Multiple sequence alignment - TraesCS1A01G015100

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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 TraesCS1A01G015100 chr1A 100.000 2742 0 0 1 2742 8240351 8237610 0.000000e+00 5064.0
1 TraesCS1A01G015100 chr1D 92.985 1454 75 11 1 1435 6767659 6766214 0.000000e+00 2095.0
2 TraesCS1A01G015100 chr1D 86.694 992 78 33 1383 2348 6766214 6765251 0.000000e+00 1051.0
3 TraesCS1A01G015100 chr1D 82.292 288 36 10 2468 2742 6765247 6764962 4.560000e-58 235.0
4 TraesCS1A01G015100 chr1B 92.674 1447 83 10 1 1425 9080337 9081782 0.000000e+00 2063.0
5 TraesCS1A01G015100 chr1B 86.047 946 67 32 1380 2298 9081788 9082695 0.000000e+00 955.0
6 TraesCS1A01G015100 chr1B 90.286 175 15 2 2570 2742 9091025 9091199 7.640000e-56 228.0
7 TraesCS1A01G015100 chr1B 91.026 78 5 2 2277 2352 9082977 9083054 1.340000e-18 104.0
8 TraesCS1A01G015100 chr1B 79.699 133 23 4 2467 2596 9083053 9083184 2.910000e-15 93.5
9 TraesCS1A01G015100 chr7A 92.188 128 9 1 2348 2475 595072412 595072538 2.170000e-41 180.0
10 TraesCS1A01G015100 chr2B 92.800 125 8 1 2348 2472 12004866 12004989 2.170000e-41 180.0
11 TraesCS1A01G015100 chr2A 93.333 120 8 0 2351 2470 606523804 606523685 7.800000e-41 178.0
12 TraesCS1A01G015100 chr2A 92.623 122 9 0 2347 2468 78845568 78845689 2.810000e-40 176.0
13 TraesCS1A01G015100 chr2A 89.286 140 13 1 2331 2470 688769153 688769290 1.010000e-39 174.0
14 TraesCS1A01G015100 chr2A 92.437 119 9 0 2351 2469 539014698 539014580 1.310000e-38 171.0
15 TraesCS1A01G015100 chr7D 91.935 124 10 0 2348 2471 57073211 57073334 1.010000e-39 174.0
16 TraesCS1A01G015100 chr5A 92.063 126 7 3 2351 2475 108623912 108623789 1.010000e-39 174.0
17 TraesCS1A01G015100 chr6D 88.732 142 13 3 2348 2487 17055123 17054983 1.310000e-38 171.0


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 TraesCS1A01G015100 chr1A 8237610 8240351 2741 True 5064.000 5064 100.000000 1 2742 1 chr1A.!!$R1 2741
1 TraesCS1A01G015100 chr1D 6764962 6767659 2697 True 1127.000 2095 87.323667 1 2742 3 chr1D.!!$R1 2741
2 TraesCS1A01G015100 chr1B 9080337 9083184 2847 False 803.875 2063 87.361500 1 2596 4 chr1B.!!$F2 2595

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
503 523 0.318762 AAGAAGAGACGGCTTCGCTT 59.681 50.0 9.62 9.62 46.13 4.68 F
1143 1180 0.035439 CTGGGGCGAAACTGGTATGT 60.035 55.0 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1700 0.182537 ACCAGCAGTTTAGCCACACA 59.817 50.0 0.00 0.00 34.23 3.72 R
2425 2852 0.843309 TGTCCCAAGCTTGTTCCTCA 59.157 50.0 24.35 12.85 0.00 3.86 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
122 124 3.941483 CCCTCTGGCACTTATTTGTACTG 59.059 47.826 0.00 0.00 0.00 2.74
163 165 1.926561 TCATCCGATCTGCTTTGTCG 58.073 50.000 0.00 0.00 35.29 4.35
229 249 7.766619 AAAGCTGAAATCTTTGTGCGAGAGC 62.767 44.000 0.00 0.00 43.85 4.09
262 282 7.009179 ACTGAAGGACATCAAACTGAGATTA 57.991 36.000 0.00 0.00 0.00 1.75
356 376 7.880195 AGTTCTATTGCTCATGTACAAAAGTCT 59.120 33.333 0.00 0.00 0.00 3.24
386 406 6.862711 AAAAAGTACTGCTTAGTTGTCTCC 57.137 37.500 0.00 0.00 36.17 3.71
394 414 4.056050 TGCTTAGTTGTCTCCGAAAGAAC 58.944 43.478 0.00 0.00 35.21 3.01
482 502 2.051692 TGCCCACTACCACAACTACTT 58.948 47.619 0.00 0.00 0.00 2.24
503 523 0.318762 AAGAAGAGACGGCTTCGCTT 59.681 50.000 9.62 9.62 46.13 4.68
533 553 0.543749 GGATAGGCACAGGAGCAACT 59.456 55.000 0.00 0.00 35.83 3.16
610 630 2.192664 ATTTGTGTGCACGGATACCA 57.807 45.000 13.13 0.00 0.00 3.25
741 761 5.879777 TGTATTTTATAGCTGTGCTGCTGAA 59.120 36.000 12.75 5.35 43.87 3.02
845 877 4.438744 GCCTCACACCACAAATAATGCTAC 60.439 45.833 0.00 0.00 0.00 3.58
846 878 4.943705 CCTCACACCACAAATAATGCTACT 59.056 41.667 0.00 0.00 0.00 2.57
1073 1110 1.150827 CGCAGCTGTTTCTCATGTCA 58.849 50.000 16.64 0.00 0.00 3.58
1125 1162 2.045926 GCCATGGCGTCCAAGTCT 60.046 61.111 23.48 0.00 36.95 3.24
1143 1180 0.035439 CTGGGGCGAAACTGGTATGT 60.035 55.000 0.00 0.00 0.00 2.29
1151 1190 3.486108 GCGAAACTGGTATGTGTATCTCG 59.514 47.826 0.00 0.00 0.00 4.04
1187 1226 1.266178 TCTTCATCTTCTCGGCACCA 58.734 50.000 0.00 0.00 0.00 4.17
1217 1256 0.103572 GCCATGGCTATTGTTGCTGG 59.896 55.000 29.98 0.00 38.26 4.85
1219 1258 1.108776 CATGGCTATTGTTGCTGGCT 58.891 50.000 0.00 0.00 0.00 4.75
1227 1266 2.355481 GTTGCTGGCTTGCTGCAC 60.355 61.111 0.00 0.00 45.15 4.57
1381 1420 3.143728 TGCTGCTGCCATACATATCTTG 58.856 45.455 13.47 0.00 38.71 3.02
1388 1427 5.407995 GCTGCCATACATATCTTGTCTTCTC 59.592 44.000 0.00 0.00 39.87 2.87
1416 1455 7.820872 AGGCCATTTATTATTATCTGCAAATGC 59.179 33.333 5.01 0.00 42.50 3.56
1454 1539 7.904558 ACTATTGATGAGTGGAGATAACTGA 57.095 36.000 0.00 0.00 0.00 3.41
1455 1540 8.489676 ACTATTGATGAGTGGAGATAACTGAT 57.510 34.615 0.00 0.00 0.00 2.90
1457 1542 9.205719 CTATTGATGAGTGGAGATAACTGATTG 57.794 37.037 0.00 0.00 0.00 2.67
1461 1546 6.796785 TGAGTGGAGATAACTGATTGATGA 57.203 37.500 0.00 0.00 0.00 2.92
1462 1547 7.186570 TGAGTGGAGATAACTGATTGATGAA 57.813 36.000 0.00 0.00 0.00 2.57
1463 1548 7.799081 TGAGTGGAGATAACTGATTGATGAAT 58.201 34.615 0.00 0.00 0.00 2.57
1464 1549 7.713942 TGAGTGGAGATAACTGATTGATGAATG 59.286 37.037 0.00 0.00 0.00 2.67
1465 1550 7.799081 AGTGGAGATAACTGATTGATGAATGA 58.201 34.615 0.00 0.00 0.00 2.57
1509 1594 3.632145 ACAAGAAGAACGGCAACATCTTT 59.368 39.130 0.00 0.00 41.10 2.52
1529 1614 7.079451 TCTTTGAGAGATGGAAGTAGGTTTT 57.921 36.000 0.00 0.00 0.00 2.43
1532 1617 6.688073 TGAGAGATGGAAGTAGGTTTTTCT 57.312 37.500 0.00 0.00 0.00 2.52
1533 1618 6.467677 TGAGAGATGGAAGTAGGTTTTTCTG 58.532 40.000 0.00 0.00 0.00 3.02
1534 1619 6.270000 TGAGAGATGGAAGTAGGTTTTTCTGA 59.730 38.462 0.00 0.00 0.00 3.27
1535 1620 7.038017 TGAGAGATGGAAGTAGGTTTTTCTGAT 60.038 37.037 0.00 0.00 0.00 2.90
1536 1621 7.694093 AGAGATGGAAGTAGGTTTTTCTGATT 58.306 34.615 0.00 0.00 0.00 2.57
1538 1623 9.449719 GAGATGGAAGTAGGTTTTTCTGATTAA 57.550 33.333 0.00 0.00 0.00 1.40
1566 1651 7.894376 AAAAGACAAATGTTAAGCCATGATG 57.106 32.000 0.00 0.00 0.00 3.07
1567 1652 6.839124 AAGACAAATGTTAAGCCATGATGA 57.161 33.333 0.00 0.00 0.00 2.92
1569 1654 8.523915 AAGACAAATGTTAAGCCATGATGATA 57.476 30.769 0.00 0.00 0.00 2.15
1570 1655 8.701908 AGACAAATGTTAAGCCATGATGATAT 57.298 30.769 0.00 0.00 0.00 1.63
1571 1656 8.573885 AGACAAATGTTAAGCCATGATGATATG 58.426 33.333 0.00 0.00 0.00 1.78
1572 1657 8.467963 ACAAATGTTAAGCCATGATGATATGA 57.532 30.769 0.00 0.00 0.00 2.15
1596 1681 9.100197 TGATATATTTGTTGTGCTAGGATAGGA 57.900 33.333 0.00 0.00 39.70 2.94
1599 1684 6.949352 ATTTGTTGTGCTAGGATAGGATTG 57.051 37.500 0.00 0.00 42.42 2.67
1600 1685 5.435686 TTGTTGTGCTAGGATAGGATTGT 57.564 39.130 0.00 0.00 42.42 2.71
1601 1686 5.435686 TGTTGTGCTAGGATAGGATTGTT 57.564 39.130 0.00 0.00 42.42 2.83
1602 1687 6.553953 TGTTGTGCTAGGATAGGATTGTTA 57.446 37.500 0.00 0.00 42.42 2.41
1603 1688 6.346096 TGTTGTGCTAGGATAGGATTGTTAC 58.654 40.000 0.00 0.00 42.42 2.50
1604 1689 6.156256 TGTTGTGCTAGGATAGGATTGTTACT 59.844 38.462 0.00 0.00 42.42 2.24
1606 1691 7.907841 TGTGCTAGGATAGGATTGTTACTTA 57.092 36.000 0.00 0.00 42.42 2.24
1607 1692 8.492415 TGTGCTAGGATAGGATTGTTACTTAT 57.508 34.615 0.00 0.00 42.42 1.73
1608 1693 8.934697 TGTGCTAGGATAGGATTGTTACTTATT 58.065 33.333 0.00 0.00 42.42 1.40
1621 1712 9.607285 GATTGTTACTTATTAGTGTTTGTGTGG 57.393 33.333 0.00 0.00 35.78 4.17
1638 1729 3.081061 TGTGGCTAAACTGCTGGTATTG 58.919 45.455 0.00 0.00 0.00 1.90
1736 1831 1.813192 CCGGAGCAGAGAGGAGAAC 59.187 63.158 0.00 0.00 0.00 3.01
1792 1898 2.680221 GCAGATGCACTCTCCAATGTCT 60.680 50.000 0.00 0.00 41.59 3.41
1827 1933 4.126437 TCAACTTTGCTCGAATTCTGACA 58.874 39.130 3.52 0.00 0.00 3.58
1896 2005 8.918202 AAAACCGAATATGGTGATACACATAT 57.082 30.769 0.00 0.00 42.89 1.78
1902 2011 8.443160 CGAATATGGTGATACACATATTTGGTC 58.557 37.037 13.22 2.31 35.86 4.02
1975 2085 0.457853 TCTGCGCGTATTGACTGGTC 60.458 55.000 8.43 0.00 0.00 4.02
1980 2090 1.799181 CGCGTATTGACTGGTCTGGAG 60.799 57.143 0.00 0.00 0.00 3.86
1998 2108 6.995091 GTCTGGAGGCTTTTGAATCTATATGT 59.005 38.462 0.00 0.00 0.00 2.29
2095 2215 2.182842 GCGATGGGTGGCACTCATC 61.183 63.158 38.73 38.73 35.30 2.92
2101 2221 1.557269 GGGTGGCACTCATCTGAGGT 61.557 60.000 18.45 0.00 46.13 3.85
2120 2240 3.312718 GCATGTGGCCCCTTTGCA 61.313 61.111 0.00 0.00 36.11 4.08
2123 2243 1.229272 ATGTGGCCCCTTTGCACAT 60.229 52.632 0.00 0.00 32.18 3.21
2160 2280 2.594592 GTGCCGCCTCAGGTTTGT 60.595 61.111 0.00 0.00 0.00 2.83
2289 2411 8.732746 AGTGATAACAAGTTTATGTATCCACC 57.267 34.615 0.00 0.00 31.71 4.61
2348 2775 7.928307 ATCGCAAAATATTAGCCATACAGAT 57.072 32.000 7.10 1.86 0.00 2.90
2350 2777 9.618890 ATCGCAAAATATTAGCCATACAGATAT 57.381 29.630 7.10 0.00 0.00 1.63
2360 2787 6.849085 AGCCATACAGATATACTCCTTCTG 57.151 41.667 0.00 0.00 42.05 3.02
2362 2789 6.784969 AGCCATACAGATATACTCCTTCTGTT 59.215 38.462 10.40 0.00 45.88 3.16
2363 2790 7.039363 AGCCATACAGATATACTCCTTCTGTTC 60.039 40.741 10.40 1.19 45.88 3.18
2364 2791 7.309177 CCATACAGATATACTCCTTCTGTTCG 58.691 42.308 10.40 4.01 45.88 3.95
2365 2792 7.175119 CCATACAGATATACTCCTTCTGTTCGA 59.825 40.741 10.40 0.00 45.88 3.71
2366 2793 8.568794 CATACAGATATACTCCTTCTGTTCGAA 58.431 37.037 10.40 0.00 45.88 3.71
2367 2794 7.406031 ACAGATATACTCCTTCTGTTCGAAA 57.594 36.000 0.00 0.00 45.88 3.46
2368 2795 7.837863 ACAGATATACTCCTTCTGTTCGAAAA 58.162 34.615 0.00 0.00 45.88 2.29
2369 2796 8.311836 ACAGATATACTCCTTCTGTTCGAAAAA 58.688 33.333 0.00 0.00 45.88 1.94
2370 2797 8.812329 CAGATATACTCCTTCTGTTCGAAAAAG 58.188 37.037 0.00 4.37 33.72 2.27
2371 2798 5.864628 ATACTCCTTCTGTTCGAAAAAGC 57.135 39.130 0.00 0.00 0.00 3.51
2372 2799 3.809905 ACTCCTTCTGTTCGAAAAAGCT 58.190 40.909 0.00 0.00 0.00 3.74
2373 2800 4.200092 ACTCCTTCTGTTCGAAAAAGCTT 58.800 39.130 0.00 0.00 0.00 3.74
2374 2801 4.035675 ACTCCTTCTGTTCGAAAAAGCTTG 59.964 41.667 0.00 0.00 0.00 4.01
2375 2802 3.945285 TCCTTCTGTTCGAAAAAGCTTGT 59.055 39.130 0.00 0.00 0.00 3.16
2376 2803 4.035208 TCCTTCTGTTCGAAAAAGCTTGTC 59.965 41.667 0.00 0.00 0.00 3.18
2377 2804 3.963383 TCTGTTCGAAAAAGCTTGTCC 57.037 42.857 0.00 0.00 0.00 4.02
2378 2805 2.616842 TCTGTTCGAAAAAGCTTGTCCC 59.383 45.455 0.00 0.00 0.00 4.46
2379 2806 2.618709 CTGTTCGAAAAAGCTTGTCCCT 59.381 45.455 0.00 0.00 0.00 4.20
2380 2807 2.616842 TGTTCGAAAAAGCTTGTCCCTC 59.383 45.455 0.00 0.00 0.00 4.30
2381 2808 2.616842 GTTCGAAAAAGCTTGTCCCTCA 59.383 45.455 0.00 0.00 0.00 3.86
2382 2809 2.925724 TCGAAAAAGCTTGTCCCTCAA 58.074 42.857 0.00 0.00 34.61 3.02
2383 2810 3.283751 TCGAAAAAGCTTGTCCCTCAAA 58.716 40.909 0.00 0.00 35.48 2.69
2384 2811 3.888930 TCGAAAAAGCTTGTCCCTCAAAT 59.111 39.130 0.00 0.00 35.48 2.32
2385 2812 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
2386 2813 4.309933 GAAAAAGCTTGTCCCTCAAATGG 58.690 43.478 0.00 0.00 35.48 3.16
2387 2814 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
2388 2815 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
2389 2816 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
2390 2817 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
2391 2818 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
2392 2819 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
2393 2820 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
2394 2821 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
2395 2822 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
2396 2823 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
2397 2824 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
2398 2825 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2399 2826 5.549228 TCCCTCAAATGGATGTATCTAGCAT 59.451 40.000 0.00 0.00 0.00 3.79
2400 2827 5.879223 CCCTCAAATGGATGTATCTAGCATC 59.121 44.000 1.37 1.37 41.30 3.91
2401 2828 6.470278 CCTCAAATGGATGTATCTAGCATCA 58.530 40.000 9.99 0.00 43.17 3.07
2402 2829 6.938596 CCTCAAATGGATGTATCTAGCATCAA 59.061 38.462 9.99 0.98 43.17 2.57
2403 2830 7.119407 CCTCAAATGGATGTATCTAGCATCAAG 59.881 40.741 9.99 0.59 43.17 3.02
2404 2831 7.512130 TCAAATGGATGTATCTAGCATCAAGT 58.488 34.615 9.99 0.00 43.17 3.16
2405 2832 7.994911 TCAAATGGATGTATCTAGCATCAAGTT 59.005 33.333 9.99 3.16 43.17 2.66
2406 2833 9.276590 CAAATGGATGTATCTAGCATCAAGTTA 57.723 33.333 9.99 0.00 43.17 2.24
2407 2834 9.499479 AAATGGATGTATCTAGCATCAAGTTAG 57.501 33.333 9.99 0.00 43.17 2.34
2408 2835 7.603180 TGGATGTATCTAGCATCAAGTTAGT 57.397 36.000 9.99 0.00 43.17 2.24
2409 2836 7.436933 TGGATGTATCTAGCATCAAGTTAGTG 58.563 38.462 9.99 0.00 43.17 2.74
2410 2837 6.367422 GGATGTATCTAGCATCAAGTTAGTGC 59.633 42.308 9.99 4.02 43.17 4.40
2412 2839 7.582667 TGTATCTAGCATCAAGTTAGTGCTA 57.417 36.000 16.22 16.22 46.54 3.49
2418 2845 6.968263 AGCATCAAGTTAGTGCTAGATAGA 57.032 37.500 11.30 0.00 46.54 1.98
2419 2846 7.537596 AGCATCAAGTTAGTGCTAGATAGAT 57.462 36.000 11.30 0.00 46.54 1.98
2420 2847 7.601856 AGCATCAAGTTAGTGCTAGATAGATC 58.398 38.462 11.30 0.00 46.54 2.75
2421 2848 6.811170 GCATCAAGTTAGTGCTAGATAGATCC 59.189 42.308 0.00 0.00 36.02 3.36
2422 2849 7.524532 GCATCAAGTTAGTGCTAGATAGATCCA 60.525 40.741 0.00 0.00 36.02 3.41
2423 2850 8.530311 CATCAAGTTAGTGCTAGATAGATCCAT 58.470 37.037 0.00 0.00 0.00 3.41
2424 2851 8.484214 TCAAGTTAGTGCTAGATAGATCCATT 57.516 34.615 0.00 0.00 0.00 3.16
2425 2852 8.928448 TCAAGTTAGTGCTAGATAGATCCATTT 58.072 33.333 0.00 0.00 0.00 2.32
2426 2853 8.986847 CAAGTTAGTGCTAGATAGATCCATTTG 58.013 37.037 0.00 0.00 0.00 2.32
2427 2854 8.484214 AGTTAGTGCTAGATAGATCCATTTGA 57.516 34.615 0.00 0.00 0.00 2.69
2428 2855 8.584157 AGTTAGTGCTAGATAGATCCATTTGAG 58.416 37.037 0.00 0.00 0.00 3.02
2429 2856 6.357579 AGTGCTAGATAGATCCATTTGAGG 57.642 41.667 0.00 0.00 0.00 3.86
2430 2857 6.080682 AGTGCTAGATAGATCCATTTGAGGA 58.919 40.000 0.00 0.00 43.01 3.71
2431 2858 6.556495 AGTGCTAGATAGATCCATTTGAGGAA 59.444 38.462 0.00 0.00 41.92 3.36
2432 2859 6.648725 GTGCTAGATAGATCCATTTGAGGAAC 59.351 42.308 0.00 0.00 41.92 3.62
2433 2860 6.327365 TGCTAGATAGATCCATTTGAGGAACA 59.673 38.462 0.00 0.00 41.92 3.18
2434 2861 7.147497 TGCTAGATAGATCCATTTGAGGAACAA 60.147 37.037 0.00 0.00 41.92 2.83
2435 2862 7.387397 GCTAGATAGATCCATTTGAGGAACAAG 59.613 40.741 0.00 0.00 41.92 3.16
2436 2863 6.060788 AGATAGATCCATTTGAGGAACAAGC 58.939 40.000 0.00 0.00 41.92 4.01
2437 2864 4.313020 AGATCCATTTGAGGAACAAGCT 57.687 40.909 0.00 0.00 41.92 3.74
2438 2865 4.670765 AGATCCATTTGAGGAACAAGCTT 58.329 39.130 0.00 0.00 41.92 3.74
2439 2866 4.461781 AGATCCATTTGAGGAACAAGCTTG 59.538 41.667 24.84 24.84 41.92 4.01
2440 2867 2.892852 TCCATTTGAGGAACAAGCTTGG 59.107 45.455 29.18 12.28 39.77 3.61
2441 2868 2.028748 CCATTTGAGGAACAAGCTTGGG 60.029 50.000 29.18 13.19 39.77 4.12
2442 2869 2.746279 TTTGAGGAACAAGCTTGGGA 57.254 45.000 29.18 4.51 39.77 4.37
2443 2870 1.981256 TTGAGGAACAAGCTTGGGAC 58.019 50.000 29.18 17.88 34.20 4.46
2444 2871 0.843309 TGAGGAACAAGCTTGGGACA 59.157 50.000 29.18 17.71 0.00 4.02
2445 2872 2.357673 TTGAGGAACAAGCTTGGGACAA 60.358 45.455 29.18 21.59 37.48 3.18
2446 2873 4.249028 TTGAGGAACAAGCTTGGGACAAG 61.249 47.826 29.18 3.71 37.48 3.16
2447 2874 6.701067 TTGAGGAACAAGCTTGGGACAAGT 62.701 45.833 29.18 4.47 37.48 3.16
2449 2876 8.774326 TTGAGGAACAAGCTTGGGACAAGTTA 62.774 42.308 29.18 5.26 37.48 2.24
2450 2877 9.975893 TTGAGGAACAAGCTTGGGACAAGTTAT 62.976 40.741 29.18 2.15 37.48 1.89
2459 2886 3.670625 TGGGACAAGTTATTTCAGACGG 58.329 45.455 0.00 0.00 31.92 4.79
2460 2887 3.325425 TGGGACAAGTTATTTCAGACGGA 59.675 43.478 0.00 0.00 31.92 4.69
2461 2888 3.933332 GGGACAAGTTATTTCAGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2462 2889 3.933332 GGACAAGTTATTTCAGACGGAGG 59.067 47.826 0.00 0.00 0.00 4.30
2463 2890 3.933332 GACAAGTTATTTCAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2464 2891 3.581332 ACAAGTTATTTCAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2465 2892 4.184629 CAAGTTATTTCAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2506 2933 1.346395 TCGCTCAAGTTTCTTGCCCTA 59.654 47.619 4.82 0.00 0.00 3.53
2513 2940 3.659183 AGTTTCTTGCCCTAGATGCAT 57.341 42.857 0.00 0.00 38.76 3.96
2514 2941 3.973425 AGTTTCTTGCCCTAGATGCATT 58.027 40.909 0.00 0.00 38.76 3.56
2515 2942 4.347607 AGTTTCTTGCCCTAGATGCATTT 58.652 39.130 0.00 0.00 38.76 2.32
2516 2943 4.774200 AGTTTCTTGCCCTAGATGCATTTT 59.226 37.500 0.00 0.00 38.76 1.82
2517 2944 5.246883 AGTTTCTTGCCCTAGATGCATTTTT 59.753 36.000 0.00 0.00 38.76 1.94
2609 3039 2.638480 AGAGTAGCAAGCCAAACACA 57.362 45.000 0.00 0.00 0.00 3.72
2610 3040 3.146104 AGAGTAGCAAGCCAAACACAT 57.854 42.857 0.00 0.00 0.00 3.21
2613 3043 3.424703 AGTAGCAAGCCAAACACATCAT 58.575 40.909 0.00 0.00 0.00 2.45
2616 3046 6.356556 AGTAGCAAGCCAAACACATCATATA 58.643 36.000 0.00 0.00 0.00 0.86
2619 3049 6.356556 AGCAAGCCAAACACATCATATAGTA 58.643 36.000 0.00 0.00 0.00 1.82
2620 3050 6.828273 AGCAAGCCAAACACATCATATAGTAA 59.172 34.615 0.00 0.00 0.00 2.24
2621 3051 7.503566 AGCAAGCCAAACACATCATATAGTAAT 59.496 33.333 0.00 0.00 0.00 1.89
2666 3108 9.958180 TCACAAATGAGAAGATGGAAATAACTA 57.042 29.630 0.00 0.00 0.00 2.24
2693 3135 6.636454 AACTTCCAACTCCCATAAGACATA 57.364 37.500 0.00 0.00 0.00 2.29
2694 3136 6.831664 ACTTCCAACTCCCATAAGACATAT 57.168 37.500 0.00 0.00 0.00 1.78
2696 3138 5.825593 TCCAACTCCCATAAGACATATCC 57.174 43.478 0.00 0.00 0.00 2.59
2697 3139 5.476983 TCCAACTCCCATAAGACATATCCT 58.523 41.667 0.00 0.00 0.00 3.24
2705 3147 5.455183 CCCATAAGACATATCCTGAGCAACA 60.455 44.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 124 3.775202 ACGATCTGTCATCACTGTAAGC 58.225 45.455 0.00 0.00 37.60 3.09
163 165 9.934190 AAAAATGACAGTTAAAACATTGAATGC 57.066 25.926 4.84 0.00 34.02 3.56
229 249 8.624776 AGTTTGATGTCCTTCAGTTTAAAGAAG 58.375 33.333 9.26 9.26 40.64 2.85
307 327 3.433598 CCAGAAGTTCAACTGTGGAGGAA 60.434 47.826 12.29 0.00 35.96 3.36
385 405 1.593196 TCACAAGCAGGTTCTTTCGG 58.407 50.000 0.00 0.00 0.00 4.30
386 406 3.904136 ATTCACAAGCAGGTTCTTTCG 57.096 42.857 0.00 0.00 0.00 3.46
394 414 5.717078 ATATTGGCATATTCACAAGCAGG 57.283 39.130 0.00 0.00 0.00 4.85
435 455 5.058149 TGCTAAAACACAACCATAGCATG 57.942 39.130 1.92 0.00 42.78 4.06
473 493 4.796618 GCCGTCTCTTCTTCAAGTAGTTGT 60.797 45.833 10.08 0.00 34.98 3.32
482 502 3.794690 CGAAGCCGTCTCTTCTTCA 57.205 52.632 0.00 0.00 40.11 3.02
503 523 0.913934 TGCCTATCCCAAGCTCCACA 60.914 55.000 0.00 0.00 0.00 4.17
533 553 7.872881 ACTAGCTTTCTTCATCGACGATAATA 58.127 34.615 10.57 0.00 0.00 0.98
584 604 4.873768 TCCGTGCACACAAATACATATG 57.126 40.909 18.64 0.00 0.00 1.78
845 877 7.965107 GCCACAGAAACAAAGAAATATGAGTAG 59.035 37.037 0.00 0.00 0.00 2.57
846 878 7.665559 AGCCACAGAAACAAAGAAATATGAGTA 59.334 33.333 0.00 0.00 0.00 2.59
999 1036 0.690744 TAGCACTGGCAGGCTCCATA 60.691 55.000 26.57 12.12 44.61 2.74
1062 1099 1.718396 CTCGCTGCTGACATGAGAAA 58.282 50.000 0.00 0.00 32.59 2.52
1091 1128 2.190578 CCGGAAGCATCCTGGTCC 59.809 66.667 6.39 0.00 44.17 4.46
1125 1162 0.322098 CACATACCAGTTTCGCCCCA 60.322 55.000 0.00 0.00 0.00 4.96
1143 1180 8.771920 AAACTGAAATTATGTGACGAGATACA 57.228 30.769 0.00 0.00 0.00 2.29
1157 1196 7.148407 GCCGAGAAGATGAAGAAACTGAAATTA 60.148 37.037 0.00 0.00 0.00 1.40
1187 1226 1.379044 GCCATGGCTACAACCAGCT 60.379 57.895 29.98 0.00 44.71 4.24
1209 1248 2.834043 TGCAGCAAGCCAGCAACA 60.834 55.556 7.23 0.00 44.83 3.33
1217 1256 3.036577 TGCTTCTGTGCAGCAAGC 58.963 55.556 19.59 19.59 44.42 4.01
1234 1273 6.265196 TCTTCAATACAACACTGGCAAGAATT 59.735 34.615 0.00 0.00 0.00 2.17
1253 1292 2.030540 GCACAAGCAGCATCTTCTTCAA 60.031 45.455 0.00 0.00 41.58 2.69
1388 1427 9.715121 ATTTGCAGATAATAATAAATGGCCTTG 57.285 29.630 3.32 0.00 0.00 3.61
1428 1467 9.421399 TCAGTTATCTCCACTCATCAATAGTTA 57.579 33.333 0.00 0.00 0.00 2.24
1430 1469 7.904558 TCAGTTATCTCCACTCATCAATAGT 57.095 36.000 0.00 0.00 0.00 2.12
1431 1470 9.205719 CAATCAGTTATCTCCACTCATCAATAG 57.794 37.037 0.00 0.00 0.00 1.73
1442 1527 8.434392 TCATCATTCATCAATCAGTTATCTCCA 58.566 33.333 0.00 0.00 0.00 3.86
1447 1532 8.404107 TGCATCATCATTCATCAATCAGTTAT 57.596 30.769 0.00 0.00 0.00 1.89
1454 1539 3.832490 CCCCTGCATCATCATTCATCAAT 59.168 43.478 0.00 0.00 0.00 2.57
1455 1540 3.117436 TCCCCTGCATCATCATTCATCAA 60.117 43.478 0.00 0.00 0.00 2.57
1457 1542 2.818432 GTCCCCTGCATCATCATTCATC 59.182 50.000 0.00 0.00 0.00 2.92
1461 1546 1.133575 CCAGTCCCCTGCATCATCATT 60.134 52.381 0.00 0.00 37.38 2.57
1462 1547 0.477204 CCAGTCCCCTGCATCATCAT 59.523 55.000 0.00 0.00 37.38 2.45
1463 1548 1.917495 CCAGTCCCCTGCATCATCA 59.083 57.895 0.00 0.00 37.38 3.07
1464 1549 1.527844 GCCAGTCCCCTGCATCATC 60.528 63.158 0.00 0.00 37.38 2.92
1465 1550 2.280404 CTGCCAGTCCCCTGCATCAT 62.280 60.000 0.00 0.00 37.38 2.45
1509 1594 6.270000 TCAGAAAAACCTACTTCCATCTCTCA 59.730 38.462 0.00 0.00 0.00 3.27
1538 1623 9.995003 TCATGGCTTAACATTTGTCTTTTTAAT 57.005 25.926 0.00 0.00 0.00 1.40
1540 1625 9.421806 CATCATGGCTTAACATTTGTCTTTTTA 57.578 29.630 0.00 0.00 0.00 1.52
1542 1627 7.669427 TCATCATGGCTTAACATTTGTCTTTT 58.331 30.769 0.00 0.00 0.00 2.27
1543 1628 7.230849 TCATCATGGCTTAACATTTGTCTTT 57.769 32.000 0.00 0.00 0.00 2.52
1545 1630 8.573885 CATATCATCATGGCTTAACATTTGTCT 58.426 33.333 0.00 0.00 0.00 3.41
1569 1654 9.896645 CCTATCCTAGCACAACAAATATATCAT 57.103 33.333 0.00 0.00 0.00 2.45
1570 1655 9.100197 TCCTATCCTAGCACAACAAATATATCA 57.900 33.333 0.00 0.00 0.00 2.15
1575 1660 7.573710 ACAATCCTATCCTAGCACAACAAATA 58.426 34.615 0.00 0.00 0.00 1.40
1577 1662 5.815581 ACAATCCTATCCTAGCACAACAAA 58.184 37.500 0.00 0.00 0.00 2.83
1579 1664 5.435686 AACAATCCTATCCTAGCACAACA 57.564 39.130 0.00 0.00 0.00 3.33
1580 1665 6.583562 AGTAACAATCCTATCCTAGCACAAC 58.416 40.000 0.00 0.00 0.00 3.32
1582 1667 6.808321 AAGTAACAATCCTATCCTAGCACA 57.192 37.500 0.00 0.00 0.00 4.57
1594 1679 9.607285 CACACAAACACTAATAAGTAACAATCC 57.393 33.333 0.00 0.00 33.48 3.01
1596 1681 8.079809 GCCACACAAACACTAATAAGTAACAAT 58.920 33.333 0.00 0.00 33.48 2.71
1597 1682 7.283580 AGCCACACAAACACTAATAAGTAACAA 59.716 33.333 0.00 0.00 33.48 2.83
1599 1684 7.198306 AGCCACACAAACACTAATAAGTAAC 57.802 36.000 0.00 0.00 33.48 2.50
1600 1685 8.905660 TTAGCCACACAAACACTAATAAGTAA 57.094 30.769 0.00 0.00 33.48 2.24
1601 1686 8.776470 GTTTAGCCACACAAACACTAATAAGTA 58.224 33.333 0.00 0.00 35.25 2.24
1602 1687 7.501225 AGTTTAGCCACACAAACACTAATAAGT 59.499 33.333 0.00 0.00 37.16 2.24
1603 1688 7.803189 CAGTTTAGCCACACAAACACTAATAAG 59.197 37.037 0.00 0.00 37.16 1.73
1604 1689 7.644490 CAGTTTAGCCACACAAACACTAATAA 58.356 34.615 0.00 0.00 37.16 1.40
1606 1691 5.507315 GCAGTTTAGCCACACAAACACTAAT 60.507 40.000 0.00 0.00 37.16 1.73
1607 1692 4.201970 GCAGTTTAGCCACACAAACACTAA 60.202 41.667 0.00 0.00 37.16 2.24
1608 1693 3.314080 GCAGTTTAGCCACACAAACACTA 59.686 43.478 0.00 0.00 37.16 2.74
1609 1694 2.099098 GCAGTTTAGCCACACAAACACT 59.901 45.455 0.00 0.00 37.16 3.55
1610 1695 2.099098 AGCAGTTTAGCCACACAAACAC 59.901 45.455 0.00 0.00 37.16 3.32
1611 1696 2.098934 CAGCAGTTTAGCCACACAAACA 59.901 45.455 0.00 0.00 37.16 2.83
1612 1697 2.543653 CCAGCAGTTTAGCCACACAAAC 60.544 50.000 0.00 0.00 35.36 2.93
1613 1698 1.680735 CCAGCAGTTTAGCCACACAAA 59.319 47.619 0.00 0.00 34.23 2.83
1615 1700 0.182537 ACCAGCAGTTTAGCCACACA 59.817 50.000 0.00 0.00 34.23 3.72
1616 1701 2.178912 TACCAGCAGTTTAGCCACAC 57.821 50.000 0.00 0.00 34.23 3.82
1621 1712 2.423538 CCCACAATACCAGCAGTTTAGC 59.576 50.000 0.00 0.00 0.00 3.09
1638 1729 1.212935 AGCACCTGAACCATATCCCAC 59.787 52.381 0.00 0.00 0.00 4.61
1736 1831 5.525012 TGGATGCTTGATGTTTCTTCTATCG 59.475 40.000 0.00 0.00 0.00 2.92
1792 1898 7.065683 TCGAGCAAAGTTGAGCATGATAAATAA 59.934 33.333 0.00 0.00 0.00 1.40
1857 1963 3.861840 TCGGTTTTCATTTTGTTTGGCA 58.138 36.364 0.00 0.00 0.00 4.92
1902 2011 3.812053 GGCATTATACTGCTGGTTCTCAG 59.188 47.826 14.00 0.00 46.03 3.35
1911 2020 3.565764 TCTGCTTGGCATTATACTGCT 57.434 42.857 14.00 0.00 41.95 4.24
1975 2085 7.284034 ACAACATATAGATTCAAAAGCCTCCAG 59.716 37.037 0.00 0.00 0.00 3.86
2095 2215 2.345760 GGGCCACATGCAACCTCAG 61.346 63.158 4.39 0.00 43.89 3.35
2101 2221 2.881528 GCAAAGGGGCCACATGCAA 61.882 57.895 25.84 0.00 43.89 4.08
2348 2775 6.698380 AGCTTTTTCGAACAGAAGGAGTATA 58.302 36.000 0.00 0.00 40.40 1.47
2350 2777 4.957296 AGCTTTTTCGAACAGAAGGAGTA 58.043 39.130 0.00 0.00 40.40 2.59
2351 2778 3.809905 AGCTTTTTCGAACAGAAGGAGT 58.190 40.909 0.00 0.00 40.40 3.85
2352 2779 4.035675 ACAAGCTTTTTCGAACAGAAGGAG 59.964 41.667 0.00 0.00 40.40 3.69
2353 2780 3.945285 ACAAGCTTTTTCGAACAGAAGGA 59.055 39.130 0.00 0.00 40.40 3.36
2354 2781 4.282873 GACAAGCTTTTTCGAACAGAAGG 58.717 43.478 0.00 0.00 40.40 3.46
2355 2782 4.282873 GGACAAGCTTTTTCGAACAGAAG 58.717 43.478 0.00 4.09 40.40 2.85
2356 2783 3.066203 GGGACAAGCTTTTTCGAACAGAA 59.934 43.478 0.00 0.00 37.01 3.02
2357 2784 2.616842 GGGACAAGCTTTTTCGAACAGA 59.383 45.455 0.00 0.00 0.00 3.41
2358 2785 2.618709 AGGGACAAGCTTTTTCGAACAG 59.381 45.455 0.00 0.00 0.00 3.16
2359 2786 2.616842 GAGGGACAAGCTTTTTCGAACA 59.383 45.455 0.00 0.00 0.00 3.18
2360 2787 2.616842 TGAGGGACAAGCTTTTTCGAAC 59.383 45.455 0.00 0.00 0.00 3.95
2361 2788 2.925724 TGAGGGACAAGCTTTTTCGAA 58.074 42.857 0.00 0.00 0.00 3.71
2362 2789 2.631160 TGAGGGACAAGCTTTTTCGA 57.369 45.000 0.00 0.00 0.00 3.71
2363 2790 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
2364 2791 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
2365 2792 3.966665 TCCATTTGAGGGACAAGCTTTTT 59.033 39.130 0.00 0.00 39.77 1.94
2366 2793 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
2367 2794 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
2368 2795 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
2369 2796 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
2370 2797 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
2371 2798 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
2372 2799 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2373 2800 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
2374 2801 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
2375 2802 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
2376 2803 5.233083 TGCTAGATACATCCATTTGAGGG 57.767 43.478 0.00 0.00 0.00 4.30
2377 2804 6.470278 TGATGCTAGATACATCCATTTGAGG 58.530 40.000 0.00 0.00 42.68 3.86
2378 2805 7.660617 ACTTGATGCTAGATACATCCATTTGAG 59.339 37.037 0.00 0.00 42.68 3.02
2379 2806 7.512130 ACTTGATGCTAGATACATCCATTTGA 58.488 34.615 0.00 0.00 42.68 2.69
2380 2807 7.741027 ACTTGATGCTAGATACATCCATTTG 57.259 36.000 0.00 0.00 42.68 2.32
2381 2808 9.499479 CTAACTTGATGCTAGATACATCCATTT 57.501 33.333 0.00 0.00 42.68 2.32
2382 2809 8.654997 ACTAACTTGATGCTAGATACATCCATT 58.345 33.333 0.00 0.00 42.68 3.16
2383 2810 8.093307 CACTAACTTGATGCTAGATACATCCAT 58.907 37.037 0.00 0.00 42.68 3.41
2384 2811 7.436933 CACTAACTTGATGCTAGATACATCCA 58.563 38.462 0.00 0.00 42.68 3.41
2385 2812 6.367422 GCACTAACTTGATGCTAGATACATCC 59.633 42.308 0.00 0.00 42.68 3.51
2386 2813 7.344910 GCACTAACTTGATGCTAGATACATC 57.655 40.000 0.00 0.00 43.46 3.06
2396 2823 6.811170 GGATCTATCTAGCACTAACTTGATGC 59.189 42.308 0.00 0.00 39.74 3.91
2397 2824 7.890515 TGGATCTATCTAGCACTAACTTGATG 58.109 38.462 0.00 0.00 34.60 3.07
2398 2825 8.663209 ATGGATCTATCTAGCACTAACTTGAT 57.337 34.615 0.00 0.00 36.37 2.57
2399 2826 8.484214 AATGGATCTATCTAGCACTAACTTGA 57.516 34.615 0.00 0.00 0.00 3.02
2400 2827 8.986847 CAAATGGATCTATCTAGCACTAACTTG 58.013 37.037 0.00 0.00 0.00 3.16
2401 2828 8.928448 TCAAATGGATCTATCTAGCACTAACTT 58.072 33.333 0.00 0.00 0.00 2.66
2402 2829 8.484214 TCAAATGGATCTATCTAGCACTAACT 57.516 34.615 0.00 0.00 0.00 2.24
2403 2830 7.816995 CCTCAAATGGATCTATCTAGCACTAAC 59.183 40.741 0.00 0.00 0.00 2.34
2404 2831 7.730332 TCCTCAAATGGATCTATCTAGCACTAA 59.270 37.037 0.00 0.00 0.00 2.24
2405 2832 7.241628 TCCTCAAATGGATCTATCTAGCACTA 58.758 38.462 0.00 0.00 0.00 2.74
2406 2833 6.080682 TCCTCAAATGGATCTATCTAGCACT 58.919 40.000 0.00 0.00 0.00 4.40
2407 2834 6.352016 TCCTCAAATGGATCTATCTAGCAC 57.648 41.667 0.00 0.00 0.00 4.40
2408 2835 6.327365 TGTTCCTCAAATGGATCTATCTAGCA 59.673 38.462 0.00 0.00 35.83 3.49
2409 2836 6.763355 TGTTCCTCAAATGGATCTATCTAGC 58.237 40.000 0.00 0.00 35.83 3.42
2410 2837 7.387397 GCTTGTTCCTCAAATGGATCTATCTAG 59.613 40.741 0.00 0.00 35.83 2.43
2411 2838 7.071698 AGCTTGTTCCTCAAATGGATCTATCTA 59.928 37.037 0.00 0.00 35.83 1.98
2412 2839 6.060788 GCTTGTTCCTCAAATGGATCTATCT 58.939 40.000 0.00 0.00 35.83 1.98
2413 2840 6.060788 AGCTTGTTCCTCAAATGGATCTATC 58.939 40.000 0.00 0.00 35.83 2.08
2414 2841 6.011122 AGCTTGTTCCTCAAATGGATCTAT 57.989 37.500 0.00 0.00 35.83 1.98
2415 2842 5.441718 AGCTTGTTCCTCAAATGGATCTA 57.558 39.130 0.00 0.00 35.83 1.98
2416 2843 4.313020 AGCTTGTTCCTCAAATGGATCT 57.687 40.909 0.00 0.00 35.83 2.75
2417 2844 4.381292 CCAAGCTTGTTCCTCAAATGGATC 60.381 45.833 24.35 0.00 36.92 3.36
2418 2845 3.512724 CCAAGCTTGTTCCTCAAATGGAT 59.487 43.478 24.35 0.00 36.92 3.41
2419 2846 2.892852 CCAAGCTTGTTCCTCAAATGGA 59.107 45.455 24.35 0.00 36.92 3.41
2420 2847 2.028748 CCCAAGCTTGTTCCTCAAATGG 60.029 50.000 24.35 10.71 35.48 3.16
2421 2848 2.892852 TCCCAAGCTTGTTCCTCAAATG 59.107 45.455 24.35 5.47 35.48 2.32
2422 2849 2.893489 GTCCCAAGCTTGTTCCTCAAAT 59.107 45.455 24.35 0.00 35.48 2.32
2423 2850 2.306847 GTCCCAAGCTTGTTCCTCAAA 58.693 47.619 24.35 0.00 35.48 2.69
2424 2851 1.214175 TGTCCCAAGCTTGTTCCTCAA 59.786 47.619 24.35 1.41 34.61 3.02
2425 2852 0.843309 TGTCCCAAGCTTGTTCCTCA 59.157 50.000 24.35 12.85 0.00 3.86
2426 2853 1.882623 CTTGTCCCAAGCTTGTTCCTC 59.117 52.381 24.35 10.65 0.00 3.71
2427 2854 1.215423 ACTTGTCCCAAGCTTGTTCCT 59.785 47.619 24.35 0.00 0.00 3.36
2428 2855 1.692411 ACTTGTCCCAAGCTTGTTCC 58.308 50.000 24.35 11.81 0.00 3.62
2429 2856 5.453567 AATAACTTGTCCCAAGCTTGTTC 57.546 39.130 24.35 14.17 0.00 3.18
2430 2857 5.362430 TGAAATAACTTGTCCCAAGCTTGTT 59.638 36.000 24.35 12.70 0.00 2.83
2431 2858 4.892934 TGAAATAACTTGTCCCAAGCTTGT 59.107 37.500 24.35 6.45 0.00 3.16
2432 2859 5.241506 TCTGAAATAACTTGTCCCAAGCTTG 59.758 40.000 19.93 19.93 0.00 4.01
2433 2860 5.241728 GTCTGAAATAACTTGTCCCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2434 2861 4.762251 GTCTGAAATAACTTGTCCCAAGCT 59.238 41.667 3.96 0.00 0.00 3.74
2435 2862 4.378459 CGTCTGAAATAACTTGTCCCAAGC 60.378 45.833 3.96 0.00 0.00 4.01
2436 2863 4.154195 CCGTCTGAAATAACTTGTCCCAAG 59.846 45.833 2.54 2.54 0.00 3.61
2437 2864 4.069304 CCGTCTGAAATAACTTGTCCCAA 58.931 43.478 0.00 0.00 0.00 4.12
2438 2865 3.325425 TCCGTCTGAAATAACTTGTCCCA 59.675 43.478 0.00 0.00 0.00 4.37
2439 2866 3.933332 CTCCGTCTGAAATAACTTGTCCC 59.067 47.826 0.00 0.00 0.00 4.46
2440 2867 3.933332 CCTCCGTCTGAAATAACTTGTCC 59.067 47.826 0.00 0.00 0.00 4.02
2441 2868 3.933332 CCCTCCGTCTGAAATAACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2442 2869 3.581332 TCCCTCCGTCTGAAATAACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2443 2870 4.184629 CTCCCTCCGTCTGAAATAACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2444 2871 3.838903 ACTCCCTCCGTCTGAAATAACTT 59.161 43.478 0.00 0.00 0.00 2.66
2445 2872 3.442076 ACTCCCTCCGTCTGAAATAACT 58.558 45.455 0.00 0.00 0.00 2.24
2446 2873 3.889520 ACTCCCTCCGTCTGAAATAAC 57.110 47.619 0.00 0.00 0.00 1.89
2447 2874 4.960469 ACATACTCCCTCCGTCTGAAATAA 59.040 41.667 0.00 0.00 0.00 1.40
2448 2875 4.543689 ACATACTCCCTCCGTCTGAAATA 58.456 43.478 0.00 0.00 0.00 1.40
2449 2876 3.375699 ACATACTCCCTCCGTCTGAAAT 58.624 45.455 0.00 0.00 0.00 2.17
2450 2877 2.816411 ACATACTCCCTCCGTCTGAAA 58.184 47.619 0.00 0.00 0.00 2.69
2451 2878 2.526888 ACATACTCCCTCCGTCTGAA 57.473 50.000 0.00 0.00 0.00 3.02
2452 2879 3.878237 ATACATACTCCCTCCGTCTGA 57.122 47.619 0.00 0.00 0.00 3.27
2453 2880 4.621991 CAAATACATACTCCCTCCGTCTG 58.378 47.826 0.00 0.00 0.00 3.51
2454 2881 3.069729 GCAAATACATACTCCCTCCGTCT 59.930 47.826 0.00 0.00 0.00 4.18
2455 2882 3.181469 TGCAAATACATACTCCCTCCGTC 60.181 47.826 0.00 0.00 0.00 4.79
2456 2883 2.769663 TGCAAATACATACTCCCTCCGT 59.230 45.455 0.00 0.00 0.00 4.69
2457 2884 3.469008 TGCAAATACATACTCCCTCCG 57.531 47.619 0.00 0.00 0.00 4.63
2458 2885 5.885912 TCTTTTGCAAATACATACTCCCTCC 59.114 40.000 13.65 0.00 0.00 4.30
2459 2886 7.420800 CATCTTTTGCAAATACATACTCCCTC 58.579 38.462 13.65 0.00 0.00 4.30
2460 2887 6.322201 CCATCTTTTGCAAATACATACTCCCT 59.678 38.462 13.65 0.00 0.00 4.20
2461 2888 6.096846 ACCATCTTTTGCAAATACATACTCCC 59.903 38.462 13.65 0.00 0.00 4.30
2462 2889 7.100458 ACCATCTTTTGCAAATACATACTCC 57.900 36.000 13.65 0.00 0.00 3.85
2463 2890 6.907212 CGACCATCTTTTGCAAATACATACTC 59.093 38.462 13.65 2.42 0.00 2.59
2464 2891 6.677920 GCGACCATCTTTTGCAAATACATACT 60.678 38.462 13.65 0.00 0.00 2.12
2465 2892 5.455525 GCGACCATCTTTTGCAAATACATAC 59.544 40.000 13.65 2.19 0.00 2.39
2635 3067 8.868522 TTTCCATCTTCTCATTTGTGATTACT 57.131 30.769 0.00 0.00 0.00 2.24
2662 3094 5.899631 TGGGAGTTGGAAGTTAACTAGTT 57.100 39.130 13.68 13.68 38.42 2.24
2666 3108 6.043938 TGTCTTATGGGAGTTGGAAGTTAACT 59.956 38.462 1.12 1.12 40.84 2.24
2669 3111 6.636454 ATGTCTTATGGGAGTTGGAAGTTA 57.364 37.500 0.00 0.00 0.00 2.24
2694 3136 9.851686 AATGAAGTTATATTATGTTGCTCAGGA 57.148 29.630 0.00 0.00 0.00 3.86
2697 3139 9.066892 GGGAATGAAGTTATATTATGTTGCTCA 57.933 33.333 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.