Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003350.1 Corchorus capsularis cultivar CVL-1 contig03358, 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, 603
Length: 1005
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Found at i:121 original size:30 final size:32
Alignment explanation
Indices: 73--132 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
63 ATGTTTTTCG
*
73 ATTGTACCCTTATTTTT-AAAACATATTTCCA
1 ATTGTACCCCTATTTTTAAAAACATATTTCCA
104 ATTGTACCCCT-TTTTTAAAAACATATTTC
1 ATTGTACCCCTATTTTTAAAAACATATTTC
133 TAAATTACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTGTACCCCTATTTTTAAAAACATATTTCCA
Found at i:204 original size:15 final size:15
Alignment explanation
Indices: 158--206 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
148 AAATAATATT
158 TTAATTATTCCATTA
1 TTAATTATTCCATTA
*
173 TT--TT-TT-AATTA
1 TTAATTATTCCATTA
*
184 TAAATTATTCCATTA
1 TTAATTATTCCATTA
199 TTAATTAT
1 TTAATTAT
207 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:356 original size:19 final size:19
Alignment explanation
Indices: 334--370 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
324 ACTATTAGTT
334 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
353 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
371 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:564 original size:22 final size:22
Alignment explanation
Indices: 536--719 Score: 169
Period size: 22 Copynumber: 8.3 Consensus size: 22
526 TGTCTCTATG
*
536 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
558 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
581 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
602 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
625 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
646 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
668 TTAGGTTATTAAAATTTCTTAGGT
1 -T-GGTTATCAAAATTTCATAGGA
** *
692 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
714 TGGTTA
1 TGGTTA
720 ATTTTCACAA
Statistics
Matches: 133, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
21 4 0.03
22 106 0.80
23 6 0.05
24 17 0.13
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:780 original size:22 final size:22
Alignment explanation
Indices: 755--880 Score: 114
Period size: 22 Copynumber: 5.7 Consensus size: 22
745 ATCAAAGAGA
*
755 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
777 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
* *
799 TTAACAGAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGCGAGG
* * *
821 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGCGAGG
* *
843 TTATCAAAATTTTATAGCGTGG
1 TTATCAAAATTTCATAGCGAGG
865 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
881 TGAAGGTTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.06
22 73 0.88
23 5 0.06
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:877 original size:44 final size:44
Alignment explanation
Indices: 755--894 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
745 ATCAAAGAGA
* * *
755 TTATCAAAATGTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGCGAGGTTATCAA-AATTTCATAGGGAGG
* * * *
799 TTAACAGAATTTCATTAG-GAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTCA-TAGCGAGGTTATC-AAAATTTCATAGGGAGG
* * * *
843 TTATCAAAATTTTATAGCGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGG
887 TTAT-AAAA
1 TTATCAAAA
895 GTCTCAATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
43 7 0.09
44 63 0.83
45 6 0.08
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGG
Done.