Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014548.1 Corchorus capsularis cultivar CVL-1 contig14569, 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: 24708
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7129 original size:20 final size:20
Alignment explanation
Indices: 7106--7146 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
7096 GACGGAAGAA
*
7106 GAAGAAGAAGAAGAA-AAATG
1 GAAG-AGAAGAAAAATAAATG
7126 GAAGAGAAGAAAAATAAATG
1 GAAGAGAAGAAAAATAAATG
7146 G
1 G
7147 TTTCTGTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.07
Consensus pattern (20 bp):
GAAGAGAAGAAAAATAAATG
Found at i:7135 original size:16 final size:17
Alignment explanation
Indices: 7109--7140 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
7099 GGAAGAAGAA
7109 GAAGAAGAAGAAAAATG
1 GAAGAAGAAGAAAAATG
7126 GAAG-AGAAGAAAAAT
1 GAAGAAGAAGAAAAAT
7141 AAATGGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (17 bp):
GAAGAAGAAGAAAAATG
Found at i:9533 original size:17 final size:15
Alignment explanation
Indices: 9500--9536 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
9490 TTTTTTTTAA
9500 AAAAAAAAATTAAAT
1 AAAAAAAAATTAAAT
9515 AAAAAAAAATTGAATAT
1 AAAAAAAAATT-AA-AT
9532 AAAAA
1 AAAAA
9537 GTTAATCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAAAAAAATTAAAT
Found at i:12760 original size:1 final size:1
Alignment explanation
Indices: 12754--12784 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
12744 GCAGTAAAGC
12754 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12785 ATTTGATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14047 original size:31 final size:30
Alignment explanation
Indices: 14009--14176 Score: 132
Period size: 31 Copynumber: 5.6 Consensus size: 30
13999 ATTGGCTAAT
*
14009 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CGAAAA
* * **
14040 TGCTCAAATAAGGGCCCGATC-TTT-GAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
*
14069 TGAC-CAAATAAGGGCCTAATGTTATCGAAAA
1 TG-CTCAAATAAGGGCCTAACGTT-TCGAAAA
* * * **
14100 TGCTCAAATAAGGGTCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCGAAAA
14129 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCGAAAA
14160 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
14177 GGTGTCAGTT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 7 0.07
29 31 0.30
30 9 0.09
31 50 0.48
32 7 0.07
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCGAAAA
Found at i:14106 original size:60 final size:60
Alignment explanation
Indices: 14013--14175 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
14003 GCTAATTGCT
*
14013 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
* * * *
14073 CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
14133 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
14176 TGGTGTCAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
Found at i:14284 original size:60 final size:60
Alignment explanation
Indices: 14203--14367 Score: 267
Period size: 60 Copynumber: 2.8 Consensus size: 60
14193 ACACATGAGA
* *
14203 CAGACCTTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGAT
1 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * * * *
14263 CGGGCCCTTATTTGAACATTTTGGCAAATGTTAGGCCCTTATTTGGTCAAATTAAAAGAT
1 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
14323 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
14368 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 94 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (60 bp):
CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:14303 original size:31 final size:31
Alignment explanation
Indices: 14210--14371 Score: 133
Period size: 31 Copynumber: 5.4 Consensus size: 31
14200 AGACAGACCT
14210 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
** **
14241 TTATTTG-GCCAAATT--CAAA-GATCGGGCCC
1 TTATTTGAG-CATTTTGGCAAACG-TTAGGCCC
* *
14270 TTATTTGAACATTTTGGCAAATGTTAGGCCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
** * * *
14301 TTATTTG-GTCAAATT---AAAAGATCAGACCC
1 TTATTTGAG-CATTTTGGCAAACG-TTAGGCCC
14330 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
14361 TTATTTGAGCA
1 TTATTTGAGCA
14372 ATTAGCCTTG
Statistics
Matches: 99, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
28 5 0.05
29 38 0.38
30 2 0.02
31 49 0.49
32 5 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (31 bp):
TTATTTGAGCATTTTGGCAAACGTTAGGCCC
Found at i:16249 original size:24 final size:25
Alignment explanation
Indices: 16222--16271 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
16212 ACAAGGCATA
16222 TATATTTTGCATAT-A-ATTTTTTTT
1 TATATTTT-CATATGACATTTTTTTT
*
16246 TATATTTTCATGTGACATTTTTTTT
1 TATATTTTCATATGACATTTTTTTT
16271 T
1 T
16272 GTAACTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 9 0.39
25 10 0.43
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (25 bp):
TATATTTTCATATGACATTTTTTTT
Done.