Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012515.1 Corchorus olitorius cultivar O-4 contig12548, 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: 7737
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:496 original size:31 final size:31
Alignment explanation
Indices: 461--523 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
451 TTGATGAATT
*
461 ACACTAAATGCTAAAGTGAATTGAAATATGC
1 ACACTAAATGCTAAAGTGAATTAAAATATGC
492 ACACTAAATGCTAAAGTGAATTAAAATATGC
1 ACACTAAATGCTAAAGTGAATTAAAATATGC
523 A
1 A
524 AATGCAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (31 bp):
ACACTAAATGCTAAAGTGAATTAAAATATGC
Found at i:749 original size:27 final size:27
Alignment explanation
Indices: 646--748 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
636 ATGTGAACTT
646 AAAATGACCAAAAATGCCCCTGAATGTG
1 AAAATGACC-AAAATGCCCCTGAATGTG
* *
674 TAAATGACCAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGTG
* * *
701 AAAATGACTAAAATGCCCCTGGACGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
*
728 CAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
749 GGTGATCCTA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 58 0.88
28 8 0.12
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTG
Found at i:1305 original size:30 final size:30
Alignment explanation
Indices: 1249--1336 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
1239 ATGAAACAAC
*
1249 GATCCTAAACCAGGATTAACAATAAAGCAGT
1 GATCCTAAACCAGGATTAA-AATAAAGCAAT
*
1280 GATCCTCAACCAGGATTAAAATAAAGCAAT
1 GATCCTAAACCAGGATTAAAATAAAGCAAT
* * *
1310 GATCCTGAACTAGGATTAAAATGAAGC
1 GATCCTAAACCAGGATTAAAATAAAGC
1337 CATAAAGCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
30 34 0.65
31 18 0.35
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (30 bp):
GATCCTAAACCAGGATTAAAATAAAGCAAT
Found at i:1732 original size:102 final size:102
Alignment explanation
Indices: 1556--1777 Score: 284
Period size: 102 Copynumber: 2.2 Consensus size: 102
1546 TGCATTTGTG
** * * * *
1556 CCCGGAGGACTTACCAATGCGAACTTTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACAT
1 CCCGGAGGTTTTAACAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTCAAACTTAAACAT
* * * **
1621 GAATCTTTGATGAAAAACTTGATGGAATGGAATGATA
66 GAATCTTTGATGAAAAAATTAATGAAATCAAATGATA
* *
1658 CCCGGAGGTTTTAACAATGCAAACTCTGAATA-GAGACCTTGAACAAGGATTTCAAACTTAAACA
1 CCCGGAGGTTTTAACAATGCAAACTCTGAAAAGGA-ACCTTAAACAAGGATTTCAAACTTAAACA
* *
1722 TGAATTTTTGATGAAAAAATTAATGAAATCAAATGGTA
65 TGAATCTTTGATGAAAAAATTAATGAAATCAAATGATA
*
1760 CCCGGAGGTTTTATCAAT
1 CCCGGAGGTTTTAACAAT
1778 TGCCCGGAGG
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 2 0.02
102 101 0.98
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (102 bp):
CCCGGAGGTTTTAACAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTCAAACTTAAACAT
GAATCTTTGATGAAAAAATTAATGAAATCAAATGATA
Found at i:1961 original size:170 final size:170
Alignment explanation
Indices: 1658--2115 Score: 699
Period size: 170 Copynumber: 2.7 Consensus size: 170
1648 TGGAATGATA
1658 CCCGGAGGT-TTTAACAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
1 CCCGGAGGTCTTTAACAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
* * *
1722 TGAATTTTTGATGAAAAAATTAATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAG
66 TGAATTTTTGATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGAAG
*
1787 GACTTACCAGAATTAATACCCGGAGTTTTCTGAACTTGTC
131 GACTTACCAGAATTAATACCCGGAGGTTTCTGAACTTGTC
* *
1827 CCCGGAGGTCTTTACCAATGCAAACTATGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
1 CCCGGAGGTCTTTAACAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
1892 TGAATTTTTGATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGAAG
66 TGAATTTTTGATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGAAG
* * *
1957 GACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTG
131 GACTTACCAGAATTAATACCCGGAGGTTTCTGAACTTGTC
* * * * * *
1997 CCCGGAGGAC-TTATCAATGCAAACTCTGAAAAGAGACCTTAAACAAGGATTT-TAACTTAAATA
1 CCCGGAGGTCTTTAACAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
* * * * *
2060 TGGATTTTTAATGAAAAACTTGACGACATGAAA-GGATACCCGGAGGTTTTATCAAT
66 TGAATTTTTGATGAAAAACTTAATGAAATGAAATGG-TACCCGGAGGTTTTATCAAT
2116 AAGCTTAAAT
Statistics
Matches: 266, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
167 2 0.01
168 57 0.21
169 47 0.18
170 160 0.60
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (170 bp):
CCCGGAGGTCTTTAACAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTCAAACTTAAACA
TGAATTTTTGATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCCGAAG
GACTTACCAGAATTAATACCCGGAGGTTTCTGAACTTGTC
Found at i:3554 original size:18 final size:17
Alignment explanation
Indices: 3527--3566 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
3517 TATTCTTTCC
*
3527 TTTTTCTTTTTTCCTTT
1 TTTTTCTTTTTTCATTT
3544 TTTTTCATTTTTTCATTT
1 TTTTTC-TTTTTTCATTT
3562 TTTTT
1 TTTTT
3567 GTGCACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTTCATTT
Found at i:3887 original size:15 final size:15
Alignment explanation
Indices: 3868--3909 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
3858 TTTATTTTGA
3868 TTTTGATTTTTTT-T
1 TTTTGATTTTTTTAT
3882 TATTTGATTTTTTTAT
1 T-TTTGATTTTTTTAT
3898 TTTTGATTTTTT
1 TTTTGATTTTTT
3910 CGAATTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.04
15 23 0.88
16 2 0.08
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (15 bp):
TTTTGATTTTTTTAT
Found at i:4307 original size:7 final size:8
Alignment explanation
Indices: 4286--4322 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
4276 AAGTGCCTTA
4286 ATTTTTTC
1 ATTTTTTC
4294 ATTTTTTTC
1 A-TTTTTTC
4303 ATTTTTTC
1 ATTTTTTC
4311 ATTTTTTC
1 ATTTTTTC
4319 ATTT
1 ATTT
4323 CATCATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:4761 original size:20 final size:18
Alignment explanation
Indices: 4736--4779 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
4726 CAGTGTTGAC
*
4736 AAAATCAAAGTTTTCACACT
1 AAAATCAAA--TTTCACACG
*
4756 AAAATCCAATTTCACACG
1 AAAATCAAATTTCACACG
4774 AAAATC
1 AAAATC
4780 CCATTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATCAAATTTCACACG
Found at i:4770 original size:18 final size:18
Alignment explanation
Indices: 4747--4785 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4737 AAATCAAAGT
*
4747 TTTCACACTAAAATCCAA
1 TTTCACACGAAAATCCAA
*
4765 TTTCACACGAAAATCCCA
1 TTTCACACGAAAATCCAA
4783 TTT
1 TTT
4786 TGAAAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (18 bp):
TTTCACACGAAAATCCAA
Done.