Multiple sequence alignment - TraesCS7B01G188700

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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 TraesCS7B01G188700 chr7B 100.000 5737 0 0 1 5737 321335828 321341564 0.000000e+00 10595.0
1 TraesCS7B01G188700 chr7B 85.559 734 70 22 4 710 727667734 727667010 0.000000e+00 736.0
2 TraesCS7B01G188700 chr7B 79.167 240 29 9 3426 3662 158367095 158366874 4.630000e-31 147.0
3 TraesCS7B01G188700 chr7D 96.889 3729 82 17 1946 5653 365321379 365317664 0.000000e+00 6213.0
4 TraesCS7B01G188700 chr7D 92.677 1188 69 14 774 1951 365322690 365321511 0.000000e+00 1696.0
5 TraesCS7B01G188700 chr7D 80.000 255 36 10 3415 3660 561513483 561513235 2.120000e-39 174.0
6 TraesCS7B01G188700 chr7D 87.603 121 10 4 1832 1951 557001125 557001241 1.000000e-27 135.0
7 TraesCS7B01G188700 chr7D 89.899 99 3 2 5639 5737 365317636 365317545 2.810000e-23 121.0
8 TraesCS7B01G188700 chr7A 94.448 1747 61 15 4002 5737 403195393 403193672 0.000000e+00 2656.0
9 TraesCS7B01G188700 chr7A 93.715 1448 57 15 1946 3364 403196833 403195391 0.000000e+00 2139.0
10 TraesCS7B01G188700 chr7A 94.516 930 46 4 1022 1951 403197889 403196965 0.000000e+00 1430.0
11 TraesCS7B01G188700 chr5B 89.524 630 51 14 86 709 421455917 421455297 0.000000e+00 784.0
12 TraesCS7B01G188700 chr5B 80.657 274 26 14 3415 3665 326916411 326916142 2.730000e-43 187.0
13 TraesCS7B01G188700 chr5B 91.736 121 10 0 1831 1951 387369381 387369261 9.890000e-38 169.0
14 TraesCS7B01G188700 chr5B 88.136 118 11 3 1835 1951 685509345 685509230 2.790000e-28 137.0
15 TraesCS7B01G188700 chr3A 86.759 725 63 16 2 699 360174906 360175624 0.000000e+00 776.0
16 TraesCS7B01G188700 chr3A 80.159 252 38 10 3420 3660 186047522 186047772 1.640000e-40 178.0
17 TraesCS7B01G188700 chr2D 86.277 736 66 20 1 709 89219542 89220269 0.000000e+00 767.0
18 TraesCS7B01G188700 chr2D 80.214 187 28 9 2097 2279 37476682 37476501 1.300000e-26 132.0
19 TraesCS7B01G188700 chr2D 82.468 154 19 5 3422 3567 611225013 611225166 1.680000e-25 128.0
20 TraesCS7B01G188700 chr4B 85.981 749 60 20 1 710 97877932 97877190 0.000000e+00 760.0
21 TraesCS7B01G188700 chr4B 88.707 611 53 12 100 702 97789217 97788615 0.000000e+00 732.0
22 TraesCS7B01G188700 chr5A 86.088 726 65 16 1 698 414783554 414782837 0.000000e+00 749.0
23 TraesCS7B01G188700 chr5A 88.273 631 59 12 86 710 461720618 461719997 0.000000e+00 741.0
24 TraesCS7B01G188700 chr5A 87.912 91 7 2 3578 3665 380222975 380222886 2.830000e-18 104.0
25 TraesCS7B01G188700 chr4A 85.655 725 69 18 14 710 302722269 302721552 0.000000e+00 730.0
26 TraesCS7B01G188700 chr1D 81.298 262 26 10 3420 3658 63609094 63609355 2.110000e-44 191.0
27 TraesCS7B01G188700 chr1D 89.412 85 5 3 3579 3660 39956545 39956462 2.830000e-18 104.0
28 TraesCS7B01G188700 chr1B 81.298 262 26 9 3417 3658 104349624 104349882 2.110000e-44 191.0
29 TraesCS7B01G188700 chr1B 78.014 282 56 5 2040 2317 600601154 600600875 7.640000e-39 172.0
30 TraesCS7B01G188700 chr4D 74.353 464 83 33 1836 2290 111559403 111559839 1.280000e-36 165.0
31 TraesCS7B01G188700 chr6B 77.992 259 39 13 3420 3660 132498482 132498224 4.630000e-31 147.0
32 TraesCS7B01G188700 chr3D 78.346 254 34 12 3426 3659 558290549 558290297 1.670000e-30 145.0
33 TraesCS7B01G188700 chr5D 77.778 261 38 12 3420 3660 267617696 267617436 5.990000e-30 143.0
34 TraesCS7B01G188700 chr5D 86.087 115 16 0 1836 1950 102039273 102039159 2.170000e-24 124.0
35 TraesCS7B01G188700 chr2B 87.603 121 14 1 1831 1951 361287982 361287863 7.750000e-29 139.0
36 TraesCS7B01G188700 chr2B 90.476 105 9 1 1829 1933 85698016 85697913 2.790000e-28 137.0
37 TraesCS7B01G188700 chr3B 90.909 99 9 0 1835 1933 4297498 4297596 3.610000e-27 134.0
38 TraesCS7B01G188700 chrUn 76.329 207 42 7 2033 2234 19252753 19252957 2.830000e-18 104.0
39 TraesCS7B01G188700 chr2A 77.901 181 25 10 3495 3661 25730701 25730880 1.320000e-16 99.0
40 TraesCS7B01G188700 chr6A 84.211 95 13 2 2200 2294 529603904 529603812 2.200000e-14 91.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G188700 chr7B 321335828 321341564 5736 False 10595.000000 10595 100.000000 1 5737 1 chr7B.!!$F1 5736
1 TraesCS7B01G188700 chr7B 727667010 727667734 724 True 736.000000 736 85.559000 4 710 1 chr7B.!!$R2 706
2 TraesCS7B01G188700 chr7D 365317545 365322690 5145 True 2676.666667 6213 93.155000 774 5737 3 chr7D.!!$R2 4963
3 TraesCS7B01G188700 chr7A 403193672 403197889 4217 True 2075.000000 2656 94.226333 1022 5737 3 chr7A.!!$R1 4715
4 TraesCS7B01G188700 chr5B 421455297 421455917 620 True 784.000000 784 89.524000 86 709 1 chr5B.!!$R3 623
5 TraesCS7B01G188700 chr3A 360174906 360175624 718 False 776.000000 776 86.759000 2 699 1 chr3A.!!$F2 697
6 TraesCS7B01G188700 chr2D 89219542 89220269 727 False 767.000000 767 86.277000 1 709 1 chr2D.!!$F1 708
7 TraesCS7B01G188700 chr4B 97877190 97877932 742 True 760.000000 760 85.981000 1 710 1 chr4B.!!$R2 709
8 TraesCS7B01G188700 chr4B 97788615 97789217 602 True 732.000000 732 88.707000 100 702 1 chr4B.!!$R1 602
9 TraesCS7B01G188700 chr5A 414782837 414783554 717 True 749.000000 749 86.088000 1 698 1 chr5A.!!$R2 697
10 TraesCS7B01G188700 chr5A 461719997 461720618 621 True 741.000000 741 88.273000 86 710 1 chr5A.!!$R3 624
11 TraesCS7B01G188700 chr4A 302721552 302722269 717 True 730.000000 730 85.655000 14 710 1 chr4A.!!$R1 696

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
748 816 0.178068 CCTGTAAGCGGCACATAGGT 59.822 55.000 1.45 0.0 0.00 3.08 F
1450 1549 1.134401 GGCTGCTTGATGCTAGGTGTA 60.134 52.381 0.00 0.0 43.37 2.90 F
1628 1727 1.420430 TCAGTTTGGAACTCCCGAGT 58.580 50.000 0.00 0.0 44.94 4.18 F
2051 2289 1.661341 GACAATGCAGCTCCGATTCT 58.339 50.000 0.00 0.0 0.00 2.40 F
2540 2783 1.684386 CTGCCTTGGCCAACAACCAA 61.684 55.000 16.05 0.0 44.86 3.67 F
2666 2909 3.104836 CCCAACCCAGGCCCATTA 58.895 61.111 0.00 0.0 0.00 1.90 F
3859 4131 3.523564 AGGCTTTTCTGGCTATTGGACTA 59.476 43.478 0.00 0.0 41.20 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2616 0.035439 GGGGCATCGTTCTTGGAGAA 60.035 55.000 0.00 0.0 0.00 2.87 R
2428 2668 0.382158 GATCTGCTCGTGATCGGACA 59.618 55.000 0.00 0.0 37.69 4.02 R
2666 2909 0.981183 TTTGTCGGTCCTGTATGGCT 59.019 50.000 0.00 0.0 35.26 4.75 R
2965 3226 4.008933 GCCCTGGAGCGTCACAGT 62.009 66.667 0.00 0.0 32.90 3.55 R
4087 4361 6.338214 TCAATAGACCTCATATGTCAGCTC 57.662 41.667 1.90 0.0 35.15 4.09 R
4628 4903 7.225931 TGTTACAAAAAGTAGGATGACAGTCAC 59.774 37.037 5.05 0.0 33.43 3.67 R
5256 5542 0.682209 CTTTGGGATGGGCCAGACAG 60.682 60.000 13.78 0.0 38.95 3.51 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
32 33 9.688592 TCAAAAATTGTTTGCAGTTTTCAAAAT 57.311 22.222 0.00 0.00 41.55 1.82
215 264 9.604626 GTTCACAAATTCAAAAATTGTTCACAA 57.395 25.926 0.00 0.00 40.51 3.33
641 708 4.520111 GCCATATCACCACAAGCATCAATA 59.480 41.667 0.00 0.00 0.00 1.90
659 726 3.814005 ATAAGGCGTAGTGGTTAGGTG 57.186 47.619 0.00 0.00 0.00 4.00
702 770 0.737715 GTGAGACCGATTGCTCGCTT 60.738 55.000 0.00 0.00 43.66 4.68
705 773 2.268298 GAGACCGATTGCTCGCTTAAA 58.732 47.619 0.00 0.00 43.66 1.52
710 778 2.223044 CCGATTGCTCGCTTAAACTTCC 60.223 50.000 0.00 0.00 43.66 3.46
711 779 2.534939 CGATTGCTCGCTTAAACTTCCG 60.535 50.000 0.00 0.00 38.20 4.30
712 780 1.153353 TTGCTCGCTTAAACTTCCGG 58.847 50.000 0.00 0.00 0.00 5.14
713 781 1.296056 TGCTCGCTTAAACTTCCGGC 61.296 55.000 0.00 0.00 0.00 6.13
714 782 1.978712 GCTCGCTTAAACTTCCGGCC 61.979 60.000 0.00 0.00 0.00 6.13
715 783 1.366854 CTCGCTTAAACTTCCGGCCC 61.367 60.000 0.00 0.00 0.00 5.80
716 784 1.673009 CGCTTAAACTTCCGGCCCA 60.673 57.895 0.00 0.00 0.00 5.36
717 785 1.029947 CGCTTAAACTTCCGGCCCAT 61.030 55.000 0.00 0.00 0.00 4.00
718 786 1.182667 GCTTAAACTTCCGGCCCATT 58.817 50.000 0.00 0.00 0.00 3.16
719 787 1.134367 GCTTAAACTTCCGGCCCATTC 59.866 52.381 0.00 0.00 0.00 2.67
720 788 1.400494 CTTAAACTTCCGGCCCATTCG 59.600 52.381 0.00 0.00 0.00 3.34
738 806 4.832608 GGGGGCGTCCTGTAAGCG 62.833 72.222 5.77 0.00 32.74 4.68
739 807 4.832608 GGGGCGTCCTGTAAGCGG 62.833 72.222 5.77 0.00 32.74 5.52
742 810 3.488090 GCGTCCTGTAAGCGGCAC 61.488 66.667 1.45 0.00 0.00 5.01
743 811 2.048597 CGTCCTGTAAGCGGCACA 60.049 61.111 1.45 0.00 0.00 4.57
744 812 1.447838 CGTCCTGTAAGCGGCACAT 60.448 57.895 1.45 0.00 0.00 3.21
745 813 0.179121 CGTCCTGTAAGCGGCACATA 60.179 55.000 1.45 0.00 0.00 2.29
746 814 1.571919 GTCCTGTAAGCGGCACATAG 58.428 55.000 1.45 0.00 0.00 2.23
747 815 0.464036 TCCTGTAAGCGGCACATAGG 59.536 55.000 1.45 6.53 0.00 2.57
748 816 0.178068 CCTGTAAGCGGCACATAGGT 59.822 55.000 1.45 0.00 0.00 3.08
757 825 4.963878 CACATAGGTGCTCCCCAC 57.036 61.111 0.00 0.00 43.90 4.61
786 854 2.325082 GCCACGACACGAGCCATTT 61.325 57.895 0.00 0.00 0.00 2.32
940 1037 9.816354 ATGAAAACAAGTAAATTTGCAGTTACT 57.184 25.926 14.18 11.64 43.96 2.24
941 1038 9.296400 TGAAAACAAGTAAATTTGCAGTTACTC 57.704 29.630 15.70 13.68 41.81 2.59
942 1039 9.296400 GAAAACAAGTAAATTTGCAGTTACTCA 57.704 29.630 15.70 0.00 41.81 3.41
943 1040 9.646427 AAAACAAGTAAATTTGCAGTTACTCAA 57.354 25.926 15.70 0.00 41.81 3.02
944 1041 9.646427 AAACAAGTAAATTTGCAGTTACTCAAA 57.354 25.926 15.70 10.59 41.81 2.69
945 1042 9.646427 AACAAGTAAATTTGCAGTTACTCAAAA 57.354 25.926 15.70 3.65 41.81 2.44
946 1043 9.646427 ACAAGTAAATTTGCAGTTACTCAAAAA 57.354 25.926 15.70 1.63 41.81 1.94
979 1076 1.202940 AGGGCAAAAGAACTGGTCTCC 60.203 52.381 0.00 0.00 34.56 3.71
1166 1265 4.025401 GTTGGAAGCCACACCGCG 62.025 66.667 0.00 0.00 30.78 6.46
1253 1352 2.885894 CCTAGGCCTCTAGAAGTTACCG 59.114 54.545 9.68 0.00 44.35 4.02
1264 1363 2.993899 AGAAGTTACCGCATTTCTCGTG 59.006 45.455 0.00 0.00 0.00 4.35
1271 1370 1.273887 GCATTTCTCGTGCGATCCG 59.726 57.895 0.00 0.00 32.29 4.18
1381 1480 7.908082 TGCGTAGTTGCATGATTAATTTTAGAC 59.092 33.333 0.00 0.00 40.62 2.59
1391 1490 9.754382 CATGATTAATTTTAGACTCCCCATTTG 57.246 33.333 0.00 0.00 0.00 2.32
1406 1505 3.382546 CCCATTTGGCTTAGGTCAATCTG 59.617 47.826 0.00 0.00 36.89 2.90
1408 1507 4.272489 CATTTGGCTTAGGTCAATCTGGA 58.728 43.478 0.00 0.00 36.89 3.86
1415 1514 4.455606 CTTAGGTCAATCTGGATGTTCCC 58.544 47.826 0.00 0.00 35.03 3.97
1424 1523 3.184628 TCTGGATGTTCCCTTGAGACAT 58.815 45.455 0.00 0.00 35.03 3.06
1425 1524 3.054875 TCTGGATGTTCCCTTGAGACATG 60.055 47.826 0.00 0.00 35.03 3.21
1450 1549 1.134401 GGCTGCTTGATGCTAGGTGTA 60.134 52.381 0.00 0.00 43.37 2.90
1454 1553 3.534554 TGCTTGATGCTAGGTGTATGTG 58.465 45.455 0.00 0.00 43.37 3.21
1482 1581 3.372060 GCTTCAGCTGTTTTGTTGGTAC 58.628 45.455 14.67 0.00 38.21 3.34
1504 1603 5.966742 CATCTGGATGTCTCGGATAACTA 57.033 43.478 2.69 0.00 34.23 2.24
1515 1614 6.485648 TGTCTCGGATAACTATCATCTTTCGA 59.514 38.462 0.00 0.00 34.40 3.71
1521 1620 6.146347 GGATAACTATCATCTTTCGACTTGCC 59.854 42.308 0.00 0.00 34.40 4.52
1523 1622 5.028549 ACTATCATCTTTCGACTTGCCAT 57.971 39.130 0.00 0.00 0.00 4.40
1533 1632 2.677836 TCGACTTGCCATTGATAAGTGC 59.322 45.455 9.32 0.00 34.99 4.40
1546 1645 3.371898 TGATAAGTGCAAGCTCGTTGATG 59.628 43.478 0.00 0.00 38.60 3.07
1566 1665 3.346315 TGGCACATGTTAAGAGTGGATG 58.654 45.455 0.00 0.00 33.98 3.51
1567 1666 2.098117 GGCACATGTTAAGAGTGGATGC 59.902 50.000 0.00 0.00 33.98 3.91
1583 1682 5.073554 AGTGGATGCATCTATTTGGTCCATA 59.926 40.000 25.28 0.00 36.73 2.74
1586 1685 5.295292 GGATGCATCTATTTGGTCCATATCG 59.705 44.000 25.28 0.00 0.00 2.92
1589 1688 5.700832 TGCATCTATTTGGTCCATATCGTTC 59.299 40.000 0.00 0.00 0.00 3.95
1596 1695 4.590850 TGGTCCATATCGTTCTCAGATG 57.409 45.455 0.00 0.00 0.00 2.90
1597 1696 3.321968 TGGTCCATATCGTTCTCAGATGG 59.678 47.826 0.00 0.00 38.75 3.51
1625 1724 2.076863 GTGATCAGTTTGGAACTCCCG 58.923 52.381 0.00 0.00 40.46 5.14
1627 1726 2.028112 TGATCAGTTTGGAACTCCCGAG 60.028 50.000 0.00 0.00 40.46 4.63
1628 1727 1.420430 TCAGTTTGGAACTCCCGAGT 58.580 50.000 0.00 0.00 44.94 4.18
1708 1807 3.055602 ACTGACAGCTATGAATCTGCACA 60.056 43.478 1.25 0.00 33.80 4.57
1833 1932 7.284261 TGATGAGACCAACATTTTGTGAGTTTA 59.716 33.333 0.00 0.00 0.00 2.01
1907 2008 5.857822 AGAGAACTGCACGGTTAATTAAC 57.142 39.130 18.30 18.30 35.50 2.01
1908 2009 5.302360 AGAGAACTGCACGGTTAATTAACA 58.698 37.500 25.59 7.75 37.92 2.41
1916 2017 5.067413 TGCACGGTTAATTAACAGAAAACCA 59.933 36.000 27.99 16.12 39.66 3.67
2037 2275 1.742761 CAACCTGCGATGAGGACAAT 58.257 50.000 0.00 0.00 36.51 2.71
2051 2289 1.661341 GACAATGCAGCTCCGATTCT 58.339 50.000 0.00 0.00 0.00 2.40
2076 2314 5.141182 ACGGAGAGCTATGAAGGAGAAATA 58.859 41.667 0.00 0.00 0.00 1.40
2377 2616 4.316823 TCCCTCCAGCCGGTCACT 62.317 66.667 1.90 0.00 0.00 3.41
2378 2617 3.322466 CCCTCCAGCCGGTCACTT 61.322 66.667 1.90 0.00 0.00 3.16
2513 2753 3.064820 GCCTCAACAACGTCTTCAAGAAA 59.935 43.478 0.00 0.00 0.00 2.52
2540 2783 1.684386 CTGCCTTGGCCAACAACCAA 61.684 55.000 16.05 0.00 44.86 3.67
2665 2908 4.720680 GCCCAACCCAGGCCCATT 62.721 66.667 0.00 0.00 45.16 3.16
2666 2909 3.104836 CCCAACCCAGGCCCATTA 58.895 61.111 0.00 0.00 0.00 1.90
3416 3687 6.931281 CCTCGCATTAAAAGATGGATCTTAGA 59.069 38.462 2.30 0.00 45.83 2.10
3417 3688 7.605691 CCTCGCATTAAAAGATGGATCTTAGAT 59.394 37.037 2.30 0.00 45.83 1.98
3698 3970 9.428097 TGCAAGTGCTAAAGATGTATGATATAG 57.572 33.333 4.69 0.00 42.66 1.31
3775 4047 7.062749 AGAACACTGTCTTACCATACTTTGA 57.937 36.000 0.00 0.00 0.00 2.69
3859 4131 3.523564 AGGCTTTTCTGGCTATTGGACTA 59.476 43.478 0.00 0.00 41.20 2.59
3869 4141 7.479579 TCTGGCTATTGGACTATAGGTAGATT 58.520 38.462 4.43 0.00 0.00 2.40
4110 4384 5.835280 TGAGCTGACATATGAGGTCTATTGA 59.165 40.000 18.87 2.43 37.56 2.57
4152 4426 5.289595 TCTGACTTGTTGTGTCATCACTAC 58.710 41.667 6.13 6.13 45.46 2.73
4362 4637 5.579511 TGCGAATGCTGATATACTCATGATG 59.420 40.000 0.00 0.00 43.34 3.07
4628 4903 3.430895 GCTTGATGGCAAAATGTTGTCTG 59.569 43.478 1.16 0.00 40.21 3.51
4651 4926 6.822442 TGTGACTGTCATCCTACTTTTTGTA 58.178 36.000 14.37 0.00 0.00 2.41
4655 4930 7.225931 TGACTGTCATCCTACTTTTTGTAACAC 59.774 37.037 6.36 0.00 0.00 3.32
4732 5007 5.465532 TTGCTGAATTAATGCACTTTCCA 57.534 34.783 0.00 0.00 36.37 3.53
4889 5165 5.454471 CCATCGAGATCATTTCCCTTTCTCT 60.454 44.000 0.00 0.00 32.50 3.10
4959 5236 3.469008 TGTTGGTTGCGGATATAGGAG 57.531 47.619 0.00 0.00 0.00 3.69
5004 5282 0.945743 GCTGTCTGTGACGTGCATGA 60.946 55.000 14.17 0.00 35.74 3.07
5043 5321 2.698274 GACAAAACCAACCACCCATCTT 59.302 45.455 0.00 0.00 0.00 2.40
5048 5326 3.258722 ACCAACCACCCATCTTGAATT 57.741 42.857 0.00 0.00 0.00 2.17
5077 5355 4.024472 GGAGGATTTTCTAGAATTCTGCGC 60.024 45.833 18.47 0.00 0.00 6.09
5239 5525 4.637483 ATAACCTTTGATTGGTCATGCG 57.363 40.909 0.00 0.00 36.69 4.73
5249 5535 1.725641 TGGTCATGCGCAACTTAGAG 58.274 50.000 17.11 0.00 0.00 2.43
5255 5541 4.806247 GTCATGCGCAACTTAGAGTAGATT 59.194 41.667 17.11 0.00 0.00 2.40
5256 5542 5.043903 TCATGCGCAACTTAGAGTAGATTC 58.956 41.667 17.11 0.00 0.00 2.52
5257 5543 4.720649 TGCGCAACTTAGAGTAGATTCT 57.279 40.909 8.16 0.00 0.00 2.40
5258 5544 4.424626 TGCGCAACTTAGAGTAGATTCTG 58.575 43.478 8.16 0.00 0.00 3.02
5283 5569 0.682209 CCCATCCCAAAGGCAGACAG 60.682 60.000 0.00 0.00 0.00 3.51
5438 5725 6.289834 TGAGACATTTCCATTGCAAACATTT 58.710 32.000 1.71 0.00 0.00 2.32
5478 5765 6.550854 AGATCAACTTTGGTTCAGAAAATCCA 59.449 34.615 0.00 0.00 32.73 3.41
5520 5807 6.839124 TGTATTTTGGCTCTCACAATTGAT 57.161 33.333 13.59 0.00 29.56 2.57
5577 5864 6.041865 CAGTTCATCCTACATCATTCTCTCCT 59.958 42.308 0.00 0.00 0.00 3.69
5672 6003 9.163894 AGGAAGATTTATCCTGTGATCTATGAA 57.836 33.333 0.00 0.00 45.60 2.57
5673 6004 9.956640 GGAAGATTTATCCTGTGATCTATGAAT 57.043 33.333 0.00 0.00 33.98 2.57
5682 6013 8.426569 TCCTGTGATCTATGAATATGATGACA 57.573 34.615 0.00 0.00 34.32 3.58
5683 6014 8.873144 TCCTGTGATCTATGAATATGATGACAA 58.127 33.333 0.00 0.00 34.88 3.18
5684 6015 9.152595 CCTGTGATCTATGAATATGATGACAAG 57.847 37.037 0.00 0.00 34.88 3.16
5685 6016 9.708092 CTGTGATCTATGAATATGATGACAAGT 57.292 33.333 0.00 0.00 34.88 3.16
5727 6058 3.328343 TCAGGGTTTCTTTCGGTGGATAA 59.672 43.478 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 255 7.721286 ACAACTTTTGACAAATTGTGAACAA 57.279 28.000 15.69 0.00 40.51 2.83
215 264 8.605746 CACAATCATGAACAACTTTTGACAAAT 58.394 29.630 0.00 0.00 0.00 2.32
226 275 9.424659 GAACAAAAATTCACAATCATGAACAAC 57.575 29.630 0.00 0.00 41.29 3.32
641 708 0.036671 GCACCTAACCACTACGCCTT 60.037 55.000 0.00 0.00 0.00 4.35
659 726 3.787458 GCACTTGTAGAGCGAGGC 58.213 61.111 0.00 0.00 32.77 4.70
689 757 2.223044 GGAAGTTTAAGCGAGCAATCGG 60.223 50.000 0.00 0.00 0.00 4.18
702 770 3.162448 CGAATGGGCCGGAAGTTTA 57.838 52.632 5.05 0.00 0.00 2.01
721 789 4.832608 CGCTTACAGGACGCCCCC 62.833 72.222 0.00 0.00 34.66 5.40
722 790 4.832608 CCGCTTACAGGACGCCCC 62.833 72.222 0.00 0.00 0.00 5.80
724 792 4.752879 TGCCGCTTACAGGACGCC 62.753 66.667 0.00 0.00 0.00 5.68
725 793 3.488090 GTGCCGCTTACAGGACGC 61.488 66.667 0.00 0.00 0.00 5.19
726 794 0.179121 TATGTGCCGCTTACAGGACG 60.179 55.000 0.00 0.00 0.00 4.79
727 795 1.571919 CTATGTGCCGCTTACAGGAC 58.428 55.000 0.00 0.00 0.00 3.85
728 796 0.464036 CCTATGTGCCGCTTACAGGA 59.536 55.000 0.00 0.00 0.00 3.86
729 797 0.178068 ACCTATGTGCCGCTTACAGG 59.822 55.000 0.00 0.00 0.00 4.00
730 798 1.290203 CACCTATGTGCCGCTTACAG 58.710 55.000 0.00 0.00 35.31 2.74
731 799 3.451793 CACCTATGTGCCGCTTACA 57.548 52.632 0.00 0.00 35.31 2.41
740 808 1.224592 GGTGGGGAGCACCTATGTG 59.775 63.158 0.00 0.00 45.65 3.21
741 809 1.229820 TGGTGGGGAGCACCTATGT 60.230 57.895 0.00 0.00 42.92 2.29
742 810 1.224592 GTGGTGGGGAGCACCTATG 59.775 63.158 0.00 0.00 42.92 2.23
743 811 2.367202 CGTGGTGGGGAGCACCTAT 61.367 63.158 0.00 0.00 42.92 2.57
744 812 3.000819 CGTGGTGGGGAGCACCTA 61.001 66.667 0.00 0.00 42.92 3.08
768 836 1.017177 TAAATGGCTCGTGTCGTGGC 61.017 55.000 9.96 9.96 44.00 5.01
769 837 1.651987 ATAAATGGCTCGTGTCGTGG 58.348 50.000 0.00 0.00 0.00 4.94
770 838 4.574759 GTTTATAAATGGCTCGTGTCGTG 58.425 43.478 0.31 0.00 0.00 4.35
771 839 3.305094 CGTTTATAAATGGCTCGTGTCGT 59.695 43.478 9.24 0.00 0.00 4.34
772 840 3.302221 CCGTTTATAAATGGCTCGTGTCG 60.302 47.826 20.82 6.96 38.17 4.35
773 841 3.001939 CCCGTTTATAAATGGCTCGTGTC 59.998 47.826 25.36 0.00 42.50 3.67
774 842 2.940410 CCCGTTTATAAATGGCTCGTGT 59.060 45.455 25.36 0.00 42.50 4.49
775 843 2.286772 GCCCGTTTATAAATGGCTCGTG 60.287 50.000 25.36 15.13 42.50 4.35
776 844 1.944709 GCCCGTTTATAAATGGCTCGT 59.055 47.619 25.36 0.00 42.50 4.18
777 845 2.218603 AGCCCGTTTATAAATGGCTCG 58.781 47.619 26.48 17.29 41.99 5.03
778 846 4.213482 CAGTAGCCCGTTTATAAATGGCTC 59.787 45.833 31.49 24.86 43.51 4.70
779 847 4.134563 CAGTAGCCCGTTTATAAATGGCT 58.865 43.478 30.82 30.82 45.25 4.75
780 848 3.881089 ACAGTAGCCCGTTTATAAATGGC 59.119 43.478 25.36 24.57 42.50 4.40
786 854 1.139455 GCCCACAGTAGCCCGTTTATA 59.861 52.381 0.00 0.00 0.00 0.98
813 881 1.562475 ACCCATTAACGTGCCTGGTAT 59.438 47.619 9.04 0.00 0.00 2.73
919 1016 9.646427 TTTTGAGTAACTGCAAATTTACTTGTT 57.354 25.926 13.51 2.85 38.40 2.83
956 1053 0.396974 ACCAGTTCTTTTGCCCTGCA 60.397 50.000 0.00 0.00 36.47 4.41
957 1054 0.315251 GACCAGTTCTTTTGCCCTGC 59.685 55.000 0.00 0.00 0.00 4.85
958 1055 1.882623 GAGACCAGTTCTTTTGCCCTG 59.117 52.381 0.00 0.00 33.22 4.45
959 1056 1.202940 GGAGACCAGTTCTTTTGCCCT 60.203 52.381 0.00 0.00 33.22 5.19
960 1057 1.248486 GGAGACCAGTTCTTTTGCCC 58.752 55.000 0.00 0.00 33.22 5.36
973 1070 1.546029 GTTTGGGAGCAAATGGAGACC 59.454 52.381 0.00 0.00 0.00 3.85
979 1076 1.273327 GGGTGAGTTTGGGAGCAAATG 59.727 52.381 0.00 0.00 0.00 2.32
1253 1352 1.273887 CGGATCGCACGAGAAATGC 59.726 57.895 0.00 0.00 39.81 3.56
1271 1370 3.051392 CTTTCGCACCGGATTGGGC 62.051 63.158 9.46 2.30 44.64 5.36
1296 1395 2.108157 ACGCTGGACACGCAAAGA 59.892 55.556 0.00 0.00 0.00 2.52
1378 1477 1.566231 CCTAAGCCAAATGGGGAGTCT 59.434 52.381 0.90 0.00 37.04 3.24
1381 1480 1.284785 TGACCTAAGCCAAATGGGGAG 59.715 52.381 0.90 0.00 37.04 4.30
1391 1490 3.567478 ACATCCAGATTGACCTAAGCC 57.433 47.619 0.00 0.00 0.00 4.35
1406 1505 3.356529 ACATGTCTCAAGGGAACATCC 57.643 47.619 0.00 0.00 35.23 3.51
1408 1507 3.828451 CCAAACATGTCTCAAGGGAACAT 59.172 43.478 0.00 0.00 0.00 2.71
1415 1514 1.068055 GCAGCCCAAACATGTCTCAAG 60.068 52.381 0.00 0.00 0.00 3.02
1424 1523 1.667151 GCATCAAGCAGCCCAAACA 59.333 52.632 0.00 0.00 44.79 2.83
1425 1524 4.584688 GCATCAAGCAGCCCAAAC 57.415 55.556 0.00 0.00 44.79 2.93
1454 1553 3.248266 CAAAACAGCTGAAGCCATTAGC 58.752 45.455 23.35 0.00 43.38 3.09
1482 1581 4.862902 AGTTATCCGAGACATCCAGATG 57.137 45.455 6.09 6.09 44.15 2.90
1495 1594 6.129062 GCAAGTCGAAAGATGATAGTTATCCG 60.129 42.308 0.00 0.00 45.19 4.18
1496 1595 6.146347 GGCAAGTCGAAAGATGATAGTTATCC 59.854 42.308 0.00 0.00 45.19 2.59
1504 1603 4.264253 TCAATGGCAAGTCGAAAGATGAT 58.736 39.130 0.00 0.00 45.19 2.45
1521 1620 4.093514 CAACGAGCTTGCACTTATCAATG 58.906 43.478 0.00 0.00 0.00 2.82
1523 1622 3.398406 TCAACGAGCTTGCACTTATCAA 58.602 40.909 0.00 0.00 0.00 2.57
1533 1632 0.806868 ATGTGCCATCAACGAGCTTG 59.193 50.000 0.00 0.00 0.00 4.01
1546 1645 2.098117 GCATCCACTCTTAACATGTGCC 59.902 50.000 0.00 0.00 0.00 5.01
1557 1656 4.445448 GGACCAAATAGATGCATCCACTCT 60.445 45.833 23.06 7.56 0.00 3.24
1566 1665 5.934625 AGAACGATATGGACCAAATAGATGC 59.065 40.000 0.00 0.00 0.00 3.91
1567 1666 7.154656 TGAGAACGATATGGACCAAATAGATG 58.845 38.462 0.00 0.00 0.00 2.90
1583 1682 5.987953 CACATGATTACCATCTGAGAACGAT 59.012 40.000 0.00 0.00 31.94 3.73
1586 1685 6.988580 TGATCACATGATTACCATCTGAGAAC 59.011 38.462 0.00 0.00 34.44 3.01
1589 1688 6.522946 ACTGATCACATGATTACCATCTGAG 58.477 40.000 0.00 0.00 34.44 3.35
1596 1695 6.375455 AGTTCCAAACTGATCACATGATTACC 59.625 38.462 0.00 0.00 41.01 2.85
1597 1696 7.383102 AGTTCCAAACTGATCACATGATTAC 57.617 36.000 0.00 0.00 41.01 1.89
1708 1807 5.222130 ACCAGAGGAATTGGTACAGTTGAAT 60.222 40.000 0.00 0.00 46.80 2.57
1907 2008 2.425668 ACGGTTTTCACCTGGTTTTCTG 59.574 45.455 0.00 0.00 41.64 3.02
1908 2009 2.730382 ACGGTTTTCACCTGGTTTTCT 58.270 42.857 0.00 0.00 41.64 2.52
1916 2017 2.809696 CGGATTGTAACGGTTTTCACCT 59.190 45.455 0.00 0.00 41.64 4.00
2037 2275 1.153765 CGTCAGAATCGGAGCTGCA 60.154 57.895 5.91 0.00 32.27 4.41
2051 2289 2.092375 TCTCCTTCATAGCTCTCCGTCA 60.092 50.000 0.00 0.00 0.00 4.35
2076 2314 1.814772 CTCTAGCGCCAGCCTAGCAT 61.815 60.000 2.29 0.00 46.67 3.79
2170 2409 0.904649 TGCCTCGGATTGTCTGTCAT 59.095 50.000 0.00 0.00 0.00 3.06
2328 2567 1.987855 GAGGATGGTGGGGTCGTCA 60.988 63.158 0.00 0.00 31.47 4.35
2377 2616 0.035439 GGGGCATCGTTCTTGGAGAA 60.035 55.000 0.00 0.00 0.00 2.87
2378 2617 1.602237 GGGGCATCGTTCTTGGAGA 59.398 57.895 0.00 0.00 0.00 3.71
2411 2650 0.664761 ACAATAGTGGCATCATGCGC 59.335 50.000 2.82 0.00 46.21 6.09
2428 2668 0.382158 GATCTGCTCGTGATCGGACA 59.618 55.000 0.00 0.00 37.69 4.02
2665 2908 1.855295 TTGTCGGTCCTGTATGGCTA 58.145 50.000 0.00 0.00 35.26 3.93
2666 2909 0.981183 TTTGTCGGTCCTGTATGGCT 59.019 50.000 0.00 0.00 35.26 4.75
2965 3226 4.008933 GCCCTGGAGCGTCACAGT 62.009 66.667 0.00 0.00 32.90 3.55
3176 3437 5.039920 ACAGGATGAGCTTGCATATTACA 57.960 39.130 0.00 0.00 39.69 2.41
3416 3687 7.569599 ATTATTTGGAACGGAGGGAGTATAT 57.430 36.000 0.00 0.00 0.00 0.86
3417 3688 7.071447 TCAATTATTTGGAACGGAGGGAGTATA 59.929 37.037 0.00 0.00 33.44 1.47
3698 3970 9.750125 AAAAATTCAATAGGAAGAACAGTTCAC 57.250 29.630 15.85 8.70 39.30 3.18
3775 4047 7.027874 TGGGAGAAACCAAAAGTCATACTAT 57.972 36.000 0.00 0.00 41.20 2.12
3826 4098 6.867550 AGCCAGAAAAGCCTCAAAATAATAC 58.132 36.000 0.00 0.00 0.00 1.89
4087 4361 6.338214 TCAATAGACCTCATATGTCAGCTC 57.662 41.667 1.90 0.00 35.15 4.09
4165 4439 8.872845 GTGTCCTGCAATAAATAAAATGAAAGG 58.127 33.333 0.00 0.00 0.00 3.11
4628 4903 7.225931 TGTTACAAAAAGTAGGATGACAGTCAC 59.774 37.037 5.05 0.00 33.43 3.67
4651 4926 8.079203 TCGAAGTTAATGCAACATTATTGTGTT 58.921 29.630 0.00 0.00 42.75 3.32
4655 4930 9.890085 CAATTCGAAGTTAATGCAACATTATTG 57.110 29.630 3.35 0.00 39.81 1.90
4712 4987 7.428020 TGATATGGAAAGTGCATTAATTCAGC 58.572 34.615 0.00 0.00 29.08 4.26
4732 5007 3.118112 CCAGAGTGCAGGGAGTTTGATAT 60.118 47.826 0.00 0.00 0.00 1.63
4889 5165 5.240623 GGACAACACAAAGGAACATCATACA 59.759 40.000 0.00 0.00 0.00 2.29
4959 5236 6.707290 AGGGGTTATAAAATGCTTTTGTTCC 58.293 36.000 0.00 2.49 34.19 3.62
5004 5282 7.255486 GGTTTTGTCCTTCTAAGCAGTTTATGT 60.255 37.037 0.00 0.00 0.00 2.29
5043 5321 7.642186 TCTAGAAAATCCTCCATTCCAATTCA 58.358 34.615 0.00 0.00 0.00 2.57
5048 5326 7.776969 CAGAATTCTAGAAAATCCTCCATTCCA 59.223 37.037 9.71 0.00 0.00 3.53
5077 5355 9.591404 GCATGAATTTCAGAAGATACTAATTCG 57.409 33.333 5.21 0.00 35.71 3.34
5239 5525 6.039616 CCAGACAGAATCTACTCTAAGTTGC 58.960 44.000 0.00 0.00 35.15 4.17
5249 5535 2.224402 GGATGGGCCAGACAGAATCTAC 60.224 54.545 13.78 0.00 35.15 2.59
5255 5541 1.139498 TTTGGGATGGGCCAGACAGA 61.139 55.000 13.78 3.09 38.95 3.41
5256 5542 0.682209 CTTTGGGATGGGCCAGACAG 60.682 60.000 13.78 0.00 38.95 3.51
5257 5543 1.383799 CTTTGGGATGGGCCAGACA 59.616 57.895 13.78 8.00 38.95 3.41
5258 5544 1.380380 CCTTTGGGATGGGCCAGAC 60.380 63.158 13.78 8.75 38.95 3.51
5283 5569 1.336240 GGCATGAATAAATCCCTGCGC 60.336 52.381 0.00 0.00 36.86 6.09
5438 5725 5.624159 AGTTGATCTGGACATGAAAACTCA 58.376 37.500 0.00 0.00 0.00 3.41
5577 5864 7.389232 TGATCTAGAGCAAGTTCTTGATTTGA 58.611 34.615 8.55 9.32 38.95 2.69
5672 6003 7.776969 ACCATAAGCAGAAACTTGTCATCATAT 59.223 33.333 0.00 0.00 0.00 1.78
5673 6004 7.112122 ACCATAAGCAGAAACTTGTCATCATA 58.888 34.615 0.00 0.00 0.00 2.15
5675 6006 5.316167 ACCATAAGCAGAAACTTGTCATCA 58.684 37.500 0.00 0.00 0.00 3.07
5676 6007 5.645497 AGACCATAAGCAGAAACTTGTCATC 59.355 40.000 0.00 0.00 0.00 2.92
5678 6009 4.756642 CAGACCATAAGCAGAAACTTGTCA 59.243 41.667 0.00 0.00 0.00 3.58
5679 6010 4.154918 CCAGACCATAAGCAGAAACTTGTC 59.845 45.833 0.00 0.00 0.00 3.18
5680 6011 4.074970 CCAGACCATAAGCAGAAACTTGT 58.925 43.478 0.00 0.00 0.00 3.16
5681 6012 3.119708 GCCAGACCATAAGCAGAAACTTG 60.120 47.826 0.00 0.00 0.00 3.16
5682 6013 3.084786 GCCAGACCATAAGCAGAAACTT 58.915 45.455 0.00 0.00 0.00 2.66
5683 6014 2.307098 AGCCAGACCATAAGCAGAAACT 59.693 45.455 0.00 0.00 0.00 2.66
5684 6015 2.716217 AGCCAGACCATAAGCAGAAAC 58.284 47.619 0.00 0.00 0.00 2.78
5685 6016 3.244875 TGAAGCCAGACCATAAGCAGAAA 60.245 43.478 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.