indices: 4252--4313 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
4242 AATAATATGG
* **
4252 AATATAAGTTTCATCTTAACATATAT
1 AATATAAGTTCCATCCCAACATATAT
* *
4278 AAAAAAAGTTCCATCCCAACATATAT
1 AATATAAGTTCCATCCCAACATATAT
4304 AATATAAGTT
1 AATATAAGTT
4314 AATTCCCTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (26 bp):
AATATAAGTTCCATCCCAACATATAT
Found at i:5231 original size:16 final size:16
Alignment explanation
Indices: 5210--5248 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
5200 GGTGAGCATC
5210 CCGGTTCGCGGTTTGA
1 CCGGTTCGCGGTTTGA
5226 CCGGTTCGCGGTTTGA
1 CCGGTTCGCGGTTTGA
5242 CCGGTTC
1 CCGGTTC
5249 AACCGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.28, G:0.36, T:0.31
Consensus pattern (16 bp):
CCGGTTCGCGGTTTGA
Found at i:11269 original size:36 final size:36
Alignment explanation
Indices: 11222--11291 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
11212 ATTTTCTCCA
11222 ATTTATTTCATCAATGTCTAAAGACATTGGCTAATC
1 ATTTATTTCATCAATGTCTAAAGACATTGGCTAATC
*
11258 ATTTATTTCATCAATGTCTCAAGACATTGGCTAA
1 ATTTATTTCATCAATGTCTAAAGACATTGGCTAA
11292 ATCTCCATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (36 bp):
ATTTATTTCATCAATGTCTAAAGACATTGGCTAATC
Done.