Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005464.1 Kokia drynarioides strain JFW-HI SEQ_119511, 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: 16642
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:700 original size:31 final size:30
Alignment explanation
Indices: 642--728 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
632 TCAAAATTTA
* * *
642 TAAAAATTACATCTTAACCCCTAAACTTTC
1 TAAAAAATACATTTTGACCCCTAAACTTTC
* *
672 TAAAAAATACATTTTGACCCCTCGAACTTTT
1 TAAAAAATACATTTTGACCCCT-AAACTTTC
* * *
703 TAGAAAACTACTTTTTGACCCTTAAA
1 TA-AAAAATACATTTTGACCCCTAAA
729 ATTTTCCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 19 0.41
31 10 0.22
32 17 0.37
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAAAAATACATTTTGACCCCTAAACTTTC
Found at i:4996 original size:12 final size:12
Alignment explanation
Indices: 4981--5014 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4971 ATCCAGAAGA
4981 AAATGCAAGAGC
1 AAATGCAAGAGC
*
4993 AAATGCAAGCGC
1 AAATGCAAGAGC
*
5005 AGATGCAAGA
1 AAATGCAAGA
5015 CCAATTAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.26, T:0.09
Consensus pattern (12 bp):
AAATGCAAGAGC
Found at i:12585 original size:40 final size:40
Alignment explanation
Indices: 12530--12699 Score: 140
Period size: 40 Copynumber: 4.3 Consensus size: 40
12520 CATTTTCGGA
*
12530 GGGCAGATTGAAGACA-ATCCAATCTCTTACCTC-GATCATG
1 GGGCAGATTAAAGACATA-CCAATCTCTTACC-CAGATCATG
12570 GGGCAGATTAAAGACATACCAATCTCTTACCCAGATCATG
1 GGGCAGATTAAAGACATACCAATCTCTTACCCAGATCATG
* * *
12610 GGGCAGATTGAAG-CAT-CAAATCTTTTACCCCA-ATCATG
1 GGGCAGATTAAAGACATACCAATCTCTTA-CCCAGATCATG
* * * * ** *
12648 AGGTAGA-T-ATGACACACTGATCTCTTAACCC-CATCATG
1 GGGCAGATTAAAGACATACCAATCTCTT-ACCCAGATCATG
*
12686 GGGCAGATTGAAGA
1 GGGCAGATTAAAGA
12700 TAGGTTGCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
36 2 0.02
37 3 0.03
38 41 0.38
39 10 0.09
40 50 0.47
41 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (40 bp):
GGGCAGATTAAAGACATACCAATCTCTTACCCAGATCATG
Found at i:12646 original size:38 final size:39
Alignment explanation
Indices: 12530--12699 Score: 170
Period size: 38 Copynumber: 4.4 Consensus size: 39
12520 CATTTTCGGA
* *
12530 GGGCAGATTGAAGACAATCCAATCTCTTACCTCGATCATG
1 GGGCAGATTGAAGAC-ATCCAATCTCTTACCCCAATCATG
*
12570 GGGCAGATTAAAGACATACCAATCTCTTA-CCCAGATCATG
1 GGGCAGATTGAAGACAT-CCAATCTCTTACCCCA-ATCATG
* *
12610 GGGCAGATTGAAG-CATCAAATCTTTTACCCCAATCATG
1 GGGCAGATTGAAGACATCCAATCTCTTACCCCAATCATG
* * * **
12648 AGGTAGATATG-ACACA-CTGATCTCTTAACCCC-ATCATG
1 GGGCAGAT-TGAAGACATCCAATCTCTT-ACCCCAATCATG
12686 GGGCAGATTGAAGA
1 GGGCAGATTGAAGA
12700 TAGGTTGCAA
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
37 2 0.02
38 43 0.40
39 20 0.19
40 43 0.40
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (39 bp):
GGGCAGATTGAAGACATCCAATCTCTTACCCCAATCATG
Found at i:15066 original size:30 final size:30
Alignment explanation
Indices: 15029--15213 Score: 146
Period size: 30 Copynumber: 6.2 Consensus size: 30
15019 TTGTTTTATT
15029 TAAAAATTATATTTTAACCCT-AAACTTTCC
1 TAAAAATTATATTTTAACCCTCAAACTTT-C
* * * * *
15059 CAAAAATTCA-AATTTGACCCTCGATCTTTC
1 TAAAAATT-ATATTTTAACCCTCAAACTTTC
* * *
15089 TAAAAATT-TCATTTTGACCCCCAAACTTTT
1 TAAAAATTAT-ATTTTAACCCTCAAACTTTC
*
15119 TAAAAATT-TCATTTTAACCCTTAAACTTT-
1 TAAAAATTAT-ATTTTAACCCTCAAACTTTC
**
15148 TAAAAATTGCATTTTAACCCTCAAACTTTC
1 TAAAAATTATATTTTAACCCTCAAACTTTC
* * * *
15178 TAAAATTTACATTTTGACCCCTAAAACTTTC
1 TAAAAATTATATTTT-AACCCTCAAACTTTC
*
15209 CAAAA
1 TAAAA
15214 TTTTGATTTC
Statistics
Matches: 127, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
29 26 0.20
30 78 0.61
31 23 0.18
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
TAAAAATTATATTTTAACCCTCAAACTTTC
Found at i:15173 original size:59 final size:59
Alignment explanation
Indices: 15027--15207 Score: 170
Period size: 60 Copynumber: 3.0 Consensus size: 59
15017 CATTGTTTTA
* * * * ** *
15027 TTTAAAAATTATATTTTAACCCT-AAACTTTCCCAAAAA-TTCAAATTTGACCCTCGATCT
1 TTTAAAAATTACATTTTAACCCTCAAACTTT-CTAAAAATTTC-ATTTTAACCCTAAAACT
* * * * *
15086 TTCTAAAAATTTCATTTTGACCCCCAAACTTTTTAAAAATTTCATTTTAACCCTTAAACT
1 TT-TAAAAATTACATTTTAACCCTCAAACTTTCTAAAAATTTCATTTTAACCCTAAAACT
* *
15146 TTTAAAAATTGCATTTTAACCCTCAAACTTTCT-AAAATTTACATTTTGACCCCTAAAACT
1 TTTAAAAATTACATTTTAACCCTCAAACTTTCTAAAAATTT-CATTTT-AACCCTAAAACT
15206 TT
1 TT
15208 CCAAAATTTT
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
58 7 0.07
59 35 0.35
60 48 0.48
61 10 0.10
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTAAAAATTACATTTTAACCCTCAAACTTTCTAAAAATTTCATTTTAACCCTAAAACT
Done.