Multiple sequence alignment - TraesCS7A01G025400

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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 TraesCS7A01G025400 chr7A 100.000 2459 0 0 1 2459 10082411 10084869 0.000000e+00 4542.0
1 TraesCS7A01G025400 chr7A 80.579 242 37 10 14 250 211154515 211154279 6.990000e-41 178.0
2 TraesCS7A01G025400 chr4A 90.580 1242 72 14 684 1906 727730198 727728983 0.000000e+00 1604.0
3 TraesCS7A01G025400 chr4A 88.251 383 30 8 4 385 727730668 727730300 6.240000e-121 444.0
4 TraesCS7A01G025400 chr4A 88.406 207 14 9 1952 2158 727728988 727728792 8.790000e-60 241.0
5 TraesCS7A01G025400 chr4A 88.125 160 18 1 2301 2459 727728735 727728576 3.230000e-44 189.0
6 TraesCS7A01G025400 chr4A 86.364 66 8 1 664 729 727730290 727730226 1.220000e-08 71.3
7 TraesCS7A01G025400 chrUn 92.100 924 41 9 684 1594 398518801 398517897 0.000000e+00 1273.0
8 TraesCS7A01G025400 chrUn 88.251 383 30 8 4 385 398519271 398518903 6.240000e-121 444.0
9 TraesCS7A01G025400 chrUn 86.018 329 30 8 1584 1906 325405078 325405396 3.030000e-89 339.0
10 TraesCS7A01G025400 chrUn 88.406 207 14 9 1952 2158 325405391 325405587 8.790000e-60 241.0
11 TraesCS7A01G025400 chrUn 88.125 160 18 1 2301 2459 325405644 325405803 3.230000e-44 189.0
12 TraesCS7A01G025400 chrUn 86.364 66 8 1 664 729 398518893 398518829 1.220000e-08 71.3
13 TraesCS7A01G025400 chr7D 96.215 502 14 5 4 502 10840101 10840600 0.000000e+00 817.0
14 TraesCS7A01G025400 chr7D 92.373 472 18 8 680 1138 10840786 10841252 0.000000e+00 656.0
15 TraesCS7A01G025400 chr7D 89.276 373 21 5 1324 1694 10841415 10841770 1.340000e-122 449.0
16 TraesCS7A01G025400 chr7D 88.012 342 36 5 1535 1873 10879848 10880187 1.370000e-107 399.0
17 TraesCS7A01G025400 chr7D 83.784 407 34 18 704 1091 10877236 10877629 8.360000e-95 357.0
18 TraesCS7A01G025400 chr7D 89.151 212 22 1 1948 2158 10880720 10880931 1.880000e-66 263.0
19 TraesCS7A01G025400 chr7D 97.744 133 2 1 502 634 10840647 10840778 6.840000e-56 228.0
20 TraesCS7A01G025400 chr7D 91.111 135 11 1 2316 2449 10881003 10881137 5.400000e-42 182.0
21 TraesCS7A01G025400 chr7D 80.000 260 36 10 4 252 78508777 78508523 6.990000e-41 178.0
22 TraesCS7A01G025400 chr6B 79.557 406 55 15 34 417 405862813 405862414 5.210000e-67 265.0
23 TraesCS7A01G025400 chr6B 77.368 190 30 8 1852 2035 638250716 638250534 1.560000e-17 100.0
24 TraesCS7A01G025400 chr1A 76.818 440 55 25 4 417 80282332 80282750 1.150000e-48 204.0
25 TraesCS7A01G025400 chr3D 79.321 324 35 17 15 333 6992684 6992388 5.360000e-47 198.0
26 TraesCS7A01G025400 chr3D 75.945 291 55 9 1843 2120 560119600 560119888 4.270000e-28 135.0
27 TraesCS7A01G025400 chr3D 80.734 109 10 3 323 420 6992378 6992270 9.430000e-10 75.0
28 TraesCS7A01G025400 chr3B 79.470 302 35 12 15 313 8506847 8506570 3.230000e-44 189.0
29 TraesCS7A01G025400 chr3B 87.179 78 7 3 324 398 816059444 816059367 4.360000e-13 86.1
30 TraesCS7A01G025400 chr4D 75.515 437 71 19 14 417 145378606 145379039 5.400000e-42 182.0
31 TraesCS7A01G025400 chr4D 74.074 243 47 11 1864 2102 501046183 501045953 4.360000e-13 86.1
32 TraesCS7A01G025400 chr1D 75.728 412 68 23 14 398 80684935 80684529 6.990000e-41 178.0
33 TraesCS7A01G025400 chr2D 78.388 273 44 13 1862 2126 495397582 495397317 1.960000e-36 163.0
34 TraesCS7A01G025400 chr2D 100.000 30 0 0 1846 1875 14887566 14887537 3.420000e-04 56.5
35 TraesCS7A01G025400 chr4B 78.571 238 44 7 18 250 413506274 413506509 1.520000e-32 150.0
36 TraesCS7A01G025400 chr4B 100.000 29 0 0 389 417 428195812 428195840 1.000000e-03 54.7
37 TraesCS7A01G025400 chr2B 77.656 273 32 14 44 313 677293812 677293566 3.300000e-29 139.0
38 TraesCS7A01G025400 chr2B 82.787 122 8 4 309 419 579978799 579978680 2.010000e-16 97.1
39 TraesCS7A01G025400 chr2B 83.810 105 6 3 324 417 54561634 54561738 3.370000e-14 89.8
40 TraesCS7A01G025400 chr6D 78.836 189 30 5 1852 2035 423389871 423389688 4.300000e-23 119.0
41 TraesCS7A01G025400 chr6A 76.410 195 29 9 1852 2035 566891978 566891790 3.370000e-14 89.8


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 TraesCS7A01G025400 chr7A 10082411 10084869 2458 False 4542.000000 4542 100.000000 1 2459 1 chr7A.!!$F1 2458
1 TraesCS7A01G025400 chr4A 727728576 727730668 2092 True 509.860000 1604 88.345200 4 2459 5 chr4A.!!$R1 2455
2 TraesCS7A01G025400 chrUn 398517897 398519271 1374 True 596.100000 1273 88.905000 4 1594 3 chrUn.!!$R1 1590
3 TraesCS7A01G025400 chrUn 325405078 325405803 725 False 256.333333 339 87.516333 1584 2459 3 chrUn.!!$F1 875
4 TraesCS7A01G025400 chr7D 10840101 10841770 1669 False 537.500000 817 93.902000 4 1694 4 chr7D.!!$F1 1690
5 TraesCS7A01G025400 chr7D 10877236 10881137 3901 False 300.250000 399 88.014500 704 2449 4 chr7D.!!$F2 1745

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
690 742 0.167908 CACACACACACACACACACC 59.832 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
1912 3863 0.108019 GGTATGGGTAGGGGAAAGCG 59.892 60.0 0.0 0.0 0.0 4.68 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
81 82 8.189460 CGTATAGTAGGAGCAAAAAGTAGAACT 58.811 37.037 0.00 0.00 0.00 3.01
96 97 6.182507 AGTAGAACTGGTTGGTTATGTTCA 57.817 37.500 0.00 0.00 39.33 3.18
230 232 6.376299 AGCATGACACTTAAATGACATCACAT 59.624 34.615 0.00 0.00 33.56 3.21
310 313 2.925563 GCCACATACAAAAGCAATCAGC 59.074 45.455 0.00 0.00 46.19 4.26
365 368 2.729194 ACCAACCAAAGTGCACTACAA 58.271 42.857 22.01 0.00 0.00 2.41
494 499 5.636903 AGCCACCAATGACTAGTAATCAT 57.363 39.130 0.00 0.00 38.47 2.45
595 647 6.044682 GCACCATTTTCCCTCTAATTCAATG 58.955 40.000 0.00 0.00 0.00 2.82
601 653 3.620488 TCCCTCTAATTCAATGTGCACC 58.380 45.455 15.69 0.00 0.00 5.01
640 692 3.543680 CGAAGGAGTCTCTCTCTCTCT 57.456 52.381 0.00 0.00 42.40 3.10
641 693 3.458189 CGAAGGAGTCTCTCTCTCTCTC 58.542 54.545 0.00 0.00 42.40 3.20
642 694 3.133003 CGAAGGAGTCTCTCTCTCTCTCT 59.867 52.174 0.00 0.00 42.40 3.10
643 695 4.698575 GAAGGAGTCTCTCTCTCTCTCTC 58.301 52.174 0.00 0.00 42.40 3.20
644 696 4.000928 AGGAGTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 42.40 3.10
645 697 3.964031 AGGAGTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 42.40 3.20
646 698 3.964031 GGAGTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 42.40 3.10
647 699 4.038642 GGAGTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 42.40 3.20
648 700 4.877773 AGTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
649 701 4.892934 AGTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
650 702 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
651 703 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
652 704 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
653 705 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
654 706 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
655 707 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
661 713 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
665 717 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
666 718 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
678 730 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
679 731 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
680 732 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
681 733 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
682 734 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
683 735 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
684 736 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
685 737 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
686 738 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
687 739 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
688 740 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
689 741 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
690 742 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
691 743 0.250510 ACACACACACACACACACCA 60.251 50.000 0.00 0.00 0.00 4.17
851 903 8.753133 TCGACATGATCTCCATATTAATTAGCT 58.247 33.333 0.00 0.00 33.31 3.32
857 909 7.547019 TGATCTCCATATTAATTAGCTTGCTCG 59.453 37.037 0.00 0.00 0.00 5.03
964 1034 2.804986 TGCCATTAGCTCACAATCCA 57.195 45.000 0.00 0.00 44.23 3.41
987 1057 1.895798 TCTCAGGTAGCCAGTTCACTG 59.104 52.381 0.00 0.00 43.40 3.66
1008 1078 3.790437 CGCCCCAGCATGAGAGGT 61.790 66.667 0.00 0.00 39.69 3.85
1074 1144 5.308825 GGATACCTTGCAGTTATAGCACAT 58.691 41.667 0.00 0.00 42.54 3.21
1084 1154 8.499403 TGCAGTTATAGCACATTGTATGTAAA 57.501 30.769 0.00 0.00 42.70 2.01
1213 1435 0.762418 TCGTTTGGAGGCTGGAAGAA 59.238 50.000 0.00 0.00 34.07 2.52
1214 1436 1.160137 CGTTTGGAGGCTGGAAGAAG 58.840 55.000 0.00 0.00 34.07 2.85
1215 1437 1.539157 GTTTGGAGGCTGGAAGAAGG 58.461 55.000 0.00 0.00 34.07 3.46
1302 1901 2.803956 GCTTAACCTACGTTTCTGCACA 59.196 45.455 0.00 0.00 33.17 4.57
1317 1916 2.016961 CACAGGCCATGTATGTCGC 58.983 57.895 5.01 0.00 41.41 5.19
1330 1929 3.827898 GTCGCCACCCTCCGAGAG 61.828 72.222 0.00 0.00 33.71 3.20
1331 1930 4.361971 TCGCCACCCTCCGAGAGT 62.362 66.667 0.00 0.00 0.00 3.24
1550 3489 9.708222 CTGATACACAATATCTTTGCTAACAAC 57.292 33.333 0.00 0.00 34.87 3.32
1587 3526 4.209080 CCGTGAGCCATTGTTTTTCTTTTC 59.791 41.667 0.00 0.00 0.00 2.29
1589 3528 5.173854 CGTGAGCCATTGTTTTTCTTTTCTC 59.826 40.000 0.00 0.00 0.00 2.87
1607 3546 3.706698 TCTCTTTTCATGATACCTCGCG 58.293 45.455 0.00 0.00 0.00 5.87
1633 3572 0.322456 CTCTTTGGGTGCCGAATGGA 60.322 55.000 0.00 0.00 37.49 3.41
1640 3579 4.695993 TGCCGAATGGAGCGCACA 62.696 61.111 11.47 9.05 37.49 4.57
1648 3587 3.058708 CGAATGGAGCGCACATGATATTT 60.059 43.478 16.72 2.79 0.00 1.40
1650 3589 5.334028 CGAATGGAGCGCACATGATATTTTA 60.334 40.000 16.72 0.00 0.00 1.52
1652 3591 5.168526 TGGAGCGCACATGATATTTTAAC 57.831 39.130 11.47 0.00 0.00 2.01
1823 3762 7.687941 AGAGAATTGGTCATTGTAAATTCGT 57.312 32.000 11.85 5.51 41.65 3.85
1824 3763 8.110860 AGAGAATTGGTCATTGTAAATTCGTT 57.889 30.769 11.85 5.92 41.65 3.85
1826 3765 8.519492 AGAATTGGTCATTGTAAATTCGTTTG 57.481 30.769 11.85 0.00 41.65 2.93
1882 3833 8.684520 ACTCAATCAAATCAAATCAGATCTTCC 58.315 33.333 0.00 0.00 0.00 3.46
1886 3837 7.779754 TCAAATCAAATCAGATCTTCCCAAA 57.220 32.000 0.00 0.00 0.00 3.28
1916 3867 9.974980 TCAAATAAATTAAAACTTTCCTCGCTT 57.025 25.926 0.00 0.00 0.00 4.68
1919 3870 8.981724 ATAAATTAAAACTTTCCTCGCTTTCC 57.018 30.769 0.00 0.00 0.00 3.13
1920 3871 4.841443 TTAAAACTTTCCTCGCTTTCCC 57.159 40.909 0.00 0.00 0.00 3.97
1921 3872 1.617322 AAACTTTCCTCGCTTTCCCC 58.383 50.000 0.00 0.00 0.00 4.81
1922 3873 0.771755 AACTTTCCTCGCTTTCCCCT 59.228 50.000 0.00 0.00 0.00 4.79
1923 3874 1.652947 ACTTTCCTCGCTTTCCCCTA 58.347 50.000 0.00 0.00 0.00 3.53
1924 3875 1.278413 ACTTTCCTCGCTTTCCCCTAC 59.722 52.381 0.00 0.00 0.00 3.18
1932 3883 0.477204 GCTTTCCCCTACCCATACCC 59.523 60.000 0.00 0.00 0.00 3.69
1997 4433 1.284785 TCTTGGCTTCCCCTACCAATG 59.715 52.381 0.00 0.00 42.35 2.82
2005 4441 3.756082 TCCCCTACCAATGCTCAAATT 57.244 42.857 0.00 0.00 0.00 1.82
2011 4447 5.452356 CCCTACCAATGCTCAAATTGAATCC 60.452 44.000 0.00 0.00 39.46 3.01
2056 4492 3.118555 TGTGGGTGTCAGATTTATACGGG 60.119 47.826 0.00 0.00 0.00 5.28
2058 4494 2.490991 GGTGTCAGATTTATACGGGCC 58.509 52.381 0.00 0.00 0.00 5.80
2073 4509 1.402787 GGGCCCGATTGATGTTGAAT 58.597 50.000 5.69 0.00 0.00 2.57
2076 4512 2.624838 GGCCCGATTGATGTTGAATCAT 59.375 45.455 0.00 0.00 31.26 2.45
2106 4543 2.047939 GCCCCAGTTGCAATGCAC 60.048 61.111 7.72 3.39 38.71 4.57
2107 4544 2.870119 GCCCCAGTTGCAATGCACA 61.870 57.895 7.72 0.00 38.71 4.57
2158 4595 6.707608 TCACGGAAGAATATCTTAGCTACGTA 59.292 38.462 0.00 0.00 36.73 3.57
2159 4596 6.796072 CACGGAAGAATATCTTAGCTACGTAC 59.204 42.308 0.00 0.00 36.73 3.67
2160 4597 6.014293 CGGAAGAATATCTTAGCTACGTACG 58.986 44.000 15.01 15.01 36.73 3.67
2161 4598 6.128715 CGGAAGAATATCTTAGCTACGTACGA 60.129 42.308 24.41 4.69 36.73 3.43
2162 4599 7.235777 GGAAGAATATCTTAGCTACGTACGAG 58.764 42.308 24.41 15.48 36.73 4.18
2163 4600 6.724694 AGAATATCTTAGCTACGTACGAGG 57.275 41.667 24.41 14.47 0.00 4.63
2164 4601 6.229733 AGAATATCTTAGCTACGTACGAGGT 58.770 40.000 24.41 20.66 0.00 3.85
2165 4602 7.382110 AGAATATCTTAGCTACGTACGAGGTA 58.618 38.462 24.41 19.69 0.00 3.08
2166 4603 7.545265 AGAATATCTTAGCTACGTACGAGGTAG 59.455 40.741 24.41 14.26 39.02 3.18
2167 4604 4.392921 TCTTAGCTACGTACGAGGTAGT 57.607 45.455 24.41 0.00 38.45 2.73
2168 4605 4.759782 TCTTAGCTACGTACGAGGTAGTT 58.240 43.478 24.41 13.45 38.45 2.24
2169 4606 5.178797 TCTTAGCTACGTACGAGGTAGTTT 58.821 41.667 24.41 8.62 38.45 2.66
2170 4607 5.643777 TCTTAGCTACGTACGAGGTAGTTTT 59.356 40.000 24.41 6.40 38.45 2.43
2171 4608 4.773323 AGCTACGTACGAGGTAGTTTTT 57.227 40.909 24.41 0.00 38.45 1.94
2218 4659 9.676861 AAAAACTACTCCAACTTTGTACTAACT 57.323 29.630 0.00 0.00 0.00 2.24
2219 4660 9.676861 AAAACTACTCCAACTTTGTACTAACTT 57.323 29.630 0.00 0.00 0.00 2.66
2220 4661 9.676861 AAACTACTCCAACTTTGTACTAACTTT 57.323 29.630 0.00 0.00 0.00 2.66
2222 4663 9.978044 ACTACTCCAACTTTGTACTAACTTTAG 57.022 33.333 0.00 0.00 36.82 1.85
2223 4664 9.978044 CTACTCCAACTTTGTACTAACTTTAGT 57.022 33.333 6.85 6.85 45.39 2.24
2245 4686 7.568199 AGTATATTGATTTTGAAACGGAGGG 57.432 36.000 0.00 0.00 0.00 4.30
2246 4687 7.343357 AGTATATTGATTTTGAAACGGAGGGA 58.657 34.615 0.00 0.00 0.00 4.20
2247 4688 6.699575 ATATTGATTTTGAAACGGAGGGAG 57.300 37.500 0.00 0.00 0.00 4.30
2271 4712 9.298250 GAGTATGTCATAAATAGTACTCCCTCA 57.702 37.037 0.00 0.00 34.65 3.86
2287 4729 2.213499 CCTCATCCCGCAATGTAAGAC 58.787 52.381 0.00 0.00 0.00 3.01
2289 4731 1.206132 TCATCCCGCAATGTAAGACGT 59.794 47.619 0.00 0.00 0.00 4.34
2290 4732 2.006888 CATCCCGCAATGTAAGACGTT 58.993 47.619 0.00 0.00 0.00 3.99
2291 4733 2.172851 TCCCGCAATGTAAGACGTTT 57.827 45.000 0.00 0.00 0.00 3.60
2292 4734 2.496111 TCCCGCAATGTAAGACGTTTT 58.504 42.857 0.00 0.00 0.00 2.43
2293 4735 2.879646 TCCCGCAATGTAAGACGTTTTT 59.120 40.909 0.00 0.00 0.00 1.94
2294 4736 2.977169 CCCGCAATGTAAGACGTTTTTG 59.023 45.455 0.00 0.00 0.00 2.44
2295 4737 2.403698 CCGCAATGTAAGACGTTTTTGC 59.596 45.455 0.00 0.00 36.88 3.68
2296 4738 3.039405 CGCAATGTAAGACGTTTTTGCA 58.961 40.909 12.09 9.58 39.42 4.08
2297 4739 3.117832 CGCAATGTAAGACGTTTTTGCAG 59.882 43.478 12.09 3.58 39.42 4.41
2298 4740 3.121362 GCAATGTAAGACGTTTTTGCAGC 60.121 43.478 7.99 4.95 39.30 5.25
2299 4741 4.290155 CAATGTAAGACGTTTTTGCAGCT 58.710 39.130 0.00 0.00 0.00 4.24
2314 4756 1.518515 GCAGCTTGCAAAAACGTCTTC 59.481 47.619 0.00 0.00 44.26 2.87
2317 4759 2.119457 GCTTGCAAAAACGTCTTCCAG 58.881 47.619 0.00 0.00 0.00 3.86
2336 4779 0.531200 GTGTGAACGGAGGGAGTAGG 59.469 60.000 0.00 0.00 0.00 3.18
2386 4829 2.035066 GCAACTTGTCACCAAAGAGCAT 59.965 45.455 0.00 0.00 0.00 3.79
2416 4859 3.998341 ACATTTCTTGCAACATGCCAATC 59.002 39.130 0.00 0.00 44.23 2.67
2429 4872 4.038282 ACATGCCAATCGTGCAATATTCAT 59.962 37.500 0.00 0.00 42.92 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.171653 TGTAACAATCCATGATAGTTGGTGAA 58.828 34.615 0.00 0.00 35.64 3.18
1 2 6.716284 TGTAACAATCCATGATAGTTGGTGA 58.284 36.000 0.00 0.00 35.64 4.02
2 3 7.572523 ATGTAACAATCCATGATAGTTGGTG 57.427 36.000 0.00 0.00 35.64 4.17
81 82 3.495331 AGCACATGAACATAACCAACCA 58.505 40.909 0.00 0.00 0.00 3.67
261 264 6.414732 TGAACTTGCTACCTTATTGCTACAT 58.585 36.000 0.00 0.00 0.00 2.29
310 313 4.096382 GGTATGTGAACAAGGCTTGTATGG 59.904 45.833 31.34 6.64 44.59 2.74
319 322 7.403312 TTGGATATTTGGTATGTGAACAAGG 57.597 36.000 0.00 0.00 0.00 3.61
399 404 6.228273 TGCTGTGAAGAACTTCTAAATTCG 57.772 37.500 14.31 0.00 40.14 3.34
467 472 8.314021 TGATTACTAGTCATTGGTGGCTATATG 58.686 37.037 0.00 0.00 41.43 1.78
494 499 8.572185 TGTTCGATTTTTGTCAAAATAGATCCA 58.428 29.630 11.44 8.34 41.79 3.41
595 647 5.637006 TCCAACATGTAAATAAGGTGCAC 57.363 39.130 8.80 8.80 0.00 4.57
601 653 5.220854 CCTTCGGCTCCAACATGTAAATAAG 60.221 44.000 0.00 0.00 0.00 1.73
629 681 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
630 682 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
632 684 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
635 687 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
636 688 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
637 689 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
638 690 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
639 691 4.403752 TGTGAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
640 692 4.160439 GTGTGAGAGAGAGAGAGAGAGAGA 59.840 50.000 0.00 0.00 0.00 3.10
641 693 4.081476 TGTGTGAGAGAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
642 694 3.837731 TGTGTGAGAGAGAGAGAGAGAGA 59.162 47.826 0.00 0.00 0.00 3.10
643 695 3.935203 GTGTGTGAGAGAGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
644 696 3.326297 TGTGTGTGAGAGAGAGAGAGAGA 59.674 47.826 0.00 0.00 0.00 3.10
645 697 3.436704 GTGTGTGTGAGAGAGAGAGAGAG 59.563 52.174 0.00 0.00 0.00 3.20
646 698 3.181450 TGTGTGTGTGAGAGAGAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
647 699 3.058293 GTGTGTGTGTGAGAGAGAGAGAG 60.058 52.174 0.00 0.00 0.00 3.20
648 700 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
649 701 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
650 702 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
651 703 2.099756 TGTGTGTGTGTGTGAGAGAGAG 59.900 50.000 0.00 0.00 0.00 3.20
652 704 2.099405 TGTGTGTGTGTGTGAGAGAGA 58.901 47.619 0.00 0.00 0.00 3.10
653 705 2.196749 GTGTGTGTGTGTGTGAGAGAG 58.803 52.381 0.00 0.00 0.00 3.20
654 706 1.548269 TGTGTGTGTGTGTGTGAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
655 707 1.660607 GTGTGTGTGTGTGTGTGAGAG 59.339 52.381 0.00 0.00 0.00 3.20
661 713 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
665 717 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
666 718 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
678 730 1.268352 GTTTGTGTGGTGTGTGTGTGT 59.732 47.619 0.00 0.00 0.00 3.72
679 731 1.727535 CGTTTGTGTGGTGTGTGTGTG 60.728 52.381 0.00 0.00 0.00 3.82
680 732 0.519519 CGTTTGTGTGGTGTGTGTGT 59.480 50.000 0.00 0.00 0.00 3.72
681 733 0.179176 CCGTTTGTGTGGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
682 734 0.606944 ACCGTTTGTGTGGTGTGTGT 60.607 50.000 0.00 0.00 37.02 3.72
683 735 1.370609 TACCGTTTGTGTGGTGTGTG 58.629 50.000 0.00 0.00 39.30 3.82
684 736 2.011222 CTTACCGTTTGTGTGGTGTGT 58.989 47.619 0.00 0.00 39.30 3.72
685 737 2.011222 ACTTACCGTTTGTGTGGTGTG 58.989 47.619 0.00 0.00 39.30 3.82
686 738 2.406596 ACTTACCGTTTGTGTGGTGT 57.593 45.000 0.00 0.00 39.30 4.16
687 739 6.730960 ATATTACTTACCGTTTGTGTGGTG 57.269 37.500 0.00 0.00 39.30 4.17
688 740 9.533253 GTATATATTACTTACCGTTTGTGTGGT 57.467 33.333 0.00 0.00 42.34 4.16
689 741 9.754382 AGTATATATTACTTACCGTTTGTGTGG 57.246 33.333 0.00 0.00 0.00 4.17
851 903 6.576662 TTTTATTATTTGGTGGTCGAGCAA 57.423 33.333 20.46 3.70 40.34 3.91
888 940 4.744136 ATCAATTGTGAGATGCATAGCG 57.256 40.909 0.00 0.00 37.14 4.26
964 1034 2.300437 GTGAACTGGCTACCTGAGAGTT 59.700 50.000 0.00 0.00 0.00 3.01
1091 1161 8.141268 TGCATCACTGAGAAATACAATCGTATA 58.859 33.333 0.00 0.00 37.34 1.47
1213 1435 0.926720 TCCTCCTGGTAGCTCCTCCT 60.927 60.000 0.00 0.00 37.07 3.69
1214 1436 0.189822 ATCCTCCTGGTAGCTCCTCC 59.810 60.000 0.00 0.00 37.07 4.30
1215 1437 1.133325 TGATCCTCCTGGTAGCTCCTC 60.133 57.143 0.00 0.00 37.07 3.71
1302 1901 1.153168 GTGGCGACATACATGGCCT 60.153 57.895 3.32 0.00 45.75 5.19
1317 1916 0.900647 AACAGACTCTCGGAGGGTGG 60.901 60.000 16.74 9.88 33.35 4.61
1330 1929 2.447244 AGCTCACAGCAGTAACAGAC 57.553 50.000 0.00 0.00 45.56 3.51
1331 1930 2.630098 AGAAGCTCACAGCAGTAACAGA 59.370 45.455 0.00 0.00 45.56 3.41
1464 2063 9.961265 ATGACTCATTTACATGAAAAGCATATG 57.039 29.630 0.00 0.00 39.04 1.78
1529 3468 7.013274 ACAGTGTTGTTAGCAAAGATATTGTGT 59.987 33.333 0.00 0.00 36.22 3.72
1531 3470 7.445402 AGACAGTGTTGTTAGCAAAGATATTGT 59.555 33.333 0.00 0.00 37.76 2.71
1533 3472 7.986085 AGACAGTGTTGTTAGCAAAGATATT 57.014 32.000 0.00 0.00 37.76 1.28
1547 3486 5.389516 GCTCACGGTATAAAAGACAGTGTTG 60.390 44.000 0.00 0.00 41.79 3.33
1550 3489 3.617263 GGCTCACGGTATAAAAGACAGTG 59.383 47.826 0.00 0.00 42.26 3.66
1587 3526 3.706698 TCGCGAGGTATCATGAAAAGAG 58.293 45.455 3.71 0.00 0.00 2.85
1589 3528 3.865745 ACTTCGCGAGGTATCATGAAAAG 59.134 43.478 23.38 8.09 0.00 2.27
1607 3546 1.266989 CGGCACCCAAAGAGAAACTTC 59.733 52.381 0.00 0.00 37.93 3.01
1633 3572 5.818136 ACAGTTAAAATATCATGTGCGCT 57.182 34.783 9.73 0.00 0.00 5.92
1804 3743 5.637387 GCCAAACGAATTTACAATGACCAAT 59.363 36.000 0.00 0.00 0.00 3.16
1807 3746 3.924073 GGCCAAACGAATTTACAATGACC 59.076 43.478 0.00 0.00 0.00 4.02
1817 3756 1.541379 GGGTGTAGGCCAAACGAATT 58.459 50.000 5.01 0.00 0.00 2.17
1823 3762 1.464395 TGGAGGGGTGTAGGCCAAA 60.464 57.895 5.01 0.00 0.00 3.28
1824 3763 2.208640 TGGAGGGGTGTAGGCCAA 59.791 61.111 5.01 0.00 0.00 4.52
1826 3765 2.609610 TGTGGAGGGGTGTAGGCC 60.610 66.667 0.00 0.00 0.00 5.19
1873 3824 9.933723 ATTTATTTGAAGTTTTGGGAAGATCTG 57.066 29.630 0.00 0.00 0.00 2.90
1912 3863 0.108019 GGTATGGGTAGGGGAAAGCG 59.892 60.000 0.00 0.00 0.00 4.68
1916 3867 2.380043 TTTGGGTATGGGTAGGGGAA 57.620 50.000 0.00 0.00 0.00 3.97
1918 3869 2.140224 TGATTTGGGTATGGGTAGGGG 58.860 52.381 0.00 0.00 0.00 4.79
1919 3870 3.963476 TTGATTTGGGTATGGGTAGGG 57.037 47.619 0.00 0.00 0.00 3.53
1920 3871 7.906199 TTTATTTGATTTGGGTATGGGTAGG 57.094 36.000 0.00 0.00 0.00 3.18
1921 3872 9.367160 AGATTTATTTGATTTGGGTATGGGTAG 57.633 33.333 0.00 0.00 0.00 3.18
1922 3873 9.722317 AAGATTTATTTGATTTGGGTATGGGTA 57.278 29.630 0.00 0.00 0.00 3.69
1923 3874 8.622572 AAGATTTATTTGATTTGGGTATGGGT 57.377 30.769 0.00 0.00 0.00 4.51
1924 3875 9.981114 GTAAGATTTATTTGATTTGGGTATGGG 57.019 33.333 0.00 0.00 0.00 4.00
1982 4418 0.255890 TGAGCATTGGTAGGGGAAGC 59.744 55.000 0.00 0.00 0.00 3.86
1997 4433 6.866480 TGGTAAGATTGGATTCAATTTGAGC 58.134 36.000 0.00 0.00 43.08 4.26
2005 4441 9.973661 TTCTAGATTTTGGTAAGATTGGATTCA 57.026 29.630 0.00 0.00 0.00 2.57
2052 4488 1.748879 CAACATCAATCGGGCCCGT 60.749 57.895 41.57 26.88 40.74 5.28
2056 4492 3.893720 GATGATTCAACATCAATCGGGC 58.106 45.455 0.00 0.00 44.00 6.13
2073 4509 5.704354 ACTGGGGCATACATATTTTGATGA 58.296 37.500 0.00 0.00 0.00 2.92
2076 4512 4.099266 GCAACTGGGGCATACATATTTTGA 59.901 41.667 0.00 0.00 0.00 2.69
2197 4638 9.978044 ACTAAAGTTAGTACAAAGTTGGAGTAG 57.022 33.333 1.81 0.00 41.92 2.57
2219 4660 9.116067 CCCTCCGTTTCAAAATCAATATACTAA 57.884 33.333 0.00 0.00 0.00 2.24
2220 4661 8.487848 TCCCTCCGTTTCAAAATCAATATACTA 58.512 33.333 0.00 0.00 0.00 1.82
2221 4662 7.343357 TCCCTCCGTTTCAAAATCAATATACT 58.657 34.615 0.00 0.00 0.00 2.12
2222 4663 7.282450 ACTCCCTCCGTTTCAAAATCAATATAC 59.718 37.037 0.00 0.00 0.00 1.47
2223 4664 7.343357 ACTCCCTCCGTTTCAAAATCAATATA 58.657 34.615 0.00 0.00 0.00 0.86
2224 4665 6.187682 ACTCCCTCCGTTTCAAAATCAATAT 58.812 36.000 0.00 0.00 0.00 1.28
2225 4666 5.566469 ACTCCCTCCGTTTCAAAATCAATA 58.434 37.500 0.00 0.00 0.00 1.90
2226 4667 4.407365 ACTCCCTCCGTTTCAAAATCAAT 58.593 39.130 0.00 0.00 0.00 2.57
2227 4668 3.827722 ACTCCCTCCGTTTCAAAATCAA 58.172 40.909 0.00 0.00 0.00 2.57
2228 4669 3.502123 ACTCCCTCCGTTTCAAAATCA 57.498 42.857 0.00 0.00 0.00 2.57
2229 4670 4.941873 ACATACTCCCTCCGTTTCAAAATC 59.058 41.667 0.00 0.00 0.00 2.17
2230 4671 4.918588 ACATACTCCCTCCGTTTCAAAAT 58.081 39.130 0.00 0.00 0.00 1.82
2231 4672 4.202377 TGACATACTCCCTCCGTTTCAAAA 60.202 41.667 0.00 0.00 0.00 2.44
2232 4673 3.325425 TGACATACTCCCTCCGTTTCAAA 59.675 43.478 0.00 0.00 0.00 2.69
2233 4674 2.901192 TGACATACTCCCTCCGTTTCAA 59.099 45.455 0.00 0.00 0.00 2.69
2234 4675 2.531771 TGACATACTCCCTCCGTTTCA 58.468 47.619 0.00 0.00 0.00 2.69
2235 4676 3.821421 ATGACATACTCCCTCCGTTTC 57.179 47.619 0.00 0.00 0.00 2.78
2236 4677 5.687166 TTTATGACATACTCCCTCCGTTT 57.313 39.130 0.00 0.00 0.00 3.60
2237 4678 5.888982 ATTTATGACATACTCCCTCCGTT 57.111 39.130 0.00 0.00 0.00 4.44
2238 4679 6.075984 ACTATTTATGACATACTCCCTCCGT 58.924 40.000 0.00 0.00 0.00 4.69
2239 4680 6.591750 ACTATTTATGACATACTCCCTCCG 57.408 41.667 0.00 0.00 0.00 4.63
2240 4681 8.653036 AGTACTATTTATGACATACTCCCTCC 57.347 38.462 0.00 0.00 0.00 4.30
2241 4682 8.741841 GGAGTACTATTTATGACATACTCCCTC 58.258 40.741 15.94 6.91 46.97 4.30
2242 4683 8.653036 GGAGTACTATTTATGACATACTCCCT 57.347 38.462 15.94 0.00 46.97 4.20
2245 4686 9.298250 TGAGGGAGTACTATTTATGACATACTC 57.702 37.037 0.00 0.00 38.42 2.59
2246 4687 9.830186 ATGAGGGAGTACTATTTATGACATACT 57.170 33.333 0.00 0.00 0.00 2.12
2271 4712 2.396590 AACGTCTTACATTGCGGGAT 57.603 45.000 0.00 0.00 0.00 3.85
2294 4736 1.518515 GAAGACGTTTTTGCAAGCTGC 59.481 47.619 0.00 0.00 45.29 5.25
2295 4737 2.119457 GGAAGACGTTTTTGCAAGCTG 58.881 47.619 0.00 0.00 0.00 4.24
2296 4738 1.748493 TGGAAGACGTTTTTGCAAGCT 59.252 42.857 0.00 0.00 0.00 3.74
2297 4739 2.119457 CTGGAAGACGTTTTTGCAAGC 58.881 47.619 0.00 0.00 34.07 4.01
2298 4740 3.108144 CACTGGAAGACGTTTTTGCAAG 58.892 45.455 0.00 0.00 37.43 4.01
2299 4741 2.490115 ACACTGGAAGACGTTTTTGCAA 59.510 40.909 0.00 0.00 37.43 4.08
2309 4751 1.605712 CCTCCGTTCACACTGGAAGAC 60.606 57.143 0.00 0.00 37.43 3.01
2314 4756 1.293498 CTCCCTCCGTTCACACTGG 59.707 63.158 0.00 0.00 0.00 4.00
2317 4759 0.531200 CCTACTCCCTCCGTTCACAC 59.469 60.000 0.00 0.00 0.00 3.82
2336 4779 6.143438 GGTGCACTACATCACATATTACGTAC 59.857 42.308 17.98 0.00 35.04 3.67
2386 4829 6.974048 GCATGTTGCAAGAAATGTGTATGATA 59.026 34.615 0.00 0.00 44.26 2.15
2429 4872 9.134734 GCTCCATTTCACACGAATAAAATAAAA 57.865 29.630 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.