Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016615.1 Corchorus olitorius cultivar O-4 contig16648, 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: 36624
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10546 original size:14 final size:14
Alignment explanation
Indices: 10485--10550 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 14
10475 TTTTTTTTGG
* *
10485 TTTTGGGGGTTCAGC
1 TTTTGGGGTTTCA-A
*
10500 TTTCGGGGTTTCAAA
1 TTTTGGGGTTTC-AA
10515 TTTATGGGGTAATTTCAA
1 TTT-TGGGG---TTTCAA
10533 TTTTGGGGTTTCAA
1 TTTTGGGGTTTCAA
10547 TTTT
1 TTTT
10551 ATAGGGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
14 10 0.24
15 13 0.31
16 5 0.12
17 5 0.12
18 5 0.12
19 4 0.10
ACGTcount: A:0.17, C:0.09, G:0.27, T:0.47
Consensus pattern (14 bp):
TTTTGGGGTTTCAA
Found at i:20563 original size:27 final size:29
Alignment explanation
Indices: 20518--20580 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
20508 AAATTATCGA
* *
20518 TTTACCCTTGGAGTTGATAAA-TTACCA-T
1 TTTACCCTTAGAGTGGATAAAGTTA-CAGT
20546 TTTACCCTTAGAG-GGATAAAGTTACAGT
1 TTTACCCTTAGAGTGGATAAAGTTACAGT
20574 TTTACCC
1 TTTACCC
20581 CTTTAACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (29 bp):
TTTACCCTTAGAGTGGATAAAGTTACAGT
Found at i:22944 original size:21 final size:21
Alignment explanation
Indices: 22905--22945 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22895 GGGCGCCCGC
* *
22905 ATGGTTTGTCTGAAGACCCAT
1 ATGGTTTGCCTGAACACCCAT
*
22926 ATGGTTTGCCTGATCACCCA
1 ATGGTTTGCCTGAACACCCA
22946 GGTACGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
ATGGTTTGCCTGAACACCCAT
Found at i:28776 original size:2 final size:2
Alignment explanation
Indices: 28769--28813 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
28759 ATCCACTTGC
*
28769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28810 TA TA
1 TA TA
28814 GTAACAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29915 original size:22 final size:23
Alignment explanation
Indices: 29885--29937 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
29875 TTTTTGCTTT
*
29885 AAAAGATTATAGA-ATT-TTTATA
1 AAAAAATTA-AGACATTATTTATA
*
29907 AAAAAATTAAGACTTTATTTATA
1 AAAAAATTAAGACATTATTTATA
29930 AATAAAAT
1 AA-AAAAT
29938 AAAAACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 10 0.38
23 8 0.31
24 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (23 bp):
AAAAAATTAAGACATTATTTATA
Found at i:29945 original size:24 final size:23
Alignment explanation
Indices: 29901--29945 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
29891 TTATAGAATT
* *
29901 TTTATAAAAAAATTAAGACTTTA
1 TTTATAAAAAAATAAAAACTTTA
29924 TTTATAAATAAAATAAAAACTT
1 TTTATAAA-AAAATAAAAACTT
29946 AACTAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
TTTATAAAAAAATAAAAACTTTA
Found at i:31899 original size:28 final size:25
Alignment explanation
Indices: 31862--31916 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
31852 TAAATAAAAT
31862 TAGTGTTTTTAGTAAAGTAAAACTATAA
1 TAGTGTTTTT-GT-AA-TAAAACTATAA
* *
31890 TAGTTTTTTTGTCATAAAACTATAA
1 TAGTGTTTTTGTAATAAAACTATAA
31915 TA
1 TA
31917 ATTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 1 0.04
27 2 0.08
28 9 0.36
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (25 bp):
TAGTGTTTTTGTAATAAAACTATAA
Found at i:33121 original size:65 final size:65
Alignment explanation
Indices: 33041--33170 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
33031 GTTTTTATAC
*
33041 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACGTAAAGTAATGTCACCAAAT
1 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
*
33106 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTGATGTCACCAAAT
1 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
33171 TTTTATACAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (65 bp):
GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
Found at i:35291 original size:100 final size:100
Alignment explanation
Indices: 35118--35322 Score: 401
Period size: 100 Copynumber: 2.0 Consensus size: 100
35108 GGGGATACAT
35118 GGCAGCCACTACCACTCGGTCCAACATATTGTGCATCGACTGCCCAAACCCTTACAAGTTTGCAA
1 GGCAGCCACTACCACTCGGTCCAACATATTGTGCATCGACTGCCCAAACCCTTACAAGTTTGCAA
35183 ACCTTTGATGCAACATCTCAACCAGTGTCATTGGG
66 ACCTTTGATGCAACATCTCAACCAGTGTCATTGGG
*
35218 GGCAGCCACTACCACTCGGTCCAACATATTGTGCATCGACTGCCCAAACCCTTACTAGTTTGCAA
1 GGCAGCCACTACCACTCGGTCCAACATATTGTGCATCGACTGCCCAAACCCTTACAAGTTTGCAA
35283 ACCTTTGATGCAACATCTCAACCAGTGTCATTGGG
66 ACCTTTGATGCAACATCTCAACCAGTGTCATTGGG
35318 GGCAG
1 GGCAG
35323 TCCAAAAACA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 104 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (100 bp):
GGCAGCCACTACCACTCGGTCCAACATATTGTGCATCGACTGCCCAAACCCTTACAAGTTTGCAA
ACCTTTGATGCAACATCTCAACCAGTGTCATTGGG
Done.