Multiple sequence alignment - TraesCS4B01G163300

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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 TraesCS4B01G163300 chr4B 100.000 5082 0 0 1 5082 333369978 333375059 0.000000e+00 9385.0
1 TraesCS4B01G163300 chr4B 97.102 1622 46 1 1 1622 333349334 333350954 0.000000e+00 2734.0
2 TraesCS4B01G163300 chr4B 94.734 1633 82 4 1 1631 238639284 238640914 0.000000e+00 2536.0
3 TraesCS4B01G163300 chr4B 94.847 1630 75 9 4 1631 403393236 403391614 0.000000e+00 2536.0
4 TraesCS4B01G163300 chr4B 94.672 1633 73 9 4 1634 637769845 637768225 0.000000e+00 2521.0
5 TraesCS4B01G163300 chr4B 95.906 171 7 0 3902 4072 20175006 20175176 1.390000e-70 278.0
6 TraesCS4B01G163300 chr7B 95.046 1635 68 11 1 1631 645860023 645861648 0.000000e+00 2558.0
7 TraesCS4B01G163300 chr7B 94.663 1630 81 6 4 1631 244119131 244117506 0.000000e+00 2523.0
8 TraesCS4B01G163300 chr7B 95.482 332 15 0 3741 4072 699508171 699508502 9.690000e-147 531.0
9 TraesCS4B01G163300 chr7B 90.265 226 18 2 4366 4587 633839201 633839426 4.980000e-75 292.0
10 TraesCS4B01G163300 chr7B 94.767 172 9 0 3901 4072 431282784 431282955 8.390000e-68 268.0
11 TraesCS4B01G163300 chr2B 94.759 1641 75 11 4 1638 292376323 292374688 0.000000e+00 2543.0
12 TraesCS4B01G163300 chr2B 94.618 1635 77 8 1 1631 595221451 595223078 0.000000e+00 2521.0
13 TraesCS4B01G163300 chr2B 92.989 1355 74 7 3352 4693 380575173 380573827 0.000000e+00 1956.0
14 TraesCS4B01G163300 chr2B 94.118 170 10 0 3901 4070 678740045 678739876 5.050000e-65 259.0
15 TraesCS4B01G163300 chr3B 94.614 1634 79 7 1 1631 660369643 660371270 0.000000e+00 2521.0
16 TraesCS4B01G163300 chr3B 94.245 1060 54 5 3135 4192 12172803 12173857 0.000000e+00 1613.0
17 TraesCS4B01G163300 chr3B 88.490 1364 86 35 2867 4216 259911328 259910022 0.000000e+00 1583.0
18 TraesCS4B01G163300 chr3B 92.683 738 54 0 1900 2637 365739969 365739232 0.000000e+00 1064.0
19 TraesCS4B01G163300 chr3B 92.580 566 37 5 2906 3467 365739232 365738668 0.000000e+00 808.0
20 TraesCS4B01G163300 chr3B 91.339 127 11 0 2701 2827 259911454 259911328 1.880000e-39 174.0
21 TraesCS4B01G163300 chr3B 91.000 100 8 1 2825 2924 259911025 259910927 3.190000e-27 134.0
22 TraesCS4B01G163300 chr4A 91.575 1828 123 16 1632 3453 610429309 610427507 0.000000e+00 2494.0
23 TraesCS4B01G163300 chr4A 89.264 1006 95 6 1632 2637 555158007 555158999 0.000000e+00 1247.0
24 TraesCS4B01G163300 chr4A 93.286 566 33 3 2906 3467 555158999 555159563 0.000000e+00 830.0
25 TraesCS4B01G163300 chr4A 94.753 324 17 0 3749 4072 306062229 306061906 5.870000e-139 505.0
26 TraesCS4B01G163300 chr4A 90.667 225 17 3 4366 4586 406188104 406187880 3.850000e-76 296.0
27 TraesCS4B01G163300 chr4A 81.818 154 15 6 1971 2119 625527705 625527850 3.210000e-22 117.0
28 TraesCS4B01G163300 chr1A 90.223 1841 149 14 1632 3467 37395784 37397598 0.000000e+00 2374.0
29 TraesCS4B01G163300 chr1A 95.082 122 6 0 3951 4072 172894257 172894136 5.190000e-45 193.0
30 TraesCS4B01G163300 chr1A 79.365 252 39 7 1643 1893 172895299 172895060 1.130000e-36 165.0
31 TraesCS4B01G163300 chr3D 89.125 1646 103 37 2693 4309 181655472 181653874 0.000000e+00 1978.0
32 TraesCS4B01G163300 chr3D 95.783 332 13 1 3741 4072 327310521 327310851 7.490000e-148 534.0
33 TraesCS4B01G163300 chr3D 91.000 100 8 1 2825 2924 181654989 181654891 3.190000e-27 134.0
34 TraesCS4B01G163300 chr3D 90.123 81 5 1 2490 2570 9496443 9496366 9.000000e-18 102.0
35 TraesCS4B01G163300 chr1B 92.671 1378 80 8 3721 5082 77723685 77725057 0.000000e+00 1965.0
36 TraesCS4B01G163300 chr1B 96.368 468 16 1 2207 2674 122829606 122830072 0.000000e+00 769.0
37 TraesCS4B01G163300 chr1B 96.154 468 18 0 2207 2674 79979097 79979564 0.000000e+00 765.0
38 TraesCS4B01G163300 chr1B 92.157 510 36 4 4575 5082 117872831 117873338 0.000000e+00 717.0
39 TraesCS4B01G163300 chr1B 97.255 255 7 0 2186 2440 217562800 217562546 2.810000e-117 433.0
40 TraesCS4B01G163300 chr2A 91.242 1256 108 2 1678 2932 132705471 132706725 0.000000e+00 1709.0
41 TraesCS4B01G163300 chr2A 92.172 511 36 4 4575 5082 391687455 391687964 0.000000e+00 719.0
42 TraesCS4B01G163300 chr2A 91.111 225 16 3 4366 4586 732302165 732301941 8.270000e-78 302.0
43 TraesCS4B01G163300 chr3A 88.744 1226 92 24 3027 4237 227365917 227367111 0.000000e+00 1458.0
44 TraesCS4B01G163300 chr3A 90.553 434 29 2 2577 2998 227365487 227365920 9.550000e-157 564.0
45 TraesCS4B01G163300 chr3A 89.412 85 9 0 2829 2913 227366068 227366152 1.930000e-19 108.0
46 TraesCS4B01G163300 chrUn 91.054 1006 77 6 1632 2637 114952524 114953516 0.000000e+00 1347.0
47 TraesCS4B01G163300 chrUn 94.523 566 26 3 2906 3467 114953516 114954080 0.000000e+00 869.0
48 TraesCS4B01G163300 chr5A 92.000 675 49 3 4413 5082 116203191 116203865 0.000000e+00 942.0
49 TraesCS4B01G163300 chr5A 92.329 365 27 1 3135 3498 116202799 116203163 7.540000e-143 518.0
50 TraesCS4B01G163300 chr7D 93.713 509 30 2 4575 5082 599756461 599755954 0.000000e+00 761.0
51 TraesCS4B01G163300 chr1D 92.955 511 31 4 4575 5082 479643631 479644139 0.000000e+00 739.0
52 TraesCS4B01G163300 chr1D 92.731 509 34 3 4575 5082 494243098 494242592 0.000000e+00 732.0
53 TraesCS4B01G163300 chr6D 92.534 509 34 3 4575 5082 47309554 47310059 0.000000e+00 726.0
54 TraesCS4B01G163300 chr6B 91.961 510 38 3 4575 5082 83737576 83738084 0.000000e+00 712.0
55 TraesCS4B01G163300 chr6B 90.129 233 17 4 4366 4593 483667220 483666989 1.070000e-76 298.0
56 TraesCS4B01G163300 chr5B 94.059 202 12 0 4378 4579 407959443 407959242 1.780000e-79 307.0
57 TraesCS4B01G163300 chr5B 90.708 226 16 4 4372 4593 653689775 653689551 3.850000e-76 296.0
58 TraesCS4B01G163300 chr5B 94.286 35 2 0 2842 2876 38047232 38047198 3.000000e-03 54.7


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 TraesCS4B01G163300 chr4B 333369978 333375059 5081 False 9385.000000 9385 100.000000 1 5082 1 chr4B.!!$F4 5081
1 TraesCS4B01G163300 chr4B 333349334 333350954 1620 False 2734.000000 2734 97.102000 1 1622 1 chr4B.!!$F3 1621
2 TraesCS4B01G163300 chr4B 238639284 238640914 1630 False 2536.000000 2536 94.734000 1 1631 1 chr4B.!!$F2 1630
3 TraesCS4B01G163300 chr4B 403391614 403393236 1622 True 2536.000000 2536 94.847000 4 1631 1 chr4B.!!$R1 1627
4 TraesCS4B01G163300 chr4B 637768225 637769845 1620 True 2521.000000 2521 94.672000 4 1634 1 chr4B.!!$R2 1630
5 TraesCS4B01G163300 chr7B 645860023 645861648 1625 False 2558.000000 2558 95.046000 1 1631 1 chr7B.!!$F3 1630
6 TraesCS4B01G163300 chr7B 244117506 244119131 1625 True 2523.000000 2523 94.663000 4 1631 1 chr7B.!!$R1 1627
7 TraesCS4B01G163300 chr2B 292374688 292376323 1635 True 2543.000000 2543 94.759000 4 1638 1 chr2B.!!$R1 1634
8 TraesCS4B01G163300 chr2B 595221451 595223078 1627 False 2521.000000 2521 94.618000 1 1631 1 chr2B.!!$F1 1630
9 TraesCS4B01G163300 chr2B 380573827 380575173 1346 True 1956.000000 1956 92.989000 3352 4693 1 chr2B.!!$R2 1341
10 TraesCS4B01G163300 chr3B 660369643 660371270 1627 False 2521.000000 2521 94.614000 1 1631 1 chr3B.!!$F2 1630
11 TraesCS4B01G163300 chr3B 12172803 12173857 1054 False 1613.000000 1613 94.245000 3135 4192 1 chr3B.!!$F1 1057
12 TraesCS4B01G163300 chr3B 365738668 365739969 1301 True 936.000000 1064 92.631500 1900 3467 2 chr3B.!!$R2 1567
13 TraesCS4B01G163300 chr3B 259910022 259911454 1432 True 630.333333 1583 90.276333 2701 4216 3 chr3B.!!$R1 1515
14 TraesCS4B01G163300 chr4A 610427507 610429309 1802 True 2494.000000 2494 91.575000 1632 3453 1 chr4A.!!$R3 1821
15 TraesCS4B01G163300 chr4A 555158007 555159563 1556 False 1038.500000 1247 91.275000 1632 3467 2 chr4A.!!$F2 1835
16 TraesCS4B01G163300 chr1A 37395784 37397598 1814 False 2374.000000 2374 90.223000 1632 3467 1 chr1A.!!$F1 1835
17 TraesCS4B01G163300 chr3D 181653874 181655472 1598 True 1056.000000 1978 90.062500 2693 4309 2 chr3D.!!$R2 1616
18 TraesCS4B01G163300 chr1B 77723685 77725057 1372 False 1965.000000 1965 92.671000 3721 5082 1 chr1B.!!$F1 1361
19 TraesCS4B01G163300 chr1B 117872831 117873338 507 False 717.000000 717 92.157000 4575 5082 1 chr1B.!!$F3 507
20 TraesCS4B01G163300 chr2A 132705471 132706725 1254 False 1709.000000 1709 91.242000 1678 2932 1 chr2A.!!$F1 1254
21 TraesCS4B01G163300 chr2A 391687455 391687964 509 False 719.000000 719 92.172000 4575 5082 1 chr2A.!!$F2 507
22 TraesCS4B01G163300 chr3A 227365487 227367111 1624 False 710.000000 1458 89.569667 2577 4237 3 chr3A.!!$F1 1660
23 TraesCS4B01G163300 chrUn 114952524 114954080 1556 False 1108.000000 1347 92.788500 1632 3467 2 chrUn.!!$F1 1835
24 TraesCS4B01G163300 chr5A 116202799 116203865 1066 False 730.000000 942 92.164500 3135 5082 2 chr5A.!!$F1 1947
25 TraesCS4B01G163300 chr7D 599755954 599756461 507 True 761.000000 761 93.713000 4575 5082 1 chr7D.!!$R1 507
26 TraesCS4B01G163300 chr1D 479643631 479644139 508 False 739.000000 739 92.955000 4575 5082 1 chr1D.!!$F1 507
27 TraesCS4B01G163300 chr1D 494242592 494243098 506 True 732.000000 732 92.731000 4575 5082 1 chr1D.!!$R1 507
28 TraesCS4B01G163300 chr6D 47309554 47310059 505 False 726.000000 726 92.534000 4575 5082 1 chr6D.!!$F1 507
29 TraesCS4B01G163300 chr6B 83737576 83738084 508 False 712.000000 712 91.961000 4575 5082 1 chr6B.!!$F1 507

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
696 707 1.002134 CCGGTGTTGCCCTGAGAAT 60.002 57.895 0.00 0.0 0.00 2.40 F
1390 1404 1.264749 TATGTTCCAGGTCGGCAGCT 61.265 55.000 0.00 0.0 33.14 4.24 F
2062 2079 0.034089 CGGGGCCTCATCCTCTTTTT 60.034 55.000 1.96 0.0 0.00 1.94 F
3514 3841 1.021390 CCTCGCTAACAACTGCCCTG 61.021 60.000 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2060 0.034089 AAAAAGAGGATGAGGCCCCG 60.034 55.000 0.00 0.00 0.00 5.73 R
2989 3289 1.176527 AAAAGACATCCATGGTGCCG 58.823 50.000 12.58 1.27 0.00 5.69 R
3849 4182 0.456653 AATCAAACATTCGGCGCTGC 60.457 50.000 12.58 0.00 0.00 5.25 R
5002 5361 1.074727 ACCACCACGGGAAATGAATCA 59.925 47.619 0.00 0.00 40.22 2.57 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
135 137 2.498885 GCTCATCAAGCCTCCCAAATTT 59.501 45.455 0.00 0.00 45.92 1.82
209 215 2.124507 TACCGCTTTGCTCAGCCCTT 62.125 55.000 0.00 0.00 36.31 3.95
390 399 1.447314 CGCCCCTAGTTTCCGTCAC 60.447 63.158 0.00 0.00 0.00 3.67
696 707 1.002134 CCGGTGTTGCCCTGAGAAT 60.002 57.895 0.00 0.00 0.00 2.40
736 747 2.709475 GGATTGTCGGTGCATCGC 59.291 61.111 16.22 10.74 0.00 4.58
897 909 7.308782 CTGCAAGGTATAATCTTTCGAAAGT 57.691 36.000 31.29 19.14 37.31 2.66
899 911 6.876789 TGCAAGGTATAATCTTTCGAAAGTCA 59.123 34.615 31.29 17.79 37.31 3.41
902 914 8.338259 CAAGGTATAATCTTTCGAAAGTCATGG 58.662 37.037 31.29 11.36 37.31 3.66
1105 1118 3.118992 TGATCATTGCTAGCTTCACGACT 60.119 43.478 17.23 0.00 0.00 4.18
1165 1179 3.721087 AGCCACCATACTTGCTTAGTT 57.279 42.857 0.00 0.00 38.33 2.24
1253 1267 3.391296 GGTAATGGGATTGCTGAGTCCTA 59.609 47.826 0.00 0.00 34.84 2.94
1349 1363 5.003804 TGCTTGTATTGGAGTTCTTCTTCC 58.996 41.667 0.00 0.00 0.00 3.46
1373 1387 2.894731 TCTGCTTCGATCAGGGGATAT 58.105 47.619 13.20 0.00 32.67 1.63
1390 1404 1.264749 TATGTTCCAGGTCGGCAGCT 61.265 55.000 0.00 0.00 33.14 4.24
1638 1654 3.626924 GGGCGTGACACCTCACCT 61.627 66.667 0.00 0.00 43.64 4.00
1660 1676 1.571955 GCCCAATTCAATCCAACCCT 58.428 50.000 0.00 0.00 0.00 4.34
1661 1677 2.625617 GGCCCAATTCAATCCAACCCTA 60.626 50.000 0.00 0.00 0.00 3.53
1769 1786 2.437897 CCTTGCCACTGCCTCCTT 59.562 61.111 0.00 0.00 36.33 3.36
1842 1859 3.695606 GCGGCCAGGAGTGTCTCA 61.696 66.667 2.24 0.00 31.08 3.27
1873 1890 2.207229 ACACCTGCGACCTGCTACA 61.207 57.895 0.00 0.00 46.63 2.74
1877 1894 3.282745 CTGCGACCTGCTACACCGT 62.283 63.158 0.00 0.00 46.63 4.83
2013 2030 1.758514 GCCTCGACCTCTCCATCCA 60.759 63.158 0.00 0.00 0.00 3.41
2014 2031 2.022240 GCCTCGACCTCTCCATCCAC 62.022 65.000 0.00 0.00 0.00 4.02
2025 2042 2.777972 CCATCCACCGCATTGCCTG 61.778 63.158 2.41 0.00 0.00 4.85
2062 2079 0.034089 CGGGGCCTCATCCTCTTTTT 60.034 55.000 1.96 0.00 0.00 1.94
2126 2143 1.728825 GCGAGATTTGTTCATTGCGCA 60.729 47.619 5.66 5.66 42.41 6.09
2139 2156 2.753989 TTGCGCATCCATTTGTATCG 57.246 45.000 12.75 0.00 0.00 2.92
2140 2157 1.662517 TGCGCATCCATTTGTATCGT 58.337 45.000 5.66 0.00 0.00 3.73
2177 2194 1.209019 ACTGCCTTTGCTCTGATCGAT 59.791 47.619 0.00 0.00 38.71 3.59
2184 2201 4.442052 CCTTTGCTCTGATCGATAGGTTGA 60.442 45.833 0.00 0.00 0.00 3.18
2233 2250 6.989169 CCCTTTTCTCCTAAGATGACATACTG 59.011 42.308 0.00 0.00 0.00 2.74
2263 2280 7.182760 TCTTTCTCTGGACCTGATTACTAGAA 58.817 38.462 0.96 0.00 0.00 2.10
2458 2475 1.423541 ACCCATGGCACTAGACAACAA 59.576 47.619 6.09 0.00 35.50 2.83
2473 2490 1.263217 CAACAACAGCAAGACCGTACC 59.737 52.381 0.00 0.00 0.00 3.34
2662 2679 7.950512 TCCAAAATTGTCTCATGCTTTTAAGA 58.049 30.769 0.00 0.00 0.00 2.10
2668 2685 4.156556 TGTCTCATGCTTTTAAGATGTGCC 59.843 41.667 0.00 0.00 0.00 5.01
2684 2713 8.922931 AAGATGTGCCATTGTGTTGATATATA 57.077 30.769 0.00 0.00 0.00 0.86
2689 2718 9.008965 TGTGCCATTGTGTTGATATATATTACC 57.991 33.333 0.00 0.00 0.00 2.85
2833 3132 1.343506 CGGACACGTACTACTTTGGC 58.656 55.000 0.00 0.00 34.81 4.52
2840 3139 2.754552 ACGTACTACTTTGGCGGACATA 59.245 45.455 0.00 0.00 0.00 2.29
2881 3180 3.044235 TCGACAATGAACATGCTGAGT 57.956 42.857 0.00 0.00 0.00 3.41
2938 3238 3.701542 CTCTGATCTGCCCAGTAGTACAA 59.298 47.826 2.52 0.00 33.57 2.41
2989 3289 8.696410 TGTTTTGTGGTTTGTTATCTTTCTTC 57.304 30.769 0.00 0.00 0.00 2.87
3065 3365 9.751542 AAAACTGATTACTAGTGGATCTATTCG 57.248 33.333 5.39 1.18 0.00 3.34
3143 3446 8.135382 AGGTTTCTCTGTGCTAGATTTACTAA 57.865 34.615 0.00 0.00 34.21 2.24
3145 3448 9.384764 GGTTTCTCTGTGCTAGATTTACTAAAT 57.615 33.333 0.00 0.00 34.21 1.40
3340 3663 5.704354 TGGCCATTGTGGATAATTCTATGT 58.296 37.500 0.00 0.00 40.96 2.29
3417 3741 8.954950 TTGTCCATAACAACAATTTCATGTTT 57.045 26.923 5.80 0.00 42.95 2.83
3498 3825 5.689383 TTACAACAAAGCTTGTGATCCTC 57.311 39.130 0.00 0.00 44.59 3.71
3514 3841 1.021390 CCTCGCTAACAACTGCCCTG 61.021 60.000 0.00 0.00 0.00 4.45
3540 3867 3.509967 TCCGCAAGTCTGAGATTGAGTAA 59.490 43.478 6.70 0.00 0.00 2.24
3544 3871 6.036470 CGCAAGTCTGAGATTGAGTAATACA 58.964 40.000 6.70 0.00 0.00 2.29
3563 3890 2.027192 ACACTATGTTGGCGAAGGTCAT 60.027 45.455 0.00 0.00 0.00 3.06
3620 3947 9.927668 ATTCCTATTTAATCCAGTTTTTGTGTG 57.072 29.630 0.00 0.00 0.00 3.82
3630 3958 3.692101 CAGTTTTTGTGTGGTGGTGAGTA 59.308 43.478 0.00 0.00 0.00 2.59
3690 4018 1.339151 CCCTTCCTACTTGGCTCACAC 60.339 57.143 0.00 0.00 35.26 3.82
3697 4025 1.717032 ACTTGGCTCACACTCCTGTA 58.283 50.000 0.00 0.00 0.00 2.74
3699 4027 2.234908 ACTTGGCTCACACTCCTGTATC 59.765 50.000 0.00 0.00 0.00 2.24
3747 4075 7.045416 TGTGGAAGTATTAGTCGTAATTGCAT 58.955 34.615 0.00 0.00 31.95 3.96
3794 4125 7.967854 TGAAATTGTGAATAAGATGGTAAAGCG 59.032 33.333 0.00 0.00 0.00 4.68
3803 4134 9.431887 GAATAAGATGGTAAAGCGGTCATAATA 57.568 33.333 0.00 0.00 0.00 0.98
3917 4251 4.931002 GCGTGTGGTAAATACTTCCAAGTA 59.069 41.667 1.66 1.66 44.84 2.24
4042 4379 5.656416 TCTGTTCCTTGTTGAATTTTCAGGT 59.344 36.000 0.00 0.00 38.61 4.00
4048 4385 6.550854 TCCTTGTTGAATTTTCAGGTGATTCT 59.449 34.615 0.00 0.00 38.61 2.40
4121 4458 1.197949 AGTGTCTCGTCTGATGTGTCG 59.802 52.381 0.00 0.00 0.00 4.35
4245 4595 2.091885 AGGTTTTGTTCCTGGCTCTTCA 60.092 45.455 0.00 0.00 33.62 3.02
4294 4644 2.833943 TGCTCTGATCAGCAGTTTCCTA 59.166 45.455 18.36 0.00 44.73 2.94
4311 4661 6.714810 AGTTTCCTATGTGTTGCTATTTGACA 59.285 34.615 0.00 0.00 0.00 3.58
4343 4693 9.698309 GTAGAGCTATGTTTTTATCATGCTCTA 57.302 33.333 21.16 21.16 44.41 2.43
4362 4712 6.070596 TGCTCTAGATTTGATGGAAAGAGTGA 60.071 38.462 0.00 0.00 0.00 3.41
4406 4756 9.289303 GTTGGCTGTTATGTATTGATTTTAGTG 57.711 33.333 0.00 0.00 0.00 2.74
4472 4822 8.410141 TCGTTCCTTTCTTGTTTGTTTTGATAT 58.590 29.630 0.00 0.00 0.00 1.63
4517 4867 5.358160 AGCTCTTCCCTTTAATGCATGTTAC 59.642 40.000 0.00 0.00 0.00 2.50
4522 4872 7.450014 TCTTCCCTTTAATGCATGTTACTTCAA 59.550 33.333 0.00 0.00 0.00 2.69
4541 4891 5.211174 TCAATGTTGTTGATTTGATGCCA 57.789 34.783 0.00 0.00 0.00 4.92
4569 4919 7.868922 TGTTCAGAAACAAGATTTTGATGGATG 59.131 33.333 2.48 0.00 42.34 3.51
4621 4971 5.982890 TGATCAGTATCAGTTGTGTCTCA 57.017 39.130 0.00 0.00 37.20 3.27
4656 5006 7.069578 ACACTCTACCTTTTCTGACTTGAGTTA 59.930 37.037 0.00 0.00 31.02 2.24
4886 5245 2.684001 ATTTCACCTTGGCATGCATG 57.316 45.000 22.70 22.70 0.00 4.06
4889 5248 1.447140 CACCTTGGCATGCATGTGC 60.447 57.895 26.79 15.96 44.31 4.57
4932 5291 6.780457 AATGAGTGTTATCAAGGAAATGGG 57.220 37.500 0.00 0.00 31.76 4.00
4953 5312 3.079578 GTTTAGGTAAACCAGCACCTCC 58.920 50.000 1.26 0.00 44.17 4.30
5002 5361 9.753674 TTATCATCTTCTTGGTTTTAGGTGATT 57.246 29.630 0.00 0.00 38.85 2.57
5005 5364 7.890127 TCATCTTCTTGGTTTTAGGTGATTGAT 59.110 33.333 0.00 0.00 0.00 2.57
5046 5405 3.037549 TGCTTGGGTTTTCCTGATGTTT 58.962 40.909 0.00 0.00 40.46 2.83
5073 5432 3.500680 GCGTTGGGTTCTGATTCACTTTA 59.499 43.478 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 137 4.349636 TGTCAAAGGTTAGAGGTTCATGGA 59.650 41.667 0.00 0.00 0.00 3.41
185 188 1.200020 GCTGAGCAAAGCGGTAACATT 59.800 47.619 0.00 0.00 32.56 2.71
259 265 6.334378 TGTGATATCCCAACCAAAATCCTA 57.666 37.500 0.00 0.00 0.00 2.94
390 399 0.037139 TCGGGAACATAACACCGGTG 60.037 55.000 32.83 32.83 45.97 4.94
579 590 0.678048 CTTAGACAAGCACTGGCCCC 60.678 60.000 0.00 0.00 42.56 5.80
696 707 3.192212 CGATAGGAGCTGCACATATCTCA 59.808 47.826 22.52 0.00 31.60 3.27
736 747 2.357517 AAGACCAGCAAGACCGCG 60.358 61.111 0.00 0.00 36.85 6.46
830 842 0.248498 TAAGCTCTCGCGATCAACGG 60.248 55.000 10.36 0.00 42.32 4.44
878 890 6.483640 GCCATGACTTTCGAAAGATTATACCT 59.516 38.462 37.54 17.35 41.60 3.08
897 909 0.250295 GCCTATAACCGCAGCCATGA 60.250 55.000 0.00 0.00 0.00 3.07
899 911 0.250467 CTGCCTATAACCGCAGCCAT 60.250 55.000 0.00 0.00 45.39 4.40
1105 1118 3.560068 GCGAGAAGAGAAACAAAGGAACA 59.440 43.478 0.00 0.00 0.00 3.18
1253 1267 4.283467 TGTTGTAGTAATCTGTGAGCCACT 59.717 41.667 6.83 0.00 35.11 4.00
1373 1387 2.818169 AAGCTGCCGACCTGGAACA 61.818 57.895 0.00 0.00 42.00 3.18
1390 1404 1.619363 ATCCACCCTGCTAGCCCAA 60.619 57.895 13.29 0.00 0.00 4.12
1638 1654 1.627834 GGTTGGATTGAATTGGGCCAA 59.372 47.619 23.33 23.33 36.35 4.52
1750 1767 3.971702 GGAGGCAGTGGCAAGGGT 61.972 66.667 20.04 0.00 43.71 4.34
1755 1772 3.177884 ACCAAGGAGGCAGTGGCA 61.178 61.111 20.04 0.00 43.71 4.92
1769 1786 0.039618 GAAGGAGGGAAATGCCACCA 59.960 55.000 9.87 0.00 38.95 4.17
1776 1793 0.543749 CGGCTGAGAAGGAGGGAAAT 59.456 55.000 0.00 0.00 0.00 2.17
1779 1796 3.077556 GCGGCTGAGAAGGAGGGA 61.078 66.667 0.00 0.00 0.00 4.20
1855 1872 2.207229 TGTAGCAGGTCGCAGGTGT 61.207 57.895 0.00 0.00 46.13 4.16
1860 1877 3.299977 ACGGTGTAGCAGGTCGCA 61.300 61.111 0.00 0.00 46.13 5.10
1884 1901 3.537206 GAGCAGCACCGGAGTTGGT 62.537 63.158 19.26 19.26 45.21 3.67
1949 1966 2.682494 GTGGGCAGGGACGTCCTA 60.682 66.667 32.52 10.72 46.12 2.94
1953 1970 4.033776 CATGGTGGGCAGGGACGT 62.034 66.667 0.00 0.00 0.00 4.34
1994 2011 2.725008 GATGGAGAGGTCGAGGCG 59.275 66.667 0.00 0.00 0.00 5.52
2043 2060 0.034089 AAAAAGAGGATGAGGCCCCG 60.034 55.000 0.00 0.00 0.00 5.73
2062 2079 1.628846 GTGGGAAGGAGTGGAGCTTAA 59.371 52.381 0.00 0.00 0.00 1.85
2071 2088 1.081277 GGGAGAGGTGGGAAGGAGT 59.919 63.158 0.00 0.00 0.00 3.85
2076 2093 1.229853 GGGAAGGGAGAGGTGGGAA 60.230 63.158 0.00 0.00 0.00 3.97
2113 2130 2.994578 CAAATGGATGCGCAATGAACAA 59.005 40.909 17.11 0.00 0.00 2.83
2120 2137 2.013400 ACGATACAAATGGATGCGCAA 58.987 42.857 17.11 0.00 0.00 4.85
2139 2156 4.425520 GCAGTCGGCCTAATATATCTCAC 58.574 47.826 0.00 0.00 36.11 3.51
2140 2157 4.720649 GCAGTCGGCCTAATATATCTCA 57.279 45.455 0.00 0.00 36.11 3.27
2157 2174 0.610174 TCGATCAGAGCAAAGGCAGT 59.390 50.000 0.00 0.00 44.61 4.40
2177 2194 3.162666 ACTCATCCGTGACTTCAACCTA 58.837 45.455 0.00 0.00 0.00 3.08
2184 2201 3.654414 GAGTTCAACTCATCCGTGACTT 58.346 45.455 13.01 0.00 44.45 3.01
2233 2250 2.039084 TCAGGTCCAGAGAAAGAAAGCC 59.961 50.000 0.00 0.00 0.00 4.35
2263 2280 9.988815 CTTGTACTCAGAACTATGGCTTATAAT 57.011 33.333 0.00 0.00 0.00 1.28
2307 2324 9.184523 CTTCTGGTAATTTGGTTCATGGTTATA 57.815 33.333 0.00 0.00 0.00 0.98
2646 2663 4.156556 TGGCACATCTTAAAAGCATGAGAC 59.843 41.667 0.00 4.80 0.00 3.36
2704 2733 9.200817 ACCAAGATAGGTGCAACATATAAAATT 57.799 29.630 3.64 0.00 44.84 1.82
2718 3017 9.319143 CTTATCTAGTTCAAACCAAGATAGGTG 57.681 37.037 11.99 6.78 42.25 4.00
2833 3132 3.181445 TGGGGAAAGGATCATTATGTCCG 60.181 47.826 0.00 0.00 39.54 4.79
2840 3139 4.506271 CGATCATCTGGGGAAAGGATCATT 60.506 45.833 0.00 0.00 32.30 2.57
2938 3238 7.986889 AGTAGCAACCAATGAAGAACAAAAATT 59.013 29.630 0.00 0.00 0.00 1.82
2956 3256 4.490743 ACAAACCACAAAACAGTAGCAAC 58.509 39.130 0.00 0.00 0.00 4.17
2989 3289 1.176527 AAAAGACATCCATGGTGCCG 58.823 50.000 12.58 1.27 0.00 5.69
3065 3365 3.255888 TGACTCATACTCGATGGCCATAC 59.744 47.826 20.84 11.53 36.08 2.39
3104 3406 7.119699 CACAGAGAAACCTACATCTATTTGCAA 59.880 37.037 0.00 0.00 0.00 4.08
3182 3502 6.079336 TCATATCCTCCAAATTGAATGGCAT 58.921 36.000 0.00 0.00 37.88 4.40
3306 3629 5.643176 TCCACAATGGCCATATGAATACAT 58.357 37.500 24.91 3.43 37.47 2.29
3340 3663 8.397906 CAGCGATATGTCAGGAGAATTTTAAAA 58.602 33.333 2.51 2.51 0.00 1.52
3357 3681 9.862371 AATCTCCTACTAATAAACAGCGATATG 57.138 33.333 0.00 0.00 0.00 1.78
3363 3687 9.825109 AGAAGAAATCTCCTACTAATAAACAGC 57.175 33.333 0.00 0.00 30.46 4.40
3417 3741 9.967346 TGTCAACCATCGAATTACAAAATAAAA 57.033 25.926 0.00 0.00 0.00 1.52
3421 3745 7.174946 AGACTGTCAACCATCGAATTACAAAAT 59.825 33.333 10.88 0.00 0.00 1.82
3481 3808 1.160137 GCGAGGATCACAAGCTTTGT 58.840 50.000 0.00 0.00 46.75 2.83
3498 3825 2.870372 GCAGGGCAGTTGTTAGCG 59.130 61.111 0.00 0.00 0.00 4.26
3540 3867 3.196901 TGACCTTCGCCAACATAGTGTAT 59.803 43.478 0.00 0.00 0.00 2.29
3544 3871 3.009723 CAATGACCTTCGCCAACATAGT 58.990 45.455 0.00 0.00 0.00 2.12
3563 3890 1.735926 TCCATGGTAGTGGTGGACAA 58.264 50.000 12.58 0.00 40.27 3.18
3620 3947 5.918608 ACATCATCTTACATACTCACCACC 58.081 41.667 0.00 0.00 0.00 4.61
3630 3958 6.040166 GGGCAGAAATGAACATCATCTTACAT 59.960 38.462 0.00 0.00 35.76 2.29
3690 4018 9.250624 GTAATAGCAACAAGTAAGATACAGGAG 57.749 37.037 0.00 0.00 0.00 3.69
3699 4027 9.169468 CACAACAAAGTAATAGCAACAAGTAAG 57.831 33.333 0.00 0.00 0.00 2.34
3836 4169 1.001815 GGCGCTGCTACTTTTGAACAA 60.002 47.619 7.64 0.00 0.00 2.83
3849 4182 0.456653 AATCAAACATTCGGCGCTGC 60.457 50.000 12.58 0.00 0.00 5.25
3917 4251 3.474600 GTCAATGATACTCAGGCAGCAT 58.525 45.455 0.00 0.00 0.00 3.79
4042 4379 3.598299 TGCGTTGATGATGTCAGAATCA 58.402 40.909 0.00 0.00 40.73 2.57
4048 4385 1.535028 GGTGTTGCGTTGATGATGTCA 59.465 47.619 0.00 0.00 34.25 3.58
4121 4458 7.337436 AGAACTACACTCTAGAACACCTCATAC 59.663 40.741 0.00 0.00 0.00 2.39
4291 4641 5.294306 ACGATGTCAAATAGCAACACATAGG 59.706 40.000 0.00 0.00 0.00 2.57
4294 4644 5.048782 ACAACGATGTCAAATAGCAACACAT 60.049 36.000 0.00 0.00 33.41 3.21
4311 4661 8.942338 TGATAAAAACATAGCTCTACAACGAT 57.058 30.769 0.00 0.00 0.00 3.73
4343 4693 5.495640 GAGGTCACTCTTTCCATCAAATCT 58.504 41.667 0.00 0.00 40.68 2.40
4362 4712 3.770933 CCAACATTTCAATCCATGGAGGT 59.229 43.478 21.33 7.80 39.02 3.85
4406 4756 2.552315 TCAGGTTTGAGCCATTTTCGAC 59.448 45.455 0.00 0.00 0.00 4.20
4472 4822 4.469945 GCTAATACAGGGCAGGTATATGGA 59.530 45.833 1.42 0.00 31.46 3.41
4517 4867 5.697178 TGGCATCAAATCAACAACATTGAAG 59.303 36.000 0.00 0.00 35.62 3.02
4522 4872 5.553123 ACATTGGCATCAAATCAACAACAT 58.447 33.333 0.00 0.00 36.36 2.71
4541 4891 8.423349 TCCATCAAAATCTTGTTTCTGAACATT 58.577 29.630 0.00 0.00 44.71 2.71
4562 4912 5.733676 AGCACAAAAATAAACCCATCCATC 58.266 37.500 0.00 0.00 0.00 3.51
4621 4971 7.506261 TCAGAAAAGGTAGAGTGTCTCTTAAGT 59.494 37.037 1.63 0.00 41.50 2.24
4775 5129 7.042950 TCTGTGTGTTAGCAGTAGTAAAAACA 58.957 34.615 0.00 0.00 34.57 2.83
4886 5245 7.391148 TTTCCATCTAAGGTGAAATAAGCAC 57.609 36.000 0.00 0.00 35.56 4.40
4889 5248 9.401058 ACTCATTTCCATCTAAGGTGAAATAAG 57.599 33.333 0.00 0.00 35.77 1.73
4932 5291 3.079578 GGAGGTGCTGGTTTACCTAAAC 58.920 50.000 0.00 0.01 46.92 2.01
4985 5344 8.421249 AATGAATCAATCACCTAAAACCAAGA 57.579 30.769 0.00 0.00 41.93 3.02
5002 5361 1.074727 ACCACCACGGGAAATGAATCA 59.925 47.619 0.00 0.00 40.22 2.57
5005 5364 1.144093 AGAACCACCACGGGAAATGAA 59.856 47.619 0.00 0.00 40.22 2.57
5046 5405 3.131223 TGAATCAGAACCCAACGCAAAAA 59.869 39.130 0.00 0.00 0.00 1.94
5050 5409 1.202758 AGTGAATCAGAACCCAACGCA 60.203 47.619 0.00 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.