Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004641.1 Kokia drynarioides strain JFW-HI SEQ_118171, 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, 779
Length: 1299
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Found at i:435 original size:216 final size:214
Alignment explanation
Indices: 10--1299 Score: 1308
Period size: 216 Copynumber: 6.1 Consensus size: 214
1 CCAACAGCC
** * * *
10 AAGAGAAACAATTCTCACGTAAATAAGTTTTTTTTTTAAAGACCAAAACTTGTTTACAAAACGAA
1 AAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* * * * *
75 AAACTATTTAGACTAAATGATGCAATTACCCGAGAAAGGAATGTTC--AAAATTGCT-AAAGGAA
66 AAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAAGGAA
* ** *
137 TGGAT-GTTATTGAATACTTTAAGGAACCGTTGTTATAAAAGAACTCGTAAAGGTTTGAAAAGTT
131 TGGATCG-TCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAG-T
*
201 TCGAAGTTCATCCAAGAACAA
194 TCGAAGTTCGTCCAAGAACAA
*
222 AGAGATAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGA-CAAAACTTGTTTACAAAAT
1 A-AG--AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
* * * * * * *
286 GACAAACAATTTAGA-AAAATGATGCGATATT-TCGAGCATAGAACGTTAAGAAAGTTGCTCGAA
63 GACAAACTATTTAGACAAAATGATGCGAT-TTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAA
* * * * * *
349 GGAATGTATCGTCTTAAATACTGTAAGGAACTGAAGTTATAAAAGAACGCGTAAAAGTTTGACAA
127 GGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAA
* * *
414 GTTCAGAAATTTGTCCAAGAAC-C
192 GTTC-GAAGTTCGTCCAAGAACAA
* * *
437 AAGCA-AAACAATTCTCACGTAAATAAGATTTTGATTCAAAGACCAAAACTTGTTTTCAAAATGA
1 AAG-AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA
* * * * * * * * *
501 CAAACTCTTTAGACCAAATGCTGCTATTTCTCAAGAATCGAACGTTCAGAAAATTGTTCGAAGGA
65 CAAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAAGGA
* * * **
566 ATGGATCATCTTGAATACTTTAAGGAACCGAAGATATGAAAGAACTCGTAAAAGTTTGACTAGTT
130 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
*
631 CGAAAGTTCGTCCGAGAACCAA
195 CG-AAGTTCGTCCAAGAA-CAA
* * * * * *
653 GAGGGAAAACAATTCTCACGTAAATAAGTTTTTAATTCAAACAACAAAACCTT-CTAACAAAATG
1 AAGAG-AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA-CTTGTTTACAAAATG
* * * *
717 ACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCACGAAGG
64 ACAAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAAGG
* * * * * * * *
782 AATGGATCGTCTTGAATGCTTTATGGAACTGAAATTATAGAAGAAGTCATAAAAGTTTGATAAGT
129 AATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGT
847 TCGGAAGTTCGTCCAAGAACTAA
194 TC-GAAGTTCGTCCAAGAAC-AA
* * * * * *
870 AAGAGAAACAATTCTCGCGAAAATAAGTATTTAATTCAAAGGCCAAAAGTTGTTCACAAAATGAC
1 AAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* * *
935 AAACTATTTAGACAAAATTATGCGATTTCCCGAGTATGGAATGTTCAGAAAATAGCTCGAAGGAA
66 AAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAAGGAA
* * *
1000 TGGATCATCTTGAATA-TTGTAAGGAACC---G--AT--------TCGTAGAAGTTTAAAAAGTT
131 TGGATCGTCTTGAATACTT-TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
* * * *
1051 CAGAAGTTCATCCAACAGC-C
195 C-GAAGTTCGTCCAAGAACAA
*** * * *
1071 AAGAGAAACAATTCTCACGTAAATAAGTTTTCGCTTTAAAGACCAAAACTTGTTTACAAAACGAA
1 AAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
* *
1136 AAACTATTTAGACTAAATGATGCGATTACCCGAGAATGGAATGTTC--AAAATTGCT-GAAAGGA
66 AAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCG-AAGGA
* *
1198 ATGGAT-GTTCTTGAATACTTCAAGGAACC-AGAGTTATAAAAGAACTCGTAAAGGTTTGAAAAG
130 ATGGATCG-TCTTGAATACTTTAAGGAACCGA-AGTTATAAAAGAACTCGTAAAAGTTTGAAAAG
*
1261 TTTGGAAGTTCGTCCAAGAACAAA
193 -TTCGAAGTTCGTCCAAGAAC-AA
1285 GAGAGAGAAACAATT
1 -A-AGAGAAACAATT
Statistics
Matches: 885, Mismatches: 150, Indels: 82
0.79 0.13 0.07
Matches are distributed among these distances:
198 1 0.00
199 36 0.04
200 2 0.00
201 95 0.11
202 1 0.00
203 31 0.04
204 2 0.00
211 2 0.00
212 64 0.07
213 61 0.07
214 142 0.16
215 55 0.06
216 213 0.24
217 176 0.20
218 4 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (214 bp):
AAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAC
AAACTATTTAGACAAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCTCGAAGGAA
TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTC
GAAGTTCGTCCAAGAACAA
Done.