Multiple sequence alignment - TraesCS6A01G018500

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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 TraesCS6A01G018500 chr6A 100.000 5689 0 0 1 5689 9046661 9040973 0.000000e+00 10506.0
1 TraesCS6A01G018500 chr6A 93.574 249 16 0 5210 5458 167492823 167492575 6.960000e-99 372.0
2 TraesCS6A01G018500 chr6A 92.667 150 7 3 5539 5688 167492552 167492407 4.470000e-51 213.0
3 TraesCS6A01G018500 chr6D 93.711 4134 164 46 286 4377 8796473 8800552 0.000000e+00 6106.0
4 TraesCS6A01G018500 chr6D 87.847 757 32 26 4430 5161 8800567 8801288 0.000000e+00 833.0
5 TraesCS6A01G018500 chr6D 90.217 184 15 1 4 184 8795131 8795314 2.650000e-58 237.0
6 TraesCS6A01G018500 chr6D 80.899 178 20 10 1509 1682 8797821 8797988 1.660000e-25 128.0
7 TraesCS6A01G018500 chr6B 92.284 3603 137 43 1532 5085 15938378 15941888 0.000000e+00 4983.0
8 TraesCS6A01G018500 chr6B 89.184 980 75 16 667 1620 15937407 15938381 0.000000e+00 1194.0
9 TraesCS6A01G018500 chr6B 89.353 479 31 8 5229 5688 15941993 15942470 8.210000e-163 584.0
10 TraesCS6A01G018500 chr6B 89.394 396 21 6 288 678 15936989 15937368 3.990000e-131 479.0
11 TraesCS6A01G018500 chr6B 84.894 470 26 10 1570 2039 632000993 632000569 3.150000e-117 433.0
12 TraesCS6A01G018500 chr6B 86.813 182 18 4 6 184 15935608 15935786 1.250000e-46 198.0
13 TraesCS6A01G018500 chr5A 86.038 1676 155 44 3118 4774 698515906 698517521 0.000000e+00 1725.0
14 TraesCS6A01G018500 chr5A 88.183 1007 82 12 1534 2529 698513741 698514721 0.000000e+00 1166.0
15 TraesCS6A01G018500 chr5A 80.215 1117 139 47 710 1784 698512265 698513341 0.000000e+00 763.0
16 TraesCS6A01G018500 chr5A 96.356 247 9 0 5209 5455 663030040 663030286 1.910000e-109 407.0
17 TraesCS6A01G018500 chr5A 94.400 250 14 0 5209 5458 153302698 153302449 8.940000e-103 385.0
18 TraesCS6A01G018500 chr5A 94.737 247 13 0 5209 5455 497666830 497667076 8.940000e-103 385.0
19 TraesCS6A01G018500 chr5A 94.422 251 12 2 5209 5458 639376808 639376559 8.940000e-103 385.0
20 TraesCS6A01G018500 chr5A 85.423 343 35 9 2631 2965 698515043 698515378 5.460000e-90 342.0
21 TraesCS6A01G018500 chr5A 94.118 153 5 3 5536 5688 663030308 663030456 4.430000e-56 230.0
22 TraesCS6A01G018500 chr5A 92.810 153 7 3 5536 5688 497667099 497667247 9.600000e-53 219.0
23 TraesCS6A01G018500 chr5A 92.667 150 7 3 5539 5688 639376536 639376391 4.470000e-51 213.0
24 TraesCS6A01G018500 chr5A 92.667 150 7 3 5539 5688 639412502 639412357 4.470000e-51 213.0
25 TraesCS6A01G018500 chr5A 92.000 150 8 3 5539 5688 153302426 153302281 2.080000e-49 207.0
26 TraesCS6A01G018500 chr5A 84.615 104 7 3 5024 5123 698517839 698517937 1.690000e-15 95.3
27 TraesCS6A01G018500 chr4B 85.603 1674 160 46 3118 4758 657167343 657165718 0.000000e+00 1681.0
28 TraesCS6A01G018500 chr4B 87.611 1017 80 17 1534 2536 657169468 657168484 0.000000e+00 1138.0
29 TraesCS6A01G018500 chr4B 78.220 1157 133 59 709 1826 657170558 657169482 1.040000e-176 630.0
30 TraesCS6A01G018500 chr4B 84.787 493 56 10 2634 3118 657168148 657167667 1.430000e-130 477.0
31 TraesCS6A01G018500 chr4B 78.646 192 33 7 1509 1699 657169683 657169499 2.780000e-23 121.0
32 TraesCS6A01G018500 chr4D 83.342 1945 187 73 3118 5006 509675522 509677385 0.000000e+00 1670.0
33 TraesCS6A01G018500 chr4D 85.967 734 62 12 1534 2251 509670298 509671006 0.000000e+00 747.0
34 TraesCS6A01G018500 chr4D 79.599 1147 126 57 710 1814 509669124 509670204 0.000000e+00 723.0
35 TraesCS6A01G018500 chr4D 85.167 418 51 8 2693 3109 509674782 509675189 8.820000e-113 418.0
36 TraesCS6A01G018500 chr4D 93.536 263 16 1 2275 2536 509674104 509674366 1.920000e-104 390.0
37 TraesCS6A01G018500 chr7B 84.894 470 26 10 1570 2039 577362756 577362332 3.150000e-117 433.0
38 TraesCS6A01G018500 chr3B 84.468 470 22 13 1570 2039 45147607 45147189 3.170000e-112 416.0
39 TraesCS6A01G018500 chr7A 96.356 247 9 0 5209 5455 110893962 110894208 1.910000e-109 407.0
40 TraesCS6A01G018500 chr7A 93.464 153 6 3 5536 5688 110894231 110894379 2.060000e-54 224.0
41 TraesCS6A01G018500 chr4A 96.266 241 9 0 5218 5458 470126234 470125994 4.130000e-106 396.0
42 TraesCS6A01G018500 chr4A 95.333 150 3 3 5539 5688 470125970 470125825 9.530000e-58 235.0
43 TraesCS6A01G018500 chr4A 76.206 311 63 8 3591 3894 660920328 660920634 2.740000e-33 154.0
44 TraesCS6A01G018500 chr3A 96.610 236 8 0 5223 5458 627673458 627673223 5.340000e-105 392.0
45 TraesCS6A01G018500 chr3A 93.464 153 6 3 5536 5688 622069602 622069750 2.060000e-54 224.0
46 TraesCS6A01G018500 chr7D 76.190 315 68 5 3591 3900 46888258 46888570 5.900000e-35 159.0
47 TraesCS6A01G018500 chr7D 75.238 315 71 4 3591 3900 46839603 46839291 5.940000e-30 143.0
48 TraesCS6A01G018500 chr3D 72.727 319 77 9 3599 3912 283316767 283317080 1.300000e-16 99.0
49 TraesCS6A01G018500 chr2D 91.667 72 4 1 4925 4994 551858311 551858240 1.300000e-16 99.0


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 TraesCS6A01G018500 chr6A 9040973 9046661 5688 True 10506.00 10506 100.0000 1 5689 1 chr6A.!!$R1 5688
1 TraesCS6A01G018500 chr6D 8795131 8801288 6157 False 1826.00 6106 88.1685 4 5161 4 chr6D.!!$F1 5157
2 TraesCS6A01G018500 chr6B 15935608 15942470 6862 False 1487.60 4983 89.4056 6 5688 5 chr6B.!!$F1 5682
3 TraesCS6A01G018500 chr5A 698512265 698517937 5672 False 818.26 1725 84.8948 710 5123 5 chr5A.!!$F3 4413
4 TraesCS6A01G018500 chr4B 657165718 657170558 4840 True 809.40 1681 82.9734 709 4758 5 chr4B.!!$R1 4049
5 TraesCS6A01G018500 chr4D 509669124 509677385 8261 False 789.60 1670 85.5222 710 5006 5 chr4D.!!$F1 4296

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
272 1456 0.037232 GGGCAGTGCGTCTCTAGTTT 60.037 55.000 9.45 0.00 0.00 2.66 F
273 1457 1.608283 GGGCAGTGCGTCTCTAGTTTT 60.608 52.381 9.45 0.00 0.00 2.43 F
1540 2931 0.463833 CGACCCCCTTCTATGTTGGC 60.464 60.000 0.00 0.00 0.00 4.52 F
2297 7442 1.177401 GTTCCCTTTCTGTGCATCCC 58.823 55.000 0.00 0.00 0.00 3.85 F
2922 8329 1.695893 CTATGGAGTTGGCACGTGCG 61.696 60.000 32.35 12.11 43.26 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 2608 0.806868 AAACAGATGGTGAGCATGCG 59.193 50.000 13.01 0.0 0.00 4.73 R
2065 4135 0.823356 GTGCAAAAGCTGGGGAGACA 60.823 55.000 0.00 0.0 0.00 3.41 R
3437 9257 1.881973 CACACACAGTGCTGCCTAATT 59.118 47.619 0.00 0.0 42.15 1.40 R
4100 9928 0.034059 CTGACCGTCTTCCACTGCTT 59.966 55.000 0.00 0.0 0.00 3.91 R
4776 10702 0.038310 CTTCTCTCCCAACCCAACCC 59.962 60.000 0.00 0.0 0.00 4.11 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
28 29 6.308766 CCAAACAATTCACAACATTAGCTAGC 59.691 38.462 6.62 6.62 0.00 3.42
45 46 5.546526 AGCTAGCCTCATATAGAGTTTTGC 58.453 41.667 12.13 0.00 43.12 3.68
78 79 9.585099 TTATTTCTGGCTAAAAGCAATTACATG 57.415 29.630 0.78 0.00 44.75 3.21
200 1339 5.380043 ACAATTAGGGCGATTTCATGATCT 58.620 37.500 0.00 0.00 0.00 2.75
212 1351 0.749049 CATGATCTGGTCGGAGCTCA 59.251 55.000 17.19 4.54 0.00 4.26
253 1437 3.148279 CGGTTCCTCCCCTCCGAG 61.148 72.222 0.00 0.00 44.86 4.63
267 1451 3.753434 CGAGGGCAGTGCGTCTCT 61.753 66.667 24.77 14.20 31.15 3.10
268 1452 2.407428 CGAGGGCAGTGCGTCTCTA 61.407 63.158 24.77 0.00 31.15 2.43
271 1455 0.900647 AGGGCAGTGCGTCTCTAGTT 60.901 55.000 9.45 0.00 0.00 2.24
272 1456 0.037232 GGGCAGTGCGTCTCTAGTTT 60.037 55.000 9.45 0.00 0.00 2.66
273 1457 1.608283 GGGCAGTGCGTCTCTAGTTTT 60.608 52.381 9.45 0.00 0.00 2.43
274 1458 2.143925 GGCAGTGCGTCTCTAGTTTTT 58.856 47.619 9.45 0.00 0.00 1.94
342 1529 1.836802 AGCCCTAGAGCAAGAAAGGAG 59.163 52.381 0.00 0.00 34.23 3.69
373 1560 3.673484 CAACCAGCTGGCCAACCG 61.673 66.667 33.06 10.75 39.70 4.44
384 1571 4.174305 CCAACCGAAGTGGGCTTT 57.826 55.556 0.00 0.00 44.64 3.51
395 1582 4.344865 GGGCTTTCACTCCGGCCA 62.345 66.667 2.24 0.00 45.68 5.36
396 1583 2.282180 GGCTTTCACTCCGGCCAA 60.282 61.111 2.24 0.00 43.59 4.52
397 1584 2.335712 GGCTTTCACTCCGGCCAAG 61.336 63.158 2.24 1.26 43.59 3.61
398 1585 2.982744 GCTTTCACTCCGGCCAAGC 61.983 63.158 2.24 4.55 33.57 4.01
399 1586 2.282180 TTTCACTCCGGCCAAGCC 60.282 61.111 2.24 0.00 46.75 4.35
422 1609 4.821589 AGCCCACGAAGCTAGCGC 62.822 66.667 9.55 0.00 39.29 5.92
522 1713 2.040359 CTTCCCTCCTCCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
770 2024 4.264638 GCGCTCCTCTCTCTCGCC 62.265 72.222 0.00 0.00 39.91 5.54
928 2229 2.061182 CTACCTACCAGAGCGCGTCC 62.061 65.000 8.43 0.00 0.00 4.79
941 2245 3.081133 CGTCCGTGATTTCCTGCG 58.919 61.111 0.00 0.00 0.00 5.18
1047 2365 4.849310 GCGGCGCCCAAGATGGTA 62.849 66.667 23.58 0.00 35.17 3.25
1074 2392 2.045045 CTCAGCGGCCCCAAATCA 60.045 61.111 0.00 0.00 0.00 2.57
1199 2531 3.427425 GCCATGTACGCAACGCCA 61.427 61.111 0.00 0.00 0.00 5.69
1268 2608 0.863144 TGAGTTTGCTTTCGCCGTAC 59.137 50.000 0.00 0.00 34.43 3.67
1424 2775 4.194312 CAACGCTGCAAAGACACG 57.806 55.556 0.00 0.00 0.00 4.49
1489 2840 5.243507 TGCCTTTGCATTTCATGTTCTAGAA 59.756 36.000 0.00 0.00 44.23 2.10
1540 2931 0.463833 CGACCCCCTTCTATGTTGGC 60.464 60.000 0.00 0.00 0.00 4.52
1550 2943 5.835280 CCCTTCTATGTTGGCTGGATTTATT 59.165 40.000 0.00 0.00 0.00 1.40
1621 3421 9.262358 GTACTCCATTTCCATTTCATAGTCTAC 57.738 37.037 0.00 0.00 0.00 2.59
1781 3833 5.203528 CCCCTTGTCTGATGGTTGAATTAT 58.796 41.667 0.00 0.00 0.00 1.28
1788 3843 9.695526 TTGTCTGATGGTTGAATTATTTTCTTG 57.304 29.630 0.00 0.00 0.00 3.02
1886 3941 9.031537 TCTTGTTTCTCAGTACCAGATACATAA 57.968 33.333 13.21 5.69 33.52 1.90
1894 3949 7.056006 TCAGTACCAGATACATAACCTCGTTA 58.944 38.462 0.00 0.00 36.09 3.18
1938 3993 3.041946 CCCATTCACTAGGTAGCTCCTT 58.958 50.000 9.58 0.00 45.67 3.36
2005 4066 4.529897 AGAAATAATGTGCATGCTCCTGA 58.470 39.130 20.33 1.51 0.00 3.86
2136 4206 4.931601 TCTTCAGTTCATGTTCCTGAATCG 59.068 41.667 18.07 11.55 42.51 3.34
2229 4299 2.432510 AGATGGAACGTCCTCAAGATCC 59.567 50.000 0.00 0.00 37.46 3.36
2296 7441 1.909700 TGTTCCCTTTCTGTGCATCC 58.090 50.000 0.00 0.00 0.00 3.51
2297 7442 1.177401 GTTCCCTTTCTGTGCATCCC 58.823 55.000 0.00 0.00 0.00 3.85
2313 7458 2.472695 TCCCTGGCGTGCAATATATC 57.527 50.000 0.00 0.00 0.00 1.63
2337 7482 3.650281 TCCCATTTCTCATTGCTGCTA 57.350 42.857 0.00 0.00 0.00 3.49
2358 7503 2.098117 AGAACTGTGAAACTGCAGCAAC 59.902 45.455 15.27 7.66 39.67 4.17
2577 7788 4.139786 CTGGAAATGCACCAGTATATGCT 58.860 43.478 12.60 0.00 46.71 3.79
2578 7789 3.884693 TGGAAATGCACCAGTATATGCTG 59.115 43.478 13.42 13.42 42.55 4.41
2586 7797 4.375272 CACCAGTATATGCTGACAAGGAG 58.625 47.826 21.02 6.00 38.70 3.69
2721 7938 5.286438 GTTGGTGGTACAATTTCTTGGTTC 58.714 41.667 0.00 0.00 44.16 3.62
2727 7944 6.039382 GTGGTACAATTTCTTGGTTCTTGACT 59.961 38.462 0.00 0.00 44.16 3.41
2871 8277 9.887406 GTTTGCTAACTTTGCTACAGTAATTTA 57.113 29.630 3.64 0.00 0.00 1.40
2922 8329 1.695893 CTATGGAGTTGGCACGTGCG 61.696 60.000 32.35 12.11 43.26 5.34
3032 8494 2.676748 TGTTTTGGGGATTGCACTCTT 58.323 42.857 3.88 0.00 0.00 2.85
3091 8553 3.599730 TGATGTCAGTACAGAGCTTGG 57.400 47.619 0.00 0.00 39.49 3.61
3352 9145 5.089970 TCTGATGACAAATCCAGTACCAG 57.910 43.478 0.00 0.00 0.00 4.00
4100 9928 0.904865 CTACCTGAGGTGGTGGAGCA 60.905 60.000 15.83 0.00 40.47 4.26
4116 9944 1.598130 GCAAGCAGTGGAAGACGGT 60.598 57.895 0.00 0.00 0.00 4.83
4126 9954 2.094182 GTGGAAGACGGTCAGATTAGCA 60.094 50.000 11.27 0.00 0.00 3.49
4366 10198 5.263968 ACAGTAGATTAATGTCGTCCCAG 57.736 43.478 0.00 0.00 30.12 4.45
4368 10200 5.043903 CAGTAGATTAATGTCGTCCCAGTG 58.956 45.833 0.00 0.00 0.00 3.66
4369 10201 4.954202 AGTAGATTAATGTCGTCCCAGTGA 59.046 41.667 0.00 0.00 0.00 3.41
4371 10203 3.769844 AGATTAATGTCGTCCCAGTGAGT 59.230 43.478 0.00 0.00 0.00 3.41
4379 10288 0.464036 GTCCCAGTGAGTGTGTGTGA 59.536 55.000 0.00 0.00 0.00 3.58
4408 10317 4.058124 GTGTGTGTGTGTGTGTCATAGAT 58.942 43.478 0.00 0.00 0.00 1.98
4413 10322 5.476945 TGTGTGTGTGTGTCATAGATAGACT 59.523 40.000 0.00 0.00 36.94 3.24
4414 10323 5.802451 GTGTGTGTGTGTCATAGATAGACTG 59.198 44.000 0.00 0.00 36.94 3.51
4415 10324 5.710099 TGTGTGTGTGTCATAGATAGACTGA 59.290 40.000 0.00 0.00 36.94 3.41
4416 10325 6.378280 TGTGTGTGTGTCATAGATAGACTGAT 59.622 38.462 0.00 0.00 36.94 2.90
4417 10326 6.694844 GTGTGTGTGTCATAGATAGACTGATG 59.305 42.308 0.00 0.00 36.94 3.07
4418 10327 6.603201 TGTGTGTGTCATAGATAGACTGATGA 59.397 38.462 0.00 0.00 36.94 2.92
4419 10328 7.286316 TGTGTGTGTCATAGATAGACTGATGAT 59.714 37.037 0.00 0.00 36.94 2.45
4420 10329 8.787852 GTGTGTGTCATAGATAGACTGATGATA 58.212 37.037 0.00 0.00 36.94 2.15
4421 10330 9.525826 TGTGTGTCATAGATAGACTGATGATAT 57.474 33.333 0.00 0.00 36.94 1.63
4422 10331 9.786105 GTGTGTCATAGATAGACTGATGATATG 57.214 37.037 0.00 0.00 36.94 1.78
4423 10332 8.964772 TGTGTCATAGATAGACTGATGATATGG 58.035 37.037 0.00 0.00 36.94 2.74
4424 10333 8.965819 GTGTCATAGATAGACTGATGATATGGT 58.034 37.037 0.00 0.00 36.94 3.55
4425 10334 9.539194 TGTCATAGATAGACTGATGATATGGTT 57.461 33.333 0.00 0.00 36.94 3.67
4439 10348 8.858094 TGATGATATGGTTAAAATTAGCATGCA 58.142 29.630 21.98 0.00 35.52 3.96
4766 10692 2.922503 GGGGGCTTGGTTGGGTTG 60.923 66.667 0.00 0.00 0.00 3.77
4767 10693 2.922503 GGGGCTTGGTTGGGTTGG 60.923 66.667 0.00 0.00 0.00 3.77
4768 10694 2.922503 GGGCTTGGTTGGGTTGGG 60.923 66.667 0.00 0.00 0.00 4.12
4769 10695 2.123033 GGCTTGGTTGGGTTGGGT 60.123 61.111 0.00 0.00 0.00 4.51
4770 10696 1.764454 GGCTTGGTTGGGTTGGGTT 60.764 57.895 0.00 0.00 0.00 4.11
4771 10697 1.445518 GCTTGGTTGGGTTGGGTTG 59.554 57.895 0.00 0.00 0.00 3.77
4772 10698 2.038814 GCTTGGTTGGGTTGGGTTGG 62.039 60.000 0.00 0.00 0.00 3.77
4773 10699 1.383248 TTGGTTGGGTTGGGTTGGG 60.383 57.895 0.00 0.00 0.00 4.12
4774 10700 2.182858 TTGGTTGGGTTGGGTTGGGT 62.183 55.000 0.00 0.00 0.00 4.51
4775 10701 1.383386 GGTTGGGTTGGGTTGGGTT 60.383 57.895 0.00 0.00 0.00 4.11
4776 10702 1.691195 GGTTGGGTTGGGTTGGGTTG 61.691 60.000 0.00 0.00 0.00 3.77
4777 10703 1.383248 TTGGGTTGGGTTGGGTTGG 60.383 57.895 0.00 0.00 0.00 3.77
4778 10704 2.525629 GGGTTGGGTTGGGTTGGG 60.526 66.667 0.00 0.00 0.00 4.12
4971 10987 9.595823 TTGGTCTTAAAAATAGAGAATACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
4993 11024 4.225717 AGAATTTTGGTTGGATTGGATGGG 59.774 41.667 0.00 0.00 0.00 4.00
5006 11037 1.053424 GGATGGGTGCCGAGGTTATA 58.947 55.000 0.00 0.00 0.00 0.98
5019 11051 5.414454 GCCGAGGTTATATATGGCATTGAAA 59.586 40.000 4.78 0.00 42.03 2.69
5097 11149 4.586421 AGCCAGATTGAGATGAGACGAATA 59.414 41.667 0.00 0.00 0.00 1.75
5111 11167 7.767250 TGAGACGAATAGAATGTGGATATCT 57.233 36.000 2.05 0.00 0.00 1.98
5132 11188 2.296073 TTTTGGGTGCGGGATTAAGT 57.704 45.000 0.00 0.00 0.00 2.24
5137 11193 2.285977 GGGTGCGGGATTAAGTTACAG 58.714 52.381 0.00 0.00 0.00 2.74
5138 11194 2.093341 GGGTGCGGGATTAAGTTACAGA 60.093 50.000 0.00 0.00 0.00 3.41
5161 11217 4.823989 AGTTGCTAATTTTCAGCTGACTGT 59.176 37.500 18.03 4.74 44.77 3.55
5162 11218 5.300286 AGTTGCTAATTTTCAGCTGACTGTT 59.700 36.000 18.03 13.24 44.77 3.16
5176 11232 2.820787 TGACTGTTGGGTTGTTCGTTTT 59.179 40.909 0.00 0.00 0.00 2.43
5192 11248 2.711885 GTTTTCTGTTTCACGGGTTCG 58.288 47.619 0.00 0.00 43.02 3.95
5195 11251 2.202905 TGTTTCACGGGTTCGCGT 60.203 55.556 5.77 8.97 40.63 6.01
5199 11255 3.851845 TTCACGGGTTCGCGTCTGG 62.852 63.158 5.77 2.52 40.63 3.86
5213 11269 1.641577 GTCTGGACGGTTATGTCTGC 58.358 55.000 0.00 0.00 38.91 4.26
5214 11270 1.067142 GTCTGGACGGTTATGTCTGCA 60.067 52.381 0.00 0.00 38.91 4.41
5215 11271 1.067142 TCTGGACGGTTATGTCTGCAC 60.067 52.381 0.00 0.00 38.91 4.57
5216 11272 0.682292 TGGACGGTTATGTCTGCACA 59.318 50.000 0.00 0.00 38.91 4.57
5217 11273 1.277842 TGGACGGTTATGTCTGCACAT 59.722 47.619 0.00 0.00 45.73 3.21
5218 11274 2.290008 TGGACGGTTATGTCTGCACATT 60.290 45.455 0.00 0.00 40.66 2.71
5219 11275 3.055747 TGGACGGTTATGTCTGCACATTA 60.056 43.478 0.00 0.00 40.66 1.90
5220 11276 4.127171 GGACGGTTATGTCTGCACATTAT 58.873 43.478 0.00 0.00 40.66 1.28
5221 11277 5.163395 TGGACGGTTATGTCTGCACATTATA 60.163 40.000 0.00 0.00 40.66 0.98
5222 11278 5.756347 GGACGGTTATGTCTGCACATTATAA 59.244 40.000 0.00 0.00 40.66 0.98
5223 11279 6.292703 GGACGGTTATGTCTGCACATTATAAC 60.293 42.308 0.00 3.26 40.66 1.89
5224 11280 5.526111 ACGGTTATGTCTGCACATTATAACC 59.474 40.000 18.51 18.51 40.66 2.85
5225 11281 5.049680 CGGTTATGTCTGCACATTATAACCC 60.050 44.000 20.58 10.82 41.94 4.11
5226 11282 5.825679 GGTTATGTCTGCACATTATAACCCA 59.174 40.000 18.07 0.00 40.66 4.51
5227 11283 6.490040 GGTTATGTCTGCACATTATAACCCAT 59.510 38.462 18.07 0.00 40.66 4.00
5238 11294 6.096705 CACATTATAACCCATGGTTGTCATGT 59.903 38.462 11.73 13.50 45.54 3.21
5258 11314 1.021202 TTTGTCGCTTGGTGTCCTTG 58.979 50.000 0.00 0.00 0.00 3.61
5299 11355 1.302832 CTGCCCCCGATTGGATAGC 60.303 63.158 0.00 0.55 37.49 2.97
5359 11415 2.423185 TGTGTTTTTGCTCCTCTGTGTG 59.577 45.455 0.00 0.00 0.00 3.82
5360 11416 1.405105 TGTTTTTGCTCCTCTGTGTGC 59.595 47.619 0.00 0.00 0.00 4.57
5362 11418 1.311859 TTTTGCTCCTCTGTGTGCAG 58.688 50.000 0.00 0.00 43.87 4.41
5381 11437 0.869880 GTTTGGCGTGGTTGTTGCTC 60.870 55.000 0.00 0.00 0.00 4.26
5384 11440 2.050985 GCGTGGTTGTTGCTCTGC 60.051 61.111 0.00 0.00 0.00 4.26
5385 11441 2.833533 GCGTGGTTGTTGCTCTGCA 61.834 57.895 0.00 0.00 36.47 4.41
5386 11442 1.726865 CGTGGTTGTTGCTCTGCAA 59.273 52.632 0.45 0.45 46.80 4.08
5418 11477 6.428159 CAGAGATAGCTAGGTTTGTTTTGTGT 59.572 38.462 0.00 0.00 0.00 3.72
5437 11496 4.877823 TGTGTCATGGCTCATATGTCTTTC 59.122 41.667 1.90 0.00 0.00 2.62
5448 11507 6.258230 TCATATGTCTTTCTGGTTTTGCAG 57.742 37.500 1.90 0.00 0.00 4.41
5484 11543 8.501580 GGTTGGTTATTCTTAGTTTGTGTAGAC 58.498 37.037 0.00 0.00 0.00 2.59
5494 11553 2.624316 TTGTGTAGACGAAGCGGTAG 57.376 50.000 0.00 0.00 0.00 3.18
5516 11575 5.468658 AGGTGAATCCCTAGCTGTACTATT 58.531 41.667 0.00 0.00 36.75 1.73
5530 11589 5.670485 CTGTACTATTTACACCATGGCTCA 58.330 41.667 13.04 0.00 0.00 4.26
5532 11591 7.368198 TGTACTATTTACACCATGGCTCATA 57.632 36.000 13.04 0.78 0.00 2.15
5534 11593 7.877612 TGTACTATTTACACCATGGCTCATATG 59.122 37.037 13.04 3.66 0.00 1.78
5539 11598 6.849085 TTACACCATGGCTCATATGTTTTT 57.151 33.333 13.04 0.00 0.00 1.94
5593 11662 0.250727 TTGTGGTGTAGCTGCCCTTC 60.251 55.000 0.00 0.00 0.00 3.46
5621 11690 3.490348 AGTGTCTTTTCCATCAGTTGGG 58.510 45.455 0.00 0.00 46.45 4.12
5624 11693 4.099419 GTGTCTTTTCCATCAGTTGGGTTT 59.901 41.667 0.00 0.00 46.45 3.27
5625 11694 5.300792 GTGTCTTTTCCATCAGTTGGGTTTA 59.699 40.000 0.00 0.00 46.45 2.01
5626 11695 5.300792 TGTCTTTTCCATCAGTTGGGTTTAC 59.699 40.000 0.00 0.00 46.45 2.01
5627 11696 4.517453 TCTTTTCCATCAGTTGGGTTTACG 59.483 41.667 0.00 0.00 46.45 3.18
5628 11697 3.495434 TTCCATCAGTTGGGTTTACGT 57.505 42.857 0.00 0.00 46.45 3.57
5629 11698 4.620589 TTCCATCAGTTGGGTTTACGTA 57.379 40.909 0.00 0.00 46.45 3.57
5643 11719 8.532186 TGGGTTTACGTACCTTGTATCTTATA 57.468 34.615 7.42 0.00 38.30 0.98
5644 11720 9.146586 TGGGTTTACGTACCTTGTATCTTATAT 57.853 33.333 7.42 0.00 38.30 0.86
5645 11721 9.415544 GGGTTTACGTACCTTGTATCTTATATG 57.584 37.037 7.42 0.00 38.30 1.78
5646 11722 8.919661 GGTTTACGTACCTTGTATCTTATATGC 58.080 37.037 0.00 0.00 35.23 3.14
5647 11723 8.919661 GTTTACGTACCTTGTATCTTATATGCC 58.080 37.037 0.00 0.00 0.00 4.40
5650 11726 6.042322 ACGTACCTTGTATCTTATATGCCCAA 59.958 38.462 0.00 0.00 0.00 4.12
5665 11741 2.224769 TGCCCAAACCTGGAAGTAGAAG 60.225 50.000 0.00 0.00 46.92 2.85
5674 11750 5.032846 ACCTGGAAGTAGAAGGATCATCAA 58.967 41.667 0.00 0.00 34.97 2.57
5688 11764 5.478332 AGGATCATCAAACCAAGAAACCTTC 59.522 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.851222 ATGTTCGCAAAACTCTATATGAGG 57.149 37.500 6.98 0.00 46.72 3.86
45 46 6.806249 TGCTTTTAGCCAGAAATAAATGTTCG 59.194 34.615 0.00 0.00 41.51 3.95
98 99 7.706607 GGGAATTATTACTGCCAAATTCACTTC 59.293 37.037 8.42 0.00 38.26 3.01
200 1339 3.838271 GCCGATGAGCTCCGACCA 61.838 66.667 12.15 0.00 0.00 4.02
252 1436 0.900647 AACTAGAGACGCACTGCCCT 60.901 55.000 0.00 0.00 0.00 5.19
253 1437 0.037232 AAACTAGAGACGCACTGCCC 60.037 55.000 0.00 0.00 0.00 5.36
275 1459 4.646945 TCTGCCACCACTACAAATGAAAAA 59.353 37.500 0.00 0.00 0.00 1.94
276 1460 4.211125 TCTGCCACCACTACAAATGAAAA 58.789 39.130 0.00 0.00 0.00 2.29
277 1461 3.820467 CTCTGCCACCACTACAAATGAAA 59.180 43.478 0.00 0.00 0.00 2.69
278 1462 3.411446 CTCTGCCACCACTACAAATGAA 58.589 45.455 0.00 0.00 0.00 2.57
279 1463 2.875672 GCTCTGCCACCACTACAAATGA 60.876 50.000 0.00 0.00 0.00 2.57
280 1464 1.470098 GCTCTGCCACCACTACAAATG 59.530 52.381 0.00 0.00 0.00 2.32
281 1465 1.826385 GCTCTGCCACCACTACAAAT 58.174 50.000 0.00 0.00 0.00 2.32
282 1466 0.602638 CGCTCTGCCACCACTACAAA 60.603 55.000 0.00 0.00 0.00 2.83
283 1467 1.005037 CGCTCTGCCACCACTACAA 60.005 57.895 0.00 0.00 0.00 2.41
284 1468 2.656646 CGCTCTGCCACCACTACA 59.343 61.111 0.00 0.00 0.00 2.74
319 1506 2.026822 CCTTTCTTGCTCTAGGGCTCAA 60.027 50.000 17.26 1.18 0.00 3.02
320 1507 1.556911 CCTTTCTTGCTCTAGGGCTCA 59.443 52.381 17.26 1.12 0.00 4.26
342 1529 2.440980 GTTGCTGGGCCCATCCTC 60.441 66.667 28.82 15.38 34.39 3.71
373 1560 0.955919 CCGGAGTGAAAGCCCACTTC 60.956 60.000 0.00 3.24 46.45 3.01
398 1585 2.742372 CTTCGTGGGCTTCGTGGG 60.742 66.667 2.55 0.00 0.00 4.61
399 1586 2.501223 TAGCTTCGTGGGCTTCGTGG 62.501 60.000 0.00 0.00 40.74 4.94
400 1587 1.078759 CTAGCTTCGTGGGCTTCGTG 61.079 60.000 0.00 0.00 40.74 4.35
401 1588 1.215647 CTAGCTTCGTGGGCTTCGT 59.784 57.895 0.00 0.00 40.74 3.85
402 1589 2.167861 GCTAGCTTCGTGGGCTTCG 61.168 63.158 7.70 0.00 40.74 3.79
403 1590 2.167861 CGCTAGCTTCGTGGGCTTC 61.168 63.158 13.93 0.00 40.74 3.86
404 1591 2.125512 CGCTAGCTTCGTGGGCTT 60.126 61.111 13.93 0.00 40.74 4.35
405 1592 4.821589 GCGCTAGCTTCGTGGGCT 62.822 66.667 13.93 0.00 43.02 5.19
574 1777 4.735132 CTTCACTTCGGCCGGCGA 62.735 66.667 27.83 18.47 0.00 5.54
770 2024 4.148825 CTGGTCGGGGAAGAGCGG 62.149 72.222 0.00 0.00 41.16 5.52
896 2197 1.445716 TAGGTAGGAGAAGAGCGCGC 61.446 60.000 26.66 26.66 0.00 6.86
954 2258 1.419107 GAGACGGCGAAACGGAATCC 61.419 60.000 16.62 0.00 38.39 3.01
1042 2360 3.866582 GAGCGCCAGCCCTACCAT 61.867 66.667 2.29 0.00 46.67 3.55
1066 2384 1.024579 ACGTAGGCGCTTGATTTGGG 61.025 55.000 7.64 0.00 42.83 4.12
1074 2392 3.823330 CGGAGGACGTAGGCGCTT 61.823 66.667 7.64 0.52 42.83 4.68
1102 2420 3.423154 GTCCTGGGCGAAGTTGCG 61.423 66.667 0.00 0.00 35.06 4.85
1136 2454 1.338200 GGACGTGGATGAGCTTGAACT 60.338 52.381 0.00 0.00 0.00 3.01
1137 2455 1.079503 GGACGTGGATGAGCTTGAAC 58.920 55.000 0.00 0.00 0.00 3.18
1216 2548 2.756283 CGAGGAGGAAGGAGCGGT 60.756 66.667 0.00 0.00 0.00 5.68
1268 2608 0.806868 AAACAGATGGTGAGCATGCG 59.193 50.000 13.01 0.00 0.00 4.73
1409 2760 1.813753 ACACGTGTCTTTGCAGCGT 60.814 52.632 17.22 0.00 36.13 5.07
1424 2775 4.385358 ACCAACCTTGTTTTCATCACAC 57.615 40.909 0.00 0.00 0.00 3.82
1515 2882 1.344763 CATAGAAGGGGGTCGATCCAC 59.655 57.143 18.43 14.45 39.32 4.02
1540 2931 9.824534 GCCAATTAAACAAACAAATAAATCCAG 57.175 29.630 0.00 0.00 0.00 3.86
1550 2943 5.606348 ACCTGAGCCAATTAAACAAACAA 57.394 34.783 0.00 0.00 0.00 2.83
1616 3412 3.064545 GCATTCATTCAGCCAGTGTAGAC 59.935 47.826 0.00 0.00 0.00 2.59
1621 3421 2.425668 TGATGCATTCATTCAGCCAGTG 59.574 45.455 0.00 0.00 31.96 3.66
1781 3833 4.821805 CCTGAGCCAAGTAAGTCAAGAAAA 59.178 41.667 0.00 0.00 0.00 2.29
1788 3843 3.402628 TCAACCTGAGCCAAGTAAGTC 57.597 47.619 0.00 0.00 0.00 3.01
1886 3941 2.027385 GAGGGTTACCGATAACGAGGT 58.973 52.381 0.00 0.00 41.52 3.85
1894 3949 0.912487 TTGCTGGGAGGGTTACCGAT 60.912 55.000 0.00 0.00 43.47 4.18
1938 3993 8.218488 ACAGTACAGGTATGAGTATGAGTATGA 58.782 37.037 0.00 0.00 0.00 2.15
2005 4066 6.094302 ACCTCCTATAAGATCCAATGGTCAT 58.906 40.000 0.00 0.00 0.00 3.06
2033 4103 1.448540 CAGGCCGTCCTACTTGCAG 60.449 63.158 0.00 0.00 41.93 4.41
2065 4135 0.823356 GTGCAAAAGCTGGGGAGACA 60.823 55.000 0.00 0.00 0.00 3.41
2085 4155 5.105392 TCCATCCTTTGAAACAACATATGCC 60.105 40.000 1.58 0.00 0.00 4.40
2136 4206 2.436824 GAGGGCGAGCCACTTTCC 60.437 66.667 16.65 0.00 37.98 3.13
2296 7441 1.003580 AGGGATATATTGCACGCCAGG 59.996 52.381 0.00 0.00 0.00 4.45
2297 7442 2.479566 AGGGATATATTGCACGCCAG 57.520 50.000 0.00 0.00 0.00 4.85
2313 7458 2.429610 CAGCAATGAGAAATGGGAAGGG 59.570 50.000 0.00 0.00 0.00 3.95
2337 7482 2.042686 TGCTGCAGTTTCACAGTTCT 57.957 45.000 16.64 0.00 36.26 3.01
2358 7503 3.285484 AGGCTTATGTCTTCATGCAAGG 58.715 45.455 0.00 0.00 35.70 3.61
2577 7788 3.328931 AGGCAATTCTTCTCTCCTTGTCA 59.671 43.478 0.00 0.00 0.00 3.58
2578 7789 3.938334 GAGGCAATTCTTCTCTCCTTGTC 59.062 47.826 0.00 0.00 0.00 3.18
2707 7924 5.888161 AGTCAGTCAAGAACCAAGAAATTGT 59.112 36.000 0.00 0.00 0.00 2.71
2765 8169 2.733026 AGGTATGTGTTTGACGCGTAAC 59.267 45.455 13.97 15.34 37.90 2.50
2871 8277 4.934797 TCAATCAGATTGGAGGGAAAGT 57.065 40.909 20.91 0.00 40.61 2.66
3005 8467 4.404073 GTGCAATCCCCAAAACATACCATA 59.596 41.667 0.00 0.00 0.00 2.74
3006 8468 3.197549 GTGCAATCCCCAAAACATACCAT 59.802 43.478 0.00 0.00 0.00 3.55
3032 8494 6.040278 CAGGTTATCAGATCAGAGCAGAGTTA 59.960 42.308 0.00 0.00 0.00 2.24
3091 8553 2.218603 TCGGTTCAAGGTTCAGCTTTC 58.781 47.619 0.00 0.00 0.00 2.62
3352 9145 3.421844 ACTACCTCTTGGTTGAAATGCC 58.578 45.455 3.90 0.00 46.05 4.40
3437 9257 1.881973 CACACACAGTGCTGCCTAATT 59.118 47.619 0.00 0.00 42.15 1.40
3459 9287 5.112686 TGAAAAGGCCATTAAAACACACAC 58.887 37.500 5.01 0.00 0.00 3.82
3460 9288 5.344743 TGAAAAGGCCATTAAAACACACA 57.655 34.783 5.01 0.00 0.00 3.72
3461 9289 5.988561 TGATGAAAAGGCCATTAAAACACAC 59.011 36.000 5.01 0.00 0.00 3.82
3462 9290 6.166984 TGATGAAAAGGCCATTAAAACACA 57.833 33.333 5.01 0.00 0.00 3.72
3463 9291 6.873076 TCATGATGAAAAGGCCATTAAAACAC 59.127 34.615 5.01 0.00 0.00 3.32
3464 9292 6.873076 GTCATGATGAAAAGGCCATTAAAACA 59.127 34.615 5.01 0.00 0.00 2.83
4100 9928 0.034059 CTGACCGTCTTCCACTGCTT 59.966 55.000 0.00 0.00 0.00 3.91
4116 9944 5.993055 TCATCCAAGACATTGCTAATCTGA 58.007 37.500 0.00 0.00 34.91 3.27
4126 9954 1.661341 GCGCTCTCATCCAAGACATT 58.339 50.000 0.00 0.00 0.00 2.71
4366 10198 1.660607 CACACACTCACACACACTCAC 59.339 52.381 0.00 0.00 0.00 3.51
4368 10200 1.660607 CACACACACTCACACACACTC 59.339 52.381 0.00 0.00 0.00 3.51
4369 10201 1.001974 ACACACACACTCACACACACT 59.998 47.619 0.00 0.00 0.00 3.55
4371 10203 1.270571 ACACACACACACTCACACACA 60.271 47.619 0.00 0.00 0.00 3.72
4379 10288 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
4413 10322 8.858094 TGCATGCTAATTTTAACCATATCATCA 58.142 29.630 20.33 0.00 0.00 3.07
4414 10323 9.865321 ATGCATGCTAATTTTAACCATATCATC 57.135 29.630 20.33 0.00 0.00 2.92
4415 10324 9.647797 CATGCATGCTAATTTTAACCATATCAT 57.352 29.630 20.33 0.00 0.00 2.45
4416 10325 8.640651 ACATGCATGCTAATTTTAACCATATCA 58.359 29.630 26.53 0.00 0.00 2.15
4417 10326 8.918658 CACATGCATGCTAATTTTAACCATATC 58.081 33.333 26.53 0.00 0.00 1.63
4418 10327 7.874016 CCACATGCATGCTAATTTTAACCATAT 59.126 33.333 26.53 0.00 0.00 1.78
4419 10328 7.069208 TCCACATGCATGCTAATTTTAACCATA 59.931 33.333 26.53 0.00 0.00 2.74
4420 10329 6.050432 CCACATGCATGCTAATTTTAACCAT 58.950 36.000 26.53 0.00 0.00 3.55
4421 10330 5.186603 TCCACATGCATGCTAATTTTAACCA 59.813 36.000 26.53 0.00 0.00 3.67
4422 10331 5.659463 TCCACATGCATGCTAATTTTAACC 58.341 37.500 26.53 0.00 0.00 2.85
4423 10332 6.757947 ACATCCACATGCATGCTAATTTTAAC 59.242 34.615 26.53 0.00 32.57 2.01
4424 10333 6.757478 CACATCCACATGCATGCTAATTTTAA 59.243 34.615 26.53 2.70 32.57 1.52
4425 10334 6.127394 ACACATCCACATGCATGCTAATTTTA 60.127 34.615 26.53 4.25 32.57 1.52
4426 10335 5.113383 CACATCCACATGCATGCTAATTTT 58.887 37.500 26.53 1.90 32.57 1.82
4427 10336 4.160814 ACACATCCACATGCATGCTAATTT 59.839 37.500 26.53 7.51 32.57 1.82
4428 10337 3.702548 ACACATCCACATGCATGCTAATT 59.297 39.130 26.53 3.52 32.57 1.40
4432 10341 0.815095 CACACATCCACATGCATGCT 59.185 50.000 26.53 11.04 32.57 3.79
4439 10348 4.139786 GCTATCAATCCACACATCCACAT 58.860 43.478 0.00 0.00 0.00 3.21
4679 10597 8.211629 AGTATTTACCATTAGCCTTACTCCTTG 58.788 37.037 0.00 0.00 0.00 3.61
4766 10692 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
4767 10693 1.383386 AACCCAACCCAACCCAACC 60.383 57.895 0.00 0.00 0.00 3.77
4768 10694 1.691195 CCAACCCAACCCAACCCAAC 61.691 60.000 0.00 0.00 0.00 3.77
4769 10695 1.383248 CCAACCCAACCCAACCCAA 60.383 57.895 0.00 0.00 0.00 4.12
4770 10696 2.283809 CCAACCCAACCCAACCCA 59.716 61.111 0.00 0.00 0.00 4.51
4771 10697 2.525629 CCCAACCCAACCCAACCC 60.526 66.667 0.00 0.00 0.00 4.11
4772 10698 1.533033 CTCCCAACCCAACCCAACC 60.533 63.158 0.00 0.00 0.00 3.77
4773 10699 0.539669 CTCTCCCAACCCAACCCAAC 60.540 60.000 0.00 0.00 0.00 3.77
4774 10700 0.699577 TCTCTCCCAACCCAACCCAA 60.700 55.000 0.00 0.00 0.00 4.12
4775 10701 0.699577 TTCTCTCCCAACCCAACCCA 60.700 55.000 0.00 0.00 0.00 4.51
4776 10702 0.038310 CTTCTCTCCCAACCCAACCC 59.962 60.000 0.00 0.00 0.00 4.11
4777 10703 0.038310 CCTTCTCTCCCAACCCAACC 59.962 60.000 0.00 0.00 0.00 3.77
4778 10704 0.609406 GCCTTCTCTCCCAACCCAAC 60.609 60.000 0.00 0.00 0.00 3.77
4971 10987 4.019411 ACCCATCCAATCCAACCAAAATTC 60.019 41.667 0.00 0.00 0.00 2.17
4993 11024 3.328382 TGCCATATATAACCTCGGCAC 57.672 47.619 7.85 0.00 44.27 5.01
5006 11037 6.608405 TCATCCAAGAAGTTTCAATGCCATAT 59.392 34.615 0.00 0.00 0.00 1.78
5019 11051 7.293073 ACAAAGCCATATATCATCCAAGAAGT 58.707 34.615 0.00 0.00 0.00 3.01
5119 11175 3.858247 ACTCTGTAACTTAATCCCGCAC 58.142 45.455 0.00 0.00 0.00 5.34
5120 11176 4.250464 CAACTCTGTAACTTAATCCCGCA 58.750 43.478 0.00 0.00 0.00 5.69
5121 11177 3.063588 GCAACTCTGTAACTTAATCCCGC 59.936 47.826 0.00 0.00 0.00 6.13
5132 11188 6.710295 TCAGCTGAAAATTAGCAACTCTGTAA 59.290 34.615 15.67 0.00 43.53 2.41
5137 11193 5.049129 ACAGTCAGCTGAAAATTAGCAACTC 60.049 40.000 20.19 0.55 45.28 3.01
5138 11194 4.823989 ACAGTCAGCTGAAAATTAGCAACT 59.176 37.500 20.19 4.66 45.28 3.16
5161 11217 4.022242 TGAAACAGAAAACGAACAACCCAA 60.022 37.500 0.00 0.00 0.00 4.12
5162 11218 3.506455 TGAAACAGAAAACGAACAACCCA 59.494 39.130 0.00 0.00 0.00 4.51
5176 11232 4.036977 GCGAACCCGTGAAACAGA 57.963 55.556 0.00 0.00 35.74 3.41
5195 11251 1.067142 GTGCAGACATAACCGTCCAGA 60.067 52.381 0.00 0.00 36.52 3.86
5199 11255 6.292703 GGTTATAATGTGCAGACATAACCGTC 60.293 42.308 22.89 9.53 42.30 4.79
5202 11258 5.825679 TGGGTTATAATGTGCAGACATAACC 59.174 40.000 26.17 26.17 42.30 2.85
5203 11259 6.935741 TGGGTTATAATGTGCAGACATAAC 57.064 37.500 16.19 16.19 42.30 1.89
5204 11260 6.489700 CCATGGGTTATAATGTGCAGACATAA 59.510 38.462 2.85 0.00 42.30 1.90
5205 11261 6.003326 CCATGGGTTATAATGTGCAGACATA 58.997 40.000 2.85 0.00 42.30 2.29
5206 11262 4.828939 CCATGGGTTATAATGTGCAGACAT 59.171 41.667 2.85 0.00 45.24 3.06
5207 11263 4.206375 CCATGGGTTATAATGTGCAGACA 58.794 43.478 2.85 0.00 36.22 3.41
5208 11264 4.207165 ACCATGGGTTATAATGTGCAGAC 58.793 43.478 18.09 0.00 27.29 3.51
5209 11265 4.518278 ACCATGGGTTATAATGTGCAGA 57.482 40.909 18.09 0.00 27.29 4.26
5210 11266 4.402155 ACAACCATGGGTTATAATGTGCAG 59.598 41.667 18.09 0.00 45.01 4.41
5211 11267 4.348486 ACAACCATGGGTTATAATGTGCA 58.652 39.130 18.09 0.00 45.01 4.57
5212 11268 4.400884 TGACAACCATGGGTTATAATGTGC 59.599 41.667 18.09 0.00 45.01 4.57
5213 11269 6.506147 CATGACAACCATGGGTTATAATGTG 58.494 40.000 18.09 0.00 45.01 3.21
5214 11270 6.713762 CATGACAACCATGGGTTATAATGT 57.286 37.500 18.09 1.56 45.01 2.71
5226 11282 2.622942 AGCGACAAAACATGACAACCAT 59.377 40.909 0.00 0.00 35.44 3.55
5227 11283 2.020720 AGCGACAAAACATGACAACCA 58.979 42.857 0.00 0.00 0.00 3.67
5238 11294 1.403679 CAAGGACACCAAGCGACAAAA 59.596 47.619 0.00 0.00 0.00 2.44
5258 11314 0.386838 AACACAAGCCAAAGCAGCTC 59.613 50.000 0.00 0.00 40.49 4.09
5299 11355 0.967380 CAGCCCCCAAACCTAGCAAG 60.967 60.000 0.00 0.00 0.00 4.01
5326 11382 5.783111 AGCAAAAACACAAGGCCTAAATAG 58.217 37.500 5.16 0.00 0.00 1.73
5330 11386 2.364002 GGAGCAAAAACACAAGGCCTAA 59.636 45.455 5.16 0.00 0.00 2.69
5359 11415 1.140804 AACAACCACGCCAAACTGC 59.859 52.632 0.00 0.00 0.00 4.40
5360 11416 1.145162 GCAACAACCACGCCAAACTG 61.145 55.000 0.00 0.00 0.00 3.16
5362 11418 0.869880 GAGCAACAACCACGCCAAAC 60.870 55.000 0.00 0.00 0.00 2.93
5381 11437 5.261209 AGCTATCTCTGAACTACTTGCAG 57.739 43.478 0.00 0.00 0.00 4.41
5384 11440 6.952773 ACCTAGCTATCTCTGAACTACTTG 57.047 41.667 0.00 0.00 0.00 3.16
5385 11441 7.397761 ACAAACCTAGCTATCTCTGAACTACTT 59.602 37.037 0.00 0.00 0.00 2.24
5386 11442 6.893005 ACAAACCTAGCTATCTCTGAACTACT 59.107 38.462 0.00 0.00 0.00 2.57
5418 11477 4.164796 ACCAGAAAGACATATGAGCCATGA 59.835 41.667 10.38 0.00 0.00 3.07
5448 11507 1.094785 ATAACCAACCGATGCAGCAC 58.905 50.000 1.53 0.00 0.00 4.40
5484 11543 0.529992 GGGATTCACCTACCGCTTCG 60.530 60.000 0.00 0.00 38.98 3.79
5494 11553 5.810080 AATAGTACAGCTAGGGATTCACC 57.190 43.478 0.00 0.00 32.45 4.02
5507 11566 5.670485 TGAGCCATGGTGTAAATAGTACAG 58.330 41.667 14.67 0.00 0.00 2.74
5516 11575 6.849085 AAAAACATATGAGCCATGGTGTAA 57.151 33.333 14.67 0.00 0.00 2.41
5539 11598 6.208797 TGCTACTAGCTCTCAACTACAGAAAA 59.791 38.462 9.49 0.00 42.97 2.29
5543 11612 5.124776 ACTTGCTACTAGCTCTCAACTACAG 59.875 44.000 9.49 0.00 42.97 2.74
5551 11620 8.125728 CAAGATTAAACTTGCTACTAGCTCTC 57.874 38.462 11.93 0.00 42.97 3.20
5593 11662 4.318332 TGATGGAAAAGACACTACAGCAG 58.682 43.478 0.00 0.00 0.00 4.24
5621 11690 8.919661 GGCATATAAGATACAAGGTACGTAAAC 58.080 37.037 0.00 0.00 0.00 2.01
5624 11693 6.720748 TGGGCATATAAGATACAAGGTACGTA 59.279 38.462 0.00 0.00 0.00 3.57
5625 11694 5.541101 TGGGCATATAAGATACAAGGTACGT 59.459 40.000 0.00 0.00 0.00 3.57
5626 11695 6.032956 TGGGCATATAAGATACAAGGTACG 57.967 41.667 0.00 0.00 0.00 3.67
5627 11696 7.174426 GGTTTGGGCATATAAGATACAAGGTAC 59.826 40.741 0.00 0.00 0.00 3.34
5628 11697 7.073215 AGGTTTGGGCATATAAGATACAAGGTA 59.927 37.037 0.00 0.00 0.00 3.08
5629 11698 6.068670 GGTTTGGGCATATAAGATACAAGGT 58.931 40.000 0.00 0.00 0.00 3.50
5643 11719 1.992557 TCTACTTCCAGGTTTGGGCAT 59.007 47.619 0.00 0.00 45.10 4.40
5644 11720 1.440618 TCTACTTCCAGGTTTGGGCA 58.559 50.000 0.00 0.00 45.10 5.36
5645 11721 2.437413 CTTCTACTTCCAGGTTTGGGC 58.563 52.381 0.00 0.00 45.10 5.36
5646 11722 2.642807 TCCTTCTACTTCCAGGTTTGGG 59.357 50.000 0.00 0.00 45.10 4.12
5647 11723 4.019321 TGATCCTTCTACTTCCAGGTTTGG 60.019 45.833 0.00 0.00 46.49 3.28
5650 11726 5.032846 TGATGATCCTTCTACTTCCAGGTT 58.967 41.667 0.00 0.00 0.00 3.50
5665 11741 5.714047 GAAGGTTTCTTGGTTTGATGATCC 58.286 41.667 0.00 0.00 32.52 3.36


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

AutoCloner maintained by Alex Coulton.