Multiple sequence alignment - TraesCS1D01G053000

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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 TraesCS1D01G053000 chr1D 100.000 2353 0 0 1 2353 33711305 33713657 0.000000e+00 4346.0
1 TraesCS1D01G053000 chr1D 85.227 528 58 13 885 1403 33663720 33664236 2.070000e-145 525.0
2 TraesCS1D01G053000 chr1D 82.534 584 58 29 822 1396 33705498 33706046 7.610000e-130 473.0
3 TraesCS1D01G053000 chr1A 83.476 1640 124 71 37 1633 32453540 32455075 0.000000e+00 1391.0
4 TraesCS1D01G053000 chr1A 90.391 562 48 2 1770 2327 32455966 32456525 0.000000e+00 734.0
5 TraesCS1D01G053000 chr1A 86.270 437 43 9 972 1404 32302194 32302617 2.130000e-125 459.0
6 TraesCS1D01G053000 chr1A 81.167 600 65 29 824 1403 32451232 32451803 2.780000e-119 438.0
7 TraesCS1D01G053000 chr1A 100.000 30 0 0 57 86 492277322 492277351 3.270000e-04 56.5
8 TraesCS1D01G053000 chr1B 84.443 1382 104 56 326 1661 51589432 51590748 0.000000e+00 1258.0
9 TraesCS1D01G053000 chr1B 81.459 658 76 26 773 1403 51299690 51300328 4.520000e-137 497.0
10 TraesCS1D01G053000 chr1B 81.716 536 64 22 885 1403 51538893 51539411 1.300000e-112 416.0
11 TraesCS1D01G053000 chr1B 82.505 463 62 10 945 1403 51546368 51546815 2.840000e-104 388.0
12 TraesCS1D01G053000 chr1B 89.527 296 25 4 38 332 51587125 51587415 1.030000e-98 370.0
13 TraesCS1D01G053000 chr1B 89.958 239 19 5 2092 2327 51591337 51591573 1.060000e-78 303.0
14 TraesCS1D01G053000 chr1B 89.881 168 11 4 165 332 51541097 51541258 6.590000e-51 211.0
15 TraesCS1D01G053000 chr1B 89.216 102 9 1 38 139 51540997 51541096 2.450000e-25 126.0
16 TraesCS1D01G053000 chr1B 92.188 64 5 0 1592 1655 51942579 51942642 8.960000e-15 91.6
17 TraesCS1D01G053000 chr1B 84.127 63 8 2 1703 1764 51590805 51590866 2.530000e-05 60.2
18 TraesCS1D01G053000 chr5D 96.875 32 1 0 56 87 242007707 242007676 1.000000e-03 54.7


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 TraesCS1D01G053000 chr1D 33711305 33713657 2352 False 4346.000000 4346 100.000000 1 2353 1 chr1D.!!$F3 2352
1 TraesCS1D01G053000 chr1D 33663720 33664236 516 False 525.000000 525 85.227000 885 1403 1 chr1D.!!$F1 518
2 TraesCS1D01G053000 chr1D 33705498 33706046 548 False 473.000000 473 82.534000 822 1396 1 chr1D.!!$F2 574
3 TraesCS1D01G053000 chr1A 32451232 32456525 5293 False 854.333333 1391 85.011333 37 2327 3 chr1A.!!$F3 2290
4 TraesCS1D01G053000 chr1B 51587125 51591573 4448 False 497.800000 1258 87.013750 38 2327 4 chr1B.!!$F5 2289
5 TraesCS1D01G053000 chr1B 51299690 51300328 638 False 497.000000 497 81.459000 773 1403 1 chr1B.!!$F1 630
6 TraesCS1D01G053000 chr1B 51538893 51541258 2365 False 251.000000 416 86.937667 38 1403 3 chr1B.!!$F4 1365

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
761 2811 0.03601 GCTCATGTGGGCAGTACTGT 60.036 55.0 23.44 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 8063 0.03563 GAACTCTGGAGGCATGTGCT 60.036 55.0 4.84 0.0 41.7 4.4 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
23 24 5.707066 AGCCTCTCTGATAAGGTTGAAAT 57.293 39.130 7.75 0.00 34.96 2.17
24 25 5.679601 AGCCTCTCTGATAAGGTTGAAATC 58.320 41.667 7.75 0.00 34.96 2.17
25 26 5.428131 AGCCTCTCTGATAAGGTTGAAATCT 59.572 40.000 7.75 0.00 34.96 2.40
26 27 5.757808 GCCTCTCTGATAAGGTTGAAATCTC 59.242 44.000 7.75 0.00 34.96 2.75
27 28 6.287525 CCTCTCTGATAAGGTTGAAATCTCC 58.712 44.000 0.00 0.00 0.00 3.71
28 29 6.126940 CCTCTCTGATAAGGTTGAAATCTCCA 60.127 42.308 0.00 0.00 0.00 3.86
29 30 6.644347 TCTCTGATAAGGTTGAAATCTCCAC 58.356 40.000 0.00 0.00 0.00 4.02
30 31 5.745227 TCTGATAAGGTTGAAATCTCCACC 58.255 41.667 0.00 0.00 37.59 4.61
31 32 4.855340 TGATAAGGTTGAAATCTCCACCC 58.145 43.478 0.00 0.00 37.99 4.61
32 33 4.290985 TGATAAGGTTGAAATCTCCACCCA 59.709 41.667 0.00 0.00 37.99 4.51
33 34 2.586648 AGGTTGAAATCTCCACCCAC 57.413 50.000 0.00 0.00 37.99 4.61
34 35 2.065799 AGGTTGAAATCTCCACCCACT 58.934 47.619 0.00 0.00 37.99 4.00
35 36 3.256704 AGGTTGAAATCTCCACCCACTA 58.743 45.455 0.00 0.00 37.99 2.74
36 37 3.264450 AGGTTGAAATCTCCACCCACTAG 59.736 47.826 0.00 0.00 37.99 2.57
37 38 3.009143 GGTTGAAATCTCCACCCACTAGT 59.991 47.826 0.00 0.00 32.27 2.57
38 39 3.981071 TGAAATCTCCACCCACTAGTG 57.019 47.619 16.34 16.34 37.51 2.74
39 40 3.248024 TGAAATCTCCACCCACTAGTGT 58.752 45.455 21.18 0.80 35.93 3.55
40 41 3.007940 TGAAATCTCCACCCACTAGTGTG 59.992 47.826 21.18 13.01 43.45 3.82
47 48 5.104444 TCTCCACCCACTAGTGTGTTTAAAA 60.104 40.000 21.18 0.00 42.34 1.52
168 170 5.391310 CGTGTAGCTCATCTTGCTTCAAAAT 60.391 40.000 0.00 0.00 39.00 1.82
169 171 6.183360 CGTGTAGCTCATCTTGCTTCAAAATA 60.183 38.462 0.00 0.00 39.00 1.40
173 175 9.017669 GTAGCTCATCTTGCTTCAAAATAAATG 57.982 33.333 0.00 0.00 41.46 2.32
174 176 6.534079 AGCTCATCTTGCTTCAAAATAAATGC 59.466 34.615 0.00 0.00 37.52 3.56
265 267 8.141909 TCATCATGTACTAAAAATCCTAGGTCG 58.858 37.037 9.08 0.00 0.00 4.79
279 281 4.583489 TCCTAGGTCGGATTTGTAGCTAAG 59.417 45.833 9.08 0.00 0.00 2.18
298 300 6.599638 AGCTAAGTCCAAGATCATTTGGTTAC 59.400 38.462 12.19 5.79 46.23 2.50
301 303 9.667107 CTAAGTCCAAGATCATTTGGTTACTTA 57.333 33.333 17.85 17.85 46.23 2.24
304 306 8.328758 AGTCCAAGATCATTTGGTTACTTATGA 58.671 33.333 12.19 0.00 46.23 2.15
332 334 3.165058 TGCTGACGGACTCAATCATAC 57.835 47.619 0.00 0.00 0.00 2.39
410 2435 3.120947 CGTATGAATCTGCTTCTCATCGC 59.879 47.826 0.00 0.00 34.75 4.58
534 2579 1.809271 GCAGCATGTGACCTCGATGAT 60.809 52.381 0.00 0.00 39.31 2.45
539 2584 1.364171 GTGACCTCGATGATCCCCG 59.636 63.158 0.00 0.00 0.00 5.73
549 2594 2.597805 GATCCCCGGCTCGCTAGA 60.598 66.667 0.00 0.00 0.00 2.43
577 2622 0.253610 ACGGGCCATTCATCGGTAAA 59.746 50.000 4.39 0.00 0.00 2.01
578 2623 1.340211 ACGGGCCATTCATCGGTAAAA 60.340 47.619 4.39 0.00 0.00 1.52
586 2631 5.067805 GCCATTCATCGGTAAAAGGAAATCT 59.932 40.000 0.00 0.00 0.00 2.40
620 2665 1.006162 ACCACTCCCTCAGTCCTACTC 59.994 57.143 0.00 0.00 30.26 2.59
625 2670 0.183014 CCCTCAGTCCTACTCCGCTA 59.817 60.000 0.00 0.00 0.00 4.26
679 2725 3.758931 GGCAACGTGGATTGGCCC 61.759 66.667 0.00 0.00 46.58 5.80
680 2726 3.758931 GCAACGTGGATTGGCCCC 61.759 66.667 0.00 0.00 34.97 5.80
681 2727 3.439540 CAACGTGGATTGGCCCCG 61.440 66.667 0.00 0.00 34.97 5.73
700 2750 4.486503 CCTGCCCTGCTCCTGCTC 62.487 72.222 0.00 0.00 40.48 4.26
701 2751 4.486503 CTGCCCTGCTCCTGCTCC 62.487 72.222 0.00 0.00 40.48 4.70
703 2753 4.486503 GCCCTGCTCCTGCTCCTG 62.487 72.222 0.00 0.00 40.48 3.86
730 2780 1.554617 TGCAGTATAGGTGAGCAGCAA 59.445 47.619 0.00 0.00 0.00 3.91
759 2809 2.376063 TGCTCATGTGGGCAGTACT 58.624 52.632 2.88 0.00 34.22 2.73
761 2811 0.036010 GCTCATGTGGGCAGTACTGT 60.036 55.000 23.44 0.00 0.00 3.55
762 2812 2.009042 GCTCATGTGGGCAGTACTGTC 61.009 57.143 23.44 21.55 0.00 3.51
763 2813 1.552337 CTCATGTGGGCAGTACTGTCT 59.448 52.381 25.74 4.20 35.13 3.41
764 2814 2.760650 CTCATGTGGGCAGTACTGTCTA 59.239 50.000 25.74 18.51 35.13 2.59
768 2818 1.900486 GTGGGCAGTACTGTCTAGGTT 59.100 52.381 25.74 0.00 35.13 3.50
786 2836 7.067008 GTCTAGGTTAGCAGCAATTAAATCCAA 59.933 37.037 0.00 0.00 0.00 3.53
802 2852 8.844441 TTAAATCCAAAAGAACACTACGTTTG 57.156 30.769 0.00 0.00 38.19 2.93
812 2862 3.533547 ACACTACGTTTGTGTTAAGCCA 58.466 40.909 17.49 0.00 45.11 4.75
816 2866 1.064357 ACGTTTGTGTTAAGCCAACGG 59.936 47.619 15.65 0.00 40.26 4.44
831 2881 1.001815 CAACGGCTTAAACACCCACAG 60.002 52.381 0.00 0.00 0.00 3.66
846 2896 1.645034 CACAGTAATCTGCCGTCTGG 58.355 55.000 0.00 0.00 44.77 3.86
895 6024 0.249911 GCTTCTCACTCACCGGTGTT 60.250 55.000 32.74 19.03 38.28 3.32
908 6037 1.676014 CCGGTGTTCATTCTCCTCCAC 60.676 57.143 0.00 0.00 0.00 4.02
916 6045 2.093973 TCATTCTCCTCCACTCGCTTTC 60.094 50.000 0.00 0.00 0.00 2.62
920 6049 2.035632 CTCCTCCACTCGCTTTCCTAT 58.964 52.381 0.00 0.00 0.00 2.57
924 6053 3.637229 CCTCCACTCGCTTTCCTATCTAA 59.363 47.826 0.00 0.00 0.00 2.10
927 6056 3.385111 CCACTCGCTTTCCTATCTAACCT 59.615 47.826 0.00 0.00 0.00 3.50
943 6086 2.754375 CTAACACAGGCCCCCGTT 59.246 61.111 0.00 2.37 0.00 4.44
963 6112 1.141234 CAGCAGCAGAGCAGATCGA 59.859 57.895 0.00 0.00 36.85 3.59
983 6142 0.250858 TCCAGTACGTCTCGGGTGAA 60.251 55.000 0.00 0.00 0.00 3.18
985 6144 0.109412 CAGTACGTCTCGGGTGAACC 60.109 60.000 0.00 0.00 0.00 3.62
1009 6171 4.916293 GCAGATCGATGGCGCCCA 62.916 66.667 26.77 12.96 38.19 5.36
1132 6300 0.829990 TGCTCCATGGACGATGCTTA 59.170 50.000 20.70 3.10 0.00 3.09
1150 6323 3.364664 GCTTAAGTTGCTTACCGTGGTTC 60.365 47.826 4.02 0.00 0.00 3.62
1191 6364 1.975407 GGGACGACGAGGACCAAGA 60.975 63.158 0.00 0.00 0.00 3.02
1192 6365 1.212229 GGACGACGAGGACCAAGAC 59.788 63.158 0.00 0.00 0.00 3.01
1404 6581 3.574445 CGCCGAGACGTCCGATCT 61.574 66.667 22.53 1.04 0.00 2.75
1405 6582 2.024871 GCCGAGACGTCCGATCTG 59.975 66.667 22.53 8.69 0.00 2.90
1406 6583 2.762234 GCCGAGACGTCCGATCTGT 61.762 63.158 22.53 0.00 0.00 3.41
1412 6606 0.167470 GACGTCCGATCTGTTCGTCA 59.833 55.000 21.28 0.00 46.65 4.35
1417 6611 0.109086 CCGATCTGTTCGTCAGTGCT 60.109 55.000 7.29 0.00 46.65 4.40
1435 6719 3.095332 TGCTGTCTGCTAGATCTGTTCT 58.905 45.455 5.18 0.00 43.37 3.01
1447 6731 1.487482 TCTGTTCTTCAGTGCGTTCG 58.513 50.000 0.00 0.00 43.97 3.95
1475 6759 0.319555 GGCAGTAGCTGTTCGTGTGA 60.320 55.000 0.00 0.00 41.70 3.58
1476 6760 0.784778 GCAGTAGCTGTTCGTGTGAC 59.215 55.000 0.00 0.00 37.91 3.67
1477 6761 1.053048 CAGTAGCTGTTCGTGTGACG 58.947 55.000 0.00 0.00 44.19 4.35
1513 6797 2.124277 AAGTAGGAAATCAACCGGGC 57.876 50.000 6.32 0.00 0.00 6.13
1517 6801 0.698818 AGGAAATCAACCGGGCTCTT 59.301 50.000 6.32 0.00 0.00 2.85
1535 6819 0.179051 TTGGTAGTTTGGTTCGCCGT 60.179 50.000 0.00 0.00 41.18 5.68
1536 6820 0.600782 TGGTAGTTTGGTTCGCCGTC 60.601 55.000 0.00 0.00 41.18 4.79
1537 6821 0.320160 GGTAGTTTGGTTCGCCGTCT 60.320 55.000 0.00 0.00 41.18 4.18
1538 6822 0.788391 GTAGTTTGGTTCGCCGTCTG 59.212 55.000 0.00 0.00 41.18 3.51
1539 6823 0.947180 TAGTTTGGTTCGCCGTCTGC 60.947 55.000 0.00 0.00 41.18 4.26
1540 6824 2.110213 TTTGGTTCGCCGTCTGCT 59.890 55.556 0.00 0.00 41.18 4.24
1541 6825 0.947180 GTTTGGTTCGCCGTCTGCTA 60.947 55.000 0.00 0.00 41.18 3.49
1542 6826 0.669318 TTTGGTTCGCCGTCTGCTAG 60.669 55.000 0.00 0.00 41.18 3.42
1545 6829 0.248539 GGTTCGCCGTCTGCTAGTAG 60.249 60.000 0.63 0.63 38.05 2.57
1557 6841 3.319972 TCTGCTAGTAGGTCGTGTTTGTT 59.680 43.478 8.07 0.00 0.00 2.83
1573 6857 0.173029 TGTTGCTGCTTTGTGTGGTG 59.827 50.000 0.00 0.00 0.00 4.17
1575 6859 1.135141 GTTGCTGCTTTGTGTGGTGAA 60.135 47.619 0.00 0.00 0.00 3.18
1576 6860 0.455410 TGCTGCTTTGTGTGGTGAAC 59.545 50.000 0.00 0.00 0.00 3.18
1577 6861 0.740737 GCTGCTTTGTGTGGTGAACT 59.259 50.000 0.00 0.00 0.00 3.01
1578 6862 1.134946 GCTGCTTTGTGTGGTGAACTT 59.865 47.619 0.00 0.00 0.00 2.66
1593 6883 8.151596 TGTGGTGAACTTGTGATGTAGTAATAA 58.848 33.333 0.00 0.00 0.00 1.40
1616 6906 0.586319 CGTTGTTTCAGCATGGACGT 59.414 50.000 0.00 0.00 36.16 4.34
1648 7675 1.577736 CATCCCCCTCTGTCTCTGTT 58.422 55.000 0.00 0.00 0.00 3.16
1649 7676 1.209019 CATCCCCCTCTGTCTCTGTTG 59.791 57.143 0.00 0.00 0.00 3.33
1661 7688 1.000843 TCTCTGTTGGTGTGATCGGTG 59.999 52.381 0.00 0.00 0.00 4.94
1662 7689 0.756294 TCTGTTGGTGTGATCGGTGT 59.244 50.000 0.00 0.00 0.00 4.16
1663 7690 1.148310 CTGTTGGTGTGATCGGTGTC 58.852 55.000 0.00 0.00 0.00 3.67
1664 7691 0.466124 TGTTGGTGTGATCGGTGTCA 59.534 50.000 0.00 0.00 0.00 3.58
1665 7692 1.134371 TGTTGGTGTGATCGGTGTCAA 60.134 47.619 0.00 0.00 0.00 3.18
1666 7693 1.944024 GTTGGTGTGATCGGTGTCAAA 59.056 47.619 0.00 0.00 0.00 2.69
1667 7694 2.333688 TGGTGTGATCGGTGTCAAAA 57.666 45.000 0.00 0.00 0.00 2.44
1668 7695 2.644676 TGGTGTGATCGGTGTCAAAAA 58.355 42.857 0.00 0.00 0.00 1.94
1669 7696 2.356382 TGGTGTGATCGGTGTCAAAAAC 59.644 45.455 0.00 0.00 0.00 2.43
1670 7697 2.601266 GGTGTGATCGGTGTCAAAAACG 60.601 50.000 0.00 0.00 0.00 3.60
1671 7698 1.003331 TGTGATCGGTGTCAAAAACGC 60.003 47.619 0.00 0.00 37.67 4.84
1673 7700 1.529438 TGATCGGTGTCAAAAACGCTC 59.471 47.619 0.00 0.00 38.49 5.03
1674 7701 1.798813 GATCGGTGTCAAAAACGCTCT 59.201 47.619 0.00 0.00 38.49 4.09
1676 7703 2.823984 TCGGTGTCAAAAACGCTCTTA 58.176 42.857 0.00 0.00 38.49 2.10
1677 7704 3.395639 TCGGTGTCAAAAACGCTCTTAT 58.604 40.909 0.00 0.00 38.49 1.73
1678 7705 3.185594 TCGGTGTCAAAAACGCTCTTATG 59.814 43.478 0.00 0.00 38.49 1.90
1680 7707 4.464112 GGTGTCAAAAACGCTCTTATGAC 58.536 43.478 0.00 0.00 38.49 3.06
1681 7708 4.213482 GGTGTCAAAAACGCTCTTATGACT 59.787 41.667 0.00 0.00 38.34 3.41
1682 7709 5.277828 GGTGTCAAAAACGCTCTTATGACTT 60.278 40.000 0.00 0.00 38.34 3.01
1683 7710 6.073440 GGTGTCAAAAACGCTCTTATGACTTA 60.073 38.462 0.00 0.00 38.34 2.24
1684 7711 7.360946 GGTGTCAAAAACGCTCTTATGACTTAT 60.361 37.037 0.00 0.00 38.34 1.73
1704 7746 7.712537 ACTTATATTATAAGACGGAGGGGGTA 58.287 38.462 23.91 0.00 0.00 3.69
1711 7753 1.280998 AGACGGAGGGGGTACATTTTG 59.719 52.381 0.00 0.00 0.00 2.44
1719 7761 2.758423 GGGGGTACATTTTGATGTGACC 59.242 50.000 2.47 4.55 36.08 4.02
1720 7762 2.758423 GGGGTACATTTTGATGTGACCC 59.242 50.000 18.64 18.64 41.87 4.46
1753 7796 3.981211 AGCTGCGTGAACATTTCATTTT 58.019 36.364 0.00 0.00 42.47 1.82
1756 7799 4.606673 GCTGCGTGAACATTTCATTTTGTG 60.607 41.667 0.00 0.00 42.47 3.33
1766 7809 6.050432 ACATTTCATTTTGTGCACATGAACT 58.950 32.000 26.22 20.55 36.80 3.01
1911 8063 3.423539 CTTGGAAGGACAATCTGGACA 57.576 47.619 0.00 0.00 0.00 4.02
1917 8069 1.632409 AGGACAATCTGGACAGCACAT 59.368 47.619 0.00 0.00 0.00 3.21
1936 8089 2.035442 GCCTCCAGAGTTCAACCGC 61.035 63.158 0.00 0.00 0.00 5.68
2012 8171 1.258445 GGTGACTCATCGTGGGGTCT 61.258 60.000 9.77 0.00 0.00 3.85
2051 8210 1.393539 GAACACACGTCCATCCAATCG 59.606 52.381 0.00 0.00 0.00 3.34
2062 8221 2.609459 CCATCCAATCGCACACTAAGAC 59.391 50.000 0.00 0.00 0.00 3.01
2085 8246 3.361644 CGTGTGCAATGCAAGATGTTTAC 59.638 43.478 10.44 0.00 41.47 2.01
2087 8248 4.148696 GTGTGCAATGCAAGATGTTTACAC 59.851 41.667 10.44 6.78 41.47 2.90
2123 8383 4.317488 ACATAAACCGCCTTTTCTTACGA 58.683 39.130 0.00 0.00 0.00 3.43
2235 8498 2.616524 ACAAGCACCTCCCTAAGTACA 58.383 47.619 0.00 0.00 0.00 2.90
2258 8521 8.696043 ACATTGCATTGTACATGACCTAATAT 57.304 30.769 12.38 0.00 0.00 1.28
2275 8538 1.924731 TATAGATCGTGAGGGCAGGG 58.075 55.000 0.00 0.00 0.00 4.45
2314 8581 1.672356 CAAACCCTCTGTGCCCTCG 60.672 63.158 0.00 0.00 0.00 4.63
2327 8594 0.527565 GCCCTCGTAAGTTCCACGTA 59.472 55.000 0.00 0.00 40.27 3.57
2328 8595 1.067635 GCCCTCGTAAGTTCCACGTAA 60.068 52.381 0.00 0.00 40.27 3.18
2329 8596 2.872370 CCCTCGTAAGTTCCACGTAAG 58.128 52.381 0.00 0.00 40.27 2.34
2331 8598 3.305608 CCCTCGTAAGTTCCACGTAAGTT 60.306 47.826 0.00 0.00 45.85 2.66
2332 8599 3.916776 CCTCGTAAGTTCCACGTAAGTTC 59.083 47.826 0.00 0.00 45.85 3.01
2333 8600 3.900941 TCGTAAGTTCCACGTAAGTTCC 58.099 45.455 0.00 0.00 45.85 3.62
2335 8602 4.792704 TCGTAAGTTCCACGTAAGTTCCAC 60.793 45.833 0.00 0.00 45.85 4.02
2343 8610 1.493772 CGTAAGTTCCACGTGCTTCA 58.506 50.000 10.91 0.00 34.74 3.02
2345 8612 3.247442 CGTAAGTTCCACGTGCTTCATA 58.753 45.455 10.91 0.00 34.74 2.15
2346 8613 3.863424 CGTAAGTTCCACGTGCTTCATAT 59.137 43.478 10.91 0.00 34.74 1.78
2347 8614 4.259810 CGTAAGTTCCACGTGCTTCATATG 60.260 45.833 10.91 0.00 34.74 1.78
2348 8615 3.610040 AGTTCCACGTGCTTCATATGA 57.390 42.857 10.91 0.00 0.00 2.15
2349 8616 4.142609 AGTTCCACGTGCTTCATATGAT 57.857 40.909 10.91 0.00 0.00 2.45
2350 8617 3.873361 AGTTCCACGTGCTTCATATGATG 59.127 43.478 10.91 10.19 0.00 3.07
2352 8619 4.664150 TCCACGTGCTTCATATGATGTA 57.336 40.909 10.91 11.75 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.679601 AGATTTCAACCTTATCAGAGAGGC 58.320 41.667 3.06 0.00 36.48 4.70
5 6 6.352222 GGTGGAGATTTCAACCTTATCAGAGA 60.352 42.308 2.40 0.00 43.21 3.10
6 7 5.819901 GGTGGAGATTTCAACCTTATCAGAG 59.180 44.000 2.40 0.00 43.21 3.35
7 8 5.339200 GGGTGGAGATTTCAACCTTATCAGA 60.339 44.000 9.60 0.00 45.48 3.27
8 9 4.884164 GGGTGGAGATTTCAACCTTATCAG 59.116 45.833 9.60 0.00 45.48 2.90
9 10 4.290985 TGGGTGGAGATTTCAACCTTATCA 59.709 41.667 9.60 0.00 45.48 2.15
10 11 4.640647 GTGGGTGGAGATTTCAACCTTATC 59.359 45.833 9.60 0.00 45.48 1.75
11 12 4.292306 AGTGGGTGGAGATTTCAACCTTAT 59.708 41.667 9.60 0.00 45.48 1.73
12 13 3.655777 AGTGGGTGGAGATTTCAACCTTA 59.344 43.478 9.60 0.00 45.48 2.69
13 14 2.447047 AGTGGGTGGAGATTTCAACCTT 59.553 45.455 9.60 0.00 45.48 3.50
14 15 2.065799 AGTGGGTGGAGATTTCAACCT 58.934 47.619 9.60 0.00 45.48 3.50
15 16 2.586648 AGTGGGTGGAGATTTCAACC 57.413 50.000 0.84 0.84 45.46 3.77
16 17 4.003648 CACTAGTGGGTGGAGATTTCAAC 58.996 47.826 15.49 0.00 33.95 3.18
17 18 3.650942 ACACTAGTGGGTGGAGATTTCAA 59.349 43.478 26.12 0.00 41.09 2.69
18 19 3.007940 CACACTAGTGGGTGGAGATTTCA 59.992 47.826 26.12 0.00 42.13 2.69
19 20 3.600388 CACACTAGTGGGTGGAGATTTC 58.400 50.000 26.12 0.00 42.13 2.17
20 21 3.703001 CACACTAGTGGGTGGAGATTT 57.297 47.619 26.12 0.00 42.13 2.17
32 33 9.528018 CATTGGAATTGTTTTAAACACACTAGT 57.472 29.630 10.28 0.00 41.97 2.57
33 34 9.528018 ACATTGGAATTGTTTTAAACACACTAG 57.472 29.630 10.28 0.00 41.97 2.57
34 35 9.307121 CACATTGGAATTGTTTTAAACACACTA 57.693 29.630 10.28 0.00 41.97 2.74
35 36 7.821846 ACACATTGGAATTGTTTTAAACACACT 59.178 29.630 10.28 0.00 41.97 3.55
36 37 7.969314 ACACATTGGAATTGTTTTAAACACAC 58.031 30.769 10.28 5.04 41.97 3.82
37 38 9.823647 ATACACATTGGAATTGTTTTAAACACA 57.176 25.926 10.28 2.55 41.97 3.72
242 244 6.608405 TCCGACCTAGGATTTTTAGTACATGA 59.392 38.462 17.98 0.00 34.92 3.07
265 267 6.349300 TGATCTTGGACTTAGCTACAAATCC 58.651 40.000 0.00 0.00 0.00 3.01
312 314 2.159099 GGTATGATTGAGTCCGTCAGCA 60.159 50.000 0.00 0.00 36.21 4.41
321 323 2.626266 TCCGCGTATGGTATGATTGAGT 59.374 45.455 4.92 0.00 0.00 3.41
324 326 3.993736 TGAATCCGCGTATGGTATGATTG 59.006 43.478 4.92 0.00 0.00 2.67
332 334 2.928361 GCGTGAATCCGCGTATGG 59.072 61.111 4.92 0.00 46.98 2.74
410 2435 1.816835 TGTACGCCTAGTCACTCCTTG 59.183 52.381 0.00 0.00 0.00 3.61
443 2488 2.197324 GGTGGGTGGCTGTGGAAA 59.803 61.111 0.00 0.00 0.00 3.13
444 2489 3.099841 TGGTGGGTGGCTGTGGAA 61.100 61.111 0.00 0.00 0.00 3.53
534 2579 4.124943 ACTCTAGCGAGCCGGGGA 62.125 66.667 2.18 0.00 41.09 4.81
539 2584 1.226717 CGTTGGACTCTAGCGAGCC 60.227 63.158 0.00 0.00 41.09 4.70
549 2594 2.798148 GAATGGCCCGTCGTTGGACT 62.798 60.000 0.00 0.00 41.16 3.85
577 2622 0.404040 TTCACGGGCCAGATTTCCTT 59.596 50.000 10.86 0.00 0.00 3.36
578 2623 0.404040 TTTCACGGGCCAGATTTCCT 59.596 50.000 10.86 0.00 0.00 3.36
586 2631 1.602323 GTGGTCATTTCACGGGCCA 60.602 57.895 4.39 0.00 0.00 5.36
735 2785 1.453379 GCCCACATGAGCAGAGCAT 60.453 57.895 0.00 0.00 0.00 3.79
746 2796 2.111384 CCTAGACAGTACTGCCCACAT 58.889 52.381 22.90 1.55 0.00 3.21
747 2797 1.203137 ACCTAGACAGTACTGCCCACA 60.203 52.381 22.90 6.44 0.00 4.17
751 2801 2.758979 TGCTAACCTAGACAGTACTGCC 59.241 50.000 22.90 12.38 0.00 4.85
759 2809 6.542370 GGATTTAATTGCTGCTAACCTAGACA 59.458 38.462 0.00 0.00 0.00 3.41
761 2811 6.658849 TGGATTTAATTGCTGCTAACCTAGA 58.341 36.000 0.00 0.00 0.00 2.43
762 2812 6.942532 TGGATTTAATTGCTGCTAACCTAG 57.057 37.500 0.00 0.00 0.00 3.02
763 2813 7.710676 TTTGGATTTAATTGCTGCTAACCTA 57.289 32.000 0.00 0.00 0.00 3.08
764 2814 6.603940 TTTGGATTTAATTGCTGCTAACCT 57.396 33.333 0.00 0.00 0.00 3.50
768 2818 7.598493 GTGTTCTTTTGGATTTAATTGCTGCTA 59.402 33.333 0.00 0.00 0.00 3.49
816 2866 4.379499 GCAGATTACTGTGGGTGTTTAAGC 60.379 45.833 0.00 0.00 45.04 3.09
846 2896 1.339151 GCTGGGCTGGTGGTATATAGC 60.339 57.143 4.94 4.94 35.49 2.97
895 6024 1.561643 AAGCGAGTGGAGGAGAATGA 58.438 50.000 0.00 0.00 0.00 2.57
908 6037 5.978322 GTGTTAGGTTAGATAGGAAAGCGAG 59.022 44.000 0.00 0.00 0.00 5.03
927 6056 2.432563 CAACGGGGGCCTGTGTTA 59.567 61.111 0.84 0.00 35.44 2.41
959 6108 1.227639 CCGAGACGTACTGGATCGAT 58.772 55.000 0.00 0.00 35.47 3.59
963 6112 0.034767 TCACCCGAGACGTACTGGAT 60.035 55.000 9.03 0.00 0.00 3.41
983 6142 0.104487 CATCGATCTGCTCAGCTGGT 59.896 55.000 15.13 0.00 0.00 4.00
985 6144 1.222766 GCCATCGATCTGCTCAGCTG 61.223 60.000 7.63 7.63 0.00 4.24
1045 6210 3.057547 CTGTGGCGACGAGGAGGAG 62.058 68.421 0.00 0.00 0.00 3.69
1083 6249 1.293498 GCTCGCTGGGAAGAGTGAA 59.707 57.895 0.00 0.00 36.88 3.18
1132 6300 1.601166 GGAACCACGGTAAGCAACTT 58.399 50.000 0.00 0.00 0.00 2.66
1150 6323 2.174107 CTGCATGCACGTCAACGG 59.826 61.111 18.46 0.00 44.95 4.44
1404 6581 0.875908 GCAGACAGCACTGACGAACA 60.876 55.000 4.31 0.00 44.79 3.18
1405 6582 1.856012 GCAGACAGCACTGACGAAC 59.144 57.895 4.31 0.00 44.79 3.95
1406 6583 4.343581 GCAGACAGCACTGACGAA 57.656 55.556 4.31 0.00 44.79 3.85
1412 6606 6.793265 AAGAACAGATCTAGCAGACAGCACT 61.793 44.000 0.00 0.00 41.53 4.40
1435 6719 2.923177 CGAACGCGAACGCACTGAA 61.923 57.895 15.93 0.00 45.53 3.02
1447 6731 3.542742 GCTACTGCCGACGAACGC 61.543 66.667 0.00 0.00 41.07 4.84
1458 6742 1.053048 CGTCACACGAACAGCTACTG 58.947 55.000 0.00 0.00 46.05 2.74
1475 6759 3.256631 ACTTTATTACGGGACACAGTCGT 59.743 43.478 0.00 0.00 40.40 4.34
1476 6760 3.841643 ACTTTATTACGGGACACAGTCG 58.158 45.455 0.00 0.00 32.65 4.18
1477 6761 5.126061 TCCTACTTTATTACGGGACACAGTC 59.874 44.000 0.00 0.00 0.00 3.51
1478 6762 5.018809 TCCTACTTTATTACGGGACACAGT 58.981 41.667 0.00 0.00 0.00 3.55
1513 6797 1.804748 GGCGAACCAAACTACCAAGAG 59.195 52.381 0.00 0.00 35.26 2.85
1517 6801 0.600782 GACGGCGAACCAAACTACCA 60.601 55.000 16.62 0.00 34.57 3.25
1535 6819 2.889045 ACAAACACGACCTACTAGCAGA 59.111 45.455 0.00 0.00 0.00 4.26
1536 6820 3.299340 ACAAACACGACCTACTAGCAG 57.701 47.619 0.00 0.00 0.00 4.24
1537 6821 3.386486 CAACAAACACGACCTACTAGCA 58.614 45.455 0.00 0.00 0.00 3.49
1538 6822 2.157085 GCAACAAACACGACCTACTAGC 59.843 50.000 0.00 0.00 0.00 3.42
1539 6823 3.428870 CAGCAACAAACACGACCTACTAG 59.571 47.826 0.00 0.00 0.00 2.57
1540 6824 3.386486 CAGCAACAAACACGACCTACTA 58.614 45.455 0.00 0.00 0.00 1.82
1541 6825 2.210116 CAGCAACAAACACGACCTACT 58.790 47.619 0.00 0.00 0.00 2.57
1542 6826 1.333791 GCAGCAACAAACACGACCTAC 60.334 52.381 0.00 0.00 0.00 3.18
1545 6829 0.100503 AAGCAGCAACAAACACGACC 59.899 50.000 0.00 0.00 0.00 4.79
1557 6841 0.455410 GTTCACCACACAAAGCAGCA 59.545 50.000 0.00 0.00 0.00 4.41
1573 6857 7.758528 ACGACCTTATTACTACATCACAAGTTC 59.241 37.037 0.00 0.00 0.00 3.01
1575 6859 7.166691 ACGACCTTATTACTACATCACAAGT 57.833 36.000 0.00 0.00 0.00 3.16
1576 6860 7.544566 ACAACGACCTTATTACTACATCACAAG 59.455 37.037 0.00 0.00 0.00 3.16
1577 6861 7.380536 ACAACGACCTTATTACTACATCACAA 58.619 34.615 0.00 0.00 0.00 3.33
1578 6862 6.927416 ACAACGACCTTATTACTACATCACA 58.073 36.000 0.00 0.00 0.00 3.58
1593 6883 1.202758 TCCATGCTGAAACAACGACCT 60.203 47.619 0.00 0.00 0.00 3.85
1616 6906 1.375396 GGGATGCAGTGCACACGTA 60.375 57.895 22.44 9.65 43.04 3.57
1648 7675 2.333688 TTTTGACACCGATCACACCA 57.666 45.000 0.00 0.00 0.00 4.17
1649 7676 2.601266 CGTTTTTGACACCGATCACACC 60.601 50.000 0.00 0.00 0.00 4.16
1676 7703 7.344871 CCCCCTCCGTCTTATAATATAAGTCAT 59.655 40.741 16.87 0.00 0.00 3.06
1677 7704 6.666546 CCCCCTCCGTCTTATAATATAAGTCA 59.333 42.308 16.87 0.00 0.00 3.41
1678 7705 6.666980 ACCCCCTCCGTCTTATAATATAAGTC 59.333 42.308 16.87 11.88 0.00 3.01
1680 7707 7.616935 TGTACCCCCTCCGTCTTATAATATAAG 59.383 40.741 12.58 12.58 0.00 1.73
1681 7708 7.477864 TGTACCCCCTCCGTCTTATAATATAA 58.522 38.462 0.00 0.00 0.00 0.98
1682 7709 7.043300 TGTACCCCCTCCGTCTTATAATATA 57.957 40.000 0.00 0.00 0.00 0.86
1683 7710 5.907421 TGTACCCCCTCCGTCTTATAATAT 58.093 41.667 0.00 0.00 0.00 1.28
1684 7711 5.337956 TGTACCCCCTCCGTCTTATAATA 57.662 43.478 0.00 0.00 0.00 0.98
1687 7714 3.909427 ATGTACCCCCTCCGTCTTATA 57.091 47.619 0.00 0.00 0.00 0.98
1688 7715 2.789323 ATGTACCCCCTCCGTCTTAT 57.211 50.000 0.00 0.00 0.00 1.73
1690 7717 1.665137 AAATGTACCCCCTCCGTCTT 58.335 50.000 0.00 0.00 0.00 3.01
1692 7719 1.279846 TCAAAATGTACCCCCTCCGTC 59.720 52.381 0.00 0.00 0.00 4.79
1694 7721 2.297701 CATCAAAATGTACCCCCTCCG 58.702 52.381 0.00 0.00 0.00 4.63
1695 7722 3.023832 CACATCAAAATGTACCCCCTCC 58.976 50.000 0.00 0.00 44.41 4.30
1698 7725 2.758423 GGTCACATCAAAATGTACCCCC 59.242 50.000 0.00 0.00 44.41 5.40
1699 7726 2.758423 GGGTCACATCAAAATGTACCCC 59.242 50.000 16.92 13.02 44.41 4.95
1700 7727 2.422127 CGGGTCACATCAAAATGTACCC 59.578 50.000 17.36 17.36 44.41 3.69
1711 7753 0.437295 CGAAAACGTCGGGTCACATC 59.563 55.000 0.00 0.00 46.45 3.06
1753 7796 3.723260 TCTTTCGTAGTTCATGTGCACA 58.277 40.909 24.08 24.08 0.00 4.57
1756 7799 7.470289 AGATATTCTTTCGTAGTTCATGTGC 57.530 36.000 0.00 0.00 0.00 4.57
1875 8027 6.633500 CTTCCAAGGAAATGTTTGTCTACA 57.367 37.500 2.78 0.00 33.34 2.74
1911 8063 0.035630 GAACTCTGGAGGCATGTGCT 60.036 55.000 4.84 0.00 41.70 4.40
1917 8069 1.371183 CGGTTGAACTCTGGAGGCA 59.629 57.895 0.00 0.00 0.00 4.75
1936 8089 3.925913 CGCTTTACCCAAATGTTTCCATG 59.074 43.478 0.00 0.00 0.00 3.66
2012 8171 0.907486 CATCCTCTGTTGCCCTCTGA 59.093 55.000 0.00 0.00 0.00 3.27
2062 8221 0.241749 ACATCTTGCATTGCACACGG 59.758 50.000 11.66 4.52 38.71 4.94
2068 8229 3.922240 CCTGTGTAAACATCTTGCATTGC 59.078 43.478 0.46 0.46 0.00 3.56
2085 8246 7.073265 CGGTTTATGTTTTACAAGTACCTGTG 58.927 38.462 7.40 0.00 0.00 3.66
2087 8248 6.081693 GCGGTTTATGTTTTACAAGTACCTG 58.918 40.000 0.00 0.00 0.00 4.00
2156 8418 5.762825 ACTTGCATAGCATTATCACTTGG 57.237 39.130 0.00 0.00 38.76 3.61
2205 8468 3.621715 GGGAGGTGCTTGTATAAACGAAG 59.378 47.826 0.00 0.00 0.00 3.79
2213 8476 4.359105 TGTACTTAGGGAGGTGCTTGTAT 58.641 43.478 0.00 0.00 0.00 2.29
2256 8519 1.427753 TCCCTGCCCTCACGATCTATA 59.572 52.381 0.00 0.00 0.00 1.31
2258 8521 0.468214 CTCCCTGCCCTCACGATCTA 60.468 60.000 0.00 0.00 0.00 1.98
2265 8528 3.686098 ATCGCTCTCCCTGCCCTCA 62.686 63.158 0.00 0.00 0.00 3.86
2275 8538 2.929531 TCTGTTGTCAGATCGCTCTC 57.070 50.000 0.00 0.00 44.58 3.20
2295 8562 1.973812 GAGGGCACAGAGGGTTTGC 60.974 63.158 0.00 0.00 35.40 3.68
2314 8581 3.426525 CGTGGAACTTACGTGGAACTTAC 59.573 47.826 0.00 0.00 36.83 2.34
2327 8594 3.937814 TCATATGAAGCACGTGGAACTT 58.062 40.909 18.88 12.11 31.75 2.66
2328 8595 3.610040 TCATATGAAGCACGTGGAACT 57.390 42.857 18.88 2.63 31.75 3.01
2329 8596 3.623060 ACATCATATGAAGCACGTGGAAC 59.377 43.478 18.88 0.00 0.00 3.62
2330 8597 3.872696 ACATCATATGAAGCACGTGGAA 58.127 40.909 18.88 0.00 0.00 3.53
2331 8598 3.541996 ACATCATATGAAGCACGTGGA 57.458 42.857 18.88 3.35 0.00 4.02


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

AutoCloner maintained by Alex Coulton.