Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011094.1 Kokia drynarioides strain JFW-HI SEQ_126067, 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: 2455
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.32
Warning! 111 characters in sequence are not A, C, G, or T
Found at i:395 original size:29 final size:28
Alignment explanation
Indices: 363--425 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
353 AAATGAGACG
363 TTTTGGATACCCGAGGGCAAAAATGGTAA
1 TTTTGGATACCC-AGGGCAAAAATGGTAA
*** **
392 TTTTGGATTTTCAGGGGTAAAATGGTAA
1 TTTTGGATACCCAGGGCAAAAATGGTAA
420 TTTTGG
1 TTTTGG
426 GAAAATTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (28 bp):
TTTTGGATACCCAGGGCAAAAATGGTAA
Found at i:558 original size:29 final size:29
Alignment explanation
Indices: 537--799 Score: 316
Period size: 29 Copynumber: 9.0 Consensus size: 29
527 AAAATGGTTA
537 TTTTGGAAGTTTTGGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGT-AAAAATGGAAT
* * *
567 TTTTGGAAGTTTCGAGGTTAAAAATGAAAT
1 TTTTGGAAGTTTTG-GGGTAAAAATGGAAT
* *
597 TTTTGGAAGTTTGGGGGAAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGTAAAAATGGAAT
** *
626 TTTTAAAAGTTTTGAGGTTAAAAATGGAAT
1 TTTTGGAAGTTTTG-GGGTAAAAATGGAAT
*
656 TTTTGGAAGTTTAGGGGTAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGTAAAAATGGAAT
* *
685 TTTTGGAAGTTTTGAGGTTAAAAAT-GATT
1 TTTTGGAAGTTTTG-GGGTAAAAATGGAAT
*
714 TTTTGGAAGTTTAGGGGTAAAAATGGAAT
1 TTTTGGAAGTTTTGGGGTAAAAATGGAAT
* *
743 TTTTGAAAGTTTTAGGGTCAAAAATGGAA-
1 TTTTGGAAGTTTTGGGGT-AAAAATGGAAT
*
772 TTTTGGAAG-TTCGAGGGTAAAAATGGAA
1 TTTTGGAAGTTTTG-GGGTAAAAATGGAA
800 ATTTCGAACA
Statistics
Matches: 199, Mismatches: 28, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
28 21 0.11
29 96 0.48
30 79 0.40
31 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTTTGGGGTAAAAATGGAAT
Found at i:622 original size:59 final size:59
Alignment explanation
Indices: 537--813 Score: 371
Period size: 59 Copynumber: 4.7 Consensus size: 59
527 AAAATGGTTA
* * * *
537 TTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGAAAT
1 TTTTGGAAGTTTGGGGGT-AAAAATGGAATTTTTGAAAGTTTTGAGGTTAAAAATGGAAT
* *
597 TTTTGGAAGTTTGGGGGAAAAAATGGAATTTTTAAAAGTTTTGAGGTTAAAAATGGAAT
1 TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGAAAGTTTTGAGGTTAAAAATGGAAT
* * *
656 TTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAAT-GATT
1 TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGAAAGTTTTGAGGTTAAAAATGGAAT
* *
714 TTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGAAAGTTTT-AGGGTCAAAAATGGAA-
1 TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGAAAGTTTTGA-GGTTAAAAATGGAAT
* * * *
772 TTTTGGAAGTTCGAGGGTAAAAATGGAAATTTCGAACAGTTT
1 TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGAA-AGTTT
814 AGAAACCTCC
Statistics
Matches: 195, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.01
58 84 0.43
59 94 0.48
60 16 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGAAAGTTTTGAGGTTAAAAATGGAAT
Found at i:802 original size:29 final size:29
Alignment explanation
Indices: 374--803 Score: 206
Period size: 29 Copynumber: 14.7 Consensus size: 29
364 TTTGGATACC
* * **
374 CGAGGGCAAAAATGGTAATTTTGGATTTT
1 CGAGGGTAAAAATGGAAATTTTGGAAGTT
* *
403 C-AGGGGT-AAAATGGTAATTTTGGGAAAATT
1 CGA-GGGTAAAAATGGAAATTTT-GG-AAGTT
* * *
433 TG-GGGTTAAAAATGGAAGTTTTAGACA-TT
1 CGAGGG-TAAAAATGGAAATTTTGGA-AGTT
* ** *
462 CGGGGGT-AAACGGGTAATTTT-GAGAGTTT
1 CGAGGGTAAAAATGGAAATTTTGGA-AG-TT
* **
491 CGA-GGTCGAAAATGGAGTTTTTGGACA-TT
1 CGAGGGT-AAAAATGGAAATTTTGGA-AGTT
** **
520 CG-GGGGCAAAATGGTTATTTTGGAAGTTT
1 CGAGGGTAAAAATGGAAATTTTGGAAG-TT
* *
549 TG-GGGTCAAAAATGGAATTTTTGGAAGTTT
1 CGAGGGT-AAAAATGGAAATTTTGGAAG-TT
*
579 CGAGGTTAAAAAT-GAAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAAA-TTTTGGAAGTT
* * * * **
608 TGGGGGAAAAAATGGAATTTTTAAAAGTTT
1 CGAGGGTAAAAATGGAAATTTTGGAAG-TT
* * *
638 TGAGGTTAAAAATGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAAATTTTGGAAGTT
* *
667 -TAGGGGTAAAAATGGAATTTTTGGAAGTTT
1 CGA-GGGTAAAAATGGAAATTTTGGAAG-TT
* * **
697 TGAGGTTAAAAAT-GATTTTTTGGAAGTT
1 CGAGGGTAAAAATGGAAATTTTGGAAGTT
* * *
725 -TAGGGGTAAAAATGGAATTTTTGAAAGTT
1 CGA-GGGTAAAAATGGAAATTTTGGAAGTT
**
754 TTAGGGTCAAAAATGG-AATTTTGGAAGTT
1 CGAGGGT-AAAAATGGAAATTTTGGAAGTT
783 CGAGGGTAAAAATGGAAATTT
1 CGAGGGTAAAAATGGAAATTT
804 CGAACAGTTT
Statistics
Matches: 313, Mismatches: 59, Indels: 58
0.73 0.14 0.13
Matches are distributed among these distances:
27 5 0.02
28 62 0.20
29 126 0.40
30 101 0.32
31 19 0.06
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
CGAGGGTAAAAATGGAAATTTTGGAAGTT
Done.