Multiple sequence alignment - TraesCS4A01G290700

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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 TraesCS4A01G290700 chr4A 100.000 2986 0 0 1 2986 594352879 594349894 0.000000e+00 5515.0
1 TraesCS4A01G290700 chr4A 93.865 326 20 0 2661 2986 594345209 594344884 2.670000e-135 492.0
2 TraesCS4A01G290700 chr4D 86.431 2373 158 72 707 2986 9069116 9071417 0.000000e+00 2447.0
3 TraesCS4A01G290700 chr4B 85.750 2400 168 75 705 2986 17016799 17019142 0.000000e+00 2377.0
4 TraesCS4A01G290700 chr2A 90.463 713 36 10 4 691 412039103 412038398 0.000000e+00 911.0
5 TraesCS4A01G290700 chr3D 90.262 688 35 13 4 665 254986094 254985413 0.000000e+00 870.0
6 TraesCS4A01G290700 chr5A 85.169 681 52 20 4 658 705448008 705447351 0.000000e+00 652.0
7 TraesCS4A01G290700 chr5A 85.600 125 18 0 1023 1147 494863170 494863294 6.720000e-27 132.0
8 TraesCS4A01G290700 chr1D 86.742 528 36 14 183 683 207139247 207138727 9.350000e-155 556.0
9 TraesCS4A01G290700 chr2B 85.556 540 42 16 183 692 800489797 800489264 1.580000e-147 532.0
10 TraesCS4A01G290700 chr2B 88.983 118 9 3 1 118 63138583 63138696 3.100000e-30 143.0
11 TraesCS4A01G290700 chr2B 79.747 79 12 3 184 261 753329433 753329508 1.000000e-03 54.7
12 TraesCS4A01G290700 chr7B 85.499 531 41 16 183 683 442537083 442537607 3.410000e-144 521.0
13 TraesCS4A01G290700 chr5B 85.499 531 40 16 183 683 214141471 214140948 1.230000e-143 520.0
14 TraesCS4A01G290700 chr5B 85.600 125 18 0 1023 1147 471852462 471852586 6.720000e-27 132.0
15 TraesCS4A01G290700 chr6B 81.556 450 54 15 270 692 57697474 57697921 7.920000e-91 344.0
16 TraesCS4A01G290700 chr6B 98.113 53 1 0 140 192 76470562 76470614 3.170000e-15 93.5
17 TraesCS4A01G290700 chr3A 89.637 193 11 7 510 694 405698142 405698333 1.380000e-58 237.0
18 TraesCS4A01G290700 chr2D 90.857 175 12 3 510 683 228432220 228432391 6.440000e-57 231.0
19 TraesCS4A01G290700 chr6A 84.127 189 24 3 4 192 485152964 485153146 8.510000e-41 178.0
20 TraesCS4A01G290700 chrUn 88.811 143 12 3 1 143 77097086 77097224 3.960000e-39 172.0
21 TraesCS4A01G290700 chr5D 82.424 165 22 6 986 1147 391730400 391730560 1.440000e-28 137.0
22 TraesCS4A01G290700 chr5D 100.000 41 0 0 183 223 525466745 525466785 3.190000e-10 76.8


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 TraesCS4A01G290700 chr4A 594349894 594352879 2985 True 5515 5515 100.000 1 2986 1 chr4A.!!$R2 2985
1 TraesCS4A01G290700 chr4D 9069116 9071417 2301 False 2447 2447 86.431 707 2986 1 chr4D.!!$F1 2279
2 TraesCS4A01G290700 chr4B 17016799 17019142 2343 False 2377 2377 85.750 705 2986 1 chr4B.!!$F1 2281
3 TraesCS4A01G290700 chr2A 412038398 412039103 705 True 911 911 90.463 4 691 1 chr2A.!!$R1 687
4 TraesCS4A01G290700 chr3D 254985413 254986094 681 True 870 870 90.262 4 665 1 chr3D.!!$R1 661
5 TraesCS4A01G290700 chr5A 705447351 705448008 657 True 652 652 85.169 4 658 1 chr5A.!!$R1 654
6 TraesCS4A01G290700 chr1D 207138727 207139247 520 True 556 556 86.742 183 683 1 chr1D.!!$R1 500
7 TraesCS4A01G290700 chr2B 800489264 800489797 533 True 532 532 85.556 183 692 1 chr2B.!!$R1 509
8 TraesCS4A01G290700 chr7B 442537083 442537607 524 False 521 521 85.499 183 683 1 chr7B.!!$F1 500
9 TraesCS4A01G290700 chr5B 214140948 214141471 523 True 520 520 85.499 183 683 1 chr5B.!!$R1 500

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
460 467 0.179153 CAAGCATCGACAGAGAGCGA 60.179 55.0 0.0 0.0 41.14 4.93 F
1354 1428 0.528924 TCCGGTACCTCAACATGTCG 59.471 55.0 10.9 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1443 0.315251 TGAACTCTGGCACTCACTCG 59.685 55.0 0.0 0.0 0.0 4.18 R
2617 2794 0.586319 AAATGACGTGTGAGGTTGCG 59.414 50.0 0.0 0.0 0.0 4.85 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
46 47 3.487202 CAACCATCGCACGACGGG 61.487 66.667 10.16 10.15 43.89 5.28
234 236 5.996644 TCCACCAGAGTTTGTTTTCTCTAA 58.003 37.500 0.00 0.00 38.74 2.10
243 245 7.661847 AGAGTTTGTTTTCTCTAAACCATCGAT 59.338 33.333 0.00 0.00 44.49 3.59
315 318 6.791887 TGCTTTCATCAGAGTTAGTTCTTG 57.208 37.500 0.00 0.00 0.00 3.02
359 362 7.534239 CGACTTTTTGCTACAACCTTATCTTTC 59.466 37.037 0.00 0.00 0.00 2.62
392 395 6.108687 GGAACCAAGGATTTCAATTGATTCC 58.891 40.000 21.93 21.93 38.96 3.01
415 418 3.286751 GGCGGCAACACAGAGCAA 61.287 61.111 3.07 0.00 0.00 3.91
416 419 2.629656 GGCGGCAACACAGAGCAAT 61.630 57.895 3.07 0.00 0.00 3.56
460 467 0.179153 CAAGCATCGACAGAGAGCGA 60.179 55.000 0.00 0.00 41.14 4.93
495 502 1.662446 GGCGACTTTCGACGGTGAA 60.662 57.895 0.00 0.00 43.74 3.18
507 514 1.228124 CGGTGAAGGCAAACAGGGA 60.228 57.895 0.00 0.00 0.00 4.20
591 624 1.357334 GGTGACAAGCGCCGAAAAA 59.643 52.632 2.29 0.00 37.43 1.94
983 1048 4.767255 GCCCACCTCACCTCGCTG 62.767 72.222 0.00 0.00 0.00 5.18
984 1049 2.997315 CCCACCTCACCTCGCTGA 60.997 66.667 0.00 0.00 0.00 4.26
985 1050 2.262915 CCACCTCACCTCGCTGAC 59.737 66.667 0.00 0.00 0.00 3.51
1202 1273 1.454295 GGTCCGTCCTCCTCTCCTC 60.454 68.421 0.00 0.00 0.00 3.71
1213 1284 0.829990 CCTCTCCTCTCTCCTTTGCC 59.170 60.000 0.00 0.00 0.00 4.52
1214 1285 1.566211 CTCTCCTCTCTCCTTTGCCA 58.434 55.000 0.00 0.00 0.00 4.92
1215 1286 1.206849 CTCTCCTCTCTCCTTTGCCAC 59.793 57.143 0.00 0.00 0.00 5.01
1216 1287 0.979665 CTCCTCTCTCCTTTGCCACA 59.020 55.000 0.00 0.00 0.00 4.17
1217 1288 0.979665 TCCTCTCTCCTTTGCCACAG 59.020 55.000 0.00 0.00 0.00 3.66
1218 1289 0.676151 CCTCTCTCCTTTGCCACAGC 60.676 60.000 0.00 0.00 40.48 4.40
1221 1292 2.670934 CTCCTTTGCCACAGCGCT 60.671 61.111 2.64 2.64 44.31 5.92
1305 1379 3.659697 CGCGCTCGTCGATCGTTC 61.660 66.667 18.46 8.82 41.67 3.95
1306 1380 3.659697 GCGCTCGTCGATCGTTCG 61.660 66.667 18.46 19.57 46.87 3.95
1307 1381 2.276493 CGCTCGTCGATCGTTCGT 60.276 61.111 24.61 0.00 45.65 3.85
1311 1385 3.558377 CGTCGATCGTTCGTCGTC 58.442 61.111 21.56 7.91 46.68 4.20
1313 1387 1.423056 GTCGATCGTTCGTCGTCCT 59.577 57.895 15.94 0.00 45.65 3.85
1354 1428 0.528924 TCCGGTACCTCAACATGTCG 59.471 55.000 10.90 0.00 0.00 4.35
1444 1518 6.072508 TCGATCTCCTTTCTCAAACATTTTGG 60.073 38.462 0.00 0.00 0.00 3.28
1518 1595 4.738124 CAAGAACTAGCTCGTCTTCATCA 58.262 43.478 0.00 0.00 0.00 3.07
1527 1604 8.035394 ACTAGCTCGTCTTCATCATCTTTTAAA 58.965 33.333 0.00 0.00 0.00 1.52
1528 1605 7.672983 AGCTCGTCTTCATCATCTTTTAAAA 57.327 32.000 0.00 0.00 0.00 1.52
1530 1607 8.017946 AGCTCGTCTTCATCATCTTTTAAAAAC 58.982 33.333 1.66 0.00 0.00 2.43
1531 1608 8.017946 GCTCGTCTTCATCATCTTTTAAAAACT 58.982 33.333 1.66 0.00 0.00 2.66
1532 1609 9.322776 CTCGTCTTCATCATCTTTTAAAAACTG 57.677 33.333 1.66 3.02 0.00 3.16
1533 1610 9.051679 TCGTCTTCATCATCTTTTAAAAACTGA 57.948 29.630 12.13 12.13 0.00 3.41
1548 1625 9.635404 TTTAAAAACTGAAAATAGGAGTCCAGA 57.365 29.630 12.86 0.00 0.00 3.86
1549 1626 7.751768 AAAAACTGAAAATAGGAGTCCAGAG 57.248 36.000 12.86 0.00 0.00 3.35
1579 1677 3.449377 TGACAAATCCGATGCAGTACCTA 59.551 43.478 0.00 0.00 0.00 3.08
1654 1755 7.321745 AGCAAAGTACTATGCATTTTACCTC 57.678 36.000 3.54 0.00 44.95 3.85
1655 1756 6.037172 AGCAAAGTACTATGCATTTTACCTCG 59.963 38.462 3.54 0.00 44.95 4.63
1656 1757 5.986004 AAGTACTATGCATTTTACCTCGC 57.014 39.130 3.54 0.00 0.00 5.03
1657 1758 5.277857 AGTACTATGCATTTTACCTCGCT 57.722 39.130 3.54 0.00 0.00 4.93
1658 1759 5.290386 AGTACTATGCATTTTACCTCGCTC 58.710 41.667 3.54 0.00 0.00 5.03
1661 1762 2.418368 TGCATTTTACCTCGCTCCAT 57.582 45.000 0.00 0.00 0.00 3.41
1662 1763 2.722094 TGCATTTTACCTCGCTCCATT 58.278 42.857 0.00 0.00 0.00 3.16
1668 1772 2.981859 TACCTCGCTCCATTTTCCTC 57.018 50.000 0.00 0.00 0.00 3.71
1698 1802 6.772770 TTCTCGTTGATTTCACGTATCAAA 57.227 33.333 12.57 2.01 42.01 2.69
1699 1803 6.148270 TCTCGTTGATTTCACGTATCAAAC 57.852 37.500 12.57 7.53 42.01 2.93
1700 1804 5.119588 TCTCGTTGATTTCACGTATCAAACC 59.880 40.000 12.57 2.96 42.01 3.27
1701 1805 4.079028 CGTTGATTTCACGTATCAAACCG 58.921 43.478 12.57 9.85 42.01 4.44
1703 1807 2.417239 TGATTTCACGTATCAAACCGGC 59.583 45.455 0.00 0.00 0.00 6.13
1705 1809 1.717194 TTCACGTATCAAACCGGCTC 58.283 50.000 0.00 0.00 0.00 4.70
1706 1810 0.604073 TCACGTATCAAACCGGCTCA 59.396 50.000 0.00 0.00 0.00 4.26
1707 1811 1.001068 TCACGTATCAAACCGGCTCAA 59.999 47.619 0.00 0.00 0.00 3.02
1708 1812 1.801771 CACGTATCAAACCGGCTCAAA 59.198 47.619 0.00 0.00 0.00 2.69
1709 1813 2.418628 CACGTATCAAACCGGCTCAAAT 59.581 45.455 0.00 0.00 0.00 2.32
1710 1814 3.078837 ACGTATCAAACCGGCTCAAATT 58.921 40.909 0.00 0.00 0.00 1.82
1711 1815 3.126343 ACGTATCAAACCGGCTCAAATTC 59.874 43.478 0.00 0.00 0.00 2.17
1712 1816 3.374058 CGTATCAAACCGGCTCAAATTCT 59.626 43.478 0.00 0.00 0.00 2.40
1713 1817 4.142687 CGTATCAAACCGGCTCAAATTCTT 60.143 41.667 0.00 0.00 0.00 2.52
1714 1818 3.641437 TCAAACCGGCTCAAATTCTTG 57.359 42.857 0.00 0.00 0.00 3.02
1723 1827 4.788100 CGGCTCAAATTCTTGTATTTCACG 59.212 41.667 0.00 0.00 33.94 4.35
1726 1830 6.370593 GCTCAAATTCTTGTATTTCACGTCA 58.629 36.000 0.00 0.00 33.94 4.35
1727 1831 6.303259 GCTCAAATTCTTGTATTTCACGTCAC 59.697 38.462 0.00 0.00 33.94 3.67
1728 1832 7.490962 TCAAATTCTTGTATTTCACGTCACT 57.509 32.000 0.00 0.00 33.94 3.41
1729 1833 7.351981 TCAAATTCTTGTATTTCACGTCACTG 58.648 34.615 0.00 0.00 33.94 3.66
1731 1835 5.651172 TTCTTGTATTTCACGTCACTGTG 57.349 39.130 0.17 0.17 41.28 3.66
1732 1836 3.493129 TCTTGTATTTCACGTCACTGTGC 59.507 43.478 2.12 0.00 39.73 4.57
1745 1849 4.044426 GTCACTGTGCATGTTTCCTTTTC 58.956 43.478 2.12 0.00 0.00 2.29
1797 1901 3.290948 ACGAGAAGATAGAGGTGAGCT 57.709 47.619 0.00 0.00 0.00 4.09
1798 1902 3.626930 ACGAGAAGATAGAGGTGAGCTT 58.373 45.455 0.00 0.00 0.00 3.74
1800 1904 4.464597 ACGAGAAGATAGAGGTGAGCTTTT 59.535 41.667 0.00 0.00 0.00 2.27
1821 1935 9.805966 GCTTTTGCATTTTGTAACCTTATTAAC 57.194 29.630 0.00 0.00 46.58 2.01
1823 1937 9.832445 TTTTGCATTTTGTAACCTTATTAACCA 57.168 25.926 0.00 0.00 0.00 3.67
1824 1938 9.482627 TTTGCATTTTGTAACCTTATTAACCAG 57.517 29.630 0.00 0.00 0.00 4.00
1831 1953 8.927675 TTGTAACCTTATTAACCAGTGACAAT 57.072 30.769 0.00 0.00 0.00 2.71
1841 1963 3.831323 ACCAGTGACAATGAAACCATCA 58.169 40.909 4.07 0.00 43.67 3.07
1895 2027 2.031069 TCAGAAGGAGATATACGCGTGC 60.031 50.000 24.59 8.59 0.00 5.34
1952 2088 4.572571 AAACCAAGACCCGCGCCA 62.573 61.111 0.00 0.00 0.00 5.69
1996 2132 0.982673 CGACCTTGATCGTGTTCGTC 59.017 55.000 0.00 0.00 37.33 4.20
2059 2195 4.668118 TTCGGTTCCACGGGCGAC 62.668 66.667 0.00 0.00 0.00 5.19
2124 2260 3.814283 GTCGTCGAGAGGAAGGTACATAT 59.186 47.826 0.00 0.00 0.00 1.78
2125 2261 4.063689 TCGTCGAGAGGAAGGTACATATC 58.936 47.826 0.00 0.00 0.00 1.63
2126 2262 3.813724 CGTCGAGAGGAAGGTACATATCA 59.186 47.826 0.00 0.00 0.00 2.15
2127 2263 4.456222 CGTCGAGAGGAAGGTACATATCAT 59.544 45.833 0.00 0.00 0.00 2.45
2128 2264 5.617973 CGTCGAGAGGAAGGTACATATCATG 60.618 48.000 0.00 0.00 0.00 3.07
2129 2265 5.241949 GTCGAGAGGAAGGTACATATCATGT 59.758 44.000 0.00 0.00 46.92 3.21
2130 2266 5.473846 TCGAGAGGAAGGTACATATCATGTC 59.526 44.000 0.00 0.00 43.67 3.06
2131 2267 5.241728 CGAGAGGAAGGTACATATCATGTCA 59.758 44.000 0.00 0.00 43.67 3.58
2133 2269 5.541868 AGAGGAAGGTACATATCATGTCAGG 59.458 44.000 0.00 0.00 43.67 3.86
2134 2270 5.219739 AGGAAGGTACATATCATGTCAGGT 58.780 41.667 0.00 0.00 43.67 4.00
2135 2271 6.382087 AGGAAGGTACATATCATGTCAGGTA 58.618 40.000 0.00 0.00 43.67 3.08
2137 2273 6.041637 GGAAGGTACATATCATGTCAGGTACA 59.958 42.308 18.71 0.00 43.67 2.90
2139 2275 7.432148 AGGTACATATCATGTCAGGTACAAA 57.568 36.000 18.71 0.00 43.67 2.83
2140 2276 7.272978 AGGTACATATCATGTCAGGTACAAAC 58.727 38.462 18.71 7.93 43.67 2.93
2141 2277 7.125811 AGGTACATATCATGTCAGGTACAAACT 59.874 37.037 18.71 9.37 43.67 2.66
2142 2278 7.769044 GGTACATATCATGTCAGGTACAAACTT 59.231 37.037 18.71 0.00 43.67 2.66
2143 2279 7.615582 ACATATCATGTCAGGTACAAACTTG 57.384 36.000 0.00 0.00 42.70 3.16
2148 2284 2.353269 TGTCAGGTACAAACTTGTTGCG 59.647 45.455 0.00 0.00 42.35 4.85
2154 2306 1.902840 ACAAACTTGTTGCGGTTTCG 58.097 45.000 0.00 0.00 38.47 3.46
2156 2308 1.843753 CAAACTTGTTGCGGTTTCGTC 59.156 47.619 0.00 0.00 38.89 4.20
2167 2319 1.126846 CGGTTTCGTCTGCAACTCATC 59.873 52.381 0.00 0.00 0.00 2.92
2169 2321 2.413453 GGTTTCGTCTGCAACTCATCTC 59.587 50.000 0.00 0.00 0.00 2.75
2178 2330 6.237942 CGTCTGCAACTCATCTCGAATAATTT 60.238 38.462 0.00 0.00 0.00 1.82
2291 2451 4.195744 TCGAGATCACATTTAAATGCGC 57.804 40.909 24.82 13.14 40.04 6.09
2298 2458 3.066621 TCACATTTAAATGCGCAGGATCC 59.933 43.478 24.82 2.48 37.86 3.36
2300 2460 1.021202 TTTAAATGCGCAGGATCCCG 58.979 50.000 18.32 7.12 37.86 5.14
2302 2462 0.179234 TAAATGCGCAGGATCCCGAA 59.821 50.000 18.32 4.09 37.86 4.30
2306 2466 3.129300 CGCAGGATCCCGAAGCTA 58.871 61.111 8.55 0.00 0.00 3.32
2307 2467 1.300233 CGCAGGATCCCGAAGCTAC 60.300 63.158 8.55 0.00 0.00 3.58
2314 2475 2.565841 GATCCCGAAGCTACAAATGCT 58.434 47.619 0.00 0.00 43.32 3.79
2329 2490 1.535833 ATGCTCGGGATCCTACGTAG 58.464 55.000 15.92 15.92 0.00 3.51
2330 2491 0.536687 TGCTCGGGATCCTACGTAGG 60.537 60.000 32.05 32.05 45.02 3.18
2349 2510 5.696270 CGTAGGAGCAATGCTATCAATGTAA 59.304 40.000 8.12 0.00 39.88 2.41
2350 2511 6.202762 CGTAGGAGCAATGCTATCAATGTAAA 59.797 38.462 8.12 0.00 39.88 2.01
2352 2527 7.035840 AGGAGCAATGCTATCAATGTAAAAG 57.964 36.000 8.12 0.00 39.88 2.27
2442 2619 2.371923 CGTGCACGCGATGAAGACA 61.372 57.895 28.16 0.00 0.00 3.41
2445 2622 0.319469 TGCACGCGATGAAGACAGAA 60.319 50.000 15.93 0.00 0.00 3.02
2502 2679 4.767255 GCACTGTGGGGCTCCGAG 62.767 72.222 10.21 0.00 35.24 4.63
2541 2718 2.427245 CCAGATCTTCGGCGGGACT 61.427 63.158 7.21 3.97 0.00 3.85
2572 2749 2.434658 CTACCTCAGGCACGTGCACA 62.435 60.000 38.60 21.72 44.36 4.57
2573 2750 1.826340 TACCTCAGGCACGTGCACAT 61.826 55.000 38.60 22.76 44.36 3.21
2583 2760 2.223456 GCACGTGCACATATAATTGCCA 60.223 45.455 34.52 0.00 41.59 4.92
2584 2761 3.362295 CACGTGCACATATAATTGCCAC 58.638 45.455 18.64 4.76 38.00 5.01
2585 2762 2.031560 ACGTGCACATATAATTGCCACG 59.968 45.455 18.64 19.94 43.06 4.94
2587 2764 3.362295 GTGCACATATAATTGCCACGTG 58.638 45.455 13.17 9.08 38.00 4.49
2589 2766 4.034626 GTGCACATATAATTGCCACGTGTA 59.965 41.667 15.65 0.00 38.00 2.90
2591 2768 4.272504 GCACATATAATTGCCACGTGTACT 59.727 41.667 15.65 0.00 32.21 2.73
2592 2769 5.464057 GCACATATAATTGCCACGTGTACTA 59.536 40.000 15.65 3.58 32.21 1.82
2595 2772 7.223971 CACATATAATTGCCACGTGTACTACTT 59.776 37.037 15.65 3.00 0.00 2.24
2597 2774 4.742438 AATTGCCACGTGTACTACTTTG 57.258 40.909 15.65 0.00 0.00 2.77
2601 2778 2.921912 GCCACGTGTACTACTTTGCGTA 60.922 50.000 15.65 0.00 0.00 4.42
2616 2793 3.708734 GTACGCACACGGGCACAC 61.709 66.667 0.00 0.00 46.04 3.82
2617 2794 4.973055 TACGCACACGGGCACACC 62.973 66.667 0.00 0.00 46.04 4.16
2636 2813 0.586319 CGCAACCTCACACGTCATTT 59.414 50.000 0.00 0.00 0.00 2.32
2637 2814 1.002900 CGCAACCTCACACGTCATTTT 60.003 47.619 0.00 0.00 0.00 1.82
2638 2815 2.650608 GCAACCTCACACGTCATTTTC 58.349 47.619 0.00 0.00 0.00 2.29
2639 2816 2.290641 GCAACCTCACACGTCATTTTCT 59.709 45.455 0.00 0.00 0.00 2.52
2642 2819 5.334879 GCAACCTCACACGTCATTTTCTATT 60.335 40.000 0.00 0.00 0.00 1.73
2643 2820 6.668323 CAACCTCACACGTCATTTTCTATTT 58.332 36.000 0.00 0.00 0.00 1.40
2645 2822 6.668323 ACCTCACACGTCATTTTCTATTTTG 58.332 36.000 0.00 0.00 0.00 2.44
2682 2880 2.733127 CGTGTACGACGGCAAATCT 58.267 52.632 0.00 0.00 44.85 2.40
2691 2889 1.675310 CGGCAAATCTCAGGTGGCA 60.675 57.895 0.00 0.00 37.67 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.114616 CGCTCGTGCTGGTTCCAG 61.115 66.667 13.88 13.88 36.97 3.86
29 30 3.487202 CCCGTCGTGCGATGGTTG 61.487 66.667 25.31 11.85 46.92 3.77
30 31 4.752879 CCCCGTCGTGCGATGGTT 62.753 66.667 25.31 0.00 46.92 3.67
118 120 0.669318 CCGCGCCTACTTTCAACTGA 60.669 55.000 0.00 0.00 0.00 3.41
154 156 3.951037 TGCGGGATGTAGCAAATTACATT 59.049 39.130 0.75 0.00 42.68 2.71
315 318 2.095718 GTCGCTCATCCAACAAAGAACC 60.096 50.000 0.00 0.00 0.00 3.62
359 362 3.967332 ATCCTTGGTTCCAGCAAATTG 57.033 42.857 0.00 0.00 34.95 2.32
442 449 0.743688 ATCGCTCTCTGTCGATGCTT 59.256 50.000 0.00 0.00 42.95 3.91
495 502 2.282462 CGCCTTCCCTGTTTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
585 617 2.021380 CGGATCGCGCCTTTTTCG 59.979 61.111 0.00 0.00 0.00 3.46
698 732 4.404654 CTTGCGGCTTCGGGCAAC 62.405 66.667 0.00 0.00 43.63 4.17
717 751 1.349627 CCGTGCTCATTGATGCGTC 59.650 57.895 0.00 0.00 0.00 5.19
801 842 5.128827 TGCCGAGAACCTGTAATAAAGATCT 59.871 40.000 0.00 0.00 0.00 2.75
904 945 1.454295 TGGCGATGGTAGGAGCGTA 60.454 57.895 0.00 0.00 0.00 4.42
968 1033 2.262915 GTCAGCGAGGTGAGGTGG 59.737 66.667 5.13 0.00 37.66 4.61
1080 1151 1.757118 TCGTAGGCCTTCTTGATGAGG 59.243 52.381 12.58 0.00 0.00 3.86
1202 1273 2.684843 GCGCTGTGGCAAAGGAGAG 61.685 63.158 6.84 0.00 38.60 3.20
1217 1288 0.733909 GGGTTCAATCAAGCAAGCGC 60.734 55.000 0.00 0.00 33.79 5.92
1218 1289 0.109132 GGGGTTCAATCAAGCAAGCG 60.109 55.000 0.00 0.00 33.79 4.68
1221 1292 2.397044 AAGGGGGTTCAATCAAGCAA 57.603 45.000 0.00 0.00 33.79 3.91
1227 1298 3.305813 GGAAACGAAAAGGGGGTTCAATC 60.306 47.826 0.00 0.00 0.00 2.67
1299 1373 1.654954 CCTGGAGGACGACGAACGAT 61.655 60.000 0.00 0.00 45.65 3.73
1304 1378 2.675423 CACCCTGGAGGACGACGA 60.675 66.667 0.00 0.00 39.89 4.20
1305 1379 3.760035 CCACCCTGGAGGACGACG 61.760 72.222 0.00 0.00 40.96 5.12
1306 1380 2.283676 TCCACCCTGGAGGACGAC 60.284 66.667 0.00 0.00 42.67 4.34
1313 1387 2.300967 GCACATCCTCCACCCTGGA 61.301 63.158 0.00 0.00 45.98 3.86
1369 1443 0.315251 TGAACTCTGGCACTCACTCG 59.685 55.000 0.00 0.00 0.00 4.18
1444 1518 1.596220 GCGGTGGTGAAACGAAGAAAC 60.596 52.381 0.00 0.00 38.12 2.78
1467 1541 3.406595 CTCCCGGTTCTGGATGGGC 62.407 68.421 0.00 0.00 41.65 5.36
1488 1562 3.257127 ACGAGCTAGTTCTTGCTTCTCTT 59.743 43.478 9.70 0.00 39.91 2.85
1527 1604 5.804771 GCCTCTGGACTCCTATTTTCAGTTT 60.805 44.000 0.00 0.00 0.00 2.66
1528 1605 4.323868 GCCTCTGGACTCCTATTTTCAGTT 60.324 45.833 0.00 0.00 0.00 3.16
1530 1607 3.454082 AGCCTCTGGACTCCTATTTTCAG 59.546 47.826 0.00 0.00 0.00 3.02
1531 1608 3.452627 GAGCCTCTGGACTCCTATTTTCA 59.547 47.826 0.00 0.00 0.00 2.69
1532 1609 3.491792 CGAGCCTCTGGACTCCTATTTTC 60.492 52.174 0.00 0.00 0.00 2.29
1533 1610 2.432510 CGAGCCTCTGGACTCCTATTTT 59.567 50.000 0.00 0.00 0.00 1.82
1547 1624 1.079503 GGATTTGTCACACGAGCCTC 58.920 55.000 0.00 0.00 0.00 4.70
1548 1625 0.670546 CGGATTTGTCACACGAGCCT 60.671 55.000 0.00 0.00 0.00 4.58
1549 1626 0.669318 TCGGATTTGTCACACGAGCC 60.669 55.000 0.00 0.00 0.00 4.70
1579 1677 0.465824 GCCTCTGGAGCATGCTGATT 60.466 55.000 28.27 0.00 33.35 2.57
1654 1755 7.433719 CGAGAATATATAGAGGAAAATGGAGCG 59.566 40.741 0.00 0.00 0.00 5.03
1655 1756 8.254508 ACGAGAATATATAGAGGAAAATGGAGC 58.745 37.037 0.00 0.00 0.00 4.70
1657 1758 9.929180 CAACGAGAATATATAGAGGAAAATGGA 57.071 33.333 0.00 0.00 0.00 3.41
1658 1759 9.929180 TCAACGAGAATATATAGAGGAAAATGG 57.071 33.333 0.00 0.00 0.00 3.16
1688 1792 1.434555 TTGAGCCGGTTTGATACGTG 58.565 50.000 1.90 0.00 0.00 4.49
1689 1793 2.172851 TTTGAGCCGGTTTGATACGT 57.827 45.000 1.90 0.00 0.00 3.57
1698 1802 4.764823 TGAAATACAAGAATTTGAGCCGGT 59.235 37.500 1.90 0.00 37.73 5.28
1699 1803 5.095490 GTGAAATACAAGAATTTGAGCCGG 58.905 41.667 0.00 0.00 37.73 6.13
1700 1804 4.788100 CGTGAAATACAAGAATTTGAGCCG 59.212 41.667 0.00 0.00 37.73 5.52
1701 1805 5.699839 ACGTGAAATACAAGAATTTGAGCC 58.300 37.500 0.00 0.00 37.73 4.70
1703 1807 7.531871 CAGTGACGTGAAATACAAGAATTTGAG 59.468 37.037 0.00 0.00 37.73 3.02
1705 1809 7.112009 CACAGTGACGTGAAATACAAGAATTTG 59.888 37.037 0.00 0.00 39.34 2.32
1706 1810 7.132213 CACAGTGACGTGAAATACAAGAATTT 58.868 34.615 0.00 0.00 39.34 1.82
1707 1811 6.658831 CACAGTGACGTGAAATACAAGAATT 58.341 36.000 0.00 0.00 39.34 2.17
1708 1812 5.334105 GCACAGTGACGTGAAATACAAGAAT 60.334 40.000 4.15 0.00 39.34 2.40
1709 1813 4.025229 GCACAGTGACGTGAAATACAAGAA 60.025 41.667 4.15 0.00 39.34 2.52
1710 1814 3.493129 GCACAGTGACGTGAAATACAAGA 59.507 43.478 4.15 0.00 39.34 3.02
1711 1815 3.247411 TGCACAGTGACGTGAAATACAAG 59.753 43.478 4.15 0.00 39.34 3.16
1712 1816 3.198872 TGCACAGTGACGTGAAATACAA 58.801 40.909 4.15 0.00 39.34 2.41
1713 1817 2.827652 TGCACAGTGACGTGAAATACA 58.172 42.857 4.15 0.00 39.34 2.29
1714 1818 3.186409 ACATGCACAGTGACGTGAAATAC 59.814 43.478 18.47 0.00 39.34 1.89
1723 1827 3.715628 AAAGGAAACATGCACAGTGAC 57.284 42.857 4.15 0.00 0.00 3.67
1726 1830 3.068590 CAGGAAAAGGAAACATGCACAGT 59.931 43.478 0.00 0.00 0.00 3.55
1727 1831 3.645884 CAGGAAAAGGAAACATGCACAG 58.354 45.455 0.00 0.00 0.00 3.66
1728 1832 2.224018 GCAGGAAAAGGAAACATGCACA 60.224 45.455 0.00 0.00 40.29 4.57
1729 1833 2.036346 AGCAGGAAAAGGAAACATGCAC 59.964 45.455 0.00 0.00 42.44 4.57
1731 1835 2.669391 CGAGCAGGAAAAGGAAACATGC 60.669 50.000 0.00 0.00 40.75 4.06
1732 1836 2.669391 GCGAGCAGGAAAAGGAAACATG 60.669 50.000 0.00 0.00 0.00 3.21
1745 1849 0.457337 GGCTGAAATTTGCGAGCAGG 60.457 55.000 12.94 0.00 32.83 4.85
1797 1901 9.832445 TGGTTAATAAGGTTACAAAATGCAAAA 57.168 25.926 0.00 0.00 0.00 2.44
1798 1902 9.482627 CTGGTTAATAAGGTTACAAAATGCAAA 57.517 29.630 0.00 0.00 0.00 3.68
1800 1904 8.085296 CACTGGTTAATAAGGTTACAAAATGCA 58.915 33.333 0.00 0.00 0.00 3.96
1817 1931 5.830457 TGATGGTTTCATTGTCACTGGTTAA 59.170 36.000 0.00 0.00 32.98 2.01
1819 1933 4.214310 TGATGGTTTCATTGTCACTGGTT 58.786 39.130 0.00 0.00 32.98 3.67
1821 1935 6.704289 ATATGATGGTTTCATTGTCACTGG 57.296 37.500 0.00 0.00 42.62 4.00
1823 1937 9.466497 AGTTAATATGATGGTTTCATTGTCACT 57.534 29.630 0.00 0.00 42.62 3.41
1831 1953 6.822442 TCGGCTAGTTAATATGATGGTTTCA 58.178 36.000 0.00 0.00 39.12 2.69
1841 1963 7.172532 TGCAATTCGAAATCGGCTAGTTAATAT 59.827 33.333 0.00 0.00 40.29 1.28
1849 1971 1.939934 CCTGCAATTCGAAATCGGCTA 59.060 47.619 0.00 0.00 40.29 3.93
1852 1974 2.279741 TCTCCTGCAATTCGAAATCGG 58.720 47.619 0.00 0.00 40.29 4.18
1996 2132 2.005537 GCGCGCACACAGAAAACAG 61.006 57.895 29.10 0.00 0.00 3.16
2052 2188 1.348250 CAATTGTCGATGTCGCCCG 59.652 57.895 0.00 0.00 39.60 6.13
2059 2195 3.484229 GGAACTTCTCGCAATTGTCGATG 60.484 47.826 20.01 15.99 35.25 3.84
2089 2225 4.373116 ACGACGCGGGTGAGCATT 62.373 61.111 10.96 0.00 36.85 3.56
2124 2260 4.036262 GCAACAAGTTTGTACCTGACATGA 59.964 41.667 0.00 0.00 41.31 3.07
2125 2261 4.290155 GCAACAAGTTTGTACCTGACATG 58.710 43.478 0.00 0.00 41.31 3.21
2126 2262 3.003275 CGCAACAAGTTTGTACCTGACAT 59.997 43.478 0.00 0.00 41.31 3.06
2127 2263 2.353269 CGCAACAAGTTTGTACCTGACA 59.647 45.455 0.00 0.00 41.31 3.58
2128 2264 2.286772 CCGCAACAAGTTTGTACCTGAC 60.287 50.000 0.00 0.00 41.31 3.51
2129 2265 1.944024 CCGCAACAAGTTTGTACCTGA 59.056 47.619 0.00 0.00 41.31 3.86
2130 2266 1.673920 ACCGCAACAAGTTTGTACCTG 59.326 47.619 0.00 0.00 41.31 4.00
2131 2267 2.047002 ACCGCAACAAGTTTGTACCT 57.953 45.000 0.00 0.00 41.31 3.08
2133 2269 2.779471 CGAAACCGCAACAAGTTTGTAC 59.221 45.455 0.00 0.00 41.31 2.90
2134 2270 2.419324 ACGAAACCGCAACAAGTTTGTA 59.581 40.909 0.00 0.00 41.31 2.41
2135 2271 1.200484 ACGAAACCGCAACAAGTTTGT 59.800 42.857 0.00 0.00 44.72 2.83
2137 2273 1.741145 AGACGAAACCGCAACAAGTTT 59.259 42.857 0.00 0.00 38.85 2.66
2139 2275 0.655733 CAGACGAAACCGCAACAAGT 59.344 50.000 0.00 0.00 0.00 3.16
2140 2276 0.657368 GCAGACGAAACCGCAACAAG 60.657 55.000 0.00 0.00 0.00 3.16
2141 2277 1.353804 GCAGACGAAACCGCAACAA 59.646 52.632 0.00 0.00 0.00 2.83
2142 2278 1.369839 TTGCAGACGAAACCGCAACA 61.370 50.000 0.00 0.00 39.32 3.33
2143 2279 1.353804 TTGCAGACGAAACCGCAAC 59.646 52.632 0.00 0.00 39.32 4.17
2148 2284 2.413453 GAGATGAGTTGCAGACGAAACC 59.587 50.000 0.00 0.00 0.00 3.27
2154 2306 6.595772 AATTATTCGAGATGAGTTGCAGAC 57.404 37.500 0.00 0.00 0.00 3.51
2156 2308 6.183360 ACCAAATTATTCGAGATGAGTTGCAG 60.183 38.462 0.00 0.84 0.00 4.41
2167 2319 4.944962 TGCACAGACCAAATTATTCGAG 57.055 40.909 0.00 0.00 0.00 4.04
2169 2321 5.046910 AGTTGCACAGACCAAATTATTCG 57.953 39.130 0.00 0.00 0.00 3.34
2178 2330 1.404181 GCTCGATAGTTGCACAGACCA 60.404 52.381 0.00 0.00 36.85 4.02
2291 2451 2.691409 TTTGTAGCTTCGGGATCCTG 57.309 50.000 15.09 15.09 0.00 3.86
2298 2458 0.652592 CCGAGCATTTGTAGCTTCGG 59.347 55.000 4.93 4.93 43.58 4.30
2300 2460 2.024176 TCCCGAGCATTTGTAGCTTC 57.976 50.000 0.00 0.00 43.58 3.86
2302 2462 1.202698 GGATCCCGAGCATTTGTAGCT 60.203 52.381 0.00 0.00 46.82 3.32
2306 2466 1.202533 CGTAGGATCCCGAGCATTTGT 60.203 52.381 8.55 0.00 0.00 2.83
2307 2467 1.202533 ACGTAGGATCCCGAGCATTTG 60.203 52.381 16.14 0.00 0.00 2.32
2329 2490 6.039717 TCCTTTTACATTGATAGCATTGCTCC 59.960 38.462 15.81 9.10 40.44 4.70
2330 2491 7.031226 TCCTTTTACATTGATAGCATTGCTC 57.969 36.000 15.81 2.42 40.44 4.26
2331 2492 7.592885 ATCCTTTTACATTGATAGCATTGCT 57.407 32.000 16.63 16.63 43.41 3.91
2332 2493 8.652810 AAATCCTTTTACATTGATAGCATTGC 57.347 30.769 0.00 0.00 0.00 3.56
2370 2545 2.627699 ACCGCCAAACACAATCTTCATT 59.372 40.909 0.00 0.00 0.00 2.57
2411 2588 3.564027 GCACGTACATCTGCGCCC 61.564 66.667 4.18 0.00 0.00 6.13
2442 2619 4.101448 ATGCCGCCGCCTTCTTCT 62.101 61.111 0.00 0.00 0.00 2.85
2487 2664 4.316823 TCCTCGGAGCCCCACAGT 62.317 66.667 0.00 0.00 0.00 3.55
2541 2718 2.587522 CTGAGGTAGATCATCGGGTCA 58.412 52.381 0.00 0.00 30.55 4.02
2572 2749 7.254658 GCAAAGTAGTACACGTGGCAATTATAT 60.255 37.037 21.57 0.00 35.78 0.86
2573 2750 6.036300 GCAAAGTAGTACACGTGGCAATTATA 59.964 38.462 21.57 0.00 35.78 0.98
2583 2760 2.574322 CGTACGCAAAGTAGTACACGT 58.426 47.619 0.52 9.07 42.26 4.49
2584 2761 1.315571 GCGTACGCAAAGTAGTACACG 59.684 52.381 33.90 3.08 42.26 4.49
2616 2793 1.227999 AATGACGTGTGAGGTTGCGG 61.228 55.000 0.00 0.00 0.00 5.69
2617 2794 0.586319 AAATGACGTGTGAGGTTGCG 59.414 50.000 0.00 0.00 0.00 4.85
2625 2802 7.357206 CCGAAACAAAATAGAAAATGACGTGTG 60.357 37.037 0.00 0.00 0.00 3.82
2636 2813 2.809119 TCGCTGCCGAAACAAAATAGAA 59.191 40.909 0.00 0.00 41.17 2.10
2637 2814 2.158841 GTCGCTGCCGAAACAAAATAGA 59.841 45.455 0.00 0.00 46.34 1.98
2638 2815 2.505866 GTCGCTGCCGAAACAAAATAG 58.494 47.619 0.00 0.00 46.34 1.73
2639 2816 1.198178 GGTCGCTGCCGAAACAAAATA 59.802 47.619 0.00 0.00 46.34 1.40
2642 2819 2.548295 GGGTCGCTGCCGAAACAAA 61.548 57.895 0.00 0.00 46.34 2.83
2643 2820 2.975799 GGGTCGCTGCCGAAACAA 60.976 61.111 0.00 0.00 46.34 2.83
2726 2924 2.105128 GATCCGTCGTCTGGCTGG 59.895 66.667 0.00 0.00 0.00 4.85
2756 2954 2.358003 GCTCGGTGCAGCTGAACT 60.358 61.111 24.24 0.00 42.31 3.01
2842 3040 1.455587 CCATGGCCGGCAGGTAATT 60.456 57.895 30.85 0.51 40.50 1.40
2844 3042 3.334891 ACCATGGCCGGCAGGTAA 61.335 61.111 29.09 10.98 40.50 2.85


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

AutoCloner maintained by Alex Coulton.