Multiple sequence alignment - TraesCS6D01G044400

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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 TraesCS6D01G044400 chr6D 100.000 2511 0 0 1 2511 18983614 18986124 0.000000e+00 4638
1 TraesCS6D01G044400 chr6D 87.338 616 53 12 95 695 450573322 450572717 0.000000e+00 682
2 TraesCS6D01G044400 chr6D 90.625 288 21 3 13 294 18958853 18959140 6.560000e-101 377
3 TraesCS6D01G044400 chr6D 95.588 68 2 1 27 93 18958591 18958658 9.500000e-20 108
4 TraesCS6D01G044400 chr6B 89.856 2159 150 33 383 2508 33037393 33039515 0.000000e+00 2710
5 TraesCS6D01G044400 chr6B 91.239 331 15 8 1 328 33037079 33037398 2.970000e-119 438
6 TraesCS6D01G044400 chr2D 88.124 1002 64 21 769 1720 534129146 534130142 0.000000e+00 1140
7 TraesCS6D01G044400 chr2D 88.243 808 67 14 931 1719 534122862 534123660 0.000000e+00 941
8 TraesCS6D01G044400 chr5A 87.980 990 68 19 769 1721 643312296 643311321 0.000000e+00 1122
9 TraesCS6D01G044400 chr5D 87.842 987 70 22 769 1721 515039901 515038931 0.000000e+00 1112
10 TraesCS6D01G044400 chr5D 91.404 698 33 10 846 1518 515094461 515093766 0.000000e+00 931
11 TraesCS6D01G044400 chr5B 87.412 993 67 25 769 1721 647879695 647878721 0.000000e+00 1088
12 TraesCS6D01G044400 chr2B 84.778 946 77 23 826 1721 776645958 776645030 0.000000e+00 887
13 TraesCS6D01G044400 chr2B 92.308 494 21 2 1039 1515 634644061 634644554 0.000000e+00 686
14 TraesCS6D01G044400 chr7B 87.701 683 62 9 859 1520 113445686 113445005 0.000000e+00 776
15 TraesCS6D01G044400 chr7D 85.981 749 76 15 861 1586 151542734 151541992 0.000000e+00 774
16 TraesCS6D01G044400 chr7A 85.200 750 81 20 861 1586 151328243 151327500 0.000000e+00 743
17 TraesCS6D01G044400 chr7A 85.738 596 44 14 117 695 734641727 734641156 2.150000e-165 592
18 TraesCS6D01G044400 chr3D 88.281 640 44 17 934 1554 594958439 594957812 0.000000e+00 737
19 TraesCS6D01G044400 chr2A 88.567 621 49 9 1116 1721 677827935 677828548 0.000000e+00 734
20 TraesCS6D01G044400 chr2A 85.714 469 41 12 117 570 779311030 779311487 2.920000e-129 472
21 TraesCS6D01G044400 chr3B 88.468 607 37 15 999 1586 798408869 798408277 0.000000e+00 702
22 TraesCS6D01G044400 chr3B 88.165 583 51 3 968 1532 496853769 496853187 0.000000e+00 678
23 TraesCS6D01G044400 chr1A 86.891 595 49 14 117 695 96432338 96432919 7.570000e-180 640
24 TraesCS6D01G044400 chr4A 90.741 108 9 1 1607 1714 639978205 639978311 2.600000e-30 143


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 TraesCS6D01G044400 chr6D 18983614 18986124 2510 False 4638.0 4638 100.0000 1 2511 1 chr6D.!!$F1 2510
1 TraesCS6D01G044400 chr6D 450572717 450573322 605 True 682.0 682 87.3380 95 695 1 chr6D.!!$R1 600
2 TraesCS6D01G044400 chr6D 18958591 18959140 549 False 242.5 377 93.1065 13 294 2 chr6D.!!$F2 281
3 TraesCS6D01G044400 chr6B 33037079 33039515 2436 False 1574.0 2710 90.5475 1 2508 2 chr6B.!!$F1 2507
4 TraesCS6D01G044400 chr2D 534129146 534130142 996 False 1140.0 1140 88.1240 769 1720 1 chr2D.!!$F2 951
5 TraesCS6D01G044400 chr2D 534122862 534123660 798 False 941.0 941 88.2430 931 1719 1 chr2D.!!$F1 788
6 TraesCS6D01G044400 chr5A 643311321 643312296 975 True 1122.0 1122 87.9800 769 1721 1 chr5A.!!$R1 952
7 TraesCS6D01G044400 chr5D 515038931 515039901 970 True 1112.0 1112 87.8420 769 1721 1 chr5D.!!$R1 952
8 TraesCS6D01G044400 chr5D 515093766 515094461 695 True 931.0 931 91.4040 846 1518 1 chr5D.!!$R2 672
9 TraesCS6D01G044400 chr5B 647878721 647879695 974 True 1088.0 1088 87.4120 769 1721 1 chr5B.!!$R1 952
10 TraesCS6D01G044400 chr2B 776645030 776645958 928 True 887.0 887 84.7780 826 1721 1 chr2B.!!$R1 895
11 TraesCS6D01G044400 chr7B 113445005 113445686 681 True 776.0 776 87.7010 859 1520 1 chr7B.!!$R1 661
12 TraesCS6D01G044400 chr7D 151541992 151542734 742 True 774.0 774 85.9810 861 1586 1 chr7D.!!$R1 725
13 TraesCS6D01G044400 chr7A 151327500 151328243 743 True 743.0 743 85.2000 861 1586 1 chr7A.!!$R1 725
14 TraesCS6D01G044400 chr7A 734641156 734641727 571 True 592.0 592 85.7380 117 695 1 chr7A.!!$R2 578
15 TraesCS6D01G044400 chr3D 594957812 594958439 627 True 737.0 737 88.2810 934 1554 1 chr3D.!!$R1 620
16 TraesCS6D01G044400 chr2A 677827935 677828548 613 False 734.0 734 88.5670 1116 1721 1 chr2A.!!$F1 605
17 TraesCS6D01G044400 chr3B 798408277 798408869 592 True 702.0 702 88.4680 999 1586 1 chr3B.!!$R2 587
18 TraesCS6D01G044400 chr3B 496853187 496853769 582 True 678.0 678 88.1650 968 1532 1 chr3B.!!$R1 564
19 TraesCS6D01G044400 chr1A 96432338 96432919 581 False 640.0 640 86.8910 117 695 1 chr1A.!!$F1 578

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
382 667 0.251077 CTTTCAGCAGGAACAGGGCT 60.251 55.0 0.0 0.0 38.7 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2316 0.185175 AGACCAGGGTGGGTGAAAAC 59.815 55.0 0.0 0.0 43.37 2.43 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
126 404 7.534085 TTTGTACAACTCTGTTTCACTACAG 57.466 36.000 8.07 0.00 45.46 2.74
224 502 4.040706 ACCACAGAAATCCATGTTTGCATT 59.959 37.500 0.00 0.00 31.99 3.56
228 506 7.092079 CACAGAAATCCATGTTTGCATTAAGA 58.908 34.615 0.00 0.00 31.99 2.10
305 588 7.636150 ACTGGATCATTGTTTTTCCTCATAG 57.364 36.000 0.00 0.00 0.00 2.23
306 589 7.177878 ACTGGATCATTGTTTTTCCTCATAGT 58.822 34.615 0.00 0.00 0.00 2.12
307 590 8.328758 ACTGGATCATTGTTTTTCCTCATAGTA 58.671 33.333 0.00 0.00 0.00 1.82
337 622 2.757868 TGGTTTTCCCAATAATGCTCCG 59.242 45.455 0.00 0.00 41.50 4.63
362 647 0.731417 CCTGAAGCAAAGCGATCTGG 59.269 55.000 8.47 8.47 34.45 3.86
382 667 0.251077 CTTTCAGCAGGAACAGGGCT 60.251 55.000 0.00 0.00 38.70 5.19
404 689 1.246737 GCAAGACAAGGGGCAGAAGG 61.247 60.000 0.00 0.00 0.00 3.46
416 701 0.749049 GCAGAAGGGATGGATTTGGC 59.251 55.000 0.00 0.00 0.00 4.52
456 749 1.145819 GCAGCCAGGATCCAGTCTC 59.854 63.158 15.82 0.00 0.00 3.36
457 750 1.336632 GCAGCCAGGATCCAGTCTCT 61.337 60.000 15.82 0.29 0.00 3.10
477 772 2.740447 CTGTGGAAGTTTAAGGCGTACC 59.260 50.000 0.00 0.00 0.00 3.34
561 856 2.665603 GTCTGGTCTGTGGAGGGC 59.334 66.667 0.00 0.00 0.00 5.19
602 897 6.088824 CACGATTAACTAAAGGACGTACAGT 58.911 40.000 0.00 0.00 0.00 3.55
603 898 6.033196 CACGATTAACTAAAGGACGTACAGTG 59.967 42.308 0.00 0.00 0.00 3.66
629 924 2.406616 CGGGCGGCTTAGTGCAAAT 61.407 57.895 9.56 0.00 45.15 2.32
646 942 5.050295 GTGCAAATATTCCTACGACTAAGCC 60.050 44.000 0.00 0.00 0.00 4.35
658 954 2.612972 CGACTAAGCCCACACACAGAAT 60.613 50.000 0.00 0.00 0.00 2.40
666 962 4.832266 AGCCCACACACAGAATTTAAATCA 59.168 37.500 0.10 0.00 0.00 2.57
672 968 7.752239 CCACACACAGAATTTAAATCAGATGAC 59.248 37.037 0.10 0.00 0.00 3.06
685 981 1.135915 CAGATGACTGGGAACGAGAGG 59.864 57.143 0.00 0.00 40.14 3.69
724 1020 8.735315 CATAAGATATACGAGGCCTATATCCAG 58.265 40.741 22.47 11.52 35.45 3.86
725 1021 6.517013 AGATATACGAGGCCTATATCCAGA 57.483 41.667 22.47 5.23 35.45 3.86
730 1026 1.203523 GAGGCCTATATCCAGAGCGTG 59.796 57.143 4.42 0.00 0.00 5.34
752 1048 4.770010 TGATTTTTGGCCTCGGTTATCTTT 59.230 37.500 3.32 0.00 0.00 2.52
758 1054 1.671328 GCCTCGGTTATCTTTGGAAGC 59.329 52.381 0.00 0.00 0.00 3.86
779 1076 4.825085 AGCAGAAAATAAGGAAACGGAACA 59.175 37.500 0.00 0.00 0.00 3.18
900 1230 2.973694 TAAATTCTCCCGGTTCCTCG 57.026 50.000 0.00 0.00 0.00 4.63
910 1245 4.222847 GTTCCTCGCCCTAGCCCG 62.223 72.222 0.00 0.00 34.57 6.13
997 1358 2.731571 CGCCTCCCAATCCTCCGAA 61.732 63.158 0.00 0.00 0.00 4.30
1006 1367 1.672854 AATCCTCCGAACGATGGCGA 61.673 55.000 0.00 0.00 41.64 5.54
1035 1396 3.030291 AGGCGAGAAGAAGATGATCACT 58.970 45.455 0.00 0.00 0.00 3.41
1114 1475 0.107456 GACCATCCGCCACATGATCT 59.893 55.000 0.00 0.00 0.00 2.75
1242 1621 3.842923 CGACGCCAGCTCCTCCAT 61.843 66.667 0.00 0.00 0.00 3.41
1314 1697 1.111116 TTCGTCAAGGTCGACCAGGT 61.111 55.000 35.00 17.76 38.89 4.00
1520 1914 5.995897 TGGGCTTTTGAGTAGAAAAGAGTAC 59.004 40.000 9.40 0.00 43.02 2.73
1554 1955 4.225984 GCACTGTTGCGTTGAATTAATGA 58.774 39.130 0.00 0.00 39.50 2.57
1559 1967 7.059488 CACTGTTGCGTTGAATTAATGAAGTAC 59.941 37.037 0.00 0.00 0.00 2.73
1565 1973 7.148474 TGCGTTGAATTAATGAAGTACTCTTCC 60.148 37.037 0.00 0.00 46.66 3.46
1571 1979 9.974750 GAATTAATGAAGTACTCTTCCTTTTCG 57.025 33.333 0.00 0.00 46.66 3.46
1612 2020 3.889520 AGAAGAAACCTATCGTGGTCC 57.110 47.619 0.00 0.00 39.83 4.46
1615 2023 1.203994 AGAAACCTATCGTGGTCCGTG 59.796 52.381 0.00 0.00 39.83 4.94
1617 2025 2.106332 CCTATCGTGGTCCGTGGC 59.894 66.667 0.00 0.00 37.94 5.01
1692 2131 8.131731 GGTAACATCATCCTTAGCTGATTTTTC 58.868 37.037 0.00 0.00 29.74 2.29
1721 2160 8.034804 GTGTGGTTTGAGATATTTTTGGCTATT 58.965 33.333 0.00 0.00 0.00 1.73
1723 2162 9.087424 GTGGTTTGAGATATTTTTGGCTATTTC 57.913 33.333 0.00 0.00 0.00 2.17
1724 2163 8.257306 TGGTTTGAGATATTTTTGGCTATTTCC 58.743 33.333 0.00 0.00 0.00 3.13
1731 2172 9.750125 AGATATTTTTGGCTATTTCCGATTTTC 57.250 29.630 0.00 0.00 0.00 2.29
1747 2188 7.272244 TCCGATTTTCTATCTACAGATTTGCA 58.728 34.615 0.00 0.00 36.05 4.08
1768 2209 5.140177 GCAAAATATCCGTCGACATGATTC 58.860 41.667 19.15 0.00 0.00 2.52
1770 2211 6.511767 GCAAAATATCCGTCGACATGATTCTT 60.512 38.462 19.15 12.20 0.00 2.52
1771 2212 6.771188 AAATATCCGTCGACATGATTCTTC 57.229 37.500 19.15 0.00 0.00 2.87
1772 2213 3.801114 ATCCGTCGACATGATTCTTCA 57.199 42.857 17.16 0.00 36.00 3.02
1773 2214 3.150848 TCCGTCGACATGATTCTTCAG 57.849 47.619 17.16 0.00 34.73 3.02
1774 2215 2.492088 TCCGTCGACATGATTCTTCAGT 59.508 45.455 17.16 0.00 34.73 3.41
1775 2216 3.056821 TCCGTCGACATGATTCTTCAGTT 60.057 43.478 17.16 0.00 34.73 3.16
1776 2217 3.679980 CCGTCGACATGATTCTTCAGTTT 59.320 43.478 17.16 0.00 34.73 2.66
1777 2218 4.434725 CCGTCGACATGATTCTTCAGTTTG 60.435 45.833 17.16 0.00 34.73 2.93
1778 2219 4.385748 CGTCGACATGATTCTTCAGTTTGA 59.614 41.667 17.16 0.00 34.73 2.69
1779 2220 5.107491 CGTCGACATGATTCTTCAGTTTGAA 60.107 40.000 17.16 0.00 34.73 2.69
1780 2221 6.401474 CGTCGACATGATTCTTCAGTTTGAAT 60.401 38.462 17.16 0.00 35.59 2.57
1781 2222 7.301054 GTCGACATGATTCTTCAGTTTGAATT 58.699 34.615 11.55 0.00 35.59 2.17
1782 2223 7.805071 GTCGACATGATTCTTCAGTTTGAATTT 59.195 33.333 11.55 0.00 35.59 1.82
1783 2224 8.017373 TCGACATGATTCTTCAGTTTGAATTTC 58.983 33.333 0.00 0.00 35.59 2.17
1787 2228 7.258022 TGATTCTTCAGTTTGAATTTCGTGA 57.742 32.000 0.00 0.00 35.59 4.35
1796 2237 1.868498 TGAATTTCGTGACCGTTGGAC 59.132 47.619 0.00 0.00 35.01 4.02
1814 2255 3.007940 TGGACCGTTGTCATGAATCTCTT 59.992 43.478 0.00 0.00 43.65 2.85
1815 2256 3.372206 GGACCGTTGTCATGAATCTCTTG 59.628 47.826 0.00 0.00 43.65 3.02
1825 2266 1.204704 TGAATCTCTTGTCCGTCGCAT 59.795 47.619 0.00 0.00 0.00 4.73
1826 2267 1.590238 GAATCTCTTGTCCGTCGCATG 59.410 52.381 0.00 0.00 0.00 4.06
1848 2289 2.661195 GAGCGGCGTACGTTTTAGTTAA 59.339 45.455 17.90 0.00 46.52 2.01
1849 2290 3.056304 AGCGGCGTACGTTTTAGTTAAA 58.944 40.909 17.90 0.00 46.52 1.52
1851 2292 3.834702 GCGGCGTACGTTTTAGTTAAAAG 59.165 43.478 17.90 0.00 46.52 2.27
1852 2293 4.375908 GCGGCGTACGTTTTAGTTAAAAGA 60.376 41.667 17.90 0.00 46.52 2.52
1854 2295 6.126079 CGGCGTACGTTTTAGTTAAAAGAAA 58.874 36.000 17.90 0.00 36.00 2.52
1855 2296 6.626882 CGGCGTACGTTTTAGTTAAAAGAAAA 59.373 34.615 17.90 0.00 36.00 2.29
1858 2299 9.754351 GCGTACGTTTTAGTTAAAAGAAAATTG 57.246 29.630 17.90 0.00 36.00 2.32
1874 2316 3.721087 AATTGGGTTACAGGTCTCCAG 57.279 47.619 0.00 0.00 0.00 3.86
1889 2331 0.184933 TCCAGTTTTCACCCACCCTG 59.815 55.000 0.00 0.00 0.00 4.45
1900 2342 2.743718 CACCCTGGTCTTGACGCT 59.256 61.111 0.00 0.00 0.00 5.07
1922 2364 0.916358 CCAGGTCCCCAAGATCCTGT 60.916 60.000 8.83 0.00 39.90 4.00
1932 2374 2.289072 CCAAGATCCTGTGTCACTTCGT 60.289 50.000 4.27 0.00 0.00 3.85
1942 2384 1.062880 TGTCACTTCGTCGTTTTTGCC 59.937 47.619 0.00 0.00 0.00 4.52
1944 2386 1.329292 TCACTTCGTCGTTTTTGCCAG 59.671 47.619 0.00 0.00 0.00 4.85
1970 2412 3.471806 GAGAGGAGGCGGGGGTTC 61.472 72.222 0.00 0.00 0.00 3.62
1971 2413 3.986116 GAGAGGAGGCGGGGGTTCT 62.986 68.421 0.00 0.00 0.00 3.01
1974 2416 4.426313 GGAGGCGGGGGTTCTTGG 62.426 72.222 0.00 0.00 0.00 3.61
1987 2429 4.821589 CTTGGGCGGCCGAGAGAC 62.822 72.222 36.18 10.82 0.00 3.36
1997 2439 1.360551 CCGAGAGACAGGTATGGCG 59.639 63.158 0.00 0.00 40.55 5.69
2001 2443 1.043673 AGAGACAGGTATGGCGACCC 61.044 60.000 4.86 0.00 40.55 4.46
2010 2452 2.668106 TATGGCGACCCTCTACCCCC 62.668 65.000 0.00 0.00 0.00 5.40
2046 2490 3.099141 GGGAACATTGTCCATGGATGTT 58.901 45.455 25.38 25.38 44.25 2.71
2067 2511 8.732746 ATGTTTTCTGTTACTCAAAGTGTACT 57.267 30.769 0.00 0.00 0.00 2.73
2069 2513 8.662141 TGTTTTCTGTTACTCAAAGTGTACTTC 58.338 33.333 0.00 0.00 34.61 3.01
2104 2548 7.145323 TCTTTAAAGCAAACTAACATTCCTGC 58.855 34.615 10.51 0.00 0.00 4.85
2108 2552 3.375299 AGCAAACTAACATTCCTGCGATC 59.625 43.478 0.00 0.00 35.00 3.69
2120 2564 3.525537 TCCTGCGATCTTTTCTTAGCTG 58.474 45.455 0.00 0.00 0.00 4.24
2123 2567 4.574013 CCTGCGATCTTTTCTTAGCTGAAT 59.426 41.667 0.00 0.00 0.00 2.57
2151 2608 4.093115 CGAAGAATATGCAGATGGCTGATC 59.907 45.833 0.00 0.00 45.17 2.92
2153 2610 1.735386 ATATGCAGATGGCTGATCGC 58.265 50.000 0.00 1.55 45.17 4.58
2162 2619 4.022603 AGATGGCTGATCGCAGATAGTAT 58.977 43.478 10.82 0.00 45.17 2.12
2165 2622 5.921962 TGGCTGATCGCAGATAGTATATT 57.078 39.130 10.82 0.00 45.17 1.28
2193 2653 5.843673 CAGAGTTATCTGTGCTCCTTAGA 57.156 43.478 0.00 0.00 46.68 2.10
2201 2661 5.843673 TCTGTGCTCCTTAGATGACTTAG 57.156 43.478 0.00 0.00 0.00 2.18
2207 2667 4.651962 GCTCCTTAGATGACTTAGGTTCCT 59.348 45.833 0.00 0.00 41.84 3.36
2220 2680 1.448013 GTTCCTGGCCTGTCTACGC 60.448 63.158 3.32 0.00 0.00 4.42
2222 2682 4.514577 CCTGGCCTGTCTACGCGG 62.515 72.222 12.47 0.00 0.00 6.46
2233 2693 2.605818 TGTCTACGCGGTAAAATCATGC 59.394 45.455 12.47 0.00 0.00 4.06
2255 2715 4.938226 GCAGAATAAAAGTAGTGTGGAGCT 59.062 41.667 0.00 0.00 0.00 4.09
2263 2723 2.499289 AGTAGTGTGGAGCTTCATCAGG 59.501 50.000 0.00 0.00 0.00 3.86
2267 2727 1.918262 TGTGGAGCTTCATCAGGGAAT 59.082 47.619 0.00 0.00 0.00 3.01
2279 2739 5.431765 TCATCAGGGAATTTGACTAGCTTC 58.568 41.667 0.00 0.00 0.00 3.86
2282 2742 2.237392 AGGGAATTTGACTAGCTTCGCT 59.763 45.455 0.00 0.00 43.41 4.93
2300 2760 2.222976 CGCTGTTGCTCTAAGCTCAATG 60.223 50.000 0.11 0.00 42.97 2.82
2325 2785 3.290710 AGCGCCAATTGACCTGAATATT 58.709 40.909 7.12 0.00 0.00 1.28
2326 2786 4.460263 AGCGCCAATTGACCTGAATATTA 58.540 39.130 7.12 0.00 0.00 0.98
2327 2787 4.516698 AGCGCCAATTGACCTGAATATTAG 59.483 41.667 7.12 0.00 0.00 1.73
2398 2858 9.860898 AACATTTTTCTAAGGATTACTGCAATC 57.139 29.630 0.00 0.00 42.12 2.67
2417 2877 6.066066 GCAATCAGCAGTTACAGTTTGTCTG 61.066 44.000 0.00 0.00 45.57 3.51
2469 2929 5.470437 TCCATTTGTATCACGTTGTAGCAAA 59.530 36.000 0.00 0.00 0.00 3.68
2470 2930 6.150307 TCCATTTGTATCACGTTGTAGCAAAT 59.850 34.615 8.24 8.24 36.06 2.32
2486 2946 2.606795 GCAAATGCTGTTTGCGGTTAGA 60.607 45.455 19.25 0.00 44.13 2.10
2496 2956 6.028146 TGTTTGCGGTTAGATTCTACTACA 57.972 37.500 0.00 0.00 0.00 2.74
2508 2968 3.308035 TCTACTACATCCGTCCCACAT 57.692 47.619 0.00 0.00 0.00 3.21
2509 2969 3.638860 TCTACTACATCCGTCCCACATT 58.361 45.455 0.00 0.00 0.00 2.71
2510 2970 4.795469 TCTACTACATCCGTCCCACATTA 58.205 43.478 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.335422 TGTCATTACAAGTGTTGCCAAATTTTT 59.665 29.630 0.00 0.00 30.91 1.94
11 12 4.991153 TGTCATTACAAGTGTTGCCAAA 57.009 36.364 0.00 0.00 30.91 3.28
12 13 4.991153 TTGTCATTACAAGTGTTGCCAA 57.009 36.364 0.00 0.00 40.69 4.52
17 18 6.942532 ACACTGATTGTCATTACAAGTGTT 57.057 33.333 9.26 0.00 46.01 3.32
30 31 7.040686 GGGACTGTAATTTTGTACACTGATTGT 60.041 37.037 0.00 0.00 42.84 2.71
126 404 8.630278 TTTACTGTTCGAGATTATGCTAGTTC 57.370 34.615 0.00 0.00 0.00 3.01
224 502 8.842280 TCGCTTTTGAAACCTTAATTCTTCTTA 58.158 29.630 0.00 0.00 0.00 2.10
228 506 7.809806 CAGATCGCTTTTGAAACCTTAATTCTT 59.190 33.333 0.00 0.00 0.00 2.52
337 622 0.519077 CGCTTTGCTTCAGGTCTTCC 59.481 55.000 0.00 0.00 0.00 3.46
382 667 3.551496 CTGCCCCTTGTCTTGCGGA 62.551 63.158 0.00 0.00 31.72 5.54
404 689 0.887933 ACAACGTGCCAAATCCATCC 59.112 50.000 0.00 0.00 0.00 3.51
416 701 3.840209 CACGCAAAGATCAATACAACGTG 59.160 43.478 0.00 0.00 41.72 4.49
456 749 2.740447 GGTACGCCTTAAACTTCCACAG 59.260 50.000 0.00 0.00 0.00 3.66
457 750 2.104451 TGGTACGCCTTAAACTTCCACA 59.896 45.455 0.00 0.00 35.27 4.17
469 764 0.526662 CGAAGAACTCTGGTACGCCT 59.473 55.000 0.00 0.00 35.27 5.52
477 772 3.414549 GGCTAGAGACGAAGAACTCTG 57.585 52.381 0.00 0.00 42.02 3.35
539 834 2.087462 CTCCACAGACCAGACGTGCA 62.087 60.000 0.00 0.00 0.00 4.57
589 884 1.005394 CCGGCACTGTACGTCCTTT 60.005 57.895 0.00 0.00 0.00 3.11
591 886 2.282674 TCCGGCACTGTACGTCCT 60.283 61.111 0.00 0.00 0.00 3.85
629 924 3.382546 GTGTGGGCTTAGTCGTAGGAATA 59.617 47.826 0.00 0.00 0.00 1.75
646 942 7.752239 GTCATCTGATTTAAATTCTGTGTGTGG 59.248 37.037 1.43 0.00 0.00 4.17
658 954 5.800296 TCGTTCCCAGTCATCTGATTTAAA 58.200 37.500 0.00 0.00 43.76 1.52
666 962 1.006043 TCCTCTCGTTCCCAGTCATCT 59.994 52.381 0.00 0.00 0.00 2.90
672 968 3.093057 CCCTATATCCTCTCGTTCCCAG 58.907 54.545 0.00 0.00 0.00 4.45
707 1003 2.724454 GCTCTGGATATAGGCCTCGTA 58.276 52.381 9.68 3.99 0.00 3.43
724 1020 0.179189 CGAGGCCAAAAATCACGCTC 60.179 55.000 5.01 0.00 0.00 5.03
725 1021 1.586154 CCGAGGCCAAAAATCACGCT 61.586 55.000 5.01 0.00 0.00 5.07
730 1026 4.983671 AAGATAACCGAGGCCAAAAATC 57.016 40.909 5.01 0.00 0.00 2.17
752 1048 4.217550 CCGTTTCCTTATTTTCTGCTTCCA 59.782 41.667 0.00 0.00 0.00 3.53
758 1054 6.735130 AGTTGTTCCGTTTCCTTATTTTCTG 58.265 36.000 0.00 0.00 0.00 3.02
779 1076 2.764547 GCCCGGCCTCCTCTAGTT 60.765 66.667 0.00 0.00 0.00 2.24
820 1119 4.497966 CGTGCTCGTTTCGTATTCATCTTA 59.502 41.667 0.00 0.00 0.00 2.10
910 1245 1.004440 AGGAGCTTCTTGGCGTGTC 60.004 57.895 0.00 0.00 37.29 3.67
917 1252 2.760374 ACGAAAGACAGGAGCTTCTTG 58.240 47.619 0.00 0.00 32.26 3.02
955 1300 1.810755 CGAAACCCTAGCAAAAGGACC 59.189 52.381 1.58 0.00 39.15 4.46
997 1358 3.064987 CTTCCTCGGTCGCCATCGT 62.065 63.158 0.00 0.00 36.96 3.73
1006 1367 0.898789 TTCTTCTCGCCTTCCTCGGT 60.899 55.000 0.00 0.00 0.00 4.69
1035 1396 0.884514 CACCGTCTGAGCTCTTGAGA 59.115 55.000 16.19 6.72 0.00 3.27
1242 1621 3.826754 CGGCGGCTGCAGTAGAGA 61.827 66.667 21.31 0.00 45.35 3.10
1314 1697 1.475403 GATGAGGTCGAAGAGGGTGA 58.525 55.000 0.00 0.00 36.95 4.02
1475 1864 1.144936 GGTTCTCCCTGCGGATCTG 59.855 63.158 0.00 0.00 37.60 2.90
1520 1914 0.905357 AACAGTGCCTAGCTAGGTGG 59.095 55.000 34.85 24.39 45.42 4.61
1554 1955 7.724287 AGTCTAAACGAAAAGGAAGAGTACTT 58.276 34.615 0.00 0.00 39.24 2.24
1559 1967 5.690857 ACGAAGTCTAAACGAAAAGGAAGAG 59.309 40.000 0.00 0.00 29.74 2.85
1565 1973 8.377681 TGCATAATACGAAGTCTAAACGAAAAG 58.622 33.333 0.00 0.00 43.93 2.27
1571 1979 9.084164 TCTTCTTGCATAATACGAAGTCTAAAC 57.916 33.333 0.00 0.00 43.93 2.01
1612 2020 2.552315 AGTTTCACAAGTAATGGCCACG 59.448 45.455 8.16 0.00 0.00 4.94
1615 2023 4.846779 TTCAGTTTCACAAGTAATGGCC 57.153 40.909 0.00 0.00 0.00 5.36
1617 2025 9.912634 ATAACAATTCAGTTTCACAAGTAATGG 57.087 29.630 0.00 0.00 33.07 3.16
1692 2131 5.160641 CAAAAATATCTCAAACCACACGGG 58.839 41.667 0.00 0.00 44.81 5.28
1721 2160 7.768582 TGCAAATCTGTAGATAGAAAATCGGAA 59.231 33.333 0.00 0.00 33.73 4.30
1723 2162 7.482654 TGCAAATCTGTAGATAGAAAATCGG 57.517 36.000 0.00 0.00 33.73 4.18
1724 2163 9.773328 TTTTGCAAATCTGTAGATAGAAAATCG 57.227 29.630 13.65 0.00 33.73 3.34
1731 2172 8.993121 ACGGATATTTTGCAAATCTGTAGATAG 58.007 33.333 19.43 6.46 37.44 2.08
1747 2188 6.761242 TGAAGAATCATGTCGACGGATATTTT 59.239 34.615 19.09 14.22 0.00 1.82
1751 2192 4.338400 ACTGAAGAATCATGTCGACGGATA 59.662 41.667 19.09 0.00 34.37 2.59
1755 2196 4.385748 TCAAACTGAAGAATCATGTCGACG 59.614 41.667 11.62 0.00 34.37 5.12
1768 2209 4.211389 CGGTCACGAAATTCAAACTGAAG 58.789 43.478 0.00 0.00 40.36 3.02
1770 2211 3.199677 ACGGTCACGAAATTCAAACTGA 58.800 40.909 0.00 0.00 44.60 3.41
1771 2212 3.602390 ACGGTCACGAAATTCAAACTG 57.398 42.857 0.00 0.00 44.60 3.16
1772 2213 3.242936 CCAACGGTCACGAAATTCAAACT 60.243 43.478 0.00 0.00 44.60 2.66
1773 2214 3.040099 CCAACGGTCACGAAATTCAAAC 58.960 45.455 0.00 0.00 44.60 2.93
1774 2215 2.943690 TCCAACGGTCACGAAATTCAAA 59.056 40.909 0.00 0.00 44.60 2.69
1775 2216 2.288458 GTCCAACGGTCACGAAATTCAA 59.712 45.455 0.00 0.00 44.60 2.69
1776 2217 1.868498 GTCCAACGGTCACGAAATTCA 59.132 47.619 0.00 0.00 44.60 2.57
1777 2218 1.196127 GGTCCAACGGTCACGAAATTC 59.804 52.381 0.00 0.00 44.60 2.17
1778 2219 1.232119 GGTCCAACGGTCACGAAATT 58.768 50.000 0.00 0.00 44.60 1.82
1779 2220 0.947180 CGGTCCAACGGTCACGAAAT 60.947 55.000 0.00 0.00 44.60 2.17
1780 2221 1.592131 CGGTCCAACGGTCACGAAA 60.592 57.895 0.00 0.00 44.60 3.46
1781 2222 2.027897 CGGTCCAACGGTCACGAA 59.972 61.111 0.00 0.00 44.60 3.85
1782 2223 2.784356 AACGGTCCAACGGTCACGA 61.784 57.895 0.00 0.00 44.60 4.35
1787 2228 0.882927 CATGACAACGGTCCAACGGT 60.883 55.000 0.00 0.00 43.65 4.83
1796 2237 3.372206 GGACAAGAGATTCATGACAACGG 59.628 47.826 0.00 0.00 0.00 4.44
1825 2266 0.733566 CTAAAACGTACGCCGCTCCA 60.734 55.000 16.72 0.00 41.42 3.86
1826 2267 0.733909 ACTAAAACGTACGCCGCTCC 60.734 55.000 16.72 0.00 41.42 4.70
1848 2289 5.538813 GGAGACCTGTAACCCAATTTTCTTT 59.461 40.000 0.00 0.00 0.00 2.52
1849 2290 5.077564 GGAGACCTGTAACCCAATTTTCTT 58.922 41.667 0.00 0.00 0.00 2.52
1851 2292 4.403734 TGGAGACCTGTAACCCAATTTTC 58.596 43.478 0.00 0.00 0.00 2.29
1852 2293 4.141018 ACTGGAGACCTGTAACCCAATTTT 60.141 41.667 0.00 0.00 33.97 1.82
1854 2295 2.986728 ACTGGAGACCTGTAACCCAATT 59.013 45.455 0.00 0.00 33.97 2.32
1855 2296 2.632537 ACTGGAGACCTGTAACCCAAT 58.367 47.619 0.00 0.00 33.97 3.16
1858 2299 3.181448 TGAAAACTGGAGACCTGTAACCC 60.181 47.826 0.00 0.00 34.63 4.11
1874 2316 0.185175 AGACCAGGGTGGGTGAAAAC 59.815 55.000 0.00 0.00 43.37 2.43
1932 2374 1.152860 TGGGCTCTGGCAAAAACGA 60.153 52.632 0.00 0.00 40.87 3.85
1942 2384 2.757508 TCCTCTCGCTGGGCTCTG 60.758 66.667 0.00 0.00 0.00 3.35
1944 2386 3.535962 CCTCCTCTCGCTGGGCTC 61.536 72.222 0.00 0.00 0.00 4.70
1970 2412 4.821589 GTCTCTCGGCCGCCCAAG 62.822 72.222 23.51 13.39 0.00 3.61
1977 2419 1.742768 CCATACCTGTCTCTCGGCC 59.257 63.158 0.00 0.00 0.00 6.13
1987 2429 0.674534 GTAGAGGGTCGCCATACCTG 59.325 60.000 0.00 0.00 39.65 4.00
1997 2439 2.832201 CGTCGGGGGTAGAGGGTC 60.832 72.222 0.00 0.00 0.00 4.46
2001 2443 1.455217 ATGGACGTCGGGGGTAGAG 60.455 63.158 9.92 0.00 0.00 2.43
2046 2490 8.958119 ATGAAGTACACTTTGAGTAACAGAAA 57.042 30.769 0.00 0.00 36.11 2.52
2095 2539 4.333926 GCTAAGAAAAGATCGCAGGAATGT 59.666 41.667 0.00 0.00 0.00 2.71
2104 2548 7.432545 TCGAACTATTCAGCTAAGAAAAGATCG 59.567 37.037 0.00 0.00 0.00 3.69
2108 2552 8.467402 TCTTCGAACTATTCAGCTAAGAAAAG 57.533 34.615 0.00 0.00 0.00 2.27
2120 2564 7.623089 GCCATCTGCATATTCTTCGAACTATTC 60.623 40.741 0.00 0.00 40.77 1.75
2123 2567 4.991056 GCCATCTGCATATTCTTCGAACTA 59.009 41.667 0.00 0.00 40.77 2.24
2151 2608 9.469807 AACTCTGAAGAAAATATACTATCTGCG 57.530 33.333 0.00 0.00 0.00 5.18
2191 2651 1.840635 GGCCAGGAACCTAAGTCATCT 59.159 52.381 0.00 0.00 0.00 2.90
2192 2652 1.840635 AGGCCAGGAACCTAAGTCATC 59.159 52.381 5.01 0.00 35.10 2.92
2193 2653 1.561542 CAGGCCAGGAACCTAAGTCAT 59.438 52.381 5.01 0.00 35.10 3.06
2201 2661 1.218316 CGTAGACAGGCCAGGAACC 59.782 63.158 5.01 0.00 0.00 3.62
2207 2667 1.534336 TTTACCGCGTAGACAGGCCA 61.534 55.000 5.01 0.00 31.75 5.36
2220 2680 9.438291 CTACTTTTATTCTGCATGATTTTACCG 57.562 33.333 0.00 0.00 0.00 4.02
2233 2693 6.650807 TGAAGCTCCACACTACTTTTATTCTG 59.349 38.462 0.00 0.00 0.00 3.02
2255 2715 5.441718 AGCTAGTCAAATTCCCTGATGAA 57.558 39.130 0.00 0.00 0.00 2.57
2279 2739 1.432514 TTGAGCTTAGAGCAACAGCG 58.567 50.000 2.47 0.00 45.56 5.18
2282 2742 5.405935 TCTACATTGAGCTTAGAGCAACA 57.594 39.130 2.47 0.00 45.56 3.33
2300 2760 1.009829 CAGGTCAATTGGCGCTCTAC 58.990 55.000 7.64 0.00 0.00 2.59
2326 2786 8.624776 GCAATACATCTTCAAAAGTATAAGGCT 58.375 33.333 0.00 0.00 0.00 4.58
2327 2787 8.624776 AGCAATACATCTTCAAAAGTATAAGGC 58.375 33.333 0.00 0.00 0.00 4.35
2398 2858 3.871006 TGTCAGACAAACTGTAACTGCTG 59.129 43.478 0.00 0.00 45.86 4.41
2409 2869 5.117592 GCATTTGCTAATGTGTCAGACAAAC 59.882 40.000 19.66 0.00 42.56 2.93
2442 2902 5.793457 GCTACAACGTGATACAAATGGAAAC 59.207 40.000 0.00 0.00 0.00 2.78
2469 2929 3.347216 AGAATCTAACCGCAAACAGCAT 58.653 40.909 0.00 0.00 46.13 3.79
2470 2930 2.778299 AGAATCTAACCGCAAACAGCA 58.222 42.857 0.00 0.00 46.13 4.41
2474 2934 6.200475 GGATGTAGTAGAATCTAACCGCAAAC 59.800 42.308 0.00 0.00 0.00 2.93
2481 2941 5.533903 TGGGACGGATGTAGTAGAATCTAAC 59.466 44.000 0.00 0.00 0.00 2.34
2486 2946 3.638860 TGTGGGACGGATGTAGTAGAAT 58.361 45.455 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.