Multiple sequence alignment - TraesCS5A01G174400

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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 TraesCS5A01G174400 chr5A 100.000 5254 0 0 1 5254 367598042 367603295 0.000000e+00 9703
1 TraesCS5A01G174400 chr5A 90.943 265 22 1 1848 2112 367599758 367600020 6.470000e-94 355
2 TraesCS5A01G174400 chr5A 90.943 265 22 1 1717 1979 367599889 367600153 6.470000e-94 355
3 TraesCS5A01G174400 chr5A 87.879 132 14 1 1981 2112 367599758 367599887 2.530000e-33 154
4 TraesCS5A01G174400 chr5A 87.879 132 14 1 1717 1846 367600022 367600153 2.530000e-33 154
5 TraesCS5A01G174400 chr5B 94.486 5132 155 56 1 5066 316368119 316373188 0.000000e+00 7792
6 TraesCS5A01G174400 chr5B 88.679 265 23 2 1848 2112 316369840 316370097 3.050000e-82 316
7 TraesCS5A01G174400 chr5B 88.060 268 22 3 1717 1979 316369971 316370233 5.110000e-80 309
8 TraesCS5A01G174400 chr5B 88.618 123 12 1 1981 2103 316369840 316369960 1.180000e-31 148
9 TraesCS5A01G174400 chr5D 94.615 5070 156 57 1 5022 278278461 278283461 0.000000e+00 7742
10 TraesCS5A01G174400 chr5D 90.875 263 22 1 1719 1979 278280315 278280577 8.370000e-93 351
11 TraesCS5A01G174400 chr5D 90.698 258 22 1 1855 2112 278280189 278280444 5.040000e-90 342
12 TraesCS5A01G174400 chr5D 87.879 132 14 1 1717 1846 278280446 278280577 2.530000e-33 154
13 TraesCS5A01G174400 chr5D 87.786 131 13 2 1982 2112 278280184 278280311 3.280000e-32 150
14 TraesCS5A01G174400 chr7D 92.806 139 9 1 5063 5201 584450657 584450794 3.210000e-47 200
15 TraesCS5A01G174400 chr7D 87.500 144 17 1 5064 5207 53745618 53745476 1.170000e-36 165
16 TraesCS5A01G174400 chr6D 90.278 144 13 1 5064 5207 291658155 291658013 2.500000e-43 187
17 TraesCS5A01G174400 chr4A 89.928 139 12 2 5063 5201 677898497 677898633 1.500000e-40 178
18 TraesCS5A01G174400 chr1D 87.324 142 16 2 5061 5201 481439376 481439516 1.510000e-35 161


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 TraesCS5A01G174400 chr5A 367598042 367603295 5253 False 2144.20 9703 91.52880 1 5254 5 chr5A.!!$F1 5253
1 TraesCS5A01G174400 chr5B 316368119 316373188 5069 False 2141.25 7792 89.96075 1 5066 4 chr5B.!!$F1 5065
2 TraesCS5A01G174400 chr5D 278278461 278283461 5000 False 1747.80 7742 90.37060 1 5022 5 chr5D.!!$F1 5021

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
612 626 0.186386 TCTCTCTCCTCCCCGATTCC 59.814 60.000 0.00 0.0 0.00 3.01 F
744 758 0.827925 ATCCAGCGATTCGAGGCCTA 60.828 55.000 4.42 0.0 0.00 3.93 F
1209 1237 1.003233 GAAGAAGGCTGGCTCGGTT 60.003 57.895 3.48 0.0 0.00 4.44 F
2044 2085 0.332632 TGCTTTTGCCTAGCCATCCT 59.667 50.000 0.00 0.0 46.87 3.24 F
3899 3955 0.034059 CACTTCCGCTCAGTGACCTT 59.966 55.000 0.00 0.0 43.90 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1909 0.839946 AGCAGAGTTTCACTGGTGGT 59.160 50.000 0.00 0.00 43.03 4.16 R
1877 1910 1.972872 AAGCAGAGTTTCACTGGTGG 58.027 50.000 0.00 0.00 43.70 4.61 R
3076 3127 4.084287 CCATTCTATGCATTAGGCCACAT 58.916 43.478 3.54 2.87 43.89 3.21 R
3950 4010 0.604780 CAAGACCCTCACCTGCACAG 60.605 60.000 0.00 0.00 0.00 3.66 R
5068 5153 0.028770 ACAACGCACGGACATGTTTG 59.971 50.000 0.00 0.84 0.00 2.93 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
111 112 3.755112 TTCACAGTCCGAAATGTACCA 57.245 42.857 0.00 0.00 0.00 3.25
257 258 2.982130 GCGAGGCTGAAGGAAGGA 59.018 61.111 0.00 0.00 0.00 3.36
287 288 2.380064 AAAGGAACTCACCATGGCAA 57.620 45.000 13.04 0.00 38.49 4.52
323 324 2.683933 GCCGGTTGAGAGGGAGGA 60.684 66.667 1.90 0.00 0.00 3.71
444 445 1.736032 CGGTTTGCTTCTAGACGAGGG 60.736 57.143 0.00 0.00 0.00 4.30
445 446 1.275573 GGTTTGCTTCTAGACGAGGGT 59.724 52.381 0.00 0.00 0.00 4.34
446 447 2.338500 GTTTGCTTCTAGACGAGGGTG 58.662 52.381 0.00 0.00 0.00 4.61
447 448 0.246635 TTGCTTCTAGACGAGGGTGC 59.753 55.000 0.00 0.00 0.00 5.01
451 459 2.613223 GCTTCTAGACGAGGGTGCTTTT 60.613 50.000 0.00 0.00 0.00 2.27
453 461 1.275291 TCTAGACGAGGGTGCTTTTGG 59.725 52.381 0.00 0.00 0.00 3.28
454 462 1.275291 CTAGACGAGGGTGCTTTTGGA 59.725 52.381 0.00 0.00 0.00 3.53
546 556 1.194781 TTGTCTCTGCCTCTCCCACC 61.195 60.000 0.00 0.00 0.00 4.61
547 557 2.039624 TCTCTGCCTCTCCCACCC 59.960 66.667 0.00 0.00 0.00 4.61
548 558 2.284921 CTCTGCCTCTCCCACCCA 60.285 66.667 0.00 0.00 0.00 4.51
549 559 2.607750 TCTGCCTCTCCCACCCAC 60.608 66.667 0.00 0.00 0.00 4.61
550 560 4.087892 CTGCCTCTCCCACCCACG 62.088 72.222 0.00 0.00 0.00 4.94
587 597 0.752658 TCGGCATCATTCCATCGTCT 59.247 50.000 0.00 0.00 0.00 4.18
598 608 6.976088 TCATTCCATCGTCTTATTCTCTCTC 58.024 40.000 0.00 0.00 0.00 3.20
599 609 6.775142 TCATTCCATCGTCTTATTCTCTCTCT 59.225 38.462 0.00 0.00 0.00 3.10
611 625 1.144093 TCTCTCTCTCCTCCCCGATTC 59.856 57.143 0.00 0.00 0.00 2.52
612 626 0.186386 TCTCTCTCCTCCCCGATTCC 59.814 60.000 0.00 0.00 0.00 3.01
613 627 0.830023 CTCTCTCCTCCCCGATTCCC 60.830 65.000 0.00 0.00 0.00 3.97
614 628 1.839296 CTCTCCTCCCCGATTCCCC 60.839 68.421 0.00 0.00 0.00 4.81
615 629 2.040884 CTCCTCCCCGATTCCCCA 60.041 66.667 0.00 0.00 0.00 4.96
616 630 2.366435 TCCTCCCCGATTCCCCAC 60.366 66.667 0.00 0.00 0.00 4.61
647 661 1.283613 ACCCATCGCACCAAATTCCTA 59.716 47.619 0.00 0.00 0.00 2.94
744 758 0.827925 ATCCAGCGATTCGAGGCCTA 60.828 55.000 4.42 0.00 0.00 3.93
815 829 4.814294 ATCGGCCGGTCGTTGCTC 62.814 66.667 29.96 0.00 0.00 4.26
889 903 7.284820 CCCTCCTTCCGGAAGTAAATAAATAA 58.715 38.462 35.89 11.86 39.29 1.40
1146 1174 2.116125 GCCAAGCCTGTCAACCCT 59.884 61.111 0.00 0.00 0.00 4.34
1209 1237 1.003233 GAAGAAGGCTGGCTCGGTT 60.003 57.895 3.48 0.00 0.00 4.44
1299 1327 2.172372 CGAGGAGGACGACGACGAT 61.172 63.158 15.32 0.00 42.66 3.73
1358 1386 2.166870 GGCACAAATCCATTGATGCTCA 59.833 45.455 12.15 0.00 41.85 4.26
1876 1909 9.926158 ACTGATAAAATCAATTTACATTGCACA 57.074 25.926 0.00 0.00 39.90 4.57
2044 2085 0.332632 TGCTTTTGCCTAGCCATCCT 59.667 50.000 0.00 0.00 46.87 3.24
2259 2300 1.686355 TTGCATTCCCTTGTTCACGT 58.314 45.000 0.00 0.00 0.00 4.49
2432 2473 1.280710 ACCATTCAAGTATGACGGCCA 59.719 47.619 2.24 0.00 34.61 5.36
2553 2600 9.255304 GTTATTTGCAGGTTTCTGTTTGATAAA 57.745 29.630 0.00 0.00 42.78 1.40
2712 2763 2.359848 TGCAAGTTCTGATGGCATATGC 59.640 45.455 19.79 19.79 41.14 3.14
2866 2917 0.914644 TTCCCAGGGAAGCTCATCTG 59.085 55.000 18.05 0.00 36.71 2.90
2988 3039 4.259930 GGGTACGCATGTTACGTAATGTTC 60.260 45.833 11.86 0.00 46.50 3.18
3040 3091 9.565213 CAGTTAATTGTCATCTGATTTTCTTCC 57.435 33.333 0.00 0.00 0.00 3.46
3076 3127 6.377146 TGACATGCTCTGTACTGTAGTATTCA 59.623 38.462 0.00 3.92 38.54 2.57
3436 3492 1.002366 ATTGTTCGTCGCTCTGATGC 58.998 50.000 0.00 0.00 33.35 3.91
3453 3509 4.318332 TGATGCAAGGTTGTAGAGACTTG 58.682 43.478 0.00 0.00 42.31 3.16
3643 3699 5.334414 CGATAATATTGGGCACAAGCTTCTC 60.334 44.000 7.78 4.64 40.49 2.87
3800 3856 7.548780 CCAAATGAAACAATGAATCCCGTATTT 59.451 33.333 0.00 0.00 0.00 1.40
3842 3898 6.295067 GGTGGCTGGTGAATTGTTAAGTTTAT 60.295 38.462 0.00 0.00 0.00 1.40
3869 3925 2.029666 CATTCCCGCTAGCCTCCG 59.970 66.667 9.66 0.00 0.00 4.63
3899 3955 0.034059 CACTTCCGCTCAGTGACCTT 59.966 55.000 0.00 0.00 43.90 3.50
3904 3960 4.142138 ACTTCCGCTCAGTGACCTTATTAG 60.142 45.833 0.00 0.00 0.00 1.73
3950 4010 8.440833 CAGTTGTAGGTGCTAAATGTAGTTTAC 58.559 37.037 0.00 0.00 0.00 2.01
4019 4079 3.819337 CCATTATGGCTGGAGATGTGAAG 59.181 47.826 0.00 0.00 35.70 3.02
4168 4228 0.813821 GCCAAGCCATGACCTTCTTC 59.186 55.000 0.00 0.00 0.00 2.87
4169 4229 1.615384 GCCAAGCCATGACCTTCTTCT 60.615 52.381 0.00 0.00 0.00 2.85
4170 4230 2.800250 CCAAGCCATGACCTTCTTCTT 58.200 47.619 0.00 0.00 0.00 2.52
4271 4331 1.273838 TGATACAAGGGGAGGTCAGCT 60.274 52.381 0.00 0.00 0.00 4.24
4304 4364 4.085107 CGTAAGAAACCAATTTTGCTGCAC 60.085 41.667 0.00 0.00 43.02 4.57
4614 4679 3.812167 GCTGGGACTTCCTTCAGTTGATT 60.812 47.826 0.00 0.00 36.20 2.57
4615 4680 4.565652 GCTGGGACTTCCTTCAGTTGATTA 60.566 45.833 0.00 0.00 36.20 1.75
4621 4686 6.258947 GGACTTCCTTCAGTTGATTATACTGC 59.741 42.308 0.00 0.00 42.12 4.40
4635 4700 7.940850 TGATTATACTGCTTCTTATTTTGGCC 58.059 34.615 0.00 0.00 0.00 5.36
4647 4712 1.954362 TTTTGGCCAGTGCAAAGCGT 61.954 50.000 5.11 0.00 40.13 5.07
4675 4740 2.459934 GTTGTAGTTGCTGTTGGTTGC 58.540 47.619 0.00 0.00 0.00 4.17
4710 4779 4.080863 ACTCTGTCAGGGTTTATTAGGCAG 60.081 45.833 0.00 0.00 0.00 4.85
4747 4816 9.762381 TGGGTTAAAGTTTGACCATAGATTTAT 57.238 29.630 25.83 0.00 35.11 1.40
4799 4868 7.396339 ACAGACATTACACTGTGATAACCTCTA 59.604 37.037 15.86 0.00 44.18 2.43
4801 4870 8.634444 AGACATTACACTGTGATAACCTCTATC 58.366 37.037 15.86 0.00 0.00 2.08
4802 4871 8.306313 ACATTACACTGTGATAACCTCTATCA 57.694 34.615 15.86 0.00 0.00 2.15
4813 4882 8.306313 TGATAACCTCTATCACAGTGTAATGT 57.694 34.615 0.00 0.00 0.00 2.71
4814 4883 8.414003 TGATAACCTCTATCACAGTGTAATGTC 58.586 37.037 0.00 0.00 0.00 3.06
4815 4884 6.859112 AACCTCTATCACAGTGTAATGTCT 57.141 37.500 0.00 0.00 0.00 3.41
4816 4885 6.214191 ACCTCTATCACAGTGTAATGTCTG 57.786 41.667 0.00 0.00 37.65 3.51
4817 4886 5.717178 ACCTCTATCACAGTGTAATGTCTGT 59.283 40.000 0.00 0.00 44.32 3.41
4823 4892 4.400529 ACAGTGTAATGTCTGTGACACA 57.599 40.909 8.26 8.26 45.65 3.72
4824 4893 4.119862 ACAGTGTAATGTCTGTGACACAC 58.880 43.478 3.56 7.08 45.65 3.82
4825 4894 4.141937 ACAGTGTAATGTCTGTGACACACT 60.142 41.667 3.56 13.20 45.65 3.55
4826 4895 4.811024 CAGTGTAATGTCTGTGACACACTT 59.189 41.667 15.17 5.44 45.65 3.16
4827 4896 5.294306 CAGTGTAATGTCTGTGACACACTTT 59.706 40.000 15.17 3.68 45.65 2.66
4828 4897 6.478673 CAGTGTAATGTCTGTGACACACTTTA 59.521 38.462 15.17 2.75 45.65 1.85
4829 4898 7.171508 CAGTGTAATGTCTGTGACACACTTTAT 59.828 37.037 15.17 0.00 45.65 1.40
4830 4899 8.364894 AGTGTAATGTCTGTGACACACTTTATA 58.635 33.333 3.56 1.50 45.65 0.98
4831 4900 9.151471 GTGTAATGTCTGTGACACACTTTATAT 57.849 33.333 3.56 0.00 45.65 0.86
4832 4901 9.719355 TGTAATGTCTGTGACACACTTTATATT 57.281 29.630 3.56 3.99 45.65 1.28
4917 4986 5.995897 ACCCAAAGTACAGAAGACACAATAC 59.004 40.000 0.00 0.00 0.00 1.89
4921 4990 7.226720 CCAAAGTACAGAAGACACAATACACTT 59.773 37.037 0.00 0.00 0.00 3.16
4924 4993 7.603651 AGTACAGAAGACACAATACACTTAGG 58.396 38.462 0.00 0.00 0.00 2.69
4927 4996 4.219944 AGAAGACACAATACACTTAGGCGA 59.780 41.667 0.00 0.00 0.00 5.54
4961 5032 7.707104 ACTTACATATGCAATGCTAAAGGAAC 58.293 34.615 6.82 0.00 0.00 3.62
4974 5045 2.222227 AAGGAACTGAAATCTGGGCC 57.778 50.000 0.00 0.00 40.86 5.80
4990 5061 0.171231 GGCCCTGAATTTGCGAGTTC 59.829 55.000 2.27 2.27 0.00 3.01
5018 5089 6.649141 GGGCACTACGATGAATTGTATTGATA 59.351 38.462 10.64 0.00 32.18 2.15
5019 5090 7.148573 GGGCACTACGATGAATTGTATTGATAG 60.149 40.741 10.64 0.00 32.18 2.08
5020 5091 7.598869 GGCACTACGATGAATTGTATTGATAGA 59.401 37.037 10.64 0.00 32.18 1.98
5021 5092 8.428536 GCACTACGATGAATTGTATTGATAGAC 58.571 37.037 10.64 0.00 32.18 2.59
5030 5115 7.169813 TGAATTGTATTGATAGACGTCATCTGC 59.830 37.037 19.50 7.98 38.49 4.26
5043 5128 0.531532 CATCTGCGGGGAGTGATGTC 60.532 60.000 0.00 0.00 33.65 3.06
5078 5163 8.810652 TTTTAATGAAACTAGCAAACATGTCC 57.189 30.769 0.00 0.00 0.00 4.02
5079 5164 4.685169 ATGAAACTAGCAAACATGTCCG 57.315 40.909 0.00 0.00 0.00 4.79
5080 5165 3.472652 TGAAACTAGCAAACATGTCCGT 58.527 40.909 0.00 0.00 0.00 4.69
5081 5166 3.249799 TGAAACTAGCAAACATGTCCGTG 59.750 43.478 0.00 0.00 0.00 4.94
5082 5167 1.156736 ACTAGCAAACATGTCCGTGC 58.843 50.000 17.10 17.10 37.26 5.34
5083 5168 0.095245 CTAGCAAACATGTCCGTGCG 59.905 55.000 18.16 6.56 41.90 5.34
5084 5169 0.601576 TAGCAAACATGTCCGTGCGT 60.602 50.000 18.16 11.87 41.90 5.24
5085 5170 1.008995 GCAAACATGTCCGTGCGTT 60.009 52.632 11.86 0.00 0.00 4.84
5086 5171 1.268113 GCAAACATGTCCGTGCGTTG 61.268 55.000 11.86 6.59 0.00 4.10
5087 5172 0.028770 CAAACATGTCCGTGCGTTGT 59.971 50.000 0.00 0.00 0.00 3.32
5088 5173 0.306533 AAACATGTCCGTGCGTTGTC 59.693 50.000 0.00 0.00 0.00 3.18
5089 5174 0.812014 AACATGTCCGTGCGTTGTCA 60.812 50.000 0.00 0.00 0.00 3.58
5090 5175 0.602638 ACATGTCCGTGCGTTGTCAT 60.603 50.000 0.00 0.00 0.00 3.06
5091 5176 0.179217 CATGTCCGTGCGTTGTCATG 60.179 55.000 0.00 0.00 0.00 3.07
5092 5177 1.298157 ATGTCCGTGCGTTGTCATGG 61.298 55.000 0.00 0.00 42.99 3.66
5093 5178 1.666553 GTCCGTGCGTTGTCATGGA 60.667 57.895 0.89 0.89 46.74 3.41
5094 5179 1.069935 TCCGTGCGTTGTCATGGAA 59.930 52.632 2.48 0.00 46.14 3.53
5095 5180 0.948623 TCCGTGCGTTGTCATGGAAG 60.949 55.000 2.48 0.00 46.14 3.46
5096 5181 0.948623 CCGTGCGTTGTCATGGAAGA 60.949 55.000 0.00 0.00 44.07 2.87
5097 5182 0.865111 CGTGCGTTGTCATGGAAGAA 59.135 50.000 0.00 0.00 0.00 2.52
5098 5183 1.262950 CGTGCGTTGTCATGGAAGAAA 59.737 47.619 0.00 0.00 0.00 2.52
5099 5184 2.286713 CGTGCGTTGTCATGGAAGAAAA 60.287 45.455 0.00 0.00 0.00 2.29
5100 5185 3.701241 GTGCGTTGTCATGGAAGAAAAA 58.299 40.909 0.00 0.00 0.00 1.94
5123 5208 8.617290 AAAATATATCTTCAACACGGGTATCC 57.383 34.615 0.00 0.00 0.00 2.59
5124 5209 6.928348 ATATATCTTCAACACGGGTATCCA 57.072 37.500 0.00 0.00 0.00 3.41
5125 5210 3.992943 ATCTTCAACACGGGTATCCAA 57.007 42.857 0.00 0.00 0.00 3.53
5126 5211 3.048337 TCTTCAACACGGGTATCCAAC 57.952 47.619 0.00 0.00 0.00 3.77
5138 5223 3.715628 GTATCCAACCATCATTGTGGC 57.284 47.619 5.51 0.00 43.27 5.01
5139 5224 2.537633 ATCCAACCATCATTGTGGCT 57.462 45.000 5.51 0.00 43.27 4.75
5140 5225 3.668141 ATCCAACCATCATTGTGGCTA 57.332 42.857 5.51 0.00 43.27 3.93
5141 5226 3.668141 TCCAACCATCATTGTGGCTAT 57.332 42.857 5.51 0.00 43.27 2.97
5142 5227 3.554934 TCCAACCATCATTGTGGCTATC 58.445 45.455 5.51 0.00 43.27 2.08
5143 5228 2.624838 CCAACCATCATTGTGGCTATCC 59.375 50.000 5.51 0.00 43.27 2.59
5144 5229 3.559069 CAACCATCATTGTGGCTATCCT 58.441 45.455 5.51 0.00 43.27 3.24
5145 5230 3.956199 CAACCATCATTGTGGCTATCCTT 59.044 43.478 5.51 0.00 43.27 3.36
5146 5231 4.255510 ACCATCATTGTGGCTATCCTTT 57.744 40.909 5.51 0.00 43.27 3.11
5147 5232 5.387113 ACCATCATTGTGGCTATCCTTTA 57.613 39.130 5.51 0.00 43.27 1.85
5148 5233 5.957132 ACCATCATTGTGGCTATCCTTTAT 58.043 37.500 5.51 0.00 43.27 1.40
5149 5234 6.006449 ACCATCATTGTGGCTATCCTTTATC 58.994 40.000 5.51 0.00 43.27 1.75
5150 5235 5.416952 CCATCATTGTGGCTATCCTTTATCC 59.583 44.000 0.00 0.00 31.43 2.59
5151 5236 4.985538 TCATTGTGGCTATCCTTTATCCC 58.014 43.478 0.00 0.00 0.00 3.85
5152 5237 3.485463 TTGTGGCTATCCTTTATCCCG 57.515 47.619 0.00 0.00 0.00 5.14
5153 5238 1.697432 TGTGGCTATCCTTTATCCCGG 59.303 52.381 0.00 0.00 0.00 5.73
5154 5239 1.975680 GTGGCTATCCTTTATCCCGGA 59.024 52.381 0.73 0.00 0.00 5.14
5155 5240 1.975680 TGGCTATCCTTTATCCCGGAC 59.024 52.381 0.73 0.00 30.90 4.79
5156 5241 1.975680 GGCTATCCTTTATCCCGGACA 59.024 52.381 0.73 0.00 30.90 4.02
5157 5242 2.370849 GGCTATCCTTTATCCCGGACAA 59.629 50.000 0.73 0.00 30.90 3.18
5158 5243 3.181448 GGCTATCCTTTATCCCGGACAAA 60.181 47.826 0.73 0.00 30.90 2.83
5159 5244 3.813724 GCTATCCTTTATCCCGGACAAAC 59.186 47.826 0.73 0.00 30.90 2.93
5160 5245 4.444449 GCTATCCTTTATCCCGGACAAACT 60.444 45.833 0.73 0.00 30.90 2.66
5161 5246 4.586306 ATCCTTTATCCCGGACAAACTT 57.414 40.909 0.73 0.00 30.90 2.66
5162 5247 3.681593 TCCTTTATCCCGGACAAACTTG 58.318 45.455 0.73 0.00 0.00 3.16
5163 5248 2.163613 CCTTTATCCCGGACAAACTTGC 59.836 50.000 0.73 0.00 0.00 4.01
5164 5249 2.871096 TTATCCCGGACAAACTTGCT 57.129 45.000 0.73 0.00 0.00 3.91
5165 5250 2.107950 TATCCCGGACAAACTTGCTG 57.892 50.000 0.73 0.00 0.00 4.41
5166 5251 0.609131 ATCCCGGACAAACTTGCTGG 60.609 55.000 0.73 5.32 33.40 4.85
5167 5252 1.528309 CCCGGACAAACTTGCTGGT 60.528 57.895 0.73 0.00 32.41 4.00
5168 5253 1.106944 CCCGGACAAACTTGCTGGTT 61.107 55.000 0.73 0.00 32.41 3.67
5176 5261 4.385358 CAAACTTGCTGGTTGGTACTTT 57.615 40.909 0.00 0.00 39.58 2.66
5177 5262 4.754322 CAAACTTGCTGGTTGGTACTTTT 58.246 39.130 0.00 0.00 39.58 2.27
5178 5263 4.385358 AACTTGCTGGTTGGTACTTTTG 57.615 40.909 0.00 0.00 0.00 2.44
5179 5264 2.693074 ACTTGCTGGTTGGTACTTTTGG 59.307 45.455 0.00 0.00 0.00 3.28
5180 5265 1.036707 TGCTGGTTGGTACTTTTGGC 58.963 50.000 0.00 0.00 0.00 4.52
5181 5266 0.317160 GCTGGTTGGTACTTTTGGCC 59.683 55.000 0.00 0.00 0.00 5.36
5182 5267 1.698506 CTGGTTGGTACTTTTGGCCA 58.301 50.000 0.00 0.00 0.00 5.36
5183 5268 1.339929 CTGGTTGGTACTTTTGGCCAC 59.660 52.381 3.88 0.00 31.19 5.01
5184 5269 1.342076 TGGTTGGTACTTTTGGCCACA 60.342 47.619 3.88 0.00 31.19 4.17
5185 5270 1.757699 GGTTGGTACTTTTGGCCACAA 59.242 47.619 3.88 3.88 34.07 3.33
5186 5271 2.482316 GGTTGGTACTTTTGGCCACAAC 60.482 50.000 19.60 19.60 36.06 3.32
5187 5272 2.145397 TGGTACTTTTGGCCACAACA 57.855 45.000 3.88 0.00 36.06 3.33
5188 5273 2.457598 TGGTACTTTTGGCCACAACAA 58.542 42.857 3.88 0.00 36.06 2.83
5189 5274 3.034635 TGGTACTTTTGGCCACAACAAT 58.965 40.909 3.88 0.00 36.06 2.71
5190 5275 3.181471 TGGTACTTTTGGCCACAACAATG 60.181 43.478 3.88 1.62 36.06 2.82
5191 5276 3.181470 GGTACTTTTGGCCACAACAATGT 60.181 43.478 3.88 8.32 41.61 2.71
5192 5277 4.038162 GGTACTTTTGGCCACAACAATGTA 59.962 41.667 3.88 7.24 37.82 2.29
5193 5278 4.053469 ACTTTTGGCCACAACAATGTAC 57.947 40.909 3.88 0.00 37.82 2.90
5194 5279 3.449018 ACTTTTGGCCACAACAATGTACA 59.551 39.130 3.88 0.00 37.82 2.90
5195 5280 4.100808 ACTTTTGGCCACAACAATGTACAT 59.899 37.500 3.88 1.41 37.82 2.29
5196 5281 5.303078 ACTTTTGGCCACAACAATGTACATA 59.697 36.000 3.88 0.00 37.82 2.29
5197 5282 4.775058 TTGGCCACAACAATGTACATAC 57.225 40.909 3.88 0.00 37.82 2.39
5198 5283 2.744741 TGGCCACAACAATGTACATACG 59.255 45.455 9.21 6.22 37.82 3.06
5199 5284 2.745281 GGCCACAACAATGTACATACGT 59.255 45.455 9.21 6.90 37.82 3.57
5200 5285 3.425625 GGCCACAACAATGTACATACGTG 60.426 47.826 9.21 12.98 37.82 4.49
5201 5286 3.742786 CCACAACAATGTACATACGTGC 58.257 45.455 9.21 0.00 37.82 5.34
5202 5287 3.187432 CCACAACAATGTACATACGTGCA 59.813 43.478 9.21 0.00 42.26 4.57
5203 5288 4.319839 CCACAACAATGTACATACGTGCAA 60.320 41.667 9.21 0.00 41.34 4.08
5204 5289 5.208503 CACAACAATGTACATACGTGCAAA 58.791 37.500 9.21 0.00 41.34 3.68
5205 5290 5.855925 CACAACAATGTACATACGTGCAAAT 59.144 36.000 9.21 0.00 41.34 2.32
5206 5291 5.855925 ACAACAATGTACATACGTGCAAATG 59.144 36.000 9.21 7.02 41.34 2.32
5207 5292 4.980590 ACAATGTACATACGTGCAAATGG 58.019 39.130 9.21 0.00 41.34 3.16
5208 5293 4.697828 ACAATGTACATACGTGCAAATGGA 59.302 37.500 9.21 0.00 41.34 3.41
5209 5294 5.356751 ACAATGTACATACGTGCAAATGGAT 59.643 36.000 9.21 0.00 41.34 3.41
5210 5295 4.873768 TGTACATACGTGCAAATGGATG 57.126 40.909 0.00 5.70 34.53 3.51
5211 5296 3.625313 TGTACATACGTGCAAATGGATGG 59.375 43.478 10.75 0.00 34.53 3.51
5212 5297 2.997980 ACATACGTGCAAATGGATGGA 58.002 42.857 10.75 0.00 0.00 3.41
5213 5298 3.554934 ACATACGTGCAAATGGATGGAT 58.445 40.909 10.75 0.00 0.00 3.41
5214 5299 3.953612 ACATACGTGCAAATGGATGGATT 59.046 39.130 10.75 0.00 0.00 3.01
5215 5300 4.402155 ACATACGTGCAAATGGATGGATTT 59.598 37.500 10.75 0.00 0.00 2.17
5216 5301 3.959535 ACGTGCAAATGGATGGATTTT 57.040 38.095 0.00 0.00 0.00 1.82
5217 5302 3.848726 ACGTGCAAATGGATGGATTTTC 58.151 40.909 0.00 0.00 0.00 2.29
5218 5303 3.511146 ACGTGCAAATGGATGGATTTTCT 59.489 39.130 0.00 0.00 0.00 2.52
5219 5304 3.861113 CGTGCAAATGGATGGATTTTCTG 59.139 43.478 0.00 0.00 0.00 3.02
5220 5305 4.380761 CGTGCAAATGGATGGATTTTCTGA 60.381 41.667 0.00 0.00 0.00 3.27
5221 5306 5.107133 GTGCAAATGGATGGATTTTCTGAG 58.893 41.667 0.00 0.00 0.00 3.35
5222 5307 5.018149 TGCAAATGGATGGATTTTCTGAGA 58.982 37.500 0.00 0.00 0.00 3.27
5223 5308 5.126545 TGCAAATGGATGGATTTTCTGAGAG 59.873 40.000 0.00 0.00 0.00 3.20
5224 5309 5.451520 GCAAATGGATGGATTTTCTGAGAGG 60.452 44.000 0.00 0.00 0.00 3.69
5225 5310 3.287867 TGGATGGATTTTCTGAGAGGC 57.712 47.619 0.00 0.00 0.00 4.70
5226 5311 2.848694 TGGATGGATTTTCTGAGAGGCT 59.151 45.455 0.00 0.00 0.00 4.58
5227 5312 3.267812 TGGATGGATTTTCTGAGAGGCTT 59.732 43.478 0.00 0.00 0.00 4.35
5228 5313 4.264083 TGGATGGATTTTCTGAGAGGCTTT 60.264 41.667 0.00 0.00 0.00 3.51
5229 5314 5.044919 TGGATGGATTTTCTGAGAGGCTTTA 60.045 40.000 0.00 0.00 0.00 1.85
5230 5315 6.067350 GGATGGATTTTCTGAGAGGCTTTAT 58.933 40.000 0.00 0.00 0.00 1.40
5231 5316 6.206438 GGATGGATTTTCTGAGAGGCTTTATC 59.794 42.308 0.00 0.00 0.00 1.75
5232 5317 5.440610 TGGATTTTCTGAGAGGCTTTATCC 58.559 41.667 0.00 0.00 0.00 2.59
5233 5318 5.192522 TGGATTTTCTGAGAGGCTTTATCCT 59.807 40.000 0.00 0.00 39.67 3.24
5234 5319 6.125719 GGATTTTCTGAGAGGCTTTATCCTT 58.874 40.000 0.00 0.00 36.38 3.36
5235 5320 6.605194 GGATTTTCTGAGAGGCTTTATCCTTT 59.395 38.462 0.00 0.00 36.38 3.11
5236 5321 7.123397 GGATTTTCTGAGAGGCTTTATCCTTTT 59.877 37.037 0.00 0.00 36.38 2.27
5237 5322 7.839680 TTTTCTGAGAGGCTTTATCCTTTTT 57.160 32.000 0.00 0.00 36.38 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 6.019748 TGAGGAGTCTTAGATTGGAGAAGTT 58.980 40.000 0.00 0.00 0.00 2.66
242 243 1.223211 GCCTCCTTCCTTCAGCCTC 59.777 63.158 0.00 0.00 0.00 4.70
257 258 1.134438 AGTTCCTTTTCCTCCCGCCT 61.134 55.000 0.00 0.00 0.00 5.52
415 416 0.040692 GAAGCAAACCGAAACCGACC 60.041 55.000 0.00 0.00 0.00 4.79
444 445 3.680786 GCCGGGGTCCAAAAGCAC 61.681 66.667 2.18 0.00 0.00 4.40
445 446 4.986708 GGCCGGGGTCCAAAAGCA 62.987 66.667 2.18 0.00 0.00 3.91
446 447 4.678743 AGGCCGGGGTCCAAAAGC 62.679 66.667 2.18 0.00 0.00 3.51
447 448 2.676471 CAGGCCGGGGTCCAAAAG 60.676 66.667 2.18 0.00 0.00 2.27
587 597 2.784095 TCGGGGAGGAGAGAGAGAATAA 59.216 50.000 0.00 0.00 0.00 1.40
598 608 2.040884 TGGGGAATCGGGGAGGAG 60.041 66.667 0.00 0.00 0.00 3.69
599 609 2.366435 GTGGGGAATCGGGGAGGA 60.366 66.667 0.00 0.00 0.00 3.71
744 758 2.898729 AATTCATCGACGGAGATGCT 57.101 45.000 14.91 5.05 45.57 3.79
889 903 6.516860 CGAAATAAACCCTAGACGATCATCCT 60.517 42.308 0.00 0.00 0.00 3.24
1146 1174 1.948611 GCAATGACAAGGGGCGTCTTA 60.949 52.381 0.00 0.00 34.37 2.10
1209 1237 3.948719 AGCTTCCCGCCCGACAAA 61.949 61.111 0.00 0.00 40.39 2.83
1358 1386 4.031129 CTGGGGCAGCAGCTGAGT 62.031 66.667 27.39 0.00 41.70 3.41
1688 1718 8.433421 TGACAGGTAAGCTTTAAATACTATGC 57.567 34.615 3.20 0.00 0.00 3.14
1805 1838 5.690464 ATTAGATGCTGAGGACTGAAGTT 57.310 39.130 0.00 0.00 0.00 2.66
1853 1886 9.149225 TGGTGTGCAATGTAAATTGATTTTATC 57.851 29.630 9.96 0.00 32.56 1.75
1873 1906 1.942657 CAGAGTTTCACTGGTGGTGTG 59.057 52.381 0.70 0.00 45.50 3.82
1874 1907 1.747206 GCAGAGTTTCACTGGTGGTGT 60.747 52.381 0.70 0.00 45.50 4.16
1875 1908 0.947244 GCAGAGTTTCACTGGTGGTG 59.053 55.000 0.70 0.00 46.60 4.17
1876 1909 0.839946 AGCAGAGTTTCACTGGTGGT 59.160 50.000 0.00 0.00 43.03 4.16
1877 1910 1.972872 AAGCAGAGTTTCACTGGTGG 58.027 50.000 0.00 0.00 43.70 4.61
2515 2561 5.836358 ACCTGCAAATAACCAAGGTTAAGAA 59.164 36.000 15.07 3.55 42.82 2.52
2712 2763 9.132521 CTTGAATTAACTGCATTTTACCAAGAG 57.867 33.333 11.12 0.00 0.00 2.85
2772 2823 6.910995 AGATCTTTGTTCAAATGAGCTTCTG 58.089 36.000 0.00 0.00 0.00 3.02
2866 2917 4.935808 CACCTCAAGTAACTTACCATGACC 59.064 45.833 0.00 0.00 0.00 4.02
3053 3104 6.775594 TGAATACTACAGTACAGAGCATGT 57.224 37.500 0.00 0.02 46.45 3.21
3076 3127 4.084287 CCATTCTATGCATTAGGCCACAT 58.916 43.478 3.54 2.87 43.89 3.21
3221 3272 6.861055 ACAGCATCAACCAACTAAAATTTACG 59.139 34.615 0.00 0.00 0.00 3.18
3436 3492 9.877178 AGTAAATATCAAGTCTCTACAACCTTG 57.123 33.333 0.00 0.00 36.49 3.61
3643 3699 1.055040 CCCTCCAGCCCATCTTAGAG 58.945 60.000 0.00 0.00 0.00 2.43
3733 3789 2.561478 TCCAACAGGCCAAGTAAGAC 57.439 50.000 5.01 0.00 0.00 3.01
3773 3829 4.526262 ACGGGATTCATTGTTTCATTTGGA 59.474 37.500 0.00 0.00 0.00 3.53
3800 3856 4.169856 AGCCACCCAAATGGATTATTAGGA 59.830 41.667 0.00 0.00 43.02 2.94
3842 3898 2.409055 GCGGGAATGCATGCAGACA 61.409 57.895 26.69 1.47 34.15 3.41
3869 3925 1.949257 CGGAAGTGTTCAACAGGGC 59.051 57.895 0.00 0.00 0.00 5.19
3950 4010 0.604780 CAAGACCCTCACCTGCACAG 60.605 60.000 0.00 0.00 0.00 3.66
4214 4274 4.046286 TGGGTTGTTCTGCAGGAAATAT 57.954 40.909 15.13 0.00 35.51 1.28
4304 4364 5.505286 CAGTTAGTTCTGTGAGCAAAACAG 58.495 41.667 7.02 7.02 45.26 3.16
4386 4447 7.542130 CCAAGTTACTTGCTGAATAAATCAACC 59.458 37.037 18.72 0.00 39.85 3.77
4614 4679 6.318648 CACTGGCCAAAATAAGAAGCAGTATA 59.681 38.462 7.01 0.00 0.00 1.47
4615 4680 5.126061 CACTGGCCAAAATAAGAAGCAGTAT 59.874 40.000 7.01 0.00 0.00 2.12
4621 4686 3.940209 TGCACTGGCCAAAATAAGAAG 57.060 42.857 7.01 0.00 40.13 2.85
4635 4700 0.862701 CACACACACGCTTTGCACTG 60.863 55.000 0.00 0.00 0.00 3.66
4647 4712 2.013400 CAGCAACTACAACCACACACA 58.987 47.619 0.00 0.00 0.00 3.72
4681 4746 6.869206 AATAAACCCTGACAGAGTAGCTAA 57.131 37.500 3.32 0.00 0.00 3.09
4683 4748 5.364157 CCTAATAAACCCTGACAGAGTAGCT 59.636 44.000 3.32 0.00 0.00 3.32
4691 4756 2.356741 GGCTGCCTAATAAACCCTGACA 60.357 50.000 12.43 0.00 0.00 3.58
4692 4757 2.092375 AGGCTGCCTAATAAACCCTGAC 60.092 50.000 21.98 0.00 28.47 3.51
4695 4760 2.205342 TGAGGCTGCCTAATAAACCCT 58.795 47.619 23.44 0.00 31.76 4.34
4710 4779 7.330946 GTCAAACTTTAACCCAAAATATGAGGC 59.669 37.037 0.00 0.00 0.00 4.70
4776 4845 8.414003 TGATAGAGGTTATCACAGTGTAATGTC 58.586 37.037 0.00 1.42 0.00 3.06
4802 4871 4.119862 GTGTGTCACAGACATTACACTGT 58.880 43.478 5.74 0.00 44.63 3.55
4803 4872 4.371786 AGTGTGTCACAGACATTACACTG 58.628 43.478 16.27 0.00 44.63 3.66
4805 4874 5.734855 AAAGTGTGTCACAGACATTACAC 57.265 39.130 7.97 12.65 44.63 2.90
4806 4875 9.719355 AATATAAAGTGTGTCACAGACATTACA 57.281 29.630 7.97 0.00 44.63 2.41
4917 4986 4.124851 AGTTACTCCATTCGCCTAAGTG 57.875 45.455 0.00 0.00 0.00 3.16
4921 4990 5.864418 ATGTAAGTTACTCCATTCGCCTA 57.136 39.130 14.00 0.00 0.00 3.93
4924 4993 5.465390 TGCATATGTAAGTTACTCCATTCGC 59.535 40.000 14.00 8.05 0.00 4.70
4927 4996 7.503566 AGCATTGCATATGTAAGTTACTCCATT 59.496 33.333 11.91 0.00 0.00 3.16
4961 5032 2.449137 ATTCAGGGCCCAGATTTCAG 57.551 50.000 27.56 2.78 0.00 3.02
4974 5045 2.095059 CCCAAGAACTCGCAAATTCAGG 60.095 50.000 0.00 0.00 0.00 3.86
4990 5061 3.009723 ACAATTCATCGTAGTGCCCAAG 58.990 45.455 0.00 0.00 0.00 3.61
5018 5089 2.362503 TCCCCGCAGATGACGTCT 60.363 61.111 17.92 1.84 37.80 4.18
5019 5090 2.105128 CTCCCCGCAGATGACGTC 59.895 66.667 9.11 9.11 0.00 4.34
5020 5091 2.680352 ACTCCCCGCAGATGACGT 60.680 61.111 0.00 0.00 0.00 4.34
5021 5092 2.021068 ATCACTCCCCGCAGATGACG 62.021 60.000 0.00 0.00 0.00 4.35
5030 5115 1.605058 AACCTCGACATCACTCCCCG 61.605 60.000 0.00 0.00 0.00 5.73
5053 5138 7.593273 CGGACATGTTTGCTAGTTTCATTAAAA 59.407 33.333 0.00 0.00 0.00 1.52
5057 5142 4.518970 ACGGACATGTTTGCTAGTTTCATT 59.481 37.500 0.00 0.00 0.00 2.57
5058 5143 4.072131 ACGGACATGTTTGCTAGTTTCAT 58.928 39.130 0.00 0.00 0.00 2.57
5059 5144 3.249799 CACGGACATGTTTGCTAGTTTCA 59.750 43.478 0.00 0.00 0.00 2.69
5060 5145 3.810373 CACGGACATGTTTGCTAGTTTC 58.190 45.455 0.00 0.00 0.00 2.78
5061 5146 2.031157 GCACGGACATGTTTGCTAGTTT 60.031 45.455 16.62 0.00 32.00 2.66
5062 5147 1.535462 GCACGGACATGTTTGCTAGTT 59.465 47.619 16.62 0.00 32.00 2.24
5064 5149 0.095245 CGCACGGACATGTTTGCTAG 59.905 55.000 19.71 7.23 32.56 3.42
5065 5150 0.601576 ACGCACGGACATGTTTGCTA 60.602 50.000 19.71 0.00 32.56 3.49
5066 5151 1.444119 AACGCACGGACATGTTTGCT 61.444 50.000 19.71 9.05 32.56 3.91
5067 5152 1.008995 AACGCACGGACATGTTTGC 60.009 52.632 14.78 14.78 0.00 3.68
5068 5153 0.028770 ACAACGCACGGACATGTTTG 59.971 50.000 0.00 0.84 0.00 2.93
5069 5154 0.306533 GACAACGCACGGACATGTTT 59.693 50.000 0.00 0.00 0.00 2.83
5070 5155 0.812014 TGACAACGCACGGACATGTT 60.812 50.000 0.00 0.00 0.00 2.71
5071 5156 0.602638 ATGACAACGCACGGACATGT 60.603 50.000 0.00 0.00 0.00 3.21
5072 5157 0.179217 CATGACAACGCACGGACATG 60.179 55.000 0.00 0.00 0.00 3.21
5073 5158 1.298157 CCATGACAACGCACGGACAT 61.298 55.000 0.00 0.00 0.00 3.06
5074 5159 1.958715 CCATGACAACGCACGGACA 60.959 57.895 0.00 0.00 0.00 4.02
5075 5160 1.225376 TTCCATGACAACGCACGGAC 61.225 55.000 0.00 0.00 0.00 4.79
5076 5161 0.948623 CTTCCATGACAACGCACGGA 60.949 55.000 0.00 0.00 0.00 4.69
5077 5162 0.948623 TCTTCCATGACAACGCACGG 60.949 55.000 0.00 0.00 0.00 4.94
5078 5163 0.865111 TTCTTCCATGACAACGCACG 59.135 50.000 0.00 0.00 0.00 5.34
5079 5164 3.347958 TTTTCTTCCATGACAACGCAC 57.652 42.857 0.00 0.00 0.00 5.34
5097 5182 9.063615 GGATACCCGTGTTGAAGATATATTTTT 57.936 33.333 0.00 0.00 0.00 1.94
5098 5183 8.215050 TGGATACCCGTGTTGAAGATATATTTT 58.785 33.333 0.00 0.00 34.29 1.82
5099 5184 7.741785 TGGATACCCGTGTTGAAGATATATTT 58.258 34.615 0.00 0.00 34.29 1.40
5100 5185 7.311092 TGGATACCCGTGTTGAAGATATATT 57.689 36.000 0.00 0.00 34.29 1.28
5101 5186 6.928348 TGGATACCCGTGTTGAAGATATAT 57.072 37.500 0.00 0.00 34.29 0.86
5102 5187 6.463331 GGTTGGATACCCGTGTTGAAGATATA 60.463 42.308 0.00 0.00 41.43 0.86
5103 5188 5.365619 GTTGGATACCCGTGTTGAAGATAT 58.634 41.667 0.00 0.00 34.29 1.63
5104 5189 4.383335 GGTTGGATACCCGTGTTGAAGATA 60.383 45.833 0.00 0.00 41.43 1.98
5105 5190 3.606687 GTTGGATACCCGTGTTGAAGAT 58.393 45.455 0.00 0.00 34.29 2.40
5106 5191 2.289819 GGTTGGATACCCGTGTTGAAGA 60.290 50.000 0.00 0.00 41.43 2.87
5107 5192 2.081462 GGTTGGATACCCGTGTTGAAG 58.919 52.381 0.00 0.00 41.43 3.02
5108 5193 2.188062 GGTTGGATACCCGTGTTGAA 57.812 50.000 0.00 0.00 41.43 2.69
5109 5194 3.940229 GGTTGGATACCCGTGTTGA 57.060 52.632 0.00 0.00 41.43 3.18
5118 5203 3.290710 AGCCACAATGATGGTTGGATAC 58.709 45.455 0.00 0.00 42.28 2.24
5119 5204 3.668141 AGCCACAATGATGGTTGGATA 57.332 42.857 0.00 0.00 42.28 2.59
5120 5205 2.537633 AGCCACAATGATGGTTGGAT 57.462 45.000 0.00 0.00 42.28 3.41
5121 5206 3.554934 GATAGCCACAATGATGGTTGGA 58.445 45.455 0.00 0.00 42.28 3.53
5122 5207 2.624838 GGATAGCCACAATGATGGTTGG 59.375 50.000 0.00 0.00 42.28 3.77
5123 5208 3.559069 AGGATAGCCACAATGATGGTTG 58.441 45.455 0.00 0.00 42.28 3.77
5124 5209 3.959495 AGGATAGCCACAATGATGGTT 57.041 42.857 0.00 0.00 42.28 3.67
5125 5210 3.959495 AAGGATAGCCACAATGATGGT 57.041 42.857 0.00 0.00 42.28 3.55
5126 5211 5.416952 GGATAAAGGATAGCCACAATGATGG 59.583 44.000 0.00 0.00 43.26 3.51
5127 5212 5.416952 GGGATAAAGGATAGCCACAATGATG 59.583 44.000 0.00 0.00 36.29 3.07
5128 5213 5.574188 GGGATAAAGGATAGCCACAATGAT 58.426 41.667 0.00 0.00 36.29 2.45
5129 5214 4.504864 CGGGATAAAGGATAGCCACAATGA 60.505 45.833 0.00 0.00 36.29 2.57
5130 5215 3.753272 CGGGATAAAGGATAGCCACAATG 59.247 47.826 0.00 0.00 36.29 2.82
5131 5216 3.244911 CCGGGATAAAGGATAGCCACAAT 60.245 47.826 0.00 0.00 36.29 2.71
5132 5217 2.105821 CCGGGATAAAGGATAGCCACAA 59.894 50.000 0.00 0.00 36.29 3.33
5133 5218 1.697432 CCGGGATAAAGGATAGCCACA 59.303 52.381 0.00 0.00 36.29 4.17
5134 5219 1.975680 TCCGGGATAAAGGATAGCCAC 59.024 52.381 0.00 0.00 36.29 5.01
5135 5220 1.975680 GTCCGGGATAAAGGATAGCCA 59.024 52.381 0.00 0.00 38.97 4.75
5136 5221 1.975680 TGTCCGGGATAAAGGATAGCC 59.024 52.381 0.00 0.00 38.97 3.93
5137 5222 3.764237 TTGTCCGGGATAAAGGATAGC 57.236 47.619 0.00 0.00 38.97 2.97
5138 5223 5.291905 AGTTTGTCCGGGATAAAGGATAG 57.708 43.478 17.90 0.00 38.97 2.08
5139 5224 5.433526 CAAGTTTGTCCGGGATAAAGGATA 58.566 41.667 17.90 0.00 38.97 2.59
5140 5225 4.270008 CAAGTTTGTCCGGGATAAAGGAT 58.730 43.478 17.90 6.07 38.97 3.24
5141 5226 3.681593 CAAGTTTGTCCGGGATAAAGGA 58.318 45.455 17.90 0.00 0.00 3.36
5142 5227 2.163613 GCAAGTTTGTCCGGGATAAAGG 59.836 50.000 17.90 12.02 0.00 3.11
5143 5228 3.081804 AGCAAGTTTGTCCGGGATAAAG 58.918 45.455 17.90 8.92 0.00 1.85
5144 5229 2.817258 CAGCAAGTTTGTCCGGGATAAA 59.183 45.455 14.13 14.13 0.00 1.40
5145 5230 2.432444 CAGCAAGTTTGTCCGGGATAA 58.568 47.619 0.00 0.00 0.00 1.75
5146 5231 1.339631 CCAGCAAGTTTGTCCGGGATA 60.340 52.381 0.00 0.00 0.00 2.59
5147 5232 0.609131 CCAGCAAGTTTGTCCGGGAT 60.609 55.000 0.00 0.00 0.00 3.85
5148 5233 1.228124 CCAGCAAGTTTGTCCGGGA 60.228 57.895 0.00 0.00 0.00 5.14
5149 5234 1.106944 AACCAGCAAGTTTGTCCGGG 61.107 55.000 0.00 0.00 0.00 5.73
5150 5235 0.030638 CAACCAGCAAGTTTGTCCGG 59.969 55.000 0.00 0.00 0.00 5.14
5151 5236 0.030638 CCAACCAGCAAGTTTGTCCG 59.969 55.000 0.00 0.00 0.00 4.79
5152 5237 1.111277 ACCAACCAGCAAGTTTGTCC 58.889 50.000 0.00 0.00 0.00 4.02
5153 5238 2.949644 AGTACCAACCAGCAAGTTTGTC 59.050 45.455 0.00 0.00 29.36 3.18
5154 5239 3.012934 AGTACCAACCAGCAAGTTTGT 57.987 42.857 0.00 2.03 31.28 2.83
5155 5240 4.385358 AAAGTACCAACCAGCAAGTTTG 57.615 40.909 0.00 0.00 0.00 2.93
5156 5241 4.382577 CCAAAAGTACCAACCAGCAAGTTT 60.383 41.667 0.00 0.00 0.00 2.66
5157 5242 3.132111 CCAAAAGTACCAACCAGCAAGTT 59.868 43.478 0.00 0.00 0.00 2.66
5158 5243 2.693074 CCAAAAGTACCAACCAGCAAGT 59.307 45.455 0.00 0.00 0.00 3.16
5159 5244 2.545742 GCCAAAAGTACCAACCAGCAAG 60.546 50.000 0.00 0.00 0.00 4.01
5160 5245 1.410882 GCCAAAAGTACCAACCAGCAA 59.589 47.619 0.00 0.00 0.00 3.91
5161 5246 1.036707 GCCAAAAGTACCAACCAGCA 58.963 50.000 0.00 0.00 0.00 4.41
5162 5247 0.317160 GGCCAAAAGTACCAACCAGC 59.683 55.000 0.00 0.00 0.00 4.85
5163 5248 1.339929 GTGGCCAAAAGTACCAACCAG 59.660 52.381 7.24 0.00 34.63 4.00
5164 5249 1.342076 TGTGGCCAAAAGTACCAACCA 60.342 47.619 7.24 0.00 34.63 3.67
5165 5250 1.404843 TGTGGCCAAAAGTACCAACC 58.595 50.000 7.24 0.00 34.63 3.77
5166 5251 2.166664 TGTTGTGGCCAAAAGTACCAAC 59.833 45.455 20.51 20.51 34.63 3.77
5167 5252 2.457598 TGTTGTGGCCAAAAGTACCAA 58.542 42.857 9.19 3.28 34.63 3.67
5168 5253 2.145397 TGTTGTGGCCAAAAGTACCA 57.855 45.000 9.19 0.00 30.94 3.25
5169 5254 3.181470 ACATTGTTGTGGCCAAAAGTACC 60.181 43.478 9.19 0.00 33.85 3.34
5170 5255 4.053469 ACATTGTTGTGGCCAAAAGTAC 57.947 40.909 9.19 0.00 33.85 2.73
5171 5256 4.645136 TGTACATTGTTGTGGCCAAAAGTA 59.355 37.500 9.19 4.94 36.53 2.24
5172 5257 3.449018 TGTACATTGTTGTGGCCAAAAGT 59.551 39.130 9.19 6.03 36.53 2.66
5173 5258 4.052159 TGTACATTGTTGTGGCCAAAAG 57.948 40.909 9.19 0.00 36.53 2.27
5174 5259 4.679373 ATGTACATTGTTGTGGCCAAAA 57.321 36.364 7.24 5.20 36.53 2.44
5175 5260 4.320567 CGTATGTACATTGTTGTGGCCAAA 60.321 41.667 14.77 0.00 36.53 3.28
5176 5261 3.189495 CGTATGTACATTGTTGTGGCCAA 59.811 43.478 14.77 0.00 36.53 4.52
5177 5262 2.744741 CGTATGTACATTGTTGTGGCCA 59.255 45.455 14.77 0.00 36.53 5.36
5178 5263 2.745281 ACGTATGTACATTGTTGTGGCC 59.255 45.455 14.77 0.00 36.53 5.36
5179 5264 3.742786 CACGTATGTACATTGTTGTGGC 58.257 45.455 14.77 0.00 36.53 5.01
5180 5265 3.187432 TGCACGTATGTACATTGTTGTGG 59.813 43.478 14.77 3.17 36.53 4.17
5181 5266 4.397064 TGCACGTATGTACATTGTTGTG 57.603 40.909 14.77 16.77 36.53 3.33
5182 5267 5.425577 TTTGCACGTATGTACATTGTTGT 57.574 34.783 14.77 5.02 39.98 3.32
5183 5268 5.285845 CCATTTGCACGTATGTACATTGTTG 59.714 40.000 14.77 9.45 0.00 3.33
5184 5269 5.182190 TCCATTTGCACGTATGTACATTGTT 59.818 36.000 14.77 0.00 0.00 2.83
5185 5270 4.697828 TCCATTTGCACGTATGTACATTGT 59.302 37.500 14.77 10.45 0.00 2.71
5186 5271 5.228579 TCCATTTGCACGTATGTACATTG 57.771 39.130 14.77 7.66 0.00 2.82
5187 5272 5.221028 CCATCCATTTGCACGTATGTACATT 60.221 40.000 14.77 0.00 0.00 2.71
5188 5273 4.275689 CCATCCATTTGCACGTATGTACAT 59.724 41.667 13.93 13.93 0.00 2.29
5189 5274 3.625313 CCATCCATTTGCACGTATGTACA 59.375 43.478 0.00 0.00 0.00 2.90
5190 5275 3.874543 TCCATCCATTTGCACGTATGTAC 59.125 43.478 0.00 0.00 0.00 2.90
5191 5276 4.143986 TCCATCCATTTGCACGTATGTA 57.856 40.909 0.00 0.00 0.00 2.29
5192 5277 2.997980 TCCATCCATTTGCACGTATGT 58.002 42.857 0.00 0.00 0.00 2.29
5193 5278 4.572985 AATCCATCCATTTGCACGTATG 57.427 40.909 0.00 0.00 0.00 2.39
5194 5279 5.360714 AGAAAATCCATCCATTTGCACGTAT 59.639 36.000 0.00 0.00 0.00 3.06
5195 5280 4.704540 AGAAAATCCATCCATTTGCACGTA 59.295 37.500 0.00 0.00 0.00 3.57
5196 5281 3.511146 AGAAAATCCATCCATTTGCACGT 59.489 39.130 0.00 0.00 0.00 4.49
5197 5282 3.861113 CAGAAAATCCATCCATTTGCACG 59.139 43.478 0.00 0.00 0.00 5.34
5198 5283 5.075858 TCAGAAAATCCATCCATTTGCAC 57.924 39.130 0.00 0.00 0.00 4.57
5199 5284 5.018149 TCTCAGAAAATCCATCCATTTGCA 58.982 37.500 0.00 0.00 0.00 4.08
5200 5285 5.451520 CCTCTCAGAAAATCCATCCATTTGC 60.452 44.000 0.00 0.00 0.00 3.68
5201 5286 5.451520 GCCTCTCAGAAAATCCATCCATTTG 60.452 44.000 0.00 0.00 0.00 2.32
5202 5287 4.648307 GCCTCTCAGAAAATCCATCCATTT 59.352 41.667 0.00 0.00 0.00 2.32
5203 5288 4.079327 AGCCTCTCAGAAAATCCATCCATT 60.079 41.667 0.00 0.00 0.00 3.16
5204 5289 3.462579 AGCCTCTCAGAAAATCCATCCAT 59.537 43.478 0.00 0.00 0.00 3.41
5205 5290 2.848694 AGCCTCTCAGAAAATCCATCCA 59.151 45.455 0.00 0.00 0.00 3.41
5206 5291 3.574354 AGCCTCTCAGAAAATCCATCC 57.426 47.619 0.00 0.00 0.00 3.51
5207 5292 6.206438 GGATAAAGCCTCTCAGAAAATCCATC 59.794 42.308 0.00 0.00 32.42 3.51
5208 5293 6.067350 GGATAAAGCCTCTCAGAAAATCCAT 58.933 40.000 0.00 0.00 32.42 3.41
5209 5294 5.192522 AGGATAAAGCCTCTCAGAAAATCCA 59.807 40.000 0.00 0.00 34.18 3.41
5210 5295 5.689835 AGGATAAAGCCTCTCAGAAAATCC 58.310 41.667 0.00 0.00 30.76 3.01
5211 5296 7.637631 AAAGGATAAAGCCTCTCAGAAAATC 57.362 36.000 0.00 0.00 37.26 2.17
5212 5297 8.427902 AAAAAGGATAAAGCCTCTCAGAAAAT 57.572 30.769 0.00 0.00 37.26 1.82
5213 5298 7.839680 AAAAAGGATAAAGCCTCTCAGAAAA 57.160 32.000 0.00 0.00 37.26 2.29


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

AutoCloner maintained by Alex Coulton.