Multiple sequence alignment - TraesCS5D01G217500

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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 TraesCS5D01G217500 chr5D 100.000 4523 0 0 330 4852 326451241 326455763 0.000000e+00 8353.0
1 TraesCS5D01G217500 chr5D 100.000 52 0 0 1 52 326450912 326450963 4.000000e-16 97.1
2 TraesCS5D01G217500 chr5B 95.006 3344 103 30 737 4039 378992829 378996149 0.000000e+00 5192.0
3 TraesCS5D01G217500 chr5B 89.310 580 51 8 4279 4852 378996314 378996888 0.000000e+00 717.0
4 TraesCS5D01G217500 chr5B 95.930 172 7 0 4057 4228 378996133 378996304 3.700000e-71 279.0
5 TraesCS5D01G217500 chr5A 95.509 3162 81 20 729 3870 429990423 429987303 0.000000e+00 4996.0
6 TraesCS5D01G217500 chr5A 89.157 581 48 12 4233 4806 429987119 429986547 0.000000e+00 710.0
7 TraesCS5D01G217500 chr5A 84.136 353 28 8 388 737 429992350 429992023 2.820000e-82 316.0
8 TraesCS5D01G217500 chr5A 83.203 256 37 5 391 641 13350476 13350222 3.780000e-56 230.0
9 TraesCS5D01G217500 chr5A 93.103 145 10 0 4057 4201 429987264 429987120 3.800000e-51 213.0
10 TraesCS5D01G217500 chr5A 94.828 58 3 0 3985 4042 429987302 429987245 1.860000e-14 91.6
11 TraesCS5D01G217500 chr6D 87.630 865 62 24 2163 3021 411181708 411182533 0.000000e+00 963.0
12 TraesCS5D01G217500 chr6D 85.971 556 57 11 3028 3565 411182579 411183131 4.210000e-160 575.0
13 TraesCS5D01G217500 chr6D 86.408 206 18 4 3566 3762 411183157 411183361 2.940000e-52 217.0
14 TraesCS5D01G217500 chr6D 86.705 173 17 6 1372 1544 411141272 411141438 2.310000e-43 187.0
15 TraesCS5D01G217500 chr6D 91.837 49 4 0 741 789 411140002 411140050 8.710000e-08 69.4
16 TraesCS5D01G217500 chr6B 86.597 858 78 23 2170 3021 617971550 617972376 0.000000e+00 913.0
17 TraesCS5D01G217500 chr6B 83.598 567 68 12 3017 3565 617972411 617972970 4.330000e-140 508.0
18 TraesCS5D01G217500 chr6B 85.159 283 31 7 844 1116 617838430 617838711 3.700000e-71 279.0
19 TraesCS5D01G217500 chr6A 87.281 456 39 9 3017 3456 555924823 555925275 2.020000e-138 503.0
20 TraesCS5D01G217500 chr6A 88.450 329 32 6 2163 2489 555792294 555791970 4.550000e-105 392.0
21 TraesCS5D01G217500 chr6A 89.869 306 22 4 2645 2950 555790750 555790454 7.620000e-103 385.0
22 TraesCS5D01G217500 chr6A 84.951 206 21 4 3566 3762 555927711 555927915 2.960000e-47 200.0
23 TraesCS5D01G217500 chr6A 91.339 127 11 0 996 1122 555813932 555813806 1.800000e-39 174.0
24 TraesCS5D01G217500 chr6A 86.503 163 14 3 2490 2648 555791010 555790852 6.460000e-39 172.0
25 TraesCS5D01G217500 chr6A 90.909 55 5 0 741 795 555830723 555830669 1.870000e-09 75.0
26 TraesCS5D01G217500 chr2D 83.333 252 37 4 394 641 541301300 541301550 1.360000e-55 228.0
27 TraesCS5D01G217500 chr7D 82.812 256 41 2 393 645 228716315 228716060 4.890000e-55 226.0
28 TraesCS5D01G217500 chr7D 83.200 250 37 4 392 637 102552510 102552262 1.760000e-54 224.0
29 TraesCS5D01G217500 chr7D 82.937 252 38 5 393 641 508309029 508309278 6.320000e-54 222.0
30 TraesCS5D01G217500 chr7D 81.648 267 40 9 380 641 274697431 274697693 3.800000e-51 213.0
31 TraesCS5D01G217500 chr2B 83.004 253 39 4 392 641 494401711 494401962 4.890000e-55 226.0
32 TraesCS5D01G217500 chr4A 82.731 249 40 3 392 637 323852262 323852510 8.180000e-53 219.0


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 TraesCS5D01G217500 chr5D 326450912 326455763 4851 False 4225.050000 8353 100.000000 1 4852 2 chr5D.!!$F1 4851
1 TraesCS5D01G217500 chr5B 378992829 378996888 4059 False 2062.666667 5192 93.415333 737 4852 3 chr5B.!!$F1 4115
2 TraesCS5D01G217500 chr5A 429986547 429992350 5803 True 1265.320000 4996 91.346600 388 4806 5 chr5A.!!$R2 4418
3 TraesCS5D01G217500 chr6D 411181708 411183361 1653 False 585.000000 963 86.669667 2163 3762 3 chr6D.!!$F2 1599
4 TraesCS5D01G217500 chr6B 617971550 617972970 1420 False 710.500000 913 85.097500 2170 3565 2 chr6B.!!$F2 1395
5 TraesCS5D01G217500 chr6A 555924823 555927915 3092 False 351.500000 503 86.116000 3017 3762 2 chr6A.!!$F1 745
6 TraesCS5D01G217500 chr6A 555790454 555792294 1840 True 316.333333 392 88.274000 2163 2950 3 chr6A.!!$R3 787

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
27 28 0.038526 TCCTTCCGACAAACTCTCGC 60.039 55.000 0.00 0.0 0.00 5.03 F
36 37 0.179215 CAAACTCTCGCGTGCCAATC 60.179 55.000 5.77 0.0 0.00 2.67 F
49 50 0.316841 GCCAATCCAGCAAACCGAAA 59.683 50.000 0.00 0.0 0.00 3.46 F
51 52 1.339610 CCAATCCAGCAAACCGAAACA 59.660 47.619 0.00 0.0 0.00 2.83 F
2073 3721 0.496841 AACTACAGGTTCCTCCCCCT 59.503 55.000 0.00 0.0 36.75 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 3322 0.107800 ATCTCTGCTGCAACTGCGAT 60.108 50.000 3.02 0.0 45.83 4.58 R
1977 3625 9.443323 TCGTCAATAGATAAAAGGAACAAATCA 57.557 29.630 0.00 0.0 0.00 2.57 R
2073 3721 5.505985 GCAACAGTTTTGTGTATCGGGTAAA 60.506 40.000 0.00 0.0 37.67 2.01 R
2114 3764 7.931407 GCCTTCCAAAATTAGAAGAAAGGAAAA 59.069 33.333 12.17 0.0 41.69 2.29 R
4065 9183 0.673985 ACAGACGACAACAGCTAGCA 59.326 50.000 18.83 0.0 0.00 3.49 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
23 24 3.228499 GGGTCCTTCCGACAAACTC 57.772 57.895 0.00 0.00 43.95 3.01
24 25 0.685660 GGGTCCTTCCGACAAACTCT 59.314 55.000 0.00 0.00 43.95 3.24
25 26 1.337917 GGGTCCTTCCGACAAACTCTC 60.338 57.143 0.00 0.00 43.95 3.20
26 27 1.669211 GGTCCTTCCGACAAACTCTCG 60.669 57.143 0.00 0.00 43.95 4.04
27 28 0.038526 TCCTTCCGACAAACTCTCGC 60.039 55.000 0.00 0.00 0.00 5.03
28 29 1.344942 CCTTCCGACAAACTCTCGCG 61.345 60.000 0.00 0.00 0.00 5.87
29 30 0.663568 CTTCCGACAAACTCTCGCGT 60.664 55.000 5.77 0.00 0.00 6.01
30 31 0.937699 TTCCGACAAACTCTCGCGTG 60.938 55.000 5.77 3.13 0.00 5.34
31 32 2.465920 CGACAAACTCTCGCGTGC 59.534 61.111 5.77 0.00 0.00 5.34
32 33 2.853914 GACAAACTCTCGCGTGCC 59.146 61.111 5.77 0.00 0.00 5.01
33 34 1.954146 GACAAACTCTCGCGTGCCA 60.954 57.895 5.77 0.00 0.00 4.92
34 35 1.495584 GACAAACTCTCGCGTGCCAA 61.496 55.000 5.77 0.00 0.00 4.52
35 36 0.884704 ACAAACTCTCGCGTGCCAAT 60.885 50.000 5.77 0.00 0.00 3.16
36 37 0.179215 CAAACTCTCGCGTGCCAATC 60.179 55.000 5.77 0.00 0.00 2.67
37 38 1.298859 AAACTCTCGCGTGCCAATCC 61.299 55.000 5.77 0.00 0.00 3.01
38 39 2.125552 CTCTCGCGTGCCAATCCA 60.126 61.111 5.77 0.00 0.00 3.41
39 40 2.125552 TCTCGCGTGCCAATCCAG 60.126 61.111 5.77 0.00 0.00 3.86
40 41 3.869272 CTCGCGTGCCAATCCAGC 61.869 66.667 5.77 0.00 0.00 4.85
41 42 4.695993 TCGCGTGCCAATCCAGCA 62.696 61.111 5.77 0.00 38.08 4.41
42 43 3.736100 CGCGTGCCAATCCAGCAA 61.736 61.111 0.00 0.00 43.02 3.91
43 44 2.650196 GCGTGCCAATCCAGCAAA 59.350 55.556 0.00 0.00 43.02 3.68
44 45 1.734117 GCGTGCCAATCCAGCAAAC 60.734 57.895 0.00 0.00 43.02 2.93
45 46 1.080569 CGTGCCAATCCAGCAAACC 60.081 57.895 0.00 0.00 43.02 3.27
46 47 1.080569 GTGCCAATCCAGCAAACCG 60.081 57.895 0.00 0.00 43.02 4.44
47 48 1.228398 TGCCAATCCAGCAAACCGA 60.228 52.632 0.00 0.00 37.28 4.69
48 49 0.825425 TGCCAATCCAGCAAACCGAA 60.825 50.000 0.00 0.00 37.28 4.30
49 50 0.316841 GCCAATCCAGCAAACCGAAA 59.683 50.000 0.00 0.00 0.00 3.46
50 51 1.934849 GCCAATCCAGCAAACCGAAAC 60.935 52.381 0.00 0.00 0.00 2.78
51 52 1.339610 CCAATCCAGCAAACCGAAACA 59.660 47.619 0.00 0.00 0.00 2.83
377 378 9.733556 TGTAAAAAGAATCTATTGAAGGTAGCA 57.266 29.630 0.00 0.00 0.00 3.49
383 384 9.466497 AAGAATCTATTGAAGGTAGCATTTTGA 57.534 29.630 0.00 0.00 0.00 2.69
384 385 9.466497 AGAATCTATTGAAGGTAGCATTTTGAA 57.534 29.630 0.00 0.00 0.00 2.69
385 386 9.508567 GAATCTATTGAAGGTAGCATTTTGAAC 57.491 33.333 0.00 0.00 0.00 3.18
386 387 7.994425 TCTATTGAAGGTAGCATTTTGAACA 57.006 32.000 0.00 0.00 0.00 3.18
414 415 4.352893 AGGCCTCCTTTAGTTTGTAGGAAA 59.647 41.667 0.00 0.00 37.61 3.13
448 449 9.503399 GAATTATATAGGGTAGGGTTTTCACAG 57.497 37.037 0.00 0.00 0.00 3.66
527 528 7.054124 GGATAGAAACCAATCCTTCACATGTA 58.946 38.462 0.00 0.00 38.92 2.29
531 532 7.661040 AGAAACCAATCCTTCACATGTAAAAG 58.339 34.615 0.00 5.61 0.00 2.27
532 533 7.505585 AGAAACCAATCCTTCACATGTAAAAGA 59.494 33.333 17.50 2.48 0.00 2.52
533 534 6.824305 ACCAATCCTTCACATGTAAAAGAG 57.176 37.500 17.50 10.20 0.00 2.85
576 577 9.011095 ACTGAATGAAGAAATGCATATCCTATG 57.989 33.333 0.00 0.00 0.00 2.23
596 597 7.558807 TCCTATGCATCAAATGACATCTCTTTT 59.441 33.333 0.19 0.00 32.25 2.27
598 599 5.957798 TGCATCAAATGACATCTCTTTTCC 58.042 37.500 0.00 0.00 0.00 3.13
603 604 7.672983 TCAAATGACATCTCTTTTCCTGTAC 57.327 36.000 0.00 0.00 0.00 2.90
611 612 6.591834 ACATCTCTTTTCCTGTACGAATTGAG 59.408 38.462 0.00 0.00 0.00 3.02
635 638 6.862711 ATGCATGTCATCTCACTTTCTATG 57.137 37.500 0.00 0.00 0.00 2.23
636 639 5.981174 TGCATGTCATCTCACTTTCTATGA 58.019 37.500 0.00 0.00 0.00 2.15
637 640 6.589135 TGCATGTCATCTCACTTTCTATGAT 58.411 36.000 0.00 0.00 31.49 2.45
638 641 7.052248 TGCATGTCATCTCACTTTCTATGATT 58.948 34.615 0.00 0.00 31.49 2.57
639 642 7.555195 TGCATGTCATCTCACTTTCTATGATTT 59.445 33.333 0.00 0.00 31.49 2.17
640 643 8.404000 GCATGTCATCTCACTTTCTATGATTTT 58.596 33.333 0.00 0.00 31.49 1.82
700 704 8.208575 AGATCCTATGGTTTTCTATTCCTACC 57.791 38.462 0.00 0.00 0.00 3.18
786 2397 1.529796 CAGGCCGGCCCAATACTAA 59.470 57.895 41.72 0.00 36.58 2.24
1110 2747 1.934220 TAGAACAGGTGAGCCTCGCG 61.934 60.000 0.00 0.00 44.97 5.87
1142 2779 1.632018 TAGGATTCCAGCAACCGGGG 61.632 60.000 6.32 0.00 0.00 5.73
1289 2926 4.163441 TCTTGTGAAGTTCCAACCATGA 57.837 40.909 0.00 0.00 0.00 3.07
1327 2964 5.391312 ACTGTGAGCTGTTTTCACTTTTT 57.609 34.783 0.00 0.00 44.08 1.94
1493 3130 2.159627 GTGGAAAAGGTATGTGCAGACG 59.840 50.000 0.00 0.00 0.00 4.18
1511 3148 5.949787 GCAGACGTGTGTTGTATAAATAACG 59.050 40.000 14.77 0.00 35.98 3.18
1586 3224 8.100164 TCATTGAATGATGAACACTTAGTACCA 58.900 33.333 3.29 0.00 33.31 3.25
1663 3301 6.631962 AGAGCCTTGTATTAGAGTGTGTTAC 58.368 40.000 0.00 0.00 0.00 2.50
1684 3322 8.311836 TGTTACCAAAATGTTTGTTCAACCTTA 58.688 29.630 0.47 0.00 33.97 2.69
1860 3500 7.288810 TGTTCTTCAGCTTATTGTGGAAATT 57.711 32.000 0.00 0.00 0.00 1.82
2073 3721 0.496841 AACTACAGGTTCCTCCCCCT 59.503 55.000 0.00 0.00 36.75 4.79
2114 3764 6.220201 ACTGTTGCAACTTTTTACTTTGTGT 58.780 32.000 28.61 7.27 0.00 3.72
2123 3777 9.805966 CAACTTTTTACTTTGTGTTTTCCTTTC 57.194 29.630 0.00 0.00 0.00 2.62
2136 3790 8.754080 TGTGTTTTCCTTTCTTCTAATTTTGGA 58.246 29.630 0.00 0.00 0.00 3.53
2160 3814 5.352284 AGGCATCTACTTCATGAAACGTAG 58.648 41.667 20.88 20.88 0.00 3.51
2302 3956 2.036217 TGTGAAAGCAATTGGCCTGAAG 59.964 45.455 3.32 0.00 46.50 3.02
2366 4020 5.477637 CCTCCTACTACCTACCTTTATCTGC 59.522 48.000 0.00 0.00 0.00 4.26
2547 5160 9.832445 TTGCAAGGTAAATGTTGGTTAATAAAA 57.168 25.926 0.00 0.00 0.00 1.52
3026 5787 9.685276 ATTTGATAGTCAATGACATACTTGGAA 57.315 29.630 16.38 0.82 36.11 3.53
3071 5833 7.439157 TGACACTGTTTTCATCTTCTATTGG 57.561 36.000 0.00 0.00 0.00 3.16
3296 6075 5.006649 TGTCTTGTTTCAGTCACTTGAATCG 59.993 40.000 0.00 0.00 36.97 3.34
3533 8615 8.928733 TCGCTAGTACAGTTAAAAATAAGTTGG 58.071 33.333 0.00 0.00 0.00 3.77
3770 8886 2.827642 GGTGCTGGAGCTGATGGC 60.828 66.667 0.00 0.00 42.66 4.40
3852 8968 2.260844 TGGCAACTTGGACTTCTGAG 57.739 50.000 0.00 0.00 37.61 3.35
3853 8969 1.490490 TGGCAACTTGGACTTCTGAGT 59.510 47.619 0.00 0.00 36.57 3.41
3923 9041 0.319900 AGTATGCCCGCATCATCGTC 60.320 55.000 5.24 0.00 37.82 4.20
3930 9048 4.585526 GCATCATCGTCGCGGGGA 62.586 66.667 6.13 4.05 0.00 4.81
3931 9049 2.340078 CATCATCGTCGCGGGGAT 59.660 61.111 6.13 6.63 0.00 3.85
3934 9052 0.895530 ATCATCGTCGCGGGGATAAT 59.104 50.000 6.13 0.00 0.00 1.28
3946 9064 1.271926 GGGGATAATTGTGCGGGCTAT 60.272 52.381 0.00 0.00 0.00 2.97
3968 9086 3.935203 TGCATCTGAACTTTAGTAGCTGC 59.065 43.478 0.00 0.00 0.00 5.25
3995 9113 7.148255 TGCTGGTGTTGTATCATGATAAAAGTC 60.148 37.037 17.12 12.80 0.00 3.01
4067 9185 6.885735 TTTTTGAGTAAAAGCTGAACTTGC 57.114 33.333 0.00 0.00 39.09 4.01
4068 9186 5.835113 TTTGAGTAAAAGCTGAACTTGCT 57.165 34.783 0.00 0.00 43.32 3.91
4069 9187 6.935741 TTTGAGTAAAAGCTGAACTTGCTA 57.064 33.333 0.00 0.00 40.22 3.49
4070 9188 6.545504 TTGAGTAAAAGCTGAACTTGCTAG 57.454 37.500 0.00 0.00 40.22 3.42
4071 9189 4.452455 TGAGTAAAAGCTGAACTTGCTAGC 59.548 41.667 8.10 8.10 40.22 3.42
4125 9243 5.222048 ACAAGAGGTGAAGGCCAAGTTATAA 60.222 40.000 5.01 0.00 0.00 0.98
4134 9252 8.784043 GTGAAGGCCAAGTTATAATACCATTAG 58.216 37.037 5.01 0.00 0.00 1.73
4181 9299 4.732285 ACACTCGCATGAACAGTAAAAG 57.268 40.909 0.00 0.00 0.00 2.27
4265 9383 8.710551 TCAACAAAATTTATAACATGCTGCAAG 58.289 29.630 6.36 4.49 0.00 4.01
4275 9393 3.909430 ACATGCTGCAAGATTTCACTTG 58.091 40.909 12.28 1.45 46.69 3.16
4373 9491 7.066284 ACACTAATACAGATGTCTTTTCATGGC 59.934 37.037 0.00 0.00 0.00 4.40
4380 9498 5.514204 CAGATGTCTTTTCATGGCGAAATTC 59.486 40.000 0.00 0.00 43.12 2.17
4381 9499 3.820689 TGTCTTTTCATGGCGAAATTCG 58.179 40.909 11.47 11.47 43.12 3.34
4383 9501 3.078097 TCTTTTCATGGCGAAATTCGGA 58.922 40.909 17.49 2.78 43.12 4.55
4392 9510 3.119990 TGGCGAAATTCGGAAAGATGTTC 60.120 43.478 17.49 0.00 40.84 3.18
4444 9565 4.618227 GCCTTATGCATTCAAAACGAACCT 60.618 41.667 3.54 0.00 40.77 3.50
4457 9578 4.400529 AACGAACCTTGGAAATTTTGCT 57.599 36.364 2.25 0.00 0.00 3.91
4478 9599 7.202016 TGCTAGATGTTAGAAAACTTGTTGG 57.798 36.000 0.00 0.00 36.51 3.77
4492 9613 8.661352 AAAACTTGTTGGTATTCATCCAAAAG 57.339 30.769 0.00 7.97 44.91 2.27
4496 9617 8.650490 ACTTGTTGGTATTCATCCAAAAGAAAT 58.350 29.630 17.38 0.00 44.91 2.17
4570 9695 4.370049 CATTTGTGAACACTTTGGCATCA 58.630 39.130 6.51 0.00 0.00 3.07
4571 9696 3.435105 TTGTGAACACTTTGGCATCAC 57.565 42.857 9.19 9.19 40.53 3.06
4572 9697 2.653726 TGTGAACACTTTGGCATCACT 58.346 42.857 15.35 0.00 40.70 3.41
4574 9699 4.203226 TGTGAACACTTTGGCATCACTTA 58.797 39.130 15.35 0.00 40.70 2.24
4578 9703 5.414454 TGAACACTTTGGCATCACTTATACC 59.586 40.000 0.00 0.00 0.00 2.73
4621 9746 2.350772 GGCATGTGTAAAGTGTCAGTGC 60.351 50.000 0.00 0.00 0.00 4.40
4634 9759 0.673333 TCAGTGCTACAATGGTGCCG 60.673 55.000 0.00 0.00 29.97 5.69
4682 9807 2.224523 TGAATGGCCATCGAGGATAACC 60.225 50.000 21.08 0.00 41.22 2.85
4684 9809 1.434188 TGGCCATCGAGGATAACCAT 58.566 50.000 0.00 0.00 41.22 3.55
4706 9831 6.037940 CCATTGAGTTCACTATGATGTTCCTG 59.962 42.308 0.00 0.00 0.00 3.86
4750 9875 1.269726 CGCAAACCCAAGAACATTGCT 60.270 47.619 7.14 0.00 43.08 3.91
4769 9894 2.168521 GCTTCCCTAATTTTCAAGGCCC 59.831 50.000 0.00 0.00 0.00 5.80
4770 9895 2.543037 TCCCTAATTTTCAAGGCCCC 57.457 50.000 0.00 0.00 0.00 5.80
4787 9912 0.109319 CCCCGTCGCAGAAAAATTGG 60.109 55.000 0.00 0.00 39.69 3.16
4797 9922 6.142320 GTCGCAGAAAAATTGGAGTGTTAAAG 59.858 38.462 0.00 0.00 39.69 1.85
4804 9929 7.530426 AAAATTGGAGTGTTAAAGATGCTCT 57.470 32.000 0.00 0.00 0.00 4.09
4808 9933 4.187694 GGAGTGTTAAAGATGCTCTGAGG 58.812 47.826 6.83 0.00 0.00 3.86
4826 9952 3.457012 TGAGGGATGATGCTTGATCTTCA 59.543 43.478 0.00 2.09 37.10 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.685660 AGAGTTTGTCGGAAGGACCC 59.314 55.000 0.00 0.00 45.46 4.46
7 8 1.699343 CGAGAGTTTGTCGGAAGGAC 58.301 55.000 0.00 0.00 46.27 3.85
8 9 0.038526 GCGAGAGTTTGTCGGAAGGA 60.039 55.000 0.00 0.00 37.91 3.36
9 10 1.344942 CGCGAGAGTTTGTCGGAAGG 61.345 60.000 0.00 0.00 37.91 3.46
10 11 0.663568 ACGCGAGAGTTTGTCGGAAG 60.664 55.000 15.93 0.00 37.91 3.46
11 12 0.937699 CACGCGAGAGTTTGTCGGAA 60.938 55.000 15.93 0.00 37.91 4.30
12 13 1.371267 CACGCGAGAGTTTGTCGGA 60.371 57.895 15.93 0.00 37.91 4.55
13 14 3.000080 GCACGCGAGAGTTTGTCGG 62.000 63.158 15.93 0.00 37.91 4.79
14 15 2.465920 GCACGCGAGAGTTTGTCG 59.534 61.111 15.93 0.00 40.50 4.35
15 16 1.495584 TTGGCACGCGAGAGTTTGTC 61.496 55.000 15.93 0.15 0.00 3.18
16 17 0.884704 ATTGGCACGCGAGAGTTTGT 60.885 50.000 15.93 0.00 0.00 2.83
17 18 0.179215 GATTGGCACGCGAGAGTTTG 60.179 55.000 15.93 0.00 0.00 2.93
18 19 1.298859 GGATTGGCACGCGAGAGTTT 61.299 55.000 15.93 0.00 0.00 2.66
19 20 1.741770 GGATTGGCACGCGAGAGTT 60.742 57.895 15.93 0.00 0.00 3.01
20 21 2.125512 GGATTGGCACGCGAGAGT 60.126 61.111 15.93 0.00 0.00 3.24
21 22 2.125552 TGGATTGGCACGCGAGAG 60.126 61.111 15.93 2.87 0.00 3.20
22 23 2.125552 CTGGATTGGCACGCGAGA 60.126 61.111 15.93 0.00 0.00 4.04
23 24 3.869272 GCTGGATTGGCACGCGAG 61.869 66.667 15.93 5.97 0.00 5.03
24 25 4.695993 TGCTGGATTGGCACGCGA 62.696 61.111 15.93 0.00 34.56 5.87
25 26 3.266230 TTTGCTGGATTGGCACGCG 62.266 57.895 3.53 3.53 39.55 6.01
26 27 1.734117 GTTTGCTGGATTGGCACGC 60.734 57.895 0.00 0.00 39.55 5.34
27 28 1.080569 GGTTTGCTGGATTGGCACG 60.081 57.895 0.00 0.00 39.55 5.34
28 29 1.080569 CGGTTTGCTGGATTGGCAC 60.081 57.895 0.00 0.00 39.55 5.01
29 30 0.825425 TTCGGTTTGCTGGATTGGCA 60.825 50.000 0.00 0.00 37.97 4.92
30 31 0.316841 TTTCGGTTTGCTGGATTGGC 59.683 50.000 0.00 0.00 0.00 4.52
31 32 1.339610 TGTTTCGGTTTGCTGGATTGG 59.660 47.619 0.00 0.00 0.00 3.16
32 33 2.791383 TGTTTCGGTTTGCTGGATTG 57.209 45.000 0.00 0.00 0.00 2.67
351 352 9.733556 TGCTACCTTCAATAGATTCTTTTTACA 57.266 29.630 0.00 0.00 0.00 2.41
357 358 9.466497 TCAAAATGCTACCTTCAATAGATTCTT 57.534 29.630 0.00 0.00 0.00 2.52
358 359 9.466497 TTCAAAATGCTACCTTCAATAGATTCT 57.534 29.630 0.00 0.00 0.00 2.40
359 360 9.508567 GTTCAAAATGCTACCTTCAATAGATTC 57.491 33.333 0.00 0.00 0.00 2.52
360 361 9.023962 TGTTCAAAATGCTACCTTCAATAGATT 57.976 29.630 0.00 0.00 0.00 2.40
361 362 8.579850 TGTTCAAAATGCTACCTTCAATAGAT 57.420 30.769 0.00 0.00 0.00 1.98
362 363 7.665559 ACTGTTCAAAATGCTACCTTCAATAGA 59.334 33.333 0.00 0.00 0.00 1.98
363 364 7.820648 ACTGTTCAAAATGCTACCTTCAATAG 58.179 34.615 0.00 0.00 0.00 1.73
364 365 7.759489 ACTGTTCAAAATGCTACCTTCAATA 57.241 32.000 0.00 0.00 0.00 1.90
365 366 6.655078 ACTGTTCAAAATGCTACCTTCAAT 57.345 33.333 0.00 0.00 0.00 2.57
366 367 7.575414 TTACTGTTCAAAATGCTACCTTCAA 57.425 32.000 0.00 0.00 0.00 2.69
367 368 7.255451 CCTTTACTGTTCAAAATGCTACCTTCA 60.255 37.037 0.00 0.00 0.00 3.02
368 369 7.084486 CCTTTACTGTTCAAAATGCTACCTTC 58.916 38.462 0.00 0.00 0.00 3.46
369 370 6.516693 GCCTTTACTGTTCAAAATGCTACCTT 60.517 38.462 0.00 0.00 0.00 3.50
370 371 5.048013 GCCTTTACTGTTCAAAATGCTACCT 60.048 40.000 0.00 0.00 0.00 3.08
371 372 5.161358 GCCTTTACTGTTCAAAATGCTACC 58.839 41.667 0.00 0.00 0.00 3.18
372 373 5.048013 AGGCCTTTACTGTTCAAAATGCTAC 60.048 40.000 0.00 0.00 0.00 3.58
373 374 5.076873 AGGCCTTTACTGTTCAAAATGCTA 58.923 37.500 0.00 0.00 0.00 3.49
374 375 3.897505 AGGCCTTTACTGTTCAAAATGCT 59.102 39.130 0.00 0.00 0.00 3.79
375 376 4.237724 GAGGCCTTTACTGTTCAAAATGC 58.762 43.478 6.77 0.00 0.00 3.56
376 377 4.524328 AGGAGGCCTTTACTGTTCAAAATG 59.476 41.667 6.77 0.00 0.00 2.32
377 378 4.740902 AGGAGGCCTTTACTGTTCAAAAT 58.259 39.130 6.77 0.00 0.00 1.82
378 379 4.178956 AGGAGGCCTTTACTGTTCAAAA 57.821 40.909 6.77 0.00 0.00 2.44
379 380 3.876309 AGGAGGCCTTTACTGTTCAAA 57.124 42.857 6.77 0.00 0.00 2.69
380 381 3.876309 AAGGAGGCCTTTACTGTTCAA 57.124 42.857 6.77 0.00 41.69 2.69
454 455 8.113462 TCCTATAAACTAAGGTGCTCCAAATTT 58.887 33.333 7.70 4.87 34.30 1.82
455 456 7.639378 TCCTATAAACTAAGGTGCTCCAAATT 58.361 34.615 7.70 0.00 34.30 1.82
456 457 7.208064 TCCTATAAACTAAGGTGCTCCAAAT 57.792 36.000 7.70 0.00 34.30 2.32
489 490 9.838339 ATTGGTTTCTATCCTACATTGTAAGAG 57.162 33.333 1.90 0.00 0.00 2.85
491 492 9.057089 GGATTGGTTTCTATCCTACATTGTAAG 57.943 37.037 0.00 0.00 40.55 2.34
576 577 6.034591 CAGGAAAAGAGATGTCATTTGATGC 58.965 40.000 0.00 0.00 0.00 3.91
596 597 3.885724 TGCATCTCAATTCGTACAGGA 57.114 42.857 0.00 0.00 0.00 3.86
598 599 4.567959 TGACATGCATCTCAATTCGTACAG 59.432 41.667 1.73 0.00 0.00 2.74
662 665 9.807921 AAACCATAGGATCTTCTAAAACAAAGA 57.192 29.630 0.00 0.00 36.05 2.52
725 729 3.270877 GCTGCTACTGCTAGGCTAAAAA 58.729 45.455 0.00 0.00 40.48 1.94
737 2348 1.449246 GCTCTGTGGGCTGCTACTG 60.449 63.158 0.00 4.10 0.00 2.74
1117 2754 2.284190 GTTGCTGGAATCCTACAGAGC 58.716 52.381 0.00 0.83 36.86 4.09
1118 2755 2.739932 CGGTTGCTGGAATCCTACAGAG 60.740 54.545 0.00 0.00 36.86 3.35
1122 2759 0.463833 CCCGGTTGCTGGAATCCTAC 60.464 60.000 0.00 0.00 29.82 3.18
1142 2779 2.495084 GCTACAGCTAAACCATAGGCC 58.505 52.381 0.00 0.00 38.21 5.19
1249 2886 4.550076 AGATCAAGCAGCAAAGAGTACT 57.450 40.909 0.00 0.00 0.00 2.73
1289 2926 5.686753 CTCACAGTACTCCTAGACACCTAT 58.313 45.833 0.00 0.00 0.00 2.57
1554 3191 5.292834 AGTGTTCATCATTCAATGAGTAGCG 59.707 40.000 6.19 0.00 43.53 4.26
1586 3224 1.072806 TGCAAGTGATCAACAGGAGCT 59.927 47.619 0.00 0.00 31.67 4.09
1663 3301 6.346518 GCGATAAGGTTGAACAAACATTTTGG 60.347 38.462 5.40 0.00 39.68 3.28
1684 3322 0.107800 ATCTCTGCTGCAACTGCGAT 60.108 50.000 3.02 0.00 45.83 4.58
1977 3625 9.443323 TCGTCAATAGATAAAAGGAACAAATCA 57.557 29.630 0.00 0.00 0.00 2.57
2073 3721 5.505985 GCAACAGTTTTGTGTATCGGGTAAA 60.506 40.000 0.00 0.00 37.67 2.01
2114 3764 7.931407 GCCTTCCAAAATTAGAAGAAAGGAAAA 59.069 33.333 12.17 0.00 41.69 2.29
2123 3777 7.872113 AGTAGATGCCTTCCAAAATTAGAAG 57.128 36.000 6.03 6.03 39.38 2.85
2136 3790 4.579869 ACGTTTCATGAAGTAGATGCCTT 58.420 39.130 8.41 0.00 0.00 4.35
2160 3814 6.762661 ACACAAGAATATGCATTTAAATGGGC 59.237 34.615 25.61 15.08 36.90 5.36
2302 3956 6.131544 ACACCACAGAAAGTACAATTGTTC 57.868 37.500 17.78 12.01 0.00 3.18
2366 4020 2.309528 ATGAGCATGCAATTGCCTTG 57.690 45.000 26.94 23.20 43.83 3.61
2781 5503 9.611284 GATCAAAATTATTATCAGCGCATGTTA 57.389 29.630 11.47 1.92 0.00 2.41
3026 5787 9.227777 GTGTCAACAAAATTCTATAAGTACCCT 57.772 33.333 0.00 0.00 0.00 4.34
3296 6075 2.420129 CCTGCACCACTCATAAGGTACC 60.420 54.545 2.73 2.73 36.07 3.34
3492 8574 7.851508 TGTACTAGCGAAAGAATCATTTATGC 58.148 34.615 0.00 0.00 0.00 3.14
3533 8615 7.865706 ACCTGTCATTCTATAACCAATTGAC 57.134 36.000 7.12 0.00 0.00 3.18
3601 8712 3.876309 AAAGTTCAAAGGTAGCCAGGA 57.124 42.857 0.00 0.00 0.00 3.86
3770 8886 3.429141 CCTTGCTGCTCGCCACTG 61.429 66.667 0.00 0.00 38.05 3.66
3923 9041 2.631428 CGCACAATTATCCCCGCG 59.369 61.111 0.00 0.00 36.47 6.46
3927 9045 1.812571 CATAGCCCGCACAATTATCCC 59.187 52.381 0.00 0.00 0.00 3.85
3930 9048 1.979855 TGCATAGCCCGCACAATTAT 58.020 45.000 0.00 0.00 33.55 1.28
3931 9049 1.879380 GATGCATAGCCCGCACAATTA 59.121 47.619 0.00 0.00 43.35 1.40
3934 9052 1.096967 CAGATGCATAGCCCGCACAA 61.097 55.000 0.00 0.00 43.35 3.33
3946 9064 3.935203 GCAGCTACTAAAGTTCAGATGCA 59.065 43.478 14.95 0.00 42.39 3.96
3968 9086 6.682423 TTTATCATGATACAACACCAGCAG 57.318 37.500 15.10 0.00 0.00 4.24
3995 9113 5.352293 TCCAATTCAACTGTTGATCGATCAG 59.648 40.000 25.95 17.91 39.84 2.90
4044 9162 6.630071 AGCAAGTTCAGCTTTTACTCAAAAA 58.370 32.000 0.00 0.00 39.87 1.94
4045 9163 6.207691 AGCAAGTTCAGCTTTTACTCAAAA 57.792 33.333 0.00 0.00 39.87 2.44
4046 9164 5.835113 AGCAAGTTCAGCTTTTACTCAAA 57.165 34.783 0.00 0.00 39.87 2.69
4047 9165 5.049405 GCTAGCAAGTTCAGCTTTTACTCAA 60.049 40.000 10.63 0.00 43.25 3.02
4048 9166 4.452455 GCTAGCAAGTTCAGCTTTTACTCA 59.548 41.667 10.63 0.00 43.25 3.41
4049 9167 4.693095 AGCTAGCAAGTTCAGCTTTTACTC 59.307 41.667 18.83 0.00 42.95 2.59
4050 9168 4.453819 CAGCTAGCAAGTTCAGCTTTTACT 59.546 41.667 18.83 0.00 42.95 2.24
4051 9169 4.214332 ACAGCTAGCAAGTTCAGCTTTTAC 59.786 41.667 18.83 0.00 42.95 2.01
4052 9170 4.389374 ACAGCTAGCAAGTTCAGCTTTTA 58.611 39.130 18.83 0.00 42.95 1.52
4053 9171 3.217626 ACAGCTAGCAAGTTCAGCTTTT 58.782 40.909 18.83 0.00 42.95 2.27
4054 9172 2.856222 ACAGCTAGCAAGTTCAGCTTT 58.144 42.857 18.83 0.00 42.95 3.51
4055 9173 2.551459 CAACAGCTAGCAAGTTCAGCTT 59.449 45.455 18.83 0.00 42.95 3.74
4056 9174 2.149578 CAACAGCTAGCAAGTTCAGCT 58.850 47.619 18.83 0.00 46.36 4.24
4057 9175 1.876156 ACAACAGCTAGCAAGTTCAGC 59.124 47.619 18.83 0.00 35.49 4.26
4058 9176 2.156504 CGACAACAGCTAGCAAGTTCAG 59.843 50.000 18.83 12.08 0.00 3.02
4059 9177 2.135139 CGACAACAGCTAGCAAGTTCA 58.865 47.619 18.83 0.00 0.00 3.18
4060 9178 2.135933 ACGACAACAGCTAGCAAGTTC 58.864 47.619 18.83 9.32 0.00 3.01
4061 9179 2.135933 GACGACAACAGCTAGCAAGTT 58.864 47.619 18.83 17.68 0.00 2.66
4062 9180 1.341531 AGACGACAACAGCTAGCAAGT 59.658 47.619 18.83 12.32 0.00 3.16
4063 9181 1.723542 CAGACGACAACAGCTAGCAAG 59.276 52.381 18.83 11.61 0.00 4.01
4064 9182 1.068588 ACAGACGACAACAGCTAGCAA 59.931 47.619 18.83 0.00 0.00 3.91
4065 9183 0.673985 ACAGACGACAACAGCTAGCA 59.326 50.000 18.83 0.00 0.00 3.49
4066 9184 2.631418 TACAGACGACAACAGCTAGC 57.369 50.000 6.62 6.62 0.00 3.42
4067 9185 3.854240 CACATACAGACGACAACAGCTAG 59.146 47.826 0.00 0.00 0.00 3.42
4068 9186 3.254903 ACACATACAGACGACAACAGCTA 59.745 43.478 0.00 0.00 0.00 3.32
4069 9187 2.035961 ACACATACAGACGACAACAGCT 59.964 45.455 0.00 0.00 0.00 4.24
4070 9188 2.404215 ACACATACAGACGACAACAGC 58.596 47.619 0.00 0.00 0.00 4.40
4071 9189 6.525355 CAAATACACATACAGACGACAACAG 58.475 40.000 0.00 0.00 0.00 3.16
4125 9243 7.461043 TGGGGAGCAGATAATTACTAATGGTAT 59.539 37.037 0.00 0.00 0.00 2.73
4134 9252 3.071602 TGAGCTGGGGAGCAGATAATTAC 59.928 47.826 0.00 0.00 37.25 1.89
4228 9346 9.585099 TTATAAATTTTGTTGATGCTCATCCAC 57.415 29.630 7.34 7.17 37.02 4.02
4230 9348 9.585099 TGTTATAAATTTTGTTGATGCTCATCC 57.415 29.630 7.34 0.00 37.02 3.51
4251 9369 5.909621 AGTGAAATCTTGCAGCATGTTAT 57.090 34.783 8.09 0.00 39.31 1.89
4275 9393 1.017387 GCCTCCACGGATGTCATTTC 58.983 55.000 0.00 0.00 33.16 2.17
4285 9403 4.641645 TTGCACAGGCCTCCACGG 62.642 66.667 0.00 0.00 40.13 4.94
4309 9427 4.895668 TGGGTACTCCAAAATACGTCTT 57.104 40.909 0.00 0.00 43.84 3.01
4343 9461 8.147704 TGAAAAGACATCTGTATTAGTGTGTCA 58.852 33.333 6.15 0.00 41.34 3.58
4351 9469 6.345298 TCGCCATGAAAAGACATCTGTATTA 58.655 36.000 0.00 0.00 0.00 0.98
4352 9470 5.185454 TCGCCATGAAAAGACATCTGTATT 58.815 37.500 0.00 0.00 0.00 1.89
4353 9471 4.769688 TCGCCATGAAAAGACATCTGTAT 58.230 39.130 0.00 0.00 0.00 2.29
4373 9491 7.623268 AAAAAGAACATCTTTCCGAATTTCG 57.377 32.000 11.81 11.81 45.19 3.46
4439 9560 6.691508 ACATCTAGCAAAATTTCCAAGGTTC 58.308 36.000 0.00 0.00 0.00 3.62
4441 9562 6.670695 AACATCTAGCAAAATTTCCAAGGT 57.329 33.333 0.00 0.00 0.00 3.50
4521 9645 4.275662 CGCGCGAACATATATTCCAAAAA 58.724 39.130 28.94 0.00 0.00 1.94
4570 9695 5.749462 AGCATCTGCAAAAGAGGTATAAGT 58.251 37.500 4.79 0.00 45.16 2.24
4571 9696 6.094603 ACAAGCATCTGCAAAAGAGGTATAAG 59.905 38.462 4.79 0.00 45.16 1.73
4572 9697 5.945784 ACAAGCATCTGCAAAAGAGGTATAA 59.054 36.000 4.79 0.00 45.16 0.98
4574 9699 4.338879 ACAAGCATCTGCAAAAGAGGTAT 58.661 39.130 4.79 0.00 45.16 2.73
4578 9703 5.100259 CCATAACAAGCATCTGCAAAAGAG 58.900 41.667 4.79 0.00 45.16 2.85
4621 9746 0.249120 TCTCCACGGCACCATTGTAG 59.751 55.000 0.00 0.00 0.00 2.74
4682 9807 6.037940 CCAGGAACATCATAGTGAACTCAATG 59.962 42.308 0.00 0.00 0.00 2.82
4684 9809 5.491070 CCAGGAACATCATAGTGAACTCAA 58.509 41.667 0.00 0.00 0.00 3.02
4706 9831 1.749258 GCACCCAAAGATCGTCCCC 60.749 63.158 0.00 0.00 0.00 4.81
4750 9875 2.561069 GGGGGCCTTGAAAATTAGGGAA 60.561 50.000 0.84 0.00 31.95 3.97
4769 9894 0.878416 TCCAATTTTTCTGCGACGGG 59.122 50.000 0.00 0.00 0.00 5.28
4770 9895 1.535462 ACTCCAATTTTTCTGCGACGG 59.465 47.619 0.00 0.00 0.00 4.79
4777 9902 7.955918 AGCATCTTTAACACTCCAATTTTTCT 58.044 30.769 0.00 0.00 0.00 2.52
4797 9922 1.348366 AGCATCATCCCTCAGAGCATC 59.652 52.381 0.00 0.00 0.00 3.91
4804 9929 3.457012 TGAAGATCAAGCATCATCCCTCA 59.543 43.478 0.00 0.00 33.29 3.86
4808 9933 6.802608 TGATTTTGAAGATCAAGCATCATCC 58.197 36.000 0.00 0.00 37.70 3.51


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

AutoCloner maintained by Alex Coulton.