Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006011.1 Corchorus capsularis cultivar CVL-1 contig06029, 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: 13147
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Found at i:2541 original size:20 final size:21
Alignment explanation
Indices: 2503--2541 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2493 AAATGCTCAG
*
2503 CTTAAGGAGTCAAACGACTTA
1 CTTAAAGAGTCAAACGACTTA
*
2524 CTTAAAGAG-CAAATGACT
1 CTTAAAGAGTCAAACGACT
2542 CAAGATCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (21 bp):
CTTAAAGAGTCAAACGACTTA
Found at i:5872 original size:156 final size:157
Alignment explanation
Indices: 5588--5942 Score: 418
Period size: 156 Copynumber: 2.3 Consensus size: 157
5578 ATCTCAAATA
* * * *
5588 GACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGAC-AGTTGAAGGAGTCAAACCAACT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAAGGAGACAAACCAACT
* * * * *
5652 TCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGGATAATCTAAG
66 TCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGAATAATCTAAG
*
5717 TCTACTGGTGG-AAAA-GT-AGCCTTGTT-G
131 TC-ACT--TGGAAAAATGTCAG-CTTATTCG
* * * *
5744 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTG-GGGAGAGAAACCTAGT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAAGGAGACAAACCAACT
* * * * **
5808 TCACTA-CCAAGGGAAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTATGTGAATGTTCTAA
66 TCACTATCCAAGAG-AGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGAATAATCTAA
* *
5872 GTCCCTTGGAAAAATTTCAGCTTATTCG
130 GTCACTTGGAAAAATGTCAGCTTATTCG
5900 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
5943 GTTTGAGGTG
Statistics
Matches: 171, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 12 0.07
156 148 0.87
157 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (157 bp):
GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGAAGGAGACAAACCAACT
TCACTATCCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGAATAATCTAAG
TCACTTGGAAAAATGTCAGCTTATTCG
Found at i:7856 original size:135 final size:135
Alignment explanation
Indices: 7610--7905 Score: 407
Period size: 135 Copynumber: 2.2 Consensus size: 135
7600 AAGACTTGGA
* * **
7610 GGGG-AAAACCAACAACTGCTTGGTGTCCAGCCCGGTGCTCTGCCTTTTCAACAAGTGAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTCTGCCCCTTCAACAAGTGAACCATC
* ** *
7674 AGGTGAACAACCCACAAGTCATGGTTGAGATTGGTCTTATCGATGAAAGGCTTGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGTCAAGATTGGTCTTATCGATGAAAGACTTGGGGGGCAAGGA
7739 CTCGG
131 CTCGG
* * * *
7744 GGGGCAAAACCACCAACTGCTTGGTGCCCAGCCTGGTCCTCTTCCCCTTCAACAAGTTAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTCTGCCCCTTCAACAAGTGAACCATC
* * *
7809 AGGTGAACAATCAACAGGTCATGGCTCAAG-TTGGTCTTATCGATGAAAGATTTGGGGGGCAAGG
66 AGGTGAACAACCAACAAGTCATGG-TCAAGATTGGTCTTATCGATGAAAGACTTGGGGGGCAAGG
7873 ACTCGG
130 ACTCGG
* * *
7879 GGGGCAACACCAACAGCCGCTTGGTGC
1 GGGGCAAAACCAACAACTGCTTGGTGC
7906 TCCACCTCTG
Statistics
Matches: 141, Mismatches: 19, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
134 4 0.03
135 134 0.95
136 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (135 bp):
GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTCTGCCCCTTCAACAAGTGAACCATC
AGGTGAACAACCAACAAGTCATGGTCAAGATTGGTCTTATCGATGAAAGACTTGGGGGGCAAGGA
CTCGG
Found at i:10778 original size:20 final size:21
Alignment explanation
Indices: 10740--10778 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
10730 AAATGCTCAG
*
10740 CTTAAGGAGTCAAACGACTTA
1 CTTAAAGAGTCAAACGACTTA
*
10761 CTTAAAGAG-CAAATGACT
1 CTTAAAGAGTCAAACGACT
10779 CAAGATCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (21 bp):
CTTAAAGAGTCAAACGACTTA
Found at i:12083 original size:182 final size:183
Alignment explanation
Indices: 11892--12302 Score: 436
Period size: 183 Copynumber: 2.3 Consensus size: 183
11882 GGTTATCTTC
* * * *
11892 ATGACCTAA-TTAACT-TACTAAACCCCCTGATTTTTGGCTTAATTAATCAATTTTGCCTAAATC
1 ATGACCTAATTTAA-TGGACTAAACCCACTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATC
* * *
11955 AGAAAAACCCCAATTCACCAAGCGAGCTAATTTGCCGCCCAAGTTGCAATTTTTGCAAAGAAGGG
65 ACAAAAACCCCAATTCACCAAGCGACCTAATTTGCCG-CCAAGTTGCAATTTTTGCAAA-AAGAG
* * *
12020 CTCA-G--CTCATTAGGGGTTGCTTGGTTT-ATCGAATTAGGTTTATGTTCATGTGAT
128 -TCACGACCT-ATTAGGGATTGCTTGATTTCATCAAATTAGGTTTATGTTCATGTGAT
* ** * *
12074 ATGACCTAATTTTATGGGTTTAACCTACTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCA
1 ATGACCTAATTTAATGGACTAAACCCACTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCA
* * ** * *
12139 CAAAAACCCTAATTTATGAAGCTACCTAATTTGCCGCCAAGTTGCAATTTTTGCAAAATGAGTCA
66 CAAAAACCCCAATTCACCAAGCGACCTAATTTGCCGCCAAGTTGCAATTTTTGCAAAAAGAGTCA
12204 CGACCTATTAGGGATTGCTTGATTTCATCAAATTAGG----T-TT-ATGTGAT
131 CGACCTATTAGGGATTGCTTGATTTCATCAAATTAGGTTTATGTTCATGTGAT
* * *
12251 ATGACCTAATTTTAT-GACGTATACCCCCTGGATTTTTGGC-TAATTTAATCAA
1 ATGACCTAATTTAATGGAC-TAAACCCACT-GATTTTTGGCTTAA-TTAATCAA
12303 ATATGCCGAA
Statistics
Matches: 193, Mismatches: 27, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
176 1 0.01
177 31 0.16
178 20 0.10
179 1 0.01
180 3 0.02
181 4 0.02
182 48 0.25
183 85 0.44
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (183 bp):
ATGACCTAATTTAATGGACTAAACCCACTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCA
CAAAAACCCCAATTCACCAAGCGACCTAATTTGCCGCCAAGTTGCAATTTTTGCAAAAAGAGTCA
CGACCTATTAGGGATTGCTTGATTTCATCAAATTAGGTTTATGTTCATGTGAT
Found at i:12146 original size:183 final size:183
Alignment explanation
Indices: 11918--12247 Score: 470
Period size: 183 Copynumber: 1.8 Consensus size: 183
11908 ACTAAACCCC
* * * *
11918 CTGATTTTTGGCTTAATTAATCAATTTTGCCTAAATCAGAAAAACCCCAATTCACCAAGCGAGCT
1 CTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCACAAAAACCCCAATTCACCAAGCGACCT
* * *
11983 AATTTGCCGCCCAAGTTGCAATTTTTGCAAAGAAGGGCTCA-G--CTCATTAGGGGTTGCTTGGT
66 AATTTGCCG-CCAAGTTGCAATTTTTGCAAA-AAGAG-TCACGACCT-ATTAGGGATTGCTTGAT
*
12045 TT-ATCGAATTAGGTTTATGTTCATGTGATATGACCTAATTTTATGGGTTTAACCTA
127 TTCATCAAATTAGGTTTATGTTCATGTGATATGACCTAATTTTATGGGTTTAACCTA
* * ** *
12101 CTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCACAAAAACCCTAATTTATGAAGCTACCT
1 CTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCACAAAAACCCCAATTCACCAAGCGACCT
*
12166 AATTTGCCGCCAAGTTGCAATTTTTGCAAAATGAGTCACGACCTATTAGGGATTGCTTGATTTCA
66 AATTTGCCGCCAAGTTGCAATTTTTGCAAAAAGAGTCACGACCTATTAGGGATTGCTTGATTTCA
12231 TCAAATTAGGTTTATGT
131 TCAAATTAGGTTTATGT
12248 GATATGACCT
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
180 3 0.02
181 4 0.03
182 38 0.29
183 84 0.65
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (183 bp):
CTGATTTTTGGCTTAATTAATCAATTTGGCCAAAATCACAAAAACCCCAATTCACCAAGCGACCT
AATTTGCCGCCAAGTTGCAATTTTTGCAAAAAGAGTCACGACCTATTAGGGATTGCTTGATTTCA
TCAAATTAGGTTTATGTTCATGTGATATGACCTAATTTTATGGGTTTAACCTA
Done.