Multiple sequence alignment - TraesCS4A01G309500

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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 TraesCS4A01G309500 chr4A 100.000 3946 0 0 377 4322 602870186 602874131 0.000000e+00 7287.0
1 TraesCS4A01G309500 chr4A 88.273 1859 166 24 2497 4322 602609135 602610974 0.000000e+00 2178.0
2 TraesCS4A01G309500 chr4A 91.884 727 59 0 3596 4322 602726157 602726883 0.000000e+00 1016.0
3 TraesCS4A01G309500 chr4A 77.281 559 120 6 1190 1746 603053638 603053085 5.390000e-84 322.0
4 TraesCS4A01G309500 chr4A 90.698 86 8 0 2345 2430 602608822 602608907 9.820000e-22 115.0
5 TraesCS4A01G309500 chr4A 92.105 76 6 0 2428 2503 602609001 602609076 1.640000e-19 108.0
6 TraesCS4A01G309500 chr4A 100.000 50 0 0 1 50 602869810 602869859 4.600000e-15 93.5
7 TraesCS4A01G309500 chr4B 93.828 1847 92 2 2497 4322 3340851 3339006 0.000000e+00 2760.0
8 TraesCS4A01G309500 chr4B 92.165 1238 96 1 830 2066 3342512 3341275 0.000000e+00 1748.0
9 TraesCS4A01G309500 chr4B 87.902 1430 163 9 631 2054 3732076 3733501 0.000000e+00 1674.0
10 TraesCS4A01G309500 chr4B 87.257 1185 144 4 3143 4322 3733780 3734962 0.000000e+00 1345.0
11 TraesCS4A01G309500 chr4B 83.287 1424 214 15 636 2042 3514570 3513154 0.000000e+00 1290.0
12 TraesCS4A01G309500 chr4B 83.825 1323 192 13 636 1942 3454482 3453166 0.000000e+00 1238.0
13 TraesCS4A01G309500 chr4B 84.351 1048 142 13 636 1668 3428005 3426965 0.000000e+00 1007.0
14 TraesCS4A01G309500 chr4B 97.516 322 8 0 2085 2406 3341284 3340963 6.320000e-153 551.0
15 TraesCS4A01G309500 chr4B 75.592 844 195 6 1207 2043 3714556 3713717 1.450000e-109 407.0
16 TraesCS4A01G309500 chr4B 100.000 57 0 0 2447 2503 3340965 3340909 5.910000e-19 106.0
17 TraesCS4A01G309500 chr4D 92.163 1863 106 16 2497 4322 1874021 1875880 0.000000e+00 2595.0
18 TraesCS4A01G309500 chr4D 93.579 1246 79 1 822 2066 1872306 1873551 0.000000e+00 1857.0
19 TraesCS4A01G309500 chr4D 84.409 1193 171 11 3139 4322 1823272 1824458 0.000000e+00 1158.0
20 TraesCS4A01G309500 chr4D 94.258 418 22 1 2085 2500 1873542 1873959 4.710000e-179 638.0
21 TraesCS4A01G309500 chr4D 79.459 628 129 0 1414 2041 2884565 2885192 3.070000e-121 446.0
22 TraesCS4A01G309500 chrUn 89.080 1859 154 17 2497 4319 47659598 47661443 0.000000e+00 2263.0
23 TraesCS4A01G309500 chrUn 89.782 1282 110 14 1222 2503 47658279 47659539 0.000000e+00 1622.0
24 TraesCS4A01G309500 chrUn 83.797 1438 206 20 638 2057 47629861 47631289 0.000000e+00 1339.0
25 TraesCS4A01G309500 chrUn 87.004 1185 147 4 3143 4322 47452166 47453348 0.000000e+00 1328.0
26 TraesCS4A01G309500 chrUn 83.357 1424 213 16 636 2042 48044510 48045926 0.000000e+00 1295.0
27 TraesCS4A01G309500 chrUn 83.287 1424 214 16 636 2042 48074781 48076197 0.000000e+00 1290.0
28 TraesCS4A01G309500 chrUn 86.303 1190 149 8 3143 4322 47631565 47632750 0.000000e+00 1282.0
29 TraesCS4A01G309500 chrUn 97.319 373 10 0 514 886 47450189 47450561 6.100000e-178 634.0
30 TraesCS4A01G309500 chrUn 96.739 92 2 1 377 468 47450109 47450199 7.490000e-33 152.0
31 TraesCS4A01G309500 chr3D 76.894 1056 215 24 1001 2040 13181569 13180527 4.850000e-159 571.0
32 TraesCS4A01G309500 chr2B 74.675 770 173 12 993 1758 2780298 2779547 5.390000e-84 322.0
33 TraesCS4A01G309500 chr2B 74.286 770 175 13 993 1758 2760775 2760025 1.950000e-78 303.0
34 TraesCS4A01G309500 chr7D 81.429 140 26 0 1586 1725 632033824 632033963 9.820000e-22 115.0


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 TraesCS4A01G309500 chr4A 602869810 602874131 4321 False 3690.250000 7287 100.000000 1 4322 2 chr4A.!!$F3 4321
1 TraesCS4A01G309500 chr4A 602726157 602726883 726 False 1016.000000 1016 91.884000 3596 4322 1 chr4A.!!$F1 726
2 TraesCS4A01G309500 chr4A 602608822 602610974 2152 False 800.333333 2178 90.358667 2345 4322 3 chr4A.!!$F2 1977
3 TraesCS4A01G309500 chr4A 603053085 603053638 553 True 322.000000 322 77.281000 1190 1746 1 chr4A.!!$R1 556
4 TraesCS4A01G309500 chr4B 3732076 3734962 2886 False 1509.500000 1674 87.579500 631 4322 2 chr4B.!!$F1 3691
5 TraesCS4A01G309500 chr4B 3339006 3342512 3506 True 1291.250000 2760 95.877250 830 4322 4 chr4B.!!$R5 3492
6 TraesCS4A01G309500 chr4B 3513154 3514570 1416 True 1290.000000 1290 83.287000 636 2042 1 chr4B.!!$R3 1406
7 TraesCS4A01G309500 chr4B 3453166 3454482 1316 True 1238.000000 1238 83.825000 636 1942 1 chr4B.!!$R2 1306
8 TraesCS4A01G309500 chr4B 3426965 3428005 1040 True 1007.000000 1007 84.351000 636 1668 1 chr4B.!!$R1 1032
9 TraesCS4A01G309500 chr4B 3713717 3714556 839 True 407.000000 407 75.592000 1207 2043 1 chr4B.!!$R4 836
10 TraesCS4A01G309500 chr4D 1872306 1875880 3574 False 1696.666667 2595 93.333333 822 4322 3 chr4D.!!$F3 3500
11 TraesCS4A01G309500 chr4D 1823272 1824458 1186 False 1158.000000 1158 84.409000 3139 4322 1 chr4D.!!$F1 1183
12 TraesCS4A01G309500 chr4D 2884565 2885192 627 False 446.000000 446 79.459000 1414 2041 1 chr4D.!!$F2 627
13 TraesCS4A01G309500 chrUn 47658279 47661443 3164 False 1942.500000 2263 89.431000 1222 4319 2 chrUn.!!$F5 3097
14 TraesCS4A01G309500 chrUn 47629861 47632750 2889 False 1310.500000 1339 85.050000 638 4322 2 chrUn.!!$F4 3684
15 TraesCS4A01G309500 chrUn 48044510 48045926 1416 False 1295.000000 1295 83.357000 636 2042 1 chrUn.!!$F1 1406
16 TraesCS4A01G309500 chrUn 48074781 48076197 1416 False 1290.000000 1290 83.287000 636 2042 1 chrUn.!!$F2 1406
17 TraesCS4A01G309500 chrUn 47450109 47453348 3239 False 704.666667 1328 93.687333 377 4322 3 chrUn.!!$F3 3945
18 TraesCS4A01G309500 chr3D 13180527 13181569 1042 True 571.000000 571 76.894000 1001 2040 1 chr3D.!!$R1 1039
19 TraesCS4A01G309500 chr2B 2779547 2780298 751 True 322.000000 322 74.675000 993 1758 1 chr2B.!!$R2 765
20 TraesCS4A01G309500 chr2B 2760025 2760775 750 True 303.000000 303 74.286000 993 1758 1 chr2B.!!$R1 765

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
49 50 0.038251 ACGCACGATCAGCTCTTTCA 60.038 50.0 0.00 0.0 0.0 2.69 F
1498 1682 0.981183 ATTGTTGGAGCGGTCAGGTA 59.019 50.0 17.59 0.0 0.0 3.08 F
2076 2284 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.0 3.72 F
2084 2292 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1999 0.320374 TCTTGTCCTCGATGGCGTTT 59.680 50.000 0.0 0.0 38.98 3.60 R
3219 3648 1.855513 CGAGTGGTAAACCGTCACAA 58.144 50.000 0.0 0.0 39.43 3.33 R
3284 3713 2.450476 GGACATCTTCCCATGCAAACT 58.550 47.619 0.0 0.0 38.70 2.66 R
3448 3880 2.890311 TCCACATGGACACAATTTCACC 59.110 45.455 0.0 0.0 39.78 4.02 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
24 25 6.672147 CCGATCTGATCTTCTTTTGTTTTGT 58.328 36.000 15.16 0.00 0.00 2.83
25 26 7.141363 CCGATCTGATCTTCTTTTGTTTTGTT 58.859 34.615 15.16 0.00 0.00 2.83
26 27 7.113965 CCGATCTGATCTTCTTTTGTTTTGTTG 59.886 37.037 15.16 0.00 0.00 3.33
27 28 7.857389 CGATCTGATCTTCTTTTGTTTTGTTGA 59.143 33.333 15.16 0.00 0.00 3.18
28 29 9.178427 GATCTGATCTTCTTTTGTTTTGTTGAG 57.822 33.333 10.37 0.00 0.00 3.02
29 30 8.055279 TCTGATCTTCTTTTGTTTTGTTGAGT 57.945 30.769 0.00 0.00 0.00 3.41
30 31 9.173021 TCTGATCTTCTTTTGTTTTGTTGAGTA 57.827 29.630 0.00 0.00 0.00 2.59
31 32 9.226345 CTGATCTTCTTTTGTTTTGTTGAGTAC 57.774 33.333 0.00 0.00 0.00 2.73
32 33 7.908082 TGATCTTCTTTTGTTTTGTTGAGTACG 59.092 33.333 0.00 0.00 0.00 3.67
33 34 6.025280 TCTTCTTTTGTTTTGTTGAGTACGC 58.975 36.000 0.00 0.00 0.00 4.42
34 35 5.298197 TCTTTTGTTTTGTTGAGTACGCA 57.702 34.783 0.00 0.00 0.00 5.24
35 36 5.090083 TCTTTTGTTTTGTTGAGTACGCAC 58.910 37.500 0.00 0.00 0.00 5.34
36 37 2.722936 TGTTTTGTTGAGTACGCACG 57.277 45.000 0.00 0.00 0.00 5.34
37 38 2.269172 TGTTTTGTTGAGTACGCACGA 58.731 42.857 0.00 0.00 0.00 4.35
38 39 2.867368 TGTTTTGTTGAGTACGCACGAT 59.133 40.909 0.00 0.00 0.00 3.73
39 40 3.060138 TGTTTTGTTGAGTACGCACGATC 60.060 43.478 0.00 0.00 0.00 3.69
40 41 2.425578 TTGTTGAGTACGCACGATCA 57.574 45.000 0.00 0.00 0.00 2.92
41 42 1.977188 TGTTGAGTACGCACGATCAG 58.023 50.000 0.00 0.00 0.00 2.90
42 43 0.640768 GTTGAGTACGCACGATCAGC 59.359 55.000 0.00 0.00 0.00 4.26
43 44 0.526211 TTGAGTACGCACGATCAGCT 59.474 50.000 0.00 0.00 0.00 4.24
44 45 0.098905 TGAGTACGCACGATCAGCTC 59.901 55.000 0.00 0.00 0.00 4.09
45 46 0.378962 GAGTACGCACGATCAGCTCT 59.621 55.000 0.00 2.13 0.00 4.09
46 47 0.811915 AGTACGCACGATCAGCTCTT 59.188 50.000 0.00 0.00 0.00 2.85
47 48 1.202582 AGTACGCACGATCAGCTCTTT 59.797 47.619 0.00 0.00 0.00 2.52
48 49 1.584308 GTACGCACGATCAGCTCTTTC 59.416 52.381 0.00 0.00 0.00 2.62
49 50 0.038251 ACGCACGATCAGCTCTTTCA 60.038 50.000 0.00 0.00 0.00 2.69
439 440 7.120789 CAATCCATGCTTTTTCCTTTACAAC 57.879 36.000 0.00 0.00 0.00 3.32
462 463 4.569943 GAATTGTTGGTAGTCTCTGCTGA 58.430 43.478 0.00 0.00 0.00 4.26
463 464 3.667497 TTGTTGGTAGTCTCTGCTGAG 57.333 47.619 14.07 14.07 41.51 3.35
464 465 2.598565 TGTTGGTAGTCTCTGCTGAGT 58.401 47.619 18.82 4.91 40.98 3.41
465 466 2.297315 TGTTGGTAGTCTCTGCTGAGTG 59.703 50.000 18.82 0.00 40.98 3.51
466 467 2.558795 GTTGGTAGTCTCTGCTGAGTGA 59.441 50.000 18.82 4.50 40.98 3.41
467 468 2.876581 TGGTAGTCTCTGCTGAGTGAA 58.123 47.619 18.82 4.38 40.98 3.18
468 469 3.435275 TGGTAGTCTCTGCTGAGTGAAT 58.565 45.455 18.82 4.54 40.98 2.57
469 470 3.445450 TGGTAGTCTCTGCTGAGTGAATC 59.555 47.826 18.82 7.57 40.98 2.52
470 471 3.699038 GGTAGTCTCTGCTGAGTGAATCT 59.301 47.826 18.82 12.69 40.98 2.40
471 472 4.884744 GGTAGTCTCTGCTGAGTGAATCTA 59.115 45.833 18.82 11.92 40.98 1.98
472 473 4.981806 AGTCTCTGCTGAGTGAATCTAC 57.018 45.455 18.82 8.91 40.98 2.59
473 474 4.339748 AGTCTCTGCTGAGTGAATCTACA 58.660 43.478 18.82 0.00 40.98 2.74
474 475 4.955450 AGTCTCTGCTGAGTGAATCTACAT 59.045 41.667 18.82 0.00 40.98 2.29
475 476 5.042593 GTCTCTGCTGAGTGAATCTACATG 58.957 45.833 18.82 0.00 40.98 3.21
476 477 4.952335 TCTCTGCTGAGTGAATCTACATGA 59.048 41.667 18.82 0.00 40.98 3.07
477 478 5.003692 TCTGCTGAGTGAATCTACATGAC 57.996 43.478 0.00 0.00 0.00 3.06
478 479 4.118410 CTGCTGAGTGAATCTACATGACC 58.882 47.826 0.00 0.00 0.00 4.02
479 480 3.515104 TGCTGAGTGAATCTACATGACCA 59.485 43.478 0.00 0.00 0.00 4.02
480 481 4.162888 TGCTGAGTGAATCTACATGACCAT 59.837 41.667 0.00 0.00 0.00 3.55
481 482 4.749099 GCTGAGTGAATCTACATGACCATC 59.251 45.833 0.00 0.00 0.00 3.51
482 483 5.282055 TGAGTGAATCTACATGACCATCC 57.718 43.478 0.00 0.00 0.00 3.51
483 484 4.964897 TGAGTGAATCTACATGACCATCCT 59.035 41.667 0.00 0.00 0.00 3.24
484 485 5.426509 TGAGTGAATCTACATGACCATCCTT 59.573 40.000 0.00 0.00 0.00 3.36
485 486 5.923204 AGTGAATCTACATGACCATCCTTC 58.077 41.667 0.00 0.00 0.00 3.46
486 487 5.664908 AGTGAATCTACATGACCATCCTTCT 59.335 40.000 0.00 0.00 0.00 2.85
487 488 6.157645 AGTGAATCTACATGACCATCCTTCTT 59.842 38.462 0.00 0.00 0.00 2.52
488 489 6.825721 GTGAATCTACATGACCATCCTTCTTT 59.174 38.462 0.00 0.00 0.00 2.52
489 490 7.337942 GTGAATCTACATGACCATCCTTCTTTT 59.662 37.037 0.00 0.00 0.00 2.27
490 491 7.554118 TGAATCTACATGACCATCCTTCTTTTC 59.446 37.037 0.00 0.00 0.00 2.29
491 492 5.745227 TCTACATGACCATCCTTCTTTTCC 58.255 41.667 0.00 0.00 0.00 3.13
492 493 4.387026 ACATGACCATCCTTCTTTTCCA 57.613 40.909 0.00 0.00 0.00 3.53
493 494 4.939255 ACATGACCATCCTTCTTTTCCAT 58.061 39.130 0.00 0.00 0.00 3.41
494 495 5.336102 ACATGACCATCCTTCTTTTCCATT 58.664 37.500 0.00 0.00 0.00 3.16
495 496 5.781818 ACATGACCATCCTTCTTTTCCATTT 59.218 36.000 0.00 0.00 0.00 2.32
496 497 6.270695 ACATGACCATCCTTCTTTTCCATTTT 59.729 34.615 0.00 0.00 0.00 1.82
497 498 6.745794 TGACCATCCTTCTTTTCCATTTTT 57.254 33.333 0.00 0.00 0.00 1.94
529 530 6.873605 TGTCACTATTGATGTGTGAAAGGTAG 59.126 38.462 0.00 0.00 41.52 3.18
582 583 5.398603 TTTGTTTTCAGTTCCAGCTCAAA 57.601 34.783 0.00 0.00 0.00 2.69
670 671 7.173218 GTCTCTCATCTCTCTAGTCGATTCAAT 59.827 40.741 0.00 0.00 0.00 2.57
776 782 2.663826 TGTTGGTGTTTGTTCAAGGC 57.336 45.000 0.00 0.00 0.00 4.35
791 798 7.292713 TGTTCAAGGCAATACTATATCGGTA 57.707 36.000 0.00 0.00 0.00 4.02
1159 1343 1.202734 TCCTTGCAGATGCTGATAGGC 60.203 52.381 6.35 0.00 42.66 3.93
1425 1609 8.538409 AATTTAAATTTGCCAAGCTAGAAGTG 57.462 30.769 7.64 0.00 0.00 3.16
1498 1682 0.981183 ATTGTTGGAGCGGTCAGGTA 59.019 50.000 17.59 0.00 0.00 3.08
1804 1991 4.047883 AGATAGGGCCCTACTTGTTGATT 58.952 43.478 34.34 14.85 0.00 2.57
1812 1999 5.003804 GCCCTACTTGTTGATTCTCTCAAA 58.996 41.667 0.00 0.00 45.27 2.69
2066 2274 1.815613 CCCAAACTCAACACACACACA 59.184 47.619 0.00 0.00 0.00 3.72
2067 2275 2.415357 CCCAAACTCAACACACACACAC 60.415 50.000 0.00 0.00 0.00 3.82
2068 2276 2.227626 CCAAACTCAACACACACACACA 59.772 45.455 0.00 0.00 0.00 3.72
2069 2277 3.233578 CAAACTCAACACACACACACAC 58.766 45.455 0.00 0.00 0.00 3.82
2070 2278 2.177394 ACTCAACACACACACACACA 57.823 45.000 0.00 0.00 0.00 3.72
2071 2279 1.804151 ACTCAACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
2072 2280 1.803555 CTCAACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
2073 2281 1.533299 TCAACACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
2074 2282 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
2075 2283 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2076 2284 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2077 2285 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2078 2286 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2079 2287 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2080 2288 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2081 2289 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2082 2290 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2083 2291 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2084 2292 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2085 2293 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2086 2294 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2087 2295 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2088 2296 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2103 2311 5.285845 CACACACACACACACTGTTAATTTG 59.714 40.000 0.00 0.00 0.00 2.32
2326 2544 6.387041 TGTCAGAAGAATAGTATGGGTACG 57.613 41.667 0.00 0.00 35.92 3.67
2352 2570 3.634397 ACACCATGCAACTATACTGCT 57.366 42.857 0.00 0.00 40.59 4.24
2387 2605 3.624900 TCAGTCTTAACACGAGTTCACG 58.375 45.455 0.18 0.00 39.15 4.35
2541 2920 5.095490 GCAACTAACATGCACATAACTTCC 58.905 41.667 0.00 0.00 43.29 3.46
2545 2924 5.945784 ACTAACATGCACATAACTTCCATGT 59.054 36.000 0.00 0.00 45.88 3.21
2583 2962 4.019681 TCAGGACCGTGTCAAATCCTAAAT 60.020 41.667 6.41 0.00 39.66 1.40
2858 3268 9.622004 ATCGATATAACTGTAGATTTTGTACCG 57.378 33.333 0.00 0.00 0.00 4.02
2860 3270 9.622004 CGATATAACTGTAGATTTTGTACCGAT 57.378 33.333 0.00 0.00 0.00 4.18
2872 3286 6.671614 TTTTGTACCGATGTTGATACCATC 57.328 37.500 0.00 0.00 36.25 3.51
2956 3378 9.719279 TTTGAAGCAACAATTTTCATTTGATTC 57.281 25.926 4.62 4.62 42.16 2.52
3039 3464 8.890718 GGTCATAAGGAGTATTAGTTTGGTTTC 58.109 37.037 0.00 0.00 0.00 2.78
3107 3532 4.142730 GCTGATCACCACTTTCAGATGTTC 60.143 45.833 3.47 0.00 39.36 3.18
3174 3603 3.764434 TCACTACAGAGGAGAATGGACAC 59.236 47.826 0.00 0.00 0.00 3.67
3219 3648 8.462589 AAATTGGGTTGCAAATTGTAGAAAAT 57.537 26.923 0.00 0.00 0.00 1.82
3284 3713 2.275134 TGCAGCAAGGAGAAATCACA 57.725 45.000 0.00 0.00 0.00 3.58
3321 3753 5.625568 ATGTCCTGAATGATGACATCTGA 57.374 39.130 16.25 0.00 44.21 3.27
3437 3869 5.103855 TCTCCCTTAAACCCAAAAAGTCTGA 60.104 40.000 0.00 0.00 0.00 3.27
3448 3880 5.049129 CCCAAAAAGTCTGAGCTAAGTCTTG 60.049 44.000 10.90 0.81 0.00 3.02
3715 4151 7.912056 TCATCCAATTTTCTTAGACTGTCTG 57.088 36.000 20.19 4.72 0.00 3.51
3835 4271 0.322546 GCCTGGGGATTCGTTGACTT 60.323 55.000 0.00 0.00 0.00 3.01
3909 4345 7.010552 GCACTAGTTGAATCTATGTACCAACTG 59.989 40.741 16.76 11.26 44.68 3.16
3916 4352 4.202245 TCTATGTACCAACTGAAGCACC 57.798 45.455 0.00 0.00 0.00 5.01
4132 4568 5.305585 TCCGAGCTCTTACAAATTTGACTT 58.694 37.500 24.64 5.12 0.00 3.01
4191 4627 2.633481 GTGTAGTCTGGAAGAGTTGGGT 59.367 50.000 0.00 0.00 46.68 4.51
4255 4691 6.942576 AGAAAATGTATCTAGTGCCTTGTTGT 59.057 34.615 0.00 0.00 0.00 3.32
4313 4749 7.939039 ACTTATCTCTCTTGGTTTGAAATGTGA 59.061 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.672147 ACAAAACAAAAGAAGATCAGATCGG 58.328 36.000 4.67 0.00 0.00 4.18
1 2 7.857389 TCAACAAAACAAAAGAAGATCAGATCG 59.143 33.333 4.67 0.00 0.00 3.69
2 3 9.178427 CTCAACAAAACAAAAGAAGATCAGATC 57.822 33.333 1.64 1.64 0.00 2.75
3 4 8.689972 ACTCAACAAAACAAAAGAAGATCAGAT 58.310 29.630 0.00 0.00 0.00 2.90
4 5 8.055279 ACTCAACAAAACAAAAGAAGATCAGA 57.945 30.769 0.00 0.00 0.00 3.27
5 6 9.226345 GTACTCAACAAAACAAAAGAAGATCAG 57.774 33.333 0.00 0.00 0.00 2.90
6 7 7.908082 CGTACTCAACAAAACAAAAGAAGATCA 59.092 33.333 0.00 0.00 0.00 2.92
7 8 7.097006 GCGTACTCAACAAAACAAAAGAAGATC 60.097 37.037 0.00 0.00 0.00 2.75
8 9 6.691388 GCGTACTCAACAAAACAAAAGAAGAT 59.309 34.615 0.00 0.00 0.00 2.40
9 10 6.025280 GCGTACTCAACAAAACAAAAGAAGA 58.975 36.000 0.00 0.00 0.00 2.87
10 11 5.797934 TGCGTACTCAACAAAACAAAAGAAG 59.202 36.000 0.00 0.00 0.00 2.85
11 12 5.569823 GTGCGTACTCAACAAAACAAAAGAA 59.430 36.000 0.00 0.00 0.00 2.52
12 13 5.090083 GTGCGTACTCAACAAAACAAAAGA 58.910 37.500 0.00 0.00 0.00 2.52
13 14 4.028830 CGTGCGTACTCAACAAAACAAAAG 60.029 41.667 1.24 0.00 0.00 2.27
14 15 3.846896 CGTGCGTACTCAACAAAACAAAA 59.153 39.130 1.24 0.00 0.00 2.44
15 16 3.124806 TCGTGCGTACTCAACAAAACAAA 59.875 39.130 1.24 0.00 0.00 2.83
16 17 2.671888 TCGTGCGTACTCAACAAAACAA 59.328 40.909 1.24 0.00 0.00 2.83
17 18 2.269172 TCGTGCGTACTCAACAAAACA 58.731 42.857 1.24 0.00 0.00 2.83
18 19 3.060138 TGATCGTGCGTACTCAACAAAAC 60.060 43.478 1.24 0.00 0.00 2.43
19 20 3.124560 TGATCGTGCGTACTCAACAAAA 58.875 40.909 1.24 0.00 0.00 2.44
20 21 2.729360 CTGATCGTGCGTACTCAACAAA 59.271 45.455 1.24 0.00 0.00 2.83
21 22 2.324860 CTGATCGTGCGTACTCAACAA 58.675 47.619 1.24 0.00 0.00 2.83
22 23 1.977188 CTGATCGTGCGTACTCAACA 58.023 50.000 1.24 0.00 0.00 3.33
23 24 0.640768 GCTGATCGTGCGTACTCAAC 59.359 55.000 1.24 0.00 0.00 3.18
24 25 0.526211 AGCTGATCGTGCGTACTCAA 59.474 50.000 1.24 0.00 35.28 3.02
25 26 0.098905 GAGCTGATCGTGCGTACTCA 59.901 55.000 1.24 0.00 35.28 3.41
26 27 0.378962 AGAGCTGATCGTGCGTACTC 59.621 55.000 1.24 0.00 35.28 2.59
27 28 0.811915 AAGAGCTGATCGTGCGTACT 59.188 50.000 1.24 4.32 35.28 2.73
28 29 1.584308 GAAAGAGCTGATCGTGCGTAC 59.416 52.381 0.00 0.00 35.28 3.67
29 30 1.201414 TGAAAGAGCTGATCGTGCGTA 59.799 47.619 0.00 0.00 35.28 4.42
30 31 0.038251 TGAAAGAGCTGATCGTGCGT 60.038 50.000 0.00 0.00 35.28 5.24
31 32 2.741930 TGAAAGAGCTGATCGTGCG 58.258 52.632 0.00 0.00 35.28 5.34
439 440 3.369147 CAGCAGAGACTACCAACAATTCG 59.631 47.826 0.00 0.00 0.00 3.34
462 463 5.664908 AGAAGGATGGTCATGTAGATTCACT 59.335 40.000 0.00 0.00 0.00 3.41
463 464 5.923204 AGAAGGATGGTCATGTAGATTCAC 58.077 41.667 0.00 0.00 0.00 3.18
464 465 6.566079 AAGAAGGATGGTCATGTAGATTCA 57.434 37.500 0.00 0.00 0.00 2.57
465 466 7.012799 GGAAAAGAAGGATGGTCATGTAGATTC 59.987 40.741 0.00 0.00 0.00 2.52
466 467 6.830838 GGAAAAGAAGGATGGTCATGTAGATT 59.169 38.462 0.00 0.00 0.00 2.40
467 468 6.069440 TGGAAAAGAAGGATGGTCATGTAGAT 60.069 38.462 0.00 0.00 0.00 1.98
468 469 5.250543 TGGAAAAGAAGGATGGTCATGTAGA 59.749 40.000 0.00 0.00 0.00 2.59
469 470 5.500234 TGGAAAAGAAGGATGGTCATGTAG 58.500 41.667 0.00 0.00 0.00 2.74
470 471 5.512942 TGGAAAAGAAGGATGGTCATGTA 57.487 39.130 0.00 0.00 0.00 2.29
471 472 4.387026 TGGAAAAGAAGGATGGTCATGT 57.613 40.909 0.00 0.00 0.00 3.21
472 473 5.927281 AATGGAAAAGAAGGATGGTCATG 57.073 39.130 0.00 0.00 0.00 3.07
473 474 6.940430 AAAATGGAAAAGAAGGATGGTCAT 57.060 33.333 0.00 0.00 0.00 3.06
474 475 6.745794 AAAAATGGAAAAGAAGGATGGTCA 57.254 33.333 0.00 0.00 0.00 4.02
496 497 6.641723 CACACATCAATAGTGACATGCAAAAA 59.358 34.615 0.00 0.00 40.16 1.94
497 498 6.016443 TCACACATCAATAGTGACATGCAAAA 60.016 34.615 0.00 0.00 40.16 2.44
498 499 5.472820 TCACACATCAATAGTGACATGCAAA 59.527 36.000 0.00 0.00 40.16 3.68
499 500 5.002516 TCACACATCAATAGTGACATGCAA 58.997 37.500 0.00 0.00 40.16 4.08
500 501 4.577875 TCACACATCAATAGTGACATGCA 58.422 39.130 0.00 0.00 40.16 3.96
501 502 5.550232 TTCACACATCAATAGTGACATGC 57.450 39.130 0.00 0.00 41.53 4.06
502 503 6.149973 ACCTTTCACACATCAATAGTGACATG 59.850 38.462 0.00 0.00 41.53 3.21
503 504 6.240894 ACCTTTCACACATCAATAGTGACAT 58.759 36.000 0.00 0.00 41.53 3.06
504 505 5.620206 ACCTTTCACACATCAATAGTGACA 58.380 37.500 0.00 0.00 41.53 3.58
505 506 6.874134 ACTACCTTTCACACATCAATAGTGAC 59.126 38.462 0.00 0.00 41.53 3.67
506 507 7.004555 ACTACCTTTCACACATCAATAGTGA 57.995 36.000 0.00 0.00 40.24 3.41
507 508 8.771920 TTACTACCTTTCACACATCAATAGTG 57.228 34.615 0.00 0.00 42.56 2.74
513 514 9.653287 CTCTTTATTACTACCTTTCACACATCA 57.347 33.333 0.00 0.00 0.00 3.07
514 515 9.099454 CCTCTTTATTACTACCTTTCACACATC 57.901 37.037 0.00 0.00 0.00 3.06
515 516 8.822805 TCCTCTTTATTACTACCTTTCACACAT 58.177 33.333 0.00 0.00 0.00 3.21
516 517 8.092687 GTCCTCTTTATTACTACCTTTCACACA 58.907 37.037 0.00 0.00 0.00 3.72
517 518 8.312564 AGTCCTCTTTATTACTACCTTTCACAC 58.687 37.037 0.00 0.00 0.00 3.82
529 530 7.750903 GCACACAAAATGAGTCCTCTTTATTAC 59.249 37.037 0.00 0.00 0.00 1.89
582 583 0.766674 TAGTTGCAGGGTCCAGTGGT 60.767 55.000 9.54 0.00 0.00 4.16
1424 1608 5.622233 CGAGTCATCTTCATGTCTTGGTACA 60.622 44.000 0.00 0.00 29.57 2.90
1425 1609 4.800993 CGAGTCATCTTCATGTCTTGGTAC 59.199 45.833 0.00 0.00 29.57 3.34
1498 1682 3.012518 CCTCAATCTTCTCGCCAACAAT 58.987 45.455 0.00 0.00 0.00 2.71
1804 1991 2.337583 CTCGATGGCGTTTTTGAGAGA 58.662 47.619 0.00 0.00 38.98 3.10
1812 1999 0.320374 TCTTGTCCTCGATGGCGTTT 59.680 50.000 0.00 0.00 38.98 3.60
2066 2274 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2067 2275 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2068 2276 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2069 2277 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2070 2278 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2071 2279 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2072 2280 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2073 2281 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2074 2282 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2075 2283 1.136000 CAGTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
2076 2284 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
2077 2285 1.155889 ACAGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 38.28 3.82
2078 2286 1.890876 AACAGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 40.26 3.72
2079 2287 4.614555 ATTAACAGTGTGTGTGTGTGTG 57.385 40.909 0.00 0.00 40.26 3.82
2080 2288 5.182190 TCAAATTAACAGTGTGTGTGTGTGT 59.818 36.000 0.00 0.00 40.26 3.72
2081 2289 5.511377 GTCAAATTAACAGTGTGTGTGTGTG 59.489 40.000 0.00 0.00 40.26 3.82
2082 2290 5.414454 AGTCAAATTAACAGTGTGTGTGTGT 59.586 36.000 0.00 0.00 40.26 3.72
2083 2291 5.879237 AGTCAAATTAACAGTGTGTGTGTG 58.121 37.500 0.00 0.00 40.26 3.82
2084 2292 6.150307 TCAAGTCAAATTAACAGTGTGTGTGT 59.850 34.615 0.00 0.00 40.26 3.72
2085 2293 6.550843 TCAAGTCAAATTAACAGTGTGTGTG 58.449 36.000 0.00 0.00 40.26 3.82
2086 2294 6.677920 GCTCAAGTCAAATTAACAGTGTGTGT 60.678 38.462 0.00 0.00 43.24 3.72
2087 2295 5.682862 GCTCAAGTCAAATTAACAGTGTGTG 59.317 40.000 0.00 0.00 0.00 3.82
2088 2296 5.590259 AGCTCAAGTCAAATTAACAGTGTGT 59.410 36.000 0.00 0.00 0.00 3.72
2326 2544 8.319059 GCAGTATAGTTGCATGGTGTACAACC 62.319 46.154 8.79 7.92 43.68 3.77
2352 2570 3.746045 AGACTGAAACTTACGGCAAGA 57.254 42.857 6.09 0.00 37.71 3.02
2541 2920 7.191551 GTCCTGATGTTGATACATTGAACATG 58.808 38.462 0.00 0.00 44.90 3.21
2545 2924 4.875536 CGGTCCTGATGTTGATACATTGAA 59.124 41.667 0.00 0.00 44.90 2.69
2583 2962 8.701895 ACTTCATCGGTTCCTGAATATAGTTTA 58.298 33.333 0.00 0.00 31.39 2.01
2872 3286 7.466805 CACATGGATGTAGTAGTGTCAATTTG 58.533 38.462 0.00 0.00 39.39 2.32
2956 3378 4.572985 TCATGGTGAAACAAGCTTTCTG 57.427 40.909 0.00 0.00 39.98 3.02
3107 3532 5.822519 TGTATAGCTTGAATAAGGGCAACAG 59.177 40.000 0.00 0.00 39.74 3.16
3174 3603 2.972625 TCCTTTAGCACATCAACCTCG 58.027 47.619 0.00 0.00 0.00 4.63
3219 3648 1.855513 CGAGTGGTAAACCGTCACAA 58.144 50.000 0.00 0.00 39.43 3.33
3284 3713 2.450476 GGACATCTTCCCATGCAAACT 58.550 47.619 0.00 0.00 38.70 2.66
3321 3753 6.990908 TCATCTGACATTGGAGATACTGAT 57.009 37.500 1.38 0.00 0.00 2.90
3437 3869 5.133221 ACACAATTTCACCAAGACTTAGCT 58.867 37.500 0.00 0.00 0.00 3.32
3448 3880 2.890311 TCCACATGGACACAATTTCACC 59.110 45.455 0.00 0.00 39.78 4.02
3715 4151 3.217681 TCCCACACCTTTGGTTTCTAC 57.782 47.619 0.00 0.00 34.44 2.59
3835 4271 5.535333 CAAAAGACGTAGACTTGGGAAGTA 58.465 41.667 0.00 0.00 42.35 2.24
3909 4345 3.282021 TGCCAAATATCTCAGGTGCTTC 58.718 45.455 0.00 0.00 0.00 3.86
3916 4352 7.718753 AGTCCTCTTTAATGCCAAATATCTCAG 59.281 37.037 0.00 0.00 0.00 3.35
4132 4568 2.378547 AGGCTGGAAACCCAAATAGTGA 59.621 45.455 0.00 0.00 32.40 3.41
4191 4627 5.694995 AGTTCATTGAGTTGGGAAAGAGAA 58.305 37.500 0.00 0.00 0.00 2.87
4255 4691 5.479893 GCATTTAGCCTTGCCTTTGCAGA 62.480 47.826 0.00 0.00 43.02 4.26


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

AutoCloner maintained by Alex Coulton.