Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013109.1 Kokia drynarioides strain JFW-HI SEQ_128128, 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: 2775
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Found at i:1408 original size:30 final size:28
Alignment explanation
Indices: 1372--1679 Score: 255
Period size: 30 Copynumber: 10.5 Consensus size: 28
1362 GACAAACAAC
*
1372 ATTTTTGGAAGGTTAGGGGCTAAAAATGGG
1 ATTTTTGGAAGGTTCGGGG-T-AAAATGGG
* *
1402 ATTTTTGGGA-GTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCG-GGGTAAAATGG-G
* *
1431 AATTTTGGAAGGTTCGAGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGT--AAAATGGG
*
1461 ATTTTTGGAA-GTTCGGGGGTAAAATGGT
1 ATTTTTGGAAGGTTC-GGGGTAAAATGGG
* *
1489 AATTTTGGAAGGTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGT--AAAATGGG
*
1519 ATTTTTGGAA-GTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCG-GGGTAAAATGG-G
*
1548 ATTTTTAGAAGGTTCGGGGCTAAAAATGGG
1 ATTTTTGGAAGGTTCGGGG-T-AAAATGGG
* *
1578 ATTTTTGGAA-GTTTGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCG-GGGTAAAATGG-G
* *
1607 ATTTTTGGAAGATTTGGGGTTAAAAATGGG
1 ATTTTTGGAAGGTTCGGGG-T-AAAATGGG
* * * **
1637 ATTTTTTGAAGTTTGGGGGTAAAATAGTA
1 ATTTTTGGAAGGTTCGGGGTAAAAT-GGG
1666 ATTTTTGGAAGGTT
1 ATTTTTGGAAGGTT
1680 TAGGGACCTC
Statistics
Matches: 228, Mismatches: 30, Indels: 41
0.76 0.10 0.14
Matches are distributed among these distances:
28 47 0.21
29 71 0.31
30 89 0.39
31 21 0.09
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (28 bp):
ATTTTTGGAAGGTTCGGGGTAAAATGGG
Found at i:1440 original size:59 final size:58
Alignment explanation
Indices: 1372--1684 Score: 430
Period size: 59 Copynumber: 5.3 Consensus size: 58
1362 GACAAACAAC
*
1372 ATTTTTGGAAGGTTAGGGGCTAAAAATGGGATTTTTGGGAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTAGGGG-TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * *
1431 AATTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTAGGGGT-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
1490 A-TTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTAGGGGT-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * *
1548 ATTTTTAGAAGGTTCGGGGCTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTA
1 ATTTTTGGAAGGTTAGGGG-TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * * * *
1607 ATTTTTGGAAGATTTGGGGTTAAAAATGGGATTTTTTGAAGTTTGGGGGTAAAATAGTA
1 ATTTTTGGAAGGTTAGGGG-TAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
1666 ATTTTTGGAAGGTTTAGGG
1 ATTTTTGGAAGG-TTAGGG
1685 ACCTCCGGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
58 56 0.24
59 168 0.73
60 6 0.03
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (58 bp):
ATTTTTGGAAGGTTAGGGGTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:1580 original size:117 final size:118
Alignment explanation
Indices: 1372--1679 Score: 460
Period size: 117 Copynumber: 2.6 Consensus size: 118
1362 GACAAACAAC
* * *
1372 ATTTTTGGAAGGTTAGGGG-CTAAAAATGGGATTTTTGGGAGTTCGAGGGTAAAATGGTAAATTT
1 ATTTTTGGAAGGTTTGGGGTC-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTT
*
1436 TGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTA
65 TGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
1490 A-TTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
1 ATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
* * *
1554 AGAAGGTTCG-GGGCTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTA
66 GGAAGGTTCGAGGTC-AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * * * *
1607 ATTTTTGGAAGATTTGGGGTTAAAAATGGGATTTTTTGAAGTTTGGGGGTAAAATAGTAATTTTT
1 ATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
1672 GGAAGGTT
66 GGAAGGTT
1680 TAGGGACCTC
Statistics
Matches: 173, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
116 3 0.02
117 104 0.60
118 66 0.38
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (118 bp):
ATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT
GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:1669 original size:29 final size:29
Alignment explanation
Indices: 1402--1676 Score: 175
Period size: 29 Copynumber: 9.4 Consensus size: 29
1392 TAAAAATGGG
* * * *
1402 ATTTTTGGGAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
* * * * **
1431 AATTTTGGAAGGTTCGAGGTCAAAA-ATGGG
1 ATTTTTGGAAGTTTGGGGGT-AAAATA-GTA
* *
1461 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
**
1490 A-TTTTGGAAGGTTT-GGGGTCAAAA-ATGGG
1 ATTTTTGGAA-GTTTGGGGGT-AAAATA-GTA
* * *
1519 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
* * * **
1548 ATTTTTAGAAGGTTCGGGGCTAAAA-ATGGG
1 ATTTTTGGAA-GTTTGGGGGTAAAATA-GTA
* *
1578 ATTTTTGGAAGTTTGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
* **
1607 ATTTTTGGAAGATTTGGGGTTAAAA-ATGGG
1 ATTTTTGGAAG-TTTGGGGGTAAAATA-GTA
*
1637 ATTTTTTGAAGTTTGGGGGTAAAATAGTA
1 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
1666 ATTTTTGGAAG
1 ATTTTTGGAAG
1677 GTTTAGGGAC
Statistics
Matches: 181, Mismatches: 50, Indels: 30
0.69 0.19 0.11
Matches are distributed among these distances:
28 13 0.07
29 91 0.50
30 77 0.43
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTTGGGGGTAAAATAGTA
Done.