Multiple sequence alignment - TraesCS5B01G284100

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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 TraesCS5B01G284100 chr5B 100.000 5347 0 0 1 5347 469970243 469975589 0.000000e+00 9875.0
1 TraesCS5B01G284100 chr5B 90.498 2210 107 34 2122 4308 467167005 467164876 0.000000e+00 2822.0
2 TraesCS5B01G284100 chr5B 96.066 1449 48 3 3 1443 15141153 15139706 0.000000e+00 2351.0
3 TraesCS5B01G284100 chr5B 90.732 205 14 3 4745 4947 467161634 467161433 8.830000e-68 268.0
4 TraesCS5B01G284100 chr5B 81.961 255 15 8 4500 4750 467164445 467164218 2.540000e-43 187.0
5 TraesCS5B01G284100 chr5B 97.222 108 2 1 2016 2123 15139704 15139598 1.180000e-41 182.0
6 TraesCS5B01G284100 chr5B 95.745 47 2 0 4308 4354 467164855 467164809 5.740000e-10 76.8
7 TraesCS5B01G284100 chr5D 92.623 3267 167 31 2122 5347 389696081 389699314 0.000000e+00 4630.0
8 TraesCS5B01G284100 chr5D 92.341 2089 93 27 2123 4173 388814484 388812425 0.000000e+00 2909.0
9 TraesCS5B01G284100 chr5D 90.137 365 17 5 4586 4947 388810414 388810066 1.760000e-124 457.0
10 TraesCS5B01G284100 chr5D 82.353 204 25 9 4195 4392 388812431 388812233 3.310000e-37 167.0
11 TraesCS5B01G284100 chr5A 93.750 1984 98 16 2423 4394 491709987 491711956 0.000000e+00 2953.0
12 TraesCS5B01G284100 chr5A 93.600 1672 85 13 2737 4399 493018141 493019799 0.000000e+00 2475.0
13 TraesCS5B01G284100 chr5A 85.771 1750 150 35 129 1817 33173467 33175178 0.000000e+00 1760.0
14 TraesCS5B01G284100 chr5A 91.366 915 51 11 4445 5345 493019804 493020704 0.000000e+00 1227.0
15 TraesCS5B01G284100 chr5A 91.182 499 28 9 2122 2609 493016778 493017271 0.000000e+00 664.0
16 TraesCS5B01G284100 chr5A 79.818 659 72 21 1190 1793 489106253 489106905 1.780000e-114 424.0
17 TraesCS5B01G284100 chr5A 85.781 429 25 16 4462 4885 491712252 491712649 6.400000e-114 422.0
18 TraesCS5B01G284100 chr5A 94.318 88 3 1 2638 2723 493017269 493017356 3.360000e-27 134.0
19 TraesCS5B01G284100 chr3D 93.651 1512 61 9 338 1817 95583904 95582396 0.000000e+00 2228.0
20 TraesCS5B01G284100 chr3D 95.130 965 36 4 2 961 264683454 264684412 0.000000e+00 1511.0
21 TraesCS5B01G284100 chr3D 91.339 889 45 4 957 1817 264686579 264687463 0.000000e+00 1186.0
22 TraesCS5B01G284100 chr3D 94.788 307 14 2 1817 2122 95582358 95582053 1.350000e-130 477.0
23 TraesCS5B01G284100 chr3D 90.584 308 13 4 1817 2123 264687501 264687793 1.400000e-105 394.0
24 TraesCS5B01G284100 chr3D 81.955 133 20 3 3737 3867 513621303 513621173 5.660000e-20 110.0
25 TraesCS5B01G284100 chr1A 86.505 1860 159 27 2 1802 532454748 532452922 0.000000e+00 1960.0
26 TraesCS5B01G284100 chr3A 86.405 1861 161 35 2 1802 65818486 65816658 0.000000e+00 1951.0
27 TraesCS5B01G284100 chr2A 86.062 1851 160 33 1 1793 596414442 596412632 0.000000e+00 1899.0
28 TraesCS5B01G284100 chr2A 85.838 1850 164 38 2 1793 431008086 431009895 0.000000e+00 1875.0
29 TraesCS5B01G284100 chr2A 81.029 680 66 18 1196 1817 505214821 505215495 2.900000e-132 483.0
30 TraesCS5B01G284100 chr2A 86.932 176 21 2 1817 1991 138831267 138831441 4.220000e-46 196.0
31 TraesCS5B01G284100 chr4D 85.892 1850 174 36 14 1802 252376651 252374828 0.000000e+00 1890.0
32 TraesCS5B01G284100 chr4D 85.398 1808 178 35 55 1802 252647854 252646073 0.000000e+00 1797.0
33 TraesCS5B01G284100 chr4D 82.704 821 81 21 1002 1773 252696920 252696112 0.000000e+00 673.0
34 TraesCS5B01G284100 chr4D 85.561 187 24 3 1630 1815 460997772 460997588 5.470000e-45 193.0
35 TraesCS5B01G284100 chr6A 92.808 1321 63 5 527 1817 35571642 35570324 0.000000e+00 1884.0
36 TraesCS5B01G284100 chr6A 94.079 304 15 3 1818 2120 35570285 35569984 4.880000e-125 459.0
37 TraesCS5B01G284100 chr2B 95.294 1020 42 2 2 1016 658919836 658918818 0.000000e+00 1613.0
38 TraesCS5B01G284100 chr2B 90.961 697 31 9 1456 2122 658918820 658918126 0.000000e+00 909.0
39 TraesCS5B01G284100 chr6B 83.495 721 53 12 1122 1793 559467685 559468388 3.540000e-171 612.0
40 TraesCS5B01G284100 chr6B 79.080 870 96 32 1196 1992 49313127 49312271 2.210000e-143 520.0
41 TraesCS5B01G284100 chr6B 90.265 226 20 2 1817 2041 559468447 559468671 1.460000e-75 294.0
42 TraesCS5B01G284100 chr7A 80.175 686 73 21 1190 1817 456202030 456201350 6.310000e-124 455.0
43 TraesCS5B01G284100 chr7B 79.818 659 72 21 1190 1793 542883090 542883742 1.780000e-114 424.0
44 TraesCS5B01G284100 chr1B 86.765 136 9 7 1837 1971 621990169 621990042 5.580000e-30 143.0
45 TraesCS5B01G284100 chr1B 87.755 49 6 0 5241 5289 618279161 618279113 2.080000e-04 58.4


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 TraesCS5B01G284100 chr5B 469970243 469975589 5346 False 9875.000000 9875 100.0000 1 5347 1 chr5B.!!$F1 5346
1 TraesCS5B01G284100 chr5B 15139598 15141153 1555 True 1266.500000 2351 96.6440 3 2123 2 chr5B.!!$R1 2120
2 TraesCS5B01G284100 chr5B 467161433 467167005 5572 True 838.450000 2822 89.7340 2122 4947 4 chr5B.!!$R2 2825
3 TraesCS5B01G284100 chr5D 389696081 389699314 3233 False 4630.000000 4630 92.6230 2122 5347 1 chr5D.!!$F1 3225
4 TraesCS5B01G284100 chr5D 388810066 388814484 4418 True 1177.666667 2909 88.2770 2123 4947 3 chr5D.!!$R1 2824
5 TraesCS5B01G284100 chr5A 33173467 33175178 1711 False 1760.000000 1760 85.7710 129 1817 1 chr5A.!!$F1 1688
6 TraesCS5B01G284100 chr5A 491709987 491712649 2662 False 1687.500000 2953 89.7655 2423 4885 2 chr5A.!!$F3 2462
7 TraesCS5B01G284100 chr5A 493016778 493020704 3926 False 1125.000000 2475 92.6165 2122 5345 4 chr5A.!!$F4 3223
8 TraesCS5B01G284100 chr5A 489106253 489106905 652 False 424.000000 424 79.8180 1190 1793 1 chr5A.!!$F2 603
9 TraesCS5B01G284100 chr3D 95582053 95583904 1851 True 1352.500000 2228 94.2195 338 2122 2 chr3D.!!$R2 1784
10 TraesCS5B01G284100 chr3D 264683454 264687793 4339 False 1030.333333 1511 92.3510 2 2123 3 chr3D.!!$F1 2121
11 TraesCS5B01G284100 chr1A 532452922 532454748 1826 True 1960.000000 1960 86.5050 2 1802 1 chr1A.!!$R1 1800
12 TraesCS5B01G284100 chr3A 65816658 65818486 1828 True 1951.000000 1951 86.4050 2 1802 1 chr3A.!!$R1 1800
13 TraesCS5B01G284100 chr2A 596412632 596414442 1810 True 1899.000000 1899 86.0620 1 1793 1 chr2A.!!$R1 1792
14 TraesCS5B01G284100 chr2A 431008086 431009895 1809 False 1875.000000 1875 85.8380 2 1793 1 chr2A.!!$F2 1791
15 TraesCS5B01G284100 chr2A 505214821 505215495 674 False 483.000000 483 81.0290 1196 1817 1 chr2A.!!$F3 621
16 TraesCS5B01G284100 chr4D 252374828 252376651 1823 True 1890.000000 1890 85.8920 14 1802 1 chr4D.!!$R1 1788
17 TraesCS5B01G284100 chr4D 252646073 252647854 1781 True 1797.000000 1797 85.3980 55 1802 1 chr4D.!!$R2 1747
18 TraesCS5B01G284100 chr4D 252696112 252696920 808 True 673.000000 673 82.7040 1002 1773 1 chr4D.!!$R3 771
19 TraesCS5B01G284100 chr6A 35569984 35571642 1658 True 1171.500000 1884 93.4435 527 2120 2 chr6A.!!$R1 1593
20 TraesCS5B01G284100 chr2B 658918126 658919836 1710 True 1261.000000 1613 93.1275 2 2122 2 chr2B.!!$R1 2120
21 TraesCS5B01G284100 chr6B 49312271 49313127 856 True 520.000000 520 79.0800 1196 1992 1 chr6B.!!$R1 796
22 TraesCS5B01G284100 chr6B 559467685 559468671 986 False 453.000000 612 86.8800 1122 2041 2 chr6B.!!$F1 919
23 TraesCS5B01G284100 chr7A 456201350 456202030 680 True 455.000000 455 80.1750 1190 1817 1 chr7A.!!$R1 627
24 TraesCS5B01G284100 chr7B 542883090 542883742 652 False 424.000000 424 79.8180 1190 1793 1 chr7B.!!$F1 603

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
818 835 2.028112 TGGAGACTTGACAGCCACATAC 60.028 50.000 0.0 0.0 0.00 2.39 F
926 945 3.165071 ACCAACCAGATTGTCAAATCCC 58.835 45.455 0.0 0.0 42.84 3.85 F
2099 4432 1.144969 GGTTTGATTGAGACGTGCGA 58.855 50.000 0.0 0.0 0.00 5.10 F
2169 4502 3.806949 TTGATAGAACTGGCTTGGGTT 57.193 42.857 0.0 0.0 0.00 4.11 F
3959 7114 0.036732 GGGTGGAAGTGAGATGTGCA 59.963 55.000 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 4087 0.107017 AGCCATAGCATTCACCGCTT 60.107 50.000 0.00 0.00 43.56 4.68 R
2554 4918 0.564171 TCATACCGGGGAGGGTGTAT 59.436 55.000 6.32 0.00 46.96 2.29 R
3881 7036 0.178903 TATCATTAGGGAGGCGGGCT 60.179 55.000 2.69 2.69 0.00 5.19 R
4081 7236 3.730761 CTGCTGCTTCACCACCGC 61.731 66.667 0.00 0.00 0.00 5.68 R
5274 12770 0.105778 TCATCACACCAGCGTCAACA 59.894 50.000 0.00 0.00 0.00 3.33 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
172 175 4.935205 GGACAACAATACATGTGTAGAGCA 59.065 41.667 9.11 0.00 42.99 4.26
406 420 2.287009 CCTTTTTCTTGCAGACGTGTCC 60.287 50.000 0.00 0.00 0.00 4.02
439 453 4.752101 ACTTTGAAGAGAAGTTCATCCGTG 59.248 41.667 5.50 0.00 36.34 4.94
653 670 7.115378 GCAGACTAAAATTTGAGTTGATGTTGG 59.885 37.037 9.66 0.00 0.00 3.77
818 835 2.028112 TGGAGACTTGACAGCCACATAC 60.028 50.000 0.00 0.00 0.00 2.39
926 945 3.165071 ACCAACCAGATTGTCAAATCCC 58.835 45.455 0.00 0.00 42.84 3.85
927 946 3.181418 ACCAACCAGATTGTCAAATCCCT 60.181 43.478 0.00 0.00 42.84 4.20
964 3155 5.122239 TGAACTCAGGAATTGTGAATAAGCG 59.878 40.000 0.00 0.00 0.00 4.68
1124 3323 5.946377 AGTTGCTTTTCCTCTAATAAGGTGG 59.054 40.000 0.00 0.00 37.69 4.61
1156 3355 4.081752 TGTTGTTGAATTGTGCAGAAAGGT 60.082 37.500 0.00 0.00 0.00 3.50
1735 4026 5.483685 TGTCTAAACTGTAATGGCACTCT 57.516 39.130 0.00 0.00 0.00 3.24
1794 4087 3.515286 CCGACGCTTCCCGCTCTA 61.515 66.667 0.00 0.00 41.76 2.43
1825 4157 2.902486 TGCTATGGCTCCCTGAAGATAG 59.098 50.000 1.68 0.00 39.59 2.08
1914 4246 4.734398 TTGTTCCAACTTTGCATTGAGT 57.266 36.364 0.01 0.00 0.00 3.41
2099 4432 1.144969 GGTTTGATTGAGACGTGCGA 58.855 50.000 0.00 0.00 0.00 5.10
2169 4502 3.806949 TTGATAGAACTGGCTTGGGTT 57.193 42.857 0.00 0.00 0.00 4.11
2226 4560 8.865590 AATGAACTGTGTTGTTTAACCATAAC 57.134 30.769 0.00 0.00 35.92 1.89
2440 4802 7.611467 ACACCTAATTCACATTGAGCTTATTCA 59.389 33.333 0.00 0.00 0.00 2.57
2483 4845 7.883391 AATTCGAGAATAGTAGAGAGGAACA 57.117 36.000 0.00 0.00 0.00 3.18
2497 4860 4.579869 AGAGGAACATATGTCACCACAAC 58.420 43.478 24.32 15.85 35.64 3.32
2730 5104 4.592942 TCAATCAACTCCTTAGCAATGCT 58.407 39.130 13.92 13.92 43.41 3.79
2796 5934 6.712547 AGGCTTCGGAATATCTTCAAATAAGG 59.287 38.462 0.00 0.00 32.70 2.69
3055 6195 5.824429 ACTTGTTTCATTGTGACATCAGTG 58.176 37.500 0.00 0.00 0.00 3.66
3074 6214 6.484288 TCAGTGACAAAATCCTATGGTCATT 58.516 36.000 0.00 0.00 40.23 2.57
3077 6217 8.090214 CAGTGACAAAATCCTATGGTCATTTTT 58.910 33.333 0.00 0.00 40.23 1.94
3103 6243 5.070313 ACACTTATTCCATTGTTGCTTTGGT 59.930 36.000 0.00 0.00 0.00 3.67
3110 6250 4.220382 TCCATTGTTGCTTTGGTGGATTAG 59.780 41.667 0.00 0.00 31.24 1.73
3246 6389 7.375834 ACATAGTTCGATGTCAAGAGTTTACA 58.624 34.615 0.00 0.00 34.97 2.41
3315 6458 6.825721 ACATATTCAACCTAGCCTTCTTTGAG 59.174 38.462 0.00 0.00 0.00 3.02
3340 6483 7.067494 AGCTTGACAAAGAGTGTGAGTATTTTT 59.933 33.333 0.00 0.00 41.96 1.94
3341 6484 7.377131 GCTTGACAAAGAGTGTGAGTATTTTTC 59.623 37.037 0.00 0.00 41.96 2.29
3342 6485 7.857734 TGACAAAGAGTGTGAGTATTTTTCA 57.142 32.000 0.00 0.00 41.96 2.69
3344 6487 8.902806 TGACAAAGAGTGTGAGTATTTTTCATT 58.097 29.630 0.00 0.00 41.96 2.57
3408 6552 5.925397 TGTGCATACATGTTGGTTTTGATTC 59.075 36.000 2.30 0.00 0.00 2.52
3692 6843 7.286316 CCTCCAATCTTTTCCTATGCTTATGTT 59.714 37.037 0.00 0.00 0.00 2.71
3696 6851 6.207691 TCTTTTCCTATGCTTATGTTTGGC 57.792 37.500 0.00 0.00 0.00 4.52
3706 6861 3.989817 GCTTATGTTTGGCTCCAAAACAG 59.010 43.478 14.97 9.76 45.86 3.16
3718 6873 5.166398 GCTCCAAAACAGATGGAAAGATTG 58.834 41.667 0.00 0.00 45.96 2.67
3734 6889 8.457261 TGGAAAGATTGTTTTGGTTGAATTTTG 58.543 29.630 0.00 0.00 0.00 2.44
3881 7036 3.804036 AGGTGTGATCGTTTTCAACAGA 58.196 40.909 0.00 0.00 0.00 3.41
3959 7114 0.036732 GGGTGGAAGTGAGATGTGCA 59.963 55.000 0.00 0.00 0.00 4.57
4034 7189 3.551046 CGTGTAGTGTCTCAAGAGTTGCT 60.551 47.826 0.00 0.00 0.00 3.91
4082 7237 9.413048 GAGTATAGTATGGATCTTTACAACAGC 57.587 37.037 0.00 0.00 0.00 4.40
4319 7495 3.873952 GGACAGCTGTTATGATCAAGGAC 59.126 47.826 22.65 2.62 0.00 3.85
4348 7524 3.005554 ACGAGAGCCTTTTGATGTGATG 58.994 45.455 0.00 0.00 0.00 3.07
4349 7525 2.223203 CGAGAGCCTTTTGATGTGATGC 60.223 50.000 0.00 0.00 0.00 3.91
4350 7526 1.741706 AGAGCCTTTTGATGTGATGCG 59.258 47.619 0.00 0.00 0.00 4.73
4351 7527 0.171903 AGCCTTTTGATGTGATGCGC 59.828 50.000 0.00 0.00 0.00 6.09
4352 7528 0.803380 GCCTTTTGATGTGATGCGCC 60.803 55.000 4.18 0.00 0.00 6.53
4353 7529 0.813184 CCTTTTGATGTGATGCGCCT 59.187 50.000 4.18 0.00 0.00 5.52
4354 7530 1.203052 CCTTTTGATGTGATGCGCCTT 59.797 47.619 4.18 0.00 0.00 4.35
4355 7531 2.353011 CCTTTTGATGTGATGCGCCTTT 60.353 45.455 4.18 0.00 0.00 3.11
4356 7532 3.319755 CTTTTGATGTGATGCGCCTTTT 58.680 40.909 4.18 0.00 0.00 2.27
4357 7533 2.350899 TTGATGTGATGCGCCTTTTG 57.649 45.000 4.18 0.00 0.00 2.44
4358 7534 1.532523 TGATGTGATGCGCCTTTTGA 58.467 45.000 4.18 0.00 0.00 2.69
4359 7535 2.093890 TGATGTGATGCGCCTTTTGAT 58.906 42.857 4.18 0.00 0.00 2.57
4360 7536 2.159352 TGATGTGATGCGCCTTTTGATG 60.159 45.455 4.18 0.00 0.00 3.07
4361 7537 1.246649 TGTGATGCGCCTTTTGATGT 58.753 45.000 4.18 0.00 0.00 3.06
4362 7538 1.068402 TGTGATGCGCCTTTTGATGTG 60.068 47.619 4.18 0.00 0.00 3.21
4363 7539 1.199789 GTGATGCGCCTTTTGATGTGA 59.800 47.619 4.18 0.00 0.00 3.58
4364 7540 2.093890 TGATGCGCCTTTTGATGTGAT 58.906 42.857 4.18 0.00 0.00 3.06
4399 7578 4.042062 TCTGTTTGATGGATGGAAGACACT 59.958 41.667 0.00 0.00 0.00 3.55
4403 7582 2.025981 TGATGGATGGAAGACACTTGGG 60.026 50.000 0.00 0.00 0.00 4.12
4433 7612 4.460034 TGAGTCGTAGTGTATACAGGCAAA 59.540 41.667 5.62 0.00 0.00 3.68
4434 7613 5.047872 TGAGTCGTAGTGTATACAGGCAAAA 60.048 40.000 5.62 0.00 0.00 2.44
4436 7615 5.810587 AGTCGTAGTGTATACAGGCAAAATG 59.189 40.000 5.62 0.00 0.00 2.32
4439 7618 6.753279 TCGTAGTGTATACAGGCAAAATGTAC 59.247 38.462 5.62 0.00 36.04 2.90
4440 7619 6.532302 CGTAGTGTATACAGGCAAAATGTACA 59.468 38.462 5.62 0.00 36.04 2.90
4443 7622 4.638421 TGTATACAGGCAAAATGTACAGGC 59.362 41.667 0.08 0.00 36.04 4.85
4444 7623 1.993956 ACAGGCAAAATGTACAGGCA 58.006 45.000 0.33 0.00 0.00 4.75
4486 9375 5.010012 ACCAAGCTGAAAAGTTGTATCCAAG 59.990 40.000 0.00 0.00 0.00 3.61
4493 9382 7.653311 GCTGAAAAGTTGTATCCAAGACAATTT 59.347 33.333 0.00 0.00 38.94 1.82
4551 9440 0.466189 ATGGTAGCGCAAAGGGGATG 60.466 55.000 11.47 0.00 0.00 3.51
4565 9455 2.157738 GGGGATGCATGATTAGCTGAC 58.842 52.381 2.46 0.00 0.00 3.51
4593 9483 2.621055 ACAGTATCTAGCCGAGCTGAAG 59.379 50.000 8.44 0.09 40.10 3.02
4621 9511 8.671384 AAATATTTAAGCTGGAACGCTGTATA 57.329 30.769 0.00 0.00 38.11 1.47
4664 9554 5.967088 AGATGTCAGCGTAAATCACTAGTT 58.033 37.500 0.00 0.00 0.00 2.24
4938 12424 2.664402 ACTGCCTCCTTCAACAACAT 57.336 45.000 0.00 0.00 0.00 2.71
4950 12436 4.291540 TCAACAACATGAAGTGCTGAAC 57.708 40.909 0.00 0.00 0.00 3.18
4955 12441 6.005583 ACAACATGAAGTGCTGAACATTAG 57.994 37.500 0.00 0.00 0.00 1.73
5048 12543 0.594602 CCGGGACTCGTTATCGCATA 59.405 55.000 0.00 0.00 37.11 3.14
5060 12555 9.646336 ACTCGTTATCGCATAATAAATTTGTTC 57.354 29.630 3.18 0.00 36.96 3.18
5097 12592 1.002624 GGGCGATTTGGACCTCACA 60.003 57.895 0.00 0.00 29.93 3.58
5160 12655 6.949352 AGTGATCAACTCTTTTGTCAACAT 57.051 33.333 0.00 0.00 31.64 2.71
5188 12683 8.256611 TCATTGATGAACTGAAGCTAGTAAAC 57.743 34.615 0.00 0.00 33.08 2.01
5274 12770 3.508845 ACGGGCTATGCTAAAATCCAT 57.491 42.857 0.00 0.00 0.00 3.41
5289 12785 0.884259 TCCATGTTGACGCTGGTGTG 60.884 55.000 0.00 0.00 0.00 3.82
5290 12786 0.884259 CCATGTTGACGCTGGTGTGA 60.884 55.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.981400 AAATAAAACGGTGCCTCGTG 57.019 45.000 2.25 0.00 43.07 4.35
145 146 1.809547 CACATGTATTGTTGTCCGCCA 59.190 47.619 0.00 0.00 36.00 5.69
406 420 8.655651 AACTTCTCTTCAAAGTCTAGTTTCAG 57.344 34.615 0.00 0.00 35.96 3.02
439 453 6.013293 AGGCATAGAAGGTAGAATTCCCATAC 60.013 42.308 0.65 0.00 0.00 2.39
653 670 9.937175 GGCTGAGATTAACATAATTGTAGAAAC 57.063 33.333 0.00 0.00 34.06 2.78
818 835 7.063074 CGGTTCAGTAGGTCAGTGTAAAATAAG 59.937 40.741 0.00 0.00 0.00 1.73
926 945 7.615582 TCCTGAGTTCAGCATAAAACAATAG 57.384 36.000 3.58 0.00 42.47 1.73
927 946 7.994425 TTCCTGAGTTCAGCATAAAACAATA 57.006 32.000 3.58 0.00 42.47 1.90
964 3155 6.966066 GCACTGATATCTTCAAAAGCTTTCTC 59.034 38.462 13.10 1.02 32.78 2.87
1124 3323 5.389098 GCACAATTCAACAACAAGCATGATC 60.389 40.000 0.00 0.00 0.00 2.92
1479 3688 1.630223 TTGGGCATGTGCAGATCAAA 58.370 45.000 7.36 0.00 44.36 2.69
1523 3740 2.380084 CCGTGCAGAAAGGCTACTAA 57.620 50.000 0.00 0.00 34.04 2.24
1622 3885 6.098982 AGGTTCATGGTAAGGACATTCTCTAG 59.901 42.308 0.00 0.00 0.00 2.43
1794 4087 0.107017 AGCCATAGCATTCACCGCTT 60.107 50.000 0.00 0.00 43.56 4.68
1825 4157 1.403780 CCTTGGATTCAAGCTGCTTGC 60.404 52.381 32.02 20.49 46.69 4.01
1835 4167 9.807921 ACTAAATTAGTTTTCTCCTTGGATTCA 57.192 29.630 0.00 0.00 34.86 2.57
1941 4274 3.831911 TCTTGGGCGAAAATCAAAGGAAT 59.168 39.130 0.00 0.00 0.00 3.01
2099 4432 4.559906 TACTAGTAAGTGTGCACGTGCAAT 60.560 41.667 42.04 28.81 44.14 3.56
2169 4502 8.085296 ACCGTGCATTTGATTTAGACAAATTAA 58.915 29.630 0.00 0.00 43.22 1.40
2192 4526 8.568732 AAACAACACAGTTCATTATTAAACCG 57.431 30.769 0.00 0.00 0.00 4.44
2287 4621 8.939201 TGTTTTTGTTTCATACATGATGTTGT 57.061 26.923 2.29 0.00 36.44 3.32
2384 4746 8.073768 TCCAACTTTAGCAAAAATCTCGTAAAG 58.926 33.333 0.00 0.00 34.87 1.85
2483 4845 6.463995 AGTTTTTGTGTTGTGGTGACATAT 57.536 33.333 0.00 0.00 46.14 1.78
2497 4860 8.930760 TGAAATCCAACACTTTTAGTTTTTGTG 58.069 29.630 0.00 0.00 35.09 3.33
2554 4918 0.564171 TCATACCGGGGAGGGTGTAT 59.436 55.000 6.32 0.00 46.96 2.29
2796 5934 1.139853 CAGGCTAGGTCAATCAGTCCC 59.860 57.143 0.00 0.00 0.00 4.46
2940 6078 0.878086 TGTCGCTCGAACATGTTGCA 60.878 50.000 17.58 0.49 0.00 4.08
2941 6079 0.234625 TTGTCGCTCGAACATGTTGC 59.765 50.000 17.58 12.45 0.00 4.17
3074 6214 9.606631 AAAGCAACAATGGAATAAGTGTAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
3077 6217 7.151308 CCAAAGCAACAATGGAATAAGTGTAA 58.849 34.615 0.00 0.00 36.27 2.41
3116 6256 4.277423 CCACAACACGAGGGTAAGATTTTT 59.723 41.667 0.00 0.00 0.00 1.94
3267 6410 0.971959 ATCGGGTACGGGTGTAAGCA 60.972 55.000 0.00 0.00 41.39 3.91
3315 6458 5.931441 AATACTCACACTCTTTGTCAAGC 57.069 39.130 0.00 0.00 35.67 4.01
3408 6552 1.138859 TGGATAGAGGCCACAATCACG 59.861 52.381 5.01 0.00 0.00 4.35
3692 6843 2.673775 TCCATCTGTTTTGGAGCCAA 57.326 45.000 0.00 0.00 38.35 4.52
3696 6851 6.336842 ACAATCTTTCCATCTGTTTTGGAG 57.663 37.500 0.00 0.00 43.87 3.86
3706 6861 7.967890 ATTCAACCAAAACAATCTTTCCATC 57.032 32.000 0.00 0.00 0.00 3.51
3718 6873 7.148836 CCTGCAAAAACAAAATTCAACCAAAAC 60.149 33.333 0.00 0.00 0.00 2.43
3881 7036 0.178903 TATCATTAGGGAGGCGGGCT 60.179 55.000 2.69 2.69 0.00 5.19
3959 7114 9.672673 GTAGCTTCAATGGGATATACAACATAT 57.327 33.333 0.00 0.00 0.00 1.78
4034 7189 4.473196 TCATAATTCTTGGTAGTCCAGGCA 59.527 41.667 0.00 0.00 45.22 4.75
4080 7235 4.254709 TGCTGCTTCACCACCGCT 62.255 61.111 0.00 0.00 0.00 5.52
4081 7236 3.730761 CTGCTGCTTCACCACCGC 61.731 66.667 0.00 0.00 0.00 5.68
4082 7237 3.730761 GCTGCTGCTTCACCACCG 61.731 66.667 8.53 0.00 36.03 4.94
4348 7524 1.135699 CGCATCACATCAAAAGGCGC 61.136 55.000 0.00 0.00 36.46 6.53
4349 7525 0.523968 CCGCATCACATCAAAAGGCG 60.524 55.000 0.00 0.00 42.35 5.52
4350 7526 0.803380 GCCGCATCACATCAAAAGGC 60.803 55.000 0.00 0.00 36.32 4.35
4351 7527 0.523968 CGCCGCATCACATCAAAAGG 60.524 55.000 0.00 0.00 0.00 3.11
4352 7528 0.523968 CCGCCGCATCACATCAAAAG 60.524 55.000 0.00 0.00 0.00 2.27
4353 7529 0.957888 TCCGCCGCATCACATCAAAA 60.958 50.000 0.00 0.00 0.00 2.44
4354 7530 1.368345 CTCCGCCGCATCACATCAAA 61.368 55.000 0.00 0.00 0.00 2.69
4355 7531 1.815003 CTCCGCCGCATCACATCAA 60.815 57.895 0.00 0.00 0.00 2.57
4356 7532 2.202919 CTCCGCCGCATCACATCA 60.203 61.111 0.00 0.00 0.00 3.07
4357 7533 3.643978 GCTCCGCCGCATCACATC 61.644 66.667 0.00 0.00 0.00 3.06
4399 7578 6.045072 ACACTACGACTCATAATTTCCCAA 57.955 37.500 0.00 0.00 0.00 4.12
4403 7582 9.395707 CCTGTATACACTACGACTCATAATTTC 57.604 37.037 0.08 0.00 0.00 2.17
4433 7612 3.306225 CCTGTGCATTTTGCCTGTACATT 60.306 43.478 0.00 0.00 44.23 2.71
4434 7613 2.231964 CCTGTGCATTTTGCCTGTACAT 59.768 45.455 0.00 0.00 44.23 2.29
4436 7615 1.885887 TCCTGTGCATTTTGCCTGTAC 59.114 47.619 0.00 0.00 44.23 2.90
4439 7618 1.404986 CCATCCTGTGCATTTTGCCTG 60.405 52.381 0.00 0.00 44.23 4.85
4440 7619 0.899720 CCATCCTGTGCATTTTGCCT 59.100 50.000 0.00 0.00 44.23 4.75
4443 7622 3.244146 TGGTTTCCATCCTGTGCATTTTG 60.244 43.478 0.00 0.00 0.00 2.44
4444 7623 2.971330 TGGTTTCCATCCTGTGCATTTT 59.029 40.909 0.00 0.00 0.00 1.82
4486 9375 7.661437 TGCCTGTATACATCCTATGAAATTGTC 59.339 37.037 5.91 0.00 0.00 3.18
4493 9382 7.517320 ACATTTTGCCTGTATACATCCTATGA 58.483 34.615 5.91 0.00 0.00 2.15
4551 9440 2.064762 CGCCTAGTCAGCTAATCATGC 58.935 52.381 0.00 0.00 0.00 4.06
4565 9455 1.465387 CGGCTAGATACTGTCGCCTAG 59.535 57.143 0.00 0.00 38.58 3.02
4593 9483 5.004726 CAGCGTTCCAGCTTAAATATTTTGC 59.995 40.000 5.91 11.17 46.80 3.68
4621 9511 9.277783 GACATCTATAAGCAGGATACAATTTGT 57.722 33.333 7.30 7.30 41.41 2.83
4679 9569 0.107456 ATGTAGAATGGCTGGCTCCG 59.893 55.000 2.00 0.00 0.00 4.63
4938 12424 6.041423 TCTCATCTAATGTTCAGCACTTCA 57.959 37.500 0.00 0.00 0.00 3.02
4950 12436 6.867550 TGCCCGTCTATATTCTCATCTAATG 58.132 40.000 0.00 0.00 0.00 1.90
4955 12441 4.461081 AGTCTGCCCGTCTATATTCTCATC 59.539 45.833 0.00 0.00 0.00 2.92
5025 12520 0.737219 CGATAACGAGTCCCGGAGTT 59.263 55.000 0.73 3.72 43.93 3.01
5048 12543 5.180492 TGACCGAGAAGCGAACAAATTTATT 59.820 36.000 0.00 0.00 44.57 1.40
5060 12555 0.730834 CACAGAGTGACCGAGAAGCG 60.731 60.000 0.00 0.00 35.23 4.68
5097 12592 2.684881 CCTTCATGAATTGCCTTACGCT 59.315 45.455 8.96 0.00 38.78 5.07
5107 12602 6.168389 GGTTTGAAAGATGCCTTCATGAATT 58.832 36.000 8.96 0.00 31.96 2.17
5177 12672 3.616802 GCCTTCTCCACGTTTACTAGCTT 60.617 47.826 0.00 0.00 0.00 3.74
5179 12674 2.269172 GCCTTCTCCACGTTTACTAGC 58.731 52.381 0.00 0.00 0.00 3.42
5188 12683 0.732880 CGTGTACTGCCTTCTCCACG 60.733 60.000 0.00 0.00 39.51 4.94
5274 12770 0.105778 TCATCACACCAGCGTCAACA 59.894 50.000 0.00 0.00 0.00 3.33
5289 12785 3.084786 CAAACCTCCCCTGACTTTCATC 58.915 50.000 0.00 0.00 0.00 2.92
5290 12786 2.225117 CCAAACCTCCCCTGACTTTCAT 60.225 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.