Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016290.1 Corchorus olitorius cultivar O-4 contig16323, 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: 15415
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:37 original size:30 final size:31
Alignment explanation
Indices: 1--58 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1 TCCCTTATG-TTTTTCTTTTGGGACAAAAAA
1 TCCCTTATGATTTTTCTTTTGGGACAAAAAA
31 TCCCTTATGATTTTTCTTTTGGGACAAA
1 TCCCTTATGATTTTTCTTTTGGGACAAA
59 TCAGTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (31 bp):
TCCCTTATGATTTTTCTTTTGGGACAAAAAA
Found at i:224 original size:29 final size:32
Alignment explanation
Indices: 182--260 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 32
172 CTCATTTTTG
* *
182 AAACGTAAGGGATTTA-TTTATCCC-GAAA-A
1 AAACATAAGGGATTTATTTTATCCCAAAAACA
*
211 AAACATAAGGGA-TTATTTTGTCCCAAAAACA
1 AAACATAAGGGATTTATTTTATCCCAAAAACA
242 AAACATAAGGGATTT-TTTT
1 AAACATAAGGGATTTATTTT
261 GGGTATTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 3 0.07
29 18 0.42
30 3 0.07
31 17 0.40
32 2 0.05
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (32 bp):
AAACATAAGGGATTTATTTTATCCCAAAAACA
Found at i:4897 original size:27 final size:27
Alignment explanation
Indices: 4867--4920 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4857 ATAGTAATTC
4867 ACTCTAGTTATTTTTCCTAGTTATTTT
1 ACTCTAGTTATTTTTCCTAGTTATTTT
4894 ACTCTAGTTATTTTTCCTAGTTATTTT
1 ACTCTAGTTATTTTTCCTAGTTATTTT
4921 TAGATTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (27 bp):
ACTCTAGTTATTTTTCCTAGTTATTTT
Found at i:4921 original size:14 final size:13
Alignment explanation
Indices: 4870--4921 Score: 86
Period size: 13 Copynumber: 3.9 Consensus size: 13
4860 GTAATTCACT
4870 CTAGTTATTTTTC
1 CTAGTTATTTTTC
*
4883 CTAGTTATTTTAC
1 CTAGTTATTTTTC
4896 TCTAGTTATTTTTC
1 -CTAGTTATTTTTC
4910 CTAGTTATTTTT
1 CTAGTTATTTTT
4922 AGATTCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 24 0.67
14 12 0.33
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.62
Consensus pattern (13 bp):
CTAGTTATTTTTC
Found at i:9108 original size:20 final size:20
Alignment explanation
Indices: 9106--9143 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9096 AAAGAAAATA
9106 AAAATAAAAATCAGAAAAAG
1 AAAATAAAAATCAGAAAAAG
9126 AAAATAAAAATCAGAAAA
1 AAAATAAAAATCAGAAAA
9144 TCAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (20 bp):
AAAATAAAAATCAGAAAAAG
Found at i:9121 original size:26 final size:27
Alignment explanation
Indices: 9076--9150 Score: 116
Period size: 26 Copynumber: 2.7 Consensus size: 27
9066 AAAAATAATT
9076 TAAAAATAAAAAAATCAGAAAAAGAAAA
1 TAAAAAT-AAAAAATCAGAAAAAGAAAA
9104 TAAAAAT-AAAAATCAGAAAAAGAAAA
1 TAAAAATAAAAAATCAGAAAAAGAAAA
*
9130 TAAAAATCAGAAAATCAGAAA
1 TAAAAAT-AAAAAATCAGAAA
9151 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 26 0.59
28 18 0.41
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.12
Consensus pattern (27 bp):
TAAAAATAAAAAATCAGAAAAAGAAAA
Found at i:10011 original size:34 final size:36
Alignment explanation
Indices: 9964--10040 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 36
9954 GGAAAATGAG
9964 TTTGGGTTCGAGTTT-AG-AGAGTGAATATGGTGAT
1 TTTGGGTTCGAGTTTAAGAAGAGTGAATATGGTGAT
* *
9998 TTTGGGTTTGAGTTTAGAGAAAGAGTGAATCTGGTGAT
1 TTTGGGTTCGAGTTTA-AG-AAGAGTGAATATGGTGAT
10036 TTTGG
1 TTTGG
10041 TGTGTTTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.38
36 2 0.05
38 21 0.57
ACGTcount: A:0.23, C:0.03, G:0.35, T:0.39
Consensus pattern (36 bp):
TTTGGGTTCGAGTTTAAGAAGAGTGAATATGGTGAT
Found at i:10206 original size:17 final size:17
Alignment explanation
Indices: 10184--10216 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10174 GAAAAGAAGG
10184 TTTTTTAATTTTCTGAT
1 TTTTTTAATTTTCTGAT
10201 TTTTTTAATTTTCTGA
1 TTTTTTAATTTTCTGA
10217 GAAGAGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTTTAATTTTCTGAT
Found at i:14199 original size:218 final size:213
Alignment explanation
Indices: 13688--14307 Score: 589
Period size: 218 Copynumber: 2.9 Consensus size: 213
13678 TAATATCATT
* ** * * * *
13688 CAATCATGCGACATTTTTTAATTAACGTCGCCTTAAGATAGGCTTTTCCAACATTTATAACAATT
1 CAATCATGCAACATTTTTTAACAAACATCGCTTTAAGATAGACTTTTCCGACATTTATAACAA-T
* * * * * * * *
13753 TTTTAAGGAATCATCG-TTTAATAAATTACATTTTAATAAATC-TCACAACATCTTGCGACTCCT
65 GTTTAAGGAAACGTCGTTTTAATATATGACATTTTAATAAA-CGTCACAATACCTTGCGACTCAT
* *** ** * *
13816 TTTAAAATTGAGTGACGTTTTTTAATTGTGTCACTCTTGTTTATACTTTTGCGATGTTTGCAGTG
129 TTTTAAATTGAGTGACGTTTTTTAATAACGTCACTCCAGTTTATACTTTTGCGACGTTTGCAGAG
* *
13881 ACGTTTTCTCAAATATCGTT
194 ACGTTTTCTCAAACATCGTC
* * * * * **
13901 CAATTATGCAACATTTTTCAACAAACATCACTTTTAAGATAGACTTTTTCGATATTTATAACGGT
1 CAATCATGCAACATTTTTTAACAAACATCGC-TTTAAGATAGACTTTTCCGACATTTATAACAAT
** * *
13966 GTTTTTCGAAAACGTCGTTTTAATATATGACATTTTAATAAACGTCACATTACCTTGCGACTCAT
65 G-TTTAAGGAAACGTCGTTTTAATATATGACATTTTAATAAACGTCACAATACCTTGCGACTCAT
* * * *
14031 TTTTAAATAGAGTGACATTTTTTTTTAATAACGTCACTCCAGTTTA-AGTTTTTGCGACGTTTGT
129 TTTTAAATTGAGTGAC---GTTTTTTAATAACGTCACTCCAGTTTATA-CTTTTGCGACGTTTGC
*
14095 AGAGACGTTTTTCTCAAACGTCGTC
190 AGAGACG-TTTTCTCAAACATCGTC
*** * *
14120 CAATCATGCATTTTTTTTTTAACAAACATCGCTTTAAGATAGACTTCTCCGACATTTATAACAAC
1 CAATCATGCA-ACATTTTTTAACAAACATCGCTTTAAGATAGACTTTTCCGACATTTATAACAAT
* * * * * *
14185 GTTTAGGGAAACGTCGTTTTAAAATATGACATTTTAATAAATGCCGCAATACCTTGCGACTCTTT
65 GTTTAAGGAAACGTCGTTTTAATATATGACATTTTAATAAACGTCACAATACCTTGCGACTCATT
* * * ** * * *
14250 TTTAATTTGAGTGATGTTTTTTAATAATGTTGCTCTAGTTTATGCTTTTGCAACGTTT
130 TTTAAATTGAGTGACGTTTTTTAATAACGTCACTCCAGTTTATACTTTTGCGACGTTT
14308 ATCTCAAAAG
Statistics
Matches: 323, Mismatches: 73, Indels: 20
0.78 0.18 0.05
Matches are distributed among these distances:
213 25 0.08
214 36 0.11
215 87 0.27
217 1 0.00
218 107 0.33
219 51 0.16
220 16 0.05
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (213 bp):
CAATCATGCAACATTTTTTAACAAACATCGCTTTAAGATAGACTTTTCCGACATTTATAACAATG
TTTAAGGAAACGTCGTTTTAATATATGACATTTTAATAAACGTCACAATACCTTGCGACTCATTT
TTAAATTGAGTGACGTTTTTTAATAACGTCACTCCAGTTTATACTTTTGCGACGTTTGCAGAGAC
GTTTTCTCAAACATCGTC
Done.