Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003269.1 Kokia drynarioides strain JFW-HI SEQ_115927, 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: 2751
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2514 original size:763 final size:758
Alignment explanation
Indices: 1042--2548 Score: 2265
Period size: 763 Copynumber: 2.0 Consensus size: 758
1032 TTACACTTCC
* * *
1042 GTGGTCAAGTAATTAAATCCAAGGGTAAAAATGAAGGAAAGATAGAGTAGATATCATATTTGATA
1 GTGGTCAAGCAATTAAATCCAAAGATAAAAATGAAGGAAAGATAGAGTAGATATCATATTTGATA
*
1107 TGGAATTAAATTGTACTTCCATAAAAACACAAATAATCAAATAATCCCAAGACTGTTTGTTTCGA
66 TGGAATTAAATTGTACTTCCATAAAAACACAAATAATCAAATAATCCCAAGACTGTTGGTTTCGA
* * * **
1172 GCTCAGTTGTTGTAGGGATTACCATAAGAATTTCCTCTGATATTATTTTCATAAAACGCATTCTC
131 GCTCAGCTATTGTAGGAATTACCATAAGAATTTCCTCTGATATTATTAACATAAAACGCATTCTC
* * *
1237 GGCATGCTTTGGACAATCTTCATGGCTATGATTGTCACCGTAAATTTCACAACAAAATGTTTGGA
196 GGCATGCTATGGACAATCTTCATAGCTATGATTGTCACCGTAAATTTCAAAACAAAATGTTTGGA
*
1302 CATCCATTTATTCTTGGATGGGAGGAACTTCACTTGTCCCCCTCATGTTTTTTTATCATATTTAC
261 CATCCATTTATTCTTGGATGGGAGCAACTTCACTTGTCCCCCTCATGTTTTTTTATCATATTTAC
* *
1367 TAACGAAGATACCTGTGCACTCATAGCTGATATAGCATCTAACTCGATAACTCCAAGGTTTGTTT
326 TAACGAAGATACCTGTGCACTCATAGATGATATAACATCTAACTCGATAACTCCAAGGTTTGTTT
*
1432 TAACTTGAGCAGCTCGAGAGATCAGATATTGGTAGTCATTCTGAGTGATACTTCTAAAATTCTCA
391 TAACTTGAGCAGCTCGAGAGATCAGATATTGGTAGTCATTCTGAGCGATACTTCTAAAATTCTCA
*
1497 CAGTTTCACAATAGGTGCAATCCAACAAAGGACCATTCGCAAATGCATCGACAAGATTTCTTGTC
456 CAGCTTCACAATAGGTGCAATCCAACAAAGGACCATTCGCAAATGCATCGACAAGATTTCTTGTC
1562 TGCATATTCAACCCATTATAAAAGATTTCGATCTAAATTTCCTGTTGAATTCCATGCATAGGACA
521 TGCATATTCAACCCATTATAAAAGATTTCGATCTAAATTTCCTGTTGAATTCCATGCATAGGACA
* * *
1627 GTGTTGAAGTAGGGTTTTGTAACGCATCCATATGGTGTGCAAATTCTCATCATCCAATTGATGAT
586 ATGTTGAAGCACGGTTTTGTAACGCATCCATATGGTGTGCAAATTCTCATCATCCAATTGATGAT
* * ** *
1692 ATGCAGTGATATCATTCCTTAGTCGAGGATTCATTATCGGAGGATTAAATTGCAAAACAAACTGG
651 ATGCAGTGATATCATTCCTTAGTCAAGCATTCATTATCGGAGGATTAAACAGAAAAACAAACT-G
*
1757 A-CGCAAGTGCATTCCATGATGCAATCGATCTAGCAGGCAATCT
715 ATCGCAAGTGAATTCCATGATGCAATCGATCTAGCAGGCAATCT
** * *
1800 GTGGTCAAGCAATTAAATCCAAAGATAGTAATGAAGGAAAGATAGATTAGATATCATATTTGATC
1 GTGGTCAAGCAATTAAATCCAAAGATAAAAATGAAGGAAAGATAGAGTAGATATCATATTTGATA
1865 TGGAATTAAATTGTACTTCCATAAAAACACAAATAATCAAATAATCCCAAGACTGTTGGTTTCGA
66 TGGAATTAAATTGTACTTCCATAAAAACACAAATAATCAAATAATCCCAAGACTGTTGGTTTCGA
* *
1930 G-TGAGCTATTGTAGGAATTACCATAAGAATTTCCTCTGATATTATTAACATAAAACGCGTTCTC
131 GCTCAGCTATTGTAGGAATTACCATAAGAATTTCCTCTGATATTATTAACATAAAACGCATTCTC
* *
1994 TGCATGCTATGGACAATCTTCATAGCTATGATTGTCATCGTAAATTTCAAAACAAAATG-TT-GA
196 GGCATGCTATGGACAATCTTCATAGCTATGATTGTCACCGTAAATTTCAAAACAAAATGTTTGGA
* **
2057 GCTATCCATTTGTTAGGCAACTTGGATGGGAGCAACTTCACTTGTCCCTTTCATG-TTTTTTATC
261 -C-ATCCATTTATT------CTTGGATGGGAGCAACTTCACTTGTCCCCCTCATGTTTTTTTATC
* * * * *
2121 ATATTTGCTAACGAAGATACTTGTGCACTCATAGATGATATAACGTCTATCTCGATAACT-TAAG
318 ATATTTACTAACGAAGATACCTGTGCACTCATAGATGATATAACATCTAACTCGATAACTCCAA-
*
2185 GGTTTGTTTTAACTTGAGCTGCTCGAGAGATCAGATATTGGTAGTCATTCTGAGCGATACTCTCT
382 GGTTTGTTTTAACTTGAGCAGCTCGAGAGATCAGATATTGGTAGTCATTCTGAGCGATACT-TCT
* * * *
2250 ATAATTCTCACAGCTTCACCATAGGTGCAGTCCAACAAAGGACCATTCGCAAATGCATCGACAAT
446 AAAATTCTCACAGCTTCACAATAGGTGCAATCCAACAAAGGACCATTCGCAAATGCATCGACAAG
** * * ** *
2315 ATTTCTTGTCTGTGTATTCAACTCATTATAAAAGATTTTGATCTGCATTTCCTTTTGAATTCCAT
511 ATTTCTTGTCTGCATATTCAACCCATTATAAAAGATTTCGATCTAAATTTCCTGTTGAATTCCAT
* * *
2380 GCATGGGACAATGTTGAAGCACGGTTTTGTAATGC-TCCCATGTGGTGTGCAAATTCTCATCATC
576 GCATAGGACAATGTTGAAGCACGGTTTTGTAACGCAT-CCATATGGTGTGCAAATTCTCATCATC
* * * * *
2444 CTATTGATGATATGTAGTGGTATCATTCCTTAGTCAAGCATTCATTGTC-GATGGATTAGACAGA
640 CAATTGATGATATGCAGTGATATCATTCCTTAGTCAAGCATTCATTATCGGA-GGATTAAACAGA
*
2508 AAAACAAACTGATTCGCAAGTGAATTCCATGATGTAATCGA
704 AAAACAAACTGA-TCGCAAGTGAATTCCATGATGCAATCGA
2549 ACCAACATGC
Statistics
Matches: 672, Mismatches: 63, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
755 2 0.00
756 3 0.00
757 120 0.18
758 123 0.18
761 2 0.00
762 127 0.19
763 270 0.40
764 25 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (758 bp):
GTGGTCAAGCAATTAAATCCAAAGATAAAAATGAAGGAAAGATAGAGTAGATATCATATTTGATA
TGGAATTAAATTGTACTTCCATAAAAACACAAATAATCAAATAATCCCAAGACTGTTGGTTTCGA
GCTCAGCTATTGTAGGAATTACCATAAGAATTTCCTCTGATATTATTAACATAAAACGCATTCTC
GGCATGCTATGGACAATCTTCATAGCTATGATTGTCACCGTAAATTTCAAAACAAAATGTTTGGA
CATCCATTTATTCTTGGATGGGAGCAACTTCACTTGTCCCCCTCATGTTTTTTTATCATATTTAC
TAACGAAGATACCTGTGCACTCATAGATGATATAACATCTAACTCGATAACTCCAAGGTTTGTTT
TAACTTGAGCAGCTCGAGAGATCAGATATTGGTAGTCATTCTGAGCGATACTTCTAAAATTCTCA
CAGCTTCACAATAGGTGCAATCCAACAAAGGACCATTCGCAAATGCATCGACAAGATTTCTTGTC
TGCATATTCAACCCATTATAAAAGATTTCGATCTAAATTTCCTGTTGAATTCCATGCATAGGACA
ATGTTGAAGCACGGTTTTGTAACGCATCCATATGGTGTGCAAATTCTCATCATCCAATTGATGAT
ATGCAGTGATATCATTCCTTAGTCAAGCATTCATTATCGGAGGATTAAACAGAAAAACAAACTGA
TCGCAAGTGAATTCCATGATGCAATCGATCTAGCAGGCAATCT
Done.