Multiple sequence alignment - TraesCS1D01G195700

Loading Multiple Alignment...

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 TraesCS1D01G195700 chr1D 100.000 3566 0 0 1 3566 275140533 275136968 0.000000e+00 6586.0
1 TraesCS1D01G195700 chr1D 97.170 106 3 0 2910 3015 275137519 275137414 2.830000e-41 180.0
2 TraesCS1D01G195700 chr1D 97.170 106 3 0 3015 3120 275137624 275137519 2.830000e-41 180.0
3 TraesCS1D01G195700 chr1A 96.346 2326 49 12 703 3015 347636083 347633781 0.000000e+00 3792.0
4 TraesCS1D01G195700 chr1A 86.304 606 43 4 1077 1682 239909152 239908587 1.090000e-174 623.0
5 TraesCS1D01G195700 chr1A 93.750 256 12 4 257 508 347637587 347637332 7.220000e-102 381.0
6 TraesCS1D01G195700 chr1A 92.800 250 14 2 1 246 347637949 347637700 3.380000e-95 359.0
7 TraesCS1D01G195700 chr1A 91.534 189 14 2 495 682 347636256 347636069 3.530000e-65 259.0
8 TraesCS1D01G195700 chr1A 87.245 196 22 3 3015 3209 347633885 347633692 1.670000e-53 220.0
9 TraesCS1D01G195700 chr1B 94.972 2307 72 15 723 3015 374330562 374328286 0.000000e+00 3578.0
10 TraesCS1D01G195700 chr1B 95.818 550 16 3 3017 3566 374328389 374327847 0.000000e+00 881.0
11 TraesCS1D01G195700 chr1B 79.837 615 52 35 98 677 374331156 374330579 2.010000e-102 383.0
12 TraesCS1D01G195700 chr1B 91.071 56 5 0 2440 2495 374322847 374322792 3.820000e-10 76.8
13 TraesCS1D01G195700 chrUn 89.587 605 52 7 1078 1682 239745056 239745649 0.000000e+00 758.0
14 TraesCS1D01G195700 chr3B 90.051 392 38 1 1078 1469 426651566 426651956 1.140000e-139 507.0
15 TraesCS1D01G195700 chr3B 91.126 293 14 1 1174 1466 823473564 823473844 1.550000e-103 387.0
16 TraesCS1D01G195700 chr3B 89.493 276 29 0 1077 1352 522027735 522027460 2.040000e-92 350.0
17 TraesCS1D01G195700 chr3B 93.333 60 4 0 1074 1133 823473511 823473570 4.900000e-14 89.8
18 TraesCS1D01G195700 chr6A 94.737 57 3 0 1261 1317 478310575 478310519 4.900000e-14 89.8
19 TraesCS1D01G195700 chr6D 96.078 51 2 0 1373 1423 337842842 337842792 2.280000e-12 84.2
20 TraesCS1D01G195700 chr6B 96.078 51 2 0 1373 1423 482470608 482470658 2.280000e-12 84.2


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 TraesCS1D01G195700 chr1D 275136968 275140533 3565 True 2315.333333 6586 98.113333 1 3566 3 chr1D.!!$R1 3565
1 TraesCS1D01G195700 chr1A 347633692 347637949 4257 True 1002.200000 3792 92.335000 1 3209 5 chr1A.!!$R2 3208
2 TraesCS1D01G195700 chr1A 239908587 239909152 565 True 623.000000 623 86.304000 1077 1682 1 chr1A.!!$R1 605
3 TraesCS1D01G195700 chr1B 374327847 374331156 3309 True 1614.000000 3578 90.209000 98 3566 3 chr1B.!!$R2 3468
4 TraesCS1D01G195700 chrUn 239745056 239745649 593 False 758.000000 758 89.587000 1078 1682 1 chrUn.!!$F1 604

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
779 2010 0.034756 AACCAAAAGGCCCATTTCGC 59.965 50.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2615 3859 0.390492 TGCAGTCAGCCCTATGATCG 59.61 55.0 0.0 0.0 44.83 3.69 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
93 95 1.433053 CTGTTTGGACGTCCGTTGCA 61.433 55.000 28.70 21.53 39.43 4.08
183 188 8.624367 TTTTATTATGTTCTCGGTTTCTTCCA 57.376 30.769 0.00 0.00 0.00 3.53
451 579 7.565450 TGCAATGAACATTCTTTCAAATACG 57.435 32.000 0.00 0.00 38.95 3.06
457 585 7.304735 TGAACATTCTTTCAAATACGTGATGG 58.695 34.615 0.00 0.00 32.42 3.51
555 1774 7.370836 CGACTAATAGTTTTGAAATGCACGATC 59.629 37.037 0.00 0.00 0.00 3.69
557 1776 8.730680 ACTAATAGTTTTGAAATGCACGATCTT 58.269 29.630 0.00 0.00 0.00 2.40
558 1777 9.559958 CTAATAGTTTTGAAATGCACGATCTTT 57.440 29.630 0.00 0.00 0.00 2.52
656 1877 0.672711 GTGGGCGTTTCACCTCCTAC 60.673 60.000 0.00 0.00 0.00 3.18
657 1878 1.078637 GGGCGTTTCACCTCCTACC 60.079 63.158 0.00 0.00 0.00 3.18
660 1881 1.217244 CGTTTCACCTCCTACCCGG 59.783 63.158 0.00 0.00 0.00 5.73
667 1888 2.428925 CCTCCTACCCGGCGCTTTA 61.429 63.158 7.64 0.00 0.00 1.85
668 1889 1.518774 CTCCTACCCGGCGCTTTAA 59.481 57.895 7.64 0.00 0.00 1.52
669 1890 0.529992 CTCCTACCCGGCGCTTTAAG 60.530 60.000 7.64 0.00 0.00 1.85
670 1891 2.178235 CCTACCCGGCGCTTTAAGC 61.178 63.158 7.64 6.92 38.02 3.09
684 1905 5.335827 GCTTTAAGCGTCAGATAGGATTG 57.664 43.478 0.00 0.00 0.00 2.67
685 1906 4.811557 GCTTTAAGCGTCAGATAGGATTGT 59.188 41.667 0.00 0.00 0.00 2.71
686 1907 5.294552 GCTTTAAGCGTCAGATAGGATTGTT 59.705 40.000 0.00 0.00 0.00 2.83
687 1908 6.183360 GCTTTAAGCGTCAGATAGGATTGTTT 60.183 38.462 0.00 0.00 0.00 2.83
688 1909 7.626452 GCTTTAAGCGTCAGATAGGATTGTTTT 60.626 37.037 0.00 0.00 0.00 2.43
689 1910 5.551760 AAGCGTCAGATAGGATTGTTTTG 57.448 39.130 0.00 0.00 0.00 2.44
690 1911 4.579869 AGCGTCAGATAGGATTGTTTTGT 58.420 39.130 0.00 0.00 0.00 2.83
691 1912 5.003804 AGCGTCAGATAGGATTGTTTTGTT 58.996 37.500 0.00 0.00 0.00 2.83
692 1913 5.473504 AGCGTCAGATAGGATTGTTTTGTTT 59.526 36.000 0.00 0.00 0.00 2.83
693 1914 6.016276 AGCGTCAGATAGGATTGTTTTGTTTT 60.016 34.615 0.00 0.00 0.00 2.43
694 1915 6.640907 GCGTCAGATAGGATTGTTTTGTTTTT 59.359 34.615 0.00 0.00 0.00 1.94
776 2007 3.582164 TGTAGAACCAAAAGGCCCATTT 58.418 40.909 0.00 0.00 0.00 2.32
777 2008 3.576550 TGTAGAACCAAAAGGCCCATTTC 59.423 43.478 0.00 0.00 0.00 2.17
778 2009 1.618343 AGAACCAAAAGGCCCATTTCG 59.382 47.619 0.00 0.00 0.00 3.46
779 2010 0.034756 AACCAAAAGGCCCATTTCGC 59.965 50.000 0.00 0.00 0.00 4.70
785 2016 4.128388 GGCCCATTTCGCCCAACG 62.128 66.667 0.00 0.00 40.78 4.10
786 2017 4.128388 GCCCATTTCGCCCAACGG 62.128 66.667 0.00 0.00 43.89 4.44
787 2018 2.675075 CCCATTTCGCCCAACGGT 60.675 61.111 0.00 0.00 43.89 4.83
788 2019 2.566010 CCATTTCGCCCAACGGTG 59.434 61.111 0.00 0.00 43.89 4.94
1743 2987 9.424319 TCTCATGACACAAAGAGTTTTATCTAC 57.576 33.333 0.00 0.00 0.00 2.59
1836 3080 1.078426 GTCCCGTGATCTTGGTGGG 60.078 63.158 0.00 0.00 41.43 4.61
2172 3416 3.861846 TGGGTATGATCTCTATGGTGCT 58.138 45.455 0.00 0.00 0.00 4.40
2457 3701 0.461135 AAATGGCATCCACGATTGGC 59.539 50.000 0.00 0.00 43.56 4.52
2615 3859 1.589716 GACTGTTCATGCCCACTGCC 61.590 60.000 0.00 0.00 40.16 4.85
2617 3861 2.359850 GTTCATGCCCACTGCCGA 60.360 61.111 0.00 0.00 40.16 5.54
2625 3869 1.372683 CCCACTGCCGATCATAGGG 59.627 63.158 0.00 0.00 33.92 3.53
2711 3955 3.219281 GGAGGTGTTGCTTAAAAGGTCA 58.781 45.455 0.00 0.00 0.00 4.02
2733 3977 8.194769 GGTCAAAGTTTTGGATTTCTCTGTTTA 58.805 33.333 4.89 0.00 38.66 2.01
2781 4025 6.863645 CCATATCTCGTATCTTGGTGTAACAG 59.136 42.308 0.00 0.00 39.98 3.16
2790 4034 7.009265 CGTATCTTGGTGTAACAGTAATGTCTG 59.991 40.741 0.00 0.00 39.98 3.51
2895 4140 6.205101 AGTGGATGCAAGATTTGATTCTTC 57.795 37.500 0.00 0.00 33.69 2.87
2916 4161 8.969121 TCTTCAAACATGTGTTTATATTGCTG 57.031 30.769 10.49 0.00 45.54 4.41
2917 4162 8.575589 TCTTCAAACATGTGTTTATATTGCTGT 58.424 29.630 10.49 0.00 45.54 4.40
2918 4163 8.518151 TTCAAACATGTGTTTATATTGCTGTG 57.482 30.769 10.49 0.00 45.54 3.66
2919 4164 7.656412 TCAAACATGTGTTTATATTGCTGTGT 58.344 30.769 10.49 0.00 45.54 3.72
2920 4165 7.594386 TCAAACATGTGTTTATATTGCTGTGTG 59.406 33.333 10.49 0.00 45.54 3.82
2921 4166 6.816134 ACATGTGTTTATATTGCTGTGTGA 57.184 33.333 0.00 0.00 0.00 3.58
2922 4167 7.395190 ACATGTGTTTATATTGCTGTGTGAT 57.605 32.000 0.00 0.00 0.00 3.06
2923 4168 7.829725 ACATGTGTTTATATTGCTGTGTGATT 58.170 30.769 0.00 0.00 0.00 2.57
2924 4169 8.955388 ACATGTGTTTATATTGCTGTGTGATTA 58.045 29.630 0.00 0.00 0.00 1.75
2925 4170 9.225201 CATGTGTTTATATTGCTGTGTGATTAC 57.775 33.333 0.00 0.00 0.00 1.89
2926 4171 8.560355 TGTGTTTATATTGCTGTGTGATTACT 57.440 30.769 0.00 0.00 0.00 2.24
2927 4172 8.450180 TGTGTTTATATTGCTGTGTGATTACTG 58.550 33.333 0.00 0.00 0.00 2.74
2928 4173 8.664798 GTGTTTATATTGCTGTGTGATTACTGA 58.335 33.333 0.00 0.00 0.00 3.41
2929 4174 9.394767 TGTTTATATTGCTGTGTGATTACTGAT 57.605 29.630 0.00 0.00 0.00 2.90
2935 4180 6.682423 TGCTGTGTGATTACTGATTATTGG 57.318 37.500 0.00 0.00 0.00 3.16
2936 4181 6.413892 TGCTGTGTGATTACTGATTATTGGA 58.586 36.000 0.00 0.00 0.00 3.53
2937 4182 6.316140 TGCTGTGTGATTACTGATTATTGGAC 59.684 38.462 0.00 0.00 0.00 4.02
2938 4183 6.510157 GCTGTGTGATTACTGATTATTGGACG 60.510 42.308 0.00 0.00 0.00 4.79
2939 4184 6.403049 TGTGTGATTACTGATTATTGGACGT 58.597 36.000 0.00 0.00 0.00 4.34
2940 4185 6.533723 TGTGTGATTACTGATTATTGGACGTC 59.466 38.462 7.13 7.13 0.00 4.34
2941 4186 6.757010 GTGTGATTACTGATTATTGGACGTCT 59.243 38.462 16.46 0.00 0.00 4.18
2942 4187 6.978659 TGTGATTACTGATTATTGGACGTCTC 59.021 38.462 16.46 6.30 0.00 3.36
2943 4188 7.147897 TGTGATTACTGATTATTGGACGTCTCT 60.148 37.037 16.46 2.97 0.00 3.10
2944 4189 7.380065 GTGATTACTGATTATTGGACGTCTCTC 59.620 40.741 16.46 0.00 0.00 3.20
2945 4190 6.769134 TTACTGATTATTGGACGTCTCTCA 57.231 37.500 16.46 1.77 0.00 3.27
2946 4191 5.255710 ACTGATTATTGGACGTCTCTCAG 57.744 43.478 16.46 17.88 35.99 3.35
2947 4192 4.098654 ACTGATTATTGGACGTCTCTCAGG 59.901 45.833 16.46 6.53 34.58 3.86
2948 4193 3.384789 TGATTATTGGACGTCTCTCAGGG 59.615 47.826 16.46 0.00 0.00 4.45
2949 4194 2.820728 TATTGGACGTCTCTCAGGGA 57.179 50.000 16.46 0.00 0.00 4.20
2950 4195 2.166907 ATTGGACGTCTCTCAGGGAT 57.833 50.000 16.46 0.00 0.00 3.85
2951 4196 1.938585 TTGGACGTCTCTCAGGGATT 58.061 50.000 16.46 0.00 0.00 3.01
2952 4197 2.820728 TGGACGTCTCTCAGGGATTA 57.179 50.000 16.46 0.00 0.00 1.75
2953 4198 2.656002 TGGACGTCTCTCAGGGATTAG 58.344 52.381 16.46 0.00 0.00 1.73
2954 4199 1.338655 GGACGTCTCTCAGGGATTAGC 59.661 57.143 16.46 0.00 0.00 3.09
2955 4200 2.303175 GACGTCTCTCAGGGATTAGCT 58.697 52.381 8.70 0.00 0.00 3.32
2956 4201 2.028130 ACGTCTCTCAGGGATTAGCTG 58.972 52.381 0.00 0.00 0.00 4.24
2957 4202 2.302260 CGTCTCTCAGGGATTAGCTGA 58.698 52.381 0.00 0.00 0.00 4.26
2958 4203 2.690497 CGTCTCTCAGGGATTAGCTGAA 59.310 50.000 0.00 0.00 0.00 3.02
2959 4204 3.320541 CGTCTCTCAGGGATTAGCTGAAT 59.679 47.826 0.00 0.00 0.00 2.57
2960 4205 4.630111 GTCTCTCAGGGATTAGCTGAATG 58.370 47.826 0.00 0.00 0.00 2.67
2961 4206 4.100808 GTCTCTCAGGGATTAGCTGAATGT 59.899 45.833 0.00 0.00 0.00 2.71
2962 4207 4.718774 TCTCTCAGGGATTAGCTGAATGTT 59.281 41.667 0.00 0.00 0.00 2.71
2963 4208 5.028549 TCTCAGGGATTAGCTGAATGTTC 57.971 43.478 0.00 0.00 0.00 3.18
2964 4209 4.718774 TCTCAGGGATTAGCTGAATGTTCT 59.281 41.667 0.00 0.00 0.00 3.01
2965 4210 5.190528 TCTCAGGGATTAGCTGAATGTTCTT 59.809 40.000 0.00 0.00 0.00 2.52
2966 4211 5.819991 TCAGGGATTAGCTGAATGTTCTTT 58.180 37.500 0.00 0.00 0.00 2.52
2967 4212 5.882557 TCAGGGATTAGCTGAATGTTCTTTC 59.117 40.000 0.00 0.00 0.00 2.62
2968 4213 5.067023 CAGGGATTAGCTGAATGTTCTTTCC 59.933 44.000 0.00 0.00 0.00 3.13
2969 4214 5.044550 AGGGATTAGCTGAATGTTCTTTCCT 60.045 40.000 0.00 0.00 0.00 3.36
2970 4215 6.158695 AGGGATTAGCTGAATGTTCTTTCCTA 59.841 38.462 0.00 0.00 0.00 2.94
2971 4216 6.484977 GGGATTAGCTGAATGTTCTTTCCTAG 59.515 42.308 0.00 0.00 0.00 3.02
2972 4217 7.275920 GGATTAGCTGAATGTTCTTTCCTAGA 58.724 38.462 0.00 0.00 0.00 2.43
2973 4218 7.770897 GGATTAGCTGAATGTTCTTTCCTAGAA 59.229 37.037 0.00 0.00 40.57 2.10
2974 4219 9.336171 GATTAGCTGAATGTTCTTTCCTAGAAT 57.664 33.333 0.00 0.00 44.39 2.40
2975 4220 6.998968 AGCTGAATGTTCTTTCCTAGAATG 57.001 37.500 0.00 0.00 44.39 2.67
2976 4221 5.884792 AGCTGAATGTTCTTTCCTAGAATGG 59.115 40.000 0.00 0.00 44.39 3.16
2977 4222 5.649831 GCTGAATGTTCTTTCCTAGAATGGT 59.350 40.000 0.00 0.00 44.39 3.55
2978 4223 6.183360 GCTGAATGTTCTTTCCTAGAATGGTC 60.183 42.308 0.00 0.00 44.39 4.02
2979 4224 6.778821 TGAATGTTCTTTCCTAGAATGGTCA 58.221 36.000 0.00 0.00 44.39 4.02
2980 4225 6.655003 TGAATGTTCTTTCCTAGAATGGTCAC 59.345 38.462 0.00 0.00 44.39 3.67
2981 4226 5.560722 TGTTCTTTCCTAGAATGGTCACA 57.439 39.130 0.00 0.00 44.39 3.58
2982 4227 6.126863 TGTTCTTTCCTAGAATGGTCACAT 57.873 37.500 0.00 0.00 44.39 3.21
2983 4228 5.939883 TGTTCTTTCCTAGAATGGTCACATG 59.060 40.000 0.00 0.00 44.39 3.21
2984 4229 6.173339 GTTCTTTCCTAGAATGGTCACATGA 58.827 40.000 0.00 0.00 44.39 3.07
2985 4230 5.982356 TCTTTCCTAGAATGGTCACATGAG 58.018 41.667 0.00 0.00 37.40 2.90
2986 4231 5.721480 TCTTTCCTAGAATGGTCACATGAGA 59.279 40.000 0.00 0.00 37.40 3.27
2987 4232 5.604758 TTCCTAGAATGGTCACATGAGAG 57.395 43.478 0.00 0.00 37.40 3.20
2988 4233 3.386078 TCCTAGAATGGTCACATGAGAGC 59.614 47.826 14.45 14.45 37.40 4.09
2989 4234 3.387374 CCTAGAATGGTCACATGAGAGCT 59.613 47.826 20.47 4.13 37.40 4.09
2990 4235 3.996921 AGAATGGTCACATGAGAGCTT 57.003 42.857 20.47 13.05 37.40 3.74
2991 4236 4.298103 AGAATGGTCACATGAGAGCTTT 57.702 40.909 20.47 19.48 37.40 3.51
2992 4237 4.660168 AGAATGGTCACATGAGAGCTTTT 58.340 39.130 20.47 14.57 37.40 2.27
2993 4238 4.699257 AGAATGGTCACATGAGAGCTTTTC 59.301 41.667 20.47 20.24 37.40 2.29
2994 4239 2.783135 TGGTCACATGAGAGCTTTTCC 58.217 47.619 20.47 6.16 36.97 3.13
2995 4240 2.087646 GGTCACATGAGAGCTTTTCCC 58.912 52.381 14.11 0.00 33.41 3.97
2996 4241 2.087646 GTCACATGAGAGCTTTTCCCC 58.912 52.381 0.00 0.00 0.00 4.81
2997 4242 1.988107 TCACATGAGAGCTTTTCCCCT 59.012 47.619 0.00 0.00 0.00 4.79
2998 4243 2.026822 TCACATGAGAGCTTTTCCCCTC 60.027 50.000 0.00 0.00 0.00 4.30
2999 4244 2.026449 CACATGAGAGCTTTTCCCCTCT 60.026 50.000 0.00 0.00 40.93 3.69
3000 4245 2.646798 ACATGAGAGCTTTTCCCCTCTT 59.353 45.455 0.00 0.00 38.48 2.85
3001 4246 2.867109 TGAGAGCTTTTCCCCTCTTG 57.133 50.000 0.00 0.00 38.48 3.02
3002 4247 1.271597 TGAGAGCTTTTCCCCTCTTGC 60.272 52.381 0.00 0.00 38.48 4.01
3003 4248 1.004161 GAGAGCTTTTCCCCTCTTGCT 59.996 52.381 0.00 0.00 38.48 3.91
3004 4249 1.004161 AGAGCTTTTCCCCTCTTGCTC 59.996 52.381 0.00 0.00 44.85 4.26
3005 4250 1.004161 GAGCTTTTCCCCTCTTGCTCT 59.996 52.381 0.00 0.00 42.28 4.09
3006 4251 1.172175 GCTTTTCCCCTCTTGCTCTG 58.828 55.000 0.00 0.00 0.00 3.35
3007 4252 1.546548 GCTTTTCCCCTCTTGCTCTGT 60.547 52.381 0.00 0.00 0.00 3.41
3008 4253 2.431454 CTTTTCCCCTCTTGCTCTGTC 58.569 52.381 0.00 0.00 0.00 3.51
3009 4254 1.734655 TTTCCCCTCTTGCTCTGTCT 58.265 50.000 0.00 0.00 0.00 3.41
3010 4255 1.270907 TTCCCCTCTTGCTCTGTCTC 58.729 55.000 0.00 0.00 0.00 3.36
3011 4256 0.115152 TCCCCTCTTGCTCTGTCTCA 59.885 55.000 0.00 0.00 0.00 3.27
3012 4257 0.979665 CCCCTCTTGCTCTGTCTCAA 59.020 55.000 0.00 0.00 0.00 3.02
3013 4258 1.558756 CCCCTCTTGCTCTGTCTCAAT 59.441 52.381 0.00 0.00 0.00 2.57
3014 4259 2.026449 CCCCTCTTGCTCTGTCTCAATT 60.026 50.000 0.00 0.00 0.00 2.32
3015 4260 3.198635 CCCCTCTTGCTCTGTCTCAATTA 59.801 47.826 0.00 0.00 0.00 1.40
3077 4322 6.484977 GGATTAGCTGAATGTTCTTTCCTAGG 59.515 42.308 0.82 0.82 0.00 3.02
3114 4359 1.734655 TTTCCCCTCTTGCTCTGTCT 58.265 50.000 0.00 0.00 0.00 3.41
3290 4536 9.575868 TTAAACAACTTGGTAAGATGGTTATGA 57.424 29.630 9.23 0.00 41.26 2.15
3291 4537 7.448748 AACAACTTGGTAAGATGGTTATGAC 57.551 36.000 4.29 0.00 35.79 3.06
3292 4538 6.539173 ACAACTTGGTAAGATGGTTATGACA 58.461 36.000 4.29 0.00 35.79 3.58
3293 4539 7.175104 ACAACTTGGTAAGATGGTTATGACAT 58.825 34.615 0.00 0.00 35.79 3.06
3294 4540 8.325787 ACAACTTGGTAAGATGGTTATGACATA 58.674 33.333 4.29 0.00 35.79 2.29
3295 4541 8.612619 CAACTTGGTAAGATGGTTATGACATAC 58.387 37.037 0.00 0.00 0.00 2.39
3408 4654 2.164338 TGCACCACACTATGTCTCGTA 58.836 47.619 0.00 0.00 0.00 3.43
3482 4728 2.094078 AGTTGCATTGCTTGTGTGTTGT 60.094 40.909 10.49 0.00 0.00 3.32
3483 4729 3.130164 AGTTGCATTGCTTGTGTGTTGTA 59.870 39.130 10.49 0.00 0.00 2.41
3484 4730 3.077229 TGCATTGCTTGTGTGTTGTAC 57.923 42.857 10.49 0.00 0.00 2.90
3485 4731 2.687425 TGCATTGCTTGTGTGTTGTACT 59.313 40.909 10.49 0.00 0.00 2.73
3554 4800 7.859325 TTATTCAACATAGGTGGCTACTTTC 57.141 36.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 2.364970 CCAAACAGGATTTGTCAAGGCA 59.635 45.455 0.00 0.00 39.73 4.75
93 95 4.147321 CAATTCCTAGGTGCCATGCTAAT 58.853 43.478 9.08 0.00 0.00 1.73
104 106 1.065418 CCGTGGAAGCAATTCCTAGGT 60.065 52.381 9.08 0.00 41.65 3.08
106 108 2.280628 GTCCGTGGAAGCAATTCCTAG 58.719 52.381 8.40 2.80 41.65 3.02
532 1751 9.559958 AAAGATCGTGCATTTCAAAACTATTAG 57.440 29.630 0.00 0.00 0.00 1.73
609 1830 3.056607 CCTTGTATGGGCTGTCAAAAAGG 60.057 47.826 0.00 0.00 0.00 3.11
611 1832 2.896685 CCCTTGTATGGGCTGTCAAAAA 59.103 45.455 0.00 0.00 40.84 1.94
667 1888 5.003804 ACAAAACAATCCTATCTGACGCTT 58.996 37.500 0.00 0.00 0.00 4.68
668 1889 4.579869 ACAAAACAATCCTATCTGACGCT 58.420 39.130 0.00 0.00 0.00 5.07
669 1890 4.946784 ACAAAACAATCCTATCTGACGC 57.053 40.909 0.00 0.00 0.00 5.19
691 1912 5.181245 CCTATCTGACGCTTTTCCTCAAAAA 59.819 40.000 0.00 0.00 35.56 1.94
692 1913 4.695455 CCTATCTGACGCTTTTCCTCAAAA 59.305 41.667 0.00 0.00 0.00 2.44
693 1914 4.020573 TCCTATCTGACGCTTTTCCTCAAA 60.021 41.667 0.00 0.00 0.00 2.69
694 1915 3.513912 TCCTATCTGACGCTTTTCCTCAA 59.486 43.478 0.00 0.00 0.00 3.02
695 1916 3.096852 TCCTATCTGACGCTTTTCCTCA 58.903 45.455 0.00 0.00 0.00 3.86
696 1917 3.712187 CTCCTATCTGACGCTTTTCCTC 58.288 50.000 0.00 0.00 0.00 3.71
697 1918 2.159028 GCTCCTATCTGACGCTTTTCCT 60.159 50.000 0.00 0.00 0.00 3.36
698 1919 2.205911 GCTCCTATCTGACGCTTTTCC 58.794 52.381 0.00 0.00 0.00 3.13
699 1920 2.605366 GTGCTCCTATCTGACGCTTTTC 59.395 50.000 0.00 0.00 0.00 2.29
700 1921 2.234908 AGTGCTCCTATCTGACGCTTTT 59.765 45.455 0.00 0.00 0.00 2.27
701 1922 1.827969 AGTGCTCCTATCTGACGCTTT 59.172 47.619 0.00 0.00 0.00 3.51
725 1946 2.421739 CTAGCCGACGGGGAATGG 59.578 66.667 17.22 0.00 38.47 3.16
727 1948 2.842936 CCCTAGCCGACGGGGAAT 60.843 66.667 17.22 0.00 42.58 3.01
778 2009 4.120331 GATGCTGCACCGTTGGGC 62.120 66.667 3.57 0.00 36.48 5.36
779 2010 3.443045 GGATGCTGCACCGTTGGG 61.443 66.667 3.57 0.00 40.11 4.12
780 2011 2.360350 AGGATGCTGCACCGTTGG 60.360 61.111 3.57 0.00 0.00 3.77
781 2012 2.693762 CCAGGATGCTGCACCGTTG 61.694 63.158 9.03 4.28 31.97 4.10
782 2013 2.360350 CCAGGATGCTGCACCGTT 60.360 61.111 9.03 0.00 31.97 4.44
783 2014 3.196207 AACCAGGATGCTGCACCGT 62.196 57.895 9.03 0.00 31.97 4.83
784 2015 2.360350 AACCAGGATGCTGCACCG 60.360 61.111 9.03 5.50 31.97 4.94
785 2016 2.345760 CCAACCAGGATGCTGCACC 61.346 63.158 9.03 8.83 41.22 5.01
786 2017 1.589716 GACCAACCAGGATGCTGCAC 61.590 60.000 9.03 0.00 41.22 4.57
787 2018 1.303561 GACCAACCAGGATGCTGCA 60.304 57.895 9.03 4.13 41.22 4.41
788 2019 2.048603 GGACCAACCAGGATGCTGC 61.049 63.158 9.03 0.00 41.22 5.25
873 2104 0.042731 TGTAGGTGGGGAAGAGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
1743 2987 5.287226 ACCGAGAAAGTGTACTTGTAGTTG 58.713 41.667 0.00 0.00 36.12 3.16
2457 3701 0.525668 GCACAGTAGGGACATCGTCG 60.526 60.000 0.00 0.00 32.65 5.12
2615 3859 0.390492 TGCAGTCAGCCCTATGATCG 59.610 55.000 0.00 0.00 44.83 3.69
2617 3861 2.038689 CAGATGCAGTCAGCCCTATGAT 59.961 50.000 0.00 0.00 44.83 2.45
2625 3869 5.300969 TGAATTAAACAGATGCAGTCAGC 57.699 39.130 0.00 0.00 45.96 4.26
2733 3977 5.920273 GGTTTCAAACAATGTCGACATCAAT 59.080 36.000 30.06 16.10 35.10 2.57
2895 4140 7.594386 TCACACAGCAATATAAACACATGTTTG 59.406 33.333 18.13 4.91 46.56 2.93
2910 4155 7.557358 TCCAATAATCAGTAATCACACAGCAAT 59.443 33.333 0.00 0.00 0.00 3.56
2911 4156 6.883756 TCCAATAATCAGTAATCACACAGCAA 59.116 34.615 0.00 0.00 0.00 3.91
2914 4159 6.535150 ACGTCCAATAATCAGTAATCACACAG 59.465 38.462 0.00 0.00 0.00 3.66
2915 4160 6.403049 ACGTCCAATAATCAGTAATCACACA 58.597 36.000 0.00 0.00 0.00 3.72
2916 4161 6.757010 AGACGTCCAATAATCAGTAATCACAC 59.243 38.462 13.01 0.00 0.00 3.82
2917 4162 6.873997 AGACGTCCAATAATCAGTAATCACA 58.126 36.000 13.01 0.00 0.00 3.58
2918 4163 7.203910 AGAGACGTCCAATAATCAGTAATCAC 58.796 38.462 13.01 0.00 0.00 3.06
2919 4164 7.068226 TGAGAGACGTCCAATAATCAGTAATCA 59.932 37.037 13.01 0.00 0.00 2.57
2920 4165 7.426410 TGAGAGACGTCCAATAATCAGTAATC 58.574 38.462 13.01 0.00 0.00 1.75
2921 4166 7.348080 TGAGAGACGTCCAATAATCAGTAAT 57.652 36.000 13.01 0.00 0.00 1.89
2922 4167 6.183360 CCTGAGAGACGTCCAATAATCAGTAA 60.183 42.308 13.01 0.00 32.86 2.24
2923 4168 5.299531 CCTGAGAGACGTCCAATAATCAGTA 59.700 44.000 13.01 0.00 32.86 2.74
2924 4169 4.098654 CCTGAGAGACGTCCAATAATCAGT 59.901 45.833 13.01 0.00 32.86 3.41
2925 4170 4.500545 CCCTGAGAGACGTCCAATAATCAG 60.501 50.000 13.01 15.12 34.18 2.90
2926 4171 3.384789 CCCTGAGAGACGTCCAATAATCA 59.615 47.826 13.01 6.84 0.00 2.57
2927 4172 3.637229 TCCCTGAGAGACGTCCAATAATC 59.363 47.826 13.01 1.63 0.00 1.75
2928 4173 3.643237 TCCCTGAGAGACGTCCAATAAT 58.357 45.455 13.01 0.00 0.00 1.28
2929 4174 3.095912 TCCCTGAGAGACGTCCAATAA 57.904 47.619 13.01 0.00 0.00 1.40
2930 4175 2.820728 TCCCTGAGAGACGTCCAATA 57.179 50.000 13.01 0.00 0.00 1.90
2931 4176 2.166907 ATCCCTGAGAGACGTCCAAT 57.833 50.000 13.01 0.00 0.00 3.16
2932 4177 1.938585 AATCCCTGAGAGACGTCCAA 58.061 50.000 13.01 0.00 0.00 3.53
2933 4178 2.656002 CTAATCCCTGAGAGACGTCCA 58.344 52.381 13.01 2.05 0.00 4.02
2934 4179 1.338655 GCTAATCCCTGAGAGACGTCC 59.661 57.143 13.01 3.77 0.00 4.79
2935 4180 2.034053 CAGCTAATCCCTGAGAGACGTC 59.966 54.545 7.70 7.70 32.03 4.34
2936 4181 2.028130 CAGCTAATCCCTGAGAGACGT 58.972 52.381 0.00 0.00 32.03 4.34
2937 4182 2.302260 TCAGCTAATCCCTGAGAGACG 58.698 52.381 0.00 0.00 34.59 4.18
2938 4183 4.100808 ACATTCAGCTAATCCCTGAGAGAC 59.899 45.833 0.00 0.00 40.16 3.36
2939 4184 4.293494 ACATTCAGCTAATCCCTGAGAGA 58.707 43.478 0.00 0.00 40.16 3.10
2940 4185 4.686191 ACATTCAGCTAATCCCTGAGAG 57.314 45.455 0.00 0.00 40.16 3.20
2941 4186 4.718774 AGAACATTCAGCTAATCCCTGAGA 59.281 41.667 0.00 0.00 40.16 3.27
2942 4187 5.033589 AGAACATTCAGCTAATCCCTGAG 57.966 43.478 0.00 0.00 40.16 3.35
2943 4188 5.441718 AAGAACATTCAGCTAATCCCTGA 57.558 39.130 0.00 0.00 37.54 3.86
2944 4189 5.067023 GGAAAGAACATTCAGCTAATCCCTG 59.933 44.000 0.00 0.00 0.00 4.45
2945 4190 5.044550 AGGAAAGAACATTCAGCTAATCCCT 60.045 40.000 0.00 0.00 0.00 4.20
2946 4191 5.196695 AGGAAAGAACATTCAGCTAATCCC 58.803 41.667 0.00 0.00 0.00 3.85
2947 4192 7.275920 TCTAGGAAAGAACATTCAGCTAATCC 58.724 38.462 0.00 0.00 0.00 3.01
2948 4193 8.723942 TTCTAGGAAAGAACATTCAGCTAATC 57.276 34.615 0.00 0.00 39.36 1.75
2949 4194 9.118300 CATTCTAGGAAAGAACATTCAGCTAAT 57.882 33.333 0.00 0.00 46.90 1.73
2950 4195 7.554118 CCATTCTAGGAAAGAACATTCAGCTAA 59.446 37.037 0.00 0.00 46.90 3.09
2951 4196 7.050377 CCATTCTAGGAAAGAACATTCAGCTA 58.950 38.462 0.00 0.00 46.90 3.32
2952 4197 5.884792 CCATTCTAGGAAAGAACATTCAGCT 59.115 40.000 0.00 0.00 46.90 4.24
2953 4198 5.649831 ACCATTCTAGGAAAGAACATTCAGC 59.350 40.000 0.00 0.00 46.90 4.26
2954 4199 6.881065 TGACCATTCTAGGAAAGAACATTCAG 59.119 38.462 0.00 0.00 46.90 3.02
2955 4200 6.655003 GTGACCATTCTAGGAAAGAACATTCA 59.345 38.462 0.00 0.00 46.90 2.57
2956 4201 6.655003 TGTGACCATTCTAGGAAAGAACATTC 59.345 38.462 0.00 0.00 46.90 2.67
2957 4202 6.542821 TGTGACCATTCTAGGAAAGAACATT 58.457 36.000 0.00 0.00 46.90 2.71
2958 4203 6.126863 TGTGACCATTCTAGGAAAGAACAT 57.873 37.500 0.00 0.00 46.90 2.71
2959 4204 5.560722 TGTGACCATTCTAGGAAAGAACA 57.439 39.130 0.00 0.00 46.90 3.18
2960 4205 6.173339 TCATGTGACCATTCTAGGAAAGAAC 58.827 40.000 0.00 0.00 46.90 3.01
2962 4207 5.721480 TCTCATGTGACCATTCTAGGAAAGA 59.279 40.000 0.00 0.00 0.00 2.52
2963 4208 5.982356 TCTCATGTGACCATTCTAGGAAAG 58.018 41.667 0.00 0.00 0.00 2.62
2964 4209 5.627735 GCTCTCATGTGACCATTCTAGGAAA 60.628 44.000 0.00 0.00 0.00 3.13
2965 4210 4.141846 GCTCTCATGTGACCATTCTAGGAA 60.142 45.833 0.00 0.00 0.00 3.36
2966 4211 3.386078 GCTCTCATGTGACCATTCTAGGA 59.614 47.826 0.00 0.00 0.00 2.94
2967 4212 3.387374 AGCTCTCATGTGACCATTCTAGG 59.613 47.826 0.00 0.00 0.00 3.02
2968 4213 4.669206 AGCTCTCATGTGACCATTCTAG 57.331 45.455 0.00 0.00 0.00 2.43
2969 4214 5.426689 AAAGCTCTCATGTGACCATTCTA 57.573 39.130 0.00 0.00 0.00 2.10
2970 4215 3.996921 AAGCTCTCATGTGACCATTCT 57.003 42.857 0.00 0.00 0.00 2.40
2971 4216 4.142513 GGAAAAGCTCTCATGTGACCATTC 60.143 45.833 0.00 0.00 0.00 2.67
2972 4217 3.760684 GGAAAAGCTCTCATGTGACCATT 59.239 43.478 0.00 0.00 0.00 3.16
2973 4218 3.350833 GGAAAAGCTCTCATGTGACCAT 58.649 45.455 0.00 0.00 0.00 3.55
2974 4219 2.553028 GGGAAAAGCTCTCATGTGACCA 60.553 50.000 0.00 0.00 0.00 4.02
2975 4220 2.087646 GGGAAAAGCTCTCATGTGACC 58.912 52.381 0.00 0.00 0.00 4.02
2976 4221 2.087646 GGGGAAAAGCTCTCATGTGAC 58.912 52.381 0.00 0.00 0.00 3.67
2977 4222 1.988107 AGGGGAAAAGCTCTCATGTGA 59.012 47.619 0.00 0.00 0.00 3.58
2978 4223 2.026449 AGAGGGGAAAAGCTCTCATGTG 60.026 50.000 0.00 0.00 0.00 3.21
2979 4224 2.273619 AGAGGGGAAAAGCTCTCATGT 58.726 47.619 0.00 0.00 0.00 3.21
2980 4225 3.015327 CAAGAGGGGAAAAGCTCTCATG 58.985 50.000 0.00 0.00 0.00 3.07
2981 4226 2.620108 GCAAGAGGGGAAAAGCTCTCAT 60.620 50.000 0.00 0.00 0.00 2.90
2982 4227 1.271597 GCAAGAGGGGAAAAGCTCTCA 60.272 52.381 0.00 0.00 0.00 3.27
2983 4228 1.004161 AGCAAGAGGGGAAAAGCTCTC 59.996 52.381 0.00 0.00 0.00 3.20
2984 4229 1.004161 GAGCAAGAGGGGAAAAGCTCT 59.996 52.381 0.00 0.00 43.68 4.09
2985 4230 1.004161 AGAGCAAGAGGGGAAAAGCTC 59.996 52.381 0.00 0.00 46.47 4.09
2986 4231 1.071434 AGAGCAAGAGGGGAAAAGCT 58.929 50.000 0.00 0.00 34.61 3.74
2987 4232 1.172175 CAGAGCAAGAGGGGAAAAGC 58.828 55.000 0.00 0.00 0.00 3.51
2988 4233 2.039613 AGACAGAGCAAGAGGGGAAAAG 59.960 50.000 0.00 0.00 0.00 2.27
2989 4234 2.039084 GAGACAGAGCAAGAGGGGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
2990 4235 1.625818 GAGACAGAGCAAGAGGGGAAA 59.374 52.381 0.00 0.00 0.00 3.13
2991 4236 1.270907 GAGACAGAGCAAGAGGGGAA 58.729 55.000 0.00 0.00 0.00 3.97
2992 4237 0.115152 TGAGACAGAGCAAGAGGGGA 59.885 55.000 0.00 0.00 0.00 4.81
2993 4238 0.979665 TTGAGACAGAGCAAGAGGGG 59.020 55.000 0.00 0.00 0.00 4.79
2994 4239 3.347077 AATTGAGACAGAGCAAGAGGG 57.653 47.619 0.00 0.00 0.00 4.30
2995 4240 5.220815 GCAATAATTGAGACAGAGCAAGAGG 60.221 44.000 0.00 0.00 0.00 3.69
2996 4241 5.585445 AGCAATAATTGAGACAGAGCAAGAG 59.415 40.000 0.00 0.00 0.00 2.85
2997 4242 5.353400 CAGCAATAATTGAGACAGAGCAAGA 59.647 40.000 0.00 0.00 0.00 3.02
2998 4243 5.123502 ACAGCAATAATTGAGACAGAGCAAG 59.876 40.000 0.00 0.00 0.00 4.01
2999 4244 5.005740 ACAGCAATAATTGAGACAGAGCAA 58.994 37.500 0.00 0.00 0.00 3.91
3000 4245 4.393990 CACAGCAATAATTGAGACAGAGCA 59.606 41.667 0.00 0.00 0.00 4.26
3001 4246 4.394300 ACACAGCAATAATTGAGACAGAGC 59.606 41.667 0.00 0.00 0.00 4.09
3002 4247 5.640783 TCACACAGCAATAATTGAGACAGAG 59.359 40.000 0.00 0.00 0.00 3.35
3003 4248 5.550290 TCACACAGCAATAATTGAGACAGA 58.450 37.500 0.00 0.00 0.00 3.41
3004 4249 5.868043 TCACACAGCAATAATTGAGACAG 57.132 39.130 0.00 0.00 0.00 3.51
3005 4250 6.822667 AATCACACAGCAATAATTGAGACA 57.177 33.333 0.00 0.00 0.00 3.41
3006 4251 7.907045 CAGTAATCACACAGCAATAATTGAGAC 59.093 37.037 0.00 0.00 0.00 3.36
3007 4252 7.823799 TCAGTAATCACACAGCAATAATTGAGA 59.176 33.333 0.00 0.00 0.00 3.27
3008 4253 7.977904 TCAGTAATCACACAGCAATAATTGAG 58.022 34.615 0.00 0.00 0.00 3.02
3009 4254 7.920160 TCAGTAATCACACAGCAATAATTGA 57.080 32.000 0.00 0.00 0.00 2.57
3014 4259 8.839343 CCAATAATCAGTAATCACACAGCAATA 58.161 33.333 0.00 0.00 0.00 1.90
3015 4260 7.557358 TCCAATAATCAGTAATCACACAGCAAT 59.443 33.333 0.00 0.00 0.00 3.56
3077 4322 2.777832 AAAGCTCTCAGGTGACCATC 57.222 50.000 3.63 0.00 0.00 3.51
3114 4359 6.993902 TCAGCTGCATTCATAGATACAATTGA 59.006 34.615 13.59 0.00 0.00 2.57
3145 4390 4.060205 GCAGCCTCAACAAAATCACAATT 58.940 39.130 0.00 0.00 0.00 2.32
3146 4391 3.069872 TGCAGCCTCAACAAAATCACAAT 59.930 39.130 0.00 0.00 0.00 2.71
3290 4536 3.751175 AGCAAACATGCGTTGTAGTATGT 59.249 39.130 10.48 0.00 46.65 2.29
3291 4537 4.340894 AGCAAACATGCGTTGTAGTATG 57.659 40.909 10.48 0.00 37.68 2.39
3292 4538 5.371115 AAAGCAAACATGCGTTGTAGTAT 57.629 34.783 10.48 0.00 37.68 2.12
3293 4539 4.319911 GGAAAGCAAACATGCGTTGTAGTA 60.320 41.667 6.71 0.00 37.68 1.82
3294 4540 3.550030 GGAAAGCAAACATGCGTTGTAGT 60.550 43.478 6.71 0.00 37.68 2.73
3295 4541 2.979813 GGAAAGCAAACATGCGTTGTAG 59.020 45.455 6.71 0.00 37.68 2.74


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

AutoCloner maintained by Alex Coulton.