Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000467.1 Kokia drynarioides strain JFW-HI SEQ_111340, 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: 6430
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:462 original size:29 final size:29
Alignment explanation
Indices: 436--609 Score: 139
Period size: 30 Copynumber: 5.9 Consensus size: 29
426 TTCGAACTTT
*
436 AAAAAATTACATTTTTGCACCCAAACTT-C
1 AAAAAATTACATTTTTAC-CCCAAACTTCC
*
465 ACAAAAATTACATTTTTACTCCTAAACTT-C
1 A-AAAAATTACATTTTTAC-CCCAAACTTCC
*
495 TAAAAATTACCA-TTTTACCCTCAAACTTCC
1 AAAAAATTA-CATTTTTACCC-CAAACTTCC
* *
525 AAAAAATTACAATTTTACCTCTAAACTTCC
1 AAAAAATTACATTTTTACC-CCAAACTTCC
**
555 --AAAATTACCA-TTTTACCCTTGAACTTCC
1 AAAAAATTA-CATTTTTACCC-CAAACTTCC
583 AAAAATATT--ATTTTTGACCCCAAACTT
1 AAAAA-ATTACATTTTT-ACCCCAAACTT
610 TTCGAAAATT
Statistics
Matches: 122, Mismatches: 10, Indels: 26
0.77 0.06 0.16
Matches are distributed among these distances:
27 1 0.01
28 25 0.20
29 34 0.28
30 58 0.48
31 4 0.03
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAAAATTACATTTTTACCCCAAACTTCC
Found at i:471 original size:30 final size:30
Alignment explanation
Indices: 437--588 Score: 142
Period size: 30 Copynumber: 5.2 Consensus size: 30
427 TCGAACTTTA
*
437 AAAAATTACATTTTTGCACC-CAAACTTCAC
1 AAAAATTACATTTTTACACCTCAAACTTC-C
* *
467 AAAAATTACATTTTTACTCCT-AAACTTCT
1 AAAAATTACATTTTTACACCTCAAACTTCC
496 AAAAATTACCA-TTTTAC-CCTCAAACTTCC
1 AAAAATTA-CATTTTTACACCTCAAACTTCC
*
525 AAAAAATTACAATTTT--ACCTCTAAACTTCC
1 -AAAAATTACATTTTTACACCTC-AAACTTCC
**
555 -AAAATTACCA-TTTTAC-CCTTGAACTTCC
1 AAAAATTA-CATTTTTACACCTCAAACTTCC
583 AAAAAT
1 AAAAAT
589 ATTATTTTTG
Statistics
Matches: 105, Mismatches: 6, Indels: 23
0.78 0.04 0.17
Matches are distributed among these distances:
28 21 0.20
29 37 0.35
30 47 0.45
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATTACATTTTTACACCTCAAACTTCC
Found at i:493 original size:59 final size:59
Alignment explanation
Indices: 457--592 Score: 188
Period size: 59 Copynumber: 2.3 Consensus size: 59
447 TTTTTGCACC
*
457 CAAACTT-CACAAAAATTACATTTTTA-CTCCTAAACTTCTAAAAATTACCATTTTACCCT
1 CAAACTTCCA-AAAAATTACAATTTTACCT-CTAAACTTCTAAAAATTACCATTTTACCCT
*
516 CAAACTTCCAAAAAATTACAATTTTACCTCTAAACTTC-CAAAATTACCATTTTACCCT
1 CAAACTTCCAAAAAATTACAATTTTACCTCTAAACTTCTAAAAATTACCATTTTACCCT
**
574 TGAACTTCCAAAAATATTA
1 CAAACTTCCAAAAA-ATTA
593 TTTTTGACCC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 31 0.44
59 35 0.50
60 4 0.06
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (59 bp):
CAAACTTCCAAAAAATTACAATTTTACCTCTAAACTTCTAAAAATTACCATTTTACCCT
Found at i:595 original size:28 final size:28
Alignment explanation
Indices: 478--596 Score: 91
Period size: 28 Copynumber: 4.1 Consensus size: 28
468 AAAATTACAT
* **
478 TTTTACTCC-TAAACTTCTAAAAATTACCA
1 TTTTAC-CCTTAAACTTCCAAAAA-TATTA
*
507 TTTTACCCTCAAACTTCCAAAAA-ATTACAA
1 TTTTACCCTTAAACTTCCAAAAATATT---A
* **
537 TTTTA-CCTCTAAACTTCCAAAATTACCA
1 TTTTACCCT-TAAACTTCCAAAAATATTA
*
565 TTTTACCCTTGAACTTCCAAAAATATTA
1 TTTTACCCTTAAACTTCCAAAAATATTA
593 TTTT
1 TTTT
597 TGACCCCAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 27 0.38
29 24 0.34
30 18 0.25
31 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (28 bp):
TTTTACCCTTAAACTTCCAAAAATATTA
Found at i:682 original size:29 final size:29
Alignment explanation
Indices: 650--849 Score: 136
Period size: 29 Copynumber: 6.8 Consensus size: 29
640 AAAATTGCAT
*
650 TTTTGTTCCTGAGTGTCCAAAAATTACCA
1 TTTTGCTCCTGAGTGTCCAAAAATTACCA
*
679 TTTTGCT-CTCGAAGTGTCC-AAAATTACCG
1 TTTTGCTCCT-G-AGTGTCCAAAAATTACCA
* * * * *
708 TTTTACTCCCGAATATCCGAAAATTACCA
1 TTTTGCTCCTGAGTGTCCAAAAATTACCA
* *
737 TTTTACCCCTCGAGTGTCCAAAAATTACCA
1 TTTTGCTCCT-GAGTGTCCAAAAATTACCA
* * * *
767 TTTGCGCCCCCGATTGTCCAAAAATTACCA
1 TTT-TGCTCCTGAGTGTCCAAAAATTACCA
* *** *
797 TTTT-ATCCTTGAACCTCCTAAAATTACCA
1 TTTTGCTCC-TGAGTGTCCAAAAATTACCA
* * **
826 TTTTACCCCTGAGCATCCAAAAAT
1 TTTTGCTCCTGAGTGTCCAAAAAT
850 CATATTTTTG
Statistics
Matches: 134, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
28 9 0.07
29 71 0.53
30 50 0.37
31 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (29 bp):
TTTTGCTCCTGAGTGTCCAAAAATTACCA
Found at i:695 original size:30 final size:29
Alignment explanation
Indices: 660--800 Score: 149
Period size: 30 Copynumber: 4.8 Consensus size: 29
650 TTTTGTTCCT
* *
660 GAGTGTCCAAAAATTACCATTTTGCTCTC
1 GAGTGTCCAAAAATTACCATTTTGCCCCC
* * *
689 GAAGTGTCC-AAAATTACCGTTTTACTCCC
1 G-AGTGTCCAAAAATTACCATTTTGCCCCC
* * * *
718 GAATATCCGAAAATTACCATTTTACCCCTC
1 GAGTGTCCAAAAATTACCATTTTGCCCC-C
*
748 GAGTGTCCAAAAATTACCATTTGCGCCCCC
1 GAGTGTCCAAAAATTACCATTT-TGCCCCC
*
778 GATTGTCCAAAAATTACCATTTT
1 GAGTGTCCAAAAATTACCATTTT
801 ATCCTTGAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.05
29 36 0.38
30 49 0.52
31 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (29 bp):
GAGTGTCCAAAAATTACCATTTTGCCCCC
Found at i:755 original size:88 final size:88
Alignment explanation
Indices: 657--849 Score: 239
Period size: 89 Copynumber: 2.2 Consensus size: 88
647 CATTTTTGTT
* * * *
657 CCTGAGTGTCCAAAAATTACCATTT-TGCTCTCGAAGTGTCC-AAAATTACCGTTTTACTCC-CG
1 CCTGAGTGTCCAAAAATTACCATTTGCGCCCCCG-AGTGTCCAAAAATTACCATTTTA-TCCTCG
*
719 AATATCCGAAAATTACCATTTTACC
64 AACATCCGAAAATTACCATTTTACC
* *
744 CCTCGAGTGTCCAAAAATTACCATTTGCGCCCCCGATTGTCCAAAAATTACCATTTTATCCTTGA
1 CCT-GAGTGTCCAAAAATTACCATTTGCGCCCCCGAGTGTCCAAAAATTACCATTTTATCCTCGA
* *
809 ACCTCCTAAAATTACCATTTTACC
65 ACATCCGAAAATTACCATTTTACC
**
833 CCTGAGCATCCAAAAAT
1 CCTGAGTGTCCAAAAAT
850 CATATTTTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
87 3 0.03
88 43 0.47
89 45 0.49
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (88 bp):
CCTGAGTGTCCAAAAATTACCATTTGCGCCCCCGAGTGTCCAAAAATTACCATTTTATCCTCGAA
CATCCGAAAATTACCATTTTACC
Done.