Multiple sequence alignment - TraesCS3B01G533200

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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 TraesCS3B01G533200 chr3B 100.000 2836 0 0 1 2836 773739736 773742571 0.000000e+00 5238.0
1 TraesCS3B01G533200 chr3B 90.758 660 33 12 1035 1679 773729125 773729771 0.000000e+00 856.0
2 TraesCS3B01G533200 chr3B 94.911 393 17 1 1234 1626 773907163 773906774 1.870000e-171 612.0
3 TraesCS3B01G533200 chr3B 79.779 272 48 6 2092 2360 258746415 258746682 1.040000e-44 191.0
4 TraesCS3B01G533200 chr3B 88.312 154 11 6 2513 2662 773729881 773730031 8.070000e-41 178.0
5 TraesCS3B01G533200 chr3B 81.818 209 26 9 473 672 773552303 773552508 6.290000e-37 165.0
6 TraesCS3B01G533200 chr3B 76.642 274 57 6 2100 2368 636267620 636267349 8.190000e-31 145.0
7 TraesCS3B01G533200 chr3A 91.689 1877 83 34 1 1828 714576796 714578648 0.000000e+00 2534.0
8 TraesCS3B01G533200 chr3A 89.779 587 45 10 1046 1626 714650847 714650270 0.000000e+00 737.0
9 TraesCS3B01G533200 chr3A 87.832 641 42 17 1035 1658 714574448 714575069 0.000000e+00 719.0
10 TraesCS3B01G533200 chr3A 88.636 396 44 1 2092 2486 714585521 714585916 5.490000e-132 481.0
11 TraesCS3B01G533200 chr3A 93.443 61 4 0 755 815 714566845 714566905 1.080000e-14 91.6
12 TraesCS3B01G533200 chr3A 84.416 77 3 6 960 1028 714559810 714559885 1.820000e-07 67.6
13 TraesCS3B01G533200 chr3D 92.129 902 36 18 987 1864 579376355 579377245 0.000000e+00 1240.0
14 TraesCS3B01G533200 chr3D 93.782 595 31 2 1035 1626 579592731 579592140 0.000000e+00 889.0
15 TraesCS3B01G533200 chr3D 87.915 662 44 18 1035 1679 579365715 579366357 0.000000e+00 747.0
16 TraesCS3B01G533200 chr3D 93.528 479 26 3 1 474 579375582 579376060 0.000000e+00 708.0
17 TraesCS3B01G533200 chr3D 88.718 585 39 6 1053 1613 579329778 579330359 0.000000e+00 689.0
18 TraesCS3B01G533200 chr3D 86.907 611 49 16 1902 2486 579377459 579378064 0.000000e+00 656.0
19 TraesCS3B01G533200 chr3D 90.090 222 17 4 738 956 579376070 579376289 1.660000e-72 283.0
20 TraesCS3B01G533200 chr3D 90.909 209 18 1 621 829 579327734 579327941 2.150000e-71 279.0
21 TraesCS3B01G533200 chr3D 83.279 305 20 9 2513 2789 579366524 579366825 4.690000e-63 252.0
22 TraesCS3B01G533200 chr3D 82.645 121 17 2 668 784 579297959 579298079 1.390000e-18 104.0
23 TraesCS3B01G533200 chr1B 84.615 312 32 11 1001 1306 378857957 378857656 2.140000e-76 296.0
24 TraesCS3B01G533200 chr4A 79.787 282 50 5 2106 2381 317085547 317085827 6.200000e-47 198.0
25 TraesCS3B01G533200 chr7A 76.989 352 69 7 2102 2442 207280984 207281334 1.040000e-44 191.0
26 TraesCS3B01G533200 chr7A 79.188 197 29 12 254 442 52343488 52343680 2.970000e-25 126.0
27 TraesCS3B01G533200 chr7A 79.188 197 29 12 254 442 52358920 52359112 2.970000e-25 126.0
28 TraesCS3B01G533200 chr5A 81.034 232 41 3 2106 2335 593713222 593712992 6.240000e-42 182.0
29 TraesCS3B01G533200 chr5A 81.081 185 29 5 265 445 374666327 374666509 2.950000e-30 143.0
30 TraesCS3B01G533200 chr2A 77.816 293 58 5 2095 2381 564216247 564216538 1.040000e-39 174.0
31 TraesCS3B01G533200 chr7B 78.327 263 51 5 2099 2356 78323579 78323840 6.290000e-37 165.0
32 TraesCS3B01G533200 chr6D 82.162 185 29 3 265 445 447891942 447892126 3.780000e-34 156.0
33 TraesCS3B01G533200 chrUn 81.675 191 30 5 265 450 79397080 79396890 1.360000e-33 154.0
34 TraesCS3B01G533200 chrUn 79.474 190 29 10 266 448 321378815 321378629 2.970000e-25 126.0
35 TraesCS3B01G533200 chr1D 80.000 190 33 4 265 449 80632771 80632582 4.930000e-28 135.0


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 TraesCS3B01G533200 chr3B 773739736 773742571 2835 False 5238.00 5238 100.0000 1 2836 1 chr3B.!!$F3 2835
1 TraesCS3B01G533200 chr3B 773729125 773730031 906 False 517.00 856 89.5350 1035 2662 2 chr3B.!!$F4 1627
2 TraesCS3B01G533200 chr3A 714574448 714578648 4200 False 1626.50 2534 89.7605 1 1828 2 chr3A.!!$F4 1827
3 TraesCS3B01G533200 chr3A 714650270 714650847 577 True 737.00 737 89.7790 1046 1626 1 chr3A.!!$R1 580
4 TraesCS3B01G533200 chr3D 579592140 579592731 591 True 889.00 889 93.7820 1035 1626 1 chr3D.!!$R1 591
5 TraesCS3B01G533200 chr3D 579375582 579378064 2482 False 721.75 1240 90.6635 1 2486 4 chr3D.!!$F4 2485
6 TraesCS3B01G533200 chr3D 579365715 579366825 1110 False 499.50 747 85.5970 1035 2789 2 chr3D.!!$F3 1754
7 TraesCS3B01G533200 chr3D 579327734 579330359 2625 False 484.00 689 89.8135 621 1613 2 chr3D.!!$F2 992

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
952 4832 0.035439 CGTGTTGGGCTGAATAGGGT 60.035 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 6841 0.179215 CAGTTTGAGCCGATCGCAAC 60.179 55.0 10.32 6.89 41.38 4.17 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
58 2407 5.892119 ACCAAGATCGACTAGATAAACCTGA 59.108 40.000 0.00 0.00 40.26 3.86
133 2482 0.608640 GACATCACCCGGACTGTTCT 59.391 55.000 0.73 0.00 0.00 3.01
294 2645 0.370273 CGGTAAAGACGCATGTGCTC 59.630 55.000 6.08 3.57 39.32 4.26
303 2654 4.415735 AGACGCATGTGCTCATATATACG 58.584 43.478 6.08 3.87 39.32 3.06
356 2709 1.837439 CACCCTAACCCTATGAGCACA 59.163 52.381 0.00 0.00 0.00 4.57
359 2712 3.527665 ACCCTAACCCTATGAGCACATTT 59.472 43.478 0.83 0.00 37.87 2.32
399 2752 9.974750 GGCATATTATCTTAAGATTAACGAAGC 57.025 33.333 22.60 16.44 36.05 3.86
424 2777 2.782222 GGGCGCCTCATAGTCGACA 61.782 63.158 28.56 4.13 31.86 4.35
475 2829 7.912778 AGCTCAGATATTTCTTTCCTCTAGT 57.087 36.000 0.00 0.00 0.00 2.57
477 2831 6.928492 GCTCAGATATTTCTTTCCTCTAGTGG 59.072 42.308 4.35 4.35 0.00 4.00
488 2842 2.037251 TCCTCTAGTGGTTGTTGCAGAC 59.963 50.000 10.56 0.00 0.00 3.51
490 2844 1.684450 TCTAGTGGTTGTTGCAGACGA 59.316 47.619 0.00 0.00 0.00 4.20
515 2869 1.615392 AGCTTGCAAGGGAAACATGAC 59.385 47.619 27.10 6.91 0.00 3.06
517 2871 0.958091 TTGCAAGGGAAACATGACGG 59.042 50.000 0.00 0.00 0.00 4.79
521 2875 0.893727 AAGGGAAACATGACGGGTGC 60.894 55.000 0.00 0.00 0.00 5.01
680 3040 3.803555 CGTTGCAGAAGAACTTCATCAC 58.196 45.455 15.43 6.70 41.84 3.06
710 3070 2.889756 GCCTTGACATTTCATTCCCCCT 60.890 50.000 0.00 0.00 0.00 4.79
713 3073 4.586001 CCTTGACATTTCATTCCCCCTATG 59.414 45.833 0.00 0.00 0.00 2.23
734 3094 3.006430 TGTGCCGGATATTATCGACATGT 59.994 43.478 5.05 0.00 0.00 3.21
736 3096 3.006430 TGCCGGATATTATCGACATGTGT 59.994 43.478 5.05 0.00 0.00 3.72
802 3162 3.672397 CAGAATTGATGCGTATCTCTCCG 59.328 47.826 14.76 0.00 34.31 4.63
849 4228 1.310216 ATGGCCGGCGTTAGTTTTCC 61.310 55.000 22.54 2.23 0.00 3.13
913 4793 4.802051 TGGGCCCGATTGAGCAGC 62.802 66.667 19.37 0.00 0.00 5.25
920 4800 0.101759 CCGATTGAGCAGCCCATTTG 59.898 55.000 0.00 0.00 0.00 2.32
952 4832 0.035439 CGTGTTGGGCTGAATAGGGT 60.035 55.000 0.00 0.00 0.00 4.34
959 4839 3.738434 TGGGCTGAATAGGGTAAGGTAA 58.262 45.455 0.00 0.00 0.00 2.85
967 4861 5.610982 TGAATAGGGTAAGGTAATGCTGGAT 59.389 40.000 0.00 0.00 0.00 3.41
976 4896 4.273318 AGGTAATGCTGGATGTCCTTTTC 58.727 43.478 0.09 0.00 36.82 2.29
989 4909 1.553704 TCCTTTTCTTAGCCGTCCCTC 59.446 52.381 0.00 0.00 0.00 4.30
990 4910 1.407025 CCTTTTCTTAGCCGTCCCTCC 60.407 57.143 0.00 0.00 0.00 4.30
992 4912 0.252558 TTTCTTAGCCGTCCCTCCCT 60.253 55.000 0.00 0.00 0.00 4.20
1023 4955 2.079925 GCATCTTCTTGTCTGGTGGTC 58.920 52.381 0.00 0.00 0.00 4.02
1051 5066 3.684413 GCCTTGACTTCATCGGGGAAATA 60.684 47.826 0.00 0.00 0.00 1.40
1095 5113 4.838152 CGGCGTGGAGGTGATGGG 62.838 72.222 0.00 0.00 0.00 4.00
1097 5115 3.399181 GCGTGGAGGTGATGGGGA 61.399 66.667 0.00 0.00 0.00 4.81
1596 5653 2.507992 CCGCAGCGTCAGGAAGAG 60.508 66.667 15.05 0.00 0.00 2.85
1758 5855 4.430765 GCATGTCCGTCCGTCCGT 62.431 66.667 0.00 0.00 0.00 4.69
1759 5856 2.202570 CATGTCCGTCCGTCCGTC 60.203 66.667 0.00 0.00 0.00 4.79
1868 5987 2.550487 GCCATAAGCGGTGTTCACA 58.450 52.632 5.32 0.00 0.00 3.58
1869 5988 0.878416 GCCATAAGCGGTGTTCACAA 59.122 50.000 5.32 0.00 0.00 3.33
1871 5990 2.680841 GCCATAAGCGGTGTTCACAATA 59.319 45.455 5.32 0.00 0.00 1.90
1873 5992 4.554723 GCCATAAGCGGTGTTCACAATATC 60.555 45.833 5.32 0.00 0.00 1.63
1874 5993 4.816385 CCATAAGCGGTGTTCACAATATCT 59.184 41.667 5.32 0.00 0.00 1.98
1898 6182 9.528018 TCTTATCTTTTTGTTAAGGCAAAACAG 57.472 29.630 4.06 5.76 44.77 3.16
1899 6183 9.528018 CTTATCTTTTTGTTAAGGCAAAACAGA 57.472 29.630 4.06 9.40 44.77 3.41
1900 6184 7.770801 ATCTTTTTGTTAAGGCAAAACAGAC 57.229 32.000 4.06 0.00 44.77 3.51
1916 6211 2.365617 ACAGACACTGATCCAAACTCGT 59.634 45.455 5.76 0.00 35.18 4.18
1920 6215 0.966920 ACTGATCCAAACTCGTCCGT 59.033 50.000 0.00 0.00 0.00 4.69
1969 6264 5.538877 TCAACCCTATCCTATCTCCAAACT 58.461 41.667 0.00 0.00 0.00 2.66
1993 6288 9.382275 ACTTCTGCACATGTTTTTCTTTAATTT 57.618 25.926 0.00 0.00 0.00 1.82
2098 6434 2.049063 GAGTTGCTCGACGTGCCT 60.049 61.111 18.25 9.55 0.00 4.75
2115 6451 3.129988 GTGCCTGGATTCTGATTTGGAAG 59.870 47.826 0.00 0.00 0.00 3.46
2128 6471 7.809238 TCTGATTTGGAAGTTGGATATGATCT 58.191 34.615 0.00 0.00 0.00 2.75
2134 6477 9.784531 TTTGGAAGTTGGATATGATCTTCTATC 57.215 33.333 0.00 0.00 36.02 2.08
2168 6511 2.818274 CTCCGGCGCCACCTTAAC 60.818 66.667 28.98 0.00 35.61 2.01
2182 6525 3.009033 CACCTTAACCCTCATCCTTCACA 59.991 47.826 0.00 0.00 0.00 3.58
2191 6534 5.044919 ACCCTCATCCTTCACAATCATGTTA 60.045 40.000 0.00 0.00 37.82 2.41
2219 6562 3.205784 TCACACAACATGTCATCACCA 57.794 42.857 0.00 0.00 40.64 4.17
2234 6577 1.979308 TCACCACCCATAAGTTTCCGA 59.021 47.619 0.00 0.00 0.00 4.55
2247 6590 8.421002 CCATAAGTTTCCGAATCCCATATTTTT 58.579 33.333 0.00 0.00 0.00 1.94
2293 6640 2.821969 CAGGCTTGGAGCACTACAAATT 59.178 45.455 2.04 0.00 44.75 1.82
2319 6666 5.422331 CCTCTCCACATCCTTACTAACTCAA 59.578 44.000 0.00 0.00 0.00 3.02
2323 6670 7.618117 TCTCCACATCCTTACTAACTCAATGTA 59.382 37.037 0.00 0.00 0.00 2.29
2326 6673 9.046296 CCACATCCTTACTAACTCAATGTATTC 57.954 37.037 0.00 0.00 0.00 1.75
2374 6721 7.496747 ACTAACTTGCTAAGAGATGATCTTCC 58.503 38.462 0.00 0.00 45.50 3.46
2405 6752 9.256228 GGAGGATATATAGATGTTGTAGACCAA 57.744 37.037 0.00 0.00 0.00 3.67
2448 6795 1.826096 TGCCCAATGACAATGTCCATG 59.174 47.619 11.24 9.41 0.00 3.66
2468 6816 2.222027 GGGCAGTATAGTTGCATGGAC 58.778 52.381 10.40 0.00 43.28 4.02
2486 6834 5.058149 TGGACATTTCAAAATCCATGTCG 57.942 39.130 2.90 0.00 44.39 4.35
2487 6835 4.522405 TGGACATTTCAAAATCCATGTCGT 59.478 37.500 2.90 0.00 44.39 4.34
2488 6836 5.010516 TGGACATTTCAAAATCCATGTCGTT 59.989 36.000 2.90 0.00 44.39 3.85
2489 6837 5.345741 GGACATTTCAAAATCCATGTCGTTG 59.654 40.000 5.33 0.00 44.39 4.10
2490 6838 5.229423 ACATTTCAAAATCCATGTCGTTGG 58.771 37.500 0.00 0.00 38.18 3.77
2497 6845 1.164411 TCCATGTCGTTGGATGTTGC 58.836 50.000 0.00 0.00 40.90 4.17
2498 6846 0.179192 CCATGTCGTTGGATGTTGCG 60.179 55.000 0.00 0.00 39.25 4.85
2499 6847 0.795698 CATGTCGTTGGATGTTGCGA 59.204 50.000 0.00 0.00 0.00 5.10
2500 6848 1.398041 CATGTCGTTGGATGTTGCGAT 59.602 47.619 0.00 0.00 35.78 4.58
2501 6849 1.075542 TGTCGTTGGATGTTGCGATC 58.924 50.000 0.00 0.00 35.78 3.69
2502 6850 0.025001 GTCGTTGGATGTTGCGATCG 59.975 55.000 11.69 11.69 35.78 3.69
2503 6851 1.081556 TCGTTGGATGTTGCGATCGG 61.082 55.000 18.30 0.00 0.00 4.18
2504 6852 1.062525 GTTGGATGTTGCGATCGGC 59.937 57.895 18.30 9.85 43.96 5.54
2505 6853 1.078497 TTGGATGTTGCGATCGGCT 60.078 52.632 18.30 0.00 44.05 5.52
2506 6854 1.089481 TTGGATGTTGCGATCGGCTC 61.089 55.000 18.30 0.16 44.05 4.70
2507 6855 1.521457 GGATGTTGCGATCGGCTCA 60.521 57.895 18.30 12.28 44.05 4.26
2508 6856 1.089481 GGATGTTGCGATCGGCTCAA 61.089 55.000 18.30 9.85 44.05 3.02
2509 6857 0.726827 GATGTTGCGATCGGCTCAAA 59.273 50.000 18.30 4.65 44.05 2.69
2510 6858 0.447801 ATGTTGCGATCGGCTCAAAC 59.552 50.000 18.30 9.98 44.05 2.93
2511 6859 0.602638 TGTTGCGATCGGCTCAAACT 60.603 50.000 18.30 0.00 44.05 2.66
2575 6923 0.438830 GCTCTGCCGTTTGTAAGTCG 59.561 55.000 0.00 0.00 0.00 4.18
2576 6924 1.779569 CTCTGCCGTTTGTAAGTCGT 58.220 50.000 0.00 0.00 0.00 4.34
2577 6925 1.719780 CTCTGCCGTTTGTAAGTCGTC 59.280 52.381 0.00 0.00 0.00 4.20
2582 6930 3.490526 TGCCGTTTGTAAGTCGTCTAAAC 59.509 43.478 0.00 0.00 0.00 2.01
2630 6982 4.511826 GTCAACTCAAGTCATTTCTCCGTT 59.488 41.667 0.00 0.00 0.00 4.44
2716 7093 3.580731 GTGCTCCAGACTTTACAGAGTC 58.419 50.000 0.00 0.00 45.05 3.36
2724 7101 1.067776 ACTTTACAGAGTCGAAGCCCG 60.068 52.381 0.00 0.00 40.25 6.13
2745 7122 6.725246 CCCGGATGAAAATACAGATACAAAC 58.275 40.000 0.73 0.00 0.00 2.93
2748 7125 7.910162 CCGGATGAAAATACAGATACAAACAAG 59.090 37.037 0.00 0.00 0.00 3.16
2757 7134 6.867662 ACAGATACAAACAAGACTTTCTGG 57.132 37.500 12.94 0.00 34.96 3.86
2784 7161 5.075858 CATGAGTACCATGCCACAAAATT 57.924 39.130 10.22 0.00 45.25 1.82
2789 7166 5.923204 AGTACCATGCCACAAAATTGAAAA 58.077 33.333 0.00 0.00 0.00 2.29
2790 7167 6.352516 AGTACCATGCCACAAAATTGAAAAA 58.647 32.000 0.00 0.00 0.00 1.94
2791 7168 6.997476 AGTACCATGCCACAAAATTGAAAAAT 59.003 30.769 0.00 0.00 0.00 1.82
2792 7169 6.316440 ACCATGCCACAAAATTGAAAAATC 57.684 33.333 0.00 0.00 0.00 2.17
2793 7170 5.826737 ACCATGCCACAAAATTGAAAAATCA 59.173 32.000 0.00 0.00 0.00 2.57
2794 7171 6.320672 ACCATGCCACAAAATTGAAAAATCAA 59.679 30.769 0.00 0.00 0.00 2.57
2795 7172 7.014422 ACCATGCCACAAAATTGAAAAATCAAT 59.986 29.630 0.00 0.00 41.59 2.57
2796 7173 8.512956 CCATGCCACAAAATTGAAAAATCAATA 58.487 29.630 4.62 0.00 39.18 1.90
2807 7184 9.887629 AATTGAAAAATCAATATATGTGCCACA 57.112 25.926 0.00 0.00 39.18 4.17
2808 7185 9.887629 ATTGAAAAATCAATATATGTGCCACAA 57.112 25.926 0.00 0.00 38.42 3.33
2809 7186 9.716531 TTGAAAAATCAATATATGTGCCACAAA 57.283 25.926 0.00 0.00 0.00 2.83
2810 7187 9.716531 TGAAAAATCAATATATGTGCCACAAAA 57.283 25.926 0.00 0.00 0.00 2.44
2814 7191 9.887629 AAATCAATATATGTGCCACAAAATTGA 57.112 25.926 23.41 23.41 38.11 2.57
2815 7192 9.887629 AATCAATATATGTGCCACAAAATTGAA 57.112 25.926 24.27 14.66 37.71 2.69
2816 7193 9.887629 ATCAATATATGTGCCACAAAATTGAAA 57.112 25.926 24.27 12.05 37.71 2.69
2817 7194 9.887629 TCAATATATGTGCCACAAAATTGAAAT 57.112 25.926 20.99 0.19 34.55 2.17
2819 7196 8.891671 ATATATGTGCCACAAAATTGAAATCC 57.108 30.769 0.00 0.00 0.00 3.01
2820 7197 3.388308 TGTGCCACAAAATTGAAATCCG 58.612 40.909 0.00 0.00 0.00 4.18
2821 7198 2.736192 GTGCCACAAAATTGAAATCCGG 59.264 45.455 0.00 0.00 0.00 5.14
2822 7199 2.630098 TGCCACAAAATTGAAATCCGGA 59.370 40.909 6.61 6.61 0.00 5.14
2823 7200 3.253230 GCCACAAAATTGAAATCCGGAG 58.747 45.455 11.34 0.00 0.00 4.63
2824 7201 3.253230 CCACAAAATTGAAATCCGGAGC 58.747 45.455 11.34 2.16 0.00 4.70
2825 7202 3.253230 CACAAAATTGAAATCCGGAGCC 58.747 45.455 11.34 1.56 0.00 4.70
2826 7203 3.056607 CACAAAATTGAAATCCGGAGCCT 60.057 43.478 11.34 0.00 0.00 4.58
2827 7204 3.578282 ACAAAATTGAAATCCGGAGCCTT 59.422 39.130 11.34 2.72 0.00 4.35
2828 7205 4.176271 CAAAATTGAAATCCGGAGCCTTC 58.824 43.478 11.34 13.05 0.00 3.46
2829 7206 2.806945 ATTGAAATCCGGAGCCTTCA 57.193 45.000 17.87 17.87 0.00 3.02
2830 7207 2.577606 TTGAAATCCGGAGCCTTCAA 57.422 45.000 24.52 24.52 35.88 2.69
2831 7208 1.821216 TGAAATCCGGAGCCTTCAAC 58.179 50.000 18.96 3.62 0.00 3.18
2832 7209 1.073125 TGAAATCCGGAGCCTTCAACA 59.927 47.619 18.96 5.66 0.00 3.33
2833 7210 1.740025 GAAATCCGGAGCCTTCAACAG 59.260 52.381 11.34 0.00 0.00 3.16
2834 7211 0.984230 AATCCGGAGCCTTCAACAGA 59.016 50.000 11.34 0.00 0.00 3.41
2835 7212 0.250513 ATCCGGAGCCTTCAACAGAC 59.749 55.000 11.34 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 2407 8.531146 GGTGCTTGCAATAATATATTTACCCAT 58.469 33.333 2.68 0.00 0.00 4.00
133 2482 2.825223 TCCTGGAAGCATCTCTTGAGA 58.175 47.619 2.59 2.59 34.56 3.27
294 2645 6.420604 TGGATGAATGTATGCGCGTATATATG 59.579 38.462 22.86 0.00 0.00 1.78
303 2654 6.742718 GTGTTTATATGGATGAATGTATGCGC 59.257 38.462 0.00 0.00 0.00 6.09
356 2709 0.674895 GCCGGCTCAGTCTGTCAAAT 60.675 55.000 22.15 0.00 0.00 2.32
359 2712 0.970427 TATGCCGGCTCAGTCTGTCA 60.970 55.000 29.70 2.45 0.00 3.58
399 2752 0.533755 CTATGAGGCGCCCTTGAAGG 60.534 60.000 26.15 3.69 31.76 3.46
437 2790 2.125912 AGCTAGCGCGTTCAGTGG 60.126 61.111 9.55 0.00 42.32 4.00
475 2829 2.535012 TACATCGTCTGCAACAACCA 57.465 45.000 0.00 0.00 0.00 3.67
477 2831 2.480419 AGCTTACATCGTCTGCAACAAC 59.520 45.455 0.00 0.00 0.00 3.32
488 2842 1.737838 TCCCTTGCAAGCTTACATCG 58.262 50.000 21.43 4.56 0.00 3.84
490 2844 3.230134 TGTTTCCCTTGCAAGCTTACAT 58.770 40.909 21.43 0.00 0.00 2.29
521 2875 3.343941 TGATTACGAAACTCCCTTGGG 57.656 47.619 0.00 0.00 0.00 4.12
680 3040 1.856629 AATGTCAAGGCCTCCCAATG 58.143 50.000 5.23 0.00 0.00 2.82
710 3070 5.105513 ACATGTCGATAATATCCGGCACATA 60.106 40.000 0.00 0.00 43.35 2.29
713 3073 3.367932 CACATGTCGATAATATCCGGCAC 59.632 47.826 0.00 0.00 43.35 5.01
736 3096 4.754618 CCAATTAAGTAGTGCGATATGGCA 59.245 41.667 8.48 8.48 41.45 4.92
802 3162 8.475639 TGTAAATGGAGATCACTAACTAAGGAC 58.524 37.037 0.00 0.00 0.00 3.85
876 4256 1.868997 CTGTAAAGCCACAGCACGG 59.131 57.895 0.00 0.00 43.56 4.94
952 4832 5.450818 AAAGGACATCCAGCATTACCTTA 57.549 39.130 0.00 0.00 38.89 2.69
959 4839 3.950395 GCTAAGAAAAGGACATCCAGCAT 59.050 43.478 0.00 0.00 38.89 3.79
967 4861 1.002773 GGGACGGCTAAGAAAAGGACA 59.997 52.381 0.00 0.00 0.00 4.02
976 4896 1.677637 GACAGGGAGGGACGGCTAAG 61.678 65.000 0.00 0.00 0.00 2.18
990 4910 4.899239 GATGCGGCGAGGGACAGG 62.899 72.222 12.98 0.00 0.00 4.00
992 4912 3.371097 GAAGATGCGGCGAGGGACA 62.371 63.158 12.98 0.00 0.00 4.02
1023 4955 1.424493 GATGAAGTCAAGGCTCGGCG 61.424 60.000 0.00 0.00 0.00 6.46
1051 5066 3.247162 GCCCAGATTTATCTCCTCCTCT 58.753 50.000 0.00 0.00 34.22 3.69
1086 5101 3.411517 CCGCCTTCCCCATCACCT 61.412 66.667 0.00 0.00 0.00 4.00
1097 5115 4.806339 CTCCTCCTCCCCCGCCTT 62.806 72.222 0.00 0.00 0.00 4.35
1370 5406 3.322466 CCGGTCCTCCCTGTTGCT 61.322 66.667 0.00 0.00 0.00 3.91
1493 5550 0.461516 TCCGTGATCTCGTACTCGCT 60.462 55.000 15.34 0.00 36.96 4.93
1494 5551 0.316032 GTCCGTGATCTCGTACTCGC 60.316 60.000 15.34 0.00 36.96 5.03
1627 5684 2.570135 CCTACCGAGTACTACTGACCC 58.430 57.143 0.00 0.00 0.00 4.46
1717 5782 1.154836 GACGAGCACAAGAAACGCG 60.155 57.895 3.53 3.53 0.00 6.01
1855 5974 6.349300 AGATAAGATATTGTGAACACCGCTT 58.651 36.000 2.46 0.00 0.00 4.68
1891 6175 5.505173 AGTTTGGATCAGTGTCTGTTTTG 57.495 39.130 0.00 0.00 32.61 2.44
1892 6176 4.273480 CGAGTTTGGATCAGTGTCTGTTTT 59.727 41.667 0.00 0.00 32.61 2.43
1894 6178 3.181465 ACGAGTTTGGATCAGTGTCTGTT 60.181 43.478 0.00 0.00 32.61 3.16
1898 6182 2.338500 GGACGAGTTTGGATCAGTGTC 58.662 52.381 0.00 0.00 0.00 3.67
1899 6183 1.336887 CGGACGAGTTTGGATCAGTGT 60.337 52.381 0.00 0.00 0.00 3.55
1900 6184 1.336887 ACGGACGAGTTTGGATCAGTG 60.337 52.381 0.00 0.00 0.00 3.66
1969 6264 9.376075 TGAAATTAAAGAAAAACATGTGCAGAA 57.624 25.926 0.00 0.00 0.00 3.02
2038 6333 7.916128 TTGTAAGATTCGAATTTCGCAAAAA 57.084 28.000 12.81 3.72 40.21 1.94
2039 6334 8.020819 AGATTGTAAGATTCGAATTTCGCAAAA 58.979 29.630 12.81 4.07 40.21 2.44
2040 6335 7.526608 AGATTGTAAGATTCGAATTTCGCAAA 58.473 30.769 12.81 4.78 40.21 3.68
2041 6336 7.072177 AGATTGTAAGATTCGAATTTCGCAA 57.928 32.000 12.81 14.33 40.21 4.85
2042 6337 6.662414 AGATTGTAAGATTCGAATTTCGCA 57.338 33.333 12.81 3.56 40.21 5.10
2043 6338 8.328864 AGTTAGATTGTAAGATTCGAATTTCGC 58.671 33.333 12.81 4.06 40.21 4.70
2050 6345 9.411801 GCATCATAGTTAGATTGTAAGATTCGA 57.588 33.333 0.00 0.00 0.00 3.71
2051 6346 9.416794 AGCATCATAGTTAGATTGTAAGATTCG 57.583 33.333 0.00 0.00 0.00 3.34
2073 6368 1.649664 GTCGAGCAACTCATGAGCAT 58.350 50.000 22.83 9.22 0.00 3.79
2098 6434 4.996793 TCCAACTTCCAAATCAGAATCCA 58.003 39.130 0.00 0.00 0.00 3.41
2128 6471 7.365117 GGAGGTCTGGAATTTGAGAAGATAGAA 60.365 40.741 0.00 0.00 0.00 2.10
2134 6477 3.265791 CGGAGGTCTGGAATTTGAGAAG 58.734 50.000 0.00 0.00 0.00 2.85
2166 6509 4.264083 ACATGATTGTGAAGGATGAGGGTT 60.264 41.667 0.00 0.00 33.85 4.11
2168 6511 3.894759 ACATGATTGTGAAGGATGAGGG 58.105 45.455 0.00 0.00 33.85 4.30
2191 6534 3.759618 TGACATGTTGTGTGATCATGCAT 59.240 39.130 0.00 0.00 42.36 3.96
2199 6542 2.877786 GTGGTGATGACATGTTGTGTGA 59.122 45.455 0.00 0.00 42.36 3.58
2201 6544 2.229792 GGTGGTGATGACATGTTGTGT 58.770 47.619 0.00 0.00 45.83 3.72
2219 6562 2.578940 TGGGATTCGGAAACTTATGGGT 59.421 45.455 0.00 0.00 0.00 4.51
2234 6577 5.765182 CGAGAGCCTGTAAAAATATGGGATT 59.235 40.000 0.00 0.00 0.00 3.01
2247 6590 2.626266 TGAAGTTGTTCGAGAGCCTGTA 59.374 45.455 0.00 0.00 35.17 2.74
2293 6640 5.590818 AGTTAGTAAGGATGTGGAGAGGAA 58.409 41.667 0.00 0.00 0.00 3.36
2319 6666 1.299541 CTCGCTTTGCCCGAATACAT 58.700 50.000 0.00 0.00 33.92 2.29
2323 6670 2.045926 AGCTCGCTTTGCCCGAAT 60.046 55.556 0.00 0.00 33.92 3.34
2326 6673 1.856265 AAAAGAGCTCGCTTTGCCCG 61.856 55.000 8.37 0.00 38.08 6.13
2356 6703 3.566351 TCGGGAAGATCATCTCTTAGCA 58.434 45.455 0.00 0.00 44.42 3.49
2358 6705 4.830046 TCCTTCGGGAAGATCATCTCTTAG 59.170 45.833 9.93 0.00 44.42 2.18
2374 6721 7.411486 ACAACATCTATATATCCTCCTTCGG 57.589 40.000 0.00 0.00 0.00 4.30
2399 6746 3.543680 ACATGCGCTACTATTTGGTCT 57.456 42.857 9.73 0.00 0.00 3.85
2400 6747 5.924475 ATAACATGCGCTACTATTTGGTC 57.076 39.130 9.73 0.00 0.00 4.02
2405 6752 7.818493 CATGACTATAACATGCGCTACTATT 57.182 36.000 9.73 0.00 38.58 1.73
2430 6777 1.758280 CCCATGGACATTGTCATTGGG 59.242 52.381 28.05 28.05 44.10 4.12
2448 6795 2.222027 GTCCATGCAACTATACTGCCC 58.778 52.381 0.00 0.00 39.13 5.36
2468 6816 5.468592 TCCAACGACATGGATTTTGAAATG 58.531 37.500 0.00 0.00 44.52 2.32
2486 6834 1.062525 GCCGATCGCAACATCCAAC 59.937 57.895 10.32 0.00 37.47 3.77
2487 6835 1.078497 AGCCGATCGCAACATCCAA 60.078 52.632 10.32 0.00 41.38 3.53
2488 6836 1.521457 GAGCCGATCGCAACATCCA 60.521 57.895 10.32 0.00 41.38 3.41
2489 6837 1.089481 TTGAGCCGATCGCAACATCC 61.089 55.000 10.32 0.00 41.38 3.51
2490 6838 0.726827 TTTGAGCCGATCGCAACATC 59.273 50.000 10.32 3.14 41.38 3.06
2491 6839 0.447801 GTTTGAGCCGATCGCAACAT 59.552 50.000 10.32 0.00 41.38 2.71
2492 6840 0.602638 AGTTTGAGCCGATCGCAACA 60.603 50.000 10.32 5.94 41.38 3.33
2493 6841 0.179215 CAGTTTGAGCCGATCGCAAC 60.179 55.000 10.32 6.89 41.38 4.17
2494 6842 0.320334 TCAGTTTGAGCCGATCGCAA 60.320 50.000 10.32 6.05 41.38 4.85
2495 6843 0.320334 TTCAGTTTGAGCCGATCGCA 60.320 50.000 10.32 0.00 41.38 5.10
2496 6844 1.009829 ATTCAGTTTGAGCCGATCGC 58.990 50.000 10.32 5.46 37.98 4.58
2497 6845 3.747099 AAATTCAGTTTGAGCCGATCG 57.253 42.857 8.51 8.51 0.00 3.69
2504 6852 7.702348 ATCCAAGGGACCAAATTCAGTTTGAG 61.702 42.308 0.00 0.00 41.34 3.02
2505 6853 5.931474 ATCCAAGGGACCAAATTCAGTTTGA 60.931 40.000 0.00 0.00 41.34 2.69
2506 6854 3.640967 TCCAAGGGACCAAATTCAGTTTG 59.359 43.478 0.00 0.00 45.44 2.93
2507 6855 3.922375 TCCAAGGGACCAAATTCAGTTT 58.078 40.909 0.00 0.00 0.00 2.66
2508 6856 3.611025 TCCAAGGGACCAAATTCAGTT 57.389 42.857 0.00 0.00 0.00 3.16
2509 6857 3.833559 ATCCAAGGGACCAAATTCAGT 57.166 42.857 0.00 0.00 32.98 3.41
2510 6858 5.240121 CAAAATCCAAGGGACCAAATTCAG 58.760 41.667 0.00 0.00 32.98 3.02
2511 6859 4.504689 GCAAAATCCAAGGGACCAAATTCA 60.505 41.667 0.00 0.00 32.98 2.57
2575 6923 9.436957 TGAGGAGAAAATGACTTATGTTTAGAC 57.563 33.333 0.00 0.00 0.00 2.59
2606 6957 4.202264 ACGGAGAAATGACTTGAGTTGACT 60.202 41.667 0.00 0.00 0.00 3.41
2619 6971 7.910162 CCTTATGTTGATGTTAACGGAGAAATG 59.090 37.037 0.26 0.00 33.28 2.32
2624 6976 6.737254 AACCTTATGTTGATGTTAACGGAG 57.263 37.500 0.26 0.00 35.31 4.63
2694 7071 2.029828 ACTCTGTAAAGTCTGGAGCACG 60.030 50.000 0.00 0.00 0.00 5.34
2695 7072 3.580731 GACTCTGTAAAGTCTGGAGCAC 58.419 50.000 0.00 0.00 42.01 4.40
2716 7093 2.285083 TGTATTTTCATCCGGGCTTCG 58.715 47.619 0.00 0.00 38.88 3.79
2724 7101 9.774742 GTCTTGTTTGTATCTGTATTTTCATCC 57.225 33.333 0.00 0.00 0.00 3.51
2745 7122 3.415212 TCATGCCTTCCAGAAAGTCTTG 58.585 45.455 0.00 0.00 32.69 3.02
2748 7125 3.064900 ACTCATGCCTTCCAGAAAGTC 57.935 47.619 0.00 0.00 32.69 3.01
2782 7159 9.887629 TTGTGGCACATATATTGATTTTTCAAT 57.112 25.926 22.73 6.47 44.52 2.57
2784 7161 9.716531 TTTTGTGGCACATATATTGATTTTTCA 57.283 25.926 22.73 0.00 44.52 2.69
2789 7166 9.887629 TTCAATTTTGTGGCACATATATTGATT 57.112 25.926 30.98 18.78 44.52 2.57
2790 7167 9.887629 TTTCAATTTTGTGGCACATATATTGAT 57.112 25.926 30.98 15.36 44.52 2.57
2791 7168 9.887629 ATTTCAATTTTGTGGCACATATATTGA 57.112 25.926 29.06 29.06 44.52 2.57
2793 7170 9.328845 GGATTTCAATTTTGTGGCACATATATT 57.671 29.630 22.73 16.92 44.52 1.28
2794 7171 7.652909 CGGATTTCAATTTTGTGGCACATATAT 59.347 33.333 22.73 12.00 44.52 0.86
2795 7172 6.977502 CGGATTTCAATTTTGTGGCACATATA 59.022 34.615 22.73 10.11 44.52 0.86
2796 7173 5.811613 CGGATTTCAATTTTGTGGCACATAT 59.188 36.000 22.73 14.88 44.52 1.78
2797 7174 5.167121 CGGATTTCAATTTTGTGGCACATA 58.833 37.500 22.73 14.47 44.52 2.29
2798 7175 3.995705 CGGATTTCAATTTTGTGGCACAT 59.004 39.130 22.73 3.32 44.52 3.21
2799 7176 3.388308 CGGATTTCAATTTTGTGGCACA 58.612 40.909 17.96 17.96 0.00 4.57
2800 7177 2.736192 CCGGATTTCAATTTTGTGGCAC 59.264 45.455 11.55 11.55 0.00 5.01
2801 7178 2.630098 TCCGGATTTCAATTTTGTGGCA 59.370 40.909 0.00 0.00 0.00 4.92
2802 7179 3.253230 CTCCGGATTTCAATTTTGTGGC 58.747 45.455 3.57 0.00 0.00 5.01
2803 7180 3.253230 GCTCCGGATTTCAATTTTGTGG 58.747 45.455 3.57 0.00 0.00 4.17
2804 7181 3.056607 AGGCTCCGGATTTCAATTTTGTG 60.057 43.478 3.57 0.00 0.00 3.33
2805 7182 3.165071 AGGCTCCGGATTTCAATTTTGT 58.835 40.909 3.57 0.00 0.00 2.83
2806 7183 3.874392 AGGCTCCGGATTTCAATTTTG 57.126 42.857 3.57 0.00 0.00 2.44
2807 7184 3.831911 TGAAGGCTCCGGATTTCAATTTT 59.168 39.130 18.43 2.05 0.00 1.82
2808 7185 3.430453 TGAAGGCTCCGGATTTCAATTT 58.570 40.909 18.43 3.36 0.00 1.82
2809 7186 3.085952 TGAAGGCTCCGGATTTCAATT 57.914 42.857 18.43 4.51 0.00 2.32
2810 7187 2.755103 GTTGAAGGCTCCGGATTTCAAT 59.245 45.455 27.41 7.88 40.43 2.57
2811 7188 2.159382 GTTGAAGGCTCCGGATTTCAA 58.841 47.619 23.90 23.90 37.25 2.69
2812 7189 1.073125 TGTTGAAGGCTCCGGATTTCA 59.927 47.619 17.38 17.38 0.00 2.69
2813 7190 1.740025 CTGTTGAAGGCTCCGGATTTC 59.260 52.381 3.57 10.44 0.00 2.17
2814 7191 1.351017 TCTGTTGAAGGCTCCGGATTT 59.649 47.619 3.57 0.00 0.00 2.17
2815 7192 0.984230 TCTGTTGAAGGCTCCGGATT 59.016 50.000 3.57 0.00 0.00 3.01
2816 7193 0.250513 GTCTGTTGAAGGCTCCGGAT 59.749 55.000 3.57 0.00 0.00 4.18
2817 7194 1.671742 GTCTGTTGAAGGCTCCGGA 59.328 57.895 2.93 2.93 0.00 5.14
2818 7195 4.285851 GTCTGTTGAAGGCTCCGG 57.714 61.111 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.