Multiple sequence alignment - TraesCS2D01G125700

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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 TraesCS2D01G125700 chr2D 100.000 3022 0 0 1 3022 73267468 73270489 0.000000e+00 5581
1 TraesCS2D01G125700 chr2D 90.211 899 82 6 1118 2013 73288524 73289419 0.000000e+00 1168
2 TraesCS2D01G125700 chr2D 85.572 804 110 6 1213 2013 73312263 73313063 0.000000e+00 837
3 TraesCS2D01G125700 chr2A 89.400 1934 128 41 117 2037 72756051 72754182 0.000000e+00 2364
4 TraesCS2D01G125700 chr2A 87.848 1185 86 27 1117 2285 72751866 72750724 0.000000e+00 1338
5 TraesCS2D01G125700 chr2A 89.866 898 87 4 1118 2013 72741491 72740596 0.000000e+00 1151
6 TraesCS2D01G125700 chr2A 87.575 499 50 9 2284 2780 72748945 72748457 4.370000e-158 568
7 TraesCS2D01G125700 chr2A 92.446 278 5 8 1860 2124 72708827 72708553 1.700000e-102 383
8 TraesCS2D01G125700 chr2A 92.647 136 7 2 2213 2347 72708512 72708379 3.070000e-45 193
9 TraesCS2D01G125700 chr2A 99.010 101 1 0 1860 1960 72709050 72708950 6.660000e-42 182
10 TraesCS2D01G125700 chr2B 90.938 1589 88 23 493 2067 111070950 111069404 0.000000e+00 2085
11 TraesCS2D01G125700 chr2B 89.934 755 72 4 1261 2013 111060473 111059721 0.000000e+00 970
12 TraesCS2D01G125700 chr2B 82.327 447 49 14 13 442 111071722 111071289 7.960000e-96 361
13 TraesCS2D01G125700 chr2B 92.481 133 10 0 2216 2348 111069285 111069153 1.110000e-44 191
14 TraesCS2D01G125700 chr3D 88.632 519 57 2 1124 1642 51443474 51443990 5.500000e-177 630
15 TraesCS2D01G125700 chr4B 85.814 571 69 4 1187 1757 408603102 408602544 2.010000e-166 595
16 TraesCS2D01G125700 chr6D 95.960 99 1 3 365 461 310124365 310124462 1.120000e-34 158
17 TraesCS2D01G125700 chr7D 94.949 99 4 1 364 461 634667326 634667228 1.450000e-33 154
18 TraesCS2D01G125700 chr7D 95.745 94 2 2 364 457 583409523 583409432 1.880000e-32 150
19 TraesCS2D01G125700 chr7D 93.137 102 6 1 364 464 583594902 583594801 6.750000e-32 148
20 TraesCS2D01G125700 chr6A 94.000 100 4 2 364 461 146548516 146548615 1.880000e-32 150
21 TraesCS2D01G125700 chr7A 92.308 104 5 2 364 464 675119493 675119390 8.730000e-31 145
22 TraesCS2D01G125700 chr7A 87.705 122 9 5 345 460 731228997 731228876 1.460000e-28 137


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 TraesCS2D01G125700 chr2D 73267468 73270489 3021 False 5581.000000 5581 100.000000 1 3022 1 chr2D.!!$F1 3021
1 TraesCS2D01G125700 chr2D 73288524 73289419 895 False 1168.000000 1168 90.211000 1118 2013 1 chr2D.!!$F2 895
2 TraesCS2D01G125700 chr2D 73312263 73313063 800 False 837.000000 837 85.572000 1213 2013 1 chr2D.!!$F3 800
3 TraesCS2D01G125700 chr2A 72748457 72756051 7594 True 1423.333333 2364 88.274333 117 2780 3 chr2A.!!$R3 2663
4 TraesCS2D01G125700 chr2A 72740596 72741491 895 True 1151.000000 1151 89.866000 1118 2013 1 chr2A.!!$R1 895
5 TraesCS2D01G125700 chr2A 72708379 72709050 671 True 252.666667 383 94.701000 1860 2347 3 chr2A.!!$R2 487
6 TraesCS2D01G125700 chr2B 111059721 111060473 752 True 970.000000 970 89.934000 1261 2013 1 chr2B.!!$R1 752
7 TraesCS2D01G125700 chr2B 111069153 111071722 2569 True 879.000000 2085 88.582000 13 2348 3 chr2B.!!$R2 2335
8 TraesCS2D01G125700 chr3D 51443474 51443990 516 False 630.000000 630 88.632000 1124 1642 1 chr3D.!!$F1 518
9 TraesCS2D01G125700 chr4B 408602544 408603102 558 True 595.000000 595 85.814000 1187 1757 1 chr4B.!!$R1 570

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
31 32 0.025001 CAACGCGTGTGCTAGCATAC 59.975 55.0 28.93 28.93 39.65 2.39 F
824 1150 0.179089 ATCGTGAGTGATGCCAGCTC 60.179 55.0 0.00 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1378 0.029567 GTGCTACCAGATCGACTCGG 59.970 60.0 0.0 0.0 0.0 4.63 R
2375 7744 0.444260 GCCTTCTTGTTCTACTGCGC 59.556 55.0 0.0 0.0 0.0 6.09 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
23 24 4.374702 CTCTGGCAACGCGTGTGC 62.375 66.667 27.16 27.16 42.51 4.57
31 32 0.025001 CAACGCGTGTGCTAGCATAC 59.975 55.000 28.93 28.93 39.65 2.39
38 39 2.876091 GTGTGCTAGCATACGAAGTCA 58.124 47.619 25.95 12.01 43.93 3.41
58 59 2.054232 TGGGCAACTTGGTAAACGAA 57.946 45.000 0.00 0.00 0.00 3.85
62 63 4.767928 TGGGCAACTTGGTAAACGAATATT 59.232 37.500 0.00 0.00 0.00 1.28
63 64 5.106078 TGGGCAACTTGGTAAACGAATATTC 60.106 40.000 5.30 5.30 0.00 1.75
94 96 9.838339 ATCTCCAAAGTTCTTATCATTATTCGT 57.162 29.630 0.00 0.00 0.00 3.85
95 97 9.667107 TCTCCAAAGTTCTTATCATTATTCGTT 57.333 29.630 0.00 0.00 0.00 3.85
111 117 9.272901 CATTATTCGTTTAAAGATTCGCAAAGA 57.727 29.630 0.00 0.00 0.00 2.52
114 120 5.912528 TCGTTTAAAGATTCGCAAAGACTC 58.087 37.500 0.00 0.00 0.00 3.36
160 166 2.508716 ACACGACTAGGTGAGGGAGATA 59.491 50.000 6.18 0.00 40.38 1.98
173 179 1.523938 GAGATAGGTGCAACGGGGC 60.524 63.158 0.00 0.00 38.12 5.80
201 208 4.501400 CCTCGGATACTGATTGTATGCACA 60.501 45.833 0.00 0.00 46.24 4.57
223 233 4.820716 CAGAAGATGGAAGAATTGCCCTAG 59.179 45.833 0.00 0.00 34.47 3.02
234 245 0.828022 TTGCCCTAGGTACATCGGTG 59.172 55.000 8.29 0.00 0.00 4.94
237 248 1.692519 GCCCTAGGTACATCGGTGATT 59.307 52.381 0.65 0.00 0.00 2.57
238 249 2.288886 GCCCTAGGTACATCGGTGATTC 60.289 54.545 0.65 0.00 0.00 2.52
239 250 2.030185 CCCTAGGTACATCGGTGATTCG 60.030 54.545 0.65 0.00 0.00 3.34
240 251 2.607282 CCTAGGTACATCGGTGATTCGC 60.607 54.545 0.65 0.00 0.00 4.70
241 252 0.821517 AGGTACATCGGTGATTCGCA 59.178 50.000 0.65 0.00 0.00 5.10
268 284 2.205022 ACCAGAACATGTGGATGTGG 57.795 50.000 9.96 9.96 42.30 4.17
286 302 3.510360 TGTGGTAGAGTTGCTCTTAGGAC 59.490 47.826 3.87 0.00 41.50 3.85
287 303 3.510360 GTGGTAGAGTTGCTCTTAGGACA 59.490 47.826 3.87 0.00 41.50 4.02
339 362 6.832520 TGCAGGAATTCTTGTTAATTAGCA 57.167 33.333 17.78 5.32 33.01 3.49
362 385 6.927381 GCAGGTAATAGAACATTGGTACGTAT 59.073 38.462 0.00 0.00 0.00 3.06
437 460 1.146041 CGATTCTCGGAATGCCCCA 59.854 57.895 4.18 0.00 36.00 4.96
578 904 2.672996 CCGGTGCTTGGGAGTTGG 60.673 66.667 0.00 0.00 0.00 3.77
579 905 2.672996 CGGTGCTTGGGAGTTGGG 60.673 66.667 0.00 0.00 0.00 4.12
580 906 2.843545 GGTGCTTGGGAGTTGGGA 59.156 61.111 0.00 0.00 0.00 4.37
581 907 1.303643 GGTGCTTGGGAGTTGGGAG 60.304 63.158 0.00 0.00 0.00 4.30
582 908 1.973812 GTGCTTGGGAGTTGGGAGC 60.974 63.158 0.00 0.00 0.00 4.70
583 909 2.156098 TGCTTGGGAGTTGGGAGCT 61.156 57.895 0.00 0.00 34.56 4.09
584 910 1.075659 GCTTGGGAGTTGGGAGCTT 59.924 57.895 0.00 0.00 0.00 3.74
585 911 1.246737 GCTTGGGAGTTGGGAGCTTG 61.247 60.000 0.00 0.00 0.00 4.01
586 912 0.610232 CTTGGGAGTTGGGAGCTTGG 60.610 60.000 0.00 0.00 0.00 3.61
587 913 2.080336 TTGGGAGTTGGGAGCTTGGG 62.080 60.000 0.00 0.00 0.00 4.12
588 914 2.356667 GGAGTTGGGAGCTTGGGG 59.643 66.667 0.00 0.00 0.00 4.96
589 915 2.231380 GGAGTTGGGAGCTTGGGGA 61.231 63.158 0.00 0.00 0.00 4.81
590 916 1.767692 GAGTTGGGAGCTTGGGGAA 59.232 57.895 0.00 0.00 0.00 3.97
591 917 0.322906 GAGTTGGGAGCTTGGGGAAG 60.323 60.000 0.00 0.00 0.00 3.46
592 918 1.068352 AGTTGGGAGCTTGGGGAAGT 61.068 55.000 0.00 0.00 0.00 3.01
609 935 4.386951 TGGATCACGTGGCGGTGG 62.387 66.667 17.00 0.00 38.46 4.61
652 978 1.302832 CCCCTCACCTGCAACACTC 60.303 63.158 0.00 0.00 0.00 3.51
695 1021 3.240631 GCACAGAAAAGAAAACGCAACTC 59.759 43.478 0.00 0.00 0.00 3.01
709 1035 3.567478 AACTCGCGCACACGGATGA 62.567 57.895 8.75 0.00 40.57 2.92
753 1079 1.401539 GCCACGAGGTGAATTTTCTGC 60.402 52.381 0.00 0.00 35.23 4.26
758 1084 1.215382 GGTGAATTTTCTGCCGCCC 59.785 57.895 0.00 0.00 0.00 6.13
791 1117 2.202797 GCCGCTCTGCAGATCGAA 60.203 61.111 34.61 6.71 35.92 3.71
824 1150 0.179089 ATCGTGAGTGATGCCAGCTC 60.179 55.000 0.00 0.00 0.00 4.09
925 1252 3.189285 GTTAAATAACGGCCGCTCTGTA 58.811 45.455 28.58 9.87 32.95 2.74
927 1254 0.822164 AATAACGGCCGCTCTGTACT 59.178 50.000 28.58 0.00 32.95 2.73
962 1289 1.514678 GCCGAGTCACATTTGCCACA 61.515 55.000 0.00 0.00 0.00 4.17
966 1293 1.131126 GAGTCACATTTGCCACATCGG 59.869 52.381 0.00 0.00 38.11 4.18
973 1300 2.779742 TTTGCCACATCGGGGGAAGG 62.780 60.000 0.00 0.00 37.05 3.46
974 1301 3.728373 GCCACATCGGGGGAAGGT 61.728 66.667 0.00 0.00 34.06 3.50
975 1302 2.372074 GCCACATCGGGGGAAGGTA 61.372 63.158 0.00 0.00 34.06 3.08
978 1305 0.689745 CACATCGGGGGAAGGTAGGA 60.690 60.000 0.00 0.00 0.00 2.94
979 1306 0.398664 ACATCGGGGGAAGGTAGGAG 60.399 60.000 0.00 0.00 0.00 3.69
980 1307 1.459730 ATCGGGGGAAGGTAGGAGC 60.460 63.158 0.00 0.00 0.00 4.70
981 1308 1.962570 ATCGGGGGAAGGTAGGAGCT 61.963 60.000 0.00 0.00 0.00 4.09
982 1309 2.134933 CGGGGGAAGGTAGGAGCTC 61.135 68.421 4.71 4.71 0.00 4.09
983 1310 2.134933 GGGGGAAGGTAGGAGCTCG 61.135 68.421 7.83 0.00 0.00 5.03
984 1311 2.134933 GGGGAAGGTAGGAGCTCGG 61.135 68.421 7.83 0.00 0.00 4.63
1019 1346 3.567797 GTTCCGAGCGATGCAGGC 61.568 66.667 4.45 4.45 0.00 4.85
1041 1368 1.359117 GCTCAGGTACGATGCGCTA 59.641 57.895 9.73 0.00 0.00 4.26
1078 1405 4.058124 TCGATCTGGTAGCACAAATATGC 58.942 43.478 0.00 0.00 46.50 3.14
1106 1433 0.394216 AATGGTCGCTGCCTGCATTA 60.394 50.000 0.00 0.00 43.06 1.90
1152 1483 3.343788 GAGAGCCGTAGTGCTGCGT 62.344 63.158 8.68 0.00 42.95 5.24
1181 1512 2.811317 GCTGGCTTCGTCGGTCAG 60.811 66.667 0.00 0.00 0.00 3.51
1184 1515 2.338984 GGCTTCGTCGGTCAGTGT 59.661 61.111 0.00 0.00 0.00 3.55
1964 5514 2.280592 GGCCACAACCTCGTCGTT 60.281 61.111 0.00 0.00 0.00 3.85
2066 5628 7.368059 ACCGGAACAAATCTGTTTATTTCTTC 58.632 34.615 9.46 0.00 45.98 2.87
2124 5687 3.878160 TTGCCAAAGAAAACCTTCGTT 57.122 38.095 0.00 0.00 36.61 3.85
2125 5688 3.430333 TGCCAAAGAAAACCTTCGTTC 57.570 42.857 0.00 0.00 36.61 3.95
2126 5689 2.755655 TGCCAAAGAAAACCTTCGTTCA 59.244 40.909 0.00 0.00 36.61 3.18
2127 5690 3.193691 TGCCAAAGAAAACCTTCGTTCAA 59.806 39.130 0.00 0.00 36.61 2.69
2130 5693 5.120986 GCCAAAGAAAACCTTCGTTCAAAAA 59.879 36.000 0.00 0.00 36.61 1.94
2131 5694 6.530567 CCAAAGAAAACCTTCGTTCAAAAAC 58.469 36.000 0.00 0.00 36.61 2.43
2132 5695 6.367695 CCAAAGAAAACCTTCGTTCAAAAACT 59.632 34.615 0.00 0.00 36.61 2.66
2133 5696 6.944557 AAGAAAACCTTCGTTCAAAAACTG 57.055 33.333 0.00 0.00 36.61 3.16
2134 5697 6.262193 AGAAAACCTTCGTTCAAAAACTGA 57.738 33.333 0.00 0.00 36.61 3.41
2135 5698 6.683715 AGAAAACCTTCGTTCAAAAACTGAA 58.316 32.000 0.00 0.00 37.91 3.02
2136 5699 7.149307 AGAAAACCTTCGTTCAAAAACTGAAA 58.851 30.769 0.00 0.00 45.67 2.69
2140 5703 8.574196 AACCTTCGTTCAAAAACTGAAATATG 57.426 30.769 0.00 0.00 45.67 1.78
2141 5704 7.712797 ACCTTCGTTCAAAAACTGAAATATGT 58.287 30.769 0.00 0.00 45.67 2.29
2143 5706 7.326063 CCTTCGTTCAAAAACTGAAATATGTCC 59.674 37.037 0.00 0.00 45.67 4.02
2144 5707 7.265647 TCGTTCAAAAACTGAAATATGTCCA 57.734 32.000 0.00 0.00 45.67 4.02
2147 5710 7.594758 CGTTCAAAAACTGAAATATGTCCACAT 59.405 33.333 0.00 0.00 45.67 3.21
2149 5712 9.906660 TTCAAAAACTGAAATATGTCCACATAC 57.093 29.630 1.42 0.00 41.21 2.39
2154 5717 8.442632 AACTGAAATATGTCCACATACATCTG 57.557 34.615 1.42 9.22 41.15 2.90
2156 5719 8.049117 ACTGAAATATGTCCACATACATCTGTT 58.951 33.333 14.19 0.53 41.15 3.16
2159 5722 8.806429 AAATATGTCCACATACATCTGTTTCA 57.194 30.769 1.42 0.00 41.15 2.69
2160 5723 8.442632 AATATGTCCACATACATCTGTTTCAG 57.557 34.615 1.42 0.00 41.15 3.02
2161 5724 4.002982 TGTCCACATACATCTGTTTCAGC 58.997 43.478 0.00 0.00 0.00 4.26
2162 5725 3.062639 GTCCACATACATCTGTTTCAGCG 59.937 47.826 0.00 0.00 0.00 5.18
2164 5727 3.062639 CCACATACATCTGTTTCAGCGAC 59.937 47.826 0.00 0.00 0.00 5.19
2165 5728 2.923655 ACATACATCTGTTTCAGCGACG 59.076 45.455 0.00 0.00 0.00 5.12
2166 5729 3.179048 CATACATCTGTTTCAGCGACGA 58.821 45.455 0.00 0.00 0.00 4.20
2167 5730 1.419374 ACATCTGTTTCAGCGACGAC 58.581 50.000 0.00 0.00 0.00 4.34
2168 5731 1.000163 ACATCTGTTTCAGCGACGACT 60.000 47.619 0.00 0.00 0.00 4.18
2169 5732 2.228103 ACATCTGTTTCAGCGACGACTA 59.772 45.455 0.00 0.00 0.00 2.59
2170 5733 3.242518 CATCTGTTTCAGCGACGACTAA 58.757 45.455 0.00 0.00 0.00 2.24
2171 5734 3.570926 TCTGTTTCAGCGACGACTAAT 57.429 42.857 0.00 0.00 0.00 1.73
2173 5736 3.057806 TCTGTTTCAGCGACGACTAATGA 60.058 43.478 0.00 0.00 0.00 2.57
2174 5737 3.644823 TGTTTCAGCGACGACTAATGAA 58.355 40.909 0.00 0.00 0.00 2.57
2176 5739 4.640805 TTTCAGCGACGACTAATGAAAC 57.359 40.909 0.00 0.00 35.55 2.78
2177 5740 2.247637 TCAGCGACGACTAATGAAACG 58.752 47.619 0.00 0.00 0.00 3.60
2178 5741 1.320555 CAGCGACGACTAATGAAACGG 59.679 52.381 0.00 0.00 0.00 4.44
2179 5742 1.200716 AGCGACGACTAATGAAACGGA 59.799 47.619 0.00 0.00 0.00 4.69
2180 5743 1.582502 GCGACGACTAATGAAACGGAG 59.417 52.381 0.00 0.00 0.00 4.63
2181 5744 2.182825 CGACGACTAATGAAACGGAGG 58.817 52.381 0.00 0.00 0.00 4.30
2182 5745 2.537401 GACGACTAATGAAACGGAGGG 58.463 52.381 0.00 0.00 0.00 4.30
2183 5746 2.165030 GACGACTAATGAAACGGAGGGA 59.835 50.000 0.00 0.00 0.00 4.20
2184 5747 2.564062 ACGACTAATGAAACGGAGGGAA 59.436 45.455 0.00 0.00 0.00 3.97
2191 5765 7.116736 ACTAATGAAACGGAGGGAATATGTTT 58.883 34.615 0.00 0.00 35.61 2.83
2195 5769 5.637809 GAAACGGAGGGAATATGTTTCAAC 58.362 41.667 10.31 0.00 44.70 3.18
2211 5785 3.361977 ACGGGCATTGGACGTTGC 61.362 61.111 1.24 1.24 37.61 4.17
2238 5825 4.464069 TTTATTTTGCGAGGGAATTGGG 57.536 40.909 0.00 0.00 0.00 4.12
2258 5845 3.551551 GGCGTTGACTTATGAAACACAC 58.448 45.455 0.00 0.00 0.00 3.82
2286 7655 0.238289 CTCCACGCAATCAACACACC 59.762 55.000 0.00 0.00 0.00 4.16
2353 7722 8.565896 AATAAGCACATTGTCTTGTAGATGAA 57.434 30.769 10.07 0.00 0.00 2.57
2356 7725 5.180117 AGCACATTGTCTTGTAGATGAACAC 59.820 40.000 0.00 0.00 0.00 3.32
2360 7729 4.607293 TGTCTTGTAGATGAACACAGCT 57.393 40.909 0.00 0.00 34.59 4.24
2362 7731 6.286240 TGTCTTGTAGATGAACACAGCTAT 57.714 37.500 0.00 0.00 35.50 2.97
2373 7742 5.222631 TGAACACAGCTATATATCGCACAG 58.777 41.667 11.43 4.00 0.00 3.66
2375 7744 5.053140 ACACAGCTATATATCGCACAGAG 57.947 43.478 11.43 3.14 0.00 3.35
2392 7761 2.665537 CAGAGCGCAGTAGAACAAGAAG 59.334 50.000 11.47 0.00 0.00 2.85
2396 7765 0.444260 GCAGTAGAACAAGAAGGCGC 59.556 55.000 0.00 0.00 0.00 6.53
2418 7787 3.461773 CCGCACCCGTCCATCTCT 61.462 66.667 0.00 0.00 0.00 3.10
2427 7796 3.775316 ACCCGTCCATCTCTACAAAAGAT 59.225 43.478 0.00 0.00 33.74 2.40
2516 7885 4.269183 CAATCCACTTGTAGGGCATGTTA 58.731 43.478 0.00 0.00 33.82 2.41
2519 7888 4.098155 TCCACTTGTAGGGCATGTTAGTA 58.902 43.478 0.00 0.00 33.82 1.82
2537 7906 6.436218 TGTTAGTATCAAGTTAGAGCTGACCA 59.564 38.462 0.00 0.00 0.00 4.02
2548 7919 4.464069 AGAGCTGACCACTCAGATAAAC 57.536 45.455 0.00 0.00 43.41 2.01
2555 7926 2.993899 ACCACTCAGATAAACGCTTTCG 59.006 45.455 0.00 0.00 42.43 3.46
2607 7978 4.782019 AAAAAGATAGGAAATGTGCGCA 57.218 36.364 5.66 5.66 0.00 6.09
2608 7979 3.764885 AAAGATAGGAAATGTGCGCAC 57.235 42.857 33.11 33.11 0.00 5.34
2609 7980 2.401583 AGATAGGAAATGTGCGCACA 57.598 45.000 41.97 41.97 46.44 4.57
2643 8014 5.187576 GGGAAAATGGATGGAAGAAACATCA 59.812 40.000 7.60 0.00 45.01 3.07
2644 8015 6.126968 GGGAAAATGGATGGAAGAAACATCAT 60.127 38.462 7.60 0.00 45.01 2.45
2647 8018 8.782339 AAAATGGATGGAAGAAACATCATTTC 57.218 30.769 7.60 0.00 45.01 2.17
2648 8019 7.484993 AATGGATGGAAGAAACATCATTTCA 57.515 32.000 7.60 0.00 45.01 2.69
2649 8020 7.670605 ATGGATGGAAGAAACATCATTTCAT 57.329 32.000 7.60 0.01 45.01 2.57
2650 8021 7.484993 TGGATGGAAGAAACATCATTTCATT 57.515 32.000 7.60 0.00 45.01 2.57
2651 8022 7.909518 TGGATGGAAGAAACATCATTTCATTT 58.090 30.769 7.60 0.00 45.01 2.32
2652 8023 8.377034 TGGATGGAAGAAACATCATTTCATTTT 58.623 29.630 7.60 0.00 45.01 1.82
2653 8024 8.662141 GGATGGAAGAAACATCATTTCATTTTG 58.338 33.333 7.60 0.00 45.01 2.44
2654 8025 7.966246 TGGAAGAAACATCATTTCATTTTGG 57.034 32.000 2.51 0.00 0.00 3.28
2668 8039 7.979115 TTTCATTTTGGTTTCTTGTACTTCG 57.021 32.000 0.00 0.00 0.00 3.79
2670 8041 5.591067 TCATTTTGGTTTCTTGTACTTCGGT 59.409 36.000 0.00 0.00 0.00 4.69
2704 8075 1.818060 TCCACCATTTACAGCACATGC 59.182 47.619 0.00 0.00 42.49 4.06
2710 8081 3.056678 CCATTTACAGCACATGCAGGAAA 60.057 43.478 4.84 8.86 43.07 3.13
2720 8091 3.504906 CACATGCAGGAAACATCTTCAGT 59.495 43.478 4.84 0.00 0.00 3.41
2735 8106 6.217693 ACATCTTCAGTAGGGGGAAATACTTT 59.782 38.462 0.00 0.00 29.77 2.66
2747 8118 6.609616 GGGGGAAATACTTTATCCAAACATGA 59.390 38.462 0.00 0.00 34.82 3.07
2781 8152 4.801147 GCAATCGCTTCTTGTATCATGA 57.199 40.909 0.00 0.00 34.30 3.07
2782 8153 5.160699 GCAATCGCTTCTTGTATCATGAA 57.839 39.130 0.00 0.00 34.30 2.57
2783 8154 5.755813 GCAATCGCTTCTTGTATCATGAAT 58.244 37.500 0.00 0.00 34.30 2.57
2784 8155 6.204359 GCAATCGCTTCTTGTATCATGAATT 58.796 36.000 0.00 0.00 34.30 2.17
2785 8156 6.694411 GCAATCGCTTCTTGTATCATGAATTT 59.306 34.615 0.00 0.00 34.30 1.82
2786 8157 7.221452 GCAATCGCTTCTTGTATCATGAATTTT 59.779 33.333 0.00 0.00 34.30 1.82
2787 8158 9.720667 CAATCGCTTCTTGTATCATGAATTTTA 57.279 29.630 0.00 0.00 29.53 1.52
2816 8187 7.489574 TGTTCCTGAATTTAAAAATGGTTGC 57.510 32.000 0.00 0.00 0.00 4.17
2817 8188 7.050377 TGTTCCTGAATTTAAAAATGGTTGCA 58.950 30.769 0.00 0.00 0.00 4.08
2818 8189 7.554118 TGTTCCTGAATTTAAAAATGGTTGCAA 59.446 29.630 0.00 0.00 0.00 4.08
2819 8190 8.401709 GTTCCTGAATTTAAAAATGGTTGCAAA 58.598 29.630 0.00 0.00 0.00 3.68
2820 8191 8.688747 TCCTGAATTTAAAAATGGTTGCAAAT 57.311 26.923 0.00 0.00 0.00 2.32
2821 8192 9.129532 TCCTGAATTTAAAAATGGTTGCAAATT 57.870 25.926 0.00 0.00 0.00 1.82
2822 8193 9.396938 CCTGAATTTAAAAATGGTTGCAAATTC 57.603 29.630 0.00 3.49 37.73 2.17
2823 8194 9.947669 CTGAATTTAAAAATGGTTGCAAATTCA 57.052 25.926 15.50 15.50 40.73 2.57
2836 8207 9.947669 TGGTTGCAAATTCAAATAAAATTCTTG 57.052 25.926 0.00 0.00 0.00 3.02
2856 8227 9.649167 ATTCTTGAATTTTTAAAGATGGCTCTG 57.351 29.630 0.00 0.00 30.41 3.35
2857 8228 8.408043 TCTTGAATTTTTAAAGATGGCTCTGA 57.592 30.769 0.00 0.00 0.00 3.27
2858 8229 8.859090 TCTTGAATTTTTAAAGATGGCTCTGAA 58.141 29.630 0.00 0.00 0.00 3.02
2859 8230 9.649167 CTTGAATTTTTAAAGATGGCTCTGAAT 57.351 29.630 0.00 0.00 0.00 2.57
2860 8231 9.643693 TTGAATTTTTAAAGATGGCTCTGAATC 57.356 29.630 0.00 0.00 0.00 2.52
2861 8232 8.805175 TGAATTTTTAAAGATGGCTCTGAATCA 58.195 29.630 0.00 0.00 0.00 2.57
2862 8233 8.992835 AATTTTTAAAGATGGCTCTGAATCAC 57.007 30.769 0.00 0.00 0.00 3.06
2863 8234 7.523293 TTTTTAAAGATGGCTCTGAATCACA 57.477 32.000 0.00 0.00 0.00 3.58
2864 8235 7.523293 TTTTAAAGATGGCTCTGAATCACAA 57.477 32.000 0.00 0.00 0.00 3.33
2865 8236 6.748333 TTAAAGATGGCTCTGAATCACAAG 57.252 37.500 0.00 0.00 0.00 3.16
2866 8237 3.996921 AGATGGCTCTGAATCACAAGT 57.003 42.857 0.00 0.00 0.00 3.16
2867 8238 4.298103 AGATGGCTCTGAATCACAAGTT 57.702 40.909 0.00 0.00 0.00 2.66
2868 8239 4.660168 AGATGGCTCTGAATCACAAGTTT 58.340 39.130 0.00 0.00 0.00 2.66
2869 8240 4.699257 AGATGGCTCTGAATCACAAGTTTC 59.301 41.667 0.00 0.00 0.00 2.78
2870 8241 3.819368 TGGCTCTGAATCACAAGTTTCA 58.181 40.909 0.00 0.00 33.61 2.69
2871 8242 4.206375 TGGCTCTGAATCACAAGTTTCAA 58.794 39.130 0.00 0.00 34.14 2.69
2872 8243 4.644234 TGGCTCTGAATCACAAGTTTCAAA 59.356 37.500 0.00 0.00 34.14 2.69
2873 8244 5.126869 TGGCTCTGAATCACAAGTTTCAAAA 59.873 36.000 0.00 0.00 34.14 2.44
2874 8245 5.689068 GGCTCTGAATCACAAGTTTCAAAAG 59.311 40.000 0.00 0.00 34.14 2.27
2875 8246 5.174579 GCTCTGAATCACAAGTTTCAAAAGC 59.825 40.000 0.00 0.00 36.38 3.51
2876 8247 5.591099 TCTGAATCACAAGTTTCAAAAGCC 58.409 37.500 0.00 0.00 34.14 4.35
2877 8248 4.692228 TGAATCACAAGTTTCAAAAGCCC 58.308 39.130 0.00 0.00 32.15 5.19
2878 8249 4.405358 TGAATCACAAGTTTCAAAAGCCCT 59.595 37.500 0.00 0.00 32.15 5.19
2879 8250 5.104982 TGAATCACAAGTTTCAAAAGCCCTT 60.105 36.000 0.00 0.00 32.15 3.95
2880 8251 4.385358 TCACAAGTTTCAAAAGCCCTTC 57.615 40.909 0.00 0.00 0.00 3.46
2881 8252 3.766591 TCACAAGTTTCAAAAGCCCTTCA 59.233 39.130 0.00 0.00 0.00 3.02
2882 8253 4.405358 TCACAAGTTTCAAAAGCCCTTCAT 59.595 37.500 0.00 0.00 0.00 2.57
2883 8254 4.508861 CACAAGTTTCAAAAGCCCTTCATG 59.491 41.667 0.00 0.00 0.00 3.07
2884 8255 4.405358 ACAAGTTTCAAAAGCCCTTCATGA 59.595 37.500 0.00 0.00 0.00 3.07
2885 8256 5.104982 ACAAGTTTCAAAAGCCCTTCATGAA 60.105 36.000 8.12 8.12 31.12 2.57
2886 8257 5.813513 AGTTTCAAAAGCCCTTCATGAAT 57.186 34.783 8.96 0.00 32.30 2.57
2887 8258 6.178607 AGTTTCAAAAGCCCTTCATGAATT 57.821 33.333 8.96 0.00 32.30 2.17
2888 8259 6.594744 AGTTTCAAAAGCCCTTCATGAATTT 58.405 32.000 8.96 3.77 32.30 1.82
2889 8260 7.056006 AGTTTCAAAAGCCCTTCATGAATTTT 58.944 30.769 8.96 9.82 32.30 1.82
2890 8261 7.557358 AGTTTCAAAAGCCCTTCATGAATTTTT 59.443 29.630 8.96 10.50 32.30 1.94
2891 8262 8.835439 GTTTCAAAAGCCCTTCATGAATTTTTA 58.165 29.630 8.96 2.11 32.30 1.52
2892 8263 8.606040 TTCAAAAGCCCTTCATGAATTTTTAG 57.394 30.769 8.96 2.97 0.00 1.85
2893 8264 7.961351 TCAAAAGCCCTTCATGAATTTTTAGA 58.039 30.769 8.96 5.08 0.00 2.10
2894 8265 8.428063 TCAAAAGCCCTTCATGAATTTTTAGAA 58.572 29.630 8.96 2.12 0.00 2.10
2895 8266 9.223099 CAAAAGCCCTTCATGAATTTTTAGAAT 57.777 29.630 8.96 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320421 ACGCGTTGCCAGAGTACATT 60.320 50.000 5.58 0.00 0.00 2.71
2 3 1.663388 CACGCGTTGCCAGAGTACA 60.663 57.895 10.22 0.00 0.00 2.90
3 4 1.663702 ACACGCGTTGCCAGAGTAC 60.664 57.895 10.22 0.00 0.00 2.73
4 5 1.663388 CACACGCGTTGCCAGAGTA 60.663 57.895 10.22 0.00 0.00 2.59
6 7 4.374702 GCACACGCGTTGCCAGAG 62.375 66.667 25.74 11.14 0.00 3.35
7 8 3.507597 TAGCACACGCGTTGCCAGA 62.508 57.895 29.57 18.88 45.49 3.86
8 9 3.015293 CTAGCACACGCGTTGCCAG 62.015 63.158 29.57 24.82 45.49 4.85
9 10 3.041351 CTAGCACACGCGTTGCCA 61.041 61.111 29.57 21.26 45.49 4.92
11 12 1.692148 TATGCTAGCACACGCGTTGC 61.692 55.000 27.55 27.55 45.49 4.17
15 16 1.137459 TTCGTATGCTAGCACACGCG 61.137 55.000 36.87 27.19 45.17 6.01
23 24 2.224042 TGCCCATGACTTCGTATGCTAG 60.224 50.000 0.00 0.00 0.00 3.42
31 32 0.523072 CCAAGTTGCCCATGACTTCG 59.477 55.000 0.00 0.00 34.04 3.79
38 39 2.279935 TCGTTTACCAAGTTGCCCAT 57.720 45.000 0.00 0.00 0.00 4.00
62 63 7.724490 TGATAAGAACTTTGGAGATGAGAGA 57.276 36.000 0.00 0.00 0.00 3.10
63 64 8.961294 AATGATAAGAACTTTGGAGATGAGAG 57.039 34.615 0.00 0.00 0.00 3.20
89 91 6.899114 AGTCTTTGCGAATCTTTAAACGAAT 58.101 32.000 0.00 0.00 0.00 3.34
94 96 5.313712 AGGGAGTCTTTGCGAATCTTTAAA 58.686 37.500 0.00 0.00 36.95 1.52
95 97 4.906618 AGGGAGTCTTTGCGAATCTTTAA 58.093 39.130 0.00 0.00 36.95 1.52
100 102 4.116238 CTCTTAGGGAGTCTTTGCGAATC 58.884 47.826 0.00 0.00 37.30 2.52
101 103 3.680196 GCTCTTAGGGAGTCTTTGCGAAT 60.680 47.826 0.00 0.00 43.62 3.34
111 117 1.561542 CATTGGGTGCTCTTAGGGAGT 59.438 52.381 0.00 0.00 43.62 3.85
136 142 3.053842 TCTCCCTCACCTAGTCGTGTAAT 60.054 47.826 0.00 0.00 35.18 1.89
173 179 2.100916 ACAATCAGTATCCGAGGGAACG 59.899 50.000 0.00 0.00 34.34 3.95
201 208 4.141298 CCTAGGGCAATTCTTCCATCTTCT 60.141 45.833 0.00 0.00 0.00 2.85
223 233 1.526887 CATGCGAATCACCGATGTACC 59.473 52.381 0.00 0.00 0.00 3.34
234 245 2.564771 TCTGGTTGGATCATGCGAATC 58.435 47.619 0.00 0.00 0.00 2.52
237 248 1.003003 TGTTCTGGTTGGATCATGCGA 59.997 47.619 0.00 0.00 0.00 5.10
238 249 1.452110 TGTTCTGGTTGGATCATGCG 58.548 50.000 0.00 0.00 0.00 4.73
239 250 2.756760 ACATGTTCTGGTTGGATCATGC 59.243 45.455 12.53 0.00 42.49 4.06
240 251 3.129813 CCACATGTTCTGGTTGGATCATG 59.870 47.826 0.00 11.55 43.46 3.07
241 252 3.010472 TCCACATGTTCTGGTTGGATCAT 59.990 43.478 0.00 0.00 0.00 2.45
268 284 4.459685 TGTCTGTCCTAAGAGCAACTCTAC 59.540 45.833 0.00 0.00 40.28 2.59
307 328 3.967332 AGAATTCCTGCAAAACATGGG 57.033 42.857 0.65 0.00 0.00 4.00
349 372 4.699925 ATGCCCTTATACGTACCAATGT 57.300 40.909 0.00 0.00 0.00 2.71
354 377 3.811497 GACCAAATGCCCTTATACGTACC 59.189 47.826 0.00 0.00 0.00 3.34
362 385 2.916934 ACCACTAGACCAAATGCCCTTA 59.083 45.455 0.00 0.00 0.00 2.69
559 870 4.660938 AACTCCCAAGCACCGGGC 62.661 66.667 6.32 6.61 44.11 6.13
574 900 0.895559 CACTTCCCCAAGCTCCCAAC 60.896 60.000 0.00 0.00 32.09 3.77
575 901 1.460255 CACTTCCCCAAGCTCCCAA 59.540 57.895 0.00 0.00 32.09 4.12
578 904 0.106967 GATCCACTTCCCCAAGCTCC 60.107 60.000 0.00 0.00 32.09 4.70
579 905 0.620556 TGATCCACTTCCCCAAGCTC 59.379 55.000 0.00 0.00 32.09 4.09
580 906 0.329596 GTGATCCACTTCCCCAAGCT 59.670 55.000 0.00 0.00 32.09 3.74
581 907 1.026718 CGTGATCCACTTCCCCAAGC 61.027 60.000 0.00 0.00 32.09 4.01
582 908 0.324943 ACGTGATCCACTTCCCCAAG 59.675 55.000 0.00 0.00 35.50 3.61
583 909 0.036164 CACGTGATCCACTTCCCCAA 59.964 55.000 10.90 0.00 31.34 4.12
584 910 1.676968 CACGTGATCCACTTCCCCA 59.323 57.895 10.90 0.00 31.34 4.96
585 911 1.078426 CCACGTGATCCACTTCCCC 60.078 63.158 19.30 0.00 31.34 4.81
586 912 1.745489 GCCACGTGATCCACTTCCC 60.745 63.158 19.30 0.00 31.34 3.97
587 913 2.100631 CGCCACGTGATCCACTTCC 61.101 63.158 19.30 0.00 31.34 3.46
588 914 2.100631 CCGCCACGTGATCCACTTC 61.101 63.158 19.30 0.00 31.34 3.01
589 915 2.047274 CCGCCACGTGATCCACTT 60.047 61.111 19.30 0.00 31.34 3.16
590 916 3.311110 ACCGCCACGTGATCCACT 61.311 61.111 19.30 0.00 31.34 4.00
591 917 3.118454 CACCGCCACGTGATCCAC 61.118 66.667 19.30 0.00 35.68 4.02
592 918 4.386951 CCACCGCCACGTGATCCA 62.387 66.667 19.30 0.00 35.68 3.41
674 1000 3.478516 CGAGTTGCGTTTTCTTTTCTGTG 59.521 43.478 0.00 0.00 34.64 3.66
676 1002 2.464016 GCGAGTTGCGTTTTCTTTTCTG 59.536 45.455 0.00 0.00 43.41 3.02
703 1029 0.107993 ATGTGTCCACAGCTCATCCG 60.108 55.000 6.27 0.00 45.48 4.18
709 1035 1.962822 CGTGCATGTGTCCACAGCT 60.963 57.895 16.88 0.00 45.48 4.24
736 1062 1.156736 CGGCAGAAAATTCACCTCGT 58.843 50.000 0.00 0.00 0.00 4.18
824 1150 1.563435 CTGTGAGCTGTGACTTGGCG 61.563 60.000 0.00 0.00 0.00 5.69
962 1289 1.459730 GCTCCTACCTTCCCCCGAT 60.460 63.158 0.00 0.00 0.00 4.18
966 1293 2.134933 CCGAGCTCCTACCTTCCCC 61.135 68.421 8.47 0.00 0.00 4.81
973 1300 3.597728 CTCCCGCCGAGCTCCTAC 61.598 72.222 8.47 0.00 0.00 3.18
974 1301 3.805497 TCTCCCGCCGAGCTCCTA 61.805 66.667 8.47 0.00 38.62 2.94
983 1310 3.036429 ATCTTGCTGGTCTCCCGCC 62.036 63.158 0.25 0.00 31.78 6.13
984 1311 1.817099 CATCTTGCTGGTCTCCCGC 60.817 63.158 0.00 0.00 0.00 6.13
988 1315 1.066858 TCGGAACATCTTGCTGGTCTC 60.067 52.381 0.00 0.00 33.21 3.36
1019 1346 1.878522 GCATCGTACCTGAGCACGG 60.879 63.158 5.25 0.00 38.66 4.94
1023 1350 0.935366 GTAGCGCATCGTACCTGAGC 60.935 60.000 11.47 9.80 39.38 4.26
1047 1374 1.434622 TACCAGATCGACTCGGCGTC 61.435 60.000 6.85 0.00 39.33 5.19
1051 1378 0.029567 GTGCTACCAGATCGACTCGG 59.970 60.000 0.00 0.00 0.00 4.63
1078 1405 1.645034 CAGCGACCATTACCACAGAG 58.355 55.000 0.00 0.00 0.00 3.35
1106 1433 2.094906 GCAACACACACAGCATGATCAT 60.095 45.455 1.18 1.18 39.69 2.45
1200 1531 2.673523 CAACCTCTGGGAGCTGGG 59.326 66.667 0.00 0.00 36.25 4.45
1202 1533 2.045536 GCCAACCTCTGGGAGCTG 60.046 66.667 0.00 0.00 46.54 4.24
2013 5563 1.537202 GATTGTGTCCCTTCACTGTGC 59.463 52.381 2.12 0.00 38.90 4.57
2014 5564 2.810274 CTGATTGTGTCCCTTCACTGTG 59.190 50.000 0.17 0.17 38.90 3.66
2015 5565 2.705658 TCTGATTGTGTCCCTTCACTGT 59.294 45.455 0.00 0.00 38.90 3.55
2072 5635 5.461032 AATAAACAGATTTCACCCGCAAA 57.539 34.783 0.00 0.00 0.00 3.68
2124 5687 9.072375 TGTATGTGGACATATTTCAGTTTTTGA 57.928 29.630 2.88 0.00 40.53 2.69
2125 5688 9.859427 ATGTATGTGGACATATTTCAGTTTTTG 57.141 29.630 2.88 0.00 40.53 2.44
2127 5690 9.466497 AGATGTATGTGGACATATTTCAGTTTT 57.534 29.630 2.88 0.00 40.18 2.43
2130 5693 7.568349 ACAGATGTATGTGGACATATTTCAGT 58.432 34.615 2.88 4.26 40.18 3.41
2131 5694 8.442632 AACAGATGTATGTGGACATATTTCAG 57.557 34.615 2.88 3.76 40.18 3.02
2132 5695 8.806429 AAACAGATGTATGTGGACATATTTCA 57.194 30.769 2.88 0.00 40.18 2.69
2133 5696 8.892723 TGAAACAGATGTATGTGGACATATTTC 58.107 33.333 2.88 8.04 40.18 2.17
2134 5697 8.806429 TGAAACAGATGTATGTGGACATATTT 57.194 30.769 2.88 0.00 40.18 1.40
2135 5698 7.012704 GCTGAAACAGATGTATGTGGACATATT 59.987 37.037 2.88 0.00 40.18 1.28
2136 5699 6.484643 GCTGAAACAGATGTATGTGGACATAT 59.515 38.462 2.88 0.00 40.18 1.78
2140 5703 3.062639 CGCTGAAACAGATGTATGTGGAC 59.937 47.826 2.81 0.00 32.44 4.02
2141 5704 3.056179 TCGCTGAAACAGATGTATGTGGA 60.056 43.478 2.81 0.00 32.44 4.02
2143 5706 3.241773 CGTCGCTGAAACAGATGTATGTG 60.242 47.826 2.81 0.00 32.44 3.21
2144 5707 2.923655 CGTCGCTGAAACAGATGTATGT 59.076 45.455 2.81 0.00 32.44 2.29
2147 5710 2.228103 AGTCGTCGCTGAAACAGATGTA 59.772 45.455 2.81 0.00 32.44 2.29
2149 5712 1.702886 AGTCGTCGCTGAAACAGATG 58.297 50.000 2.81 0.00 32.44 2.90
2152 5715 3.242518 TCATTAGTCGTCGCTGAAACAG 58.757 45.455 0.00 0.00 34.12 3.16
2154 5717 4.383679 GTTTCATTAGTCGTCGCTGAAAC 58.616 43.478 15.54 15.54 44.61 2.78
2156 5719 2.659757 CGTTTCATTAGTCGTCGCTGAA 59.340 45.455 0.00 0.00 0.00 3.02
2159 5722 1.200716 TCCGTTTCATTAGTCGTCGCT 59.799 47.619 0.00 0.00 0.00 4.93
2160 5723 1.582502 CTCCGTTTCATTAGTCGTCGC 59.417 52.381 0.00 0.00 0.00 5.19
2161 5724 2.182825 CCTCCGTTTCATTAGTCGTCG 58.817 52.381 0.00 0.00 0.00 5.12
2162 5725 2.165030 TCCCTCCGTTTCATTAGTCGTC 59.835 50.000 0.00 0.00 0.00 4.20
2164 5727 2.953466 TCCCTCCGTTTCATTAGTCG 57.047 50.000 0.00 0.00 0.00 4.18
2165 5728 6.289064 ACATATTCCCTCCGTTTCATTAGTC 58.711 40.000 0.00 0.00 0.00 2.59
2166 5729 6.248569 ACATATTCCCTCCGTTTCATTAGT 57.751 37.500 0.00 0.00 0.00 2.24
2167 5730 7.282224 TGAAACATATTCCCTCCGTTTCATTAG 59.718 37.037 10.92 0.00 46.22 1.73
2168 5731 7.113437 TGAAACATATTCCCTCCGTTTCATTA 58.887 34.615 10.92 0.00 46.22 1.90
2169 5732 5.949354 TGAAACATATTCCCTCCGTTTCATT 59.051 36.000 10.92 0.00 46.22 2.57
2170 5733 5.505780 TGAAACATATTCCCTCCGTTTCAT 58.494 37.500 10.92 0.00 46.22 2.57
2173 5736 4.155280 CGTTGAAACATATTCCCTCCGTTT 59.845 41.667 0.00 0.00 32.72 3.60
2174 5737 3.687698 CGTTGAAACATATTCCCTCCGTT 59.312 43.478 0.00 0.00 0.00 4.44
2176 5739 2.612212 CCGTTGAAACATATTCCCTCCG 59.388 50.000 0.00 0.00 0.00 4.63
2177 5740 2.949644 CCCGTTGAAACATATTCCCTCC 59.050 50.000 0.00 0.00 0.00 4.30
2178 5741 2.357952 GCCCGTTGAAACATATTCCCTC 59.642 50.000 0.00 0.00 0.00 4.30
2179 5742 2.291282 TGCCCGTTGAAACATATTCCCT 60.291 45.455 0.00 0.00 0.00 4.20
2180 5743 2.096248 TGCCCGTTGAAACATATTCCC 58.904 47.619 0.00 0.00 0.00 3.97
2181 5744 4.111916 CAATGCCCGTTGAAACATATTCC 58.888 43.478 0.00 0.00 0.00 3.01
2182 5745 4.111916 CCAATGCCCGTTGAAACATATTC 58.888 43.478 1.92 0.00 0.00 1.75
2183 5746 3.766591 TCCAATGCCCGTTGAAACATATT 59.233 39.130 1.92 0.00 0.00 1.28
2184 5747 3.130340 GTCCAATGCCCGTTGAAACATAT 59.870 43.478 1.92 0.00 0.00 1.78
2191 5765 1.228003 AACGTCCAATGCCCGTTGA 60.228 52.632 7.23 0.00 42.59 3.18
2238 5825 3.551551 GGTGTGTTTCATAAGTCAACGC 58.448 45.455 0.00 0.00 0.00 4.84
2273 5860 1.112315 TGGTGGGGTGTGTTGATTGC 61.112 55.000 0.00 0.00 0.00 3.56
2286 7655 3.244561 ACATCTCTAAACACTGTGGTGGG 60.245 47.826 13.09 2.47 46.85 4.61
2353 7722 4.617067 GCTCTGTGCGATATATAGCTGTGT 60.617 45.833 17.25 0.00 0.00 3.72
2373 7742 1.996191 CCTTCTTGTTCTACTGCGCTC 59.004 52.381 9.73 0.00 0.00 5.03
2375 7744 0.444260 GCCTTCTTGTTCTACTGCGC 59.556 55.000 0.00 0.00 0.00 6.09
2377 7746 0.444260 GCGCCTTCTTGTTCTACTGC 59.556 55.000 0.00 0.00 0.00 4.40
2380 7749 1.136336 CAACGCGCCTTCTTGTTCTAC 60.136 52.381 5.73 0.00 0.00 2.59
2403 7772 0.535335 TTGTAGAGATGGACGGGTGC 59.465 55.000 0.00 0.00 0.00 5.01
2490 7859 2.102578 GCCCTACAAGTGGATTGCAAT 58.897 47.619 12.83 12.83 43.15 3.56
2496 7865 3.523564 ACTAACATGCCCTACAAGTGGAT 59.476 43.478 0.00 0.00 28.80 3.41
2516 7885 5.020132 AGTGGTCAGCTCTAACTTGATACT 58.980 41.667 0.00 0.00 0.00 2.12
2519 7888 3.834813 TGAGTGGTCAGCTCTAACTTGAT 59.165 43.478 0.00 0.00 34.30 2.57
2588 7959 3.081061 TGTGCGCACATTTCCTATCTTT 58.919 40.909 37.86 0.00 36.21 2.52
2591 7962 3.485947 TTTGTGCGCACATTTCCTATC 57.514 42.857 40.78 12.26 41.52 2.08
2594 7965 2.593346 TTTTTGTGCGCACATTTCCT 57.407 40.000 40.78 0.00 41.52 3.36
2616 7987 5.187576 TGTTTCTTCCATCCATTTTCCCATC 59.812 40.000 0.00 0.00 0.00 3.51
2630 8001 7.507829 ACCAAAATGAAATGATGTTTCTTCCA 58.492 30.769 2.67 0.00 0.00 3.53
2631 8002 7.967890 ACCAAAATGAAATGATGTTTCTTCC 57.032 32.000 2.67 0.00 0.00 3.46
2643 8014 7.651704 CCGAAGTACAAGAAACCAAAATGAAAT 59.348 33.333 0.00 0.00 0.00 2.17
2644 8015 6.975772 CCGAAGTACAAGAAACCAAAATGAAA 59.024 34.615 0.00 0.00 0.00 2.69
2647 8018 5.827666 ACCGAAGTACAAGAAACCAAAATG 58.172 37.500 0.00 0.00 0.00 2.32
2648 8019 6.459670 AACCGAAGTACAAGAAACCAAAAT 57.540 33.333 0.00 0.00 0.00 1.82
2649 8020 5.900865 AACCGAAGTACAAGAAACCAAAA 57.099 34.783 0.00 0.00 0.00 2.44
2650 8021 5.415077 TCAAACCGAAGTACAAGAAACCAAA 59.585 36.000 0.00 0.00 0.00 3.28
2651 8022 4.942483 TCAAACCGAAGTACAAGAAACCAA 59.058 37.500 0.00 0.00 0.00 3.67
2652 8023 4.515361 TCAAACCGAAGTACAAGAAACCA 58.485 39.130 0.00 0.00 0.00 3.67
2653 8024 5.684550 ATCAAACCGAAGTACAAGAAACC 57.315 39.130 0.00 0.00 0.00 3.27
2654 8025 6.788930 CGTTATCAAACCGAAGTACAAGAAAC 59.211 38.462 0.00 0.00 31.46 2.78
2668 8039 3.816523 TGGTGGACTTTCGTTATCAAACC 59.183 43.478 0.00 0.00 31.46 3.27
2670 8041 6.642707 AAATGGTGGACTTTCGTTATCAAA 57.357 33.333 0.00 0.00 0.00 2.69
2687 8058 1.820519 CCTGCATGTGCTGTAAATGGT 59.179 47.619 6.55 0.00 42.66 3.55
2693 8064 2.268762 TGTTTCCTGCATGTGCTGTA 57.731 45.000 6.55 0.00 42.66 2.74
2694 8065 1.542915 GATGTTTCCTGCATGTGCTGT 59.457 47.619 6.55 0.00 42.66 4.40
2704 8075 3.370953 CCCCCTACTGAAGATGTTTCCTG 60.371 52.174 0.00 0.00 0.00 3.86
2710 8081 5.289510 AGTATTTCCCCCTACTGAAGATGT 58.710 41.667 0.00 0.00 0.00 3.06
2720 8091 7.286667 TGTTTGGATAAAGTATTTCCCCCTA 57.713 36.000 0.00 0.00 40.09 3.53
2735 8106 8.196771 GCTCCACAAATTATTCATGTTTGGATA 58.803 33.333 9.68 0.00 37.20 2.59
2760 8131 4.801147 TCATGATACAAGAAGCGATTGC 57.199 40.909 0.00 0.00 43.24 3.56
2790 8161 8.567104 GCAACCATTTTTAAATTCAGGAACATT 58.433 29.630 0.00 0.00 0.00 2.71
2791 8162 7.718753 TGCAACCATTTTTAAATTCAGGAACAT 59.281 29.630 0.00 0.00 0.00 2.71
2792 8163 7.050377 TGCAACCATTTTTAAATTCAGGAACA 58.950 30.769 0.00 0.00 0.00 3.18
2793 8164 7.489574 TGCAACCATTTTTAAATTCAGGAAC 57.510 32.000 0.00 0.00 0.00 3.62
2794 8165 8.511604 TTTGCAACCATTTTTAAATTCAGGAA 57.488 26.923 0.00 0.00 0.00 3.36
2795 8166 8.688747 ATTTGCAACCATTTTTAAATTCAGGA 57.311 26.923 0.00 0.00 0.00 3.86
2796 8167 9.396938 GAATTTGCAACCATTTTTAAATTCAGG 57.603 29.630 0.00 0.00 41.02 3.86
2797 8168 9.947669 TGAATTTGCAACCATTTTTAAATTCAG 57.052 25.926 15.06 0.00 43.66 3.02
2810 8181 9.947669 CAAGAATTTTATTTGAATTTGCAACCA 57.052 25.926 0.00 0.00 0.00 3.67
2830 8201 9.649167 CAGAGCCATCTTTAAAAATTCAAGAAT 57.351 29.630 0.00 0.00 31.64 2.40
2831 8202 8.859090 TCAGAGCCATCTTTAAAAATTCAAGAA 58.141 29.630 0.00 0.00 31.64 2.52
2832 8203 8.408043 TCAGAGCCATCTTTAAAAATTCAAGA 57.592 30.769 0.00 0.00 31.64 3.02
2833 8204 9.649167 ATTCAGAGCCATCTTTAAAAATTCAAG 57.351 29.630 0.00 0.00 31.64 3.02
2834 8205 9.643693 GATTCAGAGCCATCTTTAAAAATTCAA 57.356 29.630 0.00 0.00 31.64 2.69
2835 8206 8.805175 TGATTCAGAGCCATCTTTAAAAATTCA 58.195 29.630 0.00 0.00 31.64 2.57
2836 8207 9.080915 GTGATTCAGAGCCATCTTTAAAAATTC 57.919 33.333 0.00 0.00 31.64 2.17
2837 8208 8.587608 TGTGATTCAGAGCCATCTTTAAAAATT 58.412 29.630 0.00 0.00 31.64 1.82
2838 8209 8.125978 TGTGATTCAGAGCCATCTTTAAAAAT 57.874 30.769 0.00 0.00 31.64 1.82
2839 8210 7.523293 TGTGATTCAGAGCCATCTTTAAAAA 57.477 32.000 0.00 0.00 31.64 1.94
2840 8211 7.231317 ACTTGTGATTCAGAGCCATCTTTAAAA 59.769 33.333 0.00 0.00 31.64 1.52
2841 8212 6.716628 ACTTGTGATTCAGAGCCATCTTTAAA 59.283 34.615 0.00 0.00 31.64 1.52
2842 8213 6.240894 ACTTGTGATTCAGAGCCATCTTTAA 58.759 36.000 0.00 0.00 31.64 1.52
2843 8214 5.809001 ACTTGTGATTCAGAGCCATCTTTA 58.191 37.500 0.00 0.00 31.64 1.85
2844 8215 4.660168 ACTTGTGATTCAGAGCCATCTTT 58.340 39.130 0.00 0.00 31.64 2.52
2845 8216 4.298103 ACTTGTGATTCAGAGCCATCTT 57.702 40.909 0.00 0.00 31.64 2.40
2846 8217 3.996921 ACTTGTGATTCAGAGCCATCT 57.003 42.857 0.00 0.00 35.63 2.90
2847 8218 4.456911 TGAAACTTGTGATTCAGAGCCATC 59.543 41.667 0.00 0.00 31.46 3.51
2848 8219 4.401022 TGAAACTTGTGATTCAGAGCCAT 58.599 39.130 0.00 0.00 31.46 4.40
2849 8220 3.819368 TGAAACTTGTGATTCAGAGCCA 58.181 40.909 0.00 0.00 31.46 4.75
2850 8221 4.836125 TTGAAACTTGTGATTCAGAGCC 57.164 40.909 0.00 0.00 36.56 4.70
2851 8222 5.174579 GCTTTTGAAACTTGTGATTCAGAGC 59.825 40.000 0.00 0.00 38.00 4.09
2852 8223 5.689068 GGCTTTTGAAACTTGTGATTCAGAG 59.311 40.000 0.00 0.00 36.56 3.35
2853 8224 5.451798 GGGCTTTTGAAACTTGTGATTCAGA 60.452 40.000 0.00 0.00 36.56 3.27
2854 8225 4.746611 GGGCTTTTGAAACTTGTGATTCAG 59.253 41.667 0.00 0.00 36.56 3.02
2855 8226 4.405358 AGGGCTTTTGAAACTTGTGATTCA 59.595 37.500 0.00 0.00 33.99 2.57
2856 8227 4.948847 AGGGCTTTTGAAACTTGTGATTC 58.051 39.130 0.00 0.00 0.00 2.52
2857 8228 5.104982 TGAAGGGCTTTTGAAACTTGTGATT 60.105 36.000 0.00 0.00 0.00 2.57
2858 8229 4.405358 TGAAGGGCTTTTGAAACTTGTGAT 59.595 37.500 0.00 0.00 0.00 3.06
2859 8230 3.766591 TGAAGGGCTTTTGAAACTTGTGA 59.233 39.130 0.00 0.00 0.00 3.58
2860 8231 4.122143 TGAAGGGCTTTTGAAACTTGTG 57.878 40.909 0.00 0.00 0.00 3.33
2861 8232 4.405358 TCATGAAGGGCTTTTGAAACTTGT 59.595 37.500 0.00 0.00 0.00 3.16
2862 8233 4.947645 TCATGAAGGGCTTTTGAAACTTG 58.052 39.130 0.00 0.00 0.00 3.16
2863 8234 5.612725 TTCATGAAGGGCTTTTGAAACTT 57.387 34.783 3.38 0.00 0.00 2.66
2864 8235 5.813513 ATTCATGAAGGGCTTTTGAAACT 57.186 34.783 14.54 0.00 32.60 2.66
2865 8236 6.866010 AAATTCATGAAGGGCTTTTGAAAC 57.134 33.333 14.54 0.00 32.60 2.78
2866 8237 7.878547 AAAAATTCATGAAGGGCTTTTGAAA 57.121 28.000 14.54 0.00 32.60 2.69
2867 8238 8.428063 TCTAAAAATTCATGAAGGGCTTTTGAA 58.572 29.630 14.54 7.06 33.04 2.69
2868 8239 7.961351 TCTAAAAATTCATGAAGGGCTTTTGA 58.039 30.769 14.54 12.28 0.00 2.69
2869 8240 8.606040 TTCTAAAAATTCATGAAGGGCTTTTG 57.394 30.769 14.54 10.53 0.00 2.44


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

AutoCloner maintained by Alex Coulton.