Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017229.1 Corchorus olitorius cultivar O-4 contig17262, 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: 18199
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:1916 original size:452 final size:453
Alignment explanation
Indices: 1070--1980 Score: 1738
Period size: 452 Copynumber: 2.0 Consensus size: 453
1060 ATTATTATAA
1070 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
* *
1135 AAAAGTTAAAAAGTTACCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
66 AAAAGTTAAAAAGTTACCATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCCGT
*
1200 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTATTTTTTTTTTTGAAGAAT
131 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTA-TATTTTTTTTGAAGAAT
1265 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAACGT
195 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAACGT
1330 TTCTGTTTTTTGTTGGAATAATCAATTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
260 TTCTGTTTTTTGTTGGAATAATCAATTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
1395 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAAA
325 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAAA
1460 AAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
390 AAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
1524 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1589 AAAAGTT-AAAAGTTGA-CATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCCG
66 AAAAGTTAAAAAGTT-ACCATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCCG
1652 TTCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTA-ATTTTTTTTGAAGAAT
130 TTCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTATATTTTTTTTGAAGAAT
*
1716 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
195 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAACGT
1781 TTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAA
260 TTCTGTTTTTTGTTGGAATAATCAA-TTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAA
1846 CTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAA
324 CTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAA
1911 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
389 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
1976 ATAAA
1 ATAAA
1981 TCGTACTTGA
Statistics
Matches: 451, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
451 104 0.23
452 174 0.39
453 100 0.22
454 73 0.16
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (453 bp):
ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
AAAAGTTAAAAAGTTACCATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCCGT
TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTATATTTTTTTTGAAGAATT
TTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAACGTT
TCTGTTTTTTGTTGGAATAATCAATTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAACT
TCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGGCGAAAA
AGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
Found at i:2043 original size:16 final size:16
Alignment explanation
Indices: 2024--2055 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2014 TGATTGGTAT
2024 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
2040 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
2056 ATCTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Found at i:5303 original size:31 final size:31
Alignment explanation
Indices: 5265--5430 Score: 150
Period size: 31 Copynumber: 5.5 Consensus size: 31
5255 GGGCTAATTA
5265 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
* * * **
5296 CTCAAATAAGGGTCCGATC-TTT--TAATTTGG
1 CTCAAATAAGGG-CCTAACGTTTGCCAAAAT-G
*
5326 C-CAAATAAAGGCCTAACGTTTGCCAAAATG
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
* * **
5356 CTCAAATAAGGGCCCAATC-TTT--TAATTTGG
1 CTCAAATAAGGGCCTAA-CGTTTGCCAAAAT-G
5386 C-CAAATAAGGGCCTAACGTTTGCCAAAATG
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
5416 CTCAAATAAGGGCCT
1 CTCAAATAAGGGCCT
5431 GTCATCAGTT
Statistics
Matches: 103, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.34
30 8 0.08
31 50 0.49
32 5 0.05
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
CTCAAATAAGGGCCTAACGTTTGCCAAAATG
Found at i:5360 original size:60 final size:60
Alignment explanation
Indices: 5267--5429 Score: 299
Period size: 60 Copynumber: 2.7 Consensus size: 60
5257 GCTAATTACT
* *
5267 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
*
5327 CAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
5387 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
5430 TGTCATCAGT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 99 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
Found at i:5393 original size:29 final size:29
Alignment explanation
Indices: 5298--5398 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
5288 CCAAAATGCT
* *
5298 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCAATCTTTTAATTTGGC
* * * **
5327 CAAATAAAGGCCTAA-CGTTTGCCAAAAT-GC
1 CAAATAAGGGCCCAATC-TTT--TAATTTGGC
5357 TCAAATAAGGGCCCAATCTTTTAATTTGGC
1 -CAAATAAGGGCCCAATCTTTTAATTTGGC
5387 CAAATAAGGGCC
1 CAAATAAGGGCC
5399 TAACGTTTGC
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 1 0.02
29 29 0.54
30 4 0.07
31 19 0.35
32 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCCAATCTTTTAATTTGGC
Found at i:11180 original size:48 final size:48
Alignment explanation
Indices: 11124--11219 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
11114 ATTCATCAAG
*
11124 ATCCTAATATTCTTATCCTAATTATGTTTGAACTCTTTACATCCCTTT
1 ATCCTAATATTCTTAACCTAATTATGTTTGAACTCTTTACATCCCTTT
*
11172 ATCCTAATATTCTTAACCTAATTCTGTTTGAACTCTTTACATCCCTTT
1 ATCCTAATATTCTTAACCTAATTATGTTTGAACTCTTTACATCCCTTT
11220 TTTCAGGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (48 bp):
ATCCTAATATTCTTAACCTAATTATGTTTGAACTCTTTACATCCCTTT
Found at i:12647 original size:16 final size:14
Alignment explanation
Indices: 12611--12650 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
12601 AAAATTACTG
12611 ATTGAAAGTCATAT
1 ATTGAAAGTCATAT
12625 A-TGAAAGTCATAT
1 ATTGAAAGTCATAT
12638 ACCTTGAAAGTCA
1 A--TTGAAAGTCA
12651 ACATGTGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.57
14 1 0.04
16 9 0.39
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (14 bp):
ATTGAAAGTCATAT
Done.