Multiple sequence alignment - TraesCS3A01G314800

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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 TraesCS3A01G314800 chr3A 100.000 2531 0 0 1 2531 556261922 556259392 0.000000e+00 4674
1 TraesCS3A01G314800 chr3A 81.123 1086 110 52 702 1735 556354335 556353293 0.000000e+00 782
2 TraesCS3A01G314800 chr3A 78.725 1067 121 70 760 1761 556340946 556339921 1.290000e-172 616
3 TraesCS3A01G314800 chr3A 83.824 408 49 8 1066 1473 556683207 556683597 3.080000e-99 372
4 TraesCS3A01G314800 chr3A 75.532 282 61 6 8 284 667944925 667945203 5.680000e-27 132
5 TraesCS3A01G314800 chr3B 87.065 1956 148 58 604 2481 561888732 561890660 0.000000e+00 2113
6 TraesCS3A01G314800 chr3B 79.861 1152 131 63 694 1783 561840420 561841532 0.000000e+00 749
7 TraesCS3A01G314800 chr3B 79.249 959 114 53 760 1677 561592299 561593213 7.800000e-165 590
8 TraesCS3A01G314800 chr3B 87.216 485 46 4 5 489 561887003 561887471 2.860000e-149 538
9 TraesCS3A01G314800 chr3B 85.539 408 42 5 1069 1473 561039088 561038695 6.520000e-111 411
10 TraesCS3A01G314800 chr3B 81.499 427 49 16 1069 1473 561044738 561044320 8.730000e-85 324
11 TraesCS3A01G314800 chr3B 78.901 455 75 16 1895 2333 283586451 283586002 3.190000e-74 289
12 TraesCS3A01G314800 chr3B 79.268 164 30 4 2368 2530 703293175 703293015 7.400000e-21 111
13 TraesCS3A01G314800 chr3B 85.577 104 14 1 1683 1785 561596246 561596349 9.570000e-20 108
14 TraesCS3A01G314800 chr3D 86.275 1377 115 31 187 1519 429646605 429647951 0.000000e+00 1428
15 TraesCS3A01G314800 chr3D 80.072 1104 132 58 693 1747 429636910 429637974 0.000000e+00 739
16 TraesCS3A01G314800 chr3D 87.532 385 26 7 1518 1886 429648034 429648412 2.330000e-115 425
17 TraesCS3A01G314800 chr3D 86.029 408 40 5 1066 1473 428994381 428993991 3.010000e-114 422
18 TraesCS3A01G314800 chr3D 80.285 421 49 15 1069 1473 429085723 429085321 1.150000e-73 287
19 TraesCS3A01G314800 chr3D 80.054 371 54 16 2000 2356 599501290 599501654 8.980000e-65 257
20 TraesCS3A01G314800 chr3D 81.651 218 26 9 961 1169 429623693 429623905 4.330000e-38 169
21 TraesCS3A01G314800 chr3D 87.591 137 11 2 1069 1199 429044236 429044100 1.210000e-33 154
22 TraesCS3A01G314800 chr4A 81.474 475 69 14 1888 2352 738818977 738818512 3.080000e-99 372
23 TraesCS3A01G314800 chr5B 81.278 454 63 17 1895 2333 608215935 608216381 5.180000e-92 348
24 TraesCS3A01G314800 chr2B 80.531 452 76 10 1903 2343 775835811 775835361 1.120000e-88 337
25 TraesCS3A01G314800 chr2B 80.759 395 67 8 1889 2276 786257380 786256988 1.470000e-77 300
26 TraesCS3A01G314800 chr1B 79.739 459 77 12 1887 2332 67414931 67415386 4.060000e-83 318
27 TraesCS3A01G314800 chr7B 78.864 440 72 17 1891 2322 745581197 745580771 6.900000e-71 278
28 TraesCS3A01G314800 chr7B 80.802 349 52 13 1878 2218 354699531 354699872 2.500000e-65 259
29 TraesCS3A01G314800 chr7B 77.581 339 69 5 5 339 745863321 745863656 5.520000e-47 198
30 TraesCS3A01G314800 chr1A 80.508 354 53 14 1990 2333 56099045 56099392 8.980000e-65 257
31 TraesCS3A01G314800 chr7D 81.293 294 51 3 11 301 571879010 571879302 4.210000e-58 235
32 TraesCS3A01G314800 chr2D 76.761 426 86 11 64 483 592412858 592413276 2.530000e-55 226
33 TraesCS3A01G314800 chr5D 79.636 275 54 1 8 280 417046539 417046813 1.990000e-46 196
34 TraesCS3A01G314800 chr7A 80.745 161 17 8 2368 2518 690374534 690374690 2.060000e-21 113


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 TraesCS3A01G314800 chr3A 556259392 556261922 2530 True 4674.0 4674 100.0000 1 2531 1 chr3A.!!$R1 2530
1 TraesCS3A01G314800 chr3A 556353293 556354335 1042 True 782.0 782 81.1230 702 1735 1 chr3A.!!$R3 1033
2 TraesCS3A01G314800 chr3A 556339921 556340946 1025 True 616.0 616 78.7250 760 1761 1 chr3A.!!$R2 1001
3 TraesCS3A01G314800 chr3B 561887003 561890660 3657 False 1325.5 2113 87.1405 5 2481 2 chr3B.!!$F3 2476
4 TraesCS3A01G314800 chr3B 561840420 561841532 1112 False 749.0 749 79.8610 694 1783 1 chr3B.!!$F1 1089
5 TraesCS3A01G314800 chr3B 561592299 561596349 4050 False 349.0 590 82.4130 760 1785 2 chr3B.!!$F2 1025
6 TraesCS3A01G314800 chr3D 429646605 429648412 1807 False 926.5 1428 86.9035 187 1886 2 chr3D.!!$F4 1699
7 TraesCS3A01G314800 chr3D 429636910 429637974 1064 False 739.0 739 80.0720 693 1747 1 chr3D.!!$F2 1054

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
592 763 0.3199 ATGCGATCGGTCAGGTATGC 60.32 55.0 18.3 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2980 1.002659 TCGATCCTTTTGCGAGGGAAA 59.997 47.619 2.45 0.0 37.41 3.13 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
39 40 6.572254 CGTTTACGATCGTTGAAACAGAAAAT 59.428 34.615 30.87 8.39 43.02 1.82
67 68 3.624410 ACACTAAAGTCGTGGGAAACAAC 59.376 43.478 0.00 0.00 36.71 3.32
70 71 2.249844 AAGTCGTGGGAAACAACGAT 57.750 45.000 0.32 0.00 35.93 3.73
79 80 5.180271 GTGGGAAACAACGATATGAACCTA 58.820 41.667 0.00 0.00 0.00 3.08
81 82 5.046159 TGGGAAACAACGATATGAACCTACT 60.046 40.000 0.00 0.00 0.00 2.57
83 84 5.293569 GGAAACAACGATATGAACCTACTGG 59.706 44.000 0.00 0.00 39.83 4.00
98 99 5.701224 ACCTACTGGACAAAGGAAATTTCA 58.299 37.500 19.49 0.00 37.04 2.69
113 114 2.116827 TTTCAAACAGTCCACCGTGT 57.883 45.000 0.00 0.00 0.00 4.49
114 115 1.374560 TTCAAACAGTCCACCGTGTG 58.625 50.000 0.00 0.00 0.00 3.82
116 117 2.177580 AAACAGTCCACCGTGTGCG 61.178 57.895 0.00 0.00 37.95 5.34
119 120 2.048222 AGTCCACCGTGTGCGATG 60.048 61.111 0.00 0.00 41.33 3.84
129 130 2.159531 CCGTGTGCGATGAATTTGACAT 60.160 45.455 0.00 0.00 41.33 3.06
159 160 7.814107 TCATCCAAAATAGCTTCAAATGAACAC 59.186 33.333 0.00 0.00 0.00 3.32
160 161 6.148948 TCCAAAATAGCTTCAAATGAACACG 58.851 36.000 0.00 0.00 0.00 4.49
175 176 9.566624 CAAATGAACACGAAATTGAACATTTAC 57.433 29.630 0.00 0.00 35.86 2.01
203 204 3.126343 ACGAAACTACAAATTGATCGCCC 59.874 43.478 0.00 0.00 32.46 6.13
204 205 3.126171 CGAAACTACAAATTGATCGCCCA 59.874 43.478 0.00 0.00 0.00 5.36
205 206 4.201910 CGAAACTACAAATTGATCGCCCAT 60.202 41.667 0.00 0.00 0.00 4.00
225 226 4.202151 CCATATGAGACCACAACATCGAGA 60.202 45.833 3.65 0.00 0.00 4.04
231 232 3.132824 AGACCACAACATCGAGATGCATA 59.867 43.478 12.54 0.00 42.39 3.14
274 275 2.802247 TGAATCGAAGCACTCTTGTGTG 59.198 45.455 0.00 0.00 45.44 3.82
288 289 6.863126 CACTCTTGTGTGGATTAAAATTGACC 59.137 38.462 0.00 0.00 39.24 4.02
295 296 9.482627 TGTGTGGATTAAAATTGACCAATAAAC 57.517 29.630 0.00 0.00 32.32 2.01
320 321 7.042335 CGGAGAAGATTAGGAGTTAACACAAT 58.958 38.462 8.61 0.00 0.00 2.71
382 383 0.806102 TTAGGTTGCATCGCTCGAGC 60.806 55.000 27.64 27.64 37.78 5.03
410 411 1.734465 GTCTGCAGCTTTACATCGCTT 59.266 47.619 9.47 0.00 33.45 4.68
419 420 3.589988 CTTTACATCGCTTGAGTCTGGT 58.410 45.455 0.00 0.00 0.00 4.00
421 422 2.086054 ACATCGCTTGAGTCTGGTTC 57.914 50.000 0.00 0.00 0.00 3.62
423 424 0.737715 ATCGCTTGAGTCTGGTTCGC 60.738 55.000 0.00 0.00 0.00 4.70
426 427 1.668919 CGCTTGAGTCTGGTTCGCTAA 60.669 52.381 0.00 0.00 0.00 3.09
430 431 4.083271 GCTTGAGTCTGGTTCGCTAAAAAT 60.083 41.667 0.00 0.00 0.00 1.82
451 452 4.617808 TGGTCGAATCGAGAGTTTCTAG 57.382 45.455 5.25 0.00 37.60 2.43
453 454 5.181009 TGGTCGAATCGAGAGTTTCTAGTA 58.819 41.667 5.25 0.00 37.60 1.82
459 460 3.015327 TCGAGAGTTTCTAGTAGGCCAC 58.985 50.000 5.01 0.54 0.00 5.01
489 511 4.142093 GGTGCTTTGAACATCATTGCCTAT 60.142 41.667 0.00 0.00 0.00 2.57
494 516 6.860023 GCTTTGAACATCATTGCCTATACATC 59.140 38.462 0.00 0.00 0.00 3.06
540 562 1.021390 GTCTGGTTGGACCTCATGCG 61.021 60.000 0.00 0.00 39.58 4.73
542 564 2.351276 GGTTGGACCTCATGCGGT 59.649 61.111 7.19 7.19 40.80 5.68
549 571 2.202866 ACCTCATGCGGTCTACCAG 58.797 57.895 0.18 0.00 35.14 4.00
557 728 1.346395 TGCGGTCTACCAGACATGTTT 59.654 47.619 0.00 0.00 46.79 2.83
580 751 3.111853 TGACATAAGGGACATGCGATC 57.888 47.619 0.00 0.00 0.00 3.69
581 752 2.061773 GACATAAGGGACATGCGATCG 58.938 52.381 11.69 11.69 0.00 3.69
582 753 1.270305 ACATAAGGGACATGCGATCGG 60.270 52.381 18.30 2.45 0.00 4.18
584 755 0.387929 TAAGGGACATGCGATCGGTC 59.612 55.000 18.30 15.09 0.00 4.79
585 756 1.613317 AAGGGACATGCGATCGGTCA 61.613 55.000 18.30 7.62 33.26 4.02
586 757 1.592669 GGGACATGCGATCGGTCAG 60.593 63.158 18.30 4.32 33.26 3.51
587 758 1.592669 GGACATGCGATCGGTCAGG 60.593 63.158 18.30 11.36 33.26 3.86
588 759 1.141881 GACATGCGATCGGTCAGGT 59.858 57.895 18.30 14.65 0.00 4.00
589 760 0.384309 GACATGCGATCGGTCAGGTA 59.616 55.000 18.30 0.00 0.00 3.08
590 761 1.000163 GACATGCGATCGGTCAGGTAT 60.000 52.381 18.30 0.00 0.00 2.73
591 762 1.269778 ACATGCGATCGGTCAGGTATG 60.270 52.381 18.30 5.00 0.00 2.39
592 763 0.319900 ATGCGATCGGTCAGGTATGC 60.320 55.000 18.30 0.00 0.00 3.14
680 1870 2.093553 TCGTGATGGAGCATGACAATGA 60.094 45.455 0.00 0.00 35.67 2.57
683 1873 4.512571 CGTGATGGAGCATGACAATGATTA 59.487 41.667 0.00 0.00 35.67 1.75
686 1876 7.431249 GTGATGGAGCATGACAATGATTATTT 58.569 34.615 0.00 0.00 35.67 1.40
689 1879 8.657074 ATGGAGCATGACAATGATTATTTTTG 57.343 30.769 0.00 0.00 35.67 2.44
798 2004 2.732412 ATCGCAGATGAGATTACCCG 57.268 50.000 0.00 0.00 45.12 5.28
801 2008 0.603975 GCAGATGAGATTACCCGGGC 60.604 60.000 24.08 3.45 0.00 6.13
818 2025 2.347322 GCCCCGGCTTGCAAATGTA 61.347 57.895 0.00 0.00 38.26 2.29
895 2107 1.077429 GTCTCCAAGGCCATGACCC 60.077 63.158 10.18 0.00 0.00 4.46
911 2123 1.292223 CCCGAACCATGTCGTCACT 59.708 57.895 5.17 0.00 39.43 3.41
1044 2268 1.192534 GCACATATCCGCTTACGCTTC 59.807 52.381 0.00 0.00 38.22 3.86
1046 2270 2.726760 CACATATCCGCTTACGCTTCTC 59.273 50.000 0.00 0.00 38.22 2.87
1048 2272 3.238441 CATATCCGCTTACGCTTCTCTC 58.762 50.000 0.00 0.00 38.22 3.20
1049 2273 0.386113 ATCCGCTTACGCTTCTCTCC 59.614 55.000 0.00 0.00 38.22 3.71
1050 2274 0.963856 TCCGCTTACGCTTCTCTCCA 60.964 55.000 0.00 0.00 38.22 3.86
1051 2275 0.526524 CCGCTTACGCTTCTCTCCAG 60.527 60.000 0.00 0.00 38.22 3.86
1053 2277 0.108615 GCTTACGCTTCTCTCCAGCA 60.109 55.000 0.00 0.00 37.07 4.41
1055 2279 0.966179 TTACGCTTCTCTCCAGCACA 59.034 50.000 0.00 0.00 37.07 4.57
1056 2280 0.966179 TACGCTTCTCTCCAGCACAA 59.034 50.000 0.00 0.00 37.07 3.33
1058 2282 0.601046 CGCTTCTCTCCAGCACAACA 60.601 55.000 0.00 0.00 37.07 3.33
1059 2283 0.871057 GCTTCTCTCCAGCACAACAC 59.129 55.000 0.00 0.00 37.22 3.32
1061 2285 0.836606 TTCTCTCCAGCACAACACCA 59.163 50.000 0.00 0.00 0.00 4.17
1064 2288 1.152984 CTCCAGCACAACACCACCA 60.153 57.895 0.00 0.00 0.00 4.17
1067 2301 1.727511 CCAGCACAACACCACCACAG 61.728 60.000 0.00 0.00 0.00 3.66
1117 2355 0.970937 TCCTGATCGCGTCCCTTCTT 60.971 55.000 5.77 0.00 0.00 2.52
1256 2523 3.357919 GCAGTGGCTGAATGTGCA 58.642 55.556 0.00 0.00 36.96 4.57
1431 2698 1.460504 ACTGCGTCAGGATCTTCGTA 58.539 50.000 10.80 0.00 35.51 3.43
1479 2746 1.148310 CTGCCTAACACACGGTTCAG 58.852 55.000 0.00 0.00 40.96 3.02
1504 2783 0.735978 TGGACTACGCAGCATCGTTG 60.736 55.000 8.49 9.15 43.15 4.10
1547 2911 0.179000 AAAGGAGGCTGGTCGCTATG 59.821 55.000 0.00 0.00 39.13 2.23
1564 2941 1.552578 ATGCGTACACCTCTACCACA 58.447 50.000 0.00 0.00 0.00 4.17
1576 2953 5.465724 CACCTCTACCACAACTCAAGTTAAC 59.534 44.000 0.00 0.00 36.32 2.01
1590 2980 7.951591 ACTCAAGTTAACTTTGGTATTTGCAT 58.048 30.769 18.25 0.00 33.11 3.96
1615 3013 1.661112 CTCGCAAAAGGATCGAGGTTC 59.339 52.381 3.26 0.00 44.06 3.62
1621 3019 4.382147 GCAAAAGGATCGAGGTTCTAGTCT 60.382 45.833 0.00 0.00 0.00 3.24
1622 3020 4.993029 AAAGGATCGAGGTTCTAGTCTG 57.007 45.455 0.00 0.00 0.00 3.51
1623 3021 3.655615 AGGATCGAGGTTCTAGTCTGT 57.344 47.619 0.00 0.00 0.00 3.41
1624 3022 3.547746 AGGATCGAGGTTCTAGTCTGTC 58.452 50.000 0.00 0.00 0.00 3.51
1625 3023 3.054287 AGGATCGAGGTTCTAGTCTGTCA 60.054 47.826 0.00 0.00 0.00 3.58
1626 3024 3.314080 GGATCGAGGTTCTAGTCTGTCAG 59.686 52.174 0.00 0.00 0.00 3.51
1627 3025 3.420300 TCGAGGTTCTAGTCTGTCAGT 57.580 47.619 0.00 0.00 0.00 3.41
1712 6138 1.003223 GTGCGTTTACCTTGTGTGTCC 60.003 52.381 0.00 0.00 0.00 4.02
1761 6187 1.136611 GCGTTACTTTGTGTCTCGCTG 60.137 52.381 0.00 0.00 42.70 5.18
1766 6192 1.284982 CTTTGTGTCTCGCTGTCCGG 61.285 60.000 0.00 0.00 37.59 5.14
1798 6225 1.301322 TGTCGCGTCTTTGGCATGA 60.301 52.632 5.77 0.00 0.00 3.07
1804 6231 0.449388 CGTCTTTGGCATGAAGGAGC 59.551 55.000 0.00 0.00 0.00 4.70
1826 6253 4.345288 CACACAATATGACCATTTCGCTG 58.655 43.478 0.00 0.00 0.00 5.18
1838 6265 1.229428 TTTCGCTGCTTCACCTTCTG 58.771 50.000 0.00 0.00 0.00 3.02
1858 6286 1.293924 CAGCAGGCATAAGTCCTTCG 58.706 55.000 0.00 0.00 0.00 3.79
1878 6306 2.157085 CGCCTTGTTCTTTACCGTCTTC 59.843 50.000 0.00 0.00 0.00 2.87
1900 6328 8.475639 TCTTCAATACTACTACTAGCAAAAGGG 58.524 37.037 0.00 0.00 0.00 3.95
1902 6330 7.779073 TCAATACTACTACTAGCAAAAGGGTC 58.221 38.462 0.00 0.00 0.00 4.46
1908 6336 0.605319 CTAGCAAAAGGGTCCGTGCA 60.605 55.000 13.13 0.00 39.50 4.57
1920 6348 4.135570 CGTGCATTGCAACGGAAG 57.864 55.556 13.94 0.00 41.47 3.46
1948 6379 5.163281 AGATCATAATCTCTGATGGCCAC 57.837 43.478 8.16 2.36 37.75 5.01
1951 6382 3.580022 TCATAATCTCTGATGGCCACGAT 59.420 43.478 8.16 2.28 0.00 3.73
1952 6383 2.540265 AATCTCTGATGGCCACGATC 57.460 50.000 8.16 1.67 0.00 3.69
1977 6408 2.330440 TTGCTGCATCACCGACATAT 57.670 45.000 1.84 0.00 0.00 1.78
2033 6466 8.771920 ACATTTTCTGAACTCGTCAACATATA 57.228 30.769 0.00 0.00 35.22 0.86
2035 6468 9.642312 CATTTTCTGAACTCGTCAACATATATG 57.358 33.333 11.29 11.29 35.22 1.78
2080 6513 9.965748 AAATTCGTGAACACTTTTACAAAATTG 57.034 25.926 3.51 3.93 35.46 2.32
2206 6661 3.278574 TGCCGAACATTTCTAGAATGGG 58.721 45.455 5.89 3.33 32.14 4.00
2207 6662 2.033424 GCCGAACATTTCTAGAATGGGC 59.967 50.000 12.32 12.32 32.14 5.36
2215 6670 5.418840 ACATTTCTAGAATGGGCGAACATTT 59.581 36.000 5.89 1.41 40.92 2.32
2218 6673 7.455641 TTTCTAGAATGGGCGAACATTTTTA 57.544 32.000 5.89 3.35 40.92 1.52
2219 6674 7.455641 TTCTAGAATGGGCGAACATTTTTAA 57.544 32.000 0.00 0.00 40.92 1.52
2220 6675 7.455641 TCTAGAATGGGCGAACATTTTTAAA 57.544 32.000 6.48 0.00 40.92 1.52
2221 6676 8.062065 TCTAGAATGGGCGAACATTTTTAAAT 57.938 30.769 6.48 0.00 40.92 1.40
2223 6678 7.595311 AGAATGGGCGAACATTTTTAAATTC 57.405 32.000 6.48 0.00 40.92 2.17
2224 6679 6.310224 AGAATGGGCGAACATTTTTAAATTCG 59.690 34.615 14.38 14.38 40.92 3.34
2246 6705 6.205784 TCGTGGAACAATTTCTGAAATTCAC 58.794 36.000 22.00 22.36 44.16 3.18
2247 6706 5.976534 CGTGGAACAATTTCTGAAATTCACA 59.023 36.000 27.07 19.75 44.16 3.58
2250 6709 8.663911 GTGGAACAATTTCTGAAATTCACAAAA 58.336 29.630 25.10 11.80 44.16 2.44
2321 6796 5.180367 TCAGCGAACATTTTGTGAATGAA 57.820 34.783 5.82 0.00 0.00 2.57
2343 6818 9.807649 ATGAATAAACTATTTTTCAGGTCATGC 57.192 29.630 0.00 0.00 32.13 4.06
2345 6820 9.807649 GAATAAACTATTTTTCAGGTCATGCAT 57.192 29.630 0.00 0.00 0.00 3.96
2482 6966 9.605275 TTTGTTGAATCCACAAACATTTTATGA 57.395 25.926 8.33 0.00 0.00 2.15
2483 6967 9.775854 TTGTTGAATCCACAAACATTTTATGAT 57.224 25.926 0.00 0.00 0.00 2.45
2484 6968 9.775854 TGTTGAATCCACAAACATTTTATGATT 57.224 25.926 0.00 0.00 0.00 2.57
2486 6970 9.993454 TTGAATCCACAAACATTTTATGATTCA 57.007 25.926 0.00 0.00 42.79 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.725110 TCGTAAACGAGTAGATCTACACC 57.275 43.478 29.85 20.64 44.22 4.16
25 26 7.698836 AGTGTTGCATATTTTCTGTTTCAAC 57.301 32.000 0.00 0.00 34.76 3.18
30 31 7.803189 CGACTTTAGTGTTGCATATTTTCTGTT 59.197 33.333 0.00 0.00 0.00 3.16
39 40 3.007074 TCCCACGACTTTAGTGTTGCATA 59.993 43.478 0.00 0.00 37.88 3.14
67 68 5.050490 CCTTTGTCCAGTAGGTTCATATCG 58.950 45.833 0.00 0.00 35.89 2.92
70 71 6.442541 TTTCCTTTGTCCAGTAGGTTCATA 57.557 37.500 0.00 0.00 35.89 2.15
79 80 6.070824 ACTGTTTGAAATTTCCTTTGTCCAGT 60.071 34.615 15.48 13.06 0.00 4.00
81 82 6.293004 ACTGTTTGAAATTTCCTTTGTCCA 57.707 33.333 15.48 2.54 0.00 4.02
83 84 6.255670 GTGGACTGTTTGAAATTTCCTTTGTC 59.744 38.462 15.48 14.86 0.00 3.18
98 99 2.177580 CGCACACGGTGGACTGTTT 61.178 57.895 13.48 0.00 33.64 2.83
137 138 6.148948 TCGTGTTCATTTGAAGCTATTTTGG 58.851 36.000 0.00 0.00 34.27 3.28
145 146 6.019961 TGTTCAATTTCGTGTTCATTTGAAGC 60.020 34.615 0.00 0.00 34.73 3.86
149 150 9.566624 GTAAATGTTCAATTTCGTGTTCATTTG 57.433 29.630 0.00 0.00 36.04 2.32
159 160 6.848800 TCGTTCACTGTAAATGTTCAATTTCG 59.151 34.615 0.00 0.00 0.00 3.46
160 161 8.555166 TTCGTTCACTGTAAATGTTCAATTTC 57.445 30.769 0.00 0.00 0.00 2.17
175 176 6.516355 CGATCAATTTGTAGTTTCGTTCACTG 59.484 38.462 0.00 0.00 0.00 3.66
203 204 4.936891 TCTCGATGTTGTGGTCTCATATG 58.063 43.478 0.00 0.00 0.00 1.78
204 205 5.536260 CATCTCGATGTTGTGGTCTCATAT 58.464 41.667 0.00 0.00 34.23 1.78
205 206 4.737649 GCATCTCGATGTTGTGGTCTCATA 60.738 45.833 8.54 0.00 40.80 2.15
274 275 8.463607 TCTCCGTTTATTGGTCAATTTTAATCC 58.536 33.333 1.28 0.00 32.50 3.01
288 289 9.595823 TTAACTCCTAATCTTCTCCGTTTATTG 57.404 33.333 0.00 0.00 0.00 1.90
295 296 5.962433 TGTGTTAACTCCTAATCTTCTCCG 58.038 41.667 7.22 0.00 0.00 4.63
382 383 2.703675 AAAGCTGCAGACCTGGGTGG 62.704 60.000 20.43 0.00 42.93 4.61
398 399 3.589988 ACCAGACTCAAGCGATGTAAAG 58.410 45.455 0.00 0.00 0.00 1.85
410 411 3.751175 CCATTTTTAGCGAACCAGACTCA 59.249 43.478 0.00 0.00 0.00 3.41
419 420 3.927758 TCGATTCGACCATTTTTAGCGAA 59.072 39.130 4.29 0.00 43.78 4.70
421 422 3.550275 TCTCGATTCGACCATTTTTAGCG 59.450 43.478 4.29 0.00 0.00 4.26
423 424 6.648725 AACTCTCGATTCGACCATTTTTAG 57.351 37.500 4.29 0.00 0.00 1.85
426 427 5.238583 AGAAACTCTCGATTCGACCATTTT 58.761 37.500 4.29 2.73 0.00 1.82
430 431 4.008330 ACTAGAAACTCTCGATTCGACCA 58.992 43.478 4.29 0.00 0.00 4.02
451 452 1.296715 CACCCTCAGTGTGGCCTAC 59.703 63.158 3.32 3.05 41.93 3.18
474 476 6.882610 TTGGATGTATAGGCAATGATGTTC 57.117 37.500 0.00 0.00 0.00 3.18
489 511 6.665474 GCAAAAATCATGCATTTGGATGTA 57.335 33.333 11.17 0.64 43.25 2.29
515 537 2.040544 GGTCCAACCAGACCGCATG 61.041 63.158 0.00 0.00 46.57 4.06
516 538 2.351276 GGTCCAACCAGACCGCAT 59.649 61.111 0.00 0.00 46.57 4.73
522 544 1.296392 CGCATGAGGTCCAACCAGA 59.704 57.895 0.00 0.00 41.95 3.86
557 728 3.680490 TCGCATGTCCCTTATGTCAAAA 58.320 40.909 0.00 0.00 0.00 2.44
561 732 2.061773 CGATCGCATGTCCCTTATGTC 58.938 52.381 0.26 0.00 0.00 3.06
562 733 1.270305 CCGATCGCATGTCCCTTATGT 60.270 52.381 10.32 0.00 0.00 2.29
563 734 1.270305 ACCGATCGCATGTCCCTTATG 60.270 52.381 10.32 0.00 0.00 1.90
564 735 1.000955 GACCGATCGCATGTCCCTTAT 59.999 52.381 10.32 0.00 0.00 1.73
565 736 0.387929 GACCGATCGCATGTCCCTTA 59.612 55.000 10.32 0.00 0.00 2.69
569 740 1.592669 CCTGACCGATCGCATGTCC 60.593 63.158 10.32 0.00 0.00 4.02
570 741 0.384309 TACCTGACCGATCGCATGTC 59.616 55.000 10.32 12.53 0.00 3.06
571 742 1.040646 ATACCTGACCGATCGCATGT 58.959 50.000 10.32 9.02 0.00 3.21
572 743 1.422388 CATACCTGACCGATCGCATG 58.578 55.000 10.32 3.07 0.00 4.06
573 744 0.319900 GCATACCTGACCGATCGCAT 60.320 55.000 10.32 0.00 0.00 4.73
576 747 1.202417 ACTTGCATACCTGACCGATCG 60.202 52.381 8.51 8.51 0.00 3.69
580 751 2.665649 TACACTTGCATACCTGACCG 57.334 50.000 0.00 0.00 0.00 4.79
581 752 4.408182 AGATACACTTGCATACCTGACC 57.592 45.455 0.00 0.00 0.00 4.02
582 753 6.647067 GGATTAGATACACTTGCATACCTGAC 59.353 42.308 0.00 0.00 0.00 3.51
584 755 5.635280 CGGATTAGATACACTTGCATACCTG 59.365 44.000 0.00 0.00 0.00 4.00
585 756 5.538813 TCGGATTAGATACACTTGCATACCT 59.461 40.000 0.00 0.00 0.00 3.08
586 757 5.634020 GTCGGATTAGATACACTTGCATACC 59.366 44.000 0.00 0.00 0.00 2.73
587 758 5.342525 CGTCGGATTAGATACACTTGCATAC 59.657 44.000 0.00 0.00 0.00 2.39
588 759 5.458015 CGTCGGATTAGATACACTTGCATA 58.542 41.667 0.00 0.00 0.00 3.14
589 760 4.299155 CGTCGGATTAGATACACTTGCAT 58.701 43.478 0.00 0.00 0.00 3.96
590 761 3.490249 CCGTCGGATTAGATACACTTGCA 60.490 47.826 4.91 0.00 0.00 4.08
591 762 3.050619 CCGTCGGATTAGATACACTTGC 58.949 50.000 4.91 0.00 0.00 4.01
592 763 3.050619 GCCGTCGGATTAGATACACTTG 58.949 50.000 17.49 0.00 0.00 3.16
683 1873 7.662761 CGTTTCTCGTTTTTCTTGACAAAAAT 58.337 30.769 0.00 0.00 37.52 1.82
801 2008 0.173255 CTTACATTTGCAAGCCGGGG 59.827 55.000 2.18 0.00 0.00 5.73
818 2025 2.418197 CGGTATGGACATGTCGTTCCTT 60.418 50.000 19.33 7.27 0.00 3.36
895 2107 1.200252 AGAGAGTGACGACATGGTTCG 59.800 52.381 4.33 4.33 44.87 3.95
911 2123 3.396276 AGTCGATAAGATGGAGGGAGAGA 59.604 47.826 0.00 0.00 0.00 3.10
1044 2268 0.886490 GGTGGTGTTGTGCTGGAGAG 60.886 60.000 0.00 0.00 0.00 3.20
1046 2270 1.152984 TGGTGGTGTTGTGCTGGAG 60.153 57.895 0.00 0.00 0.00 3.86
1048 2272 1.727511 CTGTGGTGGTGTTGTGCTGG 61.728 60.000 0.00 0.00 0.00 4.85
1049 2273 1.729276 CTGTGGTGGTGTTGTGCTG 59.271 57.895 0.00 0.00 0.00 4.41
1050 2274 2.120909 GCTGTGGTGGTGTTGTGCT 61.121 57.895 0.00 0.00 0.00 4.40
1051 2275 2.120909 AGCTGTGGTGGTGTTGTGC 61.121 57.895 0.00 0.00 0.00 4.57
1053 2277 2.120909 GCAGCTGTGGTGGTGTTGT 61.121 57.895 16.64 0.00 37.70 3.32
1055 2279 0.756442 ATTGCAGCTGTGGTGGTGTT 60.756 50.000 16.64 0.00 37.70 3.32
1056 2280 1.152694 ATTGCAGCTGTGGTGGTGT 60.153 52.632 16.64 0.00 37.70 4.16
1058 2282 1.904865 CCATTGCAGCTGTGGTGGT 60.905 57.895 16.64 0.00 0.00 4.16
1059 2283 2.967397 CCATTGCAGCTGTGGTGG 59.033 61.111 16.64 16.01 0.00 4.61
1061 2285 2.993264 GGCCATTGCAGCTGTGGT 60.993 61.111 19.77 2.84 40.13 4.16
1064 2288 2.576832 GGTTGGCCATTGCAGCTGT 61.577 57.895 16.64 0.00 40.13 4.40
1256 2523 2.350498 GCATAACCTGCGAAACGTACAT 59.650 45.455 0.00 0.00 41.97 2.29
1504 2783 6.867662 ATTCATACATAAGTAGCAGCAACC 57.132 37.500 0.00 0.00 32.86 3.77
1547 2911 1.271656 AGTTGTGGTAGAGGTGTACGC 59.728 52.381 0.00 0.00 0.00 4.42
1558 2935 6.181908 ACCAAAGTTAACTTGAGTTGTGGTA 58.818 36.000 27.26 0.00 38.90 3.25
1564 2941 7.777095 TGCAAATACCAAAGTTAACTTGAGTT 58.223 30.769 21.22 9.88 41.73 3.01
1576 2953 4.423732 CGAGGGAAATGCAAATACCAAAG 58.576 43.478 6.17 0.00 0.00 2.77
1590 2980 1.002659 TCGATCCTTTTGCGAGGGAAA 59.997 47.619 2.45 0.00 37.41 3.13
1615 3013 3.818210 ACAGACTGACACTGACAGACTAG 59.182 47.826 10.08 10.44 38.01 2.57
1621 3019 3.195610 ACAAAGACAGACTGACACTGACA 59.804 43.478 10.08 0.00 38.55 3.58
1622 3020 3.786635 ACAAAGACAGACTGACACTGAC 58.213 45.455 10.08 0.00 38.55 3.51
1623 3021 4.202121 GGTACAAAGACAGACTGACACTGA 60.202 45.833 10.08 0.00 38.55 3.41
1624 3022 4.051922 GGTACAAAGACAGACTGACACTG 58.948 47.826 10.08 7.05 40.68 3.66
1625 3023 3.704566 TGGTACAAAGACAGACTGACACT 59.295 43.478 10.08 2.79 31.92 3.55
1626 3024 4.051922 CTGGTACAAAGACAGACTGACAC 58.948 47.826 10.08 0.38 38.70 3.67
1627 3025 3.492656 GCTGGTACAAAGACAGACTGACA 60.493 47.826 10.08 0.00 38.70 3.58
1662 3060 1.098712 GCACGACCAACTGACCCAAA 61.099 55.000 0.00 0.00 0.00 3.28
1667 3065 1.512926 ATCAAGCACGACCAACTGAC 58.487 50.000 0.00 0.00 0.00 3.51
1712 6138 2.517959 TCAGGCACAATCAAGGAAAGG 58.482 47.619 0.00 0.00 0.00 3.11
1766 6192 1.828331 GCGACACACGGACCAAACTC 61.828 60.000 0.00 0.00 42.83 3.01
1798 6225 3.719268 TGGTCATATTGTGTGCTCCTT 57.281 42.857 0.00 0.00 0.00 3.36
1804 6231 4.345288 CAGCGAAATGGTCATATTGTGTG 58.655 43.478 0.00 0.00 0.00 3.82
1838 6265 1.020437 GAAGGACTTATGCCTGCTGC 58.980 55.000 0.00 0.00 35.50 5.25
1841 6268 1.440145 GGCGAAGGACTTATGCCTGC 61.440 60.000 16.33 0.00 39.62 4.85
1848 6275 3.764237 AAGAACAAGGCGAAGGACTTA 57.236 42.857 0.00 0.00 40.42 2.24
1858 6286 3.135994 TGAAGACGGTAAAGAACAAGGC 58.864 45.455 0.00 0.00 0.00 4.35
1878 6306 6.985059 GGACCCTTTTGCTAGTAGTAGTATTG 59.015 42.308 6.47 0.00 0.00 1.90
1902 6330 1.442520 CTTCCGTTGCAATGCACGG 60.443 57.895 29.56 29.56 46.29 4.94
1927 6358 3.931468 CGTGGCCATCAGAGATTATGATC 59.069 47.826 9.72 0.00 35.20 2.92
1938 6369 4.790878 CAAAATATGATCGTGGCCATCAG 58.209 43.478 9.72 3.76 33.74 2.90
1939 6370 3.004629 GCAAAATATGATCGTGGCCATCA 59.995 43.478 9.72 9.83 34.74 3.07
1940 6371 3.254166 AGCAAAATATGATCGTGGCCATC 59.746 43.478 9.72 2.51 0.00 3.51
1948 6379 4.224433 GGTGATGCAGCAAAATATGATCG 58.776 43.478 6.05 0.00 0.00 3.69
1951 6382 3.065233 GTCGGTGATGCAGCAAAATATGA 59.935 43.478 6.05 0.00 0.00 2.15
1952 6383 3.181498 TGTCGGTGATGCAGCAAAATATG 60.181 43.478 6.05 0.00 0.00 1.78
1998 6429 8.137437 ACGAGTTCAGAAAATGTTCATGATTTT 58.863 29.630 5.42 5.42 36.04 1.82
2006 6437 5.806286 TGTTGACGAGTTCAGAAAATGTTC 58.194 37.500 0.00 0.00 34.94 3.18
2015 6446 9.034544 TGATTTCATATATGTTGACGAGTTCAG 57.965 33.333 12.42 0.00 34.94 3.02
2016 6447 8.940768 TGATTTCATATATGTTGACGAGTTCA 57.059 30.769 12.42 2.67 0.00 3.18
2017 6448 9.803130 CATGATTTCATATATGTTGACGAGTTC 57.197 33.333 12.42 0.51 34.26 3.01
2048 6481 9.193133 TGTAAAAGTGTTCACGAATTTGAAAAA 57.807 25.926 0.00 0.00 37.24 1.94
2049 6482 8.744008 TGTAAAAGTGTTCACGAATTTGAAAA 57.256 26.923 0.00 0.00 37.24 2.29
2163 6618 9.037737 CGGCAATTCATGAAAATTGATAGAAAT 57.962 29.630 20.81 0.00 45.40 2.17
2165 6620 7.770201 TCGGCAATTCATGAAAATTGATAGAA 58.230 30.769 20.81 3.57 45.40 2.10
2167 6622 7.488792 TGTTCGGCAATTCATGAAAATTGATAG 59.511 33.333 20.81 12.57 45.40 2.08
2170 6625 5.536260 TGTTCGGCAATTCATGAAAATTGA 58.464 33.333 20.81 10.17 45.40 2.57
2179 6634 6.757897 TTCTAGAAATGTTCGGCAATTCAT 57.242 33.333 1.68 0.00 38.98 2.57
2185 6640 3.278574 CCCATTCTAGAAATGTTCGGCA 58.721 45.455 9.71 0.00 34.02 5.69
2186 6641 2.033424 GCCCATTCTAGAAATGTTCGGC 59.967 50.000 9.71 11.85 34.02 5.54
2187 6642 2.287915 CGCCCATTCTAGAAATGTTCGG 59.712 50.000 9.71 6.75 34.02 4.30
2206 6661 6.074782 TGTTCCACGAATTTAAAAATGTTCGC 60.075 34.615 17.28 5.79 33.96 4.70
2207 6662 7.383050 TGTTCCACGAATTTAAAAATGTTCG 57.617 32.000 16.24 16.24 35.72 3.95
2215 6670 9.587772 TTTCAGAAATTGTTCCACGAATTTAAA 57.412 25.926 0.00 0.00 33.03 1.52
2218 6673 8.661352 AATTTCAGAAATTGTTCCACGAATTT 57.339 26.923 18.63 0.00 39.50 1.82
2219 6674 7.925483 TGAATTTCAGAAATTGTTCCACGAATT 59.075 29.630 23.27 0.00 40.97 2.17
2220 6675 7.382218 GTGAATTTCAGAAATTGTTCCACGAAT 59.618 33.333 23.27 0.00 40.97 3.34
2221 6676 6.695278 GTGAATTTCAGAAATTGTTCCACGAA 59.305 34.615 23.27 0.00 40.97 3.85
2223 6678 5.976534 TGTGAATTTCAGAAATTGTTCCACG 59.023 36.000 23.27 0.00 40.97 4.94
2224 6679 7.769272 TTGTGAATTTCAGAAATTGTTCCAC 57.231 32.000 23.27 21.90 40.97 4.02
2263 6737 9.004717 TGATCATGCATTTGAAAAATGTTCATT 57.995 25.926 12.82 0.00 0.00 2.57
2265 6739 7.964604 TGATCATGCATTTGAAAAATGTTCA 57.035 28.000 12.82 5.40 0.00 3.18
2295 6770 4.827304 TCACAAAATGTTCGCTGATTCA 57.173 36.364 0.00 0.00 0.00 2.57
2333 6808 8.800370 TGTATTAAAAAGTATGCATGACCTGA 57.200 30.769 10.16 0.00 0.00 3.86
2448 6932 3.505293 TGTGGATTCAACAAATGATCGCA 59.495 39.130 0.00 0.00 38.03 5.10
2456 6940 9.605275 TCATAAAATGTTTGTGGATTCAACAAA 57.395 25.926 14.13 14.13 0.00 2.83


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

AutoCloner maintained by Alex Coulton.