Multiple sequence alignment - TraesCS4B01G296500

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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 TraesCS4B01G296500 chr4B 100.000 2708 0 0 1 2708 582111814 582114521 0.000000e+00 5001
1 TraesCS4B01G296500 chr4A 89.349 1521 76 34 628 2108 5115608 5114134 0.000000e+00 1832
2 TraesCS4B01G296500 chr4A 84.342 281 20 8 2452 2708 5070852 5070572 1.240000e-63 254
3 TraesCS4B01G296500 chr4A 93.750 96 6 0 2363 2458 5112088 5111993 7.810000e-31 145
4 TraesCS4B01G296500 chr4D 92.928 1004 60 7 830 1831 465357724 465358718 0.000000e+00 1450
5 TraesCS4B01G296500 chr4D 90.411 365 15 8 2360 2705 465359167 465359530 1.900000e-126 462
6 TraesCS4B01G296500 chr4D 93.171 205 13 1 628 832 465357483 465357686 1.580000e-77 300
7 TraesCS4B01G296500 chr4D 87.665 227 9 4 2008 2227 465358954 465359168 2.080000e-61 246
8 TraesCS4B01G296500 chr7D 87.304 638 70 9 1 630 412151879 412152513 0.000000e+00 719
9 TraesCS4B01G296500 chr7D 87.344 640 62 12 3 629 66976208 66976841 0.000000e+00 715
10 TraesCS4B01G296500 chr7D 85.524 601 59 21 1 590 587305202 587305785 1.070000e-168 603
11 TraesCS4B01G296500 chr7D 72.043 651 161 16 1013 1651 29057370 29056729 9.970000e-40 174
12 TraesCS4B01G296500 chr5D 86.364 638 71 15 1 628 532337913 532338544 0.000000e+00 682
13 TraesCS4B01G296500 chr3D 85.824 649 80 11 1 640 474538424 474539069 0.000000e+00 678
14 TraesCS4B01G296500 chr2B 87.307 583 71 3 3 583 74254619 74254038 0.000000e+00 664
15 TraesCS4B01G296500 chr5B 88.267 554 61 3 1 551 393745953 393745401 0.000000e+00 660
16 TraesCS4B01G296500 chr5B 85.103 631 79 13 1 628 492375902 492375284 4.920000e-177 630
17 TraesCS4B01G296500 chr2D 82.972 646 80 19 1 632 47008230 47008859 8.470000e-155 556
18 TraesCS4B01G296500 chr6A 83.636 330 51 1 998 1327 111449593 111449267 9.420000e-80 307


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 TraesCS4B01G296500 chr4B 582111814 582114521 2707 False 5001.0 5001 100.00000 1 2708 1 chr4B.!!$F1 2707
1 TraesCS4B01G296500 chr4A 5111993 5115608 3615 True 988.5 1832 91.54950 628 2458 2 chr4A.!!$R2 1830
2 TraesCS4B01G296500 chr4D 465357483 465359530 2047 False 614.5 1450 91.04375 628 2705 4 chr4D.!!$F1 2077
3 TraesCS4B01G296500 chr7D 412151879 412152513 634 False 719.0 719 87.30400 1 630 1 chr7D.!!$F2 629
4 TraesCS4B01G296500 chr7D 66976208 66976841 633 False 715.0 715 87.34400 3 629 1 chr7D.!!$F1 626
5 TraesCS4B01G296500 chr7D 587305202 587305785 583 False 603.0 603 85.52400 1 590 1 chr7D.!!$F3 589
6 TraesCS4B01G296500 chr5D 532337913 532338544 631 False 682.0 682 86.36400 1 628 1 chr5D.!!$F1 627
7 TraesCS4B01G296500 chr3D 474538424 474539069 645 False 678.0 678 85.82400 1 640 1 chr3D.!!$F1 639
8 TraesCS4B01G296500 chr2B 74254038 74254619 581 True 664.0 664 87.30700 3 583 1 chr2B.!!$R1 580
9 TraesCS4B01G296500 chr5B 393745401 393745953 552 True 660.0 660 88.26700 1 551 1 chr5B.!!$R1 550
10 TraesCS4B01G296500 chr5B 492375284 492375902 618 True 630.0 630 85.10300 1 628 1 chr5B.!!$R2 627
11 TraesCS4B01G296500 chr2D 47008230 47008859 629 False 556.0 556 82.97200 1 632 1 chr2D.!!$F1 631

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
952 1032 0.179137 GCAGAAATAGCCAAACGCCC 60.179 55.0 0.0 0.0 38.78 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 4402 0.17902 CCAGAGAACCCACACAGCAA 60.179 55.0 0.0 0.0 0.0 3.91 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
20 21 2.740826 CCCCGACGCGTTCATGTT 60.741 61.111 15.53 0.00 0.00 2.71
64 65 1.205893 CGAAGAGCAAGTAGGCTTCCT 59.794 52.381 0.00 0.00 45.99 3.36
375 406 2.515991 GGCATTGAATCCCCGCGA 60.516 61.111 8.23 0.00 0.00 5.87
387 418 4.735132 CCGCGAGAAACCGAGGCA 62.735 66.667 8.23 0.00 42.10 4.75
390 421 0.804544 CGCGAGAAACCGAGGCAATA 60.805 55.000 0.00 0.00 0.00 1.90
449 481 1.131618 GCCGTTATTTCGCGCCAAAG 61.132 55.000 6.31 0.00 0.00 2.77
460 492 2.040544 CGCCAAAGTCGATTGCCCT 61.041 57.895 0.00 0.00 0.00 5.19
592 628 4.322385 GCCGGCGCTGAAAAACGT 62.322 61.111 20.25 0.00 0.00 3.99
594 630 2.604174 CCGGCGCTGAAAAACGTCT 61.604 57.895 20.25 0.00 0.00 4.18
610 650 4.052518 CTGGGGGCTGTTGGGGAG 62.053 72.222 0.00 0.00 0.00 4.30
749 790 5.124776 CGAGATTAGTCAAGTCAACTCCTCT 59.875 44.000 0.00 0.00 0.00 3.69
812 853 7.397892 TTGTGAAGTTTTACTGATTTGACCA 57.602 32.000 0.00 0.00 0.00 4.02
816 857 8.564574 GTGAAGTTTTACTGATTTGACCATACA 58.435 33.333 0.00 0.00 0.00 2.29
846 926 4.695217 TTAAAAAGCATCACGGATGACC 57.305 40.909 15.42 2.12 42.09 4.02
869 949 3.077556 AGTGATTCGCGCCTCCCT 61.078 61.111 0.00 0.00 0.00 4.20
879 959 2.370445 CGCCTCCCTGATCCCAACT 61.370 63.158 0.00 0.00 0.00 3.16
905 985 4.220821 AGCACCATATATACACTTCCTCCG 59.779 45.833 0.00 0.00 0.00 4.63
919 999 1.261238 CCTCCGAGCTCAAGTTCCCT 61.261 60.000 15.40 0.00 0.00 4.20
934 1014 3.383505 AGTTCCCTAACAAAACACAAGGC 59.616 43.478 0.00 0.00 38.12 4.35
940 1020 5.453198 CCCTAACAAAACACAAGGCAGAAAT 60.453 40.000 0.00 0.00 0.00 2.17
951 1031 3.329114 GCAGAAATAGCCAAACGCC 57.671 52.632 0.00 0.00 38.78 5.68
952 1032 0.179137 GCAGAAATAGCCAAACGCCC 60.179 55.000 0.00 0.00 38.78 6.13
953 1033 1.173043 CAGAAATAGCCAAACGCCCA 58.827 50.000 0.00 0.00 38.78 5.36
958 1038 1.591504 ATAGCCAAACGCCCAAACCG 61.592 55.000 0.00 0.00 38.78 4.44
973 1053 5.454520 CCCAAACCGTAACAAATCTTACAC 58.545 41.667 0.00 0.00 0.00 2.90
976 1056 2.738314 ACCGTAACAAATCTTACACGCC 59.262 45.455 0.00 0.00 0.00 5.68
995 1075 2.549992 GCCACACAGACACAATCCAGTA 60.550 50.000 0.00 0.00 0.00 2.74
996 1076 3.329386 CCACACAGACACAATCCAGTAG 58.671 50.000 0.00 0.00 0.00 2.57
1007 1087 1.457643 TCCAGTAGGAGATGGCCGG 60.458 63.158 0.00 0.00 39.61 6.13
1044 1124 3.080641 CTGCTGGGGTCATGGTCA 58.919 61.111 0.00 0.00 0.00 4.02
1083 1163 2.036256 AAGCTTGCCCTCGCCATT 59.964 55.556 0.00 0.00 0.00 3.16
1103 1183 1.040339 AAGGGCCTGAGCTACGAGAG 61.040 60.000 6.92 0.00 39.73 3.20
1132 1212 1.228657 GGACGTCCACAACAAGAGCC 61.229 60.000 29.75 0.00 35.64 4.70
1144 1224 0.906756 CAAGAGCCACCTCCTCCTCA 60.907 60.000 0.00 0.00 38.96 3.86
1170 1250 0.110486 ACCCCGTGCACAAGAAGATT 59.890 50.000 18.64 0.00 0.00 2.40
1238 1318 0.170561 GTGCAGTACATCGACGAGGT 59.829 55.000 19.81 19.81 0.00 3.85
1367 1447 1.004560 CGTCCAGGAGCAAGAGCAA 60.005 57.895 0.00 0.00 45.49 3.91
1488 1574 2.351276 GTCGGGCTGGTGGACATT 59.649 61.111 0.00 0.00 0.00 2.71
1513 1599 2.265739 GGAGCATGCACTCGTGGA 59.734 61.111 21.98 0.00 37.57 4.02
1802 1909 5.810074 ACCTTTTGATTGTTGTTTGTACTGC 59.190 36.000 0.00 0.00 0.00 4.40
1878 2094 0.515564 GCGGTTTACAGATGTGCGTT 59.484 50.000 0.00 0.00 0.00 4.84
1889 2105 3.067106 AGATGTGCGTTCAGTTTAGTGG 58.933 45.455 0.00 0.00 0.00 4.00
1891 2107 2.634600 TGTGCGTTCAGTTTAGTGGTT 58.365 42.857 0.00 0.00 0.00 3.67
1907 2127 5.391312 AGTGGTTATTTGATTCAACCTGC 57.609 39.130 0.00 0.00 41.89 4.85
1936 2156 3.407424 TCAGGTTTCTCACTGGACATG 57.593 47.619 0.00 0.00 35.47 3.21
1937 2157 2.038952 TCAGGTTTCTCACTGGACATGG 59.961 50.000 0.00 0.00 35.47 3.66
1945 2165 2.439701 CTGGACATGGCCTGCTGG 60.440 66.667 21.02 5.03 0.00 4.85
1948 2168 3.446570 GACATGGCCTGCTGGTGC 61.447 66.667 11.69 0.00 40.20 5.01
1961 2182 0.904649 CTGGTGCTGGATCCACTGTA 59.095 55.000 11.44 0.00 33.78 2.74
1983 2204 1.073319 TGGTTCAGGGTGAGGGGAA 60.073 57.895 0.00 0.00 0.00 3.97
1995 2216 3.519913 GGTGAGGGGAAACTGTCTAGATT 59.480 47.826 0.00 0.00 0.00 2.40
2007 2228 5.482908 ACTGTCTAGATTACTGCAAACTGG 58.517 41.667 0.00 0.00 0.00 4.00
2008 2229 4.832248 TGTCTAGATTACTGCAAACTGGG 58.168 43.478 0.00 0.00 0.00 4.45
2009 2230 4.286032 TGTCTAGATTACTGCAAACTGGGT 59.714 41.667 0.00 0.00 0.00 4.51
2010 2231 4.631813 GTCTAGATTACTGCAAACTGGGTG 59.368 45.833 0.00 0.00 0.00 4.61
2011 2232 2.795329 AGATTACTGCAAACTGGGTGG 58.205 47.619 0.00 0.00 0.00 4.61
2032 2259 3.388703 CTGCAGCCTCTGGGAGAGC 62.389 68.421 0.00 0.00 40.98 4.09
2035 2262 2.441901 AGCCTCTGGGAGAGCGAG 60.442 66.667 0.00 0.00 40.98 5.03
2097 2324 4.028490 TGGTAACTGCCCCTGCCG 62.028 66.667 0.00 0.00 36.33 5.69
2126 2361 2.865343 ACGAGAGTAAGTAATGGCGG 57.135 50.000 0.00 0.00 46.88 6.13
2127 2362 2.097825 ACGAGAGTAAGTAATGGCGGT 58.902 47.619 0.00 0.00 46.88 5.68
2128 2363 2.159282 ACGAGAGTAAGTAATGGCGGTG 60.159 50.000 0.00 0.00 46.88 4.94
2129 2364 2.798499 CGAGAGTAAGTAATGGCGGTGG 60.798 54.545 0.00 0.00 0.00 4.61
2130 2365 2.167900 GAGAGTAAGTAATGGCGGTGGT 59.832 50.000 0.00 0.00 0.00 4.16
2147 4305 2.127232 GTTGGCAGCTGGTTGGTGT 61.127 57.895 17.12 0.00 45.23 4.16
2154 4312 1.682854 CAGCTGGTTGGTGTCACAAAT 59.317 47.619 5.57 0.00 39.17 2.32
2172 4330 1.635663 ATTCGCGCTTCCGTCAAAGG 61.636 55.000 5.56 0.00 36.67 3.11
2173 4331 4.445545 CGCGCTTCCGTCAAAGGC 62.446 66.667 5.56 0.00 36.67 4.35
2174 4332 4.103103 GCGCTTCCGTCAAAGGCC 62.103 66.667 0.00 0.00 36.67 5.19
2175 4333 2.668212 CGCTTCCGTCAAAGGCCA 60.668 61.111 5.01 0.00 0.00 5.36
2176 4334 2.680913 CGCTTCCGTCAAAGGCCAG 61.681 63.158 5.01 0.00 0.00 4.85
2177 4335 1.302511 GCTTCCGTCAAAGGCCAGA 60.303 57.895 5.01 0.00 0.00 3.86
2178 4336 1.301677 GCTTCCGTCAAAGGCCAGAG 61.302 60.000 5.01 0.00 0.00 3.35
2179 4337 1.301677 CTTCCGTCAAAGGCCAGAGC 61.302 60.000 5.01 0.00 38.76 4.09
2229 4387 4.687215 GGGTCGCTGAGTGCTGCA 62.687 66.667 0.00 0.00 38.72 4.41
2230 4388 2.666190 GGTCGCTGAGTGCTGCAA 60.666 61.111 2.77 0.00 38.72 4.08
2231 4389 2.037136 GGTCGCTGAGTGCTGCAAT 61.037 57.895 2.77 1.70 38.72 3.56
2232 4390 1.423056 GTCGCTGAGTGCTGCAATC 59.577 57.895 21.92 21.92 38.72 2.67
2233 4391 1.018226 GTCGCTGAGTGCTGCAATCT 61.018 55.000 27.36 11.81 38.72 2.40
2234 4392 0.321034 TCGCTGAGTGCTGCAATCTT 60.321 50.000 27.36 4.43 38.72 2.40
2235 4393 0.179197 CGCTGAGTGCTGCAATCTTG 60.179 55.000 27.36 20.71 38.72 3.02
2254 4412 3.261441 CAAAGTGCTTGCTGTGTGG 57.739 52.632 0.00 0.00 0.00 4.17
2255 4413 0.249155 CAAAGTGCTTGCTGTGTGGG 60.249 55.000 0.00 0.00 0.00 4.61
2256 4414 0.684153 AAAGTGCTTGCTGTGTGGGT 60.684 50.000 0.00 0.00 0.00 4.51
2257 4415 0.684153 AAGTGCTTGCTGTGTGGGTT 60.684 50.000 0.00 0.00 0.00 4.11
2258 4416 1.103398 AGTGCTTGCTGTGTGGGTTC 61.103 55.000 0.00 0.00 0.00 3.62
2259 4417 1.103398 GTGCTTGCTGTGTGGGTTCT 61.103 55.000 0.00 0.00 0.00 3.01
2260 4418 0.819259 TGCTTGCTGTGTGGGTTCTC 60.819 55.000 0.00 0.00 0.00 2.87
2261 4419 0.536006 GCTTGCTGTGTGGGTTCTCT 60.536 55.000 0.00 0.00 0.00 3.10
2262 4420 1.233019 CTTGCTGTGTGGGTTCTCTG 58.767 55.000 0.00 0.00 0.00 3.35
2263 4421 0.179020 TTGCTGTGTGGGTTCTCTGG 60.179 55.000 0.00 0.00 0.00 3.86
2264 4422 1.302832 GCTGTGTGGGTTCTCTGGG 60.303 63.158 0.00 0.00 0.00 4.45
2265 4423 1.302832 CTGTGTGGGTTCTCTGGGC 60.303 63.158 0.00 0.00 0.00 5.36
2266 4424 2.055689 CTGTGTGGGTTCTCTGGGCA 62.056 60.000 0.00 0.00 0.00 5.36
2267 4425 1.600916 GTGTGGGTTCTCTGGGCAC 60.601 63.158 0.00 0.00 0.00 5.01
2268 4426 2.358737 GTGGGTTCTCTGGGCACG 60.359 66.667 0.00 0.00 0.00 5.34
2269 4427 3.636231 TGGGTTCTCTGGGCACGG 61.636 66.667 0.00 0.00 0.00 4.94
2270 4428 3.637273 GGGTTCTCTGGGCACGGT 61.637 66.667 0.00 0.00 0.00 4.83
2271 4429 2.358737 GGTTCTCTGGGCACGGTG 60.359 66.667 3.15 3.15 0.00 4.94
2272 4430 2.358737 GTTCTCTGGGCACGGTGG 60.359 66.667 10.60 0.00 0.00 4.61
2273 4431 2.847234 TTCTCTGGGCACGGTGGT 60.847 61.111 10.60 0.00 0.00 4.16
2291 4449 4.459089 GCACGGCTGGGACTCCTC 62.459 72.222 0.00 0.00 0.00 3.71
2292 4450 3.775654 CACGGCTGGGACTCCTCC 61.776 72.222 0.00 0.00 35.50 4.30
2293 4451 3.999285 ACGGCTGGGACTCCTCCT 61.999 66.667 0.00 0.00 36.68 3.69
2294 4452 3.465403 CGGCTGGGACTCCTCCTG 61.465 72.222 0.00 0.00 36.68 3.86
2295 4453 3.791586 GGCTGGGACTCCTCCTGC 61.792 72.222 0.00 0.00 44.95 4.85
2296 4454 4.154347 GCTGGGACTCCTCCTGCG 62.154 72.222 0.00 0.00 38.95 5.18
2297 4455 2.681778 CTGGGACTCCTCCTGCGT 60.682 66.667 0.00 0.00 36.68 5.24
2298 4456 2.680352 TGGGACTCCTCCTGCGTC 60.680 66.667 0.00 0.00 36.68 5.19
2299 4457 3.462678 GGGACTCCTCCTGCGTCC 61.463 72.222 0.00 0.00 45.02 4.79
2300 4458 2.363147 GGACTCCTCCTGCGTCCT 60.363 66.667 0.00 0.00 42.99 3.85
2301 4459 2.716017 GGACTCCTCCTGCGTCCTG 61.716 68.421 0.00 0.00 42.99 3.86
2302 4460 1.979693 GACTCCTCCTGCGTCCTGT 60.980 63.158 0.00 0.00 0.00 4.00
2303 4461 2.219325 GACTCCTCCTGCGTCCTGTG 62.219 65.000 0.00 0.00 0.00 3.66
2304 4462 2.997315 TCCTCCTGCGTCCTGTGG 60.997 66.667 0.00 0.00 0.00 4.17
2305 4463 4.767255 CCTCCTGCGTCCTGTGGC 62.767 72.222 0.00 0.00 0.00 5.01
2312 4470 4.988598 CGTCCTGTGGCGGCTGTT 62.989 66.667 11.43 0.00 0.00 3.16
2313 4471 3.357079 GTCCTGTGGCGGCTGTTG 61.357 66.667 11.43 0.00 0.00 3.33
2314 4472 3.555324 TCCTGTGGCGGCTGTTGA 61.555 61.111 11.43 0.00 0.00 3.18
2315 4473 2.594303 CCTGTGGCGGCTGTTGAA 60.594 61.111 11.43 0.00 0.00 2.69
2316 4474 2.639286 CTGTGGCGGCTGTTGAAC 59.361 61.111 11.43 0.00 0.00 3.18
2317 4475 2.904866 TGTGGCGGCTGTTGAACC 60.905 61.111 11.43 0.00 0.00 3.62
2322 4480 3.411351 CGGCTGTTGAACCGTCGG 61.411 66.667 10.48 10.48 44.46 4.79
2323 4481 2.280592 GGCTGTTGAACCGTCGGT 60.281 61.111 12.23 12.23 37.65 4.69
2324 4482 2.315386 GGCTGTTGAACCGTCGGTC 61.315 63.158 19.16 11.80 33.12 4.79
2325 4483 2.654912 GCTGTTGAACCGTCGGTCG 61.655 63.158 19.16 3.63 33.12 4.79
2335 4493 4.176851 GTCGGTCGGGCTCTCGTC 62.177 72.222 0.00 0.00 0.00 4.20
2338 4496 4.131088 GGTCGGGCTCTCGTCCAC 62.131 72.222 0.72 0.00 38.04 4.02
2339 4497 4.131088 GTCGGGCTCTCGTCCACC 62.131 72.222 0.00 0.00 33.27 4.61
2340 4498 4.361971 TCGGGCTCTCGTCCACCT 62.362 66.667 0.00 0.00 33.27 4.00
2341 4499 3.827898 CGGGCTCTCGTCCACCTC 61.828 72.222 0.00 0.00 33.27 3.85
2342 4500 3.827898 GGGCTCTCGTCCACCTCG 61.828 72.222 0.00 0.00 34.11 4.63
2343 4501 3.063084 GGCTCTCGTCCACCTCGT 61.063 66.667 0.00 0.00 0.00 4.18
2344 4502 2.486042 GCTCTCGTCCACCTCGTC 59.514 66.667 0.00 0.00 0.00 4.20
2345 4503 2.785921 CTCTCGTCCACCTCGTCG 59.214 66.667 0.00 0.00 0.00 5.12
2346 4504 2.031616 TCTCGTCCACCTCGTCGT 59.968 61.111 0.00 0.00 0.00 4.34
2347 4505 1.968703 CTCTCGTCCACCTCGTCGTC 61.969 65.000 0.00 0.00 0.00 4.20
2348 4506 3.364249 CTCGTCCACCTCGTCGTCG 62.364 68.421 0.00 0.00 38.55 5.12
2349 4507 4.456253 CGTCCACCTCGTCGTCGG 62.456 72.222 1.55 0.00 37.69 4.79
2350 4508 4.112341 GTCCACCTCGTCGTCGGG 62.112 72.222 1.55 0.00 37.69 5.14
2351 4509 4.334118 TCCACCTCGTCGTCGGGA 62.334 66.667 2.75 0.00 40.39 5.14
2352 4510 3.812019 CCACCTCGTCGTCGGGAG 61.812 72.222 2.75 2.15 40.39 4.30
2353 4511 2.745100 CACCTCGTCGTCGGGAGA 60.745 66.667 2.75 1.54 40.39 3.71
2494 4652 2.279784 GCGATGGAAGAGCGGGAG 60.280 66.667 0.00 0.00 0.00 4.30
2545 4703 2.272146 GGCTTCCAATCGGAGCCA 59.728 61.111 8.63 0.00 46.62 4.75
2599 4757 1.299976 CTTCGGGGTGGAAGAAGGG 59.700 63.158 0.00 0.00 44.93 3.95
2623 4781 4.436998 GAGGCGTCGGTCCTGGTG 62.437 72.222 0.00 0.00 33.24 4.17
2624 4782 4.988716 AGGCGTCGGTCCTGGTGA 62.989 66.667 0.00 0.00 31.53 4.02
2656 4832 2.361104 TCCACCCGCAATGAAGCC 60.361 61.111 0.00 0.00 0.00 4.35
2705 4881 2.739996 CGGGCCTCCTTCATGCTCT 61.740 63.158 0.84 0.00 0.00 4.09
2706 4882 1.148048 GGGCCTCCTTCATGCTCTC 59.852 63.158 0.84 0.00 0.00 3.20
2707 4883 1.148048 GGCCTCCTTCATGCTCTCC 59.852 63.158 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.776322 CGGCGCCTCCCAACATGA 62.776 66.667 26.68 0.00 0.00 3.07
114 115 0.978146 CGATGGGTGAGAGGTTCCCT 60.978 60.000 0.00 0.00 41.58 4.20
245 268 0.460311 CCCCTCGGCCGCTATATAAG 59.540 60.000 23.51 10.87 0.00 1.73
283 310 3.197790 CGCACCATCTTCCGCCAG 61.198 66.667 0.00 0.00 0.00 4.85
366 397 3.072468 TCGGTTTCTCGCGGGGAT 61.072 61.111 5.94 0.00 0.00 3.85
375 406 2.677037 CGTCCTTATTGCCTCGGTTTCT 60.677 50.000 0.00 0.00 0.00 2.52
387 418 1.226888 GCGCCTCGTCGTCCTTATT 60.227 57.895 0.00 0.00 0.00 1.40
592 628 4.608514 TCCCCAACAGCCCCCAGA 62.609 66.667 0.00 0.00 0.00 3.86
725 766 5.124776 AGAGGAGTTGACTTGACTAATCTCG 59.875 44.000 0.00 0.00 30.71 4.04
812 853 8.977505 GTGATGCTTTTTAAAATGTGTGTGTAT 58.022 29.630 13.53 0.74 0.00 2.29
816 857 5.461737 CCGTGATGCTTTTTAAAATGTGTGT 59.538 36.000 13.53 0.91 0.00 3.72
846 926 2.589492 GGCGCGAATCACTCCATCG 61.589 63.158 12.10 0.00 39.47 3.84
869 949 0.770499 TGGTGCTTGAGTTGGGATCA 59.230 50.000 0.00 0.00 0.00 2.92
879 959 6.239600 GGAGGAAGTGTATATATGGTGCTTGA 60.240 42.308 0.00 0.00 0.00 3.02
905 985 4.578928 TGTTTTGTTAGGGAACTTGAGCTC 59.421 41.667 6.82 6.82 43.67 4.09
919 999 6.212955 GCTATTTCTGCCTTGTGTTTTGTTA 58.787 36.000 0.00 0.00 0.00 2.41
934 1014 1.173043 TGGGCGTTTGGCTATTTCTG 58.827 50.000 0.00 0.00 42.94 3.02
940 1020 2.262303 CGGTTTGGGCGTTTGGCTA 61.262 57.895 0.00 0.00 42.94 3.93
946 1026 1.101331 TTTGTTACGGTTTGGGCGTT 58.899 45.000 0.00 0.00 0.00 4.84
947 1027 1.267533 GATTTGTTACGGTTTGGGCGT 59.732 47.619 0.00 0.00 0.00 5.68
948 1028 1.538075 AGATTTGTTACGGTTTGGGCG 59.462 47.619 0.00 0.00 0.00 6.13
949 1029 3.653539 AAGATTTGTTACGGTTTGGGC 57.346 42.857 0.00 0.00 0.00 5.36
950 1030 5.454520 GTGTAAGATTTGTTACGGTTTGGG 58.545 41.667 0.00 0.00 35.93 4.12
951 1031 5.141568 CGTGTAAGATTTGTTACGGTTTGG 58.858 41.667 0.00 0.00 35.93 3.28
952 1032 4.609708 GCGTGTAAGATTTGTTACGGTTTG 59.390 41.667 0.00 0.00 35.93 2.93
953 1033 4.319694 GGCGTGTAAGATTTGTTACGGTTT 60.320 41.667 0.00 0.00 35.93 3.27
958 1038 4.024725 TGTGTGGCGTGTAAGATTTGTTAC 60.025 41.667 0.00 0.00 34.07 2.50
973 1053 0.884259 TGGATTGTGTCTGTGTGGCG 60.884 55.000 0.00 0.00 0.00 5.69
976 1056 3.006859 TCCTACTGGATTGTGTCTGTGTG 59.993 47.826 0.00 0.00 37.46 3.82
995 1075 2.123077 CTCCTCCGGCCATCTCCT 60.123 66.667 2.24 0.00 0.00 3.69
996 1076 3.237741 CCTCCTCCGGCCATCTCC 61.238 72.222 2.24 0.00 0.00 3.71
1007 1087 1.069049 GCTTCAGCTCATCTCCTCCTC 59.931 57.143 0.00 0.00 38.21 3.71
1083 1163 0.257905 TCTCGTAGCTCAGGCCCTTA 59.742 55.000 0.00 0.00 39.73 2.69
1132 1212 0.906756 TTGGAGCTGAGGAGGAGGTG 60.907 60.000 0.00 0.00 0.00 4.00
1144 1224 4.643387 GTGCACGGGGTTGGAGCT 62.643 66.667 0.00 0.00 0.00 4.09
1170 1250 1.003839 GTTGTGGATGAGCACGGGA 60.004 57.895 0.00 0.00 0.00 5.14
1513 1599 2.345244 GGCCTCGATCGCCATCAT 59.655 61.111 11.09 0.00 46.27 2.45
1581 1667 2.464459 GCCGAAACGCTCCATCCAG 61.464 63.158 0.00 0.00 0.00 3.86
1726 1821 0.029700 TCACACACACACGTAGGTCG 59.970 55.000 0.00 0.00 46.00 4.79
1802 1909 4.433615 AGTATTACATCAACCTGCTGACG 58.566 43.478 0.00 0.00 0.00 4.35
1809 1916 9.917887 ACAGTAGTAGTAGTATTACATCAACCT 57.082 33.333 11.55 0.00 31.96 3.50
1878 2094 8.573035 GGTTGAATCAAATAACCACTAAACTGA 58.427 33.333 0.00 0.00 42.60 3.41
1889 2105 3.179048 GGCGCAGGTTGAATCAAATAAC 58.821 45.455 10.83 0.00 0.00 1.89
1891 2107 2.423185 CTGGCGCAGGTTGAATCAAATA 59.577 45.455 10.83 0.00 0.00 1.40
1907 2127 2.673368 GTGAGAAACCTGATAACTGGCG 59.327 50.000 0.00 0.00 38.45 5.69
1936 2156 4.437587 ATCCAGCACCAGCAGGCC 62.438 66.667 0.00 0.00 46.22 5.19
1937 2157 2.827642 GATCCAGCACCAGCAGGC 60.828 66.667 0.00 0.00 46.22 4.85
1945 2165 2.744202 CAGTTTACAGTGGATCCAGCAC 59.256 50.000 16.81 3.28 0.00 4.40
1948 2168 3.703001 ACCAGTTTACAGTGGATCCAG 57.297 47.619 16.81 7.12 45.69 3.86
1961 2182 0.478507 CCCTCACCCTGAACCAGTTT 59.521 55.000 0.00 0.00 0.00 2.66
1983 2204 5.934625 CCAGTTTGCAGTAATCTAGACAGTT 59.065 40.000 0.00 0.00 0.00 3.16
1995 2216 1.228429 GCCCACCCAGTTTGCAGTA 60.228 57.895 0.00 0.00 0.00 2.74
2035 2262 1.497722 CCGGAAGAAAGCGTTCTGC 59.502 57.895 15.83 13.68 43.59 4.26
2097 2324 1.099879 TTACTCTCGTCCTAGCGGGC 61.100 60.000 0.00 0.00 34.39 6.13
2099 2326 1.666054 ACTTACTCTCGTCCTAGCGG 58.334 55.000 0.00 0.00 0.00 5.52
2100 2327 4.319622 CCATTACTTACTCTCGTCCTAGCG 60.320 50.000 0.00 0.00 0.00 4.26
2125 2360 2.521708 AACCAGCTGCCAACCACC 60.522 61.111 8.66 0.00 0.00 4.61
2126 2361 2.730094 CAACCAGCTGCCAACCAC 59.270 61.111 8.66 0.00 0.00 4.16
2127 2362 2.521465 CCAACCAGCTGCCAACCA 60.521 61.111 8.66 0.00 0.00 3.67
2128 2363 2.521708 ACCAACCAGCTGCCAACC 60.522 61.111 8.66 0.00 0.00 3.77
2129 2364 2.075426 GACACCAACCAGCTGCCAAC 62.075 60.000 8.66 0.00 0.00 3.77
2130 2365 1.827789 GACACCAACCAGCTGCCAA 60.828 57.895 8.66 0.00 0.00 4.52
2147 4305 1.225376 ACGGAAGCGCGAATTTGTGA 61.225 50.000 12.10 0.00 0.00 3.58
2154 4312 2.314647 CCTTTGACGGAAGCGCGAA 61.315 57.895 12.10 0.00 0.00 4.70
2178 4336 1.160137 ACACTCTCGAAGCATTTGGC 58.840 50.000 0.00 0.00 45.30 4.52
2179 4337 3.365364 GGAAACACTCTCGAAGCATTTGG 60.365 47.826 0.00 0.00 0.00 3.28
2190 4348 1.079057 GAGCCGGGGAAACACTCTC 60.079 63.158 2.18 0.00 0.00 3.20
2193 4351 2.430367 GTGAGCCGGGGAAACACT 59.570 61.111 2.18 0.00 0.00 3.55
2236 4394 0.249155 CCCACACAGCAAGCACTTTG 60.249 55.000 0.00 0.00 39.88 2.77
2237 4395 0.684153 ACCCACACAGCAAGCACTTT 60.684 50.000 0.00 0.00 0.00 2.66
2238 4396 0.684153 AACCCACACAGCAAGCACTT 60.684 50.000 0.00 0.00 0.00 3.16
2239 4397 1.076777 AACCCACACAGCAAGCACT 60.077 52.632 0.00 0.00 0.00 4.40
2240 4398 1.103398 AGAACCCACACAGCAAGCAC 61.103 55.000 0.00 0.00 0.00 4.40
2241 4399 0.819259 GAGAACCCACACAGCAAGCA 60.819 55.000 0.00 0.00 0.00 3.91
2242 4400 0.536006 AGAGAACCCACACAGCAAGC 60.536 55.000 0.00 0.00 0.00 4.01
2243 4401 1.233019 CAGAGAACCCACACAGCAAG 58.767 55.000 0.00 0.00 0.00 4.01
2244 4402 0.179020 CCAGAGAACCCACACAGCAA 60.179 55.000 0.00 0.00 0.00 3.91
2245 4403 1.451504 CCAGAGAACCCACACAGCA 59.548 57.895 0.00 0.00 0.00 4.41
2246 4404 1.302832 CCCAGAGAACCCACACAGC 60.303 63.158 0.00 0.00 0.00 4.40
2247 4405 1.302832 GCCCAGAGAACCCACACAG 60.303 63.158 0.00 0.00 0.00 3.66
2248 4406 2.075566 TGCCCAGAGAACCCACACA 61.076 57.895 0.00 0.00 0.00 3.72
2249 4407 1.600916 GTGCCCAGAGAACCCACAC 60.601 63.158 0.00 0.00 0.00 3.82
2250 4408 2.836154 GTGCCCAGAGAACCCACA 59.164 61.111 0.00 0.00 0.00 4.17
2251 4409 2.358737 CGTGCCCAGAGAACCCAC 60.359 66.667 0.00 0.00 0.00 4.61
2252 4410 3.636231 CCGTGCCCAGAGAACCCA 61.636 66.667 0.00 0.00 0.00 4.51
2253 4411 3.637273 ACCGTGCCCAGAGAACCC 61.637 66.667 0.00 0.00 0.00 4.11
2254 4412 2.358737 CACCGTGCCCAGAGAACC 60.359 66.667 0.00 0.00 0.00 3.62
2255 4413 2.358737 CCACCGTGCCCAGAGAAC 60.359 66.667 0.00 0.00 0.00 3.01
2256 4414 2.847234 ACCACCGTGCCCAGAGAA 60.847 61.111 0.00 0.00 0.00 2.87
2257 4415 3.625897 CACCACCGTGCCCAGAGA 61.626 66.667 0.00 0.00 32.04 3.10
2274 4432 4.459089 GAGGAGTCCCAGCCGTGC 62.459 72.222 5.25 0.00 33.88 5.34
2275 4433 3.775654 GGAGGAGTCCCAGCCGTG 61.776 72.222 5.25 0.00 36.76 4.94
2276 4434 3.999285 AGGAGGAGTCCCAGCCGT 61.999 66.667 5.25 0.00 45.26 5.68
2277 4435 3.465403 CAGGAGGAGTCCCAGCCG 61.465 72.222 5.25 0.00 45.26 5.52
2278 4436 3.791586 GCAGGAGGAGTCCCAGCC 61.792 72.222 5.25 5.34 45.26 4.85
2279 4437 4.154347 CGCAGGAGGAGTCCCAGC 62.154 72.222 5.25 4.11 45.26 4.85
2280 4438 2.681778 ACGCAGGAGGAGTCCCAG 60.682 66.667 5.25 0.00 45.26 4.45
2281 4439 2.680352 GACGCAGGAGGAGTCCCA 60.680 66.667 5.25 0.00 45.26 4.37
2284 4442 1.979693 ACAGGACGCAGGAGGAGTC 60.980 63.158 0.00 0.00 44.58 3.36
2285 4443 2.118513 ACAGGACGCAGGAGGAGT 59.881 61.111 0.00 0.00 0.00 3.85
2286 4444 2.575993 CACAGGACGCAGGAGGAG 59.424 66.667 0.00 0.00 0.00 3.69
2287 4445 2.997315 CCACAGGACGCAGGAGGA 60.997 66.667 0.00 0.00 0.00 3.71
2288 4446 4.767255 GCCACAGGACGCAGGAGG 62.767 72.222 0.00 0.00 0.00 4.30
2295 4453 4.988598 AACAGCCGCCACAGGACG 62.989 66.667 0.00 0.00 0.00 4.79
2296 4454 3.357079 CAACAGCCGCCACAGGAC 61.357 66.667 0.00 0.00 0.00 3.85
2297 4455 3.113514 TTCAACAGCCGCCACAGGA 62.114 57.895 0.00 0.00 0.00 3.86
2298 4456 2.594303 TTCAACAGCCGCCACAGG 60.594 61.111 0.00 0.00 0.00 4.00
2299 4457 2.639286 GTTCAACAGCCGCCACAG 59.361 61.111 0.00 0.00 0.00 3.66
2300 4458 2.904866 GGTTCAACAGCCGCCACA 60.905 61.111 0.00 0.00 0.00 4.17
2301 4459 4.025401 CGGTTCAACAGCCGCCAC 62.025 66.667 0.00 0.00 41.53 5.01
2306 4464 2.280592 ACCGACGGTTCAACAGCC 60.281 61.111 15.37 0.00 27.29 4.85
2307 4465 2.654912 CGACCGACGGTTCAACAGC 61.655 63.158 22.69 5.21 35.25 4.40
2308 4466 3.534160 CGACCGACGGTTCAACAG 58.466 61.111 22.69 5.18 35.25 3.16
2318 4476 4.176851 GACGAGAGCCCGACCGAC 62.177 72.222 0.00 0.00 0.00 4.79
2321 4479 4.131088 GTGGACGAGAGCCCGACC 62.131 72.222 0.00 0.00 42.92 4.79
2322 4480 4.131088 GGTGGACGAGAGCCCGAC 62.131 72.222 0.00 0.00 35.79 4.79
2323 4481 4.361971 AGGTGGACGAGAGCCCGA 62.362 66.667 0.00 0.00 35.79 5.14
2324 4482 3.827898 GAGGTGGACGAGAGCCCG 61.828 72.222 0.00 0.00 35.79 6.13
2325 4483 3.827898 CGAGGTGGACGAGAGCCC 61.828 72.222 0.00 0.00 0.00 5.19
2326 4484 3.053849 GACGAGGTGGACGAGAGCC 62.054 68.421 0.00 0.00 34.70 4.70
2327 4485 2.486042 GACGAGGTGGACGAGAGC 59.514 66.667 0.00 0.00 34.70 4.09
2328 4486 1.968703 GACGACGAGGTGGACGAGAG 61.969 65.000 0.00 0.00 34.70 3.20
2329 4487 2.031516 GACGACGAGGTGGACGAGA 61.032 63.158 0.00 0.00 34.70 4.04
2330 4488 2.479650 GACGACGAGGTGGACGAG 59.520 66.667 0.00 0.00 34.70 4.18
2331 4489 3.417224 CGACGACGAGGTGGACGA 61.417 66.667 0.00 0.00 42.66 4.20
2332 4490 4.456253 CCGACGACGAGGTGGACG 62.456 72.222 9.28 0.00 42.66 4.79
2333 4491 4.112341 CCCGACGACGAGGTGGAC 62.112 72.222 9.28 0.00 42.66 4.02
2334 4492 4.334118 TCCCGACGACGAGGTGGA 62.334 66.667 9.28 3.81 42.66 4.02
2335 4493 3.812019 CTCCCGACGACGAGGTGG 61.812 72.222 9.28 1.16 42.66 4.61
2336 4494 2.745100 TCTCCCGACGACGAGGTG 60.745 66.667 9.28 9.28 42.66 4.00
2337 4495 2.745492 GTCTCCCGACGACGAGGT 60.745 66.667 9.28 0.00 42.66 3.85
2338 4496 2.745100 TGTCTCCCGACGACGAGG 60.745 66.667 9.28 8.57 43.21 4.63
2339 4497 2.751913 CCTGTCTCCCGACGACGAG 61.752 68.421 9.28 0.61 43.21 4.18
2340 4498 2.745100 CCTGTCTCCCGACGACGA 60.745 66.667 9.28 0.00 43.21 4.20
2341 4499 3.036783 GACCTGTCTCCCGACGACG 62.037 68.421 0.00 0.00 43.21 5.12
2342 4500 1.674980 AGACCTGTCTCCCGACGAC 60.675 63.158 0.00 0.00 43.21 4.34
2343 4501 2.755049 AGACCTGTCTCCCGACGA 59.245 61.111 0.00 0.00 43.21 4.20
2352 4510 4.803426 CAGGCGGCGAGACCTGTC 62.803 72.222 19.82 0.00 46.95 3.51
2577 4735 4.697756 CTTCCACCCCGAAGCGCA 62.698 66.667 11.47 0.00 33.33 6.09
2637 4813 3.039202 GCTTCATTGCGGGTGGACG 62.039 63.158 0.00 0.00 0.00 4.79
2638 4814 2.700773 GGCTTCATTGCGGGTGGAC 61.701 63.158 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.