Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007729.1 Kokia drynarioides strain JFW-HI SEQ_122362, 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: 9278
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Found at i:796 original size:39 final size:39
Alignment explanation
Indices: 738--812 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
728 TCTTAAGATT
*
738 TGCGTATGATTTCTATCGATTAGATGCTGCTTTTAACCA
1 TGCGTATGATTTCTATCGATCAGATGCTGCTTTTAACCA
*
777 TGCGTATGATTTCTGTCGATCAGATGCTGCTTTTAA
1 TGCGTATGATTTCTATCGATCAGATGCTGCTTTTAA
813 ACAATCACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41
Consensus pattern (39 bp):
TGCGTATGATTTCTATCGATCAGATGCTGCTTTTAACCA
Found at i:2438 original size:41 final size:41
Alignment explanation
Indices: 2392--2591 Score: 231
Period size: 41 Copynumber: 4.8 Consensus size: 41
2382 TTAACCATAT
*
2392 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAG
* * * *
2433 TCTCATTCTCATTTCAAGACATGAGTCTTCCTTATTCATAG
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAG
* * **
2474 TCTCATTCTCATCTCGAGACATGAGTCTTCTTTATTCGTAG
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAG
* **
2515 TCTCATTCTCATCTCGAGACATGAGTTTTCCATTTATAT-AATT
1 TCTCATTCTCATCTCGAGACATGAGTCTTCC--TTA-ATCAAAG
* *
2558 TCTCATGCTCAAACTCGAGACATGAGTCTTCCTT
1 TCTCATTCTC-ATCTCGAGACATGAGTCTTCCTT
2592 TTTATACACT
Statistics
Matches: 136, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
41 102 0.75
42 2 0.01
43 12 0.09
44 20 0.15
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (41 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAG
Found at i:2489 original size:82 final size:84
Alignment explanation
Indices: 2387--2591 Score: 263
Period size: 82 Copynumber: 2.5 Consensus size: 84
2377 TTCCTTTAAC
*
2387 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTCAAGA
1 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCAAGA
2452 CATGAGTCTTCC-TTAT-T
66 CATGAGTCTTCCATTATAT
* * * ** * *
2469 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCTTTATTCGTAGTCTCATTCTCATCTCGAGA
1 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCAAGA
*
2534 CATGAGTTTTCCATTTATAT
66 CATGAGTCTTCCA-TTATAT
* * *
2554 AAT-TTCTCATGCTCAAACTCGAGACATGAGTCTTCCTT
1 CATATTCTCATTCTC-ATCTCGAGACATGAGTCTTCCTT
2592 TTTATACACT
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
82 68 0.65
84 13 0.12
85 24 0.23
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (84 bp):
CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCAAGA
CATGAGTCTTCCATTATAT
Found at i:3435 original size:22 final size:21
Alignment explanation
Indices: 3388--3435 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
3378 GACATTCATA
*
3388 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
3409 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
3431 ATTAA
1 ATTAA
3436 TCAATATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:8653 original size:6 final size:6
Alignment explanation
Indices: 8607--8651 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
8597 CCCAACATCC
* * *
8607 ACACGT ACACCT ACACCT ACACCT ACACCT ACACCC ACAACT ACA
1 ACACCT ACACCT ACACCT ACACCT ACACCT ACACCT ACACCT ACA
8652 ACCACAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.38, C:0.47, G:0.02, T:0.13
Consensus pattern (6 bp):
ACACCT
Found at i:8998 original size:60 final size:58
Alignment explanation
Indices: 8789--9010 Score: 344
Period size: 60 Copynumber: 3.8 Consensus size: 58
8779 TACATTGATT
*
8789 TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATGATTTAATAAAATAGAAG
1 TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATA-AAG
* *
8848 TTATTTTGAATA-TTTTGTACATATTA-TTATATATTGTATCATTTAATAAAAT--AG
1 TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAAG
*
8902 TTCTTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAAAG
1 TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAAT-AAAG
*
8961 TTATTTTGAATATTTTTTGTACATATTATTTTTATATTGTATCATTTAAT
1 TTATTTTGAATA-TTTTTGTACACATTATTTTTATATTGTATCATTTAAT
9011 TGAGAACCCA
Statistics
Matches: 149, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
54 13 0.09
55 13 0.09
56 25 0.17
57 24 0.16
58 13 0.09
59 25 0.17
60 36 0.24
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.54
Consensus pattern (58 bp):
TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAAG
Done.