Multiple sequence alignment - TraesCS7B01G296800

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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 TraesCS7B01G296800 chr7B 100.000 5391 0 0 1 5391 533572023 533566633 0.000000e+00 9956.0
1 TraesCS7B01G296800 chr7B 75.709 247 35 15 1484 1707 268454509 268454753 3.440000e-17 100.0
2 TraesCS7B01G296800 chr7A 89.030 5196 293 116 5 5038 573098484 573093404 0.000000e+00 6181.0
3 TraesCS7B01G296800 chr7A 85.789 380 28 12 5037 5391 573093347 573092969 3.940000e-101 379.0
4 TraesCS7B01G296800 chr7A 75.304 247 36 15 1484 1707 303102172 303101928 1.600000e-15 95.3
5 TraesCS7B01G296800 chr7D 92.477 2087 101 26 3339 5391 505601486 505599422 0.000000e+00 2933.0
6 TraesCS7B01G296800 chr7D 89.412 1719 86 39 160 1827 505604911 505603238 0.000000e+00 2078.0
7 TraesCS7B01G296800 chr7D 90.941 1126 60 27 2146 3259 505602962 505601867 0.000000e+00 1476.0
8 TraesCS7B01G296800 chr7D 93.117 247 8 4 1817 2056 505603220 505602976 2.390000e-93 353.0
9 TraesCS7B01G296800 chr6D 82.456 228 38 2 1480 1706 354223515 354223741 1.180000e-46 198.0
10 TraesCS7B01G296800 chr6B 82.589 224 37 2 1484 1706 524064489 524064267 4.260000e-46 196.0
11 TraesCS7B01G296800 chr2D 82.301 226 38 2 1483 1707 557258875 557259099 1.530000e-45 195.0
12 TraesCS7B01G296800 chr2A 82.222 225 38 2 1484 1707 697290074 697290297 5.510000e-45 193.0
13 TraesCS7B01G296800 chr2B 81.858 226 37 4 1484 1707 664933892 664934115 2.560000e-43 187.0
14 TraesCS7B01G296800 chr3B 84.946 93 10 4 5173 5264 715146787 715146876 2.070000e-14 91.6
15 TraesCS7B01G296800 chr3B 100.000 29 0 0 5167 5195 29576755 29576783 3.000000e-03 54.7


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 TraesCS7B01G296800 chr7B 533566633 533572023 5390 True 9956 9956 100.00000 1 5391 1 chr7B.!!$R1 5390
1 TraesCS7B01G296800 chr7A 573092969 573098484 5515 True 3280 6181 87.40950 5 5391 2 chr7A.!!$R2 5386
2 TraesCS7B01G296800 chr7D 505599422 505604911 5489 True 1710 2933 91.48675 160 5391 4 chr7D.!!$R1 5231

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
143 144 0.035915 GTGGAGGAGAAGGAAGCCAC 60.036 60.0 0.00 0.00 38.98 5.01 F
1858 2008 0.034670 AGGAAGCTTCTGGTCATGCC 60.035 55.0 25.05 6.67 37.90 4.40 F
2375 2542 0.185901 ACTGCTTTGCCTTGGGAGAA 59.814 50.0 0.00 0.00 0.00 2.87 F
2631 2804 0.317799 GCCATGCATTGTGAACCACA 59.682 50.0 0.00 0.00 43.02 4.17 F
3015 3193 0.396001 GTCCGCCCCTCTCTTCTACT 60.396 60.0 0.00 0.00 0.00 2.57 F
3793 4306 0.620700 AGGGGCAGGTAGGGTAACTG 60.621 60.0 0.00 0.00 46.24 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2099 0.094046 CTGCGTAAACTAAACCCGCG 59.906 55.000 0.00 0.00 46.77 6.46 R
3531 4028 0.855349 CGCAGATAGACATGAACGGC 59.145 55.000 0.00 0.00 0.00 5.68 R
3762 4274 1.073923 CCTGCCCCTAGTGACACTTTT 59.926 52.381 14.50 0.00 0.00 2.27 R
3793 4306 1.086696 TTTATGGAGCTTGCACGAGC 58.913 50.000 1.95 1.95 43.02 5.03 R
4150 4668 1.153549 GGAGTCCTGGCTACGCTTG 60.154 63.158 0.41 0.00 0.00 4.01 R
5276 5880 0.782384 ACTTTGTAGCGCGAAAGTCG 59.218 50.000 21.92 5.89 37.80 4.18 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 4.972514 GAGATTGGCTCTTAGGGTTTTG 57.027 45.455 0.00 0.00 40.61 2.44
29 30 3.092301 AGATTGGCTCTTAGGGTTTTGC 58.908 45.455 0.00 0.00 0.00 3.68
36 37 3.604582 CTCTTAGGGTTTTGCAGAGGAG 58.395 50.000 0.00 0.00 0.00 3.69
52 53 1.081175 GAGCGGTTGAGCAAAAGGC 60.081 57.895 0.00 0.00 45.30 4.35
64 65 0.300193 CAAAAGGCAAAACAACGGCG 59.700 50.000 4.80 4.80 0.00 6.46
72 73 1.841342 CAAAACAACGGCGTAACACAC 59.159 47.619 15.20 0.00 0.00 3.82
74 75 1.301423 AACAACGGCGTAACACACAT 58.699 45.000 15.20 0.00 0.00 3.21
100 101 2.143419 GGATGATCGTGGCCTCCCT 61.143 63.158 3.32 0.00 0.00 4.20
113 114 2.842462 TCCCTGCACCGTCACACT 60.842 61.111 0.00 0.00 0.00 3.55
116 117 2.108976 CTGCACCGTCACACTGGT 59.891 61.111 0.00 0.00 39.66 4.00
123 124 1.154016 CGTCACACTGGTAGAGCCG 60.154 63.158 0.00 0.00 41.21 5.52
143 144 0.035915 GTGGAGGAGAAGGAAGCCAC 60.036 60.000 0.00 0.00 38.98 5.01
146 147 0.980423 GAGGAGAAGGAAGCCACAGT 59.020 55.000 0.00 0.00 0.00 3.55
147 148 0.980423 AGGAGAAGGAAGCCACAGTC 59.020 55.000 0.00 0.00 0.00 3.51
149 150 2.180276 GGAGAAGGAAGCCACAGTCTA 58.820 52.381 0.00 0.00 0.00 2.59
157 158 0.117340 AGCCACAGTCTACCCCTCTT 59.883 55.000 0.00 0.00 0.00 2.85
158 159 1.361543 AGCCACAGTCTACCCCTCTTA 59.638 52.381 0.00 0.00 0.00 2.10
204 207 0.883370 AAAAGGGAGAACGACGGCAC 60.883 55.000 0.00 0.00 0.00 5.01
214 217 2.813474 GACGGCACAGTGCGCATA 60.813 61.111 15.91 0.00 46.21 3.14
216 219 1.705337 GACGGCACAGTGCGCATATT 61.705 55.000 15.91 0.00 46.21 1.28
217 220 1.297819 CGGCACAGTGCGCATATTG 60.298 57.895 15.91 15.45 46.21 1.90
219 222 0.248215 GGCACAGTGCGCATATTGTC 60.248 55.000 15.91 8.79 46.21 3.18
225 228 1.942657 AGTGCGCATATTGTCCATGAC 59.057 47.619 15.91 0.00 0.00 3.06
230 233 4.248859 GCGCATATTGTCCATGACTATCT 58.751 43.478 0.30 0.00 31.40 1.98
234 237 6.462500 GCATATTGTCCATGACTATCTGAGT 58.538 40.000 0.00 0.00 42.90 3.41
238 241 3.956848 TGTCCATGACTATCTGAGTGAGG 59.043 47.826 0.00 0.00 39.06 3.86
539 574 7.306213 GGTCGATATATATCCGTGTCCATATG 58.694 42.308 15.61 0.00 0.00 1.78
623 681 2.110006 GATCTCCAGAAGCCCCGC 59.890 66.667 0.00 0.00 0.00 6.13
624 682 3.798954 GATCTCCAGAAGCCCCGCG 62.799 68.421 0.00 0.00 0.00 6.46
629 689 2.577059 CAGAAGCCCCGCGAGTAA 59.423 61.111 8.23 0.00 0.00 2.24
655 715 3.677689 AATCCCCTCCCCACCCTCC 62.678 68.421 0.00 0.00 0.00 4.30
659 719 4.354943 CCTCCCCACCCTCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
702 762 2.569134 GTCTCCGCTCGAGCTTGT 59.431 61.111 32.88 0.00 38.62 3.16
711 771 2.811317 CGAGCTTGTCAGTCCGCC 60.811 66.667 0.00 0.00 0.00 6.13
712 772 2.659610 GAGCTTGTCAGTCCGCCT 59.340 61.111 0.00 0.00 0.00 5.52
713 773 1.446966 GAGCTTGTCAGTCCGCCTC 60.447 63.158 0.00 0.00 0.00 4.70
715 775 2.651361 CTTGTCAGTCCGCCTCGT 59.349 61.111 0.00 0.00 0.00 4.18
724 784 4.824515 CCGCCTCGTCCTCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
819 879 3.774959 GATGGAGCCGTCGCGTCAT 62.775 63.158 5.77 0.10 41.18 3.06
834 894 0.598065 GTCATGCGTGCCTTTTTCCT 59.402 50.000 0.00 0.00 0.00 3.36
870 930 2.409012 TCTCGCGTATGCTTTGTTCAA 58.591 42.857 5.77 0.00 39.65 2.69
896 959 5.189342 TGGCAGATTGATTCTCTCTTCTTCT 59.811 40.000 0.00 0.00 29.93 2.85
960 1029 1.642762 AGGCCTTGGTTGATCAATCCT 59.357 47.619 16.06 10.37 0.00 3.24
988 1057 0.175989 GGAAGAAGATCGAAGGGCGT 59.824 55.000 0.00 0.00 41.80 5.68
991 1060 2.202756 AAGATCGAAGGGCGTCGC 60.203 61.111 9.22 9.22 40.88 5.19
1097 1180 5.096443 AGTTGCATTTTGTTTTTGGAGGA 57.904 34.783 0.00 0.00 0.00 3.71
1116 1199 0.971386 ATACGAGGACGGTGTGGTTT 59.029 50.000 0.00 0.00 44.46 3.27
1131 1219 6.745450 CGGTGTGGTTTATCAATTGTTGTATC 59.255 38.462 5.13 0.00 0.00 2.24
1133 1221 7.302524 GTGTGGTTTATCAATTGTTGTATCGT 58.697 34.615 5.13 0.00 0.00 3.73
1390 1478 1.441515 CACGTCGTCCAGGTACACG 60.442 63.158 0.00 0.00 37.36 4.49
1398 1487 0.830444 TCCAGGTACACGCCACTCTT 60.830 55.000 0.00 0.00 0.00 2.85
1427 1516 3.575506 TCCATGGCTGGATTGTGTC 57.424 52.632 6.96 0.00 46.95 3.67
1441 1530 1.813753 GTGTCGTGTGTGTGGTGCT 60.814 57.895 0.00 0.00 0.00 4.40
1442 1531 1.078778 TGTCGTGTGTGTGGTGCTT 60.079 52.632 0.00 0.00 0.00 3.91
1476 1569 0.825010 GATGGATGGGTGGACATGGC 60.825 60.000 0.00 0.00 0.00 4.40
1477 1570 1.291459 ATGGATGGGTGGACATGGCT 61.291 55.000 0.00 0.00 0.00 4.75
1480 1573 2.916527 GATGGGTGGACATGGCTGGG 62.917 65.000 0.00 0.00 0.00 4.45
1492 1585 2.203070 GCTGGGGTGCAGATACGG 60.203 66.667 0.00 0.00 0.00 4.02
1645 1738 2.203153 GGCGTCACCAACACCTGT 60.203 61.111 0.00 0.00 38.86 4.00
1651 1744 2.806745 CGTCACCAACACCTGTGAGATT 60.807 50.000 3.94 0.00 41.82 2.40
1735 1832 5.418676 CCACTCTTTCTCATCTCTTCTTCC 58.581 45.833 0.00 0.00 0.00 3.46
1759 1856 2.037251 CTCCGTCTCTTCCAAGTTCCAA 59.963 50.000 0.00 0.00 0.00 3.53
1768 1865 4.165372 TCTTCCAAGTTCCAACCTACAGTT 59.835 41.667 0.00 0.00 40.16 3.16
1776 1873 2.304761 TCCAACCTACAGTTCCATGTCC 59.695 50.000 0.00 0.00 36.18 4.02
1779 1876 0.537188 CCTACAGTTCCATGTCCGCT 59.463 55.000 0.00 0.00 34.56 5.52
1782 1879 0.249398 ACAGTTCCATGTCCGCTACC 59.751 55.000 0.00 0.00 0.00 3.18
1783 1880 0.462047 CAGTTCCATGTCCGCTACCC 60.462 60.000 0.00 0.00 0.00 3.69
1834 1984 8.181904 ACCAGAATCTCTCTATCTGAAATCTC 57.818 38.462 3.70 0.00 42.48 2.75
1858 2008 0.034670 AGGAAGCTTCTGGTCATGCC 60.035 55.000 25.05 6.67 37.90 4.40
1965 2122 1.421093 GGCGCGGGTTTAGTTTACG 59.579 57.895 8.83 0.00 0.00 3.18
2067 2224 1.200519 AAAGCAGCCGTATCCTACCA 58.799 50.000 0.00 0.00 0.00 3.25
2069 2226 1.299926 GCAGCCGTATCCTACCACG 60.300 63.158 0.00 0.00 37.89 4.94
2140 2297 4.267690 CAGCATCAACTCGCGAATAAGTTA 59.732 41.667 11.33 1.02 34.05 2.24
2141 2298 4.868171 AGCATCAACTCGCGAATAAGTTAA 59.132 37.500 11.33 0.00 34.05 2.01
2202 2362 1.827789 GCCAAGCAAGTGACCACCA 60.828 57.895 0.00 0.00 0.00 4.17
2250 2410 6.699642 GCACTAAGCCTGAGAATACTTCTTAG 59.300 42.308 0.00 0.00 41.58 2.18
2253 2413 9.127277 ACTAAGCCTGAGAATACTTCTTAGTAG 57.873 37.037 9.25 5.93 41.37 2.57
2258 2418 9.558396 GCCTGAGAATACTTCTTAGTAGTACTA 57.442 37.037 5.90 5.90 40.64 1.82
2330 2494 7.548780 ACATTTTTGTCTTGCTTTTCTTGCTTA 59.451 29.630 0.00 0.00 0.00 3.09
2331 2495 8.553696 CATTTTTGTCTTGCTTTTCTTGCTTAT 58.446 29.630 0.00 0.00 0.00 1.73
2375 2542 0.185901 ACTGCTTTGCCTTGGGAGAA 59.814 50.000 0.00 0.00 0.00 2.87
2430 2597 1.480205 CTTGCAAAAACAGCGACCAG 58.520 50.000 0.00 0.00 33.85 4.00
2596 2769 2.409975 CGGCTTGACGGAGAAACTAAA 58.590 47.619 0.00 0.00 0.00 1.85
2616 2789 0.466922 GCCCTGTCAAGCATAGCCAT 60.467 55.000 0.00 0.00 0.00 4.40
2617 2790 1.315690 CCCTGTCAAGCATAGCCATG 58.684 55.000 0.00 0.00 35.07 3.66
2628 2801 3.088194 CATAGCCATGCATTGTGAACC 57.912 47.619 0.00 0.00 0.00 3.62
2629 2802 2.212812 TAGCCATGCATTGTGAACCA 57.787 45.000 0.00 0.00 0.00 3.67
2630 2803 0.604578 AGCCATGCATTGTGAACCAC 59.395 50.000 0.00 0.00 34.56 4.16
2631 2804 0.317799 GCCATGCATTGTGAACCACA 59.682 50.000 0.00 0.00 43.02 4.17
2632 2805 1.936203 GCCATGCATTGTGAACCACAC 60.936 52.381 0.00 0.00 44.47 3.82
2646 2819 2.762745 ACCACACGTCATTAGGTTCAC 58.237 47.619 0.00 0.00 0.00 3.18
2658 2831 5.427157 TCATTAGGTTCACTATAACTGCCCA 59.573 40.000 0.00 0.00 0.00 5.36
2659 2832 5.765576 TTAGGTTCACTATAACTGCCCAA 57.234 39.130 0.00 0.00 0.00 4.12
2666 2840 6.061022 TCACTATAACTGCCCAAGATCAAA 57.939 37.500 0.00 0.00 0.00 2.69
2687 2861 4.010667 ACTTGCACGGTAAGGTTATTCA 57.989 40.909 0.00 0.00 0.00 2.57
2718 2892 5.964958 TTTCTCCTGCTACCAATCTTTTG 57.035 39.130 0.00 0.00 0.00 2.44
2806 2980 2.934570 AACTTCGGGGCTCGCGTTA 61.935 57.895 5.77 0.00 40.60 3.18
2827 3001 6.485393 GTTACCGTTAAATGCGCCTAAAATA 58.515 36.000 4.18 0.00 0.00 1.40
2841 3015 5.582689 CCTAAAATAGGCCCACTTTTCTG 57.417 43.478 0.00 0.84 39.48 3.02
2897 3071 1.869774 TTCCATCGATCCGAGCAATG 58.130 50.000 0.00 0.00 39.91 2.82
2926 3100 3.772387 TGGACCAGTATGAATTTTGCCA 58.228 40.909 0.00 0.00 39.69 4.92
2935 3109 7.820872 CCAGTATGAATTTTGCCAGAAAAGATT 59.179 33.333 0.00 0.00 39.69 2.40
2937 3111 9.860898 AGTATGAATTTTGCCAGAAAAGATTAC 57.139 29.630 0.00 0.00 0.00 1.89
2940 3114 7.495901 TGAATTTTGCCAGAAAAGATTACACA 58.504 30.769 0.00 0.00 0.00 3.72
2941 3115 8.149647 TGAATTTTGCCAGAAAAGATTACACAT 58.850 29.630 0.00 0.00 0.00 3.21
2943 3117 7.945033 TTTTGCCAGAAAAGATTACACATTC 57.055 32.000 0.00 0.00 0.00 2.67
2944 3118 6.647334 TTGCCAGAAAAGATTACACATTCA 57.353 33.333 0.00 0.00 0.00 2.57
2946 3120 7.230849 TGCCAGAAAAGATTACACATTCATT 57.769 32.000 0.00 0.00 0.00 2.57
2947 3121 7.092079 TGCCAGAAAAGATTACACATTCATTG 58.908 34.615 0.00 0.00 0.00 2.82
2950 3124 9.480053 CCAGAAAAGATTACACATTCATTGTTT 57.520 29.630 0.00 0.00 36.00 2.83
2993 3171 2.696989 AATTGCCTTTTATGCTGGCC 57.303 45.000 0.00 0.00 45.56 5.36
2998 3176 0.451783 CCTTTTATGCTGGCCGTGTC 59.548 55.000 0.00 0.00 0.00 3.67
2999 3177 0.451783 CTTTTATGCTGGCCGTGTCC 59.548 55.000 0.00 0.00 0.00 4.02
3014 3192 0.683504 TGTCCGCCCCTCTCTTCTAC 60.684 60.000 0.00 0.00 0.00 2.59
3015 3193 0.396001 GTCCGCCCCTCTCTTCTACT 60.396 60.000 0.00 0.00 0.00 2.57
3018 3196 2.164338 CCGCCCCTCTCTTCTACTATC 58.836 57.143 0.00 0.00 0.00 2.08
3042 3222 7.425606 TCATCTAAAAAGAACTTGTTCCTTGC 58.574 34.615 9.58 0.00 0.00 4.01
3054 3234 5.815740 ACTTGTTCCTTGCCTATATGTAACG 59.184 40.000 0.00 0.00 0.00 3.18
3060 3240 5.009710 TCCTTGCCTATATGTAACGAGTCAG 59.990 44.000 0.00 0.00 0.00 3.51
3061 3241 5.009710 CCTTGCCTATATGTAACGAGTCAGA 59.990 44.000 0.00 0.00 0.00 3.27
3062 3242 5.690997 TGCCTATATGTAACGAGTCAGAG 57.309 43.478 0.00 0.00 0.00 3.35
3064 3244 4.519730 GCCTATATGTAACGAGTCAGAGGT 59.480 45.833 0.00 0.00 0.00 3.85
3065 3245 5.704515 GCCTATATGTAACGAGTCAGAGGTA 59.295 44.000 0.00 0.00 0.00 3.08
3067 3247 7.573469 GCCTATATGTAACGAGTCAGAGGTAAG 60.573 44.444 0.00 0.00 0.00 2.34
3068 3248 7.660617 CCTATATGTAACGAGTCAGAGGTAAGA 59.339 40.741 0.00 0.00 0.00 2.10
3069 3249 7.876936 ATATGTAACGAGTCAGAGGTAAGAA 57.123 36.000 0.00 0.00 0.00 2.52
3150 3330 8.901472 TTAGTATATATGATGAGAACTGCCCT 57.099 34.615 0.00 0.00 0.00 5.19
3279 3459 4.440663 GCTTTTGTTTGCTCTTTCAGAGGT 60.441 41.667 3.00 0.00 42.54 3.85
3341 3822 1.270893 GCTTCGGAAAAGAGAGGGTGT 60.271 52.381 0.00 0.00 0.00 4.16
3470 3960 6.647334 TGATGCAAATTTAGGTGTTCTTGA 57.353 33.333 0.00 0.00 0.00 3.02
3499 3996 6.315642 GCAAGTTTACCATTACTAGGGAGAAC 59.684 42.308 0.00 0.00 0.00 3.01
3549 4046 1.939974 TGCCGTTCATGTCTATCTGC 58.060 50.000 0.00 0.00 0.00 4.26
3554 4051 4.109766 CCGTTCATGTCTATCTGCGTTAA 58.890 43.478 0.00 0.00 0.00 2.01
3676 4177 4.897140 TCACATCATCTTCACACATGTCA 58.103 39.130 0.00 0.00 0.00 3.58
3691 4196 5.131067 CACATGTCATCAATGGAGAGGATT 58.869 41.667 0.00 0.00 30.40 3.01
3711 4216 9.400638 GAGGATTACTAGTTAATGTTCATCTCG 57.599 37.037 0.00 0.00 29.85 4.04
3762 4274 3.037549 AGTTGCCTTGGTCCAAATTGAA 58.962 40.909 5.64 0.00 0.00 2.69
3793 4306 0.620700 AGGGGCAGGTAGGGTAACTG 60.621 60.000 0.00 0.00 46.24 3.16
3865 4381 1.271379 GGCGATGATGTATGTACCCGA 59.729 52.381 0.00 0.00 0.00 5.14
4008 4524 6.438259 TGGAAAATTCAAAACACTGTCGTA 57.562 33.333 0.00 0.00 0.00 3.43
4039 4555 3.531538 ACTACATTGATAAGTGCCGTGG 58.468 45.455 0.00 0.00 0.00 4.94
4068 4584 6.763355 ACTTGTAGTCACTTCATTCACTGAT 58.237 36.000 0.00 0.00 32.72 2.90
4138 4656 1.683441 GGACCCGACCCTGACATTT 59.317 57.895 0.00 0.00 0.00 2.32
4192 4710 1.726533 GAGAAGGGTACGGCTCCGAG 61.727 65.000 15.95 0.00 42.83 4.63
4312 4830 3.632080 AACACCCGGCCGATGACA 61.632 61.111 30.73 0.00 0.00 3.58
4471 4994 2.671963 GTCGGTTGGGACTTGGGC 60.672 66.667 0.00 0.00 34.09 5.36
4605 5131 7.933577 AGGTGGAGTGTGTGTAAATATGATATG 59.066 37.037 0.00 0.00 0.00 1.78
4787 5323 9.249457 GTCGAGATTGATATGTGAAAAGTGATA 57.751 33.333 0.00 0.00 0.00 2.15
4885 5421 4.214758 GCGGTGTGTAGTTAATTCAAGGTT 59.785 41.667 0.00 0.00 0.00 3.50
4886 5422 5.616204 GCGGTGTGTAGTTAATTCAAGGTTC 60.616 44.000 0.00 0.00 0.00 3.62
4889 5425 4.453136 TGTGTAGTTAATTCAAGGTTCGGC 59.547 41.667 0.00 0.00 0.00 5.54
4966 5502 6.488715 AGAAAGATAAGGACTTTGCCTCAAT 58.511 36.000 0.00 0.00 37.26 2.57
4981 5526 3.011818 CCTCAATCATGTGTTGCTGCTA 58.988 45.455 0.00 0.00 0.00 3.49
4998 5543 0.848942 CTACTGCTGCGACTATTGCG 59.151 55.000 0.00 0.00 34.24 4.85
5032 5577 6.757478 TGTACGTTTCAGTAATGTCTGTTTCA 59.243 34.615 0.00 0.00 37.22 2.69
5079 5682 4.210120 GCTTTCTCCTGATTATGTACTGCG 59.790 45.833 0.00 0.00 0.00 5.18
5088 5691 1.100510 TATGTACTGCGAGGCGTTCT 58.899 50.000 0.00 0.00 0.00 3.01
5098 5701 2.135933 CGAGGCGTTCTTTTCTGAAGT 58.864 47.619 0.00 0.00 0.00 3.01
5147 5751 3.133183 TGCTGGTACTATGACGGCAATTA 59.867 43.478 0.00 0.00 0.00 1.40
5260 5864 1.803922 CGGTATCGCGCAAGACACA 60.804 57.895 8.75 0.00 43.02 3.72
5276 5880 7.119360 GCAAGACACAGCAGAAAATTTAAAAC 58.881 34.615 0.00 0.00 0.00 2.43
5279 5907 6.691388 AGACACAGCAGAAAATTTAAAACGAC 59.309 34.615 0.00 0.00 0.00 4.34
5297 5925 2.348218 CGACTTTCGCGCTACAAAGTTT 60.348 45.455 22.29 7.82 41.83 2.66
5299 5927 4.433805 CGACTTTCGCGCTACAAAGTTTAT 60.434 41.667 22.29 7.01 41.83 1.40
5307 5935 4.153475 GCGCTACAAAGTTTATCACTGGAA 59.847 41.667 0.00 0.00 35.12 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.158534 TCTGCAAAACCCTAAGAGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
26 27 1.004560 CTCAACCGCTCCTCTGCAA 60.005 57.895 0.00 0.00 0.00 4.08
27 28 2.659016 CTCAACCGCTCCTCTGCA 59.341 61.111 0.00 0.00 0.00 4.41
28 29 2.817396 GCTCAACCGCTCCTCTGC 60.817 66.667 0.00 0.00 0.00 4.26
29 30 0.603707 TTTGCTCAACCGCTCCTCTG 60.604 55.000 0.00 0.00 0.00 3.35
36 37 0.529555 TTTGCCTTTTGCTCAACCGC 60.530 50.000 0.00 0.00 42.00 5.68
52 53 1.841342 GTGTGTTACGCCGTTGTTTTG 59.159 47.619 0.00 0.00 0.00 2.44
57 58 2.392933 AAATGTGTGTTACGCCGTTG 57.607 45.000 0.00 0.00 0.00 4.10
72 73 3.488047 GCCACGATCATCCACAGAAAATG 60.488 47.826 0.00 0.00 0.00 2.32
74 75 2.083774 GCCACGATCATCCACAGAAAA 58.916 47.619 0.00 0.00 0.00 2.29
100 101 1.110518 TCTACCAGTGTGACGGTGCA 61.111 55.000 0.00 0.00 36.69 4.57
105 106 1.154016 CGGCTCTACCAGTGTGACG 60.154 63.158 0.00 0.00 39.03 4.35
106 107 1.215647 CCGGCTCTACCAGTGTGAC 59.784 63.158 0.00 0.00 39.03 3.67
113 114 2.363795 CCTCCACCGGCTCTACCA 60.364 66.667 0.00 0.00 39.03 3.25
116 117 0.395862 CTTCTCCTCCACCGGCTCTA 60.396 60.000 0.00 0.00 0.00 2.43
123 124 1.201429 TGGCTTCCTTCTCCTCCACC 61.201 60.000 0.00 0.00 0.00 4.61
124 125 0.035915 GTGGCTTCCTTCTCCTCCAC 60.036 60.000 0.00 0.00 37.42 4.02
157 158 5.179881 ACCATTCCCCTCTAAACCCTATA 57.820 43.478 0.00 0.00 0.00 1.31
158 159 4.035967 ACCATTCCCCTCTAAACCCTAT 57.964 45.455 0.00 0.00 0.00 2.57
204 207 1.941975 TCATGGACAATATGCGCACTG 59.058 47.619 14.90 13.63 0.00 3.66
214 217 5.070180 CCTCACTCAGATAGTCATGGACAAT 59.930 44.000 0.00 0.00 35.76 2.71
216 219 3.956848 CCTCACTCAGATAGTCATGGACA 59.043 47.826 0.00 0.00 35.76 4.02
217 220 4.211125 TCCTCACTCAGATAGTCATGGAC 58.789 47.826 0.00 0.00 35.76 4.02
219 222 7.479352 AATATCCTCACTCAGATAGTCATGG 57.521 40.000 0.00 0.00 35.76 3.66
295 301 1.060553 CATGCTTTCACGTAATCGCGT 59.939 47.619 5.77 0.00 46.88 6.01
321 327 1.076332 AATCGTCTTTTTCCGCTCCG 58.924 50.000 0.00 0.00 0.00 4.63
702 762 2.750637 GAGGACGAGGCGGACTGA 60.751 66.667 0.00 0.00 0.00 3.41
819 879 1.795170 GCAGAGGAAAAAGGCACGCA 61.795 55.000 0.00 0.00 0.00 5.24
870 930 4.470664 AGAAGAGAGAATCAATCTGCCAGT 59.529 41.667 0.00 0.00 38.96 4.00
896 959 0.664761 ACCAAGAAGACGACGACGAA 59.335 50.000 15.32 0.00 42.66 3.85
960 1029 1.550524 CGATCTTCTTCCAGGGTCACA 59.449 52.381 0.00 0.00 0.00 3.58
988 1057 0.033642 TTTACCATGTCACCACGCGA 59.966 50.000 15.93 0.00 0.00 5.87
991 1060 3.399330 AGAACTTTACCATGTCACCACG 58.601 45.455 0.00 0.00 0.00 4.94
1097 1180 0.971386 AAACCACACCGTCCTCGTAT 59.029 50.000 0.00 0.00 35.01 3.06
1116 1199 6.091577 GGACACACACGATACAACAATTGATA 59.908 38.462 13.59 1.94 0.00 2.15
1131 1219 2.355837 CCACGAGGGACACACACG 60.356 66.667 0.00 0.00 40.01 4.49
1133 1221 0.541998 ATCTCCACGAGGGACACACA 60.542 55.000 0.00 0.00 42.15 3.72
1300 1388 2.046892 GCAGCCGAGGCAGAAGAA 60.047 61.111 17.18 0.00 44.88 2.52
1335 1423 2.888863 ACGCAGTAGGAGCAGAGC 59.111 61.111 0.00 0.00 41.94 4.09
1390 1478 4.016444 TGGATGATTTGGTTAAGAGTGGC 58.984 43.478 0.00 0.00 0.00 5.01
1427 1516 0.523125 CACAAAGCACCACACACACG 60.523 55.000 0.00 0.00 0.00 4.49
1441 1530 6.127281 CCCATCCATCAGAATTCATTCACAAA 60.127 38.462 8.44 0.00 39.23 2.83
1442 1531 5.361571 CCCATCCATCAGAATTCATTCACAA 59.638 40.000 8.44 0.00 39.23 3.33
1476 1569 2.203070 GCCGTATCTGCACCCCAG 60.203 66.667 0.00 0.00 43.17 4.45
1477 1570 4.155733 CGCCGTATCTGCACCCCA 62.156 66.667 0.00 0.00 0.00 4.96
1480 1573 2.514013 CGAACGCCGTATCTGCACC 61.514 63.158 0.00 0.00 0.00 5.01
1492 1585 1.484232 GTTGTGGTACGACGAACGC 59.516 57.895 0.00 0.00 46.94 4.84
1707 1800 4.865905 AGAGATGAGAAAGAGTGGCTAGA 58.134 43.478 0.00 0.00 0.00 2.43
1735 1832 1.551452 ACTTGGAAGAGACGGAGGAG 58.449 55.000 0.00 0.00 0.00 3.69
1759 1856 0.249398 GCGGACATGGAACTGTAGGT 59.751 55.000 0.00 0.00 0.00 3.08
1768 1865 1.760875 GAGGGGTAGCGGACATGGA 60.761 63.158 0.00 0.00 0.00 3.41
1776 1873 0.976073 TTTCAGGGAGAGGGGTAGCG 60.976 60.000 0.00 0.00 0.00 4.26
1779 1876 1.132332 TGGTTTTCAGGGAGAGGGGTA 60.132 52.381 0.00 0.00 0.00 3.69
1782 1879 2.310052 AGAATGGTTTTCAGGGAGAGGG 59.690 50.000 0.00 0.00 0.00 4.30
1783 1880 3.728385 AGAATGGTTTTCAGGGAGAGG 57.272 47.619 0.00 0.00 0.00 3.69
1834 1984 1.898472 TGACCAGAAGCTTCCTCAGAG 59.102 52.381 22.81 7.96 0.00 3.35
1875 2025 3.058160 ACTGCATTGCACTCGGGC 61.058 61.111 7.38 0.00 33.79 6.13
1949 2099 0.094046 CTGCGTAAACTAAACCCGCG 59.906 55.000 0.00 0.00 46.77 6.46
1965 2122 4.341783 AGCTGTGCCACTCCCTGC 62.342 66.667 0.00 0.00 0.00 4.85
2067 2224 0.834687 TAGAGCACACCCCTTTCCGT 60.835 55.000 0.00 0.00 0.00 4.69
2069 2226 0.984995 ACTAGAGCACACCCCTTTCC 59.015 55.000 0.00 0.00 0.00 3.13
2140 2297 0.251787 GCAACCCCCTGGAGAATGTT 60.252 55.000 0.00 0.00 34.81 2.71
2141 2298 1.384191 GCAACCCCCTGGAGAATGT 59.616 57.895 0.00 0.00 34.81 2.71
2259 2419 9.998106 CACTAGGGTGCTACTAATACAAAATAT 57.002 33.333 0.00 0.00 36.61 1.28
2330 2494 1.407989 GCTTAGCTTGGCAGAGGACAT 60.408 52.381 0.00 0.00 0.00 3.06
2331 2495 0.036010 GCTTAGCTTGGCAGAGGACA 60.036 55.000 0.00 0.00 0.00 4.02
2375 2542 1.912043 CCTTCACTCCATGTCCTCCTT 59.088 52.381 0.00 0.00 0.00 3.36
2430 2597 2.403252 TAGCTTAGCTTGGCTTGGTC 57.597 50.000 13.44 0.00 40.44 4.02
2481 2653 1.985159 TGTGTGGTCCAAGCTAATCCT 59.015 47.619 0.00 0.00 0.00 3.24
2596 2769 1.225704 GGCTATGCTTGACAGGGCT 59.774 57.895 4.56 0.00 32.43 5.19
2616 2789 0.660488 GACGTGTGGTTCACAATGCA 59.340 50.000 0.00 0.00 46.28 3.96
2617 2790 0.660488 TGACGTGTGGTTCACAATGC 59.340 50.000 0.00 0.00 46.28 3.56
2620 2793 3.135225 CCTAATGACGTGTGGTTCACAA 58.865 45.455 0.00 0.00 46.28 3.33
2621 2794 2.103432 ACCTAATGACGTGTGGTTCACA 59.897 45.455 0.00 0.00 46.44 3.58
2622 2795 2.762745 ACCTAATGACGTGTGGTTCAC 58.237 47.619 0.00 0.00 43.03 3.18
2623 2796 3.478857 AACCTAATGACGTGTGGTTCA 57.521 42.857 0.00 0.00 36.40 3.18
2625 2798 3.135994 GTGAACCTAATGACGTGTGGTT 58.864 45.455 0.00 0.00 42.85 3.67
2626 2799 2.367567 AGTGAACCTAATGACGTGTGGT 59.632 45.455 0.00 0.00 0.00 4.16
2627 2800 3.040147 AGTGAACCTAATGACGTGTGG 57.960 47.619 0.00 0.00 0.00 4.17
2628 2801 7.009265 CAGTTATAGTGAACCTAATGACGTGTG 59.991 40.741 0.00 0.00 0.00 3.82
2629 2802 7.033791 CAGTTATAGTGAACCTAATGACGTGT 58.966 38.462 0.00 0.00 0.00 4.49
2630 2803 6.019801 GCAGTTATAGTGAACCTAATGACGTG 60.020 42.308 0.00 0.00 0.00 4.49
2631 2804 6.040878 GCAGTTATAGTGAACCTAATGACGT 58.959 40.000 0.00 0.00 0.00 4.34
2632 2805 5.462398 GGCAGTTATAGTGAACCTAATGACG 59.538 44.000 0.00 0.00 0.00 4.35
2646 2819 6.678900 GCAAGTTTGATCTTGGGCAGTTATAG 60.679 42.308 8.22 0.00 43.26 1.31
2658 2831 3.502211 CCTTACCGTGCAAGTTTGATCTT 59.498 43.478 0.00 0.00 0.00 2.40
2659 2832 3.074412 CCTTACCGTGCAAGTTTGATCT 58.926 45.455 0.00 0.00 0.00 2.75
2666 2840 4.000988 CTGAATAACCTTACCGTGCAAGT 58.999 43.478 0.00 0.00 0.00 3.16
2687 2861 4.348168 TGGTAGCAGGAGAAAAGAAAGACT 59.652 41.667 0.00 0.00 0.00 3.24
2718 2892 7.987750 AGATTAGAAGAAGAAAACTTGTCCC 57.012 36.000 0.00 0.00 0.00 4.46
2720 2894 9.057089 TCCAAGATTAGAAGAAGAAAACTTGTC 57.943 33.333 0.00 0.00 33.02 3.18
2722 2896 9.061435 AGTCCAAGATTAGAAGAAGAAAACTTG 57.939 33.333 0.00 0.00 34.15 3.16
2728 2902 6.114187 TGCAGTCCAAGATTAGAAGAAGAA 57.886 37.500 0.00 0.00 0.00 2.52
2729 2903 5.745312 TGCAGTCCAAGATTAGAAGAAGA 57.255 39.130 0.00 0.00 0.00 2.87
2730 2904 6.038050 GGATTGCAGTCCAAGATTAGAAGAAG 59.962 42.308 22.46 0.00 38.20 2.85
2806 2980 4.035909 CCTATTTTAGGCGCATTTAACGGT 59.964 41.667 10.83 0.00 39.48 4.83
2827 3001 4.018415 ACATACATACAGAAAAGTGGGCCT 60.018 41.667 4.53 0.00 0.00 5.19
2830 3004 6.655003 ACAAGACATACATACAGAAAAGTGGG 59.345 38.462 0.00 0.00 0.00 4.61
2837 3011 7.265673 GGCTAGAACAAGACATACATACAGAA 58.734 38.462 0.00 0.00 0.00 3.02
2841 3015 4.982916 CCGGCTAGAACAAGACATACATAC 59.017 45.833 0.00 0.00 0.00 2.39
2897 3071 2.398588 TCATACTGGTCCATGTCCTCC 58.601 52.381 0.00 0.00 0.00 4.30
2926 3100 9.480053 CCAAACAATGAATGTGTAATCTTTTCT 57.520 29.630 0.00 0.00 42.99 2.52
2935 3109 3.894427 AGTGGCCAAACAATGAATGTGTA 59.106 39.130 7.24 0.00 42.99 2.90
2937 3111 3.389925 AGTGGCCAAACAATGAATGTG 57.610 42.857 7.24 0.00 42.99 3.21
2940 3114 4.686191 TTGAAGTGGCCAAACAATGAAT 57.314 36.364 7.24 0.00 0.00 2.57
2941 3115 4.478206 TTTGAAGTGGCCAAACAATGAA 57.522 36.364 7.24 0.00 0.00 2.57
2950 3124 2.158385 AGGTTATGGTTTGAAGTGGCCA 60.158 45.455 0.00 0.00 35.28 5.36
2963 3141 6.258507 GCATAAAAGGCAATTTCAGGTTATGG 59.741 38.462 0.00 0.00 0.00 2.74
2993 3171 3.358076 GAAGAGAGGGGCGGACACG 62.358 68.421 0.00 0.00 44.63 4.49
2998 3176 2.164338 GATAGTAGAAGAGAGGGGCGG 58.836 57.143 0.00 0.00 0.00 6.13
2999 3177 2.865079 TGATAGTAGAAGAGAGGGGCG 58.135 52.381 0.00 0.00 0.00 6.13
3018 3196 6.642540 GGCAAGGAACAAGTTCTTTTTAGATG 59.357 38.462 12.22 1.38 36.87 2.90
3028 3208 7.465513 CGTTACATATAGGCAAGGAACAAGTTC 60.466 40.741 4.39 4.39 38.80 3.01
3042 3222 7.660617 TCTTACCTCTGACTCGTTACATATAGG 59.339 40.741 0.00 0.00 0.00 2.57
3150 3330 1.352083 AGCTTCAACTCCTAGTGCCA 58.648 50.000 0.00 0.00 0.00 4.92
3279 3459 4.022416 ACTTGGCAAAAGATAATGCGTTCA 60.022 37.500 0.00 0.00 43.47 3.18
3341 3822 5.730550 AGTCAACTTTATCTGGATAACGCA 58.269 37.500 2.90 0.00 33.40 5.24
3470 3960 7.179269 TCCCTAGTAATGGTAAACTTGCAAAT 58.821 34.615 0.00 0.00 0.00 2.32
3482 3972 4.246712 TCTCGTTCTCCCTAGTAATGGT 57.753 45.455 0.00 0.00 0.00 3.55
3499 3996 7.261325 TCAAAAGAGGTATCAATCTCTTCTCG 58.739 38.462 1.59 0.00 46.13 4.04
3531 4028 0.855349 CGCAGATAGACATGAACGGC 59.145 55.000 0.00 0.00 0.00 5.68
3643 4143 8.361889 TGTGAAGATGATGTGATGAATTGTTTT 58.638 29.630 0.00 0.00 0.00 2.43
3647 4147 6.848451 TGTGTGAAGATGATGTGATGAATTG 58.152 36.000 0.00 0.00 0.00 2.32
3691 4196 8.301720 ACACAACGAGATGAACATTAACTAGTA 58.698 33.333 0.00 0.00 0.00 1.82
3711 4216 2.356796 GCAATCGCACGCACACAAC 61.357 57.895 0.00 0.00 38.36 3.32
3762 4274 1.073923 CCTGCCCCTAGTGACACTTTT 59.926 52.381 14.50 0.00 0.00 2.27
3793 4306 1.086696 TTTATGGAGCTTGCACGAGC 58.913 50.000 1.95 1.95 43.02 5.03
3796 4309 5.484173 TCTAAATTTATGGAGCTTGCACG 57.516 39.130 0.00 0.00 0.00 5.34
3847 4363 2.094700 CCCTCGGGTACATACATCATCG 60.095 54.545 0.00 0.00 0.00 3.84
3865 4381 2.158871 TCGTTGCACTTAGTGAAACCCT 60.159 45.455 25.47 0.00 46.24 4.34
4008 4524 6.203530 CACTTATCAATGTAGTCCGAATGCAT 59.796 38.462 0.00 0.00 0.00 3.96
4039 4555 8.827677 AGTGAATGAAGTGACTACAAGTAAAAC 58.172 33.333 0.00 0.00 0.00 2.43
4068 4584 1.666553 CGCCAGGAACAAGTACGCA 60.667 57.895 0.00 0.00 0.00 5.24
4150 4668 1.153549 GGAGTCCTGGCTACGCTTG 60.154 63.158 0.41 0.00 0.00 4.01
4192 4710 2.126031 GGGCTGAACGAGTCGTCC 60.126 66.667 20.18 15.29 39.99 4.79
4259 4777 3.681835 GTCAGACCACCGGACGCT 61.682 66.667 9.46 0.00 30.77 5.07
4471 4994 3.766591 ACTGGATCACTTCACTACTCAGG 59.233 47.826 0.00 0.00 0.00 3.86
4667 5201 7.523293 TCTTCACCTTATTTTCTGCATGAAA 57.477 32.000 0.00 7.09 42.33 2.69
4787 5323 8.777413 CAAACCGAGACATATACATGATGATTT 58.223 33.333 0.00 0.00 35.96 2.17
4885 5421 2.851263 ATGTTCCTGTAAGTTGCCGA 57.149 45.000 0.00 0.00 0.00 5.54
4886 5422 6.671614 TTATTATGTTCCTGTAAGTTGCCG 57.328 37.500 0.00 0.00 0.00 5.69
4966 5502 1.159285 GCAGTAGCAGCAACACATGA 58.841 50.000 0.00 0.00 41.58 3.07
4981 5526 3.786101 CGCAATAGTCGCAGCAGT 58.214 55.556 0.00 0.00 0.00 4.40
4998 5543 2.993899 ACTGAAACGTACATGTAGCTGC 59.006 45.455 5.62 0.00 0.00 5.25
4999 5544 6.310467 ACATTACTGAAACGTACATGTAGCTG 59.690 38.462 5.62 2.00 0.00 4.24
5008 5553 7.169035 TGAAACAGACATTACTGAAACGTAC 57.831 36.000 0.00 0.00 40.63 3.67
5032 5577 5.447683 CGCCAGCGCATAATTCACATATTAT 60.448 40.000 11.47 0.00 32.30 1.28
5038 5583 1.720894 CGCCAGCGCATAATTCACA 59.279 52.632 11.47 0.00 34.03 3.58
5039 5584 4.595629 CGCCAGCGCATAATTCAC 57.404 55.556 11.47 0.00 34.03 3.18
5079 5682 4.553756 AAACTTCAGAAAAGAACGCCTC 57.446 40.909 0.00 0.00 0.00 4.70
5088 5691 7.403312 TCTGATGGTTCAAAACTTCAGAAAA 57.597 32.000 18.70 2.95 42.25 2.29
5098 5701 4.922206 AGTGGCTATCTGATGGTTCAAAA 58.078 39.130 0.00 0.00 0.00 2.44
5147 5751 6.372937 GCTCTTACAACTTTAGAGGAAGCAAT 59.627 38.462 0.00 0.00 36.70 3.56
5223 5827 3.190535 ACCGCAAATTCGTTTTAGAGCAT 59.809 39.130 0.00 0.00 0.00 3.79
5250 5854 2.693797 ATTTTCTGCTGTGTCTTGCG 57.306 45.000 0.00 0.00 0.00 4.85
5260 5864 6.075046 GCGAAAGTCGTTTTAAATTTTCTGCT 60.075 34.615 0.00 0.00 42.81 4.24
5276 5880 0.782384 ACTTTGTAGCGCGAAAGTCG 59.218 50.000 21.92 5.89 37.80 4.18
5279 5907 4.781528 GTGATAAACTTTGTAGCGCGAAAG 59.218 41.667 12.10 20.92 35.64 2.62


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

AutoCloner maintained by Alex Coulton.