Multiple sequence alignment - TraesCS7A01G384900

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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 TraesCS7A01G384900 chr7A 100.000 6040 0 0 1 6040 561577708 561583747 0.000000e+00 11154.0
1 TraesCS7A01G384900 chr7A 81.772 395 37 24 2453 2840 561579682 561580048 1.270000e-76 298.0
2 TraesCS7A01G384900 chr7A 81.772 395 37 24 1975 2341 561580160 561580547 1.270000e-76 298.0
3 TraesCS7A01G384900 chr7A 89.167 120 11 1 2835 2954 561580012 561580129 1.360000e-31 148.0
4 TraesCS7A01G384900 chr7A 89.167 120 11 1 2305 2422 561580542 561580661 1.360000e-31 148.0
5 TraesCS7A01G384900 chr7D 90.752 2433 125 30 12 2420 495691736 495694092 0.000000e+00 3155.0
6 TraesCS7A01G384900 chr7D 90.973 2149 106 40 3327 5406 495694854 495696983 0.000000e+00 2813.0
7 TraesCS7A01G384900 chr7D 92.719 467 26 6 5563 6024 495703847 495704310 0.000000e+00 667.0
8 TraesCS7A01G384900 chr7D 89.620 395 31 6 2452 2840 495694156 495694546 1.510000e-135 494.0
9 TraesCS7A01G384900 chr7D 82.932 498 48 18 1929 2399 495694115 495694602 1.210000e-111 414.0
10 TraesCS7A01G384900 chr7D 84.085 377 27 18 2467 2840 495693667 495694013 3.490000e-87 333.0
11 TraesCS7A01G384900 chr7D 83.955 268 30 6 2966 3230 495694601 495694858 1.680000e-60 244.0
12 TraesCS7A01G384900 chr7D 89.116 147 13 2 2835 2981 495693977 495694120 4.810000e-41 180.0
13 TraesCS7A01G384900 chr7D 83.636 110 10 5 3227 3335 29877576 29877474 4.980000e-16 97.1
14 TraesCS7A01G384900 chr7B 90.305 2455 136 37 12 2422 524030818 524033214 0.000000e+00 3121.0
15 TraesCS7A01G384900 chr7B 90.317 2148 119 40 3327 5406 524033937 524036063 0.000000e+00 2732.0
16 TraesCS7A01G384900 chr7B 92.635 611 32 8 5419 6024 524036117 524036719 0.000000e+00 867.0
17 TraesCS7A01G384900 chr7B 90.716 377 28 5 2467 2840 524033295 524033667 4.200000e-136 496.0
18 TraesCS7A01G384900 chr7B 82.530 498 50 16 1929 2399 524033236 524033723 2.620000e-108 403.0
19 TraesCS7A01G384900 chr7B 82.927 369 32 17 2467 2832 524032789 524033129 2.740000e-78 303.0
20 TraesCS7A01G384900 chr7B 93.464 153 10 0 4904 5056 353327115 353327267 1.690000e-55 228.0
21 TraesCS7A01G384900 chr3A 97.333 975 22 3 2979 3952 616476369 616475398 0.000000e+00 1653.0
22 TraesCS7A01G384900 chr3A 96.102 590 10 2 2402 2990 616477975 616477398 0.000000e+00 950.0
23 TraesCS7A01G384900 chr3A 81.013 395 40 23 1975 2341 616477923 616477536 1.280000e-71 281.0
24 TraesCS7A01G384900 chr3A 93.506 154 10 0 4904 5057 455229382 455229229 4.710000e-56 230.0
25 TraesCS7A01G384900 chr3B 92.810 153 11 0 4904 5056 449168132 449167980 7.880000e-54 222.0
26 TraesCS7A01G384900 chr3B 85.714 203 24 3 5108 5309 279961469 279961667 6.130000e-50 209.0
27 TraesCS7A01G384900 chr5B 80.919 283 48 3 5742 6024 498882828 498882552 1.020000e-52 219.0
28 TraesCS7A01G384900 chr5A 80.986 284 46 5 5742 6024 526396504 526396228 1.020000e-52 219.0
29 TraesCS7A01G384900 chr5A 92.233 103 8 0 4954 5056 85293640 85293538 4.880000e-31 147.0
30 TraesCS7A01G384900 chr3D 91.558 154 13 0 4903 5056 9423571 9423724 4.740000e-51 213.0
31 TraesCS7A01G384900 chr4D 75.244 307 46 16 101 407 446426302 446426578 1.060000e-22 119.0
32 TraesCS7A01G384900 chr4D 83.178 107 12 3 3226 3332 385735099 385734999 6.450000e-15 93.5
33 TraesCS7A01G384900 chrUn 85.321 109 11 3 3225 3332 42338444 42338340 2.300000e-19 108.0
34 TraesCS7A01G384900 chrUn 85.321 109 11 3 3225 3332 42530505 42530609 2.300000e-19 108.0
35 TraesCS7A01G384900 chrUn 85.321 109 11 3 3225 3332 474064158 474064262 2.300000e-19 108.0
36 TraesCS7A01G384900 chr6D 84.466 103 9 3 3226 3328 324520679 324520774 1.790000e-15 95.3
37 TraesCS7A01G384900 chr6B 83.019 106 12 4 3224 3329 567471601 567471502 2.320000e-14 91.6
38 TraesCS7A01G384900 chr2D 83.495 103 10 5 3227 3329 363977841 363977936 8.340000e-14 89.8
39 TraesCS7A01G384900 chr2D 100.000 28 0 0 2430 2457 631242684 631242657 1.100000e-02 52.8
40 TraesCS7A01G384900 chr4A 97.059 34 1 0 1481 1514 607309940 607309973 2.350000e-04 58.4


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 TraesCS7A01G384900 chr7A 561577708 561583747 6039 False 11154.000000 11154 100.000000 1 6040 1 chr7A.!!$F1 6039
1 TraesCS7A01G384900 chr7A 561579682 561580661 979 False 223.000000 298 85.469500 1975 2954 4 chr7A.!!$F2 979
2 TraesCS7A01G384900 chr7D 495691736 495696983 5247 False 1090.428571 3155 87.347571 12 5406 7 chr7D.!!$F2 5394
3 TraesCS7A01G384900 chr7B 524030818 524036719 5901 False 1320.333333 3121 88.238333 12 6024 6 chr7B.!!$F2 6012
4 TraesCS7A01G384900 chr3A 616475398 616477975 2577 True 961.333333 1653 91.482667 1975 3952 3 chr3A.!!$R2 1977

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
877 936 0.179000 CCATCCCCTTCCTCAACGAG 59.821 60.000 0.0 0.0 0.0 4.18 F
1249 1318 0.698238 TCCAACCCAATCCAGTCCAG 59.302 55.000 0.0 0.0 0.0 3.86 F
1634 1703 1.915141 AAGCCACCTCCAAGATTGTG 58.085 50.000 0.0 0.0 0.0 3.33 F
1739 1808 3.349006 GTGCCAGTGTCTGCCGTG 61.349 66.667 0.0 0.0 0.0 4.94 F
3438 4588 8.473358 AAATACTTGGTTTACTGCCTACTTTT 57.527 30.769 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1808 2.143925 AGCTTGTTGGCGAGACTAAAC 58.856 47.619 0.00 0.0 37.29 2.01 R
3197 4346 3.051081 AGGCTTAGCTGAACAGAACAG 57.949 47.619 3.59 0.0 38.27 3.16 R
3438 4588 4.777896 ACCAGTAGATTCCTAAGCAAGACA 59.222 41.667 0.00 0.0 0.00 3.41 R
3714 4920 4.100035 CCTCACCTCATATGACTAGCAACA 59.900 45.833 0.00 0.0 0.00 3.33 R
5162 6403 0.608130 TCCACACAGAGAACGATGGG 59.392 55.000 0.00 0.0 0.00 4.00 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
21 22 1.433592 ACACACTAAGGAGGAGGAGGT 59.566 52.381 0.00 0.00 0.00 3.85
54 55 1.839747 TGTGTCCAACCCCTACGCT 60.840 57.895 0.00 0.00 0.00 5.07
60 61 0.834612 CCAACCCCTACGCTTGGATA 59.165 55.000 0.00 0.00 37.25 2.59
90 91 2.399856 CTCGACGAAGGAGGAGGAG 58.600 63.158 0.00 0.00 0.00 3.69
108 109 3.141272 AGGAGGACGATTAGGAGAAGGAT 59.859 47.826 0.00 0.00 0.00 3.24
118 119 1.330655 GGAGAAGGATGAGGGCGACA 61.331 60.000 0.00 0.00 0.00 4.35
137 138 1.310933 AACTAGACGACGTCGGGCAT 61.311 55.000 37.89 23.30 44.95 4.40
148 149 1.688772 GTCGGGCATCTAGGAGTGTA 58.311 55.000 0.00 0.00 0.00 2.90
156 157 0.538584 TCTAGGAGTGTAGGCGTCGA 59.461 55.000 0.00 0.00 0.00 4.20
197 209 7.370044 TGAAAACGTCGTTAAATGTCATTTG 57.630 32.000 19.10 4.70 33.82 2.32
289 312 7.601130 GCGGATTTTGGTTCCTTTTATAGTTTT 59.399 33.333 0.00 0.00 0.00 2.43
336 359 0.309302 TGAAACATGCGTTCGGTTGG 59.691 50.000 0.00 0.00 32.91 3.77
338 361 1.104577 AAACATGCGTTCGGTTGGGT 61.105 50.000 0.00 0.00 32.91 4.51
345 368 1.135603 GCGTTCGGTTGGGTTTAATCC 60.136 52.381 0.00 0.00 0.00 3.01
352 375 0.410270 TTGGGTTTAATCCGCCCCTT 59.590 50.000 0.00 0.00 41.66 3.95
371 394 7.978975 CGCCCCTTCATTATTAAAGAAAATGAA 59.021 33.333 8.83 8.83 43.65 2.57
416 447 5.860941 AAGATATGGAGGCCGTGATATAG 57.139 43.478 0.00 0.00 0.00 1.31
432 463 6.153067 GTGATATAGCGACTCTGTATTTGCT 58.847 40.000 0.00 0.00 30.45 3.91
436 467 2.232452 AGCGACTCTGTATTTGCTCACT 59.768 45.455 0.00 0.00 0.00 3.41
443 474 2.106074 TATTTGCTCACTGCCGCCG 61.106 57.895 0.00 0.00 42.00 6.46
480 512 4.972286 TCAATATGAAACGCGCTCATAG 57.028 40.909 26.15 17.98 38.75 2.23
487 519 3.816697 CGCGCTCATAGCTCGTAC 58.183 61.111 5.56 0.00 43.62 3.67
492 524 1.726251 CGCTCATAGCTCGTACATCGG 60.726 57.143 0.00 0.00 39.60 4.18
551 587 3.127589 GCGGTGTTTGTTTTGGCTAAAT 58.872 40.909 0.00 0.00 0.00 1.40
570 606 7.912773 GGCTAAATACTCAAATGAGAGCTTTTC 59.087 37.037 16.93 8.15 44.74 2.29
640 699 9.283420 GAACACAAAAGAAGAAGAAGAAAAGAG 57.717 33.333 0.00 0.00 0.00 2.85
646 705 6.816134 AGAAGAAGAAGAAAAGAGCCAATC 57.184 37.500 0.00 0.00 0.00 2.67
647 706 6.302269 AGAAGAAGAAGAAAAGAGCCAATCA 58.698 36.000 0.00 0.00 0.00 2.57
652 711 4.397417 AGAAGAAAAGAGCCAATCAATCCG 59.603 41.667 0.00 0.00 0.00 4.18
665 724 3.662117 AATCCGGGCTCCCTTTGGC 62.662 63.158 0.00 0.00 0.00 4.52
730 789 1.661112 GCAACAGCGACCAGAAGTATC 59.339 52.381 0.00 0.00 0.00 2.24
731 790 2.930887 GCAACAGCGACCAGAAGTATCA 60.931 50.000 0.00 0.00 0.00 2.15
732 791 3.525537 CAACAGCGACCAGAAGTATCAT 58.474 45.455 0.00 0.00 0.00 2.45
733 792 3.444703 ACAGCGACCAGAAGTATCATC 57.555 47.619 0.00 0.00 0.00 2.92
734 793 2.101582 ACAGCGACCAGAAGTATCATCC 59.898 50.000 0.00 0.00 0.00 3.51
841 900 1.527370 CAATCCCTTCTCCCGTCCC 59.473 63.158 0.00 0.00 0.00 4.46
877 936 0.179000 CCATCCCCTTCCTCAACGAG 59.821 60.000 0.00 0.00 0.00 4.18
1212 1271 2.149578 CCCTACGAGGTAGTATCACCG 58.850 57.143 0.00 0.00 43.84 4.94
1249 1318 0.698238 TCCAACCCAATCCAGTCCAG 59.302 55.000 0.00 0.00 0.00 3.86
1634 1703 1.915141 AAGCCACCTCCAAGATTGTG 58.085 50.000 0.00 0.00 0.00 3.33
1670 1739 5.298026 GGAATTGATCCTTCCTGCTTCTAAC 59.702 44.000 14.12 0.00 45.56 2.34
1739 1808 3.349006 GTGCCAGTGTCTGCCGTG 61.349 66.667 0.00 0.00 0.00 4.94
3438 4588 8.473358 AAATACTTGGTTTACTGCCTACTTTT 57.527 30.769 0.00 0.00 0.00 2.27
3714 4920 9.998106 AGTAGTTTACTTCATGATACACTTGTT 57.002 29.630 0.00 0.00 34.86 2.83
3989 5199 9.311916 CCTTTTTATTTCGGAATATCAAATGCA 57.688 29.630 0.00 0.00 0.00 3.96
4020 5230 8.677300 GGATGTTGCAATCTTAACAGAAGATAA 58.323 33.333 0.59 0.00 39.83 1.75
4053 5265 9.653287 ATGATAATAAGTGGTCATGGTTATACG 57.347 33.333 0.00 0.00 30.61 3.06
4055 5267 9.136952 GATAATAAGTGGTCATGGTTATACGTC 57.863 37.037 0.00 0.00 0.00 4.34
4056 5268 3.814005 AGTGGTCATGGTTATACGTCC 57.186 47.619 0.00 0.00 0.00 4.79
4078 5290 6.003950 TCCAAACTTTTGATCTCTAAGGTGG 58.996 40.000 3.17 14.10 40.55 4.61
4090 5302 6.019656 TCTCTAAGGTGGACATGAGATAGT 57.980 41.667 0.00 0.00 0.00 2.12
4118 5330 7.779754 TTTTTCCTGGAGAATGAATGATCAA 57.220 32.000 0.00 0.00 39.49 2.57
4119 5331 7.400599 TTTTCCTGGAGAATGAATGATCAAG 57.599 36.000 0.00 0.00 39.49 3.02
4120 5332 4.458397 TCCTGGAGAATGAATGATCAAGC 58.542 43.478 0.00 0.00 39.49 4.01
4121 5333 4.080186 TCCTGGAGAATGAATGATCAAGCA 60.080 41.667 0.00 0.83 39.49 3.91
4122 5334 4.276183 CCTGGAGAATGAATGATCAAGCAG 59.724 45.833 0.00 0.00 39.49 4.24
4148 5372 2.488153 GTTCTGATGCCCAGTTGGTTAC 59.512 50.000 0.00 0.00 43.38 2.50
4167 5391 2.173519 ACCCACATGAGATTTGCTTGG 58.826 47.619 0.00 0.00 0.00 3.61
4168 5392 1.134907 CCCACATGAGATTTGCTTGGC 60.135 52.381 0.00 0.00 0.00 4.52
4169 5393 1.134907 CCACATGAGATTTGCTTGGCC 60.135 52.381 0.00 0.00 0.00 5.36
4202 5426 8.742777 ACATCTGTAAATAATGAATGTGCAAGT 58.257 29.630 0.00 0.00 0.00 3.16
4206 5430 9.838975 CTGTAAATAATGAATGTGCAAGTTACA 57.161 29.630 0.00 0.00 0.00 2.41
4450 5684 7.851387 TGATTACGATTACATTGCCAGTTTA 57.149 32.000 0.00 0.00 0.00 2.01
5025 6266 7.440523 TCCTTTTGCTAGATCTCTGAAAAAC 57.559 36.000 0.00 0.00 0.00 2.43
5162 6403 1.197721 CCCGCACTGATGTTTTGAGTC 59.802 52.381 0.00 0.00 0.00 3.36
5186 6427 4.216257 CCATCGTTCTCTGTGTGGAAAATT 59.784 41.667 0.00 0.00 0.00 1.82
5193 6434 6.808008 TCTCTGTGTGGAAAATTCAGAATC 57.192 37.500 0.00 0.00 35.26 2.52
5196 6437 6.778821 TCTGTGTGGAAAATTCAGAATCCTA 58.221 36.000 0.00 0.00 33.18 2.94
5256 6497 8.401046 TCTTGTAATTTTCGTTTTGGAACTTG 57.599 30.769 0.00 0.00 33.51 3.16
5279 6520 6.120905 TGACTATTGTAGGGTAGACAGACTC 58.879 44.000 0.00 0.00 0.00 3.36
5313 6554 2.450476 AGAAATGTGCCCTTCCATCAC 58.550 47.619 0.00 0.00 0.00 3.06
5317 6558 0.409092 TGTGCCCTTCCATCACCATT 59.591 50.000 0.00 0.00 0.00 3.16
5318 6559 1.106285 GTGCCCTTCCATCACCATTC 58.894 55.000 0.00 0.00 0.00 2.67
5366 6607 9.430838 CATTCGTTCTTTTCATATCATCTGAAC 57.569 33.333 0.00 0.00 32.57 3.18
5388 6629 7.390440 TGAACATTATTTACAACCCTGTCTCTG 59.610 37.037 0.00 0.00 36.96 3.35
5391 6632 7.724061 ACATTATTTACAACCCTGTCTCTGTTT 59.276 33.333 0.00 0.00 36.96 2.83
5392 6633 8.576442 CATTATTTACAACCCTGTCTCTGTTTT 58.424 33.333 0.00 0.00 36.96 2.43
5431 6713 4.499865 CCTCGGATGACATAAACGATCAGT 60.500 45.833 9.03 0.00 32.75 3.41
5441 6723 2.717580 AACGATCAGTGACGCTTGTA 57.282 45.000 12.90 0.00 0.00 2.41
5445 6727 3.994392 ACGATCAGTGACGCTTGTATTTT 59.006 39.130 12.90 0.00 0.00 1.82
5446 6728 4.091509 ACGATCAGTGACGCTTGTATTTTC 59.908 41.667 12.90 0.00 0.00 2.29
5447 6729 4.091365 CGATCAGTGACGCTTGTATTTTCA 59.909 41.667 0.00 0.00 0.00 2.69
5448 6730 4.990543 TCAGTGACGCTTGTATTTTCAG 57.009 40.909 0.00 0.00 0.00 3.02
5449 6731 3.186409 TCAGTGACGCTTGTATTTTCAGC 59.814 43.478 0.00 0.00 0.00 4.26
5455 6737 4.065088 ACGCTTGTATTTTCAGCAAGAGA 58.935 39.130 12.61 0.00 40.68 3.10
5490 6772 2.124983 ATGAGCTGCGCGATTGGT 60.125 55.556 12.10 3.66 0.00 3.67
5498 6780 1.132640 GCGCGATTGGTGTCTTCAC 59.867 57.895 12.10 0.00 43.19 3.18
5532 6814 2.479837 TGAACGATTTGAGACGCTTGT 58.520 42.857 0.00 0.00 0.00 3.16
5533 6815 3.644823 TGAACGATTTGAGACGCTTGTA 58.355 40.909 0.00 0.00 0.00 2.41
5534 6816 4.242475 TGAACGATTTGAGACGCTTGTAT 58.758 39.130 0.00 0.00 0.00 2.29
5536 6818 5.178623 TGAACGATTTGAGACGCTTGTATTT 59.821 36.000 0.00 0.00 0.00 1.40
5537 6819 5.204673 ACGATTTGAGACGCTTGTATTTC 57.795 39.130 0.00 0.00 0.00 2.17
5538 6820 4.092968 ACGATTTGAGACGCTTGTATTTCC 59.907 41.667 0.00 0.00 0.00 3.13
5539 6821 4.092821 CGATTTGAGACGCTTGTATTTCCA 59.907 41.667 0.00 0.00 0.00 3.53
5540 6822 5.551760 ATTTGAGACGCTTGTATTTCCAG 57.448 39.130 0.00 0.00 0.00 3.86
5541 6823 2.346803 TGAGACGCTTGTATTTCCAGC 58.653 47.619 0.00 0.00 0.00 4.85
5542 6824 1.666189 GAGACGCTTGTATTTCCAGCC 59.334 52.381 0.00 0.00 0.00 4.85
5543 6825 1.003118 AGACGCTTGTATTTCCAGCCA 59.997 47.619 0.00 0.00 0.00 4.75
5544 6826 1.810151 GACGCTTGTATTTCCAGCCAA 59.190 47.619 0.00 0.00 0.00 4.52
5583 6867 6.481313 GCTGAATACATCATATGGCATCGTAT 59.519 38.462 1.65 2.22 37.44 3.06
5584 6868 7.307042 GCTGAATACATCATATGGCATCGTATC 60.307 40.741 1.65 1.42 37.44 2.24
5585 6869 6.697019 TGAATACATCATATGGCATCGTATCG 59.303 38.462 1.65 0.00 31.50 2.92
5586 6870 4.456280 ACATCATATGGCATCGTATCGT 57.544 40.909 1.65 0.00 33.60 3.73
5587 6871 5.576447 ACATCATATGGCATCGTATCGTA 57.424 39.130 1.65 0.00 33.60 3.43
5588 6872 6.149129 ACATCATATGGCATCGTATCGTAT 57.851 37.500 1.65 0.00 33.60 3.06
5634 6918 2.189594 CCTGCTTGGTGTCTTCATGA 57.810 50.000 0.00 0.00 0.00 3.07
5663 6947 0.818445 CCATCATGGACAGCTCCTGC 60.818 60.000 0.00 0.00 40.96 4.85
5747 7031 4.379243 AGCGGCTTCCTGGACACG 62.379 66.667 0.00 2.51 0.00 4.49
6024 7311 2.655364 CGTAGACGAGCATGGCGG 60.655 66.667 0.00 0.00 43.02 6.13
6025 7312 2.494918 GTAGACGAGCATGGCGGT 59.505 61.111 0.00 0.00 0.00 5.68
6026 7313 1.731700 GTAGACGAGCATGGCGGTA 59.268 57.895 0.00 0.00 0.00 4.02
6027 7314 0.317938 GTAGACGAGCATGGCGGTAG 60.318 60.000 0.00 0.00 0.00 3.18
6028 7315 0.750546 TAGACGAGCATGGCGGTAGT 60.751 55.000 0.00 0.00 33.29 2.73
6029 7316 0.750546 AGACGAGCATGGCGGTAGTA 60.751 55.000 0.00 0.00 30.51 1.82
6030 7317 0.317938 GACGAGCATGGCGGTAGTAG 60.318 60.000 0.00 0.00 30.51 2.57
6031 7318 1.007271 CGAGCATGGCGGTAGTAGG 60.007 63.158 0.00 0.00 0.00 3.18
6032 7319 1.301009 GAGCATGGCGGTAGTAGGC 60.301 63.158 0.00 0.00 0.00 3.93
6033 7320 2.661866 GCATGGCGGTAGTAGGCG 60.662 66.667 0.00 0.00 36.92 5.52
6034 7321 2.661866 CATGGCGGTAGTAGGCGC 60.662 66.667 0.00 0.00 36.92 6.53
6035 7322 2.838225 ATGGCGGTAGTAGGCGCT 60.838 61.111 7.64 0.00 36.92 5.92
6036 7323 3.151958 ATGGCGGTAGTAGGCGCTG 62.152 63.158 7.64 0.00 36.92 5.18
6037 7324 4.587189 GGCGGTAGTAGGCGCTGG 62.587 72.222 7.64 0.00 0.00 4.85
6038 7325 3.834799 GCGGTAGTAGGCGCTGGT 61.835 66.667 7.64 0.00 0.00 4.00
6039 7326 2.104331 CGGTAGTAGGCGCTGGTG 59.896 66.667 7.64 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.827969 CCTCCTCCTCCTTAGTGTGTG 59.172 57.143 0.00 0.00 0.00 3.82
1 2 1.433592 ACCTCCTCCTCCTTAGTGTGT 59.566 52.381 0.00 0.00 0.00 3.72
2 3 1.827969 CACCTCCTCCTCCTTAGTGTG 59.172 57.143 0.00 0.00 0.00 3.82
3 4 1.897647 GCACCTCCTCCTCCTTAGTGT 60.898 57.143 0.00 0.00 0.00 3.55
4 5 0.827368 GCACCTCCTCCTCCTTAGTG 59.173 60.000 0.00 0.00 0.00 2.74
5 6 0.713579 AGCACCTCCTCCTCCTTAGT 59.286 55.000 0.00 0.00 0.00 2.24
6 7 2.312390 GTAGCACCTCCTCCTCCTTAG 58.688 57.143 0.00 0.00 0.00 2.18
7 8 1.644337 TGTAGCACCTCCTCCTCCTTA 59.356 52.381 0.00 0.00 0.00 2.69
8 9 0.413832 TGTAGCACCTCCTCCTCCTT 59.586 55.000 0.00 0.00 0.00 3.36
9 10 0.032615 CTGTAGCACCTCCTCCTCCT 60.033 60.000 0.00 0.00 0.00 3.69
10 11 0.324830 ACTGTAGCACCTCCTCCTCC 60.325 60.000 0.00 0.00 0.00 4.30
21 22 1.081442 CACACGAGCGACTGTAGCA 60.081 57.895 15.17 0.00 37.01 3.49
90 91 3.257127 CCTCATCCTTCTCCTAATCGTCC 59.743 52.174 0.00 0.00 0.00 4.79
108 109 0.607217 TCGTCTAGTTGTCGCCCTCA 60.607 55.000 0.00 0.00 0.00 3.86
118 119 1.310933 ATGCCCGACGTCGTCTAGTT 61.311 55.000 33.49 12.55 37.74 2.24
137 138 0.538584 TCGACGCCTACACTCCTAGA 59.461 55.000 0.00 0.00 0.00 2.43
148 149 1.605753 TGCTATCTACATCGACGCCT 58.394 50.000 0.00 0.00 0.00 5.52
156 157 5.296780 CGTTTTCAACCCATGCTATCTACAT 59.703 40.000 0.00 0.00 0.00 2.29
223 235 4.569719 ACTATCACCGGGAACAGAATTT 57.430 40.909 6.32 0.00 0.00 1.82
228 240 6.579865 ACTATAAAACTATCACCGGGAACAG 58.420 40.000 6.32 5.05 0.00 3.16
330 353 1.659622 GGGCGGATTAAACCCAACCG 61.660 60.000 0.00 0.00 43.64 4.44
336 359 2.067365 ATGAAGGGGCGGATTAAACC 57.933 50.000 0.00 0.00 0.00 3.27
338 361 7.780745 TCTTTAATAATGAAGGGGCGGATTAAA 59.219 33.333 0.00 0.00 0.00 1.52
345 368 7.488322 TCATTTTCTTTAATAATGAAGGGGCG 58.512 34.615 0.00 0.00 35.86 6.13
381 412 8.793592 GGCCTCCATATCTTTTCGTTTATTTAT 58.206 33.333 0.00 0.00 0.00 1.40
382 413 7.041644 CGGCCTCCATATCTTTTCGTTTATTTA 60.042 37.037 0.00 0.00 0.00 1.40
391 422 3.194005 TCACGGCCTCCATATCTTTTC 57.806 47.619 0.00 0.00 0.00 2.29
416 447 2.346847 CAGTGAGCAAATACAGAGTCGC 59.653 50.000 0.00 0.00 0.00 5.19
443 474 2.042686 TTGATATGCAGACCACTGGC 57.957 50.000 0.00 0.00 43.62 4.85
445 476 7.358066 GTTTCATATTGATATGCAGACCACTG 58.642 38.462 6.19 0.00 45.91 3.66
446 477 6.203530 CGTTTCATATTGATATGCAGACCACT 59.796 38.462 6.19 0.00 39.90 4.00
480 512 1.298190 GGACGACCGATGTACGAGC 60.298 63.158 0.00 0.00 45.77 5.03
484 516 3.562505 GTCATATGGACGACCGATGTAC 58.437 50.000 14.89 10.00 36.65 2.90
640 699 2.196245 GGAGCCCGGATTGATTGGC 61.196 63.158 0.73 0.00 44.35 4.52
646 705 1.754234 CCAAAGGGAGCCCGGATTG 60.754 63.158 0.73 12.11 41.95 2.67
647 706 2.683475 CCAAAGGGAGCCCGGATT 59.317 61.111 0.73 0.00 41.95 3.01
656 715 3.179339 TTGGGTCGGCCAAAGGGA 61.179 61.111 9.07 0.00 35.59 4.20
665 724 2.943033 GTGAATAGATTGGTTGGGTCGG 59.057 50.000 0.00 0.00 0.00 4.79
718 777 3.008485 GGGATGGGATGATACTTCTGGTC 59.992 52.174 0.00 0.00 0.00 4.02
730 789 2.192979 CGTGGGTGGGATGGGATG 59.807 66.667 0.00 0.00 0.00 3.51
731 790 3.809013 GCGTGGGTGGGATGGGAT 61.809 66.667 0.00 0.00 0.00 3.85
841 900 1.885049 TGGGATGGAGAAGGGAAGAG 58.115 55.000 0.00 0.00 0.00 2.85
877 936 1.444917 GGGGGATTGGATTCGTTCGC 61.445 60.000 0.00 0.00 0.00 4.70
925 984 2.204464 AAGGGAAAGGGGAGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
926 985 2.317378 GGAAGGGAAAGGGGAGGGG 61.317 68.421 0.00 0.00 0.00 4.79
927 986 2.317378 GGGAAGGGAAAGGGGAGGG 61.317 68.421 0.00 0.00 0.00 4.30
928 987 2.317378 GGGGAAGGGAAAGGGGAGG 61.317 68.421 0.00 0.00 0.00 4.30
929 988 2.317378 GGGGGAAGGGAAAGGGGAG 61.317 68.421 0.00 0.00 0.00 4.30
930 989 2.204401 GGGGGAAGGGAAAGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
1212 1271 0.756815 GATTGGAATGGGTGGAGGGC 60.757 60.000 0.00 0.00 0.00 5.19
1276 1345 2.369477 GATTAAATTCGGGCGCGCGT 62.369 55.000 39.61 26.17 0.00 6.01
1434 1503 1.064458 GCCGTAGACGAAGAGCTCC 59.936 63.158 10.93 0.00 43.02 4.70
1445 1514 1.949847 GCTGAGGAGCTTGCCGTAGA 61.950 60.000 0.00 0.00 42.52 2.59
1467 1536 1.613630 GAGGAGCACCCCCTTCTGA 60.614 63.158 0.00 0.00 36.73 3.27
1634 1703 0.968405 TCAATTCCAGCAAACAGGGC 59.032 50.000 0.00 0.00 0.00 5.19
1670 1739 7.712639 ACAACAGATATATACACAGAGCAAAGG 59.287 37.037 0.00 0.00 0.00 3.11
1702 1771 4.457810 CACAGAGTTACACAAAATGAGCG 58.542 43.478 0.00 0.00 0.00 5.03
1739 1808 2.143925 AGCTTGTTGGCGAGACTAAAC 58.856 47.619 0.00 0.00 37.29 2.01
3056 4202 7.381766 TCAAATTGACATGTATTGGACTGAG 57.618 36.000 0.00 0.00 0.00 3.35
3197 4346 3.051081 AGGCTTAGCTGAACAGAACAG 57.949 47.619 3.59 0.00 38.27 3.16
3276 4425 5.607477 TGCTTTAGTACAGCTTTGTACAGT 58.393 37.500 16.09 2.29 45.07 3.55
3277 4426 6.158175 CTGCTTTAGTACAGCTTTGTACAG 57.842 41.667 16.09 7.90 45.07 2.74
3422 4571 5.008712 AGCAAGACAAAAGTAGGCAGTAAAC 59.991 40.000 0.00 0.00 0.00 2.01
3438 4588 4.777896 ACCAGTAGATTCCTAAGCAAGACA 59.222 41.667 0.00 0.00 0.00 3.41
3714 4920 4.100035 CCTCACCTCATATGACTAGCAACA 59.900 45.833 0.00 0.00 0.00 3.33
3969 5179 8.352201 CCTTTCTGCATTTGATATTCCGAAATA 58.648 33.333 0.00 0.00 0.00 1.40
3970 5180 7.068593 TCCTTTCTGCATTTGATATTCCGAAAT 59.931 33.333 0.00 0.00 0.00 2.17
3971 5181 6.376864 TCCTTTCTGCATTTGATATTCCGAAA 59.623 34.615 0.00 0.00 0.00 3.46
3973 5183 5.436175 TCCTTTCTGCATTTGATATTCCGA 58.564 37.500 0.00 0.00 0.00 4.55
3974 5184 5.756195 TCCTTTCTGCATTTGATATTCCG 57.244 39.130 0.00 0.00 0.00 4.30
3975 5185 7.047460 ACATCCTTTCTGCATTTGATATTCC 57.953 36.000 0.00 0.00 0.00 3.01
3976 5186 7.042925 GCAACATCCTTTCTGCATTTGATATTC 60.043 37.037 0.00 0.00 34.87 1.75
3989 5199 6.716628 TCTGTTAAGATTGCAACATCCTTTCT 59.283 34.615 0.00 0.00 34.34 2.52
3991 5201 6.899393 TCTGTTAAGATTGCAACATCCTTT 57.101 33.333 0.00 0.00 34.34 3.11
3992 5202 6.716628 TCTTCTGTTAAGATTGCAACATCCTT 59.283 34.615 0.00 5.91 34.34 3.36
4029 5241 9.136952 GACGTATAACCATGACCACTTATTATC 57.863 37.037 0.00 0.00 0.00 1.75
4039 5251 4.510571 AGTTTGGACGTATAACCATGACC 58.489 43.478 0.00 0.00 36.02 4.02
4042 5254 6.904498 TCAAAAGTTTGGACGTATAACCATG 58.096 36.000 4.04 0.00 38.66 3.66
4043 5255 7.610305 AGATCAAAAGTTTGGACGTATAACCAT 59.390 33.333 0.00 0.00 38.66 3.55
4047 5259 9.932207 TTAGAGATCAAAAGTTTGGACGTATAA 57.068 29.630 0.00 0.00 38.66 0.98
4053 5265 6.072452 CCACCTTAGAGATCAAAAGTTTGGAC 60.072 42.308 0.00 0.00 38.66 4.02
4055 5267 6.003950 TCCACCTTAGAGATCAAAAGTTTGG 58.996 40.000 4.04 4.78 38.66 3.28
4056 5268 6.486657 TGTCCACCTTAGAGATCAAAAGTTTG 59.513 38.462 0.00 0.00 39.48 2.93
4121 5333 3.446442 ACTGGGCATCAGAACAAATCT 57.554 42.857 12.38 0.00 46.18 2.40
4122 5334 3.367703 CCAACTGGGCATCAGAACAAATC 60.368 47.826 12.38 0.00 46.18 2.17
4148 5372 1.134907 GCCAAGCAAATCTCATGTGGG 60.135 52.381 0.00 0.00 0.00 4.61
4236 5470 9.599866 TCTCTACACAACCATAATAATTGTCAG 57.400 33.333 0.00 0.00 34.36 3.51
4252 5486 3.005367 TCACACGAGCATTCTCTACACAA 59.995 43.478 0.00 0.00 37.19 3.33
4432 5666 6.117911 TCACATAAACTGGCAATGTAATCG 57.882 37.500 2.43 0.00 32.70 3.34
4450 5684 1.282157 GACCCAGTAAAGCCCTCACAT 59.718 52.381 0.00 0.00 0.00 3.21
4552 5786 8.994429 AGAGAAAGTACTGAATACTCACATTG 57.006 34.615 0.00 0.00 43.79 2.82
4654 5892 4.543590 ATGGTCCTATTTCGCTATCCAG 57.456 45.455 0.00 0.00 0.00 3.86
4689 5930 7.298507 TGCATAATGAGGAACTTACGTTAAC 57.701 36.000 0.00 0.00 41.55 2.01
5025 6266 2.509336 CGCTTACTCCACTGCGGG 60.509 66.667 0.00 0.00 43.97 6.13
5162 6403 0.608130 TCCACACAGAGAACGATGGG 59.392 55.000 0.00 0.00 0.00 4.00
5214 6455 3.181451 ACAAGATGAGCAGACCAGAACAA 60.181 43.478 0.00 0.00 0.00 2.83
5215 6456 2.369860 ACAAGATGAGCAGACCAGAACA 59.630 45.455 0.00 0.00 0.00 3.18
5216 6457 3.051081 ACAAGATGAGCAGACCAGAAC 57.949 47.619 0.00 0.00 0.00 3.01
5217 6458 4.890158 TTACAAGATGAGCAGACCAGAA 57.110 40.909 0.00 0.00 0.00 3.02
5218 6459 5.426689 AATTACAAGATGAGCAGACCAGA 57.573 39.130 0.00 0.00 0.00 3.86
5227 6468 8.690840 GTTCCAAAACGAAAATTACAAGATGAG 58.309 33.333 0.00 0.00 0.00 2.90
5256 6497 5.532032 GGAGTCTGTCTACCCTACAATAGTC 59.468 48.000 0.00 0.00 0.00 2.59
5279 6520 6.428159 GGGCACATTTCTTCAGTATGTATAGG 59.572 42.308 0.00 0.00 37.40 2.57
5334 6575 8.956533 TGATATGAAAAGAACGAATGGTATGA 57.043 30.769 0.00 0.00 0.00 2.15
5335 6576 9.817365 GATGATATGAAAAGAACGAATGGTATG 57.183 33.333 0.00 0.00 0.00 2.39
5341 6582 9.166173 TGTTCAGATGATATGAAAAGAACGAAT 57.834 29.630 3.82 0.00 38.34 3.34
5366 6607 7.687941 AACAGAGACAGGGTTGTAAATAATG 57.312 36.000 0.00 0.00 37.76 1.90
5371 6612 5.502079 TCAAAACAGAGACAGGGTTGTAAA 58.498 37.500 0.00 0.00 37.76 2.01
5374 6615 3.644966 TCAAAACAGAGACAGGGTTGT 57.355 42.857 0.00 0.00 41.18 3.32
5377 6618 4.713792 AGAATCAAAACAGAGACAGGGT 57.286 40.909 0.00 0.00 0.00 4.34
5431 6713 3.812609 TCTTGCTGAAAATACAAGCGTCA 59.187 39.130 0.00 0.00 40.45 4.35
5480 6762 1.132640 GTGAAGACACCAATCGCGC 59.867 57.895 0.00 0.00 40.74 6.86
5482 6764 1.787847 CCGTGAAGACACCAATCGC 59.212 57.895 0.00 0.00 43.34 4.58
5483 6765 1.787847 GCCGTGAAGACACCAATCG 59.212 57.895 0.00 0.00 43.34 3.34
5485 6767 2.325082 GCGCCGTGAAGACACCAAT 61.325 57.895 0.00 0.00 43.34 3.16
5490 6772 2.933878 AAACCAGCGCCGTGAAGACA 62.934 55.000 2.29 0.00 0.00 3.41
5498 6780 1.154225 GTTCATGAAACCAGCGCCG 60.154 57.895 10.35 0.00 31.20 6.46
5533 6815 7.653311 GCGATTAATTAATTCTTGGCTGGAAAT 59.347 33.333 11.92 0.00 0.00 2.17
5534 6816 6.978080 GCGATTAATTAATTCTTGGCTGGAAA 59.022 34.615 11.92 0.00 0.00 3.13
5536 6818 5.827797 AGCGATTAATTAATTCTTGGCTGGA 59.172 36.000 11.92 0.00 0.00 3.86
5537 6819 5.916883 CAGCGATTAATTAATTCTTGGCTGG 59.083 40.000 24.40 14.32 40.17 4.85
5538 6820 6.728200 TCAGCGATTAATTAATTCTTGGCTG 58.272 36.000 25.28 25.28 43.94 4.85
5539 6821 6.942532 TCAGCGATTAATTAATTCTTGGCT 57.057 33.333 11.92 8.65 0.00 4.75
5540 6822 9.118236 GTATTCAGCGATTAATTAATTCTTGGC 57.882 33.333 11.92 6.58 0.00 4.52
5572 6856 3.570926 ACGAATACGATACGATGCCAT 57.429 42.857 0.00 0.00 42.66 4.40
5583 6867 2.347939 GCTCGACGTGATACGAATACGA 60.348 50.000 8.48 11.30 46.05 3.43
5584 6868 1.961214 GCTCGACGTGATACGAATACG 59.039 52.381 8.48 8.11 46.05 3.06
5585 6869 2.978013 TGCTCGACGTGATACGAATAC 58.022 47.619 8.48 0.00 46.05 1.89
5586 6870 3.249080 TCATGCTCGACGTGATACGAATA 59.751 43.478 8.48 0.00 46.05 1.75
5587 6871 2.032924 TCATGCTCGACGTGATACGAAT 59.967 45.455 8.48 0.00 46.05 3.34
5588 6872 1.399089 TCATGCTCGACGTGATACGAA 59.601 47.619 8.48 0.00 46.05 3.85
5627 6911 1.522668 TGGAAACCAGCGTCATGAAG 58.477 50.000 4.06 4.06 0.00 3.02
5634 6918 0.327924 TCCATGATGGAAACCAGCGT 59.672 50.000 12.63 0.00 45.00 5.07
5642 6926 4.652102 GCAGGAGCTGTCCATGATGGAA 62.652 54.545 17.07 5.99 46.80 3.53
5660 6944 0.392193 AGGGCATTTCTCTGTCGCAG 60.392 55.000 1.02 1.02 0.00 5.18
5663 6947 2.005451 CTCAAGGGCATTTCTCTGTCG 58.995 52.381 0.00 0.00 0.00 4.35
5747 7031 4.593864 GAGGAGATCCACGCCGCC 62.594 72.222 0.92 0.00 43.25 6.13


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

AutoCloner maintained by Alex Coulton.