Multiple sequence alignment - TraesCS4A01G096300

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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 TraesCS4A01G096300 chr4A 100.000 2605 0 0 1 2605 104392686 104390082 0.000000e+00 4811.0
1 TraesCS4A01G096300 chr4D 91.121 1419 58 30 829 2211 360467483 360468869 0.000000e+00 1860.0
2 TraesCS4A01G096300 chr4D 87.613 331 17 6 2260 2579 360469150 360469467 1.910000e-96 363.0
3 TraesCS4A01G096300 chr4B 88.652 1595 78 44 815 2368 445240356 445241888 0.000000e+00 1847.0
4 TraesCS4A01G096300 chr4B 89.940 666 58 9 1 661 445236317 445236978 0.000000e+00 850.0
5 TraesCS4A01G096300 chr4B 90.476 42 3 1 653 694 105342304 105342344 1.000000e-03 54.7
6 TraesCS4A01G096300 chr3A 92.308 78 6 0 1285 1362 608817470 608817547 7.620000e-21 111.0
7 TraesCS4A01G096300 chr3A 97.059 34 0 1 661 694 198297019 198296987 3.620000e-04 56.5
8 TraesCS4A01G096300 chr3D 83.898 118 16 3 1285 1400 465529400 465529516 2.740000e-20 110.0
9 TraesCS4A01G096300 chr3B 91.026 78 7 0 1285 1362 619061283 619061360 3.550000e-19 106.0
10 TraesCS4A01G096300 chr3B 77.966 177 26 10 337 502 776368775 776368601 5.930000e-17 99.0
11 TraesCS4A01G096300 chr2A 73.153 406 63 35 161 538 59385627 59386014 1.280000e-18 104.0
12 TraesCS4A01G096300 chr7A 75.785 223 32 18 321 533 567786687 567786477 2.760000e-15 93.5
13 TraesCS4A01G096300 chr7A 100.000 33 0 0 663 695 511579614 511579646 7.780000e-06 62.1
14 TraesCS4A01G096300 chr2B 78.014 141 26 4 401 538 649035123 649035261 1.660000e-12 84.2
15 TraesCS4A01G096300 chr2D 89.231 65 2 5 1 63 524036889 524036950 2.780000e-10 76.8
16 TraesCS4A01G096300 chr5A 84.848 66 6 4 326 389 454444066 454444003 2.160000e-06 63.9
17 TraesCS4A01G096300 chr5A 100.000 28 0 0 706 733 618965578 618965605 5.000000e-03 52.8
18 TraesCS4A01G096300 chr1B 100.000 31 0 0 664 694 371145345 371145315 1.010000e-04 58.4
19 TraesCS4A01G096300 chr1A 100.000 31 0 0 664 694 140959070 140959040 1.010000e-04 58.4
20 TraesCS4A01G096300 chr1A 94.286 35 1 1 660 694 499985471 499985438 5.000000e-03 52.8
21 TraesCS4A01G096300 chr6B 100.000 30 0 0 663 692 455903591 455903562 3.620000e-04 56.5
22 TraesCS4A01G096300 chr6A 94.595 37 1 1 659 694 170914082 170914118 3.620000e-04 56.5
23 TraesCS4A01G096300 chr7B 100.000 28 0 0 245 272 71134270 71134297 5.000000e-03 52.8
24 TraesCS4A01G096300 chr7B 94.118 34 2 0 653 686 215429283 215429316 5.000000e-03 52.8


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 TraesCS4A01G096300 chr4A 104390082 104392686 2604 True 4811.0 4811 100.000 1 2605 1 chr4A.!!$R1 2604
1 TraesCS4A01G096300 chr4D 360467483 360469467 1984 False 1111.5 1860 89.367 829 2579 2 chr4D.!!$F1 1750
2 TraesCS4A01G096300 chr4B 445236317 445241888 5571 False 1348.5 1847 89.296 1 2368 2 chr4B.!!$F2 2367

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
945 4196 1.163309 TCCAGTTCACCCCCATCCT 59.837 57.895 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 5518 0.04394 AAGCTGAGGGTGAGGGAGAT 59.956 55.0 0.0 0.0 0.0 2.75 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
56 57 4.963276 TTTGTGTTGTCTCACCTTGAAG 57.037 40.909 0.00 0.00 37.51 3.02
60 61 5.924356 TGTGTTGTCTCACCTTGAAGAATA 58.076 37.500 0.00 0.00 37.51 1.75
64 65 7.857885 GTGTTGTCTCACCTTGAAGAATAAAAG 59.142 37.037 0.00 0.00 32.81 2.27
122 124 6.661740 AATAAGTCCCCTTGTTATTACCCA 57.338 37.500 0.00 0.00 31.10 4.51
130 132 7.284716 GTCCCCTTGTTATTACCCATAAAGAAG 59.715 40.741 0.00 0.00 0.00 2.85
163 165 8.845942 AATACTAAAGAAAAACAAACGGTGAC 57.154 30.769 0.00 0.00 0.00 3.67
176 178 1.741145 ACGGTGACAAAACTTGGACAC 59.259 47.619 0.00 0.00 39.49 3.67
177 179 1.740585 CGGTGACAAAACTTGGACACA 59.259 47.619 15.36 0.00 40.81 3.72
184 186 6.252655 GTGACAAAACTTGGACACATTTACAC 59.747 38.462 11.33 0.00 39.75 2.90
218 220 7.799447 GTGCTTTTTACAACGTACATGAATACA 59.201 33.333 0.00 0.00 0.00 2.29
231 233 9.529325 CGTACATGAATACACATATAATAGGGG 57.471 37.037 0.00 0.00 0.00 4.79
241 243 8.546083 ACACATATAATAGGGGAATTTTTGCA 57.454 30.769 0.00 0.00 0.00 4.08
301 303 9.360093 CGCATTTATTACATTAAAAGGGAACAA 57.640 29.630 0.00 0.00 29.43 2.83
396 398 6.286240 ACCCTTTAAGAAGAAATGGAATGC 57.714 37.500 0.00 0.00 34.71 3.56
398 400 6.269769 ACCCTTTAAGAAGAAATGGAATGCAA 59.730 34.615 0.00 0.00 34.71 4.08
400 402 7.661027 CCCTTTAAGAAGAAATGGAATGCAAAA 59.339 33.333 0.00 0.00 34.71 2.44
593 596 6.940298 TGAATTACTAGCATTGCTATTACCCC 59.060 38.462 18.29 8.97 40.54 4.95
594 597 5.897851 TTACTAGCATTGCTATTACCCCA 57.102 39.130 18.29 0.71 40.54 4.96
677 1334 7.510549 TGCAAAAATAAGCATATACTCCCTC 57.489 36.000 0.00 0.00 35.51 4.30
678 1335 6.490040 TGCAAAAATAAGCATATACTCCCTCC 59.510 38.462 0.00 0.00 35.51 4.30
679 1336 6.348540 GCAAAAATAAGCATATACTCCCTCCG 60.349 42.308 0.00 0.00 0.00 4.63
682 1339 5.662674 ATAAGCATATACTCCCTCCGTTC 57.337 43.478 0.00 0.00 0.00 3.95
688 1650 5.621193 CATATACTCCCTCCGTTCCAAATT 58.379 41.667 0.00 0.00 0.00 1.82
690 1652 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
691 1653 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
693 1655 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
696 1658 4.082949 CCCTCCGTTCCAAATTACTTGAAC 60.083 45.833 0.00 0.00 37.17 3.18
705 1667 9.027129 GTTCCAAATTACTTGAACTAAAACCAC 57.973 33.333 0.00 0.00 37.17 4.16
706 1668 7.419204 TCCAAATTACTTGAACTAAAACCACG 58.581 34.615 0.00 0.00 37.17 4.94
707 1669 7.282675 TCCAAATTACTTGAACTAAAACCACGA 59.717 33.333 0.00 0.00 37.17 4.35
708 1670 7.377662 CCAAATTACTTGAACTAAAACCACGAC 59.622 37.037 0.00 0.00 37.17 4.34
710 1672 6.981762 TTACTTGAACTAAAACCACGACAA 57.018 33.333 0.00 0.00 0.00 3.18
712 1674 4.939439 ACTTGAACTAAAACCACGACAAGT 59.061 37.500 0.00 0.00 40.74 3.16
714 1676 6.257193 ACTTGAACTAAAACCACGACAAGTAG 59.743 38.462 0.00 0.00 42.68 2.57
716 1678 6.108015 TGAACTAAAACCACGACAAGTAGTT 58.892 36.000 0.00 0.00 36.26 2.24
717 1679 6.594937 TGAACTAAAACCACGACAAGTAGTTT 59.405 34.615 0.00 0.00 44.40 2.66
722 2098 4.870221 ACCACGACAAGTAGTTTGAAAC 57.130 40.909 0.00 0.00 39.21 2.78
724 2100 3.302870 CCACGACAAGTAGTTTGAAACGG 60.303 47.826 1.97 0.00 39.21 4.44
733 2109 4.590222 AGTAGTTTGAAACGGAGGGAGTAA 59.410 41.667 1.97 0.00 36.23 2.24
734 2110 4.635699 AGTTTGAAACGGAGGGAGTAAT 57.364 40.909 1.97 0.00 36.23 1.89
735 2111 5.750352 AGTTTGAAACGGAGGGAGTAATA 57.250 39.130 1.97 0.00 36.23 0.98
736 2112 5.731591 AGTTTGAAACGGAGGGAGTAATAG 58.268 41.667 1.97 0.00 36.23 1.73
738 2114 4.730949 TGAAACGGAGGGAGTAATAGTG 57.269 45.455 0.00 0.00 0.00 2.74
739 2115 4.091549 TGAAACGGAGGGAGTAATAGTGT 58.908 43.478 0.00 0.00 0.00 3.55
741 2117 5.895534 TGAAACGGAGGGAGTAATAGTGTAT 59.104 40.000 0.00 0.00 0.00 2.29
742 2118 6.381994 TGAAACGGAGGGAGTAATAGTGTATT 59.618 38.462 0.00 0.00 0.00 1.89
743 2119 6.803366 AACGGAGGGAGTAATAGTGTATTT 57.197 37.500 0.00 0.00 0.00 1.40
744 2120 6.158023 ACGGAGGGAGTAATAGTGTATTTG 57.842 41.667 0.00 0.00 0.00 2.32
745 2121 5.659971 ACGGAGGGAGTAATAGTGTATTTGT 59.340 40.000 0.00 0.00 0.00 2.83
746 2122 6.155737 ACGGAGGGAGTAATAGTGTATTTGTT 59.844 38.462 0.00 0.00 0.00 2.83
747 2123 7.046033 CGGAGGGAGTAATAGTGTATTTGTTT 58.954 38.462 0.00 0.00 0.00 2.83
748 2124 7.011109 CGGAGGGAGTAATAGTGTATTTGTTTG 59.989 40.741 0.00 0.00 0.00 2.93
749 2125 8.044908 GGAGGGAGTAATAGTGTATTTGTTTGA 58.955 37.037 0.00 0.00 0.00 2.69
750 2126 9.444600 GAGGGAGTAATAGTGTATTTGTTTGAA 57.555 33.333 0.00 0.00 0.00 2.69
751 2127 9.449719 AGGGAGTAATAGTGTATTTGTTTGAAG 57.550 33.333 0.00 0.00 0.00 3.02
768 2207 7.819644 TGTTTGAAGATTATGACAACAGATGG 58.180 34.615 0.00 0.00 0.00 3.51
769 2208 6.441093 TTGAAGATTATGACAACAGATGGC 57.559 37.500 0.00 0.00 37.68 4.40
777 4028 3.554934 TGACAACAGATGGCAAACTCTT 58.445 40.909 0.00 0.00 46.71 2.85
794 4045 7.148853 GCAAACTCTTAAGAACAAGCATGATTG 60.149 37.037 21.63 21.63 36.22 2.67
795 4046 7.750229 AACTCTTAAGAACAAGCATGATTGA 57.250 32.000 29.17 4.24 34.20 2.57
796 4047 7.750229 ACTCTTAAGAACAAGCATGATTGAA 57.250 32.000 29.17 12.00 34.20 2.69
797 4048 7.814642 ACTCTTAAGAACAAGCATGATTGAAG 58.185 34.615 29.17 20.09 34.20 3.02
798 4049 7.663081 ACTCTTAAGAACAAGCATGATTGAAGA 59.337 33.333 29.17 22.69 34.20 2.87
799 4050 8.571461 TCTTAAGAACAAGCATGATTGAAGAT 57.429 30.769 29.17 14.54 34.20 2.40
800 4051 9.017509 TCTTAAGAACAAGCATGATTGAAGATT 57.982 29.630 29.17 18.31 34.20 2.40
804 4055 7.201145 AGAACAAGCATGATTGAAGATTATGC 58.799 34.615 29.17 4.44 43.23 3.14
805 4056 5.839621 ACAAGCATGATTGAAGATTATGCC 58.160 37.500 29.17 0.00 43.77 4.40
806 4057 5.221382 ACAAGCATGATTGAAGATTATGCCC 60.221 40.000 29.17 0.00 43.77 5.36
807 4058 4.476297 AGCATGATTGAAGATTATGCCCA 58.524 39.130 10.83 0.00 43.77 5.36
808 4059 5.084519 AGCATGATTGAAGATTATGCCCAT 58.915 37.500 10.83 0.00 43.77 4.00
809 4060 6.250711 AGCATGATTGAAGATTATGCCCATA 58.749 36.000 10.83 0.00 43.77 2.74
810 4061 6.722590 AGCATGATTGAAGATTATGCCCATAA 59.277 34.615 10.83 3.44 43.77 1.90
811 4062 7.033791 GCATGATTGAAGATTATGCCCATAAG 58.966 38.462 0.00 0.00 38.48 1.73
812 4063 7.309621 GCATGATTGAAGATTATGCCCATAAGT 60.310 37.037 0.00 0.00 38.48 2.24
813 4064 8.582437 CATGATTGAAGATTATGCCCATAAGTT 58.418 33.333 6.83 3.42 36.79 2.66
814 4065 9.812347 ATGATTGAAGATTATGCCCATAAGTTA 57.188 29.630 6.83 0.00 36.79 2.24
815 4066 9.812347 TGATTGAAGATTATGCCCATAAGTTAT 57.188 29.630 6.83 0.00 36.79 1.89
824 4075 2.223479 GCCCATAAGTTATGTGCAACCG 60.223 50.000 21.13 5.94 39.04 4.44
851 4102 5.543507 AAATCAACAGGTGCCAACATAAA 57.456 34.783 0.00 0.00 0.00 1.40
857 4108 3.507233 ACAGGTGCCAACATAAATCTGTG 59.493 43.478 0.00 0.00 33.63 3.66
944 4195 1.303282 GTCCAGTTCACCCCCATCC 59.697 63.158 0.00 0.00 0.00 3.51
945 4196 1.163309 TCCAGTTCACCCCCATCCT 59.837 57.895 0.00 0.00 0.00 3.24
1448 4720 3.326747 GTTTCGAGCCACAGTACAGAAT 58.673 45.455 0.00 0.00 0.00 2.40
1450 4722 1.132453 TCGAGCCACAGTACAGAATCG 59.868 52.381 0.00 0.00 0.00 3.34
1480 4752 0.238817 GATGTCGAGTAGGCGGCTAG 59.761 60.000 20.35 8.21 36.72 3.42
1513 4785 7.873692 ATGTATGTACAGATCAGCCTCTTGCT 61.874 42.308 0.33 0.00 45.69 3.91
1514 4786 9.263401 ATGTATGTACAGATCAGCCTCTTGCTT 62.263 40.741 0.33 0.00 43.61 3.91
1533 4805 7.441458 TCTTGCTTACTAGGAGTCTTGTTTTTC 59.559 37.037 0.00 0.00 31.77 2.29
1534 4806 5.694910 TGCTTACTAGGAGTCTTGTTTTTCG 59.305 40.000 0.00 0.00 31.77 3.46
1548 4820 6.588373 TCTTGTTTTTCGTTTCCTTCCTTTTG 59.412 34.615 0.00 0.00 0.00 2.44
1555 4827 3.629058 GTTTCCTTCCTTTTGTTCTCGC 58.371 45.455 0.00 0.00 0.00 5.03
1575 4847 1.141881 CCATCTCTGGGACGGTTCG 59.858 63.158 0.00 0.00 39.04 3.95
1586 4858 1.137513 GACGGTTCGTGGAGAAACTG 58.862 55.000 0.00 0.00 44.23 3.16
1588 4860 1.566018 CGGTTCGTGGAGAAACTGCC 61.566 60.000 0.00 0.00 44.23 4.85
1628 4903 7.266922 AGTGATTAGTAGCAGAGTAGTTAGC 57.733 40.000 0.00 0.00 0.00 3.09
1632 4907 2.614983 AGTAGCAGAGTAGTTAGCGCTC 59.385 50.000 16.34 0.00 0.00 5.03
1636 4911 2.803451 CAGAGTAGTTAGCGCTCCAAG 58.197 52.381 16.34 0.00 0.00 3.61
1654 4929 0.252467 AGCTTAGAGGAGGTGGTGCT 60.252 55.000 0.00 0.00 0.00 4.40
1655 4930 0.107945 GCTTAGAGGAGGTGGTGCTG 60.108 60.000 0.00 0.00 0.00 4.41
1656 4931 0.107945 CTTAGAGGAGGTGGTGCTGC 60.108 60.000 0.00 0.00 0.00 5.25
1657 4932 0.835971 TTAGAGGAGGTGGTGCTGCA 60.836 55.000 0.00 0.00 0.00 4.41
1773 5057 1.065564 AGAAATCTGAGACAGGGCTGC 60.066 52.381 0.00 0.00 31.51 5.25
1774 5058 0.034670 AAATCTGAGACAGGGCTGCC 60.035 55.000 11.05 11.05 31.51 4.85
1775 5059 1.919600 AATCTGAGACAGGGCTGCCC 61.920 60.000 30.57 30.57 45.90 5.36
1813 5097 4.942852 AGCTGAAATCTAGTGGATCTTCG 58.057 43.478 0.00 0.00 32.76 3.79
1826 5110 4.512571 GTGGATCTTCGTCTACTCCTACTC 59.487 50.000 0.00 0.00 0.00 2.59
1865 5152 2.262423 AGGCTGGAAAGTTGTGACTC 57.738 50.000 0.00 0.00 34.21 3.36
1873 5160 4.346709 TGGAAAGTTGTGACTCCTGTATGA 59.653 41.667 0.00 0.00 34.21 2.15
1907 5194 2.744202 AGAAATGAGACGCCACAACATC 59.256 45.455 0.00 0.00 0.00 3.06
1908 5195 2.183478 AATGAGACGCCACAACATCA 57.817 45.000 0.00 0.00 0.00 3.07
1911 5198 1.225855 GAGACGCCACAACATCAACA 58.774 50.000 0.00 0.00 0.00 3.33
1912 5199 1.806542 GAGACGCCACAACATCAACAT 59.193 47.619 0.00 0.00 0.00 2.71
1913 5200 3.000041 GAGACGCCACAACATCAACATA 59.000 45.455 0.00 0.00 0.00 2.29
1914 5201 3.407698 AGACGCCACAACATCAACATAA 58.592 40.909 0.00 0.00 0.00 1.90
1916 5203 3.896122 ACGCCACAACATCAACATAAAC 58.104 40.909 0.00 0.00 0.00 2.01
1917 5204 3.568007 ACGCCACAACATCAACATAAACT 59.432 39.130 0.00 0.00 0.00 2.66
1918 5205 4.757657 ACGCCACAACATCAACATAAACTA 59.242 37.500 0.00 0.00 0.00 2.24
1919 5206 5.086058 CGCCACAACATCAACATAAACTAC 58.914 41.667 0.00 0.00 0.00 2.73
1920 5207 5.106712 CGCCACAACATCAACATAAACTACT 60.107 40.000 0.00 0.00 0.00 2.57
1921 5208 6.091577 CGCCACAACATCAACATAAACTACTA 59.908 38.462 0.00 0.00 0.00 1.82
1922 5209 7.201609 CGCCACAACATCAACATAAACTACTAT 60.202 37.037 0.00 0.00 0.00 2.12
1923 5210 8.458843 GCCACAACATCAACATAAACTACTATT 58.541 33.333 0.00 0.00 0.00 1.73
1924 5211 9.988350 CCACAACATCAACATAAACTACTATTC 57.012 33.333 0.00 0.00 0.00 1.75
2023 5313 5.888161 GTGGACATAAGAGGAATCAAATGGT 59.112 40.000 0.00 0.00 0.00 3.55
2104 5398 0.766288 GGATCAGGGAGGGAGAAGGG 60.766 65.000 0.00 0.00 0.00 3.95
2123 5417 1.115326 GGGCAGTAAATGGGGATGGC 61.115 60.000 0.00 0.00 35.85 4.40
2176 5470 1.005215 CCTTCTGGGACTGCCATTTCT 59.995 52.381 0.00 0.00 37.23 2.52
2211 5505 1.360192 GCCACTCCATTATTGCGCC 59.640 57.895 4.18 0.00 0.00 6.53
2212 5506 2.032981 CCACTCCATTATTGCGCCC 58.967 57.895 4.18 0.00 0.00 6.13
2213 5507 1.455383 CCACTCCATTATTGCGCCCC 61.455 60.000 4.18 0.00 0.00 5.80
2214 5508 1.152756 ACTCCATTATTGCGCCCCC 60.153 57.895 4.18 0.00 0.00 5.40
2215 5509 1.151450 CTCCATTATTGCGCCCCCT 59.849 57.895 4.18 0.00 0.00 4.79
2216 5510 0.400213 CTCCATTATTGCGCCCCCTA 59.600 55.000 4.18 0.00 0.00 3.53
2217 5511 0.109723 TCCATTATTGCGCCCCCTAC 59.890 55.000 4.18 0.00 0.00 3.18
2218 5512 0.893727 CCATTATTGCGCCCCCTACC 60.894 60.000 4.18 0.00 0.00 3.18
2219 5513 0.110486 CATTATTGCGCCCCCTACCT 59.890 55.000 4.18 0.00 0.00 3.08
2220 5514 0.400594 ATTATTGCGCCCCCTACCTC 59.599 55.000 4.18 0.00 0.00 3.85
2221 5515 2.035237 TTATTGCGCCCCCTACCTCG 62.035 60.000 4.18 0.00 0.00 4.63
2244 5548 0.906756 TCTCCCTCACCCTCAGCTTG 60.907 60.000 0.00 0.00 0.00 4.01
2247 5551 1.601171 CCTCACCCTCAGCTTGGAG 59.399 63.158 4.18 0.00 34.62 3.86
2248 5552 1.078567 CTCACCCTCAGCTTGGAGC 60.079 63.158 4.18 0.00 42.84 4.70
2249 5553 2.045536 CACCCTCAGCTTGGAGCC 60.046 66.667 4.18 0.00 43.77 4.70
2252 5556 2.438075 CCTCAGCTTGGAGCCAGC 60.438 66.667 0.00 0.00 43.77 4.85
2276 5827 1.583404 CACACAAACGCAAAACAGAGC 59.417 47.619 0.00 0.00 0.00 4.09
2296 5847 1.278238 GACCCAGAGAAATACGCACG 58.722 55.000 0.00 0.00 0.00 5.34
2297 5848 0.739813 ACCCAGAGAAATACGCACGC 60.740 55.000 0.00 0.00 0.00 5.34
2298 5849 0.739462 CCCAGAGAAATACGCACGCA 60.739 55.000 0.00 0.00 0.00 5.24
2299 5850 0.370273 CCAGAGAAATACGCACGCAC 59.630 55.000 0.00 0.00 0.00 5.34
2319 5873 3.200593 GCAGCCATGAGTGCCTCG 61.201 66.667 7.78 0.00 33.29 4.63
2334 5888 1.153549 CTCGCTTGGTGGTAGGAGC 60.154 63.158 0.00 0.00 0.00 4.70
2390 5944 2.450160 CGGCCGATGCAGTTTTTAATC 58.550 47.619 24.07 0.00 40.13 1.75
2391 5945 2.794631 CGGCCGATGCAGTTTTTAATCC 60.795 50.000 24.07 0.00 40.13 3.01
2422 5986 0.032017 AGTGGAGTAGGCCTCGGAAT 60.032 55.000 9.68 0.00 41.46 3.01
2441 6005 4.394729 GAATCCATTGTTAATAGCCGGGA 58.605 43.478 2.18 0.00 0.00 5.14
2444 6008 4.601084 TCCATTGTTAATAGCCGGGAAAA 58.399 39.130 2.18 0.00 0.00 2.29
2445 6009 5.017490 TCCATTGTTAATAGCCGGGAAAAA 58.983 37.500 2.18 0.00 0.00 1.94
2446 6010 5.105675 TCCATTGTTAATAGCCGGGAAAAAC 60.106 40.000 2.18 0.00 0.00 2.43
2454 6018 3.439008 CGGGAAAAACGGGCTGTT 58.561 55.556 5.72 5.72 44.59 3.16
2455 6019 1.284715 CGGGAAAAACGGGCTGTTC 59.715 57.895 12.95 0.00 40.84 3.18
2483 6047 2.826428 AGATCGATCAACATCAACGGG 58.174 47.619 26.47 0.00 0.00 5.28
2529 6093 1.615392 CAAGGCAGGTTTTTGCTAGCT 59.385 47.619 17.23 0.00 43.57 3.32
2537 6101 2.228103 GGTTTTTGCTAGCTGTACCACC 59.772 50.000 17.23 10.46 0.00 4.61
2538 6102 1.803334 TTTTGCTAGCTGTACCACCG 58.197 50.000 17.23 0.00 0.00 4.94
2540 6104 1.189524 TTGCTAGCTGTACCACCGGT 61.190 55.000 17.23 0.00 40.16 5.28
2579 6143 2.985456 CTTTGCCCCTCTCGCTCT 59.015 61.111 0.00 0.00 0.00 4.09
2580 6144 1.153469 CTTTGCCCCTCTCGCTCTC 60.153 63.158 0.00 0.00 0.00 3.20
2581 6145 2.897641 CTTTGCCCCTCTCGCTCTCG 62.898 65.000 0.00 0.00 0.00 4.04
2584 6148 3.591835 CCCCTCTCGCTCTCGCTC 61.592 72.222 0.00 0.00 35.26 5.03
2585 6149 3.947841 CCCTCTCGCTCTCGCTCG 61.948 72.222 0.00 0.00 35.26 5.03
2586 6150 4.605967 CCTCTCGCTCTCGCTCGC 62.606 72.222 0.00 0.00 35.26 5.03
2587 6151 3.572539 CTCTCGCTCTCGCTCGCT 61.573 66.667 0.00 0.00 35.26 4.93
2588 6152 3.506312 CTCTCGCTCTCGCTCGCTC 62.506 68.421 0.00 0.00 35.26 5.03
2589 6153 4.936248 CTCGCTCTCGCTCGCTCG 62.936 72.222 0.00 0.00 35.26 5.03
2593 6157 4.936248 CTCTCGCTCGCTCGCTCG 62.936 72.222 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.862325 TCAAGGTGAGACAACACAAATATTAT 57.138 30.769 0.00 0.00 41.88 1.28
158 160 4.385358 AATGTGTCCAAGTTTTGTCACC 57.615 40.909 9.87 0.00 34.80 4.02
163 165 6.559810 TCTGTGTAAATGTGTCCAAGTTTTG 58.440 36.000 0.00 0.00 0.00 2.44
184 186 6.567769 ACGTTGTAAAAAGCACATTTTCTG 57.432 33.333 0.00 0.00 40.27 3.02
400 402 9.486497 TGTGTGCACAATTTGTCATTATTTATT 57.514 25.926 23.59 0.00 38.56 1.40
629 632 7.326789 GCATATTGTGTGGGAATTATTTCATCG 59.673 37.037 0.20 0.00 33.23 3.84
643 646 6.964741 TGCTTATTTTTGCATATTGTGTGG 57.035 33.333 0.00 0.00 33.94 4.17
671 1328 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
673 1330 3.681593 TCAAGTAATTTGGAACGGAGGG 58.318 45.455 0.00 0.00 37.39 4.30
674 1331 4.760204 AGTTCAAGTAATTTGGAACGGAGG 59.240 41.667 0.00 0.00 37.39 4.30
675 1332 5.941948 AGTTCAAGTAATTTGGAACGGAG 57.058 39.130 0.00 0.00 37.39 4.63
676 1333 7.804843 TTTAGTTCAAGTAATTTGGAACGGA 57.195 32.000 0.00 0.00 37.39 4.69
677 1334 7.380333 GGTTTTAGTTCAAGTAATTTGGAACGG 59.620 37.037 0.00 0.00 37.39 4.44
678 1335 7.916450 TGGTTTTAGTTCAAGTAATTTGGAACG 59.084 33.333 0.00 0.00 37.39 3.95
679 1336 9.027129 GTGGTTTTAGTTCAAGTAATTTGGAAC 57.973 33.333 0.00 0.00 37.39 3.62
682 1339 7.377662 GTCGTGGTTTTAGTTCAAGTAATTTGG 59.622 37.037 0.00 0.00 37.39 3.28
688 1650 6.108015 ACTTGTCGTGGTTTTAGTTCAAGTA 58.892 36.000 0.00 0.00 41.13 2.24
690 1652 5.479716 ACTTGTCGTGGTTTTAGTTCAAG 57.520 39.130 0.00 0.00 37.58 3.02
691 1653 6.108015 ACTACTTGTCGTGGTTTTAGTTCAA 58.892 36.000 0.00 0.00 32.95 2.69
693 1655 6.594284 AACTACTTGTCGTGGTTTTAGTTC 57.406 37.500 0.00 0.00 43.77 3.01
705 1667 3.183775 CCTCCGTTTCAAACTACTTGTCG 59.816 47.826 0.00 0.00 36.34 4.35
706 1668 3.497262 CCCTCCGTTTCAAACTACTTGTC 59.503 47.826 0.00 0.00 36.34 3.18
707 1669 3.135167 TCCCTCCGTTTCAAACTACTTGT 59.865 43.478 0.00 0.00 36.34 3.16
708 1670 3.735591 TCCCTCCGTTTCAAACTACTTG 58.264 45.455 0.00 0.00 36.25 3.16
710 1672 2.970640 ACTCCCTCCGTTTCAAACTACT 59.029 45.455 0.00 0.00 0.00 2.57
712 1674 5.750352 ATTACTCCCTCCGTTTCAAACTA 57.250 39.130 0.00 0.00 0.00 2.24
714 1676 5.350640 CACTATTACTCCCTCCGTTTCAAAC 59.649 44.000 0.00 0.00 0.00 2.93
716 1678 4.529377 ACACTATTACTCCCTCCGTTTCAA 59.471 41.667 0.00 0.00 0.00 2.69
717 1679 4.091549 ACACTATTACTCCCTCCGTTTCA 58.908 43.478 0.00 0.00 0.00 2.69
722 2098 6.158023 ACAAATACACTATTACTCCCTCCG 57.842 41.667 0.00 0.00 0.00 4.63
724 2100 9.444600 TTCAAACAAATACACTATTACTCCCTC 57.555 33.333 0.00 0.00 0.00 4.30
741 2117 9.681692 CATCTGTTGTCATAATCTTCAAACAAA 57.318 29.630 0.00 0.00 0.00 2.83
742 2118 8.298854 CCATCTGTTGTCATAATCTTCAAACAA 58.701 33.333 0.00 0.00 0.00 2.83
743 2119 7.575532 GCCATCTGTTGTCATAATCTTCAAACA 60.576 37.037 0.00 0.00 0.00 2.83
744 2120 6.749118 GCCATCTGTTGTCATAATCTTCAAAC 59.251 38.462 0.00 0.00 0.00 2.93
745 2121 6.433716 TGCCATCTGTTGTCATAATCTTCAAA 59.566 34.615 0.00 0.00 0.00 2.69
746 2122 5.945191 TGCCATCTGTTGTCATAATCTTCAA 59.055 36.000 0.00 0.00 0.00 2.69
747 2123 5.499313 TGCCATCTGTTGTCATAATCTTCA 58.501 37.500 0.00 0.00 0.00 3.02
748 2124 6.441093 TTGCCATCTGTTGTCATAATCTTC 57.559 37.500 0.00 0.00 0.00 2.87
749 2125 6.435277 AGTTTGCCATCTGTTGTCATAATCTT 59.565 34.615 0.00 0.00 0.00 2.40
750 2126 5.948162 AGTTTGCCATCTGTTGTCATAATCT 59.052 36.000 0.00 0.00 0.00 2.40
751 2127 6.094603 AGAGTTTGCCATCTGTTGTCATAATC 59.905 38.462 0.00 0.00 0.00 1.75
768 2207 5.762045 TCATGCTTGTTCTTAAGAGTTTGC 58.238 37.500 5.12 9.79 0.00 3.68
769 2208 8.077991 TCAATCATGCTTGTTCTTAAGAGTTTG 58.922 33.333 9.00 4.00 0.00 2.93
770 2209 8.169977 TCAATCATGCTTGTTCTTAAGAGTTT 57.830 30.769 9.00 0.00 0.00 2.66
771 2210 7.750229 TCAATCATGCTTGTTCTTAAGAGTT 57.250 32.000 9.00 0.00 0.00 3.01
772 2211 7.663081 TCTTCAATCATGCTTGTTCTTAAGAGT 59.337 33.333 9.00 0.00 0.00 3.24
774 2213 7.984422 TCTTCAATCATGCTTGTTCTTAAGA 57.016 32.000 9.00 0.00 0.00 2.10
804 4055 3.013921 ACGGTTGCACATAACTTATGGG 58.986 45.455 12.48 9.73 42.49 4.00
805 4056 4.014847 CACGGTTGCACATAACTTATGG 57.985 45.455 12.48 4.07 40.47 2.74
824 4075 1.202510 TGGCACCTGTTGATTTTGCAC 60.203 47.619 0.00 0.00 34.76 4.57
851 4102 3.670895 CGAGTCTCTTTGCGTACACAGAT 60.671 47.826 0.00 0.00 32.32 2.90
857 4108 1.415374 TTGCGAGTCTCTTTGCGTAC 58.585 50.000 0.00 0.00 0.00 3.67
944 4195 2.422231 CGGGTGAGGCTGGAGAGAG 61.422 68.421 0.00 0.00 0.00 3.20
945 4196 2.363018 CGGGTGAGGCTGGAGAGA 60.363 66.667 0.00 0.00 0.00 3.10
1190 4450 3.177884 TGGTCCCTTGTGCTGGCT 61.178 61.111 0.00 0.00 0.00 4.75
1292 4552 3.965539 CTGCTCCTTCACCAGCCCG 62.966 68.421 0.00 0.00 34.47 6.13
1432 4694 2.423892 TCTCGATTCTGTACTGTGGCTC 59.576 50.000 0.00 0.00 0.00 4.70
1480 4752 5.670485 TGATCTGTACATACATCACCCAAC 58.330 41.667 0.00 0.00 35.36 3.77
1513 4785 7.225341 GGAAACGAAAAACAAGACTCCTAGTAA 59.775 37.037 0.00 0.00 0.00 2.24
1514 4786 6.703165 GGAAACGAAAAACAAGACTCCTAGTA 59.297 38.462 0.00 0.00 0.00 1.82
1515 4787 5.526479 GGAAACGAAAAACAAGACTCCTAGT 59.474 40.000 0.00 0.00 0.00 2.57
1516 4788 5.758784 AGGAAACGAAAAACAAGACTCCTAG 59.241 40.000 0.00 0.00 0.00 3.02
1533 4805 3.848554 GCGAGAACAAAAGGAAGGAAACG 60.849 47.826 0.00 0.00 0.00 3.60
1534 4806 3.550233 GGCGAGAACAAAAGGAAGGAAAC 60.550 47.826 0.00 0.00 0.00 2.78
1548 4820 1.144936 CCAGAGATGGGGCGAGAAC 59.855 63.158 0.00 0.00 0.00 3.01
1575 4847 0.536006 AGCACTGGCAGTTTCTCCAC 60.536 55.000 19.43 1.70 44.61 4.02
1586 4858 4.253685 TCACTAACTAATCAAGCACTGGC 58.746 43.478 0.00 0.00 41.61 4.85
1588 4860 8.709386 ACTAATCACTAACTAATCAAGCACTG 57.291 34.615 0.00 0.00 0.00 3.66
1632 4907 1.065854 CACCACCTCCTCTAAGCTTGG 60.066 57.143 9.86 6.29 0.00 3.61
1636 4911 0.107945 CAGCACCACCTCCTCTAAGC 60.108 60.000 0.00 0.00 0.00 3.09
1654 4929 0.106335 CCAAAACTTGCCCACATGCA 59.894 50.000 0.00 0.00 40.07 3.96
1655 4930 0.603439 CCCAAAACTTGCCCACATGC 60.603 55.000 0.00 0.00 0.00 4.06
1656 4931 1.047002 TCCCAAAACTTGCCCACATG 58.953 50.000 0.00 0.00 0.00 3.21
1657 4932 1.901833 GATCCCAAAACTTGCCCACAT 59.098 47.619 0.00 0.00 0.00 3.21
1693 4968 1.269448 CAACAACAACAAGATCCCCCG 59.731 52.381 0.00 0.00 0.00 5.73
1813 5097 6.205270 GCAGTACAATAGGAGTAGGAGTAGAC 59.795 46.154 0.00 0.00 0.00 2.59
1873 5160 7.441458 GGCGTCTCATTTCTTTACCTATACATT 59.559 37.037 0.00 0.00 0.00 2.71
1907 5194 7.766278 AGGAGCACAGAATAGTAGTTTATGTTG 59.234 37.037 0.00 0.00 0.00 3.33
1908 5195 7.852263 AGGAGCACAGAATAGTAGTTTATGTT 58.148 34.615 0.00 0.00 0.00 2.71
1911 5198 6.841755 AGGAGGAGCACAGAATAGTAGTTTAT 59.158 38.462 0.00 0.00 0.00 1.40
1912 5199 6.195700 AGGAGGAGCACAGAATAGTAGTTTA 58.804 40.000 0.00 0.00 0.00 2.01
1913 5200 5.026790 AGGAGGAGCACAGAATAGTAGTTT 58.973 41.667 0.00 0.00 0.00 2.66
1914 5201 4.615513 AGGAGGAGCACAGAATAGTAGTT 58.384 43.478 0.00 0.00 0.00 2.24
1916 5203 3.252215 CGAGGAGGAGCACAGAATAGTAG 59.748 52.174 0.00 0.00 0.00 2.57
1917 5204 3.118000 TCGAGGAGGAGCACAGAATAGTA 60.118 47.826 0.00 0.00 0.00 1.82
1918 5205 2.028130 CGAGGAGGAGCACAGAATAGT 58.972 52.381 0.00 0.00 0.00 2.12
1919 5206 2.302260 TCGAGGAGGAGCACAGAATAG 58.698 52.381 0.00 0.00 0.00 1.73
1920 5207 2.437085 TCGAGGAGGAGCACAGAATA 57.563 50.000 0.00 0.00 0.00 1.75
1921 5208 1.686052 GATCGAGGAGGAGCACAGAAT 59.314 52.381 0.00 0.00 0.00 2.40
1922 5209 1.107114 GATCGAGGAGGAGCACAGAA 58.893 55.000 0.00 0.00 0.00 3.02
1923 5210 0.257328 AGATCGAGGAGGAGCACAGA 59.743 55.000 0.00 0.00 0.00 3.41
1924 5211 1.110442 AAGATCGAGGAGGAGCACAG 58.890 55.000 0.00 0.00 0.00 3.66
1925 5212 0.820226 CAAGATCGAGGAGGAGCACA 59.180 55.000 0.00 0.00 0.00 4.57
1926 5213 0.820871 ACAAGATCGAGGAGGAGCAC 59.179 55.000 0.00 0.00 0.00 4.40
1928 5215 1.107114 TGACAAGATCGAGGAGGAGC 58.893 55.000 0.00 0.00 0.00 4.70
1985 5275 1.607756 TCCACTTGCGCCTCTCTCT 60.608 57.895 4.18 0.00 0.00 3.10
1986 5276 1.446966 GTCCACTTGCGCCTCTCTC 60.447 63.158 4.18 0.00 0.00 3.20
2023 5313 1.070134 CTTCGTCTTCCTCCACCACAA 59.930 52.381 0.00 0.00 0.00 3.33
2104 5398 1.115326 GCCATCCCCATTTACTGCCC 61.115 60.000 0.00 0.00 0.00 5.36
2123 5417 1.592669 GAGGATGCCATCACCGTCG 60.593 63.158 7.06 0.00 0.00 5.12
2211 5505 2.210711 GGAGATGGCGAGGTAGGGG 61.211 68.421 0.00 0.00 0.00 4.79
2212 5506 2.210711 GGGAGATGGCGAGGTAGGG 61.211 68.421 0.00 0.00 0.00 3.53
2213 5507 1.152440 AGGGAGATGGCGAGGTAGG 60.152 63.158 0.00 0.00 0.00 3.18
2214 5508 0.468214 TGAGGGAGATGGCGAGGTAG 60.468 60.000 0.00 0.00 0.00 3.18
2215 5509 0.755698 GTGAGGGAGATGGCGAGGTA 60.756 60.000 0.00 0.00 0.00 3.08
2216 5510 2.060980 GTGAGGGAGATGGCGAGGT 61.061 63.158 0.00 0.00 0.00 3.85
2217 5511 2.801631 GGTGAGGGAGATGGCGAGG 61.802 68.421 0.00 0.00 0.00 4.63
2218 5512 2.801631 GGGTGAGGGAGATGGCGAG 61.802 68.421 0.00 0.00 0.00 5.03
2219 5513 2.764128 GGGTGAGGGAGATGGCGA 60.764 66.667 0.00 0.00 0.00 5.54
2220 5514 2.765807 AGGGTGAGGGAGATGGCG 60.766 66.667 0.00 0.00 0.00 5.69
2221 5515 1.690633 TGAGGGTGAGGGAGATGGC 60.691 63.158 0.00 0.00 0.00 4.40
2222 5516 1.694133 GCTGAGGGTGAGGGAGATGG 61.694 65.000 0.00 0.00 0.00 3.51
2223 5517 0.690411 AGCTGAGGGTGAGGGAGATG 60.690 60.000 0.00 0.00 0.00 2.90
2224 5518 0.043940 AAGCTGAGGGTGAGGGAGAT 59.956 55.000 0.00 0.00 0.00 2.75
2244 5548 0.459489 TTTGTGTGTTTGCTGGCTCC 59.541 50.000 0.00 0.00 0.00 4.70
2247 5551 1.751536 GCGTTTGTGTGTTTGCTGGC 61.752 55.000 0.00 0.00 0.00 4.85
2248 5552 0.457509 TGCGTTTGTGTGTTTGCTGG 60.458 50.000 0.00 0.00 0.00 4.85
2249 5553 1.344458 TTGCGTTTGTGTGTTTGCTG 58.656 45.000 0.00 0.00 0.00 4.41
2252 5556 3.426859 TCTGTTTTGCGTTTGTGTGTTTG 59.573 39.130 0.00 0.00 0.00 2.93
2276 5827 1.278238 GTGCGTATTTCTCTGGGTCG 58.722 55.000 0.00 0.00 0.00 4.79
2296 5847 3.052082 ACTCATGGCTGCGTGTGC 61.052 61.111 0.00 0.00 43.20 4.57
2297 5848 2.865308 CACTCATGGCTGCGTGTG 59.135 61.111 0.00 0.00 34.19 3.82
2298 5849 3.052082 GCACTCATGGCTGCGTGT 61.052 61.111 6.51 0.00 39.70 4.49
2319 5873 0.902531 TACTGCTCCTACCACCAAGC 59.097 55.000 0.00 0.00 35.31 4.01
2334 5888 0.752009 TCAGGGCGTCCTAGCTACTG 60.752 60.000 9.07 0.00 42.67 2.74
2349 5903 4.247380 GGCCGGCCTCAGATCAGG 62.247 72.222 38.76 0.00 36.50 3.86
2372 5926 2.794631 CGGGATTAAAAACTGCATCGGC 60.795 50.000 0.00 0.00 41.68 5.54
2373 5927 2.422127 ACGGGATTAAAAACTGCATCGG 59.578 45.455 0.00 0.00 0.00 4.18
2374 5928 3.119990 ACACGGGATTAAAAACTGCATCG 60.120 43.478 0.00 0.00 0.00 3.84
2375 5929 4.165779 CACACGGGATTAAAAACTGCATC 58.834 43.478 0.00 0.00 0.00 3.91
2390 5944 2.666190 CCACTGACTGCACACGGG 60.666 66.667 0.00 0.00 0.00 5.28
2391 5945 1.665916 CTCCACTGACTGCACACGG 60.666 63.158 0.00 0.00 0.00 4.94
2422 5986 3.935818 TTCCCGGCTATTAACAATGGA 57.064 42.857 0.00 0.00 0.00 3.41
2441 6005 1.652563 GCTCGAACAGCCCGTTTTT 59.347 52.632 0.00 0.00 43.17 1.94
2446 6010 4.124351 TACCGCTCGAACAGCCCG 62.124 66.667 0.00 0.00 46.74 6.13
2450 6014 0.656259 TCGATCTACCGCTCGAACAG 59.344 55.000 0.00 0.00 40.64 3.16
2452 6016 1.263484 TGATCGATCTACCGCTCGAAC 59.737 52.381 25.02 0.00 45.90 3.95
2453 6017 1.589803 TGATCGATCTACCGCTCGAA 58.410 50.000 25.02 0.00 45.90 3.71
2454 6018 1.263484 GTTGATCGATCTACCGCTCGA 59.737 52.381 24.00 0.85 46.71 4.04
2455 6019 1.002792 TGTTGATCGATCTACCGCTCG 60.003 52.381 28.88 0.00 32.71 5.03
2483 6047 3.259123 ACTGTTTGATGCTTTGATTCCCC 59.741 43.478 0.00 0.00 0.00 4.81
2538 6102 1.972660 AAGGAGCGGCATGGAGTACC 61.973 60.000 1.45 0.00 0.00 3.34
2540 6104 0.178068 GAAAGGAGCGGCATGGAGTA 59.822 55.000 1.45 0.00 0.00 2.59
2542 6106 2.176273 CGAAAGGAGCGGCATGGAG 61.176 63.158 1.45 0.00 0.00 3.86
2543 6107 2.125147 CGAAAGGAGCGGCATGGA 60.125 61.111 1.45 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.