Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002869.1 Kokia drynarioides strain JFW-HI SEQ_115273, 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: 4723
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Found at i:662 original size:216 final size:215
Alignment explanation
Indices: 71--1915 Score: 1805
Period size: 216 Copynumber: 8.5 Consensus size: 215
61 CCAAGAGAGA
* * *
71 AAGTTTTTCATTCAAAGACCAAAAGTCGTTAAGAAAATGACAAAGTATTTAGACCAAATAATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * *
136 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTATCTTGAATACTTTAAGA
66 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG-
* * * * * * * *
201 AATCGAAGTTATAGAAGAACTCGTCAAAGTTTGTCAAGTT-TAGAAGTTCATCCAATATCTAAGA
130 GACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGA-AAGTTCGTCCAAGAACCAAGA
* *
265 GAGAAACAATTCTCATGTAAAT
194 GAGAAACAACTCTCACGTAAAT
* ** **
287 AAGTTTTTCATTCAAAGAGCAAAAGTTGTTTACCAAATGACAAA-TAATTTAGAAAAAAATGATG
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGT-ATTTAG-ACCAAATGATG
* * * * * ** * *
351 CGATTTTCCAATCATAAAATGTTCGAAAAATCGCTCGAAGGAATGGATCGTCATGAATACTTTAT
64 CGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAA
* * * * * * *
416 GTTACTGATGTTATAAAAAAACTCGTAAAAGTTTGCCAAGTTCGAAAGTTCGTCCAAGAACTAAG
129 G-GACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAGAACCAAG
*
481 ATAGAAACAACTCTCACGTAAAT
193 AGAGAAACAACTCTCACGTAAAT
* * * * *
504 AAGTTTTTCATTGAAAGACGAAAAGTAGTTTAGAAAATAACAAAGTATTTAAACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * * *
569 ATTTCCGGAGAATGGAATGTTCGAAAAATTACTTGAAGAAATGGATTGTCATGAATACTTTAAGG
66 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
* *
634 ACCGAAAGTTATAGATGAACTTGTAAAAGTTT-TCCAAGTTC-AGAAGTTCGTCCAAGAACCAAG
131 ACCG-AAGTTATAGAAGAACTCGTAAAAGTTTGT-CAAGTTCGA-AAGTTCGTCCAAGAACCAAG
*
697 AGAGAAACAACTCTCAGGTAAAT
193 AGAGAAACAACTCTCACGTAAAT
*
720 AAGTTTTTCATTCAAAGACCAAAAGTCGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * *
785 ATTTCCCGAGCATGAAATGTTCAAAAAATTATTCTAAGGAATGGATTATCTTGAATACTTTAAGA
66 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG-
* * * * * * * *
850 AATCGAAGTTATAGATGAACTCTTAAAAGTATGTCAAGTTTGGAAGTTCGTCTAAGAGA-CAAGA
130 GACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAGA-ACCAAGA
914 GAGAAA-AACCTCTCACGTAAAT
194 GAGAAACAA-CTCTCACGTAAAT
* * *
936 AGGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGA-CATAATGATGC
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCA-AATGATGC
* * * * *
1000 GATTTCCCGTGCTTGGAATGTTCAAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAG
65 GATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * * * ** * * **
1065 GAACTGAAGTTTTAAAAGAACTCGTAAAACTTCATCAAGTTTGGAAGTTCGTCCAAGAAAAAAAA
130 G-ACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAG--AACCAA
*
1130 GAGAGAAGCAACTCTCACGTAAAT
192 GAGAGAAACAACTCTCACGTAAAT
* * * * ** * * * * *
1154 AACTTTTTAATTTATAGACCAAAAGTCATTTACAAAATGACAAACTATTTAGACTAAATTATGCA
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * * *
1219 ATTTCTCGAGTATGGAATATTCAGAAAATTACTCGAAGGAATGGATTGTCATGAATATTTTGATA
66 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTT-A-A
* * * * * * * * * * *
1284 -GAGCAAAGTTATTGAACAACTGGTAAAAGTTTGTAAAGTTAGGAAGTTTGTCCATGATCCAAGA
129 GGACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAGAACCAAGA
* *
1348 GATAATA-AATTCTCACGTAAAT
194 GAGAA-ACAACTCTCACGTAAAT
* * * ** * * *** * *
1370 AAGTGTTTAATT-AAATGACCAAAAGTTGTATACCAAATGACGAACTAAGCAGACAAAATGATGT
1 AAGTTTTTCATTCAAA-GACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGC
* * * * * * *
1434 GATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCATGAATA-TTTAAA
65 GATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * * * * * *
1498 GAACGAAAGTTATAGAAGAACTCGTCAAAGTTTGTCATGTT-TAGAAGTTCATCCAATATCCAAG
130 GACCG-AAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGA-AAGTTCGTCCAAGAACCAAG
* * * *
1562 AGAGGAACAATTCTCATGAAAAT
193 AGAGAAACAACTCTCACGTAAAT
* * *** * *
1585 AAGTTTTTCATTCAATGACAAAAAGTTGTTTACCTAATGACAAA-TAGTTTAGA-AAAATGTTGC
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTA-TTTAGACCAAATGATGC
* * * ** * * * * *
1648 GATTTCCCAAGCAAGAAATTTTCGGAAATTTGCTCGAAGGAATGGATCGTCATGACTACTTTATG
65 GATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * * *
1713 GAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGA
130 G-ACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAGAACCAAGA
* *
1778 TAGATACAACTCTCACGTGAAA-
194 GAGAAACAACTCTCACGT-AAAT
* * *
1800 AAGTTTTTCATTCAAAGACC-AAAGTAGTTTAGAAATTGGCAAAGTATTTAGACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * *
1864 ATTTCCCGAGGATGAAATGTTCAAAAAATTTCTCTAAGGAATGGATTGTCAT
66 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCAT
1916 AATCACGTCC
Statistics
Matches: 1335, Mismatches: 259, Indels: 71
0.80 0.16 0.04
Matches are distributed among these distances:
213 1 0.00
214 89 0.07
215 250 0.19
216 640 0.48
217 179 0.13
218 170 0.13
219 5 0.00
220 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (215 bp):
AAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
ACCGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGTCCAAGAACCAAGAGA
GAAACAACTCTCACGTAAAT
Found at i:1349 original size:434 final size:433
Alignment explanation
Indices: 71--4719 Score: 2020
Period size: 432 Copynumber: 10.6 Consensus size: 433
61 CCAAGAGAGA
* * *
71 AAGTTTTTCATTCAAAGACCAAAAGTCGTTAAGAAAATGACAAAGTATTTAGACCAAATAATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * *
136 ATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTATCTTGAATACTTTAA-G
66 ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
* * ***
200 AAATCG-AAGTTATAGAAGAACTCGTCAAAGTTTGTCAAGTTTAGAAGTTCATCC-A-ATATCTA
131 AACT-GAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAA
* * * *
262 AGAGAGAAACAATTCTCATGTAAATAAGTTTTTCATTCAAAGAGCAAAAGTTGTTTACCAAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * * **
327 CAAATAATTTAGAAAAAAATGATGCGATTTTCCAATCATAAAATGTTC-GAAAAATCGCTCGAAG
260 CAAAT-ATTTAG-ACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAG-AAAATTACTCGAAG
* *
391 GAATGGATCGTCATGAATACTTT-AT-GTTA-CTGATGTTATAAAAAAACTCGTAAAAGTTTGCC
322 GAATGGATCGTCATGAATACTTTGATAG--AGC-GAAGTTATAAAAGAACTCGTAAAAGTTTGCC
* * *
453 AAGTTCGAAAGTTCGTCCAAGAACTAAGATAGAAACAACTCTCACGTAAAT
384 AAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* * * *
504 AAGTTTTTCATTGAAAGACGAAAAGTAGTTTAGAAAATAACAAAGTATTTAAACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * *
569 ATTTCCGGAGAATGGAATGTTCGAAAAATTACTTGAAGAAATGGATTGTCATGAATACTTTAAGG
66 ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
* * * * * **
634 -ACCGAAAGTTATAGATGAACTTGTAAAAGTTT-TCCAAGTTCAGAAGTTCGTCCAAG--AACCA
131 AACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGT-CAAGTTTAGAAGTTCATCCAAGATAAAAA
* *
695 AGAGAGAAACAACTCTCAGGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTAGAAAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * *
760 CAAAGTATTTAGACCAAATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTATTCTAAGGA
260 CAAA-TATTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAGAAAATTACTCGAAGGA
** * * * * * * * * * *
825 ATGGATTATCTTGAATACTTTAAGAAATCGAAGTTATAGATGAACTCTTAAAAGTATGTCAAGTT
324 ATGGATCGTCATGAATACTTTGATAGAGCGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTT
* *
890 TGGAAGTTCGTCTAAGAGA-CAAGAGAGAAAAACCTCTCACGTAAAT
389 CGGAAGTTCGTCCAAGA-ACCAAGAGAGAAAAA-CTCTCACGTAAAT
* * * *
936 AGGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGA-CATAATGATGC
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCA-AATGATGC
* * * *
1000 GATTTCCCGTGCTTGGAATGTTCAAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAG
65 GATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * * ** * * *
1065 GAACTG-AAGTTTTAAAAGAACTCGTAAAACTTCATCAAGTTTGGAAGTTCGTCCAAGAAAAAAA
130 GAACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAA
* * * * * * *
1129 AGAGAGAAGCAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTCATTTACAAAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * * * *
1194 CAAACTATTTAGACTAAATTATGCAATTTCTCGAGTATGGAATATTCAGAAAATTACTCGAAGGA
260 CAAA-TATTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAGAAAATTACTCGAAGGA
* * * ** * * **
1259 ATGGATTGTCATGAATATTTTGATAGAGCAAAGTTATTGAACAACTGGTAAAAGTTTGTAAAGTT
324 ATGGATCGTCATGAATACTTTGATAGAGCGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTT
* * * * * *
1324 AGGAAGTTTGTCCATGATCCAAGAGATAATAAATTCTCACGTAAAT
389 CGGAAGTTCGTCCAAGAACCAAGAGAGAA-AAACTCTCACGTAAAT
* * * * ** * * *** * *
1370 AAGTGTTTAATT-AAATGACCAAAAGTTGTATACCAAATGACGAACTAAGCAGACAAAATGATGT
1 AAGTTTTTCATTCAAA-GACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGC
* * * * * *
1434 GATTTTCCAAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCATGAATA-TTTAAA
65 GATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * ***
1498 GAAC-GAAAGTTATAGAAGAACTCGTCAAAGTTTGTCATGTTTAGAAGTTCATCC-A-ATATCCA
130 GAACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAA
* * * * * * **
1560 AGAGAGGAACAATTCTCATGAAAATAAGTTTTTCATTCAATGACAAAAAGTTGTTTACCTAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * * * *
1625 CAAATAGTTTAGA-AAAATGTTGCGATTTCCCAAGCAAGAAATTTTCGGAAATTTGCTCGAAGGA
260 CAAATA-TTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAGAAAATTACTCGAAGGA
* * *
1689 ATGGATCGTCATGACTACTTT-ATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGT
324 ATGGATCGTCATGAATACTTTGATAGAGC-GAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGT
* *
1753 TCGGAAGTTCGTCCAAGAACCAAGATAGATACAACTCTCACGTGAAA-
388 TCGGAAGTTCGTCCAAGAACCAAGAGAGA-AAAACTCTCACGT-AAAT
* *
1800 AAGTTTTTCATTCAAAGACC-AAAGTAGTTTAGAAATTGGCAAAGTATTTAGACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * * **
1864 ATTTCCCGAGGATGAAATGTTCAAAAAATTTCTCTAAGGAATGGATTGTCAT-AATCACGTCCAG
66 ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAAT-ACTTTAAG
* * * * *** ** * ** * *
1928 AAATTCTG---CTTGT-GCAGTTTTTATTGAAA---TGATCATAACTT-G-AGCTC--CCGAACA
130 GAA--CTGAAAGTTATAGAAG-AACTCGTAAAAGTTTG-TCA-AGTTTAGAAGTTCATCC-AAGA
* ** * ** * * * * * *
1982 TGAAATTGAGTGATTCAAAGTTCGTTTCGAAGATAAGAGATAGAACTTTGAAATCCATGCAGAGA
189 TAAAAAAGAGAGAAAC-AA---C-TCTC-ATG-T-A-A-AT--AAGTTT----TTCATTCAAAGA
* ** ** ** * ** * * *
2047 TCTCAATCCCTAAATTCGTGGATCCCAACCAAAAAGTCGTT-G---TAA-GCCTACTGATTTCCC
238 -C-C-A-----AAAGTCGTTTA-CAAAATGACAAA-TATTTAGACAAAATG-ATGC-GATTTCCC
* * * * **** * * ** * * * *
2107 CAACTTGAAAAT-TGGCAGCTTCGGTTTCTTTG-ACCAA--GAT-TTCCAAGATTTAAAACCTTG
291 GAGCATG-AAATGT-TCAG--AAAATTAC-TCGAAGGAATGGATCGT-C---A-TGAATACTTTG
* * * **** * * *
2167 ATTTTCTCGATTCTTGAAATT-TTTTGGAA-T-G-ACAAGATTGGACCAAGATTCGG--TTTCTT
346 A-----TAGA-GC--GAAGTTATAAAAGAACTCGTAAAAG-TTTG-CCAAG-TTCGGAAGTTC--
*** * * * * * *** ***
2226 GATTTACTTGGAAACAAGAAAGTGAATATTGATTTTCTTTTTCGGT
398 G---T-CCAAGAACCAAG--AGAGAA-A--AACTCTC-ACGTAAAT
* ** * * * * * * * * ** *
2272 -CGTGTTCACATT-GAGGGCCTTGGTAACGAAGTCTT-G--GATGGTCCTATTCAATCTT-G-CT
1 AAGT-TTTTCATTCAAAGACC----AAAAGTAGT-TTAGAAAAT-GACAAAGT--AT-TTAGAC-
* * * * * * * * ** * *** * **
2330 TGAATTTGCTTGGGCTTCGACCTCGTTATTGGGCCTTGAACAACTTTAATCCCATCACATTTATA
55 -CAA-ATG-ATGCGATT--TCC-CG--A----G-CATGGA-ATGTTCAA-AAAATTAC-TCGA-A
* ** * * * * * * * * * *
2395 AGCTTGAATTTGGGCCTTACGACTCGTATCAAGATTTTCATGAATACTTTAAGGAATGAAAGTTA
103 GGAATGGA-TT--G---T-C-A-T-G----AATACTTT-AAGGA-AC-TGAA--AGTTATAG-A-
* * * **
2460 TAGATGAACTGGTAAAAGTTT-TCCAAGTTCAGAAGTTCGTCCAAG-----AACCA-AGAAACAA
147 ---A-GAACTCGTAAAAGTTTGT-CAAGTTTAGAAGTTCATCCAAGATAAAAAAGAGAGAAACAA
* * * *
2518 CTCTCATGTAACTAAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGGCAAACTATTTAG
207 CTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGACAAA-TATTTAG
* * * * * * *
2583 ACATAATGATGTGA-TTCCCCATGCTTGGAATGTTC-GAAAAATTGCTCGAAGGGAA-GGATCAT
271 ACAAAATGATGCGATTTCCCGA-GCATGAAATGTTCAG-AAAATTACTCGAA-GGAATGGATCGT
** * * * * * * *
2645 CATGAATACTTT-A-AGGAAATGGAGTTTTAAAAGAACTCATGAAACTTCT-TCAAGTTCGAAAG
333 CATGAATACTTTGATA-G-AGCGAAGTTATAAAAGAACTCGTAAAAGTT-TGCCAAGTTCGGAAG
* *
2707 TTCGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAAT
395 TTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* * * * * * *
2747 AACTTTTTAATTTAGAGACCAAAAGTTGTTTAGAAACTGACAAACTATTTAGACCAAATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * * * *
2812 A-TTCCCTGTGCTTGGAATGTTCGAAAAATTGCACGATGGTAA-GGATCGTCATGAATACTTTAA
66 ATTTCCC-GAGCATGGAATGTTCAAAAAATTACTCGAAGG-AATGGATTGTCATGAATACTTTAA
* * * * * * ** * *
2875 GGAGCTG-AAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCGGAAGTTCGTCCAAG--AACA
129 GGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAA
* * * ** * * *
2937 AAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATTGACCAAAAGTTGTTTAGAAAAAG
194 AAGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATG
* * * * * * * * *
3002 ACAAACTCTTTAGACATAATGATGCAATTCCCCGTGCTTGGAATGTTC-GAAAAATTGCTTGAAG
259 ACAAA-TATTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAG-AAAATTACTCGAA-
* * * * * * *
3066 GGAA-GGATCGTCATGAATACTTT-A-AGGAACTGGAGTTTTAAAAGAACTCATGAAACTTCT-T
321 GGAATGGATCGTCATGAATACTTTGATA-GAGC-GAAGTTATAAAAGAACTCGTAAAAGTT-TGC
* *
3127 CAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAAT
383 CAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* * * * *
3179 AACTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGAC--------T------AATGATGCG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * * * * * *
3230 A-TTCCCCATGC-TTGAATGTTCGAAAAATTGCTCGAAGGAAAGGATCGTCTTGAATACTTTAAG
66 ATTTCCCGA-GCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAG
* * * * * * *
3293 GAACTG-AAGTT-TAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAGTTCATCTAAG--AACAA
130 GAACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAA
* * * * * * *
3354 AGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * * * *
3419 CAAACTATTTAGACATAATGATGCAATTCCCCGTA-CTTGGAATGTTCAAAAAATTGCTCGAAGG
260 CAAA-TATTTAGACAAAATGATGCGATTTCCCG-AGCATGAAATGTTCAGAAAATTACT------
* * * *
3483 ACGAAGGAATGGATCTTCATGAATGCTTT-ATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
317 -CGAAGGAATGGATCGTCATGAATACTTTGATAGAGC-GAAGTTATAAAAGAACTCGTAAAAGTT
* * * * * * *
3547 TACCATGTTCGAAAGTTCGTCTAAGAACCAAGATAGAAACAACTCTCATGTGAAT
380 TGCCAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* *
3602 AAATTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGAG
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* ** * * * *
3667 ATTTCCCAAGCATGGAATGTTCAAAAAATTGTTCTAAGGAATGAATTGTCTTGAATACTTTAAGA
66 ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
* * * * * **
3732 AAC-CAAAGTTTTTGAAGAACTCGTAAAAGTTTGTCAAGTTTGGAAGTTCATCTAAG--AACCAA
131 AACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAAA
* ** * * ** * *
3794 GAGAAAAACAACTCTCGCGTAAAT-AGATTTTTAATTTAAAGATAAAAAGTTGTTTAGAAAATGA
196 GAGAGAAACAACTCTCATGTAAATAAG-TTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * *
3858 AAAACTATTTAGACAAAATGACGCGATTTCCCGCGCATGGAATGTTCTA-AAAATTGCTCGAAGG
260 CAAA-TATTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTC-AGAAAATTACTCGAAGG
* * * * * ***
3922 AATGGATCGTCATGAATACTTT-A-AGGAACTGAAGTTTTAAAAGAACTTGCAAAACTTCATCAA
323 AATGGATCGTCATGAATACTTTGATA-GAGC-GAAGTTATAAAAGAACTCGTAAAAGTTTGCCAA
* * * *
3985 GTTCAGTAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAAT
386 GTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* * * * * * *
4034 AAGATTTTAATTTAGAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC--ATG-T--G
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
* * *
4094 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTTGAAGGAATGGATTGTCATGAATAATTTAAGG
66 ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
* * * * * * **
4159 AAC-AAAAGTTATAGATGAACTGGTAAAAGTTT-TCCAAGTTCAGAAGTTCGTTCAAG--AACCA
131 AACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGT-CAAGTTTAGAAGTTCATCCAAGATAAAAA
* * * **
4220 AGAGAGAAACAACTCTCACGTAAATTAGTTTTTCATTCAAAGACCAAAAGTTGTTTGGAAAATGA
195 AGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGA
* * * * * * * *
4285 CAAACTATTTTGACATAATGTTGAGA-TTCCTCGTGCTTGGAATGTTC-GAAAAATTAGTCGAAG
260 CAAA-TATTTAGACAAAATGATGCGATTTCC-CGAGCATGAAATGTTCAG-AAAATTACTCGAA-
* * * * * * * *
4348 GGAA-GGA-CTGTCTTGAATACTTT-A-AGGAACTGAAGTTTTAAAAGAAGTCGTGAAACTTCGT
321 GGAATGGATC-GTCATGAATACTTTGATA-GAGC-GAAGTTATAAAAGAACTCGTAAAAGTTTGC
* *
4409 CAAGTTCGGAAATTCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAAT
383 CAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAA-AACTCTCACGTAAAT
* * * ** * *
4461 AA-CTTTTAATTTATTGACCAAAAGTTGTTTAGAAAATGACAAACTATTTAGA-CATAATGATGC
1 AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCA-AATGATGC
* * * * * *
4524 GATTCCCCGTGCTTGGAATGTTCGAAAAATTGCTCGAAGGTAA-GGATCGTCATGAATACTTTAA
65 GATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGG-AATGGATTGTCATGAATACTTTAA
* * * * * * ** *
4588 GGAGCTG-AAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCGGAAGTTCATCCAAG--AACA
129 GGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAA
* * * * * * *
4650 AAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAAAG
194 AAGAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATG
4715 ACAAA
259 ACAAA
4720 CTCT
Statistics
Matches: 3241, Mismatches: 720, Indels: 512
0.72 0.16 0.11
Matches are distributed among these distances:
416 164 0.05
417 55 0.02
418 17 0.01
422 5 0.00
423 130 0.04
424 1 0.00
425 3 0.00
426 52 0.02
427 311 0.10
428 56 0.02
429 92 0.03
430 148 0.05
431 242 0.07
432 679 0.21
433 292 0.09
434 306 0.09
435 4 0.00
436 2 0.00
437 13 0.00
438 63 0.02
439 150 0.05
440 12 0.00
444 9 0.00
445 2 0.00
446 1 0.00
447 2 0.00
448 1 0.00
449 1 0.00
450 4 0.00
451 14 0.00
452 18 0.01
453 11 0.00
454 10 0.00
455 4 0.00
456 9 0.00
457 5 0.00
458 5 0.00
459 1 0.00
460 4 0.00
461 7 0.00
462 9 0.00
463 11 0.00
464 7 0.00
465 3 0.00
466 1 0.00
467 9 0.00
468 4 0.00
469 5 0.00
470 4 0.00
471 15 0.00
472 14 0.00
473 4 0.00
474 2 0.00
475 12 0.00
476 16 0.00
477 6 0.00
478 9 0.00
479 2 0.00
480 12 0.00
481 1 0.00
482 2 0.00
483 6 0.00
484 9 0.00
485 7 0.00
486 6 0.00
487 2 0.00
489 1 0.00
490 5 0.00
491 12 0.00
492 6 0.00
493 15 0.00
494 16 0.00
495 17 0.01
496 8 0.00
497 5 0.00
498 1 0.00
499 1 0.00
500 2 0.00
501 2 0.00
502 10 0.00
503 1 0.00
506 5 0.00
508 4 0.00
509 7 0.00
510 2 0.00
511 1 0.00
512 2 0.00
513 3 0.00
514 2 0.00
515 1 0.00
517 2 0.00
518 3 0.00
519 2 0.00
520 6 0.00
521 4 0.00
522 3 0.00
523 5 0.00
524 2 0.00
525 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (433 bp):
AAGTTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCG
ATTTCCCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATTGTCATGAATACTTTAAGG
AACTGAAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTTAGAAGTTCATCCAAGATAAAAAA
GAGAGAAACAACTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCGTTTACAAAATGAC
AAATATTTAGACAAAATGATGCGATTTCCCGAGCATGAAATGTTCAGAAAATTACTCGAAGGAAT
GGATCGTCATGAATACTTTGATAGAGCGAAGTTATAAAAGAACTCGTAAAAGTTTGCCAAGTTCG
GAAGTTCGTCCAAGAACCAAGAGAGAAAAACTCTCACGTAAAT
Found at i:2809 original size:216 final size:216
Alignment explanation
Indices: 2432--4721 Score: 2697
Period size: 216 Copynumber: 10.7 Consensus size: 216
2422 ATCAAGATTT
* * * * * *
2432 TCATGAATACTTTAAGGAA-TGAAAGTTATAGATGAACTGGTAAAAGTT-TTCCAAGTTC-AGAA
1 TCATGAATACTTTAAGGAACTG-AAGTTTTAAAAGAACTCGTGAAACTTCTT-CAAGTTCGA-AA
* * * * * * *
2494 GTTCGTCCAAGAAC---CA-AGAAACAACTCTCATGTAACTAAGTTTTTCATTCAAAGACCAAAA
63 GTTCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAA
* * *
2555 GTTGTTTAGAAAATGGCAAACTATTTAGACATAATGATGTGATTCCCCATGCTTGGAATGTTCGA
128 GTTGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGA
*
2620 AAAATTGCTCGAAGGGAAGGATCA
193 AAAATTGCTCGAAGGGAAGGATCG
* * *
2644 TCATGAATACTTTAAGGAAATGGAGTTTTAAAAGAACTCATGAAACTTCTTCAAGTTCGAAAGTT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGAAAGTT
* *
2709 CGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTAGAGACCAAAAGTT
66 CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
* *
2774 GTTTAGAAACTGACAAACTATTTAGACCA-AATGATGCGATTCCCTGTGCTTGGAATGTTCGAAA
131 GTTTAGAAAATGACAAACTATTTAGA-CATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAA
* * *
2838 AATTGCACGATGGTAAGGATCG
195 AATTGCTCGAAGGGAAGGATCG
* * *
2860 TCATGAATACTTTAAGGAGCTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCGGAAGTT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGAAAGTT
* *
2925 CGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATTGACCAAAAGTT
66 CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
* * *
2990 GTTTAGAAAAAGACAAACTCTTTAGACATAATGATGCAATTCCCCGTGCTTGGAATGTTCGAAAA
131 GTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAAA
*
3055 ATTGCTTGAAGGGAAGGATCG
196 ATTGCTCGAAGGGAAGGATCG
* *
3076 TCATGAATACTTTAAGGAACTGGAGTTTTAAAAGAACTCATGAAACTTCTTCAAGTTCGAAAGTT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGAAAGTT
3141 CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
66 CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
*
3206 GTTT-----A-G--AAA--A--T-GAC-TAATGATGCGATTCCCCATGCTT-GAATGTTCGAAAA
131 GTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAAA
*
3256 ATTGCTCGAAGGAAAGGATCG
196 ATTGCTCGAAGGGAAGGATCG
* *
3277 TCTTGAATACTTTAAGGAACTGAAG-TTTAAAAGAACTCGTGAAACTTCGTCAAGTTC-AGAAGT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGA-AAGT
* *
3340 TCATCTAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
65 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
* * *
3405 TGTTTAGAAAATGACAAACTATTTAGACATAATGATGCAATTCCCCGTACTTGGAATGTTCAAAA
130 TGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAA
*
3470 AATTGCTCGAAGGACGAAGGAATGGATCT
195 AATTGCTCG-A--A-G--GGAA-GGATCG
* * * * * * *
3499 TCATGAATGCTTTATGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT-TACCATGTTCGAAAGT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCT-TCAAGTTCGAAAGT
* * * * * * * * *
3563 TCGTCTAAGAACCAAGATAGAAACAACTCTCATGTGAATAAATTTTTCATTCAAAGACCAAAAGT
65 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
* * * * ** * *
3628 AGTTTAGAAAATGACAAAGTATTTAGACCA-AATGATGAGATTTCCCAAGCATGGAATGTTCAAA
130 TGTTTAGAAAATGACAAACTATTTAGA-CATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAA
* * * *
3692 AAATTGTTCTAA-GGAATGAATTG
194 AAATTGCTCGAAGGGAA-GGATCG
* * ** ** * * * *
3715 TCTTGAATACTTTAAGAAACCAAAGTTTTTGAAGAACTCGTAAAAGTT-TGTCAAGTTTGGAAGT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCT-TCAAGTTCGAAAGT
* * * * * * **
3779 TCATCTAAGAACCAAGAGAAAAACAACTCTCGCGTAAATAGA-TTTTTAATTTAAAGATAAAAAG
65 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATA-ACTTTTTAATTTATAGACCAAAAG
* * * * * * *
3843 TTGTTTAGAAAATGAAAAACTATTTAGACAAAATGACGCGATTTCCCGCGCATGGAATGTTCTAA
129 TTGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAA
3908 AAATTGCTCGAA-GGAATGGATCG
194 AAATTGCTCGAAGGGAA-GGATCG
* ** * *
3931 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTTGCAAAACTTCATCAAGTTC-AGTAGT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGA-AAGT
* ** *
3995 TCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTTAGAGACCAAAAGT
65 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
* * * * *
4060 TGTTTACAAAATGACAAACTATTTAGAC--CATG-T--GATTTCCCGAGCATGGAATGTTCGAAA
130 TGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAA
* * *
4120 AATTACTTGAA-GGAATGGATTG
195 AATTGCTCGAAGGGAA-GGATCG
* ** * * * * * *
4142 TCATGAATAATTTAAGGAACAAAAGTTATAGATGAACTGGTAAAAGTT-TTCCAAGTTC-AGAAG
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTT-CAAGTTCGA-AAG
* * * * * * *
4205 TTCGTTCAAGAACCAAGAGAGAAACAACTCTCACGTAAATTAGTTTTTCATTCAAAGACCAAAAG
64 TTCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAG
* * * * *
4270 TTGTTTGGAAAATGACAAACTATTTTGACATAATGTTGAGATTCCTCGTGCTTGGAATGTTCGAA
129 TTGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAA
4335 AAATTAG-TCGAAGGGAAGGA-CTG
194 AAATT-GCTCGAAGGGAAGGATC-G
* * *
4358 TCTTGAATACTTTAAGGAACTGAAGTTTTAAAAGAAGTCGTGAAACTTCGTCAAGTTCGGAAA-T
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTC-GAAAGT
*
4422 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAAC-TTTTAATTTATTGACCAAAAGT
65 TCGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
4486 TGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAA
130 TGTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAA
*
4551 AATTGCTCGAAGGTAAGGATCG
195 AATTGCTCGAAGGGAAGGATCG
* * *
4573 TCATGAATACTTTAAGGAGCTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCGGAAGTT
1 TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGAAAGTT
* *
4638 CATCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATAGACCAAAAGTT
66 CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
*
4703 GTTTAGAAAAAGACAAACT
131 GTTTAGAAAATGACAAACT
4722 CT
Statistics
Matches: 1793, Mismatches: 228, Indels: 110
0.84 0.11 0.05
Matches are distributed among these distances:
199 1 0.00
200 102 0.06
201 55 0.03
202 21 0.01
203 3 0.00
204 1 0.00
205 1 0.00
206 1 0.00
208 6 0.00
210 3 0.00
211 178 0.10
212 61 0.03
213 11 0.01
214 28 0.02
215 217 0.12
216 911 0.51
217 10 0.01
218 2 0.00
219 1 0.00
220 1 0.00
221 3 0.00
222 28 0.02
223 145 0.08
224 3 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (216 bp):
TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCTTCAAGTTCGAAAGTT
CGTCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
GTTTAGAAAATGACAAACTATTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAAA
ATTGCTCGAAGGGAAGGATCG
Found at i:4312 original size:643 final size:645
Alignment explanation
Indices: 2512--4721 Score: 2494
Period size: 639 Copynumber: 3.4 Consensus size: 645
2502 AAGAACCAAG
* * * * * * **
2512 AAACAACTCTCATGTAACTAAGTTTTTCATTCAAAGACCAAAAGTTGTTTAGAAAATGGCAAACT
1 AAACAACTCTCACGTAAATAA-CTTTTAATTTAAAGACAAAAAGTTGTTTAGAAAATGAAAAACT
* * * ** *
2577 ATTTAGACATAATGATGTGATTCCCCATGCTTGGAATGTTCGAAAAATTGCTCGAAGGGAAGGAT
65 ATTTAGACAAAATGACGCGATTCCCCGCGCATGGAATGTTCGAAAAATTGCTCGAA-GGAAGGAT
* * * * *
2642 CATCATGAATACTTTAAGGAAATGGAGTTTTAAAAGAACTCATGAAACTTCTTCAAGTTC-GAAA
129 CGTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAG-AA
* * *
2706 GTTCGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTAGAGACCAAAA
193 GTTCATCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAA
* * * * * *
2771 GTTGTTTAGAAACTGACAAACTATTTAGACCAAATGATGCGATTCCCTGTGCTTGGAATGTTCGA
258 GTTGTTTAGAAAATGACAAACTATTTAGA-CAAATGATG-AATTCCCCGTACATGGAATGTTCAA
* * * * * ** *
2836 AAAATTGC-ACGATGGTAA-GGATCGTCATGAATACTTTAAGGAGCTGAAGTTTTAAAAGAACTC
321 AAAATTACTACGAAGG-AATGGATCTTCATGAATAATTTAAGGAACAAAAGTTATAAAAGAACTC
* * *** * * * *
2899 GTGAAACTTCGTCAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATA
385 GTAAAAGTTTACCAAGTTCGAAAGTTCGTCTAAGAACCAAGAGAGAAACAACTCTCACGTAAATA
* * * ** * * *
2964 ACTTTTTAATTTATTGACCAAAAGTTGTTTAGAAAAAGACAAACTCTTTAGA-CATAATGATGCA
450 AATTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAACTATTTAGACCA-AATGATG-A
* ** * * * * *
3028 -ATTCCCCGTGCTTGGAATGTTCGAAAAATT-GCTTGAAGGGAAGGA-TCGTCATGAATACTTTA
513 GATTCCTCAAGCATGGAATGTTCAAAAAATTAG-TCGAAGGGAAGAACT-GTCTTGAATACTTTA
* *** * * * *
3090 AGGAACTGGAGTTTTAAAAGAACTCATGAAACTTCTTCAAGTTC-GAAAGTTCGTCCAAGAACAA
576 AGAAACCAAAGTTTTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAA-TTCATCCAAGAACAA
*
3154 AGAGAG
640 AGAGAA
* *
3160 AAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTTGTTTAGAAAATG----AC-
1 AAACAACTCTCACGTAAATAAC-TTTTAATTTAAAGACAAAAAGTTGTTTAGAAAATGAAAAACT
* ** *
3220 ---T------AATGATGCGATTCCCCATGC-TTGAATGTTCGAAAAATTGCTCGAAGGAAAGGAT
65 ATTTAGACAAAATGACGCGATTCCCCGCGCATGGAATGTTCGAAAAATTGCTCGAAGG-AAGGAT
*
3275 CGTCTTGAATACTTTAAGGAACTGAAG-TTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAG
129 CGTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAG
*
3339 TTCATCTAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAG
194 TTCATCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAG
*
3404 TTGTTTAGAAAATGACAAACTATTTAGACATAATGATGCAATTCCCCGTACTTGGAATGTTCAAA
259 TTGTTTAGAAAATGACAAACTATTTAGACA-AATGATG-AATTCCCCGTACATGGAATGTTCAAA
* ** * **
3469 AAATTGCTCGAAGGACGAAGGAATGGATCTTCATGAATGCTTTATGGAACTGAAGTTATAAAAGA
322 AAATTACT------ACGAAGGAATGGATCTTCATGAATAATTTAAGGAACAAAAGTTATAAAAGA
* * * *
3534 ACTCGTAAAAGTTTACCATGTTCGAAAGTTCGTCTAAGAACCAAGATAGAAACAACTCTCATGTG
381 ACTCGTAAAAGTTTACCAAGTTCGAAAGTTCGTCTAAGAACCAAGAGAGAAACAACTCTCACGTA
*
3599 AATAAATTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGAT
446 AATAAATTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAACTATTTAGACCAAATGAT
* *
3664 GAGATTTCC-CAAGCATGGAATGTTCAAAAAATT-GTTCTAA-GGAATGAATTGTCTTGAATACT
511 GAGA-TTCCTCAAGCATGGAATGTTCAAAAAATTAG-TCGAAGGGAA-GAACTGTCTTGAATACT
** * * * * *
3726 TTAAGAAACCAAAGTTTTTGAAGAACTCGTAAAAGTTTGTCAAGTTTGGAAGTTCATCTAAGAAC
573 TTAAGAAACCAAAGTTTTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAATTCATCCAAGAAC
*
3791 CAAGAGAA
638 AAAGAGAA
* * *
3799 AAACAACTCTCGCGTAAATAGATTTTTAATTTAAAGATAAAAAGTTGTTTAGAAAATGAAAAACT
1 AAACAACTCTCACGTAAATA-ACTTTTAATTTAAAGACAAAAAGTTGTTTAGAAAATGAAAAACT
* *
3864 ATTTAGACAAAATGACGCGATTTCCCGCGCATGGAATGTTCTAAAAATTGCTCGAAGGAATGGAT
65 ATTTAGACAAAATGACGCGATTCCCCGCGCATGGAATGTTCGAAAAATTGCTCGAAGGAA-GGAT
* ** * *
3929 CGTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTTGCAAAACTTCATCAAGTTCAGTAG
129 CGTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAG
* * ** *
3994 TTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGATTTTAATTTAGAGACCAAAAG
194 TTCATCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAG
* * * *
4059 TTGTTTACAAAATGACAAACTATTTAGAC-CATG-TG-ATTTCCCG-AGCATGGAATGTTCGAAA
259 TTGTTTAGAAAATGACAAACTATTTAGACAAATGATGAATTCCCCGTA-CATGGAATGTTCAAAA
* * * *
4120 AATTACT-TGAAGGAATGGAT-TGTCATGAATAATTTAAGGAACAAAAGTTATAGATGAACTGGT
323 AATTACTACGAAGGAATGGATCT-TCATGAATAATTTAAGGAACAAAAGTTATAAAAGAACTCGT
* *
4183 AAAAGTTTTCCAAGTTC-AGAAGTTCGT-TCAAGAACCAAGAGAGAAACAACTCTCACGTAAATT
387 AAAAGTTTACCAAGTTCGA-AAGTTCGTCT-AAGAACCAAGAGAGAAACAACTCTCACGTAAATA
* * * * *
4246 AGTTTTTCATTCAAAGACCAAAAGTTGTTTGGAAAATGACAAACTATTTTGA-CATAATGTTGAG
450 AATTTTTCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAACTATTTAGACCA-AATGATGAG
** * * * *
4310 ATTCCTCGTGCTTGGAATGTTCGAAAAATTAGTCGAAGGGAAGGACTGTCTTGAATACTTTAAGG
514 ATTCCTCAAGCATGGAATGTTCAAAAAATTAGTCGAAGGGAAGAACTGTCTTGAATACTTTAAGA
** * * *
4375 AACTGAAGTTTTAAAAGAAGTCGTGAAACTTCGTCAAGTTCGGAAATTCGTCCAAGAACAAAGAG
579 AACCAAAGTTTTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAATTCATCCAAGAACAAAGAG
*
4440 AG
644 AA
** * *
4442 AAACAACTCTCACGTAAATAACTTTTAATTTATTGACCAAAAGTTGTTTAGAAAATGACAAACTA
1 AAACAACTCTCACGTAAATAACTTTTAATTTAAAGACAAAAAGTTGTTTAGAAAATGAAAAACTA
* * * *
4507 TTTAGACATAATGATGCGATTCCCCGTGCTTGGAATGTTCGAAAAATTGCTCGAAGGTAAGGATC
66 TTTAGACAAAATGACGCGATTCCCCGCGCATGGAATGTTCGAAAAATTGCTCGAAGG-AAGGATC
* *
4572 GTCATGAATACTTTAAGGAGCTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCGGAAGT
130 GTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAGT
*
4637 TCATCCAAGAACAAAGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATAGACCAAAAGT
195 TCATCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGT
*
4702 TGTTTAGAAAAAGACAAACT
260 TGTTTAGAAAATGACAAACT
4722 CT
Statistics
Matches: 1342, Mismatches: 175, Indels: 96
0.83 0.11 0.06
Matches are distributed among these distances:
631 2 0.00
632 160 0.12
633 54 0.04
634 19 0.01
638 7 0.01
639 291 0.22
640 12 0.01
642 239 0.18
643 274 0.20
644 7 0.01
647 1 0.00
648 51 0.04
649 1 0.00
650 27 0.02
652 2 0.00
653 21 0.02
654 55 0.04
655 119 0.09
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (645 bp):
AAACAACTCTCACGTAAATAACTTTTAATTTAAAGACAAAAAGTTGTTTAGAAAATGAAAAACTA
TTTAGACAAAATGACGCGATTCCCCGCGCATGGAATGTTCGAAAAATTGCTCGAAGGAAGGATCG
TCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTGAAACTTCGTCAAGTTCAGAAGTT
CATCCAAGAACAAAGAGAGAAACAACTCTCACGTAAATAACTTTTTAATTTATAGACCAAAAGTT
GTTTAGAAAATGACAAACTATTTAGACAAATGATGAATTCCCCGTACATGGAATGTTCAAAAAAT
TACTACGAAGGAATGGATCTTCATGAATAATTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAA
GTTTACCAAGTTCGAAAGTTCGTCTAAGAACCAAGAGAGAAACAACTCTCACGTAAATAAATTTT
TCATTCAAAGACCAAAAGTAGTTTAGAAAATGACAAACTATTTAGACCAAATGATGAGATTCCTC
AAGCATGGAATGTTCAAAAAATTAGTCGAAGGGAAGAACTGTCTTGAATACTTTAAGAAACCAAA
GTTTTAAAAGAACTCGTAAAACTTCGTCAAGTTCGGAAATTCATCCAAGAACAAAGAGAA
Done.