Multiple sequence alignment - TraesCS6A01G151500

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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 TraesCS6A01G151500 chr6A 100.000 6028 0 0 1 6028 135434568 135440595 0.000000e+00 11132
1 TraesCS6A01G151500 chr3B 92.693 5173 289 47 1 5140 783217988 783212872 0.000000e+00 7376
2 TraesCS6A01G151500 chr3B 93.066 274 15 2 5755 6028 783212460 783212191 1.220000e-106 398
3 TraesCS6A01G151500 chr3B 87.365 277 15 8 5139 5415 783212711 783212455 3.530000e-77 300
4 TraesCS6A01G151500 chr3A 83.700 1816 223 45 2758 4534 175857318 175855537 0.000000e+00 1646
5 TraesCS6A01G151500 chr3A 82.833 1631 231 33 2753 4371 110809972 110808379 0.000000e+00 1415
6 TraesCS6A01G151500 chr3A 85.099 1114 155 9 815 1923 110812642 110811535 0.000000e+00 1127
7 TraesCS6A01G151500 chr3A 85.229 1090 148 9 815 1897 175860145 175859062 0.000000e+00 1109
8 TraesCS6A01G151500 chr3A 84.795 855 114 16 2758 3609 102091492 102092333 0.000000e+00 845
9 TraesCS6A01G151500 chr3A 84.218 678 98 9 3698 4371 102094025 102094697 0.000000e+00 651
10 TraesCS6A01G151500 chr3A 76.663 887 159 25 1886 2737 110810977 110810104 1.190000e-121 448
11 TraesCS6A01G151500 chr3A 84.058 276 41 1 5753 6028 175854153 175853881 4.630000e-66 263
12 TraesCS6A01G151500 chr3A 77.294 436 85 11 5596 6028 110807199 110806775 1.680000e-60 244
13 TraesCS6A01G151500 chr3A 82.014 278 43 4 5753 6028 102096140 102096412 4.700000e-56 230
14 TraesCS6A01G151500 chr4A 83.756 1773 221 39 2790 4525 70795219 70796961 0.000000e+00 1616
15 TraesCS6A01G151500 chr4A 85.229 1090 148 9 815 1897 70771267 70772350 0.000000e+00 1109
16 TraesCS6A01G151500 chr4A 84.058 276 40 1 5753 6028 70798355 70798626 4.630000e-66 263
17 TraesCS6A01G151500 chr1A 83.453 1807 230 41 2758 4525 255741199 255742975 0.000000e+00 1616
18 TraesCS6A01G151500 chr1A 84.567 1121 158 11 785 1897 255738339 255739452 0.000000e+00 1098
19 TraesCS6A01G151500 chr1A 83.333 276 43 1 5753 6028 255744507 255744779 1.000000e-62 252
20 TraesCS6A01G151500 chr7A 82.552 1834 234 48 2758 4534 16990786 16988982 0.000000e+00 1535
21 TraesCS6A01G151500 chr7A 84.938 1122 149 16 785 1897 67818902 67820012 0.000000e+00 1118
22 TraesCS6A01G151500 chr7A 85.140 1070 146 9 815 1877 16993607 16992544 0.000000e+00 1083
23 TraesCS6A01G151500 chr7A 84.174 853 91 20 3698 4534 67822727 67823551 0.000000e+00 787
24 TraesCS6A01G151500 chr7A 83.394 277 41 3 5753 6028 67824936 67825208 1.000000e-62 252
25 TraesCS6A01G151500 chr7A 83.394 277 41 3 5753 6028 67834271 67834543 1.000000e-62 252
26 TraesCS6A01G151500 chr5B 77.835 2504 426 81 1895 4342 600373110 600370680 0.000000e+00 1430
27 TraesCS6A01G151500 chr5B 84.870 1117 153 12 790 1897 600374596 600373487 0.000000e+00 1112
28 TraesCS6A01G151500 chr2B 80.416 1588 251 44 2767 4339 495224328 495222786 0.000000e+00 1155
29 TraesCS6A01G151500 chr2B 85.242 1118 155 10 785 1897 495226874 495225762 0.000000e+00 1142
30 TraesCS6A01G151500 chrUn 83.394 277 41 3 5753 6028 352287456 352287728 1.000000e-62 252


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 TraesCS6A01G151500 chr6A 135434568 135440595 6027 False 11132.000000 11132 100.000000 1 6028 1 chr6A.!!$F1 6027
1 TraesCS6A01G151500 chr3B 783212191 783217988 5797 True 2691.333333 7376 91.041333 1 6028 3 chr3B.!!$R1 6027
2 TraesCS6A01G151500 chr3A 175853881 175860145 6264 True 1006.000000 1646 84.329000 815 6028 3 chr3A.!!$R2 5213
3 TraesCS6A01G151500 chr3A 110806775 110812642 5867 True 808.500000 1415 80.472250 815 6028 4 chr3A.!!$R1 5213
4 TraesCS6A01G151500 chr3A 102091492 102096412 4920 False 575.333333 845 83.675667 2758 6028 3 chr3A.!!$F1 3270
5 TraesCS6A01G151500 chr4A 70771267 70772350 1083 False 1109.000000 1109 85.229000 815 1897 1 chr4A.!!$F1 1082
6 TraesCS6A01G151500 chr4A 70795219 70798626 3407 False 939.500000 1616 83.907000 2790 6028 2 chr4A.!!$F2 3238
7 TraesCS6A01G151500 chr1A 255738339 255744779 6440 False 988.666667 1616 83.784333 785 6028 3 chr1A.!!$F1 5243
8 TraesCS6A01G151500 chr7A 16988982 16993607 4625 True 1309.000000 1535 83.846000 815 4534 2 chr7A.!!$R1 3719
9 TraesCS6A01G151500 chr7A 67818902 67825208 6306 False 719.000000 1118 84.168667 785 6028 3 chr7A.!!$F2 5243
10 TraesCS6A01G151500 chr5B 600370680 600374596 3916 True 1271.000000 1430 81.352500 790 4342 2 chr5B.!!$R1 3552
11 TraesCS6A01G151500 chr2B 495222786 495226874 4088 True 1148.500000 1155 82.829000 785 4339 2 chr2B.!!$R1 3554

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
114 115 1.167851 CAAATCGGAAGCCTGCAAGA 58.832 50.000 0.0 0.0 34.07 3.02 F
1507 1514 1.971481 TGCAGCAAGAAAAGCTCAGA 58.029 45.000 0.0 0.0 41.14 3.27 F
2444 3257 1.145738 AGAAGGTCCACCAAAGTGCAT 59.854 47.619 0.0 0.0 43.09 3.96 F
3409 4419 2.609737 CCGACTTCGCTGTAAGTTTCCT 60.610 50.000 0.0 0.0 39.78 3.36 F
3771 6396 4.827692 TGTTACATGGTGCTCGTATTTCT 58.172 39.130 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2802 1.178534 GGCTTGCTTGTGCCTTGGTA 61.179 55.000 0.00 0.0 45.26 3.25 R
2959 3944 1.000163 GAGTCCGTGAACTCTGCTTCA 60.000 52.381 3.37 0.0 42.01 3.02 R
4059 6688 0.249322 CACCAAACCAGAGTCGTCGT 60.249 55.000 0.00 0.0 0.00 4.34 R
4833 8140 2.093394 TGCAAGATTTGGGGCATTCATG 60.093 45.455 0.00 0.0 0.00 3.07 R
5425 8985 4.789012 AAACCATTGCAATTCGACATCT 57.211 36.364 9.83 0.0 0.00 2.90 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
32 33 6.040278 TGTTGAACAAACATATTTCTGCTCCA 59.960 34.615 0.00 0.00 43.96 3.86
35 36 7.315142 TGAACAAACATATTTCTGCTCCATTC 58.685 34.615 0.00 0.00 0.00 2.67
38 39 5.998454 AACATATTTCTGCTCCATTCGAG 57.002 39.130 0.00 0.00 42.04 4.04
49 50 3.190874 CTCCATTCGAGCAGAACTTACC 58.809 50.000 0.00 0.00 42.39 2.85
52 53 3.941483 CCATTCGAGCAGAACTTACCATT 59.059 43.478 0.00 0.00 42.39 3.16
88 89 9.764363 TCTGCTACATACCTCTATGTTTATTTG 57.236 33.333 0.00 0.00 40.16 2.32
95 96 9.003658 CATACCTCTATGTTTATTTGGACCATC 57.996 37.037 0.00 0.00 0.00 3.51
96 97 6.969043 ACCTCTATGTTTATTTGGACCATCA 58.031 36.000 0.00 0.00 0.00 3.07
97 98 7.410174 ACCTCTATGTTTATTTGGACCATCAA 58.590 34.615 0.00 0.00 0.00 2.57
98 99 7.893302 ACCTCTATGTTTATTTGGACCATCAAA 59.107 33.333 0.00 0.00 40.37 2.69
99 100 8.917088 CCTCTATGTTTATTTGGACCATCAAAT 58.083 33.333 0.00 7.75 45.76 2.32
100 101 9.956720 CTCTATGTTTATTTGGACCATCAAATC 57.043 33.333 0.00 0.00 43.70 2.17
101 102 8.620416 TCTATGTTTATTTGGACCATCAAATCG 58.380 33.333 0.00 0.00 43.70 3.34
102 103 5.960113 TGTTTATTTGGACCATCAAATCGG 58.040 37.500 0.00 0.00 43.70 4.18
103 104 5.712446 TGTTTATTTGGACCATCAAATCGGA 59.288 36.000 0.00 0.00 43.70 4.55
104 105 6.209589 TGTTTATTTGGACCATCAAATCGGAA 59.790 34.615 0.00 0.00 43.70 4.30
114 115 1.167851 CAAATCGGAAGCCTGCAAGA 58.832 50.000 0.00 0.00 34.07 3.02
122 123 3.545703 GGAAGCCTGCAAGATAGCTTAA 58.454 45.455 0.00 0.00 45.20 1.85
217 218 9.733556 TGGAATATGGTAAACATGTATATCACC 57.266 33.333 0.00 6.75 40.82 4.02
223 224 8.500753 TGGTAAACATGTATATCACCTTTCAC 57.499 34.615 0.00 0.00 0.00 3.18
237 238 7.038154 TCACCTTTCACTTTTTATTCACTGG 57.962 36.000 0.00 0.00 0.00 4.00
247 248 9.097257 CACTTTTTATTCACTGGAAAACACATT 57.903 29.630 0.00 0.00 36.43 2.71
334 335 9.195411 GAATTTTAGTTCTGCATTGAAATGTGA 57.805 29.630 5.02 1.88 38.65 3.58
433 434 5.175126 AGTGTAATATTATTGACGTGCTCGC 59.825 40.000 8.29 1.97 41.18 5.03
478 479 8.777865 TTCATCGAGTGAAAAATAGAAGACAT 57.222 30.769 7.53 0.00 43.64 3.06
607 608 7.448748 AATAGGTTGTGTTCTTACATTCCAC 57.551 36.000 0.00 0.00 36.50 4.02
613 614 7.867305 TTGTGTTCTTACATTCCACAACTAA 57.133 32.000 0.00 0.00 40.12 2.24
619 620 7.900782 TCTTACATTCCACAACTAAGCTAAC 57.099 36.000 0.00 0.00 0.00 2.34
624 625 6.595716 ACATTCCACAACTAAGCTAACTCATC 59.404 38.462 0.00 0.00 0.00 2.92
626 627 7.476540 TTCCACAACTAAGCTAACTCATCTA 57.523 36.000 0.00 0.00 0.00 1.98
861 863 6.403866 ACATGATCATAGTTCAGAGAGGAC 57.596 41.667 8.15 0.00 0.00 3.85
1056 1063 6.262193 AGAAAGTTCAGAGTACTGCTACTC 57.738 41.667 0.00 5.24 46.70 2.59
1068 1075 2.301296 ACTGCTACTCTGCAACACTGAT 59.699 45.455 0.00 0.00 42.83 2.90
1107 1114 9.450807 ACAATAAGACTGAATGAAAAAGTTTCG 57.549 29.630 0.00 0.00 0.00 3.46
1249 1256 4.523173 TGGGATCTGTTACATACGATCCTC 59.477 45.833 22.75 16.35 45.71 3.71
1262 1269 4.808414 ACGATCCTCAAGAGATGAACAA 57.192 40.909 0.00 0.00 37.67 2.83
1289 1296 7.156876 TGAAGGTGGCTGAAACAATAATAAG 57.843 36.000 0.00 0.00 0.00 1.73
1360 1367 7.915397 TCAAGACTTCTTTTGTTTGCTTCATAC 59.085 33.333 0.00 0.00 33.11 2.39
1388 1395 8.899771 GGGTTATTTCTTAATAGCTTGTAGCAA 58.100 33.333 0.00 0.00 45.56 3.91
1507 1514 1.971481 TGCAGCAAGAAAAGCTCAGA 58.029 45.000 0.00 0.00 41.14 3.27
1586 1593 9.643693 CTTGCAGGTGAGTAATTTAATTCAAAT 57.356 29.630 0.00 0.00 38.54 2.32
1751 1759 5.568685 ATGTAGTGCCTACTATATCTGCG 57.431 43.478 11.92 0.00 41.22 5.18
1757 1765 5.011125 AGTGCCTACTATATCTGCGTTTGAT 59.989 40.000 0.00 0.00 34.74 2.57
1763 1771 7.438160 CCTACTATATCTGCGTTTGATTGTGAA 59.562 37.037 0.00 0.00 0.00 3.18
1813 1821 7.147672 TGTGAGGCAGAAGTCTGATAATGATTA 60.148 37.037 12.54 0.00 46.59 1.75
1939 2731 5.656416 AGTCATTCAGGAACAGGAAACAAAA 59.344 36.000 0.00 0.00 0.00 2.44
1970 2762 7.043590 CGTAACGAAGCTGCTACTAAATACAAT 60.044 37.037 0.90 0.00 0.00 2.71
2081 2873 2.223572 GCGCCCACTCAATATTTTCCTG 60.224 50.000 0.00 0.00 0.00 3.86
2120 2912 4.583073 GGAACAACACCAAAGAAGGTACAT 59.417 41.667 0.00 0.00 40.77 2.29
2122 2914 6.293790 GGAACAACACCAAAGAAGGTACATAC 60.294 42.308 0.00 0.00 40.77 2.39
2302 3115 6.371271 GCCAATTTGTAATAACCAAGCATTGT 59.629 34.615 0.00 0.00 46.99 2.71
2410 3223 2.184830 CATGAGCATGTCCCGGCAG 61.185 63.158 0.00 0.00 34.23 4.85
2444 3257 1.145738 AGAAGGTCCACCAAAGTGCAT 59.854 47.619 0.00 0.00 43.09 3.96
2458 3271 8.825745 CACCAAAGTGCATAAACAATTTAAAGT 58.174 29.630 0.00 0.00 35.81 2.66
2478 3291 7.617041 AAAGTGTTCTGGAAGTGAATATAGC 57.383 36.000 0.00 0.00 33.76 2.97
2521 3334 9.030301 GTGATTGTAAGTAGTTTGCAACAAAAT 57.970 29.630 0.00 0.00 42.84 1.82
2534 3348 9.548208 GTTTGCAACAAAATTTAACTTTTGCTA 57.452 25.926 23.44 10.57 45.66 3.49
2634 3457 8.776470 CAAAATGTTTCAAATTGCTGGTAAGAT 58.224 29.630 0.00 0.00 0.00 2.40
2801 3786 5.470098 ACAAGAACACCAACTAATGCACTAG 59.530 40.000 0.00 0.00 0.00 2.57
3135 4120 9.877178 AGAGGAAAATGAAGTGTAAGTATAGTG 57.123 33.333 0.00 0.00 0.00 2.74
3218 4222 8.904099 ACTATAACAGGTGCTGGATAATAAAC 57.096 34.615 0.00 0.00 35.51 2.01
3409 4419 2.609737 CCGACTTCGCTGTAAGTTTCCT 60.610 50.000 0.00 0.00 39.78 3.36
3414 4425 6.128634 CGACTTCGCTGTAAGTTTCCTAAAAT 60.129 38.462 0.00 0.00 39.78 1.82
3415 4426 7.506328 ACTTCGCTGTAAGTTTCCTAAAATT 57.494 32.000 0.00 0.00 36.26 1.82
3547 4559 6.211184 AGGAAATGAAAATGTTATGTCCAGCA 59.789 34.615 0.00 0.00 0.00 4.41
3707 6332 9.365311 CAATCAAATTACGGCGTATTAACTAAG 57.635 33.333 21.66 5.20 0.00 2.18
3771 6396 4.827692 TGTTACATGGTGCTCGTATTTCT 58.172 39.130 0.00 0.00 0.00 2.52
4024 6652 9.791820 TGAGAATGCATTCACAAGTAATATTTG 57.208 29.630 34.59 0.00 39.23 2.32
4301 6952 5.480073 TCCATTAAAGGAAACCATGGAACAG 59.520 40.000 21.47 0.00 40.39 3.16
4381 7061 9.781834 GAATTGAACAATTGGACGTGATATTTA 57.218 29.630 15.92 0.00 40.77 1.40
4562 7251 7.764901 TGTACCATAATATGCAGAACGTAACAA 59.235 33.333 0.00 0.00 0.00 2.83
4570 7259 6.747659 ATGCAGAACGTAACAAATTTCAAC 57.252 33.333 0.00 0.00 0.00 3.18
4600 7856 9.573166 TTCGAATATCATTTCCTATCCATTTGT 57.427 29.630 0.00 0.00 0.00 2.83
4615 7871 5.848406 TCCATTTGTAATTTTTCAACCGCT 58.152 33.333 0.00 0.00 0.00 5.52
4764 8036 7.692088 TCTTAGACTTGTAGTTATGCTCGTAC 58.308 38.462 0.00 0.00 0.00 3.67
4844 8151 8.907222 AAACAAATAATAATCATGAATGCCCC 57.093 30.769 0.00 0.00 0.00 5.80
4881 8189 5.856156 TGAATGTCAACCCTAAGACGTAAA 58.144 37.500 0.00 0.00 37.58 2.01
5195 8723 6.129300 GCAACACGGATTGTACATTAACAAAC 60.129 38.462 0.00 0.00 42.33 2.93
5237 8766 7.815398 TCAATGTAACAATTGATCAATGCAC 57.185 32.000 21.39 15.63 40.72 4.57
5238 8767 7.604549 TCAATGTAACAATTGATCAATGCACT 58.395 30.769 21.39 9.25 40.72 4.40
5239 8768 7.756272 TCAATGTAACAATTGATCAATGCACTC 59.244 33.333 21.39 12.41 40.72 3.51
5240 8769 5.630061 TGTAACAATTGATCAATGCACTCG 58.370 37.500 21.39 8.70 0.00 4.18
5241 8770 5.411053 TGTAACAATTGATCAATGCACTCGA 59.589 36.000 21.39 1.48 0.00 4.04
5242 8771 5.571784 AACAATTGATCAATGCACTCGAT 57.428 34.783 21.39 0.40 0.00 3.59
5243 8772 6.682423 AACAATTGATCAATGCACTCGATA 57.318 33.333 21.39 0.00 0.00 2.92
5244 8773 6.682423 ACAATTGATCAATGCACTCGATAA 57.318 33.333 21.39 0.00 0.00 1.75
5245 8774 7.268199 ACAATTGATCAATGCACTCGATAAT 57.732 32.000 21.39 0.00 0.00 1.28
5246 8775 7.136772 ACAATTGATCAATGCACTCGATAATG 58.863 34.615 21.39 12.96 0.00 1.90
5247 8776 5.678132 TTGATCAATGCACTCGATAATGG 57.322 39.130 3.38 0.00 0.00 3.16
5248 8777 4.707105 TGATCAATGCACTCGATAATGGT 58.293 39.130 0.00 0.00 0.00 3.55
5249 8778 5.125356 TGATCAATGCACTCGATAATGGTT 58.875 37.500 0.00 0.00 0.00 3.67
5250 8779 5.589855 TGATCAATGCACTCGATAATGGTTT 59.410 36.000 0.00 0.00 0.00 3.27
5251 8780 5.233957 TCAATGCACTCGATAATGGTTTG 57.766 39.130 0.00 0.00 0.00 2.93
5252 8781 4.940654 TCAATGCACTCGATAATGGTTTGA 59.059 37.500 0.00 0.00 0.00 2.69
5253 8782 5.589855 TCAATGCACTCGATAATGGTTTGAT 59.410 36.000 0.00 0.00 0.00 2.57
5254 8783 6.765512 TCAATGCACTCGATAATGGTTTGATA 59.234 34.615 0.00 0.00 0.00 2.15
5336 8891 8.576442 ACCAAACTTTCAAACAATATAGGACAG 58.424 33.333 0.00 0.00 0.00 3.51
5438 8998 8.338259 ACATTTGTATAAGAGATGTCGAATTGC 58.662 33.333 0.00 0.00 0.00 3.56
5440 9000 7.841915 TTGTATAAGAGATGTCGAATTGCAA 57.158 32.000 0.00 0.00 0.00 4.08
5441 9001 8.437360 TTGTATAAGAGATGTCGAATTGCAAT 57.563 30.769 5.99 5.99 0.00 3.56
5442 9002 7.854534 TGTATAAGAGATGTCGAATTGCAATG 58.145 34.615 13.82 1.06 0.00 2.82
5443 9003 4.627611 AAGAGATGTCGAATTGCAATGG 57.372 40.909 13.82 8.53 0.00 3.16
5444 9004 3.614092 AGAGATGTCGAATTGCAATGGT 58.386 40.909 13.82 0.00 0.00 3.55
5445 9005 4.012374 AGAGATGTCGAATTGCAATGGTT 58.988 39.130 13.82 0.00 0.00 3.67
5448 9008 6.150976 AGAGATGTCGAATTGCAATGGTTTTA 59.849 34.615 13.82 0.00 0.00 1.52
5449 9009 6.092748 AGATGTCGAATTGCAATGGTTTTAC 58.907 36.000 13.82 6.67 0.00 2.01
5450 9010 5.446143 TGTCGAATTGCAATGGTTTTACT 57.554 34.783 13.82 0.00 0.00 2.24
5452 9012 7.151999 TGTCGAATTGCAATGGTTTTACTAT 57.848 32.000 13.82 0.00 0.00 2.12
5453 9013 8.270080 TGTCGAATTGCAATGGTTTTACTATA 57.730 30.769 13.82 0.00 0.00 1.31
5455 9015 9.562583 GTCGAATTGCAATGGTTTTACTATAAA 57.437 29.630 13.82 0.00 0.00 1.40
5529 9118 8.978874 TGCTATACAATTCTATCAAACCATGT 57.021 30.769 0.00 0.00 0.00 3.21
5549 9138 9.139174 ACCATGTTTCAATTGATTACGAATTTC 57.861 29.630 9.40 0.00 0.00 2.17
5550 9139 8.594687 CCATGTTTCAATTGATTACGAATTTCC 58.405 33.333 9.40 0.00 0.00 3.13
5551 9140 8.594687 CATGTTTCAATTGATTACGAATTTCCC 58.405 33.333 9.40 0.00 0.00 3.97
5554 9143 6.825944 TCAATTGATTACGAATTTCCCACA 57.174 33.333 3.38 0.00 0.00 4.17
5556 9145 7.312154 TCAATTGATTACGAATTTCCCACAAG 58.688 34.615 3.38 0.00 0.00 3.16
5559 9148 7.747155 TTGATTACGAATTTCCCACAAGTAA 57.253 32.000 0.00 0.00 0.00 2.24
5562 9151 9.451002 TGATTACGAATTTCCCACAAGTAATTA 57.549 29.630 0.00 0.00 34.64 1.40
5563 9152 9.712359 GATTACGAATTTCCCACAAGTAATTAC 57.288 33.333 7.57 7.57 34.64 1.89
5576 9165 9.567848 CCACAAGTAATTACAAAATATGTCCAC 57.432 33.333 17.65 0.00 42.70 4.02
5724 9319 9.716507 AAATAAGACATCGAAATCAAATTACGG 57.283 29.630 0.00 0.00 0.00 4.02
5726 9321 6.978343 AGACATCGAAATCAAATTACGGAA 57.022 33.333 0.00 0.00 0.00 4.30
5727 9322 7.553881 AGACATCGAAATCAAATTACGGAAT 57.446 32.000 0.00 0.00 0.00 3.01
5736 9331 8.791355 AAATCAAATTACGGAATTTATACGGC 57.209 30.769 17.81 0.00 42.22 5.68
5740 9335 7.697291 TCAAATTACGGAATTTATACGGCAAAC 59.303 33.333 17.81 0.00 42.22 2.93
5744 9339 4.571984 ACGGAATTTATACGGCAAACCTAC 59.428 41.667 0.00 0.00 0.00 3.18
5745 9340 4.812626 CGGAATTTATACGGCAAACCTACT 59.187 41.667 0.00 0.00 0.00 2.57
5746 9341 5.295045 CGGAATTTATACGGCAAACCTACTT 59.705 40.000 0.00 0.00 0.00 2.24
5747 9342 6.183360 CGGAATTTATACGGCAAACCTACTTT 60.183 38.462 0.00 0.00 0.00 2.66
5784 9379 9.310716 ACTAACATTAATAAGACGGAACTTAGC 57.689 33.333 0.00 0.00 36.11 3.09
5789 9384 5.662674 AATAAGACGGAACTTAGCTCACT 57.337 39.130 0.00 0.00 36.11 3.41
5800 9395 7.043325 CGGAACTTAGCTCACTGATTAATACAC 60.043 40.741 0.00 0.00 0.00 2.90
5803 9398 6.758886 ACTTAGCTCACTGATTAATACACAGC 59.241 38.462 0.00 1.50 35.38 4.40
5808 9403 6.674037 GCTCACTGATTAATACACAGCAGTTG 60.674 42.308 3.22 2.18 34.66 3.16
5843 9438 8.394971 ACACACTTCATTAGTCATTTCATTGA 57.605 30.769 0.00 0.00 33.85 2.57
5953 9548 0.697854 ACCTTGACTGGACAACCCCT 60.698 55.000 0.00 0.00 34.81 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.940470 AGAAAATGGTAAGTTCTGCTCGAAT 59.060 36.000 0.00 0.00 33.45 3.34
35 36 5.390991 GGAAGAAAATGGTAAGTTCTGCTCG 60.391 44.000 0.00 0.00 32.03 5.03
38 39 5.705609 TGGAAGAAAATGGTAAGTTCTGC 57.294 39.130 0.00 0.00 32.03 4.26
41 42 6.808704 GCAGATTGGAAGAAAATGGTAAGTTC 59.191 38.462 0.00 0.00 0.00 3.01
42 43 6.494835 AGCAGATTGGAAGAAAATGGTAAGTT 59.505 34.615 0.00 0.00 0.00 2.66
49 50 7.284034 AGGTATGTAGCAGATTGGAAGAAAATG 59.716 37.037 0.00 0.00 0.00 2.32
52 53 6.156949 AGAGGTATGTAGCAGATTGGAAGAAA 59.843 38.462 0.00 0.00 0.00 2.52
88 89 1.025041 GGCTTCCGATTTGATGGTCC 58.975 55.000 0.00 0.00 0.00 4.46
95 96 1.167851 TCTTGCAGGCTTCCGATTTG 58.832 50.000 0.00 0.00 0.00 2.32
96 97 2.134789 ATCTTGCAGGCTTCCGATTT 57.865 45.000 0.00 0.00 0.00 2.17
97 98 2.843701 CTATCTTGCAGGCTTCCGATT 58.156 47.619 0.00 0.00 0.00 3.34
98 99 1.542108 GCTATCTTGCAGGCTTCCGAT 60.542 52.381 0.00 0.00 0.00 4.18
99 100 0.179073 GCTATCTTGCAGGCTTCCGA 60.179 55.000 0.00 0.00 0.00 4.55
100 101 0.179062 AGCTATCTTGCAGGCTTCCG 60.179 55.000 0.00 0.00 34.99 4.30
101 102 2.049888 AAGCTATCTTGCAGGCTTCC 57.950 50.000 0.00 0.00 40.40 3.46
102 103 5.764487 AATTAAGCTATCTTGCAGGCTTC 57.236 39.130 13.25 0.00 42.86 3.86
103 104 6.535963 AAAATTAAGCTATCTTGCAGGCTT 57.464 33.333 13.96 13.96 45.30 4.35
104 105 6.535963 AAAAATTAAGCTATCTTGCAGGCT 57.464 33.333 0.00 0.00 36.53 4.58
173 174 2.890311 TCCAGCAAACCATTGTAACAGG 59.110 45.455 0.00 0.00 38.85 4.00
184 185 5.652994 TGTTTACCATATTCCAGCAAACC 57.347 39.130 0.00 0.00 0.00 3.27
217 218 9.364989 TGTTTTCCAGTGAATAAAAAGTGAAAG 57.635 29.630 0.00 0.00 0.00 2.62
351 352 6.560253 ACCTTTGTAGTAGCAAGTGAAATG 57.440 37.500 0.00 0.00 0.00 2.32
364 365 9.582648 AACAATATTGGAGTTAACCTTTGTAGT 57.417 29.630 19.37 0.00 0.00 2.73
568 569 9.582648 ACACAACCTATTTTCTGGTTATTTACT 57.417 29.630 0.00 0.00 43.88 2.24
571 572 9.143155 AGAACACAACCTATTTTCTGGTTATTT 57.857 29.630 0.00 0.00 43.88 1.40
572 573 8.706322 AGAACACAACCTATTTTCTGGTTATT 57.294 30.769 0.00 0.00 43.88 1.40
573 574 8.706322 AAGAACACAACCTATTTTCTGGTTAT 57.294 30.769 0.00 0.00 43.88 1.89
574 575 9.059260 GTAAGAACACAACCTATTTTCTGGTTA 57.941 33.333 0.00 0.00 43.88 2.85
575 576 7.558444 TGTAAGAACACAACCTATTTTCTGGTT 59.442 33.333 0.00 0.00 46.33 3.67
593 594 6.803154 AGCTTAGTTGTGGAATGTAAGAAC 57.197 37.500 0.00 0.00 0.00 3.01
607 608 9.606631 AGGAAATTAGATGAGTTAGCTTAGTTG 57.393 33.333 0.00 0.00 0.00 3.16
612 613 6.418101 TGCAGGAAATTAGATGAGTTAGCTT 58.582 36.000 0.00 0.00 0.00 3.74
613 614 5.994250 TGCAGGAAATTAGATGAGTTAGCT 58.006 37.500 0.00 0.00 0.00 3.32
619 620 7.991084 TCCAATATGCAGGAAATTAGATGAG 57.009 36.000 0.00 0.00 0.00 2.90
807 809 5.876357 TGTTGTAGCAAATCCTAGGAAAGT 58.124 37.500 17.30 0.86 0.00 2.66
1056 1063 4.134379 AGTATCAGGATCAGTGTTGCAG 57.866 45.455 0.00 0.00 0.00 4.41
1068 1075 9.475620 TTCAGTCTTATTGTTCTAGTATCAGGA 57.524 33.333 0.00 0.00 0.00 3.86
1107 1114 4.212847 ACATCATCATCAGTTATTCGCAGC 59.787 41.667 0.00 0.00 0.00 5.25
1159 1166 7.256119 GCAGTCCAATCCTCTCAATATCTTAGA 60.256 40.741 0.00 0.00 0.00 2.10
1164 1171 4.202398 TGGCAGTCCAATCCTCTCAATATC 60.202 45.833 0.00 0.00 39.99 1.63
1222 1229 7.556844 GGATCGTATGTAACAGATCCCATTAT 58.443 38.462 11.17 0.00 44.19 1.28
1223 1230 6.931838 GGATCGTATGTAACAGATCCCATTA 58.068 40.000 11.17 0.00 44.19 1.90
1249 1256 5.278169 CCACCTTCAAGTTGTTCATCTCTTG 60.278 44.000 2.11 0.00 38.69 3.02
1262 1269 2.435372 TGTTTCAGCCACCTTCAAGT 57.565 45.000 0.00 0.00 0.00 3.16
1360 1367 8.560374 GCTACAAGCTATTAAGAAATAACCCAG 58.440 37.037 0.00 0.00 38.45 4.45
1381 1388 3.676598 GCACCATGATTTGCATTGCTACA 60.677 43.478 10.49 5.33 37.62 2.74
1388 1395 2.568062 TCTTTGGCACCATGATTTGCAT 59.432 40.909 13.70 0.00 40.75 3.96
1674 1682 4.527564 CTGTCTAAAACGAAAGCCTGTTG 58.472 43.478 0.00 0.00 0.00 3.33
1709 1717 9.823647 ACTACATAATCAGGTATGTTCAGAAAG 57.176 33.333 3.38 0.00 40.98 2.62
1710 1718 9.599866 CACTACATAATCAGGTATGTTCAGAAA 57.400 33.333 3.38 0.00 40.98 2.52
1751 1759 8.633075 TCTTTGACATCTTTTCACAATCAAAC 57.367 30.769 0.00 0.00 32.69 2.93
1757 1765 9.506018 TCTATCATCTTTGACATCTTTTCACAA 57.494 29.630 0.00 0.00 33.85 3.33
1763 1771 9.512588 ACAAGTTCTATCATCTTTGACATCTTT 57.487 29.630 0.00 0.00 33.85 2.52
1813 1821 7.427989 AATTGCACCTCATTAGATCCAAAAT 57.572 32.000 0.00 0.00 0.00 1.82
1911 2703 6.262273 TGTTTCCTGTTCCTGAATGACTTTAC 59.738 38.462 0.00 0.00 0.00 2.01
1939 2731 2.080286 AGCAGCTTCGTTACGAACAT 57.920 45.000 16.56 5.04 41.05 2.71
1970 2762 8.821894 GGTTTATTCATTGTAACAGTTGCAAAA 58.178 29.630 19.19 11.30 38.71 2.44
2010 2802 1.178534 GGCTTGCTTGTGCCTTGGTA 61.179 55.000 0.00 0.00 45.26 3.25
2081 2873 7.361799 GGTGTTGTTCCTTGTACATAAGAATCC 60.362 40.741 0.00 1.71 0.00 3.01
2153 2948 8.078596 AGTGTTAGCATTGAAAGTTCATTCTTC 58.921 33.333 0.00 0.00 37.00 2.87
2222 3017 1.139654 TGATCCTAGCACTGTGCCATC 59.860 52.381 27.74 21.78 46.52 3.51
2302 3115 5.895636 AAATTATCCGTTGCTGATGTTGA 57.104 34.783 0.00 0.00 0.00 3.18
2410 3223 4.158025 TGGACCTTCTGATCGAACTTCTAC 59.842 45.833 0.00 0.00 0.00 2.59
2444 3257 9.796120 CACTTCCAGAACACTTTAAATTGTTTA 57.204 29.630 20.76 8.29 36.06 2.01
2458 3271 4.404394 TCCGCTATATTCACTTCCAGAACA 59.596 41.667 0.00 0.00 0.00 3.18
2478 3291 5.295292 ACAATCACTATTTGAATCAGCTCCG 59.705 40.000 0.00 0.00 37.92 4.63
2593 3410 4.549458 ACATTTTGCTTTTGGATGAGTCG 58.451 39.130 0.00 0.00 0.00 4.18
2700 3524 7.993183 CCAGATAACTATGGTTGTTGGACTTAT 59.007 37.037 4.47 0.00 36.92 1.73
2756 3740 4.883585 TGTTGCATCCATATCTCCTGAAAC 59.116 41.667 0.00 0.00 0.00 2.78
2765 3749 4.398988 TGGTGTTCTTGTTGCATCCATATC 59.601 41.667 0.00 0.00 0.00 1.63
2801 3786 9.256477 TCGATATGTATTAGAACATGGTGTTTC 57.744 33.333 0.00 0.00 41.28 2.78
2823 3808 8.230486 GTGTTTGTACATTCTCAAAATCTCGAT 58.770 33.333 0.00 0.00 36.50 3.59
2825 3810 6.797033 GGTGTTTGTACATTCTCAAAATCTCG 59.203 38.462 0.00 0.00 36.50 4.04
2959 3944 1.000163 GAGTCCGTGAACTCTGCTTCA 60.000 52.381 3.37 0.00 42.01 3.02
3193 4178 8.714906 AGTTTATTATCCAGCACCTGTTATAGT 58.285 33.333 0.00 0.00 0.00 2.12
3218 4222 6.323996 TGACCTCTATGTACCTTGGTTCATAG 59.676 42.308 26.66 26.66 40.26 2.23
3771 6396 7.880105 TGTACACATTTTAGCATCATGTCAAA 58.120 30.769 0.00 0.00 0.00 2.69
4059 6688 0.249322 CACCAAACCAGAGTCGTCGT 60.249 55.000 0.00 0.00 0.00 4.34
4122 6751 6.073447 TGATAATTACCTGTGTGTGGGATT 57.927 37.500 0.00 0.00 0.00 3.01
4124 6753 5.506730 TTGATAATTACCTGTGTGTGGGA 57.493 39.130 0.00 0.00 0.00 4.37
4237 6882 5.425196 ACAAAGGCTTGAATGGCATTATT 57.575 34.783 13.65 0.00 36.33 1.40
4244 6889 3.795877 ACAACAACAAAGGCTTGAATGG 58.204 40.909 0.00 0.00 36.33 3.16
4301 6952 9.668497 AATTGTTTCTATGTAGGAAGTAGGAAC 57.332 33.333 0.00 0.00 35.46 3.62
4407 7087 9.421399 TGTCCTCAAGTATCATGAAAGTAGATA 57.579 33.333 0.00 0.00 0.00 1.98
4607 7863 8.725405 TTGTGAATATTTTATAGAGCGGTTGA 57.275 30.769 0.00 0.00 0.00 3.18
4666 7924 6.824305 ACAGGAAGTAATTTGAACAGATGG 57.176 37.500 0.00 0.00 0.00 3.51
4742 8014 5.007039 CCGTACGAGCATAACTACAAGTCTA 59.993 44.000 18.76 0.00 0.00 2.59
4749 8021 5.331902 TGTAAACCGTACGAGCATAACTAC 58.668 41.667 18.76 6.98 0.00 2.73
4827 8134 7.221450 CAAGATTTGGGGCATTCATGATTATT 58.779 34.615 0.00 0.00 0.00 1.40
4833 8140 2.093394 TGCAAGATTTGGGGCATTCATG 60.093 45.455 0.00 0.00 0.00 3.07
4843 8150 5.231702 TGACATTCATTGTGCAAGATTTGG 58.768 37.500 0.00 0.00 39.18 3.28
4844 8151 6.347079 GGTTGACATTCATTGTGCAAGATTTG 60.347 38.462 0.00 0.00 39.18 2.32
5148 8676 8.664798 GTTGCGAGGAATATGTATTATGCATTA 58.335 33.333 3.54 0.00 0.00 1.90
5225 8754 5.125356 ACCATTATCGAGTGCATTGATCAA 58.875 37.500 11.26 11.26 33.74 2.57
5230 8759 5.233957 TCAAACCATTATCGAGTGCATTG 57.766 39.130 0.00 0.00 0.00 2.82
5419 8979 6.992123 ACCATTGCAATTCGACATCTCTTATA 59.008 34.615 9.83 0.00 0.00 0.98
5425 8985 4.789012 AAACCATTGCAATTCGACATCT 57.211 36.364 9.83 0.00 0.00 2.90
5503 9085 9.578576 ACATGGTTTGATAGAATTGTATAGCAT 57.421 29.630 0.00 0.00 0.00 3.79
5518 9107 8.303156 TCGTAATCAATTGAAACATGGTTTGAT 58.697 29.630 13.09 0.00 35.84 2.57
5521 9110 9.487790 AATTCGTAATCAATTGAAACATGGTTT 57.512 25.926 13.09 2.11 0.00 3.27
5525 9114 8.594687 GGGAAATTCGTAATCAATTGAAACATG 58.405 33.333 13.09 6.25 0.00 3.21
5527 9116 7.596995 GTGGGAAATTCGTAATCAATTGAAACA 59.403 33.333 13.09 0.00 0.00 2.83
5529 9118 7.661968 TGTGGGAAATTCGTAATCAATTGAAA 58.338 30.769 13.09 1.86 0.00 2.69
5531 9120 6.825944 TGTGGGAAATTCGTAATCAATTGA 57.174 33.333 11.26 11.26 0.00 2.57
5533 9122 7.227049 ACTTGTGGGAAATTCGTAATCAATT 57.773 32.000 0.00 0.00 0.00 2.32
5537 9126 9.712359 GTAATTACTTGTGGGAAATTCGTAATC 57.288 33.333 8.41 0.00 0.00 1.75
5541 9130 7.513371 TTGTAATTACTTGTGGGAAATTCGT 57.487 32.000 16.33 0.00 0.00 3.85
5549 9138 8.744652 TGGACATATTTTGTAATTACTTGTGGG 58.255 33.333 16.33 4.18 39.18 4.61
5550 9139 9.567848 GTGGACATATTTTGTAATTACTTGTGG 57.432 33.333 16.33 3.63 39.18 4.17
5701 9296 8.481974 TTCCGTAATTTGATTTCGATGTCTTA 57.518 30.769 2.00 0.00 35.45 2.10
5702 9297 6.978343 TCCGTAATTTGATTTCGATGTCTT 57.022 33.333 2.00 0.00 35.45 3.01
5710 9305 8.898792 GCCGTATAAATTCCGTAATTTGATTTC 58.101 33.333 8.78 0.00 43.52 2.17
5784 9379 6.674037 GCAACTGCTGTGTATTAATCAGTGAG 60.674 42.308 0.00 4.90 35.28 3.51
5789 9384 4.331108 TGGCAACTGCTGTGTATTAATCA 58.669 39.130 1.06 0.00 41.70 2.57
5800 9395 3.057386 TGTGTAATGATTGGCAACTGCTG 60.057 43.478 0.00 0.00 41.70 4.41
5803 9398 4.771590 AGTGTGTAATGATTGGCAACTG 57.228 40.909 0.00 0.00 37.61 3.16
5808 9403 7.088589 ACTAATGAAGTGTGTAATGATTGGC 57.911 36.000 0.00 0.00 36.93 4.52
5843 9438 8.723942 TGTTATTTGTTTGCTTTATGTGGTTT 57.276 26.923 0.00 0.00 0.00 3.27
5908 9503 0.523335 GCAAATGTCGATCGCCAACC 60.523 55.000 11.09 0.00 0.00 3.77
6001 9596 7.338800 AGCAAACATCAAGAAGAAGAAGAAA 57.661 32.000 0.00 0.00 0.00 2.52
6002 9597 6.949352 AGCAAACATCAAGAAGAAGAAGAA 57.051 33.333 0.00 0.00 0.00 2.52
6003 9598 6.949352 AAGCAAACATCAAGAAGAAGAAGA 57.051 33.333 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.