Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003995.1 Kokia drynarioides strain JFW-HI SEQ_117107, 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: 1866
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Found at i:418 original size:30 final size:30
Alignment explanation
Indices: 384--508 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
374 TAAAAAATAA
* *
384 CATTTTGACACTTGAACTTTTCTAAAATTT
1 CATTTTGACACTTAAACTTCTCTAAAATTT
* *
414 CATTTTGACCCCTAAACTTCTCTAAAA-TT
1 CATTTTGACACTTAAACTTCTCTAAAATTT
* * * * *
443 -ATTTTTTACCCTTAAACTTTTCCAAAATTA
1 CA-TTTTGACACTTAAACTTCTCTAAAATTT
* * *
473 CATTTCGACCAC-CAAACTTCTCTAAAATTG
1 CATTTTGA-CACTTAAACTTCTCTAAAATTT
503 CATTTT
1 CATTTT
509 AACCCTTATT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.01
29 23 0.31
30 47 0.64
31 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
CATTTTGACACTTAAACTTCTCTAAAATTT
Found at i:458 original size:29 final size:30
Alignment explanation
Indices: 398--783 Score: 180
Period size: 29 Copynumber: 12.9 Consensus size: 30
388 TTGACACTTG
398 AACTTTTCTAAAATT-TCATTTTGACCCCTA
1 AACTTTTCTAAAATTAT-ATTTTGACCCCTA
* * *
428 AACTTCTCTAAAATTAT-TTTTTACCCTTA
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * *
457 AACTTTTCCAAAATTACATTTCGACCACC-A
1 AACTTTTCTAAAATTATATTTTGACC-CCTA
* ** * *
487 AACTTCTCTAAAATTGCATTTT-AACCCTT
1 AACTTTTCTAAAATTATATTTTGACCCCTA
** * * *
516 ATTTTTTTTACAAAAGTACATTTTGACCACC-A
1 AACTTTTCT--AAAATTATATTTTGACC-CCTA
* * * *
548 AACTTCTCTAAAAATACATTTTAACCCC-A
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * * *
577 AACCTTTCCAAAATTACATTTTAACCCCTA
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * * * **
607 AACTTTCCTAAAATCACATTTTAACCTTAATA
1 AACTTTTCTAAAATTATATTTTGACC--CCTA
* * * *
639 AACTTTCCAAAAATTACATCTTGA-CCCTA
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * * * *
668 AACCTTTCCAAAATCACATTTTGAACCC-A
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * *
697 AACTTTCCTAAAATTACATTTTGA-CCATA
1 AACTTTTCTAAAATTATATTTTGACCCCTA
* * * * *
726 AA-TTTTCCCATAATTACATTTTTACCTCTA
1 AACTTTT-CTAAAATTATATTTTGACCCCTA
* * *
756 AACTTTTCCAAAATTACATTTTAACCCC
1 AACTTTTCTAAAATTATATTTTGACCCC
784 AAATTCTTTG
Statistics
Matches: 276, Mismatches: 64, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
28 7 0.03
29 117 0.42
30 103 0.37
31 18 0.07
32 29 0.11
33 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
AACTTTTCTAAAATTATATTTTGACCCCTA
Found at i:544 original size:61 final size:59
Alignment explanation
Indices: 414--636 Score: 206
Period size: 59 Copynumber: 3.7 Consensus size: 59
404 TCTAAAATTT
* * *
414 CATTTTGACC-CCTAAACTTCTCTAAAATT-ATTTTTTACCCTTAAACTTTTCCAAAATTA
1 CATTTTGACCACC-AAACTTCTCTAAAATTCA-TTTTAACCCTTAAACTTTTACAAAAGTA
* ***
473 CATTTCGACCACCAAACTTCTCTAAAATTGCATTTTAACCCTTATTTTTTTTACAAAAGTA
1 CATTTTGACCACCAAACTTCTCTAAAATT-CATTTTAACCCTTA-AACTTTTACAAAAGTA
* * * * *
534 CATTTTGACCACCAAACTTCTCTAAAAATACATTTTAACCC-CAAACCTTTCCAAAATTA
1 CATTTTGACCACCAAACTTCTCT-AAAATTCATTTTAACCCTTAAACTTTTACAAAAGTA
* *
593 CATTTTAACC-CCTAAACTT-TCCTAAAATCACATTTTAA-CCTTAA
1 CATTTTGACCACC-AAACTTCT-CTAAAAT-TCATTTTAACCCTTAA
637 TAAACTTTCC
Statistics
Matches: 137, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
58 10 0.07
59 63 0.46
60 14 0.10
61 45 0.33
62 5 0.04
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (59 bp):
CATTTTGACCACCAAACTTCTCTAAAATTCATTTTAACCCTTAAACTTTTACAAAAGTA
Found at i:650 original size:120 final size:118
Alignment explanation
Indices: 402--790 Score: 348
Period size: 120 Copynumber: 3.3 Consensus size: 118
392 CACTTGAACT
* * * * * * *
402 TTTCTAAAATTTCATTTTGACCCCTAAACTTCTCTAAAATTA-TTTTTTACCCTTAAACTTTTCC
1 TTTCCAAAATTACATTTTGACCCC-AAACTTCTCTAAAAATACATTTTAACCC-CAAACCTTTCC
* * ****
466 AAAATTACATTTCGACCACC-AAAC-TTCTCTAAAATTGCATTTTAACCCTTATTTTT
64 AAAATTACATTTTGACC-CCTAAACTTTC-CTAAAATTACATTTTAA-CCTTATAAAC
* *
522 TTTACAAAAGTACATTTTGACCACCAAACTTCTCTAAAAATACATTTTAACCCCAAACCTTTCCA
1 TTTCCAAAATTACATTTTGACC-CCAAACTTCTCTAAAAATACATTTTAACCCCAAACCTTTCCA
* *
587 AAATTACATTTTAACCCCTAAACTTTCCTAAAATCACATTTTAACCTTAATAAAC
65 AAATTACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTAACCTT-ATAAAC
* * *
642 TTTCCAAAAATTACATCTTGACCCTAAACCTT-TC-CAAAATCACATTTTGAA-CCCAAA-CTTT
1 TTTCC-AAAATTACATTTTGACCCCAAA-CTTCTCTAAAAAT-ACATTTT-AACCCCAAACCTTT
* * * * * *
703 CCTAAAATTACATTTTGA-CCATAAATTTTCCCATAATTACATTTTTACC-TCTAAAC
62 CC-AAAATTACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTAACCTTATAAAC
*
759 TTTTCCAAAATTACATTTTAACCCCAAA-TTCT
1 -TTTCCAAAATTACATTTTGACCCCAAACTTCT
791 TTGAAACTTC
Statistics
Matches: 224, Mismatches: 33, Indels: 28
0.79 0.12 0.10
Matches are distributed among these distances:
115 2 0.01
116 1 0.00
117 24 0.11
118 6 0.03
119 42 0.19
120 116 0.52
121 33 0.15
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (118 bp):
TTTCCAAAATTACATTTTGACCCCAAACTTCTCTAAAAATACATTTTAACCCCAAACCTTTCCAA
AATTACATTTTGACCCCTAAACTTTCCTAAAATTACATTTTAACCTTATAAAC
Done.