Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008727.1 Corchorus capsularis cultivar CVL-1 contig08748, 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: 21089
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:1082 original size:32 final size:32
Alignment explanation
Indices: 1029--1112 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
1019 AAAATAGCCT
** *
1029 AGCCGCCCCACCGGGGCGGCCTGCCGTGG-TAA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCTGGCT-A
* *
1061 AGCTGCCCTAGTGGGGCGGCCTGCCCTGGCTA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCTGGCTA
1093 AGCCGCCCCAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
1113 TCCGCTGTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.11, C:0.38, G:0.39, T:0.12
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCTGGCTA
Found at i:14076 original size:29 final size:30
Alignment explanation
Indices: 14018--14076 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
14008 AAACAAAGAA
*
14018 GGTTATACCAATCTTCTTATTCAAATTTAC
1 GGTTATACCAATCTTCTTATTCAAAGTTAC
* *
14048 GGTT-TACCATTCTTCTTATTCAAGGTTAC
1 GGTTATACCAATCTTCTTATTCAAAGTTAC
14077 CAAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (30 bp):
GGTTATACCAATCTTCTTATTCAAAGTTAC
Found at i:16038 original size:100 final size:100
Alignment explanation
Indices: 15861--16060 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
15851 TCACTTCGGT
*
15861 TATCAAATTTCACATTTACGGTTACTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
1 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
*
15926 AAGAAACGCAGTCGATAAAATCCTTATAGAGAAGC
66 AAGAAACACAGTCGATAAAATCCTTATAGAGAAGC
15961 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
1 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
16026 AAGAAACACAGTCGATAAAATCCTTATAGAGAAGC
66 AAGAAACACAGTCGATAAAATCCTTATAGAGAAGC
16061 AAAAGTTACA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (100 bp):
TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
AAGAAACACAGTCGATAAAATCCTTATAGAGAAGC
Found at i:19183 original size:13 final size:13
Alignment explanation
Indices: 19162--19206 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
19152 TACCTGCTAA
19162 AATATTAAT-ATT
1 AATATTAATAATT
19174 AATAATTAATAATATT
1 AAT-ATTAAT-A-ATT
19190 AATATTAATAATT
1 AATATTAATAATT
19203 AATA
1 AATA
19207 ATATTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.10
13 13 0.45
14 1 0.03
15 6 0.21
16 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTAATAATT
Found at i:19187 original size:22 final size:22
Alignment explanation
Indices: 19162--19215 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
19152 TACCTGCTAA
19162 AATATTAATATTAATAATTAAT
1 AATATTAATATTAATAATTAAT
19184 AATATTAATATTAATAATTAAT
1 AATATTAATATTAATAATTAAT
19206 AATATTAATA
1 AATATTAATA
19216 ATAAGACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTAATATTAATAATTAAT
Found at i:19188 original size:16 final size:16
Alignment explanation
Indices: 19162--19217 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
19152 TACCTGCTAA
19162 AATATTAAT-ATTAAT
1 AATATTAATAATTAAT
*
19177 -A-ATTAATAA-TATT
1 AATATTAATAATTAAT
19190 AATATTAATAATTAAT
1 AATATTAATAATTAAT
19206 AATATTAATAAT
1 AATATTAATAAT
19218 AAGACAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
15 8 0.23
16 15 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTAATAATTAAT
Found at i:19215 original size:6 final size:6
Alignment explanation
Indices: 19162--19206 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
19152 TACCTGCTAA
19162 AATATT AATATT AATAATT -A-A-T AATATT AATATT AATAATT AATA
1 AATATT AATATT AAT-ATT AATATT AATATT AATATT AAT-ATT AATA
19207 ATATTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
3 1 0.03
4 2 0.06
5 1 0.03
6 21 0.62
7 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AATATT
Found at i:19861 original size:99 final size:100
Alignment explanation
Indices: 19705--19893 Score: 222
Period size: 104 Copynumber: 1.9 Consensus size: 100
19695 TGAGAACTTG
* * * *
19705 ATTTGATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTAAATTGATAATTTA-ATTCAAGGG
1 ATTTGATTTGATTCGATTCAAGGGTCGAATGACTTGATCTCAAATTGATAATTAATATTCAAGGG
19769 TCTTGACGACTCGATCTTGAATTGATGACTTGAGA
66 TCTTGACGACTCGATCTTGAATTGATGACTTGAGA
* * *
19804 ATTTGATTTGATTCGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGA-TAATTTGATT
1 ATTTGATTTGATTCGATTCAAGGGTC---GAATGACTTGATCTCAAATTGATAATTAA--T-ATT
* *
19867 CAAGGGTCTTGGCGACTTGATCTTGAA
60 CAAGGGTCTTGACGACTCGATCTTGAA
19894 CAAACAAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
99 24 0.32
100 2 0.03
101 19 0.26
102 1 0.01
104 28 0.38
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (100 bp):
ATTTGATTTGATTCGATTCAAGGGTCGAATGACTTGATCTCAAATTGATAATTAATATTCAAGGG
TCTTGACGACTCGATCTTGAATTGATGACTTGAGA
Done.