Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015134.1 Corchorus capsularis cultivar CVL-1 contig15155, 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: 56536
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:35 original size:25 final size:25
Alignment explanation
Indices: 1--117 Score: 162
Period size: 25 Copynumber: 4.7 Consensus size: 25
*
1 CGTTTGCTAAACGCAAGCGCAGGCT
1 CGTTTGCTAAACGCAAGCGCAGACT
* **
26 CGTTTGCTAAACTCAAGCATAGACT
1 CGTTTGCTAAACGCAAGCGCAGACT
*
51 CGTTTGCTAAACGCAAGCGCAGGCT
1 CGTTTGCTAAACGCAAGCGCAGACT
*
76 CGTTTGCTAAACGCAAGCGAAGACT
1 CGTTTGCTAAACGCAAGCGCAGACT
* *
101 TGTTTGCCAAACGCAAG
1 CGTTTGCTAAACGCAAG
118 AACATGAGCG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 80 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (25 bp):
CGTTTGCTAAACGCAAGCGCAGACT
Found at i:76 original size:50 final size:50
Alignment explanation
Indices: 1--117 Score: 191
Period size: 50 Copynumber: 2.3 Consensus size: 50
*
1 CGTTTGCTAAACGCAAGCGCAGGCTCGTTTGCTAAACTCAAGC-ATAGACT
1 CGTTTGCTAAACGCAAGCGCAGGCTCGTTTGCTAAACGCAAGCGA-AGACT
51 CGTTTGCTAAACGCAAGCGCAGGCTCGTTTGCTAAACGCAAGCGAAGACT
1 CGTTTGCTAAACGCAAGCGCAGGCTCGTTTGCTAAACGCAAGCGAAGACT
* *
101 TGTTTGCCAAACGCAAG
1 CGTTTGCTAAACGCAAG
118 AACATGAGCG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 62 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (50 bp):
CGTTTGCTAAACGCAAGCGCAGGCTCGTTTGCTAAACGCAAGCGAAGACT
Found at i:1253 original size:3 final size:3
Alignment explanation
Indices: 1245--1285 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1235 TGGCGCAACA
1245 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1286 AGTAGTACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21093 original size:10 final size:11
Alignment explanation
Indices: 21078--21122 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
21068 ATAGTTTTAC
21078 TGTTCTG-TTT
1 TGTTCTGTTTT
21088 TGTTCTGTTTT
1 TGTTCTGTTTT
*
21099 TGCTCTGTTTT
1 TGTTCTGTTTT
*
21110 TGTCCTGTTTT
1 TGTTCTGTTTT
21121 TG
1 TG
21123 ATCTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.00, C:0.13, G:0.20, T:0.67
Consensus pattern (11 bp):
TGTTCTGTTTT
Found at i:26845 original size:178 final size:178
Alignment explanation
Indices: 26540--26892 Score: 512
Period size: 178 Copynumber: 2.0 Consensus size: 178
26530 TTGAGGTGTA
*
26540 ATTAATCTTATTTTGGTAGAAGGTCCGGACTAATACGAAGTCAAGTCATGTCGAACAGCAAATGA
1 ATTAATCTTATTTTGGTAGAAGGCCCGGACTAATACGAAGTCAAGTCATGTCGAACAGCAAATGA
* * * *
26605 AATGGGAAAAGCTCTTCTAATGCCTATTTTCTCATTCATAAAATTCGAAATTGATGCATTGCTTA
66 AAGGGGAAAAGCTCTTCTAATGCCTATTTTCTCATTCATAAAATTCGAAATTAATACATTGCTCA
*
26670 AGGGGCATTGAGCTCATTTCACTTAATGCAATAGACATTGATAAACTG
131 AGGGGCATTGAGCTCATTTCACTCAATGCAATAGACATTGATAAACTG
* * ** *
26718 ATTAATCTTATTTTGGTAGAAGGCCCGGACTATTACGAAGTCAAGTCATGTCGGATGGTAAATGA
1 ATTAATCTTATTTTGGTAGAAGGCCCGGACTAATACGAAGTCAAGTCATGTCGAACAGCAAATGA
* * *
26783 AACGGGGAAAA-CTCTTCTAATGTCTATTTTCTCATTTATAAGATTCG-AATTCAATACATTGCT
66 AA-GGGGAAAAGCTCTTCTAATGCCTATTTTCTCATTCATAAAATTCGAAATT-AATACATTGCT
* ** *
26846 CAAGGGGTATTGAGCTCATTTCACTCAATGTGATAGACATTGGTAAA
129 CAAGGGGCATTGAGCTCATTTCACTCAATGCAATAGACATTGATAAA
26893 TTGAAGCCTA
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
177 4 0.03
178 144 0.93
179 7 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (178 bp):
ATTAATCTTATTTTGGTAGAAGGCCCGGACTAATACGAAGTCAAGTCATGTCGAACAGCAAATGA
AAGGGGAAAAGCTCTTCTAATGCCTATTTTCTCATTCATAAAATTCGAAATTAATACATTGCTCA
AGGGGCATTGAGCTCATTTCACTCAATGCAATAGACATTGATAAACTG
Found at i:49243 original size:50 final size:50
Alignment explanation
Indices: 49168--49263 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
49158 TTTTCATTGC
49168 AGATTGGATTGACTTGCAATCAAAAATTATGTAGCAAAAACGGCCCAAGA
1 AGATTGGATTGACTTGCAATCAAAAATTATGTAGCAAAAACGGCCCAAGA
49218 AGATTGGATTGACTTGCAATCAAAAATTATGTAGCAAAAACGGCCC
1 AGATTGGATTGACTTGCAATCAAAAATTATGTAGCAAAAACGGCCC
49264 GCCAATTTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTGGATTGACTTGCAATCAAAAATTATGTAGCAAAAACGGCCCAAGA
Done.