Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010042.1 Kokia drynarioides strain JFW-HI SEQ_124810, 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, 602
Length: 1004
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Found at i:427 original size:30 final size:31
Alignment explanation
Indices: 384--588 Score: 144
Period size: 30 Copynumber: 6.9 Consensus size: 31
374 GTTCGAGGGT
*
384 AAAATGGTAATTTTTAGAAGATCCGAGGTCA
1 AAAATGGTAATTTTTAGAAGATCCGGGGTCA
* * * *
415 AAAATGG-GATTTTTGGAAGTTCGGGGGT--
1 AAAATGGTAATTTTTAGAAGATCCGGGGTCA
* **
443 AAAATGGTAATTTTTAGAAGATTCGAAGTCA
1 AAAATGGTAATTTTTAGAAGATCCGGGGTCA
* * *
474 AAAAT-G-AGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGTA-ATTTTTAGAAGATCCGGGGTCA
*
502 AAAATGGTAATTTTTAGAA-AGTTCGGGGTCA
1 AAAATGGTAATTTTTAGAAGA-TCCGGGGTCA
* * * *
533 AAAATGG-GATTTTTAGAAGTTCAGGCGT--
1 AAAATGGTAATTTTTAGAAGATCCGGGGTCA
* * *
561 AAAATGGTAATTTTCAAAAGATTCGGGG
1 AAAATGGTAATTTTTAGAAGATCCGGGG
589 ATTTTTGGGA
Statistics
Matches: 129, Mismatches: 34, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
28 19 0.15
29 44 0.34
30 47 0.36
31 19 0.15
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (31 bp):
AAAATGGTAATTTTTAGAAGATCCGGGGTCA
Found at i:443 original size:59 final size:58
Alignment explanation
Indices: 354--856 Score: 527
Period size: 59 Copynumber: 8.8 Consensus size: 58
344 ATGTTCGGAA
* * *
354 TCAAAAATAGGA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATCCGAGG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA-ATTCGAGG
*
412 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAAG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA-ATTCGAGG
* *
471 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAA-TTCGAGG
* * * * *
530 TCAAAAATGGGATTTTTAGAAGTTCAGGCGTAAAATGGTAATTTTCA-AAA---GA-T
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAATTCGAGG
* * * * * * *
583 TC-----GGGGATTTTTGGGAGTGCGAGGATAAAACGGTAA-TTTTAGAAAGTTTG-GG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAA-TTCGAGG
* * * *
635 TTAAAAATGGGGTTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCG-GG
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAA-TTCGAGG
* * * *
693 GCTAAAAATGGGATTTTT-TAGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
1 TC-AAAAATGGGATTTTTGGA-AGTTCGGGGGTAAAATGGTAATTTTTAGAA-ATTCGAGG
* * *
753 -CTAAAAATGGGATTTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTGGAAGATTCGGGG
1 TC-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA-ATTCGAGG
*
811 TCAAAAATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTT
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT
857 GTAAGGTTTA
Statistics
Matches: 373, Mismatches: 51, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
47 4 0.01
48 28 0.08
52 2 0.01
53 2 0.01
54 1 0.00
57 26 0.07
58 82 0.22
59 225 0.60
60 3 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (58 bp):
TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAATTCGAGG
Found at i:668 original size:105 final size:107
Alignment explanation
Indices: 481--810 Score: 301
Period size: 105 Copynumber: 3.0 Consensus size: 107
471 TCAAAAATGA
* * * *
481 GATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGGGATTTT
1 GATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGGGATTTT
546 TAGAAGTTCAGGCGTAAAATGGTAATTTTCAAAAGATTCGGG
66 TAGAAGTTCAGGCGTAAAATGGTAATTTTCAAAAGATTCGGG
* * * *
588 GATTTTTGGGAGTGCGAGGATAAAACGGTAA-TTTTAGAAAGTT-TGGGTTAAAAATGGGGTTTT
1 GATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGGGATTTT
* * **
651 TAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAG-TTCGGG
66 TAGAAGTTCAGGCGTAAAATGGTAA-TTTTCAAAAGATTCGGG
** * * * * *
693 GCTAAAAATGGGATTTTTTAGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG-CTAA
1 G------AT----TTTTGGA-AGTGCGAGGATAAAACGGTAATTTTTAGAAAGTTCGGGGTC-AA
* ***
757 AAATGGGATTTTTGGAAGTTCAGG-GTAAAATGGTAATTTTTGGAAGATTCGGG
54 AAATGGGATTTTTAGAAGTTCAGGCGTAAAATGGTAATTTTCAAAAGATTCGGG
810 G
1 G
811 TCAAAAATGG
Statistics
Matches: 180, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
105 47 0.26
106 20 0.11
107 26 0.14
111 2 0.01
115 4 0.02
116 26 0.14
117 30 0.17
118 25 0.14
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.33
Consensus pattern (107 bp):
GATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAAGTTCGGGGTCAAAAATGGGATTTT
TAGAAGTTCAGGCGTAAAATGGTAATTTTCAAAAGATTCGGG
Found at i:693 original size:164 final size:166
Alignment explanation
Indices: 420--856 Score: 463
Period size: 164 Copynumber: 2.6 Consensus size: 166
410 GGTCAAAAAT
* * * *
420 GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCGAAGTCAAAAATGAGATT
1 GGGATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAGATTCGAAGTCAAAAATGAGATT
*
485 TTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGG-TCAAAAATGGGA-TTTTTA
66 TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGGCT-AAAAATGGGATTTTTTA
*
548 GAAGTTCAGGCGTAAAATGGTAATTTTCAAAAGATTCG
130 G-AGTGCAGGCGTAAAATGGTAATTTTCAAAAGATTCG
* * * * * *
586 GGGATTTTTGGGAGTGCGAGGATAAAACGGTAA-TTTTAGAA-AGTTTG-GGTTAAAAATGGGGT
1 GGGATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAGA-TTCGAAGTCAAAAATGAGAT
*
648 TTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGCTAAAAATGGGATTTTTTA
65 TTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGGCTAAAAATGGGATTTTTTA
* * * * *
713 GAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
130 GAGTGCAGGCGTAAAATGGTAATTTTCAAAAGATTC---G
* * * * **
753 CTAAAAATGGGATTTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAA
1 --------GGGATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAGATTCGAAGTCAAAA
* * *
817 ATGGGATTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTT
58 ATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTT
857 GTAAGGTTTA
Statistics
Matches: 226, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
164 95 0.42
165 19 0.08
166 28 0.12
167 1 0.00
174 13 0.06
175 25 0.11
176 45 0.20
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (166 bp):
GGGATTTTTGGAAGTGCGAGGATAAAACGGTAATTTTTAGAAGATTCGAAGTCAAAAATGAGATT
TTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCGGGGCTAAAAATGGGATTTTTTAG
AGTGCAGGCGTAAAATGGTAATTTTCAAAAGATTCG
Found at i:795 original size:117 final size:117
Alignment explanation
Indices: 586--864 Score: 354
Period size: 117 Copynumber: 2.4 Consensus size: 117
576 AAAAGATTCG
* * * * * * * *
586 GGGATTTTTGGGAGTGCGAGGATAAAACGGTAA-TTTTAGAAAGTTTGGGTTAAAAATGGGGTTT
1 GGGATTTTTTGGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGCTAAAAATGGGATTT
*
650 TTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAA-AGTTCGGGG-CTAAAAAT
66 TTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGA-TTCGGGGTC-AAAAAT
*
702 GGGATTTTTTAGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGCTAAAAATGGGATT
1 GGGATTTTTTGGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGCTAAAAATGGGATT
*
767 TTTGGAAGTTC-AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAAT
65 TTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAAT
* *
819 GGGA-TTTTTGGAAGTTCGGAGGTAAAATGGTAATTTTT-GTAAGGTT
1 GGGATTTTTTGG-AGTGCGGGGGTAAAATGGTAATTTTTAG-AAGGTT
865 TAAGGACCTT
Statistics
Matches: 143, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
116 35 0.24
117 82 0.57
118 26 0.18
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (117 bp):
GGGATTTTTTGGAGTGCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGCTAAAAATGGGATTT
TTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAAT
Done.