Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013813.1 Corchorus capsularis cultivar CVL-1 contig13834, 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: 22986
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:12227 original size:22 final size:22
Alignment explanation
Indices: 12202--12390 Score: 116
Period size: 22 Copynumber: 8.6 Consensus size: 22
12192 ATGATCCCAT
12202 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
12224 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* ** * * **
12246 TATGGAATTTCAAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
12268 TAT-AATTTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
12289 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
12311 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
12333 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
12354 TAATGAAATTTTGATAAACCTTCC
1 T-ATGAAATTTTGAT-AACCTTCC
*
12378 TATAAAATTTTGA
1 TATGAAATTTTGA
12391 AAATTTTCAG
Statistics
Matches: 124, Mismatches: 35, Indels: 15
0.71 0.20 0.09
Matches are distributed among these distances:
21 16 0.13
22 88 0.71
23 14 0.11
24 6 0.05
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:12388 original size:23 final size:22
Alignment explanation
Indices: 12337--12390 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
12327 CCTCAATATG
*
12337 AAATTTTGATAACTTCCTAATG
1 AAATTTTGATAACTTCCTAATA
12359 AAATTTTGATAAACCTTCCT-ATA
1 AAATTTTGAT-AA-CTTCCTAATA
12382 AAATTTTGA
1 AAATTTTGA
12391 AAATTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACTTCCTAATA
Found at i:16945 original size:12 final size:12
Alignment explanation
Indices: 16928--16958 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16918 TCTAGAGTGA
16928 TGCTTGATTAAT
1 TGCTTGATTAAT
16940 TGCTTGATTAAT
1 TGCTTGATTAAT
*
16952 TGATTGA
1 TGCTTGA
16959 ATTATATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (12 bp):
TGCTTGATTAAT
Found at i:19392 original size:7 final size:7
Alignment explanation
Indices: 19373--19445 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
19363 GTGCGAGAGG
19373 AAGAAAGA
1 AAGAAA-A
19381 AAGAAAA
1 AAGAAAA
19388 AAG--AA
1 AAGAAAA
*
19393 GAGAAAA
1 AAGAAAA
**
19400 AACTAAA
1 AAGAAAA
*
19407 AAGAATA
1 AAGAAAA
19414 AAGAATAA
1 AAGAA-AA
*
19422 ATGAATAA
1 AAGAA-AA
19430 AAGAAAA
1 AAGAAAA
19437 AA-AAAA
1 AAGAAAA
19443 AAG
1 AAG
19446 GAGAGACACG
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
5 4 0.08
6 6 0.12
7 23 0.45
8 18 0.35
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (7 bp):
AAGAAAA
Found at i:19915 original size:18 final size:18
Alignment explanation
Indices: 19892--19928 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19882 CATTGAATAC
19892 GGTGGGACTTGAACCTGA
1 GGTGGGACTTGAACCTGA
19910 GGTGGGACTTGAACCTGA
1 GGTGGGACTTGAACCTGA
19928 G
1 G
19929 ACCTTGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (18 bp):
GGTGGGACTTGAACCTGA
Found at i:21710 original size:14 final size:14
Alignment explanation
Indices: 21693--21719 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21683 TTATCGAAAA
21693 ATAATTATTATTTT
1 ATAATTATTATTTT
21707 ATAATTATTATTT
1 ATAATTATTATTT
21720 AATTCAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATAATTATTATTTT
Found at i:22877 original size:41 final size:41
Alignment explanation
Indices: 22830--22929 Score: 157
Period size: 41 Copynumber: 2.4 Consensus size: 41
22820 TAATTCAATC
*
22830 TCGTCTCGGGACGTTAAAACAGTTTTTCTTCACTT-TCAGCA
1 TCGTCTCAGGACGTTAAAACAGTTTTTCTTCA-TTGTCAGCA
* *
22871 TCGTCTCAGGACGTTAAAACAGTTTTTTTTTATTGTCAGCA
1 TCGTCTCAGGACGTTAAAACAGTTTTTCTTCATTGTCAGCA
22912 TCGTCTCAGGACGTTAAA
1 TCGTCTCAGGACGTTAAA
22930 CATTGTTACT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.04
41 53 0.96
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (41 bp):
TCGTCTCAGGACGTTAAAACAGTTTTTCTTCATTGTCAGCA
Done.