Multiple sequence alignment - TraesCS1B01G223700

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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 TraesCS1B01G223700 chr1B 100.000 2435 0 0 1 2435 401764584 401762150 0.000000e+00 4497
1 TraesCS1B01G223700 chr1B 94.339 1837 80 6 618 2435 401992767 401990936 0.000000e+00 2795
2 TraesCS1B01G223700 chr1B 89.377 979 59 21 662 1613 402039921 402038961 0.000000e+00 1190
3 TraesCS1B01G223700 chr1B 83.424 549 60 17 1904 2435 402003731 402003197 4.710000e-132 481
4 TraesCS1B01G223700 chr1B 96.207 290 9 2 1 290 377074597 377074884 7.880000e-130 473
5 TraesCS1B01G223700 chr1B 98.507 268 3 1 286 553 401993031 401992765 2.830000e-129 472
6 TraesCS1B01G223700 chr1B 95.833 288 10 2 1 288 148136168 148136453 4.740000e-127 464
7 TraesCS1B01G223700 chr1B 90.417 240 22 1 1668 1906 2770258 2770497 5.050000e-82 315
8 TraesCS1B01G223700 chr1B 90.377 239 22 1 1668 1905 465687598 465687360 1.820000e-81 313
9 TraesCS1B01G223700 chr1B 94.783 115 6 0 426 540 402040037 402039923 1.920000e-41 180
10 TraesCS1B01G223700 chr1A 89.629 1427 68 19 286 1669 372288305 372286916 0.000000e+00 1742
11 TraesCS1B01G223700 chr1A 88.061 1315 105 24 317 1595 372316770 372315472 0.000000e+00 1511
12 TraesCS1B01G223700 chr1A 89.764 127 11 2 2098 2224 372286029 372285905 6.970000e-36 161
13 TraesCS1B01G223700 chr1D 91.172 1246 72 20 426 1641 298604891 298603654 0.000000e+00 1657
14 TraesCS1B01G223700 chr1D 85.481 551 53 15 1904 2433 298598676 298598132 1.270000e-152 549
15 TraesCS1B01G223700 chr1D 84.672 548 56 15 1904 2435 298603557 298603022 2.770000e-144 521
16 TraesCS1B01G223700 chr1D 89.086 394 23 2 643 1018 298599204 298598813 2.830000e-129 472
17 TraesCS1B01G223700 chr1D 94.958 119 5 1 530 648 298599949 298599832 4.130000e-43 185
18 TraesCS1B01G223700 chr1D 91.803 122 8 1 1550 1669 298598796 298598675 4.160000e-38 169
19 TraesCS1B01G223700 chr4B 79.422 1108 140 55 537 1591 603037574 603038646 0.000000e+00 702
20 TraesCS1B01G223700 chr4B 80.570 983 122 35 695 1632 602873972 602873014 0.000000e+00 693
21 TraesCS1B01G223700 chr4D 80.648 987 122 44 695 1632 477543846 477542880 0.000000e+00 701
22 TraesCS1B01G223700 chr4D 81.714 875 89 35 645 1476 477558660 477559506 0.000000e+00 664
23 TraesCS1B01G223700 chr5B 97.241 290 7 1 1 290 508673038 508673326 7.820000e-135 490
24 TraesCS1B01G223700 chr5B 95.563 293 11 2 1 293 424338795 424338505 3.670000e-128 468
25 TraesCS1B01G223700 chr5B 95.105 286 13 1 6 291 508670742 508671026 1.330000e-122 449
26 TraesCS1B01G223700 chr5B 92.929 297 13 5 1 296 603242235 603242524 2.240000e-115 425
27 TraesCS1B01G223700 chr7B 95.862 290 10 2 1 290 451953062 451953349 3.670000e-128 468
28 TraesCS1B01G223700 chr7B 95.238 294 12 2 1 294 674764129 674763838 4.740000e-127 464
29 TraesCS1B01G223700 chr7B 89.024 246 25 2 1668 1912 414077419 414077175 1.090000e-78 303
30 TraesCS1B01G223700 chr7B 88.446 251 27 2 1657 1905 219231081 219230831 3.930000e-78 302
31 TraesCS1B01G223700 chr6B 96.441 281 9 1 1 281 264294781 264294502 1.710000e-126 462
32 TraesCS1B01G223700 chr2A 91.416 233 18 2 1677 1907 635578293 635578525 3.910000e-83 318
33 TraesCS1B01G223700 chr3D 90.377 239 22 1 1668 1905 209677726 209677488 1.820000e-81 313
34 TraesCS1B01G223700 chr3D 90.000 240 23 1 1668 1906 601830769 601831008 2.350000e-80 309
35 TraesCS1B01G223700 chr3B 88.446 251 27 2 1657 1905 110588861 110589111 3.930000e-78 302


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 TraesCS1B01G223700 chr1B 401762150 401764584 2434 True 4497.000000 4497 100.000000 1 2435 1 chr1B.!!$R1 2434
1 TraesCS1B01G223700 chr1B 401990936 401993031 2095 True 1633.500000 2795 96.423000 286 2435 2 chr1B.!!$R4 2149
2 TraesCS1B01G223700 chr1B 402038961 402040037 1076 True 685.000000 1190 92.080000 426 1613 2 chr1B.!!$R5 1187
3 TraesCS1B01G223700 chr1B 402003197 402003731 534 True 481.000000 481 83.424000 1904 2435 1 chr1B.!!$R2 531
4 TraesCS1B01G223700 chr1A 372315472 372316770 1298 True 1511.000000 1511 88.061000 317 1595 1 chr1A.!!$R1 1278
5 TraesCS1B01G223700 chr1A 372285905 372288305 2400 True 951.500000 1742 89.696500 286 2224 2 chr1A.!!$R2 1938
6 TraesCS1B01G223700 chr1D 298598132 298604891 6759 True 592.166667 1657 89.528667 426 2435 6 chr1D.!!$R1 2009
7 TraesCS1B01G223700 chr4B 603037574 603038646 1072 False 702.000000 702 79.422000 537 1591 1 chr4B.!!$F1 1054
8 TraesCS1B01G223700 chr4B 602873014 602873972 958 True 693.000000 693 80.570000 695 1632 1 chr4B.!!$R1 937
9 TraesCS1B01G223700 chr4D 477542880 477543846 966 True 701.000000 701 80.648000 695 1632 1 chr4D.!!$R1 937
10 TraesCS1B01G223700 chr4D 477558660 477559506 846 False 664.000000 664 81.714000 645 1476 1 chr4D.!!$F1 831
11 TraesCS1B01G223700 chr5B 508670742 508673326 2584 False 469.500000 490 96.173000 1 291 2 chr5B.!!$F2 290

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
589 2887 0.034337 TAAGTCCAAGCGTCCACACC 59.966 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 9335 0.102663 GCAAGCTACTACCTCCGTCC 59.897 60.0 0.0 0.0 0.0 4.79 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 2343 2.230508 CCATCAATGCAGTTTGCTCAGT 59.769 45.455 2.48 0.00 45.31 3.41
48 2345 2.574450 TCAATGCAGTTTGCTCAGTCA 58.426 42.857 2.48 0.00 45.31 3.41
218 2515 9.956720 CTTTATCTCACCTTGGCATTTTAATAG 57.043 33.333 0.00 0.00 0.00 1.73
254 2551 8.806146 ACCACTCAAGCATAATTTGATAGTTTT 58.194 29.630 0.00 0.00 34.33 2.43
424 2722 1.019673 CAAAGATGGACATGGCTCCG 58.980 55.000 0.00 0.00 32.22 4.63
551 2849 1.141053 GCCCATATTTCCGTGTCCTCT 59.859 52.381 0.00 0.00 0.00 3.69
552 2850 2.838736 CCCATATTTCCGTGTCCTCTG 58.161 52.381 0.00 0.00 0.00 3.35
553 2851 2.213499 CCATATTTCCGTGTCCTCTGC 58.787 52.381 0.00 0.00 0.00 4.26
554 2852 1.860950 CATATTTCCGTGTCCTCTGCG 59.139 52.381 0.00 0.00 0.00 5.18
555 2853 0.459585 TATTTCCGTGTCCTCTGCGC 60.460 55.000 0.00 0.00 0.00 6.09
556 2854 3.756288 TATTTCCGTGTCCTCTGCGCC 62.756 57.143 4.18 0.00 0.00 6.53
578 2876 3.492421 CGTACCGCTAACTAAGTCCAA 57.508 47.619 0.00 0.00 0.00 3.53
579 2877 3.432782 CGTACCGCTAACTAAGTCCAAG 58.567 50.000 0.00 0.00 0.00 3.61
580 2878 2.381725 ACCGCTAACTAAGTCCAAGC 57.618 50.000 0.00 0.00 0.00 4.01
584 2882 2.269172 GCTAACTAAGTCCAAGCGTCC 58.731 52.381 0.00 0.00 0.00 4.79
585 2883 2.353406 GCTAACTAAGTCCAAGCGTCCA 60.353 50.000 0.00 0.00 0.00 4.02
586 2884 2.165319 AACTAAGTCCAAGCGTCCAC 57.835 50.000 0.00 0.00 0.00 4.02
587 2885 1.045407 ACTAAGTCCAAGCGTCCACA 58.955 50.000 0.00 0.00 0.00 4.17
588 2886 1.270147 ACTAAGTCCAAGCGTCCACAC 60.270 52.381 0.00 0.00 0.00 3.82
589 2887 0.034337 TAAGTCCAAGCGTCCACACC 59.966 55.000 0.00 0.00 0.00 4.16
590 2888 2.989055 AAGTCCAAGCGTCCACACCG 62.989 60.000 0.00 0.00 0.00 4.94
610 2908 5.446143 CCGCATGGTTTATTATTGCCTAA 57.554 39.130 0.00 0.00 0.00 2.69
611 2909 5.837437 CCGCATGGTTTATTATTGCCTAAA 58.163 37.500 0.00 0.00 0.00 1.85
612 2910 6.276847 CCGCATGGTTTATTATTGCCTAAAA 58.723 36.000 0.00 0.00 0.00 1.52
613 2911 6.758886 CCGCATGGTTTATTATTGCCTAAAAA 59.241 34.615 0.00 0.00 0.00 1.94
614 2912 7.440856 CCGCATGGTTTATTATTGCCTAAAAAT 59.559 33.333 0.00 0.00 0.00 1.82
615 2913 9.469807 CGCATGGTTTATTATTGCCTAAAAATA 57.530 29.630 0.00 0.00 0.00 1.40
763 3165 5.920840 TCTCCAGAATTGATAAAGCGTATCG 59.079 40.000 6.12 0.00 0.00 2.92
859 3262 0.036732 ATCACACATGGCCACGTCTT 59.963 50.000 8.16 0.00 0.00 3.01
924 3358 6.873997 TCCATATCACCAGGCTATAAATACG 58.126 40.000 0.00 0.00 0.00 3.06
1148 3598 2.543569 CATACCATGGAGGAGGGCA 58.456 57.895 21.47 0.00 41.22 5.36
1149 3599 0.109342 CATACCATGGAGGAGGGCAC 59.891 60.000 21.47 0.00 41.22 5.01
1152 3602 4.864334 CATGGAGGAGGGCACGGC 62.864 72.222 0.00 0.00 0.00 5.68
1209 3670 3.560251 AACCTGAGGGTGTGCGCT 61.560 61.111 9.73 0.00 46.67 5.92
1426 3890 1.620822 GTCTGGTTTCACTTGCCCAT 58.379 50.000 0.00 0.00 0.00 4.00
1435 3900 3.686227 TCACTTGCCCATCCCATTAAT 57.314 42.857 0.00 0.00 0.00 1.40
1512 3990 8.706492 TTTTATTTCATCAAATGTGGATCTGC 57.294 30.769 0.00 0.00 33.95 4.26
1529 4007 0.321564 TGCTCCACTCCCACATTTCG 60.322 55.000 0.00 0.00 0.00 3.46
1544 4024 5.278266 CCACATTTCGATTGTGTAACCAGTT 60.278 40.000 20.95 0.00 42.30 3.16
1553 4043 4.893424 TGTGTAACCAGTTCTGCTTTTC 57.107 40.909 0.00 0.00 34.36 2.29
1653 9097 6.922957 CCAATTGTAGCTTCTTACTTTTTGCA 59.077 34.615 4.43 0.00 0.00 4.08
1675 9119 9.685828 TTGCAAATTTGTACAAAATACTACCTC 57.314 29.630 23.97 7.96 33.56 3.85
1676 9120 9.073475 TGCAAATTTGTACAAAATACTACCTCT 57.927 29.630 23.97 1.69 33.56 3.69
1677 9121 9.341899 GCAAATTTGTACAAAATACTACCTCTG 57.658 33.333 23.97 9.93 33.56 3.35
1680 9124 8.788325 ATTTGTACAAAATACTACCTCTGTCC 57.212 34.615 23.97 0.00 33.56 4.02
1681 9125 7.549147 TTGTACAAAATACTACCTCTGTCCT 57.451 36.000 5.64 0.00 0.00 3.85
1682 9126 6.931838 TGTACAAAATACTACCTCTGTCCTG 58.068 40.000 0.00 0.00 0.00 3.86
1683 9127 5.422214 ACAAAATACTACCTCTGTCCTGG 57.578 43.478 0.00 0.00 0.00 4.45
1684 9128 4.844655 ACAAAATACTACCTCTGTCCTGGT 59.155 41.667 0.00 0.00 40.12 4.00
1685 9129 5.309806 ACAAAATACTACCTCTGTCCTGGTT 59.690 40.000 0.00 0.00 37.74 3.67
1686 9130 6.183361 ACAAAATACTACCTCTGTCCTGGTTT 60.183 38.462 0.00 0.00 37.74 3.27
1687 9131 5.422214 AATACTACCTCTGTCCTGGTTTG 57.578 43.478 0.00 0.00 37.74 2.93
1688 9132 2.690840 ACTACCTCTGTCCTGGTTTGT 58.309 47.619 0.00 0.00 37.74 2.83
1689 9133 3.046374 ACTACCTCTGTCCTGGTTTGTT 58.954 45.455 0.00 0.00 37.74 2.83
1690 9134 4.228824 ACTACCTCTGTCCTGGTTTGTTA 58.771 43.478 0.00 0.00 37.74 2.41
1691 9135 3.771577 ACCTCTGTCCTGGTTTGTTAG 57.228 47.619 0.00 0.00 31.62 2.34
1692 9136 3.046374 ACCTCTGTCCTGGTTTGTTAGT 58.954 45.455 0.00 0.00 31.62 2.24
1693 9137 3.071167 ACCTCTGTCCTGGTTTGTTAGTC 59.929 47.826 0.00 0.00 31.62 2.59
1694 9138 3.557264 CCTCTGTCCTGGTTTGTTAGTCC 60.557 52.174 0.00 0.00 0.00 3.85
1695 9139 3.314693 TCTGTCCTGGTTTGTTAGTCCT 58.685 45.455 0.00 0.00 0.00 3.85
1696 9140 3.071023 TCTGTCCTGGTTTGTTAGTCCTG 59.929 47.826 0.00 0.00 0.00 3.86
1697 9141 2.775384 TGTCCTGGTTTGTTAGTCCTGT 59.225 45.455 0.00 0.00 0.00 4.00
1698 9142 3.201266 TGTCCTGGTTTGTTAGTCCTGTT 59.799 43.478 0.00 0.00 0.00 3.16
1699 9143 4.204799 GTCCTGGTTTGTTAGTCCTGTTT 58.795 43.478 0.00 0.00 0.00 2.83
1700 9144 4.036380 GTCCTGGTTTGTTAGTCCTGTTTG 59.964 45.833 0.00 0.00 0.00 2.93
1701 9145 3.951680 CCTGGTTTGTTAGTCCTGTTTGT 59.048 43.478 0.00 0.00 0.00 2.83
1702 9146 5.104444 TCCTGGTTTGTTAGTCCTGTTTGTA 60.104 40.000 0.00 0.00 0.00 2.41
1703 9147 5.591067 CCTGGTTTGTTAGTCCTGTTTGTAA 59.409 40.000 0.00 0.00 0.00 2.41
1704 9148 6.264518 CCTGGTTTGTTAGTCCTGTTTGTAAT 59.735 38.462 0.00 0.00 0.00 1.89
1705 9149 7.201875 CCTGGTTTGTTAGTCCTGTTTGTAATT 60.202 37.037 0.00 0.00 0.00 1.40
1706 9150 8.068892 TGGTTTGTTAGTCCTGTTTGTAATTT 57.931 30.769 0.00 0.00 0.00 1.82
1707 9151 7.976734 TGGTTTGTTAGTCCTGTTTGTAATTTG 59.023 33.333 0.00 0.00 0.00 2.32
1708 9152 7.977293 GGTTTGTTAGTCCTGTTTGTAATTTGT 59.023 33.333 0.00 0.00 0.00 2.83
1709 9153 8.803799 GTTTGTTAGTCCTGTTTGTAATTTGTG 58.196 33.333 0.00 0.00 0.00 3.33
1710 9154 6.500041 TGTTAGTCCTGTTTGTAATTTGTGC 58.500 36.000 0.00 0.00 0.00 4.57
1711 9155 6.320164 TGTTAGTCCTGTTTGTAATTTGTGCT 59.680 34.615 0.00 0.00 0.00 4.40
1712 9156 7.499563 TGTTAGTCCTGTTTGTAATTTGTGCTA 59.500 33.333 0.00 0.00 0.00 3.49
1713 9157 6.952773 AGTCCTGTTTGTAATTTGTGCTAA 57.047 33.333 0.00 0.00 0.00 3.09
1714 9158 7.341445 AGTCCTGTTTGTAATTTGTGCTAAA 57.659 32.000 0.00 0.00 0.00 1.85
1715 9159 7.951591 AGTCCTGTTTGTAATTTGTGCTAAAT 58.048 30.769 0.00 0.00 0.00 1.40
1716 9160 8.421002 AGTCCTGTTTGTAATTTGTGCTAAATT 58.579 29.630 13.92 13.92 34.55 1.82
1717 9161 9.040939 GTCCTGTTTGTAATTTGTGCTAAATTT 57.959 29.630 14.43 0.00 32.64 1.82
1718 9162 9.606631 TCCTGTTTGTAATTTGTGCTAAATTTT 57.393 25.926 14.43 0.00 32.64 1.82
1719 9163 9.649024 CCTGTTTGTAATTTGTGCTAAATTTTG 57.351 29.630 14.43 0.00 32.64 2.44
1750 9194 9.593134 AAATTTAACTGACAAAATGTTAGTGCA 57.407 25.926 8.44 0.00 44.91 4.57
1751 9195 9.762933 AATTTAACTGACAAAATGTTAGTGCAT 57.237 25.926 8.44 0.37 44.91 3.96
1752 9196 8.572828 TTTAACTGACAAAATGTTAGTGCATG 57.427 30.769 8.44 0.00 44.91 4.06
1753 9197 5.772825 ACTGACAAAATGTTAGTGCATGT 57.227 34.783 7.07 0.00 44.14 3.21
1754 9198 5.522456 ACTGACAAAATGTTAGTGCATGTG 58.478 37.500 7.07 0.00 44.14 3.21
1755 9199 5.299028 ACTGACAAAATGTTAGTGCATGTGA 59.701 36.000 7.07 0.00 44.14 3.58
1756 9200 6.141560 TGACAAAATGTTAGTGCATGTGAA 57.858 33.333 0.00 0.00 0.00 3.18
1757 9201 5.976534 TGACAAAATGTTAGTGCATGTGAAC 59.023 36.000 0.00 0.00 0.00 3.18
1758 9202 5.900425 ACAAAATGTTAGTGCATGTGAACA 58.100 33.333 7.75 7.75 36.32 3.18
1759 9203 6.336566 ACAAAATGTTAGTGCATGTGAACAA 58.663 32.000 8.95 0.00 35.56 2.83
1760 9204 6.815641 ACAAAATGTTAGTGCATGTGAACAAA 59.184 30.769 8.95 0.00 35.56 2.83
1761 9205 7.332926 ACAAAATGTTAGTGCATGTGAACAAAA 59.667 29.630 8.95 0.00 35.56 2.44
1762 9206 7.840342 AAATGTTAGTGCATGTGAACAAAAA 57.160 28.000 8.95 0.00 35.56 1.94
1763 9207 8.436046 AAATGTTAGTGCATGTGAACAAAAAT 57.564 26.923 8.95 0.00 35.56 1.82
1764 9208 8.436046 AATGTTAGTGCATGTGAACAAAAATT 57.564 26.923 8.95 0.00 35.56 1.82
1765 9209 9.539825 AATGTTAGTGCATGTGAACAAAAATTA 57.460 25.926 8.95 0.00 35.56 1.40
1766 9210 9.709495 ATGTTAGTGCATGTGAACAAAAATTAT 57.291 25.926 8.95 0.00 35.56 1.28
1770 9214 8.619146 AGTGCATGTGAACAAAAATTATATCG 57.381 30.769 0.00 0.00 0.00 2.92
1771 9215 8.243426 AGTGCATGTGAACAAAAATTATATCGT 58.757 29.630 0.00 0.00 0.00 3.73
1772 9216 8.859156 GTGCATGTGAACAAAAATTATATCGTT 58.141 29.630 0.00 0.00 0.00 3.85
1835 9279 7.783090 TTTGTGACATGCATAAACATTTTGT 57.217 28.000 0.00 0.00 33.40 2.83
1836 9280 7.783090 TTGTGACATGCATAAACATTTTGTT 57.217 28.000 0.00 0.00 43.41 2.83
1837 9281 8.877808 TTGTGACATGCATAAACATTTTGTTA 57.122 26.923 0.00 0.00 40.14 2.41
1838 9282 8.518151 TGTGACATGCATAAACATTTTGTTAG 57.482 30.769 0.00 0.00 40.14 2.34
1839 9283 8.140628 TGTGACATGCATAAACATTTTGTTAGT 58.859 29.630 0.00 0.00 40.14 2.24
1840 9284 8.977505 GTGACATGCATAAACATTTTGTTAGTT 58.022 29.630 0.00 0.00 40.14 2.24
1880 9324 9.822185 AAATTTGGCAAAGATTATAATGAGGAC 57.178 29.630 18.61 0.00 0.00 3.85
1881 9325 6.959639 TTGGCAAAGATTATAATGAGGACC 57.040 37.500 1.78 0.07 0.00 4.46
1882 9326 6.012337 TGGCAAAGATTATAATGAGGACCA 57.988 37.500 1.78 2.69 0.00 4.02
1883 9327 6.430864 TGGCAAAGATTATAATGAGGACCAA 58.569 36.000 1.78 0.00 0.00 3.67
1884 9328 7.068702 TGGCAAAGATTATAATGAGGACCAAT 58.931 34.615 1.78 0.00 0.00 3.16
1885 9329 8.224025 TGGCAAAGATTATAATGAGGACCAATA 58.776 33.333 1.78 0.00 0.00 1.90
1886 9330 9.077885 GGCAAAGATTATAATGAGGACCAATAA 57.922 33.333 1.78 0.00 0.00 1.40
1891 9335 9.799106 AGATTATAATGAGGACCAATAAACCAG 57.201 33.333 1.78 0.00 0.00 4.00
1892 9336 8.940397 ATTATAATGAGGACCAATAAACCAGG 57.060 34.615 0.00 0.00 0.00 4.45
1893 9337 4.946160 AATGAGGACCAATAAACCAGGA 57.054 40.909 0.00 0.00 0.00 3.86
1894 9338 3.713826 TGAGGACCAATAAACCAGGAC 57.286 47.619 0.00 0.00 0.00 3.85
1895 9339 2.027561 TGAGGACCAATAAACCAGGACG 60.028 50.000 0.00 0.00 0.00 4.79
1896 9340 1.280998 AGGACCAATAAACCAGGACGG 59.719 52.381 0.00 0.00 42.50 4.79
1897 9341 1.279846 GGACCAATAAACCAGGACGGA 59.720 52.381 0.00 0.00 38.63 4.69
1898 9342 2.629051 GACCAATAAACCAGGACGGAG 58.371 52.381 0.00 0.00 38.63 4.63
1899 9343 1.280998 ACCAATAAACCAGGACGGAGG 59.719 52.381 0.00 0.00 38.63 4.30
1900 9344 1.280998 CCAATAAACCAGGACGGAGGT 59.719 52.381 0.00 0.00 40.61 3.85
1901 9345 2.502538 CCAATAAACCAGGACGGAGGTA 59.497 50.000 0.00 0.00 37.07 3.08
1902 9346 3.431766 CCAATAAACCAGGACGGAGGTAG 60.432 52.174 0.00 0.00 37.07 3.18
1934 9615 4.221482 AGCTTTTTCCAGAAATGATCCACC 59.779 41.667 0.00 0.00 0.00 4.61
1970 9652 9.601810 ATTATTAACAAAGAGGGAAAAAGGAGT 57.398 29.630 0.00 0.00 0.00 3.85
1972 9654 3.566351 ACAAAGAGGGAAAAAGGAGTGG 58.434 45.455 0.00 0.00 0.00 4.00
2010 9696 5.105957 TGCAACATCACCATACACCATTAAC 60.106 40.000 0.00 0.00 0.00 2.01
2164 10546 4.695217 AACTTCGAGCAGTGTTTTCAAA 57.305 36.364 0.00 0.00 0.00 2.69
2270 10661 2.247358 CCCAAAGTGTGCCACCTAATT 58.753 47.619 0.00 0.00 34.49 1.40
2306 10697 4.039703 CACATGTTGTTGAGTTTGAGCAG 58.960 43.478 0.00 0.00 0.00 4.24
2392 10784 3.788333 CCAATTTAGGCCAGTCATGTG 57.212 47.619 5.01 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.824852 TGCCGAAGCTAGACTGATGAA 59.175 47.619 0.00 0.00 40.80 2.57
2 3 1.537776 CCTGCCGAAGCTAGACTGATG 60.538 57.143 0.00 0.00 40.80 3.07
3 4 0.749649 CCTGCCGAAGCTAGACTGAT 59.250 55.000 0.00 0.00 40.80 2.90
4 5 1.323271 CCCTGCCGAAGCTAGACTGA 61.323 60.000 0.00 0.00 40.80 3.41
16 2313 2.484062 GCATTGATGGACCCTGCCG 61.484 63.158 0.00 0.00 0.00 5.69
193 2490 8.413229 GCTATTAAAATGCCAAGGTGAGATAAA 58.587 33.333 0.00 0.00 0.00 1.40
218 2515 3.808728 TGCTTGAGTGGTAGATAATGGC 58.191 45.455 0.00 0.00 0.00 4.40
290 2587 6.795593 GTGCTCATCATTGTCATTTCGATATG 59.204 38.462 9.33 9.33 0.00 1.78
424 2722 2.424956 GGAGACCATGAATGAACAAGCC 59.575 50.000 0.00 0.00 0.00 4.35
559 2857 3.185330 GCTTGGACTTAGTTAGCGGTAC 58.815 50.000 0.00 0.00 0.00 3.34
560 2858 3.515330 GCTTGGACTTAGTTAGCGGTA 57.485 47.619 0.00 0.00 0.00 4.02
561 2859 2.381725 GCTTGGACTTAGTTAGCGGT 57.618 50.000 0.00 0.00 0.00 5.68
564 2862 2.269172 GGACGCTTGGACTTAGTTAGC 58.731 52.381 5.42 5.42 0.00 3.09
565 2863 3.251571 GTGGACGCTTGGACTTAGTTAG 58.748 50.000 0.00 0.00 0.00 2.34
566 2864 2.629137 TGTGGACGCTTGGACTTAGTTA 59.371 45.455 0.00 0.00 0.00 2.24
567 2865 1.414919 TGTGGACGCTTGGACTTAGTT 59.585 47.619 0.00 0.00 0.00 2.24
568 2866 1.045407 TGTGGACGCTTGGACTTAGT 58.955 50.000 0.00 0.00 0.00 2.24
569 2867 1.429463 GTGTGGACGCTTGGACTTAG 58.571 55.000 0.00 0.00 0.00 2.18
570 2868 0.034337 GGTGTGGACGCTTGGACTTA 59.966 55.000 0.00 0.00 0.00 2.24
571 2869 1.227853 GGTGTGGACGCTTGGACTT 60.228 57.895 0.00 0.00 0.00 3.01
572 2870 2.426023 GGTGTGGACGCTTGGACT 59.574 61.111 0.00 0.00 0.00 3.85
573 2871 3.041940 CGGTGTGGACGCTTGGAC 61.042 66.667 0.00 0.00 0.00 4.02
588 2886 5.446143 TTAGGCAATAATAAACCATGCGG 57.554 39.130 0.00 0.00 37.88 5.69
589 2887 7.763172 TTTTTAGGCAATAATAAACCATGCG 57.237 32.000 0.00 0.00 37.88 4.73
598 2896 9.586732 AGCATCAGGTATTTTTAGGCAATAATA 57.413 29.630 0.00 0.00 0.00 0.98
599 2897 8.482852 AGCATCAGGTATTTTTAGGCAATAAT 57.517 30.769 0.00 0.00 0.00 1.28
600 2898 7.896383 AGCATCAGGTATTTTTAGGCAATAA 57.104 32.000 0.00 0.00 0.00 1.40
601 2899 7.896383 AAGCATCAGGTATTTTTAGGCAATA 57.104 32.000 0.00 0.00 0.00 1.90
602 2900 6.796785 AAGCATCAGGTATTTTTAGGCAAT 57.203 33.333 0.00 0.00 0.00 3.56
603 2901 6.437162 AGAAAGCATCAGGTATTTTTAGGCAA 59.563 34.615 0.00 0.00 0.00 4.52
604 2902 5.951747 AGAAAGCATCAGGTATTTTTAGGCA 59.048 36.000 0.00 0.00 0.00 4.75
605 2903 6.095440 TGAGAAAGCATCAGGTATTTTTAGGC 59.905 38.462 0.00 0.00 0.00 3.93
606 2904 7.630242 TGAGAAAGCATCAGGTATTTTTAGG 57.370 36.000 0.00 0.00 0.00 2.69
607 2905 8.734386 AGTTGAGAAAGCATCAGGTATTTTTAG 58.266 33.333 0.00 0.00 0.00 1.85
608 2906 8.635765 AGTTGAGAAAGCATCAGGTATTTTTA 57.364 30.769 0.00 0.00 0.00 1.52
609 2907 7.530426 AGTTGAGAAAGCATCAGGTATTTTT 57.470 32.000 0.00 0.00 0.00 1.94
610 2908 7.373493 CAAGTTGAGAAAGCATCAGGTATTTT 58.627 34.615 0.00 0.00 0.00 1.82
611 2909 6.571150 GCAAGTTGAGAAAGCATCAGGTATTT 60.571 38.462 7.16 0.00 0.00 1.40
612 2910 5.105997 GCAAGTTGAGAAAGCATCAGGTATT 60.106 40.000 7.16 0.00 0.00 1.89
613 2911 4.397417 GCAAGTTGAGAAAGCATCAGGTAT 59.603 41.667 7.16 0.00 0.00 2.73
614 2912 3.753272 GCAAGTTGAGAAAGCATCAGGTA 59.247 43.478 7.16 0.00 0.00 3.08
615 2913 2.555757 GCAAGTTGAGAAAGCATCAGGT 59.444 45.455 7.16 0.00 0.00 4.00
616 2914 2.818432 AGCAAGTTGAGAAAGCATCAGG 59.182 45.455 7.16 0.00 0.00 3.86
617 2915 4.500603 AAGCAAGTTGAGAAAGCATCAG 57.499 40.909 7.16 0.00 0.00 2.90
701 3084 2.230992 GCAACACCCTTGCATGTTCATA 59.769 45.455 0.42 0.00 44.34 2.15
763 3165 8.940768 AGAGAGATAAGACAAGATTTAAGCAC 57.059 34.615 0.00 0.00 0.00 4.40
793 3196 5.817816 GGTTGTCCTCTCGATGTATCATTTT 59.182 40.000 0.00 0.00 0.00 1.82
924 3358 2.166829 TGAGAGCTTGGAGAGAGTGTC 58.833 52.381 0.00 0.00 0.00 3.67
1179 3638 2.146342 CTCAGGTTGAGCACGTTGATT 58.854 47.619 0.00 0.00 37.72 2.57
1209 3670 3.376078 AGCCCGCCGAGAACGTTA 61.376 61.111 0.00 0.00 37.88 3.18
1349 3810 3.357079 CCACAGGCACGTTGAGGC 61.357 66.667 0.00 0.00 0.00 4.70
1435 3900 0.250124 CCCAAGCAACAGTACGTCCA 60.250 55.000 0.00 0.00 0.00 4.02
1450 3923 1.403679 CAAATCTTATTCGGCGCCCAA 59.596 47.619 23.46 16.63 0.00 4.12
1512 3990 2.679837 CAATCGAAATGTGGGAGTGGAG 59.320 50.000 0.00 0.00 0.00 3.86
1544 4024 3.883830 TTGTTTGCCAAGAAAAGCAGA 57.116 38.095 0.00 0.00 40.73 4.26
1667 9111 3.853207 ACAAACCAGGACAGAGGTAGTA 58.147 45.455 0.00 0.00 37.07 1.82
1668 9112 2.690840 ACAAACCAGGACAGAGGTAGT 58.309 47.619 0.00 0.00 37.07 2.73
1669 9113 3.771577 AACAAACCAGGACAGAGGTAG 57.228 47.619 0.00 0.00 37.07 3.18
1670 9114 4.228824 ACTAACAAACCAGGACAGAGGTA 58.771 43.478 0.00 0.00 37.07 3.08
1671 9115 3.046374 ACTAACAAACCAGGACAGAGGT 58.954 45.455 0.00 0.00 40.61 3.85
1672 9116 3.557264 GGACTAACAAACCAGGACAGAGG 60.557 52.174 0.00 0.00 0.00 3.69
1673 9117 3.325135 AGGACTAACAAACCAGGACAGAG 59.675 47.826 0.00 0.00 0.00 3.35
1674 9118 3.071023 CAGGACTAACAAACCAGGACAGA 59.929 47.826 0.00 0.00 0.00 3.41
1675 9119 3.181454 ACAGGACTAACAAACCAGGACAG 60.181 47.826 0.00 0.00 0.00 3.51
1676 9120 2.775384 ACAGGACTAACAAACCAGGACA 59.225 45.455 0.00 0.00 0.00 4.02
1677 9121 3.487120 ACAGGACTAACAAACCAGGAC 57.513 47.619 0.00 0.00 0.00 3.85
1678 9122 4.204012 CAAACAGGACTAACAAACCAGGA 58.796 43.478 0.00 0.00 0.00 3.86
1679 9123 3.951680 ACAAACAGGACTAACAAACCAGG 59.048 43.478 0.00 0.00 0.00 4.45
1680 9124 6.687081 TTACAAACAGGACTAACAAACCAG 57.313 37.500 0.00 0.00 0.00 4.00
1681 9125 7.648039 AATTACAAACAGGACTAACAAACCA 57.352 32.000 0.00 0.00 0.00 3.67
1682 9126 7.977293 ACAAATTACAAACAGGACTAACAAACC 59.023 33.333 0.00 0.00 0.00 3.27
1683 9127 8.803799 CACAAATTACAAACAGGACTAACAAAC 58.196 33.333 0.00 0.00 0.00 2.93
1684 9128 7.489757 GCACAAATTACAAACAGGACTAACAAA 59.510 33.333 0.00 0.00 0.00 2.83
1685 9129 6.975772 GCACAAATTACAAACAGGACTAACAA 59.024 34.615 0.00 0.00 0.00 2.83
1686 9130 6.320164 AGCACAAATTACAAACAGGACTAACA 59.680 34.615 0.00 0.00 0.00 2.41
1687 9131 6.735130 AGCACAAATTACAAACAGGACTAAC 58.265 36.000 0.00 0.00 0.00 2.34
1688 9132 6.952773 AGCACAAATTACAAACAGGACTAA 57.047 33.333 0.00 0.00 0.00 2.24
1689 9133 8.453238 TTTAGCACAAATTACAAACAGGACTA 57.547 30.769 0.00 0.00 0.00 2.59
1690 9134 6.952773 TTAGCACAAATTACAAACAGGACT 57.047 33.333 0.00 0.00 0.00 3.85
1691 9135 8.587952 AATTTAGCACAAATTACAAACAGGAC 57.412 30.769 7.13 0.00 0.00 3.85
1692 9136 9.606631 AAAATTTAGCACAAATTACAAACAGGA 57.393 25.926 8.84 0.00 30.38 3.86
1693 9137 9.649024 CAAAATTTAGCACAAATTACAAACAGG 57.351 29.630 8.84 0.00 30.38 4.00
1724 9168 9.593134 TGCACTAACATTTTGTCAGTTAAATTT 57.407 25.926 0.00 0.00 22.66 1.82
1725 9169 9.762933 ATGCACTAACATTTTGTCAGTTAAATT 57.237 25.926 0.00 0.00 22.66 1.82
1726 9170 9.195411 CATGCACTAACATTTTGTCAGTTAAAT 57.805 29.630 0.00 0.00 22.66 1.40
1727 9171 8.194104 ACATGCACTAACATTTTGTCAGTTAAA 58.806 29.630 0.00 0.00 22.66 1.52
1728 9172 7.647318 CACATGCACTAACATTTTGTCAGTTAA 59.353 33.333 0.00 0.00 22.66 2.01
1729 9173 7.012799 TCACATGCACTAACATTTTGTCAGTTA 59.987 33.333 0.00 0.00 22.66 2.24
1730 9174 5.978919 CACATGCACTAACATTTTGTCAGTT 59.021 36.000 0.00 0.00 22.66 3.16
1731 9175 5.299028 TCACATGCACTAACATTTTGTCAGT 59.701 36.000 0.00 0.00 26.10 3.41
1732 9176 5.761003 TCACATGCACTAACATTTTGTCAG 58.239 37.500 0.00 0.00 0.00 3.51
1733 9177 5.764487 TCACATGCACTAACATTTTGTCA 57.236 34.783 0.00 0.00 0.00 3.58
1734 9178 5.976534 TGTTCACATGCACTAACATTTTGTC 59.023 36.000 0.00 0.00 0.00 3.18
1735 9179 5.900425 TGTTCACATGCACTAACATTTTGT 58.100 33.333 0.00 0.00 0.00 2.83
1736 9180 6.825284 TTGTTCACATGCACTAACATTTTG 57.175 33.333 0.00 0.00 32.31 2.44
1737 9181 7.840342 TTTTGTTCACATGCACTAACATTTT 57.160 28.000 0.00 0.00 32.31 1.82
1738 9182 7.840342 TTTTTGTTCACATGCACTAACATTT 57.160 28.000 0.00 0.00 32.31 2.32
1739 9183 8.436046 AATTTTTGTTCACATGCACTAACATT 57.564 26.923 0.00 0.00 32.31 2.71
1740 9184 9.709495 ATAATTTTTGTTCACATGCACTAACAT 57.291 25.926 0.00 0.00 32.31 2.71
1744 9188 9.715123 CGATATAATTTTTGTTCACATGCACTA 57.285 29.630 0.00 0.00 0.00 2.74
1745 9189 8.243426 ACGATATAATTTTTGTTCACATGCACT 58.757 29.630 0.00 0.00 0.00 4.40
1746 9190 8.393395 ACGATATAATTTTTGTTCACATGCAC 57.607 30.769 0.00 0.00 0.00 4.57
1747 9191 8.978564 AACGATATAATTTTTGTTCACATGCA 57.021 26.923 0.00 0.00 0.00 3.96
1809 9253 8.671921 ACAAAATGTTTATGCATGTCACAAAAA 58.328 25.926 10.16 0.00 0.00 1.94
1810 9254 8.206325 ACAAAATGTTTATGCATGTCACAAAA 57.794 26.923 10.16 0.00 0.00 2.44
1811 9255 7.783090 ACAAAATGTTTATGCATGTCACAAA 57.217 28.000 10.16 0.00 0.00 2.83
1812 9256 7.783090 AACAAAATGTTTATGCATGTCACAA 57.217 28.000 10.16 0.00 37.26 3.33
1813 9257 8.140628 ACTAACAAAATGTTTATGCATGTCACA 58.859 29.630 10.16 9.55 41.45 3.58
1814 9258 8.519492 ACTAACAAAATGTTTATGCATGTCAC 57.481 30.769 10.16 3.61 41.45 3.67
1854 9298 9.822185 GTCCTCATTATAATCTTTGCCAAATTT 57.178 29.630 0.00 0.00 0.00 1.82
1855 9299 8.424133 GGTCCTCATTATAATCTTTGCCAAATT 58.576 33.333 0.00 0.00 0.00 1.82
1856 9300 7.564660 TGGTCCTCATTATAATCTTTGCCAAAT 59.435 33.333 0.00 0.00 0.00 2.32
1857 9301 6.894654 TGGTCCTCATTATAATCTTTGCCAAA 59.105 34.615 0.00 0.00 0.00 3.28
1858 9302 6.430864 TGGTCCTCATTATAATCTTTGCCAA 58.569 36.000 0.00 0.00 0.00 4.52
1859 9303 6.012337 TGGTCCTCATTATAATCTTTGCCA 57.988 37.500 0.00 0.00 0.00 4.92
1860 9304 6.959639 TTGGTCCTCATTATAATCTTTGCC 57.040 37.500 0.00 0.00 0.00 4.52
1865 9309 9.799106 CTGGTTTATTGGTCCTCATTATAATCT 57.201 33.333 0.00 0.00 0.00 2.40
1866 9310 9.014297 CCTGGTTTATTGGTCCTCATTATAATC 57.986 37.037 0.00 0.00 0.00 1.75
1867 9311 8.732854 TCCTGGTTTATTGGTCCTCATTATAAT 58.267 33.333 0.00 0.00 0.00 1.28
1868 9312 7.996644 GTCCTGGTTTATTGGTCCTCATTATAA 59.003 37.037 0.00 0.00 0.00 0.98
1869 9313 7.514721 GTCCTGGTTTATTGGTCCTCATTATA 58.485 38.462 0.00 0.00 0.00 0.98
1870 9314 6.365520 GTCCTGGTTTATTGGTCCTCATTAT 58.634 40.000 0.00 0.00 0.00 1.28
1871 9315 5.628200 CGTCCTGGTTTATTGGTCCTCATTA 60.628 44.000 0.00 0.00 0.00 1.90
1872 9316 4.600062 GTCCTGGTTTATTGGTCCTCATT 58.400 43.478 0.00 0.00 0.00 2.57
1873 9317 3.370527 CGTCCTGGTTTATTGGTCCTCAT 60.371 47.826 0.00 0.00 0.00 2.90
1874 9318 2.027561 CGTCCTGGTTTATTGGTCCTCA 60.028 50.000 0.00 0.00 0.00 3.86
1875 9319 2.629051 CGTCCTGGTTTATTGGTCCTC 58.371 52.381 0.00 0.00 0.00 3.71
1876 9320 1.280998 CCGTCCTGGTTTATTGGTCCT 59.719 52.381 0.00 0.00 0.00 3.85
1877 9321 1.279846 TCCGTCCTGGTTTATTGGTCC 59.720 52.381 0.00 0.00 39.52 4.46
1878 9322 2.629051 CTCCGTCCTGGTTTATTGGTC 58.371 52.381 0.00 0.00 39.52 4.02
1879 9323 1.280998 CCTCCGTCCTGGTTTATTGGT 59.719 52.381 0.00 0.00 39.52 3.67
1880 9324 1.280998 ACCTCCGTCCTGGTTTATTGG 59.719 52.381 0.00 0.00 39.52 3.16
1881 9325 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
1882 9326 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
1883 9327 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
1884 9328 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
1885 9329 2.454538 CTACTACCTCCGTCCTGGTTT 58.545 52.381 0.00 0.00 39.52 3.27
1886 9330 1.959028 GCTACTACCTCCGTCCTGGTT 60.959 57.143 0.00 0.00 39.52 3.67
1887 9331 0.395448 GCTACTACCTCCGTCCTGGT 60.395 60.000 0.00 0.00 39.52 4.00
1888 9332 0.106619 AGCTACTACCTCCGTCCTGG 60.107 60.000 0.00 0.00 40.09 4.45
1889 9333 1.405821 CAAGCTACTACCTCCGTCCTG 59.594 57.143 0.00 0.00 0.00 3.86
1890 9334 1.765230 CAAGCTACTACCTCCGTCCT 58.235 55.000 0.00 0.00 0.00 3.85
1891 9335 0.102663 GCAAGCTACTACCTCCGTCC 59.897 60.000 0.00 0.00 0.00 4.79
1892 9336 0.815734 TGCAAGCTACTACCTCCGTC 59.184 55.000 0.00 0.00 0.00 4.79
1893 9337 0.818296 CTGCAAGCTACTACCTCCGT 59.182 55.000 0.00 0.00 0.00 4.69
1894 9338 3.650409 CTGCAAGCTACTACCTCCG 57.350 57.895 0.00 0.00 0.00 4.63
1946 9627 7.450323 CCACTCCTTTTTCCCTCTTTGTTAATA 59.550 37.037 0.00 0.00 0.00 0.98
1970 9652 0.393132 TGCAACTGTTCCGTTGACCA 60.393 50.000 10.37 0.00 45.40 4.02
1972 9654 1.131504 TGTTGCAACTGTTCCGTTGAC 59.868 47.619 28.61 0.00 45.40 3.18
2031 9717 0.467290 GTTGTTGGAGCACCTTCCCA 60.467 55.000 0.71 0.00 36.35 4.37
2121 10503 8.480133 AGTTTACTTAGACTTCTCTTCAAGGA 57.520 34.615 0.00 0.00 0.00 3.36
2164 10546 3.862845 GGCATTCACGTGTTGTTTTCTTT 59.137 39.130 16.51 0.00 0.00 2.52
2270 10661 3.558931 ACATGTGTCCACTTGACTTCA 57.441 42.857 17.19 2.36 44.75 3.02
2374 10766 2.624029 CCCCACATGACTGGCCTAAATT 60.624 50.000 3.32 0.00 0.00 1.82
2392 10784 1.225704 CCCTTGTCAGAGATGCCCC 59.774 63.158 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.