Multiple sequence alignment - TraesCS4B01G184600

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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 TraesCS4B01G184600 chr4B 100.000 3344 0 0 1 3344 404122798 404126141 0.000000e+00 6176.0
1 TraesCS4B01G184600 chr4D 95.316 2455 73 10 248 2701 323602296 323604709 0.000000e+00 3858.0
2 TraesCS4B01G184600 chr4D 96.133 543 17 1 2802 3344 323604756 323605294 0.000000e+00 883.0
3 TraesCS4B01G184600 chr4D 79.642 1061 174 26 1283 2331 323583319 323582289 0.000000e+00 725.0
4 TraesCS4B01G184600 chr4D 94.253 87 4 1 167 252 323600908 323600994 7.530000e-27 132.0
5 TraesCS4B01G184600 chr4A 93.756 2146 89 13 575 2701 147654226 147652107 0.000000e+00 3179.0
6 TraesCS4B01G184600 chr4A 94.555 551 22 1 2802 3344 147652062 147651512 0.000000e+00 845.0
7 TraesCS4B01G184600 chr4A 79.868 1063 168 31 1283 2331 148126606 148127636 0.000000e+00 736.0
8 TraesCS4B01G184600 chr7D 90.252 1272 100 10 1070 2335 560892445 560893698 0.000000e+00 1640.0
9 TraesCS4B01G184600 chr7D 90.051 975 79 3 1364 2338 560982799 560983755 0.000000e+00 1247.0
10 TraesCS4B01G184600 chr7A 89.494 1304 110 13 1052 2340 645038604 645039895 0.000000e+00 1624.0
11 TraesCS4B01G184600 chr7B 89.122 1287 114 17 1064 2337 608876482 608875209 0.000000e+00 1578.0
12 TraesCS4B01G184600 chr2B 77.821 257 39 11 1251 1505 773784332 773784572 3.480000e-30 143.0
13 TraesCS4B01G184600 chr1B 76.515 264 34 16 1251 1512 626036439 626036202 5.860000e-23 119.0
14 TraesCS4B01G184600 chr1A 75.875 257 36 14 1251 1505 474246680 474246912 1.270000e-19 108.0
15 TraesCS4B01G184600 chr6D 84.375 64 10 0 2162 2225 376942295 376942358 2.790000e-06 63.9
16 TraesCS4B01G184600 chr6B 84.375 64 10 0 2162 2225 563130964 563131027 2.790000e-06 63.9
17 TraesCS4B01G184600 chr6A 85.714 56 8 0 2170 2225 518546573 518546628 3.600000e-05 60.2


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 TraesCS4B01G184600 chr4B 404122798 404126141 3343 False 6176.000000 6176 100.0000 1 3344 1 chr4B.!!$F1 3343
1 TraesCS4B01G184600 chr4D 323600908 323605294 4386 False 1624.333333 3858 95.2340 167 3344 3 chr4D.!!$F1 3177
2 TraesCS4B01G184600 chr4D 323582289 323583319 1030 True 725.000000 725 79.6420 1283 2331 1 chr4D.!!$R1 1048
3 TraesCS4B01G184600 chr4A 147651512 147654226 2714 True 2012.000000 3179 94.1555 575 3344 2 chr4A.!!$R1 2769
4 TraesCS4B01G184600 chr4A 148126606 148127636 1030 False 736.000000 736 79.8680 1283 2331 1 chr4A.!!$F1 1048
5 TraesCS4B01G184600 chr7D 560892445 560893698 1253 False 1640.000000 1640 90.2520 1070 2335 1 chr7D.!!$F1 1265
6 TraesCS4B01G184600 chr7D 560982799 560983755 956 False 1247.000000 1247 90.0510 1364 2338 1 chr7D.!!$F2 974
7 TraesCS4B01G184600 chr7A 645038604 645039895 1291 False 1624.000000 1624 89.4940 1052 2340 1 chr7A.!!$F1 1288
8 TraesCS4B01G184600 chr7B 608875209 608876482 1273 True 1578.000000 1578 89.1220 1064 2337 1 chr7B.!!$R1 1273

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
950 2264 0.031585 GGTGCGGCGTCATAGTCATA 59.968 55.0 9.37 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2757 4101 0.034337 CCTCCGTCCGAAAACTTCCA 59.966 55.0 0.0 0.0 0.0 3.53 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
24 25 6.968131 TTTTCGTAAAGGATCATCTGTGAG 57.032 37.500 0.00 0.00 37.87 3.51
25 26 4.655762 TCGTAAAGGATCATCTGTGAGG 57.344 45.455 0.00 0.00 37.87 3.86
26 27 4.278310 TCGTAAAGGATCATCTGTGAGGA 58.722 43.478 0.00 0.00 37.87 3.71
27 28 4.895889 TCGTAAAGGATCATCTGTGAGGAT 59.104 41.667 0.00 0.00 37.87 3.24
28 29 6.068670 TCGTAAAGGATCATCTGTGAGGATA 58.931 40.000 0.00 0.00 37.87 2.59
29 30 6.207614 TCGTAAAGGATCATCTGTGAGGATAG 59.792 42.308 0.00 0.00 37.87 2.08
30 31 6.207614 CGTAAAGGATCATCTGTGAGGATAGA 59.792 42.308 0.00 0.00 37.87 1.98
31 32 7.093988 CGTAAAGGATCATCTGTGAGGATAGAT 60.094 40.741 0.00 0.00 37.87 1.98
33 34 4.467082 AGGATCATCTGTGAGGATAGATGC 59.533 45.833 8.87 0.00 46.19 3.91
34 35 4.222366 GGATCATCTGTGAGGATAGATGCA 59.778 45.833 8.87 0.00 46.19 3.96
35 36 5.104859 GGATCATCTGTGAGGATAGATGCAT 60.105 44.000 0.00 0.00 46.19 3.96
36 37 6.097981 GGATCATCTGTGAGGATAGATGCATA 59.902 42.308 0.00 0.00 46.19 3.14
37 38 6.923199 TCATCTGTGAGGATAGATGCATAA 57.077 37.500 0.00 0.00 46.19 1.90
38 39 6.932947 TCATCTGTGAGGATAGATGCATAAG 58.067 40.000 0.00 0.00 46.19 1.73
39 40 6.496218 TCATCTGTGAGGATAGATGCATAAGT 59.504 38.462 0.00 0.00 46.19 2.24
40 41 7.671398 TCATCTGTGAGGATAGATGCATAAGTA 59.329 37.037 0.00 0.00 46.19 2.24
41 42 7.459795 TCTGTGAGGATAGATGCATAAGTAG 57.540 40.000 0.00 0.00 0.00 2.57
42 43 7.234355 TCTGTGAGGATAGATGCATAAGTAGA 58.766 38.462 0.00 0.00 0.00 2.59
43 44 7.892771 TCTGTGAGGATAGATGCATAAGTAGAT 59.107 37.037 0.00 0.00 0.00 1.98
44 45 8.427902 TGTGAGGATAGATGCATAAGTAGATT 57.572 34.615 0.00 0.00 0.00 2.40
45 46 8.309656 TGTGAGGATAGATGCATAAGTAGATTG 58.690 37.037 0.00 0.00 0.00 2.67
46 47 8.310382 GTGAGGATAGATGCATAAGTAGATTGT 58.690 37.037 0.00 0.00 0.00 2.71
47 48 8.874156 TGAGGATAGATGCATAAGTAGATTGTT 58.126 33.333 0.00 0.00 0.00 2.83
48 49 9.364989 GAGGATAGATGCATAAGTAGATTGTTC 57.635 37.037 0.00 0.00 0.00 3.18
49 50 8.874156 AGGATAGATGCATAAGTAGATTGTTCA 58.126 33.333 0.00 0.00 0.00 3.18
50 51 9.664332 GGATAGATGCATAAGTAGATTGTTCAT 57.336 33.333 0.00 0.00 0.00 2.57
79 80 6.902224 ATTTTTCCAAAAGTTTGACCGAAG 57.098 33.333 5.34 0.00 40.55 3.79
80 81 3.430333 TTCCAAAAGTTTGACCGAAGC 57.570 42.857 5.34 0.00 40.55 3.86
81 82 2.650322 TCCAAAAGTTTGACCGAAGCT 58.350 42.857 5.34 0.00 40.55 3.74
82 83 2.616842 TCCAAAAGTTTGACCGAAGCTC 59.383 45.455 5.34 0.00 40.55 4.09
83 84 2.287608 CCAAAAGTTTGACCGAAGCTCC 60.288 50.000 5.34 0.00 40.55 4.70
84 85 2.341846 AAAGTTTGACCGAAGCTCCA 57.658 45.000 0.00 0.00 0.00 3.86
85 86 1.884235 AAGTTTGACCGAAGCTCCAG 58.116 50.000 0.00 0.00 0.00 3.86
86 87 0.603975 AGTTTGACCGAAGCTCCAGC 60.604 55.000 0.00 0.00 42.49 4.85
103 104 7.809546 GCTCCAGCTACTTTAATCCTAAATT 57.190 36.000 0.00 0.00 38.21 1.82
104 105 7.866729 GCTCCAGCTACTTTAATCCTAAATTC 58.133 38.462 0.00 0.00 38.21 2.17
105 106 7.499232 GCTCCAGCTACTTTAATCCTAAATTCA 59.501 37.037 0.00 0.00 38.21 2.57
106 107 8.964476 TCCAGCTACTTTAATCCTAAATTCAG 57.036 34.615 0.00 0.00 0.00 3.02
107 108 8.548877 TCCAGCTACTTTAATCCTAAATTCAGT 58.451 33.333 0.00 0.00 0.00 3.41
108 109 9.178758 CCAGCTACTTTAATCCTAAATTCAGTT 57.821 33.333 0.00 0.00 0.00 3.16
111 112 9.290483 GCTACTTTAATCCTAAATTCAGTTTGC 57.710 33.333 0.00 0.00 0.00 3.68
133 134 8.572828 TTGCTTACAAATTTCATATTATGCCG 57.427 30.769 0.00 0.00 31.21 5.69
134 135 6.640499 TGCTTACAAATTTCATATTATGCCGC 59.360 34.615 0.00 0.00 0.00 6.53
135 136 6.640499 GCTTACAAATTTCATATTATGCCGCA 59.360 34.615 0.00 0.00 0.00 5.69
136 137 7.329226 GCTTACAAATTTCATATTATGCCGCAT 59.671 33.333 11.38 11.38 0.00 4.73
137 138 9.195411 CTTACAAATTTCATATTATGCCGCATT 57.805 29.630 11.97 0.00 0.00 3.56
138 139 7.642071 ACAAATTTCATATTATGCCGCATTC 57.358 32.000 11.97 0.00 0.00 2.67
139 140 6.363088 ACAAATTTCATATTATGCCGCATTCG 59.637 34.615 11.97 0.00 0.00 3.34
156 157 5.607119 CATTCGGTGCAAGTAAAGTAGTT 57.393 39.130 0.00 0.00 0.00 2.24
157 158 5.618561 CATTCGGTGCAAGTAAAGTAGTTC 58.381 41.667 0.00 0.00 0.00 3.01
158 159 4.325028 TCGGTGCAAGTAAAGTAGTTCA 57.675 40.909 0.00 0.00 0.00 3.18
159 160 4.890088 TCGGTGCAAGTAAAGTAGTTCAT 58.110 39.130 0.00 0.00 0.00 2.57
160 161 5.302360 TCGGTGCAAGTAAAGTAGTTCATT 58.698 37.500 0.00 0.00 0.00 2.57
161 162 5.761234 TCGGTGCAAGTAAAGTAGTTCATTT 59.239 36.000 0.00 0.00 0.00 2.32
162 163 5.851177 CGGTGCAAGTAAAGTAGTTCATTTG 59.149 40.000 0.00 0.00 0.00 2.32
163 164 6.149633 GGTGCAAGTAAAGTAGTTCATTTGG 58.850 40.000 0.00 0.00 0.00 3.28
164 165 6.238925 GGTGCAAGTAAAGTAGTTCATTTGGT 60.239 38.462 0.00 0.00 0.00 3.67
165 166 6.856426 GTGCAAGTAAAGTAGTTCATTTGGTC 59.144 38.462 0.00 0.00 0.00 4.02
172 173 8.995220 GTAAAGTAGTTCATTTGGTCACACATA 58.005 33.333 0.00 0.00 0.00 2.29
177 178 3.088532 TCATTTGGTCACACATAAGGCC 58.911 45.455 0.00 0.00 0.00 5.19
179 180 2.897271 TTGGTCACACATAAGGCCAT 57.103 45.000 5.01 0.00 0.00 4.40
192 193 7.067494 ACACATAAGGCCATAGAAAGCTTAAAG 59.933 37.037 5.01 0.00 0.00 1.85
282 1590 6.366061 GCAAAATGTGGTTGATCTAGGAAAAC 59.634 38.462 0.00 0.00 0.00 2.43
342 1650 4.851639 ATGATTGCTTCCTACCAAGACT 57.148 40.909 0.00 0.00 0.00 3.24
358 1666 3.512033 AGACTAAGTCCAAGCGATGAC 57.488 47.619 0.00 0.00 32.18 3.06
395 1703 4.214332 CACCTTCTTTCAGTACAAAGGCTC 59.786 45.833 6.00 0.00 40.12 4.70
452 1760 2.416547 CGAGCTGTGAAGGTTATGTTGG 59.583 50.000 0.00 0.00 0.00 3.77
453 1761 3.412386 GAGCTGTGAAGGTTATGTTGGT 58.588 45.455 0.00 0.00 0.00 3.67
454 1762 3.821033 GAGCTGTGAAGGTTATGTTGGTT 59.179 43.478 0.00 0.00 0.00 3.67
455 1763 3.569701 AGCTGTGAAGGTTATGTTGGTTG 59.430 43.478 0.00 0.00 0.00 3.77
456 1764 3.305335 GCTGTGAAGGTTATGTTGGTTGG 60.305 47.826 0.00 0.00 0.00 3.77
457 1765 3.226777 TGTGAAGGTTATGTTGGTTGGG 58.773 45.455 0.00 0.00 0.00 4.12
458 1766 3.117474 TGTGAAGGTTATGTTGGTTGGGA 60.117 43.478 0.00 0.00 0.00 4.37
459 1767 3.254903 GTGAAGGTTATGTTGGTTGGGAC 59.745 47.826 0.00 0.00 0.00 4.46
460 1768 3.139397 TGAAGGTTATGTTGGTTGGGACT 59.861 43.478 0.00 0.00 0.00 3.85
461 1769 3.154827 AGGTTATGTTGGTTGGGACTG 57.845 47.619 0.00 0.00 0.00 3.51
462 1770 2.714250 AGGTTATGTTGGTTGGGACTGA 59.286 45.455 0.00 0.00 0.00 3.41
469 1777 0.984230 TGGTTGGGACTGAGGACATC 59.016 55.000 0.00 0.00 0.00 3.06
487 1795 1.131303 TCCTCCCCGTGTGGATTGTT 61.131 55.000 0.00 0.00 37.49 2.83
496 1804 3.795101 CCGTGTGGATTGTTACGAGATAC 59.205 47.826 0.00 0.00 38.72 2.24
497 1805 4.439700 CCGTGTGGATTGTTACGAGATACT 60.440 45.833 0.00 0.00 38.72 2.12
498 1806 5.220912 CCGTGTGGATTGTTACGAGATACTA 60.221 44.000 0.00 0.00 38.72 1.82
503 1811 8.638873 TGTGGATTGTTACGAGATACTATGAAT 58.361 33.333 0.00 0.00 0.00 2.57
539 1847 1.187567 AGCCCAAATGTGCACCCTTC 61.188 55.000 15.69 0.00 0.00 3.46
540 1848 1.586028 CCCAAATGTGCACCCTTCG 59.414 57.895 15.69 0.00 0.00 3.79
541 1849 1.586028 CCAAATGTGCACCCTTCGG 59.414 57.895 15.69 2.98 0.00 4.30
542 1850 1.178534 CCAAATGTGCACCCTTCGGT 61.179 55.000 15.69 0.00 46.31 4.69
556 1864 0.878523 TTCGGTGCGTTCTTGTCCAG 60.879 55.000 0.00 0.00 0.00 3.86
584 1892 4.082408 AGCAATCGCATCCATAATTCCATG 60.082 41.667 0.00 0.00 42.27 3.66
658 1971 2.804931 GCATTTGCCGTCAACGCC 60.805 61.111 0.00 0.00 38.18 5.68
679 1992 5.561339 CGCCGAAAATATGGGTTATTACCAC 60.561 44.000 2.85 0.00 46.96 4.16
723 2036 7.771183 TGTGCAATTAGGAAATGGATTAACTC 58.229 34.615 0.00 0.00 0.00 3.01
739 2052 0.681564 ACTCGTTTTGGTTGGGTGCA 60.682 50.000 0.00 0.00 0.00 4.57
741 2054 1.587613 CGTTTTGGTTGGGTGCACG 60.588 57.895 11.45 0.00 0.00 5.34
768 2082 2.417243 GGCACATGCACCTACCATTTTC 60.417 50.000 6.15 0.00 44.36 2.29
779 2093 2.420628 ACCATTTTCACATGTGCACG 57.579 45.000 21.38 7.20 0.00 5.34
780 2094 1.680735 ACCATTTTCACATGTGCACGT 59.319 42.857 21.38 9.52 0.00 4.49
846 2160 3.057736 CAGGCATTCACAAAGACTCCAAG 60.058 47.826 0.00 0.00 0.00 3.61
907 2221 2.474266 CAAACCCGACGCGTCATG 59.526 61.111 35.71 27.35 0.00 3.07
948 2262 2.183300 GGTGCGGCGTCATAGTCA 59.817 61.111 9.37 0.00 0.00 3.41
949 2263 1.227263 GGTGCGGCGTCATAGTCAT 60.227 57.895 9.37 0.00 0.00 3.06
950 2264 0.031585 GGTGCGGCGTCATAGTCATA 59.968 55.000 9.37 0.00 0.00 2.15
951 2265 1.129326 GTGCGGCGTCATAGTCATAC 58.871 55.000 9.37 0.00 0.00 2.39
952 2266 0.741915 TGCGGCGTCATAGTCATACA 59.258 50.000 9.37 0.00 0.00 2.29
953 2267 1.129326 GCGGCGTCATAGTCATACAC 58.871 55.000 9.37 0.00 0.00 2.90
1014 2328 1.522355 ATGCATGCCTCTTCCGTCG 60.522 57.895 16.68 0.00 0.00 5.12
1032 2346 2.043349 TCGGAGATGGCGGAGGAA 60.043 61.111 0.00 0.00 0.00 3.36
1569 2901 1.227380 GCTGGACGCCGAGATGAAT 60.227 57.895 0.00 0.00 0.00 2.57
1824 3156 2.997315 CTGGACCTCCTGGACGCA 60.997 66.667 0.00 0.00 36.82 5.24
2361 3693 4.339814 CCCTAGTGTCTAGTGATCAACTCC 59.660 50.000 0.00 0.00 40.56 3.85
2368 3700 5.127845 TGTCTAGTGATCAACTCCATCCTTC 59.872 44.000 0.00 0.00 40.56 3.46
2369 3701 3.922171 AGTGATCAACTCCATCCTTCC 57.078 47.619 0.00 0.00 31.64 3.46
2470 3803 1.275666 ACATGTAGCTGTAGCCACCA 58.724 50.000 0.00 0.00 43.38 4.17
2471 3804 1.839994 ACATGTAGCTGTAGCCACCAT 59.160 47.619 0.00 0.00 43.38 3.55
2472 3805 2.239654 ACATGTAGCTGTAGCCACCATT 59.760 45.455 0.00 0.00 43.38 3.16
2473 3806 2.401583 TGTAGCTGTAGCCACCATTG 57.598 50.000 0.00 0.00 43.38 2.82
2474 3807 1.628340 TGTAGCTGTAGCCACCATTGT 59.372 47.619 0.00 0.00 43.38 2.71
2475 3808 2.009774 GTAGCTGTAGCCACCATTGTG 58.990 52.381 0.00 0.00 43.38 3.33
2476 3809 0.401738 AGCTGTAGCCACCATTGTGT 59.598 50.000 0.00 0.00 43.38 3.72
2477 3810 1.628340 AGCTGTAGCCACCATTGTGTA 59.372 47.619 0.00 0.00 43.38 2.90
2478 3811 2.009774 GCTGTAGCCACCATTGTGTAG 58.990 52.381 0.00 0.00 41.09 2.74
2479 3812 2.009774 CTGTAGCCACCATTGTGTAGC 58.990 52.381 0.00 0.00 41.09 3.58
2480 3813 1.349357 TGTAGCCACCATTGTGTAGCA 59.651 47.619 0.00 0.00 41.09 3.49
2481 3814 2.026356 TGTAGCCACCATTGTGTAGCAT 60.026 45.455 0.00 0.00 41.09 3.79
2482 3815 2.220653 AGCCACCATTGTGTAGCATT 57.779 45.000 0.00 0.00 41.09 3.56
2483 3816 3.364460 AGCCACCATTGTGTAGCATTA 57.636 42.857 0.00 0.00 41.09 1.90
2484 3817 3.902218 AGCCACCATTGTGTAGCATTAT 58.098 40.909 0.00 0.00 41.09 1.28
2485 3818 4.280819 AGCCACCATTGTGTAGCATTATT 58.719 39.130 0.00 0.00 41.09 1.40
2486 3819 4.098349 AGCCACCATTGTGTAGCATTATTG 59.902 41.667 0.00 0.00 41.09 1.90
2541 3874 0.179023 TGGATGCTGCTGTGTTCACA 60.179 50.000 0.00 5.52 0.00 3.58
2571 3904 4.564782 TGCTTCATTCTTCATCTCCAGT 57.435 40.909 0.00 0.00 0.00 4.00
2607 3940 3.929414 GCTTACAGCTTATTTCAGACGC 58.071 45.455 0.00 0.00 38.45 5.19
2647 3991 3.515502 AGCTACATTGGTAAGCAGAGTGA 59.484 43.478 9.61 0.00 0.00 3.41
2662 4006 4.142071 GCAGAGTGACAGGATGAATACTGA 60.142 45.833 9.56 0.00 41.40 3.41
2702 4046 9.654663 ATGAAGTACAGTACAAGAAAATACTCC 57.345 33.333 13.37 0.00 28.91 3.85
2703 4047 8.092687 TGAAGTACAGTACAAGAAAATACTCCC 58.907 37.037 13.37 0.00 28.91 4.30
2704 4048 7.793948 AGTACAGTACAAGAAAATACTCCCT 57.206 36.000 13.37 0.00 28.91 4.20
2705 4049 7.838884 AGTACAGTACAAGAAAATACTCCCTC 58.161 38.462 13.37 0.00 28.91 4.30
2706 4050 6.051179 ACAGTACAAGAAAATACTCCCTCC 57.949 41.667 0.00 0.00 28.91 4.30
2707 4051 5.109903 CAGTACAAGAAAATACTCCCTCCG 58.890 45.833 0.00 0.00 28.91 4.63
2708 4052 4.776308 AGTACAAGAAAATACTCCCTCCGT 59.224 41.667 0.00 0.00 0.00 4.69
2709 4053 4.203654 ACAAGAAAATACTCCCTCCGTC 57.796 45.455 0.00 0.00 0.00 4.79
2710 4054 3.055312 ACAAGAAAATACTCCCTCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
2711 4055 1.755380 AGAAAATACTCCCTCCGTCCG 59.245 52.381 0.00 0.00 0.00 4.79
2712 4056 1.753073 GAAAATACTCCCTCCGTCCGA 59.247 52.381 0.00 0.00 0.00 4.55
2713 4057 1.856629 AAATACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
2714 4058 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2715 4059 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2716 4060 0.890683 TACTCCCTCCGTCCGAAAAC 59.109 55.000 0.00 0.00 0.00 2.43
2717 4061 1.079336 CTCCCTCCGTCCGAAAACC 60.079 63.158 0.00 0.00 0.00 3.27
2718 4062 1.534717 TCCCTCCGTCCGAAAACCT 60.535 57.895 0.00 0.00 0.00 3.50
2719 4063 0.251742 TCCCTCCGTCCGAAAACCTA 60.252 55.000 0.00 0.00 0.00 3.08
2720 4064 0.175073 CCCTCCGTCCGAAAACCTAG 59.825 60.000 0.00 0.00 0.00 3.02
2721 4065 1.180029 CCTCCGTCCGAAAACCTAGA 58.820 55.000 0.00 0.00 0.00 2.43
2722 4066 1.755380 CCTCCGTCCGAAAACCTAGAT 59.245 52.381 0.00 0.00 0.00 1.98
2723 4067 2.954318 CCTCCGTCCGAAAACCTAGATA 59.046 50.000 0.00 0.00 0.00 1.98
2724 4068 3.243334 CCTCCGTCCGAAAACCTAGATAC 60.243 52.174 0.00 0.00 0.00 2.24
2725 4069 3.355378 TCCGTCCGAAAACCTAGATACA 58.645 45.455 0.00 0.00 0.00 2.29
2726 4070 3.956199 TCCGTCCGAAAACCTAGATACAT 59.044 43.478 0.00 0.00 0.00 2.29
2727 4071 4.037208 TCCGTCCGAAAACCTAGATACATC 59.963 45.833 0.00 0.00 0.00 3.06
2728 4072 4.296690 CGTCCGAAAACCTAGATACATCC 58.703 47.826 0.00 0.00 0.00 3.51
2729 4073 4.202080 CGTCCGAAAACCTAGATACATCCA 60.202 45.833 0.00 0.00 0.00 3.41
2730 4074 5.509163 CGTCCGAAAACCTAGATACATCCAT 60.509 44.000 0.00 0.00 0.00 3.41
2731 4075 6.289064 GTCCGAAAACCTAGATACATCCATT 58.711 40.000 0.00 0.00 0.00 3.16
2732 4076 6.766467 GTCCGAAAACCTAGATACATCCATTT 59.234 38.462 0.00 0.00 0.00 2.32
2733 4077 6.765989 TCCGAAAACCTAGATACATCCATTTG 59.234 38.462 0.00 0.00 0.00 2.32
2734 4078 6.765989 CCGAAAACCTAGATACATCCATTTGA 59.234 38.462 0.00 0.00 0.00 2.69
2735 4079 7.041780 CCGAAAACCTAGATACATCCATTTGAG 60.042 40.741 0.00 0.00 0.00 3.02
2736 4080 7.041780 CGAAAACCTAGATACATCCATTTGAGG 60.042 40.741 0.00 0.00 0.00 3.86
2737 4081 5.832539 ACCTAGATACATCCATTTGAGGG 57.167 43.478 0.00 0.00 0.00 4.30
2738 4082 5.476983 ACCTAGATACATCCATTTGAGGGA 58.523 41.667 0.00 0.00 39.14 4.20
2739 4083 5.545723 ACCTAGATACATCCATTTGAGGGAG 59.454 44.000 0.00 0.00 37.96 4.30
2740 4084 4.989875 AGATACATCCATTTGAGGGAGG 57.010 45.455 0.00 0.00 41.79 4.30
2741 4085 3.654806 AGATACATCCATTTGAGGGAGGG 59.345 47.826 0.00 0.00 40.41 4.30
2742 4086 1.985622 ACATCCATTTGAGGGAGGGA 58.014 50.000 0.00 0.00 40.41 4.20
2743 4087 1.566231 ACATCCATTTGAGGGAGGGAC 59.434 52.381 0.00 0.00 40.41 4.46
2744 4088 1.565759 CATCCATTTGAGGGAGGGACA 59.434 52.381 0.00 0.00 37.96 4.02
2745 4089 1.753903 TCCATTTGAGGGAGGGACAA 58.246 50.000 0.00 0.00 0.00 3.18
2746 4090 1.635487 TCCATTTGAGGGAGGGACAAG 59.365 52.381 0.00 0.00 0.00 3.16
2747 4091 1.467920 CATTTGAGGGAGGGACAAGC 58.532 55.000 0.00 0.00 0.00 4.01
2748 4092 1.005215 CATTTGAGGGAGGGACAAGCT 59.995 52.381 0.00 0.00 0.00 3.74
2749 4093 1.149101 TTTGAGGGAGGGACAAGCTT 58.851 50.000 0.00 0.00 0.00 3.74
2750 4094 1.149101 TTGAGGGAGGGACAAGCTTT 58.851 50.000 0.00 0.00 0.00 3.51
2751 4095 1.149101 TGAGGGAGGGACAAGCTTTT 58.851 50.000 0.00 0.00 0.00 2.27
2752 4096 1.499007 TGAGGGAGGGACAAGCTTTTT 59.501 47.619 0.00 0.00 0.00 1.94
2753 4097 2.163509 GAGGGAGGGACAAGCTTTTTC 58.836 52.381 0.00 0.00 0.00 2.29
2754 4098 0.881796 GGGAGGGACAAGCTTTTTCG 59.118 55.000 0.00 0.00 0.00 3.46
2755 4099 0.881796 GGAGGGACAAGCTTTTTCGG 59.118 55.000 0.00 0.00 0.00 4.30
2756 4100 1.544759 GGAGGGACAAGCTTTTTCGGA 60.545 52.381 0.00 0.00 0.00 4.55
2757 4101 2.437413 GAGGGACAAGCTTTTTCGGAT 58.563 47.619 0.00 0.00 0.00 4.18
2758 4102 2.162408 GAGGGACAAGCTTTTTCGGATG 59.838 50.000 0.00 0.00 0.00 3.51
2759 4103 1.202348 GGGACAAGCTTTTTCGGATGG 59.798 52.381 0.00 0.00 0.00 3.51
2760 4104 2.159382 GGACAAGCTTTTTCGGATGGA 58.841 47.619 0.00 0.00 0.00 3.41
2761 4105 2.556622 GGACAAGCTTTTTCGGATGGAA 59.443 45.455 0.00 0.00 0.00 3.53
2762 4106 3.366374 GGACAAGCTTTTTCGGATGGAAG 60.366 47.826 0.00 0.00 35.70 3.46
2763 4107 3.222603 ACAAGCTTTTTCGGATGGAAGT 58.777 40.909 0.00 0.00 35.70 3.01
2764 4108 3.636764 ACAAGCTTTTTCGGATGGAAGTT 59.363 39.130 0.00 0.00 35.70 2.66
2765 4109 4.099419 ACAAGCTTTTTCGGATGGAAGTTT 59.901 37.500 0.00 0.00 35.70 2.66
2766 4110 4.937201 AGCTTTTTCGGATGGAAGTTTT 57.063 36.364 0.00 0.00 35.70 2.43
2767 4111 4.871513 AGCTTTTTCGGATGGAAGTTTTC 58.128 39.130 0.00 0.00 35.70 2.29
2768 4112 3.668656 GCTTTTTCGGATGGAAGTTTTCG 59.331 43.478 0.00 0.00 35.70 3.46
2769 4113 3.907894 TTTTCGGATGGAAGTTTTCGG 57.092 42.857 0.00 0.00 35.70 4.30
2770 4114 2.843401 TTCGGATGGAAGTTTTCGGA 57.157 45.000 0.00 0.00 0.00 4.55
2771 4115 2.088950 TCGGATGGAAGTTTTCGGAC 57.911 50.000 0.00 0.00 0.00 4.79
2772 4116 0.719465 CGGATGGAAGTTTTCGGACG 59.281 55.000 0.00 0.00 0.00 4.79
2773 4117 1.084289 GGATGGAAGTTTTCGGACGG 58.916 55.000 0.00 0.00 0.00 4.79
2774 4118 1.338389 GGATGGAAGTTTTCGGACGGA 60.338 52.381 0.00 0.00 0.00 4.69
2775 4119 2.000447 GATGGAAGTTTTCGGACGGAG 59.000 52.381 0.00 0.00 0.00 4.63
2776 4120 0.034337 TGGAAGTTTTCGGACGGAGG 59.966 55.000 0.00 0.00 0.00 4.30
2777 4121 0.672711 GGAAGTTTTCGGACGGAGGG 60.673 60.000 0.00 0.00 0.00 4.30
2778 4122 0.319405 GAAGTTTTCGGACGGAGGGA 59.681 55.000 0.00 0.00 0.00 4.20
2905 4273 4.403432 CACAATATTTGCAGGGGAATGACT 59.597 41.667 0.00 0.00 0.00 3.41
2906 4274 4.403432 ACAATATTTGCAGGGGAATGACTG 59.597 41.667 0.00 0.00 37.76 3.51
2907 4275 2.610438 ATTTGCAGGGGAATGACTGT 57.390 45.000 0.00 0.00 37.07 3.55
2908 4276 3.737559 ATTTGCAGGGGAATGACTGTA 57.262 42.857 0.00 0.00 37.07 2.74
2942 4314 6.644347 ACTGGAATAAAGACTGTTCGATCAT 58.356 36.000 0.00 0.00 0.00 2.45
2945 4317 6.535150 TGGAATAAAGACTGTTCGATCATCAC 59.465 38.462 0.00 0.00 0.00 3.06
3048 4420 5.343307 TTCCGTTACATTACCTTCCCTAC 57.657 43.478 0.00 0.00 0.00 3.18
3118 4498 8.357796 TGATTTTTGCGTTTGACAATTATTCA 57.642 26.923 0.00 0.00 0.00 2.57
3122 4502 4.864633 TGCGTTTGACAATTATTCAGCAA 58.135 34.783 0.00 0.00 0.00 3.91
3199 4579 1.978580 CCCTCTTACTGTCAGTTGGGT 59.021 52.381 11.54 0.00 0.00 4.51
3229 4609 4.002982 CAGTCTGCTGGTGCTAACAATAA 58.997 43.478 0.00 0.00 39.01 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.371548 CCTCACAGATGATCCTTTACGAAAAA 59.628 38.462 0.00 0.00 33.22 1.94
1 2 5.874810 CCTCACAGATGATCCTTTACGAAAA 59.125 40.000 0.00 0.00 33.22 2.29
2 3 5.186992 TCCTCACAGATGATCCTTTACGAAA 59.813 40.000 0.00 0.00 33.22 3.46
3 4 4.709886 TCCTCACAGATGATCCTTTACGAA 59.290 41.667 0.00 0.00 33.22 3.85
4 5 4.278310 TCCTCACAGATGATCCTTTACGA 58.722 43.478 0.00 0.00 33.22 3.43
5 6 4.655762 TCCTCACAGATGATCCTTTACG 57.344 45.455 0.00 0.00 33.22 3.18
6 7 7.531857 TCTATCCTCACAGATGATCCTTTAC 57.468 40.000 0.00 0.00 33.22 2.01
16 17 6.931790 ACTTATGCATCTATCCTCACAGAT 57.068 37.500 0.19 0.00 31.58 2.90
17 18 7.234355 TCTACTTATGCATCTATCCTCACAGA 58.766 38.462 0.19 0.00 0.00 3.41
18 19 7.459795 TCTACTTATGCATCTATCCTCACAG 57.540 40.000 0.19 0.00 0.00 3.66
19 20 8.309656 CAATCTACTTATGCATCTATCCTCACA 58.690 37.037 0.19 0.00 0.00 3.58
20 21 8.310382 ACAATCTACTTATGCATCTATCCTCAC 58.690 37.037 0.19 0.00 0.00 3.51
21 22 8.427902 ACAATCTACTTATGCATCTATCCTCA 57.572 34.615 0.19 0.00 0.00 3.86
22 23 9.364989 GAACAATCTACTTATGCATCTATCCTC 57.635 37.037 0.19 0.00 0.00 3.71
23 24 8.874156 TGAACAATCTACTTATGCATCTATCCT 58.126 33.333 0.19 0.00 0.00 3.24
24 25 9.664332 ATGAACAATCTACTTATGCATCTATCC 57.336 33.333 0.19 0.00 0.00 2.59
53 54 9.685828 CTTCGGTCAAACTTTTGGAAAAATATA 57.314 29.630 1.94 0.00 38.66 0.86
54 55 7.170828 GCTTCGGTCAAACTTTTGGAAAAATAT 59.829 33.333 1.94 0.00 38.66 1.28
55 56 6.477360 GCTTCGGTCAAACTTTTGGAAAAATA 59.523 34.615 1.94 0.00 38.66 1.40
56 57 5.293324 GCTTCGGTCAAACTTTTGGAAAAAT 59.707 36.000 1.94 0.00 38.66 1.82
57 58 4.627900 GCTTCGGTCAAACTTTTGGAAAAA 59.372 37.500 1.94 0.00 38.66 1.94
58 59 4.081917 AGCTTCGGTCAAACTTTTGGAAAA 60.082 37.500 1.94 0.00 38.66 2.29
59 60 3.445805 AGCTTCGGTCAAACTTTTGGAAA 59.554 39.130 1.94 0.00 38.66 3.13
60 61 3.020984 AGCTTCGGTCAAACTTTTGGAA 58.979 40.909 1.94 0.00 38.66 3.53
61 62 2.616842 GAGCTTCGGTCAAACTTTTGGA 59.383 45.455 1.94 0.00 38.66 3.53
62 63 2.287608 GGAGCTTCGGTCAAACTTTTGG 60.288 50.000 1.94 0.00 38.66 3.28
63 64 2.357637 TGGAGCTTCGGTCAAACTTTTG 59.642 45.455 0.00 0.00 39.48 2.44
64 65 2.618709 CTGGAGCTTCGGTCAAACTTTT 59.381 45.455 0.00 0.00 0.00 2.27
65 66 2.222027 CTGGAGCTTCGGTCAAACTTT 58.778 47.619 0.00 0.00 0.00 2.66
66 67 1.884235 CTGGAGCTTCGGTCAAACTT 58.116 50.000 0.00 0.00 0.00 2.66
67 68 0.603975 GCTGGAGCTTCGGTCAAACT 60.604 55.000 1.91 0.00 38.21 2.66
68 69 1.869690 GCTGGAGCTTCGGTCAAAC 59.130 57.895 1.91 0.00 38.21 2.93
69 70 4.379174 GCTGGAGCTTCGGTCAAA 57.621 55.556 1.91 0.00 38.21 2.69
76 77 7.717436 ATTTAGGATTAAAGTAGCTGGAGCTTC 59.283 37.037 6.44 1.46 40.79 3.86
77 78 7.578203 ATTTAGGATTAAAGTAGCTGGAGCTT 58.422 34.615 6.44 0.00 40.79 3.74
78 79 7.142995 ATTTAGGATTAAAGTAGCTGGAGCT 57.857 36.000 6.37 6.37 41.99 4.09
79 80 7.499232 TGAATTTAGGATTAAAGTAGCTGGAGC 59.501 37.037 0.00 0.00 35.32 4.70
80 81 8.964476 TGAATTTAGGATTAAAGTAGCTGGAG 57.036 34.615 0.00 0.00 32.58 3.86
81 82 8.548877 ACTGAATTTAGGATTAAAGTAGCTGGA 58.451 33.333 0.00 0.00 32.58 3.86
82 83 8.738645 ACTGAATTTAGGATTAAAGTAGCTGG 57.261 34.615 0.00 0.00 32.58 4.85
85 86 9.290483 GCAAACTGAATTTAGGATTAAAGTAGC 57.710 33.333 1.95 0.00 32.58 3.58
108 109 7.168972 GCGGCATAATATGAAATTTGTAAGCAA 59.831 33.333 4.14 0.00 0.00 3.91
109 110 6.640499 GCGGCATAATATGAAATTTGTAAGCA 59.360 34.615 4.14 0.00 0.00 3.91
110 111 6.640499 TGCGGCATAATATGAAATTTGTAAGC 59.360 34.615 4.14 0.00 0.00 3.09
111 112 8.746922 ATGCGGCATAATATGAAATTTGTAAG 57.253 30.769 14.96 0.00 0.00 2.34
112 113 9.190858 GAATGCGGCATAATATGAAATTTGTAA 57.809 29.630 17.00 0.00 0.00 2.41
113 114 7.536964 CGAATGCGGCATAATATGAAATTTGTA 59.463 33.333 17.00 0.00 0.00 2.41
114 115 6.363088 CGAATGCGGCATAATATGAAATTTGT 59.637 34.615 17.00 0.00 0.00 2.83
115 116 6.744418 CGAATGCGGCATAATATGAAATTTG 58.256 36.000 17.00 0.00 0.00 2.32
116 117 6.932901 CGAATGCGGCATAATATGAAATTT 57.067 33.333 17.00 0.00 0.00 1.82
134 135 5.178623 TGAACTACTTTACTTGCACCGAATG 59.821 40.000 0.00 0.00 0.00 2.67
135 136 5.302360 TGAACTACTTTACTTGCACCGAAT 58.698 37.500 0.00 0.00 0.00 3.34
136 137 4.695396 TGAACTACTTTACTTGCACCGAA 58.305 39.130 0.00 0.00 0.00 4.30
137 138 4.325028 TGAACTACTTTACTTGCACCGA 57.675 40.909 0.00 0.00 0.00 4.69
138 139 5.607119 AATGAACTACTTTACTTGCACCG 57.393 39.130 0.00 0.00 0.00 4.94
139 140 6.149633 CCAAATGAACTACTTTACTTGCACC 58.850 40.000 0.00 0.00 0.00 5.01
140 141 6.735130 ACCAAATGAACTACTTTACTTGCAC 58.265 36.000 0.00 0.00 0.00 4.57
141 142 6.544197 TGACCAAATGAACTACTTTACTTGCA 59.456 34.615 0.00 0.00 0.00 4.08
142 143 6.856426 GTGACCAAATGAACTACTTTACTTGC 59.144 38.462 0.00 0.00 0.00 4.01
143 144 7.855904 GTGTGACCAAATGAACTACTTTACTTG 59.144 37.037 0.00 0.00 0.00 3.16
144 145 7.554835 TGTGTGACCAAATGAACTACTTTACTT 59.445 33.333 0.00 0.00 0.00 2.24
145 146 7.051623 TGTGTGACCAAATGAACTACTTTACT 58.948 34.615 0.00 0.00 0.00 2.24
146 147 7.254227 TGTGTGACCAAATGAACTACTTTAC 57.746 36.000 0.00 0.00 0.00 2.01
147 148 9.562408 TTATGTGTGACCAAATGAACTACTTTA 57.438 29.630 0.00 0.00 0.00 1.85
148 149 6.959639 ATGTGTGACCAAATGAACTACTTT 57.040 33.333 0.00 0.00 0.00 2.66
149 150 7.174946 CCTTATGTGTGACCAAATGAACTACTT 59.825 37.037 0.00 0.00 0.00 2.24
150 151 6.655003 CCTTATGTGTGACCAAATGAACTACT 59.345 38.462 0.00 0.00 0.00 2.57
151 152 6.622896 GCCTTATGTGTGACCAAATGAACTAC 60.623 42.308 0.00 0.00 0.00 2.73
152 153 5.414454 GCCTTATGTGTGACCAAATGAACTA 59.586 40.000 0.00 0.00 0.00 2.24
153 154 4.218417 GCCTTATGTGTGACCAAATGAACT 59.782 41.667 0.00 0.00 0.00 3.01
154 155 4.485163 GCCTTATGTGTGACCAAATGAAC 58.515 43.478 0.00 0.00 0.00 3.18
155 156 3.509575 GGCCTTATGTGTGACCAAATGAA 59.490 43.478 0.00 0.00 0.00 2.57
156 157 3.088532 GGCCTTATGTGTGACCAAATGA 58.911 45.455 0.00 0.00 0.00 2.57
157 158 2.824936 TGGCCTTATGTGTGACCAAATG 59.175 45.455 3.32 0.00 0.00 2.32
158 159 3.168035 TGGCCTTATGTGTGACCAAAT 57.832 42.857 3.32 0.00 0.00 2.32
159 160 2.666272 TGGCCTTATGTGTGACCAAA 57.334 45.000 3.32 0.00 0.00 3.28
160 161 2.897271 ATGGCCTTATGTGTGACCAA 57.103 45.000 3.32 0.00 0.00 3.67
161 162 3.111484 TCTATGGCCTTATGTGTGACCA 58.889 45.455 3.32 0.00 0.00 4.02
162 163 3.838244 TCTATGGCCTTATGTGTGACC 57.162 47.619 3.32 0.00 0.00 4.02
163 164 4.035675 GCTTTCTATGGCCTTATGTGTGAC 59.964 45.833 3.32 0.00 0.00 3.67
164 165 4.080356 AGCTTTCTATGGCCTTATGTGTGA 60.080 41.667 3.32 0.00 0.00 3.58
165 166 4.202441 AGCTTTCTATGGCCTTATGTGTG 58.798 43.478 3.32 0.00 0.00 3.82
172 173 6.069615 TCCTACTTTAAGCTTTCTATGGCCTT 60.070 38.462 3.20 0.00 0.00 4.35
177 178 7.334421 TGCAAGTCCTACTTTAAGCTTTCTATG 59.666 37.037 3.20 0.00 36.03 2.23
179 180 6.649557 GTGCAAGTCCTACTTTAAGCTTTCTA 59.350 38.462 3.20 0.00 36.03 2.10
192 193 3.568007 TGGTTTTGATGTGCAAGTCCTAC 59.432 43.478 0.00 0.00 37.87 3.18
342 1650 0.174845 CGGGTCATCGCTTGGACTTA 59.825 55.000 0.00 0.00 34.49 2.24
358 1666 2.017049 GAAGGTGATTTGTCATCCGGG 58.983 52.381 0.00 0.00 0.00 5.73
395 1703 1.864711 ACGAACATGTGTTGTCCTTCG 59.135 47.619 0.00 4.83 40.35 3.79
419 1727 0.460284 ACAGCTCGGATTAGCCAACG 60.460 55.000 0.00 0.00 43.86 4.10
452 1760 1.280457 AGGATGTCCTCAGTCCCAAC 58.720 55.000 0.00 0.00 44.77 3.77
453 1761 3.815717 AGGATGTCCTCAGTCCCAA 57.184 52.632 0.00 0.00 44.77 4.12
469 1777 0.616371 TAACAATCCACACGGGGAGG 59.384 55.000 0.00 0.00 41.08 4.30
474 1782 2.357327 TCTCGTAACAATCCACACGG 57.643 50.000 0.00 0.00 35.21 4.94
496 1804 7.362574 GCTGCCTAACTAGGTCTCTATTCATAG 60.363 44.444 4.72 0.00 45.42 2.23
497 1805 6.434652 GCTGCCTAACTAGGTCTCTATTCATA 59.565 42.308 4.72 0.00 45.42 2.15
498 1806 5.245075 GCTGCCTAACTAGGTCTCTATTCAT 59.755 44.000 4.72 0.00 45.42 2.57
503 1811 2.424523 GGGCTGCCTAACTAGGTCTCTA 60.425 54.545 19.68 0.00 45.42 2.43
539 1847 1.284982 CTCTGGACAAGAACGCACCG 61.285 60.000 0.00 0.00 33.37 4.94
540 1848 1.569479 GCTCTGGACAAGAACGCACC 61.569 60.000 0.00 0.00 33.37 5.01
541 1849 0.601311 AGCTCTGGACAAGAACGCAC 60.601 55.000 0.00 0.00 33.37 5.34
542 1850 0.966179 TAGCTCTGGACAAGAACGCA 59.034 50.000 0.00 0.00 33.37 5.24
543 1851 1.634702 CTAGCTCTGGACAAGAACGC 58.365 55.000 0.00 0.00 33.37 4.84
544 1852 1.067565 TGCTAGCTCTGGACAAGAACG 60.068 52.381 17.23 0.00 33.37 3.95
545 1853 2.751166 TGCTAGCTCTGGACAAGAAC 57.249 50.000 17.23 0.00 33.37 3.01
546 1854 3.677148 CGATTGCTAGCTCTGGACAAGAA 60.677 47.826 17.23 0.00 33.37 2.52
547 1855 2.159184 CGATTGCTAGCTCTGGACAAGA 60.159 50.000 17.23 0.00 0.00 3.02
548 1856 2.200067 CGATTGCTAGCTCTGGACAAG 58.800 52.381 17.23 0.00 0.00 3.16
556 1864 1.805869 ATGGATGCGATTGCTAGCTC 58.194 50.000 17.23 5.01 43.34 4.09
584 1892 5.331902 CGATTTCACCATGGATGTTTGTAC 58.668 41.667 21.47 0.45 0.00 2.90
658 1971 6.262273 AGCAGTGGTAATAACCCATATTTTCG 59.738 38.462 0.00 0.00 46.16 3.46
679 1992 4.233635 GATGCGCCGCTTGAGCAG 62.234 66.667 11.67 0.00 44.55 4.24
723 2036 1.587613 CGTGCACCCAACCAAAACG 60.588 57.895 12.15 0.00 0.00 3.60
739 2052 2.046411 TGCATGTGCCCGAATCGT 60.046 55.556 0.82 0.00 41.18 3.73
741 2054 0.463654 TAGGTGCATGTGCCCGAATC 60.464 55.000 2.07 0.00 41.18 2.52
768 2082 2.861763 CAAGTAGACGTGCACATGTG 57.138 50.000 21.83 21.83 0.00 3.21
873 2187 3.183754 GTTTGGAGGTTCCGTTGTTTTG 58.816 45.455 0.00 0.00 40.17 2.44
907 2221 2.505819 TCCTGGTTAAATCAGAGAGGCC 59.494 50.000 0.00 0.00 34.36 5.19
936 2250 4.866921 TGTATGTGTATGACTATGACGCC 58.133 43.478 0.00 0.00 0.00 5.68
948 2262 6.091034 CGCTCGACTACTCTATGTATGTGTAT 59.909 42.308 0.00 0.00 0.00 2.29
949 2263 5.404667 CGCTCGACTACTCTATGTATGTGTA 59.595 44.000 0.00 0.00 0.00 2.90
950 2264 4.211584 CGCTCGACTACTCTATGTATGTGT 59.788 45.833 0.00 0.00 0.00 3.72
951 2265 4.703424 CGCTCGACTACTCTATGTATGTG 58.297 47.826 0.00 0.00 0.00 3.21
952 2266 3.186817 GCGCTCGACTACTCTATGTATGT 59.813 47.826 0.00 0.00 0.00 2.29
953 2267 3.722374 CGCGCTCGACTACTCTATGTATG 60.722 52.174 5.56 0.00 38.10 2.39
1014 2328 2.423898 TTCCTCCGCCATCTCCGAC 61.424 63.158 0.00 0.00 0.00 4.79
1019 2333 2.579201 CGTGTTCCTCCGCCATCT 59.421 61.111 0.00 0.00 0.00 2.90
1569 2901 1.371183 CAGCTTCGTCCAGAACCCA 59.629 57.895 0.00 0.00 34.66 4.51
1970 3302 0.322008 GCTCTCCAGGAACACCTTGG 60.322 60.000 0.00 0.00 30.75 3.61
2368 3700 3.740321 CACGTTCATTTCCAAACCAATGG 59.260 43.478 0.00 0.00 42.12 3.16
2369 3701 3.184178 GCACGTTCATTTCCAAACCAATG 59.816 43.478 0.00 0.00 0.00 2.82
2381 3713 3.599730 TCTGATCTCTGCACGTTCATT 57.400 42.857 0.00 0.00 0.00 2.57
2471 3804 9.356433 CATTTCACAATCAATAATGCTACACAA 57.644 29.630 0.00 0.00 0.00 3.33
2472 3805 8.522003 ACATTTCACAATCAATAATGCTACACA 58.478 29.630 0.00 0.00 31.15 3.72
2473 3806 8.915871 ACATTTCACAATCAATAATGCTACAC 57.084 30.769 0.00 0.00 31.15 2.90
2477 3810 9.793252 GACTTACATTTCACAATCAATAATGCT 57.207 29.630 0.00 0.00 31.15 3.79
2478 3811 9.571810 TGACTTACATTTCACAATCAATAATGC 57.428 29.630 0.00 0.00 31.15 3.56
2485 3818 9.283768 ACTAACATGACTTACATTTCACAATCA 57.716 29.630 0.00 0.00 37.07 2.57
2541 3874 2.010145 AGAATGAAGCATGCGTACGT 57.990 45.000 17.90 6.39 0.00 3.57
2571 3904 4.060900 CTGTAAGCTTTCTGTTGCTCTCA 58.939 43.478 3.20 0.00 38.75 3.27
2647 3991 7.482169 TCAGTAGTTTCAGTATTCATCCTGT 57.518 36.000 0.00 0.00 0.00 4.00
2701 4045 0.175073 CTAGGTTTTCGGACGGAGGG 59.825 60.000 0.00 0.00 0.00 4.30
2702 4046 1.180029 TCTAGGTTTTCGGACGGAGG 58.820 55.000 0.00 0.00 0.00 4.30
2703 4047 3.379372 TGTATCTAGGTTTTCGGACGGAG 59.621 47.826 0.00 0.00 0.00 4.63
2704 4048 3.355378 TGTATCTAGGTTTTCGGACGGA 58.645 45.455 0.00 0.00 0.00 4.69
2705 4049 3.788333 TGTATCTAGGTTTTCGGACGG 57.212 47.619 0.00 0.00 0.00 4.79
2706 4050 4.202080 TGGATGTATCTAGGTTTTCGGACG 60.202 45.833 0.00 0.00 0.00 4.79
2707 4051 5.272283 TGGATGTATCTAGGTTTTCGGAC 57.728 43.478 0.00 0.00 0.00 4.79
2708 4052 6.494666 AATGGATGTATCTAGGTTTTCGGA 57.505 37.500 0.00 0.00 0.00 4.55
2709 4053 6.765989 TCAAATGGATGTATCTAGGTTTTCGG 59.234 38.462 0.00 0.00 0.00 4.30
2710 4054 7.041780 CCTCAAATGGATGTATCTAGGTTTTCG 60.042 40.741 0.00 0.00 0.00 3.46
2711 4055 7.229506 CCCTCAAATGGATGTATCTAGGTTTTC 59.770 40.741 0.00 0.00 0.00 2.29
2712 4056 7.062957 CCCTCAAATGGATGTATCTAGGTTTT 58.937 38.462 0.00 0.00 0.00 2.43
2713 4057 6.389869 TCCCTCAAATGGATGTATCTAGGTTT 59.610 38.462 0.00 0.00 0.00 3.27
2714 4058 5.911178 TCCCTCAAATGGATGTATCTAGGTT 59.089 40.000 0.00 0.00 0.00 3.50
2715 4059 5.476983 TCCCTCAAATGGATGTATCTAGGT 58.523 41.667 0.00 0.00 0.00 3.08
2716 4060 5.046014 CCTCCCTCAAATGGATGTATCTAGG 60.046 48.000 0.00 0.00 0.00 3.02
2717 4061 5.046014 CCCTCCCTCAAATGGATGTATCTAG 60.046 48.000 0.00 0.00 0.00 2.43
2718 4062 4.846367 CCCTCCCTCAAATGGATGTATCTA 59.154 45.833 0.00 0.00 0.00 1.98
2719 4063 3.654806 CCCTCCCTCAAATGGATGTATCT 59.345 47.826 0.00 0.00 0.00 1.98
2720 4064 3.652869 TCCCTCCCTCAAATGGATGTATC 59.347 47.826 0.00 0.00 0.00 2.24
2721 4065 3.395941 GTCCCTCCCTCAAATGGATGTAT 59.604 47.826 0.00 0.00 0.00 2.29
2722 4066 2.777692 GTCCCTCCCTCAAATGGATGTA 59.222 50.000 0.00 0.00 0.00 2.29
2723 4067 1.566231 GTCCCTCCCTCAAATGGATGT 59.434 52.381 0.00 0.00 0.00 3.06
2724 4068 1.565759 TGTCCCTCCCTCAAATGGATG 59.434 52.381 0.00 0.00 0.00 3.51
2725 4069 1.985622 TGTCCCTCCCTCAAATGGAT 58.014 50.000 0.00 0.00 0.00 3.41
2726 4070 1.635487 CTTGTCCCTCCCTCAAATGGA 59.365 52.381 0.00 0.00 0.00 3.41
2727 4071 1.957113 GCTTGTCCCTCCCTCAAATGG 60.957 57.143 0.00 0.00 0.00 3.16
2728 4072 1.005215 AGCTTGTCCCTCCCTCAAATG 59.995 52.381 0.00 0.00 0.00 2.32
2729 4073 1.376649 AGCTTGTCCCTCCCTCAAAT 58.623 50.000 0.00 0.00 0.00 2.32
2730 4074 1.149101 AAGCTTGTCCCTCCCTCAAA 58.851 50.000 0.00 0.00 0.00 2.69
2731 4075 1.149101 AAAGCTTGTCCCTCCCTCAA 58.851 50.000 0.00 0.00 0.00 3.02
2732 4076 1.149101 AAAAGCTTGTCCCTCCCTCA 58.851 50.000 0.00 0.00 0.00 3.86
2733 4077 2.163509 GAAAAAGCTTGTCCCTCCCTC 58.836 52.381 0.00 0.00 0.00 4.30
2734 4078 1.545651 CGAAAAAGCTTGTCCCTCCCT 60.546 52.381 0.00 0.00 0.00 4.20
2735 4079 0.881796 CGAAAAAGCTTGTCCCTCCC 59.118 55.000 0.00 0.00 0.00 4.30
2736 4080 0.881796 CCGAAAAAGCTTGTCCCTCC 59.118 55.000 0.00 0.00 0.00 4.30
2737 4081 1.892209 TCCGAAAAAGCTTGTCCCTC 58.108 50.000 0.00 0.00 0.00 4.30
2738 4082 2.162681 CATCCGAAAAAGCTTGTCCCT 58.837 47.619 0.00 0.00 0.00 4.20
2739 4083 1.202348 CCATCCGAAAAAGCTTGTCCC 59.798 52.381 0.00 0.00 0.00 4.46
2740 4084 2.159382 TCCATCCGAAAAAGCTTGTCC 58.841 47.619 0.00 0.00 0.00 4.02
2741 4085 3.253432 ACTTCCATCCGAAAAAGCTTGTC 59.747 43.478 0.00 0.00 0.00 3.18
2742 4086 3.222603 ACTTCCATCCGAAAAAGCTTGT 58.777 40.909 0.00 0.00 0.00 3.16
2743 4087 3.923017 ACTTCCATCCGAAAAAGCTTG 57.077 42.857 0.00 0.00 0.00 4.01
2744 4088 4.937201 AAACTTCCATCCGAAAAAGCTT 57.063 36.364 0.00 0.00 0.00 3.74
2745 4089 4.556699 CGAAAACTTCCATCCGAAAAAGCT 60.557 41.667 0.00 0.00 0.00 3.74
2746 4090 3.668656 CGAAAACTTCCATCCGAAAAAGC 59.331 43.478 0.00 0.00 0.00 3.51
2747 4091 4.023536 TCCGAAAACTTCCATCCGAAAAAG 60.024 41.667 0.00 0.00 0.00 2.27
2748 4092 3.884091 TCCGAAAACTTCCATCCGAAAAA 59.116 39.130 0.00 0.00 0.00 1.94
2749 4093 3.251487 GTCCGAAAACTTCCATCCGAAAA 59.749 43.478 0.00 0.00 0.00 2.29
2750 4094 2.809696 GTCCGAAAACTTCCATCCGAAA 59.190 45.455 0.00 0.00 0.00 3.46
2751 4095 2.419667 GTCCGAAAACTTCCATCCGAA 58.580 47.619 0.00 0.00 0.00 4.30
2752 4096 1.670674 CGTCCGAAAACTTCCATCCGA 60.671 52.381 0.00 0.00 0.00 4.55
2753 4097 0.719465 CGTCCGAAAACTTCCATCCG 59.281 55.000 0.00 0.00 0.00 4.18
2754 4098 1.084289 CCGTCCGAAAACTTCCATCC 58.916 55.000 0.00 0.00 0.00 3.51
2755 4099 2.000447 CTCCGTCCGAAAACTTCCATC 59.000 52.381 0.00 0.00 0.00 3.51
2756 4100 1.338769 CCTCCGTCCGAAAACTTCCAT 60.339 52.381 0.00 0.00 0.00 3.41
2757 4101 0.034337 CCTCCGTCCGAAAACTTCCA 59.966 55.000 0.00 0.00 0.00 3.53
2758 4102 0.672711 CCCTCCGTCCGAAAACTTCC 60.673 60.000 0.00 0.00 0.00 3.46
2759 4103 0.319405 TCCCTCCGTCCGAAAACTTC 59.681 55.000 0.00 0.00 0.00 3.01
2760 4104 0.320697 CTCCCTCCGTCCGAAAACTT 59.679 55.000 0.00 0.00 0.00 2.66
2761 4105 0.830866 ACTCCCTCCGTCCGAAAACT 60.831 55.000 0.00 0.00 0.00 2.66
2762 4106 0.890683 TACTCCCTCCGTCCGAAAAC 59.109 55.000 0.00 0.00 0.00 2.43
2763 4107 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2764 4108 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
2765 4109 2.511659 CATATACTCCCTCCGTCCGAA 58.488 52.381 0.00 0.00 0.00 4.30
2766 4110 1.271762 CCATATACTCCCTCCGTCCGA 60.272 57.143 0.00 0.00 0.00 4.55
2767 4111 1.174783 CCATATACTCCCTCCGTCCG 58.825 60.000 0.00 0.00 0.00 4.79
2768 4112 2.169330 GACCATATACTCCCTCCGTCC 58.831 57.143 0.00 0.00 0.00 4.79
2769 4113 1.811359 CGACCATATACTCCCTCCGTC 59.189 57.143 0.00 0.00 0.00 4.79
2770 4114 1.906990 CGACCATATACTCCCTCCGT 58.093 55.000 0.00 0.00 0.00 4.69
2771 4115 0.526662 GCGACCATATACTCCCTCCG 59.473 60.000 0.00 0.00 0.00 4.63
2772 4116 0.896226 GGCGACCATATACTCCCTCC 59.104 60.000 0.00 0.00 0.00 4.30
2773 4117 1.819903 GAGGCGACCATATACTCCCTC 59.180 57.143 0.00 0.00 0.00 4.30
2774 4118 1.550409 GGAGGCGACCATATACTCCCT 60.550 57.143 0.00 0.00 41.41 4.20
2775 4119 0.896226 GGAGGCGACCATATACTCCC 59.104 60.000 0.00 0.00 41.41 4.30
2776 4120 1.629043 TGGAGGCGACCATATACTCC 58.371 55.000 0.00 0.00 46.14 3.85
2905 4273 9.817809 GTCTTTATTCCAGTTCTACATGATACA 57.182 33.333 0.00 0.00 0.00 2.29
2908 4276 8.543774 ACAGTCTTTATTCCAGTTCTACATGAT 58.456 33.333 0.00 0.00 0.00 2.45
2942 4314 5.871465 TTTTATATTGCTGTTGCGAGTGA 57.129 34.783 0.00 0.00 43.34 3.41
2945 4317 7.739022 TTTCATTTTATATTGCTGTTGCGAG 57.261 32.000 0.00 0.00 43.34 5.03
3118 4498 0.947244 CTTGAGTGGCGAAAGTTGCT 59.053 50.000 0.00 0.00 0.00 3.91
3122 4502 2.417719 GACATCTTGAGTGGCGAAAGT 58.582 47.619 0.00 0.00 0.00 2.66
3199 4579 1.341209 CACCAGCAGACTGTGACAGTA 59.659 52.381 19.46 0.00 45.44 2.74
3229 4609 5.496556 TGAACGGAGACCATGTTTATCATT 58.503 37.500 0.00 0.00 34.09 2.57
3244 4624 3.653344 TGATGAAAGTGTCTGAACGGAG 58.347 45.455 0.00 0.00 0.00 4.63
3246 4626 3.809832 AGTTGATGAAAGTGTCTGAACGG 59.190 43.478 0.00 0.00 0.00 4.44
3247 4627 5.409643 AAGTTGATGAAAGTGTCTGAACG 57.590 39.130 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.