Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010011.1 Kokia drynarioides strain JFW-HI SEQ_124772, 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: 31762
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2074 original size:215 final size:214
Alignment explanation
Indices: 1661--3927 Score: 2189
Period size: 215 Copynumber: 10.7 Consensus size: 214
1651 GTTTCTTTCA
* * * *
1661 TCCAAAAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACCAAAAGTTGA
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGA-CAAAACTTGT
* * * * *
1726 TAACAAAATGACAAACTATTTAGACTAAACT-ATGTGATTTTCC-GAACATGGAATG-TT-CAAA
64 TTACAAAATGACAAACTATTTAGACCAAA-TGATGCGA-TTTCCTGAGCATGGAATGTTTGGAAA
* * * * * *
1787 ATTGCTCGAAGGATTGGATTGTCTTGAATTCTTTAAGGAATCAAAGTTATAAAAGAAGTCGTAAA
127 ATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAA
* *
1852 AGTTTGACAAGTACGAAAGTTCA
192 AGTTTGACAAGTTCGAAAGTTCG
* * *
1875 TCCAAGAACCAAGATAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAGATCAAAAGTTGAT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAGA-CAAAACTTGTT
* * * *
1940 AACAAAATGAAAAACTATTTAGACAAAACT-ATGTGATTTCCTGAGCATGGAATGTTTGGAAAAT
65 TACAAAATGACAAACTATTTAGACCAAA-TGATGCGATTTCCTGAGCATGGAATGTTTGGAAAAT
* * *
2004 TGCTCGAAGGAATGGATCGACTTGAATTCTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGG
129 TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
* *
2069 TTTGACAAGTTTGAAAGTTTG
194 TTTGACAAGTTCGAAAGTTCG
* * * * * *
2090 TCTC-AGAACCAATAGAGAAACAATTCTCACATATATAAGTTTTTAACTCAAACACAAAAATTGT
1 TC-CAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACAAAACTTGT
* * * * * * *
2154 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTTGTGCGTGGAAAGCTCGTAAAAT
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAAT
* * * * * * ** *
2219 TGCTTGAAAGAATGGATTGTCTTAAATACATTAATGAACCGAAGTTATAATCGAACTCATAAAAA
129 TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT--AAA
*
2284 AGTTTGTCAAGTTC-AGAAGTTCG
192 AGTTTGACAAGTTCGA-AAGTTCG
* * *
2307 TCCAAGAACCAAGAGAGAAACAATTCTCACGCAAATAAGTTTTTAATTCTAAGACAAAAGTTGAT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACAAAACTTGTT
* * * * *
2372 AACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTAGAAATTT
65 TACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAATT
* *
2437 GCTTGAAGGAATGGATCGTCTTCAATA-TTTAAGGAACCCGAAGTTATAAAAGAACTCGTAAAAG
130 GCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CCGAAGTTATAAAAGAACTCGTAAAAG
* * *
2501 TTTGACAAGTTTGAAAATTCA
194 TTTGACAAGTTCGAAAGTTCG
* * * * *
2522 TCTC-AGAA-CTAGTAGAAAAACAATTCTCATGTAAAAAAGTTTTTAATTCAACGACAAAAATTT
1 TC-CAAGAACCAAG-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA-GAC-AAAACTT
* * * * * *
2585 GTTTACAAAATGATAAACTATTTAAATCAAATGATGCGATTTCTTGTGCATGGAATGTTTTGAAA
62 GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAA
* * * * **
2650 ATTGATCGAAGAAATGGATCGTATTGAATA-TATTAAGGAATCG-AGTTATAACGGAACTCGTAA
127 ATTGCTCGAAGGAATGGATCGTCTTGAATACT-TTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* *
2713 AAGTTTGACAAGTTCGGAAGTTTG
191 AAGTTTGACAAGTTCGAAAGTTCG
*
2737 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAGAAACTTTT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACA-AAACTTGT
* *
2802 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTAAGCGTGGAATGTTT-GAAAAT
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAA-
* * * *
2866 TTGCTTGAAGGAAAGGATCGTCTTTAATAC-TTAA-G---C-------TAACA-AA---GTAAAA
128 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAA
*
2915 GTTTGATAAGTTCGAAAGTTCG
193 GTTTGACAAGTTCGAAAGTTCG
* * * * * *
2937 TCCCAGAACCAAGAGAGAAACAATTCTCATGTAAATGAGTTTTTAATTAAAAGACTAAAACATCT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT-CAAGAC-AAAACTTGT
* * * * * *
3002 TTACAAAATGACAAACTAATTAGACAAAATGATTCAATTT-CTCGAGCATGGAATGTTCGAAAAA
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCT-GAGCATGGAATGTTTG-GAAA
* * * ** * * * * *
3066 ATT-TTCGAAGGAATGTATCATCTTGAATACTTTTAAAAAACCAAAGTAATAAAGGATCTCGTGA
127 ATTGCTCGAAGGAATGGATCGTCTTGAATAC-TTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* **
3130 AAGTTTGAAAAGTTCTTAAGTTCG
191 AAGTTTGACAAGTTCGAAAGTTCG
*
3154 TCCAAGAACCCAA-A-AGAAACAATTCTCACGTAAATATGTTTTTAATTCAAAGACCAAAACTT-
1 TCCAAGAA-CCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGA-CAAAACTTG
* * * *
3216 TTTAGAAAATGACAAACTATTTAAACCAAATGAAGTGATTTCC----C---G-A------GAAAA
63 TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAA
* * * * * *
3267 TTTCTCAAAGGAA---ATTGTCTTAAATATTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAA
128 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAA
* * *
3329 GTTTGACAAGTTTGGAAGTTCA
193 GTTTGACAAGTTCGAAAGTTCG
* * * * * *
3351 TCCCAGAACCAATAGAGAAATAATTCTCACGTAAA-AGGTTTTTAATTTAAAGACCAAAACCTGT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TTCAAGA-CAAAACTTGT
* * * * ** * *
3415 TTACAAAATGACAAACTATTTAGACCAAATTATTCAATTACCCAAACATGGAATGTTTGAAAAAT
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAAT
* * * * *
3480 TGGTCGAAAGAATGAATCGTCTTGAATACTTCAAGGAACCGAAGTTATAAAGGAACTCGTAAAAG
129 TGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
* * *
3545 TTTGACAGGTTCAAAAGTTTG
194 TTTGACAAGTTCGAAAGTTCG
* *
3566 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCACAGAAACAAACTTTT
1 TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA-AGACA-AAACTTGT
* * **
3631 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCATGAGAATGGAATGTTCAGAAAAT
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAAT
* ** * * * *
3696 TGCTC-ATAGGAATTGATAATCTTGAATACATTAATGAACTGAAGTTAT-AATGAAACTCGTAAA
129 TGCTCGA-AGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG-AACTCGTAAA
* * *
3759 AGTTTGACAAGTTCCAAAATTCA
192 AGTTTGACAAGTTCGAAAGTTCG
* * *
3782 TCCAAG-ACCTAAGAGAGAAACAATTCTCACGCAAATAAGTTTTTAATTCTAAGACAAAAGTTGA
1 TCCAAGAACC-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGACAAAACTTGT
* * * * **
3846 TAACAAAATGAAAAACTATTTAGACCAAATGATGCAATTT-TTCGAGCATGGAATGTTCAGAAAA
64 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCT-GAGCATGGAATGTTTGGAAAA
*
3910 TTACTCGAAGGAATGGAT
128 TTGCTCGAAGGAATGGAT
3928 TGATGCGAGC
Statistics
Matches: 1695, Mismatches: 278, Indels: 159
0.80 0.13 0.07
Matches are distributed among these distances:
196 4 0.00
197 73 0.04
198 66 0.04
199 2 0.00
200 156 0.09
201 11 0.01
202 9 0.01
203 2 0.00
204 4 0.00
205 1 0.00
206 2 0.00
207 1 0.00
208 1 0.00
210 1 0.00
211 1 0.00
212 18 0.01
213 64 0.04
214 67 0.04
215 662 0.39
216 334 0.20
217 212 0.13
218 4 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (214 bp):
TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAGACAAAACTTGTTT
ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTTGGAAAATTG
CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTT
TGACAAGTTCGAAAGTTCG
Found at i:2699 original size:432 final size:428
Alignment explanation
Indices: 1657--3927 Score: 2160
Period size: 432 Copynumber: 5.4 Consensus size: 428
1647 GACGGTTTCT
* * * *
1657 TTCATCCAAAAACCAAG-AGAGAAACAATTCTCACGTAAATAAGTTTTTATTTCAAAGACCAAAA
1 TTCATCCCAGAACC-AGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
* * * * ** *
1721 GTTGATAACAAAATGACAAACTATTTAGACTAAACT-ATGTGATTT-TCCGAACATGGAATG-TT
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAA-TGATGCAATTTCT-CGAGCATGGAATGTTT
* * * * * * ** * *
1783 -CAAAATTGCTCGAAGGATTGGATTGTCTTGAAT-TCTTTAAGGAATCAAAGTTATAAAAGAAGT
128 GAAAAATTGATCGAAGAAATGGATCGTCTTGAATAT-ATTAAGGAA-CCGAGTTATAAACGAACT
* * *
1846 CGTAAAAGTTTGACAAGTAC-GAAAGTTCATCCAAGAACCAAGATAGAAACAATTCTCACGTAAA
191 CGTAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAA
* * * * * *
1910 TAAGTTTTTAATTCAAGATCAAAAGTTGATAACAAAATGAAAAACTATTTAGACAAAACT-ATGT
255 TAAGTTTTTAATTCAAGA-CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAA-TGATGC
* * * * *
1974 GATTTCCTGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGACTTGAATTCTTTAAG
318 GATTTCCTGAGCATGGAATGTTTAGAAATTTGCTTGAAGGAATGGATCGTCTTGAA-TATTTAAG
*
2039 GAACCGAAGTTATAAAAGAACTCGTAAAGGTTTGACAAGTTTGAAAG
382 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAG
** * * * * * *
2086 TTTGTCTCAGAACCAATAGAGAAACAATTCTCACATATATAAGTTTTTAACTCAAACACAAAAA-
1 TTCATCCCAGAACCAGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAC
* * * * * * * *
2150 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTTGTGCGTGGAAAGCTCGTA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTTGAA
* * * * * * * *
2215 AAATTGCTTGAA-AGAATGGATTGTCTTAAATACATTAATGAACCGAAGTTATAATCGAACTCAT
131 AAATTGATCGAAGA-AATGGATCGTCTTGAATATATTAAGGAACCG-AGTTATAAACGAACTCGT
* *
2279 AAAAAAGTTTGTCAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGCAAATA
194 --AAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
2344 AGTTTTTAATTCTAAGACAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGCGAT
257 AGTTTTTAATTC-AAGACAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
2409 TTCCCGAGCATGGAATGTTTAGAAATTTGCTTGAAGGAATGGATCGTCTTCAATATTTAAGGAAC
321 TTCCTGAGCATGGAATGTTTAGAAATTTGCTTGAAGGAATGGATCGTCTTGAATATTTAAGGAA-
*
2474 CCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAA
385 CCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAG
* * * * * * *
2518 TTCATCTCAGAACTAGTAGAAAAACAATTCTCATGTAAAAAAGTTTTTAATTCAACGACAAAAAT
1 TTCATCCCAGAACCAGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAC
* * * * * *
2583 TTGTTTACAAAATGATAAACTATTTAAATCAAATGATGCGATTTCTTGTGCATGGAATGTTTTG-
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATG-TTTGA
* *
2647 AAAATTGATCGAAGAAATGGATCGTATTGAATATATTAAGGAATCGAGTTAT-AACGGAACTCGT
130 AAAATTGATCGAAGAAATGGATCGTCTTGAATATATTAAGGAACCGAGTTATAAAC-GAACTCGT
* *
2711 AAAAGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
194 AAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
*
2776 TTTTTAATTCAAAGACAGAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
259 TTTTTAATTC-AAGACA-AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * * * *
2841 TCCTAAGCGTGGAATGTTT-GAAAATTTGCTTGAAGGAAAGGATCGTCTTTAATACTTAA-G---
322 TCCTGAGCATGGAATGTTTAG-AAATTTGCTTGAAGGAATGGATCGTCTTGAATATTTAAGGAAC
* * *
2901 C-------TAACA-AA---GTAAAAGTTTGATAAGTTCGAAAG
386 CGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAG
* * * * *
2933 TTCGTCCCAGAACCAAG-AGAGAAACAATTCTCATGTAAATGAGTTTTTAATTAAAAGACTAAAA
1 TTCATCCCAGAACC-AGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAA
* * * * * *
2997 CATCTTTACAAAATGACAAACTAATTAGACAAAATGATTCAATTTCTCGAGCATGGAATGTTCGA
65 CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTTG-
* * * * * ** * * * *
3062 AAAAATT-TTCGAAGGAATGTATCATCTTGAATACTTTTAAAAAACCAAAGTAATAAAGGATCTC
129 AAAAATTGATCGAAGAAATGGATCGTCTTGAATA-TATTAAGGAACC-GAGTTATAAACGAACTC
* * **
3126 GTGAAAGTTTGAAAAGTTCTTAAGTTCGTCCAAGAACCCAA-A-AGAAACAATTCTCACGTAAAT
192 GTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAA-CCAAGAGAGAAACAATTCTCACGTAAAT
* * * * *
3189 ATGTTTTTAATTCAAAGACCAAAACTT-TTTAGAAAATGACAAACTATTTAAACCAAATGAAGTG
256 AAGTTTTTAATTC-AAGA-CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
** * *
3253 ATTTCC----C---G-A-G---A-AAATTT-CTCAAAGGAA---ATTGTCTTAAATATTTTAAGG
319 ATTTCCTGAGCATGGAATGTTTAGAAATTTGCTTGAAGGAATGGATCGTCTTGAATA-TTTAAGG
* *
3301 AACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGGAAG
383 AACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAG
* * * * *
3347 TTCATCCCAGAACCAATAGAGAAATAATTCTCACGTAAA-AGGTTTTTAATTTAAAGACCAAAAC
1 TTCATCCCAGAACCAGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAC
* * * * * * *
3411 CTGTTTACAAAATGACAAACTATTTAGACCAAATTATTCAATTACCCAAACATGGAATGTTTGAA
66 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTTGAA
* * * *
3476 AAATTGGTCGAA-AGAATGAATCGTCTTGAATACT-TCAAGGAACCGAAGTTATAAAGGAACTCG
131 AAATTGATCGAAGA-AATGGATCGTCTTGAATA-TATTAAGGAACCG-AGTTATAAACGAACTCG
* * *
3539 TAAAAGTTTGACAGGTTCAAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
193 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* *
3604 GTTTTTAATTCACAGAAACAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
258 GTTTTTAATTCA-AGACA-AAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * * * ** * *
3669 TTCATGAGAATGGAATGTTCAGAAAATTGC-TCATAGGAATTGATAATCTTGAATACATTAATGA
321 TTCCTGAGCATGGAATGTTTAGAAATTTGCTTGA-AGGAATGGATCGTCTTGAATA-TTTAAGGA
* * ** *
3733 ACTGAAGTTAT-AATGAAACTCGTAAAAGTTTGACAAGTTCCAAAA
384 ACCGAAGTTATAAAAG-AACTCGTAAAAGTTTGACAAGTTTGAAAG
* * *
3778 TTCATCCAAG-ACCTAAG-AGAGAAACAATTCTCACGCAAATAAGTTTTTAATTCTAAGAC-AAA
1 TTCATCCCAGAACC--AGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAA
* * * * * *
3840 AGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGCAATTTTTCGAGCATGGAATG-TTC
64 ACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTTG
*
3904 AGAAAATT-ACTCGAAGGAATGGAT
129 A-AAAATTGA-TCGAAGAAATGGAT
3928 TGATGCGAGC
Statistics
Matches: 1527, Mismatches: 236, Indels: 156
0.80 0.12 0.08
Matches are distributed among these distances:
398 11 0.01
399 4 0.00
400 1 0.00
401 8 0.01
402 6 0.00
403 1 0.00
406 1 0.00
407 1 0.00
408 1 0.00
410 4 0.00
411 7 0.00
412 61 0.04
413 140 0.09
414 95 0.06
415 181 0.12
416 60 0.04
417 44 0.03
418 8 0.01
419 4 0.00
421 1 0.00
422 1 0.00
423 1 0.00
426 2 0.00
427 7 0.00
428 53 0.03
429 53 0.03
430 136 0.09
431 254 0.17
432 283 0.19
433 95 0.06
434 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (428 bp):
TTCATCCCAGAACCAGTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAC
TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTTGAA
AAATTGATCGAAGAAATGGATCGTCTTGAATATATTAAGGAACCGAGTTATAAACGAACTCGTAA
AAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
TTTAATTCAAGACAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCT
GAGCATGGAATGTTTAGAAATTTGCTTGAAGGAATGGATCGTCTTGAATATTTAAGGAACCGAAG
TTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGAAAG
Found at i:3078 original size:200 final size:199
Alignment explanation
Indices: 2709--3927 Score: 589
Period size: 216 Copynumber: 5.9 Consensus size: 199
2699 AACGGAACTC
* *
2709 GTAAAAGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * * *
2774 AGTTTTTAATTCAAAGACAGAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
66 AGTTTTTAATTAAAAGACAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATGCAA
* * * * *
2839 TTTCCTAAGCGTGGAATGTTTGAAAATTTGCTTGAAGGAAAGGATCGTCTTTAATACTTAAGCTA
131 TTTCCTAAGCATGGAATGTTCGAAAATTT-CTCGAAGGAAAGGATCATCTTGAATACTTAAGCTA
2904 ACAAA
195 ACAAA
* * * *
2909 GTAAAAGTTTGATAAGTTCGAAAGTTCGTCCCAGAACCAAGAGAGAAACAATTCTCATGTAAATG
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
*
2974 AGTTTTTAATTAAAAGACTA-AAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATTCA
66 AGTTTTTAATTAAAAGAC-AGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATGCA
* * *
3038 ATTT-CTCGAGCATGGAATGTTCGAAAAAATTT-TCGAAGGAATGTATCATCTTGAATACTTTTA
130 ATTTCCT-AAGCATGGAATGTTCG--AAAATTTCTCGAAGGAAAGGATCATCTTGAATAC--TT-
* *
3101 AAAAACCAAAGTAATAAAGGA
189 ---AAGC----TAA-CAA--A
* * **
3122 TCTCGTGAAAGTTTGAAAAGTTCTTAAGTTCGTCCAAGAACCCAA-A-AGAAACAATTCTCACGT
1 ----GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA-CCAAGAGAGAAACAATTCTCACGT
* * * * * * *
3185 AAATATGTTTTTAATTCAAAGACCA-AAAC-TTTTTAGAAAATGACAAACTATTTAAACCAAATG
61 AAATAAGTTTTTAATTAAAAGA-CAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATG
* ** ** * * * * ** *
3248 AAGTGATTTCCCGAG-A--AAATTTCTCAAAGGAAATTGTCT-TAAATATTTTAAGGA--A-C-C
125 ATGCAATTTCCTAAGCATGGAATGT-TC---GAAAATT-TCTCGAAGGA----AAGGATCATCTT
* *
3305 GAAGTTA-TAAAAG--AAC-TA
181 GAA--TACT-TAAGCTAACAAA
* * * * * *
3323 GTAAAAGTTTGACAAGTTTGGAAGTTCATCCCAGAACCAATAGAGAAATAATTCTCACGTAAA-A
1 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * * * * *
3387 GGTTTTTAATTTAAAGACCA-AAACCTGTTTACAAAATGACAAACTATTTAGACCAAATTATTCA
66 AGTTTTTAATTAAAAGA-CAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATGCA
* * * * ** * * * *
3451 ATTACCCAAACATGGAATGTTTGAAAAATTGGTCGAAAGAATGAATCGTCTTGAATACTTCAAGG
130 ATTTCCTAAGCATGGAATGTTCG-AAAATTTCTCGAAGGAAAGGATCATCTTGAATACTT-AA-G
*
3516 AACCGAAGTTATAAAGGAA
192 ---C-----TA-ACA--AA
* * *
3535 CTCGTAAAAGTTTGACAGGTTCAAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
1 ---GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
* * * * * * * *
3600 ATAAGTTTTTAATTCACAGAAACAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATG
63 ATAAGTTTTTAATTAAAAGACAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATG
* * * * * ** *
3665 CGATTTCATGAGAATGGAATGTTCAGAAAATTGCTC-ATAGGAATTGATAATCTTGAATACATTA
128 CAATTTCCTAAGCATGGAATGTTC-GAAAATTTCTCGA-AGGAAAGGATCATCTTGAATAC-TTA
*
3729 ATGAACTGAAGTTATAATGAAA
190 A-G--C--------TAA-CAAA
* * * *
3751 CTCGTAAAAGTTTGACAAGTTCCAAAATTCATCCAAG-ACCTAAGAGAGAAACAATTCTCACGCA
1 ---GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-AAGAGAGAAACAATTCTCACGTA
** ** ** * * * *
3815 AATAAGTTTTTAATTCTAAGACA-AAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGAT
62 AATAAGTTTTTAATTAAAAGACAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGAT
* * * *
3879 GCAATTT-TTCGAGCATGGAATGTTCAGAAAATTACTCGAAGGAATGGAT
127 GCAATTTCCT-AAGCATGGAATGTTC-GAAAATTTCTCGAAGGAAAGGAT
3928 TGATGCGAGC
Statistics
Matches: 789, Mismatches: 149, Indels: 147
0.73 0.14 0.14
Matches are distributed among these distances:
194 3 0.00
196 6 0.01
197 59 0.07
198 70 0.09
199 3 0.00
200 153 0.19
201 6 0.01
202 9 0.01
205 2 0.00
206 3 0.00
208 1 0.00
209 1 0.00
210 3 0.00
211 4 0.01
212 5 0.01
213 3 0.00
214 8 0.01
215 181 0.23
216 219 0.28
217 40 0.05
218 7 0.01
219 3 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (199 bp):
GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
AGTTTTTAATTAAAAGACAGAAACATCTTTACAAAATGACAAACTAATTAGACAAAATGATGCAA
TTTCCTAAGCATGGAATGTTCGAAAATTTCTCGAAGGAAAGGATCATCTTGAATACTTAAGCTAA
CAAA
Found at i:6774 original size:7 final size:7
Alignment explanation
Indices: 6738--6785 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
6728 AAACCCCAAT
6738 TCCATCA
1 TCCATCA
*
6745 TCCACCA
1 TCCATCA
* *
6752 ACCATCCC
1 TCCAT-CA
6760 TACCATCA
1 T-CCATCA
6768 TCCATCA
1 TCCATCA
6775 TCCATCA
1 TCCATCA
6782 TCCA
1 TCCA
6786 CGCTACTATC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 26 0.79
8 3 0.09
9 4 0.12
ACGTcount: A:0.29, C:0.48, G:0.00, T:0.23
Consensus pattern (7 bp):
TCCATCA
Found at i:8186 original size:18 final size:18
Alignment explanation
Indices: 8152--8188 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8142 ACTCTTCTAC
*
8152 TTCTAAATGGAGTCAGAA
1 TTCTAAATGGAGACAGAA
*
8170 TTCTAAATGGGGACAGAA
1 TTCTAAATGGAGACAGAA
8188 T
1 T
8189 GCTCCTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (18 bp):
TTCTAAATGGAGACAGAA
Found at i:14302 original size:216 final size:214
Alignment explanation
Indices: 13918--15562 Score: 1135
Period size: 216 Copynumber: 7.8 Consensus size: 214
13908 GCTCACATCG
* ** *
13918 TGGATCATCTTCAATATTTTGAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTGT
1 TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAAAA-AACTCGTAAAAGTTTGACAAGT-T
* *
13983 -GGAAGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
64 CAGAAGTTCGTC-CAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* ** * * * * * *
14047 AAATTGTTTTTTACAAAATGAAAAAGTATTGAGACCAAATGATGTCATTTCTTGTGCATGGAATG
128 AAA-AGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGACATTTCTCGAGCATGGAATG
* *
14112 TTTGA-AAAATTGGTCGAAGGAA
192 TTTCAGAAAATTGCTCGAAGGAA
* * *
14134 TGGATCATCTTGAAAACATTAAGGAACTGAAGTTATAACGAAACTCGTAAAAGTTTGACAAGTTT
1 TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAA-AAAACTCGTAAAAGTTTGACAAGTTC
* * * * *
14199 AGAAGCTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGCTTTTAATTCAAAGTCC
65 AGAAGTTCGTCC-AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-AC
*
14264 AAAAGTTGATAACAAAATGAAAAACTATTT-GAACCAAATGAT-ATGATTTCTCGAGCATGGAAT
128 AAAAGTTGATAACAAAATGAAAAACTATTTAG-ACCAAATGATGA-CATTTCTCGAGCATGGAAT
* *
14327 G-TTCAAAAAATTACTCGAAGGAA
191 GTTTCAGAAAATTGCTCGAAGGAA
* * ** * * *
14350 TGGATAATCTTCAATATTTTAAGGAACCGAAGTTAT---AAA-T-GTAAAATTAGTGTGAGAAGT
1 TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAAAAAACTCGT-AAA--AGTTTGACAAGT
* * *
14410 TCAGAAGTTCATCTCAGTACCAATAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAGA
63 TCAGAAGTTCGTC-CAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * * * *
14475 CAAAATTTTGTTTACAAAATGATAAAA-TATTTAGACCAAATGATGAGATTTCTTGTGCATGGAA
127 CAAAA-GTTGATAACAAAATGA-AAAACTATTTAGACCAAATGATGACATTTCTCGAGCATGGAA
* * * *
14539 T-ATTCAGAAATTTGCACAAAGGAA
190 TGTTTCAGAAAATTGCTCGAAGGAA
** * * ** *
14563 TGGATTGTCTT-AAATACATTAAGGAACAGAAATTATAATGGAACTTGTAAAAGTTTGACAAGTT
1 TGGATCATCTTCAAA-ACATTAAGGAACTGAAGTTATAA-AAAACTCGTAAAAGTTTGACAAGTT
* * * *
14627 CGGAGGTTCGTCCAAGAACC-ATGAGAGAAACAATTCTAACGCAAATAAGTTTTTAATTCAAAGA
64 CAGAAGTTCGTCC-AGAACCAAT-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * *
14691 CCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGAT-ACGATTTCCCAAGCGTGGAA
127 -CAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGAC-ATTTCTCGAGCATGGAA
14755 TG-TTCAGAAAATTGCTCGAAGGAA
190 TGTTTCAGAAAATTGCTCGAAGGAA
* * ** * *
14779 TGGATCGTCTTCAATATTTTAAGGAAAC-GAAGTTATAAAAGAACTCGAAAAACTTTGACAAGTT
1 TGGATCATCTTCAAAACATTAAGG-AACTGAAGTTATAAAA-AACTCGTAAAAGTTTGACAAGTT
* * * *
14843 CAGAAGTTTGTCTTAGAACCACTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGAC
64 CAGAAGTTCGTC-CAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * ** * * * *
14908 -ACACTTTTTTACAAAATGACAAACTATTTAGACCAAA-GATG-CGATTTC-CTGAG-GTAGAAT
128 AAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGAC-ATTTCTC-GAGCATGGAAT
* * *
14968 G-TTCAGAAAATTGCTCAAATGTA
191 GTTTCAGAAAATTGCTCGAAGGAA
** * * * *
14991 TGGATTGTCTTGAATAC-TT-------T-AAG--GTAACAAA---GTAAAAGTTTGACAAGTTC-
1 TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAAAAAACTCGTAAAAGTTTGACAAGTTCA
* * * * *
15041 GAAAGTTTGTCCCAGAACCAAGAGAGAAACGATTCTCACGTAAATGAGTTTTTAATTCAAAGAGT
66 G-AAGTTCGT-CCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-C
** ** * * * * * * *
15106 AAAACATCTTTACAAAA--ACAAACTATTTAGACAAAATGAT-TCAATTTCCCGAGCATTGAGTG
128 AAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGAC-ATTTCTCGAGCATGGAATG
* *
15168 -TTCAAAAAAGTT-TTCGAAGGAA
192 TTTCAGAAAA-TTGCTCGAAGGAA
* * * * ** * * * * *
15190 TGGATCGTCTTGAATACTTTTAAGGAACCAAAGTGATAAAGGATCTCGTGAAAGTTTGATAAGTT
1 TGGATCATCTTCAAAAC-ATTAAGGAACTGAAGTTATAAA-AAACTCGTAAAAGTTTGACAAGTT
** * * * * *
15255 CTTAAGTTCGTCCAAGAACCCA-AGAGAAACAATTCTTACATAAATATGTTTTTAATTTAAAGAC
64 CAGAAGTTCGTCC-AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-
* * * * * *
15319 CAAAACTTGTTTATAAAATGAGAAACTATTTAGACCAAATGAAG-CAATTTCT----C-------
127 CAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGAC-ATTTCTCGAGCATGGAAT
15372 G----AGAAAATTGCTCGAAGGAA
191 GTTTCAGAAAATTGCTCGAAGGAA
* * * * ** * * *
15392 TGCATCATCTTGAATACTTTAAGGAACCAAAGTTGTAAAAGAACTAGTAAAGGTTTGACAAGTTC
1 TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAAAA-AACTCGTAAAAGTTTGACAAGTTC
* * * * * ** *
15457 GGAAGCTCGTCCCAGAACCAATCGAGAAACAATTCTCACATAAA-GAGTGCTTAATTTAAAGACC
65 AGAAGTTCGT-CCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-C
** * * *
15521 AAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATGAT
128 AAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGAT
15563 TCGATTTCCC
Statistics
Matches: 1168, Mismatches: 190, Indels: 157
0.77 0.13 0.10
Matches are distributed among these distances:
196 1 0.00
197 88 0.08
198 13 0.01
199 49 0.04
200 4 0.00
201 114 0.10
202 51 0.04
203 3 0.00
205 1 0.00
209 3 0.00
210 2 0.00
211 9 0.01
212 53 0.05
213 164 0.14
214 89 0.08
215 46 0.04
216 454 0.39
217 18 0.02
218 4 0.00
219 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (214 bp):
TGGATCATCTTCAAAACATTAAGGAACTGAAGTTATAAAAAACTCGTAAAAGTTTGACAAGTTCA
GAAGTTCGTCCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAA
AGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATGACATTTCTCGAGCATGGAATGTTTC
AGAAAATTGCTCGAAGGAA
Found at i:14783 original size:429 final size:421
Alignment explanation
Indices: 13918--15572 Score: 1513
Period size: 429 Copynumber: 3.9 Consensus size: 421
13908 GCTCACATCG
* * * *
13918 TGGATCATCTTCAATATTTTGAGGAACTGAAGTTATAAAAGAACTCGTAAA-AGTTTGACAAGTG
1 TGGATCGTCTTCAATATTTTAAGGAACCGAAGTTATAAAAG-A-T--AAAATAGTTTGACAAGT-
*
13982 T-GGAAGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
61 TCAGAAGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * **
14046 CAAATTGTTTTTTACAAAATGAAAAAGTATTGAGACCAAATGATGTCATTTCTTGTGCATGGAAT
126 CAAATT-TTGTTTACAAAATGAAAAA-TATTTAGACCAAATGATGAGATTTCTTGTGCATGGAAT
* * * **
14111 GTT-TGAAAAATTGGTCGAAGGAATGGATCATCTTGAAA-ACATTAAGGAACTGAAGTTATAACG
189 GTTCAG-AAAATTGCTCAAAGGAATGGATTGTCTT-AAATACATTAAGGAAC-GAA-TTATAA-G
** * *
14174 AAACTCGTAAAAGTTTGACAAGTTTAGAAGCTCGTCCAAGAACCAAGAGAGAAACAATTCTCACA
249 -AACT-GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACG
* *
14239 TAAATAAGCTTTTAATTCAAAGTCCAAAAGTTGATAACAAAATGAAAAACTATTT-GAACCAAAT
312 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAG-ACCAAAT
* *
14303 GATATGATTTCTCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAA
376 GATACGATTTCCCGAGCATGGAATGTTCAAAAAATT-CTCGAAGGAA
** * * *
14350 TGGATAATCTTCAATATTTTAAGGAACCGAAGTTATAAATG-TAAAATTAGTGTGAGAAGTTCAG
1 TGGATCGTCTTCAATATTTTAAGGAACCGAAGTTATAAAAGATAAAA-TAGTTTGACAAGTTCAG
* *
14414 AAGTTCATCTCAGTACCAATAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAGACAAA
65 AAGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC-AA
*
14479 ATTTTGTTTACAAAATGATAAAATATTTAGACCAAATGATGAGATTTCTTGTGCATGGAATATTC
129 ATTTTGTTTACAAAATGA-AAAATATTTAGACCAAATGATGAGATTTCTTGTGCATGGAATGTTC
* *
14544 AGAAATTTGCACAAAGGAATGGATTGTCTTAAATACATTAAGGAACAGAAATTATAATGGAACTT
193 AGAAAATTGCTCAAAGGAATGGATTGTCTTAAATACATTAAGGAAC-G-AATTATAA--GAAC-T
* * * *
14609 GTAAAAGTTTGACAAGTTCGGAGGTTCGTCCAAGAACCATGAGAGAAACAATTCTAACGCAAATA
253 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
14674 AGTTTTTAATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATACGA
318 AGTTTTTAATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATACGA
* * *
14739 TTTCCCAAGCGTGGAATGTTCAGAAAATTGCTCGAAGGAA
383 TTTCCCGAGCATGGAATGTTCAAAAAATT-CTCGAAGGAA
* *
14779 TGGATCGTCTTCAATATTTTAAGGAAACGAAGTTATAAAAGAACTCGAAAA-ACTTTGACAAGTT
1 TGGATCGTCTTCAATATTTTAAGGAACCGAAGTTATAAAAG-A-T--AAAATAGTTTGACAAGTT
** * * *
14843 CAGAAGTTTGTCTTAGAACCACTAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGAC
62 CAGAAGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
* * * * * * * *
14908 ACACTTT-TTTACAAAATGACAAACTATTTAGACCAAA-GATGCGATTTCCTGAG-GTAGAATGT
127 AAATTTTGTTTACAAAATGA-AAAATATTTAGACCAAATGATGAGATTTCTTGTGCATGGAATGT
* * * *
14970 TCAGAAAATTGCTCAAATGTATGGATTGTCTTGAATACTTTAA-G---G---TA-ACA-AA--GT
191 TCAGAAAATTGCTCAAAGGAATGGATTGTCTTAAATACATTAAGGAACGAATTATA-AGAACTGT
* * * * *
15024 AAAAGTTTGACAAGTTCGAAAGTTTGTCCCAGAACCAAGAGAGAAACGATTCTCACGTAAATGAG
255 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
** ** ** * * * * *
15089 TTTTTAATTCAAAGAGTAAAACATCTTTACAAAA--ACAAACTATTTAGACAAAATGATTCAATT
320 TTTTTAATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATACGATT
* * *
15152 TCCCGAGCATTGAGTGTTCAAAAAAGTTTTCGAAGGAA
385 TCCCGAGCATGGAATGTTCAAAAAA-TTCTCGAAGGAA
* * * * ** *
15190 TGGATCGTCTTGAATACTTTTAAGGAACCAAAGTGATAAAGGATCTCGTGAA-AGTTTGATAAGT
1 TGGATCGTCTTCAATA-TTTTAAGGAACCGAAGTTATAAAAGA--T--AAAATAGTTTGACAAGT
** * * * * * *
15254 TCTTAAGTTCGTC-CAAGAACCCA-AGAGAAACAATTCTTACATAAATATGTTTTTAATTTAAAG
61 TCAGAAGTTCATCTC-AGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
** * * *
15317 ACCAAAACTTGTTTATAAAATGAGAAACTATTTAGACCAAATGAAGCA-ATTTC---T-C-----
125 A-CAAATTTTGTTTACAAAATGA-AAAATATTTAGACCAAATGATG-AGATTTCTTGTGCATGGA
* * ** * * * *
15372 --G---AGAAAATTGCTCGAAGGAATGCATCATCTTGAATACTTTAAGGAACCAAAGTTGTAAAA
187 ATGTTCAGAAAATTGCTCAAAGGAATGGATTGTCTTAAATACATTAAGGAA-CGAA--T-TATAA
* * * ** *
15432 GAACTAGTAAAGGTTTGACAAGTTCGGAAGCTCGTCCCAGAACCAATCGAGAAACAATTCTCACA
248 GAACT-GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACG
* ** * ** * * *
15497 TAAA-GAGTGCTTAATTTAAAGACCAAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATG
312 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATG
*
15561 ATTCGATTTCCC
377 ATACGATTTCCC
15573 AATGATATGA
Statistics
Matches: 1033, Mismatches: 146, Indels: 103
0.81 0.11 0.08
Matches are distributed among these distances:
401 35 0.03
402 1 0.00
404 1 0.00
411 108 0.10
412 63 0.06
413 116 0.11
414 8 0.01
415 31 0.03
416 57 0.06
417 30 0.03
418 1 0.00
419 3 0.00
423 1 0.00
427 4 0.00
428 47 0.05
429 369 0.36
430 43 0.04
431 5 0.00
432 106 0.10
434 4 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (421 bp):
TGGATCGTCTTCAATATTTTAAGGAACCGAAGTTATAAAAGATAAAATAGTTTGACAAGTTCAGA
AGTTCATCTCAGAACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAT
TTTGTTTACAAAATGAAAAATATTTAGACCAAATGATGAGATTTCTTGTGCATGGAATGTTCAGA
AAATTGCTCAAAGGAATGGATTGTCTTAAATACATTAAGGAACGAATTATAAGAACTGTAAAAGT
TTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
ATTCAAAGACCAAAAGTTGATAACAAAATGAAAAACTATTTAGACCAAATGATACGATTTCCCGA
GCATGGAATGTTCAAAAAATTCTCGAAGGAA
Found at i:15550 original size:201 final size:202
Alignment explanation
Indices: 15181--15561 Score: 529
Period size: 201 Copynumber: 1.9 Consensus size: 202
15171 AAAAAAGTTT
* * * * *
15181 TCGAAGGAATGGATCGTCTTGAATACTTTTAAGGAACCAAAGTGATAAAGGATCTCGTGAAAGTT
1 TCGAAGGAATGCATCATCTTGAATACTTTTAAGGAACCAAAGTGATAAAAGAACTAGTGAAAGTT
* ** * * * **
15246 TGATAAGTTCTTAAGTTCGTCCAAGAACCCAAGAGAAACAATTCTTACATAAATATGTTTTTAAT
66 TGACAAGTTCGGAAGCTCGTCCAAGAACCCAAGAGAAACAATTCTCACATAAAGATGTGCTTAAT
* * * *
15311 TTAAAGACCAAAACTTGTTTATAAAATGAGAAACTATTTAGACCAAATGAAGCAATTTCTCGAGA
131 TTAAAGACCAAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATGAAGCAATTTCTCGAGA
15376 AAATTGC
196 AAATTGC
15383 TCGAAGGAATGCATCATCTTGAATAC-TTTAAGGAACCAAAGTTG-TAAAAGAACTAGT-AAAGG
1 TCGAAGGAATGCATCATCTTGAATACTTTTAAGGAACCAAAG-TGATAAAAGAACTAGTGAAA-G
*
15445 TTTGACAAGTTCGGAAGCTCGTCCCAGAA-CCAATCGAGAAACAATTCTCACATAAAGA-GTGCT
64 TTTGACAAGTTCGGAAGCTCGTCCAAGAACCCAA--GAGAAACAATTCTCACATAAAGATGTGCT
15508 TAATTTAAAGACCAAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATGA
127 TAATTTAAAGACCAAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATGA
15562 TTCGATTTCC
Statistics
Matches: 157, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
200 7 0.04
201 103 0.66
202 47 0.30
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (202 bp):
TCGAAGGAATGCATCATCTTGAATACTTTTAAGGAACCAAAGTGATAAAAGAACTAGTGAAAGTT
TGACAAGTTCGGAAGCTCGTCCAAGAACCCAAGAGAAACAATTCTCACATAAAGATGTGCTTAAT
TTAAAGACCAAAACATGTTTACAAAACGAAAAACTATTTAGACCAAATGAAGCAATTTCTCGAGA
AAATTGC
Found at i:26118 original size:12 final size:12
Alignment explanation
Indices: 26095--26127 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
26085 AGCAAAAGAA
26095 AAGAAGGAAAAAG
1 AAGAA-GAAAAAG
26108 AAGAAGAAAAAG
1 AAGAAGAAAAAG
26120 AAGAAGAA
1 AAGAAGAA
26128 GTTGTCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:30861 original size:18 final size:18
Alignment explanation
Indices: 30840--30953 Score: 120
Period size: 18 Copynumber: 6.3 Consensus size: 18
30830 ATGCTCTTAT
*
30840 GAGCTAGTATGCTTAAAC
1 GAGCTAGTATGCTCAAAC
30858 GAGCTAGTATGCTCAAAC
1 GAGCTAGTATGCTCAAAC
* * * *
30876 GAGCCACTACGCTCAAAT
1 GAGCTAGTATGCTCAAAC
* * **
30894 GAGCCAATATGCTTTAAC
1 GAGCTAGTATGCTCAAAC
30912 GAGCTAGTATGCTCAAAC
1 GAGCTAGTATGCTCAAAC
* *
30930 GAGCCAATATGCTCAAAC
1 GAGCTAGTATGCTCAAAC
*
30948 AAGCTA
1 GAGCTA
30954 ACATGCTCTG
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (18 bp):
GAGCTAGTATGCTCAAAC
Found at i:30920 original size:54 final size:54
Alignment explanation
Indices: 30838--30946 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
30828 TAATGCTCTT
* * *
30838 ATGAGCTAGTATGCTTAAACGAGCTAGTATGCTCAAACGAGCCACTACGCTCAA
1 ATGAGCCAATATGCTTAAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAA
* *
30892 ATGAGCCAATATGCTTTAACGAGCTAGTATGCTCAAACGAGCCAATATGCTCAA
1 ATGAGCCAATATGCTTAAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAA
30946 A
1 A
30947 CAAGCTAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (54 bp):
ATGAGCCAATATGCTTAAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAA
Found at i:30953 original size:36 final size:36
Alignment explanation
Indices: 30840--30971 Score: 138
Period size: 36 Copynumber: 3.7 Consensus size: 36
30830 ATGCTCTTAT
* * *
30840 GAGCTAGTATGCTTAAACGAGCTAGTATGCTCAAAC
1 GAGCTAGTATGCTCAAACGAGCCAATATGCTCAAAC
* * * * **
30876 GAGCCACTACGCTCAAATGAGCCAATATGCTTTAAC
1 GAGCTAGTATGCTCAAACGAGCCAATATGCTCAAAC
30912 GAGCTAGTATGCTCAAACGAGCCAATATGCTCAAAC
1 GAGCTAGTATGCTCAAACGAGCCAATATGCTCAAAC
* ** **
30948 AAGCTAACATGCTCTGACGAGCCA
1 GAGCTAGTATGCTCAAACGAGCCA
30972 GTAGACTCAA
Statistics
Matches: 76, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (36 bp):
GAGCTAGTATGCTCAAACGAGCCAATATGCTCAAAC
Found at i:30959 original size:18 final size:18
Alignment explanation
Indices: 30920--30961 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
30910 ACGAGCTAGT
* *
30920 ATGCTCAAACGAGCCAAT
1 ATGCTCAAACAAGCCAAC
*
30938 ATGCTCAAACAAGCTAAC
1 ATGCTCAAACAAGCCAAC
30956 ATGCTC
1 ATGCTC
30962 TGACGAGCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (18 bp):
ATGCTCAAACAAGCCAAC
Found at i:30960 original size:54 final size:54
Alignment explanation
Indices: 30848--30983 Score: 166
Period size: 54 Copynumber: 2.5 Consensus size: 54
30838 ATGAGCTAGT
* * ** *
30848 ATGCTTAAACGAGCTAGTATGCTCAAACGAGCCACTACGCTCAAATGAGCCAAT
1 ATGCTTTAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAAACAAGCCAAC
* *
30902 ATGCTTTAACGAGCTAGTATGCTCAAACGAGCCAATATGCTCAAACAAGCTAAC
1 ATGCTTTAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAAACAAGCCAAC
* * *
30956 ATGCTCTGACGAGCCAGTA-GACTCAAAC
1 ATGCTTTAACGAGCTAGTATG-CTCAAAC
30984 TTTCGTTTCT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 70 0.99
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (54 bp):
ATGCTTTAACGAGCTAGTATGCTCAAACGAGCCAATACGCTCAAACAAGCCAAC
Done.