Multiple sequence alignment - TraesCS3D01G227400

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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 TraesCS3D01G227400 chr3D 100.000 3841 0 0 1 3841 309652318 309656158 0.000000e+00 7094
1 TraesCS3D01G227400 chr3D 92.958 142 5 5 3000 3138 571057392 571057531 6.510000e-48 202
2 TraesCS3D01G227400 chr3D 92.254 142 6 5 3000 3138 5679144 5679005 3.030000e-46 196
3 TraesCS3D01G227400 chr3B 92.188 2880 83 60 73 2878 411846830 411844019 0.000000e+00 3941
4 TraesCS3D01G227400 chr3B 93.269 104 6 1 2901 3004 411843935 411843833 6.650000e-33 152
5 TraesCS3D01G227400 chr3A 93.198 2220 67 36 1 2179 429320227 429322403 0.000000e+00 3186
6 TraesCS3D01G227400 chr3A 97.853 652 9 4 2211 2857 429322402 429323053 0.000000e+00 1122
7 TraesCS3D01G227400 chr3A 95.549 674 27 1 3171 3841 125445180 125444507 0.000000e+00 1075
8 TraesCS3D01G227400 chr4D 97.037 675 17 1 3170 3841 12185767 12186441 0.000000e+00 1133
9 TraesCS3D01G227400 chr4D 96.889 675 18 1 3170 3841 505819911 505820585 0.000000e+00 1127
10 TraesCS3D01G227400 chr4D 96.296 675 22 3 3170 3841 64746845 64747519 0.000000e+00 1105
11 TraesCS3D01G227400 chr4D 90.845 142 8 5 3000 3138 357986168 357986307 6.550000e-43 185
12 TraesCS3D01G227400 chr7D 96.000 675 23 2 3170 3841 75981489 75982162 0.000000e+00 1094
13 TraesCS3D01G227400 chr4B 95.704 675 25 2 3170 3841 132857952 132857279 0.000000e+00 1083
14 TraesCS3D01G227400 chr4A 95.401 674 28 1 3171 3841 545879744 545880417 0.000000e+00 1070
15 TraesCS3D01G227400 chr5B 94.074 675 37 2 3170 3841 584324206 584324880 0.000000e+00 1022
16 TraesCS3D01G227400 chr1B 93.796 677 37 2 3170 3841 60065200 60065876 0.000000e+00 1013
17 TraesCS3D01G227400 chr1B 86.957 161 19 2 2241 2400 670202879 670203038 3.050000e-41 180
18 TraesCS3D01G227400 chr5D 92.958 142 5 5 3000 3138 24332258 24332119 6.510000e-48 202
19 TraesCS3D01G227400 chr5D 92.254 142 6 5 3000 3138 513536346 513536207 3.030000e-46 196
20 TraesCS3D01G227400 chr1D 92.958 142 5 5 3000 3138 110731652 110731513 6.510000e-48 202
21 TraesCS3D01G227400 chr1D 87.500 160 20 0 2241 2400 481603405 481603564 6.550000e-43 185
22 TraesCS3D01G227400 chr7B 90.000 140 8 4 3000 3138 67812151 67812285 3.940000e-40 176


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 TraesCS3D01G227400 chr3D 309652318 309656158 3840 False 7094.0 7094 100.0000 1 3841 1 chr3D.!!$F1 3840
1 TraesCS3D01G227400 chr3B 411843833 411846830 2997 True 2046.5 3941 92.7285 73 3004 2 chr3B.!!$R1 2931
2 TraesCS3D01G227400 chr3A 429320227 429323053 2826 False 2154.0 3186 95.5255 1 2857 2 chr3A.!!$F1 2856
3 TraesCS3D01G227400 chr3A 125444507 125445180 673 True 1075.0 1075 95.5490 3171 3841 1 chr3A.!!$R1 670
4 TraesCS3D01G227400 chr4D 12185767 12186441 674 False 1133.0 1133 97.0370 3170 3841 1 chr4D.!!$F1 671
5 TraesCS3D01G227400 chr4D 505819911 505820585 674 False 1127.0 1127 96.8890 3170 3841 1 chr4D.!!$F4 671
6 TraesCS3D01G227400 chr4D 64746845 64747519 674 False 1105.0 1105 96.2960 3170 3841 1 chr4D.!!$F2 671
7 TraesCS3D01G227400 chr7D 75981489 75982162 673 False 1094.0 1094 96.0000 3170 3841 1 chr7D.!!$F1 671
8 TraesCS3D01G227400 chr4B 132857279 132857952 673 True 1083.0 1083 95.7040 3170 3841 1 chr4B.!!$R1 671
9 TraesCS3D01G227400 chr4A 545879744 545880417 673 False 1070.0 1070 95.4010 3171 3841 1 chr4A.!!$F1 670
10 TraesCS3D01G227400 chr5B 584324206 584324880 674 False 1022.0 1022 94.0740 3170 3841 1 chr5B.!!$F1 671
11 TraesCS3D01G227400 chr1B 60065200 60065876 676 False 1013.0 1013 93.7960 3170 3841 1 chr1B.!!$F1 671

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
33 34 0.104304 AGCCATCGATAACGTGGACC 59.896 55.0 14.83 0.0 40.40 4.46 F
41 42 0.109132 ATAACGTGGACCGACCGAAC 60.109 55.0 5.19 0.0 42.61 3.95 F
470 491 0.250901 ATTTTGTGCCACGGCTCTCT 60.251 50.0 9.92 0.0 42.51 3.10 F
1849 1930 0.317938 GTCGATGCACTAGCTACCCG 60.318 60.0 0.00 0.0 42.74 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1950 1.136984 GCGGTAGTGACTGGACTCG 59.863 63.158 0.00 0.00 31.98 4.18 R
2015 2131 1.421646 AGCAAGTTCTAAGCACCAGGT 59.578 47.619 0.00 0.00 0.00 4.00 R
2196 2313 1.007721 AGGAGTATGCAGACCAGGACT 59.992 52.381 8.08 0.00 0.00 3.85 R
3020 3204 0.041839 CATTGCATTAGCGCTCGACC 60.042 55.000 16.34 1.55 46.23 4.79 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
33 34 0.104304 AGCCATCGATAACGTGGACC 59.896 55.000 14.83 0.00 40.40 4.46
41 42 0.109132 ATAACGTGGACCGACCGAAC 60.109 55.000 5.19 0.00 42.61 3.95
227 236 1.676746 CGCACTAGGCTAGACCAGTA 58.323 55.000 27.59 0.00 43.14 2.74
464 485 1.501741 CCGAGATTTTGTGCCACGG 59.498 57.895 0.00 0.00 0.00 4.94
470 491 0.250901 ATTTTGTGCCACGGCTCTCT 60.251 50.000 9.92 0.00 42.51 3.10
471 492 0.884704 TTTTGTGCCACGGCTCTCTC 60.885 55.000 9.92 0.00 42.51 3.20
472 493 1.758440 TTTGTGCCACGGCTCTCTCT 61.758 55.000 9.92 0.00 42.51 3.10
680 711 5.070313 TCCAAAGATTCCACCCTTTTTCTTG 59.930 40.000 0.00 0.00 30.89 3.02
683 714 6.650427 AAGATTCCACCCTTTTTCTTGTAC 57.350 37.500 0.00 0.00 0.00 2.90
684 715 5.953571 AGATTCCACCCTTTTTCTTGTACT 58.046 37.500 0.00 0.00 0.00 2.73
685 716 7.086685 AGATTCCACCCTTTTTCTTGTACTA 57.913 36.000 0.00 0.00 0.00 1.82
686 717 6.940867 AGATTCCACCCTTTTTCTTGTACTAC 59.059 38.462 0.00 0.00 0.00 2.73
687 718 4.976864 TCCACCCTTTTTCTTGTACTACC 58.023 43.478 0.00 0.00 0.00 3.18
688 719 4.661709 TCCACCCTTTTTCTTGTACTACCT 59.338 41.667 0.00 0.00 0.00 3.08
767 798 1.007387 GGCCCTTTTGACAAGTGCG 60.007 57.895 0.00 0.00 0.00 5.34
936 973 2.997315 TCCTCGTGCCACTCCAGG 60.997 66.667 0.00 0.00 0.00 4.45
950 987 2.490217 CAGGGTACGCGTCTGGAG 59.510 66.667 18.63 0.00 0.00 3.86
951 988 2.035312 AGGGTACGCGTCTGGAGT 59.965 61.111 18.63 0.00 0.00 3.85
1076 1117 3.305398 ACCTAGCTCACTTCGTCAAAG 57.695 47.619 0.00 0.00 41.08 2.77
1528 1596 2.736400 CGCCCGAAAAGAAGGTACGTAT 60.736 50.000 0.00 0.00 0.00 3.06
1529 1597 3.489059 CGCCCGAAAAGAAGGTACGTATA 60.489 47.826 0.00 0.00 0.00 1.47
1530 1598 4.625028 GCCCGAAAAGAAGGTACGTATAT 58.375 43.478 0.00 0.00 0.00 0.86
1531 1599 4.446719 GCCCGAAAAGAAGGTACGTATATG 59.553 45.833 0.00 0.00 0.00 1.78
1532 1600 4.446719 CCCGAAAAGAAGGTACGTATATGC 59.553 45.833 0.00 0.00 0.00 3.14
1533 1601 5.287226 CCGAAAAGAAGGTACGTATATGCT 58.713 41.667 0.00 0.00 0.00 3.79
1534 1602 5.401674 CCGAAAAGAAGGTACGTATATGCTC 59.598 44.000 0.00 0.00 0.00 4.26
1535 1603 5.401674 CGAAAAGAAGGTACGTATATGCTCC 59.598 44.000 0.00 0.00 0.00 4.70
1849 1930 0.317938 GTCGATGCACTAGCTACCCG 60.318 60.000 0.00 0.00 42.74 5.28
1861 1950 3.665675 CTACCCGGTGCACAGCCTC 62.666 68.421 20.43 0.00 0.00 4.70
1882 1991 1.401199 GAGTCCAGTCACTACCGCTAC 59.599 57.143 0.00 0.00 0.00 3.58
1886 1995 2.238144 TCCAGTCACTACCGCTACTACT 59.762 50.000 0.00 0.00 0.00 2.57
1898 2007 8.401709 ACTACCGCTACTACTTTCTGTTAATAC 58.598 37.037 0.00 0.00 0.00 1.89
1939 2048 9.823647 ATTTCTCATACGATGAAGATTTACACT 57.176 29.630 0.00 0.00 39.11 3.55
2166 2283 1.340795 ACTCCTCCGTACCAGTACCTG 60.341 57.143 2.46 0.00 32.61 4.00
2192 2309 9.949174 GTCTTAATTACTAGTAGTAGAAGCACC 57.051 37.037 11.68 4.61 31.47 5.01
2193 2310 8.834465 TCTTAATTACTAGTAGTAGAAGCACCG 58.166 37.037 11.68 0.00 31.47 4.94
2194 2311 4.889832 TTACTAGTAGTAGAAGCACCGC 57.110 45.455 11.68 0.00 31.47 5.68
2195 2312 3.002038 ACTAGTAGTAGAAGCACCGCT 57.998 47.619 11.68 0.00 42.56 5.52
2196 2313 4.148128 ACTAGTAGTAGAAGCACCGCTA 57.852 45.455 11.68 0.00 38.25 4.26
2197 2314 4.128643 ACTAGTAGTAGAAGCACCGCTAG 58.871 47.826 11.68 0.00 38.25 3.42
2238 2355 5.977129 CCTAAACTTTGTTAGCTTTGTGGTG 59.023 40.000 0.00 0.00 30.92 4.17
2417 2534 3.322466 AAGACCACCCCTGCCGAG 61.322 66.667 0.00 0.00 0.00 4.63
2516 2636 2.885861 GAGACGTCGTCCATGGCT 59.114 61.111 21.40 1.77 32.18 4.75
2525 2645 4.408821 TCCATGGCTGTGGACGGC 62.409 66.667 6.96 1.67 43.20 5.68
2870 2993 1.293498 CAGTCAACGGCTGCCTACT 59.707 57.895 17.92 11.50 0.00 2.57
2873 2996 1.067071 AGTCAACGGCTGCCTACTAAC 60.067 52.381 17.92 8.36 0.00 2.34
2878 3001 3.287867 ACGGCTGCCTACTAACTACTA 57.712 47.619 17.92 0.00 0.00 1.82
2879 3002 3.212685 ACGGCTGCCTACTAACTACTAG 58.787 50.000 17.92 0.00 0.00 2.57
2880 3003 3.212685 CGGCTGCCTACTAACTACTAGT 58.787 50.000 17.92 0.00 43.58 2.57
2881 3004 4.141620 ACGGCTGCCTACTAACTACTAGTA 60.142 45.833 17.92 1.89 41.35 1.82
2883 3006 5.128919 GGCTGCCTACTAACTACTAGTACA 58.871 45.833 12.43 0.00 41.35 2.90
2884 3007 5.591877 GGCTGCCTACTAACTACTAGTACAA 59.408 44.000 12.43 0.00 41.35 2.41
2886 3009 7.446625 GGCTGCCTACTAACTACTAGTACAATA 59.553 40.741 12.43 0.00 41.35 1.90
2887 3010 8.505625 GCTGCCTACTAACTACTAGTACAATAG 58.494 40.741 0.00 4.71 41.35 1.73
2888 3011 9.558396 CTGCCTACTAACTACTAGTACAATAGT 57.442 37.037 16.07 16.07 41.35 2.12
2951 3135 1.525995 CCACACCGAGCCAACAAGT 60.526 57.895 0.00 0.00 0.00 3.16
2970 3154 2.908073 GCTTGGCACCTGGTCGTTG 61.908 63.158 0.00 0.00 0.00 4.10
2983 3167 1.635844 GTCGTTGGATGTGCGTGATA 58.364 50.000 0.00 0.00 0.00 2.15
3008 3192 3.423154 GCGGTTGCCTCCTCAACG 61.423 66.667 0.00 0.00 45.33 4.10
3009 3193 3.423154 CGGTTGCCTCCTCAACGC 61.423 66.667 0.00 0.00 45.33 4.84
3010 3194 2.281484 GGTTGCCTCCTCAACGCA 60.281 61.111 0.00 0.00 45.33 5.24
3011 3195 1.675641 GGTTGCCTCCTCAACGCAT 60.676 57.895 0.00 0.00 45.33 4.73
3012 3196 1.503542 GTTGCCTCCTCAACGCATG 59.496 57.895 0.00 0.00 37.24 4.06
3013 3197 1.675310 TTGCCTCCTCAACGCATGG 60.675 57.895 0.00 0.00 31.44 3.66
3014 3198 2.825836 GCCTCCTCAACGCATGGG 60.826 66.667 8.44 8.44 0.00 4.00
3015 3199 2.825836 CCTCCTCAACGCATGGGC 60.826 66.667 10.10 0.00 0.00 5.36
3032 3216 4.492160 CGCCTGGTCGAGCGCTAA 62.492 66.667 11.50 0.00 46.50 3.09
3033 3217 2.107141 GCCTGGTCGAGCGCTAAT 59.893 61.111 11.50 0.00 0.00 1.73
3034 3218 2.240500 GCCTGGTCGAGCGCTAATG 61.241 63.158 11.50 3.14 0.00 1.90
3035 3219 2.240500 CCTGGTCGAGCGCTAATGC 61.241 63.158 11.50 0.33 0.00 3.56
3036 3220 1.519234 CTGGTCGAGCGCTAATGCA 60.519 57.895 11.50 0.00 39.64 3.96
3037 3221 1.079474 TGGTCGAGCGCTAATGCAA 60.079 52.632 11.50 0.00 39.64 4.08
3038 3222 0.461870 TGGTCGAGCGCTAATGCAAT 60.462 50.000 11.50 0.00 39.64 3.56
3039 3223 0.041839 GGTCGAGCGCTAATGCAATG 60.042 55.000 11.50 0.00 39.64 2.82
3040 3224 0.041839 GTCGAGCGCTAATGCAATGG 60.042 55.000 11.50 0.00 39.64 3.16
3041 3225 0.461870 TCGAGCGCTAATGCAATGGT 60.462 50.000 11.50 0.00 39.64 3.55
3042 3226 0.378257 CGAGCGCTAATGCAATGGTT 59.622 50.000 11.50 0.00 39.64 3.67
3043 3227 1.202177 CGAGCGCTAATGCAATGGTTT 60.202 47.619 11.50 0.00 39.64 3.27
3044 3228 2.731968 CGAGCGCTAATGCAATGGTTTT 60.732 45.455 11.50 0.00 39.64 2.43
3045 3229 2.854185 GAGCGCTAATGCAATGGTTTTC 59.146 45.455 11.50 0.00 39.64 2.29
3046 3230 2.493278 AGCGCTAATGCAATGGTTTTCT 59.507 40.909 8.99 0.00 39.64 2.52
3047 3231 2.854185 GCGCTAATGCAATGGTTTTCTC 59.146 45.455 0.00 0.00 39.64 2.87
3048 3232 3.100817 CGCTAATGCAATGGTTTTCTCG 58.899 45.455 0.00 0.00 39.64 4.04
3049 3233 3.438360 GCTAATGCAATGGTTTTCTCGG 58.562 45.455 0.00 0.00 39.41 4.63
3050 3234 3.119495 GCTAATGCAATGGTTTTCTCGGT 60.119 43.478 0.00 0.00 39.41 4.69
3051 3235 4.095782 GCTAATGCAATGGTTTTCTCGGTA 59.904 41.667 0.00 0.00 39.41 4.02
3052 3236 4.701956 AATGCAATGGTTTTCTCGGTAG 57.298 40.909 0.00 0.00 0.00 3.18
3053 3237 3.410631 TGCAATGGTTTTCTCGGTAGA 57.589 42.857 0.00 0.00 0.00 2.59
3054 3238 3.745799 TGCAATGGTTTTCTCGGTAGAA 58.254 40.909 0.00 0.00 40.03 2.10
3072 3256 3.432186 AAAAAGGCAGCGCTCGTT 58.568 50.000 7.13 7.97 0.00 3.85
3073 3257 2.624169 AAAAAGGCAGCGCTCGTTA 58.376 47.368 7.13 0.00 0.00 3.18
3074 3258 0.948678 AAAAAGGCAGCGCTCGTTAA 59.051 45.000 7.13 0.00 0.00 2.01
3075 3259 0.948678 AAAAGGCAGCGCTCGTTAAA 59.051 45.000 7.13 0.00 0.00 1.52
3076 3260 0.237498 AAAGGCAGCGCTCGTTAAAC 59.763 50.000 7.13 0.00 0.00 2.01
3077 3261 0.882927 AAGGCAGCGCTCGTTAAACA 60.883 50.000 7.13 0.00 0.00 2.83
3078 3262 1.132640 GGCAGCGCTCGTTAAACAG 59.867 57.895 7.13 0.00 0.00 3.16
3079 3263 1.509995 GCAGCGCTCGTTAAACAGC 60.510 57.895 7.13 0.00 0.00 4.40
3080 3264 1.901650 GCAGCGCTCGTTAAACAGCT 61.902 55.000 7.13 0.00 33.09 4.24
3081 3265 0.093705 CAGCGCTCGTTAAACAGCTC 59.906 55.000 7.13 0.00 33.09 4.09
3082 3266 0.319555 AGCGCTCGTTAAACAGCTCA 60.320 50.000 2.64 0.00 33.09 4.26
3083 3267 0.093705 GCGCTCGTTAAACAGCTCAG 59.906 55.000 0.00 0.00 33.09 3.35
3084 3268 1.698165 CGCTCGTTAAACAGCTCAGA 58.302 50.000 5.58 0.00 33.09 3.27
3085 3269 2.058798 CGCTCGTTAAACAGCTCAGAA 58.941 47.619 5.58 0.00 33.09 3.02
3086 3270 2.091277 CGCTCGTTAAACAGCTCAGAAG 59.909 50.000 5.58 0.00 33.09 2.85
3087 3271 3.318017 GCTCGTTAAACAGCTCAGAAGA 58.682 45.455 0.00 0.00 32.48 2.87
3088 3272 3.741344 GCTCGTTAAACAGCTCAGAAGAA 59.259 43.478 0.00 0.00 32.48 2.52
3089 3273 4.211374 GCTCGTTAAACAGCTCAGAAGAAA 59.789 41.667 0.00 0.00 32.48 2.52
3090 3274 5.613577 GCTCGTTAAACAGCTCAGAAGAAAG 60.614 44.000 0.00 0.00 32.48 2.62
3091 3275 5.357257 TCGTTAAACAGCTCAGAAGAAAGT 58.643 37.500 0.00 0.00 0.00 2.66
3092 3276 6.509656 TCGTTAAACAGCTCAGAAGAAAGTA 58.490 36.000 0.00 0.00 0.00 2.24
3093 3277 6.982141 TCGTTAAACAGCTCAGAAGAAAGTAA 59.018 34.615 0.00 0.00 0.00 2.24
3094 3278 7.493320 TCGTTAAACAGCTCAGAAGAAAGTAAA 59.507 33.333 0.00 0.00 0.00 2.01
3095 3279 8.120465 CGTTAAACAGCTCAGAAGAAAGTAAAA 58.880 33.333 0.00 0.00 0.00 1.52
3096 3280 9.783256 GTTAAACAGCTCAGAAGAAAGTAAAAA 57.217 29.630 0.00 0.00 0.00 1.94
3116 3300 0.808755 AAAAACTAAGCGCCCGATGG 59.191 50.000 2.29 0.00 0.00 3.51
3142 3326 4.819761 GCATCGACGCAGCCAGGA 62.820 66.667 0.00 0.00 0.00 3.86
3143 3327 2.125552 CATCGACGCAGCCAGGAA 60.126 61.111 0.00 0.00 0.00 3.36
3144 3328 2.169789 CATCGACGCAGCCAGGAAG 61.170 63.158 0.00 0.00 0.00 3.46
3145 3329 2.650116 ATCGACGCAGCCAGGAAGT 61.650 57.895 0.00 0.00 0.00 3.01
3146 3330 2.842394 ATCGACGCAGCCAGGAAGTG 62.842 60.000 0.00 0.00 0.00 3.16
3147 3331 2.343758 GACGCAGCCAGGAAGTGA 59.656 61.111 0.00 0.00 0.00 3.41
3148 3332 1.739562 GACGCAGCCAGGAAGTGAG 60.740 63.158 0.00 0.00 0.00 3.51
3149 3333 2.345244 CGCAGCCAGGAAGTGAGT 59.655 61.111 0.00 0.00 0.00 3.41
3150 3334 1.739562 CGCAGCCAGGAAGTGAGTC 60.740 63.158 0.00 0.00 0.00 3.36
3151 3335 1.376553 GCAGCCAGGAAGTGAGTCC 60.377 63.158 0.00 0.00 38.03 3.85
3153 3337 1.561643 CAGCCAGGAAGTGAGTCCTA 58.438 55.000 0.00 0.00 46.85 2.94
3154 3338 1.480137 CAGCCAGGAAGTGAGTCCTAG 59.520 57.143 0.00 0.00 46.85 3.02
3155 3339 0.176910 GCCAGGAAGTGAGTCCTAGC 59.823 60.000 0.00 0.00 46.85 3.42
3156 3340 0.457851 CCAGGAAGTGAGTCCTAGCG 59.542 60.000 0.00 0.00 46.85 4.26
3157 3341 0.179124 CAGGAAGTGAGTCCTAGCGC 60.179 60.000 0.00 0.00 46.85 5.92
3158 3342 1.142097 GGAAGTGAGTCCTAGCGCC 59.858 63.158 2.29 0.00 34.56 6.53
3159 3343 1.324005 GGAAGTGAGTCCTAGCGCCT 61.324 60.000 2.29 0.00 34.56 5.52
3160 3344 0.179124 GAAGTGAGTCCTAGCGCCTG 60.179 60.000 2.29 0.00 0.00 4.85
3161 3345 0.900647 AAGTGAGTCCTAGCGCCTGT 60.901 55.000 2.29 0.00 0.00 4.00
3162 3346 1.139947 GTGAGTCCTAGCGCCTGTC 59.860 63.158 2.29 0.00 0.00 3.51
3163 3347 1.304134 TGAGTCCTAGCGCCTGTCA 60.304 57.895 2.29 0.00 0.00 3.58
3164 3348 0.684479 TGAGTCCTAGCGCCTGTCAT 60.684 55.000 2.29 0.00 0.00 3.06
3165 3349 0.461961 GAGTCCTAGCGCCTGTCATT 59.538 55.000 2.29 0.00 0.00 2.57
3166 3350 1.681793 GAGTCCTAGCGCCTGTCATTA 59.318 52.381 2.29 0.00 0.00 1.90
3167 3351 2.297597 GAGTCCTAGCGCCTGTCATTAT 59.702 50.000 2.29 0.00 0.00 1.28
3168 3352 3.497332 AGTCCTAGCGCCTGTCATTATA 58.503 45.455 2.29 0.00 0.00 0.98
3188 3372 2.127232 TCCATGCGAGCGGATCTGA 61.127 57.895 5.48 0.00 0.00 3.27
3234 3418 3.771160 GGAAGAGGGCGCCGAGAA 61.771 66.667 22.54 0.00 0.00 2.87
3592 3776 0.257039 GAGGTGGACCATGCCTTCAT 59.743 55.000 5.16 0.00 38.89 2.57
3678 3865 1.509463 GGAGGTGTGCGACGATACA 59.491 57.895 0.00 0.00 0.00 2.29
3737 3924 1.839424 CCTGAGGGTGTCATTTTCCC 58.161 55.000 0.00 0.00 41.36 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.154150 GACAGGTACGGTTCGGTCG 60.154 63.158 0.00 0.00 36.51 4.79
41 42 0.719465 GCGTTGAATGACAGGTACGG 59.281 55.000 0.00 0.00 32.87 4.02
66 67 2.289565 GATAACTAAGTGTGCCTGCCC 58.710 52.381 0.00 0.00 0.00 5.36
227 236 5.817784 TCTCTCTAGTGTAGTTGCCTACTT 58.182 41.667 2.44 0.00 43.38 2.24
464 485 1.312815 GGCAGAGAGAGAGAGAGAGC 58.687 60.000 0.00 0.00 0.00 4.09
470 491 2.175202 GTCAAAGGGCAGAGAGAGAGA 58.825 52.381 0.00 0.00 0.00 3.10
471 492 1.898472 TGTCAAAGGGCAGAGAGAGAG 59.102 52.381 0.00 0.00 0.00 3.20
472 493 2.015456 TGTCAAAGGGCAGAGAGAGA 57.985 50.000 0.00 0.00 0.00 3.10
680 711 3.957508 AAGGGAGAGAGGAGGTAGTAC 57.042 52.381 0.00 0.00 0.00 2.73
683 714 3.449377 GTCAAAAGGGAGAGAGGAGGTAG 59.551 52.174 0.00 0.00 0.00 3.18
684 715 3.181410 TGTCAAAAGGGAGAGAGGAGGTA 60.181 47.826 0.00 0.00 0.00 3.08
685 716 2.261729 GTCAAAAGGGAGAGAGGAGGT 58.738 52.381 0.00 0.00 0.00 3.85
686 717 2.260822 TGTCAAAAGGGAGAGAGGAGG 58.739 52.381 0.00 0.00 0.00 4.30
687 718 4.566426 AATGTCAAAAGGGAGAGAGGAG 57.434 45.455 0.00 0.00 0.00 3.69
688 719 4.507335 CCAAATGTCAAAAGGGAGAGAGGA 60.507 45.833 0.00 0.00 0.00 3.71
767 798 2.344129 GGCGGGGCTCTATGCTAC 59.656 66.667 0.00 0.00 42.39 3.58
936 973 1.656652 TACTACTCCAGACGCGTACC 58.343 55.000 13.97 0.00 0.00 3.34
1528 1596 5.647658 CACAAATCAACTTGGTAGGAGCATA 59.352 40.000 0.00 0.00 0.00 3.14
1529 1597 4.460382 CACAAATCAACTTGGTAGGAGCAT 59.540 41.667 0.00 0.00 0.00 3.79
1530 1598 3.820467 CACAAATCAACTTGGTAGGAGCA 59.180 43.478 0.00 0.00 0.00 4.26
1531 1599 3.366374 GCACAAATCAACTTGGTAGGAGC 60.366 47.826 0.00 0.00 0.00 4.70
1532 1600 3.820467 TGCACAAATCAACTTGGTAGGAG 59.180 43.478 0.00 0.00 0.00 3.69
1533 1601 3.568007 GTGCACAAATCAACTTGGTAGGA 59.432 43.478 13.17 0.00 0.00 2.94
1534 1602 3.305335 GGTGCACAAATCAACTTGGTAGG 60.305 47.826 20.43 0.00 0.00 3.18
1535 1603 3.305335 GGGTGCACAAATCAACTTGGTAG 60.305 47.826 20.43 0.00 0.00 3.18
1849 1930 2.433318 GACTCGAGGCTGTGCACC 60.433 66.667 18.41 0.00 0.00 5.01
1861 1950 1.136984 GCGGTAGTGACTGGACTCG 59.863 63.158 0.00 0.00 31.98 4.18
1886 1995 9.767684 CAGTTATTGCGAATGTATTAACAGAAA 57.232 29.630 0.00 0.00 39.49 2.52
1898 2007 7.528516 CGTATGAGAAATCAGTTATTGCGAATG 59.471 37.037 0.00 0.00 0.00 2.67
1939 2048 6.669125 ATGACCAAAGGTTTGATGAAATCA 57.331 33.333 3.95 0.00 44.55 2.57
2009 2125 5.283457 AGTTCTAAGCACCAGGTCATATC 57.717 43.478 0.00 0.00 0.00 1.63
2010 2126 5.431765 CAAGTTCTAAGCACCAGGTCATAT 58.568 41.667 0.00 0.00 0.00 1.78
2011 2127 4.832248 CAAGTTCTAAGCACCAGGTCATA 58.168 43.478 0.00 0.00 0.00 2.15
2012 2128 3.679389 CAAGTTCTAAGCACCAGGTCAT 58.321 45.455 0.00 0.00 0.00 3.06
2013 2129 2.810400 GCAAGTTCTAAGCACCAGGTCA 60.810 50.000 0.00 0.00 0.00 4.02
2014 2130 1.807142 GCAAGTTCTAAGCACCAGGTC 59.193 52.381 0.00 0.00 0.00 3.85
2015 2131 1.421646 AGCAAGTTCTAAGCACCAGGT 59.578 47.619 0.00 0.00 0.00 4.00
2137 2254 2.422832 GGTACGGAGGAGTACTTGAGTG 59.577 54.545 0.00 0.00 44.59 3.51
2166 2283 9.949174 GGTGCTTCTACTACTAGTAATTAAGAC 57.051 37.037 3.76 6.21 29.00 3.01
2184 2301 1.608717 CCAGGACTAGCGGTGCTTCT 61.609 60.000 0.00 0.00 44.21 2.85
2186 2303 1.889530 GACCAGGACTAGCGGTGCTT 61.890 60.000 0.00 0.00 44.21 3.91
2188 2305 2.184579 GACCAGGACTAGCGGTGC 59.815 66.667 0.00 0.00 36.48 5.01
2189 2306 1.513158 CAGACCAGGACTAGCGGTG 59.487 63.158 0.00 0.00 31.63 4.94
2190 2307 2.352032 GCAGACCAGGACTAGCGGT 61.352 63.158 0.00 0.00 35.12 5.68
2191 2308 1.680522 ATGCAGACCAGGACTAGCGG 61.681 60.000 0.00 0.00 0.00 5.52
2192 2309 1.032794 TATGCAGACCAGGACTAGCG 58.967 55.000 0.00 0.00 0.00 4.26
2193 2310 2.035321 GAGTATGCAGACCAGGACTAGC 59.965 54.545 8.08 0.00 0.00 3.42
2194 2311 2.625790 GGAGTATGCAGACCAGGACTAG 59.374 54.545 8.08 0.00 0.00 2.57
2195 2312 2.245028 AGGAGTATGCAGACCAGGACTA 59.755 50.000 8.08 0.00 0.00 2.59
2196 2313 1.007721 AGGAGTATGCAGACCAGGACT 59.992 52.381 8.08 0.00 0.00 3.85
2197 2314 1.490574 AGGAGTATGCAGACCAGGAC 58.509 55.000 8.08 0.00 0.00 3.85
2238 2355 5.517322 CTACACTTGTAGTATCCCCTGTC 57.483 47.826 8.07 0.00 42.22 3.51
2913 3097 4.702131 GTGGTCAAGGCTTTGATGAACTAT 59.298 41.667 14.90 0.00 44.62 2.12
2915 3099 2.887152 GTGGTCAAGGCTTTGATGAACT 59.113 45.455 14.90 0.00 44.62 3.01
2951 3135 3.414136 AACGACCAGGTGCCAAGCA 62.414 57.895 0.00 0.00 35.60 3.91
2965 3149 1.635844 GTATCACGCACATCCAACGA 58.364 50.000 0.00 0.00 0.00 3.85
2970 3154 1.600663 CGAGAGGTATCACGCACATCC 60.601 57.143 0.00 0.00 32.86 3.51
3016 3200 2.107141 ATTAGCGCTCGACCAGGC 59.893 61.111 16.34 0.00 0.00 4.85
3017 3201 2.240500 GCATTAGCGCTCGACCAGG 61.241 63.158 16.34 0.00 0.00 4.45
3018 3202 1.083806 TTGCATTAGCGCTCGACCAG 61.084 55.000 16.34 0.00 46.23 4.00
3019 3203 0.461870 ATTGCATTAGCGCTCGACCA 60.462 50.000 16.34 4.72 46.23 4.02
3020 3204 0.041839 CATTGCATTAGCGCTCGACC 60.042 55.000 16.34 1.55 46.23 4.79
3021 3205 0.041839 CCATTGCATTAGCGCTCGAC 60.042 55.000 16.34 2.39 46.23 4.20
3022 3206 0.461870 ACCATTGCATTAGCGCTCGA 60.462 50.000 16.34 4.02 46.23 4.04
3023 3207 0.378257 AACCATTGCATTAGCGCTCG 59.622 50.000 16.34 4.86 46.23 5.03
3024 3208 2.566952 AAACCATTGCATTAGCGCTC 57.433 45.000 16.34 0.00 46.23 5.03
3025 3209 2.493278 AGAAAACCATTGCATTAGCGCT 59.507 40.909 17.26 17.26 46.23 5.92
3026 3210 2.854185 GAGAAAACCATTGCATTAGCGC 59.146 45.455 0.00 0.00 46.23 5.92
3027 3211 3.100817 CGAGAAAACCATTGCATTAGCG 58.899 45.455 0.00 0.00 46.23 4.26
3028 3212 3.119495 ACCGAGAAAACCATTGCATTAGC 60.119 43.478 0.00 0.00 42.57 3.09
3029 3213 4.701956 ACCGAGAAAACCATTGCATTAG 57.298 40.909 0.00 0.00 0.00 1.73
3030 3214 5.492895 TCTACCGAGAAAACCATTGCATTA 58.507 37.500 0.00 0.00 0.00 1.90
3031 3215 4.331968 TCTACCGAGAAAACCATTGCATT 58.668 39.130 0.00 0.00 0.00 3.56
3032 3216 3.950397 TCTACCGAGAAAACCATTGCAT 58.050 40.909 0.00 0.00 0.00 3.96
3033 3217 3.410631 TCTACCGAGAAAACCATTGCA 57.589 42.857 0.00 0.00 0.00 4.08
3034 3218 4.759516 TTTCTACCGAGAAAACCATTGC 57.240 40.909 0.00 0.00 46.44 3.56
3055 3239 0.948678 TTAACGAGCGCTGCCTTTTT 59.051 45.000 18.48 0.44 0.00 1.94
3056 3240 0.948678 TTTAACGAGCGCTGCCTTTT 59.051 45.000 18.48 2.44 0.00 2.27
3057 3241 0.237498 GTTTAACGAGCGCTGCCTTT 59.763 50.000 18.48 3.48 0.00 3.11
3058 3242 0.882927 TGTTTAACGAGCGCTGCCTT 60.883 50.000 18.48 5.22 0.00 4.35
3059 3243 1.291877 CTGTTTAACGAGCGCTGCCT 61.292 55.000 18.48 0.00 0.00 4.75
3060 3244 1.132640 CTGTTTAACGAGCGCTGCC 59.867 57.895 18.48 0.00 0.00 4.85
3061 3245 1.509995 GCTGTTTAACGAGCGCTGC 60.510 57.895 18.48 4.32 0.00 5.25
3062 3246 0.093705 GAGCTGTTTAACGAGCGCTG 59.906 55.000 18.48 10.31 40.34 5.18
3063 3247 0.319555 TGAGCTGTTTAACGAGCGCT 60.320 50.000 11.27 11.27 40.34 5.92
3064 3248 0.093705 CTGAGCTGTTTAACGAGCGC 59.906 55.000 0.00 0.00 40.34 5.92
3065 3249 1.698165 TCTGAGCTGTTTAACGAGCG 58.302 50.000 0.00 0.00 40.34 5.03
3066 3250 3.318017 TCTTCTGAGCTGTTTAACGAGC 58.682 45.455 0.00 10.12 35.28 5.03
3067 3251 5.463724 ACTTTCTTCTGAGCTGTTTAACGAG 59.536 40.000 0.00 0.00 0.00 4.18
3068 3252 5.357257 ACTTTCTTCTGAGCTGTTTAACGA 58.643 37.500 0.00 0.00 0.00 3.85
3069 3253 5.659048 ACTTTCTTCTGAGCTGTTTAACG 57.341 39.130 0.00 0.00 0.00 3.18
3070 3254 9.783256 TTTTTACTTTCTTCTGAGCTGTTTAAC 57.217 29.630 0.00 0.00 0.00 2.01
3097 3281 0.808755 CCATCGGGCGCTTAGTTTTT 59.191 50.000 7.64 0.00 0.00 1.94
3098 3282 2.477880 CCATCGGGCGCTTAGTTTT 58.522 52.632 7.64 0.00 0.00 2.43
3099 3283 4.218722 CCATCGGGCGCTTAGTTT 57.781 55.556 7.64 0.00 0.00 2.66
3111 3295 4.889112 ATGCCAGGGCTGCCATCG 62.889 66.667 22.05 7.41 42.51 3.84
3112 3296 2.910994 GATGCCAGGGCTGCCATC 60.911 66.667 22.05 10.52 38.09 3.51
3113 3297 4.889112 CGATGCCAGGGCTGCCAT 62.889 66.667 22.05 11.43 42.51 4.40
3125 3309 4.819761 TCCTGGCTGCGTCGATGC 62.820 66.667 22.77 22.77 0.00 3.91
3126 3310 2.125552 TTCCTGGCTGCGTCGATG 60.126 61.111 0.00 0.00 0.00 3.84
3127 3311 2.185350 CTTCCTGGCTGCGTCGAT 59.815 61.111 0.00 0.00 0.00 3.59
3128 3312 3.303135 ACTTCCTGGCTGCGTCGA 61.303 61.111 0.00 0.00 0.00 4.20
3129 3313 3.114616 CACTTCCTGGCTGCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
3130 3314 1.739562 CTCACTTCCTGGCTGCGTC 60.740 63.158 0.00 0.00 0.00 5.19
3131 3315 2.345244 CTCACTTCCTGGCTGCGT 59.655 61.111 0.00 0.00 0.00 5.24
3132 3316 1.739562 GACTCACTTCCTGGCTGCG 60.740 63.158 0.00 0.00 0.00 5.18
3133 3317 1.376553 GGACTCACTTCCTGGCTGC 60.377 63.158 0.00 0.00 32.24 5.25
3134 3318 1.480137 CTAGGACTCACTTCCTGGCTG 59.520 57.143 1.73 0.00 46.23 4.85
3135 3319 1.859302 CTAGGACTCACTTCCTGGCT 58.141 55.000 1.73 0.00 46.23 4.75
3137 3321 0.457851 CGCTAGGACTCACTTCCTGG 59.542 60.000 1.73 0.00 46.23 4.45
3138 3322 0.179124 GCGCTAGGACTCACTTCCTG 60.179 60.000 0.00 0.00 46.23 3.86
3140 3324 1.142097 GGCGCTAGGACTCACTTCC 59.858 63.158 7.64 0.00 35.66 3.46
3141 3325 0.179124 CAGGCGCTAGGACTCACTTC 60.179 60.000 7.64 0.00 0.00 3.01
3142 3326 0.900647 ACAGGCGCTAGGACTCACTT 60.901 55.000 7.64 0.00 0.00 3.16
3143 3327 1.304547 ACAGGCGCTAGGACTCACT 60.305 57.895 7.64 0.00 0.00 3.41
3144 3328 1.139947 GACAGGCGCTAGGACTCAC 59.860 63.158 7.64 0.00 0.00 3.51
3145 3329 0.684479 ATGACAGGCGCTAGGACTCA 60.684 55.000 7.64 0.67 0.00 3.41
3146 3330 0.461961 AATGACAGGCGCTAGGACTC 59.538 55.000 7.64 0.00 0.00 3.36
3147 3331 1.776662 TAATGACAGGCGCTAGGACT 58.223 50.000 7.64 0.00 0.00 3.85
3148 3332 2.821991 ATAATGACAGGCGCTAGGAC 57.178 50.000 7.64 0.00 0.00 3.85
3149 3333 3.497332 ACTATAATGACAGGCGCTAGGA 58.503 45.455 7.64 0.00 0.00 2.94
3150 3334 3.367498 GGACTATAATGACAGGCGCTAGG 60.367 52.174 7.64 0.00 0.00 3.02
3151 3335 3.255888 TGGACTATAATGACAGGCGCTAG 59.744 47.826 7.64 2.12 0.00 3.42
3152 3336 3.227614 TGGACTATAATGACAGGCGCTA 58.772 45.455 7.64 0.00 0.00 4.26
3153 3337 2.039418 TGGACTATAATGACAGGCGCT 58.961 47.619 7.64 0.00 0.00 5.92
3154 3338 2.526304 TGGACTATAATGACAGGCGC 57.474 50.000 0.00 0.00 0.00 6.53
3155 3339 2.738846 GCATGGACTATAATGACAGGCG 59.261 50.000 0.00 0.00 0.00 5.52
3156 3340 2.738846 CGCATGGACTATAATGACAGGC 59.261 50.000 0.00 0.00 35.73 4.85
3157 3341 4.240888 CTCGCATGGACTATAATGACAGG 58.759 47.826 0.00 0.00 0.00 4.00
3158 3342 3.677121 GCTCGCATGGACTATAATGACAG 59.323 47.826 0.00 0.00 0.00 3.51
3159 3343 3.653344 GCTCGCATGGACTATAATGACA 58.347 45.455 0.00 0.00 0.00 3.58
3160 3344 2.663602 CGCTCGCATGGACTATAATGAC 59.336 50.000 0.00 0.00 0.00 3.06
3161 3345 2.352715 CCGCTCGCATGGACTATAATGA 60.353 50.000 0.00 0.00 0.00 2.57
3162 3346 1.995484 CCGCTCGCATGGACTATAATG 59.005 52.381 0.00 0.00 0.00 1.90
3163 3347 1.893137 TCCGCTCGCATGGACTATAAT 59.107 47.619 0.00 0.00 0.00 1.28
3164 3348 1.324383 TCCGCTCGCATGGACTATAA 58.676 50.000 0.00 0.00 0.00 0.98
3165 3349 1.472878 GATCCGCTCGCATGGACTATA 59.527 52.381 0.00 0.00 37.02 1.31
3166 3350 0.244994 GATCCGCTCGCATGGACTAT 59.755 55.000 0.00 0.00 37.02 2.12
3167 3351 0.823769 AGATCCGCTCGCATGGACTA 60.824 55.000 0.00 0.00 37.02 2.59
3168 3352 2.130426 AGATCCGCTCGCATGGACT 61.130 57.895 0.00 0.00 37.02 3.85
3234 3418 0.252103 TCCTCCTTTACAGCGACCCT 60.252 55.000 0.00 0.00 0.00 4.34
3242 3426 0.976073 CGCCCTCCTCCTCCTTTACA 60.976 60.000 0.00 0.00 0.00 2.41
3322 3506 4.221422 GCCAGATCCGCGCCACTA 62.221 66.667 0.00 0.00 0.00 2.74
3592 3776 0.459489 GCACCTTGTTGTTGAAGCCA 59.541 50.000 0.00 0.00 0.00 4.75
3678 3865 1.134521 TGTTGTGCAGGACTTTCGTCT 60.135 47.619 0.00 0.00 40.10 4.18


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

AutoCloner maintained by Alex Coulton.