Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001980.1 Kokia drynarioides strain JFW-HI SEQ_113826, 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: 3208
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Found at i:1435 original size:29 final size:29
Alignment explanation
Indices: 1320--1630 Score: 171
Period size: 29 Copynumber: 10.9 Consensus size: 29
1310 AGTTTTGAAG
* *
1320 AGTTTG-GGGTTAAAATGTAA-TTTTGGAA
1 AGTTTGAGGGTAAAAATGTAATTTTTAG-A
* * * **
1348 AGTTTTAGGG-GAAAATGTCATTTTGGGGA
1 AGTTTGAGGGTAAAAATGTAATTTT-TAGA
* * * * * *
1377 AGTTCGA-GGTAGACATGTGATCTTTGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTAGA
1405 AGTTTGAGGGTAAAAATGTAATTTTTAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTAGA
*
1434 AGTTTG-GGAG-AAAAATGCAATTTTT---
1 AGTTTGAGG-GTAAAAATGTAATTTTTAGA
* * *
1459 AGTTTGGGGGCAAAAATCTAATTTTTAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTAGA
* * *
1488 AGTTTAAGGGTCAAAATGTGA-TTTTAGGA
1 AGTTTGAGGGTAAAAATGTAATTTTTA-GA
** *
1517 AGTTCAAGGGTAAAAAAGTAATTTTTAAGA
1 AGTTTGAGGGTAAAAATGTAATTTTT-AGA
* *
1547 AGTTCG-GGAGTAAAAATGTACTTTTTAAGA
1 AGTTTGAGG-GTAAAAATGTAATTTTT-AGA
* * * *
1577 AGTTCGGGGGTCAAAATGTGA-TTTTAGAAA
1 AGTTTGAGGGTAAAAATGTAATTTTTAG--A
* *
1607 AG-TTAAGGGTTAAAATGTAATTTT
1 AGTTTGAGGGTAAAAATGTAATTTT
1631 GGAAAGTTTG
Statistics
Matches: 222, Mismatches: 42, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
25 7 0.03
26 15 0.07
28 47 0.21
29 97 0.44
30 53 0.24
31 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AGTTTGAGGGTAAAAATGTAATTTTTAGA
Found at i:1481 original size:26 final size:25
Alignment explanation
Indices: 1405--1486 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 25
1395 GATCTTTGGA
* *
1405 AGTTTGAGGGTAAAAATGTAATTTTT
1 AGTTTG-GGGGAAAAATCTAATTTTT
*
1431 AGAAGTTTGGGAGAAAAATGC-AATTTTT
1 ---AGTTTGGGGGAAAAAT-CTAATTTTT
1459 AGTTTGGGGGCAAAAATCTAATTTTT
1 AGTTTGGGGG-AAAAATCTAATTTTT
1485 AG
1 AG
1487 AAGTTTAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
25 10 0.22
26 15 0.33
28 15 0.33
29 6 0.13
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (25 bp):
AGTTTGGGGGAAAAATCTAATTTTT
Found at i:1549 original size:30 final size:30
Alignment explanation
Indices: 1470--1630 Score: 143
Period size: 30 Copynumber: 5.5 Consensus size: 30
1460 GTTTGGGGGC
* *
1470 AAAAATCTAATTTTT-AGAAGTTTAAGGGT
1 AAAAATGTAATTTTTAAGAAGTTCAAGGGT
* * *
1499 CAAAATGTGA-TTTTAGGAAGTTCAAGGGT
1 AAAAATGTAATTTTTAAGAAGTTCAAGGGT
* *
1528 AAAAAAGTAATTTTTAAGAAGTTC-GGGAGT
1 AAAAATGTAATTTTTAAGAAGTTCAAGG-GT
* **
1558 AAAAATGTACTTTTTAAGAAGTTCGGGGGT
1 AAAAATGTAATTTTTAAGAAGTTCAAGGGT
* * *
1588 CAAAATGTGA-TTTTAGAAAAGTT-AAGGGT
1 AAAAATGTAATTTTTA-AGAAGTTCAAGGGT
*
1617 TAAAATGTAATTTT
1 AAAAATGTAATTTT
1631 GGAAAGTTTG
Statistics
Matches: 106, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.04
29 45 0.42
30 54 0.51
31 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (30 bp):
AAAAATGTAATTTTTAAGAAGTTCAAGGGT
Found at i:2722 original size:13 final size:13
Alignment explanation
Indices: 2704--2749 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2694 ATCTATTTAA
2704 TATTATACTTATT
1 TATTATACTTATT
*
2717 TATTATTAGTATATT
1 TATTA-TACT-TATT
*
2732 TATTATATTTATT
1 TATTATACTTATT
2745 TATTA
1 TATTA
2750 AAACGTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 14 0.48
14 6 0.21
15 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTATACTTATT
Found at i:2733 original size:15 final size:13
Alignment explanation
Indices: 2686--2749 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 13
2676 TTTTTATTAT
*
2686 TATTTATTATCTA
1 TATTTATTATATA
2699 T-TTAATATTATACT-
1 TATT--TATTATA-TA
2713 TATTTATTATTAGTA
1 TATTTATTA-TA-TA
*
2728 TATTTATTATATT
1 TATTTATTATATA
2741 TATTTATTA
1 TATTTATTA
2750 AAACGTTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.05
13 16 0.38
14 12 0.29
15 12 0.29
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (13 bp):
TATTTATTATATA
Done.