Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010514.1 Kokia drynarioides strain JFW-HI SEQ_125426, 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: 2447
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.35
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:23 original size:17 final size:17
Alignment explanation
Indices: 1--73 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
*
1 TAAATTCGAAATAAATT
1 TAAATTCTAAATAAATT
18 TAAATT-TAATATAAATT
1 TAAATTCTAA-ATAAATT
*
35 TAAATTTCTAAACAAATT
1 TAAA-TTCTAAATAAATT
53 T--ATTCTTAAAATAAATT
1 TAAATTC-T-AAATAAATT
70 TAAA
1 TAAA
74 GGGAGTTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 3 0.07
16 4 0.09
17 26 0.57
18 9 0.20
19 4 0.09
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTCTAAATAAATT
Found at i:591 original size:88 final size:89
Alignment explanation
Indices: 418--617 Score: 357
Period size: 88 Copynumber: 2.3 Consensus size: 89
408 ACTTGGCCTT
* *
418 CTTCTCAGTATCTCATCAGGAAGATGATCACATCGCTTTTTGTTTCAATTCGCTCCTCCGTATCT
1 CTTCTCAGTACCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCT
483 CATCCGAAAGAAGAATTTGGTTTA
66 CATCCGAAAGAAGAATTTGGTTTA
507 CTTCTCAGTACCTCATCAGGAAGATGATCACATCGCTGTTTG-TTCAATTCGCTCCTCCGTATCT
1 CTTCTCAGTACCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCT
*
571 CATCCGGAAGAAGAATTTGGTTTA
66 CATCCGAAAGAAGAATTTGGTTTA
*
595 CTTCTCAGTACCTCATCAAGAAG
1 CTTCTCAGTACCTCATCAGGAAG
618 CTAACCTTTT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
88 67 0.63
89 40 0.37
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (89 bp):
CTTCTCAGTACCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCCGTATCT
CATCCGAAAGAAGAATTTGGTTTA
Found at i:887 original size:193 final size:195
Alignment explanation
Indices: 545--997 Score: 610
Period size: 195 Copynumber: 2.3 Consensus size: 195
535 CACATCGCTG
* * * * ** *
545 TTTG-TTCAATTCGCTCCTCCGTATCTCATCCGGAAGAAGAATTTGGTTTACTTCTCAGTACCTC
1 TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTACCTC
* *
609 ATCAAGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCAAGAAGCTGGGGTTC
66 ATCAAGAAGCTAACC------T-CTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTC
* * *
674 AAGGATTTTGCTTACTTTGAGCCTCG-TTTGAGTCTTCTTCTCAGTGTTTCATCAAGAAGATGAC
124 AAGGATTTTGCTCACTTTGAGCCTCGTTTTGAGTCTTCTTCTCAGTGTCTCATCAAGAAGATAAC
738 CGCGTCA
189 CGCGTCA
*
745 TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTATCTC
1 TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTACCTC
* *
810 ATCAGGAAGCTAACC-CTTCGACCTGCTTCTCAGTATCTTC-TCAGGAAGCTGGGGTTCGAA-GA
66 ATCAAGAAGCTAACCTCTTCGACCTGCTTCTCAGTATC-TCATCAAGAAGCTGGGGTTC-AAGGA
* *
872 TTTTGCTCACTTTGAGCCTCGTTTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATAACCGCG
129 TTTTGCTCACTTTGAGCCTCG-TTTTGAGTCTTCTTCTCAGTGTCTCATCAAGAAGATAACCGCG
*
937 TCG
193 TCA
*
940 TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCAAATTTGGTTCACTTCTCA
1 TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCA
998 NNNNNNNNNN
Statistics
Matches: 229, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
193 58 0.25
194 4 0.02
195 97 0.42
200 4 0.02
201 66 0.29
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (195 bp):
TTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTACCTC
ATCAAGAAGCTAACCTCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCAAGGATT
TTGCTCACTTTGAGCCTCGTTTTGAGTCTTCTTCTCAGTGTCTCATCAAGAAGATAACCGCGTCA
Done.