Multiple sequence alignment - TraesCS3B01G145300

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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 TraesCS3B01G145300 chr3B 100.000 6769 0 0 1 6769 133807905 133801137 0.000000e+00 12501.0
1 TraesCS3B01G145300 chr3B 96.023 704 21 2 1 697 759908187 759907484 0.000000e+00 1138.0
2 TraesCS3B01G145300 chr3B 82.577 551 83 12 5048 5588 131062786 131063333 2.210000e-129 473.0
3 TraesCS3B01G145300 chr3B 80.885 565 83 14 3085 3638 133814931 133814381 8.120000e-114 422.0
4 TraesCS3B01G145300 chr3B 81.551 477 57 21 5127 5593 134997357 134996902 1.390000e-96 364.0
5 TraesCS3B01G145300 chr3B 81.132 477 59 21 5127 5593 134972335 134972790 3.000000e-93 353.0
6 TraesCS3B01G145300 chr3B 87.013 231 28 2 5129 5358 135687053 135687282 6.730000e-65 259.0
7 TraesCS3B01G145300 chr3D 94.074 4219 184 29 736 4922 84901250 84897066 0.000000e+00 6346.0
8 TraesCS3B01G145300 chr3D 94.397 696 26 5 5052 5744 84897007 84896322 0.000000e+00 1057.0
9 TraesCS3B01G145300 chr3D 78.547 895 120 40 4691 5556 84906048 84905197 2.160000e-144 523.0
10 TraesCS3B01G145300 chr3D 79.942 693 101 17 3083 3761 84908290 84907622 6.140000e-130 475.0
11 TraesCS3B01G145300 chr3D 80.216 647 93 20 3027 3649 85247234 85247869 2.880000e-123 453.0
12 TraesCS3B01G145300 chr3D 82.276 536 70 17 1345 1867 85411015 85410492 2.240000e-119 440.0
13 TraesCS3B01G145300 chr3D 80.847 543 75 16 5057 5594 85250217 85250735 3.800000e-107 399.0
14 TraesCS3B01G145300 chr3D 80.218 551 79 20 3087 3614 85408863 85408320 2.960000e-103 387.0
15 TraesCS3B01G145300 chr3D 77.105 677 125 17 3027 3693 84034149 84033493 1.390000e-96 364.0
16 TraesCS3B01G145300 chr3D 84.496 258 36 4 5103 5358 85449091 85449346 1.130000e-62 252.0
17 TraesCS3B01G145300 chr3A 92.489 2676 129 28 699 3361 101871207 101868591 0.000000e+00 3762.0
18 TraesCS3B01G145300 chr3A 96.471 1870 50 12 3392 5253 101868594 101866733 0.000000e+00 3073.0
19 TraesCS3B01G145300 chr3A 92.718 975 46 5 5795 6769 101860270 101859321 0.000000e+00 1384.0
20 TraesCS3B01G145300 chr3A 96.023 704 21 2 1 697 51882158 51881455 0.000000e+00 1138.0
21 TraesCS3B01G145300 chr3A 94.681 376 4 3 5246 5618 101866554 101866192 2.740000e-158 569.0
22 TraesCS3B01G145300 chr3A 79.721 789 104 36 4780 5556 101887199 101886455 2.800000e-143 520.0
23 TraesCS3B01G145300 chr3A 81.834 567 84 11 3083 3638 101889446 101888888 6.190000e-125 459.0
24 TraesCS3B01G145300 chr3A 82.276 536 71 20 1345 1867 102307893 102307369 6.230000e-120 442.0
25 TraesCS3B01G145300 chr3A 81.156 467 63 22 5131 5593 102279906 102280351 1.080000e-92 351.0
26 TraesCS3B01G145300 chr3A 79.642 447 66 16 3088 3518 102299089 102298652 1.430000e-76 298.0
27 TraesCS3B01G145300 chr3A 96.133 181 7 0 5619 5799 101865843 101865663 5.130000e-76 296.0
28 TraesCS3B01G145300 chr1D 96.591 704 17 2 1 697 12980491 12981194 0.000000e+00 1160.0
29 TraesCS3B01G145300 chr1D 92.647 68 5 0 6236 6303 441747971 441748038 1.550000e-16 99.0
30 TraesCS3B01G145300 chrUn 96.449 704 18 2 1 697 171011687 171010984 0.000000e+00 1155.0
31 TraesCS3B01G145300 chrUn 82.868 537 66 20 1345 1867 297431150 297431674 6.190000e-125 459.0
32 TraesCS3B01G145300 chrUn 82.868 537 66 20 1345 1867 297436102 297436626 6.190000e-125 459.0
33 TraesCS3B01G145300 chr1B 96.307 704 19 2 1 697 672544677 672543974 0.000000e+00 1149.0
34 TraesCS3B01G145300 chr1B 89.189 185 19 1 6049 6232 497275809 497275625 5.280000e-56 230.0
35 TraesCS3B01G145300 chr6B 96.165 704 20 2 1 697 596598457 596599160 0.000000e+00 1144.0
36 TraesCS3B01G145300 chr6B 91.534 189 16 0 6049 6237 454503015 454503203 1.870000e-65 261.0
37 TraesCS3B01G145300 chr4A 96.165 704 20 2 1 697 79641373 79642076 0.000000e+00 1144.0
38 TraesCS3B01G145300 chr4A 91.176 68 6 0 6237 6304 96277585 96277652 7.230000e-15 93.5
39 TraesCS3B01G145300 chr7A 96.023 704 21 2 1 697 638504263 638504966 0.000000e+00 1138.0
40 TraesCS3B01G145300 chr2B 96.023 704 19 4 1 697 391148203 391147502 0.000000e+00 1136.0
41 TraesCS3B01G145300 chr2B 91.667 72 6 0 6239 6310 653795664 653795593 4.320000e-17 100.0
42 TraesCS3B01G145300 chr2B 100.000 42 0 0 6237 6278 680323945 680323904 2.020000e-10 78.7
43 TraesCS3B01G145300 chr5D 90.476 189 16 2 6049 6237 415720617 415720431 1.460000e-61 248.0
44 TraesCS3B01G145300 chr2D 89.418 189 18 2 6049 6237 334578566 334578752 3.160000e-58 237.0
45 TraesCS3B01G145300 chr2D 91.304 69 5 1 6237 6304 567596272 567596204 7.230000e-15 93.5
46 TraesCS3B01G145300 chr7B 89.560 182 17 2 6049 6229 442058943 442059123 5.280000e-56 230.0
47 TraesCS3B01G145300 chr7D 88.770 187 17 3 6049 6232 617491509 617491694 6.830000e-55 226.0
48 TraesCS3B01G145300 chr7D 87.565 193 20 3 6049 6241 167219671 167219859 3.180000e-53 220.0
49 TraesCS3B01G145300 chr7D 89.091 55 5 1 6239 6292 227402345 227402399 4.380000e-07 67.6
50 TraesCS3B01G145300 chr4D 87.958 191 19 4 6049 6237 505256806 505256994 8.840000e-54 222.0
51 TraesCS3B01G145300 chr5B 92.754 69 5 0 6237 6305 476806600 476806668 4.320000e-17 100.0
52 TraesCS3B01G145300 chr1A 92.647 68 5 0 6237 6304 48983835 48983902 1.550000e-16 99.0


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 TraesCS3B01G145300 chr3B 133801137 133807905 6768 True 12501.00 12501 100.0000 1 6769 1 chr3B.!!$R1 6768
1 TraesCS3B01G145300 chr3B 759907484 759908187 703 True 1138.00 1138 96.0230 1 697 1 chr3B.!!$R4 696
2 TraesCS3B01G145300 chr3B 131062786 131063333 547 False 473.00 473 82.5770 5048 5588 1 chr3B.!!$F1 540
3 TraesCS3B01G145300 chr3B 133814381 133814931 550 True 422.00 422 80.8850 3085 3638 1 chr3B.!!$R2 553
4 TraesCS3B01G145300 chr3D 84896322 84908290 11968 True 2100.25 6346 86.7400 736 5744 4 chr3D.!!$R2 5008
5 TraesCS3B01G145300 chr3D 85247234 85250735 3501 False 426.00 453 80.5315 3027 5594 2 chr3D.!!$F2 2567
6 TraesCS3B01G145300 chr3D 85408320 85411015 2695 True 413.50 440 81.2470 1345 3614 2 chr3D.!!$R3 2269
7 TraesCS3B01G145300 chr3D 84033493 84034149 656 True 364.00 364 77.1050 3027 3693 1 chr3D.!!$R1 666
8 TraesCS3B01G145300 chr3A 101865663 101871207 5544 True 1925.00 3762 94.9435 699 5799 4 chr3A.!!$R5 5100
9 TraesCS3B01G145300 chr3A 101859321 101860270 949 True 1384.00 1384 92.7180 5795 6769 1 chr3A.!!$R2 974
10 TraesCS3B01G145300 chr3A 51881455 51882158 703 True 1138.00 1138 96.0230 1 697 1 chr3A.!!$R1 696
11 TraesCS3B01G145300 chr3A 101886455 101889446 2991 True 489.50 520 80.7775 3083 5556 2 chr3A.!!$R6 2473
12 TraesCS3B01G145300 chr3A 102307369 102307893 524 True 442.00 442 82.2760 1345 1867 1 chr3A.!!$R4 522
13 TraesCS3B01G145300 chr1D 12980491 12981194 703 False 1160.00 1160 96.5910 1 697 1 chr1D.!!$F1 696
14 TraesCS3B01G145300 chrUn 171010984 171011687 703 True 1155.00 1155 96.4490 1 697 1 chrUn.!!$R1 696
15 TraesCS3B01G145300 chrUn 297431150 297431674 524 False 459.00 459 82.8680 1345 1867 1 chrUn.!!$F1 522
16 TraesCS3B01G145300 chrUn 297436102 297436626 524 False 459.00 459 82.8680 1345 1867 1 chrUn.!!$F2 522
17 TraesCS3B01G145300 chr1B 672543974 672544677 703 True 1149.00 1149 96.3070 1 697 1 chr1B.!!$R2 696
18 TraesCS3B01G145300 chr6B 596598457 596599160 703 False 1144.00 1144 96.1650 1 697 1 chr6B.!!$F2 696
19 TraesCS3B01G145300 chr4A 79641373 79642076 703 False 1144.00 1144 96.1650 1 697 1 chr4A.!!$F1 696
20 TraesCS3B01G145300 chr7A 638504263 638504966 703 False 1138.00 1138 96.0230 1 697 1 chr7A.!!$F1 696
21 TraesCS3B01G145300 chr2B 391147502 391148203 701 True 1136.00 1136 96.0230 1 697 1 chr2B.!!$R1 696

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
548 549 1.613332 AATCCCCAAGCAAAGGCCC 60.613 57.895 0.00 0.00 42.56 5.80 F
1029 7343 0.253044 TCAACTACTGCCCATCTGCC 59.747 55.000 0.00 0.00 0.00 4.85 F
1759 8094 0.249398 GGTCCGGTGATGTTGCTACT 59.751 55.000 0.00 0.00 0.00 2.57 F
1874 8209 0.585838 CTAACACGCACATGCACACA 59.414 50.000 4.49 0.00 42.21 3.72 F
1876 8211 1.652167 AACACGCACATGCACACACA 61.652 50.000 4.49 0.00 42.21 3.72 F
1878 8213 2.111582 ACGCACATGCACACACACA 61.112 52.632 4.49 0.00 42.21 3.72 F
2063 8419 2.494073 AGAAGGAGTTCCAGTCGACATC 59.506 50.000 19.50 5.46 38.89 3.06 F
3989 12004 1.043816 AGCGGCATGAGTAGTAGCAT 58.956 50.000 1.45 0.00 0.00 3.79 F
3990 12005 2.239400 AGCGGCATGAGTAGTAGCATA 58.761 47.619 1.45 0.00 0.00 3.14 F
5382 13868 2.422597 TGCCAGTGTCGTCCTAATTTG 58.577 47.619 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 7816 0.042188 CGTGCAACACAGAAACTCCG 60.042 55.000 0.00 0.0 35.74 4.63 R
1888 8223 0.518636 AATCATGTGTGTGTCTGCGC 59.481 50.000 0.00 0.0 0.00 6.09 R
2771 9636 5.170748 GGATTGTTTTGATGCAAGGTAAGG 58.829 41.667 0.00 0.0 0.00 2.69 R
3064 10098 7.035004 ACATTACGCTGTTTAATCAATGCAAT 58.965 30.769 0.00 0.0 0.00 3.56 R
3094 10130 7.614192 GGAACCAGTTGGGATATAGAAAAGAAA 59.386 37.037 2.79 0.0 41.15 2.52 R
3973 11979 5.635700 GCTTACTTATGCTACTACTCATGCC 59.364 44.000 0.00 0.0 0.00 4.40 R
4141 12166 0.827507 GGCAAGCCTTTTGGTCCTGA 60.828 55.000 3.29 0.0 42.99 3.86 R
5352 13835 0.953727 GACACTGGCAATGTCAAGCA 59.046 50.000 22.87 0.0 44.87 3.91 R
5762 14628 1.071299 ACGCCTCAATGCTCACACA 59.929 52.632 0.00 0.0 0.00 3.72 R
6496 15362 0.036105 ACCATCGCTGCATGTTGAGA 60.036 50.000 0.00 0.0 0.00 3.27 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
136 137 3.972133 TGAACTATTCTCCGGGTACTGA 58.028 45.455 0.00 0.00 36.31 3.41
171 172 3.572584 CAAGCAAGTGAAGAAATCCTGC 58.427 45.455 0.00 0.00 0.00 4.85
207 208 6.490040 TGATTTACTTTCCTTTCCAAGACCTG 59.510 38.462 0.00 0.00 0.00 4.00
210 211 5.382664 ACTTTCCTTTCCAAGACCTGTAA 57.617 39.130 0.00 0.00 0.00 2.41
350 351 2.649816 ACAGCAAAGGGAAGTAGGGATT 59.350 45.455 0.00 0.00 0.00 3.01
360 361 3.282885 GAAGTAGGGATTGGCTTTCCTG 58.717 50.000 6.31 0.00 33.53 3.86
467 468 4.602340 AGTTGTAGCTTTCGAGGAGAAA 57.398 40.909 0.00 0.00 45.76 2.52
496 497 4.214310 TGAATCAAAGGGACAAGCAAAGA 58.786 39.130 0.00 0.00 0.00 2.52
548 549 1.613332 AATCCCCAAGCAAAGGCCC 60.613 57.895 0.00 0.00 42.56 5.80
723 731 3.010808 TCCGTTCAAAATCCAAGGGGTAT 59.989 43.478 0.00 0.00 34.93 2.73
731 739 2.452600 TCCAAGGGGTATGATTTGCC 57.547 50.000 0.00 0.00 34.93 4.52
1026 7340 2.906389 TCAGTTCAACTACTGCCCATCT 59.094 45.455 0.00 0.00 44.10 2.90
1029 7343 0.253044 TCAACTACTGCCCATCTGCC 59.747 55.000 0.00 0.00 0.00 4.85
1031 7345 1.264749 AACTACTGCCCATCTGCCGA 61.265 55.000 0.00 0.00 0.00 5.54
1044 7358 2.579787 GCCGACGACATCCACGAG 60.580 66.667 0.00 0.00 34.70 4.18
1054 7368 1.985662 ATCCACGAGGCCGGTAACA 60.986 57.895 1.90 0.00 40.78 2.41
1095 7412 2.351253 CCTCGAAGATAGCATCCACGAG 60.351 54.545 20.90 20.90 45.66 4.18
1193 7510 2.354203 CGTTCCCCTCCTTCTTTCTGAG 60.354 54.545 0.00 0.00 0.00 3.35
1212 7529 5.128827 TCTGAGCCCTGATTACGTTTCTAAT 59.871 40.000 0.00 0.00 0.00 1.73
1213 7530 5.116180 TGAGCCCTGATTACGTTTCTAATG 58.884 41.667 0.00 0.00 0.00 1.90
1385 7711 5.947228 TGGTCTTCTGTCTTTGCTAATTG 57.053 39.130 0.00 0.00 0.00 2.32
1388 7714 5.106515 GGTCTTCTGTCTTTGCTAATTGGTC 60.107 44.000 0.00 0.00 0.00 4.02
1389 7715 5.703130 GTCTTCTGTCTTTGCTAATTGGTCT 59.297 40.000 0.00 0.00 0.00 3.85
1390 7716 6.874134 GTCTTCTGTCTTTGCTAATTGGTCTA 59.126 38.462 0.00 0.00 0.00 2.59
1435 7765 6.599638 ACTTTGGGAAAGATATTGTACAGAGC 59.400 38.462 3.11 0.00 41.02 4.09
1558 7888 3.012518 CAAGTATTTGGTGGAGGAGCTG 58.987 50.000 0.00 0.00 0.00 4.24
1676 8011 9.135843 CAATGTTTGCCAGCATATAATATCTTG 57.864 33.333 0.00 0.00 0.00 3.02
1682 8017 7.177184 TGCCAGCATATAATATCTTGGATTGT 58.823 34.615 0.00 0.00 0.00 2.71
1759 8094 0.249398 GGTCCGGTGATGTTGCTACT 59.751 55.000 0.00 0.00 0.00 2.57
1857 8192 2.764572 CCGCTAAAGGTTCTTCTCCCTA 59.235 50.000 0.00 0.00 0.00 3.53
1874 8209 0.585838 CTAACACGCACATGCACACA 59.414 50.000 4.49 0.00 42.21 3.72
1876 8211 1.652167 AACACGCACATGCACACACA 61.652 50.000 4.49 0.00 42.21 3.72
1878 8213 2.111582 ACGCACATGCACACACACA 61.112 52.632 4.49 0.00 42.21 3.72
1883 8218 4.312231 ATGCACACACACACGCGC 62.312 61.111 5.73 0.00 0.00 6.86
1957 8313 3.263261 GCTTTGCTAGTACACTCCCTTC 58.737 50.000 0.00 0.00 0.00 3.46
1976 8332 7.427214 TCCCTTCGTTTAAATGTTTTGTTAGG 58.573 34.615 7.28 4.72 0.00 2.69
1979 8335 7.112426 CCTTCGTTTAAATGTTTTGTTAGGACG 59.888 37.037 7.28 0.00 0.00 4.79
2014 8370 7.309744 GGGATCATTTTTGTTTATCACAGGACA 60.310 37.037 0.00 0.00 36.48 4.02
2033 8389 8.343546 CAGGACACTGCATGGTAACAAAGTTT 62.344 42.308 0.00 0.00 44.81 2.66
2063 8419 2.494073 AGAAGGAGTTCCAGTCGACATC 59.506 50.000 19.50 5.46 38.89 3.06
2224 8580 6.892456 TGGGTCACCTGCATTTATTAATACAA 59.108 34.615 0.00 0.00 37.76 2.41
2248 9103 7.964604 AAATATCCGTCTTTCAGCCTAATAC 57.035 36.000 0.00 0.00 0.00 1.89
2251 9106 3.516300 TCCGTCTTTCAGCCTAATACCAA 59.484 43.478 0.00 0.00 0.00 3.67
2254 9109 4.260784 CGTCTTTCAGCCTAATACCAATGC 60.261 45.833 0.00 0.00 0.00 3.56
2337 9192 7.177216 TGGAGACACTCGTTAAGGTTAGAATTA 59.823 37.037 0.00 0.00 33.40 1.40
2764 9629 4.765339 GGAAATTGTACCTTGTGCCTAGTT 59.235 41.667 0.00 0.00 0.00 2.24
2771 9636 3.146847 ACCTTGTGCCTAGTTAAGTTGC 58.853 45.455 0.00 0.00 0.00 4.17
2928 9793 4.950205 GGATGCATCCCAATTCTCAATT 57.050 40.909 32.15 0.00 41.20 2.32
3094 10130 9.075519 CATTGATTAAACAGCGTAATGTTCATT 57.924 29.630 3.55 3.55 42.49 2.57
3379 10420 8.293867 TGTTGTTTTGTACTACTGAATATTGCC 58.706 33.333 0.00 0.00 34.20 4.52
3381 10422 9.727859 TTGTTTTGTACTACTGAATATTGCCTA 57.272 29.630 0.00 0.00 0.00 3.93
3989 12004 1.043816 AGCGGCATGAGTAGTAGCAT 58.956 50.000 1.45 0.00 0.00 3.79
3990 12005 2.239400 AGCGGCATGAGTAGTAGCATA 58.761 47.619 1.45 0.00 0.00 3.14
3991 12006 2.628178 AGCGGCATGAGTAGTAGCATAA 59.372 45.455 1.45 0.00 0.00 1.90
3992 12007 2.989840 GCGGCATGAGTAGTAGCATAAG 59.010 50.000 0.00 0.00 0.00 1.73
4503 12768 9.868277 ACTATTTGAGTAGAGTGAAAGAAGATG 57.132 33.333 0.00 0.00 36.27 2.90
4735 13005 8.699283 AGTCTTAATTAATTCACGTAGGTCAC 57.301 34.615 3.39 0.00 0.00 3.67
4906 13180 7.468084 GCTGTCCACTTTTTCTGTTTACATGTA 60.468 37.037 0.08 0.08 0.00 2.29
4996 13276 5.655532 AGCCAACCGTTCTAGTAAGAGAATA 59.344 40.000 0.00 0.00 37.75 1.75
4999 13279 6.421202 CCAACCGTTCTAGTAAGAGAATATGC 59.579 42.308 0.00 0.00 37.75 3.14
5027 13307 8.274322 CCATATCCCCATTCTGCAGTATATTAA 58.726 37.037 14.67 0.00 0.00 1.40
5085 13380 8.762426 AGTAAAGCTTTTAGACAGTTTTCTACG 58.238 33.333 18.47 0.00 0.00 3.51
5382 13868 2.422597 TGCCAGTGTCGTCCTAATTTG 58.577 47.619 0.00 0.00 0.00 2.32
5648 14514 6.765989 CCTAACGATATCAACCCAAGAATGAA 59.234 38.462 3.12 0.00 0.00 2.57
5713 14579 6.128282 GCTGACGTTTCTATTCCATTTTCTCA 60.128 38.462 0.00 0.00 0.00 3.27
5720 14586 8.576442 GTTTCTATTCCATTTTCTCACAGGAAA 58.424 33.333 0.00 0.00 41.27 3.13
5762 14628 0.976641 TTCCTGGAGAACGTGAGCAT 59.023 50.000 0.00 0.00 0.00 3.79
5772 14638 0.321034 ACGTGAGCATGTGTGAGCAT 60.321 50.000 0.00 0.00 0.00 3.79
5812 14678 4.054825 GGCCACAACATGTGCCCG 62.055 66.667 12.77 0.00 46.51 6.13
5843 14709 5.710099 CCAAATTGGAGTTAGCAGGAACTTA 59.290 40.000 6.04 0.00 40.96 2.24
5973 14839 1.692519 ACGGCCATATCCAGTCCTTAC 59.307 52.381 2.24 0.00 0.00 2.34
6008 14874 9.725019 TGAGTACTTGTGAAATTCTCAATATGT 57.275 29.630 10.37 8.16 35.22 2.29
6041 14907 9.515020 CTTGTGCAAGACTTATTTTAACTTCAA 57.485 29.630 6.08 0.00 40.79 2.69
6065 14931 8.369588 CAATGCACCGTAAAATGTACATAAAAC 58.630 33.333 9.21 6.55 0.00 2.43
6199 15065 5.988310 TCGTAAGATTACCTCAGGTGAAA 57.012 39.130 6.61 0.00 45.01 2.69
6279 15145 3.030873 TCCAAATTAAGGCCTCCATGG 57.969 47.619 5.23 4.97 39.35 3.66
6285 15151 0.326522 TAAGGCCTCCATGGAGCTCA 60.327 55.000 32.97 11.88 40.69 4.26
6297 15163 0.603569 GGAGCTCAGTCTCCGTTTGA 59.396 55.000 17.19 0.00 42.74 2.69
6312 15178 2.973224 CGTTTGACATTTTCGCCTTCTG 59.027 45.455 0.00 0.00 0.00 3.02
6380 15246 9.283768 CAGTGGCATATATAGTTTACATGGAAA 57.716 33.333 0.00 0.00 0.00 3.13
6414 15280 2.659063 GCATTTCCCTTGGCCCACC 61.659 63.158 0.00 0.00 0.00 4.61
6415 15281 1.079073 CATTTCCCTTGGCCCACCT 59.921 57.895 0.00 0.00 36.63 4.00
6433 15299 4.360405 GCTCGCCCCTTTCCCCAA 62.360 66.667 0.00 0.00 0.00 4.12
6475 15341 2.371910 CTCCGAAGAGGTGTTTCTCC 57.628 55.000 0.00 0.00 41.99 3.71
6476 15342 0.974383 TCCGAAGAGGTGTTTCTCCC 59.026 55.000 0.00 0.00 41.99 4.30
6477 15343 0.036294 CCGAAGAGGTGTTTCTCCCC 60.036 60.000 0.00 0.00 34.46 4.81
6478 15344 0.389948 CGAAGAGGTGTTTCTCCCCG 60.390 60.000 0.00 0.00 34.46 5.73
6479 15345 0.974383 GAAGAGGTGTTTCTCCCCGA 59.026 55.000 0.00 0.00 34.46 5.14
6480 15346 1.346722 GAAGAGGTGTTTCTCCCCGAA 59.653 52.381 0.00 0.00 34.46 4.30
6481 15347 0.977395 AGAGGTGTTTCTCCCCGAAG 59.023 55.000 0.00 0.00 34.46 3.79
6482 15348 0.974383 GAGGTGTTTCTCCCCGAAGA 59.026 55.000 0.00 0.00 32.21 2.87
6483 15349 0.977395 AGGTGTTTCTCCCCGAAGAG 59.023 55.000 0.00 0.00 32.21 2.85
6484 15350 0.036294 GGTGTTTCTCCCCGAAGAGG 60.036 60.000 2.38 0.00 40.63 3.69
6485 15351 0.685660 GTGTTTCTCCCCGAAGAGGT 59.314 55.000 2.38 0.00 38.74 3.85
6486 15352 0.685097 TGTTTCTCCCCGAAGAGGTG 59.315 55.000 2.38 0.00 38.74 4.00
6487 15353 0.685660 GTTTCTCCCCGAAGAGGTGT 59.314 55.000 2.38 0.00 38.74 4.16
6488 15354 1.897802 GTTTCTCCCCGAAGAGGTGTA 59.102 52.381 2.38 0.00 38.74 2.90
6489 15355 1.848652 TTCTCCCCGAAGAGGTGTAG 58.151 55.000 2.38 0.00 38.74 2.74
6490 15356 0.702902 TCTCCCCGAAGAGGTGTAGT 59.297 55.000 2.38 0.00 38.74 2.73
6491 15357 1.076677 TCTCCCCGAAGAGGTGTAGTT 59.923 52.381 2.38 0.00 38.74 2.24
6492 15358 2.309755 TCTCCCCGAAGAGGTGTAGTTA 59.690 50.000 2.38 0.00 38.74 2.24
6493 15359 3.094572 CTCCCCGAAGAGGTGTAGTTAA 58.905 50.000 0.00 0.00 38.74 2.01
6494 15360 2.827921 TCCCCGAAGAGGTGTAGTTAAC 59.172 50.000 0.00 0.00 38.74 2.01
6495 15361 2.830321 CCCCGAAGAGGTGTAGTTAACT 59.170 50.000 13.68 13.68 38.74 2.24
6496 15362 3.260128 CCCCGAAGAGGTGTAGTTAACTT 59.740 47.826 14.49 0.00 38.74 2.66
6497 15363 4.492611 CCCGAAGAGGTGTAGTTAACTTC 58.507 47.826 14.49 9.48 38.74 3.01
6498 15364 4.220163 CCCGAAGAGGTGTAGTTAACTTCT 59.780 45.833 14.49 7.19 35.68 2.85
6499 15365 5.400703 CCGAAGAGGTGTAGTTAACTTCTC 58.599 45.833 14.49 14.57 33.27 2.87
6500 15366 5.048224 CCGAAGAGGTGTAGTTAACTTCTCA 60.048 44.000 14.49 8.39 33.27 3.27
6523 15389 0.894835 TGCAGCGATGGTGAGTCTAA 59.105 50.000 1.46 0.00 32.22 2.10
6607 15473 2.672961 TGACGATGAGACATGGTTCC 57.327 50.000 0.00 0.00 0.00 3.62
6648 15514 1.638529 CTTCAGGTGGAGGAGAGTGT 58.361 55.000 0.00 0.00 0.00 3.55
6657 15523 2.027745 TGGAGGAGAGTGTGAATGAAGC 60.028 50.000 0.00 0.00 0.00 3.86
6693 15559 8.921670 CACTAAATTTAACACCTTGTTATTGGC 58.078 33.333 0.00 0.00 41.83 4.52
6712 15578 1.737793 GCCGGGTGCAACTATATATGC 59.262 52.381 2.18 1.98 42.86 3.14
6735 15601 5.565259 GCAAGTACAACTGAATTCAACATCG 59.435 40.000 9.88 0.00 0.00 3.84
6741 15607 1.295357 TGAATTCAACATCGCGCGGT 61.295 50.000 31.69 23.12 0.00 5.68
6745 15611 0.866427 TTCAACATCGCGCGGTAAAA 59.134 45.000 31.69 10.88 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.596585 CCACCCACCCGCCAGTTT 62.597 66.667 0.00 0.00 0.00 2.66
68 69 6.642131 CCCTTGTGTTGTCAAACTAATGAATG 59.358 38.462 0.00 0.00 37.19 2.67
136 137 3.095922 GCTTGGGCTTAAGCGGTAT 57.904 52.632 20.80 0.00 43.02 2.73
350 351 4.444306 CGAATACTAATCCCAGGAAAGCCA 60.444 45.833 0.00 0.00 36.29 4.75
360 361 4.389077 CAGCGAAATCCGAATACTAATCCC 59.611 45.833 0.00 0.00 41.76 3.85
467 468 5.279657 GCTTGTCCCTTTGATTCAATCCTTT 60.280 40.000 0.00 0.00 0.00 3.11
496 497 2.104451 TCCAAACATGCCATTGCTTTGT 59.896 40.909 0.00 0.00 38.71 2.83
723 731 1.218047 CGACTCCTCGGGCAAATCA 59.782 57.895 0.00 0.00 36.16 2.57
731 739 0.381089 GTGTATCCACGACTCCTCGG 59.619 60.000 0.00 0.00 44.80 4.63
789 7095 0.248949 GACACGAATCCCTACTCCGC 60.249 60.000 0.00 0.00 0.00 5.54
989 7303 0.323178 CTGAGACATGGCCAAGGCTT 60.323 55.000 19.34 1.07 41.60 4.35
1026 7340 3.336715 CTCGTGGATGTCGTCGGCA 62.337 63.158 0.14 0.14 0.00 5.69
1029 7343 2.579787 GCCTCGTGGATGTCGTCG 60.580 66.667 7.92 0.00 34.57 5.12
1031 7345 4.129737 CGGCCTCGTGGATGTCGT 62.130 66.667 7.92 0.00 34.57 4.34
1054 7368 1.408822 GGAATCGTTCATGGGAGCCTT 60.409 52.381 0.00 0.00 0.00 4.35
1193 7510 3.877508 AGCATTAGAAACGTAATCAGGGC 59.122 43.478 0.00 0.00 0.00 5.19
1273 7592 1.555533 ACCTTTGAGGGAATCGAGGTC 59.444 52.381 0.00 0.00 40.98 3.85
1409 7738 7.769044 GCTCTGTACAATATCTTTCCCAAAGTA 59.231 37.037 0.00 0.00 39.52 2.24
1410 7739 6.599638 GCTCTGTACAATATCTTTCCCAAAGT 59.400 38.462 0.00 0.00 39.52 2.66
1411 7740 6.038714 GGCTCTGTACAATATCTTTCCCAAAG 59.961 42.308 0.00 0.00 39.88 2.77
1422 7752 6.357367 CCTTTGGTAAGGCTCTGTACAATAT 58.643 40.000 0.00 0.00 44.27 1.28
1435 7765 3.146847 GTCACCACTTCCTTTGGTAAGG 58.853 50.000 0.00 0.00 46.13 2.69
1486 7816 0.042188 CGTGCAACACAGAAACTCCG 60.042 55.000 0.00 0.00 35.74 4.63
1558 7888 2.570135 GGAGCATTCACATCTCCCTTC 58.430 52.381 0.00 0.00 40.29 3.46
1600 7933 6.873997 TGAAGAAAGCGATAGATAAAGACCA 58.126 36.000 0.00 0.00 39.76 4.02
1676 8011 1.888512 AGCACATGGTCAACACAATCC 59.111 47.619 0.00 0.00 0.00 3.01
1682 8017 3.888323 ACATAACAAGCACATGGTCAACA 59.112 39.130 0.00 0.00 0.00 3.33
1689 8024 6.127925 ACCTGTGATAACATAACAAGCACATG 60.128 38.462 0.00 0.00 34.71 3.21
1759 8094 7.094975 CCACCACGATCAAGAAAATACTTAACA 60.095 37.037 0.00 0.00 0.00 2.41
1857 8192 1.063972 GTGTGTGCATGTGCGTGTT 59.936 52.632 0.00 0.00 45.83 3.32
1887 8222 0.603439 ATCATGTGTGTGTCTGCGCA 60.603 50.000 10.98 10.98 0.00 6.09
1888 8223 0.518636 AATCATGTGTGTGTCTGCGC 59.481 50.000 0.00 0.00 0.00 6.09
1892 8227 5.824624 ACTTCAAGAAATCATGTGTGTGTCT 59.175 36.000 0.00 0.00 0.00 3.41
1893 8228 6.064846 ACTTCAAGAAATCATGTGTGTGTC 57.935 37.500 0.00 0.00 0.00 3.67
1957 8313 6.906143 TCACGTCCTAACAAAACATTTAAACG 59.094 34.615 0.00 0.00 0.00 3.60
1976 8332 6.128007 ACAAAAATGATCCCATAAGTCACGTC 60.128 38.462 0.00 0.00 31.59 4.34
2014 8370 4.278419 GGAGAAACTTTGTTACCATGCAGT 59.722 41.667 0.00 0.00 0.00 4.40
2063 8419 2.073816 GGTGTTCCACGACCATAGTTG 58.926 52.381 0.00 0.00 34.83 3.16
2201 8557 9.816354 ATTTTGTATTAATAAATGCAGGTGACC 57.184 29.630 0.00 0.00 38.66 4.02
2379 9238 8.661345 TGTACATCAGAGTATAGAGATGGTAGT 58.339 37.037 0.00 0.00 41.55 2.73
2771 9636 5.170748 GGATTGTTTTGATGCAAGGTAAGG 58.829 41.667 0.00 0.00 0.00 2.69
3064 10098 7.035004 ACATTACGCTGTTTAATCAATGCAAT 58.965 30.769 0.00 0.00 0.00 3.56
3094 10130 7.614192 GGAACCAGTTGGGATATAGAAAAGAAA 59.386 37.037 2.79 0.00 41.15 2.52
3973 11979 5.635700 GCTTACTTATGCTACTACTCATGCC 59.364 44.000 0.00 0.00 0.00 4.40
3989 12004 5.812642 GCTAGCTCTTTGACATGCTTACTTA 59.187 40.000 7.70 0.00 37.02 2.24
3990 12005 4.633565 GCTAGCTCTTTGACATGCTTACTT 59.366 41.667 7.70 0.00 37.02 2.24
3991 12006 4.187694 GCTAGCTCTTTGACATGCTTACT 58.812 43.478 7.70 0.00 37.02 2.24
3992 12007 3.311048 GGCTAGCTCTTTGACATGCTTAC 59.689 47.826 15.72 0.00 37.02 2.34
4141 12166 0.827507 GGCAAGCCTTTTGGTCCTGA 60.828 55.000 3.29 0.00 42.99 3.86
4147 12172 2.102925 TCTTCTTTGGCAAGCCTTTTGG 59.897 45.455 12.96 0.00 44.18 3.28
4392 12625 1.407851 GGCATTGCTCAGATCCAGTCA 60.408 52.381 8.82 0.00 0.00 3.41
4503 12768 2.280628 CTAAACGGGCTCCATGAGAAC 58.719 52.381 0.00 0.00 0.00 3.01
4728 12998 8.875803 CAAAATTTACTTACTATGCGTGACCTA 58.124 33.333 0.00 0.00 0.00 3.08
4953 13233 6.641169 TGGCTTGTTCAATTTACATGTACA 57.359 33.333 4.68 0.00 0.00 2.90
4996 13276 2.291411 GCAGAATGGGGATATGGAGCAT 60.291 50.000 0.00 0.00 35.86 3.79
4999 13279 2.374504 ACTGCAGAATGGGGATATGGAG 59.625 50.000 23.35 0.00 35.86 3.86
5006 13286 6.297010 GGGATTAATATACTGCAGAATGGGGA 60.297 42.308 23.35 1.44 35.86 4.81
5085 13380 6.417191 TTTCTAACGCTTATTCATGGACAC 57.583 37.500 0.00 0.00 0.00 3.67
5165 13462 5.824624 CCATGACTTATTGCCTACACTCAAT 59.175 40.000 0.00 0.00 36.87 2.57
5352 13835 0.953727 GACACTGGCAATGTCAAGCA 59.046 50.000 22.87 0.00 44.87 3.91
5382 13868 7.254932 GGCCAGACTGTAAGATCAATATGAAAC 60.255 40.741 0.00 0.00 37.43 2.78
5648 14514 8.244802 GTCGATATGCAACTCAATACCTAGTAT 58.755 37.037 0.00 0.00 0.00 2.12
5713 14579 2.621070 TGAGTTCCCTAGCTTTCCTGT 58.379 47.619 0.00 0.00 0.00 4.00
5720 14586 7.385894 AATATTCTTCATGAGTTCCCTAGCT 57.614 36.000 0.00 0.00 0.00 3.32
5762 14628 1.071299 ACGCCTCAATGCTCACACA 59.929 52.632 0.00 0.00 0.00 3.72
5812 14678 6.645003 CCTGCTAACTCCAATTTGGTAAAAAC 59.355 38.462 14.98 3.83 39.03 2.43
5877 14743 3.002042 CAGTCCGAAGATGCATGATTCAC 59.998 47.826 2.46 3.99 0.00 3.18
5973 14839 9.185192 GAATTTCACAAGTACTCATTCAAAAGG 57.815 33.333 0.00 0.00 0.00 3.11
6008 14874 7.817418 AAATAAGTCTTGCACAAGGAAACTA 57.183 32.000 10.35 0.00 42.68 2.24
6041 14907 6.743627 CGTTTTATGTACATTTTACGGTGCAT 59.256 34.615 14.77 0.00 41.95 3.96
6170 15036 8.979574 CACCTGAGGTAATCTTACGATAATTTC 58.020 37.037 2.59 0.00 32.11 2.17
6175 15041 7.649533 TTTCACCTGAGGTAATCTTACGATA 57.350 36.000 2.59 0.00 32.11 2.92
6211 15077 6.828788 AGTCTATTCATCACTCAGAATGCAT 58.171 36.000 0.00 0.00 36.07 3.96
6216 15082 9.212641 CTTTTCAAGTCTATTCATCACTCAGAA 57.787 33.333 0.00 0.00 0.00 3.02
6217 15083 8.370940 ACTTTTCAAGTCTATTCATCACTCAGA 58.629 33.333 0.00 0.00 37.02 3.27
6219 15085 8.908786 AACTTTTCAAGTCTATTCATCACTCA 57.091 30.769 0.00 0.00 41.91 3.41
6221 15087 9.342308 TCAAACTTTTCAAGTCTATTCATCACT 57.658 29.630 0.00 0.00 41.91 3.41
6260 15126 2.961062 CTCCATGGAGGCCTTAATTTGG 59.039 50.000 31.14 10.64 38.51 3.28
6279 15145 1.000163 TGTCAAACGGAGACTGAGCTC 60.000 52.381 6.82 6.82 36.94 4.09
6285 15151 2.223377 GCGAAAATGTCAAACGGAGACT 59.777 45.455 5.89 0.00 36.94 3.24
6414 15280 4.803908 GGGGAAAGGGGCGAGCAG 62.804 72.222 0.00 0.00 0.00 4.24
6426 15292 2.836981 CCATGGCTATTTTGTTGGGGAA 59.163 45.455 0.00 0.00 0.00 3.97
6433 15299 4.709886 GGGTTTACTCCATGGCTATTTTGT 59.290 41.667 6.96 0.00 0.00 2.83
6459 15325 0.389948 CGGGGAGAAACACCTCTTCG 60.390 60.000 0.00 0.00 40.56 3.79
6469 15335 2.176889 CTACACCTCTTCGGGGAGAAA 58.823 52.381 7.04 0.00 39.13 2.52
6470 15336 1.076677 ACTACACCTCTTCGGGGAGAA 59.923 52.381 7.04 0.00 39.13 2.87
6471 15337 0.702902 ACTACACCTCTTCGGGGAGA 59.297 55.000 7.04 0.00 39.13 3.71
6472 15338 1.558233 AACTACACCTCTTCGGGGAG 58.442 55.000 0.00 0.00 39.13 4.30
6473 15339 2.827921 GTTAACTACACCTCTTCGGGGA 59.172 50.000 0.00 0.00 39.13 4.81
6474 15340 2.830321 AGTTAACTACACCTCTTCGGGG 59.170 50.000 6.26 0.00 44.06 5.73
6475 15341 4.220163 AGAAGTTAACTACACCTCTTCGGG 59.780 45.833 8.92 0.00 37.12 5.14
6476 15342 5.048224 TGAGAAGTTAACTACACCTCTTCGG 60.048 44.000 8.92 0.00 37.12 4.30
6477 15343 6.010294 TGAGAAGTTAACTACACCTCTTCG 57.990 41.667 8.92 0.00 37.12 3.79
6478 15344 7.208080 TGTTGAGAAGTTAACTACACCTCTTC 58.792 38.462 8.92 0.00 32.24 2.87
6479 15345 7.120923 TGTTGAGAAGTTAACTACACCTCTT 57.879 36.000 8.92 0.00 32.24 2.85
6480 15346 6.726490 TGTTGAGAAGTTAACTACACCTCT 57.274 37.500 8.92 7.51 32.24 3.69
6481 15347 6.128526 GCATGTTGAGAAGTTAACTACACCTC 60.129 42.308 8.92 12.89 0.00 3.85
6482 15348 5.701290 GCATGTTGAGAAGTTAACTACACCT 59.299 40.000 8.92 4.16 0.00 4.00
6483 15349 5.468746 TGCATGTTGAGAAGTTAACTACACC 59.531 40.000 8.92 5.08 0.00 4.16
6484 15350 6.539649 TGCATGTTGAGAAGTTAACTACAC 57.460 37.500 8.92 4.07 0.00 2.90
6485 15351 5.179368 GCTGCATGTTGAGAAGTTAACTACA 59.821 40.000 8.92 9.50 0.00 2.74
6486 15352 5.622378 GCTGCATGTTGAGAAGTTAACTAC 58.378 41.667 8.92 3.49 0.00 2.73
6487 15353 4.388773 CGCTGCATGTTGAGAAGTTAACTA 59.611 41.667 8.92 0.00 0.00 2.24
6488 15354 3.187227 CGCTGCATGTTGAGAAGTTAACT 59.813 43.478 1.12 1.12 0.00 2.24
6489 15355 3.186409 TCGCTGCATGTTGAGAAGTTAAC 59.814 43.478 0.00 0.00 0.00 2.01
6490 15356 3.398406 TCGCTGCATGTTGAGAAGTTAA 58.602 40.909 0.00 0.00 0.00 2.01
6491 15357 3.038788 TCGCTGCATGTTGAGAAGTTA 57.961 42.857 0.00 0.00 0.00 2.24
6492 15358 1.882912 TCGCTGCATGTTGAGAAGTT 58.117 45.000 0.00 0.00 0.00 2.66
6493 15359 1.736126 CATCGCTGCATGTTGAGAAGT 59.264 47.619 0.00 0.00 0.00 3.01
6494 15360 1.063616 CCATCGCTGCATGTTGAGAAG 59.936 52.381 0.00 0.00 0.00 2.85
6495 15361 1.089112 CCATCGCTGCATGTTGAGAA 58.911 50.000 0.00 0.00 0.00 2.87
6496 15362 0.036105 ACCATCGCTGCATGTTGAGA 60.036 50.000 0.00 0.00 0.00 3.27
6497 15363 0.098200 CACCATCGCTGCATGTTGAG 59.902 55.000 0.00 0.00 0.00 3.02
6498 15364 0.321475 TCACCATCGCTGCATGTTGA 60.321 50.000 0.00 4.54 0.00 3.18
6499 15365 0.098200 CTCACCATCGCTGCATGTTG 59.902 55.000 0.00 2.21 0.00 3.33
6500 15366 0.321919 ACTCACCATCGCTGCATGTT 60.322 50.000 0.00 0.00 0.00 2.71
6523 15389 0.460284 CCTTCGATACTTGTGGCGCT 60.460 55.000 7.64 0.00 0.00 5.92
6607 15473 0.817634 TTGTCAACGCTCAACCCCAG 60.818 55.000 0.00 0.00 0.00 4.45
6648 15514 1.922135 GCCCGCTTTCGCTTCATTCA 61.922 55.000 0.00 0.00 0.00 2.57
6657 15523 2.629639 AAATTTAGTGCCCGCTTTCG 57.370 45.000 0.00 0.00 0.00 3.46
6670 15536 7.091443 CGGCCAATAACAAGGTGTTAAATTTA 58.909 34.615 2.24 0.00 44.84 1.40
6693 15559 3.052455 TGCATATATAGTTGCACCCGG 57.948 47.619 6.88 0.00 43.54 5.73
6712 15578 5.565259 GCGATGTTGAATTCAGTTGTACTTG 59.435 40.000 8.41 0.17 0.00 3.16
6745 15611 4.202673 TGAGGGGGCAAGAGACTAATTTTT 60.203 41.667 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.