Multiple sequence alignment - TraesCS7B01G123600

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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 TraesCS7B01G123600 chr7B 100.000 5675 0 0 1 5675 144737751 144732077 0.000000e+00 10480.0
1 TraesCS7B01G123600 chr7B 92.794 1471 98 4 1057 2520 144813428 144811959 0.000000e+00 2122.0
2 TraesCS7B01G123600 chr7B 91.708 1423 112 4 2693 4115 145053656 145052240 0.000000e+00 1969.0
3 TraesCS7B01G123600 chr7B 89.575 1554 146 8 1068 2610 145055224 145053676 0.000000e+00 1958.0
4 TraesCS7B01G123600 chr7B 93.030 1320 89 1 2796 4115 144811932 144810616 0.000000e+00 1925.0
5 TraesCS7B01G123600 chr7B 88.052 1155 79 16 3 1128 145056342 145055218 0.000000e+00 1314.0
6 TraesCS7B01G123600 chr7B 93.997 733 38 1 4139 4865 144810640 144809908 0.000000e+00 1105.0
7 TraesCS7B01G123600 chr7B 93.179 733 35 6 4140 4866 145052263 145051540 0.000000e+00 1062.0
8 TraesCS7B01G123600 chr7B 77.472 981 187 25 3046 4009 145028609 145027646 1.790000e-154 556.0
9 TraesCS7B01G123600 chr7B 80.344 524 57 21 1 482 144814713 144814194 6.990000e-94 355.0
10 TraesCS7B01G123600 chr7B 81.768 362 62 4 4177 4536 145027523 145027164 3.320000e-77 300.0
11 TraesCS7B01G123600 chr7B 83.742 326 27 16 5042 5355 145051422 145051111 9.310000e-73 285.0
12 TraesCS7B01G123600 chr7A 94.381 4894 235 20 4 4865 183310061 183305176 0.000000e+00 7478.0
13 TraesCS7B01G123600 chr7A 92.930 1471 96 4 1057 2520 183483281 183481812 0.000000e+00 2134.0
14 TraesCS7B01G123600 chr7A 92.200 1423 108 1 2693 4115 183654449 183653030 0.000000e+00 2010.0
15 TraesCS7B01G123600 chr7A 92.879 1320 91 1 2796 4115 183481785 183480469 0.000000e+00 1914.0
16 TraesCS7B01G123600 chr7A 88.399 1543 150 11 1072 2610 183655986 183654469 0.000000e+00 1831.0
17 TraesCS7B01G123600 chr7A 89.321 1311 115 9 1050 2351 182856933 182855639 0.000000e+00 1622.0
18 TraesCS7B01G123600 chr7A 93.869 734 39 2 4138 4865 183480494 183479761 0.000000e+00 1101.0
19 TraesCS7B01G123600 chr7A 91.962 734 44 6 4138 4865 183653055 183652331 0.000000e+00 1014.0
20 TraesCS7B01G123600 chr7A 88.790 562 46 6 441 990 183656588 183656032 0.000000e+00 673.0
21 TraesCS7B01G123600 chr7A 87.220 446 31 7 3 446 183657117 183656696 8.550000e-133 484.0
22 TraesCS7B01G123600 chr7A 95.753 259 11 0 3042 3300 182855638 182855380 8.790000e-113 418.0
23 TraesCS7B01G123600 chr7A 80.916 524 52 19 1 482 183484600 183484083 2.500000e-98 370.0
24 TraesCS7B01G123600 chr7A 91.667 228 14 5 241 465 182857992 182857767 1.540000e-80 311.0
25 TraesCS7B01G123600 chr7A 90.826 218 17 3 2 217 182858537 182858321 7.190000e-74 289.0
26 TraesCS7B01G123600 chr7A 84.175 297 25 8 779 1057 182857260 182856968 9.370000e-68 268.0
27 TraesCS7B01G123600 chr7A 82.680 306 49 4 4233 4536 183641237 183640934 9.370000e-68 268.0
28 TraesCS7B01G123600 chr7A 86.603 209 21 4 5265 5470 183405553 183405349 2.060000e-54 224.0
29 TraesCS7B01G123600 chr7A 90.476 168 9 6 5212 5375 183304750 183304586 1.240000e-51 215.0
30 TraesCS7B01G123600 chr7A 82.759 174 22 6 498 664 183483980 183483808 1.270000e-31 148.0
31 TraesCS7B01G123600 chr7A 94.340 53 2 1 4866 4917 183479740 183479688 4.710000e-11 80.5
32 TraesCS7B01G123600 chr7A 100.000 37 0 0 4878 4914 183305143 183305107 1.020000e-07 69.4
33 TraesCS7B01G123600 chr7D 94.667 2794 116 19 4 2769 178862989 178860201 0.000000e+00 4303.0
34 TraesCS7B01G123600 chr7D 93.354 2859 131 16 2849 5675 178860205 178857374 0.000000e+00 4172.0
35 TraesCS7B01G123600 chr7D 92.984 1468 97 2 1059 2520 178940722 178939255 0.000000e+00 2135.0
36 TraesCS7B01G123600 chr7D 89.290 1550 151 9 1072 2610 179123587 179122042 0.000000e+00 1929.0
37 TraesCS7B01G123600 chr7D 93.030 1320 89 1 2796 4115 178939228 178937912 0.000000e+00 1925.0
38 TraesCS7B01G123600 chr7D 94.959 734 31 2 4138 4865 178937937 178937204 0.000000e+00 1146.0
39 TraesCS7B01G123600 chr7D 88.110 656 54 9 373 1011 179124245 179123597 0.000000e+00 758.0
40 TraesCS7B01G123600 chr7D 77.357 976 197 20 3046 4009 178990013 178989050 1.790000e-154 556.0
41 TraesCS7B01G123600 chr7D 85.829 374 27 13 3 373 179124653 179124303 1.930000e-99 374.0
42 TraesCS7B01G123600 chr7D 79.771 524 58 19 1 482 178942018 178941501 2.530000e-88 337.0
43 TraesCS7B01G123600 chr7D 88.636 132 13 1 5289 5420 178936819 178936690 5.890000e-35 159.0


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 TraesCS7B01G123600 chr7B 144732077 144737751 5674 True 10480.000000 10480 100.000000 1 5675 1 chr7B.!!$R1 5674
1 TraesCS7B01G123600 chr7B 144809908 144814713 4805 True 1376.750000 2122 90.041250 1 4865 4 chr7B.!!$R2 4864
2 TraesCS7B01G123600 chr7B 145051111 145056342 5231 True 1317.600000 1969 89.251200 3 5355 5 chr7B.!!$R4 5352
3 TraesCS7B01G123600 chr7B 145027164 145028609 1445 True 428.000000 556 79.620000 3046 4536 2 chr7B.!!$R3 1490
4 TraesCS7B01G123600 chr7A 183304586 183310061 5475 True 2587.466667 7478 94.952333 4 5375 3 chr7A.!!$R4 5371
5 TraesCS7B01G123600 chr7A 183652331 183657117 4786 True 1202.400000 2010 89.714200 3 4865 5 chr7A.!!$R6 4862
6 TraesCS7B01G123600 chr7A 183479688 183484600 4912 True 957.916667 2134 89.615500 1 4917 6 chr7A.!!$R5 4916
7 TraesCS7B01G123600 chr7A 182855380 182858537 3157 True 581.600000 1622 90.348400 2 3300 5 chr7A.!!$R3 3298
8 TraesCS7B01G123600 chr7D 178857374 178862989 5615 True 4237.500000 4303 94.010500 4 5675 2 chr7D.!!$R2 5671
9 TraesCS7B01G123600 chr7D 178936690 178942018 5328 True 1140.400000 2135 89.876000 1 5420 5 chr7D.!!$R3 5419
10 TraesCS7B01G123600 chr7D 179122042 179124653 2611 True 1020.333333 1929 87.743000 3 2610 3 chr7D.!!$R4 2607
11 TraesCS7B01G123600 chr7D 178989050 178990013 963 True 556.000000 556 77.357000 3046 4009 1 chr7D.!!$R1 963

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
121 123 0.735632 CTCTGGACGCAAGCTCACTC 60.736 60.000 0.00 0.0 45.62 3.51 F
1250 2537 1.067354 GGGATCGTGGACACTAAACGT 60.067 52.381 0.56 0.0 38.43 3.99 F
1765 3055 0.103937 CGGCTTTTGGGCTGAAAACA 59.896 50.000 0.00 0.0 40.74 2.83 F
2878 4180 0.321564 TTCTGAACATGTGGGAGCCG 60.322 55.000 0.00 0.0 0.00 5.52 F
2907 4209 0.591170 CGGACCGTGCTGAACAAAAT 59.409 50.000 5.48 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 2549 0.250858 CATGACAGGGTCACCAGCAA 60.251 55.0 0.00 0.0 45.65 3.91 R
2883 4185 1.017177 GTTCAGCACGGTCCGCATTA 61.017 55.0 12.28 0.0 0.00 1.90 R
3345 4647 0.039165 CCAAAGCAAAAGCTCCGGTC 60.039 55.0 0.00 0.0 0.00 4.79 R
4622 5933 0.394080 AGGACGTCTCGGGGAGTTAG 60.394 60.0 16.46 0.0 0.00 2.34 R
4876 6214 0.622665 ATTGCCTGCTTGTAGCTCCT 59.377 50.0 0.00 0.0 42.97 3.69 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
64 66 6.263617 AGTCGGATCTAGGTATTCAGAGAAAC 59.736 42.308 0.00 0.00 0.00 2.78
65 67 5.535406 TCGGATCTAGGTATTCAGAGAAACC 59.465 44.000 0.00 0.00 0.00 3.27
109 111 4.024809 GCTATTTTGGTTATCGCTCTGGAC 60.025 45.833 0.00 0.00 0.00 4.02
110 112 2.004583 TTTGGTTATCGCTCTGGACG 57.995 50.000 0.00 0.00 0.00 4.79
121 123 0.735632 CTCTGGACGCAAGCTCACTC 60.736 60.000 0.00 0.00 45.62 3.51
136 138 1.153353 CACTCGCAACCGTTTATGGT 58.847 50.000 0.00 0.00 46.67 3.55
167 172 1.734477 CTTCCCGTGTGACTGAGCG 60.734 63.158 0.00 0.00 0.00 5.03
232 543 2.032290 GTGTGTTCGGTTGTTAGGCTTC 60.032 50.000 0.00 0.00 0.00 3.86
239 550 2.668279 CGGTTGTTAGGCTTCAATGTGC 60.668 50.000 0.00 0.00 0.00 4.57
281 614 9.709387 ATGCAATTAATTTTACTAGGTACCCTT 57.291 29.630 8.74 0.00 34.61 3.95
301 635 8.375493 ACCCTTTATAATCTGTTAGTGTCTCA 57.625 34.615 0.00 0.00 0.00 3.27
388 793 8.826765 ACAAAGGGAAAGATCTAGATCACTTAA 58.173 33.333 29.83 0.00 40.22 1.85
819 1963 3.612423 GCGCTCTCTTTTGTGTTGTTTTT 59.388 39.130 0.00 0.00 0.00 1.94
917 2063 9.784531 TGAATTATCCTTGAATCCTTCAGATAC 57.215 33.333 0.00 0.00 41.38 2.24
990 2136 2.620585 GCAACTGAAAGCCTGAGACTTT 59.379 45.455 0.00 0.00 39.99 2.66
1078 2311 2.242965 AGGCAAGATCCCATCAATGTCA 59.757 45.455 0.00 0.00 0.00 3.58
1105 2392 4.524328 CCAGCAGAAATTTGTTACCCTCTT 59.476 41.667 0.00 0.00 0.00 2.85
1224 2511 4.335315 ACATACAATGCTGGATTAACACCG 59.665 41.667 0.00 0.00 0.00 4.94
1249 2536 1.636988 GGGATCGTGGACACTAAACG 58.363 55.000 0.56 0.00 38.64 3.60
1250 2537 1.067354 GGGATCGTGGACACTAAACGT 60.067 52.381 0.56 0.00 38.43 3.99
1262 2549 3.861840 CACTAAACGTGGATGGTCATCT 58.138 45.455 10.34 0.00 40.02 2.90
1306 2593 6.073058 GCATGATGGCTTTTCTGAACGATATA 60.073 38.462 0.00 0.00 0.00 0.86
1719 3009 5.642063 TGTAACTTTTGCTGCTACTATCACC 59.358 40.000 0.00 0.00 0.00 4.02
1764 3054 1.221466 GCGGCTTTTGGGCTGAAAAC 61.221 55.000 0.00 0.00 40.74 2.43
1765 3055 0.103937 CGGCTTTTGGGCTGAAAACA 59.896 50.000 0.00 0.00 40.74 2.83
1834 3124 1.919240 TCCGGCTACTTCTGTTCTCA 58.081 50.000 0.00 0.00 0.00 3.27
1836 3126 2.631062 TCCGGCTACTTCTGTTCTCAAA 59.369 45.455 0.00 0.00 0.00 2.69
2031 3321 2.502947 TGCTGCAGGATGTTGTAGAGAT 59.497 45.455 17.12 0.00 39.31 2.75
2178 3468 2.693074 GTGGTGTGTGAGAAAATTGGGT 59.307 45.455 0.00 0.00 0.00 4.51
2257 3547 4.340894 TCTTACGCAAGCAATCATCAAC 57.659 40.909 0.00 0.00 45.62 3.18
2416 3712 2.169978 TCAGATGATGAAGAGGCTGTGG 59.830 50.000 0.00 0.00 34.02 4.17
2602 3898 1.337823 GCATGGGTGTCGTGTCTAACT 60.338 52.381 0.00 0.00 34.91 2.24
2603 3899 2.337583 CATGGGTGTCGTGTCTAACTG 58.662 52.381 0.00 0.00 0.00 3.16
2699 4001 3.089284 ACCCATTACTAAGCCAAACTGC 58.911 45.455 0.00 0.00 0.00 4.40
2716 4018 2.948093 GCAAATAGCATGTGCCGTG 58.052 52.632 0.57 0.00 44.79 4.94
2723 4025 1.960763 GCATGTGCCGTGTGTCAGA 60.961 57.895 0.00 0.00 34.31 3.27
2725 4027 0.445043 CATGTGCCGTGTGTCAGATG 59.555 55.000 0.00 0.00 0.00 2.90
2734 4036 3.130633 CGTGTGTCAGATGACCAGAAAA 58.869 45.455 10.34 0.00 44.15 2.29
2746 4048 6.660521 AGATGACCAGAAAATTGCAAGTATGA 59.339 34.615 4.94 0.00 0.00 2.15
2747 4049 6.647334 TGACCAGAAAATTGCAAGTATGAA 57.353 33.333 4.94 0.00 0.00 2.57
2749 4051 6.029346 ACCAGAAAATTGCAAGTATGAAGG 57.971 37.500 4.94 4.64 0.00 3.46
2754 4056 5.927281 AAATTGCAAGTATGAAGGAGCAT 57.073 34.783 4.94 0.00 0.00 3.79
2761 4063 5.220815 GCAAGTATGAAGGAGCATTCTTCAG 60.221 44.000 17.11 8.19 39.93 3.02
2775 4077 1.685517 TCTTCAGCTGATGATCCCGAG 59.314 52.381 24.24 13.59 37.89 4.63
2789 4091 2.257207 TCCCGAGATCACTGTTCCTTT 58.743 47.619 0.00 0.00 0.00 3.11
2791 4093 3.194968 TCCCGAGATCACTGTTCCTTTAC 59.805 47.826 0.00 0.00 0.00 2.01
2792 4094 3.522553 CCGAGATCACTGTTCCTTTACC 58.477 50.000 0.00 0.00 0.00 2.85
2793 4095 3.522553 CGAGATCACTGTTCCTTTACCC 58.477 50.000 0.00 0.00 0.00 3.69
2794 4096 3.056107 CGAGATCACTGTTCCTTTACCCA 60.056 47.826 0.00 0.00 0.00 4.51
2805 4107 6.930731 TGTTCCTTTACCCAAGCAAAATATC 58.069 36.000 0.00 0.00 0.00 1.63
2810 4112 5.835113 TTACCCAAGCAAAATATCTCAGC 57.165 39.130 0.00 0.00 0.00 4.26
2814 4116 3.698040 CCAAGCAAAATATCTCAGCCAGT 59.302 43.478 0.00 0.00 0.00 4.00
2857 4159 4.040047 TGATGACATAGTGGATGAAGGGT 58.960 43.478 0.00 0.00 39.06 4.34
2864 4166 5.014123 ACATAGTGGATGAAGGGTTTTCTGA 59.986 40.000 0.00 0.00 39.06 3.27
2867 4169 3.888930 GTGGATGAAGGGTTTTCTGAACA 59.111 43.478 0.00 0.00 0.00 3.18
2873 4175 2.597455 AGGGTTTTCTGAACATGTGGG 58.403 47.619 0.00 0.00 0.00 4.61
2878 4180 0.321564 TTCTGAACATGTGGGAGCCG 60.322 55.000 0.00 0.00 0.00 5.52
2883 4185 4.415150 CATGTGGGAGCCGCTGGT 62.415 66.667 0.00 0.00 34.70 4.00
2907 4209 0.591170 CGGACCGTGCTGAACAAAAT 59.409 50.000 5.48 0.00 0.00 1.82
2909 4211 2.418628 CGGACCGTGCTGAACAAAATAT 59.581 45.455 5.48 0.00 0.00 1.28
2911 4213 4.165779 GGACCGTGCTGAACAAAATATTG 58.834 43.478 0.00 0.00 42.46 1.90
2928 4230 9.590451 CAAAATATTGTGGTTGAAGCTGATAAT 57.410 29.630 0.00 0.00 0.00 1.28
2932 4234 4.517285 TGTGGTTGAAGCTGATAATCCTC 58.483 43.478 0.00 0.00 0.00 3.71
2970 4272 8.565416 CGTATCAGTGATAACTATCCTACACAA 58.435 37.037 14.44 0.00 31.71 3.33
2981 4283 7.060383 ACTATCCTACACAATCTGAGAATGG 57.940 40.000 2.21 0.00 0.00 3.16
3002 4304 5.255687 TGGACATATTGACAGCAATCAAGT 58.744 37.500 8.42 2.04 43.43 3.16
3026 4328 1.545582 ACCCAATCAAAATGCTGACGG 59.454 47.619 0.00 0.00 0.00 4.79
3145 4447 2.558359 CCAGGTGGATTTTGGTCAAGAC 59.442 50.000 0.00 0.00 37.39 3.01
3285 4587 3.071457 TGCTCTTGAACAAGATGGTGAGA 59.929 43.478 15.99 0.00 45.40 3.27
3301 4603 4.104102 TGGTGAGAGACAAGGTTACCAAAT 59.896 41.667 3.51 0.00 34.12 2.32
3345 4647 4.030913 TGATAGTGGTCCTACTTTCCCTG 58.969 47.826 0.00 0.00 30.55 4.45
3564 4869 1.374758 CGACAACCAGACTGGGAGC 60.375 63.158 25.34 10.54 43.37 4.70
3603 4908 1.153229 GGGAAGGCGGCGTAATCTT 60.153 57.895 9.37 7.66 0.00 2.40
3616 4921 5.236478 CGGCGTAATCTTCTATTGACCATTT 59.764 40.000 0.00 0.00 0.00 2.32
3688 4993 2.072298 GTGTCTGGTCTGATGACAAGC 58.928 52.381 10.90 0.00 42.56 4.01
3943 5248 9.809096 ATATTAAACAGTCCATATATCTGAGCG 57.191 33.333 6.86 0.00 33.93 5.03
4011 5319 4.614946 TCTCTTCGATGCATGATACACTG 58.385 43.478 2.46 0.00 0.00 3.66
4088 5399 4.409247 AGAGGGTGAACAAGTAAACACTCT 59.591 41.667 11.93 11.93 46.17 3.24
4380 5691 1.667236 TCATGGCATCCATTGTCGTC 58.333 50.000 0.00 0.00 42.23 4.20
4423 5734 3.445008 TCTATCAGGAAGAAGGCTGTGT 58.555 45.455 0.00 0.00 0.00 3.72
4453 5764 5.948162 GGGGTATTGCACTTGATCATGATAT 59.052 40.000 8.54 0.00 0.00 1.63
4615 5926 0.972983 TCGGAAGCCAAGAGAGGGAG 60.973 60.000 0.00 0.00 0.00 4.30
4622 5933 1.268283 CCAAGAGAGGGAGGTGGGAC 61.268 65.000 0.00 0.00 0.00 4.46
4831 6148 5.048083 TGCCTGTTGTATGTTCTTGGAAATC 60.048 40.000 0.00 0.00 0.00 2.17
4859 6176 5.204409 AGCATGCTTGAAATTTGAACTCA 57.796 34.783 16.30 0.00 0.00 3.41
4876 6214 4.002906 ACTCAAGCCTTCGTCATGTAAA 57.997 40.909 0.00 0.00 0.00 2.01
4948 6286 3.437049 AGCAAATTCTCGGAGCAACTTAC 59.563 43.478 0.00 0.00 0.00 2.34
4949 6287 3.426292 GCAAATTCTCGGAGCAACTTACC 60.426 47.826 0.00 0.00 0.00 2.85
5091 6445 6.681777 ACAATCTTTCTGGCTTGTTCAATAC 58.318 36.000 0.00 0.00 0.00 1.89
5205 6562 3.073274 AGTTTGACCACCAGGCTTATC 57.927 47.619 0.00 0.00 39.06 1.75
5210 6567 2.290260 TGACCACCAGGCTTATCTTGTG 60.290 50.000 0.00 0.00 39.06 3.33
5248 6689 8.968242 GTGTTTTTCGCTTCTCTGATAATTTTT 58.032 29.630 0.00 0.00 0.00 1.94
5382 6838 7.909518 TGATGAAATGTTTCCCAAGAATCAAT 58.090 30.769 3.26 0.00 35.78 2.57
5450 6906 0.668401 GCCAATGTTGTGGAAGCAGC 60.668 55.000 0.00 0.00 41.65 5.25
5470 6926 4.074970 AGCTCTTTTGACTGGGTTACATG 58.925 43.478 0.00 0.00 0.00 3.21
5471 6927 3.191371 GCTCTTTTGACTGGGTTACATGG 59.809 47.826 0.00 0.00 0.00 3.66
5486 6963 5.995897 GGTTACATGGTAGTTCACTTTGTCT 59.004 40.000 0.00 0.00 0.00 3.41
5506 6983 0.969149 TGGGCTGATATCTACTGCGG 59.031 55.000 3.98 0.00 34.03 5.69
5549 7026 5.627499 AAAAATGATGCTCGAGCTTAACA 57.373 34.783 35.27 26.88 42.66 2.41
5558 7035 1.897133 TCGAGCTTAACAACCTAGCCA 59.103 47.619 0.00 0.00 35.53 4.75
5562 7039 4.518249 GAGCTTAACAACCTAGCCAGAAT 58.482 43.478 0.00 0.00 35.53 2.40
5591 7068 1.768870 GCTAGGCATTACTCCCTCCAA 59.231 52.381 0.00 0.00 32.65 3.53
5598 7075 4.098501 GGCATTACTCCCTCCAATTGAAAG 59.901 45.833 7.12 3.95 0.00 2.62
5606 7083 5.445964 TCCCTCCAATTGAAAGTATAAGGC 58.554 41.667 7.12 0.00 0.00 4.35
5617 7094 8.638685 TTGAAAGTATAAGGCGAGTTATACAC 57.361 34.615 20.64 14.61 43.79 2.90
5620 7097 8.868635 AAAGTATAAGGCGAGTTATACACTTC 57.131 34.615 20.64 3.52 43.79 3.01
5629 7106 7.919621 AGGCGAGTTATACACTTCTGTAAATAC 59.080 37.037 0.00 0.00 36.43 1.89
5669 7146 2.285827 TTTCCGGTGCAAAGTGTTTG 57.714 45.000 0.00 0.00 43.44 2.93
5670 7147 0.457851 TTCCGGTGCAAAGTGTTTGG 59.542 50.000 0.00 0.00 40.94 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 3.566351 GGTCCAGATATTTCCCTTTGGG 58.434 50.000 0.00 0.00 46.11 4.12
65 67 3.214328 CGGTCCAGATATTTCCCTTTGG 58.786 50.000 0.00 0.00 0.00 3.28
136 138 0.107214 CGGGAAGGCTGCCTCATTAA 60.107 55.000 23.61 0.00 30.89 1.40
232 543 3.687212 TCAATGGTAGGTTACGCACATTG 59.313 43.478 0.00 0.00 43.79 2.82
239 550 4.955925 TTGCATTCAATGGTAGGTTACG 57.044 40.909 0.00 0.00 0.00 3.18
274 607 9.747293 GAGACACTAACAGATTATAAAGGGTAC 57.253 37.037 0.00 0.00 0.00 3.34
281 614 9.431887 GTTGGTTGAGACACTAACAGATTATAA 57.568 33.333 0.00 0.00 37.89 0.98
284 617 6.822442 TGTTGGTTGAGACACTAACAGATTA 58.178 36.000 0.00 0.00 41.63 1.75
388 793 5.130350 CGTTATAATCTGACCCCACCAAAT 58.870 41.667 0.00 0.00 0.00 2.32
819 1963 4.104102 ACTTGGTGAAGTCTATCCCAAACA 59.896 41.667 0.00 0.00 38.01 2.83
882 2028 7.040132 GGATTCAAGGATAATTCAAGGATGGTC 60.040 40.741 0.00 0.00 0.00 4.02
917 2063 4.566426 AGAGTTTCTTGGATGGAGAAGG 57.434 45.455 0.00 0.00 34.84 3.46
990 2136 0.399833 TGTCTGCCATGTGGTTGCTA 59.600 50.000 0.35 0.00 37.57 3.49
1078 2311 4.220602 GGGTAACAAATTTCTGCTGGATGT 59.779 41.667 0.00 0.00 39.74 3.06
1224 2511 4.176752 GTCCACGATCCCCCTGGC 62.177 72.222 0.00 0.00 0.00 4.85
1249 2536 1.340405 ACCAGCAAGATGACCATCCAC 60.340 52.381 6.40 0.00 38.58 4.02
1250 2537 0.994247 ACCAGCAAGATGACCATCCA 59.006 50.000 6.40 0.00 38.58 3.41
1262 2549 0.250858 CATGACAGGGTCACCAGCAA 60.251 55.000 0.00 0.00 45.65 3.91
1306 2593 4.099266 TGCATTGCAGTAAAAGAACACCTT 59.901 37.500 7.38 0.00 33.18 3.50
1764 3054 4.398988 TGCAGCTTATTAGAACCATGGTTG 59.601 41.667 34.47 18.44 38.60 3.77
1765 3055 4.599041 TGCAGCTTATTAGAACCATGGTT 58.401 39.130 30.23 30.23 41.54 3.67
1834 3124 9.860898 ATTATAACGACGAAGGTAGTTACTTTT 57.139 29.630 0.00 0.00 43.74 2.27
2031 3321 5.585844 CACCACATAGAATGATGTTGCTACA 59.414 40.000 2.82 2.82 37.99 2.74
2178 3468 1.882912 AGCTCAATGAAAGTGCACGA 58.117 45.000 12.01 0.00 0.00 4.35
2416 3712 4.118410 CCTGACAGATGCTGTGAGTTATC 58.882 47.826 11.92 0.00 45.44 1.75
2602 3898 3.630054 CCTTCTGTAGACCCATACTCCCA 60.630 52.174 0.00 0.00 0.00 4.37
2603 3899 2.966516 CCTTCTGTAGACCCATACTCCC 59.033 54.545 0.00 0.00 0.00 4.30
2699 4001 1.199789 ACACACGGCACATGCTATTTG 59.800 47.619 3.48 0.00 41.70 2.32
2713 4015 2.438868 TTCTGGTCATCTGACACACG 57.561 50.000 12.10 0.00 46.47 4.49
2716 4018 4.022935 TGCAATTTTCTGGTCATCTGACAC 60.023 41.667 12.10 2.94 46.47 3.67
2723 4025 6.839124 TCATACTTGCAATTTTCTGGTCAT 57.161 33.333 0.00 0.00 0.00 3.06
2725 4027 6.071952 TCCTTCATACTTGCAATTTTCTGGTC 60.072 38.462 0.00 0.00 0.00 4.02
2734 4036 5.198965 AGAATGCTCCTTCATACTTGCAAT 58.801 37.500 0.00 0.00 34.07 3.56
2746 4048 3.054582 TCATCAGCTGAAGAATGCTCCTT 60.055 43.478 22.50 0.00 37.44 3.36
2747 4049 2.504585 TCATCAGCTGAAGAATGCTCCT 59.495 45.455 22.50 0.00 37.44 3.69
2749 4051 3.499157 GGATCATCAGCTGAAGAATGCTC 59.501 47.826 24.08 16.56 37.44 4.26
2754 4056 2.102084 CTCGGGATCATCAGCTGAAGAA 59.898 50.000 24.08 11.60 37.44 2.52
2775 4077 3.440522 GCTTGGGTAAAGGAACAGTGATC 59.559 47.826 0.00 0.00 36.30 2.92
2778 4080 2.582052 TGCTTGGGTAAAGGAACAGTG 58.418 47.619 0.00 0.00 36.30 3.66
2783 4085 6.951198 TGAGATATTTTGCTTGGGTAAAGGAA 59.049 34.615 0.00 0.00 43.68 3.36
2786 4088 6.268566 GCTGAGATATTTTGCTTGGGTAAAG 58.731 40.000 0.00 0.00 39.07 1.85
2789 4091 4.207165 GGCTGAGATATTTTGCTTGGGTA 58.793 43.478 0.00 0.00 0.00 3.69
2791 4093 3.025978 TGGCTGAGATATTTTGCTTGGG 58.974 45.455 0.00 0.00 0.00 4.12
2792 4094 3.698040 ACTGGCTGAGATATTTTGCTTGG 59.302 43.478 0.00 0.00 0.00 3.61
2793 4095 4.397103 TGACTGGCTGAGATATTTTGCTTG 59.603 41.667 0.00 0.00 0.00 4.01
2794 4096 4.592942 TGACTGGCTGAGATATTTTGCTT 58.407 39.130 0.00 0.00 0.00 3.91
2805 4107 2.762887 TCCATTACTCTGACTGGCTGAG 59.237 50.000 15.04 15.04 45.19 3.35
2810 4112 3.766591 AGTGTCTCCATTACTCTGACTGG 59.233 47.826 0.00 0.00 0.00 4.00
2814 4116 5.816682 TCACTAGTGTCTCCATTACTCTGA 58.183 41.667 21.99 0.00 0.00 3.27
2836 4138 4.696479 ACCCTTCATCCACTATGTCATC 57.304 45.455 0.00 0.00 36.89 2.92
2857 4159 2.238521 GGCTCCCACATGTTCAGAAAA 58.761 47.619 0.00 0.00 0.00 2.29
2864 4166 2.360350 CAGCGGCTCCCACATGTT 60.360 61.111 0.00 0.00 0.00 2.71
2867 4169 1.635817 ATTACCAGCGGCTCCCACAT 61.636 55.000 0.00 0.00 0.00 3.21
2878 4180 2.125269 ACGGTCCGCATTACCAGC 60.125 61.111 12.28 0.00 36.78 4.85
2883 4185 1.017177 GTTCAGCACGGTCCGCATTA 61.017 55.000 12.28 0.00 0.00 1.90
2907 4209 6.662755 AGGATTATCAGCTTCAACCACAATA 58.337 36.000 0.00 0.00 0.00 1.90
2909 4211 4.922206 AGGATTATCAGCTTCAACCACAA 58.078 39.130 0.00 0.00 0.00 3.33
2911 4213 3.557595 CGAGGATTATCAGCTTCAACCAC 59.442 47.826 0.00 0.00 0.00 4.16
2921 4223 6.072948 ACGAATCTCAGTACGAGGATTATCAG 60.073 42.308 12.62 7.25 42.55 2.90
2923 4225 6.243811 ACGAATCTCAGTACGAGGATTATC 57.756 41.667 12.62 0.00 42.55 1.75
2928 4230 4.700700 TGATACGAATCTCAGTACGAGGA 58.299 43.478 12.62 2.06 42.55 3.71
2947 4249 9.373450 AGATTGTGTAGGATAGTTATCACTGAT 57.627 33.333 0.00 0.00 34.06 2.90
2956 4258 7.345653 TCCATTCTCAGATTGTGTAGGATAGTT 59.654 37.037 0.00 0.00 0.00 2.24
2959 4261 6.611236 TGTCCATTCTCAGATTGTGTAGGATA 59.389 38.462 0.00 0.00 0.00 2.59
2970 4272 5.996513 GCTGTCAATATGTCCATTCTCAGAT 59.003 40.000 0.00 0.00 0.00 2.90
2981 4283 7.545362 ACTACTTGATTGCTGTCAATATGTC 57.455 36.000 5.09 0.00 42.60 3.06
3002 4304 4.634004 CGTCAGCATTTTGATTGGGTACTA 59.366 41.667 0.00 0.00 0.00 1.82
3026 4328 2.935201 AGATGCTTCTCAGTTCGAATGC 59.065 45.455 0.00 0.00 0.00 3.56
3145 4447 4.510711 AGCAGCTGAATGATGATCTTTACG 59.489 41.667 20.43 0.00 33.12 3.18
3285 4587 2.159382 CGCCATTTGGTAACCTTGTCT 58.841 47.619 0.00 0.00 37.57 3.41
3345 4647 0.039165 CCAAAGCAAAAGCTCCGGTC 60.039 55.000 0.00 0.00 0.00 4.79
3361 4663 2.538141 CCTCCCTGCAGTTCCCCAA 61.538 63.158 13.81 0.00 0.00 4.12
3564 4869 3.128938 CCAACTCCTTCTCACTAGTACCG 59.871 52.174 0.00 0.00 0.00 4.02
3603 4908 9.905713 ACAGCTAAAATAGAAATGGTCAATAGA 57.094 29.630 0.00 0.00 0.00 1.98
3973 5278 4.687948 CGAAGAGAGCAGAACTTGAATCAA 59.312 41.667 0.00 0.00 0.00 2.57
4011 5319 2.897326 ACACTTAGCCAATGGTTTTCCC 59.103 45.455 0.00 0.00 39.73 3.97
4088 5399 2.435805 ACTGAAGCTTCTGGACTCACAA 59.564 45.455 29.77 6.91 0.00 3.33
4218 5529 0.792640 CTTGGTATGCGATCGATGCC 59.207 55.000 21.57 20.45 0.00 4.40
4423 5734 2.107378 TCAAGTGCAATACCCCAAGTGA 59.893 45.455 0.00 0.00 0.00 3.41
4453 5764 2.707257 TCATGAGAGCCAGCATATCCAA 59.293 45.455 0.00 0.00 0.00 3.53
4622 5933 0.394080 AGGACGTCTCGGGGAGTTAG 60.394 60.000 16.46 0.00 0.00 2.34
4758 6069 7.613022 ACATGAAGAAAAATGCTGATAGGAGAA 59.387 33.333 0.00 0.00 0.00 2.87
4831 6148 8.500773 AGTTCAAATTTCAAGCATGCTAAAATG 58.499 29.630 28.15 22.71 0.00 2.32
4859 6176 3.600388 CTCCTTTACATGACGAAGGCTT 58.400 45.455 16.45 0.00 39.78 4.35
4876 6214 0.622665 ATTGCCTGCTTGTAGCTCCT 59.377 50.000 0.00 0.00 42.97 3.69
4948 6286 7.264373 AGCGAGTATAAAAGGATGAAAATGG 57.736 36.000 0.00 0.00 0.00 3.16
4976 6330 0.108804 TAAGAGCAACTTCCTCGGCG 60.109 55.000 0.00 0.00 39.72 6.46
5067 6421 5.796424 ATTGAACAAGCCAGAAAGATTGT 57.204 34.783 0.00 0.00 37.47 2.71
5069 6423 6.944862 AGAGTATTGAACAAGCCAGAAAGATT 59.055 34.615 0.00 0.00 0.00 2.40
5091 6445 7.658179 TGTTAGAGAACATAAAGTGCAAGAG 57.342 36.000 0.00 0.00 40.72 2.85
5160 6517 9.347240 CTTGTTTTAGATGAGAACATGGGATAT 57.653 33.333 0.00 0.00 36.82 1.63
5161 6518 8.328758 ACTTGTTTTAGATGAGAACATGGGATA 58.671 33.333 0.00 0.00 36.82 2.59
5162 6519 7.177878 ACTTGTTTTAGATGAGAACATGGGAT 58.822 34.615 0.00 0.00 36.82 3.85
5163 6520 6.542821 ACTTGTTTTAGATGAGAACATGGGA 58.457 36.000 0.00 0.00 36.82 4.37
5164 6521 6.824305 ACTTGTTTTAGATGAGAACATGGG 57.176 37.500 0.00 0.00 36.82 4.00
5165 6522 8.352201 TCAAACTTGTTTTAGATGAGAACATGG 58.648 33.333 0.00 0.00 36.82 3.66
5166 6523 9.173939 GTCAAACTTGTTTTAGATGAGAACATG 57.826 33.333 0.00 0.00 36.82 3.21
5167 6524 8.352942 GGTCAAACTTGTTTTAGATGAGAACAT 58.647 33.333 0.00 0.00 39.67 2.71
5262 6704 2.233922 GTGTGCCAGTATGTACCACTCT 59.766 50.000 0.00 0.00 31.68 3.24
5267 6722 2.356135 CTTGGTGTGCCAGTATGTACC 58.644 52.381 0.00 0.00 46.91 3.34
5382 6838 1.080093 CGCACTTCGCCTTCCAGTA 60.080 57.895 0.00 0.00 37.30 2.74
5450 6906 4.398319 ACCATGTAACCCAGTCAAAAGAG 58.602 43.478 0.00 0.00 0.00 2.85
5470 6926 2.552743 GCCCAAGACAAAGTGAACTACC 59.447 50.000 0.00 0.00 0.00 3.18
5471 6927 3.251004 CAGCCCAAGACAAAGTGAACTAC 59.749 47.826 0.00 0.00 0.00 2.73
5486 6963 1.344438 CCGCAGTAGATATCAGCCCAA 59.656 52.381 5.32 0.00 0.00 4.12
5506 6983 5.705609 TTTAGCCAGACAATGTTCCTTTC 57.294 39.130 0.00 0.00 0.00 2.62
5533 7010 2.622436 AGGTTGTTAAGCTCGAGCATC 58.378 47.619 36.87 22.92 45.16 3.91
5548 7025 5.894807 CCAAACAATATTCTGGCTAGGTTG 58.105 41.667 0.00 1.08 0.00 3.77
5558 7035 7.062957 AGTAATGCCTAGCCAAACAATATTCT 58.937 34.615 0.00 0.00 0.00 2.40
5562 7039 5.130350 GGAGTAATGCCTAGCCAAACAATA 58.870 41.667 0.00 0.00 0.00 1.90
5591 7068 9.257651 GTGTATAACTCGCCTTATACTTTCAAT 57.742 33.333 16.61 0.00 39.13 2.57
5598 7075 7.424001 ACAGAAGTGTATAACTCGCCTTATAC 58.576 38.462 12.01 12.01 38.56 1.47
5629 7106 7.165812 CGGAAAAATGGAATAGAAATACGCTTG 59.834 37.037 0.00 0.00 0.00 4.01
5636 7113 5.186797 TGCACCGGAAAAATGGAATAGAAAT 59.813 36.000 9.46 0.00 0.00 2.17
5642 7119 3.070878 ACTTTGCACCGGAAAAATGGAAT 59.929 39.130 9.46 0.00 0.00 3.01
5643 7120 2.432510 ACTTTGCACCGGAAAAATGGAA 59.567 40.909 9.46 0.00 0.00 3.53
5645 7122 2.134346 CACTTTGCACCGGAAAAATGG 58.866 47.619 9.46 0.00 0.00 3.16
5648 7125 2.996621 CAAACACTTTGCACCGGAAAAA 59.003 40.909 9.46 4.54 33.36 1.94


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

AutoCloner maintained by Alex Coulton.