Multiple sequence alignment - TraesCS7A01G322300

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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 TraesCS7A01G322300 chr7A 100.000 8831 0 0 1 8831 466258392 466249562 0.000000e+00 16308.0
1 TraesCS7A01G322300 chr7A 89.547 287 30 0 5696 5982 605840708 605840422 1.810000e-96 364.0
2 TraesCS7A01G322300 chr7A 93.836 146 8 1 1988 2133 466256341 466256197 1.490000e-52 219.0
3 TraesCS7A01G322300 chr7A 93.836 146 8 1 2052 2196 466256405 466256260 1.490000e-52 219.0
4 TraesCS7A01G322300 chr7A 91.818 110 9 0 5317 5426 406995310 406995419 4.270000e-33 154.0
5 TraesCS7A01G322300 chr7A 93.902 82 4 1 1988 2069 466256277 466256197 1.200000e-23 122.0
6 TraesCS7A01G322300 chr7A 93.902 82 4 1 2116 2196 466256405 466256324 1.200000e-23 122.0
7 TraesCS7A01G322300 chr7A 94.340 53 2 1 3828 3879 605840830 605840778 7.350000e-11 80.5
8 TraesCS7A01G322300 chr7B 94.388 7395 267 56 805 8152 419045962 419038669 0.000000e+00 11221.0
9 TraesCS7A01G322300 chr7B 94.578 332 11 3 8500 8831 419038209 419037885 2.840000e-139 507.0
10 TraesCS7A01G322300 chr7B 94.681 282 14 1 351 632 419047352 419047072 3.790000e-118 436.0
11 TraesCS7A01G322300 chr7B 83.442 308 15 15 8173 8446 419038681 419038376 4.090000e-63 254.0
12 TraesCS7A01G322300 chr7B 92.727 165 3 2 647 806 419046743 419046583 6.900000e-56 230.0
13 TraesCS7A01G322300 chr7B 91.781 146 10 2 2052 2196 419044791 419044647 1.500000e-47 202.0
14 TraesCS7A01G322300 chr7B 92.135 89 5 2 2116 2203 419044791 419044704 3.350000e-24 124.0
15 TraesCS7A01G322300 chr7B 90.909 88 7 1 1988 2075 419044727 419044641 5.600000e-22 117.0
16 TraesCS7A01G322300 chr7B 100.000 48 0 0 1 48 419047396 419047349 1.220000e-13 89.8
17 TraesCS7A01G322300 chr7D 96.187 5403 129 24 815 6179 407860465 407855102 0.000000e+00 8765.0
18 TraesCS7A01G322300 chr7D 98.192 2599 20 6 6241 8831 407854634 407852055 0.000000e+00 4514.0
19 TraesCS7A01G322300 chr7D 96.479 142 4 1 2056 2196 407859323 407859182 5.330000e-57 233.0
20 TraesCS7A01G322300 chr7D 93.458 107 5 2 5317 5421 190163219 190163113 3.300000e-34 158.0
21 TraesCS7A01G322300 chr7D 92.593 108 8 0 5312 5419 168580023 168579916 1.190000e-33 156.0
22 TraesCS7A01G322300 chr7D 95.455 88 4 0 1988 2075 407859263 407859176 3.320000e-29 141.0
23 TraesCS7A01G322300 chr7D 94.872 78 3 1 2120 2196 407859323 407859246 4.330000e-23 121.0
24 TraesCS7A01G322300 chr2D 92.357 314 22 2 39 351 439172528 439172840 6.290000e-121 446.0
25 TraesCS7A01G322300 chr6D 92.810 306 21 1 47 351 380283706 380283401 8.140000e-120 442.0
26 TraesCS7A01G322300 chr5D 92.787 305 22 0 47 351 415423871 415424175 8.140000e-120 442.0
27 TraesCS7A01G322300 chr5D 94.286 105 6 0 5313 5417 228446955 228447059 2.550000e-35 161.0
28 TraesCS7A01G322300 chr5D 92.593 108 6 2 5316 5423 415615117 415615012 4.270000e-33 154.0
29 TraesCS7A01G322300 chr4D 92.810 306 21 1 47 351 415118742 415119047 8.140000e-120 442.0
30 TraesCS7A01G322300 chr4D 92.013 313 23 2 41 351 15587327 15587639 1.050000e-118 438.0
31 TraesCS7A01G322300 chr1D 92.810 306 21 1 47 351 237617642 237617947 8.140000e-120 442.0
32 TraesCS7A01G322300 chr1D 92.508 307 22 1 48 353 493486421 493486115 1.050000e-118 438.0
33 TraesCS7A01G322300 chr1D 91.961 311 23 2 44 352 493484134 493483824 1.360000e-117 435.0
34 TraesCS7A01G322300 chr1D 91.111 315 26 2 37 351 323725962 323726274 8.190000e-115 425.0
35 TraesCS7A01G322300 chr2B 87.986 283 31 3 351 631 639993918 639993637 1.840000e-86 331.0
36 TraesCS7A01G322300 chr3D 93.333 195 13 0 438 632 567157983 567157789 1.120000e-73 289.0
37 TraesCS7A01G322300 chr3D 93.814 97 5 1 361 457 567158104 567158009 2.570000e-30 145.0
38 TraesCS7A01G322300 chr3A 95.960 99 4 0 5318 5416 156231982 156232080 2.550000e-35 161.0
39 TraesCS7A01G322300 chr5B 94.175 103 6 0 5316 5418 681819416 681819314 3.300000e-34 158.0
40 TraesCS7A01G322300 chr5B 90.123 81 7 1 3830 3909 292339900 292339980 4.360000e-18 104.0
41 TraesCS7A01G322300 chr3B 97.872 47 1 0 8347 8393 122823338 122823292 2.040000e-11 82.4


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 TraesCS7A01G322300 chr7A 466249562 466258392 8830 True 3398.000000 16308 95.095200 1 8831 5 chr7A.!!$R1 8830
1 TraesCS7A01G322300 chr7B 419037885 419047396 9511 True 1464.533333 11221 92.737889 1 8831 9 chr7B.!!$R1 8830
2 TraesCS7A01G322300 chr7D 407852055 407860465 8410 True 2754.800000 8765 96.237000 815 8831 5 chr7D.!!$R3 8016
3 TraesCS7A01G322300 chr1D 493483824 493486421 2597 True 436.500000 438 92.234500 44 353 2 chr1D.!!$R1 309

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
480 482 0.107703 TGCGCTTGTAAGGGGAGATG 60.108 55.000 9.73 0.0 39.18 2.90 F
1306 2249 0.041833 AGCAGGAGGTCAAGAGCCTA 59.958 55.000 0.00 0.0 36.29 3.93 F
2143 3087 0.174845 TTAAGCGCACGCCTATCAGT 59.825 50.000 11.47 0.0 43.17 3.41 F
2151 3095 0.176680 ACGCCTATCAGTGCTTGAGG 59.823 55.000 0.00 0.0 39.68 3.86 F
2176 3120 0.460987 ATTCTGCTGTCACCTAGCGC 60.461 55.000 0.00 0.0 44.01 5.92 F
4404 5369 2.089980 GATTCTGCTGTGATGTTGCCT 58.910 47.619 0.00 0.0 0.00 4.75 F
4469 5434 6.039493 ACGATACAGAGAAACGGTCATTATCT 59.961 38.462 0.00 0.0 0.00 1.98 F
6222 7210 3.278574 TGGTCTGGCCAATAAATTCTCG 58.721 45.455 7.01 0.0 45.94 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3125 0.164647 CTGACTGTGCTTAAGCGTGC 59.835 55.000 21.97 14.73 45.83 5.34 R
2189 3133 0.471617 ACCAGCTTCTGACTGTGCTT 59.528 50.000 0.00 0.00 32.44 3.91 R
3905 4870 2.693074 TCCTCGCATCTGTACTATTGCA 59.307 45.455 12.64 0.00 34.80 4.08 R
4046 5011 5.963253 ACATATGGACATTCCCCAATCAAAA 59.037 36.000 7.80 0.00 37.22 2.44 R
4432 5397 3.115554 TCTGTATCGTGCACATGAATCG 58.884 45.455 18.64 0.26 0.00 3.34 R
5791 6777 0.527113 CATTTGTGCGATCCAGGCAA 59.473 50.000 0.00 0.00 42.92 4.52 R
6429 7823 7.283807 TGTCTGGTCAAGATTTTATGGATGATG 59.716 37.037 0.00 0.00 37.23 3.07 R
7880 9622 1.018148 ACACGCACGATGAAACCAAA 58.982 45.000 0.00 0.00 0.00 3.28 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
44 45 4.961438 AGCTGGGAAATTCACAAATGTT 57.039 36.364 0.00 0.00 0.00 2.71
45 46 6.491745 TGTAGCTGGGAAATTCACAAATGTTA 59.508 34.615 0.00 0.00 0.00 2.41
46 47 6.418057 AGCTGGGAAATTCACAAATGTTAA 57.582 33.333 0.00 0.00 0.00 2.01
47 48 6.458210 AGCTGGGAAATTCACAAATGTTAAG 58.542 36.000 0.00 0.00 0.00 1.85
48 49 5.639082 GCTGGGAAATTCACAAATGTTAAGG 59.361 40.000 0.00 0.00 0.00 2.69
49 50 6.107901 TGGGAAATTCACAAATGTTAAGGG 57.892 37.500 0.00 0.00 0.00 3.95
50 51 4.935205 GGGAAATTCACAAATGTTAAGGGC 59.065 41.667 0.00 0.00 0.00 5.19
51 52 4.935205 GGAAATTCACAAATGTTAAGGGCC 59.065 41.667 0.00 0.00 0.00 5.80
71 72 4.640647 GGCCTCTTTGATTCGTAGGATTTT 59.359 41.667 0.00 0.00 0.00 1.82
81 82 3.058450 TCGTAGGATTTTCAAAACGCGA 58.942 40.909 15.93 0.00 0.00 5.87
94 95 6.249035 TCAAAACGCGAGAATAGGAAAAAT 57.751 33.333 15.93 0.00 0.00 1.82
241 243 8.000709 TCTAGTGCAAATGAATCCTATGGAAAT 58.999 33.333 0.00 0.00 34.34 2.17
242 244 7.427989 AGTGCAAATGAATCCTATGGAAATT 57.572 32.000 0.00 0.00 34.34 1.82
245 247 8.949177 GTGCAAATGAATCCTATGGAAATTTTT 58.051 29.630 0.00 0.00 34.34 1.94
270 272 9.451002 TTTTATGGTTTACAATCCTACGAATCA 57.549 29.630 0.00 0.00 0.00 2.57
271 273 9.451002 TTTATGGTTTACAATCCTACGAATCAA 57.549 29.630 0.00 0.00 0.00 2.57
272 274 7.931578 ATGGTTTACAATCCTACGAATCAAA 57.068 32.000 0.00 0.00 0.00 2.69
273 275 7.136289 TGGTTTACAATCCTACGAATCAAAC 57.864 36.000 0.00 0.00 0.00 2.93
274 276 6.711194 TGGTTTACAATCCTACGAATCAAACA 59.289 34.615 0.00 0.00 0.00 2.83
275 277 7.228906 TGGTTTACAATCCTACGAATCAAACAA 59.771 33.333 0.00 0.00 0.00 2.83
276 278 7.536281 GGTTTACAATCCTACGAATCAAACAAC 59.464 37.037 0.00 0.00 0.00 3.32
277 279 5.622770 ACAATCCTACGAATCAAACAACC 57.377 39.130 0.00 0.00 0.00 3.77
278 280 5.067273 ACAATCCTACGAATCAAACAACCA 58.933 37.500 0.00 0.00 0.00 3.67
279 281 5.533154 ACAATCCTACGAATCAAACAACCAA 59.467 36.000 0.00 0.00 0.00 3.67
280 282 5.880054 ATCCTACGAATCAAACAACCAAG 57.120 39.130 0.00 0.00 0.00 3.61
281 283 4.963373 TCCTACGAATCAAACAACCAAGA 58.037 39.130 0.00 0.00 0.00 3.02
282 284 5.556915 TCCTACGAATCAAACAACCAAGAT 58.443 37.500 0.00 0.00 0.00 2.40
283 285 6.703319 TCCTACGAATCAAACAACCAAGATA 58.297 36.000 0.00 0.00 0.00 1.98
284 286 6.816640 TCCTACGAATCAAACAACCAAGATAG 59.183 38.462 0.00 0.00 0.00 2.08
285 287 6.816640 CCTACGAATCAAACAACCAAGATAGA 59.183 38.462 0.00 0.00 0.00 1.98
286 288 7.333423 CCTACGAATCAAACAACCAAGATAGAA 59.667 37.037 0.00 0.00 0.00 2.10
287 289 7.504924 ACGAATCAAACAACCAAGATAGAAA 57.495 32.000 0.00 0.00 0.00 2.52
288 290 7.936584 ACGAATCAAACAACCAAGATAGAAAA 58.063 30.769 0.00 0.00 0.00 2.29
289 291 8.410141 ACGAATCAAACAACCAAGATAGAAAAA 58.590 29.630 0.00 0.00 0.00 1.94
332 334 8.956446 TCCTTCAAAATTCCTTTAAGAATCCT 57.044 30.769 0.00 0.00 35.40 3.24
333 335 9.379770 TCCTTCAAAATTCCTTTAAGAATCCTT 57.620 29.630 0.00 0.00 35.40 3.36
368 370 3.495806 GCCCTAAGAGTGCTATTCATGCT 60.496 47.826 0.00 0.00 0.00 3.79
404 406 3.247173 GTCTAGCTGCAATTGAAGGATCG 59.753 47.826 15.51 0.00 0.00 3.69
405 407 1.386533 AGCTGCAATTGAAGGATCGG 58.613 50.000 15.51 0.00 0.00 4.18
408 410 1.332997 CTGCAATTGAAGGATCGGCTC 59.667 52.381 10.34 0.00 0.00 4.70
424 426 0.896923 GCTCAAATTGGGGTGCATCA 59.103 50.000 0.00 0.00 0.00 3.07
445 447 5.858381 TCAAGTTGTGCTAGAATCAGACTT 58.142 37.500 2.11 0.00 0.00 3.01
480 482 0.107703 TGCGCTTGTAAGGGGAGATG 60.108 55.000 9.73 0.00 39.18 2.90
490 492 2.431954 AGGGGAGATGCTGATTTGTG 57.568 50.000 0.00 0.00 0.00 3.33
509 511 4.781934 TGTGAGAGATCGGAGTTCTGATA 58.218 43.478 3.51 0.00 41.75 2.15
534 536 2.894126 GAGGCTAGGAGCTGCTGTATTA 59.106 50.000 19.25 0.00 41.99 0.98
612 614 4.037923 CACATGAGTTAGCAAAGTTTGGGT 59.962 41.667 17.11 6.40 0.00 4.51
649 700 1.382522 CCAGCGATATTGTTGTGCCT 58.617 50.000 6.11 0.00 0.00 4.75
874 1817 1.593196 CCTTGACAACATGGTCACGT 58.407 50.000 4.49 0.00 46.76 4.49
948 1891 1.619807 TTCCCCTTTCCGATCGTCCC 61.620 60.000 15.09 0.00 0.00 4.46
949 1892 2.504519 CCCTTTCCGATCGTCCCC 59.495 66.667 15.09 0.00 0.00 4.81
950 1893 2.064581 CCCTTTCCGATCGTCCCCT 61.065 63.158 15.09 0.00 0.00 4.79
951 1894 1.623542 CCCTTTCCGATCGTCCCCTT 61.624 60.000 15.09 0.00 0.00 3.95
952 1895 0.179081 CCTTTCCGATCGTCCCCTTC 60.179 60.000 15.09 0.00 0.00 3.46
953 1896 0.527817 CTTTCCGATCGTCCCCTTCG 60.528 60.000 15.09 0.00 0.00 3.79
1306 2249 0.041833 AGCAGGAGGTCAAGAGCCTA 59.958 55.000 0.00 0.00 36.29 3.93
1416 2359 2.222729 CGTTCGTTCGTTCATTCATCCC 60.223 50.000 0.00 0.00 0.00 3.85
1461 2404 2.030946 GCATTGTTAACCTAGCTCGCTG 59.969 50.000 2.48 0.00 0.00 5.18
1808 2751 2.429610 GTTGGCTCGTCATAGGAAGGTA 59.570 50.000 0.00 0.00 0.00 3.08
1882 2826 4.989875 AGATGTCCCTTGGATCTATTGG 57.010 45.455 0.00 0.00 32.73 3.16
1966 2910 2.027100 AGTTTGCTACTTCCTAGTGCCC 60.027 50.000 0.00 0.00 35.78 5.36
2080 3024 0.248907 TAAGCGCACGCCTATCAGTC 60.249 55.000 11.47 0.00 43.17 3.51
2089 3033 2.552599 GCCTATCAGTCCTTAAGGCC 57.447 55.000 17.32 5.34 45.69 5.19
2139 3083 3.719214 GCTTAAGCGCACGCCTAT 58.281 55.556 12.53 1.03 43.17 2.57
2140 3084 1.565106 GCTTAAGCGCACGCCTATC 59.435 57.895 12.53 0.00 43.17 2.08
2143 3087 0.174845 TTAAGCGCACGCCTATCAGT 59.825 50.000 11.47 0.00 43.17 3.41
2144 3088 0.527600 TAAGCGCACGCCTATCAGTG 60.528 55.000 11.47 0.00 43.17 3.66
2149 3093 3.441244 CACGCCTATCAGTGCTTGA 57.559 52.632 0.00 0.00 40.85 3.02
2150 3094 1.284657 CACGCCTATCAGTGCTTGAG 58.715 55.000 0.00 0.00 39.68 3.02
2151 3095 0.176680 ACGCCTATCAGTGCTTGAGG 59.823 55.000 0.00 0.00 39.68 3.86
2152 3096 1.156645 CGCCTATCAGTGCTTGAGGC 61.157 60.000 12.04 12.04 41.46 4.70
2154 3098 1.414181 GCCTATCAGTGCTTGAGGCTA 59.586 52.381 13.89 0.00 41.58 3.93
2155 3099 2.804933 GCCTATCAGTGCTTGAGGCTAC 60.805 54.545 13.89 0.00 41.58 3.58
2156 3100 2.432146 CCTATCAGTGCTTGAGGCTACA 59.568 50.000 0.00 0.00 39.68 2.74
2157 3101 3.118629 CCTATCAGTGCTTGAGGCTACAA 60.119 47.826 0.00 0.00 39.68 2.41
2158 3102 3.641434 ATCAGTGCTTGAGGCTACAAT 57.359 42.857 0.00 0.00 39.68 2.71
2159 3103 3.423539 TCAGTGCTTGAGGCTACAATT 57.576 42.857 0.00 0.00 42.39 2.32
2160 3104 3.338249 TCAGTGCTTGAGGCTACAATTC 58.662 45.455 0.00 0.00 42.39 2.17
2161 3105 3.008375 TCAGTGCTTGAGGCTACAATTCT 59.992 43.478 0.00 0.00 42.39 2.40
2163 3107 2.086869 TGCTTGAGGCTACAATTCTGC 58.913 47.619 0.00 0.00 42.39 4.26
2164 3108 2.290514 TGCTTGAGGCTACAATTCTGCT 60.291 45.455 0.00 0.00 42.39 4.24
2167 3111 2.977914 TGAGGCTACAATTCTGCTGTC 58.022 47.619 0.00 0.00 0.00 3.51
2168 3112 2.302733 TGAGGCTACAATTCTGCTGTCA 59.697 45.455 0.00 0.00 0.00 3.58
2169 3113 2.675348 GAGGCTACAATTCTGCTGTCAC 59.325 50.000 0.00 0.00 0.00 3.67
2170 3114 1.740025 GGCTACAATTCTGCTGTCACC 59.260 52.381 0.00 0.00 0.00 4.02
2171 3115 2.616510 GGCTACAATTCTGCTGTCACCT 60.617 50.000 0.00 0.00 0.00 4.00
2172 3116 3.369471 GGCTACAATTCTGCTGTCACCTA 60.369 47.826 0.00 0.00 0.00 3.08
2173 3117 3.868077 GCTACAATTCTGCTGTCACCTAG 59.132 47.826 0.00 0.00 0.00 3.02
2174 3118 2.704572 ACAATTCTGCTGTCACCTAGC 58.295 47.619 0.00 0.00 41.49 3.42
2176 3120 0.460987 ATTCTGCTGTCACCTAGCGC 60.461 55.000 0.00 0.00 44.01 5.92
2177 3121 2.507110 TTCTGCTGTCACCTAGCGCC 62.507 60.000 2.29 0.00 44.01 6.53
2178 3122 2.997315 TGCTGTCACCTAGCGCCT 60.997 61.111 2.29 0.00 44.01 5.52
2247 3205 8.097078 AGATAATAATGATGCAAACTGAGAGC 57.903 34.615 0.00 0.00 0.00 4.09
2270 3228 7.001073 AGCTAATTCATTAACCTCTGAATCCC 58.999 38.462 3.19 0.00 40.33 3.85
2332 3290 2.100584 CAGAGGACTCACATACTCCTGC 59.899 54.545 1.75 0.00 34.35 4.85
2808 3766 2.802667 CGATTCGCTCAAGGTGCCG 61.803 63.158 0.00 0.00 0.00 5.69
2923 3881 8.971073 ACCATTACTATTTCTATTGCTTGCTTT 58.029 29.630 0.00 0.00 0.00 3.51
3066 4024 9.834628 AATTTGCTGCTCAAAATATTTCAATTG 57.165 25.926 0.10 0.00 46.60 2.32
3330 4294 9.323985 GATTAGCTTCTTGTTCAGATTATCTGT 57.676 33.333 20.09 1.67 44.58 3.41
3331 4295 9.678260 ATTAGCTTCTTGTTCAGATTATCTGTT 57.322 29.630 20.09 0.00 44.58 3.16
3332 4296 7.608308 AGCTTCTTGTTCAGATTATCTGTTC 57.392 36.000 20.09 14.58 44.58 3.18
3373 4338 2.954318 ACTTGCAGCTGATCTGTGTTTT 59.046 40.909 20.43 0.00 44.66 2.43
3723 4688 3.826637 CCAAATGAGGCCAGCAAAG 57.173 52.632 5.01 0.00 0.00 2.77
4046 5011 8.531146 CCAAACAGGTGAAATTAAATGACCTAT 58.469 33.333 3.11 0.00 35.19 2.57
4169 5134 3.117738 CCCAATCTCTTATCTGGGCTTGT 60.118 47.826 0.00 0.00 42.10 3.16
4404 5369 2.089980 GATTCTGCTGTGATGTTGCCT 58.910 47.619 0.00 0.00 0.00 4.75
4469 5434 6.039493 ACGATACAGAGAAACGGTCATTATCT 59.961 38.462 0.00 0.00 0.00 1.98
4650 5617 6.869913 AGACATCAAAAGTAACATGCCATTTG 59.130 34.615 0.00 0.00 0.00 2.32
4813 5784 9.691362 CCACTTTTATTTGTTTGTACAGCTAAT 57.309 29.630 0.00 5.26 35.28 1.73
4972 5943 7.147759 CCAGAAGAGAGGAAACTGAGATTCATA 60.148 40.741 4.84 0.00 44.43 2.15
5015 5986 8.911247 ATTTGCGAAAAGGTTTTATACTGATC 57.089 30.769 0.00 0.00 0.00 2.92
5294 6265 6.750148 ACTAGCTTATAACAGGCAGATGTAC 58.250 40.000 0.00 0.00 31.70 2.90
5356 6327 7.447238 TCCCAAAATAAGTGTCTCAACTTTAGG 59.553 37.037 0.00 0.00 40.77 2.69
5529 6514 7.550196 GCTGTTTATGGAAAAATCATGAACCAT 59.450 33.333 18.34 18.34 39.10 3.55
5565 6550 6.716934 TTGTTAAAGTTGTGAATAAGGGCA 57.283 33.333 0.00 0.00 0.00 5.36
5791 6777 6.273825 AGTTCTTCGTACGAATTGCATAGAT 58.726 36.000 29.25 6.21 33.28 1.98
5993 6979 3.868661 TGCAGCACATAATACGGTTAGTG 59.131 43.478 0.00 0.00 0.00 2.74
6099 7087 5.932303 GCATCCTGTTGTTACTTCAGAGTTA 59.068 40.000 8.35 0.00 37.33 2.24
6113 7101 8.494016 ACTTCAGAGTTAATGTAGCAAATACC 57.506 34.615 0.00 0.00 30.01 2.73
6114 7102 8.322091 ACTTCAGAGTTAATGTAGCAAATACCT 58.678 33.333 0.00 0.00 30.01 3.08
6222 7210 3.278574 TGGTCTGGCCAATAAATTCTCG 58.721 45.455 7.01 0.00 45.94 4.04
6223 7211 3.279434 GGTCTGGCCAATAAATTCTCGT 58.721 45.455 7.01 0.00 37.17 4.18
6224 7212 3.312697 GGTCTGGCCAATAAATTCTCGTC 59.687 47.826 7.01 0.00 37.17 4.20
6429 7823 1.977412 GTAAGTCTCGCACGTGAGTTC 59.023 52.381 22.23 10.90 46.40 3.01
7137 8878 2.708216 TGCAGAGACAGTTCCAACAA 57.292 45.000 0.00 0.00 0.00 2.83
7560 9302 3.857010 GCAACCTGACCTGTTTACATTGC 60.857 47.826 0.00 0.00 33.86 3.56
7880 9622 6.803320 CAGATTGCTACAACATTCGTCAATTT 59.197 34.615 0.00 0.00 0.00 1.82
7967 9709 4.751767 TTTTTGTTGGGAGCAAACAGAT 57.248 36.364 0.00 0.00 38.67 2.90
8014 9757 5.488919 GGATGGATATAGGAGGATTGGACAA 59.511 44.000 0.00 0.00 0.00 3.18
8015 9758 6.352565 GGATGGATATAGGAGGATTGGACAAG 60.353 46.154 0.00 0.00 0.00 3.16
8016 9759 5.726560 TGGATATAGGAGGATTGGACAAGA 58.273 41.667 0.00 0.00 0.00 3.02
8017 9760 5.544176 TGGATATAGGAGGATTGGACAAGAC 59.456 44.000 0.00 0.00 0.00 3.01
8506 10587 7.500892 TGAAAAGTTGGAGTGCTCAGTATAAAA 59.499 33.333 1.41 0.00 0.00 1.52
8507 10588 7.817418 AAAGTTGGAGTGCTCAGTATAAAAA 57.183 32.000 1.41 0.00 0.00 1.94
8508 10589 8.409358 AAAGTTGGAGTGCTCAGTATAAAAAT 57.591 30.769 1.41 0.00 0.00 1.82
8509 10590 7.383102 AGTTGGAGTGCTCAGTATAAAAATG 57.617 36.000 1.41 0.00 0.00 2.32
8510 10591 5.818136 TGGAGTGCTCAGTATAAAAATGC 57.182 39.130 1.41 0.00 0.00 3.56
8511 10592 5.500234 TGGAGTGCTCAGTATAAAAATGCT 58.500 37.500 1.41 0.00 0.00 3.79
8512 10593 5.945784 TGGAGTGCTCAGTATAAAAATGCTT 59.054 36.000 1.41 0.00 0.00 3.91
8513 10594 6.127925 TGGAGTGCTCAGTATAAAAATGCTTG 60.128 38.462 1.41 0.00 0.00 4.01
8514 10595 6.094048 GGAGTGCTCAGTATAAAAATGCTTGA 59.906 38.462 1.41 0.00 0.00 3.02
8564 10645 0.590195 CAGACCAGCAAGACAGCAAC 59.410 55.000 0.00 0.00 36.85 4.17
8680 10761 4.452733 CCTCCGGCGGTCCTTGTC 62.453 72.222 27.32 0.00 0.00 3.18
8681 10762 4.796231 CTCCGGCGGTCCTTGTCG 62.796 72.222 27.32 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.134081 CCTACGAATCAAAGAGGCCCTTA 59.866 47.826 0.00 0.00 34.00 2.69
45 46 2.092914 CCTACGAATCAAAGAGGCCCTT 60.093 50.000 0.00 0.00 36.47 3.95
46 47 1.486726 CCTACGAATCAAAGAGGCCCT 59.513 52.381 0.00 0.00 0.00 5.19
47 48 1.485066 TCCTACGAATCAAAGAGGCCC 59.515 52.381 0.00 0.00 0.00 5.80
48 49 2.981859 TCCTACGAATCAAAGAGGCC 57.018 50.000 0.00 0.00 0.00 5.19
49 50 5.354234 TGAAAATCCTACGAATCAAAGAGGC 59.646 40.000 0.00 0.00 0.00 4.70
50 51 6.985188 TGAAAATCCTACGAATCAAAGAGG 57.015 37.500 0.00 0.00 0.00 3.69
51 52 9.118236 GTTTTGAAAATCCTACGAATCAAAGAG 57.882 33.333 0.00 0.00 0.00 2.85
71 72 5.676532 TTTTTCCTATTCTCGCGTTTTGA 57.323 34.783 5.77 0.00 0.00 2.69
94 95 6.323996 AGACGACATTTCACTCTAATCCCATA 59.676 38.462 0.00 0.00 0.00 2.74
109 110 5.046591 TCCTGTAGGATTCAAGACGACATTT 60.047 40.000 0.00 0.00 39.78 2.32
169 171 9.287373 TCCGCTTAAACCTCTTTAAAAGAATAA 57.713 29.630 0.00 0.00 37.02 1.40
170 172 8.851541 TCCGCTTAAACCTCTTTAAAAGAATA 57.148 30.769 0.00 0.00 37.02 1.75
178 180 3.520317 TCCCATCCGCTTAAACCTCTTTA 59.480 43.478 0.00 0.00 0.00 1.85
189 191 0.625849 AGGAAACATCCCATCCGCTT 59.374 50.000 0.00 0.00 38.31 4.68
192 194 3.769739 TCATAGGAAACATCCCATCCG 57.230 47.619 0.00 0.00 38.31 4.18
245 247 9.451002 TTGATTCGTAGGATTGTAAACCATAAA 57.549 29.630 0.00 0.00 0.00 1.40
246 248 9.451002 TTTGATTCGTAGGATTGTAAACCATAA 57.549 29.630 0.00 0.00 0.00 1.90
254 256 6.231951 TGGTTGTTTGATTCGTAGGATTGTA 58.768 36.000 0.00 0.00 0.00 2.41
255 257 5.067273 TGGTTGTTTGATTCGTAGGATTGT 58.933 37.500 0.00 0.00 0.00 2.71
256 258 5.621197 TGGTTGTTTGATTCGTAGGATTG 57.379 39.130 0.00 0.00 0.00 2.67
257 259 6.001460 TCTTGGTTGTTTGATTCGTAGGATT 58.999 36.000 0.00 0.00 0.00 3.01
258 260 5.556915 TCTTGGTTGTTTGATTCGTAGGAT 58.443 37.500 0.00 0.00 0.00 3.24
259 261 4.963373 TCTTGGTTGTTTGATTCGTAGGA 58.037 39.130 0.00 0.00 0.00 2.94
260 262 5.880054 ATCTTGGTTGTTTGATTCGTAGG 57.120 39.130 0.00 0.00 0.00 3.18
261 263 7.827819 TCTATCTTGGTTGTTTGATTCGTAG 57.172 36.000 0.00 0.00 0.00 3.51
262 264 8.610248 TTTCTATCTTGGTTGTTTGATTCGTA 57.390 30.769 0.00 0.00 0.00 3.43
263 265 7.504924 TTTCTATCTTGGTTGTTTGATTCGT 57.495 32.000 0.00 0.00 0.00 3.85
264 266 8.795786 TTTTTCTATCTTGGTTGTTTGATTCG 57.204 30.769 0.00 0.00 0.00 3.34
306 308 9.552695 AGGATTCTTAAAGGAATTTTGAAGGAT 57.447 29.630 0.00 0.00 36.24 3.24
307 309 8.956446 AGGATTCTTAAAGGAATTTTGAAGGA 57.044 30.769 0.00 0.00 36.24 3.36
346 348 5.569890 CAGCATGAATAGCACTCTTAGGGC 61.570 50.000 0.00 0.00 42.45 5.19
347 349 4.063689 CAGCATGAATAGCACTCTTAGGG 58.936 47.826 0.00 0.00 39.69 3.53
348 350 4.953667 TCAGCATGAATAGCACTCTTAGG 58.046 43.478 0.00 0.00 45.97 2.69
368 370 2.462456 CTAGACAAGCAAGTGCCTCA 57.538 50.000 0.00 0.00 43.38 3.86
404 406 0.176449 GATGCACCCCAATTTGAGCC 59.824 55.000 0.00 0.00 0.00 4.70
405 407 0.896923 TGATGCACCCCAATTTGAGC 59.103 50.000 0.00 0.00 0.00 4.26
408 410 3.068560 CAACTTGATGCACCCCAATTTG 58.931 45.455 11.26 11.26 30.52 2.32
424 426 5.858381 TCAAGTCTGATTCTAGCACAACTT 58.142 37.500 0.00 0.00 0.00 2.66
445 447 5.048782 ACAAGCGCATAAACAAGATTCTTCA 60.049 36.000 11.47 0.00 0.00 3.02
480 482 3.122297 CTCCGATCTCTCACAAATCAGC 58.878 50.000 0.00 0.00 0.00 4.26
490 492 4.217550 CCCTTATCAGAACTCCGATCTCTC 59.782 50.000 0.00 0.00 0.00 3.20
509 511 2.069430 GCAGCTCCTAGCCTCCCTT 61.069 63.158 0.00 0.00 43.77 3.95
559 561 9.146984 CTTTATTACATGTCGGAGTACAGAAAA 57.853 33.333 0.00 0.00 31.70 2.29
570 572 6.478673 TCATGTGCTACTTTATTACATGTCGG 59.521 38.462 0.00 0.00 45.31 4.79
571 573 7.222805 ACTCATGTGCTACTTTATTACATGTCG 59.777 37.037 0.00 9.48 45.31 4.35
612 614 2.567862 TGGGGATTCAACCAGACCATA 58.432 47.619 0.00 0.00 31.92 2.74
710 1031 7.584987 AGAAGATGACAATTTTAAGTCGTTGG 58.415 34.615 0.00 0.00 37.58 3.77
723 1044 2.237143 TGGGCTTCGAGAAGATGACAAT 59.763 45.455 16.23 0.00 40.79 2.71
751 1072 3.982372 ATACCCTCGTGCGTGCGTG 62.982 63.158 1.25 0.00 0.00 5.34
752 1073 3.695022 GATACCCTCGTGCGTGCGT 62.695 63.158 1.25 0.00 0.00 5.24
753 1074 2.954868 GATACCCTCGTGCGTGCG 60.955 66.667 0.00 0.00 0.00 5.34
754 1075 2.585247 GGATACCCTCGTGCGTGC 60.585 66.667 0.00 0.00 0.00 5.34
949 1892 1.597461 GGTGGAAGGGAGTCCGAAG 59.403 63.158 2.26 0.00 40.96 3.79
950 1893 1.916777 GGGTGGAAGGGAGTCCGAA 60.917 63.158 2.26 0.00 40.96 4.30
951 1894 2.284405 GGGTGGAAGGGAGTCCGA 60.284 66.667 2.26 0.00 40.96 4.55
952 1895 3.400054 GGGGTGGAAGGGAGTCCG 61.400 72.222 2.26 0.00 40.96 4.79
953 1896 3.015753 GGGGGTGGAAGGGAGTCC 61.016 72.222 0.00 0.00 38.27 3.85
954 1897 1.996187 GAGGGGGTGGAAGGGAGTC 60.996 68.421 0.00 0.00 0.00 3.36
955 1898 2.062448 AAGAGGGGGTGGAAGGGAGT 62.062 60.000 0.00 0.00 0.00 3.85
956 1899 1.229984 AAGAGGGGGTGGAAGGGAG 60.230 63.158 0.00 0.00 0.00 4.30
957 1900 1.229853 GAAGAGGGGGTGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
958 1901 2.309504 GGAAGAGGGGGTGGAAGGG 61.310 68.421 0.00 0.00 0.00 3.95
1119 2062 3.229581 GCTAGCGAGCGAGCAATC 58.770 61.111 21.93 0.00 42.81 2.67
1416 2359 2.159014 CCCAATCCAATCCAGTGCAATG 60.159 50.000 7.29 7.29 0.00 2.82
1461 2404 6.966534 ATGAAATTTCCATGGGATCAGTAC 57.033 37.500 13.02 0.00 0.00 2.73
1514 2457 5.516090 TGCTTTAACAGAACAAATTCGTCC 58.484 37.500 0.00 0.00 40.04 4.79
1685 2628 0.327924 TACCCACACTTCCTGGCATG 59.672 55.000 0.00 0.00 0.00 4.06
1808 2751 7.391148 AAAGAAAACATGACGGCATAAGTAT 57.609 32.000 1.73 0.00 32.27 2.12
1962 2906 0.391130 GTGCTTACGTGAGATGGGCA 60.391 55.000 12.13 0.00 0.00 5.36
2080 3024 1.474077 GCAGAATGTGTGGCCTTAAGG 59.526 52.381 17.81 17.81 39.31 2.69
2089 3033 1.888215 AGGTGACAGCAGAATGTGTG 58.112 50.000 7.50 0.00 39.31 3.82
2144 3088 2.097142 CAGCAGAATTGTAGCCTCAAGC 59.903 50.000 0.00 0.00 44.25 4.01
2148 3092 2.675348 GTGACAGCAGAATTGTAGCCTC 59.325 50.000 0.00 0.00 0.00 4.70
2149 3093 2.616510 GGTGACAGCAGAATTGTAGCCT 60.617 50.000 0.00 0.00 0.00 4.58
2150 3094 1.740025 GGTGACAGCAGAATTGTAGCC 59.260 52.381 0.00 0.00 0.00 3.93
2151 3095 2.704572 AGGTGACAGCAGAATTGTAGC 58.295 47.619 7.50 0.00 0.00 3.58
2152 3096 3.868077 GCTAGGTGACAGCAGAATTGTAG 59.132 47.826 7.50 0.00 38.93 2.74
2154 3098 2.704572 GCTAGGTGACAGCAGAATTGT 58.295 47.619 7.50 0.00 38.93 2.71
2155 3099 1.662629 CGCTAGGTGACAGCAGAATTG 59.337 52.381 7.50 0.00 39.04 2.32
2156 3100 2.009042 GCGCTAGGTGACAGCAGAATT 61.009 52.381 7.50 0.00 39.04 2.17
2157 3101 0.460987 GCGCTAGGTGACAGCAGAAT 60.461 55.000 7.50 0.00 39.04 2.40
2158 3102 1.079819 GCGCTAGGTGACAGCAGAA 60.080 57.895 7.50 0.00 39.04 3.02
2159 3103 2.573869 GCGCTAGGTGACAGCAGA 59.426 61.111 7.50 0.00 39.04 4.26
2160 3104 1.667154 TAGGCGCTAGGTGACAGCAG 61.667 60.000 7.64 3.84 39.04 4.24
2161 3105 1.667154 CTAGGCGCTAGGTGACAGCA 61.667 60.000 7.64 0.00 39.04 4.41
2163 3107 1.736586 CCTAGGCGCTAGGTGACAG 59.263 63.158 19.08 2.71 46.15 3.51
2164 3108 3.935024 CCTAGGCGCTAGGTGACA 58.065 61.111 19.08 0.00 46.15 3.58
2174 3118 2.526120 GCTTAAGCGTGCCTAGGCG 61.526 63.158 28.28 16.34 45.51 5.52
2176 3120 0.391130 TGTGCTTAAGCGTGCCTAGG 60.391 55.000 21.97 3.67 45.83 3.02
2177 3121 1.002366 CTGTGCTTAAGCGTGCCTAG 58.998 55.000 21.97 9.80 45.83 3.02
2178 3122 0.320374 ACTGTGCTTAAGCGTGCCTA 59.680 50.000 21.97 0.63 45.83 3.93
2181 3125 0.164647 CTGACTGTGCTTAAGCGTGC 59.835 55.000 21.97 14.73 45.83 5.34
2184 3128 1.127582 GCTTCTGACTGTGCTTAAGCG 59.872 52.381 21.97 10.80 45.83 4.68
2185 3129 2.159234 CAGCTTCTGACTGTGCTTAAGC 59.841 50.000 20.84 20.84 39.62 3.09
2186 3130 2.740981 CCAGCTTCTGACTGTGCTTAAG 59.259 50.000 0.00 0.00 32.44 1.85
2187 3131 2.104792 ACCAGCTTCTGACTGTGCTTAA 59.895 45.455 0.00 0.00 32.44 1.85
2188 3132 1.694150 ACCAGCTTCTGACTGTGCTTA 59.306 47.619 0.00 0.00 32.44 3.09
2189 3133 0.471617 ACCAGCTTCTGACTGTGCTT 59.528 50.000 0.00 0.00 32.44 3.91
2247 3205 6.428159 CCGGGATTCAGAGGTTAATGAATTAG 59.572 42.308 0.00 0.73 44.18 1.73
2270 3228 8.167985 CACCAAATTGCAAAAGAAATATAACCG 58.832 33.333 1.71 0.00 0.00 4.44
2779 3737 1.139734 GCGAATCGGCTCTGTCAGA 59.860 57.895 4.35 1.78 0.00 3.27
2808 3766 2.005451 CTACACTCCACAGAGCATTGC 58.995 52.381 0.00 0.00 44.65 3.56
3066 4024 9.567848 TTGTCTCAGATTCTGTTAAACAAAAAC 57.432 29.630 13.23 0.00 32.61 2.43
3373 4338 8.464404 AGTCGTAACACATCTAATTAAGCACTA 58.536 33.333 0.00 0.00 0.00 2.74
3723 4688 8.519526 AGATTACTAGCAGAGCATAGACAATAC 58.480 37.037 0.00 0.00 0.00 1.89
3905 4870 2.693074 TCCTCGCATCTGTACTATTGCA 59.307 45.455 12.64 0.00 34.80 4.08
4004 4969 7.940178 CCTGTTTGGTTACAAGGTAATTTTC 57.060 36.000 0.00 0.00 37.97 2.29
4043 5008 6.736110 ATGGACATTCCCCAATCAAAATAG 57.264 37.500 0.00 0.00 37.22 1.73
4046 5011 5.963253 ACATATGGACATTCCCCAATCAAAA 59.037 36.000 7.80 0.00 37.22 2.44
4432 5397 3.115554 TCTGTATCGTGCACATGAATCG 58.884 45.455 18.64 0.26 0.00 3.34
4813 5784 5.951148 TCATATTGAGGACAAAAGGCAATGA 59.049 36.000 0.00 0.00 39.54 2.57
4972 5943 5.868801 CGCAAATTTATGAAAATCCCAGTGT 59.131 36.000 0.00 0.00 34.12 3.55
5015 5986 4.843220 ATGCAGTTCTGAACTTTCAAGG 57.157 40.909 19.89 9.27 40.46 3.61
5294 6265 2.295885 CTTGGCAATCTTAGAGGGCAG 58.704 52.381 0.00 4.92 37.13 4.85
5458 6443 5.414454 TCAATTGGCCAGTGATTGTACTTAC 59.586 40.000 22.23 0.00 33.60 2.34
5529 6514 8.452534 CACAACTTTAACAAACCAGTACAGTTA 58.547 33.333 0.00 0.00 0.00 2.24
5565 6550 8.486210 TCATTTTGCAGTTAGGATATGAGTAGT 58.514 33.333 0.00 0.00 0.00 2.73
5791 6777 0.527113 CATTTGTGCGATCCAGGCAA 59.473 50.000 0.00 0.00 42.92 4.52
5993 6979 7.816995 AGATGAGACAACAAGAGATGAAAGTAC 59.183 37.037 0.00 0.00 0.00 2.73
6429 7823 7.283807 TGTCTGGTCAAGATTTTATGGATGATG 59.716 37.037 0.00 0.00 37.23 3.07
7137 8878 6.756542 GCATTTTCAACTGGAGTAACTTTTGT 59.243 34.615 0.00 0.00 0.00 2.83
7560 9302 2.441532 CCCTGCAATGCCAGAGGG 60.442 66.667 13.74 13.74 39.42 4.30
7880 9622 1.018148 ACACGCACGATGAAACCAAA 58.982 45.000 0.00 0.00 0.00 3.28
7967 9709 3.245371 ACAAAGGCCTCCAAGAATGATCA 60.245 43.478 5.23 0.00 0.00 2.92
8014 9757 2.621055 GTGTCTGTCTGTCTGTCTGTCT 59.379 50.000 0.00 0.00 0.00 3.41
8015 9758 2.603412 CGTGTCTGTCTGTCTGTCTGTC 60.603 54.545 0.00 0.00 0.00 3.51
8016 9759 1.335182 CGTGTCTGTCTGTCTGTCTGT 59.665 52.381 0.00 0.00 0.00 3.41
8017 9760 1.335415 CCGTGTCTGTCTGTCTGTCTG 60.335 57.143 0.00 0.00 0.00 3.51
8508 10589 8.892723 CCATATTTATACAACAACTCTCAAGCA 58.107 33.333 0.00 0.00 0.00 3.91
8509 10590 8.893727 ACCATATTTATACAACAACTCTCAAGC 58.106 33.333 0.00 0.00 0.00 4.01
8512 10593 9.817809 GAGACCATATTTATACAACAACTCTCA 57.182 33.333 0.00 0.00 0.00 3.27
8564 10645 3.757493 ACTTCACCAACTACTCTACTCCG 59.243 47.826 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.