Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002059.1 Kokia drynarioides strain JFW-HI SEQ_113957, 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, 637
Length: 1062
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Found at i:857 original size:431 final size:425
Alignment explanation
Indices: 89--1053 Score: 1002
Period size: 431 Copynumber: 2.3 Consensus size: 425
79 AAAGTTGTCG
* * * * * * *
89 AAGAACTCGTAAAAGTTCGACCAGTTC-GTAAGTTCGTACTAGAACCACA-AGAGGAACAATTCT
1 AAGAACTCGTAAAAGTTTGACAAGTTCAG-AAGTT-ATCCAAAAACCA-AGAGAGAAACAATTCT
* * * * * * * * *
152 CACGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGAAAAAGTTTTTGGACCG
63 CACGTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGATTACA-AATGAAAAACTATTTAGACCA
* * * * * * *** * *
217 AATGATACGA-TTCCCGAGCATGGAAAGTTCAAAAAATTGGTCGAAGGAATGGATCATCTTGAGT
127 AACGATGCGATTTCCCAAGCGTAGAATGTTGGGAAAATTGCTCGAAGGAATGGATCATCTTGAAT
* * * * *
281 ACTCTCAGGAACTTAAGTTACAAAAGAGCTATTAAATGTTCCGCAAGTACGAAAGTTCGTCCAAG
192 ACTCTAAGGAACTGAAGTTACAAAAGAACTATTAAAAGTTCCGCAAGTACGAAACTTCGTCCAAG
*** * * *
346 AACCGTGATAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAATTGTTTAGAA
257 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAAAGACCAAAAATTGGTTAGAA
* * * * *
411 AATGATAACCTATTTAGACCAAATGATGTC-A-TTTCTCGGGCATGGAATGCTT-GAAAAATTGC
322 AATGACAAACTATTTAGACCAAATAATG-CGATTTTC-CGAGCATGGAATG-TTCGAAAAACTG-
* *
473 ACAAAGGAATGGATCACCTTTAATAGTTTAAGGAACCGAAGTTATAA
383 ---AAGGAA-GGATCACCTTGAATAATTTAAGGAACCGAAGTTATAA
* * *
520 AGGAACT-GATAAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTGT
1 AAGAACTCG-T-AAAAGTTTGACAAGTTCAGAAGTT-ATCCAAAAACCAAGAGAGAAACAATTCT
* **
584 CATGTAAAT-A-TTTTAAATTCAAAGACGGAAAGTTGATTACGAAATGAAAAACTATTTAGACCA
63 CACGTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGATTAC-AAATGAAAAACTATTTAGACCA
*
647 AACGATGCGATTTCCCAAGCGTAGAATGTTGGGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
127 AACGATGCGATTTCCCAAGCGTAGAATGTTGGGAAAATTGCTCGAAGGAATGGATCATCTTGAAT
* * * * *
712 ACTTTAAGGAACTGAAGTTATAAAAGAATTCA-TAAAAGCTT-GGCAAGTTCGAAACTTCAG-CC
192 ACTCTAAGGAACTGAAGTTACAAAAGAACT-ATTAAAAG-TTCCGCAAGTACGAAACTTC-GTCC
* * * ** *
774 AAGAACAAAGAGAGAAACAGTTCTCATGTAAATAAGTTTTTAATACATAGTGCAAAAGTTGGTTA
254 AAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAAAGACCAAAAATTGGTTA
*
839 CG-AAATGACAAACTATTTAGACCAAATAATGCGATTTTCCGAGCATTGAATGTTCGAAAAACTG
319 -GAAAATGACAAACTATTTAGACCAAATAATGCGATTTTCCGAGCATGGAATGTTCGAAAAACTG
*** ** *
903 GTTGAAGGATCGGCTTGAATAATTTAAGGAACTGAAGTTATAA
383 AAGGAAGGATCACCTTGAATAATTTAAGGAACCGAAGTTATAA
*
946 AAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTATCCAAAAACCAAGAGAGAAACAATTCTCAC
1 AAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTATCCAAAAACCAAGAGAGAAACAATTCTCAC
* *
1011 GTAAATAAGTTTTCAATTCAAAGACCAAAAGTTGTTTACAAAT
66 GTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGATTACAAAT
1054 TTAAAAAAA
Statistics
Matches: 442, Mismatches: 76, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
424 34 0.08
425 28 0.06
426 65 0.15
427 4 0.01
430 54 0.12
431 197 0.45
432 59 0.13
433 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (425 bp):
AAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTATCCAAAAACCAAGAGAGAAACAATTCTCAC
GTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGATTACAAATGAAAAACTATTTAGACCAAACG
ATGCGATTTCCCAAGCGTAGAATGTTGGGAAAATTGCTCGAAGGAATGGATCATCTTGAATACTC
TAAGGAACTGAAGTTACAAAAGAACTATTAAAAGTTCCGCAAGTACGAAACTTCGTCCAAGAACA
AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAAAGACCAAAAATTGGTTAGAAAATG
ACAAACTATTTAGACCAAATAATGCGATTTTCCGAGCATGGAATGTTCGAAAAACTGAAGGAAGG
ATCACCTTGAATAATTTAAGGAACCGAAGTTATAA
Found at i:873 original size:216 final size:214
Alignment explanation
Indices: 4--1053 Score: 878
Period size: 215 Copynumber: 4.9 Consensus size: 214
1 AAA
* * * * * * **
4 GATGCGATTTTCGGAGCATGGAATGTTCAGAAAATGGCTCAAAGGAATGGAT-AGTCTTGAACGC
1 GATGCGATTTCCCGAGCATAGAATGTT-GGAAAATTGCTCGAAGGAATGGATCA-TCTTGAATAC
* * ** * ** * * * * * *
68 ATTGAGGAACCAAAGTTGTCGAAGAACTCGTAAAAGTTCGACCAGTTCGTAAGTTC-GTACTAGA
64 TTTAAGGAACTGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCAG-CCAAGA
* * * *
132 ACCACA-AGAGGAACAATTCTCACGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTAC-A
128 ACCA-AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC-AAAAGTTGATTACGA
* * * *
195 TAATGAAAAAGTTTTTGGACCGAAT
191 -AATGAAAAACTATTTAGACCAAAT
* * * ** * *
220 GATACGA-TTCCCGAGCATGGAAAGTTCAAAAAATTGGTCGAAGGAATGGATCATCTTGAGTACT
1 GATGCGATTTCCCGAGCATAGAATGTT-GGAAAATTGCTCGAAGGAATGGATCATCTTGAATACT
* * * * * * * *
284 CTCAGGAACTTAAGTTACAAAAGAGCT-ATTAAATGTTCCG-CAAGTACGAAAGTTC-GTCCAAG
65 TTAAGGAACTGAAGTTATAAAAGAACTCA-TAAAAGTT-TGACAAGTTCGAAAGTTCAG-CCAAG
** * * *
346 AACCGTGATAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAATTGTTTA-GA
127 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CAAAAGTTGATTACG-
* *
410 AAATGATAACCTATTTAGACCAAAT
190 AAATGAAAAACTATTTAGACCAAAT
* * * * * * * * *
435 GATGTC-ATTTCTCGGGCATGGAATGCTTGAAAAATTGCACAAAGGAATGGATCACCTTTAATAG
1 GATG-CGATTTCCCGAGCATAGAATG-TTGGAAAATTGCTCGAAGGAATGGATCATCTTGAATAC
* * * *
499 TTTAAGGAACCGAAGTTATAAAGGAACTGATAAAAAGTTTGACAAGTTC-AGAAGTTCATCCAAG
64 TTTAAGGAACTGAAGTTATAAAAGAACTCAT-AAAAGTTTGACAAGTTCGA-AAGTTCAGCCAAG
* * * *
563 AACCAAGAGAGAAACAATTGTCATGTAAAT-A-TTTTAAATTCAAAGACGGAAAGTTGATTACGA
127 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC-AAAAGTTGATTACGA
*
626 AATGAAAAACTATTTAGACCAAAC
191 AATGAAAAACTATTTAGACCAAAT
* * *
650 GATGCGATTTCCCAAGCGTAGAATGTTGGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACT
1 GATGCGATTTCCCGAGCATAGAATGTT-GGAAAATTGCTCGAAGGAATGGATCATCTTGAATACT
* * * *
715 TTAAGGAACTGAAGTTATAAAAGAATTCATAAAAGCTTGGCAAGTTCGAAACTTCAGCCAAGAAC
65 TTAAGGAACTGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCAGCCAAGAAC
* * * * * * *
780 AAAGAGAGAAACAGTTCTCATGTAAATAAGTTTTTAATACATAGTGCAAAAGTTGGTTACGAAAT
130 CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-ACAAAAGTTGATTACGAAAT
*
845 GACAAACTATTTAGACCAAAT
194 GAAAAACTATTTAGACCAAAT
* * * * * *** ** *
866 AATGCGATTTTCCGAGCATTGAATGTTCGAAAA--ACT-GGTTGAA-GGATCGGCTTGAATAATT
1 GATGCGATTTCCCGAGCATAGAATGTTGGAAAATTGCTCGAAGGAATGGATCATCTTGAATACTT
* * * *
927 TAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTT-ATCCAAAAACC
66 TAAGGAACTGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCAGCCAAGAACC
* *
991 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTCAATTCAAAGACCAAAAGTTGTTTAC-AAAT
131 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CAAAAGTTGATTACGAAAT
1054 TTAAAAAAA
Statistics
Matches: 675, Mismatches: 135, Indels: 55
0.78 0.16 0.06
Matches are distributed among these distances:
209 4 0.01
210 59 0.09
211 63 0.09
212 4 0.01
213 2 0.00
214 57 0.08
215 286 0.42
216 148 0.22
217 52 0.08
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (214 bp):
GATGCGATTTCCCGAGCATAGAATGTTGGAAAATTGCTCGAAGGAATGGATCATCTTGAATACTT
TAAGGAACTGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCAGCCAAGAACC
AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAGTTGATTACGAAATGA
AAAACTATTTAGACCAAAT
Done.