Multiple sequence alignment - TraesCS3A01G253300

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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 TraesCS3A01G253300 chr3A 100.000 2669 0 0 1 2669 474680303 474677635 0.000000e+00 4929.0
1 TraesCS3A01G253300 chr3A 83.594 128 14 7 2438 2560 474677767 474677642 2.170000e-21 113.0
2 TraesCS3A01G253300 chr3A 83.594 128 14 7 2537 2662 474677866 474677744 2.170000e-21 113.0
3 TraesCS3A01G253300 chr3D 93.388 2057 82 27 639 2669 355707343 355705315 0.000000e+00 2996.0
4 TraesCS3A01G253300 chr3D 86.239 218 22 6 309 525 355707698 355707488 2.070000e-56 230.0
5 TraesCS3A01G253300 chr3D 91.824 159 8 2 655 813 355709833 355709680 1.610000e-52 217.0
6 TraesCS3A01G253300 chr3D 83.465 127 16 5 2537 2662 355705546 355705424 2.170000e-21 113.0
7 TraesCS3A01G253300 chr3D 84.348 115 14 4 2438 2550 355705447 355705335 2.810000e-20 110.0
8 TraesCS3A01G253300 chr3B 97.784 722 16 0 1001 1722 456675875 456675154 0.000000e+00 1245.0
9 TraesCS3A01G253300 chr3B 90.726 744 43 22 1941 2669 456674982 456674250 0.000000e+00 968.0
10 TraesCS3A01G253300 chr3B 89.560 364 12 3 655 1001 456676267 456675913 3.150000e-119 438.0
11 TraesCS3A01G253300 chr3B 86.486 111 8 7 2455 2560 456674365 456674257 6.040000e-22 115.0
12 TraesCS3A01G253300 chr3B 82.677 127 17 5 2537 2662 456674481 456674359 1.010000e-19 108.0
13 TraesCS3A01G253300 chr2D 86.756 891 83 22 804 1669 60765910 60765030 0.000000e+00 959.0
14 TraesCS3A01G253300 chr2A 90.625 672 54 5 1001 1669 61295976 61295311 0.000000e+00 883.0
15 TraesCS3A01G253300 chr2A 77.619 210 24 10 796 983 61296246 61296038 3.630000e-19 106.0
16 TraesCS3A01G253300 chr2B 84.828 870 115 15 804 1669 95219827 95218971 0.000000e+00 859.0
17 TraesCS3A01G253300 chr1B 84.314 102 16 0 2425 2526 614184013 614183912 1.690000e-17 100.0
18 TraesCS3A01G253300 chr1D 83.495 103 15 2 2425 2526 448283857 448283756 7.870000e-16 95.3
19 TraesCS3A01G253300 chr1D 87.143 70 8 1 2419 2488 332703275 332703343 7.920000e-11 78.7
20 TraesCS3A01G253300 chr1A 83.495 103 15 2 2425 2526 544177349 544177248 7.870000e-16 95.3


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 TraesCS3A01G253300 chr3A 474677635 474680303 2668 True 1718.333333 4929 89.062667 1 2669 3 chr3A.!!$R1 2668
1 TraesCS3A01G253300 chr3D 355705315 355709833 4518 True 733.200000 2996 87.852800 309 2669 5 chr3D.!!$R1 2360
2 TraesCS3A01G253300 chr3B 456674250 456676267 2017 True 574.800000 1245 89.446600 655 2669 5 chr3B.!!$R1 2014
3 TraesCS3A01G253300 chr2D 60765030 60765910 880 True 959.000000 959 86.756000 804 1669 1 chr2D.!!$R1 865
4 TraesCS3A01G253300 chr2A 61295311 61296246 935 True 494.500000 883 84.122000 796 1669 2 chr2A.!!$R1 873
5 TraesCS3A01G253300 chr2B 95218971 95219827 856 True 859.000000 859 84.828000 804 1669 1 chr2B.!!$R1 865

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
167 168 0.030504 CAAAATGTGCCTGCGTGTGA 59.969 50.0 0.00 0.00 0.0 3.58 F
637 2550 0.108329 AGAAAGGTGTATGTCCGCGG 60.108 55.0 22.12 22.12 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 3411 2.027625 GTTGGTCGCCGAGGTGAAG 61.028 63.158 6.99 0.0 36.33 3.02 R
2528 4578 1.101635 CAGACCGGGAGCTACATCGA 61.102 60.000 6.32 0.0 0.00 3.59 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
41 42 7.269435 GCTTTATAATGAAGCACACAAACTG 57.731 36.000 7.92 0.00 46.67 3.16
42 43 6.863126 GCTTTATAATGAAGCACACAAACTGT 59.137 34.615 7.92 0.00 46.67 3.55
55 56 5.691508 CACAAACTGTGCTTCTTGAAAAG 57.308 39.130 0.00 0.00 43.06 2.27
56 57 5.163513 CACAAACTGTGCTTCTTGAAAAGT 58.836 37.500 0.00 0.00 42.59 2.66
57 58 5.061311 CACAAACTGTGCTTCTTGAAAAGTG 59.939 40.000 0.00 0.00 42.59 3.16
58 59 5.048083 ACAAACTGTGCTTCTTGAAAAGTGA 60.048 36.000 0.00 0.00 46.34 3.41
59 60 5.643379 AACTGTGCTTCTTGAAAAGTGAA 57.357 34.783 0.00 0.00 46.34 3.18
60 61 5.643379 ACTGTGCTTCTTGAAAAGTGAAA 57.357 34.783 0.00 0.00 46.34 2.69
64 65 7.094377 ACTGTGCTTCTTGAAAAGTGAAAAGTA 60.094 33.333 0.00 0.00 46.34 2.24
65 66 7.771183 TGTGCTTCTTGAAAAGTGAAAAGTAT 58.229 30.769 0.00 0.00 46.34 2.12
66 67 8.250332 TGTGCTTCTTGAAAAGTGAAAAGTATT 58.750 29.630 0.00 0.00 46.34 1.89
67 68 8.746751 GTGCTTCTTGAAAAGTGAAAAGTATTC 58.253 33.333 0.00 0.00 46.34 1.75
68 69 8.465999 TGCTTCTTGAAAAGTGAAAAGTATTCA 58.534 29.630 0.00 0.00 46.34 2.57
69 70 8.746751 GCTTCTTGAAAAGTGAAAAGTATTCAC 58.253 33.333 12.21 12.21 46.34 3.18
82 83 9.444600 TGAAAAGTATTCACAAACTATACTCCC 57.555 33.333 0.00 0.00 34.81 4.30
83 84 9.444600 GAAAAGTATTCACAAACTATACTCCCA 57.555 33.333 0.00 0.00 34.81 4.37
84 85 9.802039 AAAAGTATTCACAAACTATACTCCCAA 57.198 29.630 0.00 0.00 34.81 4.12
85 86 8.788325 AAGTATTCACAAACTATACTCCCAAC 57.212 34.615 0.00 0.00 34.81 3.77
86 87 7.913789 AGTATTCACAAACTATACTCCCAACA 58.086 34.615 0.00 0.00 31.23 3.33
88 89 7.687941 ATTCACAAACTATACTCCCAACAAG 57.312 36.000 0.00 0.00 0.00 3.16
89 90 6.182507 TCACAAACTATACTCCCAACAAGT 57.817 37.500 0.00 0.00 0.00 3.16
90 91 5.995282 TCACAAACTATACTCCCAACAAGTG 59.005 40.000 0.00 0.00 0.00 3.16
91 92 5.995282 CACAAACTATACTCCCAACAAGTGA 59.005 40.000 0.00 0.00 0.00 3.41
92 93 6.485313 CACAAACTATACTCCCAACAAGTGAA 59.515 38.462 0.00 0.00 0.00 3.18
94 95 8.380099 ACAAACTATACTCCCAACAAGTGAATA 58.620 33.333 0.00 0.00 0.00 1.75
96 97 6.583562 ACTATACTCCCAACAAGTGAATAGC 58.416 40.000 0.00 0.00 0.00 2.97
97 98 3.788227 ACTCCCAACAAGTGAATAGCA 57.212 42.857 0.00 0.00 0.00 3.49
109 110 4.228912 GTGAATAGCACAGTTTTGCACT 57.771 40.909 0.00 0.00 46.91 4.40
116 117 2.569259 CAGTTTTGCACTGCGTGTG 58.431 52.632 9.76 7.72 46.70 3.82
117 118 0.098552 CAGTTTTGCACTGCGTGTGA 59.901 50.000 12.91 0.00 46.70 3.58
119 120 2.983758 CAGTTTTGCACTGCGTGTGAAA 60.984 45.455 12.91 6.43 46.70 2.69
155 156 8.621532 TCTAATAGAAGTGAAGTGCAAAATGT 57.378 30.769 0.00 0.00 0.00 2.71
156 157 8.506437 TCTAATAGAAGTGAAGTGCAAAATGTG 58.494 33.333 0.00 0.00 0.00 3.21
166 167 2.508743 CAAAATGTGCCTGCGTGTG 58.491 52.632 0.00 0.00 0.00 3.82
167 168 0.030504 CAAAATGTGCCTGCGTGTGA 59.969 50.000 0.00 0.00 0.00 3.58
170 171 2.133742 AATGTGCCTGCGTGTGAAGC 62.134 55.000 0.00 0.00 0.00 3.86
171 172 3.279116 GTGCCTGCGTGTGAAGCA 61.279 61.111 0.00 0.00 42.99 3.91
173 174 1.003959 TGCCTGCGTGTGAAGCATA 60.004 52.632 0.00 0.00 44.26 3.14
174 175 1.020861 TGCCTGCGTGTGAAGCATAG 61.021 55.000 0.00 0.00 44.26 2.23
175 176 1.021390 GCCTGCGTGTGAAGCATAGT 61.021 55.000 0.00 0.00 44.26 2.12
176 177 1.442769 CCTGCGTGTGAAGCATAGTT 58.557 50.000 0.00 0.00 44.26 2.24
177 178 1.129251 CCTGCGTGTGAAGCATAGTTG 59.871 52.381 0.00 0.00 44.26 3.16
178 179 1.800586 CTGCGTGTGAAGCATAGTTGT 59.199 47.619 0.00 0.00 44.26 3.32
179 180 1.530720 TGCGTGTGAAGCATAGTTGTG 59.469 47.619 0.00 0.00 40.01 3.33
180 181 1.725931 GCGTGTGAAGCATAGTTGTGC 60.726 52.381 0.00 0.00 45.38 4.57
191 192 4.003648 GCATAGTTGTGCTTCAGGTTAGT 58.996 43.478 0.00 0.00 41.82 2.24
192 193 4.455877 GCATAGTTGTGCTTCAGGTTAGTT 59.544 41.667 0.00 0.00 41.82 2.24
193 194 5.048713 GCATAGTTGTGCTTCAGGTTAGTTT 60.049 40.000 0.00 0.00 41.82 2.66
195 196 7.308348 GCATAGTTGTGCTTCAGGTTAGTTTTA 60.308 37.037 0.00 0.00 41.82 1.52
196 197 8.564574 CATAGTTGTGCTTCAGGTTAGTTTTAA 58.435 33.333 0.00 0.00 0.00 1.52
198 199 7.832769 AGTTGTGCTTCAGGTTAGTTTTAAAA 58.167 30.769 0.00 0.00 0.00 1.52
199 200 8.308207 AGTTGTGCTTCAGGTTAGTTTTAAAAA 58.692 29.630 1.31 0.00 0.00 1.94
221 222 5.453567 AAATAGTTGTGCTTCTGGTTTCC 57.546 39.130 0.00 0.00 0.00 3.13
222 223 1.308998 AGTTGTGCTTCTGGTTTCCG 58.691 50.000 0.00 0.00 0.00 4.30
223 224 1.021968 GTTGTGCTTCTGGTTTCCGT 58.978 50.000 0.00 0.00 0.00 4.69
224 225 1.404035 GTTGTGCTTCTGGTTTCCGTT 59.596 47.619 0.00 0.00 0.00 4.44
226 227 2.096248 TGTGCTTCTGGTTTCCGTTTT 58.904 42.857 0.00 0.00 0.00 2.43
228 229 3.113322 GTGCTTCTGGTTTCCGTTTTTC 58.887 45.455 0.00 0.00 0.00 2.29
229 230 3.020984 TGCTTCTGGTTTCCGTTTTTCT 58.979 40.909 0.00 0.00 0.00 2.52
232 233 4.676986 GCTTCTGGTTTCCGTTTTTCTGTT 60.677 41.667 0.00 0.00 0.00 3.16
234 235 3.379057 TCTGGTTTCCGTTTTTCTGTTCC 59.621 43.478 0.00 0.00 0.00 3.62
235 236 3.090037 TGGTTTCCGTTTTTCTGTTCCA 58.910 40.909 0.00 0.00 0.00 3.53
236 237 3.129638 TGGTTTCCGTTTTTCTGTTCCAG 59.870 43.478 0.00 0.00 0.00 3.86
237 238 3.113322 GTTTCCGTTTTTCTGTTCCAGC 58.887 45.455 0.00 0.00 0.00 4.85
238 239 2.341846 TCCGTTTTTCTGTTCCAGCT 57.658 45.000 0.00 0.00 0.00 4.24
239 240 2.218603 TCCGTTTTTCTGTTCCAGCTC 58.781 47.619 0.00 0.00 0.00 4.09
240 241 2.158813 TCCGTTTTTCTGTTCCAGCTCT 60.159 45.455 0.00 0.00 0.00 4.09
242 243 3.066760 CCGTTTTTCTGTTCCAGCTCTTT 59.933 43.478 0.00 0.00 0.00 2.52
243 244 4.440112 CCGTTTTTCTGTTCCAGCTCTTTT 60.440 41.667 0.00 0.00 0.00 2.27
244 245 5.102313 CGTTTTTCTGTTCCAGCTCTTTTT 58.898 37.500 0.00 0.00 0.00 1.94
245 246 5.004726 CGTTTTTCTGTTCCAGCTCTTTTTG 59.995 40.000 0.00 0.00 0.00 2.44
246 247 4.654091 TTTCTGTTCCAGCTCTTTTTGG 57.346 40.909 0.00 0.00 35.74 3.28
247 248 3.297134 TCTGTTCCAGCTCTTTTTGGT 57.703 42.857 0.00 0.00 35.89 3.67
248 249 3.631250 TCTGTTCCAGCTCTTTTTGGTT 58.369 40.909 0.00 0.00 35.89 3.67
249 250 4.023291 TCTGTTCCAGCTCTTTTTGGTTT 58.977 39.130 0.00 0.00 35.89 3.27
250 251 5.197451 TCTGTTCCAGCTCTTTTTGGTTTA 58.803 37.500 0.00 0.00 35.89 2.01
252 253 5.841810 TGTTCCAGCTCTTTTTGGTTTATG 58.158 37.500 0.00 0.00 35.89 1.90
253 254 5.362430 TGTTCCAGCTCTTTTTGGTTTATGT 59.638 36.000 0.00 0.00 35.89 2.29
254 255 6.127196 TGTTCCAGCTCTTTTTGGTTTATGTT 60.127 34.615 0.00 0.00 35.89 2.71
255 256 6.478512 TCCAGCTCTTTTTGGTTTATGTTT 57.521 33.333 0.00 0.00 35.89 2.83
256 257 6.883744 TCCAGCTCTTTTTGGTTTATGTTTT 58.116 32.000 0.00 0.00 35.89 2.43
257 258 7.334858 TCCAGCTCTTTTTGGTTTATGTTTTT 58.665 30.769 0.00 0.00 35.89 1.94
282 283 7.328277 TCTAAATCATCCAAACCCATTAACG 57.672 36.000 0.00 0.00 0.00 3.18
284 285 4.981806 ATCATCCAAACCCATTAACGTG 57.018 40.909 0.00 0.00 0.00 4.49
285 286 3.085533 TCATCCAAACCCATTAACGTGG 58.914 45.455 0.00 0.00 39.05 4.94
298 299 7.795482 CCATTAACGTGGGATTTAGTTCATA 57.205 36.000 0.00 0.00 35.55 2.15
299 300 7.861630 CCATTAACGTGGGATTTAGTTCATAG 58.138 38.462 0.00 0.00 35.55 2.23
300 301 7.713507 CCATTAACGTGGGATTTAGTTCATAGA 59.286 37.037 0.00 0.00 35.55 1.98
302 303 8.882415 TTAACGTGGGATTTAGTTCATAGATC 57.118 34.615 0.00 0.00 0.00 2.75
303 304 6.732896 ACGTGGGATTTAGTTCATAGATCT 57.267 37.500 0.00 0.00 0.00 2.75
305 306 5.859114 CGTGGGATTTAGTTCATAGATCTCG 59.141 44.000 0.00 0.00 29.69 4.04
306 307 6.294010 CGTGGGATTTAGTTCATAGATCTCGA 60.294 42.308 0.00 0.00 29.69 4.04
308 309 7.543868 GTGGGATTTAGTTCATAGATCTCGATG 59.456 40.741 0.00 0.00 29.69 3.84
309 310 7.233553 TGGGATTTAGTTCATAGATCTCGATGT 59.766 37.037 0.00 0.00 29.69 3.06
310 311 7.543868 GGGATTTAGTTCATAGATCTCGATGTG 59.456 40.741 0.00 0.00 32.00 3.21
311 312 8.300286 GGATTTAGTTCATAGATCTCGATGTGA 58.700 37.037 0.00 0.00 32.00 3.58
312 313 9.340695 GATTTAGTTCATAGATCTCGATGTGAG 57.659 37.037 0.00 0.00 46.72 3.51
467 2288 7.832685 TCATCACCAAAGAAGATGAGAATGAAT 59.167 33.333 0.00 0.00 42.17 2.57
556 2469 3.482783 GGAAGCAGCAGACGTCGC 61.483 66.667 19.92 19.92 0.00 5.19
564 2477 2.179267 CAGACGTCGCAGCAGCTA 59.821 61.111 10.46 0.00 39.10 3.32
567 2480 1.064946 GACGTCGCAGCAGCTAGAT 59.935 57.895 0.00 0.00 39.10 1.98
578 2491 1.857837 GCAGCTAGATTCGAAGAGCAC 59.142 52.381 23.56 15.06 38.43 4.40
583 2496 0.176680 AGATTCGAAGAGCACCGCAT 59.823 50.000 3.35 0.00 38.43 4.73
586 2499 3.257561 CGAAGAGCACCGCATCCG 61.258 66.667 0.00 0.00 0.00 4.18
587 2500 2.184322 GAAGAGCACCGCATCCGA 59.816 61.111 0.00 0.00 36.29 4.55
588 2501 1.227380 GAAGAGCACCGCATCCGAT 60.227 57.895 0.00 0.00 36.29 4.18
589 2502 0.811616 GAAGAGCACCGCATCCGATT 60.812 55.000 0.00 0.00 36.29 3.34
590 2503 1.091771 AAGAGCACCGCATCCGATTG 61.092 55.000 0.00 0.00 36.29 2.67
591 2504 2.514592 AGCACCGCATCCGATTGG 60.515 61.111 0.00 0.00 36.29 3.16
592 2505 4.256090 GCACCGCATCCGATTGGC 62.256 66.667 0.00 0.00 36.29 4.52
593 2506 2.823593 CACCGCATCCGATTGGCA 60.824 61.111 0.00 0.00 36.29 4.92
594 2507 2.188829 CACCGCATCCGATTGGCAT 61.189 57.895 0.00 0.00 36.29 4.40
595 2508 1.893808 ACCGCATCCGATTGGCATC 60.894 57.895 0.00 0.00 36.29 3.91
596 2509 1.598962 CCGCATCCGATTGGCATCT 60.599 57.895 0.00 0.00 36.29 2.90
597 2510 1.168407 CCGCATCCGATTGGCATCTT 61.168 55.000 0.00 0.00 36.29 2.40
598 2511 0.664761 CGCATCCGATTGGCATCTTT 59.335 50.000 0.00 0.00 36.29 2.52
599 2512 1.066002 CGCATCCGATTGGCATCTTTT 59.934 47.619 0.00 0.00 36.29 2.27
600 2513 2.480073 CGCATCCGATTGGCATCTTTTT 60.480 45.455 0.00 0.00 36.29 1.94
635 2548 4.499037 AAAAAGAAAGGTGTATGTCCGC 57.501 40.909 0.00 0.00 0.00 5.54
636 2549 1.722011 AAGAAAGGTGTATGTCCGCG 58.278 50.000 0.00 0.00 0.00 6.46
637 2550 0.108329 AGAAAGGTGTATGTCCGCGG 60.108 55.000 22.12 22.12 0.00 6.46
638 2551 1.078708 AAAGGTGTATGTCCGCGGG 60.079 57.895 27.83 6.80 0.00 6.13
639 2552 3.675619 AAGGTGTATGTCCGCGGGC 62.676 63.158 26.05 26.05 0.00 6.13
689 2602 4.896028 CGCGCCGCACACAAACAA 62.896 61.111 10.75 0.00 0.00 2.83
743 2656 1.710996 CCATACGGGGCCCAATGGTA 61.711 60.000 32.22 22.72 34.12 3.25
769 2682 3.000080 CTCGACAGCGACAAACGGC 62.000 63.158 0.00 0.00 42.51 5.68
884 2829 1.091771 CAGTCATCACCCGTGCATCC 61.092 60.000 0.00 0.00 0.00 3.51
930 2882 2.579207 TATAGTGAACGAGCTGCACC 57.421 50.000 1.02 0.00 33.14 5.01
1500 3516 4.025401 CTCAACGTTGGCACCGGC 62.025 66.667 27.02 0.00 40.13 6.13
1902 3934 1.271379 TGTGTCTCCGTGTACATGACC 59.729 52.381 16.87 8.84 0.00 4.02
1918 3950 1.984424 TGACCATGTTCACCAGGATGA 59.016 47.619 0.00 0.00 39.69 2.92
1931 3963 1.203052 CAGGATGACAAATGGGTGCAC 59.797 52.381 8.80 8.80 39.69 4.57
1990 4028 9.886132 GAGACACTAGGATTCCAACTTTATTAA 57.114 33.333 5.29 0.00 0.00 1.40
2031 4071 0.719015 ATGGAAGGGAGGAGTCAGGA 59.281 55.000 0.00 0.00 0.00 3.86
2036 4076 0.043940 AGGGAGGAGTCAGGAATGCT 59.956 55.000 0.00 0.00 0.00 3.79
2349 4399 1.738700 GCACACAAAAACCACACAGGG 60.739 52.381 0.00 0.00 43.89 4.45
2368 4418 2.930682 GGGTCATCTTTAGAACGTCTGC 59.069 50.000 0.00 0.00 0.00 4.26
2376 4426 2.812358 TAGAACGTCTGCTGCAAGAA 57.188 45.000 3.02 0.00 34.07 2.52
2377 4427 2.175878 AGAACGTCTGCTGCAAGAAT 57.824 45.000 3.02 0.00 34.07 2.40
2378 4428 1.802960 AGAACGTCTGCTGCAAGAATG 59.197 47.619 3.02 0.53 34.07 2.67
2379 4429 1.532868 GAACGTCTGCTGCAAGAATGT 59.467 47.619 3.02 1.18 34.07 2.71
2380 4430 0.870393 ACGTCTGCTGCAAGAATGTG 59.130 50.000 3.02 0.00 34.07 3.21
2381 4431 1.150827 CGTCTGCTGCAAGAATGTGA 58.849 50.000 3.02 0.00 34.07 3.58
2382 4432 1.136141 CGTCTGCTGCAAGAATGTGAC 60.136 52.381 3.02 4.87 34.07 3.67
2384 4434 2.291465 GTCTGCTGCAAGAATGTGACAA 59.709 45.455 3.02 0.00 34.07 3.18
2385 4435 2.551032 TCTGCTGCAAGAATGTGACAAG 59.449 45.455 3.02 0.00 34.07 3.16
2387 4437 2.551032 TGCTGCAAGAATGTGACAAGAG 59.449 45.455 0.00 0.00 34.07 2.85
2388 4438 2.810274 GCTGCAAGAATGTGACAAGAGA 59.190 45.455 0.00 0.00 34.07 3.10
2390 4440 4.437121 GCTGCAAGAATGTGACAAGAGATC 60.437 45.833 0.00 0.00 34.07 2.75
2391 4441 4.903054 TGCAAGAATGTGACAAGAGATCT 58.097 39.130 0.00 0.00 0.00 2.75
2393 4443 5.766670 TGCAAGAATGTGACAAGAGATCTTT 59.233 36.000 0.00 0.00 33.11 2.52
2395 4445 6.622462 GCAAGAATGTGACAAGAGATCTTTCC 60.622 42.308 0.00 0.00 33.11 3.13
2396 4446 5.495640 AGAATGTGACAAGAGATCTTTCCC 58.504 41.667 0.00 0.00 33.11 3.97
2397 4447 3.703001 TGTGACAAGAGATCTTTCCCC 57.297 47.619 0.00 0.00 33.11 4.81
2398 4448 3.251484 TGTGACAAGAGATCTTTCCCCT 58.749 45.455 0.00 0.00 33.11 4.79
2399 4449 4.425772 TGTGACAAGAGATCTTTCCCCTA 58.574 43.478 0.00 0.00 33.11 3.53
2400 4450 4.844085 TGTGACAAGAGATCTTTCCCCTAA 59.156 41.667 0.00 0.00 33.11 2.69
2401 4451 5.046304 TGTGACAAGAGATCTTTCCCCTAAG 60.046 44.000 0.00 0.00 33.11 2.18
2402 4452 5.187967 GTGACAAGAGATCTTTCCCCTAAGA 59.812 44.000 0.00 0.00 38.43 2.10
2403 4453 5.785423 TGACAAGAGATCTTTCCCCTAAGAA 59.215 40.000 0.00 0.00 37.66 2.52
2404 4454 6.070538 TGACAAGAGATCTTTCCCCTAAGAAG 60.071 42.308 0.00 0.00 37.66 2.85
2405 4455 6.026186 ACAAGAGATCTTTCCCCTAAGAAGA 58.974 40.000 0.00 0.00 37.66 2.87
2406 4456 6.502158 ACAAGAGATCTTTCCCCTAAGAAGAA 59.498 38.462 0.00 0.00 37.66 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.643379 TTCACTTTTCAAGAAGCACAGTT 57.357 34.783 0.00 0.00 0.00 3.16
39 40 6.095377 ACTTTTCACTTTTCAAGAAGCACAG 58.905 36.000 0.00 0.00 0.00 3.66
40 41 6.024552 ACTTTTCACTTTTCAAGAAGCACA 57.975 33.333 0.00 0.00 0.00 4.57
41 42 8.634475 AATACTTTTCACTTTTCAAGAAGCAC 57.366 30.769 0.00 0.00 0.00 4.40
42 43 8.465999 TGAATACTTTTCACTTTTCAAGAAGCA 58.534 29.630 0.00 0.00 0.00 3.91
44 45 9.787532 TGTGAATACTTTTCACTTTTCAAGAAG 57.212 29.630 16.72 0.00 46.53 2.85
56 57 9.444600 GGGAGTATAGTTTGTGAATACTTTTCA 57.555 33.333 0.00 0.00 36.74 2.69
57 58 9.444600 TGGGAGTATAGTTTGTGAATACTTTTC 57.555 33.333 0.00 0.00 36.74 2.29
58 59 9.802039 TTGGGAGTATAGTTTGTGAATACTTTT 57.198 29.630 0.00 0.00 36.74 2.27
59 60 9.227777 GTTGGGAGTATAGTTTGTGAATACTTT 57.772 33.333 0.00 0.00 36.74 2.66
60 61 8.380099 TGTTGGGAGTATAGTTTGTGAATACTT 58.620 33.333 0.00 0.00 36.74 2.24
64 65 7.174946 CACTTGTTGGGAGTATAGTTTGTGAAT 59.825 37.037 0.00 0.00 0.00 2.57
65 66 6.485313 CACTTGTTGGGAGTATAGTTTGTGAA 59.515 38.462 0.00 0.00 0.00 3.18
66 67 5.995282 CACTTGTTGGGAGTATAGTTTGTGA 59.005 40.000 0.00 0.00 0.00 3.58
67 68 5.995282 TCACTTGTTGGGAGTATAGTTTGTG 59.005 40.000 0.00 0.00 0.00 3.33
68 69 6.182507 TCACTTGTTGGGAGTATAGTTTGT 57.817 37.500 0.00 0.00 0.00 2.83
69 70 7.687941 ATTCACTTGTTGGGAGTATAGTTTG 57.312 36.000 0.00 0.00 0.00 2.93
70 71 7.553044 GCTATTCACTTGTTGGGAGTATAGTTT 59.447 37.037 0.00 0.00 0.00 2.66
71 72 7.048512 GCTATTCACTTGTTGGGAGTATAGTT 58.951 38.462 0.00 0.00 0.00 2.24
72 73 6.156256 TGCTATTCACTTGTTGGGAGTATAGT 59.844 38.462 0.00 0.00 0.00 2.12
73 74 6.480320 GTGCTATTCACTTGTTGGGAGTATAG 59.520 42.308 0.00 0.00 42.38 1.31
74 75 6.070481 TGTGCTATTCACTTGTTGGGAGTATA 60.070 38.462 0.00 0.00 45.81 1.47
75 76 5.186198 GTGCTATTCACTTGTTGGGAGTAT 58.814 41.667 0.00 0.00 42.38 2.12
76 77 4.041075 TGTGCTATTCACTTGTTGGGAGTA 59.959 41.667 0.00 0.00 45.81 2.59
77 78 3.181445 TGTGCTATTCACTTGTTGGGAGT 60.181 43.478 0.00 0.00 45.81 3.85
78 79 3.411446 TGTGCTATTCACTTGTTGGGAG 58.589 45.455 0.00 0.00 45.81 4.30
79 80 3.181445 ACTGTGCTATTCACTTGTTGGGA 60.181 43.478 0.00 0.00 45.81 4.37
80 81 3.149196 ACTGTGCTATTCACTTGTTGGG 58.851 45.455 0.00 0.00 45.81 4.12
81 82 4.836125 AACTGTGCTATTCACTTGTTGG 57.164 40.909 0.00 0.00 45.81 3.77
82 83 5.051508 GCAAAACTGTGCTATTCACTTGTTG 60.052 40.000 0.00 0.00 45.81 3.33
83 84 5.043248 GCAAAACTGTGCTATTCACTTGTT 58.957 37.500 0.00 0.00 45.81 2.83
84 85 4.097741 TGCAAAACTGTGCTATTCACTTGT 59.902 37.500 0.00 0.00 45.81 3.16
85 86 4.442073 GTGCAAAACTGTGCTATTCACTTG 59.558 41.667 0.00 0.00 45.81 3.16
86 87 4.339247 AGTGCAAAACTGTGCTATTCACTT 59.661 37.500 0.00 0.00 45.81 3.16
88 89 4.228912 AGTGCAAAACTGTGCTATTCAC 57.771 40.909 0.00 0.00 45.17 3.18
129 130 9.066892 ACATTTTGCACTTCACTTCTATTAGAA 57.933 29.630 6.01 6.01 32.50 2.10
130 131 8.506437 CACATTTTGCACTTCACTTCTATTAGA 58.494 33.333 0.00 0.00 0.00 2.10
148 149 0.030504 TCACACGCAGGCACATTTTG 59.969 50.000 0.00 0.00 0.00 2.44
149 150 0.743688 TTCACACGCAGGCACATTTT 59.256 45.000 0.00 0.00 0.00 1.82
150 151 0.311790 CTTCACACGCAGGCACATTT 59.688 50.000 0.00 0.00 0.00 2.32
151 152 1.951510 CTTCACACGCAGGCACATT 59.048 52.632 0.00 0.00 0.00 2.71
152 153 2.620112 GCTTCACACGCAGGCACAT 61.620 57.895 0.00 0.00 0.00 3.21
153 154 3.279116 GCTTCACACGCAGGCACA 61.279 61.111 0.00 0.00 0.00 4.57
155 156 1.003959 TATGCTTCACACGCAGGCA 60.004 52.632 0.00 0.00 41.22 4.75
156 157 1.021390 ACTATGCTTCACACGCAGGC 61.021 55.000 0.00 0.00 41.22 4.85
158 159 1.800586 ACAACTATGCTTCACACGCAG 59.199 47.619 0.00 0.00 41.22 5.18
159 160 1.530720 CACAACTATGCTTCACACGCA 59.469 47.619 0.00 0.00 42.25 5.24
160 161 1.725931 GCACAACTATGCTTCACACGC 60.726 52.381 0.00 0.00 42.62 5.34
170 171 6.560253 AAACTAACCTGAAGCACAACTATG 57.440 37.500 0.00 0.00 0.00 2.23
171 172 8.685838 TTAAAACTAACCTGAAGCACAACTAT 57.314 30.769 0.00 0.00 0.00 2.12
173 174 7.399245 TTTAAAACTAACCTGAAGCACAACT 57.601 32.000 0.00 0.00 0.00 3.16
174 175 8.468720 TTTTTAAAACTAACCTGAAGCACAAC 57.531 30.769 0.00 0.00 0.00 3.32
198 199 5.507315 CGGAAACCAGAAGCACAACTATTTT 60.507 40.000 0.00 0.00 0.00 1.82
199 200 4.023193 CGGAAACCAGAAGCACAACTATTT 60.023 41.667 0.00 0.00 0.00 1.40
200 201 3.502211 CGGAAACCAGAAGCACAACTATT 59.498 43.478 0.00 0.00 0.00 1.73
201 202 3.074412 CGGAAACCAGAAGCACAACTAT 58.926 45.455 0.00 0.00 0.00 2.12
202 203 2.158871 ACGGAAACCAGAAGCACAACTA 60.159 45.455 0.00 0.00 0.00 2.24
204 205 1.021968 ACGGAAACCAGAAGCACAAC 58.978 50.000 0.00 0.00 0.00 3.32
205 206 1.757682 AACGGAAACCAGAAGCACAA 58.242 45.000 0.00 0.00 0.00 3.33
206 207 1.757682 AAACGGAAACCAGAAGCACA 58.242 45.000 0.00 0.00 0.00 4.57
207 208 2.863401 AAAACGGAAACCAGAAGCAC 57.137 45.000 0.00 0.00 0.00 4.40
208 209 3.020984 AGAAAAACGGAAACCAGAAGCA 58.979 40.909 0.00 0.00 0.00 3.91
209 210 3.181490 ACAGAAAAACGGAAACCAGAAGC 60.181 43.478 0.00 0.00 0.00 3.86
211 212 4.142337 GGAACAGAAAAACGGAAACCAGAA 60.142 41.667 0.00 0.00 0.00 3.02
212 213 3.379057 GGAACAGAAAAACGGAAACCAGA 59.621 43.478 0.00 0.00 0.00 3.86
214 215 3.090037 TGGAACAGAAAAACGGAAACCA 58.910 40.909 0.00 0.00 0.00 3.67
215 216 3.786516 TGGAACAGAAAAACGGAAACC 57.213 42.857 0.00 0.00 0.00 3.27
229 230 5.362430 ACATAAACCAAAAAGAGCTGGAACA 59.638 36.000 0.00 0.00 36.49 3.18
232 233 6.478512 AAACATAAACCAAAAAGAGCTGGA 57.521 33.333 0.00 0.00 36.49 3.86
255 256 9.936759 GTTAATGGGTTTGGATGATTTAGAAAA 57.063 29.630 0.00 0.00 0.00 2.29
256 257 8.247562 CGTTAATGGGTTTGGATGATTTAGAAA 58.752 33.333 0.00 0.00 0.00 2.52
257 258 7.394923 ACGTTAATGGGTTTGGATGATTTAGAA 59.605 33.333 0.00 0.00 0.00 2.10
258 259 6.887545 ACGTTAATGGGTTTGGATGATTTAGA 59.112 34.615 0.00 0.00 0.00 2.10
259 260 6.972328 CACGTTAATGGGTTTGGATGATTTAG 59.028 38.462 0.00 0.00 0.00 1.85
260 261 6.127591 CCACGTTAATGGGTTTGGATGATTTA 60.128 38.462 0.00 0.00 35.95 1.40
261 262 5.337169 CCACGTTAATGGGTTTGGATGATTT 60.337 40.000 0.00 0.00 35.95 2.17
262 263 4.159506 CCACGTTAATGGGTTTGGATGATT 59.840 41.667 0.00 0.00 35.95 2.57
263 264 3.699038 CCACGTTAATGGGTTTGGATGAT 59.301 43.478 0.00 0.00 35.95 2.45
264 265 3.085533 CCACGTTAATGGGTTTGGATGA 58.914 45.455 0.00 0.00 35.95 2.92
265 266 3.502191 CCACGTTAATGGGTTTGGATG 57.498 47.619 0.00 0.00 35.95 3.51
275 276 8.657074 TCTATGAACTAAATCCCACGTTAATG 57.343 34.615 0.00 0.00 0.00 1.90
276 277 9.490379 GATCTATGAACTAAATCCCACGTTAAT 57.510 33.333 0.00 0.00 0.00 1.40
277 278 8.701895 AGATCTATGAACTAAATCCCACGTTAA 58.298 33.333 0.00 0.00 0.00 2.01
278 279 8.246430 AGATCTATGAACTAAATCCCACGTTA 57.754 34.615 0.00 0.00 0.00 3.18
280 281 6.515200 CGAGATCTATGAACTAAATCCCACGT 60.515 42.308 0.00 0.00 0.00 4.49
282 283 6.982852 TCGAGATCTATGAACTAAATCCCAC 58.017 40.000 0.00 0.00 0.00 4.61
284 285 7.543868 CACATCGAGATCTATGAACTAAATCCC 59.456 40.741 11.65 0.00 0.00 3.85
285 286 8.300286 TCACATCGAGATCTATGAACTAAATCC 58.700 37.037 11.65 0.00 0.00 3.01
286 287 9.340695 CTCACATCGAGATCTATGAACTAAATC 57.659 37.037 11.65 0.00 45.45 2.17
287 288 9.072375 TCTCACATCGAGATCTATGAACTAAAT 57.928 33.333 11.65 0.00 46.18 1.40
330 1443 5.531634 ACTGTGCGTTCAAATCATGATTTT 58.468 33.333 27.30 12.74 38.84 1.82
331 1444 5.125100 ACTGTGCGTTCAAATCATGATTT 57.875 34.783 24.83 24.83 41.33 2.17
333 1446 4.771590 AACTGTGCGTTCAAATCATGAT 57.228 36.364 1.18 1.18 38.03 2.45
344 1457 8.810652 ACATTTTATCATTTAAACTGTGCGTT 57.189 26.923 0.00 0.00 37.47 4.84
345 1458 8.810652 AACATTTTATCATTTAAACTGTGCGT 57.189 26.923 0.00 0.00 32.90 5.24
395 2118 4.452455 ACATTTGTCACAATCCGAGAGTTC 59.548 41.667 0.00 0.00 0.00 3.01
422 2243 1.511887 CAAGTGGCGCGTTGTATGC 60.512 57.895 8.43 0.00 0.00 3.14
430 2251 2.476051 GTGATGACAAGTGGCGCG 59.524 61.111 0.00 0.00 0.00 6.86
484 2305 9.168451 TGCCATATTTCGAAATCACTAGTTAAA 57.832 29.630 25.89 5.92 0.00 1.52
492 2313 4.900635 ACCTGCCATATTTCGAAATCAC 57.099 40.909 25.89 14.25 0.00 3.06
499 2320 1.408702 CCCCAAACCTGCCATATTTCG 59.591 52.381 0.00 0.00 0.00 3.46
530 2443 0.389426 CTGCTGCTTCCATTTGTGGC 60.389 55.000 0.00 0.00 0.00 5.01
556 2469 2.126467 GCTCTTCGAATCTAGCTGCTG 58.874 52.381 13.43 2.51 32.18 4.41
564 2477 0.176680 ATGCGGTGCTCTTCGAATCT 59.823 50.000 0.00 0.00 0.00 2.40
567 2480 1.447838 GGATGCGGTGCTCTTCGAA 60.448 57.895 0.00 0.00 0.00 3.71
578 2491 1.168407 AAGATGCCAATCGGATGCGG 61.168 55.000 6.82 0.00 37.92 5.69
614 2527 3.058501 CGCGGACATACACCTTTCTTTTT 60.059 43.478 0.00 0.00 0.00 1.94
615 2528 2.482721 CGCGGACATACACCTTTCTTTT 59.517 45.455 0.00 0.00 0.00 2.27
616 2529 2.073816 CGCGGACATACACCTTTCTTT 58.926 47.619 0.00 0.00 0.00 2.52
617 2530 1.674817 CCGCGGACATACACCTTTCTT 60.675 52.381 24.07 0.00 0.00 2.52
618 2531 0.108329 CCGCGGACATACACCTTTCT 60.108 55.000 24.07 0.00 0.00 2.52
619 2532 1.087771 CCCGCGGACATACACCTTTC 61.088 60.000 30.73 0.00 0.00 2.62
620 2533 1.078708 CCCGCGGACATACACCTTT 60.079 57.895 30.73 0.00 0.00 3.11
621 2534 2.582436 CCCGCGGACATACACCTT 59.418 61.111 30.73 0.00 0.00 3.50
622 2535 4.157120 GCCCGCGGACATACACCT 62.157 66.667 30.73 0.00 0.00 4.00
743 2656 1.678101 TGTCGCTGTCGAGATCATGAT 59.322 47.619 8.25 8.25 46.46 2.45
769 2682 0.638746 GGCTATGTTGTTCGTCGTCG 59.361 55.000 0.00 0.00 38.55 5.12
778 2691 1.077716 GCGGAAGGGGCTATGTTGT 60.078 57.895 0.00 0.00 0.00 3.32
884 2829 2.622629 CGATGAACGCAGCATCCG 59.377 61.111 0.00 0.00 39.10 4.18
930 2882 3.058016 GTGATCTTGGTGGTGACATTGTG 60.058 47.826 0.00 0.00 46.14 3.33
997 3010 1.560860 GAGCGAGCCGATGCCATTAC 61.561 60.000 0.00 0.00 38.69 1.89
1395 3411 2.027625 GTTGGTCGCCGAGGTGAAG 61.028 63.158 6.99 0.00 36.33 3.02
1500 3516 4.147322 GCCATGAACACGGCGTCG 62.147 66.667 10.85 8.42 38.82 5.12
1708 3724 2.135664 ACGAATACGGATACTGCAGC 57.864 50.000 15.27 0.00 44.46 5.25
1902 3934 4.381185 CCATTTGTCATCCTGGTGAACATG 60.381 45.833 0.00 0.00 0.00 3.21
1951 3983 7.209340 TCCTAGTGTCTCTTCTGTAATCCTA 57.791 40.000 0.00 0.00 0.00 2.94
1961 3993 5.669164 AGTTGGAATCCTAGTGTCTCTTC 57.331 43.478 0.00 0.00 0.00 2.87
1990 4028 3.119316 TGCTTGTTTCCGTGTTCACAATT 60.119 39.130 3.87 0.00 0.00 2.32
2036 4076 4.016444 GACCTAGACAAATGCCCAATGAA 58.984 43.478 0.00 0.00 0.00 2.57
2176 4224 4.369182 GACCAGGGATTACTAATCGTGTG 58.631 47.826 3.21 1.38 38.82 3.82
2177 4225 3.387050 GGACCAGGGATTACTAATCGTGT 59.613 47.826 3.21 0.00 38.82 4.49
2349 4399 3.061429 GCAGCAGACGTTCTAAAGATGAC 59.939 47.826 0.00 0.00 0.00 3.06
2368 4418 4.936411 AGATCTCTTGTCACATTCTTGCAG 59.064 41.667 0.00 0.00 0.00 4.41
2376 4426 3.848975 AGGGGAAAGATCTCTTGTCACAT 59.151 43.478 0.00 0.00 36.12 3.21
2377 4427 3.251484 AGGGGAAAGATCTCTTGTCACA 58.749 45.455 0.00 0.00 36.12 3.58
2378 4428 3.990959 AGGGGAAAGATCTCTTGTCAC 57.009 47.619 0.00 0.00 36.12 3.67
2379 4429 5.342017 TCTTAGGGGAAAGATCTCTTGTCA 58.658 41.667 0.00 0.00 36.12 3.58
2380 4430 5.941555 TCTTAGGGGAAAGATCTCTTGTC 57.058 43.478 0.00 0.00 36.12 3.18
2381 4431 6.026186 TCTTCTTAGGGGAAAGATCTCTTGT 58.974 40.000 0.00 0.00 35.48 3.16
2382 4432 6.552445 TCTTCTTAGGGGAAAGATCTCTTG 57.448 41.667 0.00 0.00 35.48 3.02
2384 4434 7.459444 TCTTTTCTTCTTAGGGGAAAGATCTCT 59.541 37.037 0.00 0.00 35.48 3.10
2385 4435 7.625469 TCTTTTCTTCTTAGGGGAAAGATCTC 58.375 38.462 0.00 0.00 35.48 2.75
2387 4437 8.681806 CATTCTTTTCTTCTTAGGGGAAAGATC 58.318 37.037 9.16 0.00 35.48 2.75
2388 4438 8.173412 ACATTCTTTTCTTCTTAGGGGAAAGAT 58.827 33.333 9.16 1.40 35.48 2.40
2390 4440 7.767250 ACATTCTTTTCTTCTTAGGGGAAAG 57.233 36.000 0.00 0.00 31.88 2.62
2391 4441 9.074576 GTTACATTCTTTTCTTCTTAGGGGAAA 57.925 33.333 0.00 0.00 0.00 3.13
2393 4443 7.751646 TGTTACATTCTTTTCTTCTTAGGGGA 58.248 34.615 0.00 0.00 0.00 4.81
2395 4445 9.846248 CATTGTTACATTCTTTTCTTCTTAGGG 57.154 33.333 0.00 0.00 0.00 3.53
2400 4450 9.574516 AGGTACATTGTTACATTCTTTTCTTCT 57.425 29.630 0.00 0.00 0.00 2.85
2401 4451 9.612620 CAGGTACATTGTTACATTCTTTTCTTC 57.387 33.333 0.00 0.00 0.00 2.87
2402 4452 8.082242 GCAGGTACATTGTTACATTCTTTTCTT 58.918 33.333 0.00 0.00 0.00 2.52
2403 4453 7.230510 TGCAGGTACATTGTTACATTCTTTTCT 59.769 33.333 0.00 0.00 0.00 2.52
2404 4454 7.326063 GTGCAGGTACATTGTTACATTCTTTTC 59.674 37.037 0.00 0.00 0.00 2.29
2405 4455 7.145323 GTGCAGGTACATTGTTACATTCTTTT 58.855 34.615 0.00 0.00 0.00 2.27
2406 4456 6.567701 CGTGCAGGTACATTGTTACATTCTTT 60.568 38.462 0.00 0.00 0.00 2.52
2528 4578 1.101635 CAGACCGGGAGCTACATCGA 61.102 60.000 6.32 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.