Multiple sequence alignment - TraesCS2B01G504900

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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 TraesCS2B01G504900 chr2B 100.000 4703 0 0 1 4703 699106747 699111449 0.000000e+00 8685.0
1 TraesCS2B01G504900 chr2D 94.097 4083 205 17 1 4058 580191095 580195166 0.000000e+00 6172.0
2 TraesCS2B01G504900 chr2A 91.067 2597 177 27 2121 4691 718119194 718121761 0.000000e+00 3459.0
3 TraesCS2B01G504900 chr2A 94.044 722 40 1 890 1608 718117702 718118423 0.000000e+00 1092.0
4 TraesCS2B01G504900 chr2A 93.534 232 11 4 2 233 718117148 718117375 4.510000e-90 342.0
5 TraesCS2B01G504900 chr4A 82.499 3257 498 41 523 3733 531387113 531383883 0.000000e+00 2791.0
6 TraesCS2B01G504900 chr4A 83.367 2970 440 28 966 3889 531680587 531677626 0.000000e+00 2699.0
7 TraesCS2B01G504900 chr4A 81.360 2441 376 36 1478 3889 532215676 532218066 0.000000e+00 1914.0
8 TraesCS2B01G504900 chr4A 76.607 949 163 30 998 1914 626302344 626301423 7.130000e-128 468.0
9 TraesCS2B01G504900 chr4A 89.189 74 8 0 4402 4475 532218596 532218669 5.010000e-15 93.5
10 TraesCS2B01G504900 chr4B 83.988 2929 420 25 966 3853 95069187 95072107 0.000000e+00 2765.0
11 TraesCS2B01G504900 chr4B 81.541 3115 513 32 998 4067 94791598 94788501 0.000000e+00 2510.0
12 TraesCS2B01G504900 chr4D 83.670 2970 431 28 966 3889 64537953 64540914 0.000000e+00 2748.0
13 TraesCS2B01G504900 chr4D 81.837 1470 250 11 1013 2476 64356167 64354709 0.000000e+00 1219.0
14 TraesCS2B01G504900 chr4D 80.348 1435 217 35 2472 3871 64349333 64347929 0.000000e+00 1027.0
15 TraesCS2B01G504900 chr4D 88.636 88 8 1 4402 4487 64340094 64340007 6.440000e-19 106.0
16 TraesCS2B01G504900 chrUn 95.048 828 28 4 378 1193 77012756 77013582 0.000000e+00 1290.0
17 TraesCS2B01G504900 chrUn 94.807 828 30 4 378 1193 76993128 76993954 0.000000e+00 1279.0
18 TraesCS2B01G504900 chrUn 95.250 800 26 3 406 1193 396331612 396330813 0.000000e+00 1256.0
19 TraesCS2B01G504900 chrUn 96.730 581 18 1 614 1193 360279780 360280360 0.000000e+00 966.0
20 TraesCS2B01G504900 chr6B 96.730 581 18 1 614 1193 76423316 76423896 0.000000e+00 966.0
21 TraesCS2B01G504900 chr7B 84.127 315 45 4 3596 3908 23663674 23663363 2.750000e-77 300.0
22 TraesCS2B01G504900 chr3B 74.785 349 75 7 982 1320 573979269 573978924 1.360000e-30 145.0
23 TraesCS2B01G504900 chr7A 90.323 62 1 4 221 281 625535712 625535769 5.050000e-10 76.8
24 TraesCS2B01G504900 chr5D 95.652 46 1 1 234 279 482103314 482103358 6.530000e-09 73.1
25 TraesCS2B01G504900 chr5D 100.000 29 0 0 234 262 11299598 11299570 2.000000e-03 54.7
26 TraesCS2B01G504900 chr7D 93.617 47 2 1 237 283 58800481 58800526 8.440000e-08 69.4
27 TraesCS2B01G504900 chr7D 95.000 40 1 1 238 277 452702998 452703036 1.410000e-05 62.1
28 TraesCS2B01G504900 chr1A 89.286 56 3 3 234 288 58710004 58709951 3.040000e-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 TraesCS2B01G504900 chr2B 699106747 699111449 4702 False 8685.00 8685 100.000000 1 4703 1 chr2B.!!$F1 4702
1 TraesCS2B01G504900 chr2D 580191095 580195166 4071 False 6172.00 6172 94.097000 1 4058 1 chr2D.!!$F1 4057
2 TraesCS2B01G504900 chr2A 718117148 718121761 4613 False 1631.00 3459 92.881667 2 4691 3 chr2A.!!$F1 4689
3 TraesCS2B01G504900 chr4A 531383883 531387113 3230 True 2791.00 2791 82.499000 523 3733 1 chr4A.!!$R1 3210
4 TraesCS2B01G504900 chr4A 531677626 531680587 2961 True 2699.00 2699 83.367000 966 3889 1 chr4A.!!$R2 2923
5 TraesCS2B01G504900 chr4A 532215676 532218669 2993 False 1003.75 1914 85.274500 1478 4475 2 chr4A.!!$F1 2997
6 TraesCS2B01G504900 chr4A 626301423 626302344 921 True 468.00 468 76.607000 998 1914 1 chr4A.!!$R3 916
7 TraesCS2B01G504900 chr4B 95069187 95072107 2920 False 2765.00 2765 83.988000 966 3853 1 chr4B.!!$F1 2887
8 TraesCS2B01G504900 chr4B 94788501 94791598 3097 True 2510.00 2510 81.541000 998 4067 1 chr4B.!!$R1 3069
9 TraesCS2B01G504900 chr4D 64537953 64540914 2961 False 2748.00 2748 83.670000 966 3889 1 chr4D.!!$F1 2923
10 TraesCS2B01G504900 chr4D 64354709 64356167 1458 True 1219.00 1219 81.837000 1013 2476 1 chr4D.!!$R3 1463
11 TraesCS2B01G504900 chr4D 64347929 64349333 1404 True 1027.00 1027 80.348000 2472 3871 1 chr4D.!!$R2 1399
12 TraesCS2B01G504900 chrUn 77012756 77013582 826 False 1290.00 1290 95.048000 378 1193 1 chrUn.!!$F2 815
13 TraesCS2B01G504900 chrUn 76993128 76993954 826 False 1279.00 1279 94.807000 378 1193 1 chrUn.!!$F1 815
14 TraesCS2B01G504900 chrUn 396330813 396331612 799 True 1256.00 1256 95.250000 406 1193 1 chrUn.!!$R1 787
15 TraesCS2B01G504900 chrUn 360279780 360280360 580 False 966.00 966 96.730000 614 1193 1 chrUn.!!$F3 579
16 TraesCS2B01G504900 chr6B 76423316 76423896 580 False 966.00 966 96.730000 614 1193 1 chr6B.!!$F1 579

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
113 114 0.695462 TCCTGCTCCATAGGCCACAT 60.695 55.0 5.01 0.0 35.23 3.21 F
1371 1431 0.613260 TTGCGGATGAGGTAGTTGCT 59.387 50.0 0.00 0.0 0.00 3.91 F
1914 2440 1.131638 ATCTCCAAGGAAGCCGCATA 58.868 50.0 0.00 0.0 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2366 0.835276 CCTGCTCCCAGACATCATCA 59.165 55.0 0.0 0.0 41.77 3.07 R
2259 2795 1.230324 ACAAGAAGCAGTTTCGGAGC 58.770 50.0 0.0 0.0 40.86 4.70 R
3818 4387 0.664166 CACAAGTGCCGACAAATGCC 60.664 55.0 0.0 0.0 0.00 4.40 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
71 72 2.421424 GCAGAATTGATCACACTGGTCC 59.579 50.000 18.31 5.03 0.00 4.46
113 114 0.695462 TCCTGCTCCATAGGCCACAT 60.695 55.000 5.01 0.00 35.23 3.21
121 122 4.263068 GCTCCATAGGCCACATACTACAAT 60.263 45.833 5.01 0.00 0.00 2.71
128 129 6.412362 AGGCCACATACTACAATTCTCTAG 57.588 41.667 5.01 0.00 0.00 2.43
215 216 1.905215 AGCTCTGTGCCATGTAGTCTT 59.095 47.619 0.00 0.00 44.23 3.01
268 269 3.978855 TCAGCGACAATTAATACGGATCG 59.021 43.478 10.14 6.92 0.00 3.69
295 296 4.041691 GGGAGTAGATAAATTAGCAGCCCA 59.958 45.833 0.00 0.00 0.00 5.36
299 300 2.438021 AGATAAATTAGCAGCCCACCGA 59.562 45.455 0.00 0.00 0.00 4.69
322 323 7.974501 CCGATTCATTTACTAGACTAGTTGTGT 59.025 37.037 19.99 6.47 40.14 3.72
329 330 7.578310 TTACTAGACTAGTTGTGTTCTGTGT 57.422 36.000 19.99 0.00 40.14 3.72
403 404 1.073923 CTTACATGGTATCCTGGGGGC 59.926 57.143 0.00 0.00 0.00 5.80
446 447 5.927115 ACGAAAATCTTTCTGTAGTCCTGAC 59.073 40.000 0.00 0.00 0.00 3.51
626 639 2.036217 CTGAACGTTGTTTGTGATGCG 58.964 47.619 5.00 0.00 0.00 4.73
1203 1239 4.164221 ACTGTATACCTGATGGACAAAGGG 59.836 45.833 0.00 0.00 35.24 3.95
1210 1246 1.075374 TGATGGACAAAGGGGTCAAGG 59.925 52.381 0.00 0.00 39.59 3.61
1317 1371 4.228912 ACAAAGTCGCCTGAAGAAATTG 57.771 40.909 0.00 0.00 0.00 2.32
1370 1430 1.668419 ATTGCGGATGAGGTAGTTGC 58.332 50.000 0.00 0.00 0.00 4.17
1371 1431 0.613260 TTGCGGATGAGGTAGTTGCT 59.387 50.000 0.00 0.00 0.00 3.91
1396 1456 3.055240 AGAGGAGGAGATTGAGCAAGTTG 60.055 47.826 0.00 0.00 0.00 3.16
1458 1518 2.093973 CGCTGACCCACTTACTGAGATT 60.094 50.000 0.00 0.00 0.00 2.40
1536 1596 7.693969 AGTAGGAATTGAAGAAAACAGGATG 57.306 36.000 0.00 0.00 46.00 3.51
1555 1615 4.783621 TGCTGACCGGATGGCTGC 62.784 66.667 9.46 10.59 39.70 5.25
1811 2335 9.799106 TGACTTGAAAAAGGAAATAGAGAAGAT 57.201 29.630 0.00 0.00 0.00 2.40
1860 2384 2.093075 ACTTGATGATGTCTGGGAGCAG 60.093 50.000 0.00 0.00 0.00 4.24
1873 2399 2.023404 TGGGAGCAGGAGGTATACTTCA 60.023 50.000 16.01 0.00 0.00 3.02
1914 2440 1.131638 ATCTCCAAGGAAGCCGCATA 58.868 50.000 0.00 0.00 0.00 3.14
1971 2497 1.889530 CTTCTCCCACCCGTCACCTC 61.890 65.000 0.00 0.00 0.00 3.85
2130 2666 4.339247 CCTCTAGCAATTGTTACCATTGGG 59.661 45.833 7.78 0.58 41.29 4.12
2259 2795 2.751166 ACCATGACCTTTCAGACGAG 57.249 50.000 0.00 0.00 34.35 4.18
2263 2799 0.603569 TGACCTTTCAGACGAGCTCC 59.396 55.000 8.47 0.00 0.00 4.70
2314 2850 2.571653 CCTGAAGACTACCCCATGTCAA 59.428 50.000 0.00 0.00 35.81 3.18
2357 2893 2.124060 TTGCGGAAGGCTTTGTGCA 61.124 52.632 15.12 15.12 45.15 4.57
2554 3090 6.082338 GCTTCAACAGATGATTACAACACAG 58.918 40.000 0.00 0.00 38.03 3.66
2604 3158 2.087646 GAATGGAAAGAGGACACTGCC 58.912 52.381 0.00 0.00 0.00 4.85
2706 3267 4.106029 TGCATCGAACTACCTTACTGTC 57.894 45.455 0.00 0.00 0.00 3.51
2775 3336 4.184629 GGTCTCAGTTCAATCTGCGTTAT 58.815 43.478 0.00 0.00 35.63 1.89
3149 3710 3.699038 GCTACCCTTTCAAATATGCCACA 59.301 43.478 0.00 0.00 0.00 4.17
3191 3752 2.092753 GTGCAAGGGATGAGAATGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
3638 4205 2.895404 AGTGCTTGCACAAGGATTTCAT 59.105 40.909 24.82 0.34 40.79 2.57
3675 4242 2.029838 ACGGAATGCATCAGAAGACC 57.970 50.000 0.00 0.00 0.00 3.85
3694 4261 1.548582 CCCTGCATGTTCCAGAGGTTT 60.549 52.381 0.00 0.00 32.03 3.27
3695 4262 2.290896 CCCTGCATGTTCCAGAGGTTTA 60.291 50.000 0.00 0.00 32.03 2.01
3727 4295 1.738099 CAGGTCGGTTCTTCCTGCG 60.738 63.158 0.00 0.00 41.46 5.18
3756 4324 2.014857 CTTGGATGGTGCATCTGTCAG 58.985 52.381 0.00 0.00 40.39 3.51
3769 4337 1.655484 CTGTCAGTCACAGTTGTGCA 58.345 50.000 7.38 0.00 46.81 4.57
3786 4354 6.482308 AGTTGTGCAGTACTTTTAATCGTTCT 59.518 34.615 0.00 0.00 0.00 3.01
3818 4387 4.567959 TGTGATTATTGATGTCGTCAGCAG 59.432 41.667 0.26 0.00 41.05 4.24
3826 4395 0.534877 TGTCGTCAGCAGGCATTTGT 60.535 50.000 0.00 0.00 0.00 2.83
3830 4400 2.180017 CAGCAGGCATTTGTCGGC 59.820 61.111 0.00 0.00 41.09 5.54
3835 4405 0.387622 CAGGCATTTGTCGGCACTTG 60.388 55.000 0.00 0.00 0.00 3.16
3837 4407 0.664166 GGCATTTGTCGGCACTTGTG 60.664 55.000 0.00 0.00 0.00 3.33
3844 4415 0.580104 GTCGGCACTTGTGTGTGTAC 59.420 55.000 2.61 0.00 45.44 2.90
3905 4482 1.348696 GAGGTCCCCGTCTGGTTTTAA 59.651 52.381 0.00 0.00 0.00 1.52
3906 4483 1.350019 AGGTCCCCGTCTGGTTTTAAG 59.650 52.381 0.00 0.00 0.00 1.85
3908 4485 2.420642 GTCCCCGTCTGGTTTTAAGTC 58.579 52.381 0.00 0.00 0.00 3.01
3909 4486 2.048601 TCCCCGTCTGGTTTTAAGTCA 58.951 47.619 0.00 0.00 0.00 3.41
3911 4488 3.839490 TCCCCGTCTGGTTTTAAGTCATA 59.161 43.478 0.00 0.00 0.00 2.15
3912 4489 3.937079 CCCCGTCTGGTTTTAAGTCATAC 59.063 47.826 0.00 0.00 0.00 2.39
3922 4540 9.547753 CTGGTTTTAAGTCATACTATGTGCTAT 57.452 33.333 0.00 0.00 0.00 2.97
4035 4655 5.105063 TCTTGATCTTTGTCGCTGTATGAG 58.895 41.667 0.00 0.00 0.00 2.90
4043 4663 2.034685 TGTCGCTGTATGAGCCTATGAC 59.965 50.000 0.00 0.00 46.01 3.06
4060 4680 1.003580 TGACCTGATTCACCAAGAGGC 59.996 52.381 0.00 0.00 39.06 4.70
4082 4702 4.673580 GCATTACACTGTCATTTCAGCAGG 60.674 45.833 0.00 0.00 38.84 4.85
4084 4704 2.498167 ACACTGTCATTTCAGCAGGTC 58.502 47.619 0.00 0.00 38.84 3.85
4085 4705 1.462283 CACTGTCATTTCAGCAGGTCG 59.538 52.381 0.00 0.00 38.84 4.79
4096 4716 4.539152 CAGGTCGTGCATTTGTGC 57.461 55.556 0.00 0.00 0.00 4.57
4102 4722 1.072219 GTCGTGCATTTGTGCGTTTTG 60.072 47.619 0.00 0.00 37.69 2.44
4114 4734 2.031157 GTGCGTTTTGCTGATTAGGTGT 60.031 45.455 0.00 0.00 46.63 4.16
4126 4746 6.095377 GCTGATTAGGTGTTCAAATTTCAGG 58.905 40.000 0.00 0.00 0.00 3.86
4127 4747 6.024552 TGATTAGGTGTTCAAATTTCAGGC 57.975 37.500 0.00 0.00 0.00 4.85
4134 4754 6.041979 AGGTGTTCAAATTTCAGGCTAACAAT 59.958 34.615 0.00 0.00 0.00 2.71
4171 4803 9.547753 AGTATCATTTATTAGTAGCACTTGTGG 57.452 33.333 2.81 0.00 0.00 4.17
4172 4804 7.807977 ATCATTTATTAGTAGCACTTGTGGG 57.192 36.000 2.81 0.00 0.00 4.61
4173 4805 6.717289 TCATTTATTAGTAGCACTTGTGGGT 58.283 36.000 2.81 0.00 0.00 4.51
4174 4806 6.597672 TCATTTATTAGTAGCACTTGTGGGTG 59.402 38.462 2.81 0.00 39.91 4.61
4175 4807 5.492855 TTATTAGTAGCACTTGTGGGTGT 57.507 39.130 2.81 0.00 39.21 4.16
4176 4808 3.849563 TTAGTAGCACTTGTGGGTGTT 57.150 42.857 2.81 0.00 39.21 3.32
4177 4809 2.729028 AGTAGCACTTGTGGGTGTTT 57.271 45.000 2.81 0.00 39.21 2.83
4178 4810 3.012934 AGTAGCACTTGTGGGTGTTTT 57.987 42.857 2.81 0.00 39.21 2.43
4179 4811 2.687935 AGTAGCACTTGTGGGTGTTTTG 59.312 45.455 2.81 0.00 39.21 2.44
4180 4812 0.175531 AGCACTTGTGGGTGTTTTGC 59.824 50.000 2.81 0.00 39.21 3.68
4181 4813 1.145162 GCACTTGTGGGTGTTTTGCG 61.145 55.000 2.81 0.00 39.21 4.85
4182 4814 0.527385 CACTTGTGGGTGTTTTGCGG 60.527 55.000 0.00 0.00 33.04 5.69
4183 4815 1.067250 CTTGTGGGTGTTTTGCGGG 59.933 57.895 0.00 0.00 0.00 6.13
4184 4816 1.671901 CTTGTGGGTGTTTTGCGGGT 61.672 55.000 0.00 0.00 0.00 5.28
4216 4880 2.637872 CCAGTTTGAAGGGGACAGACTA 59.362 50.000 0.00 0.00 32.76 2.59
4219 4887 3.075148 GTTTGAAGGGGACAGACTAAGC 58.925 50.000 0.00 0.00 0.00 3.09
4247 4915 8.139350 TCATTTTGGTTCATCTTGATATGATGC 58.861 33.333 0.00 0.00 40.59 3.91
4251 4919 5.163174 TGGTTCATCTTGATATGATGCCTGA 60.163 40.000 0.00 0.00 40.59 3.86
4252 4920 5.180868 GGTTCATCTTGATATGATGCCTGAC 59.819 44.000 0.00 0.00 40.59 3.51
4254 4922 5.548406 TCATCTTGATATGATGCCTGACAG 58.452 41.667 0.00 0.00 40.59 3.51
4261 4929 5.541484 TGATATGATGCCTGACAGACACTAT 59.459 40.000 3.32 0.00 0.00 2.12
4272 4940 4.464244 TGACAGACACTATGGAGAAGGAAG 59.536 45.833 0.00 0.00 0.00 3.46
4281 4949 7.181125 ACACTATGGAGAAGGAAGACAAAGTAT 59.819 37.037 0.00 0.00 0.00 2.12
4282 4950 7.708752 CACTATGGAGAAGGAAGACAAAGTATC 59.291 40.741 0.00 0.00 0.00 2.24
4285 4953 7.020827 TGGAGAAGGAAGACAAAGTATCATT 57.979 36.000 0.00 0.00 0.00 2.57
4287 4955 7.944554 TGGAGAAGGAAGACAAAGTATCATTTT 59.055 33.333 0.00 0.00 0.00 1.82
4288 4956 8.239998 GGAGAAGGAAGACAAAGTATCATTTTG 58.760 37.037 0.00 0.00 40.48 2.44
4292 4976 6.151817 AGGAAGACAAAGTATCATTTTGCTCC 59.848 38.462 0.00 2.97 38.72 4.70
4339 5023 4.695455 ACAGTTTTCCTGGACATGAATACG 59.305 41.667 0.00 0.00 46.06 3.06
4345 5029 3.069586 TCCTGGACATGAATACGTCATCC 59.930 47.826 0.00 0.00 44.01 3.51
4346 5030 3.052745 CTGGACATGAATACGTCATCCG 58.947 50.000 0.00 0.00 44.01 4.18
4357 5041 2.175530 CGTCATCCGTACTGTGAGAC 57.824 55.000 0.00 0.00 0.00 3.36
4361 5045 4.660105 GTCATCCGTACTGTGAGACTAAC 58.340 47.826 0.00 0.00 0.00 2.34
4384 5069 6.688637 CTGATATCAGGAAAATTGCAGTCA 57.311 37.500 22.89 0.00 40.20 3.41
4396 5081 7.814107 GGAAAATTGCAGTCAGAAATGTCAATA 59.186 33.333 0.00 0.00 0.00 1.90
4400 5085 8.743085 ATTGCAGTCAGAAATGTCAATATAGT 57.257 30.769 0.00 0.00 0.00 2.12
4489 5174 2.468532 GCAAGTGTGTTTTGCTACGT 57.531 45.000 0.00 0.00 45.64 3.57
4490 5175 3.595709 GCAAGTGTGTTTTGCTACGTA 57.404 42.857 0.00 0.00 45.64 3.57
4491 5176 3.285745 GCAAGTGTGTTTTGCTACGTAC 58.714 45.455 0.00 0.00 45.64 3.67
4492 5177 3.528121 CAAGTGTGTTTTGCTACGTACG 58.472 45.455 15.01 15.01 0.00 3.67
4493 5178 2.813061 AGTGTGTTTTGCTACGTACGT 58.187 42.857 25.98 25.98 0.00 3.57
4494 5179 3.963665 AGTGTGTTTTGCTACGTACGTA 58.036 40.909 25.41 25.41 0.00 3.57
4495 5180 3.730715 AGTGTGTTTTGCTACGTACGTAC 59.269 43.478 23.60 19.21 0.00 3.67
4496 5181 3.049206 TGTGTTTTGCTACGTACGTACC 58.951 45.455 23.60 17.83 0.00 3.34
4497 5182 3.049206 GTGTTTTGCTACGTACGTACCA 58.951 45.455 23.60 20.21 0.00 3.25
4498 5183 3.674753 GTGTTTTGCTACGTACGTACCAT 59.325 43.478 23.60 10.84 0.00 3.55
4499 5184 3.919804 TGTTTTGCTACGTACGTACCATC 59.080 43.478 23.60 15.69 0.00 3.51
4510 5195 5.163713 ACGTACGTACCATCTTTTAGAGGAC 60.164 44.000 21.41 0.00 0.00 3.85
4520 5205 5.422214 TCTTTTAGAGGACACAAGGATCC 57.578 43.478 2.48 2.48 34.98 3.36
4533 5218 4.449743 CACAAGGATCCAAAACTTGCAATG 59.550 41.667 15.82 0.00 44.01 2.82
4547 5232 1.300266 GCAATGGCAATGCAACACCC 61.300 55.000 22.06 0.00 43.29 4.61
4551 5236 2.258286 GCAATGCAACACCCGTCC 59.742 61.111 0.00 0.00 0.00 4.79
4552 5237 2.560861 CAATGCAACACCCGTCCG 59.439 61.111 0.00 0.00 0.00 4.79
4559 5244 0.882927 CAACACCCGTCCGTTCATGT 60.883 55.000 0.00 0.00 0.00 3.21
4580 5265 3.375299 GTCAGTTATGGTGGTCTGCATTC 59.625 47.826 0.00 0.00 0.00 2.67
4588 5273 1.869767 GTGGTCTGCATTCGATCATCC 59.130 52.381 0.00 0.00 0.00 3.51
4604 5289 5.007039 CGATCATCCTGGTATTGTTTGAGTG 59.993 44.000 0.00 0.00 0.00 3.51
4607 5292 5.705441 TCATCCTGGTATTGTTTGAGTGAAC 59.295 40.000 0.00 0.00 0.00 3.18
4649 5334 6.730960 CCGTGTGGTACATAGTTTAATGTT 57.269 37.500 0.00 0.00 44.52 2.71
4650 5335 7.136289 CCGTGTGGTACATAGTTTAATGTTT 57.864 36.000 0.00 0.00 44.52 2.83
4651 5336 7.586747 CCGTGTGGTACATAGTTTAATGTTTT 58.413 34.615 0.00 0.00 44.52 2.43
4652 5337 8.077386 CCGTGTGGTACATAGTTTAATGTTTTT 58.923 33.333 0.00 0.00 44.52 1.94
4691 5376 1.342672 ACACCTGGTGAACCGAACCT 61.343 55.000 32.30 4.34 38.60 3.50
4692 5377 0.682852 CACCTGGTGAACCGAACCTA 59.317 55.000 22.33 0.00 38.60 3.08
4693 5378 1.278127 CACCTGGTGAACCGAACCTAT 59.722 52.381 22.33 0.00 38.60 2.57
4694 5379 1.278127 ACCTGGTGAACCGAACCTATG 59.722 52.381 0.00 0.00 38.60 2.23
4695 5380 1.553248 CCTGGTGAACCGAACCTATGA 59.447 52.381 0.00 0.00 38.60 2.15
4696 5381 2.027561 CCTGGTGAACCGAACCTATGAA 60.028 50.000 0.00 0.00 38.60 2.57
4697 5382 3.370527 CCTGGTGAACCGAACCTATGAAT 60.371 47.826 0.00 0.00 38.60 2.57
4698 5383 3.869065 TGGTGAACCGAACCTATGAATC 58.131 45.455 0.00 0.00 38.60 2.52
4699 5384 3.203716 GGTGAACCGAACCTATGAATCC 58.796 50.000 0.00 0.00 34.66 3.01
4700 5385 3.370103 GGTGAACCGAACCTATGAATCCA 60.370 47.826 0.00 0.00 34.66 3.41
4701 5386 3.621715 GTGAACCGAACCTATGAATCCAC 59.378 47.826 0.00 0.00 0.00 4.02
4702 5387 3.203716 GAACCGAACCTATGAATCCACC 58.796 50.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.537625 GTCGAACATCAGACTATGCAGC 59.462 50.000 0.00 0.00 34.74 5.25
71 72 1.595489 GCGCTTACATGCCGAATGAAG 60.595 52.381 0.00 5.81 38.72 3.02
121 122 7.147880 GCTAACCAATACTCACCTTCTAGAGAA 60.148 40.741 0.00 0.00 35.83 2.87
128 129 5.086104 TCAGCTAACCAATACTCACCTTC 57.914 43.478 0.00 0.00 0.00 3.46
262 263 0.038455 ATCTACTCCCTCCCGATCCG 59.962 60.000 0.00 0.00 0.00 4.18
268 269 5.569832 GCTGCTAATTTATCTACTCCCTCCC 60.570 48.000 0.00 0.00 0.00 4.30
295 296 7.974501 CACAACTAGTCTAGTAAATGAATCGGT 59.025 37.037 12.99 0.00 38.26 4.69
322 323 3.407424 ACTCTAAGCATGCACACAGAA 57.593 42.857 21.98 0.00 0.00 3.02
329 330 1.401409 GCGCAAAACTCTAAGCATGCA 60.401 47.619 21.98 0.00 33.55 3.96
403 404 0.752054 TTGCAGGAAGTTTGGCAAGG 59.248 50.000 0.00 0.00 40.94 3.61
446 447 5.443824 CGATTGTCATCTCTTTTGACTGTCG 60.444 44.000 2.98 12.91 43.12 4.35
626 639 9.495572 AGAAATACCCAATCGAAGAGATAAATC 57.504 33.333 0.00 0.00 43.63 2.17
886 912 2.177016 AGTTTATACCCCTTGGCCCATC 59.823 50.000 0.00 0.00 33.59 3.51
1203 1239 1.287739 TCCCCAATCCAATCCTTGACC 59.712 52.381 0.00 0.00 0.00 4.02
1210 1246 1.680338 CGGACTTCCCCAATCCAATC 58.320 55.000 0.00 0.00 32.35 2.67
1317 1371 8.593492 AAACTGCATAATCTTTTCCTTTCAAC 57.407 30.769 0.00 0.00 0.00 3.18
1370 1430 3.295093 TGCTCAATCTCCTCCTCTACAG 58.705 50.000 0.00 0.00 0.00 2.74
1371 1431 3.388552 TGCTCAATCTCCTCCTCTACA 57.611 47.619 0.00 0.00 0.00 2.74
1396 1456 5.004061 GCAACCAACGTTCTTTCAACTTTAC 59.996 40.000 0.00 0.00 0.00 2.01
1413 1473 1.531365 CTGGAAGGGCTGCAACCAA 60.531 57.895 8.71 0.00 0.00 3.67
1458 1518 3.234630 CTGGGACCGCCGTCTTTCA 62.235 63.158 5.18 1.85 39.15 2.69
1536 1596 2.045926 AGCCATCCGGTCAGCAAC 60.046 61.111 0.00 0.00 33.28 4.17
1555 1615 2.554462 TGTTCTCCGTCTCTTCAGAGTG 59.446 50.000 3.73 0.00 42.60 3.51
1748 2272 1.682702 CCATGCCTGCTGACAATGGTA 60.683 52.381 9.51 0.00 0.00 3.25
1826 2350 9.708092 AGACATCATCAAGTACAATCAGATATG 57.292 33.333 0.00 0.00 0.00 1.78
1842 2366 0.835276 CCTGCTCCCAGACATCATCA 59.165 55.000 0.00 0.00 41.77 3.07
1860 2384 8.507249 GCATCACATATTTTGAAGTATACCTCC 58.493 37.037 0.00 0.00 0.00 4.30
1873 2399 8.302515 AGATTCTGGAAAGCATCACATATTTT 57.697 30.769 0.00 0.00 0.00 1.82
1914 2440 3.518590 GTCCTTCCGTGTCGTAATGATT 58.481 45.455 0.00 0.00 0.00 2.57
1971 2497 4.121691 CTCAATGGCAGGAGCTCG 57.878 61.111 7.83 0.00 41.70 5.03
2172 2708 3.123621 CGTGTCCAAGCTGATTGTACTTC 59.876 47.826 4.82 0.00 37.17 3.01
2259 2795 1.230324 ACAAGAAGCAGTTTCGGAGC 58.770 50.000 0.00 0.00 40.86 4.70
2263 2799 2.543848 TGCAGTACAAGAAGCAGTTTCG 59.456 45.455 0.00 0.00 40.86 3.46
2357 2893 2.289506 GGCGTGTTCTTTCCCTTACTCT 60.290 50.000 0.00 0.00 0.00 3.24
2554 3090 3.966154 ACAGACGACGAATATCCATCAC 58.034 45.455 0.00 0.00 0.00 3.06
2775 3336 1.449956 GGTGCGCCGTAACCCAATA 60.450 57.895 4.18 0.00 0.00 1.90
3149 3710 5.287226 CACAAAGAAGCAAGCTTGAAAGAT 58.713 37.500 30.39 9.88 36.26 2.40
3191 3752 2.234143 GGAGAGCCTCAAAGCAAAGTT 58.766 47.619 0.00 0.00 34.23 2.66
3381 3942 4.982999 TGTTAAGTCTCAGATACGTGAGC 58.017 43.478 0.00 0.00 43.28 4.26
3638 4205 2.551287 CCGTTGGTGTCCCATTGACTTA 60.551 50.000 0.00 0.00 44.75 2.24
3675 4242 1.915141 AAACCTCTGGAACATGCAGG 58.085 50.000 0.00 0.00 36.40 4.85
3694 4261 2.294512 CGACCTGCTGCATCTAGACATA 59.705 50.000 1.31 0.00 0.00 2.29
3695 4262 1.068281 CGACCTGCTGCATCTAGACAT 59.932 52.381 1.31 0.00 0.00 3.06
3727 4295 0.673644 CACCATCCAAGACCGACACC 60.674 60.000 0.00 0.00 0.00 4.16
3818 4387 0.664166 CACAAGTGCCGACAAATGCC 60.664 55.000 0.00 0.00 0.00 4.40
3844 4415 8.122472 ACCAAACTTTTGAGGAGTAAATATGG 57.878 34.615 3.17 0.00 40.55 2.74
3980 4598 8.777413 CCACATATAAGATGAAATGTTCGACAT 58.223 33.333 0.00 0.00 41.31 3.06
4035 4655 3.118261 TCTTGGTGAATCAGGTCATAGGC 60.118 47.826 0.00 0.00 0.00 3.93
4043 4663 2.431954 ATGCCTCTTGGTGAATCAGG 57.568 50.000 0.00 0.00 35.27 3.86
4060 4680 4.456911 ACCTGCTGAAATGACAGTGTAATG 59.543 41.667 0.00 0.00 39.73 1.90
4091 4711 2.621055 ACCTAATCAGCAAAACGCACAA 59.379 40.909 0.00 0.00 46.13 3.33
4096 4716 4.481930 TGAACACCTAATCAGCAAAACG 57.518 40.909 0.00 0.00 0.00 3.60
4102 4722 6.095377 CCTGAAATTTGAACACCTAATCAGC 58.905 40.000 0.00 0.00 0.00 4.26
4155 4787 4.367039 AACACCCACAAGTGCTACTAAT 57.633 40.909 0.00 0.00 41.67 1.73
4160 4792 1.407258 GCAAAACACCCACAAGTGCTA 59.593 47.619 0.00 0.00 41.67 3.49
4168 4800 0.963225 AATACCCGCAAAACACCCAC 59.037 50.000 0.00 0.00 0.00 4.61
4170 4802 1.746787 CCTAATACCCGCAAAACACCC 59.253 52.381 0.00 0.00 0.00 4.61
4171 4803 2.421073 GACCTAATACCCGCAAAACACC 59.579 50.000 0.00 0.00 0.00 4.16
4172 4804 2.421073 GGACCTAATACCCGCAAAACAC 59.579 50.000 0.00 0.00 0.00 3.32
4173 4805 2.306512 AGGACCTAATACCCGCAAAACA 59.693 45.455 0.00 0.00 0.00 2.83
4174 4806 2.941064 GAGGACCTAATACCCGCAAAAC 59.059 50.000 0.00 0.00 0.00 2.43
4175 4807 2.092807 GGAGGACCTAATACCCGCAAAA 60.093 50.000 0.00 0.00 0.00 2.44
4176 4808 1.487558 GGAGGACCTAATACCCGCAAA 59.512 52.381 0.00 0.00 0.00 3.68
4177 4809 1.125633 GGAGGACCTAATACCCGCAA 58.874 55.000 0.00 0.00 0.00 4.85
4178 4810 0.031917 TGGAGGACCTAATACCCGCA 60.032 55.000 0.00 0.00 37.04 5.69
4179 4811 0.680061 CTGGAGGACCTAATACCCGC 59.320 60.000 0.00 0.00 37.04 6.13
4180 4812 2.083628 ACTGGAGGACCTAATACCCG 57.916 55.000 0.00 0.00 37.04 5.28
4181 4813 3.778629 TCAAACTGGAGGACCTAATACCC 59.221 47.826 0.00 0.00 37.04 3.69
4182 4814 5.429130 CTTCAAACTGGAGGACCTAATACC 58.571 45.833 0.00 0.00 37.04 2.73
4183 4815 5.429130 CCTTCAAACTGGAGGACCTAATAC 58.571 45.833 0.00 0.00 37.04 1.89
4184 4816 4.473559 CCCTTCAAACTGGAGGACCTAATA 59.526 45.833 2.26 0.00 37.04 0.98
4216 4880 6.349243 TCAAGATGAACCAAAATGATGCTT 57.651 33.333 0.00 0.00 0.00 3.91
4247 4915 3.131933 CCTTCTCCATAGTGTCTGTCAGG 59.868 52.174 0.00 0.00 0.00 3.86
4251 4919 4.464597 GTCTTCCTTCTCCATAGTGTCTGT 59.535 45.833 0.00 0.00 0.00 3.41
4252 4920 4.464244 TGTCTTCCTTCTCCATAGTGTCTG 59.536 45.833 0.00 0.00 0.00 3.51
4254 4922 5.407407 TTGTCTTCCTTCTCCATAGTGTC 57.593 43.478 0.00 0.00 0.00 3.67
4261 4929 6.627087 ATGATACTTTGTCTTCCTTCTCCA 57.373 37.500 0.00 0.00 0.00 3.86
4272 4940 6.624423 ACATGGAGCAAAATGATACTTTGTC 58.376 36.000 0.00 0.00 36.38 3.18
4281 4949 4.933505 TTGTCAACATGGAGCAAAATGA 57.066 36.364 0.00 0.00 0.00 2.57
4282 4950 6.256975 CCATATTGTCAACATGGAGCAAAATG 59.743 38.462 16.62 0.00 41.53 2.32
4285 4953 5.015515 TCCATATTGTCAACATGGAGCAAA 58.984 37.500 19.61 0.00 42.55 3.68
4287 4955 4.233632 TCCATATTGTCAACATGGAGCA 57.766 40.909 19.61 0.44 42.55 4.26
4292 4976 3.205338 TCCGCTCCATATTGTCAACATG 58.795 45.455 0.00 0.00 0.00 3.21
4339 5023 4.395542 AGTTAGTCTCACAGTACGGATGAC 59.604 45.833 0.00 5.09 0.00 3.06
4345 5029 7.247929 TGATATCAGTTAGTCTCACAGTACG 57.752 40.000 0.00 0.00 0.00 3.67
4346 5030 7.499563 TCCTGATATCAGTTAGTCTCACAGTAC 59.500 40.741 27.03 0.00 42.27 2.73
4347 5031 7.574607 TCCTGATATCAGTTAGTCTCACAGTA 58.425 38.462 27.03 0.55 42.27 2.74
4348 5032 6.427441 TCCTGATATCAGTTAGTCTCACAGT 58.573 40.000 27.03 0.00 42.27 3.55
4349 5033 6.951062 TCCTGATATCAGTTAGTCTCACAG 57.049 41.667 27.03 10.48 42.27 3.66
4357 5041 8.218338 ACTGCAATTTTCCTGATATCAGTTAG 57.782 34.615 27.03 14.73 42.27 2.34
4361 5045 6.541278 TCTGACTGCAATTTTCCTGATATCAG 59.459 38.462 23.53 23.53 43.40 2.90
4396 5081 3.356290 GGGCAGGAAACAACATCACTAT 58.644 45.455 0.00 0.00 0.00 2.12
4398 5083 1.620822 GGGCAGGAAACAACATCACT 58.379 50.000 0.00 0.00 0.00 3.41
4400 5085 0.187117 TGGGGCAGGAAACAACATCA 59.813 50.000 0.00 0.00 0.00 3.07
4463 5148 2.854185 GCAAAACACACTTGCTGAACTC 59.146 45.455 0.41 0.00 44.66 3.01
4486 5171 4.943705 TCCTCTAAAAGATGGTACGTACGT 59.056 41.667 25.98 25.98 0.00 3.57
4488 5173 6.032717 GTGTCCTCTAAAAGATGGTACGTAC 58.967 44.000 17.56 17.56 0.00 3.67
4489 5174 5.711506 TGTGTCCTCTAAAAGATGGTACGTA 59.288 40.000 0.00 0.00 0.00 3.57
4490 5175 4.525487 TGTGTCCTCTAAAAGATGGTACGT 59.475 41.667 0.00 0.00 0.00 3.57
4491 5176 5.068234 TGTGTCCTCTAAAAGATGGTACG 57.932 43.478 0.00 0.00 0.00 3.67
4492 5177 5.875359 CCTTGTGTCCTCTAAAAGATGGTAC 59.125 44.000 0.00 0.00 0.00 3.34
4493 5178 5.783360 TCCTTGTGTCCTCTAAAAGATGGTA 59.217 40.000 0.00 0.00 0.00 3.25
4494 5179 4.597507 TCCTTGTGTCCTCTAAAAGATGGT 59.402 41.667 0.00 0.00 0.00 3.55
4495 5180 5.165961 TCCTTGTGTCCTCTAAAAGATGG 57.834 43.478 0.00 0.00 0.00 3.51
4496 5181 5.819901 GGATCCTTGTGTCCTCTAAAAGATG 59.180 44.000 3.84 0.00 0.00 2.90
4497 5182 5.488919 TGGATCCTTGTGTCCTCTAAAAGAT 59.511 40.000 14.23 0.00 35.49 2.40
4498 5183 4.844085 TGGATCCTTGTGTCCTCTAAAAGA 59.156 41.667 14.23 0.00 35.49 2.52
4499 5184 5.165961 TGGATCCTTGTGTCCTCTAAAAG 57.834 43.478 14.23 0.00 35.49 2.27
4510 5195 3.731652 TGCAAGTTTTGGATCCTTGTG 57.268 42.857 14.23 3.92 38.24 3.33
4533 5218 2.258286 GACGGGTGTTGCATTGCC 59.742 61.111 6.12 0.00 0.00 4.52
4543 5228 1.005512 TGACATGAACGGACGGGTG 60.006 57.895 0.00 0.00 0.00 4.61
4545 5230 0.320421 AACTGACATGAACGGACGGG 60.320 55.000 0.00 0.00 0.00 5.28
4547 5232 2.603110 CCATAACTGACATGAACGGACG 59.397 50.000 0.00 0.00 0.00 4.79
4551 5236 3.334691 ACCACCATAACTGACATGAACG 58.665 45.455 0.00 0.00 0.00 3.95
4552 5237 4.393062 CAGACCACCATAACTGACATGAAC 59.607 45.833 0.00 0.00 32.90 3.18
4559 5244 3.609853 GAATGCAGACCACCATAACTGA 58.390 45.455 0.00 0.00 32.90 3.41
4580 5265 5.007039 CACTCAAACAATACCAGGATGATCG 59.993 44.000 0.00 0.00 39.69 3.69
4588 5273 3.188460 CCGGTTCACTCAAACAATACCAG 59.812 47.826 0.00 0.00 0.00 4.00
4604 5289 4.213674 GTTTCGTGTAATTCAACCGGTTC 58.786 43.478 19.24 5.60 0.00 3.62
4607 5292 2.411806 CGGTTTCGTGTAATTCAACCGG 60.412 50.000 12.84 0.00 45.40 5.28
4650 5335 6.793203 GTGTTGCGAATAACGATCAGTAAAAA 59.207 34.615 0.00 0.00 45.77 1.94
4651 5336 6.301108 GTGTTGCGAATAACGATCAGTAAAA 58.699 36.000 0.00 0.00 45.77 1.52
4652 5337 5.163933 GGTGTTGCGAATAACGATCAGTAAA 60.164 40.000 0.00 0.00 45.77 2.01
4653 5338 4.327898 GGTGTTGCGAATAACGATCAGTAA 59.672 41.667 0.00 0.00 45.77 2.24
4654 5339 3.861113 GGTGTTGCGAATAACGATCAGTA 59.139 43.478 0.00 0.00 45.77 2.74
4655 5340 2.671396 GGTGTTGCGAATAACGATCAGT 59.329 45.455 0.00 0.00 45.77 3.41
4656 5341 2.930040 AGGTGTTGCGAATAACGATCAG 59.070 45.455 0.00 0.00 45.77 2.90
4657 5342 2.670905 CAGGTGTTGCGAATAACGATCA 59.329 45.455 0.00 0.00 45.77 2.92
4658 5343 2.030457 CCAGGTGTTGCGAATAACGATC 59.970 50.000 0.00 0.00 45.77 3.69
4659 5344 2.006888 CCAGGTGTTGCGAATAACGAT 58.993 47.619 0.00 0.00 45.77 3.73
4660 5345 1.270412 ACCAGGTGTTGCGAATAACGA 60.270 47.619 0.00 0.00 45.77 3.85
4661 5346 1.136085 CACCAGGTGTTGCGAATAACG 60.136 52.381 11.99 0.00 45.66 3.18


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

AutoCloner maintained by Alex Coulton.