Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014854.1 Corchorus olitorius cultivar O-4 contig14887, 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: 24201
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:541 original size:13 final size:13
Alignment explanation
Indices: 523--547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
513 TTTTTCTCTT
523 TTTTATTTATTTA
1 TTTTATTTATTTA
536 TTTTATTTATTT
1 TTTTATTTATTT
548 TTTATTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:1672 original size:42 final size:42
Alignment explanation
Indices: 1624--1710 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
1614 AAATGCAATC
1624 TAATGAGACAAGGTAAGACAATGCCAATATAACTAAAATGGG
1 TAATGAGACAAGGTAAGACAATGCCAATATAACTAAAATGGG
1666 TAATGAGACAAGGTAAGACAATGCCAATATAACTAAAATGGG
1 TAATGAGACAAGGTAAGACAATGCCAATATAACTAAAATGGG
1708 TAA
1 TAA
1711 CATTTATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (42 bp):
TAATGAGACAAGGTAAGACAATGCCAATATAACTAAAATGGG
Found at i:12480 original size:18 final size:18
Alignment explanation
Indices: 12457--12515 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
12447 TAATTTGGAA
12457 TTATTTATGATTTGGGCT
1 TTATTTATGATTTGGGCT
*
12475 TTATTTACT-ACTTGGGCTT
1 TTATTTA-TGATTTGGGC-T
*
12494 TTATTTATGCATTTGGGTT
1 TTATTTATG-ATTTGGGCT
12513 TTA
1 TTA
12516 CATTGCTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 15 0.44
19 13 0.38
20 6 0.18
ACGTcount: A:0.17, C:0.08, G:0.19, T:0.56
Consensus pattern (18 bp):
TTATTTATGATTTGGGCT
Found at i:12694 original size:2 final size:2
Alignment explanation
Indices: 12687--12724 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12677 ATTTCTTGTG
12687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12725 TACTATGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13500 original size:36 final size:36
Alignment explanation
Indices: 13419--13589 Score: 202
Period size: 36 Copynumber: 4.8 Consensus size: 36
13409 TGTTCAATTT
* * *
13419 AGTTTTCAAATAGGGAAAGTTCCCACCAGGTTT-T-
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTCTA
* *
13453 AGTTTTCAAGTTGGGAAAGTTCCCAACAAGTTTCTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTCTA
* * *
13489 AGTTTTCAAGTTGGGAAAGATCCCATCAAGTTTTTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTCTA
* * * *
13525 AGTTTTCAAATTGGGATAGTTCCTATTCAATTTTCAA
1 AGTTTTCAAATTGGGAAAGTTCCCA-TCAAGTTTCTA
*
13562 AGTTTTTAAATTGGGAAAGTTCCCATCA
1 AGTTTTCAAATTGGGAAAGTTCCCATCA
13590 GGTTGTAGTT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
34 29 0.25
35 1 0.01
36 57 0.49
37 30 0.26
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (36 bp):
AGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTCTA
Found at i:13586 original size:73 final size:71
Alignment explanation
Indices: 13419--13617 Score: 222
Period size: 72 Copynumber: 2.8 Consensus size: 71
13409 TGTTCAATTT
* * *
13419 AGTTTTCAAATAGGGAAAGTTCCCA-CCAGGTTTTAGTTTTCAAGTTGGGAAAGTTCCCAACAAG
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
*
13483 TTTCTA
66 TTTCAA
* * * * * *
13489 AGTTTTCAAGTTGGGAAAGATCCCATCAAGTTTTTAAGTTTTCAAATTGGGATAGTTCCTATTCA
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGGTTTT-AGTTTTCAAATTGGGAAAGTTCCCA-ACA
*
13554 ATTTTCAA
64 AGTTTCAA
* * * *
13562 AGTTTTTAAATTGGGAAAGTTCCCATC-AGGTTGTAGTTTTCGATTTAGGGAAAGTT
1 AGTTTTCAAATTGGGAAAGTTCCCATCAAGGTTTTAGTTTTCAAATT-GGGAAAGTT
13618 TCCGTCATTT
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
70 22 0.21
71 17 0.16
72 35 0.33
73 32 0.30
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (71 bp):
AGTTTTCAAATTGGGAAAGTTCCCATCAAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
TTTCAA
Found at i:19026 original size:25 final size:25
Alignment explanation
Indices: 18998--19049 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
18988 CGAGCAAAGA
*
18998 AAATTACCCCTTAACATGCCTATTT
1 AAATTACCCCTTAACATGCCTAATT
19023 AAATTACCCCTTAACATGCCTAATT
1 AAATTACCCCTTAACATGCCTAATT
19048 AA
1 AA
19050 TTTTTTGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATTACCCCTTAACATGCCTAATT
Found at i:19940 original size:21 final size:22
Alignment explanation
Indices: 19900--19940 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19890 GACAAACTCG
*
19900 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
19922 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
19941 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Done.