Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014247.1 Corchorus capsularis cultivar CVL-1 contig14268, 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: 42048
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1729 original size:42 final size:42
Alignment explanation
Indices: 1683--1783 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
1673 CATGGAGCAA
* * *
1683 CCGGCCATGACCGGCCAACGCATGGGAAATCGCACGGGCCAT
1 CCGGCCATAACCGGCCAACACACGGGAAATCGCACGGGCCAT
* * **
1725 CCGGCCATAACCGGTCATCACACGGGCCATCGCACGGGCCAT
1 CCGGCCATAACCGGCCAACACACGGGAAATCGCACGGGCCAT
1767 CCGGCCATAACCGGCCA
1 CCGGCCATAACCGGCCA
1784 CTTGACCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.10
Consensus pattern (42 bp):
CCGGCCATAACCGGCCAACACACGGGAAATCGCACGGGCCAT
Found at i:6657 original size:5 final size:6
Alignment explanation
Indices: 6628--6654 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6618 CCTAACATAG
6628 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
6655 TAATCTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:6902 original size:62 final size:61
Alignment explanation
Indices: 6786--6916 Score: 140
Period size: 62 Copynumber: 2.1 Consensus size: 61
6776 AAACCAGTCT
* ** **
6786 TAAATTGAAGCAAATTAACATGAACAGGCCTCAAATCGCAGAGATCTACCATAATCAAGCAA
1 TAAATTGAAGCAAATCAACATGAACAGGCCTCAAATCGCAGAGAAATAAAATAAT-AAGCAA
* * * *
6848 TAAATTGTAA-CAAATCAACATGAACATGCCTCAAATCGTAGTA-AAATAAAATAATAAGGAG
1 TAAATTG-AAGCAAATCAACATGAACAGGCCTCAAATCGCAG-AGAAATAAAATAATAAGCAA
6909 TAAATTGA
1 TAAATTGA
6917 GAAGGGAAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
60 1 0.02
61 11 0.19
62 43 0.74
63 3 0.05
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (61 bp):
TAAATTGAAGCAAATCAACATGAACAGGCCTCAAATCGCAGAGAAATAAAATAATAAGCAA
Found at i:9339 original size:18 final size:18
Alignment explanation
Indices: 9316--9353 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9306 TTAACGATGA
9316 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
9334 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
9352 AC
1 AC
9354 CACAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:21192 original size:22 final size:22
Alignment explanation
Indices: 21166--21217 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21156 AATTGATTTC
*
21166 TTAA-TTAGTATTTTAGTTTAGT
1 TTAATTTAGT-TTTTACTTTAGT
*
21188 TTAATTTAGTTTTTACTTTACT
1 TTAATTTAGTTTTTACTTTAGT
*
21210 TTTATTTA
1 TTAATTTA
21218 ATTGCTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (22 bp):
TTAATTTAGTTTTTACTTTAGT
Found at i:25745 original size:22 final size:22
Alignment explanation
Indices: 25714--25779 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
25704 AATTTATTAC
25714 TTTTATCTTTTAATTTTTCGTTA
1 TTTT-TCTTTTAATTTTTCGTTA
*
25737 TTTTTCTTTTAATTTTTCTTTA
1 TTTTTCTTTTAATTTTTCGTTA
25759 TTTTTCTTTTAATTTTTCGTT
1 TTTTTCTTTTAATTTTTCGTT
25780 TCTTTTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 37 0.90
23 4 0.10
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTCTTTTAATTTTTCGTTA
Found at i:25752 original size:11 final size:11
Alignment explanation
Indices: 25719--25774 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
25709 ATTACTTTTA
25719 TCTTTTAATTT
1 TCTTTTAATTT
* *
25730 T-TCGTTATTTT
1 TCT-TTTAATTT
25741 TCTTTTAATTT
1 TCTTTTAATTT
*
25752 T-TCTTTATTTT
1 TCT-TTTAATTT
25763 TCTTTTAATTT
1 TCTTTTAATTT
25774 T
1 T
25775 TCGTTTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 2 0.06
11 31 0.89
12 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (11 bp):
TCTTTTAATTT
Found at i:25753 original size:12 final size:12
Alignment explanation
Indices: 25714--25776 Score: 80
Period size: 12 Copynumber: 5.5 Consensus size: 12
25704 AATTTATTAC
25714 TTTTATCTTTTAA
1 TTTT-TCTTTTAA
*
25727 TTTTTC-GTT-A
1 TTTTTCTTTTAA
25737 TTTTTCTTTTAA
1 TTTTTCTTTTAA
25749 TTTTTC-TTT-A
1 TTTTTCTTTTAA
25759 TTTTTCTTTTAA
1 TTTTTCTTTTAA
25771 TTTTTC
1 TTTTTC
25777 GTTTCTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
10 14 0.32
11 10 0.23
12 16 0.36
13 4 0.09
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTCTTTTAA
Found at i:25785 original size:11 final size:11
Alignment explanation
Indices: 25726--25785 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 11
25716 TTATCTTTTA
25726 ATTTTTCG-TT
1 ATTTTTCGTTT
*
25736 ATTTTTCTTTT
1 ATTTTTCGTTT
25747 AATTTTTC-TTT
1 -ATTTTTCGTTT
*
25758 ATTTTTCTTTT
1 ATTTTTCGTTT
25769 AATTTTTCGTTT
1 -ATTTTTCGTTT
*
25781 CTTTT
1 ATTTT
25786 GTTTTTAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.33
11 12 0.28
12 17 0.40
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (11 bp):
ATTTTTCGTTT
Found at i:25785 original size:22 final size:21
Alignment explanation
Indices: 25714--25790 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 21
25704 AATTTATTAC
*
25714 TTTTATCTTTTAATTTTTCGT
1 TTTTTTCTTTTAATTTTTCGT
*
25735 TATTTTTCTTTTAATTTTTCTT
1 T-TTTTTCTTTTAATTTTTCGT
25757 TATTTTTCTTTTAATTTTTCGT
1 T-TTTTTCTTTTAATTTTTCGT
*
25779 TTCTTTTGTTTT
1 TT-TTTTCTTTT
25791 TAGTTTACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 2 0.04
22 48 0.96
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTTCTTTTAATTTTTCGT
Found at i:25796 original size:16 final size:17
Alignment explanation
Indices: 25761--25802 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
25751 TTTCTTTATT
*
25761 TTTCTTTTAATTTTTCG
1 TTTCTTTTAATTTTTAG
*
25778 TTTCTTTT-GTTTTTAG
1 TTTCTTTTAATTTTTAG
25794 TTTACTTTT
1 TTT-CTTTT
25803 TAGTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTCTTTTAATTTTTAG
Found at i:31903 original size:26 final size:25
Alignment explanation
Indices: 31870--31918 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
31860 GTCCCTCTTG
* *
31870 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGCGTTAGTAACCTC
*
31895 AAAAGAAAAAGGGCGTTAGTAACC
1 AAAA-AAAAAGAGCGTTAGTAACC
31919 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGCGTTAGTAACCTC
Done.