Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007580.1 Kokia drynarioides strain JFW-HI SEQ_122210, 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: 2257
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Found at i:396 original size:216 final size:216
Alignment explanation
Indices: 1--1380 Score: 911
Period size: 216 Copynumber: 6.5 Consensus size: 216
* * * * * * *
1 CGAGAATGTAATGTTCGAAAAATTGCTCGAAGGAGTGGATCATCTTTATTACTTTAAGGAAACGA
1 CGAGAATGGAATGTTAGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATCGA
66 AGTTATAAAAGAACTCG-AAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAAC
66 AGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAAC
* * * *
130 CATTCTCACGTAAATAATTTTTTAATTCAAAGACCAAAAGTT-TGTTACAAAAGGACAAACTATT
131 AATTCTCACATAAATAAGTTTTTAATTCAAAGACTAAAAGTTGT-TTACAAAAGGACAAACTATT
* *
194 TTGACCAAATGATGCGATTTTT
195 TGGACCAAATGATGCGATTTCT
* * * *
216 CGAGCATCGAATGTTAGGAAAATTGCTCGAAGGAATCGATCCTCTTGAATACTTTAAGGAATCGA
1 CGAGAATGGAATGTTAGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATCGA
* * * *
281 AGTTTTAAAAGAACTCGAAAAAGCTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAAC
66 AGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAAC
* * * *
346 AATTCTCACATAATTTAGTTTTTAATCCAAAGACTAAAAGTTGTTTACAAAAGGA-AAATTTATT
131 AATTCTCACATAAATAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAAGGACAAA-CTATT
*
410 TGGACCAAATGATGCTATTTCT
195 TGGACCAAATGATGCGATTTCT
* * * * * *
432 CGATAATGGAATGTTCA-AAAAATTGCTTGAAGGAAAGGA-AC-C--G-A-A-GTT--GTGAA-A
1 CGAGAATGGAATGTT-AGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAG-GAATC
* * ** * * ** **** *
486 GAACTCA-AAAA-ATTTTG-AAAA-TTTCG-GAAGTTCGGCCAAGAACCAAGAGAGAAACAATTC
64 GAAGTTATAAAAGAACTCGAAAAAGTTT-GAAAAGTTCGG--AAGTTCGGCCA-AGAACCAA---
* * * * * * *
546 TCACATAAATAAGTTTTTAATCTAATGACCAA-AAGTTGTTTAGA---AAATGAC-AGATTA-TT
122 -GAGAGAAACAA--TTCTCA-C--AT-A--AATAAGTT-TTTA-ATTCAAA-GACTA-A-AAGTT
* * * *** * * * *
605 -TTGGACCAAATGATGTGA-TTTTTCGA--TAATG--G-AATTT-T
173 GTT-TACAAAAGGA-CAAACTATTTGGACCAAATGATGCGATTTCT
** * *
643 CGA-AA---AA--TT------A-T--TCGAAATAATGGATCGTCTTAAATACTTTAAGGAATCGA
1 CGAGAATGGAATGTTAGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATCGA
* * * *
693 AGTTATAAAAGAACTCAAAAAAGTTTAAAAAGTTCGAAAGTTCGGCCAAGAACAAAGAGAGAAAC
66 AGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAAC
* * * * * *
758 AATTCTTACATAAATAAGCTTTTAATTCAAAGA-TCAAATGTTTTTTAAAAAAGGACAAACTGTT
131 AATTCTCACATAAATAAGTTTTTAATTCAAAGACT-AAAAGTTGTTTACAAAAGGACAAACTATT
* *
822 TGGACCAAATGGTGTC-ATATCT
195 TGGACCAAATGATG-CGATTTCT
** * * * * * *
844 CGAGGCTGGAATGTTTGGAAAATTG-TCGGGAGGAATCGATCATCTTGATTACTTTAAGGAATCG
1 CGAGAATGGAATGTTAGAAAAATTGCTC-GAAGGAATGGATCCTCTTGAATACTTTAAGGAATCG
* * * * * *
908 AAGTTATAAAAGAACTAGAAAAATTTTCACAAGTTCGGAAGTTTGGCCAAGAACGAAGAGA-AAA
65 AAGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAA
* * * * * * * *
972 -AATTCTCAAATAAATAAGTTTTTAATCCAAAGACCAACAGTTCTTTACAAAATGACATATTATT
130 CAATTCTCACATAAATAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAAGGACAAACTATT
* *
1036 TGGACCATAA-GATGTGATTTCC
195 TGGACCA-AATGATGCGATTTCT
* * *
1058 CGAGAAGGGAATGTTTA-AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGAAATCG
1 CGAGAATGGAATG-TTAGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATCG
* ** *
1122 AAGTTATAAAGGAACTCGAAAAAGTTTGAAAAGTTCAAAAATTCGGCCAAGAACCAAGAGAGAAA
65 AAGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAA
* * * * *
1187 TC-ATTCTCACGTAAATAAGTTTTTAATTCAAAGATTGAAAGTTTTTTTCAAAAGGACAAACTAT
130 -CAATTCTCACATAAATAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAAGGACAAACTAT
* *
1251 TTGGTCCAAATGATG-GAATTTCC
194 TTGGACCAAATGATGCG-ATTTCT
* *
1274 CGAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATCGATCCTCTTGAATACTTTAAGGAA-CT
1 CGAGAATGGAATGTT-AGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATC-
* *
1337 GAAGTTTTAAAAGAACTC-AAAAATGTTT-AACAAGTGCGGAAGTT
64 GAAGTTATAAAAGAACTCGAAAAA-GTTTGAA-AAGTTCGGAAGTT
1381 TGGTGATAGC
Statistics
Matches: 882, Mismatches: 193, Indels: 179
0.70 0.15 0.14
Matches are distributed among these distances:
193 1 0.00
194 7 0.01
195 21 0.02
196 16 0.02
197 6 0.01
198 2 0.00
199 3 0.00
200 7 0.01
201 5 0.01
202 8 0.01
203 12 0.01
204 8 0.01
205 18 0.02
206 21 0.02
207 16 0.02
208 7 0.01
209 12 0.01
210 10 0.01
211 5 0.01
212 9 0.01
213 3 0.00
214 165 0.19
215 107 0.12
216 380 0.43
217 25 0.03
218 6 0.01
219 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (216 bp):
CGAGAATGGAATGTTAGAAAAATTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAATCGA
AGTTATAAAAGAACTCGAAAAAGTTTGAAAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAAC
AATTCTCACATAAATAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAAGGACAAACTATTT
GGACCAAATGATGCGATTTCT
Found at i:1123 original size:214 final size:214
Alignment explanation
Indices: 466--1380 Score: 955
Period size: 216 Copynumber: 4.2 Consensus size: 214
456 GCTTGAAGGA
* * * * *
466 AAGGAACCGAAGTTGTGAAAGAACTCAAAAAATTTTGAAAATTTCGGAAGTTCGGCCAAGAACCA
1 AAGGAATCGAAGTTATAAAAGAACT-AAAAAATTTTAAAAAGTTCGGAAGTTCGGCCAAGAACCA
* * * * *
531 AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCTAATGACCAAAAGTTGTTTAGAAAATGA
65 AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACC-AAAGTTTTTTACAAAAGGA
* * ** * * ** *
596 CAGATTATTTTGGACCAAATGATGTGATTTTTCGATAATGGAAT-TTTCGAAAAATTATTCGAAA
129 CAAACTA-TTTGGACCAAATGATGTGATTTCCCGAGAATGGAATGTTT-AAAAAATTGCTCGAAG
* * *
660 TAATGGATCGTCTTAAATACTTT
192 GAATCGATCGTCTTGAATACTTT
* * *
683 AAGGAATCGAAGTTATAAAAGAACTCAAAAAAGTTTAAAAAGTTCGAAAGTTCGGCCAAGAACAA
1 AAGGAATCGAAGTTATAAAAGAACT-AAAAAATTTTAAAAAGTTCGGAAGTTCGGCCAAGAACCA
* * * * *
748 AGAGAGAAACAATTCTTACATAAATAAGCTTTTAATTCAAAGATCAAATGTTTTTTAAAAAAGGA
65 AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAA-GTTTTTTACAAAAGGA
* * * * * ** ** *
813 CAAACTGTTTGGACCAAATGGTGTCATATCTCGAGGCTGGAATGTTTGGAAAATTG-TCGGGAGG
129 CAAACTATTTGGACCAAATGATGTGATTTCCCGAGAATGGAATGTTTAAAAAATTGCTC-GAAGG
* *
877 AATCGATCATCTTGATTACTTT
193 AATCGATCGTCTTGAATACTTT
* * * *
899 AAGGAATCGAAGTTATAAAAGAACTAGAAAAATTTTCACAAGTTCGGAAGTTTGGCCAAGAACGA
1 AAGGAATCGAAGTTATAAAAGAACTA-AAAAATTTTAAAAAGTTCGGAAGTTCGGCCAAGAACCA
* * *
964 AGAGA-AAA-AATTCTCAAATAAATAAGTTTTTAATCCAAAGACCAACAGTTCTTTACAAAATGA
65 AGAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAA-AGTTTTTTACAAAAGGA
* * *
1027 CATATTATTTGGACCATAA-GATGTGATTTCCCGAGAAGGGAATGTTTAAAAAATTGCTCGAAGG
129 CAAACTATTTGGACCA-AATGATGTGATTTCCCGAGAATGGAATGTTTAAAAAATTGCTCGAAGG
*
1091 AATGGATCGTCTTGAATACTTT
193 AATCGATCGTCTTGAATACTTT
* * * * * ** *
1113 AAGAAATCGAAGTTATAAAGGAACTCGAAAAAGTTTGAAAAGTTCAAAAATTCGGCCAAGAACCA
1 AAGGAATCGAAGTTATAAAAGAACT-AAAAAATTTTAAAAAGTTCGGAAGTTCGGCCAAGAACCA
* * ** *
1178 AGAGAGAAATC-ATTCTCACGTAAATAAGTTTTTAATTCAAAGATTGAAAGTTTTTTTCAAAAGG
65 AGAGAGAAA-CAATTCTCACATAAATAAGTTTTTAATCCAAAGA-CCAAAGTTTTTTACAAAAGG
* * * *
1242 ACAAACTATTTGGTCCAAATGATG-GAATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAG
128 ACAAACTATTTGGACCAAATGATGTG-ATTTCCCGAGAATGGAATGTTTAAAAAATTGCTCGAAG
*
1306 GAATCGATCCTCTTGAATACTTT
192 GAATCGATCGTCTTGAATACTTT
* * * *
1329 AAGGAA-CTGAAGTTTTAAAAGAACTCAAAAATGTTTAACAAGTGCGGAAGTT
1 AAGGAATC-GAAGTTATAAAAGAACTAAAAAAT-TTTAAAAAGTTCGGAAGTT
1381 TGGTGATAGC
Statistics
Matches: 577, Mismatches: 105, Indels: 33
0.81 0.15 0.05
Matches are distributed among these distances:
214 167 0.29
215 23 0.04
216 269 0.47
217 118 0.20
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (214 bp):
AAGGAATCGAAGTTATAAAAGAACTAAAAAATTTTAAAAAGTTCGGAAGTTCGGCCAAGAACCAA
GAGAGAAACAATTCTCACATAAATAAGTTTTTAATCCAAAGACCAAAGTTTTTTACAAAAGGACA
AACTATTTGGACCAAATGATGTGATTTCCCGAGAATGGAATGTTTAAAAAATTGCTCGAAGGAAT
CGATCGTCTTGAATACTTT
Done.