Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013089.1 Kokia drynarioides strain JFW-HI SEQ_128107, 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: 3325
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1657 original size:24 final size:24
Alignment explanation
Indices: 1629--1701 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1619 TAGACTAATA
* * * *
1629 AGAGTTTGACTAAAAAAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
1653 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
1677 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
1701 A
1 A
1702 AATAAAAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.23
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:2547 original size:24 final size:24
Alignment explanation
Indices: 2519--2589 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
2509 TAGACTAATA
* * *
2519 AGAGTTTGACTAAAATAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
*
2543 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
2567 AGAGTTTAACTGAAACAAATAAA
1 AGAGTTTAACTGAAACAAATAAA
2590 CAAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:3316 original size:894 final size:840
Alignment explanation
Indices: 1590--3325 Score: 2799
Period size: 894 Copynumber: 2.0 Consensus size: 840
1580 ATAGGCTAAA
1590 TTTTTAGGTCAAATAATAATAAAATAATCTAGACTAATAAGAGTTTGACTAAAAAAAATAAATAG
1 TTTTTAGGTCAAATAATAATAAAATAATCTAGACTAATAAGAGTTTGACTAAAAAAAATAAATAG
1655 AGTTTAATTGAAACAAATAAACAGAGTTTAACTGAAACAAATAAACAAATAAAAAGCAAGCAACC
66 AGTTTAATTGAAACAAATAAACAGAGTTTAACTGAAACAAATAAACAAATAAAAAGCAAGCAACC
**
1720 CACAACTACAAACTCAAATGGCTTCTTAAAAAGTGACTGAAATTACCCTGAAAACTAGAAAACAC
131 CACAACTACAAACTCAAATGAATTCTTAAAAAGTGACTGAAATTACCCTGAAAACTAGAAAACAC
1785 ACTAGAAATGTTGTAAACACACTCAAATTTGGCTCCAAAGGCTACTCTTTATTTGTTCTTAGATT
196 ACTAGAAATGTTGTAAACACACTCAAATTTGGCTCCAAAGGCTACTCTTTATTTGTTCTTAGATT
1850 GAGACCGGAATGCTTTGTTCATGCTTGAAGAAATTATGTGGATCAACCTTTGTTTTTATGTTAAT
261 GAGACCGGAATGCTTTGTTCATGCTTGAAGAAATTATGTGGATCAACCTTTGTTTTTATGTTAAT
1915 TAACTTATCAAAATTATTCTTAAAATATTTTCGACCTCAAACAGTTGCTTTTCCATAACTTATTT
326 TAACTTATCAAAATTATTCTTAAAATATTTTCGACCTCAAACAGTTGCTTTTCCATAACTTATTT
1980 CACCGTCCTTGTTGTTGATTCCAATATCATCGTCTCTGTAACAAACATATGCTCCTCGTGGAGAT
391 CACCGTCCTTGTTGTTGATTCCAATATCATCGTCTCTGTAACAAACATATGCTCCTCGTGGAGAT
2045 TTCGAAACATAAGGTGTCAAAAAGCCGTAAAACTTTCTTATCCAATTCACATACCTTTGGGAATT
456 TTCGAAACATAAGGTGTCAAAAAGCCGTAAAACTTTCTTATCCAATTCACATACCTTTGGGAATT
2110 TATGCTTTCTTCTCCATCCCACCCTGTGTATGCAATATGGTATAAGTTTCCATCTCTGTGTGGGA
521 TATGCTTTCTTCTCCATCCCACCCTGTGTATGCAATATGGTATAAGTTTCCATCTCTGTGTGGGA
2175 ATTGGGTTGCAAATTCTGGGATTTTCGCCATTTTTCCTCCATAAGCAATGAAAGCCATGGCTGTC
586 ATTGGGTTGCAAATTCTGGGATTTTCGCCATTTTTCCTCCATAAGCAATGAAAGCCATGGCTGTC
2240 GTTTCTACATCTTCTTCACAAAGCTTAGACCAAATCTTTTCGAATCCAGCTTTTGGAATTGGGTT
651 GTTTCTACATCTTCTTCACAAAGCTTAGACCAAATCTTTTCGAATCCAGCTTTTGGAATTGGGTT
2305 TTTAACATAATCTAATTTTGTTTTGAATGATGGAGCATTGAGAGGTGATTTGTAACTCCAAGTGA
716 TTTAACATAATCTAATTTTGTTTTGAATGATGGAGCATTGAGAGGTGATTTGTAACTCCAAGTGA
2370 AACATCGATCGATTTGTTTTGGATTTGCCCAAAATAAAGAATCGATTCAATCCAACTCAT
781 AACATCGATCGATTTGTTTTGGATTTGCCCAAAATAAAGAATCGATTCAATCCAACTCAT
*********** * *
2430 TTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT-TTAGGTCAAAT
1 TT---------------------------------------TTTAGGTCAAATAATA-AT--AA-
** *
2494 AATAATAAAATAATCTAGACTAATAAGAGTTTGACTAAAATAAATAAATAGAGTTTAATTGAAAC
23 AATAATCTA--------GACTAATAAGAGTTTGACTAAAAAAAATAAATAGAGTTTAATTGAAAC
*
2559 AAATAAATAGAGTTTAACTGAAACAAATAAACAAATAAAAAGCAAGCAACCCACAACTACAAACT
80 AAATAAACAGAGTTTAACTGAAACAAATAAACAAATAAAAAGCAAGCAACCCACAACTACAAACT
2624 CAAATAAATGAATTCTTAAAAAGTGACTGAAATTACCCTGAAAACTAGAAAACACACTAGAAATG
145 C----AAATGAATTCTTAAAAAGTGACTGAAATTACCCTGAAAACTAGAAAACACACTAGAAATG
2689 TTGTAAACACACTCAAATTTGGCTCCAAAGGCTACTCTTTATTTGTTCTTAGATTGAGACCGGAA
206 TTGTAAACACACTCAAATTTGGCTCCAAAGGCTACTCTTTATTTGTTCTTAGATTGAGACCGGAA
2754 TGCTTTGTTCATGCTTGAAGAAATTATGTGGATCAACCTTTGTTTTTATGTTAATTAACTTATCA
271 TGCTTTGTTCATGCTTGAAGAAATTATGTGGATCAACCTTTGTTTTTATGTTAATTAACTTATCA
2819 AAATTATTCTTAAAATATTTTCGACCTCAAACAGTTGCTTTTCCATAACTTATTTCACCGTCCTT
336 AAATTATTCTTAAAATATTTTCGACCTCAAACAGTTGCTTTTCCATAACTTATTTCACCGTCCTT
2884 GTTGTTGATTCCAATATCATCGTCTCTGTAACAAACATATGCTCCTCGTGGAGATTTCGAAACAT
401 GTTGTTGATTCCAATATCATCGTCTCTGTAACAAACATATGCTCCTCGTGGAGATTTCGAAACAT
2949 AAGGTGTCAAAAAGCCGTAAAACTTTCTTATCCAATTCACATACCTTTGGGAATTTATGCTTTCT
466 AAGGTGTCAAAAAGCCGTAAAACTTTCTTATCCAATTCACATACCTTTGGGAATTTATGCTTTCT
3014 TCTCCATCCCACCCTGTGTATGCAATATGGTATAAGTTTCCATCTCTGTGTGGGAATTGGGTTGC
531 TCTCCATCCCACCCTGTGTATGCAATATGGTATAAGTTTCCATCTCTGTGTGGGAATTGGGTTGC
3079 AAATTCTGGGATTTTCGCCATTTTTCCTCCATAAGCAATGAAAGCCATGGCTGTCGTTTCTACAT
596 AAATTCTGGGATTTTCGCCATTTTTCCTCCATAAGCAATGAAAGCCATGGCTGTCGTTTCTACAT
3144 CTTCTTCACAAAGCTTAGACCAAATCTTTTCGAATCCAGCTTTTGGAATTGGGTTTTTAACATAA
661 CTTCTTCACAAAGCTTAGACCAAATCTTTTCGAATCCAGCTTTTGGAATTGGGTTTTTAACATAA
3209 TCTAATTTTGTTTTGAATGATGGAGCATTGAGAGGTGATTTGTAACTCCAAGTGAAACATCGATC
726 TCTAATTTTGTTTTGAATGATGGAGCATTGAGAGGTGATTTGTAACTCCAAGTGAAACATCGATC
3274 GATTTGTTTTGGATTTGCCCAAAATAAAGAATCGATTCAATCCAACTCAT
791 GATTTGTTTTGGATTTGCCCAAAATAAAGAATCGATTCAATCCAACTCAT
3324 TT
1 TT
Statistics
Matches: 822, Mismatches: 19, Indels: 56
0.92 0.02 0.06
Matches are distributed among these distances:
840 2 0.00
878 2 0.00
879 2 0.00
881 2 0.00
882 7 0.01
890 112 0.14
894 695 0.85
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.33
Consensus pattern (840 bp):
TTTTTAGGTCAAATAATAATAAAATAATCTAGACTAATAAGAGTTTGACTAAAAAAAATAAATAG
AGTTTAATTGAAACAAATAAACAGAGTTTAACTGAAACAAATAAACAAATAAAAAGCAAGCAACC
CACAACTACAAACTCAAATGAATTCTTAAAAAGTGACTGAAATTACCCTGAAAACTAGAAAACAC
ACTAGAAATGTTGTAAACACACTCAAATTTGGCTCCAAAGGCTACTCTTTATTTGTTCTTAGATT
GAGACCGGAATGCTTTGTTCATGCTTGAAGAAATTATGTGGATCAACCTTTGTTTTTATGTTAAT
TAACTTATCAAAATTATTCTTAAAATATTTTCGACCTCAAACAGTTGCTTTTCCATAACTTATTT
CACCGTCCTTGTTGTTGATTCCAATATCATCGTCTCTGTAACAAACATATGCTCCTCGTGGAGAT
TTCGAAACATAAGGTGTCAAAAAGCCGTAAAACTTTCTTATCCAATTCACATACCTTTGGGAATT
TATGCTTTCTTCTCCATCCCACCCTGTGTATGCAATATGGTATAAGTTTCCATCTCTGTGTGGGA
ATTGGGTTGCAAATTCTGGGATTTTCGCCATTTTTCCTCCATAAGCAATGAAAGCCATGGCTGTC
GTTTCTACATCTTCTTCACAAAGCTTAGACCAAATCTTTTCGAATCCAGCTTTTGGAATTGGGTT
TTTAACATAATCTAATTTTGTTTTGAATGATGGAGCATTGAGAGGTGATTTGTAACTCCAAGTGA
AACATCGATCGATTTGTTTTGGATTTGCCCAAAATAAAGAATCGATTCAATCCAACTCAT
Done.