Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001754.1 Kokia drynarioides strain JFW-HI SEQ_113469, 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: 27717
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1419 original size:7 final size:7
Alignment explanation
Indices: 1407--1431 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1397 TCTATTCAGA
1407 TGATTGT
1 TGATTGT
1414 TGATTGT
1 TGATTGT
1421 TGATTGT
1 TGATTGT
1428 TGAT
1 TGAT
1432 GTGGTATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (7 bp):
TGATTGT
Found at i:3571 original size:28 final size:28
Alignment explanation
Indices: 3531--3585 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3521 ATTGGGATTT
* * * *
3531 TTTTATAATTTATAAAATTTTAAATTAA
1 TTTTAAAAATTATAAAAATATAAATTAA
3559 TTTTAAAAATTATAAAAATATAAATTA
1 TTTTAAAAATTATAAAAATATAAATTA
3586 TTAAAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTAAAAATTATAAAAATATAAATTAA
Found at i:3585 original size:15 final size:17
Alignment explanation
Indices: 3564--3604 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3554 ATTAATTTTA
3564 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
3580 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
3596 AAAATTATA
1 AAAATTATA
3605 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:4805 original size:63 final size:63
Alignment explanation
Indices: 4702--4827 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
4692 TATGCCCCTG
* *
4702 ATAACTATGAACTAAAAAATAATGGTATAATAAACCTAAATTTAATAAAATAATTTTAATAAT
1 ATAACTATGAACTAAAAAATAACGGTATAATAAACCTAAATTTAACAAAATAATTTTAATAAT
* * *
4765 ATAACTATGAACTAAAAAA-AACCGGTATAATATACGTAAATTTAACACAATAATTTTAATAAT
1 ATAACTATGAACTAAAAAATAA-CGGTATAATAAACCTAAATTTAACAAAATAATTTTAATAAT
4828 GAAAACAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 2 0.04
63 55 0.96
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.32
Consensus pattern (63 bp):
ATAACTATGAACTAAAAAATAACGGTATAATAAACCTAAATTTAACAAAATAATTTTAATAAT
Found at i:5132 original size:16 final size:18
Alignment explanation
Indices: 5111--5143 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5101 TTTTATTTTT
5111 TTTAAT-ATTT-TTTATG
1 TTTAATAATTTCTTTATG
5127 TTTAATAATTTCTTTAT
1 TTTAATAATTTCTTTAT
5144 TTTGAACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTAATAATTTCTTTATG
Found at i:19309 original size:36 final size:37
Alignment explanation
Indices: 19269--19349 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
19259 GTGATATGAT
* **
19269 GAGTACATCTGTGGTGAAAT-CCAACAAATGATTAAA
1 GAGTACATCTATAATGAAATACCAACAAATGATTAAA
**
19305 GAGTACATCTATAATGAAATACCTTCAAATGATTAAA
1 GAGTACATCTATAATGAAATACCAACAAATGATTAAA
19342 GAGTACAT
1 GAGTACAT
19350 ATATGCTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 17 0.44
37 22 0.56
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (37 bp):
GAGTACATCTATAATGAAATACCAACAAATGATTAAA
Found at i:24136 original size:6 final size:6
Alignment explanation
Indices: 24115--24191 Score: 84
Period size: 6 Copynumber: 13.0 Consensus size: 6
24105 AAAGGTGCAT
* * * * *
24115 AATAAA GATGAA AATAAA AATAAA AAT-AA AATGAA AATGAA AATGAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
* *
24162 AATGAA AATAAA AATAAA AATAAA ACTAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
24192 TATACTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
5 5 0.08
6 59 0.92
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:24138 original size:18 final size:18
Alignment explanation
Indices: 24115--24191 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
24105 AAAGGTGCAT
*
24115 AATAAAGATGAAAATAAA
1 AATAAAAATGAAAATAAA
*
24133 AATAAAAAT-AAAATGAA
1 AATAAAAATGAAAATAAA
* *
24150 AATGAAAATGAAAATGAA
1 AATAAAAATGAAAATAAA
*
24168 AATAAAAATAAAAATAAA
1 AATAAAAATGAAAATAAA
*
24186 ACTAAA
1 AATAAA
24192 TATACTAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 15 0.29
18 36 0.71
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (18 bp):
AATAAAAATGAAAATAAA
Found at i:26066 original size:25 final size:25
Alignment explanation
Indices: 26010--26068 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
26000 CTTTTATATT
*
26010 CTCCTCCCCACTTTCTCTTCCTTTTT
1 CTCCT-CCCACTTTCTCTTCCTTTTC
* *
26036 CACCTCCCATTTTCTC-TCCTTTTC
1 CTCCTCCCACTTTCTCTTCCTTTTC
26060 CTTCCTCCC
1 C-TCCTCCC
26069 TCCCCATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 8 0.29
25 16 0.57
26 4 0.14
ACGTcount: A:0.05, C:0.49, G:0.00, T:0.46
Consensus pattern (25 bp):
CTCCTCCCACTTTCTCTTCCTTTTC
Done.