Multiple sequence alignment - TraesCS1A01G099700

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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 TraesCS1A01G099700 chr1A 100.000 3095 0 0 1 3095 96366555 96363461 0.000000e+00 5716.0
1 TraesCS1A01G099700 chr1A 91.719 797 57 8 1 793 224095728 224096519 0.000000e+00 1098.0
2 TraesCS1A01G099700 chr1A 90.625 800 70 5 1 795 68376178 68376977 0.000000e+00 1057.0
3 TraesCS1A01G099700 chr1D 93.204 1913 74 20 796 2701 79091140 79093003 0.000000e+00 2761.0
4 TraesCS1A01G099700 chr1D 90.613 799 68 5 1 792 469552182 469552980 0.000000e+00 1053.0
5 TraesCS1A01G099700 chr1D 94.545 275 11 4 2763 3035 79093004 79093276 3.690000e-114 422.0
6 TraesCS1A01G099700 chr1B 91.173 1926 124 22 803 2726 129998416 130000297 0.000000e+00 2573.0
7 TraesCS1A01G099700 chr1B 92.308 39 3 0 2934 2972 130000493 130000531 4.310000e-04 56.5
8 TraesCS1A01G099700 chr4A 93.734 798 42 6 1 793 609567385 609566591 0.000000e+00 1190.0
9 TraesCS1A01G099700 chr5A 92.105 798 59 4 1 794 64788612 64789409 0.000000e+00 1122.0
10 TraesCS1A01G099700 chr5A 89.750 800 72 7 1 794 311940411 311941206 0.000000e+00 1014.0
11 TraesCS1A01G099700 chr5A 89.987 789 72 6 10 794 648315123 648314338 0.000000e+00 1013.0
12 TraesCS1A01G099700 chr5A 88.636 132 12 3 2470 2601 610378906 610378778 1.150000e-34 158.0
13 TraesCS1A01G099700 chr2A 91.332 796 61 7 1 792 568402130 568401339 0.000000e+00 1081.0
14 TraesCS1A01G099700 chr6D 90.062 805 68 10 2 798 17103311 17102511 0.000000e+00 1033.0
15 TraesCS1A01G099700 chr6D 89.344 122 10 3 2481 2601 436674967 436674848 1.920000e-32 150.0
16 TraesCS1A01G099700 chr5D 76.780 323 60 13 2285 2601 437359104 437358791 1.910000e-37 167.0
17 TraesCS1A01G099700 chr3A 76.543 324 58 15 2285 2601 6788398 6788710 8.880000e-36 161.0
18 TraesCS1A01G099700 chr3A 88.636 132 12 3 2470 2601 597624259 597624131 1.150000e-34 158.0
19 TraesCS1A01G099700 chr7D 76.308 325 58 15 2285 2601 455434184 455433871 4.130000e-34 156.0
20 TraesCS1A01G099700 chrUn 100.000 30 0 0 2540 2569 300484564 300484593 4.310000e-04 56.5


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 TraesCS1A01G099700 chr1A 96363461 96366555 3094 True 5716.00 5716 100.0000 1 3095 1 chr1A.!!$R1 3094
1 TraesCS1A01G099700 chr1A 224095728 224096519 791 False 1098.00 1098 91.7190 1 793 1 chr1A.!!$F2 792
2 TraesCS1A01G099700 chr1A 68376178 68376977 799 False 1057.00 1057 90.6250 1 795 1 chr1A.!!$F1 794
3 TraesCS1A01G099700 chr1D 79091140 79093276 2136 False 1591.50 2761 93.8745 796 3035 2 chr1D.!!$F2 2239
4 TraesCS1A01G099700 chr1D 469552182 469552980 798 False 1053.00 1053 90.6130 1 792 1 chr1D.!!$F1 791
5 TraesCS1A01G099700 chr1B 129998416 130000531 2115 False 1314.75 2573 91.7405 803 2972 2 chr1B.!!$F1 2169
6 TraesCS1A01G099700 chr4A 609566591 609567385 794 True 1190.00 1190 93.7340 1 793 1 chr4A.!!$R1 792
7 TraesCS1A01G099700 chr5A 64788612 64789409 797 False 1122.00 1122 92.1050 1 794 1 chr5A.!!$F1 793
8 TraesCS1A01G099700 chr5A 311940411 311941206 795 False 1014.00 1014 89.7500 1 794 1 chr5A.!!$F2 793
9 TraesCS1A01G099700 chr5A 648314338 648315123 785 True 1013.00 1013 89.9870 10 794 1 chr5A.!!$R2 784
10 TraesCS1A01G099700 chr2A 568401339 568402130 791 True 1081.00 1081 91.3320 1 792 1 chr2A.!!$R1 791
11 TraesCS1A01G099700 chr6D 17102511 17103311 800 True 1033.00 1033 90.0620 2 798 1 chr6D.!!$R1 796

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
893 911 2.022195 TCGGTCTCTTTGATACGGAGG 58.978 52.381 0.00 0.0 0.0 4.30 F
1554 1572 0.390124 TTTTCGCCGCGGGTAGATAT 59.610 50.000 29.38 0.0 0.0 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2093 0.036732 TTACCTGCTGCTGTTCCTGG 59.963 55.0 0.00 0.0 0.00 4.45 R
2525 2561 0.179073 AGTGCACTGAAGAGCAACGT 60.179 50.0 20.97 0.0 42.84 3.99 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
162 164 9.595823 AATACGTGTGCAACTAGACTAAATTAT 57.404 29.630 0.00 0.00 38.04 1.28
176 178 8.863872 AGACTAAATTATAAGCCAACTGTGTT 57.136 30.769 0.00 0.00 0.00 3.32
248 252 6.705782 CAATTAGACTACGTTACATGCCAAG 58.294 40.000 0.00 0.00 0.00 3.61
267 271 5.735922 GCCAAGTAAACATCAATGTGTGTGT 60.736 40.000 0.00 0.00 41.61 3.72
287 291 8.853126 TGTGTGTAACTAGACTACATTACAAGT 58.147 33.333 12.88 0.00 38.79 3.16
521 528 7.773864 TTTTATCGAAACATACTTATGCGGA 57.226 32.000 0.00 0.00 37.19 5.54
658 665 4.412207 ACGTGAAGCTGTTTCTTTCAAAC 58.588 39.130 5.84 0.00 36.71 2.93
741 753 5.832539 ATACTTATGCATGGCTAGGAAGT 57.167 39.130 10.16 11.40 0.00 3.01
751 763 2.682494 TAGGAAGTCCGGCCGCTT 60.682 61.111 22.85 19.23 42.08 4.68
754 767 2.265904 GGAAGTCCGGCCGCTTTTT 61.266 57.895 22.85 10.99 0.00 1.94
795 811 6.237901 GGCCACTTTTTAGATTTTGGGAAAT 58.762 36.000 0.00 0.00 38.16 2.17
798 814 8.882736 GCCACTTTTTAGATTTTGGGAAATATG 58.117 33.333 0.00 0.00 35.65 1.78
799 815 9.382275 CCACTTTTTAGATTTTGGGAAATATGG 57.618 33.333 0.00 0.00 35.65 2.74
854 870 3.149196 CAAAGTGGCAAGTGGTAGACAT 58.851 45.455 0.00 0.00 0.00 3.06
872 888 2.741486 ATTGTTGGGCCGTGCGTAGT 62.741 55.000 0.00 0.00 0.00 2.73
893 911 2.022195 TCGGTCTCTTTGATACGGAGG 58.978 52.381 0.00 0.00 0.00 4.30
1107 1125 4.081030 GCCTCGACGACGACGACA 62.081 66.667 17.84 0.00 43.81 4.35
1108 1126 2.096030 CCTCGACGACGACGACAG 59.904 66.667 17.84 9.73 43.81 3.51
1109 1127 2.096030 CTCGACGACGACGACAGG 59.904 66.667 17.84 5.77 43.81 4.00
1161 1179 4.742201 TCGCCGCCAGCAGAGAAC 62.742 66.667 0.00 0.00 44.04 3.01
1167 1185 2.752358 CCAGCAGAGAACCCAGCA 59.248 61.111 0.00 0.00 0.00 4.41
1263 1281 1.980052 CCTTACAGAGGTTGCCGGA 59.020 57.895 5.05 0.00 40.95 5.14
1447 1465 4.463788 CCAGGGCCATTGGGGGTC 62.464 72.222 15.94 0.00 37.04 4.46
1554 1572 0.390124 TTTTCGCCGCGGGTAGATAT 59.610 50.000 29.38 0.00 0.00 1.63
1559 1577 2.126071 CGCGGGTAGATATGGGCG 60.126 66.667 0.00 0.00 37.56 6.13
1604 1622 4.909696 TCGAGGAGCTGAAGAAAGATAG 57.090 45.455 0.00 0.00 0.00 2.08
1618 1636 7.290948 TGAAGAAAGATAGGAGATGCTTGGATA 59.709 37.037 0.00 0.00 0.00 2.59
1653 1671 1.556911 ACTGTCTTGGACATGCTAGGG 59.443 52.381 0.71 0.00 41.94 3.53
1656 1674 2.642311 TGTCTTGGACATGCTAGGGAAA 59.358 45.455 0.00 0.00 37.67 3.13
1670 1688 1.602605 GGAAAGTTGGTCGGGTGGG 60.603 63.158 0.00 0.00 0.00 4.61
1681 1699 2.573340 GGGTGGGCGAAATGCTTG 59.427 61.111 0.00 0.00 45.43 4.01
1740 1758 5.528320 TCCTGACATCGTGACGTATAATACA 59.472 40.000 4.40 0.00 0.00 2.29
1774 1792 1.277842 TGCGTAGGCTTGGAAGATTGA 59.722 47.619 9.11 0.00 40.82 2.57
1824 1842 0.820226 TTGAGAGAGGCATCAGTCCG 59.180 55.000 0.00 0.00 0.00 4.79
1984 2002 0.755327 AAAAGCTGGGCGGTTTGAGT 60.755 50.000 0.00 0.00 42.12 3.41
2075 2093 0.405973 AAGTCCAAGGGAAGAAGGGC 59.594 55.000 0.00 0.00 31.38 5.19
2120 2138 5.635120 AGCAGAAAAGTTATCTTCCAGGTT 58.365 37.500 0.00 0.00 32.90 3.50
2124 2142 7.141363 CAGAAAAGTTATCTTCCAGGTTTGTG 58.859 38.462 0.00 0.00 32.90 3.33
2162 2180 3.677648 CAACAGCTGCTGGCACCC 61.678 66.667 31.00 0.00 44.79 4.61
2177 2198 2.222013 ACCCAGTTCCCGACTTCCC 61.222 63.158 0.00 0.00 36.10 3.97
2191 2212 3.041946 GACTTCCCATGGATACTGGTCT 58.958 50.000 15.22 0.00 34.28 3.85
2198 2219 2.489938 TGGATACTGGTCTTGTTGGC 57.510 50.000 0.00 0.00 37.61 4.52
2202 2223 2.543777 TACTGGTCTTGTTGGCTGAC 57.456 50.000 0.00 0.00 0.00 3.51
2203 2224 0.546122 ACTGGTCTTGTTGGCTGACA 59.454 50.000 0.00 0.00 32.84 3.58
2204 2225 1.143684 ACTGGTCTTGTTGGCTGACAT 59.856 47.619 0.00 0.00 32.84 3.06
2205 2226 1.808945 CTGGTCTTGTTGGCTGACATC 59.191 52.381 0.00 0.00 32.84 3.06
2206 2227 1.421268 TGGTCTTGTTGGCTGACATCT 59.579 47.619 0.00 0.00 32.84 2.90
2207 2228 2.158623 TGGTCTTGTTGGCTGACATCTT 60.159 45.455 0.00 0.00 32.84 2.40
2208 2229 2.485814 GGTCTTGTTGGCTGACATCTTC 59.514 50.000 0.00 0.00 32.84 2.87
2209 2230 3.141398 GTCTTGTTGGCTGACATCTTCA 58.859 45.455 0.00 0.00 0.00 3.02
2302 2323 7.332926 CAGTAGCTTGATGATTACAAAGACACT 59.667 37.037 0.00 0.00 0.00 3.55
2308 2329 6.614160 TGATGATTACAAAGACACTGCAATG 58.386 36.000 0.00 0.00 0.00 2.82
2309 2330 6.430616 TGATGATTACAAAGACACTGCAATGA 59.569 34.615 0.26 0.00 0.00 2.57
2310 2331 6.822667 TGATTACAAAGACACTGCAATGAT 57.177 33.333 0.26 0.00 0.00 2.45
2311 2332 6.845302 TGATTACAAAGACACTGCAATGATC 58.155 36.000 0.26 0.00 0.00 2.92
2312 2333 5.627499 TTACAAAGACACTGCAATGATCC 57.373 39.130 0.26 0.00 0.00 3.36
2313 2334 3.759581 ACAAAGACACTGCAATGATCCT 58.240 40.909 0.26 0.00 0.00 3.24
2314 2335 3.504906 ACAAAGACACTGCAATGATCCTG 59.495 43.478 0.26 0.00 0.00 3.86
2315 2336 2.414994 AGACACTGCAATGATCCTGG 57.585 50.000 0.26 0.00 0.00 4.45
2316 2337 1.911357 AGACACTGCAATGATCCTGGA 59.089 47.619 0.26 0.00 0.00 3.86
2317 2338 2.093075 AGACACTGCAATGATCCTGGAG 60.093 50.000 0.26 10.66 38.16 3.86
2318 2339 1.022735 CACTGCAATGATCCTGGAGC 58.977 55.000 4.68 4.68 35.80 4.70
2319 2340 0.917533 ACTGCAATGATCCTGGAGCT 59.082 50.000 13.80 0.00 35.80 4.09
2320 2341 2.121948 ACTGCAATGATCCTGGAGCTA 58.878 47.619 13.80 0.00 35.80 3.32
2321 2342 2.158842 ACTGCAATGATCCTGGAGCTAC 60.159 50.000 13.80 0.00 35.80 3.58
2322 2343 1.839354 TGCAATGATCCTGGAGCTACA 59.161 47.619 13.80 0.00 0.00 2.74
2335 2371 0.176680 AGCTACAGACCTGAATGGCG 59.823 55.000 3.76 0.00 40.22 5.69
2478 2514 0.323629 TGCCCGTTACTGGAAAGAGG 59.676 55.000 0.00 0.00 0.00 3.69
2479 2515 0.392595 GCCCGTTACTGGAAAGAGGG 60.393 60.000 0.00 5.07 40.27 4.30
2514 2550 5.186797 TCTGAACTTGTGGGTGTCAAATTTT 59.813 36.000 0.00 0.00 0.00 1.82
2515 2551 5.799213 TGAACTTGTGGGTGTCAAATTTTT 58.201 33.333 0.00 0.00 0.00 1.94
2525 2561 7.011857 GTGGGTGTCAAATTTTTCAGCATTTTA 59.988 33.333 17.42 2.98 0.00 1.52
2722 2760 5.118286 CACTATGTGTCTGTCAATATGCCA 58.882 41.667 0.00 0.00 0.00 4.92
2726 2764 4.587891 TGTGTCTGTCAATATGCCATGAA 58.412 39.130 0.00 0.00 0.00 2.57
2728 2766 4.637534 GTGTCTGTCAATATGCCATGAACT 59.362 41.667 0.00 0.00 0.00 3.01
2730 2768 4.274459 GTCTGTCAATATGCCATGAACTCC 59.726 45.833 0.00 0.00 0.00 3.85
2731 2769 4.164796 TCTGTCAATATGCCATGAACTCCT 59.835 41.667 0.00 0.00 0.00 3.69
2733 2771 5.368145 TGTCAATATGCCATGAACTCCTAC 58.632 41.667 0.00 0.00 0.00 3.18
2734 2772 5.130975 TGTCAATATGCCATGAACTCCTACT 59.869 40.000 0.00 0.00 0.00 2.57
2735 2773 5.698545 GTCAATATGCCATGAACTCCTACTC 59.301 44.000 0.00 0.00 0.00 2.59
2736 2774 4.899352 ATATGCCATGAACTCCTACTCC 57.101 45.455 0.00 0.00 0.00 3.85
2737 2775 1.204146 TGCCATGAACTCCTACTCCC 58.796 55.000 0.00 0.00 0.00 4.30
2738 2776 1.273838 TGCCATGAACTCCTACTCCCT 60.274 52.381 0.00 0.00 0.00 4.20
2739 2777 2.023404 TGCCATGAACTCCTACTCCCTA 60.023 50.000 0.00 0.00 0.00 3.53
2740 2778 2.630580 GCCATGAACTCCTACTCCCTAG 59.369 54.545 0.00 0.00 0.00 3.02
2741 2779 3.691603 GCCATGAACTCCTACTCCCTAGA 60.692 52.174 0.00 0.00 0.00 2.43
2742 2780 4.746466 CCATGAACTCCTACTCCCTAGAT 58.254 47.826 0.00 0.00 0.00 1.98
2743 2781 5.151454 CCATGAACTCCTACTCCCTAGATT 58.849 45.833 0.00 0.00 0.00 2.40
2744 2782 5.604650 CCATGAACTCCTACTCCCTAGATTT 59.395 44.000 0.00 0.00 0.00 2.17
2745 2783 6.100424 CCATGAACTCCTACTCCCTAGATTTT 59.900 42.308 0.00 0.00 0.00 1.82
2746 2784 7.366011 CCATGAACTCCTACTCCCTAGATTTTT 60.366 40.741 0.00 0.00 0.00 1.94
2801 2839 2.219080 TGGTGTGATGCCATGTCATT 57.781 45.000 0.00 0.00 0.00 2.57
2808 2846 2.101750 TGATGCCATGTCATTTCCATGC 59.898 45.455 0.00 0.00 38.67 4.06
2811 2849 2.273557 GCCATGTCATTTCCATGCAAC 58.726 47.619 0.00 0.00 38.67 4.17
2857 2895 2.764128 GGGGTGCTGGATCGAGGA 60.764 66.667 6.88 0.07 0.00 3.71
2891 2929 5.202746 TGCTCTCCTAGGGACTAACTTTA 57.797 43.478 9.46 0.00 42.17 1.85
2899 2937 8.912614 TCCTAGGGACTAACTTTAGAAGATTT 57.087 34.615 9.46 0.00 42.17 2.17
2998 3069 7.946655 TTCAGAATGTATGCTCGTATTTAGG 57.053 36.000 0.00 0.00 37.40 2.69
3003 3074 4.603985 TGTATGCTCGTATTTAGGTCACG 58.396 43.478 0.00 0.00 37.03 4.35
3008 3079 3.922240 GCTCGTATTTAGGTCACGAAACA 59.078 43.478 0.00 0.00 43.40 2.83
3009 3080 4.565564 GCTCGTATTTAGGTCACGAAACAT 59.434 41.667 0.00 0.00 43.40 2.71
3026 3097 5.432885 AAACATTACAAAGTCCTGAACCG 57.567 39.130 0.00 0.00 0.00 4.44
3027 3098 4.081322 ACATTACAAAGTCCTGAACCGT 57.919 40.909 0.00 0.00 0.00 4.83
3028 3099 5.217978 ACATTACAAAGTCCTGAACCGTA 57.782 39.130 0.00 0.00 0.00 4.02
3029 3100 4.992951 ACATTACAAAGTCCTGAACCGTAC 59.007 41.667 0.00 0.00 0.00 3.67
3030 3101 4.669206 TTACAAAGTCCTGAACCGTACA 57.331 40.909 0.00 0.00 0.00 2.90
3032 3103 3.463944 ACAAAGTCCTGAACCGTACAAG 58.536 45.455 0.00 0.00 0.00 3.16
3033 3104 2.165319 AAGTCCTGAACCGTACAAGC 57.835 50.000 0.00 0.00 0.00 4.01
3034 3105 1.045407 AGTCCTGAACCGTACAAGCA 58.955 50.000 0.00 0.00 0.00 3.91
3035 3106 1.623811 AGTCCTGAACCGTACAAGCAT 59.376 47.619 0.00 0.00 0.00 3.79
3036 3107 1.732259 GTCCTGAACCGTACAAGCATG 59.268 52.381 0.00 0.00 0.00 4.06
3037 3108 1.621317 TCCTGAACCGTACAAGCATGA 59.379 47.619 0.00 0.00 0.00 3.07
3038 3109 2.236146 TCCTGAACCGTACAAGCATGAT 59.764 45.455 0.00 0.00 0.00 2.45
3039 3110 3.009723 CCTGAACCGTACAAGCATGATT 58.990 45.455 0.00 0.00 0.00 2.57
3040 3111 4.081365 TCCTGAACCGTACAAGCATGATTA 60.081 41.667 0.00 0.00 0.00 1.75
3041 3112 4.634004 CCTGAACCGTACAAGCATGATTAA 59.366 41.667 0.00 0.00 0.00 1.40
3042 3113 5.220662 CCTGAACCGTACAAGCATGATTAAG 60.221 44.000 0.00 0.00 0.00 1.85
3043 3114 4.094294 TGAACCGTACAAGCATGATTAAGC 59.906 41.667 0.00 0.00 0.00 3.09
3044 3115 3.605634 ACCGTACAAGCATGATTAAGCA 58.394 40.909 0.00 0.00 0.00 3.91
3045 3116 3.623060 ACCGTACAAGCATGATTAAGCAG 59.377 43.478 0.00 0.00 0.00 4.24
3046 3117 3.871006 CCGTACAAGCATGATTAAGCAGA 59.129 43.478 0.00 0.00 0.00 4.26
3047 3118 4.332543 CCGTACAAGCATGATTAAGCAGAA 59.667 41.667 0.00 0.00 0.00 3.02
3048 3119 5.008019 CCGTACAAGCATGATTAAGCAGAAT 59.992 40.000 0.00 0.00 0.00 2.40
3049 3120 6.202762 CCGTACAAGCATGATTAAGCAGAATA 59.797 38.462 0.00 0.00 0.00 1.75
3050 3121 7.254761 CCGTACAAGCATGATTAAGCAGAATAA 60.255 37.037 0.00 0.00 0.00 1.40
3051 3122 7.584123 CGTACAAGCATGATTAAGCAGAATAAC 59.416 37.037 0.00 0.00 0.00 1.89
3052 3123 7.395190 ACAAGCATGATTAAGCAGAATAACA 57.605 32.000 0.00 0.00 0.00 2.41
3053 3124 7.829725 ACAAGCATGATTAAGCAGAATAACAA 58.170 30.769 0.00 0.00 0.00 2.83
3054 3125 8.306038 ACAAGCATGATTAAGCAGAATAACAAA 58.694 29.630 0.00 0.00 0.00 2.83
3055 3126 8.804743 CAAGCATGATTAAGCAGAATAACAAAG 58.195 33.333 0.00 0.00 0.00 2.77
3056 3127 8.284945 AGCATGATTAAGCAGAATAACAAAGA 57.715 30.769 0.00 0.00 0.00 2.52
3057 3128 8.404000 AGCATGATTAAGCAGAATAACAAAGAG 58.596 33.333 0.00 0.00 0.00 2.85
3058 3129 7.167136 GCATGATTAAGCAGAATAACAAAGAGC 59.833 37.037 0.00 0.00 0.00 4.09
3059 3130 7.686438 TGATTAAGCAGAATAACAAAGAGCA 57.314 32.000 0.00 0.00 0.00 4.26
3060 3131 7.530010 TGATTAAGCAGAATAACAAAGAGCAC 58.470 34.615 0.00 0.00 0.00 4.40
3061 3132 6.875948 TTAAGCAGAATAACAAAGAGCACA 57.124 33.333 0.00 0.00 0.00 4.57
3062 3133 4.756084 AGCAGAATAACAAAGAGCACAC 57.244 40.909 0.00 0.00 0.00 3.82
3063 3134 4.392940 AGCAGAATAACAAAGAGCACACT 58.607 39.130 0.00 0.00 0.00 3.55
3064 3135 5.551233 AGCAGAATAACAAAGAGCACACTA 58.449 37.500 0.00 0.00 0.00 2.74
3065 3136 5.997746 AGCAGAATAACAAAGAGCACACTAA 59.002 36.000 0.00 0.00 0.00 2.24
3066 3137 6.486657 AGCAGAATAACAAAGAGCACACTAAA 59.513 34.615 0.00 0.00 0.00 1.85
3067 3138 7.175641 AGCAGAATAACAAAGAGCACACTAAAT 59.824 33.333 0.00 0.00 0.00 1.40
3068 3139 8.450964 GCAGAATAACAAAGAGCACACTAAATA 58.549 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 0.602638 TTGGCAGGACACTAGTTGCG 60.603 55.000 10.37 0.00 33.32 4.85
162 164 4.884744 ACACACATAAACACAGTTGGCTTA 59.115 37.500 0.00 0.00 0.00 3.09
173 175 4.878971 ACACTAGTTGCACACACATAAACA 59.121 37.500 0.00 0.00 0.00 2.83
176 178 4.062293 GGACACTAGTTGCACACACATAA 58.938 43.478 0.00 0.00 0.00 1.90
248 252 8.984764 TCTAGTTACACACACATTGATGTTTAC 58.015 33.333 0.00 0.00 39.39 2.01
445 450 4.447290 TGTGCAACTTCAGTACTGCTTTA 58.553 39.130 18.45 0.00 38.04 1.85
514 521 8.506168 AGATTTTTGAAACTAGATTCCGCATA 57.494 30.769 9.96 0.00 0.00 3.14
521 528 6.147164 TGCGACGAGATTTTTGAAACTAGATT 59.853 34.615 0.00 0.00 0.00 2.40
618 625 7.470289 TTCACGTCCAATTATTTTGGTTTTG 57.530 32.000 4.42 1.34 40.40 2.44
635 642 3.944422 TGAAAGAAACAGCTTCACGTC 57.056 42.857 0.00 0.00 36.40 4.34
674 681 7.589395 TGTCGTTATCAGCATTTAATGTGTTT 58.411 30.769 6.81 0.90 0.00 2.83
724 736 1.344438 CGGACTTCCTAGCCATGCATA 59.656 52.381 0.00 0.00 0.00 3.14
751 763 3.497118 CCGCGCACTAATTGATGAAAAA 58.503 40.909 8.75 0.00 0.00 1.94
754 767 0.376852 GCCGCGCACTAATTGATGAA 59.623 50.000 8.75 0.00 0.00 2.57
836 852 2.106511 ACAATGTCTACCACTTGCCACT 59.893 45.455 0.00 0.00 0.00 4.00
837 853 2.504367 ACAATGTCTACCACTTGCCAC 58.496 47.619 0.00 0.00 0.00 5.01
838 854 2.884012 CAACAATGTCTACCACTTGCCA 59.116 45.455 0.00 0.00 0.00 4.92
839 855 2.228822 CCAACAATGTCTACCACTTGCC 59.771 50.000 0.00 0.00 0.00 4.52
840 856 2.228822 CCCAACAATGTCTACCACTTGC 59.771 50.000 0.00 0.00 0.00 4.01
841 857 2.228822 GCCCAACAATGTCTACCACTTG 59.771 50.000 0.00 0.00 0.00 3.16
842 858 2.514803 GCCCAACAATGTCTACCACTT 58.485 47.619 0.00 0.00 0.00 3.16
843 859 1.271926 GGCCCAACAATGTCTACCACT 60.272 52.381 0.00 0.00 0.00 4.00
854 870 2.666862 CTACGCACGGCCCAACAA 60.667 61.111 0.00 0.00 0.00 2.83
872 888 2.426024 CCTCCGTATCAAAGAGACCGAA 59.574 50.000 0.00 0.00 0.00 4.30
893 911 1.979155 GGGAAGCTGGCTTGGGTTC 60.979 63.158 12.79 0.00 39.54 3.62
1092 1110 2.096030 CCTGTCGTCGTCGTCGAG 59.904 66.667 14.63 4.70 46.96 4.04
1094 1112 3.417224 TCCCTGTCGTCGTCGTCG 61.417 66.667 5.50 5.50 38.33 5.12
1107 1125 3.152400 GATACCGCGGGTGTCCCT 61.152 66.667 31.76 9.01 42.67 4.20
1152 1170 2.350514 GCTGCTGGGTTCTCTGCT 59.649 61.111 0.00 0.00 33.58 4.24
1161 1179 4.559063 CCCTGATCCGCTGCTGGG 62.559 72.222 9.91 0.25 37.01 4.45
1167 1185 4.841617 TCGCTCCCCTGATCCGCT 62.842 66.667 0.00 0.00 0.00 5.52
1447 1465 8.763049 TTGAGTAACAGTTCATTGTCATCTAG 57.237 34.615 0.00 0.00 0.00 2.43
1554 1572 1.891919 GCATTTATCGAGGCGCCCA 60.892 57.895 26.15 8.02 0.00 5.36
1559 1577 5.368256 AATGATCAAGCATTTATCGAGGC 57.632 39.130 0.00 0.00 35.01 4.70
1604 1622 3.817647 GGTGACAATATCCAAGCATCTCC 59.182 47.826 0.00 0.00 0.00 3.71
1618 1636 4.156455 AGACAGTGTTGAAGGTGACAAT 57.844 40.909 0.00 0.00 0.00 2.71
1653 1671 2.265904 GCCCACCCGACCAACTTTC 61.266 63.158 0.00 0.00 0.00 2.62
1670 1688 1.678970 ACCTCCCCAAGCATTTCGC 60.679 57.895 0.00 0.00 42.91 4.70
1681 1699 1.225704 CCATCAGCTTCACCTCCCC 59.774 63.158 0.00 0.00 0.00 4.81
1740 1758 2.418746 CCTACGCAGGCAGTTTATCACT 60.419 50.000 0.00 0.00 34.35 3.41
1824 1842 2.470257 CGCGGTATACGTTCTCAAATCC 59.530 50.000 0.00 0.00 46.52 3.01
1984 2002 2.831685 TCGGTGAGCTTTTCTGCTAA 57.168 45.000 0.00 0.00 44.17 3.09
2016 2034 2.094417 GCCTAACAAATCAGACGCACTC 59.906 50.000 0.00 0.00 0.00 3.51
2075 2093 0.036732 TTACCTGCTGCTGTTCCTGG 59.963 55.000 0.00 0.00 0.00 4.45
2124 2142 5.027190 TGCATCGCATGTGAAGGAATCAC 62.027 47.826 13.91 1.72 45.61 3.06
2158 2176 1.003718 GGAAGTCGGGAACTGGGTG 60.004 63.158 0.00 0.00 38.58 4.61
2162 2180 0.392998 CCATGGGAAGTCGGGAACTG 60.393 60.000 2.85 0.00 38.58 3.16
2169 2190 1.762957 ACCAGTATCCATGGGAAGTCG 59.237 52.381 13.02 0.00 42.48 4.18
2177 2198 2.684881 GCCAACAAGACCAGTATCCATG 59.315 50.000 0.00 0.00 0.00 3.66
2243 2264 5.071115 ACTTTGTAGTTCTCTGCTTCTTCCT 59.929 40.000 0.00 0.00 0.00 3.36
2244 2265 5.301555 ACTTTGTAGTTCTCTGCTTCTTCC 58.698 41.667 0.00 0.00 0.00 3.46
2302 2323 1.839354 TGTAGCTCCAGGATCATTGCA 59.161 47.619 0.00 0.00 0.00 4.08
2308 2329 1.686052 CAGGTCTGTAGCTCCAGGATC 59.314 57.143 6.45 0.00 33.14 3.36
2309 2330 1.289231 TCAGGTCTGTAGCTCCAGGAT 59.711 52.381 6.45 0.00 33.14 3.24
2310 2331 0.704664 TCAGGTCTGTAGCTCCAGGA 59.295 55.000 6.45 0.00 33.14 3.86
2311 2332 1.561643 TTCAGGTCTGTAGCTCCAGG 58.438 55.000 6.45 0.00 33.14 4.45
2312 2333 2.158986 CCATTCAGGTCTGTAGCTCCAG 60.159 54.545 0.00 0.00 0.00 3.86
2313 2334 1.833630 CCATTCAGGTCTGTAGCTCCA 59.166 52.381 0.00 0.00 0.00 3.86
2314 2335 1.474143 GCCATTCAGGTCTGTAGCTCC 60.474 57.143 0.00 0.00 40.61 4.70
2315 2336 1.804372 CGCCATTCAGGTCTGTAGCTC 60.804 57.143 0.00 0.00 40.61 4.09
2316 2337 0.176680 CGCCATTCAGGTCTGTAGCT 59.823 55.000 0.00 0.00 40.61 3.32
2317 2338 0.108138 ACGCCATTCAGGTCTGTAGC 60.108 55.000 0.00 0.00 40.61 3.58
2318 2339 3.068165 TGATACGCCATTCAGGTCTGTAG 59.932 47.826 0.00 0.00 40.61 2.74
2319 2340 3.028130 TGATACGCCATTCAGGTCTGTA 58.972 45.455 0.00 0.00 40.61 2.74
2320 2341 1.831106 TGATACGCCATTCAGGTCTGT 59.169 47.619 0.00 0.00 40.61 3.41
2321 2342 2.602257 TGATACGCCATTCAGGTCTG 57.398 50.000 0.00 0.00 40.61 3.51
2322 2343 2.700371 TCATGATACGCCATTCAGGTCT 59.300 45.455 0.00 0.00 40.61 3.85
2335 2371 1.146041 TGGCCTGCGGTCATGATAC 59.854 57.895 3.32 0.00 29.54 2.24
2478 2514 2.281484 TTCAGAGCACAACGGCCC 60.281 61.111 0.00 0.00 0.00 5.80
2479 2515 1.166531 AAGTTCAGAGCACAACGGCC 61.167 55.000 0.00 0.00 0.00 6.13
2525 2561 0.179073 AGTGCACTGAAGAGCAACGT 60.179 50.000 20.97 0.00 42.84 3.99
2672 2709 1.676006 GGCCCACGATTTGTAAGATGG 59.324 52.381 0.00 0.00 0.00 3.51
2703 2740 4.784177 TCATGGCATATTGACAGACACAT 58.216 39.130 0.00 0.00 39.76 3.21
2712 2750 5.221722 GGAGTAGGAGTTCATGGCATATTGA 60.222 44.000 0.00 0.00 0.00 2.57
2722 2760 7.757242 AAAAATCTAGGGAGTAGGAGTTCAT 57.243 36.000 0.00 0.00 0.00 2.57
2750 2788 4.035909 GGAGTAGGAGTTGTTTCGCAAAAA 59.964 41.667 0.00 0.00 39.03 1.94
2751 2789 3.562557 GGAGTAGGAGTTGTTTCGCAAAA 59.437 43.478 0.00 0.00 39.03 2.44
2752 2790 3.135994 GGAGTAGGAGTTGTTTCGCAAA 58.864 45.455 0.00 0.00 39.03 3.68
2753 2791 2.549349 GGGAGTAGGAGTTGTTTCGCAA 60.549 50.000 0.00 0.00 34.16 4.85
2754 2792 1.001633 GGGAGTAGGAGTTGTTTCGCA 59.998 52.381 0.00 0.00 0.00 5.10
2755 2793 1.275573 AGGGAGTAGGAGTTGTTTCGC 59.724 52.381 0.00 0.00 0.00 4.70
2756 2794 4.015084 TCTAGGGAGTAGGAGTTGTTTCG 58.985 47.826 0.00 0.00 0.00 3.46
2757 2795 5.657302 TCATCTAGGGAGTAGGAGTTGTTTC 59.343 44.000 0.00 0.00 0.00 2.78
2758 2796 5.590818 TCATCTAGGGAGTAGGAGTTGTTT 58.409 41.667 0.00 0.00 0.00 2.83
2759 2797 5.208294 TCATCTAGGGAGTAGGAGTTGTT 57.792 43.478 0.00 0.00 0.00 2.83
2760 2798 4.883021 TCATCTAGGGAGTAGGAGTTGT 57.117 45.455 0.00 0.00 0.00 3.32
2761 2799 4.526262 CCATCATCTAGGGAGTAGGAGTTG 59.474 50.000 0.00 0.00 0.00 3.16
2808 2846 2.862512 ACTTCAACAAACTGCACGTTG 58.137 42.857 7.05 7.05 41.07 4.10
2811 2849 3.543494 CAGAAACTTCAACAAACTGCACG 59.457 43.478 0.00 0.00 0.00 5.34
2857 2895 3.641434 AGGAGAGCATGCAGTAAACAT 57.359 42.857 21.98 0.00 0.00 2.71
2891 2929 9.559958 CGTTTGCATTCACTTATTAAATCTTCT 57.440 29.630 0.00 0.00 0.00 2.85
2899 2937 5.353123 GGACTCCGTTTGCATTCACTTATTA 59.647 40.000 0.00 0.00 0.00 0.98
2901 2939 3.689649 GGACTCCGTTTGCATTCACTTAT 59.310 43.478 0.00 0.00 0.00 1.73
2975 3046 7.050970 ACCTAAATACGAGCATACATTCTGA 57.949 36.000 0.00 0.00 0.00 3.27
2998 3069 5.235616 TCAGGACTTTGTAATGTTTCGTGAC 59.764 40.000 0.00 0.00 0.00 3.67
3003 3074 5.008316 ACGGTTCAGGACTTTGTAATGTTTC 59.992 40.000 0.00 0.00 0.00 2.78
3008 3079 5.217978 TGTACGGTTCAGGACTTTGTAAT 57.782 39.130 0.00 0.00 0.00 1.89
3009 3080 4.669206 TGTACGGTTCAGGACTTTGTAA 57.331 40.909 0.00 0.00 0.00 2.41
3026 3097 8.397906 TGTTATTCTGCTTAATCATGCTTGTAC 58.602 33.333 0.00 0.00 0.00 2.90
3027 3098 8.504812 TGTTATTCTGCTTAATCATGCTTGTA 57.495 30.769 0.00 0.00 0.00 2.41
3028 3099 7.395190 TGTTATTCTGCTTAATCATGCTTGT 57.605 32.000 0.00 0.00 0.00 3.16
3029 3100 8.692110 TTTGTTATTCTGCTTAATCATGCTTG 57.308 30.769 0.00 0.00 0.00 4.01
3030 3101 8.742777 TCTTTGTTATTCTGCTTAATCATGCTT 58.257 29.630 0.00 0.00 0.00 3.91
3032 3103 7.167136 GCTCTTTGTTATTCTGCTTAATCATGC 59.833 37.037 0.00 0.00 0.00 4.06
3033 3104 8.186163 TGCTCTTTGTTATTCTGCTTAATCATG 58.814 33.333 0.00 0.00 0.00 3.07
3034 3105 8.186821 GTGCTCTTTGTTATTCTGCTTAATCAT 58.813 33.333 0.00 0.00 0.00 2.45
3035 3106 7.174772 TGTGCTCTTTGTTATTCTGCTTAATCA 59.825 33.333 0.00 0.00 0.00 2.57
3036 3107 7.483059 GTGTGCTCTTTGTTATTCTGCTTAATC 59.517 37.037 0.00 0.00 0.00 1.75
3037 3108 7.175641 AGTGTGCTCTTTGTTATTCTGCTTAAT 59.824 33.333 0.00 0.00 0.00 1.40
3038 3109 6.486657 AGTGTGCTCTTTGTTATTCTGCTTAA 59.513 34.615 0.00 0.00 0.00 1.85
3039 3110 5.997746 AGTGTGCTCTTTGTTATTCTGCTTA 59.002 36.000 0.00 0.00 0.00 3.09
3040 3111 4.823989 AGTGTGCTCTTTGTTATTCTGCTT 59.176 37.500 0.00 0.00 0.00 3.91
3041 3112 4.392940 AGTGTGCTCTTTGTTATTCTGCT 58.607 39.130 0.00 0.00 0.00 4.24
3042 3113 4.756084 AGTGTGCTCTTTGTTATTCTGC 57.244 40.909 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.