Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011646.1 Kokia drynarioides strain JFW-HI SEQ_126638, 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: 6942
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:664 original size:29 final size:29
Alignment explanation
Indices: 613--960 Score: 385
Period size: 29 Copynumber: 11.8 Consensus size: 29
603 GAAGGTCCCT
*
613 AAACTGTCCGAAAATAT-CATTTTTACCCCC
1 AAACT-TCCAAAAAT-TCCATTTTTACCCCC
* * * **
643 GAACTTCTAAAAATTCCATTTTTGACTCAG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
673 AAACTGCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
702 AAACTTCCAAAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
732 AAACTTTCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
761 AAACTTCCAAAAATTCCATTTTTTA-CCCC
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
* *
790 AAAATGTCTAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* ** *
820 GAACTTCCAAAAATTCCATTTTTGACTTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
850 AAACTTCCAAAAATTCCATTTTTACACCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
879 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
908 AAACCTCCAAAATTTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
938 AAATTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
961 GCCCTCGAAT
Statistics
Matches: 267, Mismatches: 42, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.00
29 140 0.52
30 119 0.45
31 7 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:707 original size:59 final size:58
Alignment explanation
Indices: 613--960 Score: 398
Period size: 59 Copynumber: 5.9 Consensus size: 58
603 GAAGGTCCCT
* * *
613 AAACTGTCCGAAAATAT-CATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTGACTCA
1 AAACTG-CCAAAAAT-TCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACTCA
*
672 GAAACTGCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCA
1 -AAACTGCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA-CTCA
** * * *
732 AAACTTTCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCCCA
1 AAACTGCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA-CTCA
* *
791 AAA-TGTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACTTCA
1 AAACTG-CCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGAC-TCA
* * *
850 AAACTTCCAAAAATTCCATTTTTACACCCAAACTTCCAAAAATTCCATTTTT-ACCCCTA
1 AAACTGCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA-CTC-A
* * * * *
909 AACCT-CCAAAATTTCCATTTTTAACCCCAAAATTTTCAAAAATTACCATTTT
1 AAACTGCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATT-CCATTTT
961 GCCCTCGAAT
Statistics
Matches: 252, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
58 21 0.08
59 213 0.85
60 18 0.07
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTGCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACTCA
Found at i:773 original size:88 final size:88
Alignment explanation
Indices: 613--960 Score: 391
Period size: 88 Copynumber: 3.9 Consensus size: 88
603 GAAGGTCCCT
* ** * * **
613 AAACTGTCCGAAAATAT-CATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTGACTCAGAAAC
1 AAACT-TCCAAAAAT-TCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCCTCAAAC
*
677 TGCCAAAAATTCCATTTTTACCCCC
64 TTCCAAAAATTCCATTTTTACCCCC
* *
702 AAACTTCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAATTCCATTTTT-ACCCTCAAACT
1 AAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTGACCCTCAAACT
766 TCCAAAAATTCCATTTTTTA-CCCC
65 TCCAAAAATTCCA-TTTTTACCCCC
* * ** *
790 AAAATGTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA-CTTCAAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCCTC-AAAC
*
854 TTCCAAAAATTCCATTTTTACACCC
64 TTCCAAAAATTCCATTTTTACCCCC
* * * * *
879 AAACTTCCAAAAATTCCATTTTTACCCCTAAACCTCCAAAATTTCCATTTTTAACCC-CAAAATT
1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCCTC-AAACT
*
943 TTCAAAAATTACCATTTT
65 TCCAAAAATT-CCATTTT
961 GCCCTCGAAT
Statistics
Matches: 222, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
87 1 0.00
88 135 0.61
89 86 0.39
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (88 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTGACCCTCAAACTT
CCAAAAATTCCATTTTTACCCCC
Found at i:1036 original size:29 final size:28
Alignment explanation
Indices: 630--1076 Score: 317
Period size: 29 Copynumber: 15.2 Consensus size: 28
620 CCGAAAATAT
* *
630 CATTTTTACCCCCGAACTTCTAAAAATTC
1 CATTTTTACCCCC-AAATTCCAAAAATTC
* ** *
659 CATTTTTGACTCAGAAACTGCCAAAAATTC
1 CATTTTT-ACCCCCAAA-TTCCAAAAATTC
689 CATTTTTACCCCCAAACTTCCAAAAATTC
1 CATTTTTACCCCCAAA-TTCCAAAAATTC
* * *
718 CATTTTTAACCTCAAAACTTTCAAAAATTC
1 CATTTTT-ACCCCCAAA-TTCCAAAAATTC
*
748 CATTTTTACCCTCAAACTTCCAAAAATTC
1 CATTTTTACCCCCAAA-TTCCAAAAATTC
* *
777 CATTTTTTACCCCAAAATGTCTAAAAATTC
1 CA-TTTTTACCCCCAAAT-TCCAAAAATTC
*
807 CATTTTTACCCCCGAACTTCCAAAAATTC
1 CATTTTTACCCCC-AAATTCCAAAAATTC
** *
836 CATTTTTGACTTCAAAACTTCCAAAAATTC
1 CATTTTT-ACCCCCAAA-TTCCAAAAATTC
*
866 CATTTTTACACCCAAACTTCCAAAAATTC
1 CATTTTTACCCCCAAA-TTCCAAAAATTC
* * *
895 CATTTTTACCCCTAAACCTCCAAAATTTC
1 CATTTTTACCCCCAAA-TTCCAAAAATTC
* *
924 CATTTTTAACCCCAAAATTTTCAAAAATTAC
1 CATTTTT-ACCCCCAAA-TTCCAAAAATT-C
* * * *
955 CA-TTTTGCCCTCGAATGTCCAAAACTT-
1 CATTTTTACCCCCAAAT-TCCAAAAATTC
* * * *
982 CATTTTTGGCCTCAAAACTCTC-AAAATTAC
1 CATTTTT-ACCCCCAAATTC-CAAAAATT-C
* *
1012 C-TTTTTACCCCCAAATGTCTAAAAATTT
1 CATTTTTACCCCCAAAT-TCCAAAAATTC
* * * *
1040 CATTATTAACCTCAAATTTTTCCAAAAATAC
1 CATTTTTACCCCCAAA---TTCCAAAAATTC
1071 CATTTT
1 CATTTT
1077 CCCTCGAGAA
Statistics
Matches: 332, Mismatches: 64, Indels: 42
0.76 0.15 0.10
Matches are distributed among these distances:
27 2 0.01
28 19 0.06
29 178 0.54
30 116 0.35
31 16 0.05
32 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
CATTTTTACCCCCAAATTCCAAAAATTC
Found at i:5375 original size:22 final size:21
Alignment explanation
Indices: 5334--5376 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5324 CCTAGACAAA
*
5334 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
5355 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
5377 GCAAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Done.