Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004935.1 Corchorus capsularis cultivar CVL-1 contig04953, 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: 15017
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10681 original size:3 final size:3
Alignment explanation
Indices: 10673--10699 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10663 GGTATGGGAG
10673 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
10700 TCTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:14439 original size:40 final size:40
Alignment explanation
Indices: 14395--14542 Score: 167
Period size: 40 Copynumber: 3.8 Consensus size: 40
14385 GATAATCTTC
*
14395 CGTTGTGTGTGGGGAGCATCACTGCCAAGACTTGCGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGACTTGCGTCTG
* *
14435 CGTTGTGTGTGGGGAGCATCACTTCCGAGATTTGCGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGACTTGCGTCTG
* * * * * *
14475 CGATGTATTTGGGGAGCATCACTGTCGAG-GTTCACGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGACTT-GCGTCTG
* *
14515 CG-T-TGTGTGGTGAGCATCACTGTCGAGA
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGA
14543 GCTGTTGTCG
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
38 21 0.23
39 3 0.03
40 69 0.74
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (40 bp):
CGTTGTGTGTGGGGAGCATCACTGCCGAGACTTGCGTCTG
Found at i:14537 original size:38 final size:40
Alignment explanation
Indices: 14395--14671 Score: 160
Period size: 40 Copynumber: 6.7 Consensus size: 40
14385 GATAATCTTC
* * * * *
14395 CGTTGTGTGTGGGGAGCATCACTGCCAAGACTT-GCGTCTG
1 CGTTGTGTGTGGTGAGCATCACTGTCGAG-GTTCACGTCTG
* * **
14435 CGTTGTGTGTGGGGAGCATCACT-TCCGAGATTTGCGTCTG
1 CGTTGTGTGTGGTGAGCATCACTGT-CGAGGTTCACGTCTG
* * * *
14475 CGATGTATTTGGGGAGCATCACTGTCGAGGTTCACGTCTG
1 CGTTGTGTGTGGTGAGCATCACTGTCGAGGTTCACGTCTG
*
14515 CG-T-TGTGTGGTGAGCATCACTGTCGAGAGCTGTTGTCGAGAGTC-G
1 CGTTGTGTGTGGTGAGCATCACTGTC--GAG--G-T-TC-A-CGTCTG
*
14560 CGTTGTGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGT-T-
1 CGTTGT--G-TGT----G-GTGAGCATCACTGTCGAGGTTCACGTCTG
* * *
14606 TG-TGTTTGTGGTGAGCATCACTGTCGAGGGTCACGTCTG
1 CGTTGTGTGTGGTGAGCATCACTGTCGAGGTTCACGTCTG
14645 CG-T-TGTGTGGTGAGCATCACTGTCGAG
1 CGTTGTGTGTGGTGAGCATCACTGTCGAG
14672 AGCCGTTGTC
Statistics
Matches: 194, Mismatches: 19, Indels: 50
0.74 0.07 0.19
Matches are distributed among these distances:
37 26 0.13
38 43 0.22
39 5 0.03
40 70 0.36
41 1 0.01
42 4 0.02
43 1 0.01
44 2 0.01
45 7 0.04
46 5 0.03
47 3 0.02
48 1 0.01
49 3 0.02
50 3 0.02
51 1 0.01
53 3 0.02
54 1 0.01
55 15 0.08
ACGTcount: A:0.15, C:0.20, G:0.35, T:0.30
Consensus pattern (40 bp):
CGTTGTGTGTGGTGAGCATCACTGTCGAGGTTCACGTCTG
Found at i:14629 original size:37 final size:38
Alignment explanation
Indices: 14579--14671 Score: 161
Period size: 37 Copynumber: 2.5 Consensus size: 38
14569 TTGTCAACGT
* *
14579 GTGAGCATCACTGTCGAGGGTCACGTTTGTGTT-TGTG
1 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTG
14616 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTG
1 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTG
14654 GTGAGCATCACTGTCGAG
1 GTGAGCATCACTGTCGAG
14672 AGCCGTTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
37 31 0.58
38 22 0.42
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.30
Consensus pattern (38 bp):
GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTG
Found at i:14721 original size:130 final size:131
Alignment explanation
Indices: 14488--14764 Score: 502
Period size: 130 Copynumber: 2.1 Consensus size: 131
14478 TGTATTTGGG
* *
14488 GAGCATCACTGTCGAGGTTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCTGTTGTCG
1 GAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGTCG
* * *
14553 AGAGTCGCGTTGTGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGTTTGTGTT-TGTGG
66 AGAGTCGCGTTATGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGG
14617 T
131 T
14618 GAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGTCG
1 GAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGTCG
14683 AGAGTCGCGTTATGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGG
66 AGAGTCGCGTTATGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGG
14748 T
131 T
14749 GAGCATCACTGTCGAG
1 GAGCATCACTGTCGAG
14765 AGCCGTTGTC
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
130 119 0.84
131 22 0.16
ACGTcount: A:0.16, C:0.21, G:0.35, T:0.29
Consensus pattern (131 bp):
GAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGTCG
AGAGTCGCGTTATGCGTTGTCAACGTGTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGG
T
Found at i:14725 original size:42 final size:38
Alignment explanation
Indices: 14678--14766 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 38
14668 CGAGAGCCGT
*
14678 TGTCGAGAGTCGCGTTATGCGTTGTCAACGT-GTGAGCATCAC
1 TGTCGAGAGTCACG-TATGCGTTGT----GTGGTGAGCATCAC
* *
14720 TGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCAC
1 TGTCGAGAGTCACGTATGCGTTGTGTGGTGAGCATCAC
14758 TGTCGAGAG
1 TGTCGAGAG
14767 CCGTTGTCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 2 0.05
38 19 0.45
41 9 0.21
42 12 0.29
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (38 bp):
TGTCGAGAGTCACGTATGCGTTGTGTGGTGAGCATCAC
Found at i:14775 original size:93 final size:93
Alignment explanation
Indices: 14616--14819 Score: 390
Period size: 93 Copynumber: 2.2 Consensus size: 93
14606 TGTGTTTGTG
14616 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGT
1 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGT
14681 CGAGAGTCGCGTTATGCGTTGTCAACGT
66 CGAGAGTCGCGTTATGCGTTGTCAACGT
14709 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGT
1 GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGT
* *
14774 CGAGAGTCGTGTTGTGCGTTGTCAACGT
66 CGAGAGTCGCGTTATGCGTTGTCAACGT
14802 GTGAGCATCACTGTCGAG
1 GTGAGCATCACTGTCGAG
14820 AGCCGTTGTC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 109 1.00
ACGTcount: A:0.16, C:0.21, G:0.35, T:0.28
Consensus pattern (93 bp):
GTGAGCATCACTGTCGAGGGTCACGTCTGCGTTGTGTGGTGAGCATCACTGTCGAGAGCCGTTGT
CGAGAGTCGCGTTATGCGTTGTCAACGT
Found at i:14809 original size:55 final size:55
Alignment explanation
Indices: 14747--14876 Score: 251
Period size: 55 Copynumber: 2.4 Consensus size: 55
14737 GCGTTGTGTG
*
14747 GTGAGCATCACTGTCGAGAGCCGTTGTCGAGAGTCGTGTTGTGCGTTGTCAACGT
1 GTGAGCATCACTGTCGAGAGCCGTTGTCGAGAGTCGCGTTGTGCGTTGTCAACGT
14802 GTGAGCATCACTGTCGAGAGCCGTTGTCGAGAGTCGCGTTGTGCGTTGTCAACGT
1 GTGAGCATCACTGTCGAGAGCCGTTGTCGAGAGTCGCGTTGTGCGTTGTCAACGT
14857 GTGAGCATCACTGTCGAGAG
1 GTGAGCATCACTGTCGAGAG
14877 TTGTGTGGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.18, C:0.21, G:0.35, T:0.27
Consensus pattern (55 bp):
GTGAGCATCACTGTCGAGAGCCGTTGTCGAGAGTCGCGTTGTGCGTTGTCAACGT
Found at i:14927 original size:38 final size:38
Alignment explanation
Indices: 14876--15017 Score: 248
Period size: 38 Copynumber: 3.7 Consensus size: 38
14866 ACTGTCGAGA
* * * *
14876 GTTGTGTGGTGAGCATCACTGTCGAGGGCCCCGTNTGC
1 GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
14914 GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
1 GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
14952 GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
1 GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
14990 GTTGTGTGGTGAGCATCACTGTCGAGAG
1 GTTGTGTGGTGAGCATCACTGTCGAGAG
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 100 1.00
ACGTcount: A:0.13, C:0.20, G:0.37, T:0.28
Consensus pattern (38 bp):
GTTGTGTGGTGAGCATCACTGTCGAGAGTCGCGTCTGC
Done.