Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006818.1 Corchorus capsularis cultivar CVL-1 contig06839, 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: 37361
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Found at i:241 original size:2 final size:2
Alignment explanation
Indices: 234--273 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
224 TGTCTGCGGC
*
234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
274 GTGTGTGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4968 original size:67 final size:66
Alignment explanation
Indices: 4826--5179 Score: 406
Period size: 67 Copynumber: 5.3 Consensus size: 66
4816 TCGGGCAGTC
* * ** * * *
4826 CGTCTTATTTAAGTTCACGATTCAAGGATCG-TTCAATTTTTTTATAAAACTGTCTCAATGGAGA
1 CGTCTTATTT-AGTTTACGATTCAAGGATCGTTTTAA--TTTTGGTAAAACGGTCTCGAGGGAGA
*
4890 CGTC
63 CGTT
* * * * * *
4894 CGTCTTATTCTAGTATACGATTCATGGATCG-TTCAATTTTTGATAAAACGGTCTCAATGGAGAC
1 CGTCTTATT-TAGTTTACGATTCAAGGATCGTTTTAA-TTTTGGTAAAACGGTCTCGAGGGAGAC
4958 GTT
64 GTT
* *
4961 CGTCTTATTTAAATTTACGATTCAAGGATCGTTTTAATTTTGGTGAAACGGTCTCGAGGGAGACG
1 CGTCTTATTT-AGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
5026 TT
65 TT
** *
5028 CGTCTTACTGAAATTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
1 CGTCTTA-TTTAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
5093 TT
65 TT
* * *
5095 CGTCTTACTTAAGTTTACGATTTAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGATG
1 CGTCTTA-TTTAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
5160 TT
65 TT
*
5162 CGTCTTACTTAAGTTTAC
1 CGTCTTA-TTTAGTTTAC
5180 TTAAGTTCTA
Statistics
Matches: 261, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
66 1 0.00
67 223 0.85
68 36 0.14
69 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (66 bp):
CGTCTTATTTAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACGT
T
Found at i:5069 original size:134 final size:134
Alignment explanation
Indices: 4826--5179 Score: 451
Period size: 134 Copynumber: 2.6 Consensus size: 134
4816 TCGGGCAGTC
* * ** * * *
4826 CGTCTTATTTAAGTTCACGATTCAAGGATCG-TTCAATTTTTTTATAAAACTGTCTCAATGGAGA
1 CGTCTTATTTAAGTTTACGATTCAAGGATCGTTTTAA--TTTTGGTAAAACGGTCTCGAGGGAGA
* * * * * *
4890 CGTCCGTCTTATTCTAGTATACGATTCATGGATCGTTCAATTTTTGATAAAACGGTCTCAATGGA
64 CGTTCGTCTTACTCAAGTTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCAAGGGA
4955 GACGTT
129 GACGTT
* *
4961 CGTCTTATTTAAATTTACGATTCAAGGATCGTTTTAATTTTGGTGAAACGGTCTCGAGGGAGACG
1 CGTCTTATTTAAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
* * * * *
5026 TTCGTCTTACTGAAATTTACGATTCAAGGATCGTTTTAA-TTTTGGTAAAACGGTCTCGAGGGAG
66 TTCGTCTTACTCAAGTTTACGATTCAAGGATCG-TTCAATTTTTGATAAAACGGTCTCAAGGGAG
5090 ACGTT
130 ACGTT
* * *
5095 CGTCTTACTTAAGTTTACGATTTAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGATG
1 CGTCTTATTTAAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
*
5160 TTCGTCTTACTTAAGTTTAC
66 TTCGTCTTACTCAAGTTTAC
5180 TTAAGTTCTA
Statistics
Matches: 190, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
134 153 0.81
135 33 0.17
136 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (134 bp):
CGTCTTATTTAAGTTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACG
TTCGTCTTACTCAAGTTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCAAGGGAGA
CGTT
Found at i:12040 original size:2 final size:2
Alignment explanation
Indices: 12033--12076 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
12023 ATACTCAACA
12033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
12076 A
1 A
12077 CTTGTACTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14937 original size:22 final size:22
Alignment explanation
Indices: 14886--14943 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
14876 TCGGTTTATG
*
14886 TAGATTATTAGTTTAATTATCA
1 TAGATTATTAGTTTAATTAACA
* *
14908 TATA-TATTAGTTATAA-TAAGA
1 TAGATTATTAGTT-TAATTAACA
14929 TAGATTATTAGTTTA
1 TAGATTATTAGTTTA
14944 TTATAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
TAGATTATTAGTTTAATTAACA
Found at i:15710 original size:2 final size:2
Alignment explanation
Indices: 15705--15729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15695 GGGGAACAAA
15705 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15730 GGAAAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18811 original size:25 final size:25
Alignment explanation
Indices: 18778--18830 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
18768 TTTAGTTTAC
*
18778 TAGTAGTATATTTTATGACTTTGAT
1 TAGTAGTATATTTTACGACTTTGAT
18803 TAGTAGTATATTTTACGACTTTGAT
1 TAGTAGTATATTTTACGACTTTGAT
18828 TAG
1 TAG
18831 AAAATGTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (25 bp):
TAGTAGTATATTTTACGACTTTGAT
Found at i:21426 original size:6 final size:6
Alignment explanation
Indices: 21406--21448 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
21396 CTAAGCAAAG
*
21406 TAAAT- TAAATG TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
21449 TAGCAATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:35207 original size:15 final size:15
Alignment explanation
Indices: 35184--35241 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
35174 ACAACATGAA
*
35184 TGTTCGCACCATAGT
1 TGTTCGCACCATTGT
*
35199 TGTTTGCACCATTGT
1 TGTTCGCACCATTGT
*
35214 TGTTTGCACCATTGT
1 TGTTCGCACCATTGT
35229 TGTTCGCACCATT
1 TGTTCGCACCATT
35242 CACCCTAGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (15 bp):
TGTTCGCACCATTGT
Done.