Multiple sequence alignment - TraesCS3B01G550900

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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 TraesCS3B01G550900 chr3B 100.000 5366 0 0 1 5366 785696584 785691219 0.000000e+00 9910.0
1 TraesCS3B01G550900 chr3B 83.487 3476 509 43 972 4420 786136800 786140237 0.000000e+00 3179.0
2 TraesCS3B01G550900 chr3D 95.127 3673 150 13 230 3899 587951107 587947461 0.000000e+00 5764.0
3 TraesCS3B01G550900 chr3D 94.979 936 37 7 4433 5366 587946661 587945734 0.000000e+00 1459.0
4 TraesCS3B01G550900 chr3D 94.891 548 28 0 3894 4441 587947382 587946835 0.000000e+00 857.0
5 TraesCS3B01G550900 chr3A 96.279 2956 86 7 1900 4838 717853805 717850857 0.000000e+00 4828.0
6 TraesCS3B01G550900 chr3A 92.464 1619 83 21 231 1840 717855387 717853799 0.000000e+00 2278.0
7 TraesCS3B01G550900 chr3A 83.251 1218 176 22 3300 4503 717901208 717902411 0.000000e+00 1094.0
8 TraesCS3B01G550900 chr3A 80.952 1029 161 22 2224 3236 717898942 717899951 0.000000e+00 782.0
9 TraesCS3B01G550900 chr3A 82.334 917 139 13 973 1876 717884908 717885814 0.000000e+00 774.0
10 TraesCS3B01G550900 chr6B 97.817 229 5 0 1 229 705488563 705488791 3.890000e-106 396.0
11 TraesCS3B01G550900 chr6B 95.238 231 9 1 1 229 5678984 5679214 1.100000e-96 364.0
12 TraesCS3B01G550900 chr2B 97.009 234 6 1 1 233 785279256 785279023 5.040000e-105 392.0
13 TraesCS3B01G550900 chr5B 96.070 229 9 0 1 229 476149605 476149377 1.820000e-99 374.0
14 TraesCS3B01G550900 chr5B 95.652 230 9 1 1 230 648258458 648258230 8.490000e-98 368.0
15 TraesCS3B01G550900 chr5B 94.872 234 8 4 1 233 19731262 19731032 3.950000e-96 363.0
16 TraesCS3B01G550900 chr4B 95.708 233 8 2 2 232 516953881 516953649 1.820000e-99 374.0
17 TraesCS3B01G550900 chr6D 95.652 230 9 1 1 230 375311124 375310896 8.490000e-98 368.0
18 TraesCS3B01G550900 chr7D 95.633 229 9 1 1 229 63450520 63450293 3.050000e-97 366.0
19 TraesCS3B01G550900 chrUn 100.000 28 0 0 4741 4768 31808131 31808104 1.000000e-02 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 TraesCS3B01G550900 chr3B 785691219 785696584 5365 True 9910.000000 9910 100.0000 1 5366 1 chr3B.!!$R1 5365
1 TraesCS3B01G550900 chr3B 786136800 786140237 3437 False 3179.000000 3179 83.4870 972 4420 1 chr3B.!!$F1 3448
2 TraesCS3B01G550900 chr3D 587945734 587951107 5373 True 2693.333333 5764 94.9990 230 5366 3 chr3D.!!$R1 5136
3 TraesCS3B01G550900 chr3A 717850857 717855387 4530 True 3553.000000 4828 94.3715 231 4838 2 chr3A.!!$R1 4607
4 TraesCS3B01G550900 chr3A 717898942 717902411 3469 False 938.000000 1094 82.1015 2224 4503 2 chr3A.!!$F2 2279
5 TraesCS3B01G550900 chr3A 717884908 717885814 906 False 774.000000 774 82.3340 973 1876 1 chr3A.!!$F1 903

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
905 914 0.250640 AGTACTGCTTGCTGCTTGCT 60.251 50.0 15.63 2.9 43.37 3.91 F
2588 2636 0.107654 AAGGTGGCTATCGGCTTCAC 60.108 55.0 0.00 0.0 41.46 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 2933 0.482446 TGGGATGGCACCAGAAAGTT 59.518 50.0 8.11 0.0 33.23 2.66 R
4383 5729 1.531423 ACAGTTCTTCATGCAGCCAG 58.469 50.0 0.00 0.0 0.00 4.85 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
28 29 9.542462 TTTGGCTAATATAGTGTGAATAGTGAC 57.458 33.333 0.00 0.00 0.00 3.67
29 30 7.667557 TGGCTAATATAGTGTGAATAGTGACC 58.332 38.462 0.00 0.00 0.00 4.02
30 31 7.509318 TGGCTAATATAGTGTGAATAGTGACCT 59.491 37.037 0.00 0.00 0.00 3.85
31 32 9.021807 GGCTAATATAGTGTGAATAGTGACCTA 57.978 37.037 0.00 0.00 0.00 3.08
39 40 8.478775 AGTGTGAATAGTGACCTATAATAGCA 57.521 34.615 0.00 0.00 32.57 3.49
40 41 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
41 42 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
77 78 6.639671 TTTTTGTTGTGAGGTCAATTTTCG 57.360 33.333 0.00 0.00 0.00 3.46
78 79 4.974368 TTGTTGTGAGGTCAATTTTCGT 57.026 36.364 0.00 0.00 0.00 3.85
79 80 4.974368 TGTTGTGAGGTCAATTTTCGTT 57.026 36.364 0.00 0.00 0.00 3.85
80 81 5.317733 TGTTGTGAGGTCAATTTTCGTTT 57.682 34.783 0.00 0.00 0.00 3.60
81 82 5.715070 TGTTGTGAGGTCAATTTTCGTTTT 58.285 33.333 0.00 0.00 0.00 2.43
82 83 6.159988 TGTTGTGAGGTCAATTTTCGTTTTT 58.840 32.000 0.00 0.00 0.00 1.94
107 108 9.459640 TTTTTCTCGTCGAGATTTATATACCAG 57.540 33.333 24.78 0.00 38.56 4.00
108 109 7.741027 TTCTCGTCGAGATTTATATACCAGT 57.259 36.000 24.78 0.00 38.56 4.00
109 110 7.130303 TCTCGTCGAGATTTATATACCAGTG 57.870 40.000 20.85 0.00 33.35 3.66
110 111 5.696822 TCGTCGAGATTTATATACCAGTGC 58.303 41.667 0.00 0.00 0.00 4.40
111 112 5.239963 TCGTCGAGATTTATATACCAGTGCA 59.760 40.000 0.00 0.00 0.00 4.57
112 113 5.918576 CGTCGAGATTTATATACCAGTGCAA 59.081 40.000 0.00 0.00 0.00 4.08
113 114 6.419710 CGTCGAGATTTATATACCAGTGCAAA 59.580 38.462 0.00 0.00 0.00 3.68
114 115 7.042992 CGTCGAGATTTATATACCAGTGCAAAA 60.043 37.037 0.00 0.00 0.00 2.44
115 116 8.276325 GTCGAGATTTATATACCAGTGCAAAAG 58.724 37.037 0.00 0.00 0.00 2.27
116 117 7.985184 TCGAGATTTATATACCAGTGCAAAAGT 59.015 33.333 0.00 0.00 0.00 2.66
117 118 9.256477 CGAGATTTATATACCAGTGCAAAAGTA 57.744 33.333 0.00 0.00 0.00 2.24
122 123 9.727859 TTTATATACCAGTGCAAAAGTAAGTCA 57.272 29.630 0.00 0.00 0.00 3.41
123 124 9.727859 TTATATACCAGTGCAAAAGTAAGTCAA 57.272 29.630 0.00 0.00 0.00 3.18
124 125 4.900635 ACCAGTGCAAAAGTAAGTCAAG 57.099 40.909 0.00 0.00 0.00 3.02
125 126 4.270008 ACCAGTGCAAAAGTAAGTCAAGT 58.730 39.130 0.00 0.00 0.00 3.16
126 127 4.096382 ACCAGTGCAAAAGTAAGTCAAGTG 59.904 41.667 0.00 0.00 0.00 3.16
127 128 4.096382 CCAGTGCAAAAGTAAGTCAAGTGT 59.904 41.667 0.00 0.00 0.00 3.55
128 129 5.393027 CCAGTGCAAAAGTAAGTCAAGTGTT 60.393 40.000 0.00 0.00 0.00 3.32
129 130 6.092748 CAGTGCAAAAGTAAGTCAAGTGTTT 58.907 36.000 0.00 0.00 0.00 2.83
130 131 6.586082 CAGTGCAAAAGTAAGTCAAGTGTTTT 59.414 34.615 0.00 0.00 0.00 2.43
131 132 6.586082 AGTGCAAAAGTAAGTCAAGTGTTTTG 59.414 34.615 0.00 0.00 37.74 2.44
132 133 6.364976 GTGCAAAAGTAAGTCAAGTGTTTTGT 59.635 34.615 0.00 0.00 37.26 2.83
133 134 6.584563 TGCAAAAGTAAGTCAAGTGTTTTGTC 59.415 34.615 0.00 0.00 37.26 3.18
134 135 6.584563 GCAAAAGTAAGTCAAGTGTTTTGTCA 59.415 34.615 0.00 0.00 37.26 3.58
135 136 7.115663 GCAAAAGTAAGTCAAGTGTTTTGTCAA 59.884 33.333 0.00 0.00 37.26 3.18
136 137 8.973378 CAAAAGTAAGTCAAGTGTTTTGTCAAA 58.027 29.630 0.00 0.00 32.65 2.69
137 138 9.535878 AAAAGTAAGTCAAGTGTTTTGTCAAAA 57.464 25.926 6.65 6.65 0.00 2.44
138 139 9.705290 AAAGTAAGTCAAGTGTTTTGTCAAAAT 57.295 25.926 13.65 0.00 32.22 1.82
141 142 9.783256 GTAAGTCAAGTGTTTTGTCAAAATAGT 57.217 29.630 13.65 11.04 32.22 2.12
143 144 8.911247 AGTCAAGTGTTTTGTCAAAATAGTTC 57.089 30.769 19.36 12.43 34.29 3.01
144 145 8.739972 AGTCAAGTGTTTTGTCAAAATAGTTCT 58.260 29.630 19.36 13.92 34.29 3.01
145 146 9.353999 GTCAAGTGTTTTGTCAAAATAGTTCTT 57.646 29.630 19.36 11.77 34.29 2.52
148 149 9.797556 AAGTGTTTTGTCAAAATAGTTCTTACC 57.202 29.630 17.46 2.76 31.98 2.85
149 150 9.185680 AGTGTTTTGTCAAAATAGTTCTTACCT 57.814 29.630 13.65 0.34 32.22 3.08
214 215 2.949644 GGTGCATATACAACCAGGAACC 59.050 50.000 0.00 0.00 0.00 3.62
215 216 3.616219 GTGCATATACAACCAGGAACCA 58.384 45.455 0.00 0.00 0.00 3.67
216 217 4.013728 GTGCATATACAACCAGGAACCAA 58.986 43.478 0.00 0.00 0.00 3.67
217 218 4.461081 GTGCATATACAACCAGGAACCAAA 59.539 41.667 0.00 0.00 0.00 3.28
218 219 4.704540 TGCATATACAACCAGGAACCAAAG 59.295 41.667 0.00 0.00 0.00 2.77
219 220 4.705023 GCATATACAACCAGGAACCAAAGT 59.295 41.667 0.00 0.00 0.00 2.66
220 221 5.393027 GCATATACAACCAGGAACCAAAGTG 60.393 44.000 0.00 0.00 0.00 3.16
221 222 2.525105 ACAACCAGGAACCAAAGTGT 57.475 45.000 0.00 0.00 0.00 3.55
222 223 3.655615 ACAACCAGGAACCAAAGTGTA 57.344 42.857 0.00 0.00 0.00 2.90
223 224 4.178956 ACAACCAGGAACCAAAGTGTAT 57.821 40.909 0.00 0.00 0.00 2.29
224 225 4.542697 ACAACCAGGAACCAAAGTGTATT 58.457 39.130 0.00 0.00 0.00 1.89
225 226 4.959839 ACAACCAGGAACCAAAGTGTATTT 59.040 37.500 0.00 0.00 0.00 1.40
226 227 5.068591 ACAACCAGGAACCAAAGTGTATTTC 59.931 40.000 0.00 0.00 0.00 2.17
227 228 4.149598 ACCAGGAACCAAAGTGTATTTCC 58.850 43.478 0.00 0.00 36.71 3.13
228 229 3.509967 CCAGGAACCAAAGTGTATTTCCC 59.490 47.826 0.00 0.00 37.09 3.97
256 257 6.619801 AAGAGAAGCGTAAAACATTTCAGT 57.380 33.333 0.00 0.00 0.00 3.41
309 310 3.596214 AGCGTTCAAACCATATCGAACT 58.404 40.909 0.00 0.00 36.46 3.01
314 315 5.220228 CGTTCAAACCATATCGAACTGAGTC 60.220 44.000 0.00 0.00 36.46 3.36
414 420 1.675552 AGTGACTTTTGGTCCAACGG 58.324 50.000 2.98 2.65 43.89 4.44
499 508 7.616313 ACCCTCAGATATTTATCGAATTCCTC 58.384 38.462 0.00 0.00 37.76 3.71
517 526 4.759782 TCCTCGAGGATTCATCTTGTTTC 58.240 43.478 30.49 0.00 39.78 2.78
522 531 5.047021 TCGAGGATTCATCTTGTTTCAGAGT 60.047 40.000 0.00 0.00 0.00 3.24
526 535 6.876257 AGGATTCATCTTGTTTCAGAGTGTAC 59.124 38.462 0.00 0.00 0.00 2.90
574 583 4.326255 GGGTGCACCAATCTCCTG 57.674 61.111 35.78 0.00 39.85 3.86
585 594 2.516923 CAATCTCCTGACACGTCGTAC 58.483 52.381 0.00 0.00 0.00 3.67
601 610 1.556564 GTACATCGGATCCACACACG 58.443 55.000 13.41 0.00 0.00 4.49
609 618 2.287427 CGGATCCACACACGGTATAGAC 60.287 54.545 13.41 0.00 0.00 2.59
634 643 1.939969 TTTTTCATCAACGCGTACGC 58.060 45.000 29.83 29.83 45.53 4.42
667 676 6.680810 TCAAGGAAGCAACTCAATTTGTATG 58.319 36.000 0.00 0.00 0.00 2.39
669 678 4.523943 AGGAAGCAACTCAATTTGTATGCA 59.476 37.500 18.59 0.00 36.30 3.96
670 679 5.186409 AGGAAGCAACTCAATTTGTATGCAT 59.814 36.000 18.59 3.79 36.30 3.96
671 680 5.290158 GGAAGCAACTCAATTTGTATGCATG 59.710 40.000 10.16 0.00 36.30 4.06
672 681 4.178540 AGCAACTCAATTTGTATGCATGC 58.821 39.130 11.82 11.82 36.30 4.06
673 682 3.927758 GCAACTCAATTTGTATGCATGCA 59.072 39.130 25.04 25.04 34.10 3.96
674 683 4.569162 GCAACTCAATTTGTATGCATGCAT 59.431 37.500 33.92 33.92 40.19 3.96
675 684 5.501736 GCAACTCAATTTGTATGCATGCATG 60.502 40.000 37.43 23.24 37.82 4.06
676 685 5.585820 ACTCAATTTGTATGCATGCATGA 57.414 34.783 37.43 25.76 37.82 3.07
677 686 6.156748 ACTCAATTTGTATGCATGCATGAT 57.843 33.333 37.43 23.43 37.82 2.45
678 687 5.983118 ACTCAATTTGTATGCATGCATGATG 59.017 36.000 37.43 25.14 37.82 3.07
679 688 6.150396 TCAATTTGTATGCATGCATGATGA 57.850 33.333 37.43 26.57 37.82 2.92
680 689 6.574350 TCAATTTGTATGCATGCATGATGAA 58.426 32.000 37.43 25.92 37.82 2.57
681 690 6.699642 TCAATTTGTATGCATGCATGATGAAG 59.300 34.615 37.43 22.52 37.82 3.02
701 710 3.831112 AGATGATACACGATGATCTGCG 58.169 45.455 6.30 6.30 37.15 5.18
817 826 7.412891 CGATTTTACAGATCATGGCGCATATAA 60.413 37.037 10.83 0.00 0.00 0.98
829 838 4.138817 GGCGCATATAAACGTACGAATTG 58.861 43.478 24.41 10.98 0.00 2.32
834 843 5.333568 GCATATAAACGTACGAATTGTCCCC 60.334 44.000 24.41 0.00 0.00 4.81
839 848 1.369625 GTACGAATTGTCCCCAGCTG 58.630 55.000 6.78 6.78 0.00 4.24
888 897 5.472820 GGCACTAACGATCATACCTACTAGT 59.527 44.000 0.00 0.00 0.00 2.57
899 908 5.299531 TCATACCTACTAGTACTGCTTGCTG 59.700 44.000 5.39 0.00 0.00 4.41
900 909 2.166664 ACCTACTAGTACTGCTTGCTGC 59.833 50.000 5.39 0.00 43.25 5.25
901 910 2.428890 CCTACTAGTACTGCTTGCTGCT 59.571 50.000 5.39 0.00 43.37 4.24
902 911 3.118956 CCTACTAGTACTGCTTGCTGCTT 60.119 47.826 5.39 0.00 43.37 3.91
903 912 2.693069 ACTAGTACTGCTTGCTGCTTG 58.307 47.619 5.39 0.00 43.37 4.01
904 913 1.396301 CTAGTACTGCTTGCTGCTTGC 59.604 52.381 5.39 5.85 43.37 4.01
905 914 0.250640 AGTACTGCTTGCTGCTTGCT 60.251 50.000 15.63 2.90 43.37 3.91
908 917 1.134075 CTGCTTGCTGCTTGCTACG 59.866 57.895 15.63 0.00 43.37 3.51
964 973 7.230712 CAGAAACCCAAAAGGACTACTGTAAAT 59.769 37.037 0.00 0.00 39.89 1.40
1230 1257 2.626780 CGTGTCGCTGTCCCTCTCA 61.627 63.158 0.00 0.00 0.00 3.27
1377 1410 3.329542 GAGATGGAGGTGCGGCCAA 62.330 63.158 2.24 0.00 40.61 4.52
1585 1624 1.579429 GACAACAACATCACCGGCC 59.421 57.895 0.00 0.00 0.00 6.13
1710 1749 2.959707 GGAGTCACTTGATCTATCCGGT 59.040 50.000 0.00 0.00 0.00 5.28
1715 1754 6.750148 AGTCACTTGATCTATCCGGTAATTC 58.250 40.000 0.00 0.00 0.00 2.17
1851 1890 1.562942 TCGCTCTCCTACCTCAACCTA 59.437 52.381 0.00 0.00 0.00 3.08
1986 2025 0.391661 GTCGGCTTGCCAATCTGAGA 60.392 55.000 12.45 0.00 0.00 3.27
1998 2037 4.774124 CCAATCTGAGAATGCTGGACTTA 58.226 43.478 0.00 0.00 0.00 2.24
2364 2407 5.578005 ACTGCAAGAATCTGAAATGGATG 57.422 39.130 0.00 0.00 37.43 3.51
2588 2636 0.107654 AAGGTGGCTATCGGCTTCAC 60.108 55.000 0.00 0.00 41.46 3.18
2621 2674 3.120683 CCACATATATACTTGCGCAACGG 60.121 47.826 21.02 13.59 0.00 4.44
2714 2767 2.037772 ACCGGATGGCTAGCAAGAATAG 59.962 50.000 18.24 1.65 39.70 1.73
2744 2797 0.756903 ACACGGGTATACATCCTGGC 59.243 55.000 5.01 0.00 35.79 4.85
2856 2910 7.906199 ACTTGGTAAGATGAACTATCTAGCT 57.094 36.000 0.00 0.00 45.41 3.32
2879 2933 5.840243 ATCATGAATCTTCGGCAAAATCA 57.160 34.783 0.00 0.00 0.00 2.57
3018 3072 7.371159 TGTCGGAGATTGATCTATCATACAAC 58.629 38.462 17.62 9.98 40.67 3.32
3065 3119 0.039618 GGATCCCTTGCCACTTTCCA 59.960 55.000 0.00 0.00 0.00 3.53
3263 4519 8.621532 ATTTTATTGTACTGCATATCGTGGAT 57.378 30.769 0.00 0.00 0.00 3.41
3397 4653 7.502226 GTGAAGATTACATGTTGGGATATGGAA 59.498 37.037 2.30 0.00 32.56 3.53
3473 4729 1.453155 GTTCTTGACATGCGGTCCAT 58.547 50.000 5.94 0.00 46.38 3.41
3644 4900 3.052082 CTGCTCACAACAGGGCGG 61.052 66.667 0.00 0.00 0.00 6.13
3742 4998 1.812571 ACCATGAAATCGTCTTGCACC 59.187 47.619 0.00 0.00 31.48 5.01
3820 5076 5.472148 CAGATTTTGGCATTGCAAGACTAA 58.528 37.500 11.39 0.44 0.00 2.24
4186 5529 1.977056 TGTCGTGGATAGACGGCTAT 58.023 50.000 11.56 11.56 44.34 2.97
4383 5729 2.238521 TGATTGGTCAACCTTGCTTCC 58.761 47.619 0.10 0.00 36.82 3.46
4424 5770 5.416326 TGTTTCGGAGAAAGAAAAAGGACAA 59.584 36.000 0.00 0.00 45.90 3.18
4587 6115 4.512571 AGCGTTTGGATGTACGTAAACTTT 59.487 37.500 0.00 0.00 39.80 2.66
4666 6195 3.476552 TCTATCATCGGTGCCCATTTTC 58.523 45.455 0.00 0.00 0.00 2.29
4888 6417 5.985530 CAGGAGAAAACTTTGGTGATTTTCC 59.014 40.000 5.33 0.00 41.29 3.13
4903 6432 1.999648 TTTCCCAAGCAACATGAGCT 58.000 45.000 10.82 10.82 45.97 4.09
4907 6436 1.681166 CCCAAGCAACATGAGCTAGCT 60.681 52.381 19.45 19.45 42.53 3.32
4929 6458 3.188786 GCAAGCGCTCCCACTACG 61.189 66.667 12.06 0.00 34.30 3.51
4946 6475 5.163561 CCACTACGGGTTTTACGGACTATTA 60.164 44.000 0.00 0.00 35.23 0.98
5014 6543 4.607293 TTGTGAGAAGTACTGAGTGCAT 57.393 40.909 3.02 0.00 0.00 3.96
5054 6583 1.001974 GGGGGCAGTCCAACAATTTTC 59.998 52.381 0.00 0.00 37.22 2.29
5244 6773 8.429493 AATTTTCTTCTCTCCTTTTGCTTTTG 57.571 30.769 0.00 0.00 0.00 2.44
5299 6829 7.022055 TCTTCACATACACGTTGAACATTTT 57.978 32.000 0.00 0.00 0.00 1.82
5322 6852 7.401484 TTTTGAACACAAGTTGAACAGTTTC 57.599 32.000 10.54 3.47 38.30 2.78
5330 6860 5.531287 ACAAGTTGAACAGTTTCCAGATACC 59.469 40.000 10.54 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.542462 GTCACTATTCACACTATATTAGCCAAA 57.458 33.333 0.00 0.00 0.00 3.28
3 4 8.148351 GGTCACTATTCACACTATATTAGCCAA 58.852 37.037 0.00 0.00 0.00 4.52
4 5 7.509318 AGGTCACTATTCACACTATATTAGCCA 59.491 37.037 0.00 0.00 0.00 4.75
5 6 7.897864 AGGTCACTATTCACACTATATTAGCC 58.102 38.462 0.00 0.00 0.00 3.93
13 14 9.582648 TGCTATTATAGGTCACTATTCACACTA 57.417 33.333 1.12 0.00 40.35 2.74
14 15 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
15 16 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
54 55 6.159988 ACGAAAATTGACCTCACAACAAAAA 58.840 32.000 0.00 0.00 32.50 1.94
55 56 5.715070 ACGAAAATTGACCTCACAACAAAA 58.285 33.333 0.00 0.00 32.50 2.44
56 57 5.317733 ACGAAAATTGACCTCACAACAAA 57.682 34.783 0.00 0.00 32.50 2.83
57 58 4.974368 ACGAAAATTGACCTCACAACAA 57.026 36.364 0.00 0.00 32.50 2.83
58 59 4.974368 AACGAAAATTGACCTCACAACA 57.026 36.364 0.00 0.00 32.50 3.33
59 60 6.641176 AAAAACGAAAATTGACCTCACAAC 57.359 33.333 0.00 0.00 32.50 3.32
81 82 9.459640 CTGGTATATAAATCTCGACGAGAAAAA 57.540 33.333 29.68 17.95 42.27 1.94
82 83 8.627403 ACTGGTATATAAATCTCGACGAGAAAA 58.373 33.333 29.68 18.28 42.27 2.29
83 84 8.074370 CACTGGTATATAAATCTCGACGAGAAA 58.926 37.037 29.68 18.61 42.27 2.52
84 85 7.582352 CACTGGTATATAAATCTCGACGAGAA 58.418 38.462 29.68 15.33 42.27 2.87
85 86 6.348295 GCACTGGTATATAAATCTCGACGAGA 60.348 42.308 28.36 28.36 43.20 4.04
86 87 5.795939 GCACTGGTATATAAATCTCGACGAG 59.204 44.000 18.91 18.91 0.00 4.18
87 88 5.239963 TGCACTGGTATATAAATCTCGACGA 59.760 40.000 0.00 0.00 0.00 4.20
88 89 5.458015 TGCACTGGTATATAAATCTCGACG 58.542 41.667 0.00 0.00 0.00 5.12
89 90 7.709269 TTTGCACTGGTATATAAATCTCGAC 57.291 36.000 0.00 0.00 0.00 4.20
90 91 7.985184 ACTTTTGCACTGGTATATAAATCTCGA 59.015 33.333 0.00 0.00 0.00 4.04
91 92 8.142994 ACTTTTGCACTGGTATATAAATCTCG 57.857 34.615 0.00 0.00 0.00 4.04
96 97 9.727859 TGACTTACTTTTGCACTGGTATATAAA 57.272 29.630 0.00 0.00 0.00 1.40
97 98 9.727859 TTGACTTACTTTTGCACTGGTATATAA 57.272 29.630 0.00 0.00 0.00 0.98
98 99 9.378551 CTTGACTTACTTTTGCACTGGTATATA 57.621 33.333 0.00 0.00 0.00 0.86
99 100 7.883311 ACTTGACTTACTTTTGCACTGGTATAT 59.117 33.333 0.00 0.00 0.00 0.86
100 101 7.172532 CACTTGACTTACTTTTGCACTGGTATA 59.827 37.037 0.00 0.00 0.00 1.47
101 102 6.017109 CACTTGACTTACTTTTGCACTGGTAT 60.017 38.462 0.00 0.00 0.00 2.73
102 103 5.295787 CACTTGACTTACTTTTGCACTGGTA 59.704 40.000 0.00 0.00 0.00 3.25
103 104 4.096382 CACTTGACTTACTTTTGCACTGGT 59.904 41.667 0.00 0.00 0.00 4.00
104 105 4.096382 ACACTTGACTTACTTTTGCACTGG 59.904 41.667 0.00 0.00 0.00 4.00
105 106 5.235305 ACACTTGACTTACTTTTGCACTG 57.765 39.130 0.00 0.00 0.00 3.66
106 107 5.897377 AACACTTGACTTACTTTTGCACT 57.103 34.783 0.00 0.00 0.00 4.40
107 108 6.364976 ACAAAACACTTGACTTACTTTTGCAC 59.635 34.615 0.00 0.00 33.72 4.57
108 109 6.451393 ACAAAACACTTGACTTACTTTTGCA 58.549 32.000 0.00 0.00 33.72 4.08
109 110 6.584563 TGACAAAACACTTGACTTACTTTTGC 59.415 34.615 0.00 0.00 33.72 3.68
110 111 8.514136 TTGACAAAACACTTGACTTACTTTTG 57.486 30.769 0.00 0.00 35.61 2.44
111 112 9.535878 TTTTGACAAAACACTTGACTTACTTTT 57.464 25.926 9.30 0.00 0.00 2.27
112 113 9.705290 ATTTTGACAAAACACTTGACTTACTTT 57.295 25.926 15.36 0.00 32.37 2.66
115 116 9.783256 ACTATTTTGACAAAACACTTGACTTAC 57.217 29.630 15.36 0.00 32.37 2.34
117 118 9.353999 GAACTATTTTGACAAAACACTTGACTT 57.646 29.630 15.36 0.00 32.37 3.01
118 119 8.739972 AGAACTATTTTGACAAAACACTTGACT 58.260 29.630 15.36 7.03 32.37 3.41
119 120 8.911247 AGAACTATTTTGACAAAACACTTGAC 57.089 30.769 15.36 5.14 32.37 3.18
122 123 9.797556 GGTAAGAACTATTTTGACAAAACACTT 57.202 29.630 15.36 15.89 32.37 3.16
123 124 9.185680 AGGTAAGAACTATTTTGACAAAACACT 57.814 29.630 15.36 3.23 32.37 3.55
185 186 6.061022 TGGTTGTATATGCACCCTATATGG 57.939 41.667 8.77 0.00 0.00 2.74
186 187 6.070251 TCCTGGTTGTATATGCACCCTATATG 60.070 42.308 8.77 0.00 0.00 1.78
187 188 6.029431 TCCTGGTTGTATATGCACCCTATAT 58.971 40.000 8.77 0.00 0.00 0.86
188 189 5.407936 TCCTGGTTGTATATGCACCCTATA 58.592 41.667 8.77 0.00 0.00 1.31
189 190 4.239495 TCCTGGTTGTATATGCACCCTAT 58.761 43.478 8.77 0.00 0.00 2.57
190 191 3.659841 TCCTGGTTGTATATGCACCCTA 58.340 45.455 8.77 0.00 0.00 3.53
191 192 2.487775 TCCTGGTTGTATATGCACCCT 58.512 47.619 8.77 0.00 0.00 4.34
192 193 2.949644 GTTCCTGGTTGTATATGCACCC 59.050 50.000 0.12 0.12 0.00 4.61
193 194 2.949644 GGTTCCTGGTTGTATATGCACC 59.050 50.000 0.00 0.00 0.00 5.01
194 195 3.616219 TGGTTCCTGGTTGTATATGCAC 58.384 45.455 0.00 0.00 0.00 4.57
195 196 4.308526 TTGGTTCCTGGTTGTATATGCA 57.691 40.909 0.00 0.00 0.00 3.96
196 197 4.705023 ACTTTGGTTCCTGGTTGTATATGC 59.295 41.667 0.00 0.00 0.00 3.14
197 198 5.710099 ACACTTTGGTTCCTGGTTGTATATG 59.290 40.000 0.00 0.00 0.00 1.78
198 199 5.887754 ACACTTTGGTTCCTGGTTGTATAT 58.112 37.500 0.00 0.00 0.00 0.86
199 200 5.313280 ACACTTTGGTTCCTGGTTGTATA 57.687 39.130 0.00 0.00 0.00 1.47
200 201 4.178956 ACACTTTGGTTCCTGGTTGTAT 57.821 40.909 0.00 0.00 0.00 2.29
201 202 3.655615 ACACTTTGGTTCCTGGTTGTA 57.344 42.857 0.00 0.00 0.00 2.41
202 203 2.525105 ACACTTTGGTTCCTGGTTGT 57.475 45.000 0.00 0.00 0.00 3.32
203 204 5.508994 GGAAATACACTTTGGTTCCTGGTTG 60.509 44.000 0.00 0.00 0.00 3.77
204 205 4.587262 GGAAATACACTTTGGTTCCTGGTT 59.413 41.667 0.00 0.00 0.00 3.67
205 206 4.149598 GGAAATACACTTTGGTTCCTGGT 58.850 43.478 0.00 0.00 0.00 4.00
206 207 3.509967 GGGAAATACACTTTGGTTCCTGG 59.490 47.826 0.00 0.00 0.00 4.45
207 208 3.509967 GGGGAAATACACTTTGGTTCCTG 59.490 47.826 0.00 0.00 0.00 3.86
208 209 3.401342 AGGGGAAATACACTTTGGTTCCT 59.599 43.478 0.00 0.00 0.00 3.36
209 210 3.774734 AGGGGAAATACACTTTGGTTCC 58.225 45.455 0.00 0.00 0.00 3.62
210 211 8.050930 TCTTATAGGGGAAATACACTTTGGTTC 58.949 37.037 0.00 0.00 0.00 3.62
211 212 7.935405 TCTTATAGGGGAAATACACTTTGGTT 58.065 34.615 0.00 0.00 0.00 3.67
212 213 7.404980 TCTCTTATAGGGGAAATACACTTTGGT 59.595 37.037 0.00 0.00 0.00 3.67
213 214 7.802117 TCTCTTATAGGGGAAATACACTTTGG 58.198 38.462 0.00 0.00 0.00 3.28
214 215 9.331282 CTTCTCTTATAGGGGAAATACACTTTG 57.669 37.037 0.00 0.00 0.00 2.77
215 216 7.993758 GCTTCTCTTATAGGGGAAATACACTTT 59.006 37.037 0.00 0.00 0.00 2.66
216 217 7.510407 GCTTCTCTTATAGGGGAAATACACTT 58.490 38.462 0.00 0.00 0.00 3.16
217 218 6.239345 CGCTTCTCTTATAGGGGAAATACACT 60.239 42.308 0.00 0.00 0.00 3.55
218 219 5.927115 CGCTTCTCTTATAGGGGAAATACAC 59.073 44.000 0.00 0.00 0.00 2.90
219 220 5.601313 ACGCTTCTCTTATAGGGGAAATACA 59.399 40.000 0.00 0.00 0.00 2.29
220 221 6.099159 ACGCTTCTCTTATAGGGGAAATAC 57.901 41.667 0.00 0.00 0.00 1.89
221 222 7.844493 TTACGCTTCTCTTATAGGGGAAATA 57.156 36.000 0.00 0.00 0.00 1.40
222 223 6.742559 TTACGCTTCTCTTATAGGGGAAAT 57.257 37.500 0.00 0.00 0.00 2.17
223 224 6.549433 TTTACGCTTCTCTTATAGGGGAAA 57.451 37.500 0.00 0.00 35.52 3.13
224 225 6.070653 TGTTTTACGCTTCTCTTATAGGGGAA 60.071 38.462 0.00 0.00 0.00 3.97
225 226 5.422970 TGTTTTACGCTTCTCTTATAGGGGA 59.577 40.000 0.00 0.00 0.00 4.81
226 227 5.667466 TGTTTTACGCTTCTCTTATAGGGG 58.333 41.667 0.00 0.00 0.00 4.79
227 228 7.787725 AATGTTTTACGCTTCTCTTATAGGG 57.212 36.000 0.00 0.00 0.00 3.53
228 229 8.879759 TGAAATGTTTTACGCTTCTCTTATAGG 58.120 33.333 0.00 0.00 0.00 2.57
331 337 3.723260 TCGTCAGCAGTAATTTGTGTCA 58.277 40.909 0.00 0.00 0.00 3.58
414 420 3.441572 ACTACAGCAGAATTGTTCATGGC 59.558 43.478 0.00 0.00 0.00 4.40
499 508 5.063186 CACTCTGAAACAAGATGAATCCTCG 59.937 44.000 0.00 0.00 0.00 4.63
505 514 5.924356 TGGTACACTCTGAAACAAGATGAA 58.076 37.500 0.00 0.00 0.00 2.57
517 526 5.062183 CACGTGAAACATATGGTACACTCTG 59.938 44.000 10.90 12.91 38.03 3.35
522 531 3.665190 TGCACGTGAAACATATGGTACA 58.335 40.909 22.23 0.00 39.84 2.90
526 535 5.671742 TGATATGCACGTGAAACATATGG 57.328 39.130 23.39 0.00 37.17 2.74
573 582 1.063027 GATCCGATGTACGACGTGTCA 59.937 52.381 11.56 10.26 45.77 3.58
574 583 1.596464 GGATCCGATGTACGACGTGTC 60.596 57.143 11.56 5.34 45.77 3.67
585 594 0.458260 TACCGTGTGTGGATCCGATG 59.542 55.000 7.39 0.00 0.00 3.84
601 610 9.438291 CGTTGATGAAAAATGATTGTCTATACC 57.562 33.333 0.00 0.00 0.00 2.73
609 618 5.274777 CGTACGCGTTGATGAAAAATGATTG 60.275 40.000 20.78 0.00 0.00 2.67
634 643 2.169832 TGCTTCCTTGAAAGAGGACG 57.830 50.000 0.00 0.00 45.30 4.79
667 676 5.391449 GTGTATCATCTTCATCATGCATGC 58.609 41.667 22.25 11.82 31.70 4.06
669 678 5.544650 TCGTGTATCATCTTCATCATGCAT 58.455 37.500 0.00 0.00 0.00 3.96
670 679 4.947645 TCGTGTATCATCTTCATCATGCA 58.052 39.130 0.00 0.00 0.00 3.96
671 680 5.636543 TCATCGTGTATCATCTTCATCATGC 59.363 40.000 0.00 0.00 0.00 4.06
672 681 7.760340 AGATCATCGTGTATCATCTTCATCATG 59.240 37.037 0.00 0.00 0.00 3.07
673 682 7.760340 CAGATCATCGTGTATCATCTTCATCAT 59.240 37.037 0.00 0.00 0.00 2.45
674 683 7.088905 CAGATCATCGTGTATCATCTTCATCA 58.911 38.462 0.00 0.00 0.00 3.07
675 684 6.034790 GCAGATCATCGTGTATCATCTTCATC 59.965 42.308 0.00 0.00 0.00 2.92
676 685 5.868258 GCAGATCATCGTGTATCATCTTCAT 59.132 40.000 0.00 0.00 0.00 2.57
677 686 5.225642 GCAGATCATCGTGTATCATCTTCA 58.774 41.667 0.00 0.00 0.00 3.02
678 687 4.323070 CGCAGATCATCGTGTATCATCTTC 59.677 45.833 0.00 0.00 0.00 2.87
679 688 4.233005 CGCAGATCATCGTGTATCATCTT 58.767 43.478 0.00 0.00 0.00 2.40
680 689 3.831112 CGCAGATCATCGTGTATCATCT 58.169 45.455 0.00 0.00 0.00 2.90
681 690 2.343843 GCGCAGATCATCGTGTATCATC 59.656 50.000 0.30 0.00 0.00 2.92
817 826 1.942586 GCTGGGGACAATTCGTACGTT 60.943 52.381 16.05 0.00 42.06 3.99
829 838 2.358737 CGTGTTCCAGCTGGGGAC 60.359 66.667 32.23 27.80 46.54 4.46
834 843 2.375766 GCTCGTCGTGTTCCAGCTG 61.376 63.158 6.78 6.78 0.00 4.24
839 848 2.737376 GGTGGCTCGTCGTGTTCC 60.737 66.667 0.00 0.00 0.00 3.62
899 908 1.721926 GAGTGAACACTCGTAGCAAGC 59.278 52.381 17.19 0.00 46.93 4.01
1230 1257 4.296729 ACGTCGAGTGGGACCCCT 62.297 66.667 8.45 4.46 36.94 4.79
1359 1392 2.819984 TTTGGCCGCACCTCCATCTC 62.820 60.000 0.00 0.00 40.22 2.75
1360 1393 2.424842 TTTTGGCCGCACCTCCATCT 62.425 55.000 0.00 0.00 40.22 2.90
1362 1395 1.978617 CTTTTGGCCGCACCTCCAT 60.979 57.895 0.00 0.00 40.22 3.41
1385 1418 3.691342 CGGACAGGTCAAGCCCGA 61.691 66.667 1.41 0.00 42.49 5.14
1386 1419 4.760047 CCGGACAGGTCAAGCCCG 62.760 72.222 0.00 0.00 39.85 6.13
1392 1425 2.425592 CTGTTGCCGGACAGGTCA 59.574 61.111 14.14 7.51 42.58 4.02
1585 1624 2.360949 ATCCAGCTGAGATCGCCGTG 62.361 60.000 17.39 0.00 0.00 4.94
1710 1749 1.760613 ACCTCGCCGGAGATTGAATTA 59.239 47.619 8.83 0.00 43.27 1.40
1715 1754 2.892425 GCACCTCGCCGGAGATTG 60.892 66.667 8.83 10.35 43.27 2.67
1851 1890 3.809832 CACCAGAGAAGTTGTTGTTCGAT 59.190 43.478 0.00 0.00 0.00 3.59
1986 2025 3.003480 GTTCGAGCTTAAGTCCAGCATT 58.997 45.455 4.02 0.00 39.99 3.56
2118 2161 3.416156 GAGGCTTTCACAGTTGGAGATT 58.584 45.455 0.00 0.00 0.00 2.40
2323 2366 1.664151 GTTCATCAATTCGGACGGGAC 59.336 52.381 0.00 0.00 0.00 4.46
2331 2374 5.737757 CAGATTCTTGCAGTTCATCAATTCG 59.262 40.000 0.00 0.00 0.00 3.34
2595 2646 2.929161 GCGCAAGTATATATGTGGCCGA 60.929 50.000 0.30 0.00 41.68 5.54
2621 2674 1.226323 CATTTGCTGCTCTGCTCGC 60.226 57.895 0.00 0.00 0.00 5.03
2714 2767 0.533308 TACCCGTGTGAAGTTGCACC 60.533 55.000 0.00 0.00 37.99 5.01
2744 2797 1.067565 TCAAAGTGTGCTCTCCGCTAG 60.068 52.381 0.00 0.00 40.11 3.42
2856 2910 6.940831 TGATTTTGCCGAAGATTCATGATA 57.059 33.333 0.00 0.00 0.00 2.15
2879 2933 0.482446 TGGGATGGCACCAGAAAGTT 59.518 50.000 8.11 0.00 33.23 2.66
3018 3072 2.810274 CGGTATTGATCCATTCAGCCTG 59.190 50.000 0.00 0.00 35.27 4.85
3065 3119 3.370840 TGTTTGCATATTGGCTCTCCT 57.629 42.857 0.00 0.00 34.04 3.69
3263 4519 4.989797 TCTTGCCGTTGTCGACTTTATTTA 59.010 37.500 17.92 0.00 39.71 1.40
3397 4653 2.618045 CCTTGAATACCTTTCCGTGGCT 60.618 50.000 0.00 0.00 0.00 4.75
3644 4900 2.359531 TCGTGGAACCCAAATTGTGTTC 59.640 45.455 11.92 11.92 38.08 3.18
3662 4918 2.558795 AGCATAACACACAGTCTCTCGT 59.441 45.455 0.00 0.00 0.00 4.18
3820 5076 4.987285 CGCAGAGTTATCATCAGCTTGTAT 59.013 41.667 0.00 0.00 0.00 2.29
4149 5492 3.434641 CGACATGAACAAGTTGATCTGCT 59.565 43.478 10.54 0.00 0.00 4.24
4186 5529 2.364647 TGTCCATGTCAAAGCATTGCAA 59.635 40.909 11.91 0.00 36.45 4.08
4383 5729 1.531423 ACAGTTCTTCATGCAGCCAG 58.469 50.000 0.00 0.00 0.00 4.85
4601 6129 7.093684 GGCATTACTACTTTATGTCCCCAAAAA 60.094 37.037 0.00 0.00 0.00 1.94
4607 6135 6.592870 AGAAGGCATTACTACTTTATGTCCC 58.407 40.000 0.00 0.00 0.00 4.46
4801 6330 9.023962 AGCCACTATTTCATTTGACAAATCTTA 57.976 29.630 10.52 0.00 0.00 2.10
4861 6390 4.229304 TCACCAAAGTTTTCTCCTGACA 57.771 40.909 0.00 0.00 0.00 3.58
4888 6417 1.747709 AGCTAGCTCATGTTGCTTGG 58.252 50.000 12.68 13.12 41.46 3.61
4907 6436 4.465480 TGGGAGCGCTTGCGCATA 62.465 61.111 35.35 18.72 45.69 3.14
4929 6458 4.097892 TCCGACTAATAGTCCGTAAAACCC 59.902 45.833 14.17 0.00 42.12 4.11
4946 6475 3.393800 CAATTCATCGCCTTATCCGACT 58.606 45.455 0.00 0.00 37.56 4.18
4990 6519 5.714047 TGCACTCAGTACTTCTCACAATAG 58.286 41.667 0.00 0.00 0.00 1.73
4992 6521 4.607293 TGCACTCAGTACTTCTCACAAT 57.393 40.909 0.00 0.00 0.00 2.71
4993 6522 4.309933 CATGCACTCAGTACTTCTCACAA 58.690 43.478 0.00 0.00 0.00 3.33
4994 6523 3.862264 GCATGCACTCAGTACTTCTCACA 60.862 47.826 14.21 0.00 0.00 3.58
4995 6524 2.670414 GCATGCACTCAGTACTTCTCAC 59.330 50.000 14.21 0.00 0.00 3.51
4996 6525 2.354103 GGCATGCACTCAGTACTTCTCA 60.354 50.000 21.36 0.00 0.00 3.27
5002 6531 0.321564 TGTGGGCATGCACTCAGTAC 60.322 55.000 22.81 11.08 0.00 2.73
5004 6533 0.467844 TTTGTGGGCATGCACTCAGT 60.468 50.000 22.56 0.00 0.00 3.41
5014 6543 1.271871 CCATAGAGGTGTTTGTGGGCA 60.272 52.381 0.00 0.00 0.00 5.36
5036 6565 1.001974 GGGAAAATTGTTGGACTGCCC 59.998 52.381 0.00 0.00 0.00 5.36
5038 6567 2.365293 ACTGGGAAAATTGTTGGACTGC 59.635 45.455 0.00 0.00 0.00 4.40
5048 6577 9.154632 AGAACCATTAGTAAAACTGGGAAAATT 57.845 29.630 6.08 0.00 32.89 1.82
5054 6583 6.954232 TCCTAGAACCATTAGTAAAACTGGG 58.046 40.000 6.08 0.00 32.89 4.45
5218 6747 8.886719 CAAAAGCAAAAGGAGAGAAGAAAATTT 58.113 29.630 0.00 0.00 0.00 1.82
5219 6748 8.260114 TCAAAAGCAAAAGGAGAGAAGAAAATT 58.740 29.630 0.00 0.00 0.00 1.82
5224 6753 6.966534 ATTCAAAAGCAAAAGGAGAGAAGA 57.033 33.333 0.00 0.00 0.00 2.87
5227 6756 6.098124 TGGAAATTCAAAAGCAAAAGGAGAGA 59.902 34.615 0.00 0.00 0.00 3.10
5228 6757 6.282930 TGGAAATTCAAAAGCAAAAGGAGAG 58.717 36.000 0.00 0.00 0.00 3.20
5299 6829 5.923684 GGAAACTGTTCAACTTGTGTTCAAA 59.076 36.000 0.00 0.00 35.25 2.69
5318 6848 3.404899 TGTTCAACGGGTATCTGGAAAC 58.595 45.455 0.00 0.00 0.00 2.78
5322 6852 6.693315 AAAATATGTTCAACGGGTATCTGG 57.307 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.