Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006782.1 Kokia drynarioides strain JFW-HI SEQ_121381, 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: 22342
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4881 original size:38 final size:38
Alignment explanation
Indices: 4830--4902 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
4820 TTTTGAGGAA
4830 AAGAAATCTCTAAGAACCCTCCAAAAACCAATAGATTT
1 AAGAAATCTCTAAGAACCCTCCAAAAACCAATAGATTT
*
4868 AAGAAATCTCTAAGAACCCTCCAAAAGCCAATAGA
1 AAGAAATCTCTAAGAACCCTCCAAAAACCAATAGA
4903 ATTCTAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.48, C:0.25, G:0.10, T:0.18
Consensus pattern (38 bp):
AAGAAATCTCTAAGAACCCTCCAAAAACCAATAGATTT
Found at i:8358 original size:55 final size:55
Alignment explanation
Indices: 8293--8404 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
8283 AATAAAAGAG
8293 ACCAAAGACGTAATTACACCAAGGTAAAAAAGTCCAAGCGGTGGAGGATATGATT
1 ACCAAAGACGTAATTACACCAAGGTAAAAAAGTCCAAGCGGTGGAGGATATGATT
8348 ACCAAAGACGTAATTACACCAAGGTAAAAAAGTCCAAGCGGTGGAGGATATGATT
1 ACCAAAGACGTAATTACACCAAGGTAAAAAAGTCCAAGCGGTGGAGGATATGATT
8403 AC
1 AC
8405 ATTCCACTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (55 bp):
ACCAAAGACGTAATTACACCAAGGTAAAAAAGTCCAAGCGGTGGAGGATATGATT
Found at i:9279 original size:16 final size:16
Alignment explanation
Indices: 9258--9289 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9248 GGTAATTTTT
*
9258 ATGTTAAAGGATTAAA
1 ATGTTAAAGGAATAAA
9274 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
9290 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:9857 original size:53 final size:53
Alignment explanation
Indices: 9743--10041 Score: 322
Period size: 53 Copynumber: 5.7 Consensus size: 53
9733 CCGTGAATGA
* * * *
9743 AAAAGGTTCGATGACTAC-GTATCATCGTGAG-TATATGAATCCT-TCATGGATT
1 AAAAGGTCCGATGACT-CTGTGTCATCGTGAGTTATATGAATCCTATTACGGA-T
* *
9795 ATGAA-GTCCGATGACTAC-GTGTCATCGTGAGGTATATGAATCCTATTACGGAT
1 A-AAAGGTCCGATGACT-CTGTGTCATCGTGAGTTATATGAATCCTATTACGGAT
* *
9848 AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTACGGAT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGAT
* * * *
9901 TACAGGTCTGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGA-T
* * * **
9955 ACAA-GTCCGATGACTCTGTGTCATCATGAGTTACATGAATCCTATTATAGAT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGAT
* * * *
10007 TAGAGGTTCGATGATTCTGTGTCATCGTGAGTTAT
1 AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
10042 CAAATGTGAA
Statistics
Matches: 212, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
52 30 0.14
53 175 0.83
54 7 0.03
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (53 bp):
AAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGAT
Found at i:9927 original size:106 final size:107
Alignment explanation
Indices: 9743--10037 Score: 368
Period size: 106 Copynumber: 2.8 Consensus size: 107
9733 CCGTGAATGA
* * * * * *
9743 AAAAGGTTCGATGACTACGTATCATCGTGAG-TATATGAATCC-TTCATGGATTATGAAGTCCGA
1 AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTATGGATTA-GAGGTCTGA
*
9806 TGACTAC-GTGTCATCGTGAGGTATATGAATCCTATTACGGA-T
65 TGACT-CTGTGTCATCGTGAGGTATATGAATCCTATTACAGATT
* *
9848 AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTACGGATTACAGGTCTGAT
1 AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTATGGATTAGAGGTCTGAT
*
9913 GACTCTGTGTCATCGTGAGTTATATGAATCCTATTACAGATT
66 GACTCTGTGTCATCGTGAGGTATATGAATCCTATTACAGATT
* * * * * *
9955 ACAA-GTCCGATGACTCTGTGTCATCATGAGTTACATGAATCCTATTATAGATTAGAGGT-TCGA
1 AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTATGGATTAGAGGTCT-GA
*
10018 TGATTCTGTGTCATCGTGAG
65 TGACTCTGTGTCATCGTGAG
10038 TTATCAAATG
Statistics
Matches: 166, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
105 30 0.18
106 123 0.74
107 13 0.08
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (107 bp):
AAAAGGTCCGATGACTCCGTGTCATCGTGAGTTATATGAATCCTTTTATGGATTAGAGGTCTGAT
GACTCTGTGTCATCGTGAGGTATATGAATCCTATTACAGATT
Found at i:20201 original size:6 final size:6
Alignment explanation
Indices: 20190--20217 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20180 ATGTTCTCAA
20190 TCTTGT TCTTGT TCTTGT TCTTGT TCTT
1 TCTTGT TCTTGT TCTTGT TCTTGT TCTT
20218 CTTAATCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (6 bp):
TCTTGT
Found at i:20510 original size:20 final size:19
Alignment explanation
Indices: 20485--20530 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
20475 TTAGAAATAT
*
20485 TAAAATATTAAATAATTAAA
1 TAAAATATTAAA-AATAAAA
*
20505 TAAAATTTTAAAAATAAAA
1 TAAAATATTAAAAATAAAA
20524 TATAAAT
1 TA-AAAT
20531 GTCATAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATATTAAAAATAAAA
Done.