Multiple sequence alignment - TraesCS4A01G215900

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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 TraesCS4A01G215900 chr4A 100.000 2264 0 0 1 2264 514407623 514405360 0.000000e+00 4181.0
1 TraesCS4A01G215900 chr4A 93.371 1750 93 7 1 1749 698023513 698021786 0.000000e+00 2567.0
2 TraesCS4A01G215900 chr4A 98.500 200 1 2 2066 2264 27238007 27238205 3.580000e-93 351.0
3 TraesCS4A01G215900 chr4A 97.101 207 5 1 2059 2264 286244721 286244515 4.630000e-92 348.0
4 TraesCS4A01G215900 chr4A 97.537 203 3 2 2063 2264 459739109 459739310 1.660000e-91 346.0
5 TraesCS4A01G215900 chr4A 89.109 101 11 0 1925 2025 514389451 514389351 2.360000e-25 126.0
6 TraesCS4A01G215900 chr4A 95.745 47 2 0 1925 1971 514388918 514388872 2.410000e-10 76.8
7 TraesCS4A01G215900 chr7D 96.472 2041 63 5 1 2039 16799690 16797657 0.000000e+00 3362.0
8 TraesCS4A01G215900 chr3B 95.785 1803 67 8 1 1802 40993579 40991785 0.000000e+00 2900.0
9 TraesCS4A01G215900 chr6A 92.547 2026 124 7 1 2022 387215233 387217235 0.000000e+00 2880.0
10 TraesCS4A01G215900 chr6A 98.000 200 3 1 2066 2264 65320725 65320924 1.660000e-91 346.0
11 TraesCS4A01G215900 chr4B 93.455 1910 88 20 1 1880 664037777 664035875 0.000000e+00 2800.0
12 TraesCS4A01G215900 chr5B 94.630 1732 89 3 1 1731 426532764 426534492 0.000000e+00 2680.0
13 TraesCS4A01G215900 chr5B 91.504 1942 128 25 1 1917 658084104 658086033 0.000000e+00 2638.0
14 TraesCS4A01G215900 chr5B 93.463 1545 93 5 1 1538 16010576 16012119 0.000000e+00 2287.0
15 TraesCS4A01G215900 chr5B 91.111 45 4 0 1927 1971 578835228 578835184 6.750000e-06 62.1
16 TraesCS4A01G215900 chr2B 95.096 1713 65 6 1 1712 649657454 649655760 0.000000e+00 2680.0
17 TraesCS4A01G215900 chr2B 93.802 1791 96 9 1 1779 579908106 579909893 0.000000e+00 2678.0
18 TraesCS4A01G215900 chr2A 98.500 200 2 1 2066 2264 87291277 87291476 3.580000e-93 351.0
19 TraesCS4A01G215900 chr2A 98.500 200 2 1 2066 2264 162515400 162515201 3.580000e-93 351.0
20 TraesCS4A01G215900 chr3A 98.010 201 2 2 2065 2264 162485343 162485542 4.630000e-92 348.0
21 TraesCS4A01G215900 chr7A 97.512 201 4 1 2065 2264 240819298 240819498 2.150000e-90 342.0
22 TraesCS4A01G215900 chr1A 97.512 201 3 2 2065 2264 347413643 347413842 2.150000e-90 342.0
23 TraesCS4A01G215900 chr7B 91.379 116 9 1 1925 2040 720233870 720233756 8.370000e-35 158.0
24 TraesCS4A01G215900 chr7B 88.793 116 13 0 1925 2040 720233728 720233613 2.340000e-30 143.0
25 TraesCS4A01G215900 chr5A 96.104 77 3 0 1806 1882 288267388 288267312 2.360000e-25 126.0
26 TraesCS4A01G215900 chr5A 90.909 77 3 1 1806 1882 606689577 606689649 1.430000e-17 100.0


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 TraesCS4A01G215900 chr4A 514405360 514407623 2263 True 4181 4181 100.000 1 2264 1 chr4A.!!$R2 2263
1 TraesCS4A01G215900 chr4A 698021786 698023513 1727 True 2567 2567 93.371 1 1749 1 chr4A.!!$R3 1748
2 TraesCS4A01G215900 chr7D 16797657 16799690 2033 True 3362 3362 96.472 1 2039 1 chr7D.!!$R1 2038
3 TraesCS4A01G215900 chr3B 40991785 40993579 1794 True 2900 2900 95.785 1 1802 1 chr3B.!!$R1 1801
4 TraesCS4A01G215900 chr6A 387215233 387217235 2002 False 2880 2880 92.547 1 2022 1 chr6A.!!$F2 2021
5 TraesCS4A01G215900 chr4B 664035875 664037777 1902 True 2800 2800 93.455 1 1880 1 chr4B.!!$R1 1879
6 TraesCS4A01G215900 chr5B 426532764 426534492 1728 False 2680 2680 94.630 1 1731 1 chr5B.!!$F2 1730
7 TraesCS4A01G215900 chr5B 658084104 658086033 1929 False 2638 2638 91.504 1 1917 1 chr5B.!!$F3 1916
8 TraesCS4A01G215900 chr5B 16010576 16012119 1543 False 2287 2287 93.463 1 1538 1 chr5B.!!$F1 1537
9 TraesCS4A01G215900 chr2B 649655760 649657454 1694 True 2680 2680 95.096 1 1712 1 chr2B.!!$R1 1711
10 TraesCS4A01G215900 chr2B 579908106 579909893 1787 False 2678 2678 93.802 1 1779 1 chr2B.!!$F1 1778

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
480 482 0.179032 ATGTGGAGTGTGCGGTCAAA 60.179 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1575 0.033504 TGCTTCTTCCGCTCGTTCTT 59.966 50.0 0.0 0.0 0.0 2.52 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
290 291 3.230134 CCCTTTCTTGGACCAATCACAA 58.770 45.455 7.54 0.00 0.00 3.33
327 328 1.981495 GCCCTCATATTAGGCCAGACT 59.019 52.381 5.01 0.00 41.00 3.24
461 462 2.501723 GGAGGCTCCTGACACTATCAAA 59.498 50.000 26.44 0.00 36.69 2.69
467 468 4.623886 GCTCCTGACACTATCAAATGTGGA 60.624 45.833 0.00 0.00 36.69 4.02
477 479 0.238289 CAAATGTGGAGTGTGCGGTC 59.762 55.000 0.00 0.00 0.00 4.79
480 482 0.179032 ATGTGGAGTGTGCGGTCAAA 60.179 50.000 0.00 0.00 0.00 2.69
587 589 3.178540 AAGAGGTGACGGTGGTGGC 62.179 63.158 0.00 0.00 0.00 5.01
643 645 0.606604 GGTCGTAGAGGGAGCACAAA 59.393 55.000 0.00 0.00 36.95 2.83
670 672 3.418995 AGAGGTGCTAGTGTTCGTAGAA 58.581 45.455 0.00 0.00 45.90 2.10
876 944 5.147162 GCCTTCGATTATTTGCTTAATCCG 58.853 41.667 0.00 0.00 35.89 4.18
1016 1086 1.322538 GGCATGGCTTCATCCGGTTT 61.323 55.000 12.86 0.00 0.00 3.27
1073 1143 1.605058 CCGAAGACGTGGATGGAGGT 61.605 60.000 0.00 0.00 37.88 3.85
1459 1536 0.608035 GTCCTTTGCACGGGGATTGA 60.608 55.000 5.02 0.00 0.00 2.57
1478 1570 4.169102 GCATGAGCGTCGTGAGAA 57.831 55.556 0.00 0.00 45.01 2.87
1479 1571 1.994467 GCATGAGCGTCGTGAGAAG 59.006 57.895 0.00 0.00 45.01 2.85
1480 1572 1.416813 GCATGAGCGTCGTGAGAAGG 61.417 60.000 0.00 0.00 45.01 3.46
1481 1573 0.171231 CATGAGCGTCGTGAGAAGGA 59.829 55.000 0.00 0.00 45.01 3.36
1482 1574 0.453793 ATGAGCGTCGTGAGAAGGAG 59.546 55.000 0.00 0.00 45.01 3.69
1483 1575 0.605589 TGAGCGTCGTGAGAAGGAGA 60.606 55.000 0.00 0.00 45.01 3.71
1484 1576 0.522180 GAGCGTCGTGAGAAGGAGAA 59.478 55.000 0.00 0.00 45.01 2.87
1485 1577 0.523966 AGCGTCGTGAGAAGGAGAAG 59.476 55.000 0.00 0.00 45.01 2.85
1486 1578 0.522180 GCGTCGTGAGAAGGAGAAGA 59.478 55.000 0.00 0.00 45.01 2.87
1487 1579 1.068472 GCGTCGTGAGAAGGAGAAGAA 60.068 52.381 0.00 0.00 45.01 2.52
1488 1580 2.586900 CGTCGTGAGAAGGAGAAGAAC 58.413 52.381 0.00 0.00 45.01 3.01
1489 1581 2.586900 GTCGTGAGAAGGAGAAGAACG 58.413 52.381 0.00 0.00 45.01 3.95
1490 1582 2.225963 GTCGTGAGAAGGAGAAGAACGA 59.774 50.000 0.00 0.00 45.01 3.85
1491 1583 2.484651 TCGTGAGAAGGAGAAGAACGAG 59.515 50.000 0.00 0.00 37.03 4.18
1494 1586 0.528470 AGAAGGAGAAGAACGAGCGG 59.472 55.000 0.00 0.00 0.00 5.52
1502 1594 0.033504 AAGAACGAGCGGAAGAAGCA 59.966 50.000 0.00 0.00 37.01 3.91
1656 1771 2.380064 AGACAAATGGAAAGGCACCA 57.620 45.000 0.00 0.00 41.83 4.17
1661 1776 1.408969 AATGGAAAGGCACCAACGTT 58.591 45.000 0.00 0.00 40.93 3.99
1771 1916 5.525745 ACATCGTGTGTGAACTTGTTATTCA 59.474 36.000 0.00 0.00 40.28 2.57
1815 1960 7.849804 ACTACTTATGTGCAACCTATTTGAG 57.150 36.000 0.00 0.00 37.39 3.02
1942 2148 3.066190 CAGACGCCACGGTCCCTA 61.066 66.667 0.00 0.00 37.66 3.53
1969 2175 1.692762 GGGTCCCTATCCAGAGAGCAA 60.693 57.143 0.00 0.00 0.00 3.91
1970 2176 2.119495 GGTCCCTATCCAGAGAGCAAA 58.881 52.381 0.00 0.00 0.00 3.68
1971 2177 2.505819 GGTCCCTATCCAGAGAGCAAAA 59.494 50.000 0.00 0.00 0.00 2.44
1972 2178 3.054361 GGTCCCTATCCAGAGAGCAAAAA 60.054 47.826 0.00 0.00 0.00 1.94
2005 2212 2.796483 TATGCACACCCAGACGCCAC 62.796 60.000 0.00 0.00 0.00 5.01
2033 2240 0.398318 GCATCTGGGTCCCTATCCAC 59.602 60.000 10.00 0.00 30.58 4.02
2039 2246 0.691078 GGGTCCCTATCCACAGAGCA 60.691 60.000 0.00 0.00 0.00 4.26
2040 2247 1.204146 GGTCCCTATCCACAGAGCAA 58.796 55.000 0.00 0.00 0.00 3.91
2041 2248 1.559682 GGTCCCTATCCACAGAGCAAA 59.440 52.381 0.00 0.00 0.00 3.68
2042 2249 2.026262 GGTCCCTATCCACAGAGCAAAA 60.026 50.000 0.00 0.00 0.00 2.44
2043 2250 3.372025 GGTCCCTATCCACAGAGCAAAAT 60.372 47.826 0.00 0.00 0.00 1.82
2044 2251 4.273318 GTCCCTATCCACAGAGCAAAATT 58.727 43.478 0.00 0.00 0.00 1.82
2045 2252 4.336713 GTCCCTATCCACAGAGCAAAATTC 59.663 45.833 0.00 0.00 0.00 2.17
2046 2253 3.633986 CCCTATCCACAGAGCAAAATTCC 59.366 47.826 0.00 0.00 0.00 3.01
2047 2254 4.272489 CCTATCCACAGAGCAAAATTCCA 58.728 43.478 0.00 0.00 0.00 3.53
2048 2255 4.337555 CCTATCCACAGAGCAAAATTCCAG 59.662 45.833 0.00 0.00 0.00 3.86
2049 2256 3.228188 TCCACAGAGCAAAATTCCAGT 57.772 42.857 0.00 0.00 0.00 4.00
2050 2257 3.565307 TCCACAGAGCAAAATTCCAGTT 58.435 40.909 0.00 0.00 0.00 3.16
2051 2258 3.960102 TCCACAGAGCAAAATTCCAGTTT 59.040 39.130 0.00 0.00 0.00 2.66
2052 2259 4.053295 CCACAGAGCAAAATTCCAGTTTG 58.947 43.478 0.00 0.00 38.69 2.93
2076 2283 6.146601 CAAATATGCACATGTAACATCCCA 57.853 37.500 14.88 1.74 0.00 4.37
2077 2284 6.571605 CAAATATGCACATGTAACATCCCAA 58.428 36.000 14.88 1.44 0.00 4.12
2078 2285 6.788598 AATATGCACATGTAACATCCCAAA 57.211 33.333 14.88 1.13 0.00 3.28
2079 2286 6.788598 ATATGCACATGTAACATCCCAAAA 57.211 33.333 14.88 0.53 0.00 2.44
2080 2287 5.680594 ATGCACATGTAACATCCCAAAAT 57.319 34.783 0.00 0.00 0.00 1.82
2081 2288 5.480642 TGCACATGTAACATCCCAAAATT 57.519 34.783 0.00 0.00 0.00 1.82
2082 2289 5.477510 TGCACATGTAACATCCCAAAATTC 58.522 37.500 0.00 0.00 0.00 2.17
2083 2290 5.245751 TGCACATGTAACATCCCAAAATTCT 59.754 36.000 0.00 0.00 0.00 2.40
2084 2291 6.435591 TGCACATGTAACATCCCAAAATTCTA 59.564 34.615 0.00 0.00 0.00 2.10
2085 2292 7.039434 TGCACATGTAACATCCCAAAATTCTAA 60.039 33.333 0.00 0.00 0.00 2.10
2086 2293 7.816995 GCACATGTAACATCCCAAAATTCTAAA 59.183 33.333 0.00 0.00 0.00 1.85
2087 2294 9.874205 CACATGTAACATCCCAAAATTCTAAAT 57.126 29.630 0.00 0.00 0.00 1.40
2136 2343 9.985730 ATAGATGATTGTTTGTTTGATTGTTGT 57.014 25.926 0.00 0.00 0.00 3.32
2137 2344 8.133754 AGATGATTGTTTGTTTGATTGTTGTG 57.866 30.769 0.00 0.00 0.00 3.33
2138 2345 7.765360 AGATGATTGTTTGTTTGATTGTTGTGT 59.235 29.630 0.00 0.00 0.00 3.72
2139 2346 7.058298 TGATTGTTTGTTTGATTGTTGTGTG 57.942 32.000 0.00 0.00 0.00 3.82
2140 2347 6.870439 TGATTGTTTGTTTGATTGTTGTGTGA 59.130 30.769 0.00 0.00 0.00 3.58
2141 2348 7.548427 TGATTGTTTGTTTGATTGTTGTGTGAT 59.452 29.630 0.00 0.00 0.00 3.06
2142 2349 7.664082 TTGTTTGTTTGATTGTTGTGTGATT 57.336 28.000 0.00 0.00 0.00 2.57
2143 2350 7.058298 TGTTTGTTTGATTGTTGTGTGATTG 57.942 32.000 0.00 0.00 0.00 2.67
2144 2351 6.870439 TGTTTGTTTGATTGTTGTGTGATTGA 59.130 30.769 0.00 0.00 0.00 2.57
2145 2352 7.548427 TGTTTGTTTGATTGTTGTGTGATTGAT 59.452 29.630 0.00 0.00 0.00 2.57
2146 2353 8.389603 GTTTGTTTGATTGTTGTGTGATTGATT 58.610 29.630 0.00 0.00 0.00 2.57
2147 2354 7.466193 TGTTTGATTGTTGTGTGATTGATTG 57.534 32.000 0.00 0.00 0.00 2.67
2148 2355 7.263496 TGTTTGATTGTTGTGTGATTGATTGA 58.737 30.769 0.00 0.00 0.00 2.57
2149 2356 7.435784 TGTTTGATTGTTGTGTGATTGATTGAG 59.564 33.333 0.00 0.00 0.00 3.02
2150 2357 6.638096 TGATTGTTGTGTGATTGATTGAGT 57.362 33.333 0.00 0.00 0.00 3.41
2151 2358 6.440436 TGATTGTTGTGTGATTGATTGAGTG 58.560 36.000 0.00 0.00 0.00 3.51
2152 2359 6.262720 TGATTGTTGTGTGATTGATTGAGTGA 59.737 34.615 0.00 0.00 0.00 3.41
2153 2360 6.448207 TTGTTGTGTGATTGATTGAGTGAA 57.552 33.333 0.00 0.00 0.00 3.18
2154 2361 6.448207 TGTTGTGTGATTGATTGAGTGAAA 57.552 33.333 0.00 0.00 0.00 2.69
2155 2362 7.041635 TGTTGTGTGATTGATTGAGTGAAAT 57.958 32.000 0.00 0.00 0.00 2.17
2156 2363 7.490840 TGTTGTGTGATTGATTGAGTGAAATT 58.509 30.769 0.00 0.00 0.00 1.82
2157 2364 7.648908 TGTTGTGTGATTGATTGAGTGAAATTC 59.351 33.333 0.00 0.00 0.00 2.17
2158 2365 7.274603 TGTGTGATTGATTGAGTGAAATTCA 57.725 32.000 0.00 0.00 0.00 2.57
2159 2366 7.714703 TGTGTGATTGATTGAGTGAAATTCAA 58.285 30.769 0.00 0.00 46.79 2.69
2160 2367 8.196103 TGTGTGATTGATTGAGTGAAATTCAAA 58.804 29.630 0.00 0.00 45.86 2.69
2161 2368 9.033481 GTGTGATTGATTGAGTGAAATTCAAAA 57.967 29.630 0.00 0.00 45.86 2.44
2162 2369 9.033481 TGTGATTGATTGAGTGAAATTCAAAAC 57.967 29.630 0.00 0.00 45.86 2.43
2163 2370 9.252962 GTGATTGATTGAGTGAAATTCAAAACT 57.747 29.630 0.00 0.00 45.86 2.66
2164 2371 9.820725 TGATTGATTGAGTGAAATTCAAAACTT 57.179 25.926 0.00 0.00 45.86 2.66
2185 2392 9.599866 AAACTTTTTGAAAGTTAAATGAGAGGG 57.400 29.630 16.48 0.00 39.36 4.30
2186 2393 8.533569 ACTTTTTGAAAGTTAAATGAGAGGGA 57.466 30.769 0.44 0.00 0.00 4.20
2187 2394 8.977412 ACTTTTTGAAAGTTAAATGAGAGGGAA 58.023 29.630 0.44 0.00 0.00 3.97
2188 2395 9.987272 CTTTTTGAAAGTTAAATGAGAGGGAAT 57.013 29.630 0.00 0.00 0.00 3.01
2195 2402 9.822727 AAAGTTAAATGAGAGGGAATAAAAGGA 57.177 29.630 0.00 0.00 0.00 3.36
2196 2403 8.809468 AGTTAAATGAGAGGGAATAAAAGGAC 57.191 34.615 0.00 0.00 0.00 3.85
2197 2404 8.615705 AGTTAAATGAGAGGGAATAAAAGGACT 58.384 33.333 0.00 0.00 0.00 3.85
2198 2405 9.244292 GTTAAATGAGAGGGAATAAAAGGACTT 57.756 33.333 0.00 0.00 0.00 3.01
2199 2406 9.822727 TTAAATGAGAGGGAATAAAAGGACTTT 57.177 29.630 0.00 0.00 0.00 2.66
2200 2407 7.946381 AATGAGAGGGAATAAAAGGACTTTC 57.054 36.000 0.00 0.00 31.45 2.62
2201 2408 5.816682 TGAGAGGGAATAAAAGGACTTTCC 58.183 41.667 0.00 0.00 37.49 3.13
2207 2414 6.665992 GGAATAAAAGGACTTTCCCAAACT 57.334 37.500 0.00 0.00 37.19 2.66
2208 2415 7.062749 GGAATAAAAGGACTTTCCCAAACTT 57.937 36.000 0.00 0.00 37.19 2.66
2209 2416 7.506114 GGAATAAAAGGACTTTCCCAAACTTT 58.494 34.615 0.00 0.00 37.19 2.66
2210 2417 7.656137 GGAATAAAAGGACTTTCCCAAACTTTC 59.344 37.037 0.00 0.00 37.19 2.62
2211 2418 7.669089 ATAAAAGGACTTTCCCAAACTTTCA 57.331 32.000 0.00 0.00 37.19 2.69
2212 2419 5.339008 AAAGGACTTTCCCAAACTTTCAC 57.661 39.130 0.00 0.00 37.19 3.18
2213 2420 3.296854 AGGACTTTCCCAAACTTTCACC 58.703 45.455 0.00 0.00 37.19 4.02
2214 2421 3.052869 AGGACTTTCCCAAACTTTCACCT 60.053 43.478 0.00 0.00 37.19 4.00
2215 2422 3.704566 GGACTTTCCCAAACTTTCACCTT 59.295 43.478 0.00 0.00 0.00 3.50
2216 2423 4.161565 GGACTTTCCCAAACTTTCACCTTT 59.838 41.667 0.00 0.00 0.00 3.11
2217 2424 5.338056 GGACTTTCCCAAACTTTCACCTTTT 60.338 40.000 0.00 0.00 0.00 2.27
2218 2425 6.121776 ACTTTCCCAAACTTTCACCTTTTT 57.878 33.333 0.00 0.00 0.00 1.94
2219 2426 5.937540 ACTTTCCCAAACTTTCACCTTTTTG 59.062 36.000 0.00 0.00 0.00 2.44
2220 2427 3.867857 TCCCAAACTTTCACCTTTTTGC 58.132 40.909 0.00 0.00 0.00 3.68
2221 2428 3.261897 TCCCAAACTTTCACCTTTTTGCA 59.738 39.130 0.00 0.00 0.00 4.08
2222 2429 4.080638 TCCCAAACTTTCACCTTTTTGCAT 60.081 37.500 0.00 0.00 0.00 3.96
2223 2430 4.639755 CCCAAACTTTCACCTTTTTGCATT 59.360 37.500 0.00 0.00 0.00 3.56
2224 2431 5.125257 CCCAAACTTTCACCTTTTTGCATTT 59.875 36.000 0.00 0.00 0.00 2.32
2225 2432 6.350027 CCCAAACTTTCACCTTTTTGCATTTT 60.350 34.615 0.00 0.00 0.00 1.82
2226 2433 6.527372 CCAAACTTTCACCTTTTTGCATTTTG 59.473 34.615 0.00 0.00 0.00 2.44
2227 2434 7.303998 CAAACTTTCACCTTTTTGCATTTTGA 58.696 30.769 0.00 0.00 0.00 2.69
2228 2435 7.628769 AACTTTCACCTTTTTGCATTTTGAT 57.371 28.000 0.00 0.00 0.00 2.57
2229 2436 7.250445 ACTTTCACCTTTTTGCATTTTGATC 57.750 32.000 0.00 0.00 0.00 2.92
2230 2437 7.049754 ACTTTCACCTTTTTGCATTTTGATCT 58.950 30.769 0.00 0.00 0.00 2.75
2231 2438 7.225341 ACTTTCACCTTTTTGCATTTTGATCTC 59.775 33.333 0.00 0.00 0.00 2.75
2232 2439 5.540911 TCACCTTTTTGCATTTTGATCTCC 58.459 37.500 0.00 0.00 0.00 3.71
2233 2440 5.305128 TCACCTTTTTGCATTTTGATCTCCT 59.695 36.000 0.00 0.00 0.00 3.69
2234 2441 5.993441 CACCTTTTTGCATTTTGATCTCCTT 59.007 36.000 0.00 0.00 0.00 3.36
2235 2442 5.993441 ACCTTTTTGCATTTTGATCTCCTTG 59.007 36.000 0.00 0.00 0.00 3.61
2236 2443 6.183360 ACCTTTTTGCATTTTGATCTCCTTGA 60.183 34.615 0.00 0.00 0.00 3.02
2237 2444 6.707161 CCTTTTTGCATTTTGATCTCCTTGAA 59.293 34.615 0.00 0.00 0.00 2.69
2238 2445 7.389607 CCTTTTTGCATTTTGATCTCCTTGAAT 59.610 33.333 0.00 0.00 0.00 2.57
2239 2446 8.680039 TTTTTGCATTTTGATCTCCTTGAATT 57.320 26.923 0.00 0.00 0.00 2.17
2240 2447 7.894376 TTTGCATTTTGATCTCCTTGAATTC 57.106 32.000 0.00 0.00 0.00 2.17
2241 2448 6.593268 TGCATTTTGATCTCCTTGAATTCA 57.407 33.333 3.38 3.38 0.00 2.57
2242 2449 6.995364 TGCATTTTGATCTCCTTGAATTCAA 58.005 32.000 19.45 19.45 0.00 2.69
2243 2450 7.443477 TGCATTTTGATCTCCTTGAATTCAAA 58.557 30.769 20.82 7.48 35.23 2.69
2244 2451 8.098286 TGCATTTTGATCTCCTTGAATTCAAAT 58.902 29.630 20.82 11.87 36.50 2.32
2245 2452 8.943002 GCATTTTGATCTCCTTGAATTCAAATT 58.057 29.630 20.82 5.26 36.50 1.82
2251 2458 9.918630 TGATCTCCTTGAATTCAAATTCTTTTC 57.081 29.630 20.82 12.27 43.97 2.29
2252 2459 9.918630 GATCTCCTTGAATTCAAATTCTTTTCA 57.081 29.630 20.82 0.00 43.97 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 295 0.042581 TGAGGGCCATGGTACTCAGA 59.957 55.000 26.58 12.64 35.24 3.27
327 328 2.158310 TGGTCTCCACCTTCAGAAGAGA 60.158 50.000 12.14 3.85 44.17 3.10
394 395 1.146930 ATGCCAGTGTATCCAGCCG 59.853 57.895 0.00 0.00 0.00 5.52
461 462 0.179032 TTTGACCGCACACTCCACAT 60.179 50.000 0.00 0.00 0.00 3.21
467 468 2.113139 CCCCTTTGACCGCACACT 59.887 61.111 0.00 0.00 0.00 3.55
477 479 0.523072 CGCTCATTGTGTCCCCTTTG 59.477 55.000 0.00 0.00 0.00 2.77
480 482 1.918293 TCCGCTCATTGTGTCCCCT 60.918 57.895 0.00 0.00 0.00 4.79
526 528 3.207778 CCACCTCCACGACTTGTTTTTA 58.792 45.455 0.00 0.00 0.00 1.52
587 589 1.006102 ACTTGTGCTTCCTCGACCG 60.006 57.895 0.00 0.00 0.00 4.79
643 645 2.223803 ACACTAGCACCTCTAGCACT 57.776 50.000 0.00 0.00 46.93 4.40
670 672 3.093057 CACCTCTAGCACTTGTACTCCT 58.907 50.000 0.00 0.00 0.00 3.69
749 787 1.672356 GTGCTTGCTCGACCACCAT 60.672 57.895 0.00 0.00 0.00 3.55
860 928 6.549364 TCAACCATCCGGATTAAGCAAATAAT 59.451 34.615 16.19 0.00 35.59 1.28
1073 1143 1.699634 CCTTCTCCTTGTCCAACCTGA 59.300 52.381 0.00 0.00 0.00 3.86
1459 1536 0.038251 TTCTCACGACGCTCATGCTT 60.038 50.000 0.00 0.00 36.97 3.91
1477 1569 0.966920 TTCCGCTCGTTCTTCTCCTT 59.033 50.000 0.00 0.00 0.00 3.36
1478 1570 0.528470 CTTCCGCTCGTTCTTCTCCT 59.472 55.000 0.00 0.00 0.00 3.69
1479 1571 0.526662 TCTTCCGCTCGTTCTTCTCC 59.473 55.000 0.00 0.00 0.00 3.71
1480 1572 2.255316 CTTCTTCCGCTCGTTCTTCTC 58.745 52.381 0.00 0.00 0.00 2.87
1481 1573 1.670380 GCTTCTTCCGCTCGTTCTTCT 60.670 52.381 0.00 0.00 0.00 2.85
1482 1574 0.716666 GCTTCTTCCGCTCGTTCTTC 59.283 55.000 0.00 0.00 0.00 2.87
1483 1575 0.033504 TGCTTCTTCCGCTCGTTCTT 59.966 50.000 0.00 0.00 0.00 2.52
1484 1576 0.247736 ATGCTTCTTCCGCTCGTTCT 59.752 50.000 0.00 0.00 0.00 3.01
1485 1577 0.371645 CATGCTTCTTCCGCTCGTTC 59.628 55.000 0.00 0.00 0.00 3.95
1486 1578 0.037326 TCATGCTTCTTCCGCTCGTT 60.037 50.000 0.00 0.00 0.00 3.85
1487 1579 0.459237 CTCATGCTTCTTCCGCTCGT 60.459 55.000 0.00 0.00 0.00 4.18
1488 1580 1.760268 GCTCATGCTTCTTCCGCTCG 61.760 60.000 0.00 0.00 36.03 5.03
1489 1581 0.742281 TGCTCATGCTTCTTCCGCTC 60.742 55.000 0.00 0.00 40.48 5.03
1490 1582 0.321919 TTGCTCATGCTTCTTCCGCT 60.322 50.000 0.00 0.00 40.48 5.52
1491 1583 0.098376 CTTGCTCATGCTTCTTCCGC 59.902 55.000 0.00 0.00 40.48 5.54
1494 1586 2.937799 CCTCTCTTGCTCATGCTTCTTC 59.062 50.000 0.00 0.00 40.48 2.87
1502 1594 1.220206 CGTGCCCTCTCTTGCTCAT 59.780 57.895 0.00 0.00 0.00 2.90
1656 1771 2.029380 TCGACAGTCCATCATCAACGTT 60.029 45.455 0.00 0.00 0.00 3.99
1661 1776 2.728007 AGTCTCGACAGTCCATCATCA 58.272 47.619 0.00 0.00 0.00 3.07
1815 1960 9.190858 TGAACAAAACATAGTTTGCACATAATC 57.809 29.630 0.00 0.00 41.33 1.75
1942 2148 1.457831 GGATAGGGACCCAGACGCT 60.458 63.158 14.60 0.00 34.98 5.07
1987 2194 3.952508 TGGCGTCTGGGTGTGCAT 61.953 61.111 0.00 0.00 0.00 3.96
2016 2223 1.580658 TCTGTGGATAGGGACCCAGAT 59.419 52.381 14.60 5.36 33.35 2.90
2053 2260 6.146601 TGGGATGTTACATGTGCATATTTG 57.853 37.500 9.11 0.00 0.00 2.32
2054 2261 6.788598 TTGGGATGTTACATGTGCATATTT 57.211 33.333 9.11 0.00 0.00 1.40
2055 2262 6.788598 TTTGGGATGTTACATGTGCATATT 57.211 33.333 9.11 0.00 0.00 1.28
2056 2263 6.788598 TTTTGGGATGTTACATGTGCATAT 57.211 33.333 9.11 0.00 0.00 1.78
2057 2264 6.788598 ATTTTGGGATGTTACATGTGCATA 57.211 33.333 9.11 0.00 0.00 3.14
2058 2265 5.680594 ATTTTGGGATGTTACATGTGCAT 57.319 34.783 9.11 12.66 0.00 3.96
2059 2266 5.245751 AGAATTTTGGGATGTTACATGTGCA 59.754 36.000 9.11 8.01 0.00 4.57
2060 2267 5.723295 AGAATTTTGGGATGTTACATGTGC 58.277 37.500 9.11 1.72 0.00 4.57
2061 2268 9.874205 ATTTAGAATTTTGGGATGTTACATGTG 57.126 29.630 9.11 0.00 0.00 3.21
2110 2317 9.985730 ACAACAATCAAACAAACAATCATCTAT 57.014 25.926 0.00 0.00 0.00 1.98
2111 2318 9.247126 CACAACAATCAAACAAACAATCATCTA 57.753 29.630 0.00 0.00 0.00 1.98
2112 2319 7.765360 ACACAACAATCAAACAAACAATCATCT 59.235 29.630 0.00 0.00 0.00 2.90
2113 2320 7.847078 CACACAACAATCAAACAAACAATCATC 59.153 33.333 0.00 0.00 0.00 2.92
2114 2321 7.548427 TCACACAACAATCAAACAAACAATCAT 59.452 29.630 0.00 0.00 0.00 2.45
2115 2322 6.870439 TCACACAACAATCAAACAAACAATCA 59.130 30.769 0.00 0.00 0.00 2.57
2116 2323 7.288317 TCACACAACAATCAAACAAACAATC 57.712 32.000 0.00 0.00 0.00 2.67
2117 2324 7.846644 ATCACACAACAATCAAACAAACAAT 57.153 28.000 0.00 0.00 0.00 2.71
2118 2325 7.386025 TCAATCACACAACAATCAAACAAACAA 59.614 29.630 0.00 0.00 0.00 2.83
2119 2326 6.870439 TCAATCACACAACAATCAAACAAACA 59.130 30.769 0.00 0.00 0.00 2.83
2120 2327 7.288317 TCAATCACACAACAATCAAACAAAC 57.712 32.000 0.00 0.00 0.00 2.93
2121 2328 8.388853 CAATCAATCACACAACAATCAAACAAA 58.611 29.630 0.00 0.00 0.00 2.83
2122 2329 7.763071 TCAATCAATCACACAACAATCAAACAA 59.237 29.630 0.00 0.00 0.00 2.83
2123 2330 7.263496 TCAATCAATCACACAACAATCAAACA 58.737 30.769 0.00 0.00 0.00 2.83
2124 2331 7.436080 ACTCAATCAATCACACAACAATCAAAC 59.564 33.333 0.00 0.00 0.00 2.93
2125 2332 7.435784 CACTCAATCAATCACACAACAATCAAA 59.564 33.333 0.00 0.00 0.00 2.69
2126 2333 6.919115 CACTCAATCAATCACACAACAATCAA 59.081 34.615 0.00 0.00 0.00 2.57
2127 2334 6.262720 TCACTCAATCAATCACACAACAATCA 59.737 34.615 0.00 0.00 0.00 2.57
2128 2335 6.671190 TCACTCAATCAATCACACAACAATC 58.329 36.000 0.00 0.00 0.00 2.67
2129 2336 6.638096 TCACTCAATCAATCACACAACAAT 57.362 33.333 0.00 0.00 0.00 2.71
2130 2337 6.448207 TTCACTCAATCAATCACACAACAA 57.552 33.333 0.00 0.00 0.00 2.83
2131 2338 6.448207 TTTCACTCAATCAATCACACAACA 57.552 33.333 0.00 0.00 0.00 3.33
2132 2339 7.648908 TGAATTTCACTCAATCAATCACACAAC 59.351 33.333 0.00 0.00 0.00 3.32
2133 2340 7.714703 TGAATTTCACTCAATCAATCACACAA 58.285 30.769 0.00 0.00 0.00 3.33
2134 2341 7.274603 TGAATTTCACTCAATCAATCACACA 57.725 32.000 0.00 0.00 0.00 3.72
2135 2342 8.578308 TTTGAATTTCACTCAATCAATCACAC 57.422 30.769 0.00 0.00 32.98 3.82
2136 2343 9.033481 GTTTTGAATTTCACTCAATCAATCACA 57.967 29.630 0.00 0.00 32.98 3.58
2137 2344 9.252962 AGTTTTGAATTTCACTCAATCAATCAC 57.747 29.630 0.00 0.00 32.98 3.06
2138 2345 9.820725 AAGTTTTGAATTTCACTCAATCAATCA 57.179 25.926 0.00 0.00 32.98 2.57
2159 2366 9.599866 CCCTCTCATTTAACTTTCAAAAAGTTT 57.400 29.630 19.49 3.38 40.58 2.66
2160 2367 8.977412 TCCCTCTCATTTAACTTTCAAAAAGTT 58.023 29.630 18.60 18.60 42.53 2.66
2161 2368 8.533569 TCCCTCTCATTTAACTTTCAAAAAGT 57.466 30.769 0.00 0.00 0.00 2.66
2162 2369 9.987272 ATTCCCTCTCATTTAACTTTCAAAAAG 57.013 29.630 0.00 0.00 0.00 2.27
2169 2376 9.822727 TCCTTTTATTCCCTCTCATTTAACTTT 57.177 29.630 0.00 0.00 0.00 2.66
2170 2377 9.244292 GTCCTTTTATTCCCTCTCATTTAACTT 57.756 33.333 0.00 0.00 0.00 2.66
2171 2378 8.615705 AGTCCTTTTATTCCCTCTCATTTAACT 58.384 33.333 0.00 0.00 0.00 2.24
2172 2379 8.809468 AGTCCTTTTATTCCCTCTCATTTAAC 57.191 34.615 0.00 0.00 0.00 2.01
2173 2380 9.822727 AAAGTCCTTTTATTCCCTCTCATTTAA 57.177 29.630 0.00 0.00 0.00 1.52
2174 2381 9.462606 GAAAGTCCTTTTATTCCCTCTCATTTA 57.537 33.333 0.00 0.00 32.11 1.40
2175 2382 7.397476 GGAAAGTCCTTTTATTCCCTCTCATTT 59.603 37.037 0.00 0.00 36.21 2.32
2176 2383 6.892456 GGAAAGTCCTTTTATTCCCTCTCATT 59.108 38.462 0.00 0.00 36.21 2.57
2177 2384 6.427441 GGAAAGTCCTTTTATTCCCTCTCAT 58.573 40.000 0.00 0.00 36.21 2.90
2178 2385 5.816682 GGAAAGTCCTTTTATTCCCTCTCA 58.183 41.667 0.00 0.00 36.21 3.27
2184 2391 6.665992 AGTTTGGGAAAGTCCTTTTATTCC 57.334 37.500 0.00 0.00 40.48 3.01
2185 2392 8.201464 TGAAAGTTTGGGAAAGTCCTTTTATTC 58.799 33.333 0.00 0.00 36.57 1.75
2186 2393 7.985184 GTGAAAGTTTGGGAAAGTCCTTTTATT 59.015 33.333 0.00 0.00 36.57 1.40
2187 2394 7.418597 GGTGAAAGTTTGGGAAAGTCCTTTTAT 60.419 37.037 0.00 0.00 36.57 1.40
2188 2395 6.127281 GGTGAAAGTTTGGGAAAGTCCTTTTA 60.127 38.462 0.00 0.00 36.57 1.52
2189 2396 5.338056 GGTGAAAGTTTGGGAAAGTCCTTTT 60.338 40.000 0.00 0.00 36.57 2.27
2190 2397 4.161565 GGTGAAAGTTTGGGAAAGTCCTTT 59.838 41.667 0.00 0.00 36.57 3.11
2191 2398 3.704566 GGTGAAAGTTTGGGAAAGTCCTT 59.295 43.478 0.00 0.00 36.57 3.36
2192 2399 3.052869 AGGTGAAAGTTTGGGAAAGTCCT 60.053 43.478 0.00 0.00 36.57 3.85
2193 2400 3.296854 AGGTGAAAGTTTGGGAAAGTCC 58.703 45.455 0.00 0.00 35.23 3.85
2194 2401 5.339008 AAAGGTGAAAGTTTGGGAAAGTC 57.661 39.130 0.00 0.00 0.00 3.01
2195 2402 5.755409 AAAAGGTGAAAGTTTGGGAAAGT 57.245 34.783 0.00 0.00 0.00 2.66
2196 2403 5.163764 GCAAAAAGGTGAAAGTTTGGGAAAG 60.164 40.000 0.00 0.00 32.73 2.62
2197 2404 4.697828 GCAAAAAGGTGAAAGTTTGGGAAA 59.302 37.500 0.00 0.00 32.73 3.13
2198 2405 4.257731 GCAAAAAGGTGAAAGTTTGGGAA 58.742 39.130 0.00 0.00 32.73 3.97
2199 2406 3.261897 TGCAAAAAGGTGAAAGTTTGGGA 59.738 39.130 0.00 0.00 32.73 4.37
2200 2407 3.604582 TGCAAAAAGGTGAAAGTTTGGG 58.395 40.909 0.00 0.00 32.73 4.12
2201 2408 5.816449 AATGCAAAAAGGTGAAAGTTTGG 57.184 34.783 0.00 0.00 32.73 3.28
2202 2409 7.303998 TCAAAATGCAAAAAGGTGAAAGTTTG 58.696 30.769 0.00 0.00 34.74 2.93
2203 2410 7.446001 TCAAAATGCAAAAAGGTGAAAGTTT 57.554 28.000 0.00 0.00 0.00 2.66
2204 2411 7.553760 AGATCAAAATGCAAAAAGGTGAAAGTT 59.446 29.630 0.00 0.00 0.00 2.66
2205 2412 7.049754 AGATCAAAATGCAAAAAGGTGAAAGT 58.950 30.769 0.00 0.00 0.00 2.66
2206 2413 7.307573 GGAGATCAAAATGCAAAAAGGTGAAAG 60.308 37.037 0.00 0.00 0.00 2.62
2207 2414 6.482973 GGAGATCAAAATGCAAAAAGGTGAAA 59.517 34.615 0.00 0.00 0.00 2.69
2208 2415 5.990996 GGAGATCAAAATGCAAAAAGGTGAA 59.009 36.000 0.00 0.00 0.00 3.18
2209 2416 5.305128 AGGAGATCAAAATGCAAAAAGGTGA 59.695 36.000 0.00 0.00 0.00 4.02
2210 2417 5.544650 AGGAGATCAAAATGCAAAAAGGTG 58.455 37.500 0.00 0.00 0.00 4.00
2211 2418 5.813513 AGGAGATCAAAATGCAAAAAGGT 57.186 34.783 0.00 0.00 0.00 3.50
2212 2419 6.225318 TCAAGGAGATCAAAATGCAAAAAGG 58.775 36.000 0.00 0.00 0.00 3.11
2213 2420 7.718272 TTCAAGGAGATCAAAATGCAAAAAG 57.282 32.000 0.00 0.00 0.00 2.27
2214 2421 8.680039 AATTCAAGGAGATCAAAATGCAAAAA 57.320 26.923 0.00 0.00 0.00 1.94
2215 2422 7.932491 TGAATTCAAGGAGATCAAAATGCAAAA 59.068 29.630 5.45 0.00 0.00 2.44
2216 2423 7.443477 TGAATTCAAGGAGATCAAAATGCAAA 58.557 30.769 5.45 0.00 0.00 3.68
2217 2424 6.995364 TGAATTCAAGGAGATCAAAATGCAA 58.005 32.000 5.45 0.00 0.00 4.08
2218 2425 6.593268 TGAATTCAAGGAGATCAAAATGCA 57.407 33.333 5.45 0.00 0.00 3.96
2219 2426 7.894376 TTTGAATTCAAGGAGATCAAAATGC 57.106 32.000 19.64 0.00 37.14 3.56
2225 2432 9.918630 GAAAAGAATTTGAATTCAAGGAGATCA 57.081 29.630 19.64 5.07 45.59 2.92
2226 2433 9.918630 TGAAAAGAATTTGAATTCAAGGAGATC 57.081 29.630 19.64 14.11 45.59 2.75


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

AutoCloner maintained by Alex Coulton.