Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002683.1 Kokia drynarioides strain JFW-HI SEQ_114950, 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, 811
Length: 1352
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.31
Found at i:222 original size:96 final size:96
Alignment explanation
Indices: 50--241 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
40 TTTTGGGAAA
** * *
50 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGAAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTCCACCTAGAAAGTTAAGGCACAATATTTCA
* *
115 GAATCGAAGAT-AAGGAAACATTGTCTCGATT
66 GAATCGAAGATAAAAGAAA-ATTGCCTCGATT
* * ** **
146 AAGGATATTCGATTATTTCGATTTGAGGAAAAATTCCACCTAGTGAGTTAAGGCACAA-ATTTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTCCACCTAGAAAGTTAAGGCACAATATTTCA
210 GAAACTCG-AGATAAAAGAAAATTGCCTCGATT
66 G-AA-TCGAAGATAAAAGAAAATTGCCTCGATT
242 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 5 0.06
96 67 0.83
97 9 0.11
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTCCACCTAGAAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAAAATTGCCTCGATT
Found at i:504 original size:29 final size:29
Alignment explanation
Indices: 465--1022 Score: 245
Period size: 29 Copynumber: 18.8 Consensus size: 29
455 CTCGGATACC
*
465 CGAGGGT-AAAATGGTAATTTTGGGAA-AT
1 CGAGGGTAAAAATGG-AATTTTTGGAAGAT
* * *
493 CGAGGTTAAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
*
522 CGAGGGTAAAAATGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
** * * *
551 TTAGCGTAAAAAATGGGATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
* ** *
581 CGGGGGTAAAAGCGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * *** *
611 CGA-GGTCAAAATGGTATTTTCAAAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
* * * *
639 CGTGGGTAAAAATGGAATTCTTGAAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * * * *
669 TG-GGGTTAAAAATGGGATTTTCGAAAGTT
1 CGAGGG-TAAAAATGGAATTTTTGGAAGAT
* * *
698 CGGGGGTAAAAAT-TAATTTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAA-TTTTTGGAAG-AT
* * * * *
728 C-AAGGTAAAAAATGGGATTTTCGAAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
* * *
757 CGAGGGGTAAAAATGAAATTTTTGGGAGTTT
1 CGA-GGGTAAAAATGGAATTTTTGGAAG-AT
* ** * * *
788 TG-GCATCAAAAATGGGATTTTTAGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
* *
817 CGGGGGTAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * * *
847 TG-GGGTTAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
* * * * *
875 TGAGGTTAAAAATGGATTTTTTGGTAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
** * * *
904 TTAGGGTTAAAATGGGATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* *
934 CGAAAGTTTGGGGTAAAAATGGAATTTTTGGGAGTTT
1 CG--A-----GGGTAAAAATGGAATTTTTGGAAG-AT
* * *
971 TG-GGGTCAAAAATGAAATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
1000 CGAGGGT-AAAATGGAATTTTTGG
1 CGAGGGTAAAAATGGAATTTTTGG
1023 GAGTTTTGGG
Statistics
Matches: 413, Mismatches: 88, Indels: 58
0.74 0.16 0.10
Matches are distributed among these distances:
28 39 0.09
29 211 0.51
30 130 0.31
31 7 0.02
32 1 0.00
37 25 0.06
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
CGAGGGTAAAAATGGAATTTTTGGAAGAT
Found at i:577 original size:59 final size:58
Alignment explanation
Indices: 499--1050 Score: 568
Period size: 58 Copynumber: 9.3 Consensus size: 58
489 AAATCGAGGT
* *
499 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGCG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* ** * *
557 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAGCGGAATTTTTGGAAGTTTCGAGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * *** * * *
616 TCAAAATGGTATTTTCAAAAGTTCGTGGGTAAAAATGGAATTCTTGAAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * ***
674 TTAAAAATGGGATTTTCGAAAGTTCGGGGGTAAAAAT-TAATTTTTTGGAAGTTTCAAGG
1 -TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTGGGG
* * * * **
733 TAAAAAATGGGATTTTCGAAAGTTCGAGGGGTAAAAATGAAATTTTTGGGAGTTTTGGCA
1 T-AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* *
793 TCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * * *
852 TTAAAATGGGATTTTTGGAAGTTTGAGGTTAAAAATGGATTTTTTGGTAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* *
910 TTAAAATGGGATTTTTGGAAGTTTCGAAAGTTTGGGGTAAAAATGGAATTTTTGGGAGTTTTGGG
1 TAAAAATGGGATTTTTGGAAG-TTCG--A-----GGGTAAAAATGGAATTTTTGGAAGTTTTGGG
975 G
58 G
** *
976 TCAAAAATGAAATTTTTGGAAGTTCGAGGGT-AAAATGGAATTTTTGGGAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
*
1034 TTAAAAATTGGATTTTT
1 -TAAAAATGGGATTTTT
1051 AAATGTTCGG
Statistics
Matches: 413, Mismatches: 65, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
58 158 0.38
59 157 0.38
60 44 0.11
61 3 0.01
64 1 0.00
66 33 0.08
67 17 0.04
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (58 bp):
TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
Found at i:970 original size:95 final size:95
Alignment explanation
Indices: 845--1028 Score: 244
Period size: 95 Copynumber: 1.9 Consensus size: 95
835 TTTTGGAAGT
* * * * * * **
845 TTTGGGGTTAAAATGGGATTTTTGGAAG-TTTGAGGTTAAAAATGGATTTTTTGGTAGTTTTAGG
1 TTTGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTCGAGG
*
909 GTTAAAATGGGATTTTTGGAAGTTTCGAAAG
66 G-TAAAATGGAATTTTTGGAAGTTTCGAAAG
* *
940 TTTGGGGTAAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGAAATTTTTGGAAGTTCGAGG
1 TTTGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTCGAGG
*
1005 GTAAAATGGAATTTTTGGGAGTTT
66 GTAAAATGGAATTTTTGGAAGTTT
1029 TGGGGTTAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
95 46 0.61
96 30 0.39
ACGTcount: A:0.28, C:0.02, G:0.31, T:0.39
Consensus pattern (95 bp):
TTTGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGAAATTTTTGGAAGTTCGAGG
GTAAAATGGAATTTTTGGAAGTTTCGAAAG
Found at i:1049 original size:30 final size:29
Alignment explanation
Indices: 940--1050 Score: 138
Period size: 30 Copynumber: 3.8 Consensus size: 29
930 GTTTCGAAAG
940 TTTGGGGTAAAAATGGAATTTTTGGGAGT
1 TTTGGGGTAAAAATGGAATTTTTGGGAGT
* *
969 TTTGGGGTCAAAAATGAAATTTTTGGAAG-
1 TTTGGGGT-AAAAATGGAATTTTTGGGAGT
*
998 TTCGAGGGT-AAAATGGAATTTTTGGGAGT
1 TTTG-GGGTAAAAATGGAATTTTTGGGAGT
1027 TTTGGGGTTAAAAATTGG-ATTTTT
1 TTTGGGG-TAAAAA-TGGAATTTTT
1051 AAATGTTCGG
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
28 20 0.29
29 15 0.21
30 32 0.46
31 3 0.04
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.39
Consensus pattern (29 bp):
TTTGGGGTAAAAATGGAATTTTTGGGAGT
Found at i:1059 original size:58 final size:57
Alignment explanation
Indices: 935--1068 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 57
925 TGGAAGTTTC
*
935 GAAAGTTTGGGGTAAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGAAATTTTT
1 GAAAGTTCGGGGT-AAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGAAATTTTT
* * *
993 GGAAGTTCGAGGGTAAAATGGAATTTTTGGGAGTTTTGGGGTTAAAAATTG-GATTTTT
1 GAAAGTTCG-GGGTAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAA-TGAAATTTTT
1051 -AAATGTTCGGAGGTAAAA
1 GAAA-GTTCGG-GGTAAAA
1069 ACAAAATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
57 3 0.04
58 58 0.87
59 6 0.09
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (57 bp):
GAAAGTTCGGGGTAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAATGAAATTTTT
Done.