Multiple sequence alignment - TraesCS7A01G282100

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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 TraesCS7A01G282100 chr7A 100.000 2448 0 0 1 2448 307565194 307567641 0.000000e+00 4521.0
1 TraesCS7A01G282100 chr7A 83.520 625 99 4 1 624 258376384 258375763 4.540000e-162 580.0
2 TraesCS7A01G282100 chr7A 91.667 336 27 1 289 624 727608556 727608222 4.770000e-127 464.0
3 TraesCS7A01G282100 chr7A 89.583 144 15 0 2305 2448 307623069 307623212 1.500000e-42 183.0
4 TraesCS7A01G282100 chr7B 96.811 1066 25 9 736 1795 263670479 263669417 0.000000e+00 1772.0
5 TraesCS7A01G282100 chr7B 97.059 34 1 0 624 657 263670894 263670861 9.450000e-05 58.4
6 TraesCS7A01G282100 chr7D 93.362 1175 28 19 739 1888 274260651 274261800 0.000000e+00 1692.0
7 TraesCS7A01G282100 chr7D 89.143 525 47 7 1786 2304 422574405 422574925 0.000000e+00 645.0
8 TraesCS7A01G282100 chr7D 88.966 145 15 1 2305 2448 335597433 335597289 6.960000e-41 178.0
9 TraesCS7A01G282100 chr7D 89.286 140 14 1 2310 2448 281106174 281106313 9.000000e-40 174.0
10 TraesCS7A01G282100 chr7D 88.276 145 15 2 2305 2448 315076562 315076705 3.240000e-39 172.0
11 TraesCS7A01G282100 chr7D 100.000 61 0 0 687 747 274259049 274259109 1.990000e-21 113.0
12 TraesCS7A01G282100 chr7D 100.000 38 0 0 624 661 274258960 274258997 1.210000e-08 71.3
13 TraesCS7A01G282100 chr1D 87.360 625 72 6 1 623 67989703 67989084 0.000000e+00 710.0
14 TraesCS7A01G282100 chr1D 88.571 140 15 1 2310 2448 223845661 223845522 4.190000e-38 169.0
15 TraesCS7A01G282100 chrUn 86.762 627 81 2 1 626 40999077 40999702 0.000000e+00 697.0
16 TraesCS7A01G282100 chr4D 90.680 515 41 5 1796 2304 465442206 465441693 0.000000e+00 678.0
17 TraesCS7A01G282100 chr4D 89.484 523 44 7 1789 2304 37340674 37341192 0.000000e+00 651.0
18 TraesCS7A01G282100 chr4D 90.000 140 13 1 2310 2448 90337042 90337181 1.930000e-41 180.0
19 TraesCS7A01G282100 chr3A 90.272 514 47 2 1794 2304 735609553 735610066 0.000000e+00 669.0
20 TraesCS7A01G282100 chr3A 90.272 514 44 4 1796 2304 501568445 501567933 0.000000e+00 667.0
21 TraesCS7A01G282100 chr5D 90.272 514 45 3 1796 2304 328727138 328726625 0.000000e+00 667.0
22 TraesCS7A01G282100 chr5D 90.078 514 46 3 1796 2304 487411278 487410765 0.000000e+00 662.0
23 TraesCS7A01G282100 chr2D 90.078 514 46 3 1796 2304 616993006 616992493 0.000000e+00 662.0
24 TraesCS7A01G282100 chr2D 89.286 140 14 1 2310 2448 352425749 352425610 9.000000e-40 174.0
25 TraesCS7A01G282100 chr6B 89.768 518 45 6 1794 2304 626303564 626304080 0.000000e+00 656.0
26 TraesCS7A01G282100 chr6A 92.191 461 36 0 79 539 432262790 432262330 0.000000e+00 652.0
27 TraesCS7A01G282100 chr2A 92.876 379 27 0 1 379 386090919 386091297 3.560000e-153 551.0
28 TraesCS7A01G282100 chr2A 91.235 251 21 1 374 624 386095037 386095286 8.380000e-90 340.0
29 TraesCS7A01G282100 chr2A 92.593 54 1 1 624 677 625288335 625288285 9.390000e-10 75.0
30 TraesCS7A01G282100 chr3B 76.923 624 123 19 10 624 176425345 176424734 3.900000e-88 335.0
31 TraesCS7A01G282100 chr3D 89.333 150 13 3 2301 2448 225746916 225746768 4.160000e-43 185.0
32 TraesCS7A01G282100 chr6D 88.194 144 17 0 2305 2448 167422329 167422472 3.240000e-39 172.0


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 TraesCS7A01G282100 chr7A 307565194 307567641 2447 False 4521.000000 4521 100.000000 1 2448 1 chr7A.!!$F1 2447
1 TraesCS7A01G282100 chr7A 258375763 258376384 621 True 580.000000 580 83.520000 1 624 1 chr7A.!!$R1 623
2 TraesCS7A01G282100 chr7B 263669417 263670894 1477 True 915.200000 1772 96.935000 624 1795 2 chr7B.!!$R1 1171
3 TraesCS7A01G282100 chr7D 422574405 422574925 520 False 645.000000 645 89.143000 1786 2304 1 chr7D.!!$F3 518
4 TraesCS7A01G282100 chr7D 274258960 274261800 2840 False 625.433333 1692 97.787333 624 1888 3 chr7D.!!$F4 1264
5 TraesCS7A01G282100 chr1D 67989084 67989703 619 True 710.000000 710 87.360000 1 623 1 chr1D.!!$R1 622
6 TraesCS7A01G282100 chrUn 40999077 40999702 625 False 697.000000 697 86.762000 1 626 1 chrUn.!!$F1 625
7 TraesCS7A01G282100 chr4D 465441693 465442206 513 True 678.000000 678 90.680000 1796 2304 1 chr4D.!!$R1 508
8 TraesCS7A01G282100 chr4D 37340674 37341192 518 False 651.000000 651 89.484000 1789 2304 1 chr4D.!!$F1 515
9 TraesCS7A01G282100 chr3A 735609553 735610066 513 False 669.000000 669 90.272000 1794 2304 1 chr3A.!!$F1 510
10 TraesCS7A01G282100 chr3A 501567933 501568445 512 True 667.000000 667 90.272000 1796 2304 1 chr3A.!!$R1 508
11 TraesCS7A01G282100 chr5D 328726625 328727138 513 True 667.000000 667 90.272000 1796 2304 1 chr5D.!!$R1 508
12 TraesCS7A01G282100 chr5D 487410765 487411278 513 True 662.000000 662 90.078000 1796 2304 1 chr5D.!!$R2 508
13 TraesCS7A01G282100 chr2D 616992493 616993006 513 True 662.000000 662 90.078000 1796 2304 1 chr2D.!!$R2 508
14 TraesCS7A01G282100 chr6B 626303564 626304080 516 False 656.000000 656 89.768000 1794 2304 1 chr6B.!!$F1 510
15 TraesCS7A01G282100 chr2A 386090919 386095286 4367 False 445.500000 551 92.055500 1 624 2 chr2A.!!$F1 623
16 TraesCS7A01G282100 chr3B 176424734 176425345 611 True 335.000000 335 76.923000 10 624 1 chr3B.!!$R1 614

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
128 129 0.179084 GCATCCGGAACCTCGAATCA 60.179 55.0 9.01 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 7673 1.005037 CTAGTTCGCCCACACAGCA 60.005 57.895 0.0 0.0 0.0 4.41 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
50 51 2.008329 CTCATGCTCCAGAACAAGCTC 58.992 52.381 0.00 0.00 39.31 4.09
70 71 2.401766 GGTGCAATGACAGGCTCCG 61.402 63.158 7.09 0.00 34.44 4.63
74 75 3.706373 AATGACAGGCTCCGGCGT 61.706 61.111 6.01 0.00 39.81 5.68
128 129 0.179084 GCATCCGGAACCTCGAATCA 60.179 55.000 9.01 0.00 0.00 2.57
135 136 2.604914 CGGAACCTCGAATCATCAAGTG 59.395 50.000 0.00 0.00 0.00 3.16
196 197 0.535780 ACAGTCAGTACGTGGACGGA 60.536 55.000 18.31 5.77 44.95 4.69
295 296 1.993369 GCAACAAGATGGCGTAGGGC 61.993 60.000 1.39 1.39 42.51 5.19
314 315 2.225491 GGCAAACATCACGCTCTTGTTA 59.775 45.455 0.00 0.00 33.44 2.41
319 320 4.193826 ACATCACGCTCTTGTTACTCAT 57.806 40.909 0.00 0.00 0.00 2.90
512 4258 3.777106 TCTTGTCACTTGAGGATTGCT 57.223 42.857 0.00 0.00 0.00 3.91
539 4285 1.443828 GCAAGTCCTCGGATCCTCC 59.556 63.158 10.75 0.00 0.00 4.30
553 4301 0.558220 TCCTCCGGATCCTCATCACT 59.442 55.000 3.57 0.00 0.00 3.41
564 4315 5.478332 GGATCCTCATCACTTTGGTTTTTCT 59.522 40.000 3.84 0.00 0.00 2.52
565 4316 6.015095 GGATCCTCATCACTTTGGTTTTTCTT 60.015 38.462 3.84 0.00 0.00 2.52
596 4347 7.758528 GCTTTCTGCTAATGATCAATGAAAAGT 59.241 33.333 0.00 0.00 38.95 2.66
662 4750 5.793030 ATAGGTGTCTCCACATTACTAGC 57.207 43.478 0.00 0.00 43.71 3.42
664 4752 3.195825 AGGTGTCTCCACATTACTAGCAC 59.804 47.826 0.00 0.00 43.71 4.40
666 4754 4.425520 GTGTCTCCACATTACTAGCACTC 58.574 47.826 0.00 0.00 41.44 3.51
669 4757 4.888239 GTCTCCACATTACTAGCACTCCTA 59.112 45.833 0.00 0.00 0.00 2.94
670 4758 9.281119 GTGTCTCCACATTACTAGCACTCCTAG 62.281 48.148 0.00 0.00 43.58 3.02
767 6432 1.654105 CGACTTAAGATGACGTGGCAC 59.346 52.381 10.09 7.79 0.00 5.01
856 6521 2.915869 ACTCCTCATCCCCTTACAACA 58.084 47.619 0.00 0.00 0.00 3.33
872 6537 2.761208 ACAACAGGAATCGGTAGAGAGG 59.239 50.000 0.00 0.00 0.00 3.69
886 6555 2.412591 AGAGAGGGAGAGAGAGAGAGG 58.587 57.143 0.00 0.00 0.00 3.69
936 6605 2.958818 TCGTCTTGGCTACCATATCCT 58.041 47.619 0.00 0.00 31.53 3.24
1450 7125 0.035439 TCGGATTCCTTGCTTGACCC 60.035 55.000 0.30 0.00 0.00 4.46
1630 7320 7.390440 CAGTTAAACTTCAGTTCCATGTGGATA 59.610 37.037 1.98 0.00 44.98 2.59
1842 7536 1.825622 TTTGCACATCGCCCACACA 60.826 52.632 0.00 0.00 41.33 3.72
1862 7557 7.601130 CCACACATCTTGATTCATGTTGATTTT 59.399 33.333 14.26 0.00 30.48 1.82
1976 7673 2.598394 ATGCGGTTTGCCAGCTGT 60.598 55.556 13.81 0.00 45.60 4.40
2035 7733 1.153842 CTAGTCCACGCGCATGTGA 60.154 57.895 15.84 3.91 42.55 3.58
2036 7734 0.735978 CTAGTCCACGCGCATGTGAA 60.736 55.000 15.84 0.00 42.55 3.18
2038 7736 2.280457 TCCACGCGCATGTGAACA 60.280 55.556 15.84 0.00 42.55 3.18
2060 7758 1.001633 ACTACTTTTCGCCCACACGAT 59.998 47.619 0.00 0.00 42.54 3.73
2065 7763 1.828461 TTTCGCCCACACGATACCCA 61.828 55.000 0.00 0.00 42.54 4.51
2075 7773 3.305094 CACACGATACCCATACGTTGTTC 59.695 47.826 0.00 0.00 38.18 3.18
2160 7858 2.143925 GCTAGACGGCAACTTCAGTTT 58.856 47.619 0.00 0.00 37.30 2.66
2273 7972 4.870363 ACACACATGGCAACTATTGTTTC 58.130 39.130 0.00 0.00 33.52 2.78
2304 8003 4.968259 TGGCAAGTAGTTAATGACACACT 58.032 39.130 0.00 0.00 0.00 3.55
2305 8004 4.754618 TGGCAAGTAGTTAATGACACACTG 59.245 41.667 0.00 0.00 0.00 3.66
2306 8005 4.755123 GGCAAGTAGTTAATGACACACTGT 59.245 41.667 0.00 0.00 0.00 3.55
2307 8006 5.334105 GGCAAGTAGTTAATGACACACTGTG 60.334 44.000 7.68 7.68 39.75 3.66
2308 8007 5.465390 GCAAGTAGTTAATGACACACTGTGA 59.535 40.000 16.30 0.00 36.96 3.58
2309 8008 6.346919 GCAAGTAGTTAATGACACACTGTGAG 60.347 42.308 16.30 9.44 36.96 3.51
2310 8009 6.650427 AGTAGTTAATGACACACTGTGAGA 57.350 37.500 16.30 2.03 36.96 3.27
2311 8010 7.233389 AGTAGTTAATGACACACTGTGAGAT 57.767 36.000 16.30 4.29 36.96 2.75
2312 8011 7.671302 AGTAGTTAATGACACACTGTGAGATT 58.329 34.615 16.30 13.78 36.96 2.40
2313 8012 7.815068 AGTAGTTAATGACACACTGTGAGATTC 59.185 37.037 16.30 3.58 36.96 2.52
2314 8013 6.524734 AGTTAATGACACACTGTGAGATTCA 58.475 36.000 16.30 9.13 36.96 2.57
2315 8014 6.648310 AGTTAATGACACACTGTGAGATTCAG 59.352 38.462 16.30 0.00 36.96 3.02
2316 8015 3.391506 TGACACACTGTGAGATTCAGG 57.608 47.619 16.30 0.00 36.96 3.86
2317 8016 2.037641 TGACACACTGTGAGATTCAGGG 59.962 50.000 16.30 0.00 41.53 4.45
2318 8017 1.271054 ACACACTGTGAGATTCAGGGC 60.271 52.381 16.30 0.00 39.65 5.19
2319 8018 1.002888 CACACTGTGAGATTCAGGGCT 59.997 52.381 15.86 0.00 39.65 5.19
2320 8019 1.277557 ACACTGTGAGATTCAGGGCTC 59.722 52.381 15.86 0.00 39.65 4.70
2321 8020 0.908198 ACTGTGAGATTCAGGGCTCC 59.092 55.000 0.00 0.00 37.25 4.70
2322 8021 0.179089 CTGTGAGATTCAGGGCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2323 8022 1.522580 GTGAGATTCAGGGCTCCGC 60.523 63.158 0.00 0.00 0.00 5.54
2324 8023 1.989508 TGAGATTCAGGGCTCCGCA 60.990 57.895 0.00 0.00 0.00 5.69
2325 8024 1.227497 GAGATTCAGGGCTCCGCAG 60.227 63.158 0.00 0.00 0.00 5.18
2326 8025 1.680522 GAGATTCAGGGCTCCGCAGA 61.681 60.000 0.00 0.00 0.00 4.26
2327 8026 1.522580 GATTCAGGGCTCCGCAGAC 60.523 63.158 0.00 0.00 0.00 3.51
2332 8031 4.785453 GGGCTCCGCAGACCCAAG 62.785 72.222 0.00 0.00 43.28 3.61
2333 8032 3.706373 GGCTCCGCAGACCCAAGA 61.706 66.667 0.00 0.00 0.00 3.02
2334 8033 2.347490 GCTCCGCAGACCCAAGAA 59.653 61.111 0.00 0.00 0.00 2.52
2335 8034 1.302511 GCTCCGCAGACCCAAGAAA 60.303 57.895 0.00 0.00 0.00 2.52
2336 8035 1.301677 GCTCCGCAGACCCAAGAAAG 61.302 60.000 0.00 0.00 0.00 2.62
2337 8036 0.674895 CTCCGCAGACCCAAGAAAGG 60.675 60.000 0.00 0.00 0.00 3.11
2338 8037 1.073199 CCGCAGACCCAAGAAAGGT 59.927 57.895 0.00 0.00 41.50 3.50
2339 8038 0.537371 CCGCAGACCCAAGAAAGGTT 60.537 55.000 0.00 0.00 37.88 3.50
2340 8039 0.875059 CGCAGACCCAAGAAAGGTTC 59.125 55.000 0.00 0.00 37.88 3.62
2341 8040 0.875059 GCAGACCCAAGAAAGGTTCG 59.125 55.000 0.00 0.00 37.88 3.95
2342 8041 1.523758 CAGACCCAAGAAAGGTTCGG 58.476 55.000 0.00 0.00 37.88 4.30
2343 8042 1.071699 CAGACCCAAGAAAGGTTCGGA 59.928 52.381 0.00 0.00 37.88 4.55
2344 8043 1.071857 AGACCCAAGAAAGGTTCGGAC 59.928 52.381 0.00 0.00 37.88 4.79
2345 8044 1.071857 GACCCAAGAAAGGTTCGGACT 59.928 52.381 0.00 0.00 37.88 3.85
2346 8045 1.071857 ACCCAAGAAAGGTTCGGACTC 59.928 52.381 0.00 0.00 32.05 3.36
2347 8046 1.348036 CCCAAGAAAGGTTCGGACTCT 59.652 52.381 0.00 0.00 34.02 3.24
2348 8047 2.417719 CCAAGAAAGGTTCGGACTCTG 58.582 52.381 0.00 0.00 34.02 3.35
2349 8048 2.417719 CAAGAAAGGTTCGGACTCTGG 58.582 52.381 0.00 0.00 34.02 3.86
2350 8049 0.977395 AGAAAGGTTCGGACTCTGGG 59.023 55.000 0.00 0.00 34.02 4.45
2351 8050 0.036294 GAAAGGTTCGGACTCTGGGG 60.036 60.000 0.00 0.00 0.00 4.96
2352 8051 2.125766 AAAGGTTCGGACTCTGGGGC 62.126 60.000 0.00 0.00 0.00 5.80
2353 8052 4.452733 GGTTCGGACTCTGGGGCG 62.453 72.222 0.00 0.00 0.00 6.13
2367 8066 4.135493 GGCGCGTGCGAAGAACTC 62.135 66.667 19.66 0.00 44.10 3.01
2368 8067 3.403057 GCGCGTGCGAAGAACTCA 61.403 61.111 19.66 0.00 42.83 3.41
2369 8068 2.938823 GCGCGTGCGAAGAACTCAA 61.939 57.895 19.66 0.00 42.83 3.02
2370 8069 1.154836 CGCGTGCGAAGAACTCAAC 60.155 57.895 8.89 0.00 42.83 3.18
2371 8070 1.204312 GCGTGCGAAGAACTCAACC 59.796 57.895 0.00 0.00 0.00 3.77
2372 8071 1.222115 GCGTGCGAAGAACTCAACCT 61.222 55.000 0.00 0.00 0.00 3.50
2373 8072 0.784778 CGTGCGAAGAACTCAACCTC 59.215 55.000 0.00 0.00 0.00 3.85
2374 8073 1.149148 GTGCGAAGAACTCAACCTCC 58.851 55.000 0.00 0.00 0.00 4.30
2375 8074 0.034896 TGCGAAGAACTCAACCTCCC 59.965 55.000 0.00 0.00 0.00 4.30
2376 8075 0.673956 GCGAAGAACTCAACCTCCCC 60.674 60.000 0.00 0.00 0.00 4.81
2377 8076 0.685097 CGAAGAACTCAACCTCCCCA 59.315 55.000 0.00 0.00 0.00 4.96
2378 8077 1.338200 CGAAGAACTCAACCTCCCCAG 60.338 57.143 0.00 0.00 0.00 4.45
2379 8078 0.402121 AAGAACTCAACCTCCCCAGC 59.598 55.000 0.00 0.00 0.00 4.85
2380 8079 1.002011 GAACTCAACCTCCCCAGCC 60.002 63.158 0.00 0.00 0.00 4.85
2381 8080 1.464198 AACTCAACCTCCCCAGCCT 60.464 57.895 0.00 0.00 0.00 4.58
2382 8081 0.178873 AACTCAACCTCCCCAGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
2383 8082 0.910088 ACTCAACCTCCCCAGCCTAC 60.910 60.000 0.00 0.00 0.00 3.18
2384 8083 1.615424 TCAACCTCCCCAGCCTACC 60.615 63.158 0.00 0.00 0.00 3.18
2385 8084 1.923395 CAACCTCCCCAGCCTACCA 60.923 63.158 0.00 0.00 0.00 3.25
2386 8085 1.151677 AACCTCCCCAGCCTACCAA 60.152 57.895 0.00 0.00 0.00 3.67
2387 8086 1.498176 AACCTCCCCAGCCTACCAAC 61.498 60.000 0.00 0.00 0.00 3.77
2388 8087 1.616628 CCTCCCCAGCCTACCAACT 60.617 63.158 0.00 0.00 0.00 3.16
2389 8088 1.627297 CCTCCCCAGCCTACCAACTC 61.627 65.000 0.00 0.00 0.00 3.01
2390 8089 0.909610 CTCCCCAGCCTACCAACTCA 60.910 60.000 0.00 0.00 0.00 3.41
2391 8090 0.253160 TCCCCAGCCTACCAACTCAT 60.253 55.000 0.00 0.00 0.00 2.90
2392 8091 0.181350 CCCCAGCCTACCAACTCATC 59.819 60.000 0.00 0.00 0.00 2.92
2393 8092 0.179073 CCCAGCCTACCAACTCATCG 60.179 60.000 0.00 0.00 0.00 3.84
2394 8093 0.811616 CCAGCCTACCAACTCATCGC 60.812 60.000 0.00 0.00 0.00 4.58
2395 8094 0.176680 CAGCCTACCAACTCATCGCT 59.823 55.000 0.00 0.00 0.00 4.93
2396 8095 0.461961 AGCCTACCAACTCATCGCTC 59.538 55.000 0.00 0.00 0.00 5.03
2397 8096 0.461961 GCCTACCAACTCATCGCTCT 59.538 55.000 0.00 0.00 0.00 4.09
2398 8097 1.537135 GCCTACCAACTCATCGCTCTC 60.537 57.143 0.00 0.00 0.00 3.20
2399 8098 1.751351 CCTACCAACTCATCGCTCTCA 59.249 52.381 0.00 0.00 0.00 3.27
2400 8099 2.480416 CCTACCAACTCATCGCTCTCAC 60.480 54.545 0.00 0.00 0.00 3.51
2401 8100 0.109086 ACCAACTCATCGCTCTCACG 60.109 55.000 0.00 0.00 0.00 4.35
2403 8102 1.263776 CAACTCATCGCTCTCACGAC 58.736 55.000 0.00 0.00 46.28 4.34
2404 8103 0.171455 AACTCATCGCTCTCACGACC 59.829 55.000 0.00 0.00 46.28 4.79
2405 8104 0.678366 ACTCATCGCTCTCACGACCT 60.678 55.000 0.00 0.00 46.28 3.85
2406 8105 1.300481 CTCATCGCTCTCACGACCTA 58.700 55.000 0.00 0.00 46.28 3.08
2407 8106 1.262950 CTCATCGCTCTCACGACCTAG 59.737 57.143 0.00 0.00 46.28 3.02
2408 8107 0.317436 CATCGCTCTCACGACCTAGC 60.317 60.000 0.00 0.00 46.28 3.42
2409 8108 0.464735 ATCGCTCTCACGACCTAGCT 60.465 55.000 0.00 0.00 46.28 3.32
2410 8109 1.090625 TCGCTCTCACGACCTAGCTC 61.091 60.000 0.00 0.00 37.09 4.09
2411 8110 1.353804 GCTCTCACGACCTAGCTCG 59.646 63.158 5.90 5.90 39.68 5.03
2412 8111 1.090625 GCTCTCACGACCTAGCTCGA 61.091 60.000 14.23 0.00 37.11 4.04
2413 8112 0.653636 CTCTCACGACCTAGCTCGAC 59.346 60.000 14.23 0.00 37.11 4.20
2414 8113 1.082679 TCTCACGACCTAGCTCGACG 61.083 60.000 14.23 5.11 37.11 5.12
2415 8114 1.079612 TCACGACCTAGCTCGACGA 60.080 57.895 14.23 7.23 37.11 4.20
2416 8115 0.671472 TCACGACCTAGCTCGACGAA 60.671 55.000 14.23 0.00 37.11 3.85
2417 8116 0.520827 CACGACCTAGCTCGACGAAC 60.521 60.000 14.23 0.00 37.11 3.95
2418 8117 1.296722 CGACCTAGCTCGACGAACG 60.297 63.158 0.95 0.00 44.09 3.95
2419 8118 1.062206 GACCTAGCTCGACGAACGG 59.938 63.158 0.00 0.00 42.82 4.44
2420 8119 2.320339 GACCTAGCTCGACGAACGGG 62.320 65.000 0.00 5.47 46.38 5.28
2421 8120 2.110967 CCTAGCTCGACGAACGGGA 61.111 63.158 10.28 0.00 46.62 5.14
2422 8121 1.651240 CCTAGCTCGACGAACGGGAA 61.651 60.000 10.28 0.00 46.62 3.97
2423 8122 0.248134 CTAGCTCGACGAACGGGAAG 60.248 60.000 10.28 3.77 46.62 3.46
2424 8123 0.674581 TAGCTCGACGAACGGGAAGA 60.675 55.000 10.28 0.00 46.62 2.87
2425 8124 1.080974 GCTCGACGAACGGGAAGAA 60.081 57.895 10.28 0.00 46.62 2.52
2426 8125 1.071567 GCTCGACGAACGGGAAGAAG 61.072 60.000 10.28 0.29 46.62 2.85
2427 8126 0.520404 CTCGACGAACGGGAAGAAGA 59.480 55.000 0.00 0.00 46.62 2.87
2428 8127 0.520404 TCGACGAACGGGAAGAAGAG 59.480 55.000 0.00 0.00 42.82 2.85
2429 8128 0.456312 CGACGAACGGGAAGAAGAGG 60.456 60.000 0.00 0.00 38.46 3.69
2430 8129 0.108756 GACGAACGGGAAGAAGAGGG 60.109 60.000 0.00 0.00 0.00 4.30
2431 8130 0.541296 ACGAACGGGAAGAAGAGGGA 60.541 55.000 0.00 0.00 0.00 4.20
2432 8131 0.108756 CGAACGGGAAGAAGAGGGAC 60.109 60.000 0.00 0.00 0.00 4.46
2433 8132 0.974383 GAACGGGAAGAAGAGGGACA 59.026 55.000 0.00 0.00 0.00 4.02
2434 8133 0.685660 AACGGGAAGAAGAGGGACAC 59.314 55.000 0.00 0.00 0.00 3.67
2435 8134 0.471211 ACGGGAAGAAGAGGGACACA 60.471 55.000 0.00 0.00 0.00 3.72
2436 8135 0.905357 CGGGAAGAAGAGGGACACAT 59.095 55.000 0.00 0.00 0.00 3.21
2437 8136 1.134670 CGGGAAGAAGAGGGACACATC 60.135 57.143 0.00 0.00 0.00 3.06
2438 8137 1.909302 GGGAAGAAGAGGGACACATCA 59.091 52.381 0.00 0.00 0.00 3.07
2439 8138 2.093235 GGGAAGAAGAGGGACACATCAG 60.093 54.545 0.00 0.00 0.00 2.90
2440 8139 2.569404 GGAAGAAGAGGGACACATCAGT 59.431 50.000 0.00 0.00 0.00 3.41
2441 8140 3.008485 GGAAGAAGAGGGACACATCAGTT 59.992 47.826 0.00 0.00 0.00 3.16
2442 8141 4.505742 GGAAGAAGAGGGACACATCAGTTT 60.506 45.833 0.00 0.00 0.00 2.66
2443 8142 5.280011 GGAAGAAGAGGGACACATCAGTTTA 60.280 44.000 0.00 0.00 0.00 2.01
2444 8143 5.153950 AGAAGAGGGACACATCAGTTTAC 57.846 43.478 0.00 0.00 0.00 2.01
2445 8144 3.983044 AGAGGGACACATCAGTTTACC 57.017 47.619 0.00 0.00 0.00 2.85
2446 8145 2.572104 AGAGGGACACATCAGTTTACCC 59.428 50.000 0.00 0.00 34.18 3.69
2447 8146 2.304761 GAGGGACACATCAGTTTACCCA 59.695 50.000 0.00 0.00 35.51 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.310933 GGAGCCTGTCATTGCACCAG 61.311 60.000 6.21 0.00 38.03 4.00
70 71 1.595929 TTCTTCCAACCACGACGCC 60.596 57.895 0.00 0.00 0.00 5.68
74 75 0.748450 ACTCGTTCTTCCAACCACGA 59.252 50.000 0.00 0.00 39.27 4.35
128 129 3.593442 TCCCAAAACAGGTCACTTGAT 57.407 42.857 0.00 0.00 0.00 2.57
166 167 1.507140 ACTGACTGTTTCCCAGACCA 58.493 50.000 0.00 0.00 44.49 4.02
180 181 2.251600 AGTCCGTCCACGTACTGAC 58.748 57.895 5.23 5.23 37.16 3.51
196 197 3.151022 GCGCTAGGGAGGAGCAGT 61.151 66.667 11.61 0.00 40.09 4.40
295 296 4.211164 TGAGTAACAAGAGCGTGATGTTTG 59.789 41.667 5.73 0.00 38.22 2.93
301 302 3.838120 CAGATGAGTAACAAGAGCGTGA 58.162 45.455 0.00 0.00 0.00 4.35
314 315 1.693062 CATAGCTCCCAGCAGATGAGT 59.307 52.381 0.00 0.00 45.56 3.41
319 320 1.690283 TGCCATAGCTCCCAGCAGA 60.690 57.895 0.00 0.00 45.56 4.26
360 361 2.772515 AGGCACTTGGTATACTTCTCCC 59.227 50.000 2.25 0.00 27.25 4.30
434 4180 2.801631 GCTCCCGATGCAGGTAGCT 61.802 63.158 2.67 0.00 45.94 3.32
437 4183 3.161450 GGGCTCCCGATGCAGGTA 61.161 66.667 0.00 0.00 0.00 3.08
512 4258 1.754745 GAGGACTTGCCACAGACCA 59.245 57.895 0.00 0.00 40.02 4.02
539 4285 2.698855 ACCAAAGTGATGAGGATCCG 57.301 50.000 5.98 0.00 0.00 4.18
553 4301 5.868801 CAGAAAGCAGTGAAGAAAAACCAAA 59.131 36.000 0.00 0.00 0.00 3.28
677 4774 8.207545 AGTTGGAAGTAAAACCAAATGCAATTA 58.792 29.630 0.00 0.00 45.75 1.40
767 6432 4.588528 TCCCTTGGTCTTTTTCCATTTCTG 59.411 41.667 0.00 0.00 34.75 3.02
856 6521 2.107552 CTCTCCCTCTCTACCGATTCCT 59.892 54.545 0.00 0.00 0.00 3.36
872 6537 0.261696 AAGCCCCTCTCTCTCTCTCC 59.738 60.000 0.00 0.00 0.00 3.71
886 6555 2.991540 GGTGTCCAGCCAAAGCCC 60.992 66.667 0.00 0.00 41.25 5.19
936 6605 1.407299 CCGTGCAGAATGAGAATGGGA 60.407 52.381 0.00 0.00 39.69 4.37
1564 7239 5.476599 CCACAAGAGAAGAGAAGAGAAGAGA 59.523 44.000 0.00 0.00 0.00 3.10
1565 7240 5.476599 TCCACAAGAGAAGAGAAGAGAAGAG 59.523 44.000 0.00 0.00 0.00 2.85
1630 7320 6.024247 AGATACATCATCTGTCCATCCATCT 58.976 40.000 0.00 0.00 42.69 2.90
1748 7438 2.261671 GGCGTGACGGATCAGTGT 59.738 61.111 7.25 0.00 34.75 3.55
1810 7502 1.358402 GCAAACATGCCACACGTGA 59.642 52.632 25.01 0.00 38.75 4.35
1862 7557 7.594758 CAGATTTCTTTAGGATTCGTGCAAAAA 59.405 33.333 0.00 0.00 0.00 1.94
1976 7673 1.005037 CTAGTTCGCCCACACAGCA 60.005 57.895 0.00 0.00 0.00 4.41
2035 7733 3.018149 TGTGGGCGAAAAGTAGTTTGTT 58.982 40.909 0.00 0.00 0.00 2.83
2036 7734 2.356695 GTGTGGGCGAAAAGTAGTTTGT 59.643 45.455 0.00 0.00 0.00 2.83
2038 7736 1.600485 CGTGTGGGCGAAAAGTAGTTT 59.400 47.619 0.00 0.00 0.00 2.66
2060 7758 2.739287 GCCATCGAACAACGTATGGGTA 60.739 50.000 13.30 0.00 43.19 3.69
2297 7996 2.693069 CCCTGAATCTCACAGTGTGTC 58.307 52.381 22.29 13.09 34.79 3.67
2304 8003 1.900351 CGGAGCCCTGAATCTCACA 59.100 57.895 0.00 0.00 0.00 3.58
2305 8004 4.844420 CGGAGCCCTGAATCTCAC 57.156 61.111 0.00 0.00 0.00 3.51
2318 8017 0.674895 CCTTTCTTGGGTCTGCGGAG 60.675 60.000 0.00 0.00 0.00 4.63
2319 8018 1.374947 CCTTTCTTGGGTCTGCGGA 59.625 57.895 0.00 0.00 0.00 5.54
2320 8019 0.537371 AACCTTTCTTGGGTCTGCGG 60.537 55.000 0.00 0.00 35.83 5.69
2321 8020 0.875059 GAACCTTTCTTGGGTCTGCG 59.125 55.000 0.00 0.00 40.53 5.18
2322 8021 0.875059 CGAACCTTTCTTGGGTCTGC 59.125 55.000 0.00 0.00 41.49 4.26
2323 8022 1.071699 TCCGAACCTTTCTTGGGTCTG 59.928 52.381 0.00 0.00 41.49 3.51
2324 8023 1.071857 GTCCGAACCTTTCTTGGGTCT 59.928 52.381 0.00 0.00 41.49 3.85
2325 8024 1.071857 AGTCCGAACCTTTCTTGGGTC 59.928 52.381 0.00 0.00 40.31 4.46
2326 8025 1.071857 GAGTCCGAACCTTTCTTGGGT 59.928 52.381 0.00 0.00 38.94 4.51
2327 8026 1.348036 AGAGTCCGAACCTTTCTTGGG 59.652 52.381 0.00 0.00 0.00 4.12
2328 8027 2.417719 CAGAGTCCGAACCTTTCTTGG 58.582 52.381 0.00 0.00 0.00 3.61
2329 8028 2.417719 CCAGAGTCCGAACCTTTCTTG 58.582 52.381 0.00 0.00 0.00 3.02
2330 8029 1.348036 CCCAGAGTCCGAACCTTTCTT 59.652 52.381 0.00 0.00 0.00 2.52
2331 8030 0.977395 CCCAGAGTCCGAACCTTTCT 59.023 55.000 0.00 0.00 0.00 2.52
2332 8031 0.036294 CCCCAGAGTCCGAACCTTTC 60.036 60.000 0.00 0.00 0.00 2.62
2333 8032 2.067197 CCCCAGAGTCCGAACCTTT 58.933 57.895 0.00 0.00 0.00 3.11
2334 8033 2.593956 GCCCCAGAGTCCGAACCTT 61.594 63.158 0.00 0.00 0.00 3.50
2335 8034 3.003763 GCCCCAGAGTCCGAACCT 61.004 66.667 0.00 0.00 0.00 3.50
2336 8035 4.452733 CGCCCCAGAGTCCGAACC 62.453 72.222 0.00 0.00 0.00 3.62
2350 8049 4.135493 GAGTTCTTCGCACGCGCC 62.135 66.667 5.73 0.00 39.59 6.53
2351 8050 2.938823 TTGAGTTCTTCGCACGCGC 61.939 57.895 5.73 0.00 39.59 6.86
2352 8051 1.154836 GTTGAGTTCTTCGCACGCG 60.155 57.895 3.53 3.53 41.35 6.01
2353 8052 1.204312 GGTTGAGTTCTTCGCACGC 59.796 57.895 0.00 0.00 0.00 5.34
2354 8053 0.784778 GAGGTTGAGTTCTTCGCACG 59.215 55.000 0.00 0.00 0.00 5.34
2355 8054 1.149148 GGAGGTTGAGTTCTTCGCAC 58.851 55.000 0.00 0.00 0.00 5.34
2356 8055 0.034896 GGGAGGTTGAGTTCTTCGCA 59.965 55.000 0.00 0.00 0.00 5.10
2357 8056 0.673956 GGGGAGGTTGAGTTCTTCGC 60.674 60.000 0.00 0.00 0.00 4.70
2358 8057 0.685097 TGGGGAGGTTGAGTTCTTCG 59.315 55.000 0.00 0.00 0.00 3.79
2359 8058 1.611936 GCTGGGGAGGTTGAGTTCTTC 60.612 57.143 0.00 0.00 0.00 2.87
2360 8059 0.402121 GCTGGGGAGGTTGAGTTCTT 59.598 55.000 0.00 0.00 0.00 2.52
2361 8060 1.492993 GGCTGGGGAGGTTGAGTTCT 61.493 60.000 0.00 0.00 0.00 3.01
2362 8061 1.002011 GGCTGGGGAGGTTGAGTTC 60.002 63.158 0.00 0.00 0.00 3.01
2363 8062 0.178873 TAGGCTGGGGAGGTTGAGTT 60.179 55.000 0.00 0.00 0.00 3.01
2364 8063 0.910088 GTAGGCTGGGGAGGTTGAGT 60.910 60.000 0.00 0.00 0.00 3.41
2365 8064 1.627297 GGTAGGCTGGGGAGGTTGAG 61.627 65.000 0.00 0.00 0.00 3.02
2366 8065 1.615424 GGTAGGCTGGGGAGGTTGA 60.615 63.158 0.00 0.00 0.00 3.18
2367 8066 1.497309 TTGGTAGGCTGGGGAGGTTG 61.497 60.000 0.00 0.00 0.00 3.77
2368 8067 1.151677 TTGGTAGGCTGGGGAGGTT 60.152 57.895 0.00 0.00 0.00 3.50
2369 8068 1.923909 GTTGGTAGGCTGGGGAGGT 60.924 63.158 0.00 0.00 0.00 3.85
2370 8069 1.616628 AGTTGGTAGGCTGGGGAGG 60.617 63.158 0.00 0.00 0.00 4.30
2371 8070 0.909610 TGAGTTGGTAGGCTGGGGAG 60.910 60.000 0.00 0.00 0.00 4.30
2372 8071 0.253160 ATGAGTTGGTAGGCTGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
2373 8072 0.181350 GATGAGTTGGTAGGCTGGGG 59.819 60.000 0.00 0.00 0.00 4.96
2374 8073 0.179073 CGATGAGTTGGTAGGCTGGG 60.179 60.000 0.00 0.00 0.00 4.45
2375 8074 0.811616 GCGATGAGTTGGTAGGCTGG 60.812 60.000 0.00 0.00 0.00 4.85
2376 8075 0.176680 AGCGATGAGTTGGTAGGCTG 59.823 55.000 0.00 0.00 0.00 4.85
2377 8076 0.461961 GAGCGATGAGTTGGTAGGCT 59.538 55.000 0.00 0.00 0.00 4.58
2378 8077 0.461961 AGAGCGATGAGTTGGTAGGC 59.538 55.000 0.00 0.00 0.00 3.93
2379 8078 1.751351 TGAGAGCGATGAGTTGGTAGG 59.249 52.381 0.00 0.00 0.00 3.18
2380 8079 2.792890 CGTGAGAGCGATGAGTTGGTAG 60.793 54.545 0.00 0.00 0.00 3.18
2381 8080 1.132453 CGTGAGAGCGATGAGTTGGTA 59.868 52.381 0.00 0.00 0.00 3.25
2382 8081 0.109086 CGTGAGAGCGATGAGTTGGT 60.109 55.000 0.00 0.00 0.00 3.67
2383 8082 0.171231 TCGTGAGAGCGATGAGTTGG 59.829 55.000 0.00 0.00 35.83 3.77
2384 8083 1.263776 GTCGTGAGAGCGATGAGTTG 58.736 55.000 0.00 0.00 43.07 3.16
2385 8084 3.704381 GTCGTGAGAGCGATGAGTT 57.296 52.632 0.00 0.00 43.07 3.01
2394 8093 0.653636 GTCGAGCTAGGTCGTGAGAG 59.346 60.000 35.39 13.76 43.49 3.20
2395 8094 1.082679 CGTCGAGCTAGGTCGTGAGA 61.083 60.000 35.39 19.33 40.93 3.27
2396 8095 1.082679 TCGTCGAGCTAGGTCGTGAG 61.083 60.000 35.39 27.42 40.93 3.51
2397 8096 0.671472 TTCGTCGAGCTAGGTCGTGA 60.671 55.000 35.39 30.36 40.93 4.35
2398 8097 0.520827 GTTCGTCGAGCTAGGTCGTG 60.521 60.000 35.39 28.99 40.93 4.35
2399 8098 1.792941 GTTCGTCGAGCTAGGTCGT 59.207 57.895 35.39 0.00 40.93 4.34
2400 8099 1.296722 CGTTCGTCGAGCTAGGTCG 60.297 63.158 32.85 32.85 42.86 4.79
2401 8100 1.062206 CCGTTCGTCGAGCTAGGTC 59.938 63.158 12.04 12.04 42.86 3.85
2402 8101 2.404995 CCCGTTCGTCGAGCTAGGT 61.405 63.158 7.51 0.00 42.86 3.08
2403 8102 1.651240 TTCCCGTTCGTCGAGCTAGG 61.651 60.000 7.51 7.91 42.86 3.02
2404 8103 0.248134 CTTCCCGTTCGTCGAGCTAG 60.248 60.000 7.51 0.00 42.86 3.42
2405 8104 0.674581 TCTTCCCGTTCGTCGAGCTA 60.675 55.000 7.51 0.00 42.86 3.32
2406 8105 1.521450 TTCTTCCCGTTCGTCGAGCT 61.521 55.000 7.51 0.00 42.86 4.09
2407 8106 1.071567 CTTCTTCCCGTTCGTCGAGC 61.072 60.000 0.00 0.00 42.86 5.03
2408 8107 0.520404 TCTTCTTCCCGTTCGTCGAG 59.480 55.000 0.00 0.00 42.86 4.04
2409 8108 0.520404 CTCTTCTTCCCGTTCGTCGA 59.480 55.000 0.00 0.00 42.86 4.20
2410 8109 0.456312 CCTCTTCTTCCCGTTCGTCG 60.456 60.000 0.00 0.00 39.52 5.12
2411 8110 0.108756 CCCTCTTCTTCCCGTTCGTC 60.109 60.000 0.00 0.00 0.00 4.20
2412 8111 0.541296 TCCCTCTTCTTCCCGTTCGT 60.541 55.000 0.00 0.00 0.00 3.85
2413 8112 0.108756 GTCCCTCTTCTTCCCGTTCG 60.109 60.000 0.00 0.00 0.00 3.95
2414 8113 0.974383 TGTCCCTCTTCTTCCCGTTC 59.026 55.000 0.00 0.00 0.00 3.95
2415 8114 0.685660 GTGTCCCTCTTCTTCCCGTT 59.314 55.000 0.00 0.00 0.00 4.44
2416 8115 0.471211 TGTGTCCCTCTTCTTCCCGT 60.471 55.000 0.00 0.00 0.00 5.28
2417 8116 0.905357 ATGTGTCCCTCTTCTTCCCG 59.095 55.000 0.00 0.00 0.00 5.14
2418 8117 1.909302 TGATGTGTCCCTCTTCTTCCC 59.091 52.381 0.00 0.00 0.00 3.97
2419 8118 2.569404 ACTGATGTGTCCCTCTTCTTCC 59.431 50.000 0.00 0.00 0.00 3.46
2420 8119 3.971245 ACTGATGTGTCCCTCTTCTTC 57.029 47.619 0.00 0.00 0.00 2.87
2421 8120 4.713792 AAACTGATGTGTCCCTCTTCTT 57.286 40.909 0.00 0.00 0.00 2.52
2422 8121 4.020128 GGTAAACTGATGTGTCCCTCTTCT 60.020 45.833 0.00 0.00 0.00 2.85
2423 8122 4.254492 GGTAAACTGATGTGTCCCTCTTC 58.746 47.826 0.00 0.00 0.00 2.87
2424 8123 3.009143 GGGTAAACTGATGTGTCCCTCTT 59.991 47.826 0.00 0.00 32.42 2.85
2425 8124 2.572104 GGGTAAACTGATGTGTCCCTCT 59.428 50.000 0.00 0.00 32.42 3.69
2426 8125 2.304761 TGGGTAAACTGATGTGTCCCTC 59.695 50.000 0.00 0.00 34.54 4.30
2427 8126 2.344592 TGGGTAAACTGATGTGTCCCT 58.655 47.619 0.00 0.00 34.54 4.20
2428 8127 2.871096 TGGGTAAACTGATGTGTCCC 57.129 50.000 0.00 0.00 34.26 4.46


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

AutoCloner maintained by Alex Coulton.