Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012789.1 Kokia drynarioides strain JFW-HI SEQ_127802, 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: 3308
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2626 original size:59 final size:58
Alignment explanation
Indices: 2516--2779 Score: 257
Period size: 59 Copynumber: 4.5 Consensus size: 58
2506 ATTTTAAACA
* * * * ** * ** *
2516 TTCGGGGGTAAAAGGGTAA-TTTTGGTAGATTCAGGGTTTAAAATGGGATTTTTTTAAC
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GAGTCAAAAATGGAATTTTTGGAAG
* *
2574 TTGGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAAGTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCG-AGTCAAAAATGGAATTTTTGGAAG
* * * * * *
2633 TTCGAGGGTAAAATGATAATTTTTGGAAGTTTTTGGGTCAAAAAT-GAAATTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAG-GTTCGAGTCAAAAATGGAATTTTTGGAAG
2691 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTTCGGAGTCAAAAATGGAATTTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGG-TTC-GAGTCAAAAATGGAATTTTTGG-AAG
*
2752 TTC-GGGGTCAAAGATGG-GATTTTTGGAA
1 TTCGGGGGT-AAA-ATGGTAATTTTTGGAA
2780 ATTAAGGGGT
Statistics
Matches: 172, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
58 58 0.34
59 74 0.43
60 17 0.10
61 19 0.11
62 4 0.02
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (58 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGTCAAAAATGGAATTTTTGGAAG
Found at i:2636 original size:29 final size:29
Alignment explanation
Indices: 2583--3048 Score: 326
Period size: 29 Copynumber: 15.8 Consensus size: 29
2573 CTTGGGGGGT
*
2583 AAAATGGTAATTTTTGGAAGGTTCGAAGTCA
1 AAAATGG-AATTTTTGGAA-GTTCGAGGTCA
*
2614 AAAATGGGATTTTTGGAAGTTCGAGGGT--
1 AAAATGGAATTTTTGGAAGTTCGA-GGTCA
* *
2642 AAAATGATAATTTTTGGAAGTTTTTG-GGTCA
1 AAAATG-GAATTTTTGGAAG--TTCGAGGTCA
* *
2673 AAAAT-GAAATTTTGGAAGTTCGGGGGT--
1 AAAATGGAATTTTTGGAAGTTC-GAGGTCA
2700 AAAATGGTAATTTTTGGAAGGTTTCG-GAGTCA
1 AAAATGG-AATTTTTGGAA-G-TTCGAG-GTCA
*
2732 AAAATGGAATTTTTGGAAAGTTCGGGGTCA
1 AAAATGGAATTTTTGG-AAGTTCGAGGTCA
* * * * *
2762 AAGATGGGATTTTTGGAAATTAAGGGGT--
1 AAAATGGAATTTTTGGAAGTT-CGAGGTCA
2790 AAAATGGTAATTTTTGGAAAGTTCG-GGTTCA
1 AAAATGG-AATTTTTGG-AAGTTCGAGG-TCA
* *
2821 AAAATGGGATTTTT-GAAGTTCGGGGGT--
1 AAAATGGAATTTTTGGAAGTTC-GAGGTCA
*
2848 AAAATGGAAATTTTTAGAAGGTTCGAGGTCA
1 AAAATGG-AATTTTTGGAA-GTTCGAGGTCA
* *
2879 AAAATGGGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGAATTTTTGGAAGTTC-GAGGTCA
* *
2907 AAAATGGTATTTTTTAGAAGTTTCGAGGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGTCA
*
2938 AAAAT-GAGATTTTTGGAAGTTCAAGGGT--
1 AAAATGGA-ATTTTTGGAAGTTCGA-GGTCA
2966 AAAATGGTAATTTTTGGAAAGTTCG-GGTTCA
1 AAAATGG-AATTTTTGG-AAGTTCGAGG-TCA
*
2997 AAATTGGAATTTTTGGAAGTTCGAGGGT--
1 AAAATGGAATTTTTGGAAGTTCGA-GGTCA
3025 AAAATGGTAATTTTTGGAGAGTTC
1 AAAATGG-AATTTTTGGA-AGTTC
3049 AAGGACCTCC
Statistics
Matches: 355, Mismatches: 33, Indels: 95
0.73 0.07 0.20
Matches are distributed among these distances:
27 14 0.04
28 48 0.14
29 118 0.33
30 110 0.31
31 56 0.16
32 9 0.03
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGTCA
Found at i:2762 original size:148 final size:148
Alignment explanation
Indices: 2583--2958 Score: 439
Period size: 148 Copynumber: 2.5 Consensus size: 148
2573 CTTGGGGGGT
* **
2583 AAAATGGTAATTTTTGGAAGGTTCGAAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
* *
2648 ATAATTTTTGGAAGTTTTTGGG-TCAAAAATGAAATTTTGGAAGTTCGGGGGTAAAATGGTAATT
65 ATAATTTTTGGAAGTTTTCGGGTTCAAAAATGAAATTTTGGAAGTTCGGGGGTAAAATGGAAATT
*
2712 TTTGGAAGGTTTCG-GAGTCA
130 TTTAGAAGG-TTCGAG-GTCA
* * *
2732 AAAATGGAATTTTTGGAAAGTTCGGGGTCAAAGATGGGATTTTTGGAAATT-AAGGGGTAAAATG
1 AAAATGGAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATG
* ** *
2796 GTAATTTTTGGAAAG--TTCGGGTTCAAAAATGGGATTTTTGAAGTTCGGGGGTAAAATGGAAAT
65 ATAATTTTTGG-AAGTTTTCGGGTTCAAAAATGAAATTTTGGAAGTTCGGGGGTAAAATGGAAAT
2859 TTTTAGAAGGTTCGAGGTCA
129 TTTTAGAAGGTTCGAGGTCA
* * *
2879 AAAATGGGATTTTTGG-AAGTTCGGGGGT--AAAATGGTATTTTTTAGAAGTTTCGA-GGTCAAA
1 AAAATGGAATTTTTGGAAAGTTC-GGGGTCAAAAATGGGA-TTTTTGGAAG-TTCGAGGGT--AA
*
2940 AATGA-GATTTTTGGAAGTT
61 AATGATAATTTTTGGAAGTT
2959 CAAGGGTAAA
Statistics
Matches: 194, Mismatches: 21, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
145 7 0.04
146 20 0.10
147 44 0.23
148 113 0.58
149 10 0.05
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (148 bp):
AAAATGGAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGA
TAATTTTTGGAAGTTTTCGGGTTCAAAAATGAAATTTTGGAAGTTCGGGGGTAAAATGGAAATTT
TTAGAAGGTTCGAGGTCA
Found at i:2822 original size:59 final size:58
Alignment explanation
Indices: 2732--3048 Score: 383
Period size: 59 Copynumber: 5.4 Consensus size: 58
2722 TTCGGAGTCA
* *
2732 AAAATGG-AATTTTTGGAAAGTTCGGGGTCAAAGATGGGATTTTTGGAAATTAAGGGGT
1 AAAATGGTAATTTTTGGAAAGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTAAGGGGT
**
2790 AAAATGGTAATTTTTGGAAAGTTCGGGTTCAAAAATGGGATTTTT-GAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGG-TCAAAAATGGGATTTTTGGAAGTTAAGGGGT
* * * **
2848 AAAATGGAAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCG-GGTCAAAAATGGGATTTTTGGAAGTTAAGGGGT
* * *
2907 AAAATGGTATTTTTTAG-AAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCAA-GGGT
1 AAAATGGTAATTTTTGGAAAG-TTCG-GGTCAAAAATGGGATTTTTGGAAGTT-AAGGGGT
* * *
2966 AAAATGGTAATTTTTGGAAAGTTCGGGTTCAAAATTGGAATTTTTGGAAGTT-CGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGG-TCAAAAATGGGATTTTTGGAAGTTAAG-GGGT
*
3025 AAAATGGTAATTTTTGGAGAGTTC
1 AAAATGGTAATTTTTGGAAAGTTC
3049 AAGGACCTCC
Statistics
Matches: 229, Mismatches: 20, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
58 63 0.28
59 163 0.71
60 3 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAGTTCGGGTCAAAAATGGGATTTTTGGAAGTTAAGGGGT
Done.