Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015134.1 Corchorus olitorius cultivar O-4 contig15167, 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: 40890
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:132 original size:24 final size:24
Alignment explanation
Indices: 97--142 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
87 AAATTGTATT
97 ACGGCGTCTAGACGCCGCTATATG
1 ACGGCGTCTAGACGCCGCTATATG
* *
121 ACGGCGTTTAGACGCCGTTATA
1 ACGGCGTCTAGACGCCGCTATA
143 CAGATAGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (24 bp):
ACGGCGTCTAGACGCCGCTATATG
Found at i:728 original size:16 final size:16
Alignment explanation
Indices: 703--733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
693 TCTGTTTTTT
*
703 GTTTTTGTTTTGTTTC
1 GTTTTCGTTTTGTTTC
719 GTTTTCGTTTTGTTT
1 GTTTTCGTTTTGTTT
734 TTGTTACGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.74
Consensus pattern (16 bp):
GTTTTCGTTTTGTTTC
Found at i:6543 original size:106 final size:108
Alignment explanation
Indices: 6353--6569 Score: 332
Period size: 106 Copynumber: 2.0 Consensus size: 108
6343 GAAGTGTACA
* *
6353 AACTTGGTATGTCCAATTTGCTAATTTTAGTCTGTTTAAAGCATAATAATTTTTTGCATTTCTAA
1 AACTTGGTATGTCCAATTTGCCAATTGTAG-CTGTTTAAAGC--AATAATTTTTTGCATTTCTAA
*
6418 AAGGTAGCCTTTTGTGAATGTATGGCTTC-AGAATTTTAAGTTCTTT
63 AAGGTAGCCTTTTGTGAATGTATGGCATCTA-AATTTTAAGTTCTTT
* *
6464 AACTTGGTATGTCCACTTTGCCAATTGTAG-TGTTTAAAGC-ATAATTTTTTGCCTTTCTAAAAG
1 AACTTGGTATGTCCAATTTGCCAATTGTAGCTGTTTAAAGCAATAATTTTTTGCATTTCTAAAAG
6527 GTAGCCTTTTGTGAATGTATGGCATCTAAATTTTAAGTTCTTT
66 GTAGCCTTTTGTGAATGTATGGCATCTAAATTTTAAGTTCTTT
6570 CTCTTAAGGG
Statistics
Matches: 100, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
106 62 0.62
107 1 0.01
109 10 0.10
111 27 0.27
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (108 bp):
AACTTGGTATGTCCAATTTGCCAATTGTAGCTGTTTAAAGCAATAATTTTTTGCATTTCTAAAAG
GTAGCCTTTTGTGAATGTATGGCATCTAAATTTTAAGTTCTTT
Found at i:17423 original size:25 final size:25
Alignment explanation
Indices: 17391--17444 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
17381 AATCAATTCT
17391 GCAAATCTGTCAAGCTATGATCAAG
1 GCAAATCTGTCAAGCTATGATCAAG
*
17416 GCAAATCTGTCAAGTTATGATCAAG
1 GCAAATCTGTCAAGCTATGATCAAG
17441 GCAA
1 GCAA
17445 TCAAAGCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (25 bp):
GCAAATCTGTCAAGCTATGATCAAG
Found at i:17465 original size:26 final size:24
Alignment explanation
Indices: 17401--17472 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 24
17391 GCAAATCTGT
* *
17401 CAAGCTATGATCAAGGCAAATCTGT
1 CAAGCTATGATCAAGGC-AATCAGC
*
17426 CAAGTTATGATCAAGGCAATCAAAGC
1 CAAGCTATGATCAAGGCAATC--AGC
* *
17452 CAAGCTATGGTCAATGCAATC
1 CAAGCTATGATCAAGGCAATC
17473 TGTTAAACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 4 0.10
25 16 0.41
26 19 0.49
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (24 bp):
CAAGCTATGATCAAGGCAATCAGC
Found at i:28866 original size:29 final size:30
Alignment explanation
Indices: 28834--28906 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
28824 TATGGGATTT
*
28834 ATTTGTCCCAAAA-AAAAGTTAAGAGGCCA
1 ATTTTTCCCAAAAGAAAAGTTAAGAGGCCA
* * *
28863 ATTTTTCCCAAAATGGATAGTTAAGGGGCCA
1 ATTTTTCCCAAAA-GAAAAGTTAAGAGGCCA
28894 ATTTTTCCCAAAA
1 ATTTTTCCCAAAA
28907 TGGATAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 12 0.32
31 26 0.68
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (30 bp):
ATTTTTCCCAAAAGAAAAGTTAAGAGGCCA
Found at i:28893 original size:31 final size:31
Alignment explanation
Indices: 28850--28928 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
28840 CCCAAAAAAA
*
28850 AGTTAAGAGGCCAATTTTTCCCAAAATGGAT
1 AGTTAAGGGGCCAATTTTTCCCAAAATGGAT
28881 AGTTAAGGGGCCAATTTTTCCCAAAATGGAT
1 AGTTAAGGGGCCAATTTTTCCCAAAATGGAT
*
28912 AGTTAAGGGGCTAATTT
1 AGTTAAGGGGCCAATTT
28929 GGGTATTAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (31 bp):
AGTTAAGGGGCCAATTTTTCCCAAAATGGAT
Found at i:31364 original size:48 final size:48
Alignment explanation
Indices: 31311--31449 Score: 224
Period size: 48 Copynumber: 2.9 Consensus size: 48
31301 AATCTTAAGC
*
31311 GCCAATTACCGGTCATCCAAGACTTAACTCATGGAGTGATGGATTTAA
1 GCCAATTACCGGTCATCCAAGACTTAACTCATGGAGTGATGGACTTAA
* *
31359 GCCAATTACCGATCATCCAAGACTTAACTCATGGAGTGATAGACTTAA
1 GCCAATTACCGGTCATCCAAGACTTAACTCATGGAGTGATGGACTTAA
* * *
31407 ACCAATTACCGGCCATCCAAGACTTAACTCATGGAATGATGGA
1 GCCAATTACCGGTCATCCAAGACTTAACTCATGGAGTGATGGA
31450 GTGCAAGGTC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (48 bp):
GCCAATTACCGGTCATCCAAGACTTAACTCATGGAGTGATGGACTTAA
Found at i:33342 original size:106 final size:102
Alignment explanation
Indices: 33159--33349 Score: 294
Period size: 106 Copynumber: 1.8 Consensus size: 102
33149 AGCACATAAT
*
33159 ATGAAATCGATTGTGCTATATATGTTTGCTAAAGAAAAGGCTTTATTCTATCAAATTTTTGTGGT
1 ATGAAATCAATTGTGCTATATATGTTTGCTAAAGAAAAGGCTTTATTCTATCAAATTTTTGTGGT
*
33224 AATTCCAATTCCACGATTTCTTATACACACACACGAC
66 AATTCCAATTCCACCATTTCTTATACACACACACGAC
*
33261 ATGAAATCAATTGTGCTCTATATGTTTGGGTGCTAAAGAAAAGGCTTTATT-TAATCAAATTTTT
1 ATGAAATCAATTGTGCTATATATG-TT---TGCTAAAGAAAAGGCTTTATTCT-ATCAAATTTTT
*
33325 GTGGTAATTCCAGTTCCACCATTTC
61 GTGGTAATTCCAATTCCACCATTTC
33350 CCAATCCTCT
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
102 22 0.28
103 2 0.03
105 1 0.01
106 55 0.69
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (102 bp):
ATGAAATCAATTGTGCTATATATGTTTGCTAAAGAAAAGGCTTTATTCTATCAAATTTTTGTGGT
AATTCCAATTCCACCATTTCTTATACACACACACGAC
Found at i:33771 original size:46 final size:47
Alignment explanation
Indices: 33719--33814 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
33709 AGACAACTCA
* *
33719 TTAATTTTCTAAAATTCTA-TCCCAATAAAATCTCAAATTTGGGGAC
1 TTAATTTTCTAAAATCCTACTCACAATAAAATCTCAAATTTGGGGAC
33765 TTAATTTTCTAAAATCCTACTCACAATAAAATCTCAAATTTGGGGAC
1 TTAATTTTCTAAAATCCTACTCACAATAAAATCTCAAATTTGGGGAC
33812 TTA
1 TTA
33815 CCCTTTATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 18 0.38
47 29 0.62
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (47 bp):
TTAATTTTCTAAAATCCTACTCACAATAAAATCTCAAATTTGGGGAC
Found at i:36526 original size:64 final size:63
Alignment explanation
Indices: 36452--36583 Score: 221
Period size: 64 Copynumber: 2.1 Consensus size: 63
36442 TTTTTCATAA
*
36452 ATAAACAACACTACAATTTAAATAAGGGAA-TTGATGAAATTGGGAACATATAATATAATAATAT
1 ATAAACAACACTACAATTTAAATAAGGAAATTTGATGAAATTGGGAAC--ATAATATAATAATAT
*
36516 ATAAACAACACTACAATTTAAATAAGGAAATTTGATGAAATTGGGAACATAATATAGTAATAT
1 ATAAACAACACTACAATTTAAATAAGGAAATTTGATGAAATTGGGAACATAATATAATAATAT
36579 ATAAA
1 ATAAA
36584 TTATTGAGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
63 19 0.29
64 29 0.45
65 17 0.26
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (63 bp):
ATAAACAACACTACAATTTAAATAAGGAAATTTGATGAAATTGGGAACATAATATAATAATAT
Done.