Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013427.1 Kokia drynarioides strain JFW-HI SEQ_128453, 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: 2320
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.26
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:564 original size:216 final size:217
Alignment explanation
Indices: 8--839 Score: 1180
Period size: 216 Copynumber: 3.9 Consensus size: 217
1 TTGCTCG
8 AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAAC-AGTAAAAGTTTGAC
1 AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAC
* * * *
72 AAGTTCGAAAGTTGGTACAATG-ACAAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTC
66 AAGTTCGAAAGTTCGTCCAATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
* * * *
136 AAAGAGCAAAAGTTGTCTGCTAAATGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCAT
131 AAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCAT
* *
201 GGAAAATTCGAAAAATTGCTGA
196 GGAATATTTGAAAAATTGCTGA
* * *
223 AATGAATGGATCGTCTTGAATACTATAAGGATCCAAAGTTAT---A-AACTAGTAAAAGTTTGAC
1 AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAC
284 AAGTTCGAAAGTTCGTCCAA-GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
66 AAGTTCGAAAGTTCGTCCAATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
* * * * * *
348 AAAGACCAATACATGTTTGCAAAATGACAAACTATTTAGGCCAAATGGTGCGATTTGCTGAGCTT
131 AAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCAT
413 GGAATATTTGAAAAATTGCTCG-
196 GGAATATTTGAAAAATTGCT-GA
* * * * *
435 AAGGAACGAATCGTCTTGAATAATTTATGGATCCAAAGTTATAAATGAACTAGTAAAATTTTGAC
1 AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAC
500 AAGTTCGAAAGTTCGTCCAA-GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
66 AAGTTCGAAAGTTCGTCCAATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
* ** * *
564 AACGAAAAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATGTGATTTGCCGAGCAT
131 AAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCAT
* *
629 GGAATA-ATCAGAAAATTGCTGA
196 GGAATATTTGA-AAAATTGCTGA
* * * * *
651 AATGAATGGATCGTCTTGAATACTTTAAGGTTCCAAAGTTATAAAAAAACTAGTAAAAGGTTGAC
1 AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAC
* *
716 AAGTTCGGAAGTTCGTCCAAGAATGAACAAAGAGAGAAACAATTATCACGTAAATAAGTTTTTAA
66 AAGTTCGAAAGTTCGTCC---AATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* * *
781 TTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAGTGACGCGATTT
128 TTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTT
840 CCCAANNNNN
Statistics
Matches: 544, Mismatches: 60, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
211 4 0.01
212 182 0.33
213 1 0.00
215 42 0.08
216 222 0.41
219 2 0.00
220 91 0.17
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (217 bp):
AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGAC
AAGTTCGAAAGTTCGTCCAATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
AAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTGCCGAGCAT
GGAATATTTGAAAAATTGCTGA
Found at i:1268 original size:216 final size:216
Alignment explanation
Indices: 895--1815 Score: 1281
Period size: 216 Copynumber: 4.3 Consensus size: 216
885 NNNNNNNNNN
* * * *
895 ATTTGCCGAGCATGGTAT-ATTTGAAAAATTGCTCG-AAGGAATGGATCGTCTTGAATAATTTAA
1 ATTTGCCGAGCATGGAATAATTCGAAAAATTGCT-GAAATGAATGGATCGTCTTGAATACTTTAA
* *
958 GGATCCAAAGTTATAAAAAAATAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGA
65 GGATCCAAAGTTATAAAAAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGA
* * **
1023 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAACGAAAAAAACTTGTTTGCAAAACGACAA
130 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAACGACAA
* *
1088 ACTATTTAGATCAAATGATGTG
195 ACTATTTAGACCAAATGATGCG
1110 ATTTGCCGAGCATGGAATAA-TC-AGAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAA
1 ATTTGCCGAGCATGGAATAATTCGA-AAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAA
1173 GGATCCAAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAG
65 GGATCCAAAGTTATAAAA-AACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAG
* * *
1238 AGAGAAACAATTGTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCTAAATGACA
129 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAACGACA
*
1303 AACTCTTTAGACCAAATGATGCG
194 AACTATTTAGACCAAATGATGCG
* *
1326 ATTTGCCGAGCA-CGAAAAATTCGAAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAAG
1 ATTTGCCGAGCATGGAATAATTCGAAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAAG
* * *
1390 GATCCAAAGTTAT---AAACTAGTAAATGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAAGAG
66 GATCCAAAGTTATAAAAAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAG
*
1452 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAACTTGTTTGCAAAACGACAAA
131 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAACGACAAA
*
1517 CTATTTAGACCAAATGATACG
196 CTATTTAGACCAAATGATGCG
* * * * * *
1538 ATTTACTGAG-ATTGGAA-AATTTGGAAAATTACTAAAATGAATGGATCGTCTTGAATACTTTAA
1 ATTTGCCGAGCA-TGGAATAATTCGAAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAA
* * *
1601 GGTTCCAAAGTTATAAAAGAACTAGTAAAAGGTTGTCAGGTTCGAAAGTTCGTCCAAGAACAAAG
65 GGATCCAAAGTTATAAAA-AACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAG
* * * *
1666 AGAGAAACAATTGTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTACAAAATGACA
129 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAACGACA
* * *
1731 AACTATTTAGACCAAGTAACGCG
194 AACTATTTAGACCAAATGATGCG
* * * * * * * *
1754 ATTTCCCAAGGATGGAAT-GTTCGAAAAATTGCTCTAAA-AAATGGATCTTGTTGAATACTTTA
1 ATTTGCCGAGCATGGAATAATTCGAAAAATTGCT-GAAATGAATGGATCGTCTTGAATACTTTA
1816 GGGAACTGAA
Statistics
Matches: 631, Mismatches: 60, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
211 1 0.00
212 188 0.30
213 4 0.01
214 2 0.00
215 77 0.12
216 354 0.56
217 5 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
ATTTGCCGAGCATGGAATAATTCGAAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAAG
GATCCAAAGTTATAAAAAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAG
AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAACGACAAA
CTATTTAGACCAAATGATGCG
Found at i:1695 original size:428 final size:429
Alignment explanation
Indices: 917--2217 Score: 1460
Period size: 428 Copynumber: 3.0 Consensus size: 429
907 TGGTATATTT
917 GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAAAATAG
1 GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTAT--AAAAATAG
*
982 TAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
64 TAAAAGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
* * **
1047 GTTTTTAATTTAACGAAAAAAACTTGTTTGCAAAACGACAAACTATTTAGATCAAATGATGTGAT
129 GTTTTTAATTCAACGAAAAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATACGAT
* * *
1112 TTGCCGAGCATGGAATAATCAGAAAATTGCTGAAATGAATGGATCGTCTTGAATACTTTAAGGAT
194 TTACCGAGCATGGAATAATCAGAAAATTACTAAAATGAATGGATCGTCTTGAATACTTTAAGGAT
1177 CCAAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAG
259 CCAAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAG
* * *
1242 AAACAATTGTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCTAAATGACAAACT
324 AAACAATTGTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTACAAAATGACAAACT
*
1307 CTTTAGACCAAATGATGCGATTTGCCGAGCACGAAAAATTC
389 ATTTAGACCAAATGATGCGATTTGCCGAGCACGAAAAATTC
* * *
1348 GAAAAATTGCT-GAAATGAATGGATCGTCTTGAATACTTTAAGGATCCAAAGTTAT-AAACTAGT
1 GAAAAATTGCTCG-AAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAATAGT
*
1411 AAATGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAG
65 AAAAGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAG
**
1476 TTTTTAATTCAACGACCAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATACGATT
130 TTTTTAATTCAACGAAAAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATACGATT
* ** *
1541 TACTGAG-ATTGGAA-AATTTGGAAAATTACTAAAATGAATGGATCGTCTTGAATACTTTAAGGT
195 TACCGAGCA-TGGAATAA-TCAGAAAATTACTAAAATGAATGGATCGTCTTGAATACTTTAAGGA
* *
1604 TCCAAAGTTATAAAAGAACTAGTAAAAGGTTGTCAGGTTCGAAAGTTCGTCCAAGAACAAAGAGA
258 TCCAAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGA
1669 GAAACAATTGTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTACAAAATGACAAAC
323 GAAACAATTGTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTACAAAATGACAAAC
* * * * * * * * **
1734 TATTTAGACCAAGTAACGCGATTTCCCAAGGATGGAATGTTC
388 TATTTAGACCAAATGATGCGATTTGCCGAGCACGAAAAATTC
* ** * * * * * **
1776 GAAAAATTGCTCTAAAAAATGGATCTTGTTGAATACTTTAGGGAACTGAAGTTA-AAANNNNNNN
1 GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAA-------
********************** * *
1840 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGAAAGTTCGTCAAAGAACAAA
59 ---------------------AATAGTAAAAGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAA
* *
1905 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAACGAAAAAAACTTGTTTGCAAAACAAC
103 GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAACGAAAAAAACTTGTTTGCAAAACGAC
* ** * ** *
1970 AAACTATTTAGATCAAATGATGTGATTTGCCGAGCATGGAATAATCAGAAAATTGTTGAAATGAA
168 AAACTATTTAGACCAAATGATACGATTTACCGAGCATGGAATAATCAGAAAATTACTAAAATGAA
* * *
2035 TGGATCGTCTTGACTACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAACGGTTGATAAGTTC
233 TGGATCGTCTTGAATACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTC
* * * *
2100 GGAAGTTCGTCCAAGAATGAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTCAAA
298 GAAAGTTCGTCC---AA-GAACAAAGAGAGAAACAATTGTCACGTAAATAAGTTTTTAATTAAAA
* *
2165 GACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAGTGACGCGATTT
359 GACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
2218 CCCAAGGATG
Statistics
Matches: 739, Mismatches: 92, Indels: 49
0.84 0.10 0.06
Matches are distributed among these distances:
427 3 0.00
428 382 0.52
430 1 0.00
431 51 0.07
456 201 0.27
457 3 0.00
459 2 0.00
460 96 0.13
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.26
Consensus pattern (429 bp):
GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATAATTTAAGGATCCAAAGTTATAAAAATAGTA
AAAGTTTGACAAGTTCAAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAACGAAAAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATACGATTT
ACCGAGCATGGAATAATCAGAAAATTACTAAAATGAATGGATCGTCTTGAATACTTTAAGGATCC
AAAGTTATAAAAGAACTAGTAAAAGGTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAA
ACAATTGTCACGTAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
TTAGACCAAATGATGCGATTTGCCGAGCACGAAAAATTC
Found at i:2289 original size:220 final size:220
Alignment explanation
Indices: 1898--2320 Score: 510
Period size: 220 Copynumber: 1.9 Consensus size: 220
1888 GTTCGTCAAA
* * * *
1898 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAACGAAAAAAACTTGTTTGCA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTCAAAGAAAAAAACTTGTTTACA
* * * * * *
1963 AAACAACAAACTATTTAGATCAAATGATGTGATTTGCCGAGCATGGAATAATCAGAAAATTGTTG
66 AAACAACAAACTATTTAGACCAAATGACGCGATTTCCCAAGCATGGAATAATCAGAAAATTCTTG
* * * * * *
2028 AAATGAATGGATCGTCTTGACTACTTTAAGGATCCAAAGTTATAAAAGAACTAGTAAACGGTTGA
131 AAATAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACCAGTAAAAGGTTGA
*
2093 TAAGTTCGGAAGTTCGTCCAAGAAT
196 CAAGTTCGGAAGTTCGTCCAAGAAT
**
2118 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTCAAAGACCAAAACTTGTTTACA
1 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTCAAAGAAAAAAACTTGTTTACA
** * * **
2183 AAATGACAAACTATTTAGACCAAGTGACGCGATTTCCCAAGGATGGAATGTTC-GAAAAATTACT
66 AAACAACAAACTATTTAGACCAAATGACGCGATTTCCCAAGCATGGAATAATCAG-AAAATT-CT
* * * * * * *
2247 CT-AAA-AAATGGATCTTGTTTAATACTTTAGGGAACTAAAGTTAAAAAATAACCCGTAAAAGGT
129 -TGAAATAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACCAGTAAAAGGT
2310 TGACAAGTTCG
193 TGACAAGTTCG
Statistics
Matches: 168, Mismatches: 32, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
219 1 0.01
220 162 0.96
221 4 0.02
222 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (220 bp):
GAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTCAAAGAAAAAAACTTGTTTACA
AAACAACAAACTATTTAGACCAAATGACGCGATTTCCCAAGCATGGAATAATCAGAAAATTCTTG
AAATAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACCAGTAAAAGGTTGA
CAAGTTCGGAAGTTCGTCCAAGAAT
Done.