Multiple sequence alignment - TraesCS2D01G259300

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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 TraesCS2D01G259300 chr2D 100.000 7861 0 0 1 7861 315413730 315421590 0.000000e+00 14517.0
1 TraesCS2D01G259300 chr2D 100.000 130 0 0 7732 7861 28836148 28836019 2.830000e-59 241.0
2 TraesCS2D01G259300 chr2B 97.245 6207 135 21 689 6882 383273605 383279788 0.000000e+00 10482.0
3 TraesCS2D01G259300 chr2B 95.668 831 26 5 6898 7728 383279774 383280594 0.000000e+00 1327.0
4 TraesCS2D01G259300 chr2A 97.029 4376 93 13 1741 6085 419651947 419647578 0.000000e+00 7326.0
5 TraesCS2D01G259300 chr2A 97.701 783 16 2 677 1459 419654225 419653445 0.000000e+00 1345.0
6 TraesCS2D01G259300 chr2A 98.663 748 10 0 6138 6885 419647577 419646830 0.000000e+00 1327.0
7 TraesCS2D01G259300 chr2A 94.737 836 34 7 6898 7730 419646847 419646019 0.000000e+00 1291.0
8 TraesCS2D01G259300 chr2A 95.076 264 7 2 1486 1749 419653448 419653191 2.040000e-110 411.0
9 TraesCS2D01G259300 chr2A 94.872 39 1 1 4521 4559 43502298 43502335 8.520000e-05 60.2
10 TraesCS2D01G259300 chr4B 89.731 633 55 8 49 673 585685026 585684396 0.000000e+00 800.0
11 TraesCS2D01G259300 chr4B 90.580 276 18 7 1044 1312 74853015 74852741 7.500000e-95 359.0
12 TraesCS2D01G259300 chr4B 85.597 243 28 6 80 321 117022102 117021866 1.690000e-61 248.0
13 TraesCS2D01G259300 chr4B 79.372 223 28 15 4673 4884 95703758 95703973 2.960000e-29 141.0
14 TraesCS2D01G259300 chr4B 85.047 107 16 0 4162 4268 95676082 95676188 8.340000e-20 110.0
15 TraesCS2D01G259300 chr4B 96.078 51 2 0 3 53 585693824 585693774 5.050000e-12 84.2
16 TraesCS2D01G259300 chr5A 83.871 682 87 17 4 673 261913998 261913328 5.180000e-176 628.0
17 TraesCS2D01G259300 chr5A 72.578 733 161 32 2363 3079 594143762 594143054 3.720000e-48 204.0
18 TraesCS2D01G259300 chr5A 96.000 50 2 0 1248 1297 625752797 625752748 1.820000e-11 82.4
19 TraesCS2D01G259300 chr5A 97.727 44 1 0 1254 1297 605801924 605801881 8.460000e-10 76.8
20 TraesCS2D01G259300 chr5B 78.822 628 88 31 81 675 109768808 109768193 1.600000e-101 381.0
21 TraesCS2D01G259300 chr5B 72.245 735 160 35 2363 3079 582165323 582164615 3.750000e-43 187.0
22 TraesCS2D01G259300 chr4D 89.552 201 21 0 5449 5649 65145950 65146150 1.010000e-63 255.0
23 TraesCS2D01G259300 chr4D 85.981 107 15 0 4162 4268 65126859 65126965 1.790000e-21 115.0
24 TraesCS2D01G259300 chr5D 72.192 730 169 28 2363 3079 475013842 475013134 8.050000e-45 193.0
25 TraesCS2D01G259300 chr5D 89.655 58 4 2 7734 7790 350684289 350684345 1.090000e-08 73.1
26 TraesCS2D01G259300 chr6B 96.154 52 2 0 1246 1297 539277904 539277853 1.410000e-12 86.1
27 TraesCS2D01G259300 chr1D 94.231 52 3 0 1246 1297 90393942 90393891 6.540000e-11 80.5
28 TraesCS2D01G259300 chr6A 95.745 47 2 0 1248 1294 212355948 212355994 8.460000e-10 76.8
29 TraesCS2D01G259300 chr3D 95.833 48 1 1 627 674 37671363 37671317 8.460000e-10 76.8
30 TraesCS2D01G259300 chr1B 92.308 52 4 0 1246 1297 453199756 453199705 3.040000e-09 75.0
31 TraesCS2D01G259300 chr3A 89.286 56 6 0 618 673 662511909 662511964 3.940000e-08 71.3
32 TraesCS2D01G259300 chr6D 90.000 50 3 2 7679 7727 69917059 69917107 6.590000e-06 63.9


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 TraesCS2D01G259300 chr2D 315413730 315421590 7860 False 14517.0 14517 100.0000 1 7861 1 chr2D.!!$F1 7860
1 TraesCS2D01G259300 chr2B 383273605 383280594 6989 False 5904.5 10482 96.4565 689 7728 2 chr2B.!!$F1 7039
2 TraesCS2D01G259300 chr2A 419646019 419654225 8206 True 2340.0 7326 96.6412 677 7730 5 chr2A.!!$R1 7053
3 TraesCS2D01G259300 chr4B 585684396 585685026 630 True 800.0 800 89.7310 49 673 1 chr4B.!!$R3 624
4 TraesCS2D01G259300 chr5A 261913328 261913998 670 True 628.0 628 83.8710 4 673 1 chr5A.!!$R1 669
5 TraesCS2D01G259300 chr5A 594143054 594143762 708 True 204.0 204 72.5780 2363 3079 1 chr5A.!!$R2 716
6 TraesCS2D01G259300 chr5B 109768193 109768808 615 True 381.0 381 78.8220 81 675 1 chr5B.!!$R1 594

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
550 608 0.810031 GCGATATGCGTTGACCCAGT 60.810 55.000 0.00 0.00 43.41 4.00 F
616 676 1.071542 TCCACGAAAGGCAATCAGACA 59.928 47.619 0.00 0.00 0.00 3.41 F
1453 1513 2.034376 AGCTGGAGACGACGGACT 59.966 61.111 0.00 0.00 0.00 3.85 F
2019 3374 1.068610 TGGTTTACCTCCGTTCGTACG 60.069 52.381 9.53 9.53 41.21 3.67 F
3376 4743 3.152341 AGCACCTTTCTGAGAATTGGTG 58.848 45.455 28.24 28.24 45.33 4.17 F
4137 5505 4.024218 GCACTCCTGCATTTGATATCACTC 60.024 45.833 4.48 0.00 43.62 3.51 F
4605 5984 4.094294 TGGACTTGTTTTTGAGTCGAACAG 59.906 41.667 0.00 0.00 42.46 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1541 0.036765 TATTTGCAACGACGCCCTCT 60.037 50.000 0.00 0.00 0.00 3.69 R
1482 1542 0.096454 GTATTTGCAACGACGCCCTC 59.904 55.000 0.00 0.00 0.00 4.30 R
2255 3619 1.004440 GTCTGACCTGTCACCCTGC 60.004 63.158 0.00 0.00 35.46 4.85 R
3908 5276 0.452987 GTGCATGATGGTTGATGCGT 59.547 50.000 0.00 0.00 46.66 5.24 R
4719 6098 3.037549 TCAAAAATTTGTGGAGTGGCCT 58.962 40.909 8.51 0.00 39.18 5.19 R
5983 7363 1.072331 CTACCACAGAAACACAGGCCT 59.928 52.381 0.00 0.00 0.00 5.19 R
6872 8252 2.357327 TTTGAGACAATGCATGCAGC 57.643 45.000 26.69 14.59 45.96 5.25 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
19 20 2.024871 TTTTTGTTGCGACCGCCG 59.975 55.556 12.08 0.00 41.09 6.46
69 71 6.454795 GTGGCAAGAACAATCATTTTTCCTA 58.545 36.000 0.00 0.00 0.00 2.94
72 74 6.587608 GGCAAGAACAATCATTTTTCCTACAG 59.412 38.462 0.00 0.00 0.00 2.74
83 85 6.266558 TCATTTTTCCTACAGCTGCCTTTTTA 59.733 34.615 15.27 0.00 0.00 1.52
235 246 3.139077 ACGACCAGAGACACCATTTTTC 58.861 45.455 0.00 0.00 0.00 2.29
310 327 1.742761 CGAAGCAGATGTGGATGGTT 58.257 50.000 0.00 0.00 39.67 3.67
330 347 4.096382 GGTTGTCGGAAGTATTGCAATCAT 59.904 41.667 16.86 2.52 35.47 2.45
367 413 1.522092 CGGGGTAGAGCTGCAATCA 59.478 57.895 1.02 0.00 0.00 2.57
413 460 1.139520 GCATCCGTGTTGCAATCCC 59.860 57.895 0.59 0.00 39.90 3.85
506 562 2.094494 GGACGACACATGTGAGATGAGT 60.094 50.000 31.94 19.21 0.00 3.41
524 582 3.695060 TGAGTTAAGGTTAGCGGAGAGAG 59.305 47.826 0.00 0.00 0.00 3.20
550 608 0.810031 GCGATATGCGTTGACCCAGT 60.810 55.000 0.00 0.00 43.41 4.00
552 610 1.739035 CGATATGCGTTGACCCAGTGT 60.739 52.381 0.00 0.00 34.64 3.55
561 619 1.841556 GACCCAGTGTGGTGGAGGA 60.842 63.158 7.90 0.00 40.44 3.71
575 633 3.413327 GTGGAGGAGGAGAAAGAAAACC 58.587 50.000 0.00 0.00 0.00 3.27
604 664 1.141645 CATCGAACGGTTCCACGAAA 58.858 50.000 14.83 0.00 38.22 3.46
616 676 1.071542 TCCACGAAAGGCAATCAGACA 59.928 47.619 0.00 0.00 0.00 3.41
694 754 2.877691 GCCAAACTCATGCGGACC 59.122 61.111 0.00 0.00 0.00 4.46
750 810 4.387598 CCATCAGTGGCAAAAATGGAAAA 58.612 39.130 14.82 0.00 39.39 2.29
786 846 2.049156 CTGGCGCGAGTTGACTGA 60.049 61.111 12.10 0.00 0.00 3.41
1037 1097 2.125512 CTCCAAGACCGCCTTCCG 60.126 66.667 0.00 0.00 31.42 4.30
1108 1168 4.056125 CCACCTCGCGCTCACAGA 62.056 66.667 5.56 0.00 0.00 3.41
1453 1513 2.034376 AGCTGGAGACGACGGACT 59.966 61.111 0.00 0.00 0.00 3.85
1521 1614 7.730364 AATACCGAGGTAATGTTGATTCATC 57.270 36.000 6.04 0.00 33.99 2.92
1522 1615 5.097742 ACCGAGGTAATGTTGATTCATCA 57.902 39.130 0.00 0.11 34.44 3.07
1523 1616 5.684704 ACCGAGGTAATGTTGATTCATCAT 58.315 37.500 4.68 4.68 36.56 2.45
1707 1800 5.053145 GGATTGACATGTGTAGGAAGCTAG 58.947 45.833 1.15 0.00 0.00 3.42
1708 1801 5.395768 GGATTGACATGTGTAGGAAGCTAGT 60.396 44.000 1.15 0.00 0.00 2.57
1709 1802 6.183360 GGATTGACATGTGTAGGAAGCTAGTA 60.183 42.308 1.15 0.00 0.00 1.82
1842 3189 2.308570 TGCAATCCAACCATCTACAGGT 59.691 45.455 0.00 0.00 42.34 4.00
1866 3213 5.834169 AGAAGTAGCTAATAGTCGAAAGCC 58.166 41.667 0.00 0.00 35.54 4.35
1925 3280 4.175962 AGGTTAGAAATGAAGGGACAGGA 58.824 43.478 0.00 0.00 0.00 3.86
2019 3374 1.068610 TGGTTTACCTCCGTTCGTACG 60.069 52.381 9.53 9.53 41.21 3.67
2255 3619 5.064707 CGGGTTCTTACTAATCATGTGGTTG 59.935 44.000 0.00 0.00 0.00 3.77
3146 4513 3.802866 TGCAAAAACAGGGAATTTGACC 58.197 40.909 1.95 0.00 36.41 4.02
3374 4741 4.154918 GTGTAGCACCTTTCTGAGAATTGG 59.845 45.833 11.53 11.53 0.00 3.16
3376 4743 3.152341 AGCACCTTTCTGAGAATTGGTG 58.848 45.455 28.24 28.24 45.33 4.17
3955 5323 9.636789 ACTTACCCTTGTCTGTTTATTTTACTT 57.363 29.630 0.00 0.00 0.00 2.24
3973 5341 7.633193 TTTACTTTGTTCTGGCTGAGTTTAA 57.367 32.000 0.00 0.00 0.00 1.52
4008 5376 4.221926 TGGTTGTGTGAATGTTCATTCG 57.778 40.909 17.09 0.00 39.73 3.34
4042 5410 8.049117 ACTTGCTCTAGATGAATTTACATTGGA 58.951 33.333 0.00 0.00 0.00 3.53
4137 5505 4.024218 GCACTCCTGCATTTGATATCACTC 60.024 45.833 4.48 0.00 43.62 3.51
4378 5746 6.238842 CCAACTGAGGCAACCATCTAAATATG 60.239 42.308 0.00 0.00 37.17 1.78
4379 5747 6.006275 ACTGAGGCAACCATCTAAATATGT 57.994 37.500 0.00 0.00 37.17 2.29
4380 5748 6.058183 ACTGAGGCAACCATCTAAATATGTC 58.942 40.000 0.00 0.00 37.17 3.06
4382 5750 7.071196 ACTGAGGCAACCATCTAAATATGTCTA 59.929 37.037 0.00 0.00 37.17 2.59
4383 5751 7.445121 TGAGGCAACCATCTAAATATGTCTAG 58.555 38.462 0.00 0.00 37.17 2.43
4384 5752 6.234177 AGGCAACCATCTAAATATGTCTAGC 58.766 40.000 0.00 0.00 37.17 3.42
4386 5754 6.656693 GGCAACCATCTAAATATGTCTAGCAT 59.343 38.462 5.25 5.25 41.42 3.79
4391 5759 8.803235 ACCATCTAAATATGTCTAGCATTACGA 58.197 33.333 5.22 0.00 38.94 3.43
4392 5760 9.809096 CCATCTAAATATGTCTAGCATTACGAT 57.191 33.333 5.22 0.88 38.94 3.73
4585 5964 9.559732 CAGAACCAATAATTACAGATGTATGGA 57.440 33.333 13.79 0.00 32.68 3.41
4605 5984 4.094294 TGGACTTGTTTTTGAGTCGAACAG 59.906 41.667 0.00 0.00 42.46 3.16
4719 6098 7.499321 TCCGCAATAACTTTGTTAAGAGAAA 57.501 32.000 0.00 0.00 35.30 2.52
4985 6364 4.388485 TGGATTGCATACATACGATTGCT 58.612 39.130 0.00 0.00 36.10 3.91
5049 6428 5.165961 AGTACACTATCCAAAGCATGTGT 57.834 39.130 0.00 0.00 40.90 3.72
5242 6621 4.412858 TGGTTCCCCTAACAAAAGTAGACA 59.587 41.667 0.00 0.00 40.08 3.41
5393 6773 5.227569 TGGTGACTCTTTATTCAGCAGAA 57.772 39.130 0.00 0.00 43.48 3.02
5893 7273 7.148018 TGCATGATATTCTCAAAGAAAAGGTCC 60.148 37.037 0.00 0.00 37.82 4.46
6121 7501 5.680619 TGGTAATCTGGGTATGAACATCAC 58.319 41.667 0.00 0.00 0.00 3.06
6868 8248 8.554490 AAGGAGGTTCTCTTCTAAGCATATAA 57.446 34.615 0.00 0.00 29.15 0.98
6869 8249 8.189119 AGGAGGTTCTCTTCTAAGCATATAAG 57.811 38.462 0.00 0.00 26.83 1.73
6870 8250 7.234577 AGGAGGTTCTCTTCTAAGCATATAAGG 59.765 40.741 0.00 0.00 26.83 2.69
6871 8251 7.015779 GGAGGTTCTCTTCTAAGCATATAAGGT 59.984 40.741 0.00 0.00 0.00 3.50
6872 8252 7.731054 AGGTTCTCTTCTAAGCATATAAGGTG 58.269 38.462 0.00 0.00 0.00 4.00
6873 8253 6.425417 GGTTCTCTTCTAAGCATATAAGGTGC 59.575 42.308 0.00 0.00 42.81 5.01
6880 8260 2.342910 GCATATAAGGTGCTGCATGC 57.657 50.000 11.82 11.82 39.45 4.06
6891 8271 2.357327 GCTGCATGCATTGTCTCAAA 57.643 45.000 22.97 0.00 42.31 2.69
6892 8272 2.679450 GCTGCATGCATTGTCTCAAAA 58.321 42.857 22.97 0.00 42.31 2.44
6893 8273 3.061322 GCTGCATGCATTGTCTCAAAAA 58.939 40.909 22.97 0.00 42.31 1.94
7027 8407 9.554395 GAAAGAAAGGAAATATAAGAGAGGGAG 57.446 37.037 0.00 0.00 0.00 4.30
7063 8443 7.111353 CGCAGCTAGAAACTTTATAAGGATC 57.889 40.000 0.98 0.10 0.00 3.36
7117 8497 2.494888 TCCATGCAGATCCCTTCCTA 57.505 50.000 0.00 0.00 0.00 2.94
7135 8515 3.067106 CCTACACCAACAGTCATGTGAC 58.933 50.000 5.01 5.01 45.08 3.67
7156 8542 6.801377 GTGACAGAAAACATCAATATTTCGCA 59.199 34.615 0.00 0.00 37.95 5.10
7158 8544 7.094848 TGACAGAAAACATCAATATTTCGCAGA 60.095 33.333 0.00 0.00 37.95 4.26
7160 8546 6.193410 CAGAAAACATCAATATTTCGCAGACG 59.807 38.462 0.00 0.00 37.95 4.18
7161 8547 3.592381 ACATCAATATTTCGCAGACGC 57.408 42.857 0.00 0.00 39.84 5.19
7162 8548 2.287915 ACATCAATATTTCGCAGACGCC 59.712 45.455 0.00 0.00 39.84 5.68
7163 8549 0.927537 TCAATATTTCGCAGACGCCG 59.072 50.000 0.00 0.00 39.84 6.46
7164 8550 0.650512 CAATATTTCGCAGACGCCGT 59.349 50.000 0.00 0.00 39.84 5.68
7165 8551 0.928229 AATATTTCGCAGACGCCGTC 59.072 50.000 9.71 9.71 39.84 4.79
7231 8617 1.003812 CCCCACAGTTTATCGGGTTGA 59.996 52.381 0.00 0.00 36.92 3.18
7294 8680 3.686726 GGCTGTCAAGACTCAAAGTATGG 59.313 47.826 1.53 0.00 0.00 2.74
7311 8697 2.636647 TGGTGACAACTGAATGCTGA 57.363 45.000 0.00 0.00 37.44 4.26
7605 8994 6.727394 TCTATACATTGGCCAAAAGTAACCT 58.273 36.000 27.64 18.40 0.00 3.50
7720 9109 6.311735 ACTCCCTAATTTTAAAAGCCTCACA 58.688 36.000 6.79 0.00 0.00 3.58
7730 9119 6.855763 TTAAAAGCCTCACAATCAATGGAT 57.144 33.333 0.00 0.00 34.43 3.41
7731 9120 5.750352 AAAAGCCTCACAATCAATGGATT 57.250 34.783 0.00 0.00 44.51 3.01
7732 9121 6.855763 AAAAGCCTCACAATCAATGGATTA 57.144 33.333 0.00 0.00 41.78 1.75
7733 9122 7.427989 AAAAGCCTCACAATCAATGGATTAT 57.572 32.000 0.00 0.00 41.78 1.28
7734 9123 7.427989 AAAGCCTCACAATCAATGGATTATT 57.572 32.000 0.00 0.00 41.78 1.40
7735 9124 7.427989 AAGCCTCACAATCAATGGATTATTT 57.572 32.000 0.00 0.00 41.78 1.40
7736 9125 7.427989 AGCCTCACAATCAATGGATTATTTT 57.572 32.000 0.00 0.00 41.78 1.82
7737 9126 8.537728 AGCCTCACAATCAATGGATTATTTTA 57.462 30.769 0.00 0.00 41.78 1.52
7738 9127 8.416329 AGCCTCACAATCAATGGATTATTTTAC 58.584 33.333 0.00 0.00 41.78 2.01
7739 9128 8.196771 GCCTCACAATCAATGGATTATTTTACA 58.803 33.333 0.00 0.00 41.78 2.41
7740 9129 9.740239 CCTCACAATCAATGGATTATTTTACAG 57.260 33.333 0.00 0.00 41.78 2.74
7745 9134 9.965824 CAATCAATGGATTATTTTACAGTACCC 57.034 33.333 0.00 0.00 41.78 3.69
7746 9135 9.936329 AATCAATGGATTATTTTACAGTACCCT 57.064 29.630 0.00 0.00 41.89 4.34
7747 9136 8.746052 TCAATGGATTATTTTACAGTACCCTG 57.254 34.615 0.00 0.00 44.68 4.45
7748 9137 7.777910 TCAATGGATTATTTTACAGTACCCTGG 59.222 37.037 0.00 0.00 43.36 4.45
7749 9138 6.645884 TGGATTATTTTACAGTACCCTGGT 57.354 37.500 0.00 0.00 43.36 4.00
7750 9139 7.752518 TGGATTATTTTACAGTACCCTGGTA 57.247 36.000 0.00 0.00 43.36 3.25
7760 9149 2.675583 GTACCCTGGTACTCCCTAAGG 58.324 57.143 17.35 0.00 45.30 2.69
7761 9150 0.342313 ACCCTGGTACTCCCTAAGGG 59.658 60.000 4.48 4.48 45.16 3.95
7762 9151 0.342313 CCCTGGTACTCCCTAAGGGT 59.658 60.000 0.00 0.00 44.74 4.34
7763 9152 1.691801 CCCTGGTACTCCCTAAGGGTC 60.692 61.905 0.00 0.00 44.74 4.46
7764 9153 1.691801 CCTGGTACTCCCTAAGGGTCC 60.692 61.905 0.00 0.00 44.74 4.46
7765 9154 1.291335 CTGGTACTCCCTAAGGGTCCT 59.709 57.143 0.00 0.00 44.74 3.85
7766 9155 1.007963 TGGTACTCCCTAAGGGTCCTG 59.992 57.143 0.00 0.00 44.74 3.86
7767 9156 1.008084 GGTACTCCCTAAGGGTCCTGT 59.992 57.143 0.00 0.00 44.74 4.00
7768 9157 2.108970 GTACTCCCTAAGGGTCCTGTG 58.891 57.143 0.00 0.00 44.74 3.66
7769 9158 0.252742 ACTCCCTAAGGGTCCTGTGG 60.253 60.000 0.00 0.00 44.74 4.17
7770 9159 0.042731 CTCCCTAAGGGTCCTGTGGA 59.957 60.000 0.00 6.30 44.74 4.02
7771 9160 0.042731 TCCCTAAGGGTCCTGTGGAG 59.957 60.000 0.00 2.33 44.74 3.86
7772 9161 0.252742 CCCTAAGGGTCCTGTGGAGT 60.253 60.000 9.25 0.00 38.25 3.85
7773 9162 1.007963 CCCTAAGGGTCCTGTGGAGTA 59.992 57.143 9.25 0.00 38.25 2.59
7774 9163 2.108970 CCTAAGGGTCCTGTGGAGTAC 58.891 57.143 3.42 0.00 29.39 2.73
7775 9164 2.108970 CTAAGGGTCCTGTGGAGTACC 58.891 57.143 0.00 0.00 29.39 3.34
7776 9165 0.192566 AAGGGTCCTGTGGAGTACCA 59.807 55.000 0.00 0.00 44.76 3.25
7789 9178 4.913784 TGGAGTACCAAGTAAATCCAACC 58.086 43.478 7.25 0.00 43.91 3.77
7790 9179 3.937079 GGAGTACCAAGTAAATCCAACCG 59.063 47.826 0.00 0.00 35.97 4.44
7791 9180 4.564199 GGAGTACCAAGTAAATCCAACCGT 60.564 45.833 0.00 0.00 35.97 4.83
7792 9181 4.320870 AGTACCAAGTAAATCCAACCGTG 58.679 43.478 0.00 0.00 0.00 4.94
7810 9199 8.857694 CAACCGTGGATATTAAAGGGTATTAT 57.142 34.615 0.00 0.00 32.04 1.28
7811 9200 9.947433 CAACCGTGGATATTAAAGGGTATTATA 57.053 33.333 0.00 0.00 32.04 0.98
7813 9202 9.551339 ACCGTGGATATTAAAGGGTATTATAGA 57.449 33.333 0.00 0.00 30.58 1.98
7841 9230 8.928270 TTTTACAATTTATGTTGGTGTTTCGT 57.072 26.923 0.00 0.00 43.63 3.85
7842 9231 8.928270 TTTACAATTTATGTTGGTGTTTCGTT 57.072 26.923 0.00 0.00 43.63 3.85
7843 9232 8.928270 TTACAATTTATGTTGGTGTTTCGTTT 57.072 26.923 0.00 0.00 43.63 3.60
7845 9234 8.928270 ACAATTTATGTTGGTGTTTCGTTTAA 57.072 26.923 0.00 0.00 40.06 1.52
7846 9235 8.809478 ACAATTTATGTTGGTGTTTCGTTTAAC 58.191 29.630 0.00 0.00 40.06 2.01
7847 9236 7.933728 ATTTATGTTGGTGTTTCGTTTAACC 57.066 32.000 0.00 0.00 0.00 2.85
7848 9237 6.696441 TTATGTTGGTGTTTCGTTTAACCT 57.304 33.333 0.00 0.00 33.65 3.50
7849 9238 7.798596 TTATGTTGGTGTTTCGTTTAACCTA 57.201 32.000 0.00 0.00 33.65 3.08
7850 9239 6.696441 ATGTTGGTGTTTCGTTTAACCTAA 57.304 33.333 0.00 0.00 33.65 2.69
7851 9240 6.121613 TGTTGGTGTTTCGTTTAACCTAAG 57.878 37.500 0.00 0.00 33.65 2.18
7852 9241 4.816786 TGGTGTTTCGTTTAACCTAAGC 57.183 40.909 0.00 0.00 33.65 3.09
7853 9242 3.565063 TGGTGTTTCGTTTAACCTAAGCC 59.435 43.478 0.00 0.00 33.65 4.35
7854 9243 3.817084 GGTGTTTCGTTTAACCTAAGCCT 59.183 43.478 0.00 0.00 0.00 4.58
7855 9244 4.996758 GGTGTTTCGTTTAACCTAAGCCTA 59.003 41.667 0.00 0.00 0.00 3.93
7856 9245 5.106948 GGTGTTTCGTTTAACCTAAGCCTAC 60.107 44.000 0.00 0.00 0.00 3.18
7857 9246 5.698089 GTGTTTCGTTTAACCTAAGCCTACT 59.302 40.000 0.00 0.00 0.00 2.57
7858 9247 5.928264 TGTTTCGTTTAACCTAAGCCTACTC 59.072 40.000 0.00 0.00 0.00 2.59
7859 9248 5.726980 TTCGTTTAACCTAAGCCTACTCA 57.273 39.130 0.00 0.00 0.00 3.41
7860 9249 5.726980 TCGTTTAACCTAAGCCTACTCAA 57.273 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.212900 GATTGTTCTTGCCACCGCCC 62.213 60.000 0.00 0.00 0.00 6.13
41 42 1.212751 GATTGTTCTTGCCACCGCC 59.787 57.895 0.00 0.00 0.00 6.13
46 47 5.549742 AGGAAAAATGATTGTTCTTGCCA 57.450 34.783 7.92 0.00 0.00 4.92
69 71 4.341366 AGCAAAATAAAAAGGCAGCTGT 57.659 36.364 16.64 0.00 0.00 4.40
72 74 5.465056 TGTTGTAGCAAAATAAAAAGGCAGC 59.535 36.000 0.00 0.00 0.00 5.25
167 178 0.396435 AACACATCGCAGGTTCCAGA 59.604 50.000 0.00 0.00 0.00 3.86
295 312 0.729116 CGACAACCATCCACATCTGC 59.271 55.000 0.00 0.00 0.00 4.26
310 327 3.627123 CCATGATTGCAATACTTCCGACA 59.373 43.478 12.97 3.71 0.00 4.35
367 413 2.682856 GACTCGATCTTCTGCTCTCTGT 59.317 50.000 0.00 0.00 0.00 3.41
444 491 1.372499 GGTTACAGCACTGTCGCGA 60.372 57.895 3.71 3.71 43.74 5.87
506 562 4.200874 CTCTCTCTCTCCGCTAACCTTAA 58.799 47.826 0.00 0.00 0.00 1.85
524 582 1.001268 TCAACGCATATCGCTCCTCTC 60.001 52.381 0.00 0.00 43.23 3.20
550 608 1.132849 TCTTTCTCCTCCTCCACCACA 60.133 52.381 0.00 0.00 0.00 4.17
552 610 2.415983 TTCTTTCTCCTCCTCCACCA 57.584 50.000 0.00 0.00 0.00 4.17
561 619 5.262455 AGCCTATTGGTTTTCTTTCTCCT 57.738 39.130 0.00 0.00 35.27 3.69
575 633 3.093717 ACCGTTCGATGTAGCCTATTG 57.906 47.619 0.00 0.00 0.00 1.90
604 664 0.835941 CCCTAGCTGTCTGATTGCCT 59.164 55.000 0.00 0.00 0.00 4.75
690 750 7.694093 AGATATATGAAATGAAAGGAGGGTCC 58.306 38.462 0.00 0.00 36.58 4.46
694 754 9.956640 AAGCTAGATATATGAAATGAAAGGAGG 57.043 33.333 0.00 0.00 0.00 4.30
750 810 1.228154 GGAACCCGTCCACTGCTTT 60.228 57.895 0.00 0.00 46.97 3.51
786 846 5.320277 CATCCAGGAAGAAGGAAGTCTTTT 58.680 41.667 0.00 0.00 37.98 2.27
1005 1065 2.125512 GAGCGCTTCCACCACGAT 60.126 61.111 13.26 0.00 0.00 3.73
1466 1526 3.701604 CTCTCGTTCCCGCCTTCCG 62.702 68.421 0.00 0.00 0.00 4.30
1467 1527 2.184579 CTCTCGTTCCCGCCTTCC 59.815 66.667 0.00 0.00 0.00 3.46
1468 1528 2.184579 CCTCTCGTTCCCGCCTTC 59.815 66.667 0.00 0.00 0.00 3.46
1469 1529 3.391382 CCCTCTCGTTCCCGCCTT 61.391 66.667 0.00 0.00 0.00 4.35
1473 1533 4.493747 GACGCCCTCTCGTTCCCG 62.494 72.222 0.00 0.00 43.42 5.14
1474 1534 4.493747 CGACGCCCTCTCGTTCCC 62.494 72.222 0.00 0.00 43.42 3.97
1475 1535 3.745803 ACGACGCCCTCTCGTTCC 61.746 66.667 0.00 0.00 41.58 3.62
1478 1538 4.719369 GCAACGACGCCCTCTCGT 62.719 66.667 0.00 0.00 46.20 4.18
1479 1539 4.717629 TGCAACGACGCCCTCTCG 62.718 66.667 0.00 0.00 37.17 4.04
1480 1540 1.298859 ATTTGCAACGACGCCCTCTC 61.299 55.000 0.00 0.00 0.00 3.20
1481 1541 0.036765 TATTTGCAACGACGCCCTCT 60.037 50.000 0.00 0.00 0.00 3.69
1482 1542 0.096454 GTATTTGCAACGACGCCCTC 59.904 55.000 0.00 0.00 0.00 4.30
1483 1543 1.303091 GGTATTTGCAACGACGCCCT 61.303 55.000 0.00 0.00 0.00 5.19
1484 1544 1.135939 GGTATTTGCAACGACGCCC 59.864 57.895 0.00 0.00 0.00 6.13
1707 1800 8.438676 AGTATAATTCACTGCAATCCTTGTAC 57.561 34.615 0.00 0.00 0.00 2.90
1708 1801 9.542462 GTAGTATAATTCACTGCAATCCTTGTA 57.458 33.333 3.47 0.00 0.00 2.41
1709 1802 7.499232 GGTAGTATAATTCACTGCAATCCTTGT 59.501 37.037 9.42 0.00 31.02 3.16
1842 3189 6.771749 AGGCTTTCGACTATTAGCTACTTCTA 59.228 38.462 0.00 0.00 34.16 2.10
1866 3213 2.756760 AGTGGCCAAACAATCATAGCAG 59.243 45.455 7.24 0.00 0.00 4.24
1925 3280 6.041409 TCAGAGAATGTTCTGACTTCTGAACT 59.959 38.462 22.18 9.38 46.42 3.01
2019 3374 5.414360 TGTTCTTCAGTCAGATGTCATAGC 58.586 41.667 0.00 0.00 0.00 2.97
2114 3469 3.244422 ACCGGTCAGCAAATGAGACTTAA 60.244 43.478 0.00 0.00 39.07 1.85
2115 3470 2.301870 ACCGGTCAGCAAATGAGACTTA 59.698 45.455 0.00 0.00 39.07 2.24
2255 3619 1.004440 GTCTGACCTGTCACCCTGC 60.004 63.158 0.00 0.00 35.46 4.85
2326 3690 1.911357 TCGGTGGTGACTAGAGGTAGA 59.089 52.381 0.00 0.00 0.00 2.59
2465 3829 2.161012 ACGTCAGCATTGCTCAATCTTG 59.839 45.455 8.54 0.00 36.40 3.02
3146 4513 5.244626 ACCAATGGAACTGATTGAAAAGAGG 59.755 40.000 6.16 0.00 0.00 3.69
3425 4792 1.542915 AGGCAGCTTGTAACTTGCATG 59.457 47.619 0.00 0.00 38.27 4.06
3548 4915 7.625553 CACAAGAAATACTTAGCTCAGCATAC 58.374 38.462 0.00 0.00 37.03 2.39
3908 5276 0.452987 GTGCATGATGGTTGATGCGT 59.547 50.000 0.00 0.00 46.66 5.24
3955 5323 7.606456 CCTAGTAATTAAACTCAGCCAGAACAA 59.394 37.037 0.00 0.00 0.00 2.83
3973 5341 7.490657 TCACACAACCATTCTACCTAGTAAT 57.509 36.000 0.00 0.00 0.00 1.89
4008 5376 6.727824 TTCATCTAGAGCAAGTACAAAAGC 57.272 37.500 0.00 0.00 0.00 3.51
4042 5410 5.644188 TGAAAAATTCATCCAAGTCCTCCT 58.356 37.500 0.00 0.00 34.08 3.69
4137 5505 7.119116 TCACTTACTTTTACATACATGCCACAG 59.881 37.037 0.00 0.00 0.00 3.66
4378 5746 4.872664 AGCCACTAATCGTAATGCTAGAC 58.127 43.478 0.00 0.00 0.00 2.59
4379 5747 5.768662 ACTAGCCACTAATCGTAATGCTAGA 59.231 40.000 19.14 0.00 41.85 2.43
4380 5748 6.015027 ACTAGCCACTAATCGTAATGCTAG 57.985 41.667 12.61 12.61 43.25 3.42
4382 5750 4.939052 ACTAGCCACTAATCGTAATGCT 57.061 40.909 0.00 0.00 0.00 3.79
4383 5751 4.809426 ACAACTAGCCACTAATCGTAATGC 59.191 41.667 0.00 0.00 0.00 3.56
4384 5752 6.238103 CCAACAACTAGCCACTAATCGTAATG 60.238 42.308 0.00 0.00 0.00 1.90
4386 5754 5.047164 TCCAACAACTAGCCACTAATCGTAA 60.047 40.000 0.00 0.00 0.00 3.18
4389 5757 3.857052 TCCAACAACTAGCCACTAATCG 58.143 45.455 0.00 0.00 0.00 3.34
4391 5759 4.943705 CACATCCAACAACTAGCCACTAAT 59.056 41.667 0.00 0.00 0.00 1.73
4392 5760 4.323417 CACATCCAACAACTAGCCACTAA 58.677 43.478 0.00 0.00 0.00 2.24
4585 5964 3.689649 AGCTGTTCGACTCAAAAACAAGT 59.310 39.130 0.00 0.00 32.89 3.16
4719 6098 3.037549 TCAAAAATTTGTGGAGTGGCCT 58.962 40.909 8.51 0.00 39.18 5.19
4778 6157 7.734865 TGTCAACAGGGTATAATGAGAGGATAT 59.265 37.037 0.00 0.00 0.00 1.63
4793 6172 3.366052 ACAGAAAAGTGTCAACAGGGT 57.634 42.857 0.00 0.00 0.00 4.34
5049 6428 4.562757 GCGGCCCATGTAAGATGTAATAGA 60.563 45.833 0.00 0.00 0.00 1.98
5242 6621 3.873910 CCTTTCAGGTCACATATCGGTT 58.126 45.455 0.00 0.00 0.00 4.44
5393 6773 6.203723 GCCTCAAGAATGCTAATTAACTCGAT 59.796 38.462 0.00 0.00 0.00 3.59
5513 6893 3.724508 AGACTCCAGATATCAACAGCG 57.275 47.619 5.32 0.00 0.00 5.18
5697 7077 1.266989 GGTGAAGCTCTTCCGTTTTGG 59.733 52.381 7.12 0.00 38.77 3.28
5846 7226 5.881447 GCATTTATTTGCATGCCAATTTCA 58.119 33.333 20.76 7.24 42.31 2.69
5983 7363 1.072331 CTACCACAGAAACACAGGCCT 59.928 52.381 0.00 0.00 0.00 5.19
6872 8252 2.357327 TTTGAGACAATGCATGCAGC 57.643 45.000 26.69 14.59 45.96 5.25
7027 8407 1.455030 CTAGCTGCGCGAGATTTCATC 59.545 52.381 12.10 0.00 33.20 2.92
7063 8443 1.660607 CACTATTACCACGTGCAGCTG 59.339 52.381 10.91 10.11 0.00 4.24
7117 8497 2.170397 TCTGTCACATGACTGTTGGTGT 59.830 45.455 12.98 0.00 44.99 4.16
7135 8515 6.193410 CGTCTGCGAAATATTGATGTTTTCTG 59.807 38.462 0.00 0.00 41.33 3.02
7136 8516 6.250819 CGTCTGCGAAATATTGATGTTTTCT 58.749 36.000 0.00 0.00 41.33 2.52
7156 8542 1.469308 CTAGAAGTTCAGACGGCGTCT 59.531 52.381 34.91 34.91 44.44 4.18
7158 8544 1.245732 ACTAGAAGTTCAGACGGCGT 58.754 50.000 14.65 14.65 0.00 5.68
7160 8546 5.408356 TCAATTACTAGAAGTTCAGACGGC 58.592 41.667 5.50 0.00 0.00 5.68
7161 8547 5.517054 GCTCAATTACTAGAAGTTCAGACGG 59.483 44.000 5.50 0.00 0.00 4.79
7162 8548 6.093404 TGCTCAATTACTAGAAGTTCAGACG 58.907 40.000 5.50 0.00 0.00 4.18
7163 8549 6.035542 GCTGCTCAATTACTAGAAGTTCAGAC 59.964 42.308 5.50 0.00 0.00 3.51
7164 8550 6.102663 GCTGCTCAATTACTAGAAGTTCAGA 58.897 40.000 5.50 0.00 0.00 3.27
7165 8551 5.871524 TGCTGCTCAATTACTAGAAGTTCAG 59.128 40.000 5.50 3.46 0.00 3.02
7211 8597 1.003812 TCAACCCGATAAACTGTGGGG 59.996 52.381 5.28 3.09 46.38 4.96
7245 8631 7.715249 TGACAAAAACATCTAGTCTTTGCTACT 59.285 33.333 0.00 0.00 0.00 2.57
7246 8632 7.861630 TGACAAAAACATCTAGTCTTTGCTAC 58.138 34.615 0.00 0.00 0.00 3.58
7247 8633 7.173218 CCTGACAAAAACATCTAGTCTTTGCTA 59.827 37.037 0.00 0.00 0.00 3.49
7248 8634 6.016777 CCTGACAAAAACATCTAGTCTTTGCT 60.017 38.462 0.00 0.00 0.00 3.91
7294 8680 4.754372 TTCATCAGCATTCAGTTGTCAC 57.246 40.909 0.00 0.00 0.00 3.67
7599 8988 4.137116 TCCATACTCATGCACAGGTTAC 57.863 45.455 0.00 0.00 0.00 2.50
7605 8994 4.193865 CAGACAATCCATACTCATGCACA 58.806 43.478 0.00 0.00 0.00 4.57
7720 9109 9.936329 AGGGTACTGTAAAATAATCCATTGATT 57.064 29.630 0.00 0.00 43.56 2.57
7754 9143 2.108970 GTACTCCACAGGACCCTTAGG 58.891 57.143 0.00 0.00 40.04 2.69
7761 9150 4.612264 TTTACTTGGTACTCCACAGGAC 57.388 45.455 0.00 0.00 44.22 3.85
7762 9151 4.224370 GGATTTACTTGGTACTCCACAGGA 59.776 45.833 0.00 0.00 44.22 3.86
7763 9152 4.019681 TGGATTTACTTGGTACTCCACAGG 60.020 45.833 0.00 0.00 44.22 4.00
7764 9153 5.160607 TGGATTTACTTGGTACTCCACAG 57.839 43.478 0.00 0.00 44.22 3.66
7765 9154 5.310451 GTTGGATTTACTTGGTACTCCACA 58.690 41.667 0.00 0.00 44.22 4.17
7766 9155 4.698780 GGTTGGATTTACTTGGTACTCCAC 59.301 45.833 0.00 4.83 44.22 4.02
7767 9156 4.563993 CGGTTGGATTTACTTGGTACTCCA 60.564 45.833 0.00 0.00 42.66 3.86
7768 9157 3.937079 CGGTTGGATTTACTTGGTACTCC 59.063 47.826 0.00 0.00 0.00 3.85
7769 9158 4.390909 CACGGTTGGATTTACTTGGTACTC 59.609 45.833 0.00 0.00 0.00 2.59
7770 9159 4.320870 CACGGTTGGATTTACTTGGTACT 58.679 43.478 0.00 0.00 0.00 2.73
7771 9160 4.673534 CACGGTTGGATTTACTTGGTAC 57.326 45.455 0.00 0.00 0.00 3.34
7784 9173 3.893521 ACCCTTTAATATCCACGGTTGG 58.106 45.455 0.00 0.00 45.56 3.77
7785 9174 8.857694 ATAATACCCTTTAATATCCACGGTTG 57.142 34.615 0.00 0.00 0.00 3.77
7787 9176 9.551339 TCTATAATACCCTTTAATATCCACGGT 57.449 33.333 0.00 0.00 0.00 4.83
7815 9204 9.535878 ACGAAACACCAACATAAATTGTAAAAT 57.464 25.926 0.00 0.00 37.68 1.82
7816 9205 8.928270 ACGAAACACCAACATAAATTGTAAAA 57.072 26.923 0.00 0.00 37.68 1.52
7817 9206 8.928270 AACGAAACACCAACATAAATTGTAAA 57.072 26.923 0.00 0.00 37.68 2.01
7818 9207 8.928270 AAACGAAACACCAACATAAATTGTAA 57.072 26.923 0.00 0.00 37.68 2.41
7820 9209 8.809478 GTTAAACGAAACACCAACATAAATTGT 58.191 29.630 0.00 0.00 41.53 2.71
7821 9210 8.270111 GGTTAAACGAAACACCAACATAAATTG 58.730 33.333 0.00 0.00 0.00 2.32
7822 9211 8.198778 AGGTTAAACGAAACACCAACATAAATT 58.801 29.630 0.00 0.00 0.00 1.82
7823 9212 7.718525 AGGTTAAACGAAACACCAACATAAAT 58.281 30.769 0.00 0.00 0.00 1.40
7824 9213 7.098074 AGGTTAAACGAAACACCAACATAAA 57.902 32.000 0.00 0.00 0.00 1.40
7825 9214 6.696441 AGGTTAAACGAAACACCAACATAA 57.304 33.333 0.00 0.00 0.00 1.90
7826 9215 7.520292 GCTTAGGTTAAACGAAACACCAACATA 60.520 37.037 0.00 0.00 0.00 2.29
7827 9216 6.696441 TTAGGTTAAACGAAACACCAACAT 57.304 33.333 0.00 0.00 0.00 2.71
7828 9217 5.448904 GCTTAGGTTAAACGAAACACCAACA 60.449 40.000 0.00 0.00 0.00 3.33
7829 9218 4.971830 GCTTAGGTTAAACGAAACACCAAC 59.028 41.667 0.00 0.00 0.00 3.77
7830 9219 4.036616 GGCTTAGGTTAAACGAAACACCAA 59.963 41.667 0.00 0.00 0.00 3.67
7831 9220 3.565063 GGCTTAGGTTAAACGAAACACCA 59.435 43.478 0.00 0.00 0.00 4.17
7832 9221 3.817084 AGGCTTAGGTTAAACGAAACACC 59.183 43.478 0.00 0.00 0.00 4.16
7833 9222 5.698089 AGTAGGCTTAGGTTAAACGAAACAC 59.302 40.000 0.00 0.00 0.00 3.32
7834 9223 5.857268 AGTAGGCTTAGGTTAAACGAAACA 58.143 37.500 0.00 0.00 0.00 2.83
7835 9224 5.928264 TGAGTAGGCTTAGGTTAAACGAAAC 59.072 40.000 0.00 0.00 0.00 2.78
7836 9225 6.100404 TGAGTAGGCTTAGGTTAAACGAAA 57.900 37.500 0.00 0.00 0.00 3.46
7837 9226 5.726980 TGAGTAGGCTTAGGTTAAACGAA 57.273 39.130 0.00 0.00 0.00 3.85
7838 9227 5.726980 TTGAGTAGGCTTAGGTTAAACGA 57.273 39.130 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.