Multiple sequence alignment - TraesCS7A01G402200

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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 TraesCS7A01G402200 chr7A 100.000 5420 0 0 1 5420 581371487 581376906 0.000000e+00 10009.0
1 TraesCS7A01G402200 chr7A 88.043 92 11 0 5329 5420 695840851 695840942 5.740000e-20 110.0
2 TraesCS7A01G402200 chr7A 87.097 93 12 0 5328 5420 286747041 286746949 7.420000e-19 106.0
3 TraesCS7A01G402200 chr7A 78.443 167 18 11 5270 5418 34157573 34157739 5.780000e-15 93.5
4 TraesCS7A01G402200 chr7A 95.918 49 2 0 2285 2333 356367785 356367737 4.500000e-11 80.5
5 TraesCS7A01G402200 chr7A 86.301 73 5 4 5164 5235 403443549 403443617 2.090000e-09 75.0
6 TraesCS7A01G402200 chr7D 94.546 4327 154 24 1 4279 510610671 510614963 0.000000e+00 6608.0
7 TraesCS7A01G402200 chr7D 95.238 546 16 8 4266 4808 510615001 510615539 0.000000e+00 856.0
8 TraesCS7A01G402200 chr7D 93.261 371 20 4 4836 5202 510615531 510615900 4.780000e-150 542.0
9 TraesCS7A01G402200 chr7D 89.247 93 10 0 5328 5420 515487135 515487043 3.430000e-22 117.0
10 TraesCS7A01G402200 chr7D 93.651 63 3 1 5270 5331 83871368 83871430 5.780000e-15 93.5
11 TraesCS7A01G402200 chr7B 94.262 3677 130 31 633 4279 539216167 539219792 0.000000e+00 5546.0
12 TraesCS7A01G402200 chr7B 93.884 981 49 8 4266 5243 539219830 539220802 0.000000e+00 1469.0
13 TraesCS7A01G402200 chr7B 87.576 660 28 22 1 631 539215494 539216128 0.000000e+00 715.0
14 TraesCS7A01G402200 chr7B 95.918 98 4 0 2762 2859 685247258 685247161 5.620000e-35 159.0
15 TraesCS7A01G402200 chr7B 87.037 54 4 2 5176 5229 45001821 45001871 2.110000e-04 58.4
16 TraesCS7A01G402200 chr1A 90.411 292 19 5 483 774 439488133 439487851 5.130000e-100 375.0
17 TraesCS7A01G402200 chr1A 88.742 302 25 5 473 774 31697790 31697498 1.440000e-95 361.0
18 TraesCS7A01G402200 chr1A 87.719 285 26 6 487 771 534010893 534010618 1.880000e-84 324.0
19 TraesCS7A01G402200 chr1A 86.000 100 10 2 5321 5420 45268576 45268671 2.670000e-18 104.0
20 TraesCS7A01G402200 chr1A 100.000 28 0 0 365 392 31697892 31697865 1.000000e-02 52.8
21 TraesCS7A01G402200 chr1A 100.000 28 0 0 365 392 534011009 534010982 1.000000e-02 52.8
22 TraesCS7A01G402200 chr3B 89.298 299 23 6 473 771 685090021 685090310 3.080000e-97 366.0
23 TraesCS7A01G402200 chr3B 88.079 302 27 6 473 774 615703923 615704215 3.110000e-92 350.0
24 TraesCS7A01G402200 chr3B 87.417 302 28 7 473 774 509217127 509216836 6.720000e-89 339.0
25 TraesCS7A01G402200 chr3B 95.238 63 2 1 5270 5331 5315284 5315346 1.240000e-16 99.0
26 TraesCS7A01G402200 chr3B 96.429 56 0 2 5272 5326 738635520 738635574 2.080000e-14 91.6
27 TraesCS7A01G402200 chr3B 100.000 28 0 0 365 392 615703821 615703848 1.000000e-02 52.8
28 TraesCS7A01G402200 chr1D 89.333 300 19 7 478 774 418606557 418606268 1.110000e-96 364.0
29 TraesCS7A01G402200 chr1D 94.898 98 5 0 2763 2860 392556677 392556580 2.610000e-33 154.0
30 TraesCS7A01G402200 chr1D 89.247 93 10 0 5328 5420 110976093 110976001 3.430000e-22 117.0
31 TraesCS7A01G402200 chr1D 85.938 64 6 2 5176 5239 44694130 44694190 1.260000e-06 65.8
32 TraesCS7A01G402200 chr2B 88.581 289 24 5 483 771 632573728 632574007 5.200000e-90 342.0
33 TraesCS7A01G402200 chr2B 92.373 118 5 3 2756 2873 206114721 206114834 1.210000e-36 165.0
34 TraesCS7A01G402200 chr2B 91.228 57 4 1 2281 2337 375174364 375174309 5.820000e-10 76.8
35 TraesCS7A01G402200 chr6B 88.014 292 26 6 483 774 304065666 304065384 2.420000e-88 337.0
36 TraesCS7A01G402200 chr4B 91.818 110 8 1 2762 2871 642195650 642195542 9.400000e-33 152.0
37 TraesCS7A01G402200 chr1B 94.845 97 5 0 2763 2859 411568789 411568693 9.400000e-33 152.0
38 TraesCS7A01G402200 chr1B 88.750 80 6 1 5164 5243 4638280 4638204 1.610000e-15 95.3
39 TraesCS7A01G402200 chr6D 93.878 98 6 0 2763 2860 41640905 41640808 1.220000e-31 148.0
40 TraesCS7A01G402200 chr6D 92.308 52 4 0 2282 2333 4632425 4632476 2.090000e-09 75.0
41 TraesCS7A01G402200 chr5A 90.000 110 10 1 2762 2871 680118330 680118222 2.040000e-29 141.0
42 TraesCS7A01G402200 chr5A 89.474 95 8 2 5328 5420 687654662 687654568 9.540000e-23 119.0
43 TraesCS7A01G402200 chr2D 93.258 89 5 1 319 407 645284911 645284998 4.410000e-26 130.0
44 TraesCS7A01G402200 chr2D 85.417 96 14 0 5325 5420 575434214 575434309 3.450000e-17 100.0
45 TraesCS7A01G402200 chr2A 88.542 96 11 0 5325 5420 561288475 561288570 3.430000e-22 117.0
46 TraesCS7A01G402200 chr2A 80.473 169 15 3 5270 5420 27349010 27349178 4.440000e-21 113.0
47 TraesCS7A01G402200 chr2A 86.458 96 13 0 5325 5420 713708984 713709079 7.420000e-19 106.0
48 TraesCS7A01G402200 chr2A 92.308 52 2 1 2282 2333 593496841 593496890 7.530000e-09 73.1
49 TraesCS7A01G402200 chr6A 78.947 171 15 15 5269 5420 54075987 54075819 4.470000e-16 97.1
50 TraesCS7A01G402200 chr3D 88.462 78 4 2 5254 5326 278453897 278453974 7.480000e-14 89.8
51 TraesCS7A01G402200 chr3D 94.231 52 3 0 2285 2336 217588811 217588760 4.500000e-11 80.5
52 TraesCS7A01G402200 chrUn 92.063 63 4 1 5270 5331 308484556 308484494 2.690000e-13 87.9
53 TraesCS7A01G402200 chrUn 88.000 75 6 2 5255 5326 134258702 134258628 9.670000e-13 86.1
54 TraesCS7A01G402200 chrUn 92.727 55 1 3 5171 5225 26971341 26971290 5.820000e-10 76.8
55 TraesCS7A01G402200 chr3A 94.118 51 3 0 2285 2335 291804526 291804576 1.620000e-10 78.7
56 TraesCS7A01G402200 chr3A 88.889 54 3 2 5176 5229 6364042 6364092 4.530000e-06 63.9
57 TraesCS7A01G402200 chr4D 92.593 54 1 2 2285 2338 220358612 220358662 2.090000e-09 75.0
58 TraesCS7A01G402200 chr4A 88.889 63 4 2 5176 5238 478742208 478742149 2.090000e-09 75.0
59 TraesCS7A01G402200 chr5B 82.090 67 7 4 5176 5242 616223032 616222971 1.000000e-02 52.8


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 TraesCS7A01G402200 chr7A 581371487 581376906 5419 False 10009.000000 10009 100.000000 1 5420 1 chr7A.!!$F3 5419
1 TraesCS7A01G402200 chr7D 510610671 510615900 5229 False 2668.666667 6608 94.348333 1 5202 3 chr7D.!!$F2 5201
2 TraesCS7A01G402200 chr7B 539215494 539220802 5308 False 2576.666667 5546 91.907333 1 5243 3 chr7B.!!$F2 5242

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
840 920 0.521735 CAGGATCCGCGATGATCGTA 59.478 55.000 16.83 3.03 42.81 3.43 F
1101 1197 1.134175 CGTGCTCTCTCTTTCTCCTCC 59.866 57.143 0.00 0.00 0.00 4.30 F
2330 2429 0.252057 ACCGGGCTGCCCTTAATTTT 60.252 50.000 33.39 8.27 42.67 1.82 F
3152 3269 0.173708 CCTGCTGGTCCGTCTCTTAC 59.826 60.000 0.51 0.00 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1743 0.248866 GGGCCACGAACACAAAACTG 60.249 55.000 4.39 0.00 0.00 3.16 R
2538 2637 0.880278 CTATGGGTCGTGCATTCCCG 60.880 60.000 15.58 4.05 43.75 5.14 R
3266 3383 0.250234 ACTCCGTCCATGTGTCCATG 59.750 55.000 0.00 0.00 46.65 3.66 R
4738 4908 1.411246 AGTGTACACAACGCCTCTGAA 59.589 47.619 27.06 0.00 39.57 3.02 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
47 48 0.673985 TCGGCTGGATCAGATAACCG 59.326 55.000 0.00 6.56 35.70 4.44
83 84 3.939592 GTGCTAAAGCTTAAATCCGGACT 59.060 43.478 6.12 0.00 42.66 3.85
86 87 5.114081 GCTAAAGCTTAAATCCGGACTGTA 58.886 41.667 6.12 0.00 38.21 2.74
199 208 5.367937 ACATCTATCAAAGAGGCATGGTAGT 59.632 40.000 0.00 0.00 39.70 2.73
209 218 5.024118 AGAGGCATGGTAGTTACAAGTAGT 58.976 41.667 0.00 0.00 0.00 2.73
210 219 6.192773 AGAGGCATGGTAGTTACAAGTAGTA 58.807 40.000 0.00 0.00 0.00 1.82
211 220 6.096564 AGAGGCATGGTAGTTACAAGTAGTAC 59.903 42.308 0.00 0.00 30.91 2.73
249 258 2.668550 AAGGCGAGCCGGAACAAC 60.669 61.111 5.05 0.00 41.95 3.32
347 363 1.003355 CCTTCTCCTTGGCGAGCAA 60.003 57.895 0.00 0.00 0.00 3.91
648 720 3.161450 TAGAGGTGGATGGGGCGC 61.161 66.667 0.00 0.00 0.00 6.53
689 761 0.616111 GTCCAGAGCAGAGGAAGGGA 60.616 60.000 0.00 0.00 35.29 4.20
698 770 1.694525 GAGGAAGGGAAGGGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
699 771 2.696504 GGAAGGGAAGGGGAGGGG 60.697 72.222 0.00 0.00 0.00 4.79
700 772 2.459710 GAAGGGAAGGGGAGGGGA 59.540 66.667 0.00 0.00 0.00 4.81
701 773 1.694525 GAAGGGAAGGGGAGGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
814 891 2.035626 CCGGCCCATGGACTTGTT 59.964 61.111 15.22 0.00 0.00 2.83
840 920 0.521735 CAGGATCCGCGATGATCGTA 59.478 55.000 16.83 3.03 42.81 3.43
852 939 1.153429 GATCGTAGTGGGCCGCTTT 60.153 57.895 26.87 8.07 0.00 3.51
1082 1175 3.463690 CGGTTACACGTGGACGCG 61.464 66.667 21.57 17.36 44.43 6.01
1101 1197 1.134175 CGTGCTCTCTCTTTCTCCTCC 59.866 57.143 0.00 0.00 0.00 4.30
1111 1207 2.296471 TCTTTCTCCTCCTTGTGACGAC 59.704 50.000 0.00 0.00 0.00 4.34
1394 1491 2.563086 GAATCAGTTGCGCGGTTCCG 62.563 60.000 8.83 6.90 0.00 4.30
1487 1584 2.679716 GGATTGGGCAGGCACTCT 59.320 61.111 0.00 0.00 34.60 3.24
1511 1609 7.444183 TCTTGGAGTTCACTTTGGTAGTTTATG 59.556 37.037 0.00 0.00 33.85 1.90
1568 1666 6.698008 TGTTTGGATTGGTGTATGATCATC 57.302 37.500 12.53 4.90 0.00 2.92
1601 1699 5.840243 TGGATTGTTATTCTGAATGCCAG 57.160 39.130 13.01 0.00 44.27 4.85
1629 1727 9.936329 ATGTAGGATTTCCAATTTTACCTGTAT 57.064 29.630 0.00 0.00 38.89 2.29
1645 1743 4.040952 ACCTGTATACCTGATTGCCTGATC 59.959 45.833 0.00 0.00 0.00 2.92
1661 1759 3.303990 CCTGATCAGTTTTGTGTTCGTGG 60.304 47.826 21.11 0.00 0.00 4.94
1668 1766 0.394488 TTTGTGTTCGTGGCCCTGAA 60.394 50.000 0.00 0.47 0.00 3.02
1683 1781 3.435026 GCCCTGAATAAACTGGCATCCTA 60.435 47.826 0.00 0.00 0.00 2.94
1684 1782 4.137543 CCCTGAATAAACTGGCATCCTAC 58.862 47.826 0.00 0.00 0.00 3.18
1758 1856 7.963532 TCCTAGGGTGATTAAAGCATAGTTAG 58.036 38.462 9.46 0.00 31.73 2.34
1780 1878 2.028883 GCGTAGACCGTTCAAATAGTGC 59.971 50.000 0.00 0.00 39.32 4.40
1793 1891 6.993786 TCAAATAGTGCGATTGGTGAATTA 57.006 33.333 0.00 0.00 0.00 1.40
1857 1955 0.516877 CTACATGTGTGGGTGTTGCG 59.483 55.000 9.11 0.00 0.00 4.85
2060 2159 4.435137 TCCCAAAGATTGTAGAAGGAGGA 58.565 43.478 0.00 0.00 0.00 3.71
2150 2249 9.142014 TGTATTTCCCCCTCAAAATATACAATG 57.858 33.333 0.00 0.00 31.87 2.82
2292 2391 5.630121 TCTTTTAGATTTCTTGACCCTGCA 58.370 37.500 0.00 0.00 0.00 4.41
2330 2429 0.252057 ACCGGGCTGCCCTTAATTTT 60.252 50.000 33.39 8.27 42.67 1.82
2427 2526 1.279496 AGCACAGCATACAGGAAGGA 58.721 50.000 0.00 0.00 0.00 3.36
2538 2637 7.439655 GGGATCAACACTATGACTGATTCTTAC 59.560 40.741 0.00 0.00 30.82 2.34
2547 2646 3.055458 TGACTGATTCTTACGGGAATGCA 60.055 43.478 0.00 0.00 36.24 3.96
2602 2701 3.320610 TCCTCTCCCCTGAATCTACTG 57.679 52.381 0.00 0.00 0.00 2.74
2747 2848 7.444792 GGAGATTCTATTTTGTCTGCATCTCAT 59.555 37.037 7.85 0.00 37.99 2.90
2760 2861 7.278646 TGTCTGCATCTCATACTAACATTTCAC 59.721 37.037 0.00 0.00 0.00 3.18
2816 2917 7.498900 CAGCCTCTATACAATGTAAAATGGACA 59.501 37.037 0.00 0.00 0.00 4.02
2831 2932 3.475566 TGGACATTGTATAGAGGCTGC 57.524 47.619 0.00 0.00 0.00 5.25
2852 2953 3.246699 GCGTCAATTAATTCGGATCGGAA 59.753 43.478 16.94 16.94 0.00 4.30
3107 3224 2.891580 ACTGGAGACTTACGACACACAT 59.108 45.455 0.00 0.00 0.00 3.21
3152 3269 0.173708 CCTGCTGGTCCGTCTCTTAC 59.826 60.000 0.51 0.00 0.00 2.34
3182 3299 9.076781 CCCATCCATTTCATTATGTATTGTACA 57.923 33.333 0.00 0.00 43.80 2.90
3266 3383 4.753107 TCTGTTCCTGAACGTTGTTAATCC 59.247 41.667 5.00 0.00 43.94 3.01
3301 3418 1.339055 GGAGTTGGCACTGTAGCATCA 60.339 52.381 0.00 0.00 35.83 3.07
3541 3659 4.144297 TGGAAAGAAGTGATGGAGGTTTG 58.856 43.478 0.00 0.00 0.00 2.93
3710 3828 1.683025 CATTCATGGGCAGGCCACA 60.683 57.895 20.07 10.85 37.98 4.17
3826 3944 3.764160 GATCCTGGCCCAGCTTCCG 62.764 68.421 4.81 0.00 0.00 4.30
3934 4052 9.098355 GTAAACTACATCTTGCATGATAGTTCA 57.902 33.333 21.74 11.67 36.00 3.18
4026 4145 4.058124 CTGTTCCGTGTGATATACCCATG 58.942 47.826 0.00 0.00 0.00 3.66
4192 4311 8.021396 GTGTGTGTTCCTTTTATCCTACAAATC 58.979 37.037 0.00 0.00 0.00 2.17
4216 4335 5.343249 GGAAACTGTATTGCATGAACCATC 58.657 41.667 0.00 0.00 0.00 3.51
4225 4344 8.596293 TGTATTGCATGAACCATCTCTATCATA 58.404 33.333 0.00 0.00 31.59 2.15
4251 4370 6.262944 TGTGTGTGCAATCTTTCTGTTTATCT 59.737 34.615 0.00 0.00 0.00 1.98
4275 4394 8.997323 TCTAGGTATAACTCGTGATTAGCTAAC 58.003 37.037 8.70 3.84 0.00 2.34
4441 4609 3.428589 GCATCATCCTTTTCCTGTCTTGC 60.429 47.826 0.00 0.00 0.00 4.01
4517 4685 7.120285 AGCACTTATATGATCCCATTCATTTCG 59.880 37.037 0.00 0.00 37.51 3.46
4565 4733 5.872963 TCAGTTATCTCATGCATTAGCCAT 58.127 37.500 0.00 0.00 41.13 4.40
4719 4889 2.690173 TGGTCGGTTAAATGTTTGCG 57.310 45.000 0.00 0.00 0.00 4.85
4738 4908 1.668751 CGTGCAACTTACCTGTTGTGT 59.331 47.619 8.78 0.00 46.33 3.72
4765 4935 1.659098 GCGTTGTGTACACTAGGATGC 59.341 52.381 26.71 20.58 0.00 3.91
4815 4986 5.953183 TGCAATGTTGTGTCTGGAAATATC 58.047 37.500 0.00 0.00 0.00 1.63
4852 5023 0.514691 GCTGTGTTCTGCTCGAAAGG 59.485 55.000 0.00 0.00 35.98 3.11
4945 5116 8.817092 TTATAGATGTTGGTTCCCTTTTTAGG 57.183 34.615 0.00 0.00 0.00 2.69
5033 5204 1.136085 CGTGTGCGGTATGGTTTGAAG 60.136 52.381 0.00 0.00 0.00 3.02
5182 5357 6.052405 TGGTTATTGTGTATTACCTCCGTT 57.948 37.500 0.00 0.00 36.96 4.44
5203 5378 9.893634 TCCGTTCCAAATTATTTGTCTTAGATA 57.106 29.630 15.40 0.00 38.98 1.98
5251 5428 9.435688 TCTAACACTATAACGTGTAACTCTACA 57.564 33.333 0.00 0.00 46.71 2.74
5305 5482 9.889128 TCTTCAATCATGATAGTACAATGAACA 57.111 29.630 9.04 0.00 34.96 3.18
5308 5485 9.835389 TCAATCATGATAGTACAATGAACATCA 57.165 29.630 9.04 0.00 0.00 3.07
5338 5515 7.823149 ATAAAAATTACAACTAGCGACGACT 57.177 32.000 0.00 0.00 0.00 4.18
5339 5516 8.915871 ATAAAAATTACAACTAGCGACGACTA 57.084 30.769 0.00 0.00 0.00 2.59
5340 5517 6.623223 AAAATTACAACTAGCGACGACTAC 57.377 37.500 0.00 0.00 0.00 2.73
5341 5518 4.952262 ATTACAACTAGCGACGACTACA 57.048 40.909 0.00 0.00 0.00 2.74
5342 5519 4.747540 TTACAACTAGCGACGACTACAA 57.252 40.909 0.00 0.00 0.00 2.41
5343 5520 3.631145 ACAACTAGCGACGACTACAAA 57.369 42.857 0.00 0.00 0.00 2.83
5344 5521 4.170292 ACAACTAGCGACGACTACAAAT 57.830 40.909 0.00 0.00 0.00 2.32
5345 5522 5.300969 ACAACTAGCGACGACTACAAATA 57.699 39.130 0.00 0.00 0.00 1.40
5346 5523 5.091431 ACAACTAGCGACGACTACAAATAC 58.909 41.667 0.00 0.00 0.00 1.89
5347 5524 5.106396 ACAACTAGCGACGACTACAAATACT 60.106 40.000 0.00 0.00 0.00 2.12
5348 5525 5.557891 ACTAGCGACGACTACAAATACTT 57.442 39.130 0.00 0.00 0.00 2.24
5349 5526 6.668541 ACTAGCGACGACTACAAATACTTA 57.331 37.500 0.00 0.00 0.00 2.24
5350 5527 7.076842 ACTAGCGACGACTACAAATACTTAA 57.923 36.000 0.00 0.00 0.00 1.85
5351 5528 7.185453 ACTAGCGACGACTACAAATACTTAAG 58.815 38.462 0.00 0.00 0.00 1.85
5352 5529 4.797349 AGCGACGACTACAAATACTTAAGC 59.203 41.667 1.29 0.00 0.00 3.09
5353 5530 4.316240 GCGACGACTACAAATACTTAAGCG 60.316 45.833 1.29 0.00 0.00 4.68
5354 5531 5.023920 CGACGACTACAAATACTTAAGCGA 58.976 41.667 1.29 0.00 0.00 4.93
5355 5532 5.169208 CGACGACTACAAATACTTAAGCGAG 59.831 44.000 1.29 0.00 0.00 5.03
5356 5533 5.947443 ACGACTACAAATACTTAAGCGAGT 58.053 37.500 1.29 0.00 0.00 4.18
5357 5534 6.385033 ACGACTACAAATACTTAAGCGAGTT 58.615 36.000 1.29 0.00 0.00 3.01
5358 5535 6.307318 ACGACTACAAATACTTAAGCGAGTTG 59.693 38.462 13.61 13.61 0.00 3.16
5359 5536 6.525628 CGACTACAAATACTTAAGCGAGTTGA 59.474 38.462 19.29 7.28 0.00 3.18
5360 5537 7.061441 CGACTACAAATACTTAAGCGAGTTGAA 59.939 37.037 19.29 0.00 0.00 2.69
5361 5538 8.240883 ACTACAAATACTTAAGCGAGTTGAAG 57.759 34.615 19.29 5.95 0.00 3.02
5362 5539 6.481954 ACAAATACTTAAGCGAGTTGAAGG 57.518 37.500 19.29 0.61 0.00 3.46
5363 5540 5.106673 ACAAATACTTAAGCGAGTTGAAGGC 60.107 40.000 19.29 0.00 0.00 4.35
5364 5541 1.809684 ACTTAAGCGAGTTGAAGGCC 58.190 50.000 1.29 0.00 0.00 5.19
5365 5542 1.087501 CTTAAGCGAGTTGAAGGCCC 58.912 55.000 0.00 0.00 0.00 5.80
5366 5543 0.672401 TTAAGCGAGTTGAAGGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
5387 5564 2.770048 CCCTCATCGCCCCTCCTT 60.770 66.667 0.00 0.00 0.00 3.36
5388 5565 2.812619 CCCTCATCGCCCCTCCTTC 61.813 68.421 0.00 0.00 0.00 3.46
5389 5566 2.066393 CCTCATCGCCCCTCCTTCA 61.066 63.158 0.00 0.00 0.00 3.02
5390 5567 1.414061 CCTCATCGCCCCTCCTTCAT 61.414 60.000 0.00 0.00 0.00 2.57
5391 5568 0.034616 CTCATCGCCCCTCCTTCATC 59.965 60.000 0.00 0.00 0.00 2.92
5392 5569 0.690744 TCATCGCCCCTCCTTCATCA 60.691 55.000 0.00 0.00 0.00 3.07
5393 5570 0.250209 CATCGCCCCTCCTTCATCAG 60.250 60.000 0.00 0.00 0.00 2.90
5394 5571 0.399091 ATCGCCCCTCCTTCATCAGA 60.399 55.000 0.00 0.00 0.00 3.27
5395 5572 1.045350 TCGCCCCTCCTTCATCAGAG 61.045 60.000 0.00 0.00 0.00 3.35
5396 5573 1.148048 GCCCCTCCTTCATCAGAGC 59.852 63.158 0.00 0.00 0.00 4.09
5397 5574 1.835693 CCCCTCCTTCATCAGAGCC 59.164 63.158 0.00 0.00 0.00 4.70
5398 5575 1.445095 CCCTCCTTCATCAGAGCCG 59.555 63.158 0.00 0.00 0.00 5.52
5399 5576 1.445095 CCTCCTTCATCAGAGCCGG 59.555 63.158 0.00 0.00 0.00 6.13
5400 5577 1.445095 CTCCTTCATCAGAGCCGGG 59.555 63.158 2.18 0.00 0.00 5.73
5401 5578 2.203126 CCTTCATCAGAGCCGGGC 60.203 66.667 12.11 12.11 0.00 6.13
5402 5579 2.586245 CTTCATCAGAGCCGGGCA 59.414 61.111 23.09 0.00 0.00 5.36
5403 5580 1.078214 CTTCATCAGAGCCGGGCAA 60.078 57.895 23.09 3.52 0.00 4.52
5404 5581 0.677731 CTTCATCAGAGCCGGGCAAA 60.678 55.000 23.09 3.31 0.00 3.68
5405 5582 0.251121 TTCATCAGAGCCGGGCAAAA 60.251 50.000 23.09 3.70 0.00 2.44
5406 5583 0.960364 TCATCAGAGCCGGGCAAAAC 60.960 55.000 23.09 9.43 0.00 2.43
5407 5584 0.962356 CATCAGAGCCGGGCAAAACT 60.962 55.000 23.09 11.60 0.00 2.66
5408 5585 0.251341 ATCAGAGCCGGGCAAAACTT 60.251 50.000 23.09 0.00 0.00 2.66
5409 5586 1.172180 TCAGAGCCGGGCAAAACTTG 61.172 55.000 23.09 9.58 0.00 3.16
5410 5587 1.152756 AGAGCCGGGCAAAACTTGT 60.153 52.632 23.09 0.00 0.00 3.16
5411 5588 0.755327 AGAGCCGGGCAAAACTTGTT 60.755 50.000 23.09 0.00 0.00 2.83
5412 5589 0.597377 GAGCCGGGCAAAACTTGTTG 60.597 55.000 23.09 0.00 0.00 3.33
5413 5590 1.142965 GCCGGGCAAAACTTGTTGT 59.857 52.632 15.62 0.00 0.00 3.32
5414 5591 0.386113 GCCGGGCAAAACTTGTTGTA 59.614 50.000 15.62 0.00 0.00 2.41
5415 5592 1.601914 GCCGGGCAAAACTTGTTGTAG 60.602 52.381 15.62 0.00 0.00 2.74
5416 5593 1.679153 CCGGGCAAAACTTGTTGTAGT 59.321 47.619 0.00 0.00 0.00 2.73
5417 5594 2.879646 CCGGGCAAAACTTGTTGTAGTA 59.120 45.455 0.00 0.00 0.00 1.82
5418 5595 3.058501 CCGGGCAAAACTTGTTGTAGTAG 60.059 47.826 0.00 0.00 0.00 2.57
5419 5596 3.810941 CGGGCAAAACTTGTTGTAGTAGA 59.189 43.478 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.987912 CAGCCGAAAACCAAATGTAAATGT 59.012 37.500 0.00 0.00 0.00 2.71
47 48 1.176527 TAGCACTCCAATTTGCCTGC 58.823 50.000 0.00 0.00 39.75 4.85
83 84 3.512724 GCCTGTTAGTACCTTGGTCTACA 59.487 47.826 0.00 0.00 0.00 2.74
86 87 2.616524 TGCCTGTTAGTACCTTGGTCT 58.383 47.619 0.00 0.00 0.00 3.85
199 208 9.224267 CTGTTAGGTGAGTAGTACTACTTGTAA 57.776 37.037 31.14 22.19 45.63 2.41
209 218 3.276857 CCGAGCTGTTAGGTGAGTAGTA 58.723 50.000 0.00 0.00 0.00 1.82
210 219 2.093106 CCGAGCTGTTAGGTGAGTAGT 58.907 52.381 0.00 0.00 0.00 2.73
211 220 1.405821 CCCGAGCTGTTAGGTGAGTAG 59.594 57.143 0.00 0.00 0.00 2.57
245 254 4.583871 GTGATTTCCTCTCATCCTGTTGT 58.416 43.478 0.00 0.00 0.00 3.32
249 258 3.131933 ACTCGTGATTTCCTCTCATCCTG 59.868 47.826 0.00 0.00 0.00 3.86
347 363 3.450115 GGAGGTACGAGGCGCACT 61.450 66.667 10.83 3.39 0.00 4.40
628 664 2.064581 GCCCCATCCACCTCTACGT 61.065 63.158 0.00 0.00 0.00 3.57
674 746 0.620121 CCCTTCCCTTCCTCTGCTCT 60.620 60.000 0.00 0.00 0.00 4.09
698 770 3.846254 TCCTCCCGATCCCCCTCC 61.846 72.222 0.00 0.00 0.00 4.30
699 771 2.524640 GTCCTCCCGATCCCCCTC 60.525 72.222 0.00 0.00 0.00 4.30
700 772 4.541648 CGTCCTCCCGATCCCCCT 62.542 72.222 0.00 0.00 0.00 4.79
781 858 2.556287 GGAAGCAGCCGTCGTTTG 59.444 61.111 0.00 0.00 0.00 2.93
814 891 2.928988 ATCGCGGATCCTGGTCCAGA 62.929 60.000 21.23 6.96 38.21 3.86
840 920 4.974721 CCACCAAAGCGGCCCACT 62.975 66.667 0.00 0.00 39.03 4.00
852 939 2.595463 GCTGCTTGCTGTCCACCA 60.595 61.111 0.00 0.00 38.95 4.17
913 1006 2.600470 GGCCGGCCACTCCTTTTT 60.600 61.111 40.73 0.00 35.81 1.94
914 1007 3.897122 TGGCCGGCCACTCCTTTT 61.897 61.111 44.23 0.00 41.89 2.27
1082 1175 2.456577 AGGAGGAGAAAGAGAGAGCAC 58.543 52.381 0.00 0.00 0.00 4.40
1431 1528 2.304761 ACACAGGTACGATTTCCACCAT 59.695 45.455 0.00 0.00 34.62 3.55
1487 1584 6.488683 CCATAAACTACCAAAGTGAACTCCAA 59.511 38.462 0.00 0.00 38.88 3.53
1568 1666 6.206243 CAGAATAACAATCCAATAGCCCTCTG 59.794 42.308 0.00 0.00 0.00 3.35
1601 1699 6.980397 CAGGTAAAATTGGAAATCCTACATGC 59.020 38.462 0.44 0.00 36.82 4.06
1645 1743 0.248866 GGGCCACGAACACAAAACTG 60.249 55.000 4.39 0.00 0.00 3.16
1661 1759 1.683385 GGATGCCAGTTTATTCAGGGC 59.317 52.381 0.00 0.00 44.82 5.19
1668 1766 5.823045 GTGCTTTAGTAGGATGCCAGTTTAT 59.177 40.000 0.00 0.00 0.00 1.40
1683 1781 6.656693 AGCAGAAAGTAATGATGTGCTTTAGT 59.343 34.615 0.00 0.00 40.33 2.24
1684 1782 7.081526 AGCAGAAAGTAATGATGTGCTTTAG 57.918 36.000 0.00 0.00 40.33 1.85
1780 1878 8.853345 CAAAAGAACTGATTAATTCACCAATCG 58.147 33.333 0.00 0.00 34.52 3.34
1793 1891 7.516198 AACTACAGATGCAAAAGAACTGATT 57.484 32.000 0.00 0.00 33.53 2.57
1857 1955 2.548057 TCCAGTCTTGTTGTTGCGAATC 59.452 45.455 0.00 0.00 0.00 2.52
2039 2138 4.844349 TCCTCCTTCTACAATCTTTGGG 57.156 45.455 0.00 0.00 34.12 4.12
2060 2159 8.680903 CCAAGTAATTCTAGCATCTGTTTGAAT 58.319 33.333 0.00 0.00 33.82 2.57
2115 2214 3.780850 GAGGGGGAAATACAGGAGAAGAA 59.219 47.826 0.00 0.00 0.00 2.52
2150 2249 1.168714 CCAAGGGTGCTTAACTGCTC 58.831 55.000 0.00 0.00 0.00 4.26
2292 2391 2.261671 CACGTAGCTCCCGCTTGT 59.738 61.111 5.69 0.00 46.47 3.16
2330 2429 9.460019 TTCCTCATGTATATTGTGTCAATCAAA 57.540 29.630 0.00 0.00 0.00 2.69
2427 2526 3.245229 TGCAACAAAGTGGATGGGAGTAT 60.245 43.478 0.00 0.00 0.00 2.12
2538 2637 0.880278 CTATGGGTCGTGCATTCCCG 60.880 60.000 15.58 4.05 43.75 5.14
2602 2701 7.378728 GCACCAAAAACTACTAATTGACACTTC 59.621 37.037 0.00 0.00 0.00 3.01
2724 2825 9.270640 AGTATGAGATGCAGACAAAATAGAATC 57.729 33.333 0.00 0.00 41.13 2.52
2747 2848 6.127535 CGGAGGGAGTAAGTGAAATGTTAGTA 60.128 42.308 0.00 0.00 0.00 1.82
2760 2861 1.688772 TTCGGATCGGAGGGAGTAAG 58.311 55.000 2.99 0.00 0.00 2.34
2816 2917 3.819564 TTGACGCAGCCTCTATACAAT 57.180 42.857 0.00 0.00 0.00 2.71
2831 2932 4.084537 CCTTCCGATCCGAATTAATTGACG 60.085 45.833 5.17 3.90 0.00 4.35
3107 3224 4.383989 GGGGCAATTTGGAAAATATCAGCA 60.384 41.667 0.00 0.00 0.00 4.41
3152 3269 9.647797 CAATACATAATGAAATGGATGGGAATG 57.352 33.333 0.00 0.00 30.51 2.67
3198 3315 6.889198 AGAGGCTGAATATGTAGCTACAAAA 58.111 36.000 29.26 20.40 39.99 2.44
3266 3383 0.250234 ACTCCGTCCATGTGTCCATG 59.750 55.000 0.00 0.00 46.65 3.66
3675 3793 7.287950 CCATGAATGGTAATAATTCGTACACG 58.712 38.462 0.82 0.00 43.05 4.49
3710 3828 1.272425 TGGGTCGAATCTTGGGCAAAT 60.272 47.619 0.00 0.00 0.00 2.32
3826 3944 3.260884 TCCCTGTTAGAGGTGTTCATGAC 59.739 47.826 0.00 0.00 40.87 3.06
4026 4145 4.737855 TCCTATACAAGCAGGACAAGAC 57.262 45.455 0.00 0.00 35.99 3.01
4192 4311 3.190327 TGGTTCATGCAATACAGTTTCCG 59.810 43.478 0.00 0.00 0.00 4.30
4216 4335 7.725818 AAGATTGCACACACATATGATAGAG 57.274 36.000 10.38 0.52 0.00 2.43
4225 4344 4.924305 AACAGAAAGATTGCACACACAT 57.076 36.364 0.00 0.00 0.00 3.21
4251 4370 8.681486 TGTTAGCTAATCACGAGTTATACCTA 57.319 34.615 9.88 0.00 0.00 3.08
4263 4382 9.722056 CAAGAATAAACCATGTTAGCTAATCAC 57.278 33.333 9.88 0.00 0.00 3.06
4275 4394 8.816640 AAAGTACAAAGCAAGAATAAACCATG 57.183 30.769 0.00 0.00 0.00 3.66
4350 4518 2.298729 GGGCTTGTACTTTGGAAATGCA 59.701 45.455 0.00 0.00 0.00 3.96
4517 4685 3.013921 TGAAAGGCGTATGGAAATGGAC 58.986 45.455 0.00 0.00 0.00 4.02
4565 4733 3.458118 ACCGAATAATCCTGAATCACCCA 59.542 43.478 0.00 0.00 0.00 4.51
4738 4908 1.411246 AGTGTACACAACGCCTCTGAA 59.589 47.619 27.06 0.00 39.57 3.02
4765 4935 2.602878 CCCGAATAATATCACCCGACG 58.397 52.381 0.00 0.00 0.00 5.12
4852 5023 5.503846 GCATGAAACCAAACAACCATTGAAC 60.504 40.000 0.00 0.00 0.00 3.18
4945 5116 4.615223 GCTCGGGTTTTGGATGAAAGTTAC 60.615 45.833 0.00 0.00 0.00 2.50
5026 5197 1.822506 GGGACTAGCACCCTTCAAAC 58.177 55.000 15.77 0.00 43.65 2.93
5060 5233 5.353938 GGGAAAAAGGTTTACAGTTTGACC 58.646 41.667 0.00 0.00 0.00 4.02
5279 5456 9.889128 TGTTCATTGTACTATCATGATTGAAGA 57.111 29.630 21.64 14.65 34.96 2.87
5282 5459 9.835389 TGATGTTCATTGTACTATCATGATTGA 57.165 29.630 21.64 11.26 36.00 2.57
5312 5489 9.357652 AGTCGTCGCTAGTTGTAATTTTTATTA 57.642 29.630 0.00 0.00 0.00 0.98
5313 5490 8.248117 AGTCGTCGCTAGTTGTAATTTTTATT 57.752 30.769 0.00 0.00 0.00 1.40
5314 5491 7.823149 AGTCGTCGCTAGTTGTAATTTTTAT 57.177 32.000 0.00 0.00 0.00 1.40
5315 5492 7.807433 TGTAGTCGTCGCTAGTTGTAATTTTTA 59.193 33.333 0.00 0.00 0.00 1.52
5316 5493 6.642131 TGTAGTCGTCGCTAGTTGTAATTTTT 59.358 34.615 0.00 0.00 0.00 1.94
5317 5494 6.151691 TGTAGTCGTCGCTAGTTGTAATTTT 58.848 36.000 0.00 0.00 0.00 1.82
5318 5495 5.702865 TGTAGTCGTCGCTAGTTGTAATTT 58.297 37.500 0.00 0.00 0.00 1.82
5319 5496 5.300969 TGTAGTCGTCGCTAGTTGTAATT 57.699 39.130 0.00 0.00 0.00 1.40
5320 5497 4.952262 TGTAGTCGTCGCTAGTTGTAAT 57.048 40.909 0.00 0.00 0.00 1.89
5321 5498 4.747540 TTGTAGTCGTCGCTAGTTGTAA 57.252 40.909 0.00 0.00 0.00 2.41
5322 5499 4.747540 TTTGTAGTCGTCGCTAGTTGTA 57.252 40.909 0.00 0.00 0.00 2.41
5323 5500 3.631145 TTTGTAGTCGTCGCTAGTTGT 57.369 42.857 0.00 0.00 0.00 3.32
5324 5501 5.330295 AGTATTTGTAGTCGTCGCTAGTTG 58.670 41.667 0.00 0.00 0.00 3.16
5325 5502 5.557891 AGTATTTGTAGTCGTCGCTAGTT 57.442 39.130 0.00 0.00 0.00 2.24
5326 5503 5.557891 AAGTATTTGTAGTCGTCGCTAGT 57.442 39.130 0.00 0.00 0.00 2.57
5327 5504 6.140422 GCTTAAGTATTTGTAGTCGTCGCTAG 59.860 42.308 4.02 0.00 0.00 3.42
5328 5505 5.967674 GCTTAAGTATTTGTAGTCGTCGCTA 59.032 40.000 4.02 0.00 0.00 4.26
5329 5506 4.797349 GCTTAAGTATTTGTAGTCGTCGCT 59.203 41.667 4.02 0.00 0.00 4.93
5330 5507 4.316240 CGCTTAAGTATTTGTAGTCGTCGC 60.316 45.833 4.02 0.00 0.00 5.19
5331 5508 5.023920 TCGCTTAAGTATTTGTAGTCGTCG 58.976 41.667 4.02 0.00 0.00 5.12
5332 5509 6.026513 ACTCGCTTAAGTATTTGTAGTCGTC 58.973 40.000 4.02 0.00 0.00 4.20
5333 5510 5.947443 ACTCGCTTAAGTATTTGTAGTCGT 58.053 37.500 4.02 0.00 0.00 4.34
5334 5511 6.525628 TCAACTCGCTTAAGTATTTGTAGTCG 59.474 38.462 4.02 0.00 0.00 4.18
5335 5512 7.807687 TCAACTCGCTTAAGTATTTGTAGTC 57.192 36.000 4.02 0.00 0.00 2.59
5336 5513 7.331193 CCTTCAACTCGCTTAAGTATTTGTAGT 59.669 37.037 4.02 0.00 0.00 2.73
5337 5514 7.674240 GCCTTCAACTCGCTTAAGTATTTGTAG 60.674 40.741 4.02 6.92 0.00 2.74
5338 5515 6.091713 GCCTTCAACTCGCTTAAGTATTTGTA 59.908 38.462 4.02 0.00 0.00 2.41
5339 5516 5.106673 GCCTTCAACTCGCTTAAGTATTTGT 60.107 40.000 4.02 0.00 0.00 2.83
5340 5517 5.324697 GCCTTCAACTCGCTTAAGTATTTG 58.675 41.667 4.02 4.42 0.00 2.32
5341 5518 4.395231 GGCCTTCAACTCGCTTAAGTATTT 59.605 41.667 4.02 0.00 0.00 1.40
5342 5519 3.939592 GGCCTTCAACTCGCTTAAGTATT 59.060 43.478 4.02 0.00 0.00 1.89
5343 5520 3.532542 GGCCTTCAACTCGCTTAAGTAT 58.467 45.455 4.02 0.00 0.00 2.12
5344 5521 2.354403 GGGCCTTCAACTCGCTTAAGTA 60.354 50.000 0.84 0.00 0.00 2.24
5345 5522 1.610886 GGGCCTTCAACTCGCTTAAGT 60.611 52.381 0.84 0.00 0.00 2.24
5346 5523 1.087501 GGGCCTTCAACTCGCTTAAG 58.912 55.000 0.84 0.00 0.00 1.85
5347 5524 0.672401 CGGGCCTTCAACTCGCTTAA 60.672 55.000 0.84 0.00 0.00 1.85
5348 5525 1.079405 CGGGCCTTCAACTCGCTTA 60.079 57.895 0.84 0.00 0.00 3.09
5349 5526 2.358737 CGGGCCTTCAACTCGCTT 60.359 61.111 0.84 0.00 0.00 4.68
5370 5547 2.770048 AAGGAGGGGCGATGAGGG 60.770 66.667 0.00 0.00 0.00 4.30
5371 5548 1.414061 ATGAAGGAGGGGCGATGAGG 61.414 60.000 0.00 0.00 0.00 3.86
5372 5549 0.034616 GATGAAGGAGGGGCGATGAG 59.965 60.000 0.00 0.00 0.00 2.90
5373 5550 0.690744 TGATGAAGGAGGGGCGATGA 60.691 55.000 0.00 0.00 0.00 2.92
5374 5551 0.250209 CTGATGAAGGAGGGGCGATG 60.250 60.000 0.00 0.00 0.00 3.84
5375 5552 0.399091 TCTGATGAAGGAGGGGCGAT 60.399 55.000 0.00 0.00 0.00 4.58
5376 5553 1.001631 TCTGATGAAGGAGGGGCGA 59.998 57.895 0.00 0.00 0.00 5.54
5377 5554 1.445095 CTCTGATGAAGGAGGGGCG 59.555 63.158 0.00 0.00 0.00 6.13
5378 5555 1.148048 GCTCTGATGAAGGAGGGGC 59.852 63.158 0.00 0.00 0.00 5.80
5379 5556 1.835693 GGCTCTGATGAAGGAGGGG 59.164 63.158 0.00 0.00 0.00 4.79
5380 5557 1.445095 CGGCTCTGATGAAGGAGGG 59.555 63.158 0.00 0.00 0.00 4.30
5381 5558 1.445095 CCGGCTCTGATGAAGGAGG 59.555 63.158 0.00 0.00 0.00 4.30
5382 5559 1.445095 CCCGGCTCTGATGAAGGAG 59.555 63.158 0.00 0.00 0.00 3.69
5383 5560 2.735772 GCCCGGCTCTGATGAAGGA 61.736 63.158 0.71 0.00 0.00 3.36
5384 5561 2.203126 GCCCGGCTCTGATGAAGG 60.203 66.667 0.71 0.00 0.00 3.46
5385 5562 0.677731 TTTGCCCGGCTCTGATGAAG 60.678 55.000 11.61 0.00 0.00 3.02
5386 5563 0.251121 TTTTGCCCGGCTCTGATGAA 60.251 50.000 11.61 0.00 0.00 2.57
5387 5564 0.960364 GTTTTGCCCGGCTCTGATGA 60.960 55.000 11.61 0.00 0.00 2.92
5388 5565 0.962356 AGTTTTGCCCGGCTCTGATG 60.962 55.000 11.61 0.00 0.00 3.07
5389 5566 0.251341 AAGTTTTGCCCGGCTCTGAT 60.251 50.000 11.61 0.00 0.00 2.90
5390 5567 1.150536 AAGTTTTGCCCGGCTCTGA 59.849 52.632 11.61 0.00 0.00 3.27
5391 5568 1.286880 CAAGTTTTGCCCGGCTCTG 59.713 57.895 11.61 0.00 0.00 3.35
5392 5569 0.755327 AACAAGTTTTGCCCGGCTCT 60.755 50.000 11.61 1.30 0.00 4.09
5393 5570 0.597377 CAACAAGTTTTGCCCGGCTC 60.597 55.000 11.61 0.00 0.00 4.70
5394 5571 1.326951 ACAACAAGTTTTGCCCGGCT 61.327 50.000 11.61 0.00 0.00 5.52
5395 5572 0.386113 TACAACAAGTTTTGCCCGGC 59.614 50.000 1.04 1.04 0.00 6.13
5396 5573 1.679153 ACTACAACAAGTTTTGCCCGG 59.321 47.619 0.00 0.00 0.00 5.73
5397 5574 3.810941 TCTACTACAACAAGTTTTGCCCG 59.189 43.478 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.