Multiple sequence alignment - TraesCS5D01G354500

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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 TraesCS5D01G354500 chr5D 100.000 2315 0 0 1 2315 436605327 436607641 0.000000e+00 4276.0
1 TraesCS5D01G354500 chr5D 86.468 436 46 10 987 1419 436621444 436621869 1.250000e-127 466.0
2 TraesCS5D01G354500 chr5D 93.478 46 3 0 779 824 436621235 436621280 4.130000e-08 69.4
3 TraesCS5D01G354500 chr5A 94.366 1136 45 6 850 1979 551190790 551191912 0.000000e+00 1725.0
4 TraesCS5D01G354500 chr5A 93.492 968 50 8 656 1620 551058714 551059671 0.000000e+00 1426.0
5 TraesCS5D01G354500 chr5A 92.607 771 44 5 850 1620 551244929 551245686 0.000000e+00 1096.0
6 TraesCS5D01G354500 chr5A 93.223 605 28 5 850 1454 551435678 551436269 0.000000e+00 878.0
7 TraesCS5D01G354500 chr5A 85.289 605 61 21 824 1419 551193982 551194567 1.180000e-167 599.0
8 TraesCS5D01G354500 chr5A 93.750 384 18 1 1609 1986 551059898 551060281 2.580000e-159 571.0
9 TraesCS5D01G354500 chr5A 92.448 384 21 4 1609 1986 551245912 551246293 2.020000e-150 542.0
10 TraesCS5D01G354500 chr5A 90.566 159 12 2 1 157 551189506 551189663 8.380000e-50 207.0
11 TraesCS5D01G354500 chr5A 92.053 151 2 6 543 692 551058553 551058694 1.080000e-48 204.0
12 TraesCS5D01G354500 chr5A 91.026 156 7 6 1 152 551243674 551243826 1.080000e-48 204.0
13 TraesCS5D01G354500 chr5A 80.208 288 38 13 547 824 551244654 551244932 5.050000e-47 198.0
14 TraesCS5D01G354500 chr5A 92.562 121 6 2 547 667 551190479 551190596 1.100000e-38 171.0
15 TraesCS5D01G354500 chr5A 90.909 121 7 2 547 667 551435166 551435282 2.380000e-35 159.0
16 TraesCS5D01G354500 chr5A 95.349 43 2 0 782 824 551248188 551248230 4.130000e-08 69.4
17 TraesCS5D01G354500 chr5A 93.023 43 3 0 782 824 551063600 551063642 1.920000e-06 63.9
18 TraesCS5D01G354500 chr5A 92.683 41 3 0 784 824 551193913 551193953 2.480000e-05 60.2
19 TraesCS5D01G354500 chr5B 92.819 933 41 10 547 1461 530723861 530724785 0.000000e+00 1328.0
20 TraesCS5D01G354500 chr5B 92.075 858 39 16 850 1699 530780439 530781275 0.000000e+00 1181.0
21 TraesCS5D01G354500 chr5B 92.130 432 26 5 1472 1895 530725192 530725623 9.150000e-169 603.0
22 TraesCS5D01G354500 chr5B 83.699 638 68 21 734 1343 530797929 530798558 9.280000e-159 569.0
23 TraesCS5D01G354500 chr5B 87.112 419 39 6 935 1345 530762650 530763061 5.830000e-126 460.0
24 TraesCS5D01G354500 chr5B 90.000 160 13 2 1 158 530779187 530779345 1.080000e-48 204.0
25 TraesCS5D01G354500 chr5B 97.917 96 2 0 1891 1986 530743986 530744081 1.420000e-37 167.0
26 TraesCS5D01G354500 chr5B 90.741 108 9 1 2099 2206 407241992 407242098 2.400000e-30 143.0
27 TraesCS5D01G354500 chr3B 82.390 477 66 13 1612 2076 85412801 85412331 1.290000e-107 399.0
28 TraesCS5D01G354500 chr3B 85.758 330 37 7 1753 2076 357683280 357683605 7.920000e-90 340.0
29 TraesCS5D01G354500 chr3A 82.062 485 67 13 1606 2076 748417539 748417061 1.670000e-106 396.0
30 TraesCS5D01G354500 chr3A 91.837 98 7 1 2098 2195 357059850 357059754 4.010000e-28 135.0
31 TraesCS5D01G354500 chr6A 87.336 229 24 4 2091 2315 49750891 49750664 8.210000e-65 257.0
32 TraesCS5D01G354500 chr1B 86.932 176 18 4 2144 2315 542687179 542687005 2.350000e-45 193.0
33 TraesCS5D01G354500 chr4A 76.517 379 60 13 1698 2071 146703005 146703359 1.830000e-41 180.0
34 TraesCS5D01G354500 chr7D 88.991 109 10 2 2099 2206 586688270 586688163 1.440000e-27 134.0
35 TraesCS5D01G354500 chr2A 88.889 108 11 1 2099 2206 733098786 733098680 5.190000e-27 132.0
36 TraesCS5D01G354500 chr4B 97.222 36 1 0 1600 1635 458319858 458319823 6.910000e-06 62.1


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 TraesCS5D01G354500 chr5D 436605327 436607641 2314 False 4276.000 4276 100.0000 1 2315 1 chr5D.!!$F1 2314
1 TraesCS5D01G354500 chr5D 436621235 436621869 634 False 267.700 466 89.9730 779 1419 2 chr5D.!!$F2 640
2 TraesCS5D01G354500 chr5A 551058553 551063642 5089 False 566.225 1426 93.0795 543 1986 4 chr5A.!!$F1 1443
3 TraesCS5D01G354500 chr5A 551189506 551194567 5061 False 552.440 1725 91.0932 1 1979 5 chr5A.!!$F2 1978
4 TraesCS5D01G354500 chr5A 551435166 551436269 1103 False 518.500 878 92.0660 547 1454 2 chr5A.!!$F4 907
5 TraesCS5D01G354500 chr5A 551243674 551248230 4556 False 421.880 1096 90.3276 1 1986 5 chr5A.!!$F3 1985
6 TraesCS5D01G354500 chr5B 530723861 530725623 1762 False 965.500 1328 92.4745 547 1895 2 chr5B.!!$F5 1348
7 TraesCS5D01G354500 chr5B 530779187 530781275 2088 False 692.500 1181 91.0375 1 1699 2 chr5B.!!$F6 1698
8 TraesCS5D01G354500 chr5B 530797929 530798558 629 False 569.000 569 83.6990 734 1343 1 chr5B.!!$F4 609

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
45 46 0.398098 GAAGGATCACCCTCCCGGTA 60.398 60.0 0.0 0.0 46.14 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 3362 0.606604 GGGAGCTTTGTCGTGGACTA 59.393 55.0 0.0 0.0 33.15 2.59 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
45 46 0.398098 GAAGGATCACCCTCCCGGTA 60.398 60.000 0.00 0.00 46.14 4.02
51 52 1.492764 TCACCCTCCCGGTAATCTTC 58.507 55.000 0.00 0.00 46.14 2.87
109 112 2.648059 AGGTGATAGGCTTTGACATGC 58.352 47.619 0.00 0.00 0.00 4.06
115 118 5.346822 GTGATAGGCTTTGACATGCTTTTTG 59.653 40.000 0.00 0.00 0.00 2.44
119 122 4.943093 AGGCTTTGACATGCTTTTTGTTTT 59.057 33.333 0.00 0.00 0.00 2.43
120 123 5.415389 AGGCTTTGACATGCTTTTTGTTTTT 59.585 32.000 0.00 0.00 0.00 1.94
128 131 7.082700 ACATGCTTTTTGTTTTTCCGAAAAT 57.917 28.000 7.12 0.00 37.12 1.82
129 132 7.534282 ACATGCTTTTTGTTTTTCCGAAAATT 58.466 26.923 7.12 0.00 37.12 1.82
141 144 4.075963 TCCGAAAATTAGGATAACCCCG 57.924 45.455 0.00 0.00 36.73 5.73
187 190 2.399217 CACGCACGCACGCATATT 59.601 55.556 0.00 0.00 36.19 1.28
216 274 3.733337 AGTATGCGTCCATTCTCAATCC 58.267 45.455 0.00 0.00 32.85 3.01
230 288 4.005650 TCTCAATCCAACATCTCACAAGC 58.994 43.478 0.00 0.00 0.00 4.01
231 289 3.753815 TCAATCCAACATCTCACAAGCA 58.246 40.909 0.00 0.00 0.00 3.91
244 302 7.609146 ACATCTCACAAGCAAAGATTTCAGATA 59.391 33.333 0.00 0.00 0.00 1.98
248 306 8.515695 TCACAAGCAAAGATTTCAGATATCAT 57.484 30.769 5.32 0.00 0.00 2.45
249 307 8.403236 TCACAAGCAAAGATTTCAGATATCATG 58.597 33.333 5.32 0.93 0.00 3.07
261 319 8.421249 TTTCAGATATCATGGAAGTTGGTTTT 57.579 30.769 5.32 0.00 0.00 2.43
262 320 9.527157 TTTCAGATATCATGGAAGTTGGTTTTA 57.473 29.630 5.32 0.00 0.00 1.52
263 321 9.699410 TTCAGATATCATGGAAGTTGGTTTTAT 57.301 29.630 5.32 0.00 0.00 1.40
545 989 2.102749 CCCCGCGCATGACATTTG 59.897 61.111 8.75 0.00 0.00 2.32
567 1011 5.302357 GCCAAGTGCATATTTATCTAGGC 57.698 43.478 0.00 0.00 40.77 3.93
577 1021 7.922278 TGCATATTTATCTAGGCAAGCAAAAAG 59.078 33.333 0.00 0.00 35.66 2.27
583 1027 8.816640 TTATCTAGGCAAGCAAAAAGAAAAAG 57.183 30.769 0.00 0.00 0.00 2.27
584 1028 5.600696 TCTAGGCAAGCAAAAAGAAAAAGG 58.399 37.500 0.00 0.00 0.00 3.11
585 1029 4.486125 AGGCAAGCAAAAAGAAAAAGGA 57.514 36.364 0.00 0.00 0.00 3.36
824 1732 2.314415 TTAATACGCCCCCGCCTGTC 62.314 60.000 0.00 0.00 38.22 3.51
833 1741 3.646715 CCGCCTGTCCCCCAGAAA 61.647 66.667 0.00 0.00 44.49 2.52
834 1742 2.434331 CGCCTGTCCCCCAGAAAA 59.566 61.111 0.00 0.00 44.49 2.29
835 1743 1.971695 CGCCTGTCCCCCAGAAAAC 60.972 63.158 0.00 0.00 44.49 2.43
836 1744 1.152830 GCCTGTCCCCCAGAAAACA 59.847 57.895 0.00 0.00 44.49 2.83
837 1745 0.469144 GCCTGTCCCCCAGAAAACAA 60.469 55.000 0.00 0.00 44.49 2.83
838 1746 2.032151 GCCTGTCCCCCAGAAAACAAA 61.032 52.381 0.00 0.00 44.49 2.83
839 1747 2.393646 CCTGTCCCCCAGAAAACAAAA 58.606 47.619 0.00 0.00 44.49 2.44
840 1748 2.972021 CCTGTCCCCCAGAAAACAAAAT 59.028 45.455 0.00 0.00 44.49 1.82
841 1749 4.156477 CCTGTCCCCCAGAAAACAAAATA 58.844 43.478 0.00 0.00 44.49 1.40
842 1750 4.021456 CCTGTCCCCCAGAAAACAAAATAC 60.021 45.833 0.00 0.00 44.49 1.89
843 1751 3.570550 TGTCCCCCAGAAAACAAAATACG 59.429 43.478 0.00 0.00 0.00 3.06
844 1752 3.570975 GTCCCCCAGAAAACAAAATACGT 59.429 43.478 0.00 0.00 0.00 3.57
845 1753 4.761227 GTCCCCCAGAAAACAAAATACGTA 59.239 41.667 0.00 0.00 0.00 3.57
846 1754 5.416639 GTCCCCCAGAAAACAAAATACGTAT 59.583 40.000 1.14 1.14 0.00 3.06
847 1755 6.011481 TCCCCCAGAAAACAAAATACGTATT 58.989 36.000 15.07 15.07 0.00 1.89
848 1756 7.121020 GTCCCCCAGAAAACAAAATACGTATTA 59.879 37.037 20.62 0.00 0.00 0.98
849 1757 7.121020 TCCCCCAGAAAACAAAATACGTATTAC 59.879 37.037 20.62 7.23 0.00 1.89
850 1758 7.121611 CCCCCAGAAAACAAAATACGTATTACT 59.878 37.037 20.62 8.87 0.00 2.24
851 1759 7.966204 CCCCAGAAAACAAAATACGTATTACTG 59.034 37.037 20.62 20.62 0.00 2.74
852 1760 8.508875 CCCAGAAAACAAAATACGTATTACTGT 58.491 33.333 20.62 21.19 0.00 3.55
897 1806 1.369321 CGCTAGGGCTTCATCTCCC 59.631 63.158 0.00 0.00 42.94 4.30
903 1812 1.591863 GGCTTCATCTCCCGTACGC 60.592 63.158 10.49 0.00 0.00 4.42
1097 2029 0.956633 TGGGTCTATATCGCGGTGTC 59.043 55.000 6.13 0.00 0.00 3.67
1100 2032 1.612463 GGTCTATATCGCGGTGTCCTT 59.388 52.381 6.13 0.00 0.00 3.36
1642 3217 4.685169 ACGGAAGCAAACATGTTATGAG 57.315 40.909 12.39 3.85 0.00 2.90
1649 3224 2.428171 CAAACATGTTATGAGGGCCCTG 59.572 50.000 34.59 16.26 0.00 4.45
1777 3362 1.069049 GCAACAACAATGCCAGGACTT 59.931 47.619 0.00 0.00 37.85 3.01
1998 3824 3.642141 ACAACATTTGTCAAAGGACCCT 58.358 40.909 16.39 0.00 43.65 4.34
2019 3845 8.344939 ACCCTATTTTTATAACAGATCTGGGA 57.655 34.615 26.08 13.86 34.19 4.37
2044 3871 7.856145 ATCTAAGAAGCAACTCATTACCTTG 57.144 36.000 0.00 0.00 0.00 3.61
2072 3899 5.353123 ACACCTTTATTACAAGCATACACGG 59.647 40.000 0.00 0.00 0.00 4.94
2076 3903 6.238374 CCTTTATTACAAGCATACACGGAAGG 60.238 42.308 0.00 0.00 0.00 3.46
2078 3905 0.981183 ACAAGCATACACGGAAGGGA 59.019 50.000 0.00 0.00 38.45 4.20
2079 3906 1.349688 ACAAGCATACACGGAAGGGAA 59.650 47.619 0.00 0.00 38.45 3.97
2080 3907 2.224670 ACAAGCATACACGGAAGGGAAA 60.225 45.455 0.00 0.00 38.45 3.13
2081 3908 2.109425 AGCATACACGGAAGGGAAAC 57.891 50.000 0.00 0.00 38.45 2.78
2083 3910 1.942586 GCATACACGGAAGGGAAACGT 60.943 52.381 0.00 0.00 42.17 3.99
2089 3916 3.976758 GAAGGGAAACGTTCGGGG 58.023 61.111 0.00 0.00 44.29 5.73
2090 3917 2.281970 AAGGGAAACGTTCGGGGC 60.282 61.111 0.00 0.00 31.66 5.80
2112 3939 4.083862 AGACCGGCCGAAGCTTCC 62.084 66.667 30.73 6.74 39.73 3.46
2120 3947 3.488090 CGAAGCTTCCGCCGGTTC 61.488 66.667 20.62 0.00 36.60 3.62
2123 3950 3.178540 AAGCTTCCGCCGGTTCAGT 62.179 57.895 1.63 0.00 36.60 3.41
2125 3952 2.434359 CTTCCGCCGGTTCAGTCC 60.434 66.667 1.63 0.00 0.00 3.85
2127 3954 3.524648 TTCCGCCGGTTCAGTCCAC 62.525 63.158 1.63 0.00 0.00 4.02
2156 5045 2.202610 CGATCCACTCGCGAGCAA 60.203 61.111 34.83 20.76 41.14 3.91
2162 5051 4.280494 ACTCGCGAGCAACCACGT 62.280 61.111 34.83 11.93 0.00 4.49
2187 5076 0.962356 GGTGGACCCGAGACGAACTA 60.962 60.000 0.00 0.00 0.00 2.24
2189 5078 0.037303 TGGACCCGAGACGAACTAGT 59.963 55.000 0.00 0.00 0.00 2.57
2191 5080 0.731994 GACCCGAGACGAACTAGTCC 59.268 60.000 0.00 0.00 41.83 3.85
2192 5081 0.327591 ACCCGAGACGAACTAGTCCT 59.672 55.000 0.00 0.00 41.83 3.85
2194 5083 1.015868 CCGAGACGAACTAGTCCTCC 58.984 60.000 0.00 0.00 41.83 4.30
2195 5084 1.407162 CCGAGACGAACTAGTCCTCCT 60.407 57.143 0.00 0.00 41.83 3.69
2196 5085 2.158986 CCGAGACGAACTAGTCCTCCTA 60.159 54.545 0.00 0.00 41.83 2.94
2197 5086 2.865551 CGAGACGAACTAGTCCTCCTAC 59.134 54.545 0.00 0.00 41.83 3.18
2199 7778 2.235898 AGACGAACTAGTCCTCCTACGT 59.764 50.000 0.00 0.00 41.83 3.57
2202 7781 4.775236 ACGAACTAGTCCTCCTACGTTAT 58.225 43.478 0.00 0.00 0.00 1.89
2203 7782 4.813697 ACGAACTAGTCCTCCTACGTTATC 59.186 45.833 0.00 0.00 0.00 1.75
2204 7783 4.213059 CGAACTAGTCCTCCTACGTTATCC 59.787 50.000 0.00 0.00 0.00 2.59
2209 7788 3.204831 AGTCCTCCTACGTTATCCCTTCT 59.795 47.826 0.00 0.00 0.00 2.85
2214 7793 5.126699 TCCTACGTTATCCCTTCTTCTCT 57.873 43.478 0.00 0.00 0.00 3.10
2215 7794 5.131784 TCCTACGTTATCCCTTCTTCTCTC 58.868 45.833 0.00 0.00 0.00 3.20
2216 7795 4.278919 CCTACGTTATCCCTTCTTCTCTCC 59.721 50.000 0.00 0.00 0.00 3.71
2217 7796 3.032459 ACGTTATCCCTTCTTCTCTCCC 58.968 50.000 0.00 0.00 0.00 4.30
2222 7801 1.219393 CCTTCTTCTCTCCCACGCC 59.781 63.158 0.00 0.00 0.00 5.68
2226 7805 3.708220 CTTCTCTCCCACGCCGCTC 62.708 68.421 0.00 0.00 0.00 5.03
2235 7814 2.026301 ACGCCGCTCGCTCTTATC 59.974 61.111 0.00 0.00 43.23 1.75
2236 7815 2.731348 CGCCGCTCGCTCTTATCC 60.731 66.667 0.00 0.00 34.21 2.59
2237 7816 2.356433 GCCGCTCGCTCTTATCCC 60.356 66.667 0.00 0.00 0.00 3.85
2238 7817 2.340443 CCGCTCGCTCTTATCCCC 59.660 66.667 0.00 0.00 0.00 4.81
2240 7819 1.742768 CGCTCGCTCTTATCCCCTT 59.257 57.895 0.00 0.00 0.00 3.95
2241 7820 0.105039 CGCTCGCTCTTATCCCCTTT 59.895 55.000 0.00 0.00 0.00 3.11
2242 7821 1.473434 CGCTCGCTCTTATCCCCTTTT 60.473 52.381 0.00 0.00 0.00 2.27
2245 7824 3.723260 CTCGCTCTTATCCCCTTTTCTC 58.277 50.000 0.00 0.00 0.00 2.87
2247 7826 2.159085 CGCTCTTATCCCCTTTTCTCGT 60.159 50.000 0.00 0.00 0.00 4.18
2249 7828 4.262079 CGCTCTTATCCCCTTTTCTCGTAT 60.262 45.833 0.00 0.00 0.00 3.06
2250 7829 5.612351 GCTCTTATCCCCTTTTCTCGTATT 58.388 41.667 0.00 0.00 0.00 1.89
2252 7831 6.463190 GCTCTTATCCCCTTTTCTCGTATTCT 60.463 42.308 0.00 0.00 0.00 2.40
2253 7832 7.433537 TCTTATCCCCTTTTCTCGTATTCTT 57.566 36.000 0.00 0.00 0.00 2.52
2254 7833 7.858498 TCTTATCCCCTTTTCTCGTATTCTTT 58.142 34.615 0.00 0.00 0.00 2.52
2255 7834 8.326529 TCTTATCCCCTTTTCTCGTATTCTTTT 58.673 33.333 0.00 0.00 0.00 2.27
2256 7835 8.873186 TTATCCCCTTTTCTCGTATTCTTTTT 57.127 30.769 0.00 0.00 0.00 1.94
2257 7836 6.569179 TCCCCTTTTCTCGTATTCTTTTTG 57.431 37.500 0.00 0.00 0.00 2.44
2258 7837 5.048294 TCCCCTTTTCTCGTATTCTTTTTGC 60.048 40.000 0.00 0.00 0.00 3.68
2259 7838 5.048013 CCCCTTTTCTCGTATTCTTTTTGCT 60.048 40.000 0.00 0.00 0.00 3.91
2262 7841 7.096065 CCCTTTTCTCGTATTCTTTTTGCTTTG 60.096 37.037 0.00 0.00 0.00 2.77
2263 7842 7.647715 CCTTTTCTCGTATTCTTTTTGCTTTGA 59.352 33.333 0.00 0.00 0.00 2.69
2264 7843 8.560576 TTTTCTCGTATTCTTTTTGCTTTGAG 57.439 30.769 0.00 0.00 0.00 3.02
2265 7844 5.689819 TCTCGTATTCTTTTTGCTTTGAGC 58.310 37.500 0.00 0.00 42.82 4.26
2266 7845 5.470098 TCTCGTATTCTTTTTGCTTTGAGCT 59.530 36.000 1.29 0.00 42.97 4.09
2267 7846 5.689819 TCGTATTCTTTTTGCTTTGAGCTC 58.310 37.500 6.82 6.82 42.97 4.09
2268 7847 4.853743 CGTATTCTTTTTGCTTTGAGCTCC 59.146 41.667 12.15 0.00 42.97 4.70
2269 7848 3.733443 TTCTTTTTGCTTTGAGCTCCC 57.267 42.857 12.15 0.00 42.97 4.30
2270 7849 1.608590 TCTTTTTGCTTTGAGCTCCCG 59.391 47.619 12.15 0.13 42.97 5.14
2271 7850 0.031994 TTTTTGCTTTGAGCTCCCGC 59.968 50.000 12.15 11.38 42.97 6.13
2272 7851 2.128853 TTTTGCTTTGAGCTCCCGCG 62.129 55.000 12.15 0.00 42.97 6.46
2275 7854 4.767255 CTTTGAGCTCCCGCGCCT 62.767 66.667 12.15 0.00 42.32 5.52
2277 7856 4.760047 TTGAGCTCCCGCGCCTTC 62.760 66.667 12.15 0.00 42.32 3.46
2289 7868 3.512516 GCCTTCGCCTGCACATCC 61.513 66.667 0.00 0.00 0.00 3.51
2291 7870 1.817099 CCTTCGCCTGCACATCCTC 60.817 63.158 0.00 0.00 0.00 3.71
2292 7871 1.220206 CTTCGCCTGCACATCCTCT 59.780 57.895 0.00 0.00 0.00 3.69
2293 7872 0.461548 CTTCGCCTGCACATCCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
2295 7874 0.175760 TCGCCTGCACATCCTCTAAC 59.824 55.000 0.00 0.00 0.00 2.34
2296 7875 0.176680 CGCCTGCACATCCTCTAACT 59.823 55.000 0.00 0.00 0.00 2.24
2299 7878 1.661341 CTGCACATCCTCTAACTGGC 58.339 55.000 0.00 0.00 0.00 4.85
2300 7879 0.983467 TGCACATCCTCTAACTGGCA 59.017 50.000 0.00 0.00 0.00 4.92
2301 7880 1.065926 TGCACATCCTCTAACTGGCAG 60.066 52.381 14.16 14.16 0.00 4.85
2302 7881 1.661341 CACATCCTCTAACTGGCAGC 58.339 55.000 15.89 0.00 0.00 5.25
2303 7882 0.543749 ACATCCTCTAACTGGCAGCC 59.456 55.000 15.89 3.66 0.00 4.85
2304 7883 0.835941 CATCCTCTAACTGGCAGCCT 59.164 55.000 15.89 4.51 0.00 4.58
2305 7884 2.042464 CATCCTCTAACTGGCAGCCTA 58.958 52.381 15.89 5.56 0.00 3.93
2308 7887 4.133526 TCCTCTAACTGGCAGCCTATAT 57.866 45.455 15.89 0.00 0.00 0.86
2309 7888 4.493618 TCCTCTAACTGGCAGCCTATATT 58.506 43.478 15.89 2.48 0.00 1.28
2310 7889 4.528596 TCCTCTAACTGGCAGCCTATATTC 59.471 45.833 15.89 0.00 0.00 1.75
2311 7890 4.530161 CCTCTAACTGGCAGCCTATATTCT 59.470 45.833 15.89 0.00 0.00 2.40
2312 7891 5.012561 CCTCTAACTGGCAGCCTATATTCTT 59.987 44.000 15.89 0.11 0.00 2.52
2313 7892 6.102897 TCTAACTGGCAGCCTATATTCTTC 57.897 41.667 15.89 0.00 0.00 2.87
2314 7893 5.841237 TCTAACTGGCAGCCTATATTCTTCT 59.159 40.000 15.89 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.381420 TCTTGTATCCTTTCTCTCCGAAGATT 59.619 38.462 0.00 0.00 32.21 2.40
51 52 4.116238 GCTTCTTGTATCCTTTCTCTCCG 58.884 47.826 0.00 0.00 0.00 4.63
87 90 3.181493 GCATGTCAAAGCCTATCACCTTG 60.181 47.826 0.00 0.00 0.00 3.61
88 91 3.019564 GCATGTCAAAGCCTATCACCTT 58.980 45.455 0.00 0.00 0.00 3.50
115 118 7.037438 GGGGTTATCCTAATTTTCGGAAAAAC 58.963 38.462 18.78 10.11 35.01 2.43
119 122 4.453751 CGGGGTTATCCTAATTTTCGGAA 58.546 43.478 0.00 0.00 35.33 4.30
120 123 3.181452 CCGGGGTTATCCTAATTTTCGGA 60.181 47.826 0.00 0.00 36.30 4.55
128 131 0.765519 GAGGCCCGGGGTTATCCTAA 60.766 60.000 25.28 0.00 35.33 2.69
129 132 1.152183 GAGGCCCGGGGTTATCCTA 60.152 63.158 25.28 0.00 35.33 2.94
141 144 3.207669 CGCTCAATGCAGAGGCCC 61.208 66.667 0.00 0.00 43.06 5.80
169 172 3.716856 AATATGCGTGCGTGCGTGC 62.717 57.895 5.07 1.68 37.81 5.34
173 176 2.718609 GCGAATATGCGTGCGTGC 60.719 61.111 4.71 0.00 0.00 5.34
181 184 3.890705 GCATACTAGTCGCGAATATGC 57.109 47.619 26.38 26.38 40.81 3.14
203 261 5.188434 GTGAGATGTTGGATTGAGAATGGA 58.812 41.667 0.00 0.00 0.00 3.41
216 274 6.210796 TGAAATCTTTGCTTGTGAGATGTTG 58.789 36.000 0.00 0.00 30.91 3.33
230 288 9.731819 CAACTTCCATGATATCTGAAATCTTTG 57.268 33.333 3.98 3.14 0.00 2.77
231 289 8.910944 CCAACTTCCATGATATCTGAAATCTTT 58.089 33.333 3.98 0.00 0.00 2.52
493 591 1.069906 GCACTAAACTCACGCAGTTGG 60.070 52.381 1.29 1.64 45.32 3.77
526 624 2.406616 AAATGTCATGCGCGGGGTC 61.407 57.895 8.83 0.00 0.00 4.46
545 989 4.761739 TGCCTAGATAAATATGCACTTGGC 59.238 41.667 14.02 14.02 44.80 4.52
567 1011 7.485595 CCAAATGTTCCTTTTTCTTTTTGCTTG 59.514 33.333 0.00 0.00 0.00 4.01
577 1021 8.607441 AAGCTTATTCCAAATGTTCCTTTTTC 57.393 30.769 0.00 0.00 0.00 2.29
583 1027 8.352942 CCACTATAAGCTTATTCCAAATGTTCC 58.647 37.037 23.47 0.00 0.00 3.62
584 1028 8.352942 CCCACTATAAGCTTATTCCAAATGTTC 58.647 37.037 23.47 0.00 0.00 3.18
585 1029 7.201911 GCCCACTATAAGCTTATTCCAAATGTT 60.202 37.037 23.47 0.00 0.00 2.71
719 1498 2.883122 ACGTACCTGGGCCAAAAATA 57.117 45.000 8.04 0.00 0.00 1.40
824 1732 5.907866 ATACGTATTTTGTTTTCTGGGGG 57.092 39.130 1.14 0.00 0.00 5.40
825 1733 7.966204 CAGTAATACGTATTTTGTTTTCTGGGG 59.034 37.037 24.81 0.00 0.00 4.96
826 1734 8.508875 ACAGTAATACGTATTTTGTTTTCTGGG 58.491 33.333 24.81 5.90 0.00 4.45
903 1812 2.285834 GGTGATTAAATCGAGCTGCGTG 60.286 50.000 0.00 0.00 41.80 5.34
1097 2029 1.884926 GCGAAGATGCCGAGGAAGG 60.885 63.158 0.00 0.00 0.00 3.46
1439 2380 5.515626 GCCTTTGACAATCTAGTACGTACAG 59.484 44.000 26.55 19.97 0.00 2.74
1476 2813 6.589135 ACTATTAGTGTTAAAATCGAGGGGG 58.411 40.000 0.00 0.00 0.00 5.40
1642 3217 0.685458 ATTGCATCTTGACAGGGCCC 60.685 55.000 16.46 16.46 0.00 5.80
1649 3224 5.353400 TCTTCTGACATCATTGCATCTTGAC 59.647 40.000 0.00 0.00 0.00 3.18
1777 3362 0.606604 GGGAGCTTTGTCGTGGACTA 59.393 55.000 0.00 0.00 33.15 2.59
2019 3845 7.885399 ACAAGGTAATGAGTTGCTTCTTAGATT 59.115 33.333 0.00 0.00 0.00 2.40
2044 3871 7.749126 GTGTATGCTTGTAATAAAGGTGTTGAC 59.251 37.037 0.00 0.00 0.00 3.18
2072 3899 2.330372 GCCCCGAACGTTTCCCTTC 61.330 63.158 0.46 0.00 0.00 3.46
2094 3921 2.815647 GAAGCTTCGGCCGGTCTG 60.816 66.667 27.83 13.86 43.01 3.51
2108 3935 2.434359 GGACTGAACCGGCGGAAG 60.434 66.667 35.78 26.57 0.00 3.46
2109 3936 3.235481 TGGACTGAACCGGCGGAA 61.235 61.111 35.78 16.55 0.00 4.30
2110 3937 3.998672 GTGGACTGAACCGGCGGA 61.999 66.667 35.78 9.74 0.00 5.54
2140 3967 2.167861 GGTTGCTCGCGAGTGGATC 61.168 63.158 34.46 19.35 0.00 3.36
2141 3968 2.125512 GGTTGCTCGCGAGTGGAT 60.126 61.111 34.46 0.00 0.00 3.41
2142 3969 3.611674 TGGTTGCTCGCGAGTGGA 61.612 61.111 34.46 19.13 0.00 4.02
2143 3970 3.414700 GTGGTTGCTCGCGAGTGG 61.415 66.667 34.46 13.77 0.00 4.00
2144 3971 3.767230 CGTGGTTGCTCGCGAGTG 61.767 66.667 34.46 14.55 42.50 3.51
2145 3972 4.280494 ACGTGGTTGCTCGCGAGT 62.280 61.111 34.46 12.67 42.50 4.18
2168 5057 0.962356 TAGTTCGTCTCGGGTCCACC 60.962 60.000 0.00 0.00 0.00 4.61
2170 5059 0.037303 ACTAGTTCGTCTCGGGTCCA 59.963 55.000 0.00 0.00 0.00 4.02
2176 5065 2.027003 AGGAGGACTAGTTCGTCTCG 57.973 55.000 0.00 0.00 38.87 4.04
2181 5070 4.213059 GGATAACGTAGGAGGACTAGTTCG 59.787 50.000 0.00 0.00 30.77 3.95
2182 5071 4.518590 GGGATAACGTAGGAGGACTAGTTC 59.481 50.000 0.00 0.00 30.77 3.01
2184 5073 3.721050 AGGGATAACGTAGGAGGACTAGT 59.279 47.826 0.00 0.00 30.77 2.57
2187 5076 3.204831 AGAAGGGATAACGTAGGAGGACT 59.795 47.826 0.00 0.00 0.00 3.85
2189 5078 3.967467 AGAAGGGATAACGTAGGAGGA 57.033 47.619 0.00 0.00 0.00 3.71
2191 5080 5.134661 AGAGAAGAAGGGATAACGTAGGAG 58.865 45.833 0.00 0.00 0.00 3.69
2192 5081 5.126699 AGAGAAGAAGGGATAACGTAGGA 57.873 43.478 0.00 0.00 0.00 2.94
2194 5083 4.278919 GGGAGAGAAGAAGGGATAACGTAG 59.721 50.000 0.00 0.00 0.00 3.51
2195 5084 4.213513 GGGAGAGAAGAAGGGATAACGTA 58.786 47.826 0.00 0.00 0.00 3.57
2196 5085 3.032459 GGGAGAGAAGAAGGGATAACGT 58.968 50.000 0.00 0.00 0.00 3.99
2197 5086 3.031736 TGGGAGAGAAGAAGGGATAACG 58.968 50.000 0.00 0.00 0.00 3.18
2199 7778 3.031736 CGTGGGAGAGAAGAAGGGATAA 58.968 50.000 0.00 0.00 0.00 1.75
2202 7781 1.258445 GCGTGGGAGAGAAGAAGGGA 61.258 60.000 0.00 0.00 0.00 4.20
2203 7782 1.219393 GCGTGGGAGAGAAGAAGGG 59.781 63.158 0.00 0.00 0.00 3.95
2204 7783 1.219393 GGCGTGGGAGAGAAGAAGG 59.781 63.158 0.00 0.00 0.00 3.46
2209 7788 3.760035 GAGCGGCGTGGGAGAGAA 61.760 66.667 9.37 0.00 0.00 2.87
2222 7801 0.105039 AAAGGGGATAAGAGCGAGCG 59.895 55.000 0.00 0.00 0.00 5.03
2226 7805 2.159085 ACGAGAAAAGGGGATAAGAGCG 60.159 50.000 0.00 0.00 0.00 5.03
2228 7807 7.056844 AGAATACGAGAAAAGGGGATAAGAG 57.943 40.000 0.00 0.00 0.00 2.85
2230 7809 8.507524 AAAAGAATACGAGAAAAGGGGATAAG 57.492 34.615 0.00 0.00 0.00 1.73
2232 7811 7.148137 GCAAAAAGAATACGAGAAAAGGGGATA 60.148 37.037 0.00 0.00 0.00 2.59
2235 7814 5.048013 AGCAAAAAGAATACGAGAAAAGGGG 60.048 40.000 0.00 0.00 0.00 4.79
2236 7815 6.013842 AGCAAAAAGAATACGAGAAAAGGG 57.986 37.500 0.00 0.00 0.00 3.95
2237 7816 7.647715 TCAAAGCAAAAAGAATACGAGAAAAGG 59.352 33.333 0.00 0.00 0.00 3.11
2238 7817 8.560576 TCAAAGCAAAAAGAATACGAGAAAAG 57.439 30.769 0.00 0.00 0.00 2.27
2240 7819 6.636850 GCTCAAAGCAAAAAGAATACGAGAAA 59.363 34.615 0.00 0.00 41.89 2.52
2241 7820 6.017109 AGCTCAAAGCAAAAAGAATACGAGAA 60.017 34.615 1.29 0.00 45.56 2.87
2242 7821 5.470098 AGCTCAAAGCAAAAAGAATACGAGA 59.530 36.000 1.29 0.00 45.56 4.04
2245 7824 4.853743 GGAGCTCAAAGCAAAAAGAATACG 59.146 41.667 17.19 0.00 45.56 3.06
2247 7826 4.082787 CGGGAGCTCAAAGCAAAAAGAATA 60.083 41.667 17.19 0.00 45.56 1.75
2249 7828 2.034558 CGGGAGCTCAAAGCAAAAAGAA 59.965 45.455 17.19 0.00 45.56 2.52
2250 7829 1.608590 CGGGAGCTCAAAGCAAAAAGA 59.391 47.619 17.19 0.00 45.56 2.52
2273 7852 1.817099 GAGGATGTGCAGGCGAAGG 60.817 63.158 0.00 0.00 0.00 3.46
2274 7853 0.461548 TAGAGGATGTGCAGGCGAAG 59.538 55.000 0.00 0.00 0.00 3.79
2275 7854 0.901827 TTAGAGGATGTGCAGGCGAA 59.098 50.000 0.00 0.00 0.00 4.70
2277 7856 0.176680 AGTTAGAGGATGTGCAGGCG 59.823 55.000 0.00 0.00 0.00 5.52
2278 7857 1.661341 CAGTTAGAGGATGTGCAGGC 58.339 55.000 0.00 0.00 0.00 4.85
2279 7858 1.745141 GCCAGTTAGAGGATGTGCAGG 60.745 57.143 0.00 0.00 0.00 4.85
2280 7859 1.065926 TGCCAGTTAGAGGATGTGCAG 60.066 52.381 0.00 0.00 0.00 4.41
2281 7860 0.983467 TGCCAGTTAGAGGATGTGCA 59.017 50.000 0.00 0.00 0.00 4.57
2282 7861 1.661341 CTGCCAGTTAGAGGATGTGC 58.339 55.000 0.00 0.00 0.00 4.57
2283 7862 1.661341 GCTGCCAGTTAGAGGATGTG 58.339 55.000 0.00 0.00 0.00 3.21
2284 7863 0.543749 GGCTGCCAGTTAGAGGATGT 59.456 55.000 15.17 0.00 0.00 3.06
2286 7865 2.478872 TAGGCTGCCAGTTAGAGGAT 57.521 50.000 22.65 0.00 0.00 3.24
2287 7866 2.478872 ATAGGCTGCCAGTTAGAGGA 57.521 50.000 22.65 0.00 0.00 3.71
2289 7868 5.736951 AGAATATAGGCTGCCAGTTAGAG 57.263 43.478 22.65 0.00 0.00 2.43
2291 7870 6.107901 AGAAGAATATAGGCTGCCAGTTAG 57.892 41.667 22.65 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.