Multiple sequence alignment - TraesCS2A01G546100

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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 TraesCS2A01G546100 chr2A 100.000 2895 0 0 1 2895 755072980 755075874 0.000000e+00 5347.0
1 TraesCS2A01G546100 chr2A 98.253 458 8 0 242 699 739853252 739853709 0.000000e+00 802.0
2 TraesCS2A01G546100 chr2A 97.211 251 6 1 1 250 739852825 739853075 9.590000e-115 424.0
3 TraesCS2A01G546100 chr2A 97.674 43 0 1 1493 1534 703998897 703998939 4.000000e-09 73.1
4 TraesCS2A01G546100 chr1A 98.011 704 10 2 1 700 569251765 569251062 0.000000e+00 1219.0
5 TraesCS2A01G546100 chr4A 98.006 702 12 2 1 700 624838535 624839236 0.000000e+00 1218.0
6 TraesCS2A01G546100 chr7A 97.466 671 16 1 1 670 90026621 90027291 0.000000e+00 1144.0
7 TraesCS2A01G546100 chr7D 91.990 799 51 5 699 1495 534628629 534627842 0.000000e+00 1109.0
8 TraesCS2A01G546100 chr7D 89.394 528 53 2 2319 2843 534627172 534626645 0.000000e+00 662.0
9 TraesCS2A01G546100 chr7D 83.552 687 76 26 1540 2216 534627833 534627174 2.470000e-170 608.0
10 TraesCS2A01G546100 chr7D 89.474 57 3 2 1486 1539 232932455 232932511 5.180000e-08 69.4
11 TraesCS2A01G546100 chr2B 88.019 843 53 23 699 1494 765568423 765569264 0.000000e+00 953.0
12 TraesCS2A01G546100 chr2B 85.351 669 65 15 1493 2128 765569305 765569973 0.000000e+00 662.0
13 TraesCS2A01G546100 chr2B 88.762 525 48 7 2380 2895 765570284 765570806 1.460000e-177 632.0
14 TraesCS2A01G546100 chr2D 92.220 437 20 5 699 1123 623857707 623858141 8.870000e-170 606.0
15 TraesCS2A01G546100 chr2D 85.294 476 37 14 1595 2040 623885439 623885911 7.310000e-126 460.0
16 TraesCS2A01G546100 chr2D 89.535 258 17 3 1240 1495 623885149 623885398 4.660000e-83 318.0
17 TraesCS2A01G546100 chr2D 92.000 125 5 2 1123 1242 623858174 623858298 1.380000e-38 171.0
18 TraesCS2A01G546100 chr2D 91.837 49 3 1 1494 1542 36111377 36111330 1.860000e-07 67.6
19 TraesCS2A01G546100 chr5B 81.739 115 19 1 2387 2499 393754895 393755009 8.540000e-16 95.3
20 TraesCS2A01G546100 chr5B 100.000 40 0 0 1491 1530 546857635 546857596 1.110000e-09 75.0
21 TraesCS2A01G546100 chr3B 73.705 251 59 6 2390 2634 779308526 779308277 1.100000e-14 91.6
22 TraesCS2A01G546100 chr3A 95.556 45 2 0 1491 1535 12748692 12748736 4.000000e-09 73.1
23 TraesCS2A01G546100 chr1D 100.000 39 0 0 1493 1531 206041031 206041069 4.000000e-09 73.1
24 TraesCS2A01G546100 chr3D 95.455 44 2 0 1493 1536 548271383 548271340 1.440000e-08 71.3
25 TraesCS2A01G546100 chr1B 91.667 48 4 0 1486 1533 662787563 662787516 1.860000e-07 67.6


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 TraesCS2A01G546100 chr2A 755072980 755075874 2894 False 5347.0 5347 100.000000 1 2895 1 chr2A.!!$F2 2894
1 TraesCS2A01G546100 chr2A 739852825 739853709 884 False 613.0 802 97.732000 1 699 2 chr2A.!!$F3 698
2 TraesCS2A01G546100 chr1A 569251062 569251765 703 True 1219.0 1219 98.011000 1 700 1 chr1A.!!$R1 699
3 TraesCS2A01G546100 chr4A 624838535 624839236 701 False 1218.0 1218 98.006000 1 700 1 chr4A.!!$F1 699
4 TraesCS2A01G546100 chr7A 90026621 90027291 670 False 1144.0 1144 97.466000 1 670 1 chr7A.!!$F1 669
5 TraesCS2A01G546100 chr7D 534626645 534628629 1984 True 793.0 1109 88.312000 699 2843 3 chr7D.!!$R1 2144
6 TraesCS2A01G546100 chr2B 765568423 765570806 2383 False 749.0 953 87.377333 699 2895 3 chr2B.!!$F1 2196
7 TraesCS2A01G546100 chr2D 623885149 623885911 762 False 389.0 460 87.414500 1240 2040 2 chr2D.!!$F2 800
8 TraesCS2A01G546100 chr2D 623857707 623858298 591 False 388.5 606 92.110000 699 1242 2 chr2D.!!$F1 543

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
943 1145 0.393537 CAAGTGCAGGTGGATCCTCC 60.394 60.0 23.03 23.03 46.24 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2255 0.037046 GAACGAAAACTAGCCCCGGA 60.037 55.0 0.73 0.0 0.0 5.14 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
229 231 3.736433 CGACTCCTTGCAATCGAATCTCT 60.736 47.826 13.54 0.00 36.70 3.10
505 692 8.168725 ACAGTAGGGTAGGATCGAATCTTATAA 58.831 37.037 0.00 0.00 0.00 0.98
586 773 4.758674 TCTATTCGGGAGTCTATTACACCG 59.241 45.833 0.00 0.00 46.33 4.94
660 847 0.941463 CTGATGTGCGGCCGAGATAC 60.941 60.000 33.48 21.07 0.00 2.24
664 851 1.153628 GTGCGGCCGAGATACAAGT 60.154 57.895 33.48 0.00 0.00 3.16
890 1089 4.105217 TCCATTGATCACATAGCCTCCATT 59.895 41.667 0.00 0.00 0.00 3.16
893 1092 4.347360 TGATCACATAGCCTCCATTCTG 57.653 45.455 0.00 0.00 0.00 3.02
925 1124 1.277273 CAGATCCAGCACTCCAAGACA 59.723 52.381 0.00 0.00 0.00 3.41
943 1145 0.393537 CAAGTGCAGGTGGATCCTCC 60.394 60.000 23.03 23.03 46.24 4.30
971 1173 1.589716 AAATGCACGCCAAGGCTCTC 61.590 55.000 9.73 0.00 39.32 3.20
976 1178 4.749310 CGCCAAGGCTCTCAGCGT 62.749 66.667 9.73 0.00 43.62 5.07
1030 1232 0.687354 AGGAGCTTCCTTCGCTCAAA 59.313 50.000 13.26 0.00 46.91 2.69
1059 1261 1.662629 CAACTGCTGGAGAACTATGCG 59.337 52.381 2.24 0.00 0.00 4.73
1087 1289 5.758296 CAGCATTTCTGGGTACGTACATTAT 59.242 40.000 26.02 8.26 39.15 1.28
1121 1356 4.183865 TGATCATTAGTTCGGTTGCTCTG 58.816 43.478 0.00 0.00 0.00 3.35
1134 1369 2.688794 GCTCTGCCAGCTGCTTCAC 61.689 63.158 8.66 0.00 45.83 3.18
1242 1493 2.083183 GCATACGGCAAGCGTTACA 58.917 52.632 0.00 0.00 43.97 2.41
1280 1531 1.806542 GCTTCTGAATCACCGCTTCAA 59.193 47.619 0.00 0.00 32.53 2.69
1289 1540 1.606668 TCACCGCTTCAAATCAACACC 59.393 47.619 0.00 0.00 0.00 4.16
1386 1637 0.969409 GCCAGATTTCTGCTGCCCTT 60.969 55.000 1.90 0.00 42.47 3.95
1402 1653 2.003072 CCCTTTGCCCCCTCCATATAT 58.997 52.381 0.00 0.00 0.00 0.86
1413 1664 3.456277 CCCTCCATATATAGGCAAGTCCC 59.544 52.174 0.00 0.00 34.51 4.46
1417 1668 4.104086 CCATATATAGGCAAGTCCCCTCA 58.896 47.826 0.00 0.00 33.88 3.86
1451 1712 3.959535 TGCAATTCCCCTTAGCTTTTG 57.040 42.857 0.00 0.00 0.00 2.44
1452 1713 2.566724 TGCAATTCCCCTTAGCTTTTGG 59.433 45.455 0.00 0.00 0.00 3.28
1453 1714 2.677902 GCAATTCCCCTTAGCTTTTGGC 60.678 50.000 0.00 0.00 42.19 4.52
1454 1715 1.866015 ATTCCCCTTAGCTTTTGGCC 58.134 50.000 0.00 0.00 43.05 5.36
1455 1716 0.783850 TTCCCCTTAGCTTTTGGCCT 59.216 50.000 3.32 0.00 43.05 5.19
1456 1717 0.783850 TCCCCTTAGCTTTTGGCCTT 59.216 50.000 3.32 0.00 43.05 4.35
1457 1718 1.149077 TCCCCTTAGCTTTTGGCCTTT 59.851 47.619 3.32 0.00 43.05 3.11
1458 1719 1.977854 CCCCTTAGCTTTTGGCCTTTT 59.022 47.619 3.32 0.00 43.05 2.27
1479 1740 6.371809 TTTACTGAACTTTTTCGAGCATGT 57.628 33.333 0.00 0.00 34.04 3.21
1496 1757 5.252969 GCATGTGCTCCAAATTTCATCTA 57.747 39.130 0.00 0.00 38.21 1.98
1497 1758 5.653507 GCATGTGCTCCAAATTTCATCTAA 58.346 37.500 0.00 0.00 38.21 2.10
1544 1847 7.836479 AGGGAGTACATTATAGAAGTGTACC 57.164 40.000 14.05 9.03 45.73 3.34
1612 1915 3.765511 TGGTAACAGGTCGTTGCTACTAT 59.234 43.478 0.00 0.00 46.17 2.12
1657 1960 0.873054 TCTATCCGAATCTCGCCGAC 59.127 55.000 0.00 0.00 38.82 4.79
1675 1978 3.428180 CCGACTATCTCAAGGGCGATATG 60.428 52.174 0.00 0.00 0.00 1.78
1693 1996 1.669760 GACCGCACATGGAACCGAA 60.670 57.895 0.00 0.00 0.00 4.30
1701 2004 2.556189 CACATGGAACCGAAAATGTGGA 59.444 45.455 11.64 0.00 43.90 4.02
1709 2012 1.750206 CCGAAAATGTGGATGGCATGA 59.250 47.619 3.81 0.00 0.00 3.07
1784 2087 6.656693 AGCAAAACTCAACAGCTACTATGAAT 59.343 34.615 0.00 0.00 33.06 2.57
1796 2099 7.123397 ACAGCTACTATGAATCAGACTCTTCAA 59.877 37.037 0.00 0.00 35.20 2.69
1828 2134 3.876914 GGCCATTCATACTTGATGACGAA 59.123 43.478 0.00 0.00 44.53 3.85
1833 2139 6.758416 CCATTCATACTTGATGACGAAGAGAA 59.242 38.462 0.00 0.00 44.53 2.87
1834 2140 7.254252 CCATTCATACTTGATGACGAAGAGAAC 60.254 40.741 0.00 0.00 44.53 3.01
1873 2179 1.030457 CCTCCATCTTGCCATTCTGC 58.970 55.000 0.00 0.00 0.00 4.26
1906 2221 1.133025 CTGGCGTAAATCTTTGGGCTG 59.867 52.381 0.00 1.53 0.00 4.85
1908 2223 0.179137 GCGTAAATCTTTGGGCTGCC 60.179 55.000 11.05 11.05 0.00 4.85
2010 2361 5.619086 GCCGTGTTAGTTTGCTATTTGATGT 60.619 40.000 0.00 0.00 0.00 3.06
2015 2366 7.962918 GTGTTAGTTTGCTATTTGATGTGTAGG 59.037 37.037 0.00 0.00 0.00 3.18
2074 2425 9.826574 AATTCTGAAATATCAATTGTGGGATTG 57.173 29.630 5.13 0.00 38.16 2.67
2096 2447 1.064803 TGCAACTTTCGCACGTTGAAT 59.935 42.857 8.52 0.00 42.24 2.57
2119 2471 9.561270 GAATCCTATTTTAAGTGCTTTGAGAAC 57.439 33.333 0.00 0.00 0.00 3.01
2128 2480 4.662145 AGTGCTTTGAGAACGAGTTTTTG 58.338 39.130 0.00 0.00 0.00 2.44
2133 2664 6.690957 TGCTTTGAGAACGAGTTTTTGTTATG 59.309 34.615 0.00 0.00 30.90 1.90
2145 2676 9.726232 CGAGTTTTTGTTATGATGATGATCATT 57.274 29.630 13.08 0.00 45.51 2.57
2158 2689 6.558771 TGATGATCATTTATTAGTTGCGGG 57.441 37.500 10.14 0.00 0.00 6.13
2160 2691 6.204688 TGATGATCATTTATTAGTTGCGGGAC 59.795 38.462 10.14 0.00 0.00 4.46
2161 2692 5.432645 TGATCATTTATTAGTTGCGGGACA 58.567 37.500 0.00 0.00 0.00 4.02
2164 2695 5.492895 TCATTTATTAGTTGCGGGACAAGA 58.507 37.500 0.00 0.00 39.50 3.02
2165 2696 5.584649 TCATTTATTAGTTGCGGGACAAGAG 59.415 40.000 0.00 0.00 39.50 2.85
2166 2697 1.739067 ATTAGTTGCGGGACAAGAGC 58.261 50.000 0.00 0.00 39.50 4.09
2178 2709 0.804989 ACAAGAGCGTGCATTTAGCC 59.195 50.000 0.00 0.00 44.83 3.93
2190 2721 5.449041 CGTGCATTTAGCCAAACATACTCAT 60.449 40.000 0.00 0.00 44.83 2.90
2196 2727 4.443978 AGCCAAACATACTCATAGCCAT 57.556 40.909 0.00 0.00 0.00 4.40
2206 2737 3.861846 ACTCATAGCCATATCCCTCACA 58.138 45.455 0.00 0.00 0.00 3.58
2213 2744 3.202818 AGCCATATCCCTCACATTGACAA 59.797 43.478 0.00 0.00 0.00 3.18
2216 2747 4.336433 CCATATCCCTCACATTGACAACAC 59.664 45.833 0.00 0.00 0.00 3.32
2217 2748 2.270352 TCCCTCACATTGACAACACC 57.730 50.000 0.00 0.00 0.00 4.16
2218 2749 1.492599 TCCCTCACATTGACAACACCA 59.507 47.619 0.00 0.00 0.00 4.17
2219 2750 1.881973 CCCTCACATTGACAACACCAG 59.118 52.381 0.00 0.00 0.00 4.00
2228 2759 1.327303 GACAACACCAGGGCAATTCA 58.673 50.000 0.00 0.00 0.00 2.57
2229 2760 1.895131 GACAACACCAGGGCAATTCAT 59.105 47.619 0.00 0.00 0.00 2.57
2233 2764 1.895131 ACACCAGGGCAATTCATTGTC 59.105 47.619 1.59 0.00 41.47 3.18
2243 2774 4.518217 GCAATTCATTGTCGATACCTTCG 58.482 43.478 1.59 0.00 42.32 3.79
2263 2794 2.040544 CCTCCATCGTTGTGGTGGC 61.041 63.158 10.66 0.00 43.62 5.01
2264 2795 2.358125 TCCATCGTTGTGGTGGCG 60.358 61.111 4.64 0.00 40.27 5.69
2265 2796 3.430862 CCATCGTTGTGGTGGCGG 61.431 66.667 0.00 0.00 34.46 6.13
2266 2797 3.430862 CATCGTTGTGGTGGCGGG 61.431 66.667 0.00 0.00 0.00 6.13
2283 2814 4.347453 GCCCAGCTGCCAAACACG 62.347 66.667 8.66 0.00 0.00 4.49
2284 2815 2.594303 CCCAGCTGCCAAACACGA 60.594 61.111 8.66 0.00 0.00 4.35
2285 2816 2.639286 CCAGCTGCCAAACACGAC 59.361 61.111 8.66 0.00 0.00 4.34
2286 2817 2.249309 CAGCTGCCAAACACGACG 59.751 61.111 0.00 0.00 0.00 5.12
2287 2818 2.972505 AGCTGCCAAACACGACGG 60.973 61.111 0.00 0.00 0.00 4.79
2288 2819 4.025401 GCTGCCAAACACGACGGG 62.025 66.667 0.00 0.00 0.00 5.28
2289 2820 3.353836 CTGCCAAACACGACGGGG 61.354 66.667 0.43 0.00 0.00 5.73
2290 2821 4.939368 TGCCAAACACGACGGGGG 62.939 66.667 0.43 0.00 0.00 5.40
2291 2822 4.629523 GCCAAACACGACGGGGGA 62.630 66.667 0.43 0.00 0.00 4.81
2292 2823 2.349755 CCAAACACGACGGGGGAT 59.650 61.111 0.43 0.00 0.00 3.85
2293 2824 1.743995 CCAAACACGACGGGGGATC 60.744 63.158 0.43 0.00 0.00 3.36
2294 2825 1.295423 CAAACACGACGGGGGATCT 59.705 57.895 0.43 0.00 0.00 2.75
2295 2826 0.739813 CAAACACGACGGGGGATCTC 60.740 60.000 0.43 0.00 0.00 2.75
2296 2827 0.903454 AAACACGACGGGGGATCTCT 60.903 55.000 0.43 0.00 0.00 3.10
2297 2828 1.605058 AACACGACGGGGGATCTCTG 61.605 60.000 0.43 0.00 0.00 3.35
2298 2829 2.052690 CACGACGGGGGATCTCTGT 61.053 63.158 0.00 0.00 0.00 3.41
2299 2830 1.753463 ACGACGGGGGATCTCTGTC 60.753 63.158 14.45 14.45 37.21 3.51
2300 2831 2.491022 CGACGGGGGATCTCTGTCC 61.491 68.421 16.98 0.78 37.25 4.02
2301 2832 1.075896 GACGGGGGATCTCTGTCCT 60.076 63.158 13.84 0.00 38.38 3.85
2302 2833 1.381872 ACGGGGGATCTCTGTCCTG 60.382 63.158 0.00 0.00 38.38 3.86
2303 2834 2.136878 CGGGGGATCTCTGTCCTGG 61.137 68.421 0.00 0.00 38.38 4.45
2304 2835 1.003573 GGGGGATCTCTGTCCTGGT 59.996 63.158 0.00 0.00 38.38 4.00
2305 2836 1.341156 GGGGGATCTCTGTCCTGGTG 61.341 65.000 0.00 0.00 38.38 4.17
2306 2837 1.341156 GGGGATCTCTGTCCTGGTGG 61.341 65.000 0.00 0.00 38.38 4.61
2307 2838 0.325671 GGGATCTCTGTCCTGGTGGA 60.326 60.000 0.00 0.00 40.69 4.02
2308 2839 1.694048 GGGATCTCTGTCCTGGTGGAT 60.694 57.143 0.00 0.00 45.29 3.41
2309 2840 1.415659 GGATCTCTGTCCTGGTGGATG 59.584 57.143 0.00 0.00 45.29 3.51
2310 2841 2.114616 GATCTCTGTCCTGGTGGATGT 58.885 52.381 0.00 0.00 45.29 3.06
2311 2842 1.561643 TCTCTGTCCTGGTGGATGTC 58.438 55.000 0.00 0.00 45.29 3.06
2312 2843 1.077828 TCTCTGTCCTGGTGGATGTCT 59.922 52.381 0.00 0.00 45.29 3.41
2313 2844 1.905215 CTCTGTCCTGGTGGATGTCTT 59.095 52.381 0.00 0.00 45.29 3.01
2314 2845 1.902508 TCTGTCCTGGTGGATGTCTTC 59.097 52.381 0.00 0.00 45.29 2.87
2315 2846 1.905215 CTGTCCTGGTGGATGTCTTCT 59.095 52.381 0.00 0.00 45.29 2.85
2316 2847 1.625315 TGTCCTGGTGGATGTCTTCTG 59.375 52.381 0.00 0.00 45.29 3.02
2317 2848 0.615331 TCCTGGTGGATGTCTTCTGC 59.385 55.000 0.00 0.00 37.46 4.26
2327 2858 4.704833 TCTTCTGCTGGCGGCCAC 62.705 66.667 19.77 15.46 40.92 5.01
2349 2880 1.405105 GTTGTGTGTTCTGGCATGTGT 59.595 47.619 0.00 0.00 0.00 3.72
2360 2891 2.046988 CATGTGTGCTCTGCGGGA 60.047 61.111 0.00 0.00 0.00 5.14
2449 2980 2.230508 GTGTCGACAACATCCTAGGACA 59.769 50.000 21.95 1.36 40.80 4.02
2459 2990 3.775316 ACATCCTAGGACATCGTTCCTTT 59.225 43.478 15.42 0.00 44.22 3.11
2477 3008 0.952280 TTTTTGGCGGCGTCATTGTA 59.048 45.000 17.58 0.00 0.00 2.41
2484 3015 1.873903 GCGGCGTCATTGTAGATCCAT 60.874 52.381 9.37 0.00 0.00 3.41
2510 3041 2.939103 CCTCCATCGTGGTTTCAATCTC 59.061 50.000 4.33 0.00 39.03 2.75
2535 3067 5.395214 GGGTTGTCAAGGTGAAAATTCAAGT 60.395 40.000 0.00 0.00 39.21 3.16
2539 3071 6.033341 TGTCAAGGTGAAAATTCAAGTTTCG 58.967 36.000 5.88 0.00 39.21 3.46
2546 3078 3.515071 AAATTCAAGTTTCGACGTCGG 57.485 42.857 35.05 19.30 40.29 4.79
2565 3097 2.434884 CGAAGCAGGCATCGGTGT 60.435 61.111 10.70 0.00 34.13 4.16
2566 3098 2.456119 CGAAGCAGGCATCGGTGTC 61.456 63.158 10.70 0.00 34.13 3.67
2573 3105 2.264794 GCATCGGTGTCGTTCCCT 59.735 61.111 0.00 0.00 37.69 4.20
2574 3106 1.514087 GCATCGGTGTCGTTCCCTA 59.486 57.895 0.00 0.00 37.69 3.53
2577 3109 0.533951 ATCGGTGTCGTTCCCTAACC 59.466 55.000 0.00 0.00 37.69 2.85
2637 3169 0.687920 TTGGATGTCGGTGGCTTACA 59.312 50.000 0.00 0.00 0.00 2.41
2651 3183 5.066505 GGTGGCTTACATGGATTTCTAGTTG 59.933 44.000 0.00 0.00 0.00 3.16
2655 3187 5.006746 GCTTACATGGATTTCTAGTTGGTCG 59.993 44.000 0.00 0.00 0.00 4.79
2673 3205 3.659092 CAACTGCGCGGCCTCAAA 61.659 61.111 18.15 0.00 0.00 2.69
2678 3210 3.972276 GCGCGGCCTCAAAACCAA 61.972 61.111 8.83 0.00 0.00 3.67
2692 3224 6.985645 CCTCAAAACCAATGTGAAAATCAGAA 59.014 34.615 0.00 0.00 0.00 3.02
2702 3234 2.224523 TGAAAATCAGAACGGTGGCTCT 60.225 45.455 0.00 0.00 0.00 4.09
2714 3246 2.679059 CGGTGGCTCTGAAATCTCATGT 60.679 50.000 0.00 0.00 0.00 3.21
2719 3251 4.020307 TGGCTCTGAAATCTCATGTGTGTA 60.020 41.667 0.00 0.00 0.00 2.90
2720 3252 4.937620 GGCTCTGAAATCTCATGTGTGTAA 59.062 41.667 0.00 0.00 0.00 2.41
2721 3253 5.064452 GGCTCTGAAATCTCATGTGTGTAAG 59.936 44.000 0.00 0.00 0.00 2.34
2722 3254 5.064452 GCTCTGAAATCTCATGTGTGTAAGG 59.936 44.000 0.00 0.00 0.00 2.69
2723 3255 4.937620 TCTGAAATCTCATGTGTGTAAGGC 59.062 41.667 0.00 0.00 0.00 4.35
2724 3256 4.650734 TGAAATCTCATGTGTGTAAGGCA 58.349 39.130 0.00 0.00 0.00 4.75
2854 3391 5.864628 AATTAAAGAGCTCTTGTCGGTTC 57.135 39.130 29.09 0.00 36.12 3.62
2860 3397 3.056465 AGAGCTCTTGTCGGTTCCTAAAG 60.056 47.826 11.45 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.202698 GCTCACCTCCTCAACACAACT 60.203 52.381 0.00 0.00 0.00 3.16
229 231 2.159099 CCTCATGAGCCTTTACAGCGTA 60.159 50.000 17.76 0.00 34.64 4.42
505 692 1.839747 TCGTACTGTGGGGCCAAGT 60.840 57.895 4.39 8.48 0.00 3.16
586 773 3.386078 TGTCAGATCTGCAAGGTATCTCC 59.614 47.826 18.36 0.00 0.00 3.71
660 847 2.353376 CGTTGCCCGCACAACTTG 60.353 61.111 14.38 0.00 46.21 3.16
664 851 1.225376 CTAACTCGTTGCCCGCACAA 61.225 55.000 0.00 0.00 36.19 3.33
890 1089 1.260538 ATCTGAGCGCCTTGTCCAGA 61.261 55.000 2.29 8.16 38.12 3.86
893 1092 1.522580 GGATCTGAGCGCCTTGTCC 60.523 63.158 2.29 1.77 0.00 4.02
943 1145 2.787249 CGTGCATTTCAGGAGCCG 59.213 61.111 0.00 0.00 32.56 5.52
971 1173 1.734477 CTTCCTCGACACCACGCTG 60.734 63.158 0.00 0.00 0.00 5.18
976 1178 2.215942 TGATCTCTTCCTCGACACCA 57.784 50.000 0.00 0.00 0.00 4.17
1059 1261 0.727398 GTACCCAGAAATGCTGCGAC 59.273 55.000 0.00 0.00 43.50 5.19
1087 1289 9.190858 CCGAACTAATGATCAAATCAAAACAAA 57.809 29.630 0.00 0.00 43.50 2.83
1107 1309 1.302033 CTGGCAGAGCAACCGAACT 60.302 57.895 9.42 0.00 0.00 3.01
1121 1356 0.170561 CATCAAGTGAAGCAGCTGGC 59.829 55.000 17.12 7.98 45.30 4.85
1134 1369 1.681327 AGCAAGCAGGGCCATCAAG 60.681 57.895 6.18 0.00 0.00 3.02
1155 1401 6.619852 ACCCTATATCTTGGTTCCTACAACAT 59.380 38.462 0.00 0.00 0.00 2.71
1220 1471 2.703409 CGCTTGCCGTATGCTGTC 59.297 61.111 0.00 0.00 42.00 3.51
1242 1493 2.522185 AGCAGCCATGAAATTGACAGT 58.478 42.857 0.00 0.00 0.00 3.55
1280 1531 2.039084 AGCGAAGAAGAGGGTGTTGATT 59.961 45.455 0.00 0.00 0.00 2.57
1289 1540 1.929836 CCGAATTCAGCGAAGAAGAGG 59.070 52.381 6.22 0.00 0.00 3.69
1386 1637 2.205342 GCCTATATATGGAGGGGGCAA 58.795 52.381 4.10 0.00 38.16 4.52
1397 1648 5.430089 GGAATGAGGGGACTTGCCTATATAT 59.570 44.000 0.00 0.00 44.43 0.86
1402 1653 1.213296 GGAATGAGGGGACTTGCCTA 58.787 55.000 0.00 0.00 44.43 3.93
1451 1712 5.177725 TCGAAAAAGTTCAGTAAAAGGCC 57.822 39.130 0.00 0.00 32.89 5.19
1452 1713 4.675565 GCTCGAAAAAGTTCAGTAAAAGGC 59.324 41.667 0.00 0.00 32.89 4.35
1453 1714 5.816919 TGCTCGAAAAAGTTCAGTAAAAGG 58.183 37.500 0.00 0.00 32.89 3.11
1454 1715 6.912591 ACATGCTCGAAAAAGTTCAGTAAAAG 59.087 34.615 0.00 0.00 32.89 2.27
1455 1716 6.690957 CACATGCTCGAAAAAGTTCAGTAAAA 59.309 34.615 0.00 0.00 32.89 1.52
1456 1717 6.198687 CACATGCTCGAAAAAGTTCAGTAAA 58.801 36.000 0.00 0.00 32.89 2.01
1457 1718 5.747565 CACATGCTCGAAAAAGTTCAGTAA 58.252 37.500 0.00 0.00 32.89 2.24
1458 1719 4.319477 GCACATGCTCGAAAAAGTTCAGTA 60.319 41.667 0.00 0.00 38.21 2.74
1479 1740 4.458989 AGCGTTTAGATGAAATTTGGAGCA 59.541 37.500 0.00 0.00 0.00 4.26
1496 1757 8.601476 CCTTCGTAAAGAAATATAAGAGCGTTT 58.399 33.333 0.00 0.00 38.57 3.60
1497 1758 7.224167 CCCTTCGTAAAGAAATATAAGAGCGTT 59.776 37.037 0.00 0.00 38.57 4.84
1544 1847 7.796838 TGATTGTTGATTCAGTAAAAGAGACG 58.203 34.615 0.00 0.00 0.00 4.18
1639 1942 0.875728 AGTCGGCGAGATTCGGATAG 59.124 55.000 11.20 0.00 40.84 2.08
1642 1945 0.873054 GATAGTCGGCGAGATTCGGA 59.127 55.000 11.20 0.00 40.84 4.55
1657 1960 3.428180 CGGTCATATCGCCCTTGAGATAG 60.428 52.174 0.00 0.00 36.82 2.08
1675 1978 1.231958 TTTCGGTTCCATGTGCGGTC 61.232 55.000 0.00 0.00 0.00 4.79
1693 1996 5.068636 GTCTCTATCATGCCATCCACATTT 58.931 41.667 0.00 0.00 0.00 2.32
1701 2004 5.307456 ACAAGATCTGTCTCTATCATGCCAT 59.693 40.000 0.00 0.00 29.87 4.40
1784 2087 1.000163 GCTCCACGTTGAAGAGTCTGA 60.000 52.381 0.00 0.00 0.00 3.27
1796 2099 4.778143 GAATGGCCGGCTCCACGT 62.778 66.667 28.56 8.00 39.25 4.49
1828 2134 1.303398 TGGTCTCCGAGCGTTCTCT 60.303 57.895 0.00 0.00 37.19 3.10
1833 2139 0.319641 GAAAAGTGGTCTCCGAGCGT 60.320 55.000 0.00 0.00 32.15 5.07
1834 2140 0.038159 AGAAAAGTGGTCTCCGAGCG 60.038 55.000 0.00 0.00 32.15 5.03
1906 2221 7.844482 AGTATATCGTTTACAACATTAACGGC 58.156 34.615 0.00 0.00 43.39 5.68
1908 2223 8.203346 CGGAGTATATCGTTTACAACATTAACG 58.797 37.037 0.00 0.00 44.26 3.18
1926 2250 2.624838 CGAAAACTAGCCCCGGAGTATA 59.375 50.000 0.73 0.00 0.00 1.47
1927 2251 1.411612 CGAAAACTAGCCCCGGAGTAT 59.588 52.381 0.73 0.00 0.00 2.12
1928 2252 0.819582 CGAAAACTAGCCCCGGAGTA 59.180 55.000 0.73 0.00 0.00 2.59
1929 2253 1.190178 ACGAAAACTAGCCCCGGAGT 61.190 55.000 0.73 0.00 0.00 3.85
1931 2255 0.037046 GAACGAAAACTAGCCCCGGA 60.037 55.000 0.73 0.00 0.00 5.14
2010 2361 6.328356 AGGTGAAAGCTTAGCTTGCCTACA 62.328 45.833 25.36 16.32 46.63 2.74
2074 2425 1.298339 AACGTGCGAAAGTTGCAGC 60.298 52.632 0.00 0.00 44.21 5.25
2096 2447 6.932400 TCGTTCTCAAAGCACTTAAAATAGGA 59.068 34.615 0.00 0.00 0.00 2.94
2133 2664 7.119699 TCCCGCAACTAATAAATGATCATCATC 59.880 37.037 9.06 0.00 35.76 2.92
2145 2676 3.267483 GCTCTTGTCCCGCAACTAATAA 58.733 45.455 0.00 0.00 32.90 1.40
2158 2689 1.202076 GGCTAAATGCACGCTCTTGTC 60.202 52.381 0.00 0.00 45.15 3.18
2160 2691 0.804364 TGGCTAAATGCACGCTCTTG 59.196 50.000 0.00 0.00 45.15 3.02
2161 2692 1.533625 TTGGCTAAATGCACGCTCTT 58.466 45.000 0.00 0.00 45.15 2.85
2164 2695 0.958091 TGTTTGGCTAAATGCACGCT 59.042 45.000 0.00 0.00 45.15 5.07
2165 2696 1.994916 ATGTTTGGCTAAATGCACGC 58.005 45.000 0.00 0.00 45.15 5.34
2166 2697 4.142708 TGAGTATGTTTGGCTAAATGCACG 60.143 41.667 0.00 0.00 45.15 5.34
2178 2709 6.715280 AGGGATATGGCTATGAGTATGTTTG 58.285 40.000 0.00 0.00 0.00 2.93
2190 2721 3.973305 TGTCAATGTGAGGGATATGGCTA 59.027 43.478 0.00 0.00 0.00 3.93
2196 2727 3.329225 TGGTGTTGTCAATGTGAGGGATA 59.671 43.478 0.00 0.00 0.00 2.59
2206 2737 2.014010 ATTGCCCTGGTGTTGTCAAT 57.986 45.000 0.00 0.00 0.00 2.57
2213 2744 1.895131 GACAATGAATTGCCCTGGTGT 59.105 47.619 2.92 0.00 41.38 4.16
2216 2747 1.462616 TCGACAATGAATTGCCCTGG 58.537 50.000 2.92 0.00 41.38 4.45
2217 2748 3.003689 GGTATCGACAATGAATTGCCCTG 59.996 47.826 2.92 0.00 41.38 4.45
2218 2749 3.117888 AGGTATCGACAATGAATTGCCCT 60.118 43.478 2.92 0.00 41.38 5.19
2219 2750 3.214328 AGGTATCGACAATGAATTGCCC 58.786 45.455 2.92 0.00 41.38 5.36
2243 2774 0.673644 CCACCACAACGATGGAGGTC 60.674 60.000 8.72 0.00 43.50 3.85
2266 2797 4.347453 CGTGTTTGGCAGCTGGGC 62.347 66.667 17.12 9.25 43.73 5.36
2268 2799 2.639286 GTCGTGTTTGGCAGCTGG 59.361 61.111 17.12 0.00 0.00 4.85
2269 2800 2.249309 CGTCGTGTTTGGCAGCTG 59.751 61.111 10.11 10.11 0.00 4.24
2270 2801 2.972505 CCGTCGTGTTTGGCAGCT 60.973 61.111 0.00 0.00 0.00 4.24
2271 2802 4.025401 CCCGTCGTGTTTGGCAGC 62.025 66.667 0.00 0.00 0.00 5.25
2272 2803 3.353836 CCCCGTCGTGTTTGGCAG 61.354 66.667 0.00 0.00 0.00 4.85
2273 2804 4.939368 CCCCCGTCGTGTTTGGCA 62.939 66.667 0.00 0.00 0.00 4.92
2274 2805 3.912745 ATCCCCCGTCGTGTTTGGC 62.913 63.158 0.00 0.00 0.00 4.52
2275 2806 1.743995 GATCCCCCGTCGTGTTTGG 60.744 63.158 0.00 0.00 0.00 3.28
2276 2807 0.739813 GAGATCCCCCGTCGTGTTTG 60.740 60.000 0.00 0.00 0.00 2.93
2277 2808 0.903454 AGAGATCCCCCGTCGTGTTT 60.903 55.000 0.00 0.00 0.00 2.83
2278 2809 1.305046 AGAGATCCCCCGTCGTGTT 60.305 57.895 0.00 0.00 0.00 3.32
2279 2810 2.052690 CAGAGATCCCCCGTCGTGT 61.053 63.158 0.00 0.00 0.00 4.49
2280 2811 2.005960 GACAGAGATCCCCCGTCGTG 62.006 65.000 0.00 0.00 0.00 4.35
2281 2812 1.753463 GACAGAGATCCCCCGTCGT 60.753 63.158 0.00 0.00 0.00 4.34
2282 2813 2.491022 GGACAGAGATCCCCCGTCG 61.491 68.421 0.00 0.00 31.94 5.12
2283 2814 1.075896 AGGACAGAGATCCCCCGTC 60.076 63.158 0.00 0.00 39.91 4.79
2284 2815 1.381872 CAGGACAGAGATCCCCCGT 60.382 63.158 0.00 0.00 39.91 5.28
2285 2816 2.136878 CCAGGACAGAGATCCCCCG 61.137 68.421 0.00 0.00 39.91 5.73
2286 2817 1.003573 ACCAGGACAGAGATCCCCC 59.996 63.158 0.00 0.00 39.91 5.40
2287 2818 1.341156 CCACCAGGACAGAGATCCCC 61.341 65.000 0.00 0.00 39.91 4.81
2288 2819 0.325671 TCCACCAGGACAGAGATCCC 60.326 60.000 0.00 0.00 39.61 3.85
2289 2820 3.306902 TCCACCAGGACAGAGATCC 57.693 57.895 0.00 0.00 39.61 3.36
2299 2830 0.617413 AGCAGAAGACATCCACCAGG 59.383 55.000 0.00 0.00 0.00 4.45
2300 2831 1.678123 CCAGCAGAAGACATCCACCAG 60.678 57.143 0.00 0.00 0.00 4.00
2301 2832 0.325933 CCAGCAGAAGACATCCACCA 59.674 55.000 0.00 0.00 0.00 4.17
2302 2833 1.028868 GCCAGCAGAAGACATCCACC 61.029 60.000 0.00 0.00 0.00 4.61
2303 2834 1.364626 CGCCAGCAGAAGACATCCAC 61.365 60.000 0.00 0.00 0.00 4.02
2304 2835 1.078918 CGCCAGCAGAAGACATCCA 60.079 57.895 0.00 0.00 0.00 3.41
2305 2836 1.817099 CCGCCAGCAGAAGACATCC 60.817 63.158 0.00 0.00 0.00 3.51
2306 2837 2.467826 GCCGCCAGCAGAAGACATC 61.468 63.158 0.00 0.00 42.97 3.06
2307 2838 2.437359 GCCGCCAGCAGAAGACAT 60.437 61.111 0.00 0.00 42.97 3.06
2308 2839 4.704833 GGCCGCCAGCAGAAGACA 62.705 66.667 3.91 0.00 46.50 3.41
2309 2840 4.704833 TGGCCGCCAGCAGAAGAC 62.705 66.667 8.43 0.00 46.50 3.01
2310 2841 4.704833 GTGGCCGCCAGCAGAAGA 62.705 66.667 13.92 0.00 46.50 2.87
2317 2848 3.663176 CACAACTGTGGCCGCCAG 61.663 66.667 13.92 16.88 42.10 4.85
2327 2858 1.677576 ACATGCCAGAACACACAACTG 59.322 47.619 0.00 0.00 0.00 3.16
2328 2859 1.677576 CACATGCCAGAACACACAACT 59.322 47.619 0.00 0.00 0.00 3.16
2388 2919 2.391389 GGCTTTCACCCGAAGCTCG 61.391 63.158 8.52 0.00 46.64 5.03
2459 2990 0.519519 CTACAATGACGCCGCCAAAA 59.480 50.000 0.00 0.00 0.00 2.44
2465 2996 2.154854 ATGGATCTACAATGACGCCG 57.845 50.000 0.00 0.00 0.00 6.46
2472 3003 5.715439 TGGAGGTGAAATGGATCTACAAT 57.285 39.130 0.00 0.00 0.00 2.71
2477 3008 2.774234 ACGATGGAGGTGAAATGGATCT 59.226 45.455 0.00 0.00 0.00 2.75
2484 3015 2.158740 TGAAACCACGATGGAGGTGAAA 60.159 45.455 10.46 0.00 40.96 2.69
2510 3041 3.067461 TGAATTTTCACCTTGACAACCCG 59.933 43.478 0.00 0.00 31.01 5.28
2539 3071 2.504244 CCTGCTTCGACCGACGTC 60.504 66.667 5.18 5.18 43.13 4.34
2546 3078 2.125512 ACCGATGCCTGCTTCGAC 60.126 61.111 23.69 0.00 43.36 4.20
2554 3086 2.264794 GGAACGACACCGATGCCT 59.735 61.111 0.00 0.00 39.50 4.75
2565 3097 1.565067 GAGGAAGGGTTAGGGAACGA 58.435 55.000 0.00 0.00 36.32 3.85
2566 3098 0.540454 GGAGGAAGGGTTAGGGAACG 59.460 60.000 0.00 0.00 36.32 3.95
2603 3135 4.451900 ACATCCAATGAAAGACCGTATCC 58.548 43.478 0.00 0.00 0.00 2.59
2637 3169 3.627395 TGCGACCAACTAGAAATCCAT 57.373 42.857 0.00 0.00 0.00 3.41
2672 3204 5.163457 ACCGTTCTGATTTTCACATTGGTTT 60.163 36.000 0.00 0.00 0.00 3.27
2673 3205 4.340950 ACCGTTCTGATTTTCACATTGGTT 59.659 37.500 0.00 0.00 0.00 3.67
2678 3210 2.228822 GCCACCGTTCTGATTTTCACAT 59.771 45.455 0.00 0.00 0.00 3.21
2692 3224 0.976641 TGAGATTTCAGAGCCACCGT 59.023 50.000 0.00 0.00 0.00 4.83
2702 3234 4.650734 TGCCTTACACACATGAGATTTCA 58.349 39.130 0.00 0.00 37.81 2.69
2714 3246 3.120321 ACAAAGACGATGCCTTACACA 57.880 42.857 0.00 0.00 0.00 3.72
2719 3251 2.851195 AGTGAACAAAGACGATGCCTT 58.149 42.857 0.00 0.00 0.00 4.35
2720 3252 2.549754 CAAGTGAACAAAGACGATGCCT 59.450 45.455 0.00 0.00 0.00 4.75
2721 3253 2.548057 TCAAGTGAACAAAGACGATGCC 59.452 45.455 0.00 0.00 0.00 4.40
2722 3254 3.248602 ACTCAAGTGAACAAAGACGATGC 59.751 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.