Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011901.1 Corchorus capsularis cultivar CVL-1 contig11922, 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: 19688
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:879 original size:33 final size:33
Alignment explanation
Indices: 808--926 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
798 AAAGGATCGT
* * *
808 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCGT
1 GTGGCCGGTTGTGGCCGGACATGTCC-ATGTCGC
* * *
841 TTGGCCGGTTGTAGCCGGCCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
874 GTGGCCGG-TGATGGCCGGACATGTCCATGTCGC
1 GTGGCCGGTTG-TGGCCGGACATGTCCATGTCGC
907 GTGGCCGGTCTTGTGGCCGG
1 GTGGCCGG--TTGTGGCCGG
927 TGTTGCTTGG
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.04
33 61 0.84
35 7 0.10
36 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
Found at i:4283 original size:21 final size:20
Alignment explanation
Indices: 4255--4309 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
4245 TCTCAACAAA
* * *
4255 GCCTCATTGATTTTCATTTG
1 GCCTCATTCAATTTCACTTG
4275 GCCTGCATTCAATTTCACTTG
1 GCCT-CATTCAATTTCACTTG
4296 GCCTTCATTCAATT
1 GCC-TCATTCAATT
4310 GCAACTGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 25 0.83
22 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44
Consensus pattern (20 bp):
GCCTCATTCAATTTCACTTG
Found at i:11635 original size:35 final size:35
Alignment explanation
Indices: 11545--11795 Score: 367
Period size: 35 Copynumber: 7.1 Consensus size: 35
11535 GAAGTGAGAA
* *
11545 AAGTGAGTCGGTAAATAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
* * * * *
11580 GAGTAAAATCAGTTAGTAACTTAATTCAGGGTAATT
1 AAGT-GAGTCAGTAATTAACTTAATTCAGGGTAATT
11616 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
11651 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
*
11686 AAGTGAGTCAGTAATCAACCTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATTAA-CTTAATTCAGGGTAATT
* *
11722 AAGTGATTCAGTAATCAACTTTAATTCAGGGTAATT
1 AAGTGAGTCAGTAATTAAC-TTAATTCAGGGTAATT
* *
11758 AAGTGAGTCAGTAGTTAACTTAATTCAGGATAATT
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
11793 AAG
1 AAG
11796 ATCGACTTAA
Statistics
Matches: 196, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
35 101 0.52
36 95 0.48
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (35 bp):
AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATT
Found at i:11709 original size:71 final size:70
Alignment explanation
Indices: 11545--11795 Score: 367
Period size: 71 Copynumber: 3.5 Consensus size: 70
11535 GAAGTGAGAA
* * * * * *
11545 AAGTGAGTCGGTAAATAACTTAATTCAGGGTAATTGAGTAAAATCAGTTAGTAACTTAATTCAGG
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATTAAGT-GAATCAGTAATTAACTTAATTCAGG
11610 GTAATT
65 GTAATT
*
11616 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATTAACTTAATTCAGGG
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTGAATCAGTAATTAACTTAATTCAGGG
11681 TAATT
66 TAATT
* * *
11686 AAGTGAGTCAGTAATCAACCTTAATTCAGGGTAATTAAGTGATTCAGTAATCAACTTTAATTCAG
1 AAGTGAGTCAGTAATTAA-CTTAATTCAGGGTAATTAAGTGAATCAGTAATTAAC-TTAATTCAG
11751 GGTAATT
64 GGTAATT
* *
11758 AAGTGAGTCAGTAGTTAACTTAATTCAGGATAATTAAG
1 AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATTAAG
11796 ATCGACTTAA
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
70 44 0.27
71 89 0.54
72 32 0.19
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (70 bp):
AAGTGAGTCAGTAATTAACTTAATTCAGGGTAATTAAGTGAATCAGTAATTAACTTAATTCAGGG
TAATT
Found at i:16279 original size:8 final size:8
Alignment explanation
Indices: 16258--16298 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
16248 GTCCCCATCC
16258 AAATAA-A
1 AAATAATA
16265 AAA-AATA
1 AAATAATA
16272 AAATAATA
1 AAATAATA
16280 AAATAATA
1 AAATAATA
16288 AAATAATA
1 AAATAATA
16296 AAA
1 AAA
16299 AAGAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 2 0.06
7 7 0.22
8 23 0.72
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATAATA
Found at i:16319 original size:14 final size:15
Alignment explanation
Indices: 16296--16330 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16286 TAAAATAATA
16296 AAAAAGAAGAAAAAG
1 AAAAAGAAGAAAAAG
*
16311 AAAAA-AAGAAGAAG
1 AAAAAGAAGAAAAAG
16325 AAAAAG
1 AAAAAG
16331 CACTCGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAAG
Done.