Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011169.1 Corchorus capsularis cultivar CVL-1 contig11190, 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: 12205
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3335 original size:45 final size:47
Alignment explanation
Indices: 3240--3335 Score: 115
Period size: 48 Copynumber: 2.1 Consensus size: 47
3230 GCTGTTAATG
* * * *
3240 AAGAAGAAAGCCCTCTGGCCAAAGAAGGAGAAAGGTAGAAGGAGGGAA
1 AAGAAGAAAGCCCTCTGGCAAAAGAAGGAGAAACG-AGAAGCAAGGAA
* *
3288 AAGAAGAAAGTCCTTTGGCAAAAGAAGGAG-AACG-GAAGCAAGGAA
1 AAGAAGAAAGCCCTCTGGCAAAAGAAGGAGAAACGAGAAGCAAGGAA
3333 AAG
1 AAG
3336 GCAGGAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 12 0.29
47 3 0.07
48 27 0.64
ACGTcount: A:0.48, C:0.11, G:0.33, T:0.07
Consensus pattern (47 bp):
AAGAAGAAAGCCCTCTGGCAAAAGAAGGAGAAACGAGAAGCAAGGAA
Found at i:3522 original size:150 final size:143
Alignment explanation
Indices: 3288--3633 Score: 523
Period size: 150 Copynumber: 2.4 Consensus size: 143
3278 AAGGAGGGAA
* * *
3288 AAGAAGAAAGTCCTTTGGCAAAAGAAGGAGAACGGAAGCAAGGAAAAGGCAGGAACATAGACACC
1 AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAG-AAGGAAAAGGCAGGAACATAGACACC
*
3353 ACTCAAGAAGAAAGCTCTGACAAGCAAGAATCGAAATCAAAAGAAAGGGTTGCGG-AGAAGAAGG
65 ACTCAAGAAGAAAGCTCTGACAAGCAAGAATCGAAATAAAAAGAAAGGGTTG-GGAAGAAGAAGG
3417 AAAGCGATGTTAAGG
129 AAAGCGATGTTAAGG
3432 AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAGAAAGGAAACGGCAGCGCTAGGAACATA
1 AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAG-AAGGAAA----AG-GC-AGGAACATA
* *
3497 GACACCACTCAAGAAGAAAGTTCTGACAAGCAAGAATCGAAATAAAAAGGAAGGGTTGGGAAGAA
59 GACACCACTCAAGAAGAAAGCTCTGACAAGCAAGAATCGAAATAAAAAGAAAGGGTTGGGAAGAA
* *
3562 GAAGGAAAGCGTTGTTAAGT
124 GAAGGAAAGCGATGTTAAGG
*
3582 AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAGAAGGAAAATGCAGG
1 AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAGAAGGAAAAGGCAGG
3634 GACACCACCC
Statistics
Matches: 185, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
143 3 0.02
144 44 0.24
145 1 0.01
148 2 0.01
149 11 0.06
150 124 0.67
ACGTcount: A:0.46, C:0.14, G:0.29, T:0.11
Consensus pattern (143 bp):
AAGAAGAAAGCCCTTTGGCCAAAGAAGGAGAACAGAAGAAGGAAAAGGCAGGAACATAGACACCA
CTCAAGAAGAAAGCTCTGACAAGCAAGAATCGAAATAAAAAGAAAGGGTTGGGAAGAAGAAGGAA
AGCGATGTTAAGG
Found at i:6120 original size:30 final size:29
Alignment explanation
Indices: 6047--6124 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
6037 ACTTGTAGCG
** *
6047 TTTGGACGGTTTGCCCTCTGAACTTCAAT
1 TTTGGACATTTTGCCCCCTGAACTTCAAT
6076 TTTGGACATTTTGCCCCCTGAACTTCAAT
1 TTTGGACATTTTGCCCCCTGAACTTCAAT
*
6105 TTTGGGACTTTTTGCCCCCT
1 TTT-GGACATTTTGCCCCCT
6125 CAGGTTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 29 0.66
30 15 0.34
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCCTGAACTTCAAT
Found at i:6348 original size:29 final size:29
Alignment explanation
Indices: 6306--6369 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
6296 GCAGAACATC
* *
6306 CCAAAATTGAAGTTCAGGGGGTAAAATGT
1 CCAAAATTGAAGTTCAGGGGGCAAAACGT
*
6335 CCAAAATTGAAGTTTAGGGGGCAAAACGT
1 CCAAAATTGAAGTTCAGGGGGCAAAACGT
6364 CCAAAA
1 CCAAAA
6370 ACTACAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (29 bp):
CCAAAATTGAAGTTCAGGGGGCAAAACGT
Found at i:8780 original size:15 final size:15
Alignment explanation
Indices: 8716--8780 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
8706 TCCAAACAAA
*
8716 GAATTTGAAATTATT
1 GAATTTCAAATTATT
*
8731 AAATTTCAAATTATT
1 GAATTTCAAATTATT
* * **
8746 -CATTCCCAAA-TAAA
1 GAATT-TCAAATTATT
8760 GAATTTCAAATTATT
1 GAATTTCAAATTATT
8775 GAATTT
1 GAATTT
8781 AAAAATCTTA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
14 9 0.24
15 28 0.76
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (15 bp):
GAATTTCAAATTATT
Found at i:12169 original size:33 final size:33
Alignment explanation
Indices: 12127--12201 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
12117 TACACTGAGT
* *
12127 CTCCCCACTA-GGACGGCTCAGCCACGGCGGAGC
1 CTCCCCACTAGGGA-GGCTCAACCACGGCGAAGC
12160 CTCCCCACTAGGGAGGCTCAACCACGGCGAAGC
1 CTCCCCACTAGGGAGGCTCAACCACGGCGAAGC
12193 CTCCCCACT
1 CTCCCCACT
12202 GGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.20, C:0.44, G:0.25, T:0.11
Consensus pattern (33 bp):
CTCCCCACTAGGGAGGCTCAACCACGGCGAAGC
Done.