Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021541.1 Corchorus olitorius cultivar O-4 contig21574, 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: 45252
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6620 original size:63 final size:63
Alignment explanation
Indices: 6550--6673 Score: 239
Period size: 63 Copynumber: 2.0 Consensus size: 63
6540 TTTTTACGAT
6550 AATATTATCGGTCACTTGATTTTTTGTTTATAGCATCATAACCTTTAAACCTCTACTCTAAAA
1 AATATTATCGGTCACTTGATTTTTTGTTTATAGCATCATAACCTTTAAACCTCTACTCTAAAA
*
6613 AATATTATTGGTCACTTGATTTTTTGTTTATAGCATCATAACCTTTAAACCTCTACTCTAA
1 AATATTATCGGTCACTTGATTTTTTGTTTATAGCATCATAACCTTTAAACCTCTACTCTAA
6674 CCTTTTTTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.43
Consensus pattern (63 bp):
AATATTATCGGTCACTTGATTTTTTGTTTATAGCATCATAACCTTTAAACCTCTACTCTAAAA
Found at i:13082 original size:105 final size:106
Alignment explanation
Indices: 12903--13164 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 106
12893 AATTTTTCTA
* ** *
12903 ACCCTTAAAATAAAATTTTAATTTTAATTT-GTGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
12966 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
13006 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
13071 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* *
13113 ACCCTTAAAATAAAAATAAAATATTAATTTGAGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
13165 AGGCTAAACT
Statistics
Matches: 145, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 37 0.26
107 67 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:13200 original size:10 final size:10
Alignment explanation
Indices: 13187--13216 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13177 ATAAAAAAAT
13187 AAAAAAAGAA
1 AAAAAAAGAA
13197 AAAAAAAGAA
1 AAAAAAAGAA
*
13207 AAAAAGAGAA
1 AAAAAAAGAA
13217 GAGAAGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:13223 original size:18 final size:18
Alignment explanation
Indices: 13179--13213 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13169 TAAACTTAAT
*
13179 AAAAAAATAAAAAAAGAA
1 AAAAAAAGAAAAAAAGAA
13197 AAAAAAAGAAAAAAAGA
1 AAAAAAAGAAAAAAAGA
13214 GAAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAGAA
Found at i:13309 original size:23 final size:24
Alignment explanation
Indices: 13283--13332 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
13273 AATTCACTGT
*
13283 TAATTGGGTGAC-G-TGTCAAGCAA
1 TAATTGGG-GACAGATGTCAAACAA
*
13306 TAATTTGGGACAGATGTCAAACAA
1 TAATTGGGGACAGATGTCAAACAA
13330 TAA
1 TAA
13333 GTTAGGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 8 0.35
24 12 0.52
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (24 bp):
TAATTGGGGACAGATGTCAAACAA
Found at i:13700 original size:157 final size:157
Alignment explanation
Indices: 13503--13814 Score: 520
Period size: 157 Copynumber: 2.0 Consensus size: 157
13493 CATGTATTTT
* *
13503 TATTATTATATTCATGTATTTTTATTATATTCTTCAATCTCTTAATATACCCTAATCTAAATTGA
1 TATTATTATATTCATATATTTTTATTATATTCTTCAATCTCTTAATATACCCTAATCCAAATTGA
13568 AATTTCACGAAGAAAAAAACGTTAAGGTTACAAATTGAAATTCCAAGTTCAAA-TAAAATTCCAA
66 AATTTCACGAAGAAAAAAACGTTAAGGTTACAAATTGAAATTCCAAGTTCAAATTAAAATTCCAA
*
13632 TACTAAAAAAAA-GTGAAGGAATACCATG
131 TA--AAAAAAAATGTGAAGGAACACCATG
*
13660 TATTTTTATATTCATATATTTTTATTATATTCTTCAATCTCTTAATATACCCTAATCCAAATTGA
1 TATTATTATATTCATATATTTTTATTATATTCTTCAATCTCTTAATATACCCTAATCCAAATTGA
* * * *
13725 AATTTCATGAAGAAAAAAACGTTGAGGTTACAAATTGAAATTCCAAGTTCAAATTGAAATTCTAA
66 AATTTCACGAAGAAAAAAACGTTAAGGTTACAAATTGAAATTCCAAGTTCAAATTAAAATTCCAA
13790 TAAAAAAAAATGTGAAGGAACACCA
131 TAAAAAAAAATGTGAAGGAACACCA
13815 ACAAATTCAA
Statistics
Matches: 145, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
156 8 0.06
157 126 0.87
158 11 0.08
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (157 bp):
TATTATTATATTCATATATTTTTATTATATTCTTCAATCTCTTAATATACCCTAATCCAAATTGA
AATTTCACGAAGAAAAAAACGTTAAGGTTACAAATTGAAATTCCAAGTTCAAATTAAAATTCCAA
TAAAAAAAAATGTGAAGGAACACCATG
Found at i:13988 original size:21 final size:21
Alignment explanation
Indices: 13959--14003 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13949 AATCGCACAA
13959 TCAGGGTTTC-ACAAATTGACT
1 TCAGGGTTTCAAC-AATTGACT
* *
13980 TCAGTGTTTCAACAATTGGCT
1 TCAGGGTTTCAACAATTGACT
14001 TCA
1 TCA
14004 CGAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
TCAGGGTTTCAACAATTGACT
Found at i:15467 original size:11 final size:11
Alignment explanation
Indices: 15451--15485 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
15441 TTTTTTGTAA
15451 TTAGAAGAGTT
1 TTAGAAGAGTT
15462 TTAGAAGAGTT
1 TTAGAAGAGTT
*
15473 TTAGAAGGGTT
1 TTAGAAGAGTT
15484 TT
1 TT
15486 GTTTTGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (11 bp):
TTAGAAGAGTT
Found at i:21680 original size:18 final size:18
Alignment explanation
Indices: 21657--21699 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
21647 GACTATTGCC
21657 TTGCTTTGATAAATATGA
1 TTGCTTTGATAAATATGA
*
21675 TTGCTTTGATAAATATTA
1 TTGCTTTGATAAATATGA
21693 TTG-TTTG
1 TTGCTTTG
21700 TGATGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (18 bp):
TTGCTTTGATAAATATGA
Found at i:36431 original size:2 final size:2
Alignment explanation
Indices: 36424--36460 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36414 TCGCCAACTT
36424 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
36461 CTTCTTGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40584 original size:27 final size:27
Alignment explanation
Indices: 40560--40632 Score: 146
Period size: 27 Copynumber: 2.7 Consensus size: 27
40550 TGTGAACTTA
40560 AAATGACTAAAATGCCCCTGAAACTGC
1 AAATGACTAAAATGCCCCTGAAACTGC
40587 AAATGACTAAAATGCCCCTGAAACTGC
1 AAATGACTAAAATGCCCCTGAAACTGC
40614 AAATGACTAAAATGCCCCT
1 AAATGACTAAAATGCCCCT
40633 AGATTCTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAAACTGC
Done.