Multiple sequence alignment - TraesCS6B01G079000

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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 TraesCS6B01G079000 chr6B 100.000 2312 0 0 1 2312 55652224 55649913 0.000000e+00 4270.0
1 TraesCS6B01G079000 chr6B 86.330 951 85 23 706 1649 55436274 55437186 0.000000e+00 994.0
2 TraesCS6B01G079000 chr6B 89.807 726 47 9 707 1431 55695535 55694836 0.000000e+00 905.0
3 TraesCS6B01G079000 chr6B 86.053 717 49 31 722 1431 54663201 54662529 0.000000e+00 723.0
4 TraesCS6B01G079000 chr6B 85.216 717 48 34 723 1431 54877222 54876556 0.000000e+00 684.0
5 TraesCS6B01G079000 chr6B 78.337 457 59 21 1 422 54828468 54828017 2.280000e-65 259.0
6 TraesCS6B01G079000 chr6B 88.942 208 15 5 1338 1542 67120971 67121173 1.370000e-62 250.0
7 TraesCS6B01G079000 chr6B 100.000 34 0 0 610 643 55695565 55695532 1.920000e-06 63.9
8 TraesCS6B01G079000 chr6A 86.980 1513 119 32 722 2198 31264722 31263252 0.000000e+00 1631.0
9 TraesCS6B01G079000 chr6A 83.882 1185 109 41 637 1802 28666862 28665741 0.000000e+00 1055.0
10 TraesCS6B01G079000 chr6A 86.510 934 71 30 754 1674 28640811 28641702 0.000000e+00 976.0
11 TraesCS6B01G079000 chr6A 88.739 595 56 9 652 1244 28773875 28773290 0.000000e+00 717.0
12 TraesCS6B01G079000 chr6A 85.352 710 60 29 723 1431 29081708 29082374 0.000000e+00 695.0
13 TraesCS6B01G079000 chr6A 82.770 621 50 29 1 600 28667447 28666863 3.430000e-138 501.0
14 TraesCS6B01G079000 chr6A 81.804 621 50 28 1 600 28640150 28640728 1.620000e-126 462.0
15 TraesCS6B01G079000 chrUn 86.570 1385 124 30 724 2057 103772377 103771004 0.000000e+00 1471.0
16 TraesCS6B01G079000 chrUn 91.278 837 64 3 709 1541 103670323 103671154 0.000000e+00 1133.0
17 TraesCS6B01G079000 chr7A 83.811 803 88 24 725 1501 628524954 628524168 0.000000e+00 725.0
18 TraesCS6B01G079000 chr1B 81.967 915 97 34 762 1649 398836461 398837334 0.000000e+00 713.0
19 TraesCS6B01G079000 chr2D 80.357 112 18 3 2142 2252 133477249 133477141 5.290000e-12 82.4
20 TraesCS6B01G079000 chr3A 100.000 28 0 0 238 265 130864293 130864266 4.000000e-03 52.8


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 TraesCS6B01G079000 chr6B 55649913 55652224 2311 True 4270.00 4270 100.0000 1 2312 1 chr6B.!!$R4 2311
1 TraesCS6B01G079000 chr6B 55436274 55437186 912 False 994.00 994 86.3300 706 1649 1 chr6B.!!$F1 943
2 TraesCS6B01G079000 chr6B 54662529 54663201 672 True 723.00 723 86.0530 722 1431 1 chr6B.!!$R1 709
3 TraesCS6B01G079000 chr6B 54876556 54877222 666 True 684.00 684 85.2160 723 1431 1 chr6B.!!$R3 708
4 TraesCS6B01G079000 chr6B 55694836 55695565 729 True 484.45 905 94.9035 610 1431 2 chr6B.!!$R5 821
5 TraesCS6B01G079000 chr6A 31263252 31264722 1470 True 1631.00 1631 86.9800 722 2198 1 chr6A.!!$R2 1476
6 TraesCS6B01G079000 chr6A 28665741 28667447 1706 True 778.00 1055 83.3260 1 1802 2 chr6A.!!$R3 1801
7 TraesCS6B01G079000 chr6A 28640150 28641702 1552 False 719.00 976 84.1570 1 1674 2 chr6A.!!$F2 1673
8 TraesCS6B01G079000 chr6A 28773290 28773875 585 True 717.00 717 88.7390 652 1244 1 chr6A.!!$R1 592
9 TraesCS6B01G079000 chr6A 29081708 29082374 666 False 695.00 695 85.3520 723 1431 1 chr6A.!!$F1 708
10 TraesCS6B01G079000 chrUn 103771004 103772377 1373 True 1471.00 1471 86.5700 724 2057 1 chrUn.!!$R1 1333
11 TraesCS6B01G079000 chrUn 103670323 103671154 831 False 1133.00 1133 91.2780 709 1541 1 chrUn.!!$F1 832
12 TraesCS6B01G079000 chr7A 628524168 628524954 786 True 725.00 725 83.8110 725 1501 1 chr7A.!!$R1 776
13 TraesCS6B01G079000 chr1B 398836461 398837334 873 False 713.00 713 81.9670 762 1649 1 chr1B.!!$F1 887

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
80 81 0.172803 GTGATCCTGCTCGTACCGTT 59.827 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1719 0.319469 CAACACGGTGGATTTTGGGC 60.319 55.0 13.48 0.0 0.0 5.36 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
33 34 4.009675 TGGCGAAAATCTAACAGAGCAAT 58.990 39.130 0.00 0.00 0.00 3.56
49 50 2.182842 AATCGGAGCGCAAGATGGC 61.183 57.895 11.47 0.00 43.02 4.40
80 81 0.172803 GTGATCCTGCTCGTACCGTT 59.827 55.000 0.00 0.00 0.00 4.44
103 105 3.986006 TCCAAACCGCTCGCTCGT 61.986 61.111 0.00 0.00 0.00 4.18
104 106 3.041940 CCAAACCGCTCGCTCGTT 61.042 61.111 0.00 0.00 0.00 3.85
215 230 6.830838 AGGGAGCAGATATTAGTTTTTGGAAG 59.169 38.462 0.00 0.00 0.00 3.46
297 313 8.451748 GTTCTCATGAACTAAATTTGGTCTACC 58.548 37.037 7.72 0.00 46.56 3.18
314 330 6.981559 TGGTCTACCTGTTTTAAAATGTTTGC 59.018 34.615 3.52 0.00 36.82 3.68
317 333 9.040939 GTCTACCTGTTTTAAAATGTTTGCAAT 57.959 29.630 0.00 0.00 0.00 3.56
472 491 5.038033 GCGAAACCAATAAACAAACACAGA 58.962 37.500 0.00 0.00 0.00 3.41
476 495 7.895767 CGAAACCAATAAACAAACACAGAAAAC 59.104 33.333 0.00 0.00 0.00 2.43
486 505 6.212955 ACAAACACAGAAAACATAAATCCGG 58.787 36.000 0.00 0.00 0.00 5.14
499 518 5.418840 ACATAAATCCGGAAGCTTCACAAAT 59.581 36.000 27.02 12.00 0.00 2.32
507 526 2.270352 AGCTTCACAAATCCCGTTGA 57.730 45.000 0.00 0.00 32.59 3.18
511 530 4.116238 GCTTCACAAATCCCGTTGAAAAA 58.884 39.130 0.00 0.00 32.59 1.94
575 597 3.950397 TGAGCCAGTCATTTAACGGAAT 58.050 40.909 0.00 0.00 0.00 3.01
581 603 5.344933 GCCAGTCATTTAACGGAATTGTTTC 59.655 40.000 0.00 0.00 33.32 2.78
593 615 4.519540 GAATTGTTTCCAAGCTGCCTTA 57.480 40.909 0.00 0.00 33.17 2.69
620 642 5.385509 TTTATGTTTACTTCCAAGCTGCC 57.614 39.130 0.00 0.00 0.00 4.85
621 643 2.656947 TGTTTACTTCCAAGCTGCCT 57.343 45.000 0.00 0.00 0.00 4.75
622 644 3.780804 TGTTTACTTCCAAGCTGCCTA 57.219 42.857 0.00 0.00 0.00 3.93
623 645 3.674997 TGTTTACTTCCAAGCTGCCTAG 58.325 45.455 0.00 0.00 0.00 3.02
624 646 3.010420 GTTTACTTCCAAGCTGCCTAGG 58.990 50.000 3.67 3.67 0.00 3.02
625 647 0.541863 TACTTCCAAGCTGCCTAGGC 59.458 55.000 27.71 27.71 42.35 3.93
626 648 1.452833 CTTCCAAGCTGCCTAGGCC 60.453 63.158 30.81 16.45 41.09 5.19
627 649 2.202236 CTTCCAAGCTGCCTAGGCCA 62.202 60.000 30.81 17.33 41.09 5.36
628 650 1.788518 TTCCAAGCTGCCTAGGCCAA 61.789 55.000 30.81 12.64 41.09 4.52
629 651 2.048603 CCAAGCTGCCTAGGCCAAC 61.049 63.158 30.81 19.24 41.09 3.77
630 652 2.045926 AAGCTGCCTAGGCCAACG 60.046 61.111 30.81 16.79 41.09 4.10
631 653 3.628646 AAGCTGCCTAGGCCAACGG 62.629 63.158 30.81 15.70 41.09 4.44
733 763 1.267832 GCAACTCGCGAGAAAACACAA 60.268 47.619 40.58 0.00 41.32 3.33
829 867 2.167398 ATATTCCATCCGACGGCCCG 62.167 60.000 9.66 0.00 0.00 6.13
894 936 1.347707 TCGCAGCTATAAATCCCCCAG 59.652 52.381 0.00 0.00 0.00 4.45
1325 1396 2.754658 CTAGGTCACGCCGGTCCT 60.755 66.667 1.90 6.43 43.70 3.85
1438 1547 0.040958 GCTGCTGTCTGTTGTTTCGG 60.041 55.000 0.00 0.00 0.00 4.30
1556 1677 2.198827 ATCTTGTCAATGCGTTCCCA 57.801 45.000 0.00 0.00 0.00 4.37
1582 1713 2.030457 CCCATTGTTCGTCGCTGTAATC 59.970 50.000 0.00 0.00 0.00 1.75
1588 1719 2.561733 TCGTCGCTGTAATCTTCTGG 57.438 50.000 0.00 0.00 0.00 3.86
1624 1755 5.278071 CCGTGTTGGATTTAGTTTGCAGTAA 60.278 40.000 0.00 0.00 42.00 2.24
1657 1789 3.760151 TCCCTGCATTTCTGAATGTCAAG 59.240 43.478 0.00 0.00 43.67 3.02
1675 1814 3.503363 TCAAGTGTCAAATGCTCACCATC 59.497 43.478 0.00 0.00 31.43 3.51
1697 1836 3.438087 CAGCCGATTCAAAACTCAGATGT 59.562 43.478 0.00 0.00 0.00 3.06
1699 1838 4.631813 AGCCGATTCAAAACTCAGATGTAC 59.368 41.667 0.00 0.00 0.00 2.90
1701 1840 5.671329 GCCGATTCAAAACTCAGATGTACAC 60.671 44.000 0.00 0.00 0.00 2.90
1703 1842 5.408299 CGATTCAAAACTCAGATGTACACCA 59.592 40.000 0.00 0.00 0.00 4.17
1704 1843 6.073276 CGATTCAAAACTCAGATGTACACCAA 60.073 38.462 0.00 0.00 0.00 3.67
1706 1845 6.801539 TCAAAACTCAGATGTACACCAATC 57.198 37.500 0.00 0.00 0.00 2.67
1707 1846 5.705441 TCAAAACTCAGATGTACACCAATCC 59.295 40.000 0.00 0.00 0.00 3.01
1708 1847 3.914426 ACTCAGATGTACACCAATCCC 57.086 47.619 0.00 0.00 0.00 3.85
1709 1848 3.454858 ACTCAGATGTACACCAATCCCT 58.545 45.455 0.00 0.00 0.00 4.20
1710 1849 3.198635 ACTCAGATGTACACCAATCCCTG 59.801 47.826 0.00 0.00 0.00 4.45
1714 1874 2.897271 TGTACACCAATCCCTGCATT 57.103 45.000 0.00 0.00 0.00 3.56
1725 1885 5.163426 CCAATCCCTGCATTGCTGTTAATAA 60.163 40.000 10.49 0.00 33.08 1.40
1726 1886 4.981806 TCCCTGCATTGCTGTTAATAAC 57.018 40.909 10.49 0.00 0.00 1.89
1727 1887 4.339748 TCCCTGCATTGCTGTTAATAACA 58.660 39.130 10.49 5.66 39.52 2.41
1730 1890 6.605194 TCCCTGCATTGCTGTTAATAACATTA 59.395 34.615 10.49 0.00 41.26 1.90
1732 1892 7.927629 CCCTGCATTGCTGTTAATAACATTATT 59.072 33.333 10.49 2.60 41.26 1.40
1764 1930 3.052036 CTGCCAATTGAACCAAGTTTCG 58.948 45.455 7.12 0.00 0.00 3.46
1772 1938 8.028938 CCAATTGAACCAAGTTTCGAATAAGAT 58.971 33.333 7.12 0.00 0.00 2.40
1878 2058 9.058174 TGTTTTCGAAAATAGAAGTTGACCATA 57.942 29.630 24.93 0.00 0.00 2.74
1895 2075 7.275888 TGACCATATGATGCATCTTTTAACC 57.724 36.000 26.32 11.93 0.00 2.85
1918 2105 1.246056 GCAGCTGATTTCTGTGGCCA 61.246 55.000 20.43 0.00 34.21 5.36
1931 2118 7.531857 TTTCTGTGGCCAAACATAGATTTTA 57.468 32.000 7.24 0.00 38.21 1.52
2033 2225 5.296151 AGAAGTTGGAAGACATGAACTGA 57.704 39.130 0.00 0.00 0.00 3.41
2046 2238 2.838736 TGAACTGAAGTGGAGCTCAAC 58.161 47.619 13.83 13.83 0.00 3.18
2060 2252 4.156556 GGAGCTCAACATGCAAACATTAGA 59.843 41.667 17.19 0.00 32.87 2.10
2089 2281 0.545171 TGTCCGGGTTTGGTGTACAA 59.455 50.000 0.00 0.00 37.28 2.41
2092 2284 1.202675 TCCGGGTTTGGTGTACAACTC 60.203 52.381 13.07 0.00 39.19 3.01
2106 2298 1.628846 ACAACTCACCCATGTACTCCC 59.371 52.381 0.00 0.00 0.00 4.30
2107 2299 1.628340 CAACTCACCCATGTACTCCCA 59.372 52.381 0.00 0.00 0.00 4.37
2108 2300 2.038863 ACTCACCCATGTACTCCCAA 57.961 50.000 0.00 0.00 0.00 4.12
2109 2301 1.909302 ACTCACCCATGTACTCCCAAG 59.091 52.381 0.00 0.00 0.00 3.61
2117 2309 4.443457 CCCATGTACTCCCAAGTAGTCATG 60.443 50.000 0.00 8.25 39.68 3.07
2119 2311 5.362717 CCATGTACTCCCAAGTAGTCATGTA 59.637 44.000 11.84 0.00 39.03 2.29
2163 2355 3.076079 TGCCTGAATGCTGAGATTTCA 57.924 42.857 0.00 0.00 0.00 2.69
2187 2379 4.336433 GGCTTCCTGAAATGATTGATCGAA 59.664 41.667 0.00 0.00 0.00 3.71
2188 2380 5.163622 GGCTTCCTGAAATGATTGATCGAAA 60.164 40.000 0.00 0.00 0.00 3.46
2194 2386 7.494298 TCCTGAAATGATTGATCGAAAACGATA 59.506 33.333 5.14 0.00 0.00 2.92
2206 2398 8.856247 TGATCGAAAACGATAATATATGAACGG 58.144 33.333 4.90 0.00 0.00 4.44
2207 2399 8.752766 ATCGAAAACGATAATATATGAACGGT 57.247 30.769 4.90 0.00 0.00 4.83
2208 2400 9.844790 ATCGAAAACGATAATATATGAACGGTA 57.155 29.630 4.90 0.00 0.00 4.02
2209 2401 9.333497 TCGAAAACGATAATATATGAACGGTAG 57.667 33.333 4.90 0.00 0.00 3.18
2210 2402 9.121517 CGAAAACGATAATATATGAACGGTAGT 57.878 33.333 4.90 0.00 0.00 2.73
2226 2418 9.715121 TGAACGGTAGTTATAGAATTTGAAACT 57.285 29.630 0.00 0.00 41.34 2.66
2227 2419 9.968743 GAACGGTAGTTATAGAATTTGAAACTG 57.031 33.333 0.00 0.00 41.34 3.16
2228 2420 8.488651 ACGGTAGTTATAGAATTTGAAACTGG 57.511 34.615 0.00 0.00 32.85 4.00
2229 2421 8.316214 ACGGTAGTTATAGAATTTGAAACTGGA 58.684 33.333 0.00 0.00 32.85 3.86
2230 2422 8.818057 CGGTAGTTATAGAATTTGAAACTGGAG 58.182 37.037 0.00 0.00 32.85 3.86
2231 2423 9.886132 GGTAGTTATAGAATTTGAAACTGGAGA 57.114 33.333 0.00 0.00 32.85 3.71
2234 2426 9.793259 AGTTATAGAATTTGAAACTGGAGAACA 57.207 29.630 0.00 0.00 0.00 3.18
2245 2437 2.760374 CTGGAGAACAGTGTGGAGAAC 58.240 52.381 0.00 0.00 42.42 3.01
2246 2438 2.366916 CTGGAGAACAGTGTGGAGAACT 59.633 50.000 0.00 0.00 42.42 3.01
2255 2447 5.139435 CAGTGTGGAGAACTGTATTGAGA 57.861 43.478 0.00 0.00 40.17 3.27
2256 2448 5.728471 CAGTGTGGAGAACTGTATTGAGAT 58.272 41.667 0.00 0.00 40.17 2.75
2257 2449 6.169094 CAGTGTGGAGAACTGTATTGAGATT 58.831 40.000 0.00 0.00 40.17 2.40
2258 2450 6.652481 CAGTGTGGAGAACTGTATTGAGATTT 59.348 38.462 0.00 0.00 40.17 2.17
2259 2451 6.652481 AGTGTGGAGAACTGTATTGAGATTTG 59.348 38.462 0.00 0.00 0.00 2.32
2260 2452 5.939883 TGTGGAGAACTGTATTGAGATTTGG 59.060 40.000 0.00 0.00 0.00 3.28
2261 2453 6.173339 GTGGAGAACTGTATTGAGATTTGGA 58.827 40.000 0.00 0.00 0.00 3.53
2262 2454 6.825721 GTGGAGAACTGTATTGAGATTTGGAT 59.174 38.462 0.00 0.00 0.00 3.41
2263 2455 6.825213 TGGAGAACTGTATTGAGATTTGGATG 59.175 38.462 0.00 0.00 0.00 3.51
2264 2456 6.825721 GGAGAACTGTATTGAGATTTGGATGT 59.174 38.462 0.00 0.00 0.00 3.06
2265 2457 7.011857 GGAGAACTGTATTGAGATTTGGATGTC 59.988 40.741 0.00 0.00 0.00 3.06
2266 2458 7.628234 AGAACTGTATTGAGATTTGGATGTCT 58.372 34.615 0.00 0.00 0.00 3.41
2267 2459 8.105829 AGAACTGTATTGAGATTTGGATGTCTT 58.894 33.333 0.00 0.00 0.00 3.01
2268 2460 8.641498 AACTGTATTGAGATTTGGATGTCTTT 57.359 30.769 0.00 0.00 0.00 2.52
2269 2461 8.641498 ACTGTATTGAGATTTGGATGTCTTTT 57.359 30.769 0.00 0.00 0.00 2.27
2270 2462 9.739276 ACTGTATTGAGATTTGGATGTCTTTTA 57.261 29.630 0.00 0.00 0.00 1.52
2276 2468 9.912634 TTGAGATTTGGATGTCTTTTATTTCAC 57.087 29.630 0.00 0.00 0.00 3.18
2277 2469 8.522830 TGAGATTTGGATGTCTTTTATTTCACC 58.477 33.333 0.00 0.00 0.00 4.02
2278 2470 8.421249 AGATTTGGATGTCTTTTATTTCACCA 57.579 30.769 0.00 0.00 0.00 4.17
2279 2471 9.039165 AGATTTGGATGTCTTTTATTTCACCAT 57.961 29.630 0.00 0.00 0.00 3.55
2280 2472 9.090692 GATTTGGATGTCTTTTATTTCACCATG 57.909 33.333 0.00 0.00 0.00 3.66
2281 2473 6.528537 TGGATGTCTTTTATTTCACCATGG 57.471 37.500 11.19 11.19 0.00 3.66
2282 2474 5.105392 TGGATGTCTTTTATTTCACCATGGC 60.105 40.000 13.04 0.00 0.00 4.40
2283 2475 5.127682 GGATGTCTTTTATTTCACCATGGCT 59.872 40.000 13.04 0.00 0.00 4.75
2284 2476 5.643379 TGTCTTTTATTTCACCATGGCTC 57.357 39.130 13.04 0.00 0.00 4.70
2285 2477 5.076182 TGTCTTTTATTTCACCATGGCTCA 58.924 37.500 13.04 0.00 0.00 4.26
2286 2478 5.183713 TGTCTTTTATTTCACCATGGCTCAG 59.816 40.000 13.04 0.00 0.00 3.35
2287 2479 5.183904 GTCTTTTATTTCACCATGGCTCAGT 59.816 40.000 13.04 0.00 0.00 3.41
2288 2480 6.374333 GTCTTTTATTTCACCATGGCTCAGTA 59.626 38.462 13.04 0.00 0.00 2.74
2289 2481 6.599244 TCTTTTATTTCACCATGGCTCAGTAG 59.401 38.462 13.04 0.00 0.00 2.57
2299 2491 3.760035 CTCAGTAGCACCGCCCGT 61.760 66.667 0.00 0.00 0.00 5.28
2300 2492 3.989698 CTCAGTAGCACCGCCCGTG 62.990 68.421 0.00 0.00 46.03 4.94
2301 2493 4.373116 CAGTAGCACCGCCCGTGT 62.373 66.667 0.98 0.00 44.97 4.49
2302 2494 2.677524 AGTAGCACCGCCCGTGTA 60.678 61.111 0.98 0.00 44.97 2.90
2303 2495 2.507769 GTAGCACCGCCCGTGTAC 60.508 66.667 0.98 0.00 44.97 2.90
2304 2496 2.990395 TAGCACCGCCCGTGTACA 60.990 61.111 0.00 0.00 44.97 2.90
2305 2497 2.352821 TAGCACCGCCCGTGTACAT 61.353 57.895 0.00 0.00 44.97 2.29
2306 2498 1.890625 TAGCACCGCCCGTGTACATT 61.891 55.000 0.00 0.00 44.97 2.71
2307 2499 2.329614 GCACCGCCCGTGTACATTT 61.330 57.895 0.00 0.00 44.97 2.32
2308 2500 1.858372 GCACCGCCCGTGTACATTTT 61.858 55.000 0.00 0.00 44.97 1.82
2309 2501 0.109964 CACCGCCCGTGTACATTTTG 60.110 55.000 0.00 0.00 37.73 2.44
2310 2502 1.154112 CCGCCCGTGTACATTTTGC 60.154 57.895 0.00 0.00 0.00 3.68
2311 2503 1.576920 CGCCCGTGTACATTTTGCA 59.423 52.632 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.385751 AGGATCACTCGTACCATGCG 59.614 55.000 0.00 0.00 0.00 4.73
158 160 9.811995 AACTTTTAGAAAATGTTTTAGGTCACC 57.188 29.630 0.00 0.00 0.00 4.02
326 342 8.614469 TGTGGAAATTTTTGAAAGTGAAAACT 57.386 26.923 0.00 0.00 0.00 2.66
327 343 9.670719 TTTGTGGAAATTTTTGAAAGTGAAAAC 57.329 25.926 0.00 0.00 0.00 2.43
346 362 9.712305 TTTTGTGAACTTCTTTAAATTTGTGGA 57.288 25.926 0.00 0.00 0.00 4.02
434 453 0.311790 TTCGCTTACGTTCCGTCTGT 59.688 50.000 0.00 0.00 41.54 3.41
440 459 4.666928 TTATTGGTTTCGCTTACGTTCC 57.333 40.909 0.00 0.00 41.18 3.62
441 460 5.442402 TGTTTATTGGTTTCGCTTACGTTC 58.558 37.500 0.00 0.00 41.18 3.95
442 461 5.421212 TGTTTATTGGTTTCGCTTACGTT 57.579 34.783 0.00 0.00 41.18 3.99
443 462 5.421212 TTGTTTATTGGTTTCGCTTACGT 57.579 34.783 0.00 0.00 41.18 3.57
444 463 5.681982 TGTTTGTTTATTGGTTTCGCTTACG 59.318 36.000 0.00 0.00 42.01 3.18
445 464 6.472808 TGTGTTTGTTTATTGGTTTCGCTTAC 59.527 34.615 0.00 0.00 0.00 2.34
446 465 6.561614 TGTGTTTGTTTATTGGTTTCGCTTA 58.438 32.000 0.00 0.00 0.00 3.09
447 466 5.411781 TGTGTTTGTTTATTGGTTTCGCTT 58.588 33.333 0.00 0.00 0.00 4.68
448 467 5.000012 TGTGTTTGTTTATTGGTTTCGCT 58.000 34.783 0.00 0.00 0.00 4.93
449 468 5.038033 TCTGTGTTTGTTTATTGGTTTCGC 58.962 37.500 0.00 0.00 0.00 4.70
450 469 7.513190 TTTCTGTGTTTGTTTATTGGTTTCG 57.487 32.000 0.00 0.00 0.00 3.46
451 470 8.713271 TGTTTTCTGTGTTTGTTTATTGGTTTC 58.287 29.630 0.00 0.00 0.00 2.78
472 491 5.242838 TGTGAAGCTTCCGGATTTATGTTTT 59.757 36.000 23.42 0.00 0.00 2.43
476 495 4.963276 TTGTGAAGCTTCCGGATTTATG 57.037 40.909 23.42 0.00 0.00 1.90
486 505 2.552315 TCAACGGGATTTGTGAAGCTTC 59.448 45.455 19.89 19.89 0.00 3.86
532 551 9.928236 GCTCATGTAAAGATTCTATTGTTTCTC 57.072 33.333 0.00 0.00 0.00 2.87
534 553 8.677300 TGGCTCATGTAAAGATTCTATTGTTTC 58.323 33.333 0.00 0.00 0.00 2.78
535 554 8.579850 TGGCTCATGTAAAGATTCTATTGTTT 57.420 30.769 0.00 0.00 0.00 2.83
536 555 7.831193 ACTGGCTCATGTAAAGATTCTATTGTT 59.169 33.333 0.00 0.00 0.00 2.83
537 556 7.341805 ACTGGCTCATGTAAAGATTCTATTGT 58.658 34.615 0.00 0.00 0.00 2.71
538 557 7.496920 TGACTGGCTCATGTAAAGATTCTATTG 59.503 37.037 0.00 0.00 0.00 1.90
599 621 4.662278 AGGCAGCTTGGAAGTAAACATAA 58.338 39.130 0.00 0.00 0.00 1.90
600 622 4.301072 AGGCAGCTTGGAAGTAAACATA 57.699 40.909 0.00 0.00 0.00 2.29
601 623 3.160679 AGGCAGCTTGGAAGTAAACAT 57.839 42.857 0.00 0.00 0.00 2.71
602 624 2.656947 AGGCAGCTTGGAAGTAAACA 57.343 45.000 0.00 0.00 0.00 2.83
603 625 3.010420 CCTAGGCAGCTTGGAAGTAAAC 58.990 50.000 0.00 0.00 0.00 2.01
604 626 2.618045 GCCTAGGCAGCTTGGAAGTAAA 60.618 50.000 29.33 0.00 41.49 2.01
605 627 1.065418 GCCTAGGCAGCTTGGAAGTAA 60.065 52.381 29.33 0.00 41.49 2.24
606 628 0.541863 GCCTAGGCAGCTTGGAAGTA 59.458 55.000 29.33 0.00 41.49 2.24
607 629 1.301293 GCCTAGGCAGCTTGGAAGT 59.699 57.895 29.33 0.00 41.49 3.01
608 630 1.452833 GGCCTAGGCAGCTTGGAAG 60.453 63.158 34.09 0.00 44.11 3.46
609 631 1.788518 TTGGCCTAGGCAGCTTGGAA 61.789 55.000 34.09 11.97 44.11 3.53
610 632 2.230653 TTGGCCTAGGCAGCTTGGA 61.231 57.895 34.09 9.19 44.11 3.53
611 633 2.048603 GTTGGCCTAGGCAGCTTGG 61.049 63.158 34.09 0.00 44.11 3.61
612 634 2.401766 CGTTGGCCTAGGCAGCTTG 61.402 63.158 34.09 15.95 44.11 4.01
613 635 2.045926 CGTTGGCCTAGGCAGCTT 60.046 61.111 34.09 0.00 44.11 3.74
614 636 4.101448 CCGTTGGCCTAGGCAGCT 62.101 66.667 34.09 0.00 44.11 4.24
625 647 1.153549 GACAGCTCTAGCCCGTTGG 60.154 63.158 0.00 0.00 43.38 3.77
626 648 0.037326 TTGACAGCTCTAGCCCGTTG 60.037 55.000 0.00 0.00 43.38 4.10
627 649 0.037232 GTTGACAGCTCTAGCCCGTT 60.037 55.000 0.00 0.00 43.38 4.44
628 650 1.592223 GTTGACAGCTCTAGCCCGT 59.408 57.895 0.00 0.00 43.38 5.28
629 651 1.517257 CGTTGACAGCTCTAGCCCG 60.517 63.158 0.00 0.00 43.38 6.13
630 652 1.153549 CCGTTGACAGCTCTAGCCC 60.154 63.158 0.00 0.00 43.38 5.19
631 653 1.153549 CCCGTTGACAGCTCTAGCC 60.154 63.158 0.00 0.00 43.38 3.93
632 654 0.037232 AACCCGTTGACAGCTCTAGC 60.037 55.000 0.00 0.00 42.49 3.42
633 655 1.732732 CGAACCCGTTGACAGCTCTAG 60.733 57.143 0.00 0.00 0.00 2.43
634 656 0.242825 CGAACCCGTTGACAGCTCTA 59.757 55.000 0.00 0.00 0.00 2.43
635 657 1.006102 CGAACCCGTTGACAGCTCT 60.006 57.895 0.00 0.00 0.00 4.09
793 831 1.595311 TATGAATGGCTGGGAGTGGT 58.405 50.000 0.00 0.00 0.00 4.16
933 977 1.318886 TGTTGCTGGTGGTGGTTGTG 61.319 55.000 0.00 0.00 0.00 3.33
1325 1396 2.180769 CGCGAGGTGGATTCGACA 59.819 61.111 0.00 0.00 40.36 4.35
1438 1547 1.787155 CATTCCACGCTAGCGATACAC 59.213 52.381 41.33 0.00 42.83 2.90
1556 1677 2.095263 CAGCGACGAACAATGGGAAATT 60.095 45.455 0.00 0.00 0.00 1.82
1582 1713 0.897621 GGTGGATTTTGGGCCAGAAG 59.102 55.000 15.30 0.00 34.22 2.85
1588 1719 0.319469 CAACACGGTGGATTTTGGGC 60.319 55.000 13.48 0.00 0.00 5.36
1609 1740 7.653647 TGGTTCGAATTTACTGCAAACTAAAT 58.346 30.769 0.00 0.00 0.00 1.40
1612 1743 6.128117 GGATGGTTCGAATTTACTGCAAACTA 60.128 38.462 0.00 0.00 0.00 2.24
1624 1755 2.442236 ATGCAGGGATGGTTCGAATT 57.558 45.000 0.00 0.00 0.00 2.17
1657 1789 2.415090 GCTGATGGTGAGCATTTGACAC 60.415 50.000 0.00 0.00 36.40 3.67
1675 1814 3.438087 ACATCTGAGTTTTGAATCGGCTG 59.562 43.478 0.00 0.00 0.00 4.85
1697 1836 1.005805 AGCAATGCAGGGATTGGTGTA 59.994 47.619 15.76 0.00 41.39 2.90
1699 1838 2.587080 AGCAATGCAGGGATTGGTG 58.413 52.632 15.76 0.00 41.39 4.17
1701 1840 0.899720 AACAGCAATGCAGGGATTGG 59.100 50.000 8.35 2.75 34.42 3.16
1703 1842 5.421693 TGTTATTAACAGCAATGCAGGGATT 59.578 36.000 8.35 0.00 36.25 3.01
1704 1843 4.955450 TGTTATTAACAGCAATGCAGGGAT 59.045 37.500 8.35 0.00 36.25 3.85
1706 1845 4.717233 TGTTATTAACAGCAATGCAGGG 57.283 40.909 8.35 0.00 36.25 4.45
1707 1846 8.876275 AATAATGTTATTAACAGCAATGCAGG 57.124 30.769 8.35 1.12 45.95 4.85
1725 1885 4.263727 TGGCAGACCACAGGTTAATAATGT 60.264 41.667 0.00 0.00 42.67 2.71
1726 1886 4.269183 TGGCAGACCACAGGTTAATAATG 58.731 43.478 0.00 0.00 42.67 1.90
1727 1887 4.584638 TGGCAGACCACAGGTTAATAAT 57.415 40.909 0.00 0.00 42.67 1.28
1741 1907 3.733443 AACTTGGTTCAATTGGCAGAC 57.267 42.857 5.42 0.10 0.00 3.51
1764 1930 5.474532 TCAATGGGCAGCACATATCTTATTC 59.525 40.000 11.57 0.00 0.00 1.75
1772 1938 1.408683 GGTCTCAATGGGCAGCACATA 60.409 52.381 11.57 0.00 0.00 2.29
1843 2023 7.678194 TCTATTTTCGAAAACAAGCAACAAG 57.322 32.000 24.68 10.97 0.00 3.16
1878 2058 3.316308 GCCTCGGTTAAAAGATGCATCAT 59.684 43.478 27.81 14.43 0.00 2.45
1895 2075 0.725686 CACAGAAATCAGCTGCCTCG 59.274 55.000 9.47 4.71 36.86 4.63
1918 2105 9.520515 AGATGTGACTGGTTAAAATCTATGTTT 57.479 29.630 0.00 0.00 0.00 2.83
1931 2118 5.827797 TGCTTAGAAAAAGATGTGACTGGTT 59.172 36.000 0.00 0.00 0.00 3.67
2033 2225 1.985473 TTGCATGTTGAGCTCCACTT 58.015 45.000 17.93 9.69 0.00 3.16
2046 2238 4.201753 CGGTGAGTCTCTAATGTTTGCATG 60.202 45.833 0.65 0.00 35.15 4.06
2084 2276 3.369157 GGGAGTACATGGGTGAGTTGTAC 60.369 52.174 0.00 4.67 43.77 2.90
2089 2281 1.909302 CTTGGGAGTACATGGGTGAGT 59.091 52.381 0.00 0.00 0.00 3.41
2092 2284 2.838202 ACTACTTGGGAGTACATGGGTG 59.162 50.000 0.00 0.00 37.33 4.61
2135 2327 3.429492 TCAGCATTCAGGCAATAACCAA 58.571 40.909 0.00 0.00 35.83 3.67
2136 2328 3.018856 CTCAGCATTCAGGCAATAACCA 58.981 45.455 0.00 0.00 35.83 3.67
2137 2329 3.282021 TCTCAGCATTCAGGCAATAACC 58.718 45.455 0.00 0.00 35.83 2.85
2163 2355 3.881688 CGATCAATCATTTCAGGAAGCCT 59.118 43.478 0.00 0.00 0.00 4.58
2200 2392 9.715121 AGTTTCAAATTCTATAACTACCGTTCA 57.285 29.630 0.00 0.00 34.59 3.18
2201 2393 9.968743 CAGTTTCAAATTCTATAACTACCGTTC 57.031 33.333 0.00 0.00 34.59 3.95
2202 2394 8.943002 CCAGTTTCAAATTCTATAACTACCGTT 58.057 33.333 0.00 0.00 37.15 4.44
2203 2395 8.316214 TCCAGTTTCAAATTCTATAACTACCGT 58.684 33.333 0.00 0.00 0.00 4.83
2204 2396 8.712285 TCCAGTTTCAAATTCTATAACTACCG 57.288 34.615 0.00 0.00 0.00 4.02
2205 2397 9.886132 TCTCCAGTTTCAAATTCTATAACTACC 57.114 33.333 0.00 0.00 0.00 3.18
2208 2400 9.793259 TGTTCTCCAGTTTCAAATTCTATAACT 57.207 29.630 0.00 0.00 0.00 2.24
2226 2418 2.103094 CAGTTCTCCACACTGTTCTCCA 59.897 50.000 0.00 0.00 37.47 3.86
2227 2419 2.760374 CAGTTCTCCACACTGTTCTCC 58.240 52.381 0.00 0.00 37.47 3.71
2233 2425 5.139435 TCTCAATACAGTTCTCCACACTG 57.861 43.478 0.00 0.00 46.18 3.66
2234 2426 6.365970 AATCTCAATACAGTTCTCCACACT 57.634 37.500 0.00 0.00 0.00 3.55
2235 2427 6.128172 CCAAATCTCAATACAGTTCTCCACAC 60.128 42.308 0.00 0.00 0.00 3.82
2236 2428 5.939883 CCAAATCTCAATACAGTTCTCCACA 59.060 40.000 0.00 0.00 0.00 4.17
2237 2429 6.173339 TCCAAATCTCAATACAGTTCTCCAC 58.827 40.000 0.00 0.00 0.00 4.02
2238 2430 6.373005 TCCAAATCTCAATACAGTTCTCCA 57.627 37.500 0.00 0.00 0.00 3.86
2239 2431 6.825721 ACATCCAAATCTCAATACAGTTCTCC 59.174 38.462 0.00 0.00 0.00 3.71
2240 2432 7.768120 AGACATCCAAATCTCAATACAGTTCTC 59.232 37.037 0.00 0.00 0.00 2.87
2241 2433 7.628234 AGACATCCAAATCTCAATACAGTTCT 58.372 34.615 0.00 0.00 0.00 3.01
2242 2434 7.856145 AGACATCCAAATCTCAATACAGTTC 57.144 36.000 0.00 0.00 0.00 3.01
2243 2435 8.641498 AAAGACATCCAAATCTCAATACAGTT 57.359 30.769 0.00 0.00 0.00 3.16
2244 2436 8.641498 AAAAGACATCCAAATCTCAATACAGT 57.359 30.769 0.00 0.00 0.00 3.55
2250 2442 9.912634 GTGAAATAAAAGACATCCAAATCTCAA 57.087 29.630 0.00 0.00 0.00 3.02
2251 2443 8.522830 GGTGAAATAAAAGACATCCAAATCTCA 58.477 33.333 0.00 0.00 0.00 3.27
2252 2444 8.522830 TGGTGAAATAAAAGACATCCAAATCTC 58.477 33.333 0.00 0.00 0.00 2.75
2253 2445 8.421249 TGGTGAAATAAAAGACATCCAAATCT 57.579 30.769 0.00 0.00 0.00 2.40
2254 2446 9.090692 CATGGTGAAATAAAAGACATCCAAATC 57.909 33.333 0.00 0.00 0.00 2.17
2255 2447 8.042515 CCATGGTGAAATAAAAGACATCCAAAT 58.957 33.333 2.57 0.00 0.00 2.32
2256 2448 7.385267 CCATGGTGAAATAAAAGACATCCAAA 58.615 34.615 2.57 0.00 0.00 3.28
2257 2449 6.574073 GCCATGGTGAAATAAAAGACATCCAA 60.574 38.462 14.67 0.00 0.00 3.53
2258 2450 5.105392 GCCATGGTGAAATAAAAGACATCCA 60.105 40.000 14.67 0.00 0.00 3.41
2259 2451 5.127682 AGCCATGGTGAAATAAAAGACATCC 59.872 40.000 14.67 0.00 0.00 3.51
2260 2452 6.127647 TGAGCCATGGTGAAATAAAAGACATC 60.128 38.462 14.67 0.00 0.00 3.06
2261 2453 5.716228 TGAGCCATGGTGAAATAAAAGACAT 59.284 36.000 14.67 0.00 0.00 3.06
2262 2454 5.076182 TGAGCCATGGTGAAATAAAAGACA 58.924 37.500 14.67 0.00 0.00 3.41
2263 2455 5.183904 ACTGAGCCATGGTGAAATAAAAGAC 59.816 40.000 14.67 0.00 0.00 3.01
2264 2456 5.324409 ACTGAGCCATGGTGAAATAAAAGA 58.676 37.500 14.67 0.00 0.00 2.52
2265 2457 5.649782 ACTGAGCCATGGTGAAATAAAAG 57.350 39.130 14.67 1.50 0.00 2.27
2266 2458 5.125417 GCTACTGAGCCATGGTGAAATAAAA 59.875 40.000 14.67 0.00 43.49 1.52
2267 2459 4.640201 GCTACTGAGCCATGGTGAAATAAA 59.360 41.667 14.67 0.00 43.49 1.40
2268 2460 4.199310 GCTACTGAGCCATGGTGAAATAA 58.801 43.478 14.67 0.00 43.49 1.40
2269 2461 3.808728 GCTACTGAGCCATGGTGAAATA 58.191 45.455 14.67 0.46 43.49 1.40
2270 2462 2.648059 GCTACTGAGCCATGGTGAAAT 58.352 47.619 14.67 0.00 43.49 2.17
2271 2463 2.113860 GCTACTGAGCCATGGTGAAA 57.886 50.000 14.67 0.00 43.49 2.69
2272 2464 3.861341 GCTACTGAGCCATGGTGAA 57.139 52.632 14.67 0.00 43.49 3.18
2282 2474 3.760035 ACGGGCGGTGCTACTGAG 61.760 66.667 0.00 0.00 0.00 3.35
2283 2475 4.063967 CACGGGCGGTGCTACTGA 62.064 66.667 12.41 0.00 40.33 3.41
2291 2483 1.858372 GCAAAATGTACACGGGCGGT 61.858 55.000 0.00 0.00 0.00 5.68
2292 2484 1.154112 GCAAAATGTACACGGGCGG 60.154 57.895 0.00 0.00 0.00 6.13
2293 2485 1.576920 TGCAAAATGTACACGGGCG 59.423 52.632 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.