Multiple sequence alignment - TraesCS6A01G081800

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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 TraesCS6A01G081800 chr6A 100.000 3538 0 0 1 3538 50410588 50407051 0.000000e+00 6534.0
1 TraesCS6A01G081800 chr6A 98.914 3224 29 4 320 3538 50466863 50463641 0.000000e+00 5755.0
2 TraesCS6A01G081800 chr6A 94.992 1797 61 9 899 2680 50866277 50864495 0.000000e+00 2793.0
3 TraesCS6A01G081800 chr6A 94.861 1401 44 7 929 2309 50250638 50249246 0.000000e+00 2163.0
4 TraesCS6A01G081800 chr6A 93.448 641 37 4 2899 3538 594997386 594996750 0.000000e+00 946.0
5 TraesCS6A01G081800 chr6A 93.814 194 11 1 2304 2497 50206594 50206402 1.240000e-74 291.0
6 TraesCS6A01G081800 chr6A 86.528 193 8 10 2722 2896 457318033 457317841 2.790000e-46 196.0
7 TraesCS6A01G081800 chr6A 85.870 184 8 1 2731 2896 512826584 512826401 2.810000e-41 180.0
8 TraesCS6A01G081800 chr6A 95.495 111 3 2 2619 2727 50197012 50196902 3.630000e-40 176.0
9 TraesCS6A01G081800 chr6A 91.803 122 9 1 2505 2626 50198248 50198128 6.070000e-38 169.0
10 TraesCS6A01G081800 chr6A 92.632 95 7 0 2802 2896 596602174 596602080 1.710000e-28 137.0
11 TraesCS6A01G081800 chr6A 97.674 43 1 0 2679 2721 50505756 50505714 1.360000e-09 75.0
12 TraesCS6A01G081800 chrUn 94.701 1887 65 19 743 2629 114233443 114235294 0.000000e+00 2898.0
13 TraesCS6A01G081800 chrUn 85.083 181 9 3 591 754 114196620 114196799 6.070000e-38 169.0
14 TraesCS6A01G081800 chrUn 92.593 108 5 2 2615 2721 114235310 114235415 6.120000e-33 152.0
15 TraesCS6A01G081800 chr4A 94.264 645 33 4 2896 3538 589103498 589104140 0.000000e+00 983.0
16 TraesCS6A01G081800 chr4A 91.641 323 26 1 1 323 729133736 729134057 2.510000e-121 446.0
17 TraesCS6A01G081800 chr4A 92.391 276 17 3 320 592 654590063 654589789 1.190000e-104 390.0
18 TraesCS6A01G081800 chr4A 81.858 226 39 2 2170 2394 687627012 687626788 4.660000e-44 189.0
19 TraesCS6A01G081800 chr4A 76.190 378 78 10 2024 2394 687660983 687660611 4.660000e-44 189.0
20 TraesCS6A01G081800 chr4A 80.973 226 41 2 2170 2394 687706550 687706326 1.010000e-40 178.0
21 TraesCS6A01G081800 chr1A 93.808 646 34 6 2896 3538 3262702 3263344 0.000000e+00 966.0
22 TraesCS6A01G081800 chr1A 85.492 193 10 10 2722 2896 488618619 488618427 6.030000e-43 185.0
23 TraesCS6A01G081800 chr5A 93.653 646 36 3 2894 3538 378278423 378277782 0.000000e+00 961.0
24 TraesCS6A01G081800 chr2A 93.199 647 37 5 2893 3538 374049071 374049711 0.000000e+00 944.0
25 TraesCS6A01G081800 chr2A 92.049 654 42 5 2894 3538 460083973 460084625 0.000000e+00 911.0
26 TraesCS6A01G081800 chr2A 92.117 647 43 4 2893 3538 77189105 77188466 0.000000e+00 905.0
27 TraesCS6A01G081800 chr2A 78.919 370 69 8 2030 2393 535413391 535413757 3.530000e-60 243.0
28 TraesCS6A01G081800 chr2A 91.549 71 6 0 2718 2788 97849202 97849272 8.080000e-17 99.0
29 TraesCS6A01G081800 chr5B 92.012 651 39 6 2892 3538 412655157 412654516 0.000000e+00 902.0
30 TraesCS6A01G081800 chr5B 93.730 319 20 0 1 319 13739597 13739279 2.470000e-131 479.0
31 TraesCS6A01G081800 chr5B 92.945 326 16 7 1 323 38135110 38134789 5.350000e-128 468.0
32 TraesCS6A01G081800 chr5B 90.312 320 29 1 1 320 557072397 557072080 5.460000e-113 418.0
33 TraesCS6A01G081800 chr5B 90.312 320 29 2 1 319 688472651 688472333 5.460000e-113 418.0
34 TraesCS6A01G081800 chr5B 93.116 276 14 4 320 592 225884568 225884841 1.980000e-107 399.0
35 TraesCS6A01G081800 chr5B 95.161 248 12 0 320 567 654603557 654603804 3.310000e-105 392.0
36 TraesCS6A01G081800 chr5B 91.912 272 20 1 323 592 97892975 97892704 2.580000e-101 379.0
37 TraesCS6A01G081800 chr5B 87.778 90 10 1 2719 2808 614636219 614636307 1.740000e-18 104.0
38 TraesCS6A01G081800 chr5B 89.610 77 8 0 2712 2788 366499685 366499761 8.080000e-17 99.0
39 TraesCS6A01G081800 chr5B 88.750 80 6 3 2711 2788 520109282 520109204 1.050000e-15 95.3
40 TraesCS6A01G081800 chr3B 94.062 320 18 1 1 320 799751035 799751353 5.310000e-133 484.0
41 TraesCS6A01G081800 chr2B 92.835 321 21 2 1 320 739549424 739549743 6.920000e-127 464.0
42 TraesCS6A01G081800 chr2B 92.029 276 18 3 320 592 307286629 307286903 5.540000e-103 385.0
43 TraesCS6A01G081800 chr1B 90.654 321 28 2 1 320 678419018 678418699 3.260000e-115 425.0
44 TraesCS6A01G081800 chr1B 93.116 276 15 3 320 592 391945626 391945352 5.500000e-108 401.0
45 TraesCS6A01G081800 chr1B 100.000 30 0 0 606 635 598379413 598379384 4.930000e-04 56.5
46 TraesCS6A01G081800 chr1B 100.000 30 0 0 606 635 598394672 598394643 4.930000e-04 56.5
47 TraesCS6A01G081800 chr1B 100.000 30 0 0 606 635 598409929 598409900 4.930000e-04 56.5
48 TraesCS6A01G081800 chr7B 90.312 320 29 2 1 319 739428442 739428124 5.460000e-113 418.0
49 TraesCS6A01G081800 chr7B 77.119 236 45 9 2161 2393 374530226 374530455 1.030000e-25 128.0
50 TraesCS6A01G081800 chr7B 89.474 76 7 1 2724 2799 721417734 721417808 1.050000e-15 95.3
51 TraesCS6A01G081800 chr7D 95.635 252 11 0 320 571 550353184 550352933 4.250000e-109 405.0
52 TraesCS6A01G081800 chr7D 76.132 243 49 9 2161 2400 379091453 379091689 6.200000e-23 119.0
53 TraesCS6A01G081800 chr7D 95.714 70 3 0 2718 2787 558892992 558893061 2.890000e-21 113.0
54 TraesCS6A01G081800 chr5D 94.444 252 14 0 320 571 448737738 448737989 4.280000e-104 388.0
55 TraesCS6A01G081800 chr5D 95.714 70 3 0 2718 2787 454269499 454269568 2.890000e-21 113.0
56 TraesCS6A01G081800 chr2D 84.756 164 7 9 2751 2896 545767532 545767695 7.910000e-32 148.0
57 TraesCS6A01G081800 chr2D 78.302 106 18 5 2214 2318 69275950 69276051 2.950000e-06 63.9
58 TraesCS6A01G081800 chr4B 93.684 95 6 0 2802 2896 5973400 5973306 3.680000e-30 143.0
59 TraesCS6A01G081800 chr4B 98.485 66 1 0 2722 2787 5973519 5973454 2.230000e-22 117.0
60 TraesCS6A01G081800 chr7A 100.000 28 0 0 608 635 245593424 245593397 6.000000e-03 52.8


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 TraesCS6A01G081800 chr6A 50407051 50410588 3537 True 6534 6534 100.000 1 3538 1 chr6A.!!$R3 3537
1 TraesCS6A01G081800 chr6A 50463641 50466863 3222 True 5755 5755 98.914 320 3538 1 chr6A.!!$R4 3218
2 TraesCS6A01G081800 chr6A 50864495 50866277 1782 True 2793 2793 94.992 899 2680 1 chr6A.!!$R6 1781
3 TraesCS6A01G081800 chr6A 50249246 50250638 1392 True 2163 2163 94.861 929 2309 1 chr6A.!!$R2 1380
4 TraesCS6A01G081800 chr6A 594996750 594997386 636 True 946 946 93.448 2899 3538 1 chr6A.!!$R9 639
5 TraesCS6A01G081800 chrUn 114233443 114235415 1972 False 1525 2898 93.647 743 2721 2 chrUn.!!$F2 1978
6 TraesCS6A01G081800 chr4A 589103498 589104140 642 False 983 983 94.264 2896 3538 1 chr4A.!!$F1 642
7 TraesCS6A01G081800 chr1A 3262702 3263344 642 False 966 966 93.808 2896 3538 1 chr1A.!!$F1 642
8 TraesCS6A01G081800 chr5A 378277782 378278423 641 True 961 961 93.653 2894 3538 1 chr5A.!!$R1 644
9 TraesCS6A01G081800 chr2A 374049071 374049711 640 False 944 944 93.199 2893 3538 1 chr2A.!!$F2 645
10 TraesCS6A01G081800 chr2A 460083973 460084625 652 False 911 911 92.049 2894 3538 1 chr2A.!!$F3 644
11 TraesCS6A01G081800 chr2A 77188466 77189105 639 True 905 905 92.117 2893 3538 1 chr2A.!!$R1 645
12 TraesCS6A01G081800 chr5B 412654516 412655157 641 True 902 902 92.012 2892 3538 1 chr5B.!!$R4 646

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
159 160 0.033504 ATATGCAGTTAGGCCGACGG 59.966 55.0 10.29 10.29 0.00 4.79 F
227 228 0.110464 GGCTATAGTACGCCGACGAC 60.110 60.0 0.00 0.00 43.93 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 2515 8.650143 ACAAACTCCCTGATTATTACATTTGT 57.350 30.769 0.0 0.0 33.08 2.83 R
2715 2772 8.184192 AGATGTGAAATAGCAAATCCGTTTTAG 58.816 33.333 0.0 0.0 33.79 1.85 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
25 26 3.849951 CGTGGCCTGCGGACCTAT 61.850 66.667 3.32 0.00 0.00 2.57
26 27 2.203070 GTGGCCTGCGGACCTATG 60.203 66.667 3.32 0.00 0.00 2.23
27 28 4.175337 TGGCCTGCGGACCTATGC 62.175 66.667 3.32 0.00 0.00 3.14
28 29 4.937431 GGCCTGCGGACCTATGCC 62.937 72.222 0.00 0.00 0.00 4.40
65 66 2.959275 CCGTCGGCATAGTTCTGAC 58.041 57.895 0.00 0.00 36.69 3.51
74 75 3.491267 GGCATAGTTCTGACGATGTTAGC 59.509 47.826 0.00 0.00 39.98 3.09
75 76 3.491267 GCATAGTTCTGACGATGTTAGCC 59.509 47.826 0.00 0.00 39.98 3.93
76 77 4.682787 CATAGTTCTGACGATGTTAGCCA 58.317 43.478 0.00 0.00 35.10 4.75
77 78 3.238108 AGTTCTGACGATGTTAGCCAG 57.762 47.619 0.00 0.00 0.00 4.85
78 79 2.093973 AGTTCTGACGATGTTAGCCAGG 60.094 50.000 0.00 0.00 0.00 4.45
79 80 0.824109 TCTGACGATGTTAGCCAGGG 59.176 55.000 0.00 0.00 0.00 4.45
80 81 0.179073 CTGACGATGTTAGCCAGGGG 60.179 60.000 0.00 0.00 0.00 4.79
81 82 1.146263 GACGATGTTAGCCAGGGGG 59.854 63.158 0.00 0.00 37.18 5.40
100 101 3.571216 TTGCCGGGCCCACTGTTA 61.571 61.111 24.92 0.00 0.00 2.41
101 102 2.913117 TTGCCGGGCCCACTGTTAT 61.913 57.895 24.92 0.00 0.00 1.89
102 103 2.828549 GCCGGGCCCACTGTTATG 60.829 66.667 24.92 1.64 0.00 1.90
103 104 2.828549 CCGGGCCCACTGTTATGC 60.829 66.667 24.92 0.00 0.00 3.14
104 105 2.828549 CGGGCCCACTGTTATGCC 60.829 66.667 24.92 3.95 43.26 4.40
105 106 2.828549 GGGCCCACTGTTATGCCG 60.829 66.667 19.95 0.00 44.96 5.69
106 107 2.270850 GGCCCACTGTTATGCCGA 59.729 61.111 0.00 0.00 33.59 5.54
107 108 2.112815 GGCCCACTGTTATGCCGAC 61.113 63.158 0.00 0.00 33.59 4.79
108 109 2.461110 GCCCACTGTTATGCCGACG 61.461 63.158 0.00 0.00 0.00 5.12
109 110 1.813753 CCCACTGTTATGCCGACGG 60.814 63.158 10.29 10.29 0.00 4.79
119 120 3.849953 GCCGACGGCGCTTGTAAG 61.850 66.667 25.24 4.48 39.62 2.34
141 142 4.873129 CGGCAGCTGTCGGCGTAT 62.873 66.667 32.36 0.00 46.26 3.06
142 143 3.478724 CGGCAGCTGTCGGCGTATA 62.479 63.158 32.36 0.00 46.26 1.47
143 144 2.749110 CGGCAGCTGTCGGCGTATAT 62.749 60.000 32.36 0.00 46.26 0.86
146 147 4.336581 GCTGTCGGCGTATATGCA 57.663 55.556 18.41 0.00 36.28 3.96
147 148 2.145225 GCTGTCGGCGTATATGCAG 58.855 57.895 18.41 14.44 36.28 4.41
148 149 0.597637 GCTGTCGGCGTATATGCAGT 60.598 55.000 18.41 0.00 36.28 4.40
149 150 1.852942 CTGTCGGCGTATATGCAGTT 58.147 50.000 18.41 0.00 36.28 3.16
150 151 2.860971 GCTGTCGGCGTATATGCAGTTA 60.861 50.000 18.41 7.37 36.28 2.24
151 152 2.980476 CTGTCGGCGTATATGCAGTTAG 59.020 50.000 18.41 12.36 36.28 2.34
152 153 2.287970 TGTCGGCGTATATGCAGTTAGG 60.288 50.000 18.41 1.07 36.28 2.69
153 154 1.068474 CGGCGTATATGCAGTTAGGC 58.932 55.000 18.41 12.49 36.28 3.93
154 155 1.439679 GGCGTATATGCAGTTAGGCC 58.560 55.000 20.16 20.16 40.80 5.19
155 156 1.068474 GCGTATATGCAGTTAGGCCG 58.932 55.000 12.17 0.34 34.15 6.13
156 157 1.336517 GCGTATATGCAGTTAGGCCGA 60.337 52.381 12.17 0.00 34.15 5.54
157 158 2.325761 CGTATATGCAGTTAGGCCGAC 58.674 52.381 0.00 0.00 0.00 4.79
158 159 2.325761 GTATATGCAGTTAGGCCGACG 58.674 52.381 0.00 0.00 0.00 5.12
159 160 0.033504 ATATGCAGTTAGGCCGACGG 59.966 55.000 10.29 10.29 0.00 4.79
169 170 2.960129 GCCGACGGCCGTTCTATG 60.960 66.667 34.65 19.22 44.06 2.23
170 171 2.960129 CCGACGGCCGTTCTATGC 60.960 66.667 34.65 17.58 36.31 3.14
171 172 2.960129 CGACGGCCGTTCTATGCC 60.960 66.667 34.65 16.77 44.41 4.40
178 179 4.609995 CGTTCTATGCCAACGGGT 57.390 55.556 0.00 0.00 42.36 5.28
179 180 2.086510 CGTTCTATGCCAACGGGTG 58.913 57.895 0.00 0.00 42.36 4.61
180 181 1.800681 GTTCTATGCCAACGGGTGC 59.199 57.895 0.00 0.00 36.17 5.01
181 182 1.377987 TTCTATGCCAACGGGTGCC 60.378 57.895 0.00 0.00 36.17 5.01
196 197 2.583593 GCCGTCGGCTTAGCTCTG 60.584 66.667 28.98 0.00 46.69 3.35
197 198 2.885861 CCGTCGGCTTAGCTCTGT 59.114 61.111 3.59 0.00 0.00 3.41
198 199 1.517257 CCGTCGGCTTAGCTCTGTG 60.517 63.158 3.59 0.00 0.00 3.66
199 200 1.213013 CGTCGGCTTAGCTCTGTGT 59.787 57.895 3.59 0.00 0.00 3.72
200 201 0.450583 CGTCGGCTTAGCTCTGTGTA 59.549 55.000 3.59 0.00 0.00 2.90
201 202 1.532090 CGTCGGCTTAGCTCTGTGTAG 60.532 57.143 3.59 0.00 0.00 2.74
202 203 0.456221 TCGGCTTAGCTCTGTGTAGC 59.544 55.000 3.59 0.00 43.11 3.58
203 204 0.528684 CGGCTTAGCTCTGTGTAGCC 60.529 60.000 3.59 0.00 46.16 3.93
204 205 0.179070 GGCTTAGCTCTGTGTAGCCC 60.179 60.000 3.59 0.00 44.38 5.19
205 206 0.528684 GCTTAGCTCTGTGTAGCCCG 60.529 60.000 0.00 0.00 43.86 6.13
206 207 1.103803 CTTAGCTCTGTGTAGCCCGA 58.896 55.000 0.00 0.00 43.86 5.14
207 208 0.815734 TTAGCTCTGTGTAGCCCGAC 59.184 55.000 0.00 0.00 43.86 4.79
208 209 1.374343 TAGCTCTGTGTAGCCCGACG 61.374 60.000 0.00 0.00 43.86 5.12
209 210 2.490217 CTCTGTGTAGCCCGACGG 59.510 66.667 6.99 6.99 0.00 4.79
220 221 1.208614 CCCGACGGCTATAGTACGC 59.791 63.158 8.86 9.63 0.00 4.42
221 222 1.208614 CCGACGGCTATAGTACGCC 59.791 63.158 15.69 5.03 42.86 5.68
226 227 2.238353 GGCTATAGTACGCCGACGA 58.762 57.895 0.00 0.00 43.93 4.20
227 228 0.110464 GGCTATAGTACGCCGACGAC 60.110 60.000 0.00 0.00 43.93 4.34
228 229 0.110464 GCTATAGTACGCCGACGACC 60.110 60.000 0.00 0.00 43.93 4.79
229 230 1.220529 CTATAGTACGCCGACGACCA 58.779 55.000 0.00 0.00 43.93 4.02
230 231 1.194098 CTATAGTACGCCGACGACCAG 59.806 57.143 0.00 0.00 43.93 4.00
231 232 0.462581 ATAGTACGCCGACGACCAGA 60.463 55.000 0.00 0.00 43.93 3.86
232 233 0.673333 TAGTACGCCGACGACCAGAA 60.673 55.000 0.00 0.00 43.93 3.02
233 234 1.799121 GTACGCCGACGACCAGAAC 60.799 63.158 0.00 0.00 43.93 3.01
234 235 2.981560 TACGCCGACGACCAGAACC 61.982 63.158 0.00 0.00 43.93 3.62
235 236 4.351938 CGCCGACGACCAGAACCA 62.352 66.667 0.00 0.00 43.93 3.67
236 237 2.432628 GCCGACGACCAGAACCAG 60.433 66.667 0.00 0.00 0.00 4.00
237 238 2.261671 CCGACGACCAGAACCAGG 59.738 66.667 0.00 0.00 0.00 4.45
238 239 2.432628 CGACGACCAGAACCAGGC 60.433 66.667 0.00 0.00 0.00 4.85
239 240 2.932234 CGACGACCAGAACCAGGCT 61.932 63.158 0.00 0.00 0.00 4.58
240 241 1.374758 GACGACCAGAACCAGGCTG 60.375 63.158 7.75 7.75 0.00 4.85
241 242 2.100879 GACGACCAGAACCAGGCTGT 62.101 60.000 14.43 0.00 0.00 4.40
242 243 1.374758 CGACCAGAACCAGGCTGTC 60.375 63.158 14.43 5.33 0.00 3.51
243 244 1.374758 GACCAGAACCAGGCTGTCG 60.375 63.158 14.43 1.04 0.00 4.35
244 245 2.046892 CCAGAACCAGGCTGTCGG 60.047 66.667 14.43 6.04 0.00 4.79
245 246 2.743928 CAGAACCAGGCTGTCGGC 60.744 66.667 14.43 0.00 40.90 5.54
246 247 3.241530 AGAACCAGGCTGTCGGCA 61.242 61.111 14.43 0.00 44.01 5.69
247 248 2.045926 GAACCAGGCTGTCGGCAT 60.046 61.111 14.43 0.00 44.01 4.40
248 249 1.220749 GAACCAGGCTGTCGGCATA 59.779 57.895 14.43 0.00 44.01 3.14
249 250 0.811616 GAACCAGGCTGTCGGCATAG 60.812 60.000 14.43 0.00 44.01 2.23
250 251 2.590007 CCAGGCTGTCGGCATAGC 60.590 66.667 14.43 0.00 44.01 2.97
251 252 2.503061 CAGGCTGTCGGCATAGCT 59.497 61.111 6.28 0.00 44.01 3.32
252 253 1.593750 CAGGCTGTCGGCATAGCTC 60.594 63.158 6.28 0.00 44.01 4.09
253 254 2.280457 GGCTGTCGGCATAGCTCC 60.280 66.667 5.89 0.00 44.01 4.70
261 262 2.611012 GGCATAGCTCCGAAGAAGC 58.389 57.895 0.00 0.00 39.24 3.86
262 263 0.882484 GGCATAGCTCCGAAGAAGCC 60.882 60.000 0.00 0.00 40.62 4.35
263 264 1.218230 GCATAGCTCCGAAGAAGCCG 61.218 60.000 0.00 0.00 40.62 5.52
264 265 0.385751 CATAGCTCCGAAGAAGCCGA 59.614 55.000 0.00 0.00 40.62 5.54
265 266 0.386113 ATAGCTCCGAAGAAGCCGAC 59.614 55.000 0.00 0.00 40.62 4.79
266 267 1.989966 TAGCTCCGAAGAAGCCGACG 61.990 60.000 0.00 0.00 40.62 5.12
267 268 2.202623 CTCCGAAGAAGCCGACGG 60.203 66.667 10.29 10.29 45.61 4.79
288 289 2.637025 CCGTCGGCACTGTTTTGG 59.363 61.111 0.00 0.00 0.00 3.28
289 290 2.051345 CGTCGGCACTGTTTTGGC 60.051 61.111 0.00 0.00 38.68 4.52
290 291 2.335011 GTCGGCACTGTTTTGGCC 59.665 61.111 0.00 0.00 44.27 5.36
293 294 2.335011 GGCACTGTTTTGGCCGTC 59.665 61.111 0.00 0.00 38.04 4.79
294 295 2.051345 GCACTGTTTTGGCCGTCG 60.051 61.111 0.00 0.00 0.00 5.12
295 296 2.637025 CACTGTTTTGGCCGTCGG 59.363 61.111 6.99 6.99 0.00 4.79
296 297 2.593436 ACTGTTTTGGCCGTCGGG 60.593 61.111 14.38 0.00 0.00 5.14
297 298 3.361977 CTGTTTTGGCCGTCGGGG 61.362 66.667 14.38 0.00 39.58 5.73
298 299 4.192453 TGTTTTGGCCGTCGGGGT 62.192 61.111 14.38 0.00 38.44 4.95
299 300 2.032376 GTTTTGGCCGTCGGGGTA 59.968 61.111 14.38 0.00 38.44 3.69
300 301 2.036571 GTTTTGGCCGTCGGGGTAG 61.037 63.158 14.38 0.00 38.44 3.18
301 302 3.905437 TTTTGGCCGTCGGGGTAGC 62.905 63.158 14.38 0.00 38.44 3.58
313 314 4.832608 GGTAGCGCCCTGTTCCGG 62.833 72.222 2.29 0.00 0.00 5.14
314 315 4.078516 GTAGCGCCCTGTTCCGGT 62.079 66.667 2.29 0.00 38.78 5.28
315 316 2.362760 TAGCGCCCTGTTCCGGTA 60.363 61.111 2.29 0.00 36.51 4.02
316 317 2.420568 TAGCGCCCTGTTCCGGTAG 61.421 63.158 2.29 0.00 36.51 3.18
317 318 4.078516 GCGCCCTGTTCCGGTAGT 62.079 66.667 0.00 0.00 0.00 2.73
318 319 2.125673 CGCCCTGTTCCGGTAGTG 60.126 66.667 0.00 0.00 0.00 2.74
436 437 2.432510 AGGCGAGTTCTGAATTAGAGGG 59.567 50.000 0.00 0.00 36.61 4.30
455 456 7.465900 AGAGGGTTTGGAGGATAATAAATGA 57.534 36.000 0.00 0.00 0.00 2.57
580 581 5.253330 CAAGCACCCTTTTATTCACCTAGA 58.747 41.667 0.00 0.00 0.00 2.43
2494 2515 2.906939 GCCTCACACGTGCATGCAA 61.907 57.895 24.58 4.38 0.00 4.08
2715 2772 5.949233 ATTTGCGAGTTTGTCAAGTTTTC 57.051 34.783 0.00 0.00 0.00 2.29
3203 3274 1.544825 CGGCCTTCTCCTCCTTGACA 61.545 60.000 0.00 0.00 0.00 3.58
3299 3373 1.514087 GCATAAGACGACGACCCCA 59.486 57.895 0.00 0.00 0.00 4.96
3418 3493 1.077787 CCTGGCACGCCCATTCTAA 60.078 57.895 5.42 0.00 44.33 2.10
3433 3508 2.025418 CTAAGGCCGCGTCGTTGTT 61.025 57.895 4.92 0.00 0.00 2.83
3513 3588 2.124653 GAGCCGACGAGGAGGAGA 60.125 66.667 0.00 0.00 45.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.760047 GCAGGCCACGTCACCGAT 62.760 66.667 5.01 0.00 37.88 4.18
14 15 2.279517 GTCGGCATAGGTCCGCAG 60.280 66.667 5.55 0.00 46.05 5.18
15 16 4.201679 CGTCGGCATAGGTCCGCA 62.202 66.667 5.55 0.00 46.05 5.69
16 17 4.944372 CCGTCGGCATAGGTCCGC 62.944 72.222 0.00 1.58 46.05 5.54
47 48 0.866061 CGTCAGAACTATGCCGACGG 60.866 60.000 10.29 10.29 44.21 4.79
48 49 2.566997 CGTCAGAACTATGCCGACG 58.433 57.895 0.00 0.00 42.79 5.12
49 50 2.120232 CATCGTCAGAACTATGCCGAC 58.880 52.381 0.00 0.00 0.00 4.79
50 51 1.749063 ACATCGTCAGAACTATGCCGA 59.251 47.619 0.00 0.00 33.09 5.54
51 52 2.209838 ACATCGTCAGAACTATGCCG 57.790 50.000 0.00 0.00 33.09 5.69
52 53 3.491267 GCTAACATCGTCAGAACTATGCC 59.509 47.826 0.00 0.00 33.09 4.40
53 54 3.491267 GGCTAACATCGTCAGAACTATGC 59.509 47.826 0.00 0.00 33.09 3.14
54 55 4.682787 TGGCTAACATCGTCAGAACTATG 58.317 43.478 0.00 0.00 35.32 2.23
55 56 4.202161 CCTGGCTAACATCGTCAGAACTAT 60.202 45.833 0.00 0.00 36.22 2.12
56 57 3.130516 CCTGGCTAACATCGTCAGAACTA 59.869 47.826 0.00 0.00 36.22 2.24
57 58 2.093973 CCTGGCTAACATCGTCAGAACT 60.094 50.000 0.00 0.00 36.22 3.01
58 59 2.271800 CCTGGCTAACATCGTCAGAAC 58.728 52.381 0.00 0.00 36.22 3.01
59 60 1.207089 CCCTGGCTAACATCGTCAGAA 59.793 52.381 0.00 0.00 36.22 3.02
60 61 0.824109 CCCTGGCTAACATCGTCAGA 59.176 55.000 0.00 0.00 36.22 3.27
61 62 0.179073 CCCCTGGCTAACATCGTCAG 60.179 60.000 0.00 0.00 34.00 3.51
62 63 1.622607 CCCCCTGGCTAACATCGTCA 61.623 60.000 0.00 0.00 0.00 4.35
63 64 1.146263 CCCCCTGGCTAACATCGTC 59.854 63.158 0.00 0.00 0.00 4.20
64 65 3.320359 CCCCCTGGCTAACATCGT 58.680 61.111 0.00 0.00 0.00 3.73
82 83 3.853698 TAACAGTGGGCCCGGCAAC 62.854 63.158 19.37 9.94 0.00 4.17
83 84 2.913117 ATAACAGTGGGCCCGGCAA 61.913 57.895 19.37 0.00 0.00 4.52
84 85 3.334891 ATAACAGTGGGCCCGGCA 61.335 61.111 19.37 0.00 0.00 5.69
85 86 2.828549 CATAACAGTGGGCCCGGC 60.829 66.667 19.37 13.10 0.00 6.13
86 87 2.828549 GCATAACAGTGGGCCCGG 60.829 66.667 19.37 12.13 0.00 5.73
87 88 2.828549 GGCATAACAGTGGGCCCG 60.829 66.667 19.37 5.25 40.55 6.13
88 89 2.828549 CGGCATAACAGTGGGCCC 60.829 66.667 17.59 17.59 43.50 5.80
89 90 2.112815 GTCGGCATAACAGTGGGCC 61.113 63.158 0.00 0.00 42.98 5.80
90 91 2.461110 CGTCGGCATAACAGTGGGC 61.461 63.158 0.00 0.00 0.00 5.36
91 92 1.813753 CCGTCGGCATAACAGTGGG 60.814 63.158 0.00 0.00 0.00 4.61
92 93 3.794270 CCGTCGGCATAACAGTGG 58.206 61.111 0.00 0.00 0.00 4.00
102 103 3.849953 CTTACAAGCGCCGTCGGC 61.850 66.667 26.69 26.69 46.75 5.54
103 104 3.849953 GCTTACAAGCGCCGTCGG 61.850 66.667 6.99 6.99 42.88 4.79
124 125 2.749110 ATATACGCCGACAGCTGCCG 62.749 60.000 16.16 16.16 40.39 5.69
125 126 1.006102 ATATACGCCGACAGCTGCC 60.006 57.895 15.27 0.16 40.39 4.85
126 127 1.891060 GCATATACGCCGACAGCTGC 61.891 60.000 15.27 5.81 40.39 5.25
127 128 0.597377 TGCATATACGCCGACAGCTG 60.597 55.000 13.48 13.48 40.39 4.24
128 129 0.319040 CTGCATATACGCCGACAGCT 60.319 55.000 0.00 0.00 40.39 4.24
129 130 0.597637 ACTGCATATACGCCGACAGC 60.598 55.000 0.00 0.00 38.52 4.40
130 131 1.852942 AACTGCATATACGCCGACAG 58.147 50.000 0.00 0.00 0.00 3.51
131 132 2.287970 CCTAACTGCATATACGCCGACA 60.288 50.000 0.00 0.00 0.00 4.35
132 133 2.325761 CCTAACTGCATATACGCCGAC 58.674 52.381 0.00 0.00 0.00 4.79
133 134 1.336517 GCCTAACTGCATATACGCCGA 60.337 52.381 0.00 0.00 0.00 5.54
134 135 1.068474 GCCTAACTGCATATACGCCG 58.932 55.000 0.00 0.00 0.00 6.46
135 136 1.439679 GGCCTAACTGCATATACGCC 58.560 55.000 0.00 0.00 0.00 5.68
136 137 1.068474 CGGCCTAACTGCATATACGC 58.932 55.000 0.00 0.00 0.00 4.42
137 138 2.325761 GTCGGCCTAACTGCATATACG 58.674 52.381 0.00 0.00 0.00 3.06
138 139 2.325761 CGTCGGCCTAACTGCATATAC 58.674 52.381 0.00 0.00 0.00 1.47
139 140 1.271379 CCGTCGGCCTAACTGCATATA 59.729 52.381 0.00 0.00 0.00 0.86
140 141 0.033504 CCGTCGGCCTAACTGCATAT 59.966 55.000 0.00 0.00 0.00 1.78
141 142 1.440060 CCGTCGGCCTAACTGCATA 59.560 57.895 0.00 0.00 0.00 3.14
142 143 2.186903 CCGTCGGCCTAACTGCAT 59.813 61.111 0.00 0.00 0.00 3.96
143 144 4.752879 GCCGTCGGCCTAACTGCA 62.753 66.667 26.23 0.00 44.06 4.41
153 154 2.960129 GCATAGAACGGCCGTCGG 60.960 66.667 34.29 19.49 44.45 4.79
154 155 2.960129 GGCATAGAACGGCCGTCG 60.960 66.667 34.29 18.28 40.93 5.12
161 162 1.977594 GCACCCGTTGGCATAGAACG 61.978 60.000 2.57 2.57 44.59 3.95
162 163 1.800681 GCACCCGTTGGCATAGAAC 59.199 57.895 0.00 0.00 33.59 3.01
163 164 4.312052 GCACCCGTTGGCATAGAA 57.688 55.556 0.00 0.00 33.59 2.10
180 181 1.517257 CACAGAGCTAAGCCGACGG 60.517 63.158 10.29 10.29 0.00 4.79
181 182 0.450583 TACACAGAGCTAAGCCGACG 59.549 55.000 0.00 0.00 0.00 5.12
182 183 1.799548 GCTACACAGAGCTAAGCCGAC 60.800 57.143 0.00 0.00 39.50 4.79
183 184 0.456221 GCTACACAGAGCTAAGCCGA 59.544 55.000 0.00 0.00 39.50 5.54
184 185 0.528684 GGCTACACAGAGCTAAGCCG 60.529 60.000 0.00 0.00 42.98 5.52
185 186 3.371087 GGCTACACAGAGCTAAGCC 57.629 57.895 0.00 0.00 45.37 4.35
186 187 0.528684 CGGGCTACACAGAGCTAAGC 60.529 60.000 0.00 0.00 42.43 3.09
187 188 1.103803 TCGGGCTACACAGAGCTAAG 58.896 55.000 0.00 0.00 42.43 2.18
188 189 0.815734 GTCGGGCTACACAGAGCTAA 59.184 55.000 0.00 0.00 42.43 3.09
189 190 1.374343 CGTCGGGCTACACAGAGCTA 61.374 60.000 0.00 0.00 42.43 3.32
190 191 2.701780 CGTCGGGCTACACAGAGCT 61.702 63.158 0.00 0.00 42.43 4.09
191 192 2.202623 CGTCGGGCTACACAGAGC 60.203 66.667 0.00 0.00 42.05 4.09
192 193 2.490217 CCGTCGGGCTACACAGAG 59.510 66.667 2.34 0.00 0.00 3.35
202 203 1.208614 GCGTACTATAGCCGTCGGG 59.791 63.158 14.38 0.00 0.00 5.14
203 204 1.208614 GGCGTACTATAGCCGTCGG 59.791 63.158 6.99 6.99 44.22 4.79
204 205 4.834828 GGCGTACTATAGCCGTCG 57.165 61.111 12.38 7.78 44.22 5.12
209 210 0.110464 GGTCGTCGGCGTACTATAGC 60.110 60.000 10.18 0.00 39.49 2.97
210 211 1.194098 CTGGTCGTCGGCGTACTATAG 59.806 57.143 10.18 0.00 39.49 1.31
211 212 1.202521 TCTGGTCGTCGGCGTACTATA 60.203 52.381 10.18 0.00 39.49 1.31
212 213 0.462581 TCTGGTCGTCGGCGTACTAT 60.463 55.000 10.18 0.00 39.49 2.12
213 214 0.673333 TTCTGGTCGTCGGCGTACTA 60.673 55.000 10.18 3.52 39.49 1.82
214 215 1.968017 TTCTGGTCGTCGGCGTACT 60.968 57.895 10.18 0.00 39.49 2.73
215 216 1.799121 GTTCTGGTCGTCGGCGTAC 60.799 63.158 10.18 6.37 39.49 3.67
216 217 2.562912 GTTCTGGTCGTCGGCGTA 59.437 61.111 10.18 0.00 39.49 4.42
217 218 4.353437 GGTTCTGGTCGTCGGCGT 62.353 66.667 10.18 0.00 39.49 5.68
218 219 4.351938 TGGTTCTGGTCGTCGGCG 62.352 66.667 1.15 1.15 39.92 6.46
219 220 2.432628 CTGGTTCTGGTCGTCGGC 60.433 66.667 0.00 0.00 0.00 5.54
220 221 2.261671 CCTGGTTCTGGTCGTCGG 59.738 66.667 0.00 0.00 0.00 4.79
221 222 2.432628 GCCTGGTTCTGGTCGTCG 60.433 66.667 0.00 0.00 0.00 5.12
222 223 1.374758 CAGCCTGGTTCTGGTCGTC 60.375 63.158 0.00 0.00 0.00 4.20
223 224 2.100879 GACAGCCTGGTTCTGGTCGT 62.101 60.000 0.00 0.00 35.94 4.34
224 225 1.374758 GACAGCCTGGTTCTGGTCG 60.375 63.158 0.00 0.00 35.94 4.79
225 226 1.374758 CGACAGCCTGGTTCTGGTC 60.375 63.158 0.00 0.00 35.94 4.02
226 227 2.743718 CGACAGCCTGGTTCTGGT 59.256 61.111 0.00 0.00 35.94 4.00
227 228 2.046892 CCGACAGCCTGGTTCTGG 60.047 66.667 0.00 0.00 35.94 3.86
228 229 2.743928 GCCGACAGCCTGGTTCTG 60.744 66.667 0.00 0.00 37.56 3.02
229 230 1.264749 TATGCCGACAGCCTGGTTCT 61.265 55.000 0.00 0.00 42.71 3.01
230 231 0.811616 CTATGCCGACAGCCTGGTTC 60.812 60.000 0.00 0.00 42.71 3.62
231 232 1.221840 CTATGCCGACAGCCTGGTT 59.778 57.895 0.00 0.00 42.71 3.67
232 233 2.903357 CTATGCCGACAGCCTGGT 59.097 61.111 0.00 0.00 42.71 4.00
233 234 2.590007 GCTATGCCGACAGCCTGG 60.590 66.667 0.00 0.00 42.71 4.45
234 235 1.593750 GAGCTATGCCGACAGCCTG 60.594 63.158 0.00 0.00 42.71 4.85
235 236 2.801631 GGAGCTATGCCGACAGCCT 61.802 63.158 0.00 0.00 42.71 4.58
236 237 2.280457 GGAGCTATGCCGACAGCC 60.280 66.667 0.00 0.00 42.71 4.85
243 244 0.882484 GGCTTCTTCGGAGCTATGCC 60.882 60.000 0.00 0.00 0.00 4.40
244 245 1.218230 CGGCTTCTTCGGAGCTATGC 61.218 60.000 0.00 0.00 0.00 3.14
245 246 0.385751 TCGGCTTCTTCGGAGCTATG 59.614 55.000 0.00 0.00 0.00 2.23
246 247 0.386113 GTCGGCTTCTTCGGAGCTAT 59.614 55.000 0.00 0.00 0.00 2.97
247 248 1.807886 GTCGGCTTCTTCGGAGCTA 59.192 57.895 0.00 0.00 0.00 3.32
248 249 2.574399 GTCGGCTTCTTCGGAGCT 59.426 61.111 0.00 0.00 0.00 4.09
249 250 2.881352 CGTCGGCTTCTTCGGAGC 60.881 66.667 0.00 0.00 0.00 4.70
250 251 2.202623 CCGTCGGCTTCTTCGGAG 60.203 66.667 0.00 0.00 44.86 4.63
251 252 4.430765 GCCGTCGGCTTCTTCGGA 62.431 66.667 28.98 0.00 46.69 4.55
271 272 2.637025 CCAAAACAGTGCCGACGG 59.363 61.111 10.29 10.29 0.00 4.79
272 273 2.051345 GCCAAAACAGTGCCGACG 60.051 61.111 0.00 0.00 0.00 5.12
273 274 2.335011 GGCCAAAACAGTGCCGAC 59.665 61.111 0.00 0.00 35.08 4.79
276 277 2.335011 GACGGCCAAAACAGTGCC 59.665 61.111 2.24 0.00 41.85 5.01
277 278 2.051345 CGACGGCCAAAACAGTGC 60.051 61.111 2.24 0.00 0.00 4.40
278 279 2.637025 CCGACGGCCAAAACAGTG 59.363 61.111 2.24 0.00 0.00 3.66
279 280 2.593436 CCCGACGGCCAAAACAGT 60.593 61.111 8.86 0.00 0.00 3.55
280 281 2.734948 TACCCCGACGGCCAAAACAG 62.735 60.000 8.86 0.00 33.26 3.16
281 282 2.734948 CTACCCCGACGGCCAAAACA 62.735 60.000 8.86 0.00 33.26 2.83
282 283 2.032376 TACCCCGACGGCCAAAAC 59.968 61.111 8.86 0.00 33.26 2.43
283 284 2.348243 CTACCCCGACGGCCAAAA 59.652 61.111 8.86 0.00 33.26 2.44
284 285 4.397832 GCTACCCCGACGGCCAAA 62.398 66.667 8.86 0.00 33.26 3.28
296 297 4.832608 CCGGAACAGGGCGCTACC 62.833 72.222 7.64 0.00 37.93 3.18
297 298 2.624437 CTACCGGAACAGGGCGCTAC 62.624 65.000 9.46 0.00 35.02 3.58
298 299 2.362760 TACCGGAACAGGGCGCTA 60.363 61.111 9.46 0.00 35.02 4.26
299 300 3.771160 CTACCGGAACAGGGCGCT 61.771 66.667 9.46 0.00 35.02 5.92
300 301 4.078516 ACTACCGGAACAGGGCGC 62.079 66.667 9.46 0.00 35.02 6.53
301 302 2.125673 CACTACCGGAACAGGGCG 60.126 66.667 9.46 0.00 35.02 6.13
302 303 0.672711 GTTCACTACCGGAACAGGGC 60.673 60.000 9.46 0.00 43.16 5.19
303 304 0.974383 AGTTCACTACCGGAACAGGG 59.026 55.000 9.46 2.97 45.45 4.45
304 305 2.824341 ACTAGTTCACTACCGGAACAGG 59.176 50.000 9.46 1.17 45.45 4.00
305 306 3.757493 AGACTAGTTCACTACCGGAACAG 59.243 47.826 9.46 4.49 45.45 3.16
306 307 3.759581 AGACTAGTTCACTACCGGAACA 58.240 45.455 9.46 0.00 45.45 3.18
307 308 4.217118 TCAAGACTAGTTCACTACCGGAAC 59.783 45.833 9.46 0.53 43.82 3.62
308 309 4.401022 TCAAGACTAGTTCACTACCGGAA 58.599 43.478 9.46 0.00 0.00 4.30
309 310 4.008330 CTCAAGACTAGTTCACTACCGGA 58.992 47.826 9.46 0.00 0.00 5.14
310 311 4.008330 TCTCAAGACTAGTTCACTACCGG 58.992 47.826 0.00 0.00 0.00 5.28
311 312 4.972201 GTCTCAAGACTAGTTCACTACCG 58.028 47.826 0.00 0.00 41.65 4.02
580 581 4.701286 GGATGGTACTCCCTCCGT 57.299 61.111 0.00 0.00 38.42 4.69
2494 2515 8.650143 ACAAACTCCCTGATTATTACATTTGT 57.350 30.769 0.00 0.00 33.08 2.83
2715 2772 8.184192 AGATGTGAAATAGCAAATCCGTTTTAG 58.816 33.333 0.00 0.00 33.79 1.85
3418 3493 4.903010 ACAACAACGACGCGGCCT 62.903 61.111 12.47 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.