Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014557.1 Corchorus olitorius cultivar O-4 contig14590, 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: 38836
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1009 original size:15 final size:15
Alignment explanation
Indices: 968--1013 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
958 TTTGACAGTG
*
968 ATAATTGTGATAATT
1 ATAATTATGATAATT
*
983 AT-A-TAAGATAATT
1 ATAATTATGATAATT
*
996 ATAATTTTGATAATT
1 ATAATTATGATAATT
1011 ATA
1 ATA
1014 TATGCTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (15 bp):
ATAATTATGATAATT
Found at i:8308 original size:12 final size:12
Alignment explanation
Indices: 8291--8324 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
8281 ACCTTTCCTC
8291 TCCTTGATTTTT
1 TCCTTGATTTTT
8303 TCCTTGATTTTT
1 TCCTTGATTTTT
*
8315 TCTTTGATTT
1 TCCTTGATTT
8325 CTTGAACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.15, G:0.09, T:0.68
Consensus pattern (12 bp):
TCCTTGATTTTT
Found at i:30394 original size:31 final size:33
Alignment explanation
Indices: 30328--30404 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 33
30318 TTCTTTTTAT
*
30328 TCAAATTGCAACTTAAACTTGTAAATAATTAGTA
1 TCAAATTGCACCTTAAACTTGT-AATAATTAGTA
* *
30362 TCAAATTGCACCTTAAATTTGT-AT-TTTAGTA
1 TCAAATTGCACCTTAAACTTGTAATAATTAGTA
*
30393 TCAAATAGCACC
1 TCAAATTGCACC
30405 CTGCACATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 17 0.44
32 2 0.05
34 20 0.51
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (33 bp):
TCAAATTGCACCTTAAACTTGTAATAATTAGTA
Found at i:32939 original size:13 final size:13
Alignment explanation
Indices: 32921--32950 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
32911 CTTGAACTTG
32921 AACTATATATAAA
1 AACTATATATAAA
32934 AACTATATATAAA
1 AACTATATATAAA
32947 AACT
1 AACT
32951 TTTTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (13 bp):
AACTATATATAAA
Found at i:34645 original size:42 final size:42
Alignment explanation
Indices: 34586--34667 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
34576 CGGCCAACCC
34586 TAAACCATGTAACATTAGCGAGAGTTTAAATATTTCCCTCCT
1 TAAACCATGTAACATTAGCGAGAGTTTAAATATTTCCCTCCT
34628 TAAACCATGTAACATTAGCGAGAGTTTAAATATTTCCCTC
1 TAAACCATGTAACATTAGCGAGAGTTTAAATATTTCCCTC
34668 GTTTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (42 bp):
TAAACCATGTAACATTAGCGAGAGTTTAAATATTTCCCTCCT
Found at i:37695 original size:58 final size:58
Alignment explanation
Indices: 37600--37716 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
37590 ACGATTTGGC
*
37600 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAA
1 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAGTGAAAAAACCATCAAAAA
* *
37658 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAGTGAAAAAACCTTTAAAAA
1 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAGTGAAAAAACCATCAAAAA
37716 A
1 A
37717 AAGTTTATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.17
Consensus pattern (58 bp):
ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAGTGAAAAAACCATCAAAAA
Found at i:38350 original size:333 final size:332
Alignment explanation
Indices: 37741--38836 Score: 1689
Period size: 334 Copynumber: 3.3 Consensus size: 332
37731 AAGTTTTTTT
*
37741 GAAGCGTAAAAAGCCCTTCAATATTTTAGGCATTGAATTATATATTTTTGTGAGTATTGTGGCAA
1 GAAGCGTAAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTGTGAGTATTGTGGCAA
* * *
37806 AAAATGGAGGAAAGAATTTTCGGGTCAGTTTTTTCAAAAATTTCAACCGAAATCGTGTACTAACC
66 AAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACC
* * *
37871 ATCATGATTTTTGGCTAAAAAAGCGCTA-TGGGACCCCGGCTCAGTTTTGCATGATTTTTAGTGC
131 ATCATGATTTTTGGCTAAAAATGCGCTATTGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGTTC
* * * *
37935 CAAGACTCCTTGAAATATCTTTAGTCATTTAACCAAATCTCAGTCGCAATGGGTTTAAGGATTTG
195 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTG
* * * *
38000 TTTTTACGAGTATCTGAATCATGTTCCGATTTACTTAAAAAATAATTTGGAAAAATTTTGAAAAA
260 TTTTTGCGAGCATCTGAATCATGTTCCGATTTAATTAAAAATTAATTTGGAAAAATTTTGAAAAA
38065 CGATATTA
325 CGATATTA
* *
38073 GAAGCGTAAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCA
1 GAAGCGTAAAAAGCCCTTCAATATTTTTGGCATTGAATTATATA-TTTTTGTGAGTATTGTGGCA
** *
38138 AAAAATGGAGGAAAAAATTTTCGAATTAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
65 AAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
* * * * *
38203 CATCATGATTTTTGCCTAAAAATGCGCTATTGTGCCACGGCTAAGTTTTGCATTATTTTTGGTTC
130 CATCATGATTTTTGGCTAAAAATGCGCTATTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTTC
* * *
38268 CAAAACTCCTTGATATATCTTTATTCATCTAACCAAATCCCAGCCGCAATGGATTTAAGGATTTG
195 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTG
* **
38333 TTTTTGCGAGCATCTGAATCATGTTCCGATTTTAGTTAAAAATTAATTTGGAAAAATTTTGAAGG
260 TTTTTGCGAGCATCTGAATCATGTTCCGA-TTTAATTAAAAATTAATTTGGAAAAATTTTGAAAA
38398 ACGATATTA
324 ACGATATTA
38407 GAAGCGTAAAAA-CCCTTCAAT-TATTTTGGCATTGAATTATATAATTTTTTGTGAGTATTGTGG
1 GAAGCGTAAAAAGCCCTTCAATAT-TTTTGGCATTGAATTATAT-A-TTTTTGTGAGTATTGTGG
*
38470 CAAAAAATGGAGTAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTA
63 CAAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTA
*
38535 ACCATCATGATTTTTGGCTAAAAATGCGCTATGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGT
128 ACCATCATGATTTTTGGCTAAAAATGCGCTATTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGT
38600 GT-CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGAT
193 -TCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGAT
* * * *
38664 TTGCTTTTGCGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATTTCGA
257 TTGTTTTTGCGAGCATCTGAATCATGTTCCGATTTAATTAAAAATTAATTTGG-AAAAATTTTGA
38729 AAAACGATATTA
321 AAAACGATATTA
* * *
38741 GAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTGTGAGTATTGTGGCCA
1 GAAGCGTAAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTGTGAGTATTGTGGCAA
* * *
38806 AAAGTTGAGG-AAAAATGTTTTGGGTCAGTTT
66 AAAATGGAGGAAAAAAT-TTTCGGGTCAGTTT
Statistics
Matches: 696, Mismatches: 58, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
332 49 0.07
333 303 0.44
334 315 0.45
335 28 0.04
336 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (332 bp):
GAAGCGTAAAAAGCCCTTCAATATTTTTGGCATTGAATTATATATTTTTGTGAGTATTGTGGCAA
AAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACC
ATCATGATTTTTGGCTAAAAATGCGCTATTGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTTCC
AAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTGT
TTTTGCGAGCATCTGAATCATGTTCCGATTTAATTAAAAATTAATTTGGAAAAATTTTGAAAAAC
GATATTA
Done.