Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006999.1 Kokia drynarioides strain JFW-HI SEQ_121605, 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: 2352
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Found at i:192 original size:29 final size:29
Alignment explanation
Indices: 153--710 Score: 265
Period size: 29 Copynumber: 18.8 Consensus size: 29
143 CTCGGATACC
*
153 CGAGGGT-AAAATGGTAATTTTGGGAA-AT
1 CGAGGGTAAAAATGG-AATTTTTGGAAGAT
* * *
181 CGAGGTTAAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
*
210 CGAGGGTAAAAATGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
** * * *
239 TTAGCGTAAAAAATGGGATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
* ** *
269 CGGGGGTAAAAGCGGAATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * *** *
299 CGA-GGTCAAAATGGTATTTTCAAAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
* * * *
327 CGTGGGTAAAAATGGAATTCTTGAAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * * *
357 TG-GGGTTAAAAATGGGATTTTTGAAAGTT
1 CGAGGG-TAAAAATGGAATTTTTGGAAGAT
* * *
386 CGGGGGTAAAAAT-TAATTTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAA-TTTTTGGAAG-AT
* * * *
416 CGA-GGTAAAAAATGGGATTTTCGAAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
* * *
445 CGAGGGGTAAAAATGAAATTTTTGGGAGTTT
1 CGA-GGGTAAAAATGGAATTTTTGGAAG-AT
* ** * * *
476 TG-GCATCAAAAATGGGATTTTTAGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
*
505 CG-GGCGTAAAAATGGAATTTTTGGAAGTTT
1 CGAGG-GTAAAAATGGAATTTTTGGAAG-AT
* * * *
535 TG-GGGTTAAAATGGGATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
* *
563 CGAGGGTAAAAATGGAATTTTTGGTAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGAT
** * * *
592 TTAGGGTTAAAATGGGATTTTTGGAAGTTT
1 CGAGGGTAAAAATGGAATTTTTGGAAG-AT
* * * *
622 TGAAAGTTTGGGGTAAAAATTGAATTTTTGGTAGTTT
1 CG--A-----GGGTAAAAATGGAATTTTTGGAAG-AT
* *
659 TG-GGGTCAAAAATGGAATTTTTGGAAGTT
1 CGAGGGT-AAAAATGGAATTTTTGGAAGAT
*
688 CGAGAGT-AAAATGGAATTTTTGG
1 CGAGGGTAAAAATGGAATTTTTGG
711 GAGTTTTGGG
Statistics
Matches: 420, Mismatches: 81, Indels: 58
0.75 0.14 0.10
Matches are distributed among these distances:
28 39 0.09
29 216 0.51
30 132 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:265 original size:59 final size:58
Alignment explanation
Indices: 187--738 Score: 588
Period size: 58 Copynumber: 9.3 Consensus size: 58
177 AAATCGAGGT
* *
187 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGCG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* ** * *
245 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAGCGGAATTTTTGGAAGTTTCGAGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * *** * * *
304 TCAAAATGGTATTTTCAAAAGTTCGTGGGTAAAAATGGAATTCTTGAAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * * *
362 TTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAAT-TAATTTTTTGGAAGTTTCGAGG
1 -TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTGGGG
* * * * **
421 TAAAAAATGGGATTTTCGAAAGTTCGAGGGGTAAAAATGAAATTTTTGGGAGTTTTGGCA
1 T-AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
*
481 TCAAAAATGGGATTTTTAGAAGTTCG-GGCGTAAAAATGGAATTTTTGGAAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * *
540 TTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGTAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
* * * *
598 TTAAAATGGGATTTTTGGAAGTTTTGAAAGTTTGGGGTAAAAATTGAATTTTTGGTAGTTTTGGG
1 TAAAAATGGGATTTTTGGAAG-TTCG--A-----GGGTAAAAATGGAATTTTTGGAAGTTTTGGG
663 G
58 G
* * *
664 TCAAAAATGGAATTTTTGGAAGTTCGAGAGT-AAAATGGAATTTTTGGGAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
*
722 TTAAAAATTGGATTTTT
1 -TAAAAATGGGATTTTT
739 AAATGTTCGG
Statistics
Matches: 416, Mismatches: 60, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
58 160 0.38
59 155 0.37
60 45 0.11
61 3 0.01
64 1 0.00
66 34 0.08
67 18 0.04
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (58 bp):
TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGG
Found at i:659 original size:66 final size:68
Alignment explanation
Indices: 552--687 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 68
542 AAAATGGGAT
* * *
552 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGTAGTTTTAGGGT-TAAAATGGGATTTTTGG
1 TTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGTAGTTTTAGGGTCAAAAATGGAATTTTTGG
616 AAG
66 AAG
* * *
619 TTTTGAAAGTTTG-GGGTAAAAATTGAATTTTTGGTAGTTTTGGGGTCAAAAATGGAATTTTTGG
1 TTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGTAGTTTTAGGGTCAAAAATGGAATTTTTGG
683 AAG
66 AAG
686 TT
1 TT
688 CGAGAGTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
66 31 0.50
67 31 0.50
ACGTcount: A:0.29, C:0.01, G:0.29, T:0.40
Consensus pattern (68 bp):
TTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGTAGTTTTAGGGTCAAAAATGGAATTTTTGG
AAG
Found at i:707 original size:95 final size:96
Alignment explanation
Indices: 517--718 Score: 248
Period size: 95 Copynumber: 2.1 Consensus size: 96
507 GGCGTAAAAA
* * * *
517 TGGAATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATT
1 TGGAAGTTTTGAAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATT
* ** * *
582 TTTGGTAGTTTTAGGGTTAAAATGGGATTTT
66 TTTGGAAGTTCGAGAGTTAAAATGGAATTTT
* * *
613 TGGAAGTTTTGAAAG-TTTGGGGTAAAAATTGAATTTTTGGTAGTTTTG-GGGTCAAAAATGGAA
1 TGGAAGTTTTGAAAGTTTTGGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAA
676 TTTTTGGAAGTTCGAGAG-TAAAATGGAATTTT
64 TTTTTGGAAGTTCGAGAGTTAAAATGGAATTTT
*
708 TGGGAGTTTTG
1 TGGAAGTTTTG
719 GGGTTAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
95 51 0.56
96 40 0.44
ACGTcount: A:0.28, C:0.01, G:0.31, T:0.40
Consensus pattern (96 bp):
TGGAAGTTTTGAAAGTTTTGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATT
TTTGGAAGTTCGAGAGTTAAAATGGAATTTT
Found at i:737 original size:30 final size:29
Alignment explanation
Indices: 613--738 Score: 125
Period size: 28 Copynumber: 4.3 Consensus size: 29
603 ATGGGATTTT
* *
613 TGGAAGTTTTGAAAG-TTTGGGGTAAAAA
1 TGGAATTTTTGGAAGTTTTGGGGTAAAAA
* *
641 TTGAATTTTTGGTAGTTTTGGGGTCAAAAA
1 TGGAATTTTTGGAAGTTTTGGGGT-AAAAA
* *
671 TGGAATTTTTGGAAG-TTCGAGAGT-AAAA
1 TGGAATTTTTGGAAGTTTTG-GGGTAAAAA
*
699 TGGAATTTTTGGGAGTTTTGGGGTTAAAAA
1 TGGAATTTTTGGAAGTTTTGGGG-TAAAAA
729 TTGG-ATTTTT
1 -TGGAATTTTT
739 AAATGTTCGG
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
28 31 0.39
29 15 0.19
30 31 0.39
31 3 0.04
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (29 bp):
TGGAATTTTTGGAAGTTTTGGGGTAAAAA
Found at i:747 original size:58 final size:58
Alignment explanation
Indices: 613--756 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 58
603 ATGGGATTTT
* * * *
613 TGGAAGTTTTGAAAGTTTGG-GGTAAAAATTGAATTTTTGGTAGTTTTGGGGTCAAAAA
1 TGGAATTTTTGAAAGTTCGGAGGT-AAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAA
* *
671 TGGAATTTTTGGAAGTTC-GAGAGTAAAATGGAATTTTTGGGAGTTTTGGGGTTAAAAA
1 TGGAATTTTTGAAAGTTCGGAG-GTAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAA
729 TTGG-ATTTTT-AAATGTTCGGAGGTAAAA
1 -TGGAATTTTTGAAA-GTTCGGAGGTAAAA
757 ACAAAATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
57 3 0.04
58 63 0.85
59 8 0.11
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (58 bp):
TGGAATTTTTGAAAGTTCGGAGGTAAAATGGAATTTTTGGGAGTTTTGGGGTCAAAAA
Found at i:1724 original size:18 final size:17
Alignment explanation
Indices: 1692--1744 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
1682 ATTTTCCTTT
*
1692 TATTATTATTTTATTAA
1 TATTATTGTTTTATTAA
1709 TATTATTGTATTTATT-A
1 TATTATTGT-TTTATTAA
1726 TATTTATTGTTATTATTAA
1 TA-TTATTGTT-TTATTAA
1745 AACGTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 12 0.39
18 18 0.58
19 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TATTATTGTTTTATTAA
Done.