Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014098.1 Kokia drynarioides strain JFW-HI SEQ_129129, 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: 1880
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Found at i:849 original size:96 final size:96
Alignment explanation
Indices: 666--852 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
656 GGGAAAAAAA
**
666 TATTCGATTATGTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATC
1 TATTCGATTATGTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATC
* *
731 GAAGATAAGGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAGAAACATTACCTCGATTAAGGG
* * * *
762 TATTCGATTATTTCGATTTGAAGAAAAATTGTACCTAGTAAGTTAAGGCGCAAATTTTTTA-AAT
1 TATTCGATTATGTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGC-AATATTTCAGAA-
*
826 TCG-AGATAAA-AGAATATTACCTCGATT
64 TCGAAGATAAAGA-AACATTACCTCGATT
853 TTAAAGTCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 1 0.01
96 68 0.86
97 10 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (96 bp):
TATTCGATTATGTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATC
GAAGATAAAGAAACATTACCTCGATTAAGGG
Found at i:1318 original size:59 final size:58
Alignment explanation
Indices: 1226--1552 Score: 433
Period size: 59 Copynumber: 5.5 Consensus size: 58
1216 TTTTTGAACA
1226 TTAGGAGGT-AAAATGGTAATTTTT-GAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGT
1 TTAGG-GGTAAAAATGG-AATTTTTAGAAGTTTTGGGGTCAAAAATGG-ATTTTTGGAAGT
* * *
1285 TTAGGGCTAAAAATGGAATTTTTAAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGT
1 TTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAT-GGATTTTTGGAAGT
** *
1344 TTAAAGGTAAAATTGGAATTTTTAGAAGTTTTGGGGTCAAAAATTGGATTTTTGGAAGT
1 TTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAA-TGGATTTTTGGAAGT
* * *
1403 TTGGGGGTAAAAATGGAATTTTTAGAAGTTTCGGGATCAAAAATGGGATTTTTGGAAGT
1 TTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAT-GGATTTTTGGAAGT
* * * *
1462 TTGGGGGTAAAAATAGAATTTTTAGAAGTTTTGGGGTTAGAAATTGGATTTTTGGAAGT
1 TTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCA-AAAATGGATTTTTGGAAGT
* *
1521 TTAGGGGTAAAAATGAAATTTTTGGATAGTTT
1 TTAGGGGTAAAAATGGAATTTTTAGA-AGTTT
1553 AGGGACCTTC
Statistics
Matches: 237, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
58 10 0.04
59 215 0.91
60 12 0.05
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (58 bp):
TTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGATTTTTGGAAGT
Found at i:1552 original size:30 final size:29
Alignment explanation
Indices: 1226--1556 Score: 346
Period size: 29 Copynumber: 11.2 Consensus size: 29
1216 TTTTTGAACA
1226 TTAGGAGGT-AAAATGGTAATTTTT-GAAGT
1 TTAGG-GGTAAAAATGG-AATTTTTGGAAGT
*
1255 TTTGGGGTCAAAAATGGAATTTTTGGAAGT
1 TTAGGGGT-AAAAATGGAATTTTTGGAAGT
* **
1285 TTAGGGCTAAAAATGGAATTTTTAAAAGT
1 TTAGGGGTAAAAATGGAATTTTTGGAAGT
* *
1314 TTTGGGGTTAAAAATGGGATTTTTGGAAGT
1 TTAGGGG-TAAAAATGGAATTTTTGGAAGT
** * *
1344 TTAAAGGTAAAATTGGAATTTTTAGAAGT
1 TTAGGGGTAAAAATGGAATTTTTGGAAGT
*
1373 TTTGGGGTCAAAAATTGG-ATTTTTGGAAGT
1 TTAGGGGT-AAAAA-TGGAATTTTTGGAAGT
* *
1403 TTGGGGGTAAAAATGGAATTTTTAGAAGT
1 TTAGGGGTAAAAATGGAATTTTTGGAAGT
* * *
1432 TTCGGGATCAAAAATGGGATTTTTGGAAGT
1 TTAGGGGT-AAAAATGGAATTTTTGGAAGT
* * *
1462 TTGGGGGTAAAAATAGAATTTTTAGAAGT
1 TTAGGGGTAAAAATGGAATTTTTGGAAGT
* *
1491 TTTGGGGTTAGAAATTGG-ATTTTTGGAAGT
1 TTAGGGG-TA-AAAATGGAATTTTTGGAAGT
*
1521 TTAGGGGTAAAAATGAAATTTTTGGATAGT
1 TTAGGGGTAAAAATGGAATTTTTGGA-AGT
1551 TTAGGG
1 TTAGGG
1557 ACCTTCAAGG
Statistics
Matches: 251, Mismatches: 39, Indels: 23
0.80 0.12 0.07
Matches are distributed among these distances:
28 11 0.04
29 116 0.46
30 116 0.46
31 8 0.03
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
TTAGGGGTAAAAATGGAATTTTTGGAAGT
Done.