Multiple sequence alignment - TraesCS5B01G417800

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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 TraesCS5B01G417800 chr5B 100.000 2639 0 0 1 2639 592835672 592838310 0.000000e+00 4874
1 TraesCS5B01G417800 chr5B 78.531 531 91 15 979 1506 606751917 606752427 7.040000e-86 327
2 TraesCS5B01G417800 chr5B 79.758 331 50 9 1329 1647 605531360 605531035 9.510000e-55 224
3 TraesCS5B01G417800 chr5B 82.800 250 37 5 1275 1521 606822241 606822487 4.420000e-53 219
4 TraesCS5B01G417800 chr5A 92.610 1042 68 4 650 1682 603529162 603530203 0.000000e+00 1489
5 TraesCS5B01G417800 chr5A 82.321 922 137 19 860 1776 603503340 603504240 0.000000e+00 776
6 TraesCS5B01G417800 chr5A 87.335 529 59 6 3 529 603528340 603528862 1.350000e-167 599
7 TraesCS5B01G417800 chr5A 86.863 510 40 14 1745 2240 603530216 603530712 1.790000e-151 545
8 TraesCS5B01G417800 chr5A 91.495 388 27 4 2227 2612 603530728 603531111 1.800000e-146 529
9 TraesCS5B01G417800 chr5A 80.889 225 34 2 416 639 411428521 411428737 4.520000e-38 169
10 TraesCS5B01G417800 chr5D 93.333 690 42 3 998 1683 482907143 482907832 0.000000e+00 1016
11 TraesCS5B01G417800 chr5D 84.560 693 98 8 993 1683 482900664 482901349 0.000000e+00 678
12 TraesCS5B01G417800 chr5D 87.934 547 49 11 1853 2396 482908367 482908899 1.720000e-176 628
13 TraesCS5B01G417800 chr5D 94.942 257 11 1 697 953 482906881 482907135 4.090000e-108 401
14 TraesCS5B01G417800 chr5D 84.872 390 34 9 16 405 482903476 482903840 1.150000e-98 370
15 TraesCS5B01G417800 chr5D 89.503 181 16 1 2431 2611 482908901 482909078 2.640000e-55 226
16 TraesCS5B01G417800 chr1D 85.859 198 27 1 416 612 32759159 32758962 2.660000e-50 209
17 TraesCS5B01G417800 chr3D 82.479 234 31 6 416 642 522296124 522295894 2.070000e-46 196
18 TraesCS5B01G417800 chr7A 84.343 198 29 2 416 612 706365211 706365407 2.680000e-45 193
19 TraesCS5B01G417800 chr2B 82.174 230 33 4 416 638 373111949 373111721 9.640000e-45 191
20 TraesCS5B01G417800 chr4D 82.018 228 32 4 416 642 452544356 452544137 4.490000e-43 185
21 TraesCS5B01G417800 chr4D 82.323 198 32 3 416 612 469197909 469198104 4.520000e-38 169
22 TraesCS5B01G417800 chr6B 81.579 228 31 3 416 642 545282175 545282392 7.510000e-41 178
23 TraesCS5B01G417800 chr4B 82.323 198 33 2 416 612 589027387 589027583 1.260000e-38 171
24 TraesCS5B01G417800 chr2D 80.435 230 38 3 416 638 304267584 304267355 4.520000e-38 169
25 TraesCS5B01G417800 chr2D 79.130 230 38 4 416 639 603133595 603133820 1.640000e-32 150
26 TraesCS5B01G417800 chr7B 76.068 234 46 6 416 642 557182739 557182509 2.150000e-21 113


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 TraesCS5B01G417800 chr5B 592835672 592838310 2638 False 4874.000000 4874 100.000000 1 2639 1 chr5B.!!$F1 2638
1 TraesCS5B01G417800 chr5B 606751917 606752427 510 False 327.000000 327 78.531000 979 1506 1 chr5B.!!$F2 527
2 TraesCS5B01G417800 chr5A 603528340 603531111 2771 False 790.500000 1489 89.575750 3 2612 4 chr5A.!!$F3 2609
3 TraesCS5B01G417800 chr5A 603503340 603504240 900 False 776.000000 776 82.321000 860 1776 1 chr5A.!!$F2 916
4 TraesCS5B01G417800 chr5D 482900664 482909078 8414 False 553.166667 1016 89.190667 16 2611 6 chr5D.!!$F1 2595

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
541 4842 0.171007 GACCGCCAAACATGGACATG 59.829 55.0 10.57 10.57 44.15 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 8495 0.031994 TTGCAAAAGAAGAAGCGGGC 59.968 50.0 0.0 0.0 0.0 6.13 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
22 23 5.750352 ATCTTGGGAGCATCAATTTTGTT 57.250 34.783 0.00 0.00 36.25 2.83
23 2820 5.138125 TCTTGGGAGCATCAATTTTGTTC 57.862 39.130 0.00 0.00 36.25 3.18
28 2825 7.060383 TGGGAGCATCAATTTTGTTCTTTTA 57.940 32.000 0.00 0.00 36.25 1.52
34 2831 7.768120 AGCATCAATTTTGTTCTTTTAACCACA 59.232 29.630 0.00 0.00 0.00 4.17
60 2857 7.405292 ACTTCCATGAAAGTGATTCCAAGATA 58.595 34.615 0.00 0.00 38.06 1.98
76 2873 8.514136 TTCCAAGATAAAAATTTGTAAGCACG 57.486 30.769 0.00 0.00 0.00 5.34
187 2984 5.435291 CTCATTTGAGACCAAGCTAAGGAT 58.565 41.667 11.80 0.48 44.74 3.24
194 2991 3.390639 AGACCAAGCTAAGGATCTCCATG 59.609 47.826 11.80 0.00 38.89 3.66
261 3058 5.237996 GCATACTGCTAATGATGTGATGTGT 59.762 40.000 0.00 0.00 40.96 3.72
263 3060 4.194640 ACTGCTAATGATGTGATGTGTCC 58.805 43.478 0.00 0.00 0.00 4.02
287 3084 5.335583 CCCTCATGTCGTGCAATTTTTCTTA 60.336 40.000 0.00 0.00 0.00 2.10
304 3101 5.452078 TTCTTAGGTGAACAAAGCCAATG 57.548 39.130 0.00 0.00 0.00 2.82
350 3147 1.003118 CCCGACATGAAAGGGTTCTCA 59.997 52.381 14.01 0.00 40.27 3.27
408 3205 7.686371 GCCTCAGAACAAAGAGATCATCATCTA 60.686 40.741 0.00 0.00 39.71 1.98
413 3210 5.288015 ACAAAGAGATCATCATCTACGCTG 58.712 41.667 0.00 0.00 39.71 5.18
420 3217 5.709631 AGATCATCATCTACGCTGTGAGTAT 59.290 40.000 0.00 0.00 37.63 2.12
427 3224 0.179073 ACGCTGTGAGTATGGCATCC 60.179 55.000 1.65 0.00 0.00 3.51
432 3229 1.409064 TGTGAGTATGGCATCCGAGAC 59.591 52.381 1.65 0.00 0.00 3.36
451 3973 3.793144 GCGGCGCCTTGAGTCTTG 61.793 66.667 26.68 6.32 0.00 3.02
453 3975 1.080093 CGGCGCCTTGAGTCTTGTA 60.080 57.895 26.68 0.00 0.00 2.41
460 3982 1.676014 CCTTGAGTCTTGTAAGCCGGG 60.676 57.143 2.18 0.00 0.00 5.73
463 3985 0.458025 GAGTCTTGTAAGCCGGGTCG 60.458 60.000 6.62 0.00 0.00 4.79
465 3987 1.012486 GTCTTGTAAGCCGGGTCGTG 61.012 60.000 6.62 0.00 0.00 4.35
466 3988 1.740296 CTTGTAAGCCGGGTCGTGG 60.740 63.158 6.62 0.00 0.00 4.94
483 4005 3.913107 GCCCATGCCCTCCTCTAT 58.087 61.111 0.00 0.00 0.00 1.98
484 4006 1.682257 GCCCATGCCCTCCTCTATC 59.318 63.158 0.00 0.00 0.00 2.08
487 4009 1.627834 CCCATGCCCTCCTCTATCTTC 59.372 57.143 0.00 0.00 0.00 2.87
496 4018 1.107538 CCTCTATCTTCCCGGCGACA 61.108 60.000 9.30 0.00 0.00 4.35
497 4019 0.312416 CTCTATCTTCCCGGCGACAG 59.688 60.000 9.30 0.30 0.00 3.51
501 4023 4.452733 CTTCCCGGCGACAGGACC 62.453 72.222 9.30 0.00 0.00 4.46
512 4035 1.048601 GACAGGACCAACACTCTGGA 58.951 55.000 0.00 0.00 38.96 3.86
534 4835 3.055719 CAGCCGACCGCCAAACAT 61.056 61.111 0.00 0.00 38.78 2.71
535 4836 3.055719 AGCCGACCGCCAAACATG 61.056 61.111 0.00 0.00 38.78 3.21
536 4837 4.114997 GCCGACCGCCAAACATGG 62.115 66.667 0.00 0.00 0.00 3.66
537 4838 2.359354 CCGACCGCCAAACATGGA 60.359 61.111 0.00 0.00 0.00 3.41
538 4839 2.686816 CCGACCGCCAAACATGGAC 61.687 63.158 0.00 0.00 0.00 4.02
539 4840 1.963855 CGACCGCCAAACATGGACA 60.964 57.895 0.00 0.00 0.00 4.02
540 4841 1.305219 CGACCGCCAAACATGGACAT 61.305 55.000 0.00 0.00 0.00 3.06
541 4842 0.171007 GACCGCCAAACATGGACATG 59.829 55.000 10.57 10.57 44.15 3.21
542 4843 1.250154 ACCGCCAAACATGGACATGG 61.250 55.000 15.94 0.71 42.91 3.66
545 4846 1.512230 CCAAACATGGACATGGCGG 59.488 57.895 15.94 9.24 42.91 6.13
546 4847 0.964860 CCAAACATGGACATGGCGGA 60.965 55.000 15.94 0.00 42.91 5.54
568 4869 1.376295 GGACGAGCCCCGCTTAAAA 60.376 57.895 0.00 0.00 39.88 1.52
573 4874 1.470890 CGAGCCCCGCTTAAAAATCAA 59.529 47.619 0.00 0.00 39.88 2.57
575 4876 3.428862 CGAGCCCCGCTTAAAAATCAATT 60.429 43.478 0.00 0.00 39.88 2.32
619 5545 7.228314 TGGATTTAAGGTGTCTAGATATCCG 57.772 40.000 0.00 0.00 33.40 4.18
639 5565 5.590145 TCCGGATGTGAAATGCATTATTTG 58.410 37.500 13.39 0.00 39.06 2.32
643 5569 5.174398 GGATGTGAAATGCATTATTTGAGCG 59.826 40.000 13.39 0.00 39.06 5.03
644 5570 3.858812 TGTGAAATGCATTATTTGAGCGC 59.141 39.130 13.39 0.00 39.06 5.92
647 5573 2.129823 ATGCATTATTTGAGCGCTGC 57.870 45.000 18.48 11.41 0.00 5.25
653 5579 2.238847 TATTTGAGCGCTGCGGGAGT 62.239 55.000 24.61 0.00 0.00 3.85
654 5580 3.708426 TATTTGAGCGCTGCGGGAGTT 62.708 52.381 24.61 0.00 0.00 3.01
667 5630 0.688087 GGGAGTTGGAGGAGTCGGAT 60.688 60.000 0.00 0.00 0.00 4.18
725 6292 1.683943 CCCATTCATCTGCACCGATT 58.316 50.000 0.00 0.00 0.00 3.34
737 6306 1.202177 GCACCGATTACACCAATGCAG 60.202 52.381 0.00 0.00 0.00 4.41
748 6317 5.880054 ACACCAATGCAGACTTAATACAC 57.120 39.130 0.00 0.00 0.00 2.90
780 6349 2.096406 CGCGGACGCATTCAACTG 59.904 61.111 17.35 0.00 42.06 3.16
822 6391 2.580867 GCTGCTGTCGCTACCTCG 60.581 66.667 0.00 0.00 36.97 4.63
841 6410 2.394563 GGCCAGAGACAAGAAGCGC 61.395 63.158 0.00 0.00 0.00 5.92
907 6480 1.679305 GTCGAGCTCTGTCCCTCCA 60.679 63.158 12.85 0.00 0.00 3.86
953 6527 5.236478 GCTAGAAGCAAAGTACACAAGTCAA 59.764 40.000 0.00 0.00 41.89 3.18
981 6555 8.614469 AAGCTATTGTAATCATTTCTCTAGGC 57.386 34.615 0.00 0.00 0.00 3.93
1033 6607 2.874315 CGCTCGTCGTCGCAATCA 60.874 61.111 0.00 0.00 36.96 2.57
1152 6726 2.436109 GCCTGGGCTGAGACCAAA 59.564 61.111 9.11 0.00 41.95 3.28
1205 6781 3.245229 TGCATAACCACTGAACCATTCCT 60.245 43.478 0.00 0.00 0.00 3.36
1211 6787 0.693049 ACTGAACCATTCCTTCCGCT 59.307 50.000 0.00 0.00 0.00 5.52
1212 6788 1.089920 CTGAACCATTCCTTCCGCTG 58.910 55.000 0.00 0.00 0.00 5.18
1225 6805 3.120385 CGCTGGCACGCTTGATCA 61.120 61.111 0.00 0.00 0.00 2.92
1255 6835 0.871722 TCTGCGACGGGAAACAAATG 59.128 50.000 0.00 0.00 0.00 2.32
1290 6870 6.005823 CCAATCCCTCATGCTAATTATGTCA 58.994 40.000 0.00 0.00 0.00 3.58
1314 6894 0.879765 CAGTGTTCGAGTACGGGACT 59.120 55.000 0.00 0.00 42.90 3.85
1317 6897 0.892358 TGTTCGAGTACGGGACTGCT 60.892 55.000 0.00 0.00 39.06 4.24
1323 6903 2.687200 TACGGGACTGCTGGCCAT 60.687 61.111 18.40 7.27 0.00 4.40
1648 7228 1.519719 GTGCTCTAGGCTCCCACTG 59.480 63.158 0.00 0.00 42.39 3.66
1654 7234 2.374830 CTAGGCTCCCACTGCATCGG 62.375 65.000 0.00 0.00 0.00 4.18
1683 7263 6.127140 GGTTTCTACTACATATGTGACCCACT 60.127 42.308 18.81 0.00 35.11 4.00
1684 7264 6.710597 TTCTACTACATATGTGACCCACTC 57.289 41.667 18.81 0.00 35.11 3.51
1691 7271 2.430367 GTGACCCACTCACCCACC 59.570 66.667 0.00 0.00 43.35 4.61
1692 7272 3.238497 TGACCCACTCACCCACCG 61.238 66.667 0.00 0.00 0.00 4.94
1693 7273 2.920912 GACCCACTCACCCACCGA 60.921 66.667 0.00 0.00 0.00 4.69
1694 7274 2.923035 ACCCACTCACCCACCGAG 60.923 66.667 0.00 0.00 36.53 4.63
1695 7275 2.603473 CCCACTCACCCACCGAGA 60.603 66.667 0.00 0.00 34.47 4.04
1696 7276 2.650116 CCCACTCACCCACCGAGAG 61.650 68.421 0.00 0.00 34.47 3.20
1697 7277 2.262915 CACTCACCCACCGAGAGC 59.737 66.667 0.00 0.00 34.47 4.09
1701 7281 3.680786 CACCCACCGAGAGCGTCA 61.681 66.667 0.00 0.00 35.23 4.35
1703 7283 2.202797 CCCACCGAGAGCGTCATG 60.203 66.667 0.00 0.00 35.23 3.07
1720 7300 0.593128 ATGTTTGGTCGTGCTGCTTC 59.407 50.000 0.00 0.00 0.00 3.86
1721 7301 0.463654 TGTTTGGTCGTGCTGCTTCT 60.464 50.000 0.00 0.00 0.00 2.85
1722 7302 0.235926 GTTTGGTCGTGCTGCTTCTC 59.764 55.000 0.00 0.00 0.00 2.87
1723 7303 0.179059 TTTGGTCGTGCTGCTTCTCA 60.179 50.000 0.00 0.00 0.00 3.27
1724 7304 0.035317 TTGGTCGTGCTGCTTCTCAT 59.965 50.000 0.00 0.00 0.00 2.90
1725 7305 0.671472 TGGTCGTGCTGCTTCTCATG 60.671 55.000 0.00 0.00 0.00 3.07
1726 7306 0.671781 GGTCGTGCTGCTTCTCATGT 60.672 55.000 0.00 0.00 0.00 3.21
1727 7307 0.441533 GTCGTGCTGCTTCTCATGTG 59.558 55.000 0.00 0.00 0.00 3.21
1734 7315 2.871022 GCTGCTTCTCATGTGGTATCAG 59.129 50.000 0.00 0.00 0.00 2.90
1750 7331 8.965819 TGTGGTATCAGCATTATTGTTGTTATT 58.034 29.630 2.08 0.00 35.72 1.40
1790 7371 3.821841 CCCTTGAATTTTTCTTCGGTCG 58.178 45.455 0.00 0.00 0.00 4.79
1834 7415 6.080406 GCTTAGCATAAAAGTGTGAGTGTTC 58.920 40.000 0.00 0.00 0.00 3.18
1837 7418 6.305693 AGCATAAAAGTGTGAGTGTTCTTC 57.694 37.500 0.00 0.00 0.00 2.87
1846 7429 6.159988 AGTGTGAGTGTTCTTCTATTAGTGC 58.840 40.000 0.00 0.00 0.00 4.40
1849 7432 6.159988 GTGAGTGTTCTTCTATTAGTGCAGT 58.840 40.000 0.00 0.00 0.00 4.40
1851 7434 7.813148 GTGAGTGTTCTTCTATTAGTGCAGTAA 59.187 37.037 16.13 16.13 0.00 2.24
1891 7893 4.650588 TCATATTGCTCCCTTGAAAATGGG 59.349 41.667 0.00 0.00 44.66 4.00
1899 7902 5.760131 CTCCCTTGAAAATGGGTTCTCTAT 58.240 41.667 0.00 0.00 43.74 1.98
1957 7960 3.963129 ACAACACAAACCCTCAAAGAGA 58.037 40.909 0.00 0.00 0.00 3.10
1963 7966 5.480422 ACACAAACCCTCAAAGAGAGTTTTT 59.520 36.000 4.24 0.00 37.32 1.94
1999 8002 2.870435 GCGTCCCAAACAGTGTACAGAT 60.870 50.000 0.00 0.00 0.00 2.90
2015 8018 8.947115 AGTGTACAGATATTAACTTTCCAAAGC 58.053 33.333 0.00 0.00 39.63 3.51
2016 8019 8.182227 GTGTACAGATATTAACTTTCCAAAGCC 58.818 37.037 0.00 0.00 39.63 4.35
2018 8021 7.396540 ACAGATATTAACTTTCCAAAGCCAG 57.603 36.000 0.00 0.00 39.63 4.85
2019 8022 6.127619 ACAGATATTAACTTTCCAAAGCCAGC 60.128 38.462 0.00 0.00 39.63 4.85
2020 8023 6.096001 CAGATATTAACTTTCCAAAGCCAGCT 59.904 38.462 0.00 0.00 39.63 4.24
2021 8024 6.665248 AGATATTAACTTTCCAAAGCCAGCTT 59.335 34.615 0.00 0.00 39.63 3.74
2022 8025 2.896745 AACTTTCCAAAGCCAGCTTG 57.103 45.000 5.50 0.68 39.63 4.01
2023 8026 1.043022 ACTTTCCAAAGCCAGCTTGG 58.957 50.000 5.50 9.63 39.63 3.61
2140 8145 6.747414 TTCTTAGCTAGAGAATGGGCAATA 57.253 37.500 11.83 0.00 33.51 1.90
2142 8147 7.136822 TCTTAGCTAGAGAATGGGCAATAAA 57.863 36.000 0.00 0.00 0.00 1.40
2143 8148 7.573710 TCTTAGCTAGAGAATGGGCAATAAAA 58.426 34.615 0.00 0.00 0.00 1.52
2144 8149 8.220559 TCTTAGCTAGAGAATGGGCAATAAAAT 58.779 33.333 0.00 0.00 0.00 1.82
2145 8150 8.766994 TTAGCTAGAGAATGGGCAATAAAATT 57.233 30.769 0.00 0.00 0.00 1.82
2146 8151 7.282332 AGCTAGAGAATGGGCAATAAAATTC 57.718 36.000 0.00 0.00 0.00 2.17
2147 8152 6.266330 AGCTAGAGAATGGGCAATAAAATTCC 59.734 38.462 0.00 0.00 30.83 3.01
2148 8153 5.876651 AGAGAATGGGCAATAAAATTCCC 57.123 39.130 0.00 0.00 39.22 3.97
2156 8169 4.225042 GGGCAATAAAATTCCCAGTCCTTT 59.775 41.667 0.00 0.00 38.62 3.11
2211 8224 9.682465 ATGAGAAGATTGATTGAGAAATTCAGA 57.318 29.630 0.00 0.00 37.07 3.27
2233 8275 7.445402 TCAGAAAGTATTGTTCTTTTCCTCCAG 59.555 37.037 0.00 0.00 35.62 3.86
2262 8304 3.367806 GGCTTCTCCAAAAGATTCCTTGC 60.368 47.826 0.00 0.00 32.82 4.01
2293 8335 4.828939 ACTTGAACAAGATTCCTGCAATCA 59.171 37.500 19.35 0.00 43.27 2.57
2307 8349 4.474113 CTGCAATCAGAAAAGAAGACAGC 58.526 43.478 0.00 0.00 42.95 4.40
2309 8351 4.023450 TGCAATCAGAAAAGAAGACAGCAG 60.023 41.667 0.00 0.00 0.00 4.24
2337 8380 4.157840 CCATCCTAAAGCTTTAACCACCAC 59.842 45.833 19.10 0.00 0.00 4.16
2338 8381 3.404899 TCCTAAAGCTTTAACCACCACG 58.595 45.455 19.10 5.74 0.00 4.94
2370 8413 5.497474 GGTTAATCCAAGAGCTTCAACCTA 58.503 41.667 0.00 0.00 33.10 3.08
2399 8442 4.389992 CAGAAGAAACATTTCTCGCAGCTA 59.610 41.667 7.32 0.00 46.22 3.32
2452 8495 7.414984 GCTTCATCTTTGAGATAAACTCCAAGG 60.415 40.741 0.00 0.00 43.89 3.61
2474 8517 2.229784 CCCGCTTCTTCTTTTGCAATCT 59.770 45.455 0.00 0.00 0.00 2.40
2511 8554 3.447586 ACATCACTATACGCCACAAGACT 59.552 43.478 0.00 0.00 0.00 3.24
2514 8557 3.257375 TCACTATACGCCACAAGACTTGT 59.743 43.478 15.23 15.23 46.75 3.16
2522 8565 2.293399 GCCACAAGACTTGTAACTTGGG 59.707 50.000 20.17 16.24 45.03 4.12
2523 8566 3.815809 CCACAAGACTTGTAACTTGGGA 58.184 45.455 20.17 0.00 46.52 4.37
2524 8567 3.815401 CCACAAGACTTGTAACTTGGGAG 59.185 47.826 20.17 5.19 46.52 4.30
2525 8568 4.451900 CACAAGACTTGTAACTTGGGAGT 58.548 43.478 20.17 0.00 46.52 3.85
2526 8569 4.273480 CACAAGACTTGTAACTTGGGAGTG 59.727 45.833 20.17 0.48 46.52 3.51
2527 8570 3.127425 AGACTTGTAACTTGGGAGTGC 57.873 47.619 0.00 0.00 35.91 4.40
2537 8580 4.255510 ACTTGGGAGTGCATATTTGGAT 57.744 40.909 0.00 0.00 33.99 3.41
2612 8655 1.855213 ATTGTGCGTCGCAACTGCAT 61.855 50.000 23.58 6.75 41.47 3.96
2613 8656 2.202222 GTGCGTCGCAACTGCATC 60.202 61.111 23.58 3.46 41.47 3.91
2614 8657 3.776849 TGCGTCGCAACTGCATCG 61.777 61.111 19.38 6.80 42.21 3.84
2615 8658 3.478394 GCGTCGCAACTGCATCGA 61.478 61.111 13.44 0.00 42.21 3.59
2616 8659 2.391821 CGTCGCAACTGCATCGAC 59.608 61.111 16.03 16.03 46.23 4.20
2617 8660 3.862124 GTCGCAACTGCATCGACT 58.138 55.556 17.69 0.00 46.21 4.18
2618 8661 3.030209 GTCGCAACTGCATCGACTA 57.970 52.632 17.69 0.00 46.21 2.59
2619 8662 1.560923 GTCGCAACTGCATCGACTAT 58.439 50.000 17.69 0.00 46.21 2.12
2620 8663 1.256376 GTCGCAACTGCATCGACTATG 59.744 52.381 17.69 0.00 46.21 2.23
2621 8664 1.135112 TCGCAACTGCATCGACTATGT 60.135 47.619 2.12 0.00 42.21 2.29
2622 8665 1.660607 CGCAACTGCATCGACTATGTT 59.339 47.619 2.12 0.00 42.21 2.71
2623 8666 2.535534 CGCAACTGCATCGACTATGTTG 60.536 50.000 14.71 14.71 42.21 3.33
2624 8667 2.223112 GCAACTGCATCGACTATGTTGG 60.223 50.000 18.29 6.72 41.59 3.77
2625 8668 3.261580 CAACTGCATCGACTATGTTGGA 58.738 45.455 12.46 0.00 37.93 3.53
2626 8669 3.610040 ACTGCATCGACTATGTTGGAA 57.390 42.857 0.00 0.00 37.93 3.53
2627 8670 3.937814 ACTGCATCGACTATGTTGGAAA 58.062 40.909 0.00 0.00 37.93 3.13
2628 8671 4.517285 ACTGCATCGACTATGTTGGAAAT 58.483 39.130 0.00 0.00 37.93 2.17
2629 8672 5.670485 ACTGCATCGACTATGTTGGAAATA 58.330 37.500 0.00 0.00 37.93 1.40
2630 8673 6.291377 ACTGCATCGACTATGTTGGAAATAT 58.709 36.000 0.00 0.00 37.93 1.28
2631 8674 6.767902 ACTGCATCGACTATGTTGGAAATATT 59.232 34.615 0.00 0.00 37.93 1.28
2632 8675 7.931407 ACTGCATCGACTATGTTGGAAATATTA 59.069 33.333 0.00 0.00 37.93 0.98
2633 8676 8.310406 TGCATCGACTATGTTGGAAATATTAG 57.690 34.615 0.00 0.00 37.93 1.73
2634 8677 7.095229 TGCATCGACTATGTTGGAAATATTAGC 60.095 37.037 0.00 0.00 37.93 3.09
2635 8678 7.118390 GCATCGACTATGTTGGAAATATTAGCT 59.882 37.037 0.00 0.00 37.93 3.32
2636 8679 9.639601 CATCGACTATGTTGGAAATATTAGCTA 57.360 33.333 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.834496 AGAACAAAATTGATGCTCCCAAGA 59.166 37.500 0.00 0.00 0.00 3.02
22 23 7.123547 ACTTTCATGGAAGTTGTGGTTAAAAGA 59.876 33.333 14.00 0.00 36.49 2.52
23 2820 7.222611 CACTTTCATGGAAGTTGTGGTTAAAAG 59.777 37.037 17.16 4.63 37.76 2.27
28 2825 4.277476 TCACTTTCATGGAAGTTGTGGTT 58.723 39.130 17.16 0.00 37.76 3.67
34 2831 6.070656 TCTTGGAATCACTTTCATGGAAGTT 58.929 36.000 17.16 2.72 37.76 2.66
60 2857 6.170675 TGTTTTGCGTGCTTACAAATTTTT 57.829 29.167 0.00 0.00 35.81 1.94
69 2866 7.332003 CATTAAGAAATGTTTTGCGTGCTTA 57.668 32.000 0.00 0.00 38.15 3.09
179 2976 2.050144 TGGGACATGGAGATCCTTAGC 58.950 52.381 0.00 0.00 35.15 3.09
261 3058 0.327924 AATTGCACGACATGAGGGGA 59.672 50.000 0.00 0.00 0.00 4.81
263 3060 3.057315 AGAAAAATTGCACGACATGAGGG 60.057 43.478 0.00 0.00 0.00 4.30
287 3084 1.608590 CGTCATTGGCTTTGTTCACCT 59.391 47.619 0.00 0.00 0.00 4.00
334 3131 2.107204 AGCAGTGAGAACCCTTTCATGT 59.893 45.455 0.00 0.00 33.72 3.21
408 3205 0.179073 GGATGCCATACTCACAGCGT 60.179 55.000 0.00 0.00 0.00 5.07
413 3210 1.600663 CGTCTCGGATGCCATACTCAC 60.601 57.143 0.00 0.00 0.00 3.51
444 3241 0.458025 CGACCCGGCTTACAAGACTC 60.458 60.000 0.00 0.00 0.00 3.36
450 3972 4.382320 GCCACGACCCGGCTTACA 62.382 66.667 0.00 0.00 46.56 2.41
466 3988 0.839853 AGATAGAGGAGGGCATGGGC 60.840 60.000 0.00 0.00 40.13 5.36
477 3999 1.107538 TGTCGCCGGGAAGATAGAGG 61.108 60.000 2.18 0.00 0.00 3.69
496 4018 0.398318 GCTTCCAGAGTGTTGGTCCT 59.602 55.000 0.00 0.00 39.35 3.85
497 4019 0.951040 CGCTTCCAGAGTGTTGGTCC 60.951 60.000 0.00 0.00 39.35 4.46
501 4023 1.864862 CTGCGCTTCCAGAGTGTTG 59.135 57.895 9.73 0.00 38.18 3.33
522 4823 0.171007 CATGTCCATGTTTGGCGGTC 59.829 55.000 0.00 0.00 43.29 4.79
526 4827 4.917474 GCCATGTCCATGTTTGGC 57.083 55.556 6.53 8.96 46.94 4.52
527 4828 0.964860 TCCGCCATGTCCATGTTTGG 60.965 55.000 6.53 5.26 45.15 3.28
528 4829 0.452987 CTCCGCCATGTCCATGTTTG 59.547 55.000 6.53 0.00 37.11 2.93
529 4830 1.315257 GCTCCGCCATGTCCATGTTT 61.315 55.000 6.53 0.00 37.11 2.83
530 4831 1.750399 GCTCCGCCATGTCCATGTT 60.750 57.895 6.53 0.00 37.11 2.71
531 4832 2.124570 GCTCCGCCATGTCCATGT 60.125 61.111 6.53 0.00 37.11 3.21
554 4855 3.801114 ATTGATTTTTAAGCGGGGCTC 57.199 42.857 0.00 0.00 38.25 4.70
558 4859 6.668796 GCAACGTAAATTGATTTTTAAGCGGG 60.669 38.462 0.00 0.00 0.00 6.13
602 5528 4.524714 CACATCCGGATATCTAGACACCTT 59.475 45.833 18.63 0.00 0.00 3.50
607 5533 5.578727 GCATTTCACATCCGGATATCTAGAC 59.421 44.000 18.63 0.00 0.00 2.59
613 5539 7.707624 AATAATGCATTTCACATCCGGATAT 57.292 32.000 18.63 1.59 0.00 1.63
619 5545 5.174398 CGCTCAAATAATGCATTTCACATCC 59.826 40.000 18.75 1.59 34.49 3.51
643 5569 3.672295 CTCCTCCAACTCCCGCAGC 62.672 68.421 0.00 0.00 0.00 5.25
644 5570 2.232298 GACTCCTCCAACTCCCGCAG 62.232 65.000 0.00 0.00 0.00 5.18
647 5573 2.711922 CCGACTCCTCCAACTCCCG 61.712 68.421 0.00 0.00 0.00 5.14
653 5579 1.974957 TGACAAATCCGACTCCTCCAA 59.025 47.619 0.00 0.00 0.00 3.53
654 5580 1.639722 TGACAAATCCGACTCCTCCA 58.360 50.000 0.00 0.00 0.00 3.86
655 5581 2.762535 TTGACAAATCCGACTCCTCC 57.237 50.000 0.00 0.00 0.00 4.30
667 5630 1.002201 TCTACCGCCGGATTTGACAAA 59.998 47.619 11.71 2.48 0.00 2.83
725 6292 5.878116 GGTGTATTAAGTCTGCATTGGTGTA 59.122 40.000 0.00 0.00 0.00 2.90
780 6349 1.135024 CAGTGGTGGCAATTGTATGGC 60.135 52.381 7.40 0.00 45.44 4.40
822 6391 1.743252 CGCTTCTTGTCTCTGGCCC 60.743 63.158 0.00 0.00 0.00 5.80
907 6480 5.594926 GCTCTGGCTTTGCATGTAATATTT 58.405 37.500 0.00 0.00 35.22 1.40
939 6513 7.499232 ACAATAGCTTTCTTGACTTGTGTACTT 59.501 33.333 0.00 0.00 0.00 2.24
975 6549 2.619177 CGAGTAAGCAGCTAAGCCTAGA 59.381 50.000 0.00 0.00 34.23 2.43
981 6555 2.941453 TCACCGAGTAAGCAGCTAAG 57.059 50.000 0.00 0.00 0.00 2.18
1152 6726 1.885850 GTCGCCGACCACAAACTGT 60.886 57.895 5.81 0.00 0.00 3.55
1182 6756 3.701040 GGAATGGTTCAGTGGTTATGCAT 59.299 43.478 3.79 3.79 0.00 3.96
1205 6781 3.899981 ATCAAGCGTGCCAGCGGAA 62.900 57.895 0.00 0.00 43.00 4.30
1211 6787 0.035317 AGAAGTGATCAAGCGTGCCA 59.965 50.000 0.00 0.00 0.00 4.92
1212 6788 1.129437 GAAGAAGTGATCAAGCGTGCC 59.871 52.381 0.00 0.00 0.00 5.01
1225 6805 1.068194 CCGTCGCAGAGAAGAAGAAGT 60.068 52.381 0.00 0.00 36.95 3.01
1255 6835 1.137675 GAGGGATTGGCAGGCAATTTC 59.862 52.381 22.33 16.74 0.00 2.17
1290 6870 1.614385 CGTACTCGAACACTGCGATT 58.386 50.000 0.00 0.00 39.71 3.34
1323 6903 3.238497 CCCACCTCCACCACGTCA 61.238 66.667 0.00 0.00 0.00 4.35
1623 7203 3.201494 GCCTAGAGCACGAGCAGA 58.799 61.111 7.77 0.00 45.49 4.26
1648 7228 1.739067 AGTAGAAACCTTGCCGATGC 58.261 50.000 0.00 0.00 38.26 3.91
1654 7234 6.258068 GGTCACATATGTAGTAGAAACCTTGC 59.742 42.308 8.32 0.00 0.00 4.01
1683 7263 3.371063 GACGCTCTCGGTGGGTGA 61.371 66.667 0.00 0.00 40.69 4.02
1684 7264 3.006756 ATGACGCTCTCGGTGGGTG 62.007 63.158 0.00 0.00 40.69 4.61
1686 7266 2.202797 CATGACGCTCTCGGTGGG 60.203 66.667 0.00 0.00 40.69 4.61
1687 7267 0.670546 AAACATGACGCTCTCGGTGG 60.671 55.000 0.00 0.00 40.69 4.61
1689 7269 0.670546 CCAAACATGACGCTCTCGGT 60.671 55.000 0.00 0.00 40.69 4.69
1690 7270 0.670546 ACCAAACATGACGCTCTCGG 60.671 55.000 0.00 0.00 40.69 4.63
1691 7271 0.716108 GACCAAACATGACGCTCTCG 59.284 55.000 0.00 0.00 42.43 4.04
1692 7272 0.716108 CGACCAAACATGACGCTCTC 59.284 55.000 0.00 0.00 0.00 3.20
1693 7273 0.033504 ACGACCAAACATGACGCTCT 59.966 50.000 0.00 0.00 0.00 4.09
1694 7274 0.163788 CACGACCAAACATGACGCTC 59.836 55.000 0.00 0.00 0.00 5.03
1695 7275 1.841663 GCACGACCAAACATGACGCT 61.842 55.000 0.00 0.00 0.00 5.07
1696 7276 1.440353 GCACGACCAAACATGACGC 60.440 57.895 0.00 0.00 0.00 5.19
1697 7277 0.110688 CAGCACGACCAAACATGACG 60.111 55.000 0.00 0.00 0.00 4.35
1701 7281 0.593128 GAAGCAGCACGACCAAACAT 59.407 50.000 0.00 0.00 0.00 2.71
1703 7283 0.235926 GAGAAGCAGCACGACCAAAC 59.764 55.000 0.00 0.00 0.00 2.93
1720 7300 6.872628 ACAATAATGCTGATACCACATGAG 57.127 37.500 0.00 0.00 0.00 2.90
1721 7301 6.602803 ACAACAATAATGCTGATACCACATGA 59.397 34.615 0.00 0.00 0.00 3.07
1722 7302 6.798482 ACAACAATAATGCTGATACCACATG 58.202 36.000 0.00 0.00 0.00 3.21
1723 7303 7.408756 AACAACAATAATGCTGATACCACAT 57.591 32.000 0.00 0.00 0.00 3.21
1724 7304 6.832520 AACAACAATAATGCTGATACCACA 57.167 33.333 0.00 0.00 0.00 4.17
1750 7331 6.879993 TCAAGGGCTAAAATTCACAACGTATA 59.120 34.615 0.00 0.00 0.00 1.47
1751 7332 5.708230 TCAAGGGCTAAAATTCACAACGTAT 59.292 36.000 0.00 0.00 0.00 3.06
1752 7333 5.064558 TCAAGGGCTAAAATTCACAACGTA 58.935 37.500 0.00 0.00 0.00 3.57
1753 7334 3.886505 TCAAGGGCTAAAATTCACAACGT 59.113 39.130 0.00 0.00 0.00 3.99
1766 7347 4.403734 ACCGAAGAAAAATTCAAGGGCTA 58.596 39.130 0.00 0.00 0.00 3.93
1810 7391 5.613358 ACACTCACACTTTTATGCTAAGC 57.387 39.130 0.00 0.00 0.00 3.09
1822 7403 6.159988 GCACTAATAGAAGAACACTCACACT 58.840 40.000 0.00 0.00 0.00 3.55
1843 7426 8.687824 ATATGCACTGTTTTTAATTACTGCAC 57.312 30.769 0.00 0.00 36.30 4.57
1930 7933 6.869388 TCTTTGAGGGTTTGTGTTGTAAAAAC 59.131 34.615 0.00 0.00 33.57 2.43
1970 7973 4.038642 ACACTGTTTGGGACGCAAATAAAT 59.961 37.500 19.20 6.64 0.00 1.40
1980 7983 7.822822 AGTTAATATCTGTACACTGTTTGGGAC 59.177 37.037 0.00 0.00 0.00 4.46
1999 8002 5.047377 CCAAGCTGGCTTTGGAAAGTTAATA 60.047 40.000 4.98 0.00 38.28 0.98
2015 8018 4.702131 ACTCTAATTGTAAAGCCAAGCTGG 59.298 41.667 0.00 0.00 39.62 4.85
2016 8019 5.645497 AGACTCTAATTGTAAAGCCAAGCTG 59.355 40.000 0.00 0.00 39.62 4.24
2018 8021 7.611213 TTAGACTCTAATTGTAAAGCCAAGC 57.389 36.000 0.00 0.00 0.00 4.01
2019 8022 8.178313 GCTTTAGACTCTAATTGTAAAGCCAAG 58.822 37.037 12.14 0.00 45.06 3.61
2020 8023 8.040716 GCTTTAGACTCTAATTGTAAAGCCAA 57.959 34.615 12.14 0.00 45.06 4.52
2021 8024 7.611213 GCTTTAGACTCTAATTGTAAAGCCA 57.389 36.000 12.14 0.00 45.06 4.75
2024 8027 7.550906 AGCAGGCTTTAGACTCTAATTGTAAAG 59.449 37.037 0.00 0.00 34.96 1.85
2025 8028 7.394816 AGCAGGCTTTAGACTCTAATTGTAAA 58.605 34.615 0.00 0.00 0.00 2.01
2026 8029 6.947464 AGCAGGCTTTAGACTCTAATTGTAA 58.053 36.000 0.00 0.00 0.00 2.41
2027 8030 6.546428 AGCAGGCTTTAGACTCTAATTGTA 57.454 37.500 0.00 0.00 0.00 2.41
2028 8031 5.428184 AGCAGGCTTTAGACTCTAATTGT 57.572 39.130 0.00 0.00 0.00 2.71
2029 8032 5.065731 CCAAGCAGGCTTTAGACTCTAATTG 59.934 44.000 3.30 0.53 33.42 2.32
2030 8033 5.189180 CCAAGCAGGCTTTAGACTCTAATT 58.811 41.667 3.30 0.00 33.42 1.40
2031 8034 4.775236 CCAAGCAGGCTTTAGACTCTAAT 58.225 43.478 3.30 0.00 33.42 1.73
2032 8035 4.207891 CCAAGCAGGCTTTAGACTCTAA 57.792 45.455 3.30 0.00 33.42 2.10
2074 8077 9.376075 CTTCTTCTAGTCTTCAATCTTATGCAA 57.624 33.333 0.00 0.00 0.00 4.08
2140 8145 5.952347 GTCTATCCAAAGGACTGGGAATTTT 59.048 40.000 0.00 0.00 37.06 1.82
2142 8147 4.079730 GGTCTATCCAAAGGACTGGGAATT 60.080 45.833 0.00 0.00 37.06 2.17
2143 8148 3.459969 GGTCTATCCAAAGGACTGGGAAT 59.540 47.826 0.00 0.00 37.06 3.01
2144 8149 2.844348 GGTCTATCCAAAGGACTGGGAA 59.156 50.000 0.00 0.00 37.06 3.97
2145 8150 2.045885 AGGTCTATCCAAAGGACTGGGA 59.954 50.000 0.00 0.00 37.06 4.37
2146 8151 2.482494 AGGTCTATCCAAAGGACTGGG 58.518 52.381 0.00 0.00 37.06 4.45
2147 8152 5.896073 ATTAGGTCTATCCAAAGGACTGG 57.104 43.478 0.00 0.00 39.02 4.00
2148 8153 7.281100 GTGAAATTAGGTCTATCCAAAGGACTG 59.719 40.741 0.00 0.00 39.02 3.51
2156 8169 8.375493 ACTACTTGTGAAATTAGGTCTATCCA 57.625 34.615 0.00 0.00 39.02 3.41
2211 8224 7.290813 AGACTGGAGGAAAAGAACAATACTTT 58.709 34.615 0.00 0.00 38.91 2.66
2214 8227 5.644206 GGAGACTGGAGGAAAAGAACAATAC 59.356 44.000 0.00 0.00 0.00 1.89
2242 8284 4.522022 ACAGCAAGGAATCTTTTGGAGAAG 59.478 41.667 0.00 0.00 38.06 2.85
2243 8285 4.473444 ACAGCAAGGAATCTTTTGGAGAA 58.527 39.130 0.00 0.00 38.06 2.87
2293 8335 3.244387 GGGACTCTGCTGTCTTCTTTTCT 60.244 47.826 0.00 0.00 37.16 2.52
2307 8349 3.922171 AAGCTTTAGGATGGGACTCTG 57.078 47.619 0.00 0.00 0.00 3.35
2309 8351 4.882427 GGTTAAAGCTTTAGGATGGGACTC 59.118 45.833 17.91 4.10 0.00 3.36
2337 8380 5.031066 TCTTGGATTAACCCTATCAACCG 57.969 43.478 0.00 0.00 38.00 4.44
2338 8381 4.822350 GCTCTTGGATTAACCCTATCAACC 59.178 45.833 0.00 0.00 38.00 3.77
2340 8383 5.975988 AGCTCTTGGATTAACCCTATCAA 57.024 39.130 0.00 0.00 38.00 2.57
2347 8390 4.336280 AGGTTGAAGCTCTTGGATTAACC 58.664 43.478 0.00 0.00 37.25 2.85
2370 8413 5.743872 GCGAGAAATGTTTCTTCTGTTTTGT 59.256 36.000 9.20 0.00 46.84 2.83
2452 8495 0.031994 TTGCAAAAGAAGAAGCGGGC 59.968 50.000 0.00 0.00 0.00 6.13
2474 8517 5.670792 AGTGATGTTACTTACAATCCGGA 57.329 39.130 6.61 6.61 40.89 5.14
2487 8530 5.126545 AGTCTTGTGGCGTATAGTGATGTTA 59.873 40.000 0.00 0.00 0.00 2.41
2489 8532 3.447586 AGTCTTGTGGCGTATAGTGATGT 59.552 43.478 0.00 0.00 0.00 3.06
2511 8554 5.184864 CCAAATATGCACTCCCAAGTTACAA 59.815 40.000 0.00 0.00 31.71 2.41
2514 8557 5.186256 TCCAAATATGCACTCCCAAGTTA 57.814 39.130 0.00 0.00 31.71 2.24
2522 8565 3.126001 TCGGGATCCAAATATGCACTC 57.874 47.619 15.23 0.00 0.00 3.51
2523 8566 3.576078 TTCGGGATCCAAATATGCACT 57.424 42.857 15.23 0.00 0.00 4.40
2524 8567 3.004734 CCTTTCGGGATCCAAATATGCAC 59.995 47.826 15.23 0.00 37.23 4.57
2525 8568 3.221771 CCTTTCGGGATCCAAATATGCA 58.778 45.455 15.23 0.00 37.23 3.96
2526 8569 3.923017 CCTTTCGGGATCCAAATATGC 57.077 47.619 15.23 0.00 37.23 3.14


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

AutoCloner maintained by Alex Coulton.