Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014594.1 Corchorus olitorius cultivar O-4 contig14627, 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: 8576
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:3115 original size:179 final size:177
Alignment explanation
Indices: 2845--3182 Score: 473
Period size: 179 Copynumber: 1.9 Consensus size: 177
2835 CCAATTAAGG
* *
2845 TGATTTAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGCAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
2910 AATTTAATGTTTTAAATATCAAAAATGCTTCCAAAAAATTTGTTGTTTCGCTTAACGGGAAATAG
66 AATCTAATGTTTCAAATATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGCTTAAC-GGAAATAG
* *
2975 ACGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
130 -CAGTCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * *
3024 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
3089 AATCTAATG-TTCAAGGTATAAAAAATGTTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATCTAATGTTTCAA-ATATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGCTTAACGGAAATAG
*
3153 CAGTCCTCTTAATATTACATAATTTGTGCT
130 CAGTCCACTTAATATTACATAATTTGTGCT
3183 TATGGTGGAA
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
176 3 0.02
177 23 0.16
178 12 0.09
179 102 0.73
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (177 bp):
TGATTCAAGTCTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATCTAATGTTTCAAATATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGCTTAACGGAAATAGC
AGTCCACTTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:4178 original size:60 final size:58
Alignment explanation
Indices: 4102--4261 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 58
4092 GCTAATTACT
** * *
4102 CAAATAAGGGTTTAACGTTTGCCAAAATGCTCAATTAAGTG-CCCGATATTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTG--AAAATGCTCAAATAAG-GACCCAATATTTTAATTTGGC
* *
4162 CAAATAAGGGCCTAACGTTATTGAAAATGCTTAAATAAGGACCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-T-TTGAAAATGCTCAAATAAGGACCCAATATTTTAATTTGGC
4222 CAAATAAGGGCCTAACGTTATGGAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACGTT-T-GAAAATGCTCAAATAAGG
4262 GCCTGTTGTC
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
58 1 0.01
59 3 0.03
60 80 0.91
61 1 0.01
62 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (58 bp):
CAAATAAGGGCCTAACGTTTGAAAATGCTCAAATAAGGACCCAATATTTTAATTTGGC
Found at i:4201 original size:31 final size:31
Alignment explanation
Indices: 4162--4265 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
4152 TTAATTTGGC
4162 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
* * * **
4193 TAAATAAGGACCCAATC-TT-TT-AATTTGGC-
1 CAAATAAGGGCCTAA-CGTTATTGAAAAT-GCT
*
4222 CAAATAAGGGCCTAACGTTATGGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
4253 CAAATAAGGGCCT
1 CAAATAAGGGCCT
4266 GTTGTCGAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 1 0.02
29 17 0.30
30 7 0.12
31 30 0.54
32 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATTGAAAATGCT
Found at i:4342 original size:31 final size:31
Alignment explanation
Indices: 4304--4377 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
4294 AACTGACGTC
4304 AGGCCCTTATTTCAACATTTTCGATAATGTT
1 AGGCCCTTATTTCAACATTTTCGATAATGTT
4335 AGGCCCTTATTTCAACATTTTCGATAATGTT
1 AGGCCCTTATTTCAACATTTTCGATAATGTT
4366 AGGCCCTTATTT
1 AGGCCCTTATTT
4378 GGCCAAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (31 bp):
AGGCCCTTATTTCAACATTTTCGATAATGTT
Found at i:4414 original size:60 final size:60
Alignment explanation
Indices: 4336--4475 Score: 217
Period size: 60 Copynumber: 2.3 Consensus size: 60
4326 GATAATGTTA
* * * * *
4336 GGCCCTTATTTCAACATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCCATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
4396 GGCCCTTATTTGAGCATTTTCCATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATTG
1 GGCCCTTATTTGAGCATTTTCCATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
4456 GGACCTTATTTGAGCATTTT
1 GGCCCTTATTTGAGCATTTT
4476 GGCAAACTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCCATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:8501 original size:13 final size:13
Alignment explanation
Indices: 8483--8507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8473 ATAACATGAC
8483 ACTAGTAAATAAT
1 ACTAGTAAATAAT
8496 ACTAGTAAATAA
1 ACTAGTAAATAA
8508 CAATCTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTAGTAAATAAT
Found at i:8549 original size:2 final size:2
Alignment explanation
Indices: 8544--8574 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8534 AGATCCATGT
8544 TA TA 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 TA TA T
8575 GG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.