Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005694.1 Kokia drynarioides strain JFW-HI SEQ_119898, 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, 623
Length: 1039
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.40
Found at i:447 original size:29 final size:29
Alignment explanation
Indices: 398--676 Score: 300
Period size: 29 Copynumber: 9.6 Consensus size: 29
388 CTAAATTTTA
398 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
**
428 CAAAAATTCCATTTTTACCCTTGAAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
*
458 CAAAAATT--ATATTTTACCCCAAAACTTA
1 CAAAAATTCCAT-TTTTACCCCAAAACTTC
*
486 CAAAAATTACATTTTTACCCC-AAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
*
514 CAAAAATTCCATTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
543 CAAAAATTACATTTTTACACCC-GAACTTC
1 CAAAAATTCCATTTTTAC-CCCAAAACTTC
* ** *
572 CAAAAATTACATTTTTACCCCTGAACCTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
601 CAAAAATTCCATTTTTTAACCCTAAAACTTT
1 CAAAAATTCCA-TTTTT-ACCCCAAAACTTC
* **
632 CAAAAATTACC-CTTTTACCCCCGAA-TGTC
1 CAAAAATT-CCATTTTTACCCCAAAACT-TC
661 CAAAAATTCCATTTTT
1 CAAAAATTCCATTTTT
677 GATCCCGATT
Statistics
Matches: 213, Mismatches: 24, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
28 47 0.22
29 103 0.48
30 45 0.21
31 16 0.08
32 2 0.01
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:698 original size:30 final size:27
Alignment explanation
Indices: 659--746 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 27
649 CCCCCGAATG
659 TCCAAAAATTCCATTTTTGATCCCGATT
1 TCCAAAAATTCC-TTTTTGATCCCGATT
* * *
687 TCCCTAAAAATTACTATTTT-ACCCCCGGATG
1 T-CC-AAAAATTCCT-TTTTGA-TCCC-GATT
718 TCCAAAAATTCCGTTTTTGATCCCGATT
1 TCCAAAAATTCC-TTTTTGATCCCGATT
746 T
1 T
747 TTTTTAAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
28 5 0.11
29 19 0.40
30 19 0.40
31 4 0.09
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (27 bp):
TCCAAAAATTCCTTTTTGATCCCGATT
Found at i:707 original size:59 final size:59
Alignment explanation
Indices: 633--851 Score: 223
Period size: 59 Copynumber: 3.7 Consensus size: 59
623 TAAAACTTTC
*
633 AAAAATTACCCTTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTCCCT
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTCCCT
* * * ***
692 AAAAATTACTATTTTACCCCCGGATGTCCAAAAATTCCGTTTTTGATCCCGATTTTTTT
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTCCCT
* * * * * * *
751 TAAAGTTACCGTTTTACCCCCGAGT-TCTAAAAATTCCATTTTTAACCCCGAACTTTCCC-
1 AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCG-A-TTTCCCT
* *
810 -AAAATTATCATTTTGCCCCCGAGA-GTCC-AAAATTACCATTTT
1 AAAAATTACCATTTTACCCCCGA-ATGTCCAAAAATT-CCATTTT
852 GCCCTCCGGA
Statistics
Matches: 129, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
58 45 0.35
59 81 0.63
60 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGATCCCGATTTCCCT
Found at i:707 original size:89 final size:87
Alignment explanation
Indices: 398--676 Score: 278
Period size: 86 Copynumber: 3.2 Consensus size: 87
388 CTAAATTTTA
* ** * * * **
398 CAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTTGAAACTTCCAAAA
1 CAAAAATTACATTTTT-ACCCCTGAACCTCCAAAAATTCTATTTTAACCC-CAAAACTTCCAAAA
* * *
463 ATTATA-TTTTAC-CCCAAAACTTA
64 ATTACACTTTTACACCC-GAACTTC
* * * *
486 CAAAAATTACATTTTTACCCC-AAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAAT
1 CAAAAATTACATTTTTACCCCTGAACCTCCAAAAATTCTATTTTAACCCCAAAACTTCCAAAAAT
*
550 TACATTTTTACACCCGAACTTC
66 TACACTTTTACACCCGAACTTC
* * *
572 CAAAAATTACATTTTTACCCCTGAACCTCCAAAAATTCCATTTTTTAACCCTAAAACTTTCAAAA
1 CAAAAATTACATTTTTACCCCTGAACCTCCAAAAATT-C-TATTTTAACCCCAAAACTTCCAAAA
* *
637 ATTACCCTTTTACCCCCGAA-TGTC
64 ATTACACTTTTACACCCGAACT-TC
*
661 CAAAAATTCCATTTTT
1 CAAAAATTACATTTTT
677 GATCCCGATT
Statistics
Matches: 167, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
85 17 0.10
86 58 0.35
87 21 0.13
88 17 0.10
89 54 0.32
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (87 bp):
CAAAAATTACATTTTTACCCCTGAACCTCCAAAAATTCTATTTTAACCCCAAAACTTCCAAAAAT
TACACTTTTACACCCGAACTTC
Found at i:829 original size:58 final size:57
Alignment explanation
Indices: 425--851 Score: 273
Period size: 58 Copynumber: 7.3 Consensus size: 57
415 ACCCCAAAAC
* * ** *
425 TTCCAAAAATTCCATTTTTACCCTTGAAAC-TTCCAAAAATTA-TATTTTACCCCAAAAC
1 TTCCAAAAATTCCATTTTTACCC-CG-AACTTTCCAAAAATTACCATTTTACCCC-CGAG
* * * ** *
483 TTACAAAAATTACATTTTTACCCCAAAC-TTCCAAAAATT-CCATTTTGACCCCAAAAC
1 TTCCAAAAATTCCATTTTTACCCCGAACTTTCCAAAAATTACCATTTT-ACCCC-CGAG
* * *
540 TTCCAAAAATTACATTTTTACACCCGAAC-TTCCAAAAATTA-CATTTTTACCCCTGAAC
1 TTCCAAAAATTCCATTTTTAC-CCCGAACTTTCCAAAAATTACCA-TTTTACCCCCG-AG
* ** * *
598 CTCCAAAAATTCCATTTTTTAACCCTAAAACTTT-CAAAAATTACCCTTTTACCCCCGAA
1 TTCCAAAAATTCCA-TTTTT-ACCC-CGAACTTTCCAAAAATTACCATTTTACCCCCGAG
* *
657 TGTCCAAAAATTCCATTTTTGATCCCG-A-TTTCCCTAAAAATTACTATTTTACCCCCG-G
1 T-TCCAAAAATTCCATTTTT-ACCCCGAACTTT-CC-AAAAATTACCATTTTACCCCCGAG
* * ** *** * *
715 ATGTCCAAAAATTCCGTTTTTGATCCCGATTTTTTTTAAAGTTACCGTTTTACCCCCGAG
1 -T-TCCAAAAATTCCATTTTT-ACCCCGAACTTTCCAAAAATTACCATTTTACCCCCGAG
* * * *
775 TTCTAAAAATTCCATTTTTAACCCCGAACTTTCCCAAAATTATCATTTTGCCCCCGAG
1 TTCCAAAAATTCCATTTTT-ACCCCGAACTTTCCAAAAATTACCATTTTACCCCCGAG
*
833 AGTCC-AAAATTACCATTTT
1 -TTCCAAAAATT-CCATTTT
852 GCCCTCCGGA
Statistics
Matches: 301, Mismatches: 47, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
56 22 0.07
57 31 0.10
58 110 0.37
59 94 0.31
60 38 0.13
61 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
TTCCAAAAATTCCATTTTTACCCCGAACTTTCCAAAAATTACCATTTTACCCCCGAG
Done.