Multiple sequence alignment - TraesCS5D01G418300

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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 TraesCS5D01G418300 chr5D 100.000 3980 0 0 1 3980 480341861 480345840 0.000000e+00 7350
1 TraesCS5D01G418300 chr5A 96.077 1555 54 2 2433 3980 598816722 598818276 0.000000e+00 2527
2 TraesCS5D01G418300 chr5A 90.340 1470 78 30 864 2309 598815294 598816723 0.000000e+00 1869
3 TraesCS5D01G418300 chr5B 92.912 1566 77 22 2437 3980 588396120 588397673 0.000000e+00 2246
4 TraesCS5D01G418300 chr5B 92.695 1451 57 20 869 2308 588394704 588396116 0.000000e+00 2047
5 TraesCS5D01G418300 chr5B 85.000 820 104 11 1 810 588387856 588388666 0.000000e+00 815
6 TraesCS5D01G418300 chr5B 84.160 726 86 17 1 712 659981736 659982446 0.000000e+00 676
7 TraesCS5D01G418300 chr6A 84.615 871 105 17 1 861 441810664 441811515 0.000000e+00 839
8 TraesCS5D01G418300 chr1D 83.216 852 106 22 4 834 490935770 490934935 0.000000e+00 747
9 TraesCS5D01G418300 chr3B 82.114 861 123 20 11 854 787423666 787424512 0.000000e+00 708
10 TraesCS5D01G418300 chr3B 95.683 139 5 1 2304 2441 583843958 583843820 5.180000e-54 222
11 TraesCS5D01G418300 chr3B 93.836 146 4 4 2308 2452 748784614 748784755 8.660000e-52 215
12 TraesCS5D01G418300 chr7D 81.352 858 111 30 1 838 78759663 78760491 0.000000e+00 652
13 TraesCS5D01G418300 chr7D 92.361 144 10 1 2295 2437 503403835 503403692 1.880000e-48 204
14 TraesCS5D01G418300 chr2B 85.913 575 58 16 1 561 676079445 676080010 3.430000e-165 592
15 TraesCS5D01G418300 chr2B 95.588 136 4 2 2308 2443 104014174 104014041 2.410000e-52 217
16 TraesCS5D01G418300 chr6D 81.259 731 94 34 1 707 421864774 421865485 5.810000e-153 551
17 TraesCS5D01G418300 chr1B 81.025 722 105 26 1 706 528487424 528488129 2.700000e-151 545
18 TraesCS5D01G418300 chr2D 80.543 663 94 23 3 653 572644607 572645246 1.000000e-130 477
19 TraesCS5D01G418300 chr3A 97.710 131 3 0 2308 2438 182282951 182282821 4.000000e-55 226
20 TraesCS5D01G418300 chr1A 95.652 138 5 1 2308 2445 3261592 3261728 1.860000e-53 220
21 TraesCS5D01G418300 chr3D 94.406 143 6 2 2303 2444 532240139 532239998 6.700000e-53 219
22 TraesCS5D01G418300 chr7B 94.366 142 6 2 2308 2449 141892781 141892642 2.410000e-52 217
23 TraesCS5D01G418300 chr2A 92.715 151 7 4 2294 2442 65193131 65192983 8.660000e-52 215


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 TraesCS5D01G418300 chr5D 480341861 480345840 3979 False 7350.0 7350 100.0000 1 3980 1 chr5D.!!$F1 3979
1 TraesCS5D01G418300 chr5A 598815294 598818276 2982 False 2198.0 2527 93.2085 864 3980 2 chr5A.!!$F1 3116
2 TraesCS5D01G418300 chr5B 588394704 588397673 2969 False 2146.5 2246 92.8035 869 3980 2 chr5B.!!$F3 3111
3 TraesCS5D01G418300 chr5B 588387856 588388666 810 False 815.0 815 85.0000 1 810 1 chr5B.!!$F1 809
4 TraesCS5D01G418300 chr5B 659981736 659982446 710 False 676.0 676 84.1600 1 712 1 chr5B.!!$F2 711
5 TraesCS5D01G418300 chr6A 441810664 441811515 851 False 839.0 839 84.6150 1 861 1 chr6A.!!$F1 860
6 TraesCS5D01G418300 chr1D 490934935 490935770 835 True 747.0 747 83.2160 4 834 1 chr1D.!!$R1 830
7 TraesCS5D01G418300 chr3B 787423666 787424512 846 False 708.0 708 82.1140 11 854 1 chr3B.!!$F2 843
8 TraesCS5D01G418300 chr7D 78759663 78760491 828 False 652.0 652 81.3520 1 838 1 chr7D.!!$F1 837
9 TraesCS5D01G418300 chr2B 676079445 676080010 565 False 592.0 592 85.9130 1 561 1 chr2B.!!$F1 560
10 TraesCS5D01G418300 chr6D 421864774 421865485 711 False 551.0 551 81.2590 1 707 1 chr6D.!!$F1 706
11 TraesCS5D01G418300 chr1B 528487424 528488129 705 False 545.0 545 81.0250 1 706 1 chr1B.!!$F1 705
12 TraesCS5D01G418300 chr2D 572644607 572645246 639 False 477.0 477 80.5430 3 653 1 chr2D.!!$F1 650

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
740 848 0.179073 AGCTAACCTATGTGCAGCCG 60.179 55.000 0.0 0.0 35.14 5.52 F
1265 1375 0.179073 CGGACACCACCATCATCTCC 60.179 60.000 0.0 0.0 0.00 3.71 F
2328 2467 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.0 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2550 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
2413 2552 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.0 44.66 1.40 R
3524 3687 1.632409 AGCTGAGGAGATTGCCAAGAA 59.368 47.619 0.00 0.0 0.00 2.52 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
140 142 0.786435 AAGCCATTCCACCCTTTCCT 59.214 50.000 0.00 0.00 0.00 3.36
145 147 2.440409 CATTCCACCCTTTCCTCACTG 58.560 52.381 0.00 0.00 0.00 3.66
150 153 1.134438 ACCCTTTCCTCACTGGGGTC 61.134 60.000 0.00 0.00 46.28 4.46
288 296 0.388520 GGCATTTGACAACGAAGCCC 60.389 55.000 7.72 0.00 32.60 5.19
301 309 2.424246 ACGAAGCCCGAAAGAACAAAAA 59.576 40.909 2.99 0.00 41.76 1.94
310 318 5.221244 CCCGAAAGAACAAAAAGATGGAGTT 60.221 40.000 0.00 0.00 0.00 3.01
312 320 6.459573 CCGAAAGAACAAAAAGATGGAGTTGA 60.460 38.462 0.00 0.00 0.00 3.18
363 372 4.080975 AGGCAAGGATCTGAAGAAGAAGAG 60.081 45.833 0.00 0.00 38.79 2.85
368 399 5.588845 AGGATCTGAAGAAGAAGAGGAAGA 58.411 41.667 0.00 0.00 38.79 2.87
377 418 1.278699 AGAAGAGGAAGAAGCAGCAGG 59.721 52.381 0.00 0.00 0.00 4.85
381 422 0.903942 AGGAAGAAGCAGCAGGAGAG 59.096 55.000 0.00 0.00 0.00 3.20
488 580 1.739035 GCATCGACGATGAACCTTCCA 60.739 52.381 35.61 0.00 42.09 3.53
496 588 5.293324 CGACGATGAACCTTCCATTATTCAA 59.707 40.000 0.00 0.00 34.88 2.69
603 709 5.872617 TGTTCAGATTATGTTGGTAAGGTCG 59.127 40.000 0.00 0.00 0.00 4.79
659 767 4.584327 GGTTGCAACCTAACATCAAGTT 57.416 40.909 36.26 0.00 45.75 2.66
719 827 6.478129 ACGGGTCAAAATTAGTTTCCTCATA 58.522 36.000 0.00 0.00 0.00 2.15
736 844 4.202253 CCTCATACAGCTAACCTATGTGCA 60.202 45.833 0.00 0.00 0.00 4.57
738 846 2.029838 ACAGCTAACCTATGTGCAGC 57.970 50.000 0.00 0.00 34.91 5.25
740 848 0.179073 AGCTAACCTATGTGCAGCCG 60.179 55.000 0.00 0.00 35.14 5.52
741 849 0.462047 GCTAACCTATGTGCAGCCGT 60.462 55.000 0.00 0.00 30.71 5.68
742 850 1.290203 CTAACCTATGTGCAGCCGTG 58.710 55.000 0.00 0.00 0.00 4.94
771 879 3.890756 ACCAAACAATGTGCAGAAGATGA 59.109 39.130 0.00 0.00 0.00 2.92
775 883 6.090358 CCAAACAATGTGCAGAAGATGATTTC 59.910 38.462 0.00 0.00 0.00 2.17
780 888 5.426689 TGTGCAGAAGATGATTTCTAGGT 57.573 39.130 0.00 0.00 35.70 3.08
785 893 7.334421 GTGCAGAAGATGATTTCTAGGTTGTTA 59.666 37.037 0.00 0.00 35.70 2.41
798 907 2.644798 AGGTTGTTATTCTCAGCCAGGT 59.355 45.455 0.00 0.00 38.37 4.00
856 965 3.115556 GGCAACCAAGCACGTTCA 58.884 55.556 0.00 0.00 35.83 3.18
857 966 1.659794 GGCAACCAAGCACGTTCAT 59.340 52.632 0.00 0.00 35.83 2.57
858 967 0.878416 GGCAACCAAGCACGTTCATA 59.122 50.000 0.00 0.00 35.83 2.15
859 968 1.135689 GGCAACCAAGCACGTTCATAG 60.136 52.381 0.00 0.00 35.83 2.23
860 969 1.804151 GCAACCAAGCACGTTCATAGA 59.196 47.619 0.00 0.00 0.00 1.98
861 970 2.412847 GCAACCAAGCACGTTCATAGAC 60.413 50.000 0.00 0.00 0.00 2.59
862 971 3.067106 CAACCAAGCACGTTCATAGACT 58.933 45.455 0.00 0.00 0.00 3.24
863 972 2.960819 ACCAAGCACGTTCATAGACTC 58.039 47.619 0.00 0.00 0.00 3.36
864 973 2.563179 ACCAAGCACGTTCATAGACTCT 59.437 45.455 0.00 0.00 0.00 3.24
865 974 2.926200 CCAAGCACGTTCATAGACTCTG 59.074 50.000 0.00 0.00 0.00 3.35
1050 1160 3.753434 CCGTCCACTCGCTCAGCT 61.753 66.667 0.00 0.00 0.00 4.24
1052 1162 2.183046 GTCCACTCGCTCAGCTCC 59.817 66.667 0.00 0.00 0.00 4.70
1265 1375 0.179073 CGGACACCACCATCATCTCC 60.179 60.000 0.00 0.00 0.00 3.71
1267 1377 1.561542 GGACACCACCATCATCTCCTT 59.438 52.381 0.00 0.00 0.00 3.36
1315 1426 2.093764 CCTCATCGTCTTGCTTTCCTCT 60.094 50.000 0.00 0.00 0.00 3.69
1319 1430 1.964223 TCGTCTTGCTTTCCTCTCTGT 59.036 47.619 0.00 0.00 0.00 3.41
1452 1563 2.614057 CCTTCTCGGTATTGTCCAATGC 59.386 50.000 2.80 1.40 33.47 3.56
1453 1564 3.535561 CTTCTCGGTATTGTCCAATGCT 58.464 45.455 7.81 0.00 34.46 3.79
1454 1565 3.179443 TCTCGGTATTGTCCAATGCTC 57.821 47.619 7.81 0.00 34.46 4.26
1455 1566 2.158957 TCTCGGTATTGTCCAATGCTCC 60.159 50.000 7.81 4.96 34.46 4.70
1457 1568 2.026729 TCGGTATTGTCCAATGCTCCAA 60.027 45.455 7.81 0.00 34.46 3.53
1460 1571 4.685924 GGTATTGTCCAATGCTCCAATTG 58.314 43.478 0.00 0.00 37.30 2.32
1461 1572 2.747396 TTGTCCAATGCTCCAATTGC 57.253 45.000 0.00 0.00 36.42 3.56
1463 1574 2.250031 TGTCCAATGCTCCAATTGCTT 58.750 42.857 0.00 0.00 36.42 3.91
1464 1575 3.429492 TGTCCAATGCTCCAATTGCTTA 58.571 40.909 0.00 0.00 36.42 3.09
1465 1576 3.193267 TGTCCAATGCTCCAATTGCTTAC 59.807 43.478 0.00 0.00 36.42 2.34
1466 1577 2.760092 TCCAATGCTCCAATTGCTTACC 59.240 45.455 0.00 0.00 36.42 2.85
1467 1578 2.762327 CCAATGCTCCAATTGCTTACCT 59.238 45.455 0.00 0.00 36.42 3.08
1468 1579 3.196254 CCAATGCTCCAATTGCTTACCTT 59.804 43.478 0.00 0.00 36.42 3.50
1469 1580 4.402155 CCAATGCTCCAATTGCTTACCTTA 59.598 41.667 0.00 0.00 36.42 2.69
1470 1581 5.343249 CAATGCTCCAATTGCTTACCTTAC 58.657 41.667 0.00 0.00 31.19 2.34
1471 1582 4.301072 TGCTCCAATTGCTTACCTTACT 57.699 40.909 0.00 0.00 0.00 2.24
1472 1583 4.261801 TGCTCCAATTGCTTACCTTACTC 58.738 43.478 0.00 0.00 0.00 2.59
1473 1584 4.261801 GCTCCAATTGCTTACCTTACTCA 58.738 43.478 0.00 0.00 0.00 3.41
1474 1585 4.333926 GCTCCAATTGCTTACCTTACTCAG 59.666 45.833 0.00 0.00 0.00 3.35
1475 1586 5.491982 CTCCAATTGCTTACCTTACTCAGT 58.508 41.667 0.00 0.00 0.00 3.41
1476 1587 5.488341 TCCAATTGCTTACCTTACTCAGTC 58.512 41.667 0.00 0.00 0.00 3.51
1477 1588 4.636206 CCAATTGCTTACCTTACTCAGTCC 59.364 45.833 0.00 0.00 0.00 3.85
1478 1589 5.491982 CAATTGCTTACCTTACTCAGTCCT 58.508 41.667 0.00 0.00 0.00 3.85
1479 1590 4.803098 TTGCTTACCTTACTCAGTCCTC 57.197 45.455 0.00 0.00 0.00 3.71
1480 1591 3.774734 TGCTTACCTTACTCAGTCCTCA 58.225 45.455 0.00 0.00 0.00 3.86
1483 1594 2.696526 ACCTTACTCAGTCCTCACCA 57.303 50.000 0.00 0.00 0.00 4.17
1500 1613 1.696988 CCAAATTTGGTGCACTACGC 58.303 50.000 26.34 0.00 43.43 4.42
1508 1621 2.578369 GTGCACTACGCCAGATACG 58.422 57.895 10.32 0.00 41.33 3.06
1515 1628 2.098770 ACTACGCCAGATACGTTTCTCC 59.901 50.000 5.47 0.03 41.93 3.71
1805 1924 1.609072 TGCTCGACGATAAGGATCCTG 59.391 52.381 17.02 5.00 0.00 3.86
1823 1942 2.486982 CCTGTCAAGGTTGAAGCTGATG 59.513 50.000 0.00 0.00 39.21 3.07
1866 1985 4.256110 CAGTAGGTTCATTGCAGACATCA 58.744 43.478 0.00 0.00 0.00 3.07
1890 2009 3.986277 AGAAGCTTGCCAAATTTCTGTG 58.014 40.909 2.10 0.00 0.00 3.66
1901 2020 6.589523 TGCCAAATTTCTGTGTATTATTGTGC 59.410 34.615 0.00 0.00 0.00 4.57
1912 2038 6.651643 TGTGTATTATTGTGCCGAGTAAACTT 59.348 34.615 0.00 0.00 0.00 2.66
1913 2039 7.818446 TGTGTATTATTGTGCCGAGTAAACTTA 59.182 33.333 0.00 0.00 0.00 2.24
1914 2040 8.823818 GTGTATTATTGTGCCGAGTAAACTTAT 58.176 33.333 0.00 0.00 0.00 1.73
1915 2041 9.037737 TGTATTATTGTGCCGAGTAAACTTATC 57.962 33.333 0.00 0.00 0.00 1.75
1946 2072 7.721286 TTTTTGTGGCAAAATTGATCGTTAT 57.279 28.000 7.70 0.00 0.00 1.89
2025 2153 4.029520 AGCTCAGTGATGATAGGTGAGTT 58.970 43.478 0.00 0.00 37.54 3.01
2062 2190 5.596845 TGCCAATCAACTTGTTTCTTTACC 58.403 37.500 0.00 0.00 32.61 2.85
2313 2452 9.403583 TCACAGGTTATTTTCATATTTACTCCC 57.596 33.333 0.00 0.00 0.00 4.30
2314 2453 9.408648 CACAGGTTATTTTCATATTTACTCCCT 57.591 33.333 0.00 0.00 0.00 4.20
2315 2454 9.628500 ACAGGTTATTTTCATATTTACTCCCTC 57.372 33.333 0.00 0.00 0.00 4.30
2316 2455 9.067986 CAGGTTATTTTCATATTTACTCCCTCC 57.932 37.037 0.00 0.00 0.00 4.30
2317 2456 7.937394 AGGTTATTTTCATATTTACTCCCTCCG 59.063 37.037 0.00 0.00 0.00 4.63
2318 2457 7.718314 GGTTATTTTCATATTTACTCCCTCCGT 59.282 37.037 0.00 0.00 0.00 4.69
2319 2458 8.771766 GTTATTTTCATATTTACTCCCTCCGTC 58.228 37.037 0.00 0.00 0.00 4.79
2320 2459 4.950205 TTCATATTTACTCCCTCCGTCC 57.050 45.455 0.00 0.00 0.00 4.79
2321 2460 2.889045 TCATATTTACTCCCTCCGTCCG 59.111 50.000 0.00 0.00 0.00 4.79
2322 2461 2.734755 TATTTACTCCCTCCGTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
2323 2462 1.856629 ATTTACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
2324 2463 1.631405 TTTACTCCCTCCGTCCGAAA 58.369 50.000 0.00 0.00 0.00 3.46
2325 2464 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
2326 2465 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2327 2466 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2328 2467 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2329 2468 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2330 2469 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2331 2470 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2332 2471 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2333 2472 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2334 2473 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2335 2474 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2336 2475 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2337 2476 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2338 2477 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2339 2478 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2340 2479 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2341 2480 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2342 2481 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2343 2482 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2344 2483 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2345 2484 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2346 2485 8.800972 CGAAAATACTTGTCATCAAAATGGATG 58.199 33.333 0.00 0.00 44.78 3.51
2359 2498 9.826574 CATCAAAATGGATGAAAAAGGATGTAT 57.173 29.630 0.00 0.00 46.00 2.29
2361 2500 9.258629 TCAAAATGGATGAAAAAGGATGTATCT 57.741 29.630 0.00 0.00 0.00 1.98
2366 2505 8.964476 TGGATGAAAAAGGATGTATCTAGAAC 57.036 34.615 0.00 0.00 0.00 3.01
2367 2506 8.772250 TGGATGAAAAAGGATGTATCTAGAACT 58.228 33.333 0.00 0.00 0.00 3.01
2388 2527 9.406113 AGAACTAAAATACGTCTAGATACACCT 57.594 33.333 0.00 0.00 0.00 4.00
2389 2528 9.662545 GAACTAAAATACGTCTAGATACACCTC 57.337 37.037 0.00 0.00 0.00 3.85
2390 2529 8.164058 ACTAAAATACGTCTAGATACACCTCC 57.836 38.462 0.00 0.00 0.00 4.30
2391 2530 7.997803 ACTAAAATACGTCTAGATACACCTCCT 59.002 37.037 0.00 0.00 0.00 3.69
2392 2531 7.657023 AAAATACGTCTAGATACACCTCCTT 57.343 36.000 0.00 0.00 0.00 3.36
2393 2532 7.657023 AAATACGTCTAGATACACCTCCTTT 57.343 36.000 0.00 0.00 0.00 3.11
2394 2533 7.657023 AATACGTCTAGATACACCTCCTTTT 57.343 36.000 0.00 0.00 0.00 2.27
2395 2534 8.757982 AATACGTCTAGATACACCTCCTTTTA 57.242 34.615 0.00 0.00 0.00 1.52
2396 2535 8.937207 ATACGTCTAGATACACCTCCTTTTAT 57.063 34.615 0.00 0.00 0.00 1.40
2397 2536 7.274603 ACGTCTAGATACACCTCCTTTTATC 57.725 40.000 0.00 0.00 0.00 1.75
2398 2537 6.264970 ACGTCTAGATACACCTCCTTTTATCC 59.735 42.308 0.00 0.00 0.00 2.59
2399 2538 6.264744 CGTCTAGATACACCTCCTTTTATCCA 59.735 42.308 0.00 0.00 0.00 3.41
2400 2539 7.039644 CGTCTAGATACACCTCCTTTTATCCAT 60.040 40.741 0.00 0.00 0.00 3.41
2401 2540 8.652290 GTCTAGATACACCTCCTTTTATCCATT 58.348 37.037 0.00 0.00 0.00 3.16
2402 2541 9.225682 TCTAGATACACCTCCTTTTATCCATTT 57.774 33.333 0.00 0.00 0.00 2.32
2403 2542 9.853177 CTAGATACACCTCCTTTTATCCATTTT 57.147 33.333 0.00 0.00 0.00 1.82
2404 2543 8.525290 AGATACACCTCCTTTTATCCATTTTG 57.475 34.615 0.00 0.00 0.00 2.44
2405 2544 8.336235 AGATACACCTCCTTTTATCCATTTTGA 58.664 33.333 0.00 0.00 0.00 2.69
2406 2545 9.136323 GATACACCTCCTTTTATCCATTTTGAT 57.864 33.333 0.00 0.00 0.00 2.57
2407 2546 7.174107 ACACCTCCTTTTATCCATTTTGATG 57.826 36.000 0.00 0.00 0.00 3.07
2408 2547 6.953520 ACACCTCCTTTTATCCATTTTGATGA 59.046 34.615 0.00 0.00 0.00 2.92
2409 2548 7.093771 ACACCTCCTTTTATCCATTTTGATGAC 60.094 37.037 0.00 0.00 0.00 3.06
2410 2549 6.953520 ACCTCCTTTTATCCATTTTGATGACA 59.046 34.615 0.00 0.00 0.00 3.58
2411 2550 7.454380 ACCTCCTTTTATCCATTTTGATGACAA 59.546 33.333 0.00 0.00 0.00 3.18
2412 2551 7.977853 CCTCCTTTTATCCATTTTGATGACAAG 59.022 37.037 0.00 0.00 37.32 3.16
2413 2552 8.421249 TCCTTTTATCCATTTTGATGACAAGT 57.579 30.769 0.00 0.00 37.32 3.16
2414 2553 9.527157 TCCTTTTATCCATTTTGATGACAAGTA 57.473 29.630 0.00 0.00 37.32 2.24
2420 2559 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2421 2560 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2422 2561 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2423 2562 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2424 2563 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2425 2564 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2426 2565 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2427 2566 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2428 2567 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2429 2568 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2430 2569 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2431 2570 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2532 2674 8.995027 AGGATTTAAATACCAATGCTGATGTA 57.005 30.769 6.80 0.00 30.54 2.29
2548 2690 3.132289 TGATGTACCCATTCCTCGACTTC 59.868 47.826 0.00 0.00 0.00 3.01
2569 2711 9.678941 GACTTCCCTTACAAAAAGAGTTTTATG 57.321 33.333 0.00 0.00 35.12 1.90
2639 2781 4.110482 CGTAAGCTAGTAAATTCGCTGGT 58.890 43.478 0.00 0.00 32.22 4.00
2875 3020 1.321474 TTGCTTGCCTCTGGTCTTTG 58.679 50.000 0.00 0.00 0.00 2.77
2886 3031 2.158623 TCTGGTCTTTGCTCACCATTGT 60.159 45.455 0.00 0.00 41.97 2.71
3363 3522 1.227823 CTGGGTTTGAGTGCGACCA 60.228 57.895 0.00 0.00 35.11 4.02
3486 3649 6.825721 CAGAGGCTTCTACCAAATACAATCTT 59.174 38.462 0.00 0.00 30.73 2.40
3524 3687 4.624913 TCCTCTGGATTAATCTCCACTGT 58.375 43.478 14.95 0.00 40.43 3.55
3825 3988 4.540099 AGGATTCCTTCAAGAACCCATACA 59.460 41.667 0.00 0.00 30.90 2.29
3888 4051 5.009710 GGTCATCCAGTCAACATCTCGTATA 59.990 44.000 0.00 0.00 0.00 1.47
3900 4063 4.830046 ACATCTCGTATATCAGCAGGAACT 59.170 41.667 0.00 0.00 43.88 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 6.613271 TGGCTTCTGATCTAGGATCTTAAACT 59.387 38.462 8.66 0.00 0.00 2.66
140 142 0.550914 AACAAGCTTGACCCCAGTGA 59.449 50.000 32.50 0.00 0.00 3.41
145 147 1.692411 ACAAGAACAAGCTTGACCCC 58.308 50.000 32.50 16.60 46.31 4.95
288 296 6.414987 GTCAACTCCATCTTTTTGTTCTTTCG 59.585 38.462 0.00 0.00 0.00 3.46
301 309 2.936919 TGCTTGTGTCAACTCCATCT 57.063 45.000 0.00 0.00 0.00 2.90
363 372 0.107752 CCTCTCCTGCTGCTTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
368 399 0.903942 CTCTTCCTCTCCTGCTGCTT 59.096 55.000 0.00 0.00 0.00 3.91
377 418 3.954258 CTCTTCCTCTTCCTCTTCCTCTC 59.046 52.174 0.00 0.00 0.00 3.20
381 422 3.108847 TCCTCTTCCTCTTCCTCTTCC 57.891 52.381 0.00 0.00 0.00 3.46
438 526 2.026822 TGCAAGTCCATCTTCCTCTTCC 60.027 50.000 0.00 0.00 33.63 3.46
522 622 4.866508 TCCTACCTACTATCAAATGGCG 57.133 45.455 0.00 0.00 0.00 5.69
648 756 5.364778 AGGCGCACATATAACTTGATGTTA 58.635 37.500 10.83 0.00 44.22 2.41
719 827 1.407437 GGCTGCACATAGGTTAGCTGT 60.407 52.381 11.80 0.00 35.83 4.40
741 849 1.047596 ACATTGTTTGGTGCCCTGCA 61.048 50.000 0.00 0.00 35.60 4.41
742 850 0.600782 CACATTGTTTGGTGCCCTGC 60.601 55.000 0.00 0.00 0.00 4.85
743 851 3.591979 CACATTGTTTGGTGCCCTG 57.408 52.632 0.00 0.00 0.00 4.45
748 856 3.713858 TCTTCTGCACATTGTTTGGTG 57.286 42.857 0.00 0.00 38.05 4.17
756 864 6.421485 ACCTAGAAATCATCTTCTGCACATT 58.579 36.000 0.00 0.00 39.71 2.71
766 874 9.829507 CTGAGAATAACAACCTAGAAATCATCT 57.170 33.333 0.00 0.00 42.48 2.90
771 879 6.721318 TGGCTGAGAATAACAACCTAGAAAT 58.279 36.000 0.00 0.00 0.00 2.17
775 883 4.080863 ACCTGGCTGAGAATAACAACCTAG 60.081 45.833 0.00 0.00 0.00 3.02
780 888 2.642311 TGGACCTGGCTGAGAATAACAA 59.358 45.455 0.00 0.00 0.00 2.83
785 893 1.064906 CACATGGACCTGGCTGAGAAT 60.065 52.381 0.00 0.00 0.00 2.40
814 923 2.932498 TCGATTTTGACTGCATTGCAC 58.068 42.857 7.38 0.00 33.79 4.57
848 957 2.668457 CCAACAGAGTCTATGAACGTGC 59.332 50.000 0.43 0.00 0.00 5.34
862 971 6.530120 TGTGCTTTTAGAATACTCCAACAGA 58.470 36.000 0.00 0.00 0.00 3.41
863 972 6.801539 TGTGCTTTTAGAATACTCCAACAG 57.198 37.500 0.00 0.00 0.00 3.16
864 973 7.284489 AGTTTGTGCTTTTAGAATACTCCAACA 59.716 33.333 0.00 0.00 0.00 3.33
865 974 7.591426 CAGTTTGTGCTTTTAGAATACTCCAAC 59.409 37.037 0.00 0.00 0.00 3.77
976 1085 4.619227 CCGTGTGGGCCTCAACGT 62.619 66.667 10.32 0.00 0.00 3.99
1035 1145 2.183046 GGAGCTGAGCGAGTGGAC 59.817 66.667 0.00 0.00 0.00 4.02
1131 1241 3.611674 GGGCGCTAGAGGAGGCTC 61.612 72.222 7.64 5.78 39.97 4.70
1136 1246 2.123683 CTCAGGGGCGCTAGAGGA 60.124 66.667 7.64 6.24 0.00 3.71
1265 1375 2.469516 GCCATGACCGGCGGTTAAG 61.470 63.158 34.58 25.47 43.52 1.85
1299 1409 1.964223 ACAGAGAGGAAAGCAAGACGA 59.036 47.619 0.00 0.00 0.00 4.20
1300 1410 2.447244 ACAGAGAGGAAAGCAAGACG 57.553 50.000 0.00 0.00 0.00 4.18
1301 1411 3.471680 ACAACAGAGAGGAAAGCAAGAC 58.528 45.455 0.00 0.00 0.00 3.01
1315 1426 1.020861 CCAGCTGCGCATACAACAGA 61.021 55.000 12.24 0.00 33.10 3.41
1319 1430 3.133464 GCCCAGCTGCGCATACAA 61.133 61.111 18.38 0.00 0.00 2.41
1422 1533 2.685380 CCGAGAAGGTCCTGGGCT 60.685 66.667 0.00 0.00 34.51 5.19
1444 1555 3.429410 GGTAAGCAATTGGAGCATTGGAC 60.429 47.826 7.72 0.00 0.00 4.02
1452 1563 5.491982 ACTGAGTAAGGTAAGCAATTGGAG 58.508 41.667 7.72 0.00 0.00 3.86
1453 1564 5.488341 GACTGAGTAAGGTAAGCAATTGGA 58.512 41.667 7.72 0.00 0.00 3.53
1454 1565 4.636206 GGACTGAGTAAGGTAAGCAATTGG 59.364 45.833 7.72 0.00 0.00 3.16
1455 1566 5.491982 AGGACTGAGTAAGGTAAGCAATTG 58.508 41.667 0.00 0.00 0.00 2.32
1457 1568 4.777896 TGAGGACTGAGTAAGGTAAGCAAT 59.222 41.667 0.00 0.00 0.00 3.56
1460 1571 3.119065 GGTGAGGACTGAGTAAGGTAAGC 60.119 52.174 0.00 0.00 0.00 3.09
1461 1572 4.087182 TGGTGAGGACTGAGTAAGGTAAG 58.913 47.826 0.00 0.00 0.00 2.34
1463 1574 3.820195 TGGTGAGGACTGAGTAAGGTA 57.180 47.619 0.00 0.00 0.00 3.08
1464 1575 2.696526 TGGTGAGGACTGAGTAAGGT 57.303 50.000 0.00 0.00 0.00 3.50
1465 1576 4.559862 ATTTGGTGAGGACTGAGTAAGG 57.440 45.455 0.00 0.00 0.00 2.69
1466 1577 5.182001 CCAAATTTGGTGAGGACTGAGTAAG 59.818 44.000 26.34 0.00 43.43 2.34
1467 1578 5.070001 CCAAATTTGGTGAGGACTGAGTAA 58.930 41.667 26.34 0.00 43.43 2.24
1468 1579 4.651778 CCAAATTTGGTGAGGACTGAGTA 58.348 43.478 26.34 0.00 43.43 2.59
1469 1580 3.490348 CCAAATTTGGTGAGGACTGAGT 58.510 45.455 26.34 0.00 43.43 3.41
1492 1605 1.587034 GAAACGTATCTGGCGTAGTGC 59.413 52.381 0.00 0.00 42.10 4.40
1493 1606 3.106672 GAGAAACGTATCTGGCGTAGTG 58.893 50.000 0.00 0.00 42.10 2.74
1494 1607 2.098770 GGAGAAACGTATCTGGCGTAGT 59.901 50.000 0.00 0.00 42.10 2.73
1495 1608 2.728922 GGAGAAACGTATCTGGCGTAG 58.271 52.381 0.00 0.00 42.10 3.51
1496 1609 1.064505 CGGAGAAACGTATCTGGCGTA 59.935 52.381 0.00 0.00 42.10 4.42
1498 1611 1.480219 GCGGAGAAACGTATCTGGCG 61.480 60.000 0.00 0.00 35.98 5.69
1499 1612 0.459585 TGCGGAGAAACGTATCTGGC 60.460 55.000 0.00 0.00 35.98 4.85
1500 1613 2.004583 TTGCGGAGAAACGTATCTGG 57.995 50.000 0.00 0.00 35.98 3.86
1501 1614 3.370978 ACAATTGCGGAGAAACGTATCTG 59.629 43.478 5.05 0.00 35.98 2.90
1502 1615 3.370978 CACAATTGCGGAGAAACGTATCT 59.629 43.478 5.05 0.00 35.98 1.98
1503 1616 3.369756 TCACAATTGCGGAGAAACGTATC 59.630 43.478 5.05 0.00 35.98 2.24
1504 1617 3.124636 GTCACAATTGCGGAGAAACGTAT 59.875 43.478 5.05 0.00 35.98 3.06
1505 1618 2.477375 GTCACAATTGCGGAGAAACGTA 59.523 45.455 5.05 0.00 35.98 3.57
1506 1619 1.263217 GTCACAATTGCGGAGAAACGT 59.737 47.619 5.05 0.00 35.98 3.99
1507 1620 1.399727 GGTCACAATTGCGGAGAAACG 60.400 52.381 5.05 0.00 0.00 3.60
1508 1621 1.880027 AGGTCACAATTGCGGAGAAAC 59.120 47.619 5.05 0.00 0.00 2.78
1509 1622 2.270352 AGGTCACAATTGCGGAGAAA 57.730 45.000 5.05 0.00 0.00 2.52
1515 1628 0.040514 TTGCGAAGGTCACAATTGCG 60.041 50.000 5.05 0.00 0.00 4.85
1805 1924 1.200948 GGCATCAGCTTCAACCTTGAC 59.799 52.381 0.00 0.00 41.70 3.18
1823 1942 0.750911 ATTAGCTCTGCAAGGCTGGC 60.751 55.000 19.33 7.01 40.05 4.85
1866 1985 4.141869 ACAGAAATTTGGCAAGCTTCTTGT 60.142 37.500 18.10 16.27 0.00 3.16
1890 2009 8.212495 CGATAAGTTTACTCGGCACAATAATAC 58.788 37.037 0.00 0.00 0.00 1.89
1946 2072 6.372659 GTCAGAGAATGATCTGCAAGGTTAAA 59.627 38.462 0.00 0.00 45.25 1.52
2073 2201 2.687935 ACACACAGAATTGGTTGGACAC 59.312 45.455 0.00 0.00 0.00 3.67
2074 2202 3.011566 ACACACAGAATTGGTTGGACA 57.988 42.857 0.00 0.00 0.00 4.02
2075 2203 4.385358 AAACACACAGAATTGGTTGGAC 57.615 40.909 0.00 0.00 0.00 4.02
2173 2303 7.435068 AAAGTGGTTACATCAGTACAATCAC 57.565 36.000 0.00 0.00 0.00 3.06
2184 2314 6.273071 AGCAAGTTGAAAAAGTGGTTACATC 58.727 36.000 7.16 0.00 0.00 3.06
2307 2446 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2308 2447 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2309 2448 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2310 2449 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2311 2450 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2312 2451 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2313 2452 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2314 2453 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2315 2454 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2316 2455 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2317 2456 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2318 2457 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2319 2458 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2320 2459 8.800972 CATCCATTTTGATGACAAGTATTTTCG 58.199 33.333 0.00 0.00 43.94 3.46
2321 2460 9.859427 TCATCCATTTTGATGACAAGTATTTTC 57.141 29.630 0.00 0.00 44.65 2.29
2333 2472 9.826574 ATACATCCTTTTTCATCCATTTTGATG 57.173 29.630 0.00 0.00 42.84 3.07
2335 2474 9.258629 AGATACATCCTTTTTCATCCATTTTGA 57.741 29.630 0.00 0.00 0.00 2.69
2340 2479 9.566432 GTTCTAGATACATCCTTTTTCATCCAT 57.434 33.333 0.00 0.00 0.00 3.41
2341 2480 8.772250 AGTTCTAGATACATCCTTTTTCATCCA 58.228 33.333 0.00 0.00 0.00 3.41
2362 2501 9.406113 AGGTGTATCTAGACGTATTTTAGTTCT 57.594 33.333 0.00 0.00 0.00 3.01
2363 2502 9.662545 GAGGTGTATCTAGACGTATTTTAGTTC 57.337 37.037 0.00 0.00 0.00 3.01
2364 2503 8.628280 GGAGGTGTATCTAGACGTATTTTAGTT 58.372 37.037 0.00 0.00 0.00 2.24
2365 2504 7.997803 AGGAGGTGTATCTAGACGTATTTTAGT 59.002 37.037 0.00 0.00 0.00 2.24
2366 2505 8.393671 AGGAGGTGTATCTAGACGTATTTTAG 57.606 38.462 0.00 0.00 0.00 1.85
2367 2506 8.757982 AAGGAGGTGTATCTAGACGTATTTTA 57.242 34.615 0.00 0.00 0.00 1.52
2368 2507 7.657023 AAGGAGGTGTATCTAGACGTATTTT 57.343 36.000 0.00 0.00 0.00 1.82
2369 2508 7.657023 AAAGGAGGTGTATCTAGACGTATTT 57.343 36.000 0.00 0.00 0.00 1.40
2370 2509 7.657023 AAAAGGAGGTGTATCTAGACGTATT 57.343 36.000 0.00 0.00 0.00 1.89
2371 2510 8.937207 ATAAAAGGAGGTGTATCTAGACGTAT 57.063 34.615 0.00 0.00 0.00 3.06
2372 2511 7.446625 GGATAAAAGGAGGTGTATCTAGACGTA 59.553 40.741 0.00 0.00 0.00 3.57
2373 2512 6.264970 GGATAAAAGGAGGTGTATCTAGACGT 59.735 42.308 0.00 0.00 0.00 4.34
2374 2513 6.264744 TGGATAAAAGGAGGTGTATCTAGACG 59.735 42.308 0.00 0.00 0.00 4.18
2375 2514 7.598759 TGGATAAAAGGAGGTGTATCTAGAC 57.401 40.000 0.00 0.00 0.00 2.59
2376 2515 8.798975 AATGGATAAAAGGAGGTGTATCTAGA 57.201 34.615 0.00 0.00 0.00 2.43
2377 2516 9.853177 AAAATGGATAAAAGGAGGTGTATCTAG 57.147 33.333 0.00 0.00 0.00 2.43
2378 2517 9.627123 CAAAATGGATAAAAGGAGGTGTATCTA 57.373 33.333 0.00 0.00 0.00 1.98
2379 2518 8.336235 TCAAAATGGATAAAAGGAGGTGTATCT 58.664 33.333 0.00 0.00 0.00 1.98
2380 2519 8.519799 TCAAAATGGATAAAAGGAGGTGTATC 57.480 34.615 0.00 0.00 0.00 2.24
2381 2520 8.917088 CATCAAAATGGATAAAAGGAGGTGTAT 58.083 33.333 0.00 0.00 0.00 2.29
2382 2521 8.112822 TCATCAAAATGGATAAAAGGAGGTGTA 58.887 33.333 0.00 0.00 33.42 2.90
2383 2522 6.953520 TCATCAAAATGGATAAAAGGAGGTGT 59.046 34.615 0.00 0.00 33.42 4.16
2384 2523 7.093814 TGTCATCAAAATGGATAAAAGGAGGTG 60.094 37.037 0.00 0.00 33.42 4.00
2385 2524 6.953520 TGTCATCAAAATGGATAAAAGGAGGT 59.046 34.615 0.00 0.00 33.42 3.85
2386 2525 7.408756 TGTCATCAAAATGGATAAAAGGAGG 57.591 36.000 0.00 0.00 33.42 4.30
2387 2526 8.526147 ACTTGTCATCAAAATGGATAAAAGGAG 58.474 33.333 0.00 0.00 33.42 3.69
2388 2527 8.421249 ACTTGTCATCAAAATGGATAAAAGGA 57.579 30.769 0.00 0.00 33.42 3.36
2394 2533 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2395 2534 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2396 2535 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2397 2536 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2398 2537 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2399 2538 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2400 2539 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2401 2540 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2402 2541 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2403 2542 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2404 2543 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2405 2544 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2406 2545 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2407 2546 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2408 2547 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2409 2548 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2410 2549 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2411 2550 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2412 2551 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2413 2552 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2414 2553 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2415 2554 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2416 2555 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
2417 2556 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
2418 2557 1.817447 GAATATACTCCCTCCGTCCGG 59.183 57.143 0.00 0.00 0.00 5.14
2419 2558 2.792878 AGAATATACTCCCTCCGTCCG 58.207 52.381 0.00 0.00 0.00 4.79
2420 2559 5.774184 AGTAAAGAATATACTCCCTCCGTCC 59.226 44.000 0.00 0.00 0.00 4.79
2421 2560 6.264970 ACAGTAAAGAATATACTCCCTCCGTC 59.735 42.308 0.00 0.00 31.33 4.79
2422 2561 6.040616 CACAGTAAAGAATATACTCCCTCCGT 59.959 42.308 0.00 0.00 31.33 4.69
2423 2562 6.264744 TCACAGTAAAGAATATACTCCCTCCG 59.735 42.308 0.00 0.00 31.33 4.63
2424 2563 7.598759 TCACAGTAAAGAATATACTCCCTCC 57.401 40.000 0.00 0.00 31.33 4.30
2425 2564 9.886132 TTTTCACAGTAAAGAATATACTCCCTC 57.114 33.333 0.00 0.00 31.33 4.30
2426 2565 9.892130 CTTTTCACAGTAAAGAATATACTCCCT 57.108 33.333 0.00 0.00 35.16 4.20
2427 2566 9.668497 ACTTTTCACAGTAAAGAATATACTCCC 57.332 33.333 3.25 0.00 36.38 4.30
2532 2674 0.252742 AGGGAAGTCGAGGAATGGGT 60.253 55.000 0.00 0.00 0.00 4.51
2594 2736 4.640771 AGACTCCAAAGCAGTTCCATAA 57.359 40.909 0.00 0.00 0.00 1.90
2599 2741 2.484889 ACGAAGACTCCAAAGCAGTTC 58.515 47.619 0.00 0.00 0.00 3.01
2639 2781 6.526526 TGCAGTACATTGAAGTTGGTAAGTA 58.473 36.000 0.00 0.00 0.00 2.24
2654 2796 5.879223 CCTTCATCTTCTTTCTGCAGTACAT 59.121 40.000 14.67 0.00 0.00 2.29
2818 2961 2.799978 GGCAGGAAAACAAAACGATTGG 59.200 45.455 9.76 0.00 0.00 3.16
3524 3687 1.632409 AGCTGAGGAGATTGCCAAGAA 59.368 47.619 0.00 0.00 0.00 2.52
3693 3856 3.505680 ACTTTATGAACAAGAATGCGGCA 59.494 39.130 4.58 4.58 0.00 5.69
3825 3988 6.884836 GTGGGTATGTTCCTGAAAGAAATACT 59.115 38.462 0.00 0.00 34.07 2.12
3888 4051 4.713814 TCATTGACTAGAGTTCCTGCTGAT 59.286 41.667 0.00 0.00 0.00 2.90
3900 4063 6.040054 CCATGATGGCAAAATCATTGACTAGA 59.960 38.462 0.00 0.00 43.28 2.43


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

AutoCloner maintained by Alex Coulton.