Multiple sequence alignment - TraesCS5B01G519100

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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 TraesCS5B01G519100 chr5B 100.000 3405 0 0 1 3405 681921246 681924650 0.000000e+00 6288
1 TraesCS5B01G519100 chr5B 96.504 801 24 3 1 797 63252398 63251598 0.000000e+00 1321
2 TraesCS5B01G519100 chr5B 89.474 209 22 0 1706 1914 681922801 681923009 7.240000e-67 265
3 TraesCS5B01G519100 chr5B 89.474 209 22 0 1556 1764 681922951 681923159 7.240000e-67 265
4 TraesCS5B01G519100 chr4A 93.523 1019 44 11 835 1839 628515251 628514241 0.000000e+00 1496
5 TraesCS5B01G519100 chr4A 91.393 639 45 4 1631 2267 628514524 628513894 0.000000e+00 867
6 TraesCS5B01G519100 chr4A 89.189 592 58 2 2614 3200 201645998 201645408 0.000000e+00 734
7 TraesCS5B01G519100 chr4A 91.787 207 17 0 1706 1912 628514524 628514318 4.300000e-74 289
8 TraesCS5B01G519100 chr4A 88.725 204 23 0 3202 3405 201645344 201645141 2.030000e-62 250
9 TraesCS5B01G519100 chr4A 88.152 211 17 5 2254 2457 628513685 628513476 9.440000e-61 244
10 TraesCS5B01G519100 chr4A 86.538 208 26 2 1556 1762 628514449 628514243 9.510000e-56 228
11 TraesCS5B01G519100 chr4A 82.836 134 23 0 1556 1689 628514374 628514241 1.660000e-23 121
12 TraesCS5B01G519100 chr5D 94.298 947 40 8 902 1834 539859367 539860313 0.000000e+00 1437
13 TraesCS5B01G519100 chr5D 92.975 669 41 5 1631 2296 539860035 539860700 0.000000e+00 970
14 TraesCS5B01G519100 chr5D 92.157 204 16 0 1706 1909 539860035 539860238 4.300000e-74 289
15 TraesCS5B01G519100 chr5D 88.050 159 17 1 2458 2614 539861245 539861403 1.610000e-43 187
16 TraesCS5B01G519100 chr5D 93.878 98 3 2 823 918 539853787 539853883 9.850000e-31 145
17 TraesCS5B01G519100 chr5D 85.714 126 18 0 1556 1681 539860185 539860310 2.130000e-27 134
18 TraesCS5B01G519100 chr4B 96.746 799 24 2 1 797 273095144 273095942 0.000000e+00 1330
19 TraesCS5B01G519100 chr4B 95.941 813 25 7 1 808 28682315 28681506 0.000000e+00 1312
20 TraesCS5B01G519100 chr4B 79.331 329 63 3 2877 3200 3509948 3509620 3.420000e-55 226
21 TraesCS5B01G519100 chr4B 79.027 329 64 3 2877 3200 3449891 3449563 1.590000e-53 220
22 TraesCS5B01G519100 chr3B 96.638 803 24 3 1 800 94487359 94488161 0.000000e+00 1330
23 TraesCS5B01G519100 chr3B 96.384 802 27 2 1 800 22550423 22549622 0.000000e+00 1319
24 TraesCS5B01G519100 chr3A 96.750 800 22 4 1 797 522043412 522044210 0.000000e+00 1330
25 TraesCS5B01G519100 chr2B 96.509 802 24 4 1 798 699182396 699181595 0.000000e+00 1323
26 TraesCS5B01G519100 chr2B 96.163 808 26 5 1 805 118826285 118827090 0.000000e+00 1315
27 TraesCS5B01G519100 chr5A 95.941 813 27 4 1 807 664389669 664388857 0.000000e+00 1314
28 TraesCS5B01G519100 chrUn 79.755 326 61 3 2877 3197 312015071 312015396 7.350000e-57 231
29 TraesCS5B01G519100 chrUn 79.448 326 62 3 2877 3197 48049113 48049438 3.420000e-55 226
30 TraesCS5B01G519100 chrUn 79.448 326 62 3 2877 3197 48082950 48083275 3.420000e-55 226
31 TraesCS5B01G519100 chrUn 79.828 233 42 3 2877 3104 369374217 369374449 7.560000e-37 165


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 TraesCS5B01G519100 chr5B 681921246 681924650 3404 False 2272.666667 6288 92.982667 1 3405 3 chr5B.!!$F1 3404
1 TraesCS5B01G519100 chr5B 63251598 63252398 800 True 1321.000000 1321 96.504000 1 797 1 chr5B.!!$R1 796
2 TraesCS5B01G519100 chr4A 628513476 628515251 1775 True 540.833333 1496 89.038167 835 2457 6 chr4A.!!$R2 1622
3 TraesCS5B01G519100 chr4A 201645141 201645998 857 True 492.000000 734 88.957000 2614 3405 2 chr4A.!!$R1 791
4 TraesCS5B01G519100 chr5D 539859367 539861403 2036 False 603.400000 1437 90.638800 902 2614 5 chr5D.!!$F2 1712
5 TraesCS5B01G519100 chr4B 273095144 273095942 798 False 1330.000000 1330 96.746000 1 797 1 chr4B.!!$F1 796
6 TraesCS5B01G519100 chr4B 28681506 28682315 809 True 1312.000000 1312 95.941000 1 808 1 chr4B.!!$R3 807
7 TraesCS5B01G519100 chr3B 94487359 94488161 802 False 1330.000000 1330 96.638000 1 800 1 chr3B.!!$F1 799
8 TraesCS5B01G519100 chr3B 22549622 22550423 801 True 1319.000000 1319 96.384000 1 800 1 chr3B.!!$R1 799
9 TraesCS5B01G519100 chr3A 522043412 522044210 798 False 1330.000000 1330 96.750000 1 797 1 chr3A.!!$F1 796
10 TraesCS5B01G519100 chr2B 699181595 699182396 801 True 1323.000000 1323 96.509000 1 798 1 chr2B.!!$R1 797
11 TraesCS5B01G519100 chr2B 118826285 118827090 805 False 1315.000000 1315 96.163000 1 805 1 chr2B.!!$F1 804
12 TraesCS5B01G519100 chr5A 664388857 664389669 812 True 1314.000000 1314 95.941000 1 807 1 chr5A.!!$R1 806

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
800 815 2.162608 TGGGCGTTAACATTTCCGATTG 59.837 45.455 6.39 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 3314 0.179054 GGGCTATTGAGTCCCCGAAC 60.179 60.0 0.0 0.0 42.21 3.95 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
86 87 5.121298 GCAGGAATCTTTTTGGATTTTCAGC 59.879 40.000 0.00 0.00 36.24 4.26
274 279 4.193090 TGTTTACACCGAAGTTGTCATGT 58.807 39.130 0.00 0.00 0.00 3.21
800 815 2.162608 TGGGCGTTAACATTTCCGATTG 59.837 45.455 6.39 0.00 0.00 2.67
801 816 2.420722 GGGCGTTAACATTTCCGATTGA 59.579 45.455 6.39 0.00 0.00 2.57
802 817 3.119779 GGGCGTTAACATTTCCGATTGAA 60.120 43.478 6.39 0.00 0.00 2.69
804 819 5.099575 GGCGTTAACATTTCCGATTGAATT 58.900 37.500 6.39 0.00 31.67 2.17
806 821 6.748198 GGCGTTAACATTTCCGATTGAATTTA 59.252 34.615 6.39 0.00 31.67 1.40
807 822 7.434013 GGCGTTAACATTTCCGATTGAATTTAT 59.566 33.333 6.39 0.00 31.67 1.40
808 823 9.440784 GCGTTAACATTTCCGATTGAATTTATA 57.559 29.630 6.39 0.00 31.67 0.98
935 950 4.458989 TCCATCGATTTGGACTTTTCTTGG 59.541 41.667 3.55 0.00 40.90 3.61
1007 1022 4.624364 TGTCACAGGCGGGCACAG 62.624 66.667 3.78 0.00 0.00 3.66
1019 1045 0.732538 GGGCACAGCAAACATAACGC 60.733 55.000 0.00 0.00 0.00 4.84
1218 1247 2.457743 TACCACGCCGGCAACTTCAT 62.458 55.000 28.98 7.00 39.03 2.57
1228 1257 1.603455 CAACTTCATGGGGGCGTGT 60.603 57.895 0.00 0.00 0.00 4.49
1538 1567 3.145551 GGAAGGACGCCTCCGCTA 61.146 66.667 0.00 0.00 42.22 4.26
1681 1710 1.648116 ATGCTGGCCCAAACAGAAAT 58.352 45.000 0.00 0.00 38.20 2.17
1742 1771 3.803082 CCGGCGACACCAATGCTG 61.803 66.667 9.30 0.00 39.03 4.41
1743 1772 2.741985 CGGCGACACCAATGCTGA 60.742 61.111 0.00 0.00 39.03 4.26
1744 1773 2.870372 GGCGACACCAATGCTGAC 59.130 61.111 0.00 0.00 38.86 3.51
1745 1774 1.965930 GGCGACACCAATGCTGACA 60.966 57.895 0.00 0.00 38.86 3.58
1746 1775 1.207593 GCGACACCAATGCTGACAC 59.792 57.895 0.00 0.00 0.00 3.67
1747 1776 1.506309 GCGACACCAATGCTGACACA 61.506 55.000 0.00 0.00 0.00 3.72
1748 1777 0.943673 CGACACCAATGCTGACACAA 59.056 50.000 0.00 0.00 0.00 3.33
1749 1778 1.333308 CGACACCAATGCTGACACAAA 59.667 47.619 0.00 0.00 0.00 2.83
1750 1779 2.731217 GACACCAATGCTGACACAAAC 58.269 47.619 0.00 0.00 0.00 2.93
1751 1780 2.098614 ACACCAATGCTGACACAAACA 58.901 42.857 0.00 0.00 0.00 2.83
1752 1781 2.099592 ACACCAATGCTGACACAAACAG 59.900 45.455 0.00 0.00 38.27 3.16
1753 1782 2.358582 CACCAATGCTGACACAAACAGA 59.641 45.455 0.00 0.00 37.54 3.41
1754 1783 3.023119 ACCAATGCTGACACAAACAGAA 58.977 40.909 0.00 0.00 37.54 3.02
1755 1784 3.446873 ACCAATGCTGACACAAACAGAAA 59.553 39.130 0.00 0.00 37.54 2.52
1756 1785 3.798337 CCAATGCTGACACAAACAGAAAC 59.202 43.478 0.00 0.00 37.54 2.78
1757 1786 4.422840 CAATGCTGACACAAACAGAAACA 58.577 39.130 0.00 0.00 37.54 2.83
1758 1787 3.763097 TGCTGACACAAACAGAAACAG 57.237 42.857 0.00 0.00 37.54 3.16
1759 1788 3.081061 TGCTGACACAAACAGAAACAGT 58.919 40.909 0.00 0.00 37.54 3.55
1760 1789 3.126858 TGCTGACACAAACAGAAACAGTC 59.873 43.478 0.00 0.00 37.54 3.51
1761 1790 3.487544 GCTGACACAAACAGAAACAGTCC 60.488 47.826 0.00 0.00 37.54 3.85
1762 1791 3.013921 TGACACAAACAGAAACAGTCCC 58.986 45.455 0.00 0.00 0.00 4.46
1763 1792 2.357952 GACACAAACAGAAACAGTCCCC 59.642 50.000 0.00 0.00 0.00 4.81
1764 1793 1.681264 CACAAACAGAAACAGTCCCCC 59.319 52.381 0.00 0.00 0.00 5.40
1765 1794 1.569072 ACAAACAGAAACAGTCCCCCT 59.431 47.619 0.00 0.00 0.00 4.79
1767 1796 0.178990 AACAGAAACAGTCCCCCTGC 60.179 55.000 0.00 0.00 45.68 4.85
1768 1797 1.303643 CAGAAACAGTCCCCCTGCC 60.304 63.158 0.00 0.00 45.68 4.85
1769 1798 2.359975 GAAACAGTCCCCCTGCCG 60.360 66.667 0.00 0.00 45.68 5.69
1770 1799 3.920093 GAAACAGTCCCCCTGCCGG 62.920 68.421 0.00 0.00 45.68 6.13
1815 1844 3.925238 CGCCGGCGACACTAATGC 61.925 66.667 44.86 1.62 42.83 3.56
1989 2018 2.280524 CGCCAAAGGACACGGACA 60.281 61.111 0.00 0.00 0.00 4.02
2158 2187 2.357034 GTCCTGGAAGCGTTCGCA 60.357 61.111 18.95 0.00 0.00 5.10
2187 2216 1.381928 GCCCGATGAGAGACACCGTA 61.382 60.000 0.00 0.00 32.92 4.02
2223 2252 1.499049 GGGAGAAGACACGTGAACAC 58.501 55.000 25.01 10.68 0.00 3.32
2224 2253 1.499049 GGAGAAGACACGTGAACACC 58.501 55.000 25.01 13.16 0.00 4.16
2314 2570 8.300286 TCTGATAGAGTAGAATTTTAGCATCCG 58.700 37.037 0.00 0.00 0.00 4.18
2332 2588 5.163622 GCATCCGGCATTATATAAACAGCAT 60.164 40.000 15.41 3.45 43.97 3.79
2333 2589 6.625740 GCATCCGGCATTATATAAACAGCATT 60.626 38.462 15.41 0.00 43.97 3.56
2350 2606 6.721318 ACAGCATTCCCTAGTTGATTCTAAA 58.279 36.000 0.00 0.00 0.00 1.85
2423 2681 1.344438 TCGAAGAAGAAGAAGCTGCCA 59.656 47.619 0.00 0.00 0.00 4.92
2430 2688 3.930634 AGAAGAAGCTGCCATGTTTTC 57.069 42.857 0.00 0.00 0.00 2.29
2444 2702 5.481105 CCATGTTTTCATTATTGTGTGGCT 58.519 37.500 0.00 0.00 38.64 4.75
2459 2717 2.062177 GGCTTGCCCCATGCTCATT 61.062 57.895 0.00 0.00 42.00 2.57
2460 2718 1.143183 GCTTGCCCCATGCTCATTG 59.857 57.895 0.00 0.00 42.00 2.82
2461 2719 1.820581 CTTGCCCCATGCTCATTGG 59.179 57.895 0.00 0.00 42.00 3.16
2462 2720 1.682451 CTTGCCCCATGCTCATTGGG 61.682 60.000 13.17 13.17 44.42 4.12
2464 2722 2.428925 GCCCCATGCTCATTGGGTG 61.429 63.158 17.29 9.55 43.71 4.61
2465 2723 1.759299 CCCCATGCTCATTGGGTGG 60.759 63.158 10.09 0.00 41.19 4.61
2466 2724 1.759299 CCCATGCTCATTGGGTGGG 60.759 63.158 0.00 0.00 43.16 4.61
2467 2725 1.000739 CCATGCTCATTGGGTGGGT 59.999 57.895 0.00 0.00 0.00 4.51
2468 2726 1.039233 CCATGCTCATTGGGTGGGTC 61.039 60.000 0.00 0.00 0.00 4.46
2498 3184 8.085296 AGGAATAAGAACAATATAGTCTGCGAG 58.915 37.037 0.00 0.00 0.00 5.03
2510 3198 0.666374 TCTGCGAGTCGACTCACAAA 59.334 50.000 37.14 23.38 43.00 2.83
2524 3212 4.793201 ACTCACAAAGAAGTTTAGGCCTT 58.207 39.130 12.58 0.00 0.00 4.35
2533 3221 6.791867 AGAAGTTTAGGCCTTCTTTGTTTT 57.208 33.333 12.58 0.00 44.78 2.43
2538 3226 8.349568 AGTTTAGGCCTTCTTTGTTTTATAGG 57.650 34.615 12.58 0.00 0.00 2.57
2568 3256 6.969828 AAATCATACGAAGAGGAAAGTCAC 57.030 37.500 0.00 0.00 0.00 3.67
2571 3259 2.821991 ACGAAGAGGAAAGTCACAGG 57.178 50.000 0.00 0.00 0.00 4.00
2581 3269 8.324191 AGAGGAAAGTCACAGGAAATGATATA 57.676 34.615 0.00 0.00 0.00 0.86
2626 3314 7.262772 TGAATAGGAATAACTAGTGTGGAACG 58.737 38.462 0.00 0.00 42.39 3.95
2630 3318 4.325472 GGAATAACTAGTGTGGAACGTTCG 59.675 45.833 21.34 8.68 42.39 3.95
2648 3336 1.839894 GGGGACTCAATAGCCCTGG 59.160 63.158 0.00 0.00 38.45 4.45
2649 3337 0.694444 GGGGACTCAATAGCCCTGGA 60.694 60.000 0.00 0.00 38.45 3.86
2652 3340 1.112113 GACTCAATAGCCCTGGACGA 58.888 55.000 0.00 0.00 0.00 4.20
2740 3428 2.871096 TGGAGGTTGTAATGGTGGAC 57.129 50.000 0.00 0.00 0.00 4.02
2754 3442 0.034059 GTGGACCTGGTGACTCACTG 59.966 60.000 2.82 3.04 34.40 3.66
2758 3446 1.294780 CCTGGTGACTCACTGCCTC 59.705 63.158 9.08 0.00 34.40 4.70
2759 3447 1.080230 CTGGTGACTCACTGCCTCG 60.080 63.158 9.08 0.00 34.40 4.63
2761 3449 2.262915 GTGACTCACTGCCTCGGG 59.737 66.667 1.58 0.00 0.00 5.14
2793 3481 6.490566 TGAAAATTTCTTCTACTTACCGGC 57.509 37.500 0.00 0.00 0.00 6.13
2797 3485 3.587797 TTCTTCTACTTACCGGCAGTG 57.412 47.619 15.68 7.16 0.00 3.66
2814 3502 0.704664 GTGGGAACAAGGGGAGGAAT 59.295 55.000 0.00 0.00 46.06 3.01
2816 3504 2.514160 GTGGGAACAAGGGGAGGAATAT 59.486 50.000 0.00 0.00 46.06 1.28
2818 3506 3.052944 TGGGAACAAGGGGAGGAATATTG 60.053 47.826 0.00 0.00 37.44 1.90
2828 3516 0.532862 AGGAATATTGCTCGCGTGGG 60.533 55.000 5.77 0.00 0.00 4.61
2844 3532 2.189499 GGGATGCCTCGATGGTTGC 61.189 63.158 0.00 0.00 38.35 4.17
2854 3542 1.341209 TCGATGGTTGCTATCTCGCAT 59.659 47.619 0.00 0.00 40.04 4.73
2862 3550 2.306847 TGCTATCTCGCATCCACACTA 58.693 47.619 0.00 0.00 34.44 2.74
2869 3557 1.621317 TCGCATCCACACTACAAGGAA 59.379 47.619 0.00 0.00 34.62 3.36
2882 3570 3.934457 ACAAGGAAAATGCCTTAACGG 57.066 42.857 0.00 0.00 46.29 4.44
2902 3590 1.886542 GCCTTAGTCAAACACTTGGGG 59.113 52.381 0.00 0.00 36.43 4.96
2934 3622 2.289072 GGTGGATCACCGATGTCTATGG 60.289 54.545 1.01 0.00 44.95 2.74
2936 3624 2.248248 GGATCACCGATGTCTATGGGA 58.752 52.381 0.00 0.00 35.86 4.37
2953 3641 3.613030 TGGGACACAACATGATCATGAG 58.387 45.455 36.37 28.53 41.20 2.90
2962 3650 4.603989 ACATGATCATGAGAAGATCGCT 57.396 40.909 36.37 11.84 43.73 4.93
2965 3653 5.821470 ACATGATCATGAGAAGATCGCTTTT 59.179 36.000 36.37 10.74 43.73 2.27
2993 3686 4.037446 AGGAGCGACATAAGAGAACTCATC 59.963 45.833 4.64 0.00 0.00 2.92
2997 3690 3.046390 GACATAAGAGAACTCATCGCCG 58.954 50.000 4.64 0.00 0.00 6.46
3007 3700 2.104572 CTCATCGCCGGACCATGGAT 62.105 60.000 21.47 1.98 0.00 3.41
3026 3719 2.461300 TGGTGGTGGGTGATTTCAAA 57.539 45.000 0.00 0.00 0.00 2.69
3029 3722 2.698274 GGTGGTGGGTGATTTCAAACTT 59.302 45.455 0.00 0.00 0.00 2.66
3040 3733 6.106003 GTGATTTCAAACTTTTGGTGAACCT 58.894 36.000 0.37 0.00 38.66 3.50
3047 3740 3.288092 ACTTTTGGTGAACCTGGAAGAC 58.712 45.455 0.00 0.00 34.07 3.01
3057 3750 4.770010 TGAACCTGGAAGACAAAAACAACT 59.230 37.500 0.00 0.00 34.07 3.16
3070 3763 6.805713 ACAAAAACAACTCCCTCATTAACAG 58.194 36.000 0.00 0.00 0.00 3.16
3090 3783 1.463650 GCGAATGATGGCGCGTTTTC 61.464 55.000 8.43 2.46 43.96 2.29
3125 3818 7.227156 TCAACTTCTTAGAGCTGAAGGAAATT 58.773 34.615 14.13 0.00 42.67 1.82
3140 3833 7.378181 TGAAGGAAATTTACTTGAATGGAAGC 58.622 34.615 20.53 3.35 29.60 3.86
3149 3842 5.171339 ACTTGAATGGAAGCAGATACACT 57.829 39.130 0.00 0.00 0.00 3.55
3168 3861 0.034896 TTGGTCAAACGAGAGGGAGC 59.965 55.000 0.00 0.00 0.00 4.70
3170 3863 0.250513 GGTCAAACGAGAGGGAGCAT 59.749 55.000 0.00 0.00 0.00 3.79
3194 3887 1.156736 CTTTGGAGCGAATTGACCGT 58.843 50.000 0.00 0.00 0.00 4.83
3200 3893 1.390463 GAGCGAATTGACCGTGTCTTC 59.610 52.381 5.77 2.28 33.15 2.87
3207 3962 1.441682 GACCGTGTCTTCGTCCGAC 60.442 63.158 0.00 0.00 0.00 4.79
3219 3974 1.239296 CGTCCGACCACTGTCCACTA 61.239 60.000 0.00 0.00 38.32 2.74
3220 3975 0.243095 GTCCGACCACTGTCCACTAC 59.757 60.000 0.00 0.00 38.32 2.73
3222 3977 1.352017 TCCGACCACTGTCCACTACTA 59.648 52.381 0.00 0.00 38.32 1.82
3223 3978 2.025605 TCCGACCACTGTCCACTACTAT 60.026 50.000 0.00 0.00 38.32 2.12
3278 4033 3.944015 AGATTCAAATTCGAGGCCTTCTG 59.056 43.478 6.77 0.00 0.00 3.02
3279 4034 2.113860 TCAAATTCGAGGCCTTCTGG 57.886 50.000 6.77 0.00 0.00 3.86
3306 4061 0.958091 CCGAGGGTTTCATGCAAACA 59.042 50.000 17.03 0.00 45.66 2.83
3328 4083 3.231734 CAGGATGCGTGGAGTTCAA 57.768 52.632 0.00 0.00 0.00 2.69
3345 4100 0.897621 CAATTCCAAGGGAGGGCAAC 59.102 55.000 0.00 0.00 31.21 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 228 6.265876 TGGCAATTCATATGCAATAGACATGT 59.734 34.615 0.00 0.00 45.60 3.21
346 351 4.406456 AGTTTATGGTTCATGGCAACTCA 58.594 39.130 0.00 0.00 37.61 3.41
349 354 8.442384 CAATTTTAGTTTATGGTTCATGGCAAC 58.558 33.333 0.00 0.00 0.00 4.17
571 585 7.851228 ACTAGACCTCATGTTGATATGTTTCA 58.149 34.615 0.00 0.00 0.00 2.69
702 717 6.450545 CCACGTATGAATAGATGACATCAGT 58.549 40.000 17.57 2.70 0.00 3.41
827 842 9.676195 CAAACATGTGTCATAAGTGATAAAACA 57.324 29.630 0.00 0.00 36.60 2.83
828 843 9.891828 TCAAACATGTGTCATAAGTGATAAAAC 57.108 29.630 0.00 0.00 36.60 2.43
833 848 9.453572 ACTAATCAAACATGTGTCATAAGTGAT 57.546 29.630 0.00 0.00 36.60 3.06
869 884 6.904463 TTCGGCTATGTACCATCTAACATA 57.096 37.500 0.00 0.00 37.50 2.29
870 885 5.801531 TTCGGCTATGTACCATCTAACAT 57.198 39.130 0.00 0.00 39.56 2.71
871 886 5.801531 ATTCGGCTATGTACCATCTAACA 57.198 39.130 0.00 0.00 0.00 2.41
872 887 7.352739 CAAAATTCGGCTATGTACCATCTAAC 58.647 38.462 0.00 0.00 0.00 2.34
947 962 1.522355 CGCAAGCGGGAGATGTCAT 60.522 57.895 6.55 0.00 35.56 3.06
950 965 1.153628 GTACGCAAGCGGGAGATGT 60.154 57.895 19.30 0.00 44.69 3.06
971 986 0.521242 ACGATTACACGCGACGTACC 60.521 55.000 15.93 7.43 38.32 3.34
984 999 1.216977 CCCGCCTGTGACACGATTA 59.783 57.895 0.22 0.00 0.00 1.75
1007 1022 2.152078 GCGGCTGCGTTATGTTTGC 61.152 57.895 0.00 0.00 0.00 3.68
1030 1056 4.101790 CGTTCGTGCATGGTGCCC 62.102 66.667 5.98 0.00 44.23 5.36
1670 1699 2.420022 CAGGCGGACTATTTCTGTTTGG 59.580 50.000 0.00 0.00 32.41 3.28
1741 1770 3.013921 GGGACTGTTTCTGTTTGTGTCA 58.986 45.455 0.00 0.00 0.00 3.58
1742 1771 2.357952 GGGGACTGTTTCTGTTTGTGTC 59.642 50.000 0.00 0.00 0.00 3.67
1743 1772 2.375146 GGGGACTGTTTCTGTTTGTGT 58.625 47.619 0.00 0.00 0.00 3.72
1744 1773 1.681264 GGGGGACTGTTTCTGTTTGTG 59.319 52.381 0.00 0.00 0.00 3.33
1745 1774 1.569072 AGGGGGACTGTTTCTGTTTGT 59.431 47.619 0.00 0.00 0.00 2.83
1746 1775 1.956477 CAGGGGGACTGTTTCTGTTTG 59.044 52.381 0.00 0.00 42.42 2.93
1747 1776 2.364972 CAGGGGGACTGTTTCTGTTT 57.635 50.000 0.00 0.00 42.42 2.83
1797 1826 3.261951 CATTAGTGTCGCCGGCGG 61.262 66.667 44.95 28.06 40.25 6.13
1798 1827 3.925238 GCATTAGTGTCGCCGGCG 61.925 66.667 42.13 42.13 41.35 6.46
1799 1828 3.573491 GGCATTAGTGTCGCCGGC 61.573 66.667 19.07 19.07 35.79 6.13
1805 1834 2.546368 TGTTTGTGTCGGCATTAGTGTC 59.454 45.455 0.00 0.00 0.00 3.67
1806 1835 2.548057 CTGTTTGTGTCGGCATTAGTGT 59.452 45.455 0.00 0.00 0.00 3.55
1807 1836 2.805671 TCTGTTTGTGTCGGCATTAGTG 59.194 45.455 0.00 0.00 0.00 2.74
1808 1837 3.120321 TCTGTTTGTGTCGGCATTAGT 57.880 42.857 0.00 0.00 0.00 2.24
1809 1838 4.219033 GTTTCTGTTTGTGTCGGCATTAG 58.781 43.478 0.00 0.00 0.00 1.73
1810 1839 3.628032 TGTTTCTGTTTGTGTCGGCATTA 59.372 39.130 0.00 0.00 0.00 1.90
1811 1840 2.425312 TGTTTCTGTTTGTGTCGGCATT 59.575 40.909 0.00 0.00 0.00 3.56
1812 1841 2.020720 TGTTTCTGTTTGTGTCGGCAT 58.979 42.857 0.00 0.00 0.00 4.40
1813 1842 1.400142 CTGTTTCTGTTTGTGTCGGCA 59.600 47.619 0.00 0.00 0.00 5.69
1814 1843 1.400494 ACTGTTTCTGTTTGTGTCGGC 59.600 47.619 0.00 0.00 0.00 5.54
1815 1844 2.031683 GGACTGTTTCTGTTTGTGTCGG 59.968 50.000 0.00 0.00 0.00 4.79
1944 1973 2.647297 GCCTGTTTCTGCCTGTGC 59.353 61.111 0.00 0.00 38.26 4.57
2004 2033 1.150567 GCAGTGCCAGCAGTAGATCG 61.151 60.000 2.85 0.00 0.00 3.69
2187 2216 3.710722 CCAGGAGCCAGCGGAGTT 61.711 66.667 0.00 0.00 0.00 3.01
2314 2570 6.840780 AGGGAATGCTGTTTATATAATGCC 57.159 37.500 0.00 0.00 0.00 4.40
2326 2582 4.851639 AGAATCAACTAGGGAATGCTGT 57.148 40.909 0.00 0.00 0.00 4.40
2332 2588 8.660295 TCTAGTGTTTAGAATCAACTAGGGAA 57.340 34.615 7.97 0.00 0.00 3.97
2333 2589 8.660295 TTCTAGTGTTTAGAATCAACTAGGGA 57.340 34.615 7.97 0.00 0.00 4.20
2423 2681 5.409214 GCAAGCCACACAATAATGAAAACAT 59.591 36.000 0.00 0.00 0.00 2.71
2430 2688 1.134729 GGGGCAAGCCACACAATAATG 60.135 52.381 13.87 0.00 39.85 1.90
2459 2717 2.184194 TATTCCTCCCGACCCACCCA 62.184 60.000 0.00 0.00 0.00 4.51
2460 2718 0.984432 TTATTCCTCCCGACCCACCC 60.984 60.000 0.00 0.00 0.00 4.61
2461 2719 0.468648 CTTATTCCTCCCGACCCACC 59.531 60.000 0.00 0.00 0.00 4.61
2462 2720 1.492764 TCTTATTCCTCCCGACCCAC 58.507 55.000 0.00 0.00 0.00 4.61
2464 2722 1.835531 TGTTCTTATTCCTCCCGACCC 59.164 52.381 0.00 0.00 0.00 4.46
2465 2723 3.622166 TTGTTCTTATTCCTCCCGACC 57.378 47.619 0.00 0.00 0.00 4.79
2466 2724 7.668492 ACTATATTGTTCTTATTCCTCCCGAC 58.332 38.462 0.00 0.00 0.00 4.79
2467 2725 7.728981 AGACTATATTGTTCTTATTCCTCCCGA 59.271 37.037 0.00 0.00 0.00 5.14
2468 2726 7.815068 CAGACTATATTGTTCTTATTCCTCCCG 59.185 40.741 0.00 0.00 0.00 5.14
2498 3184 4.084485 GCCTAAACTTCTTTGTGAGTCGAC 60.084 45.833 7.70 7.70 0.00 4.20
2538 3226 8.488651 TTTCCTCTTCGTATGATTTTTCTACC 57.511 34.615 0.00 0.00 0.00 3.18
2547 3235 5.394663 CCTGTGACTTTCCTCTTCGTATGAT 60.395 44.000 0.00 0.00 0.00 2.45
2553 3241 3.386768 TTCCTGTGACTTTCCTCTTCG 57.613 47.619 0.00 0.00 0.00 3.79
2557 3245 8.831550 GTTATATCATTTCCTGTGACTTTCCTC 58.168 37.037 0.00 0.00 0.00 3.71
2596 3284 9.658799 CCACACTAGTTATTCCTATTCATATGG 57.341 37.037 2.13 0.00 0.00 2.74
2626 3314 0.179054 GGGCTATTGAGTCCCCGAAC 60.179 60.000 0.00 0.00 42.21 3.95
2648 3336 4.784329 TGATAGATTGCACTACGATCGTC 58.216 43.478 26.48 11.05 43.18 4.20
2649 3337 4.830826 TGATAGATTGCACTACGATCGT 57.169 40.909 25.94 25.94 43.18 3.73
2652 3340 5.163405 ACCACTTGATAGATTGCACTACGAT 60.163 40.000 0.00 0.00 0.00 3.73
2705 3393 5.331876 ACCTCCAATTTCGTCTCTAGAAG 57.668 43.478 0.00 0.00 0.00 2.85
2707 3395 4.527038 ACAACCTCCAATTTCGTCTCTAGA 59.473 41.667 0.00 0.00 0.00 2.43
2709 3397 4.884668 ACAACCTCCAATTTCGTCTCTA 57.115 40.909 0.00 0.00 0.00 2.43
2740 3428 1.294780 GAGGCAGTGAGTCACCAGG 59.705 63.158 19.71 10.79 34.49 4.45
2754 3442 7.549134 AGAAATTTTCAAATTTATTCCCGAGGC 59.451 33.333 11.53 0.00 45.70 4.70
2782 3470 0.899720 TTCCCACTGCCGGTAAGTAG 59.100 55.000 11.05 5.00 0.00 2.57
2788 3476 2.113139 CTTGTTCCCACTGCCGGT 59.887 61.111 1.90 0.00 0.00 5.28
2789 3477 2.672996 CCTTGTTCCCACTGCCGG 60.673 66.667 0.00 0.00 0.00 6.13
2793 3481 1.133809 TCCTCCCCTTGTTCCCACTG 61.134 60.000 0.00 0.00 0.00 3.66
2797 3485 3.566351 CAATATTCCTCCCCTTGTTCCC 58.434 50.000 0.00 0.00 0.00 3.97
2814 3502 1.887242 GCATCCCACGCGAGCAATA 60.887 57.895 15.93 0.00 0.00 1.90
2823 3511 2.280389 CCATCGAGGCATCCCACG 60.280 66.667 0.00 0.00 45.09 4.94
2828 3516 2.072298 GATAGCAACCATCGAGGCATC 58.928 52.381 0.00 0.00 43.14 3.91
2844 3532 3.990318 TGTAGTGTGGATGCGAGATAG 57.010 47.619 0.00 0.00 0.00 2.08
2854 3542 3.153919 GGCATTTTCCTTGTAGTGTGGA 58.846 45.455 0.00 0.00 0.00 4.02
2862 3550 3.934457 CCGTTAAGGCATTTTCCTTGT 57.066 42.857 5.38 0.00 45.51 3.16
2882 3570 1.886542 CCCCAAGTGTTTGACTAAGGC 59.113 52.381 0.00 0.00 36.36 4.35
2902 3590 1.152673 GATCCACCATTGGGCTCCC 60.153 63.158 7.78 0.00 44.11 4.30
2925 3613 8.387599 CATGATCATGTTGTGTCCCATAGACAT 61.388 40.741 24.87 0.00 44.07 3.06
2932 3620 3.263937 TCTCATGATCATGTTGTGTCCCA 59.736 43.478 30.01 10.86 39.72 4.37
2934 3622 5.181009 TCTTCTCATGATCATGTTGTGTCC 58.819 41.667 30.01 0.00 39.72 4.02
2936 3624 5.522824 CGATCTTCTCATGATCATGTTGTGT 59.477 40.000 30.01 15.82 40.03 3.72
2953 3641 3.303659 GCTCCTGCATAAAAGCGATCTTC 60.304 47.826 0.00 0.00 39.41 2.87
2962 3650 4.765273 TCTTATGTCGCTCCTGCATAAAA 58.235 39.130 0.00 0.00 39.64 1.52
2965 3653 3.222603 TCTCTTATGTCGCTCCTGCATA 58.777 45.455 0.00 0.00 39.64 3.14
3007 3700 2.035632 GTTTGAAATCACCCACCACCA 58.964 47.619 0.00 0.00 0.00 4.17
3009 3702 4.400529 AAAGTTTGAAATCACCCACCAC 57.599 40.909 0.00 0.00 0.00 4.16
3026 3719 3.288092 GTCTTCCAGGTTCACCAAAAGT 58.712 45.455 0.00 0.00 38.89 2.66
3029 3722 3.374042 TTGTCTTCCAGGTTCACCAAA 57.626 42.857 0.00 0.00 38.89 3.28
3040 3733 3.951680 GAGGGAGTTGTTTTTGTCTTCCA 59.048 43.478 0.00 0.00 0.00 3.53
3047 3740 6.215845 CCTGTTAATGAGGGAGTTGTTTTTG 58.784 40.000 0.00 0.00 0.00 2.44
3057 3750 2.503765 TCATTCGCCTGTTAATGAGGGA 59.496 45.455 5.82 0.27 37.23 4.20
3086 3779 1.398692 AGTTGAGCTTTGCCCGAAAA 58.601 45.000 0.00 0.00 0.00 2.29
3090 3783 0.954452 AAGAAGTTGAGCTTTGCCCG 59.046 50.000 0.00 0.00 37.59 6.13
3116 3809 7.378181 TGCTTCCATTCAAGTAAATTTCCTTC 58.622 34.615 0.00 0.00 0.00 3.46
3125 3818 6.711277 AGTGTATCTGCTTCCATTCAAGTAA 58.289 36.000 0.00 0.00 0.00 2.24
3140 3833 4.556233 TCTCGTTTGACCAAGTGTATCTG 58.444 43.478 0.00 0.00 0.00 2.90
3149 3842 0.034896 GCTCCCTCTCGTTTGACCAA 59.965 55.000 0.00 0.00 0.00 3.67
3168 3861 0.729116 ATTCGCTCCAAAGTCGCATG 59.271 50.000 0.00 0.00 0.00 4.06
3170 3863 0.516877 CAATTCGCTCCAAAGTCGCA 59.483 50.000 0.00 0.00 0.00 5.10
3194 3887 1.105167 ACAGTGGTCGGACGAAGACA 61.105 55.000 1.43 0.00 40.20 3.41
3200 3893 1.239296 TAGTGGACAGTGGTCGGACG 61.239 60.000 1.43 0.00 45.28 4.79
3219 3974 8.514594 CACAAGTCAACATTTATGTCCAATAGT 58.485 33.333 0.00 0.00 40.80 2.12
3220 3975 8.514594 ACACAAGTCAACATTTATGTCCAATAG 58.485 33.333 0.00 0.00 40.80 1.73
3222 3977 7.288810 ACACAAGTCAACATTTATGTCCAAT 57.711 32.000 0.00 0.00 40.80 3.16
3223 3978 6.707440 ACACAAGTCAACATTTATGTCCAA 57.293 33.333 0.00 0.00 40.80 3.53
3229 3984 5.127031 GCCCCATACACAAGTCAACATTTAT 59.873 40.000 0.00 0.00 0.00 1.40
3234 3989 1.880221 CGCCCCATACACAAGTCAACA 60.880 52.381 0.00 0.00 0.00 3.33
3243 3998 2.325583 TGAATCTTCGCCCCATACAC 57.674 50.000 0.00 0.00 0.00 2.90
3278 4033 0.107800 GAAACCCTCGGCCTTAGTCC 60.108 60.000 0.00 0.00 0.00 3.85
3279 4034 0.611714 TGAAACCCTCGGCCTTAGTC 59.388 55.000 0.00 0.00 0.00 2.59
3288 4043 1.608590 ACTGTTTGCATGAAACCCTCG 59.391 47.619 14.25 6.61 43.04 4.63
3306 4061 2.116983 AACTCCACGCATCCTGCACT 62.117 55.000 0.00 0.00 45.36 4.40
3312 4067 1.401905 GGAATTGAACTCCACGCATCC 59.598 52.381 0.00 0.00 32.77 3.51
3318 4073 3.084786 CTCCCTTGGAATTGAACTCCAC 58.915 50.000 0.00 0.00 42.76 4.02
3326 4081 0.897621 GTTGCCCTCCCTTGGAATTG 59.102 55.000 0.00 0.00 0.00 2.32
3327 4082 0.252239 GGTTGCCCTCCCTTGGAATT 60.252 55.000 0.00 0.00 0.00 2.17
3328 4083 1.388133 GGTTGCCCTCCCTTGGAAT 59.612 57.895 0.00 0.00 0.00 3.01
3371 4126 3.040414 CTCTTCGCCGTCGCTCTCA 62.040 63.158 0.00 0.00 35.26 3.27


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

AutoCloner maintained by Alex Coulton.