Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010730.1 Corchorus olitorius cultivar O-4 contig10762, 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: 6259
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Found at i:247 original size:28 final size:30
Alignment explanation
Indices: 211--283 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
201 CTCATTTTTG
* *
211 AAACGTAAGGGATTAATTTGTCCC-GAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
239 AAACATAAGGGATTATTTTGTCCCAAAATCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
270 AAACATAAGGGATT
1 AAACATAAGGGATT
284 TTTTTGGGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.56
29 2 0.05
31 15 0.38
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:3450 original size:26 final size:27
Alignment explanation
Indices: 3394--3465 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
3384 AAAGTCACCT
**
3394 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTGCACACTA
* * *
3421 A-GGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTGCACACTA
*
3447 AGGGGCATGTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
3466 TAAGTCCACT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACACTA
Found at i:5512 original size:154 final size:154
Alignment explanation
Indices: 5139--6259 Score: 1906
Period size: 154 Copynumber: 7.2 Consensus size: 154
5129 ATTCGTATCA
* *
5139 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATGGTGAGATTAATCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* * *
5204 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCAATTAGTTCCGTTT
66 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
*
5269 TGAATCGTCTTCAATTTTGGCAAAC
131 TGAATCGTCTTCGA-TTTGGCAAAC
* *
5294 CTCAATGCTTTTCTTTCCATTGCTTAAGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
5359 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGG-CCATTAGTTCCGTA
66 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGGCCCATTAGTTCCGTT
* * *
5423 TTGCATTGTCTTCCATTTGGCAAAC
130 TTGAATCGTCTTCGATTTGGCAAAC
* *
5448 CTAAATGCATTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* *
5513 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTCGTTCCGTTT
66 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
*
5578 TGAATCGTTTTCGATTTGGCAAAC
131 TGAATCGTCTTCGATTTGGCAAAC
* *
5602 C-CAAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATT
1 CTC-AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
*
5666 GTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
65 GTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
5731 TTGAATCGTCTTCGATTTGGCAAAC
130 TTGAATCGTCTTCGATTTGGCAAAC
*
5756 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTATGGTGAGATTAGTCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
5821 TGAAG-TTTTAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTT
66 TGAAGTTTTTAA-CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
5885 TTGAATCGTCTTCGATTTGGCAAAC
130 TTGAATCGTCTTCGATTTGGCAAAC
5910 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* *
5975 AGAAGTTTTTAGCTCATTTGGAACACTTGCTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
66 TGAAGTTTTTAACTCATTTGGAACACTTG-TTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTT
6040 TTGAATCGTCTTCGATTTGGCAAAC
130 TTGAATCGTCTTCGATTTGGCAAAC
6065 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
6130 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGGCCCATTAGTTCCGTT
66 TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGGCCCATTAGTTCCGTT
6195 TTGAATCGTCTTCGATTTGGCAAAC
130 TTGAATCGTCTTCGATTTGGCAAAC
* *
6220 CTCAATGCTTTTCATTCAAGTTGTTTTATGGCCTAACTAT
1 CTCAATGCTTTTCTTTCCA-TTG-TTTATGGCCTAACTAT
Statistics
Matches: 913, Mismatches: 43, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
153 9 0.01
154 535 0.59
155 347 0.38
156 6 0.01
157 16 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
TGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
TGAATCGTCTTCGATTTGGCAAAC
Done.