Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004990.1 Kokia drynarioides strain JFW-HI SEQ_118741, 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: 7638
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:5317 original size:41 final size:41
Alignment explanation
Indices: 5260--5341 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
5250 AAGAACATAG
*
5260 AAACCTCTGGCATATTTTAACTTAAATTCAAATGAATTTTT
1 AAACCTCTAGCATATTTTAACTTAAATTCAAATGAATTTTT
5301 AAACCTCTAGCATATTTTAACTTAAATTCAAATGAATTTTT
1 AAACCTCTAGCATATTTTAACTTAAATTCAAATGAATTTTT
5342 TACTCATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (41 bp):
AAACCTCTAGCATATTTTAACTTAAATTCAAATGAATTTTT
Found at i:5877 original size:45 final size:45
Alignment explanation
Indices: 5810--6352 Score: 623
Period size: 45 Copynumber: 12.2 Consensus size: 45
5800 ACTACAAAGA
* *
5810 AATATTTACCATATCATGCATATCATATAGCATAATTAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * * *
5855 AATATTTATCATATTATACATATCGTATAGCATAA-CTAATAAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATC-AATCAAAT
* * * * **
5900 AATATTTACCATATCATACATATTGTATAACACAATCAATCAAGC
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* *
5945 AAAATTTACCATATTATGCATATCGTATAGC---AT-AATC-AAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * *
5985 AGTATTTACCATATCATGCATATCGTATAGCATCATTAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* *
6030 AATAGTTACCATATCATACATATCGTATAGCATAATCAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * *
6075 AATATTTACCATATCATGCATACCGTATAGCTTGATCAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * * *
6120 ACTATTTACTATATCATGCATATCATATAGCATAATCAATCAAGT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * *
6165 AATATTTATCATATCATGCATATCGTATAGCTTGATCAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
* * * * *
6210 ACTATTTACCATATCATGCCTATCGTATAACTTGATCAATCAAAT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
** **
6255 AATATTTATTATATCATGCATATCGTA-ATGTGTAATCAATCAAAT
1 AATATTTACCATATCATGCATATCGTATA-GCATAATCAATCAAAT
** * * *
6300 AATATTTACCATATCATGTGTATCATATAGCATAATTAATCAATT
1 AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
*
6345 AGTATTTA
1 AATATTTA
6353 GAAAAATCAA
Statistics
Matches: 419, Mismatches: 70, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
40 29 0.07
41 4 0.01
42 2 0.00
43 2 0.00
44 5 0.01
45 375 0.89
46 2 0.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (45 bp):
AATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAAT
Found at i:6005 original size:175 final size:177
Alignment explanation
Indices: 5811--6335 Score: 590
Period size: 175 Copynumber: 3.0 Consensus size: 177
5801 CTACAAAGAA
* * *
5811 ATATTTACCATATCATGCATATCATATAGCATAATTAATCAAATAATATTTATCATATTATACAT
1 ATATTTACCATATCATGCATATCGTATAGCATAATTAATCAAATAATATTTACCATATCATACAT
**
5876 ATCGTATAGCATAA-CTAATAAAATAATATTTACCATATCATACATATTGTATAACACAATCAAT
66 ATCGTATAGCATAATC-AATAAAATAATATTTACCATATCATACATACCGTATAACACAATCAAT
* * *
5940 CAAGCAAAATTTACCATATTATGCATATCGTATAGCATAATCAAT-AG
130 CAAACAAAATTTACCATATCATGCATATCATATAGCATAATCAATAAG
* *
5987 -TATTTACCATATCATGCATATCGTATAGCATCATTAATCAAATAATAGTTACCATATCATACAT
1 ATATTTACCATATCATGCATATCGTATAGCATAATTAATCAAATAATATTTACCATATCATACAT
* * * ***
6051 ATCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATACCGTATAGCTTGATCAATC
66 ATCGTATAGCATAATCAATAAAATAATATTTACCATATCATACATACCGTATAACACAATCAATC
* ** *
6116 AAATACTATTTACTATATCATGCATATCATATAGCATAATCAATCAAG
131 AAACAAAATTTACCATATCATGCATATCATATAGCATAATCAAT-AAG
* * * * * *
6164 TAATATTTATCATATCATGCATATCGTATAGCTTGATCAATCAAATACTATTTACCATATCATGC
1 --ATATTTACCATATCATGCATATCGTATAGCATAATTAATCAAATAATATTTACCATATCATAC
* * * * * ** * * ****
6229 CTATCGTATAACTTGATCAATCAAATAATATTTATTATATCATGCATATCGTA-ATGTGTAATCA
64 ATATCGTATAGCATAATCAATAAAATAATATTTACCATATCATACATACCGTATA-ACACAATCA
* * **
6293 ATCAAATAATATTTACCATATCATGTGTATCATATAGCATAAT
128 ATCAAACAAAATTTACCATATCATGCATATCATATAGCATAAT
6336 TAATCAATTA
Statistics
Matches: 301, Mismatches: 41, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
175 151 0.50
176 1 0.00
177 2 0.01
179 1 0.00
180 146 0.49
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (177 bp):
ATATTTACCATATCATGCATATCGTATAGCATAATTAATCAAATAATATTTACCATATCATACAT
ATCGTATAGCATAATCAATAAAATAATATTTACCATATCATACATACCGTATAACACAATCAATC
AAACAAAATTTACCATATCATGCATATCATATAGCATAATCAATAAG
Found at i:7237 original size:19 final size:19
Alignment explanation
Indices: 7213--7250 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
7203 TCGAAGCAAC
7213 TAAGATTAAAATAAGAGTA
1 TAAGATTAAAATAAGAGTA
7232 TAAGATTAAAATAAGAGTA
1 TAAGATTAAAATAAGAGTA
7251 ATTGTTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (19 bp):
TAAGATTAAAATAAGAGTA
Done.