Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000547.1 Kokia drynarioides strain JFW-HI SEQ_111451, 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: 2580
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:440 original size:216 final size:216
Alignment explanation
Indices: 90--2301 Score: 2068
Period size: 216 Copynumber: 10.3 Consensus size: 216
80 GTATGGAGGG
* * * * *
90 ATGGATCGTCTTAAATACTTTAAGAAACCGATGTTATACAAGAAATCGTAAAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * ** * * * * * * * * *
155 TGAAAGCTCGGCCGAGAACGAATAGACAAATAAATCTCACATAAATAAGTTTTTAAATCGAAGAC
66 CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * *
220 CAAAAGTTTTTTTACAAAATGACAAACTATTTAGACGAAAAGATGCGATTTCCCGAGCGTAGAAT
131 CAAAAG-TTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCCCGAGCATAGAAT
*
285 GTTCGAAAAATTGCTCAAAGGA
195 GTTCGAAAAATTGCTCGAAGGA
* * ** *
307 ATGGATCGTCATG-ATACTTTAAGGTATTGAAGTTATAAAAGAACTTGTAAAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * *
371 TGGAAGTTCATCGAAGAACCAATAG-GCAAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGA
66 CGGAAGTTCATCCAAGAACCAAGAGAG-AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * * * *
435 CCAAAAGTTGTTTACAAATATCATAAACTATTTAGACCATATGATGGGA-TTCGCCGAGCATGGA
130 CCAAAAGTTGTTTACAAA-ATGACAAACTATTTAGACCAAAAGATGCGATTTC-CCGAGCATAGA
* * ***
499 ATGTTTGGAAAATT--TC--TTTA
193 ATGTTCGAAAAATTGCTCGAAGGA
* ** *
519 A--GATCATCTTGAATACTTTAAGGAACCGAAGTTATTCAAGAACTCGTACAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* ** * * * *
582 TGGAAGTTTGTCTAAAAACCAAGAGAGAATCAATTCTCATGTAAATAAGTTTTTAATTCAAAGAC
66 CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * * * ** *
647 CAAAAGTTATTTAAAAAATGATAAACTATTTGGACGAAAAGATGCGATTTCTTG-GACATTGAAT
131 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCCCGAG-CATAGAAT
* * *
711 GTTCGGAAAATTTCTGGAAGGA
195 GTTCGAAAAATTGCTCGAAGGA
* * *
733 ATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAA-AATCTCATAAAAGTTTGACAAGT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA-CTCGTAAAAGTTTGACAAGT
* * * * *
797 TCGGAAGTTCATCCAAGAACCAACAGAGAAACAATTCTGAGGTGAATAAGTTTTTAAATCAAAGA
65 TCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * ** *
862 CCAAAAGTTGTTTACAAAATGA-ATAACTGTTTGGA-CAAAATGATGCTCTTTCCCGAGCATGGA
130 CCAAAAGTTGTTTACAAAATGACA-AACTATTTAGACCAAAA-GATGCGATTTCCCGAGCATAGA
** *
925 ATGTTCGGGAAATTACTCGAAGGA
193 ATGTTCGAAAAATTGCTCGAAGGA
* * * ** *
949 ATGGACCGTCTTGAATACTTTAAGAAACCAAAGTTATTCAAGAGC-CAGTAAAAGTTTGACAAG-
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC-GTAAAAGTTTGACAAGT
* *
1012 T------TTCATCCAAGAACCAAGAGAGAAACAATTCT-ATGTAAATAATTTTTTAATTCAAAGA
65 TCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * * ** * * *
1070 CCTAAAGTTGTTTACAAAATAACAAA-TTTGTTGGACCAATTGATGCGATTTCCCGAACTTTGAA
130 CCAAAAGTTGTTTACAAAATGACAAACTAT-TTAGACCAAAAGATGCGATTTCCCGAGCATAGAA
* *
1134 AGTTCGAAAAATTGCTCGATGGA
194 TGTTCGAAAAATTGCTCGAAGGA
* * ** * *
1157 ATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATTCAAGAACTCATACAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * *
1222 CGCAAGTT-AGTCCAAGAACCAAGAGAGAATCAATTCTCACGTAAATAACTTTTTAAATCAAAGA
66 CGGAAGTTCA-TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * ** *
1286 CCAAAAGTTGTTTACAAAATGGCAAACTATTTATG--CAAAATTATGTGATTTCTTGAACA-A-A
130 CCAAAAGTTGTTTACAAAATGACAAACTATTTA-GACCAAAA-GATGCGATTTCCCGAGCATAGA
* * * * * *
1347 AGGTTAG-AAAATTACCCAAAGGG
193 ATGTTCGAAAAATTGCTCGAAGGA
* * ** * * * *
1370 ATGGACCGTCTTGAATAATTTAAGGAATTGATGTTATAAAAGAACACATGAAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * *
1435 CGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCAAACAC
66 CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * *
1500 CAAAACTTGTTTACAAACTGACAAACTATTTAGA-CAAAATTATGCGATTTCCTGAGCATAGAAT
131 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAA-GATGCGATTTCCCGAGCATAGAAT
1564 GTTCG-AAAATTGCTCGAAGGA
195 GTTCGAAAAATTGCTCGAAGGA
* * * * * *
1585 ATAGATCATCTTGAATACTTTCAGGAACCGAAGTAATAAAAGAAATCGCAAAAGTTTGACAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * * *
1650 CGGATGTTCGTCCAAGAGCCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAAC
66 CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
** * * * * * *
1715 CAAAACATGGTTACGAAATGACAAACTTTTTAGACCATACGATGCAATTTTTCGAACACTCTTAC
131 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGA--TTT------C-C---C
* *
1780 GAGCATGGAGTGTTCGAAAAATT-CTCGAAGGA
184 GAGCATAGAATGTTCGAAAAATTGCTCGAAGGA
* * * ** *
1812 ATAGATTGTCTTGAATACTGTAAGGTGCCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * *
1877 CAGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTGAAAGAC
66 CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
*** * * *
1942 CAAATCCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCATGGAAAT
131 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCCCGAGCATAG-AAT
* * *
2007 CTTCGAAAAACTGCCCGAAGGA
195 GTTCGAAAAATTGCTCGAAGGA
* * * * *
2029 ATGGATCGTCTTGAATACTTTAAGGAATCTAAGTTATAAAACAACTAGTAAAAGTTT-AAAATGT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-GT
* * * **
2093 TCGGAAGTTCGTCTAAGAACAAAGAGAGAAACTGTTCTCACGTAAATAAGTTTTTAATTCAAAGA
65 TCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * **
2158 ACAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTT-CTAAGGCA-AGG
130 CCAAAAGT-TGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCCCGA-GCATA-G
* * *
2219 AATGTTTGGAAAATAGCTCGAAGGA
192 AATGTTCGAAAAATTGCTCGAAGGA
* * * * * *
2244 ATGGATCATCATGATTACCTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAAGTTT
1 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT-AAAAGTTT
2302 NNNNNNNNNN
Statistics
Matches: 1642, Mismatches: 293, Indels: 121
0.80 0.14 0.06
Matches are distributed among these distances:
207 2 0.00
208 138 0.08
209 37 0.02
210 51 0.03
211 117 0.07
212 5 0.00
213 173 0.11
214 13 0.01
215 283 0.17
216 500 0.30
217 138 0.08
218 1 0.00
219 1 0.00
223 1 0.00
224 1 0.00
225 3 0.00
227 172 0.10
228 6 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
CGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCCCGAGCATAGAATG
TTCGAAAAATTGCTCGAAGGA
Found at i:1215 original size:424 final size:427
Alignment explanation
Indices: 90--2301 Score: 2031
Period size: 424 Copynumber: 5.1 Consensus size: 427
80 GTATGGAGGG
* * * * * *
90 ATGGATCGTCTTAAATACTTTAAGAAACCGATGTTATACAAGAAATCGTAAAAGTTTGACAAGTT
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-T
* ** * * * * * * * * *
155 TGAAAGCTCGGCCGAGAACGAATAGACAAATAAATCTCACATAAATAAGTTTTTAAATCGAAGAC
65 T---A-TTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * *
220 CAAAAGTTTTTTTACAAAATGACAAACTATTTAGACGAAAAGATGCGATTTCCCGAGCGTAGAAT
126 CAAAAG-TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAAT
* * * * *
285 GTTCGAAAAATTGCTCAAAGGAATGGATCGTCATG-ATACTTTAAGGTATTGAAGTTATAAAAGA
190 GTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGA
** * * *
349 ACTTGTAAAAGTTTGACAAGTTTGGAAGTTCATCGAAGAACCAATAG-GCAAACAATTCTCACGT
255 ACTCATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAG-AAACAATTCTCACGT
* * *
413 AAATAAGTTTTTAATTGAAAGACCAAAAGTTGTTTACAAATATCATAAACTATTTAGACCATATG
319 AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA-ATGA-AAACTATTTAGACCAAATG
** * * **
478 ATGGGA-TTCGCCGAGCATGGAATGTTTGGAAAATTTCTTTAA-G-
382 ATGCTATTTCGCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGA
* ** *
521 AT----CATCTTGAATACTTTAAGGAACCGAAGTTATTCAAGAACTCGTACAAGTTTGACAAGTT
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-T
** * * * *
582 TGGAAGTTTGTCTAAAAACCAAGAGAGAATCAATTCTCATGTAAATAAGTTTTTAATTCAAAGAC
65 T---A-TTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * * * * ** *
647 CAAAAGTTATTTAAAAAATGATAAACTATTTGGACGAAAAGATGCGATTTCTTG-GACATTGAAT
126 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAG-CATAGAAT
* * * * *
711 GTTCGGAAAATTTCTGGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAA-A
190 GTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGA
* * *
775 ATCTCATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAACAGAGAAACAATTCTGAGGT
255 A-CTCATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGT
* * * * *
840 GAATAAGTTTTTAAATCAAAGACCAAAAGTTGTTTACAAAATGAATAACTGTTTGGACAAAATGA
319 AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAA-AACTATTTAGACCAAATGA
* *
905 TGCTCTTTC-CCGAGCATGGAATGTTCGGGAAATTACTCGAAGGA
383 TGCTATTTCGCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGA
* * ** *
949 ATGGACCGTCTTGAATACTTTAAGAAACCAAAGTTATTCAAGAGC-CAGTAAAAGTTTGACAAG-
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC-GTAAAAGTTTGACAAGT
* * *
1012 T-TTCATCCAAGAACCAAGAGAGAAACAATTCT-ATGTAAATAATTTTTTAATTCAAAGACCTAA
65 TATTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* * * * * * * *
1075 AGTTGTTTACAAAATAACAAA-TTTGTTGGACCAATTGATGCGATTTCCCGAACTTTGAAAGTTC
130 AGTTGTTTACAAAATGACAAACTAT-TTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTC
* **
1139 GAAAAATTGCTCGATGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATTCAAGAACTC
194 GAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTC
* * *
1204 ATACAAGTTTGACAAGTTCGCAAGTT-AGTCCAAGAACCAAGAGAGAATCAATTCTCACGTAAAT
259 ATAAAAGTTTGACAAGTTCGGAAGTTCA-TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* * * * *
1268 AACTTTTTAAATCAAAGACCAAAAGTTGTTTACAAAATGGCAAACTATTTATG-CAAAATTATG-
323 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT-GAAAACTATTTA-GACCAAATGATGC
** * * * * * * *
1331 TGATTTC-TTGAACA--AAAGGTT-AGAAAATTACCCAAAGGG
386 T-ATTTCGCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGA
* ** * * * *
1370 ATGGACCGTCTTGAATAATTTAAGGAATTGATGTTATAAAAGAACACATGAAAGTTTGACAAGTT
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* *
1435 CGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCAAACAC
66 ----A-TTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * * *
1500 CAAAACTTGTTTACAAACTGACAAACTATTTAGACAAAATTATGCGATTTCCTGAGCATAGAATG
126 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATG
* * * *
1565 TTCG-AAAATTGCTCGAAGGAATAGATCATCTTGAATACTTTCAGGAACCGAAGTAATAAAAGAA
191 TTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAA
* ** * * * *
1629 ATCGCAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAATTCTTACGTAA
256 CTCATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
* ** * * * * *
1694 ATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAATGACAAACTTTTTAGACCATACGATG
321 ATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGA-AAACTATTTAGACCAAATGATG
* * *
1759 CAATTTTTCGAACACTCTTACGAGCATGGAGTGTTCGAAAAATT-CTCGAAGGA
385 C--TATTTCG------C---CGAGCATGGAATGTTCGGAAAATTACTCGAAGGA
* ** * ** *
1812 ATAGATTGTCTTGAATACTGTAAGGTGCCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * *
1877 CAGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTGAAAGAC
66 ----A-TTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
*** * *
1942 CAAATCCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCATGGAAAT
126 CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAG-AAT
* * * * * *
2007 CTTCGAAAAACTGCCCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCTAAGTTATAAAACA
190 GTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGA
* * * * **
2072 ACT-AGTAAAAGTTT-AAAATGTTCGGAAGTTCGTCTAAGAACAAAGAGAGAAACTGTTCTCACG
255 ACTCA-TAAAAGTTTGACAA-GTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACG
* *
2135 TAAATAAGTTTTTAATTCAAAGAACAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAAT
318 TAAATAAGTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGA-AAACTATTTAGACCAAAT
* *** * *
2198 GATGCGATTTCTAAG-GCAAGGAATGTTTGGAAAA-TAGCTCGAAGGA
381 GATGCTATTTCGCCGAGCATGGAATGTTCGGAAAATTA-CTCGAAGGA
* * * * * * *
2244 ATGGATCATCATGATTACCTTCAGGAACCGAAGTTATAAAAGAAATCGTAAAAAGTTT
1 ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT-AAAAGTTT
2302 NNNNNNNNNN
Statistics
Matches: 1453, Mismatches: 271, Indels: 112
0.79 0.15 0.06
Matches are distributed among these distances:
421 63 0.04
422 7 0.00
423 4 0.00
424 246 0.17
425 33 0.02
426 126 0.09
427 226 0.16
428 189 0.13
429 75 0.05
430 8 0.01
431 19 0.01
432 98 0.07
433 8 0.01
440 4 0.00
441 4 0.00
442 172 0.12
443 46 0.03
444 125 0.09
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (427 bp):
ATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
ATTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
GTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATAGAATGTTCGA
AAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCAT
AAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAACTATTTAGACCAAATGATGCTATTT
CGCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGA
Found at i:1963 original size:227 final size:215
Alignment explanation
Indices: 1779--2301 Score: 568
Period size: 217 Copynumber: 2.4 Consensus size: 215
1769 AACACTCTTA
* * * **
1779 CGAGCATGGAGTGTTCGAAAAATTCTCGAAGGAATAGATTGTCTTGAATACTGTAAGGTGCCGAA
1 CGAGCATGGAATGTTCGAAAAATTCTCGAAGGAATAGATCGTCTTGAATACTTTAAGGAACCGAA
* **
1844 GTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTTCACCCAAGAACCAAGAGAGAAACA
66 GTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACA
* * * *
1909 ATTCTCACGTAAATAAGGTTTTAATTGAAAGACCAAATCCTGTTTACAAAATGACAAACTATTCA
131 ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAATCATGTTTACAAAATGACAAACTATTTA
* *
1974 GACCAAATGATGCGATTTCC
196 GACCAAACGATGCAATTTCC
* * * * * *
1994 CGAGCATGGAAATCTTCGAAAAACTGCCCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCT
1 CGAGCATGG-AATGTTCGAAAAA-TTCTCGAAGGAATAGATCGTCTTGAATACTTTAAGGAACCG
* * * *
2059 AAGTTATAAAACAACTAGTAAAAGTTT-AAAATGTTCGGAAGTTCGTCTAAGAACAAAGAGAGAA
64 AAGTTATAAAAGAACTCGTAAAAGTTTGAAAA-GTTCGGAAGTTCGTCCAAGAACCAAGAGAGAA
** * *
2123 ACTGTTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAAT-AT-TTTTCAAAATGACAAACTA
128 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-ACCAAATCATGTTTACAAAATGACAAACTA
* *
2186 TTTAGACCAAATGATGCGATTT-C
192 TTTAGACCAAACGATGCAATTTCC
** * * * * * * * * * *
2209 TAAGGCAAGGAATGTTTGGAAAATAGCTCGAAGGAATGGATCATCATGATTACCTTCAGGAACCG
1 CGA-GCATGGAATGTTCGAAAAAT-TCTCGAAGGAATAGATCGTCTTGAATACTTTAAGGAACCG
*
2274 AAGTTATAAAAGAAATCGTAAAAAGTTT
64 AAGTTATAAAAGAACTCGT-AAAAGTTT
2302 NNNNNNNNNN
Statistics
Matches: 258, Mismatches: 43, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
214 1 0.00
215 69 0.27
216 67 0.26
217 115 0.45
218 6 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (215 bp):
CGAGCATGGAATGTTCGAAAAATTCTCGAAGGAATAGATCGTCTTGAATACTTTAAGGAACCGAA
GTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACA
ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAATCATGTTTACAAAATGACAAACTATTTA
GACCAAACGATGCAATTTCC
Found at i:2338 original size:216 final size:217
Alignment explanation
Indices: 1017--2301 Score: 762
Period size: 215 Copynumber: 5.9 Consensus size: 217
1007 ACAAGTTTCA
* * ** *
1017 TCCAAGAACCAAGAGAGAAACAATTCT-ATGTAAATAATTTTTTAATTCAAAGACCTAAAGT--T
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGA-C-AAAATCAT
* * ** * ** * *** *
1079 GTTTACAAAATAACAAA-TTTGTTGGACCAATTGATGCGATTTCCCGAACTTTGAAA-GTTCGAA
64 GTTTACAAAATGACAAACTAT-TCAGACCAAATGATGCGATTTCAAGAGCAAGGAAATCTTCGAA
* * * * * * ** * *
1142 AAATTGCTCGATGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATTCAAGAACTCA-T
128 AAACTGCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAAAT-AGT
* * * *
1206 ACAAGTTTGACAA-GTTCGCAAGTTAG
192 AAAAGTTT-AAAATGTTCGGAAGTTCG
* * ** *
1232 TCCAAGAACCAAGAGAGAATCAATTCTCACGTAAATAACTTTTTAAATCAAAGACCAAAAGT--T
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGA-CAAAA-TCAT
* * * * * ** * ** *
1295 GTTTACAAAATGGCAAACTATTTATG-CAAAATTATGTGATTTCTTGAAC-A--AAAGGTTAG-A
64 GTTTACAAAATGACAAACTATTCA-GACCAAATGATGCGATTTCAAGAGCAAGGAAATCTTCGAA
* * * * * * * ** ** * * *
1355 AAATTACCCAAAGGGATGGACCGTCTTGAATAATTTAAGGAATTGATGTTATAAAAGAACACA-T
128 AAACTGCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAA-ATAGT
* * * *
1419 GAAAGTTTGACAA-GTTCGAAAGTTCA
192 AAAAGTTT-AAAATGTTCGGAAGTTCG
* * *
1445 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA-GTTTCTAATTCAAACACCAAAA-CTT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTT-TAATTCAAAGA-CAAAATCAT
* * * * ** *
1508 GTTTACAAACTGACAAACTATTTAGACAAAATTATGCGATTTCCTGAGCATA-G-AATGTTCG-A
64 GTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCAAGAGCA-AGGAAATCTTCGAA
* * * * * * * * * *
1570 AAATTGCTCGAAGGAATAGATCATCTTGAATACTTTCAGGAACCGAAGTAATAAAAGAAATCGCA
128 AAACTGCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAAATAGTA
* *
1635 AAAGTTTGACAA-GTTCGGATGTTCG
193 AAAGTTT-AAAATGTTCGGAAGTTCG
* * * * *
1660 TCCAAGAGCCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAA-CATG
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGA-CAAAATCATG
* * * * * * * *
1724 GTTACGAAATGACAAACTTTTTAGACCATACGATGCAATTTTTCGAACACTCTTACGAGCATGG-
65 TTTACAAAATGACAAACTATTCAGACCAAATGATGCGA--TTT----CA-----A-GAGCAAGGA
* * * * * ** * **
1788 AGTGTTCGAAAAA-TTCTCGAAGGAATAGATTGTCTTGAATA-CTGTAAGGTGCCGAAGTTATAA
118 AATCTTCGAAAAACTGCCCGAAGGAATGGATCATCATGAATACCT-TAAGGAACCGAAGTTATAA
* * * * *
1851 AAGAACTCGTAAAAGTTTGAAAA-GTTCAGAAGTTCA
182 AACAAATAGTAAAAGTTT-AAAATGTTCGGAAGTTCG
* * * * *
1887 CCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTGAAAGACCAAATCCTGT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGACAAAATCATGT
** *
1952 TTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCATGGAAATCTTCGAAAAA
66 TTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCAAGAGCAAGGAAATCTTCGAAAAA
* * * * * *
2017 CTGCCCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCTAAGTTATAAAACAACTAGTAAAA
131 CTGCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAAATAGTAAAA
2082 GTTTAAAATGTTCGGAAGTTCG
196 GTTTAAAATGTTCGGAAGTTCG
* ** *
2104 TCTAAGAACAAAGAGAGAAACTGTTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAAT-AT-
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAG-ACAAAATCATG
* * * * *
2167 TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTAAG-GCAAGG-AATGTTTGGAA
65 TTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTC-AAGAGCAAGGAAATCTTCGAAA
* * * * *
2230 AA-TAGCTCGAAGGAATGGATCATCATGATTACCTTCAGGAACCGAAGTTATAAAAGAAATCGTA
129 AACT-GCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAAATAGT-
2294 AAAAGTTT
192 AAAAGTTT
2302 NNNNNNNNNN
Statistics
Matches: 872, Mismatches: 159, Indels: 77
0.79 0.14 0.07
Matches are distributed among these distances:
212 4 0.00
213 169 0.19
214 6 0.01
215 255 0.29
216 132 0.15
217 120 0.14
218 7 0.01
221 2 0.00
225 3 0.00
226 5 0.01
227 165 0.19
228 4 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (217 bp):
TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGACAAAATCATGT
TTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCAAGAGCAAGGAAATCTTCGAAAAA
CTGCCCGAAGGAATGGATCATCATGAATACCTTAAGGAACCGAAGTTATAAAACAAATAGTAAAA
GTTTAAAATGTTCGGAAGTTCG
Found at i:2421 original size:60 final size:61
Alignment explanation
Indices: 2315--2548 Score: 274
Period size: 62 Copynumber: 3.8 Consensus size: 61
2305 NNNNNNNNNN
* * * * *
2315 GTTCGTCCAAGAACCAAGAGAGAATCAATTCTTACATAAAATAAGTTTTTGACAAGCTC-GAAA
1 GTTCGTCCAAGAA-CAAGAGAGAAGCAATACTCACGT-AAATAAGTTTTTGACAAGTTCAG-AA
* *
2378 GTTCGTCCAAGAACTAGAGAGAAGCAATACT-ACGTAAATAAGTTATTGACAAGTTCAGAA
1 GTTCGTCCAAGAACAAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCAGAA
* *
2438 GTTCGTCCAAAAACTAAGAGAGAAGCAATACTCACGTAAATAAGGTTTTGACAAGTTCAGAA
1 GTTCGTCCAAGAAC-AAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCAGAA
* * * * * *
2500 GTTCCTCCAAGATCCAAGAGAGAACCAATTCTCTCGTAGATAAGTTTTT
1 GTTCGTCCAAGA-ACAAGAGAGAAGCAATACTCACGTAAATAAGTTTTT
2549 AATTCAGCGA
Statistics
Matches: 149, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
60 34 0.23
61 20 0.13
62 81 0.54
63 14 0.09
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (61 bp):
GTTCGTCCAAGAACAAGAGAGAAGCAATACTCACGTAAATAAGTTTTTGACAAGTTCAGAA
Done.