Multiple sequence alignment - TraesCS2A01G547000

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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 TraesCS2A01G547000 chr2A 100.000 4097 0 0 499 4595 755368257 755364161 0.000000e+00 7566
1 TraesCS2A01G547000 chr2A 84.363 793 90 17 3335 4116 755045619 755046388 0.000000e+00 747
2 TraesCS2A01G547000 chr2A 100.000 173 0 0 1 173 755368755 755368583 2.060000e-83 320
3 TraesCS2A01G547000 chr2A 84.000 125 19 1 1429 1553 755427864 755427741 8.080000e-23 119
4 TraesCS2A01G547000 chr2B 93.976 1660 87 10 2946 4595 765921940 765920284 0.000000e+00 2499
5 TraesCS2A01G547000 chr2B 91.460 1007 72 13 1865 2865 765922936 765921938 0.000000e+00 1371
6 TraesCS2A01G547000 chr2B 94.588 850 35 7 924 1763 765923908 765923060 0.000000e+00 1304
7 TraesCS2A01G547000 chr2B 93.333 150 9 1 3 151 568660340 568660191 2.150000e-53 220
8 TraesCS2A01G547000 chr2D 93.908 1658 88 12 2946 4595 624096444 624094792 0.000000e+00 2490
9 TraesCS2A01G547000 chr2D 93.188 734 37 8 921 1642 624098616 624097884 0.000000e+00 1066
10 TraesCS2A01G547000 chr2D 88.127 598 60 8 1947 2534 624097470 624096874 0.000000e+00 701
11 TraesCS2A01G547000 chr7D 91.747 1660 111 19 2946 4595 534336058 534334415 0.000000e+00 2283
12 TraesCS2A01G547000 chr7D 90.457 1006 62 16 1866 2865 534337033 534336056 0.000000e+00 1295
13 TraesCS2A01G547000 chr7D 92.966 853 41 9 921 1763 534338001 534337158 0.000000e+00 1225
14 TraesCS2A01G547000 chr4B 88.679 424 35 6 1953 2366 378001367 378001787 5.310000e-139 505
15 TraesCS2A01G547000 chr4B 88.208 424 37 6 1953 2366 14570294 14569874 1.150000e-135 494
16 TraesCS2A01G547000 chr4B 91.038 212 19 0 2946 3157 378002199 378002410 2.090000e-73 287
17 TraesCS2A01G547000 chr4B 89.238 223 24 0 2946 3168 14569462 14569240 3.500000e-71 279
18 TraesCS2A01G547000 chr4B 90.303 165 16 0 619 783 174441577 174441741 2.780000e-52 217
19 TraesCS2A01G547000 chr4B 96.512 86 3 0 2864 2949 437940379 437940464 4.790000e-30 143
20 TraesCS2A01G547000 chr4B 91.579 95 8 0 2857 2951 453246339 453246245 1.040000e-26 132
21 TraesCS2A01G547000 chr4D 91.667 252 12 7 581 828 58912220 58911974 1.580000e-89 340
22 TraesCS2A01G547000 chr4D 95.890 146 5 1 1 145 58912940 58912795 7.690000e-58 235
23 TraesCS2A01G547000 chr4D 95.294 85 4 0 2864 2948 485409435 485409351 8.020000e-28 135
24 TraesCS2A01G547000 chr6B 87.019 208 22 3 619 825 560634803 560634600 3.580000e-56 230
25 TraesCS2A01G547000 chr6B 92.949 156 11 0 1 156 560657791 560657636 1.290000e-55 228
26 TraesCS2A01G547000 chr6B 92.715 151 10 1 7 156 560635139 560634989 2.780000e-52 217
27 TraesCS2A01G547000 chr6B 88.827 179 16 2 619 796 560657163 560656988 2.780000e-52 217
28 TraesCS2A01G547000 chrUn 90.566 159 12 3 1 158 50283951 50284107 1.680000e-49 207
29 TraesCS2A01G547000 chrUn 88.608 158 18 0 3011 3168 256117885 256117728 4.690000e-45 193
30 TraesCS2A01G547000 chrUn 88.608 158 18 0 3011 3168 342150559 342150716 4.690000e-45 193
31 TraesCS2A01G547000 chrUn 88.608 158 18 0 3011 3168 342153049 342153206 4.690000e-45 193
32 TraesCS2A01G547000 chr3B 88.506 174 11 7 1 170 818189207 818189039 7.800000e-48 202
33 TraesCS2A01G547000 chr1D 88.889 162 18 0 3007 3168 437804163 437804324 2.800000e-47 200
34 TraesCS2A01G547000 chr1D 96.471 85 3 0 2864 2948 6335508 6335592 1.720000e-29 141
35 TraesCS2A01G547000 chr5B 87.931 174 12 7 1 170 487469118 487469286 3.630000e-46 196
36 TraesCS2A01G547000 chr5B 95.455 88 4 0 2861 2948 429030605 429030692 1.720000e-29 141
37 TraesCS2A01G547000 chr5B 91.579 95 7 1 2856 2949 100033885 100033979 3.730000e-26 130
38 TraesCS2A01G547000 chr7A 87.356 174 13 7 1 170 11039325 11039157 1.690000e-44 191
39 TraesCS2A01G547000 chr3A 87.356 174 13 7 1 170 550444599 550444431 1.690000e-44 191
40 TraesCS2A01G547000 chr5A 84.906 159 13 7 571 725 569992927 569993078 2.860000e-32 150
41 TraesCS2A01G547000 chr5A 91.579 95 7 1 2854 2948 339739756 339739849 3.730000e-26 130
42 TraesCS2A01G547000 chr6A 95.604 91 4 0 2862 2952 101438364 101438274 3.700000e-31 147
43 TraesCS2A01G547000 chr6A 92.632 95 5 2 2862 2955 511530184 511530091 8.020000e-28 135


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 TraesCS2A01G547000 chr2A 755364161 755368755 4594 True 3943.000000 7566 100.000000 1 4595 2 chr2A.!!$R2 4594
1 TraesCS2A01G547000 chr2A 755045619 755046388 769 False 747.000000 747 84.363000 3335 4116 1 chr2A.!!$F1 781
2 TraesCS2A01G547000 chr2B 765920284 765923908 3624 True 1724.666667 2499 93.341333 924 4595 3 chr2B.!!$R2 3671
3 TraesCS2A01G547000 chr2D 624094792 624098616 3824 True 1419.000000 2490 91.741000 921 4595 3 chr2D.!!$R1 3674
4 TraesCS2A01G547000 chr7D 534334415 534338001 3586 True 1601.000000 2283 91.723333 921 4595 3 chr7D.!!$R1 3674
5 TraesCS2A01G547000 chr4B 378001367 378002410 1043 False 396.000000 505 89.858500 1953 3157 2 chr4B.!!$F3 1204
6 TraesCS2A01G547000 chr4B 14569240 14570294 1054 True 386.500000 494 88.723000 1953 3168 2 chr4B.!!$R2 1215
7 TraesCS2A01G547000 chr4D 58911974 58912940 966 True 287.500000 340 93.778500 1 828 2 chr4D.!!$R2 827
8 TraesCS2A01G547000 chr6B 560634600 560635139 539 True 223.500000 230 89.867000 7 825 2 chr6B.!!$R1 818
9 TraesCS2A01G547000 chr6B 560656988 560657791 803 True 222.500000 228 90.888000 1 796 2 chr6B.!!$R2 795

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
806 1292 0.661187 GCGACGTACGACCAGAAACA 60.661 55.000 24.41 0.0 45.77 2.83 F
807 1293 1.324718 CGACGTACGACCAGAAACAG 58.675 55.000 24.41 0.0 45.77 3.16 F
1348 1872 1.517361 CTCATCCGGCAGTACAGCA 59.483 57.895 12.66 0.0 35.83 4.41 F
2446 3171 1.004185 GAGCATGCAAGCACGTAGATG 60.004 52.381 21.98 0.0 36.85 2.90 F
3072 3925 1.021202 TGCGTGAAAAACTGTGGGAG 58.979 50.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 3151 1.004185 CATCTACGTGCTTGCATGCTC 60.004 52.381 23.31 18.87 0.00 4.26 R
2436 3161 1.990563 ACAAACGCTACATCTACGTGC 59.009 47.619 0.00 0.00 40.44 5.34 R
2926 3776 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71 R
3445 4298 0.179034 GGGGCAGAGACCTTGCTATG 60.179 60.000 0.00 0.00 0.00 2.23 R
4382 5272 0.401356 TTCTGCACCTGCTTGGATCA 59.599 50.000 0.00 0.76 42.66 2.92 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
593 1079 4.806339 CTCTTCCTCCCCGCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
647 1133 3.764466 CCCTCTTCACGGAGCGCT 61.764 66.667 11.27 11.27 32.43 5.92
783 1269 4.500375 CCTCAGGGACTTTTCTGCAAAAAG 60.500 45.833 21.93 21.93 41.63 2.27
788 1274 2.809446 ACTTTTCTGCAAAAAGTCGGC 58.191 42.857 22.81 0.00 44.50 5.54
789 1275 1.780860 CTTTTCTGCAAAAAGTCGGCG 59.219 47.619 18.25 0.00 33.72 6.46
804 1290 1.081242 GGCGACGTACGACCAGAAA 60.081 57.895 24.41 0.00 45.37 2.52
806 1292 0.661187 GCGACGTACGACCAGAAACA 60.661 55.000 24.41 0.00 45.77 2.83
807 1293 1.324718 CGACGTACGACCAGAAACAG 58.675 55.000 24.41 0.00 45.77 3.16
809 1295 2.096268 CGACGTACGACCAGAAACAGTA 60.096 50.000 24.41 0.00 45.77 2.74
811 1297 2.248487 CGTACGACCAGAAACAGTAGC 58.752 52.381 10.44 0.00 0.00 3.58
813 1299 2.726832 ACGACCAGAAACAGTAGCTC 57.273 50.000 0.00 0.00 0.00 4.09
1113 1621 2.041265 TTCCTCCTCCTCAGGCCC 59.959 66.667 0.00 0.00 40.12 5.80
1117 1625 3.284251 TCCTCCTCAGGCCCTCCA 61.284 66.667 0.00 0.00 40.12 3.86
1118 1626 2.040043 CCTCCTCAGGCCCTCCAT 60.040 66.667 0.00 0.00 30.98 3.41
1120 1628 2.040464 TCCTCAGGCCCTCCATCC 60.040 66.667 0.00 0.00 33.74 3.51
1122 1630 3.554342 CTCAGGCCCTCCATCCCG 61.554 72.222 0.00 0.00 33.74 5.14
1130 1651 3.878667 CTCCATCCCGCCCTTCCC 61.879 72.222 0.00 0.00 0.00 3.97
1163 1684 3.238497 CACCACCGACCCTGACCA 61.238 66.667 0.00 0.00 0.00 4.02
1168 1692 4.373116 CCGACCCTGACCACCACG 62.373 72.222 0.00 0.00 0.00 4.94
1348 1872 1.517361 CTCATCCGGCAGTACAGCA 59.483 57.895 12.66 0.00 35.83 4.41
1533 2057 1.925888 CAGGAAGGAGGGGAATGGG 59.074 63.158 0.00 0.00 0.00 4.00
1542 2066 2.449450 GGGGAATGGGGACTACCGG 61.449 68.421 0.00 0.00 41.60 5.28
1763 2287 6.094881 GCATAGCTGGTTAAGTTTCATGGTTA 59.905 38.462 0.00 0.00 0.00 2.85
1764 2288 7.679638 GCATAGCTGGTTAAGTTTCATGGTTAG 60.680 40.741 0.00 0.00 0.00 2.34
1765 2289 4.459337 AGCTGGTTAAGTTTCATGGTTAGC 59.541 41.667 0.00 0.00 0.00 3.09
1766 2290 4.217550 GCTGGTTAAGTTTCATGGTTAGCA 59.782 41.667 0.00 0.00 0.00 3.49
1767 2291 5.105756 GCTGGTTAAGTTTCATGGTTAGCAT 60.106 40.000 0.00 0.00 0.00 3.79
1769 2293 7.385778 TGGTTAAGTTTCATGGTTAGCATAC 57.614 36.000 0.00 0.00 0.00 2.39
1770 2294 7.172342 TGGTTAAGTTTCATGGTTAGCATACT 58.828 34.615 0.00 0.00 0.00 2.12
1773 2297 9.158233 GTTAAGTTTCATGGTTAGCATACTGTA 57.842 33.333 0.00 0.00 0.00 2.74
1774 2298 9.727859 TTAAGTTTCATGGTTAGCATACTGTAA 57.272 29.630 0.00 0.00 0.00 2.41
1775 2299 8.630054 AAGTTTCATGGTTAGCATACTGTAAA 57.370 30.769 0.00 0.00 0.00 2.01
1776 2300 8.807948 AGTTTCATGGTTAGCATACTGTAAAT 57.192 30.769 0.00 0.00 0.00 1.40
1781 2305 8.710239 TCATGGTTAGCATACTGTAAATTAGGA 58.290 33.333 0.00 0.00 0.00 2.94
1785 2309 9.338622 GGTTAGCATACTGTAAATTAGGACAAT 57.661 33.333 0.00 0.00 0.00 2.71
1787 2311 9.899661 TTAGCATACTGTAAATTAGGACAATGT 57.100 29.630 0.00 0.00 0.00 2.71
1788 2312 8.438676 AGCATACTGTAAATTAGGACAATGTC 57.561 34.615 4.51 4.51 0.00 3.06
1789 2313 8.046708 AGCATACTGTAAATTAGGACAATGTCA 58.953 33.333 15.86 0.00 33.68 3.58
1790 2314 8.338259 GCATACTGTAAATTAGGACAATGTCAG 58.662 37.037 15.86 3.74 33.68 3.51
1791 2315 9.383519 CATACTGTAAATTAGGACAATGTCAGT 57.616 33.333 15.86 9.36 36.58 3.41
1793 2317 7.224297 ACTGTAAATTAGGACAATGTCAGTGT 58.776 34.615 15.86 5.45 33.68 3.55
1794 2318 7.173218 ACTGTAAATTAGGACAATGTCAGTGTG 59.827 37.037 11.24 0.00 33.68 3.82
1796 2320 5.947228 AATTAGGACAATGTCAGTGTGTG 57.053 39.130 11.24 0.00 33.68 3.82
1829 2402 8.876181 TGCCTATTAGCACAATTTAGTATAGGA 58.124 33.333 0.00 0.00 38.00 2.94
1863 2483 9.336171 ACTGTAATTTTATTTGCACAATTTGGT 57.664 25.926 0.78 0.00 0.00 3.67
1870 2490 9.646427 TTTTATTTGCACAATTTGGTATAGGAC 57.354 29.630 0.78 0.00 0.00 3.85
1893 2599 8.947115 GGACAGAAACTTATATTAGCACAGTTT 58.053 33.333 0.00 0.00 39.76 2.66
1936 2643 7.744087 TGTACTTTTATGCAAGTGAAGTGAT 57.256 32.000 14.54 0.00 37.57 3.06
1943 2650 3.151554 TGCAAGTGAAGTGATGCAGAAT 58.848 40.909 0.00 0.00 43.32 2.40
1961 2670 7.215789 TGCAGAATCATTTGGTGTATTGTTTT 58.784 30.769 0.00 0.00 0.00 2.43
2200 2909 5.300034 TCAAGTGTCATTGCTGAAAGATGTT 59.700 36.000 0.00 0.00 34.07 2.71
2263 2972 1.886542 GAAAATATGGATCGCCCCACC 59.113 52.381 0.00 0.00 39.34 4.61
2396 3113 4.658713 CACATCTTGTGCTTGACTGTAG 57.341 45.455 0.00 0.00 41.89 2.74
2439 3164 4.100707 TCATAAAAGAGCATGCAAGCAC 57.899 40.909 21.98 10.19 36.85 4.40
2443 3168 1.081892 AAGAGCATGCAAGCACGTAG 58.918 50.000 21.98 0.00 36.85 3.51
2446 3171 1.004185 GAGCATGCAAGCACGTAGATG 60.004 52.381 21.98 0.00 36.85 2.90
2450 3175 1.640428 TGCAAGCACGTAGATGTAGC 58.360 50.000 0.00 0.00 0.00 3.58
2614 3424 6.765915 ATTCTACTTCAAAATCTTCCAGGC 57.234 37.500 0.00 0.00 0.00 4.85
2697 3513 9.896645 TCTATATTTATTCCAGGAAGCATCATC 57.103 33.333 8.20 0.00 0.00 2.92
2751 3567 4.892934 ACCATTTTGCTTTCAACAGGACTA 59.107 37.500 0.00 0.00 30.75 2.59
2753 3569 6.041979 ACCATTTTGCTTTCAACAGGACTATT 59.958 34.615 0.00 0.00 30.75 1.73
2755 3571 8.087750 CCATTTTGCTTTCAACAGGACTATTTA 58.912 33.333 0.00 0.00 30.75 1.40
2756 3572 9.643693 CATTTTGCTTTCAACAGGACTATTTAT 57.356 29.630 0.00 0.00 30.75 1.40
2758 3574 6.662414 TGCTTTCAACAGGACTATTTATCG 57.338 37.500 0.00 0.00 0.00 2.92
2759 3575 5.064707 TGCTTTCAACAGGACTATTTATCGC 59.935 40.000 0.00 0.00 0.00 4.58
2760 3576 5.294552 GCTTTCAACAGGACTATTTATCGCT 59.705 40.000 0.00 0.00 0.00 4.93
2775 3591 5.712217 TTATCGCTTTATGCAGTGTACAC 57.288 39.130 18.56 18.56 43.06 2.90
2865 3715 7.444487 AGACTAGGTTGTTCCTTTGATTTGTAC 59.556 37.037 0.00 0.00 45.67 2.90
2866 3716 7.287810 ACTAGGTTGTTCCTTTGATTTGTACT 58.712 34.615 0.00 0.00 45.67 2.73
2867 3717 6.635030 AGGTTGTTCCTTTGATTTGTACTC 57.365 37.500 0.00 0.00 45.67 2.59
2868 3718 5.535030 AGGTTGTTCCTTTGATTTGTACTCC 59.465 40.000 0.00 0.00 45.67 3.85
2869 3719 5.278808 GGTTGTTCCTTTGATTTGTACTCCC 60.279 44.000 0.00 0.00 0.00 4.30
2870 3720 5.319043 TGTTCCTTTGATTTGTACTCCCT 57.681 39.130 0.00 0.00 0.00 4.20
2871 3721 5.313712 TGTTCCTTTGATTTGTACTCCCTC 58.686 41.667 0.00 0.00 0.00 4.30
2872 3722 5.073144 TGTTCCTTTGATTTGTACTCCCTCT 59.927 40.000 0.00 0.00 0.00 3.69
2873 3723 5.165961 TCCTTTGATTTGTACTCCCTCTG 57.834 43.478 0.00 0.00 0.00 3.35
2874 3724 4.597507 TCCTTTGATTTGTACTCCCTCTGT 59.402 41.667 0.00 0.00 0.00 3.41
2875 3725 4.938226 CCTTTGATTTGTACTCCCTCTGTC 59.062 45.833 0.00 0.00 0.00 3.51
2876 3726 4.553330 TTGATTTGTACTCCCTCTGTCC 57.447 45.455 0.00 0.00 0.00 4.02
2877 3727 2.838202 TGATTTGTACTCCCTCTGTCCC 59.162 50.000 0.00 0.00 0.00 4.46
2878 3728 2.409064 TTTGTACTCCCTCTGTCCCA 57.591 50.000 0.00 0.00 0.00 4.37
2879 3729 2.642171 TTGTACTCCCTCTGTCCCAT 57.358 50.000 0.00 0.00 0.00 4.00
2880 3730 3.769189 TTGTACTCCCTCTGTCCCATA 57.231 47.619 0.00 0.00 0.00 2.74
2881 3731 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
2882 3732 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
2883 3733 3.967326 TGTACTCCCTCTGTCCCATAATG 59.033 47.826 0.00 0.00 0.00 1.90
2884 3734 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2885 3735 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2886 3736 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2887 3737 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2888 3738 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2889 3739 5.476983 TCCCTCTGTCCCATAATGTAAGAT 58.523 41.667 0.00 0.00 0.00 2.40
2890 3740 5.307976 TCCCTCTGTCCCATAATGTAAGATG 59.692 44.000 0.00 0.00 0.00 2.90
2891 3741 4.999950 CCTCTGTCCCATAATGTAAGATGC 59.000 45.833 0.00 0.00 0.00 3.91
2892 3742 5.221803 CCTCTGTCCCATAATGTAAGATGCT 60.222 44.000 0.00 0.00 0.00 3.79
2893 3743 6.252599 TCTGTCCCATAATGTAAGATGCTT 57.747 37.500 0.00 0.00 0.00 3.91
2894 3744 6.662755 TCTGTCCCATAATGTAAGATGCTTT 58.337 36.000 0.00 0.00 0.00 3.51
2895 3745 7.118723 TCTGTCCCATAATGTAAGATGCTTTT 58.881 34.615 0.00 0.00 0.00 2.27
2896 3746 7.615365 TCTGTCCCATAATGTAAGATGCTTTTT 59.385 33.333 0.00 0.00 0.00 1.94
2897 3747 7.546358 TGTCCCATAATGTAAGATGCTTTTTG 58.454 34.615 0.00 0.00 0.00 2.44
2898 3748 7.395772 TGTCCCATAATGTAAGATGCTTTTTGA 59.604 33.333 0.00 0.00 0.00 2.69
2899 3749 7.702348 GTCCCATAATGTAAGATGCTTTTTGAC 59.298 37.037 0.00 0.00 0.00 3.18
2900 3750 7.395772 TCCCATAATGTAAGATGCTTTTTGACA 59.604 33.333 0.00 0.00 0.00 3.58
2901 3751 7.489113 CCCATAATGTAAGATGCTTTTTGACAC 59.511 37.037 0.00 0.00 0.00 3.67
2902 3752 8.246180 CCATAATGTAAGATGCTTTTTGACACT 58.754 33.333 0.00 0.00 0.00 3.55
2905 3755 7.744087 ATGTAAGATGCTTTTTGACACTACA 57.256 32.000 0.00 0.00 0.00 2.74
2906 3756 6.954944 TGTAAGATGCTTTTTGACACTACAC 58.045 36.000 0.00 0.00 0.00 2.90
2907 3757 5.438761 AAGATGCTTTTTGACACTACACC 57.561 39.130 0.00 0.00 0.00 4.16
2908 3758 4.460263 AGATGCTTTTTGACACTACACCA 58.540 39.130 0.00 0.00 0.00 4.17
2909 3759 4.516698 AGATGCTTTTTGACACTACACCAG 59.483 41.667 0.00 0.00 0.00 4.00
2910 3760 3.616219 TGCTTTTTGACACTACACCAGT 58.384 40.909 0.00 0.00 38.32 4.00
2942 3792 2.605257 TCCTACATTATGGGACGGAGG 58.395 52.381 0.00 0.00 31.72 4.30
2943 3793 1.623811 CCTACATTATGGGACGGAGGG 59.376 57.143 0.00 0.00 0.00 4.30
2944 3794 2.605257 CTACATTATGGGACGGAGGGA 58.395 52.381 0.00 0.00 0.00 4.20
2945 3795 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2946 3796 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2947 3797 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3072 3925 1.021202 TGCGTGAAAAACTGTGGGAG 58.979 50.000 0.00 0.00 0.00 4.30
3445 4298 3.866910 TGAGTACGAAAACAGTCACCAAC 59.133 43.478 0.00 0.00 0.00 3.77
3446 4299 3.864243 AGTACGAAAACAGTCACCAACA 58.136 40.909 0.00 0.00 0.00 3.33
3809 4675 9.405587 GAAGAAATTGTCCATTTGAAACGAATA 57.594 29.630 0.00 0.00 35.02 1.75
3920 4806 0.976641 GCTTCAAAGGGGAAAAGGGG 59.023 55.000 0.00 0.00 0.00 4.79
4078 4966 5.084519 TCAGTTACAGGAATACACTCCACT 58.915 41.667 0.00 0.00 38.02 4.00
4105 4993 4.430423 GCCAGCGCAACGAGAACG 62.430 66.667 11.47 0.00 39.23 3.95
4135 5023 2.729479 CGCCTGATCCCAGCTGACT 61.729 63.158 17.39 0.00 39.07 3.41
4138 5026 0.907486 CCTGATCCCAGCTGACTTGA 59.093 55.000 17.39 6.48 39.07 3.02
4209 5097 3.118992 AGAGAGAATACATCAGCAACGCA 60.119 43.478 0.00 0.00 0.00 5.24
4279 5169 0.830648 CAGATAGCAGGAACCCGGAA 59.169 55.000 0.73 0.00 0.00 4.30
4423 5313 2.476619 ACTCAGCGAAAACGAACAGATG 59.523 45.455 0.00 0.00 0.00 2.90
4431 5321 4.260620 CGAAAACGAACAGATGGTCAAGTT 60.261 41.667 0.00 0.00 0.00 2.66
4432 5322 5.050634 CGAAAACGAACAGATGGTCAAGTTA 60.051 40.000 0.00 0.00 0.00 2.24
4433 5323 6.347402 CGAAAACGAACAGATGGTCAAGTTAT 60.347 38.462 0.00 0.00 0.00 1.89
4436 5326 8.561738 AAACGAACAGATGGTCAAGTTATATT 57.438 30.769 0.00 0.00 0.00 1.28
4455 5346 2.631160 TGGGTGTTACAGAACCTGTG 57.369 50.000 9.64 0.00 45.01 3.66
4474 5365 3.332187 TGTGACCCATTTCCATCTTACCA 59.668 43.478 0.00 0.00 0.00 3.25
4483 5374 1.227527 CATCTTACCATCGCCGCCA 60.228 57.895 0.00 0.00 0.00 5.69
4503 5394 3.069300 CCACTCATCATCGACAAGGAGAT 59.931 47.826 15.12 0.00 0.00 2.75
4573 5464 3.315470 GCACGATGACATAGTACAGAGGA 59.685 47.826 0.50 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
784 1270 3.792047 CTGGTCGTACGTCGCCGA 61.792 66.667 16.05 3.75 38.10 5.54
785 1271 2.784957 TTTCTGGTCGTACGTCGCCG 62.785 60.000 16.05 11.78 38.10 6.46
786 1272 1.081242 TTTCTGGTCGTACGTCGCC 60.081 57.895 16.05 15.72 39.67 5.54
788 1274 1.324718 CTGTTTCTGGTCGTACGTCG 58.675 55.000 16.05 0.00 41.41 5.12
789 1275 2.412421 ACTGTTTCTGGTCGTACGTC 57.588 50.000 16.05 9.80 0.00 4.34
898 1384 9.624037 GGTATCTCTATCTCTATATCTCCCCTA 57.376 40.741 0.00 0.00 0.00 3.53
899 1385 7.236847 CGGTATCTCTATCTCTATATCTCCCCT 59.763 44.444 0.00 0.00 0.00 4.79
900 1386 7.236019 TCGGTATCTCTATCTCTATATCTCCCC 59.764 44.444 0.00 0.00 0.00 4.81
901 1387 8.197592 TCGGTATCTCTATCTCTATATCTCCC 57.802 42.308 0.00 0.00 0.00 4.30
902 1388 9.485206 GTTCGGTATCTCTATCTCTATATCTCC 57.515 40.741 0.00 0.00 0.00 3.71
908 1394 9.747898 AATTCAGTTCGGTATCTCTATCTCTAT 57.252 33.333 0.00 0.00 0.00 1.98
909 1395 9.575868 AAATTCAGTTCGGTATCTCTATCTCTA 57.424 33.333 0.00 0.00 0.00 2.43
910 1396 8.472007 AAATTCAGTTCGGTATCTCTATCTCT 57.528 34.615 0.00 0.00 0.00 3.10
911 1397 7.535940 CGAAATTCAGTTCGGTATCTCTATCTC 59.464 40.741 1.51 0.00 45.21 2.75
912 1398 7.364200 CGAAATTCAGTTCGGTATCTCTATCT 58.636 38.462 1.51 0.00 45.21 1.98
913 1399 7.555639 CGAAATTCAGTTCGGTATCTCTATC 57.444 40.000 1.51 0.00 45.21 2.08
1113 1621 3.878667 GGGAAGGGCGGGATGGAG 61.879 72.222 0.00 0.00 0.00 3.86
1348 1872 2.352032 GCAGGAGCCAGTACTCGGT 61.352 63.158 11.47 2.78 37.57 4.69
1440 1964 1.566018 CGAAGAAGGGCACGAACACC 61.566 60.000 0.00 0.00 0.00 4.16
1533 2057 4.208686 CTCTGGCGCCGGTAGTCC 62.209 72.222 33.59 1.60 0.00 3.85
1722 2246 5.355071 CAGCTATGCTAACCTTGATTCACAA 59.645 40.000 0.00 0.00 36.40 3.33
1763 2287 8.046708 TGACATTGTCCTAATTTACAGTATGCT 58.953 33.333 14.05 0.00 42.53 3.79
1764 2288 8.208718 TGACATTGTCCTAATTTACAGTATGC 57.791 34.615 14.05 0.00 42.53 3.14
1765 2289 9.383519 ACTGACATTGTCCTAATTTACAGTATG 57.616 33.333 14.05 0.00 46.00 2.39
1766 2290 9.383519 CACTGACATTGTCCTAATTTACAGTAT 57.616 33.333 14.05 0.00 34.32 2.12
1767 2291 8.372459 ACACTGACATTGTCCTAATTTACAGTA 58.628 33.333 14.05 0.00 34.32 2.74
1769 2293 7.173218 ACACACTGACATTGTCCTAATTTACAG 59.827 37.037 14.05 4.83 0.00 2.74
1770 2294 6.995686 ACACACTGACATTGTCCTAATTTACA 59.004 34.615 14.05 0.00 0.00 2.41
1773 2297 5.827797 ACACACACTGACATTGTCCTAATTT 59.172 36.000 14.05 0.00 0.00 1.82
1774 2298 5.239306 CACACACACTGACATTGTCCTAATT 59.761 40.000 14.05 0.00 0.00 1.40
1775 2299 4.756642 CACACACACTGACATTGTCCTAAT 59.243 41.667 14.05 0.00 0.00 1.73
1776 2300 4.126437 CACACACACTGACATTGTCCTAA 58.874 43.478 14.05 0.00 0.00 2.69
1778 2302 2.092968 ACACACACACTGACATTGTCCT 60.093 45.455 14.05 0.00 0.00 3.85
1779 2303 2.032054 CACACACACACTGACATTGTCC 59.968 50.000 14.05 0.00 0.00 4.02
1781 2305 2.710377 ACACACACACACTGACATTGT 58.290 42.857 0.00 0.00 0.00 2.71
1785 2309 2.209273 GCATACACACACACACTGACA 58.791 47.619 0.00 0.00 0.00 3.58
1787 2311 1.416030 AGGCATACACACACACACTGA 59.584 47.619 0.00 0.00 0.00 3.41
1788 2312 1.882912 AGGCATACACACACACACTG 58.117 50.000 0.00 0.00 0.00 3.66
1789 2313 3.981071 ATAGGCATACACACACACACT 57.019 42.857 0.00 0.00 0.00 3.55
1790 2314 4.034048 GCTAATAGGCATACACACACACAC 59.966 45.833 0.00 0.00 0.00 3.82
1791 2315 4.188462 GCTAATAGGCATACACACACACA 58.812 43.478 0.00 0.00 0.00 3.72
1793 2317 4.188462 GTGCTAATAGGCATACACACACA 58.812 43.478 0.00 0.00 44.34 3.72
1794 2318 4.188462 TGTGCTAATAGGCATACACACAC 58.812 43.478 0.00 0.00 44.34 3.82
1796 2320 6.377327 AATTGTGCTAATAGGCATACACAC 57.623 37.500 0.00 0.00 44.34 3.82
1844 2464 9.646427 GTCCTATACCAAATTGTGCAAATAAAA 57.354 29.630 0.00 0.00 0.00 1.52
1845 2465 8.807118 TGTCCTATACCAAATTGTGCAAATAAA 58.193 29.630 0.00 0.00 0.00 1.40
1846 2466 8.354711 TGTCCTATACCAAATTGTGCAAATAA 57.645 30.769 0.00 0.00 0.00 1.40
1847 2467 7.831690 TCTGTCCTATACCAAATTGTGCAAATA 59.168 33.333 0.00 0.00 0.00 1.40
1848 2468 6.663093 TCTGTCCTATACCAAATTGTGCAAAT 59.337 34.615 0.00 0.00 0.00 2.32
1893 2599 8.428186 AAGTACAATGTTTCTCTCGTTTACAA 57.572 30.769 0.00 0.00 0.00 2.41
1894 2600 8.428186 AAAGTACAATGTTTCTCTCGTTTACA 57.572 30.769 0.00 0.00 0.00 2.41
1936 2643 5.981088 ACAATACACCAAATGATTCTGCA 57.019 34.783 0.00 0.00 0.00 4.41
1943 2650 7.493971 CACCAAGAAAAACAATACACCAAATGA 59.506 33.333 0.00 0.00 0.00 2.57
1961 2670 4.834496 AGGCAAATCAATCTTCACCAAGAA 59.166 37.500 0.00 0.00 42.14 2.52
2086 2795 3.500448 TCAACCACCAGTAGAATTGCA 57.500 42.857 0.00 0.00 0.00 4.08
2224 2933 1.291033 TCTGATAGGTGCAGGGTAGGT 59.709 52.381 0.00 0.00 34.20 3.08
2263 2972 2.355209 GGCTCCCTTGAAGTACAGAAGG 60.355 54.545 9.54 9.54 0.00 3.46
2337 3054 9.349713 AGATAAACCTTTCCAAATATAATGCGA 57.650 29.630 0.00 0.00 0.00 5.10
2367 3084 3.708403 AGCACAAGATGTGATCCAGAA 57.292 42.857 14.29 0.00 44.55 3.02
2385 3102 2.760374 AGTGCAAGTCTACAGTCAAGC 58.240 47.619 0.00 0.00 0.00 4.01
2393 3110 9.495754 GAAATTAATGATGAAGTGCAAGTCTAC 57.504 33.333 0.00 0.00 0.00 2.59
2395 3112 8.114331 TGAAATTAATGATGAAGTGCAAGTCT 57.886 30.769 0.00 0.00 0.00 3.24
2396 3113 8.922058 ATGAAATTAATGATGAAGTGCAAGTC 57.078 30.769 0.00 0.00 0.00 3.01
2426 3151 1.004185 CATCTACGTGCTTGCATGCTC 60.004 52.381 23.31 18.87 0.00 4.26
2436 3161 1.990563 ACAAACGCTACATCTACGTGC 59.009 47.619 0.00 0.00 40.44 5.34
2439 3164 5.450376 AAATGACAAACGCTACATCTACG 57.550 39.130 0.00 0.00 0.00 3.51
2443 3168 7.061752 AGAAGTAAATGACAAACGCTACATC 57.938 36.000 0.00 0.00 0.00 3.06
2446 3171 6.884187 TCAAGAAGTAAATGACAAACGCTAC 58.116 36.000 0.00 0.00 0.00 3.58
2450 3175 5.049405 AGGCTCAAGAAGTAAATGACAAACG 60.049 40.000 0.00 0.00 0.00 3.60
2600 3410 5.665916 ATAACAAGGCCTGGAAGATTTTG 57.334 39.130 16.25 3.59 34.07 2.44
2610 3420 2.880890 GCCTCACATATAACAAGGCCTG 59.119 50.000 5.69 2.82 45.45 4.85
2614 3424 5.220710 AGCTAGCCTCACATATAACAAGG 57.779 43.478 12.13 0.00 0.00 3.61
2758 3574 6.561614 TCTACTAGTGTACACTGCATAAAGC 58.438 40.000 33.77 1.72 42.52 3.51
2759 3575 8.244802 AGTTCTACTAGTGTACACTGCATAAAG 58.755 37.037 33.77 24.42 42.52 1.85
2760 3576 8.118976 AGTTCTACTAGTGTACACTGCATAAA 57.881 34.615 33.77 20.35 42.52 1.40
2775 3591 6.209788 ACAAAGAACCTCAGGAGTTCTACTAG 59.790 42.308 0.00 0.00 36.55 2.57
2873 3723 7.702348 GTCAAAAAGCATCTTACATTATGGGAC 59.298 37.037 0.00 0.00 0.00 4.46
2874 3724 7.395772 TGTCAAAAAGCATCTTACATTATGGGA 59.604 33.333 0.00 0.00 0.00 4.37
2875 3725 7.489113 GTGTCAAAAAGCATCTTACATTATGGG 59.511 37.037 0.00 0.00 0.00 4.00
2876 3726 8.246180 AGTGTCAAAAAGCATCTTACATTATGG 58.754 33.333 0.00 0.00 0.00 2.74
2879 3729 9.278978 TGTAGTGTCAAAAAGCATCTTACATTA 57.721 29.630 0.00 0.00 0.00 1.90
2880 3730 8.076178 GTGTAGTGTCAAAAAGCATCTTACATT 58.924 33.333 0.00 0.00 0.00 2.71
2881 3731 7.308589 GGTGTAGTGTCAAAAAGCATCTTACAT 60.309 37.037 0.00 0.00 0.00 2.29
2882 3732 6.017440 GGTGTAGTGTCAAAAAGCATCTTACA 60.017 38.462 0.00 0.00 0.00 2.41
2883 3733 6.017440 TGGTGTAGTGTCAAAAAGCATCTTAC 60.017 38.462 0.00 0.00 0.00 2.34
2884 3734 6.058833 TGGTGTAGTGTCAAAAAGCATCTTA 58.941 36.000 0.00 0.00 0.00 2.10
2885 3735 4.887071 TGGTGTAGTGTCAAAAAGCATCTT 59.113 37.500 0.00 0.00 0.00 2.40
2886 3736 4.460263 TGGTGTAGTGTCAAAAAGCATCT 58.540 39.130 0.00 0.00 0.00 2.90
2887 3737 4.275936 ACTGGTGTAGTGTCAAAAAGCATC 59.724 41.667 0.00 0.00 38.49 3.91
2888 3738 4.207165 ACTGGTGTAGTGTCAAAAAGCAT 58.793 39.130 0.00 0.00 38.49 3.79
2889 3739 3.616219 ACTGGTGTAGTGTCAAAAAGCA 58.384 40.909 0.00 0.00 38.49 3.91
2921 3771 2.299297 CCTCCGTCCCATAATGTAGGAC 59.701 54.545 0.00 0.00 45.49 3.85
2922 3772 2.605257 CCTCCGTCCCATAATGTAGGA 58.395 52.381 0.00 0.00 0.00 2.94
2923 3773 1.623811 CCCTCCGTCCCATAATGTAGG 59.376 57.143 0.00 0.00 0.00 3.18
2924 3774 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
2925 3775 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2926 3776 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2927 3777 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2928 3778 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2929 3779 4.294168 AGATATACTCCCTCCGTCCCATAA 59.706 45.833 0.00 0.00 0.00 1.90
2930 3780 3.856813 AGATATACTCCCTCCGTCCCATA 59.143 47.826 0.00 0.00 0.00 2.74
2931 3781 2.655407 AGATATACTCCCTCCGTCCCAT 59.345 50.000 0.00 0.00 0.00 4.00
2932 3782 2.071372 AGATATACTCCCTCCGTCCCA 58.929 52.381 0.00 0.00 0.00 4.37
2933 3783 2.041350 TCAGATATACTCCCTCCGTCCC 59.959 54.545 0.00 0.00 0.00 4.46
2934 3784 3.244981 ACTCAGATATACTCCCTCCGTCC 60.245 52.174 0.00 0.00 0.00 4.79
2935 3785 3.754323 CACTCAGATATACTCCCTCCGTC 59.246 52.174 0.00 0.00 0.00 4.79
2936 3786 3.394940 TCACTCAGATATACTCCCTCCGT 59.605 47.826 0.00 0.00 0.00 4.69
2937 3787 4.022413 TCACTCAGATATACTCCCTCCG 57.978 50.000 0.00 0.00 0.00 4.63
2938 3788 5.390387 ACTTCACTCAGATATACTCCCTCC 58.610 45.833 0.00 0.00 0.00 4.30
2939 3789 7.722285 AGTTACTTCACTCAGATATACTCCCTC 59.278 40.741 0.00 0.00 0.00 4.30
2940 3790 7.588169 AGTTACTTCACTCAGATATACTCCCT 58.412 38.462 0.00 0.00 0.00 4.20
2941 3791 7.826918 AGTTACTTCACTCAGATATACTCCC 57.173 40.000 0.00 0.00 0.00 4.30
3072 3925 2.695359 TCAGGCTCGTTAACCATCAAC 58.305 47.619 0.00 0.00 0.00 3.18
3445 4298 0.179034 GGGGCAGAGACCTTGCTATG 60.179 60.000 0.00 0.00 0.00 2.23
3446 4299 0.621571 TGGGGCAGAGACCTTGCTAT 60.622 55.000 0.00 0.00 0.00 2.97
3564 4417 1.745489 GCACCGAAGTGGGATGGAC 60.745 63.158 0.00 0.00 44.69 4.02
3567 4420 0.680921 AATGGCACCGAAGTGGGATG 60.681 55.000 0.00 0.00 44.69 3.51
3652 4506 6.732896 TTTGCAACTACCAGGGAAAAATAA 57.267 33.333 0.00 0.00 0.00 1.40
3654 4508 5.823861 ATTTGCAACTACCAGGGAAAAAT 57.176 34.783 0.00 0.00 0.00 1.82
3748 4612 1.355971 CCCGTACAACAACTCATCGG 58.644 55.000 0.00 0.00 36.85 4.18
3809 4675 2.243810 GATCCGTATCCAGCCTTCTCT 58.756 52.381 0.00 0.00 0.00 3.10
3829 4695 9.995957 TTCAACAATTTGTACCAATATACATCG 57.004 29.630 1.76 0.00 35.04 3.84
3920 4806 2.087646 GGCACCAGAAGTTTCTCATCC 58.912 52.381 0.00 0.00 34.74 3.51
4105 4993 2.872858 GGATCAGGCGATTGGTAAACTC 59.127 50.000 0.00 0.00 29.66 3.01
4135 5023 2.811431 CTCGTGGCTTGGTTACATTCAA 59.189 45.455 0.00 0.00 0.00 2.69
4138 5026 2.851263 TCTCGTGGCTTGGTTACATT 57.149 45.000 0.00 0.00 0.00 2.71
4174 5062 8.908786 ATGTATTCTCTCTGTTTTCTTGTTGA 57.091 30.769 0.00 0.00 0.00 3.18
4209 5097 2.161855 TGCCTTGACAGAATTTCGCAT 58.838 42.857 0.00 0.00 0.00 4.73
4279 5169 1.137404 GAGCGCCGCAATGTTCATT 59.863 52.632 13.36 0.00 0.00 2.57
4375 5265 1.272872 ACCTGCTTGGATCATGGCTTT 60.273 47.619 0.00 0.00 39.71 3.51
4382 5272 0.401356 TTCTGCACCTGCTTGGATCA 59.599 50.000 0.00 0.76 42.66 2.92
4423 5313 7.107542 TCTGTAACACCCAATATAACTTGACC 58.892 38.462 0.00 0.00 0.00 4.02
4431 5321 6.213802 TCACAGGTTCTGTAACACCCAATATA 59.786 38.462 0.00 0.00 43.43 0.86
4432 5322 5.013704 TCACAGGTTCTGTAACACCCAATAT 59.986 40.000 0.00 0.00 43.43 1.28
4433 5323 4.348461 TCACAGGTTCTGTAACACCCAATA 59.652 41.667 0.00 0.00 43.43 1.90
4436 5326 2.120312 TCACAGGTTCTGTAACACCCA 58.880 47.619 0.00 0.00 43.43 4.51
4455 5346 3.815401 CGATGGTAAGATGGAAATGGGTC 59.185 47.826 0.00 0.00 0.00 4.46
4474 5365 1.301244 GATGATGAGTGGCGGCGAT 60.301 57.895 12.98 0.00 0.00 4.58
4483 5374 3.956848 TCATCTCCTTGTCGATGATGAGT 59.043 43.478 0.00 0.00 40.62 3.41
4513 5404 2.203788 TTCTGGCGTGACTCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
4573 5464 1.280421 GACAGGGAATTGCTGAGAGGT 59.720 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.