Multiple sequence alignment - TraesCS5B01G429000

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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 TraesCS5B01G429000 chr5B 100.000 4533 0 0 521 5053 604291732 604287200 0.000000e+00 8371.0
1 TraesCS5B01G429000 chr5B 100.000 139 0 0 1 139 604292252 604292114 1.810000e-64 257.0
2 TraesCS5B01G429000 chr5D 91.077 2544 126 30 638 3123 490181216 490178716 0.000000e+00 3347.0
3 TraesCS5B01G429000 chr5D 92.053 906 45 7 3253 4135 490178511 490177610 0.000000e+00 1249.0
4 TraesCS5B01G429000 chr5D 87.107 923 73 22 4173 5053 490177185 490176267 0.000000e+00 1003.0
5 TraesCS5B01G429000 chr5D 92.701 137 10 0 3122 3258 490178686 490178550 1.110000e-46 198.0
6 TraesCS5B01G429000 chr5D 97.872 47 1 0 4129 4175 490177353 490177307 1.170000e-11 82.4
7 TraesCS5B01G429000 chr5A 88.852 1830 112 45 521 2295 611835370 611833578 0.000000e+00 2165.0
8 TraesCS5B01G429000 chr5A 93.804 1033 40 12 3122 4135 611832678 611831651 0.000000e+00 1531.0
9 TraesCS5B01G429000 chr5A 90.940 883 54 10 2254 3123 611833577 611832708 0.000000e+00 1164.0
10 TraesCS5B01G429000 chr5A 76.991 452 70 25 4550 4994 79276623 79276199 1.420000e-55 228.0
11 TraesCS5B01G429000 chr5A 78.187 353 60 15 4550 4897 692380933 692381273 5.130000e-50 209.0
12 TraesCS5B01G429000 chr5A 77.027 370 69 16 4536 4897 608273944 608274305 1.110000e-46 198.0
13 TraesCS5B01G429000 chrUn 79.275 883 141 32 4172 5021 363549454 363550327 3.390000e-161 579.0
14 TraesCS5B01G429000 chrUn 78.587 892 140 33 4172 5021 362996883 362997765 4.450000e-150 542.0
15 TraesCS5B01G429000 chr3A 79.275 883 141 32 4172 5021 1245289 1244416 3.390000e-161 579.0
16 TraesCS5B01G429000 chr3A 78.587 892 140 33 4172 5021 1257641 1256759 4.450000e-150 542.0
17 TraesCS5B01G429000 chr2A 75.036 693 125 26 4240 4897 136636256 136636935 1.390000e-70 278.0
18 TraesCS5B01G429000 chr2A 78.512 121 24 2 1889 2008 369202396 369202277 1.510000e-10 78.7


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 TraesCS5B01G429000 chr5B 604287200 604292252 5052 True 4314.00 8371 100.000000 1 5053 2 chr5B.!!$R1 5052
1 TraesCS5B01G429000 chr5D 490176267 490181216 4949 True 1175.88 3347 92.162000 638 5053 5 chr5D.!!$R1 4415
2 TraesCS5B01G429000 chr5A 611831651 611835370 3719 True 1620.00 2165 91.198667 521 4135 3 chr5A.!!$R2 3614
3 TraesCS5B01G429000 chrUn 363549454 363550327 873 False 579.00 579 79.275000 4172 5021 1 chrUn.!!$F2 849
4 TraesCS5B01G429000 chrUn 362996883 362997765 882 False 542.00 542 78.587000 4172 5021 1 chrUn.!!$F1 849
5 TraesCS5B01G429000 chr3A 1244416 1245289 873 True 579.00 579 79.275000 4172 5021 1 chr3A.!!$R1 849
6 TraesCS5B01G429000 chr3A 1256759 1257641 882 True 542.00 542 78.587000 4172 5021 1 chr3A.!!$R2 849
7 TraesCS5B01G429000 chr2A 136636256 136636935 679 False 278.00 278 75.036000 4240 4897 1 chr2A.!!$F1 657

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
707 746 0.105039 CGCGAGGGAAAGGCTAGATT 59.895 55.0 0.0 0.0 0.00 2.40 F
2295 2434 0.598065 AGATTTTGGTTGTGCCTCGC 59.402 50.0 0.0 0.0 38.35 5.03 F
2907 3064 0.107654 GCTGCGTGGGAGATAAACCT 60.108 55.0 0.0 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2444 0.251073 GCCCAGCCAAGATTTGCAAT 59.749 50.0 0.00 0.00 0.0 3.56 R
3633 3868 0.179000 CCTGTGGAGTAGTCATGGCC 59.821 60.0 0.00 0.00 0.0 5.36 R
4183 4844 0.846427 AATCCTTGTGAGCTCCCCCA 60.846 55.0 12.15 2.27 0.0 4.96 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
19 20 2.480224 AACGACGACGAACAGAAAGA 57.520 45.000 15.32 0.00 42.66 2.52
20 21 2.701073 ACGACGACGAACAGAAAGAT 57.299 45.000 15.32 0.00 42.66 2.40
21 22 2.316792 ACGACGACGAACAGAAAGATG 58.683 47.619 15.32 0.00 42.66 2.90
22 23 1.649171 CGACGACGAACAGAAAGATGG 59.351 52.381 0.00 0.00 42.66 3.51
23 24 1.390463 GACGACGAACAGAAAGATGGC 59.610 52.381 0.00 0.00 0.00 4.40
24 25 0.366871 CGACGAACAGAAAGATGGCG 59.633 55.000 0.00 0.00 0.00 5.69
25 26 1.429463 GACGAACAGAAAGATGGCGT 58.571 50.000 0.00 0.00 37.80 5.68
26 27 1.126846 GACGAACAGAAAGATGGCGTG 59.873 52.381 0.00 0.00 36.10 5.34
27 28 0.179215 CGAACAGAAAGATGGCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
28 29 1.160137 GAACAGAAAGATGGCGTGCT 58.840 50.000 0.00 0.00 0.00 4.40
29 30 2.346803 GAACAGAAAGATGGCGTGCTA 58.653 47.619 0.00 0.00 0.00 3.49
30 31 1.726853 ACAGAAAGATGGCGTGCTAC 58.273 50.000 0.00 0.00 0.00 3.58
31 32 1.001974 ACAGAAAGATGGCGTGCTACA 59.998 47.619 0.00 0.00 0.00 2.74
32 33 2.076100 CAGAAAGATGGCGTGCTACAA 58.924 47.619 0.00 0.00 0.00 2.41
33 34 2.483877 CAGAAAGATGGCGTGCTACAAA 59.516 45.455 0.00 0.00 0.00 2.83
34 35 3.058293 CAGAAAGATGGCGTGCTACAAAA 60.058 43.478 0.00 0.00 0.00 2.44
35 36 3.758554 AGAAAGATGGCGTGCTACAAAAT 59.241 39.130 0.00 0.00 0.00 1.82
36 37 4.941263 AGAAAGATGGCGTGCTACAAAATA 59.059 37.500 0.00 0.00 0.00 1.40
37 38 5.414454 AGAAAGATGGCGTGCTACAAAATAA 59.586 36.000 0.00 0.00 0.00 1.40
38 39 5.637006 AAGATGGCGTGCTACAAAATAAA 57.363 34.783 0.00 0.00 0.00 1.40
39 40 5.637006 AGATGGCGTGCTACAAAATAAAA 57.363 34.783 0.00 0.00 0.00 1.52
40 41 6.019779 AGATGGCGTGCTACAAAATAAAAA 57.980 33.333 0.00 0.00 0.00 1.94
41 42 6.630071 AGATGGCGTGCTACAAAATAAAAAT 58.370 32.000 0.00 0.00 0.00 1.82
42 43 7.767261 AGATGGCGTGCTACAAAATAAAAATA 58.233 30.769 0.00 0.00 0.00 1.40
43 44 8.247562 AGATGGCGTGCTACAAAATAAAAATAA 58.752 29.630 0.00 0.00 0.00 1.40
44 45 8.764524 ATGGCGTGCTACAAAATAAAAATAAA 57.235 26.923 0.00 0.00 0.00 1.40
45 46 8.589335 TGGCGTGCTACAAAATAAAAATAAAA 57.411 26.923 0.00 0.00 0.00 1.52
46 47 9.042008 TGGCGTGCTACAAAATAAAAATAAAAA 57.958 25.926 0.00 0.00 0.00 1.94
55 56 9.958234 ACAAAATAAAAATAAAAATGGTGTGGC 57.042 25.926 0.00 0.00 0.00 5.01
56 57 9.404348 CAAAATAAAAATAAAAATGGTGTGGCC 57.596 29.630 0.00 0.00 37.90 5.36
64 65 3.569210 TGGTGTGGCCAGGACAGG 61.569 66.667 5.11 0.00 43.61 4.00
72 73 4.463879 CCAGGACAGGCCAGCTCG 62.464 72.222 5.01 0.00 40.02 5.03
85 86 4.418470 GCTCGCGCGCAAACGTAA 62.418 61.111 32.61 3.74 42.83 3.18
86 87 2.169091 CTCGCGCGCAAACGTAAA 59.831 55.556 32.61 2.86 42.83 2.01
87 88 1.437411 CTCGCGCGCAAACGTAAAA 60.437 52.632 32.61 1.98 42.83 1.52
88 89 0.987848 CTCGCGCGCAAACGTAAAAA 60.988 50.000 32.61 1.35 42.83 1.94
115 116 2.821366 CAGGAGTGGCGGCACATC 60.821 66.667 38.86 30.32 0.00 3.06
116 117 4.457496 AGGAGTGGCGGCACATCG 62.457 66.667 38.86 0.00 0.00 3.84
117 118 4.760047 GGAGTGGCGGCACATCGT 62.760 66.667 38.86 22.02 0.00 3.73
118 119 2.183300 GAGTGGCGGCACATCGTA 59.817 61.111 38.86 1.15 0.00 3.43
119 120 1.878522 GAGTGGCGGCACATCGTAG 60.879 63.158 38.86 0.00 0.00 3.51
120 121 2.183300 GTGGCGGCACATCGTAGA 59.817 61.111 34.40 0.00 45.75 2.59
121 122 2.165301 GTGGCGGCACATCGTAGAC 61.165 63.158 34.40 5.93 42.51 2.59
122 123 2.954868 GGCGGCACATCGTAGACG 60.955 66.667 3.07 0.00 42.51 4.18
123 124 2.202570 GCGGCACATCGTAGACGT 60.203 61.111 1.46 0.00 42.51 4.34
124 125 1.063006 GCGGCACATCGTAGACGTA 59.937 57.895 1.46 0.00 42.51 3.57
125 126 0.928908 GCGGCACATCGTAGACGTAG 60.929 60.000 1.46 0.00 42.51 3.51
126 127 0.654160 CGGCACATCGTAGACGTAGA 59.346 55.000 1.46 0.00 42.51 2.59
127 128 1.594034 CGGCACATCGTAGACGTAGAC 60.594 57.143 1.46 0.00 42.51 2.59
128 129 1.594034 GGCACATCGTAGACGTAGACG 60.594 57.143 13.92 13.92 42.51 4.18
133 134 1.359848 TCGTAGACGTAGACGAACCC 58.640 55.000 18.87 0.00 44.56 4.11
134 135 0.375106 CGTAGACGTAGACGAACCCC 59.625 60.000 14.74 0.00 41.60 4.95
135 136 0.735471 GTAGACGTAGACGAACCCCC 59.265 60.000 9.41 0.00 43.02 5.40
541 542 2.627945 GACCGTATGCCACTGAATCAA 58.372 47.619 0.00 0.00 0.00 2.57
542 543 3.206150 GACCGTATGCCACTGAATCAAT 58.794 45.455 0.00 0.00 0.00 2.57
543 544 3.620488 ACCGTATGCCACTGAATCAATT 58.380 40.909 0.00 0.00 0.00 2.32
586 592 0.395312 TTTTCCCGCGAGAAGTTCCT 59.605 50.000 8.23 0.00 0.00 3.36
623 629 4.277476 TGAGAAAAACACCACACAATCCT 58.723 39.130 0.00 0.00 0.00 3.24
631 637 1.956477 ACCACACAATCCTCAAGTTGC 59.044 47.619 0.00 0.00 0.00 4.17
645 670 2.281414 TTGCCAAGCTAGTGCGCA 60.281 55.556 5.66 5.66 45.42 6.09
652 677 1.001378 CAAGCTAGTGCGCACCTTTTT 60.001 47.619 35.51 21.88 45.42 1.94
707 746 0.105039 CGCGAGGGAAAGGCTAGATT 59.895 55.000 0.00 0.00 0.00 2.40
711 750 3.560481 GCGAGGGAAAGGCTAGATTAAAC 59.440 47.826 0.00 0.00 0.00 2.01
733 772 6.331369 ACCAAATCAAATCAAATCGTGAGT 57.669 33.333 0.00 0.00 40.43 3.41
735 774 5.574055 CCAAATCAAATCAAATCGTGAGTGG 59.426 40.000 0.00 0.00 40.43 4.00
797 836 3.936203 TGGAAAGCTCACCGGCGT 61.936 61.111 6.01 0.00 37.29 5.68
813 855 1.405461 GCGTGATGCAATGATGATGC 58.595 50.000 0.00 0.00 45.45 3.91
814 856 1.929038 GCGTGATGCAATGATGATGCC 60.929 52.381 0.00 0.00 45.45 4.40
815 857 1.662026 CGTGATGCAATGATGATGCCG 60.662 52.381 0.00 0.00 43.16 5.69
983 1040 3.647771 ACCACTCCCCGCCTTTCC 61.648 66.667 0.00 0.00 0.00 3.13
984 1041 4.426313 CCACTCCCCGCCTTTCCC 62.426 72.222 0.00 0.00 0.00 3.97
985 1042 4.426313 CACTCCCCGCCTTTCCCC 62.426 72.222 0.00 0.00 0.00 4.81
986 1043 4.677151 ACTCCCCGCCTTTCCCCT 62.677 66.667 0.00 0.00 0.00 4.79
987 1044 3.798511 CTCCCCGCCTTTCCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
993 1050 2.947217 GCCTTTCCCCTCCCCCTT 60.947 66.667 0.00 0.00 0.00 3.95
1138 1198 4.181010 CCCCCATGGACCAGCTCG 62.181 72.222 15.22 0.00 35.39 5.03
1158 1218 4.862823 GACCCCTCCCCCTCCTCG 62.863 77.778 0.00 0.00 0.00 4.63
1161 1221 4.075793 CCCTCCCCCTCCTCGTCA 62.076 72.222 0.00 0.00 0.00 4.35
1162 1222 2.283809 CCTCCCCCTCCTCGTCAT 59.716 66.667 0.00 0.00 0.00 3.06
1164 1224 1.834822 CTCCCCCTCCTCGTCATCC 60.835 68.421 0.00 0.00 0.00 3.51
1165 1225 2.283809 CCCCCTCCTCGTCATCCT 59.716 66.667 0.00 0.00 0.00 3.24
1166 1226 2.136878 CCCCCTCCTCGTCATCCTG 61.137 68.421 0.00 0.00 0.00 3.86
1167 1227 2.801631 CCCCTCCTCGTCATCCTGC 61.802 68.421 0.00 0.00 0.00 4.85
1296 1356 3.068881 CGGGTTGAGGAGCTGGAA 58.931 61.111 0.00 0.00 0.00 3.53
1566 1626 2.962253 GCATCCTACCACTCGCGC 60.962 66.667 0.00 0.00 0.00 6.86
1658 1718 3.822192 CCACGCGGACCAGATCGA 61.822 66.667 12.47 0.00 0.00 3.59
1669 1729 1.032657 CCAGATCGACGACCTGGTCT 61.033 60.000 27.55 10.86 41.81 3.85
1758 1824 1.277557 GAGGAGGAAGAGCAAGAGCAA 59.722 52.381 0.00 0.00 45.49 3.91
1803 1869 0.806868 TCGAGTACACGGTGGATGTC 59.193 55.000 13.48 4.47 0.00 3.06
1929 1995 2.482374 GACAGAGCGGCAATGCAC 59.518 61.111 7.79 0.00 37.31 4.57
1947 2013 2.105930 AGAGAGATTGCGGCGCTC 59.894 61.111 33.26 22.64 33.15 5.03
2037 2103 6.998074 TCTCTGAGAGGAAAAGCATTGTTAAA 59.002 34.615 9.97 0.00 0.00 1.52
2070 2136 1.439644 GGCGAAGAGATTCTCGGCT 59.560 57.895 19.53 6.55 45.53 5.52
2093 2159 8.204160 GGCTTTAGGAATTTGCAAGGTATAATT 58.796 33.333 0.00 0.00 0.00 1.40
2171 2237 1.685302 AACATCGTTCGTGCATTTGC 58.315 45.000 0.00 0.00 42.50 3.68
2205 2294 5.882557 CAGGTGCTAACTTCAGAATATTGGT 59.117 40.000 0.00 0.00 0.00 3.67
2237 2326 4.080356 TGGAGCCTAGCACATTTGTAGAAT 60.080 41.667 0.00 0.00 0.00 2.40
2241 2338 7.254932 GGAGCCTAGCACATTTGTAGAATTTAG 60.255 40.741 0.00 0.00 0.00 1.85
2295 2434 0.598065 AGATTTTGGTTGTGCCTCGC 59.402 50.000 0.00 0.00 38.35 5.03
2324 2463 0.251073 ATTGCAAATCTTGGCTGGGC 59.749 50.000 1.71 0.00 0.00 5.36
2325 2464 2.157305 TTGCAAATCTTGGCTGGGCG 62.157 55.000 0.00 0.00 0.00 6.13
2326 2465 2.182537 CAAATCTTGGCTGGGCGC 59.817 61.111 0.00 0.00 38.13 6.53
2327 2466 3.443045 AAATCTTGGCTGGGCGCG 61.443 61.111 0.00 0.00 40.44 6.86
2423 2562 2.138656 GAAGCAGCAAGGCACCAGTG 62.139 60.000 0.00 0.00 35.83 3.66
2432 2571 2.826128 CAAGGCACCAGTGAGTACTCTA 59.174 50.000 23.01 7.59 34.07 2.43
2552 2691 2.694628 AGTGCATGAACTTGCTTTGGAA 59.305 40.909 0.00 0.00 43.18 3.53
2569 2708 6.500684 TTTGGAAGTGTGATTATCAGCTTC 57.499 37.500 21.06 21.06 38.12 3.86
2586 2725 5.880332 TCAGCTTCTGTACTCTTTGTTGTTT 59.120 36.000 0.00 0.00 32.61 2.83
2591 2730 6.578020 TCTGTACTCTTTGTTGTTTACACG 57.422 37.500 0.00 0.00 36.21 4.49
2697 2836 9.529823 TTAGTTTGTGTCTCTTATTAGGAGAGA 57.470 33.333 5.81 2.47 45.44 3.10
2734 2873 5.465935 TCGTTTGGTGGATTCATTTTTAGC 58.534 37.500 0.00 0.00 0.00 3.09
2738 2877 5.811399 TGGTGGATTCATTTTTAGCTACG 57.189 39.130 0.00 0.00 0.00 3.51
2770 2920 3.844211 TGGGAGACTATGTGCTTAAGGTT 59.156 43.478 4.29 0.00 0.00 3.50
2800 2950 2.135933 GTACACTGGAGAGTTGCACAC 58.864 52.381 0.00 0.00 0.00 3.82
2816 2966 2.843077 CACACTTGCAGAATAGTTGCG 58.157 47.619 0.00 0.00 44.40 4.85
2871 3021 2.311542 TGGTGGTGGCCTAGATGAAATT 59.688 45.455 3.32 0.00 0.00 1.82
2880 3030 5.957168 TGGCCTAGATGAAATTGGATTTTGA 59.043 36.000 3.32 0.00 31.47 2.69
2885 3035 9.933723 CCTAGATGAAATTGGATTTTGAAAGTT 57.066 29.630 0.00 0.00 31.47 2.66
2906 3063 1.095807 GGCTGCGTGGGAGATAAACC 61.096 60.000 0.00 0.00 0.00 3.27
2907 3064 0.107654 GCTGCGTGGGAGATAAACCT 60.108 55.000 0.00 0.00 0.00 3.50
3164 3353 8.070171 ACAAATTTGTGAAGTGAATAGAGTTCG 58.930 33.333 22.71 0.00 40.49 3.95
3175 3364 6.649557 AGTGAATAGAGTTCGTTTACCAAAGG 59.350 38.462 0.00 0.00 0.00 3.11
3246 3435 7.110155 ACAGACTGAACTCCTTTTCTTGTTAA 58.890 34.615 10.08 0.00 0.00 2.01
3261 3495 9.621629 TTTTCTTGTTAACCTTTCATCTAGACA 57.378 29.630 2.48 0.00 0.00 3.41
3283 3517 8.370940 AGACATGGTAGTAATGAGATACAATGG 58.629 37.037 0.00 0.00 35.85 3.16
3331 3565 8.344831 TGATATGTCTGTTCTGTTTTTCTGTTG 58.655 33.333 0.00 0.00 0.00 3.33
3455 3689 2.173519 CCACCCTTGAGTAGTTCGGTA 58.826 52.381 0.00 0.00 0.00 4.02
3487 3721 1.699083 TGCCACTGTTCTCATCCTTGA 59.301 47.619 0.00 0.00 0.00 3.02
3539 3774 2.930682 GTGGTTGCTCTCCGTAATCTTC 59.069 50.000 0.00 0.00 0.00 2.87
3615 3850 6.268847 ACCTATGATTATCCTTCTTCGCTCTT 59.731 38.462 0.00 0.00 0.00 2.85
3616 3851 7.158021 CCTATGATTATCCTTCTTCGCTCTTT 58.842 38.462 0.00 0.00 0.00 2.52
3633 3868 2.034053 TCTTTTGCAACCCTAAACTGCG 59.966 45.455 0.00 0.00 38.97 5.18
3670 3905 1.194495 GGTATACGTTCGGCTTGTCG 58.806 55.000 0.00 0.00 0.00 4.35
3673 3908 0.457337 ATACGTTCGGCTTGTCGACC 60.457 55.000 14.12 0.00 39.01 4.79
3804 4039 5.034554 ACACATGTAAATGCAGAACTTCG 57.965 39.130 0.00 0.00 0.00 3.79
3856 4091 4.206404 GTGCATTGCATTCTTTGATGATCG 59.794 41.667 15.49 0.00 41.91 3.69
3864 4099 5.741040 GCATTCTTTGATGATCGGTTTCTTC 59.259 40.000 0.00 0.00 0.00 2.87
3911 4146 4.396790 GGTATTGGCGATGTAAGTTTTGGA 59.603 41.667 0.00 0.00 0.00 3.53
3948 4183 5.586243 AGCTTGCTGTATAGTGTGTTATTGG 59.414 40.000 0.00 0.00 0.00 3.16
3990 4225 7.072263 AGCTTGTAATATGGAGCTAACTGAT 57.928 36.000 0.00 0.00 43.21 2.90
4071 4345 7.721286 ACTTCACTCTTCAGATTTGTACTTG 57.279 36.000 0.00 0.00 0.00 3.16
4102 4376 6.452242 TCTTGAACTAGCATCGTGACTTAAA 58.548 36.000 0.00 0.00 0.00 1.52
4183 4844 7.356089 TGTGTCCGGTATAATACAGAGAAAT 57.644 36.000 0.00 0.00 0.00 2.17
4187 4848 5.247564 TCCGGTATAATACAGAGAAATGGGG 59.752 44.000 0.00 0.00 0.00 4.96
4206 4867 2.363683 GGGAGCTCACAAGGATTCAAG 58.636 52.381 17.19 0.00 0.00 3.02
4229 4890 2.367567 TCAAGACCTCGCACTTAAAGGT 59.632 45.455 0.00 0.00 46.03 3.50
4250 4911 0.989890 CGCGTTACTAGCCACTTGAC 59.010 55.000 0.00 0.00 0.00 3.18
4420 5089 6.035070 ACGAAATTTGAGCACACATTTTTG 57.965 33.333 9.20 8.01 36.79 2.44
4421 5090 5.809562 ACGAAATTTGAGCACACATTTTTGA 59.190 32.000 9.20 0.00 36.79 2.69
4457 5126 9.566624 CACAATTTCGAAACATGAACAATTTAC 57.433 29.630 24.45 0.00 0.00 2.01
4536 5225 3.786516 TTGTTTGTCCCGTTTTCCTTC 57.213 42.857 0.00 0.00 0.00 3.46
4540 5229 4.948621 TGTTTGTCCCGTTTTCCTTCTTTA 59.051 37.500 0.00 0.00 0.00 1.85
4541 5230 5.418209 TGTTTGTCCCGTTTTCCTTCTTTAA 59.582 36.000 0.00 0.00 0.00 1.52
4547 5236 7.492994 TGTCCCGTTTTCCTTCTTTAAAATTTG 59.507 33.333 0.00 0.00 0.00 2.32
4549 5238 7.492994 TCCCGTTTTCCTTCTTTAAAATTTGTG 59.507 33.333 0.00 0.00 0.00 3.33
4552 5241 9.683651 CGTTTTCCTTCTTTAAAATTTGTGAAC 57.316 29.630 0.00 0.00 0.00 3.18
4897 5619 9.920826 GTTGATTCATTTTTCTCCTTTTTGAAC 57.079 29.630 0.00 0.00 0.00 3.18
4909 5631 9.862149 TTCTCCTTTTTGAACTTTATTACTCCT 57.138 29.630 0.00 0.00 0.00 3.69
4922 5644 9.965824 ACTTTATTACTCCTTTTGAAACATGTG 57.034 29.630 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.480224 TCTTTCTGTTCGTCGTCGTT 57.520 45.000 1.33 0.00 38.33 3.85
1 2 2.316792 CATCTTTCTGTTCGTCGTCGT 58.683 47.619 1.33 0.00 38.33 4.34
2 3 1.649171 CCATCTTTCTGTTCGTCGTCG 59.351 52.381 0.00 0.00 38.55 5.12
3 4 1.390463 GCCATCTTTCTGTTCGTCGTC 59.610 52.381 0.00 0.00 0.00 4.20
4 5 1.429463 GCCATCTTTCTGTTCGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
5 6 0.366871 CGCCATCTTTCTGTTCGTCG 59.633 55.000 0.00 0.00 0.00 5.12
6 7 1.126846 CACGCCATCTTTCTGTTCGTC 59.873 52.381 0.00 0.00 0.00 4.20
7 8 1.148310 CACGCCATCTTTCTGTTCGT 58.852 50.000 0.00 0.00 0.00 3.85
8 9 0.179215 GCACGCCATCTTTCTGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
9 10 1.160137 AGCACGCCATCTTTCTGTTC 58.840 50.000 0.00 0.00 0.00 3.18
10 11 2.076863 GTAGCACGCCATCTTTCTGTT 58.923 47.619 0.00 0.00 0.00 3.16
11 12 1.001974 TGTAGCACGCCATCTTTCTGT 59.998 47.619 0.00 0.00 0.00 3.41
12 13 1.725641 TGTAGCACGCCATCTTTCTG 58.274 50.000 0.00 0.00 0.00 3.02
13 14 2.472695 TTGTAGCACGCCATCTTTCT 57.527 45.000 0.00 0.00 0.00 2.52
14 15 3.552604 TTTTGTAGCACGCCATCTTTC 57.447 42.857 0.00 0.00 0.00 2.62
15 16 5.637006 TTATTTTGTAGCACGCCATCTTT 57.363 34.783 0.00 0.00 0.00 2.52
16 17 5.637006 TTTATTTTGTAGCACGCCATCTT 57.363 34.783 0.00 0.00 0.00 2.40
17 18 5.637006 TTTTATTTTGTAGCACGCCATCT 57.363 34.783 0.00 0.00 0.00 2.90
18 19 6.885735 ATTTTTATTTTGTAGCACGCCATC 57.114 33.333 0.00 0.00 0.00 3.51
19 20 8.764524 TTTATTTTTATTTTGTAGCACGCCAT 57.235 26.923 0.00 0.00 0.00 4.40
20 21 8.589335 TTTTATTTTTATTTTGTAGCACGCCA 57.411 26.923 0.00 0.00 0.00 5.69
29 30 9.958234 GCCACACCATTTTTATTTTTATTTTGT 57.042 25.926 0.00 0.00 0.00 2.83
30 31 9.404348 GGCCACACCATTTTTATTTTTATTTTG 57.596 29.630 0.00 0.00 38.86 2.44
31 32 9.136323 TGGCCACACCATTTTTATTTTTATTTT 57.864 25.926 0.00 0.00 46.36 1.82
32 33 8.697507 TGGCCACACCATTTTTATTTTTATTT 57.302 26.923 0.00 0.00 46.36 1.40
55 56 4.463879 CGAGCTGGCCTGTCCTGG 62.464 72.222 11.69 0.00 34.64 4.45
69 70 0.987848 TTTTTACGTTTGCGCGCGAG 60.988 50.000 37.18 19.93 42.83 5.03
70 71 1.011463 TTTTTACGTTTGCGCGCGA 60.011 47.368 37.18 23.83 42.83 5.87
71 72 3.500968 TTTTTACGTTTGCGCGCG 58.499 50.000 28.44 28.44 42.83 6.86
85 86 3.119137 GCCACTCCTGCGGATTTATTTTT 60.119 43.478 0.00 0.00 0.00 1.94
86 87 2.427095 GCCACTCCTGCGGATTTATTTT 59.573 45.455 0.00 0.00 0.00 1.82
87 88 2.024414 GCCACTCCTGCGGATTTATTT 58.976 47.619 0.00 0.00 0.00 1.40
88 89 1.680338 GCCACTCCTGCGGATTTATT 58.320 50.000 0.00 0.00 0.00 1.40
89 90 3.403936 GCCACTCCTGCGGATTTAT 57.596 52.632 0.00 0.00 0.00 1.40
90 91 4.954933 GCCACTCCTGCGGATTTA 57.045 55.556 0.00 0.00 0.00 1.40
98 99 2.821366 GATGTGCCGCCACTCCTG 60.821 66.667 0.00 0.00 42.54 3.86
99 100 4.457496 CGATGTGCCGCCACTCCT 62.457 66.667 0.00 0.00 42.54 3.69
100 101 3.365291 TACGATGTGCCGCCACTCC 62.365 63.158 0.00 0.00 42.54 3.85
101 102 1.878522 CTACGATGTGCCGCCACTC 60.879 63.158 0.00 0.00 42.54 3.51
102 103 2.184322 CTACGATGTGCCGCCACT 59.816 61.111 0.00 0.00 42.54 4.00
103 104 2.165301 GTCTACGATGTGCCGCCAC 61.165 63.158 0.00 0.00 42.40 5.01
104 105 2.183300 GTCTACGATGTGCCGCCA 59.817 61.111 0.00 0.00 0.00 5.69
105 106 2.327002 TACGTCTACGATGTGCCGCC 62.327 60.000 9.86 0.00 43.02 6.13
106 107 0.928908 CTACGTCTACGATGTGCCGC 60.929 60.000 9.86 0.00 43.02 6.53
107 108 0.654160 TCTACGTCTACGATGTGCCG 59.346 55.000 9.86 0.00 43.02 5.69
108 109 1.594034 CGTCTACGTCTACGATGTGCC 60.594 57.143 15.31 0.00 41.55 5.01
109 110 1.325640 TCGTCTACGTCTACGATGTGC 59.674 52.381 18.11 0.00 42.74 4.57
110 111 3.340552 GTTCGTCTACGTCTACGATGTG 58.659 50.000 21.36 0.00 46.44 3.21
111 112 2.349886 GGTTCGTCTACGTCTACGATGT 59.650 50.000 21.36 0.00 46.44 3.06
112 113 2.286067 GGGTTCGTCTACGTCTACGATG 60.286 54.545 21.36 7.73 46.44 3.84
113 114 1.936547 GGGTTCGTCTACGTCTACGAT 59.063 52.381 21.36 0.00 46.44 3.73
114 115 1.359848 GGGTTCGTCTACGTCTACGA 58.640 55.000 18.11 18.11 45.64 3.43
115 116 0.375106 GGGGTTCGTCTACGTCTACG 59.625 60.000 14.49 14.49 46.33 3.51
116 117 0.735471 GGGGGTTCGTCTACGTCTAC 59.265 60.000 0.00 0.00 40.80 2.59
117 118 3.175133 GGGGGTTCGTCTACGTCTA 57.825 57.895 0.00 0.00 40.80 2.59
118 119 4.009015 GGGGGTTCGTCTACGTCT 57.991 61.111 0.00 0.00 40.80 4.18
560 566 3.435671 ACTTCTCGCGGGAAAATAAACAG 59.564 43.478 23.67 10.74 0.00 3.16
605 611 4.466015 ACTTGAGGATTGTGTGGTGTTTTT 59.534 37.500 0.00 0.00 0.00 1.94
623 629 1.238439 GCACTAGCTTGGCAACTTGA 58.762 50.000 14.26 0.00 37.91 3.02
631 637 1.237285 AAAGGTGCGCACTAGCTTGG 61.237 55.000 36.84 0.00 36.15 3.61
652 677 1.862911 AGAGGAGGAGCAGGGAGATAA 59.137 52.381 0.00 0.00 0.00 1.75
653 678 1.146774 CAGAGGAGGAGCAGGGAGATA 59.853 57.143 0.00 0.00 0.00 1.98
654 679 0.105555 CAGAGGAGGAGCAGGGAGAT 60.106 60.000 0.00 0.00 0.00 2.75
655 680 1.309347 CAGAGGAGGAGCAGGGAGA 59.691 63.158 0.00 0.00 0.00 3.71
656 681 0.617249 AACAGAGGAGGAGCAGGGAG 60.617 60.000 0.00 0.00 0.00 4.30
657 682 0.616111 GAACAGAGGAGGAGCAGGGA 60.616 60.000 0.00 0.00 0.00 4.20
658 683 0.617249 AGAACAGAGGAGGAGCAGGG 60.617 60.000 0.00 0.00 0.00 4.45
659 684 1.206849 GAAGAACAGAGGAGGAGCAGG 59.793 57.143 0.00 0.00 0.00 4.85
660 685 1.206849 GGAAGAACAGAGGAGGAGCAG 59.793 57.143 0.00 0.00 0.00 4.24
661 686 1.270907 GGAAGAACAGAGGAGGAGCA 58.729 55.000 0.00 0.00 0.00 4.26
662 687 0.539518 GGGAAGAACAGAGGAGGAGC 59.460 60.000 0.00 0.00 0.00 4.70
663 688 1.199615 GGGGAAGAACAGAGGAGGAG 58.800 60.000 0.00 0.00 0.00 3.69
666 691 2.784347 GTTTGGGGAAGAACAGAGGAG 58.216 52.381 0.00 0.00 0.00 3.69
707 746 8.356657 ACTCACGATTTGATTTGATTTGGTTTA 58.643 29.630 0.00 0.00 32.17 2.01
711 750 5.574055 CCACTCACGATTTGATTTGATTTGG 59.426 40.000 0.00 0.00 32.17 3.28
733 772 3.918253 AAGAATGAAGCGGCCGCCA 62.918 57.895 44.47 35.44 43.17 5.69
735 774 0.388520 AAAAAGAATGAAGCGGCCGC 60.389 50.000 42.34 42.34 42.33 6.53
797 836 0.955905 CCGGCATCATCATTGCATCA 59.044 50.000 0.00 0.00 41.95 3.07
802 844 1.829096 TGGGCCGGCATCATCATTG 60.829 57.895 30.85 0.00 0.00 2.82
803 845 1.829533 GTGGGCCGGCATCATCATT 60.830 57.895 30.85 0.00 0.00 2.57
813 855 4.499633 AATAAGCGGGTGGGCCGG 62.500 66.667 0.00 0.00 38.05 6.13
814 856 2.900337 GAATAAGCGGGTGGGCCG 60.900 66.667 0.00 0.00 34.97 6.13
815 857 2.518587 GGAATAAGCGGGTGGGCC 60.519 66.667 0.00 0.00 0.00 5.80
983 1040 4.845307 GGGAGGGAAGGGGGAGGG 62.845 77.778 0.00 0.00 0.00 4.30
984 1041 4.845307 GGGGAGGGAAGGGGGAGG 62.845 77.778 0.00 0.00 0.00 4.30
991 1048 3.682292 CTTTCGGCGGGGAGGGAAG 62.682 68.421 7.21 0.00 0.00 3.46
992 1049 3.712907 CTTTCGGCGGGGAGGGAA 61.713 66.667 7.21 0.00 0.00 3.97
1140 1200 4.500826 GAGGAGGGGGAGGGGTCC 62.501 77.778 0.00 0.00 0.00 4.46
1144 1204 3.396822 ATGACGAGGAGGGGGAGGG 62.397 68.421 0.00 0.00 0.00 4.30
1147 1207 2.282446 GGATGACGAGGAGGGGGA 59.718 66.667 0.00 0.00 0.00 4.81
1148 1208 2.136878 CAGGATGACGAGGAGGGGG 61.137 68.421 0.00 0.00 39.69 5.40
1284 1344 4.087892 GCCGCTTCCAGCTCCTCA 62.088 66.667 0.00 0.00 39.60 3.86
1641 1701 3.822192 TCGATCTGGTCCGCGTGG 61.822 66.667 9.28 9.28 0.00 4.94
1656 1716 4.477975 GGCGAGACCAGGTCGTCG 62.478 72.222 25.42 25.42 39.69 5.12
1657 1717 4.131088 GGGCGAGACCAGGTCGTC 62.131 72.222 14.32 5.29 41.36 4.20
1709 1769 0.609957 TTTCACCTCCATGCCAGCAG 60.610 55.000 0.00 0.00 0.00 4.24
1836 1902 1.078001 CACGTATTCCCCCACCACC 60.078 63.158 0.00 0.00 0.00 4.61
1848 1914 1.469335 CGGCTACATCCCCCACGTAT 61.469 60.000 0.00 0.00 0.00 3.06
1929 1995 2.202851 AGCGCCGCAATCTCTCTG 60.203 61.111 13.36 0.00 0.00 3.35
2037 2103 2.597510 GCCGGGACAACAGCCTTT 60.598 61.111 2.18 0.00 0.00 3.11
2145 2211 2.096466 TGCACGAACGATGTTTGCTAAG 60.096 45.455 0.14 0.00 34.18 2.18
2158 2224 4.340894 TGAGATTAGCAAATGCACGAAC 57.659 40.909 8.28 0.00 45.16 3.95
2171 2237 6.577103 TGAAGTTAGCACCTGATGAGATTAG 58.423 40.000 0.00 0.00 0.00 1.73
2205 2294 3.016736 GTGCTAGGCTCCAAATTTAGCA 58.983 45.455 13.55 9.70 43.02 3.49
2295 2434 5.568482 CCAAGATTTGCAATGCATTTCATG 58.432 37.500 12.58 11.73 38.76 3.07
2305 2444 0.251073 GCCCAGCCAAGATTTGCAAT 59.749 50.000 0.00 0.00 0.00 3.56
2326 2465 2.892425 GATTCTGTGCCGCTCCCG 60.892 66.667 0.00 0.00 0.00 5.14
2327 2466 1.817099 CTGATTCTGTGCCGCTCCC 60.817 63.158 0.00 0.00 0.00 4.30
2328 2467 0.391661 TTCTGATTCTGTGCCGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
2329 2468 1.661341 ATTCTGATTCTGTGCCGCTC 58.339 50.000 0.00 0.00 0.00 5.03
2330 2469 2.119801 AATTCTGATTCTGTGCCGCT 57.880 45.000 0.00 0.00 0.00 5.52
2335 2474 9.472361 AAGAAATGTCAAAATTCTGATTCTGTG 57.528 29.630 0.00 0.00 33.86 3.66
2389 2528 7.385752 CCTTGCTGCTTCAATTCAAAAGAAATA 59.614 33.333 0.00 0.00 0.00 1.40
2423 2562 9.096160 GCACCCTAAAAATAGTTTAGAGTACTC 57.904 37.037 15.41 15.41 34.74 2.59
2432 2571 7.961326 ATCATCAGCACCCTAAAAATAGTTT 57.039 32.000 0.00 0.00 0.00 2.66
2552 2691 6.379703 AGAGTACAGAAGCTGATAATCACACT 59.620 38.462 0.82 0.00 35.18 3.55
2569 2708 6.578020 TCGTGTAAACAACAAAGAGTACAG 57.422 37.500 0.00 0.00 40.63 2.74
2612 2751 6.207417 CCCAGTCACTAAATTGTCAACTCAAT 59.793 38.462 0.00 0.00 39.35 2.57
2697 2836 6.993902 TCCACCAAACGAGAAGTACTTTTATT 59.006 34.615 10.02 0.00 0.00 1.40
2734 2873 5.831702 AGTCTCCCAAATGTACTACGTAG 57.168 43.478 20.97 20.97 0.00 3.51
2738 2877 5.753921 GCACATAGTCTCCCAAATGTACTAC 59.246 44.000 0.00 0.00 31.55 2.73
2770 2920 7.817962 GCAACTCTCCAGTGTACTAAAATTAGA 59.182 37.037 7.17 0.00 32.02 2.10
2800 2950 2.245096 GCAACGCAACTATTCTGCAAG 58.755 47.619 0.00 0.00 39.91 4.01
2871 3021 3.465871 GCAGCCAAACTTTCAAAATCCA 58.534 40.909 0.00 0.00 0.00 3.41
2880 3030 1.454847 TCCCACGCAGCCAAACTTT 60.455 52.632 0.00 0.00 0.00 2.66
2885 3035 0.326595 TTTATCTCCCACGCAGCCAA 59.673 50.000 0.00 0.00 0.00 4.52
3072 3230 5.163550 TGACCACGATGGATTACTACTGAAG 60.164 44.000 10.46 0.00 40.96 3.02
3161 3350 6.939132 TTTGACATACCTTTGGTAAACGAA 57.061 33.333 0.26 0.40 41.85 3.85
3164 3353 6.687604 AGCATTTGACATACCTTTGGTAAAC 58.312 36.000 0.26 0.00 41.85 2.01
3175 3364 9.708222 CTGAAGTATTGTTAGCATTTGACATAC 57.292 33.333 0.00 0.00 0.00 2.39
3208 3397 5.812642 AGTTCAGTCTGTAGTTGTGAACAAG 59.187 40.000 14.13 0.00 46.18 3.16
3246 3435 7.973048 TTACTACCATGTCTAGATGAAAGGT 57.027 36.000 0.00 3.33 32.52 3.50
3261 3495 6.936900 GTGCCATTGTATCTCATTACTACCAT 59.063 38.462 0.00 0.00 0.00 3.55
3283 3517 7.990541 TCATGCAACATATATTTTCAAGTGC 57.009 32.000 0.00 0.00 0.00 4.40
3331 3565 3.831715 AGTTTCAGCTCCAAATAACGC 57.168 42.857 0.00 0.00 0.00 4.84
3384 3618 7.752686 GCAAAGGCAGTTGAAAAATAAACAAAA 59.247 29.630 5.24 0.00 40.72 2.44
3455 3689 5.018809 AGAACAGTGGCAATGTTATGGAAT 58.981 37.500 30.33 9.56 40.86 3.01
3496 3730 7.546667 ACCACTGCAGCAAAGATATAAAAATTG 59.453 33.333 15.27 0.00 0.00 2.32
3539 3774 4.274147 TGGTAGTAGAGCTTCTTCTCCAG 58.726 47.826 0.00 0.00 33.66 3.86
3615 3850 0.671251 CCGCAGTTTAGGGTTGCAAA 59.329 50.000 0.00 0.00 37.69 3.68
3616 3851 1.801309 GCCGCAGTTTAGGGTTGCAA 61.801 55.000 0.00 0.00 37.69 4.08
3633 3868 0.179000 CCTGTGGAGTAGTCATGGCC 59.821 60.000 0.00 0.00 0.00 5.36
3673 3908 1.672356 CAGGAGGCCAAGGAACGTG 60.672 63.158 5.01 0.00 37.63 4.49
3774 4009 4.804108 TGCATTTACATGTGTTTGGCTAC 58.196 39.130 9.11 0.00 32.28 3.58
3856 4091 3.066203 TCAGCCAAAACGAAGAAGAAACC 59.934 43.478 0.00 0.00 0.00 3.27
3864 4099 3.795561 CTGTACTCAGCCAAAACGAAG 57.204 47.619 0.00 0.00 34.79 3.79
3888 4123 4.396790 TCCAAAACTTACATCGCCAATACC 59.603 41.667 0.00 0.00 0.00 2.73
3948 4183 3.033368 GCTATGCAAGCCTAGTAGTCC 57.967 52.381 9.03 0.00 46.25 3.85
3976 4211 1.536922 CGCACGATCAGTTAGCTCCAT 60.537 52.381 0.00 0.00 0.00 3.41
3990 4225 2.279851 CCACAACTCACCGCACGA 60.280 61.111 0.00 0.00 0.00 4.35
4071 4345 6.017933 CACGATGCTAGTTCAAGATCAAAAC 58.982 40.000 0.00 0.00 0.00 2.43
4183 4844 0.846427 AATCCTTGTGAGCTCCCCCA 60.846 55.000 12.15 2.27 0.00 4.96
4187 4848 1.742268 GCTTGAATCCTTGTGAGCTCC 59.258 52.381 12.15 3.09 0.00 4.70
4206 4867 2.080286 TTAAGTGCGAGGTCTTGAGC 57.920 50.000 0.00 0.00 0.00 4.26
4229 4890 1.011968 CAAGTGGCTAGTAACGCGCA 61.012 55.000 5.73 0.00 0.00 6.09
4347 5015 9.360514 CATTTCAAATTGTTCACATTTTTCTCG 57.639 29.630 0.00 0.00 29.96 4.04
4457 5126 7.448588 TTGTTCATGTTTTGAAAGATGTTCG 57.551 32.000 11.76 0.00 45.71 3.95
4541 5230 9.804758 TCACGGTTTAAAATAGTTCACAAATTT 57.195 25.926 0.00 0.00 0.00 1.82
4547 5236 6.962686 AGGTTCACGGTTTAAAATAGTTCAC 58.037 36.000 0.00 0.00 0.00 3.18
4549 5238 8.861033 AAAAGGTTCACGGTTTAAAATAGTTC 57.139 30.769 0.00 0.00 0.00 3.01
4554 5243 9.872721 TTTAAGAAAAGGTTCACGGTTTAAAAT 57.127 25.926 0.00 0.00 36.09 1.82
4621 5331 7.954835 TCATGGATTTGAAAAACAGAGTTCAT 58.045 30.769 0.00 0.00 33.90 2.57
4662 5372 9.545611 GTTCGTAAAAGTTGAAAAGAGTTTGTA 57.454 29.630 0.00 0.00 0.00 2.41
4756 5469 1.226018 CCAAGCGTTCGCGGATTTC 60.226 57.895 6.13 0.00 41.67 2.17
4897 5619 9.965824 ACACATGTTTCAAAAGGAGTAATAAAG 57.034 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.