Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018020.1 Corchorus olitorius cultivar O-4 contig18053, 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: 10617
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:642 original size:16 final size:16
Alignment explanation
Indices: 619--671 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
609 TGTAATTGCA
*
619 TATTCAATTCCCTCCT
1 TATTCAATTCCCACCT
*
635 TTTTCAATTCCCACCT
1 TATTCAATTCCCACCT
* * *
651 TATGCAATTCCTACTT
1 TATTCAATTCCCACCT
667 TATTC
1 TATTC
672 CACCGAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.21, C:0.32, G:0.02, T:0.45
Consensus pattern (16 bp):
TATTCAATTCCCACCT
Found at i:1525 original size:32 final size:32
Alignment explanation
Indices: 1480--1573 Score: 170
Period size: 32 Copynumber: 2.9 Consensus size: 32
1470 TTTGAATCAC
*
1480 CCATTATATCCTTATTTTTCGAATATATTTTA
1 CCATTATACCCTTATTTTTCGAATATATTTTA
*
1512 CCATTATACCCTTATTTTTTGAATATATTTTA
1 CCATTATACCCTTATTTTTCGAATATATTTTA
1544 CCATTATACCCTTATTTTTCGAATATATTT
1 CCATTATACCCTTATTTTTCGAATATATTT
1574 CTTAAATGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (32 bp):
CCATTATACCCTTATTTTTCGAATATATTTTA
Found at i:1777 original size:16 final size:17
Alignment explanation
Indices: 1758--1789 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1748 CATTTAATTA
1758 AATT-TTTTATTTTTAT
1 AATTATTTTATTTTTAT
1774 AATTATTTTATTTTTA
1 AATTATTTTATTTTTA
1790 CCATTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
AATTATTTTATTTTTAT
Found at i:1795 original size:17 final size:17
Alignment explanation
Indices: 1758--1796 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1748 CATTTAATTA
*
1758 AATT-TTTTATTTTTAT
1 AATTATTTTATTTTTAC
1774 AATTATTTTATTTTTAC
1 AATTATTTTATTTTTAC
*
1791 CATTAT
1 AATTAT
1797 AATTTACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTATTTTATTTTTAC
Found at i:2330 original size:16 final size:16
Alignment explanation
Indices: 2311--2341 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2301 TTGTGTCCAA
2311 GTCATTTCAGGTTCGG
1 GTCATTTCAGGTTCGG
*
2327 GTCATTTCAGTTTCG
1 GTCATTTCAGGTTCG
2342 AATTGGGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.42
Consensus pattern (16 bp):
GTCATTTCAGGTTCGG
Found at i:2744 original size:22 final size:22
Alignment explanation
Indices: 2716--2762 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2706 TATCCTTATA
* *
2716 ACTATTTTATTTTTACCATTTT
1 ACTATTTTACTTTTACAATTTT
*
2738 ACTATTTTACTTTTATAATTTT
1 ACTATTTTACTTTTACAATTTT
2760 ACT
1 ACT
2763 CAACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (22 bp):
ACTATTTTACTTTTACAATTTT
Found at i:3799 original size:17 final size:17
Alignment explanation
Indices: 3767--3800 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3757 CTTTCATTAC
*
3767 ATTAATTAAAATTATAA
1 ATTAATTAAAAGTATAA
*
3784 ATTAATTAATAGTATAA
1 ATTAATTAAAAGTATAA
3801 GTATCCATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTAATTAAAAGTATAA
Found at i:4057 original size:51 final size:51
Alignment explanation
Indices: 4002--4108 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
3992 ACGTTTAGCA
* * **
4002 AATTTAATAAA-ATTATAATAATAATAATATAAATTTTATTGAATAAATGAT
1 AATTTAA-AAAGATTAAAATAATAACAATATAAATTTTATTGAATAAAACAT
* * * *
4053 AATTTAAAAAGGTTAAAATTATAACAATTTGAATTTTATTGAATAAAACAT
1 AATTTAAAAAGATTAAAATAATAACAATATAAATTTTATTGAATAAAACAT
4104 AATTT
1 AATTT
4109 TAGTTTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 3 0.06
51 44 0.94
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (51 bp):
AATTTAAAAAGATTAAAATAATAACAATATAAATTTTATTGAATAAAACAT
Found at i:4539 original size:77 final size:77
Alignment explanation
Indices: 4458--4614 Score: 278
Period size: 77 Copynumber: 2.0 Consensus size: 77
4448 AACTCTATTT
* * *
4458 TTATTTAATTCAATCTAATATCTTTATAGCTATTTATTTTTTACCATTTTACTATTTTAATTAAA
1 TTATTTAATTCAATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAA
4523 AACTTATATATA
66 AACTTATATATA
*
4535 TTATTTAATTCAATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAG
1 TTATTTAATTCAATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAA
4600 AACTTATATATA
66 AACTTATATATA
4612 TTA
1 TTA
4615 GAATTTTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (77 bp):
TTATTTAATTCAATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAA
AACTTATATATA
Found at i:5234 original size:57 final size:57
Alignment explanation
Indices: 5166--5309 Score: 243
Period size: 57 Copynumber: 2.5 Consensus size: 57
5156 GCGGGTTGGA
5166 CGGGATTTGAGTCATCTAGGTTCAGGTCAAATGAGTCAGGTAATTTCCTCGGGTCATT
1 CGGG-TTTGAGTCATCTAGGTTCAGGTCAAATGAGTCAGGTAATTTCCTCGGGTCATT
*
5224 CGGGTTTGAGTCATCTAGGTTCAGGTCAAATGAGTCAGGTAATTTTCTCGGGTCATT
1 CGGGTTTGAGTCATCTAGGTTCAGGTCAAATGAGTCAGGTAATTTCCTCGGGTCATT
* *
5281 CGGGTTTCAGCTCATCTGGGTTCAGGTCA
1 CGGGTTTGAG-TCATCTAGGTTCAGGTCA
5310 TTCGGGTCTC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
57 61 0.74
58 21 0.26
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (57 bp):
CGGGTTTGAGTCATCTAGGTTCAGGTCAAATGAGTCAGGTAATTTCCTCGGGTCATT
Found at i:5316 original size:15 final size:15
Alignment explanation
Indices: 5274--5316 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5264 AATTTTCTCG
5274 GGTCATTCGGGTTTCA
1 GGTCATTCGGG-TTCA
*
5290 GCTCA-TCTGGGTTCA
1 GGTCATTC-GGGTTCA
5305 GGTCATTCGGGT
1 GGTCATTCGGGT
5317 CTCGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.21, G:0.33, T:0.35
Consensus pattern (15 bp):
GGTCATTCGGGTTCA
Done.