Multiple sequence alignment - TraesCS2D01G544300

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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 TraesCS2D01G544300 chr2D 100.000 3749 0 0 1 3749 621553379 621549631 0.000000e+00 6924.0
1 TraesCS2D01G544300 chr2D 82.329 730 112 15 1676 2397 621583012 621582292 5.320000e-173 617.0
2 TraesCS2D01G544300 chr2D 91.244 434 33 4 2087 2518 499308609 499309039 1.500000e-163 586.0
3 TraesCS2D01G544300 chr2D 92.478 226 15 2 1054 1278 621572095 621571871 4.670000e-84 322.0
4 TraesCS2D01G544300 chr2D 77.591 357 36 20 2704 3053 499309066 499309385 3.850000e-40 176.0
5 TraesCS2D01G544300 chr2D 84.746 177 24 3 460 634 11542162 11542337 1.380000e-39 174.0
6 TraesCS2D01G544300 chr2B 91.390 3136 158 48 674 3749 762508552 762505469 0.000000e+00 4193.0
7 TraesCS2D01G544300 chr2B 94.992 639 24 3 1 637 762513402 762512770 0.000000e+00 996.0
8 TraesCS2D01G544300 chr2B 80.323 930 136 37 1799 2698 762801114 762800202 0.000000e+00 660.0
9 TraesCS2D01G544300 chr2B 78.642 1016 138 52 1743 2721 762916221 762915248 5.360000e-168 601.0
10 TraesCS2D01G544300 chr2B 86.780 469 55 3 877 1341 762538634 762538169 2.000000e-142 516.0
11 TraesCS2D01G544300 chr2B 76.998 613 84 33 2292 2870 762789765 762789176 7.870000e-77 298.0
12 TraesCS2D01G544300 chr2B 84.848 297 35 9 1867 2158 763039944 763039653 1.320000e-74 291.0
13 TraesCS2D01G544300 chr2B 84.706 255 28 6 2293 2536 762793611 762793357 1.040000e-60 244.0
14 TraesCS2D01G544300 chr2B 87.879 66 7 1 1787 1852 762794044 762793980 4.020000e-10 76.8
15 TraesCS2D01G544300 chr2A 86.164 1207 110 27 1893 3077 753256364 753255193 0.000000e+00 1251.0
16 TraesCS2D01G544300 chr2A 89.074 659 31 9 707 1349 753257423 753256790 0.000000e+00 780.0
17 TraesCS2D01G544300 chr2A 78.578 1111 166 51 1676 2744 753403343 753402263 0.000000e+00 667.0
18 TraesCS2D01G544300 chr2A 86.604 530 19 13 3237 3749 753255163 753254669 4.260000e-149 538.0
19 TraesCS2D01G544300 chr2A 84.475 438 58 9 6 435 753258010 753257575 1.240000e-114 424.0
20 TraesCS2D01G544300 chr2A 79.532 171 30 4 1685 1851 753256640 753256471 2.370000e-22 117.0
21 TraesCS2D01G544300 chr4A 90.783 434 35 4 2087 2518 153777677 153777247 3.250000e-160 575.0
22 TraesCS2D01G544300 chr1D 85.185 216 21 8 430 637 82332863 82333075 1.050000e-50 211.0
23 TraesCS2D01G544300 chr3D 83.871 217 26 6 429 637 493038555 493038340 8.210000e-47 198.0
24 TraesCS2D01G544300 chr7D 83.410 217 27 6 430 637 471219405 471219189 3.820000e-45 193.0
25 TraesCS2D01G544300 chr7D 83.333 216 27 5 430 637 603581024 603581238 1.370000e-44 191.0
26 TraesCS2D01G544300 chr5B 83.636 220 21 7 429 637 366053611 366053396 3.820000e-45 193.0
27 TraesCS2D01G544300 chr5D 82.192 219 29 9 428 638 460749933 460749717 2.980000e-41 180.0
28 TraesCS2D01G544300 chr4D 82.439 205 24 5 440 637 460955074 460955273 6.440000e-38 169.0
29 TraesCS2D01G544300 chr5A 84.685 111 9 6 429 532 281895890 281895999 1.840000e-18 104.0
30 TraesCS2D01G544300 chr5A 94.444 36 2 0 429 464 449020943 449020978 5.230000e-04 56.5
31 TraesCS2D01G544300 chr3B 79.279 111 9 6 430 532 53557919 53557815 8.690000e-07 65.8
32 TraesCS2D01G544300 chr7A 94.595 37 0 2 429 464 548624843 548624878 5.230000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G544300 chr2D 621549631 621553379 3748 True 6924.000000 6924 100.000000 1 3749 1 chr2D.!!$R1 3748
1 TraesCS2D01G544300 chr2D 621582292 621583012 720 True 617.000000 617 82.329000 1676 2397 1 chr2D.!!$R3 721
2 TraesCS2D01G544300 chr2D 499308609 499309385 776 False 381.000000 586 84.417500 2087 3053 2 chr2D.!!$F2 966
3 TraesCS2D01G544300 chr2B 762505469 762508552 3083 True 4193.000000 4193 91.390000 674 3749 1 chr2B.!!$R1 3075
4 TraesCS2D01G544300 chr2B 762512770 762513402 632 True 996.000000 996 94.992000 1 637 1 chr2B.!!$R2 636
5 TraesCS2D01G544300 chr2B 762800202 762801114 912 True 660.000000 660 80.323000 1799 2698 1 chr2B.!!$R4 899
6 TraesCS2D01G544300 chr2B 762915248 762916221 973 True 601.000000 601 78.642000 1743 2721 1 chr2B.!!$R5 978
7 TraesCS2D01G544300 chr2B 762789176 762794044 4868 True 206.266667 298 83.194333 1787 2870 3 chr2B.!!$R7 1083
8 TraesCS2D01G544300 chr2A 753402263 753403343 1080 True 667.000000 667 78.578000 1676 2744 1 chr2A.!!$R1 1068
9 TraesCS2D01G544300 chr2A 753254669 753258010 3341 True 622.000000 1251 85.169800 6 3749 5 chr2A.!!$R2 3743

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
702 711 0.459934 CGTAACGCAATCCCCCGTAA 60.460 55.000 0.00 0.00 36.56 3.18 F
1405 1439 1.266718 TGATTCAGAAACAACCGCTGC 59.733 47.619 0.00 0.00 0.00 5.25 F
1550 1629 0.588252 TGAAGCTTGCTTCGCACTTC 59.412 50.000 24.43 10.49 40.05 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1629 0.390472 GGGGAGCAGTCTCAGAAACG 60.390 60.0 0.00 0.00 41.13 3.60 R
2702 4864 0.107066 TGACGATGATGGCCTTGCAT 60.107 50.0 3.32 4.64 0.00 3.96 R
2833 4999 0.244450 CCAAAGCATTCGTGTGGCAT 59.756 50.0 0.00 0.00 0.00 4.40 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
219 224 2.869192 GGACTTGCATCTTTCTCCGATC 59.131 50.000 0.00 0.00 0.00 3.69
254 259 4.099881 CCCGCCAGTAACCTACTTGTAATA 59.900 45.833 0.00 0.00 36.76 0.98
256 261 5.068198 CCGCCAGTAACCTACTTGTAATAGA 59.932 44.000 0.00 0.00 36.76 1.98
259 264 8.355169 CGCCAGTAACCTACTTGTAATAGAATA 58.645 37.037 0.00 0.00 36.76 1.75
292 298 8.194769 TGAATGCAAACTTCATACTCGAGTATA 58.805 33.333 32.06 19.70 39.06 1.47
391 398 5.997746 TGTGTTCTTTTCCTCAGTGATAAGG 59.002 40.000 0.00 0.00 0.00 2.69
427 435 3.778629 ACTGGTCGAATTATGTTAGGGGT 59.221 43.478 0.00 0.00 0.00 4.95
477 485 6.407623 GTCCACTTTTGCGTTAAATTTTGAC 58.592 36.000 0.00 0.00 0.00 3.18
480 488 6.181944 CACTTTTGCGTTAAATTTTGACCAC 58.818 36.000 0.00 0.00 0.00 4.16
489 497 8.211838 GCGTTAAATTTTGACCACAGATTTAAC 58.788 33.333 19.42 19.42 42.89 2.01
514 522 9.691362 ACTAACAAAATGTTAATTCATGTCACC 57.309 29.630 4.68 0.00 41.70 4.02
638 647 5.359009 TGACACTAAATACGAAGGGACTAGG 59.641 44.000 0.00 0.00 38.49 3.02
639 648 5.513233 ACACTAAATACGAAGGGACTAGGA 58.487 41.667 0.00 0.00 38.49 2.94
640 649 5.593502 ACACTAAATACGAAGGGACTAGGAG 59.406 44.000 0.00 0.00 38.49 3.69
642 651 3.684408 AATACGAAGGGACTAGGAGGT 57.316 47.619 0.00 0.00 38.49 3.85
643 652 4.803329 AATACGAAGGGACTAGGAGGTA 57.197 45.455 0.00 0.00 38.49 3.08
644 653 2.732844 ACGAAGGGACTAGGAGGTAG 57.267 55.000 0.00 0.00 38.49 3.18
647 656 2.033372 GAAGGGACTAGGAGGTAGTGC 58.967 57.143 0.00 0.00 46.73 4.40
702 711 0.459934 CGTAACGCAATCCCCCGTAA 60.460 55.000 0.00 0.00 36.56 3.18
834 851 2.561526 GGGGGTAGGGTGAGGGTATATC 60.562 59.091 0.00 0.00 0.00 1.63
840 857 1.749634 GGGTGAGGGTATATCCGATCG 59.250 57.143 8.51 8.51 37.00 3.69
1231 1265 1.747709 TTCGACGGGGAAACAAACAA 58.252 45.000 0.00 0.00 0.00 2.83
1232 1266 1.747709 TCGACGGGGAAACAAACAAA 58.252 45.000 0.00 0.00 0.00 2.83
1245 1279 5.635549 AACAAACAAAGCTGCGATTTTAC 57.364 34.783 0.00 0.00 0.00 2.01
1351 1385 2.428890 ACCGCTGTAATTCTCTCCTCAG 59.571 50.000 0.00 0.00 0.00 3.35
1356 1390 5.517054 CGCTGTAATTCTCTCCTCAGTTTAC 59.483 44.000 0.00 0.00 0.00 2.01
1405 1439 1.266718 TGATTCAGAAACAACCGCTGC 59.733 47.619 0.00 0.00 0.00 5.25
1482 1516 7.201600 GCCTATTTTCATTCTCTCTTCAGTGTC 60.202 40.741 0.00 0.00 0.00 3.67
1515 1574 8.348285 TGTTGCTAAAATAATTGGCTAGTCTT 57.652 30.769 0.00 0.00 0.00 3.01
1516 1575 9.456147 TGTTGCTAAAATAATTGGCTAGTCTTA 57.544 29.630 0.00 0.00 0.00 2.10
1532 1611 7.185453 GCTAGTCTTATTTGCTGTCAGAAATG 58.815 38.462 3.32 0.00 0.00 2.32
1544 1623 3.058708 TGTCAGAAATGAAGCTTGCTTCG 60.059 43.478 24.43 12.88 36.21 3.79
1550 1629 0.588252 TGAAGCTTGCTTCGCACTTC 59.412 50.000 24.43 10.49 40.05 3.01
1559 1638 1.136502 GCTTCGCACTTCGTTTCTGAG 60.137 52.381 0.00 0.00 39.67 3.35
1591 1670 6.329197 CCCCCTCCAGTAAATAATCAGTAGAA 59.671 42.308 0.00 0.00 0.00 2.10
1607 1686 1.078143 GAATGGAACTGCCGGAGCT 60.078 57.895 5.05 0.00 40.66 4.09
1610 1689 0.687757 ATGGAACTGCCGGAGCTCTA 60.688 55.000 14.64 0.00 40.66 2.43
1713 1792 6.854892 CACTTCAGAACAACATGAAATCAGAC 59.145 38.462 0.00 0.00 35.14 3.51
1788 1867 2.049248 ACCGCTTGCGCCAAATTG 60.049 55.556 4.18 0.00 0.00 2.32
1797 3774 1.337071 TGCGCCAAATTGACCGTTTTA 59.663 42.857 4.18 0.00 0.00 1.52
1871 3929 9.605955 CAGAGTATTAGAACTCAGAATATGACG 57.394 37.037 6.76 0.00 46.89 4.35
2012 4092 2.109774 AGAGATGAGCAAGGAGTCCTG 58.890 52.381 13.89 8.32 32.13 3.86
2226 4348 1.694150 AGCAAGTGTTCTGCTCTACCA 59.306 47.619 0.00 0.00 32.98 3.25
2336 4464 1.675720 AACAACAGCCCAGCAACCAC 61.676 55.000 0.00 0.00 0.00 4.16
2397 4525 6.072838 TGCAAATGTCTTGTCTCTGAATTCTC 60.073 38.462 7.05 0.00 0.00 2.87
2535 4663 4.980573 TCAAGGTGGTACAAAAGCATACT 58.019 39.130 0.00 0.00 44.16 2.12
2698 4860 5.687970 CGTCTAGGGATCTCTCAAGGAACTA 60.688 48.000 0.00 0.00 38.49 2.24
2702 4864 5.594777 AGGGATCTCTCAAGGAACTAAAGA 58.405 41.667 0.00 0.00 38.49 2.52
2724 4886 1.957668 CAAGGCCATCATCGTCATCA 58.042 50.000 5.01 0.00 0.00 3.07
2754 4919 4.576873 CACGAAGATCTCCACTAGCTAGAA 59.423 45.833 27.45 10.84 0.00 2.10
2760 4925 9.509956 GAAGATCTCCACTAGCTAGAATACTTA 57.490 37.037 27.45 6.60 0.00 2.24
2765 4930 9.422681 TCTCCACTAGCTAGAATACTTAACAAT 57.577 33.333 27.45 0.00 0.00 2.71
2792 4957 2.103263 GGGTATCACTTCTAGGTGGCAG 59.897 54.545 0.00 0.00 37.75 4.85
2793 4958 2.766828 GGTATCACTTCTAGGTGGCAGT 59.233 50.000 0.00 0.00 37.75 4.40
2794 4959 3.958798 GGTATCACTTCTAGGTGGCAGTA 59.041 47.826 0.00 0.00 37.75 2.74
2799 4964 4.286032 TCACTTCTAGGTGGCAGTACATTT 59.714 41.667 0.00 0.00 37.75 2.32
2801 4966 3.906720 TCTAGGTGGCAGTACATTTCC 57.093 47.619 0.00 0.00 0.00 3.13
2808 4973 3.435671 GTGGCAGTACATTTCCACTACAC 59.564 47.826 14.56 0.00 44.09 2.90
2809 4974 3.007635 GGCAGTACATTTCCACTACACC 58.992 50.000 0.00 0.00 0.00 4.16
2824 4989 5.344743 ACTACACCAGTGACCTGAATATG 57.655 43.478 4.48 0.00 41.50 1.78
2833 4999 7.092891 ACCAGTGACCTGAATATGAGTTTATCA 60.093 37.037 0.00 0.00 41.50 2.15
2872 5040 5.902613 TGGAACATGATCCAATGAAAGAC 57.097 39.130 21.41 0.00 46.36 3.01
2877 5046 7.543520 GGAACATGATCCAATGAAAGACTTTTC 59.456 37.037 16.67 0.00 39.97 2.29
2892 5061 8.438676 AAAGACTTTTCTATGATATCCAACGG 57.561 34.615 0.00 0.00 0.00 4.44
2902 5071 9.046846 TCTATGATATCCAACGGAAGGATTATT 57.953 33.333 10.23 0.00 43.21 1.40
2903 5072 9.672673 CTATGATATCCAACGGAAGGATTATTT 57.327 33.333 10.23 0.00 43.21 1.40
2905 5074 8.760980 TGATATCCAACGGAAGGATTATTTTT 57.239 30.769 10.23 0.00 43.21 1.94
2906 5075 8.629158 TGATATCCAACGGAAGGATTATTTTTG 58.371 33.333 10.23 0.00 43.21 2.44
2908 5077 6.902771 TCCAACGGAAGGATTATTTTTGAA 57.097 33.333 0.00 0.00 0.00 2.69
2909 5078 6.919721 TCCAACGGAAGGATTATTTTTGAAG 58.080 36.000 0.00 0.00 0.00 3.02
2912 5081 6.510879 ACGGAAGGATTATTTTTGAAGGTC 57.489 37.500 0.00 0.00 0.00 3.85
2913 5082 6.246163 ACGGAAGGATTATTTTTGAAGGTCT 58.754 36.000 0.00 0.00 0.00 3.85
2914 5083 7.399634 ACGGAAGGATTATTTTTGAAGGTCTA 58.600 34.615 0.00 0.00 0.00 2.59
2915 5084 7.886446 ACGGAAGGATTATTTTTGAAGGTCTAA 59.114 33.333 0.00 0.00 0.00 2.10
2916 5085 8.182227 CGGAAGGATTATTTTTGAAGGTCTAAC 58.818 37.037 0.00 0.00 0.00 2.34
2917 5086 8.182227 GGAAGGATTATTTTTGAAGGTCTAACG 58.818 37.037 0.00 0.00 0.00 3.18
2918 5087 7.625828 AGGATTATTTTTGAAGGTCTAACGG 57.374 36.000 0.00 0.00 0.00 4.44
2919 5088 7.399634 AGGATTATTTTTGAAGGTCTAACGGA 58.600 34.615 0.00 0.00 0.00 4.69
2920 5089 7.886446 AGGATTATTTTTGAAGGTCTAACGGAA 59.114 33.333 0.00 0.00 0.00 4.30
2921 5090 8.182227 GGATTATTTTTGAAGGTCTAACGGAAG 58.818 37.037 0.00 0.00 0.00 3.46
2922 5091 5.959618 ATTTTTGAAGGTCTAACGGAAGG 57.040 39.130 0.00 0.00 0.00 3.46
2923 5092 4.693042 TTTTGAAGGTCTAACGGAAGGA 57.307 40.909 0.00 0.00 0.00 3.36
2924 5093 4.903045 TTTGAAGGTCTAACGGAAGGAT 57.097 40.909 0.00 0.00 0.00 3.24
2925 5094 4.903045 TTGAAGGTCTAACGGAAGGATT 57.097 40.909 0.00 0.00 0.00 3.01
2926 5095 6.363167 TTTGAAGGTCTAACGGAAGGATTA 57.637 37.500 0.00 0.00 0.00 1.75
2927 5096 6.555463 TTGAAGGTCTAACGGAAGGATTAT 57.445 37.500 0.00 0.00 0.00 1.28
2928 5097 5.914033 TGAAGGTCTAACGGAAGGATTATG 58.086 41.667 0.00 0.00 0.00 1.90
2929 5098 5.659525 TGAAGGTCTAACGGAAGGATTATGA 59.340 40.000 0.00 0.00 0.00 2.15
2930 5099 6.326583 TGAAGGTCTAACGGAAGGATTATGAT 59.673 38.462 0.00 0.00 0.00 2.45
2931 5100 7.507956 TGAAGGTCTAACGGAAGGATTATGATA 59.492 37.037 0.00 0.00 0.00 2.15
2947 5116 8.993121 GGATTATGATATACAGTTGACCAGTTG 58.007 37.037 0.00 0.00 0.00 3.16
2948 5117 7.786178 TTATGATATACAGTTGACCAGTTGC 57.214 36.000 0.00 0.00 0.00 4.17
2950 5119 6.538945 TGATATACAGTTGACCAGTTGCTA 57.461 37.500 0.00 0.00 0.00 3.49
2954 5130 0.764890 AGTTGACCAGTTGCTAGCCA 59.235 50.000 13.29 0.00 0.00 4.75
2975 5155 3.885724 TCTCAATTCGTGTGCCTGATA 57.114 42.857 0.00 0.00 0.00 2.15
3080 5264 3.061403 GTGTTATCTTTGCGATCGTACCG 60.061 47.826 17.81 5.80 33.48 4.02
3096 5280 7.201679 CGATCGTACCGAGATATTTAACCCTAT 60.202 40.741 7.03 0.00 39.91 2.57
3212 5398 6.899393 TTTTTACTTCTGATTGGCAGTGAT 57.101 33.333 0.00 0.00 45.14 3.06
3213 5399 6.899393 TTTTACTTCTGATTGGCAGTGATT 57.101 33.333 0.00 0.00 45.14 2.57
3214 5400 6.500684 TTTACTTCTGATTGGCAGTGATTC 57.499 37.500 0.00 0.00 45.14 2.52
3215 5401 4.298103 ACTTCTGATTGGCAGTGATTCT 57.702 40.909 0.00 0.00 45.14 2.40
3216 5402 4.660168 ACTTCTGATTGGCAGTGATTCTT 58.340 39.130 0.00 0.00 45.14 2.52
3217 5403 4.699257 ACTTCTGATTGGCAGTGATTCTTC 59.301 41.667 0.00 0.00 45.14 2.87
3218 5404 4.564782 TCTGATTGGCAGTGATTCTTCT 57.435 40.909 0.00 0.00 45.14 2.85
3219 5405 4.914983 TCTGATTGGCAGTGATTCTTCTT 58.085 39.130 0.00 0.00 45.14 2.52
3220 5406 4.940046 TCTGATTGGCAGTGATTCTTCTTC 59.060 41.667 0.00 0.00 45.14 2.87
3221 5407 4.914983 TGATTGGCAGTGATTCTTCTTCT 58.085 39.130 0.00 0.00 0.00 2.85
3222 5408 5.319453 TGATTGGCAGTGATTCTTCTTCTT 58.681 37.500 0.00 0.00 0.00 2.52
3223 5409 5.771666 TGATTGGCAGTGATTCTTCTTCTTT 59.228 36.000 0.00 0.00 0.00 2.52
3224 5410 6.266103 TGATTGGCAGTGATTCTTCTTCTTTT 59.734 34.615 0.00 0.00 0.00 2.27
3225 5411 6.469782 TTGGCAGTGATTCTTCTTCTTTTT 57.530 33.333 0.00 0.00 0.00 1.94
3333 5521 1.154073 GAGTAGACGCGTCCGCTTT 60.154 57.895 34.08 18.72 39.32 3.51
3343 5531 0.243907 CGTCCGCTTTCTCTTCTCCA 59.756 55.000 0.00 0.00 0.00 3.86
3611 5799 2.042843 CAGTACGCCTCCCCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
3612 5800 2.128507 CAGTACGCCTCCCCTCCTC 61.129 68.421 0.00 0.00 0.00 3.71
3613 5801 3.217743 GTACGCCTCCCCTCCTCG 61.218 72.222 0.00 0.00 0.00 4.63
3614 5802 3.736224 TACGCCTCCCCTCCTCGT 61.736 66.667 0.00 0.00 37.19 4.18
3615 5803 3.711059 TACGCCTCCCCTCCTCGTC 62.711 68.421 0.00 0.00 34.97 4.20
3616 5804 4.824515 CGCCTCCCCTCCTCGTCT 62.825 72.222 0.00 0.00 0.00 4.18
3617 5805 2.835895 GCCTCCCCTCCTCGTCTC 60.836 72.222 0.00 0.00 0.00 3.36
3618 5806 3.011885 CCTCCCCTCCTCGTCTCT 58.988 66.667 0.00 0.00 0.00 3.10
3619 5807 1.152839 CCTCCCCTCCTCGTCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
3658 5867 1.940613 CGAATTTCGAGGGGAATGGTC 59.059 52.381 13.45 0.00 43.74 4.02
3684 5893 7.362056 CCTTCGCTTCATCTAATTTTGAGGAAA 60.362 37.037 8.75 0.00 34.53 3.13
3742 5965 1.067060 TGGTTCGATATCCACGAGCTG 59.933 52.381 0.00 0.00 40.72 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 224 3.217743 GGCGGGACCTCTACCTCG 61.218 72.222 0.00 0.00 34.51 4.63
254 259 9.013229 TGAAGTTTGCATTCATACAACTATTCT 57.987 29.630 0.00 0.00 31.86 2.40
292 298 6.626302 TCGACTTTTTCTTTTGTGGAAACAT 58.374 32.000 0.00 0.00 46.14 2.71
427 435 3.377253 AATCAGGACGGAGGTAGTACA 57.623 47.619 2.06 0.00 0.00 2.90
439 447 6.389906 CAAAAGTGGACCAATAAATCAGGAC 58.610 40.000 0.00 0.00 0.00 3.85
489 497 9.689976 TGGTGACATGAATTAACATTTTGTTAG 57.310 29.630 0.00 0.00 38.68 2.34
610 619 8.019656 AGTCCCTTCGTATTTAGTGTCATATT 57.980 34.615 0.00 0.00 0.00 1.28
627 636 2.033372 GCACTACCTCCTAGTCCCTTC 58.967 57.143 0.00 0.00 32.90 3.46
670 679 2.304751 CGTTACGCCCCTCAAATACT 57.695 50.000 0.00 0.00 0.00 2.12
776 793 4.473520 CTGGAACCATCGCCCGCT 62.474 66.667 0.00 0.00 0.00 5.52
817 834 3.446442 TCGGATATACCCTCACCCTAC 57.554 52.381 0.00 0.00 34.64 3.18
1103 1137 2.701163 GAAGTAGGGCGCGATCTGGG 62.701 65.000 12.10 0.00 0.00 4.45
1184 1218 2.639286 CAAGTGTTGGGTGAGCGC 59.361 61.111 0.00 0.00 0.00 5.92
1231 1265 3.365364 GCAACTGAGTAAAATCGCAGCTT 60.365 43.478 0.00 0.00 38.46 3.74
1232 1266 2.160417 GCAACTGAGTAAAATCGCAGCT 59.840 45.455 0.00 0.00 38.46 4.24
1245 1279 2.285486 GCAAATCGATCGAGCAACTGAG 60.285 50.000 23.84 8.08 0.00 3.35
1351 1385 2.294979 CGGCTATTTCTGGGGGTAAAC 58.705 52.381 0.00 0.00 0.00 2.01
1356 1390 0.472471 TAAGCGGCTATTTCTGGGGG 59.528 55.000 1.35 0.00 0.00 5.40
1405 1439 3.611057 GCAGTGAACTGAGCAGGAAATTG 60.611 47.826 14.58 0.00 46.59 2.32
1501 1560 7.109501 TGACAGCAAATAAGACTAGCCAATTA 58.890 34.615 0.00 0.00 0.00 1.40
1508 1567 8.484641 TCATTTCTGACAGCAAATAAGACTAG 57.515 34.615 0.00 0.00 0.00 2.57
1512 1571 6.432162 AGCTTCATTTCTGACAGCAAATAAGA 59.568 34.615 13.15 6.55 37.68 2.10
1515 1574 6.384224 CAAGCTTCATTTCTGACAGCAAATA 58.616 36.000 0.00 0.00 37.68 1.40
1516 1575 5.227908 CAAGCTTCATTTCTGACAGCAAAT 58.772 37.500 0.00 2.73 37.68 2.32
1544 1623 1.193426 GCAGTCTCAGAAACGAAGTGC 59.807 52.381 0.00 0.00 45.00 4.40
1550 1629 0.390472 GGGGAGCAGTCTCAGAAACG 60.390 60.000 0.00 0.00 41.13 3.60
1559 1638 0.617820 TTACTGGAGGGGGAGCAGTC 60.618 60.000 0.00 0.00 0.00 3.51
1591 1670 0.687757 TAGAGCTCCGGCAGTTCCAT 60.688 55.000 10.93 0.00 41.70 3.41
1664 1743 4.705023 ACAGTGCAAAAGACACTAAACCTT 59.295 37.500 0.00 0.00 46.44 3.50
1788 1867 5.064834 GGTCATGAGGATTCTTAAAACGGTC 59.935 44.000 0.00 0.00 0.00 4.79
1797 3774 6.487828 TCTTTGAATGGTCATGAGGATTCTT 58.512 36.000 19.98 1.92 32.48 2.52
2226 4348 2.748465 GCACACCCACCTAAAGTCTTGT 60.748 50.000 0.00 0.00 0.00 3.16
2535 4663 5.765677 TCCAATTCAACGGTTATGACTTCAA 59.234 36.000 0.00 0.00 0.00 2.69
2698 4860 1.679680 CGATGATGGCCTTGCATCTTT 59.320 47.619 22.00 4.71 37.00 2.52
2702 4864 0.107066 TGACGATGATGGCCTTGCAT 60.107 50.000 3.32 4.64 0.00 3.96
2760 4925 9.408648 CCTAGAAGTGATACCCATAAAATTGTT 57.591 33.333 0.00 0.00 0.00 2.83
2765 4930 6.634039 GCCACCTAGAAGTGATACCCATAAAA 60.634 42.308 1.10 0.00 40.34 1.52
2776 4941 2.884320 TGTACTGCCACCTAGAAGTGA 58.116 47.619 1.10 0.00 40.34 3.41
2779 4944 4.192317 GGAAATGTACTGCCACCTAGAAG 58.808 47.826 0.00 0.00 0.00 2.85
2808 4973 7.275183 TGATAAACTCATATTCAGGTCACTGG 58.725 38.462 0.00 0.00 44.99 4.00
2809 4974 8.771766 CATGATAAACTCATATTCAGGTCACTG 58.228 37.037 0.00 0.00 42.91 3.66
2822 4987 3.872696 TCGTGTGGCATGATAAACTCAT 58.127 40.909 0.00 0.00 45.78 2.90
2824 4989 4.591202 CATTCGTGTGGCATGATAAACTC 58.409 43.478 0.00 0.00 0.00 3.01
2833 4999 0.244450 CCAAAGCATTCGTGTGGCAT 59.756 50.000 0.00 0.00 0.00 4.40
2871 5039 6.992715 CCTTCCGTTGGATATCATAGAAAAGT 59.007 38.462 4.83 0.00 0.00 2.66
2872 5040 7.217200 TCCTTCCGTTGGATATCATAGAAAAG 58.783 38.462 4.83 1.78 0.00 2.27
2877 5046 9.672673 AAATAATCCTTCCGTTGGATATCATAG 57.327 33.333 4.83 0.00 42.93 2.23
2892 5061 8.182227 CCGTTAGACCTTCAAAAATAATCCTTC 58.818 37.037 0.00 0.00 0.00 3.46
2902 5071 4.693042 TCCTTCCGTTAGACCTTCAAAA 57.307 40.909 0.00 0.00 0.00 2.44
2903 5072 4.903045 ATCCTTCCGTTAGACCTTCAAA 57.097 40.909 0.00 0.00 0.00 2.69
2905 5074 5.659525 TCATAATCCTTCCGTTAGACCTTCA 59.340 40.000 0.00 0.00 0.00 3.02
2906 5075 6.158023 TCATAATCCTTCCGTTAGACCTTC 57.842 41.667 0.00 0.00 0.00 3.46
2908 5077 8.968969 GTATATCATAATCCTTCCGTTAGACCT 58.031 37.037 0.00 0.00 0.00 3.85
2909 5078 8.746530 TGTATATCATAATCCTTCCGTTAGACC 58.253 37.037 0.00 0.00 0.00 3.85
2913 5082 9.923143 CAACTGTATATCATAATCCTTCCGTTA 57.077 33.333 0.00 0.00 0.00 3.18
2914 5083 8.647796 TCAACTGTATATCATAATCCTTCCGTT 58.352 33.333 0.00 0.00 0.00 4.44
2915 5084 8.088981 GTCAACTGTATATCATAATCCTTCCGT 58.911 37.037 0.00 0.00 0.00 4.69
2916 5085 7.545965 GGTCAACTGTATATCATAATCCTTCCG 59.454 40.741 0.00 0.00 0.00 4.30
2917 5086 8.375506 TGGTCAACTGTATATCATAATCCTTCC 58.624 37.037 0.00 0.00 0.00 3.46
2918 5087 9.429359 CTGGTCAACTGTATATCATAATCCTTC 57.571 37.037 0.00 0.00 0.00 3.46
2919 5088 8.938883 ACTGGTCAACTGTATATCATAATCCTT 58.061 33.333 0.00 0.00 0.00 3.36
2920 5089 8.497910 ACTGGTCAACTGTATATCATAATCCT 57.502 34.615 0.00 0.00 0.00 3.24
2921 5090 8.993121 CAACTGGTCAACTGTATATCATAATCC 58.007 37.037 0.00 0.00 0.00 3.01
2922 5091 8.499162 GCAACTGGTCAACTGTATATCATAATC 58.501 37.037 0.00 0.00 0.00 1.75
2923 5092 8.213679 AGCAACTGGTCAACTGTATATCATAAT 58.786 33.333 0.00 0.00 0.00 1.28
2924 5093 7.564793 AGCAACTGGTCAACTGTATATCATAA 58.435 34.615 0.00 0.00 0.00 1.90
2925 5094 7.124573 AGCAACTGGTCAACTGTATATCATA 57.875 36.000 0.00 0.00 0.00 2.15
2926 5095 5.994250 AGCAACTGGTCAACTGTATATCAT 58.006 37.500 0.00 0.00 0.00 2.45
2927 5096 5.420725 AGCAACTGGTCAACTGTATATCA 57.579 39.130 0.00 0.00 0.00 2.15
2928 5097 5.463724 GCTAGCAACTGGTCAACTGTATATC 59.536 44.000 10.63 0.00 0.00 1.63
2929 5098 5.360591 GCTAGCAACTGGTCAACTGTATAT 58.639 41.667 10.63 0.00 0.00 0.86
2930 5099 4.382685 GGCTAGCAACTGGTCAACTGTATA 60.383 45.833 18.24 0.00 0.00 1.47
2931 5100 3.600388 GCTAGCAACTGGTCAACTGTAT 58.400 45.455 10.63 0.00 0.00 2.29
2947 5116 2.286294 CACACGAATTGAGATGGCTAGC 59.714 50.000 6.04 6.04 0.00 3.42
2948 5117 2.286294 GCACACGAATTGAGATGGCTAG 59.714 50.000 0.00 0.00 0.00 3.42
2950 5119 1.089920 GCACACGAATTGAGATGGCT 58.910 50.000 0.00 0.00 0.00 4.75
2954 5130 2.768253 TCAGGCACACGAATTGAGAT 57.232 45.000 0.00 0.00 0.00 2.75
2975 5155 5.617751 GCATCAACGAATAACAGAGCAAGTT 60.618 40.000 0.00 0.00 0.00 2.66
3194 5380 4.298103 AGAATCACTGCCAATCAGAAGT 57.702 40.909 0.00 0.00 45.72 3.01
3202 5388 6.469782 AAAAAGAAGAAGAATCACTGCCAA 57.530 33.333 0.00 0.00 0.00 4.52
3223 5409 2.360844 TCACTGCCGTTGTCTCAAAAA 58.639 42.857 0.00 0.00 0.00 1.94
3224 5410 2.031258 TCACTGCCGTTGTCTCAAAA 57.969 45.000 0.00 0.00 0.00 2.44
3225 5411 2.254546 ATCACTGCCGTTGTCTCAAA 57.745 45.000 0.00 0.00 0.00 2.69
3226 5412 2.143122 GAATCACTGCCGTTGTCTCAA 58.857 47.619 0.00 0.00 0.00 3.02
3227 5413 1.344438 AGAATCACTGCCGTTGTCTCA 59.656 47.619 0.00 0.00 0.00 3.27
3228 5414 2.086054 AGAATCACTGCCGTTGTCTC 57.914 50.000 0.00 0.00 0.00 3.36
3229 5415 2.037772 AGAAGAATCACTGCCGTTGTCT 59.962 45.455 0.00 0.00 0.00 3.41
3230 5416 2.417719 AGAAGAATCACTGCCGTTGTC 58.582 47.619 0.00 0.00 0.00 3.18
3231 5417 2.550830 AGAAGAATCACTGCCGTTGT 57.449 45.000 0.00 0.00 0.00 3.32
3232 5418 2.673368 GGTAGAAGAATCACTGCCGTTG 59.327 50.000 0.00 0.00 0.00 4.10
3233 5419 2.301870 TGGTAGAAGAATCACTGCCGTT 59.698 45.455 9.06 0.00 40.77 4.44
3234 5420 1.899814 TGGTAGAAGAATCACTGCCGT 59.100 47.619 9.06 0.00 40.77 5.68
3235 5421 2.093973 AGTGGTAGAAGAATCACTGCCG 60.094 50.000 9.06 0.00 40.77 5.69
3333 5521 2.009424 CTGCGGCGATGGAGAAGAGA 62.009 60.000 12.98 0.00 0.00 3.10
3611 5799 0.178973 TGTGAAGGTGGGAGAGACGA 60.179 55.000 0.00 0.00 0.00 4.20
3612 5800 0.244994 CTGTGAAGGTGGGAGAGACG 59.755 60.000 0.00 0.00 0.00 4.18
3613 5801 0.036858 GCTGTGAAGGTGGGAGAGAC 60.037 60.000 0.00 0.00 0.00 3.36
3614 5802 1.194781 GGCTGTGAAGGTGGGAGAGA 61.195 60.000 0.00 0.00 0.00 3.10
3615 5803 1.197430 AGGCTGTGAAGGTGGGAGAG 61.197 60.000 0.00 0.00 0.00 3.20
3616 5804 1.152030 AGGCTGTGAAGGTGGGAGA 60.152 57.895 0.00 0.00 0.00 3.71
3617 5805 1.298014 GAGGCTGTGAAGGTGGGAG 59.702 63.158 0.00 0.00 0.00 4.30
3618 5806 0.842030 ATGAGGCTGTGAAGGTGGGA 60.842 55.000 0.00 0.00 0.00 4.37
3619 5807 0.393537 GATGAGGCTGTGAAGGTGGG 60.394 60.000 0.00 0.00 0.00 4.61
3658 5867 5.586243 TCCTCAAAATTAGATGAAGCGAAGG 59.414 40.000 0.00 0.00 0.00 3.46
3684 5893 4.260702 CGCCATCTGCAAAAACAACAATTT 60.261 37.500 0.00 0.00 41.33 1.82


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

AutoCloner maintained by Alex Coulton.