Multiple sequence alignment - TraesCS5A01G491200

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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 TraesCS5A01G491200 chr5A 100.000 3898 0 0 1 3898 660202115 660206012 0.000000e+00 7199
1 TraesCS5A01G491200 chr5A 81.910 796 89 29 1685 2456 660251584 660252348 4.280000e-174 621
2 TraesCS5A01G491200 chr5A 86.975 476 32 12 675 1147 660250224 660250672 3.470000e-140 508
3 TraesCS5A01G491200 chr4D 91.640 2835 163 47 122 2914 482361393 482358591 0.000000e+00 3855
4 TraesCS5A01G491200 chr4D 85.793 908 77 30 678 1553 482255645 482254758 0.000000e+00 915
5 TraesCS5A01G491200 chr4D 82.618 932 97 34 1562 2456 482254654 482253751 0.000000e+00 763
6 TraesCS5A01G491200 chr4D 85.846 325 37 6 210 533 482328502 482328186 1.740000e-88 337
7 TraesCS5A01G491200 chr4B 92.185 755 39 10 2161 2914 612209737 612209002 0.000000e+00 1050
8 TraesCS5A01G491200 chr4B 93.260 638 37 6 1473 2107 612210365 612209731 0.000000e+00 935
9 TraesCS5A01G491200 chr4B 82.139 1019 119 28 1473 2456 612178090 612177100 0.000000e+00 815
10 TraesCS5A01G491200 chr4B 83.605 799 70 39 678 1468 612178896 612178151 0.000000e+00 693
11 TraesCS5A01G491200 chr4B 84.722 720 46 40 753 1417 612211084 612210374 0.000000e+00 662
12 TraesCS5A01G491200 chr4B 98.413 63 1 0 698 760 612212554 612212492 1.140000e-20 111
13 TraesCS5A01G491200 chr2B 80.777 952 157 23 2920 3863 215954748 215955681 0.000000e+00 721
14 TraesCS5A01G491200 chr2B 81.023 880 138 17 2915 3784 538959224 538958364 0.000000e+00 673
15 TraesCS5A01G491200 chr2B 76.281 995 189 30 2911 3898 168957201 168958155 1.630000e-133 486
16 TraesCS5A01G491200 chr2B 79.351 678 126 12 2919 3593 361716297 361715631 7.630000e-127 464
17 TraesCS5A01G491200 chr2B 80.360 611 116 4 3174 3781 180806040 180805431 9.870000e-126 460
18 TraesCS5A01G491200 chr2B 80.942 467 72 14 2914 3373 367735880 367736336 1.720000e-93 353
19 TraesCS5A01G491200 chr2B 74.055 979 185 43 2915 3881 291365783 291364862 1.740000e-88 337
20 TraesCS5A01G491200 chr7D 79.072 970 163 29 2915 3873 303542837 303543777 7.110000e-177 630
21 TraesCS5A01G491200 chr7D 80.882 612 102 9 2914 3523 554573119 554572521 5.900000e-128 468
22 TraesCS5A01G491200 chr7D 92.913 127 7 2 2 128 17126417 17126293 2.390000e-42 183
23 TraesCS5A01G491200 chr7D 91.538 130 8 2 2 131 509692249 509692375 4.000000e-40 176
24 TraesCS5A01G491200 chr2A 78.068 880 162 26 2915 3782 426881483 426880623 9.590000e-146 527
25 TraesCS5A01G491200 chr2A 77.139 678 122 25 2911 3581 119371039 119371690 2.860000e-96 363
26 TraesCS5A01G491200 chr2A 89.899 99 10 0 2915 3013 475378649 475378747 1.140000e-25 128
27 TraesCS5A01G491200 chr3B 77.727 880 153 38 2924 3784 347008570 347007715 2.090000e-137 499
28 TraesCS5A01G491200 chr3B 76.966 890 164 27 2915 3791 398379672 398378811 1.640000e-128 470
29 TraesCS5A01G491200 chr7B 76.932 880 160 26 2915 3784 375165235 375166081 9.870000e-126 460
30 TraesCS5A01G491200 chr2D 80.998 421 57 10 2914 3333 141322626 141322228 2.920000e-81 313
31 TraesCS5A01G491200 chr2D 81.746 252 41 3 3537 3784 355284090 355284340 5.110000e-49 206
32 TraesCS5A01G491200 chr2D 93.701 127 7 1 2 128 628953562 628953687 5.140000e-44 189
33 TraesCS5A01G491200 chr3A 93.023 129 9 0 1 129 568965971 568965843 5.140000e-44 189
34 TraesCS5A01G491200 chr7A 93.600 125 8 0 2 126 719461681 719461557 1.850000e-43 187
35 TraesCS5A01G491200 chr1D 92.969 128 8 1 2 129 202847715 202847589 6.650000e-43 185
36 TraesCS5A01G491200 chr3D 92.800 125 8 1 2 126 113789921 113790044 3.090000e-41 180
37 TraesCS5A01G491200 chr1A 92.126 127 10 0 2 128 77616566 77616440 3.090000e-41 180
38 TraesCS5A01G491200 chr1A 90.977 133 11 1 1 132 578325448 578325316 1.110000e-40 178


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 TraesCS5A01G491200 chr5A 660202115 660206012 3897 False 7199.0 7199 100.0000 1 3898 1 chr5A.!!$F1 3897
1 TraesCS5A01G491200 chr5A 660250224 660252348 2124 False 564.5 621 84.4425 675 2456 2 chr5A.!!$F2 1781
2 TraesCS5A01G491200 chr4D 482358591 482361393 2802 True 3855.0 3855 91.6400 122 2914 1 chr4D.!!$R2 2792
3 TraesCS5A01G491200 chr4D 482253751 482255645 1894 True 839.0 915 84.2055 678 2456 2 chr4D.!!$R3 1778
4 TraesCS5A01G491200 chr4B 612177100 612178896 1796 True 754.0 815 82.8720 678 2456 2 chr4B.!!$R1 1778
5 TraesCS5A01G491200 chr4B 612209002 612212554 3552 True 689.5 1050 92.1450 698 2914 4 chr4B.!!$R2 2216
6 TraesCS5A01G491200 chr2B 215954748 215955681 933 False 721.0 721 80.7770 2920 3863 1 chr2B.!!$F2 943
7 TraesCS5A01G491200 chr2B 538958364 538959224 860 True 673.0 673 81.0230 2915 3784 1 chr2B.!!$R4 869
8 TraesCS5A01G491200 chr2B 168957201 168958155 954 False 486.0 486 76.2810 2911 3898 1 chr2B.!!$F1 987
9 TraesCS5A01G491200 chr2B 361715631 361716297 666 True 464.0 464 79.3510 2919 3593 1 chr2B.!!$R3 674
10 TraesCS5A01G491200 chr2B 180805431 180806040 609 True 460.0 460 80.3600 3174 3781 1 chr2B.!!$R1 607
11 TraesCS5A01G491200 chr2B 291364862 291365783 921 True 337.0 337 74.0550 2915 3881 1 chr2B.!!$R2 966
12 TraesCS5A01G491200 chr7D 303542837 303543777 940 False 630.0 630 79.0720 2915 3873 1 chr7D.!!$F1 958
13 TraesCS5A01G491200 chr7D 554572521 554573119 598 True 468.0 468 80.8820 2914 3523 1 chr7D.!!$R2 609
14 TraesCS5A01G491200 chr2A 426880623 426881483 860 True 527.0 527 78.0680 2915 3782 1 chr2A.!!$R1 867
15 TraesCS5A01G491200 chr2A 119371039 119371690 651 False 363.0 363 77.1390 2911 3581 1 chr2A.!!$F1 670
16 TraesCS5A01G491200 chr3B 347007715 347008570 855 True 499.0 499 77.7270 2924 3784 1 chr3B.!!$R1 860
17 TraesCS5A01G491200 chr3B 398378811 398379672 861 True 470.0 470 76.9660 2915 3791 1 chr3B.!!$R2 876
18 TraesCS5A01G491200 chr7B 375165235 375166081 846 False 460.0 460 76.9320 2915 3784 1 chr7B.!!$F1 869

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
105 106 0.608035 TTTTAGCGCCTTCTGTGGGG 60.608 55.0 2.29 0.0 42.18 4.96 F
1090 2584 0.105709 GGGAGGGAGGGAGAAGAGAG 60.106 65.0 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 4138 0.245539 TATATGGTCTTAGGCCGCGC 59.754 55.0 0.0 0.0 0.00 6.86 R
3023 5186 1.550130 CCCGAACCTGGGTAGCTCAA 61.550 60.0 0.0 0.0 44.76 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
40 41 4.758251 CGCGACTGGGTGGCATCA 62.758 66.667 0.00 0.00 37.11 3.07
41 42 3.127533 GCGACTGGGTGGCATCAC 61.128 66.667 0.00 0.00 42.91 3.06
42 43 2.815211 CGACTGGGTGGCATCACG 60.815 66.667 0.00 0.00 44.50 4.35
91 92 2.807247 CCCAGGGGGCGATTTTTAG 58.193 57.895 0.00 0.00 35.35 1.85
92 93 1.391933 CCCAGGGGGCGATTTTTAGC 61.392 60.000 0.00 0.00 35.35 3.09
93 94 1.724582 CCAGGGGGCGATTTTTAGCG 61.725 60.000 0.00 0.00 0.00 4.26
100 101 1.815132 GCGATTTTTAGCGCCTTCTG 58.185 50.000 2.29 0.00 46.93 3.02
101 102 1.130561 GCGATTTTTAGCGCCTTCTGT 59.869 47.619 2.29 0.00 46.93 3.41
102 103 2.774007 CGATTTTTAGCGCCTTCTGTG 58.226 47.619 2.29 0.00 0.00 3.66
103 104 2.476185 CGATTTTTAGCGCCTTCTGTGG 60.476 50.000 2.29 0.00 0.00 4.17
104 105 1.243902 TTTTTAGCGCCTTCTGTGGG 58.756 50.000 2.29 0.00 0.00 4.61
105 106 0.608035 TTTTAGCGCCTTCTGTGGGG 60.608 55.000 2.29 0.00 42.18 4.96
109 110 4.659172 CGCCTTCTGTGGGGCCAA 62.659 66.667 4.39 0.00 45.01 4.52
110 111 2.991540 GCCTTCTGTGGGGCCAAC 60.992 66.667 3.33 3.33 42.30 3.77
111 112 2.672996 CCTTCTGTGGGGCCAACG 60.673 66.667 6.56 1.40 0.00 4.10
112 113 3.365265 CTTCTGTGGGGCCAACGC 61.365 66.667 6.56 3.84 0.00 4.84
164 165 8.203485 TGTGCTTTCTTTATTTTTCAGGATTGT 58.797 29.630 0.00 0.00 0.00 2.71
216 217 9.745018 TCTGGATGATTTAGAAAAACATCTTCT 57.255 29.630 16.95 0.00 35.60 2.85
258 259 4.579869 ACAGTGGTGTAATCAACTGATCC 58.420 43.478 8.54 0.00 34.05 3.36
289 290 8.664211 AGTCTCTTTATTTTGAACGAACTTCT 57.336 30.769 0.00 0.00 0.00 2.85
335 336 3.632145 AGGGCAACTTGTTAGAACACTTG 59.368 43.478 0.00 1.83 38.92 3.16
338 339 5.273944 GGCAACTTGTTAGAACACTTGAAG 58.726 41.667 12.91 0.00 38.92 3.02
352 353 8.696374 AGAACACTTGAAGATTATAAGATCCGA 58.304 33.333 0.00 0.00 0.00 4.55
417 419 2.027469 CCCCCTACTTGTATTATCCGCC 60.027 54.545 0.00 0.00 0.00 6.13
491 493 2.254546 TGCACGGTCAGAAGATTGTT 57.745 45.000 0.00 0.00 0.00 2.83
492 494 1.872952 TGCACGGTCAGAAGATTGTTG 59.127 47.619 0.00 0.00 0.00 3.33
493 495 1.873591 GCACGGTCAGAAGATTGTTGT 59.126 47.619 0.00 0.00 0.00 3.32
505 507 9.261180 TCAGAAGATTGTTGTGTACTAGAAAAG 57.739 33.333 0.00 0.00 0.00 2.27
508 510 6.238648 AGATTGTTGTGTACTAGAAAAGGGG 58.761 40.000 0.00 0.00 0.00 4.79
544 547 6.530181 CACTCACAGTTAATTACAGTGCGATA 59.470 38.462 7.64 0.00 42.25 2.92
548 551 8.245491 TCACAGTTAATTACAGTGCGATAAGTA 58.755 33.333 0.00 0.00 42.25 2.24
622 625 1.409661 CCGGGAAAAGGTATGGAAGGG 60.410 57.143 0.00 0.00 0.00 3.95
684 689 4.433805 CGCTTGTAGTATTGTTGTCCGTTC 60.434 45.833 0.00 0.00 0.00 3.95
974 2398 6.018588 CGCATACACCTAATCCGTAATTTTGA 60.019 38.462 0.00 0.00 0.00 2.69
1064 2548 3.572255 GTCACACCAGAGAGAGAGAAAGT 59.428 47.826 0.00 0.00 0.00 2.66
1072 2556 4.637534 CAGAGAGAGAGAAAGTGAGAGAGG 59.362 50.000 0.00 0.00 0.00 3.69
1076 2560 3.023832 GAGAGAAAGTGAGAGAGGGAGG 58.976 54.545 0.00 0.00 0.00 4.30
1080 2564 0.338120 AAGTGAGAGAGGGAGGGAGG 59.662 60.000 0.00 0.00 0.00 4.30
1085 2579 0.556380 AGAGAGGGAGGGAGGGAGAA 60.556 60.000 0.00 0.00 0.00 2.87
1089 2583 0.556380 AGGGAGGGAGGGAGAAGAGA 60.556 60.000 0.00 0.00 0.00 3.10
1090 2584 0.105709 GGGAGGGAGGGAGAAGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
1091 2585 0.930726 GGAGGGAGGGAGAAGAGAGA 59.069 60.000 0.00 0.00 0.00 3.10
1097 2596 2.422945 GGAGGGAGAAGAGAGAGAGGAC 60.423 59.091 0.00 0.00 0.00 3.85
1100 2599 2.285977 GGAGAAGAGAGAGAGGACGAC 58.714 57.143 0.00 0.00 0.00 4.34
1107 2606 2.011856 GAGAGAGGACGACGACGACG 62.012 65.000 17.60 17.60 42.66 5.12
1109 2608 2.011856 GAGAGGACGACGACGACGAG 62.012 65.000 25.15 9.88 42.66 4.18
1257 2764 2.945668 GCTTATTCACCAGAATCGGCTT 59.054 45.455 0.00 0.00 43.26 4.35
1279 2786 0.380733 GCCGCTGGCTAATTACAACC 59.619 55.000 11.61 0.00 46.69 3.77
1280 2787 2.017113 GCCGCTGGCTAATTACAACCT 61.017 52.381 11.61 0.00 46.69 3.50
1286 2793 4.683400 GCTGGCTAATTACAACCTCAGCTA 60.683 45.833 0.00 0.00 41.91 3.32
1291 2803 6.049149 GCTAATTACAACCTCAGCTACATCA 58.951 40.000 0.00 0.00 0.00 3.07
1294 2806 9.935241 CTAATTACAACCTCAGCTACATCATAT 57.065 33.333 0.00 0.00 0.00 1.78
1303 2815 9.314133 ACCTCAGCTACATCATATAGTGAATAA 57.686 33.333 0.00 0.00 40.97 1.40
1346 2858 2.783284 CGTCATGTTTAATTCGGCATGC 59.217 45.455 9.90 9.90 38.72 4.06
1445 2971 0.675522 CCCTTACGATGCAACCGGTT 60.676 55.000 15.86 15.86 0.00 4.44
1510 3095 2.410730 GGATCACGTTAACCTGTTGTCG 59.589 50.000 0.00 0.74 0.00 4.35
1525 3113 2.075761 GTCGGTGGGAAAATCGACG 58.924 57.895 0.00 0.00 41.60 5.12
1560 3243 7.709149 AAGCTAAGTCCAATTTAGAAAGCAT 57.291 32.000 0.00 0.00 31.26 3.79
1638 3329 3.721087 AAGTCGATTTTGTGGGAGGAT 57.279 42.857 0.00 0.00 0.00 3.24
1710 3822 7.556275 GGTTGTTGGATCTTAATCTAATGACCA 59.444 37.037 11.09 0.00 38.55 4.02
1711 3823 8.616076 GTTGTTGGATCTTAATCTAATGACCAG 58.384 37.037 0.00 0.00 35.19 4.00
1733 3845 3.439129 GGAAAACCGACTTACCCAAGATG 59.561 47.826 0.00 0.00 35.60 2.90
1763 3875 8.296713 TCTAAAAACACATAGAAAATGAGGTGC 58.703 33.333 0.00 0.00 0.00 5.01
1785 3897 7.358066 GTGCCATGTAAGAAGTCATGAATATG 58.642 38.462 0.00 0.00 42.52 1.78
1812 3927 0.879090 GCCGGTTCAAAACTTCCGAT 59.121 50.000 1.90 0.00 44.86 4.18
1828 3943 5.297527 ACTTCCGATACAAAGGAAAAACGTT 59.702 36.000 0.00 0.00 44.89 3.99
1878 3995 3.135530 ACATAGGAGAAAGCCCTCATGTC 59.864 47.826 0.00 0.00 35.30 3.06
1919 4039 7.999679 TGCTATGGAATTTTCTTTACCTGATG 58.000 34.615 0.00 0.00 0.00 3.07
1980 4102 9.959749 TCGCAATTTTTCCTATATGAATTTACC 57.040 29.630 0.00 0.00 0.00 2.85
1996 4138 8.348285 TGAATTTACCCATTCAAAGTTCTAGG 57.652 34.615 0.00 0.00 39.69 3.02
2076 4220 5.707298 ACATGGATCGTTCTTTGATTCTTGT 59.293 36.000 0.00 0.00 35.82 3.16
2159 4305 7.954788 TTGAAAATAAAATACCTTGGTGCAC 57.045 32.000 8.80 8.80 0.00 4.57
2226 4372 4.037803 TGATCATTGGCCCATGAATTAACG 59.962 41.667 22.32 0.00 0.00 3.18
2233 4385 3.438360 GCCCATGAATTAACGCTCTTTG 58.562 45.455 0.00 0.00 0.00 2.77
2395 4547 4.006989 CCGGTGATGAAAAGGAACATGTA 58.993 43.478 0.00 0.00 0.00 2.29
2532 4685 8.764287 GTTTTATTTTGGGAAGTTTCTCACATG 58.236 33.333 0.00 0.00 37.41 3.21
2584 4737 6.250344 ACGAAAAACTTAGTTCCCTTATGC 57.750 37.500 0.00 0.00 0.00 3.14
2652 4805 2.443255 TCATATTTCCCCTCTTCCAGGC 59.557 50.000 0.00 0.00 41.80 4.85
2661 4814 1.065418 CCTCTTCCAGGCAATTACCGT 60.065 52.381 0.00 0.00 34.56 4.83
2728 4881 4.789075 GCTGTGCCGCTTGCCATG 62.789 66.667 0.00 0.00 40.16 3.66
2730 4883 3.620300 CTGTGCCGCTTGCCATGTG 62.620 63.158 0.00 0.00 40.16 3.21
2786 4939 4.137543 CTCTTGGCCTTGTACTTTCAAGT 58.862 43.478 3.32 0.00 42.01 3.16
2817 4970 9.542462 GGCTCACTAATGATTTATGTACTACAA 57.458 33.333 0.00 0.00 33.22 2.41
2839 4993 7.967771 CAATCATGTATTGTTCAAATACGCA 57.032 32.000 8.75 0.00 40.19 5.24
2840 4994 8.564648 CAATCATGTATTGTTCAAATACGCAT 57.435 30.769 8.75 0.00 40.19 4.73
2914 5068 5.103043 TGTCTCCCTCTATCAATTACTCCCT 60.103 44.000 0.00 0.00 0.00 4.20
2915 5069 5.245075 GTCTCCCTCTATCAATTACTCCCTG 59.755 48.000 0.00 0.00 0.00 4.45
2916 5070 5.103043 TCTCCCTCTATCAATTACTCCCTGT 60.103 44.000 0.00 0.00 0.00 4.00
2917 5071 5.148502 TCCCTCTATCAATTACTCCCTGTC 58.851 45.833 0.00 0.00 0.00 3.51
2918 5072 4.021894 CCCTCTATCAATTACTCCCTGTCG 60.022 50.000 0.00 0.00 0.00 4.35
2919 5073 4.021894 CCTCTATCAATTACTCCCTGTCGG 60.022 50.000 0.00 0.00 0.00 4.79
3023 5186 2.688507 CTAGGCACGACAAAGACACAT 58.311 47.619 0.00 0.00 0.00 3.21
3142 5307 0.668535 GGCTCTTGGGTGTCAACAAC 59.331 55.000 0.00 0.00 0.00 3.32
3143 5308 1.388547 GCTCTTGGGTGTCAACAACA 58.611 50.000 0.00 0.00 34.61 3.33
3150 5325 0.030638 GGTGTCAACAACAGCGCAAT 59.969 50.000 11.47 0.00 45.61 3.56
3162 5337 2.717485 CGCAATGGGCCGATCAAG 59.283 61.111 0.00 0.00 40.31 3.02
3164 5339 1.453745 GCAATGGGCCGATCAAGGA 60.454 57.895 0.00 0.00 36.11 3.36
3165 5340 1.450531 GCAATGGGCCGATCAAGGAG 61.451 60.000 0.00 0.00 36.11 3.69
3166 5341 1.152881 AATGGGCCGATCAAGGAGC 60.153 57.895 0.00 0.00 0.00 4.70
3167 5342 2.631012 AATGGGCCGATCAAGGAGCC 62.631 60.000 0.00 0.00 44.99 4.70
3169 5344 2.512896 GGCCGATCAAGGAGCCAT 59.487 61.111 0.00 0.00 45.07 4.40
3170 5345 1.599240 GGCCGATCAAGGAGCCATC 60.599 63.158 0.00 0.00 45.07 3.51
3171 5346 1.449353 GCCGATCAAGGAGCCATCT 59.551 57.895 0.00 0.00 0.00 2.90
3172 5347 0.179034 GCCGATCAAGGAGCCATCTT 60.179 55.000 0.00 0.00 0.00 2.40
3184 5382 1.925255 AGCCATCTTCCAATCCCTTGA 59.075 47.619 0.00 0.00 34.04 3.02
3187 5385 4.077822 GCCATCTTCCAATCCCTTGATAG 58.922 47.826 0.00 0.00 34.04 2.08
3197 5395 2.588877 CTTGATAGGGTGGCCGCG 60.589 66.667 10.86 0.00 0.00 6.46
3383 5588 2.259818 CTCCGTCTTGCAGCGTCT 59.740 61.111 6.64 0.00 0.00 4.18
3398 5603 0.596577 CGTCTTCGTCCTGGTCTTCA 59.403 55.000 0.00 0.00 0.00 3.02
3410 5615 2.886523 CTGGTCTTCATTCACCAAAGCA 59.113 45.455 0.00 0.00 42.28 3.91
3635 5866 1.271217 GGTGGTACTTGGTGAAGTCCC 60.271 57.143 0.00 0.00 41.75 4.46
3645 5877 0.680061 GTGAAGTCCCTTGTCGGAGT 59.320 55.000 0.00 0.00 37.15 3.85
3720 5952 0.984995 GGGCTACCTCTTGAGTTGGT 59.015 55.000 0.00 0.00 37.83 3.67
3753 5985 4.429522 TGGGCCGCATGCAGATGT 62.430 61.111 19.57 0.00 43.89 3.06
3771 6003 1.461849 TCCCGTGGTACCCTGGTTT 60.462 57.895 10.07 0.00 0.00 3.27
3784 6016 2.359975 GGTTTCCACTGGGCCGAG 60.360 66.667 14.03 14.03 0.00 4.63
3795 6027 2.043248 GGCCGAGAGTAGTCCCCA 60.043 66.667 0.00 0.00 0.00 4.96
3800 6032 1.311747 GAGAGTAGTCCCCAGGCCT 59.688 63.158 0.00 0.00 0.00 5.19
3834 6066 0.671781 CTGCCTGTTGAGGGACGAAG 60.672 60.000 0.00 0.00 40.19 3.79
3853 6085 4.525949 GACGCGGGGCCTAAGACC 62.526 72.222 12.47 0.00 0.00 3.85
3859 6091 3.073101 GGGCCTAAGACCGTCGGT 61.073 66.667 18.94 18.94 39.44 4.69
3881 6113 0.821517 CATGCAAGGACACATGGCAT 59.178 50.000 0.00 0.00 45.33 4.40
3883 6115 0.038599 TGCAAGGACACATGGCATCT 59.961 50.000 0.00 0.00 0.00 2.90
3886 6118 0.107508 AAGGACACATGGCATCTCGG 60.108 55.000 0.00 0.00 0.00 4.63
3888 6120 2.512286 ACACATGGCATCTCGGCG 60.512 61.111 0.00 0.00 45.16 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.110352 CGGCGCCTACGGGATTTTT 61.110 57.895 26.68 0.00 40.57 1.94
7 8 2.512974 CGGCGCCTACGGGATTTT 60.513 61.111 26.68 0.00 40.57 1.82
23 24 4.758251 TGATGCCACCCAGTCGCG 62.758 66.667 0.00 0.00 0.00 5.87
24 25 3.127533 GTGATGCCACCCAGTCGC 61.128 66.667 0.00 0.00 37.33 5.19
25 26 2.815211 CGTGATGCCACCCAGTCG 60.815 66.667 0.00 0.00 40.12 4.18
26 27 3.127533 GCGTGATGCCACCCAGTC 61.128 66.667 0.00 0.00 40.12 3.51
74 75 1.724582 CGCTAAAAATCGCCCCCTGG 61.725 60.000 0.00 0.00 0.00 4.45
75 76 1.727467 CGCTAAAAATCGCCCCCTG 59.273 57.895 0.00 0.00 0.00 4.45
76 77 2.119029 GCGCTAAAAATCGCCCCCT 61.119 57.895 0.00 0.00 45.01 4.79
77 78 2.411701 GCGCTAAAAATCGCCCCC 59.588 61.111 0.00 0.00 45.01 5.40
82 83 2.476185 CCACAGAAGGCGCTAAAAATCG 60.476 50.000 7.64 0.00 0.00 3.34
83 84 2.159379 CCCACAGAAGGCGCTAAAAATC 60.159 50.000 7.64 0.00 0.00 2.17
84 85 1.818674 CCCACAGAAGGCGCTAAAAAT 59.181 47.619 7.64 0.00 0.00 1.82
85 86 1.243902 CCCACAGAAGGCGCTAAAAA 58.756 50.000 7.64 0.00 0.00 1.94
86 87 0.608035 CCCCACAGAAGGCGCTAAAA 60.608 55.000 7.64 0.00 0.00 1.52
87 88 1.002624 CCCCACAGAAGGCGCTAAA 60.003 57.895 7.64 0.00 0.00 1.85
88 89 2.668632 CCCCACAGAAGGCGCTAA 59.331 61.111 7.64 0.00 0.00 3.09
89 90 4.096003 GCCCCACAGAAGGCGCTA 62.096 66.667 7.64 0.00 39.87 4.26
94 95 2.672996 CGTTGGCCCCACAGAAGG 60.673 66.667 0.00 0.00 0.00 3.46
95 96 3.365265 GCGTTGGCCCCACAGAAG 61.365 66.667 0.00 0.00 0.00 2.85
105 106 1.986575 GAGCATCTTCAGGCGTTGGC 61.987 60.000 0.00 0.00 38.90 4.52
106 107 2.093216 GAGCATCTTCAGGCGTTGG 58.907 57.895 0.00 0.00 34.54 3.77
118 119 3.068873 ACATCGAAGTCCCTTAGAGCATC 59.931 47.826 0.00 0.00 29.57 3.91
119 120 3.034635 ACATCGAAGTCCCTTAGAGCAT 58.965 45.455 0.00 0.00 29.57 3.79
120 121 2.166459 CACATCGAAGTCCCTTAGAGCA 59.834 50.000 0.00 0.00 29.57 4.26
216 217 9.535878 CCACTGTTTAAACCTAGCAATTAAAAA 57.464 29.630 15.59 3.11 32.21 1.94
222 223 5.137551 ACACCACTGTTTAAACCTAGCAAT 58.862 37.500 15.59 0.00 0.00 3.56
281 282 3.318017 CCGGCCTCATTATAGAAGTTCG 58.682 50.000 0.00 0.00 0.00 3.95
289 290 1.202758 CCACTTGCCGGCCTCATTATA 60.203 52.381 26.77 0.00 0.00 0.98
316 317 6.119144 TCTTCAAGTGTTCTAACAAGTTGC 57.881 37.500 1.81 0.00 41.21 4.17
326 327 8.696374 TCGGATCTTATAATCTTCAAGTGTTCT 58.304 33.333 0.00 0.00 0.00 3.01
396 398 2.027469 GGCGGATAATACAAGTAGGGGG 60.027 54.545 0.00 0.00 0.00 5.40
406 408 8.331730 ACTTAAAATACCATGGCGGATAATAC 57.668 34.615 13.04 0.00 38.63 1.89
414 416 4.578516 TGGATGACTTAAAATACCATGGCG 59.421 41.667 13.04 0.00 0.00 5.69
417 419 6.511767 GCTCGTGGATGACTTAAAATACCATG 60.512 42.308 0.00 0.00 35.20 3.66
454 456 4.333649 CGTGCAATGAGGATAAGTGACATT 59.666 41.667 0.00 0.00 0.00 2.71
455 457 3.873361 CGTGCAATGAGGATAAGTGACAT 59.127 43.478 0.00 0.00 0.00 3.06
491 493 5.836024 AACATCCCCTTTTCTAGTACACA 57.164 39.130 0.00 0.00 0.00 3.72
492 494 5.646793 GGAAACATCCCCTTTTCTAGTACAC 59.353 44.000 0.00 0.00 33.10 2.90
493 495 5.311121 TGGAAACATCCCCTTTTCTAGTACA 59.689 40.000 0.00 0.00 33.10 2.90
562 565 7.119846 CCCTTCAGACTTTAAGTTCAATGTAGG 59.880 40.741 0.00 8.58 0.00 3.18
573 576 3.583086 TCCTGTCCCCTTCAGACTTTAAG 59.417 47.826 0.00 0.00 35.21 1.85
577 580 1.981495 CTTCCTGTCCCCTTCAGACTT 59.019 52.381 0.00 0.00 35.21 3.01
578 581 1.132689 ACTTCCTGTCCCCTTCAGACT 60.133 52.381 0.00 0.00 35.21 3.24
622 625 5.860716 GCAGAATGATTGAACTCCAAAAGTC 59.139 40.000 0.00 0.00 39.69 3.01
630 633 3.063180 CCGACTGCAGAATGATTGAACTC 59.937 47.826 23.35 1.25 39.69 3.01
635 638 1.325640 CGTCCGACTGCAGAATGATTG 59.674 52.381 23.35 0.52 39.69 2.67
684 689 4.457257 AGGAAAAGGATTTCTCAAGCTTCG 59.543 41.667 0.00 0.00 43.65 3.79
1016 2440 0.463620 GTTGTTTGCTGCCTTGGGAA 59.536 50.000 0.00 0.00 0.00 3.97
1064 2548 1.230650 TCCCTCCCTCCCTCTCTCA 60.231 63.158 0.00 0.00 0.00 3.27
1072 2556 0.930726 TCTCTCTTCTCCCTCCCTCC 59.069 60.000 0.00 0.00 0.00 4.30
1076 2560 1.850345 TCCTCTCTCTCTTCTCCCTCC 59.150 57.143 0.00 0.00 0.00 4.30
1080 2564 2.285977 GTCGTCCTCTCTCTCTTCTCC 58.714 57.143 0.00 0.00 0.00 3.71
1085 2579 0.458889 CGTCGTCGTCCTCTCTCTCT 60.459 60.000 0.00 0.00 0.00 3.10
1089 2583 2.093473 CGTCGTCGTCGTCCTCTCT 61.093 63.158 3.67 0.00 38.33 3.10
1090 2584 2.011856 CTCGTCGTCGTCGTCCTCTC 62.012 65.000 11.41 0.00 38.33 3.20
1091 2585 2.048784 TCGTCGTCGTCGTCCTCT 60.049 61.111 11.41 0.00 38.33 3.69
1097 2596 3.703939 CTGCTCCTCGTCGTCGTCG 62.704 68.421 5.50 5.50 38.33 5.12
1100 2599 3.102107 CTCCTGCTCCTCGTCGTCG 62.102 68.421 0.00 0.00 38.55 5.12
1107 2606 1.457455 CCTCCTCCTCCTGCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
1109 2608 1.002274 TTCCTCCTCCTCCTGCTCC 59.998 63.158 0.00 0.00 0.00 4.70
1234 2740 2.682856 GCCGATTCTGGTGAATAAGCAA 59.317 45.455 0.00 0.00 42.43 3.91
1237 2743 5.335127 CAAAAGCCGATTCTGGTGAATAAG 58.665 41.667 0.00 0.00 42.43 1.73
1294 2806 8.539544 TCACCTCATGAGTTCATTTATTCACTA 58.460 33.333 21.11 0.00 33.61 2.74
1311 2823 1.931841 CATGACGAAGCTCACCTCATG 59.068 52.381 13.62 13.62 34.07 3.07
1356 2868 2.205022 TTCCCTGATGAAAGGCAGTG 57.795 50.000 0.00 0.00 35.85 3.66
1382 2907 2.146342 GCTCTCAAGCTAACAACTGCA 58.854 47.619 0.00 0.00 45.55 4.41
1427 2953 0.446222 CAACCGGTTGCATCGTAAGG 59.554 55.000 32.87 6.99 33.45 2.69
1465 2994 9.905713 TCCTAACAATAAATTGAGCTTCTGTAT 57.094 29.630 9.60 0.00 40.14 2.29
1468 2997 8.896744 TGATCCTAACAATAAATTGAGCTTCTG 58.103 33.333 9.60 0.00 40.14 3.02
1470 2999 7.852945 CGTGATCCTAACAATAAATTGAGCTTC 59.147 37.037 9.60 0.70 40.14 3.86
1484 3069 4.877378 ACAGGTTAACGTGATCCTAACA 57.123 40.909 29.54 0.00 35.83 2.41
1510 3095 1.515081 TTGTCGTCGATTTTCCCACC 58.485 50.000 0.00 0.00 0.00 4.61
1577 3260 7.974675 TCAGTCAACTTACATTTAGCTATTGC 58.025 34.615 0.00 0.00 40.05 3.56
1587 3270 8.891671 AATTGCAAATTCAGTCAACTTACATT 57.108 26.923 1.71 0.00 0.00 2.71
1638 3329 3.358111 TCTTGCCCATCCAATCGTTTA 57.642 42.857 0.00 0.00 0.00 2.01
1710 3822 2.707257 TCTTGGGTAAGTCGGTTTTCCT 59.293 45.455 0.00 0.00 35.10 3.36
1711 3823 3.130280 TCTTGGGTAAGTCGGTTTTCC 57.870 47.619 0.00 0.00 35.38 3.13
1760 3872 5.824904 ATTCATGACTTCTTACATGGCAC 57.175 39.130 0.00 0.00 42.53 5.01
1763 3875 7.741027 AGCATATTCATGACTTCTTACATGG 57.259 36.000 0.00 0.00 42.53 3.66
1785 3897 2.065906 TTTTGAACCGGCGGTGAAGC 62.066 55.000 34.87 21.71 35.34 3.86
1828 3943 5.487488 CCCCCTACATATGCCTATAACTCAA 59.513 44.000 1.58 0.00 0.00 3.02
1857 3973 3.390639 AGACATGAGGGCTTTCTCCTATG 59.609 47.826 0.00 0.00 34.21 2.23
1878 3995 7.587037 TCCATAGCATTTTGGAGGAAAATAG 57.413 36.000 0.00 0.00 41.50 1.73
1919 4039 2.435805 TGCTCATCAGGGTTCCTATGAC 59.564 50.000 0.00 0.00 29.64 3.06
1980 4102 1.062587 CGCGCCTAGAACTTTGAATGG 59.937 52.381 0.00 0.00 0.00 3.16
1996 4138 0.245539 TATATGGTCTTAGGCCGCGC 59.754 55.000 0.00 0.00 0.00 6.86
2190 4336 6.998673 GGGCCAATGATCAGTTTAATAGTAGT 59.001 38.462 4.39 0.00 0.00 2.73
2191 4337 6.998074 TGGGCCAATGATCAGTTTAATAGTAG 59.002 38.462 2.13 0.00 0.00 2.57
2226 4372 4.260051 GCGGGTTAAAACAAAACAAAGAGC 60.260 41.667 0.00 0.00 0.00 4.09
2233 4385 3.439895 TCCTGCGGGTTAAAACAAAAC 57.560 42.857 12.43 0.00 0.00 2.43
2417 4570 9.797642 TTCACAGATCATAATTTGTGCCTATAT 57.202 29.630 5.81 0.00 43.98 0.86
2418 4571 9.276590 CTTCACAGATCATAATTTGTGCCTATA 57.723 33.333 5.81 0.00 43.98 1.31
2419 4572 7.776969 ACTTCACAGATCATAATTTGTGCCTAT 59.223 33.333 5.81 0.00 43.98 2.57
2652 4805 7.487509 TGATATTTGTGCAATTGACGGTAATTG 59.512 33.333 10.34 17.28 46.03 2.32
2661 4814 6.343716 ACAAGGTGATATTTGTGCAATTGA 57.656 33.333 10.34 0.00 36.26 2.57
2726 4879 9.883142 TTTCCTTTTCTTGACAAAATTACACAT 57.117 25.926 0.00 0.00 0.00 3.21
2817 4970 7.706159 ACATGCGTATTTGAACAATACATGAT 58.294 30.769 0.00 0.00 33.81 2.45
2834 4988 8.561212 ACATTCAAAGTACTTAAAACATGCGTA 58.439 29.630 8.92 0.00 0.00 4.42
2881 5035 6.581388 TGATAGAGGGAGACATGGAATTTT 57.419 37.500 0.00 0.00 0.00 1.82
2882 5036 6.581388 TTGATAGAGGGAGACATGGAATTT 57.419 37.500 0.00 0.00 0.00 1.82
2885 5039 6.846505 AGTAATTGATAGAGGGAGACATGGAA 59.153 38.462 0.00 0.00 0.00 3.53
2914 5068 2.680805 GCTCAGAATCAATTCCCCGACA 60.681 50.000 0.00 0.00 37.51 4.35
2915 5069 1.943340 GCTCAGAATCAATTCCCCGAC 59.057 52.381 0.00 0.00 37.51 4.79
2916 5070 1.839994 AGCTCAGAATCAATTCCCCGA 59.160 47.619 0.00 0.00 37.51 5.14
2917 5071 2.338577 AGCTCAGAATCAATTCCCCG 57.661 50.000 0.00 0.00 37.51 5.73
2918 5072 3.134458 CGTAGCTCAGAATCAATTCCCC 58.866 50.000 0.00 0.00 37.51 4.81
2919 5073 3.134458 CCGTAGCTCAGAATCAATTCCC 58.866 50.000 0.00 0.00 37.51 3.97
2920 5074 3.134458 CCCGTAGCTCAGAATCAATTCC 58.866 50.000 0.00 0.00 37.51 3.01
2921 5075 4.060038 TCCCGTAGCTCAGAATCAATTC 57.940 45.455 0.00 0.00 37.06 2.17
2922 5076 4.487714 TTCCCGTAGCTCAGAATCAATT 57.512 40.909 0.00 0.00 0.00 2.32
3023 5186 1.550130 CCCGAACCTGGGTAGCTCAA 61.550 60.000 0.00 0.00 44.76 3.02
3123 5286 0.668535 GTTGTTGACACCCAAGAGCC 59.331 55.000 0.00 0.00 35.03 4.70
3142 5307 3.957535 GATCGGCCCATTGCGCTG 61.958 66.667 9.73 0.00 42.61 5.18
3143 5308 3.993614 TTGATCGGCCCATTGCGCT 62.994 57.895 9.73 0.00 42.61 5.92
3150 5325 3.797353 GGCTCCTTGATCGGCCCA 61.797 66.667 0.00 0.00 38.77 5.36
3162 5337 0.849417 AGGGATTGGAAGATGGCTCC 59.151 55.000 0.00 0.00 0.00 4.70
3164 5339 1.925255 TCAAGGGATTGGAAGATGGCT 59.075 47.619 0.00 0.00 0.00 4.75
3165 5340 2.442236 TCAAGGGATTGGAAGATGGC 57.558 50.000 0.00 0.00 0.00 4.40
3166 5341 4.660168 CCTATCAAGGGATTGGAAGATGG 58.340 47.826 0.00 0.00 45.75 3.51
3197 5395 2.851805 GCACCTATAAAAGTGGCAGC 57.148 50.000 0.00 0.00 34.48 5.25
3383 5588 2.289444 GGTGAATGAAGACCAGGACGAA 60.289 50.000 0.00 0.00 31.97 3.85
3410 5615 2.371658 AGCAAGTCCCAAAGCTTTCT 57.628 45.000 9.23 0.00 32.52 2.52
3524 5737 3.430862 CGGGTCACGTGCCCATTG 61.431 66.667 33.02 20.61 46.40 2.82
3609 5836 1.414919 TCACCAAGTACCACCACAGTC 59.585 52.381 0.00 0.00 0.00 3.51
3635 5866 2.266055 GAGGGGCACTCCGACAAG 59.734 66.667 5.13 0.00 40.49 3.16
3745 5977 1.594833 GTACCACGGGACATCTGCA 59.405 57.895 0.00 0.00 0.00 4.41
3771 6003 1.379977 CTACTCTCGGCCCAGTGGA 60.380 63.158 11.95 0.00 0.00 4.02
3784 6016 2.736826 GCAGGCCTGGGGACTACTC 61.737 68.421 33.46 10.16 40.42 2.59
3816 6048 1.371183 CTTCGTCCCTCAACAGGCA 59.629 57.895 0.00 0.00 38.72 4.75
3853 6085 2.819595 CCTTGCATGGGACCGACG 60.820 66.667 10.81 0.00 0.00 5.12
3859 6091 3.269578 CATGTGTCCTTGCATGGGA 57.730 52.632 17.95 11.38 38.90 4.37
3864 6096 0.038599 AGATGCCATGTGTCCTTGCA 59.961 50.000 0.00 0.00 0.00 4.08
3875 6107 4.241555 GTCCCGCCGAGATGCCAT 62.242 66.667 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.