Multiple sequence alignment - TraesCS6D01G223000

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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 TraesCS6D01G223000 chr6D 100.000 4884 0 0 1 4884 315179708 315174825 0.000000e+00 9020.0
1 TraesCS6D01G223000 chr6D 94.878 449 18 2 253 696 7553795 7554243 0.000000e+00 697.0
2 TraesCS6D01G223000 chr6D 82.989 435 50 18 4122 4544 86383936 86383514 5.970000e-99 372.0
3 TraesCS6D01G223000 chr6D 82.784 273 45 2 1113 1384 315193691 315193420 4.880000e-60 243.0
4 TraesCS6D01G223000 chr6D 86.667 135 12 4 4751 4884 315175297 315175426 1.420000e-30 145.0
5 TraesCS6D01G223000 chr6A 94.488 3175 128 29 757 3909 452100293 452097144 0.000000e+00 4850.0
6 TraesCS6D01G223000 chr6A 97.253 182 4 1 3760 3941 452095901 452095721 1.710000e-79 307.0
7 TraesCS6D01G223000 chr6A 96.703 182 6 0 3760 3941 452093866 452093685 2.210000e-78 303.0
8 TraesCS6D01G223000 chr6A 96.667 150 5 0 3760 3909 452096494 452096345 2.920000e-62 250.0
9 TraesCS6D01G223000 chr6A 82.784 273 45 2 1113 1384 452267025 452266754 4.880000e-60 243.0
10 TraesCS6D01G223000 chr6A 96.117 103 4 0 4007 4109 452016856 452016754 8.410000e-38 169.0
11 TraesCS6D01G223000 chr6A 94.175 103 6 0 4007 4109 452095080 452094978 1.820000e-34 158.0
12 TraesCS6D01G223000 chr6A 86.111 72 1 2 3943 4014 452095189 452095127 8.770000e-08 69.4
13 TraesCS6D01G223000 chr6B 93.621 3057 119 33 876 3910 512234260 512237262 0.000000e+00 4495.0
14 TraesCS6D01G223000 chr6B 93.166 439 29 1 259 696 14127970 14128408 1.150000e-180 643.0
15 TraesCS6D01G223000 chr3D 96.694 726 17 3 1 719 552257218 552257943 0.000000e+00 1201.0
16 TraesCS6D01G223000 chr3D 93.521 355 16 5 4242 4593 18622180 18621830 5.600000e-144 521.0
17 TraesCS6D01G223000 chr3D 92.938 354 22 3 369 721 5654189 5654540 3.370000e-141 512.0
18 TraesCS6D01G223000 chr3D 96.053 228 8 1 496 722 564531927 564531700 2.150000e-98 370.0
19 TraesCS6D01G223000 chrUn 96.122 722 20 4 7 721 305660926 305660206 0.000000e+00 1171.0
20 TraesCS6D01G223000 chrUn 96.122 722 20 4 7 721 342936783 342936063 0.000000e+00 1171.0
21 TraesCS6D01G223000 chr2A 94.587 702 28 3 7 698 19573467 19572766 0.000000e+00 1077.0
22 TraesCS6D01G223000 chr2A 86.562 320 38 5 1066 1384 640269887 640270202 1.010000e-91 348.0
23 TraesCS6D01G223000 chr2A 87.671 73 5 3 1293 1363 680261761 680261831 1.130000e-11 82.4
24 TraesCS6D01G223000 chr2D 91.863 553 27 12 4135 4681 614367997 614367457 0.000000e+00 756.0
25 TraesCS6D01G223000 chr2D 85.110 544 48 19 4144 4680 522147625 522148142 4.330000e-145 525.0
26 TraesCS6D01G223000 chr2D 83.844 359 50 8 1047 1403 493177186 493176834 7.830000e-88 335.0
27 TraesCS6D01G223000 chr2D 89.904 208 13 5 4677 4884 614366320 614366121 1.350000e-65 261.0
28 TraesCS6D01G223000 chr2D 86.528 193 22 4 4695 4884 522168473 522168664 4.950000e-50 209.0
29 TraesCS6D01G223000 chr2D 87.879 132 12 3 4751 4881 614367721 614367849 8.470000e-33 152.0
30 TraesCS6D01G223000 chr5D 89.576 566 38 18 4122 4681 216054908 216054358 0.000000e+00 699.0
31 TraesCS6D01G223000 chr5D 89.286 112 9 3 4773 4884 216054641 216054749 2.370000e-28 137.0
32 TraesCS6D01G223000 chr2B 88.752 569 49 13 4120 4681 801180207 801180767 0.000000e+00 682.0
33 TraesCS6D01G223000 chr2B 85.443 316 37 8 1072 1384 581471104 581470795 2.190000e-83 320.0
34 TraesCS6D01G223000 chr2B 87.500 136 10 6 4750 4884 801180497 801180368 3.050000e-32 150.0
35 TraesCS6D01G223000 chr1B 84.190 525 61 14 4169 4679 323662105 323662621 1.580000e-134 490.0
36 TraesCS6D01G223000 chr7D 82.155 566 75 18 4122 4680 607202409 607202955 3.440000e-126 462.0
37 TraesCS6D01G223000 chr7D 82.258 186 28 4 1488 1671 531439811 531439993 6.550000e-34 156.0
38 TraesCS6D01G223000 chr5B 94.318 264 11 4 464 725 380799895 380800156 7.610000e-108 401.0
39 TraesCS6D01G223000 chr3A 79.885 522 64 27 4163 4680 71232269 71232753 1.300000e-90 344.0
40 TraesCS6D01G223000 chr4B 85.374 294 33 7 4392 4680 647406673 647406961 3.700000e-76 296.0
41 TraesCS6D01G223000 chr7B 82.044 362 50 14 4144 4496 719457842 719458197 1.330000e-75 294.0
42 TraesCS6D01G223000 chr7A 82.258 186 28 4 1488 1671 611728481 611728663 6.550000e-34 156.0
43 TraesCS6D01G223000 chr7A 84.127 126 17 2 1495 1620 611911340 611911462 8.590000e-23 119.0
44 TraesCS6D01G223000 chr5A 77.692 260 50 8 1112 1367 689897019 689897274 8.470000e-33 152.0
45 TraesCS6D01G223000 chr4A 90.698 43 2 2 1105 1145 535940693 535940735 6.830000e-04 56.5
46 TraesCS6D01G223000 chr4A 100.000 28 0 0 1105 1132 7883519 7883546 9.000000e-03 52.8


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 TraesCS6D01G223000 chr6D 315174825 315179708 4883 True 9020.000000 9020 100.000000 1 4884 1 chr6D.!!$R2 4883
1 TraesCS6D01G223000 chr6A 452093685 452100293 6608 True 989.566667 4850 94.232833 757 4109 6 chr6A.!!$R3 3352
2 TraesCS6D01G223000 chr6B 512234260 512237262 3002 False 4495.000000 4495 93.621000 876 3910 1 chr6B.!!$F2 3034
3 TraesCS6D01G223000 chr3D 552257218 552257943 725 False 1201.000000 1201 96.694000 1 719 1 chr3D.!!$F2 718
4 TraesCS6D01G223000 chrUn 305660206 305660926 720 True 1171.000000 1171 96.122000 7 721 1 chrUn.!!$R1 714
5 TraesCS6D01G223000 chrUn 342936063 342936783 720 True 1171.000000 1171 96.122000 7 721 1 chrUn.!!$R2 714
6 TraesCS6D01G223000 chr2A 19572766 19573467 701 True 1077.000000 1077 94.587000 7 698 1 chr2A.!!$R1 691
7 TraesCS6D01G223000 chr2D 522147625 522148142 517 False 525.000000 525 85.110000 4144 4680 1 chr2D.!!$F1 536
8 TraesCS6D01G223000 chr2D 614366121 614367997 1876 True 508.500000 756 90.883500 4135 4884 2 chr2D.!!$R2 749
9 TraesCS6D01G223000 chr5D 216054358 216054908 550 True 699.000000 699 89.576000 4122 4681 1 chr5D.!!$R1 559
10 TraesCS6D01G223000 chr2B 801180207 801180767 560 False 682.000000 682 88.752000 4120 4681 1 chr2B.!!$F1 561
11 TraesCS6D01G223000 chr1B 323662105 323662621 516 False 490.000000 490 84.190000 4169 4679 1 chr1B.!!$F1 510
12 TraesCS6D01G223000 chr7D 607202409 607202955 546 False 462.000000 462 82.155000 4122 4680 1 chr7D.!!$F2 558

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
746 757 0.039527 GTCGCCACCCATTTGTCAAC 60.040 55.0 0.00 0.0 0.00 3.18 F
1659 1683 0.037447 GGCTCCTCAACTTGCTTCCT 59.963 55.0 0.00 0.0 0.00 3.36 F
3410 3453 0.179076 TACAGTCATGGGCTGCATCG 60.179 55.0 15.04 0.0 37.47 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1952 0.517316 CGCCTTCAAACCTGTACAGC 59.483 55.0 17.86 2.6 0.0 4.40 R
3634 3677 0.104304 CCATCGGAAGGGGAACGTAG 59.896 60.0 0.00 0.0 0.0 3.51 R
4611 7267 5.931294 TGGTGATACTAGTGTGTGGAAAAA 58.069 37.5 5.39 0.0 0.0 1.94 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
276 286 0.179084 TGCTAATCGTACTGCTGGGC 60.179 55.000 0.00 0.00 0.00 5.36
291 301 1.302993 GGGCGTGGTATGGTGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
559 569 8.156994 ACGGAGATCTCAGTTACTCTTATTAC 57.843 38.462 23.85 0.20 34.43 1.89
626 636 0.745845 GTACTCCTCGGACTGCGGTA 60.746 60.000 0.00 0.00 0.00 4.02
637 647 2.029623 GACTGCGGTATGGTTAGGAGA 58.970 52.381 0.00 0.00 0.00 3.71
699 710 7.232534 TGCACCACCTTAAGTAATGAGATTTTT 59.767 33.333 0.97 0.00 0.00 1.94
711 722 2.167662 GAGATTTTTCTTTCCCCCGCA 58.832 47.619 0.00 0.00 0.00 5.69
712 723 2.164422 GAGATTTTTCTTTCCCCCGCAG 59.836 50.000 0.00 0.00 0.00 5.18
742 753 2.518426 TGGTCGCCACCCATTTGT 59.482 55.556 0.00 0.00 42.99 2.83
743 754 1.602323 TGGTCGCCACCCATTTGTC 60.602 57.895 0.00 0.00 42.99 3.18
744 755 1.602323 GGTCGCCACCCATTTGTCA 60.602 57.895 0.00 0.00 36.54 3.58
745 756 1.175983 GGTCGCCACCCATTTGTCAA 61.176 55.000 0.00 0.00 36.54 3.18
746 757 0.039527 GTCGCCACCCATTTGTCAAC 60.040 55.000 0.00 0.00 0.00 3.18
747 758 0.179004 TCGCCACCCATTTGTCAACT 60.179 50.000 0.00 0.00 0.00 3.16
748 759 0.240945 CGCCACCCATTTGTCAACTC 59.759 55.000 0.00 0.00 0.00 3.01
749 760 1.620822 GCCACCCATTTGTCAACTCT 58.379 50.000 0.00 0.00 0.00 3.24
750 761 1.963515 GCCACCCATTTGTCAACTCTT 59.036 47.619 0.00 0.00 0.00 2.85
751 762 2.365293 GCCACCCATTTGTCAACTCTTT 59.635 45.455 0.00 0.00 0.00 2.52
752 763 3.552890 GCCACCCATTTGTCAACTCTTTC 60.553 47.826 0.00 0.00 0.00 2.62
753 764 3.636300 CCACCCATTTGTCAACTCTTTCA 59.364 43.478 0.00 0.00 0.00 2.69
754 765 4.261741 CCACCCATTTGTCAACTCTTTCAG 60.262 45.833 0.00 0.00 0.00 3.02
755 766 3.891366 ACCCATTTGTCAACTCTTTCAGG 59.109 43.478 0.00 0.00 0.00 3.86
760 771 5.596836 TTTGTCAACTCTTTCAGGCAATT 57.403 34.783 0.00 0.00 0.00 2.32
774 785 0.373716 GCAATTAAGAGTGGTCGCCG 59.626 55.000 0.00 0.00 0.00 6.46
775 786 1.722011 CAATTAAGAGTGGTCGCCGT 58.278 50.000 0.00 0.00 0.00 5.68
779 790 1.592400 TAAGAGTGGTCGCCGTCCAG 61.592 60.000 2.60 0.00 35.49 3.86
793 805 1.795286 CGTCCAGCTGTCAACTCTTTC 59.205 52.381 13.81 0.00 0.00 2.62
809 821 5.702349 CTCTTTCAGGCAATCAAGAGTTT 57.298 39.130 6.74 0.00 38.21 2.66
811 823 6.469782 TCTTTCAGGCAATCAAGAGTTTTT 57.530 33.333 0.00 0.00 0.00 1.94
871 883 2.450160 GTCAAGACGCTGTTTTGTTGG 58.550 47.619 10.19 0.00 31.04 3.77
973 987 1.376553 GGTGAGAGCCTTCTGCCAC 60.377 63.158 0.00 0.00 42.71 5.01
1053 1067 1.742880 GATTGAGCAGTGCGAGGCA 60.743 57.895 10.00 4.22 35.60 4.75
1230 1250 2.903855 GGCATCATCCCCACGCTG 60.904 66.667 0.00 0.00 0.00 5.18
1427 1449 1.449601 CACGCCGTTTAGCATCCCT 60.450 57.895 0.00 0.00 0.00 4.20
1466 1490 0.175760 GTCCACGGCTGCATCTAGAA 59.824 55.000 0.50 0.00 0.00 2.10
1467 1491 0.175760 TCCACGGCTGCATCTAGAAC 59.824 55.000 0.50 0.00 0.00 3.01
1468 1492 0.108186 CCACGGCTGCATCTAGAACA 60.108 55.000 0.50 0.00 0.00 3.18
1469 1493 1.473965 CCACGGCTGCATCTAGAACAT 60.474 52.381 0.50 0.00 0.00 2.71
1659 1683 0.037447 GGCTCCTCAACTTGCTTCCT 59.963 55.000 0.00 0.00 0.00 3.36
1675 1699 1.423584 TCCTCTCAGAAAGGTGTGCA 58.576 50.000 0.00 0.00 35.29 4.57
1690 1714 2.215363 GTGTGCAAAAATCGTTCAACGG 59.785 45.455 10.69 0.00 42.81 4.44
1700 1727 1.135373 TCGTTCAACGGATCAGCTCTC 60.135 52.381 10.69 0.00 42.81 3.20
1701 1728 1.402852 CGTTCAACGGATCAGCTCTCA 60.403 52.381 0.61 0.00 38.08 3.27
1756 1783 4.928661 CACAGTACCATGTGCTTTACTC 57.071 45.455 2.65 0.00 43.69 2.59
1757 1784 3.684788 CACAGTACCATGTGCTTTACTCC 59.315 47.826 2.65 0.00 43.69 3.85
1758 1785 3.583086 ACAGTACCATGTGCTTTACTCCT 59.417 43.478 0.00 0.00 30.46 3.69
1759 1786 4.775780 ACAGTACCATGTGCTTTACTCCTA 59.224 41.667 0.00 0.00 30.46 2.94
1760 1787 5.109903 CAGTACCATGTGCTTTACTCCTAC 58.890 45.833 0.00 0.00 0.00 3.18
1778 1805 8.950208 ACTCCTACATTCTACTCTAATTTTGC 57.050 34.615 0.00 0.00 0.00 3.68
1825 1852 5.469479 CATTGACCAATGGTAAACTGAACC 58.531 41.667 4.23 0.00 43.25 3.62
1877 1904 8.993121 ACTCATAGTTTAAATGTGACAGACTTG 58.007 33.333 0.00 0.00 0.00 3.16
1896 1923 4.162131 ACTTGCACACCCTTTCTCAATTTT 59.838 37.500 0.00 0.00 0.00 1.82
1913 1940 9.981114 TCTCAATTTTATCATCTTATACTCGCA 57.019 29.630 0.00 0.00 0.00 5.10
1915 1942 8.988934 TCAATTTTATCATCTTATACTCGCACC 58.011 33.333 0.00 0.00 0.00 5.01
1944 1973 0.517316 GCTGTACAGGTTTGAAGGCG 59.483 55.000 23.95 0.00 0.00 5.52
1947 1976 3.395639 CTGTACAGGTTTGAAGGCGTAA 58.604 45.455 15.49 0.00 0.00 3.18
1997 2026 7.099120 ACAATTTTATTGCTCCAATGAAGACC 58.901 34.615 0.94 0.00 35.54 3.85
2002 2031 3.334583 TGCTCCAATGAAGACCTACAC 57.665 47.619 0.00 0.00 0.00 2.90
2003 2032 2.906389 TGCTCCAATGAAGACCTACACT 59.094 45.455 0.00 0.00 0.00 3.55
2004 2033 3.055819 TGCTCCAATGAAGACCTACACTC 60.056 47.826 0.00 0.00 0.00 3.51
2020 2049 6.092748 CCTACACTCAAAACACCATTTATGC 58.907 40.000 0.00 0.00 0.00 3.14
2023 2052 3.260632 ACTCAAAACACCATTTATGCCCC 59.739 43.478 0.00 0.00 0.00 5.80
2024 2053 2.569404 TCAAAACACCATTTATGCCCCC 59.431 45.455 0.00 0.00 0.00 5.40
2044 2075 2.553247 CCCTTTCTTTGTCCCCTCTGAC 60.553 54.545 0.00 0.00 35.77 3.51
2224 2255 2.159043 AGTCTTGGCGATACATGGTGAG 60.159 50.000 0.00 0.00 0.00 3.51
2366 2397 6.150641 GTGGGTTTCTACAATTCCCTACTTTC 59.849 42.308 0.00 0.00 38.95 2.62
2457 2488 6.138761 GCTAATTTGTCTCATGCCTAATTCG 58.861 40.000 0.00 0.00 0.00 3.34
2923 2965 7.595819 TTAATTCCTTCCACATTTTGTCACT 57.404 32.000 0.00 0.00 0.00 3.41
2981 3023 6.753744 GGCAAATGAGGATACAGTTTCATTTC 59.246 38.462 7.99 4.84 44.20 2.17
3058 3101 1.830279 ATGCCGGATATGCCTCATTG 58.170 50.000 5.05 0.00 0.00 2.82
3410 3453 0.179076 TACAGTCATGGGCTGCATCG 60.179 55.000 15.04 0.00 37.47 3.84
3412 3455 1.028330 CAGTCATGGGCTGCATCGTT 61.028 55.000 0.50 0.00 0.00 3.85
3550 3593 3.606065 CTCTGCACTGCCAAAGCGC 62.606 63.158 0.00 0.00 44.31 5.92
3567 3610 2.969016 CTGCCTCGAGCTGTCTGT 59.031 61.111 6.99 0.00 44.23 3.41
3631 3674 2.025418 CTCGCCGCAAAAGTACCGT 61.025 57.895 0.00 0.00 0.00 4.83
3634 3677 0.179243 CGCCGCAAAAGTACCGTAAC 60.179 55.000 0.00 0.00 0.00 2.50
3724 3767 0.984230 TGGGGAGCTTGGTAGTCTTG 59.016 55.000 0.00 0.00 0.00 3.02
3725 3768 0.253327 GGGGAGCTTGGTAGTCTTGG 59.747 60.000 0.00 0.00 0.00 3.61
3726 3769 0.393132 GGGAGCTTGGTAGTCTTGGC 60.393 60.000 0.00 0.00 0.00 4.52
3741 3784 0.609957 TTGGCCTGGCACAAGATGAG 60.610 55.000 22.05 0.00 38.70 2.90
3742 3785 2.413142 GGCCTGGCACAAGATGAGC 61.413 63.158 22.05 0.00 38.70 4.26
3745 3788 1.030488 CCTGGCACAAGATGAGCAGG 61.030 60.000 2.41 0.00 38.70 4.85
3891 5325 2.168521 CACCGGGAAGCTAGAGAAATGA 59.831 50.000 6.32 0.00 0.00 2.57
3941 5375 5.471456 GTGCAATGGGAGTATTTAGGATGAG 59.529 44.000 0.00 0.00 0.00 2.90
3951 5915 5.812642 AGTATTTAGGATGAGCTGTTGTTCG 59.187 40.000 0.00 0.00 0.00 3.95
3976 5940 6.158598 ACATTTGCAACATCCAAGAATGTAC 58.841 36.000 0.00 0.00 38.92 2.90
3977 5941 6.015180 ACATTTGCAACATCCAAGAATGTACT 60.015 34.615 0.00 0.00 38.92 2.73
3978 5942 5.375417 TTGCAACATCCAAGAATGTACTG 57.625 39.130 0.00 0.00 38.92 2.74
3979 5943 4.397420 TGCAACATCCAAGAATGTACTGT 58.603 39.130 0.00 0.00 38.92 3.55
3980 5944 5.555966 TGCAACATCCAAGAATGTACTGTA 58.444 37.500 0.00 0.00 38.92 2.74
3981 5945 5.643348 TGCAACATCCAAGAATGTACTGTAG 59.357 40.000 0.00 0.00 38.92 2.74
3982 5946 5.643777 GCAACATCCAAGAATGTACTGTAGT 59.356 40.000 0.00 0.00 38.92 2.73
4007 5971 7.860872 GTCTGTAGATAAGTTTGGTTTTGTTGG 59.139 37.037 0.00 0.00 0.00 3.77
4008 5972 7.013846 TCTGTAGATAAGTTTGGTTTTGTTGGG 59.986 37.037 0.00 0.00 0.00 4.12
4009 5973 6.834451 TGTAGATAAGTTTGGTTTTGTTGGGA 59.166 34.615 0.00 0.00 0.00 4.37
4011 5975 6.758254 AGATAAGTTTGGTTTTGTTGGGATG 58.242 36.000 0.00 0.00 0.00 3.51
4013 5977 4.835284 AGTTTGGTTTTGTTGGGATGTT 57.165 36.364 0.00 0.00 0.00 2.71
4014 5978 4.512484 AGTTTGGTTTTGTTGGGATGTTG 58.488 39.130 0.00 0.00 0.00 3.33
4015 5979 4.019771 AGTTTGGTTTTGTTGGGATGTTGT 60.020 37.500 0.00 0.00 0.00 3.32
4016 5980 3.533606 TGGTTTTGTTGGGATGTTGTG 57.466 42.857 0.00 0.00 0.00 3.33
4017 5981 2.834549 TGGTTTTGTTGGGATGTTGTGT 59.165 40.909 0.00 0.00 0.00 3.72
4060 6076 3.511540 CACTTGACTGAGGGTAGTGATCA 59.488 47.826 0.00 0.00 38.74 2.92
4061 6077 3.766591 ACTTGACTGAGGGTAGTGATCAG 59.233 47.826 0.00 0.08 44.81 2.90
4088 6104 0.180642 GGGGGCTTAGTAAGAGTGGC 59.819 60.000 14.27 0.00 0.00 5.01
4106 6122 4.706962 AGTGGCAAATTCTCTACCAAATCC 59.293 41.667 0.00 0.00 30.82 3.01
4109 6125 5.721000 TGGCAAATTCTCTACCAAATCCATT 59.279 36.000 0.00 0.00 0.00 3.16
4111 6127 6.758416 GGCAAATTCTCTACCAAATCCATTTC 59.242 38.462 0.00 0.00 0.00 2.17
4115 6131 8.986929 AATTCTCTACCAAATCCATTTCTAGG 57.013 34.615 0.00 0.00 0.00 3.02
4116 6132 7.749377 TTCTCTACCAAATCCATTTCTAGGA 57.251 36.000 0.00 0.00 39.97 2.94
4117 6133 7.125792 TCTCTACCAAATCCATTTCTAGGAC 57.874 40.000 0.00 0.00 38.13 3.85
4118 6134 6.672218 TCTCTACCAAATCCATTTCTAGGACA 59.328 38.462 0.00 0.00 38.13 4.02
4438 6504 8.114331 AGAAACATGCTCACATAAAAAGATCA 57.886 30.769 0.00 0.00 33.67 2.92
4570 6707 8.623180 GTTGTTTTTCGTTTTCCATTTTTGTTC 58.377 29.630 0.00 0.00 0.00 3.18
4611 7267 7.417116 GCTCACATCAAGATAATTGACCCAAAT 60.417 37.037 0.00 0.00 0.00 2.32
4800 8601 9.959775 TTTTGTTGAATCGAACAATAAACAAAC 57.040 25.926 20.67 6.65 43.56 2.93
4801 8602 8.689251 TTGTTGAATCGAACAATAAACAAACA 57.311 26.923 12.59 3.44 40.18 2.83
4802 8603 8.689251 TGTTGAATCGAACAATAAACAAACAA 57.311 26.923 10.64 0.00 32.84 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.634896 GGAGCTTTGTCATGTGTAATCTTG 58.365 41.667 0.00 0.00 0.00 3.02
5 6 4.393062 CGGAGCTTTGTCATGTGTAATCTT 59.607 41.667 0.00 0.00 0.00 2.40
276 286 0.035598 TCCCACAACACCATACCACG 59.964 55.000 0.00 0.00 0.00 4.94
451 461 1.227380 GTGGCCTCTAGCATCACCG 60.227 63.158 3.32 0.00 46.50 4.94
462 472 1.671379 GGTTCCGTTCAGTGGCCTC 60.671 63.158 3.32 0.00 0.00 4.70
535 545 7.308710 GGGTAATAAGAGTAACTGAGATCTCCG 60.309 44.444 20.03 15.99 0.00 4.63
559 569 7.437793 TGACTAACTTTATTTTTGGTACGGG 57.562 36.000 0.00 0.00 0.00 5.28
626 636 3.700038 CGTCTGTACCTTCTCCTAACCAT 59.300 47.826 0.00 0.00 0.00 3.55
637 647 5.365619 AGTTCACAATTTCGTCTGTACCTT 58.634 37.500 0.00 0.00 0.00 3.50
699 710 3.831651 TTTTTCTGCGGGGGAAAGA 57.168 47.368 0.00 0.00 34.73 2.52
725 736 1.602323 GACAAATGGGTGGCGACCA 60.602 57.895 20.36 7.69 45.25 4.02
726 737 1.175983 TTGACAAATGGGTGGCGACC 61.176 55.000 9.83 9.83 42.27 4.79
727 738 0.039527 GTTGACAAATGGGTGGCGAC 60.040 55.000 0.00 0.00 33.72 5.19
728 739 0.179004 AGTTGACAAATGGGTGGCGA 60.179 50.000 0.00 0.00 0.00 5.54
729 740 0.240945 GAGTTGACAAATGGGTGGCG 59.759 55.000 0.00 0.00 0.00 5.69
730 741 1.620822 AGAGTTGACAAATGGGTGGC 58.379 50.000 0.00 0.00 0.00 5.01
731 742 3.636300 TGAAAGAGTTGACAAATGGGTGG 59.364 43.478 0.00 0.00 0.00 4.61
732 743 4.261741 CCTGAAAGAGTTGACAAATGGGTG 60.262 45.833 0.00 0.00 34.07 4.61
733 744 3.891366 CCTGAAAGAGTTGACAAATGGGT 59.109 43.478 0.00 0.00 34.07 4.51
734 745 3.305608 GCCTGAAAGAGTTGACAAATGGG 60.306 47.826 0.00 0.00 34.07 4.00
735 746 3.318839 TGCCTGAAAGAGTTGACAAATGG 59.681 43.478 0.00 0.00 34.07 3.16
736 747 4.572985 TGCCTGAAAGAGTTGACAAATG 57.427 40.909 0.00 0.00 34.07 2.32
737 748 5.796424 ATTGCCTGAAAGAGTTGACAAAT 57.204 34.783 0.00 0.00 34.07 2.32
738 749 5.596836 AATTGCCTGAAAGAGTTGACAAA 57.403 34.783 0.00 0.00 34.07 2.83
739 750 6.545666 TCTTAATTGCCTGAAAGAGTTGACAA 59.454 34.615 0.00 0.00 34.07 3.18
740 751 6.061441 TCTTAATTGCCTGAAAGAGTTGACA 58.939 36.000 0.00 0.00 34.07 3.58
741 752 6.560253 TCTTAATTGCCTGAAAGAGTTGAC 57.440 37.500 0.00 0.00 34.07 3.18
742 753 6.808008 CTCTTAATTGCCTGAAAGAGTTGA 57.192 37.500 5.57 0.00 39.93 3.18
746 757 5.006386 ACCACTCTTAATTGCCTGAAAGAG 58.994 41.667 10.51 10.51 46.69 2.85
747 758 4.985538 ACCACTCTTAATTGCCTGAAAGA 58.014 39.130 0.00 0.00 34.07 2.52
748 759 4.142816 CGACCACTCTTAATTGCCTGAAAG 60.143 45.833 0.00 0.00 0.00 2.62
749 760 3.751175 CGACCACTCTTAATTGCCTGAAA 59.249 43.478 0.00 0.00 0.00 2.69
750 761 3.334691 CGACCACTCTTAATTGCCTGAA 58.665 45.455 0.00 0.00 0.00 3.02
751 762 2.935238 GCGACCACTCTTAATTGCCTGA 60.935 50.000 0.00 0.00 0.00 3.86
752 763 1.398390 GCGACCACTCTTAATTGCCTG 59.602 52.381 0.00 0.00 0.00 4.85
753 764 1.679032 GGCGACCACTCTTAATTGCCT 60.679 52.381 0.00 0.00 38.42 4.75
754 765 0.733150 GGCGACCACTCTTAATTGCC 59.267 55.000 0.00 0.00 34.50 4.52
755 766 0.373716 CGGCGACCACTCTTAATTGC 59.626 55.000 0.00 0.00 0.00 3.56
760 771 1.592400 CTGGACGGCGACCACTCTTA 61.592 60.000 26.29 5.36 33.57 2.10
774 785 2.805099 CTGAAAGAGTTGACAGCTGGAC 59.195 50.000 19.93 13.35 34.07 4.02
775 786 2.224378 CCTGAAAGAGTTGACAGCTGGA 60.224 50.000 19.93 0.29 34.07 3.86
779 790 1.597742 TGCCTGAAAGAGTTGACAGC 58.402 50.000 0.00 0.00 34.07 4.40
812 824 9.183368 ACCTCCAAAAAGCAATAATTTCAAAAA 57.817 25.926 0.00 0.00 0.00 1.94
820 832 4.082245 CGGTCACCTCCAAAAAGCAATAAT 60.082 41.667 0.00 0.00 0.00 1.28
827 839 1.852067 CGCCGGTCACCTCCAAAAAG 61.852 60.000 1.90 0.00 0.00 2.27
847 859 2.097466 ACAAAACAGCGTCTTGACCAAG 59.903 45.455 3.47 3.47 39.71 3.61
849 861 1.745232 ACAAAACAGCGTCTTGACCA 58.255 45.000 2.53 0.00 0.00 4.02
851 863 2.159435 ACCAACAAAACAGCGTCTTGAC 60.159 45.455 2.53 0.00 0.00 3.18
852 864 2.088423 ACCAACAAAACAGCGTCTTGA 58.912 42.857 2.53 0.00 0.00 3.02
853 865 2.559998 ACCAACAAAACAGCGTCTTG 57.440 45.000 0.00 0.00 0.00 3.02
860 872 5.587043 TGTCCTACACTAACCAACAAAACAG 59.413 40.000 0.00 0.00 0.00 3.16
861 873 5.498393 TGTCCTACACTAACCAACAAAACA 58.502 37.500 0.00 0.00 0.00 2.83
871 883 5.758924 CAAAAAGGCTTGTCCTACACTAAC 58.241 41.667 0.00 0.00 46.94 2.34
896 908 3.619483 CGCCACAATATACGAACTCCAAA 59.381 43.478 0.00 0.00 0.00 3.28
1155 1175 4.463879 AAGCCGATGAGCAGCGCT 62.464 61.111 2.64 2.64 43.88 5.92
1312 1332 4.785453 CTCCTGGCGGGTGAAGGC 62.785 72.222 13.14 0.00 36.25 4.35
1323 1343 1.080705 GACGACGGTGTTCTCCTGG 60.081 63.158 0.00 0.00 0.00 4.45
1427 1449 5.046878 TGGACTAATTAAGAAAGACTCGGCA 60.047 40.000 0.00 0.00 0.00 5.69
1432 1454 5.046520 AGCCGTGGACTAATTAAGAAAGACT 60.047 40.000 0.00 0.00 0.00 3.24
1466 1490 4.584325 GCACACAATATTCCCCATGTATGT 59.416 41.667 0.00 0.00 0.00 2.29
1467 1491 4.320421 CGCACACAATATTCCCCATGTATG 60.320 45.833 0.00 0.00 0.00 2.39
1468 1492 3.820467 CGCACACAATATTCCCCATGTAT 59.180 43.478 0.00 0.00 0.00 2.29
1469 1493 3.210227 CGCACACAATATTCCCCATGTA 58.790 45.455 0.00 0.00 0.00 2.29
1577 1601 1.545706 CCCGGGCTCCTTATAGCTCC 61.546 65.000 8.08 0.00 40.04 4.70
1659 1683 4.261155 CGATTTTTGCACACCTTTCTGAGA 60.261 41.667 0.00 0.00 0.00 3.27
1675 1699 3.502211 AGCTGATCCGTTGAACGATTTTT 59.498 39.130 20.47 0.00 46.05 1.94
1690 1714 2.669300 TTGCAGAGTGAGAGCTGATC 57.331 50.000 0.00 0.00 34.06 2.92
1700 1727 6.022163 AGAAAATCCTGAATTTGCAGAGTG 57.978 37.500 0.00 0.00 37.64 3.51
1701 1728 6.661304 AAGAAAATCCTGAATTTGCAGAGT 57.339 33.333 0.00 0.00 37.64 3.24
1755 1782 8.540388 AGTGCAAAATTAGAGTAGAATGTAGGA 58.460 33.333 0.00 0.00 0.00 2.94
1756 1783 8.723942 AGTGCAAAATTAGAGTAGAATGTAGG 57.276 34.615 0.00 0.00 0.00 3.18
1757 1784 8.821894 GGAGTGCAAAATTAGAGTAGAATGTAG 58.178 37.037 0.00 0.00 0.00 2.74
1758 1785 8.318412 TGGAGTGCAAAATTAGAGTAGAATGTA 58.682 33.333 0.00 0.00 0.00 2.29
1759 1786 7.168219 TGGAGTGCAAAATTAGAGTAGAATGT 58.832 34.615 0.00 0.00 0.00 2.71
1760 1787 7.615582 TGGAGTGCAAAATTAGAGTAGAATG 57.384 36.000 0.00 0.00 0.00 2.67
1778 1805 4.488126 AACGAAAATGTGACATGGAGTG 57.512 40.909 0.00 0.00 0.00 3.51
1877 1904 6.024552 TGATAAAATTGAGAAAGGGTGTGC 57.975 37.500 0.00 0.00 0.00 4.57
1896 1923 6.413783 TTTGGGTGCGAGTATAAGATGATA 57.586 37.500 0.00 0.00 0.00 2.15
1923 1950 2.162681 GCCTTCAAACCTGTACAGCAT 58.837 47.619 17.86 4.67 0.00 3.79
1924 1951 1.604604 GCCTTCAAACCTGTACAGCA 58.395 50.000 17.86 0.00 0.00 4.41
1925 1952 0.517316 CGCCTTCAAACCTGTACAGC 59.483 55.000 17.86 2.60 0.00 4.40
1926 1953 1.878953 ACGCCTTCAAACCTGTACAG 58.121 50.000 16.34 16.34 0.00 2.74
1927 1954 3.472283 TTACGCCTTCAAACCTGTACA 57.528 42.857 0.00 0.00 0.00 2.90
1928 1955 4.214758 ACATTTACGCCTTCAAACCTGTAC 59.785 41.667 0.00 0.00 0.00 2.90
1970 1999 8.437742 GTCTTCATTGGAGCAATAAAATTGTTG 58.562 33.333 1.94 0.00 32.35 3.33
1972 2001 7.038799 AGGTCTTCATTGGAGCAATAAAATTGT 60.039 33.333 1.94 0.00 32.35 2.71
1973 2002 7.325694 AGGTCTTCATTGGAGCAATAAAATTG 58.674 34.615 0.00 0.00 32.35 2.32
1975 2004 7.615365 TGTAGGTCTTCATTGGAGCAATAAAAT 59.385 33.333 0.00 0.00 32.35 1.82
1979 2008 5.189736 AGTGTAGGTCTTCATTGGAGCAATA 59.810 40.000 0.00 0.00 32.35 1.90
1986 2015 5.530915 TGTTTTGAGTGTAGGTCTTCATTGG 59.469 40.000 0.00 0.00 0.00 3.16
1987 2016 6.430451 GTGTTTTGAGTGTAGGTCTTCATTG 58.570 40.000 0.00 0.00 0.00 2.82
1988 2017 5.531287 GGTGTTTTGAGTGTAGGTCTTCATT 59.469 40.000 0.00 0.00 0.00 2.57
1997 2026 6.092748 GGCATAAATGGTGTTTTGAGTGTAG 58.907 40.000 0.00 0.00 0.00 2.74
2002 2031 3.369366 GGGGGCATAAATGGTGTTTTGAG 60.369 47.826 0.00 0.00 0.00 3.02
2003 2032 2.569404 GGGGGCATAAATGGTGTTTTGA 59.431 45.455 0.00 0.00 0.00 2.69
2004 2033 2.984562 GGGGGCATAAATGGTGTTTTG 58.015 47.619 0.00 0.00 0.00 2.44
2023 2052 1.705186 TCAGAGGGGACAAAGAAAGGG 59.295 52.381 0.00 0.00 0.00 3.95
2024 2053 2.784347 GTCAGAGGGGACAAAGAAAGG 58.216 52.381 0.00 0.00 37.73 3.11
2025 2054 2.037251 TCGTCAGAGGGGACAAAGAAAG 59.963 50.000 0.00 0.00 37.66 2.62
2029 2060 2.744202 CAAATCGTCAGAGGGGACAAAG 59.256 50.000 0.00 0.00 37.66 2.77
2031 2062 1.610624 GCAAATCGTCAGAGGGGACAA 60.611 52.381 0.00 0.00 37.66 3.18
2036 2067 1.303309 GGATGCAAATCGTCAGAGGG 58.697 55.000 0.00 0.00 32.27 4.30
2044 2075 2.800629 GCCTGAAATGGGATGCAAATCG 60.801 50.000 0.00 0.00 0.00 3.34
2197 2228 5.480422 ACCATGTATCGCCAAGACTATGATA 59.520 40.000 0.00 0.00 0.00 2.15
2210 2241 2.545526 CCATGAACTCACCATGTATCGC 59.454 50.000 0.00 0.00 39.66 4.58
2224 2255 2.941720 GAGATGAAGTCAGGCCATGAAC 59.058 50.000 5.01 0.00 40.43 3.18
2366 2397 2.500229 TGTTTCCAAGCCTTTAGACCG 58.500 47.619 0.00 0.00 0.00 4.79
2940 2982 1.007502 GCCGCTGCAATTCACACAA 60.008 52.632 0.00 0.00 37.47 3.33
3410 3453 2.792542 GCAAGAATGTAGATGGCGCAAC 60.793 50.000 10.83 0.00 0.00 4.17
3412 3455 1.016627 GCAAGAATGTAGATGGCGCA 58.983 50.000 10.83 0.00 0.00 6.09
3418 3461 7.279758 GCTTTGTAGAAGAGCAAGAATGTAGAT 59.720 37.037 0.00 0.00 36.45 1.98
3550 3593 1.013005 CAACAGACAGCTCGAGGCAG 61.013 60.000 15.58 6.16 44.79 4.85
3634 3677 0.104304 CCATCGGAAGGGGAACGTAG 59.896 60.000 0.00 0.00 0.00 3.51
3724 3767 2.413142 GCTCATCTTGTGCCAGGCC 61.413 63.158 9.64 0.00 31.28 5.19
3725 3768 1.654954 CTGCTCATCTTGTGCCAGGC 61.655 60.000 3.66 3.66 36.15 4.85
3726 3769 1.030488 CCTGCTCATCTTGTGCCAGG 61.030 60.000 0.00 0.00 39.22 4.45
3742 3785 3.710722 AGCGTGGCCTCCTTCCTG 61.711 66.667 3.32 0.00 0.00 3.86
3745 3788 4.400961 AGCAGCGTGGCCTCCTTC 62.401 66.667 3.32 0.00 0.00 3.46
3891 5325 3.059097 AGCTATCCATCCATGAAACCCT 58.941 45.455 0.00 0.00 0.00 4.34
3941 5375 2.118228 TGCAAATGTCGAACAACAGC 57.882 45.000 0.00 0.00 31.50 4.40
3951 5915 5.232463 ACATTCTTGGATGTTGCAAATGTC 58.768 37.500 0.00 0.00 36.92 3.06
3976 5940 9.490379 AAAACCAAACTTATCTACAGACTACAG 57.510 33.333 0.00 0.00 0.00 2.74
3977 5941 9.268268 CAAAACCAAACTTATCTACAGACTACA 57.732 33.333 0.00 0.00 0.00 2.74
3978 5942 9.269453 ACAAAACCAAACTTATCTACAGACTAC 57.731 33.333 0.00 0.00 0.00 2.73
3979 5943 9.841295 AACAAAACCAAACTTATCTACAGACTA 57.159 29.630 0.00 0.00 0.00 2.59
3980 5944 8.621286 CAACAAAACCAAACTTATCTACAGACT 58.379 33.333 0.00 0.00 0.00 3.24
3981 5945 7.860872 CCAACAAAACCAAACTTATCTACAGAC 59.139 37.037 0.00 0.00 0.00 3.51
3982 5946 7.013846 CCCAACAAAACCAAACTTATCTACAGA 59.986 37.037 0.00 0.00 0.00 3.41
4007 5971 8.519526 TCAGATATGGTTTTAAACACAACATCC 58.480 33.333 10.14 1.23 0.00 3.51
4060 6076 1.981259 ACTAAGCCCCCAATACACCT 58.019 50.000 0.00 0.00 0.00 4.00
4061 6077 3.457012 TCTTACTAAGCCCCCAATACACC 59.543 47.826 0.00 0.00 0.00 4.16
4206 6224 5.717038 AAAGCGAACATTTTTGGAACTTG 57.283 34.783 0.00 0.00 0.00 3.16
4434 6500 8.902735 GTTCGGAAATTTAAGAAGTGTTTGATC 58.097 33.333 7.74 0.00 0.00 2.92
4438 6504 9.594478 AAATGTTCGGAAATTTAAGAAGTGTTT 57.406 25.926 7.74 7.03 0.00 2.83
4596 7252 7.659390 TGTGTGGAAAAATTTGGGTCAATTATC 59.341 33.333 0.00 0.00 0.00 1.75
4611 7267 5.931294 TGGTGATACTAGTGTGTGGAAAAA 58.069 37.500 5.39 0.00 0.00 1.94
4767 8568 6.489469 TGTTCGATTCAACAAAAATGTTCG 57.511 33.333 0.00 0.00 33.21 3.95


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

AutoCloner maintained by Alex Coulton.