Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011843.1 Corchorus capsularis cultivar CVL-1 contig11864, 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: 3816
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:1962 original size:14 final size:15
Alignment explanation
Indices: 1945--1982 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1935 AAGAAAAAAT
*
1945 TTTCAAGAAAATG-C
1 TTTCAAAAAAATGAC
1959 TTTCAAAAAAATGAC
1 TTTCAAAAAAATGAC
1974 TTTCAAAAA
1 TTTCAAAAA
1983 TGAGAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (15 bp):
TTTCAAAAAAATGAC
Found at i:3712 original size:38 final size:37
Alignment explanation
Indices: 3609--3813 Score: 144
Period size: 37 Copynumber: 5.5 Consensus size: 37
3599 AAAAAATTCA
** *
3609 GTCTCATCAAAA-CCTTGTTCAAGATTTCTGTTTAAGT
1 GTCTCAT-AAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * *
3646 GTCTCATCAAATCCTTATTTAAGGTCCCTATTTAGGT
1 GTCTCATAAAATCCTTGTTCAAGATCCCTGTTTAGGT
*
3683 GTTTCATAAAAATCCTTGTTCAAGATCCCTGTTTAGGT
1 GTCTCAT-AAAATCCTTGTTCAAGATCCCTGTTTAGGT
* ** * * * * * *
3721 TTCTTGTCAAATCCATGTTTAAGGTTCATGTTTAGGT
1 GTCTCATAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * *
3758 GTCTTATTAAATCCTTATTTAAGGTCCCTGTTTAGGT
1 GTCTCATAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* *
3795 TTC-CTATCAAATCCTTGTT
1 GTCTC-ATAAAATCCTTGTT
3814 TAA
Statistics
Matches: 130, Mismatches: 35, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
36 3 0.02
37 99 0.76
38 28 0.22
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (37 bp):
GTCTCATAAAATCCTTGTTCAAGATCCCTGTTTAGGT
Found at i:3715 original size:75 final size:75
Alignment explanation
Indices: 3612--3816 Score: 220
Period size: 75 Copynumber: 2.7 Consensus size: 75
3602 AAATTCAGTC
** * * * *
3612 TCATCAAAA-CCTTGTTCAAGATTTCTGTTTAAGTGTCTCATCAAATCCTTATTTAAGGTCCCTA
1 TCAT-AAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTCATCAAATCCTTGTTTAAGGTCCATA
3676 TTTAGGTGT-T
65 TTTAGGTGTCT
** * * *
3686 TCATAAAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTTGTCAAATCCATGTTTAAGGTTCATG
1 TCAT-AAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTCATCAAATCCTTGTTTAAGGTCCATA
3751 TTTAGGTGTCT
65 TTTAGGTGTCT
* * * *
3762 T-ATTAAATCCTTATTTAAGGTCCCTGTTTAGGTTTC-CTATCAAATCCTTGTTTAA
1 TCATAAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTC-ATCAAATCCTTGTTTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
74 52 0.48
75 55 0.50
76 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (75 bp):
TCATAAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTCATCAAATCCTTGTTTAAGGTCCATAT
TTAGGTGTCT
Found at i:3739 original size:24 final size:27
Alignment explanation
Indices: 3697--3746 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
3687 CATAAAAATC
*
3697 CTTGTTCAAGATCCCTGTTT-AGGTTT
1 CTTGTTCAAGATCCATGTTTAAGGTTT
3723 CTTG-TCAA-ATCCATGTTTAAGGTT
1 CTTGTTCAAGATCCATGTTTAAGGTT
3747 CATGTTTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (27 bp):
CTTGTTCAAGATCCATGTTTAAGGTTT
Found at i:3753 original size:37 final size:37
Alignment explanation
Indices: 3637--3816 Score: 164
Period size: 37 Copynumber: 4.8 Consensus size: 37
3627 TCAAGATTTC
* * * * *
3637 TGTTTAAGTGTCTCATCAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCA
* * * * * *
3674 TATTTAGGTGTT-TCATAAAAATCCTTGTTCAAGATCCC
1 TGTTTAGGT-TTCTTAT-CAAATCCTTGTTTAAGGTCCA
* * *
3712 TGTTTAGGTTTCTTGTCAAATCCATGTTTAAGGTTCA
1 TGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCA
* * * *
3749 TGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCCC
1 TGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCA
*
3786 TGTTTAGGTTTCCTATCAAATCCTTGTTTAA
1 TGTTTAGGTTTCTTATCAAATCCTTGTTTAA
Statistics
Matches: 113, Mismatches: 27, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
37 85 0.75
38 28 0.25
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (37 bp):
TGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCA
Found at i:3805 original size:74 final size:75
Alignment explanation
Indices: 3612--3816 Score: 211
Period size: 74 Copynumber: 2.8 Consensus size: 75
3602 AAATTCAGTC
* * ** * * * *
3612 TCATCAAAA-CCTTGTTCAAGATTTCTGTTTAAGTGT-CTCATCAAATCCTTATTTAAGGTCCCT
1 TCATAAAAATCCTTATTCAAGATCCCTGTTTAGGTTTCCT-ATCAAATCCTTGTTTAAGGTCCAT
3675 ATTTAGGTGTT
65 ATTTAGGTGTT
* * * * * *
3686 TCATAAAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTTGTCAAATCCATGTTTAAGGTTCATG
1 TCATAAAAATCCTTATTCAAGATCCCTGTTTAGGTTTCCTATCAAATCCTTGTTTAAGGTCCATA
3751 TTTAGGTGTCT
66 TTTAGGTGT-T
* * *
3762 T-AT-TAAATCCTTATTTAAGGTCCCTGTTTAGGTTTCCTATCAAATCCTTGTTTAA
1 TCATAAAAATCCTTATTCAAGATCCCTGTTTAGGTTTCCTATCAAATCCTTGTTTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
74 53 0.49
75 53 0.49
76 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (75 bp):
TCATAAAAATCCTTATTCAAGATCCCTGTTTAGGTTTCCTATCAAATCCTTGTTTAAGGTCCATA
TTTAGGTGTT
Done.