Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007273.1 Kokia drynarioides strain JFW-HI SEQ_121889, 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: 7254
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:688 original size:117 final size:117
Alignment explanation
Indices: 475--712 Score: 352
Period size: 117 Copynumber: 2.0 Consensus size: 117
465 TGTCTCACGG
* * * * *
475 TTTCGTTATATTGAAGCTCCCAATCCCGTAAACTACTGTCCTTGGAGTCAATTTTCTCTACAAGG
1 TTTCCTTATATCGAAGCTCCCAATCCCGCAAACCACTGTCCTTGGAGTCAATTTTCGCTACAAGG
* *
540 CCATCAACGAGTCTTTGAAGAGCTACGGTTGTCTCATCATATTTATGTTCCA
66 CCATCAACGAGTCTTTGAAGAGCCACCGTTGTCTCATCATATTTATGTTCCA
592 TTTCCTTATATCGAAGCTCCCAATCCCGCAAACCACTGTCCTTGGAGTCAATTTTCGCTACAAGG
1 TTTCCTTATATCGAAGCTCCCAATCCCGCAAACCACTGTCCTTGGAGTCAATTTTCGCTACAAGG
* * ** *
657 CCATCGACGAGT-TCTTGAAGAGCCGCCGTTGTCTTGTCATATTTATGTTCCT
66 CCATCAACGAGTCT-TTGAAGAGCCACCGTTGTCTCATCATATTTATGTTCCA
709 TTTC
1 TTTC
713 GGACAACTGT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 1 0.01
117 107 0.99
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (117 bp):
TTTCCTTATATCGAAGCTCCCAATCCCGCAAACCACTGTCCTTGGAGTCAATTTTCGCTACAAGG
CCATCAACGAGTCTTTGAAGAGCCACCGTTGTCTCATCATATTTATGTTCCA
Found at i:1635 original size:57 final size:56
Alignment explanation
Indices: 1526--1636 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 56
1516 GTTGGCCCAT
* *
1526 TTAATTTTTAAAAAATAGAATTTAATTAAAAAAATACATATTTAAAGAATAATTAA
1 TTAATTTTTAAAAAATAGAATTTAATTAAAAAAAGACATATTTAAAAAATAATTAA
* * *
1582 TTAATTTTTGAAAAATATAATTTAAATT-AAATAAGACATA-TTAATTAAAATAATT
1 TTAATTTTTAAAAAATAGAATTT-AATTAAAAAAAGACATATTTAA--AAAATAATT
1637 GAAGGGCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 4 0.09
56 31 0.66
57 12 0.26
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (56 bp):
TTAATTTTTAAAAAATAGAATTTAATTAAAAAAAGACATATTTAAAAAATAATTAA
Found at i:5511 original size:71 final size:72
Alignment explanation
Indices: 5388--5576 Score: 183
Period size: 71 Copynumber: 2.6 Consensus size: 72
5378 TGTCATGGTA
* * * * * *
5388 AACAGAAACAGTGAGTTCCACGACCTGGGC-CTACAGGCGTGGGCTGGACCGTGTGGGT-ACTCT
1 AACAGAAACAGTGAGTTACACGATCTGGGCAC-ACGGGCATGGGCTAGACCGTGT-GATCACTCT
5451 -AA-TTTGTG
64 AAAGTTT-TG
* *
5459 AACAGAAACAGTGAGTTACACGGTCTGGGCACACGGGCATGTGCTA-AGCCGTGTGATCACTCTG
1 AACAGAAACAGTGAGTTACACGATCTGGGCACACGGGCATGGGCTAGA-CCGTGTGATCACTCT-
5523 AAAGTTTTG
64 AAAGTTTTG
* *
5532 AA-ATGCAAACAGTGAGTTACACGATCTGGACACACGGGCGTGGGC
1 AACA-G-AAACAGTGAGTTACACGATCTGGGCACACGGGCATGGGC
5577 CTAACTGTGT
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
70 3 0.03
71 48 0.49
72 2 0.02
73 7 0.07
74 38 0.39
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (72 bp):
AACAGAAACAGTGAGTTACACGATCTGGGCACACGGGCATGGGCTAGACCGTGTGATCACTCTAA
AGTTTTG
Done.