Multiple sequence alignment - TraesCS1D01G282000

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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 TraesCS1D01G282000 chr1D 100.000 2246 0 0 1 2246 379585056 379582811 0.000000e+00 4148
1 TraesCS1D01G282000 chr1B 88.472 1891 99 46 1 1831 509005507 509003676 0.000000e+00 2174
2 TraesCS1D01G282000 chr1B 94.776 268 12 2 1838 2105 509003559 509003294 1.240000e-112 416
3 TraesCS1D01G282000 chr1A 86.733 2005 124 53 1 1953 480751672 480749758 0.000000e+00 2098
4 TraesCS1D01G282000 chr1A 91.964 112 6 2 1994 2105 480749568 480749460 1.070000e-33 154
5 TraesCS1D01G282000 chr1A 85.294 102 10 3 1 102 480753388 480753292 1.420000e-17 100


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 TraesCS1D01G282000 chr1D 379582811 379585056 2245 True 4148 4148 100.000 1 2246 1 chr1D.!!$R1 2245
1 TraesCS1D01G282000 chr1B 509003294 509005507 2213 True 1295 2174 91.624 1 2105 2 chr1B.!!$R1 2104
2 TraesCS1D01G282000 chr1A 480749460 480753388 3928 True 784 2098 87.997 1 2105 3 chr1A.!!$R1 2104

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
877 2625 0.343372 TAAGCCCATGTCCTCCTCCT 59.657 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 3886 0.038526 GACAATGTCCGTGAGTCCGT 60.039 55.0 1.1 0.0 0.0 4.69 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
48 49 2.607180 GCCGCTCATTCTCTTCTTCTTC 59.393 50.000 0.00 0.00 0.00 2.87
49 50 3.678529 GCCGCTCATTCTCTTCTTCTTCT 60.679 47.826 0.00 0.00 0.00 2.85
50 51 4.111916 CCGCTCATTCTCTTCTTCTTCTC 58.888 47.826 0.00 0.00 0.00 2.87
111 1822 2.037620 GCCCGATCAGCATCTCCAGT 62.038 60.000 0.00 0.00 0.00 4.00
217 1928 2.099098 CGCCATCTTCCCCATTGTTTAC 59.901 50.000 0.00 0.00 0.00 2.01
218 1929 3.365472 GCCATCTTCCCCATTGTTTACT 58.635 45.455 0.00 0.00 0.00 2.24
223 1934 1.816074 TCCCCATTGTTTACTCACGC 58.184 50.000 0.00 0.00 0.00 5.34
357 2068 3.713889 GTGAGATCACGCTGAACTTTC 57.286 47.619 0.00 0.00 37.10 2.62
358 2069 2.413453 GTGAGATCACGCTGAACTTTCC 59.587 50.000 0.00 0.00 37.10 3.13
384 2095 1.064621 CATGGCAGCGATTTTCCGG 59.935 57.895 0.00 0.00 0.00 5.14
474 2185 6.639563 AGGTTTGTGTTTGCTTATCTTTTGT 58.360 32.000 0.00 0.00 0.00 2.83
534 2251 3.424962 GCCGAGAAATTACAGCAACTGAC 60.425 47.826 0.78 0.00 35.18 3.51
535 2252 3.997021 CCGAGAAATTACAGCAACTGACT 59.003 43.478 0.78 0.00 35.18 3.41
536 2253 4.143030 CCGAGAAATTACAGCAACTGACTG 60.143 45.833 0.78 0.00 41.08 3.51
537 2254 4.686091 CGAGAAATTACAGCAACTGACTGA 59.314 41.667 0.78 0.00 38.55 3.41
541 2258 7.945134 AGAAATTACAGCAACTGACTGAAAAT 58.055 30.769 0.78 0.00 38.55 1.82
542 2259 9.066892 AGAAATTACAGCAACTGACTGAAAATA 57.933 29.630 0.78 0.00 38.55 1.40
574 2303 0.668535 ACTTGGAAAACTCGCCTTGC 59.331 50.000 0.00 0.00 0.00 4.01
607 2336 0.890996 CCTTGCGTTCAAGCCTCCTT 60.891 55.000 0.00 0.00 46.38 3.36
618 2354 3.036045 GCCTCCTTCCCCTCCCCTA 62.036 68.421 0.00 0.00 0.00 3.53
652 2392 6.070824 CCATAGCCCCAATGATTAATTAACCC 60.071 42.308 0.00 0.00 0.00 4.11
658 2398 6.722129 CCCCAATGATTAATTAACCCGGAATA 59.278 38.462 0.73 0.00 0.00 1.75
659 2399 7.233757 CCCCAATGATTAATTAACCCGGAATAA 59.766 37.037 0.73 1.57 0.00 1.40
672 2412 3.368531 CCCGGAATAATGTCCTAGCTAGC 60.369 52.174 15.74 6.62 35.31 3.42
675 2415 5.163602 CCGGAATAATGTCCTAGCTAGCTAG 60.164 48.000 35.39 35.39 44.07 3.42
677 2417 5.186021 GGAATAATGTCCTAGCTAGCTAGCA 59.814 44.000 39.50 30.44 43.35 3.49
678 2418 6.627065 GGAATAATGTCCTAGCTAGCTAGCAG 60.627 46.154 39.50 31.78 43.35 4.24
679 2419 8.930239 GGAATAATGTCCTAGCTAGCTAGCAGT 61.930 44.444 39.50 30.26 43.35 4.40
689 2429 4.250116 CTAGCTAGCAGTTACCCTGATG 57.750 50.000 18.83 0.00 44.49 3.07
691 2431 3.107601 AGCTAGCAGTTACCCTGATGAA 58.892 45.455 18.83 0.00 44.49 2.57
692 2432 3.713764 AGCTAGCAGTTACCCTGATGAAT 59.286 43.478 18.83 0.00 44.49 2.57
693 2433 4.164988 AGCTAGCAGTTACCCTGATGAATT 59.835 41.667 18.83 0.00 44.49 2.17
694 2434 4.513318 GCTAGCAGTTACCCTGATGAATTC 59.487 45.833 10.63 0.00 44.49 2.17
695 2435 3.891049 AGCAGTTACCCTGATGAATTCC 58.109 45.455 2.27 0.00 44.49 3.01
696 2436 2.952310 GCAGTTACCCTGATGAATTCCC 59.048 50.000 2.27 0.00 44.49 3.97
697 2437 3.372025 GCAGTTACCCTGATGAATTCCCT 60.372 47.826 2.27 0.00 44.49 4.20
698 2438 4.860022 CAGTTACCCTGATGAATTCCCTT 58.140 43.478 2.27 0.00 44.49 3.95
699 2439 4.641989 CAGTTACCCTGATGAATTCCCTTG 59.358 45.833 2.27 0.00 44.49 3.61
700 2440 4.292306 AGTTACCCTGATGAATTCCCTTGT 59.708 41.667 2.27 0.00 0.00 3.16
701 2441 5.491078 AGTTACCCTGATGAATTCCCTTGTA 59.509 40.000 2.27 0.00 0.00 2.41
702 2442 4.946160 ACCCTGATGAATTCCCTTGTAA 57.054 40.909 2.27 0.00 0.00 2.41
703 2443 5.472301 ACCCTGATGAATTCCCTTGTAAT 57.528 39.130 2.27 0.00 0.00 1.89
704 2444 6.590656 ACCCTGATGAATTCCCTTGTAATA 57.409 37.500 2.27 0.00 0.00 0.98
705 2445 6.605119 ACCCTGATGAATTCCCTTGTAATAG 58.395 40.000 2.27 0.00 0.00 1.73
706 2446 6.160459 ACCCTGATGAATTCCCTTGTAATAGT 59.840 38.462 2.27 0.00 0.00 2.12
707 2447 7.349859 ACCCTGATGAATTCCCTTGTAATAGTA 59.650 37.037 2.27 0.00 0.00 1.82
708 2448 7.661847 CCCTGATGAATTCCCTTGTAATAGTAC 59.338 40.741 2.27 0.00 0.00 2.73
709 2449 7.661847 CCTGATGAATTCCCTTGTAATAGTACC 59.338 40.741 2.27 0.00 0.00 3.34
710 2450 7.514721 TGATGAATTCCCTTGTAATAGTACCC 58.485 38.462 2.27 0.00 0.00 3.69
711 2451 6.256643 TGAATTCCCTTGTAATAGTACCCC 57.743 41.667 2.27 0.00 0.00 4.95
717 2457 4.344390 CCCTTGTAATAGTACCCCTGAGTC 59.656 50.000 0.00 0.00 0.00 3.36
718 2458 4.344390 CCTTGTAATAGTACCCCTGAGTCC 59.656 50.000 0.00 0.00 0.00 3.85
722 2462 1.690010 TAGTACCCCTGAGTCCCTGA 58.310 55.000 0.00 0.00 0.00 3.86
737 2477 1.266718 CCCTGACACGACACATTTTGG 59.733 52.381 0.00 0.00 0.00 3.28
797 2545 3.244249 ACAATTATCCTTCCTAGGCGAGC 60.244 47.826 2.96 0.00 41.69 5.03
827 2575 3.838565 TGGTCTCTGATCTCTATCCACC 58.161 50.000 0.00 0.00 0.00 4.61
829 2577 2.817258 GTCTCTGATCTCTATCCACCCG 59.183 54.545 0.00 0.00 0.00 5.28
876 2624 1.213296 TTAAGCCCATGTCCTCCTCC 58.787 55.000 0.00 0.00 0.00 4.30
877 2625 0.343372 TAAGCCCATGTCCTCCTCCT 59.657 55.000 0.00 0.00 0.00 3.69
878 2626 1.277580 AAGCCCATGTCCTCCTCCTG 61.278 60.000 0.00 0.00 0.00 3.86
948 2696 4.349930 AGTGTTGTCCCAATAACCACTACT 59.650 41.667 0.00 0.00 0.00 2.57
949 2697 5.544948 AGTGTTGTCCCAATAACCACTACTA 59.455 40.000 0.00 0.00 0.00 1.82
951 2699 5.181009 GTTGTCCCAATAACCACTACTACC 58.819 45.833 0.00 0.00 0.00 3.18
1077 2825 3.827898 GTCTCCCTCGCCGACCTG 61.828 72.222 0.00 0.00 0.00 4.00
1246 2994 0.107456 GGAGCATGGATCGTGGTGAT 59.893 55.000 6.21 0.00 41.06 3.06
1276 3024 1.211190 GAAGCGCAGAAAGGCCAAG 59.789 57.895 11.47 0.00 0.00 3.61
1348 3102 3.665871 CGAGTACATGCAGATACGATGTG 59.334 47.826 0.00 0.00 32.59 3.21
1354 3108 2.837498 TGCAGATACGATGTGGATTGG 58.163 47.619 0.00 0.00 0.00 3.16
1357 3111 3.133691 CAGATACGATGTGGATTGGTGG 58.866 50.000 0.00 0.00 0.00 4.61
1358 3112 3.038280 AGATACGATGTGGATTGGTGGA 58.962 45.455 0.00 0.00 0.00 4.02
1359 3113 3.454447 AGATACGATGTGGATTGGTGGAA 59.546 43.478 0.00 0.00 0.00 3.53
1361 3115 2.159382 ACGATGTGGATTGGTGGAAAC 58.841 47.619 0.00 0.00 0.00 2.78
1364 3118 2.286365 TGTGGATTGGTGGAAACCTC 57.714 50.000 0.00 0.00 0.00 3.85
1365 3119 1.496857 TGTGGATTGGTGGAAACCTCA 59.503 47.619 0.00 0.00 0.00 3.86
1430 3185 4.619437 TTGTGTGTGCTATACATGCATG 57.381 40.909 25.09 25.09 42.24 4.06
1460 3239 8.970020 TGGTATTTCAATTCAGCTTGTAATGAT 58.030 29.630 0.00 0.00 31.32 2.45
1484 3263 4.574421 TGTCAACTGTAAATATGGGATGCG 59.426 41.667 0.00 0.00 0.00 4.73
1485 3264 4.574828 GTCAACTGTAAATATGGGATGCGT 59.425 41.667 0.00 0.00 0.00 5.24
1650 3439 0.445436 GCGAGTGTCAAGCATCAAGG 59.555 55.000 0.00 0.00 0.00 3.61
1733 3523 5.324739 TCTCGTTTTCAGTTCGAAATCAC 57.675 39.130 0.00 0.00 43.12 3.06
1832 3629 9.959749 GAATAACTTTGGTTGAAAAGATGTACA 57.040 29.630 0.00 0.00 39.12 2.90
1833 3630 9.965824 AATAACTTTGGTTGAAAAGATGTACAG 57.034 29.630 0.33 0.00 39.12 2.74
1834 3631 7.404671 AACTTTGGTTGAAAAGATGTACAGT 57.595 32.000 0.33 0.00 39.12 3.55
1835 3632 8.514330 AACTTTGGTTGAAAAGATGTACAGTA 57.486 30.769 0.33 0.00 39.12 2.74
1836 3633 8.691661 ACTTTGGTTGAAAAGATGTACAGTAT 57.308 30.769 0.33 0.00 39.12 2.12
1875 3784 3.434940 TGGACACTCTGTGCTACTCTA 57.565 47.619 0.00 0.00 39.59 2.43
1967 3886 0.321564 CAGTTCATCTTCCGCCCACA 60.322 55.000 0.00 0.00 0.00 4.17
2013 4071 9.352784 CGCCTGAATTTCATCTTTGTTAAATTA 57.647 29.630 0.00 0.00 33.03 1.40
2038 4096 2.093394 TCGATATCCCCGCAAAAACAGA 60.093 45.455 0.00 0.00 0.00 3.41
2100 4158 3.525862 AGAAACCCTCTCATCCTTGACT 58.474 45.455 0.00 0.00 0.00 3.41
2105 4163 3.102972 CCCTCTCATCCTTGACTTCTCA 58.897 50.000 0.00 0.00 0.00 3.27
2106 4164 3.710677 CCCTCTCATCCTTGACTTCTCAT 59.289 47.826 0.00 0.00 0.00 2.90
2107 4165 4.443175 CCCTCTCATCCTTGACTTCTCATG 60.443 50.000 0.00 0.00 0.00 3.07
2108 4166 4.121317 CTCTCATCCTTGACTTCTCATGC 58.879 47.826 0.00 0.00 0.00 4.06
2109 4167 3.516700 TCTCATCCTTGACTTCTCATGCA 59.483 43.478 0.00 0.00 0.00 3.96
2110 4168 3.870274 TCATCCTTGACTTCTCATGCAG 58.130 45.455 0.00 0.00 0.00 4.41
2111 4169 3.516700 TCATCCTTGACTTCTCATGCAGA 59.483 43.478 0.00 0.00 0.00 4.26
2112 4170 4.163649 TCATCCTTGACTTCTCATGCAGAT 59.836 41.667 0.00 0.00 0.00 2.90
2113 4171 3.870274 TCCTTGACTTCTCATGCAGATG 58.130 45.455 0.00 0.00 33.32 2.90
2114 4172 3.262660 TCCTTGACTTCTCATGCAGATGT 59.737 43.478 11.06 11.06 41.22 3.06
2115 4173 4.008330 CCTTGACTTCTCATGCAGATGTT 58.992 43.478 11.96 1.90 39.16 2.71
2116 4174 4.094590 CCTTGACTTCTCATGCAGATGTTC 59.905 45.833 11.96 8.18 39.16 3.18
2117 4175 3.603532 TGACTTCTCATGCAGATGTTCC 58.396 45.455 11.96 5.06 39.16 3.62
2118 4176 3.008266 TGACTTCTCATGCAGATGTTCCA 59.992 43.478 11.96 6.73 39.16 3.53
2119 4177 4.197750 GACTTCTCATGCAGATGTTCCAT 58.802 43.478 11.96 0.00 39.16 3.41
2120 4178 4.597004 ACTTCTCATGCAGATGTTCCATT 58.403 39.130 0.00 0.00 36.34 3.16
2121 4179 4.639310 ACTTCTCATGCAGATGTTCCATTC 59.361 41.667 0.00 0.00 36.34 2.67
2122 4180 4.224991 TCTCATGCAGATGTTCCATTCA 57.775 40.909 0.00 0.00 0.00 2.57
2123 4181 4.196971 TCTCATGCAGATGTTCCATTCAG 58.803 43.478 0.00 0.00 0.00 3.02
2124 4182 4.080751 TCTCATGCAGATGTTCCATTCAGA 60.081 41.667 0.00 0.00 0.00 3.27
2125 4183 4.788679 TCATGCAGATGTTCCATTCAGAT 58.211 39.130 0.00 0.00 0.00 2.90
2126 4184 4.578928 TCATGCAGATGTTCCATTCAGATG 59.421 41.667 0.00 0.00 0.00 2.90
2127 4185 4.224991 TGCAGATGTTCCATTCAGATGA 57.775 40.909 0.00 0.00 35.16 2.92
2128 4186 4.788679 TGCAGATGTTCCATTCAGATGAT 58.211 39.130 0.00 0.00 35.16 2.45
2129 4187 4.820173 TGCAGATGTTCCATTCAGATGATC 59.180 41.667 0.00 0.00 35.16 2.92
2130 4188 5.064558 GCAGATGTTCCATTCAGATGATCT 58.935 41.667 0.00 0.00 35.16 2.75
2131 4189 6.183361 TGCAGATGTTCCATTCAGATGATCTA 60.183 38.462 0.00 0.00 35.16 1.98
2132 4190 6.369340 GCAGATGTTCCATTCAGATGATCTAG 59.631 42.308 0.00 0.00 35.16 2.43
2133 4191 7.668492 CAGATGTTCCATTCAGATGATCTAGA 58.332 38.462 0.00 0.00 35.16 2.43
2134 4192 7.815549 CAGATGTTCCATTCAGATGATCTAGAG 59.184 40.741 0.00 0.00 35.16 2.43
2135 4193 6.416631 TGTTCCATTCAGATGATCTAGAGG 57.583 41.667 0.00 0.00 35.16 3.69
2136 4194 5.221601 TGTTCCATTCAGATGATCTAGAGGC 60.222 44.000 0.00 0.00 35.16 4.70
2137 4195 3.509184 TCCATTCAGATGATCTAGAGGCG 59.491 47.826 0.00 0.00 35.16 5.52
2138 4196 3.252400 CATTCAGATGATCTAGAGGCGC 58.748 50.000 0.00 0.00 35.16 6.53
2139 4197 1.986882 TCAGATGATCTAGAGGCGCA 58.013 50.000 10.83 0.00 0.00 6.09
2140 4198 1.885233 TCAGATGATCTAGAGGCGCAG 59.115 52.381 10.83 0.00 0.00 5.18
2141 4199 1.885233 CAGATGATCTAGAGGCGCAGA 59.115 52.381 10.83 3.09 0.00 4.26
2142 4200 2.095110 CAGATGATCTAGAGGCGCAGAG 60.095 54.545 10.83 0.00 0.00 3.35
2143 4201 2.158559 GATGATCTAGAGGCGCAGAGA 58.841 52.381 10.83 5.96 0.00 3.10
2144 4202 1.603456 TGATCTAGAGGCGCAGAGAG 58.397 55.000 10.83 0.32 0.00 3.20
2145 4203 1.133945 TGATCTAGAGGCGCAGAGAGT 60.134 52.381 10.83 0.00 0.00 3.24
2146 4204 2.104963 TGATCTAGAGGCGCAGAGAGTA 59.895 50.000 10.83 0.00 0.00 2.59
2147 4205 2.940994 TCTAGAGGCGCAGAGAGTAT 57.059 50.000 10.83 0.00 0.00 2.12
2148 4206 4.020128 TGATCTAGAGGCGCAGAGAGTATA 60.020 45.833 10.83 0.00 0.00 1.47
2149 4207 3.932822 TCTAGAGGCGCAGAGAGTATAG 58.067 50.000 10.83 0.00 0.00 1.31
2150 4208 2.649531 AGAGGCGCAGAGAGTATAGT 57.350 50.000 10.83 0.00 0.00 2.12
2151 4209 2.500229 AGAGGCGCAGAGAGTATAGTC 58.500 52.381 10.83 0.00 0.00 2.59
2152 4210 2.158740 AGAGGCGCAGAGAGTATAGTCA 60.159 50.000 10.83 0.00 0.00 3.41
2153 4211 2.619177 GAGGCGCAGAGAGTATAGTCAA 59.381 50.000 10.83 0.00 0.00 3.18
2154 4212 2.359531 AGGCGCAGAGAGTATAGTCAAC 59.640 50.000 10.83 3.93 0.00 3.18
2155 4213 2.099263 GGCGCAGAGAGTATAGTCAACA 59.901 50.000 10.83 0.00 0.00 3.33
2156 4214 3.243569 GGCGCAGAGAGTATAGTCAACAT 60.244 47.826 10.83 0.00 0.00 2.71
2157 4215 3.733224 GCGCAGAGAGTATAGTCAACATG 59.267 47.826 0.30 0.00 0.00 3.21
2158 4216 4.294232 CGCAGAGAGTATAGTCAACATGG 58.706 47.826 10.21 0.51 0.00 3.66
2159 4217 4.054671 GCAGAGAGTATAGTCAACATGGC 58.945 47.826 10.21 5.68 0.00 4.40
2160 4218 4.294232 CAGAGAGTATAGTCAACATGGCG 58.706 47.826 10.21 0.00 0.00 5.69
2161 4219 3.954904 AGAGAGTATAGTCAACATGGCGT 59.045 43.478 10.21 0.00 0.00 5.68
2162 4220 4.402793 AGAGAGTATAGTCAACATGGCGTT 59.597 41.667 10.21 0.00 38.83 4.84
2173 4231 3.135414 ACATGGCGTTGATGAAATTCG 57.865 42.857 0.00 0.00 0.00 3.34
2174 4232 2.487762 ACATGGCGTTGATGAAATTCGT 59.512 40.909 0.00 0.00 0.00 3.85
2175 4233 3.687212 ACATGGCGTTGATGAAATTCGTA 59.313 39.130 0.00 0.00 0.00 3.43
2176 4234 3.733024 TGGCGTTGATGAAATTCGTAC 57.267 42.857 0.00 0.00 0.00 3.67
2177 4235 3.067833 TGGCGTTGATGAAATTCGTACA 58.932 40.909 0.00 0.00 0.00 2.90
2178 4236 3.120477 TGGCGTTGATGAAATTCGTACAC 60.120 43.478 0.00 0.00 0.00 2.90
2179 4237 3.120477 GGCGTTGATGAAATTCGTACACA 60.120 43.478 0.00 0.00 0.00 3.72
2180 4238 4.436852 GGCGTTGATGAAATTCGTACACAT 60.437 41.667 0.00 0.00 0.00 3.21
2181 4239 5.086058 GCGTTGATGAAATTCGTACACATT 58.914 37.500 0.00 0.00 0.00 2.71
2182 4240 5.567534 GCGTTGATGAAATTCGTACACATTT 59.432 36.000 0.00 0.00 0.00 2.32
2183 4241 6.451054 GCGTTGATGAAATTCGTACACATTTG 60.451 38.462 4.38 0.00 0.00 2.32
2184 4242 6.577055 CGTTGATGAAATTCGTACACATTTGT 59.423 34.615 4.38 0.00 40.02 2.83
2185 4243 7.742525 CGTTGATGAAATTCGTACACATTTGTA 59.257 33.333 4.38 0.00 37.15 2.41
2186 4244 9.388346 GTTGATGAAATTCGTACACATTTGTAA 57.612 29.630 4.38 0.00 40.00 2.41
2188 4246 9.767684 TGATGAAATTCGTACACATTTGTAATC 57.232 29.630 4.38 5.79 40.00 1.75
2189 4247 9.988350 GATGAAATTCGTACACATTTGTAATCT 57.012 29.630 4.38 0.00 40.00 2.40
2190 4248 9.988350 ATGAAATTCGTACACATTTGTAATCTC 57.012 29.630 4.38 0.00 40.00 2.75
2191 4249 8.994170 TGAAATTCGTACACATTTGTAATCTCA 58.006 29.630 4.38 0.00 40.00 3.27
2192 4250 9.820229 GAAATTCGTACACATTTGTAATCTCAA 57.180 29.630 4.38 0.00 40.00 3.02
2196 4254 9.605955 TTCGTACACATTTGTAATCTCAAATTG 57.394 29.630 0.00 7.11 42.88 2.32
2197 4255 7.748683 TCGTACACATTTGTAATCTCAAATTGC 59.251 33.333 0.00 0.00 42.88 3.56
2198 4256 7.008266 CGTACACATTTGTAATCTCAAATTGCC 59.992 37.037 0.00 1.32 42.88 4.52
2199 4257 6.996509 ACACATTTGTAATCTCAAATTGCCT 58.003 32.000 2.52 0.00 42.88 4.75
2200 4258 6.869913 ACACATTTGTAATCTCAAATTGCCTG 59.130 34.615 2.52 0.00 42.88 4.85
2201 4259 7.092079 CACATTTGTAATCTCAAATTGCCTGA 58.908 34.615 2.52 0.00 42.88 3.86
2202 4260 7.062605 CACATTTGTAATCTCAAATTGCCTGAC 59.937 37.037 2.52 0.00 42.88 3.51
2203 4261 6.899393 TTTGTAATCTCAAATTGCCTGACT 57.101 33.333 0.00 0.00 33.23 3.41
2204 4262 6.899393 TTGTAATCTCAAATTGCCTGACTT 57.101 33.333 0.00 0.00 0.00 3.01
2205 4263 6.500684 TGTAATCTCAAATTGCCTGACTTC 57.499 37.500 0.00 0.00 0.00 3.01
2206 4264 6.240894 TGTAATCTCAAATTGCCTGACTTCT 58.759 36.000 0.00 0.00 0.00 2.85
2207 4265 6.716628 TGTAATCTCAAATTGCCTGACTTCTT 59.283 34.615 0.00 0.00 0.00 2.52
2208 4266 6.661304 AATCTCAAATTGCCTGACTTCTTT 57.339 33.333 0.00 0.00 0.00 2.52
2209 4267 7.765695 AATCTCAAATTGCCTGACTTCTTTA 57.234 32.000 0.00 0.00 0.00 1.85
2210 4268 7.765695 ATCTCAAATTGCCTGACTTCTTTAA 57.234 32.000 0.00 0.00 0.00 1.52
2211 4269 6.970484 TCTCAAATTGCCTGACTTCTTTAAC 58.030 36.000 0.00 0.00 0.00 2.01
2212 4270 5.757886 TCAAATTGCCTGACTTCTTTAACG 58.242 37.500 0.00 0.00 0.00 3.18
2213 4271 4.766404 AATTGCCTGACTTCTTTAACGG 57.234 40.909 0.00 0.00 0.00 4.44
2214 4272 2.922740 TGCCTGACTTCTTTAACGGT 57.077 45.000 0.00 0.00 0.00 4.83
2215 4273 2.489971 TGCCTGACTTCTTTAACGGTG 58.510 47.619 0.00 0.00 0.00 4.94
2216 4274 2.158871 TGCCTGACTTCTTTAACGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
2217 4275 2.876550 GCCTGACTTCTTTAACGGTGTT 59.123 45.455 0.00 0.00 0.00 3.32
2218 4276 3.059120 GCCTGACTTCTTTAACGGTGTTC 60.059 47.826 0.00 0.00 0.00 3.18
2219 4277 3.497262 CCTGACTTCTTTAACGGTGTTCC 59.503 47.826 0.00 0.00 0.00 3.62
2220 4278 4.124238 CTGACTTCTTTAACGGTGTTCCA 58.876 43.478 0.00 0.00 0.00 3.53
2221 4279 4.124238 TGACTTCTTTAACGGTGTTCCAG 58.876 43.478 0.00 0.00 0.00 3.86
2222 4280 3.473625 ACTTCTTTAACGGTGTTCCAGG 58.526 45.455 0.00 0.00 0.00 4.45
2223 4281 3.118149 ACTTCTTTAACGGTGTTCCAGGT 60.118 43.478 0.00 0.00 0.00 4.00
2224 4282 4.101430 ACTTCTTTAACGGTGTTCCAGGTA 59.899 41.667 0.00 0.00 0.00 3.08
2225 4283 4.261578 TCTTTAACGGTGTTCCAGGTAG 57.738 45.455 0.00 0.00 0.00 3.18
2226 4284 3.896888 TCTTTAACGGTGTTCCAGGTAGA 59.103 43.478 0.00 0.00 0.00 2.59
2227 4285 3.947910 TTAACGGTGTTCCAGGTAGAG 57.052 47.619 0.00 0.00 0.00 2.43
2228 4286 1.713297 AACGGTGTTCCAGGTAGAGT 58.287 50.000 0.00 0.00 0.00 3.24
2229 4287 1.713297 ACGGTGTTCCAGGTAGAGTT 58.287 50.000 0.00 0.00 0.00 3.01
2230 4288 2.880443 ACGGTGTTCCAGGTAGAGTTA 58.120 47.619 0.00 0.00 0.00 2.24
2231 4289 2.560105 ACGGTGTTCCAGGTAGAGTTAC 59.440 50.000 0.00 0.00 0.00 2.50
2232 4290 2.559668 CGGTGTTCCAGGTAGAGTTACA 59.440 50.000 0.00 0.00 0.00 2.41
2233 4291 3.613432 CGGTGTTCCAGGTAGAGTTACAC 60.613 52.174 0.00 0.00 35.04 2.90
2234 4292 3.322828 GGTGTTCCAGGTAGAGTTACACA 59.677 47.826 0.00 0.00 36.91 3.72
2235 4293 4.202284 GGTGTTCCAGGTAGAGTTACACAA 60.202 45.833 0.00 0.00 36.91 3.33
2236 4294 4.748600 GTGTTCCAGGTAGAGTTACACAAC 59.251 45.833 0.00 0.00 35.66 3.32
2237 4295 4.406326 TGTTCCAGGTAGAGTTACACAACA 59.594 41.667 0.00 0.00 37.10 3.33
2238 4296 5.104859 TGTTCCAGGTAGAGTTACACAACAA 60.105 40.000 0.00 0.00 37.10 2.83
2239 4297 5.617528 TCCAGGTAGAGTTACACAACAAA 57.382 39.130 0.00 0.00 37.10 2.83
2240 4298 5.991861 TCCAGGTAGAGTTACACAACAAAA 58.008 37.500 0.00 0.00 37.10 2.44
2241 4299 6.597562 TCCAGGTAGAGTTACACAACAAAAT 58.402 36.000 0.00 0.00 37.10 1.82
2242 4300 6.708949 TCCAGGTAGAGTTACACAACAAAATC 59.291 38.462 0.00 0.00 37.10 2.17
2243 4301 6.485313 CCAGGTAGAGTTACACAACAAAATCA 59.515 38.462 0.00 0.00 37.10 2.57
2244 4302 7.307989 CCAGGTAGAGTTACACAACAAAATCAG 60.308 40.741 0.00 0.00 37.10 2.90
2245 4303 7.441157 CAGGTAGAGTTACACAACAAAATCAGA 59.559 37.037 0.00 0.00 37.10 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.398960 GGTTCGTACCGGATCGTATCG 60.399 57.143 9.46 1.87 34.01 2.92
48 49 6.869421 TGTTTTTCTTCTTCTTTTTGCGAG 57.131 33.333 0.00 0.00 0.00 5.03
49 50 6.183359 CGTTGTTTTTCTTCTTCTTTTTGCGA 60.183 34.615 0.00 0.00 0.00 5.10
50 51 5.945824 CGTTGTTTTTCTTCTTCTTTTTGCG 59.054 36.000 0.00 0.00 0.00 4.85
64 1775 6.797033 CAGTTCATACCAGATCGTTGTTTTTC 59.203 38.462 0.00 0.00 0.00 2.29
111 1822 0.972883 GCTGGGGTTTGTTTATGGCA 59.027 50.000 0.00 0.00 0.00 4.92
204 1915 1.349688 AGCGTGAGTAAACAATGGGGA 59.650 47.619 0.00 0.00 0.00 4.81
338 2049 2.300152 AGGAAAGTTCAGCGTGATCTCA 59.700 45.455 0.00 0.00 0.00 3.27
355 2066 3.643595 CTGCCATGGCGGGAAGGAA 62.644 63.158 34.36 13.06 45.51 3.36
356 2067 4.113815 CTGCCATGGCGGGAAGGA 62.114 66.667 34.36 13.82 45.51 3.36
410 2121 5.617252 TGGTCGAGTTCTTTTTATCCAACT 58.383 37.500 0.00 0.00 0.00 3.16
444 2155 1.362355 CAAACACAAACCTCCGCCC 59.638 57.895 0.00 0.00 0.00 6.13
474 2185 1.602237 GCCTACAGCTTACCTGCCA 59.398 57.895 0.00 0.00 45.78 4.92
502 2213 3.660501 AATTTCTCGGCTGAAAAACCC 57.339 42.857 0.00 0.00 39.08 4.11
534 2251 2.734606 TGGACAGCGACGTTATTTTCAG 59.265 45.455 0.00 0.00 0.00 3.02
535 2252 2.477375 GTGGACAGCGACGTTATTTTCA 59.523 45.455 0.00 0.00 0.00 2.69
536 2253 2.735134 AGTGGACAGCGACGTTATTTTC 59.265 45.455 0.00 0.00 0.00 2.29
537 2254 2.762745 AGTGGACAGCGACGTTATTTT 58.237 42.857 0.00 0.00 0.00 1.82
541 2258 0.319211 CCAAGTGGACAGCGACGTTA 60.319 55.000 0.00 0.00 37.39 3.18
542 2259 1.594293 CCAAGTGGACAGCGACGTT 60.594 57.895 0.00 0.00 37.39 3.99
574 2303 1.457346 GCAAGGGATGGTCAGTCTTG 58.543 55.000 0.00 0.00 38.18 3.02
652 2392 4.792521 AGCTAGCTAGGACATTATTCCG 57.207 45.455 17.69 0.00 41.04 4.30
677 2417 4.292306 ACAAGGGAATTCATCAGGGTAACT 59.708 41.667 7.93 0.00 0.00 2.24
678 2418 4.600062 ACAAGGGAATTCATCAGGGTAAC 58.400 43.478 7.93 0.00 0.00 2.50
679 2419 4.946160 ACAAGGGAATTCATCAGGGTAA 57.054 40.909 7.93 0.00 0.00 2.85
680 2420 6.590656 ATTACAAGGGAATTCATCAGGGTA 57.409 37.500 7.93 0.00 0.00 3.69
681 2421 4.946160 TTACAAGGGAATTCATCAGGGT 57.054 40.909 7.93 0.38 0.00 4.34
682 2422 6.605119 ACTATTACAAGGGAATTCATCAGGG 58.395 40.000 7.93 0.00 0.00 4.45
683 2423 7.661847 GGTACTATTACAAGGGAATTCATCAGG 59.338 40.741 7.93 0.00 0.00 3.86
684 2424 7.661847 GGGTACTATTACAAGGGAATTCATCAG 59.338 40.741 7.93 0.00 0.00 2.90
686 2426 6.940867 GGGGTACTATTACAAGGGAATTCATC 59.059 42.308 7.93 0.00 0.00 2.92
687 2427 6.624021 AGGGGTACTATTACAAGGGAATTCAT 59.376 38.462 7.93 0.00 0.00 2.57
689 2429 6.100714 TCAGGGGTACTATTACAAGGGAATTC 59.899 42.308 0.00 0.00 0.00 2.17
691 2431 5.544682 TCAGGGGTACTATTACAAGGGAAT 58.455 41.667 0.00 0.00 0.00 3.01
692 2432 4.962839 TCAGGGGTACTATTACAAGGGAA 58.037 43.478 0.00 0.00 0.00 3.97
693 2433 4.015918 ACTCAGGGGTACTATTACAAGGGA 60.016 45.833 0.00 0.00 0.00 4.20
694 2434 4.296056 ACTCAGGGGTACTATTACAAGGG 58.704 47.826 0.00 0.00 0.00 3.95
695 2435 4.344390 GGACTCAGGGGTACTATTACAAGG 59.656 50.000 0.00 0.00 0.00 3.61
696 2436 4.344390 GGGACTCAGGGGTACTATTACAAG 59.656 50.000 0.00 0.00 0.00 3.16
697 2437 4.015918 AGGGACTCAGGGGTACTATTACAA 60.016 45.833 0.00 0.00 0.00 2.41
698 2438 3.534747 AGGGACTCAGGGGTACTATTACA 59.465 47.826 0.00 0.00 0.00 2.41
699 2439 3.896272 CAGGGACTCAGGGGTACTATTAC 59.104 52.174 0.00 0.00 34.60 1.89
700 2440 3.795545 TCAGGGACTCAGGGGTACTATTA 59.204 47.826 0.00 0.00 34.60 0.98
701 2441 2.590611 TCAGGGACTCAGGGGTACTATT 59.409 50.000 0.00 0.00 34.60 1.73
702 2442 2.091222 GTCAGGGACTCAGGGGTACTAT 60.091 54.545 0.00 0.00 34.60 2.12
703 2443 1.287146 GTCAGGGACTCAGGGGTACTA 59.713 57.143 0.00 0.00 34.60 1.82
704 2444 0.041386 GTCAGGGACTCAGGGGTACT 59.959 60.000 0.00 0.00 34.60 2.73
705 2445 0.252103 TGTCAGGGACTCAGGGGTAC 60.252 60.000 0.00 0.00 34.60 3.34
706 2446 0.252103 GTGTCAGGGACTCAGGGGTA 60.252 60.000 0.00 0.00 34.60 3.69
707 2447 1.536662 GTGTCAGGGACTCAGGGGT 60.537 63.158 0.00 0.00 34.60 4.95
708 2448 2.650116 CGTGTCAGGGACTCAGGGG 61.650 68.421 0.00 0.00 34.60 4.79
709 2449 1.606601 TCGTGTCAGGGACTCAGGG 60.607 63.158 0.00 0.00 34.60 4.45
710 2450 1.179174 TGTCGTGTCAGGGACTCAGG 61.179 60.000 5.76 0.00 34.60 3.86
711 2451 0.039074 GTGTCGTGTCAGGGACTCAG 60.039 60.000 5.76 0.00 34.60 3.35
717 2457 1.266718 CCAAAATGTGTCGTGTCAGGG 59.733 52.381 0.00 0.00 0.00 4.45
718 2458 1.946768 ACCAAAATGTGTCGTGTCAGG 59.053 47.619 0.00 0.00 0.00 3.86
722 2462 4.097135 TCAATCAACCAAAATGTGTCGTGT 59.903 37.500 0.00 0.00 0.00 4.49
737 2477 4.636206 ACCTTAGCTCCGAAATCAATCAAC 59.364 41.667 0.00 0.00 0.00 3.18
797 2545 2.169352 AGATCAGAGACCAAATGGGACG 59.831 50.000 4.17 0.00 41.15 4.79
827 2575 0.036875 AAAACAGAAGAGGCCTCCGG 59.963 55.000 29.54 17.38 0.00 5.14
829 2577 1.539157 CCAAAACAGAAGAGGCCTCC 58.461 55.000 29.54 15.08 0.00 4.30
834 2582 1.074566 AGGGAGCCAAAACAGAAGAGG 59.925 52.381 0.00 0.00 0.00 3.69
835 2583 2.575805 AGGGAGCCAAAACAGAAGAG 57.424 50.000 0.00 0.00 0.00 2.85
837 2585 4.406648 AAAAAGGGAGCCAAAACAGAAG 57.593 40.909 0.00 0.00 0.00 2.85
876 2624 0.873054 GATGAATGATGGCGAGGCAG 59.127 55.000 5.43 0.00 0.00 4.85
877 2625 0.535780 GGATGAATGATGGCGAGGCA 60.536 55.000 0.88 0.88 0.00 4.75
878 2626 1.239968 GGGATGAATGATGGCGAGGC 61.240 60.000 0.00 0.00 0.00 4.70
948 2696 1.634459 AGAAGACGGTGGAGAGAGGTA 59.366 52.381 0.00 0.00 0.00 3.08
949 2697 0.406361 AGAAGACGGTGGAGAGAGGT 59.594 55.000 0.00 0.00 0.00 3.85
951 2699 2.163412 CTGAAGAAGACGGTGGAGAGAG 59.837 54.545 0.00 0.00 0.00 3.20
993 2741 3.017581 AGGCCCTCCATGACACCC 61.018 66.667 0.00 0.00 33.74 4.61
997 2745 1.453669 GGATGAGGCCCTCCATGAC 59.546 63.158 8.62 0.00 33.74 3.06
1223 2971 1.512996 CCACGATCCATGCTCCATGC 61.513 60.000 0.00 0.00 40.20 4.06
1246 2994 2.813172 TCTGCGCTTCAATCACAATCAA 59.187 40.909 9.73 0.00 0.00 2.57
1276 3024 4.154195 TGCTTCGCTCTGTTTCCTTTATTC 59.846 41.667 0.00 0.00 0.00 1.75
1354 3108 2.492088 GGCCAATACTTGAGGTTTCCAC 59.508 50.000 0.00 0.00 0.00 4.02
1357 3111 3.628032 GCTAGGCCAATACTTGAGGTTTC 59.372 47.826 5.01 0.00 0.00 2.78
1358 3112 3.267031 AGCTAGGCCAATACTTGAGGTTT 59.733 43.478 5.01 0.00 0.00 3.27
1359 3113 2.846827 AGCTAGGCCAATACTTGAGGTT 59.153 45.455 5.01 0.00 0.00 3.50
1361 3115 4.636249 CTTAGCTAGGCCAATACTTGAGG 58.364 47.826 5.01 0.00 0.00 3.86
1364 3118 4.078639 AGCTTAGCTAGGCCAATACTTG 57.921 45.455 22.94 0.00 36.99 3.16
1365 3119 5.888982 TTAGCTTAGCTAGGCCAATACTT 57.111 39.130 22.94 6.50 42.34 2.24
1435 3190 9.807649 AATCATTACAAGCTGAATTGAAATACC 57.192 29.630 0.00 0.00 34.20 2.73
1460 3239 5.065859 CGCATCCCATATTTACAGTTGACAA 59.934 40.000 0.00 0.00 0.00 3.18
1484 3263 2.202756 CGGAGGTCCTGCGCTTAC 60.203 66.667 20.48 3.69 38.60 2.34
1485 3264 1.945354 CTTCGGAGGTCCTGCGCTTA 61.945 60.000 26.55 13.58 44.59 3.09
1508 3287 7.178451 TCTGACACTATACATTTCTTCACAGGA 59.822 37.037 0.00 0.00 0.00 3.86
1831 3628 6.510746 TGTTTCTTGCGATTCGATATACTG 57.489 37.500 10.88 0.00 0.00 2.74
1832 3629 6.146184 CCATGTTTCTTGCGATTCGATATACT 59.854 38.462 10.88 0.00 0.00 2.12
1833 3630 6.145534 TCCATGTTTCTTGCGATTCGATATAC 59.854 38.462 10.88 0.48 0.00 1.47
1834 3631 6.145534 GTCCATGTTTCTTGCGATTCGATATA 59.854 38.462 10.88 0.00 0.00 0.86
1835 3632 5.050091 GTCCATGTTTCTTGCGATTCGATAT 60.050 40.000 10.88 0.00 0.00 1.63
1836 3633 4.270084 GTCCATGTTTCTTGCGATTCGATA 59.730 41.667 10.88 0.00 0.00 2.92
1860 3769 3.264706 TGGAGACTAGAGTAGCACAGAGT 59.735 47.826 0.00 0.00 0.00 3.24
1861 3770 3.879998 TGGAGACTAGAGTAGCACAGAG 58.120 50.000 0.00 0.00 0.00 3.35
1967 3886 0.038526 GACAATGTCCGTGAGTCCGT 60.039 55.000 1.10 0.00 0.00 4.69
2013 4071 2.702592 TTTGCGGGGATATCGAACTT 57.297 45.000 0.00 0.00 0.00 2.66
2113 4171 5.237048 GCCTCTAGATCATCTGAATGGAAC 58.763 45.833 0.00 0.00 33.42 3.62
2114 4172 4.021632 CGCCTCTAGATCATCTGAATGGAA 60.022 45.833 0.00 0.00 33.42 3.53
2115 4173 3.509184 CGCCTCTAGATCATCTGAATGGA 59.491 47.826 0.00 0.00 33.42 3.41
2116 4174 3.847542 CGCCTCTAGATCATCTGAATGG 58.152 50.000 0.00 0.00 33.42 3.16
2117 4175 3.252400 GCGCCTCTAGATCATCTGAATG 58.748 50.000 0.00 0.00 0.00 2.67
2118 4176 2.896044 TGCGCCTCTAGATCATCTGAAT 59.104 45.455 4.18 0.00 0.00 2.57
2119 4177 2.295629 CTGCGCCTCTAGATCATCTGAA 59.704 50.000 4.18 0.00 0.00 3.02
2120 4178 1.885233 CTGCGCCTCTAGATCATCTGA 59.115 52.381 4.18 0.00 0.00 3.27
2121 4179 1.885233 TCTGCGCCTCTAGATCATCTG 59.115 52.381 4.18 0.00 0.00 2.90
2122 4180 2.161855 CTCTGCGCCTCTAGATCATCT 58.838 52.381 4.18 0.00 0.00 2.90
2123 4181 2.158559 TCTCTGCGCCTCTAGATCATC 58.841 52.381 4.18 0.00 0.00 2.92
2124 4182 2.161855 CTCTCTGCGCCTCTAGATCAT 58.838 52.381 4.18 0.00 0.00 2.45
2125 4183 1.133945 ACTCTCTGCGCCTCTAGATCA 60.134 52.381 4.18 0.00 0.00 2.92
2126 4184 1.604604 ACTCTCTGCGCCTCTAGATC 58.395 55.000 4.18 0.00 0.00 2.75
2127 4185 2.940994 TACTCTCTGCGCCTCTAGAT 57.059 50.000 4.18 0.00 0.00 1.98
2128 4186 2.940994 ATACTCTCTGCGCCTCTAGA 57.059 50.000 4.18 0.00 0.00 2.43
2129 4187 3.670625 ACTATACTCTCTGCGCCTCTAG 58.329 50.000 4.18 0.00 0.00 2.43
2130 4188 3.071167 TGACTATACTCTCTGCGCCTCTA 59.929 47.826 4.18 0.00 0.00 2.43
2131 4189 2.158740 TGACTATACTCTCTGCGCCTCT 60.159 50.000 4.18 0.00 0.00 3.69
2132 4190 2.222886 TGACTATACTCTCTGCGCCTC 58.777 52.381 4.18 0.00 0.00 4.70
2133 4191 2.350057 TGACTATACTCTCTGCGCCT 57.650 50.000 4.18 0.00 0.00 5.52
2134 4192 2.099263 TGTTGACTATACTCTCTGCGCC 59.901 50.000 4.18 0.00 0.00 6.53
2135 4193 3.422417 TGTTGACTATACTCTCTGCGC 57.578 47.619 0.00 0.00 0.00 6.09
2136 4194 4.294232 CCATGTTGACTATACTCTCTGCG 58.706 47.826 0.00 0.00 0.00 5.18
2137 4195 4.054671 GCCATGTTGACTATACTCTCTGC 58.945 47.826 0.00 0.00 0.00 4.26
2138 4196 4.202060 ACGCCATGTTGACTATACTCTCTG 60.202 45.833 0.00 0.00 0.00 3.35
2139 4197 3.954904 ACGCCATGTTGACTATACTCTCT 59.045 43.478 0.00 0.00 0.00 3.10
2140 4198 4.308899 ACGCCATGTTGACTATACTCTC 57.691 45.455 0.00 0.00 0.00 3.20
2141 4199 4.737855 AACGCCATGTTGACTATACTCT 57.262 40.909 0.00 0.00 40.00 3.24
2152 4210 3.057596 ACGAATTTCATCAACGCCATGTT 60.058 39.130 0.00 0.00 43.09 2.71
2153 4211 2.487762 ACGAATTTCATCAACGCCATGT 59.512 40.909 0.00 0.00 0.00 3.21
2154 4212 3.135414 ACGAATTTCATCAACGCCATG 57.865 42.857 0.00 0.00 0.00 3.66
2155 4213 3.687212 TGTACGAATTTCATCAACGCCAT 59.313 39.130 0.00 0.00 0.00 4.40
2156 4214 3.067833 TGTACGAATTTCATCAACGCCA 58.932 40.909 0.00 0.00 0.00 5.69
2157 4215 3.120477 TGTGTACGAATTTCATCAACGCC 60.120 43.478 0.00 0.00 0.00 5.68
2158 4216 4.060288 TGTGTACGAATTTCATCAACGC 57.940 40.909 0.00 0.00 0.00 4.84
2159 4217 6.577055 ACAAATGTGTACGAATTTCATCAACG 59.423 34.615 0.00 0.00 35.72 4.10
2160 4218 7.851822 ACAAATGTGTACGAATTTCATCAAC 57.148 32.000 0.00 0.00 35.72 3.18
2162 4220 9.767684 GATTACAAATGTGTACGAATTTCATCA 57.232 29.630 0.00 0.00 40.00 3.07
2163 4221 9.988350 AGATTACAAATGTGTACGAATTTCATC 57.012 29.630 0.00 0.00 40.00 2.92
2164 4222 9.988350 GAGATTACAAATGTGTACGAATTTCAT 57.012 29.630 0.00 0.00 40.00 2.57
2165 4223 8.994170 TGAGATTACAAATGTGTACGAATTTCA 58.006 29.630 0.00 0.00 40.00 2.69
2166 4224 9.820229 TTGAGATTACAAATGTGTACGAATTTC 57.180 29.630 0.00 0.00 40.00 2.17
2170 4228 9.605955 CAATTTGAGATTACAAATGTGTACGAA 57.394 29.630 0.00 0.00 45.71 3.85
2171 4229 7.748683 GCAATTTGAGATTACAAATGTGTACGA 59.251 33.333 0.00 0.00 45.71 3.43
2172 4230 7.008266 GGCAATTTGAGATTACAAATGTGTACG 59.992 37.037 0.00 0.00 45.71 3.67
2173 4231 8.028938 AGGCAATTTGAGATTACAAATGTGTAC 58.971 33.333 0.00 0.00 45.71 2.90
2174 4232 8.028354 CAGGCAATTTGAGATTACAAATGTGTA 58.972 33.333 0.00 0.00 45.71 2.90
2175 4233 6.869913 CAGGCAATTTGAGATTACAAATGTGT 59.130 34.615 0.00 0.00 45.71 3.72
2176 4234 7.062605 GTCAGGCAATTTGAGATTACAAATGTG 59.937 37.037 0.00 0.00 45.71 3.21
2177 4235 7.039504 AGTCAGGCAATTTGAGATTACAAATGT 60.040 33.333 0.00 0.00 45.71 2.71
2178 4236 7.318141 AGTCAGGCAATTTGAGATTACAAATG 58.682 34.615 0.00 0.00 45.71 2.32
2180 4238 6.899393 AGTCAGGCAATTTGAGATTACAAA 57.101 33.333 0.00 0.00 42.58 2.83
2181 4239 6.716628 AGAAGTCAGGCAATTTGAGATTACAA 59.283 34.615 0.00 0.00 0.00 2.41
2182 4240 6.240894 AGAAGTCAGGCAATTTGAGATTACA 58.759 36.000 0.00 0.00 0.00 2.41
2183 4241 6.749923 AGAAGTCAGGCAATTTGAGATTAC 57.250 37.500 0.00 0.00 0.00 1.89
2184 4242 7.765695 AAAGAAGTCAGGCAATTTGAGATTA 57.234 32.000 0.00 0.00 0.00 1.75
2185 4243 6.661304 AAAGAAGTCAGGCAATTTGAGATT 57.339 33.333 0.00 0.00 0.00 2.40
2186 4244 7.573843 CGTTAAAGAAGTCAGGCAATTTGAGAT 60.574 37.037 0.00 0.00 0.00 2.75
2187 4245 6.293407 CGTTAAAGAAGTCAGGCAATTTGAGA 60.293 38.462 0.00 0.00 0.00 3.27
2188 4246 5.853282 CGTTAAAGAAGTCAGGCAATTTGAG 59.147 40.000 0.00 0.00 0.00 3.02
2189 4247 5.278266 CCGTTAAAGAAGTCAGGCAATTTGA 60.278 40.000 0.00 0.00 0.00 2.69
2190 4248 4.917415 CCGTTAAAGAAGTCAGGCAATTTG 59.083 41.667 0.00 0.00 0.00 2.32
2191 4249 4.583073 ACCGTTAAAGAAGTCAGGCAATTT 59.417 37.500 0.00 0.00 0.00 1.82
2192 4250 4.023193 CACCGTTAAAGAAGTCAGGCAATT 60.023 41.667 0.00 0.00 0.00 2.32
2193 4251 3.502211 CACCGTTAAAGAAGTCAGGCAAT 59.498 43.478 0.00 0.00 0.00 3.56
2194 4252 2.875933 CACCGTTAAAGAAGTCAGGCAA 59.124 45.455 0.00 0.00 0.00 4.52
2195 4253 2.158871 ACACCGTTAAAGAAGTCAGGCA 60.159 45.455 0.00 0.00 0.00 4.75
2196 4254 2.490991 ACACCGTTAAAGAAGTCAGGC 58.509 47.619 0.00 0.00 0.00 4.85
2197 4255 3.497262 GGAACACCGTTAAAGAAGTCAGG 59.503 47.826 0.00 0.00 0.00 3.86
2198 4256 4.124238 TGGAACACCGTTAAAGAAGTCAG 58.876 43.478 0.00 0.00 0.00 3.51
2199 4257 4.124238 CTGGAACACCGTTAAAGAAGTCA 58.876 43.478 0.00 0.00 0.00 3.41
2200 4258 3.497262 CCTGGAACACCGTTAAAGAAGTC 59.503 47.826 0.00 0.00 0.00 3.01
2201 4259 3.118149 ACCTGGAACACCGTTAAAGAAGT 60.118 43.478 0.00 0.00 0.00 3.01
2202 4260 3.473625 ACCTGGAACACCGTTAAAGAAG 58.526 45.455 0.00 0.00 0.00 2.85
2203 4261 3.564053 ACCTGGAACACCGTTAAAGAA 57.436 42.857 0.00 0.00 0.00 2.52
2204 4262 3.896888 TCTACCTGGAACACCGTTAAAGA 59.103 43.478 0.00 0.00 0.00 2.52
2205 4263 4.243270 CTCTACCTGGAACACCGTTAAAG 58.757 47.826 0.00 0.00 0.00 1.85
2206 4264 3.642848 ACTCTACCTGGAACACCGTTAAA 59.357 43.478 0.00 0.00 0.00 1.52
2207 4265 3.233507 ACTCTACCTGGAACACCGTTAA 58.766 45.455 0.00 0.00 0.00 2.01
2208 4266 2.880443 ACTCTACCTGGAACACCGTTA 58.120 47.619 0.00 0.00 0.00 3.18
2209 4267 1.713297 ACTCTACCTGGAACACCGTT 58.287 50.000 0.00 0.00 0.00 4.44
2210 4268 1.713297 AACTCTACCTGGAACACCGT 58.287 50.000 0.00 0.00 0.00 4.83
2211 4269 2.559668 TGTAACTCTACCTGGAACACCG 59.440 50.000 0.00 0.00 0.00 4.94
2212 4270 3.322828 TGTGTAACTCTACCTGGAACACC 59.677 47.826 0.00 0.00 38.04 4.16
2213 4271 4.595762 TGTGTAACTCTACCTGGAACAC 57.404 45.455 0.00 3.95 38.04 3.32
2214 4272 4.406326 TGTTGTGTAACTCTACCTGGAACA 59.594 41.667 0.00 0.00 38.04 3.18
2215 4273 4.952460 TGTTGTGTAACTCTACCTGGAAC 58.048 43.478 0.00 0.00 38.04 3.62
2216 4274 5.617528 TTGTTGTGTAACTCTACCTGGAA 57.382 39.130 0.00 0.00 38.04 3.53
2217 4275 5.617528 TTTGTTGTGTAACTCTACCTGGA 57.382 39.130 0.00 0.00 38.04 3.86
2218 4276 6.485313 TGATTTTGTTGTGTAACTCTACCTGG 59.515 38.462 0.00 0.00 38.04 4.45
2219 4277 7.441157 TCTGATTTTGTTGTGTAACTCTACCTG 59.559 37.037 0.00 0.00 38.04 4.00
2220 4278 7.506114 TCTGATTTTGTTGTGTAACTCTACCT 58.494 34.615 0.00 0.00 38.04 3.08
2221 4279 7.724305 TCTGATTTTGTTGTGTAACTCTACC 57.276 36.000 0.00 0.00 38.04 3.18


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

AutoCloner maintained by Alex Coulton.