Multiple sequence alignment - TraesCS2A01G278600

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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 TraesCS2A01G278600 chr2A 100.000 2043 0 0 1641 3683 461495861 461493819 0.000000e+00 3773.0
1 TraesCS2A01G278600 chr2A 100.000 1232 0 0 1 1232 461497501 461496270 0.000000e+00 2276.0
2 TraesCS2A01G278600 chr2B 91.749 1515 71 26 1641 3130 413080488 413079003 0.000000e+00 2056.0
3 TraesCS2A01G278600 chr2B 94.776 536 16 4 706 1232 413081095 413080563 0.000000e+00 824.0
4 TraesCS2A01G278600 chr2B 87.295 488 43 11 212 685 627316134 627315652 1.160000e-149 540.0
5 TraesCS2A01G278600 chr2B 94.545 55 3 0 2326 2380 413079771 413079717 6.550000e-13 86.1
6 TraesCS2A01G278600 chr7A 96.589 557 12 3 3131 3683 668000972 668001525 0.000000e+00 917.0
7 TraesCS2A01G278600 chr7A 86.096 187 25 1 490 676 725225906 725225721 2.240000e-47 200.0
8 TraesCS2A01G278600 chr7A 86.719 128 17 0 3131 3258 34720019 34720146 3.830000e-30 143.0
9 TraesCS2A01G278600 chr2D 95.510 490 15 4 749 1232 347815084 347814596 0.000000e+00 776.0
10 TraesCS2A01G278600 chr2D 85.771 759 71 22 1641 2380 347814522 347813782 0.000000e+00 769.0
11 TraesCS2A01G278600 chr2D 89.620 395 34 6 2544 2934 347813695 347813304 2.550000e-136 496.0
12 TraesCS2A01G278600 chr2D 81.121 339 35 10 376 687 388321004 388320668 1.020000e-60 244.0
13 TraesCS2A01G278600 chr4A 82.706 717 71 23 1 683 6251867 6252564 4.100000e-164 588.0
14 TraesCS2A01G278600 chr3A 81.564 716 78 25 1 683 704404786 704405480 3.240000e-150 542.0
15 TraesCS2A01G278600 chr3A 81.295 278 38 7 407 683 493646321 493646057 2.880000e-51 213.0
16 TraesCS2A01G278600 chr3A 81.667 240 31 9 457 683 32991336 32991097 1.750000e-43 187.0
17 TraesCS2A01G278600 chr6A 86.136 339 38 7 361 690 224331840 224332178 1.260000e-94 357.0
18 TraesCS2A01G278600 chr6A 89.873 79 5 2 3169 3246 516152771 516152847 8.420000e-17 99.0
19 TraesCS2A01G278600 chr5A 86.905 252 31 2 435 685 581375826 581376076 7.790000e-72 281.0
20 TraesCS2A01G278600 chr5A 91.406 128 11 0 3131 3258 325804445 325804318 3.780000e-40 176.0
21 TraesCS2A01G278600 chr6B 82.105 285 41 8 407 683 9312955 9312673 6.150000e-58 235.0
22 TraesCS2A01G278600 chr6B 90.840 131 11 1 3129 3258 23475249 23475119 1.360000e-39 174.0
23 TraesCS2A01G278600 chr7D 81.911 293 27 8 407 683 206107131 206106849 1.330000e-54 224.0
24 TraesCS2A01G278600 chr6D 82.353 255 40 5 433 684 189744206 189743954 2.230000e-52 217.0
25 TraesCS2A01G278600 chr6D 87.117 163 21 0 523 685 100370221 100370383 6.280000e-43 185.0
26 TraesCS2A01G278600 chr1B 87.730 163 20 0 523 685 151486691 151486529 1.350000e-44 191.0
27 TraesCS2A01G278600 chr1B 87.117 163 21 0 523 685 489008424 489008586 6.280000e-43 185.0
28 TraesCS2A01G278600 chr1B 81.513 238 31 4 461 685 277317405 277317168 2.260000e-42 183.0
29 TraesCS2A01G278600 chr1B 86.275 102 10 3 3146 3245 18355433 18355532 1.400000e-19 108.0
30 TraesCS2A01G278600 chr1A 86.957 161 21 0 523 683 5141576 5141416 8.120000e-42 182.0
31 TraesCS2A01G278600 chr3D 79.795 292 23 14 407 684 137460514 137460245 2.920000e-41 180.0
32 TraesCS2A01G278600 chr5B 91.406 128 11 0 3131 3258 612298720 612298593 3.780000e-40 176.0
33 TraesCS2A01G278600 chr5B 90.909 132 11 1 3128 3258 703797379 703797248 3.780000e-40 176.0
34 TraesCS2A01G278600 chr1D 94.737 76 4 0 3131 3206 486748293 486748218 6.460000e-23 119.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G278600 chr2A 461493819 461497501 3682 True 3024.500000 3773 100.000000 1 3683 2 chr2A.!!$R1 3682
1 TraesCS2A01G278600 chr2B 413079003 413081095 2092 True 988.700000 2056 93.690000 706 3130 3 chr2B.!!$R2 2424
2 TraesCS2A01G278600 chr7A 668000972 668001525 553 False 917.000000 917 96.589000 3131 3683 1 chr7A.!!$F2 552
3 TraesCS2A01G278600 chr2D 347813304 347815084 1780 True 680.333333 776 90.300333 749 2934 3 chr2D.!!$R2 2185
4 TraesCS2A01G278600 chr4A 6251867 6252564 697 False 588.000000 588 82.706000 1 683 1 chr4A.!!$F1 682
5 TraesCS2A01G278600 chr3A 704404786 704405480 694 False 542.000000 542 81.564000 1 683 1 chr3A.!!$F1 682

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
107 116 0.179020 ATGCAATAGCGGCTGCCTTA 60.179 50.0 15.55 9.55 46.23 2.69 F
344 403 0.242017 GTTGGGCTGCTGCTTAACTG 59.758 55.0 15.64 0.00 39.59 3.16 F
747 806 0.255890 TGAAGTGCTTATGGGCCTCC 59.744 55.0 4.53 0.00 0.00 4.30 F
2119 2198 0.548510 ATCCTTCTAACCTGGCTGGC 59.451 55.0 10.71 0.00 40.22 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 1910 0.249741 ACGTAAAGAACCGCAGCACT 60.250 50.000 0.00 0.00 0.00 4.40 R
2217 2296 1.076485 GCATCCCAGCTCCCACAAT 60.076 57.895 0.00 0.00 0.00 2.71 R
2517 2598 0.321387 ATCCAGCAGAGCACACAGTG 60.321 55.000 0.00 0.00 36.51 3.66 R
2954 3045 0.040058 ATGCTCAATGGCCACTTCCA 59.960 50.000 8.16 1.93 40.97 3.53 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
25 26 1.359848 CGTCATGTGTCCTACCAAGC 58.640 55.000 0.00 0.00 0.00 4.01
28 29 2.744202 GTCATGTGTCCTACCAAGCTTG 59.256 50.000 19.93 19.93 0.00 4.01
63 64 1.865865 GCACTAGCTATTAGGCGCAA 58.134 50.000 10.83 0.00 37.91 4.85
99 108 1.511850 TCCAATCGATGCAATAGCGG 58.488 50.000 0.00 0.00 46.23 5.52
105 114 1.895707 GATGCAATAGCGGCTGCCT 60.896 57.895 15.55 4.17 46.23 4.75
106 115 1.450531 GATGCAATAGCGGCTGCCTT 61.451 55.000 15.55 5.40 46.23 4.35
107 116 0.179020 ATGCAATAGCGGCTGCCTTA 60.179 50.000 15.55 9.55 46.23 2.69
108 117 0.179020 TGCAATAGCGGCTGCCTTAT 60.179 50.000 15.55 11.45 46.23 1.73
109 118 0.519077 GCAATAGCGGCTGCCTTATC 59.481 55.000 15.55 3.15 44.31 1.75
110 119 1.879796 GCAATAGCGGCTGCCTTATCT 60.880 52.381 15.55 10.47 44.31 1.98
111 120 1.802960 CAATAGCGGCTGCCTTATCTG 59.197 52.381 15.55 10.87 44.31 2.90
112 121 0.322975 ATAGCGGCTGCCTTATCTGG 59.677 55.000 15.55 0.00 44.31 3.86
113 122 0.759060 TAGCGGCTGCCTTATCTGGA 60.759 55.000 15.55 0.00 44.31 3.86
114 123 1.889573 GCGGCTGCCTTATCTGGAC 60.890 63.158 17.92 0.00 33.98 4.02
115 124 1.826024 CGGCTGCCTTATCTGGACT 59.174 57.895 17.92 0.00 0.00 3.85
116 125 1.040646 CGGCTGCCTTATCTGGACTA 58.959 55.000 17.92 0.00 0.00 2.59
117 126 1.000283 CGGCTGCCTTATCTGGACTAG 60.000 57.143 17.92 0.00 0.00 2.57
118 127 2.043227 GGCTGCCTTATCTGGACTAGT 58.957 52.381 12.43 0.00 0.00 2.57
119 128 2.036604 GGCTGCCTTATCTGGACTAGTC 59.963 54.545 14.87 14.87 0.00 2.59
120 129 2.962421 GCTGCCTTATCTGGACTAGTCT 59.038 50.000 21.88 5.25 0.00 3.24
121 130 3.386402 GCTGCCTTATCTGGACTAGTCTT 59.614 47.826 21.88 7.89 0.00 3.01
122 131 4.739137 GCTGCCTTATCTGGACTAGTCTTG 60.739 50.000 21.88 14.49 0.00 3.02
123 132 4.610333 TGCCTTATCTGGACTAGTCTTGA 58.390 43.478 21.88 18.73 0.00 3.02
180 227 1.078709 CGTCGTTGTCTCATTGCCAT 58.921 50.000 0.00 0.00 0.00 4.40
182 229 2.095768 CGTCGTTGTCTCATTGCCATTT 60.096 45.455 0.00 0.00 0.00 2.32
191 238 4.872124 GTCTCATTGCCATTTTCATTTCCC 59.128 41.667 0.00 0.00 0.00 3.97
192 239 4.531339 TCTCATTGCCATTTTCATTTCCCA 59.469 37.500 0.00 0.00 0.00 4.37
193 240 5.190132 TCTCATTGCCATTTTCATTTCCCAT 59.810 36.000 0.00 0.00 0.00 4.00
194 241 5.817784 TCATTGCCATTTTCATTTCCCATT 58.182 33.333 0.00 0.00 0.00 3.16
195 242 6.246919 TCATTGCCATTTTCATTTCCCATTT 58.753 32.000 0.00 0.00 0.00 2.32
196 243 6.720288 TCATTGCCATTTTCATTTCCCATTTT 59.280 30.769 0.00 0.00 0.00 1.82
197 244 6.973460 TTGCCATTTTCATTTCCCATTTTT 57.027 29.167 0.00 0.00 0.00 1.94
219 266 8.464770 TTTTTAGAATGCCATTCTCATTTTCG 57.535 30.769 22.62 0.00 46.17 3.46
229 276 5.065090 CCATTCTCATTTTCGTGTGCTATCA 59.935 40.000 0.00 0.00 0.00 2.15
236 283 0.939419 TCGTGTGCTATCATGCATGC 59.061 50.000 22.25 11.82 45.23 4.06
249 296 0.734309 TGCATGCAAAGCAGGATACG 59.266 50.000 20.30 0.00 43.36 3.06
256 303 2.699954 CAAAGCAGGATACGAGTTGGT 58.300 47.619 0.00 0.00 46.39 3.67
259 306 1.751924 AGCAGGATACGAGTTGGTCTC 59.248 52.381 0.00 0.00 46.39 3.36
260 307 1.476891 GCAGGATACGAGTTGGTCTCA 59.523 52.381 0.00 0.00 42.88 3.27
295 342 3.686016 ACTGCCCGAAATGTTATTCTGT 58.314 40.909 0.00 0.00 0.00 3.41
317 376 2.034687 GGGCTTGAGGCTGCTCAA 59.965 61.111 11.93 11.93 40.59 3.02
341 400 1.631405 AATGTTGGGCTGCTGCTTAA 58.369 45.000 15.64 8.07 39.59 1.85
344 403 0.242017 GTTGGGCTGCTGCTTAACTG 59.758 55.000 15.64 0.00 39.59 3.16
352 411 4.260948 GGCTGCTGCTTAACTGCTTATTAG 60.261 45.833 15.64 0.00 43.25 1.73
356 415 9.745011 GCTGCTGCTTAACTGCTTATTAGCATT 62.745 40.741 6.89 0.00 45.28 3.56
369 428 8.678593 GCTTATTAGCATTTAAGGACCTTACT 57.321 34.615 13.76 9.92 46.95 2.24
382 441 1.340405 ACCTTACTAGGAGCGACCGAA 60.340 52.381 0.00 0.00 45.05 4.30
385 444 3.436496 CTTACTAGGAGCGACCGAAAAG 58.564 50.000 0.00 0.00 44.74 2.27
421 480 3.364366 GCAAAGATACATGCATCGCTACC 60.364 47.826 0.00 0.00 42.12 3.18
422 481 2.354109 AGATACATGCATCGCTACCG 57.646 50.000 0.00 0.00 0.00 4.02
484 543 1.822506 TCACCAAAACGTCCACACAA 58.177 45.000 0.00 0.00 0.00 3.33
493 552 7.650104 ACCAAAACGTCCACACAAAATATAAAG 59.350 33.333 0.00 0.00 0.00 1.85
552 611 1.107945 CATGGGCAGAACATCATGCA 58.892 50.000 0.00 0.00 44.37 3.96
563 622 4.410228 AGAACATCATGCACATACCCTACT 59.590 41.667 0.00 0.00 0.00 2.57
586 645 4.410883 TCATGACTAATCGGGTTACCCATT 59.589 41.667 21.58 19.13 45.83 3.16
611 670 5.513233 GGCTTACCCATGGATGAATATGAT 58.487 41.667 15.22 0.00 0.00 2.45
614 673 6.832384 GCTTACCCATGGATGAATATGATGAT 59.168 38.462 15.22 0.00 0.00 2.45
631 690 4.919510 TGATGATCCATACCCTACCCATTT 59.080 41.667 0.00 0.00 0.00 2.32
644 703 2.035626 CATTTGGGTCGGGTGCCT 59.964 61.111 0.00 0.00 0.00 4.75
647 706 1.142060 CATTTGGGTCGGGTGCCTATA 59.858 52.381 0.00 0.00 0.00 1.31
648 707 1.287217 TTTGGGTCGGGTGCCTATAA 58.713 50.000 0.00 0.00 0.00 0.98
649 708 1.287217 TTGGGTCGGGTGCCTATAAA 58.713 50.000 0.00 0.00 0.00 1.40
659 718 2.279918 CCTATAAACGCGGCCGCT 60.280 61.111 43.60 29.94 39.32 5.52
660 719 1.885850 CCTATAAACGCGGCCGCTT 60.886 57.895 43.60 35.39 39.32 4.68
685 744 4.415783 GGATTGCCGGGTTGAGTT 57.584 55.556 2.18 0.00 0.00 3.01
686 745 3.562397 GGATTGCCGGGTTGAGTTA 57.438 52.632 2.18 0.00 0.00 2.24
687 746 1.828979 GGATTGCCGGGTTGAGTTAA 58.171 50.000 2.18 0.00 0.00 2.01
688 747 1.471287 GGATTGCCGGGTTGAGTTAAC 59.529 52.381 2.18 0.00 38.60 2.01
699 758 3.725490 GTTGAGTTAACCCTATAGCCGG 58.275 50.000 0.00 0.00 33.01 6.13
700 759 1.690352 TGAGTTAACCCTATAGCCGGC 59.310 52.381 21.89 21.89 0.00 6.13
701 760 0.677842 AGTTAACCCTATAGCCGGCG 59.322 55.000 23.20 8.17 0.00 6.46
702 761 0.947660 GTTAACCCTATAGCCGGCGC 60.948 60.000 23.20 0.00 0.00 6.53
703 762 2.103339 TTAACCCTATAGCCGGCGCC 62.103 60.000 23.20 19.07 34.57 6.53
704 763 4.936081 ACCCTATAGCCGGCGCCT 62.936 66.667 26.68 12.36 34.57 5.52
734 793 2.918712 ATAGGAATCGGGCTGAAGTG 57.081 50.000 0.00 0.00 0.00 3.16
747 806 0.255890 TGAAGTGCTTATGGGCCTCC 59.744 55.000 4.53 0.00 0.00 4.30
787 846 2.094757 TTTTGAGGAGGAGACGCGCA 62.095 55.000 5.73 0.00 0.00 6.09
800 859 1.596752 CGCGCATGGGCCAATAGTA 60.597 57.895 26.94 0.00 36.38 1.82
815 875 4.337763 CAATAGTACACGTACCACGAGTC 58.662 47.826 5.61 0.00 41.27 3.36
1017 1085 2.027561 AGCAATGGGTAAGACGCTAACA 60.028 45.455 0.00 0.00 31.67 2.41
1714 1782 1.134877 TGATCTCGCAGAAGCAGAAGG 60.135 52.381 0.00 0.00 42.27 3.46
1761 1829 4.180946 CGTCTCCCGCTCGACCTG 62.181 72.222 0.00 0.00 0.00 4.00
1819 1888 1.081892 CAAGCACCAGGTGATCTTCG 58.918 55.000 24.96 8.84 35.23 3.79
1832 1901 2.104170 GATCTTCGTTCCTCCCTGTCT 58.896 52.381 0.00 0.00 0.00 3.41
1833 1902 2.893215 TCTTCGTTCCTCCCTGTCTA 57.107 50.000 0.00 0.00 0.00 2.59
1841 1910 5.131642 TCGTTCCTCCCTGTCTATCTACTTA 59.868 44.000 0.00 0.00 0.00 2.24
1850 1919 3.315470 TGTCTATCTACTTAGTGCTGCGG 59.685 47.826 0.00 0.00 0.00 5.69
1882 1959 4.392138 GTGGAAGCGCTCTAGTTTGTTATT 59.608 41.667 12.06 0.00 0.00 1.40
1885 1962 4.928661 AGCGCTCTAGTTTGTTATTGTG 57.071 40.909 2.64 0.00 0.00 3.33
1916 1993 8.076178 AGTTGTCAAATTCTTTTCGTTAGATGG 58.924 33.333 0.00 0.00 0.00 3.51
1938 2015 8.757982 ATGGTGAGATTAGTAAAATTGATGCT 57.242 30.769 0.00 0.00 0.00 3.79
1987 2066 9.897744 ATGTTGTATTTTCTTGTGTAAGACATG 57.102 29.630 0.00 0.00 42.41 3.21
2062 2141 3.312421 ACATGGCACTGTATTTCGTATGC 59.688 43.478 0.00 0.00 0.00 3.14
2119 2198 0.548510 ATCCTTCTAACCTGGCTGGC 59.451 55.000 10.71 0.00 40.22 4.85
2191 2270 5.534207 TCTTGTGTTGGCTTGATGAAATT 57.466 34.783 0.00 0.00 0.00 1.82
2204 2283 8.992073 GGCTTGATGAAATTCAGTTTGTATTTT 58.008 29.630 1.10 0.00 29.43 1.82
2217 2296 9.119418 TCAGTTTGTATTTTTCAGTCTGATTGA 57.881 29.630 2.68 0.00 0.00 2.57
2251 2330 4.947388 TGGGATGCTGGTTTACTTTGTATC 59.053 41.667 0.00 0.00 0.00 2.24
2319 2400 7.715249 TGTAGTATTCTTTTCTGCTTGTGTCTT 59.285 33.333 0.00 0.00 0.00 3.01
2326 2407 8.445275 TCTTTTCTGCTTGTGTCTTGTTAATA 57.555 30.769 0.00 0.00 0.00 0.98
2517 2598 4.649674 TCCATCTGAGGGTATGTGTTACTC 59.350 45.833 8.37 0.00 0.00 2.59
2534 2621 0.949588 CTCACTGTGTGCTCTGCTGG 60.950 60.000 7.79 0.00 32.98 4.85
2544 2631 3.390311 TGTGCTCTGCTGGATTCTATCAT 59.610 43.478 0.00 0.00 0.00 2.45
2551 2638 6.519382 TCTGCTGGATTCTATCATGTTAGTG 58.481 40.000 10.00 0.00 0.00 2.74
2808 2896 5.066375 TCCTGCATGAAATTCGAACTTATGG 59.934 40.000 0.00 0.00 0.00 2.74
2887 2975 8.967664 TGTATGTTGTTAGTTTCCAGTTAACT 57.032 30.769 1.12 1.12 39.13 2.24
2890 2978 7.690952 TGTTGTTAGTTTCCAGTTAACTTGT 57.309 32.000 5.07 0.00 37.12 3.16
2945 3036 7.223582 TGTGATGGTTTTCGTACGTTAAAGTTA 59.776 33.333 16.05 6.91 0.00 2.24
2946 3037 8.223100 GTGATGGTTTTCGTACGTTAAAGTTAT 58.777 33.333 16.05 10.60 0.00 1.89
2947 3038 8.434661 TGATGGTTTTCGTACGTTAAAGTTATC 58.565 33.333 16.05 16.93 0.00 1.75
2948 3039 7.945033 TGGTTTTCGTACGTTAAAGTTATCT 57.055 32.000 16.05 0.00 0.00 1.98
2950 3041 9.469807 TGGTTTTCGTACGTTAAAGTTATCTTA 57.530 29.630 16.05 0.00 33.09 2.10
2964 3055 6.775594 AGTTATCTTAAAATGGAAGTGGCC 57.224 37.500 0.00 0.00 0.00 5.36
2965 3056 6.252995 AGTTATCTTAAAATGGAAGTGGCCA 58.747 36.000 0.00 0.00 43.23 5.36
2966 3057 7.400052 AAGTTATCTTAAAATGGAAGTGGCCAT 59.600 33.333 9.72 0.00 40.06 4.40
2971 3062 2.892025 ATGGAAGTGGCCATTGAGC 58.108 52.632 9.72 0.00 46.29 4.26
2972 3063 0.040058 ATGGAAGTGGCCATTGAGCA 59.960 50.000 9.72 0.00 46.29 4.26
2973 3064 0.040058 TGGAAGTGGCCATTGAGCAT 59.960 50.000 9.72 0.00 31.66 3.79
2989 3080 0.464373 GCATCATCGGTGGTGGATGT 60.464 55.000 11.67 0.00 41.54 3.06
2990 3081 1.586422 CATCATCGGTGGTGGATGTC 58.414 55.000 0.00 0.00 41.54 3.06
2992 3083 0.536724 TCATCGGTGGTGGATGTCTG 59.463 55.000 0.00 0.00 41.54 3.51
2993 3084 0.250234 CATCGGTGGTGGATGTCTGT 59.750 55.000 0.00 0.00 37.18 3.41
3026 3119 8.824756 TCAGTTATCAGATAGTGGTCTAGTTT 57.175 34.615 0.00 0.00 0.00 2.66
3032 3125 7.482169 TCAGATAGTGGTCTAGTTTGACATT 57.518 36.000 0.00 0.00 38.61 2.71
3033 3126 7.907389 TCAGATAGTGGTCTAGTTTGACATTT 58.093 34.615 0.00 0.00 38.61 2.32
3034 3127 7.819415 TCAGATAGTGGTCTAGTTTGACATTTG 59.181 37.037 0.00 0.00 38.61 2.32
3040 3133 5.359576 TGGTCTAGTTTGACATTTGCTTGTT 59.640 36.000 0.00 0.00 38.61 2.83
3046 3139 1.336440 TGACATTTGCTTGTTCACCCG 59.664 47.619 0.00 0.00 0.00 5.28
3050 3143 0.102120 TTTGCTTGTTCACCCGCTTG 59.898 50.000 0.00 0.00 0.00 4.01
3055 3159 2.223340 GCTTGTTCACCCGCTTGATATG 60.223 50.000 0.00 0.00 0.00 1.78
3063 3167 3.058708 CACCCGCTTGATATGTTATGCAG 60.059 47.826 0.00 0.00 0.00 4.41
3094 3198 4.658901 TGAGGGAAGGACTACTTGAAAGTT 59.341 41.667 0.21 0.00 40.21 2.66
3126 3230 4.987912 ACTTTTGGGAACATATTGTTTGCG 59.012 37.500 0.00 0.00 41.28 4.85
3139 3243 2.691984 GTTTGCGTATGGGAAACGTT 57.308 45.000 0.00 0.00 45.11 3.99
3347 3451 4.876107 ACAAAGGGTTGATATTGAGCTACG 59.124 41.667 0.00 0.00 38.20 3.51
3444 3548 1.336887 CGACAAGTCGTTCTCATGGGT 60.337 52.381 14.03 0.00 46.99 4.51
3549 3657 3.911698 TGACCAGCGACGCACACT 61.912 61.111 23.70 0.00 0.00 3.55
3622 3730 4.730949 TTGCTGCGTCCTAGTAGTAAAT 57.269 40.909 0.00 0.00 0.00 1.40
3627 3735 3.449737 TGCGTCCTAGTAGTAAATGCCTT 59.550 43.478 0.00 0.00 0.00 4.35
3628 3736 4.049869 GCGTCCTAGTAGTAAATGCCTTC 58.950 47.826 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.901827 TGGTAGGACACATGACGCAT 59.098 50.000 0.00 0.00 0.00 4.73
13 14 0.764890 ACAGCAAGCTTGGTAGGACA 59.235 50.000 29.24 0.00 37.09 4.02
19 20 3.893326 AAAAAGAACAGCAAGCTTGGT 57.107 38.095 24.96 24.96 39.91 3.67
63 64 1.153628 GAAGTGGCTACCGCGATGT 60.154 57.895 8.23 0.00 39.30 3.06
99 108 2.962421 AGACTAGTCCAGATAAGGCAGC 59.038 50.000 19.38 0.00 0.00 5.25
105 114 6.964464 AGAGACTCAAGACTAGTCCAGATAA 58.036 40.000 19.38 0.00 43.64 1.75
106 115 6.569127 AGAGACTCAAGACTAGTCCAGATA 57.431 41.667 19.38 0.48 43.64 1.98
107 116 5.450818 AGAGACTCAAGACTAGTCCAGAT 57.549 43.478 19.38 7.54 43.64 2.90
108 117 4.919774 AGAGACTCAAGACTAGTCCAGA 57.080 45.455 19.38 15.53 43.64 3.86
109 118 8.918202 ATATAAGAGACTCAAGACTAGTCCAG 57.082 38.462 19.38 14.54 43.64 3.86
111 120 9.444600 CCTATATAAGAGACTCAAGACTAGTCC 57.555 40.741 19.38 2.89 43.64 3.85
112 121 8.943002 GCCTATATAAGAGACTCAAGACTAGTC 58.057 40.741 15.41 15.41 43.06 2.59
113 122 7.604927 CGCCTATATAAGAGACTCAAGACTAGT 59.395 40.741 5.02 0.00 0.00 2.57
114 123 7.820386 TCGCCTATATAAGAGACTCAAGACTAG 59.180 40.741 5.02 0.00 0.00 2.57
115 124 7.677892 TCGCCTATATAAGAGACTCAAGACTA 58.322 38.462 5.02 0.00 0.00 2.59
116 125 6.535540 TCGCCTATATAAGAGACTCAAGACT 58.464 40.000 5.02 0.00 0.00 3.24
117 126 6.804770 TCGCCTATATAAGAGACTCAAGAC 57.195 41.667 5.02 0.00 0.00 3.01
118 127 6.072397 GCTTCGCCTATATAAGAGACTCAAGA 60.072 42.308 5.02 0.00 0.00 3.02
119 128 6.072175 AGCTTCGCCTATATAAGAGACTCAAG 60.072 42.308 5.02 0.00 0.00 3.02
120 129 5.770663 AGCTTCGCCTATATAAGAGACTCAA 59.229 40.000 5.02 0.00 0.00 3.02
121 130 5.182190 CAGCTTCGCCTATATAAGAGACTCA 59.818 44.000 5.02 0.00 0.00 3.41
122 131 5.636837 CAGCTTCGCCTATATAAGAGACTC 58.363 45.833 0.00 0.00 0.00 3.36
123 132 4.082463 GCAGCTTCGCCTATATAAGAGACT 60.082 45.833 0.00 0.00 0.00 3.24
200 247 4.560035 CACACGAAAATGAGAATGGCATTC 59.440 41.667 28.54 28.54 35.06 2.67
201 248 4.487948 CACACGAAAATGAGAATGGCATT 58.512 39.130 13.54 13.54 37.56 3.56
202 249 3.674138 GCACACGAAAATGAGAATGGCAT 60.674 43.478 0.00 0.00 0.00 4.40
203 250 2.351641 GCACACGAAAATGAGAATGGCA 60.352 45.455 0.00 0.00 0.00 4.92
204 251 2.095059 AGCACACGAAAATGAGAATGGC 60.095 45.455 0.00 0.00 0.00 4.40
205 252 3.837213 AGCACACGAAAATGAGAATGG 57.163 42.857 0.00 0.00 0.00 3.16
206 253 6.110543 TGATAGCACACGAAAATGAGAATG 57.889 37.500 0.00 0.00 0.00 2.67
207 254 6.722301 CATGATAGCACACGAAAATGAGAAT 58.278 36.000 0.00 0.00 0.00 2.40
208 255 5.447683 GCATGATAGCACACGAAAATGAGAA 60.448 40.000 0.00 0.00 0.00 2.87
209 256 4.034394 GCATGATAGCACACGAAAATGAGA 59.966 41.667 0.00 0.00 0.00 3.27
210 257 4.201841 TGCATGATAGCACACGAAAATGAG 60.202 41.667 0.00 0.00 40.11 2.90
211 258 3.688673 TGCATGATAGCACACGAAAATGA 59.311 39.130 0.00 0.00 40.11 2.57
212 259 4.018649 TGCATGATAGCACACGAAAATG 57.981 40.909 0.00 0.00 40.11 2.32
229 276 1.335810 CGTATCCTGCTTTGCATGCAT 59.664 47.619 23.37 6.28 38.13 3.96
236 283 2.673368 GACCAACTCGTATCCTGCTTTG 59.327 50.000 0.00 0.00 0.00 2.77
249 296 2.772287 CCTCCAAAGTGAGACCAACTC 58.228 52.381 0.00 0.00 45.11 3.01
256 303 4.330056 TGGGCCTCCAAAGTGAGA 57.670 55.556 4.53 0.00 40.73 3.27
278 325 5.527582 CCCTCTAACAGAATAACATTTCGGG 59.472 44.000 0.00 0.00 0.00 5.14
295 342 0.911525 AGCAGCCTCAAGCCCTCTAA 60.912 55.000 0.00 0.00 45.47 2.10
317 376 1.538047 CAGCAGCCCAACATTACTGT 58.462 50.000 0.00 0.00 37.12 3.55
352 411 5.057819 GCTCCTAGTAAGGTCCTTAAATGC 58.942 45.833 13.12 8.30 44.09 3.56
356 415 3.950395 GTCGCTCCTAGTAAGGTCCTTAA 59.050 47.826 13.12 0.00 44.09 1.85
362 421 0.254178 TCGGTCGCTCCTAGTAAGGT 59.746 55.000 0.00 0.00 44.09 3.50
369 428 3.604875 ATTTCTTTTCGGTCGCTCCTA 57.395 42.857 0.00 0.00 0.00 2.94
421 480 2.912025 AACAACCCAAGGCTGCCG 60.912 61.111 13.96 0.85 0.00 5.69
422 481 0.251165 TAGAACAACCCAAGGCTGCC 60.251 55.000 11.65 11.65 0.00 4.85
468 527 7.650104 ACTTTATATTTTGTGTGGACGTTTTGG 59.350 33.333 0.00 0.00 0.00 3.28
508 567 7.166167 GGGTCACCCGATTAATATTAGTGATT 58.834 38.462 14.18 0.00 35.45 2.57
510 569 6.105397 GGGTCACCCGATTAATATTAGTGA 57.895 41.667 0.00 9.33 32.13 3.41
528 587 0.034186 GATGTTCTGCCCATGGGTCA 60.034 55.000 31.58 26.04 37.65 4.02
539 598 3.548770 AGGGTATGTGCATGATGTTCTG 58.451 45.455 0.00 0.00 0.00 3.02
552 611 5.477291 CCGATTAGTCATGAGTAGGGTATGT 59.523 44.000 10.12 0.00 0.00 2.29
611 670 3.397618 CCAAATGGGTAGGGTATGGATCA 59.602 47.826 0.00 0.00 0.00 2.92
631 690 0.542805 GTTTATAGGCACCCGACCCA 59.457 55.000 0.00 0.00 0.00 4.51
683 742 0.947660 GCGCCGGCTATAGGGTTAAC 60.948 60.000 26.68 0.00 35.83 2.01
684 743 1.368579 GCGCCGGCTATAGGGTTAA 59.631 57.895 26.68 0.00 35.83 2.01
685 744 2.576832 GGCGCCGGCTATAGGGTTA 61.577 63.158 26.68 0.00 39.81 2.85
686 745 3.937447 GGCGCCGGCTATAGGGTT 61.937 66.667 26.68 0.00 39.81 4.11
687 746 4.936081 AGGCGCCGGCTATAGGGT 62.936 66.667 26.68 0.00 36.44 4.34
688 747 1.823169 TTAAGGCGCCGGCTATAGGG 61.823 60.000 26.68 8.84 37.50 3.53
689 748 0.389948 CTTAAGGCGCCGGCTATAGG 60.390 60.000 26.68 9.69 37.50 2.57
690 749 0.317479 ACTTAAGGCGCCGGCTATAG 59.683 55.000 26.68 16.27 37.50 1.31
691 750 0.032952 CACTTAAGGCGCCGGCTATA 59.967 55.000 26.68 9.04 37.50 1.31
692 751 1.227556 CACTTAAGGCGCCGGCTAT 60.228 57.895 26.68 10.12 37.50 2.97
693 752 2.185867 CACTTAAGGCGCCGGCTA 59.814 61.111 26.68 11.44 37.50 3.93
701 760 2.614829 TCCTATTCGGCACTTAAGGC 57.385 50.000 7.53 7.36 0.00 4.35
702 761 3.741344 CGATTCCTATTCGGCACTTAAGG 59.259 47.826 7.53 0.00 33.05 2.69
703 762 4.974103 CGATTCCTATTCGGCACTTAAG 57.026 45.455 0.00 0.00 33.05 1.85
734 793 0.954452 CATTTCGGAGGCCCATAAGC 59.046 55.000 0.00 0.00 0.00 3.09
747 806 7.634048 TCAAAAGAAAAACAAAATCGCATTTCG 59.366 29.630 0.00 0.00 40.15 3.46
787 846 2.103601 GGTACGTGTACTATTGGCCCAT 59.896 50.000 0.00 0.00 36.36 4.00
894 954 3.196039 TGCGTGCGGGTTATATATATGGT 59.804 43.478 5.44 0.00 0.00 3.55
1674 1742 2.034879 CGTGAGCACCCTCGCAATT 61.035 57.895 5.28 0.00 46.51 2.32
1720 1788 1.001633 GTTCTTGTACGCCTCCCTCAA 59.998 52.381 0.00 0.00 0.00 3.02
1819 1888 6.263617 CACTAAGTAGATAGACAGGGAGGAAC 59.736 46.154 0.00 0.00 0.00 3.62
1832 1901 3.952323 AGAACCGCAGCACTAAGTAGATA 59.048 43.478 0.00 0.00 0.00 1.98
1833 1902 2.761208 AGAACCGCAGCACTAAGTAGAT 59.239 45.455 0.00 0.00 0.00 1.98
1841 1910 0.249741 ACGTAAAGAACCGCAGCACT 60.250 50.000 0.00 0.00 0.00 4.40
1850 1919 1.126296 GAGCGCTTCCACGTAAAGAAC 59.874 52.381 13.26 4.83 34.88 3.01
1882 1959 8.332464 CGAAAAGAATTTGACAACTAGTACACA 58.668 33.333 0.00 0.00 39.02 3.72
2036 2115 3.623060 ACGAAATACAGTGCCATGTCATC 59.377 43.478 0.00 0.00 34.56 2.92
2037 2116 3.609853 ACGAAATACAGTGCCATGTCAT 58.390 40.909 0.00 0.00 34.56 3.06
2062 2141 3.423154 GCGAACGACTGGGCAAGG 61.423 66.667 0.00 0.00 0.00 3.61
2084 2163 4.705023 AGAAGGATTTCATAAACCCAACCG 59.295 41.667 0.00 0.00 35.70 4.44
2119 2198 7.434307 CAGCAATCCTTACAAATGCTAATTCAG 59.566 37.037 0.00 0.00 44.97 3.02
2130 2209 6.240894 AGAGATTCACAGCAATCCTTACAAA 58.759 36.000 0.00 0.00 33.79 2.83
2191 2270 9.119418 TCAATCAGACTGAAAAATACAAACTGA 57.881 29.630 9.70 0.00 35.70 3.41
2204 2283 4.582869 CTCCCACAATCAATCAGACTGAA 58.417 43.478 9.70 0.00 0.00 3.02
2217 2296 1.076485 GCATCCCAGCTCCCACAAT 60.076 57.895 0.00 0.00 0.00 2.71
2251 2330 5.688823 TCAAAAAGACAAGTGCGATACATG 58.311 37.500 0.00 0.00 34.29 3.21
2326 2407 8.263940 ACTTACGCAGTTAAACATAACATGAT 57.736 30.769 0.00 0.00 37.78 2.45
2358 2439 8.856153 TTAGGCAGTTAAACACAAGATGATAA 57.144 30.769 0.00 0.00 0.00 1.75
2413 2494 6.127111 ACTGAGAGCACAGATTGATATTCAGT 60.127 38.462 11.41 0.00 40.84 3.41
2421 2502 6.935167 TGTTATTACTGAGAGCACAGATTGA 58.065 36.000 11.41 0.00 40.63 2.57
2490 2571 5.255397 ACACATACCCTCAGATGGAAAAA 57.745 39.130 0.00 0.00 0.00 1.94
2517 2598 0.321387 ATCCAGCAGAGCACACAGTG 60.321 55.000 0.00 0.00 36.51 3.66
2534 2621 6.259608 AGCACTTGCACTAACATGATAGAATC 59.740 38.462 16.18 5.72 45.16 2.52
2544 2631 4.337836 TGATCAAAAGCACTTGCACTAACA 59.662 37.500 3.62 0.00 45.16 2.41
2551 2638 4.512571 ACCAAAATGATCAAAAGCACTTGC 59.487 37.500 0.00 0.00 42.49 4.01
2691 2779 0.725117 CTCGGCCGGTAAAACATGTC 59.275 55.000 27.83 0.00 0.00 3.06
2808 2896 9.081997 GCAGCTATAGATCATAGTGTCAATAAC 57.918 37.037 3.21 0.00 39.17 1.89
2887 2975 0.102120 CAAGGCGCTTCCACAAACAA 59.898 50.000 7.64 0.00 37.29 2.83
2890 2978 0.102120 CAACAAGGCGCTTCCACAAA 59.898 50.000 7.64 0.00 37.29 2.83
2954 3045 0.040058 ATGCTCAATGGCCACTTCCA 59.960 50.000 8.16 1.93 40.97 3.53
2956 3047 1.466856 TGATGCTCAATGGCCACTTC 58.533 50.000 8.16 3.18 0.00 3.01
2958 3049 1.688772 GATGATGCTCAATGGCCACT 58.311 50.000 8.16 0.00 0.00 4.00
2959 3050 0.309922 CGATGATGCTCAATGGCCAC 59.690 55.000 8.16 0.00 0.00 5.01
2960 3051 0.820482 CCGATGATGCTCAATGGCCA 60.820 55.000 8.56 8.56 0.00 5.36
2961 3052 0.820891 ACCGATGATGCTCAATGGCC 60.821 55.000 0.00 0.00 30.55 5.36
2962 3053 0.309922 CACCGATGATGCTCAATGGC 59.690 55.000 0.00 0.00 30.55 4.40
2963 3054 0.949397 CCACCGATGATGCTCAATGG 59.051 55.000 0.00 0.00 32.82 3.16
2964 3055 1.332686 CACCACCGATGATGCTCAATG 59.667 52.381 0.00 0.00 0.00 2.82
2965 3056 1.671979 CACCACCGATGATGCTCAAT 58.328 50.000 0.00 0.00 0.00 2.57
2966 3057 0.392863 CCACCACCGATGATGCTCAA 60.393 55.000 0.00 0.00 0.00 3.02
2967 3058 1.221566 CCACCACCGATGATGCTCA 59.778 57.895 0.00 0.00 0.00 4.26
2968 3059 0.107456 ATCCACCACCGATGATGCTC 59.893 55.000 0.00 0.00 0.00 4.26
2969 3060 0.179037 CATCCACCACCGATGATGCT 60.179 55.000 0.00 0.00 39.64 3.79
2970 3061 0.464373 ACATCCACCACCGATGATGC 60.464 55.000 4.88 0.00 39.64 3.91
2971 3062 1.139654 AGACATCCACCACCGATGATG 59.860 52.381 4.88 0.00 39.64 3.07
2972 3063 1.139654 CAGACATCCACCACCGATGAT 59.860 52.381 4.88 0.00 39.64 2.45
2973 3064 0.536724 CAGACATCCACCACCGATGA 59.463 55.000 4.88 0.00 39.64 2.92
2989 3080 6.041423 TCTGATAACTGATGCAGAAACAGA 57.959 37.500 16.03 6.07 34.71 3.41
2990 3081 6.922247 ATCTGATAACTGATGCAGAAACAG 57.078 37.500 0.82 10.09 40.38 3.16
2992 3083 7.042187 CCACTATCTGATAACTGATGCAGAAAC 60.042 40.741 0.82 0.00 40.38 2.78
2993 3084 6.988580 CCACTATCTGATAACTGATGCAGAAA 59.011 38.462 0.82 0.00 40.38 2.52
3026 3119 1.336440 CGGGTGAACAAGCAAATGTCA 59.664 47.619 0.00 0.00 31.81 3.58
3032 3125 0.749818 TCAAGCGGGTGAACAAGCAA 60.750 50.000 0.00 0.00 0.00 3.91
3033 3126 0.537143 ATCAAGCGGGTGAACAAGCA 60.537 50.000 0.00 0.00 0.00 3.91
3034 3127 1.448985 TATCAAGCGGGTGAACAAGC 58.551 50.000 0.00 0.00 0.00 4.01
3040 3133 3.138304 GCATAACATATCAAGCGGGTGA 58.862 45.455 0.00 0.00 0.00 4.02
3046 3139 6.204301 ACACAGATCTGCATAACATATCAAGC 59.796 38.462 22.83 0.00 34.99 4.01
3050 3143 6.368243 CCTCACACAGATCTGCATAACATATC 59.632 42.308 22.83 0.00 33.20 1.63
3055 3159 3.118629 TCCCTCACACAGATCTGCATAAC 60.119 47.826 22.83 0.00 0.00 1.89
3063 3167 2.183679 AGTCCTTCCCTCACACAGATC 58.816 52.381 0.00 0.00 0.00 2.75
3094 3198 9.814899 CAATATGTTCCCAAAAGTTATTATGCA 57.185 29.630 0.00 0.00 0.00 3.96
3126 3230 1.068816 GGTGTGCAACGTTTCCCATAC 60.069 52.381 0.00 4.98 42.39 2.39
3347 3451 0.601841 TCAAAAAGGACTCGCCGGTC 60.602 55.000 1.90 0.00 43.43 4.79
3393 3497 1.039233 AAATGCCTCATTGGAGCCGG 61.039 55.000 0.00 0.00 39.96 6.13
3420 3524 1.847818 TGAGAACGACTTGTCGGTTG 58.152 50.000 23.99 0.68 37.45 3.77
3428 3532 1.276421 CCAGACCCATGAGAACGACTT 59.724 52.381 0.00 0.00 0.00 3.01
3444 3548 2.623878 TCGCAAAAGGTTACACCAGA 57.376 45.000 0.00 0.00 41.95 3.86
3499 3603 2.104281 AGTCCCAGCAAAACTACTCGTT 59.896 45.455 0.00 0.00 37.47 3.85
3570 3678 3.052036 CCTGTCCAAGCAAAACAATTCG 58.948 45.455 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.