Multiple sequence alignment - TraesCS2B01G096500

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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 TraesCS2B01G096500 chr2B 100.000 4240 0 0 1 4240 56779644 56775405 0.000000e+00 7830.0
1 TraesCS2B01G096500 chr2B 87.887 355 43 0 1560 1914 292616392 292616038 6.560000e-113 418.0
2 TraesCS2B01G096500 chr2B 87.887 355 43 0 1560 1914 292623270 292622916 6.560000e-113 418.0
3 TraesCS2B01G096500 chr2B 86.260 262 24 10 869 1122 203466602 203466859 1.500000e-69 274.0
4 TraesCS2B01G096500 chr2B 70.856 748 160 49 25 739 171818082 171817360 2.070000e-23 121.0
5 TraesCS2B01G096500 chr2B 91.860 86 6 1 661 746 711135486 711135402 7.450000e-23 119.0
6 TraesCS2B01G096500 chr2D 92.555 2861 162 29 759 3588 34275839 34272999 0.000000e+00 4056.0
7 TraesCS2B01G096500 chr2D 92.901 648 33 7 3584 4231 34272856 34272222 0.000000e+00 929.0
8 TraesCS2B01G096500 chr2A 89.688 1571 95 31 914 2424 37218420 37216857 0.000000e+00 1941.0
9 TraesCS2B01G096500 chr2A 94.898 1176 55 5 2470 3642 37216849 37215676 0.000000e+00 1834.0
10 TraesCS2B01G096500 chr2A 94.171 549 28 3 3683 4231 37215675 37215131 0.000000e+00 833.0
11 TraesCS2B01G096500 chr5B 89.665 687 51 9 908 1587 316762163 316762836 0.000000e+00 857.0
12 TraesCS2B01G096500 chr5B 97.727 44 1 0 3557 3600 13559339 13559382 4.550000e-10 76.8
13 TraesCS2B01G096500 chr5B 95.455 44 2 0 3557 3600 13555275 13555318 2.120000e-08 71.3
14 TraesCS2B01G096500 chr3A 86.119 670 67 16 26 686 746210484 746211136 0.000000e+00 699.0
15 TraesCS2B01G096500 chr3A 96.552 87 3 0 621 707 746211138 746211224 1.230000e-30 145.0
16 TraesCS2B01G096500 chr5A 81.906 724 102 24 26 740 402824554 402825257 6.110000e-163 584.0
17 TraesCS2B01G096500 chr6B 90.741 216 16 3 908 1122 160729123 160729335 6.940000e-73 285.0
18 TraesCS2B01G096500 chr6B 90.278 216 17 4 908 1122 719484523 719484311 3.230000e-71 279.0
19 TraesCS2B01G096500 chr6B 91.133 203 14 3 908 1109 116214648 116214847 5.400000e-69 272.0
20 TraesCS2B01G096500 chr6B 91.860 86 7 0 661 746 423098119 423098204 2.070000e-23 121.0
21 TraesCS2B01G096500 chr3B 89.352 216 19 3 908 1122 504523121 504522909 6.990000e-68 268.0
22 TraesCS2B01G096500 chr3B 100.000 65 0 0 682 746 123362352 123362288 2.070000e-23 121.0
23 TraesCS2B01G096500 chr7B 90.640 203 15 4 908 1109 66447494 66447295 2.510000e-67 267.0
24 TraesCS2B01G096500 chr7B 90.148 203 16 3 908 1109 639551170 639551369 1.170000e-65 261.0
25 TraesCS2B01G096500 chr1D 88.525 122 12 2 620 740 465599123 465599003 3.420000e-31 147.0
26 TraesCS2B01G096500 chr1B 91.579 95 7 1 661 755 409681261 409681168 3.440000e-26 130.0
27 TraesCS2B01G096500 chr3D 89.773 88 5 3 661 746 331403144 331403229 4.480000e-20 110.0
28 TraesCS2B01G096500 chr6D 88.636 88 9 1 628 714 11572948 11572861 5.800000e-19 106.0


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 TraesCS2B01G096500 chr2B 56775405 56779644 4239 True 7830.0 7830 100.0000 1 4240 1 chr2B.!!$R1 4239
1 TraesCS2B01G096500 chr2D 34272222 34275839 3617 True 2492.5 4056 92.7280 759 4231 2 chr2D.!!$R1 3472
2 TraesCS2B01G096500 chr2A 37215131 37218420 3289 True 1536.0 1941 92.9190 914 4231 3 chr2A.!!$R1 3317
3 TraesCS2B01G096500 chr5B 316762163 316762836 673 False 857.0 857 89.6650 908 1587 1 chr5B.!!$F3 679
4 TraesCS2B01G096500 chr3A 746210484 746211224 740 False 422.0 699 91.3355 26 707 2 chr3A.!!$F1 681
5 TraesCS2B01G096500 chr5A 402824554 402825257 703 False 584.0 584 81.9060 26 740 1 chr5A.!!$F1 714

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
749 885 0.174845 CCGAATAGGAACCAGCACGA 59.825 55.0 0.0 0.0 45.0 4.35 F
1374 1525 0.036306 ATCGCCCCTTTCGTTCTGTT 59.964 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1812 0.681733 GTCCTGCTTGTCTCTCCACA 59.318 55.000 0.00 0.00 0.0 4.17 R
3356 3564 1.001293 ACGCCGCATACTCATCATGAT 59.999 47.619 1.18 1.18 0.0 2.45 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
20 21 3.101643 TGCTGTATGTACTCTGGTCCT 57.898 47.619 0.00 0.00 0.00 3.85
21 22 3.441101 TGCTGTATGTACTCTGGTCCTT 58.559 45.455 0.00 0.00 0.00 3.36
22 23 3.838317 TGCTGTATGTACTCTGGTCCTTT 59.162 43.478 0.00 0.00 0.00 3.11
23 24 4.184629 GCTGTATGTACTCTGGTCCTTTG 58.815 47.826 0.00 0.00 0.00 2.77
24 25 4.081642 GCTGTATGTACTCTGGTCCTTTGA 60.082 45.833 0.00 0.00 0.00 2.69
49 50 7.583860 AAAAAGTTCACCGAATTTCGAAAAA 57.416 28.000 19.91 7.78 43.74 1.94
50 51 6.806120 AAAGTTCACCGAATTTCGAAAAAG 57.194 33.333 19.91 8.93 43.74 2.27
51 52 5.494632 AGTTCACCGAATTTCGAAAAAGT 57.505 34.783 19.91 7.12 43.74 2.66
52 53 5.886992 AGTTCACCGAATTTCGAAAAAGTT 58.113 33.333 19.91 4.70 43.74 2.66
53 54 5.969435 AGTTCACCGAATTTCGAAAAAGTTC 59.031 36.000 19.91 12.93 43.74 3.01
54 55 5.487153 TCACCGAATTTCGAAAAAGTTCA 57.513 34.783 19.91 0.00 43.74 3.18
55 56 5.267776 TCACCGAATTTCGAAAAAGTTCAC 58.732 37.500 19.91 1.27 43.74 3.18
56 57 4.439776 CACCGAATTTCGAAAAAGTTCACC 59.560 41.667 19.91 0.00 43.74 4.02
57 58 3.662186 CCGAATTTCGAAAAAGTTCACCG 59.338 43.478 19.91 9.06 43.74 4.94
58 59 4.520078 CGAATTTCGAAAAAGTTCACCGA 58.480 39.130 15.66 0.00 43.74 4.69
59 60 4.965158 CGAATTTCGAAAAAGTTCACCGAA 59.035 37.500 15.66 0.00 43.74 4.30
60 61 5.623673 CGAATTTCGAAAAAGTTCACCGAAT 59.376 36.000 15.66 0.00 43.74 3.34
61 62 6.141685 CGAATTTCGAAAAAGTTCACCGAATT 59.858 34.615 15.66 0.00 43.74 2.17
62 63 6.986424 ATTTCGAAAAAGTTCACCGAATTC 57.014 33.333 15.66 0.00 38.72 2.17
63 64 4.123276 TCGAAAAAGTTCACCGAATTCG 57.877 40.909 20.92 20.92 39.43 3.34
194 217 6.702716 AGTTCACCAAATTCGGAAAAAGTA 57.297 33.333 0.00 0.00 0.00 2.24
260 284 4.602995 TCAAATTCGGAAAAAGTTCACCG 58.397 39.130 0.00 0.00 45.61 4.94
327 392 2.610374 CGGAAAAAGTTCACCGAGTTCA 59.390 45.455 0.00 0.00 46.94 3.18
328 393 3.064271 CGGAAAAAGTTCACCGAGTTCAA 59.936 43.478 0.00 0.00 46.94 2.69
330 395 5.588240 GGAAAAAGTTCACCGAGTTCAAAT 58.412 37.500 0.00 0.00 35.25 2.32
331 396 6.040247 GGAAAAAGTTCACCGAGTTCAAATT 58.960 36.000 0.00 0.00 35.25 1.82
332 397 6.533723 GGAAAAAGTTCACCGAGTTCAAATTT 59.466 34.615 0.00 0.00 35.25 1.82
333 398 7.064134 GGAAAAAGTTCACCGAGTTCAAATTTT 59.936 33.333 0.00 0.00 35.25 1.82
334 399 7.899178 AAAAGTTCACCGAGTTCAAATTTTT 57.101 28.000 0.00 0.00 0.00 1.94
428 494 9.695526 AATTCAAGAAAATGTCATCGATTTTGA 57.304 25.926 0.00 0.00 34.00 2.69
449 515 9.677567 TTTTGAAGAAATATTCGTGAAGGAAAG 57.322 29.630 0.00 0.00 34.02 2.62
465 531 5.934935 AGGAAAGAAGTTTCGCGAATTTA 57.065 34.783 24.05 4.74 42.78 1.40
466 532 6.308371 AGGAAAGAAGTTTCGCGAATTTAA 57.692 33.333 24.05 4.30 42.78 1.52
467 533 6.731164 AGGAAAGAAGTTTCGCGAATTTAAA 58.269 32.000 24.05 3.86 42.78 1.52
468 534 7.197703 AGGAAAGAAGTTTCGCGAATTTAAAA 58.802 30.769 24.05 2.99 42.78 1.52
469 535 7.703197 AGGAAAGAAGTTTCGCGAATTTAAAAA 59.297 29.630 24.05 2.13 42.78 1.94
533 600 9.833182 GAAATAAAAAGGTGAAAACAAGCAAAA 57.167 25.926 0.00 0.00 0.00 2.44
559 626 2.094675 CATGAAAGGATGTGGTGGGTC 58.905 52.381 0.00 0.00 0.00 4.46
565 632 3.659089 GATGTGGTGGGTCGGTCGG 62.659 68.421 0.00 0.00 0.00 4.79
576 643 3.751246 CGGTCGGGGCGTCTTACA 61.751 66.667 0.00 0.00 0.00 2.41
613 680 1.513622 GGTTCGAGACCCAGCTCTC 59.486 63.158 5.71 0.00 43.06 3.20
618 685 2.757917 AGACCCAGCTCTCGCTCC 60.758 66.667 0.00 0.00 45.15 4.70
714 850 1.456544 CGTTAGCGAAAACGCCTGTAA 59.543 47.619 10.85 1.53 44.83 2.41
740 876 1.808891 GCTAAAGGCGCCGAATAGGAA 60.809 52.381 26.61 8.91 45.00 3.36
741 877 1.865340 CTAAAGGCGCCGAATAGGAAC 59.135 52.381 23.20 0.00 45.00 3.62
742 878 0.746923 AAAGGCGCCGAATAGGAACC 60.747 55.000 23.20 0.00 45.00 3.62
743 879 1.906105 AAGGCGCCGAATAGGAACCA 61.906 55.000 23.20 0.00 45.00 3.67
744 880 1.887707 GGCGCCGAATAGGAACCAG 60.888 63.158 12.58 0.00 45.00 4.00
745 881 2.534903 GCGCCGAATAGGAACCAGC 61.535 63.158 0.00 0.00 45.00 4.85
746 882 1.153449 CGCCGAATAGGAACCAGCA 60.153 57.895 0.00 0.00 45.00 4.41
747 883 1.429148 CGCCGAATAGGAACCAGCAC 61.429 60.000 0.00 0.00 45.00 4.40
748 884 1.429148 GCCGAATAGGAACCAGCACG 61.429 60.000 0.00 0.00 45.00 5.34
749 885 0.174845 CCGAATAGGAACCAGCACGA 59.825 55.000 0.00 0.00 45.00 4.35
750 886 1.560923 CGAATAGGAACCAGCACGAG 58.439 55.000 0.00 0.00 0.00 4.18
751 887 1.802880 CGAATAGGAACCAGCACGAGG 60.803 57.143 0.00 0.00 0.00 4.63
752 888 1.480954 GAATAGGAACCAGCACGAGGA 59.519 52.381 0.00 0.00 0.00 3.71
753 889 1.115467 ATAGGAACCAGCACGAGGAG 58.885 55.000 0.00 0.00 0.00 3.69
754 890 0.970937 TAGGAACCAGCACGAGGAGG 60.971 60.000 0.00 0.00 0.00 4.30
755 891 2.283529 GGAACCAGCACGAGGAGGA 61.284 63.158 0.00 0.00 0.00 3.71
756 892 1.079750 GAACCAGCACGAGGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
757 893 1.534235 AACCAGCACGAGGAGGACT 60.534 57.895 0.00 0.00 0.00 3.85
810 946 1.727467 GCAACGTTGTGACAAGGCT 59.273 52.632 27.78 3.00 0.00 4.58
813 949 2.047151 AACGTTGTGACAAGGCTGCG 62.047 55.000 16.91 10.35 0.00 5.18
972 1112 2.098680 CTCGTCGTCGTCTCTGCC 59.901 66.667 1.33 0.00 38.33 4.85
1026 1173 4.361971 TGCCGGACCTCCTCTCGT 62.362 66.667 5.05 0.00 0.00 4.18
1238 1389 3.423154 GTTGCTCGACTTGGCCGG 61.423 66.667 0.00 0.00 0.00 6.13
1262 1413 1.124839 GTTTTGCTTGCTTGCGTATGC 59.875 47.619 0.00 0.00 43.20 3.14
1340 1491 6.258507 CCATGCGCATATATTCAGTAGCATAA 59.741 38.462 24.84 0.00 41.42 1.90
1374 1525 0.036306 ATCGCCCCTTTCGTTCTGTT 59.964 50.000 0.00 0.00 0.00 3.16
1375 1526 0.179040 TCGCCCCTTTCGTTCTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
1376 1527 1.070445 TCGCCCCTTTCGTTCTGTTTA 59.930 47.619 0.00 0.00 0.00 2.01
1396 1547 5.586155 TTATACTTGTGGAAGGACCCAAA 57.414 39.130 0.00 0.00 38.06 3.28
1438 1606 7.039784 TCCAATGTTAGGTTCAGAAAATTCAGG 60.040 37.037 0.00 0.00 0.00 3.86
1460 1629 5.987347 AGGAATTGTTTGCTGAATGAAGTTG 59.013 36.000 0.00 0.00 31.54 3.16
1489 1685 5.291128 ACACGGACATGATTTTTAGATCGTC 59.709 40.000 0.00 0.00 0.00 4.20
1516 1712 5.299279 ACAAACAACCTCTCAGTTAACCATG 59.701 40.000 0.88 0.00 0.00 3.66
1613 1812 2.556144 ATATGCATGATGAGCACCGT 57.444 45.000 10.16 0.00 45.95 4.83
1676 1875 3.056328 GTTCCTGGCCGCCAACTC 61.056 66.667 14.45 0.86 30.80 3.01
1686 1885 2.230940 CGCCAACTCGTATCGCCTG 61.231 63.158 0.00 0.00 0.00 4.85
1733 1932 0.250901 GTCTCTTCCTGCCCTGCAAA 60.251 55.000 0.00 0.00 38.41 3.68
1738 1937 1.243342 TTCCTGCCCTGCAAATCACG 61.243 55.000 0.00 0.00 38.41 4.35
1744 1943 0.670546 CCCTGCAAATCACGAGTCGT 60.671 55.000 13.56 13.56 42.36 4.34
1949 2148 4.727507 ATGGTGTTTGTTTGCTGTAACA 57.272 36.364 0.00 0.00 36.30 2.41
1952 2151 5.105752 TGGTGTTTGTTTGCTGTAACAATC 58.894 37.500 11.31 11.06 44.76 2.67
1954 2153 3.794028 TGTTTGTTTGCTGTAACAATCGC 59.206 39.130 11.31 7.36 44.76 4.58
1965 2164 0.527565 AACAATCGCAATGGTGGCTC 59.472 50.000 0.00 0.00 0.00 4.70
1979 2178 1.751927 GGCTCCACTGCTGGAATGG 60.752 63.158 0.00 0.00 46.63 3.16
1983 2182 1.004044 CTCCACTGCTGGAATGGTTCT 59.996 52.381 0.00 0.00 46.63 3.01
2037 2236 8.070171 CAGTTCAAAAATCTCTATGTCGTTGTT 58.930 33.333 0.00 0.00 0.00 2.83
2049 2248 2.206750 GTCGTTGTTGCTGTTCCTACA 58.793 47.619 0.00 0.00 0.00 2.74
2061 2260 3.411446 TGTTCCTACAGTGGAGCAAATG 58.589 45.455 0.00 0.00 42.84 2.32
2072 2271 4.156008 AGTGGAGCAAATGGAATCGTTTAC 59.844 41.667 0.00 0.00 31.46 2.01
2095 2294 9.772973 TTACTCAGTCTTATTTCAAGTAAGCAA 57.227 29.630 0.00 0.00 0.00 3.91
2254 2453 1.897133 TGCTCAAAATTGCTCATGCCT 59.103 42.857 0.00 0.00 38.71 4.75
2330 2530 3.189910 GCATCTGACACACATCAACACAT 59.810 43.478 0.00 0.00 0.00 3.21
2412 2614 5.619132 TTCACATGCTTCCAGATCTATCA 57.381 39.130 0.00 0.00 0.00 2.15
2430 2632 7.767250 TCTATCACTGCACTATATGTAGCTT 57.233 36.000 0.00 0.00 44.44 3.74
2474 2676 5.183713 TGTTGCAAATGCTGTAGCTCTAAAT 59.816 36.000 0.00 0.00 42.66 1.40
2514 2716 1.513158 CTGTGTCTGTAGCGGGAGG 59.487 63.158 0.00 0.00 0.00 4.30
2527 2729 0.390472 CGGGAGGAAGCAGTTCAGTC 60.390 60.000 0.00 0.00 33.93 3.51
2541 2743 4.040829 CAGTTCAGTCCATGGATGCCTATA 59.959 45.833 19.62 0.00 0.00 1.31
2686 2889 9.771915 CAGTTTTGAATTATTTGCAAGTTTTGT 57.228 25.926 0.00 0.00 0.00 2.83
2721 2924 5.418310 AAACAACTCAAATGGTAGACACG 57.582 39.130 0.00 0.00 0.00 4.49
2777 2980 8.653338 CAATCATTTTTCTAAAGCATGGTTGAG 58.347 33.333 14.91 14.91 35.55 3.02
2789 2992 1.208706 TGGTTGAGGACAGTTCACCA 58.791 50.000 0.00 0.00 0.00 4.17
2803 3006 2.654749 TCACCATAGACAAGTGCTCG 57.345 50.000 0.00 0.00 0.00 5.03
2831 3034 6.799512 GCTCAAACATAATTATTGTGCCTCT 58.200 36.000 10.93 0.00 37.51 3.69
2832 3035 6.914757 GCTCAAACATAATTATTGTGCCTCTC 59.085 38.462 10.93 0.00 37.51 3.20
2833 3036 7.201767 GCTCAAACATAATTATTGTGCCTCTCT 60.202 37.037 10.93 0.00 37.51 3.10
2834 3037 8.213518 TCAAACATAATTATTGTGCCTCTCTC 57.786 34.615 1.60 0.00 0.00 3.20
2835 3038 7.828717 TCAAACATAATTATTGTGCCTCTCTCA 59.171 33.333 1.60 0.00 0.00 3.27
2836 3039 8.627403 CAAACATAATTATTGTGCCTCTCTCAT 58.373 33.333 1.60 0.00 0.00 2.90
2837 3040 7.741027 ACATAATTATTGTGCCTCTCTCATG 57.259 36.000 1.60 0.00 0.00 3.07
2838 3041 7.512130 ACATAATTATTGTGCCTCTCTCATGA 58.488 34.615 1.60 0.00 0.00 3.07
2840 3043 6.690194 AATTATTGTGCCTCTCTCATGAAC 57.310 37.500 0.00 0.00 0.00 3.18
2882 3086 8.485976 ACTATTCAAGAATGAGAACTAAGCAC 57.514 34.615 5.59 0.00 36.78 4.40
2888 3092 6.360370 AGAATGAGAACTAAGCACTTACCA 57.640 37.500 0.00 0.00 0.00 3.25
2890 3094 5.746990 ATGAGAACTAAGCACTTACCAGT 57.253 39.130 0.00 0.00 0.00 4.00
2894 3098 6.927381 TGAGAACTAAGCACTTACCAGTTTAC 59.073 38.462 0.05 0.00 0.00 2.01
2925 3129 6.084326 GAGAAGTCCTCCATTCTCTGATAC 57.916 45.833 7.51 0.00 45.19 2.24
2926 3130 4.898861 AGAAGTCCTCCATTCTCTGATACC 59.101 45.833 0.00 0.00 29.80 2.73
2949 3153 3.120234 TGCTCTGTACAATTTGTCATGCG 60.120 43.478 5.07 0.00 0.00 4.73
3338 3546 5.105752 GTCAGAGAACTGTATGCCTACTTG 58.894 45.833 0.74 0.00 43.81 3.16
3343 3551 5.725362 AGAACTGTATGCCTACTTGTTCTC 58.275 41.667 22.06 9.95 42.07 2.87
3353 3561 4.518249 CCTACTTGTTCTCCCATTCTTCC 58.482 47.826 0.00 0.00 0.00 3.46
3356 3564 4.803452 ACTTGTTCTCCCATTCTTCCAAA 58.197 39.130 0.00 0.00 0.00 3.28
3483 3692 2.162408 ACTTCTTTTGCCGAGCTAATGC 59.838 45.455 0.00 0.00 40.05 3.56
3494 3703 2.456119 GCTAATGCGCACGCTCAGT 61.456 57.895 14.90 0.00 42.51 3.41
3616 3967 8.302438 TCAGAAGTACAGTAGTTAAGTTAAGCC 58.698 37.037 0.25 0.00 0.00 4.35
3636 3987 3.887716 GCCACATATTCTGGAAGCAAGAT 59.112 43.478 0.88 0.00 0.00 2.40
3637 3988 5.065914 GCCACATATTCTGGAAGCAAGATA 58.934 41.667 0.88 0.00 0.00 1.98
3638 3989 5.049129 GCCACATATTCTGGAAGCAAGATAC 60.049 44.000 0.88 0.00 0.00 2.24
3645 3996 3.133003 TCTGGAAGCAAGATACTACCTGC 59.867 47.826 0.00 0.00 0.00 4.85
3648 3999 3.181450 GGAAGCAAGATACTACCTGCCAT 60.181 47.826 0.00 0.00 0.00 4.40
3658 4009 3.356290 ACTACCTGCCATGATGAAAACC 58.644 45.455 0.00 0.00 0.00 3.27
3708 4059 4.139038 CCTGATGCATTCACATGATACCA 58.861 43.478 0.00 0.00 31.07 3.25
3743 4094 3.630312 GGCAGGCAAATTAAGGTCGATTA 59.370 43.478 0.00 0.00 0.00 1.75
3759 4110 4.679197 GTCGATTAGCTACTGAATCTGCAG 59.321 45.833 7.63 7.63 41.63 4.41
3774 4125 0.994247 TGCAGTGGGATGAACTCCAT 59.006 50.000 0.00 0.00 46.98 3.41
3796 4147 0.905357 ACTGCCGAAGCTATTGGTCT 59.095 50.000 0.00 0.00 40.80 3.85
3940 4291 4.981806 TTTACTGCAAAAAGTCAGCTGT 57.018 36.364 14.67 0.00 42.02 4.40
4014 4365 4.577677 TTGAACGGCAGCCCAGCA 62.578 61.111 5.63 0.00 35.83 4.41
4020 4371 2.590007 GGCAGCCCAGCATACTCG 60.590 66.667 0.00 0.00 35.83 4.18
4172 4523 2.430244 GTGTCGTGTCGTCCGCAT 60.430 61.111 0.00 0.00 0.00 4.73
4204 4555 4.946157 CAGATGCAGAAATAGGAACCACTT 59.054 41.667 0.00 0.00 0.00 3.16
4231 4582 2.564771 TGCAGCTGGCTTCACATATAC 58.435 47.619 17.12 0.00 45.15 1.47
4232 4583 2.171237 TGCAGCTGGCTTCACATATACT 59.829 45.455 17.12 0.00 45.15 2.12
4233 4584 2.805099 GCAGCTGGCTTCACATATACTC 59.195 50.000 17.12 0.00 40.25 2.59
4234 4585 3.397482 CAGCTGGCTTCACATATACTCC 58.603 50.000 5.57 0.00 0.00 3.85
4235 4586 2.370189 AGCTGGCTTCACATATACTCCC 59.630 50.000 0.00 0.00 0.00 4.30
4236 4587 2.370189 GCTGGCTTCACATATACTCCCT 59.630 50.000 0.00 0.00 0.00 4.20
4237 4588 3.556004 GCTGGCTTCACATATACTCCCTC 60.556 52.174 0.00 0.00 0.00 4.30
4238 4589 2.972713 TGGCTTCACATATACTCCCTCC 59.027 50.000 0.00 0.00 0.00 4.30
4239 4590 2.028930 GGCTTCACATATACTCCCTCCG 60.029 54.545 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.101643 AGGACCAGAGTACATACAGCA 57.898 47.619 0.00 0.00 0.00 4.41
1 2 4.081642 TCAAAGGACCAGAGTACATACAGC 60.082 45.833 0.00 0.00 0.00 4.40
2 3 5.661056 TCAAAGGACCAGAGTACATACAG 57.339 43.478 0.00 0.00 0.00 2.74
3 4 6.428083 TTTCAAAGGACCAGAGTACATACA 57.572 37.500 0.00 0.00 0.00 2.29
4 5 7.739498 TTTTTCAAAGGACCAGAGTACATAC 57.261 36.000 0.00 0.00 0.00 2.39
37 38 6.986424 ATTCGGTGAACTTTTTCGAAATTC 57.014 33.333 12.12 12.88 41.93 2.17
40 41 4.965158 CGAATTCGGTGAACTTTTTCGAAA 59.035 37.500 20.16 6.47 41.93 3.46
42 43 4.123276 CGAATTCGGTGAACTTTTTCGA 57.877 40.909 20.16 0.00 34.40 3.71
56 57 4.520078 TCGTTGAACTTTTTCCGAATTCG 58.480 39.130 20.92 20.92 39.44 3.34
57 58 5.507974 ACTCGTTGAACTTTTTCCGAATTC 58.492 37.500 0.00 0.00 28.84 2.17
58 59 5.494632 ACTCGTTGAACTTTTTCCGAATT 57.505 34.783 0.00 0.00 28.84 2.17
59 60 5.494632 AACTCGTTGAACTTTTTCCGAAT 57.505 34.783 0.00 0.00 28.84 3.34
60 61 4.492895 CGAACTCGTTGAACTTTTTCCGAA 60.493 41.667 0.00 0.00 28.84 4.30
61 62 3.000523 CGAACTCGTTGAACTTTTTCCGA 59.999 43.478 0.00 0.00 34.11 4.55
62 63 3.000523 TCGAACTCGTTGAACTTTTTCCG 59.999 43.478 0.00 0.00 40.80 4.30
63 64 4.525411 TCGAACTCGTTGAACTTTTTCC 57.475 40.909 0.00 0.00 40.80 3.13
64 65 6.842081 TTTTCGAACTCGTTGAACTTTTTC 57.158 33.333 0.00 0.00 40.80 2.29
95 97 4.573201 ACGGTGAACTTTTTCTGAATTCGA 59.427 37.500 0.04 0.00 32.36 3.71
97 99 8.073768 TGAATACGGTGAACTTTTTCTGAATTC 58.926 33.333 0.00 0.00 32.36 2.17
103 105 7.562454 TTTCTGAATACGGTGAACTTTTTCT 57.438 32.000 0.00 0.00 32.36 2.52
185 208 4.996062 TCGAATTCGGTGTACTTTTTCC 57.004 40.909 26.47 0.00 40.29 3.13
299 343 4.212636 TCGGTGAACTTTTTCCGAATTCTC 59.787 41.667 3.52 0.00 46.96 2.87
428 494 8.622948 ACTTCTTTCCTTCACGAATATTTCTT 57.377 30.769 0.00 0.00 0.00 2.52
504 570 9.225436 TGCTTGTTTTCACCTTTTTATTTCTTT 57.775 25.926 0.00 0.00 0.00 2.52
559 626 3.751246 TGTAAGACGCCCCGACCG 61.751 66.667 0.00 0.00 0.00 4.79
565 632 2.460757 TGGTTTAGTGTAAGACGCCC 57.539 50.000 0.00 0.00 0.00 6.13
613 680 0.389025 AAACTGCAAAAAGGGGAGCG 59.611 50.000 0.00 0.00 0.00 5.03
616 683 5.941555 TTTCTAAAACTGCAAAAAGGGGA 57.058 34.783 0.00 0.00 0.00 4.81
641 708 4.826556 CCCAGTTTTGACTTGTTTTTCCA 58.173 39.130 0.00 0.00 0.00 3.53
642 709 3.621268 GCCCAGTTTTGACTTGTTTTTCC 59.379 43.478 0.00 0.00 0.00 3.13
732 868 1.480954 TCCTCGTGCTGGTTCCTATTC 59.519 52.381 0.00 0.00 0.00 1.75
740 876 1.979693 GAGTCCTCCTCGTGCTGGT 60.980 63.158 0.00 0.00 0.00 4.00
741 877 2.716017 GGAGTCCTCCTCGTGCTGG 61.716 68.421 0.41 0.00 46.16 4.85
742 878 2.888863 GGAGTCCTCCTCGTGCTG 59.111 66.667 0.41 0.00 46.16 4.41
751 887 5.334646 GGAATGTTAAAAACGTGGAGTCCTC 60.335 44.000 11.33 5.88 0.00 3.71
752 888 4.517832 GGAATGTTAAAAACGTGGAGTCCT 59.482 41.667 11.33 0.00 0.00 3.85
753 889 4.612033 CGGAATGTTAAAAACGTGGAGTCC 60.612 45.833 0.73 0.73 0.00 3.85
754 890 4.211794 TCGGAATGTTAAAAACGTGGAGTC 59.788 41.667 0.00 0.00 0.00 3.36
755 891 4.128643 TCGGAATGTTAAAAACGTGGAGT 58.871 39.130 0.00 0.00 0.00 3.85
756 892 4.735662 TCGGAATGTTAAAAACGTGGAG 57.264 40.909 0.00 0.00 0.00 3.86
757 893 5.496133 TTTCGGAATGTTAAAAACGTGGA 57.504 34.783 0.00 0.00 0.00 4.02
784 920 2.203153 ACAACGTTGCGCCCTCTT 60.203 55.556 27.61 2.90 0.00 2.85
785 921 2.972505 CACAACGTTGCGCCCTCT 60.973 61.111 27.61 3.70 0.00 3.69
867 1003 0.621082 GAAGAAGGGTGAGGAAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
868 1004 0.250513 CGAAGAAGGGTGAGGAAGGG 59.749 60.000 0.00 0.00 0.00 3.95
956 1092 3.429141 GGGCAGAGACGACGACGA 61.429 66.667 15.32 0.00 42.66 4.20
957 1093 4.477975 GGGGCAGAGACGACGACG 62.478 72.222 5.58 5.58 45.75 5.12
958 1094 4.477975 CGGGGCAGAGACGACGAC 62.478 72.222 0.00 0.00 0.00 4.34
1238 1389 1.860326 ACGCAAGCAAGCAAAACATTC 59.140 42.857 1.32 0.00 45.62 2.67
1262 1413 1.233019 GAATCCCCATCAGCACATCG 58.767 55.000 0.00 0.00 0.00 3.84
1340 1491 2.919043 GATTCCTCCGGGCATGGT 59.081 61.111 0.00 0.00 0.00 3.55
1374 1525 5.515886 CCTTTGGGTCCTTCCACAAGTATAA 60.516 44.000 0.00 0.00 36.38 0.98
1375 1526 4.018779 CCTTTGGGTCCTTCCACAAGTATA 60.019 45.833 0.00 0.00 36.38 1.47
1376 1527 3.245264 CCTTTGGGTCCTTCCACAAGTAT 60.245 47.826 0.00 0.00 36.38 2.12
1396 1547 1.127567 TGGAACCACACAGCTAGCCT 61.128 55.000 12.13 0.00 0.00 4.58
1438 1606 5.464389 AGCAACTTCATTCAGCAAACAATTC 59.536 36.000 0.00 0.00 0.00 2.17
1460 1629 3.559238 AAAATCATGTCCGTGTTCAGC 57.441 42.857 0.00 0.00 0.00 4.26
1489 1685 5.050567 GGTTAACTGAGAGGTTGTTTGTACG 60.051 44.000 5.42 0.00 0.00 3.67
1546 1744 2.954318 CGGAGCCATCAAGATCCAATTT 59.046 45.455 0.00 0.00 0.00 1.82
1613 1812 0.681733 GTCCTGCTTGTCTCTCCACA 59.318 55.000 0.00 0.00 0.00 4.17
1676 1875 1.135083 ACAGGAAGTTCAGGCGATACG 60.135 52.381 5.01 0.00 0.00 3.06
1686 1885 4.339814 ACAGGAGATATCGACAGGAAGTTC 59.660 45.833 0.00 0.00 0.00 3.01
1738 1937 3.369147 CACCACAGAATCATTCACGACTC 59.631 47.826 0.00 0.00 0.00 3.36
1744 1943 4.022935 GCAAAGACACCACAGAATCATTCA 60.023 41.667 0.00 0.00 0.00 2.57
1888 2087 2.540383 ACATAGCAGGGAAGAGTGTCA 58.460 47.619 0.00 0.00 0.00 3.58
1919 2118 4.321601 GCAAACAAACACCATACCAGCATA 60.322 41.667 0.00 0.00 0.00 3.14
1926 2125 5.583495 TGTTACAGCAAACAAACACCATAC 58.417 37.500 0.00 0.00 36.45 2.39
1949 2148 1.001020 TGGAGCCACCATTGCGATT 60.001 52.632 0.00 0.00 44.64 3.34
1965 2164 1.542915 CAAGAACCATTCCAGCAGTGG 59.457 52.381 0.00 0.00 46.63 4.00
1968 2167 2.608752 GCAACAAGAACCATTCCAGCAG 60.609 50.000 0.00 0.00 0.00 4.24
1971 2170 2.029649 CCTGCAACAAGAACCATTCCAG 60.030 50.000 0.00 0.00 0.00 3.86
1979 2178 2.863704 GCATTCACCCTGCAACAAGAAC 60.864 50.000 0.00 0.00 39.46 3.01
1983 2182 2.818111 TGCATTCACCCTGCAACAA 58.182 47.368 0.00 0.00 46.06 2.83
2002 2201 5.472820 AGAGATTTTTGAACTGCCTCTTCAG 59.527 40.000 0.00 0.00 39.86 3.02
2049 2248 2.496899 ACGATTCCATTTGCTCCACT 57.503 45.000 0.00 0.00 0.00 4.00
2061 2260 8.475331 TGAAATAAGACTGAGTAAACGATTCC 57.525 34.615 0.00 0.00 0.00 3.01
2072 2271 8.316640 AGTTGCTTACTTGAAATAAGACTGAG 57.683 34.615 0.00 0.00 31.29 3.35
2095 2294 9.672673 CCCAGCACTAGCAAAATATATATTAGT 57.327 33.333 8.39 5.39 45.49 2.24
2103 2302 3.669939 ACCCCAGCACTAGCAAAATAT 57.330 42.857 0.00 0.00 45.49 1.28
2241 2440 1.471119 CTCCACAGGCATGAGCAATT 58.529 50.000 4.84 0.00 44.61 2.32
2446 2648 3.122297 GCTACAGCATTTGCAACAACAA 58.878 40.909 0.00 0.00 45.16 2.83
2447 2649 2.361757 AGCTACAGCATTTGCAACAACA 59.638 40.909 0.00 0.00 45.16 3.33
2448 2650 2.982470 GAGCTACAGCATTTGCAACAAC 59.018 45.455 0.00 0.00 45.16 3.32
2449 2651 2.886523 AGAGCTACAGCATTTGCAACAA 59.113 40.909 0.00 0.00 45.16 2.83
2450 2652 2.507484 AGAGCTACAGCATTTGCAACA 58.493 42.857 0.00 0.00 45.16 3.33
2451 2653 4.685169 TTAGAGCTACAGCATTTGCAAC 57.315 40.909 0.00 0.00 45.16 4.17
2452 2654 5.902613 ATTTAGAGCTACAGCATTTGCAA 57.097 34.783 5.20 0.00 45.16 4.08
2453 2655 5.902613 AATTTAGAGCTACAGCATTTGCA 57.097 34.783 5.20 0.00 45.16 4.08
2474 2676 5.351465 CAGGCGAGAAATCACTTAGCTTAAA 59.649 40.000 0.00 0.00 0.00 1.52
2514 2716 2.479566 TCCATGGACTGAACTGCTTC 57.520 50.000 11.44 0.00 0.00 3.86
2527 2729 4.686972 CACTCGTATATAGGCATCCATGG 58.313 47.826 4.97 4.97 0.00 3.66
2541 2743 3.570550 GGAATAGAGGTGAGCACTCGTAT 59.429 47.826 0.16 0.00 39.90 3.06
2628 2830 2.133553 CAGTAGCCAAGAGATCATGCG 58.866 52.381 0.00 0.00 0.00 4.73
2630 2832 4.669206 AGTCAGTAGCCAAGAGATCATG 57.331 45.455 0.00 0.00 0.00 3.07
2721 2924 5.979517 GGCAAGGCAAATGATTGTACTTATC 59.020 40.000 0.00 0.00 38.85 1.75
2777 2980 3.997021 CACTTGTCTATGGTGAACTGTCC 59.003 47.826 0.00 0.00 33.32 4.02
2789 2992 1.827969 AGCCTTCGAGCACTTGTCTAT 59.172 47.619 0.00 0.00 34.23 1.98
2803 3006 6.476706 GGCACAATAATTATGTTTGAGCCTTC 59.523 38.462 21.69 5.63 46.79 3.46
2831 3034 6.880529 TGCATAGAATCAAGTTGTTCATGAGA 59.119 34.615 19.54 0.00 0.00 3.27
2832 3035 7.080353 TGCATAGAATCAAGTTGTTCATGAG 57.920 36.000 19.54 10.94 0.00 2.90
2833 3036 7.175467 AGTTGCATAGAATCAAGTTGTTCATGA 59.825 33.333 19.54 0.00 0.00 3.07
2834 3037 7.310664 AGTTGCATAGAATCAAGTTGTTCATG 58.689 34.615 15.75 15.76 0.00 3.07
2835 3038 7.458409 AGTTGCATAGAATCAAGTTGTTCAT 57.542 32.000 15.75 8.12 0.00 2.57
2836 3039 6.882610 AGTTGCATAGAATCAAGTTGTTCA 57.117 33.333 15.75 6.77 0.00 3.18
2837 3040 9.495754 GAATAGTTGCATAGAATCAAGTTGTTC 57.504 33.333 2.11 6.44 0.00 3.18
2838 3041 9.013229 TGAATAGTTGCATAGAATCAAGTTGTT 57.987 29.630 2.11 0.00 0.00 2.83
2840 3043 9.499585 CTTGAATAGTTGCATAGAATCAAGTTG 57.500 33.333 17.27 0.00 38.32 3.16
2888 3092 6.014413 GGAGGACTTCTCAAGTTAGGTAAACT 60.014 42.308 0.00 0.00 43.43 2.66
2890 3094 5.842328 TGGAGGACTTCTCAAGTTAGGTAAA 59.158 40.000 0.00 0.00 43.03 2.01
2894 3098 5.188751 AGAATGGAGGACTTCTCAAGTTAGG 59.811 44.000 0.00 0.00 43.03 2.69
2925 3129 4.673580 GCATGACAAATTGTACAGAGCAGG 60.674 45.833 0.00 0.00 0.00 4.85
2926 3130 4.409570 GCATGACAAATTGTACAGAGCAG 58.590 43.478 0.00 0.00 0.00 4.24
2964 3168 7.591426 GTGTTCACTGTTCACCAATAGATTTTC 59.409 37.037 0.00 0.00 0.00 2.29
3338 3546 5.653769 TCATGATTTGGAAGAATGGGAGAAC 59.346 40.000 0.00 0.00 0.00 3.01
3343 3551 5.597182 ACTCATCATGATTTGGAAGAATGGG 59.403 40.000 5.16 0.00 0.00 4.00
3353 3561 3.666111 CGCCGCATACTCATCATGATTTG 60.666 47.826 5.16 4.34 0.00 2.32
3356 3564 1.001293 ACGCCGCATACTCATCATGAT 59.999 47.619 1.18 1.18 0.00 2.45
3483 3692 1.139734 ACCATAGACTGAGCGTGCG 59.860 57.895 0.00 0.00 0.00 5.34
3616 3967 7.386299 GGTAGTATCTTGCTTCCAGAATATGTG 59.614 40.741 0.00 0.00 0.00 3.21
3636 3987 4.018870 TGGTTTTCATCATGGCAGGTAGTA 60.019 41.667 0.00 0.00 0.00 1.82
3637 3988 3.245229 TGGTTTTCATCATGGCAGGTAGT 60.245 43.478 0.00 0.00 0.00 2.73
3638 3989 3.355378 TGGTTTTCATCATGGCAGGTAG 58.645 45.455 0.00 0.00 0.00 3.18
3708 4059 2.996631 TGCCTGCCAAACAACAAAATT 58.003 38.095 0.00 0.00 0.00 1.82
3743 4094 1.209019 CCCACTGCAGATTCAGTAGCT 59.791 52.381 23.35 0.00 44.81 3.32
3788 4139 0.101759 GTAGCCGACGCAGACCAATA 59.898 55.000 0.00 0.00 37.52 1.90
3796 4147 2.566529 CAGTCAGTAGCCGACGCA 59.433 61.111 0.00 0.00 38.46 5.24
3921 4272 4.439974 CCAAACAGCTGACTTTTTGCAGTA 60.440 41.667 23.35 0.00 40.64 2.74
3932 4283 2.602217 CGTGTTAAGCCAAACAGCTGAC 60.602 50.000 23.35 4.99 44.11 3.51
3940 4291 0.800012 GATCGCCGTGTTAAGCCAAA 59.200 50.000 0.00 0.00 0.00 3.28
4014 4365 1.065491 TGTGCCATCTTTGCCGAGTAT 60.065 47.619 0.00 0.00 0.00 2.12
4020 4371 0.242017 GTCAGTGTGCCATCTTTGCC 59.758 55.000 0.00 0.00 0.00 4.52
4204 4555 1.300971 GAAGCCAGCTGCATCGTTCA 61.301 55.000 8.66 0.00 44.83 3.18


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

AutoCloner maintained by Alex Coulton.