Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005550.1 Corchorus capsularis cultivar CVL-1 contig05568, 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: 13976
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:89 original size:22 final size:22
Alignment explanation
Indices: 57--104 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
47 TTGTGATAAT
* *
57 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
*
79 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
101 TAAC
1 TAAC
105 TTGATTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:128 original size:24 final size:24
Alignment explanation
Indices: 91--238 Score: 77
Period size: 22 Copynumber: 6.6 Consensus size: 24
81 ACCAACCTAA
* *
91 GAAATTTTAATAACTTGAT-TCTAT
1 GAAATTTTGATAACTTCATAT-TAT
*
115 GAAATTTTGGTAAC--CATATTAT
1 GAAATTTTGATAACTTCATATTAT
*
137 GAAATTTTGATAACTTC-CA-TAT
1 GAAATTTTGATAACTTCATATTAT
* * *
159 GAAATTTTGGTAA--TCACACTAT
1 GAAATTTTGATAACTTCATATTAT
* * *
181 -AGAATTTTGATAACCTC--CTCAT
1 GA-AATTTTGATAACTTCATATTAT
* * *
203 GAAATTATAATAAC--CATTTTAT
1 GAAATTTTGATAACTTCATATTAT
225 GAAATTTTGATAAC
1 GAAATTTTGATAAC
239 CACATAGAGA
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
20 3 0.03
21 3 0.03
22 73 0.75
23 3 0.03
24 15 0.15
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (24 bp):
GAAATTTTGATAACTTCATATTAT
Found at i:129 original size:46 final size:46
Alignment explanation
Indices: 65--152 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
55 ATTAACCACC
65 CTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACTTGATT
1 CTATGAAATTTCAATAACCATA-CTAAGAAATTTTAATAACTTGATT
*** * * *
111 CTATGAAATTTTGGTAACCATATTATGAAATTTTGATAACTT
1 CTATGAAATTTCAATAACCATACTAAGAAATTTTAATAACTT
153 CCATATGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
46 34 0.97
47 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (46 bp):
CTATGAAATTTCAATAACCATACTAAGAAATTTTAATAACTTGATT
Found at i:140 original size:22 final size:22
Alignment explanation
Indices: 112--240 Score: 95
Period size: 22 Copynumber: 5.9 Consensus size: 22
102 AACTTGATTC
*
112 TATGAAATTTTGGTAACCATAT
1 TATGAAATTTTGATAACCATAT
*
134 TATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTTGATAAC--CATAT
* * * *
156 TATGAAATTTTGGTAATCACAC
1 TATGAAATTTTGATAACCATAT
*
178 TAT-AGAATTTTGATAACC-TCCT
1 TATGA-AATTTTGATAACCAT-AT
* * * *
200 CATGAAATTATAATAACCATTT
1 TATGAAATTTTGATAACCATAT
222 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
241 CATAGAGACA
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 75 0.90
23 3 0.04
24 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAT
Found at i:187 original size:44 final size:43
Alignment explanation
Indices: 111--239 Score: 134
Period size: 44 Copynumber: 3.0 Consensus size: 43
101 TAACTTGATT
* * *
111 CTATGAAATTTTGGTAACCATATTATGAAATTTTGATAACTTC
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
*
154 CATATGAAATTTTGGTAATCACACTAT-AGAATTTTGATAACCTC
1 C-TATGAAATTTTGGTAACCACACTATGA-AATTTTGATAACCTC
* ** ***
198 CTCATGAAATTATAATAACCATTTTATGAAATTTTGATAACC
1 CT-ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
240 ACATAGAGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 3 0.04
44 67 0.94
45 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (43 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
Found at i:668 original size:37 final size:37
Alignment explanation
Indices: 578--674 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
568 ATCTAAGAGC
* *
578 AAATAGGACGTTGGAGAAAAAATACAAAAAGCAAAATT
1 AAATAGGACGTTGGA-AACAAAGACAAAAAGCAAAATT
* ** *
616 AAATAGAAAAATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAG-GACGTTGGAAACAAAGACAAAAAGCAAAATT
654 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
675 AAACCAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
37 12 0.24
38 31 0.63
39 6 0.12
ACGTcount: A:0.59, C:0.08, G:0.19, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:6835 original size:30 final size:31
Alignment explanation
Indices: 6780--6848 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
6770 CATATACTCC
6780 AAGGAGTATATAGTTTGCATATATAGTAGGAAGG
1 AAGGAGTATATAGTTTG---ATATAGTAGGAAGG
6814 AAGGAGTATATAGTTTG-TATAGTAGGAAGG
1 AAGGAGTATATAGTTTGATATAGTAGGAAGG
6844 AAGGA
1 AAGGA
6849 AATGGATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 18 0.51
34 17 0.49
ACGTcount: A:0.39, C:0.01, G:0.32, T:0.28
Consensus pattern (31 bp):
AAGGAGTATATAGTTTGATATAGTAGGAAGG
Found at i:6849 original size:34 final size:33
Alignment explanation
Indices: 6780--6849 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
6770 CATATACTCC
*
6780 AAGGAGTATATAGTTTGCATATATAGTAGGAAGG
1 AAGGAGTATATAGTTTG-ATATATAGAAGGAAGG
6814 AAGGAGTATATAGTTTG-TATAGTAGGAAGGAAGG
1 AAGGAGTATATAGTTTGATATA-TA-GAAGGAAGG
6848 AA
1 AA
6850 ATGGATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 4 0.12
33 2 0.06
34 27 0.82
ACGTcount: A:0.40, C:0.01, G:0.31, T:0.27
Consensus pattern (33 bp):
AAGGAGTATATAGTTTGATATATAGAAGGAAGG
Done.