Multiple sequence alignment - TraesCS7B01G364100

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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 TraesCS7B01G364100 chr7B 100.000 3933 0 0 1 3933 627057755 627053823 0.000000e+00 7263.0
1 TraesCS7B01G364100 chr7B 95.050 101 3 2 2174 2274 697607726 697607628 1.460000e-34 158.0
2 TraesCS7B01G364100 chr7B 77.711 166 34 3 3667 3830 55030198 55030362 8.990000e-17 99.0
3 TraesCS7B01G364100 chr7D 94.824 2106 69 14 1 2091 571199029 571196949 0.000000e+00 3249.0
4 TraesCS7B01G364100 chr7D 91.872 972 49 19 2271 3222 571196888 571195927 0.000000e+00 1330.0
5 TraesCS7B01G364100 chr7D 83.067 750 71 23 3219 3933 571195434 571194706 7.170000e-177 630.0
6 TraesCS7B01G364100 chr7D 84.946 93 9 5 3291 3378 431077424 431077332 5.410000e-14 89.8
7 TraesCS7B01G364100 chr7A 94.523 1990 85 8 1 1981 660411059 660409085 0.000000e+00 3049.0
8 TraesCS7B01G364100 chr7A 93.573 918 37 15 2260 3159 660408990 660408077 0.000000e+00 1349.0
9 TraesCS7B01G364100 chr7A 84.652 632 64 19 3158 3762 660407973 660407348 2.020000e-167 599.0
10 TraesCS7B01G364100 chr6B 90.980 765 56 8 1213 1974 699029750 699028996 0.000000e+00 1018.0
11 TraesCS7B01G364100 chr6B 90.783 217 18 2 2273 2489 699028652 699028438 4.970000e-74 289.0
12 TraesCS7B01G364100 chr2B 96.970 99 2 1 2166 2264 142245678 142245581 8.740000e-37 165.0
13 TraesCS7B01G364100 chr4B 97.872 94 2 0 2172 2265 262945667 262945760 3.140000e-36 163.0
14 TraesCS7B01G364100 chr4B 96.939 98 2 1 2166 2263 603516250 603516346 3.140000e-36 163.0
15 TraesCS7B01G364100 chr1B 94.393 107 4 2 2164 2269 660748492 660748387 3.140000e-36 163.0
16 TraesCS7B01G364100 chr1B 94.175 103 4 2 2167 2269 651554677 651554577 5.260000e-34 156.0
17 TraesCS7B01G364100 chr6D 92.035 113 7 2 2159 2271 216847263 216847373 1.460000e-34 158.0
18 TraesCS7B01G364100 chr3B 95.050 101 3 2 2172 2272 250575928 250576026 1.460000e-34 158.0
19 TraesCS7B01G364100 chr3B 94.595 37 2 0 3342 3378 38792627 38792591 1.530000e-04 58.4
20 TraesCS7B01G364100 chr1D 88.525 122 11 3 2143 2261 62864387 62864508 1.140000e-30 145.0
21 TraesCS7B01G364100 chr2D 90.566 53 2 2 3753 3803 378766523 378766472 2.540000e-07 67.6
22 TraesCS7B01G364100 chr3A 100.000 28 0 0 3756 3783 90295317 90295344 7.000000e-03 52.8


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 TraesCS7B01G364100 chr7B 627053823 627057755 3932 True 7263.000000 7263 100.0000 1 3933 1 chr7B.!!$R1 3932
1 TraesCS7B01G364100 chr7D 571194706 571199029 4323 True 1736.333333 3249 89.9210 1 3933 3 chr7D.!!$R2 3932
2 TraesCS7B01G364100 chr7A 660407348 660411059 3711 True 1665.666667 3049 90.9160 1 3762 3 chr7A.!!$R1 3761
3 TraesCS7B01G364100 chr6B 699028438 699029750 1312 True 653.500000 1018 90.8815 1213 2489 2 chr6B.!!$R1 1276

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
182 184 1.003116 CTGTGCAAAGCTGTCAGTGAC 60.003 52.381 16.68 16.68 0.00 3.67 F
1038 1061 0.949105 TTTTCAAGAGGACGAGCGGC 60.949 55.000 0.00 0.00 0.00 6.53 F
2117 2200 0.475475 CAAGGGCTGCATAGGGATGA 59.525 55.000 0.50 0.00 34.73 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1594 0.032540 GAAGGGTTTGTGCAAGGCTG 59.967 55.0 0.00 0.0 0.0 4.85 R
2498 2719 0.106719 ATACAATGGTTCAGGCCGGG 60.107 55.0 2.18 0.0 0.0 5.73 R
3279 4120 0.033228 TGCATTTTGAAACCGGGCTG 59.967 50.0 6.32 0.0 0.0 4.85 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 9.933723 CAAAGAGACCATTTGGATTAGAAAAAT 57.066 29.630 3.01 0.00 38.94 1.82
43 44 8.298729 AGAGACCATTTGGATTAGAAAAATCC 57.701 34.615 3.01 9.38 44.99 3.01
182 184 1.003116 CTGTGCAAAGCTGTCAGTGAC 60.003 52.381 16.68 16.68 0.00 3.67
210 212 4.069304 TGATGGGTAAAACTCCAGAAACG 58.931 43.478 0.00 0.00 36.38 3.60
256 258 3.826157 TGCTTAAGTGGCTTTGCTGTTAT 59.174 39.130 4.02 0.00 0.00 1.89
262 264 1.477700 TGGCTTTGCTGTTATGATGGC 59.522 47.619 0.00 0.00 0.00 4.40
339 343 3.377172 CCTCCACTGTTAAATTTAGCCCG 59.623 47.826 9.27 3.89 0.00 6.13
340 344 2.750712 TCCACTGTTAAATTTAGCCCGC 59.249 45.455 9.27 0.00 0.00 6.13
345 349 5.637387 CACTGTTAAATTTAGCCCGCAATTT 59.363 36.000 9.27 3.97 36.69 1.82
350 354 8.035394 TGTTAAATTTAGCCCGCAATTTATGAA 58.965 29.630 9.27 0.00 35.67 2.57
436 440 3.439129 GCAAACTACCCGAGCAGTATTTT 59.561 43.478 0.00 0.00 0.00 1.82
460 464 6.436843 AACTTGAATTCTGTGTTTCGACTT 57.563 33.333 7.05 0.00 0.00 3.01
472 476 9.491675 TCTGTGTTTCGACTTTTATTATTACCA 57.508 29.630 0.00 0.00 0.00 3.25
540 544 9.154847 TGCATATAGAATATCCGAGTCAAAATG 57.845 33.333 0.00 0.00 0.00 2.32
710 725 5.772521 ACCTAAAATGTTTGACTCACATGC 58.227 37.500 0.00 0.00 34.97 4.06
1038 1061 0.949105 TTTTCAAGAGGACGAGCGGC 60.949 55.000 0.00 0.00 0.00 6.53
1499 1525 7.905265 TCTCTGATATTTCCCATGAGAATCTC 58.095 38.462 2.75 2.75 34.92 2.75
1544 1570 2.637947 GAAGGAAGCCACAAGATCCTC 58.362 52.381 0.00 0.00 41.39 3.71
1609 1635 8.370940 CCTTCTAGGTAGATTATCATTGCTGAA 58.629 37.037 0.00 0.00 31.32 3.02
1649 1675 7.765695 TGTTCCTAGAAAAATTTCAGATGCT 57.234 32.000 8.47 0.00 39.61 3.79
1706 1732 4.146058 CGGCATAGCAGCATCCAA 57.854 55.556 0.00 0.00 35.83 3.53
1760 1786 1.538876 TGTTGCCCAGGGACTAGCT 60.539 57.895 10.89 0.00 37.72 3.32
1958 1984 6.093495 CCATTTAATCGAACCTGTCTGCTTTA 59.907 38.462 0.00 0.00 0.00 1.85
1962 1988 4.859304 TCGAACCTGTCTGCTTTACTAA 57.141 40.909 0.00 0.00 0.00 2.24
1975 2006 7.537649 GTCTGCTTTACTAAATGTTTACTTGCC 59.462 37.037 0.00 0.00 0.00 4.52
1976 2007 6.375377 TGCTTTACTAAATGTTTACTTGCCG 58.625 36.000 0.00 0.00 0.00 5.69
1977 2008 6.016943 TGCTTTACTAAATGTTTACTTGCCGT 60.017 34.615 0.00 0.00 0.00 5.68
1978 2009 6.859508 GCTTTACTAAATGTTTACTTGCCGTT 59.140 34.615 0.00 0.00 0.00 4.44
1979 2010 7.380333 GCTTTACTAAATGTTTACTTGCCGTTT 59.620 33.333 0.00 0.00 0.00 3.60
1980 2011 9.240159 CTTTACTAAATGTTTACTTGCCGTTTT 57.760 29.630 0.00 0.00 0.00 2.43
1981 2012 8.563289 TTACTAAATGTTTACTTGCCGTTTTG 57.437 30.769 0.00 0.00 0.00 2.44
1982 2013 5.980715 ACTAAATGTTTACTTGCCGTTTTGG 59.019 36.000 0.00 0.00 42.50 3.28
1983 2014 2.873133 TGTTTACTTGCCGTTTTGGG 57.127 45.000 0.00 0.00 38.63 4.12
1984 2015 1.409427 TGTTTACTTGCCGTTTTGGGG 59.591 47.619 0.00 0.00 38.63 4.96
1985 2016 1.409790 GTTTACTTGCCGTTTTGGGGT 59.590 47.619 0.00 0.00 38.63 4.95
1986 2017 2.622470 GTTTACTTGCCGTTTTGGGGTA 59.378 45.455 0.00 0.00 38.63 3.69
1987 2018 2.653234 TACTTGCCGTTTTGGGGTAA 57.347 45.000 0.00 0.00 38.63 2.85
1988 2019 1.777941 ACTTGCCGTTTTGGGGTAAA 58.222 45.000 0.00 0.00 38.63 2.01
1989 2020 2.108970 ACTTGCCGTTTTGGGGTAAAA 58.891 42.857 0.00 0.00 38.63 1.52
1990 2021 2.500504 ACTTGCCGTTTTGGGGTAAAAA 59.499 40.909 0.00 0.00 39.79 1.94
2066 2097 7.496529 TGTTAGTTTGTCTGATCCTTTGAAG 57.503 36.000 0.00 0.00 0.00 3.02
2092 2175 2.891580 TGGGTGATAGGCTCTTATCGAC 59.108 50.000 0.00 0.00 33.63 4.20
2093 2176 2.095161 GGGTGATAGGCTCTTATCGACG 60.095 54.545 0.00 0.00 33.63 5.12
2103 2186 3.372954 CTCTTATCGACGTAAGCAAGGG 58.627 50.000 10.47 0.00 45.62 3.95
2104 2187 1.859080 CTTATCGACGTAAGCAAGGGC 59.141 52.381 0.00 0.00 45.62 5.19
2117 2200 0.475475 CAAGGGCTGCATAGGGATGA 59.525 55.000 0.50 0.00 34.73 2.92
2119 2202 2.306805 CAAGGGCTGCATAGGGATGATA 59.693 50.000 0.50 0.00 34.73 2.15
2185 2402 9.862149 AAAATGAAAATATTATACTCCCTCCGT 57.138 29.630 0.00 0.00 0.00 4.69
2186 2403 9.862149 AAATGAAAATATTATACTCCCTCCGTT 57.138 29.630 0.00 0.00 0.00 4.44
2187 2404 9.503399 AATGAAAATATTATACTCCCTCCGTTC 57.497 33.333 0.00 0.00 0.00 3.95
2188 2405 7.447594 TGAAAATATTATACTCCCTCCGTTCC 58.552 38.462 0.00 0.00 0.00 3.62
2189 2406 7.071447 TGAAAATATTATACTCCCTCCGTTCCA 59.929 37.037 0.00 0.00 0.00 3.53
2190 2407 7.383156 AAATATTATACTCCCTCCGTTCCAA 57.617 36.000 0.00 0.00 0.00 3.53
2191 2408 7.383156 AATATTATACTCCCTCCGTTCCAAA 57.617 36.000 0.00 0.00 0.00 3.28
2192 2409 5.703730 ATTATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
2193 2410 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
2194 2411 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
2195 2412 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2196 2413 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2197 2414 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2198 2415 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2199 2416 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2200 2417 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
2201 2418 4.757149 CCCTCCGTTCCAAAATAGATGATC 59.243 45.833 0.00 0.00 0.00 2.92
2202 2419 4.757149 CCTCCGTTCCAAAATAGATGATCC 59.243 45.833 0.00 0.00 0.00 3.36
2203 2420 5.366482 TCCGTTCCAAAATAGATGATCCA 57.634 39.130 0.00 0.00 0.00 3.41
2204 2421 5.750524 TCCGTTCCAAAATAGATGATCCAA 58.249 37.500 0.00 0.00 0.00 3.53
2205 2422 5.588648 TCCGTTCCAAAATAGATGATCCAAC 59.411 40.000 0.00 0.00 0.00 3.77
2206 2423 5.590259 CCGTTCCAAAATAGATGATCCAACT 59.410 40.000 0.00 0.00 0.00 3.16
2207 2424 6.095440 CCGTTCCAAAATAGATGATCCAACTT 59.905 38.462 0.00 0.00 0.00 2.66
2208 2425 7.362920 CCGTTCCAAAATAGATGATCCAACTTT 60.363 37.037 0.00 0.00 0.00 2.66
2209 2426 7.485913 CGTTCCAAAATAGATGATCCAACTTTG 59.514 37.037 0.00 0.00 0.00 2.77
2210 2427 8.306761 GTTCCAAAATAGATGATCCAACTTTGT 58.693 33.333 0.00 0.00 0.00 2.83
2211 2428 9.527157 TTCCAAAATAGATGATCCAACTTTGTA 57.473 29.630 0.00 0.00 0.00 2.41
2212 2429 8.956426 TCCAAAATAGATGATCCAACTTTGTAC 58.044 33.333 0.00 0.00 0.00 2.90
2213 2430 8.960591 CCAAAATAGATGATCCAACTTTGTACT 58.039 33.333 0.00 0.00 0.00 2.73
2246 2463 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2247 2464 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2248 2465 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2249 2466 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2250 2467 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2251 2468 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2252 2469 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2253 2470 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2254 2471 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2255 2472 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2256 2473 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2257 2474 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2258 2475 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2293 2510 9.692325 AATTAGATATCTCCTCTGTTGCTTTTT 57.308 29.630 8.95 0.00 0.00 1.94
2303 2520 5.296780 CCTCTGTTGCTTTTTCTCACTGTAA 59.703 40.000 0.00 0.00 0.00 2.41
2304 2521 6.183360 CCTCTGTTGCTTTTTCTCACTGTAAA 60.183 38.462 0.00 0.00 0.00 2.01
2446 2663 6.034591 CACTGATACAAAACTACCCTACGAG 58.965 44.000 0.00 0.00 0.00 4.18
2473 2694 7.487822 TCAGATTCTTCTTGAGAAGGTACAT 57.512 36.000 18.01 7.72 46.99 2.29
2497 2718 6.542821 TGACCCTGTTCTAAATTGTTCATCT 58.457 36.000 0.00 0.00 0.00 2.90
2498 2719 6.655003 TGACCCTGTTCTAAATTGTTCATCTC 59.345 38.462 0.00 0.00 0.00 2.75
2499 2720 5.946377 ACCCTGTTCTAAATTGTTCATCTCC 59.054 40.000 0.00 0.00 0.00 3.71
2500 2721 5.358160 CCCTGTTCTAAATTGTTCATCTCCC 59.642 44.000 0.00 0.00 0.00 4.30
2502 2723 4.941263 TGTTCTAAATTGTTCATCTCCCGG 59.059 41.667 0.00 0.00 0.00 5.73
2504 2725 1.474330 AAATTGTTCATCTCCCGGCC 58.526 50.000 0.00 0.00 0.00 6.13
2505 2726 0.625849 AATTGTTCATCTCCCGGCCT 59.374 50.000 0.00 0.00 0.00 5.19
2506 2727 0.107017 ATTGTTCATCTCCCGGCCTG 60.107 55.000 0.00 0.00 0.00 4.85
2507 2728 1.198094 TTGTTCATCTCCCGGCCTGA 61.198 55.000 0.00 0.00 0.00 3.86
2508 2729 1.198094 TGTTCATCTCCCGGCCTGAA 61.198 55.000 0.00 0.00 0.00 3.02
2509 2730 0.744771 GTTCATCTCCCGGCCTGAAC 60.745 60.000 15.14 15.14 40.27 3.18
2511 2732 2.285368 ATCTCCCGGCCTGAACCA 60.285 61.111 0.00 0.00 0.00 3.67
2513 2734 1.281925 ATCTCCCGGCCTGAACCATT 61.282 55.000 0.00 0.00 0.00 3.16
2516 2737 1.202099 TCCCGGCCTGAACCATTGTA 61.202 55.000 0.00 0.00 0.00 2.41
2517 2738 0.106719 CCCGGCCTGAACCATTGTAT 60.107 55.000 0.00 0.00 0.00 2.29
2519 2740 2.099405 CCGGCCTGAACCATTGTATTT 58.901 47.619 0.00 0.00 0.00 1.40
2520 2741 3.283751 CCGGCCTGAACCATTGTATTTA 58.716 45.455 0.00 0.00 0.00 1.40
2522 2743 4.158764 CCGGCCTGAACCATTGTATTTAAA 59.841 41.667 0.00 0.00 0.00 1.52
2523 2744 5.336849 CCGGCCTGAACCATTGTATTTAAAA 60.337 40.000 0.00 0.00 0.00 1.52
2524 2745 6.337356 CGGCCTGAACCATTGTATTTAAAAT 58.663 36.000 0.00 0.00 0.00 1.82
2525 2746 7.416890 CCGGCCTGAACCATTGTATTTAAAATA 60.417 37.037 0.00 0.00 0.00 1.40
2526 2747 8.141268 CGGCCTGAACCATTGTATTTAAAATAT 58.859 33.333 0.00 0.00 0.00 1.28
2527 2748 9.476202 GGCCTGAACCATTGTATTTAAAATATC 57.524 33.333 0.00 0.00 0.00 1.63
2550 2783 8.915057 ATCAAGATTACTGATTACCAATCCTG 57.085 34.615 0.00 0.00 37.09 3.86
2797 3030 2.359967 CCGGGACTTCAGGGACCTC 61.360 68.421 0.00 0.00 0.00 3.85
2905 3138 2.607750 ACCCGCACCTCCATCACT 60.608 61.111 0.00 0.00 0.00 3.41
3085 3319 8.515414 GCCTTCATACTTTCATTCACTTTACTT 58.485 33.333 0.00 0.00 0.00 2.24
3135 3375 8.792633 TGATTGTTTCTCTGTATAAAAGGGTTG 58.207 33.333 0.00 0.00 0.00 3.77
3182 3526 2.688507 ACCAAGCTCATGTAGTTCACG 58.311 47.619 0.00 0.00 0.00 4.35
3213 3557 0.392998 CTCCCCCAAAGGTCATCACG 60.393 60.000 0.00 0.00 0.00 4.35
3225 4066 2.029020 GGTCATCACGCAGCCTATATGA 60.029 50.000 0.00 0.00 0.00 2.15
3230 4071 4.541973 TCACGCAGCCTATATGAATCAT 57.458 40.909 0.00 0.00 0.00 2.45
3246 4087 4.332543 TGAATCATTGTATGCACTTCGACC 59.667 41.667 0.00 0.00 0.00 4.79
3279 4120 0.246635 TTGGAGACCGAGCTACAAGC 59.753 55.000 0.00 0.00 42.84 4.01
3283 4124 1.811679 GACCGAGCTACAAGCAGCC 60.812 63.158 1.22 0.00 45.56 4.85
3304 4146 3.188254 CCCGGTTTCAAAATGCATTTTCC 59.812 43.478 29.92 25.38 37.86 3.13
3349 4193 8.637196 TTTTTGTGAACACCCATACACATATA 57.363 30.769 0.00 0.00 41.67 0.86
3380 4224 8.741101 TGTATCTGCAAAATTTCATAACACAC 57.259 30.769 0.00 0.00 0.00 3.82
3382 4226 7.878477 ATCTGCAAAATTTCATAACACACTG 57.122 32.000 0.00 0.00 0.00 3.66
3383 4227 6.215121 TCTGCAAAATTTCATAACACACTGG 58.785 36.000 0.00 0.00 0.00 4.00
3384 4228 4.749099 TGCAAAATTTCATAACACACTGGC 59.251 37.500 0.00 0.00 0.00 4.85
3385 4229 4.143347 GCAAAATTTCATAACACACTGGCG 60.143 41.667 0.00 0.00 0.00 5.69
3387 4231 3.829886 ATTTCATAACACACTGGCGTG 57.170 42.857 7.71 7.71 46.63 5.34
3388 4232 0.871722 TTCATAACACACTGGCGTGC 59.128 50.000 8.93 0.00 45.10 5.34
3453 4312 1.486726 TGTTGTTGGGCCGGAATTTTT 59.513 42.857 5.05 0.00 0.00 1.94
3501 4364 8.508800 AATATTTTCAAACGTTTATTCACGCA 57.491 26.923 14.20 0.00 44.37 5.24
3537 4400 9.515226 AACATGTACAGTATAAGTTTCCATGTT 57.485 29.630 12.71 12.71 34.74 2.71
3581 4458 8.346476 TGACATTTGTTTTTCTTCAAATACCG 57.654 30.769 0.00 0.00 40.70 4.02
3588 4465 0.544697 TCTTCAAATACCGAGCCCCC 59.455 55.000 0.00 0.00 0.00 5.40
3589 4466 0.546598 CTTCAAATACCGAGCCCCCT 59.453 55.000 0.00 0.00 0.00 4.79
3601 4478 4.052518 CCCCCTGGAGCTTGGGTG 62.053 72.222 16.05 4.54 41.82 4.61
3626 4503 5.474189 CCATTGGCATTTTCCATTTCAACTT 59.526 36.000 0.00 0.00 35.77 2.66
3640 4517 6.311935 CCATTTCAACTTGCAGTATTCCATTG 59.688 38.462 0.00 0.00 0.00 2.82
3675 4552 0.486879 ATTCTTCCCCCAAACTGCCA 59.513 50.000 0.00 0.00 0.00 4.92
3676 4553 0.178964 TTCTTCCCCCAAACTGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
3739 4616 5.360714 CCAGCCCATTTGTGTAGATAACATT 59.639 40.000 0.00 0.00 41.10 2.71
3763 4640 3.732048 ACTATTCCATCCGGTTTTGGT 57.268 42.857 16.69 5.40 34.48 3.67
3772 4649 4.566070 CCATCCGGTTTTGGTAACCTTCTA 60.566 45.833 0.00 0.00 38.15 2.10
3905 4787 7.588143 ATCGTGTTTTCAAATTTTGTTCACA 57.412 28.000 8.89 7.29 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.634118 TCCAAATGGTCTCTTTGATTGACT 58.366 37.500 0.00 0.00 35.99 3.41
41 42 2.589157 CCGTTAGGCCACCACAGGA 61.589 63.158 5.01 0.00 0.00 3.86
42 43 2.046314 CCGTTAGGCCACCACAGG 60.046 66.667 5.01 0.00 0.00 4.00
182 184 4.069304 TGGAGTTTTACCCATCAGAAACG 58.931 43.478 0.00 0.00 37.15 3.60
256 258 3.338249 GTGCTCTTAGAAACTGCCATCA 58.662 45.455 0.00 0.00 0.00 3.07
262 264 3.026630 TGTCGGTGCTCTTAGAAACTG 57.973 47.619 0.00 0.00 0.00 3.16
339 343 8.512138 ACTAACAGGTAACAGTTCATAAATTGC 58.488 33.333 0.00 0.00 43.62 3.56
340 344 9.825972 CACTAACAGGTAACAGTTCATAAATTG 57.174 33.333 0.00 0.00 43.62 2.32
345 349 8.426489 AGAAACACTAACAGGTAACAGTTCATA 58.574 33.333 0.00 0.00 43.62 2.15
350 354 6.229936 TCAGAAACACTAACAGGTAACAGT 57.770 37.500 0.00 0.00 38.34 3.55
436 440 7.548196 AAGTCGAAACACAGAATTCAAGTTA 57.452 32.000 8.44 0.00 0.00 2.24
505 509 7.124147 TCGGATATTCTATATGCACAAGATGGA 59.876 37.037 0.00 0.00 0.00 3.41
540 544 5.859521 TGCCAATGTTTAAATTGACATGC 57.140 34.783 3.59 0.00 39.46 4.06
562 566 6.344500 GTCAGAATGTCACATTGGAGACTAT 58.656 40.000 8.05 0.00 35.87 2.12
1038 1061 0.307760 GACCAGTTTGTTGCTGACCG 59.692 55.000 0.00 0.00 36.12 4.79
1499 1525 2.226437 ACAACAGCCATAAAGCTTGACG 59.774 45.455 0.00 0.00 42.61 4.35
1568 1594 0.032540 GAAGGGTTTGTGCAAGGCTG 59.967 55.000 0.00 0.00 0.00 4.85
1609 1635 7.974504 TCTAGGAACAAAAGAATACAGAGGTT 58.025 34.615 0.00 0.00 0.00 3.50
1649 1675 3.561313 GGCAAGGACCAAGAAGGATTACA 60.561 47.826 0.00 0.00 41.22 2.41
1706 1732 5.723672 TCACTCGAGTTCTCCAGTTAAAT 57.276 39.130 17.26 0.00 0.00 1.40
1760 1786 0.899720 GGACACCGTCATGGAGGTAA 59.100 55.000 11.70 0.00 42.00 2.85
1784 1810 3.569849 TCCCGGTGGACAACATGT 58.430 55.556 0.00 0.00 35.03 3.21
1934 1960 5.551760 AAGCAGACAGGTTCGATTAAATG 57.448 39.130 0.00 0.00 30.75 2.32
1958 1984 5.980715 CCAAAACGGCAAGTAAACATTTAGT 59.019 36.000 0.00 0.00 0.00 2.24
1962 1988 3.493524 CCCCAAAACGGCAAGTAAACATT 60.494 43.478 0.00 0.00 0.00 2.71
2002 2033 9.787435 AGAACAGAAACACAAGTAAATATACCA 57.213 29.630 0.00 0.00 32.08 3.25
2044 2075 9.273016 CTAACTTCAAAGGATCAGACAAACTAA 57.727 33.333 0.00 0.00 0.00 2.24
2066 2097 5.565045 CGATAAGAGCCTATCACCCACTAAC 60.565 48.000 0.00 0.00 0.00 2.34
2103 2186 6.579666 TGAAAAATATCATCCCTATGCAGC 57.420 37.500 0.00 0.00 32.76 5.25
2170 2387 5.703730 TTTTGGAACGGAGGGAGTATAAT 57.296 39.130 0.00 0.00 0.00 1.28
2174 2391 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2175 2392 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2176 2393 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2177 2394 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2178 2395 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
2179 2396 4.757149 GGATCATCTATTTTGGAACGGAGG 59.243 45.833 0.00 0.00 0.00 4.30
2180 2397 5.368145 TGGATCATCTATTTTGGAACGGAG 58.632 41.667 0.00 0.00 0.00 4.63
2181 2398 5.366482 TGGATCATCTATTTTGGAACGGA 57.634 39.130 0.00 0.00 0.00 4.69
2182 2399 5.590259 AGTTGGATCATCTATTTTGGAACGG 59.410 40.000 0.00 0.00 0.00 4.44
2183 2400 6.683974 AGTTGGATCATCTATTTTGGAACG 57.316 37.500 0.00 0.00 0.00 3.95
2184 2401 8.306761 ACAAAGTTGGATCATCTATTTTGGAAC 58.693 33.333 11.01 0.00 0.00 3.62
2185 2402 8.421249 ACAAAGTTGGATCATCTATTTTGGAA 57.579 30.769 11.01 0.00 0.00 3.53
2186 2403 8.956426 GTACAAAGTTGGATCATCTATTTTGGA 58.044 33.333 11.01 2.87 0.00 3.53
2187 2404 8.960591 AGTACAAAGTTGGATCATCTATTTTGG 58.039 33.333 11.01 0.00 0.00 3.28
2220 2437 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2221 2438 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2222 2439 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2223 2440 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2224 2441 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2225 2442 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2226 2443 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2227 2444 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2228 2445 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2229 2446 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2230 2447 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2231 2448 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2232 2449 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2233 2450 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2234 2451 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2235 2452 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2236 2453 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2237 2454 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2238 2455 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2239 2456 7.731688 ACTATATACTCCCTCCGTTCCAAAATA 59.268 37.037 0.00 0.00 0.00 1.40
2240 2457 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
2241 2458 5.901276 ACTATATACTCCCTCCGTTCCAAAA 59.099 40.000 0.00 0.00 0.00 2.44
2242 2459 5.461327 ACTATATACTCCCTCCGTTCCAAA 58.539 41.667 0.00 0.00 0.00 3.28
2243 2460 5.070823 ACTATATACTCCCTCCGTTCCAA 57.929 43.478 0.00 0.00 0.00 3.53
2244 2461 4.736611 ACTATATACTCCCTCCGTTCCA 57.263 45.455 0.00 0.00 0.00 3.53
2245 2462 7.715266 ATTAACTATATACTCCCTCCGTTCC 57.285 40.000 0.00 0.00 0.00 3.62
2293 2510 3.888323 TGCAGGCAAAATTTACAGTGAGA 59.112 39.130 0.00 0.00 0.00 3.27
2303 2520 3.500343 AGTAACCTCTGCAGGCAAAATT 58.500 40.909 15.13 3.10 45.05 1.82
2304 2521 3.160679 AGTAACCTCTGCAGGCAAAAT 57.839 42.857 15.13 0.00 45.05 1.82
2473 2694 6.542821 AGATGAACAATTTAGAACAGGGTCA 58.457 36.000 0.00 0.00 0.00 4.02
2497 2718 1.202099 TACAATGGTTCAGGCCGGGA 61.202 55.000 2.18 0.00 0.00 5.14
2498 2719 0.106719 ATACAATGGTTCAGGCCGGG 60.107 55.000 2.18 0.00 0.00 5.73
2499 2720 1.762708 AATACAATGGTTCAGGCCGG 58.237 50.000 0.00 0.00 0.00 6.13
2500 2721 4.974368 TTAAATACAATGGTTCAGGCCG 57.026 40.909 0.00 0.00 0.00 6.13
2525 2746 8.497745 ACAGGATTGGTAATCAGTAATCTTGAT 58.502 33.333 12.74 0.00 38.27 2.57
2526 2747 7.861629 ACAGGATTGGTAATCAGTAATCTTGA 58.138 34.615 12.74 0.00 38.27 3.02
2527 2748 7.989741 AGACAGGATTGGTAATCAGTAATCTTG 59.010 37.037 0.00 0.00 40.40 3.02
2528 2749 8.095452 AGACAGGATTGGTAATCAGTAATCTT 57.905 34.615 4.19 0.00 39.71 2.40
2529 2750 7.682787 AGACAGGATTGGTAATCAGTAATCT 57.317 36.000 4.19 0.00 39.71 2.40
2531 2752 7.127955 AGGAAGACAGGATTGGTAATCAGTAAT 59.872 37.037 4.19 0.00 39.71 1.89
2532 2753 6.443849 AGGAAGACAGGATTGGTAATCAGTAA 59.556 38.462 4.19 0.00 39.71 2.24
2534 2755 4.785376 AGGAAGACAGGATTGGTAATCAGT 59.215 41.667 4.19 2.21 39.71 3.41
2535 2756 5.130145 AGAGGAAGACAGGATTGGTAATCAG 59.870 44.000 4.19 0.00 39.71 2.90
2536 2757 5.032846 AGAGGAAGACAGGATTGGTAATCA 58.967 41.667 4.19 0.00 39.71 2.57
2543 2769 2.235650 TCTGCAGAGGAAGACAGGATTG 59.764 50.000 13.74 0.00 0.00 2.67
2544 2770 2.544721 TCTGCAGAGGAAGACAGGATT 58.455 47.619 13.74 0.00 0.00 3.01
2545 2771 2.244486 TCTGCAGAGGAAGACAGGAT 57.756 50.000 13.74 0.00 0.00 3.24
2550 2783 0.389166 CCACGTCTGCAGAGGAAGAC 60.389 60.000 36.00 16.16 45.01 3.01
2831 3064 2.264480 CGCCACGATGGAGGTCAA 59.736 61.111 8.04 0.00 40.96 3.18
3004 3237 3.059982 GGAAAAACCTGGGCTGCC 58.940 61.111 11.05 11.05 35.41 4.85
3148 3388 9.193806 ACATGAGCTTGGTTTCTATTGATAAAT 57.806 29.630 0.00 0.00 0.00 1.40
3213 3557 6.094464 TGCATACAATGATTCATATAGGCTGC 59.906 38.462 19.69 14.89 0.00 5.25
3225 4066 3.627577 GGGTCGAAGTGCATACAATGATT 59.372 43.478 0.00 0.00 0.00 2.57
3230 4071 0.604073 TCGGGTCGAAGTGCATACAA 59.396 50.000 0.00 0.00 31.06 2.41
3246 4087 1.630244 CTCCAAAAGCTCGCACTCGG 61.630 60.000 0.00 0.00 36.13 4.63
3279 4120 0.033228 TGCATTTTGAAACCGGGCTG 59.967 50.000 6.32 0.00 0.00 4.85
3283 4124 3.812053 TGGAAAATGCATTTTGAAACCGG 59.188 39.130 35.57 0.00 39.86 5.28
3475 4338 9.608617 TGCGTGAATAAACGTTTGAAAATATTA 57.391 25.926 23.46 0.00 45.32 0.98
3581 4458 4.120755 CCAAGCTCCAGGGGGCTC 62.121 72.222 14.17 0.00 37.87 4.70
3588 4465 1.304713 AATGGCACCCAAGCTCCAG 60.305 57.895 0.00 0.00 36.95 3.86
3589 4466 1.607178 CAATGGCACCCAAGCTCCA 60.607 57.895 0.00 0.00 36.95 3.86
3626 4503 4.036262 GGCGATAAACAATGGAATACTGCA 59.964 41.667 0.00 0.00 0.00 4.41
3640 4517 0.317020 GAATGGCAGCGGCGATAAAC 60.317 55.000 12.98 0.00 37.49 2.01
3739 4616 4.519213 CAAAACCGGATGGAATAGTACCA 58.481 43.478 9.46 0.00 41.83 3.25
3747 4624 2.108601 AGGTTACCAAAACCGGATGGAA 59.891 45.455 25.28 15.11 44.82 3.53
3748 4625 1.706305 AGGTTACCAAAACCGGATGGA 59.294 47.619 25.28 11.23 44.82 3.41


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

AutoCloner maintained by Alex Coulton.