Multiple sequence alignment - TraesCS3B01G465300

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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 TraesCS3B01G465300 chr3B 100.000 4622 0 0 1 4622 708364914 708360293 0.000000e+00 8536.0
1 TraesCS3B01G465300 chr3B 84.688 738 90 19 3755 4487 2150417 2149698 0.000000e+00 715.0
2 TraesCS3B01G465300 chr3B 95.349 43 1 1 3687 3729 421611845 421611804 2.980000e-07 67.6
3 TraesCS3B01G465300 chr3D 90.861 2473 169 28 1 2454 536140779 536143213 0.000000e+00 3262.0
4 TraesCS3B01G465300 chr3D 95.068 1176 47 6 2472 3646 536143200 536144365 0.000000e+00 1840.0
5 TraesCS3B01G465300 chr3D 79.603 353 60 10 2741 3090 536244007 536244350 4.620000e-60 243.0
6 TraesCS3B01G465300 chr3D 95.968 124 4 1 4500 4622 536147568 536147691 2.820000e-47 200.0
7 TraesCS3B01G465300 chr3D 77.183 355 69 10 2739 3090 535650887 535650542 3.650000e-46 196.0
8 TraesCS3B01G465300 chr3D 85.906 149 10 7 2280 2427 536165151 536165289 1.040000e-31 148.0
9 TraesCS3B01G465300 chr3A 92.661 1935 114 14 1 1921 671680642 671678722 0.000000e+00 2761.0
10 TraesCS3B01G465300 chr3A 93.929 1120 45 8 2570 3672 671678729 671677616 0.000000e+00 1670.0
11 TraesCS3B01G465300 chr3A 77.968 758 137 22 2739 3487 671661127 671660391 9.120000e-122 448.0
12 TraesCS3B01G465300 chr3A 88.341 223 18 3 2710 2925 671659871 671659650 1.280000e-65 261.0
13 TraesCS3B01G465300 chr3A 79.213 356 60 12 2739 3090 671722974 671723319 7.730000e-58 235.0
14 TraesCS3B01G465300 chr3A 86.802 197 12 5 2240 2427 671660214 671660023 1.690000e-49 207.0
15 TraesCS3B01G465300 chr3A 76.554 354 73 8 2739 3090 670834572 670834227 7.900000e-43 185.0
16 TraesCS3B01G465300 chr3A 96.703 91 3 0 4496 4586 671677614 671677524 8.010000e-33 152.0
17 TraesCS3B01G465300 chr3A 91.837 49 3 1 3687 3735 117293177 117293224 2.980000e-07 67.6
18 TraesCS3B01G465300 chr1D 82.880 882 128 9 2739 3613 419999923 419999058 0.000000e+00 771.0
19 TraesCS3B01G465300 chr1B 83.804 815 121 8 2739 3546 566983427 566982617 0.000000e+00 763.0
20 TraesCS3B01G465300 chr1B 96.078 51 1 1 3688 3738 422548751 422548800 1.070000e-11 82.4
21 TraesCS3B01G465300 chr1B 97.500 40 1 0 3574 3613 566982610 566982571 8.300000e-08 69.4
22 TraesCS3B01G465300 chr7D 85.734 729 94 8 3755 4479 617760122 617759400 0.000000e+00 761.0
23 TraesCS3B01G465300 chr7D 80.543 221 39 4 1906 2124 600272109 600271891 2.860000e-37 167.0
24 TraesCS3B01G465300 chr7D 90.541 74 6 1 3687 3760 139187093 139187021 3.810000e-16 97.1
25 TraesCS3B01G465300 chr5D 85.637 738 90 16 3755 4484 27490786 27490057 0.000000e+00 761.0
26 TraesCS3B01G465300 chr5D 81.019 216 40 1 1925 2140 26521904 26521690 2.210000e-38 171.0
27 TraesCS3B01G465300 chr5D 79.747 237 44 3 1906 2140 26472466 26472232 7.950000e-38 169.0
28 TraesCS3B01G465300 chr5D 80.093 216 42 1 1925 2140 26506263 26506049 4.790000e-35 159.0
29 TraesCS3B01G465300 chr6D 85.464 743 91 13 3755 4488 143137448 143138182 0.000000e+00 758.0
30 TraesCS3B01G465300 chr2D 85.210 737 88 16 3755 4483 650057987 650057264 0.000000e+00 737.0
31 TraesCS3B01G465300 chr2D 94.915 59 2 1 3689 3747 450370259 450370202 1.770000e-14 91.6
32 TraesCS3B01G465300 chr6A 84.005 744 97 17 3755 4487 122817194 122817926 0.000000e+00 695.0
33 TraesCS3B01G465300 chr7A 85.440 625 83 7 3757 4377 696118219 696117599 1.080000e-180 643.0
34 TraesCS3B01G465300 chr7A 83.881 639 87 11 3850 4487 207084801 207085424 3.080000e-166 595.0
35 TraesCS3B01G465300 chr1A 84.337 664 89 12 3818 4479 60798697 60799347 1.810000e-178 636.0
36 TraesCS3B01G465300 chr1A 84.188 234 37 0 1906 2139 405673160 405673393 1.290000e-55 228.0
37 TraesCS3B01G465300 chr1A 81.526 249 41 4 1906 2150 172189161 172188914 2.820000e-47 200.0
38 TraesCS3B01G465300 chr1A 93.333 45 2 1 3687 3731 60797057 60797100 1.070000e-06 65.8
39 TraesCS3B01G465300 chr4D 80.508 236 42 4 1906 2140 198604490 198604258 1.320000e-40 178.0
40 TraesCS3B01G465300 chr4D 90.196 51 5 0 1907 1957 71063233 71063283 2.980000e-07 67.6
41 TraesCS3B01G465300 chr2B 82.418 91 14 2 3670 3760 104897402 104897490 1.380000e-10 78.7
42 TraesCS3B01G465300 chr4A 95.652 46 1 1 3687 3732 210955621 210955665 6.410000e-09 73.1
43 TraesCS3B01G465300 chr4A 91.837 49 3 1 3687 3735 944863 944910 2.980000e-07 67.6


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 TraesCS3B01G465300 chr3B 708360293 708364914 4621 True 8536.000000 8536 100.000000 1 4622 1 chr3B.!!$R3 4621
1 TraesCS3B01G465300 chr3B 2149698 2150417 719 True 715.000000 715 84.688000 3755 4487 1 chr3B.!!$R1 732
2 TraesCS3B01G465300 chr3D 536140779 536147691 6912 False 1767.333333 3262 93.965667 1 4622 3 chr3D.!!$F3 4621
3 TraesCS3B01G465300 chr3A 671677524 671680642 3118 True 1527.666667 2761 94.431000 1 4586 3 chr3A.!!$R3 4585
4 TraesCS3B01G465300 chr3A 671659650 671661127 1477 True 305.333333 448 84.370333 2240 3487 3 chr3A.!!$R2 1247
5 TraesCS3B01G465300 chr1D 419999058 419999923 865 True 771.000000 771 82.880000 2739 3613 1 chr1D.!!$R1 874
6 TraesCS3B01G465300 chr1B 566982571 566983427 856 True 416.200000 763 90.652000 2739 3613 2 chr1B.!!$R1 874
7 TraesCS3B01G465300 chr7D 617759400 617760122 722 True 761.000000 761 85.734000 3755 4479 1 chr7D.!!$R3 724
8 TraesCS3B01G465300 chr5D 27490057 27490786 729 True 761.000000 761 85.637000 3755 4484 1 chr5D.!!$R4 729
9 TraesCS3B01G465300 chr6D 143137448 143138182 734 False 758.000000 758 85.464000 3755 4488 1 chr6D.!!$F1 733
10 TraesCS3B01G465300 chr2D 650057264 650057987 723 True 737.000000 737 85.210000 3755 4483 1 chr2D.!!$R2 728
11 TraesCS3B01G465300 chr6A 122817194 122817926 732 False 695.000000 695 84.005000 3755 4487 1 chr6A.!!$F1 732
12 TraesCS3B01G465300 chr7A 696117599 696118219 620 True 643.000000 643 85.440000 3757 4377 1 chr7A.!!$R1 620
13 TraesCS3B01G465300 chr7A 207084801 207085424 623 False 595.000000 595 83.881000 3850 4487 1 chr7A.!!$F1 637
14 TraesCS3B01G465300 chr1A 60797057 60799347 2290 False 350.900000 636 88.835000 3687 4479 2 chr1A.!!$F2 792

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
772 782 0.172578 CACGACATAAGTCTCCGCCA 59.827 55.0 0.00 0.00 42.73 5.69 F
1423 1437 0.258774 TTTGGAATAGGAGGCTGGCC 59.741 55.0 3.00 3.00 0.00 5.36 F
2247 2276 1.467875 GTAGCACGATCAGTACTGCG 58.532 55.0 18.45 18.09 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 2736 0.109412 GCATCCTGCAAGCAGTTCAC 60.109 55.000 19.60 4.32 44.26 3.18 R
2991 3036 1.807165 GCTCATGAAGTCGCTCGCA 60.807 57.895 0.00 0.00 0.00 5.10 R
4030 8779 0.389817 TCCATTTGTCTGACCGAGCG 60.390 55.000 5.17 0.00 0.00 5.03 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
188 190 8.347771 CCGATTGATATGATGACATTGTCTTTT 58.652 33.333 17.26 3.17 37.87 2.27
302 304 6.783708 ACCACCACAAAACTTCAAAATCTA 57.216 33.333 0.00 0.00 0.00 1.98
369 374 2.749621 CAAGGTAGAAGGTGAATGGTGC 59.250 50.000 0.00 0.00 0.00 5.01
419 424 1.761198 GTTTAGCATCGAGGGTAGGGT 59.239 52.381 9.10 0.00 0.00 4.34
429 434 0.195096 AGGGTAGGGTTTGGTGGAGA 59.805 55.000 0.00 0.00 0.00 3.71
438 443 1.065410 TTTGGTGGAGAGGGGAGCAA 61.065 55.000 0.00 0.00 0.00 3.91
485 490 9.100197 ACCCATCTTCTTGTTTTATTTTGGTAT 57.900 29.630 0.00 0.00 0.00 2.73
489 494 8.129496 TCTTCTTGTTTTATTTTGGTATCCCC 57.871 34.615 0.00 0.00 0.00 4.81
490 495 7.953493 TCTTCTTGTTTTATTTTGGTATCCCCT 59.047 33.333 0.00 0.00 0.00 4.79
688 697 8.374327 AGACCGCCTTATAAATACAATGTAAC 57.626 34.615 0.00 0.00 0.00 2.50
690 699 6.487668 ACCGCCTTATAAATACAATGTAACCC 59.512 38.462 0.00 0.00 0.00 4.11
694 703 8.287503 GCCTTATAAATACAATGTAACCCGAAG 58.712 37.037 0.00 0.00 0.00 3.79
706 715 1.698506 ACCCGAAGTGGATTTTTGCA 58.301 45.000 0.00 0.00 42.00 4.08
772 782 0.172578 CACGACATAAGTCTCCGCCA 59.827 55.000 0.00 0.00 42.73 5.69
833 843 7.027874 TCAAAACCCATAGAAACCTACAGAT 57.972 36.000 0.00 0.00 0.00 2.90
834 844 6.884295 TCAAAACCCATAGAAACCTACAGATG 59.116 38.462 0.00 0.00 0.00 2.90
848 858 4.835056 CCTACAGATGTCCATATCCTCACA 59.165 45.833 0.00 0.00 0.00 3.58
854 864 4.743057 TGTCCATATCCTCACACTGAAG 57.257 45.455 0.00 0.00 0.00 3.02
1033 1043 3.640029 TCTCTCCAACACGGTAAAGTTCT 59.360 43.478 0.00 0.00 35.57 3.01
1100 1110 6.067263 TCATCGGTTTGTAAAGTTTTGGAG 57.933 37.500 0.00 0.00 0.00 3.86
1125 1135 4.636206 GCAACCACTATAACCCTCTTTCTG 59.364 45.833 0.00 0.00 0.00 3.02
1297 1307 6.466812 TCCATATGATGTGTAGCATTTCGAT 58.533 36.000 3.65 0.00 38.06 3.59
1299 1309 6.369615 CCATATGATGTGTAGCATTTCGATGA 59.630 38.462 3.65 0.00 38.06 2.92
1309 1319 4.852138 AGCATTTCGATGATTCCATTTCG 58.148 39.130 0.00 0.00 32.09 3.46
1345 1355 9.016438 CACATATGACATGATTGAATCCCATAA 57.984 33.333 10.38 0.00 0.00 1.90
1359 1373 7.829725 TGAATCCCATAATCACTTTGTTTCAG 58.170 34.615 0.00 0.00 0.00 3.02
1403 1417 7.873719 TCCCTTGTATTACATGGTGTATTTG 57.126 36.000 21.12 9.12 40.63 2.32
1423 1437 0.258774 TTTGGAATAGGAGGCTGGCC 59.741 55.000 3.00 3.00 0.00 5.36
1544 1562 9.000486 ACTTTAAGTAGGCTTGTTCATTTAGTC 58.000 33.333 0.00 0.00 36.22 2.59
1566 1584 2.103263 CCCTATTGGTGTAGTGAGCTCC 59.897 54.545 12.15 2.40 0.00 4.70
1765 1786 3.448660 GGATTGGAAGGGGTCTCAAAATG 59.551 47.826 0.00 0.00 0.00 2.32
1788 1809 6.422333 TGATTAGGATGTGCAAATGGAGTTA 58.578 36.000 0.00 0.00 0.00 2.24
1808 1829 7.172703 GGAGTTATCGGGGTAGAAACAATAATG 59.827 40.741 0.00 0.00 0.00 1.90
1854 1875 9.988350 AACAATATTAACTGACGATCAATTCAC 57.012 29.630 0.00 0.00 0.00 3.18
1863 1884 5.109210 TGACGATCAATTCACGATTTAGCT 58.891 37.500 0.00 0.00 0.00 3.32
1870 1891 7.899178 TCAATTCACGATTTAGCTAGAAACA 57.101 32.000 0.00 0.00 0.00 2.83
1934 1958 7.369551 TCCAAATATATAGGGCCTAATACGG 57.630 40.000 18.91 15.50 0.00 4.02
1937 1961 8.050930 CCAAATATATAGGGCCTAATACGGTTT 58.949 37.037 18.91 10.98 0.00 3.27
1966 1990 4.879545 GTCACCTCTGACCACAAGTTAAAA 59.120 41.667 0.00 0.00 41.06 1.52
1995 2019 5.199723 ACATATGGCATGGATGTTACACAA 58.800 37.500 10.98 0.00 29.46 3.33
1998 2022 2.230992 TGGCATGGATGTTACACAAAGC 59.769 45.455 0.00 0.00 0.00 3.51
2004 2028 6.459985 GCATGGATGTTACACAAAGCATATGA 60.460 38.462 6.97 0.00 0.00 2.15
2098 2122 3.940209 TCAATGGTCAAATGCAACCTC 57.060 42.857 6.83 0.00 36.47 3.85
2139 2163 8.191110 ACCCTATATATTTGGATGAAGGGAGTA 58.809 37.037 16.59 0.00 44.39 2.59
2174 2198 4.456358 GCATGAATTTGCGCGTGA 57.544 50.000 8.43 0.00 32.06 4.35
2201 2225 7.979444 ACGAAAGGAAGATTGACATTTTAGA 57.021 32.000 0.00 0.00 0.00 2.10
2202 2226 8.391075 ACGAAAGGAAGATTGACATTTTAGAA 57.609 30.769 0.00 0.00 0.00 2.10
2203 2227 8.507249 ACGAAAGGAAGATTGACATTTTAGAAG 58.493 33.333 0.00 0.00 0.00 2.85
2204 2228 7.483059 CGAAAGGAAGATTGACATTTTAGAAGC 59.517 37.037 0.00 0.00 0.00 3.86
2205 2229 8.414629 AAAGGAAGATTGACATTTTAGAAGCT 57.585 30.769 0.00 0.00 0.00 3.74
2206 2230 7.388460 AGGAAGATTGACATTTTAGAAGCTG 57.612 36.000 0.00 0.00 0.00 4.24
2209 2233 4.400567 AGATTGACATTTTAGAAGCTGGCC 59.599 41.667 0.00 0.00 0.00 5.36
2238 2267 3.143279 CGAAACAAAACGTAGCACGATC 58.857 45.455 14.18 0.00 46.05 3.69
2243 2272 3.671928 ACAAAACGTAGCACGATCAGTAC 59.328 43.478 14.18 0.00 46.05 2.73
2247 2276 1.467875 GTAGCACGATCAGTACTGCG 58.532 55.000 18.45 18.09 0.00 5.18
2267 2296 2.166459 CGAATCAGCCCTGTAACTCTCA 59.834 50.000 0.00 0.00 0.00 3.27
2307 2336 7.926674 AATGGATCAAAATTTTGTGGGATTC 57.073 32.000 25.98 14.05 39.18 2.52
2319 2348 6.392625 TTTGTGGGATTCGACTAGATCTAG 57.607 41.667 25.26 25.26 39.04 2.43
2343 2372 8.767478 AGAAATTTAATGAGGATGTGCAAAAG 57.233 30.769 0.00 0.00 0.00 2.27
2375 2404 5.475719 TCGACGGAATCAGAAACAATAACT 58.524 37.500 0.00 0.00 0.00 2.24
2389 2418 8.091449 AGAAACAATAACTGAGTAGAGTGAAGG 58.909 37.037 2.47 0.00 0.00 3.46
2404 2433 6.176183 AGAGTGAAGGAGGAATACAACATTG 58.824 40.000 0.00 0.00 0.00 2.82
2417 2446 7.148407 GGAATACAACATTGACTAGTGACCAAG 60.148 40.741 0.00 0.00 0.00 3.61
2452 2481 9.992442 TGGGGTTTAATTAATTACCAAGATACA 57.008 29.630 17.89 7.27 0.00 2.29
2457 2486 8.999905 TTAATTAATTACCAAGATACACCCCC 57.000 34.615 7.43 0.00 0.00 5.40
2508 2537 8.581263 CACATAAAATCTTTTCAATGCTTCGAG 58.419 33.333 0.00 0.00 0.00 4.04
2520 2549 7.615582 TCAATGCTTCGAGAATATTTGAGTT 57.384 32.000 0.00 0.00 0.00 3.01
2593 2622 8.732746 AAAGTATATCCAGCGTTAAATGTTCT 57.267 30.769 0.00 0.00 0.00 3.01
2624 2653 8.087136 TCATAGTATCGTCCTACTGTAGTACTG 58.913 40.741 18.14 5.69 33.96 2.74
2630 2660 5.185828 TCGTCCTACTGTAGTACTGTACTCA 59.814 44.000 22.79 17.95 40.14 3.41
2663 2693 9.859152 AAAAATTGGAGAGATATTCTTAGAGGG 57.141 33.333 0.00 0.00 35.87 4.30
2707 2748 2.201732 CACGTTAGTGTGTGAACTGCT 58.798 47.619 0.00 0.00 43.15 4.24
2708 2749 2.607635 CACGTTAGTGTGTGAACTGCTT 59.392 45.455 0.00 0.00 43.15 3.91
2769 2810 4.802051 CCCATGGTGGCCACGGAG 62.802 72.222 29.08 19.59 39.54 4.63
2991 3036 0.534412 CGTCCATGAACCTGAGCTCT 59.466 55.000 16.19 0.00 0.00 4.09
3093 3138 1.270907 ACAGCTTCCTCTTCACGGAT 58.729 50.000 0.00 0.00 0.00 4.18
3240 3288 1.082561 CGTGAAGTCGACGAACCGA 60.083 57.895 10.46 0.00 39.21 4.69
3381 3432 1.658114 CGTCCAGTTCCTCGACACA 59.342 57.895 0.00 0.00 0.00 3.72
3672 6901 3.192466 ACGTCGCACTTTAAGTTGACTT 58.808 40.909 18.75 11.04 39.85 3.01
3673 6902 3.000925 ACGTCGCACTTTAAGTTGACTTG 59.999 43.478 18.75 10.76 37.40 3.16
3674 6903 3.244345 CGTCGCACTTTAAGTTGACTTGA 59.756 43.478 18.75 0.00 37.40 3.02
3675 6904 4.606232 CGTCGCACTTTAAGTTGACTTGAG 60.606 45.833 18.75 7.00 37.40 3.02
3676 6905 4.506654 GTCGCACTTTAAGTTGACTTGAGA 59.493 41.667 15.72 1.54 37.40 3.27
3677 6906 4.506654 TCGCACTTTAAGTTGACTTGAGAC 59.493 41.667 6.64 3.15 37.40 3.36
3678 6907 4.508124 CGCACTTTAAGTTGACTTGAGACT 59.492 41.667 6.64 0.00 37.40 3.24
3679 6908 5.690409 CGCACTTTAAGTTGACTTGAGACTA 59.310 40.000 6.64 0.00 37.40 2.59
3680 6909 6.200286 CGCACTTTAAGTTGACTTGAGACTAA 59.800 38.462 6.64 0.00 37.40 2.24
3681 6910 7.095607 CGCACTTTAAGTTGACTTGAGACTAAT 60.096 37.037 6.64 0.00 37.40 1.73
3682 6911 8.012241 GCACTTTAAGTTGACTTGAGACTAATG 58.988 37.037 6.64 1.36 37.40 1.90
3683 6912 9.046296 CACTTTAAGTTGACTTGAGACTAATGT 57.954 33.333 6.64 0.00 37.40 2.71
3686 6915 9.706691 TTTAAGTTGACTTGAGACTAATGTAGG 57.293 33.333 6.64 0.00 37.40 3.18
3687 6916 5.725362 AGTTGACTTGAGACTAATGTAGGC 58.275 41.667 0.00 0.00 0.00 3.93
3688 6917 7.178628 TAAGTTGACTTGAGACTAATGTAGGCT 59.821 37.037 6.64 0.00 41.17 4.58
3689 6918 6.014156 AGTTGACTTGAGACTAATGTAGGCTT 60.014 38.462 0.00 0.00 46.40 4.35
3690 6919 5.967088 TGACTTGAGACTAATGTAGGCTTC 58.033 41.667 0.00 0.00 46.40 3.86
3691 6920 5.000012 ACTTGAGACTAATGTAGGCTTCG 58.000 43.478 0.00 0.00 46.40 3.79
3692 6921 3.438297 TGAGACTAATGTAGGCTTCGC 57.562 47.619 0.00 0.00 46.40 4.70
3726 6955 6.472887 TCTTCACTCGTGGGATTAATTCTTT 58.527 36.000 0.00 0.00 0.00 2.52
3780 7230 6.798315 TTTTTCGTTTGATATTGTACCGGA 57.202 33.333 9.46 0.00 0.00 5.14
3786 7236 6.819649 TCGTTTGATATTGTACCGGATTCTTT 59.180 34.615 9.46 0.00 0.00 2.52
3794 7244 7.703058 ATTGTACCGGATTCTTTTTGAAGAT 57.297 32.000 9.46 0.00 38.18 2.40
3872 7325 2.223443 TCTGCCTTGGTGCCAGCTA 61.223 57.895 0.00 0.00 0.00 3.32
3889 7342 2.038557 AGCTAGTGGTGGTCGTTTGAAT 59.961 45.455 0.00 0.00 0.00 2.57
3894 7347 3.576982 AGTGGTGGTCGTTTGAATCTCTA 59.423 43.478 0.00 0.00 0.00 2.43
3903 7356 6.349445 GGTCGTTTGAATCTCTAGAGAAGTCA 60.349 42.308 25.77 25.33 41.36 3.41
3915 7368 9.616156 TCTCTAGAGAAGTCATATTCTACGTTT 57.384 33.333 20.31 0.00 39.63 3.60
3916 7369 9.658475 CTCTAGAGAAGTCATATTCTACGTTTG 57.342 37.037 15.05 0.00 39.63 2.93
3966 8712 2.281345 GGATCGGCCCATGAGCTG 60.281 66.667 0.71 0.71 40.71 4.24
4030 8779 2.234913 TTTTCTCCGCTCGCCCTACC 62.235 60.000 0.00 0.00 0.00 3.18
4355 9133 4.782019 AAGCGCTCATGAATTAAAACCA 57.218 36.364 12.06 0.00 0.00 3.67
4363 9142 8.424731 CGCTCATGAATTAAAACCAGTAAAAAC 58.575 33.333 0.00 0.00 0.00 2.43
4421 9203 0.744414 CCTTACATGCAGGTCCCACG 60.744 60.000 7.56 0.00 0.00 4.94
4469 9513 3.009916 AGAGTGCTTCAAATCATGGGAGT 59.990 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.689553 CACACTTTTGGGCCAGTTTT 57.310 45.000 6.23 0.00 0.00 2.43
188 190 5.183140 GCCTGTAGGATTTGCTTCTTACAAA 59.817 40.000 1.17 0.00 37.62 2.83
192 194 4.568072 TGCCTGTAGGATTTGCTTCTTA 57.432 40.909 1.17 0.00 37.39 2.10
302 304 4.910195 TGTCTGGTTCAGCAATAATCACT 58.090 39.130 0.00 0.00 0.00 3.41
314 316 2.484770 CGGTCCTTTCTTGTCTGGTTCA 60.485 50.000 0.00 0.00 0.00 3.18
380 385 9.899661 TGCTAAACAATTGTAGATAATAGTGGT 57.100 29.630 12.39 0.00 0.00 4.16
402 407 1.760613 CAAACCCTACCCTCGATGCTA 59.239 52.381 0.00 0.00 0.00 3.49
419 424 1.065410 TTGCTCCCCTCTCCACCAAA 61.065 55.000 0.00 0.00 0.00 3.28
429 434 0.982852 TCCGATGTCATTGCTCCCCT 60.983 55.000 0.00 0.00 0.00 4.79
438 443 1.417890 GAGGGGTGATTCCGATGTCAT 59.582 52.381 0.00 0.00 37.00 3.06
485 490 1.064825 GGTTTTGAGAGGTGAGGGGA 58.935 55.000 0.00 0.00 0.00 4.81
489 494 3.519510 TCCTATGGGTTTTGAGAGGTGAG 59.480 47.826 0.00 0.00 0.00 3.51
490 495 3.526899 TCCTATGGGTTTTGAGAGGTGA 58.473 45.455 0.00 0.00 0.00 4.02
569 576 7.972277 GCTGACTAATTGGAAATATATGCATGG 59.028 37.037 10.16 0.00 0.00 3.66
688 697 2.810439 TTGCAAAAATCCACTTCGGG 57.190 45.000 0.00 0.00 34.36 5.14
690 699 3.058450 TGCATTGCAAAAATCCACTTCG 58.942 40.909 9.33 0.00 34.76 3.79
772 782 6.980397 GTCTTCAATCCACAATTTCACAAAGT 59.020 34.615 0.00 0.00 0.00 2.66
833 843 4.081476 CACTTCAGTGTGAGGATATGGACA 60.081 45.833 0.00 0.00 40.96 4.02
834 844 4.437239 CACTTCAGTGTGAGGATATGGAC 58.563 47.826 0.00 0.00 40.96 4.02
848 858 6.360370 TTCTAAAGATGTAGGCACTTCAGT 57.640 37.500 0.00 0.00 39.55 3.41
854 864 9.780186 ATTATTACCTTCTAAAGATGTAGGCAC 57.220 33.333 0.00 0.00 0.00 5.01
972 982 5.304686 TGGATTTATAGGGTGTCCATGAC 57.695 43.478 0.00 0.00 34.23 3.06
1005 1015 5.779529 TTACCGTGTTGGAGAGATATACC 57.220 43.478 0.00 0.00 42.00 2.73
1009 1019 5.479375 AGAACTTTACCGTGTTGGAGAGATA 59.521 40.000 0.00 0.00 42.00 1.98
1083 1093 5.062934 GGTTGCACTCCAAAACTTTACAAAC 59.937 40.000 0.00 0.00 34.68 2.93
1100 1110 3.629142 AGAGGGTTATAGTGGTTGCAC 57.371 47.619 0.00 0.00 0.00 4.57
1125 1135 2.828128 GCTGGCGAGCACCAATAGC 61.828 63.158 16.60 0.00 45.46 2.97
1183 1193 0.820871 TTTTGTTTTGGTGCTCGCCT 59.179 45.000 0.86 0.00 0.00 5.52
1192 1202 9.244799 GTTAGAGTTTCCACTATTTTGTTTTGG 57.755 33.333 0.00 0.00 31.22 3.28
1297 1307 6.207614 TGTGTTTTCATACCGAAATGGAATCA 59.792 34.615 0.00 0.00 43.12 2.57
1299 1309 6.582677 TGTGTTTTCATACCGAAATGGAAT 57.417 33.333 0.00 0.00 43.12 3.01
1309 1319 9.454585 CAATCATGTCATATGTGTTTTCATACC 57.545 33.333 1.90 0.00 33.87 2.73
1345 1355 5.354234 ACGAGAAACACTGAAACAAAGTGAT 59.646 36.000 10.35 0.00 46.55 3.06
1359 1373 5.044558 GGGATCTATCTCAACGAGAAACAC 58.955 45.833 0.00 0.00 42.27 3.32
1403 1417 1.393603 GCCAGCCTCCTATTCCAAAC 58.606 55.000 0.00 0.00 0.00 2.93
1423 1437 2.602878 TGACTAGCCGCGAGTAAAAAG 58.397 47.619 8.23 0.00 0.00 2.27
1544 1562 2.103263 GAGCTCACTACACCAATAGGGG 59.897 54.545 9.40 0.00 46.87 4.79
1566 1584 1.675552 AACACCTGGAAAGGACGTTG 58.324 50.000 0.00 0.00 30.93 4.10
1668 1689 9.692325 ATCTGCCAAGAAGTTCTTATATCTTTT 57.308 29.630 17.62 0.00 33.78 2.27
1675 1696 5.105595 GCCAAATCTGCCAAGAAGTTCTTAT 60.106 40.000 17.62 5.02 33.78 1.73
1682 1703 3.604875 AATGCCAAATCTGCCAAGAAG 57.395 42.857 0.00 0.00 35.59 2.85
1737 1758 4.265124 TGAGACCCCTTCCAATCCTAGTAA 60.265 45.833 0.00 0.00 0.00 2.24
1748 1769 4.889995 CCTAATCATTTTGAGACCCCTTCC 59.110 45.833 0.00 0.00 0.00 3.46
1751 1772 5.194537 ACATCCTAATCATTTTGAGACCCCT 59.805 40.000 0.00 0.00 0.00 4.79
1765 1786 5.841957 AACTCCATTTGCACATCCTAATC 57.158 39.130 0.00 0.00 0.00 1.75
1788 1809 5.132144 ACTCCATTATTGTTTCTACCCCGAT 59.868 40.000 0.00 0.00 0.00 4.18
1833 1854 8.642908 AATCGTGAATTGATCGTCAGTTAATA 57.357 30.769 0.00 0.00 0.00 0.98
1854 1875 6.673316 GCTTTCCTGTGTTTCTAGCTAAATCG 60.673 42.308 0.00 0.00 0.00 3.34
1966 1990 9.752228 TGTAACATCCATGCCATATGTTATTAT 57.248 29.630 13.43 0.00 43.89 1.28
2004 2028 9.774742 GAAACTTCTTTCGCATATGAATTTAGT 57.225 29.630 6.97 0.00 0.00 2.24
2157 2181 2.103898 TATCACGCGCAAATTCATGC 57.896 45.000 5.73 0.00 42.94 4.06
2160 2184 1.727335 TCGTTATCACGCGCAAATTCA 59.273 42.857 5.73 0.00 46.70 2.57
2220 2249 3.128349 ACTGATCGTGCTACGTTTTGTT 58.872 40.909 0.00 0.00 43.14 2.83
2227 2256 1.467875 GCAGTACTGATCGTGCTACG 58.532 55.000 27.08 2.79 44.19 3.51
2238 2267 0.176680 AGGGCTGATTCGCAGTACTG 59.823 55.000 18.93 18.93 46.62 2.74
2247 2276 3.895232 TGAGAGTTACAGGGCTGATTC 57.105 47.619 0.00 0.00 0.00 2.52
2286 2315 5.576774 GTCGAATCCCACAAAATTTTGATCC 59.423 40.000 32.20 14.62 40.55 3.36
2319 2348 7.818930 TCCTTTTGCACATCCTCATTAAATTTC 59.181 33.333 0.00 0.00 0.00 2.17
2343 2372 0.806492 GATTCCGTCGAGGCAAGTCC 60.806 60.000 0.00 0.00 40.77 3.85
2354 2383 6.369065 ACTCAGTTATTGTTTCTGATTCCGTC 59.631 38.462 0.00 0.00 37.54 4.79
2375 2404 5.827756 TGTATTCCTCCTTCACTCTACTCA 58.172 41.667 0.00 0.00 0.00 3.41
2389 2418 6.535508 GGTCACTAGTCAATGTTGTATTCCTC 59.464 42.308 0.00 0.00 0.00 3.71
2404 2433 8.095169 CCCCAATTATATACTTGGTCACTAGTC 58.905 40.741 23.22 0.00 40.28 2.59
2496 2525 7.615582 AACTCAAATATTCTCGAAGCATTGA 57.384 32.000 0.00 0.00 0.00 2.57
2497 2526 9.773328 TTAAACTCAAATATTCTCGAAGCATTG 57.227 29.630 0.00 0.00 0.00 2.82
2528 2557 9.034800 ACACACATTATTGGAGAAATATTTGGT 57.965 29.630 5.17 0.00 30.74 3.67
2609 2638 7.013823 ACTTGAGTACAGTACTACAGTAGGA 57.986 40.000 13.51 0.00 39.59 2.94
2624 2653 9.052759 TCTCTCCAATTTTTGTTACTTGAGTAC 57.947 33.333 0.00 0.00 0.00 2.73
2698 2736 0.109412 GCATCCTGCAAGCAGTTCAC 60.109 55.000 19.60 4.32 44.26 3.18
2946 2987 2.050350 CGTCGGGAGGAGGTAGCAA 61.050 63.158 0.00 0.00 0.00 3.91
2991 3036 1.807165 GCTCATGAAGTCGCTCGCA 60.807 57.895 0.00 0.00 0.00 5.10
3240 3288 2.434884 CGCAGCATCTCCACCGTT 60.435 61.111 0.00 0.00 0.00 4.44
3692 6921 3.952628 GAGTGAAGAACGGCCCGGG 62.953 68.421 19.09 19.09 0.00 5.73
3696 6925 2.027625 CCACGAGTGAAGAACGGCC 61.028 63.158 4.59 0.00 0.00 6.13
3731 6960 7.380536 ACAACCGACCGCAATAATATATTAGA 58.619 34.615 10.79 0.00 0.00 2.10
3732 6961 7.591006 ACAACCGACCGCAATAATATATTAG 57.409 36.000 10.79 0.25 0.00 1.73
3733 6962 7.966246 AACAACCGACCGCAATAATATATTA 57.034 32.000 7.62 7.62 0.00 0.98
3734 6963 6.870971 AACAACCGACCGCAATAATATATT 57.129 33.333 2.97 2.97 0.00 1.28
3735 6964 6.870971 AAACAACCGACCGCAATAATATAT 57.129 33.333 0.00 0.00 0.00 0.86
3737 6966 5.570234 AAAACAACCGACCGCAATAATAT 57.430 34.783 0.00 0.00 0.00 1.28
3739 6968 3.926821 AAAACAACCGACCGCAATAAT 57.073 38.095 0.00 0.00 0.00 1.28
3827 7279 4.980573 TGTAAAGACACCACAATAAGGCT 58.019 39.130 0.00 0.00 0.00 4.58
3830 7282 7.173218 AGACACATGTAAAGACACCACAATAAG 59.827 37.037 0.00 0.00 38.76 1.73
3833 7286 5.239306 CAGACACATGTAAAGACACCACAAT 59.761 40.000 0.00 0.00 38.76 2.71
3872 7325 2.368875 AGAGATTCAAACGACCACCACT 59.631 45.455 0.00 0.00 0.00 4.00
3889 7342 9.616156 AAACGTAGAATATGACTTCTCTAGAGA 57.384 33.333 18.76 18.76 36.82 3.10
3894 7347 9.877178 ATTTCAAACGTAGAATATGACTTCTCT 57.123 29.630 4.45 0.00 36.82 3.10
3909 7362 6.148948 CAGCAATTCCAGAATTTCAAACGTA 58.851 36.000 2.86 0.00 38.84 3.57
3915 7368 7.122501 TGTTATAGCAGCAATTCCAGAATTTCA 59.877 33.333 2.86 0.00 38.84 2.69
3916 7369 7.433425 GTGTTATAGCAGCAATTCCAGAATTTC 59.567 37.037 2.86 0.00 38.84 2.17
3921 7380 5.102953 AGTGTTATAGCAGCAATTCCAGA 57.897 39.130 0.00 0.00 0.00 3.86
3922 7381 4.877823 TGAGTGTTATAGCAGCAATTCCAG 59.122 41.667 0.00 0.00 0.00 3.86
4030 8779 0.389817 TCCATTTGTCTGACCGAGCG 60.390 55.000 5.17 0.00 0.00 5.03
4322 9100 7.754069 TTCATGAGCGCTTATTAAAATTTGG 57.246 32.000 13.26 0.00 0.00 3.28
4355 9133 8.042286 TCCCCTTCTCTCTTTAAGTTTTTACT 57.958 34.615 0.00 0.00 0.00 2.24
4425 9207 0.534203 TGTTTCGAGAGTTGTGGGGC 60.534 55.000 0.00 0.00 0.00 5.80
4435 9217 1.040646 AGCACTCTGGTGTTTCGAGA 58.959 50.000 0.00 0.00 44.65 4.04
4451 9233 5.324409 ACTAAACTCCCATGATTTGAAGCA 58.676 37.500 0.00 0.00 0.00 3.91
4493 9537 9.854668 TGATAGCTAAGTTCAAGTCTATCTAGT 57.145 33.333 0.00 0.00 34.59 2.57
4512 9556 7.898636 AGCTAGAAGGATTAAGGTATGATAGCT 59.101 37.037 0.00 0.00 37.00 3.32
4516 9560 8.497910 TTGAGCTAGAAGGATTAAGGTATGAT 57.502 34.615 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.