Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013740.1 Corchorus olitorius cultivar O-4 contig13773, 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: 52396
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Found at i:445 original size:68 final size:68
Alignment explanation
Indices: 349--484 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
339 AATATGTAGT
*
349 ATATATATTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAAGACAAAAAAAGTTCAAACTAA
1 ATATATATTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAAGACAAAAAAAGTTCAAACCAA
414 GCC
66 GCC
*
417 ATATATATTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAGGACAAAAAAAGTTCAAACCAA
1 ATATATATTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAAGACAAAAAAAGTTCAAACCAA
482 GCC
66 GCC
485 TCCTCCTCGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.21
Consensus pattern (68 bp):
ATATATATTTTTGGTAATTAACCAAGTGAGAAAAGACAGAAAAAGACAAAAAAAGTTCAAACCAA
GCC
Found at i:12664 original size:26 final size:26
Alignment explanation
Indices: 12635--12686 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12625 TGGACCGTGG
*
12635 GAAAAAAGTTTTAAGTAAATAAAAAT
1 GAAAAAAGTTATAAGTAAATAAAAAT
12661 GAAAAAAGTTATAAGTAAATAAAAAT
1 GAAAAAAGTTATAAGTAAATAAAAAT
12687 TAATTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (26 bp):
GAAAAAAGTTATAAGTAAATAAAAAT
Found at i:18044 original size:2 final size:2
Alignment explanation
Indices: 18037--18073 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18027 TGGTCCACAG
18037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18074 TGAAAAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22474 original size:2 final size:2
Alignment explanation
Indices: 22467--22502 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
22457 AATGAAGAAA
*
22467 AT AT AT AT AT AT AT AC 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
22503 CACATAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22897 original size:227 final size:227
Alignment explanation
Indices: 22502--22957 Score: 903
Period size: 227 Copynumber: 2.0 Consensus size: 227
22492 TATATATATA
22502 TCACATAACCTCTACATCTTTCCGAAGAAAAAGAATGGAAAGAAAATAATAATTCCATCCTTCTC
1 TCACATAACCTCTACATCTTTCCGAAGAAAAAGAATGGAAAGAAAATAATAATTCCATCCTTCTC
*
22567 TCTGTTCCCAAGAAGTTACAGGTTAACAAATTTATTAGAAGTGATAAGGTTTTAAATAAGAAACA
66 TCTGTTCCCAAGAAGTTACAGGTTAACAAATTCATTAGAAGTGATAAGGTTTTAAATAAGAAACA
22632 AGTATCTAGGGCGTTTAAAAACCTATCTCGCCATTTTTGTTGTTGCAGATTAATGATGGTTTTTC
131 AGTATCTAGGGCGTTTAAAAACCTATCTCGCCATTTTTGTTGTTGCAGATTAATGATGGTTTTTC
22697 TAGTGAAAAAAGGTGAATGTATATGATCTAGG
196 TAGTGAAAAAAGGTGAATGTATATGATCTAGG
22729 TCACATAACCTCTACATCTTTCCGAAGAAAAAGAATGGAAAGAAAATAATAATTCCATCCTTCTC
1 TCACATAACCTCTACATCTTTCCGAAGAAAAAGAATGGAAAGAAAATAATAATTCCATCCTTCTC
22794 TCTGTTCCCAAGAAGTTACAGGTTAACAAATTCATTAGAAGTGATAAGGTTTTAAATAAGAAACA
66 TCTGTTCCCAAGAAGTTACAGGTTAACAAATTCATTAGAAGTGATAAGGTTTTAAATAAGAAACA
22859 AGTATCTAGGGCGTTTAAAAACCTATCTCGCCATTTTTGTTGTTGCAGATTAATGATGGTTTTTC
131 AGTATCTAGGGCGTTTAAAAACCTATCTCGCCATTTTTGTTGTTGCAGATTAATGATGGTTTTTC
22924 TAGTGAAAAAAGGTGAATGTATATGATCTAGG
196 TAGTGAAAAAAGGTGAATGTATATGATCTAGG
22956 TC
1 TC
22958 CCAGGGATTT
Statistics
Matches: 228, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 228 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (227 bp):
TCACATAACCTCTACATCTTTCCGAAGAAAAAGAATGGAAAGAAAATAATAATTCCATCCTTCTC
TCTGTTCCCAAGAAGTTACAGGTTAACAAATTCATTAGAAGTGATAAGGTTTTAAATAAGAAACA
AGTATCTAGGGCGTTTAAAAACCTATCTCGCCATTTTTGTTGTTGCAGATTAATGATGGTTTTTC
TAGTGAAAAAAGGTGAATGTATATGATCTAGG
Found at i:27568 original size:73 final size:74
Alignment explanation
Indices: 27478--27626 Score: 246
Period size: 76 Copynumber: 2.0 Consensus size: 74
27468 CAGACTTAAA
* * *
27478 CGTGTTAACGAGTTA-TTGATAGAATTAATCTTAATATTTTCTTGAAGTAGAGTGACGTGTCATT
1 CGTGTTAACGAGTTATTTGATAGAATCAATCTTAACATTTTCTTGAAGGAGAGTGACGTGTCATT
27542 TACCCTATT
66 TACCCTATT
27551 CGTGTTAACGAGTTATTGTTGATAGAATCAATCTTAACATTTTCTTGAAGGAGAGTGACGTGTCA
1 CGTGTTAACGAGTTA-T-TTGATAGAATCAATCTTAACATTTTCTTGAAGGAGAGTGACGTGTCA
27616 TTTACCCTATT
64 TTTACCCTATT
27627 TTCAAGAAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 15 0.21
76 55 0.79
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (74 bp):
CGTGTTAACGAGTTATTTGATAGAATCAATCTTAACATTTTCTTGAAGGAGAGTGACGTGTCATT
TACCCTATT
Found at i:31084 original size:19 final size:19
Alignment explanation
Indices: 31064--31100 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31054 AATTAATTAT
31064 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
31082 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
31101 CTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:33620 original size:17 final size:17
Alignment explanation
Indices: 33598--33641 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
33588 AATTTGTTTT
33598 TGTTTTTTTTTTTAAAC
1 TGTTTTTTTTTTTAAAC
** *
33615 TGTTTTCATTTTTAATC
1 TGTTTTTTTTTTTAAAC
33632 T-TTTTTTTTT
1 TGTTTTTTTTT
33642 CTTTTGGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (17 bp):
TGTTTTTTTTTTTAAAC
Found at i:36683 original size:33 final size:34
Alignment explanation
Indices: 36646--36716 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
36636 CGGTGGTGGC
*
36646 TTTGGGAG-CTTTGGTTCAGGTCGTTCTACTGGA
1 TTTGGGAGACTTTGGTTCAGGTCATTCTACTGGA
36679 TTT-GGAGACTTTGGTTCAGGTCATTCTACTGGA
1 TTTGGGAGACTTTGGTTCAGGTCATTCTACTGGA
36712 TTTGG
1 TTTGG
36717 TGATCGTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 4 0.11
33 30 0.86
34 1 0.03
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (34 bp):
TTTGGGAGACTTTGGTTCAGGTCATTCTACTGGA
Found at i:38182 original size:30 final size:30
Alignment explanation
Indices: 38148--38207 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
38138 AAGAATAAAA
*
38148 ACAGCAACGAGAAATTGAAGAAGACACAGG
1 ACAGCAACGAGAAATTAAAGAAGACACAGG
38178 ACAGCAACGAGAAATTAAAGAAGACACAGG
1 ACAGCAACGAGAAATTAAAGAAGACACAGG
38208 TTTTACGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.25, T:0.07
Consensus pattern (30 bp):
ACAGCAACGAGAAATTAAAGAAGACACAGG
Found at i:46560 original size:20 final size:20
Alignment explanation
Indices: 46535--46575 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
46525 ACATTACCTC
46535 AGTGCTGGATAAGCCTTTCA
1 AGTGCTGGATAAGCCTTTCA
46555 AGTGCTGGATAAGCCTTTCA
1 AGTGCTGGATAAGCCTTTCA
46575 A
1 A
46576 TGAATCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCTGGATAAGCCTTTCA
Found at i:52351 original size:2 final size:2
Alignment explanation
Indices: 52344--52390 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
52334 GCTCAAGGGA
52344 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52386 AG AG A
1 AG AG A
52391 TACATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.