Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019782.1 Corchorus olitorius cultivar O-4 contig19815, 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: 16838
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:4521 original size:16 final size:17
Alignment explanation
Indices: 4500--4533 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4490 ATACGTATAA
*
4500 ATTATAT-TTAATAAAT
1 ATTATATATTAACAAAT
4516 ATTATATATTAACAAAT
1 ATTATATATTAACAAAT
4533 A
1 A
4534 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATTAACAAAT
Found at i:8854 original size:84 final size:84
Alignment explanation
Indices: 8709--8871 Score: 222
Period size: 84 Copynumber: 1.9 Consensus size: 84
8699 TTTGCTTGTG
* * ** * * *
8709 AGTTCAATCAAAATTCTAATTTTTTCTTTTTCTTAATTTTACACCAGCAACTTTTTTACATT-T-
1 AGTTCAATCAAAATGCTAATTTTTACTTTTTCTTAATTCCACACCAACAACTTCTTAACATTATA
8772 TATATAAACTTACTTTGCA
66 TATATAAACTTACTTTGCA
8791 AGTTCAATCAAAATGCTAATCTTTTACTTTTTTCTTAATTCCACACCAACAACTTCTTAACATTA
1 AGTTCAATCAAAATGCTAAT-TTTTAC-TTTTTCTTAATTCCACACCAACAACTTCTTAACATTA
*
8856 TATATATATACTTACT
64 TATATATAAACTTACT
8872 CGTTTGTCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 19 0.28
83 5 0.07
84 31 0.45
85 1 0.01
86 13 0.19
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (84 bp):
AGTTCAATCAAAATGCTAATTTTTACTTTTTCTTAATTCCACACCAACAACTTCTTAACATTATA
TATATAAACTTACTTTGCA
Found at i:12377 original size:51 final size:51
Alignment explanation
Indices: 12321--12421 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
12311 CATATTTTTT
* *
12321 TTGTTT-AGATCTTGTCTCAGGACA-ATCAAACACTCTTTTAGTGTTTTTCTC
1 TTGTTTCA-ATCTTGTCTCAGGACATA-AAAACACTCTATTAGTGTTTTTCTC
* * *
12372 TTGTTTCAATCTTGTCTCCGGACATAAAAACACTGTATTCGTGTTTTTCT
1 TTGTTTCAATCTTGTCTCAGGACATAAAAACACTCTATTAGTGTTTTTCT
12422 TTCAGAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (51 bp):
TTGTTTCAATCTTGTCTCAGGACATAAAAACACTCTATTAGTGTTTTTCTC
Found at i:15241 original size:87 final size:87
Alignment explanation
Indices: 15083--15249 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 87
15073 ATTGAATGTG
* * * ** *
15083 ATCTTCCTAATGGAGTTATGGGTGGTTATGGTGCAAAATCTTTGAAAAATATTATGGTAGAGGGT
1 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAATATTATGGTAGAGGAT
15148 AGTTTGAATTCAAATTTTAGTA
66 AGTTTGAATTCAAATTTTAGTA
* * *
15170 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAACTGA-TGTGGTGGAGGA
1 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAAT-ATTATGGTAGAGGA
* *
15234 TATTTTGATTTCAAAT
65 TAGTTTGAATTCAAAT
15250 CAGAGTGGTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (87 bp):
ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAATATTATGGTAGAGGAT
AGTTTGAATTCAAATTTTAGTA
Found at i:15267 original size:87 final size:87
Alignment explanation
Indices: 15083--15269 Score: 205
Period size: 87 Copynumber: 2.1 Consensus size: 87
15073 ATTGAATGTG
* * * ** *
15083 ATCTTCCTAATGGAGTTATGGGTGGTTATGGTGCAAAATCTTTGAAAAATATTATGGTAGAGGGT
1 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAATATTATGGTAGAGGAT
***
15148 AGTTTGAATTCAAATTTTAGTA
66 AGTTTGAATTCAAATCAGAGTA
* * *
15170 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAACTGA-TGTGGTGGAGGA
1 ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAAT-ATTATGGTAGAGGA
* * *
15234 TATTTTGATTTCAAATCAGAGTG
65 TAGTTTGAATTCAAATCAGAGTA
* *
15257 GTCTTGCTAATGG
1 ATCTTCCTAATGG
15270 GAATATGGCA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
87 81 0.99
88 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (87 bp):
ATCTTCCTAATGGAGTTATGGCTAGTAATAATGCAAAATCTTTGAAAAATATTATGGTAGAGGAT
AGTTTGAATTCAAATCAGAGTA
Found at i:15904 original size:15 final size:15
Alignment explanation
Indices: 15884--15922 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
15874 GGTTTGATTT
15884 TTGTTG-TTCTTTGTG
1 TTGTTGTTTC-TTGTG
15899 TTGTTGTTTCTTGTG
1 TTGTTGTTTCTTGTG
*
15914 TTGATGTTT
1 TTGTTGTTT
15923 GTTTGTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.03, C:0.05, G:0.26, T:0.67
Consensus pattern (15 bp):
TTGTTGTTTCTTGTG
Found at i:16416 original size:18 final size:18
Alignment explanation
Indices: 16393--16432 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
16383 CCATCAACTA
16393 TATAACCAATTATCAAAC
1 TATAACCAATTATCAAAC
16411 TATAACCAATTATCAAAC
1 TATAACCAATTATCAAAC
16429 TATA
1 TATA
16433 TTGTGCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (18 bp):
TATAACCAATTATCAAAC
Found at i:16696 original size:29 final size:30
Alignment explanation
Indices: 16664--16730 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
16654 ATGCAATTTG
16664 GGATATAACGTTAC-AAAACAAGCAATTAA
1 GGATATAACGTTACAAAAACAAGCAATTAA
* *
16693 GGATATAATGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAGCAATTAA
16724 GGATATA
1 GGATATA
16731 GTCCGTCAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
31 21 0.62
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAGCAATTAA
Done.