Multiple sequence alignment - TraesCS3B01G196100

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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 TraesCS3B01G196100 chr3B 100.000 2433 0 0 1 2433 222803235 222805667 0.000000e+00 4494.0
1 TraesCS3B01G196100 chr3B 100.000 178 0 0 2684 2861 222805918 222806095 2.130000e-86 329.0
2 TraesCS3B01G196100 chr3B 98.182 110 2 0 2752 2861 809415805 809415914 2.910000e-45 193.0
3 TraesCS3B01G196100 chr3B 100.000 48 0 0 2386 2433 202593527 202593574 3.930000e-14 89.8
4 TraesCS3B01G196100 chr3B 100.000 46 0 0 2388 2433 809415285 809415330 5.080000e-13 86.1
5 TraesCS3B01G196100 chr3D 93.703 2001 64 18 1 1966 152481649 152483622 0.000000e+00 2940.0
6 TraesCS3B01G196100 chr3D 82.090 201 21 6 2021 2211 152483720 152483915 1.060000e-34 158.0
7 TraesCS3B01G196100 chr3A 89.823 2260 119 28 1 2211 178256482 178254285 0.000000e+00 2796.0
8 TraesCS3B01G196100 chr3A 96.154 52 0 2 2384 2433 583745009 583744958 1.830000e-12 84.2
9 TraesCS3B01G196100 chr1B 100.000 178 0 0 2684 2861 61639849 61639672 2.130000e-86 329.0
10 TraesCS3B01G196100 chr1B 98.182 110 2 0 2752 2861 61639143 61639034 2.910000e-45 193.0
11 TraesCS3B01G196100 chr1D 96.629 178 6 0 2684 2861 492510099 492509922 2.160000e-76 296.0
12 TraesCS3B01G196100 chr1D 100.000 48 0 0 2386 2433 2147296 2147343 3.930000e-14 89.8
13 TraesCS3B01G196100 chr1D 92.982 57 2 2 2378 2433 103480631 103480576 6.570000e-12 82.4
14 TraesCS3B01G196100 chr4D 96.629 178 5 1 2684 2861 3299024 3298848 7.750000e-76 294.0
15 TraesCS3B01G196100 chr5B 96.067 178 7 0 2684 2861 82040409 82040586 1.000000e-74 291.0
16 TraesCS3B01G196100 chr5B 100.000 48 0 0 2386 2433 596724392 596724345 3.930000e-14 89.8
17 TraesCS3B01G196100 chr4A 98.125 160 3 0 2702 2861 598328144 598327985 2.170000e-71 279.0
18 TraesCS3B01G196100 chr6D 100.000 48 0 0 2386 2433 25659593 25659546 3.930000e-14 89.8
19 TraesCS3B01G196100 chr7B 96.154 52 0 2 2384 2433 495037496 495037445 1.830000e-12 84.2
20 TraesCS3B01G196100 chr5D 97.959 49 0 1 2386 2433 379268574 379268526 1.830000e-12 84.2


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 TraesCS3B01G196100 chr3B 222803235 222806095 2860 False 2411.5 4494 100.0000 1 2861 2 chr3B.!!$F2 2860
1 TraesCS3B01G196100 chr3D 152481649 152483915 2266 False 1549.0 2940 87.8965 1 2211 2 chr3D.!!$F1 2210
2 TraesCS3B01G196100 chr3A 178254285 178256482 2197 True 2796.0 2796 89.8230 1 2211 1 chr3A.!!$R1 2210
3 TraesCS3B01G196100 chr1B 61639034 61639849 815 True 261.0 329 99.0910 2684 2861 2 chr1B.!!$R1 177

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
43 45 0.322906 CTTTGGTCAGGAGAAGGGGC 60.323 60.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2140 0.249676 ACATCCTGCTCACTGCTCAG 59.75 55.0 0.0 0.0 43.37 3.35 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
43 45 0.322906 CTTTGGTCAGGAGAAGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
60 62 1.490621 GGCATGTTGTGTTGTTGAGC 58.509 50.000 0.00 0.00 0.00 4.26
98 100 5.712917 ACCTTGAAATCGGCTAATTGGTTTA 59.287 36.000 0.00 0.00 0.00 2.01
138 140 5.125356 TGATATTATAGCCATGCCCATTCG 58.875 41.667 0.00 0.00 0.00 3.34
221 226 2.151502 TTGTGTGAGGAAAAAGCCCA 57.848 45.000 0.00 0.00 0.00 5.36
432 447 4.729227 AACGGTTTGTTTCACCTGATTT 57.271 36.364 0.00 0.00 37.59 2.17
434 449 5.079689 ACGGTTTGTTTCACCTGATTTTT 57.920 34.783 0.00 0.00 31.32 1.94
478 493 2.972625 TGTGAGCTCCGGATTTGTAAG 58.027 47.619 12.15 0.00 0.00 2.34
553 577 5.871524 TCTGAAGAAGACATACAACTGATGC 59.128 40.000 0.00 0.00 0.00 3.91
589 613 3.383825 GCTGATGCATTCTGGAAGGATTT 59.616 43.478 0.00 0.00 39.41 2.17
729 753 1.207593 GAAGACACGTGGTGCATGC 59.792 57.895 21.57 11.82 36.98 4.06
732 756 3.295228 GACACGTGGTGCATGCGTC 62.295 63.158 21.57 8.49 36.98 5.19
809 841 7.993101 ACTACGTGTACTGATTATATGTGTGT 58.007 34.615 0.00 0.00 0.00 3.72
810 842 9.112725 ACTACGTGTACTGATTATATGTGTGTA 57.887 33.333 0.00 0.00 0.00 2.90
812 844 8.797266 ACGTGTACTGATTATATGTGTGTATG 57.203 34.615 0.00 0.00 0.00 2.39
1398 1443 4.264638 GCCACCACGTTGCACCAC 62.265 66.667 0.00 0.00 0.00 4.16
1724 1772 1.595993 AAGAGCAGCGCGAGGTAAGA 61.596 55.000 12.10 0.00 41.81 2.10
1760 1808 5.556915 TCATTAATTCTTCCGTTGAGGTGT 58.443 37.500 0.00 0.00 41.99 4.16
1781 1829 0.321021 GGTTTGCATTGCATGGTGGA 59.679 50.000 12.95 0.00 38.76 4.02
1782 1830 1.065998 GGTTTGCATTGCATGGTGGAT 60.066 47.619 12.95 0.00 38.76 3.41
1783 1831 2.168106 GGTTTGCATTGCATGGTGGATA 59.832 45.455 12.95 0.00 38.76 2.59
1784 1832 3.181463 GGTTTGCATTGCATGGTGGATAT 60.181 43.478 12.95 0.00 38.76 1.63
1785 1833 4.039004 GGTTTGCATTGCATGGTGGATATA 59.961 41.667 12.95 0.00 38.76 0.86
1786 1834 5.279607 GGTTTGCATTGCATGGTGGATATAT 60.280 40.000 12.95 0.00 38.76 0.86
1819 1867 2.159653 GGCTTCTTCTATGCGTTGTGTG 60.160 50.000 0.00 0.00 0.00 3.82
1888 1957 2.371510 GCTATGGGAGAAGATGAAGGCT 59.628 50.000 0.00 0.00 0.00 4.58
1905 1974 5.360714 TGAAGGCTGAAATTCAACTGTTTCT 59.639 36.000 0.00 0.00 35.80 2.52
1908 1977 6.739112 AGGCTGAAATTCAACTGTTTCTTAC 58.261 36.000 0.00 0.00 35.80 2.34
1920 1989 9.047371 TCAACTGTTTCTTACGAAATTCATGTA 57.953 29.630 0.00 0.00 40.91 2.29
1933 2002 8.814235 ACGAAATTCATGTACTAATTAGGAACG 58.186 33.333 16.73 11.11 0.00 3.95
1940 2009 5.448654 TGTACTAATTAGGAACGAGCCCTA 58.551 41.667 16.73 0.00 35.30 3.53
1941 2010 4.933505 ACTAATTAGGAACGAGCCCTAC 57.066 45.455 16.73 0.00 36.10 3.18
1942 2011 3.640498 ACTAATTAGGAACGAGCCCTACC 59.360 47.826 16.73 0.00 36.10 3.18
2026 2154 2.346365 TGCCTGAGCAGTGAGCAG 59.654 61.111 0.00 0.00 46.52 4.24
2033 2161 3.791539 GCAGTGAGCAGGATGTCG 58.208 61.111 0.00 0.00 44.79 4.35
2050 2180 6.018180 AGGATGTCGAAAGTTCAGTGTAAAAC 60.018 38.462 0.00 0.00 0.00 2.43
2052 2182 4.333372 TGTCGAAAGTTCAGTGTAAAACCC 59.667 41.667 0.00 0.00 0.00 4.11
2075 2205 5.418840 CCCAGCTTTGTATAACTGGTGATTT 59.581 40.000 7.10 0.00 46.80 2.17
2076 2206 6.071391 CCCAGCTTTGTATAACTGGTGATTTT 60.071 38.462 7.10 0.00 46.80 1.82
2077 2207 7.378181 CCAGCTTTGTATAACTGGTGATTTTT 58.622 34.615 0.00 0.00 43.86 1.94
2112 2242 3.072944 GCTAGAAGATGACCCATGCATC 58.927 50.000 0.00 4.20 41.85 3.91
2120 2250 4.965814 GATGACCCATGCATCTTAGAGAA 58.034 43.478 0.00 0.00 39.18 2.87
2122 2252 4.711399 TGACCCATGCATCTTAGAGAATG 58.289 43.478 0.00 0.00 0.00 2.67
2125 2255 5.128919 ACCCATGCATCTTAGAGAATGTTC 58.871 41.667 0.00 0.00 0.00 3.18
2126 2256 5.104193 ACCCATGCATCTTAGAGAATGTTCT 60.104 40.000 0.00 0.00 41.00 3.01
2164 2294 0.543277 TAAGCAGCTGGTCATCCTGG 59.457 55.000 20.46 0.00 33.97 4.45
2171 2309 1.834263 GCTGGTCATCCTGGTAGAACT 59.166 52.381 7.48 0.00 33.97 3.01
2178 2316 5.513267 GGTCATCCTGGTAGAACTTCAGTTT 60.513 44.000 0.00 0.00 38.56 2.66
2180 2318 5.544176 TCATCCTGGTAGAACTTCAGTTTCT 59.456 40.000 0.00 0.00 38.56 2.52
2185 2323 6.017852 CCTGGTAGAACTTCAGTTTCTTTCAC 60.018 42.308 0.00 0.00 38.56 3.18
2201 2339 7.801716 TTCTTTCACTATTATCCATTTCGGG 57.198 36.000 0.00 0.00 34.36 5.14
2206 2344 6.895782 TCACTATTATCCATTTCGGGAAAGT 58.104 36.000 0.05 0.00 41.12 2.66
2211 2349 9.938280 CTATTATCCATTTCGGGAAAGTACATA 57.062 33.333 0.00 0.00 41.12 2.29
2212 2350 8.848474 ATTATCCATTTCGGGAAAGTACATAG 57.152 34.615 0.00 0.00 41.12 2.23
2213 2351 5.031066 TCCATTTCGGGAAAGTACATAGG 57.969 43.478 0.00 0.00 32.90 2.57
2214 2352 4.134563 CCATTTCGGGAAAGTACATAGGG 58.865 47.826 0.00 0.00 33.32 3.53
2215 2353 4.141574 CCATTTCGGGAAAGTACATAGGGA 60.142 45.833 0.00 0.00 33.32 4.20
2216 2354 5.456186 CCATTTCGGGAAAGTACATAGGGAT 60.456 44.000 0.00 0.00 33.32 3.85
2217 2355 5.703730 TTTCGGGAAAGTACATAGGGATT 57.296 39.130 0.00 0.00 0.00 3.01
2218 2356 6.811634 TTTCGGGAAAGTACATAGGGATTA 57.188 37.500 0.00 0.00 0.00 1.75
2219 2357 6.811634 TTCGGGAAAGTACATAGGGATTAA 57.188 37.500 0.00 0.00 0.00 1.40
2220 2358 6.811634 TCGGGAAAGTACATAGGGATTAAA 57.188 37.500 0.00 0.00 0.00 1.52
2221 2359 7.197901 TCGGGAAAGTACATAGGGATTAAAA 57.802 36.000 0.00 0.00 0.00 1.52
2222 2360 7.631933 TCGGGAAAGTACATAGGGATTAAAAA 58.368 34.615 0.00 0.00 0.00 1.94
2223 2361 7.553760 TCGGGAAAGTACATAGGGATTAAAAAC 59.446 37.037 0.00 0.00 0.00 2.43
2224 2362 7.337436 CGGGAAAGTACATAGGGATTAAAAACA 59.663 37.037 0.00 0.00 0.00 2.83
2225 2363 8.464404 GGGAAAGTACATAGGGATTAAAAACAC 58.536 37.037 0.00 0.00 0.00 3.32
2226 2364 9.016438 GGAAAGTACATAGGGATTAAAAACACA 57.984 33.333 0.00 0.00 0.00 3.72
2229 2367 9.747898 AAGTACATAGGGATTAAAAACACATGA 57.252 29.630 0.00 0.00 0.00 3.07
2230 2368 9.747898 AGTACATAGGGATTAAAAACACATGAA 57.252 29.630 0.00 0.00 0.00 2.57
2231 2369 9.783256 GTACATAGGGATTAAAAACACATGAAC 57.217 33.333 0.00 0.00 0.00 3.18
2232 2370 8.415950 ACATAGGGATTAAAAACACATGAACA 57.584 30.769 0.00 0.00 0.00 3.18
2233 2371 8.522830 ACATAGGGATTAAAAACACATGAACAG 58.477 33.333 0.00 0.00 0.00 3.16
2234 2372 8.739039 CATAGGGATTAAAAACACATGAACAGA 58.261 33.333 0.00 0.00 0.00 3.41
2235 2373 7.219484 AGGGATTAAAAACACATGAACAGAG 57.781 36.000 0.00 0.00 0.00 3.35
2236 2374 7.004086 AGGGATTAAAAACACATGAACAGAGA 58.996 34.615 0.00 0.00 0.00 3.10
2237 2375 7.175641 AGGGATTAAAAACACATGAACAGAGAG 59.824 37.037 0.00 0.00 0.00 3.20
2238 2376 7.040409 GGGATTAAAAACACATGAACAGAGAGT 60.040 37.037 0.00 0.00 0.00 3.24
2239 2377 7.805071 GGATTAAAAACACATGAACAGAGAGTG 59.195 37.037 0.00 0.00 36.34 3.51
2240 2378 7.624360 TTAAAAACACATGAACAGAGAGTGT 57.376 32.000 0.00 0.00 44.53 3.55
2268 2406 6.830114 TTTAATGCGTGGTTTTGTTTTAGG 57.170 33.333 0.00 0.00 0.00 2.69
2269 2407 2.873133 TGCGTGGTTTTGTTTTAGGG 57.127 45.000 0.00 0.00 0.00 3.53
2270 2408 2.376109 TGCGTGGTTTTGTTTTAGGGA 58.624 42.857 0.00 0.00 0.00 4.20
2271 2409 2.758979 TGCGTGGTTTTGTTTTAGGGAA 59.241 40.909 0.00 0.00 0.00 3.97
2272 2410 3.181485 TGCGTGGTTTTGTTTTAGGGAAG 60.181 43.478 0.00 0.00 0.00 3.46
2273 2411 3.377439 CGTGGTTTTGTTTTAGGGAAGC 58.623 45.455 0.00 0.00 0.00 3.86
2274 2412 3.181485 CGTGGTTTTGTTTTAGGGAAGCA 60.181 43.478 0.00 0.00 0.00 3.91
2275 2413 4.500716 CGTGGTTTTGTTTTAGGGAAGCAT 60.501 41.667 0.00 0.00 31.50 3.79
2276 2414 4.988540 GTGGTTTTGTTTTAGGGAAGCATC 59.011 41.667 0.00 0.00 31.50 3.91
2277 2415 4.651503 TGGTTTTGTTTTAGGGAAGCATCA 59.348 37.500 0.00 0.00 0.00 3.07
2278 2416 4.988540 GGTTTTGTTTTAGGGAAGCATCAC 59.011 41.667 0.00 0.00 0.00 3.06
2279 2417 4.864704 TTTGTTTTAGGGAAGCATCACC 57.135 40.909 0.00 0.00 0.00 4.02
2280 2418 3.806949 TGTTTTAGGGAAGCATCACCT 57.193 42.857 4.70 4.70 38.40 4.00
2281 2419 4.112634 TGTTTTAGGGAAGCATCACCTT 57.887 40.909 4.62 0.00 35.84 3.50
2282 2420 4.479158 TGTTTTAGGGAAGCATCACCTTT 58.521 39.130 4.62 0.00 35.84 3.11
2283 2421 4.898861 TGTTTTAGGGAAGCATCACCTTTT 59.101 37.500 4.62 0.00 35.84 2.27
2284 2422 5.365314 TGTTTTAGGGAAGCATCACCTTTTT 59.635 36.000 4.62 0.00 35.84 1.94
2302 2440 2.746279 TTTTGAACCTGAGGGAAGCA 57.254 45.000 2.38 0.00 36.25 3.91
2303 2441 2.978156 TTTGAACCTGAGGGAAGCAT 57.022 45.000 2.38 0.00 36.25 3.79
2304 2442 2.496899 TTGAACCTGAGGGAAGCATC 57.503 50.000 2.38 0.00 36.25 3.91
2305 2443 1.361204 TGAACCTGAGGGAAGCATCA 58.639 50.000 2.38 0.00 36.25 3.07
2306 2444 1.003580 TGAACCTGAGGGAAGCATCAC 59.996 52.381 2.38 0.00 36.25 3.06
2307 2445 1.280421 GAACCTGAGGGAAGCATCACT 59.720 52.381 2.38 0.00 43.86 3.41
2308 2446 1.366319 ACCTGAGGGAAGCATCACTT 58.634 50.000 2.38 0.00 40.23 3.16
2309 2447 1.004044 ACCTGAGGGAAGCATCACTTG 59.996 52.381 2.38 0.00 40.23 3.16
2310 2448 1.280133 CCTGAGGGAAGCATCACTTGA 59.720 52.381 0.00 0.00 40.23 3.02
2311 2449 2.630158 CTGAGGGAAGCATCACTTGAG 58.370 52.381 0.00 0.00 40.23 3.02
2312 2450 2.235650 CTGAGGGAAGCATCACTTGAGA 59.764 50.000 0.00 0.00 40.23 3.27
2313 2451 2.235650 TGAGGGAAGCATCACTTGAGAG 59.764 50.000 0.00 0.00 40.23 3.20
2314 2452 1.558756 AGGGAAGCATCACTTGAGAGG 59.441 52.381 0.00 0.00 35.03 3.69
2315 2453 1.377536 GGAAGCATCACTTGAGAGGC 58.622 55.000 0.00 0.00 45.01 4.70
2316 2454 1.339438 GGAAGCATCACTTGAGAGGCA 60.339 52.381 7.35 0.00 46.90 4.75
2317 2455 2.641305 GAAGCATCACTTGAGAGGCAT 58.359 47.619 7.35 0.00 46.90 4.40
2318 2456 2.803030 AGCATCACTTGAGAGGCATT 57.197 45.000 7.35 0.00 46.90 3.56
2319 2457 2.366533 AGCATCACTTGAGAGGCATTG 58.633 47.619 7.35 0.00 46.90 2.82
2320 2458 1.202268 GCATCACTTGAGAGGCATTGC 60.202 52.381 0.00 0.00 44.15 3.56
2331 2469 3.851620 GGCATTGCCGTGATGTATG 57.148 52.632 12.82 0.00 39.62 2.39
2332 2470 1.024271 GGCATTGCCGTGATGTATGT 58.976 50.000 12.82 0.00 39.62 2.29
2333 2471 1.002468 GGCATTGCCGTGATGTATGTC 60.002 52.381 12.82 0.00 39.62 3.06
2334 2472 1.942657 GCATTGCCGTGATGTATGTCT 59.057 47.619 0.00 0.00 0.00 3.41
2335 2473 2.032549 GCATTGCCGTGATGTATGTCTC 60.033 50.000 0.00 0.00 0.00 3.36
2336 2474 3.197265 CATTGCCGTGATGTATGTCTCA 58.803 45.455 0.00 0.00 0.00 3.27
2337 2475 2.584492 TGCCGTGATGTATGTCTCAG 57.416 50.000 0.00 0.00 0.00 3.35
2338 2476 2.099405 TGCCGTGATGTATGTCTCAGA 58.901 47.619 0.00 0.00 0.00 3.27
2339 2477 2.695147 TGCCGTGATGTATGTCTCAGAT 59.305 45.455 0.00 0.00 0.00 2.90
2340 2478 3.055591 GCCGTGATGTATGTCTCAGATG 58.944 50.000 0.00 0.00 0.00 2.90
2341 2479 3.243535 GCCGTGATGTATGTCTCAGATGA 60.244 47.826 0.00 0.00 0.00 2.92
2342 2480 4.737649 GCCGTGATGTATGTCTCAGATGAA 60.738 45.833 0.00 0.00 0.00 2.57
2343 2481 5.351458 CCGTGATGTATGTCTCAGATGAAA 58.649 41.667 0.00 0.00 0.00 2.69
2344 2482 5.987953 CCGTGATGTATGTCTCAGATGAAAT 59.012 40.000 0.00 0.00 0.00 2.17
2345 2483 6.145209 CCGTGATGTATGTCTCAGATGAAATC 59.855 42.308 0.00 0.00 46.04 2.17
2370 2508 8.397906 TCAATAGCAAAATCATCTAAACTTCCG 58.602 33.333 0.00 0.00 0.00 4.30
2371 2509 8.397906 CAATAGCAAAATCATCTAAACTTCCGA 58.602 33.333 0.00 0.00 0.00 4.55
2372 2510 6.428385 AGCAAAATCATCTAAACTTCCGAG 57.572 37.500 0.00 0.00 0.00 4.63
2373 2511 5.940470 AGCAAAATCATCTAAACTTCCGAGT 59.060 36.000 0.00 0.00 37.87 4.18
2375 2513 6.743172 GCAAAATCATCTAAACTTCCGAGTTC 59.257 38.462 0.00 0.00 45.18 3.01
2376 2514 7.573096 GCAAAATCATCTAAACTTCCGAGTTCA 60.573 37.037 0.00 0.00 45.18 3.18
2377 2515 7.602517 AAATCATCTAAACTTCCGAGTTCAG 57.397 36.000 0.00 0.00 45.18 3.02
2378 2516 5.073311 TCATCTAAACTTCCGAGTTCAGG 57.927 43.478 0.00 0.00 45.18 3.86
2379 2517 3.314541 TCTAAACTTCCGAGTTCAGGC 57.685 47.619 0.00 0.00 45.18 4.85
2380 2518 2.631062 TCTAAACTTCCGAGTTCAGGCA 59.369 45.455 0.00 0.00 45.18 4.75
2381 2519 1.594331 AAACTTCCGAGTTCAGGCAC 58.406 50.000 0.00 0.00 45.18 5.01
2382 2520 0.759346 AACTTCCGAGTTCAGGCACT 59.241 50.000 0.00 0.00 42.35 4.40
2384 2522 4.759995 AACTTCCGAGTTCAGGCACTGG 62.760 54.545 2.86 0.00 46.57 4.00
2405 2543 1.943293 TTTTTGACGGTGCTACGGC 59.057 52.632 5.66 2.68 43.68 5.68
2412 2550 4.151582 GGTGCTACGGCGGGCTTA 62.152 66.667 22.80 6.00 42.25 3.09
2413 2551 2.889018 GTGCTACGGCGGGCTTAC 60.889 66.667 22.80 13.01 42.25 2.34
2414 2552 4.501714 TGCTACGGCGGGCTTACG 62.502 66.667 22.80 0.00 42.25 3.18
2425 2563 3.497031 GCTTACGCCGGCCTGAAC 61.497 66.667 23.46 3.95 0.00 3.18
2426 2564 2.818274 CTTACGCCGGCCTGAACC 60.818 66.667 23.46 0.00 0.00 3.62
2427 2565 3.310860 CTTACGCCGGCCTGAACCT 62.311 63.158 23.46 0.00 0.00 3.50
2428 2566 2.798148 CTTACGCCGGCCTGAACCTT 62.798 60.000 23.46 0.00 0.00 3.50
2429 2567 2.400269 TTACGCCGGCCTGAACCTTT 62.400 55.000 23.46 0.00 0.00 3.11
2430 2568 2.400269 TACGCCGGCCTGAACCTTTT 62.400 55.000 23.46 0.00 0.00 2.27
2431 2569 2.962569 GCCGGCCTGAACCTTTTC 59.037 61.111 18.11 0.00 0.00 2.29
2432 2570 1.901464 GCCGGCCTGAACCTTTTCA 60.901 57.895 18.11 0.00 39.55 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.399330 TCCTGACCAAAGTTGAATCGAC 58.601 45.455 0.00 0.00 0.00 4.20
43 45 4.383649 GCATAAGCTCAACAACACAACATG 59.616 41.667 0.00 0.00 37.91 3.21
78 80 7.122055 ACAGAATAAACCAATTAGCCGATTTCA 59.878 33.333 0.00 0.00 0.00 2.69
84 86 5.123186 TGTGACAGAATAAACCAATTAGCCG 59.877 40.000 0.00 0.00 0.00 5.52
138 140 7.280652 CCATAAAATTTGATCCATTCACCCAAC 59.719 37.037 0.00 0.00 32.84 3.77
221 226 3.171528 GGTCACTTACCCAGAAGTACCT 58.828 50.000 0.00 0.00 43.16 3.08
269 274 2.288825 GCCAAAGGCCCAAAGTAAGAAC 60.289 50.000 0.00 0.00 44.06 3.01
451 466 0.104855 TCCGGAGCTCACATATGTGC 59.895 55.000 27.71 18.60 45.25 4.57
466 481 5.666969 TGATTAATCGCTTACAAATCCGG 57.333 39.130 10.80 0.00 0.00 5.14
467 482 9.265938 CATTATGATTAATCGCTTACAAATCCG 57.734 33.333 10.80 0.00 0.00 4.18
478 493 6.201517 ACAGCACAACATTATGATTAATCGC 58.798 36.000 10.80 4.12 0.00 4.58
553 577 3.508762 GCATCAGCAGAAAAGAACATGG 58.491 45.455 0.00 0.00 41.58 3.66
729 753 2.028766 GACGCATGCATGGAGTGACG 62.029 60.000 27.34 21.62 0.00 4.35
732 756 1.426621 GTGACGCATGCATGGAGTG 59.573 57.895 27.34 11.39 0.00 3.51
810 842 9.647797 TTCTACTGATACATCGTACAAAAACAT 57.352 29.630 0.00 0.00 0.00 2.71
812 844 9.136952 ACTTCTACTGATACATCGTACAAAAAC 57.863 33.333 0.00 0.00 0.00 2.43
1393 1438 3.362797 CTGCTGCTGCTGGTGGTG 61.363 66.667 17.00 0.00 40.48 4.17
1396 1441 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
1593 1641 3.069946 TACCCGGCCATCGTCGTT 61.070 61.111 2.24 0.00 37.11 3.85
1701 1749 2.489285 CTCGCGCTGCTCTTCTCT 59.511 61.111 5.56 0.00 0.00 3.10
1760 1808 1.549620 CCACCATGCAATGCAAACCTA 59.450 47.619 13.45 0.00 44.97 3.08
1908 1977 9.027129 TCGTTCCTAATTAGTACATGAATTTCG 57.973 33.333 11.50 7.38 0.00 3.46
1920 1989 3.640498 GGTAGGGCTCGTTCCTAATTAGT 59.360 47.826 11.50 0.00 38.47 2.24
1925 1994 1.829222 CTTGGTAGGGCTCGTTCCTAA 59.171 52.381 0.00 0.00 38.47 2.69
1933 2002 3.118223 AGAAGCAATACTTGGTAGGGCTC 60.118 47.826 0.00 0.00 41.14 4.70
1940 2009 7.775053 TTTTATTCCAGAAGCAATACTTGGT 57.225 32.000 0.00 0.00 44.43 3.67
1966 2035 3.568007 TGAAGCAACAGCGAAACCTATTT 59.432 39.130 0.00 0.00 0.00 1.40
1967 2036 3.146066 TGAAGCAACAGCGAAACCTATT 58.854 40.909 0.00 0.00 0.00 1.73
1969 2038 2.248280 TGAAGCAACAGCGAAACCTA 57.752 45.000 0.00 0.00 0.00 3.08
1970 2039 1.537202 GATGAAGCAACAGCGAAACCT 59.463 47.619 0.00 0.00 0.00 3.50
1971 2040 1.537202 AGATGAAGCAACAGCGAAACC 59.463 47.619 0.00 0.00 0.00 3.27
1972 2041 2.977405 AGATGAAGCAACAGCGAAAC 57.023 45.000 0.00 0.00 0.00 2.78
1973 2042 3.988379 AAAGATGAAGCAACAGCGAAA 57.012 38.095 0.00 0.00 0.00 3.46
1975 2044 3.988379 AAAAAGATGAAGCAACAGCGA 57.012 38.095 0.00 0.00 0.00 4.93
1997 2116 1.068679 GCTCAGGCAGAAGAAAAGCAC 60.069 52.381 0.00 0.00 38.54 4.40
1999 2118 1.242076 TGCTCAGGCAGAAGAAAAGC 58.758 50.000 0.00 0.00 44.28 3.51
2012 2140 0.249676 ACATCCTGCTCACTGCTCAG 59.750 55.000 0.00 0.00 43.37 3.35
2020 2148 2.037121 TGAACTTTCGACATCCTGCTCA 59.963 45.455 0.00 0.00 0.00 4.26
2021 2149 2.670414 CTGAACTTTCGACATCCTGCTC 59.330 50.000 0.00 0.00 0.00 4.26
2022 2150 2.037772 ACTGAACTTTCGACATCCTGCT 59.962 45.455 0.00 0.00 0.00 4.24
2023 2151 2.158449 CACTGAACTTTCGACATCCTGC 59.842 50.000 0.00 0.00 0.00 4.85
2024 2152 3.393800 ACACTGAACTTTCGACATCCTG 58.606 45.455 0.00 0.00 0.00 3.86
2025 2153 3.753294 ACACTGAACTTTCGACATCCT 57.247 42.857 0.00 0.00 0.00 3.24
2026 2154 5.917541 TTTACACTGAACTTTCGACATCC 57.082 39.130 0.00 0.00 0.00 3.51
2030 2158 4.260907 GGGGTTTTACACTGAACTTTCGAC 60.261 45.833 0.00 0.00 0.00 4.20
2033 2161 4.499188 GCTGGGGTTTTACACTGAACTTTC 60.499 45.833 0.00 0.00 0.00 2.62
2103 2233 5.374921 AGAACATTCTCTAAGATGCATGGG 58.625 41.667 2.46 0.00 29.94 4.00
2178 2316 7.131907 TCCCGAAATGGATAATAGTGAAAGA 57.868 36.000 0.00 0.00 42.00 2.52
2180 2318 7.832187 ACTTTCCCGAAATGGATAATAGTGAAA 59.168 33.333 0.00 0.00 42.00 2.69
2185 2323 8.848474 ATGTACTTTCCCGAAATGGATAATAG 57.152 34.615 0.00 0.00 42.00 1.73
2197 2335 6.811634 TTTAATCCCTATGTACTTTCCCGA 57.188 37.500 0.00 0.00 0.00 5.14
2198 2336 7.337436 TGTTTTTAATCCCTATGTACTTTCCCG 59.663 37.037 0.00 0.00 0.00 5.14
2206 2344 9.521841 TGTTCATGTGTTTTTAATCCCTATGTA 57.478 29.630 0.00 0.00 0.00 2.29
2211 2349 7.004086 TCTCTGTTCATGTGTTTTTAATCCCT 58.996 34.615 0.00 0.00 0.00 4.20
2212 2350 7.040409 ACTCTCTGTTCATGTGTTTTTAATCCC 60.040 37.037 0.00 0.00 0.00 3.85
2213 2351 7.805071 CACTCTCTGTTCATGTGTTTTTAATCC 59.195 37.037 0.00 0.00 0.00 3.01
2214 2352 8.345565 ACACTCTCTGTTCATGTGTTTTTAATC 58.654 33.333 0.00 0.00 38.51 1.75
2215 2353 8.225603 ACACTCTCTGTTCATGTGTTTTTAAT 57.774 30.769 0.00 0.00 38.51 1.40
2216 2354 7.624360 ACACTCTCTGTTCATGTGTTTTTAA 57.376 32.000 0.00 0.00 38.51 1.52
2217 2355 7.624360 AACACTCTCTGTTCATGTGTTTTTA 57.376 32.000 0.00 0.00 45.72 1.52
2218 2356 6.515272 AACACTCTCTGTTCATGTGTTTTT 57.485 33.333 0.00 0.00 45.72 1.94
2243 2381 7.201617 CCCTAAAACAAAACCACGCATTAAAAA 60.202 33.333 0.00 0.00 0.00 1.94
2244 2382 6.258068 CCCTAAAACAAAACCACGCATTAAAA 59.742 34.615 0.00 0.00 0.00 1.52
2245 2383 5.753921 CCCTAAAACAAAACCACGCATTAAA 59.246 36.000 0.00 0.00 0.00 1.52
2246 2384 5.068723 TCCCTAAAACAAAACCACGCATTAA 59.931 36.000 0.00 0.00 0.00 1.40
2247 2385 4.583489 TCCCTAAAACAAAACCACGCATTA 59.417 37.500 0.00 0.00 0.00 1.90
2248 2386 3.385111 TCCCTAAAACAAAACCACGCATT 59.615 39.130 0.00 0.00 0.00 3.56
2249 2387 2.959707 TCCCTAAAACAAAACCACGCAT 59.040 40.909 0.00 0.00 0.00 4.73
2250 2388 2.376109 TCCCTAAAACAAAACCACGCA 58.624 42.857 0.00 0.00 0.00 5.24
2251 2389 3.377439 CTTCCCTAAAACAAAACCACGC 58.623 45.455 0.00 0.00 0.00 5.34
2252 2390 3.181485 TGCTTCCCTAAAACAAAACCACG 60.181 43.478 0.00 0.00 0.00 4.94
2253 2391 4.394439 TGCTTCCCTAAAACAAAACCAC 57.606 40.909 0.00 0.00 0.00 4.16
2254 2392 4.651503 TGATGCTTCCCTAAAACAAAACCA 59.348 37.500 0.00 0.00 0.00 3.67
2255 2393 4.988540 GTGATGCTTCCCTAAAACAAAACC 59.011 41.667 0.00 0.00 0.00 3.27
2256 2394 4.988540 GGTGATGCTTCCCTAAAACAAAAC 59.011 41.667 0.00 0.00 0.00 2.43
2257 2395 4.898861 AGGTGATGCTTCCCTAAAACAAAA 59.101 37.500 7.56 0.00 0.00 2.44
2258 2396 4.479158 AGGTGATGCTTCCCTAAAACAAA 58.521 39.130 7.56 0.00 0.00 2.83
2259 2397 4.112634 AGGTGATGCTTCCCTAAAACAA 57.887 40.909 7.56 0.00 0.00 2.83
2260 2398 3.806949 AGGTGATGCTTCCCTAAAACA 57.193 42.857 7.56 0.00 0.00 2.83
2261 2399 5.468540 AAAAGGTGATGCTTCCCTAAAAC 57.531 39.130 9.18 0.00 0.00 2.43
2282 2420 3.025322 TGCTTCCCTCAGGTTCAAAAA 57.975 42.857 0.00 0.00 0.00 1.94
2283 2421 2.746279 TGCTTCCCTCAGGTTCAAAA 57.254 45.000 0.00 0.00 0.00 2.44
2284 2422 2.108075 TGATGCTTCCCTCAGGTTCAAA 59.892 45.455 0.00 0.00 0.00 2.69
2285 2423 1.704628 TGATGCTTCCCTCAGGTTCAA 59.295 47.619 0.00 0.00 0.00 2.69
2286 2424 1.003580 GTGATGCTTCCCTCAGGTTCA 59.996 52.381 0.00 0.00 0.00 3.18
2287 2425 1.280421 AGTGATGCTTCCCTCAGGTTC 59.720 52.381 0.00 0.00 0.00 3.62
2288 2426 1.366319 AGTGATGCTTCCCTCAGGTT 58.634 50.000 0.00 0.00 0.00 3.50
2289 2427 1.004044 CAAGTGATGCTTCCCTCAGGT 59.996 52.381 0.00 0.00 34.69 4.00
2290 2428 1.280133 TCAAGTGATGCTTCCCTCAGG 59.720 52.381 0.00 0.00 34.69 3.86
2291 2429 2.235650 TCTCAAGTGATGCTTCCCTCAG 59.764 50.000 0.00 0.00 34.69 3.35
2292 2430 2.235650 CTCTCAAGTGATGCTTCCCTCA 59.764 50.000 0.00 0.00 34.69 3.86
2293 2431 2.419851 CCTCTCAAGTGATGCTTCCCTC 60.420 54.545 0.00 0.00 34.69 4.30
2294 2432 1.558756 CCTCTCAAGTGATGCTTCCCT 59.441 52.381 0.00 0.00 34.69 4.20
2295 2433 2.016096 GCCTCTCAAGTGATGCTTCCC 61.016 57.143 0.00 0.00 34.69 3.97
2296 2434 1.339438 TGCCTCTCAAGTGATGCTTCC 60.339 52.381 0.00 0.00 34.69 3.46
2297 2435 2.105006 TGCCTCTCAAGTGATGCTTC 57.895 50.000 0.00 0.00 34.69 3.86
2298 2436 2.753452 CAATGCCTCTCAAGTGATGCTT 59.247 45.455 0.00 0.00 38.08 3.91
2299 2437 2.366533 CAATGCCTCTCAAGTGATGCT 58.633 47.619 0.00 0.00 0.00 3.79
2300 2438 1.202268 GCAATGCCTCTCAAGTGATGC 60.202 52.381 0.00 0.00 0.00 3.91
2301 2439 1.404391 GGCAATGCCTCTCAAGTGATG 59.596 52.381 18.47 0.00 46.69 3.07
2302 2440 1.760192 GGCAATGCCTCTCAAGTGAT 58.240 50.000 18.47 0.00 46.69 3.06
2303 2441 3.254629 GGCAATGCCTCTCAAGTGA 57.745 52.632 18.47 0.00 46.69 3.41
2313 2451 1.002468 GACATACATCACGGCAATGCC 60.002 52.381 15.52 15.52 46.75 4.40
2314 2452 1.942657 AGACATACATCACGGCAATGC 59.057 47.619 0.00 0.00 0.00 3.56
2315 2453 3.197265 TGAGACATACATCACGGCAATG 58.803 45.455 0.00 0.00 0.00 2.82
2316 2454 3.132824 TCTGAGACATACATCACGGCAAT 59.867 43.478 0.00 0.00 0.00 3.56
2317 2455 2.495669 TCTGAGACATACATCACGGCAA 59.504 45.455 0.00 0.00 0.00 4.52
2318 2456 2.099405 TCTGAGACATACATCACGGCA 58.901 47.619 0.00 0.00 0.00 5.69
2319 2457 2.871182 TCTGAGACATACATCACGGC 57.129 50.000 0.00 0.00 0.00 5.68
2320 2458 4.574599 TCATCTGAGACATACATCACGG 57.425 45.455 0.00 0.00 0.00 4.94
2321 2459 6.698766 TGATTTCATCTGAGACATACATCACG 59.301 38.462 0.00 0.00 0.00 4.35
2322 2460 8.429493 TTGATTTCATCTGAGACATACATCAC 57.571 34.615 0.00 0.00 0.00 3.06
2325 2463 9.217278 GCTATTGATTTCATCTGAGACATACAT 57.783 33.333 0.00 0.00 0.00 2.29
2326 2464 8.206189 TGCTATTGATTTCATCTGAGACATACA 58.794 33.333 0.00 0.00 0.00 2.29
2327 2465 8.599055 TGCTATTGATTTCATCTGAGACATAC 57.401 34.615 0.00 0.00 0.00 2.39
2328 2466 9.617523 TTTGCTATTGATTTCATCTGAGACATA 57.382 29.630 0.00 0.00 0.00 2.29
2329 2467 8.515695 TTTGCTATTGATTTCATCTGAGACAT 57.484 30.769 0.00 0.00 0.00 3.06
2330 2468 7.926674 TTTGCTATTGATTTCATCTGAGACA 57.073 32.000 0.00 0.00 0.00 3.41
2331 2469 9.448294 GATTTTGCTATTGATTTCATCTGAGAC 57.552 33.333 0.00 0.00 0.00 3.36
2332 2470 9.181061 TGATTTTGCTATTGATTTCATCTGAGA 57.819 29.630 0.00 0.00 0.00 3.27
2333 2471 9.967346 ATGATTTTGCTATTGATTTCATCTGAG 57.033 29.630 0.00 0.00 0.00 3.35
2334 2472 9.961265 GATGATTTTGCTATTGATTTCATCTGA 57.039 29.630 0.00 0.00 36.76 3.27
2335 2473 9.967346 AGATGATTTTGCTATTGATTTCATCTG 57.033 29.630 10.38 0.00 44.04 2.90
2344 2482 8.397906 CGGAAGTTTAGATGATTTTGCTATTGA 58.602 33.333 0.00 0.00 0.00 2.57
2345 2483 8.397906 TCGGAAGTTTAGATGATTTTGCTATTG 58.602 33.333 0.00 0.00 0.00 1.90
2346 2484 8.506168 TCGGAAGTTTAGATGATTTTGCTATT 57.494 30.769 0.00 0.00 0.00 1.73
2347 2485 7.770897 ACTCGGAAGTTTAGATGATTTTGCTAT 59.229 33.333 0.00 0.00 28.74 2.97
2348 2486 7.103641 ACTCGGAAGTTTAGATGATTTTGCTA 58.896 34.615 0.00 0.00 28.74 3.49
2349 2487 5.940470 ACTCGGAAGTTTAGATGATTTTGCT 59.060 36.000 0.00 0.00 28.74 3.91
2350 2488 6.183309 ACTCGGAAGTTTAGATGATTTTGC 57.817 37.500 0.00 0.00 28.74 3.68
2351 2489 7.806690 TGAACTCGGAAGTTTAGATGATTTTG 58.193 34.615 0.00 0.00 45.80 2.44
2352 2490 7.119846 CCTGAACTCGGAAGTTTAGATGATTTT 59.880 37.037 10.60 0.00 46.73 1.82
2353 2491 6.595716 CCTGAACTCGGAAGTTTAGATGATTT 59.404 38.462 10.60 0.00 46.73 2.17
2354 2492 6.109359 CCTGAACTCGGAAGTTTAGATGATT 58.891 40.000 10.60 0.00 46.73 2.57
2355 2493 5.665459 CCTGAACTCGGAAGTTTAGATGAT 58.335 41.667 10.60 0.00 46.73 2.45
2356 2494 4.620803 GCCTGAACTCGGAAGTTTAGATGA 60.621 45.833 10.60 0.00 46.73 2.92
2357 2495 3.619038 GCCTGAACTCGGAAGTTTAGATG 59.381 47.826 10.60 0.00 46.73 2.90
2358 2496 3.260884 TGCCTGAACTCGGAAGTTTAGAT 59.739 43.478 10.60 0.00 46.73 1.98
2359 2497 2.631062 TGCCTGAACTCGGAAGTTTAGA 59.369 45.455 10.60 0.00 46.73 2.10
2360 2498 2.737252 GTGCCTGAACTCGGAAGTTTAG 59.263 50.000 3.77 3.77 45.80 1.85
2361 2499 2.367567 AGTGCCTGAACTCGGAAGTTTA 59.632 45.455 0.00 0.00 45.80 2.01
2362 2500 1.141053 AGTGCCTGAACTCGGAAGTTT 59.859 47.619 0.00 0.00 45.80 2.66
2364 2502 0.034059 CAGTGCCTGAACTCGGAAGT 59.966 55.000 0.00 0.00 37.32 3.01
2365 2503 0.671781 CCAGTGCCTGAACTCGGAAG 60.672 60.000 4.00 0.00 32.44 3.46
2366 2504 1.371183 CCAGTGCCTGAACTCGGAA 59.629 57.895 4.00 0.00 32.44 4.30
2367 2505 1.407656 AACCAGTGCCTGAACTCGGA 61.408 55.000 4.00 0.00 32.44 4.55
2368 2506 0.535102 AAACCAGTGCCTGAACTCGG 60.535 55.000 4.00 0.00 32.44 4.63
2369 2507 1.308998 AAAACCAGTGCCTGAACTCG 58.691 50.000 4.00 0.00 32.44 4.18
2387 2525 1.833434 CGCCGTAGCACCGTCAAAAA 61.833 55.000 0.00 0.00 39.83 1.94
2388 2526 2.311701 CGCCGTAGCACCGTCAAAA 61.312 57.895 0.00 0.00 39.83 2.44
2389 2527 2.735478 CGCCGTAGCACCGTCAAA 60.735 61.111 0.00 0.00 39.83 2.69
2390 2528 4.728102 CCGCCGTAGCACCGTCAA 62.728 66.667 0.00 0.00 39.83 3.18
2395 2533 4.151582 TAAGCCCGCCGTAGCACC 62.152 66.667 0.00 0.00 39.83 5.01
2396 2534 2.889018 GTAAGCCCGCCGTAGCAC 60.889 66.667 0.00 0.00 39.83 4.40
2397 2535 4.501714 CGTAAGCCCGCCGTAGCA 62.502 66.667 0.00 0.00 39.83 3.49
2409 2547 2.798148 AAGGTTCAGGCCGGCGTAAG 62.798 60.000 23.15 10.93 43.44 2.34
2410 2548 2.400269 AAAGGTTCAGGCCGGCGTAA 62.400 55.000 23.15 12.08 0.00 3.18
2411 2549 2.400269 AAAAGGTTCAGGCCGGCGTA 62.400 55.000 23.15 4.02 0.00 4.42
2412 2550 3.785122 AAAAGGTTCAGGCCGGCGT 62.785 57.895 22.54 20.09 0.00 5.68
2413 2551 2.978018 GAAAAGGTTCAGGCCGGCG 61.978 63.158 22.54 7.85 33.61 6.46
2414 2552 1.901464 TGAAAAGGTTCAGGCCGGC 60.901 57.895 21.18 21.18 38.88 6.13
2415 2553 4.492604 TGAAAAGGTTCAGGCCGG 57.507 55.556 0.00 0.00 38.88 6.13


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

AutoCloner maintained by Alex Coulton.