Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006035.1 Corchorus capsularis cultivar CVL-1 contig06053, 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: 34548
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:7019 original size:153 final size:147
Alignment explanation
Indices: 6747--7024 Score: 400
Period size: 153 Copynumber: 1.9 Consensus size: 147
6737 ATTGATCCAT
*
6747 GATTTGATTCTGATATAATTGATCTTGATGAACAAATTCTCCAAAATTCGTCTGACAAGTGCTAC
1 GATTTGATTCTGATATAATTCATCTTGATGAACAAATTCTCCAAAATTCGTCTGACAAGTGCTAC
*
6812 TTGCATCCAACGCATGATTAACACAAACTTTCTTCATAGCCGACATCCCAGCTCCATTAACATCA
66 TTGCATCCAACGCATGATCAACACAAACTTTCTTCATAGCCGACATCCCAGCTCCATTAACATCA
6877 CCAATATATGCAGAGTG
131 CCAATATATGCAGAGTG
6894 GATTTGATTCTGATCAT-ATTCATCTTGATGAACAATTAATTCTCCAAAATTCAGAT-T-ACAAG
1 GATTTGATTCTGAT-ATAATTCATCTTGATGAAC-A--AATTCTCCAAAATTC-G-TCTGACAAG
* * * *
6956 TACTGTTACTTGCATCTAACGCATGATCAACACATACTTTCTTCATAGCCGACATTCCAGCTCCA
60 ---TGCTACTTGCATCCAACGCATGATCAACACAAACTTTCTTCATAGCCGACATCCCAGCTCCA
7021 TTAA
122 TTAA
7025 TAATATCATC
Statistics
Matches: 116, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
147 29 0.25
148 3 0.03
150 20 0.17
151 2 0.02
152 1 0.01
153 61 0.53
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (147 bp):
GATTTGATTCTGATATAATTCATCTTGATGAACAAATTCTCCAAAATTCGTCTGACAAGTGCTAC
TTGCATCCAACGCATGATCAACACAAACTTTCTTCATAGCCGACATCCCAGCTCCATTAACATCA
CCAATATATGCAGAGTG
Found at i:9926 original size:31 final size:31
Alignment explanation
Indices: 9885--9963 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 31
9875 CGTTTCTGTT
9885 TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
*
9916 TTTAGACTCAAATTGAG-CAACTTTTGAAAGG
1 TTTAGGCTCAAATTG-GTCAACTTTTGAAAGG
9947 TTTAGGCTCAAATTGGT
1 TTTAGGCTCAAATTGGT
9964 GACTAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 42 0.95
32 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
Found at i:11241 original size:31 final size:31
Alignment explanation
Indices: 11203--11265 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11193 AACTGAACTA
*
11203 ACTCAAACATCCAAGATCTGAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
11234 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
11265 A
1 A
11266 TTGATAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:20823 original size:1 final size:1
Alignment explanation
Indices: 20817--20841 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20807 TGTACATTTC
20817 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
20842 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27267 original size:168 final size:168
Alignment explanation
Indices: 26983--27286 Score: 427
Period size: 168 Copynumber: 1.8 Consensus size: 168
26973 GTCATCCAAT
* * * *
26983 TGACGCGCGTCTCCTACGGAGACTTCCGCCTCACTGAGGCACCGATCTGGAGCAGGATACTTGGG
1 TGACGAGCGTCTCCCACGGAGACTTCCGCCTCACTAAGGCACCGATCTGGAGCAGGACACTTGGG
* * * *
27048 GGGCAGGAGCCTATCAATACAGTGCAACCCTCCCATGTGAACCTCCAATCGGACGAACGCGATCG
66 GGGCAGGAGCCTATCAACACAGAGCAACCCTCCCATGTGAACCCCCAATCGGACGAACGCGATCA
27113 CCAAATATTCAAAATCACAAATCGACAAGGTGCAGATC
131 CCAAATATTCAAAATCACAAATCGACAAGGTGCAGATC
* * *
27151 TGACGAGCGTCTCCCGCGGTGACTTCCGCCTCAGC-AAGGCACCGATCTGGGGCAGGACACTTGG
1 TGACGAGCGTCTCCCACGGAGACTTCCGCCTCA-CTAAGGCACCGATCTGGAGCAGGACACTTGG
* *
27215 GGGGCATGAGCCT-TACAACATAGAGCAA-CCTCCCCACT-TGAACCCCCAATCGGACGAACGCG
65 GGGGCAGGAGCCTAT-CAACACAGAGCAACCCT-CCCA-TGTGAACCCCCAATCGGACGAACGCG
27277 ATCACCAAAT
127 ATCACCAAAT
27287 TATCAAGTCA
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
167 4 0.03
168 113 0.95
169 2 0.02
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.17
Consensus pattern (168 bp):
TGACGAGCGTCTCCCACGGAGACTTCCGCCTCACTAAGGCACCGATCTGGAGCAGGACACTTGGG
GGGCAGGAGCCTATCAACACAGAGCAACCCTCCCATGTGAACCCCCAATCGGACGAACGCGATCA
CCAAATATTCAAAATCACAAATCGACAAGGTGCAGATC
Found at i:27450 original size:151 final size:151
Alignment explanation
Indices: 27175--27450 Score: 335
Period size: 151 Copynumber: 1.8 Consensus size: 151
27165 CGCGGTGACT
* * * *
27175 TCCGCCTCAGCAAGGCACCGATCTGGGGCAGGACACTTGGGGGGCATGAGCCTTACAACATAGAG
1 TCCGCCTCAGCAAGGCAACGATCTGGGGCAAGACACTTGGGGGGAATGAGCCTTACAACACAGAG
* **
27240 CAACCTCCCCACTTGAACCCCCAATCGGACGAACGCGATCACCAAATTATCAAGTCACAAGCTGA
66 CAACCTCCCCACTTAAACCCCCAATCGGACGAACGCGATCACCAAATTATCAAACCACAAGCTGA
27305 CAAACGTCTCCCATGAAGACC
131 CAAACGTCTCCCATGAAGACC
* * * * * *
27326 TCCGCCTTAGCGAGTCAACGATTTGGGGCAAGACACTTGGGGGGAATGAGCC-TATCAATACAGT
1 TCCGCCTCAGCAAGGCAACGATCTGGGGCAAGACACTTGGGGGGAATGAGCCTTA-CAACACAGA
* * * *
27390 GCAACC-CTCCCA-TGTAAACCTCCAATCGGATGAACGCGATTACCGAA-TATTCAAACCACAA
65 GCAACCTC-CCCACT-TAAACCCCCAATCGGACGAACGCGATCACCAAATTA-TCAAACCACAA
27451 TTGACAATGC
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
150 6 0.06
151 98 0.94
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (151 bp):
TCCGCCTCAGCAAGGCAACGATCTGGGGCAAGACACTTGGGGGGAATGAGCCTTACAACACAGAG
CAACCTCCCCACTTAAACCCCCAATCGGACGAACGCGATCACCAAATTATCAAACCACAAGCTGA
CAAACGTCTCCCATGAAGACC
Done.