Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003846.1 Kokia drynarioides strain JFW-HI SEQ_116866, 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, 884
Length: 1474
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Found at i:396 original size:29 final size:28
Alignment explanation
Indices: 363--950 Score: 244
Period size: 30 Copynumber: 20.0 Consensus size: 28
353 ATTTTGAGAA
*
363 AATTCGGGGTTAAAAATGGAATTTTTAG
1 AATTCGGGGTTAAAAATGGAATTTTTGG
*
391 ACATTCGGGG-T-AAAAGGGTAA-TTTTGAG
1 A-ATTCGGGGTTAAAAATGG-AATTTTTG-G
* * * ** * * *
419 AGTTTCGAGATCGAAAATAGAGTTTTTAG
1 A-ATTCGGGGTTAAAAATGGAATTTTTGG
* *
448 ACATCCGAGGG-CAA-AATGGTAATTTTTGG
1 A-ATTCG-GGGTTAAAAATGG-AATTTTTGG
* * * *
477 AGGTTTCAGGGTCAAAAATGGGATTTTTGG
1 A--ATTCGGGGTTAAAAATGGAATTTTTGG
* *
507 AAGTTCGGGGGTAAAAATAGAATTTTTGG
1 AA-TTCGGGGTTAAAAATGGAATTTTTGG
* **
536 AAGTCTCGGGGTCAAAAATGGGGTTTTTGG
1 AA-T-TCGGGGTTAAAAATGGAATTTTTGG
* *
566 AAGTTCGAGGG-TGAAAACGGAATTTTTGGG
1 AA-TTCG-GGGTTAAAAATGGAATTTTT-GG
* * * * *
596 AGTTTCGAGGTCAAAAATGGGATTTTTTG
1 A-ATTCGGGGTTAAAAATGGAATTTTTGG
* *
625 AAGTTCGGGGGTAAAAATGGAATTTTTGA
1 AA-TTCGGGGTTAAAAATGGAATTTTTGG
* *
654 AAGTCTCGGGGTCAAAAATAGG-GTTTTTGG
1 AA-T-TCGGGGTTAAAAAT-GGAATTTTTGG
* * **
684 AAGTTCGAGGG-TGAAAATGGAATGATGGGG
1 AA-TTCG-GGGTTAAAAATGGAAT-TTTTGG
* * *
714 AGTTTCGGGGTCAAAAATGGGATTTTTGG
1 A-ATTCGGGGTTAAAAATGGAATTTTTGG
*
743 AAGTTC-GAGTGTAAAAATGGAATTTTTGG
1 AA-TTCGGGGT-TAAAAATGGAATTTTTGG
* **
772 AAGTTTTGGGGTTAAAAATGGGGTTTTTGG
1 AA--TTCGGGGTTAAAAATGGAATTTTTGG
* *
802 AAATTTAGGGGTAAAAAACT-GAATTTTTGGG
1 -AA-TTCGGGGTTAAAAA-TGGAATTTTT-GG
* * * *
833 AGTTTCGAGGTAAAAAATGGGATTTTTGG
1 A-ATTCGGGGTTAAAAATGGAATTTTTGG
862 AAGTTCGAGGG-TAAAAATGGAATTTTTGG
1 AA-TTCG-GGGTTAAAAATGGAATTTTTGG
* * ** *
891 AAGTTTCGGGATAAAAAATGGGGTTTTTGA
1 AA--TTCGGGGTTAAAAATGGAATTTTTGG
* * *
921 AAGTTCGGGGGTGAAAACGGAATTTTTGG
1 AA-TTCGGGGTTAAAAATGGAATTTTTGG
950 A
1 A
951 CAATTTAGGG
Statistics
Matches: 414, Mismatches: 108, Indels: 75
0.69 0.18 0.13
Matches are distributed among these distances:
27 10 0.02
28 20 0.05
29 178 0.43
30 191 0.46
31 15 0.04
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.32
Consensus pattern (28 bp):
AATTCGGGGTTAAAAATGGAATTTTTGG
Found at i:425 original size:28 final size:27
Alignment explanation
Indices: 306--419 Score: 97
Period size: 28 Copynumber: 4.0 Consensus size: 27
296 TTTTTCGGAT
*
306 ATTCGGGGGCAAAATGGTAATTTTG-GA
1 ATTC-GGGGTAAAATGGTAATTTTGAGA
* *
333 TTCTCGAGGGTGAAATGGTAATTTTGAGAAA
1 AT-TCG-GGGTAAAATGGTAATTTTGAG--A
*
364 ATTCGGGGTTAAAAATGG-AATTTTTAGA
1 ATTCGGGG-T-AAAATGGTAATTTTGAGA
*
392 CATTCGGGGTAAAAGGGTAATTTTGAGA
1 -ATTCGGGGTAAAATGGTAATTTTGAGA
420 GTTTCGAGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 8 0.11
28 30 0.43
29 12 0.17
30 12 0.17
31 8 0.11
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (27 bp):
ATTCGGGGTAAAATGGTAATTTTGAGA
Found at i:503 original size:30 final size:29
Alignment explanation
Indices: 460--925 Score: 326
Period size: 30 Copynumber: 15.7 Consensus size: 29
450 ATCCGAGGGC
* *
460 AAAATGGTAATTTTTGGAGGTTTCAGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTCAGGGT-A
*
491 AAAATGGGATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTC-AGGGTA
* * * *
520 AAAATAGAATTTTTGGAAGTCTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCAGGGT-A
* *
550 AAAATGGGGTTTTTGGAAG-TTCGAGGGTG
1 AAAATGGGATTTTTGGAAGTTTC-AGGGTA
* * *
579 AAAACGGAATTTTTGGGAGTTTC-GAGGTCA
1 AAAATGGGATTTTTGGAAGTTTCAG-GGT-A
* *
609 AAAATGGGATTTTTTGAAG-TTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTTC-AGGGTA
* * * *
638 AAAATGGAATTTTTGAAAGTCTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCAGGGT-A
*
668 AAAATAGGG-TTTTTGGAAG-TTCGAGGGTG
1 AAAAT-GGGATTTTTGGAAGTTTC-AGGGTA
* ** * * *
697 AAAATGGAATGATGGGGAGTTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGTTTCAGGGT-A
*
727 AAAATGGGATTTTTGGAAG-TTCGAGTGTA
1 AAAATGGGATTTTTGGAAGTTTC-AGGGTA
* **
756 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGGATTTTTGGAAGTTTCAGGG-TA
* *
786 AAAATGGGGTTTTTGGAAATTT-AGGGGTAA
1 AAAATGGGATTTTTGGAAGTTTCA-GGGT-A
* *
816 AAAACT-GAATTTTTGGGAGTTTC-GAGGTAA
1 AAAA-TGGGATTTTTGGAAGTTTCAG-GGT-A
846 AAAATGGGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTTC-AGGGTA
*
875 AAAATGGAATTTTTGGAAGTTTC-GGGATAA
1 AAAATGGGATTTTTGGAAGTTTCAGGG-T-A
* *
905 AAAATGGGGTTTTTGAAAGTT
1 AAAATGGGATTTTTGGAAGTT
926 CGGGGGTGAA
Statistics
Matches: 343, Mismatches: 62, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.02
29 138 0.40
30 187 0.55
31 12 0.03
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTTCAGGGTA
Found at i:504 original size:59 final size:59
Alignment explanation
Indices: 460--950 Score: 553
Period size: 59 Copynumber: 8.3 Consensus size: 59
450 ATCCGAGGGC
* *
460 AAAATGGTAATTTTTGGAGGTTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGG-AATTTTTGGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * * *
520 AAAATAGAATTTTTGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTG
1 AAAATGGAATTTTTGGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * *
579 AAAACGGAATTTTTGG-GAGTTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAG-GTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * *
638 AAAATGGAATTTTTGAAAGTCTCGGGGTCAAAAATAGGG-TTTTTGGAAGTTCGAGGGTG
1 AAAATGGAATTTTTGGAGGTTTCGGGGTCAAAAAT-GGGATTTTTGGAAGTTCGAGGGTA
** * *
697 AAAATGGAA-TGATGGGGAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGTGTA
1 AAAATGGAATTTTTGGAG-GTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * * * *
756 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGGTTTTTGGAAATT-TAGGGGTAA
1 AAAATGGAATTTTTGGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT-A
* *
816 AAAACT-GAATTTTTGG-GAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAA-TGGAATTTTTGGAG-GTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * * * * *
875 AAAATGGAATTTTTGGAAGTTTCGGGATAAAAAATGGGGTTTTTGAAAGTTCGGGGGTG
1 AAAATGGAATTTTTGGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
*
934 AAAACGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
951 CAATTTAGGG
Statistics
Matches: 361, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
58 8 0.02
59 291 0.81
60 60 0.17
61 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAGGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
Found at i:590 original size:118 final size:118
Alignment explanation
Indices: 468--949 Score: 682
Period size: 118 Copynumber: 4.1 Consensus size: 118
458 GCAAAATGGT
* *
468 AATTTTT-GGAGGTTTC-AGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATT
1 AATTTTTGGGA-GTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATT
531 TTTGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAACGG
64 TTTGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAACGG
* *
586 AATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTT
1 AATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
* * *
651 TGAAAGTCTCGGGGTCAAAAATAGGGTTTTTGGAAGTTCGAGGGTGAAAATGG
66 TGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAACGG
** * * *
704 AATGATGGGGAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGTGTAAAAATGGAATTTT
1 AATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
* * * * * * *
769 TGGAAGTTTTGGGGTTAAAAATGGGGTTTTTGGAAATT-TAGGGGTAAAAAACTG
66 TGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGA-GGGT-GAAAACGG
*
823 AATTTTTGGGAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
1 AATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
* * * * *
888 TGGAAGTTTCGGGATAAAAAATGGGGTTTTTGAAAGTTCGGGGGTGAAAACGG
66 TGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAACGG
941 AATTTTTGG
1 AATTTTTGG
950 ACAATTTAGG
Statistics
Matches: 322, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
117 1 0.00
118 216 0.67
119 105 0.33
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (118 bp):
AATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
TGGAAGTCTCGGGGTCAAAAATGGGGTTTTTGGAAGTTCGAGGGTGAAAACGG
Done.