Multiple sequence alignment - TraesCS4D01G245000

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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 TraesCS4D01G245000 chr4D 100.000 5876 0 0 1 5876 409645891 409640016 0.000000e+00 10852
1 TraesCS4D01G245000 chr4B 93.472 5438 207 54 1 5331 506138238 506143634 0.000000e+00 7939
2 TraesCS4D01G245000 chr4B 95.324 278 7 3 5602 5876 506144070 506144344 2.510000e-118 436
3 TraesCS4D01G245000 chr4B 98.421 190 3 0 5452 5641 506143882 506144071 9.440000e-88 335
4 TraesCS4D01G245000 chr4B 95.050 101 5 0 5327 5427 56355640 56355740 6.090000e-35 159
5 TraesCS4D01G245000 chr4B 95.050 101 5 0 5327 5427 64948661 64948561 6.090000e-35 159
6 TraesCS4D01G245000 chr4A 94.068 3827 143 45 1561 5331 64143282 64147080 0.000000e+00 5733
7 TraesCS4D01G245000 chr4A 91.551 1302 56 25 164 1433 64141605 64142884 0.000000e+00 1746
8 TraesCS4D01G245000 chr4A 93.925 214 10 1 5434 5644 64147095 64147308 2.640000e-83 320
9 TraesCS4D01G245000 chr4A 93.478 92 4 2 5787 5876 64147389 64147480 1.030000e-27 135
10 TraesCS4D01G245000 chr4A 89.655 87 5 4 5670 5756 64147308 64147390 2.240000e-19 108
11 TraesCS4D01G245000 chr1D 93.850 439 21 5 2145 2581 340641524 340641090 0.000000e+00 656
12 TraesCS4D01G245000 chr5B 97.030 101 3 0 5327 5427 277078976 277079076 2.820000e-38 171
13 TraesCS4D01G245000 chr3B 96.040 101 4 0 5327 5427 523210012 523209912 1.310000e-36 165
14 TraesCS4D01G245000 chr3B 93.396 106 7 0 5322 5427 822718767 822718662 2.190000e-34 158
15 TraesCS4D01G245000 chr2A 94.340 106 5 1 5323 5427 73898551 73898446 1.690000e-35 161
16 TraesCS4D01G245000 chr2A 93.396 106 7 0 5322 5427 333768830 333768725 2.190000e-34 158
17 TraesCS4D01G245000 chr2A 91.892 111 9 0 5317 5427 180979275 180979165 7.880000e-34 156
18 TraesCS4D01G245000 chr3A 91.964 112 8 1 5317 5427 1921363 1921252 7.880000e-34 156


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 TraesCS4D01G245000 chr4D 409640016 409645891 5875 True 10852.000000 10852 100.0000 1 5876 1 chr4D.!!$R1 5875
1 TraesCS4D01G245000 chr4B 506138238 506144344 6106 False 2903.333333 7939 95.7390 1 5876 3 chr4B.!!$F2 5875
2 TraesCS4D01G245000 chr4A 64141605 64147480 5875 False 1608.400000 5733 92.5354 164 5876 5 chr4A.!!$F1 5712

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
124 125 0.671472 GATGATCGATCGCCCATGCA 60.671 55.000 20.03 9.39 37.32 3.96 F
263 272 1.226746 GTCCACTAGCTTGTGCGTTT 58.773 50.000 21.04 0.00 45.42 3.60 F
955 992 2.126463 CCTGAACGAGCGAGCGAA 60.126 61.111 4.36 0.00 34.83 4.70 F
1788 2102 1.169661 AACCTTCCACGAAATGCGCA 61.170 50.000 14.96 14.96 46.04 6.09 F
2124 2440 0.878523 CTTGTCGAAAGGCGTCACCA 60.879 55.000 0.00 0.00 43.14 4.17 F
3867 4201 1.005340 GTCCATGAGAAGCAGCTTCG 58.995 55.000 26.14 13.79 44.34 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1241 1.210234 ATCAACGAGATGCATGGGACA 59.790 47.619 2.46 0.0 38.2 4.02 R
1217 1258 1.533625 CGCAAGGTGGAAGGAAATCA 58.466 50.000 0.00 0.0 0.0 2.57 R
1993 2309 1.845809 GCCAGTGACACGCAAAGGAG 61.846 60.000 0.00 0.0 0.0 3.69 R
3402 3730 3.181465 ACGGACTGAAATACATAGGCAGG 60.181 47.826 0.00 0.0 0.0 4.85 R
3877 4215 0.321122 CCCAGTTCAGCACACTCTCC 60.321 60.000 0.00 0.0 0.0 3.71 R
5222 5595 2.159282 TCGGTAAGAAGAATGACCTCGC 60.159 50.000 0.00 0.0 0.0 5.03 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
26 27 2.262211 GCTTCCCAGCAAATTAAAGCG 58.738 47.619 0.00 0.00 46.49 4.68
30 31 1.349234 CCAGCAAATTAAAGCGTGCC 58.651 50.000 0.00 0.00 37.73 5.01
124 125 0.671472 GATGATCGATCGCCCATGCA 60.671 55.000 20.03 9.39 37.32 3.96
220 225 4.796231 ACGGCACTGACGGATCGC 62.796 66.667 9.60 0.00 39.02 4.58
263 272 1.226746 GTCCACTAGCTTGTGCGTTT 58.773 50.000 21.04 0.00 45.42 3.60
612 639 7.987268 AAAAACTTCGATTCCTTTCTGTTTC 57.013 32.000 0.00 0.00 0.00 2.78
613 640 6.944234 AAACTTCGATTCCTTTCTGTTTCT 57.056 33.333 0.00 0.00 0.00 2.52
741 774 4.493547 TGTTGTTGTTGAGAAAAAGCTGG 58.506 39.130 0.00 0.00 0.00 4.85
758 791 7.446001 AAAGCTGGTTTATTTCTTGAGAGAG 57.554 36.000 2.51 0.00 32.44 3.20
955 992 2.126463 CCTGAACGAGCGAGCGAA 60.126 61.111 4.36 0.00 34.83 4.70
958 995 2.501222 GAACGAGCGAGCGAACGA 60.501 61.111 15.54 0.00 35.09 3.85
1125 1166 4.467084 GCGGCGGAGGATGTTCCA 62.467 66.667 9.78 0.00 39.61 3.53
1217 1258 1.679944 CCTTGTCCCATGCATCTCGTT 60.680 52.381 0.00 0.00 0.00 3.85
1610 1924 3.274288 CAGTCCTGATTTTAGGCAGTCC 58.726 50.000 0.00 0.00 37.76 3.85
1729 2043 4.449131 ACTTCGGTCTACAGTATCGATCA 58.551 43.478 0.00 0.00 0.00 2.92
1749 2063 5.957842 TCACTTGATTTGGACATGTAACC 57.042 39.130 0.00 0.00 0.00 2.85
1788 2102 1.169661 AACCTTCCACGAAATGCGCA 61.170 50.000 14.96 14.96 46.04 6.09
1906 2222 5.764131 TGATTCGGTTACATTGGTGTTTTC 58.236 37.500 0.00 0.00 39.77 2.29
1911 2227 6.847400 TCGGTTACATTGGTGTTTTCATATG 58.153 36.000 0.00 0.00 39.77 1.78
1945 2261 9.832445 AGAAGATCTAAAGTAACAGTGTTTTCA 57.168 29.630 14.90 0.00 0.00 2.69
1993 2309 3.751698 ACAAAGGCTTCTGTTCCGAATAC 59.248 43.478 0.00 0.00 0.00 1.89
2005 2321 1.274167 TCCGAATACTCCTTTGCGTGT 59.726 47.619 0.00 0.00 0.00 4.49
2010 2326 2.148916 TACTCCTTTGCGTGTCACTG 57.851 50.000 0.65 0.00 0.00 3.66
2057 2373 1.642037 CCAGGCACATGCTGAGTTCG 61.642 60.000 3.48 0.00 41.70 3.95
2124 2440 0.878523 CTTGTCGAAAGGCGTCACCA 60.879 55.000 0.00 0.00 43.14 4.17
2140 2456 1.624813 CACCACAGCCCCATTTTGATT 59.375 47.619 0.00 0.00 0.00 2.57
2141 2457 2.038820 CACCACAGCCCCATTTTGATTT 59.961 45.455 0.00 0.00 0.00 2.17
2142 2458 2.710471 ACCACAGCCCCATTTTGATTTT 59.290 40.909 0.00 0.00 0.00 1.82
2178 2494 5.250200 TGAGTATGTTCCCCATTTACACAC 58.750 41.667 0.00 0.00 34.86 3.82
2180 2496 5.007682 AGTATGTTCCCCATTTACACACAC 58.992 41.667 0.00 0.00 34.86 3.82
2185 2501 4.927978 TCCCCATTTACACACACAAAAG 57.072 40.909 0.00 0.00 0.00 2.27
2186 2502 4.537751 TCCCCATTTACACACACAAAAGA 58.462 39.130 0.00 0.00 0.00 2.52
2384 2702 4.084641 GCTACTGCTCTGAGATTTAATGCG 60.085 45.833 9.28 0.00 36.03 4.73
2490 2808 2.166459 CTCGAAAGTCTGCATCTACCCA 59.834 50.000 0.00 0.00 0.00 4.51
2544 2862 5.298527 TGAAGAAGATGCCATCATTAGCAAG 59.701 40.000 7.56 0.00 43.36 4.01
2658 2976 6.873605 TCTCGCAATATACCTGGTTTCATATG 59.126 38.462 3.84 0.00 0.00 1.78
3003 3331 9.947669 GCTATCCATGATGCTAATTCATATTTC 57.052 33.333 0.00 0.00 32.63 2.17
3079 3407 3.769844 ACCTAACGATCAGATCACTTGGT 59.230 43.478 11.12 9.47 0.00 3.67
3225 3553 9.007901 GGAATATGGATATCTGTTTTCAAGGAG 57.992 37.037 2.05 0.00 0.00 3.69
3242 3570 6.611381 TCAAGGAGAAATATTTGAAGCGTTG 58.389 36.000 5.17 9.47 0.00 4.10
3345 3673 1.973281 CATGGGTGTCACTGGTGCC 60.973 63.158 2.35 0.00 0.00 5.01
3413 3741 4.119556 AGCATCTAGACCTGCCTATGTA 57.880 45.455 13.51 0.00 39.22 2.29
3461 3789 6.608808 CCCATTCCATCTTTTTCTTCAGGTAT 59.391 38.462 0.00 0.00 0.00 2.73
3630 3964 3.152341 CTGGAAATGGCTCTGAAAGTGT 58.848 45.455 0.00 0.00 33.76 3.55
3827 4161 2.357952 CAGGTCAGATTGCCATGTCATG 59.642 50.000 5.79 5.79 0.00 3.07
3842 4176 6.185511 CCATGTCATGCTCCCATAGATTAAT 58.814 40.000 7.35 0.00 0.00 1.40
3843 4177 6.662234 CCATGTCATGCTCCCATAGATTAATT 59.338 38.462 7.35 0.00 0.00 1.40
3844 4178 7.830697 CCATGTCATGCTCCCATAGATTAATTA 59.169 37.037 7.35 0.00 0.00 1.40
3867 4201 1.005340 GTCCATGAGAAGCAGCTTCG 58.995 55.000 26.14 13.79 44.34 3.79
3877 4215 0.814457 AGCAGCTTCGGTAGAGACTG 59.186 55.000 0.00 0.00 35.50 3.51
4000 4338 1.670811 CTCGTGTTCTGCAGGTTTGTT 59.329 47.619 15.13 0.00 34.79 2.83
4011 4349 6.058833 TCTGCAGGTTTGTTACAGTTGATTA 58.941 36.000 15.13 0.00 0.00 1.75
4030 4368 5.418840 TGATTATTGCCACTTCTCCCTTTTC 59.581 40.000 0.00 0.00 0.00 2.29
4031 4369 1.995376 TTGCCACTTCTCCCTTTTCC 58.005 50.000 0.00 0.00 0.00 3.13
4051 4390 1.029947 CCCCCTAGAACGCGCAAAAT 61.030 55.000 5.73 0.00 0.00 1.82
4054 4393 1.465689 CCCTAGAACGCGCAAAATGTG 60.466 52.381 5.73 0.00 0.00 3.21
4134 4479 0.178876 TTCTGGGGATGGGTCTCACA 60.179 55.000 0.00 0.00 0.00 3.58
4237 4582 1.153349 CCGGTAAGAGCCTTGGCTC 60.153 63.158 28.67 28.67 37.11 4.70
4248 4593 1.683385 GCCTTGGCTCTTCAAAACACT 59.317 47.619 4.11 0.00 0.00 3.55
4249 4594 2.101415 GCCTTGGCTCTTCAAAACACTT 59.899 45.455 4.11 0.00 0.00 3.16
4251 4596 3.381272 CCTTGGCTCTTCAAAACACTTGA 59.619 43.478 0.00 0.00 0.00 3.02
4304 4649 5.305644 AGGATTCGGACACTGAATATAGCTT 59.694 40.000 0.00 0.00 36.24 3.74
4317 4664 6.430864 TGAATATAGCTTTGTTTGGGGATGA 58.569 36.000 0.00 0.00 0.00 2.92
4324 4671 4.262592 GCTTTGTTTGGGGATGATCAGTTT 60.263 41.667 0.09 0.00 0.00 2.66
4423 4770 2.037772 CTCTGCATACTCCATGGTACCC 59.962 54.545 12.58 0.00 34.97 3.69
4426 4773 3.646162 CTGCATACTCCATGGTACCCTAA 59.354 47.826 12.58 0.00 34.97 2.69
4433 4780 5.544682 ACTCCATGGTACCCTAAATCCTTA 58.455 41.667 12.58 0.00 0.00 2.69
4449 4797 6.780457 AATCCTTACACAGCAGCATAAATT 57.220 33.333 0.00 0.00 0.00 1.82
4482 4830 2.528041 ACTTGTCCCGAGACTGAAAC 57.472 50.000 0.00 0.00 43.91 2.78
4485 4833 1.699730 TGTCCCGAGACTGAAACTGA 58.300 50.000 0.00 0.00 43.91 3.41
4531 4879 1.346395 GTGGCGTCCATATCCATACCA 59.654 52.381 1.90 0.00 35.28 3.25
4654 5002 2.673258 TGATACGATGCTCCACCCTAA 58.327 47.619 0.00 0.00 0.00 2.69
4673 5025 0.419459 ACCCCCTCCTCATCACTTCT 59.581 55.000 0.00 0.00 0.00 2.85
4680 5032 4.653341 CCCTCCTCATCACTTCTTCAGTAT 59.347 45.833 0.00 0.00 32.76 2.12
4681 5033 5.835819 CCCTCCTCATCACTTCTTCAGTATA 59.164 44.000 0.00 0.00 32.76 1.47
4786 5139 6.017400 TCTCTGTGAAATCCTTGCAAAATC 57.983 37.500 0.00 0.00 0.00 2.17
5016 5380 4.141482 GCTTGGGGTATTGGAGTTAGATGA 60.141 45.833 0.00 0.00 0.00 2.92
5017 5381 5.456763 GCTTGGGGTATTGGAGTTAGATGAT 60.457 44.000 0.00 0.00 0.00 2.45
5018 5382 5.567037 TGGGGTATTGGAGTTAGATGATG 57.433 43.478 0.00 0.00 0.00 3.07
5188 5559 6.015350 ACATTGGTCTATCCCTAGTTATGTCG 60.015 42.308 0.00 0.00 34.77 4.35
5215 5588 6.406692 TTCCTCTCTTAATCCTTGTATCGG 57.593 41.667 0.00 0.00 0.00 4.18
5222 5595 6.675026 TCTTAATCCTTGTATCGGATGTACG 58.325 40.000 0.00 0.00 40.31 3.67
5227 5600 0.589708 TGTATCGGATGTACGCGAGG 59.410 55.000 15.93 0.00 0.00 4.63
5228 5601 0.590195 GTATCGGATGTACGCGAGGT 59.410 55.000 15.93 0.00 0.00 3.85
5239 5612 3.441222 TGTACGCGAGGTCATTCTTCTTA 59.559 43.478 15.93 0.00 0.00 2.10
5285 5658 7.521529 TCGAGCTGAGAAATAAAATTGTCTTG 58.478 34.615 0.00 0.00 0.00 3.02
5326 5701 5.357742 AACAAACCTCCAAGCTGAAAATT 57.642 34.783 0.00 0.00 0.00 1.82
5331 5706 6.819397 AACCTCCAAGCTGAAAATTAGTAC 57.181 37.500 0.00 0.00 0.00 2.73
5333 5708 6.543735 ACCTCCAAGCTGAAAATTAGTACTT 58.456 36.000 0.00 0.00 0.00 2.24
5334 5709 6.655425 ACCTCCAAGCTGAAAATTAGTACTTC 59.345 38.462 0.00 0.00 0.00 3.01
5337 5712 6.879458 TCCAAGCTGAAAATTAGTACTTCCTC 59.121 38.462 0.00 0.00 0.00 3.71
5341 5716 7.454225 AGCTGAAAATTAGTACTTCCTCTGTT 58.546 34.615 0.00 0.00 0.00 3.16
5344 5719 8.603242 TGAAAATTAGTACTTCCTCTGTTCAC 57.397 34.615 0.00 0.00 0.00 3.18
5345 5720 8.429641 TGAAAATTAGTACTTCCTCTGTTCACT 58.570 33.333 0.00 0.00 0.00 3.41
5354 5729 9.152595 GTACTTCCTCTGTTCACTTTTATAAGG 57.847 37.037 0.00 0.00 35.61 2.69
5357 5732 5.250774 TCCTCTGTTCACTTTTATAAGGCCT 59.749 40.000 0.00 0.00 35.61 5.19
5358 5733 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
5360 5735 7.610305 CCTCTGTTCACTTTTATAAGGCCTTTA 59.390 37.037 26.08 12.91 35.61 1.85
5361 5736 8.927675 TCTGTTCACTTTTATAAGGCCTTTAA 57.072 30.769 26.08 17.88 35.61 1.52
5363 5738 8.927675 TGTTCACTTTTATAAGGCCTTTAAGA 57.072 30.769 26.08 14.94 35.61 2.10
5364 5739 8.789762 TGTTCACTTTTATAAGGCCTTTAAGAC 58.210 33.333 26.08 15.04 35.61 3.01
5365 5740 8.789762 GTTCACTTTTATAAGGCCTTTAAGACA 58.210 33.333 26.08 4.20 35.61 3.41
5372 5747 9.747898 TTTATAAGGCCTTTAAGACATTTCAGA 57.252 29.630 26.08 0.00 0.00 3.27
5376 5751 6.012745 AGGCCTTTAAGACATTTCAGACAAT 58.987 36.000 0.00 0.00 0.00 2.71
5377 5752 6.071728 AGGCCTTTAAGACATTTCAGACAATG 60.072 38.462 0.00 0.00 39.67 2.82
5379 5754 6.583806 GCCTTTAAGACATTTCAGACAATGTG 59.416 38.462 12.82 2.69 45.55 3.21
5380 5755 6.583806 CCTTTAAGACATTTCAGACAATGTGC 59.416 38.462 12.82 7.29 45.55 4.57
5381 5756 6.631971 TTAAGACATTTCAGACAATGTGCA 57.368 33.333 12.82 0.00 45.55 4.57
5383 5758 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
5384 5759 5.904941 AGACATTTCAGACAATGTGCAAAA 58.095 33.333 12.82 0.00 45.55 2.44
5385 5760 5.750067 AGACATTTCAGACAATGTGCAAAAC 59.250 36.000 12.82 2.36 45.55 2.43
5386 5761 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
5387 5762 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
5388 5763 4.717233 TTCAGACAATGTGCAAAACAGT 57.283 36.364 0.00 0.00 43.64 3.55
5389 5764 4.291540 TCAGACAATGTGCAAAACAGTC 57.708 40.909 0.00 0.00 43.64 3.51
5390 5765 3.066621 TCAGACAATGTGCAAAACAGTCC 59.933 43.478 0.00 0.00 43.64 3.85
5391 5766 3.023119 AGACAATGTGCAAAACAGTCCA 58.977 40.909 0.00 0.00 43.64 4.02
5393 5768 4.099881 AGACAATGTGCAAAACAGTCCATT 59.900 37.500 0.00 0.00 43.64 3.16
5394 5769 4.768583 ACAATGTGCAAAACAGTCCATTT 58.231 34.783 0.00 0.00 43.64 2.32
5395 5770 5.184711 ACAATGTGCAAAACAGTCCATTTT 58.815 33.333 0.00 0.00 43.64 1.82
5396 5771 5.064962 ACAATGTGCAAAACAGTCCATTTTG 59.935 36.000 5.96 5.96 45.68 2.44
5398 5773 4.431809 TGTGCAAAACAGTCCATTTTGAG 58.568 39.130 13.00 0.00 45.75 3.02
5399 5774 4.081752 TGTGCAAAACAGTCCATTTTGAGT 60.082 37.500 13.00 0.00 45.75 3.41
5400 5775 4.869861 GTGCAAAACAGTCCATTTTGAGTT 59.130 37.500 13.00 0.00 45.75 3.01
5401 5776 4.869297 TGCAAAACAGTCCATTTTGAGTTG 59.131 37.500 13.00 0.00 45.75 3.16
5402 5777 4.869861 GCAAAACAGTCCATTTTGAGTTGT 59.130 37.500 13.00 0.00 45.75 3.32
5403 5778 5.005682 GCAAAACAGTCCATTTTGAGTTGTC 59.994 40.000 13.00 0.00 45.75 3.18
5406 5781 7.639113 AAACAGTCCATTTTGAGTTGTCTAA 57.361 32.000 0.00 0.00 0.00 2.10
5407 5782 7.639113 AACAGTCCATTTTGAGTTGTCTAAA 57.361 32.000 0.00 0.00 32.92 1.85
5408 5783 7.639113 ACAGTCCATTTTGAGTTGTCTAAAA 57.361 32.000 0.00 0.00 32.28 1.52
5409 5784 7.480810 ACAGTCCATTTTGAGTTGTCTAAAAC 58.519 34.615 0.00 0.00 32.28 2.43
5410 5785 6.632834 CAGTCCATTTTGAGTTGTCTAAAACG 59.367 38.462 0.00 0.00 32.28 3.60
5411 5786 6.540914 AGTCCATTTTGAGTTGTCTAAAACGA 59.459 34.615 0.00 0.00 32.28 3.85
5412 5787 6.631636 GTCCATTTTGAGTTGTCTAAAACGAC 59.368 38.462 0.00 0.00 41.93 4.34
5423 5798 8.307031 GTTGTCTAAAACGACTTACAAAAGTG 57.693 34.615 0.00 0.00 46.09 3.16
5426 5801 8.170553 TGTCTAAAACGACTTACAAAAGTGAAC 58.829 33.333 0.00 0.00 46.09 3.18
5428 5803 8.938906 TCTAAAACGACTTACAAAAGTGAACTT 58.061 29.630 0.00 0.00 46.09 2.66
5430 5805 7.790861 AAACGACTTACAAAAGTGAACTTTG 57.209 32.000 9.11 6.53 46.09 2.77
5432 5807 7.599630 ACGACTTACAAAAGTGAACTTTGTA 57.400 32.000 9.11 10.34 46.09 2.41
5666 6209 3.544684 CAGTTGATGGCTGCCATAACTA 58.455 45.455 32.21 20.45 45.26 2.24
5667 6210 3.947196 CAGTTGATGGCTGCCATAACTAA 59.053 43.478 32.21 23.88 45.26 2.24
5668 6211 3.947834 AGTTGATGGCTGCCATAACTAAC 59.052 43.478 32.02 29.23 45.26 2.34
5723 6266 8.598916 TGTCTGAGAAGGTATTATTTGTTACCA 58.401 33.333 2.29 0.00 35.15 3.25
5747 6291 2.038557 GTGTTGGAGGATAGTGTGTGGT 59.961 50.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.262211 CGCTTTAATTTGCTGGGAAGC 58.738 47.619 0.00 0.00 36.92 3.86
19 20 1.284408 CGGCAAAGGCACGCTTTAA 59.716 52.632 0.00 0.00 43.71 1.52
20 21 0.603172 TACGGCAAAGGCACGCTTTA 60.603 50.000 0.00 0.00 43.71 1.85
26 27 1.352156 CTCTCGTACGGCAAAGGCAC 61.352 60.000 16.52 0.00 43.71 5.01
30 31 2.455032 CTCATCTCTCGTACGGCAAAG 58.545 52.381 16.52 5.33 0.00 2.77
61 62 2.483106 GGCCGGAAAGAGTTTCTGTTAC 59.517 50.000 5.05 0.00 43.06 2.50
263 272 1.619526 GCCGTTACGTTGCGTGATCA 61.620 55.000 3.52 0.00 41.39 2.92
440 462 1.227089 CTGCCGACGAGAATGGAGG 60.227 63.158 0.00 0.00 0.00 4.30
560 587 0.603975 AAGAGCAGGAAAGCGACCAC 60.604 55.000 0.00 0.00 40.15 4.16
640 673 1.459592 GTTATGTGTGCGTGTGGTCTC 59.540 52.381 0.00 0.00 0.00 3.36
641 674 1.508632 GTTATGTGTGCGTGTGGTCT 58.491 50.000 0.00 0.00 0.00 3.85
720 753 4.494484 ACCAGCTTTTTCTCAACAACAAC 58.506 39.130 0.00 0.00 0.00 3.32
723 756 7.770801 AATAAACCAGCTTTTTCTCAACAAC 57.229 32.000 0.00 0.00 0.00 3.32
724 757 8.257306 AGAAATAAACCAGCTTTTTCTCAACAA 58.743 29.630 0.00 0.00 32.66 2.83
727 760 8.474025 TCAAGAAATAAACCAGCTTTTTCTCAA 58.526 29.630 0.00 0.00 36.03 3.02
728 761 8.006298 TCAAGAAATAAACCAGCTTTTTCTCA 57.994 30.769 0.00 0.00 36.03 3.27
730 763 8.237811 TCTCAAGAAATAAACCAGCTTTTTCT 57.762 30.769 0.00 0.00 38.04 2.52
731 764 8.352942 TCTCTCAAGAAATAAACCAGCTTTTTC 58.647 33.333 0.00 0.00 0.00 2.29
732 765 8.237811 TCTCTCAAGAAATAAACCAGCTTTTT 57.762 30.769 0.00 0.00 0.00 1.94
741 774 9.818796 GTGAAATGTCTCTCTCAAGAAATAAAC 57.181 33.333 0.00 0.00 0.00 2.01
819 852 0.250124 TCACATGGAAAGGCGAACGT 60.250 50.000 0.00 0.00 0.00 3.99
888 921 0.752054 GAGGAGGGATGAGAGCACAG 59.248 60.000 0.00 0.00 0.00 3.66
961 998 1.676529 TGAGAGGTCGATCGATCAACC 59.323 52.381 28.86 25.20 34.04 3.77
963 1000 1.950216 CCTGAGAGGTCGATCGATCAA 59.050 52.381 28.86 11.30 0.00 2.57
964 1001 1.598882 CCTGAGAGGTCGATCGATCA 58.401 55.000 28.86 21.90 0.00 2.92
965 1002 0.239879 GCCTGAGAGGTCGATCGATC 59.760 60.000 22.50 21.62 37.80 3.69
966 1003 0.466372 TGCCTGAGAGGTCGATCGAT 60.466 55.000 22.50 5.91 37.80 3.59
967 1004 0.679960 TTGCCTGAGAGGTCGATCGA 60.680 55.000 15.15 15.15 37.80 3.59
968 1005 0.248825 CTTGCCTGAGAGGTCGATCG 60.249 60.000 9.36 9.36 37.80 3.69
1200 1241 1.210234 ATCAACGAGATGCATGGGACA 59.790 47.619 2.46 0.00 38.20 4.02
1217 1258 1.533625 CGCAAGGTGGAAGGAAATCA 58.466 50.000 0.00 0.00 0.00 2.57
1610 1924 5.621193 ACATATCCGGAAATTCCCTTGTAG 58.379 41.667 9.01 0.00 31.13 2.74
1729 2043 3.756434 CCGGTTACATGTCCAAATCAAGT 59.244 43.478 0.00 0.00 0.00 3.16
1788 2102 2.296190 GCAAAGGTGAAAATTCTCCGGT 59.704 45.455 0.00 0.00 43.68 5.28
1945 2261 9.160496 TGATGCACAAAAGAACAAATAAAAACT 57.840 25.926 0.00 0.00 0.00 2.66
1993 2309 1.845809 GCCAGTGACACGCAAAGGAG 61.846 60.000 0.00 0.00 0.00 3.69
2005 2321 5.483811 TGTATAACGAGAAATTGCCAGTGA 58.516 37.500 0.00 0.00 0.00 3.41
2010 2326 6.560711 ACCAATTGTATAACGAGAAATTGCC 58.439 36.000 4.43 0.00 37.06 4.52
2057 2373 9.750125 ATTTCAAGGTAACAAAATGAAGAGAAC 57.250 29.630 0.00 0.00 41.41 3.01
2150 2466 6.778069 TGTAAATGGGGAACATACTCAAAACA 59.222 34.615 0.00 0.00 39.40 2.83
2178 2494 7.019774 TCAAGAGAATCACACTTCTTTTGTG 57.980 36.000 13.46 0.00 43.04 3.33
2180 2496 8.400947 TCTTTCAAGAGAATCACACTTCTTTTG 58.599 33.333 9.56 9.56 43.49 2.44
2185 2501 8.770438 AGTATCTTTCAAGAGAATCACACTTC 57.230 34.615 0.00 0.00 38.66 3.01
2186 2502 8.370940 TGAGTATCTTTCAAGAGAATCACACTT 58.629 33.333 9.61 0.00 43.62 3.16
2384 2702 7.418840 TGAAAAATTGTGCACATATTTCACC 57.581 32.000 30.79 22.77 32.38 4.02
2490 2808 3.904571 TGATGTTGTTACGCTAACGAGT 58.095 40.909 0.00 0.00 43.93 4.18
2544 2862 9.216117 TCTTTGCTGTTATTTTCTTCTAGGTAC 57.784 33.333 0.00 0.00 0.00 3.34
2658 2976 9.406828 GGTCAAATCAAATTACTGTTTAGGAAC 57.593 33.333 0.00 0.00 36.29 3.62
3003 3331 5.305386 TCCTGGAATAGTGTGATGTAGATGG 59.695 44.000 0.00 0.00 0.00 3.51
3225 3553 7.740519 ATGTTAGCAACGCTTCAAATATTTC 57.259 32.000 0.00 0.00 40.44 2.17
3402 3730 3.181465 ACGGACTGAAATACATAGGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
3403 3731 4.051922 GACGGACTGAAATACATAGGCAG 58.948 47.826 0.00 0.00 0.00 4.85
3404 3732 3.181469 GGACGGACTGAAATACATAGGCA 60.181 47.826 0.00 0.00 0.00 4.75
3413 3741 4.562963 GGAGTTGTTAGGACGGACTGAAAT 60.563 45.833 0.00 0.00 0.00 2.17
3461 3789 8.031277 CGACATATCAAGATCATGGTTATCAGA 58.969 37.037 0.00 0.00 0.00 3.27
3842 4176 5.620738 AGCTGCTTCTCATGGACTAATAA 57.379 39.130 0.00 0.00 0.00 1.40
3843 4177 5.605534 GAAGCTGCTTCTCATGGACTAATA 58.394 41.667 29.91 0.00 37.49 0.98
3844 4178 4.450053 GAAGCTGCTTCTCATGGACTAAT 58.550 43.478 29.91 0.00 37.49 1.73
3867 4201 1.474879 GCACACTCTCCAGTCTCTACC 59.525 57.143 0.00 0.00 0.00 3.18
3877 4215 0.321122 CCCAGTTCAGCACACTCTCC 60.321 60.000 0.00 0.00 0.00 3.71
4000 4338 5.880332 GGAGAAGTGGCAATAATCAACTGTA 59.120 40.000 0.00 0.00 0.00 2.74
4011 4349 2.529632 GGAAAAGGGAGAAGTGGCAAT 58.470 47.619 0.00 0.00 0.00 3.56
4043 4382 1.929836 TGAACCAAACACATTTTGCGC 59.070 42.857 0.00 0.00 0.00 6.09
4051 4390 5.885352 TCTTCTTCTCAATGAACCAAACACA 59.115 36.000 0.00 0.00 0.00 3.72
4054 4393 5.563671 GCCTCTTCTTCTCAATGAACCAAAC 60.564 44.000 0.00 0.00 0.00 2.93
4086 4430 2.342910 GCTGCAAGGTGAAAGACATG 57.657 50.000 0.00 0.00 0.00 3.21
4134 4479 0.827925 TGAAGAGACCGAGCACCACT 60.828 55.000 0.00 0.00 0.00 4.00
4237 4582 6.632834 CGTATGGAGTTTCAAGTGTTTTGAAG 59.367 38.462 3.00 0.00 39.30 3.02
4248 4593 5.419155 AGTCATCTCTCGTATGGAGTTTCAA 59.581 40.000 0.00 0.00 43.60 2.69
4249 4594 4.950475 AGTCATCTCTCGTATGGAGTTTCA 59.050 41.667 0.00 0.00 43.60 2.69
4251 4596 7.589958 AATAGTCATCTCTCGTATGGAGTTT 57.410 36.000 0.00 0.00 43.60 2.66
4304 4649 4.222336 ACAAACTGATCATCCCCAAACAA 58.778 39.130 0.00 0.00 0.00 2.83
4317 4664 2.031919 TGCCGGCGACAAACTGAT 59.968 55.556 23.90 0.00 0.00 2.90
4423 4770 6.925610 TTATGCTGCTGTGTAAGGATTTAG 57.074 37.500 0.00 0.00 0.00 1.85
4426 4773 6.780457 AATTTATGCTGCTGTGTAAGGATT 57.220 33.333 0.00 0.00 0.00 3.01
4449 4797 4.274950 CGGGACAAGTTTCAGAGCTAAAAA 59.725 41.667 0.00 0.00 0.00 1.94
4482 4830 3.698040 CTGAAGGTTTCCATGGGATTCAG 59.302 47.826 16.93 16.93 38.15 3.02
4485 4833 3.105959 CCTGAAGGTTTCCATGGGATT 57.894 47.619 13.02 0.00 0.00 3.01
4531 4879 1.614317 GCAGAAAGGTACACCAGGCAT 60.614 52.381 0.38 0.00 38.89 4.40
4546 4894 0.250684 TGAATCCCTTGTGCGCAGAA 60.251 50.000 19.71 19.71 0.00 3.02
4640 4988 1.532238 GGGGTTAGGGTGGAGCATC 59.468 63.158 0.00 0.00 0.00 3.91
4654 5002 0.419459 AGAAGTGATGAGGAGGGGGT 59.581 55.000 0.00 0.00 0.00 4.95
4673 5025 8.311836 GGATACCGAAGAAATGGATATACTGAA 58.688 37.037 0.00 0.00 0.00 3.02
5188 5559 8.604890 CGATACAAGGATTAAGAGAGGAAAAAC 58.395 37.037 0.00 0.00 0.00 2.43
5215 5588 2.493713 AGAATGACCTCGCGTACATC 57.506 50.000 5.77 0.44 0.00 3.06
5222 5595 2.159282 TCGGTAAGAAGAATGACCTCGC 60.159 50.000 0.00 0.00 0.00 5.03
5239 5612 4.261031 CGAAAACAAAACCTCATCTTCGGT 60.261 41.667 0.00 0.00 32.83 4.69
5331 5706 6.094186 GGCCTTATAAAAGTGAACAGAGGAAG 59.906 42.308 0.00 0.00 0.00 3.46
5333 5708 5.250774 AGGCCTTATAAAAGTGAACAGAGGA 59.749 40.000 0.00 0.00 0.00 3.71
5334 5709 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
5337 5712 9.010029 TCTTAAAGGCCTTATAAAAGTGAACAG 57.990 33.333 20.84 5.01 0.00 3.16
5341 5716 9.528489 AATGTCTTAAAGGCCTTATAAAAGTGA 57.472 29.630 20.84 9.87 0.00 3.41
5351 5726 5.385198 TGTCTGAAATGTCTTAAAGGCCTT 58.615 37.500 13.78 13.78 0.00 4.35
5352 5727 4.985538 TGTCTGAAATGTCTTAAAGGCCT 58.014 39.130 0.00 0.00 0.00 5.19
5354 5729 6.583806 CACATTGTCTGAAATGTCTTAAAGGC 59.416 38.462 12.25 0.00 45.47 4.35
5357 5732 7.036996 TGCACATTGTCTGAAATGTCTTAAA 57.963 32.000 12.25 0.00 45.47 1.52
5358 5733 6.631971 TGCACATTGTCTGAAATGTCTTAA 57.368 33.333 12.25 0.00 45.47 1.85
5360 5735 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
5361 5736 5.518848 TTTGCACATTGTCTGAAATGTCT 57.481 34.783 12.25 0.00 45.47 3.41
5364 5739 5.521010 ACTGTTTTGCACATTGTCTGAAATG 59.479 36.000 0.00 9.50 42.21 2.32
5365 5740 5.663456 ACTGTTTTGCACATTGTCTGAAAT 58.337 33.333 0.00 0.00 33.76 2.17
5369 5744 3.181488 TGGACTGTTTTGCACATTGTCTG 60.181 43.478 0.00 0.00 33.15 3.51
5370 5745 3.023119 TGGACTGTTTTGCACATTGTCT 58.977 40.909 0.00 0.00 33.15 3.41
5372 5747 4.405116 AATGGACTGTTTTGCACATTGT 57.595 36.364 0.00 0.00 33.76 2.71
5376 5751 4.081752 ACTCAAAATGGACTGTTTTGCACA 60.082 37.500 6.49 0.00 43.04 4.57
5377 5752 4.432712 ACTCAAAATGGACTGTTTTGCAC 58.567 39.130 6.49 0.00 43.04 4.57
5379 5754 4.869861 ACAACTCAAAATGGACTGTTTTGC 59.130 37.500 6.49 0.00 43.04 3.68
5380 5755 6.332630 AGACAACTCAAAATGGACTGTTTTG 58.667 36.000 5.27 5.27 44.10 2.44
5381 5756 6.530019 AGACAACTCAAAATGGACTGTTTT 57.470 33.333 0.00 0.00 0.00 2.43
5383 5758 7.639113 TTTAGACAACTCAAAATGGACTGTT 57.361 32.000 0.00 0.00 0.00 3.16
5384 5759 7.480810 GTTTTAGACAACTCAAAATGGACTGT 58.519 34.615 0.00 0.00 0.00 3.55
5385 5760 6.632834 CGTTTTAGACAACTCAAAATGGACTG 59.367 38.462 0.00 0.00 0.00 3.51
5386 5761 6.540914 TCGTTTTAGACAACTCAAAATGGACT 59.459 34.615 0.00 0.00 31.88 3.85
5387 5762 6.631636 GTCGTTTTAGACAACTCAAAATGGAC 59.368 38.462 0.00 0.00 40.65 4.02
5388 5763 6.540914 AGTCGTTTTAGACAACTCAAAATGGA 59.459 34.615 0.00 0.00 43.24 3.41
5389 5764 6.725246 AGTCGTTTTAGACAACTCAAAATGG 58.275 36.000 0.00 0.00 43.24 3.16
5390 5765 9.155053 GTAAGTCGTTTTAGACAACTCAAAATG 57.845 33.333 0.00 0.00 43.24 2.32
5391 5766 8.885722 TGTAAGTCGTTTTAGACAACTCAAAAT 58.114 29.630 0.00 0.00 43.24 1.82
5393 5768 7.830940 TGTAAGTCGTTTTAGACAACTCAAA 57.169 32.000 0.00 0.00 43.24 2.69
5394 5769 7.830940 TTGTAAGTCGTTTTAGACAACTCAA 57.169 32.000 0.00 0.00 43.24 3.02
5395 5770 7.830940 TTTGTAAGTCGTTTTAGACAACTCA 57.169 32.000 0.00 0.00 43.24 3.41
5396 5771 8.385858 ACTTTTGTAAGTCGTTTTAGACAACTC 58.614 33.333 0.00 0.00 40.60 3.01
5398 5773 8.170553 TCACTTTTGTAAGTCGTTTTAGACAAC 58.829 33.333 0.00 0.00 42.67 3.32
5399 5774 8.254178 TCACTTTTGTAAGTCGTTTTAGACAA 57.746 30.769 0.00 0.00 42.67 3.18
5400 5775 7.830940 TCACTTTTGTAAGTCGTTTTAGACA 57.169 32.000 0.00 0.00 42.67 3.41
5401 5776 8.385858 AGTTCACTTTTGTAAGTCGTTTTAGAC 58.614 33.333 0.00 0.00 42.67 2.59
5402 5777 8.483307 AGTTCACTTTTGTAAGTCGTTTTAGA 57.517 30.769 0.00 0.00 42.67 2.10
5403 5778 9.550811 AAAGTTCACTTTTGTAAGTCGTTTTAG 57.449 29.630 0.00 0.00 43.07 1.85
5406 5781 7.364970 ACAAAGTTCACTTTTGTAAGTCGTTT 58.635 30.769 2.01 0.00 43.07 3.60
5407 5782 6.905578 ACAAAGTTCACTTTTGTAAGTCGTT 58.094 32.000 2.01 0.00 43.07 3.85
5408 5783 6.490566 ACAAAGTTCACTTTTGTAAGTCGT 57.509 33.333 2.01 0.00 43.07 4.34
5409 5784 7.681903 AGTACAAAGTTCACTTTTGTAAGTCG 58.318 34.615 10.95 0.00 43.07 4.18
5410 5785 9.911980 GTAGTACAAAGTTCACTTTTGTAAGTC 57.088 33.333 10.95 2.06 43.07 3.01
5411 5786 9.662947 AGTAGTACAAAGTTCACTTTTGTAAGT 57.337 29.630 10.95 0.79 43.07 2.24
5419 5794 9.609346 ACAACATAAGTAGTACAAAGTTCACTT 57.391 29.630 2.52 0.00 37.91 3.16
5420 5795 9.609346 AACAACATAAGTAGTACAAAGTTCACT 57.391 29.630 2.52 0.00 0.00 3.41
5428 5803 8.249638 TGGCGTATAACAACATAAGTAGTACAA 58.750 33.333 2.52 0.00 0.00 2.41
5430 5805 7.917505 AGTGGCGTATAACAACATAAGTAGTAC 59.082 37.037 0.00 0.00 0.00 2.73
5432 5807 6.870769 AGTGGCGTATAACAACATAAGTAGT 58.129 36.000 0.00 0.00 0.00 2.73
5468 5970 3.903090 TCTGTTCCGACCTAAAAGGGTAA 59.097 43.478 0.00 0.00 40.58 2.85
5666 6209 7.520614 GCACATACTTTAAGAGCTTGAGTTGTT 60.521 37.037 0.00 0.00 0.00 2.83
5667 6210 6.073003 GCACATACTTTAAGAGCTTGAGTTGT 60.073 38.462 0.00 7.73 0.00 3.32
5668 6211 6.073058 TGCACATACTTTAAGAGCTTGAGTTG 60.073 38.462 0.00 7.32 0.00 3.16
5723 6266 4.326826 CACACACTATCCTCCAACACAAT 58.673 43.478 0.00 0.00 0.00 2.71
5793 6337 8.613482 GGATAGTTCTTTGCCTAAGATTGTAAC 58.387 37.037 0.00 0.00 42.32 2.50


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

AutoCloner maintained by Alex Coulton.