Multiple sequence alignment - TraesCS4D01G182800

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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 TraesCS4D01G182800 chr4D 100.000 2504 0 0 1 2504 319703224 319700721 0.000000e+00 4625.0
1 TraesCS4D01G182800 chr4B 95.869 1767 29 8 1 1749 401880423 401882163 0.000000e+00 2819.0
2 TraesCS4D01G182800 chr4B 93.627 204 7 2 2307 2504 401884101 401884304 1.460000e-77 300.0
3 TraesCS4D01G182800 chr4B 85.833 240 15 4 1751 1979 401883879 401884110 1.160000e-58 237.0
4 TraesCS4D01G182800 chr4A 93.224 1712 69 26 309 1979 153778850 153780555 0.000000e+00 2475.0
5 TraesCS4D01G182800 chr4A 94.044 319 13 4 1 317 153775968 153776282 1.740000e-131 479.0
6 TraesCS4D01G182800 chr4A 90.323 93 5 1 2307 2395 153780546 153780638 4.380000e-23 119.0
7 TraesCS4D01G182800 chr4A 89.394 66 6 1 1796 1860 22749336 22749271 5.740000e-12 82.4
8 TraesCS4D01G182800 chr7D 96.238 319 11 1 1990 2307 156079535 156079853 2.850000e-144 521.0
9 TraesCS4D01G182800 chr7D 95.370 324 14 1 1990 2312 262758865 262758542 4.780000e-142 514.0
10 TraesCS4D01G182800 chr7D 88.608 79 8 1 1783 1860 593265134 593265056 7.370000e-16 95.3
11 TraesCS4D01G182800 chr2B 95.706 326 11 3 1978 2301 691015615 691015939 2.850000e-144 521.0
12 TraesCS4D01G182800 chr1D 95.963 322 12 1 1990 2310 218258741 218259062 2.850000e-144 521.0
13 TraesCS4D01G182800 chr1D 95.938 320 12 1 1988 2306 7423856 7424175 3.690000e-143 518.0
14 TraesCS4D01G182800 chr1D 95.925 319 12 1 1990 2307 359693216 359693534 1.330000e-142 516.0
15 TraesCS4D01G182800 chr1D 94.595 333 16 2 1975 2306 432685943 432685612 4.780000e-142 514.0
16 TraesCS4D01G182800 chr2D 95.679 324 13 1 1990 2312 534851832 534852155 1.030000e-143 520.0
17 TraesCS4D01G182800 chr2D 90.566 53 4 1 1811 1862 109704179 109704127 4.470000e-08 69.4
18 TraesCS4D01G182800 chr3D 94.545 330 17 1 1978 2306 15618068 15617739 2.220000e-140 508.0
19 TraesCS4D01G182800 chr3D 80.488 82 14 2 1780 1860 482504996 482504916 7.480000e-06 62.1
20 TraesCS4D01G182800 chr7B 85.034 147 21 1 2358 2504 481696157 481696012 5.580000e-32 148.0
21 TraesCS4D01G182800 chr7B 88.608 79 8 1 1783 1860 431680289 431680367 7.370000e-16 95.3
22 TraesCS4D01G182800 chr1A 86.420 81 10 1 1783 1862 466926305 466926385 1.230000e-13 87.9
23 TraesCS4D01G182800 chr6A 85.366 82 11 1 1779 1859 232331693 232331774 1.600000e-12 84.2
24 TraesCS4D01G182800 chr5B 87.500 72 8 1 1790 1860 28207671 28207600 5.740000e-12 82.4
25 TraesCS4D01G182800 chr5D 88.235 68 4 1 2322 2385 447522950 447523017 7.430000e-11 78.7
26 TraesCS4D01G182800 chr6D 100.000 39 0 0 2347 2385 412973702 412973740 3.450000e-09 73.1
27 TraesCS4D01G182800 chr3B 83.333 78 12 1 1783 1859 443362652 443362729 1.240000e-08 71.3


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 TraesCS4D01G182800 chr4D 319700721 319703224 2503 True 4625.000000 4625 100.000000 1 2504 1 chr4D.!!$R1 2503
1 TraesCS4D01G182800 chr4B 401880423 401884304 3881 False 1118.666667 2819 91.776333 1 2504 3 chr4B.!!$F1 2503
2 TraesCS4D01G182800 chr4A 153775968 153780638 4670 False 1024.333333 2475 92.530333 1 2395 3 chr4A.!!$F1 2394

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
896 3493 0.756815 CAAAATAGCCTCCCAGCCCC 60.757 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
2185 6512 0.178992 CCTGAGTTTTGAGCCCACCA 60.179 55.0 0.0 0.0 0.0 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.289010 CCCATGGTTGAAAGCTGGTTTC 60.289 50.000 21.84 21.84 44.41 2.78
166 168 2.737252 GGGAGCATTCGTATCCGATTTC 59.263 50.000 0.00 0.00 43.80 2.17
239 241 5.276536 GCGTTTGTCACCCTATACGTATTTC 60.277 44.000 14.33 0.00 0.00 2.17
395 2978 2.652382 TTTCCTCCACACGCGCTCAA 62.652 55.000 5.73 0.00 0.00 3.02
607 3190 3.189010 AACCAAGCGCCGAAAACCG 62.189 57.895 2.29 0.00 38.18 4.44
702 3285 1.003839 ACATCACCCGCGTTGACAT 60.004 52.632 4.92 0.00 0.00 3.06
896 3493 0.756815 CAAAATAGCCTCCCAGCCCC 60.757 60.000 0.00 0.00 0.00 5.80
959 3556 1.039785 ATCTAGCTCTGCGGCTGTCA 61.040 55.000 0.00 0.00 43.01 3.58
1436 4033 2.693074 TGATAAGTATGGCTGCTGACGA 59.307 45.455 0.00 0.00 0.00 4.20
1613 4210 3.669536 TGGCGTGAGATTGATTGTTGTA 58.330 40.909 0.00 0.00 0.00 2.41
1668 4265 7.502696 TGTATCGTAGCTGTTACCCATAAAAT 58.497 34.615 0.00 0.00 0.00 1.82
1669 4266 7.654520 TGTATCGTAGCTGTTACCCATAAAATC 59.345 37.037 0.00 0.00 0.00 2.17
1670 4267 5.045215 TCGTAGCTGTTACCCATAAAATCG 58.955 41.667 0.00 0.00 0.00 3.34
1734 4335 5.529800 TGGAAACTTAAACAAGTGCTCTACC 59.470 40.000 0.00 0.00 32.47 3.18
1749 4350 1.207791 CTACCCTCCTGCAGGTCATT 58.792 55.000 31.58 17.09 41.51 2.57
1760 6075 4.832266 CCTGCAGGTCATTATACTCTCTCT 59.168 45.833 25.53 0.00 0.00 3.10
1830 6146 4.778143 GACCCATTGCGGCGGAGT 62.778 66.667 9.78 0.00 0.00 3.85
1894 6215 4.275689 TCAGAAAACAGCACTACATTGTGG 59.724 41.667 0.00 0.00 38.31 4.17
1901 6222 2.147958 GCACTACATTGTGGAACGGAA 58.852 47.619 7.20 0.00 42.39 4.30
1906 6227 1.697432 ACATTGTGGAACGGAAGGAGA 59.303 47.619 0.00 0.00 42.39 3.71
1982 6309 6.051179 AGAAAAGAAGACAGTGGGTATACC 57.949 41.667 13.99 13.99 40.81 2.73
1983 6310 5.785940 AGAAAAGAAGACAGTGGGTATACCT 59.214 40.000 21.25 0.66 41.11 3.08
1984 6311 5.422214 AAAGAAGACAGTGGGTATACCTG 57.578 43.478 21.25 14.09 41.11 4.00
1985 6312 3.375699 AGAAGACAGTGGGTATACCTGG 58.624 50.000 21.25 10.69 41.11 4.45
1986 6313 1.497161 AGACAGTGGGTATACCTGGC 58.503 55.000 21.25 14.01 41.11 4.85
1987 6314 0.468648 GACAGTGGGTATACCTGGCC 59.531 60.000 21.25 0.00 41.11 5.36
1988 6315 0.252974 ACAGTGGGTATACCTGGCCA 60.253 55.000 21.25 4.71 41.11 5.36
1989 6316 1.140312 CAGTGGGTATACCTGGCCAT 58.860 55.000 21.25 0.00 41.11 4.40
1990 6317 1.140312 AGTGGGTATACCTGGCCATG 58.860 55.000 21.25 6.06 41.11 3.66
1991 6318 0.110486 GTGGGTATACCTGGCCATGG 59.890 60.000 21.25 13.05 41.11 3.66
1992 6319 1.065410 TGGGTATACCTGGCCATGGG 61.065 60.000 21.25 16.10 41.11 4.00
1993 6320 2.426305 GGGTATACCTGGCCATGGGC 62.426 65.000 30.65 30.65 41.80 5.36
2025 6352 4.473643 CCCACGGCAGAAAACTGA 57.526 55.556 0.00 0.00 0.00 3.41
2026 6353 2.247790 CCCACGGCAGAAAACTGAG 58.752 57.895 0.00 0.00 0.00 3.35
2027 6354 1.237285 CCCACGGCAGAAAACTGAGG 61.237 60.000 0.00 0.00 0.00 3.86
2028 6355 1.576421 CACGGCAGAAAACTGAGGC 59.424 57.895 0.00 0.00 0.00 4.70
2029 6356 1.600916 ACGGCAGAAAACTGAGGCC 60.601 57.895 0.00 0.00 41.20 5.19
2030 6357 2.335712 CGGCAGAAAACTGAGGCCC 61.336 63.158 0.00 0.00 41.58 5.80
2031 6358 1.228552 GGCAGAAAACTGAGGCCCA 60.229 57.895 0.00 0.00 38.70 5.36
2039 6366 3.086600 CTGAGGCCCAGTCCCTCC 61.087 72.222 11.85 0.00 46.69 4.30
2040 6367 3.931631 CTGAGGCCCAGTCCCTCCA 62.932 68.421 11.85 0.00 46.69 3.86
2041 6368 3.086600 GAGGCCCAGTCCCTCCAG 61.087 72.222 0.00 0.00 42.46 3.86
2042 6369 4.748798 AGGCCCAGTCCCTCCAGG 62.749 72.222 0.00 0.00 0.00 4.45
2046 6373 4.748798 CCAGTCCCTCCAGGCCCT 62.749 72.222 0.00 0.00 34.51 5.19
2047 6374 2.368594 CAGTCCCTCCAGGCCCTA 59.631 66.667 0.00 0.00 34.51 3.53
2048 6375 2.066999 CAGTCCCTCCAGGCCCTAC 61.067 68.421 0.00 0.00 34.51 3.18
2049 6376 2.768769 GTCCCTCCAGGCCCTACC 60.769 72.222 0.00 0.00 39.61 3.18
2050 6377 3.289211 TCCCTCCAGGCCCTACCA 61.289 66.667 0.00 0.00 43.14 3.25
2051 6378 2.039405 CCCTCCAGGCCCTACCAT 60.039 66.667 0.00 0.00 43.14 3.55
2052 6379 2.150051 CCCTCCAGGCCCTACCATC 61.150 68.421 0.00 0.00 43.14 3.51
2053 6380 2.511452 CCTCCAGGCCCTACCATCG 61.511 68.421 0.00 0.00 43.14 3.84
2054 6381 2.445845 TCCAGGCCCTACCATCGG 60.446 66.667 0.00 0.00 43.14 4.18
2055 6382 3.560251 CCAGGCCCTACCATCGGG 61.560 72.222 0.00 0.00 44.89 5.14
2060 6387 3.468063 CCCTACCATCGGGCCTAC 58.532 66.667 0.84 0.00 37.90 3.18
2061 6388 1.152312 CCCTACCATCGGGCCTACT 60.152 63.158 0.84 0.00 37.90 2.57
2062 6389 0.763223 CCCTACCATCGGGCCTACTT 60.763 60.000 0.84 0.00 37.90 2.24
2063 6390 1.129058 CCTACCATCGGGCCTACTTT 58.871 55.000 0.84 0.00 37.90 2.66
2064 6391 1.489230 CCTACCATCGGGCCTACTTTT 59.511 52.381 0.84 0.00 37.90 2.27
2065 6392 2.484947 CCTACCATCGGGCCTACTTTTC 60.485 54.545 0.84 0.00 37.90 2.29
2066 6393 0.988832 ACCATCGGGCCTACTTTTCA 59.011 50.000 0.84 0.00 37.90 2.69
2067 6394 1.353022 ACCATCGGGCCTACTTTTCAA 59.647 47.619 0.84 0.00 37.90 2.69
2068 6395 2.017049 CCATCGGGCCTACTTTTCAAG 58.983 52.381 0.84 0.00 0.00 3.02
2069 6396 1.401905 CATCGGGCCTACTTTTCAAGC 59.598 52.381 0.84 0.00 0.00 4.01
2070 6397 0.322187 TCGGGCCTACTTTTCAAGCC 60.322 55.000 0.84 0.00 43.09 4.35
2072 6399 3.356814 GGCCTACTTTTCAAGCCCA 57.643 52.632 0.00 0.00 37.66 5.36
2073 6400 1.627864 GGCCTACTTTTCAAGCCCAA 58.372 50.000 0.00 0.00 37.66 4.12
2074 6401 1.546029 GGCCTACTTTTCAAGCCCAAG 59.454 52.381 0.00 0.00 37.66 3.61
2075 6402 1.067565 GCCTACTTTTCAAGCCCAAGC 60.068 52.381 0.00 0.00 40.32 4.01
2076 6403 1.546029 CCTACTTTTCAAGCCCAAGCC 59.454 52.381 0.00 0.00 41.25 4.35
2077 6404 1.546029 CTACTTTTCAAGCCCAAGCCC 59.454 52.381 0.00 0.00 41.25 5.19
2078 6405 1.290009 CTTTTCAAGCCCAAGCCCG 59.710 57.895 0.00 0.00 41.25 6.13
2079 6406 2.158561 CTTTTCAAGCCCAAGCCCGG 62.159 60.000 0.00 0.00 41.25 5.73
2087 6414 2.043450 CCAAGCCCGGCCCATTTA 60.043 61.111 5.55 0.00 0.00 1.40
2088 6415 1.684049 CCAAGCCCGGCCCATTTAA 60.684 57.895 5.55 0.00 0.00 1.52
2089 6416 1.048160 CCAAGCCCGGCCCATTTAAT 61.048 55.000 5.55 0.00 0.00 1.40
2090 6417 1.698506 CAAGCCCGGCCCATTTAATA 58.301 50.000 5.55 0.00 0.00 0.98
2091 6418 2.035632 CAAGCCCGGCCCATTTAATAA 58.964 47.619 5.55 0.00 0.00 1.40
2092 6419 2.432510 CAAGCCCGGCCCATTTAATAAA 59.567 45.455 5.55 0.00 0.00 1.40
2093 6420 2.753247 AGCCCGGCCCATTTAATAAAA 58.247 42.857 5.55 0.00 0.00 1.52
2094 6421 3.108376 AGCCCGGCCCATTTAATAAAAA 58.892 40.909 5.55 0.00 0.00 1.94
2095 6422 3.133901 AGCCCGGCCCATTTAATAAAAAG 59.866 43.478 5.55 0.00 0.00 2.27
2096 6423 3.462982 CCCGGCCCATTTAATAAAAAGC 58.537 45.455 0.00 0.00 0.00 3.51
2097 6424 3.462982 CCGGCCCATTTAATAAAAAGCC 58.537 45.455 0.00 11.63 36.61 4.35
2098 6425 3.462982 CGGCCCATTTAATAAAAAGCCC 58.537 45.455 14.36 3.45 36.62 5.19
2099 6426 3.133901 CGGCCCATTTAATAAAAAGCCCT 59.866 43.478 14.36 0.00 36.62 5.19
2100 6427 4.450976 GGCCCATTTAATAAAAAGCCCTG 58.549 43.478 10.93 0.00 35.14 4.45
2101 6428 4.163268 GGCCCATTTAATAAAAAGCCCTGA 59.837 41.667 10.93 0.00 35.14 3.86
2102 6429 5.338789 GGCCCATTTAATAAAAAGCCCTGAA 60.339 40.000 10.93 0.00 35.14 3.02
2103 6430 6.176896 GCCCATTTAATAAAAAGCCCTGAAA 58.823 36.000 0.00 0.00 0.00 2.69
2104 6431 6.657117 GCCCATTTAATAAAAAGCCCTGAAAA 59.343 34.615 0.00 0.00 0.00 2.29
2105 6432 7.148255 GCCCATTTAATAAAAAGCCCTGAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
2106 6433 7.148255 CCCATTTAATAAAAAGCCCTGAAAAGC 60.148 37.037 0.00 0.00 0.00 3.51
2107 6434 7.148255 CCATTTAATAAAAAGCCCTGAAAAGCC 60.148 37.037 0.00 0.00 0.00 4.35
2108 6435 3.981071 ATAAAAAGCCCTGAAAAGCCC 57.019 42.857 0.00 0.00 0.00 5.19
2109 6436 1.806496 AAAAAGCCCTGAAAAGCCCT 58.194 45.000 0.00 0.00 0.00 5.19
2110 6437 1.806496 AAAAGCCCTGAAAAGCCCTT 58.194 45.000 0.00 0.00 0.00 3.95
2111 6438 2.694616 AAAGCCCTGAAAAGCCCTTA 57.305 45.000 0.00 0.00 0.00 2.69
2112 6439 2.222227 AAGCCCTGAAAAGCCCTTAG 57.778 50.000 0.00 0.00 0.00 2.18
2113 6440 0.332972 AGCCCTGAAAAGCCCTTAGG 59.667 55.000 0.00 0.00 0.00 2.69
2144 6471 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
2145 6472 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
2146 6473 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
2147 6474 0.323087 GCCGGGCCTCTTCCTTAAAA 60.323 55.000 8.12 0.00 0.00 1.52
2148 6475 1.685180 GCCGGGCCTCTTCCTTAAAAT 60.685 52.381 8.12 0.00 0.00 1.82
2149 6476 2.024414 CCGGGCCTCTTCCTTAAAATG 58.976 52.381 0.84 0.00 0.00 2.32
2150 6477 1.405463 CGGGCCTCTTCCTTAAAATGC 59.595 52.381 0.84 0.00 0.00 3.56
2151 6478 1.757118 GGGCCTCTTCCTTAAAATGCC 59.243 52.381 0.84 0.00 36.92 4.40
2152 6479 2.456577 GGCCTCTTCCTTAAAATGCCA 58.543 47.619 0.00 0.00 37.58 4.92
2153 6480 2.831526 GGCCTCTTCCTTAAAATGCCAA 59.168 45.455 0.00 0.00 37.58 4.52
2154 6481 3.452264 GGCCTCTTCCTTAAAATGCCAAT 59.548 43.478 0.00 0.00 37.58 3.16
2155 6482 4.649218 GGCCTCTTCCTTAAAATGCCAATA 59.351 41.667 0.00 0.00 37.58 1.90
2156 6483 5.305386 GGCCTCTTCCTTAAAATGCCAATAT 59.695 40.000 0.00 0.00 37.58 1.28
2157 6484 6.218746 GCCTCTTCCTTAAAATGCCAATATG 58.781 40.000 0.00 0.00 0.00 1.78
2158 6485 6.218746 CCTCTTCCTTAAAATGCCAATATGC 58.781 40.000 0.00 0.00 0.00 3.14
2159 6486 6.160576 TCTTCCTTAAAATGCCAATATGCC 57.839 37.500 0.00 0.00 0.00 4.40
2160 6487 5.660417 TCTTCCTTAAAATGCCAATATGCCA 59.340 36.000 0.00 0.00 0.00 4.92
2161 6488 5.946942 TCCTTAAAATGCCAATATGCCAA 57.053 34.783 0.00 0.00 0.00 4.52
2162 6489 5.916318 TCCTTAAAATGCCAATATGCCAAG 58.084 37.500 0.00 0.00 0.00 3.61
2163 6490 5.424895 TCCTTAAAATGCCAATATGCCAAGT 59.575 36.000 0.00 0.00 0.00 3.16
2164 6491 5.754890 CCTTAAAATGCCAATATGCCAAGTC 59.245 40.000 0.00 0.00 0.00 3.01
2165 6492 3.825143 AAATGCCAATATGCCAAGTCC 57.175 42.857 0.00 0.00 0.00 3.85
2166 6493 2.457813 ATGCCAATATGCCAAGTCCA 57.542 45.000 0.00 0.00 0.00 4.02
2167 6494 2.228545 TGCCAATATGCCAAGTCCAA 57.771 45.000 0.00 0.00 0.00 3.53
2168 6495 2.101783 TGCCAATATGCCAAGTCCAAG 58.898 47.619 0.00 0.00 0.00 3.61
2169 6496 1.202452 GCCAATATGCCAAGTCCAAGC 60.202 52.381 0.00 0.00 0.00 4.01
2170 6497 1.410153 CCAATATGCCAAGTCCAAGCC 59.590 52.381 0.00 0.00 0.00 4.35
2171 6498 1.410153 CAATATGCCAAGTCCAAGCCC 59.590 52.381 0.00 0.00 0.00 5.19
2172 6499 0.466189 ATATGCCAAGTCCAAGCCCG 60.466 55.000 0.00 0.00 0.00 6.13
2173 6500 1.847798 TATGCCAAGTCCAAGCCCGT 61.848 55.000 0.00 0.00 0.00 5.28
2174 6501 3.056328 GCCAAGTCCAAGCCCGTC 61.056 66.667 0.00 0.00 0.00 4.79
2175 6502 2.359975 CCAAGTCCAAGCCCGTCC 60.360 66.667 0.00 0.00 0.00 4.79
2176 6503 2.429930 CAAGTCCAAGCCCGTCCA 59.570 61.111 0.00 0.00 0.00 4.02
2177 6504 1.672356 CAAGTCCAAGCCCGTCCAG 60.672 63.158 0.00 0.00 0.00 3.86
2178 6505 2.895424 AAGTCCAAGCCCGTCCAGG 61.895 63.158 0.00 0.00 40.63 4.45
2189 6516 4.729918 GTCCAGGCCCTGCTGGTG 62.730 72.222 4.81 0.37 41.28 4.17
2196 6523 3.970410 CCCTGCTGGTGGGCTCAA 61.970 66.667 9.00 0.00 37.99 3.02
2197 6524 2.115910 CCTGCTGGTGGGCTCAAA 59.884 61.111 0.51 0.00 0.00 2.69
2198 6525 1.531365 CCTGCTGGTGGGCTCAAAA 60.531 57.895 0.51 0.00 0.00 2.44
2199 6526 1.662044 CTGCTGGTGGGCTCAAAAC 59.338 57.895 0.00 0.00 0.00 2.43
2200 6527 0.825010 CTGCTGGTGGGCTCAAAACT 60.825 55.000 0.00 0.00 0.00 2.66
2201 6528 0.823356 TGCTGGTGGGCTCAAAACTC 60.823 55.000 0.00 0.00 0.00 3.01
2202 6529 0.823356 GCTGGTGGGCTCAAAACTCA 60.823 55.000 0.00 0.00 0.00 3.41
2203 6530 1.242076 CTGGTGGGCTCAAAACTCAG 58.758 55.000 0.00 0.00 0.00 3.35
2204 6531 0.178992 TGGTGGGCTCAAAACTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
2205 6532 1.527433 GGTGGGCTCAAAACTCAGGC 61.527 60.000 0.00 0.00 34.44 4.85
2207 6534 3.686760 GGCTCAAAACTCAGGCCC 58.313 61.111 0.00 0.00 37.12 5.80
2208 6535 1.228552 GGCTCAAAACTCAGGCCCA 60.229 57.895 0.00 0.00 37.12 5.36
2209 6536 0.827507 GGCTCAAAACTCAGGCCCAA 60.828 55.000 0.00 0.00 37.12 4.12
2210 6537 0.600057 GCTCAAAACTCAGGCCCAAG 59.400 55.000 0.00 0.00 0.00 3.61
2211 6538 0.600057 CTCAAAACTCAGGCCCAAGC 59.400 55.000 0.00 0.00 38.76 4.01
2233 6560 2.757099 CCCACAGGCAAGCCCATC 60.757 66.667 7.62 0.00 36.58 3.51
2234 6561 3.136123 CCACAGGCAAGCCCATCG 61.136 66.667 7.62 0.00 36.58 3.84
2235 6562 3.136123 CACAGGCAAGCCCATCGG 61.136 66.667 7.62 0.00 36.58 4.18
2255 6582 2.278332 GCCTAGGCCCTGGATTTTAG 57.722 55.000 24.19 0.33 34.56 1.85
2256 6583 1.202940 GCCTAGGCCCTGGATTTTAGG 60.203 57.143 24.19 10.45 34.56 2.69
2262 6589 3.520623 CCTGGATTTTAGGGCTGGG 57.479 57.895 0.00 0.00 0.00 4.45
2263 6590 0.756815 CCTGGATTTTAGGGCTGGGC 60.757 60.000 0.00 0.00 0.00 5.36
2304 6631 3.313874 CCGGAGATGGCCAGAACT 58.686 61.111 13.05 10.74 0.00 3.01
2305 6632 2.516448 CCGGAGATGGCCAGAACTA 58.484 57.895 13.05 0.00 0.00 2.24
2306 6633 0.830648 CCGGAGATGGCCAGAACTAA 59.169 55.000 13.05 0.00 0.00 2.24
2307 6634 1.473434 CCGGAGATGGCCAGAACTAAC 60.473 57.143 13.05 6.54 0.00 2.34
2308 6635 1.207089 CGGAGATGGCCAGAACTAACA 59.793 52.381 13.05 0.00 0.00 2.41
2309 6636 2.739932 CGGAGATGGCCAGAACTAACAG 60.740 54.545 13.05 0.00 0.00 3.16
2318 6645 3.244457 GCCAGAACTAACAGTGGGTAAGT 60.244 47.826 0.00 0.00 0.00 2.24
2456 6793 1.678627 CCTCCTTCATCGTCATCGTCT 59.321 52.381 0.00 0.00 38.33 4.18
2463 6800 0.658368 ATCGTCATCGTCTGAGGTCG 59.342 55.000 9.20 3.07 40.04 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.659427 TATTCTCGTGCCGACGGTAG 59.341 55.000 16.73 8.39 46.11 3.18
166 168 5.647589 TGTTTCTCACTTACCTAGTATGCG 58.352 41.667 0.00 0.00 34.56 4.73
239 241 4.785301 ACCACCAGTCAAATATGGATGAG 58.215 43.478 0.00 0.00 39.02 2.90
338 2917 1.005512 TAACACCACGCGCATGTCT 60.006 52.632 5.73 2.40 0.00 3.41
395 2978 2.559668 TGTTCGATCCACCTTACGTTCT 59.440 45.455 0.00 0.00 0.00 3.01
721 3304 1.116536 TTCGTGGAGGTGGTGCACTA 61.117 55.000 17.98 8.10 45.11 2.74
928 3525 2.011881 GCTAGATCGGAAGCGCGAC 61.012 63.158 12.10 0.04 0.00 5.19
959 3556 2.680370 GGGAAATGGGGAGCCTCGT 61.680 63.158 0.00 0.00 0.00 4.18
1519 4116 4.517832 TCAAGTCTAGTGCTTTACAGTCGA 59.482 41.667 0.00 0.00 32.79 4.20
1687 4288 6.706270 CCAAGGATACACGCATAGTATCTTTT 59.294 38.462 15.51 10.13 42.18 2.27
1817 6132 2.559998 ATTTTTACTCCGCCGCAATG 57.440 45.000 0.00 0.00 0.00 2.82
1819 6134 4.035441 GGTATAATTTTTACTCCGCCGCAA 59.965 41.667 0.00 0.00 0.00 4.85
1822 6137 4.812626 AGTGGTATAATTTTTACTCCGCCG 59.187 41.667 0.00 0.00 0.00 6.46
1894 6215 6.746120 TGCTAGTAATATTCTCCTTCCGTTC 58.254 40.000 0.00 0.00 0.00 3.95
1901 6222 6.183361 ACCTCTCCTGCTAGTAATATTCTCCT 60.183 42.308 0.00 0.00 0.00 3.69
1906 6227 5.088026 GGGACCTCTCCTGCTAGTAATATT 58.912 45.833 0.00 0.00 36.68 1.28
1973 6300 1.065410 CCCATGGCCAGGTATACCCA 61.065 60.000 18.65 9.54 36.42 4.51
1974 6301 1.767692 CCCATGGCCAGGTATACCC 59.232 63.158 18.65 3.62 36.42 3.69
1975 6302 1.074951 GCCCATGGCCAGGTATACC 59.925 63.158 17.55 14.54 44.06 2.73
1976 6303 4.821935 GCCCATGGCCAGGTATAC 57.178 61.111 17.55 0.00 44.06 1.47
2008 6335 1.237285 CCTCAGTTTTCTGCCGTGGG 61.237 60.000 0.00 0.00 46.59 4.61
2009 6336 1.856265 GCCTCAGTTTTCTGCCGTGG 61.856 60.000 0.00 0.00 46.59 4.94
2010 6337 1.576421 GCCTCAGTTTTCTGCCGTG 59.424 57.895 0.00 0.00 46.59 4.94
2011 6338 1.600916 GGCCTCAGTTTTCTGCCGT 60.601 57.895 0.00 0.00 46.59 5.68
2012 6339 2.335712 GGGCCTCAGTTTTCTGCCG 61.336 63.158 0.84 0.00 46.59 5.69
2013 6340 1.228552 TGGGCCTCAGTTTTCTGCC 60.229 57.895 4.53 0.00 46.59 4.85
2014 6341 2.261215 CTGGGCCTCAGTTTTCTGC 58.739 57.895 4.53 0.00 46.59 4.26
2023 6350 3.931631 CTGGAGGGACTGGGCCTCA 62.932 68.421 4.53 0.00 41.55 3.86
2024 6351 3.086600 CTGGAGGGACTGGGCCTC 61.087 72.222 4.53 0.00 41.55 4.70
2025 6352 4.748798 CCTGGAGGGACTGGGCCT 62.749 72.222 4.53 0.00 41.55 5.19
2029 6356 3.332393 TAGGGCCTGGAGGGACTGG 62.332 68.421 18.53 0.00 44.42 4.00
2030 6357 2.066999 GTAGGGCCTGGAGGGACTG 61.067 68.421 18.53 0.00 44.42 3.51
2031 6358 2.369001 GTAGGGCCTGGAGGGACT 59.631 66.667 18.53 0.00 44.42 3.85
2032 6359 2.768769 GGTAGGGCCTGGAGGGAC 60.769 72.222 18.53 4.57 44.23 4.46
2033 6360 2.621672 GATGGTAGGGCCTGGAGGGA 62.622 65.000 18.53 0.00 38.35 4.20
2034 6361 2.039405 ATGGTAGGGCCTGGAGGG 60.039 66.667 18.53 0.00 38.35 4.30
2035 6362 2.511452 CGATGGTAGGGCCTGGAGG 61.511 68.421 18.53 0.00 38.35 4.30
2036 6363 2.511452 CCGATGGTAGGGCCTGGAG 61.511 68.421 18.53 1.24 38.35 3.86
2037 6364 2.445845 CCGATGGTAGGGCCTGGA 60.446 66.667 18.53 0.00 38.35 3.86
2038 6365 3.560251 CCCGATGGTAGGGCCTGG 61.560 72.222 18.53 7.41 42.77 4.45
2044 6371 1.129058 AAAGTAGGCCCGATGGTAGG 58.871 55.000 0.00 0.00 0.00 3.18
2045 6372 2.169769 TGAAAAGTAGGCCCGATGGTAG 59.830 50.000 0.00 0.00 0.00 3.18
2046 6373 2.189676 TGAAAAGTAGGCCCGATGGTA 58.810 47.619 0.00 0.00 0.00 3.25
2047 6374 0.988832 TGAAAAGTAGGCCCGATGGT 59.011 50.000 0.00 0.00 0.00 3.55
2048 6375 2.017049 CTTGAAAAGTAGGCCCGATGG 58.983 52.381 0.00 0.00 39.70 3.51
2061 6388 2.206536 CCGGGCTTGGGCTTGAAAA 61.207 57.895 0.00 0.00 38.73 2.29
2062 6389 2.600173 CCGGGCTTGGGCTTGAAA 60.600 61.111 0.00 0.00 38.73 2.69
2069 6396 3.670629 TAAATGGGCCGGGCTTGGG 62.671 63.158 28.80 0.00 0.00 4.12
2070 6397 1.048160 ATTAAATGGGCCGGGCTTGG 61.048 55.000 28.80 0.00 0.00 3.61
2071 6398 1.698506 TATTAAATGGGCCGGGCTTG 58.301 50.000 28.80 0.00 0.00 4.01
2072 6399 2.463047 TTATTAAATGGGCCGGGCTT 57.537 45.000 28.80 16.88 0.00 4.35
2073 6400 2.463047 TTTATTAAATGGGCCGGGCT 57.537 45.000 28.80 10.65 0.00 5.19
2074 6401 3.462982 CTTTTTATTAAATGGGCCGGGC 58.537 45.455 22.00 22.00 0.00 6.13
2075 6402 3.462982 GCTTTTTATTAAATGGGCCGGG 58.537 45.455 2.18 0.00 0.00 5.73
2076 6403 3.462982 GGCTTTTTATTAAATGGGCCGG 58.537 45.455 0.00 0.00 30.28 6.13
2077 6404 3.133901 AGGGCTTTTTATTAAATGGGCCG 59.866 43.478 19.07 0.00 41.93 6.13
2078 6405 4.163268 TCAGGGCTTTTTATTAAATGGGCC 59.837 41.667 18.27 18.27 39.77 5.80
2079 6406 5.351948 TCAGGGCTTTTTATTAAATGGGC 57.648 39.130 0.00 0.00 0.00 5.36
2080 6407 7.148255 GCTTTTCAGGGCTTTTTATTAAATGGG 60.148 37.037 0.00 0.00 0.00 4.00
2081 6408 7.148255 GGCTTTTCAGGGCTTTTTATTAAATGG 60.148 37.037 0.00 0.00 0.00 3.16
2082 6409 7.148255 GGGCTTTTCAGGGCTTTTTATTAAATG 60.148 37.037 0.00 0.00 0.00 2.32
2083 6410 6.884295 GGGCTTTTCAGGGCTTTTTATTAAAT 59.116 34.615 0.00 0.00 0.00 1.40
2084 6411 6.043822 AGGGCTTTTCAGGGCTTTTTATTAAA 59.956 34.615 0.00 0.00 0.00 1.52
2085 6412 5.546110 AGGGCTTTTCAGGGCTTTTTATTAA 59.454 36.000 0.00 0.00 0.00 1.40
2086 6413 5.090845 AGGGCTTTTCAGGGCTTTTTATTA 58.909 37.500 0.00 0.00 0.00 0.98
2087 6414 3.909995 AGGGCTTTTCAGGGCTTTTTATT 59.090 39.130 0.00 0.00 0.00 1.40
2088 6415 3.520696 AGGGCTTTTCAGGGCTTTTTAT 58.479 40.909 0.00 0.00 0.00 1.40
2089 6416 2.970987 AGGGCTTTTCAGGGCTTTTTA 58.029 42.857 0.00 0.00 0.00 1.52
2090 6417 1.806496 AGGGCTTTTCAGGGCTTTTT 58.194 45.000 0.00 0.00 0.00 1.94
2091 6418 1.806496 AAGGGCTTTTCAGGGCTTTT 58.194 45.000 0.00 0.00 0.00 2.27
2092 6419 2.529632 CTAAGGGCTTTTCAGGGCTTT 58.470 47.619 0.00 0.00 33.62 3.51
2093 6420 1.272704 CCTAAGGGCTTTTCAGGGCTT 60.273 52.381 0.00 0.00 0.00 4.35
2094 6421 0.332972 CCTAAGGGCTTTTCAGGGCT 59.667 55.000 0.00 0.00 0.00 5.19
2095 6422 0.684479 CCCTAAGGGCTTTTCAGGGC 60.684 60.000 4.44 0.00 39.62 5.19
2096 6423 3.596362 CCCTAAGGGCTTTTCAGGG 57.404 57.895 3.08 3.08 40.10 4.45
2128 6455 0.323087 TTTTAAGGAAGAGGCCCGGC 60.323 55.000 0.00 0.00 0.00 6.13
2129 6456 2.024414 CATTTTAAGGAAGAGGCCCGG 58.976 52.381 0.00 0.00 0.00 5.73
2130 6457 1.405463 GCATTTTAAGGAAGAGGCCCG 59.595 52.381 0.00 0.00 0.00 6.13
2131 6458 1.757118 GGCATTTTAAGGAAGAGGCCC 59.243 52.381 0.00 0.00 34.17 5.80
2132 6459 2.456577 TGGCATTTTAAGGAAGAGGCC 58.543 47.619 0.00 0.00 40.51 5.19
2133 6460 4.743057 ATTGGCATTTTAAGGAAGAGGC 57.257 40.909 0.00 0.00 0.00 4.70
2134 6461 6.218746 GCATATTGGCATTTTAAGGAAGAGG 58.781 40.000 0.00 0.00 0.00 3.69
2135 6462 6.218746 GGCATATTGGCATTTTAAGGAAGAG 58.781 40.000 0.00 0.00 43.14 2.85
2136 6463 6.160576 GGCATATTGGCATTTTAAGGAAGA 57.839 37.500 0.00 0.00 43.14 2.87
2149 6476 1.202452 GCTTGGACTTGGCATATTGGC 60.202 52.381 0.00 0.00 44.03 4.52
2150 6477 1.410153 GGCTTGGACTTGGCATATTGG 59.590 52.381 0.00 0.00 0.00 3.16
2151 6478 1.410153 GGGCTTGGACTTGGCATATTG 59.590 52.381 0.00 0.00 0.00 1.90
2152 6479 1.780503 GGGCTTGGACTTGGCATATT 58.219 50.000 0.00 0.00 0.00 1.28
2153 6480 0.466189 CGGGCTTGGACTTGGCATAT 60.466 55.000 0.00 0.00 0.00 1.78
2154 6481 1.077787 CGGGCTTGGACTTGGCATA 60.078 57.895 0.00 0.00 0.00 3.14
2155 6482 2.361610 CGGGCTTGGACTTGGCAT 60.362 61.111 0.00 0.00 0.00 4.40
2156 6483 3.842925 GACGGGCTTGGACTTGGCA 62.843 63.158 0.00 0.00 0.00 4.92
2157 6484 3.056328 GACGGGCTTGGACTTGGC 61.056 66.667 0.00 0.00 0.00 4.52
2158 6485 2.359975 GGACGGGCTTGGACTTGG 60.360 66.667 0.00 0.00 0.00 3.61
2159 6486 1.672356 CTGGACGGGCTTGGACTTG 60.672 63.158 0.00 0.00 0.00 3.16
2160 6487 2.750350 CTGGACGGGCTTGGACTT 59.250 61.111 0.00 0.00 0.00 3.01
2161 6488 3.322466 CCTGGACGGGCTTGGACT 61.322 66.667 0.00 0.00 0.00 3.85
2180 6507 1.531365 TTTTGAGCCCACCAGCAGG 60.531 57.895 0.00 0.00 42.21 4.85
2181 6508 0.825010 AGTTTTGAGCCCACCAGCAG 60.825 55.000 0.00 0.00 34.23 4.24
2182 6509 0.823356 GAGTTTTGAGCCCACCAGCA 60.823 55.000 0.00 0.00 34.23 4.41
2183 6510 0.823356 TGAGTTTTGAGCCCACCAGC 60.823 55.000 0.00 0.00 0.00 4.85
2184 6511 1.242076 CTGAGTTTTGAGCCCACCAG 58.758 55.000 0.00 0.00 0.00 4.00
2185 6512 0.178992 CCTGAGTTTTGAGCCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2186 6513 1.527433 GCCTGAGTTTTGAGCCCACC 61.527 60.000 0.00 0.00 0.00 4.61
2187 6514 1.527433 GGCCTGAGTTTTGAGCCCAC 61.527 60.000 0.00 0.00 37.66 4.61
2188 6515 1.228552 GGCCTGAGTTTTGAGCCCA 60.229 57.895 0.00 0.00 37.66 5.36
2189 6516 3.686760 GGCCTGAGTTTTGAGCCC 58.313 61.111 0.00 0.00 37.66 5.19
2190 6517 0.827507 TTGGGCCTGAGTTTTGAGCC 60.828 55.000 4.53 0.00 43.09 4.70
2191 6518 0.600057 CTTGGGCCTGAGTTTTGAGC 59.400 55.000 4.53 0.00 0.00 4.26
2192 6519 0.600057 GCTTGGGCCTGAGTTTTGAG 59.400 55.000 4.53 0.00 0.00 3.02
2193 6520 2.732289 GCTTGGGCCTGAGTTTTGA 58.268 52.632 4.53 0.00 0.00 2.69
2216 6543 2.757099 GATGGGCTTGCCTGTGGG 60.757 66.667 11.71 0.00 0.00 4.61
2217 6544 3.136123 CGATGGGCTTGCCTGTGG 61.136 66.667 11.71 0.00 0.00 4.17
2218 6545 3.136123 CCGATGGGCTTGCCTGTG 61.136 66.667 11.71 0.00 0.00 3.66
2219 6546 4.431131 CCCGATGGGCTTGCCTGT 62.431 66.667 11.71 0.42 35.35 4.00
2236 6563 1.202940 CCTAAAATCCAGGGCCTAGGC 60.203 57.143 26.55 26.55 41.06 3.93
2237 6564 1.425448 CCCTAAAATCCAGGGCCTAGG 59.575 57.143 5.28 10.90 46.27 3.02
2238 6565 2.959465 CCCTAAAATCCAGGGCCTAG 57.041 55.000 5.28 0.00 46.27 3.02
2244 6571 0.756815 GCCCAGCCCTAAAATCCAGG 60.757 60.000 0.00 0.00 0.00 4.45
2245 6572 0.756815 GGCCCAGCCCTAAAATCCAG 60.757 60.000 0.00 0.00 44.06 3.86
2246 6573 1.309688 GGCCCAGCCCTAAAATCCA 59.690 57.895 0.00 0.00 44.06 3.41
2247 6574 4.277552 GGCCCAGCCCTAAAATCC 57.722 61.111 0.00 0.00 44.06 3.01
2287 6614 0.830648 TTAGTTCTGGCCATCTCCGG 59.169 55.000 5.51 0.00 0.00 5.14
2288 6615 1.207089 TGTTAGTTCTGGCCATCTCCG 59.793 52.381 5.51 0.00 0.00 4.63
2289 6616 2.237392 ACTGTTAGTTCTGGCCATCTCC 59.763 50.000 5.51 0.00 0.00 3.71
2290 6617 3.265791 CACTGTTAGTTCTGGCCATCTC 58.734 50.000 5.51 0.00 0.00 2.75
2291 6618 2.026822 CCACTGTTAGTTCTGGCCATCT 60.027 50.000 5.51 8.22 0.00 2.90
2292 6619 2.359900 CCACTGTTAGTTCTGGCCATC 58.640 52.381 5.51 0.00 0.00 3.51
2293 6620 1.004745 CCCACTGTTAGTTCTGGCCAT 59.995 52.381 5.51 0.00 0.00 4.40
2294 6621 0.400213 CCCACTGTTAGTTCTGGCCA 59.600 55.000 4.71 4.71 0.00 5.36
2295 6622 0.400594 ACCCACTGTTAGTTCTGGCC 59.599 55.000 0.00 0.00 0.00 5.36
2296 6623 3.244457 ACTTACCCACTGTTAGTTCTGGC 60.244 47.826 0.00 0.00 33.16 4.85
2297 6624 4.618920 ACTTACCCACTGTTAGTTCTGG 57.381 45.455 0.00 0.00 33.16 3.86
2298 6625 5.930569 GGTTACTTACCCACTGTTAGTTCTG 59.069 44.000 0.00 0.00 41.43 3.02
2299 6626 6.106648 GGTTACTTACCCACTGTTAGTTCT 57.893 41.667 0.00 0.00 41.43 3.01
2342 6669 3.365969 GGTGAACTGATTTTTGGTAGCGG 60.366 47.826 0.00 0.00 0.00 5.52
2348 6675 3.324556 ACCATGGGTGAACTGATTTTTGG 59.675 43.478 18.09 0.00 32.98 3.28
2456 6793 0.246635 GGCTTTGCTAGACGACCTCA 59.753 55.000 0.00 0.00 0.00 3.86
2463 6800 2.109126 CCGCTGGGCTTTGCTAGAC 61.109 63.158 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.