Multiple sequence alignment - TraesCS2A01G328800

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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 TraesCS2A01G328800 chr2A 100.000 2969 0 0 1 2969 560784822 560781854 0.000000e+00 5483.0
1 TraesCS2A01G328800 chr2A 100.000 82 0 0 2888 2969 560776831 560776750 5.130000e-33 152.0
2 TraesCS2A01G328800 chr2B 91.264 1820 71 29 325 2081 504468022 504469816 0.000000e+00 2399.0
3 TraesCS2A01G328800 chr2B 89.844 256 24 2 325 580 504444376 504444629 7.930000e-86 327.0
4 TraesCS2A01G328800 chr2B 91.213 239 14 5 2652 2887 504470713 504470947 4.780000e-83 318.0
5 TraesCS2A01G328800 chr2B 92.308 195 10 3 2080 2269 504469886 504470080 3.770000e-69 272.0
6 TraesCS2A01G328800 chr2B 90.659 182 16 1 2267 2448 504470255 504470435 1.060000e-59 241.0
7 TraesCS2A01G328800 chr2B 93.750 112 4 2 2456 2564 504470598 504470709 6.580000e-37 165.0
8 TraesCS2A01G328800 chr2B 96.875 96 3 0 2566 2661 653585435 653585340 8.520000e-36 161.0
9 TraesCS2A01G328800 chr2B 86.614 127 8 6 203 320 504467553 504467679 6.680000e-27 132.0
10 TraesCS2A01G328800 chr2B 92.683 82 6 0 2886 2967 401283979 401284060 5.200000e-23 119.0
11 TraesCS2A01G328800 chr2B 92.500 80 6 0 2888 2967 401286683 401286762 6.720000e-22 115.0
12 TraesCS2A01G328800 chr2B 86.111 108 6 6 222 320 504443926 504444033 1.130000e-19 108.0
13 TraesCS2A01G328800 chr2D 91.266 1809 59 30 322 2081 427570339 427572097 0.000000e+00 2374.0
14 TraesCS2A01G328800 chr2D 84.363 518 29 25 2080 2565 427572157 427572654 7.500000e-126 460.0
15 TraesCS2A01G328800 chr2D 90.295 237 16 5 2652 2887 427572657 427572887 1.340000e-78 303.0
16 TraesCS2A01G328800 chr2D 85.128 195 15 9 1 183 405280790 405280598 1.410000e-43 187.0
17 TraesCS2A01G328800 chr2D 91.304 115 7 3 2567 2680 107899778 107899890 1.430000e-33 154.0
18 TraesCS2A01G328800 chr3B 89.205 176 10 5 1 167 758844930 758845105 8.340000e-51 211.0
19 TraesCS2A01G328800 chr7B 87.568 185 11 4 1 173 608187238 608187054 1.400000e-48 204.0
20 TraesCS2A01G328800 chr1B 87.500 184 14 5 1 175 470727647 470727830 1.400000e-48 204.0
21 TraesCS2A01G328800 chr1B 85.632 174 16 5 1 166 6668718 6668890 1.090000e-39 174.0
22 TraesCS2A01G328800 chr1B 96.875 96 2 1 2564 2659 618002459 618002553 3.060000e-35 159.0
23 TraesCS2A01G328800 chr1A 87.166 187 12 6 1 175 522187512 522187698 5.020000e-48 202.0
24 TraesCS2A01G328800 chr1A 91.096 146 11 2 2 145 93368545 93368400 2.330000e-46 196.0
25 TraesCS2A01G328800 chr7A 87.931 174 13 4 1 166 10222569 10222742 6.490000e-47 198.0
26 TraesCS2A01G328800 chr7A 96.875 96 3 0 2567 2662 608875110 608875205 8.520000e-36 161.0
27 TraesCS2A01G328800 chr6D 88.050 159 11 4 1 151 420707214 420707056 6.540000e-42 182.0
28 TraesCS2A01G328800 chr6D 91.892 111 8 1 2544 2654 434509242 434509351 1.430000e-33 154.0
29 TraesCS2A01G328800 chr4D 95.146 103 4 1 2561 2662 5081569 5081671 8.520000e-36 161.0
30 TraesCS2A01G328800 chr3D 97.849 93 2 0 2565 2657 535746945 535746853 8.520000e-36 161.0
31 TraesCS2A01G328800 chr1D 91.892 111 7 2 2551 2661 440409661 440409769 1.430000e-33 154.0
32 TraesCS2A01G328800 chr6B 92.381 105 7 1 2544 2648 657939632 657939735 6.630000e-32 148.0
33 TraesCS2A01G328800 chr6B 92.500 80 6 0 2888 2967 464713821 464713900 6.720000e-22 115.0
34 TraesCS2A01G328800 chr6B 92.500 80 6 0 2888 2967 464718915 464718994 6.720000e-22 115.0
35 TraesCS2A01G328800 chrUn 100.000 29 0 0 1809 1837 356020608 356020636 1.000000e-03 54.7


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 TraesCS2A01G328800 chr2A 560781854 560784822 2968 True 5483.000000 5483 100.000000 1 2969 1 chr2A.!!$R2 2968
1 TraesCS2A01G328800 chr2B 504467553 504470947 3394 False 587.833333 2399 90.968000 203 2887 6 chr2B.!!$F3 2684
2 TraesCS2A01G328800 chr2B 504443926 504444629 703 False 217.500000 327 87.977500 222 580 2 chr2B.!!$F2 358
3 TraesCS2A01G328800 chr2D 427570339 427572887 2548 False 1045.666667 2374 88.641333 322 2887 3 chr2D.!!$F2 2565


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
23 24 0.036875 AGCAGGACACAAACCCTAGC 59.963 55.0 0.00 0.0 0.0 3.42 F
24 25 0.250727 GCAGGACACAAACCCTAGCA 60.251 55.0 0.00 0.0 31.5 3.49 F
185 186 0.453782 CGGCGGCGGTAAAAAGAAAG 60.454 55.0 25.36 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1434 0.604780 CCGGATGATGCTGATGGTCC 60.605 60.000 0.0 0.0 0.0 4.46 R
1917 2333 1.290009 GTGTGATTGTGCTTGGCCC 59.710 57.895 0.0 0.0 0.0 5.80 R
2101 2589 1.334960 CGTTGTTTACAGCCTTGCAGG 60.335 52.381 0.0 0.0 38.8 4.85 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
19 20 2.633860 CTGAGCAGGACACAAACCC 58.366 57.895 0.00 0.00 0.00 4.11
20 21 0.109342 CTGAGCAGGACACAAACCCT 59.891 55.000 0.00 0.00 0.00 4.34
21 22 1.347707 CTGAGCAGGACACAAACCCTA 59.652 52.381 0.00 0.00 0.00 3.53
22 23 1.347707 TGAGCAGGACACAAACCCTAG 59.652 52.381 0.00 0.00 0.00 3.02
23 24 0.036875 AGCAGGACACAAACCCTAGC 59.963 55.000 0.00 0.00 0.00 3.42
24 25 0.250727 GCAGGACACAAACCCTAGCA 60.251 55.000 0.00 0.00 31.50 3.49
25 26 1.817740 GCAGGACACAAACCCTAGCAA 60.818 52.381 0.00 0.00 31.50 3.91
26 27 2.582052 CAGGACACAAACCCTAGCAAA 58.418 47.619 0.00 0.00 0.00 3.68
27 28 2.955660 CAGGACACAAACCCTAGCAAAA 59.044 45.455 0.00 0.00 0.00 2.44
28 29 2.956333 AGGACACAAACCCTAGCAAAAC 59.044 45.455 0.00 0.00 0.00 2.43
29 30 2.956333 GGACACAAACCCTAGCAAAACT 59.044 45.455 0.00 0.00 0.00 2.66
30 31 3.243401 GGACACAAACCCTAGCAAAACTG 60.243 47.826 0.00 0.00 0.00 3.16
31 32 3.361786 ACACAAACCCTAGCAAAACTGT 58.638 40.909 0.00 0.00 0.00 3.55
32 33 4.528920 ACACAAACCCTAGCAAAACTGTA 58.471 39.130 0.00 0.00 0.00 2.74
33 34 4.951094 ACACAAACCCTAGCAAAACTGTAA 59.049 37.500 0.00 0.00 0.00 2.41
34 35 5.067283 ACACAAACCCTAGCAAAACTGTAAG 59.933 40.000 0.00 0.00 42.29 2.34
35 36 5.298276 CACAAACCCTAGCAAAACTGTAAGA 59.702 40.000 0.00 0.00 37.43 2.10
36 37 5.889289 ACAAACCCTAGCAAAACTGTAAGAA 59.111 36.000 0.00 0.00 37.43 2.52
37 38 6.378848 ACAAACCCTAGCAAAACTGTAAGAAA 59.621 34.615 0.00 0.00 37.43 2.52
38 39 6.387041 AACCCTAGCAAAACTGTAAGAAAC 57.613 37.500 0.00 0.00 37.43 2.78
39 40 4.514066 ACCCTAGCAAAACTGTAAGAAACG 59.486 41.667 0.00 0.00 37.43 3.60
40 41 4.753107 CCCTAGCAAAACTGTAAGAAACGA 59.247 41.667 0.00 0.00 37.43 3.85
41 42 5.333875 CCCTAGCAAAACTGTAAGAAACGAC 60.334 44.000 0.00 0.00 37.43 4.34
42 43 5.465724 CCTAGCAAAACTGTAAGAAACGACT 59.534 40.000 0.00 0.00 37.43 4.18
43 44 6.643770 CCTAGCAAAACTGTAAGAAACGACTA 59.356 38.462 0.00 0.00 37.43 2.59
44 45 6.913873 AGCAAAACTGTAAGAAACGACTAA 57.086 33.333 0.00 0.00 37.43 2.24
45 46 7.311364 AGCAAAACTGTAAGAAACGACTAAA 57.689 32.000 0.00 0.00 37.43 1.85
46 47 7.754625 AGCAAAACTGTAAGAAACGACTAAAA 58.245 30.769 0.00 0.00 37.43 1.52
47 48 8.238631 AGCAAAACTGTAAGAAACGACTAAAAA 58.761 29.630 0.00 0.00 37.43 1.94
48 49 8.309019 GCAAAACTGTAAGAAACGACTAAAAAC 58.691 33.333 0.00 0.00 37.43 2.43
49 50 8.509923 CAAAACTGTAAGAAACGACTAAAAACG 58.490 33.333 0.00 0.00 37.43 3.60
50 51 7.524294 AACTGTAAGAAACGACTAAAAACGA 57.476 32.000 0.00 0.00 37.43 3.85
51 52 7.524294 ACTGTAAGAAACGACTAAAAACGAA 57.476 32.000 0.00 0.00 37.43 3.85
52 53 7.615790 ACTGTAAGAAACGACTAAAAACGAAG 58.384 34.615 0.00 0.00 37.43 3.79
53 54 6.413269 TGTAAGAAACGACTAAAAACGAAGC 58.587 36.000 0.00 0.00 0.00 3.86
54 55 4.463515 AGAAACGACTAAAAACGAAGCC 57.536 40.909 0.00 0.00 0.00 4.35
55 56 3.249320 AGAAACGACTAAAAACGAAGCCC 59.751 43.478 0.00 0.00 0.00 5.19
56 57 2.538512 ACGACTAAAAACGAAGCCCT 57.461 45.000 0.00 0.00 0.00 5.19
57 58 2.410939 ACGACTAAAAACGAAGCCCTC 58.589 47.619 0.00 0.00 0.00 4.30
58 59 1.730612 CGACTAAAAACGAAGCCCTCC 59.269 52.381 0.00 0.00 0.00 4.30
59 60 2.082231 GACTAAAAACGAAGCCCTCCC 58.918 52.381 0.00 0.00 0.00 4.30
60 61 1.084289 CTAAAAACGAAGCCCTCCCG 58.916 55.000 0.00 0.00 0.00 5.14
61 62 0.956902 TAAAAACGAAGCCCTCCCGC 60.957 55.000 0.00 0.00 0.00 6.13
62 63 4.717313 AAACGAAGCCCTCCCGCC 62.717 66.667 0.00 0.00 0.00 6.13
81 82 2.514824 GCCCTTGCCGAGATCCAC 60.515 66.667 0.00 0.00 0.00 4.02
82 83 2.190578 CCCTTGCCGAGATCCACC 59.809 66.667 0.00 0.00 0.00 4.61
83 84 2.202932 CCTTGCCGAGATCCACCG 60.203 66.667 0.00 0.00 0.00 4.94
84 85 2.892425 CTTGCCGAGATCCACCGC 60.892 66.667 0.00 0.00 0.00 5.68
85 86 4.812476 TTGCCGAGATCCACCGCG 62.812 66.667 0.00 0.00 0.00 6.46
90 91 4.593864 GAGATCCACCGCGCCCTC 62.594 72.222 0.00 0.00 0.00 4.30
92 93 4.241555 GATCCACCGCGCCCTCAT 62.242 66.667 0.00 0.00 0.00 2.90
93 94 4.552365 ATCCACCGCGCCCTCATG 62.552 66.667 0.00 0.00 0.00 3.07
112 113 4.475444 CCCTAGGGCCACCGGAGA 62.475 72.222 16.90 0.00 43.47 3.71
113 114 2.840102 CCTAGGGCCACCGGAGAG 60.840 72.222 9.46 0.00 43.47 3.20
115 116 3.352748 TAGGGCCACCGGAGAGGA 61.353 66.667 9.46 0.00 45.00 3.71
116 117 2.664835 CTAGGGCCACCGGAGAGGAT 62.665 65.000 9.46 0.00 45.00 3.24
117 118 2.946988 TAGGGCCACCGGAGAGGATG 62.947 65.000 9.46 0.00 45.00 3.51
118 119 4.554036 GGCCACCGGAGAGGATGC 62.554 72.222 9.46 0.00 45.00 3.91
119 120 4.899239 GCCACCGGAGAGGATGCG 62.899 72.222 9.46 0.00 45.00 4.73
143 144 2.032681 GCGGGAGGCAGAAACACT 59.967 61.111 0.00 0.00 42.87 3.55
144 145 1.295423 GCGGGAGGCAGAAACACTA 59.705 57.895 0.00 0.00 42.87 2.74
145 146 0.741221 GCGGGAGGCAGAAACACTAG 60.741 60.000 0.00 0.00 42.87 2.57
146 147 0.608640 CGGGAGGCAGAAACACTAGT 59.391 55.000 0.00 0.00 0.00 2.57
147 148 1.002087 CGGGAGGCAGAAACACTAGTT 59.998 52.381 0.00 0.00 40.40 2.24
166 167 3.745723 TTTTTGTGGAGGAGGAGGC 57.254 52.632 0.00 0.00 0.00 4.70
167 168 0.250727 TTTTTGTGGAGGAGGAGGCG 60.251 55.000 0.00 0.00 0.00 5.52
168 169 2.124507 TTTTGTGGAGGAGGAGGCGG 62.125 60.000 0.00 0.00 0.00 6.13
181 182 4.470170 GGCGGCGGCGGTAAAAAG 62.470 66.667 33.02 2.30 41.24 2.27
182 183 3.424859 GCGGCGGCGGTAAAAAGA 61.425 61.111 33.02 0.00 0.00 2.52
183 184 2.968639 GCGGCGGCGGTAAAAAGAA 61.969 57.895 33.02 0.00 0.00 2.52
184 185 1.575423 CGGCGGCGGTAAAAAGAAA 59.425 52.632 25.36 0.00 0.00 2.52
185 186 0.453782 CGGCGGCGGTAAAAAGAAAG 60.454 55.000 25.36 0.00 0.00 2.62
186 187 0.594602 GGCGGCGGTAAAAAGAAAGT 59.405 50.000 9.78 0.00 0.00 2.66
187 188 1.001048 GGCGGCGGTAAAAAGAAAGTT 60.001 47.619 9.78 0.00 0.00 2.66
188 189 2.544277 GGCGGCGGTAAAAAGAAAGTTT 60.544 45.455 9.78 0.00 0.00 2.66
189 190 3.304592 GGCGGCGGTAAAAAGAAAGTTTA 60.305 43.478 9.78 0.00 0.00 2.01
190 191 4.478699 GCGGCGGTAAAAAGAAAGTTTAT 58.521 39.130 9.78 0.00 0.00 1.40
191 192 4.919168 GCGGCGGTAAAAAGAAAGTTTATT 59.081 37.500 9.78 0.00 0.00 1.40
192 193 5.403166 GCGGCGGTAAAAAGAAAGTTTATTT 59.597 36.000 9.78 2.38 0.00 1.40
193 194 6.399249 GCGGCGGTAAAAAGAAAGTTTATTTC 60.399 38.462 9.78 0.00 0.00 2.17
194 195 6.637658 CGGCGGTAAAAAGAAAGTTTATTTCA 59.362 34.615 8.57 0.00 0.00 2.69
195 196 7.327518 CGGCGGTAAAAAGAAAGTTTATTTCAT 59.672 33.333 8.57 4.43 0.00 2.57
196 197 8.644619 GGCGGTAAAAAGAAAGTTTATTTCATC 58.355 33.333 8.57 0.77 0.00 2.92
197 198 9.187455 GCGGTAAAAAGAAAGTTTATTTCATCA 57.813 29.630 8.57 0.00 0.00 3.07
235 236 9.040939 TCAATACGATATTAACACTGTCAATGG 57.959 33.333 0.00 0.00 0.00 3.16
367 716 5.897377 AAGTCAACCCAATATTTTCTCGG 57.103 39.130 0.00 0.00 0.00 4.63
371 720 6.151144 AGTCAACCCAATATTTTCTCGGAAAG 59.849 38.462 0.00 0.00 0.00 2.62
383 732 2.556622 TCTCGGAAAGCCATTTTGGTTC 59.443 45.455 0.00 0.00 40.46 3.62
396 745 0.958091 TTGGTTCCGGTGCATTTCAG 59.042 50.000 0.00 0.00 0.00 3.02
428 777 4.982916 CGAAGATGGAGTAATAAACCTCGG 59.017 45.833 0.00 0.00 0.00 4.63
455 804 1.702491 GGTTGGGATTGCGCGAGTAC 61.702 60.000 12.10 0.00 0.00 2.73
531 880 1.342672 GCCCGTATCCCCTCCTTCAA 61.343 60.000 0.00 0.00 0.00 2.69
709 1069 0.751452 GGCTGGCCAGTAGTAGTACC 59.249 60.000 32.81 19.10 35.81 3.34
734 1094 4.618965 AGTACCGCTCCGAAATCTAATTC 58.381 43.478 0.00 0.00 0.00 2.17
737 1097 2.544267 CCGCTCCGAAATCTAATTCCAC 59.456 50.000 0.00 0.00 0.00 4.02
746 1107 6.238648 CCGAAATCTAATTCCACCCATAACAC 60.239 42.308 0.00 0.00 0.00 3.32
776 1137 3.539253 CATTAACTGCATGCGCCTC 57.461 52.632 14.09 0.00 37.32 4.70
777 1138 1.019673 CATTAACTGCATGCGCCTCT 58.980 50.000 14.09 0.00 37.32 3.69
778 1139 1.019673 ATTAACTGCATGCGCCTCTG 58.980 50.000 14.09 0.38 37.32 3.35
779 1140 1.647545 TTAACTGCATGCGCCTCTGC 61.648 55.000 14.09 16.91 37.32 4.26
780 1141 2.526450 TAACTGCATGCGCCTCTGCT 62.526 55.000 22.03 9.27 39.16 4.24
781 1142 3.877357 CTGCATGCGCCTCTGCTG 61.877 66.667 22.03 18.68 39.16 4.41
782 1143 4.397832 TGCATGCGCCTCTGCTGA 62.398 61.111 22.03 5.69 39.16 4.26
804 1165 3.839353 CTGCCCCGGATCAGATGGC 62.839 68.421 15.19 15.85 42.49 4.40
806 1167 2.851102 CCCCGGATCAGATGGCCT 60.851 66.667 0.73 0.00 0.00 5.19
808 1169 2.746359 CCGGATCAGATGGCCTCC 59.254 66.667 3.32 0.00 0.00 4.30
810 1171 2.888447 CGGATCAGATGGCCTCCCC 61.888 68.421 3.32 0.00 0.00 4.81
811 1172 1.463018 GGATCAGATGGCCTCCCCT 60.463 63.158 3.32 0.00 0.00 4.79
812 1173 1.487850 GGATCAGATGGCCTCCCCTC 61.488 65.000 3.32 0.00 0.00 4.30
813 1174 1.463018 ATCAGATGGCCTCCCCTCC 60.463 63.158 3.32 0.00 0.00 4.30
814 1175 2.998668 ATCAGATGGCCTCCCCTCCC 62.999 65.000 3.32 0.00 0.00 4.30
815 1176 3.381049 AGATGGCCTCCCCTCCCT 61.381 66.667 3.32 0.00 0.00 4.20
869 1236 3.737172 AGTGCGCACGCCCATTTC 61.737 61.111 32.94 7.87 41.09 2.17
883 1250 2.641815 CCCATTTCAAATCCCCACCAAA 59.358 45.455 0.00 0.00 0.00 3.28
917 1284 1.301677 GCCAGAGTTTTCGGAGCAGG 61.302 60.000 0.00 0.00 0.00 4.85
1060 1451 1.544982 CCAGGACCATCAGCATCATCC 60.545 57.143 0.00 0.00 0.00 3.51
1170 1570 1.276844 GCGGATGCATCTAACGTGC 59.723 57.895 25.28 15.35 42.15 5.34
1430 1834 1.550374 AGGGGGAAGAGGAGGAGGA 60.550 63.158 0.00 0.00 0.00 3.71
1473 1877 2.841988 GGGGAGGAGCAGAGCGAT 60.842 66.667 0.00 0.00 0.00 4.58
1749 2153 2.513259 GGAGGACGACCACCACCAA 61.513 63.158 14.86 0.00 44.54 3.67
1978 2394 7.703621 CCTTGCACATAAATTAGACAGAAATGG 59.296 37.037 0.00 0.00 0.00 3.16
2081 2498 9.612620 CTTTTGTTTATACTGATTCACTGGTTC 57.387 33.333 0.00 0.00 0.00 3.62
2101 2589 8.420374 TGGTTCTCATTTGTATTCGATACTTC 57.580 34.615 0.00 0.00 36.70 3.01
2169 2660 1.133637 TGGGCAGTTGGAGCAGTAAAA 60.134 47.619 0.00 0.00 0.00 1.52
2261 2756 1.302752 CACTGCTGCCTGGCTACAA 60.303 57.895 21.03 0.00 0.00 2.41
2311 2983 2.923634 ATTGCCCAGGCCTGAGATGC 62.924 60.000 34.91 27.11 41.09 3.91
2335 3007 3.737774 GTGCATTCAAAGCTTCAGTTTCC 59.262 43.478 0.00 0.00 0.00 3.13
2337 3009 4.099881 TGCATTCAAAGCTTCAGTTTCCTT 59.900 37.500 0.00 0.00 0.00 3.36
2356 3028 1.737838 TGAACTGTTGATGATCGCCC 58.262 50.000 0.00 0.00 0.00 6.13
2368 3040 1.171308 GATCGCCCCATGGATCAATG 58.829 55.000 15.22 2.74 39.07 2.82
2369 3041 0.896940 ATCGCCCCATGGATCAATGC 60.897 55.000 15.22 4.87 0.00 3.56
2435 3107 6.434340 ACGAGAGAGTATGTTATGCATGGATA 59.566 38.462 10.16 2.31 38.47 2.59
2484 3318 7.931578 TGTAATCGGTGAAATCCTTTTATGT 57.068 32.000 0.00 0.00 0.00 2.29
2565 3402 9.569122 ACTATTCCTAAAGTGTACATGTGTTTT 57.431 29.630 9.11 6.31 0.00 2.43
2569 3406 8.597662 TCCTAAAGTGTACATGTGTTTTCTAC 57.402 34.615 9.11 0.00 0.00 2.59
2570 3407 8.426489 TCCTAAAGTGTACATGTGTTTTCTACT 58.574 33.333 9.11 0.00 0.00 2.57
2571 3408 8.709646 CCTAAAGTGTACATGTGTTTTCTACTC 58.290 37.037 9.11 0.00 0.00 2.59
2572 3409 7.492352 AAAGTGTACATGTGTTTTCTACTCC 57.508 36.000 9.11 0.00 0.00 3.85
2573 3410 5.548406 AGTGTACATGTGTTTTCTACTCCC 58.452 41.667 9.11 0.00 0.00 4.30
2574 3411 5.307196 AGTGTACATGTGTTTTCTACTCCCT 59.693 40.000 9.11 0.00 0.00 4.20
2575 3412 5.638234 GTGTACATGTGTTTTCTACTCCCTC 59.362 44.000 9.11 0.00 0.00 4.30
2576 3413 4.287766 ACATGTGTTTTCTACTCCCTCC 57.712 45.455 0.00 0.00 0.00 4.30
2577 3414 3.262420 CATGTGTTTTCTACTCCCTCCG 58.738 50.000 0.00 0.00 0.00 4.63
2578 3415 2.322658 TGTGTTTTCTACTCCCTCCGT 58.677 47.619 0.00 0.00 0.00 4.69
2579 3416 2.701951 TGTGTTTTCTACTCCCTCCGTT 59.298 45.455 0.00 0.00 0.00 4.44
2580 3417 3.243975 TGTGTTTTCTACTCCCTCCGTTC 60.244 47.826 0.00 0.00 0.00 3.95
2581 3418 2.301009 TGTTTTCTACTCCCTCCGTTCC 59.699 50.000 0.00 0.00 0.00 3.62
2582 3419 2.301009 GTTTTCTACTCCCTCCGTTCCA 59.699 50.000 0.00 0.00 0.00 3.53
2583 3420 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
2584 3421 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
2585 3422 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
2586 3423 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
2587 3424 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
2588 3425 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2589 3426 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2590 3427 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2591 3428 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2592 3429 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2593 3430 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2594 3431 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2595 3432 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2596 3433 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2597 3434 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2598 3435 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2599 3436 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2600 3437 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2601 3438 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2602 3439 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2603 3440 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2604 3441 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2605 3442 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2606 3443 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2607 3444 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2608 3445 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2609 3446 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2610 3447 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2611 3448 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2612 3449 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2613 3450 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2614 3451 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2615 3452 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2628 3465 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2629 3466 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2630 3467 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2631 3468 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2632 3469 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2633 3470 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2634 3471 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2635 3472 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2636 3473 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2637 3474 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2638 3475 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2639 3476 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2640 3477 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2641 3478 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2642 3479 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2643 3480 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2644 3481 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2645 3482 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2646 3483 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2647 3484 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2648 3485 2.564062 ACGAGTAATTTGGAACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
2649 3486 3.007182 ACGAGTAATTTGGAACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
2650 3487 3.617263 CGAGTAATTTGGAACGGAGGAAG 59.383 47.826 0.00 0.00 0.00 3.46
2651 3488 4.576879 GAGTAATTTGGAACGGAGGAAGT 58.423 43.478 0.00 0.00 0.00 3.01
2652 3489 5.622914 CGAGTAATTTGGAACGGAGGAAGTA 60.623 44.000 0.00 0.00 0.00 2.24
2653 3490 5.731591 AGTAATTTGGAACGGAGGAAGTAG 58.268 41.667 0.00 0.00 0.00 2.57
2654 3491 3.629142 ATTTGGAACGGAGGAAGTAGG 57.371 47.619 0.00 0.00 0.00 3.18
2659 3496 3.136992 TGGAACGGAGGAAGTAGGTTTTT 59.863 43.478 0.00 0.00 0.00 1.94
2715 3553 1.722011 CTAAACGCCGAACTGTGGAT 58.278 50.000 0.00 0.00 0.00 3.41
2738 3576 3.064958 GGCTCATCAAGTCATCATGTGTG 59.935 47.826 0.00 0.00 0.00 3.82
2785 3623 6.003326 TGTCATCACTTATTCTTTGCTTGGA 58.997 36.000 0.00 0.00 0.00 3.53
2786 3624 6.072508 TGTCATCACTTATTCTTTGCTTGGAC 60.073 38.462 0.00 0.00 0.00 4.02
2798 3636 3.347958 TGCTTGGACGTTTGCTAAAAG 57.652 42.857 0.00 0.00 0.00 2.27
2806 3645 6.334202 TGGACGTTTGCTAAAAGAACATTTT 58.666 32.000 0.00 0.00 0.00 1.82
2845 3684 4.214545 CGTACTTTTGCTTGACATGGGTAA 59.785 41.667 0.00 0.00 0.00 2.85
2850 3689 7.151976 ACTTTTGCTTGACATGGGTAATTTAC 58.848 34.615 0.00 0.00 0.00 2.01
2856 3695 6.806739 GCTTGACATGGGTAATTTACTTTGAC 59.193 38.462 6.52 3.96 0.00 3.18
2863 3702 6.263516 GGGTAATTTACTTTGACCCTGTTC 57.736 41.667 6.52 0.00 45.44 3.18
2887 3726 2.802774 CGCTGGAAAACAAAATGCCTGT 60.803 45.455 0.00 0.00 0.00 4.00
2888 3727 2.545106 GCTGGAAAACAAAATGCCTGTG 59.455 45.455 0.00 0.00 0.00 3.66
2889 3728 3.795877 CTGGAAAACAAAATGCCTGTGT 58.204 40.909 0.00 0.00 0.00 3.72
2890 3729 3.791245 TGGAAAACAAAATGCCTGTGTC 58.209 40.909 0.00 0.00 0.00 3.67
2891 3730 3.196469 TGGAAAACAAAATGCCTGTGTCA 59.804 39.130 0.00 0.00 0.00 3.58
2892 3731 3.803778 GGAAAACAAAATGCCTGTGTCAG 59.196 43.478 0.00 0.00 0.00 3.51
2893 3732 2.514205 AACAAAATGCCTGTGTCAGC 57.486 45.000 0.00 0.00 0.00 4.26
2894 3733 0.311790 ACAAAATGCCTGTGTCAGCG 59.688 50.000 0.00 0.00 0.00 5.18
2895 3734 0.311790 CAAAATGCCTGTGTCAGCGT 59.688 50.000 0.00 0.00 0.00 5.07
2896 3735 0.593128 AAAATGCCTGTGTCAGCGTC 59.407 50.000 0.00 0.00 0.00 5.19
2897 3736 1.237285 AAATGCCTGTGTCAGCGTCC 61.237 55.000 0.00 0.00 0.00 4.79
2898 3737 3.612247 ATGCCTGTGTCAGCGTCCC 62.612 63.158 0.00 0.00 0.00 4.46
2899 3738 4.008933 GCCTGTGTCAGCGTCCCT 62.009 66.667 0.00 0.00 0.00 4.20
2900 3739 2.646175 GCCTGTGTCAGCGTCCCTA 61.646 63.158 0.00 0.00 0.00 3.53
2901 3740 1.972198 CCTGTGTCAGCGTCCCTAA 59.028 57.895 0.00 0.00 0.00 2.69
2902 3741 0.389948 CCTGTGTCAGCGTCCCTAAC 60.390 60.000 0.00 0.00 0.00 2.34
2911 3750 4.525949 GTCCCTAACGAGGCCGGC 62.526 72.222 21.18 21.18 42.21 6.13
2930 3769 3.437795 CGCAAGGCAGCTCCAAGG 61.438 66.667 5.21 0.00 37.29 3.61
2931 3770 2.034687 GCAAGGCAGCTCCAAGGA 59.965 61.111 5.21 0.00 37.29 3.36
2932 3771 1.379576 GCAAGGCAGCTCCAAGGAT 60.380 57.895 5.21 0.00 37.29 3.24
2933 3772 1.382692 GCAAGGCAGCTCCAAGGATC 61.383 60.000 5.21 0.00 37.29 3.36
2934 3773 0.750911 CAAGGCAGCTCCAAGGATCC 60.751 60.000 2.48 2.48 37.29 3.36
2935 3774 0.918310 AAGGCAGCTCCAAGGATCCT 60.918 55.000 9.02 9.02 37.29 3.24
2936 3775 1.153005 GGCAGCTCCAAGGATCCTG 60.153 63.158 17.02 9.57 34.01 3.86
2937 3776 1.606531 GCAGCTCCAAGGATCCTGT 59.393 57.895 17.02 2.57 0.00 4.00
2938 3777 0.463474 GCAGCTCCAAGGATCCTGTC 60.463 60.000 17.02 3.01 0.00 3.51
2939 3778 1.202330 CAGCTCCAAGGATCCTGTCT 58.798 55.000 17.02 5.39 0.00 3.41
2940 3779 1.138661 CAGCTCCAAGGATCCTGTCTC 59.861 57.143 17.02 4.13 0.00 3.36
2941 3780 0.467804 GCTCCAAGGATCCTGTCTCC 59.532 60.000 17.02 0.33 0.00 3.71
2942 3781 1.871418 CTCCAAGGATCCTGTCTCCA 58.129 55.000 17.02 0.00 35.08 3.86
2943 3782 1.484240 CTCCAAGGATCCTGTCTCCAC 59.516 57.143 17.02 0.00 35.08 4.02
2944 3783 0.176680 CCAAGGATCCTGTCTCCACG 59.823 60.000 17.02 0.00 35.08 4.94
2945 3784 1.186200 CAAGGATCCTGTCTCCACGA 58.814 55.000 17.02 0.00 35.08 4.35
2946 3785 1.134965 CAAGGATCCTGTCTCCACGAC 60.135 57.143 17.02 0.00 43.14 4.34
2947 3786 0.684805 AGGATCCTGTCTCCACGACC 60.685 60.000 15.29 0.00 42.13 4.79
2948 3787 1.677637 GGATCCTGTCTCCACGACCC 61.678 65.000 3.84 0.00 42.13 4.46
2949 3788 1.677637 GATCCTGTCTCCACGACCCC 61.678 65.000 0.00 0.00 42.13 4.95
2950 3789 3.760035 CCTGTCTCCACGACCCCG 61.760 72.222 0.00 0.00 42.13 5.73
2951 3790 4.436998 CTGTCTCCACGACCCCGC 62.437 72.222 0.00 0.00 42.13 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.109342 AGGGTTTGTGTCCTGCTCAG 59.891 55.000 0.00 0.00 31.11 3.35
2 3 1.347707 CTAGGGTTTGTGTCCTGCTCA 59.652 52.381 0.00 0.00 34.75 4.26
3 4 1.946283 GCTAGGGTTTGTGTCCTGCTC 60.946 57.143 0.00 0.00 34.75 4.26
4 5 0.036875 GCTAGGGTTTGTGTCCTGCT 59.963 55.000 0.00 0.00 34.75 4.24
5 6 0.250727 TGCTAGGGTTTGTGTCCTGC 60.251 55.000 0.00 0.00 34.75 4.85
6 7 2.270352 TTGCTAGGGTTTGTGTCCTG 57.730 50.000 0.00 0.00 34.75 3.86
7 8 2.956333 GTTTTGCTAGGGTTTGTGTCCT 59.044 45.455 0.00 0.00 37.18 3.85
8 9 2.956333 AGTTTTGCTAGGGTTTGTGTCC 59.044 45.455 0.00 0.00 0.00 4.02
9 10 3.380320 ACAGTTTTGCTAGGGTTTGTGTC 59.620 43.478 0.00 0.00 0.00 3.67
10 11 3.361786 ACAGTTTTGCTAGGGTTTGTGT 58.638 40.909 0.00 0.00 0.00 3.72
11 12 5.298276 TCTTACAGTTTTGCTAGGGTTTGTG 59.702 40.000 0.00 0.00 0.00 3.33
12 13 5.442391 TCTTACAGTTTTGCTAGGGTTTGT 58.558 37.500 0.00 0.00 0.00 2.83
13 14 6.385649 TTCTTACAGTTTTGCTAGGGTTTG 57.614 37.500 0.00 0.00 0.00 2.93
14 15 6.459161 CGTTTCTTACAGTTTTGCTAGGGTTT 60.459 38.462 0.00 0.00 0.00 3.27
15 16 5.008316 CGTTTCTTACAGTTTTGCTAGGGTT 59.992 40.000 0.00 0.00 0.00 4.11
16 17 4.514066 CGTTTCTTACAGTTTTGCTAGGGT 59.486 41.667 0.00 0.00 0.00 4.34
17 18 4.753107 TCGTTTCTTACAGTTTTGCTAGGG 59.247 41.667 0.00 0.00 0.00 3.53
18 19 5.465724 AGTCGTTTCTTACAGTTTTGCTAGG 59.534 40.000 0.00 0.00 0.00 3.02
19 20 6.526566 AGTCGTTTCTTACAGTTTTGCTAG 57.473 37.500 0.00 0.00 0.00 3.42
20 21 8.422973 TTTAGTCGTTTCTTACAGTTTTGCTA 57.577 30.769 0.00 0.00 0.00 3.49
21 22 6.913873 TTAGTCGTTTCTTACAGTTTTGCT 57.086 33.333 0.00 0.00 0.00 3.91
22 23 7.958112 TTTTAGTCGTTTCTTACAGTTTTGC 57.042 32.000 0.00 0.00 0.00 3.68
23 24 8.509923 CGTTTTTAGTCGTTTCTTACAGTTTTG 58.490 33.333 0.00 0.00 0.00 2.44
24 25 8.442384 TCGTTTTTAGTCGTTTCTTACAGTTTT 58.558 29.630 0.00 0.00 0.00 2.43
25 26 7.962917 TCGTTTTTAGTCGTTTCTTACAGTTT 58.037 30.769 0.00 0.00 0.00 2.66
26 27 7.524294 TCGTTTTTAGTCGTTTCTTACAGTT 57.476 32.000 0.00 0.00 0.00 3.16
27 28 7.524294 TTCGTTTTTAGTCGTTTCTTACAGT 57.476 32.000 0.00 0.00 0.00 3.55
28 29 6.568965 GCTTCGTTTTTAGTCGTTTCTTACAG 59.431 38.462 0.00 0.00 0.00 2.74
29 30 6.413269 GCTTCGTTTTTAGTCGTTTCTTACA 58.587 36.000 0.00 0.00 0.00 2.41
30 31 5.842843 GGCTTCGTTTTTAGTCGTTTCTTAC 59.157 40.000 0.00 0.00 0.00 2.34
31 32 5.050159 GGGCTTCGTTTTTAGTCGTTTCTTA 60.050 40.000 0.00 0.00 0.00 2.10
32 33 4.260907 GGGCTTCGTTTTTAGTCGTTTCTT 60.261 41.667 0.00 0.00 0.00 2.52
33 34 3.249320 GGGCTTCGTTTTTAGTCGTTTCT 59.751 43.478 0.00 0.00 0.00 2.52
34 35 3.249320 AGGGCTTCGTTTTTAGTCGTTTC 59.751 43.478 0.00 0.00 0.00 2.78
35 36 3.208594 AGGGCTTCGTTTTTAGTCGTTT 58.791 40.909 0.00 0.00 0.00 3.60
36 37 2.804527 GAGGGCTTCGTTTTTAGTCGTT 59.195 45.455 0.00 0.00 0.00 3.85
37 38 2.410939 GAGGGCTTCGTTTTTAGTCGT 58.589 47.619 0.00 0.00 0.00 4.34
38 39 1.730612 GGAGGGCTTCGTTTTTAGTCG 59.269 52.381 0.00 0.00 0.00 4.18
39 40 2.082231 GGGAGGGCTTCGTTTTTAGTC 58.918 52.381 0.00 0.00 0.00 2.59
40 41 1.609841 CGGGAGGGCTTCGTTTTTAGT 60.610 52.381 0.00 0.00 0.00 2.24
41 42 1.084289 CGGGAGGGCTTCGTTTTTAG 58.916 55.000 0.00 0.00 0.00 1.85
42 43 0.956902 GCGGGAGGGCTTCGTTTTTA 60.957 55.000 0.00 0.00 0.00 1.52
43 44 2.265904 GCGGGAGGGCTTCGTTTTT 61.266 57.895 0.00 0.00 0.00 1.94
44 45 2.671963 GCGGGAGGGCTTCGTTTT 60.672 61.111 0.00 0.00 0.00 2.43
45 46 4.717313 GGCGGGAGGGCTTCGTTT 62.717 66.667 0.00 0.00 38.40 3.60
64 65 2.514824 GTGGATCTCGGCAAGGGC 60.515 66.667 0.00 0.00 40.13 5.19
65 66 2.190578 GGTGGATCTCGGCAAGGG 59.809 66.667 0.00 0.00 0.00 3.95
66 67 2.202932 CGGTGGATCTCGGCAAGG 60.203 66.667 0.00 0.00 0.00 3.61
67 68 2.892425 GCGGTGGATCTCGGCAAG 60.892 66.667 12.88 0.00 0.00 4.01
68 69 4.812476 CGCGGTGGATCTCGGCAA 62.812 66.667 0.00 0.00 0.00 4.52
73 74 4.593864 GAGGGCGCGGTGGATCTC 62.594 72.222 8.83 0.00 0.00 2.75
75 76 4.241555 ATGAGGGCGCGGTGGATC 62.242 66.667 8.83 0.00 0.00 3.36
76 77 4.552365 CATGAGGGCGCGGTGGAT 62.552 66.667 8.83 0.00 0.00 3.41
95 96 4.475444 TCTCCGGTGGCCCTAGGG 62.475 72.222 24.89 24.89 38.57 3.53
96 97 2.840102 CTCTCCGGTGGCCCTAGG 60.840 72.222 0.06 0.06 0.00 3.02
97 98 2.664835 ATCCTCTCCGGTGGCCCTAG 62.665 65.000 0.00 0.00 0.00 3.02
98 99 2.711899 ATCCTCTCCGGTGGCCCTA 61.712 63.158 0.00 0.00 0.00 3.53
99 100 4.095400 ATCCTCTCCGGTGGCCCT 62.095 66.667 0.00 0.00 0.00 5.19
100 101 3.866582 CATCCTCTCCGGTGGCCC 61.867 72.222 0.00 0.00 0.00 5.80
101 102 4.554036 GCATCCTCTCCGGTGGCC 62.554 72.222 0.00 0.00 0.00 5.36
102 103 4.899239 CGCATCCTCTCCGGTGGC 62.899 72.222 0.00 0.00 0.00 5.01
103 104 4.227134 CCGCATCCTCTCCGGTGG 62.227 72.222 0.00 2.66 37.36 4.61
104 105 4.899239 GCCGCATCCTCTCCGGTG 62.899 72.222 0.00 0.00 43.70 4.94
123 124 2.747855 GTTTCTGCCTCCCGCTGG 60.748 66.667 0.00 0.00 38.78 4.85
124 125 2.032528 TGTTTCTGCCTCCCGCTG 59.967 61.111 0.00 0.00 38.78 5.18
125 126 1.192146 TAGTGTTTCTGCCTCCCGCT 61.192 55.000 0.00 0.00 38.78 5.52
126 127 0.741221 CTAGTGTTTCTGCCTCCCGC 60.741 60.000 0.00 0.00 38.31 6.13
127 128 0.608640 ACTAGTGTTTCTGCCTCCCG 59.391 55.000 0.00 0.00 0.00 5.14
128 129 2.861147 AACTAGTGTTTCTGCCTCCC 57.139 50.000 0.00 0.00 31.37 4.30
148 149 0.250727 CGCCTCCTCCTCCACAAAAA 60.251 55.000 0.00 0.00 0.00 1.94
149 150 1.374947 CGCCTCCTCCTCCACAAAA 59.625 57.895 0.00 0.00 0.00 2.44
150 151 2.592993 CCGCCTCCTCCTCCACAAA 61.593 63.158 0.00 0.00 0.00 2.83
151 152 3.003173 CCGCCTCCTCCTCCACAA 61.003 66.667 0.00 0.00 0.00 3.33
164 165 4.470170 CTTTTTACCGCCGCCGCC 62.470 66.667 0.00 0.00 0.00 6.13
165 166 2.460837 TTTCTTTTTACCGCCGCCGC 62.461 55.000 0.00 0.00 0.00 6.53
166 167 0.453782 CTTTCTTTTTACCGCCGCCG 60.454 55.000 0.00 0.00 0.00 6.46
167 168 0.594602 ACTTTCTTTTTACCGCCGCC 59.405 50.000 0.00 0.00 0.00 6.13
168 169 2.410785 AACTTTCTTTTTACCGCCGC 57.589 45.000 0.00 0.00 0.00 6.53
169 170 6.637658 TGAAATAAACTTTCTTTTTACCGCCG 59.362 34.615 0.08 0.00 0.00 6.46
170 171 7.933728 TGAAATAAACTTTCTTTTTACCGCC 57.066 32.000 0.08 0.00 0.00 6.13
171 172 9.187455 TGATGAAATAAACTTTCTTTTTACCGC 57.813 29.630 0.08 0.00 0.00 5.68
215 216 8.587952 TCATACCATTGACAGTGTTAATATCG 57.412 34.615 12.47 6.56 0.00 2.92
322 332 9.036980 ACTTTATTCTCAATGAGTACCAGTAGT 57.963 33.333 10.36 4.27 0.00 2.73
323 333 9.522804 GACTTTATTCTCAATGAGTACCAGTAG 57.477 37.037 10.36 3.71 0.00 2.57
367 716 1.343142 ACCGGAACCAAAATGGCTTTC 59.657 47.619 9.46 0.00 42.67 2.62
371 720 1.374125 GCACCGGAACCAAAATGGC 60.374 57.895 9.46 0.00 42.67 4.40
383 732 2.393764 GTTTGAACTGAAATGCACCGG 58.606 47.619 0.00 0.00 0.00 5.28
396 745 1.798813 ACTCCATCTTCGCGTTTGAAC 59.201 47.619 5.77 0.00 0.00 3.18
428 777 1.434696 CAATCCCAACCATCGCTGC 59.565 57.895 0.00 0.00 0.00 5.25
455 804 1.332180 ACACGTCGCGTTGTGATACG 61.332 55.000 29.96 22.01 44.09 3.06
522 871 1.860950 CGTACGCATCATTGAAGGAGG 59.139 52.381 0.52 0.00 0.00 4.30
531 880 1.139816 CGTCTGCACGTACGCATCAT 61.140 55.000 16.72 0.00 42.06 2.45
549 898 1.977594 GCTTGCCCGTGGTATGAACG 61.978 60.000 0.00 0.00 40.70 3.95
555 904 1.481901 TTACCAGCTTGCCCGTGGTA 61.482 55.000 7.77 7.77 42.99 3.25
558 907 1.802636 CATTACCAGCTTGCCCGTG 59.197 57.895 0.00 0.00 0.00 4.94
674 1034 3.419759 CCGAAGCCGAACCAACCG 61.420 66.667 0.00 0.00 38.22 4.44
698 1058 2.483889 GCGGTACTCGGGTACTACTACT 60.484 54.545 24.19 0.00 45.41 2.57
699 1059 1.867865 GCGGTACTCGGGTACTACTAC 59.132 57.143 24.19 7.10 45.41 2.73
700 1060 1.762957 AGCGGTACTCGGGTACTACTA 59.237 52.381 24.19 0.00 45.41 1.82
734 1094 0.322098 TTGCCGAGTGTTATGGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
737 1097 1.308998 GGATTGCCGAGTGTTATGGG 58.691 55.000 0.00 0.00 0.00 4.00
779 1140 3.746949 GATCCGGGGCAGCAGTCAG 62.747 68.421 0.00 0.00 0.00 3.51
780 1141 3.785859 GATCCGGGGCAGCAGTCA 61.786 66.667 0.00 0.00 0.00 3.41
781 1142 3.746949 CTGATCCGGGGCAGCAGTC 62.747 68.421 0.00 0.00 0.00 3.51
782 1143 3.790437 CTGATCCGGGGCAGCAGT 61.790 66.667 0.00 0.00 0.00 4.40
804 1165 1.345715 ATTAACGCAGGGAGGGGAGG 61.346 60.000 0.00 0.00 33.80 4.30
806 1167 1.342672 GGATTAACGCAGGGAGGGGA 61.343 60.000 0.00 0.00 33.80 4.81
808 1169 1.148498 GGGATTAACGCAGGGAGGG 59.852 63.158 0.00 0.00 0.00 4.30
810 1171 0.810031 CACGGGATTAACGCAGGGAG 60.810 60.000 0.00 0.00 34.00 4.30
811 1172 1.219664 CACGGGATTAACGCAGGGA 59.780 57.895 0.00 0.00 34.00 4.20
812 1173 2.469516 GCACGGGATTAACGCAGGG 61.470 63.158 0.00 0.00 34.00 4.45
813 1174 2.469516 GGCACGGGATTAACGCAGG 61.470 63.158 0.00 0.00 34.00 4.85
814 1175 3.098555 GGCACGGGATTAACGCAG 58.901 61.111 0.00 0.00 34.00 5.18
852 1219 3.737172 GAAATGGGCGTGCGCACT 61.737 61.111 35.27 17.26 46.30 4.40
869 1236 1.623311 GGAGGTTTTGGTGGGGATTTG 59.377 52.381 0.00 0.00 0.00 2.32
883 1250 1.842381 CTGGCGGAAGGAAGGAGGTT 61.842 60.000 0.00 0.00 0.00 3.50
970 1337 1.476110 CCAGACCTCCTCCTAGACGAG 60.476 61.905 0.00 0.00 0.00 4.18
986 1353 0.382158 GTGCATCTCGTCGATCCAGA 59.618 55.000 0.00 0.00 0.00 3.86
1043 1434 0.604780 CCGGATGATGCTGATGGTCC 60.605 60.000 0.00 0.00 0.00 4.46
1060 1451 1.374252 CGTTCTTGGTGAGGTCCCG 60.374 63.158 0.00 0.00 0.00 5.14
1170 1570 3.172099 CTGCACACACGCACACAGG 62.172 63.158 0.00 0.00 36.86 4.00
1272 1676 2.540910 TCCAGGTCCTCCTCCCCT 60.541 66.667 0.00 0.00 43.07 4.79
1664 2068 4.180946 CCTCCTCCTCGTGCGACG 62.181 72.222 2.79 2.79 44.19 5.12
1731 2135 2.513259 TTGGTGGTGGTCGTCCTCC 61.513 63.158 12.18 12.18 44.92 4.30
1866 2270 1.814527 GACGACGAGGCCCAGTATT 59.185 57.895 0.00 0.00 0.00 1.89
1917 2333 1.290009 GTGTGATTGTGCTTGGCCC 59.710 57.895 0.00 0.00 0.00 5.80
2081 2498 6.479990 TGCAGGAAGTATCGAATACAAATGAG 59.520 38.462 0.00 0.00 38.21 2.90
2101 2589 1.334960 CGTTGTTTACAGCCTTGCAGG 60.335 52.381 0.00 0.00 38.80 4.85
2186 2677 5.132502 TGTCATCATACCAATGTTCCATCC 58.867 41.667 0.00 0.00 34.50 3.51
2198 2689 9.520204 CCAGAATTAAACATTTGTCATCATACC 57.480 33.333 0.00 0.00 0.00 2.73
2202 2697 7.093814 CCTCCCAGAATTAAACATTTGTCATCA 60.094 37.037 0.00 0.00 0.00 3.07
2203 2698 7.122650 TCCTCCCAGAATTAAACATTTGTCATC 59.877 37.037 0.00 0.00 0.00 2.92
2204 2699 6.953520 TCCTCCCAGAATTAAACATTTGTCAT 59.046 34.615 0.00 0.00 0.00 3.06
2205 2700 6.310941 TCCTCCCAGAATTAAACATTTGTCA 58.689 36.000 0.00 0.00 0.00 3.58
2206 2701 6.834168 TCCTCCCAGAATTAAACATTTGTC 57.166 37.500 0.00 0.00 0.00 3.18
2208 2703 7.123247 AGACATCCTCCCAGAATTAAACATTTG 59.877 37.037 0.00 0.00 0.00 2.32
2311 2983 3.637998 ACTGAAGCTTTGAATGCACAG 57.362 42.857 19.65 19.65 40.21 3.66
2335 3007 2.096496 GGGCGATCATCAACAGTTCAAG 59.904 50.000 0.00 0.00 0.00 3.02
2337 3009 1.678728 GGGGCGATCATCAACAGTTCA 60.679 52.381 0.00 0.00 0.00 3.18
2356 3028 3.028850 AGGTGAAAGCATTGATCCATGG 58.971 45.455 4.97 4.97 36.26 3.66
2441 3113 8.074370 CGATTACAAACTAGAATACGAGATGGA 58.926 37.037 0.00 0.00 0.00 3.41
2448 3120 7.745022 TTCACCGATTACAAACTAGAATACG 57.255 36.000 0.00 0.00 0.00 3.06
2451 3123 8.047310 AGGATTTCACCGATTACAAACTAGAAT 58.953 33.333 0.00 0.00 34.73 2.40
2452 3124 7.391620 AGGATTTCACCGATTACAAACTAGAA 58.608 34.615 0.00 0.00 34.73 2.10
2484 3318 7.872993 GGAATAATCCTCGATTACTCACAATGA 59.127 37.037 5.52 0.00 42.93 2.57
2565 3402 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
2566 3403 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
2569 3406 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2570 3407 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2571 3408 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2572 3409 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2573 3410 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2574 3411 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2575 3412 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2576 3413 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2577 3414 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2578 3415 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2579 3416 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2580 3417 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2581 3418 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2582 3419 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2583 3420 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2584 3421 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2585 3422 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2586 3423 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2587 3424 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2588 3425 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2589 3426 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2590 3427 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2591 3428 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2604 3441 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2605 3442 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2606 3443 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2607 3444 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2608 3445 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2609 3446 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2610 3447 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2611 3448 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2612 3449 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2613 3450 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2614 3451 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2615 3452 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2616 3453 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2617 3454 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2618 3455 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2619 3456 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2620 3457 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2621 3458 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2622 3459 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2623 3460 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2624 3461 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2625 3462 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2626 3463 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2627 3464 2.564062 TCCTCCGTTCCAAATTACTCGT 59.436 45.455 0.00 0.00 0.00 4.18
2628 3465 3.241067 TCCTCCGTTCCAAATTACTCG 57.759 47.619 0.00 0.00 0.00 4.18
2629 3466 4.576879 ACTTCCTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2630 3467 4.635699 ACTTCCTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2631 3468 4.874396 CCTACTTCCTCCGTTCCAAATTAC 59.126 45.833 0.00 0.00 0.00 1.89
2632 3469 4.533311 ACCTACTTCCTCCGTTCCAAATTA 59.467 41.667 0.00 0.00 0.00 1.40
2633 3470 3.329814 ACCTACTTCCTCCGTTCCAAATT 59.670 43.478 0.00 0.00 0.00 1.82
2634 3471 2.910977 ACCTACTTCCTCCGTTCCAAAT 59.089 45.455 0.00 0.00 0.00 2.32
2635 3472 2.332117 ACCTACTTCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
2636 3473 2.019807 ACCTACTTCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2637 3474 2.019807 AACCTACTTCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2638 3475 3.413846 AAAACCTACTTCCTCCGTTCC 57.586 47.619 0.00 0.00 0.00 3.62
2639 3476 5.545588 ACTAAAAACCTACTTCCTCCGTTC 58.454 41.667 0.00 0.00 0.00 3.95
2640 3477 5.557576 ACTAAAAACCTACTTCCTCCGTT 57.442 39.130 0.00 0.00 0.00 4.44
2641 3478 6.041979 TGTTACTAAAAACCTACTTCCTCCGT 59.958 38.462 0.00 0.00 0.00 4.69
2642 3479 6.458210 TGTTACTAAAAACCTACTTCCTCCG 58.542 40.000 0.00 0.00 0.00 4.63
2643 3480 7.716560 TGTTGTTACTAAAAACCTACTTCCTCC 59.283 37.037 0.21 0.00 0.00 4.30
2644 3481 8.667076 TGTTGTTACTAAAAACCTACTTCCTC 57.333 34.615 0.21 0.00 0.00 3.71
2645 3482 9.465199 TTTGTTGTTACTAAAAACCTACTTCCT 57.535 29.630 0.21 0.00 0.00 3.36
2715 3553 3.275999 CACATGATGACTTGATGAGCCA 58.724 45.455 0.00 0.00 0.00 4.75
2738 3576 8.130307 ACACTTTCATTTTCAGCACAAAATAC 57.870 30.769 5.55 0.00 34.77 1.89
2785 3623 7.464045 GCTTCAAAATGTTCTTTTAGCAAACGT 60.464 33.333 0.00 0.00 0.00 3.99
2786 3624 6.840789 GCTTCAAAATGTTCTTTTAGCAAACG 59.159 34.615 0.00 0.00 0.00 3.60
2798 3636 4.449068 TCAGAGACGAGCTTCAAAATGTTC 59.551 41.667 0.00 0.00 0.00 3.18
2830 3669 6.491745 TCAAAGTAAATTACCCATGTCAAGCA 59.508 34.615 0.00 0.00 0.00 3.91
2845 3684 4.324267 CGAGGAACAGGGTCAAAGTAAAT 58.676 43.478 0.00 0.00 0.00 1.40
2850 3689 0.035458 AGCGAGGAACAGGGTCAAAG 59.965 55.000 0.00 0.00 0.00 2.77
2863 3702 2.061028 GCATTTTGTTTTCCAGCGAGG 58.939 47.619 0.00 0.00 39.47 4.63
2894 3733 4.525949 GCCGGCCTCGTTAGGGAC 62.526 72.222 18.11 0.00 43.87 4.46
2912 3751 3.437795 CTTGGAGCTGCCTTGCGG 61.438 66.667 1.53 0.00 37.63 5.69
2913 3752 3.437795 CCTTGGAGCTGCCTTGCG 61.438 66.667 1.53 0.00 37.63 4.85
2914 3753 1.379576 ATCCTTGGAGCTGCCTTGC 60.380 57.895 1.53 0.00 37.63 4.01
2915 3754 0.750911 GGATCCTTGGAGCTGCCTTG 60.751 60.000 3.84 0.00 37.63 3.61
2916 3755 0.918310 AGGATCCTTGGAGCTGCCTT 60.918 55.000 9.02 0.00 37.63 4.35
2917 3756 1.307691 AGGATCCTTGGAGCTGCCT 60.308 57.895 9.02 1.86 37.63 4.75
2918 3757 1.153005 CAGGATCCTTGGAGCTGCC 60.153 63.158 13.00 0.00 37.10 4.85
2919 3758 0.463474 GACAGGATCCTTGGAGCTGC 60.463 60.000 13.00 0.00 0.00 5.25
2920 3759 1.138661 GAGACAGGATCCTTGGAGCTG 59.861 57.143 13.00 1.97 0.00 4.24
2921 3760 1.494960 GAGACAGGATCCTTGGAGCT 58.505 55.000 13.00 4.91 0.00 4.09
2922 3761 0.467804 GGAGACAGGATCCTTGGAGC 59.532 60.000 13.00 0.48 33.77 4.70
2923 3762 1.484240 GTGGAGACAGGATCCTTGGAG 59.516 57.143 13.00 2.98 44.46 3.86
2924 3763 1.573108 GTGGAGACAGGATCCTTGGA 58.427 55.000 13.00 0.00 44.46 3.53



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

AutoCloner maintained by Alex Coulton.