Multiple sequence alignment - TraesCS5A01G135900

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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 TraesCS5A01G135900 chr5A 100.000 4152 0 0 1 4152 307204641 307208792 0.000000e+00 7668.0
1 TraesCS5A01G135900 chr5A 88.344 163 19 0 2985 3147 307207517 307207679 3.270000e-46 196.0
2 TraesCS5A01G135900 chr5A 88.344 163 19 0 2877 3039 307207625 307207787 3.270000e-46 196.0
3 TraesCS5A01G135900 chr5A 81.731 208 31 3 465 665 575592842 575593049 2.570000e-37 167.0
4 TraesCS5A01G135900 chr5A 90.654 107 8 2 3042 3147 307207520 307207625 1.560000e-29 141.0
5 TraesCS5A01G135900 chr5A 90.654 107 8 2 2880 2985 307207682 307207787 1.560000e-29 141.0
6 TraesCS5A01G135900 chr5A 100.000 34 0 0 1333 1366 307205865 307205898 3.470000e-06 63.9
7 TraesCS5A01G135900 chr5A 100.000 34 0 0 1225 1258 307205973 307206006 3.470000e-06 63.9
8 TraesCS5A01G135900 chr5A 96.970 33 1 0 388 420 275259663 275259631 5.800000e-04 56.5
9 TraesCS5A01G135900 chr5B 90.211 3228 144 53 1 3147 254492614 254495750 0.000000e+00 4052.0
10 TraesCS5A01G135900 chr5B 90.994 1288 86 16 2877 4152 254495588 254496857 0.000000e+00 1709.0
11 TraesCS5A01G135900 chr5B 89.513 267 28 0 2880 3146 254495537 254495803 5.140000e-89 339.0
12 TraesCS5A01G135900 chr5B 90.187 214 21 0 2880 3093 254495645 254495858 3.160000e-71 279.0
13 TraesCS5A01G135900 chr5B 81.017 295 33 10 394 676 594738530 594738247 3.250000e-51 213.0
14 TraesCS5A01G135900 chr5B 89.571 163 17 0 2985 3147 254495480 254495642 1.510000e-49 207.0
15 TraesCS5A01G135900 chr5B 88.785 107 12 0 3041 3147 254495482 254495588 9.370000e-27 132.0
16 TraesCS5A01G135900 chr5B 87.671 73 2 5 1258 1325 254493987 254494057 1.240000e-10 78.7
17 TraesCS5A01G135900 chr5B 100.000 34 0 0 1333 1366 254493781 254493814 3.470000e-06 63.9
18 TraesCS5A01G135900 chr5B 100.000 34 0 0 1225 1258 254493889 254493922 3.470000e-06 63.9
19 TraesCS5A01G135900 chr5D 93.363 1552 74 10 1468 2991 228551668 228553218 0.000000e+00 2268.0
20 TraesCS5A01G135900 chr5D 91.837 637 48 4 3041 3676 228553106 228553739 0.000000e+00 885.0
21 TraesCS5A01G135900 chr5D 92.164 587 20 9 677 1257 228551050 228551616 0.000000e+00 806.0
22 TraesCS5A01G135900 chr5D 94.748 457 21 3 3698 4152 228553734 228554189 0.000000e+00 708.0
23 TraesCS5A01G135900 chr5D 80.810 667 57 26 24 677 228550404 228551012 1.360000e-124 457.0
24 TraesCS5A01G135900 chr5D 86.869 99 12 1 413 510 256412712 256412614 4.390000e-20 110.0
25 TraesCS5A01G135900 chr5D 96.610 59 2 0 1335 1393 228551586 228551644 9.500000e-17 99.0
26 TraesCS5A01G135900 chr4A 82.520 246 36 3 433 672 170422042 170421798 4.210000e-50 209.0
27 TraesCS5A01G135900 chr4A 88.462 78 7 2 3592 3668 601184826 601184902 4.420000e-15 93.5
28 TraesCS5A01G135900 chr4A 91.935 62 5 0 3608 3669 363081160 363081221 2.060000e-13 87.9
29 TraesCS5A01G135900 chr4A 83.158 95 10 6 3586 3678 485464433 485464343 9.570000e-12 82.4
30 TraesCS5A01G135900 chr4A 100.000 28 0 0 393 420 726350626 726350653 8.000000e-03 52.8
31 TraesCS5A01G135900 chr3A 83.628 226 30 3 437 655 589390483 589390258 5.440000e-49 206.0
32 TraesCS5A01G135900 chr6D 79.401 267 38 9 417 672 71025022 71025282 5.520000e-39 172.0
33 TraesCS5A01G135900 chr6D 83.721 86 10 3 3592 3676 429012227 429012145 1.240000e-10 78.7
34 TraesCS5A01G135900 chr4B 77.922 308 37 9 394 671 494690255 494689949 3.320000e-36 163.0
35 TraesCS5A01G135900 chr4B 87.129 101 11 2 412 511 44366999 44367098 3.390000e-21 113.0
36 TraesCS5A01G135900 chr4B 84.314 102 12 4 412 511 625960560 625960461 3.420000e-16 97.1
37 TraesCS5A01G135900 chr4B 91.935 62 5 0 3608 3669 232097808 232097869 2.060000e-13 87.9
38 TraesCS5A01G135900 chr4B 88.732 71 5 2 3610 3678 551684756 551684687 2.660000e-12 84.2
39 TraesCS5A01G135900 chr4B 89.552 67 5 1 3608 3672 551744966 551744900 2.660000e-12 84.2
40 TraesCS5A01G135900 chr1B 77.850 307 36 14 395 670 684003045 684002740 1.190000e-35 161.0
41 TraesCS5A01G135900 chr7A 79.556 225 40 3 437 655 669397359 669397135 5.560000e-34 156.0
42 TraesCS5A01G135900 chr1A 82.707 133 15 6 412 542 385670188 385670062 1.220000e-20 111.0
43 TraesCS5A01G135900 chrUn 83.200 125 13 4 413 530 3241676 3241799 1.580000e-19 108.0
44 TraesCS5A01G135900 chrUn 79.646 113 23 0 2 114 314914383 314914271 9.570000e-12 82.4
45 TraesCS5A01G135900 chrUn 80.000 110 22 0 2 111 350107087 350107196 9.570000e-12 82.4
46 TraesCS5A01G135900 chr2D 100.000 29 0 0 392 420 502525583 502525555 2.000000e-03 54.7
47 TraesCS5A01G135900 chr4D 100.000 28 0 0 393 420 25590056 25590029 8.000000e-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 TraesCS5A01G135900 chr5A 307204641 307208792 4151 False 1209.971429 7668 93.999429 1 4152 7 chr5A.!!$F2 4151
1 TraesCS5A01G135900 chr5B 254492614 254496857 4243 False 769.388889 4052 91.881333 1 4152 9 chr5B.!!$F1 4151
2 TraesCS5A01G135900 chr5D 228550404 228554189 3785 False 870.500000 2268 91.588667 24 4152 6 chr5D.!!$F1 4128

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
690 724 0.102120 TTTGCGGAAACACCAAGCAG 59.898 50.0 0.00 0.00 36.63 4.24 F
1860 2023 0.531753 TACAGCAGAAGTTGTGCGCA 60.532 50.0 18.26 5.66 46.06 6.09 F
2065 2247 0.100146 GCAAGTGCTGCCTATGCTTC 59.900 55.0 11.73 0.00 46.13 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2230 0.622665 AGGAAGCATAGGCAGCACTT 59.377 50.0 0.67 0.0 44.61 3.16 R
2901 3102 0.031616 CTCCCCTTCCTCTGGTAGCT 60.032 60.0 0.00 0.0 0.00 3.32 R
3319 3628 0.102300 AACAAGTTCGGGCAACAAGC 59.898 50.0 0.00 0.0 44.65 4.01 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
49 50 9.916397 GTACAACAAGTTAAGCATATACACATC 57.084 33.333 0.00 0.00 0.00 3.06
140 141 3.117663 ACCTAAGCTTCAAGGGTGTCAAA 60.118 43.478 17.71 0.00 37.18 2.69
158 159 6.761714 GTGTCAAATTCATCTTACCCGTAGAT 59.238 38.462 0.00 0.00 0.00 1.98
237 239 4.287720 CGCCTTTCCAAAGTAAAACTCAC 58.712 43.478 0.00 0.00 34.20 3.51
245 247 9.505995 TTTCCAAAGTAAAACTCACGATTAAAC 57.494 29.630 0.00 0.00 0.00 2.01
423 436 4.986708 GGGCAGCCCGACCCAAAA 62.987 66.667 17.05 0.00 46.22 2.44
424 437 2.915137 GGCAGCCCGACCCAAAAA 60.915 61.111 0.00 0.00 0.00 1.94
486 508 3.154589 GGGTCTAGGTTTTGAGCCG 57.845 57.895 0.00 0.00 40.36 5.52
530 553 1.786579 GCTGTTTTTGCGCTTTACTGG 59.213 47.619 9.73 0.00 0.00 4.00
532 555 3.701241 CTGTTTTTGCGCTTTACTGGAA 58.299 40.909 9.73 0.00 0.00 3.53
561 595 0.250597 GGACTTTTGTAGTGGCGGGT 60.251 55.000 0.00 0.00 37.17 5.28
584 618 2.979678 AGGCTTGGGTCTGAAAAGTAGA 59.020 45.455 0.00 0.00 0.00 2.59
592 626 2.227388 GTCTGAAAAGTAGACCCGACGA 59.773 50.000 0.00 0.00 38.85 4.20
677 711 1.686355 TGGCCAGGTATAATTTGCGG 58.314 50.000 0.00 0.00 0.00 5.69
678 712 1.213182 TGGCCAGGTATAATTTGCGGA 59.787 47.619 0.00 0.00 0.00 5.54
680 714 2.691011 GGCCAGGTATAATTTGCGGAAA 59.309 45.455 4.04 4.04 0.00 3.13
681 715 3.490249 GGCCAGGTATAATTTGCGGAAAC 60.490 47.826 3.52 0.00 0.00 2.78
682 716 3.129638 GCCAGGTATAATTTGCGGAAACA 59.870 43.478 3.52 0.00 0.00 2.83
683 717 4.668289 CCAGGTATAATTTGCGGAAACAC 58.332 43.478 3.52 0.68 0.00 3.32
684 718 4.439563 CCAGGTATAATTTGCGGAAACACC 60.440 45.833 3.52 9.84 0.00 4.16
685 719 4.156922 CAGGTATAATTTGCGGAAACACCA 59.843 41.667 19.34 2.95 38.90 4.17
686 720 4.767928 AGGTATAATTTGCGGAAACACCAA 59.232 37.500 19.34 1.81 38.90 3.67
687 721 5.099575 GGTATAATTTGCGGAAACACCAAG 58.900 41.667 3.52 0.00 38.90 3.61
688 722 1.864565 AATTTGCGGAAACACCAAGC 58.135 45.000 3.52 0.00 38.90 4.01
689 723 0.749649 ATTTGCGGAAACACCAAGCA 59.250 45.000 3.52 0.00 38.90 3.91
690 724 0.102120 TTTGCGGAAACACCAAGCAG 59.898 50.000 0.00 0.00 36.63 4.24
691 725 1.034838 TTGCGGAAACACCAAGCAGT 61.035 50.000 0.00 0.00 36.63 4.40
692 726 1.282875 GCGGAAACACCAAGCAGTC 59.717 57.895 0.00 0.00 38.90 3.51
693 727 1.949257 CGGAAACACCAAGCAGTCC 59.051 57.895 0.00 0.00 38.90 3.85
694 728 1.515521 CGGAAACACCAAGCAGTCCC 61.516 60.000 0.00 0.00 38.90 4.46
695 729 1.515521 GGAAACACCAAGCAGTCCCG 61.516 60.000 0.00 0.00 38.79 5.14
696 730 1.515521 GAAACACCAAGCAGTCCCGG 61.516 60.000 0.00 0.00 0.00 5.73
697 731 4.643387 ACACCAAGCAGTCCCGGC 62.643 66.667 0.00 0.00 0.00 6.13
706 740 4.824515 AGTCCCGGCCCGAGAGAG 62.825 72.222 3.71 0.00 0.00 3.20
707 741 4.816984 GTCCCGGCCCGAGAGAGA 62.817 72.222 3.71 0.00 0.00 3.10
722 814 2.817258 AGAGAGAAAGAGAGTCGTGGTG 59.183 50.000 0.00 0.00 0.00 4.17
842 941 1.153449 TCCATCCGCGTTCATCCAC 60.153 57.895 4.92 0.00 0.00 4.02
928 1031 3.181482 ACGAGGATGACTGTAATGCTCTG 60.181 47.826 20.41 16.42 39.57 3.35
1119 1227 3.388350 GTCGGTAATCCCCTCATTCTTCT 59.612 47.826 0.00 0.00 0.00 2.85
1192 1301 3.146847 CCGAGGATTAATTAAGCACCCC 58.853 50.000 14.91 5.76 0.00 4.95
1285 1394 2.230940 CGGCTACAGATTGCGACGG 61.231 63.158 0.00 0.00 0.00 4.79
1389 1499 7.344093 TGTCCTCATCTCTGAATCAGACTATTT 59.656 37.037 9.18 0.00 35.39 1.40
1433 1543 5.359009 GCCTTTTACCTAAATGGGGACTTAC 59.641 44.000 10.29 0.00 39.53 2.34
1457 1567 1.883084 CCGGCTACAGATTGCGACC 60.883 63.158 0.00 0.00 0.00 4.79
1460 1570 1.153628 GCTACAGATTGCGACCGGT 60.154 57.895 6.92 6.92 0.00 5.28
1570 1689 1.777101 CGAAGGATCGGCTCATTCTC 58.223 55.000 4.96 0.00 45.32 2.87
1575 1694 1.576356 GATCGGCTCATTCTCGCTTT 58.424 50.000 0.00 0.00 0.00 3.51
1645 1764 1.559368 CATGATTGGCCACCTTTCCA 58.441 50.000 3.88 0.00 0.00 3.53
1646 1765 1.479323 CATGATTGGCCACCTTTCCAG 59.521 52.381 3.88 0.00 33.32 3.86
1647 1766 0.899717 TGATTGGCCACCTTTCCAGC 60.900 55.000 3.88 0.00 33.32 4.85
1648 1767 1.937546 GATTGGCCACCTTTCCAGCG 61.938 60.000 3.88 0.00 33.32 5.18
1649 1768 4.659172 TGGCCACCTTTCCAGCGG 62.659 66.667 0.00 0.00 0.00 5.52
1652 1773 3.365265 CCACCTTTCCAGCGGCAC 61.365 66.667 1.45 0.00 0.00 5.01
1691 1822 3.202001 CGGGCGCGGATGTGAATT 61.202 61.111 16.41 0.00 0.00 2.17
1702 1833 3.549794 GGATGTGAATTCAGAAGGGGAG 58.450 50.000 8.80 0.00 0.00 4.30
1733 1865 6.411376 AGTTTTCGACACCATGGTAATCATA 58.589 36.000 19.28 6.66 34.12 2.15
1734 1866 6.315393 AGTTTTCGACACCATGGTAATCATAC 59.685 38.462 19.28 10.58 34.12 2.39
1784 1940 1.064463 GGCATCAAGGATCCCAGTGAA 60.064 52.381 8.55 0.00 0.00 3.18
1786 1942 2.356535 GCATCAAGGATCCCAGTGAAGT 60.357 50.000 8.55 0.00 0.00 3.01
1797 1953 1.146637 CAGTGAAGTGAGCACTCAGC 58.853 55.000 3.27 0.00 44.28 4.26
1843 2006 6.371548 TGGCAAGTTTTATGTGACTCAGATAC 59.628 38.462 0.00 0.00 0.00 2.24
1860 2023 0.531753 TACAGCAGAAGTTGTGCGCA 60.532 50.000 18.26 5.66 46.06 6.09
1907 2082 1.228956 TGCAAGCTTTGGCCATCCT 60.229 52.632 6.09 0.00 39.73 3.24
2013 2195 9.672673 GGGCTTTGAATAGCATCTTATAGATTA 57.327 33.333 0.00 0.00 43.02 1.75
2048 2230 3.787676 CCGCATTTCGCTCACGCA 61.788 61.111 0.00 0.00 39.84 5.24
2049 2231 2.173141 CGCATTTCGCTCACGCAA 59.827 55.556 0.00 0.00 39.84 4.85
2065 2247 0.100146 GCAAGTGCTGCCTATGCTTC 59.900 55.000 11.73 0.00 46.13 3.86
2117 2315 3.435327 TGCAATACTTGTTCGTGATGTCC 59.565 43.478 0.00 0.00 0.00 4.02
2118 2316 3.684788 GCAATACTTGTTCGTGATGTCCT 59.315 43.478 0.00 0.00 0.00 3.85
2119 2317 4.201724 GCAATACTTGTTCGTGATGTCCTC 60.202 45.833 0.00 0.00 0.00 3.71
2120 2318 5.171476 CAATACTTGTTCGTGATGTCCTCT 58.829 41.667 0.00 0.00 0.00 3.69
2121 2319 3.753294 ACTTGTTCGTGATGTCCTCTT 57.247 42.857 0.00 0.00 0.00 2.85
2122 2320 3.393800 ACTTGTTCGTGATGTCCTCTTG 58.606 45.455 0.00 0.00 0.00 3.02
2123 2321 3.069586 ACTTGTTCGTGATGTCCTCTTGA 59.930 43.478 0.00 0.00 0.00 3.02
2124 2322 3.026630 TGTTCGTGATGTCCTCTTGAC 57.973 47.619 0.00 0.00 44.72 3.18
2125 2323 2.628178 TGTTCGTGATGTCCTCTTGACT 59.372 45.455 0.00 0.00 44.75 3.41
2126 2324 3.069586 TGTTCGTGATGTCCTCTTGACTT 59.930 43.478 0.00 0.00 44.75 3.01
2127 2325 3.303881 TCGTGATGTCCTCTTGACTTG 57.696 47.619 0.00 0.00 44.75 3.16
2128 2326 2.628178 TCGTGATGTCCTCTTGACTTGT 59.372 45.455 0.00 0.00 44.75 3.16
2129 2327 3.069586 TCGTGATGTCCTCTTGACTTGTT 59.930 43.478 0.00 0.00 44.75 2.83
2130 2328 3.809832 CGTGATGTCCTCTTGACTTGTTT 59.190 43.478 0.00 0.00 44.75 2.83
2131 2329 4.319046 CGTGATGTCCTCTTGACTTGTTTG 60.319 45.833 0.00 0.00 44.75 2.93
2132 2330 3.565482 TGATGTCCTCTTGACTTGTTTGC 59.435 43.478 0.00 0.00 44.75 3.68
2161 2359 6.788243 ACACATGTGCTAATATGTTGTCATG 58.212 36.000 25.68 0.00 36.11 3.07
2162 2360 6.375174 ACACATGTGCTAATATGTTGTCATGT 59.625 34.615 25.68 0.00 43.08 3.21
2230 2431 2.653234 ATGCTGGAGATGGAATGGTC 57.347 50.000 0.00 0.00 0.00 4.02
2250 2451 2.167693 TCATCCATTTTACGAGAGCGGT 59.832 45.455 0.00 0.00 43.17 5.68
2599 2800 3.181490 ACTTCGCGATATACTGCAAGACA 60.181 43.478 10.88 0.00 37.43 3.41
2866 3067 2.203549 CTCTTCCTCAAGGGGCCACC 62.204 65.000 0.00 0.57 40.67 4.61
2895 3096 1.228367 CTGCAACACCAGGAGGCTT 60.228 57.895 0.00 0.00 39.06 4.35
2899 3100 2.464403 AACACCAGGAGGCTTGCCT 61.464 57.895 14.69 14.69 39.06 4.75
2910 3111 1.599047 GCTTGCCTGAGCTACCAGA 59.401 57.895 4.03 0.00 39.57 3.86
2931 3132 1.819288 GGAAGGGGAGCTTGCTAAAAC 59.181 52.381 0.00 0.00 0.00 2.43
2971 3172 0.905357 TGGAGCTACCAGGAGAAAGC 59.095 55.000 0.00 0.00 44.64 3.51
2994 3195 1.269051 GCTTGCTAAAACGGCAACACT 60.269 47.619 0.00 0.00 43.50 3.55
2995 3196 2.031508 GCTTGCTAAAACGGCAACACTA 60.032 45.455 0.00 0.00 43.50 2.74
3006 3207 1.517257 CAACACTAGGAGGCTCGCG 60.517 63.158 8.69 0.00 0.00 5.87
3025 3226 2.747443 GGAGCTACCAGGGGAAGGC 61.747 68.421 0.00 0.00 38.79 4.35
3058 3259 2.270986 GGCAACACCAGGAGGCTTG 61.271 63.158 0.00 0.00 39.06 4.01
3071 3272 2.046314 GCTTGCCGGAGCTACCAA 60.046 61.111 5.05 0.00 39.57 3.67
3077 3278 1.988015 CCGGAGCTACCAAGGGAAA 59.012 57.895 0.00 0.00 38.90 3.13
3079 3280 0.744771 CGGAGCTACCAAGGGAAAGC 60.745 60.000 0.00 6.35 38.90 3.51
3149 3458 3.612795 AAGGGGGACTTGCTAAAAAGT 57.387 42.857 0.00 0.00 43.08 2.66
3183 3492 1.065358 CTGCGGTATTGTCGTTCGTT 58.935 50.000 0.00 0.00 0.00 3.85
3223 3532 3.939740 TGCTGCTCAATTCCCTTATCT 57.060 42.857 0.00 0.00 0.00 1.98
3248 3557 2.253603 GTTCCACGCAATTCTTCATGC 58.746 47.619 0.00 0.00 39.17 4.06
3286 3595 0.905357 AAGAGGTTGGTCGATCTGGG 59.095 55.000 0.00 0.00 0.00 4.45
3319 3628 9.455847 GATTTGCTGCTTAATCCACTTATTAAG 57.544 33.333 13.52 10.57 45.84 1.85
3329 3638 3.761752 TCCACTTATTAAGCTTGTTGCCC 59.238 43.478 9.86 0.00 44.23 5.36
3334 3643 1.975660 TTAAGCTTGTTGCCCGAACT 58.024 45.000 9.86 0.00 44.23 3.01
3352 3661 7.544217 GCCCGAACTTGTTCATGTAAATTAATT 59.456 33.333 13.05 0.00 0.00 1.40
3375 3684 7.672983 TTTACCTCTGAAAGAAGTAGCAATG 57.327 36.000 0.00 0.00 46.34 2.82
3377 3686 3.063180 CCTCTGAAAGAAGTAGCAATGCG 59.937 47.826 0.00 0.00 46.34 4.73
3380 3689 2.742053 TGAAAGAAGTAGCAATGCGTCC 59.258 45.455 0.00 0.00 0.00 4.79
3385 3694 2.185004 AGTAGCAATGCGTCCACTTT 57.815 45.000 0.00 0.00 0.00 2.66
3395 3704 1.535462 GCGTCCACTTTGCTTGTATGT 59.465 47.619 0.00 0.00 0.00 2.29
3415 3724 9.051679 TGTATGTAATGTTATGATGTAAGGTGC 57.948 33.333 0.00 0.00 0.00 5.01
3416 3725 9.051679 GTATGTAATGTTATGATGTAAGGTGCA 57.948 33.333 0.00 0.00 0.00 4.57
3537 3846 1.913419 TCCCCTTCCACAAGTATCCAC 59.087 52.381 0.00 0.00 0.00 4.02
3606 3915 2.586258 ATCACCTCTGTTCCGAATCG 57.414 50.000 0.00 0.00 0.00 3.34
3679 3988 1.271102 ACAAGCACACCAAACACGTTT 59.729 42.857 0.00 0.00 0.00 3.60
3686 3995 4.693155 CACACCAAACACGTTTTTCAAAC 58.307 39.130 0.00 0.00 0.00 2.93
3689 3998 5.293569 ACACCAAACACGTTTTTCAAACAAA 59.706 32.000 0.00 0.00 0.00 2.83
3691 4000 6.687105 CACCAAACACGTTTTTCAAACAAAAA 59.313 30.769 0.00 0.00 0.00 1.94
3742 4052 9.520204 TGATTCAGAAAAAGTTTTGAACATCTC 57.480 29.630 0.61 0.00 39.78 2.75
3754 4064 8.960591 AGTTTTGAACATCTCATAATTCGGAAT 58.039 29.630 0.00 0.00 32.78 3.01
3758 4068 7.053498 TGAACATCTCATAATTCGGAATGGAA 58.947 34.615 3.59 0.00 0.00 3.53
3821 4132 3.328343 TCCTTCCCCAACTTGTCGAATAA 59.672 43.478 0.00 0.00 0.00 1.40
3852 4163 5.189928 TGTCCTTTCTCAGTTGCAGTTTTA 58.810 37.500 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.025480 AGTGTTTAACAACTAAAGTCCGCG 60.025 41.667 0.00 0.00 33.58 6.46
140 141 8.968969 GGTCTATTATCTACGGGTAAGATGAAT 58.031 37.037 0.00 0.00 0.00 2.57
158 159 1.227147 GCGCCGCACAGGTCTATTA 60.227 57.895 3.15 0.00 43.70 0.98
237 239 8.868744 TGACTTTGCTAAAATACGTTTAATCG 57.131 30.769 0.00 4.42 31.22 3.34
245 247 6.077838 GTCAACCTGACTTTGCTAAAATACG 58.922 40.000 0.00 0.00 43.73 3.06
358 363 8.184192 CACCTTTTCATTCATACGCTTCTTTAT 58.816 33.333 0.00 0.00 0.00 1.40
459 472 0.691413 AACCTAGACCCAGGCCTAGC 60.691 60.000 3.98 0.00 39.53 3.42
461 483 1.913419 CAAAACCTAGACCCAGGCCTA 59.087 52.381 3.98 0.00 39.53 3.93
462 484 0.698818 CAAAACCTAGACCCAGGCCT 59.301 55.000 0.00 0.00 39.53 5.19
471 493 1.975680 ACCTTCGGCTCAAAACCTAGA 59.024 47.619 0.00 0.00 0.00 2.43
503 526 3.922640 GCAAAAACAGCGGGCCCA 61.923 61.111 24.92 0.00 0.00 5.36
530 553 4.717313 AAGTCCGCCGGGCCTTTC 62.717 66.667 14.55 1.75 0.00 2.62
532 555 4.280019 AAAAGTCCGCCGGGCCTT 62.280 61.111 14.55 8.34 0.00 4.35
561 595 1.494721 ACTTTTCAGACCCAAGCCTGA 59.505 47.619 0.00 0.00 37.61 3.86
572 606 2.227388 GTCGTCGGGTCTACTTTTCAGA 59.773 50.000 0.00 0.00 0.00 3.27
605 639 0.606673 GAAAACTCAGGCCCGAGCTT 60.607 55.000 16.28 7.38 39.73 3.74
606 640 1.003233 GAAAACTCAGGCCCGAGCT 60.003 57.895 16.28 0.05 39.73 4.09
677 711 1.515521 CCGGGACTGCTTGGTGTTTC 61.516 60.000 0.00 0.00 0.00 2.78
678 712 1.528309 CCGGGACTGCTTGGTGTTT 60.528 57.895 0.00 0.00 0.00 2.83
680 714 4.643387 GCCGGGACTGCTTGGTGT 62.643 66.667 2.18 0.00 35.10 4.16
689 723 4.824515 CTCTCTCGGGCCGGGACT 62.825 72.222 27.67 0.00 31.17 3.85
690 724 4.816984 TCTCTCTCGGGCCGGGAC 62.817 72.222 27.67 0.00 31.17 4.46
691 725 3.595428 TTTCTCTCTCGGGCCGGGA 62.595 63.158 29.35 29.35 34.26 5.14
692 726 3.075005 TTTCTCTCTCGGGCCGGG 61.075 66.667 27.98 25.48 0.00 5.73
693 727 2.010582 CTCTTTCTCTCTCGGGCCGG 62.011 65.000 27.98 17.02 0.00 6.13
694 728 1.032657 TCTCTTTCTCTCTCGGGCCG 61.033 60.000 22.51 22.51 0.00 6.13
695 729 0.744281 CTCTCTTTCTCTCTCGGGCC 59.256 60.000 0.00 0.00 0.00 5.80
696 730 1.404035 GACTCTCTTTCTCTCTCGGGC 59.596 57.143 0.00 0.00 0.00 6.13
697 731 1.668751 CGACTCTCTTTCTCTCTCGGG 59.331 57.143 0.00 0.00 0.00 5.14
698 732 2.095213 CACGACTCTCTTTCTCTCTCGG 59.905 54.545 0.00 0.00 0.00 4.63
699 733 2.095213 CCACGACTCTCTTTCTCTCTCG 59.905 54.545 0.00 0.00 0.00 4.04
700 734 3.078837 ACCACGACTCTCTTTCTCTCTC 58.921 50.000 0.00 0.00 0.00 3.20
701 735 2.817258 CACCACGACTCTCTTTCTCTCT 59.183 50.000 0.00 0.00 0.00 3.10
702 736 2.094957 CCACCACGACTCTCTTTCTCTC 60.095 54.545 0.00 0.00 0.00 3.20
703 737 1.889829 CCACCACGACTCTCTTTCTCT 59.110 52.381 0.00 0.00 0.00 3.10
704 738 1.614413 ACCACCACGACTCTCTTTCTC 59.386 52.381 0.00 0.00 0.00 2.87
705 739 1.614413 GACCACCACGACTCTCTTTCT 59.386 52.381 0.00 0.00 0.00 2.52
706 740 1.666311 CGACCACCACGACTCTCTTTC 60.666 57.143 0.00 0.00 0.00 2.62
707 741 0.314302 CGACCACCACGACTCTCTTT 59.686 55.000 0.00 0.00 0.00 2.52
898 1001 2.092291 GTCATCCTCGTCGCGCAAA 61.092 57.895 8.75 0.00 0.00 3.68
928 1031 4.554036 GCAGAGATCACCGGGGCC 62.554 72.222 6.32 0.00 0.00 5.80
1192 1301 0.304705 GCGTGAGATTAATGGTGGCG 59.695 55.000 0.00 0.00 0.00 5.69
1400 1510 5.385509 TTTAGGTAAAAGGCATTGCAGAC 57.614 39.130 11.39 0.52 0.00 3.51
1433 1543 0.096976 CAATCTGTAGCCGGCAAACG 59.903 55.000 31.54 20.16 43.80 3.60
1628 1747 0.899717 GCTGGAAAGGTGGCCAATCA 60.900 55.000 7.24 0.00 32.95 2.57
1652 1773 2.981909 CAGTGGTGCTGGTGCTGG 60.982 66.667 0.00 0.00 41.42 4.85
1686 1817 1.988107 AGTGCTCCCCTTCTGAATTCA 59.012 47.619 8.12 8.12 0.00 2.57
1691 1822 0.979665 CTCAAGTGCTCCCCTTCTGA 59.020 55.000 0.00 0.00 0.00 3.27
1702 1833 1.668751 TGGTGTCGAAAACTCAAGTGC 59.331 47.619 0.00 0.00 0.00 4.40
1733 1865 0.636101 AGCAGAGGAGATCCCAGAGT 59.364 55.000 0.00 0.00 37.41 3.24
1734 1866 2.673775 TAGCAGAGGAGATCCCAGAG 57.326 55.000 0.00 0.00 37.41 3.35
1843 2006 0.728129 CATGCGCACAACTTCTGCTG 60.728 55.000 14.90 0.00 32.03 4.41
1860 2023 7.362056 CGATTCTTAACCAGATTGAACAACCAT 60.362 37.037 0.00 0.00 0.00 3.55
1907 2082 6.858993 GTCGAAAGCCAAATTACAAATGTACA 59.141 34.615 0.00 0.00 0.00 2.90
1972 2154 5.876357 TCAAAGCCCACTAGTCTAACAAAT 58.124 37.500 0.00 0.00 0.00 2.32
2013 2195 3.118261 TGCGGCTTGAGAAGGAAGATATT 60.118 43.478 0.00 0.00 0.00 1.28
2048 2230 0.622665 AGGAAGCATAGGCAGCACTT 59.377 50.000 0.67 0.00 44.61 3.16
2049 2231 1.415659 CTAGGAAGCATAGGCAGCACT 59.584 52.381 0.67 0.00 44.61 4.40
2065 2247 2.032894 CGTATGCATGGCGAAAACTAGG 60.033 50.000 10.16 0.00 0.00 3.02
2117 2315 5.163764 TGTGTACAAGCAAACAAGTCAAGAG 60.164 40.000 0.00 0.00 0.00 2.85
2118 2316 4.697828 TGTGTACAAGCAAACAAGTCAAGA 59.302 37.500 0.00 0.00 0.00 3.02
2119 2317 4.980590 TGTGTACAAGCAAACAAGTCAAG 58.019 39.130 0.00 0.00 0.00 3.02
2120 2318 5.105957 ACATGTGTACAAGCAAACAAGTCAA 60.106 36.000 0.00 0.00 0.00 3.18
2121 2319 4.397730 ACATGTGTACAAGCAAACAAGTCA 59.602 37.500 0.00 0.00 0.00 3.41
2122 2320 4.734854 CACATGTGTACAAGCAAACAAGTC 59.265 41.667 18.03 0.00 0.00 3.01
2123 2321 4.671377 CACATGTGTACAAGCAAACAAGT 58.329 39.130 18.03 0.00 0.00 3.16
2124 2322 3.486841 GCACATGTGTACAAGCAAACAAG 59.513 43.478 26.01 0.00 0.00 3.16
2125 2323 3.130164 AGCACATGTGTACAAGCAAACAA 59.870 39.130 26.01 0.00 0.00 2.83
2126 2324 2.687425 AGCACATGTGTACAAGCAAACA 59.313 40.909 26.01 0.00 0.00 2.83
2127 2325 3.354089 AGCACATGTGTACAAGCAAAC 57.646 42.857 26.01 6.22 0.00 2.93
2128 2326 5.703978 ATTAGCACATGTGTACAAGCAAA 57.296 34.783 26.01 9.88 0.00 3.68
2129 2327 6.374053 ACATATTAGCACATGTGTACAAGCAA 59.626 34.615 26.01 10.51 34.15 3.91
2130 2328 5.879777 ACATATTAGCACATGTGTACAAGCA 59.120 36.000 26.01 10.46 34.15 3.91
2131 2329 6.363577 ACATATTAGCACATGTGTACAAGC 57.636 37.500 26.01 11.38 34.15 4.01
2132 2330 7.751732 ACAACATATTAGCACATGTGTACAAG 58.248 34.615 26.01 12.97 35.59 3.16
2191 2392 7.179694 CCAGCATATATCCCTGAAAAATGGAAT 59.820 37.037 10.21 0.00 0.00 3.01
2230 2431 2.550978 ACCGCTCTCGTAAAATGGATG 58.449 47.619 0.00 0.00 0.00 3.51
2250 2451 3.164268 CCTGTCCCAATTTCATGTCCAA 58.836 45.455 0.00 0.00 0.00 3.53
2458 2659 2.758770 TAGTGCACGTTCCTCCACGC 62.759 60.000 12.01 0.00 44.37 5.34
2484 2685 2.570706 GCTGAGCAGCGTCAGAGA 59.429 61.111 20.03 0.00 46.02 3.10
2599 2800 1.376683 AGTCTCGACGAGCAGCTCT 60.377 57.895 20.11 7.43 36.20 4.09
2665 2866 1.166531 AAGAAGCCACCGCACTGAAC 61.167 55.000 0.00 0.00 37.52 3.18
2866 3067 2.743928 GTTGCAGTCTCCGCCTGG 60.744 66.667 0.00 0.00 0.00 4.45
2878 3079 1.529010 CAAGCCTCCTGGTGTTGCA 60.529 57.895 0.00 0.00 35.27 4.08
2895 3096 0.252239 TTCCTCTGGTAGCTCAGGCA 60.252 55.000 0.00 0.00 41.70 4.75
2899 3100 0.325671 CCCCTTCCTCTGGTAGCTCA 60.326 60.000 0.00 0.00 0.00 4.26
2900 3101 0.032017 TCCCCTTCCTCTGGTAGCTC 60.032 60.000 0.00 0.00 0.00 4.09
2901 3102 0.031616 CTCCCCTTCCTCTGGTAGCT 60.032 60.000 0.00 0.00 0.00 3.32
2910 3111 1.372501 TTTAGCAAGCTCCCCTTCCT 58.627 50.000 0.00 0.00 0.00 3.36
2931 3132 4.335647 AGCCTCCTGGTGTTGCCG 62.336 66.667 0.00 0.00 41.21 5.69
2965 3166 2.096218 CGTTTTAGCAAGCTCGCTTTCT 60.096 45.455 3.51 8.71 43.56 2.52
2969 3170 1.912371 GCCGTTTTAGCAAGCTCGCT 61.912 55.000 3.76 3.76 46.26 4.93
2971 3172 0.237235 TTGCCGTTTTAGCAAGCTCG 59.763 50.000 0.00 0.00 44.95 5.03
3006 3207 2.073101 CCTTCCCCTGGTAGCTCCC 61.073 68.421 0.00 0.00 34.77 4.30
3025 3226 2.634982 TTGCCATTTTAGCAAGCTCG 57.365 45.000 0.00 0.00 44.95 5.03
3058 3259 2.193087 TTTCCCTTGGTAGCTCCGGC 62.193 60.000 0.00 0.00 39.52 6.13
3071 3272 0.324943 TTAGCAAGCTCGCTTTCCCT 59.675 50.000 3.51 2.09 43.56 4.20
3077 3278 1.912371 GCCGTTTTAGCAAGCTCGCT 61.912 55.000 3.76 3.76 46.26 4.93
3079 3280 0.237235 TTGCCGTTTTAGCAAGCTCG 59.763 50.000 0.00 0.00 44.95 5.03
3128 3437 3.923648 ACTTTTTAGCAAGTCCCCCTTT 58.076 40.909 0.00 0.00 30.76 3.11
3149 3458 7.334921 ACAATACCGCAGCTAAATAACACTTTA 59.665 33.333 0.00 0.00 0.00 1.85
3183 3492 3.306225 GCAATCCTCACAAAGCCAAATCA 60.306 43.478 0.00 0.00 0.00 2.57
3286 3595 3.536158 TTAAGCAGCAAATCGTCACAC 57.464 42.857 0.00 0.00 0.00 3.82
3319 3628 0.102300 AACAAGTTCGGGCAACAAGC 59.898 50.000 0.00 0.00 44.65 4.01
3324 3633 1.686355 ACATGAACAAGTTCGGGCAA 58.314 45.000 0.00 0.00 42.28 4.52
3352 3661 5.643777 GCATTGCTACTTCTTTCAGAGGTAA 59.356 40.000 0.16 0.00 36.54 2.85
3359 3668 2.742053 GGACGCATTGCTACTTCTTTCA 59.258 45.455 7.12 0.00 0.00 2.69
3375 3684 1.535462 ACATACAAGCAAAGTGGACGC 59.465 47.619 0.00 0.00 0.00 5.19
3377 3686 6.254281 ACATTACATACAAGCAAAGTGGAC 57.746 37.500 0.00 0.00 0.00 4.02
3395 3704 8.574251 AGTTTGCACCTTACATCATAACATTA 57.426 30.769 0.00 0.00 0.00 1.90
3537 3846 1.072965 AGGAAGCACCAGAAACTCCAG 59.927 52.381 2.96 0.00 42.04 3.86
3626 3935 6.887626 TCAGCACGTATGTAGTCCATATTA 57.112 37.500 0.00 0.00 38.29 0.98
3729 4039 9.013490 CATTCCGAATTATGAGATGTTCAAAAC 57.987 33.333 0.00 0.00 39.77 2.43
3730 4040 8.190122 CCATTCCGAATTATGAGATGTTCAAAA 58.810 33.333 0.00 0.00 39.77 2.44
3733 4043 6.591001 TCCATTCCGAATTATGAGATGTTCA 58.409 36.000 0.00 0.00 40.85 3.18
3742 4052 6.992715 AGTTACTCCTTCCATTCCGAATTATG 59.007 38.462 0.00 0.00 0.00 1.90
3754 4064 8.840200 ATAGAACATAAGAGTTACTCCTTCCA 57.160 34.615 8.96 0.00 0.00 3.53
3758 4068 8.788806 CGATGATAGAACATAAGAGTTACTCCT 58.211 37.037 8.96 0.00 0.00 3.69
3821 4132 2.836981 ACTGAGAAAGGACATGCTAGCT 59.163 45.455 17.23 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.