Multiple sequence alignment - TraesCS2B01G141800

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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 TraesCS2B01G141800 chr2B 100.000 4821 0 0 1 4821 108236461 108231641 0.000000e+00 8903
1 TraesCS2B01G141800 chr2A 88.011 3153 217 71 1 3066 70875760 70872682 0.000000e+00 3579
2 TraesCS2B01G141800 chr2A 94.419 1738 85 9 3089 4821 70872694 70870964 0.000000e+00 2662
3 TraesCS2B01G141800 chr2D 88.505 2810 161 59 467 3175 71764371 71761623 0.000000e+00 3251
4 TraesCS2B01G141800 chr2D 94.498 1654 72 13 3177 4821 71761522 71759879 0.000000e+00 2532
5 TraesCS2B01G141800 chr5B 90.435 575 46 6 1015 1583 13216553 13217124 0.000000e+00 749
6 TraesCS2B01G141800 chr5B 89.446 578 52 6 1015 1586 638033498 638032924 0.000000e+00 721
7 TraesCS2B01G141800 chr5B 87.313 134 4 4 4673 4806 319885796 319885916 1.810000e-29 141
8 TraesCS2B01G141800 chr1B 89.792 578 49 8 1015 1586 663566258 663565685 0.000000e+00 732
9 TraesCS2B01G141800 chr3B 89.391 575 52 7 1015 1583 26976162 26976733 0.000000e+00 715
10 TraesCS2B01G141800 chr3B 86.505 578 54 12 1040 1599 483420008 483420579 8.870000e-172 614
11 TraesCS2B01G141800 chr4D 78.495 279 60 0 3543 3821 263948729 263948451 2.960000e-42 183
12 TraesCS2B01G141800 chr4B 78.967 271 55 2 3537 3806 359724000 359724269 2.960000e-42 183
13 TraesCS2B01G141800 chr1A 91.667 120 7 2 1470 1586 69816005 69815886 3.860000e-36 163
14 TraesCS2B01G141800 chr1A 87.786 131 3 4 4676 4806 102168647 102168530 1.810000e-29 141
15 TraesCS2B01G141800 chr3A 92.174 115 6 2 1475 1586 35609619 35609505 4.990000e-35 159


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 TraesCS2B01G141800 chr2B 108231641 108236461 4820 True 8903.0 8903 100.0000 1 4821 1 chr2B.!!$R1 4820
1 TraesCS2B01G141800 chr2A 70870964 70875760 4796 True 3120.5 3579 91.2150 1 4821 2 chr2A.!!$R1 4820
2 TraesCS2B01G141800 chr2D 71759879 71764371 4492 True 2891.5 3251 91.5015 467 4821 2 chr2D.!!$R1 4354
3 TraesCS2B01G141800 chr5B 13216553 13217124 571 False 749.0 749 90.4350 1015 1583 1 chr5B.!!$F1 568
4 TraesCS2B01G141800 chr5B 638032924 638033498 574 True 721.0 721 89.4460 1015 1586 1 chr5B.!!$R1 571
5 TraesCS2B01G141800 chr1B 663565685 663566258 573 True 732.0 732 89.7920 1015 1586 1 chr1B.!!$R1 571
6 TraesCS2B01G141800 chr3B 26976162 26976733 571 False 715.0 715 89.3910 1015 1583 1 chr3B.!!$F1 568
7 TraesCS2B01G141800 chr3B 483420008 483420579 571 False 614.0 614 86.5050 1040 1599 1 chr3B.!!$F2 559

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
102 106 0.036577 GGATGGCGGAGATGATGAGG 60.037 60.0 0.00 0.00 0.00 3.86 F
791 838 0.104855 TCCCTGTCTGCACGCATATC 59.895 55.0 0.00 0.00 0.00 1.63 F
792 839 0.179076 CCCTGTCTGCACGCATATCA 60.179 55.0 0.00 0.00 0.00 2.15 F
1443 1519 0.326143 TGCTACTCCATGGTGGCCTA 60.326 55.0 17.76 1.17 41.88 3.93 F
2835 2984 1.305201 GAAAACCAGCAGTTCCGACA 58.695 50.0 0.00 0.00 37.88 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2106 0.675633 AGCAACAAAGCCACATGGTC 59.324 50.000 0.00 0.0 37.57 4.02 R
2034 2167 1.210478 GCATCTCTTGGTCCAGGCTAA 59.790 52.381 0.00 0.0 0.00 3.09 R
2305 2438 1.599576 GCAGGTCTGACTCCCCTTC 59.400 63.158 7.85 0.0 0.00 3.46 R
3351 3601 0.528924 TACGCCGCAACATAGTCAGT 59.471 50.000 0.00 0.0 0.00 3.41 R
4172 4426 1.008938 ACAGCAACCTATCCTCCTCCT 59.991 52.381 0.00 0.0 0.00 3.69 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
35 39 5.898630 AACAAAAATCAACAATACACGGC 57.101 34.783 0.00 0.00 0.00 5.68
43 47 4.337145 TCAACAATACACGGCCCTAAAAT 58.663 39.130 0.00 0.00 0.00 1.82
53 57 4.022329 CACGGCCCTAAAATGAAAGAAACT 60.022 41.667 0.00 0.00 0.00 2.66
62 66 9.774742 CCTAAAATGAAAGAAACTTAATCCTCG 57.225 33.333 0.00 0.00 0.00 4.63
65 69 5.607119 TGAAAGAAACTTAATCCTCGCAC 57.393 39.130 0.00 0.00 0.00 5.34
89 93 1.303309 CGATGTCTGGAAAGGATGGC 58.697 55.000 0.00 0.00 0.00 4.40
95 99 0.471617 CTGGAAAGGATGGCGGAGAT 59.528 55.000 0.00 0.00 0.00 2.75
102 106 0.036577 GGATGGCGGAGATGATGAGG 60.037 60.000 0.00 0.00 0.00 3.86
103 107 0.972134 GATGGCGGAGATGATGAGGA 59.028 55.000 0.00 0.00 0.00 3.71
104 108 0.683973 ATGGCGGAGATGATGAGGAC 59.316 55.000 0.00 0.00 0.00 3.85
105 109 0.687427 TGGCGGAGATGATGAGGACA 60.687 55.000 0.00 0.00 0.00 4.02
109 113 1.001924 CGGAGATGATGAGGACACGAG 60.002 57.143 0.00 0.00 0.00 4.18
110 114 2.302260 GGAGATGATGAGGACACGAGA 58.698 52.381 0.00 0.00 0.00 4.04
111 115 2.690497 GGAGATGATGAGGACACGAGAA 59.310 50.000 0.00 0.00 0.00 2.87
112 116 3.243367 GGAGATGATGAGGACACGAGAAG 60.243 52.174 0.00 0.00 0.00 2.85
113 117 3.625853 AGATGATGAGGACACGAGAAGA 58.374 45.455 0.00 0.00 0.00 2.87
114 118 3.631686 AGATGATGAGGACACGAGAAGAG 59.368 47.826 0.00 0.00 0.00 2.85
115 119 3.073274 TGATGAGGACACGAGAAGAGA 57.927 47.619 0.00 0.00 0.00 3.10
116 120 3.625853 TGATGAGGACACGAGAAGAGAT 58.374 45.455 0.00 0.00 0.00 2.75
117 121 3.629855 TGATGAGGACACGAGAAGAGATC 59.370 47.826 0.00 0.00 0.00 2.75
118 122 3.073274 TGAGGACACGAGAAGAGATCA 57.927 47.619 0.00 0.00 0.00 2.92
119 123 2.750166 TGAGGACACGAGAAGAGATCAC 59.250 50.000 0.00 0.00 0.00 3.06
154 158 1.285280 TGGTTAGGAGGGTGGATGTG 58.715 55.000 0.00 0.00 0.00 3.21
157 161 2.188817 GTTAGGAGGGTGGATGTGTCT 58.811 52.381 0.00 0.00 0.00 3.41
183 187 2.630580 GCCCACCAGAAATTAAACACCA 59.369 45.455 0.00 0.00 0.00 4.17
222 227 5.008415 AGCATGCATGTCTCATAAAGTAAGC 59.992 40.000 26.79 7.42 0.00 3.09
225 230 7.571026 CATGCATGTCTCATAAAGTAAGCTAC 58.429 38.462 18.91 0.00 0.00 3.58
234 239 9.804758 TCTCATAAAGTAAGCTACTCTTTTAGC 57.195 33.333 13.25 0.00 44.27 3.09
242 247 6.546428 AAGCTACTCTTTTAGCATGAGGTA 57.454 37.500 0.00 0.00 46.04 3.08
249 254 6.127310 ACTCTTTTAGCATGAGGTAACGAGAT 60.127 38.462 0.00 3.41 46.39 2.75
274 279 7.297391 TGTTTGTGATGACTTTGTCAATATCG 58.703 34.615 4.46 0.00 45.96 2.92
280 285 7.651304 GTGATGACTTTGTCAATATCGAGATCT 59.349 37.037 0.00 0.00 45.96 2.75
287 292 5.592054 TGTCAATATCGAGATCTGTTGACC 58.408 41.667 17.12 5.01 42.72 4.02
300 305 3.454447 TCTGTTGACCCAGTCTCTCAAAA 59.546 43.478 0.00 0.00 34.02 2.44
301 306 3.808728 TGTTGACCCAGTCTCTCAAAAG 58.191 45.455 0.00 0.00 33.15 2.27
313 318 3.509967 TCTCTCAAAAGTGCTCATACGGA 59.490 43.478 0.00 0.00 0.00 4.69
324 330 1.341209 CTCATACGGATAGGCTGCACA 59.659 52.381 0.50 0.00 0.00 4.57
327 333 0.249868 TACGGATAGGCTGCACATGC 60.250 55.000 0.50 0.00 42.50 4.06
339 345 1.068832 GCACATGCATGCGTTCACAG 61.069 55.000 26.53 0.67 41.59 3.66
341 347 1.138036 CATGCATGCGTTCACAGGG 59.862 57.895 14.93 0.00 0.00 4.45
345 351 0.955428 GCATGCGTTCACAGGGAAGA 60.955 55.000 0.00 0.00 35.82 2.87
346 352 1.522668 CATGCGTTCACAGGGAAGAA 58.477 50.000 0.00 0.00 35.82 2.52
359 365 4.141711 ACAGGGAAGAATATATGTGCGTGT 60.142 41.667 5.76 5.76 0.00 4.49
360 366 5.069914 ACAGGGAAGAATATATGTGCGTGTA 59.930 40.000 8.45 0.00 30.24 2.90
361 367 6.166279 CAGGGAAGAATATATGTGCGTGTAT 58.834 40.000 0.00 0.00 0.00 2.29
362 368 6.091305 CAGGGAAGAATATATGTGCGTGTATG 59.909 42.308 0.00 0.00 0.00 2.39
363 369 5.932303 GGGAAGAATATATGTGCGTGTATGT 59.068 40.000 0.00 0.00 0.00 2.29
364 370 6.128553 GGGAAGAATATATGTGCGTGTATGTG 60.129 42.308 0.00 0.00 0.00 3.21
365 371 6.645003 GGAAGAATATATGTGCGTGTATGTGA 59.355 38.462 0.00 0.00 0.00 3.58
366 372 7.170828 GGAAGAATATATGTGCGTGTATGTGAA 59.829 37.037 0.00 0.00 0.00 3.18
367 373 7.408132 AGAATATATGTGCGTGTATGTGAAC 57.592 36.000 0.00 0.00 0.00 3.18
387 393 1.002544 CGTTTGCCTCCCTCTTCTCTT 59.997 52.381 0.00 0.00 0.00 2.85
388 394 2.705730 GTTTGCCTCCCTCTTCTCTTC 58.294 52.381 0.00 0.00 0.00 2.87
389 395 1.280457 TTGCCTCCCTCTTCTCTTCC 58.720 55.000 0.00 0.00 0.00 3.46
390 396 0.415429 TGCCTCCCTCTTCTCTTCCT 59.585 55.000 0.00 0.00 0.00 3.36
391 397 1.203364 TGCCTCCCTCTTCTCTTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
392 398 2.044492 TGCCTCCCTCTTCTCTTCCTTA 59.956 50.000 0.00 0.00 0.00 2.69
393 399 3.108376 GCCTCCCTCTTCTCTTCCTTAA 58.892 50.000 0.00 0.00 0.00 1.85
394 400 3.519913 GCCTCCCTCTTCTCTTCCTTAAA 59.480 47.826 0.00 0.00 0.00 1.52
395 401 4.019231 GCCTCCCTCTTCTCTTCCTTAAAA 60.019 45.833 0.00 0.00 0.00 1.52
396 402 5.739959 CCTCCCTCTTCTCTTCCTTAAAAG 58.260 45.833 0.00 0.00 0.00 2.27
431 437 8.739972 TCTGCAAAGGAAACTAATTTTATCTCC 58.260 33.333 0.00 0.00 42.68 3.71
433 439 9.747898 TGCAAAGGAAACTAATTTTATCTCCTA 57.252 29.630 0.00 0.00 42.68 2.94
491 513 7.615403 AGAAAAGGAAAATGGCCTTATCTTTC 58.385 34.615 3.32 5.05 44.72 2.62
521 543 5.341169 TGAAAATGGGCTTATCTTTTCCCT 58.659 37.500 0.00 0.00 39.49 4.20
523 545 3.602205 ATGGGCTTATCTTTTCCCTCC 57.398 47.619 0.00 0.00 39.49 4.30
603 639 8.287350 AGGAGTACTATATTTGACCAGGTAAGA 58.713 37.037 0.00 0.00 0.00 2.10
732 774 2.034878 TGGGCACAGCACAATTTTGTA 58.965 42.857 0.00 0.00 39.83 2.41
733 775 2.035704 TGGGCACAGCACAATTTTGTAG 59.964 45.455 0.00 0.00 39.83 2.74
734 776 2.061028 GGCACAGCACAATTTTGTAGC 58.939 47.619 0.00 3.26 39.91 3.58
781 828 1.339438 CCACATCCTTGTCCCTGTCTG 60.339 57.143 0.00 0.00 32.34 3.51
783 830 0.325933 CATCCTTGTCCCTGTCTGCA 59.674 55.000 0.00 0.00 0.00 4.41
784 831 0.326264 ATCCTTGTCCCTGTCTGCAC 59.674 55.000 0.00 0.00 0.00 4.57
785 832 1.669115 CCTTGTCCCTGTCTGCACG 60.669 63.158 0.00 0.00 0.00 5.34
788 835 2.046892 GTCCCTGTCTGCACGCAT 60.047 61.111 0.00 0.00 0.00 4.73
789 836 1.218047 GTCCCTGTCTGCACGCATA 59.782 57.895 0.00 0.00 0.00 3.14
790 837 0.179073 GTCCCTGTCTGCACGCATAT 60.179 55.000 0.00 0.00 0.00 1.78
791 838 0.104855 TCCCTGTCTGCACGCATATC 59.895 55.000 0.00 0.00 0.00 1.63
792 839 0.179076 CCCTGTCTGCACGCATATCA 60.179 55.000 0.00 0.00 0.00 2.15
793 840 0.933097 CCTGTCTGCACGCATATCAC 59.067 55.000 0.00 0.00 0.00 3.06
868 917 0.673333 CCATATTGATGCCGCCGCTA 60.673 55.000 0.00 0.00 35.36 4.26
881 930 0.654683 GCCGCTACAGAGAATTGCAG 59.345 55.000 0.00 0.00 0.00 4.41
882 931 0.654683 CCGCTACAGAGAATTGCAGC 59.345 55.000 0.00 0.00 34.74 5.25
974 1034 3.074369 GGGTTGGGCGGATTTGGG 61.074 66.667 0.00 0.00 0.00 4.12
975 1035 2.283604 GGTTGGGCGGATTTGGGT 60.284 61.111 0.00 0.00 0.00 4.51
1393 1469 4.856607 CTCGTTCGCTCGCTCCCC 62.857 72.222 0.00 0.00 0.00 4.81
1438 1514 0.538584 TCAGCTGCTACTCCATGGTG 59.461 55.000 12.58 12.42 0.00 4.17
1443 1519 0.326143 TGCTACTCCATGGTGGCCTA 60.326 55.000 17.76 1.17 41.88 3.93
1459 1535 5.758784 GGTGGCCTAGTGTTCATATTAAGTC 59.241 44.000 3.32 0.00 0.00 3.01
1460 1536 6.408206 GGTGGCCTAGTGTTCATATTAAGTCT 60.408 42.308 3.32 0.00 0.00 3.24
1494 1572 7.068593 TCACCAAAGTTTTTCTCTGTTGATGAT 59.931 33.333 0.00 0.00 0.00 2.45
1495 1573 7.168637 CACCAAAGTTTTTCTCTGTTGATGATG 59.831 37.037 0.00 0.00 0.00 3.07
1501 1579 8.446273 AGTTTTTCTCTGTTGATGATGTTATCG 58.554 33.333 0.00 0.00 0.00 2.92
1504 1582 7.704789 TTCTCTGTTGATGATGTTATCGATG 57.295 36.000 8.54 0.00 0.00 3.84
1538 1619 8.186821 AGTAATTCAAGAGCAATTAGTTGATGC 58.813 33.333 1.56 0.00 37.53 3.91
1593 1674 5.743872 GCGATTGTGTTCAGTTTTTCTTTCT 59.256 36.000 0.00 0.00 0.00 2.52
1657 1738 2.410939 ACGTAGCGACCCTTCTTTTTC 58.589 47.619 0.00 0.00 0.00 2.29
1685 1766 4.781775 TGGAAGGTGTCAAAGAAAGGTA 57.218 40.909 0.00 0.00 0.00 3.08
1695 1777 6.912591 GTGTCAAAGAAAGGTATGTGTGAAAG 59.087 38.462 0.00 0.00 0.00 2.62
1700 1782 6.681729 AGAAAGGTATGTGTGAAAGGAGTA 57.318 37.500 0.00 0.00 0.00 2.59
1773 1880 6.883217 AGTAGTAGTTGAGACCGAGAAATACA 59.117 38.462 0.00 0.00 0.00 2.29
1795 1902 5.643777 ACATCCGTATTGAGAAGAAACTTGG 59.356 40.000 0.00 0.00 0.00 3.61
1833 1940 8.700973 AGTAAATAATGACTGGTTGTTTGGTTT 58.299 29.630 0.00 0.00 0.00 3.27
1834 1941 9.968870 GTAAATAATGACTGGTTGTTTGGTTTA 57.031 29.630 0.00 0.00 0.00 2.01
1837 1944 8.927675 ATAATGACTGGTTGTTTGGTTTAGTA 57.072 30.769 0.00 0.00 0.00 1.82
1838 1945 7.833285 AATGACTGGTTGTTTGGTTTAGTAT 57.167 32.000 0.00 0.00 0.00 2.12
1958 2090 6.127897 CCATCCTTTTTAGAACAGTGATGTCC 60.128 42.308 0.00 0.00 0.00 4.02
1974 2106 9.778993 CAGTGATGTCCAATTCAAGTTTTATAG 57.221 33.333 0.00 0.00 0.00 1.31
2034 2167 9.750783 TGAACTTACTTATACCTCTCTAACACT 57.249 33.333 0.00 0.00 0.00 3.55
2145 2278 2.290641 TGGTATGCGTTTCTCATTGGGT 60.291 45.455 0.00 0.00 0.00 4.51
2146 2279 3.055021 TGGTATGCGTTTCTCATTGGGTA 60.055 43.478 0.00 0.00 0.00 3.69
2147 2280 4.134563 GGTATGCGTTTCTCATTGGGTAT 58.865 43.478 0.00 0.00 0.00 2.73
2260 2393 1.967319 CACGCAAATACCATAGGCCT 58.033 50.000 11.78 11.78 0.00 5.19
2305 2438 5.402398 TCACTTGACAAGACTGATATGTCG 58.598 41.667 21.95 0.00 44.95 4.35
2317 2450 2.959030 TGATATGTCGAAGGGGAGTCAG 59.041 50.000 0.00 0.00 0.00 3.51
2413 2546 7.333174 TCAGCGACATACATAAGATCAAAACAA 59.667 33.333 0.00 0.00 0.00 2.83
2618 2751 5.426833 GGGATCTAGGTATGCCATCTTATGT 59.573 44.000 1.54 0.00 37.32 2.29
2648 2781 8.331730 ACCCTTCCATTACGTAAATTATATGC 57.668 34.615 12.81 0.00 0.00 3.14
2649 2782 7.940137 ACCCTTCCATTACGTAAATTATATGCA 59.060 33.333 12.81 0.00 0.00 3.96
2760 2893 6.294397 CGTAACCCCTGACCATAACTACTATC 60.294 46.154 0.00 0.00 0.00 2.08
2784 2917 3.127030 GCAGTGCTGATAACAACCTTACC 59.873 47.826 8.18 0.00 0.00 2.85
2785 2918 4.579869 CAGTGCTGATAACAACCTTACCT 58.420 43.478 0.00 0.00 0.00 3.08
2832 2965 4.497473 TTTATGAAAACCAGCAGTTCCG 57.503 40.909 0.00 0.00 37.88 4.30
2835 2984 1.305201 GAAAACCAGCAGTTCCGACA 58.695 50.000 0.00 0.00 37.88 4.35
3062 3211 4.717778 TGGTAGTGGGTAAGCAAAGCTATA 59.282 41.667 0.00 0.00 38.25 1.31
3163 3312 7.222805 AGTGTAATTATGTCACGTATGAAGCAG 59.777 37.037 0.00 0.00 36.31 4.24
3182 3331 9.177608 TGAAGCAGCACTAACTAATTTTATCAT 57.822 29.630 0.00 0.00 0.00 2.45
3276 3526 4.286808 CCCCCAGTTCCATTTCAAAGAAAT 59.713 41.667 0.00 0.00 0.00 2.17
3351 3601 8.324110 CTTTGTGTAAGAAGTCTCACCAAGACA 61.324 40.741 7.84 0.00 45.25 3.41
3368 3622 1.014044 ACACTGACTATGTTGCGGCG 61.014 55.000 0.51 0.51 0.00 6.46
3460 3714 2.738213 AAGGAGGCACAGCTCCAACG 62.738 60.000 9.13 0.00 41.98 4.10
3466 3720 2.031163 ACAGCTCCAACGCAGACC 59.969 61.111 0.00 0.00 0.00 3.85
3784 4038 0.602638 TTCAGGCGTTTGCGATCTGT 60.603 50.000 0.00 0.00 44.10 3.41
3811 4065 2.483877 CAGCTTCGACACCAAATTAGCA 59.516 45.455 3.11 0.00 0.00 3.49
4003 4257 5.958955 AGTTAGCTTCAATCCAGCATTTTC 58.041 37.500 0.00 0.00 39.99 2.29
4182 4436 2.493099 ATGAGAAGCAGGAGGAGGAT 57.507 50.000 0.00 0.00 0.00 3.24
4189 4443 0.107643 GCAGGAGGAGGATAGGTTGC 59.892 60.000 0.00 0.00 0.00 4.17
4318 4573 4.594970 TGTGTATTGGAAATACCCAGGTG 58.405 43.478 0.00 0.00 37.53 4.00
4474 4733 6.547880 TGGAATCAGTTTTTAACAGCAAGGTA 59.452 34.615 0.00 0.00 0.00 3.08
4494 4753 7.617041 AGGTAAGAGAATTATGTCAAACTGC 57.383 36.000 0.00 0.00 0.00 4.40
4521 4780 5.240623 TGCAATTCGGTTCACTGTAAATTCT 59.759 36.000 0.00 0.00 0.00 2.40
4566 4825 4.248174 TGATATGGATGCCAGGAAAACA 57.752 40.909 0.00 0.00 36.75 2.83
4587 4846 4.345859 AGGGAACTGAATTAACACGACA 57.654 40.909 0.00 0.00 41.13 4.35
4626 4885 7.987649 ACATCAGTTGAAAATTTTGCATTTGT 58.012 26.923 8.47 1.13 0.00 2.83
4640 4899 5.648178 TGCATTTGTATTTGCAGTGATCT 57.352 34.783 0.00 0.00 43.54 2.75
4641 4900 6.756299 TGCATTTGTATTTGCAGTGATCTA 57.244 33.333 0.00 0.00 43.54 1.98
4759 5018 4.657436 ATACACTTGAACTCTCGATCCC 57.343 45.455 0.00 0.00 0.00 3.85
4761 5020 2.632996 ACACTTGAACTCTCGATCCCAA 59.367 45.455 0.00 0.00 0.00 4.12
4762 5021 3.071023 ACACTTGAACTCTCGATCCCAAA 59.929 43.478 0.00 0.00 0.00 3.28
4764 5023 4.515191 CACTTGAACTCTCGATCCCAAAAA 59.485 41.667 0.00 0.00 0.00 1.94
4797 5057 8.572185 CGGATCGGATCATAGTATTTCATATCT 58.428 37.037 18.99 0.00 0.00 1.98
4798 5058 9.906660 GGATCGGATCATAGTATTTCATATCTC 57.093 37.037 18.99 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.959749 TGTATTGTTGATTTTTGTTACCTCTTC 57.040 29.630 0.00 0.00 0.00 2.87
15 17 3.677596 GGGCCGTGTATTGTTGATTTTTG 59.322 43.478 0.00 0.00 0.00 2.44
43 47 4.454504 GGTGCGAGGATTAAGTTTCTTTCA 59.545 41.667 0.00 0.00 0.00 2.69
65 69 2.802667 CTTTCCAGACATCGCGCGG 61.803 63.158 31.69 17.77 0.00 6.46
70 74 1.303309 GCCATCCTTTCCAGACATCG 58.697 55.000 0.00 0.00 0.00 3.84
76 80 0.471617 ATCTCCGCCATCCTTTCCAG 59.528 55.000 0.00 0.00 0.00 3.86
89 93 1.001924 CTCGTGTCCTCATCATCTCCG 60.002 57.143 0.00 0.00 0.00 4.63
95 99 3.073274 TCTCTTCTCGTGTCCTCATCA 57.927 47.619 0.00 0.00 0.00 3.07
102 106 4.797868 CAGATTGTGATCTCTTCTCGTGTC 59.202 45.833 0.00 0.00 40.67 3.67
103 107 4.381398 CCAGATTGTGATCTCTTCTCGTGT 60.381 45.833 0.00 0.00 40.67 4.49
104 108 4.111198 CCAGATTGTGATCTCTTCTCGTG 58.889 47.826 0.00 0.00 40.67 4.35
105 109 4.019858 TCCAGATTGTGATCTCTTCTCGT 58.980 43.478 0.00 0.00 40.67 4.18
109 113 4.512198 CAGCATCCAGATTGTGATCTCTTC 59.488 45.833 0.00 0.00 40.67 2.87
110 114 4.452825 CAGCATCCAGATTGTGATCTCTT 58.547 43.478 0.00 0.00 40.67 2.85
111 115 3.181453 CCAGCATCCAGATTGTGATCTCT 60.181 47.826 0.00 0.00 40.67 3.10
112 116 3.139850 CCAGCATCCAGATTGTGATCTC 58.860 50.000 0.00 0.00 40.67 2.75
113 117 2.775960 TCCAGCATCCAGATTGTGATCT 59.224 45.455 0.00 0.00 43.43 2.75
114 118 3.204306 TCCAGCATCCAGATTGTGATC 57.796 47.619 0.00 0.00 0.00 2.92
115 119 3.487372 CATCCAGCATCCAGATTGTGAT 58.513 45.455 0.00 0.00 0.00 3.06
116 120 2.422377 CCATCCAGCATCCAGATTGTGA 60.422 50.000 0.00 0.00 0.00 3.58
117 121 1.954382 CCATCCAGCATCCAGATTGTG 59.046 52.381 0.00 0.00 0.00 3.33
118 122 1.567649 ACCATCCAGCATCCAGATTGT 59.432 47.619 0.00 0.00 0.00 2.71
119 123 2.359981 ACCATCCAGCATCCAGATTG 57.640 50.000 0.00 0.00 0.00 2.67
154 158 4.489306 AATTTCTGGTGGGCTAGTAGAC 57.511 45.455 0.00 0.00 0.00 2.59
157 161 5.941647 GTGTTTAATTTCTGGTGGGCTAGTA 59.058 40.000 0.00 0.00 0.00 1.82
191 195 1.808343 GAGACATGCATGCTTGTGTCA 59.192 47.619 37.59 14.81 42.51 3.58
198 202 5.008415 GCTTACTTTATGAGACATGCATGCT 59.992 40.000 26.53 22.42 0.00 3.79
199 203 5.008415 AGCTTACTTTATGAGACATGCATGC 59.992 40.000 26.53 18.25 0.00 4.06
200 204 6.615264 AGCTTACTTTATGAGACATGCATG 57.385 37.500 25.09 25.09 0.00 4.06
201 205 7.504403 AGTAGCTTACTTTATGAGACATGCAT 58.496 34.615 0.00 0.00 34.86 3.96
222 227 6.561614 TCGTTACCTCATGCTAAAAGAGTAG 58.438 40.000 0.00 0.00 0.00 2.57
225 230 5.651530 TCTCGTTACCTCATGCTAAAAGAG 58.348 41.667 0.00 0.00 0.00 2.85
234 239 4.929211 TCACAAACATCTCGTTACCTCATG 59.071 41.667 0.00 0.00 36.59 3.07
236 241 4.594123 TCACAAACATCTCGTTACCTCA 57.406 40.909 0.00 0.00 36.59 3.86
242 247 5.296780 ACAAAGTCATCACAAACATCTCGTT 59.703 36.000 0.00 0.00 40.50 3.85
249 254 7.172361 TCGATATTGACAAAGTCATCACAAACA 59.828 33.333 0.12 0.00 42.40 2.83
274 279 3.096092 AGAGACTGGGTCAACAGATCTC 58.904 50.000 0.00 13.17 41.12 2.75
280 285 3.199946 ACTTTTGAGAGACTGGGTCAACA 59.800 43.478 0.52 0.00 34.60 3.33
287 292 3.117491 TGAGCACTTTTGAGAGACTGG 57.883 47.619 0.00 0.00 0.00 4.00
300 305 1.615883 CAGCCTATCCGTATGAGCACT 59.384 52.381 0.00 0.00 0.00 4.40
301 306 1.937108 GCAGCCTATCCGTATGAGCAC 60.937 57.143 0.00 0.00 0.00 4.40
324 330 0.608856 TTCCCTGTGAACGCATGCAT 60.609 50.000 19.57 5.46 0.00 3.96
327 333 1.522668 TTCTTCCCTGTGAACGCATG 58.477 50.000 0.00 0.00 0.00 4.06
328 334 2.496899 ATTCTTCCCTGTGAACGCAT 57.503 45.000 0.00 0.00 0.00 4.73
332 338 5.050091 CGCACATATATTCTTCCCTGTGAAC 60.050 44.000 4.78 0.00 36.89 3.18
339 345 5.932303 ACATACACGCACATATATTCTTCCC 59.068 40.000 0.00 0.00 0.00 3.97
341 347 7.637709 TCACATACACGCACATATATTCTTC 57.362 36.000 0.00 0.00 0.00 2.87
345 351 5.751509 ACGTTCACATACACGCACATATATT 59.248 36.000 0.00 0.00 40.16 1.28
346 352 5.286438 ACGTTCACATACACGCACATATAT 58.714 37.500 0.00 0.00 40.16 0.86
359 365 1.349688 AGGGAGGCAAACGTTCACATA 59.650 47.619 0.00 0.00 0.00 2.29
360 366 0.110486 AGGGAGGCAAACGTTCACAT 59.890 50.000 0.00 0.00 0.00 3.21
361 367 0.534203 GAGGGAGGCAAACGTTCACA 60.534 55.000 0.00 0.00 0.00 3.58
362 368 0.250338 AGAGGGAGGCAAACGTTCAC 60.250 55.000 0.00 0.00 0.00 3.18
363 369 0.472471 AAGAGGGAGGCAAACGTTCA 59.528 50.000 0.00 0.00 0.00 3.18
364 370 1.157585 GAAGAGGGAGGCAAACGTTC 58.842 55.000 0.00 0.00 0.00 3.95
365 371 0.765510 AGAAGAGGGAGGCAAACGTT 59.234 50.000 0.00 0.00 0.00 3.99
366 372 0.321996 GAGAAGAGGGAGGCAAACGT 59.678 55.000 0.00 0.00 0.00 3.99
367 373 0.610687 AGAGAAGAGGGAGGCAAACG 59.389 55.000 0.00 0.00 0.00 3.60
407 413 8.650143 AGGAGATAAAATTAGTTTCCTTTGCA 57.350 30.769 0.00 0.00 0.00 4.08
491 513 9.657419 AAAAGATAAGCCCATTTTCATGTAAAG 57.343 29.630 3.81 0.00 0.00 1.85
579 615 8.910944 TGTCTTACCTGGTCAAATATAGTACTC 58.089 37.037 0.63 0.00 0.00 2.59
603 639 5.716228 TGTTTATGGCATTTTCCTCTGATGT 59.284 36.000 4.78 0.00 0.00 3.06
681 717 6.038271 CAGGGAAATTGTGCTGGTACTAATAC 59.962 42.308 0.00 0.00 0.00 1.89
726 768 3.568007 AGGAACAAGAATGCGCTACAAAA 59.432 39.130 9.73 0.00 0.00 2.44
732 774 1.168714 GGAAGGAACAAGAATGCGCT 58.831 50.000 9.73 0.00 0.00 5.92
733 775 0.171231 GGGAAGGAACAAGAATGCGC 59.829 55.000 0.00 0.00 0.00 6.09
734 776 1.740025 GAGGGAAGGAACAAGAATGCG 59.260 52.381 0.00 0.00 0.00 4.73
781 828 0.378257 CTTGGTGGTGATATGCGTGC 59.622 55.000 0.00 0.00 0.00 5.34
783 830 0.748005 GGCTTGGTGGTGATATGCGT 60.748 55.000 0.00 0.00 0.00 5.24
784 831 1.775039 CGGCTTGGTGGTGATATGCG 61.775 60.000 0.00 0.00 0.00 4.73
785 832 2.024918 CGGCTTGGTGGTGATATGC 58.975 57.895 0.00 0.00 0.00 3.14
788 835 0.177141 GTAGCGGCTTGGTGGTGATA 59.823 55.000 8.26 0.00 0.00 2.15
789 836 1.078426 GTAGCGGCTTGGTGGTGAT 60.078 57.895 8.26 0.00 0.00 3.06
790 837 2.345991 GTAGCGGCTTGGTGGTGA 59.654 61.111 8.26 0.00 0.00 4.02
791 838 2.746277 GGTAGCGGCTTGGTGGTG 60.746 66.667 8.26 0.00 0.00 4.17
792 839 4.029809 GGGTAGCGGCTTGGTGGT 62.030 66.667 8.26 0.00 0.00 4.16
793 840 3.561120 TTGGGTAGCGGCTTGGTGG 62.561 63.158 8.26 0.00 0.00 4.61
868 917 0.250901 AACGGGCTGCAATTCTCTGT 60.251 50.000 0.50 0.00 0.00 3.41
881 930 3.134127 GCTGGGATGTCAACGGGC 61.134 66.667 0.00 0.00 0.00 6.13
882 931 2.819595 CGCTGGGATGTCAACGGG 60.820 66.667 0.00 0.00 0.00 5.28
921 970 2.488153 CCAAGAAACTGACGGATTTCCC 59.512 50.000 0.00 0.00 35.77 3.97
922 971 2.095212 GCCAAGAAACTGACGGATTTCC 60.095 50.000 0.00 0.00 35.77 3.13
924 973 2.554032 CTGCCAAGAAACTGACGGATTT 59.446 45.455 0.00 0.00 0.00 2.17
925 974 2.154462 CTGCCAAGAAACTGACGGATT 58.846 47.619 0.00 0.00 0.00 3.01
926 975 1.611673 CCTGCCAAGAAACTGACGGAT 60.612 52.381 0.00 0.00 0.00 4.18
927 976 0.250295 CCTGCCAAGAAACTGACGGA 60.250 55.000 0.00 0.00 0.00 4.69
928 977 0.250295 TCCTGCCAAGAAACTGACGG 60.250 55.000 0.00 0.00 0.00 4.79
929 978 1.813513 ATCCTGCCAAGAAACTGACG 58.186 50.000 0.00 0.00 0.00 4.35
930 979 2.160417 CGAATCCTGCCAAGAAACTGAC 59.840 50.000 0.00 0.00 0.00 3.51
932 981 1.470098 CCGAATCCTGCCAAGAAACTG 59.530 52.381 0.00 0.00 0.00 3.16
933 982 1.073923 ACCGAATCCTGCCAAGAAACT 59.926 47.619 0.00 0.00 0.00 2.66
959 1019 2.969827 CACCCAAATCCGCCCAAC 59.030 61.111 0.00 0.00 0.00 3.77
1361 1433 1.104577 ACGAGAGAGGGATTCGGAGC 61.105 60.000 0.00 0.00 38.58 4.70
1438 1514 7.272978 TCAAGACTTAATATGAACACTAGGCC 58.727 38.462 0.00 0.00 0.00 5.19
1459 1535 8.624776 AGAGAAAAACTTTGGTGACTAATCAAG 58.375 33.333 0.00 0.00 36.31 3.02
1460 1536 8.405531 CAGAGAAAAACTTTGGTGACTAATCAA 58.594 33.333 0.00 0.00 36.31 2.57
1501 1579 9.973450 TTGCTCTTGAATTACTAGTAGATCATC 57.027 33.333 16.10 7.59 0.00 2.92
1538 1619 5.746245 TGAAGTTTGCCAAAAATAGACGTTG 59.254 36.000 0.00 0.00 0.00 4.10
1593 1674 6.096141 TCAAAAGGCACTCACACAATTCTAAA 59.904 34.615 0.00 0.00 38.49 1.85
1657 1738 2.584835 TTGACACCTTCCAATCAGGG 57.415 50.000 0.00 0.00 38.24 4.45
1685 1766 5.538813 TGACAGTAGTACTCCTTTCACACAT 59.461 40.000 0.00 0.00 0.00 3.21
1695 1777 7.492352 AAAACAAACATGACAGTAGTACTCC 57.508 36.000 0.00 0.00 0.00 3.85
1745 1850 6.645790 TTCTCGGTCTCAACTACTACTTTT 57.354 37.500 0.00 0.00 0.00 2.27
1773 1880 6.049955 TCCAAGTTTCTTCTCAATACGGAT 57.950 37.500 0.00 0.00 0.00 4.18
1834 1941 9.672673 GACATTGGGCATTTCATACTATATACT 57.327 33.333 0.00 0.00 0.00 2.12
1837 1944 8.796475 GTTGACATTGGGCATTTCATACTATAT 58.204 33.333 0.00 0.00 0.00 0.86
1838 1945 7.998383 AGTTGACATTGGGCATTTCATACTATA 59.002 33.333 0.00 0.00 0.00 1.31
1879 2002 1.209127 CCCGTTTGACAATGACCGC 59.791 57.895 0.00 0.00 0.00 5.68
1958 2090 7.489113 GCCACATGGTCTATAAAACTTGAATTG 59.511 37.037 0.00 0.00 37.57 2.32
1974 2106 0.675633 AGCAACAAAGCCACATGGTC 59.324 50.000 0.00 0.00 37.57 4.02
2019 2151 4.896482 CCAGGCTAAGTGTTAGAGAGGTAT 59.104 45.833 0.00 0.00 35.20 2.73
2033 2166 2.744494 GCATCTCTTGGTCCAGGCTAAG 60.744 54.545 0.00 1.92 0.00 2.18
2034 2167 1.210478 GCATCTCTTGGTCCAGGCTAA 59.790 52.381 0.00 0.00 0.00 3.09
2186 2319 4.993584 TGCTGCACAAAGAAAAAGAAACAA 59.006 33.333 0.00 0.00 0.00 2.83
2188 2321 4.627035 AGTGCTGCACAAAGAAAAAGAAAC 59.373 37.500 31.90 1.67 36.74 2.78
2219 2352 2.303022 CAGCAAGTAGGAACTTCCCAGA 59.697 50.000 4.01 0.00 44.28 3.86
2260 2393 7.931407 AGTGAAATTAGATATTCGGTGCATGTA 59.069 33.333 0.00 0.00 0.00 2.29
2305 2438 1.599576 GCAGGTCTGACTCCCCTTC 59.400 63.158 7.85 0.00 0.00 3.46
2378 2511 4.371855 TGTATGTCGCTGAAGGAACTAG 57.628 45.455 0.00 0.00 38.49 2.57
2413 2546 3.825328 AGGTTTCTCTGCTTCAACATGT 58.175 40.909 0.00 0.00 0.00 3.21
2618 2751 5.495926 TTTACGTAATGGAAGGGTTACCA 57.504 39.130 9.18 0.00 40.13 3.25
2649 2782 9.515020 CCAGAAAATATACAAAAATATGTGCGT 57.485 29.630 0.00 0.00 34.75 5.24
2734 2867 2.823959 AGTTATGGTCAGGGGTTACGA 58.176 47.619 0.00 0.00 0.00 3.43
2760 2893 2.430465 AGGTTGTTATCAGCACTGCAG 58.570 47.619 13.48 13.48 0.00 4.41
2802 2935 8.592809 ACTGCTGGTTTTCATAAATGGAAATTA 58.407 29.630 0.00 0.00 37.58 1.40
2814 2947 1.880027 GTCGGAACTGCTGGTTTTCAT 59.120 47.619 0.00 0.00 38.41 2.57
3088 3237 6.891908 AGTGGTGCTTCCTACATGATAATTTT 59.108 34.615 0.00 0.00 37.07 1.82
3090 3239 6.006275 AGTGGTGCTTCCTACATGATAATT 57.994 37.500 0.00 0.00 37.07 1.40
3200 3450 5.804639 AGTTAGTGGTGCTTCATACATGAA 58.195 37.500 0.00 4.66 43.94 2.57
3276 3526 9.733556 ATAATTAGTTAGTGTCATGTGGTTTCA 57.266 29.630 0.00 0.00 0.00 2.69
3339 3589 4.152647 ACATAGTCAGTGTCTTGGTGAGA 58.847 43.478 0.00 0.00 0.00 3.27
3340 3590 4.527509 ACATAGTCAGTGTCTTGGTGAG 57.472 45.455 0.00 0.00 0.00 3.51
3345 3595 2.413112 CCGCAACATAGTCAGTGTCTTG 59.587 50.000 0.00 0.00 0.00 3.02
3351 3601 0.528924 TACGCCGCAACATAGTCAGT 59.471 50.000 0.00 0.00 0.00 3.41
3352 3602 1.852942 ATACGCCGCAACATAGTCAG 58.147 50.000 0.00 0.00 0.00 3.51
3353 3603 2.303163 AATACGCCGCAACATAGTCA 57.697 45.000 0.00 0.00 0.00 3.41
3354 3604 2.849502 GCAAATACGCCGCAACATAGTC 60.850 50.000 0.00 0.00 0.00 2.59
3368 3622 2.165641 GGCCCCTACAACAAGCAAATAC 59.834 50.000 0.00 0.00 0.00 1.89
3460 3714 1.206831 GAAAGGAAACGCGGTCTGC 59.793 57.895 12.47 0.00 41.47 4.26
3466 3720 2.414161 GGGATTGAAGAAAGGAAACGCG 60.414 50.000 3.53 3.53 0.00 6.01
3628 3882 4.096984 ACCAGCTGAAAGTTTTTCACTGAG 59.903 41.667 17.39 17.16 35.12 3.35
3688 3942 3.282745 CTGGAGGGTGGTGTCGTCG 62.283 68.421 0.00 0.00 0.00 5.12
3772 4026 1.392853 CTGCTGAGACAGATCGCAAAC 59.607 52.381 2.81 0.00 40.25 2.93
3784 4038 1.290324 GGTGTCGAAGCTGCTGAGA 59.710 57.895 1.35 2.75 0.00 3.27
3811 4065 2.094659 CGCACCTCTTCATTCGCGT 61.095 57.895 5.77 0.00 38.03 6.01
4003 4257 2.767505 GGATATCCTTAACACCCAGCG 58.232 52.381 14.97 0.00 0.00 5.18
4172 4426 1.008938 ACAGCAACCTATCCTCCTCCT 59.991 52.381 0.00 0.00 0.00 3.69
4189 4443 8.986847 CATTTAACAGGATATCAAGCTCTACAG 58.013 37.037 4.83 0.00 0.00 2.74
4240 4494 2.035321 ACAAATTTAACCACACCCAGCG 59.965 45.455 0.00 0.00 0.00 5.18
4318 4573 4.273318 ACCAGGTAGAAAATCATGCTTCC 58.727 43.478 0.00 0.00 0.00 3.46
4474 4733 6.676456 GCATCGCAGTTTGACATAATTCTCTT 60.676 38.462 0.00 0.00 0.00 2.85
4494 4753 1.464608 ACAGTGAACCGAATTGCATCG 59.535 47.619 2.68 2.68 42.37 3.84
4521 4780 5.707242 TCAAAATTGTAATTACCGCCACA 57.293 34.783 13.01 0.00 0.00 4.17
4566 4825 4.062991 GTGTCGTGTTAATTCAGTTCCCT 58.937 43.478 0.00 0.00 0.00 4.20
4771 5031 8.572185 AGATATGAAATACTATGATCCGATCCG 58.428 37.037 5.91 0.00 0.00 4.18
4789 5049 8.925338 CCCAGATGATATGAGATGAGATATGAA 58.075 37.037 0.00 0.00 0.00 2.57
4790 5050 7.015389 GCCCAGATGATATGAGATGAGATATGA 59.985 40.741 0.00 0.00 0.00 2.15
4791 5051 7.015779 AGCCCAGATGATATGAGATGAGATATG 59.984 40.741 0.00 0.00 0.00 1.78
4794 5054 5.129650 CAGCCCAGATGATATGAGATGAGAT 59.870 44.000 0.00 0.00 0.00 2.75
4797 5057 4.422984 TCAGCCCAGATGATATGAGATGA 58.577 43.478 0.00 0.00 0.00 2.92
4798 5058 4.820894 TCAGCCCAGATGATATGAGATG 57.179 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.