Multiple sequence alignment - TraesCS5D01G272600

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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 TraesCS5D01G272600 chr5D 100.000 3711 0 0 1 3711 375451424 375455134 0.000000e+00 6854.0
1 TraesCS5D01G272600 chr5D 87.413 1430 139 24 693 2112 375589446 375590844 0.000000e+00 1605.0
2 TraesCS5D01G272600 chr5D 89.336 1069 92 13 1072 2133 375576989 375578042 0.000000e+00 1323.0
3 TraesCS5D01G272600 chr5D 95.245 652 25 4 1566 2216 375590858 375591504 0.000000e+00 1027.0
4 TraesCS5D01G272600 chr5D 79.570 558 38 32 2180 2678 375591503 375592043 2.760000e-86 329.0
5 TraesCS5D01G272600 chr5D 92.453 106 6 2 604 708 139287195 139287299 2.310000e-32 150.0
6 TraesCS5D01G272600 chr5D 92.233 103 6 2 607 708 170395510 170395409 1.070000e-30 145.0
7 TraesCS5D01G272600 chr5D 78.261 253 21 15 4 238 375588762 375588998 8.360000e-27 132.0
8 TraesCS5D01G272600 chr5D 90.667 75 4 2 611 684 170399820 170399748 3.050000e-16 97.1
9 TraesCS5D01G272600 chr5A 85.788 1745 180 38 485 2203 476769280 476770982 0.000000e+00 1786.0
10 TraesCS5D01G272600 chr5A 91.273 1249 72 17 1611 2829 476759461 476760702 0.000000e+00 1668.0
11 TraesCS5D01G272600 chr5A 83.182 1546 140 44 60 1554 476757968 476759444 0.000000e+00 1304.0
12 TraesCS5D01G272600 chr5A 80.747 857 105 29 2864 3703 299569805 299568992 6.810000e-172 614.0
13 TraesCS5D01G272600 chr5A 86.651 427 43 7 2864 3283 92215238 92215657 9.390000e-126 460.0
14 TraesCS5D01G272600 chr5A 86.136 339 35 9 2459 2788 476771233 476771568 4.560000e-94 355.0
15 TraesCS5D01G272600 chr5A 81.746 252 22 5 4 249 476769035 476769268 4.890000e-44 189.0
16 TraesCS5D01G272600 chr5A 91.743 109 7 2 601 708 648947347 648947454 2.310000e-32 150.0
17 TraesCS5D01G272600 chr5B 86.467 1633 114 48 1 1576 448302750 448304332 0.000000e+00 1692.0
18 TraesCS5D01G272600 chr5B 94.745 609 24 6 1611 2216 448304330 448304933 0.000000e+00 941.0
19 TraesCS5D01G272600 chr5B 81.069 861 111 27 2864 3704 680313267 680314095 1.120000e-179 640.0
20 TraesCS5D01G272600 chr5B 84.514 607 49 20 2286 2862 448305595 448306186 3.240000e-155 558.0
21 TraesCS5D01G272600 chr5B 89.340 394 37 3 1814 2203 448440182 448440574 1.200000e-134 490.0
22 TraesCS5D01G272600 chr5B 85.970 335 33 10 2457 2782 448440806 448441135 2.740000e-91 346.0
23 TraesCS5D01G272600 chr5B 89.091 55 6 0 2206 2260 448305483 448305537 6.650000e-08 69.4
24 TraesCS5D01G272600 chr6B 86.505 867 87 14 2860 3711 658601473 658600622 0.000000e+00 926.0
25 TraesCS5D01G272600 chr6B 82.580 752 102 19 2970 3705 127615937 127616675 1.450000e-178 636.0
26 TraesCS5D01G272600 chr4B 86.092 870 101 11 2860 3711 2222224 2223091 0.000000e+00 918.0
27 TraesCS5D01G272600 chr4B 85.998 857 93 19 2864 3708 7853179 7852338 0.000000e+00 893.0
28 TraesCS5D01G272600 chrUn 84.642 879 100 15 2864 3711 86429565 86428691 0.000000e+00 843.0
29 TraesCS5D01G272600 chrUn 92.500 40 2 1 813 852 363329703 363329741 5.180000e-04 56.5
30 TraesCS5D01G272600 chr1B 83.391 873 82 19 2861 3711 594918090 594918921 0.000000e+00 750.0
31 TraesCS5D01G272600 chr1B 85.500 600 65 14 2860 3446 473006992 473007582 1.140000e-169 606.0
32 TraesCS5D01G272600 chr1B 95.122 41 1 1 812 852 119630227 119630188 3.090000e-06 63.9
33 TraesCS5D01G272600 chr3D 82.984 858 97 22 2864 3709 175649433 175648613 0.000000e+00 730.0
34 TraesCS5D01G272600 chr7D 88.758 596 56 7 2860 3446 572807314 572807907 0.000000e+00 719.0
35 TraesCS5D01G272600 chr7D 80.543 884 125 24 2861 3708 20626056 20626928 1.450000e-178 636.0
36 TraesCS5D01G272600 chr2D 86.767 597 60 9 2864 3444 276908447 276907854 0.000000e+00 647.0
37 TraesCS5D01G272600 chr7B 87.067 549 55 8 3178 3711 667763759 667764306 1.140000e-169 606.0
38 TraesCS5D01G272600 chr7B 88.811 143 12 3 607 748 394822552 394822413 4.930000e-39 172.0
39 TraesCS5D01G272600 chr7B 87.500 64 7 1 813 876 394822411 394822349 5.140000e-09 73.1
40 TraesCS5D01G272600 chr3B 86.932 528 47 11 2864 3382 2307291 2306777 1.160000e-159 573.0
41 TraesCS5D01G272600 chr3B 88.971 136 13 2 607 741 328606122 328606256 2.290000e-37 167.0
42 TraesCS5D01G272600 chr6D 90.837 251 19 2 1952 2202 84555744 84555990 2.140000e-87 333.0
43 TraesCS5D01G272600 chr6D 84.146 328 38 8 2334 2650 84558858 84559182 4.660000e-79 305.0
44 TraesCS5D01G272600 chr6D 87.413 143 14 3 607 748 374766037 374765898 1.070000e-35 161.0
45 TraesCS5D01G272600 chr6D 93.204 103 5 2 607 708 62242540 62242439 2.310000e-32 150.0
46 TraesCS5D01G272600 chr6D 89.000 100 9 2 2200 2298 84558495 84558593 5.030000e-24 122.0
47 TraesCS5D01G272600 chr2B 88.811 143 12 3 607 748 118089766 118089627 4.930000e-39 172.0
48 TraesCS5D01G272600 chr2B 87.500 64 7 1 813 876 118089625 118089563 5.140000e-09 73.1
49 TraesCS5D01G272600 chr7A 89.394 132 13 1 611 741 679417912 679418043 8.250000e-37 165.0
50 TraesCS5D01G272600 chr7A 89.655 58 5 1 813 870 679418050 679418106 5.140000e-09 73.1


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 TraesCS5D01G272600 chr5D 375451424 375455134 3710 False 6854.000000 6854 100.000000 1 3711 1 chr5D.!!$F2 3710
1 TraesCS5D01G272600 chr5D 375576989 375578042 1053 False 1323.000000 1323 89.336000 1072 2133 1 chr5D.!!$F3 1061
2 TraesCS5D01G272600 chr5D 375588762 375592043 3281 False 773.250000 1605 85.122250 4 2678 4 chr5D.!!$F4 2674
3 TraesCS5D01G272600 chr5A 476757968 476760702 2734 False 1486.000000 1668 87.227500 60 2829 2 chr5A.!!$F3 2769
4 TraesCS5D01G272600 chr5A 476769035 476771568 2533 False 776.666667 1786 84.556667 4 2788 3 chr5A.!!$F4 2784
5 TraesCS5D01G272600 chr5A 299568992 299569805 813 True 614.000000 614 80.747000 2864 3703 1 chr5A.!!$R1 839
6 TraesCS5D01G272600 chr5B 448302750 448306186 3436 False 815.100000 1692 88.704250 1 2862 4 chr5B.!!$F2 2861
7 TraesCS5D01G272600 chr5B 680313267 680314095 828 False 640.000000 640 81.069000 2864 3704 1 chr5B.!!$F1 840
8 TraesCS5D01G272600 chr5B 448440182 448441135 953 False 418.000000 490 87.655000 1814 2782 2 chr5B.!!$F3 968
9 TraesCS5D01G272600 chr6B 658600622 658601473 851 True 926.000000 926 86.505000 2860 3711 1 chr6B.!!$R1 851
10 TraesCS5D01G272600 chr6B 127615937 127616675 738 False 636.000000 636 82.580000 2970 3705 1 chr6B.!!$F1 735
11 TraesCS5D01G272600 chr4B 2222224 2223091 867 False 918.000000 918 86.092000 2860 3711 1 chr4B.!!$F1 851
12 TraesCS5D01G272600 chr4B 7852338 7853179 841 True 893.000000 893 85.998000 2864 3708 1 chr4B.!!$R1 844
13 TraesCS5D01G272600 chrUn 86428691 86429565 874 True 843.000000 843 84.642000 2864 3711 1 chrUn.!!$R1 847
14 TraesCS5D01G272600 chr1B 594918090 594918921 831 False 750.000000 750 83.391000 2861 3711 1 chr1B.!!$F2 850
15 TraesCS5D01G272600 chr1B 473006992 473007582 590 False 606.000000 606 85.500000 2860 3446 1 chr1B.!!$F1 586
16 TraesCS5D01G272600 chr3D 175648613 175649433 820 True 730.000000 730 82.984000 2864 3709 1 chr3D.!!$R1 845
17 TraesCS5D01G272600 chr7D 572807314 572807907 593 False 719.000000 719 88.758000 2860 3446 1 chr7D.!!$F2 586
18 TraesCS5D01G272600 chr7D 20626056 20626928 872 False 636.000000 636 80.543000 2861 3708 1 chr7D.!!$F1 847
19 TraesCS5D01G272600 chr2D 276907854 276908447 593 True 647.000000 647 86.767000 2864 3444 1 chr2D.!!$R1 580
20 TraesCS5D01G272600 chr7B 667763759 667764306 547 False 606.000000 606 87.067000 3178 3711 1 chr7B.!!$F1 533
21 TraesCS5D01G272600 chr3B 2306777 2307291 514 True 573.000000 573 86.932000 2864 3382 1 chr3B.!!$R1 518
22 TraesCS5D01G272600 chr6D 84555744 84559182 3438 False 253.333333 333 87.994333 1952 2650 3 chr6D.!!$F1 698

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
450 586 1.144057 CAGGGATCCGTGGTAGCAC 59.856 63.158 24.05 15.12 0.00 4.4 F
1524 1702 0.320771 ATTCTGTCACCGGTGAGTGC 60.321 55.000 37.04 25.09 40.75 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1803 0.328450 ACCATCCCCAGGAATGCCTA 60.328 55.0 0.00 0.00 44.80 3.93 R
3172 7399 0.040603 AGAAGGACGACGACGACAAC 60.041 55.0 15.32 3.49 42.66 3.32 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
134 169 3.080121 CCTGAGCTTCTCCGGCCT 61.080 66.667 0.00 0.00 28.87 5.19
135 170 2.498726 CTGAGCTTCTCCGGCCTC 59.501 66.667 0.00 0.00 0.00 4.70
136 171 3.077556 TGAGCTTCTCCGGCCTCC 61.078 66.667 0.00 0.00 0.00 4.30
137 172 3.077556 GAGCTTCTCCGGCCTCCA 61.078 66.667 0.00 0.00 0.00 3.86
138 173 3.378399 GAGCTTCTCCGGCCTCCAC 62.378 68.421 0.00 0.00 0.00 4.02
139 174 4.475135 GCTTCTCCGGCCTCCACC 62.475 72.222 0.00 0.00 0.00 4.61
140 175 3.003173 CTTCTCCGGCCTCCACCA 61.003 66.667 0.00 0.00 0.00 4.17
141 176 2.528127 TTCTCCGGCCTCCACCAA 60.528 61.111 0.00 0.00 0.00 3.67
142 177 2.804828 CTTCTCCGGCCTCCACCAAC 62.805 65.000 0.00 0.00 0.00 3.77
143 178 4.410400 CTCCGGCCTCCACCAACC 62.410 72.222 0.00 0.00 0.00 3.77
248 332 2.731374 CGAATCTCCCGCTCCCTC 59.269 66.667 0.00 0.00 0.00 4.30
249 333 2.127869 CGAATCTCCCGCTCCCTCA 61.128 63.158 0.00 0.00 0.00 3.86
250 334 1.745264 GAATCTCCCGCTCCCTCAG 59.255 63.158 0.00 0.00 0.00 3.35
251 335 1.753368 GAATCTCCCGCTCCCTCAGG 61.753 65.000 0.00 0.00 0.00 3.86
327 421 1.446016 AGTAGGTGCCCTGGAACTTT 58.554 50.000 0.00 0.00 34.61 2.66
330 424 3.591977 AGTAGGTGCCCTGGAACTTTATT 59.408 43.478 0.00 0.00 34.61 1.40
331 425 3.542969 AGGTGCCCTGGAACTTTATTT 57.457 42.857 0.00 0.00 29.57 1.40
332 426 4.668138 AGGTGCCCTGGAACTTTATTTA 57.332 40.909 0.00 0.00 29.57 1.40
333 427 4.341487 AGGTGCCCTGGAACTTTATTTAC 58.659 43.478 0.00 0.00 29.57 2.01
344 438 9.167311 CTGGAACTTTATTTACAGTATGAAGCT 57.833 33.333 0.00 0.00 39.69 3.74
401 511 2.797156 GAGTACTCAACTGCAGTGTGTG 59.203 50.000 22.49 20.80 39.07 3.82
406 516 3.198068 CTCAACTGCAGTGTGTGTACTT 58.802 45.455 22.49 0.00 0.00 2.24
422 532 3.510753 TGTACTTGCCAGGTGACGTTATA 59.489 43.478 0.00 0.00 0.00 0.98
450 586 1.144057 CAGGGATCCGTGGTAGCAC 59.856 63.158 24.05 15.12 0.00 4.40
462 598 1.211212 TGGTAGCACTAGAGCTCGGTA 59.789 52.381 18.43 0.00 45.26 4.02
468 604 2.860582 GCACTAGAGCTCGGTATTCTGC 60.861 54.545 8.37 7.20 0.00 4.26
478 614 4.678309 GCTCGGTATTCTGCTGACTAGTTT 60.678 45.833 0.00 0.00 0.00 2.66
523 659 3.440127 TGATTTGGGAGGGGAATTCAAC 58.560 45.455 7.93 0.00 0.00 3.18
545 681 6.959606 ACTGTAGGAGCATATTATGGGAAT 57.040 37.500 5.84 0.00 0.00 3.01
548 684 7.667219 ACTGTAGGAGCATATTATGGGAATTTG 59.333 37.037 5.84 0.00 0.00 2.32
551 687 6.012745 AGGAGCATATTATGGGAATTTGACC 58.987 40.000 5.84 0.00 0.00 4.02
552 688 5.774690 GGAGCATATTATGGGAATTTGACCA 59.225 40.000 5.84 0.74 41.76 4.02
559 695 7.660030 ATTATGGGAATTTGACCAGTTTAGG 57.340 36.000 4.21 0.00 40.67 2.69
577 720 7.920682 CAGTTTAGGTTGTATGCAGTTTCTTTT 59.079 33.333 0.00 0.00 0.00 2.27
578 721 9.127277 AGTTTAGGTTGTATGCAGTTTCTTTTA 57.873 29.630 0.00 0.00 0.00 1.52
579 722 9.908152 GTTTAGGTTGTATGCAGTTTCTTTTAT 57.092 29.630 0.00 0.00 0.00 1.40
590 742 5.343325 GCAGTTTCTTTTATAGCTTGTGTGC 59.657 40.000 0.00 0.00 0.00 4.57
701 853 3.363084 GCTAATTCGCTAAAGGTCGATGC 60.363 47.826 0.00 0.00 34.48 3.91
742 896 4.365514 TGCAATCTCCTGGTTGAGTAAA 57.634 40.909 0.12 0.00 33.93 2.01
762 916 5.482686 AAATTTTCACACCAACATTGCAC 57.517 34.783 0.00 0.00 0.00 4.57
765 919 3.815856 TTCACACCAACATTGCACATT 57.184 38.095 0.00 0.00 0.00 2.71
767 921 2.692041 TCACACCAACATTGCACATTCA 59.308 40.909 0.00 0.00 0.00 2.57
768 922 3.054166 CACACCAACATTGCACATTCAG 58.946 45.455 0.00 0.00 0.00 3.02
798 952 7.559486 TGTATCATCTGTAGCAGTTCTGAAAT 58.441 34.615 3.84 0.00 32.61 2.17
803 957 8.918116 TCATCTGTAGCAGTTCTGAAATATACT 58.082 33.333 3.84 4.21 32.61 2.12
845 1004 5.370679 TGCTACTGTCACATGATGCATATT 58.629 37.500 0.00 0.00 0.00 1.28
861 1020 5.614308 TGCATATTATGGTTCTCAGACCTG 58.386 41.667 5.84 0.00 40.47 4.00
870 1029 3.432890 GGTTCTCAGACCTGGGATCAATC 60.433 52.174 0.00 0.00 40.24 2.67
876 1035 3.323403 CAGACCTGGGATCAATCTACTCC 59.677 52.174 0.00 0.00 0.00 3.85
893 1052 2.223971 ACTCCTACTTCGGTGTGTTGTG 60.224 50.000 0.00 0.00 30.16 3.33
897 1056 4.121317 CCTACTTCGGTGTGTTGTGTTAA 58.879 43.478 0.00 0.00 0.00 2.01
902 1061 6.391537 ACTTCGGTGTGTTGTGTTAATTTTT 58.608 32.000 0.00 0.00 0.00 1.94
944 1104 5.413833 CAGTGCTCTCATGTTCCACTAATTT 59.586 40.000 9.48 0.00 35.20 1.82
952 1112 7.882791 TCTCATGTTCCACTAATTTTTAGCTGA 59.117 33.333 0.00 0.00 0.00 4.26
1016 1176 4.093952 GATGCTGCTGCGTTGCGT 62.094 61.111 11.91 6.53 43.34 5.24
1083 1249 1.486726 CCTAGCCAGTTACAAGGAGGG 59.513 57.143 0.00 0.00 0.00 4.30
1118 1284 2.241941 TGGCCTTATGGAAGCATTCTCA 59.758 45.455 3.32 0.00 46.56 3.27
1128 1294 1.366679 AGCATTCTCACTCACATGCG 58.633 50.000 0.00 0.00 45.58 4.73
1241 1407 2.159014 TGGAGCAACAGTCTAAACACGT 60.159 45.455 0.00 0.00 0.00 4.49
1321 1487 7.824779 ACAAGTTTTCTAGTATTAGCTGGAAGG 59.175 37.037 0.00 0.00 37.30 3.46
1328 1494 3.451178 AGTATTAGCTGGAAGGCGAGAAA 59.549 43.478 0.00 0.00 37.29 2.52
1332 1498 1.021920 GCTGGAAGGCGAGAAAGACC 61.022 60.000 0.00 0.00 0.00 3.85
1344 1510 4.561105 CGAGAAAGACCAGAAGTTTAGCT 58.439 43.478 0.00 0.00 0.00 3.32
1370 1536 2.938956 ATAGGAGGTACAGGCATTGC 57.061 50.000 0.00 0.00 0.00 3.56
1371 1537 1.879575 TAGGAGGTACAGGCATTGCT 58.120 50.000 8.82 0.00 0.00 3.91
1420 1586 1.377202 GCAAATGCTGAGGGTCCGA 60.377 57.895 0.00 0.00 38.21 4.55
1442 1608 1.800805 GATGATGGCATCGGTACCAG 58.199 55.000 21.65 5.03 41.31 4.00
1443 1609 1.070758 GATGATGGCATCGGTACCAGT 59.929 52.381 21.65 0.00 41.31 4.00
1444 1610 1.783071 TGATGGCATCGGTACCAGTA 58.217 50.000 21.65 0.00 39.88 2.74
1445 1611 1.411246 TGATGGCATCGGTACCAGTAC 59.589 52.381 21.65 0.00 39.88 2.73
1446 1612 6.880243 GATGATGGCATCGGTACCAGTACC 62.880 54.167 21.65 15.71 43.30 3.34
1524 1702 0.320771 ATTCTGTCACCGGTGAGTGC 60.321 55.000 37.04 25.09 40.75 4.40
1624 1803 0.389391 CTGTCTCACACAAGACCCGT 59.611 55.000 1.88 0.00 44.17 5.28
1770 1951 7.526142 TTGGTATGTTTGTAATGTAAAGCCA 57.474 32.000 0.00 0.00 0.00 4.75
1812 1995 8.939929 TGAATATTGTTCTCAACACTGAAGATC 58.060 33.333 0.00 0.00 41.97 2.75
1825 2009 7.410120 ACACTGAAGATCTTTTTCTTGGTTT 57.590 32.000 9.87 0.00 36.10 3.27
1829 2013 7.340487 ACTGAAGATCTTTTTCTTGGTTTGTCT 59.660 33.333 9.87 0.00 36.10 3.41
1835 2019 7.931578 TCTTTTTCTTGGTTTGTCTTGTCTA 57.068 32.000 0.00 0.00 0.00 2.59
1838 2022 9.586435 CTTTTTCTTGGTTTGTCTTGTCTAAAT 57.414 29.630 0.00 0.00 0.00 1.40
1917 2101 6.183361 ACAGAGACTGAATGGTTAGTTCCTTT 60.183 38.462 5.76 0.00 35.18 3.11
2164 2923 7.334671 TGAGTAGTAGTATTAGCCATGATCTCG 59.665 40.741 0.00 0.00 0.00 4.04
2256 6117 6.216569 TGCAACAAGTTGTTTCACTTTTACA 58.783 32.000 18.59 3.90 38.77 2.41
2272 6143 6.573725 CACTTTTACATTCGCAAGTCAGTAAC 59.426 38.462 0.00 0.00 39.48 2.50
2292 6163 8.063200 AGTAACACTGATGTAGCACAATACTA 57.937 34.615 0.00 0.00 38.45 1.82
2308 6205 7.912250 GCACAATACTAATTCTCATTGACCTTG 59.088 37.037 10.93 0.00 33.56 3.61
2360 6260 3.805267 CCTCAAGGTGCTGCGATC 58.195 61.111 0.00 0.00 0.00 3.69
2445 6557 7.441890 AGACACGTCGATGAGAATCTATTAT 57.558 36.000 12.58 0.00 32.57 1.28
2448 6560 6.863645 ACACGTCGATGAGAATCTATTATTGG 59.136 38.462 12.58 0.00 34.92 3.16
2450 6562 6.208797 ACGTCGATGAGAATCTATTATTGGGA 59.791 38.462 12.58 0.00 34.92 4.37
2451 6563 6.749578 CGTCGATGAGAATCTATTATTGGGAG 59.250 42.308 0.00 0.00 34.92 4.30
2454 6580 8.740906 TCGATGAGAATCTATTATTGGGAGTAC 58.259 37.037 0.00 0.00 34.92 2.73
2523 6667 5.416947 AGGTACAAAGGCAGTAAGAATACG 58.583 41.667 0.00 0.00 37.11 3.06
2575 6722 0.531532 ATATGCGCGAAGAAGCAGCT 60.532 50.000 12.10 0.00 44.57 4.24
2614 6761 1.633774 CGGAGTATGGCCAGGAGTAT 58.366 55.000 13.05 0.00 0.00 2.12
2650 6797 3.534357 ATCCGAGTCCTCTATCATGGT 57.466 47.619 0.00 0.00 0.00 3.55
2687 6834 2.838736 CGCTGCATATACCAGGAAACT 58.161 47.619 0.00 0.00 46.44 2.66
2731 6884 3.565307 ACATTTGGAGCTCTGAAACCAA 58.435 40.909 14.64 5.91 40.05 3.67
2795 6950 6.095377 GCTTCCCAAATACATTTTCTGTCAG 58.905 40.000 0.00 0.00 39.39 3.51
2833 6991 2.440409 TGAGCTTCTTCCATTTGGAGC 58.560 47.619 0.00 0.21 46.36 4.70
2842 7000 6.363167 TCTTCCATTTGGAGCATCATTTTT 57.637 33.333 0.00 0.00 46.36 1.94
3043 7214 4.432712 GGCTAAAATTCGGCAAACATGAT 58.567 39.130 0.00 0.00 0.00 2.45
3066 7239 3.270877 AGATTCGGCAAACAGGACATAC 58.729 45.455 0.00 0.00 0.00 2.39
3071 7244 2.552315 CGGCAAACAGGACATACACTTT 59.448 45.455 0.00 0.00 0.00 2.66
3084 7260 4.630069 ACATACACTTTGGCGTTCTACATC 59.370 41.667 0.00 0.00 0.00 3.06
3157 7339 0.741221 GGCCGAAGAACTCGCTGAAT 60.741 55.000 0.00 0.00 46.71 2.57
3631 7967 0.348370 AGTGGGAGGAGGATTGGGAT 59.652 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.151710 TCGTGACGGGCCCATAGG 61.152 66.667 24.92 12.71 0.00 2.57
69 84 2.321719 GGAGGGGATTGGTCTACTCTC 58.678 57.143 0.00 0.00 31.93 3.20
133 168 1.852626 AGGGGAAGGGTTGGTGGAG 60.853 63.158 0.00 0.00 0.00 3.86
134 169 2.160171 CAGGGGAAGGGTTGGTGGA 61.160 63.158 0.00 0.00 0.00 4.02
135 170 2.440599 CAGGGGAAGGGTTGGTGG 59.559 66.667 0.00 0.00 0.00 4.61
136 171 1.497309 TAGCAGGGGAAGGGTTGGTG 61.497 60.000 0.00 0.00 0.00 4.17
137 172 1.151677 TAGCAGGGGAAGGGTTGGT 60.152 57.895 0.00 0.00 0.00 3.67
138 173 1.303282 GTAGCAGGGGAAGGGTTGG 59.697 63.158 0.00 0.00 0.00 3.77
139 174 1.303282 GGTAGCAGGGGAAGGGTTG 59.697 63.158 0.00 0.00 0.00 3.77
140 175 1.929088 GGGTAGCAGGGGAAGGGTT 60.929 63.158 0.00 0.00 0.00 4.11
141 176 2.286197 GGGTAGCAGGGGAAGGGT 60.286 66.667 0.00 0.00 0.00 4.34
142 177 3.480133 CGGGTAGCAGGGGAAGGG 61.480 72.222 0.00 0.00 0.00 3.95
219 281 1.646189 GAGATTCGCACCTTGAGACC 58.354 55.000 0.00 0.00 0.00 3.85
224 308 3.799753 CGGGAGATTCGCACCTTG 58.200 61.111 0.00 0.00 0.00 3.61
242 326 0.252012 AGACACCTGACCTGAGGGAG 60.252 60.000 2.38 0.00 37.45 4.30
247 331 3.009033 CCCAAATTAGACACCTGACCTGA 59.991 47.826 0.00 0.00 0.00 3.86
248 332 3.347216 CCCAAATTAGACACCTGACCTG 58.653 50.000 0.00 0.00 0.00 4.00
249 333 2.290960 GCCCAAATTAGACACCTGACCT 60.291 50.000 0.00 0.00 0.00 3.85
250 334 2.092323 GCCCAAATTAGACACCTGACC 58.908 52.381 0.00 0.00 0.00 4.02
251 335 2.749621 CAGCCCAAATTAGACACCTGAC 59.250 50.000 0.00 0.00 0.00 3.51
317 408 8.398665 GCTTCATACTGTAAATAAAGTTCCAGG 58.601 37.037 0.00 0.00 0.00 4.45
327 421 9.273016 GGCAATCTAAGCTTCATACTGTAAATA 57.727 33.333 0.00 0.00 0.00 1.40
330 424 6.055588 GGGCAATCTAAGCTTCATACTGTAA 58.944 40.000 0.00 0.00 0.00 2.41
331 425 5.130311 TGGGCAATCTAAGCTTCATACTGTA 59.870 40.000 0.00 0.00 0.00 2.74
332 426 4.080356 TGGGCAATCTAAGCTTCATACTGT 60.080 41.667 0.00 0.00 0.00 3.55
333 427 4.454678 TGGGCAATCTAAGCTTCATACTG 58.545 43.478 0.00 0.00 0.00 2.74
401 511 2.443887 TAACGTCACCTGGCAAGTAC 57.556 50.000 0.00 0.00 0.00 2.73
406 516 1.484653 AGCATATAACGTCACCTGGCA 59.515 47.619 0.00 0.00 0.00 4.92
422 532 1.043816 CGGATCCCTGTAGACAGCAT 58.956 55.000 6.06 0.00 42.47 3.79
450 586 2.881513 TCAGCAGAATACCGAGCTCTAG 59.118 50.000 12.85 5.58 34.61 2.43
462 598 2.746362 GCAGCAAACTAGTCAGCAGAAT 59.254 45.455 18.30 0.00 0.00 2.40
468 604 1.723542 CACGAGCAGCAAACTAGTCAG 59.276 52.381 0.00 0.00 0.00 3.51
478 614 0.239082 CATTTCAAGCACGAGCAGCA 59.761 50.000 7.77 0.00 45.49 4.41
523 659 7.884877 TCAAATTCCCATAATATGCTCCTACAG 59.115 37.037 0.00 0.00 0.00 2.74
545 681 5.133941 TGCATACAACCTAAACTGGTCAAA 58.866 37.500 0.00 0.00 39.83 2.69
548 684 4.324267 ACTGCATACAACCTAAACTGGTC 58.676 43.478 0.00 0.00 39.83 4.02
551 687 6.560253 AGAAACTGCATACAACCTAAACTG 57.440 37.500 0.00 0.00 0.00 3.16
552 688 7.582667 AAAGAAACTGCATACAACCTAAACT 57.417 32.000 0.00 0.00 0.00 2.66
559 695 9.065871 CAAGCTATAAAAGAAACTGCATACAAC 57.934 33.333 0.00 0.00 0.00 3.32
577 720 1.204704 ACTGAGCGCACACAAGCTATA 59.795 47.619 11.47 0.00 44.69 1.31
578 721 0.036952 ACTGAGCGCACACAAGCTAT 60.037 50.000 11.47 0.00 44.69 2.97
579 722 0.601057 TACTGAGCGCACACAAGCTA 59.399 50.000 11.47 0.00 44.69 3.32
581 724 0.095935 CATACTGAGCGCACACAAGC 59.904 55.000 11.47 0.00 0.00 4.01
590 742 4.017380 ACTAGTTCGAACATACTGAGCG 57.983 45.455 28.78 9.02 0.00 5.03
627 779 3.903530 ACAGGAAGAAAGGTCCCAATT 57.096 42.857 0.00 0.00 35.59 2.32
701 853 0.678395 AGCATAGAGGCTGATGACCG 59.322 55.000 9.61 0.00 43.89 4.79
742 896 4.134379 TGTGCAATGTTGGTGTGAAAAT 57.866 36.364 0.00 0.00 0.00 1.82
762 916 6.585702 GCTACAGATGATACAGCTACTGAATG 59.414 42.308 0.78 0.00 35.18 2.67
765 919 5.133221 TGCTACAGATGATACAGCTACTGA 58.867 41.667 0.78 0.00 35.18 3.41
767 921 5.136828 ACTGCTACAGATGATACAGCTACT 58.863 41.667 0.78 0.00 35.18 2.57
768 922 5.446143 ACTGCTACAGATGATACAGCTAC 57.554 43.478 0.78 0.00 35.18 3.58
845 1004 2.940514 TCCCAGGTCTGAGAACCATA 57.059 50.000 0.00 0.00 42.12 2.74
861 1020 4.218852 CCGAAGTAGGAGTAGATTGATCCC 59.781 50.000 0.00 0.00 33.30 3.85
870 1029 3.255149 ACAACACACCGAAGTAGGAGTAG 59.745 47.826 0.00 0.00 33.35 2.57
876 1035 5.917541 ATTAACACAACACACCGAAGTAG 57.082 39.130 0.00 0.00 0.00 2.57
902 1061 9.842775 AGAGCACTGATTCATCTCAAATATAAA 57.157 29.630 11.04 0.00 0.00 1.40
903 1062 9.486497 GAGAGCACTGATTCATCTCAAATATAA 57.514 33.333 9.22 0.00 37.07 0.98
904 1063 8.645110 TGAGAGCACTGATTCATCTCAAATATA 58.355 33.333 12.95 0.00 42.43 0.86
905 1064 7.506971 TGAGAGCACTGATTCATCTCAAATAT 58.493 34.615 12.95 0.00 42.43 1.28
944 1104 3.197766 ACATGTTCGGAGGATCAGCTAAA 59.802 43.478 0.00 0.00 36.25 1.85
952 1112 4.398319 ACTGAAAAACATGTTCGGAGGAT 58.602 39.130 12.39 0.00 35.66 3.24
1083 1249 0.607489 AGGCCATGCTCTGTGACAAC 60.607 55.000 5.01 0.00 0.00 3.32
1118 1284 2.233676 TGATAACTGACCGCATGTGAGT 59.766 45.455 8.11 3.85 43.83 3.41
1128 1294 5.010617 ACCCATTTTTGTGTGATAACTGACC 59.989 40.000 0.00 0.00 0.00 4.02
1321 1487 3.123790 GCTAAACTTCTGGTCTTTCTCGC 59.876 47.826 0.00 0.00 0.00 5.03
1366 1532 3.057946 GCGAAACTCAAGGAAAGAGCAAT 60.058 43.478 0.00 0.00 36.58 3.56
1367 1533 2.290641 GCGAAACTCAAGGAAAGAGCAA 59.709 45.455 0.00 0.00 36.58 3.91
1370 1536 3.134458 ACTGCGAAACTCAAGGAAAGAG 58.866 45.455 0.00 0.00 39.04 2.85
1371 1537 3.194005 ACTGCGAAACTCAAGGAAAGA 57.806 42.857 0.00 0.00 0.00 2.52
1420 1586 1.003580 GGTACCGATGCCATCATCCAT 59.996 52.381 5.40 0.00 44.83 3.41
1436 1602 3.340928 GAATTGTGGGTGGTACTGGTAC 58.659 50.000 2.58 2.58 35.40 3.34
1437 1603 2.306512 GGAATTGTGGGTGGTACTGGTA 59.693 50.000 0.00 0.00 0.00 3.25
1438 1604 1.074889 GGAATTGTGGGTGGTACTGGT 59.925 52.381 0.00 0.00 0.00 4.00
1439 1605 1.834188 GGAATTGTGGGTGGTACTGG 58.166 55.000 0.00 0.00 0.00 4.00
1440 1606 1.002659 TCGGAATTGTGGGTGGTACTG 59.997 52.381 0.00 0.00 0.00 2.74
1441 1607 1.354101 TCGGAATTGTGGGTGGTACT 58.646 50.000 0.00 0.00 0.00 2.73
1442 1608 2.188062 TTCGGAATTGTGGGTGGTAC 57.812 50.000 0.00 0.00 0.00 3.34
1443 1609 2.306219 TGATTCGGAATTGTGGGTGGTA 59.694 45.455 4.47 0.00 0.00 3.25
1444 1610 1.074727 TGATTCGGAATTGTGGGTGGT 59.925 47.619 4.47 0.00 0.00 4.16
1445 1611 1.832883 TGATTCGGAATTGTGGGTGG 58.167 50.000 4.47 0.00 0.00 4.61
1446 1612 2.358898 GGATGATTCGGAATTGTGGGTG 59.641 50.000 4.47 0.00 0.00 4.61
1447 1613 2.025416 TGGATGATTCGGAATTGTGGGT 60.025 45.455 4.47 0.00 0.00 4.51
1448 1614 2.358898 GTGGATGATTCGGAATTGTGGG 59.641 50.000 4.47 0.00 0.00 4.61
1449 1615 3.282021 AGTGGATGATTCGGAATTGTGG 58.718 45.455 4.47 0.00 0.00 4.17
1450 1616 5.118990 ACTAGTGGATGATTCGGAATTGTG 58.881 41.667 4.47 0.00 0.00 3.33
1451 1617 5.359194 ACTAGTGGATGATTCGGAATTGT 57.641 39.130 4.47 0.00 0.00 2.71
1452 1618 5.586243 ACAACTAGTGGATGATTCGGAATTG 59.414 40.000 3.64 0.00 0.00 2.32
1453 1619 5.586243 CACAACTAGTGGATGATTCGGAATT 59.414 40.000 3.64 0.00 44.69 2.17
1624 1803 0.328450 ACCATCCCCAGGAATGCCTA 60.328 55.000 0.00 0.00 44.80 3.93
1767 1946 5.643379 TTCATCAAAAGTATGACCTTGGC 57.357 39.130 0.00 0.00 33.18 4.52
1812 1995 8.980143 TTTAGACAAGACAAACCAAGAAAAAG 57.020 30.769 0.00 0.00 0.00 2.27
1855 2039 4.770795 ACTCATCAGCAACCTACCAATAC 58.229 43.478 0.00 0.00 0.00 1.89
1861 2045 6.818644 TCTTGATAAACTCATCAGCAACCTAC 59.181 38.462 0.00 0.00 36.34 3.18
1917 2101 5.470098 GTGAAGAAAGAACAACAGCAGGATA 59.530 40.000 0.00 0.00 0.00 2.59
2107 2859 9.691362 TTAAAATGCCTATCTCAACAGAAAAAC 57.309 29.630 0.00 0.00 30.24 2.43
2147 2906 8.723942 AAATATTCCGAGATCATGGCTAATAC 57.276 34.615 0.00 0.00 0.00 1.89
2148 2907 9.383519 GAAAATATTCCGAGATCATGGCTAATA 57.616 33.333 0.00 0.00 0.00 0.98
2149 2908 7.884877 TGAAAATATTCCGAGATCATGGCTAAT 59.115 33.333 0.00 0.00 34.49 1.73
2272 6143 8.654230 AGAATTAGTATTGTGCTACATCAGTG 57.346 34.615 0.00 0.00 0.00 3.66
2360 6260 2.544267 GGAGTGAAGACAGAAAACCACG 59.456 50.000 0.00 0.00 0.00 4.94
2410 6522 3.766151 TCGACGTGTCTATTGGAACATC 58.234 45.455 0.00 0.00 39.30 3.06
2421 6533 5.759506 AATAGATTCTCATCGACGTGTCT 57.240 39.130 0.00 0.00 34.17 3.41
2423 6535 6.863645 CCAATAATAGATTCTCATCGACGTGT 59.136 38.462 0.00 0.00 34.17 4.49
2460 6594 7.363181 GGCCGGATTTTAAAACTAAACCTACAT 60.363 37.037 5.05 0.00 0.00 2.29
2481 6615 1.374505 CAATGTTGCAAAGGGCCGG 60.375 57.895 0.00 0.00 43.89 6.13
2523 6667 2.159517 GGCATCCTGAAACACAACGATC 60.160 50.000 0.00 0.00 0.00 3.69
2575 6722 1.934589 CGATCGCTATCAAACCACCA 58.065 50.000 0.26 0.00 31.93 4.17
2650 6797 0.455410 GCGCTTCATAATGGCCACAA 59.545 50.000 8.16 0.00 0.00 3.33
2687 6834 0.178921 AGTCTTGACCTGGGCTCAGA 60.179 55.000 17.43 0.00 43.49 3.27
2731 6884 4.820173 GGCCAAGAACTTACTACAACTGTT 59.180 41.667 0.00 0.00 0.00 3.16
2733 6886 4.642429 AGGCCAAGAACTTACTACAACTG 58.358 43.478 5.01 0.00 0.00 3.16
2795 6950 8.519492 GAAGCTCAATGATTCTGACTATACTC 57.481 38.462 0.00 0.00 38.01 2.59
2924 7088 0.170116 CCAAGCCGATTTTTAGCGCA 59.830 50.000 11.47 0.00 0.00 6.09
3011 7180 4.499399 GCCGAATTTTAGCCGATTTTCTTC 59.501 41.667 0.00 0.00 0.00 2.87
3043 7214 3.410631 TGTCCTGTTTGCCGAATCTTA 57.589 42.857 0.00 0.00 0.00 2.10
3066 7239 4.749245 AAAGATGTAGAACGCCAAAGTG 57.251 40.909 0.00 0.00 0.00 3.16
3071 7244 7.324935 TCTATGTAAAAAGATGTAGAACGCCA 58.675 34.615 0.00 0.00 0.00 5.69
3122 7303 1.384989 GGCCTGTAGTCGCAGCTCTA 61.385 60.000 0.00 0.00 35.28 2.43
3128 7310 1.529152 TTCTTCGGCCTGTAGTCGCA 61.529 55.000 0.00 0.00 0.00 5.10
3172 7399 0.040603 AGAAGGACGACGACGACAAC 60.041 55.000 15.32 3.49 42.66 3.32
3173 7400 0.236711 GAGAAGGACGACGACGACAA 59.763 55.000 15.32 0.00 42.66 3.18
3174 7401 1.572085 GGAGAAGGACGACGACGACA 61.572 60.000 15.32 0.00 42.66 4.35
3345 7621 1.782201 TTGGGCACAGCTGGAGATGT 61.782 55.000 19.93 0.00 46.68 3.06
3438 7748 1.215382 CTCACCGCCATGAAGACGA 59.785 57.895 0.00 0.00 0.00 4.20
3575 7890 2.357517 CTTCAGCGTCAAGGCCGT 60.358 61.111 0.00 0.00 0.00 5.68
3631 7967 1.380515 CGGCTCCTCTTCCTCCTCA 60.381 63.158 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.