Multiple sequence alignment - TraesCS7B01G148400

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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 TraesCS7B01G148400 chr7B 100.000 3390 0 0 1 3390 196275553 196278942 0.000000e+00 6261.0
1 TraesCS7B01G148400 chr7B 96.552 116 4 0 1 116 122956874 122956989 3.450000e-45 193.0
2 TraesCS7B01G148400 chr7A 93.502 2724 122 18 129 2823 218266534 218263837 0.000000e+00 3999.0
3 TraesCS7B01G148400 chr7A 93.780 209 13 0 3182 3390 218263627 218263419 7.060000e-82 315.0
4 TraesCS7B01G148400 chr7A 79.235 183 38 0 3208 3390 6300140 6299958 9.870000e-26 128.0
5 TraesCS7B01G148400 chr7A 100.000 28 0 0 3161 3188 218263692 218263665 6.000000e-03 52.8
6 TraesCS7B01G148400 chr7D 94.540 2088 72 15 117 2189 205954963 205952903 0.000000e+00 3186.0
7 TraesCS7B01G148400 chr7D 94.529 658 25 7 2175 2823 205951116 205950461 0.000000e+00 1005.0
8 TraesCS7B01G148400 chr7D 95.957 371 15 0 2818 3188 205950370 205950000 1.350000e-168 603.0
9 TraesCS7B01G148400 chr7D 95.631 206 9 0 3185 3390 205949959 205949754 7.010000e-87 331.0
10 TraesCS7B01G148400 chrUn 94.879 371 19 0 2818 3188 214044866 214044496 6.310000e-162 580.0
11 TraesCS7B01G148400 chrUn 94.879 371 19 0 2818 3188 240300219 240300589 6.310000e-162 580.0
12 TraesCS7B01G148400 chrUn 93.548 372 24 0 2818 3189 45773306 45772935 3.820000e-154 555.0
13 TraesCS7B01G148400 chrUn 95.146 206 10 0 3185 3390 214044455 214044250 3.260000e-85 326.0
14 TraesCS7B01G148400 chrUn 94.737 209 11 0 3182 3390 240300627 240300835 3.260000e-85 326.0
15 TraesCS7B01G148400 chrUn 93.204 206 14 0 3185 3390 45772895 45772690 1.530000e-78 303.0
16 TraesCS7B01G148400 chrUn 87.671 219 20 4 2611 2823 45773614 45773397 7.260000e-62 248.0
17 TraesCS7B01G148400 chrUn 93.985 133 8 0 2691 2823 214045089 214044957 5.740000e-48 202.0
18 TraesCS7B01G148400 chrUn 93.985 133 8 0 2691 2823 240299996 240300128 5.740000e-48 202.0
19 TraesCS7B01G148400 chr3D 93.817 372 23 0 2818 3189 592868787 592868416 8.210000e-156 560.0
20 TraesCS7B01G148400 chr3D 93.817 372 23 0 2818 3189 592874528 592874157 8.210000e-156 560.0
21 TraesCS7B01G148400 chr3D 93.689 206 13 0 3185 3390 592868376 592868171 3.290000e-80 309.0
22 TraesCS7B01G148400 chr3D 93.689 206 13 0 3185 3390 592874117 592873912 3.290000e-80 309.0
23 TraesCS7B01G148400 chr3D 87.671 219 20 4 2611 2823 592869095 592868878 7.260000e-62 248.0
24 TraesCS7B01G148400 chr3D 87.671 219 20 4 2611 2823 592874836 592874619 7.260000e-62 248.0
25 TraesCS7B01G148400 chr3B 96.581 117 3 1 1 116 668117444 668117560 3.450000e-45 193.0
26 TraesCS7B01G148400 chr3B 95.726 117 4 1 1 116 77704993 77704877 1.610000e-43 187.0
27 TraesCS7B01G148400 chr5D 95.726 117 4 1 1 116 21461491 21461607 1.610000e-43 187.0
28 TraesCS7B01G148400 chr5B 95.690 116 5 0 1 116 8972998 8972883 1.610000e-43 187.0
29 TraesCS7B01G148400 chr5B 94.828 116 6 0 1 116 61158500 61158615 7.470000e-42 182.0
30 TraesCS7B01G148400 chr3A 95.690 116 5 0 1 116 710804038 710804153 1.610000e-43 187.0
31 TraesCS7B01G148400 chr1B 95.726 117 4 1 1 116 312036768 312036884 1.610000e-43 187.0
32 TraesCS7B01G148400 chr4A 94.828 116 6 0 1 116 590373376 590373491 7.470000e-42 182.0
33 TraesCS7B01G148400 chr2A 83.784 185 30 0 3206 3390 764771020 764771204 3.480000e-40 176.0
34 TraesCS7B01G148400 chr1A 77.224 281 61 3 2912 3190 530516113 530516392 9.730000e-36 161.0
35 TraesCS7B01G148400 chr2D 77.947 263 50 7 2926 3184 602704992 602704734 1.260000e-34 158.0


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 TraesCS7B01G148400 chr7B 196275553 196278942 3389 False 6261.000000 6261 100.000000 1 3390 1 chr7B.!!$F2 3389
1 TraesCS7B01G148400 chr7A 218263419 218266534 3115 True 1455.600000 3999 95.760667 129 3390 3 chr7A.!!$R2 3261
2 TraesCS7B01G148400 chr7D 205949754 205954963 5209 True 1281.250000 3186 95.164250 117 3390 4 chr7D.!!$R1 3273
3 TraesCS7B01G148400 chrUn 214044250 214045089 839 True 369.333333 580 94.670000 2691 3390 3 chrUn.!!$R2 699
4 TraesCS7B01G148400 chrUn 240299996 240300835 839 False 369.333333 580 94.533667 2691 3390 3 chrUn.!!$F1 699
5 TraesCS7B01G148400 chrUn 45772690 45773614 924 True 368.666667 555 91.474333 2611 3390 3 chrUn.!!$R1 779
6 TraesCS7B01G148400 chr3D 592868171 592869095 924 True 372.333333 560 91.725667 2611 3390 3 chr3D.!!$R1 779
7 TraesCS7B01G148400 chr3D 592873912 592874836 924 True 372.333333 560 91.725667 2611 3390 3 chr3D.!!$R2 779

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
57 58 0.107459 GGCCACCCTGAAGAGCTTAG 60.107 60.0 0.00 0.00 0.0 2.18 F
58 59 0.615850 GCCACCCTGAAGAGCTTAGT 59.384 55.0 0.00 0.00 0.0 2.24 F
1387 1401 0.646895 GCGTGCATGCTTTAATTGGC 59.353 50.0 23.72 6.67 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1028 1.741706 AGCAACTCGCCAATCATCAAG 59.258 47.619 0.0 0.0 44.04 3.02 R
2029 2058 2.645838 AGTGTGTTGATGGTGAGCTT 57.354 45.000 0.0 0.0 0.00 3.74 R
2665 4511 1.066430 TGCCTCGGTAACCTGATTGAC 60.066 52.381 0.0 0.0 0.00 3.18 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
20 21 2.634639 TGCCTTAACTCTAGGGACCA 57.365 50.000 0.00 0.00 33.19 4.02
21 22 2.467880 TGCCTTAACTCTAGGGACCAG 58.532 52.381 0.00 0.00 33.19 4.00
22 23 1.139256 GCCTTAACTCTAGGGACCAGC 59.861 57.143 0.00 0.00 33.19 4.85
23 24 1.763545 CCTTAACTCTAGGGACCAGCC 59.236 57.143 0.00 0.00 0.00 4.85
24 25 1.409427 CTTAACTCTAGGGACCAGCCG 59.591 57.143 0.00 0.00 37.63 5.52
25 26 1.041447 TAACTCTAGGGACCAGCCGC 61.041 60.000 0.00 0.00 37.63 6.53
26 27 3.541713 CTCTAGGGACCAGCCGCC 61.542 72.222 0.00 0.00 37.63 6.13
27 28 4.392166 TCTAGGGACCAGCCGCCA 62.392 66.667 0.00 0.00 37.63 5.69
28 29 3.164269 CTAGGGACCAGCCGCCAT 61.164 66.667 0.00 0.00 37.63 4.40
29 30 3.466791 CTAGGGACCAGCCGCCATG 62.467 68.421 0.00 0.00 37.63 3.66
31 32 4.740822 GGGACCAGCCGCCATGTT 62.741 66.667 0.00 0.00 37.63 2.71
32 33 2.676471 GGACCAGCCGCCATGTTT 60.676 61.111 0.00 0.00 0.00 2.83
33 34 2.568090 GACCAGCCGCCATGTTTG 59.432 61.111 0.00 0.00 0.00 2.93
34 35 2.990967 ACCAGCCGCCATGTTTGG 60.991 61.111 0.00 0.00 46.66 3.28
35 36 2.990967 CCAGCCGCCATGTTTGGT 60.991 61.111 0.00 0.00 45.57 3.67
36 37 2.573083 CCAGCCGCCATGTTTGGTT 61.573 57.895 0.00 0.00 45.57 3.67
37 38 1.247419 CCAGCCGCCATGTTTGGTTA 61.247 55.000 0.00 0.00 45.57 2.85
38 39 0.171007 CAGCCGCCATGTTTGGTTAG 59.829 55.000 0.00 0.00 45.57 2.34
39 40 0.965363 AGCCGCCATGTTTGGTTAGG 60.965 55.000 0.00 0.00 45.57 2.69
40 41 1.510844 CCGCCATGTTTGGTTAGGC 59.489 57.895 0.00 0.00 45.57 3.93
41 42 1.510844 CGCCATGTTTGGTTAGGCC 59.489 57.895 0.00 0.00 45.57 5.19
42 43 1.247419 CGCCATGTTTGGTTAGGCCA 61.247 55.000 5.01 0.00 45.57 5.36
49 50 4.341199 TGGTTAGGCCACCCTGAA 57.659 55.556 5.01 0.00 43.61 3.02
50 51 2.074967 TGGTTAGGCCACCCTGAAG 58.925 57.895 5.01 0.00 43.61 3.02
51 52 0.474854 TGGTTAGGCCACCCTGAAGA 60.475 55.000 5.01 0.00 43.61 2.87
52 53 0.253327 GGTTAGGCCACCCTGAAGAG 59.747 60.000 5.01 0.00 42.90 2.85
53 54 0.393132 GTTAGGCCACCCTGAAGAGC 60.393 60.000 5.01 0.00 42.90 4.09
54 55 0.547712 TTAGGCCACCCTGAAGAGCT 60.548 55.000 5.01 0.00 42.90 4.09
55 56 0.547712 TAGGCCACCCTGAAGAGCTT 60.548 55.000 5.01 0.00 42.90 3.74
56 57 0.547712 AGGCCACCCTGAAGAGCTTA 60.548 55.000 5.01 0.00 40.94 3.09
57 58 0.107459 GGCCACCCTGAAGAGCTTAG 60.107 60.000 0.00 0.00 0.00 2.18
58 59 0.615850 GCCACCCTGAAGAGCTTAGT 59.384 55.000 0.00 0.00 0.00 2.24
59 60 1.003696 GCCACCCTGAAGAGCTTAGTT 59.996 52.381 0.00 0.00 0.00 2.24
60 61 2.553247 GCCACCCTGAAGAGCTTAGTTT 60.553 50.000 0.00 0.00 0.00 2.66
61 62 3.339141 CCACCCTGAAGAGCTTAGTTTC 58.661 50.000 0.00 0.00 0.00 2.78
62 63 2.996621 CACCCTGAAGAGCTTAGTTTCG 59.003 50.000 0.00 0.00 0.00 3.46
63 64 2.633481 ACCCTGAAGAGCTTAGTTTCGT 59.367 45.455 0.00 0.00 0.00 3.85
64 65 3.254892 CCCTGAAGAGCTTAGTTTCGTC 58.745 50.000 0.00 0.00 0.00 4.20
65 66 3.254892 CCTGAAGAGCTTAGTTTCGTCC 58.745 50.000 0.00 0.00 0.00 4.79
66 67 3.254892 CTGAAGAGCTTAGTTTCGTCCC 58.745 50.000 0.00 0.00 0.00 4.46
67 68 2.897969 TGAAGAGCTTAGTTTCGTCCCT 59.102 45.455 0.00 0.00 0.00 4.20
68 69 3.254892 GAAGAGCTTAGTTTCGTCCCTG 58.745 50.000 0.00 0.00 0.00 4.45
69 70 2.249139 AGAGCTTAGTTTCGTCCCTGT 58.751 47.619 0.00 0.00 0.00 4.00
70 71 3.428532 AGAGCTTAGTTTCGTCCCTGTA 58.571 45.455 0.00 0.00 0.00 2.74
71 72 3.830755 AGAGCTTAGTTTCGTCCCTGTAA 59.169 43.478 0.00 0.00 0.00 2.41
72 73 4.282703 AGAGCTTAGTTTCGTCCCTGTAAA 59.717 41.667 0.00 0.00 0.00 2.01
73 74 4.313282 AGCTTAGTTTCGTCCCTGTAAAC 58.687 43.478 0.00 0.00 34.13 2.01
74 75 3.122445 GCTTAGTTTCGTCCCTGTAAACG 59.878 47.826 0.00 0.00 37.99 3.60
75 76 2.896745 AGTTTCGTCCCTGTAAACGT 57.103 45.000 0.00 0.00 39.78 3.99
76 77 3.183793 AGTTTCGTCCCTGTAAACGTT 57.816 42.857 0.00 0.00 39.78 3.99
77 78 2.867975 AGTTTCGTCCCTGTAAACGTTG 59.132 45.455 0.00 0.00 39.78 4.10
78 79 2.600470 TTCGTCCCTGTAAACGTTGT 57.400 45.000 0.00 0.00 39.78 3.32
79 80 1.855513 TCGTCCCTGTAAACGTTGTG 58.144 50.000 0.00 0.00 39.78 3.33
80 81 1.408340 TCGTCCCTGTAAACGTTGTGA 59.592 47.619 0.00 0.00 39.78 3.58
81 82 1.523934 CGTCCCTGTAAACGTTGTGAC 59.476 52.381 0.00 1.10 34.30 3.67
96 97 4.613866 CGTTGTGACGGGTTAATAAAAAGC 59.386 41.667 0.00 0.00 45.32 3.51
97 98 5.561339 CGTTGTGACGGGTTAATAAAAAGCT 60.561 40.000 0.00 0.00 45.32 3.74
98 99 6.210796 GTTGTGACGGGTTAATAAAAAGCTT 58.789 36.000 0.00 0.00 0.00 3.74
99 100 6.394025 TGTGACGGGTTAATAAAAAGCTTT 57.606 33.333 5.69 5.69 0.00 3.51
100 101 6.210078 TGTGACGGGTTAATAAAAAGCTTTG 58.790 36.000 13.54 0.00 0.00 2.77
101 102 5.118050 GTGACGGGTTAATAAAAAGCTTTGC 59.882 40.000 13.54 0.00 0.00 3.68
102 103 4.231439 ACGGGTTAATAAAAAGCTTTGCG 58.769 39.130 13.54 0.00 0.00 4.85
103 104 4.023021 ACGGGTTAATAAAAAGCTTTGCGA 60.023 37.500 13.54 1.21 0.00 5.10
104 105 4.557301 CGGGTTAATAAAAAGCTTTGCGAG 59.443 41.667 13.54 0.00 0.00 5.03
105 106 5.466819 GGGTTAATAAAAAGCTTTGCGAGT 58.533 37.500 13.54 3.07 0.00 4.18
106 107 5.924254 GGGTTAATAAAAAGCTTTGCGAGTT 59.076 36.000 13.54 5.37 0.00 3.01
107 108 6.422701 GGGTTAATAAAAAGCTTTGCGAGTTT 59.577 34.615 13.54 4.61 0.00 2.66
108 109 7.280769 GGTTAATAAAAAGCTTTGCGAGTTTG 58.719 34.615 13.54 0.00 0.00 2.93
109 110 4.972286 ATAAAAAGCTTTGCGAGTTTGC 57.028 36.364 13.54 0.00 0.00 3.68
110 111 1.570813 AAAAGCTTTGCGAGTTTGCC 58.429 45.000 13.54 0.00 0.00 4.52
111 112 0.746659 AAAGCTTTGCGAGTTTGCCT 59.253 45.000 11.80 0.00 0.00 4.75
112 113 1.604604 AAGCTTTGCGAGTTTGCCTA 58.395 45.000 0.00 0.00 0.00 3.93
113 114 1.604604 AGCTTTGCGAGTTTGCCTAA 58.395 45.000 0.00 0.00 0.00 2.69
114 115 1.953686 AGCTTTGCGAGTTTGCCTAAA 59.046 42.857 0.00 0.00 0.00 1.85
115 116 2.360801 AGCTTTGCGAGTTTGCCTAAAA 59.639 40.909 0.00 0.00 0.00 1.52
123 124 2.699251 GTTTGCCTAAAACGTCCCTG 57.301 50.000 0.00 0.00 38.92 4.45
124 125 2.223745 GTTTGCCTAAAACGTCCCTGA 58.776 47.619 0.00 0.00 38.92 3.86
310 311 1.635663 GCATTCACTTACGCGCCAGT 61.636 55.000 5.73 5.28 0.00 4.00
337 338 2.492012 GCTGCAGATGAAGGTATCCTG 58.508 52.381 20.43 0.00 32.13 3.86
426 428 2.162208 CACCCGTTCGCTAGTACTGTAA 59.838 50.000 5.39 0.00 0.00 2.41
451 464 6.599638 AGCTTTATCAAGTGTATTCTTCACCC 59.400 38.462 0.00 0.00 36.58 4.61
452 465 6.599638 GCTTTATCAAGTGTATTCTTCACCCT 59.400 38.462 0.00 0.00 36.58 4.34
453 466 7.769044 GCTTTATCAAGTGTATTCTTCACCCTA 59.231 37.037 0.00 0.00 36.58 3.53
454 467 9.838339 CTTTATCAAGTGTATTCTTCACCCTAT 57.162 33.333 0.00 0.00 36.58 2.57
500 514 5.336690 CGGGGTCATTTCTTCATTGTCAATT 60.337 40.000 0.00 0.00 0.00 2.32
525 539 5.756195 ACGCATGATACAGTTTGCATAAT 57.244 34.783 0.00 0.00 34.80 1.28
607 621 6.808704 GCCTTTTCCTGCTAAGAAAGTAAATG 59.191 38.462 0.00 0.00 34.84 2.32
635 649 8.129496 TCTGAATTTCGGGTACTGCATATATA 57.871 34.615 5.41 0.00 32.53 0.86
638 652 9.378551 TGAATTTCGGGTACTGCATATATATTC 57.621 33.333 0.00 0.00 32.53 1.75
639 653 9.601217 GAATTTCGGGTACTGCATATATATTCT 57.399 33.333 0.00 0.00 32.53 2.40
697 711 4.698575 TGTGCTGTTACTGTGTTACATGA 58.301 39.130 0.00 0.00 0.00 3.07
744 758 5.412904 GGATTAGCAAGCACTTGTAAACTCT 59.587 40.000 11.77 2.46 42.31 3.24
836 850 1.144503 ACCATCATGAATCCCCTCTGC 59.855 52.381 0.00 0.00 0.00 4.26
837 851 1.144298 CCATCATGAATCCCCTCTGCA 59.856 52.381 0.00 0.00 0.00 4.41
838 852 2.505405 CATCATGAATCCCCTCTGCAG 58.495 52.381 7.63 7.63 0.00 4.41
839 853 1.588239 TCATGAATCCCCTCTGCAGT 58.412 50.000 14.67 0.00 0.00 4.40
840 854 1.487976 TCATGAATCCCCTCTGCAGTC 59.512 52.381 14.67 2.21 0.00 3.51
841 855 1.489649 CATGAATCCCCTCTGCAGTCT 59.510 52.381 14.67 0.00 0.00 3.24
842 856 0.907486 TGAATCCCCTCTGCAGTCTG 59.093 55.000 14.67 5.43 0.00 3.51
963 977 5.596772 AGGTGATCTAAAGCTAACTCTCCTC 59.403 44.000 0.00 0.00 0.00 3.71
1014 1028 1.303309 CACCGATGGAGATGCTTTCC 58.697 55.000 0.00 0.00 35.20 3.13
1026 1040 3.383825 AGATGCTTTCCTTGATGATTGGC 59.616 43.478 0.00 0.00 0.00 4.52
1188 1202 5.559770 TCTGTTCCTAATTCACTGCATTCA 58.440 37.500 0.00 0.00 0.00 2.57
1387 1401 0.646895 GCGTGCATGCTTTAATTGGC 59.353 50.000 23.72 6.67 0.00 4.52
1411 1425 5.584913 TGCCCCTCAGGAATTAAATTGTTA 58.415 37.500 0.00 0.00 38.24 2.41
1458 1472 5.862924 AAACTTTGGGCATATCGATATCG 57.137 39.130 19.14 19.14 41.45 2.92
1499 1513 3.469739 TCAAGACAAACCGGTTCCTTAC 58.530 45.455 22.53 10.65 0.00 2.34
1708 1729 6.926272 CCTAGACTATGTCTGGACTTTATTGC 59.074 42.308 11.71 0.00 42.49 3.56
1759 1788 8.770828 AGTGATATTTTTCAACGGATATTACGG 58.229 33.333 5.86 0.00 35.23 4.02
1873 1902 8.023050 AGAAACTCAAAATATGACTCTGTTCG 57.977 34.615 0.00 0.00 33.47 3.95
1911 1940 4.282496 TGTTGTTTACACCATCCCTTGTT 58.718 39.130 0.00 0.00 0.00 2.83
1912 1941 4.712337 TGTTGTTTACACCATCCCTTGTTT 59.288 37.500 0.00 0.00 0.00 2.83
1913 1942 5.187967 TGTTGTTTACACCATCCCTTGTTTT 59.812 36.000 0.00 0.00 0.00 2.43
1914 1943 5.941555 TGTTTACACCATCCCTTGTTTTT 57.058 34.783 0.00 0.00 0.00 1.94
2029 2058 5.007528 GCAAAAGCTGGCATAACTTTTTCAA 59.992 36.000 15.97 0.00 40.63 2.69
2032 2061 4.309933 AGCTGGCATAACTTTTTCAAAGC 58.690 39.130 0.00 0.00 0.00 3.51
2047 2076 2.618241 TCAAAGCTCACCATCAACACAC 59.382 45.455 0.00 0.00 0.00 3.82
2071 2100 6.940298 ACTTTAGAGTTGCCAACTTGCTATTA 59.060 34.615 12.09 1.23 43.03 0.98
2085 2114 9.294030 CAACTTGCTATTAATGGAGAAACATTC 57.706 33.333 2.52 0.00 41.12 2.67
2100 2129 4.860802 AACATTCCATGGACCTGTGATA 57.139 40.909 23.42 5.55 33.60 2.15
2107 2136 3.135348 CCATGGACCTGTGATATGACACT 59.865 47.826 5.56 0.00 40.87 3.55
2109 2138 4.471904 TGGACCTGTGATATGACACTTC 57.528 45.455 0.00 0.00 40.87 3.01
2173 2204 2.754472 GTGGGTTTTTCCTTGTCATGC 58.246 47.619 0.00 0.00 36.25 4.06
2178 2209 5.248020 TGGGTTTTTCCTTGTCATGCATATT 59.752 36.000 0.00 0.00 36.25 1.28
2217 4049 9.987272 TGTGTCCATATGAATTCTAACTATGAG 57.013 33.333 3.65 4.43 0.00 2.90
2507 4347 9.770097 TTCCATGCAAACTAAAAATAATTGTCA 57.230 25.926 0.00 0.00 0.00 3.58
2521 4361 9.995003 AAAATAATTGTCAATTGCTGAAACCTA 57.005 25.926 19.10 0.00 35.22 3.08
2555 4395 8.372521 GCATATTTAAAAAGGACGTGACAATTG 58.627 33.333 3.24 3.24 0.00 2.32
2710 4557 6.862711 ACTCATAGATGACATGCATTCTTG 57.137 37.500 0.00 0.00 37.34 3.02
2780 4627 7.576666 GCATTGTTCTGTTCCATTGGTGTATTA 60.577 37.037 1.86 0.00 0.00 0.98
3032 4975 6.873605 CCAAATATCCAAAAGTTCCTTGAACC 59.126 38.462 3.47 0.00 42.85 3.62
3047 4990 1.414919 TGAACCGCAGTTGTAACTCCT 59.585 47.619 0.00 0.00 37.08 3.69
3083 5026 0.036952 TGCCTCGAGAAGCTCCAAAG 60.037 55.000 15.71 0.00 0.00 2.77
3195 5182 3.497640 CAGATAAGCAAGGCACTGATAGC 59.502 47.826 0.00 0.00 40.86 2.97
3255 5242 7.975616 CCATTTGAAATGAATTCGTAGACCAAT 59.024 33.333 18.82 0.00 41.18 3.16
3327 5314 5.513094 CCTGTGGTTCACTTGAGAAAGGATA 60.513 44.000 0.00 0.00 35.11 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.041946 CTGGTCCCTAGAGTTAAGGCAT 58.958 50.000 0.00 0.00 32.34 4.40
2 3 1.139256 GCTGGTCCCTAGAGTTAAGGC 59.861 57.143 0.00 0.00 32.34 4.35
5 6 1.481871 CGGCTGGTCCCTAGAGTTAA 58.518 55.000 0.00 0.00 0.00 2.01
7 8 2.359967 GCGGCTGGTCCCTAGAGTT 61.360 63.158 0.00 0.00 0.00 3.01
8 9 2.760385 GCGGCTGGTCCCTAGAGT 60.760 66.667 0.00 0.00 0.00 3.24
9 10 3.541713 GGCGGCTGGTCCCTAGAG 61.542 72.222 0.00 0.00 0.00 2.43
10 11 3.696518 ATGGCGGCTGGTCCCTAGA 62.697 63.158 11.43 0.00 0.00 2.43
11 12 3.164269 ATGGCGGCTGGTCCCTAG 61.164 66.667 11.43 0.00 0.00 3.02
12 13 3.479203 CATGGCGGCTGGTCCCTA 61.479 66.667 11.43 0.00 0.00 3.53
14 15 4.740822 AACATGGCGGCTGGTCCC 62.741 66.667 11.43 0.00 0.00 4.46
15 16 2.676471 AAACATGGCGGCTGGTCC 60.676 61.111 11.43 0.00 0.00 4.46
16 17 2.568090 CAAACATGGCGGCTGGTC 59.432 61.111 11.43 0.00 0.00 4.02
17 18 2.990967 CCAAACATGGCGGCTGGT 60.991 61.111 11.43 5.30 0.00 4.00
18 19 1.247419 TAACCAAACATGGCGGCTGG 61.247 55.000 11.43 11.76 0.00 4.85
19 20 0.171007 CTAACCAAACATGGCGGCTG 59.829 55.000 11.43 8.69 0.00 4.85
20 21 0.965363 CCTAACCAAACATGGCGGCT 60.965 55.000 11.43 0.00 0.00 5.52
21 22 1.510844 CCTAACCAAACATGGCGGC 59.489 57.895 0.00 0.00 0.00 6.53
22 23 1.510844 GCCTAACCAAACATGGCGG 59.489 57.895 0.00 0.00 33.96 6.13
23 24 1.510844 GGCCTAACCAAACATGGCG 59.489 57.895 0.00 0.00 44.07 5.69
33 34 0.253327 CTCTTCAGGGTGGCCTAACC 59.747 60.000 3.32 3.45 39.71 2.85
34 35 0.393132 GCTCTTCAGGGTGGCCTAAC 60.393 60.000 3.32 0.00 0.00 2.34
35 36 0.547712 AGCTCTTCAGGGTGGCCTAA 60.548 55.000 3.32 0.00 0.00 2.69
36 37 0.547712 AAGCTCTTCAGGGTGGCCTA 60.548 55.000 3.32 0.00 0.00 3.93
37 38 0.547712 TAAGCTCTTCAGGGTGGCCT 60.548 55.000 3.32 0.00 0.00 5.19
38 39 0.107459 CTAAGCTCTTCAGGGTGGCC 60.107 60.000 0.00 0.00 0.00 5.36
39 40 0.615850 ACTAAGCTCTTCAGGGTGGC 59.384 55.000 0.00 0.00 0.00 5.01
40 41 3.339141 GAAACTAAGCTCTTCAGGGTGG 58.661 50.000 0.00 0.00 0.00 4.61
41 42 2.996621 CGAAACTAAGCTCTTCAGGGTG 59.003 50.000 0.00 0.00 0.00 4.61
42 43 2.633481 ACGAAACTAAGCTCTTCAGGGT 59.367 45.455 0.00 0.00 0.00 4.34
43 44 3.254892 GACGAAACTAAGCTCTTCAGGG 58.745 50.000 0.00 0.00 0.00 4.45
44 45 3.254892 GGACGAAACTAAGCTCTTCAGG 58.745 50.000 0.00 0.00 0.00 3.86
45 46 3.056465 AGGGACGAAACTAAGCTCTTCAG 60.056 47.826 0.00 0.00 0.00 3.02
46 47 2.897969 AGGGACGAAACTAAGCTCTTCA 59.102 45.455 0.00 0.00 0.00 3.02
47 48 3.254892 CAGGGACGAAACTAAGCTCTTC 58.745 50.000 0.00 0.00 0.00 2.87
48 49 2.633481 ACAGGGACGAAACTAAGCTCTT 59.367 45.455 0.00 0.00 0.00 2.85
49 50 2.249139 ACAGGGACGAAACTAAGCTCT 58.751 47.619 0.00 0.00 0.00 4.09
50 51 2.745515 ACAGGGACGAAACTAAGCTC 57.254 50.000 0.00 0.00 0.00 4.09
51 52 4.313282 GTTTACAGGGACGAAACTAAGCT 58.687 43.478 0.00 0.00 31.71 3.74
52 53 3.122445 CGTTTACAGGGACGAAACTAAGC 59.878 47.826 0.00 0.00 41.53 3.09
53 54 4.301628 ACGTTTACAGGGACGAAACTAAG 58.698 43.478 2.69 0.00 41.53 2.18
54 55 4.320608 ACGTTTACAGGGACGAAACTAA 57.679 40.909 2.69 0.00 41.53 2.24
55 56 4.050553 CAACGTTTACAGGGACGAAACTA 58.949 43.478 0.00 0.00 41.53 2.24
56 57 2.867975 CAACGTTTACAGGGACGAAACT 59.132 45.455 0.00 0.00 41.53 2.66
57 58 2.609002 ACAACGTTTACAGGGACGAAAC 59.391 45.455 0.00 0.00 41.53 2.78
58 59 2.608546 CACAACGTTTACAGGGACGAAA 59.391 45.455 0.00 0.00 41.53 3.46
59 60 2.159128 TCACAACGTTTACAGGGACGAA 60.159 45.455 0.00 0.00 41.53 3.85
60 61 1.408340 TCACAACGTTTACAGGGACGA 59.592 47.619 0.00 0.00 41.53 4.20
61 62 1.523934 GTCACAACGTTTACAGGGACG 59.476 52.381 0.00 0.00 44.34 4.79
62 63 1.523934 CGTCACAACGTTTACAGGGAC 59.476 52.381 8.32 8.32 43.94 4.46
63 64 1.855513 CGTCACAACGTTTACAGGGA 58.144 50.000 0.00 0.00 43.94 4.20
74 75 5.765176 AGCTTTTTATTAACCCGTCACAAC 58.235 37.500 0.00 0.00 0.00 3.32
75 76 6.394025 AAGCTTTTTATTAACCCGTCACAA 57.606 33.333 0.00 0.00 0.00 3.33
76 77 6.210078 CAAAGCTTTTTATTAACCCGTCACA 58.790 36.000 9.53 0.00 0.00 3.58
77 78 5.118050 GCAAAGCTTTTTATTAACCCGTCAC 59.882 40.000 9.53 0.00 0.00 3.67
78 79 5.224135 GCAAAGCTTTTTATTAACCCGTCA 58.776 37.500 9.53 0.00 0.00 4.35
79 80 4.322539 CGCAAAGCTTTTTATTAACCCGTC 59.677 41.667 9.53 0.00 0.00 4.79
80 81 4.023021 TCGCAAAGCTTTTTATTAACCCGT 60.023 37.500 9.53 0.00 0.00 5.28
81 82 4.477780 TCGCAAAGCTTTTTATTAACCCG 58.522 39.130 9.53 1.98 0.00 5.28
82 83 5.466819 ACTCGCAAAGCTTTTTATTAACCC 58.533 37.500 9.53 0.00 0.00 4.11
83 84 7.280769 CAAACTCGCAAAGCTTTTTATTAACC 58.719 34.615 9.53 0.00 0.00 2.85
84 85 6.785633 GCAAACTCGCAAAGCTTTTTATTAAC 59.214 34.615 9.53 0.00 0.00 2.01
85 86 6.074034 GGCAAACTCGCAAAGCTTTTTATTAA 60.074 34.615 9.53 0.00 0.00 1.40
86 87 5.404066 GGCAAACTCGCAAAGCTTTTTATTA 59.596 36.000 9.53 0.00 0.00 0.98
87 88 4.211164 GGCAAACTCGCAAAGCTTTTTATT 59.789 37.500 9.53 0.00 0.00 1.40
88 89 3.740832 GGCAAACTCGCAAAGCTTTTTAT 59.259 39.130 9.53 0.00 0.00 1.40
89 90 3.120041 GGCAAACTCGCAAAGCTTTTTA 58.880 40.909 9.53 0.00 0.00 1.52
90 91 1.933181 GGCAAACTCGCAAAGCTTTTT 59.067 42.857 9.53 0.00 0.00 1.94
91 92 1.136891 AGGCAAACTCGCAAAGCTTTT 59.863 42.857 9.53 0.00 0.00 2.27
92 93 0.746659 AGGCAAACTCGCAAAGCTTT 59.253 45.000 5.69 5.69 0.00 3.51
93 94 1.604604 TAGGCAAACTCGCAAAGCTT 58.395 45.000 0.00 0.00 0.00 3.74
94 95 1.604604 TTAGGCAAACTCGCAAAGCT 58.395 45.000 0.00 0.00 0.00 3.74
95 96 2.415697 TTTAGGCAAACTCGCAAAGC 57.584 45.000 0.00 0.00 0.00 3.51
96 97 2.719046 CGTTTTAGGCAAACTCGCAAAG 59.281 45.455 0.00 0.00 42.51 2.77
97 98 2.097791 ACGTTTTAGGCAAACTCGCAAA 59.902 40.909 0.00 0.00 42.51 3.68
98 99 1.671845 ACGTTTTAGGCAAACTCGCAA 59.328 42.857 0.00 0.00 42.51 4.85
99 100 1.262151 GACGTTTTAGGCAAACTCGCA 59.738 47.619 0.00 0.00 42.51 5.10
100 101 1.399343 GGACGTTTTAGGCAAACTCGC 60.399 52.381 0.00 0.00 42.51 5.03
101 102 1.196127 GGGACGTTTTAGGCAAACTCG 59.804 52.381 0.00 0.00 42.51 4.18
102 103 2.225727 CAGGGACGTTTTAGGCAAACTC 59.774 50.000 0.00 0.00 42.51 3.01
103 104 2.158726 TCAGGGACGTTTTAGGCAAACT 60.159 45.455 0.00 0.00 42.51 2.66
104 105 2.223745 TCAGGGACGTTTTAGGCAAAC 58.776 47.619 0.00 0.00 41.42 2.93
105 106 2.642154 TCAGGGACGTTTTAGGCAAA 57.358 45.000 0.00 0.00 0.00 3.68
106 107 2.617021 GGATCAGGGACGTTTTAGGCAA 60.617 50.000 0.00 0.00 0.00 4.52
107 108 1.065709 GGATCAGGGACGTTTTAGGCA 60.066 52.381 0.00 0.00 0.00 4.75
108 109 1.664873 GGATCAGGGACGTTTTAGGC 58.335 55.000 0.00 0.00 0.00 3.93
109 110 1.935933 CGGATCAGGGACGTTTTAGG 58.064 55.000 0.00 0.00 0.00 2.69
110 111 1.134788 AGCGGATCAGGGACGTTTTAG 60.135 52.381 0.00 0.00 0.00 1.85
111 112 0.899720 AGCGGATCAGGGACGTTTTA 59.100 50.000 0.00 0.00 0.00 1.52
112 113 0.391263 GAGCGGATCAGGGACGTTTT 60.391 55.000 0.00 0.00 0.00 2.43
113 114 1.218316 GAGCGGATCAGGGACGTTT 59.782 57.895 0.00 0.00 0.00 3.60
114 115 2.893398 GAGCGGATCAGGGACGTT 59.107 61.111 0.00 0.00 0.00 3.99
115 116 3.518998 CGAGCGGATCAGGGACGT 61.519 66.667 0.00 0.00 0.00 4.34
116 117 3.209812 TCGAGCGGATCAGGGACG 61.210 66.667 0.00 0.00 0.00 4.79
117 118 2.413765 GTCGAGCGGATCAGGGAC 59.586 66.667 0.00 0.00 0.00 4.46
118 119 2.833582 GGTCGAGCGGATCAGGGA 60.834 66.667 0.00 0.00 0.00 4.20
119 120 3.147595 TGGTCGAGCGGATCAGGG 61.148 66.667 10.46 0.00 30.49 4.45
120 121 2.105128 GTGGTCGAGCGGATCAGG 59.895 66.667 10.46 0.00 36.14 3.86
121 122 2.105128 GGTGGTCGAGCGGATCAG 59.895 66.667 10.46 0.00 36.14 2.90
122 123 3.458163 GGGTGGTCGAGCGGATCA 61.458 66.667 10.46 0.00 31.88 2.92
123 124 4.222847 GGGGTGGTCGAGCGGATC 62.223 72.222 10.46 0.58 0.00 3.36
190 191 1.445942 GCTGCCGGCTATTCCTACA 59.554 57.895 29.70 1.91 38.06 2.74
212 213 0.840722 GAGGGGTCCAGGGAAGAACA 60.841 60.000 0.00 0.00 0.00 3.18
310 311 2.864378 CTTCATCTGCAGCCTGGCGA 62.864 60.000 13.96 4.61 36.28 5.54
337 338 1.865340 ACGAGCGAACTTTTTGGAGAC 59.135 47.619 0.00 0.00 0.00 3.36
426 428 6.599638 GGGTGAAGAATACACTTGATAAAGCT 59.400 38.462 0.00 0.00 38.20 3.74
500 514 3.855858 TGCAAACTGTATCATGCGTAGA 58.144 40.909 0.00 0.00 41.61 2.59
525 539 1.006086 CTAATGATGACGCCAACGCA 58.994 50.000 0.00 0.00 45.53 5.24
566 580 9.525409 CAGGAAAAGGCATATTCATTCTAAAAG 57.475 33.333 0.00 0.00 0.00 2.27
607 621 2.418976 GCAGTACCCGAAATTCAGAACC 59.581 50.000 0.00 0.00 0.00 3.62
635 649 6.574350 CATACTTGAGGTTTACGAGGAGAAT 58.426 40.000 0.00 0.00 0.00 2.40
638 652 4.113354 GCATACTTGAGGTTTACGAGGAG 58.887 47.826 0.00 0.00 0.00 3.69
639 653 3.512329 TGCATACTTGAGGTTTACGAGGA 59.488 43.478 0.00 0.00 0.00 3.71
697 711 0.324368 TCTGTAGAGGACACCGGCAT 60.324 55.000 0.00 0.00 33.31 4.40
821 835 1.489649 AGACTGCAGAGGGGATTCATG 59.510 52.381 23.35 0.00 0.00 3.07
836 850 0.325933 TGAGGGGTTGATGCAGACTG 59.674 55.000 0.00 0.00 0.00 3.51
837 851 1.211457 GATGAGGGGTTGATGCAGACT 59.789 52.381 0.00 0.00 0.00 3.24
838 852 1.211457 AGATGAGGGGTTGATGCAGAC 59.789 52.381 0.00 0.00 0.00 3.51
839 853 1.211212 CAGATGAGGGGTTGATGCAGA 59.789 52.381 0.00 0.00 0.00 4.26
840 854 1.064906 ACAGATGAGGGGTTGATGCAG 60.065 52.381 0.00 0.00 0.00 4.41
841 855 0.994247 ACAGATGAGGGGTTGATGCA 59.006 50.000 0.00 0.00 0.00 3.96
842 856 2.019984 GAACAGATGAGGGGTTGATGC 58.980 52.381 0.00 0.00 0.00 3.91
963 977 0.657368 GAAGTCAAAACAGTGCCGCG 60.657 55.000 0.00 0.00 0.00 6.46
1011 1025 2.749076 CAACTCGCCAATCATCAAGGAA 59.251 45.455 0.00 0.00 0.00 3.36
1014 1028 1.741706 AGCAACTCGCCAATCATCAAG 59.258 47.619 0.00 0.00 44.04 3.02
1387 1401 4.026052 ACAATTTAATTCCTGAGGGGCAG 58.974 43.478 0.00 0.00 44.49 4.85
1458 1472 2.808206 CCCCTCACCGTATCCCTGC 61.808 68.421 0.00 0.00 0.00 4.85
1556 1570 4.415596 ACAGCAAATAATCAACTCCCCAA 58.584 39.130 0.00 0.00 0.00 4.12
1613 1628 7.801716 ATTGAAGTAACAAGTGCTAGTTTCA 57.198 32.000 0.00 0.00 33.22 2.69
1708 1729 4.992951 TCTTATATGCACTGCTAGCACATG 59.007 41.667 22.84 19.86 45.95 3.21
1759 1788 3.817647 AGACAACAGCAGAACTTCCATTC 59.182 43.478 0.00 0.00 0.00 2.67
1817 1846 4.437967 TCCTAGATGGCAATGGATATCCA 58.562 43.478 26.49 26.49 42.68 3.41
2029 2058 2.645838 AGTGTGTTGATGGTGAGCTT 57.354 45.000 0.00 0.00 0.00 3.74
2032 2061 5.300752 ACTCTAAAGTGTGTTGATGGTGAG 58.699 41.667 0.00 0.00 33.32 3.51
2047 2076 5.886960 ATAGCAAGTTGGCAACTCTAAAG 57.113 39.130 31.24 19.12 41.91 1.85
2085 2114 3.135348 AGTGTCATATCACAGGTCCATGG 59.865 47.826 4.97 4.97 40.37 3.66
2173 2204 6.095377 GGACACAGAAAAAGCAAGGAATATG 58.905 40.000 0.00 0.00 0.00 1.78
2178 2209 3.011566 TGGACACAGAAAAAGCAAGGA 57.988 42.857 0.00 0.00 0.00 3.36
2217 4049 5.754890 CCCATTGATTTTAGCCTTAATGCAC 59.245 40.000 5.50 0.00 0.00 4.57
2313 4153 4.363138 CAGAGATTTATCGTGTAGCTGCA 58.637 43.478 0.00 0.00 0.00 4.41
2360 4200 5.298197 GCATCATCAGCCATATCTTTCAG 57.702 43.478 0.00 0.00 0.00 3.02
2452 4292 9.804758 AGGTTTCGACTATATTCAGAAGTAAAG 57.195 33.333 0.00 0.00 0.00 1.85
2507 4347 5.945784 TGCTTACAGATAGGTTTCAGCAATT 59.054 36.000 0.00 0.00 33.18 2.32
2511 4351 7.736447 AATATGCTTACAGATAGGTTTCAGC 57.264 36.000 0.00 0.00 0.00 4.26
2521 4361 9.174166 ACGTCCTTTTTAAATATGCTTACAGAT 57.826 29.630 0.00 0.00 0.00 2.90
2600 4441 6.658849 TCCTGCCTCAGTAAAAATTGCTATA 58.341 36.000 0.00 0.00 0.00 1.31
2665 4511 1.066430 TGCCTCGGTAACCTGATTGAC 60.066 52.381 0.00 0.00 0.00 3.18
2710 4557 4.882427 TCAGTAGGCGATATAGTATGGAGC 59.118 45.833 0.00 0.00 0.00 4.70
2780 4627 4.942761 AGTGATGCAAACTGTGGAAAAT 57.057 36.364 4.71 0.00 0.00 1.82
2987 4930 2.652590 GATCCGGAGTACTACCACACT 58.347 52.381 11.34 0.00 0.00 3.55
3047 4990 2.109774 GGCATCCCCATTGATCAAACA 58.890 47.619 13.09 0.00 0.00 2.83
3083 5026 3.126000 GCCTCACAGCAAAAGTATCAGAC 59.874 47.826 0.00 0.00 0.00 3.51
3195 5182 1.931841 CATCTTCATGTCAGCACTCCG 59.068 52.381 0.00 0.00 0.00 4.63
3255 5242 5.312120 GTCTCGAGACAGAAGTTCCATTA 57.688 43.478 34.97 0.00 44.18 1.90


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

AutoCloner maintained by Alex Coulton.