Multiple sequence alignment - TraesCS6A01G291500

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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 TraesCS6A01G291500 chr6A 100.000 5315 0 0 1 5315 523062744 523068058 0.000000e+00 9816.0
1 TraesCS6A01G291500 chr6B 94.380 1548 75 10 2909 4446 570148606 570150151 0.000000e+00 2366.0
2 TraesCS6A01G291500 chr6B 84.629 1158 102 38 706 1834 570147498 570148608 0.000000e+00 1083.0
3 TraesCS6A01G291500 chr6B 92.276 246 19 0 4638 4883 570150599 570150844 3.050000e-92 350.0
4 TraesCS6A01G291500 chr6B 82.368 397 33 10 4923 5315 570150845 570151208 1.440000e-80 311.0
5 TraesCS6A01G291500 chr6B 91.111 45 4 0 1694 1738 143457869 143457825 1.600000e-05 62.1
6 TraesCS6A01G291500 chr6D 95.749 1435 48 9 2909 4331 381547452 381548885 0.000000e+00 2300.0
7 TraesCS6A01G291500 chr6D 88.229 1852 144 41 1 1834 381545659 381547454 0.000000e+00 2145.0
8 TraesCS6A01G291500 chr6D 91.896 691 44 5 4637 5315 381549433 381550123 0.000000e+00 955.0
9 TraesCS6A01G291500 chr6D 86.348 293 20 6 4338 4622 381549077 381549357 8.650000e-78 302.0
10 TraesCS6A01G291500 chr5A 89.091 1100 101 10 1833 2913 579822691 579821592 0.000000e+00 1349.0
11 TraesCS6A01G291500 chr5A 79.287 449 64 16 1830 2274 37970767 37971190 2.420000e-73 287.0
12 TraesCS6A01G291500 chr5A 75.656 686 100 30 1833 2473 535706587 535705924 4.050000e-71 279.0
13 TraesCS6A01G291500 chr5A 93.023 43 3 0 1694 1736 552545989 552545947 4.440000e-06 63.9
14 TraesCS6A01G291500 chr2D 90.563 657 54 2 1834 2482 567649323 567648667 0.000000e+00 863.0
15 TraesCS6A01G291500 chr2D 91.489 47 3 1 1694 1739 562758253 562758207 4.440000e-06 63.9
16 TraesCS6A01G291500 chr3A 90.554 614 58 0 1833 2446 348998717 348998104 0.000000e+00 813.0
17 TraesCS6A01G291500 chr7A 79.287 449 66 16 1831 2275 466321449 466321874 6.730000e-74 289.0
18 TraesCS6A01G291500 chr7A 83.513 279 28 8 2636 2911 466322250 466322513 1.480000e-60 244.0
19 TraesCS6A01G291500 chr7A 100.000 34 0 0 1702 1735 626609469 626609436 4.440000e-06 63.9
20 TraesCS6A01G291500 chr2B 78.215 381 66 10 2103 2473 632610103 632610476 1.490000e-55 228.0
21 TraesCS6A01G291500 chr5B 86.420 162 21 1 2281 2442 491298667 491298507 5.470000e-40 176.0
22 TraesCS6A01G291500 chr5B 91.736 121 10 0 2279 2399 574666774 574666654 9.150000e-38 169.0
23 TraesCS6A01G291500 chr5B 87.023 131 16 1 2792 2922 574662839 574662710 4.290000e-31 147.0
24 TraesCS6A01G291500 chr5B 94.340 53 3 0 2470 2522 491298511 491298459 1.230000e-11 82.4
25 TraesCS6A01G291500 chr7B 89.062 128 12 2 2792 2918 246524527 246524653 1.980000e-34 158.0
26 TraesCS6A01G291500 chr7B 93.750 64 4 0 2336 2399 246520787 246520850 4.380000e-16 97.1
27 TraesCS6A01G291500 chr1D 76.557 273 53 5 3680 3947 97778243 97777977 7.180000e-29 139.0
28 TraesCS6A01G291500 chr4B 95.745 47 2 0 1690 1736 613320143 613320097 5.710000e-10 76.8
29 TraesCS6A01G291500 chr3D 95.652 46 2 0 1695 1740 56848816 56848861 2.050000e-09 75.0
30 TraesCS6A01G291500 chr7D 86.154 65 7 2 4465 4528 500764055 500763992 9.550000e-08 69.4
31 TraesCS6A01G291500 chr7D 88.235 51 6 0 1694 1744 365391685 365391635 1.600000e-05 62.1
32 TraesCS6A01G291500 chr5D 93.023 43 3 0 1694 1736 11219917 11219959 4.440000e-06 63.9
33 TraesCS6A01G291500 chr4A 95.000 40 2 0 1697 1736 447781203 447781242 4.440000e-06 63.9


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 TraesCS6A01G291500 chr6A 523062744 523068058 5314 False 9816.0 9816 100.00000 1 5315 1 chr6A.!!$F1 5314
1 TraesCS6A01G291500 chr6B 570147498 570151208 3710 False 1027.5 2366 88.41325 706 5315 4 chr6B.!!$F1 4609
2 TraesCS6A01G291500 chr6D 381545659 381550123 4464 False 1425.5 2300 90.55550 1 5315 4 chr6D.!!$F1 5314
3 TraesCS6A01G291500 chr5A 579821592 579822691 1099 True 1349.0 1349 89.09100 1833 2913 1 chr5A.!!$R3 1080
4 TraesCS6A01G291500 chr5A 535705924 535706587 663 True 279.0 279 75.65600 1833 2473 1 chr5A.!!$R1 640
5 TraesCS6A01G291500 chr2D 567648667 567649323 656 True 863.0 863 90.56300 1834 2482 1 chr2D.!!$R2 648
6 TraesCS6A01G291500 chr3A 348998104 348998717 613 True 813.0 813 90.55400 1833 2446 1 chr3A.!!$R1 613
7 TraesCS6A01G291500 chr7A 466321449 466322513 1064 False 266.5 289 81.40000 1831 2911 2 chr7A.!!$F1 1080

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
826 836 3.551846 ACCCTGAACAGTTTTTGTCGAT 58.448 40.909 0.00 0.0 39.73 3.59 F
1565 1621 0.251916 TAATTCAGTGTGGGCCTCCG 59.748 55.000 4.53 0.0 35.24 4.63 F
2611 2868 0.033208 TTGGGTCCAATGGAGATGCC 60.033 55.000 0.27 0.0 29.39 4.40 F
2679 2936 0.104304 CTTGGCTCGTATACCCGCTT 59.896 55.000 9.94 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2031 0.036875 GTGGAGTTGGAACCAGAGGG 59.963 60.0 0.00 0.0 36.82 4.30 R
2669 2926 0.103572 GAAGCGGTCAAGCGGGTATA 59.896 55.0 3.61 0.0 43.00 1.47 R
4204 4481 0.185901 TCCCCTGCTCTTTTGTTGCT 59.814 50.0 0.00 0.0 0.00 3.91 R
4354 4818 0.188342 AACATGGCCCAGAGGTTGTT 59.812 50.0 0.00 0.0 34.57 2.83 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
262 263 9.518906 AATTTTGGAGCAATTTTTGAAATTCAC 57.481 25.926 0.00 0.00 0.00 3.18
278 279 8.071122 TGAAATTCACGAACAATTTTTGGATC 57.929 30.769 0.00 0.00 34.30 3.36
287 288 4.148838 ACAATTTTTGGATCGGAGACCAA 58.851 39.130 13.07 13.07 42.64 3.67
294 295 4.627284 TGGATCGGAGACCAACTTTAAA 57.373 40.909 4.58 0.00 42.51 1.52
303 304 5.952347 GGAGACCAACTTTAAATCTGGGAAT 59.048 40.000 16.22 5.48 32.94 3.01
307 308 9.547279 AGACCAACTTTAAATCTGGGAATAATT 57.453 29.630 16.22 0.00 32.94 1.40
322 323 6.951198 TGGGAATAATTTTTGGAACTAGCAGA 59.049 34.615 0.00 0.00 0.00 4.26
340 341 9.822185 ACTAGCAGACATTTCTTTTGAATTTTT 57.178 25.926 0.00 0.00 38.37 1.94
439 440 4.277423 TGAAAAATCGGGAAACACTTCTCC 59.723 41.667 0.00 0.00 0.00 3.71
444 445 3.827722 TCGGGAAACACTTCTCCAATTT 58.172 40.909 0.00 0.00 32.95 1.82
445 446 3.568007 TCGGGAAACACTTCTCCAATTTG 59.432 43.478 0.00 0.00 32.95 2.32
597 598 9.822185 AGATTTTTCAAATTCACAGCTACTTTT 57.178 25.926 0.00 0.00 0.00 2.27
598 599 9.853921 GATTTTTCAAATTCACAGCTACTTTTG 57.146 29.630 0.00 0.00 0.00 2.44
604 605 8.855110 TCAAATTCACAGCTACTTTTGGAAATA 58.145 29.630 0.00 0.00 0.00 1.40
606 607 6.569179 TTCACAGCTACTTTTGGAAATACC 57.431 37.500 0.00 0.00 39.54 2.73
642 643 5.098893 TCAAACTCGTGAACCATTTTTGTG 58.901 37.500 0.00 0.00 0.00 3.33
651 652 5.814705 GTGAACCATTTTTGTGTCCATGAAA 59.185 36.000 0.00 0.00 0.00 2.69
656 657 9.571816 AACCATTTTTGTGTCCATGAAAATATT 57.428 25.926 0.00 0.00 32.25 1.28
673 674 9.142014 TGAAAATATTTTGGATATTCGGACCAT 57.858 29.630 17.98 0.00 33.56 3.55
688 689 5.252547 TCGGACCATTTTCTGAATTCATGA 58.747 37.500 8.96 6.08 0.00 3.07
689 690 5.887598 TCGGACCATTTTCTGAATTCATGAT 59.112 36.000 8.96 0.00 0.00 2.45
693 694 7.820872 GGACCATTTTCTGAATTCATGATTGTT 59.179 33.333 8.96 0.00 0.00 2.83
727 730 6.031003 CCGAGAATATTTTTCAAACGTGAACG 59.969 38.462 0.40 0.40 43.52 3.95
746 751 9.199184 CGTGAACGTTTTGAAATATGAGAATAG 57.801 33.333 0.46 0.00 34.11 1.73
826 836 3.551846 ACCCTGAACAGTTTTTGTCGAT 58.448 40.909 0.00 0.00 39.73 3.59
837 847 5.574830 CAGTTTTTGTCGATTTTGTGGTTCA 59.425 36.000 0.00 0.00 0.00 3.18
849 859 7.169645 CGATTTTGTGGTTCATGAACATTTCTT 59.830 33.333 33.42 16.10 42.85 2.52
951 983 4.152964 GGGTTCCCCGCGTAGGTC 62.153 72.222 4.92 3.87 38.74 3.85
1114 1165 2.949177 TCCAAGCTTACAAAGGCTCA 57.051 45.000 0.00 0.00 37.87 4.26
1333 1384 2.005451 CAACAAGATGGCGAGGAAGAG 58.995 52.381 0.00 0.00 0.00 2.85
1349 1400 1.115930 AGAGCGTCAAGGACACCACT 61.116 55.000 0.00 0.00 32.09 4.00
1410 1461 6.836527 TGGAAAATTTTCTACTGGGTTCTTGA 59.163 34.615 25.86 0.00 37.35 3.02
1430 1484 3.299503 GAATGGGTGGGTGCTTATGATT 58.700 45.455 0.00 0.00 0.00 2.57
1433 1487 1.136891 GGGTGGGTGCTTATGATTTGC 59.863 52.381 0.00 0.00 0.00 3.68
1440 1494 2.096496 GTGCTTATGATTTGCTGCGTCT 59.904 45.455 0.00 0.00 0.00 4.18
1517 1571 4.096984 CCTTGAGATTTTGCAGGTATGGTC 59.903 45.833 0.00 0.00 0.00 4.02
1540 1594 2.533266 CACTTAGGTGTGCTGTCAGT 57.467 50.000 0.93 0.00 38.54 3.41
1560 1616 5.105473 TCAGTAGTAGTAATTCAGTGTGGGC 60.105 44.000 0.00 0.00 0.00 5.36
1565 1621 0.251916 TAATTCAGTGTGGGCCTCCG 59.748 55.000 4.53 0.00 35.24 4.63
1577 1633 2.093341 TGGGCCTCCGTTATGTAACTTC 60.093 50.000 4.53 0.00 34.12 3.01
1587 1643 5.406175 CCGTTATGTAACTTCGGAAAACAGA 59.594 40.000 0.00 0.00 43.22 3.41
1588 1644 6.073657 CCGTTATGTAACTTCGGAAAACAGAA 60.074 38.462 0.00 0.00 43.22 3.02
1589 1645 7.007697 CGTTATGTAACTTCGGAAAACAGAAG 58.992 38.462 0.00 0.00 46.66 2.85
1590 1646 7.095940 CGTTATGTAACTTCGGAAAACAGAAGA 60.096 37.037 14.56 0.00 44.76 2.87
1591 1647 8.553696 GTTATGTAACTTCGGAAAACAGAAGAA 58.446 33.333 14.56 2.88 44.76 2.52
1592 1648 6.988622 TGTAACTTCGGAAAACAGAAGAAA 57.011 33.333 14.56 2.61 44.76 2.52
1654 1710 0.323725 ATTCCTGACGGGCAAGCATT 60.324 50.000 0.00 0.00 34.39 3.56
1673 1729 4.327087 GCATTAGCCATTTTGTAAGTGTGC 59.673 41.667 0.00 0.00 33.58 4.57
1696 1752 5.533482 CAGTAGTGCTTGAGTGAAAGTAGT 58.467 41.667 0.00 0.00 31.43 2.73
1698 1754 4.672587 AGTGCTTGAGTGAAAGTAGTGA 57.327 40.909 0.00 0.00 0.00 3.41
1699 1755 5.220710 AGTGCTTGAGTGAAAGTAGTGAT 57.779 39.130 0.00 0.00 0.00 3.06
1700 1756 4.993584 AGTGCTTGAGTGAAAGTAGTGATG 59.006 41.667 0.00 0.00 0.00 3.07
1701 1757 4.752101 GTGCTTGAGTGAAAGTAGTGATGT 59.248 41.667 0.00 0.00 0.00 3.06
1702 1758 5.926542 GTGCTTGAGTGAAAGTAGTGATGTA 59.073 40.000 0.00 0.00 0.00 2.29
1703 1759 6.423905 GTGCTTGAGTGAAAGTAGTGATGTAA 59.576 38.462 0.00 0.00 0.00 2.41
1704 1760 6.989759 TGCTTGAGTGAAAGTAGTGATGTAAA 59.010 34.615 0.00 0.00 0.00 2.01
1705 1761 7.042051 TGCTTGAGTGAAAGTAGTGATGTAAAC 60.042 37.037 0.00 0.00 0.00 2.01
1706 1762 7.402811 TTGAGTGAAAGTAGTGATGTAAACG 57.597 36.000 0.00 0.00 0.00 3.60
1707 1763 5.404366 TGAGTGAAAGTAGTGATGTAAACGC 59.596 40.000 0.00 0.00 0.00 4.84
1709 1765 6.684686 AGTGAAAGTAGTGATGTAAACGCTA 58.315 36.000 0.00 0.00 29.98 4.26
1711 1767 7.817962 AGTGAAAGTAGTGATGTAAACGCTATT 59.182 33.333 0.00 0.00 34.20 1.73
1712 1768 9.079833 GTGAAAGTAGTGATGTAAACGCTATTA 57.920 33.333 0.00 0.00 34.20 0.98
1713 1769 9.811995 TGAAAGTAGTGATGTAAACGCTATTAT 57.188 29.630 0.00 0.00 34.20 1.28
1729 1785 9.490379 AACGCTATTATATTTCTTTACAGAGGG 57.510 33.333 0.00 0.00 0.00 4.30
1730 1786 8.867097 ACGCTATTATATTTCTTTACAGAGGGA 58.133 33.333 0.00 0.00 0.00 4.20
1731 1787 9.360093 CGCTATTATATTTCTTTACAGAGGGAG 57.640 37.037 0.00 0.00 0.00 4.30
1741 1797 9.537852 TTTCTTTACAGAGGGAGTACTGTATTA 57.462 33.333 0.00 0.00 45.05 0.98
1784 1840 7.170320 TCCTAAAACAAAGTACTACTGCTTTCG 59.830 37.037 0.00 0.00 33.19 3.46
1849 1905 0.406750 TGTACTCCCTCCGTTCCTCA 59.593 55.000 0.00 0.00 0.00 3.86
1860 1916 2.035449 TCCGTTCCTCAATATAGTGCGG 59.965 50.000 2.76 2.76 38.20 5.69
1861 1917 2.404215 CGTTCCTCAATATAGTGCGGG 58.596 52.381 9.18 7.37 0.00 6.13
1911 1967 6.841119 TGTAGTGCGTATTAACTACTTTCGA 58.159 36.000 12.65 0.00 45.87 3.71
1942 1998 1.295423 GAACTAGCCCCGCAACAGA 59.705 57.895 0.00 0.00 0.00 3.41
1944 2000 0.328258 AACTAGCCCCGCAACAGAAT 59.672 50.000 0.00 0.00 0.00 2.40
1975 2031 1.301009 CGCTCGCCTTTATCCCCTC 60.301 63.158 0.00 0.00 0.00 4.30
1980 2036 0.764752 CGCCTTTATCCCCTCCCTCT 60.765 60.000 0.00 0.00 0.00 3.69
2147 2209 4.697756 CCTTCGCTTCCACGGCCA 62.698 66.667 2.24 0.00 0.00 5.36
2197 2266 3.147595 CTCCGCCTCCACATCCGA 61.148 66.667 0.00 0.00 0.00 4.55
2275 2505 1.479730 CATCTGCTGCTAGTGTCTCCA 59.520 52.381 0.00 0.00 0.00 3.86
2503 2760 1.450312 CTTCTCCACGTCCATGCCC 60.450 63.158 0.00 0.00 0.00 5.36
2511 2768 3.211963 GTCCATGCCCGCATCCAC 61.212 66.667 0.00 0.00 33.90 4.02
2514 2771 3.576356 CATGCCCGCATCCACGTC 61.576 66.667 0.00 0.00 33.90 4.34
2515 2772 4.856801 ATGCCCGCATCCACGTCC 62.857 66.667 0.00 0.00 29.42 4.79
2535 2792 1.802880 CGGCGTCAATCGATTTCCTCT 60.803 52.381 8.21 0.00 42.86 3.69
2611 2868 0.033208 TTGGGTCCAATGGAGATGCC 60.033 55.000 0.27 0.00 29.39 4.40
2629 2886 0.392193 CCGATTTCACAGCTGCTCCT 60.392 55.000 15.27 0.00 0.00 3.69
2630 2887 0.725686 CGATTTCACAGCTGCTCCTG 59.274 55.000 15.27 4.46 38.78 3.86
2675 2932 1.608283 GCATCCTTGGCTCGTATACCC 60.608 57.143 0.00 0.00 0.00 3.69
2676 2933 0.966920 ATCCTTGGCTCGTATACCCG 59.033 55.000 0.00 0.00 0.00 5.28
2677 2934 1.300697 CCTTGGCTCGTATACCCGC 60.301 63.158 0.00 0.00 0.00 6.13
2678 2935 1.740285 CTTGGCTCGTATACCCGCT 59.260 57.895 9.94 0.00 0.00 5.52
2679 2936 0.104304 CTTGGCTCGTATACCCGCTT 59.896 55.000 9.94 0.00 0.00 4.68
2680 2937 0.179094 TTGGCTCGTATACCCGCTTG 60.179 55.000 9.94 0.00 0.00 4.01
2681 2938 1.038681 TGGCTCGTATACCCGCTTGA 61.039 55.000 9.94 0.00 0.00 3.02
2682 2939 0.596859 GGCTCGTATACCCGCTTGAC 60.597 60.000 9.94 0.00 0.00 3.18
2713 2978 2.256461 GGCTTTGCTTGCTGGTCG 59.744 61.111 0.00 0.00 0.00 4.79
2844 3112 2.319472 GCTTTCTCGTCCAAAATGCAC 58.681 47.619 0.00 0.00 0.00 4.57
2866 3134 1.237533 CCAGCGCATGCATTGGTATA 58.762 50.000 22.96 0.00 46.23 1.47
2869 3137 2.485038 CAGCGCATGCATTGGTATATGA 59.515 45.455 19.57 0.00 46.23 2.15
2933 3201 8.537016 AGTATGGTTTAGTGAACACTTAGCATA 58.463 33.333 22.30 22.30 42.54 3.14
2936 3204 5.935789 GGTTTAGTGAACACTTAGCATACCA 59.064 40.000 12.66 0.00 42.54 3.25
2996 3267 9.499479 CTTATCTGATAGTATTGCAATCTGGTT 57.501 33.333 16.86 0.00 0.00 3.67
3002 3273 5.435686 AGTATTGCAATCTGGTTGGACTA 57.564 39.130 16.86 0.00 37.93 2.59
3019 3290 8.509690 GGTTGGACTATGTTACTTTTAAGAACC 58.490 37.037 0.00 0.00 0.00 3.62
3089 3361 5.430089 AGACAGGGCCATCTACTTATTCTTT 59.570 40.000 6.18 0.00 0.00 2.52
3090 3362 5.440610 ACAGGGCCATCTACTTATTCTTTG 58.559 41.667 6.18 0.00 0.00 2.77
3091 3363 5.191722 ACAGGGCCATCTACTTATTCTTTGA 59.808 40.000 6.18 0.00 0.00 2.69
3092 3364 5.762218 CAGGGCCATCTACTTATTCTTTGAG 59.238 44.000 6.18 0.00 0.00 3.02
3298 3574 6.463360 TGTGAATGCTCATCAGTAGTTAACA 58.537 36.000 8.61 0.00 33.05 2.41
3299 3575 6.934083 TGTGAATGCTCATCAGTAGTTAACAA 59.066 34.615 8.61 0.00 33.05 2.83
3300 3576 7.443879 TGTGAATGCTCATCAGTAGTTAACAAA 59.556 33.333 8.61 0.00 33.05 2.83
3386 3662 5.592282 TCAAGTAGGTTGACAAAGCATGAAA 59.408 36.000 0.00 0.00 40.45 2.69
3916 4193 1.780503 AGAACAAGGGCAAGCAAACT 58.219 45.000 0.00 0.00 0.00 2.66
4085 4362 0.249398 TTTCTCCCCGCACTTAGAGC 59.751 55.000 0.00 0.00 0.00 4.09
4097 4374 3.004210 GCACTTAGAGCGATGAGATCAGA 59.996 47.826 0.00 0.00 37.82 3.27
4148 4425 7.062749 TGTAGTATCTGAACTTGAGTTTGGT 57.937 36.000 0.00 0.00 38.56 3.67
4159 4436 4.762251 ACTTGAGTTTGGTAGGATGCTTTC 59.238 41.667 0.00 0.00 0.00 2.62
4204 4481 5.937975 TGTGGATGTTCATCTACTGATCA 57.062 39.130 22.70 0.00 37.83 2.92
4267 4544 6.386927 ACATTCTGAATCCTGGTATAGTTCCA 59.613 38.462 0.00 0.00 0.00 3.53
4270 4547 6.830912 TCTGAATCCTGGTATAGTTCCATTG 58.169 40.000 0.00 0.00 34.26 2.82
4303 4581 0.175531 GTGCCTGTTTGGTTGCTTGT 59.824 50.000 0.00 0.00 38.35 3.16
4313 4592 7.012232 CCTGTTTGGTTGCTTGTATCAAAATTT 59.988 33.333 0.00 0.00 0.00 1.82
4316 4595 6.841443 TGGTTGCTTGTATCAAAATTTGTG 57.159 33.333 5.56 0.00 0.00 3.33
4323 4602 6.617105 GCTTGTATCAAAATTTGTGCTCTTGC 60.617 38.462 5.56 1.15 40.20 4.01
4334 4613 0.841961 TGCTCTTGCATCTATGGCCT 59.158 50.000 3.32 0.00 45.31 5.19
4351 4815 1.611673 GCCTGACTTAGCTTGGCTGAA 60.612 52.381 0.00 0.00 40.10 3.02
4354 4818 4.517285 CCTGACTTAGCTTGGCTGAATAA 58.483 43.478 0.00 0.00 40.10 1.40
4356 4820 5.163713 CCTGACTTAGCTTGGCTGAATAAAC 60.164 44.000 0.00 0.00 40.10 2.01
4362 4828 3.507622 AGCTTGGCTGAATAAACAACCTC 59.492 43.478 0.00 0.00 37.57 3.85
4383 4850 1.973515 TGGGCCATGTTGTGCAATTTA 59.026 42.857 0.00 0.00 0.00 1.40
4404 4876 1.243902 TTCGTTTGGTCCCTTGCATC 58.756 50.000 0.00 0.00 0.00 3.91
4409 4881 2.045926 GGTCCCTTGCATCGCACT 60.046 61.111 0.00 0.00 38.71 4.40
4428 4900 4.445385 GCACTGTTGATCAATTTTGTGTCC 59.555 41.667 12.12 0.00 0.00 4.02
4454 5115 1.604755 GTTGTTTGGACGGCATGTGTA 59.395 47.619 0.00 0.00 0.00 2.90
4457 5118 1.196808 GTTTGGACGGCATGTGTAGTG 59.803 52.381 0.00 0.00 0.00 2.74
4462 5123 2.353406 GGACGGCATGTGTAGTGTAAGT 60.353 50.000 0.00 0.00 0.00 2.24
4467 5128 3.679980 GGCATGTGTAGTGTAAGTGTGAG 59.320 47.826 0.00 0.00 0.00 3.51
4484 5145 3.132925 GTGAGCAAATGCAAACCACAAT 58.867 40.909 8.28 0.00 45.16 2.71
4608 5270 8.763356 CACAATTAACACAACACATTAGCAATT 58.237 29.630 0.00 0.00 0.00 2.32
4645 5373 7.113658 ACATTAGAATGGTACGATCTTGACT 57.886 36.000 7.16 0.00 40.70 3.41
4650 5378 5.356190 AGAATGGTACGATCTTGACTACGAA 59.644 40.000 0.00 0.00 0.00 3.85
4668 5396 0.819259 AATATGTCGCCGGCAAGCAT 60.819 50.000 28.98 26.03 0.00 3.79
4722 5450 1.172180 ACCATCACCACCTTGTTGCG 61.172 55.000 0.00 0.00 0.00 4.85
4744 5472 1.303888 CTGCTGAACCTGCACCCAT 60.304 57.895 0.00 0.00 34.77 4.00
4801 5529 2.186076 CGAGACAGCCGAATGTAGAAC 58.814 52.381 0.00 0.00 32.25 3.01
4816 5544 1.911766 GAACCACCTCCTCGGGACA 60.912 63.158 0.00 0.00 36.97 4.02
4883 5611 5.410746 TCGTTCTTGATCTACACGTAGAACT 59.589 40.000 17.02 0.00 44.44 3.01
4930 5658 1.427020 CTCAAGCTTTAGCCTGCGC 59.573 57.895 0.00 0.00 43.38 6.09
4952 5680 1.593469 CAAGCATGAGCAGAGACATCG 59.407 52.381 0.00 0.00 45.49 3.84
5068 5802 2.368875 ACTCGGTCTTCATCACCTTGTT 59.631 45.455 0.00 0.00 0.00 2.83
5076 5810 6.295688 GGTCTTCATCACCTTGTTAGTTAGGA 60.296 42.308 0.00 0.00 35.45 2.94
5083 5817 5.364446 TCACCTTGTTAGTTAGGAAGACACA 59.636 40.000 0.00 0.00 35.45 3.72
5143 5879 5.578336 ACAGTGTACATCAATGAACTGATCG 59.422 40.000 16.22 2.90 43.71 3.69
5177 5913 7.859377 GTGCATTAGTATGATCAAATGAACTGG 59.141 37.037 17.98 6.00 35.73 4.00
5191 5927 4.019792 TGAACTGGTCATAGCAATGTGT 57.980 40.909 0.00 0.00 34.50 3.72
5205 5941 4.022589 AGCAATGTGTGTTTCCTTGATCAG 60.023 41.667 0.00 0.00 0.00 2.90
5227 5963 3.376234 GTGCACTGATCATAGCAATGTGT 59.624 43.478 19.87 0.00 38.91 3.72
5228 5964 3.375922 TGCACTGATCATAGCAATGTGTG 59.624 43.478 16.97 9.86 33.48 3.82
5231 5967 5.620654 GCACTGATCATAGCAATGTGTGTTT 60.621 40.000 12.99 0.00 34.50 2.83
5232 5968 6.025896 CACTGATCATAGCAATGTGTGTTTC 58.974 40.000 0.00 0.00 34.50 2.78
5287 6023 1.522668 TGGACACATAGCAAGCACAC 58.477 50.000 0.00 0.00 0.00 3.82
5288 6024 1.202746 TGGACACATAGCAAGCACACA 60.203 47.619 0.00 0.00 0.00 3.72
5305 6045 4.632153 CACACATACCAATCCTAGCCTAC 58.368 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 220 9.316730 CTCCAAAATTTCAAAAATGTTCTCAGA 57.683 29.630 0.00 0.00 0.00 3.27
221 222 7.551974 TGCTCCAAAATTTCAAAAATGTTCTCA 59.448 29.630 0.00 0.00 0.00 3.27
262 263 4.403453 GTCTCCGATCCAAAAATTGTTCG 58.597 43.478 0.00 5.99 35.47 3.95
273 274 4.627284 TTTAAAGTTGGTCTCCGATCCA 57.373 40.909 0.00 0.00 0.00 3.41
278 279 3.689649 CCCAGATTTAAAGTTGGTCTCCG 59.310 47.826 15.69 1.79 0.00 4.63
294 295 7.619302 TGCTAGTTCCAAAAATTATTCCCAGAT 59.381 33.333 0.00 0.00 0.00 2.90
303 304 9.077885 AGAAATGTCTGCTAGTTCCAAAAATTA 57.922 29.630 0.00 0.00 30.83 1.40
307 308 6.959639 AAGAAATGTCTGCTAGTTCCAAAA 57.040 33.333 0.00 0.00 33.05 2.44
417 418 4.277423 TGGAGAAGTGTTTCCCGATTTTTC 59.723 41.667 0.00 0.00 33.64 2.29
418 419 4.211920 TGGAGAAGTGTTTCCCGATTTTT 58.788 39.130 0.00 0.00 33.64 1.94
425 426 4.937201 ACAAATTGGAGAAGTGTTTCCC 57.063 40.909 0.00 0.00 33.64 3.97
428 429 9.665719 AAATGTTAACAAATTGGAGAAGTGTTT 57.334 25.926 13.23 0.53 0.00 2.83
590 591 6.753107 ATGTTCCGGTATTTCCAAAAGTAG 57.247 37.500 0.00 0.00 35.57 2.57
593 594 8.996024 AAAATATGTTCCGGTATTTCCAAAAG 57.004 30.769 0.00 0.00 31.26 2.27
597 598 7.704578 TGAAAAATATGTTCCGGTATTTCCA 57.295 32.000 0.00 4.20 31.26 3.53
598 599 8.865978 GTTTGAAAAATATGTTCCGGTATTTCC 58.134 33.333 0.00 1.79 31.26 3.13
604 605 5.239963 ACGAGTTTGAAAAATATGTTCCGGT 59.760 36.000 0.00 0.00 0.00 5.28
606 607 6.367421 TCACGAGTTTGAAAAATATGTTCCG 58.633 36.000 0.00 0.00 0.00 4.30
642 643 9.410556 CCGAATATCCAAAATATTTTCATGGAC 57.589 33.333 18.19 8.25 0.00 4.02
651 652 9.981114 GAAAATGGTCCGAATATCCAAAATATT 57.019 29.630 0.00 0.00 34.80 1.28
656 657 6.184068 TCAGAAAATGGTCCGAATATCCAAA 58.816 36.000 0.00 0.00 34.80 3.28
659 660 6.884280 ATTCAGAAAATGGTCCGAATATCC 57.116 37.500 0.00 0.00 0.00 2.59
815 824 6.254589 TCATGAACCACAAAATCGACAAAAAC 59.745 34.615 0.00 0.00 0.00 2.43
826 836 9.658799 TTTAAGAAATGTTCATGAACCACAAAA 57.341 25.926 30.66 19.17 40.46 2.44
863 873 4.436718 CGGCCCTTGTTTTTCTTTGTTTTG 60.437 41.667 0.00 0.00 0.00 2.44
868 878 1.217001 GCGGCCCTTGTTTTTCTTTG 58.783 50.000 0.00 0.00 0.00 2.77
936 961 4.503314 CCGACCTACGCGGGGAAC 62.503 72.222 23.53 15.85 44.87 3.62
947 979 1.291335 AGACCTCCTATTTCCCGACCT 59.709 52.381 0.00 0.00 0.00 3.85
948 980 1.687660 GAGACCTCCTATTTCCCGACC 59.312 57.143 0.00 0.00 0.00 4.79
949 981 2.668625 AGAGACCTCCTATTTCCCGAC 58.331 52.381 0.00 0.00 0.00 4.79
950 982 3.751245 GCTAGAGACCTCCTATTTCCCGA 60.751 52.174 0.00 0.00 0.00 5.14
951 983 2.559231 GCTAGAGACCTCCTATTTCCCG 59.441 54.545 0.00 0.00 0.00 5.14
1197 1248 3.130160 CGAGCCCTTCTTGCTGCC 61.130 66.667 0.00 0.00 39.69 4.85
1333 1384 1.961277 CCAGTGGTGTCCTTGACGC 60.961 63.158 0.00 0.00 41.69 5.19
1349 1400 2.766925 AACTCACCAGCCCTTGCCA 61.767 57.895 0.00 0.00 38.69 4.92
1410 1461 3.403228 AATCATAAGCACCCACCCATT 57.597 42.857 0.00 0.00 0.00 3.16
1430 1484 0.667993 CCTGGAAAAAGACGCAGCAA 59.332 50.000 0.00 0.00 0.00 3.91
1433 1487 1.069906 CGAACCTGGAAAAAGACGCAG 60.070 52.381 0.00 0.00 0.00 5.18
1440 1494 1.611491 GGCATGTCGAACCTGGAAAAA 59.389 47.619 0.00 0.00 0.00 1.94
1531 1585 6.208797 ACACTGAATTACTACTACTGACAGCA 59.791 38.462 1.25 0.00 0.00 4.41
1537 1591 5.109903 GCCCACACTGAATTACTACTACTG 58.890 45.833 0.00 0.00 0.00 2.74
1538 1592 4.161754 GGCCCACACTGAATTACTACTACT 59.838 45.833 0.00 0.00 0.00 2.57
1539 1593 4.161754 AGGCCCACACTGAATTACTACTAC 59.838 45.833 0.00 0.00 0.00 2.73
1540 1594 4.359105 AGGCCCACACTGAATTACTACTA 58.641 43.478 0.00 0.00 0.00 1.82
1560 1616 3.788333 TCCGAAGTTACATAACGGAGG 57.212 47.619 0.00 3.17 45.87 4.30
1565 1621 8.080083 TCTTCTGTTTTCCGAAGTTACATAAC 57.920 34.615 0.00 0.00 40.43 1.89
1614 1670 6.394345 AATTCAGGATCACCTTCCTAAACT 57.606 37.500 0.00 0.00 44.54 2.66
1615 1671 5.590663 GGAATTCAGGATCACCTTCCTAAAC 59.409 44.000 7.93 0.00 44.54 2.01
1654 1710 4.141287 ACTGCACACTTACAAAATGGCTA 58.859 39.130 0.00 0.00 0.00 3.93
1664 1720 3.390135 TCAAGCACTACTGCACACTTAC 58.610 45.455 0.00 0.00 46.97 2.34
1673 1729 5.403766 CACTACTTTCACTCAAGCACTACTG 59.596 44.000 0.00 0.00 0.00 2.74
1703 1759 9.490379 CCCTCTGTAAAGAAATATAATAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
1704 1760 8.867097 TCCCTCTGTAAAGAAATATAATAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
1705 1761 9.360093 CTCCCTCTGTAAAGAAATATAATAGCG 57.640 37.037 0.00 0.00 0.00 4.26
1711 1767 9.710818 ACAGTACTCCCTCTGTAAAGAAATATA 57.289 33.333 0.00 0.00 42.13 0.86
1712 1768 8.611051 ACAGTACTCCCTCTGTAAAGAAATAT 57.389 34.615 0.00 0.00 42.13 1.28
1713 1769 9.710818 ATACAGTACTCCCTCTGTAAAGAAATA 57.289 33.333 8.67 0.00 45.84 1.40
1714 1770 6.936968 ACAGTACTCCCTCTGTAAAGAAAT 57.063 37.500 0.00 0.00 42.13 2.17
1715 1771 8.431910 AATACAGTACTCCCTCTGTAAAGAAA 57.568 34.615 8.67 0.00 45.84 2.52
1716 1772 9.537852 TTAATACAGTACTCCCTCTGTAAAGAA 57.462 33.333 8.67 2.55 45.84 2.52
1717 1773 9.186837 CTTAATACAGTACTCCCTCTGTAAAGA 57.813 37.037 8.67 0.00 45.84 2.52
1718 1774 8.414778 CCTTAATACAGTACTCCCTCTGTAAAG 58.585 40.741 8.67 8.59 45.84 1.85
1719 1775 8.117956 TCCTTAATACAGTACTCCCTCTGTAAA 58.882 37.037 8.67 0.97 45.84 2.01
1720 1776 7.645942 TCCTTAATACAGTACTCCCTCTGTAA 58.354 38.462 8.67 0.00 45.84 2.41
1721 1777 7.217028 TCCTTAATACAGTACTCCCTCTGTA 57.783 40.000 7.34 7.34 46.45 2.74
1722 1778 6.088541 TCCTTAATACAGTACTCCCTCTGT 57.911 41.667 0.00 0.00 45.21 3.41
1723 1779 7.094118 GCTATCCTTAATACAGTACTCCCTCTG 60.094 44.444 0.00 0.00 37.65 3.35
1724 1780 6.949463 GCTATCCTTAATACAGTACTCCCTCT 59.051 42.308 0.00 0.00 0.00 3.69
1725 1781 6.949463 AGCTATCCTTAATACAGTACTCCCTC 59.051 42.308 0.00 0.00 0.00 4.30
1726 1782 6.865520 AGCTATCCTTAATACAGTACTCCCT 58.134 40.000 0.00 0.00 0.00 4.20
1727 1783 7.339976 CCTAGCTATCCTTAATACAGTACTCCC 59.660 44.444 0.00 0.00 0.00 4.30
1728 1784 7.148035 GCCTAGCTATCCTTAATACAGTACTCC 60.148 44.444 0.00 0.00 0.00 3.85
1729 1785 7.612633 AGCCTAGCTATCCTTAATACAGTACTC 59.387 40.741 0.00 0.00 36.99 2.59
1730 1786 7.471890 AGCCTAGCTATCCTTAATACAGTACT 58.528 38.462 0.00 0.00 36.99 2.73
1731 1787 7.706100 AGCCTAGCTATCCTTAATACAGTAC 57.294 40.000 0.00 0.00 36.99 2.73
1732 1788 8.171400 AGAAGCCTAGCTATCCTTAATACAGTA 58.829 37.037 0.00 0.00 38.25 2.74
1733 1789 7.013834 AGAAGCCTAGCTATCCTTAATACAGT 58.986 38.462 0.00 0.00 38.25 3.55
1734 1790 7.363443 GGAGAAGCCTAGCTATCCTTAATACAG 60.363 44.444 11.59 0.00 39.83 2.74
1735 1791 6.437793 GGAGAAGCCTAGCTATCCTTAATACA 59.562 42.308 11.59 0.00 39.83 2.29
1736 1792 6.666113 AGGAGAAGCCTAGCTATCCTTAATAC 59.334 42.308 14.44 0.82 46.20 1.89
1741 1797 3.628832 AGGAGAAGCCTAGCTATCCTT 57.371 47.619 14.44 5.77 46.20 3.36
1784 1840 7.369803 TCATTCTATTGAGAGCAGACAAAAC 57.630 36.000 0.00 0.00 31.77 2.43
1816 1872 4.080356 AGGGAGTACATGCTTGCTTAATGA 60.080 41.667 0.00 0.00 0.00 2.57
1901 1957 2.798847 GTCCAAAAGCGTCGAAAGTAGT 59.201 45.455 0.00 0.00 0.00 2.73
1909 1965 1.203313 GTTCCGTCCAAAAGCGTCG 59.797 57.895 0.00 0.00 0.00 5.12
1911 1967 1.792006 CTAGTTCCGTCCAAAAGCGT 58.208 50.000 0.00 0.00 0.00 5.07
1942 1998 4.398598 GCGTTGCGTGCGGGAATT 62.399 61.111 0.00 0.00 0.00 2.17
1975 2031 0.036875 GTGGAGTTGGAACCAGAGGG 59.963 60.000 0.00 0.00 36.82 4.30
1980 2036 2.112297 GCCGTGGAGTTGGAACCA 59.888 61.111 0.00 0.00 0.00 3.67
2160 2222 0.385751 ACACCGGTATCAGATGCGAG 59.614 55.000 6.87 0.00 0.00 5.03
2275 2505 2.283388 CAGGGGCACAGTGGCAAT 60.283 61.111 27.09 12.91 45.76 3.56
2421 2659 3.843240 GCTGCTCGCGAAACTCGG 61.843 66.667 11.33 6.05 40.84 4.63
2514 2771 0.810031 AGGAAATCGATTGACGCCGG 60.810 55.000 12.25 0.00 42.26 6.13
2515 2772 0.577269 GAGGAAATCGATTGACGCCG 59.423 55.000 12.25 0.00 42.26 6.46
2593 2850 1.614711 GGCATCTCCATTGGACCCA 59.385 57.895 0.00 0.00 34.01 4.51
2611 2868 0.725686 CAGGAGCAGCTGTGAAATCG 59.274 55.000 16.64 0.00 0.00 3.34
2629 2886 2.047750 TAGCCATGCACGCGTTCA 60.048 55.556 15.13 15.13 0.00 3.18
2630 2887 2.703409 CTAGCCATGCACGCGTTC 59.297 61.111 10.22 5.06 0.00 3.95
2669 2926 0.103572 GAAGCGGTCAAGCGGGTATA 59.896 55.000 3.61 0.00 43.00 1.47
2675 2932 2.358737 AAGGGAAGCGGTCAAGCG 60.359 61.111 0.00 0.00 43.00 4.68
2676 2933 2.982744 GCAAGGGAAGCGGTCAAGC 61.983 63.158 0.00 0.00 37.41 4.01
2677 2934 2.335712 GGCAAGGGAAGCGGTCAAG 61.336 63.158 0.00 0.00 0.00 3.02
2678 2935 2.282180 GGCAAGGGAAGCGGTCAA 60.282 61.111 0.00 0.00 0.00 3.18
2679 2936 4.697756 CGGCAAGGGAAGCGGTCA 62.698 66.667 0.00 0.00 0.00 4.02
2697 2962 1.370900 CACGACCAGCAAGCAAAGC 60.371 57.895 0.00 0.00 0.00 3.51
2812 3080 3.661648 GAAAGCCCCCAGCCTCCA 61.662 66.667 0.00 0.00 45.47 3.86
2866 3134 4.621991 AGTGCGCGTAGATTTTATCTCAT 58.378 39.130 8.43 0.00 40.76 2.90
2869 3137 5.434352 TCTAGTGCGCGTAGATTTTATCT 57.566 39.130 13.73 0.00 43.33 1.98
2881 3149 1.071239 CATTCCGAAATCTAGTGCGCG 60.071 52.381 0.00 0.00 0.00 6.86
2933 3201 3.719924 CATGTTGACAAGCAAATGTGGT 58.280 40.909 0.00 0.00 38.44 4.16
2936 3204 3.455990 TGCATGTTGACAAGCAAATGT 57.544 38.095 11.14 0.00 45.88 2.71
2956 3224 3.457380 TCAGATAAGCCTCCAAAGATGCT 59.543 43.478 0.00 0.00 44.81 3.79
2957 3225 3.813443 TCAGATAAGCCTCCAAAGATGC 58.187 45.455 0.00 0.00 34.14 3.91
2996 3267 7.669427 TCGGTTCTTAAAAGTAACATAGTCCA 58.331 34.615 0.00 0.00 0.00 4.02
3002 3273 9.374838 ACGATATTCGGTTCTTAAAAGTAACAT 57.625 29.630 1.69 0.00 45.59 2.71
3019 3290 9.181805 ACATAGTATTTCAACTCACGATATTCG 57.818 33.333 0.00 0.00 46.93 3.34
3056 3327 0.331278 TGGCCCTGTCTAACATTGGG 59.669 55.000 0.00 0.00 36.83 4.12
3089 3361 5.606348 AGCCACCAAAACATAAAAACTCA 57.394 34.783 0.00 0.00 0.00 3.41
3090 3362 7.307160 GCTTAAGCCACCAAAACATAAAAACTC 60.307 37.037 17.00 0.00 34.31 3.01
3091 3363 6.481976 GCTTAAGCCACCAAAACATAAAAACT 59.518 34.615 17.00 0.00 34.31 2.66
3092 3364 6.258947 TGCTTAAGCCACCAAAACATAAAAAC 59.741 34.615 24.30 0.00 41.18 2.43
3272 3548 5.869753 AACTACTGATGAGCATTCACAAC 57.130 39.130 0.00 0.00 35.83 3.32
3300 3576 8.917088 CCTAAACCCATCATCAAAATATTCAGT 58.083 33.333 0.00 0.00 0.00 3.41
3386 3662 1.140312 TCAACCAAGGTCTGCTTCCT 58.860 50.000 0.00 0.00 36.81 3.36
3757 4034 9.765795 AGATGCATTATCTACCAACTTTAGTAC 57.234 33.333 0.00 0.00 44.32 2.73
3787 4064 9.130661 TGTTCAGTTTCAGGAATTCTTAAATGA 57.869 29.630 5.23 2.54 0.00 2.57
3916 4193 2.038659 CTGTCCTTGGCCCTTTTGAAA 58.961 47.619 0.00 0.00 0.00 2.69
3998 4275 1.134818 CACAACCTATAGCCGTGCTCA 60.135 52.381 1.46 0.00 40.44 4.26
4085 4362 3.492309 CCCCTCAAACTCTGATCTCATCG 60.492 52.174 0.00 0.00 32.14 3.84
4097 4374 2.278245 TGACCATCATCCCCTCAAACT 58.722 47.619 0.00 0.00 0.00 2.66
4186 4463 5.814188 TGTTGCTGATCAGTAGATGAACATC 59.186 40.000 23.38 9.87 42.53 3.06
4204 4481 0.185901 TCCCCTGCTCTTTTGTTGCT 59.814 50.000 0.00 0.00 0.00 3.91
4241 4518 7.092444 TGGAACTATACCAGGATTCAGAATGTT 60.092 37.037 0.00 0.00 33.22 2.71
4267 4544 1.396996 GCACATAACGTTCCTCGCAAT 59.603 47.619 2.82 0.00 44.19 3.56
4270 4547 0.739813 AGGCACATAACGTTCCTCGC 60.740 55.000 2.82 3.97 36.36 5.03
4288 4566 7.481275 AATTTTGATACAAGCAACCAAACAG 57.519 32.000 0.00 0.00 0.00 3.16
4316 4595 1.202734 TCAGGCCATAGATGCAAGAGC 60.203 52.381 5.01 0.00 42.57 4.09
4323 4602 4.063689 CAAGCTAAGTCAGGCCATAGATG 58.936 47.826 5.01 0.00 0.00 2.90
4334 4613 5.312895 TGTTTATTCAGCCAAGCTAAGTCA 58.687 37.500 0.00 0.00 36.40 3.41
4351 4815 2.042979 ACATGGCCCAGAGGTTGTTTAT 59.957 45.455 0.00 0.00 34.57 1.40
4354 4818 0.188342 AACATGGCCCAGAGGTTGTT 59.812 50.000 0.00 0.00 34.57 2.83
4356 4820 0.540365 ACAACATGGCCCAGAGGTTG 60.540 55.000 18.63 18.63 43.24 3.77
4362 4828 0.322322 AATTGCACAACATGGCCCAG 59.678 50.000 0.00 0.00 0.00 4.45
4383 4850 1.698506 TGCAAGGGACCAAACGAAAT 58.301 45.000 0.00 0.00 0.00 2.17
4404 4876 4.043750 ACACAAAATTGATCAACAGTGCG 58.956 39.130 21.52 12.71 0.00 5.34
4409 4881 4.909696 ACGGACACAAAATTGATCAACA 57.090 36.364 11.07 0.00 0.00 3.33
4428 4900 0.863957 GCCGTCCAAACAACACAACG 60.864 55.000 0.00 0.00 0.00 4.10
4454 5115 3.213506 TGCATTTGCTCACACTTACACT 58.786 40.909 3.94 0.00 42.66 3.55
4457 5118 3.735746 GGTTTGCATTTGCTCACACTTAC 59.264 43.478 3.94 0.00 42.66 2.34
4462 5123 1.479730 TGTGGTTTGCATTTGCTCACA 59.520 42.857 3.94 9.85 42.66 3.58
4467 5128 3.967203 ACAATTGTGGTTTGCATTTGC 57.033 38.095 11.07 0.00 42.50 3.68
4484 5145 2.998670 CACATTGCACACAACCAAACAA 59.001 40.909 0.00 0.00 38.99 2.83
4608 5270 8.777578 ACCATTCTAATGTAGGTATCTGTGTA 57.222 34.615 2.25 0.00 34.60 2.90
4626 5288 4.880120 TCGTAGTCAAGATCGTACCATTCT 59.120 41.667 0.00 0.00 0.00 2.40
4630 5292 6.261603 ACATATTCGTAGTCAAGATCGTACCA 59.738 38.462 0.00 0.00 0.00 3.25
4650 5378 1.227943 ATGCTTGCCGGCGACATAT 60.228 52.632 23.90 9.57 34.52 1.78
4668 5396 0.979665 CTTCTGCTGGAAGGACCTCA 59.020 55.000 0.00 0.00 45.55 3.86
4703 5431 1.172180 CGCAACAAGGTGGTGATGGT 61.172 55.000 0.00 0.00 37.20 3.55
4722 5450 1.008079 GTGCAGGTTCAGCAGTTGC 60.008 57.895 0.00 0.00 43.63 4.17
4744 5472 2.500229 GCTGGCAAGTGGTGTAACTAA 58.500 47.619 0.00 0.00 36.74 2.24
4801 5529 3.077556 CCTGTCCCGAGGAGGTGG 61.078 72.222 0.00 0.00 38.74 4.61
4831 5559 0.543410 TCGCCTTCCTGGTTGTCCTA 60.543 55.000 0.00 0.00 38.35 2.94
4883 5611 1.064003 ATAGAACCAGTGCCACACCA 58.936 50.000 0.00 0.00 34.49 4.17
4930 5658 0.035725 TGTCTCTGCTCATGCTTGGG 60.036 55.000 0.00 0.00 40.48 4.12
4940 5668 4.521062 GGCGGCGATGTCTCTGCT 62.521 66.667 12.98 0.00 33.71 4.24
4958 5686 2.798364 GGAGGAGGAAGCCGGTAGC 61.798 68.421 1.90 0.00 44.25 3.58
4960 5688 2.042230 GGGAGGAGGAAGCCGGTA 60.042 66.667 1.90 0.00 0.00 4.02
4964 5692 3.471806 GTCGGGGAGGAGGAAGCC 61.472 72.222 0.00 0.00 0.00 4.35
4965 5693 2.034048 GATGTCGGGGAGGAGGAAGC 62.034 65.000 0.00 0.00 0.00 3.86
4968 5702 1.230497 GAGATGTCGGGGAGGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
5068 5802 4.737578 ACTGACCTGTGTCTTCCTAACTA 58.262 43.478 0.00 0.00 42.28 2.24
5076 5810 3.118956 GCTATGCTACTGACCTGTGTCTT 60.119 47.826 0.00 0.00 42.28 3.01
5083 5817 4.080356 TCCATTTTGCTATGCTACTGACCT 60.080 41.667 0.00 0.00 0.00 3.85
5143 5879 4.898829 TCATACTAATGCACATTGCCAC 57.101 40.909 6.13 0.00 44.23 5.01
5158 5894 7.443575 GCTATGACCAGTTCATTTGATCATACT 59.556 37.037 0.00 0.00 42.87 2.12
5177 5913 5.048782 TCAAGGAAACACACATTGCTATGAC 60.049 40.000 15.23 0.00 35.65 3.06
5191 5927 2.880268 CAGTGCACTGATCAAGGAAACA 59.120 45.455 38.12 0.00 46.59 2.83
5205 5941 3.376234 ACACATTGCTATGATCAGTGCAC 59.624 43.478 20.45 9.40 35.01 4.57
5213 5949 5.711506 TCAAGGAAACACACATTGCTATGAT 59.288 36.000 15.23 0.00 35.65 2.45
5216 5952 5.711506 TGATCAAGGAAACACACATTGCTAT 59.288 36.000 0.00 0.00 0.00 2.97
5227 5963 5.725325 TCAATGCATTGATCAAGGAAACA 57.275 34.783 33.08 12.16 41.51 2.83
5265 6001 2.086869 GTGCTTGCTATGTGTCCATGT 58.913 47.619 0.00 0.00 32.29 3.21
5287 6023 4.588951 TCAGTGTAGGCTAGGATTGGTATG 59.411 45.833 0.00 0.00 0.00 2.39
5288 6024 4.816126 TCAGTGTAGGCTAGGATTGGTAT 58.184 43.478 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.