Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002549.1 Kokia drynarioides strain JFW-HI SEQ_114737, 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: 2816
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Found at i:814 original size:216 final size:215
Alignment explanation
Indices: 1--1874 Score: 1928
Period size: 216 Copynumber: 8.7 Consensus size: 215
* * * * * * * ** *
1 GATCGTCTTAAACACTTTAAGGAACCGAACTTTTAAAAGAGCTTGTAAAAGTTTGACAAATGCGA
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* ** * * *
66 AAGTACATATAAGAACCAAAAGAGAACCAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* * * * * * **
131 AACTCGTTTACAAAATGACAAACTATTGAAAACAAATGATGTGATTTC-CTAGGCATGGTATGTT
131 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGA-GCATGAAATGTT
** *
195 C-AAAATTTTTTCAAAGGAATG
195 CAAAAATTGATT-GAAGGAATG
* * * * ** * *
216 GATCGACTTGATTATTTTATGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
** * * * *
281 AAGTTCATCCAAGAAATAAGAGAGAAACAATTCTCAGGTAAACAAGTTTTTAATTCGAAGAC-CA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* * * *
345 AACGTTGTTTACAAAATGATAAACTATTAAGACCAAATGATGCA-ATTTCCCGAGGATGAAATGT
131 AAC-TTGTTTACAAAATGACAAACTATTTAGACCAAATGATG-AGATTTCTCGAGCATGAAATGT
** *
409 TCGAAAAA-CAACTCGAAGGAATG
194 TC-AAAAATTGA-TTGAAGGAATG
* * * * *
432 GATCGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAGGAACTCGTAATAGTTTTACTAGTTTGG
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* * * * *
497 AAGTTCATCCAAGAACCAATA-A-ATACAATTCTGATGTAAATAAGTTTTTAATTCAAAGACCAA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* *
560 AACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTC
131 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGAAATGTTC
*
625 GAAAAATTGATTGAAGGATTG
196 -AAAAATTGATTGAAGGAATG
* * * * *
646 GA-CTGTCTTGAATACTTTAAGGAATCGAATTTATAAAAGAACTCATAAAAGTTTGACATGTTTT
1 GATC-GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * *
710 GAAGTTCATCCAAGAACCATGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACAA
65 GAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTA
* * *
775 AAACTTGTTTACATAATGACAAACTATTTAGATCAAATGATGCGATTTCTCGAGCATGAAATGTT
130 AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGAAATGTT
* *
840 CAGAAAATTGCTTGGAGGAATG
195 CA-AAAATTGATTGAAGGAATG
* * * * * * * *
862 GATCATCTTGAATACTTTCAGGAATCGAAGTTATAAAAGAACTCATAAAAGTTTTACCACTTTGA
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
** ** * * *
927 AAGTTTGTCCAAGAACCAAGAGAGAAAGTATTCTAACGTAAATAAGTTTTCAATTCAAAGACCAA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* * * * *
992 AACATATTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGAAATGTTC
131 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGAAATGTTC
* *
1057 GAGAAATT-ACTCGAAGGAATG
196 -AAAAATTGA-TTGAAGGAATG
* * * * * *
1078 GATTGTCTTGAATACTTTAAGGAACCGAAGTTATGAAAGAACTTGTAAAAGTTTGACTAGTTCGA
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* * *
1143 AAGTTCGTGCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* * * *
1208 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATAATGAAATTTC-CTGTGTAT-AGAATGT
131 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTC-GAGCATGA-AATGT
* *
1271 T-AAGAATATTGCTTGAAAG-ATG
194 TCAA-AA-ATTGATTGAAGGAATG
* * * * * * * * ***
1293 GATCTTCTTGAATTCTTTATGGAA-C-------TAATACAACTCATAAAAGTTTTACCAGTTCAA
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* *** *
1350 AAGTTCATCCAAGAACCAAGAGGGAAAGTTTTCTCACGTAAATAAGTTTTTAATTTAAAGACTAA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
* * * * * * *
1415 AAGTTGTTTAGAAAACGAAAAACTATTTAGACCAAATGATGTGATTTCTCGACCTTGAAATGTTC
131 AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGAAATGTTC
*
1480 GAAAAATTTATTGAAGGAATG
196 -AAAAATTGATTGAAGGAATG
* * * *
1501 GATCATCTTGAATACTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGACAAGTGTGG
1 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* * * *
1566 AAGTTCGTCCAAGAACCAAGATAGAAACATTTCTCTA-TTAAATAAGTTTTTAATTCAAAGACTA
66 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTC-ACGTAAATAAGTTTTTAATTCAAAGACTA
*
1630 AAACTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGTA-ATTTCTCGAGCATGAAATGT
130 AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG-AGATTTCTCGAGCATGAAATGT
* * **
1694 TCAGAAAATAGCTCAAAGGAATG
194 TCA-AAAATTGATTGAAGGAATG
* * * * *
1717 GATCATCTTGAATACTTTAAGTAACC-ATGGTTGTAAAAGAACTCGTAAAAGTTTGACAAGTGTG
1 GATCGTCTTGAATACTTTAAGGAACCGA-AGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * * * * *
1781 GAAGTTCGTCCAAGAACCAAGATAGAGATAATTCTCAGGTAAATAAG-TTTTATTTCAAAGACTA
65 GAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTA
* *
1845 AAATTTGTTTACAAACA-GACAAATTATTTA
130 AAACTTGTTTACAAA-ATGACAAACTATTTA
1875 CTGAGTTGGA
Statistics
Matches: 1391, Mismatches: 228, Indels: 80
0.82 0.13 0.05
Matches are distributed among these distances:
207 139 0.10
208 28 0.02
209 3 0.00
213 2 0.00
214 181 0.13
215 231 0.17
216 799 0.57
217 8 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (215 bp):
GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAA
AACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGAGATTTCTCGAGCATGAAATGTTC
AAAAATTGATTGAAGGAATG
Found at i:1578 original size:639 final size:634
Alignment explanation
Indices: 76--1874 Score: 2113
Period size: 639 Copynumber: 2.8 Consensus size: 634
66 AAGTACATAT
* * * * *
76 AAGAACCAAAAGAGAACCAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAAAACTCGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAACTTGTTTA
* * * ** *
141 CAAAATGACAAACTATTGAAAACAAATGATGTGATTTC-CTAGGCATGGTATGTTC-AAAATTTT
66 CAAAATGACAAACTATTTAGAACAAATGATGTGATTTCTCGA-GCATGAAATGTTCAAAAATTTA
* * * * *
204 TTCAAAGGAATGGATCGA-CTTGATTATTTTATGGAATTGAAGTTATAAAAGAACTCGTAAAAGT
130 TT-GAAGGAATGGATC-ATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGT
* ** * *
268 TTGACAAGTTCGAAAGTTCATCCAAGAAATAAGAGAGAAACAATTCTCAGGTAAACAAGTTTTTA
193 TTGACAAGTT-GAAAGTTCGTCCAAGAACCAAGAGAGAAA-AATTCT-AAGTAAATAAGTTTTTA
* * *
333 ATTCGAAGACC-AAACGTTGTTTACAAAATGATAAACTATTAAGACCAAATGATGCAATTTCCCG
255 ATTCAAAGACCAAAAC-TTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCCCG
* * *
397 AGGATGAAATGTTCGA-AAAACAACTCGAAGGAATGGATCGTCTTGAAAACTTTAAGGAACCGAA
319 AGCATGAAATGTTCGAGAAAA-TACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA
* * * * *
461 GTTATAAAGGAACTCGTAATAGTTTTACTAGTTTGGAAGTTCATCCAAGAACCAATAA-ATACAA
383 GTTATAAA-GAACTCGTAAAAGTTTGACTAG-TTGGAAGTTCGTCCAAGAACCAAGAAGAAACAA
* * *
525 TTCTGATGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAG
446 TTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAG
* * * *
590 ACCAAATGATGAGATTTCTCGAGCATGGAATGTTCGAAAAATTGATTGAAGGATTGGACTGTCTT
511 ACCAAATAATGAAATTTCTCGAGCATAGAATGTTC-AAAAATTGATTGAAAGATTGGACTGTCTT
* ***
655 GAATACTTTAAGGAATCGAATTTATAAAAGAACTCATAAAAGTTTGACATGTTTTGAAGTTCATC
575 GAATACTTTAAGGAATC------ATAAAACAACTCATAAAAGTTTGACATGTTCAAAAGTTCATC
720 C
634 C
* *
721 AAGAACCATGAGAGAAACAATTCTCACGTAAATAAGTTTTT-ATTTCAAAGACAAAAACTTGTTT
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTT-AAAGACTAAAACTTGTTT
* * * *
785 ACATAATGACAAACTATTTAGATCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATTG
65 ACAAAATGACAAACTATTTAGAACAAATGATGTGATTTCTCGAGCATGAAATGTTCA-AAAATTT
* * * *
850 CTTGGAGGAATGGATCATCTTGAATACTTTCAGGAATCGAAGTTATAAAAGAACTCATAAAAGTT
129 ATTGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTT
* ** * * *
915 TTACCACTTTGAAAGTTTGTCCAAGAACCAAGAGAGAAAGTATTCTAACGTAAATAAGTTTTCAA
194 TGA-CAAGTTGAAAGTTCGTCCAAGAACCAAGAGAGAAA-AATTCTAA-GTAAATAAGTTTTTAA
* * *
980 TTCAAAGACCAAAACATATTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAG
256 TTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCCCGAG
* *
1045 CATGAAATGTTCGAGAAATTACTCGAAGGAATGGATTGTCTTGAATACTTTAAGGAACCGAAGTT
321 CATGAAATGTTCGAGAAAATACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTT
* * *
1110 ATGAAAGAACTTGTAAAAGTTTGACTAGTTCGAAAGTTCGTGCAAGAACCAAGAGAGAAACAATT
386 AT-AAAGAACTCGTAAAAGTTTGACTAGTT-GGAAGTTCGTCCAAGAACCAAGA-AGAAACAATT
1175 CTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGAC
448 CTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGAC
* * *
1240 CAAATAATGAAATTTC-CTGTGTATAGAATGTT-AAGAATATTGCTTGAAAGA-TGGATCT-TCT
513 CAAATAATGAAATTTCTC-GAGCATAGAATGTTCAA-AA-ATTGATTGAAAGATTGGA-CTGTCT
* * * *
1301 TGAATTCTTTATGGAA-C-TAATACAACTCATAAAAGTTTTACCA-GTTCAAAAGTTCATCC
574 TGAATACTTTAAGGAATCATAAAACAACTCATAAAAGTTTGA-CATGTTCAAAAGTTCATCC
* *** *
1360 AAGAACCAAGAGGGAAAGTTTTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAAGTTGTTTA
1 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAACTTGTTTA
* * * * * *
1425 GAAAACGAAAAACTATTTAGACCAAATGATGTGATTTCTCGACCTTGAAATGTTCGAAAAATTTA
66 CAAAATGACAAACTATTTAGAACAAATGATGTGATTTCTCGAGCATGAAATGTTC-AAAAATTTA
* * *
1490 TTGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTT
130 TTGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTT
* * * * *
1555 GACAAGTGTGGAAGTTCGTCCAAGAACCAAGATAGAAACATTTCTCTATTAAATAAGTTTTTAAT
195 GACAAGT-TGAAAGTTCGTCCAAGAACCAAGAGAGAAA-AATTCT-AAGTAAATAAGTTTTTAAT
* * * * *
1620 TCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGTAATTTCTCGAGC
257 TCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCCCGAGC
* * * *
1685 ATGAAATGTTC-AGAAAATAGCTCAAAGGAATGGATCATCTTGAATACTTTAAGTAACC-ATGGT
322 ATGAAATGTTCGAGAAAATA-CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGA-AGT
* * * *
1748 TGTAAAAGAACTCGTAAAAGTTTGACAAGTGTGGAAGTTCGTCCAAGAACCAAGATAGAGATAAT
385 TAT-AAAGAACTCGTAAAAGTTTGACTAGT-TGGAAGTTCGTCCAAGAACCAAGA-AGAAACAAT
* * * * *
1813 TCTCAGGTAAATAAG-TTTTATTTCAAAGACTAAAATTTGTTTACAAACA-GACAAATTATTTA
447 TCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA-ATGACAAACTATTTA
1875 CTGAGTTGGA
Statistics
Matches: 991, Mismatches: 137, Indels: 59
0.83 0.12 0.05
Matches are distributed among these distances:
638 52 0.05
639 418 0.42
640 9 0.01
644 3 0.00
645 102 0.10
646 253 0.26
647 47 0.05
648 107 0.11
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (634 bp):
AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACTAAAACTTGTTTA
CAAAATGACAAACTATTTAGAACAAATGATGTGATTTCTCGAGCATGAAATGTTCAAAAATTTAT
TGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTG
ACAAGTTGAAAGTTCGTCCAAGAACCAAGAGAGAAAAATTCTAAGTAAATAAGTTTTTAATTCAA
AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTCCCGAGCATGA
AATGTTCGAGAAAATACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
GAACTCGTAAAAGTTTGACTAGTTGGAAGTTCGTCCAAGAACCAAGAAGAAACAATTCTCACGTA
AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATAAT
GAAATTTCTCGAGCATAGAATGTTCAAAAATTGATTGAAAGATTGGACTGTCTTGAATACTTTAA
GGAATCATAAAACAACTCATAAAAGTTTGACATGTTCAAAAGTTCATCC
Found at i:1690 original size:855 final size:847
Alignment explanation
Indices: 14--2111 Score: 2316
Period size: 855 Copynumber: 2.5 Consensus size: 847
4 CGTCTTAAAC
* * * ** * * * * **
14 ACTTTAAGGAACCGA-ACTTTTAAAAGAGCTTGTAAAAGTTTGACAAATGCGAAAGTACATATAA
1 ACTTTAAGGAACC-ATAGTTATAAAAGAACTCATAAAAGTTTGACAACTGTGAAAGTTCGTCCAA
* *
78 GAACCAAAAGAGAACCA-ATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAAAACTCGTTTAC
65 GAACCAAGAGAGAA--ATATTCTCACGTAAATAAG-TTTTAATTCAAAGACTAAAACT-GTTTAC
* * *
142 AAAATGACAAACTATTGAAAACAAATGATGTGATTTCCTAGGCATGGTATGTTC-A-AAATTTTT
126 AAAATGACAAACTATT--TAACAAATGATG-GATTTCC-A-GCAT-GAATGTTCGAGAAA-TTTC
* * * * **
205 TCAAAGGAATGGATCGACTTGATTATTTTATGGAATTGAAGTTATAAAAGAACTCGTAAAAGTTT
184 TCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTT
** * *
270 GACAAGTTCGAAAGTTCATCCAAGAAATAAGAGAGAAACAATTCTCAGGTAAACAAGTTTTTAAT
249 GACAAGTTCGAAAGTTCAT-CAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* * * *
335 TCGAAGACC-AAACGTTGTTTACAAAATGATAAACTATTAAGACCAAATGATGCAATTTCCCGAG
313 TCAAAGACCAAAAC-TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCCTGAG
*
399 GATGAAATGTTCGAAAAACAACTCGAAGGAATGGATCGTCTTGAAAACTTTAAGGAACCGAAGTT
377 GATGAAATGTTC-AAAAACAACTCGAAAGAATGGATCGTCTTGAAAACTTTAAGGAACC--A--T
* * * * *** *
464 ATAAAGGAACTCGTAATAGTTTTACTAGTTTGGAAGTTCATCCAAGAACCAATAAATACAATTCT
437 ATAAAGCAACTCATAAAAGTTTTACCAGTTCAAAAGTTCATCCAAGAACCAAGAAATACAATTCT
* * *
529 GATGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCA
502 CACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAACGAAAAACTATTTAGACCA
* * * *
594 AATGATGAGATTTCTCGAGCATGGAATGTTCGAAAAATTGATTGAAGGATTGGACTGTCTTGAAT
567 AATGATGAGATTTCTCGACCATGAAATGTTCGAAAAATTGATTGAAGGAATGGACTATCTTGAAT
* * * * * *
659 ACTTTAAGGAATCGAATTTATAAAAGAACTCATAAAAGTTTGACATGTTTTGAAGTTCATCCAAG
632 ACTTTAAGGAACCAAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTGTGGAAGTTCATCCAAG
* * *
724 AACCATGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACAAAAACTTGTTTACAT
697 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAA
* * * * **
789 AATGACAAACTATTTAGATCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATTGCTTG
762 AATGACAAACTATTTAAACCAAATGATGCAATTTCTCGAGCATGAAATGTTCAGAAAATAGCTCA
*
854 GAGGAATGGATCATCTTGAAT
827 AAGGAATGGATCATCTTGAAT
* * * * * *
875 ACTTTCAGGAATCGA-AGTTATAAAAGAACTCATAAAAGTTTTACCACTTTGAAAGTTTGTCCAA
1 ACTTTAAGGAA-CCATAGTTATAAAAGAACTCATAAAAGTTTGACAACTGTGAAAGTTCGTCCAA
* * *
939 GAACCAAGAGAGAAAGTATTCTAACGTAAATAAGTTTTCAATTCAAAGACCAAAACATATTTACA
65 GAACCAAGAGAGAAA-TATTCTCACGTAAATAAGTTTT-AATTCAAAGACTAAAAC-TGTTTACA
* *
1004 AAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGAAATGTTCGAGAAATTACTC
127 AAATGACAAACTATTTA-A-CAAATGATG-GATTT-CC-AGCATG-AATGTTCGAGAAATTTCTC
* * * *
1069 GAAGGAATGGATTGTCTTGAATACTTTAAGGAACCGAAGTTATGAAAGAACTTGTAAAAGTTTGA
186 AAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGA
* *
1134 CTAGTTCGAAAGTTCGTGCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
251 CAAGTTCGAAAGTTCAT-CAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
* * * *
1199 AAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATAATGAAATTTCCTGTGTAT
315 AAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCCTGAGGAT
*** * * ** * *
1264 -AGAATGTT-AAGAATATTGCTTGAAAG-ATGGATCTTCTTGAATTCTTTATGGAA-C-TA-ATA
380 GA-AATGTTCAA-AA-ACAACTCGAAAGAATGGATCGTCTTGAAAACTTTAAGGAACCATATAAA
***
1323 -CAACTCATAAAAGTTTTACCAGTTCAAAAGTTCATCCAAGAACCAAGAGGGAA-AGTTTTCTCA
442 GCAACTCATAAAAGTTTTACCAGTTCAAAAGTTCATCCAAGAACCAAGA---AATACAATTCTCA
* * * *
1386 CGTAAATAAGTTTTTAATTTAAAGACTAAAAGTTGTTTAGAAAACGAAAAACTATTTAGACCAAA
504 CGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAACGAAAAACTATTTAGACCAAA
* * *
1451 TGATGTGATTTCTCGACCTTGAAATGTTCGAAAAATTTATTGAAGGAATGGA-TCATCTTGAATA
569 TGATGAGATTTCTCGACCATGAAATGTTCGAAAAATTGATTGAAGGAATGGACT-ATCTTGAATA
* * *
1515 CTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGACAAGTGTGGAAGTTCGTCCAAGA
633 CTTTAAGGAACCAAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTGTGGAAGTTCATCCAAGA
* * * *
1580 ACCAAGATAGAAACATTTCTCTA-TTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAA
698 ACCAAGAGAGAAACAATTCTC-ACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAA
*
1644 AATGACAAACTATTTAAACCAAATGATGTAATTTCTCGAGCATGAAATGTTCAGAAAATAGCTCA
762 AATGACAAACTATTTAAACCAAATGATGCAATTTCTCGAGCATGAAATGTTCAGAAAATAGCTCA
1709 AAGGAATGGATCATCTTGAAT
827 AAGGAATGGATCATCTTGAAT
* * * * * *
1730 ACTTTAAGTAACCATGGTTGTAAAAGAACTCGTAAAAGTTTGACAAGTGTGGAAGTTCGTCCAAG
1 ACTTTAAGGAACCATAGTTATAAAAGAACTCATAAAAGTTTGACAACTGTGAAAGTTCGTCCAAG
* * * * *
1795 AACCAAGATAGAGATAATTCTCAGGTAAATAAGTTTTATTTCAAAGACTAAAATTTGTTTACAAA
66 AACCAAGAGAGAAAT-ATTCTCACGTAAATAAGTTTTAATTCAAAGACTAAAA-CTGTTTACAAA
* *
1860 CA-GACAAATTATTT-AC---TGA--G--TT---G---GAATGTTCG-GAAAATTTCTCAAAAGA
129 -ATGACAAACTATTTAACAAATGATGGATTTCCAGCATGAATGTTCGAG-AAATTTCTCAAAGGA
* * * * ** * *
1909 ATGGATCGTCTTAAACACTTTAAGGAACCAAAGTTCTAAAAGTTCTCGTAAAAGTTTGACAAATG
192 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
* * *
1974 CGGAAGTACATCTAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGAC
257 CGAAAGTTCATC-AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * * * **
2039 TAAAACTTTTTTACAAAATGACAAACTATTTAAACCAAATGATGCGATTTCCTGAGCATGGTATG
321 CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCCTGAGGATGAAATG
2104 TTCAAAAA
386 TTCAAAAA
2112 ATTTCACGAA
Statistics
Matches: 1045, Mismatches: 164, Indels: 84
0.81 0.13 0.06
Matches are distributed among these distances:
833 3 0.00
834 190 0.18
835 3 0.00
838 1 0.00
843 2 0.00
845 1 0.00
848 3 0.00
851 1 0.00
852 1 0.00
853 40 0.04
854 39 0.04
855 393 0.38
856 3 0.00
859 2 0.00
860 9 0.01
861 159 0.15
862 188 0.18
863 7 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (847 bp):
ACTTTAAGGAACCATAGTTATAAAAGAACTCATAAAAGTTTGACAACTGTGAAAGTTCGTCCAAG
AACCAAGAGAGAAATATTCTCACGTAAATAAGTTTTAATTCAAAGACTAAAACTGTTTACAAAAT
GACAAACTATTTAACAAATGATGGATTTCCAGCATGAATGTTCGAGAAATTTCTCAAAGGAATGG
ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
AGTTCATCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCCTGAGGATGAAATGTTCAA
AAACAACTCGAAAGAATGGATCGTCTTGAAAACTTTAAGGAACCATATAAAGCAACTCATAAAAG
TTTTACCAGTTCAAAAGTTCATCCAAGAACCAAGAAATACAATTCTCACGTAAATAAGTTTTTAA
TTCAAAGACCAAAACTTGTTTACAAAACGAAAAACTATTTAGACCAAATGATGAGATTTCTCGAC
CATGAAATGTTCGAAAAATTGATTGAAGGAATGGACTATCTTGAATACTTTAAGGAACCAAAGTT
ATAAAAGAACTCATAAAAGTTTGACAAGTGTGGAAGTTCATCCAAGAACCAAGAGAGAAACAATT
CTCACGTAAATAAGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAACTATTTAAAC
CAAATGATGCAATTTCTCGAGCATGAAATGTTCAGAAAATAGCTCAAAGGAATGGATCATCTTGA
AT
Found at i:2021 original size:195 final size:196
Alignment explanation
Indices: 1689--2070 Score: 509
Period size: 195 Copynumber: 2.0 Consensus size: 196
1679 TCGAGCATGA
* * * * ** *
1689 AATGTTCAGAAAATAGCTCAAAGGAATGGATCATCTTGAATACTTTAAGTAACCATGGTTGTAAA
1 AATGTTCAGAAAATAGCTCAAAAGAATGGATCATCTTAAACACTTTAAGGAACCAAAGTTCTAAA
* * * * * * *
1754 AGAACTCGTAAAAGTTTGACAAGTGTGGAAGTTCGTCCAAGAACCAAGATAGAGATAATTCTCAG
66 AGAACTCGTAAAAGTTTGACAAATGCGGAAGTACATCCAAGAACCAAGAGAGAAACAATTCTCAG
* *
1819 GTAAATAAG-TTTTATTTCAAAGACTAAAA-TTTGTTTACAAACA-GACAAATTATTTACTGAGT
131 GTAAATAAGTTTTTAATTCAAAGACTAAAACTTT-TTTACAAA-ATGACAAACTATTTACTGAGT
1881 TGG
194 TGG
* ** *
1884 AATGTTCGGAAAATTTCTCAAAAGAATGGATCGTCTTAAACACTTTAAGGAACCAAAGTTCTAAA
1 AATGTTCAGAAAATAGCTCAAAAGAATGGATCATCTTAAACACTTTAAGGAACCAAAGTTCTAAA
** * *
1949 AGTTCTCGTAAAAGTTTGACAAATGCGGAAGTACATCTAAGAACCAAGAGAGAAACAATTCTCAT
66 AGAACTCGTAAAAGTTTGACAAATGCGGAAGTACATCCAAGAACCAAGAGAGAAACAATTCTCAG
2014 GTAAATAAGTTTTTAATTCAAAGACTAAAACTTTTTTACAAAATGACAAACTATTTA
131 GTAAATAAGTTTTTAATTCAAAGACTAAAACTTTTTTACAAAATGACAAACTATTTA
2071 AACCAAATGA
Statistics
Matches: 160, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
195 118 0.74
196 39 0.24
197 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (196 bp):
AATGTTCAGAAAATAGCTCAAAAGAATGGATCATCTTAAACACTTTAAGGAACCAAAGTTCTAAA
AGAACTCGTAAAAGTTTGACAAATGCGGAAGTACATCCAAGAACCAAGAGAGAAACAATTCTCAG
GTAAATAAGTTTTTAATTCAAAGACTAAAACTTTTTTACAAAATGACAAACTATTTACTGAGTTG
G
Done.