Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013195.1 Kokia drynarioides strain JFW-HI SEQ_128214, 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: 28964
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:435 original size:26 final size:26
Alignment explanation
Indices: 386--437 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
376 TTATCCTTAA
* * * *
386 AATTTTTAATTAATTTATTTTAAAAT
1 AATTTTTAATGAATTAAATATAAAAT
412 AATTTTTAATGAATTAAATATAAAAT
1 AATTTTTAATGAATTAAATATAAAAT
438 TAAAATCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AATTTTTAATGAATTAAATATAAAAT
Found at i:14194 original size:101 final size:101
Alignment explanation
Indices: 14019--14222 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 101
14009 GCAAAATGGA
* *
14019 TGGCAAGAATTTTCTGAGTATTTCTCTCTCAATTATGGGCATCTTCTGGTTTTCAAATATGAAGG
1 TGGCAAAAATTTTCTGAGTATTTCTCACTCAATTATGGGCATCTTCTGGTTTTCAAATATGAAGG
14084 TAATGGAAAGTTTCTGGTACTCATATTTGATACGAG
66 TAATGGAAAGTTTCTGGTACTCATATTTGATACGAG
14120 TGGCAAAAATTTTCTGAGTATTTCTCACTCAATTATGGGCATCTTCTGGTTTTCAAATATGAAGG
1 TGGCAAAAATTTTCTGAGTATTTCTCACTCAATTATGGGCATCTTCTGGTTTTCAAATATGAAGG
14185 TAATGGAAAGTTTCTGGTACTCATATTTGATACGAG
66 TAATGGAAAGTTTCTGGTACTCATATTTGATACGAG
14221 TG
1 TG
14223 CATCAGAGAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (101 bp):
TGGCAAAAATTTTCTGAGTATTTCTCACTCAATTATGGGCATCTTCTGGTTTTCAAATATGAAGG
TAATGGAAAGTTTCTGGTACTCATATTTGATACGAG
Found at i:14725 original size:168 final size:168
Alignment explanation
Indices: 14231--14733 Score: 718
Period size: 168 Copynumber: 3.0 Consensus size: 168
14221 TGCATCAGAG
* *
14231 ATTGAATATCCATGCAAGAGCCATATTGAAGATCAGAAGAGTGATGATCAAATGTGTCTAAAACC
1 ATTGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACC
* * * *
14296 TGTCAAGGAAGAACCTAAAGATGATGTTTGTGATAAACCCTTGTATGGGACTCCTTCATGCAAGG
66 TGTCAAGGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGG
* * * *
14361 AAACTAAGAGGAAGAAATCACGATCACTACGTTCTAAC
131 AAACTAGGAGGAAGAAATCACGATCACAATGTTCTAAA
* * * * *
14399 ACTGAATATCTATGCAAGAGCTATATTGAAGATCATAAGAGTGATGATCAATTGTGTCTAAAACC
1 ATTGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACC
* * *
14464 TGTCAAGGAAGAAGCTAAAGATGGTGTTTATGATGAAACCTTGTATGAGACTCCTCCATGCAAGG
66 TGTCAAGGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGG
* * *
14529 AAGCTAGGAGGAATAAATCACAATCACAATGTTCTAAA
131 AAACTAGGAGGAAGAAATCACGATCACAATGTTCTAAA
* * *
14567 ATTGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGAAGATCAAGTGAGTCTAAAACC
1 ATTGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACC
** * *
14632 CATCAAAGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTCTATGAGACTCCTCCATGCAAGG
66 TGTCAAGGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGG
* * * *
14697 AAACTAGGAAGCAGAAACCGCGATCACAATGTTCTAA
131 AAACTAGGAGGAAGAAATCACGATCACAATGTTCTAA
14734 TCCTCGAAAG
Statistics
Matches: 295, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
168 295 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (168 bp):
ATTGAATATCAATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAAATGTGTCTAAAACC
TGTCAAGGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGG
AAACTAGGAGGAAGAAATCACGATCACAATGTTCTAAA
Found at i:23793 original size:12 final size:12
Alignment explanation
Indices: 23776--23808 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
23766 AAAAATTTAA
23776 TTTAATAATTAT
1 TTTAATAATTAT
23788 TTTAATAA-TAT
1 TTTAATAATTAT
*
23799 TTTATTAATT
1 TTTAATAATT
23809 TAATCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAATAATTAT
Found at i:23823 original size:17 final size:17
Alignment explanation
Indices: 23801--23835 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23791 AATAATATTT
23801 TATT-AATTTAATCTTAA
1 TATTAAATTTAAT-TTAA
23818 TATTAAATTTAATTTAA
1 TATTAAATTTAATTTAA
23835 T
1 T
23836 GTTTATCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTAAATTTAATTTAA
Found at i:24582 original size:26 final size:26
Alignment explanation
Indices: 24548--24604 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
24538 TATATTATAT
*
24548 GAAG-TGGTTTCGAGGTGGATATAGC
1 GAAGATGGTTTCGAGGTGAATATAGC
*
24573 GAAGATGGTTTCGGGGTGAATATAGC
1 GAAGATGGTTTCGAGGTGAATATAGC
24599 GAAGAT
1 GAAGAT
24605 TAGGTGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.28, C:0.07, G:0.39, T:0.26
Consensus pattern (26 bp):
GAAGATGGTTTCGAGGTGAATATAGC
Found at i:25062 original size:20 final size:19
Alignment explanation
Indices: 25021--25066 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25011 AATTATATTG
25021 AATA-TTGAATATGATAAA
1 AATATTTGAATATGATAAA
* *
25039 AATATTTGAAGTATTATAAT
1 AATATTTGAA-TATGATAAA
25059 AATATTTG
1 AATATTTG
25067 TATGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (19 bp):
AATATTTGAATATGATAAA
Done.