Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009184.1 Kokia drynarioides strain JFW-HI SEQ_123889, 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: 14580
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2814 original size:29 final size:28
Alignment explanation
Indices: 2771--2846 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 28
2761 ATTTGAGTTA
2771 AAATCAAAATTTCATGTAA-ATAATTACACC
1 AAATCAAAA-TTCATGTAACA-AATTACA-C
*
2801 AAATCAAAATTCATATAACAAATTACAC
1 AAATCAAAATTCATGTAACAAATTACAC
2829 ATTATATCAAAATTCATG
1 A--A-ATCAAAATTCATG
2847 CGTAGTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 2 0.05
29 15 0.38
30 11 0.28
31 12 0.30
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (28 bp):
AAATCAAAATTCATGTAACAAATTACAC
Found at i:4707 original size:76 final size:76
Alignment explanation
Indices: 4581--4883 Score: 570
Period size: 76 Copynumber: 4.0 Consensus size: 76
4571 TATTCTCTTA
*
4581 AATTAGGGGTTGTAGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
1 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
*
4646 GTGGATTTCTC
66 GTGGTTTTCTC
4657 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
1 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
4722 GTGGTTTTCTC
66 GTGGTTTTCTC
4733 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
1 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
*
4798 GTGGTTTTCTT
66 GTGGTTTTCTC
*
4809 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGGAGGGTATTT
1 AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
4874 GTGGTTTTCT
66 GTGGTTTTCT
4884 GTAAGTTCAC
Statistics
Matches: 223, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 223 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (76 bp):
AATTAGGGGTTGTTGATGGATATTGTAGGGTTGACAAGTAGAGTTAGTGTTCTTGTAGGGTATTT
GTGGTTTTCTC
Found at i:10479 original size:23 final size:24
Alignment explanation
Indices: 10453--10509 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
10443 TATAACTTAT
*
10453 TATTAATATTTTAATATAT-GAAA
1 TATTAATATTTAAATATATCGAAA
* *
10476 TATTAAT-TTTAAATATTTCTAAA
1 TATTAATATTTAAATATATCGAAA
10499 TAATTAATATT
1 T-ATTAATATT
10510 AATTATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 11 0.39
24 6 0.21
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTAATATTTAAATATATCGAAA
Found at i:10511 original size:24 final size:23
Alignment explanation
Indices: 10473--10517 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
10463 TTAATATATG
*
10473 AAATATTAATTTTAAATATTTCT
1 AAATATTAATATTAAATATTTCT
*
10496 AAATAATTAATATTAATTATTT
1 AAAT-ATTAATATTAAATATTT
10518 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTCT
Found at i:10523 original size:24 final size:23
Alignment explanation
Indices: 10473--10528 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
10463 TTAATATATG
* **
10473 AAATATTAATTTTAAATATTTCT
1 AAATATTAATATTAAATATTTAA
*
10496 AAATAATTAATATTAATTATTTAA
1 AAAT-ATTAATATTAAATATTTAA
10520 AAAT-TTAAT
1 AAATATTAAT
10529 TAGATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.18
23 4 0.14
24 19 0.68
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAA
Found at i:10901 original size:74 final size:74
Alignment explanation
Indices: 10799--10947 Score: 244
Period size: 74 Copynumber: 2.0 Consensus size: 74
10789 TCCAAATGAT
* * *
10799 GTTTATTTAGTATTCTTTAAAATAAAAAAAACTTATTTAATAAAAAAATTATTTTAAAAGCTTAG
1 GTTTATTTAGTATCCTTTAAAACAAAAAAAACTTATTTAATAAAAAAATTATTCTAAAAGCTTAG
*
10864 CTCAACACA
66 CCCAACACA
* *
10873 GTTTGTTTAGTATCCTTTAAAACCAAAAAAACTTATTTAATAAAAAAATTATTCTAAAAGCTTAG
1 GTTTATTTAGTATCCTTTAAAACAAAAAAAACTTATTTAATAAAAAAATTATTCTAAAAGCTTAG
10938 CCCAACACA
66 CCCAACACA
10947 G
1 G
10948 CCTTAATAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (74 bp):
GTTTATTTAGTATCCTTTAAAACAAAAAAAACTTATTTAATAAAAAAATTATTCTAAAAGCTTAG
CCCAACACA
Found at i:11845 original size:59 final size:58
Alignment explanation
Indices: 11723--11898 Score: 318
Period size: 59 Copynumber: 3.0 Consensus size: 58
11713 TCCTTTACTT
11723 TGAGATTGAGAGTTCTGTGGCTATTGTCAATT-GTGTGATAAAGAAAGCTATGGGTAC
1 TGAGATTGAGAGTTCTGTGGCTATTGTCAATTGGTGTGATAAAGAAAGCTATGGGTAC
*
11780 TGAGATTGAGAGTTCTGCGGCTATTGTCAATTGCGTGTGATAAAGAAAGCTATGGGTAC
1 TGAGATTGAGAGTTCTGTGGCTATTGTCAATTG-GTGTGATAAAGAAAGCTATGGGTAC
11839 TGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGCTATGGGTAC
1 TGAGATTGAGAGTTCTGTGGCTATTGTCAATTG-GTGTGATAAAGAAAGCTATGGGTAC
11898 T
1 T
11899 ATGGCTTGAT
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
57 31 0.27
59 83 0.73
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (58 bp):
TGAGATTGAGAGTTCTGTGGCTATTGTCAATTGGTGTGATAAAGAAAGCTATGGGTAC
Done.