Multiple sequence alignment - TraesCS6B01G336900

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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 TraesCS6B01G336900 chr6B 100.000 4375 0 0 1 4375 593266663 593262289 0.000000e+00 8080
1 TraesCS6B01G336900 chr6B 95.872 751 31 0 3625 4375 171027067 171026317 0.000000e+00 1216
2 TraesCS6B01G336900 chr6B 95.872 751 31 0 3625 4375 643243037 643242287 0.000000e+00 1216
3 TraesCS6B01G336900 chr6B 93.411 516 29 5 1 514 583683010 583682498 0.000000e+00 760
4 TraesCS6B01G336900 chr6D 89.590 2123 137 48 510 2581 396610593 396608504 0.000000e+00 2619
5 TraesCS6B01G336900 chr6D 94.100 678 25 8 2966 3630 396608049 396607374 0.000000e+00 1016
6 TraesCS6B01G336900 chr6D 91.271 527 40 4 1 522 175236319 175236844 0.000000e+00 713
7 TraesCS6B01G336900 chr6D 90.547 402 28 4 2577 2972 396608473 396608076 1.390000e-144 523
8 TraesCS6B01G336900 chr6A 88.249 1302 79 37 510 1769 542936620 542935351 0.000000e+00 1489
9 TraesCS6B01G336900 chr6A 91.480 892 41 9 2763 3630 542934001 542933121 0.000000e+00 1194
10 TraesCS6B01G336900 chr6A 89.374 847 52 20 1764 2581 542935114 542934277 0.000000e+00 1031
11 TraesCS6B01G336900 chr6A 94.375 160 8 1 2577 2736 542934245 542934087 1.220000e-60 244
12 TraesCS6B01G336900 chr2A 96.680 753 24 1 3624 4375 583020579 583021331 0.000000e+00 1251
13 TraesCS6B01G336900 chr7A 96.405 751 27 0 3625 4375 666848444 666847694 0.000000e+00 1238
14 TraesCS6B01G336900 chr1B 96.005 751 30 0 3625 4375 77620600 77621350 0.000000e+00 1221
15 TraesCS6B01G336900 chr5A 95.739 751 32 0 3625 4375 32844407 32845157 0.000000e+00 1210
16 TraesCS6B01G336900 chr5A 95.606 751 33 0 3625 4375 693471210 693470460 0.000000e+00 1205
17 TraesCS6B01G336900 chr4B 95.739 751 32 0 3625 4375 367311802 367311052 0.000000e+00 1210
18 TraesCS6B01G336900 chr1A 95.606 751 33 0 3625 4375 3510697 3511447 0.000000e+00 1205
19 TraesCS6B01G336900 chr3B 93.424 517 33 1 1 517 725396822 725396307 0.000000e+00 765
20 TraesCS6B01G336900 chr2B 93.725 510 32 0 1 510 504884763 504885272 0.000000e+00 765
21 TraesCS6B01G336900 chr2B 92.308 507 38 1 4 509 675957995 675957489 0.000000e+00 719
22 TraesCS6B01G336900 chr2B 83.688 141 17 5 1949 2087 8034280 8034416 1.280000e-25 128
23 TraesCS6B01G336900 chr2B 83.688 141 17 5 1949 2087 8198204 8198340 1.280000e-25 128
24 TraesCS6B01G336900 chr2B 91.667 72 6 0 1982 2053 9029805 9029734 2.780000e-17 100
25 TraesCS6B01G336900 chr7B 92.982 513 35 1 1 513 54281526 54281015 0.000000e+00 747
26 TraesCS6B01G336900 chr7B 92.338 509 39 0 1 509 330992113 330991605 0.000000e+00 725
27 TraesCS6B01G336900 chr7D 92.172 511 37 3 1 510 601703236 601702728 0.000000e+00 719
28 TraesCS6B01G336900 chr3D 91.908 519 34 8 1 513 262984257 262984773 0.000000e+00 719
29 TraesCS6B01G336900 chrUn 83.688 141 17 5 1949 2087 372165980 372165844 1.280000e-25 128
30 TraesCS6B01G336900 chrUn 81.119 143 22 4 1951 2092 15462928 15463066 4.630000e-20 110
31 TraesCS6B01G336900 chrUn 80.000 145 24 4 1951 2094 15940340 15940480 7.740000e-18 102
32 TraesCS6B01G336900 chr2D 84.615 104 12 3 1951 2053 2753926 2754026 2.780000e-17 100


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 TraesCS6B01G336900 chr6B 593262289 593266663 4374 True 8080.0 8080 100.000000 1 4375 1 chr6B.!!$R3 4374
1 TraesCS6B01G336900 chr6B 171026317 171027067 750 True 1216.0 1216 95.872000 3625 4375 1 chr6B.!!$R1 750
2 TraesCS6B01G336900 chr6B 643242287 643243037 750 True 1216.0 1216 95.872000 3625 4375 1 chr6B.!!$R4 750
3 TraesCS6B01G336900 chr6B 583682498 583683010 512 True 760.0 760 93.411000 1 514 1 chr6B.!!$R2 513
4 TraesCS6B01G336900 chr6D 396607374 396610593 3219 True 1386.0 2619 91.412333 510 3630 3 chr6D.!!$R1 3120
5 TraesCS6B01G336900 chr6D 175236319 175236844 525 False 713.0 713 91.271000 1 522 1 chr6D.!!$F1 521
6 TraesCS6B01G336900 chr6A 542933121 542936620 3499 True 989.5 1489 90.869500 510 3630 4 chr6A.!!$R1 3120
7 TraesCS6B01G336900 chr2A 583020579 583021331 752 False 1251.0 1251 96.680000 3624 4375 1 chr2A.!!$F1 751
8 TraesCS6B01G336900 chr7A 666847694 666848444 750 True 1238.0 1238 96.405000 3625 4375 1 chr7A.!!$R1 750
9 TraesCS6B01G336900 chr1B 77620600 77621350 750 False 1221.0 1221 96.005000 3625 4375 1 chr1B.!!$F1 750
10 TraesCS6B01G336900 chr5A 32844407 32845157 750 False 1210.0 1210 95.739000 3625 4375 1 chr5A.!!$F1 750
11 TraesCS6B01G336900 chr5A 693470460 693471210 750 True 1205.0 1205 95.606000 3625 4375 1 chr5A.!!$R1 750
12 TraesCS6B01G336900 chr4B 367311052 367311802 750 True 1210.0 1210 95.739000 3625 4375 1 chr4B.!!$R1 750
13 TraesCS6B01G336900 chr1A 3510697 3511447 750 False 1205.0 1205 95.606000 3625 4375 1 chr1A.!!$F1 750
14 TraesCS6B01G336900 chr3B 725396307 725396822 515 True 765.0 765 93.424000 1 517 1 chr3B.!!$R1 516
15 TraesCS6B01G336900 chr2B 504884763 504885272 509 False 765.0 765 93.725000 1 510 1 chr2B.!!$F3 509
16 TraesCS6B01G336900 chr2B 675957489 675957995 506 True 719.0 719 92.308000 4 509 1 chr2B.!!$R2 505
17 TraesCS6B01G336900 chr7B 54281015 54281526 511 True 747.0 747 92.982000 1 513 1 chr7B.!!$R1 512
18 TraesCS6B01G336900 chr7B 330991605 330992113 508 True 725.0 725 92.338000 1 509 1 chr7B.!!$R2 508
19 TraesCS6B01G336900 chr7D 601702728 601703236 508 True 719.0 719 92.172000 1 510 1 chr7D.!!$R1 509
20 TraesCS6B01G336900 chr3D 262984257 262984773 516 False 719.0 719 91.908000 1 513 1 chr3D.!!$F1 512

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
618 631 1.135315 CATGACGTGGGCTCCAATTTG 60.135 52.381 0.00 0.00 34.18 2.32 F
1168 1200 1.146485 CCTCCTCCTCTCTCGCGTA 59.854 63.158 5.77 0.00 0.00 4.42 F
1561 1596 0.177836 CCGGTGATCCTGTGTATGCA 59.822 55.000 0.00 0.00 0.00 3.96 F
1907 2221 0.249120 CACCCGAGCTCAACCACATA 59.751 55.000 15.40 0.00 0.00 2.29 F
2459 2777 0.252479 AGCTGATCAGGTTCAGGCTG 59.748 55.000 21.55 8.58 42.78 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 1561 0.182537 CCGGATACCATCTTGGGCAA 59.817 55.000 0.00 0.00 43.37 4.52 R
2440 2758 0.252479 CAGCCTGAACCTGATCAGCT 59.748 55.000 17.76 7.38 44.43 4.24 R
2840 3269 0.540454 GTAGCAACCCCCTAGTGGTC 59.460 60.000 1.93 0.00 34.15 4.02 R
3344 3831 1.078214 CCGACACACAGGGCATGAT 60.078 57.895 5.99 0.00 0.00 2.45 R
4258 4756 1.719529 TAGTCCCGACCTTGGTGAAA 58.280 50.000 0.00 0.00 0.00 2.69 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 1.996191 CTGCTTTTAGCTGGTCGTCTC 59.004 52.381 0.00 0.00 42.97 3.36
189 200 2.597510 GGAGGGTTGGTGTGTGGC 60.598 66.667 0.00 0.00 0.00 5.01
201 212 4.641645 TGTGGCTTGCGGTGGGAG 62.642 66.667 0.00 0.00 0.00 4.30
265 276 2.808206 GGCGATGGAGGTAGGGGTG 61.808 68.421 0.00 0.00 0.00 4.61
524 536 3.523972 GGGACCCTAAATCAAAGAGACCT 59.476 47.826 2.09 0.00 0.00 3.85
558 570 1.273327 GGCAACACAGGGAATGGAAAG 59.727 52.381 0.00 0.00 0.00 2.62
559 571 1.963515 GCAACACAGGGAATGGAAAGT 59.036 47.619 0.00 0.00 0.00 2.66
560 572 2.365293 GCAACACAGGGAATGGAAAGTT 59.635 45.455 0.00 0.00 0.00 2.66
562 574 2.597455 ACACAGGGAATGGAAAGTTGG 58.403 47.619 0.00 0.00 0.00 3.77
563 575 2.176798 ACACAGGGAATGGAAAGTTGGA 59.823 45.455 0.00 0.00 0.00 3.53
565 577 3.640967 CACAGGGAATGGAAAGTTGGAAA 59.359 43.478 0.00 0.00 0.00 3.13
566 578 4.284234 CACAGGGAATGGAAAGTTGGAAAT 59.716 41.667 0.00 0.00 0.00 2.17
568 580 3.840078 AGGGAATGGAAAGTTGGAAATGG 59.160 43.478 0.00 0.00 0.00 3.16
569 581 3.582647 GGGAATGGAAAGTTGGAAATGGT 59.417 43.478 0.00 0.00 0.00 3.55
570 582 4.322725 GGGAATGGAAAGTTGGAAATGGTC 60.323 45.833 0.00 0.00 0.00 4.02
571 583 4.283212 GGAATGGAAAGTTGGAAATGGTCA 59.717 41.667 0.00 0.00 0.00 4.02
572 584 5.473039 GAATGGAAAGTTGGAAATGGTCAG 58.527 41.667 0.00 0.00 0.00 3.51
575 587 3.255888 GGAAAGTTGGAAATGGTCAGGAC 59.744 47.826 0.00 0.00 0.00 3.85
576 588 3.593442 AAGTTGGAAATGGTCAGGACA 57.407 42.857 1.41 0.00 0.00 4.02
596 609 2.260844 TTCCATCCGCTCCAATCATC 57.739 50.000 0.00 0.00 0.00 2.92
600 613 2.501261 CATCCGCTCCAATCATCACAT 58.499 47.619 0.00 0.00 0.00 3.21
617 630 1.176527 CATGACGTGGGCTCCAATTT 58.823 50.000 0.00 0.00 34.18 1.82
618 631 1.135315 CATGACGTGGGCTCCAATTTG 60.135 52.381 0.00 0.00 34.18 2.32
625 638 2.299867 GTGGGCTCCAATTTGAACACAT 59.700 45.455 0.00 0.00 34.18 3.21
632 645 6.161381 GCTCCAATTTGAACACATGAAAGAT 58.839 36.000 0.00 0.00 0.00 2.40
636 649 9.076781 TCCAATTTGAACACATGAAAGATAGAA 57.923 29.630 0.00 0.00 0.00 2.10
732 750 3.378427 CCTAAATTCTGCCCCGAAAAGAG 59.622 47.826 0.00 0.00 0.00 2.85
968 1000 3.126686 GCGCCAAAAATAAACCCGTACTA 59.873 43.478 0.00 0.00 0.00 1.82
979 1011 1.153005 CCGTACTACCTCTCCGCCT 60.153 63.158 0.00 0.00 0.00 5.52
1142 1174 4.363999 CTCTTCGCTCTCGGTAATTGATT 58.636 43.478 0.00 0.00 36.13 2.57
1149 1181 2.092968 TCTCGGTAATTGATTGCTGGCT 60.093 45.455 1.63 0.00 30.87 4.75
1150 1182 2.288666 TCGGTAATTGATTGCTGGCTC 58.711 47.619 1.63 0.00 30.87 4.70
1168 1200 1.146485 CCTCCTCCTCTCTCGCGTA 59.854 63.158 5.77 0.00 0.00 4.42
1207 1240 1.525995 CTTGTTGGGCACACTCCGT 60.526 57.895 0.00 0.00 33.98 4.69
1213 1246 2.347490 GGCACACTCCGTCATGGT 59.653 61.111 0.00 0.00 39.52 3.55
1282 1315 5.355350 GTGTTATTAAGCTGGAGCATTGACT 59.645 40.000 0.65 0.00 45.16 3.41
1458 1491 5.647658 CCATGGTCAGTAACATTAAGCTTCA 59.352 40.000 0.00 0.00 0.00 3.02
1512 1547 8.851541 ATTTCAGATTATTTGTTGTGGCAATT 57.148 26.923 0.00 0.00 0.00 2.32
1515 1550 7.035004 TCAGATTATTTGTTGTGGCAATTAGC 58.965 34.615 0.00 0.00 44.65 3.09
1526 1561 4.955450 TGTGGCAATTAGCTCCATAATGTT 59.045 37.500 0.00 0.00 44.79 2.71
1528 1563 5.750067 GTGGCAATTAGCTCCATAATGTTTG 59.250 40.000 0.00 0.00 44.79 2.93
1538 1573 3.705579 TCCATAATGTTTGCCCAAGATGG 59.294 43.478 0.00 0.00 37.25 3.51
1543 1578 2.733956 TGTTTGCCCAAGATGGTATCC 58.266 47.619 0.00 0.00 35.17 2.59
1555 1590 1.119684 TGGTATCCGGTGATCCTGTG 58.880 55.000 0.00 0.00 32.18 3.66
1556 1591 1.120530 GGTATCCGGTGATCCTGTGT 58.879 55.000 0.00 0.00 32.18 3.72
1558 1593 2.897969 GGTATCCGGTGATCCTGTGTAT 59.102 50.000 0.00 0.00 32.18 2.29
1559 1594 3.306088 GGTATCCGGTGATCCTGTGTATG 60.306 52.174 0.00 0.00 32.18 2.39
1560 1595 0.464036 TCCGGTGATCCTGTGTATGC 59.536 55.000 0.00 0.00 0.00 3.14
1561 1596 0.177836 CCGGTGATCCTGTGTATGCA 59.822 55.000 0.00 0.00 0.00 3.96
1562 1597 1.202687 CCGGTGATCCTGTGTATGCAT 60.203 52.381 3.79 3.79 0.00 3.96
1563 1598 1.869132 CGGTGATCCTGTGTATGCATG 59.131 52.381 10.16 0.00 0.00 4.06
1564 1599 2.742856 CGGTGATCCTGTGTATGCATGT 60.743 50.000 10.16 0.00 0.00 3.21
1565 1600 3.492482 CGGTGATCCTGTGTATGCATGTA 60.492 47.826 10.16 0.00 0.00 2.29
1566 1601 3.809832 GGTGATCCTGTGTATGCATGTAC 59.190 47.826 10.16 8.77 0.00 2.90
1567 1602 4.443457 GGTGATCCTGTGTATGCATGTACT 60.443 45.833 10.16 0.00 0.00 2.73
1568 1603 4.747108 GTGATCCTGTGTATGCATGTACTC 59.253 45.833 10.16 1.98 0.00 2.59
1586 1621 2.149578 CTCTGTTCTCTGCTTGTTGGG 58.850 52.381 0.00 0.00 0.00 4.12
1639 1687 0.456221 ATCGGTAGGTCGTTCTGCTG 59.544 55.000 0.00 0.00 0.00 4.41
1640 1688 1.805945 CGGTAGGTCGTTCTGCTGC 60.806 63.158 0.00 0.00 0.00 5.25
1651 1699 2.346847 CGTTCTGCTGCTTAGTGTGATC 59.653 50.000 0.00 0.00 0.00 2.92
1658 1706 6.881065 TCTGCTGCTTAGTGTGATCTTTATTT 59.119 34.615 0.00 0.00 0.00 1.40
1660 1708 7.885297 TGCTGCTTAGTGTGATCTTTATTTTT 58.115 30.769 0.00 0.00 0.00 1.94
1672 1720 9.759259 GTGATCTTTATTTTTAAAATGCCAAGC 57.241 29.630 12.62 0.95 0.00 4.01
1673 1721 9.499479 TGATCTTTATTTTTAAAATGCCAAGCA 57.501 25.926 12.62 3.22 44.86 3.91
1700 1753 9.658475 TTACAGATTTGAAGTTTTATGTTCACG 57.342 29.630 0.00 0.00 32.40 4.35
1724 1777 5.757808 GTGTTGTGCCATTTGGTAGAAAAAT 59.242 36.000 0.00 0.00 35.08 1.82
1725 1778 6.259829 GTGTTGTGCCATTTGGTAGAAAAATT 59.740 34.615 0.00 0.00 35.08 1.82
1729 1782 3.689161 GCCATTTGGTAGAAAAATTGGCC 59.311 43.478 0.00 0.00 36.39 5.36
1734 1790 7.609532 CCATTTGGTAGAAAAATTGGCCAATTA 59.390 33.333 37.45 22.48 39.88 1.40
1738 1794 8.367660 TGGTAGAAAAATTGGCCAATTATGTA 57.632 30.769 37.45 27.93 39.88 2.29
1739 1795 8.816894 TGGTAGAAAAATTGGCCAATTATGTAA 58.183 29.630 37.45 22.71 39.88 2.41
1786 2085 2.368221 CCCCTTGTTCTTTTTGGATGCA 59.632 45.455 0.00 0.00 0.00 3.96
1824 2123 5.805486 GGTTTTCCTCCGATTATTTTTCTGC 59.195 40.000 0.00 0.00 36.94 4.26
1834 2138 7.437862 TCCGATTATTTTTCTGCCATATTTTGC 59.562 33.333 0.00 0.00 0.00 3.68
1846 2150 9.585099 TCTGCCATATTTTGCTACTAATTTTTG 57.415 29.630 0.00 0.00 0.00 2.44
1857 2162 7.535139 TGCTACTAATTTTTGAGTGCCATAAC 58.465 34.615 0.00 0.00 0.00 1.89
1861 2168 7.748847 ACTAATTTTTGAGTGCCATAACGTAG 58.251 34.615 0.00 0.00 0.00 3.51
1872 2179 6.651643 AGTGCCATAACGTAGTGTTCAAAATA 59.348 34.615 0.00 0.00 45.00 1.40
1907 2221 0.249120 CACCCGAGCTCAACCACATA 59.751 55.000 15.40 0.00 0.00 2.29
1911 2225 3.016736 CCCGAGCTCAACCACATATTTT 58.983 45.455 15.40 0.00 0.00 1.82
1915 2229 4.396166 CGAGCTCAACCACATATTTTCCTT 59.604 41.667 15.40 0.00 0.00 3.36
1917 2231 6.093495 CGAGCTCAACCACATATTTTCCTTAA 59.907 38.462 15.40 0.00 0.00 1.85
1918 2232 7.158099 AGCTCAACCACATATTTTCCTTAAC 57.842 36.000 0.00 0.00 0.00 2.01
1919 2233 6.948309 AGCTCAACCACATATTTTCCTTAACT 59.052 34.615 0.00 0.00 0.00 2.24
1920 2234 7.029563 GCTCAACCACATATTTTCCTTAACTG 58.970 38.462 0.00 0.00 0.00 3.16
2051 2368 1.153086 GCTTGGATCCTCGGCACAT 60.153 57.895 14.23 0.00 0.00 3.21
2093 2410 7.607991 CAGGTCAGTTTCAGTATTATCAACCTT 59.392 37.037 0.00 0.00 30.08 3.50
2122 2439 1.822581 GACAACGTTTGCCACAGAAC 58.177 50.000 0.00 0.00 0.00 3.01
2129 2447 0.884704 TTTGCCACAGAACGGAGAGC 60.885 55.000 0.00 0.00 0.00 4.09
2141 2459 2.464459 GGAGAGCGAAATGGCACCG 61.464 63.158 0.00 0.00 34.64 4.94
2162 2480 3.585862 GAACCGATGGCGATGTATACAT 58.414 45.455 18.31 18.31 40.82 2.29
2177 2495 4.625311 TGTATACATGAGTGTTGCTTGTCG 59.375 41.667 0.08 0.00 39.77 4.35
2284 2602 2.659244 TCCCGTCGTGCGTTGTTC 60.659 61.111 0.00 0.00 39.32 3.18
2305 2623 6.939730 TGTTCCTGCATCTGTACTGAATTTTA 59.060 34.615 6.54 0.00 0.00 1.52
2310 2628 8.680903 CCTGCATCTGTACTGAATTTTAGATTT 58.319 33.333 6.54 0.00 0.00 2.17
2312 2630 8.461222 TGCATCTGTACTGAATTTTAGATTTGG 58.539 33.333 6.54 0.00 0.00 3.28
2389 2707 2.676750 CGACATCTTCGGGGACATTTCA 60.677 50.000 0.00 0.00 44.60 2.69
2395 2713 0.464036 TCGGGGACATTTCATCGAGG 59.536 55.000 0.00 0.00 0.00 4.63
2428 2746 2.026262 GGAGGCACTGGAGAAATTACCA 60.026 50.000 0.00 0.00 41.55 3.25
2446 2764 2.941453 CACACTACGTGGTAGCTGAT 57.059 50.000 3.52 0.00 42.34 2.90
2447 2765 2.798680 CACACTACGTGGTAGCTGATC 58.201 52.381 3.52 0.00 42.34 2.92
2448 2766 2.163613 CACACTACGTGGTAGCTGATCA 59.836 50.000 3.52 0.00 42.34 2.92
2449 2767 2.423892 ACACTACGTGGTAGCTGATCAG 59.576 50.000 18.84 18.84 39.51 2.90
2450 2768 2.025155 ACTACGTGGTAGCTGATCAGG 58.975 52.381 23.89 7.99 39.51 3.86
2451 2769 2.025155 CTACGTGGTAGCTGATCAGGT 58.975 52.381 28.82 28.82 40.38 4.00
2459 2777 0.252479 AGCTGATCAGGTTCAGGCTG 59.748 55.000 21.55 8.58 42.78 4.85
2486 2804 0.676736 GGGCAAATCGGGTGAAAACA 59.323 50.000 0.00 0.00 0.00 2.83
2533 2853 9.482627 CAGGTACAATTATCATAAGAACCTCTC 57.517 37.037 0.00 0.00 32.61 3.20
2553 2877 4.037923 TCTCAGTTTGCCCTTCATTTTGTC 59.962 41.667 0.00 0.00 0.00 3.18
2554 2878 3.960102 TCAGTTTGCCCTTCATTTTGTCT 59.040 39.130 0.00 0.00 0.00 3.41
2565 2889 7.633553 GCCCTTCATTTTGTCTAAGGCAAATAT 60.634 37.037 0.00 0.00 37.71 1.28
2594 2960 0.259356 AGGAAACGGGGAACAAACCA 59.741 50.000 0.00 0.00 0.00 3.67
2630 3000 5.065988 TCACAGAAGAACCTAAAACACAAGC 59.934 40.000 0.00 0.00 0.00 4.01
2674 3044 4.780815 TGAAGTTAATGTGGCTCCCATAG 58.219 43.478 0.00 0.00 35.28 2.23
2770 3199 4.642437 TGAGACTCCATAGCTGAGTACTTG 59.358 45.833 5.25 0.00 42.94 3.16
2840 3269 1.752683 AGCAGAGTACCTACCAGTCG 58.247 55.000 0.00 0.00 0.00 4.18
2850 3279 1.390565 CTACCAGTCGACCACTAGGG 58.609 60.000 13.01 7.15 44.81 3.53
2933 3362 9.120538 AGATGAAACTTTGTGCTAAAGACTAAA 57.879 29.630 17.17 3.71 0.00 1.85
2939 3368 8.451908 ACTTTGTGCTAAAGACTAAAGTTCAT 57.548 30.769 17.17 0.00 35.52 2.57
2940 3369 8.560374 ACTTTGTGCTAAAGACTAAAGTTCATC 58.440 33.333 17.17 0.00 35.52 2.92
2972 3436 9.841295 TTCTGTAACAAAATTCACCTAGTACTT 57.159 29.630 0.00 0.00 0.00 2.24
3029 3493 6.710295 TCACTGTGACATTAAACTGCAATACT 59.290 34.615 6.36 0.00 0.00 2.12
3068 3532 0.839946 AGAGAGGTGCAACAACCACT 59.160 50.000 3.64 0.00 42.97 4.00
3069 3533 1.230324 GAGAGGTGCAACAACCACTC 58.770 55.000 3.64 3.48 46.25 3.51
3080 3544 2.774687 ACAACCACTCCGTTTATGTCC 58.225 47.619 0.00 0.00 0.00 4.02
3105 3571 9.191995 CCTCGTTAGATTTTTAAAAGCAATTGT 57.808 29.630 8.40 0.00 0.00 2.71
3135 3601 4.570369 CGGATTTCATACCAATTTTTGCCC 59.430 41.667 0.00 0.00 0.00 5.36
3417 3904 0.103937 CGATCTGAGTTCTCTGCCCC 59.896 60.000 1.53 0.00 0.00 5.80
3435 3925 3.308188 GCCCCAGGAGTTAGTTGTGTAAT 60.308 47.826 0.00 0.00 0.00 1.89
3553 4050 3.568007 TCCAAGCAAGTGGAAATGTACAC 59.432 43.478 0.00 0.00 44.91 2.90
3621 4118 0.464373 CACGGCTGCCATAGGATGTT 60.464 55.000 20.29 0.00 0.00 2.71
3768 4265 2.313317 AGGGGACGCGAATACTCAATA 58.687 47.619 15.93 0.00 0.00 1.90
4091 4589 5.867716 GTCGAGTTCTATAAAAAGTGCTGGA 59.132 40.000 0.00 0.00 0.00 3.86
4192 4690 5.045213 TGGAACTATCACATTGCTCCCTAAA 60.045 40.000 0.00 0.00 0.00 1.85
4195 4693 7.396540 AACTATCACATTGCTCCCTAAAAAG 57.603 36.000 0.00 0.00 0.00 2.27
4258 4756 7.154656 GCCTCCTCAATGTTAGTTTCAAAATT 58.845 34.615 0.00 0.00 0.00 1.82
4307 4805 1.812235 ACAGATTGCGCATTCTGTGA 58.188 45.000 43.58 20.32 45.11 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 212 0.766288 AGAGCAGATCCTTAGGGCCC 60.766 60.000 16.46 16.46 0.00 5.80
209 220 1.203441 TGGCAACCAGAGCAGATCCT 61.203 55.000 0.00 0.00 0.00 3.24
265 276 2.122167 ATCGTCTCCCACCTCTCGC 61.122 63.158 0.00 0.00 0.00 5.03
524 536 3.698539 TGTGTTGCCATGAAAAAGACTCA 59.301 39.130 0.00 0.00 0.00 3.41
530 542 2.392662 TCCCTGTGTTGCCATGAAAAA 58.607 42.857 0.00 0.00 0.00 1.94
549 561 5.467035 TGACCATTTCCAACTTTCCATTC 57.533 39.130 0.00 0.00 0.00 2.67
558 570 3.193479 GGAATGTCCTGACCATTTCCAAC 59.807 47.826 14.13 0.00 35.60 3.77
559 571 3.181424 TGGAATGTCCTGACCATTTCCAA 60.181 43.478 17.20 7.37 39.10 3.53
560 572 2.378208 TGGAATGTCCTGACCATTTCCA 59.622 45.455 16.26 16.26 39.42 3.53
562 574 3.633986 GGATGGAATGTCCTGACCATTTC 59.366 47.826 0.00 0.00 42.23 2.17
563 575 3.635591 GGATGGAATGTCCTGACCATTT 58.364 45.455 0.00 0.00 42.23 2.32
565 577 1.141657 CGGATGGAATGTCCTGACCAT 59.858 52.381 0.00 0.00 44.40 3.55
566 578 0.541392 CGGATGGAATGTCCTGACCA 59.459 55.000 0.00 0.00 37.46 4.02
568 580 0.179000 AGCGGATGGAATGTCCTGAC 59.821 55.000 0.00 0.00 37.46 3.51
569 581 0.465705 GAGCGGATGGAATGTCCTGA 59.534 55.000 0.00 0.00 37.46 3.86
570 582 0.533755 GGAGCGGATGGAATGTCCTG 60.534 60.000 0.00 0.00 37.46 3.86
571 583 0.982852 TGGAGCGGATGGAATGTCCT 60.983 55.000 0.00 0.00 37.46 3.85
572 584 0.107214 TTGGAGCGGATGGAATGTCC 60.107 55.000 0.00 0.00 36.96 4.02
575 587 1.971481 TGATTGGAGCGGATGGAATG 58.029 50.000 0.00 0.00 0.00 2.67
576 588 2.107031 TGATGATTGGAGCGGATGGAAT 59.893 45.455 0.00 0.00 0.00 3.01
600 613 0.109532 TCAAATTGGAGCCCACGTCA 59.890 50.000 0.00 0.00 30.78 4.35
636 649 6.937436 ACCTCGTGTGAGTATTTTCTTTTT 57.063 33.333 0.00 0.00 40.85 1.94
732 750 1.205893 CTCTCTGTGTTGGTAGAGGCC 59.794 57.143 0.00 0.00 40.59 5.19
813 838 2.158957 GGCTTCCCGTGATGAAGTGATA 60.159 50.000 0.00 0.00 41.03 2.15
968 1000 1.456705 GAGGATCAGGCGGAGAGGT 60.457 63.158 0.00 0.00 33.17 3.85
1066 1098 2.284405 CCTGGGGAGGTACACGGT 60.284 66.667 0.00 0.00 0.00 4.83
1142 1174 2.364842 GAGGAGGAGGAGCCAGCA 60.365 66.667 0.00 0.00 40.02 4.41
1149 1181 1.335882 TACGCGAGAGAGGAGGAGGA 61.336 60.000 15.93 0.00 34.13 3.71
1150 1182 1.146485 TACGCGAGAGAGGAGGAGG 59.854 63.158 15.93 0.00 34.13 4.30
1207 1240 1.221566 CACATGCTCGGGACCATGA 59.778 57.895 9.55 0.00 40.92 3.07
1213 1246 0.684535 TTCAGAACACATGCTCGGGA 59.315 50.000 0.00 0.00 0.00 5.14
1458 1491 1.707427 GATAGCATCAAGGGGGTGGAT 59.293 52.381 0.00 0.00 0.00 3.41
1497 1532 3.577848 TGGAGCTAATTGCCACAACAAAT 59.422 39.130 0.00 0.00 44.23 2.32
1512 1547 3.660970 TGGGCAAACATTATGGAGCTA 57.339 42.857 0.00 0.00 0.00 3.32
1515 1550 4.202182 CCATCTTGGGCAAACATTATGGAG 60.202 45.833 0.00 0.00 36.13 3.86
1526 1561 0.182537 CCGGATACCATCTTGGGCAA 59.817 55.000 0.00 0.00 43.37 4.52
1528 1563 0.535102 CACCGGATACCATCTTGGGC 60.535 60.000 9.46 0.00 43.37 5.36
1538 1573 3.861131 GCATACACAGGATCACCGGATAC 60.861 52.174 9.46 0.00 41.83 2.24
1543 1578 1.869132 CATGCATACACAGGATCACCG 59.131 52.381 0.00 0.00 41.83 4.94
1555 1590 4.505922 GCAGAGAACAGAGTACATGCATAC 59.494 45.833 0.00 0.00 32.79 2.39
1556 1591 4.403752 AGCAGAGAACAGAGTACATGCATA 59.596 41.667 0.00 0.00 34.93 3.14
1558 1593 2.564504 AGCAGAGAACAGAGTACATGCA 59.435 45.455 0.00 0.00 34.93 3.96
1559 1594 3.244033 AGCAGAGAACAGAGTACATGC 57.756 47.619 0.00 0.00 0.00 4.06
1560 1595 4.564041 ACAAGCAGAGAACAGAGTACATG 58.436 43.478 0.00 0.00 0.00 3.21
1561 1596 4.881019 ACAAGCAGAGAACAGAGTACAT 57.119 40.909 0.00 0.00 0.00 2.29
1562 1597 4.371786 CAACAAGCAGAGAACAGAGTACA 58.628 43.478 0.00 0.00 0.00 2.90
1563 1598 3.743396 CCAACAAGCAGAGAACAGAGTAC 59.257 47.826 0.00 0.00 0.00 2.73
1564 1599 3.244215 CCCAACAAGCAGAGAACAGAGTA 60.244 47.826 0.00 0.00 0.00 2.59
1565 1600 2.486191 CCCAACAAGCAGAGAACAGAGT 60.486 50.000 0.00 0.00 0.00 3.24
1566 1601 2.149578 CCCAACAAGCAGAGAACAGAG 58.850 52.381 0.00 0.00 0.00 3.35
1567 1602 1.815408 GCCCAACAAGCAGAGAACAGA 60.815 52.381 0.00 0.00 0.00 3.41
1568 1603 0.595095 GCCCAACAAGCAGAGAACAG 59.405 55.000 0.00 0.00 0.00 3.16
1586 1621 2.811307 TGGCATAAGGCATTCAGGC 58.189 52.632 0.00 0.00 46.46 4.85
1622 1657 1.805945 GCAGCAGAACGACCTACCG 60.806 63.158 0.00 0.00 0.00 4.02
1675 1723 8.832521 ACGTGAACATAAAACTTCAAATCTGTA 58.167 29.630 0.00 0.00 0.00 2.74
1676 1724 7.643764 CACGTGAACATAAAACTTCAAATCTGT 59.356 33.333 10.90 0.00 0.00 3.41
1677 1725 7.643764 ACACGTGAACATAAAACTTCAAATCTG 59.356 33.333 25.01 0.00 0.00 2.90
1678 1726 7.703328 ACACGTGAACATAAAACTTCAAATCT 58.297 30.769 25.01 0.00 0.00 2.40
1679 1727 7.908193 ACACGTGAACATAAAACTTCAAATC 57.092 32.000 25.01 0.00 0.00 2.17
1680 1728 7.757624 ACAACACGTGAACATAAAACTTCAAAT 59.242 29.630 25.01 0.00 0.00 2.32
1681 1729 7.085116 ACAACACGTGAACATAAAACTTCAAA 58.915 30.769 25.01 0.00 0.00 2.69
1749 1805 4.220821 ACAAGGGGTAGCAGATATGTATCG 59.779 45.833 0.00 0.00 37.76 2.92
1750 1806 5.746990 ACAAGGGGTAGCAGATATGTATC 57.253 43.478 0.00 0.00 0.00 2.24
1759 1815 3.005791 CCAAAAAGAACAAGGGGTAGCAG 59.994 47.826 0.00 0.00 0.00 4.24
1834 2138 7.748847 ACGTTATGGCACTCAAAAATTAGTAG 58.251 34.615 0.00 0.00 0.00 2.57
1839 2143 6.016610 ACACTACGTTATGGCACTCAAAAATT 60.017 34.615 0.00 0.00 0.00 1.82
1843 2147 3.997762 ACACTACGTTATGGCACTCAAA 58.002 40.909 0.00 0.00 0.00 2.69
1846 2150 3.581755 TGAACACTACGTTATGGCACTC 58.418 45.455 0.00 0.00 38.19 3.51
1850 2155 6.959311 CACTATTTTGAACACTACGTTATGGC 59.041 38.462 0.00 0.00 38.19 4.40
1857 2162 4.753107 ACCCACACTATTTTGAACACTACG 59.247 41.667 0.00 0.00 0.00 3.51
1861 2168 4.911514 ACACCCACACTATTTTGAACAC 57.088 40.909 0.00 0.00 0.00 3.32
1947 2264 4.067972 TGAACTTTCTTAGAGGCGTGTT 57.932 40.909 0.00 0.00 0.00 3.32
2122 2439 2.464459 GGTGCCATTTCGCTCTCCG 61.464 63.158 0.00 0.00 38.61 4.63
2123 2440 2.464459 CGGTGCCATTTCGCTCTCC 61.464 63.158 0.00 0.00 0.00 3.71
2129 2447 1.366111 ATCGGTTCGGTGCCATTTCG 61.366 55.000 0.00 0.00 0.00 3.46
2141 2459 3.021269 TGTATACATCGCCATCGGTTC 57.979 47.619 0.08 0.00 36.13 3.62
2162 2480 1.134818 ACACTCGACAAGCAACACTCA 60.135 47.619 0.00 0.00 0.00 3.41
2177 2495 1.317613 TCACCAAATGCACCACACTC 58.682 50.000 0.00 0.00 0.00 3.51
2284 2602 7.798596 ATCTAAAATTCAGTACAGATGCAGG 57.201 36.000 0.00 0.00 0.00 4.85
2319 2637 2.156917 TGCTGAGCTGTTTGATGAAGG 58.843 47.619 5.83 0.00 0.00 3.46
2389 2707 2.435693 CCTCGAAAGCCCCCTCGAT 61.436 63.158 0.00 0.00 42.73 3.59
2395 2713 4.491409 GCCTCCCTCGAAAGCCCC 62.491 72.222 0.00 0.00 0.00 5.80
2405 2723 1.376649 AATTTCTCCAGTGCCTCCCT 58.623 50.000 0.00 0.00 0.00 4.20
2440 2758 0.252479 CAGCCTGAACCTGATCAGCT 59.748 55.000 17.76 7.38 44.43 4.24
2446 2764 1.537397 AGCCTCAGCCTGAACCTGA 60.537 57.895 0.00 0.00 41.25 3.86
2447 2765 1.078567 GAGCCTCAGCCTGAACCTG 60.079 63.158 0.00 0.00 41.25 4.00
2448 2766 1.537397 TGAGCCTCAGCCTGAACCT 60.537 57.895 0.00 0.00 41.25 3.50
2449 2767 1.078567 CTGAGCCTCAGCCTGAACC 60.079 63.158 9.13 0.00 37.72 3.62
2450 2768 1.078567 CCTGAGCCTCAGCCTGAAC 60.079 63.158 16.49 0.00 42.98 3.18
2451 2769 2.296365 CCCTGAGCCTCAGCCTGAA 61.296 63.158 16.49 0.00 42.98 3.02
2459 2777 1.821332 CCGATTTGCCCTGAGCCTC 60.821 63.158 0.00 0.00 42.71 4.70
2533 2853 4.326504 AGACAAAATGAAGGGCAAACTG 57.673 40.909 0.00 0.00 0.00 3.16
2594 2960 8.697507 AGGTTCTTCTGTGAAAATTATGAACT 57.302 30.769 0.00 0.00 33.86 3.01
2601 2967 8.527810 TGTGTTTTAGGTTCTTCTGTGAAAATT 58.472 29.630 0.00 0.00 0.00 1.82
2607 2973 5.163663 TGCTTGTGTTTTAGGTTCTTCTGTG 60.164 40.000 0.00 0.00 0.00 3.66
2624 2994 2.354510 TCTTGTTTTCCGACTGCTTGTG 59.645 45.455 0.00 0.00 0.00 3.33
2630 3000 6.898041 TCAACATAATCTTGTTTTCCGACTG 58.102 36.000 0.00 0.00 37.73 3.51
2743 3113 4.545678 ACTCAGCTATGGAGTCTCAAGAT 58.454 43.478 1.47 0.00 41.63 2.40
2750 3120 3.702045 ACCAAGTACTCAGCTATGGAGTC 59.298 47.826 14.56 2.35 44.14 3.36
2840 3269 0.540454 GTAGCAACCCCCTAGTGGTC 59.460 60.000 1.93 0.00 34.15 4.02
2850 3279 3.378427 CAGCTGGAAAATAGTAGCAACCC 59.622 47.826 5.57 0.00 38.59 4.11
2933 3362 5.707242 TGTTACAGAAGACTCGATGAACT 57.293 39.130 0.00 0.00 0.00 3.01
2939 3368 6.202188 GGTGAATTTTGTTACAGAAGACTCGA 59.798 38.462 0.00 0.00 0.00 4.04
2940 3369 6.202954 AGGTGAATTTTGTTACAGAAGACTCG 59.797 38.462 0.00 0.00 0.00 4.18
2972 3436 4.781775 TTGGTCCTAGGTGAGTTTTCAA 57.218 40.909 9.08 1.04 34.49 2.69
3068 3532 5.587388 AATCTAACGAGGACATAAACGGA 57.413 39.130 0.00 0.00 0.00 4.69
3069 3533 6.657836 AAAATCTAACGAGGACATAAACGG 57.342 37.500 0.00 0.00 0.00 4.44
3135 3601 1.330521 ACCGCATTGCATTTAGTAGCG 59.669 47.619 9.69 0.00 42.93 4.26
3344 3831 1.078214 CCGACACACAGGGCATGAT 60.078 57.895 5.99 0.00 0.00 2.45
3417 3904 7.010552 GCAGACATATTACACAACTAACTCCTG 59.989 40.741 0.00 0.00 0.00 3.86
3435 3925 8.706322 TTCTACATTGTATAGGAGCAGACATA 57.294 34.615 0.00 0.00 0.00 2.29
3545 4042 9.357161 TGTAAAAGAAAATACCAGGTGTACATT 57.643 29.630 0.76 0.00 30.62 2.71
3553 4050 7.220108 GCGCTTAATGTAAAAGAAAATACCAGG 59.780 37.037 0.00 0.00 0.00 4.45
3621 4118 3.509575 AGGCAGCAAAATCGTGGATTTAA 59.490 39.130 4.20 0.00 40.77 1.52
3768 4265 2.564062 CCATTGGCAATCAGGTGAAAGT 59.436 45.455 10.36 0.00 0.00 2.66
4066 4563 5.869888 CCAGCACTTTTTATAGAACTCGACT 59.130 40.000 0.00 0.00 0.00 4.18
4091 4589 6.553476 GGTAGCAAATCCCCCTTAATAATGTT 59.447 38.462 0.00 0.00 0.00 2.71
4192 4690 5.258841 TCAATTCTCACAGCATCCATCTTT 58.741 37.500 0.00 0.00 0.00 2.52
4195 4693 3.003482 GCTCAATTCTCACAGCATCCATC 59.997 47.826 0.00 0.00 0.00 3.51
4258 4756 1.719529 TAGTCCCGACCTTGGTGAAA 58.280 50.000 0.00 0.00 0.00 2.69
4307 4805 1.972795 AGCAGTTTGGGATTGTTGCAT 59.027 42.857 0.00 0.00 34.17 3.96


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

AutoCloner maintained by Alex Coulton.