Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010226.1 Kokia drynarioides strain JFW-HI SEQ_125055, 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, 605
Length: 1009
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Found at i:795 original size:431 final size:429
Alignment explanation
Indices: 161--982 Score: 1018
Period size: 431 Copynumber: 1.9 Consensus size: 429
151 ACTAGTTCGT
* * *
161 AAGTTCGTCCGAGAACCAAGAGAGAGACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAA
1 AAGTTCGTCCAAAAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAA
*
226 AATTTGTTTACAAAATCACAAACTATTTAGACCGAAAGATGCGATTTTCAGAGCATGGAATGTTC
66 AAATTGTTTACAAAATCACAAACTATTTAGACCGAAAGATGCGATTTTCAGAGCATGGAATGTT-
* * * *
291 AGAAAATGGATCAAAGGAATGGATAGTCTTGAATACTTTGAGGAACCAAAGTTATAAAATAACTC
130 AGAAAATGCATCAAAGGAATGGATAGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
** * *
356 GTAAAAGTTCGAGTAG-TTCGTAAGTTCGTCCTAGAACCACA-AGAGAAACAATTCTCACGTAAA
195 GTAAAAGTTCGACAAGTTTAG-AAGTTCGTCCAAGAACCA-AGAGAGAAACAATTCTCACGTAAA
* * * * * * * ** *
419 TAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACAAAGTTTTTAGACTGAATGATAA
258 TA--TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACGATAA
* * * *
484 GA-TTCCCAAGCATGGAAAGTTCAAAAAATTGGTCAAAGGAATGGATCGTCTTGAGTACTCTCAG
321 GATTTCCCAAGCATAGAAAGTTCAAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTCTAAG
548 GAACTTAAGATACAAAATAGCTATTAAATGTTCCTCAAGTACGA
386 GAACTTAAGATACAAAATAGCTATTAAATGTTCCTCAAGTACGA
* *
592 AAGTTCGTCCAAAAACCATGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTTCGAAGACCA
1 AAGTTCGTCCAAAAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTT-AAAGACCA
* * * * *
656 AAAATTGTTTAGAAAATGATAACCTATTTAGACC-AAATGATGTC-ATTTCTC-GAGCATGGATT
65 AAAATTGTTTACAAAATCACAAACTATTTAGACCGAAA-GATG-CGATTT-TCAGAGCATGGAAT
* * *
718 GCTT-GAAAATTGCA-CAAAGGAATGGATCA-CCTTTAATAGTTTAAGGAACCGAAGTTATAAAA
127 G-TTAGAAAA-TGCATCAAAGGAATGGAT-AGCCTTGAATACTTTAAGGAACCAAAGTTATAAAA
* * *
780 GAACT-GATAAAAAGTTTGACAAGTTTAGAAGTTCTTCCAAGAACCAAGAGAGAAACAATTGTCA
189 GAACTCG-T-AAAAGTTCGACAAGTTTAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
*
844 TGTAAATATTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACG
252 CGTAAATATTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACG
** * * * * *
909 ATGTGATTTCCCAAGCATAGAATGTTCGAGAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
317 ATAAGATTTCCCAAGCATAGAAAGTTCAAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTC
974 TAAGGAACT
382 TAAGGAACT
983 GAAGTTATAA
Statistics
Matches: 332, Mismatches: 47, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
429 52 0.16
430 122 0.37
431 150 0.45
432 8 0.02
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (429 bp):
AAGTTCGTCCAAAAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAA
AAATTGTTTACAAAATCACAAACTATTTAGACCGAAAGATGCGATTTTCAGAGCATGGAATGTTA
GAAAATGCATCAAAGGAATGGATAGCCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
TAAAAGTTCGACAAGTTTAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAT
TTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACGATAAGATTT
CCCAAGCATAGAAAGTTCAAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTCTAAGGAACT
TAAGATACAAAATAGCTATTAAATGTTCCTCAAGTACGA
Found at i:989 original size:215 final size:217
Alignment explanation
Indices: 142--1006 Score: 860
Period size: 215 Copynumber: 4.0 Consensus size: 217
132 TCAAAGTCGT
* * * * *
142 AAAAGTTTGACTAGTTCGTAAGTTCGTCCGAGAACCAAGAGAGAGACAATTCTCACGTAAATAAG
1 AAAAGTTCGACAAGTTAGTAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * *
207 TTTTTAATTTAAAGACCAAAATTTGTTTACAAAATCACAAACTATTTAGACCGAAA-GATGCGAT
66 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC-AAATGATGTGAT
* * * * *
271 TT-TCAGAGCATGGAATGTTC-AGAAAATGGATCAAAGGAATGGATAGTCTTGAATACTTTGAGG
130 TTCCCA-AGCATGGAATGTTCGAG-AAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGG
* *
334 AACCAAAGTTATAAAATAACTCG-T-
193 AACCGAAGTTATAAAAGAACT-GATA
** * * *
358 AAAAGTTCGAGTAGTTCGTAAGTTCGTCCTAGAACCACA-AGAGAAACAATTCTCACGTAAATAG
1 AAAAGTTCGACAAGTTAGTAAGTTCGTCCAAGAACCA-AGAGAGAAACAATTCTCACGTAAATAA
* * * * * ** **
422 GTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACAAAGTTTTTAGACTGAATGATAAGA-
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGAT
* * * * * * *
486 TTCCCAAGCATGGAAAGTTCAAAAAATTGGTCAAAGGAATGGATCGTCTTGAGTACTCTCAGGAA
130 TTCCCAAGCATGGAATGTTCGAGAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAA
** * * * * *
551 CTTAAGATACAAAATAGCT-ATT
195 CCGAAGTTATAAAAGAACTGATA
* ** * * *
573 AAATGTTCCTCAAG-TACGAAAGTTCGTCCAAAAACCATGAGAGAAACAATTCTCACGTAAATAA
1 AAAAGTTCGACAAGTTA-GTAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * * * *
637 G-TTTTAATTTCGAAGACCAAAAATTGTTTAGAAAATGATAACCTATTTAGACCAAATGATGTCA
65 GTTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGA
* * * * ** * *
701 TTTCTCGAGCATGGATTGCTT-GA-AAATTGCACAAAGGAATGGATCACCTTTAATAGTTTAAGG
129 TTTCCCAAGCATGGAATG-TTCGAGAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGG
764 AACCGAAGTTATAAAAGAACTGATA
193 AACCGAAGTTATAAAAGAACTGATA
* * * *
789 AAAAGTTTGACAAGTTTAG-AAGTTCTTCCAAGAACCAAGAGAGAAACAATTGTCATGTAAAT-A
1 AAAAGTTCGACAAG-TTAGTAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * *
852 -TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAACTATTTAGACCAAACGATGTGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGAT
* *
916 TTCCCAAGCATAGAATGTTCGAGAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
130 TTCCCAAGCATGGAATGTTCGAGAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* *
981 CTGAAGTTATAAAAGAACTCATA
195 CCGAAGTTATAAAAGAACTGATA
1004 AAA
1 AAA
1007 GCT
Statistics
Matches: 526, Mismatches: 106, Indels: 35
0.79 0.16 0.05
Matches are distributed among these distances:
213 2 0.00
214 71 0.13
215 274 0.52
216 173 0.33
217 4 0.01
218 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (217 bp):
AAAAGTTCGACAAGTTAGTAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATT
TCCCAAGCATGGAATGTTCGAGAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
CGAAGTTATAAAAGAACTGATA
Done.