Multiple sequence alignment - TraesCS1D01G385300

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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 TraesCS1D01G385300 chr1D 100.000 3425 0 0 1 3425 458730434 458727010 0.000000e+00 6325.0
1 TraesCS1D01G385300 chr1D 81.818 88 13 3 136 221 418203983 418204069 1.710000e-08 71.3
2 TraesCS1D01G385300 chr1A 88.901 1874 148 40 834 2691 551157606 551155777 0.000000e+00 2254.0
3 TraesCS1D01G385300 chr1A 92.235 528 37 3 2899 3423 551154546 551154020 0.000000e+00 745.0
4 TraesCS1D01G385300 chr1A 99.200 125 0 1 478 601 551157785 551157661 1.240000e-54 224.0
5 TraesCS1D01G385300 chr1A 95.413 109 5 0 2793 2901 551155405 551155297 1.260000e-39 174.0
6 TraesCS1D01G385300 chr1A 89.916 119 12 0 3193 3311 520942838 520942956 1.650000e-33 154.0
7 TraesCS1D01G385300 chr1A 93.000 100 7 0 280 379 551157954 551157855 2.750000e-31 147.0
8 TraesCS1D01G385300 chr1A 93.750 48 3 0 387 434 551157827 551157780 4.740000e-09 73.1
9 TraesCS1D01G385300 chr1B 89.706 1768 128 28 834 2573 630467586 630465845 0.000000e+00 2207.0
10 TraesCS1D01G385300 chr1B 86.983 1452 126 27 996 2431 630263448 630262044 0.000000e+00 1576.0
11 TraesCS1D01G385300 chr1B 82.850 414 24 10 235 601 630468058 630467645 9.160000e-86 327.0
12 TraesCS1D01G385300 chr1B 87.023 262 27 3 2899 3160 630356923 630356669 4.320000e-74 289.0
13 TraesCS1D01G385300 chr1B 84.242 165 19 4 2737 2901 630357788 630357631 1.650000e-33 154.0
14 TraesCS1D01G385300 chr1B 83.486 109 12 4 138 240 350726802 350726910 2.810000e-16 97.1
15 TraesCS1D01G385300 chr1B 100.000 30 0 0 2537 2566 630261954 630261925 4.770000e-04 56.5
16 TraesCS1D01G385300 chr4D 96.983 232 6 1 606 836 29362912 29363143 4.140000e-104 388.0
17 TraesCS1D01G385300 chr4D 96.983 232 6 1 606 836 29363515 29363746 4.140000e-104 388.0
18 TraesCS1D01G385300 chr4D 96.121 232 8 1 606 836 30751247 30751016 8.970000e-101 377.0
19 TraesCS1D01G385300 chr4D 86.765 136 17 1 3176 3311 63228392 63228258 2.130000e-32 150.0
20 TraesCS1D01G385300 chr4D 83.125 160 27 0 3184 3343 491966466 491966307 2.750000e-31 147.0
21 TraesCS1D01G385300 chr2D 96.943 229 6 1 606 833 9160848 9160620 1.930000e-102 383.0
22 TraesCS1D01G385300 chr2D 97.727 220 4 1 615 833 520536763 520536544 8.970000e-101 377.0
23 TraesCS1D01G385300 chr2D 95.652 230 7 2 606 834 520537794 520538021 1.940000e-97 366.0
24 TraesCS1D01G385300 chr5D 96.507 229 7 1 606 833 425665318 425665090 8.970000e-101 377.0
25 TraesCS1D01G385300 chr5D 95.319 235 9 2 600 833 215022688 215022921 4.170000e-99 372.0
26 TraesCS1D01G385300 chr5D 94.894 235 10 2 600 832 37655999 37656233 1.940000e-97 366.0
27 TraesCS1D01G385300 chr5D 91.304 138 12 0 3176 3313 424623520 424623657 4.510000e-44 189.0
28 TraesCS1D01G385300 chr5D 82.407 108 13 6 1997 2101 366780895 366780791 4.710000e-14 89.8
29 TraesCS1D01G385300 chr4B 89.844 256 24 2 2919 3174 16686641 16686388 9.160000e-86 327.0
30 TraesCS1D01G385300 chr6D 78.824 255 43 6 3176 3423 289516785 289516535 9.840000e-36 161.0
31 TraesCS1D01G385300 chr6D 87.591 137 17 0 3176 3312 274342645 274342781 3.540000e-35 159.0
32 TraesCS1D01G385300 chr3D 90.000 120 12 0 3194 3313 46100630 46100749 4.580000e-34 156.0
33 TraesCS1D01G385300 chr7D 81.529 157 28 1 3176 3332 398046827 398046982 9.980000e-26 128.0
34 TraesCS1D01G385300 chr5A 78.182 165 32 4 1991 2153 513959875 513959713 6.050000e-18 102.0
35 TraesCS1D01G385300 chr5A 81.081 111 15 6 1997 2104 468907488 468907381 2.190000e-12 84.2
36 TraesCS1D01G385300 chr2A 84.158 101 9 4 142 236 61487336 61487237 1.310000e-14 91.6
37 TraesCS1D01G385300 chr2A 83.516 91 10 3 155 240 25042502 25042412 2.830000e-11 80.5
38 TraesCS1D01G385300 chr5B 82.407 108 13 6 1997 2101 433945674 433945570 4.710000e-14 89.8
39 TraesCS1D01G385300 chr5B 84.722 72 7 3 145 213 229078781 229078851 6.130000e-08 69.4
40 TraesCS1D01G385300 chr3B 82.692 104 13 2 141 239 377000284 377000181 1.690000e-13 87.9
41 TraesCS1D01G385300 chr7B 87.324 71 7 2 145 213 483862287 483862357 2.830000e-11 80.5
42 TraesCS1D01G385300 chr7B 79.091 110 17 6 1991 2097 572958461 572958355 1.710000e-08 71.3
43 TraesCS1D01G385300 chr7A 79.091 110 17 6 1991 2097 612756423 612756317 1.710000e-08 71.3
44 TraesCS1D01G385300 chr7A 86.364 66 5 3 151 213 65540106 65540170 6.130000e-08 69.4
45 TraesCS1D01G385300 chr2B 84.211 76 8 3 141 213 678379099 678379173 1.710000e-08 71.3


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 TraesCS1D01G385300 chr1D 458727010 458730434 3424 True 6325.00 6325 100.000000 1 3425 1 chr1D.!!$R1 3424
1 TraesCS1D01G385300 chr1A 551154020 551157954 3934 True 602.85 2254 93.749833 280 3423 6 chr1A.!!$R1 3143
2 TraesCS1D01G385300 chr1B 630465845 630468058 2213 True 1267.00 2207 86.278000 235 2573 2 chr1B.!!$R3 2338
3 TraesCS1D01G385300 chr1B 630261925 630263448 1523 True 816.25 1576 93.491500 996 2566 2 chr1B.!!$R1 1570
4 TraesCS1D01G385300 chr1B 630356669 630357788 1119 True 221.50 289 85.632500 2737 3160 2 chr1B.!!$R2 423
5 TraesCS1D01G385300 chr4D 29362912 29363746 834 False 388.00 388 96.983000 606 836 2 chr4D.!!$F1 230

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
392 413 0.535102 AGTGACTTTGCGGAAGGTGG 60.535 55.000 9.62 0.00 39.79 4.61 F
758 810 1.065926 TCTGGAGCAATGCTGGTACTG 60.066 52.381 14.48 4.56 39.88 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2529 1.273606 CGTGTCAACTCCACCAGATCT 59.726 52.381 0.00 0.0 0.00 2.75 R
2510 2696 0.105224 ACAACGGTGTCGGACAATGA 59.895 50.000 13.23 0.0 41.39 2.57 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
126 127 8.519492 AACTTCGAATTATCATGGTTTTTGTG 57.481 30.769 0.00 0.00 0.00 3.33
127 128 7.090173 ACTTCGAATTATCATGGTTTTTGTGG 58.910 34.615 0.00 0.00 0.00 4.17
128 129 5.960113 TCGAATTATCATGGTTTTTGTGGG 58.040 37.500 0.00 0.00 0.00 4.61
129 130 5.712446 TCGAATTATCATGGTTTTTGTGGGA 59.288 36.000 0.00 0.00 0.00 4.37
130 131 6.209589 TCGAATTATCATGGTTTTTGTGGGAA 59.790 34.615 0.00 0.00 0.00 3.97
131 132 7.041107 CGAATTATCATGGTTTTTGTGGGAAT 58.959 34.615 0.00 0.00 0.00 3.01
132 133 7.548780 CGAATTATCATGGTTTTTGTGGGAATT 59.451 33.333 0.00 0.00 0.00 2.17
133 134 8.564509 AATTATCATGGTTTTTGTGGGAATTG 57.435 30.769 0.00 0.00 0.00 2.32
134 135 5.822132 ATCATGGTTTTTGTGGGAATTGA 57.178 34.783 0.00 0.00 0.00 2.57
135 136 5.822132 TCATGGTTTTTGTGGGAATTGAT 57.178 34.783 0.00 0.00 0.00 2.57
136 137 6.185114 TCATGGTTTTTGTGGGAATTGATT 57.815 33.333 0.00 0.00 0.00 2.57
137 138 7.308450 TCATGGTTTTTGTGGGAATTGATTA 57.692 32.000 0.00 0.00 0.00 1.75
138 139 7.739825 TCATGGTTTTTGTGGGAATTGATTAA 58.260 30.769 0.00 0.00 0.00 1.40
139 140 8.213679 TCATGGTTTTTGTGGGAATTGATTAAA 58.786 29.630 0.00 0.00 0.00 1.52
140 141 8.844244 CATGGTTTTTGTGGGAATTGATTAAAA 58.156 29.630 0.00 0.00 0.00 1.52
141 142 8.986929 TGGTTTTTGTGGGAATTGATTAAAAT 57.013 26.923 0.00 0.00 0.00 1.82
157 158 9.847224 TTGATTAAAATACTATTCCCTCTGTCC 57.153 33.333 0.00 0.00 0.00 4.02
158 159 8.437575 TGATTAAAATACTATTCCCTCTGTCCC 58.562 37.037 0.00 0.00 0.00 4.46
159 160 7.758820 TTAAAATACTATTCCCTCTGTCCCA 57.241 36.000 0.00 0.00 0.00 4.37
160 161 6.652205 AAAATACTATTCCCTCTGTCCCAA 57.348 37.500 0.00 0.00 0.00 4.12
161 162 6.652205 AAATACTATTCCCTCTGTCCCAAA 57.348 37.500 0.00 0.00 0.00 3.28
162 163 6.652205 AATACTATTCCCTCTGTCCCAAAA 57.348 37.500 0.00 0.00 0.00 2.44
163 164 6.848562 ATACTATTCCCTCTGTCCCAAAAT 57.151 37.500 0.00 0.00 0.00 1.82
164 165 7.947782 ATACTATTCCCTCTGTCCCAAAATA 57.052 36.000 0.00 0.00 0.00 1.40
165 166 6.848562 ACTATTCCCTCTGTCCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
166 167 6.605119 ACTATTCCCTCTGTCCCAAAATATG 58.395 40.000 0.00 0.00 0.00 1.78
167 168 4.946160 TTCCCTCTGTCCCAAAATATGT 57.054 40.909 0.00 0.00 0.00 2.29
168 169 4.503714 TCCCTCTGTCCCAAAATATGTC 57.496 45.455 0.00 0.00 0.00 3.06
169 170 4.111577 TCCCTCTGTCCCAAAATATGTCT 58.888 43.478 0.00 0.00 0.00 3.41
170 171 4.540099 TCCCTCTGTCCCAAAATATGTCTT 59.460 41.667 0.00 0.00 0.00 3.01
171 172 5.729229 TCCCTCTGTCCCAAAATATGTCTTA 59.271 40.000 0.00 0.00 0.00 2.10
172 173 6.216662 TCCCTCTGTCCCAAAATATGTCTTAA 59.783 38.462 0.00 0.00 0.00 1.85
173 174 6.318900 CCCTCTGTCCCAAAATATGTCTTAAC 59.681 42.308 0.00 0.00 0.00 2.01
174 175 7.112779 CCTCTGTCCCAAAATATGTCTTAACT 58.887 38.462 0.00 0.00 0.00 2.24
175 176 7.611855 CCTCTGTCCCAAAATATGTCTTAACTT 59.388 37.037 0.00 0.00 0.00 2.66
176 177 8.934023 TCTGTCCCAAAATATGTCTTAACTTT 57.066 30.769 0.00 0.00 0.00 2.66
179 180 9.802039 TGTCCCAAAATATGTCTTAACTTTAGT 57.198 29.630 0.00 0.00 0.00 2.24
215 216 8.388484 ACTAAAGTTAGTACAAAGTCGAGAGA 57.612 34.615 1.81 0.00 41.92 3.10
228 229 3.646736 TCGAGAGACTTATGGGACAGA 57.353 47.619 0.00 0.00 37.01 3.41
229 230 3.546724 TCGAGAGACTTATGGGACAGAG 58.453 50.000 0.00 0.00 37.01 3.35
230 231 3.685835 TCGAGAGACTTATGGGACAGAGG 60.686 52.174 0.00 0.00 37.01 3.69
231 232 6.751211 TCGAGAGACTTATGGGACAGAGGG 62.751 54.167 0.00 0.00 37.01 4.30
243 244 6.001449 TGGGACAGAGGGAGTATTATTTTG 57.999 41.667 0.00 0.00 0.00 2.44
257 258 7.480810 AGTATTATTTTGAGATTCCGGTTTGC 58.519 34.615 0.00 0.00 0.00 3.68
274 275 5.599732 GGTTTGCCAATACATGCATGATTA 58.400 37.500 32.75 16.06 37.33 1.75
347 348 2.042162 AGGGAACAGCATGAGATTGGTT 59.958 45.455 0.00 0.00 39.69 3.67
348 349 2.827921 GGGAACAGCATGAGATTGGTTT 59.172 45.455 0.00 0.00 39.69 3.27
392 413 0.535102 AGTGACTTTGCGGAAGGTGG 60.535 55.000 9.62 0.00 39.79 4.61
464 490 3.008157 TGTTAACCTAAGGCCGATGACAA 59.992 43.478 2.48 0.00 0.00 3.18
467 493 1.906574 ACCTAAGGCCGATGACAAGAA 59.093 47.619 0.00 0.00 0.00 2.52
601 653 3.335356 ATGAACCCGAGCTGCCTGG 62.335 63.158 0.00 0.00 0.00 4.45
602 654 4.021925 GAACCCGAGCTGCCTGGT 62.022 66.667 0.00 3.61 0.00 4.00
603 655 3.959991 GAACCCGAGCTGCCTGGTC 62.960 68.421 0.00 0.00 39.62 4.02
758 810 1.065926 TCTGGAGCAATGCTGGTACTG 60.066 52.381 14.48 4.56 39.88 2.74
786 838 5.669430 CGTAAAAATTAGCAATCGTGGTACG 59.331 40.000 0.00 0.00 44.19 3.67
897 957 5.396324 CCGGCTCCCTATATATAACATGCAA 60.396 44.000 0.00 0.00 0.00 4.08
917 977 2.859165 ATGTACACCCAGTTCCACAG 57.141 50.000 0.00 0.00 0.00 3.66
932 1001 2.291465 TCCACAGACACACGTACACTAC 59.709 50.000 0.00 0.00 0.00 2.73
937 1006 1.532868 GACACACGTACACTACCGAGT 59.467 52.381 0.00 0.00 35.80 4.18
980 1055 2.745152 GCCACAGACCAAACACTACACT 60.745 50.000 0.00 0.00 0.00 3.55
987 1062 4.058817 GACCAAACACTACACTCTCCTTG 58.941 47.826 0.00 0.00 0.00 3.61
994 1069 1.241990 TACACTCTCCTTGCGTCGCT 61.242 55.000 19.50 0.00 0.00 4.93
1090 1242 2.813908 GCCACGTGAACCCGCTAG 60.814 66.667 19.30 0.00 0.00 3.42
1096 1248 2.992689 TGAACCCGCTAGTCCGCA 60.993 61.111 0.00 0.00 0.00 5.69
1237 1401 4.671549 GCGACGACGACCACGACA 62.672 66.667 12.29 0.00 42.66 4.35
1240 1404 2.352333 GACGACGACCACGACAACG 61.352 63.158 0.00 0.00 42.66 4.10
1243 1407 1.594269 CGACGACCACGACAACGAAG 61.594 60.000 0.00 0.00 42.66 3.79
1249 1416 2.019951 CACGACAACGAAGACCGGG 61.020 63.158 6.32 0.00 43.93 5.73
1277 1444 4.289379 CGATGACATGCTGCGGCG 62.289 66.667 13.96 0.51 42.25 6.46
1672 1839 1.228657 GCTCGTCAACACCTTCCACC 61.229 60.000 0.00 0.00 0.00 4.61
1766 1933 3.697439 ATGATGAACCGGCCGTGGG 62.697 63.158 26.12 11.78 0.00 4.61
2253 2420 3.136123 CCGGAGGCAGTGGCAATG 61.136 66.667 20.04 11.15 46.14 2.82
2282 2449 4.035102 AAGGGCGTGGAAGGAGGC 62.035 66.667 0.00 0.00 0.00 4.70
2358 2525 4.443266 GACTTCCTGCGAGCGCCT 62.443 66.667 12.70 0.00 41.09 5.52
2359 2526 3.064987 GACTTCCTGCGAGCGCCTA 62.065 63.158 12.70 0.00 41.09 3.93
2360 2527 2.583593 CTTCCTGCGAGCGCCTAC 60.584 66.667 12.70 0.00 41.09 3.18
2362 2529 2.835701 CTTCCTGCGAGCGCCTACAA 62.836 60.000 12.70 0.00 41.09 2.41
2468 2653 5.880887 GTCCTATCCCTTCGAGAACATTTTT 59.119 40.000 0.00 0.00 0.00 1.94
2510 2696 2.665165 TGAACCATGCTCCAACACTTT 58.335 42.857 0.00 0.00 0.00 2.66
2573 2759 0.109532 TTGGCTCGTCACCCATGAAA 59.890 50.000 0.00 0.00 36.31 2.69
2574 2760 0.327924 TGGCTCGTCACCCATGAAAT 59.672 50.000 0.00 0.00 36.31 2.17
2575 2761 0.734889 GGCTCGTCACCCATGAAATG 59.265 55.000 0.00 0.00 46.21 2.32
2576 2762 1.453155 GCTCGTCACCCATGAAATGT 58.547 50.000 0.00 0.00 44.81 2.71
2577 2763 1.131126 GCTCGTCACCCATGAAATGTG 59.869 52.381 0.00 0.00 44.81 3.21
2578 2764 2.698803 CTCGTCACCCATGAAATGTGA 58.301 47.619 0.00 0.00 44.81 3.58
2579 2765 3.273434 CTCGTCACCCATGAAATGTGAT 58.727 45.455 0.00 0.00 44.81 3.06
2581 2767 3.689161 TCGTCACCCATGAAATGTGATTC 59.311 43.478 0.00 0.00 44.81 2.52
2584 2770 4.634004 GTCACCCATGAAATGTGATTCGTA 59.366 41.667 0.00 0.00 44.81 3.43
2585 2771 4.634004 TCACCCATGAAATGTGATTCGTAC 59.366 41.667 0.00 0.00 44.81 3.67
2642 2836 2.156098 GTCACGTCTTGTCTCCTCTCT 58.844 52.381 0.00 0.00 0.00 3.10
2661 2855 6.187727 TCTCTTGGCTCCTTTTCTAGAAAA 57.812 37.500 25.24 25.24 37.90 2.29
2680 2874 0.107456 AGACATTGGGAGCGCCTATG 59.893 55.000 2.29 16.31 34.48 2.23
2685 2879 1.686325 TTGGGAGCGCCTATGAGACC 61.686 60.000 2.29 0.00 0.00 3.85
2686 2880 2.737830 GGAGCGCCTATGAGACCC 59.262 66.667 2.29 0.00 0.00 4.46
2691 2885 1.017387 GCGCCTATGAGACCCTTTTG 58.983 55.000 0.00 0.00 0.00 2.44
2694 3182 2.420022 CGCCTATGAGACCCTTTTGTTG 59.580 50.000 0.00 0.00 0.00 3.33
2697 3185 4.321230 GCCTATGAGACCCTTTTGTTGTTG 60.321 45.833 0.00 0.00 0.00 3.33
2700 3188 4.448537 TGAGACCCTTTTGTTGTTGTTG 57.551 40.909 0.00 0.00 0.00 3.33
2706 3194 3.370672 CCCTTTTGTTGTTGTTGTTGAGC 59.629 43.478 0.00 0.00 0.00 4.26
2714 3202 3.221771 TGTTGTTGTTGAGCAAGCCTAT 58.778 40.909 0.00 0.00 37.83 2.57
2754 3243 1.338769 ACAAATGCGACCTCCTGTACC 60.339 52.381 0.00 0.00 0.00 3.34
2764 3253 1.609841 CCTCCTGTACCCGACCAAAAC 60.610 57.143 0.00 0.00 0.00 2.43
2769 3258 1.154197 GTACCCGACCAAAACTCAGC 58.846 55.000 0.00 0.00 0.00 4.26
2781 3270 2.584418 CTCAGCTCGCGGTGATGG 60.584 66.667 7.86 0.00 45.65 3.51
2782 3271 4.147449 TCAGCTCGCGGTGATGGG 62.147 66.667 6.13 0.00 42.30 4.00
2791 3280 2.971598 CGGTGATGGGCCCTCTTGT 61.972 63.158 25.70 3.37 0.00 3.16
2860 3349 7.715686 CCATCTACTACCTCCTTTCCAAAATAC 59.284 40.741 0.00 0.00 0.00 1.89
2867 3356 4.438744 CCTCCTTTCCAAAATACATGACGC 60.439 45.833 0.00 0.00 0.00 5.19
3084 4365 3.763097 ATTTGCATGTCCATGTACACG 57.237 42.857 0.00 0.00 40.80 4.49
3182 4463 2.687935 GTGGTGGTGTAATATTGCTGGG 59.312 50.000 5.11 0.00 0.00 4.45
3220 4501 1.101635 CGACGTAGGCCTCATCCTGA 61.102 60.000 9.68 0.00 37.01 3.86
3237 4518 0.620410 TGAATGGACCCGAGGATGGT 60.620 55.000 0.00 0.00 39.32 3.55
3238 4519 0.179045 GAATGGACCCGAGGATGGTG 60.179 60.000 0.00 0.00 35.85 4.17
3241 4522 2.732619 GGACCCGAGGATGGTGGTC 61.733 68.421 0.00 0.00 45.25 4.02
3327 4696 3.263259 AGCTTGCAGGGCCTCCTT 61.263 61.111 0.95 0.00 42.67 3.36
3343 4712 1.684049 CTTCTCCGGCACCTCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
3348 4717 0.836400 TCCGGCACCTCCTCTTTCTT 60.836 55.000 0.00 0.00 0.00 2.52
3351 4720 2.092914 CCGGCACCTCCTCTTTCTTAAT 60.093 50.000 0.00 0.00 0.00 1.40
3355 4724 3.282885 CACCTCCTCTTTCTTAATGGGC 58.717 50.000 0.00 0.00 0.00 5.36
3357 4726 3.201045 ACCTCCTCTTTCTTAATGGGCTC 59.799 47.826 0.00 0.00 0.00 4.70
3381 4750 2.765689 TCCTCCTCCTCTTCATCCTC 57.234 55.000 0.00 0.00 0.00 3.71
3385 4754 1.036707 CCTCCTCTTCATCCTCCGAC 58.963 60.000 0.00 0.00 0.00 4.79
3424 4793 4.090057 GCGAAACGAGCAGCCCAC 62.090 66.667 0.00 0.00 34.19 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 8.977505 CACAAAAACCATGATAATTCGAAGTTT 58.022 29.630 2.37 2.77 0.00 2.66
101 102 7.598493 CCACAAAAACCATGATAATTCGAAGTT 59.402 33.333 2.37 0.82 0.00 2.66
102 103 7.090173 CCACAAAAACCATGATAATTCGAAGT 58.910 34.615 3.35 3.02 0.00 3.01
103 104 6.531240 CCCACAAAAACCATGATAATTCGAAG 59.469 38.462 3.35 0.00 0.00 3.79
104 105 6.209589 TCCCACAAAAACCATGATAATTCGAA 59.790 34.615 0.00 0.00 0.00 3.71
105 106 5.712446 TCCCACAAAAACCATGATAATTCGA 59.288 36.000 0.00 0.00 0.00 3.71
106 107 5.960113 TCCCACAAAAACCATGATAATTCG 58.040 37.500 0.00 0.00 0.00 3.34
107 108 8.667463 CAATTCCCACAAAAACCATGATAATTC 58.333 33.333 0.00 0.00 0.00 2.17
108 109 8.381636 TCAATTCCCACAAAAACCATGATAATT 58.618 29.630 0.00 0.00 0.00 1.40
109 110 7.915930 TCAATTCCCACAAAAACCATGATAAT 58.084 30.769 0.00 0.00 0.00 1.28
110 111 7.308450 TCAATTCCCACAAAAACCATGATAA 57.692 32.000 0.00 0.00 0.00 1.75
111 112 6.924913 TCAATTCCCACAAAAACCATGATA 57.075 33.333 0.00 0.00 0.00 2.15
112 113 5.822132 TCAATTCCCACAAAAACCATGAT 57.178 34.783 0.00 0.00 0.00 2.45
113 114 5.822132 ATCAATTCCCACAAAAACCATGA 57.178 34.783 0.00 0.00 0.00 3.07
114 115 7.976135 TTAATCAATTCCCACAAAAACCATG 57.024 32.000 0.00 0.00 0.00 3.66
115 116 8.986929 TTTTAATCAATTCCCACAAAAACCAT 57.013 26.923 0.00 0.00 0.00 3.55
116 117 8.986929 ATTTTAATCAATTCCCACAAAAACCA 57.013 26.923 0.00 0.00 0.00 3.67
131 132 9.847224 GGACAGAGGGAATAGTATTTTAATCAA 57.153 33.333 0.00 0.00 0.00 2.57
132 133 8.437575 GGGACAGAGGGAATAGTATTTTAATCA 58.562 37.037 0.00 0.00 0.00 2.57
133 134 8.437575 TGGGACAGAGGGAATAGTATTTTAATC 58.562 37.037 0.00 0.00 0.00 1.75
134 135 8.344939 TGGGACAGAGGGAATAGTATTTTAAT 57.655 34.615 0.00 0.00 0.00 1.40
135 136 7.758820 TGGGACAGAGGGAATAGTATTTTAA 57.241 36.000 0.00 0.00 0.00 1.52
136 137 7.758820 TTGGGACAGAGGGAATAGTATTTTA 57.241 36.000 0.00 0.00 42.39 1.52
137 138 6.652205 TTGGGACAGAGGGAATAGTATTTT 57.348 37.500 0.00 0.00 42.39 1.82
138 139 6.652205 TTTGGGACAGAGGGAATAGTATTT 57.348 37.500 0.00 0.00 42.39 1.40
139 140 6.652205 TTTTGGGACAGAGGGAATAGTATT 57.348 37.500 0.00 0.00 42.39 1.89
140 141 6.848562 ATTTTGGGACAGAGGGAATAGTAT 57.151 37.500 0.00 0.00 42.39 2.12
141 142 7.349859 ACATATTTTGGGACAGAGGGAATAGTA 59.650 37.037 0.00 0.00 42.39 1.82
142 143 6.160459 ACATATTTTGGGACAGAGGGAATAGT 59.840 38.462 0.00 0.00 42.39 2.12
143 144 6.605119 ACATATTTTGGGACAGAGGGAATAG 58.395 40.000 0.00 0.00 42.39 1.73
144 145 6.389869 AGACATATTTTGGGACAGAGGGAATA 59.610 38.462 0.00 0.00 42.39 1.75
145 146 5.194537 AGACATATTTTGGGACAGAGGGAAT 59.805 40.000 0.00 0.00 42.39 3.01
146 147 4.540099 AGACATATTTTGGGACAGAGGGAA 59.460 41.667 0.00 0.00 42.39 3.97
147 148 4.111577 AGACATATTTTGGGACAGAGGGA 58.888 43.478 0.00 0.00 42.39 4.20
148 149 4.510167 AGACATATTTTGGGACAGAGGG 57.490 45.455 0.00 0.00 42.39 4.30
149 150 7.112779 AGTTAAGACATATTTTGGGACAGAGG 58.887 38.462 0.00 0.00 42.39 3.69
150 151 8.567285 AAGTTAAGACATATTTTGGGACAGAG 57.433 34.615 0.00 0.00 42.39 3.35
151 152 8.934023 AAAGTTAAGACATATTTTGGGACAGA 57.066 30.769 0.00 0.00 42.39 3.41
153 154 9.802039 ACTAAAGTTAAGACATATTTTGGGACA 57.198 29.630 0.00 0.00 0.00 4.02
189 190 9.494271 TCTCTCGACTTTGTACTAACTTTAGTA 57.506 33.333 4.98 4.98 43.36 1.82
190 191 8.288913 GTCTCTCGACTTTGTACTAACTTTAGT 58.711 37.037 6.85 6.85 40.64 2.24
191 192 8.658171 GTCTCTCGACTTTGTACTAACTTTAG 57.342 38.462 0.00 0.00 37.19 1.85
207 208 3.280295 TCTGTCCCATAAGTCTCTCGAC 58.720 50.000 0.00 0.00 40.54 4.20
208 209 3.546724 CTCTGTCCCATAAGTCTCTCGA 58.453 50.000 0.00 0.00 0.00 4.04
209 210 2.621055 CCTCTGTCCCATAAGTCTCTCG 59.379 54.545 0.00 0.00 0.00 4.04
210 211 2.962421 CCCTCTGTCCCATAAGTCTCTC 59.038 54.545 0.00 0.00 0.00 3.20
211 212 2.587777 TCCCTCTGTCCCATAAGTCTCT 59.412 50.000 0.00 0.00 0.00 3.10
212 213 2.962421 CTCCCTCTGTCCCATAAGTCTC 59.038 54.545 0.00 0.00 0.00 3.36
213 214 2.316372 ACTCCCTCTGTCCCATAAGTCT 59.684 50.000 0.00 0.00 0.00 3.24
214 215 2.753247 ACTCCCTCTGTCCCATAAGTC 58.247 52.381 0.00 0.00 0.00 3.01
215 216 2.950990 ACTCCCTCTGTCCCATAAGT 57.049 50.000 0.00 0.00 0.00 2.24
216 217 7.560796 AATAATACTCCCTCTGTCCCATAAG 57.439 40.000 0.00 0.00 0.00 1.73
217 218 7.947782 AAATAATACTCCCTCTGTCCCATAA 57.052 36.000 0.00 0.00 0.00 1.90
218 219 7.570982 TCAAAATAATACTCCCTCTGTCCCATA 59.429 37.037 0.00 0.00 0.00 2.74
219 220 6.389869 TCAAAATAATACTCCCTCTGTCCCAT 59.610 38.462 0.00 0.00 0.00 4.00
220 221 5.729229 TCAAAATAATACTCCCTCTGTCCCA 59.271 40.000 0.00 0.00 0.00 4.37
221 222 6.099845 TCTCAAAATAATACTCCCTCTGTCCC 59.900 42.308 0.00 0.00 0.00 4.46
222 223 7.125792 TCTCAAAATAATACTCCCTCTGTCC 57.874 40.000 0.00 0.00 0.00 4.02
223 224 9.267084 GAATCTCAAAATAATACTCCCTCTGTC 57.733 37.037 0.00 0.00 0.00 3.51
224 225 8.214364 GGAATCTCAAAATAATACTCCCTCTGT 58.786 37.037 0.00 0.00 0.00 3.41
225 226 7.386299 CGGAATCTCAAAATAATACTCCCTCTG 59.614 40.741 0.00 0.00 0.00 3.35
226 227 7.445945 CGGAATCTCAAAATAATACTCCCTCT 58.554 38.462 0.00 0.00 0.00 3.69
227 228 6.651225 CCGGAATCTCAAAATAATACTCCCTC 59.349 42.308 0.00 0.00 0.00 4.30
228 229 6.101296 ACCGGAATCTCAAAATAATACTCCCT 59.899 38.462 9.46 0.00 0.00 4.20
229 230 6.296803 ACCGGAATCTCAAAATAATACTCCC 58.703 40.000 9.46 0.00 0.00 4.30
230 231 7.803279 AACCGGAATCTCAAAATAATACTCC 57.197 36.000 9.46 0.00 0.00 3.85
231 232 7.644157 GCAAACCGGAATCTCAAAATAATACTC 59.356 37.037 9.46 0.00 0.00 2.59
232 233 7.416326 GGCAAACCGGAATCTCAAAATAATACT 60.416 37.037 9.46 0.00 0.00 2.12
233 234 6.695713 GGCAAACCGGAATCTCAAAATAATAC 59.304 38.462 9.46 0.00 0.00 1.89
239 240 2.311463 TGGCAAACCGGAATCTCAAAA 58.689 42.857 9.46 0.00 39.70 2.44
243 244 3.013921 TGTATTGGCAAACCGGAATCTC 58.986 45.455 9.46 0.00 39.70 2.75
257 258 7.879070 AGTAAAGCTAATCATGCATGTATTGG 58.121 34.615 25.43 22.40 0.00 3.16
295 296 6.979817 GCCAATCATGCATGTATTTTGAGTTA 59.020 34.615 25.43 2.66 0.00 2.24
347 348 2.283529 GGAGTGCTCCCGAGTCCAA 61.284 63.158 6.98 0.00 43.94 3.53
348 349 2.680352 GGAGTGCTCCCGAGTCCA 60.680 66.667 6.98 0.00 43.94 4.02
392 413 2.253603 GCGTCCAGAAATGTCAAATGC 58.746 47.619 0.00 0.00 0.00 3.56
601 653 8.915871 ACTTTGCATGTAATCACATAAATGAC 57.084 30.769 0.00 0.00 43.73 3.06
719 771 5.654650 TCCAGACTTTTGCAAAAAGGTCTAA 59.345 36.000 30.74 23.27 44.11 2.10
758 810 5.506832 CCACGATTGCTAATTTTTACGTGTC 59.493 40.000 0.09 0.00 44.93 3.67
897 957 2.708861 TCTGTGGAACTGGGTGTACATT 59.291 45.455 0.00 0.00 38.04 2.71
904 964 0.180406 GTGTGTCTGTGGAACTGGGT 59.820 55.000 0.00 0.00 38.04 4.51
917 977 1.532868 ACTCGGTAGTGTACGTGTGTC 59.467 52.381 0.00 0.00 35.78 3.67
937 1006 1.430632 GCCGACGAGATCAACCGTA 59.569 57.895 0.00 0.00 39.30 4.02
980 1055 1.211969 GTGTAGCGACGCAAGGAGA 59.788 57.895 23.70 0.00 46.39 3.71
994 1069 0.894835 TCTTGGCAGCTCATCGTGTA 59.105 50.000 0.00 0.00 0.00 2.90
1127 1279 2.359570 GACGGTGGTGAAGGTGACGT 62.360 60.000 0.00 0.00 35.64 4.34
1202 1366 1.805945 CGCAGGTGGTACTCGAAGC 60.806 63.158 0.00 0.00 0.00 3.86
1203 1367 1.805945 GCGCAGGTGGTACTCGAAG 60.806 63.158 0.30 0.00 0.00 3.79
1231 1395 2.019951 CCCGGTCTTCGTTGTCGTG 61.020 63.158 0.00 0.00 38.33 4.35
1236 1400 2.125673 ATCGCCCGGTCTTCGTTG 60.126 61.111 0.00 0.00 37.11 4.10
1237 1401 2.125673 CATCGCCCGGTCTTCGTT 60.126 61.111 0.00 0.00 37.11 3.85
1240 1404 2.202892 GGTCATCGCCCGGTCTTC 60.203 66.667 0.00 0.00 0.00 2.87
1249 1416 2.280186 GTCATCGGGGGTCATCGC 60.280 66.667 0.00 0.00 0.00 4.58
1644 1811 1.374252 GTTGACGAGCACCCACGAT 60.374 57.895 0.00 0.00 0.00 3.73
1936 2103 4.083862 GGACTCCGGCAGGTGGAC 62.084 72.222 9.76 3.41 39.05 4.02
2101 2268 4.137872 CCACCACGGGTACGCGAT 62.138 66.667 35.08 18.32 46.04 4.58
2265 2432 4.035102 GCCTCCTTCCACGCCCTT 62.035 66.667 0.00 0.00 0.00 3.95
2358 2525 3.901222 TGTCAACTCCACCAGATCTTGTA 59.099 43.478 0.00 0.00 0.00 2.41
2359 2526 2.705658 TGTCAACTCCACCAGATCTTGT 59.294 45.455 0.00 0.00 0.00 3.16
2360 2527 3.070018 GTGTCAACTCCACCAGATCTTG 58.930 50.000 0.00 0.00 0.00 3.02
2362 2529 1.273606 CGTGTCAACTCCACCAGATCT 59.726 52.381 0.00 0.00 0.00 2.75
2431 2601 6.607004 AGGGATAGGACGGATTATTGTTAG 57.393 41.667 0.00 0.00 0.00 2.34
2468 2653 3.565307 AGCTCCTCATTGGTTCAACAAA 58.435 40.909 0.00 0.00 37.07 2.83
2469 2654 3.228188 AGCTCCTCATTGGTTCAACAA 57.772 42.857 0.00 0.00 37.07 2.83
2510 2696 0.105224 ACAACGGTGTCGGACAATGA 59.895 50.000 13.23 0.00 41.39 2.57
2574 2760 5.725362 TCCACATTATGTGTACGAATCACA 58.275 37.500 21.84 12.33 46.45 3.58
2575 2761 6.844696 ATCCACATTATGTGTACGAATCAC 57.155 37.500 21.84 0.00 46.45 3.06
2576 2762 7.947282 TCTATCCACATTATGTGTACGAATCA 58.053 34.615 21.84 4.25 46.45 2.57
2577 2763 7.062371 GCTCTATCCACATTATGTGTACGAATC 59.938 40.741 21.84 4.96 46.45 2.52
2578 2764 6.868864 GCTCTATCCACATTATGTGTACGAAT 59.131 38.462 21.84 10.66 46.45 3.34
2579 2765 6.183360 TGCTCTATCCACATTATGTGTACGAA 60.183 38.462 21.84 5.86 46.45 3.85
2581 2767 5.528870 TGCTCTATCCACATTATGTGTACG 58.471 41.667 21.84 8.81 46.45 3.67
2584 2770 6.653020 TCTTTGCTCTATCCACATTATGTGT 58.347 36.000 21.84 8.83 46.45 3.72
2661 2855 0.107456 CATAGGCGCTCCCAATGTCT 59.893 55.000 7.64 0.00 35.39 3.41
2680 2874 4.450082 ACAACAACAACAAAAGGGTCTC 57.550 40.909 0.00 0.00 0.00 3.36
2685 2879 3.993081 TGCTCAACAACAACAACAAAAGG 59.007 39.130 0.00 0.00 0.00 3.11
2686 2880 5.588568 TTGCTCAACAACAACAACAAAAG 57.411 34.783 0.00 0.00 31.73 2.27
2691 2885 1.926510 GGCTTGCTCAACAACAACAAC 59.073 47.619 0.00 0.00 33.68 3.32
2694 3182 3.568538 CATAGGCTTGCTCAACAACAAC 58.431 45.455 0.00 0.00 33.68 3.32
2697 3185 1.466360 CGCATAGGCTTGCTCAACAAC 60.466 52.381 15.99 0.00 40.54 3.32
2700 3188 0.375106 GTCGCATAGGCTTGCTCAAC 59.625 55.000 15.99 9.77 40.54 3.18
2706 3194 0.179000 AAGGAGGTCGCATAGGCTTG 59.821 55.000 0.00 0.00 38.10 4.01
2754 3243 2.153913 CGAGCTGAGTTTTGGTCGG 58.846 57.895 0.00 0.00 46.26 4.79
2764 3253 2.584418 CCATCACCGCGAGCTGAG 60.584 66.667 8.23 0.00 0.00 3.35
2785 3274 0.109342 ACCAGAGTGCCCAACAAGAG 59.891 55.000 0.00 0.00 0.00 2.85
2786 3275 0.550914 AACCAGAGTGCCCAACAAGA 59.449 50.000 0.00 0.00 0.00 3.02
2787 3276 0.670162 CAACCAGAGTGCCCAACAAG 59.330 55.000 0.00 0.00 0.00 3.16
2791 3280 0.036732 CTAGCAACCAGAGTGCCCAA 59.963 55.000 0.00 0.00 0.00 4.12
2797 3286 1.417890 ACAAGTGCTAGCAACCAGAGT 59.582 47.619 21.29 9.62 0.00 3.24
2860 3349 2.283298 AGCATCTACCAAAGCGTCATG 58.717 47.619 0.00 0.00 0.00 3.07
2867 3356 4.479619 GAGTTGCAAAGCATCTACCAAAG 58.520 43.478 0.00 0.00 38.49 2.77
2921 4202 9.817809 TGTGCAATTTTAACCATTGTTTACTTA 57.182 25.926 0.00 0.00 35.87 2.24
3037 4318 7.120789 TGTAATGCGATTTCTATGCACTATG 57.879 36.000 0.00 0.00 42.11 2.23
3039 4320 8.825667 TTATGTAATGCGATTTCTATGCACTA 57.174 30.769 0.00 0.00 42.11 2.74
3041 4322 8.955061 AATTATGTAATGCGATTTCTATGCAC 57.045 30.769 0.00 0.00 42.11 4.57
3110 4391 4.968181 TCTAGCGACGATTAATCTTCAACG 59.032 41.667 18.78 13.99 0.00 4.10
3136 4417 6.974048 CCATGAGATGCAATTTATTTTCGACA 59.026 34.615 0.00 0.00 0.00 4.35
3182 4463 1.809684 GAGGCCAACCAGTAGTTCAC 58.190 55.000 5.01 0.00 36.18 3.18
3220 4501 1.635817 CCACCATCCTCGGGTCCATT 61.636 60.000 0.00 0.00 36.19 3.16
3227 4508 2.187946 GCAGACCACCATCCTCGG 59.812 66.667 0.00 0.00 0.00 4.63
3327 4696 1.229209 AAAGAGGAGGTGCCGGAGA 60.229 57.895 5.05 0.00 43.43 3.71
3355 4724 0.341609 AAGAGGAGGAGGAAGGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
3357 4726 0.043334 TGAAGAGGAGGAGGAAGGGG 59.957 60.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.