Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001050.1 Kokia drynarioides strain JFW-HI SEQ_112284, 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, 642
Length: 1071
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Found at i:277 original size:29 final size:29
Alignment explanation
Indices: 245--305 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
235 AAAATGAGAC
245 TTTTTGAATACCCGAGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
* * * *
274 -TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
302 TTTT
1 TTTT
306 GGGAAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (29 bp):
TTTTTGAATACCCGAGGGCAAAATGGTAA
Found at i:360 original size:59 final size:59
Alignment explanation
Indices: 283--517 Score: 206
Period size: 59 Copynumber: 4.0 Consensus size: 59
273 ATTTTGGATT
* * * * *
283 CTCGGGGGCAAAATGGTAA-TTTTGGGAAAGTTCGAGGTTAAAAATGGAATTTTTAAACA
1 CTCGAGGGTAAAATGGTAACTTTT-GGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
* * * * *
342 CTCGAGGGTAAAACGGTAACTTTTGAAAAAATCG-GGATCAAAAACGGAATTTTTGGACA
1 CTCGAGGGTAAAATGGTAACTTTTGGAAAGATCGAGG-TCAAAAATGGAATTTTTAGACA
* * * * *
401 TTCGAGGGTAAAATAGTAATTTTTAGGAAA-ATCGAGATCAAAAATGGAATTTTTGGACA
1 CTCGAGGGTAAAATGGTAACTTTT-GGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
* * * ** * * *
460 TTCGGGGGTGAAATGGTATTTTTTTGAAAGTTTCGAGGTCAAAAATAGAATTTTTAGA
1 CTCGAGGGTAAAATGGTAACTTTTGGAAAG-ATCGAGGTCAAAAATGGAATTTTTAGA
518 GGTTCAAGGG
Statistics
Matches: 144, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
58 6 0.04
59 106 0.74
60 32 0.22
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.30
Consensus pattern (59 bp):
CTCGAGGGTAAAATGGTAACTTTTGGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
Found at i:413 original size:29 final size:29
Alignment explanation
Indices: 313--468 Score: 86
Period size: 29 Copynumber: 5.3 Consensus size: 29
303 TTTGGGAAAG
* * **
313 TTCGAGGTTAAAAATGGAATTTTTAAACA
1 TTCGAGGGTAAAAACGGAATTTTTGGACA
* * * *
342 CTCGAGGGT-AAAACGGTAACTTTTGAAAAA
1 TTCGAGGGTAAAAACGG-AATTTTTG-GACA
* *
372 ATCG-GGATCAAAAACGGAATTTTTGGACA
1 TTCGAGGGT-AAAAACGGAATTTTTGGACA
* *
401 TTCGAGGGTAAAATA-GTAATTTTTAGGAAA
1 TTCGAGGGTAAAA-ACGGAATTTTT-GGACA
* * *
431 ATCGA-GATCAAAAATGGAATTTTTGGACA
1 TTCGAGGGT-AAAAACGGAATTTTTGGACA
*
460 TTCGGGGGT
1 TTCGAGGGT
469 GAAATGGTAT
Statistics
Matches: 95, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
28 6 0.06
29 43 0.45
30 39 0.41
31 7 0.07
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (29 bp):
TTCGAGGGTAAAAACGGAATTTTTGGACA
Found at i:514 original size:30 final size:29
Alignment explanation
Indices: 480--759 Score: 148
Period size: 29 Copynumber: 9.4 Consensus size: 29
470 AAATGGTATT
*
480 TTTTTGAAAGTTTCGAGGTCAAAAATAGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAAT-GAA
* * *
510 TTTTTAG-AGGTTCAAGGGT-AAAAATGCAA
1 TTTTTGGAAGTTTCGA-GGTCAAAAATG-AA
* * * *
539 TTTTTTGGAATTTTTGGGGTTAAAAATGTAA
1 -TTTTTGGAAGTTTCGAGGTCAAAAATG-AA
*
570 TTTTTGGAAGTTTATG-GGT-AAAAATGTAA
1 TTTTTGGAAGTTT-CGAGGTCAAAAATG-AA
*
599 TTTTTGGAAGTTT-TAGGGTC-AAAATGAAA
1 TTTTTGGAAGTTTCGA-GGTCAAAAATG-AA
* * *
628 TTTTTGGAAGTTTAGGGGT-AAAAATATAA
1 TTTTTGGAAGTTTCGAGGTCAAAAAT-GAA
* **
657 TTTTCGGAAGTTTCGAGGGAAAAAATGGAA
1 TTTTTGGAAGTTTCGAGGTCAAAAAT-GAA
*
687 TTTTTGGAAGTTT-GA-G-CATAAATATATAA
1 TTTTTGGAAGTTTCGAGGTCA-AAA-AT-GAA
* * **
716 TTTTCGAAAGTTTTAAGGTCAAAAATGAAA
1 TTTTTGGAAGTTTCGAGGTCAAAAATG-AA
*
746 ATTTTGGACAGTTT
1 TTTTTGGA-AGTTT
760 AGGGACCTCC
Statistics
Matches: 196, Mismatches: 34, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 103 0.53
30 62 0.32
31 23 0.12
32 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
TTTTTGGAAGTTTCGAGGTCAAAAATGAA
Found at i:592 original size:29 final size:29
Alignment explanation
Indices: 525--699 Score: 194
Period size: 29 Copynumber: 5.9 Consensus size: 29
515 AGAGGTTCAA
* *
525 GGGTAAAAATGCAATTTTTTGGAA-TTTTT
1 GGGTAAAAATGTAA-TTTTTGGAAGTTTAT
554 GGGGTTAAAAATGTAATTTTTGGAAGTTTAT
1 -GGG-TAAAAATGTAATTTTTGGAAGTTTAT
585 GGGTAAAAATGTAATTTTTGGAAGTTT-T
1 GGGTAAAAATGTAATTTTTGGAAGTTTAT
* * *
613 AGGGTCAAAATGAAATTTTTGGAAGTTTAG
1 -GGGTAAAAATGTAATTTTTGGAAGTTTAT
* *
643 GGGTAAAAATATAATTTTCGGAAGTTTCGA-
1 GGGTAAAAATGTAATTTTTGGAAGTTT--AT
* *
673 GGGAAAAAATGGAATTTTTGGAAGTTT
1 GGGTAAAAATGTAATTTTTGGAAGTTT
700 GAGCATAAAT
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
28 1 0.01
29 72 0.57
30 38 0.30
31 15 0.12
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAT
Found at i:714 original size:59 final size:58
Alignment explanation
Indices: 560--763 Score: 221
Period size: 59 Copynumber: 3.5 Consensus size: 58
550 TTTTGGGGTT
* * * * * *
560 AAAAATGTAATTTTTGGAAGTTTATGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCGGAAGTTTGAGGGA
*
618 CAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCGGAAGTTTCGAGGGA
1 AAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCGGAAGTTT-GAGGGA
* ** * * * **
677 AAAAATGGAATTTTTGGAAGTTT-GAGCATAAATATATAATTTTCGAAAGTTTTAAGGTC
1 AAAAATGAAATTTTTGGAAGTTTAG-GGGTAAAAATATAATTTTCGGAAG-TTTGAGGGA
*
736 AAAAATGAAAATTTTGGACAGTTTAGGG
1 AAAAATGAAATTTTTGGA-AGTTTAGGG
764 ACCTCCAGGG
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
58 48 0.39
59 64 0.52
60 9 0.07
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (58 bp):
AAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCGGAAGTTTGAGGGA
Done.