Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009464.1 Kokia drynarioides strain JFW-HI SEQ_124171, 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, 809
Length: 1349
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Found at i:464 original size:59 final size:59
Alignment explanation
Indices: 403--783 Score: 366
Period size: 59 Copynumber: 6.5 Consensus size: 59
393 TTTAGACATC
* * * * *
403 CGGGAGTAAGATAGTAATTTTTGGATGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTC
1 CGGGAGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * * * * *
462 CGGGAGTAAAATGATAATTTCTAGAAGGTTCGAGGTCAAAATTGAGATTTTTGGAACTT
1 CGGGAGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * *
521 CGGGGGTAAAATGGTATTTTTTGGAAGGTTC-AGAGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGAGTAAAATGGTAATTTTTGGAAGGTTCGAG-GTCAAAAATGGGATTTTTGGAAGTT
* * * *
580 CGGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTT
1 CGGGAGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * * * **
639 CGAGG-GTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATTGGGGTTTTTGGACTTT
1 CG-GGAGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * *
698 CGAGG-GTAAAAATGG-GATTTTTGGAA-GTTCGGGGGT--AAAATGGTAATTTTTGGAAGGTT
1 CG-GGAGT-AAAATGGTAATTTTTGGAAGGTTC-GAGGTCAAAAATGG-GATTTTTGGAA-GTT
*
757 CGGG-GTCAAAAATGG-GATTTTTGGAAG
1 CGGGAGT--AAAATGGTAATTTTTGGAAG
784 TTTAGGGGTA
Statistics
Matches: 276, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
57 6 0.02
58 18 0.07
59 242 0.88
60 10 0.04
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.33
Consensus pattern (59 bp):
CGGGAGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:481 original size:29 final size:29
Alignment explanation
Indices: 449--811 Score: 171
Period size: 30 Copynumber: 12.4 Consensus size: 29
439 CAAAAATGGG
*
449 ATTTTTGGAAGTCCGGGAGTAAAATGATA
1 ATTTTTGGAAGTTCGGGAGTAAAATGATA
* * * *
478 ATTTCTAGAAGGTTCGAG-GTCAAAATTGA-G
1 ATTTTTGGAA-GTTCGGGAGT-AAAA-TGATA
* * *
508 ATTTTTGGAACTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGGGAGTAAAATGATA
* * *
537 TTTTTTGGAAGGTTC-AGAGTCAAAAATGA-G
1 ATTTTTGGAA-GTTCGGGAGT--AAAATGATA
* *
567 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGGGAGTAAAATGATA
* **
596 ATTTTTGGAAGGTTTGGG-GTTAAAAATG-GG
1 ATTTTTGGAA-GTTCGGGAG-T-AAAATGATA
*
626 ATTTTTGGAAGTTCGAGG-GTAAAATGGTA
1 ATTTTTGGAAGTTCG-GGAGTAAAATGATA
* **
655 ATTTTTAGAAGGTTCGGG-GTCAAAATTG-GG
1 ATTTTTGGAA-GTTCGGGAGT-AAAA-TGATA
* ** **
685 GTTTTTGGACTTTCGAGG-GTAAAAATG-GG
1 ATTTTTGGAAGTTCG-GGAGT-AAAATGATA
* *
714 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGGGAGTAAAATGATA
**
743 ATTTTTGGAAGGTTCGGG-GTCAAAAATG-GG
1 ATTTTTGGAA-GTTCGGGAGT--AAAATGATA
* *
773 ATTTTTGGAAGTTTAGGG-GTAAAATGGTA
1 ATTTTTGGAAG-TTCGGGAGTAAAATGATA
802 A-TTTTGGAAG
1 ATTTTTGGAAG
812 GTTTGGGGTC
Statistics
Matches: 262, Mismatches: 46, Indels: 53
0.73 0.13 0.15
Matches are distributed among these distances:
28 37 0.14
29 100 0.38
30 102 0.39
31 23 0.09
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGGGAGTAAAATGATA
Found at i:581 original size:88 final size:87
Alignment explanation
Indices: 440--811 Score: 357
Period size: 88 Copynumber: 4.2 Consensus size: 87
430 TTTCGAGGTC
* * * * *
440 AAAAATGGGATTTTTGGAAGTCCG-GGAGTAAAATGATAATTTCTAGAAGGTTCGAGGTCAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATG-GAATTTTTGGAAGGTTCGGGGTCAAAAT
504 TGAGATTTTTGGAACTTCGGGGGT
64 TGAGATTTTTGGAACTTCGGGGGT
* *
528 -AAAATGGTATTTTTTGGAAGGTTC-AGAGTCAAAAAT-GAGATTTTTGGAA-GTTCGGGGGT-A
1 AAAAATGGGA-TTTTTGGAA-GTTCGAGGGT--AAAATGGA-ATTTTTGGAAGGTTC-GGGGTCA
* * * *
588 AAATGGTA-ATTTTTGGAAGGTTTGGGGTT
60 AAATTG-AGATTTTTGGAA-CTTCGGGGGT
*
617 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG-AATTTTTGGAAGGTTCGGGGTCAAAATT
* * *
682 GGGGTTTTTGG-ACTTTCGAGGGT
65 GAGATTTTTGGAAC-TTCGGGGGT
* *
705 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG-AATTTTTGGAAGGTTCGGGGTCAAAATT
* * **
770 GGGATTTTTGGAAGTTTAGGGGT
65 GAGATTTTTGGAACTTCGGGGGT
* *
793 -AAAATGGTAATTTTGGAAG
1 AAAAATGGGATTTTTGGAAG
812 GTTTGGGGTC
Statistics
Matches: 235, Mismatches: 31, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
87 30 0.13
88 136 0.58
89 56 0.24
90 13 0.06
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (87 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTGGAAGGTTCGGGGTCAAAATTG
AGATTTTTGGAACTTCGGGGGT
Found at i:705 original size:118 final size:116
Alignment explanation
Indices: 416--825 Score: 391
Period size: 118 Copynumber: 3.5 Consensus size: 116
406 GAGTAAGATA
* * * * *
416 GTAATTTTTGGATGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTCCGGGAGTAAAATGATAATT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG-GTAAAATGGTAATT
* * * * * * *
481 TCTAGAAGGTTCGAGGTCAAAATTGAGATTTTTGGAACTTCGGGGGTAAAATG
65 TTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATG
* * * *
534 GTATTTTTTGGAAGGTTCAGAGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAATGGTAATT
*
599 TTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATG
65 TTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATG
* * * ** *
652 GTAATTTTTAGAAGGTTCGGGGTCAAAATTGGGGTTTTTGGACTTTCGAGGGTAAAAATGG-GAT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT-AAAATGGTAAT
* *
716 TTTTGGAA-GTTCGGGGGT-AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATG
64 TTTTGGAAGGTTCGGGGTTAAAAATGG-GATTTTTGGAA-GTTCGGGGT--AAAATG
* * * * * * *
771 G-GATTTTTGGAAGTTTAGGGGT--AAAATGGTAATTTTGGAAGGTTTGGGGTCAAAT
1 GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAA-GTTCGGGGTAAAAT
826 ATTATTAGAA
Statistics
Matches: 241, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
115 4 0.02
116 24 0.10
117 27 0.11
118 169 0.70
119 17 0.07
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (116 bp):
GTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTT
TTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATG
Found at i:793 original size:147 final size:146
Alignment explanation
Indices: 558--824 Score: 455
Period size: 147 Copynumber: 1.8 Consensus size: 146
548 GTTCAGAGTC
* *
558 AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAAT
1 AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
*
623 GGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAATTGGGGTT
66 GGGATTTTTGGAAGTTAGAGGGTAAAATGGTAA-TTTTAGAAGGTTCGGGGTCAAAATTGGGGTT
688 TTTGGACTTTCGAGGGT
130 TTTGGACTTTCGAGGGT
*
705 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
1 AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
* *
770 GGGATTTTTGGAAGTTTAG-GGGTAAAATGGTAATTTTGGAAGGTTTGGGGTCAAA
66 GGGATTTTTGGAAG-TTAGAGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTCAAA
825 TATTATTAGA
Statistics
Matches: 113, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
146 20 0.18
147 90 0.80
148 3 0.03
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.34
Consensus pattern (146 bp):
AAAAATGAGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT
GGGATTTTTGGAAGTTAGAGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTCAAAATTGGGGTTT
TTGGACTTTCGAGGGT
Done.