Multiple sequence alignment - TraesCS1A01G152100

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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 TraesCS1A01G152100 chr1A 100.000 4703 0 0 1 4703 261246313 261251015 0.000000e+00 8685.0
1 TraesCS1A01G152100 chr1A 79.391 427 66 15 4276 4701 533665365 533664960 9.960000e-72 281.0
2 TraesCS1A01G152100 chr1A 77.127 529 86 22 1 511 309397734 309398245 1.670000e-69 274.0
3 TraesCS1A01G152100 chr1A 77.597 308 56 8 4396 4703 471963982 471963688 1.740000e-39 174.0
4 TraesCS1A01G152100 chr1A 73.348 454 88 26 1090 1534 21986865 21986436 2.280000e-28 137.0
5 TraesCS1A01G152100 chr1B 90.157 4267 219 74 513 4700 300720069 300724213 0.000000e+00 5367.0
6 TraesCS1A01G152100 chr1B 77.467 537 92 14 1 513 418073596 418073065 1.280000e-75 294.0
7 TraesCS1A01G152100 chr1B 81.967 183 33 0 4521 4703 288157228 288157046 6.300000e-34 156.0
8 TraesCS1A01G152100 chr1D 91.027 2396 145 25 2328 4703 204798215 204800560 0.000000e+00 3169.0
9 TraesCS1A01G152100 chr1D 91.854 2087 118 26 1 2048 204796116 204798189 0.000000e+00 2865.0
10 TraesCS1A01G152100 chr1D 84.401 609 75 14 4100 4703 204803110 204803703 8.770000e-162 580.0
11 TraesCS1A01G152100 chr1D 79.319 411 69 12 4296 4703 372522795 372522398 1.670000e-69 274.0
12 TraesCS1A01G152100 chr1D 75.479 522 109 15 4190 4703 205136077 205136587 2.190000e-58 237.0
13 TraesCS1A01G152100 chr1D 85.581 215 30 1 4 217 215618732 215618518 1.700000e-54 224.0
14 TraesCS1A01G152100 chr1D 74.298 463 86 23 1081 1534 20568371 20568809 1.050000e-36 165.0
15 TraesCS1A01G152100 chr1D 73.622 508 90 22 4205 4703 118473873 118473401 6.300000e-34 156.0
16 TraesCS1A01G152100 chr7D 90.643 342 31 1 2971 3311 49493748 49493407 2.000000e-123 453.0
17 TraesCS1A01G152100 chr7D 92.035 226 17 1 2971 3195 49430872 49430647 2.730000e-82 316.0
18 TraesCS1A01G152100 chr7D 77.348 543 87 16 1 515 30126829 30127363 5.950000e-74 289.0
19 TraesCS1A01G152100 chr7D 75.855 497 107 13 4190 4681 213456802 213457290 1.690000e-59 241.0
20 TraesCS1A01G152100 chr7D 93.798 129 7 1 3178 3306 49427516 49427389 4.800000e-45 193.0
21 TraesCS1A01G152100 chr7D 80.745 161 27 4 351 511 494670376 494670220 6.390000e-24 122.0
22 TraesCS1A01G152100 chr5D 80.784 536 78 15 1 515 242582210 242581679 3.410000e-106 396.0
23 TraesCS1A01G152100 chr5D 75.952 499 91 17 4190 4686 510350082 510349611 3.660000e-56 230.0
24 TraesCS1A01G152100 chr5D 75.734 511 95 16 26 513 529088318 529087814 3.660000e-56 230.0
25 TraesCS1A01G152100 chr5D 75.224 335 67 12 4318 4648 35965940 35965618 1.360000e-30 145.0
26 TraesCS1A01G152100 chr4D 80.228 526 67 23 10 513 46113170 46113680 1.240000e-95 361.0
27 TraesCS1A01G152100 chr4D 78.531 177 29 9 4187 4358 63956858 63957030 1.790000e-19 108.0
28 TraesCS1A01G152100 chr4D 80.000 100 19 1 4190 4288 509018383 509018482 6.530000e-09 73.1
29 TraesCS1A01G152100 chr7A 80.556 396 60 9 4309 4700 77479815 77480197 5.950000e-74 289.0
30 TraesCS1A01G152100 chr7A 83.682 239 34 3 1 238 121065550 121065316 2.200000e-53 220.0
31 TraesCS1A01G152100 chr6B 76.200 521 102 15 4188 4703 616475165 616475668 6.040000e-64 255.0
32 TraesCS1A01G152100 chr6B 74.632 272 61 6 1000 1267 693063993 693063726 3.850000e-21 113.0
33 TraesCS1A01G152100 chr6B 78.075 187 28 13 4183 4363 595230303 595230482 6.440000e-19 106.0
34 TraesCS1A01G152100 chr2D 76.023 513 79 27 31 511 638848901 638848401 4.740000e-55 226.0
35 TraesCS1A01G152100 chr7B 75.975 487 85 21 46 511 654021853 654022328 6.130000e-54 222.0
36 TraesCS1A01G152100 chr5B 79.253 241 45 3 26 262 289055728 289055967 3.770000e-36 163.0
37 TraesCS1A01G152100 chr4A 79.592 196 32 6 261 452 524170237 524170046 2.950000e-27 134.0
38 TraesCS1A01G152100 chr6D 74.539 271 63 4 1000 1267 455830648 455830381 3.850000e-21 113.0
39 TraesCS1A01G152100 chr6A 73.978 269 68 2 1000 1267 602624821 602624554 1.790000e-19 108.0
40 TraesCS1A01G152100 chr2B 80.992 121 20 3 4188 4306 158629538 158629657 5.010000e-15 93.5
41 TraesCS1A01G152100 chr3B 82.524 103 15 3 4188 4288 769951338 769951439 2.330000e-13 87.9


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 TraesCS1A01G152100 chr1A 261246313 261251015 4702 False 8685.000000 8685 100.0000 1 4703 1 chr1A.!!$F1 4702
1 TraesCS1A01G152100 chr1A 309397734 309398245 511 False 274.000000 274 77.1270 1 511 1 chr1A.!!$F2 510
2 TraesCS1A01G152100 chr1B 300720069 300724213 4144 False 5367.000000 5367 90.1570 513 4700 1 chr1B.!!$F1 4187
3 TraesCS1A01G152100 chr1B 418073065 418073596 531 True 294.000000 294 77.4670 1 513 1 chr1B.!!$R2 512
4 TraesCS1A01G152100 chr1D 204796116 204803703 7587 False 2204.666667 3169 89.0940 1 4703 3 chr1D.!!$F3 4702
5 TraesCS1A01G152100 chr1D 205136077 205136587 510 False 237.000000 237 75.4790 4190 4703 1 chr1D.!!$F2 513
6 TraesCS1A01G152100 chr7D 30126829 30127363 534 False 289.000000 289 77.3480 1 515 1 chr7D.!!$F1 514
7 TraesCS1A01G152100 chr7D 49427389 49430872 3483 True 254.500000 316 92.9165 2971 3306 2 chr7D.!!$R3 335
8 TraesCS1A01G152100 chr5D 242581679 242582210 531 True 396.000000 396 80.7840 1 515 1 chr5D.!!$R2 514
9 TraesCS1A01G152100 chr5D 529087814 529088318 504 True 230.000000 230 75.7340 26 513 1 chr5D.!!$R4 487
10 TraesCS1A01G152100 chr4D 46113170 46113680 510 False 361.000000 361 80.2280 10 513 1 chr4D.!!$F1 503
11 TraesCS1A01G152100 chr6B 616475165 616475668 503 False 255.000000 255 76.2000 4188 4703 1 chr6B.!!$F2 515
12 TraesCS1A01G152100 chr2D 638848401 638848901 500 True 226.000000 226 76.0230 31 511 1 chr2D.!!$R1 480

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
474 540 0.315059 CACGACGCAAACAGACACAC 60.315 55.0 0.0 0.0 0.0 3.82 F
1781 1870 0.651031 GTTTGAGACGCCCGAATAGC 59.349 55.0 0.0 0.0 0.0 2.97 F
2171 2297 0.512952 CACTTTGCAGTACACCGAGC 59.487 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1955 0.249073 CAGAATAGCTCACCGGACGG 60.249 60.0 9.46 9.56 42.03 4.79 R
2632 2768 0.461135 GCAGAGAAGAGGCAGAGGAG 59.539 60.0 0.00 0.00 0.00 3.69 R
3705 6994 2.046009 TACGTGAAGTTGCTGGGCCA 62.046 55.0 5.85 5.85 0.00 5.36 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
39 40 2.966309 GCAACTTCGTCCCTTGCGG 61.966 63.158 0.00 0.00 31.61 5.69
41 42 3.178540 AACTTCGTCCCTTGCGGCT 62.179 57.895 0.00 0.00 0.00 5.52
76 77 2.358737 CTTCCGCTTGGCCGACTT 60.359 61.111 0.00 0.00 0.00 3.01
77 78 2.668212 TTCCGCTTGGCCGACTTG 60.668 61.111 0.00 0.00 0.00 3.16
91 92 0.398318 GACTTGACTGCCCACTCCTT 59.602 55.000 0.00 0.00 0.00 3.36
189 204 2.184322 GATGCTGGACGAGGCGAA 59.816 61.111 0.00 0.00 0.00 4.70
278 341 1.354368 GAGGAAGGGAAATGGTGGACA 59.646 52.381 0.00 0.00 0.00 4.02
279 342 1.786441 AGGAAGGGAAATGGTGGACAA 59.214 47.619 0.00 0.00 0.00 3.18
413 479 1.708027 GGACGAAAATCAGACGCGG 59.292 57.895 12.47 0.00 0.00 6.46
474 540 0.315059 CACGACGCAAACAGACACAC 60.315 55.000 0.00 0.00 0.00 3.82
495 561 1.359459 GCAGACGAAATGGGTCGACC 61.359 60.000 27.04 27.04 43.86 4.79
523 589 2.751806 AGTTGCTCTTAAAGGCTCATGC 59.248 45.455 0.00 0.00 38.76 4.06
568 634 5.009631 TGGAAATCATACCCTGAAACACAG 58.990 41.667 0.00 0.00 45.36 3.66
580 646 4.067896 CTGAAACACAGTGGAGCTACAAT 58.932 43.478 0.00 0.00 41.30 2.71
655 721 0.934496 TTTGTCGAACGCAGGTGAAG 59.066 50.000 0.00 0.00 0.00 3.02
688 754 9.573133 AACGAAGAAAAATATAAGCAGGAAATG 57.427 29.630 0.00 0.00 0.00 2.32
782 848 3.139025 CCATTAATCTCCCATCCACACCT 59.861 47.826 0.00 0.00 0.00 4.00
815 881 4.152647 CCCACTCCACACTATCTATAGCA 58.847 47.826 0.00 0.00 33.68 3.49
1104 1171 2.186903 CGGCGGTGCTATCTGGTT 59.813 61.111 0.00 0.00 0.00 3.67
1173 1240 1.521457 GTGCGGCGAGATCATCCAA 60.521 57.895 12.98 0.00 0.00 3.53
1422 1489 2.430921 GTGGACCTGCTCGTCGTG 60.431 66.667 0.00 0.00 33.30 4.35
1527 1594 4.415150 CTCACCGGCATGGGCTGT 62.415 66.667 0.00 0.00 45.29 4.40
1626 1709 3.181507 GCATTATCTTCTCTGTTGCGCAA 60.182 43.478 21.02 21.02 0.00 4.85
1685 1773 3.568007 TGGATTCAACCAGCACTAACAAC 59.432 43.478 0.00 0.00 34.77 3.32
1688 1776 3.552132 TCAACCAGCACTAACAACTGA 57.448 42.857 0.00 0.00 33.10 3.41
1726 1814 4.807631 TCGCTCGATCCGGGTCCA 62.808 66.667 9.71 0.00 0.00 4.02
1735 1823 1.956629 ATCCGGGTCCAAGCGTAGTG 61.957 60.000 0.00 0.00 0.00 2.74
1781 1870 0.651031 GTTTGAGACGCCCGAATAGC 59.349 55.000 0.00 0.00 0.00 2.97
1853 1957 4.765281 CAATTTATTTGCTGTGCATCCG 57.235 40.909 0.00 0.00 38.76 4.18
1974 2096 6.015856 AGGTAGATGATCTTTCTCGTACCATG 60.016 42.308 0.00 0.00 0.00 3.66
1978 2100 3.767131 TGATCTTTCTCGTACCATGTCCA 59.233 43.478 0.00 0.00 0.00 4.02
2051 2174 1.538876 CCCAGGACAAGGACTCCCA 60.539 63.158 0.00 0.00 33.88 4.37
2052 2175 0.916358 CCCAGGACAAGGACTCCCAT 60.916 60.000 0.00 0.00 33.88 4.00
2054 2177 2.196595 CCAGGACAAGGACTCCCATTA 58.803 52.381 0.00 0.00 33.88 1.90
2063 2186 7.213178 ACAAGGACTCCCATTAAAGATGTAT 57.787 36.000 0.00 0.00 33.88 2.29
2064 2187 8.331931 ACAAGGACTCCCATTAAAGATGTATA 57.668 34.615 0.00 0.00 33.88 1.47
2065 2188 8.211629 ACAAGGACTCCCATTAAAGATGTATAC 58.788 37.037 0.00 0.00 33.88 1.47
2067 2190 8.511748 AGGACTCCCATTAAAGATGTATACAT 57.488 34.615 18.31 18.31 35.34 2.29
2083 2206 5.823570 TGTATACATATTTTTCCCACCCGTG 59.176 40.000 0.08 0.00 0.00 4.94
2093 2216 1.064611 TCCCACCCGTGAACTTTGAAA 60.065 47.619 0.00 0.00 0.00 2.69
2095 2218 1.066454 CCACCCGTGAACTTTGAAACC 59.934 52.381 0.00 0.00 0.00 3.27
2115 2241 2.806244 CCCAAGAAAGTAGACACAACCG 59.194 50.000 0.00 0.00 0.00 4.44
2116 2242 3.493699 CCCAAGAAAGTAGACACAACCGA 60.494 47.826 0.00 0.00 0.00 4.69
2117 2243 3.741344 CCAAGAAAGTAGACACAACCGAG 59.259 47.826 0.00 0.00 0.00 4.63
2118 2244 4.369182 CAAGAAAGTAGACACAACCGAGT 58.631 43.478 0.00 0.00 0.00 4.18
2119 2245 5.508489 CCAAGAAAGTAGACACAACCGAGTA 60.508 44.000 0.00 0.00 0.00 2.59
2120 2246 5.118642 AGAAAGTAGACACAACCGAGTAC 57.881 43.478 0.00 0.00 0.00 2.73
2121 2247 4.581824 AGAAAGTAGACACAACCGAGTACA 59.418 41.667 0.00 0.00 0.00 2.90
2122 2248 4.500603 AAGTAGACACAACCGAGTACAG 57.499 45.455 0.00 0.00 0.00 2.74
2123 2249 3.484407 AGTAGACACAACCGAGTACAGT 58.516 45.455 0.00 0.00 0.00 3.55
2124 2250 4.645535 AGTAGACACAACCGAGTACAGTA 58.354 43.478 0.00 0.00 0.00 2.74
2125 2251 3.911661 AGACACAACCGAGTACAGTAC 57.088 47.619 2.05 2.05 0.00 2.73
2126 2252 3.216800 AGACACAACCGAGTACAGTACA 58.783 45.455 13.37 0.00 0.00 2.90
2127 2253 3.004106 AGACACAACCGAGTACAGTACAC 59.996 47.826 13.37 5.80 0.00 2.90
2128 2254 2.954318 ACACAACCGAGTACAGTACACT 59.046 45.455 13.37 0.00 0.00 3.55
2129 2255 3.382546 ACACAACCGAGTACAGTACACTT 59.617 43.478 13.37 0.00 0.00 3.16
2130 2256 4.142093 ACACAACCGAGTACAGTACACTTT 60.142 41.667 13.37 0.60 0.00 2.66
2131 2257 4.807304 CACAACCGAGTACAGTACACTTTT 59.193 41.667 13.37 0.27 0.00 2.27
2132 2258 5.292589 CACAACCGAGTACAGTACACTTTTT 59.707 40.000 13.37 0.00 0.00 1.94
2171 2297 0.512952 CACTTTGCAGTACACCGAGC 59.487 55.000 0.00 0.00 0.00 5.03
2191 2317 5.556355 AGCGGTACCTTGCTATTTTTAAC 57.444 39.130 12.13 0.00 40.28 2.01
2222 2348 9.753674 ATAAGAAGAACCATAAATTCCAACTCA 57.246 29.630 0.00 0.00 0.00 3.41
2269 2399 1.002868 CACTCACCTGCCTCCCAAG 60.003 63.158 0.00 0.00 0.00 3.61
2288 2418 1.609555 AGACGAGCGGATCCATCTTAC 59.390 52.381 13.41 0.00 0.00 2.34
2297 2430 3.256136 CGGATCCATCTTACCCTGTAGTC 59.744 52.174 13.41 0.00 0.00 2.59
2309 2442 3.251484 CCCTGTAGTCCCATATGACCAT 58.749 50.000 3.65 0.00 35.83 3.55
2310 2443 3.261897 CCCTGTAGTCCCATATGACCATC 59.738 52.174 3.65 0.00 35.83 3.51
2311 2444 3.261897 CCTGTAGTCCCATATGACCATCC 59.738 52.174 3.65 0.00 35.83 3.51
2318 2451 4.080863 GTCCCATATGACCATCCTATCCAC 60.081 50.000 3.65 0.00 0.00 4.02
2326 2459 3.328931 GACCATCCTATCCACCATGTGAT 59.671 47.826 0.00 0.00 35.23 3.06
2337 2470 4.080413 TCCACCATGTGATGCTAGATCAAA 60.080 41.667 0.00 0.00 35.23 2.69
2390 2523 7.010183 GCAGAATAAATGTTAGTAACAGCGAGA 59.990 37.037 19.87 5.38 45.95 4.04
2410 2543 2.112279 TGGTGAAGTTACCTGTCCCT 57.888 50.000 0.00 0.00 41.43 4.20
2554 2690 2.737252 GTTCGCTTTTAGTAGCTGCAGT 59.263 45.455 16.64 4.79 39.03 4.40
2580 2716 1.094073 GCAGTAGCAGATGGGTGCAG 61.094 60.000 0.00 0.00 46.60 4.41
2630 2766 2.260743 GTGGACGGACGAACCTCC 59.739 66.667 0.00 2.59 36.88 4.30
2631 2767 2.116772 TGGACGGACGAACCTCCT 59.883 61.111 0.00 0.00 37.09 3.69
2632 2768 1.975407 TGGACGGACGAACCTCCTC 60.975 63.158 0.00 3.72 37.09 3.71
2633 2769 1.678300 GGACGGACGAACCTCCTCT 60.678 63.158 0.00 0.00 34.98 3.69
2634 2770 1.655885 GGACGGACGAACCTCCTCTC 61.656 65.000 0.00 0.00 34.98 3.20
2651 2787 0.461135 CTCCTCTGCCTCTTCTCTGC 59.539 60.000 0.00 0.00 0.00 4.26
2666 2802 2.514592 TGCCTCTTGCGCCATAGC 60.515 61.111 4.18 1.75 45.60 2.97
2696 2832 0.872021 GCAGAGAGTAATGGCGTCCG 60.872 60.000 0.00 0.00 0.00 4.79
2745 2886 0.458889 CGTCCATGCCAAATTGCCAG 60.459 55.000 0.00 0.00 0.00 4.85
2802 2943 5.331532 CGGAAATGTTTCTTGTTTTTCGCTC 60.332 40.000 5.56 0.00 37.35 5.03
2846 2987 8.030913 TCTAGTCTAGGGGTAAAAATTGATCC 57.969 38.462 7.05 0.00 0.00 3.36
2877 3018 7.599630 ACAATGTGCATGGTAAAAATTGATC 57.400 32.000 0.00 0.00 0.00 2.92
2878 3019 6.594937 ACAATGTGCATGGTAAAAATTGATCC 59.405 34.615 0.00 0.00 0.00 3.36
3705 6994 0.251354 ACATGAGCGCCTTGTGATCT 59.749 50.000 2.29 0.00 32.64 2.75
3732 7021 2.923655 AGCAACTTCACGTACATGATCG 59.076 45.455 0.00 6.22 0.00 3.69
3888 7177 4.899239 CCGTGATGGAGGAGCGGC 62.899 72.222 0.00 0.00 42.00 6.53
3935 7227 2.231529 CGGGGGATGTGTTGTTTTGTA 58.768 47.619 0.00 0.00 0.00 2.41
3936 7228 2.823154 CGGGGGATGTGTTGTTTTGTAT 59.177 45.455 0.00 0.00 0.00 2.29
3937 7229 3.257127 CGGGGGATGTGTTGTTTTGTATT 59.743 43.478 0.00 0.00 0.00 1.89
3938 7230 4.262249 CGGGGGATGTGTTGTTTTGTATTT 60.262 41.667 0.00 0.00 0.00 1.40
3939 7231 5.616270 GGGGGATGTGTTGTTTTGTATTTT 58.384 37.500 0.00 0.00 0.00 1.82
3940 7232 6.516860 CGGGGGATGTGTTGTTTTGTATTTTA 60.517 38.462 0.00 0.00 0.00 1.52
4042 7334 6.887545 AGTGTCCGGTTAATTAATCAATGGAA 59.112 34.615 9.11 0.00 0.00 3.53
4136 7449 2.143925 GGTCTTGCGGATATACCTTGC 58.856 52.381 0.00 0.00 36.31 4.01
4179 7492 1.269448 GTTGCCAACCGACACAATGAT 59.731 47.619 0.00 0.00 0.00 2.45
4184 7497 3.874543 GCCAACCGACACAATGATATACA 59.125 43.478 0.00 0.00 0.00 2.29
4203 10634 2.375174 ACAAGTAAGGGCATCTCCAACA 59.625 45.455 0.00 0.00 36.21 3.33
4233 10664 4.142687 CGTAAATTTTCTCCCGCATCTGTT 60.143 41.667 0.00 0.00 0.00 3.16
4234 10665 4.871933 AAATTTTCTCCCGCATCTGTTT 57.128 36.364 0.00 0.00 0.00 2.83
4243 10674 3.863681 GCATCTGTTTGCGGACAAA 57.136 47.368 0.00 0.00 43.45 2.83
4264 10697 0.387929 GGACCAGTCCGCGAATATGA 59.612 55.000 8.23 0.00 40.36 2.15
4266 10699 1.859080 GACCAGTCCGCGAATATGAAC 59.141 52.381 8.23 0.00 0.00 3.18
4268 10701 1.535226 CCAGTCCGCGAATATGAACGA 60.535 52.381 8.23 0.00 0.00 3.85
4288 10721 2.264794 GAGTCCGCCATCCAACGT 59.735 61.111 0.00 0.00 0.00 3.99
4292 10725 1.228003 TCCGCCATCCAACGTTGTT 60.228 52.632 25.63 11.03 0.00 2.83
4293 10726 0.820074 TCCGCCATCCAACGTTGTTT 60.820 50.000 25.63 10.66 0.00 2.83
4304 10738 2.892373 ACGTTGTTTGCATACATCCG 57.108 45.000 20.28 20.28 0.00 4.18
4310 10744 3.351740 TGTTTGCATACATCCGGACAAT 58.648 40.909 6.12 0.00 0.00 2.71
4366 10800 5.722263 TCGGACGGATTTCATTGTAAGTTA 58.278 37.500 0.00 0.00 0.00 2.24
4368 10802 5.808540 CGGACGGATTTCATTGTAAGTTAGA 59.191 40.000 0.00 0.00 0.00 2.10
4447 10882 9.871175 AAATAAAACATAAACCCTATACCGGAT 57.129 29.630 9.46 0.00 0.00 4.18
4454 10889 3.839323 ACCCTATACCGGATGACCATA 57.161 47.619 9.46 0.00 35.59 2.74
4460 10895 5.768662 CCTATACCGGATGACCATATCGTAT 59.231 44.000 9.46 0.00 35.59 3.06
4468 10903 0.391228 ACCATATCGTATGCGTGGCA 59.609 50.000 10.54 0.00 44.86 4.92
4474 10909 2.813179 CGTATGCGTGGCAGCCTTC 61.813 63.158 14.15 5.04 43.65 3.46
4500 10935 1.063412 CGCATTGTCGTCTTCGTCGA 61.063 55.000 0.00 0.00 38.33 4.20
4537 10972 2.128507 GGTCCCTCCAGCGGTAGAG 61.129 68.421 2.86 2.86 35.97 2.43
4603 11038 0.963856 TCGCAGAGGAACCGCTCTAA 60.964 55.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.970974 GCAGTCAAGTCGGCCAAGC 61.971 63.158 2.24 0.00 0.00 4.01
76 77 3.160585 CCAAGGAGTGGGCAGTCA 58.839 61.111 0.00 0.00 44.64 3.41
91 92 3.182590 AAGAAGCAGCTGACGCCCA 62.183 57.895 20.43 0.00 36.60 5.36
177 192 3.068691 CCTCCTTCGCCTCGTCCA 61.069 66.667 0.00 0.00 0.00 4.02
220 241 4.592192 CCGCTCGCCATGGACGAT 62.592 66.667 24.74 0.00 39.12 3.73
252 285 1.619669 ATTTCCCTTCCTCCCGCCT 60.620 57.895 0.00 0.00 0.00 5.52
302 365 3.327754 CGCGCGAACTATTCCCCG 61.328 66.667 28.94 0.00 0.00 5.73
328 393 1.556564 CACAAACACGAGACAGACGT 58.443 50.000 0.00 0.00 44.83 4.34
474 540 2.452813 CGACCCATTTCGTCTGCGG 61.453 63.158 0.00 0.00 38.89 5.69
495 561 2.484264 CCTTTAAGAGCAACTCCAACGG 59.516 50.000 0.00 0.00 0.00 4.44
568 634 3.895232 TCAGAGGAATTGTAGCTCCAC 57.105 47.619 0.00 0.00 33.83 4.02
580 646 4.136796 CCAATTATGGCGATTCAGAGGAA 58.863 43.478 0.00 0.00 40.58 3.36
688 754 2.677337 GGCTCATGAGAAGCTTCTTCAC 59.323 50.000 29.02 17.24 37.73 3.18
782 848 3.324108 GAGTGGGGTTGCCGGGTA 61.324 66.667 2.18 0.00 0.00 3.69
832 898 2.894765 GCTTAGACCTATGGACCTCCTC 59.105 54.545 0.00 0.00 36.82 3.71
972 1039 2.415168 CAGCGAGGAGAGATCTATCGAC 59.585 54.545 18.08 11.07 37.42 4.20
1102 1169 2.729882 CCTTGTAGCACACGTAGTCAAC 59.270 50.000 0.00 0.00 41.61 3.18
1104 1171 1.271379 CCCTTGTAGCACACGTAGTCA 59.729 52.381 0.00 0.00 41.61 3.41
1173 1240 2.281761 CCCAGCAGCTTGTTCCGT 60.282 61.111 0.00 0.00 0.00 4.69
1422 1489 1.439679 GGGAGAACATGGACACGTTC 58.560 55.000 3.29 3.29 41.48 3.95
1527 1594 4.221422 GCGATGAGGGTGGCGCTA 62.221 66.667 7.64 0.00 45.41 4.26
1626 1709 3.765511 TGGACACTAGCCGTTGTATTAGT 59.234 43.478 0.00 0.00 0.00 2.24
1693 1781 2.733127 CGAGAGCCGAGCGTAAAAA 58.267 52.632 0.00 0.00 41.76 1.94
1694 1782 4.470876 CGAGAGCCGAGCGTAAAA 57.529 55.556 0.00 0.00 41.76 1.52
1726 1814 1.668047 GCTTGTCGTACCACTACGCTT 60.668 52.381 0.00 0.00 44.64 4.68
1783 1872 4.325970 GCTTTTGCCTGCCAATGCAATG 62.326 50.000 8.37 0.00 45.96 2.82
1849 1953 0.674534 GAATAGCTCACCGGACGGAT 59.325 55.000 18.80 0.00 38.96 4.18
1851 1955 0.249073 CAGAATAGCTCACCGGACGG 60.249 60.000 9.46 9.56 42.03 4.79
1853 1957 2.288518 GGATCAGAATAGCTCACCGGAC 60.289 54.545 9.46 0.00 0.00 4.79
1931 2047 1.000731 CCTAGTGCCATCTAGCTCAGC 59.999 57.143 0.00 0.00 36.89 4.26
1974 2096 1.078426 CTCCCGGGTGACAATGGAC 60.078 63.158 22.86 0.00 0.00 4.02
1978 2100 1.358152 TTCTTCTCCCGGGTGACAAT 58.642 50.000 24.67 0.00 0.00 2.71
2054 2177 9.143155 GGGTGGGAAAAATATGTATACATCTTT 57.857 33.333 21.49 19.78 37.76 2.52
2063 2186 4.571369 TCACGGGTGGGAAAAATATGTA 57.429 40.909 0.00 0.00 0.00 2.29
2064 2187 3.443145 TCACGGGTGGGAAAAATATGT 57.557 42.857 0.00 0.00 0.00 2.29
2065 2188 3.761752 AGTTCACGGGTGGGAAAAATATG 59.238 43.478 0.00 0.00 0.00 1.78
2067 2190 3.512219 AGTTCACGGGTGGGAAAAATA 57.488 42.857 0.00 0.00 0.00 1.40
2069 2192 2.146920 AAGTTCACGGGTGGGAAAAA 57.853 45.000 0.00 0.00 0.00 1.94
2078 2201 1.394618 TGGGTTTCAAAGTTCACGGG 58.605 50.000 0.00 0.00 0.00 5.28
2083 2206 7.148137 TGTCTACTTTCTTGGGTTTCAAAGTTC 60.148 37.037 1.53 0.00 39.32 3.01
2093 2216 3.743269 CGGTTGTGTCTACTTTCTTGGGT 60.743 47.826 0.00 0.00 0.00 4.51
2095 2218 3.724374 TCGGTTGTGTCTACTTTCTTGG 58.276 45.455 0.00 0.00 0.00 3.61
2130 2256 3.857157 ACTGTACTGCTCCCTCAAAAA 57.143 42.857 0.00 0.00 0.00 1.94
2131 2257 3.644265 TGTACTGTACTGCTCCCTCAAAA 59.356 43.478 17.98 0.00 0.00 2.44
2132 2258 3.006537 GTGTACTGTACTGCTCCCTCAAA 59.993 47.826 17.98 0.00 0.00 2.69
2133 2259 2.561419 GTGTACTGTACTGCTCCCTCAA 59.439 50.000 17.98 0.00 0.00 3.02
2134 2260 2.168496 GTGTACTGTACTGCTCCCTCA 58.832 52.381 17.98 0.00 0.00 3.86
2135 2261 2.448453 AGTGTACTGTACTGCTCCCTC 58.552 52.381 17.98 0.97 0.00 4.30
2136 2262 2.606751 AGTGTACTGTACTGCTCCCT 57.393 50.000 17.98 3.18 0.00 4.20
2137 2263 3.326747 CAAAGTGTACTGTACTGCTCCC 58.673 50.000 17.98 1.20 0.00 4.30
2138 2264 2.737252 GCAAAGTGTACTGTACTGCTCC 59.263 50.000 17.98 6.23 0.00 4.70
2139 2265 3.390135 TGCAAAGTGTACTGTACTGCTC 58.610 45.455 22.34 10.97 0.00 4.26
2140 2266 3.181465 ACTGCAAAGTGTACTGTACTGCT 60.181 43.478 22.34 16.03 0.00 4.24
2171 2297 5.329493 GCTGTTAAAAATAGCAAGGTACCG 58.671 41.667 6.18 0.00 44.08 4.02
2191 2317 8.469200 TGGAATTTATGGTTCTTCTTATTGCTG 58.531 33.333 0.00 0.00 0.00 4.41
2198 2324 8.477419 TTGAGTTGGAATTTATGGTTCTTCTT 57.523 30.769 0.00 0.00 0.00 2.52
2199 2325 8.477419 TTTGAGTTGGAATTTATGGTTCTTCT 57.523 30.769 0.00 0.00 0.00 2.85
2200 2326 9.541143 TTTTTGAGTTGGAATTTATGGTTCTTC 57.459 29.630 0.00 0.00 0.00 2.87
2233 2359 3.356290 AGTGGGCACTGAATTTATGGTC 58.644 45.455 0.00 0.00 40.75 4.02
2246 2376 3.909086 GAGGCAGGTGAGTGGGCAC 62.909 68.421 0.00 0.00 38.05 5.01
2269 2399 1.336056 GGTAAGATGGATCCGCTCGTC 60.336 57.143 7.39 0.24 0.00 4.20
2288 2418 2.689658 TGGTCATATGGGACTACAGGG 58.310 52.381 2.13 0.00 37.91 4.45
2297 2430 3.200825 GGTGGATAGGATGGTCATATGGG 59.799 52.174 2.13 0.00 0.00 4.00
2309 2442 2.411583 AGCATCACATGGTGGATAGGA 58.588 47.619 0.00 0.00 39.92 2.94
2310 2443 2.945080 AGCATCACATGGTGGATAGG 57.055 50.000 0.00 0.00 39.92 2.57
2311 2444 4.879197 TCTAGCATCACATGGTGGATAG 57.121 45.455 0.00 0.00 42.16 2.08
2318 2451 6.206829 ACATGATTTGATCTAGCATCACATGG 59.793 38.462 21.60 13.06 35.82 3.66
2326 2459 6.485648 CCTTCATCACATGATTTGATCTAGCA 59.514 38.462 0.00 0.00 39.39 3.49
2337 2470 2.242965 TCTTGGCCCTTCATCACATGAT 59.757 45.455 0.00 0.00 39.39 2.45
2580 2716 0.104304 ATATTCACGCACCGTCTCCC 59.896 55.000 0.00 0.00 38.32 4.30
2591 2727 2.027569 CGTCCACGTCAACATATTCACG 59.972 50.000 0.00 0.00 38.24 4.35
2630 2766 2.026641 CAGAGAAGAGGCAGAGGAGAG 58.973 57.143 0.00 0.00 0.00 3.20
2631 2767 1.959508 GCAGAGAAGAGGCAGAGGAGA 60.960 57.143 0.00 0.00 0.00 3.71
2632 2768 0.461135 GCAGAGAAGAGGCAGAGGAG 59.539 60.000 0.00 0.00 0.00 3.69
2633 2769 0.975040 GGCAGAGAAGAGGCAGAGGA 60.975 60.000 0.00 0.00 0.00 3.71
2634 2770 0.977108 AGGCAGAGAAGAGGCAGAGG 60.977 60.000 0.00 0.00 0.00 3.69
2666 2802 4.427096 TTACTCTCTGCTCTTCACTTCG 57.573 45.455 0.00 0.00 0.00 3.79
2778 2919 4.502645 AGCGAAAAACAAGAAACATTTCCG 59.497 37.500 0.68 0.00 37.92 4.30
2802 2943 6.787225 ACTAGAAAGTACTACAGATTCGCAG 58.213 40.000 0.00 2.19 32.84 5.18
2846 2987 3.281341 ACCATGCACATTGTAAACACG 57.719 42.857 0.00 0.00 0.00 4.49
3705 6994 2.046009 TACGTGAAGTTGCTGGGCCA 62.046 55.000 5.85 5.85 0.00 5.36
3732 7021 8.125448 ACCGAGTATACGTAGAAATTAAGTGAC 58.875 37.037 0.08 0.00 0.00 3.67
3888 7177 4.201812 CCCACAGAAGTGTACAATAATGCG 60.202 45.833 0.00 0.00 44.39 4.73
3935 7227 9.418045 CATGGACACCGAAAACTTTAATAAAAT 57.582 29.630 0.00 0.00 0.00 1.82
3936 7228 8.414778 ACATGGACACCGAAAACTTTAATAAAA 58.585 29.630 0.00 0.00 0.00 1.52
3937 7229 7.942990 ACATGGACACCGAAAACTTTAATAAA 58.057 30.769 0.00 0.00 0.00 1.40
3938 7230 7.513371 ACATGGACACCGAAAACTTTAATAA 57.487 32.000 0.00 0.00 0.00 1.40
3939 7231 7.513371 AACATGGACACCGAAAACTTTAATA 57.487 32.000 0.00 0.00 0.00 0.98
3940 7232 6.399639 AACATGGACACCGAAAACTTTAAT 57.600 33.333 0.00 0.00 0.00 1.40
3973 7265 5.913137 AACAACACAACCAATTCTTCAGA 57.087 34.783 0.00 0.00 0.00 3.27
4136 7449 9.545611 CAACAACAAAAAGAAGAAAATGAAAGG 57.454 29.630 0.00 0.00 0.00 3.11
4179 7492 5.427157 TGTTGGAGATGCCCTTACTTGTATA 59.573 40.000 0.00 0.00 34.97 1.47
4184 7497 2.619074 GCTGTTGGAGATGCCCTTACTT 60.619 50.000 0.00 0.00 34.97 2.24
4203 10634 2.823747 GGGAGAAAATTTACGGGTTGCT 59.176 45.455 0.00 0.00 0.00 3.91
4233 10664 1.228124 CTGGTCCCTTTGTCCGCAA 60.228 57.895 0.00 0.00 0.00 4.85
4234 10665 2.391724 GACTGGTCCCTTTGTCCGCA 62.392 60.000 0.00 0.00 0.00 5.69
4243 10674 0.759436 ATATTCGCGGACTGGTCCCT 60.759 55.000 6.13 0.00 46.96 4.20
4264 10697 2.683933 ATGGCGGACTCCCTCGTT 60.684 61.111 0.00 0.00 0.00 3.85
4266 10699 3.917760 GGATGGCGGACTCCCTCG 61.918 72.222 0.00 0.00 0.00 4.63
4268 10701 2.285368 TTGGATGGCGGACTCCCT 60.285 61.111 0.00 0.00 0.00 4.20
4288 10721 2.784347 TGTCCGGATGTATGCAAACAA 58.216 42.857 7.81 0.00 32.02 2.83
4292 10725 6.707440 AAATTATTGTCCGGATGTATGCAA 57.293 33.333 7.81 6.38 0.00 4.08
4293 10726 7.809546 TTAAATTATTGTCCGGATGTATGCA 57.190 32.000 7.81 0.00 0.00 3.96
4304 10738 8.819974 TCGTCCGATTAGTTTAAATTATTGTCC 58.180 33.333 0.00 0.00 0.00 4.02
4424 10859 7.933033 GTCATCCGGTATAGGGTTTATGTTTTA 59.067 37.037 0.00 0.00 0.00 1.52
4430 10865 4.495565 TGGTCATCCGGTATAGGGTTTAT 58.504 43.478 0.00 0.00 36.30 1.40
4447 10882 1.604438 GCCACGCATACGATATGGTCA 60.604 52.381 0.00 0.00 43.93 4.02
4454 10889 2.588877 GGCTGCCACGCATACGAT 60.589 61.111 15.17 0.00 43.93 3.73
4500 10935 1.640428 CACTACAACGACGATGGCAT 58.360 50.000 10.02 0.00 0.00 4.40
4513 10948 1.982395 CGCTGGAGGGACCACTACA 60.982 63.158 0.00 0.00 44.64 2.74
4516 10951 3.233919 TACCGCTGGAGGGACCACT 62.234 63.158 1.50 0.00 44.64 4.00
4553 10988 1.525995 CACCGGACAAGGCTGTTGT 60.526 57.895 9.46 4.88 35.30 3.32
4588 11023 1.006162 AGGAGTTAGAGCGGTTCCTCT 59.994 52.381 0.00 0.00 44.12 3.69
4594 11029 0.037232 GCAACAGGAGTTAGAGCGGT 60.037 55.000 0.00 0.00 35.85 5.68


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

AutoCloner maintained by Alex Coulton.