Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013017.1 Kokia drynarioides strain JFW-HI SEQ_128035, 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: 1770
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:624 original size:216 final size:217
Alignment explanation
Indices: 18--773 Score: 1118
Period size: 216 Copynumber: 3.5 Consensus size: 217
8 GCAAAGATAA
* *
18 AAAATAACTAGTAAAAGTTTGACAAGTT-TGAAAGTTCGTCCAAGAACAAAGAGACAAACAATTC
1 AAAATAACTAGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTC
* * * *
82 TCACATATATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGGAAAATGATAAACTATTTAGACC
66 TCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTGCAAAATGATAAACTATTTAGACC
* * *
147 AAATGATGCGATATCCCAAGCATTGAATGTTCGAAAAATTGTTCGGAAGAATAGATCGTCCTGAA
131 AAATGATGCGATATCCCAAGCATGGAATGTTCGAAAAATTGTTCGAAAGAATAGATCGTCTTGAA
*
212 CACTTTAAGGATCCGATGTTAT
196 TACTTTAAGGATCCGATGTTAT
234 AAAATAACTAGTAAAAGTTTGACAAGTTCA-AAAGTTCGTCCAAG---AAAGAGAGAAACAATTC
1 AAAATAACTAGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTC
* * *
295 TCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTGGAAAATGATAAACTATTTAGAAC
66 TCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTGCAAAATGATAAACTATTTAGACC
* *
360 AAATGATGCGATATCCCAAGCATGGAATGTTTGAAATATTGTTCGAAAGAATAGATCGTCTTGAA
131 AAATGATGCGATATCCCAAGCATGGAATGTTCGAAAAATTGTTCGAAAGAATAGATCGTCTTGAA
425 TACTTTAAGGATCCGATGTTAT
196 TACTTTAAGGATCCGATGTTAT
*
447 AAAATAACTAGTAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACAAAGACAGAAACAATTC
1 AAAATAACTAGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTC
* * *
511 TCACGTAAATAATTTTTTAATTCAAAGAACAAAACTTATTTGCAAAATGACAAACTATTTAGACC
66 TCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTGCAAAATGATAAACTATTTAGACC
* * * ** * * *
576 AAATGATGCGATTTCCCGAGCAGGGAATGTTCGAAAAAAAGCTCGAAAGAATGGATCGTCTTGAT
131 AAATGATGCGATATCCCAAGCATGGAATGTTCGAAAAATTGTTCGAAAGAATAGATCGTCTTGAA
*
641 TA-ATT-AGGAATCCGATGTTAAT
196 TACTTTAAGG-ATCCGATGTT-AT
* *
663 CAAA-GACATAGTAAAAGTTTGACAAGTTC-GAAAGTTCGTCCAAGAACAAAGAGAGAAACAATT
1 AAAATAAC-TAGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATT
* *
726 CTCACGTAAATAAGTTTTTTAATTCAAAGAACAGAACTTGTTTACAAA
65 CTCACGTAAATAAG-TTTTTAATTCAAAGAACAAAACTTGTTTGCAAA
774 GTGANNNNNN
Statistics
Matches: 493, Mismatches: 37, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
213 201 0.41
214 3 0.01
215 15 0.03
216 244 0.49
217 30 0.06
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (217 bp):
AAAATAACTAGTAAAAGTTTGACAAGTTCAGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTC
TCACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTGCAAAATGATAAACTATTTAGACC
AAATGATGCGATATCCCAAGCATGGAATGTTCGAAAAATTGTTCGAAAGAATAGATCGTCTTGAA
TACTTTAAGGATCCGATGTTAT
Found at i:1312 original size:216 final size:217
Alignment explanation
Indices: 831--1770 Score: 1098
Period size: 216 Copynumber: 4.4 Consensus size: 217
821 NNNNNNNAAC
* * * *
831 AAAGACCTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAAAGAGAAACAATTCTC
1 AAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTC
* * *
896 ACGTAAATAAGTTTTTAATTCAAAGAACAGAACTTGTTTACAAAGTGACAAACTATTTTAGACCA
66 ACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATCTTAGACCA
* * ** * * * * * *
961 AATGATGCGATTTCCTGAGCATTGAGTGTTCGAAAAATAGCTCTAAGGAATGGATCTTGATGAAT
131 AATGATGCAATATCCCAAGCATTGAATGTTCGAAAAATAGCTCGAAAGAATAGATCGTCATGAAT
* *
1026 ACTCTATGGAAGCAAAGTTAAA
196 ACTCTAAGGAACCAAAGTTAAA
* * *
1048 AAATAACTCGTAAAAGTTTGACAAGTT-TGAAAGTTCGTCCATGAACAAAGAGAGAAACAATTCT
1 AAAGAACTCGTAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCT
* * * *
1112 TACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGATAAACTA-CTTAGACC
65 CACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATCTTAGACC
* * * *
1176 AAATGATGCAATATCCCAAGCATGGAATGTTCGAAAAATTGTTCGAAAGAATAGATCGTCTTGAA
130 AAATGATGCAATATCCCAAGCATTGAATGTTCGAAAAATAGCTCGAAAGAATAGATCGTCATGAA
* * * * *
1241 TACTTTAAGGATCCGATGTTATA
195 TACTCTAAGGAACCAAAGTTAAA
* *
1264 AAAGAACTTGTAACAGTTTGACAAGTTCAGAAGTTCGTCCAAGAAC-AA-AGAGAAACAATTCTC
1 AAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTC
* * *
1327 ACGTAAATAAGTTTTTAATTCAAAGAACAGAACTTGTTTACAAAGTGACAAACTATTTTAGACCA
66 ACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATCTTAGACCA
* * ** * * * * *
1392 AATGATGCGATTTCCTGAGCATTGAGTGTTCGAAAAATAGCTC-TAAGTAATGGATCTTGATGAA
131 AATGATGCAATATCCCAAGCATTGAATGTTCGAAAAATAGCTCGAAAG-AATAGATCGTCATGAA
* *
1456 TACTCTATGGAAGCAAAGTTAAA
195 TACTCTAAGGAACCAAAGTTAAA
* * *
1479 AAATAACTCGTAAAAGTTTGACAAGTT-TGAAAGTTCGTCCATGAACAAAGAGAGAAACAATTCT
1 AAAGAACTCGTAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCT
* * * *
1543 TACGTAAATAAG-TTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGATAAACTA-CTTAGACC
65 CACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATCTTAGACC
*
1606 AAATGATGCAATATCCCAAGCA-TGAA--TT-G-----T---TCGAAAGAATAGATCGTCTTGAA
130 AAATGATGCAATATCCCAAGCATTGAATGTTCGAAAAATAGCTCGAAAGAATAGATCGTCATGAA
* * * *
1659 TACAT-TAAGGATCCGATGTTATA
195 TAC-TCTAAGGAACCAAAGTTAAA
* *
1682 AAAGAACTTGTAACAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGA-AAA-AATTCTC
1 AAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTC
1745 ACGTAAATAAGTTTTTAATTCAAAGA
66 ACGTAAATAAGTTTTTAATTCAAAGA
Statistics
Matches: 612, Mismatches: 100, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
201 17 0.03
202 17 0.03
203 75 0.12
204 5 0.01
206 1 0.00
211 1 0.00
212 2 0.00
214 71 0.12
215 137 0.22
216 154 0.25
217 132 0.22
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (217 bp):
AAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTC
ACGTAAATAAGTTTTTAATTCAAAGAACAAAACTTGTTTACAAAATGACAAACTATCTTAGACCA
AATGATGCAATATCCCAAGCATTGAATGTTCGAAAAATAGCTCGAAAGAATAGATCGTCATGAAT
ACTCTAAGGAACCAAAGTTAAA
Done.