Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011216.1 Corchorus capsularis cultivar CVL-1 contig11237, 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: 27921
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:10773 original size:11 final size:11
Alignment explanation
Indices: 10757--10793 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
10747 GTGGGATAAA
10757 TTTTGTTTTTT
1 TTTTGTTTTTT
10768 TTTTGTTTTTT
1 TTTTGTTTTTT
10779 TTTTGTTTTTT
1 TTTTGTTTTTT
10790 TTTT
1 TTTT
10794 CTGCTCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:13160 original size:50 final size:48
Alignment explanation
Indices: 13084--13300 Score: 161
Period size: 48 Copynumber: 4.5 Consensus size: 48
13074 AAAGCGAACT
* * * *
13084 TGCCTTTCATCCGGAAAGGGCATTTTAAGAAAAAAAACGAGTAAAACT-AA
1 TGCCTTCCATCCGGGAAGGGCGTTTT-AGAAAAAAAA-G-GTAAAAATCAA
* * *
13134 TGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAG
1 TGCCTTCCATCCGGGAAGGGCGTTTTAGAAAAAAAAGGTAAAAATCAA
* * ** * *
13182 TGCCTTCCGTCCGGGAAGGGCGTTTTGAGAAAAACAA-GTAATGATTAG
1 TGCCTTCCATCCGGGAAGGGCGTTTT-AGAAAAAAAAGGTAAAAATCAA
* * * * * *
13230 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAA-GTAAAGATGAA
1 TGCCTTCCATCCGGGAAGGGCGTTTT-AGAAA-AAAAAGGTAAAAATCAA
* * *
13279 TGGCTTCCGTCTGGGAAGGGCG
1 TGCCTTCCATCCGGGAAGGGCG
13301 CTTTGGGAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
47 7 0.05
48 65 0.46
49 47 0.33
50 23 0.16
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (48 bp):
TGCCTTCCATCCGGGAAGGGCGTTTTAGAAAAAAAAGGTAAAAATCAA
Found at i:13286 original size:49 final size:49
Alignment explanation
Indices: 13132--13718 Score: 529
Period size: 49 Copynumber: 11.9 Consensus size: 49
13122 GAGTAAAACT
* * * * * *
13132 AATGCCTTCCATCCGGGAAGGGCGTTTTAGGAAA-AACAGGTAAAAATC
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * * *
13180 AGTGCCTTCCGTCCGGGAAGGGCGTTTTGAGAAA-AACAAGTAATGATT
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * *
13228 AGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAAGTAAAGATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * *
13277 AATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAGATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * * *
13326 AATGTCTTCCGTCTGGGAAAGGCGTTTTGAGAAATAGCAAGTAAAGATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * *
13375 AATGGCTTCTGTCTGTGAAGGGCGCTTTGGGAAATAACAAGTAAAGATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * *
13424 AATGGCTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGCAAGTAAAGATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * * * * *
13473 AATGGTTTCTGTCTGGGAAGAGCGCTTTGGGAAATAGCAAGTAAAAATG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
* * * *
13522 AATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAA-AAGAAAATAAAAATTG
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAA-CAAGTAAAGA-TG
* * * * ** * *
13572 AGTGCCTTCTGTCCGGGACGGGCGTTTTGGGGAAA-AGTTAA-TAAAAATA
1 AATGGCTTCCGTCCGGGAAGGGCGTTTT-GGGAAATA-ACAAGTAAAGATG
* * * * * * *
13621 AACGCCTTCCATCCGGGAAGGGCGTTCTGGGAAA-AAGCGAGTAAAAATTA
1 AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAA-CAAGTAAAGA-TG
* *
13671 AATAGCGCCTTCCGTCCGGGAAGGGTGTTTTGGGAAATAGCAAGTAAA
1 AAT-G-G-CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAA
13719 AACTGAAAGC
Statistics
Matches: 454, Mismatches: 73, Indels: 19
0.83 0.13 0.03
Matches are distributed among these distances:
48 81 0.18
49 294 0.65
50 35 0.08
51 10 0.02
53 33 0.07
54 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.24
Consensus pattern (49 bp):
AATGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATG
Found at i:18359 original size:172 final size:173
Alignment explanation
Indices: 18148--18479 Score: 553
Period size: 172 Copynumber: 1.9 Consensus size: 173
18138 TAAAAGTGGG
*
18148 AAAAATAAAATAATTATAAAAATATTGAATCTAATTAAATTAAAATAGAGTTTTTAGTAAAATAA
1 AAAAATAAAATAATTATAAAAATATTGAATCTAATTAAATGAAAATAGAGTTTTTAGTAAAATAA
*
18213 AACTGTATATTAA-AATATTTTAATATATCCAAGCTTTTAATAAAAAATAGTAAAATGGTAAAAA
66 AACTGTATATTAATAA-ACTTTAATATATCCAAGCTTTTAATAAAAAATAGTAAAATGGTAAAAA
18277 TAAAGTAACT-ATAAAAATATTAGATTTAATTCCTTTTTAAATTT
130 TAAAGTAA-TAATAAAAATATTAGATTTAATTCCTTTTTAAATTT
* * *
18321 AAAAATAAAATAATTAT-AAAATATTGAATTTAATTAAATGAAAATGGAGTTTTTAGTTAAATAA
1 AAAAATAAAATAATTATAAAAATATTGAATCTAATTAAATGAAAATAGAGTTTTTAGTAAAATAA
* *
18385 AACTGTATATTAATAAACTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGTAAAAAT
66 AACTGTATATTAATAAACTTTAATATATCCAAGCTTTTAATAAAAAATAGTAAAATGGTAAAAAT
*
18450 AAAGTAATAATAAAGATATTAGATTTAATT
131 AAAGTAATAATAAAAATATTAGATTTAATT
18480 AAATAAAAAT
Statistics
Matches: 149, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
171 1 0.01
172 129 0.87
173 19 0.13
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (173 bp):
AAAAATAAAATAATTATAAAAATATTGAATCTAATTAAATGAAAATAGAGTTTTTAGTAAAATAA
AACTGTATATTAATAAACTTTAATATATCCAAGCTTTTAATAAAAAATAGTAAAATGGTAAAAAT
AAAGTAATAATAAAAATATTAGATTTAATTCCTTTTTAAATTT
Found at i:21291 original size:6 final size:6
Alignment explanation
Indices: 21286--21315 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21276 TGTTGTTGGT
*
21286 GGTGGT GGTGGA GGTGGA GGTGGA GGTGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
21316 ATCAGAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.67, T:0.20
Consensus pattern (6 bp):
GGTGGA
Found at i:23239 original size:42 final size:42
Alignment explanation
Indices: 23180--23267 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
23170 AGAGAAGGCA
*
23180 AACACAGCAAAAATTTTCAACTCTCTTGTATTGATTTCTGAT
1 AACACAACAAAAATTTTCAACTCTCTTGTATTGATTTCTGAT
*
23222 AACACAACAAATATTTTCAACTCTCTTGTATTGATTTCTGAT
1 AACACAACAAAAATTTTCAACTCTCTTGTATTGATTTCTGAT
23264 AACA
1 AACA
23268 AGTTAGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (42 bp):
AACACAACAAAAATTTTCAACTCTCTTGTATTGATTTCTGAT
Done.