Multiple sequence alignment - TraesCS4B01G312000

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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 TraesCS4B01G312000 chr4B 100.000 3086 0 0 1 3086 601774159 601777244 0.000000e+00 5699.0
1 TraesCS4B01G312000 chr4D 92.515 1857 106 16 633 2480 477150379 477152211 0.000000e+00 2628.0
2 TraesCS4B01G312000 chr4D 84.868 152 14 8 475 625 477150163 477150306 8.920000e-31 145.0
3 TraesCS4B01G312000 chr4A 93.471 1501 69 14 622 2116 683929664 683931141 0.000000e+00 2202.0
4 TraesCS4B01G312000 chr4A 89.655 145 5 5 475 611 683929456 683929598 3.160000e-40 176.0
5 TraesCS4B01G312000 chr1A 84.125 989 137 13 884 1864 554875305 554876281 0.000000e+00 939.0
6 TraesCS4B01G312000 chr1A 88.732 71 4 1 741 811 554875209 554875275 1.970000e-12 84.2
7 TraesCS4B01G312000 chr1B 84.336 881 123 11 993 1864 637948857 637949731 0.000000e+00 848.0
8 TraesCS4B01G312000 chr1B 89.545 220 17 4 2680 2893 166094384 166094165 1.090000e-69 274.0
9 TraesCS4B01G312000 chr1B 89.024 82 5 1 730 811 637948618 637948695 7.040000e-17 99.0
10 TraesCS4B01G312000 chr1B 97.368 38 1 0 1269 1306 637894359 637894322 7.140000e-07 65.8
11 TraesCS4B01G312000 chrUn 94.387 481 26 1 1 481 23714552 23714073 0.000000e+00 737.0
12 TraesCS4B01G312000 chr5A 90.580 414 31 5 2680 3086 32136102 32135690 2.710000e-150 542.0
13 TraesCS4B01G312000 chr7B 90.819 403 27 9 2689 3086 134314080 134314477 5.860000e-147 531.0
14 TraesCS4B01G312000 chr7B 85.507 414 38 15 2680 3086 158041698 158042096 2.210000e-111 412.0
15 TraesCS4B01G312000 chr1D 90.073 413 27 8 2680 3086 125103793 125103389 9.800000e-145 523.0
16 TraesCS4B01G312000 chr1D 91.860 86 6 1 2587 2671 125103947 125103862 5.410000e-23 119.0
17 TraesCS4B01G312000 chr3A 89.526 401 34 5 2689 3086 361624285 361624680 4.590000e-138 501.0
18 TraesCS4B01G312000 chr3D 88.750 400 37 4 2689 3086 277929640 277929247 1.660000e-132 483.0
19 TraesCS4B01G312000 chr3D 89.402 368 34 4 2715 3080 532080966 532081330 2.800000e-125 459.0
20 TraesCS4B01G312000 chr7D 89.091 385 28 8 2680 3059 70096212 70095837 1.680000e-127 466.0
21 TraesCS4B01G312000 chr7D 80.952 84 8 6 2275 2356 599716293 599716216 3.320000e-05 60.2
22 TraesCS4B01G312000 chr7A 85.158 411 51 7 2680 3086 203860747 203861151 2.210000e-111 412.0
23 TraesCS4B01G312000 chr7A 82.105 475 40 28 1 474 55921438 55921868 6.290000e-97 364.0
24 TraesCS4B01G312000 chr5B 91.724 290 10 6 166 443 680986938 680986651 1.040000e-104 390.0
25 TraesCS4B01G312000 chr5B 93.886 229 14 0 1 229 493602696 493602468 2.280000e-91 346.0
26 TraesCS4B01G312000 chr5B 93.785 177 11 0 296 472 493600258 493600082 1.820000e-67 267.0
27 TraesCS4B01G312000 chr5B 88.789 223 16 6 1 214 680987057 680986835 6.560000e-67 265.0
28 TraesCS4B01G312000 chr3B 82.353 119 14 7 2244 2360 501422506 501422393 2.530000e-16 97.1
29 TraesCS4B01G312000 chr2D 86.905 84 11 0 2244 2327 15133426 15133343 9.110000e-16 95.3
30 TraesCS4B01G312000 chr2D 91.837 49 4 0 1051 1099 528089311 528089359 5.520000e-08 69.4
31 TraesCS4B01G312000 chr2A 85.227 88 5 4 1014 1100 672939421 672939501 1.970000e-12 84.2
32 TraesCS4B01G312000 chr2B 93.750 48 3 0 1052 1099 626056990 626057037 4.270000e-09 73.1
33 TraesCS4B01G312000 chr6D 85.075 67 8 1 2243 2307 48866817 48866751 1.990000e-07 67.6
34 TraesCS4B01G312000 chr6A 84.848 66 4 2 2243 2308 65800425 65800484 9.240000e-06 62.1


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 TraesCS4B01G312000 chr4B 601774159 601777244 3085 False 5699.0 5699 100.0000 1 3086 1 chr4B.!!$F1 3085
1 TraesCS4B01G312000 chr4D 477150163 477152211 2048 False 1386.5 2628 88.6915 475 2480 2 chr4D.!!$F1 2005
2 TraesCS4B01G312000 chr4A 683929456 683931141 1685 False 1189.0 2202 91.5630 475 2116 2 chr4A.!!$F1 1641
3 TraesCS4B01G312000 chr1A 554875209 554876281 1072 False 511.6 939 86.4285 741 1864 2 chr1A.!!$F1 1123
4 TraesCS4B01G312000 chr1B 637948618 637949731 1113 False 473.5 848 86.6800 730 1864 2 chr1B.!!$F1 1134
5 TraesCS4B01G312000 chr1D 125103389 125103947 558 True 321.0 523 90.9665 2587 3086 2 chr1D.!!$R1 499
6 TraesCS4B01G312000 chr5B 493600082 493602696 2614 True 306.5 346 93.8355 1 472 2 chr5B.!!$R1 471

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
944 3173 0.494788 GCGACGAAATCACTCGATCG 59.505 55.0 9.36 9.36 41.44 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2518 4783 0.035458 CATGGGATAGCGAGGGGAAC 59.965 60.0 0.0 0.0 0.0 3.62 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
20 21 1.893137 ACGGTGATGCTCTTGAGTACA 59.107 47.619 0.00 0.00 0.00 2.90
21 22 2.497675 ACGGTGATGCTCTTGAGTACAT 59.502 45.455 0.00 0.00 0.00 2.29
141 142 4.864334 GCGGTGGCCATGGAGAGG 62.864 72.222 18.40 0.51 0.00 3.69
144 145 2.616458 GGTGGCCATGGAGAGGGTT 61.616 63.158 18.40 0.00 0.00 4.11
164 165 1.183549 GACAGTAGAGGAGGCGGAAA 58.816 55.000 0.00 0.00 0.00 3.13
188 189 3.716195 TGGTGACCATGGCCGAGG 61.716 66.667 13.04 11.50 0.00 4.63
229 230 0.796312 AAGCGGCAACAACGACTATG 59.204 50.000 1.45 0.00 0.00 2.23
230 231 1.019278 AGCGGCAACAACGACTATGG 61.019 55.000 1.45 0.00 0.00 2.74
231 232 1.423845 CGGCAACAACGACTATGGC 59.576 57.895 0.00 0.00 35.24 4.40
232 233 1.800681 GGCAACAACGACTATGGCC 59.199 57.895 0.00 0.00 32.71 5.36
233 234 1.423845 GCAACAACGACTATGGCCG 59.576 57.895 0.00 0.00 0.00 6.13
258 2167 4.742201 GCAGCAACGGAGAGCGGA 62.742 66.667 0.00 0.00 37.20 5.54
259 2168 2.048222 CAGCAACGGAGAGCGGAA 60.048 61.111 0.00 0.00 37.20 4.30
272 2181 3.744719 CGGAAGCCACGACGGAGA 61.745 66.667 0.00 0.00 36.56 3.71
274 2183 2.507324 GAAGCCACGACGGAGAGC 60.507 66.667 0.00 0.00 36.56 4.09
278 2187 3.744719 CCACGACGGAGAGCGGAA 61.745 66.667 0.00 0.00 36.56 4.30
279 2188 2.202492 CACGACGGAGAGCGGAAG 60.202 66.667 0.00 0.00 33.86 3.46
292 2201 4.090057 GGAAGCGGCAACAGCGAC 62.090 66.667 1.45 0.00 40.31 5.19
293 2202 3.345808 GAAGCGGCAACAGCGACA 61.346 61.111 1.45 0.00 40.31 4.35
294 2203 2.892334 GAAGCGGCAACAGCGACAA 61.892 57.895 1.45 0.00 40.31 3.18
305 2449 4.195308 GCGACAATAACCGCCTGA 57.805 55.556 0.00 0.00 45.06 3.86
307 2451 1.860676 GCGACAATAACCGCCTGATA 58.139 50.000 0.00 0.00 45.06 2.15
317 2461 1.404391 ACCGCCTGATAGTCTAACACG 59.596 52.381 0.00 0.00 0.00 4.49
408 2552 1.992233 TACCGCGTACGTCCCACATC 61.992 60.000 17.90 0.00 37.70 3.06
428 2572 3.033764 GAGCCGAACGAACGCACA 61.034 61.111 0.00 0.00 0.00 4.57
429 2573 3.000080 GAGCCGAACGAACGCACAG 62.000 63.158 0.00 0.00 0.00 3.66
447 2591 3.895204 CGATACAGAGAGCGCACG 58.105 61.111 11.47 0.00 0.00 5.34
577 2721 3.788797 GCGTAATGCAGTATGGTGCTTTC 60.789 47.826 14.70 0.00 44.32 2.62
609 2761 8.988934 GTGTTAAAGAGAGAACAATGTGTGATA 58.011 33.333 0.00 0.00 37.31 2.15
610 2762 9.208022 TGTTAAAGAGAGAACAATGTGTGATAG 57.792 33.333 0.00 0.00 32.74 2.08
611 2763 8.660373 GTTAAAGAGAGAACAATGTGTGATAGG 58.340 37.037 0.00 0.00 0.00 2.57
612 2764 6.611613 AAGAGAGAACAATGTGTGATAGGA 57.388 37.500 0.00 0.00 0.00 2.94
613 2765 6.219417 AGAGAGAACAATGTGTGATAGGAG 57.781 41.667 0.00 0.00 0.00 3.69
625 2777 2.943690 GTGATAGGAGTAGCACACGAGA 59.056 50.000 0.00 0.00 43.74 4.04
629 2781 9.736671 TGTGATAGGAGTAGCACACGAGAGTAT 62.737 44.444 0.00 0.00 46.14 2.12
692 2911 4.559386 GTATGACTGCACGCGCGC 62.559 66.667 32.58 23.91 42.97 6.86
814 3033 2.425773 CGCGATTAATGCAGGCGC 60.426 61.111 0.00 0.00 43.78 6.53
830 3049 4.410743 GCAGGCCAAGCAAGCGTC 62.411 66.667 14.58 0.00 0.00 5.19
831 3050 4.093952 CAGGCCAAGCAAGCGTCG 62.094 66.667 5.01 0.00 0.00 5.12
832 3051 4.314440 AGGCCAAGCAAGCGTCGA 62.314 61.111 5.01 0.00 0.00 4.20
836 3055 2.594962 CCAAGCAAGCGTCGACGTT 61.595 57.895 35.48 29.35 42.22 3.99
839 3058 1.548973 AAGCAAGCGTCGACGTTCTG 61.549 55.000 35.48 28.36 42.22 3.02
944 3173 0.494788 GCGACGAAATCACTCGATCG 59.505 55.000 9.36 9.36 41.44 3.69
945 3174 1.854828 GCGACGAAATCACTCGATCGA 60.855 52.381 18.32 18.32 40.99 3.59
1177 3430 1.264295 GAGGTACTTCCCTGACGGTT 58.736 55.000 0.00 0.00 41.55 4.44
1178 3431 1.204231 GAGGTACTTCCCTGACGGTTC 59.796 57.143 0.00 0.00 41.55 3.62
1217 3470 6.127479 GCTGGTTGGATATCTATCTACCTCTG 60.127 46.154 9.17 2.86 37.79 3.35
1224 3477 7.667635 TGGATATCTATCTACCTCTGTCTTGTG 59.332 40.741 2.05 0.00 33.28 3.33
1479 3732 0.614697 TCTTCACGGAGCCCATCTCA 60.615 55.000 0.00 0.00 43.70 3.27
1489 3742 1.985614 CCCATCTCACTGCTGGTCA 59.014 57.895 0.00 0.00 30.30 4.02
1569 3822 0.317603 CAGACGTCACGTTCGAGGTT 60.318 55.000 19.50 0.00 41.37 3.50
1727 3986 1.684248 GGCCATGCTCCACTTCATCTT 60.684 52.381 0.00 0.00 0.00 2.40
1870 4132 0.179156 CAATCACATGGACGCAAGCC 60.179 55.000 0.00 0.00 45.62 4.35
2006 4268 1.086634 GGCTTCGAGCATGTGAGGAC 61.087 60.000 8.71 0.00 44.75 3.85
2043 4306 2.151202 CTAAGGAGCTCGTTGCCAAAA 58.849 47.619 27.49 9.02 44.23 2.44
2177 4440 4.773323 ACTTCTATTTGTGCTGCCTTTC 57.227 40.909 0.00 0.00 0.00 2.62
2179 4442 3.153369 TCTATTTGTGCTGCCTTTCCA 57.847 42.857 0.00 0.00 0.00 3.53
2180 4443 3.700538 TCTATTTGTGCTGCCTTTCCAT 58.299 40.909 0.00 0.00 0.00 3.41
2181 4444 2.754946 ATTTGTGCTGCCTTTCCATG 57.245 45.000 0.00 0.00 0.00 3.66
2188 4452 2.025037 TGCTGCCTTTCCATGGTAGATT 60.025 45.455 12.58 0.00 39.22 2.40
2207 4471 7.173390 GGTAGATTATCAGTGGCCAAAACTATC 59.827 40.741 7.24 2.76 0.00 2.08
2208 4472 6.662755 AGATTATCAGTGGCCAAAACTATCA 58.337 36.000 7.24 0.00 0.00 2.15
2212 4476 2.095059 CAGTGGCCAAAACTATCAGTGC 60.095 50.000 7.24 0.00 0.00 4.40
2236 4500 4.944962 TGCAAAGGTCGAACTTATCATG 57.055 40.909 17.70 12.15 0.00 3.07
2239 4503 4.391830 GCAAAGGTCGAACTTATCATGTCA 59.608 41.667 17.70 0.00 0.00 3.58
2241 4505 5.661056 AAGGTCGAACTTATCATGTCAGA 57.339 39.130 15.61 0.00 0.00 3.27
2242 4506 5.661056 AGGTCGAACTTATCATGTCAGAA 57.339 39.130 0.00 0.00 0.00 3.02
2261 4525 7.609146 TGTCAGAATTGCTAAATCTCAGTTGAT 59.391 33.333 0.00 0.00 0.00 2.57
2264 4528 8.456471 CAGAATTGCTAAATCTCAGTTGATTGA 58.544 33.333 0.00 0.00 36.84 2.57
2265 4529 8.675504 AGAATTGCTAAATCTCAGTTGATTGAG 58.324 33.333 0.00 0.00 44.74 3.02
2297 4561 5.150342 AGTCTCGATCGATGCTATATTCG 57.850 43.478 19.78 2.67 36.72 3.34
2298 4562 4.632251 AGTCTCGATCGATGCTATATTCGT 59.368 41.667 19.78 0.00 36.74 3.85
2300 4564 4.630069 TCTCGATCGATGCTATATTCGTGA 59.370 41.667 19.78 4.49 36.74 4.35
2312 4576 8.310406 TGCTATATTCGTGAGATTTTACATGG 57.690 34.615 0.00 0.00 41.60 3.66
2395 4659 3.757184 TCATGCGGATGAAAACAATTCG 58.243 40.909 17.99 0.00 35.55 3.34
2396 4660 2.627863 TGCGGATGAAAACAATTCGG 57.372 45.000 0.00 0.00 0.00 4.30
2399 4663 3.243569 TGCGGATGAAAACAATTCGGTTT 60.244 39.130 0.00 0.00 42.49 3.27
2403 4667 5.633182 CGGATGAAAACAATTCGGTTTCATT 59.367 36.000 23.05 13.73 39.93 2.57
2405 4669 6.183359 GGATGAAAACAATTCGGTTTCATTCG 60.183 38.462 23.05 0.00 39.93 3.34
2416 4680 3.049912 GGTTTCATTCGTGTTTTGAGCC 58.950 45.455 0.00 0.00 0.00 4.70
2418 4682 0.237235 TCATTCGTGTTTTGAGCCGC 59.763 50.000 0.00 0.00 0.00 6.53
2423 4687 3.047280 TGTTTTGAGCCGCGCGAT 61.047 55.556 34.63 20.30 0.00 4.58
2439 4704 1.257415 GCGATCTGTGCTTGAGATTCG 59.743 52.381 0.00 0.00 29.97 3.34
2446 4711 4.024893 TCTGTGCTTGAGATTCGTGTTTTC 60.025 41.667 0.00 0.00 0.00 2.29
2448 4713 3.251004 GTGCTTGAGATTCGTGTTTTCCT 59.749 43.478 0.00 0.00 0.00 3.36
2449 4714 3.498397 TGCTTGAGATTCGTGTTTTCCTC 59.502 43.478 0.00 0.00 0.00 3.71
2450 4715 3.748568 GCTTGAGATTCGTGTTTTCCTCT 59.251 43.478 0.00 0.00 0.00 3.69
2451 4716 4.214332 GCTTGAGATTCGTGTTTTCCTCTT 59.786 41.667 0.00 0.00 0.00 2.85
2452 4717 5.278022 GCTTGAGATTCGTGTTTTCCTCTTT 60.278 40.000 0.00 0.00 0.00 2.52
2453 4718 6.693315 TTGAGATTCGTGTTTTCCTCTTTT 57.307 33.333 0.00 0.00 0.00 2.27
2454 4719 6.693315 TGAGATTCGTGTTTTCCTCTTTTT 57.307 33.333 0.00 0.00 0.00 1.94
2455 4720 6.494842 TGAGATTCGTGTTTTCCTCTTTTTG 58.505 36.000 0.00 0.00 0.00 2.44
2456 4721 5.831997 AGATTCGTGTTTTCCTCTTTTTGG 58.168 37.500 0.00 0.00 0.00 3.28
2457 4722 5.359860 AGATTCGTGTTTTCCTCTTTTTGGT 59.640 36.000 0.00 0.00 0.00 3.67
2458 4723 4.625972 TCGTGTTTTCCTCTTTTTGGTC 57.374 40.909 0.00 0.00 0.00 4.02
2459 4724 3.379057 TCGTGTTTTCCTCTTTTTGGTCC 59.621 43.478 0.00 0.00 0.00 4.46
2460 4725 3.129638 CGTGTTTTCCTCTTTTTGGTCCA 59.870 43.478 0.00 0.00 0.00 4.02
2461 4726 4.430007 GTGTTTTCCTCTTTTTGGTCCAC 58.570 43.478 0.00 0.00 0.00 4.02
2462 4727 4.159693 GTGTTTTCCTCTTTTTGGTCCACT 59.840 41.667 0.00 0.00 0.00 4.00
2463 4728 4.775253 TGTTTTCCTCTTTTTGGTCCACTT 59.225 37.500 0.00 0.00 0.00 3.16
2464 4729 5.109210 GTTTTCCTCTTTTTGGTCCACTTG 58.891 41.667 0.00 0.00 0.00 3.16
2465 4730 2.944129 TCCTCTTTTTGGTCCACTTGG 58.056 47.619 0.00 0.00 0.00 3.61
2466 4731 2.512056 TCCTCTTTTTGGTCCACTTGGA 59.488 45.455 0.00 0.00 43.08 3.53
2476 4741 2.702592 TCCACTTGGACGTTGAGTTT 57.297 45.000 0.00 0.00 39.78 2.66
2477 4742 2.557317 TCCACTTGGACGTTGAGTTTC 58.443 47.619 0.00 0.00 39.78 2.78
2478 4743 2.169769 TCCACTTGGACGTTGAGTTTCT 59.830 45.455 0.00 0.00 39.78 2.52
2479 4744 2.943033 CCACTTGGACGTTGAGTTTCTT 59.057 45.455 0.00 0.00 37.39 2.52
2514 4779 5.984725 TCACTTGGACACTGAGTTTTCTTA 58.015 37.500 0.00 0.00 0.00 2.10
2515 4780 6.591935 TCACTTGGACACTGAGTTTTCTTAT 58.408 36.000 0.00 0.00 0.00 1.73
2516 4781 6.706270 TCACTTGGACACTGAGTTTTCTTATC 59.294 38.462 0.00 0.00 0.00 1.75
2517 4782 5.696724 ACTTGGACACTGAGTTTTCTTATCG 59.303 40.000 0.00 0.00 0.00 2.92
2518 4783 4.566004 TGGACACTGAGTTTTCTTATCGG 58.434 43.478 0.00 0.00 0.00 4.18
2519 4784 4.039973 TGGACACTGAGTTTTCTTATCGGT 59.960 41.667 0.00 0.00 32.79 4.69
2520 4785 4.995487 GGACACTGAGTTTTCTTATCGGTT 59.005 41.667 0.00 0.00 30.13 4.44
2521 4786 5.120363 GGACACTGAGTTTTCTTATCGGTTC 59.880 44.000 0.00 0.00 30.13 3.62
2522 4787 4.995487 ACACTGAGTTTTCTTATCGGTTCC 59.005 41.667 0.00 0.00 30.13 3.62
2523 4788 4.392138 CACTGAGTTTTCTTATCGGTTCCC 59.608 45.833 0.00 0.00 30.13 3.97
2524 4789 3.939592 CTGAGTTTTCTTATCGGTTCCCC 59.060 47.826 0.00 0.00 0.00 4.81
2525 4790 3.585732 TGAGTTTTCTTATCGGTTCCCCT 59.414 43.478 0.00 0.00 0.00 4.79
2526 4791 4.190001 GAGTTTTCTTATCGGTTCCCCTC 58.810 47.826 0.00 0.00 0.00 4.30
2527 4792 2.934553 GTTTTCTTATCGGTTCCCCTCG 59.065 50.000 0.00 0.00 0.00 4.63
2528 4793 0.462789 TTCTTATCGGTTCCCCTCGC 59.537 55.000 0.00 0.00 0.00 5.03
2529 4794 0.396695 TCTTATCGGTTCCCCTCGCT 60.397 55.000 0.00 0.00 0.00 4.93
2530 4795 1.133699 TCTTATCGGTTCCCCTCGCTA 60.134 52.381 0.00 0.00 0.00 4.26
2531 4796 1.893801 CTTATCGGTTCCCCTCGCTAT 59.106 52.381 0.00 0.00 0.00 2.97
2532 4797 1.542492 TATCGGTTCCCCTCGCTATC 58.458 55.000 0.00 0.00 0.00 2.08
2533 4798 1.186267 ATCGGTTCCCCTCGCTATCC 61.186 60.000 0.00 0.00 0.00 2.59
2534 4799 2.868986 CGGTTCCCCTCGCTATCCC 61.869 68.421 0.00 0.00 0.00 3.85
2535 4800 1.764854 GGTTCCCCTCGCTATCCCA 60.765 63.158 0.00 0.00 0.00 4.37
2536 4801 1.128188 GGTTCCCCTCGCTATCCCAT 61.128 60.000 0.00 0.00 0.00 4.00
2537 4802 0.035458 GTTCCCCTCGCTATCCCATG 59.965 60.000 0.00 0.00 0.00 3.66
2538 4803 0.399949 TTCCCCTCGCTATCCCATGT 60.400 55.000 0.00 0.00 0.00 3.21
2539 4804 0.832135 TCCCCTCGCTATCCCATGTC 60.832 60.000 0.00 0.00 0.00 3.06
2540 4805 1.290324 CCCTCGCTATCCCATGTCG 59.710 63.158 0.00 0.00 0.00 4.35
2541 4806 1.290324 CCTCGCTATCCCATGTCGG 59.710 63.158 0.00 0.00 0.00 4.79
2542 4807 1.464376 CCTCGCTATCCCATGTCGGT 61.464 60.000 0.00 0.00 0.00 4.69
2543 4808 0.039074 CTCGCTATCCCATGTCGGTC 60.039 60.000 0.00 0.00 0.00 4.79
2544 4809 1.006102 CGCTATCCCATGTCGGTCC 60.006 63.158 0.00 0.00 0.00 4.46
2545 4810 1.744320 CGCTATCCCATGTCGGTCCA 61.744 60.000 0.00 0.00 0.00 4.02
2546 4811 0.249911 GCTATCCCATGTCGGTCCAC 60.250 60.000 0.00 0.00 0.00 4.02
2547 4812 1.119684 CTATCCCATGTCGGTCCACA 58.880 55.000 0.00 0.00 0.00 4.17
2548 4813 1.484653 CTATCCCATGTCGGTCCACAA 59.515 52.381 0.00 0.00 0.00 3.33
2549 4814 0.695924 ATCCCATGTCGGTCCACAAA 59.304 50.000 0.00 0.00 0.00 2.83
2550 4815 0.036164 TCCCATGTCGGTCCACAAAG 59.964 55.000 0.00 0.00 0.00 2.77
2551 4816 0.250727 CCCATGTCGGTCCACAAAGT 60.251 55.000 0.00 0.00 0.00 2.66
2552 4817 1.156736 CCATGTCGGTCCACAAAGTC 58.843 55.000 0.00 0.00 0.00 3.01
2553 4818 1.542328 CCATGTCGGTCCACAAAGTCA 60.542 52.381 0.00 0.00 0.00 3.41
2554 4819 2.426522 CATGTCGGTCCACAAAGTCAT 58.573 47.619 0.00 0.00 0.00 3.06
2555 4820 3.595173 CATGTCGGTCCACAAAGTCATA 58.405 45.455 0.00 0.00 0.00 2.15
2556 4821 3.973206 TGTCGGTCCACAAAGTCATAT 57.027 42.857 0.00 0.00 0.00 1.78
2557 4822 4.280436 TGTCGGTCCACAAAGTCATATT 57.720 40.909 0.00 0.00 0.00 1.28
2558 4823 4.000325 TGTCGGTCCACAAAGTCATATTG 59.000 43.478 0.00 0.00 0.00 1.90
2559 4824 4.000988 GTCGGTCCACAAAGTCATATTGT 58.999 43.478 0.00 0.00 41.50 2.71
2567 4832 5.235305 ACAAAGTCATATTGTGCGATTCC 57.765 39.130 0.00 0.00 39.43 3.01
2568 4833 4.201812 ACAAAGTCATATTGTGCGATTCCG 60.202 41.667 0.00 0.00 39.43 4.30
2569 4834 3.179443 AGTCATATTGTGCGATTCCGT 57.821 42.857 0.00 0.00 38.24 4.69
2570 4835 2.866156 AGTCATATTGTGCGATTCCGTG 59.134 45.455 0.00 0.00 38.24 4.94
2571 4836 2.863740 GTCATATTGTGCGATTCCGTGA 59.136 45.455 0.00 0.00 38.24 4.35
2572 4837 3.494626 GTCATATTGTGCGATTCCGTGAT 59.505 43.478 0.00 0.00 38.24 3.06
2573 4838 3.494251 TCATATTGTGCGATTCCGTGATG 59.506 43.478 0.00 0.00 38.24 3.07
2574 4839 1.737838 ATTGTGCGATTCCGTGATGT 58.262 45.000 0.00 0.00 38.24 3.06
2575 4840 2.371910 TTGTGCGATTCCGTGATGTA 57.628 45.000 0.00 0.00 38.24 2.29
2576 4841 1.635844 TGTGCGATTCCGTGATGTAC 58.364 50.000 0.00 0.00 38.24 2.90
2577 4842 0.928229 GTGCGATTCCGTGATGTACC 59.072 55.000 0.00 0.00 38.24 3.34
2578 4843 0.526739 TGCGATTCCGTGATGTACCG 60.527 55.000 0.00 0.00 38.24 4.02
2579 4844 1.213094 GCGATTCCGTGATGTACCGG 61.213 60.000 0.00 0.00 45.55 5.28
2580 4845 1.213094 CGATTCCGTGATGTACCGGC 61.213 60.000 0.00 0.00 43.87 6.13
2581 4846 0.179094 GATTCCGTGATGTACCGGCA 60.179 55.000 0.00 0.00 43.87 5.69
2582 4847 0.250793 ATTCCGTGATGTACCGGCAA 59.749 50.000 0.00 0.00 43.87 4.52
2583 4848 0.250793 TTCCGTGATGTACCGGCAAT 59.749 50.000 0.00 0.00 43.87 3.56
2584 4849 1.112950 TCCGTGATGTACCGGCAATA 58.887 50.000 0.00 0.00 43.87 1.90
2585 4850 1.481363 TCCGTGATGTACCGGCAATAA 59.519 47.619 0.00 0.00 43.87 1.40
2671 4937 9.988815 AATTGAATACCTAGTCTAATACAGCTG 57.011 33.333 13.48 13.48 0.00 4.24
2672 4938 6.982852 TGAATACCTAGTCTAATACAGCTGC 58.017 40.000 15.27 0.00 0.00 5.25
2674 4940 7.942894 TGAATACCTAGTCTAATACAGCTGCTA 59.057 37.037 15.27 6.05 0.00 3.49
2675 4941 7.690952 ATACCTAGTCTAATACAGCTGCTAC 57.309 40.000 15.27 3.17 0.00 3.58
2678 5004 7.288560 ACCTAGTCTAATACAGCTGCTACTTA 58.711 38.462 15.27 5.74 0.00 2.24
2687 5013 8.425577 AATACAGCTGCTACTTAATGTTACAG 57.574 34.615 15.27 0.00 35.08 2.74
2710 5040 4.500545 GCTCACTCTCTCTTTTCTCACACA 60.501 45.833 0.00 0.00 0.00 3.72
2712 5042 4.402474 TCACTCTCTCTTTTCTCACACACA 59.598 41.667 0.00 0.00 0.00 3.72
2713 5043 5.069648 TCACTCTCTCTTTTCTCACACACAT 59.930 40.000 0.00 0.00 0.00 3.21
2726 5056 3.444388 TCACACACATGCATGCATATGTT 59.556 39.130 35.67 24.85 40.69 2.71
2760 5090 2.198827 TGCGAACAAATCCATGGACT 57.801 45.000 18.99 1.87 0.00 3.85
2860 5190 1.673009 CCCGGCGCCAAGACTTTTA 60.673 57.895 28.98 0.00 0.00 1.52
2950 5281 9.712305 TGAAATAAACCTGTTTCACTTGAAAAA 57.288 25.926 5.98 0.31 44.58 1.94
2953 5284 9.665719 AATAAACCTGTTTCACTTGAAAAATGT 57.334 25.926 5.98 1.99 44.58 2.71
2954 5285 6.966435 AACCTGTTTCACTTGAAAAATGTG 57.034 33.333 5.98 0.00 44.58 3.21
2955 5286 6.036577 ACCTGTTTCACTTGAAAAATGTGT 57.963 33.333 5.98 0.00 44.58 3.72
2956 5287 6.463360 ACCTGTTTCACTTGAAAAATGTGTT 58.537 32.000 5.98 0.00 44.58 3.32
2957 5288 6.589907 ACCTGTTTCACTTGAAAAATGTGTTC 59.410 34.615 5.98 0.00 44.58 3.18
2988 5319 6.979817 TGAAACAAGACAATGGAAGTGAAATG 59.020 34.615 0.00 0.00 34.17 2.32
2990 5321 6.076981 ACAAGACAATGGAAGTGAAATGTC 57.923 37.500 0.00 0.00 34.17 3.06
3004 5335 5.124776 AGTGAAATGTCGGTTTTGAAAGTGA 59.875 36.000 0.00 0.00 0.00 3.41
3005 5336 5.802956 GTGAAATGTCGGTTTTGAAAGTGAA 59.197 36.000 0.00 0.00 0.00 3.18
3065 5397 7.925043 ACGATTATTTGGTAATGTGTAACCA 57.075 32.000 0.00 0.00 43.99 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.117285 AGATAACATGTACTCAAGAGCATCA 57.883 36.000 0.00 0.00 37.82 3.07
20 21 5.481473 AGCCACACCATCAAAAAGATAACAT 59.519 36.000 0.00 0.00 34.43 2.71
21 22 4.832266 AGCCACACCATCAAAAAGATAACA 59.168 37.500 0.00 0.00 34.43 2.41
141 142 0.173708 CGCCTCCTCTACTGTCAACC 59.826 60.000 0.00 0.00 0.00 3.77
144 145 0.039180 TTCCGCCTCCTCTACTGTCA 59.961 55.000 0.00 0.00 0.00 3.58
170 171 2.436646 CTCGGCCATGGTCACCAC 60.437 66.667 18.31 0.00 35.80 4.16
207 208 3.342627 TCGTTGTTGCCGCTTCCG 61.343 61.111 0.00 0.00 0.00 4.30
221 222 3.537874 GCCCTCGGCCATAGTCGT 61.538 66.667 2.24 0.00 44.06 4.34
243 2152 2.262915 CTTCCGCTCTCCGTTGCT 59.737 61.111 0.00 0.00 34.38 3.91
244 2153 3.491652 GCTTCCGCTCTCCGTTGC 61.492 66.667 0.00 0.00 34.38 4.17
246 2155 3.311110 TGGCTTCCGCTCTCCGTT 61.311 61.111 0.00 0.00 36.09 4.44
251 2160 4.421479 CGTCGTGGCTTCCGCTCT 62.421 66.667 0.00 0.00 36.09 4.09
255 2164 3.685214 CTCTCCGTCGTGGCTTCCG 62.685 68.421 0.00 0.00 37.80 4.30
256 2165 2.182030 CTCTCCGTCGTGGCTTCC 59.818 66.667 0.00 0.00 37.80 3.46
258 2167 4.421479 CGCTCTCCGTCGTGGCTT 62.421 66.667 0.00 0.00 37.80 4.35
262 2171 2.202492 CTTCCGCTCTCCGTCGTG 60.202 66.667 0.00 0.00 34.38 4.35
263 2172 4.117661 GCTTCCGCTCTCCGTCGT 62.118 66.667 0.00 0.00 34.38 4.34
268 2177 4.760047 TTGCCGCTTCCGCTCTCC 62.760 66.667 0.00 0.00 0.00 3.71
276 2185 2.187599 ATTGTCGCTGTTGCCGCTTC 62.188 55.000 0.00 0.00 35.36 3.86
278 2187 0.953471 TTATTGTCGCTGTTGCCGCT 60.953 50.000 0.00 0.00 35.36 5.52
279 2188 0.793104 GTTATTGTCGCTGTTGCCGC 60.793 55.000 0.00 0.00 35.36 6.53
280 2189 0.179200 GGTTATTGTCGCTGTTGCCG 60.179 55.000 0.00 0.00 35.36 5.69
281 2190 0.179200 CGGTTATTGTCGCTGTTGCC 60.179 55.000 0.00 0.00 35.36 4.52
282 2191 3.290098 CGGTTATTGTCGCTGTTGC 57.710 52.632 0.00 0.00 0.00 4.17
289 2198 3.050619 GACTATCAGGCGGTTATTGTCG 58.949 50.000 0.00 0.00 0.00 4.35
292 2201 5.462398 GTGTTAGACTATCAGGCGGTTATTG 59.538 44.000 0.00 0.00 0.00 1.90
293 2202 5.598769 GTGTTAGACTATCAGGCGGTTATT 58.401 41.667 0.00 0.00 0.00 1.40
294 2203 4.261489 CGTGTTAGACTATCAGGCGGTTAT 60.261 45.833 1.43 0.00 0.00 1.89
305 2449 1.667724 CGGACGGTCGTGTTAGACTAT 59.332 52.381 0.00 0.00 40.76 2.12
307 2451 1.871772 CGGACGGTCGTGTTAGACT 59.128 57.895 0.00 0.00 40.76 3.24
347 2491 4.746115 GGGATATTTATTGTGCGTACGTGA 59.254 41.667 17.90 0.58 0.00 4.35
355 2499 4.892934 TGGTTGAGGGGATATTTATTGTGC 59.107 41.667 0.00 0.00 0.00 4.57
428 2572 1.064946 GTGCGCTCTCTGTATCGCT 59.935 57.895 9.73 0.00 46.73 4.93
429 2573 2.289375 CGTGCGCTCTCTGTATCGC 61.289 63.158 9.73 0.00 46.78 4.58
447 2591 2.811317 CTTGGCGTGGACGAGCTC 60.811 66.667 2.73 2.73 43.02 4.09
473 2617 2.186125 CTAGGACCGGTTTCGCCC 59.814 66.667 9.42 4.48 34.56 6.13
557 2701 3.694072 TGGAAAGCACCATACTGCATTAC 59.306 43.478 0.00 0.00 39.86 1.89
558 2702 3.947196 CTGGAAAGCACCATACTGCATTA 59.053 43.478 0.00 0.00 39.86 1.90
577 2721 2.737252 GTTCTCTCTTTAACACGGCTGG 59.263 50.000 0.00 0.00 0.00 4.85
609 2761 2.783609 TACTCTCGTGTGCTACTCCT 57.216 50.000 0.00 0.00 0.00 3.69
610 2762 2.033550 CCATACTCTCGTGTGCTACTCC 59.966 54.545 0.00 0.00 31.62 3.85
611 2763 2.683867 ACCATACTCTCGTGTGCTACTC 59.316 50.000 0.00 0.00 31.62 2.59
612 2764 2.423892 CACCATACTCTCGTGTGCTACT 59.576 50.000 0.00 0.00 31.62 2.57
613 2765 2.798680 CACCATACTCTCGTGTGCTAC 58.201 52.381 0.00 0.00 31.62 3.58
692 2911 1.221021 GGTACCTTTGCCGAGGAGG 59.779 63.158 4.06 0.00 39.25 4.30
814 3033 4.093952 CGACGCTTGCTTGGCCTG 62.094 66.667 3.32 0.00 0.00 4.85
817 3036 4.430423 CGTCGACGCTTGCTTGGC 62.430 66.667 26.59 0.00 0.00 4.52
818 3037 2.480426 GAACGTCGACGCTTGCTTGG 62.480 60.000 35.92 8.80 44.43 3.61
819 3038 1.154836 GAACGTCGACGCTTGCTTG 60.155 57.895 35.92 9.56 44.43 4.01
820 3039 1.299926 AGAACGTCGACGCTTGCTT 60.300 52.632 35.92 22.76 44.43 3.91
821 3040 2.016704 CAGAACGTCGACGCTTGCT 61.017 57.895 35.92 23.75 44.43 3.91
824 3043 0.385723 GAGTCAGAACGTCGACGCTT 60.386 55.000 35.92 27.15 44.43 4.68
825 3044 1.207085 GAGTCAGAACGTCGACGCT 59.793 57.895 35.92 26.30 44.43 5.07
826 3045 1.796749 GGAGTCAGAACGTCGACGC 60.797 63.158 35.92 21.50 44.43 5.19
828 3047 0.725118 CACGGAGTCAGAACGTCGAC 60.725 60.000 5.18 5.18 41.61 4.20
829 3048 1.572941 CACGGAGTCAGAACGTCGA 59.427 57.895 0.00 0.00 41.61 4.20
830 3049 2.081212 GCACGGAGTCAGAACGTCG 61.081 63.158 0.00 0.00 41.61 5.12
831 3050 0.318784 AAGCACGGAGTCAGAACGTC 60.319 55.000 0.00 0.00 41.61 4.34
832 3051 0.104304 AAAGCACGGAGTCAGAACGT 59.896 50.000 0.00 0.00 41.61 3.99
836 3055 0.318441 CTGGAAAGCACGGAGTCAGA 59.682 55.000 0.00 0.00 41.61 3.27
839 3058 2.383527 CGCTGGAAAGCACGGAGTC 61.384 63.158 0.00 0.00 41.61 3.36
871 3090 8.447053 GCTTCTGAGGTTCTTAAACTTCTTATG 58.553 37.037 2.74 0.00 40.96 1.90
944 3173 0.179070 GAGCCTGGGAAGAACGGATC 60.179 60.000 0.00 0.00 0.00 3.36
945 3174 1.908483 GAGCCTGGGAAGAACGGAT 59.092 57.895 0.00 0.00 0.00 4.18
1446 3699 2.111384 GTGAAGATCTCCCTAGGCACA 58.889 52.381 2.05 0.00 0.00 4.57
1551 3804 0.317603 CAACCTCGAACGTGACGTCT 60.318 55.000 12.37 1.31 39.99 4.18
1554 3807 1.002250 CTCCAACCTCGAACGTGACG 61.002 60.000 2.24 2.24 0.00 4.35
1569 3822 2.357034 GCAAACGTCTCGCCTCCA 60.357 61.111 0.00 0.00 0.00 3.86
1727 3986 2.640302 GGCGGCAGAGAGTCTGTGA 61.640 63.158 20.86 0.00 45.94 3.58
1905 4167 2.032528 TTGAGCCCGCAACAGGAG 59.967 61.111 0.00 0.00 0.00 3.69
2043 4306 4.219288 GCCTGTCTCAAATCAAGGTGAAAT 59.781 41.667 0.00 0.00 0.00 2.17
2145 4408 9.587772 CAGCACAAATAGAAGTACTAGTACATT 57.412 33.333 29.87 21.28 38.48 2.71
2177 4440 3.072915 TGGCCACTGATAATCTACCATGG 59.927 47.826 11.19 11.19 0.00 3.66
2179 4442 5.387113 TTTGGCCACTGATAATCTACCAT 57.613 39.130 3.88 0.00 0.00 3.55
2180 4443 4.853468 TTTGGCCACTGATAATCTACCA 57.147 40.909 3.88 0.00 0.00 3.25
2181 4444 5.193679 AGTTTTGGCCACTGATAATCTACC 58.806 41.667 3.88 0.00 0.00 3.18
2188 4452 5.185454 CACTGATAGTTTTGGCCACTGATA 58.815 41.667 3.88 0.00 0.00 2.15
2207 4471 1.725641 TCGACCTTTGCATAGCACTG 58.274 50.000 0.00 0.00 38.71 3.66
2208 4472 2.076863 GTTCGACCTTTGCATAGCACT 58.923 47.619 0.00 0.00 38.71 4.40
2212 4476 6.258727 ACATGATAAGTTCGACCTTTGCATAG 59.741 38.462 0.00 0.00 0.00 2.23
2236 4500 7.369803 TCAACTGAGATTTAGCAATTCTGAC 57.630 36.000 0.00 0.00 0.00 3.51
2239 4503 8.571461 TCAATCAACTGAGATTTAGCAATTCT 57.429 30.769 0.00 0.00 36.13 2.40
2241 4505 8.571461 TCTCAATCAACTGAGATTTAGCAATT 57.429 30.769 0.00 0.00 45.45 2.32
2267 4531 5.753744 AGCATCGATCGAGACTTAGTTAAG 58.246 41.667 23.84 2.75 39.18 1.85
2268 4532 5.752892 AGCATCGATCGAGACTTAGTTAA 57.247 39.130 23.84 0.00 0.00 2.01
2269 4533 8.719560 ATATAGCATCGATCGAGACTTAGTTA 57.280 34.615 23.84 10.69 0.00 2.24
2273 4537 6.313164 ACGAATATAGCATCGATCGAGACTTA 59.687 38.462 23.84 15.67 41.43 2.24
2276 4540 4.726229 CACGAATATAGCATCGATCGAGAC 59.274 45.833 23.84 16.99 41.43 3.36
2278 4542 4.898370 TCACGAATATAGCATCGATCGAG 58.102 43.478 23.84 15.68 41.43 4.04
2281 4545 7.748031 AAATCTCACGAATATAGCATCGATC 57.252 36.000 11.05 0.00 41.43 3.69
2282 4546 9.077674 GTAAAATCTCACGAATATAGCATCGAT 57.922 33.333 11.05 0.00 41.43 3.59
2349 4613 9.244799 GAAATTAGGCAATTCGGTATAAAAAGG 57.755 33.333 0.00 0.00 33.09 3.11
2358 4622 3.489059 CGCATGAAATTAGGCAATTCGGT 60.489 43.478 0.00 0.00 33.09 4.69
2395 4659 3.049912 GGCTCAAAACACGAATGAAACC 58.950 45.455 0.00 0.00 0.00 3.27
2396 4660 2.719046 CGGCTCAAAACACGAATGAAAC 59.281 45.455 0.00 0.00 0.00 2.78
2399 4663 0.237235 GCGGCTCAAAACACGAATGA 59.763 50.000 0.00 0.00 0.00 2.57
2403 4667 4.007940 GCGCGGCTCAAAACACGA 62.008 61.111 8.83 0.00 0.00 4.35
2405 4669 3.308878 ATCGCGCGGCTCAAAACAC 62.309 57.895 31.69 0.00 0.00 3.32
2416 4680 3.135382 CTCAAGCACAGATCGCGCG 62.135 63.158 26.76 26.76 0.00 6.86
2418 4682 1.257415 GAATCTCAAGCACAGATCGCG 59.743 52.381 0.00 0.00 29.82 5.87
2423 4687 2.820059 ACACGAATCTCAAGCACAGA 57.180 45.000 0.00 0.00 0.00 3.41
2439 4704 4.159693 AGTGGACCAAAAAGAGGAAAACAC 59.840 41.667 0.00 0.00 0.00 3.32
2446 4711 2.944129 TCCAAGTGGACCAAAAAGAGG 58.056 47.619 0.00 0.00 39.78 3.69
2457 4722 2.169769 AGAAACTCAACGTCCAAGTGGA 59.830 45.455 0.00 0.00 43.08 4.02
2458 4723 2.561569 AGAAACTCAACGTCCAAGTGG 58.438 47.619 0.00 0.00 0.00 4.00
2459 4724 4.616181 AAAGAAACTCAACGTCCAAGTG 57.384 40.909 0.00 0.00 0.00 3.16
2460 4725 5.638596 AAAAAGAAACTCAACGTCCAAGT 57.361 34.783 0.00 0.00 0.00 3.16
2487 4752 1.141053 ACTCAGTGTCCAAGTGAACCC 59.859 52.381 0.00 0.00 37.79 4.11
2491 4756 4.487714 AGAAAACTCAGTGTCCAAGTGA 57.512 40.909 0.00 0.00 36.75 3.41
2493 4758 5.696724 CGATAAGAAAACTCAGTGTCCAAGT 59.303 40.000 0.00 0.00 0.00 3.16
2498 4763 5.120363 GGAACCGATAAGAAAACTCAGTGTC 59.880 44.000 0.00 0.00 0.00 3.67
2518 4783 0.035458 CATGGGATAGCGAGGGGAAC 59.965 60.000 0.00 0.00 0.00 3.62
2519 4784 0.399949 ACATGGGATAGCGAGGGGAA 60.400 55.000 0.00 0.00 0.00 3.97
2520 4785 0.832135 GACATGGGATAGCGAGGGGA 60.832 60.000 0.00 0.00 0.00 4.81
2521 4786 1.674057 GACATGGGATAGCGAGGGG 59.326 63.158 0.00 0.00 0.00 4.79
2522 4787 1.290324 CGACATGGGATAGCGAGGG 59.710 63.158 0.00 0.00 0.00 4.30
2523 4788 1.290324 CCGACATGGGATAGCGAGG 59.710 63.158 0.00 0.00 0.00 4.63
2524 4789 0.039074 GACCGACATGGGATAGCGAG 60.039 60.000 0.00 0.00 44.64 5.03
2525 4790 1.461091 GGACCGACATGGGATAGCGA 61.461 60.000 0.00 0.00 44.64 4.93
2526 4791 1.006102 GGACCGACATGGGATAGCG 60.006 63.158 0.00 0.00 44.64 4.26
2527 4792 0.249911 GTGGACCGACATGGGATAGC 60.250 60.000 0.00 0.00 44.64 2.97
2528 4793 1.119684 TGTGGACCGACATGGGATAG 58.880 55.000 0.00 0.00 44.64 2.08
2529 4794 1.574263 TTGTGGACCGACATGGGATA 58.426 50.000 0.00 0.00 44.64 2.59
2530 4795 0.695924 TTTGTGGACCGACATGGGAT 59.304 50.000 0.00 0.00 44.64 3.85
2531 4796 0.036164 CTTTGTGGACCGACATGGGA 59.964 55.000 0.00 0.00 44.64 4.37
2532 4797 0.250727 ACTTTGTGGACCGACATGGG 60.251 55.000 0.00 0.00 44.64 4.00
2533 4798 1.156736 GACTTTGTGGACCGACATGG 58.843 55.000 0.00 0.00 46.41 3.66
2534 4799 1.877637 TGACTTTGTGGACCGACATG 58.122 50.000 0.00 0.00 0.00 3.21
2535 4800 2.859165 ATGACTTTGTGGACCGACAT 57.141 45.000 0.00 0.00 0.00 3.06
2536 4801 3.973206 ATATGACTTTGTGGACCGACA 57.027 42.857 0.00 0.00 0.00 4.35
2537 4802 4.000988 ACAATATGACTTTGTGGACCGAC 58.999 43.478 0.00 0.00 36.02 4.79
2538 4803 4.000325 CACAATATGACTTTGTGGACCGA 59.000 43.478 8.33 0.00 46.46 4.69
2539 4804 4.340894 CACAATATGACTTTGTGGACCG 57.659 45.455 8.33 0.00 46.46 4.79
2545 4810 4.201812 CGGAATCGCACAATATGACTTTGT 60.202 41.667 0.00 0.00 37.79 2.83
2546 4811 4.201812 ACGGAATCGCACAATATGACTTTG 60.202 41.667 0.00 0.00 40.63 2.77
2547 4812 3.938963 ACGGAATCGCACAATATGACTTT 59.061 39.130 0.00 0.00 40.63 2.66
2548 4813 3.309682 CACGGAATCGCACAATATGACTT 59.690 43.478 0.00 0.00 40.63 3.01
2549 4814 2.866156 CACGGAATCGCACAATATGACT 59.134 45.455 0.00 0.00 40.63 3.41
2550 4815 2.863740 TCACGGAATCGCACAATATGAC 59.136 45.455 0.00 0.00 40.63 3.06
2551 4816 3.172229 TCACGGAATCGCACAATATGA 57.828 42.857 0.00 0.00 40.63 2.15
2552 4817 3.248363 ACATCACGGAATCGCACAATATG 59.752 43.478 0.00 0.00 40.63 1.78
2553 4818 3.466836 ACATCACGGAATCGCACAATAT 58.533 40.909 0.00 0.00 40.63 1.28
2554 4819 2.899976 ACATCACGGAATCGCACAATA 58.100 42.857 0.00 0.00 40.63 1.90
2555 4820 1.737838 ACATCACGGAATCGCACAAT 58.262 45.000 0.00 0.00 40.63 2.71
2556 4821 1.996898 GTACATCACGGAATCGCACAA 59.003 47.619 0.00 0.00 40.63 3.33
2557 4822 1.635844 GTACATCACGGAATCGCACA 58.364 50.000 0.00 0.00 40.63 4.57
2558 4823 0.928229 GGTACATCACGGAATCGCAC 59.072 55.000 0.00 0.00 40.63 5.34
2559 4824 0.526739 CGGTACATCACGGAATCGCA 60.527 55.000 0.00 0.00 40.63 5.10
2560 4825 2.213483 CGGTACATCACGGAATCGC 58.787 57.895 0.00 0.00 40.63 4.58
2567 4832 2.478894 GGATTATTGCCGGTACATCACG 59.521 50.000 1.90 0.00 0.00 4.35
2568 4833 3.472652 TGGATTATTGCCGGTACATCAC 58.527 45.455 1.90 0.00 0.00 3.06
2569 4834 3.847671 TGGATTATTGCCGGTACATCA 57.152 42.857 1.90 0.00 0.00 3.07
2570 4835 4.332819 GCTATGGATTATTGCCGGTACATC 59.667 45.833 1.90 0.00 32.34 3.06
2571 4836 4.019321 AGCTATGGATTATTGCCGGTACAT 60.019 41.667 1.90 0.00 38.13 2.29
2572 4837 3.326588 AGCTATGGATTATTGCCGGTACA 59.673 43.478 1.90 0.00 38.13 2.90
2573 4838 3.684788 CAGCTATGGATTATTGCCGGTAC 59.315 47.826 1.90 0.00 38.13 3.34
2574 4839 3.868369 GCAGCTATGGATTATTGCCGGTA 60.868 47.826 1.90 0.00 38.13 4.02
2575 4840 2.783135 CAGCTATGGATTATTGCCGGT 58.217 47.619 1.90 0.00 38.13 5.28
2576 4841 1.470098 GCAGCTATGGATTATTGCCGG 59.530 52.381 0.00 0.00 38.13 6.13
2577 4842 2.430465 AGCAGCTATGGATTATTGCCG 58.570 47.619 0.00 0.00 38.13 5.69
2578 4843 4.861102 AAAGCAGCTATGGATTATTGCC 57.139 40.909 0.00 0.00 38.13 4.52
2579 4844 7.206981 TCTTAAAGCAGCTATGGATTATTGC 57.793 36.000 0.00 0.00 37.73 3.56
2580 4845 9.837525 GAATCTTAAAGCAGCTATGGATTATTG 57.162 33.333 0.00 0.00 0.00 1.90
2581 4846 8.725148 CGAATCTTAAAGCAGCTATGGATTATT 58.275 33.333 0.00 0.00 0.00 1.40
2582 4847 7.335422 CCGAATCTTAAAGCAGCTATGGATTAT 59.665 37.037 0.00 0.00 0.00 1.28
2583 4848 6.650807 CCGAATCTTAAAGCAGCTATGGATTA 59.349 38.462 0.00 0.00 0.00 1.75
2584 4849 5.471456 CCGAATCTTAAAGCAGCTATGGATT 59.529 40.000 0.00 4.05 0.00 3.01
2585 4850 4.999950 CCGAATCTTAAAGCAGCTATGGAT 59.000 41.667 0.00 0.00 0.00 3.41
2618 4883 8.527810 TGTATAGCAAAAAGGGGAAAATTAGTG 58.472 33.333 0.00 0.00 0.00 2.74
2647 4913 7.287927 AGCAGCTGTATTAGACTAGGTATTCAA 59.712 37.037 16.64 0.00 0.00 2.69
2656 4922 9.132923 ACATTAAGTAGCAGCTGTATTAGACTA 57.867 33.333 16.64 3.19 0.00 2.59
2671 4937 6.334202 AGAGTGAGCTGTAACATTAAGTAGC 58.666 40.000 0.00 0.00 0.00 3.58
2672 4938 7.767261 AGAGAGTGAGCTGTAACATTAAGTAG 58.233 38.462 0.00 0.00 0.00 2.57
2674 4940 6.435904 AGAGAGAGTGAGCTGTAACATTAAGT 59.564 38.462 0.00 0.00 0.00 2.24
2675 4941 6.862209 AGAGAGAGTGAGCTGTAACATTAAG 58.138 40.000 0.00 0.00 0.00 1.85
2678 5004 5.736951 AAGAGAGAGTGAGCTGTAACATT 57.263 39.130 0.00 0.00 0.00 2.71
2687 5013 3.987220 GTGTGAGAAAAGAGAGAGTGAGC 59.013 47.826 0.00 0.00 0.00 4.26
2844 5174 1.128692 CTTCTAAAAGTCTTGGCGCCG 59.871 52.381 23.90 8.74 0.00 6.46
2845 5175 2.152016 ACTTCTAAAAGTCTTGGCGCC 58.848 47.619 22.73 22.73 42.10 6.53
2846 5176 5.145059 GTTTACTTCTAAAAGTCTTGGCGC 58.855 41.667 0.00 0.00 44.64 6.53
2936 5267 9.316859 CAAAAGAACACATTTTTCAAGTGAAAC 57.683 29.630 5.98 0.00 43.01 2.78
2950 5281 6.686630 TGTCTTGTTTCACAAAAGAACACAT 58.313 32.000 0.00 0.00 37.69 3.21
2951 5282 6.078202 TGTCTTGTTTCACAAAAGAACACA 57.922 33.333 0.00 0.00 37.69 3.72
2952 5283 7.411804 CCATTGTCTTGTTTCACAAAAGAACAC 60.412 37.037 0.00 0.00 37.69 3.32
2953 5284 6.589523 CCATTGTCTTGTTTCACAAAAGAACA 59.410 34.615 0.00 0.00 37.69 3.18
2954 5285 6.811170 TCCATTGTCTTGTTTCACAAAAGAAC 59.189 34.615 0.00 0.00 37.69 3.01
2955 5286 6.929625 TCCATTGTCTTGTTTCACAAAAGAA 58.070 32.000 0.00 0.00 37.69 2.52
2956 5287 6.522625 TCCATTGTCTTGTTTCACAAAAGA 57.477 33.333 0.00 0.00 37.69 2.52
2957 5288 6.813152 ACTTCCATTGTCTTGTTTCACAAAAG 59.187 34.615 0.00 0.00 37.69 2.27
2973 5304 4.503741 AACCGACATTTCACTTCCATTG 57.496 40.909 0.00 0.00 0.00 2.82
2975 5306 4.582656 TCAAAACCGACATTTCACTTCCAT 59.417 37.500 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.