Multiple sequence alignment - TraesCS4A01G426900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G426900 chr4A 100.000 4279 0 0 1 4279 698056797 698052519 0.000000e+00 7902.0
1 TraesCS4A01G426900 chr4A 80.627 1275 201 32 2312 3550 646324863 646326127 0.000000e+00 944.0
2 TraesCS4A01G426900 chr4A 81.458 480 76 8 2532 3004 646481968 646482441 8.680000e-102 381.0
3 TraesCS4A01G426900 chr4A 84.169 379 31 14 1015 1387 698361983 698362338 1.470000e-89 340.0
4 TraesCS4A01G426900 chr4A 81.166 446 58 10 17 462 698359062 698359481 6.860000e-88 335.0
5 TraesCS4A01G426900 chr4A 87.823 271 33 0 17 287 698368112 698368382 6.900000e-83 318.0
6 TraesCS4A01G426900 chr4A 77.013 596 72 31 777 1334 698354395 698354963 9.060000e-72 281.0
7 TraesCS4A01G426900 chr4A 86.100 259 29 4 2041 2295 646324414 646324669 5.450000e-69 272.0
8 TraesCS4A01G426900 chr4A 77.547 481 72 21 956 1408 646586440 646586912 1.530000e-64 257.0
9 TraesCS4A01G426900 chr4A 84.186 215 19 7 1842 2047 698362822 698363030 1.210000e-45 195.0
10 TraesCS4A01G426900 chr4A 78.438 320 29 15 956 1247 646346989 646347296 5.690000e-39 172.0
11 TraesCS4A01G426900 chr4A 88.158 152 9 4 1301 1452 698369113 698369255 5.690000e-39 172.0
12 TraesCS4A01G426900 chr4A 83.432 169 20 6 1807 1967 646514318 646514486 2.670000e-32 150.0
13 TraesCS4A01G426900 chr4A 86.607 112 6 3 1341 1452 698088561 698088459 9.720000e-22 115.0
14 TraesCS4A01G426900 chr4A 96.774 62 2 0 554 615 622891130 622891191 2.100000e-18 104.0
15 TraesCS4A01G426900 chr4A 96.774 62 2 0 554 615 622892157 622892218 2.100000e-18 104.0
16 TraesCS4A01G426900 chr4A 96.774 62 2 0 554 615 622959204 622959265 2.100000e-18 104.0
17 TraesCS4A01G426900 chr4A 96.667 60 2 0 554 613 622969036 622969095 2.720000e-17 100.0
18 TraesCS4A01G426900 chr4A 100.000 28 0 0 997 1024 698487482 698487509 8.000000e-03 52.8
19 TraesCS4A01G426900 chr7A 93.091 1983 101 25 2310 4276 31074441 31076403 0.000000e+00 2870.0
20 TraesCS4A01G426900 chr7A 91.742 775 46 11 1559 2315 31073503 31074277 0.000000e+00 1061.0
21 TraesCS4A01G426900 chr7A 87.631 857 62 15 619 1452 31072631 31073466 0.000000e+00 955.0
22 TraesCS4A01G426900 chr7A 82.667 675 80 19 995 1641 715007266 715006601 8.030000e-157 564.0
23 TraesCS4A01G426900 chr7A 79.095 641 92 23 2317 2934 116527263 116527884 1.850000e-108 403.0
24 TraesCS4A01G426900 chr7A 81.614 446 52 9 17 462 31065205 31065620 4.100000e-90 342.0
25 TraesCS4A01G426900 chr7A 82.532 395 47 19 1455 1831 31066386 31066776 1.150000e-85 327.0
26 TraesCS4A01G426900 chr7A 88.710 248 18 5 4034 4275 40099323 40099566 1.160000e-75 294.0
27 TraesCS4A01G426900 chr7A 77.650 434 64 20 2439 2866 116585716 116586122 2.570000e-57 233.0
28 TraesCS4A01G426900 chr7A 85.507 207 16 5 1017 1216 31065979 31066178 2.020000e-48 204.0
29 TraesCS4A01G426900 chr7A 83.019 106 7 4 1243 1344 31066176 31066274 7.620000e-13 86.1
30 TraesCS4A01G426900 chr7D 92.404 1988 112 15 2310 4276 30500982 30502951 0.000000e+00 2798.0
31 TraesCS4A01G426900 chr7D 89.931 1748 91 28 619 2315 30499105 30500818 0.000000e+00 2174.0
32 TraesCS4A01G426900 chr7D 80.201 1495 239 41 2310 3777 111277772 111279236 0.000000e+00 1068.0
33 TraesCS4A01G426900 chr7D 86.853 464 52 4 3 462 30498589 30499047 1.060000e-140 510.0
34 TraesCS4A01G426900 chr7D 89.320 412 26 6 2945 3345 30470200 30470604 6.390000e-138 501.0
35 TraesCS4A01G426900 chr7D 86.134 476 51 9 1832 2297 30469681 30470151 2.300000e-137 499.0
36 TraesCS4A01G426900 chr7D 84.706 510 59 12 951 1452 30477981 30478479 3.840000e-135 492.0
37 TraesCS4A01G426900 chr7D 86.147 462 44 12 3 462 30485238 30485681 8.320000e-132 481.0
38 TraesCS4A01G426900 chr7D 78.682 516 67 27 625 1114 30485744 30486242 1.930000e-78 303.0
39 TraesCS4A01G426900 chr7D 84.615 195 28 2 1895 2088 30410825 30411018 4.370000e-45 193.0
40 TraesCS4A01G426900 chr7D 80.000 260 35 14 3950 4195 111399803 111400059 4.400000e-40 176.0
41 TraesCS4A01G426900 chr7D 80.476 210 17 11 4068 4274 111406595 111406783 5.770000e-29 139.0
42 TraesCS4A01G426900 chr7D 95.556 45 2 0 4104 4148 111313605 111313649 5.940000e-09 73.1
43 TraesCS4A01G426900 chr7D 100.000 28 0 0 997 1024 30390623 30390650 8.000000e-03 52.8
44 TraesCS4A01G426900 chr7B 79.507 1015 158 34 2310 3304 70871245 70872229 0.000000e+00 676.0
45 TraesCS4A01G426900 chr7B 79.026 267 33 15 3946 4191 70866227 70866491 1.230000e-35 161.0
46 TraesCS4A01G426900 chr1B 81.138 668 91 18 995 1635 51392364 51393023 1.780000e-138 503.0
47 TraesCS4A01G426900 chr3A 80.240 668 79 21 995 1635 581431687 581432328 1.810000e-123 453.0
48 TraesCS4A01G426900 chr4D 95.455 66 1 1 557 620 20577868 20577803 2.100000e-18 104.0
49 TraesCS4A01G426900 chr4D 95.161 62 3 0 554 615 25492971 25493032 9.790000e-17 99.0
50 TraesCS4A01G426900 chr2D 96.774 62 2 0 554 615 30454213 30454152 2.100000e-18 104.0
51 TraesCS4A01G426900 chr1D 95.161 62 3 0 554 615 225396072 225396011 9.790000e-17 99.0
52 TraesCS4A01G426900 chr1D 95.161 62 3 0 554 615 356143451 356143390 9.790000e-17 99.0
53 TraesCS4A01G426900 chr3B 100.000 29 0 0 516 544 64244615 64244643 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G426900 chr4A 698052519 698056797 4278 True 7902.000000 7902 100.000000 1 4279 1 chr4A.!!$R1 4278
1 TraesCS4A01G426900 chr4A 646324414 646326127 1713 False 608.000000 944 83.363500 2041 3550 2 chr4A.!!$F10 1509
2 TraesCS4A01G426900 chr4A 698359062 698363030 3968 False 290.000000 340 83.173667 17 2047 3 chr4A.!!$F11 2030
3 TraesCS4A01G426900 chr4A 698354395 698354963 568 False 281.000000 281 77.013000 777 1334 1 chr4A.!!$F7 557
4 TraesCS4A01G426900 chr4A 698368112 698369255 1143 False 245.000000 318 87.990500 17 1452 2 chr4A.!!$F12 1435
5 TraesCS4A01G426900 chr7A 31072631 31076403 3772 False 1628.666667 2870 90.821333 619 4276 3 chr7A.!!$F5 3657
6 TraesCS4A01G426900 chr7A 715006601 715007266 665 True 564.000000 564 82.667000 995 1641 1 chr7A.!!$R1 646
7 TraesCS4A01G426900 chr7A 116527263 116527884 621 False 403.000000 403 79.095000 2317 2934 1 chr7A.!!$F2 617
8 TraesCS4A01G426900 chr7A 31065205 31066776 1571 False 239.775000 342 83.168000 17 1831 4 chr7A.!!$F4 1814
9 TraesCS4A01G426900 chr7D 30498589 30502951 4362 False 1827.333333 2798 89.729333 3 4276 3 chr7D.!!$F10 4273
10 TraesCS4A01G426900 chr7D 111277772 111279236 1464 False 1068.000000 1068 80.201000 2310 3777 1 chr7D.!!$F4 1467
11 TraesCS4A01G426900 chr7D 30469681 30470604 923 False 500.000000 501 87.727000 1832 3345 2 chr7D.!!$F8 1513
12 TraesCS4A01G426900 chr7D 30485238 30486242 1004 False 392.000000 481 82.414500 3 1114 2 chr7D.!!$F9 1111
13 TraesCS4A01G426900 chr7B 70871245 70872229 984 False 676.000000 676 79.507000 2310 3304 1 chr7B.!!$F2 994
14 TraesCS4A01G426900 chr1B 51392364 51393023 659 False 503.000000 503 81.138000 995 1635 1 chr1B.!!$F1 640
15 TraesCS4A01G426900 chr3A 581431687 581432328 641 False 453.000000 453 80.240000 995 1635 1 chr3A.!!$F1 640

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
902 2423 0.033208 AACCCAATCACCATCGCCAT 60.033 50.0 0.0 0.0 0.00 4.40 F
1561 3929 0.104672 TGGACTCCCTTCCAAGACCA 60.105 55.0 0.0 0.0 43.04 4.02 F
1723 4111 0.105964 ACAAGTTCGCTGCTGTACCA 59.894 50.0 0.0 0.0 0.00 3.25 F
1908 4335 0.674534 ATCGGGAGTATTCGAGGTGC 59.325 55.0 0.0 0.0 38.83 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 4233 1.137086 GGCGAGACTATTCTTGAGGCA 59.863 52.381 1.55 0.0 35.41 4.75 R
2565 5225 1.494960 AGCAGGTTCTCTCCTCCATC 58.505 55.000 0.00 0.0 35.37 3.51 R
2738 5410 3.451178 AGGCTGTGGTCACTACGAATAAT 59.549 43.478 2.66 0.0 0.00 1.28 R
3848 6581 3.928375 GGTGCCTTTTGTATTTGCATCAG 59.072 43.478 0.00 0.0 33.35 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.767759 CCATTGGGTGTGGAAGGATC 58.232 55.000 0.00 0.00 39.12 3.36
129 130 0.750911 CTTTCCTGATGCCTCCCAGC 60.751 60.000 0.00 0.00 0.00 4.85
152 153 5.676079 GCCATACGTGTTTGCTAACATCATT 60.676 40.000 16.56 4.81 45.41 2.57
153 154 6.457663 GCCATACGTGTTTGCTAACATCATTA 60.458 38.462 16.56 6.65 45.41 1.90
177 178 5.508567 TGATTATGTGTCCACCATCATGTT 58.491 37.500 0.00 0.00 0.00 2.71
246 247 6.148315 TGAAGAGAGAGTTATGTGCAAATGTG 59.852 38.462 0.00 0.00 0.00 3.21
250 251 7.392673 AGAGAGAGTTATGTGCAAATGTGAAAT 59.607 33.333 0.00 0.00 0.00 2.17
251 252 7.310664 AGAGAGTTATGTGCAAATGTGAAATG 58.689 34.615 0.00 0.00 0.00 2.32
252 253 5.865552 AGAGTTATGTGCAAATGTGAAATGC 59.134 36.000 0.00 0.00 40.45 3.56
253 254 5.539979 AGTTATGTGCAAATGTGAAATGCA 58.460 33.333 0.00 0.00 46.97 3.96
257 258 3.679824 TGCAAATGTGAAATGCATGGA 57.320 38.095 0.00 0.00 44.52 3.41
258 259 4.209307 TGCAAATGTGAAATGCATGGAT 57.791 36.364 0.00 0.00 44.52 3.41
259 260 3.935828 TGCAAATGTGAAATGCATGGATG 59.064 39.130 0.00 0.00 44.52 3.51
260 261 4.185394 GCAAATGTGAAATGCATGGATGA 58.815 39.130 0.00 0.00 39.81 2.92
261 262 4.632251 GCAAATGTGAAATGCATGGATGAA 59.368 37.500 0.00 0.00 39.81 2.57
273 286 3.608707 GCATGGATGAATGAATGCGAGAC 60.609 47.826 0.00 0.00 36.41 3.36
324 337 9.706691 CGAACATGGTGTAAAATATATAGGAGT 57.293 33.333 0.00 0.00 0.00 3.85
355 372 5.411361 GTGTAGTTTAGGCATGTCACATGAA 59.589 40.000 22.56 4.05 0.00 2.57
356 373 5.643348 TGTAGTTTAGGCATGTCACATGAAG 59.357 40.000 22.56 0.00 0.00 3.02
367 384 1.555075 TCACATGAAGAGGTAGGTGGC 59.445 52.381 0.00 0.00 0.00 5.01
398 415 4.574674 AAAATGCACAGGGTAGAGATGA 57.425 40.909 0.00 0.00 0.00 2.92
400 417 1.937191 TGCACAGGGTAGAGATGACA 58.063 50.000 0.00 0.00 0.00 3.58
426 443 4.154195 CCGGCTTCTATATAAACACATGCC 59.846 45.833 0.00 0.00 0.00 4.40
434 451 8.716646 TCTATATAAACACATGCCATATTCCG 57.283 34.615 0.00 0.00 0.00 4.30
493 1847 5.346281 GTGATCCAGAAAACTAACTCGACAG 59.654 44.000 0.00 0.00 0.00 3.51
505 1859 6.094061 ACTAACTCGACAGATTAGTTTCAGC 58.906 40.000 0.00 0.00 36.03 4.26
506 1860 4.521130 ACTCGACAGATTAGTTTCAGCA 57.479 40.909 0.00 0.00 0.00 4.41
507 1861 4.883083 ACTCGACAGATTAGTTTCAGCAA 58.117 39.130 0.00 0.00 0.00 3.91
508 1862 4.926238 ACTCGACAGATTAGTTTCAGCAAG 59.074 41.667 0.00 0.00 0.00 4.01
509 1863 5.134202 TCGACAGATTAGTTTCAGCAAGA 57.866 39.130 0.00 0.00 0.00 3.02
510 1864 4.923871 TCGACAGATTAGTTTCAGCAAGAC 59.076 41.667 0.00 0.00 0.00 3.01
511 1865 4.686091 CGACAGATTAGTTTCAGCAAGACA 59.314 41.667 0.00 0.00 0.00 3.41
512 1866 5.349817 CGACAGATTAGTTTCAGCAAGACAT 59.650 40.000 0.00 0.00 0.00 3.06
513 1867 6.454848 CGACAGATTAGTTTCAGCAAGACATC 60.455 42.308 0.00 0.00 0.00 3.06
514 1868 5.645497 ACAGATTAGTTTCAGCAAGACATCC 59.355 40.000 0.00 0.00 0.00 3.51
515 1869 4.872691 AGATTAGTTTCAGCAAGACATCCG 59.127 41.667 0.00 0.00 0.00 4.18
516 1870 2.839486 AGTTTCAGCAAGACATCCGA 57.161 45.000 0.00 0.00 0.00 4.55
517 1871 3.340814 AGTTTCAGCAAGACATCCGAT 57.659 42.857 0.00 0.00 0.00 4.18
518 1872 4.471904 AGTTTCAGCAAGACATCCGATA 57.528 40.909 0.00 0.00 0.00 2.92
519 1873 4.832248 AGTTTCAGCAAGACATCCGATAA 58.168 39.130 0.00 0.00 0.00 1.75
520 1874 5.245531 AGTTTCAGCAAGACATCCGATAAA 58.754 37.500 0.00 0.00 0.00 1.40
521 1875 5.705441 AGTTTCAGCAAGACATCCGATAAAA 59.295 36.000 0.00 0.00 0.00 1.52
522 1876 6.375455 AGTTTCAGCAAGACATCCGATAAAAT 59.625 34.615 0.00 0.00 0.00 1.82
523 1877 6.757897 TTCAGCAAGACATCCGATAAAATT 57.242 33.333 0.00 0.00 0.00 1.82
524 1878 6.122850 TCAGCAAGACATCCGATAAAATTG 57.877 37.500 0.00 0.00 0.00 2.32
525 1879 5.066375 TCAGCAAGACATCCGATAAAATTGG 59.934 40.000 0.00 0.00 34.94 3.16
526 1880 5.066375 CAGCAAGACATCCGATAAAATTGGA 59.934 40.000 0.00 0.00 46.63 3.53
527 1881 5.652014 AGCAAGACATCCGATAAAATTGGAA 59.348 36.000 0.00 0.00 45.74 3.53
528 1882 5.743872 GCAAGACATCCGATAAAATTGGAAC 59.256 40.000 0.00 0.00 45.74 3.62
529 1883 5.734855 AGACATCCGATAAAATTGGAACG 57.265 39.130 0.00 0.00 45.74 3.95
530 1884 4.574828 AGACATCCGATAAAATTGGAACGG 59.425 41.667 0.00 0.00 45.74 4.44
531 1885 4.266714 ACATCCGATAAAATTGGAACGGT 58.733 39.130 0.00 0.00 45.74 4.83
532 1886 5.430007 ACATCCGATAAAATTGGAACGGTA 58.570 37.500 0.00 0.00 45.74 4.02
533 1887 5.295045 ACATCCGATAAAATTGGAACGGTAC 59.705 40.000 0.00 0.00 45.74 3.34
534 1888 4.829968 TCCGATAAAATTGGAACGGTACA 58.170 39.130 0.00 0.00 39.91 2.90
535 1889 5.243981 TCCGATAAAATTGGAACGGTACAA 58.756 37.500 0.00 0.00 39.91 2.41
536 1890 5.704515 TCCGATAAAATTGGAACGGTACAAA 59.295 36.000 0.06 0.00 39.91 2.83
537 1891 6.025280 CCGATAAAATTGGAACGGTACAAAG 58.975 40.000 0.06 0.00 35.72 2.77
538 1892 6.128227 CCGATAAAATTGGAACGGTACAAAGA 60.128 38.462 0.06 0.00 35.72 2.52
539 1893 7.299586 CGATAAAATTGGAACGGTACAAAGAA 58.700 34.615 0.06 0.00 0.00 2.52
540 1894 7.480542 CGATAAAATTGGAACGGTACAAAGAAG 59.519 37.037 0.06 0.00 0.00 2.85
541 1895 6.702716 AAAATTGGAACGGTACAAAGAAGA 57.297 33.333 0.06 0.00 0.00 2.87
542 1896 6.894339 AAATTGGAACGGTACAAAGAAGAT 57.106 33.333 0.06 0.00 0.00 2.40
543 1897 6.894339 AATTGGAACGGTACAAAGAAGATT 57.106 33.333 0.06 0.00 0.00 2.40
544 1898 7.989416 AATTGGAACGGTACAAAGAAGATTA 57.011 32.000 0.06 0.00 0.00 1.75
545 1899 7.611213 ATTGGAACGGTACAAAGAAGATTAG 57.389 36.000 0.06 0.00 0.00 1.73
546 1900 4.933400 TGGAACGGTACAAAGAAGATTAGC 59.067 41.667 0.00 0.00 0.00 3.09
547 1901 4.933400 GGAACGGTACAAAGAAGATTAGCA 59.067 41.667 0.00 0.00 0.00 3.49
548 1902 5.585047 GGAACGGTACAAAGAAGATTAGCAT 59.415 40.000 0.00 0.00 0.00 3.79
549 1903 6.422776 AACGGTACAAAGAAGATTAGCATG 57.577 37.500 0.00 0.00 0.00 4.06
550 1904 4.876107 ACGGTACAAAGAAGATTAGCATGG 59.124 41.667 0.00 0.00 0.00 3.66
551 1905 4.260784 CGGTACAAAGAAGATTAGCATGGC 60.261 45.833 0.00 0.00 0.00 4.40
552 1906 4.036852 GGTACAAAGAAGATTAGCATGGCC 59.963 45.833 0.00 0.00 0.00 5.36
553 1907 3.700538 ACAAAGAAGATTAGCATGGCCA 58.299 40.909 8.56 8.56 0.00 5.36
554 1908 4.284178 ACAAAGAAGATTAGCATGGCCAT 58.716 39.130 14.09 14.09 0.00 4.40
555 1909 5.448654 ACAAAGAAGATTAGCATGGCCATA 58.551 37.500 20.30 2.40 0.00 2.74
556 1910 5.893255 ACAAAGAAGATTAGCATGGCCATAA 59.107 36.000 20.30 10.20 0.00 1.90
557 1911 6.380846 ACAAAGAAGATTAGCATGGCCATAAA 59.619 34.615 20.30 13.57 0.00 1.40
558 1912 7.093377 ACAAAGAAGATTAGCATGGCCATAAAA 60.093 33.333 20.30 13.19 0.00 1.52
559 1913 7.607615 AAGAAGATTAGCATGGCCATAAAAT 57.392 32.000 20.30 17.35 0.00 1.82
560 1914 7.607615 AGAAGATTAGCATGGCCATAAAATT 57.392 32.000 20.30 11.87 0.00 1.82
561 1915 7.439381 AGAAGATTAGCATGGCCATAAAATTG 58.561 34.615 20.30 7.79 0.00 2.32
562 1916 6.105397 AGATTAGCATGGCCATAAAATTGG 57.895 37.500 20.30 5.13 39.94 3.16
563 1917 5.840149 AGATTAGCATGGCCATAAAATTGGA 59.160 36.000 20.30 0.00 39.25 3.53
564 1918 5.946942 TTAGCATGGCCATAAAATTGGAA 57.053 34.783 20.30 1.57 39.25 3.53
565 1919 4.141233 AGCATGGCCATAAAATTGGAAC 57.859 40.909 20.30 0.00 39.25 3.62
566 1920 2.865551 GCATGGCCATAAAATTGGAACG 59.134 45.455 20.30 2.07 39.25 3.95
567 1921 3.456280 CATGGCCATAAAATTGGAACGG 58.544 45.455 20.30 0.00 39.25 4.44
568 1922 2.530701 TGGCCATAAAATTGGAACGGT 58.469 42.857 0.00 0.00 39.25 4.83
569 1923 3.698289 TGGCCATAAAATTGGAACGGTA 58.302 40.909 0.00 0.00 39.25 4.02
570 1924 3.444388 TGGCCATAAAATTGGAACGGTAC 59.556 43.478 0.00 0.00 39.25 3.34
571 1925 3.444388 GGCCATAAAATTGGAACGGTACA 59.556 43.478 0.00 0.00 39.25 2.90
572 1926 4.439563 GGCCATAAAATTGGAACGGTACAG 60.440 45.833 0.00 0.00 39.25 2.74
573 1927 4.396790 GCCATAAAATTGGAACGGTACAGA 59.603 41.667 0.00 0.00 39.25 3.41
574 1928 5.448632 GCCATAAAATTGGAACGGTACAGAG 60.449 44.000 0.00 0.00 39.25 3.35
575 1929 5.878116 CCATAAAATTGGAACGGTACAGAGA 59.122 40.000 0.00 0.00 39.25 3.10
576 1930 6.373216 CCATAAAATTGGAACGGTACAGAGAA 59.627 38.462 0.00 0.00 39.25 2.87
577 1931 5.941948 AAAATTGGAACGGTACAGAGAAG 57.058 39.130 0.00 0.00 0.00 2.85
578 1932 4.884668 AATTGGAACGGTACAGAGAAGA 57.115 40.909 0.00 0.00 0.00 2.87
579 1933 5.422214 AATTGGAACGGTACAGAGAAGAT 57.578 39.130 0.00 0.00 0.00 2.40
580 1934 4.884668 TTGGAACGGTACAGAGAAGATT 57.115 40.909 0.00 0.00 0.00 2.40
581 1935 5.988310 TTGGAACGGTACAGAGAAGATTA 57.012 39.130 0.00 0.00 0.00 1.75
582 1936 5.578005 TGGAACGGTACAGAGAAGATTAG 57.422 43.478 0.00 0.00 0.00 1.73
583 1937 4.142227 TGGAACGGTACAGAGAAGATTAGC 60.142 45.833 0.00 0.00 0.00 3.09
584 1938 4.142227 GGAACGGTACAGAGAAGATTAGCA 60.142 45.833 0.00 0.00 0.00 3.49
585 1939 5.452077 GGAACGGTACAGAGAAGATTAGCAT 60.452 44.000 0.00 0.00 0.00 3.79
586 1940 4.938080 ACGGTACAGAGAAGATTAGCATG 58.062 43.478 0.00 0.00 0.00 4.06
587 1941 4.202161 ACGGTACAGAGAAGATTAGCATGG 60.202 45.833 0.00 0.00 0.00 3.66
588 1942 4.061596 GGTACAGAGAAGATTAGCATGGC 58.938 47.826 0.00 0.00 0.00 4.40
589 1943 3.205784 ACAGAGAAGATTAGCATGGCC 57.794 47.619 0.00 0.00 0.00 5.36
590 1944 2.158696 ACAGAGAAGATTAGCATGGCCC 60.159 50.000 0.00 0.00 0.00 5.80
591 1945 1.423161 AGAGAAGATTAGCATGGCCCC 59.577 52.381 0.00 0.00 0.00 5.80
592 1946 1.423161 GAGAAGATTAGCATGGCCCCT 59.577 52.381 0.00 0.00 0.00 4.79
593 1947 1.144503 AGAAGATTAGCATGGCCCCTG 59.855 52.381 0.00 0.00 0.00 4.45
594 1948 0.468771 AAGATTAGCATGGCCCCTGC 60.469 55.000 17.40 17.40 39.97 4.85
595 1949 2.203394 ATTAGCATGGCCCCTGCG 60.203 61.111 18.59 0.00 44.38 5.18
608 1962 3.970721 CTGCGCAAGGATGACACA 58.029 55.556 13.05 0.00 36.74 3.72
609 1963 1.499056 CTGCGCAAGGATGACACAC 59.501 57.895 13.05 0.00 36.74 3.82
610 1964 1.227793 TGCGCAAGGATGACACACA 60.228 52.632 8.16 0.00 38.28 3.72
611 1965 0.817229 TGCGCAAGGATGACACACAA 60.817 50.000 8.16 0.00 38.28 3.33
612 1966 0.310543 GCGCAAGGATGACACACAAA 59.689 50.000 0.30 0.00 38.28 2.83
613 1967 1.268999 GCGCAAGGATGACACACAAAA 60.269 47.619 0.30 0.00 38.28 2.44
614 1968 2.797792 GCGCAAGGATGACACACAAAAA 60.798 45.455 0.30 0.00 38.28 1.94
665 2020 2.817839 GCAACCCCAGTTCCACTAACAT 60.818 50.000 0.00 0.00 40.83 2.71
668 2023 5.261216 CAACCCCAGTTCCACTAACATAAT 58.739 41.667 0.00 0.00 40.83 1.28
669 2024 6.419791 CAACCCCAGTTCCACTAACATAATA 58.580 40.000 0.00 0.00 40.83 0.98
673 2028 6.887545 CCCCAGTTCCACTAACATAATAAACA 59.112 38.462 0.00 0.00 40.83 2.83
674 2029 7.067008 CCCCAGTTCCACTAACATAATAAACAG 59.933 40.741 0.00 0.00 40.83 3.16
675 2030 7.610305 CCCAGTTCCACTAACATAATAAACAGT 59.390 37.037 0.00 0.00 40.83 3.55
676 2031 8.450964 CCAGTTCCACTAACATAATAAACAGTG 58.549 37.037 0.00 0.00 40.83 3.66
677 2032 8.999431 CAGTTCCACTAACATAATAAACAGTGT 58.001 33.333 0.00 0.00 40.83 3.55
678 2033 9.569122 AGTTCCACTAACATAATAAACAGTGTT 57.431 29.630 1.64 1.64 40.83 3.32
679 2034 9.821662 GTTCCACTAACATAATAAACAGTGTTC 57.178 33.333 9.40 0.00 38.05 3.18
680 2035 9.562408 TTCCACTAACATAATAAACAGTGTTCA 57.438 29.630 9.40 0.00 36.34 3.18
681 2036 9.214957 TCCACTAACATAATAAACAGTGTTCAG 57.785 33.333 9.40 0.00 36.34 3.02
682 2037 7.962918 CCACTAACATAATAAACAGTGTTCAGC 59.037 37.037 9.40 0.00 36.34 4.26
683 2038 8.503196 CACTAACATAATAAACAGTGTTCAGCA 58.497 33.333 9.40 0.00 36.34 4.41
707 2088 7.201688 GCAGTTCATGTACCCAAAAACAAAAAT 60.202 33.333 0.00 0.00 0.00 1.82
757 2140 2.178912 TAACCTCCTCTGTTTTGCCG 57.821 50.000 0.00 0.00 0.00 5.69
764 2147 3.280295 TCCTCTGTTTTGCCGTGTTTTA 58.720 40.909 0.00 0.00 0.00 1.52
792 2186 5.398122 GGTACAACATTCAACACGTGATTTG 59.602 40.000 25.01 17.21 35.70 2.32
849 2356 5.470098 CCCCAATCACATCCGAGTATAAAAG 59.530 44.000 0.00 0.00 0.00 2.27
853 2364 5.925506 TCACATCCGAGTATAAAAGTGGA 57.074 39.130 0.00 0.00 0.00 4.02
902 2423 0.033208 AACCCAATCACCATCGCCAT 60.033 50.000 0.00 0.00 0.00 4.40
903 2424 0.466189 ACCCAATCACCATCGCCATC 60.466 55.000 0.00 0.00 0.00 3.51
904 2425 1.509644 CCCAATCACCATCGCCATCG 61.510 60.000 0.00 0.00 0.00 3.84
905 2426 1.280746 CAATCACCATCGCCATCGC 59.719 57.895 0.00 0.00 35.26 4.58
1315 3656 1.136891 GCAAAGCAGTGGGTGAGTTTT 59.863 47.619 0.00 0.00 0.00 2.43
1432 3775 0.690762 GAGTGGGGCAACAGGTAGAA 59.309 55.000 0.00 0.00 39.74 2.10
1452 3795 8.827677 GGTAGAAATGATAGTGTGGTGTTTATC 58.172 37.037 0.00 0.00 0.00 1.75
1453 3796 7.539712 AGAAATGATAGTGTGGTGTTTATCG 57.460 36.000 0.00 0.00 0.00 2.92
1561 3929 0.104672 TGGACTCCCTTCCAAGACCA 60.105 55.000 0.00 0.00 43.04 4.02
1586 3954 1.019673 CAGATTGGCCCATTCACTCG 58.980 55.000 0.00 0.00 0.00 4.18
1712 4100 8.425577 AGGAAGATACAATCATAACAAGTTCG 57.574 34.615 0.00 0.00 0.00 3.95
1714 4102 7.011482 GGAAGATACAATCATAACAAGTTCGCT 59.989 37.037 0.00 0.00 0.00 4.93
1723 4111 0.105964 ACAAGTTCGCTGCTGTACCA 59.894 50.000 0.00 0.00 0.00 3.25
1774 4162 4.830046 TGCTATTCTCCTGATAGGACTGAC 59.170 45.833 0.00 0.00 40.06 3.51
1908 4335 0.674534 ATCGGGAGTATTCGAGGTGC 59.325 55.000 0.00 0.00 38.83 5.01
1967 4396 5.695851 ACTAAAACCTGAACTTCTGCATG 57.304 39.130 0.00 0.00 0.00 4.06
2236 4672 1.763546 TTGGCGATGTCAGTGTCCCA 61.764 55.000 0.00 0.00 0.00 4.37
2257 4693 5.944007 CCCAAAGTTAGTTGCTTATACAGGT 59.056 40.000 0.00 0.00 0.00 4.00
2308 4749 9.487442 TGTAATTAGCTTTTATTCCCCATTTCT 57.513 29.630 0.00 0.00 0.00 2.52
2326 4947 7.199766 CCATTTCTTGTGCACTTTAAACTGTA 58.800 34.615 19.41 0.00 0.00 2.74
2353 4975 6.433093 GGTACACTAAAACAAGGGAATCACAT 59.567 38.462 0.00 0.00 0.00 3.21
2377 5001 9.254133 CATTAGTAGAATGTAACACATCTGGAG 57.746 37.037 1.32 0.00 37.97 3.86
2387 5011 2.232452 ACACATCTGGAGTCGAAAGAGG 59.768 50.000 0.00 0.00 43.49 3.69
2403 5033 9.367444 GTCGAAAGAGGAGATAATTTAAGAACA 57.633 33.333 0.00 0.00 43.49 3.18
2409 5045 8.951243 AGAGGAGATAATTTAAGAACAACTTGC 58.049 33.333 0.00 0.00 39.38 4.01
2451 5091 5.901413 ATCTACCATCAACCATCTCACAT 57.099 39.130 0.00 0.00 0.00 3.21
2565 5225 4.219725 ACTTTGGACAATTTAACATCCCGG 59.780 41.667 0.00 0.00 0.00 5.73
2645 5312 4.755266 TGGTAAGCCTATGGAAGAAGTC 57.245 45.455 0.00 0.00 35.27 3.01
2660 5328 5.238868 GGAAGAAGTCTTTTGGTTACCTGTC 59.761 44.000 2.07 0.00 36.11 3.51
2701 5369 6.374417 AATAGCAGAAGGACTTAAGGTGAA 57.626 37.500 7.53 0.00 0.00 3.18
2703 5371 5.048846 AGCAGAAGGACTTAAGGTGAAAA 57.951 39.130 7.53 0.00 0.00 2.29
2732 5401 7.875041 ACACTATATTTCAGCAGTATAGCAAGG 59.125 37.037 0.00 0.00 33.66 3.61
2738 5410 2.432146 CAGCAGTATAGCAAGGACAGGA 59.568 50.000 0.00 0.00 36.85 3.86
2745 5417 6.587990 CAGTATAGCAAGGACAGGATTATTCG 59.412 42.308 0.00 0.00 0.00 3.34
2749 5423 4.406003 AGCAAGGACAGGATTATTCGTAGT 59.594 41.667 0.00 0.00 0.00 2.73
2750 5424 4.508124 GCAAGGACAGGATTATTCGTAGTG 59.492 45.833 0.00 0.00 0.00 2.74
2752 5426 5.517322 AGGACAGGATTATTCGTAGTGAC 57.483 43.478 0.00 0.00 0.00 3.67
2763 5437 2.453521 TCGTAGTGACCACAGCCTAAT 58.546 47.619 2.78 0.00 0.00 1.73
2771 5445 5.247564 AGTGACCACAGCCTAATACTTGTAA 59.752 40.000 2.78 0.00 0.00 2.41
2782 5460 9.255029 AGCCTAATACTTGTAATGTGGAATTTT 57.745 29.630 0.00 0.00 0.00 1.82
3384 6095 4.036352 GTGATCCTTAGCTTCGAAGTACG 58.964 47.826 25.24 13.53 44.09 3.67
3393 6105 4.053295 AGCTTCGAAGTACGCAAAACTTA 58.947 39.130 25.24 0.00 42.26 2.24
3500 6212 6.520272 TGTGGGAACAAAATGGTGAATAAAG 58.480 36.000 0.00 0.00 46.06 1.85
3597 6328 7.665559 TCTCAAGTATGCAAAATGGTAAGACTT 59.334 33.333 0.00 0.00 0.00 3.01
3599 6330 9.290988 TCAAGTATGCAAAATGGTAAGACTTAA 57.709 29.630 0.00 0.00 0.00 1.85
3685 6418 5.852282 AAATAGCAGTGTTTTCTGTGGTT 57.148 34.783 0.00 0.00 37.70 3.67
3711 6444 5.156355 CAACTTCCATGTGCACTATTTCAC 58.844 41.667 19.41 0.00 0.00 3.18
3816 6549 6.556495 AGAAGGTTAGATGATCATAAGAGGCA 59.444 38.462 8.54 0.00 0.00 4.75
3843 6576 1.614903 TGCCTGGTGCTTCAGAATTTG 59.385 47.619 8.16 0.00 42.00 2.32
3848 6581 1.203287 GGTGCTTCAGAATTTGAGCCC 59.797 52.381 0.00 0.00 37.07 5.19
3855 6588 2.097036 CAGAATTTGAGCCCTGATGCA 58.903 47.619 0.00 0.00 0.00 3.96
3883 6616 1.219393 GGCACCTGCTAGACCTGTC 59.781 63.158 0.00 0.00 41.70 3.51
3920 6666 7.800380 GCAAGGTAATTCTGATCATCAATAACG 59.200 37.037 0.00 0.00 0.00 3.18
3942 6688 8.833231 AACGAAAAATCATTTCTAGAGAGTGA 57.167 30.769 0.00 6.34 0.00 3.41
3944 6690 8.877779 ACGAAAAATCATTTCTAGAGAGTGATG 58.122 33.333 13.84 6.58 34.05 3.07
4057 6809 5.793030 AGGCTTACTTGTATAGTAGCTGG 57.207 43.478 0.00 0.00 40.35 4.85
4058 6810 5.455872 AGGCTTACTTGTATAGTAGCTGGA 58.544 41.667 0.00 0.00 40.35 3.86
4060 6812 5.068723 GGCTTACTTGTATAGTAGCTGGACA 59.931 44.000 0.00 0.00 40.35 4.02
4276 7028 2.714250 TCTGAATTGTTGTACCAGGGGT 59.286 45.455 0.00 0.00 40.16 4.95
4277 7029 3.139397 TCTGAATTGTTGTACCAGGGGTT 59.861 43.478 0.00 0.00 37.09 4.11
4278 7030 3.226777 TGAATTGTTGTACCAGGGGTTG 58.773 45.455 0.00 0.00 37.09 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.194640 TGCAAACATGAGAGCTCCTAATC 58.805 43.478 10.93 1.45 0.00 1.75
1 2 4.197750 CTGCAAACATGAGAGCTCCTAAT 58.802 43.478 10.93 0.00 0.00 1.73
11 12 3.278367 CAGTTGGACTGCAAACATGAG 57.722 47.619 0.00 0.00 39.62 2.90
74 75 1.767759 GGATCCTTCCACACCCAATG 58.232 55.000 3.84 0.00 42.12 2.82
92 93 6.582295 CAGGAAAGAAACAAATACGTGAATGG 59.418 38.462 0.00 0.00 0.00 3.16
152 153 6.840527 ACATGATGGTGGACACATAATCATA 58.159 36.000 18.64 2.87 38.70 2.15
153 154 5.698104 ACATGATGGTGGACACATAATCAT 58.302 37.500 15.69 15.69 40.08 2.45
246 247 4.149922 CGCATTCATTCATCCATGCATTTC 59.850 41.667 0.00 0.00 41.86 2.17
250 251 2.292292 CTCGCATTCATTCATCCATGCA 59.708 45.455 0.00 0.00 41.86 3.96
251 252 2.551032 TCTCGCATTCATTCATCCATGC 59.449 45.455 0.00 0.00 38.96 4.06
252 253 3.363673 CGTCTCGCATTCATTCATCCATG 60.364 47.826 0.00 0.00 0.00 3.66
253 254 2.804527 CGTCTCGCATTCATTCATCCAT 59.195 45.455 0.00 0.00 0.00 3.41
254 255 2.159114 TCGTCTCGCATTCATTCATCCA 60.159 45.455 0.00 0.00 0.00 3.41
255 256 2.473816 TCGTCTCGCATTCATTCATCC 58.526 47.619 0.00 0.00 0.00 3.51
256 257 3.120752 CCATCGTCTCGCATTCATTCATC 60.121 47.826 0.00 0.00 0.00 2.92
257 258 2.804527 CCATCGTCTCGCATTCATTCAT 59.195 45.455 0.00 0.00 0.00 2.57
258 259 2.204237 CCATCGTCTCGCATTCATTCA 58.796 47.619 0.00 0.00 0.00 2.57
259 260 1.528586 CCCATCGTCTCGCATTCATTC 59.471 52.381 0.00 0.00 0.00 2.67
260 261 1.586422 CCCATCGTCTCGCATTCATT 58.414 50.000 0.00 0.00 0.00 2.57
261 262 0.882042 GCCCATCGTCTCGCATTCAT 60.882 55.000 0.00 0.00 0.00 2.57
273 286 2.237751 CGCGTAGGAAAGCCCATCG 61.238 63.158 0.00 0.00 37.41 3.84
324 337 4.287585 ACATGCCTAAACTACACTTACCCA 59.712 41.667 0.00 0.00 0.00 4.51
355 372 4.772886 ATTAATTTCGCCACCTACCTCT 57.227 40.909 0.00 0.00 0.00 3.69
356 373 6.930667 TTTATTAATTTCGCCACCTACCTC 57.069 37.500 0.00 0.00 0.00 3.85
367 384 8.402472 TCTACCCTGTGCATTTTATTAATTTCG 58.598 33.333 0.00 0.00 0.00 3.46
398 415 3.389983 TGTTTATATAGAAGCCGGGCTGT 59.610 43.478 24.63 15.71 39.62 4.40
400 417 3.389983 TGTGTTTATATAGAAGCCGGGCT 59.610 43.478 17.69 17.69 42.56 5.19
426 443 4.336433 AGTGAAACAGAATGGCGGAATATG 59.664 41.667 0.00 0.00 43.62 1.78
433 450 4.944962 TGATAAGTGAAACAGAATGGCG 57.055 40.909 0.00 0.00 43.62 5.69
434 451 6.441093 TCATGATAAGTGAAACAGAATGGC 57.559 37.500 0.00 0.00 43.62 4.40
493 1847 4.870426 TCGGATGTCTTGCTGAAACTAATC 59.130 41.667 0.00 0.00 0.00 1.75
505 1859 5.965334 CGTTCCAATTTTATCGGATGTCTTG 59.035 40.000 0.00 0.03 0.00 3.02
506 1860 5.065988 CCGTTCCAATTTTATCGGATGTCTT 59.934 40.000 0.00 0.00 40.29 3.01
507 1861 4.574828 CCGTTCCAATTTTATCGGATGTCT 59.425 41.667 0.00 0.00 40.29 3.41
508 1862 4.334481 ACCGTTCCAATTTTATCGGATGTC 59.666 41.667 13.36 0.00 40.90 3.06
509 1863 4.266714 ACCGTTCCAATTTTATCGGATGT 58.733 39.130 13.36 0.00 40.90 3.06
510 1864 4.893424 ACCGTTCCAATTTTATCGGATG 57.107 40.909 13.36 0.00 40.90 3.51
511 1865 5.430007 TGTACCGTTCCAATTTTATCGGAT 58.570 37.500 13.36 0.00 40.90 4.18
512 1866 4.829968 TGTACCGTTCCAATTTTATCGGA 58.170 39.130 13.36 0.00 40.90 4.55
513 1867 5.548706 TTGTACCGTTCCAATTTTATCGG 57.451 39.130 0.00 0.00 42.94 4.18
514 1868 6.833839 TCTTTGTACCGTTCCAATTTTATCG 58.166 36.000 0.00 0.00 0.00 2.92
515 1869 8.508875 TCTTCTTTGTACCGTTCCAATTTTATC 58.491 33.333 0.00 0.00 0.00 1.75
516 1870 8.398878 TCTTCTTTGTACCGTTCCAATTTTAT 57.601 30.769 0.00 0.00 0.00 1.40
517 1871 7.804843 TCTTCTTTGTACCGTTCCAATTTTA 57.195 32.000 0.00 0.00 0.00 1.52
518 1872 6.702716 TCTTCTTTGTACCGTTCCAATTTT 57.297 33.333 0.00 0.00 0.00 1.82
519 1873 6.894339 ATCTTCTTTGTACCGTTCCAATTT 57.106 33.333 0.00 0.00 0.00 1.82
520 1874 6.894339 AATCTTCTTTGTACCGTTCCAATT 57.106 33.333 0.00 0.00 0.00 2.32
521 1875 6.093633 GCTAATCTTCTTTGTACCGTTCCAAT 59.906 38.462 0.00 0.00 0.00 3.16
522 1876 5.410439 GCTAATCTTCTTTGTACCGTTCCAA 59.590 40.000 0.00 0.00 0.00 3.53
523 1877 4.933400 GCTAATCTTCTTTGTACCGTTCCA 59.067 41.667 0.00 0.00 0.00 3.53
524 1878 4.933400 TGCTAATCTTCTTTGTACCGTTCC 59.067 41.667 0.00 0.00 0.00 3.62
525 1879 6.456988 CCATGCTAATCTTCTTTGTACCGTTC 60.457 42.308 0.00 0.00 0.00 3.95
526 1880 5.354234 CCATGCTAATCTTCTTTGTACCGTT 59.646 40.000 0.00 0.00 0.00 4.44
527 1881 4.876107 CCATGCTAATCTTCTTTGTACCGT 59.124 41.667 0.00 0.00 0.00 4.83
528 1882 4.260784 GCCATGCTAATCTTCTTTGTACCG 60.261 45.833 0.00 0.00 0.00 4.02
529 1883 4.036852 GGCCATGCTAATCTTCTTTGTACC 59.963 45.833 0.00 0.00 0.00 3.34
530 1884 4.640201 TGGCCATGCTAATCTTCTTTGTAC 59.360 41.667 0.00 0.00 0.00 2.90
531 1885 4.854173 TGGCCATGCTAATCTTCTTTGTA 58.146 39.130 0.00 0.00 0.00 2.41
532 1886 3.700538 TGGCCATGCTAATCTTCTTTGT 58.299 40.909 0.00 0.00 0.00 2.83
533 1887 4.931661 ATGGCCATGCTAATCTTCTTTG 57.068 40.909 20.04 0.00 0.00 2.77
534 1888 7.422465 TTTTATGGCCATGCTAATCTTCTTT 57.578 32.000 29.04 0.00 0.00 2.52
535 1889 7.607615 ATTTTATGGCCATGCTAATCTTCTT 57.392 32.000 29.04 0.00 0.00 2.52
536 1890 7.439381 CAATTTTATGGCCATGCTAATCTTCT 58.561 34.615 29.04 6.88 0.00 2.85
537 1891 6.647895 CCAATTTTATGGCCATGCTAATCTTC 59.352 38.462 29.04 0.00 32.78 2.87
538 1892 6.327104 TCCAATTTTATGGCCATGCTAATCTT 59.673 34.615 29.04 12.25 40.46 2.40
539 1893 5.840149 TCCAATTTTATGGCCATGCTAATCT 59.160 36.000 29.04 1.85 40.46 2.40
540 1894 6.100404 TCCAATTTTATGGCCATGCTAATC 57.900 37.500 29.04 0.00 40.46 1.75
541 1895 6.290605 GTTCCAATTTTATGGCCATGCTAAT 58.709 36.000 29.04 19.57 40.46 1.73
542 1896 5.669477 GTTCCAATTTTATGGCCATGCTAA 58.331 37.500 29.04 18.24 40.46 3.09
543 1897 4.202101 CGTTCCAATTTTATGGCCATGCTA 60.202 41.667 29.04 12.89 40.46 3.49
544 1898 3.430651 CGTTCCAATTTTATGGCCATGCT 60.431 43.478 29.04 5.35 40.46 3.79
545 1899 2.865551 CGTTCCAATTTTATGGCCATGC 59.134 45.455 29.04 0.00 40.46 4.06
546 1900 3.118811 ACCGTTCCAATTTTATGGCCATG 60.119 43.478 29.04 11.85 40.46 3.66
547 1901 3.103742 ACCGTTCCAATTTTATGGCCAT 58.896 40.909 24.45 24.45 40.46 4.40
548 1902 2.530701 ACCGTTCCAATTTTATGGCCA 58.469 42.857 8.56 8.56 40.46 5.36
549 1903 3.444388 TGTACCGTTCCAATTTTATGGCC 59.556 43.478 0.00 0.00 40.46 5.36
550 1904 4.396790 TCTGTACCGTTCCAATTTTATGGC 59.603 41.667 0.00 0.00 40.46 4.40
551 1905 5.878116 TCTCTGTACCGTTCCAATTTTATGG 59.122 40.000 0.00 0.00 42.12 2.74
552 1906 6.978343 TCTCTGTACCGTTCCAATTTTATG 57.022 37.500 0.00 0.00 0.00 1.90
553 1907 7.391620 TCTTCTCTGTACCGTTCCAATTTTAT 58.608 34.615 0.00 0.00 0.00 1.40
554 1908 6.761312 TCTTCTCTGTACCGTTCCAATTTTA 58.239 36.000 0.00 0.00 0.00 1.52
555 1909 5.617252 TCTTCTCTGTACCGTTCCAATTTT 58.383 37.500 0.00 0.00 0.00 1.82
556 1910 5.223449 TCTTCTCTGTACCGTTCCAATTT 57.777 39.130 0.00 0.00 0.00 1.82
557 1911 4.884668 TCTTCTCTGTACCGTTCCAATT 57.115 40.909 0.00 0.00 0.00 2.32
558 1912 5.422214 AATCTTCTCTGTACCGTTCCAAT 57.578 39.130 0.00 0.00 0.00 3.16
559 1913 4.884668 AATCTTCTCTGTACCGTTCCAA 57.115 40.909 0.00 0.00 0.00 3.53
560 1914 4.142227 GCTAATCTTCTCTGTACCGTTCCA 60.142 45.833 0.00 0.00 0.00 3.53
561 1915 4.142227 TGCTAATCTTCTCTGTACCGTTCC 60.142 45.833 0.00 0.00 0.00 3.62
562 1916 4.995124 TGCTAATCTTCTCTGTACCGTTC 58.005 43.478 0.00 0.00 0.00 3.95
563 1917 5.352284 CATGCTAATCTTCTCTGTACCGTT 58.648 41.667 0.00 0.00 0.00 4.44
564 1918 4.202161 CCATGCTAATCTTCTCTGTACCGT 60.202 45.833 0.00 0.00 0.00 4.83
565 1919 4.302455 CCATGCTAATCTTCTCTGTACCG 58.698 47.826 0.00 0.00 0.00 4.02
566 1920 4.061596 GCCATGCTAATCTTCTCTGTACC 58.938 47.826 0.00 0.00 0.00 3.34
567 1921 4.061596 GGCCATGCTAATCTTCTCTGTAC 58.938 47.826 0.00 0.00 0.00 2.90
568 1922 3.071602 GGGCCATGCTAATCTTCTCTGTA 59.928 47.826 4.39 0.00 0.00 2.74
569 1923 2.158696 GGGCCATGCTAATCTTCTCTGT 60.159 50.000 4.39 0.00 0.00 3.41
570 1924 2.502295 GGGCCATGCTAATCTTCTCTG 58.498 52.381 4.39 0.00 0.00 3.35
571 1925 1.423161 GGGGCCATGCTAATCTTCTCT 59.577 52.381 4.39 0.00 0.00 3.10
572 1926 1.423161 AGGGGCCATGCTAATCTTCTC 59.577 52.381 4.39 0.00 0.00 2.87
573 1927 1.144503 CAGGGGCCATGCTAATCTTCT 59.855 52.381 4.75 0.00 0.00 2.85
574 1928 1.613836 CAGGGGCCATGCTAATCTTC 58.386 55.000 4.75 0.00 0.00 2.87
575 1929 0.468771 GCAGGGGCCATGCTAATCTT 60.469 55.000 33.99 0.00 40.59 2.40
576 1930 1.152368 GCAGGGGCCATGCTAATCT 59.848 57.895 33.99 1.91 40.59 2.40
577 1931 2.263741 CGCAGGGGCCATGCTAATC 61.264 63.158 36.49 11.88 41.61 1.75
578 1932 2.203394 CGCAGGGGCCATGCTAAT 60.203 61.111 36.49 0.00 41.61 1.73
587 1941 4.802051 TCATCCTTGCGCAGGGGC 62.802 66.667 34.94 0.86 44.12 5.80
588 1942 2.825836 GTCATCCTTGCGCAGGGG 60.826 66.667 34.94 27.37 44.12 4.79
589 1943 2.046023 TGTCATCCTTGCGCAGGG 60.046 61.111 31.27 31.27 44.12 4.45
590 1944 1.672030 TGTGTCATCCTTGCGCAGG 60.672 57.895 13.36 13.36 45.64 4.85
591 1945 1.229975 TGTGTGTCATCCTTGCGCAG 61.230 55.000 11.31 4.92 0.00 5.18
592 1946 0.817229 TTGTGTGTCATCCTTGCGCA 60.817 50.000 5.66 5.66 0.00 6.09
593 1947 0.310543 TTTGTGTGTCATCCTTGCGC 59.689 50.000 0.00 0.00 0.00 6.09
594 1948 2.772568 TTTTGTGTGTCATCCTTGCG 57.227 45.000 0.00 0.00 0.00 4.85
639 1993 1.152333 GGAACTGGGGTTGCCCTTT 60.152 57.895 4.02 0.00 44.66 3.11
665 2020 7.228507 ACATGAACTGCTGAACACTGTTTATTA 59.771 33.333 0.00 0.00 30.47 0.98
668 2023 4.881273 ACATGAACTGCTGAACACTGTTTA 59.119 37.500 0.00 0.00 30.47 2.01
669 2024 3.696051 ACATGAACTGCTGAACACTGTTT 59.304 39.130 0.00 0.00 30.47 2.83
673 2028 3.403038 GGTACATGAACTGCTGAACACT 58.597 45.455 0.00 0.00 0.00 3.55
674 2029 2.484264 GGGTACATGAACTGCTGAACAC 59.516 50.000 0.00 0.00 0.00 3.32
675 2030 2.105649 TGGGTACATGAACTGCTGAACA 59.894 45.455 0.00 0.00 0.00 3.18
676 2031 2.778299 TGGGTACATGAACTGCTGAAC 58.222 47.619 0.00 0.00 0.00 3.18
677 2032 3.500448 TTGGGTACATGAACTGCTGAA 57.500 42.857 0.00 0.00 0.00 3.02
678 2033 3.500448 TTTGGGTACATGAACTGCTGA 57.500 42.857 0.00 0.00 0.00 4.26
679 2034 4.202101 TGTTTTTGGGTACATGAACTGCTG 60.202 41.667 0.00 0.00 0.00 4.41
680 2035 3.957497 TGTTTTTGGGTACATGAACTGCT 59.043 39.130 0.00 0.00 0.00 4.24
681 2036 4.314740 TGTTTTTGGGTACATGAACTGC 57.685 40.909 0.00 0.00 0.00 4.40
682 2037 7.602517 TTTTTGTTTTTGGGTACATGAACTG 57.397 32.000 0.00 0.00 0.00 3.16
683 2038 9.892130 TTATTTTTGTTTTTGGGTACATGAACT 57.108 25.926 0.00 0.00 0.00 3.01
725 2106 6.993902 ACAGAGGAGGTTATTCGTTGTTTTTA 59.006 34.615 0.00 0.00 0.00 1.52
728 2109 4.969484 ACAGAGGAGGTTATTCGTTGTTT 58.031 39.130 0.00 0.00 0.00 2.83
729 2110 4.618920 ACAGAGGAGGTTATTCGTTGTT 57.381 40.909 0.00 0.00 0.00 2.83
730 2111 4.618920 AACAGAGGAGGTTATTCGTTGT 57.381 40.909 0.00 0.00 0.00 3.32
731 2112 5.689819 CAAAACAGAGGAGGTTATTCGTTG 58.310 41.667 0.00 0.00 0.00 4.10
732 2113 4.215613 GCAAAACAGAGGAGGTTATTCGTT 59.784 41.667 0.00 0.00 0.00 3.85
733 2114 3.751698 GCAAAACAGAGGAGGTTATTCGT 59.248 43.478 0.00 0.00 0.00 3.85
734 2115 3.127030 GGCAAAACAGAGGAGGTTATTCG 59.873 47.826 0.00 0.00 0.00 3.34
735 2116 3.127030 CGGCAAAACAGAGGAGGTTATTC 59.873 47.826 0.00 0.00 0.00 1.75
736 2117 3.081804 CGGCAAAACAGAGGAGGTTATT 58.918 45.455 0.00 0.00 0.00 1.40
737 2118 2.039879 ACGGCAAAACAGAGGAGGTTAT 59.960 45.455 0.00 0.00 0.00 1.89
738 2119 1.418637 ACGGCAAAACAGAGGAGGTTA 59.581 47.619 0.00 0.00 0.00 2.85
739 2120 0.182775 ACGGCAAAACAGAGGAGGTT 59.817 50.000 0.00 0.00 0.00 3.50
740 2121 0.535102 CACGGCAAAACAGAGGAGGT 60.535 55.000 0.00 0.00 0.00 3.85
757 2140 4.275443 TGAATGTTGTACCGGGTAAAACAC 59.725 41.667 34.31 25.53 45.29 3.32
764 2147 2.223745 GTGTTGAATGTTGTACCGGGT 58.776 47.619 6.32 4.46 0.00 5.28
792 2186 1.187567 AGGATTTGTGCCACCAAGCC 61.188 55.000 7.81 7.81 0.00 4.35
803 2197 4.081198 GGATGTCTCTGTCAGAGGATTTGT 60.081 45.833 26.16 9.60 42.54 2.83
849 2356 1.639298 GGTGATGAGCGTGCTTCCAC 61.639 60.000 0.00 4.94 38.62 4.02
853 2364 0.322975 AGAAGGTGATGAGCGTGCTT 59.677 50.000 0.00 0.00 0.00 3.91
905 2426 4.351938 TCTGTGGTCCGCGAACCG 62.352 66.667 10.84 0.00 42.62 4.44
906 2427 2.737376 GTCTGTGGTCCGCGAACC 60.737 66.667 7.94 7.94 39.94 3.62
907 2428 2.737376 GGTCTGTGGTCCGCGAAC 60.737 66.667 8.23 0.00 0.00 3.95
908 2429 3.220999 CTGGTCTGTGGTCCGCGAA 62.221 63.158 8.23 0.00 0.00 4.70
929 2450 4.210331 AGATGGGGCAGTTTAATTAGCTG 58.790 43.478 0.00 12.20 0.00 4.24
1146 3480 0.094216 CGACGTACGACATGACGAGT 59.906 55.000 24.41 18.21 45.77 4.18
1315 3656 4.280677 CCAAAAAGTCAACTAGGAATGCCA 59.719 41.667 0.00 0.00 36.29 4.92
1432 3775 6.640518 AGTCGATAAACACCACACTATCATT 58.359 36.000 0.00 0.00 0.00 2.57
1452 3795 5.582269 TCAGGCATCTCTAAATTTCAAGTCG 59.418 40.000 0.00 0.00 0.00 4.18
1453 3796 6.992063 TCAGGCATCTCTAAATTTCAAGTC 57.008 37.500 0.00 0.00 0.00 3.01
1561 3929 2.037144 GAATGGGCCAATCTGCATTCT 58.963 47.619 11.89 0.00 28.46 2.40
1586 3954 6.405842 CCCTTTCCATAGCTGTTATCCAAAAC 60.406 42.308 0.00 0.00 0.00 2.43
1674 4061 9.794685 GATTGTATCTTCCTTTTCCATTTTCTC 57.205 33.333 0.00 0.00 0.00 2.87
1774 4162 1.685517 TCATGGAGCTCGAATGAGAGG 59.314 52.381 20.87 2.53 45.57 3.69
1784 4172 6.578023 ACTGAAATACTTAGTCATGGAGCTC 58.422 40.000 4.71 4.71 0.00 4.09
1822 4215 7.333528 TGAGGCAATTGGAAGATAAATACAC 57.666 36.000 7.72 0.00 0.00 2.90
1837 4230 3.873952 GCGAGACTATTCTTGAGGCAATT 59.126 43.478 1.55 0.00 35.41 2.32
1840 4233 1.137086 GGCGAGACTATTCTTGAGGCA 59.863 52.381 1.55 0.00 35.41 4.75
1908 4335 6.364976 TCCTGTCAATGCGTATATAACATTCG 59.635 38.462 8.58 0.00 31.82 3.34
1967 4396 5.509840 CCTCCATATAACAGCAGGAGTGTAC 60.510 48.000 0.00 0.00 43.37 2.90
2131 4567 4.281182 ACATCGAGGAGAGTTTGTACAGTT 59.719 41.667 3.06 0.00 0.00 3.16
2236 4672 6.238648 AGCACCTGTATAAGCAACTAACTTT 58.761 36.000 0.00 0.00 0.00 2.66
2257 4693 1.985159 AGTACCTTCCATGTCCAAGCA 59.015 47.619 0.00 0.00 0.00 3.91
2308 4749 6.542735 TGTACCATACAGTTTAAAGTGCACAA 59.457 34.615 21.04 1.11 34.06 3.33
2326 4947 6.433093 GTGATTCCCTTGTTTTAGTGTACCAT 59.567 38.462 0.00 0.00 0.00 3.55
2353 4975 8.362464 ACTCCAGATGTGTTACATTCTACTAA 57.638 34.615 0.00 0.00 39.27 2.24
2377 5001 9.367444 TGTTCTTAAATTATCTCCTCTTTCGAC 57.633 33.333 0.00 0.00 0.00 4.20
2387 5011 9.860898 AATGGCAAGTTGTTCTTAAATTATCTC 57.139 29.630 4.48 0.00 34.66 2.75
2431 5071 4.774124 ACATGTGAGATGGTTGATGGTAG 58.226 43.478 0.00 0.00 0.00 3.18
2451 5091 5.983720 GTCTTGTTAAGTAGTGAGCTCAACA 59.016 40.000 20.19 14.43 0.00 3.33
2457 5097 5.164954 CAGAGGTCTTGTTAAGTAGTGAGC 58.835 45.833 0.00 0.00 0.00 4.26
2565 5225 1.494960 AGCAGGTTCTCTCCTCCATC 58.505 55.000 0.00 0.00 35.37 3.51
2618 5278 4.534500 TCTTCCATAGGCTTACCAACTGAA 59.466 41.667 0.00 0.00 39.06 3.02
2645 5312 3.724374 TGAGTCGACAGGTAACCAAAAG 58.276 45.455 19.50 0.00 37.17 2.27
2660 5328 3.837213 ATTTTGAACCATGCTGAGTCG 57.163 42.857 0.00 0.00 0.00 4.18
2732 5401 5.041940 GTGGTCACTACGAATAATCCTGTC 58.958 45.833 0.00 0.00 0.00 3.51
2738 5410 3.451178 AGGCTGTGGTCACTACGAATAAT 59.549 43.478 2.66 0.00 0.00 1.28
2745 5417 5.109903 CAAGTATTAGGCTGTGGTCACTAC 58.890 45.833 0.00 0.00 0.00 2.73
2749 5423 5.748670 TTACAAGTATTAGGCTGTGGTCA 57.251 39.130 0.00 0.00 0.00 4.02
2750 5424 6.037172 CACATTACAAGTATTAGGCTGTGGTC 59.963 42.308 0.00 0.00 0.00 4.02
2752 5426 5.296780 CCACATTACAAGTATTAGGCTGTGG 59.703 44.000 0.00 3.75 43.43 4.17
2763 5437 9.357161 ACCTACAAAAATTCCACATTACAAGTA 57.643 29.630 0.00 0.00 0.00 2.24
2771 5445 5.838521 AGGTTGACCTACAAAAATTCCACAT 59.161 36.000 0.00 0.00 46.48 3.21
3077 5778 5.066505 AGGAGATGTTGTTGTCTGTTGAAAC 59.933 40.000 0.00 0.00 0.00 2.78
3384 6095 9.516314 ACTTAATTCTTCTGTTGTAAGTTTTGC 57.484 29.630 0.00 0.00 29.71 3.68
3393 6105 9.052759 ACGTTGAATACTTAATTCTTCTGTTGT 57.947 29.630 0.00 0.00 43.83 3.32
3478 6190 5.841237 TCCTTTATTCACCATTTTGTTCCCA 59.159 36.000 0.00 0.00 0.00 4.37
3500 6212 4.642429 AGGACTGTAACAACATTCTGTCC 58.358 43.478 10.54 10.54 43.93 4.02
3599 6330 9.893305 GCAAACTGTTGATAACTAATTAACACT 57.107 29.630 0.00 0.00 38.69 3.55
3685 6418 6.488344 TGAAATAGTGCACATGGAAGTTGTTA 59.512 34.615 21.04 0.00 0.00 2.41
3843 6576 4.427312 CTTTTGTATTTGCATCAGGGCTC 58.573 43.478 0.00 0.00 34.04 4.70
3848 6581 3.928375 GGTGCCTTTTGTATTTGCATCAG 59.072 43.478 0.00 0.00 33.35 2.90
3855 6588 4.459337 GTCTAGCAGGTGCCTTTTGTATTT 59.541 41.667 0.00 0.00 43.38 1.40
3883 6616 5.463061 CAGAATTACCTTGCCACACTTTTTG 59.537 40.000 0.00 0.00 0.00 2.44
3920 6666 9.985318 CACATCACTCTCTAGAAATGATTTTTC 57.015 33.333 9.33 0.00 31.37 2.29
4057 6809 9.912634 TGGATTTTGAGATGATAAAACTTTGTC 57.087 29.630 0.00 0.00 0.00 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.