Multiple sequence alignment - TraesCS3A01G516100

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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 TraesCS3A01G516100 chr3A 100.000 3813 0 0 1 3813 733918392 733914580 0.000000e+00 7042.0
1 TraesCS3A01G516100 chr3A 92.440 2262 127 13 848 3070 733860209 733857953 0.000000e+00 3190.0
2 TraesCS3A01G516100 chr3A 81.526 2176 287 49 458 2560 733726352 733724219 0.000000e+00 1685.0
3 TraesCS3A01G516100 chr3A 81.257 1846 273 40 701 2487 733333047 733334878 0.000000e+00 1424.0
4 TraesCS3A01G516100 chr3A 82.482 1547 239 19 969 2490 733436441 733437980 0.000000e+00 1327.0
5 TraesCS3A01G516100 chr3A 82.704 1509 222 23 865 2347 733732363 733730868 0.000000e+00 1304.0
6 TraesCS3A01G516100 chr3A 84.000 1350 167 30 843 2175 733472530 733473847 0.000000e+00 1251.0
7 TraesCS3A01G516100 chr3A 80.156 1280 205 27 1234 2487 733185892 733187148 0.000000e+00 911.0
8 TraesCS3A01G516100 chr3A 90.196 459 22 4 3076 3527 733857918 733857476 9.180000e-161 577.0
9 TraesCS3A01G516100 chr3A 78.581 761 112 28 1994 2722 733715333 733714592 4.490000e-124 455.0
10 TraesCS3A01G516100 chr3A 98.571 70 1 0 366 435 9082311 9082242 1.440000e-24 124.0
11 TraesCS3A01G516100 chr3D 94.415 2041 83 6 680 2692 604288535 604286498 0.000000e+00 3109.0
12 TraesCS3A01G516100 chr3D 81.874 2124 293 50 458 2539 604259597 604257524 0.000000e+00 1705.0
13 TraesCS3A01G516100 chr3D 81.716 2133 298 52 467 2560 604144127 604142048 0.000000e+00 1694.0
14 TraesCS3A01G516100 chr3D 81.469 2137 300 45 486 2565 604253253 604251156 0.000000e+00 1664.0
15 TraesCS3A01G516100 chr3D 83.966 1659 219 26 848 2484 603962780 603964413 0.000000e+00 1546.0
16 TraesCS3A01G516100 chr3D 80.529 1890 267 52 859 2694 604237040 604235198 0.000000e+00 1358.0
17 TraesCS3A01G516100 chr3D 91.631 466 17 10 1 461 604289533 604289085 3.230000e-175 625.0
18 TraesCS3A01G516100 chr3D 94.359 195 6 1 458 647 604288734 604288540 1.040000e-75 294.0
19 TraesCS3A01G516100 chr3D 94.737 38 2 0 3119 3156 604256075 604256038 4.110000e-05 60.2
20 TraesCS3A01G516100 chr3B 91.130 2266 146 16 851 3070 811181899 811179643 0.000000e+00 3020.0
21 TraesCS3A01G516100 chr3B 81.536 2161 304 46 458 2565 811141662 811139544 0.000000e+00 1692.0
22 TraesCS3A01G516100 chr3B 81.757 2072 282 54 458 2487 811153996 811151979 0.000000e+00 1644.0
23 TraesCS3A01G516100 chr3B 83.236 1712 239 28 848 2534 811079468 811081156 0.000000e+00 1528.0
24 TraesCS3A01G516100 chr3B 82.245 1639 243 32 888 2487 810978015 810979644 0.000000e+00 1371.0
25 TraesCS3A01G516100 chr3B 80.914 1598 238 33 957 2520 811112835 811111271 0.000000e+00 1199.0
26 TraesCS3A01G516100 chr3B 84.390 205 25 5 578 779 811178685 811178485 1.080000e-45 195.0
27 TraesCS3A01G516100 chr3B 83.854 192 30 1 476 666 811135757 811135566 8.410000e-42 182.0
28 TraesCS3A01G516100 chr3B 93.519 108 4 3 458 563 811182243 811182137 1.420000e-34 158.0
29 TraesCS3A01G516100 chrUn 84.784 1735 204 32 848 2565 42260202 42261893 0.000000e+00 1687.0
30 TraesCS3A01G516100 chr4A 96.897 290 8 1 3525 3813 608075172 608075461 5.730000e-133 484.0
31 TraesCS3A01G516100 chr4A 87.975 158 19 0 3524 3681 56470266 56470423 1.810000e-43 187.0
32 TraesCS3A01G516100 chr7A 94.828 290 14 1 3524 3813 642338353 642338641 5.810000e-123 451.0
33 TraesCS3A01G516100 chr7A 86.552 290 39 0 3524 3813 631521534 631521823 1.710000e-83 320.0
34 TraesCS3A01G516100 chr7A 96.319 163 6 0 273 435 621330740 621330902 6.280000e-68 268.0
35 TraesCS3A01G516100 chr7D 93.080 289 20 0 3525 3813 38811724 38812012 1.270000e-114 424.0
36 TraesCS3A01G516100 chr7D 87.582 153 19 0 3525 3677 548338229 548338381 1.090000e-40 178.0
37 TraesCS3A01G516100 chr7D 85.075 67 4 4 3752 3812 531769438 531769504 3.180000e-06 63.9
38 TraesCS3A01G516100 chr6B 93.950 281 16 1 3525 3805 704409011 704408732 1.270000e-114 424.0
39 TraesCS3A01G516100 chr5D 87.582 153 19 0 3525 3677 505021268 505021420 1.090000e-40 178.0
40 TraesCS3A01G516100 chr4D 86.928 153 20 0 3525 3677 509205572 509205724 5.060000e-39 172.0
41 TraesCS3A01G516100 chr2D 100.000 36 0 0 3778 3813 615993400 615993435 2.460000e-07 67.6


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 TraesCS3A01G516100 chr3A 733914580 733918392 3812 True 7042.000000 7042 100.000000 1 3813 1 chr3A.!!$R5 3812
1 TraesCS3A01G516100 chr3A 733857476 733860209 2733 True 1883.500000 3190 91.318000 848 3527 2 chr3A.!!$R6 2679
2 TraesCS3A01G516100 chr3A 733724219 733726352 2133 True 1685.000000 1685 81.526000 458 2560 1 chr3A.!!$R3 2102
3 TraesCS3A01G516100 chr3A 733333047 733334878 1831 False 1424.000000 1424 81.257000 701 2487 1 chr3A.!!$F2 1786
4 TraesCS3A01G516100 chr3A 733436441 733437980 1539 False 1327.000000 1327 82.482000 969 2490 1 chr3A.!!$F3 1521
5 TraesCS3A01G516100 chr3A 733730868 733732363 1495 True 1304.000000 1304 82.704000 865 2347 1 chr3A.!!$R4 1482
6 TraesCS3A01G516100 chr3A 733472530 733473847 1317 False 1251.000000 1251 84.000000 843 2175 1 chr3A.!!$F4 1332
7 TraesCS3A01G516100 chr3A 733185892 733187148 1256 False 911.000000 911 80.156000 1234 2487 1 chr3A.!!$F1 1253
8 TraesCS3A01G516100 chr3A 733714592 733715333 741 True 455.000000 455 78.581000 1994 2722 1 chr3A.!!$R2 728
9 TraesCS3A01G516100 chr3D 604142048 604144127 2079 True 1694.000000 1694 81.716000 467 2560 1 chr3D.!!$R1 2093
10 TraesCS3A01G516100 chr3D 603962780 603964413 1633 False 1546.000000 1546 83.966000 848 2484 1 chr3D.!!$F1 1636
11 TraesCS3A01G516100 chr3D 604235198 604237040 1842 True 1358.000000 1358 80.529000 859 2694 1 chr3D.!!$R2 1835
12 TraesCS3A01G516100 chr3D 604286498 604289533 3035 True 1342.666667 3109 93.468333 1 2692 3 chr3D.!!$R4 2691
13 TraesCS3A01G516100 chr3D 604251156 604259597 8441 True 1143.066667 1705 86.026667 458 3156 3 chr3D.!!$R3 2698
14 TraesCS3A01G516100 chr3B 811151979 811153996 2017 True 1644.000000 1644 81.757000 458 2487 1 chr3B.!!$R2 2029
15 TraesCS3A01G516100 chr3B 811079468 811081156 1688 False 1528.000000 1528 83.236000 848 2534 1 chr3B.!!$F2 1686
16 TraesCS3A01G516100 chr3B 810978015 810979644 1629 False 1371.000000 1371 82.245000 888 2487 1 chr3B.!!$F1 1599
17 TraesCS3A01G516100 chr3B 811111271 811112835 1564 True 1199.000000 1199 80.914000 957 2520 1 chr3B.!!$R1 1563
18 TraesCS3A01G516100 chr3B 811178485 811182243 3758 True 1124.333333 3020 89.679667 458 3070 3 chr3B.!!$R4 2612
19 TraesCS3A01G516100 chr3B 811135566 811141662 6096 True 937.000000 1692 82.695000 458 2565 2 chr3B.!!$R3 2107
20 TraesCS3A01G516100 chrUn 42260202 42261893 1691 False 1687.000000 1687 84.784000 848 2565 1 chrUn.!!$F1 1717

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
276 282 0.968901 TCGAACCCTAGACACGGCAT 60.969 55.000 0.0 0.0 0.00 4.40 F
333 339 2.049433 CGTCCTGCGTTCGTTCCT 60.049 61.111 0.0 0.0 35.54 3.36 F
2125 9015 0.824759 CCTCCAGTAAACTCTCCCCG 59.175 60.000 0.0 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 9015 1.216122 GATCAGGTGATCGAGCAAGC 58.784 55.000 4.22 0.00 41.15 4.01 R
2467 9412 3.070429 CGGGAGCATGCTTATCAAAAC 57.930 47.619 23.61 5.90 0.00 2.43 R
3724 12757 0.385849 TGCTTGATGCGCGTCTTTTG 60.386 50.000 28.53 16.56 46.63 2.44 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
98 100 7.928706 ACATTTGGGATCGATTGTTTTGTAAAA 59.071 29.630 0.00 0.00 0.00 1.52
188 194 4.530857 GGCGCCCGCTCTGTACAT 62.531 66.667 18.11 0.00 41.60 2.29
189 195 3.264897 GCGCCCGCTCTGTACATG 61.265 66.667 5.27 0.00 38.26 3.21
212 218 4.697756 CCCAAAGTGCGCTCGGGA 62.698 66.667 24.17 0.00 39.44 5.14
276 282 0.968901 TCGAACCCTAGACACGGCAT 60.969 55.000 0.00 0.00 0.00 4.40
333 339 2.049433 CGTCCTGCGTTCGTTCCT 60.049 61.111 0.00 0.00 35.54 3.36
446 452 3.435186 GTCCGCTTTGCTCCCTGC 61.435 66.667 0.00 0.00 43.25 4.85
587 956 6.500684 TCCTCAACTAGAATTGCATTTGAC 57.499 37.500 0.00 0.00 0.00 3.18
874 1306 6.211384 CCTAAATTCCCATCTCTTGGTTGTTT 59.789 38.462 0.00 0.00 44.83 2.83
886 1320 6.533367 TCTCTTGGTTGTTTGTTATTTGTTGC 59.467 34.615 0.00 0.00 0.00 4.17
953 1402 9.601971 TTTTGCGTCTATTGTATTTTTAGTGAC 57.398 29.630 0.00 0.00 0.00 3.67
971 7751 2.302733 TGACACATGTGGTAGACTGCAT 59.697 45.455 28.64 4.36 34.19 3.96
1034 7820 8.462016 ACAGTTTAATATGGATTCTGAAGCAAC 58.538 33.333 8.03 1.86 0.00 4.17
1190 7977 5.131142 CCTTATCAAGTACTTGGAGGGATGT 59.869 44.000 30.35 12.15 40.78 3.06
1425 8216 3.653352 GGCCAAGGTATAAGATTCCCTCT 59.347 47.826 0.00 0.00 34.96 3.69
1879 8695 5.823861 TTATCTCCAGCATTACTATGGCA 57.176 39.130 0.00 0.00 33.92 4.92
2096 8984 7.389053 CCTAACTTAAAGAAGCTTGAGATGTGT 59.611 37.037 2.10 0.00 35.97 3.72
2125 9015 0.824759 CCTCCAGTAAACTCTCCCCG 59.175 60.000 0.00 0.00 0.00 5.73
2252 9191 0.890683 GGTGGGCATTCAAGGACTTG 59.109 55.000 5.72 5.72 41.71 3.16
2413 9358 3.340814 AAGGACTGTAGCATGGTTCTG 57.659 47.619 1.12 4.70 0.00 3.02
2467 9412 1.586154 GGGCCAAGGTCATTGTCACG 61.586 60.000 4.39 0.00 37.17 4.35
2610 9626 6.059484 GGAAATTCGGTGGGAATACTTGATA 58.941 40.000 0.00 0.00 44.59 2.15
2807 9885 8.755696 TTCATGGTTTTAGCAAATATGTGAAC 57.244 30.769 0.00 0.00 0.00 3.18
2981 10119 3.902261 TTCTATATCGCCGTCGCTTTA 57.098 42.857 0.00 0.00 35.26 1.85
3070 10214 9.527157 TCAAAACAATTCACATAATTAGGAGGA 57.473 29.630 3.76 0.00 0.00 3.71
3071 10215 9.573133 CAAAACAATTCACATAATTAGGAGGAC 57.427 33.333 3.76 0.00 0.00 3.85
3073 10217 8.511604 AACAATTCACATAATTAGGAGGACTG 57.488 34.615 3.76 0.00 0.00 3.51
3074 10218 7.056635 ACAATTCACATAATTAGGAGGACTGG 58.943 38.462 3.76 0.00 0.00 4.00
3179 10791 2.969821 TCCAGCTTTGCTTTTAGGGA 57.030 45.000 0.00 0.00 36.40 4.20
3213 11074 7.765695 AATATGTCCATTATCGGCAAGAAAT 57.234 32.000 0.00 0.00 0.00 2.17
3222 11083 7.115378 CCATTATCGGCAAGAAATTAAGAATGC 59.885 37.037 0.00 0.00 0.00 3.56
3320 11187 7.630242 TCTTCATTTTGGTGTGATTATCTCC 57.370 36.000 0.00 0.00 0.00 3.71
3334 11201 8.424918 TGTGATTATCTCCTTTAGGATTGTCTC 58.575 37.037 0.00 0.00 44.46 3.36
3357 11224 3.202818 TGTTTGGACCATGAGGCATAGAT 59.797 43.478 0.00 0.00 39.06 1.98
3358 11225 3.497103 TTGGACCATGAGGCATAGATG 57.503 47.619 0.00 0.00 39.06 2.90
3359 11226 2.693210 TGGACCATGAGGCATAGATGA 58.307 47.619 0.00 0.00 39.06 2.92
3360 11227 2.636403 TGGACCATGAGGCATAGATGAG 59.364 50.000 0.00 0.00 39.06 2.90
3361 11228 2.902486 GGACCATGAGGCATAGATGAGA 59.098 50.000 0.00 0.00 39.06 3.27
3362 11229 3.326006 GGACCATGAGGCATAGATGAGAA 59.674 47.826 0.00 0.00 39.06 2.87
3363 11230 4.563168 GGACCATGAGGCATAGATGAGAAG 60.563 50.000 0.00 0.00 39.06 2.85
3364 11231 4.229639 ACCATGAGGCATAGATGAGAAGA 58.770 43.478 0.00 0.00 39.06 2.87
3365 11232 4.657504 ACCATGAGGCATAGATGAGAAGAA 59.342 41.667 0.00 0.00 39.06 2.52
3366 11233 4.996122 CCATGAGGCATAGATGAGAAGAAC 59.004 45.833 0.00 0.00 0.00 3.01
3367 11234 4.679373 TGAGGCATAGATGAGAAGAACC 57.321 45.455 0.00 0.00 0.00 3.62
3368 11235 4.033009 TGAGGCATAGATGAGAAGAACCA 58.967 43.478 0.00 0.00 0.00 3.67
3369 11236 4.657504 TGAGGCATAGATGAGAAGAACCAT 59.342 41.667 0.00 0.00 0.00 3.55
3370 11237 5.840693 TGAGGCATAGATGAGAAGAACCATA 59.159 40.000 0.00 0.00 0.00 2.74
3371 11238 6.107901 AGGCATAGATGAGAAGAACCATAC 57.892 41.667 0.00 0.00 0.00 2.39
3474 11342 5.192927 AGTGTGAGAAACAAATGTGGAAGA 58.807 37.500 0.00 0.00 41.57 2.87
3510 11378 1.476007 AAGAGGCGCACTGAGGACTT 61.476 55.000 10.83 0.56 0.00 3.01
3528 11396 4.442192 GGACTTCAATCAGGTGCCTACTAG 60.442 50.000 0.00 0.00 0.00 2.57
3529 11397 4.353777 ACTTCAATCAGGTGCCTACTAGA 58.646 43.478 0.00 0.00 0.00 2.43
3530 11398 4.965532 ACTTCAATCAGGTGCCTACTAGAT 59.034 41.667 0.00 0.00 0.00 1.98
3531 11399 5.426833 ACTTCAATCAGGTGCCTACTAGATT 59.573 40.000 0.00 0.00 33.64 2.40
3532 11400 5.282055 TCAATCAGGTGCCTACTAGATTG 57.718 43.478 16.56 16.56 42.51 2.67
3534 11402 2.398588 TCAGGTGCCTACTAGATTGGG 58.601 52.381 0.00 0.00 0.00 4.12
3535 11403 2.023404 TCAGGTGCCTACTAGATTGGGA 60.023 50.000 0.00 0.00 0.00 4.37
3536 11404 2.975489 CAGGTGCCTACTAGATTGGGAT 59.025 50.000 0.00 0.00 0.00 3.85
3537 11405 3.007398 CAGGTGCCTACTAGATTGGGATC 59.993 52.174 0.00 0.00 0.00 3.36
3538 11406 2.028930 GGTGCCTACTAGATTGGGATCG 60.029 54.545 0.00 0.00 37.37 3.69
3539 11407 1.618837 TGCCTACTAGATTGGGATCGC 59.381 52.381 2.14 2.14 37.37 4.58
3540 11408 1.402984 GCCTACTAGATTGGGATCGCG 60.403 57.143 0.00 0.00 37.37 5.87
3543 11411 1.367471 CTAGATTGGGATCGCGCCA 59.633 57.895 0.00 0.00 37.37 5.69
3545 11413 0.320683 TAGATTGGGATCGCGCCATG 60.321 55.000 0.00 0.00 37.37 3.66
3567 11435 4.717313 GAGGGTGCCGGTCCCAAC 62.717 72.222 29.22 21.14 46.82 3.77
3570 11438 4.941309 GGTGCCGGTCCCAACGTT 62.941 66.667 1.90 0.00 0.00 3.99
3571 11439 2.903350 GTGCCGGTCCCAACGTTT 60.903 61.111 1.90 0.00 0.00 3.60
3572 11440 2.124236 TGCCGGTCCCAACGTTTT 60.124 55.556 1.90 0.00 0.00 2.43
3573 11441 2.333581 GCCGGTCCCAACGTTTTG 59.666 61.111 1.90 0.00 0.00 2.44
3585 11453 3.733727 CCAACGTTTTGGTTAAGCATGTC 59.266 43.478 8.40 1.38 46.63 3.06
3586 11454 3.262135 ACGTTTTGGTTAAGCATGTCG 57.738 42.857 8.40 14.32 0.00 4.35
3587 11455 2.614983 ACGTTTTGGTTAAGCATGTCGT 59.385 40.909 18.43 18.43 0.00 4.34
3588 11456 2.970609 CGTTTTGGTTAAGCATGTCGTG 59.029 45.455 8.40 0.00 0.00 4.35
3601 11469 2.736144 TGTCGTGCCAAGTTAGTAGG 57.264 50.000 0.00 0.00 0.00 3.18
3602 11470 2.241160 TGTCGTGCCAAGTTAGTAGGA 58.759 47.619 0.00 0.00 0.00 2.94
3603 11471 2.230508 TGTCGTGCCAAGTTAGTAGGAG 59.769 50.000 0.00 0.00 0.00 3.69
3604 11472 2.230750 GTCGTGCCAAGTTAGTAGGAGT 59.769 50.000 0.00 0.00 0.00 3.85
3605 11473 2.230508 TCGTGCCAAGTTAGTAGGAGTG 59.769 50.000 0.00 0.00 0.00 3.51
3606 11474 2.029290 CGTGCCAAGTTAGTAGGAGTGT 60.029 50.000 0.00 0.00 0.00 3.55
3607 11475 3.192001 CGTGCCAAGTTAGTAGGAGTGTA 59.808 47.826 0.00 0.00 0.00 2.90
3608 11476 4.142227 CGTGCCAAGTTAGTAGGAGTGTAT 60.142 45.833 0.00 0.00 0.00 2.29
3609 11477 5.066893 CGTGCCAAGTTAGTAGGAGTGTATA 59.933 44.000 0.00 0.00 0.00 1.47
3610 11478 6.238953 CGTGCCAAGTTAGTAGGAGTGTATAT 60.239 42.308 0.00 0.00 0.00 0.86
3611 11479 7.498443 GTGCCAAGTTAGTAGGAGTGTATATT 58.502 38.462 0.00 0.00 0.00 1.28
3612 11480 7.985752 GTGCCAAGTTAGTAGGAGTGTATATTT 59.014 37.037 0.00 0.00 0.00 1.40
3613 11481 9.204337 TGCCAAGTTAGTAGGAGTGTATATTTA 57.796 33.333 0.00 0.00 0.00 1.40
3614 11482 9.694137 GCCAAGTTAGTAGGAGTGTATATTTAG 57.306 37.037 0.00 0.00 0.00 1.85
3615 11483 9.694137 CCAAGTTAGTAGGAGTGTATATTTAGC 57.306 37.037 0.00 0.00 0.00 3.09
3616 11484 9.395707 CAAGTTAGTAGGAGTGTATATTTAGCG 57.604 37.037 0.00 0.00 0.00 4.26
3617 11485 8.688747 AGTTAGTAGGAGTGTATATTTAGCGT 57.311 34.615 0.00 0.00 0.00 5.07
3618 11486 9.784531 AGTTAGTAGGAGTGTATATTTAGCGTA 57.215 33.333 0.00 0.00 0.00 4.42
3621 11489 8.859236 AGTAGGAGTGTATATTTAGCGTATGA 57.141 34.615 0.00 0.00 0.00 2.15
3622 11490 9.293404 AGTAGGAGTGTATATTTAGCGTATGAA 57.707 33.333 0.00 0.00 0.00 2.57
3625 11493 9.640963 AGGAGTGTATATTTAGCGTATGAATTC 57.359 33.333 0.00 0.00 0.00 2.17
3626 11494 9.419297 GGAGTGTATATTTAGCGTATGAATTCA 57.581 33.333 11.26 11.26 0.00 2.57
3679 11547 9.412460 AGAAATATTCATTTGTGATAGAAGGCA 57.588 29.630 0.00 0.00 34.44 4.75
3681 11549 9.976511 AAATATTCATTTGTGATAGAAGGCATG 57.023 29.630 0.00 0.00 33.01 4.06
3682 11550 8.929260 ATATTCATTTGTGATAGAAGGCATGA 57.071 30.769 0.00 0.00 0.00 3.07
3683 11551 6.688637 TTCATTTGTGATAGAAGGCATGAG 57.311 37.500 0.00 0.00 0.00 2.90
3687 11555 8.212995 TCATTTGTGATAGAAGGCATGAGATTA 58.787 33.333 0.00 0.00 0.00 1.75
3691 11559 9.716531 TTGTGATAGAAGGCATGAGATTATAAG 57.283 33.333 0.00 0.00 0.00 1.73
3692 11560 8.316946 TGTGATAGAAGGCATGAGATTATAAGG 58.683 37.037 0.00 0.00 0.00 2.69
3693 11561 7.279758 GTGATAGAAGGCATGAGATTATAAGGC 59.720 40.741 0.00 0.00 0.00 4.35
3694 11562 5.573380 AGAAGGCATGAGATTATAAGGCA 57.427 39.130 0.00 0.00 0.00 4.75
3695 11563 5.945310 AGAAGGCATGAGATTATAAGGCAA 58.055 37.500 0.00 0.00 0.00 4.52
3696 11564 5.767168 AGAAGGCATGAGATTATAAGGCAAC 59.233 40.000 0.00 0.00 0.00 4.17
3698 11566 5.638133 AGGCATGAGATTATAAGGCAACAT 58.362 37.500 0.00 0.00 41.41 2.71
3715 11583 8.314143 AGGCAACATAAAATTCAGAATGTTTG 57.686 30.769 3.77 5.57 39.80 2.93
3717 11585 9.202273 GGCAACATAAAATTCAGAATGTTTGTA 57.798 29.630 3.77 0.00 39.80 2.41
3724 12757 8.871686 AAAATTCAGAATGTTTGTAAGACCAC 57.128 30.769 0.00 0.00 37.40 4.16
3728 12761 7.397892 TCAGAATGTTTGTAAGACCACAAAA 57.602 32.000 3.19 0.00 46.81 2.44
3730 12763 7.338196 TCAGAATGTTTGTAAGACCACAAAAGA 59.662 33.333 3.19 0.00 46.81 2.52
3731 12764 7.432252 CAGAATGTTTGTAAGACCACAAAAGAC 59.568 37.037 3.19 0.00 46.81 3.01
3732 12765 5.224562 TGTTTGTAAGACCACAAAAGACG 57.775 39.130 3.19 0.00 46.81 4.18
3734 12767 1.862201 TGTAAGACCACAAAAGACGCG 59.138 47.619 3.53 3.53 0.00 6.01
3736 12769 1.092921 AAGACCACAAAAGACGCGCA 61.093 50.000 5.73 0.00 0.00 6.09
3739 12772 1.163420 ACCACAAAAGACGCGCATCA 61.163 50.000 6.14 0.00 0.00 3.07
3741 12774 1.321016 CACAAAAGACGCGCATCAAG 58.679 50.000 6.14 0.00 0.00 3.02
3743 12776 0.385849 CAAAAGACGCGCATCAAGCA 60.386 50.000 6.14 0.00 46.13 3.91
3744 12777 0.385974 AAAAGACGCGCATCAAGCAC 60.386 50.000 6.14 0.00 46.13 4.40
3747 12780 1.793613 GACGCGCATCAAGCACAAC 60.794 57.895 5.73 0.00 46.13 3.32
3749 12782 1.154169 CGCGCATCAAGCACAACAT 60.154 52.632 8.75 0.00 46.13 2.71
3759 12792 7.044510 CGCATCAAGCACAACATAAAAGAATAG 60.045 37.037 0.00 0.00 46.13 1.73
3762 12795 7.816640 TCAAGCACAACATAAAAGAATAGACC 58.183 34.615 0.00 0.00 0.00 3.85
3763 12796 7.446931 TCAAGCACAACATAAAAGAATAGACCA 59.553 33.333 0.00 0.00 0.00 4.02
3764 12797 7.759489 AGCACAACATAAAAGAATAGACCAA 57.241 32.000 0.00 0.00 0.00 3.67
3765 12798 8.177119 AGCACAACATAAAAGAATAGACCAAA 57.823 30.769 0.00 0.00 0.00 3.28
3766 12799 8.637986 AGCACAACATAAAAGAATAGACCAAAA 58.362 29.630 0.00 0.00 0.00 2.44
3767 12800 8.915654 GCACAACATAAAAGAATAGACCAAAAG 58.084 33.333 0.00 0.00 0.00 2.27
3768 12801 8.915654 CACAACATAAAAGAATAGACCAAAAGC 58.084 33.333 0.00 0.00 0.00 3.51
3769 12802 8.637986 ACAACATAAAAGAATAGACCAAAAGCA 58.362 29.630 0.00 0.00 0.00 3.91
3770 12803 9.474920 CAACATAAAAGAATAGACCAAAAGCAA 57.525 29.630 0.00 0.00 0.00 3.91
3771 12804 9.476202 AACATAAAAGAATAGACCAAAAGCAAC 57.524 29.630 0.00 0.00 0.00 4.17
3772 12805 8.637986 ACATAAAAGAATAGACCAAAAGCAACA 58.362 29.630 0.00 0.00 0.00 3.33
3775 13743 8.962884 AAAAGAATAGACCAAAAGCAACATTT 57.037 26.923 0.00 0.00 0.00 2.32
3785 13753 9.294030 GACCAAAAGCAACATTTAATAGATCAG 57.706 33.333 0.00 0.00 0.00 2.90
3787 13755 8.469200 CCAAAAGCAACATTTAATAGATCAGGA 58.531 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 9.618890 TTGGATGTTTGGATGTTTGAATTTAAA 57.381 25.926 0.00 0.00 0.00 1.52
47 49 9.050601 GTTTGGATGTTTGGATGTTTGAATTTA 57.949 29.630 0.00 0.00 0.00 1.40
49 51 7.052873 TGTTTGGATGTTTGGATGTTTGAATT 58.947 30.769 0.00 0.00 0.00 2.17
50 52 6.590068 TGTTTGGATGTTTGGATGTTTGAAT 58.410 32.000 0.00 0.00 0.00 2.57
51 53 5.982356 TGTTTGGATGTTTGGATGTTTGAA 58.018 33.333 0.00 0.00 0.00 2.69
52 54 5.604758 TGTTTGGATGTTTGGATGTTTGA 57.395 34.783 0.00 0.00 0.00 2.69
53 55 6.864360 AATGTTTGGATGTTTGGATGTTTG 57.136 33.333 0.00 0.00 0.00 2.93
54 56 7.261829 CAAATGTTTGGATGTTTGGATGTTT 57.738 32.000 0.00 0.00 34.59 2.83
55 57 6.864360 CAAATGTTTGGATGTTTGGATGTT 57.136 33.333 0.00 0.00 34.59 2.71
98 100 7.913297 CGTACATCATTAAAAATCGTTTGGGAT 59.087 33.333 0.00 0.00 0.00 3.85
258 264 0.806102 CATGCCGTGTCTAGGGTTCG 60.806 60.000 0.00 0.00 34.32 3.95
305 311 3.536917 CAGGACGCCGGATGCCTA 61.537 66.667 5.05 0.00 36.24 3.93
319 325 2.556287 GCAAGGAACGAACGCAGG 59.444 61.111 0.00 0.00 0.00 4.85
324 330 0.955919 CAGAGGGGCAAGGAACGAAC 60.956 60.000 0.00 0.00 0.00 3.95
420 426 1.810030 CAAAGCGGACCTACGGAGC 60.810 63.158 0.00 0.00 0.00 4.70
440 446 0.691078 AAGAATCTAGCGGGCAGGGA 60.691 55.000 0.00 0.00 0.00 4.20
446 452 4.920640 TTCACTCTAAGAATCTAGCGGG 57.079 45.455 0.00 0.00 0.00 6.13
576 945 2.713877 GGCCAAATGGTCAAATGCAAT 58.286 42.857 0.00 0.00 40.23 3.56
587 956 2.568090 GTCAGCGTGGCCAAATGG 59.432 61.111 7.24 0.00 38.53 3.16
831 1256 0.108756 GGGAGAAGTGCGGACAGTAC 60.109 60.000 10.52 0.00 35.57 2.73
874 1306 6.183360 TGTTCCTAGCAAAGCAACAAATAACA 60.183 34.615 0.00 0.00 0.00 2.41
886 1320 5.725362 AGTAGTAGCTTGTTCCTAGCAAAG 58.275 41.667 0.00 0.00 41.11 2.77
935 1376 9.773328 CCACATGTGTCACTAAAAATACAATAG 57.227 33.333 23.79 0.00 0.00 1.73
953 1402 1.399440 GCATGCAGTCTACCACATGTG 59.601 52.381 19.31 19.31 41.51 3.21
971 7751 3.115390 AGACAGGGAGCCTAAATTAGCA 58.885 45.455 0.00 0.00 29.64 3.49
1034 7820 3.000727 CTGGCCTTTTTACAGGTACTCG 58.999 50.000 3.32 0.00 34.60 4.18
1075 7862 1.065854 GCTAAGTCTGTCTGTGCCCAT 60.066 52.381 0.00 0.00 0.00 4.00
1190 7977 2.187100 TCACTGGCATGTCAGTCCATA 58.813 47.619 29.62 12.90 45.24 2.74
1425 8216 3.973206 TCACCGATAGAAAAGAGGCAA 57.027 42.857 0.00 0.00 39.76 4.52
1879 8695 7.093112 ACACAGATTAGTTAGAGGCAGAAGAAT 60.093 37.037 0.00 0.00 0.00 2.40
2096 8984 5.720041 AGAGTTTACTGGAGGCATACTTACA 59.280 40.000 0.00 0.00 0.00 2.41
2125 9015 1.216122 GATCAGGTGATCGAGCAAGC 58.784 55.000 4.22 0.00 41.15 4.01
2467 9412 3.070429 CGGGAGCATGCTTATCAAAAC 57.930 47.619 23.61 5.90 0.00 2.43
2610 9626 2.297033 GGACAACAATTGCTGACACCAT 59.703 45.455 15.55 0.00 0.00 3.55
2807 9885 5.088680 ACCATACAATTTGATGCCTTTGG 57.911 39.130 2.79 0.00 0.00 3.28
2970 10108 3.002348 AGCTGAATATTTAAAGCGACGGC 59.998 43.478 11.03 3.00 40.63 5.68
3027 10171 5.009210 TGTTTTGAGGTAAAAACTGGATCCG 59.991 40.000 7.39 4.62 45.90 4.18
3070 10214 6.070538 ACTGAATAGTTGTAGCTGATTCCAGT 60.071 38.462 0.00 0.00 36.94 4.00
3071 10215 6.344500 ACTGAATAGTTGTAGCTGATTCCAG 58.656 40.000 0.00 0.00 37.37 3.86
3073 10217 8.894768 ATAACTGAATAGTTGTAGCTGATTCC 57.105 34.615 0.00 0.00 46.28 3.01
3169 10781 7.939588 ACATATTTATCCAGTCTCCCTAAAAGC 59.060 37.037 0.00 0.00 0.00 3.51
3213 11074 7.018826 GTGTTAACATAGCAACGCATTCTTAA 58.981 34.615 12.26 0.00 35.67 1.85
3222 11083 4.201551 CCGTAGTGTGTTAACATAGCAACG 60.202 45.833 12.26 16.55 38.92 4.10
3320 11187 5.412904 GGTCCAAACAGAGACAATCCTAAAG 59.587 44.000 0.00 0.00 34.58 1.85
3334 11201 1.843368 ATGCCTCATGGTCCAAACAG 58.157 50.000 0.00 0.00 35.27 3.16
3385 11252 2.768492 GGAATGCAAGGAGGCGCTG 61.768 63.158 7.64 0.00 36.28 5.18
3386 11253 2.439156 GGAATGCAAGGAGGCGCT 60.439 61.111 7.64 0.00 36.28 5.92
3388 11255 3.204827 CGGGAATGCAAGGAGGCG 61.205 66.667 0.00 0.00 36.28 5.52
3398 11265 3.093835 TAGGGGTGGCCGGGAATG 61.094 66.667 2.18 0.00 0.00 2.67
3412 11279 4.256920 CACAAGTCATCTTCAACCCTAGG 58.743 47.826 0.06 0.06 0.00 3.02
3423 11290 3.008813 ACTCTTCCATGCACAAGTCATCT 59.991 43.478 0.00 0.00 0.00 2.90
3474 11342 4.401925 CCTCTTCCTCTTCAACCACAATT 58.598 43.478 0.00 0.00 0.00 2.32
3510 11378 4.101585 CCAATCTAGTAGGCACCTGATTGA 59.898 45.833 20.76 8.52 41.94 2.57
3528 11396 2.620112 CCATGGCGCGATCCCAATC 61.620 63.158 12.10 0.00 35.67 2.67
3529 11397 2.595463 CCATGGCGCGATCCCAAT 60.595 61.111 12.10 0.00 35.67 3.16
3550 11418 4.717313 GTTGGGACCGGCACCCTC 62.717 72.222 29.42 20.89 46.82 4.30
3555 11423 2.124236 AAAACGTTGGGACCGGCA 60.124 55.556 0.00 0.00 0.00 5.69
3556 11424 2.333581 CAAAACGTTGGGACCGGC 59.666 61.111 0.00 0.00 0.00 6.13
3564 11432 3.420576 CGACATGCTTAACCAAAACGTTG 59.579 43.478 0.00 0.00 34.25 4.10
3565 11433 3.065648 ACGACATGCTTAACCAAAACGTT 59.934 39.130 0.00 0.00 0.00 3.99
3567 11435 2.970609 CACGACATGCTTAACCAAAACG 59.029 45.455 0.00 0.00 0.00 3.60
3583 11451 2.230750 ACTCCTACTAACTTGGCACGAC 59.769 50.000 0.00 0.00 0.00 4.34
3585 11453 2.029290 ACACTCCTACTAACTTGGCACG 60.029 50.000 0.00 0.00 0.00 5.34
3586 11454 3.679824 ACACTCCTACTAACTTGGCAC 57.320 47.619 0.00 0.00 0.00 5.01
3587 11455 7.670605 AATATACACTCCTACTAACTTGGCA 57.329 36.000 0.00 0.00 0.00 4.92
3588 11456 9.694137 CTAAATATACACTCCTACTAACTTGGC 57.306 37.037 0.00 0.00 0.00 4.52
3589 11457 9.694137 GCTAAATATACACTCCTACTAACTTGG 57.306 37.037 0.00 0.00 0.00 3.61
3591 11459 9.129532 ACGCTAAATATACACTCCTACTAACTT 57.870 33.333 0.00 0.00 0.00 2.66
3592 11460 8.688747 ACGCTAAATATACACTCCTACTAACT 57.311 34.615 0.00 0.00 0.00 2.24
3595 11463 9.948964 TCATACGCTAAATATACACTCCTACTA 57.051 33.333 0.00 0.00 0.00 1.82
3596 11464 8.859236 TCATACGCTAAATATACACTCCTACT 57.141 34.615 0.00 0.00 0.00 2.57
3599 11467 9.640963 GAATTCATACGCTAAATATACACTCCT 57.359 33.333 0.00 0.00 0.00 3.69
3600 11468 9.419297 TGAATTCATACGCTAAATATACACTCC 57.581 33.333 3.38 0.00 0.00 3.85
3613 11481 9.853555 TTTTTATCATGTTTGAATTCATACGCT 57.146 25.926 19.77 10.11 34.96 5.07
3656 11524 9.358406 TCATGCCTTCTATCACAAATGAATATT 57.642 29.630 0.00 0.00 38.69 1.28
3660 11528 6.417258 TCTCATGCCTTCTATCACAAATGAA 58.583 36.000 0.00 0.00 38.69 2.57
3661 11529 5.993055 TCTCATGCCTTCTATCACAAATGA 58.007 37.500 0.00 0.00 39.83 2.57
3662 11530 6.879276 ATCTCATGCCTTCTATCACAAATG 57.121 37.500 0.00 0.00 0.00 2.32
3665 11533 9.716531 CTTATAATCTCATGCCTTCTATCACAA 57.283 33.333 0.00 0.00 0.00 3.33
3666 11534 8.316946 CCTTATAATCTCATGCCTTCTATCACA 58.683 37.037 0.00 0.00 0.00 3.58
3667 11535 7.279758 GCCTTATAATCTCATGCCTTCTATCAC 59.720 40.741 0.00 0.00 0.00 3.06
3668 11536 7.038088 TGCCTTATAATCTCATGCCTTCTATCA 60.038 37.037 0.00 0.00 0.00 2.15
3671 11539 6.686484 TGCCTTATAATCTCATGCCTTCTA 57.314 37.500 0.00 0.00 0.00 2.10
3672 11540 5.573380 TGCCTTATAATCTCATGCCTTCT 57.427 39.130 0.00 0.00 0.00 2.85
3673 11541 5.532406 TGTTGCCTTATAATCTCATGCCTTC 59.468 40.000 0.00 0.00 0.00 3.46
3674 11542 5.448654 TGTTGCCTTATAATCTCATGCCTT 58.551 37.500 0.00 0.00 0.00 4.35
3676 11544 5.972107 ATGTTGCCTTATAATCTCATGCC 57.028 39.130 0.00 0.00 0.00 4.40
3689 11557 8.776470 CAAACATTCTGAATTTTATGTTGCCTT 58.224 29.630 0.00 0.00 40.14 4.35
3690 11558 7.933033 ACAAACATTCTGAATTTTATGTTGCCT 59.067 29.630 0.00 0.00 40.14 4.75
3691 11559 8.086851 ACAAACATTCTGAATTTTATGTTGCC 57.913 30.769 0.00 0.00 40.14 4.52
3698 11566 9.959749 GTGGTCTTACAAACATTCTGAATTTTA 57.040 29.630 0.00 0.00 0.00 1.52
3705 11573 7.432252 GTCTTTTGTGGTCTTACAAACATTCTG 59.568 37.037 3.78 0.00 46.73 3.02
3706 11574 7.480810 GTCTTTTGTGGTCTTACAAACATTCT 58.519 34.615 3.78 0.00 46.73 2.40
3707 11575 6.413818 CGTCTTTTGTGGTCTTACAAACATTC 59.586 38.462 3.78 0.00 46.73 2.67
3708 11576 6.262601 CGTCTTTTGTGGTCTTACAAACATT 58.737 36.000 3.78 0.00 46.73 2.71
3709 11577 5.732247 GCGTCTTTTGTGGTCTTACAAACAT 60.732 40.000 3.78 0.00 46.73 2.71
3710 11578 4.437659 GCGTCTTTTGTGGTCTTACAAACA 60.438 41.667 3.78 0.00 46.73 2.83
3711 11579 4.033019 GCGTCTTTTGTGGTCTTACAAAC 58.967 43.478 3.78 0.00 46.73 2.93
3712 11580 3.242478 CGCGTCTTTTGTGGTCTTACAAA 60.242 43.478 0.00 0.00 45.78 2.83
3713 11581 2.285756 CGCGTCTTTTGTGGTCTTACAA 59.714 45.455 0.00 0.00 38.69 2.41
3715 11583 1.398071 GCGCGTCTTTTGTGGTCTTAC 60.398 52.381 8.43 0.00 0.00 2.34
3717 11585 1.092921 TGCGCGTCTTTTGTGGTCTT 61.093 50.000 8.43 0.00 0.00 3.01
3718 11586 0.884704 ATGCGCGTCTTTTGTGGTCT 60.885 50.000 8.43 0.00 0.00 3.85
3719 11587 0.452784 GATGCGCGTCTTTTGTGGTC 60.453 55.000 22.31 0.00 0.00 4.02
3722 11590 1.321016 CTTGATGCGCGTCTTTTGTG 58.679 50.000 28.53 9.73 0.00 3.33
3724 12757 0.385849 TGCTTGATGCGCGTCTTTTG 60.386 50.000 28.53 16.56 46.63 2.44
3734 12767 6.956299 ATTCTTTTATGTTGTGCTTGATGC 57.044 33.333 0.00 0.00 43.25 3.91
3736 12769 8.462016 GGTCTATTCTTTTATGTTGTGCTTGAT 58.538 33.333 0.00 0.00 0.00 2.57
3739 12772 7.759489 TGGTCTATTCTTTTATGTTGTGCTT 57.241 32.000 0.00 0.00 0.00 3.91
3741 12774 8.810652 TTTTGGTCTATTCTTTTATGTTGTGC 57.189 30.769 0.00 0.00 0.00 4.57
3743 12776 8.637986 TGCTTTTGGTCTATTCTTTTATGTTGT 58.362 29.630 0.00 0.00 0.00 3.32
3744 12777 9.474920 TTGCTTTTGGTCTATTCTTTTATGTTG 57.525 29.630 0.00 0.00 0.00 3.33
3747 12780 9.643693 ATGTTGCTTTTGGTCTATTCTTTTATG 57.356 29.630 0.00 0.00 0.00 1.90
3759 12792 9.294030 CTGATCTATTAAATGTTGCTTTTGGTC 57.706 33.333 0.00 0.00 0.00 4.02
3766 12799 9.851686 TGTAATCCTGATCTATTAAATGTTGCT 57.148 29.630 0.00 0.00 0.00 3.91
3777 13745 9.911788 AAATGACTTGTTGTAATCCTGATCTAT 57.088 29.630 0.00 0.00 0.00 1.98
3779 13747 9.911788 ATAAATGACTTGTTGTAATCCTGATCT 57.088 29.630 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.