Multiple sequence alignment - TraesCS2D01G079500

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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 TraesCS2D01G079500 chr2D 100.000 2579 0 0 1 2579 33946587 33949165 0.000000e+00 4763
1 TraesCS2D01G079500 chr2D 92.941 85 6 0 1 85 634858863 634858779 9.690000e-25 124
2 TraesCS2D01G079500 chrUn 84.660 1043 80 41 893 1866 276814200 276813169 0.000000e+00 966
3 TraesCS2D01G079500 chrUn 94.643 112 4 2 2430 2539 276813155 276813044 3.410000e-39 172
4 TraesCS2D01G079500 chrUn 96.053 76 3 0 9 84 47459961 47460036 9.690000e-25 124
5 TraesCS2D01G079500 chr2B 84.660 1043 80 41 893 1866 56236400 56237431 0.000000e+00 966
6 TraesCS2D01G079500 chr2B 84.162 764 68 29 893 1623 56166000 56166743 0.000000e+00 691
7 TraesCS2D01G079500 chr2B 84.842 475 33 16 2127 2579 56167346 56167803 2.360000e-120 442
8 TraesCS2D01G079500 chr2B 88.168 262 26 4 575 833 56165737 56165996 8.960000e-80 307
9 TraesCS2D01G079500 chr2B 84.615 286 30 9 209 488 56165441 56165718 3.270000e-69 272
10 TraesCS2D01G079500 chr2B 85.845 219 27 3 611 827 56219422 56219638 2.000000e-56 230
11 TraesCS2D01G079500 chr2B 94.643 112 4 2 2430 2539 56237445 56237556 3.410000e-39 172
12 TraesCS2D01G079500 chr2B 85.294 136 16 3 1979 2113 56167226 56167358 1.240000e-28 137
13 TraesCS2D01G079500 chr2B 92.683 82 5 1 1 82 393024117 393024037 1.620000e-22 117
14 TraesCS2D01G079500 chr2A 88.131 733 55 17 961 1674 36880327 36881046 0.000000e+00 843
15 TraesCS2D01G079500 chr2A 86.605 433 45 9 2124 2546 36881779 36882208 1.400000e-127 466
16 TraesCS2D01G079500 chr2A 79.328 387 37 26 481 832 36879908 36880286 5.550000e-57 231
17 TraesCS2D01G079500 chr2A 82.873 181 31 0 1807 1987 646626846 646627026 2.050000e-36 163
18 TraesCS2D01G079500 chr7A 84.324 185 29 0 1803 1987 534442693 534442877 5.670000e-42 182
19 TraesCS2D01G079500 chr7A 82.162 185 33 0 1803 1987 214307106 214307290 2.660000e-35 159
20 TraesCS2D01G079500 chr6B 83.333 186 29 2 1803 1987 30352728 30352912 1.230000e-38 171
21 TraesCS2D01G079500 chr1D 83.333 180 30 0 1803 1982 36550607 36550786 1.590000e-37 167
22 TraesCS2D01G079500 chr3B 82.540 189 25 4 1803 1987 441626135 441625951 2.660000e-35 159
23 TraesCS2D01G079500 chr3B 93.750 80 5 0 1 80 5497675 5497754 1.250000e-23 121
24 TraesCS2D01G079500 chr5D 82.632 190 22 8 1803 1987 355210130 355209947 9.550000e-35 158
25 TraesCS2D01G079500 chr5D 81.720 186 32 2 1802 1987 344989278 344989095 1.240000e-33 154
26 TraesCS2D01G079500 chr5D 82.011 189 26 4 1803 1987 371278938 371278754 1.240000e-33 154
27 TraesCS2D01G079500 chr7D 91.667 84 7 0 1 84 56464450 56464367 1.620000e-22 117
28 TraesCS2D01G079500 chr7D 91.765 85 6 1 1 85 106718252 106718169 1.620000e-22 117
29 TraesCS2D01G079500 chr1B 91.566 83 7 0 1 83 41772372 41772454 5.830000e-22 115
30 TraesCS2D01G079500 chr1B 95.588 68 3 0 9 76 686736725 686736792 2.710000e-20 110
31 TraesCS2D01G079500 chr5A 87.000 100 11 2 1 100 358352583 358352486 7.540000e-21 111


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 TraesCS2D01G079500 chr2D 33946587 33949165 2578 False 4763.000000 4763 100.0000 1 2579 1 chr2D.!!$F1 2578
1 TraesCS2D01G079500 chrUn 276813044 276814200 1156 True 569.000000 966 89.6515 893 2539 2 chrUn.!!$R1 1646
2 TraesCS2D01G079500 chr2B 56236400 56237556 1156 False 569.000000 966 89.6515 893 2539 2 chr2B.!!$F3 1646
3 TraesCS2D01G079500 chr2B 56165441 56167803 2362 False 369.800000 691 85.4162 209 2579 5 chr2B.!!$F2 2370
4 TraesCS2D01G079500 chr2A 36879908 36882208 2300 False 513.333333 843 84.6880 481 2546 3 chr2A.!!$F2 2065

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
207 208 0.034186 AGGGGCATGCAATTTCTCGA 60.034 50.0 21.36 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 2325 0.824109 GTCATCGTCCCTCCATCACA 59.176 55.0 0.0 0.0 0.0 3.58 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
26 27 9.263538 CACTGTAGAGGTAGTAACATAGACTAG 57.736 40.741 0.00 0.00 30.08 2.57
27 28 8.991275 ACTGTAGAGGTAGTAACATAGACTAGT 58.009 37.037 0.00 0.00 30.08 2.57
64 65 9.359653 TGTTACTACTTTAAGTTACTCTCCACT 57.640 33.333 1.94 0.00 31.82 4.00
68 69 9.750783 ACTACTTTAAGTTACTCTCCACTATGA 57.249 33.333 1.94 0.00 0.00 2.15
70 71 7.838884 ACTTTAAGTTACTCTCCACTATGACC 58.161 38.462 0.00 0.00 0.00 4.02
71 72 7.453752 ACTTTAAGTTACTCTCCACTATGACCA 59.546 37.037 0.00 0.00 0.00 4.02
72 73 5.923733 AAGTTACTCTCCACTATGACCAG 57.076 43.478 0.00 0.00 0.00 4.00
73 74 3.702045 AGTTACTCTCCACTATGACCAGC 59.298 47.826 0.00 0.00 0.00 4.85
74 75 1.490574 ACTCTCCACTATGACCAGCC 58.509 55.000 0.00 0.00 0.00 4.85
75 76 1.007721 ACTCTCCACTATGACCAGCCT 59.992 52.381 0.00 0.00 0.00 4.58
76 77 1.686052 CTCTCCACTATGACCAGCCTC 59.314 57.143 0.00 0.00 0.00 4.70
77 78 1.007118 TCTCCACTATGACCAGCCTCA 59.993 52.381 0.00 0.00 0.00 3.86
78 79 1.137872 CTCCACTATGACCAGCCTCAC 59.862 57.143 0.00 0.00 0.00 3.51
79 80 0.904649 CCACTATGACCAGCCTCACA 59.095 55.000 0.00 0.00 0.00 3.58
80 81 1.406069 CCACTATGACCAGCCTCACAC 60.406 57.143 0.00 0.00 0.00 3.82
81 82 0.532573 ACTATGACCAGCCTCACACG 59.467 55.000 0.00 0.00 0.00 4.49
82 83 0.532573 CTATGACCAGCCTCACACGT 59.467 55.000 0.00 0.00 0.00 4.49
83 84 1.749063 CTATGACCAGCCTCACACGTA 59.251 52.381 0.00 0.00 0.00 3.57
84 85 0.246635 ATGACCAGCCTCACACGTAC 59.753 55.000 0.00 0.00 0.00 3.67
85 86 1.443872 GACCAGCCTCACACGTACG 60.444 63.158 15.01 15.01 0.00 3.67
86 87 2.126071 CCAGCCTCACACGTACGG 60.126 66.667 21.06 11.05 0.00 4.02
87 88 2.649034 CAGCCTCACACGTACGGT 59.351 61.111 21.06 11.73 0.00 4.83
95 96 4.563630 CACGTACGGTGCTGCTTA 57.436 55.556 21.06 0.00 40.33 3.09
96 97 2.817035 CACGTACGGTGCTGCTTAA 58.183 52.632 21.06 0.00 40.33 1.85
97 98 0.713883 CACGTACGGTGCTGCTTAAG 59.286 55.000 21.06 0.00 40.33 1.85
119 120 4.782019 CAAGGCAATTTGCTACTACCAA 57.218 40.909 20.06 0.00 44.28 3.67
120 121 5.132897 CAAGGCAATTTGCTACTACCAAA 57.867 39.130 20.06 0.00 44.28 3.28
121 122 5.537188 CAAGGCAATTTGCTACTACCAAAA 58.463 37.500 20.06 0.00 44.28 2.44
122 123 5.799827 AGGCAATTTGCTACTACCAAAAA 57.200 34.783 20.06 0.00 44.28 1.94
139 140 3.252979 AAAAATGGTCGTACCCCGG 57.747 52.632 0.00 0.00 37.50 5.73
140 141 0.322726 AAAAATGGTCGTACCCCGGG 60.323 55.000 15.80 15.80 37.50 5.73
141 142 2.825075 AAAATGGTCGTACCCCGGGC 62.825 60.000 17.73 0.00 37.50 6.13
161 162 4.626081 ACAGCCAGCTCGCGGTTT 62.626 61.111 6.13 0.00 33.07 3.27
162 163 4.093952 CAGCCAGCTCGCGGTTTG 62.094 66.667 6.13 1.64 0.00 2.93
163 164 4.314440 AGCCAGCTCGCGGTTTGA 62.314 61.111 6.13 0.00 0.00 2.69
164 165 3.353836 GCCAGCTCGCGGTTTGAA 61.354 61.111 6.13 0.00 0.00 2.69
165 166 2.556287 CCAGCTCGCGGTTTGAAC 59.444 61.111 6.13 0.00 0.00 3.18
166 167 2.250939 CCAGCTCGCGGTTTGAACA 61.251 57.895 6.13 0.00 0.00 3.18
167 168 1.205064 CAGCTCGCGGTTTGAACAG 59.795 57.895 6.13 0.00 0.00 3.16
168 169 2.127232 GCTCGCGGTTTGAACAGC 60.127 61.111 6.13 8.62 44.86 4.40
169 170 2.607892 GCTCGCGGTTTGAACAGCT 61.608 57.895 6.13 0.00 45.88 4.24
170 171 1.205064 CTCGCGGTTTGAACAGCTG 59.795 57.895 13.48 13.48 45.88 4.24
171 172 1.221466 CTCGCGGTTTGAACAGCTGA 61.221 55.000 23.35 12.63 45.88 4.26
172 173 1.082756 CGCGGTTTGAACAGCTGAC 60.083 57.895 23.35 14.31 45.88 3.51
173 174 1.771073 CGCGGTTTGAACAGCTGACA 61.771 55.000 23.35 16.83 45.88 3.58
174 175 0.380378 GCGGTTTGAACAGCTGACAA 59.620 50.000 23.35 21.46 44.88 3.18
175 176 1.597937 GCGGTTTGAACAGCTGACAAG 60.598 52.381 23.35 14.22 44.88 3.16
176 177 1.939934 CGGTTTGAACAGCTGACAAGA 59.060 47.619 23.35 12.96 0.00 3.02
177 178 2.286418 CGGTTTGAACAGCTGACAAGAC 60.286 50.000 23.35 20.96 0.00 3.01
178 179 2.033424 GGTTTGAACAGCTGACAAGACC 59.967 50.000 23.35 24.45 0.00 3.85
179 180 1.967319 TTGAACAGCTGACAAGACCC 58.033 50.000 23.35 0.47 0.00 4.46
180 181 0.249868 TGAACAGCTGACAAGACCCG 60.250 55.000 23.35 0.00 0.00 5.28
181 182 1.569479 GAACAGCTGACAAGACCCGC 61.569 60.000 23.35 0.00 0.00 6.13
182 183 2.743928 CAGCTGACAAGACCCGCC 60.744 66.667 8.42 0.00 0.00 6.13
183 184 4.379243 AGCTGACAAGACCCGCCG 62.379 66.667 0.00 0.00 0.00 6.46
184 185 4.373116 GCTGACAAGACCCGCCGA 62.373 66.667 0.00 0.00 0.00 5.54
185 186 2.342279 CTGACAAGACCCGCCGAA 59.658 61.111 0.00 0.00 0.00 4.30
186 187 1.301401 CTGACAAGACCCGCCGAAA 60.301 57.895 0.00 0.00 0.00 3.46
187 188 1.291877 CTGACAAGACCCGCCGAAAG 61.292 60.000 0.00 0.00 0.00 2.62
188 189 1.005394 GACAAGACCCGCCGAAAGA 60.005 57.895 0.00 0.00 0.00 2.52
189 190 1.004918 ACAAGACCCGCCGAAAGAG 60.005 57.895 0.00 0.00 0.00 2.85
190 191 1.741770 CAAGACCCGCCGAAAGAGG 60.742 63.158 0.00 0.00 0.00 3.69
198 199 2.045045 CCGAAAGAGGGGCATGCA 60.045 61.111 21.36 0.00 0.00 3.96
199 200 1.678635 CCGAAAGAGGGGCATGCAA 60.679 57.895 21.36 0.00 0.00 4.08
200 201 1.039233 CCGAAAGAGGGGCATGCAAT 61.039 55.000 21.36 3.85 0.00 3.56
201 202 0.819582 CGAAAGAGGGGCATGCAATT 59.180 50.000 21.36 3.08 0.00 2.32
202 203 1.205417 CGAAAGAGGGGCATGCAATTT 59.795 47.619 21.36 11.72 0.00 1.82
203 204 2.736400 CGAAAGAGGGGCATGCAATTTC 60.736 50.000 21.36 17.98 0.00 2.17
204 205 2.242882 AAGAGGGGCATGCAATTTCT 57.757 45.000 21.36 13.08 0.00 2.52
205 206 1.772836 AGAGGGGCATGCAATTTCTC 58.227 50.000 21.36 16.40 0.00 2.87
206 207 0.383231 GAGGGGCATGCAATTTCTCG 59.617 55.000 21.36 0.00 0.00 4.04
207 208 0.034186 AGGGGCATGCAATTTCTCGA 60.034 50.000 21.36 0.00 0.00 4.04
226 227 2.417933 CGACCTTGAATGAGCCTGAAAG 59.582 50.000 0.00 0.00 0.00 2.62
231 232 0.098376 GAATGAGCCTGAAAGCAGCG 59.902 55.000 0.00 0.00 40.91 5.18
261 262 1.787847 GAGTTGGCCATTGTCGACG 59.212 57.895 6.09 0.00 35.52 5.12
286 287 0.106335 CTGCTGTCTCTGGGCATAGG 59.894 60.000 0.00 0.00 35.37 2.57
312 321 0.709467 CAAATGTTTCATGGTGCGCG 59.291 50.000 0.00 0.00 0.00 6.86
313 322 1.008361 AAATGTTTCATGGTGCGCGC 61.008 50.000 27.26 27.26 0.00 6.86
314 323 2.817470 AATGTTTCATGGTGCGCGCC 62.817 55.000 32.83 32.83 0.00 6.53
337 346 2.586079 CCGATTCCGACGCAGCAT 60.586 61.111 0.00 0.00 38.22 3.79
363 372 3.990469 CCGCTCGAATTAGATGCATTAGT 59.010 43.478 0.00 0.00 0.00 2.24
364 373 4.143242 CCGCTCGAATTAGATGCATTAGTG 60.143 45.833 0.00 0.00 0.00 2.74
375 385 6.884280 AGATGCATTAGTGGCTTATTAACC 57.116 37.500 0.00 0.00 0.00 2.85
381 391 1.280998 AGTGGCTTATTAACCGGCTGT 59.719 47.619 0.00 0.00 0.00 4.40
392 402 3.114616 CGGCTGTCTGGTTCGCTG 61.115 66.667 0.00 0.00 0.00 5.18
399 409 0.601558 GTCTGGTTCGCTGACCTGTA 59.398 55.000 6.87 0.00 40.47 2.74
400 410 0.888619 TCTGGTTCGCTGACCTGTAG 59.111 55.000 6.87 0.00 40.47 2.74
401 411 0.603569 CTGGTTCGCTGACCTGTAGT 59.396 55.000 6.87 0.00 40.47 2.73
429 439 1.326548 CTTAATTGGGCTCGTACGTGC 59.673 52.381 28.92 28.92 0.00 5.34
455 465 1.001888 ATGCCATTGCCATCCACCA 59.998 52.632 0.00 0.00 36.33 4.17
456 466 1.046472 ATGCCATTGCCATCCACCAG 61.046 55.000 0.00 0.00 36.33 4.00
465 475 1.673626 GCCATCCACCAGCACATTTTG 60.674 52.381 0.00 0.00 0.00 2.44
475 485 3.591979 CACATTTTGCAGGTGGGTG 57.408 52.632 0.00 0.00 0.00 4.61
482 492 4.729918 GCAGGTGGGTGGCTCTGG 62.730 72.222 0.00 0.00 0.00 3.86
484 494 4.990910 AGGTGGGTGGCTCTGGCT 62.991 66.667 0.00 0.00 38.73 4.75
485 495 4.729918 GGTGGGTGGCTCTGGCTG 62.730 72.222 0.00 0.00 38.73 4.85
527 537 4.461431 CCATATACTGTTGCATGCATGGAT 59.539 41.667 27.34 18.13 34.84 3.41
532 545 1.746787 TGTTGCATGCATGGATGAGTC 59.253 47.619 29.10 17.18 0.00 3.36
540 553 2.426406 ATGGATGAGTCGGCAGCGA 61.426 57.895 0.00 0.00 0.00 4.93
543 556 1.587613 GATGAGTCGGCAGCGAGTC 60.588 63.158 11.82 11.82 38.44 3.36
567 593 4.873810 TGCCACAGCACGTTGGCT 62.874 61.111 25.08 12.14 46.52 4.75
600 631 5.525484 ACACAGTGGATGGAGGTAGTATAA 58.475 41.667 5.31 0.00 0.00 0.98
639 670 3.721706 GTGGAGTGGGAGCTGGGG 61.722 72.222 0.00 0.00 0.00 4.96
643 682 3.412624 GAGTGGGAGCTGGGGATGC 62.413 68.421 0.00 0.00 0.00 3.91
703 743 3.049227 GGCCAACCGCATTTTCATC 57.951 52.632 0.00 0.00 40.31 2.92
746 792 0.459489 GCTCAAGCTCTGACTCGGAT 59.541 55.000 0.00 0.00 38.21 4.18
748 794 1.066908 CTCAAGCTCTGACTCGGATCC 59.933 57.143 0.00 0.00 0.00 3.36
750 796 0.681564 AAGCTCTGACTCGGATCCGT 60.682 55.000 32.15 15.85 40.74 4.69
752 798 2.026522 CTCTGACTCGGATCCGTCC 58.973 63.158 32.15 21.55 41.40 4.79
753 799 0.748367 CTCTGACTCGGATCCGTCCA 60.748 60.000 32.15 24.41 45.37 4.02
755 801 1.001269 TGACTCGGATCCGTCCAGT 60.001 57.895 32.15 27.17 45.37 4.00
756 802 1.313091 TGACTCGGATCCGTCCAGTG 61.313 60.000 32.15 17.95 45.37 3.66
757 803 2.005960 GACTCGGATCCGTCCAGTGG 62.006 65.000 32.15 16.35 45.37 4.00
786 834 0.385029 CAGCTCGTCTCCATCTCCTG 59.615 60.000 0.00 0.00 0.00 3.86
833 881 6.434652 AGCTTCTTCGCCCGCTATATATATAT 59.565 38.462 10.10 10.10 0.00 0.86
834 882 7.610692 AGCTTCTTCGCCCGCTATATATATATA 59.389 37.037 11.21 11.21 0.00 0.86
835 883 8.407064 GCTTCTTCGCCCGCTATATATATATAT 58.593 37.037 17.37 17.37 33.68 0.86
934 982 1.144565 CTCGATCAAGTGAGCCTGCG 61.145 60.000 0.00 0.00 0.00 5.18
939 987 0.465460 TCAAGTGAGCCTGCGGTTTT 60.465 50.000 0.00 0.00 0.00 2.43
940 988 0.385390 CAAGTGAGCCTGCGGTTTTT 59.615 50.000 0.00 0.00 0.00 1.94
941 989 0.385390 AAGTGAGCCTGCGGTTTTTG 59.615 50.000 0.00 0.00 0.00 2.44
942 990 0.751643 AGTGAGCCTGCGGTTTTTGT 60.752 50.000 0.00 0.00 0.00 2.83
943 991 0.948678 GTGAGCCTGCGGTTTTTGTA 59.051 50.000 0.00 0.00 0.00 2.41
945 993 0.240145 GAGCCTGCGGTTTTTGTACC 59.760 55.000 0.00 0.00 34.72 3.34
946 994 0.179001 AGCCTGCGGTTTTTGTACCT 60.179 50.000 0.00 0.00 35.97 3.08
948 996 1.198408 GCCTGCGGTTTTTGTACCTAC 59.802 52.381 0.00 0.00 35.97 3.18
949 997 1.808343 CCTGCGGTTTTTGTACCTACC 59.192 52.381 0.00 0.00 35.97 3.18
951 999 3.078837 CTGCGGTTTTTGTACCTACCAT 58.921 45.455 0.00 0.00 35.97 3.55
952 1000 3.075884 TGCGGTTTTTGTACCTACCATC 58.924 45.455 0.00 0.00 35.97 3.51
953 1001 3.075884 GCGGTTTTTGTACCTACCATCA 58.924 45.455 0.00 0.00 35.97 3.07
957 1005 5.182380 CGGTTTTTGTACCTACCATCACATT 59.818 40.000 0.00 0.00 35.97 2.71
958 1006 6.617879 GGTTTTTGTACCTACCATCACATTC 58.382 40.000 0.00 0.00 35.23 2.67
959 1007 6.207810 GGTTTTTGTACCTACCATCACATTCA 59.792 38.462 0.00 0.00 35.23 2.57
1050 1112 2.743928 GTGCGTGCCCTCCTCTTG 60.744 66.667 0.00 0.00 0.00 3.02
1063 1125 2.920912 TCTTGGGCGTCTTCGGGT 60.921 61.111 0.00 0.00 37.56 5.28
1237 1302 2.364842 GCTCCTCCTCCTCCTGCA 60.365 66.667 0.00 0.00 0.00 4.41
1316 1399 1.540267 GCAGTACTGTGGAAGACGAGA 59.460 52.381 23.44 0.00 0.00 4.04
1443 1540 1.216710 CTGCCTCCAGGAGTTCGAC 59.783 63.158 15.86 0.22 37.39 4.20
1583 1702 0.531974 TCACACGGCTGTTGACCTTC 60.532 55.000 0.00 0.00 0.00 3.46
1588 1707 3.423154 GCTGTTGACCTTCCGGCG 61.423 66.667 0.00 0.00 0.00 6.46
1590 1709 1.738099 CTGTTGACCTTCCGGCGAG 60.738 63.158 9.30 0.00 0.00 5.03
1623 1743 4.630111 TGTGATTTCAGATGTTTTTGGCC 58.370 39.130 0.00 0.00 0.00 5.36
1626 1774 5.349543 GTGATTTCAGATGTTTTTGGCCATC 59.650 40.000 6.09 0.00 38.17 3.51
1719 2189 2.034558 CCAGTGAAAAGTCAACCGCAAT 59.965 45.455 0.00 0.00 34.87 3.56
1801 2284 6.423001 ACGAGCTTTGAATAGTAACTTTCGTT 59.577 34.615 0.00 0.00 33.23 3.85
1816 2299 2.536761 TCGTTTTCCCGACTGTCAAT 57.463 45.000 8.73 0.00 30.63 2.57
1822 2305 5.334569 CGTTTTCCCGACTGTCAATTACAAT 60.335 40.000 8.73 0.00 37.74 2.71
1825 2310 7.931578 TTTCCCGACTGTCAATTACAATAAT 57.068 32.000 8.73 0.00 37.74 1.28
1832 2317 8.764287 CGACTGTCAATTACAATAATATCTGCA 58.236 33.333 8.73 0.00 37.74 4.41
1899 2384 1.721926 GCTTCAGTGCTTGTAGTCGTC 59.278 52.381 0.00 0.00 0.00 4.20
1901 2386 0.386858 TCAGTGCTTGTAGTCGTCGC 60.387 55.000 0.00 0.00 0.00 5.19
1909 2394 1.063811 GTAGTCGTCGCTAGGTGGC 59.936 63.158 0.00 0.00 0.00 5.01
1914 2399 2.412112 GTCGCTAGGTGGCCTACG 59.588 66.667 3.32 0.00 34.61 3.51
1915 2400 2.831742 TCGCTAGGTGGCCTACGG 60.832 66.667 3.32 0.00 34.20 4.02
1921 2406 0.974010 TAGGTGGCCTACGGACTTGG 60.974 60.000 3.32 0.00 34.61 3.61
1922 2407 2.288025 GGTGGCCTACGGACTTGGA 61.288 63.158 3.32 0.00 0.00 3.53
1923 2408 1.623542 GGTGGCCTACGGACTTGGAT 61.624 60.000 3.32 0.00 0.00 3.41
1924 2409 0.462047 GTGGCCTACGGACTTGGATG 60.462 60.000 3.32 0.00 0.00 3.51
1925 2410 0.907704 TGGCCTACGGACTTGGATGT 60.908 55.000 3.32 0.00 0.00 3.06
1927 2412 1.483415 GGCCTACGGACTTGGATGTAA 59.517 52.381 0.00 0.00 0.00 2.41
1929 2414 3.391049 GCCTACGGACTTGGATGTAATC 58.609 50.000 0.00 0.00 44.55 1.75
1940 2425 7.281100 GGACTTGGATGTAATCTTTACTTCTGG 59.719 40.741 10.99 6.37 44.71 3.86
1952 2437 8.974060 ATCTTTACTTCTGGTGTTCTTTGTAA 57.026 30.769 0.00 0.00 0.00 2.41
1963 2448 9.988350 CTGGTGTTCTTTGTAATATATTGACAC 57.012 33.333 8.28 10.03 0.00 3.67
1988 2514 9.865321 ACTTGATGAATACATTGAAAGATTTGG 57.135 29.630 0.00 0.00 36.82 3.28
2034 2560 8.825745 TCTGGATGAAAAACAAAGTAAAATTGC 58.174 29.630 0.00 0.00 0.00 3.56
2043 2569 6.806120 ACAAAGTAAAATTGCAACTTCGAC 57.194 33.333 0.00 0.00 32.42 4.20
2046 2572 6.806120 AAGTAAAATTGCAACTTCGACAAC 57.194 33.333 0.00 0.00 0.00 3.32
2113 2639 8.677148 TTTTGCATAGAATACCATAGAAGTCC 57.323 34.615 0.00 0.00 0.00 3.85
2114 2640 6.360370 TGCATAGAATACCATAGAAGTCCC 57.640 41.667 0.00 0.00 0.00 4.46
2115 2641 5.248477 TGCATAGAATACCATAGAAGTCCCC 59.752 44.000 0.00 0.00 0.00 4.81
2116 2642 5.624738 GCATAGAATACCATAGAAGTCCCCG 60.625 48.000 0.00 0.00 0.00 5.73
2117 2643 4.194678 AGAATACCATAGAAGTCCCCGA 57.805 45.455 0.00 0.00 0.00 5.14
2118 2644 4.553678 AGAATACCATAGAAGTCCCCGAA 58.446 43.478 0.00 0.00 0.00 4.30
2119 2645 4.966805 AGAATACCATAGAAGTCCCCGAAA 59.033 41.667 0.00 0.00 0.00 3.46
2120 2646 5.427481 AGAATACCATAGAAGTCCCCGAAAA 59.573 40.000 0.00 0.00 0.00 2.29
2121 2647 5.703730 ATACCATAGAAGTCCCCGAAAAA 57.296 39.130 0.00 0.00 0.00 1.94
2183 2709 3.614616 GCGAGTATAATGCTAGACCATGC 59.385 47.826 0.00 0.00 0.00 4.06
2204 2730 5.806286 TGCTCGTTACAAAAAGTTTCAGAG 58.194 37.500 0.00 0.00 0.00 3.35
2253 2785 5.741011 TCAATGTGGGTATGACTAGGTTTC 58.259 41.667 0.00 0.00 0.00 2.78
2254 2786 5.249622 TCAATGTGGGTATGACTAGGTTTCA 59.750 40.000 0.00 0.00 0.00 2.69
2284 2831 9.863845 TGTATTTTCGTCTATGTTTCTCATGTA 57.136 29.630 0.00 0.00 37.91 2.29
2334 2881 4.898320 AGAAACCTTTTGATTGGATTGGC 58.102 39.130 0.00 0.00 0.00 4.52
2355 2902 2.092995 CACATGCATGAAAATGTTGCGG 59.907 45.455 32.75 1.77 39.23 5.69
2360 2907 0.595588 ATGAAAATGTTGCGGCGTCA 59.404 45.000 9.37 4.08 0.00 4.35
2367 2914 1.349627 GTTGCGGCGTCATCATCAG 59.650 57.895 9.37 0.00 0.00 2.90
2389 2936 5.123820 CAGAACCGCTTCCATTGAGATAAAA 59.876 40.000 0.00 0.00 0.00 1.52
2492 3039 8.912787 TTCACGCATTTTGAGTTTTTACTTTA 57.087 26.923 0.00 0.00 0.00 1.85
2547 3110 6.334102 ACAATTAGACAAATACCCGCAAAA 57.666 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.263538 CTAGTCTATGTTACTACCTCTACAGTG 57.736 40.741 0.00 0.00 0.00 3.66
1 2 8.991275 ACTAGTCTATGTTACTACCTCTACAGT 58.009 37.037 0.00 0.00 0.00 3.55
38 39 9.359653 AGTGGAGAGTAACTTAAAGTAGTAACA 57.640 33.333 0.00 0.00 0.00 2.41
42 43 9.750783 TCATAGTGGAGAGTAACTTAAAGTAGT 57.249 33.333 0.00 0.00 0.00 2.73
44 45 8.964772 GGTCATAGTGGAGAGTAACTTAAAGTA 58.035 37.037 0.00 0.00 0.00 2.24
45 46 7.453752 TGGTCATAGTGGAGAGTAACTTAAAGT 59.546 37.037 0.00 0.00 0.00 2.66
46 47 7.837863 TGGTCATAGTGGAGAGTAACTTAAAG 58.162 38.462 0.00 0.00 0.00 1.85
47 48 7.578955 GCTGGTCATAGTGGAGAGTAACTTAAA 60.579 40.741 0.00 0.00 0.00 1.52
48 49 6.127423 GCTGGTCATAGTGGAGAGTAACTTAA 60.127 42.308 0.00 0.00 0.00 1.85
49 50 5.360144 GCTGGTCATAGTGGAGAGTAACTTA 59.640 44.000 0.00 0.00 0.00 2.24
50 51 4.160626 GCTGGTCATAGTGGAGAGTAACTT 59.839 45.833 0.00 0.00 0.00 2.66
51 52 3.702045 GCTGGTCATAGTGGAGAGTAACT 59.298 47.826 0.00 0.00 0.00 2.24
52 53 3.181474 GGCTGGTCATAGTGGAGAGTAAC 60.181 52.174 0.00 0.00 0.00 2.50
53 54 3.031736 GGCTGGTCATAGTGGAGAGTAA 58.968 50.000 0.00 0.00 0.00 2.24
54 55 2.245028 AGGCTGGTCATAGTGGAGAGTA 59.755 50.000 0.00 0.00 0.00 2.59
55 56 1.007721 AGGCTGGTCATAGTGGAGAGT 59.992 52.381 0.00 0.00 0.00 3.24
56 57 1.686052 GAGGCTGGTCATAGTGGAGAG 59.314 57.143 0.00 0.00 0.00 3.20
57 58 1.007118 TGAGGCTGGTCATAGTGGAGA 59.993 52.381 0.00 0.00 0.00 3.71
58 59 1.137872 GTGAGGCTGGTCATAGTGGAG 59.862 57.143 0.00 0.00 0.00 3.86
59 60 1.195115 GTGAGGCTGGTCATAGTGGA 58.805 55.000 0.00 0.00 0.00 4.02
60 61 0.904649 TGTGAGGCTGGTCATAGTGG 59.095 55.000 0.00 0.00 0.00 4.00
61 62 1.737029 CGTGTGAGGCTGGTCATAGTG 60.737 57.143 0.00 0.00 0.00 2.74
62 63 0.532573 CGTGTGAGGCTGGTCATAGT 59.467 55.000 0.00 0.00 0.00 2.12
63 64 0.532573 ACGTGTGAGGCTGGTCATAG 59.467 55.000 0.00 0.00 0.00 2.23
64 65 1.475280 GTACGTGTGAGGCTGGTCATA 59.525 52.381 0.00 0.00 0.00 2.15
65 66 0.246635 GTACGTGTGAGGCTGGTCAT 59.753 55.000 0.00 0.00 0.00 3.06
66 67 1.663739 GTACGTGTGAGGCTGGTCA 59.336 57.895 0.00 0.00 0.00 4.02
67 68 1.443872 CGTACGTGTGAGGCTGGTC 60.444 63.158 7.22 0.00 0.00 4.02
68 69 2.649034 CGTACGTGTGAGGCTGGT 59.351 61.111 7.22 0.00 0.00 4.00
69 70 2.126071 CCGTACGTGTGAGGCTGG 60.126 66.667 15.21 0.00 0.00 4.85
70 71 1.733041 CACCGTACGTGTGAGGCTG 60.733 63.158 23.91 6.04 37.73 4.85
71 72 2.649034 CACCGTACGTGTGAGGCT 59.351 61.111 23.91 0.00 37.73 4.58
72 73 3.110178 GCACCGTACGTGTGAGGC 61.110 66.667 29.12 16.68 44.97 4.70
73 74 1.733041 CAGCACCGTACGTGTGAGG 60.733 63.158 29.12 19.68 44.97 3.86
74 75 2.372690 GCAGCACCGTACGTGTGAG 61.373 63.158 29.12 22.68 44.97 3.51
75 76 2.355363 GCAGCACCGTACGTGTGA 60.355 61.111 29.12 0.00 44.97 3.58
76 77 0.665068 TAAGCAGCACCGTACGTGTG 60.665 55.000 23.91 23.91 44.97 3.82
77 78 0.032403 TTAAGCAGCACCGTACGTGT 59.968 50.000 15.21 8.99 44.97 4.49
78 79 0.713883 CTTAAGCAGCACCGTACGTG 59.286 55.000 15.21 13.20 46.03 4.49
79 80 3.117589 CTTAAGCAGCACCGTACGT 57.882 52.632 15.21 0.00 0.00 3.57
88 89 5.249637 GCAAATTGCCTTGCTTAAGCAGC 62.250 47.826 27.82 27.08 46.66 5.25
89 90 2.414138 GCAAATTGCCTTGCTTAAGCAG 59.586 45.455 27.82 19.28 46.66 4.24
90 91 2.415776 GCAAATTGCCTTGCTTAAGCA 58.584 42.857 26.06 26.06 46.66 3.91
98 99 4.782019 TTGGTAGTAGCAAATTGCCTTG 57.218 40.909 15.04 0.00 46.52 3.61
99 100 5.799827 TTTTGGTAGTAGCAAATTGCCTT 57.200 34.783 24.02 3.10 46.52 4.35
100 101 5.799827 TTTTTGGTAGTAGCAAATTGCCT 57.200 34.783 24.02 8.11 46.52 4.75
144 145 4.626081 AAACCGCGAGCTGGCTGT 62.626 61.111 19.00 15.42 31.35 4.40
145 146 4.093952 CAAACCGCGAGCTGGCTG 62.094 66.667 19.00 14.72 0.00 4.85
146 147 3.825160 TTCAAACCGCGAGCTGGCT 62.825 57.895 19.00 0.00 0.00 4.75
147 148 3.353836 TTCAAACCGCGAGCTGGC 61.354 61.111 8.23 11.17 0.00 4.85
148 149 2.175184 CTGTTCAAACCGCGAGCTGG 62.175 60.000 8.23 0.00 0.00 4.85
149 150 1.205064 CTGTTCAAACCGCGAGCTG 59.795 57.895 8.23 0.54 0.00 4.24
150 151 2.607892 GCTGTTCAAACCGCGAGCT 61.608 57.895 8.23 0.00 29.78 4.09
151 152 2.127232 GCTGTTCAAACCGCGAGC 60.127 61.111 8.23 1.01 29.78 5.03
152 153 1.205064 CAGCTGTTCAAACCGCGAG 59.795 57.895 8.23 0.00 42.87 5.03
153 154 1.227409 TCAGCTGTTCAAACCGCGA 60.227 52.632 14.67 2.86 42.87 5.87
154 155 1.082756 GTCAGCTGTTCAAACCGCG 60.083 57.895 14.67 0.00 42.87 6.46
155 156 0.380378 TTGTCAGCTGTTCAAACCGC 59.620 50.000 14.67 1.53 39.11 5.68
156 157 1.939934 TCTTGTCAGCTGTTCAAACCG 59.060 47.619 14.67 9.07 0.00 4.44
157 158 2.033424 GGTCTTGTCAGCTGTTCAAACC 59.967 50.000 14.67 20.80 0.00 3.27
158 159 2.033424 GGGTCTTGTCAGCTGTTCAAAC 59.967 50.000 14.67 17.21 0.00 2.93
159 160 2.297701 GGGTCTTGTCAGCTGTTCAAA 58.702 47.619 14.67 8.73 0.00 2.69
160 161 1.810031 CGGGTCTTGTCAGCTGTTCAA 60.810 52.381 14.67 17.81 0.00 2.69
161 162 0.249868 CGGGTCTTGTCAGCTGTTCA 60.250 55.000 14.67 11.60 0.00 3.18
162 163 1.569479 GCGGGTCTTGTCAGCTGTTC 61.569 60.000 14.67 9.03 0.00 3.18
163 164 1.598130 GCGGGTCTTGTCAGCTGTT 60.598 57.895 14.67 0.00 0.00 3.16
164 165 2.031163 GCGGGTCTTGTCAGCTGT 59.969 61.111 14.67 0.00 0.00 4.40
165 166 2.743928 GGCGGGTCTTGTCAGCTG 60.744 66.667 7.63 7.63 0.00 4.24
166 167 4.379243 CGGCGGGTCTTGTCAGCT 62.379 66.667 0.00 0.00 0.00 4.24
167 168 3.876589 TTCGGCGGGTCTTGTCAGC 62.877 63.158 7.21 0.00 0.00 4.26
168 169 1.291877 CTTTCGGCGGGTCTTGTCAG 61.292 60.000 7.21 0.00 0.00 3.51
169 170 1.301401 CTTTCGGCGGGTCTTGTCA 60.301 57.895 7.21 0.00 0.00 3.58
170 171 1.005394 TCTTTCGGCGGGTCTTGTC 60.005 57.895 7.21 0.00 0.00 3.18
171 172 1.004918 CTCTTTCGGCGGGTCTTGT 60.005 57.895 7.21 0.00 0.00 3.16
172 173 1.741770 CCTCTTTCGGCGGGTCTTG 60.742 63.158 7.21 0.00 0.00 3.02
173 174 2.663196 CCTCTTTCGGCGGGTCTT 59.337 61.111 7.21 0.00 0.00 3.01
174 175 3.391382 CCCTCTTTCGGCGGGTCT 61.391 66.667 7.21 0.00 33.16 3.85
175 176 4.468689 CCCCTCTTTCGGCGGGTC 62.469 72.222 7.21 0.00 36.18 4.46
180 181 3.521796 GCATGCCCCTCTTTCGGC 61.522 66.667 6.36 0.00 45.92 5.54
181 182 1.039233 ATTGCATGCCCCTCTTTCGG 61.039 55.000 16.68 0.00 0.00 4.30
182 183 0.819582 AATTGCATGCCCCTCTTTCG 59.180 50.000 16.68 0.00 0.00 3.46
183 184 2.498885 AGAAATTGCATGCCCCTCTTTC 59.501 45.455 16.68 15.27 0.00 2.62
184 185 2.498885 GAGAAATTGCATGCCCCTCTTT 59.501 45.455 16.68 7.43 0.00 2.52
185 186 2.105766 GAGAAATTGCATGCCCCTCTT 58.894 47.619 16.68 1.10 0.00 2.85
186 187 1.772836 GAGAAATTGCATGCCCCTCT 58.227 50.000 16.68 11.55 0.00 3.69
187 188 0.383231 CGAGAAATTGCATGCCCCTC 59.617 55.000 16.68 12.49 0.00 4.30
188 189 0.034186 TCGAGAAATTGCATGCCCCT 60.034 50.000 16.68 4.68 0.00 4.79
189 190 0.101219 GTCGAGAAATTGCATGCCCC 59.899 55.000 16.68 0.00 0.00 5.80
190 191 0.101219 GGTCGAGAAATTGCATGCCC 59.899 55.000 16.68 0.36 0.00 5.36
191 192 1.098050 AGGTCGAGAAATTGCATGCC 58.902 50.000 16.68 0.00 0.00 4.40
192 193 2.162208 TCAAGGTCGAGAAATTGCATGC 59.838 45.455 11.82 11.82 0.00 4.06
193 194 4.424061 TTCAAGGTCGAGAAATTGCATG 57.576 40.909 0.00 0.00 0.00 4.06
194 195 4.701651 TCATTCAAGGTCGAGAAATTGCAT 59.298 37.500 0.00 0.00 0.00 3.96
195 196 4.071423 TCATTCAAGGTCGAGAAATTGCA 58.929 39.130 0.00 0.00 0.00 4.08
196 197 4.656041 CTCATTCAAGGTCGAGAAATTGC 58.344 43.478 0.00 0.00 0.00 3.56
197 198 4.437930 GGCTCATTCAAGGTCGAGAAATTG 60.438 45.833 0.00 0.00 0.00 2.32
198 199 3.691609 GGCTCATTCAAGGTCGAGAAATT 59.308 43.478 0.00 0.00 0.00 1.82
199 200 3.054802 AGGCTCATTCAAGGTCGAGAAAT 60.055 43.478 0.00 0.00 0.00 2.17
200 201 2.303022 AGGCTCATTCAAGGTCGAGAAA 59.697 45.455 0.00 0.00 0.00 2.52
201 202 1.902508 AGGCTCATTCAAGGTCGAGAA 59.097 47.619 0.00 0.00 0.00 2.87
202 203 1.205655 CAGGCTCATTCAAGGTCGAGA 59.794 52.381 0.00 0.00 0.00 4.04
203 204 1.205655 TCAGGCTCATTCAAGGTCGAG 59.794 52.381 0.00 0.00 0.00 4.04
204 205 1.266178 TCAGGCTCATTCAAGGTCGA 58.734 50.000 0.00 0.00 0.00 4.20
205 206 2.099141 TTCAGGCTCATTCAAGGTCG 57.901 50.000 0.00 0.00 0.00 4.79
206 207 2.163211 GCTTTCAGGCTCATTCAAGGTC 59.837 50.000 0.00 0.00 0.00 3.85
207 208 2.165998 GCTTTCAGGCTCATTCAAGGT 58.834 47.619 0.00 0.00 0.00 3.50
261 262 1.079266 CCAGAGACAGCAGCAGGAC 60.079 63.158 0.00 0.00 0.00 3.85
286 287 2.299867 ACCATGAAACATTTGGACCAGC 59.700 45.455 0.00 0.00 34.52 4.85
320 329 2.586079 ATGCTGCGTCGGAATCGG 60.586 61.111 0.00 0.00 36.95 4.18
322 331 1.218230 GAGGATGCTGCGTCGGAATC 61.218 60.000 15.13 7.35 0.00 2.52
323 332 1.227380 GAGGATGCTGCGTCGGAAT 60.227 57.895 15.13 1.95 0.00 3.01
324 333 2.184322 GAGGATGCTGCGTCGGAA 59.816 61.111 15.13 0.00 0.00 4.30
325 334 3.838271 GGAGGATGCTGCGTCGGA 61.838 66.667 15.13 0.00 0.00 4.55
328 337 4.521062 AGCGGAGGATGCTGCGTC 62.521 66.667 27.24 19.39 44.79 5.19
329 338 4.521062 GAGCGGAGGATGCTGCGT 62.521 66.667 27.24 15.19 44.18 5.24
331 340 2.985512 ATTCGAGCGGAGGATGCTGC 62.986 60.000 0.00 0.00 44.18 5.25
332 341 0.531532 AATTCGAGCGGAGGATGCTG 60.532 55.000 0.00 0.00 44.18 4.41
334 343 1.000163 TCTAATTCGAGCGGAGGATGC 60.000 52.381 0.00 0.00 0.00 3.91
337 346 1.000163 GCATCTAATTCGAGCGGAGGA 60.000 52.381 0.00 0.00 0.00 3.71
363 372 1.557832 AGACAGCCGGTTAATAAGCCA 59.442 47.619 1.90 0.00 0.00 4.75
364 373 1.940613 CAGACAGCCGGTTAATAAGCC 59.059 52.381 1.90 0.00 0.00 4.35
375 385 3.114616 CAGCGAACCAGACAGCCG 61.115 66.667 0.00 0.00 0.00 5.52
381 391 0.888619 CTACAGGTCAGCGAACCAGA 59.111 55.000 12.34 0.00 42.12 3.86
386 396 2.426024 GGATGTACTACAGGTCAGCGAA 59.574 50.000 0.00 0.00 0.00 4.70
392 402 7.210873 CCAATTAAGAGGATGTACTACAGGTC 58.789 42.308 0.00 0.00 0.00 3.85
399 409 4.202264 CGAGCCCAATTAAGAGGATGTACT 60.202 45.833 0.00 0.00 0.00 2.73
400 410 4.058817 CGAGCCCAATTAAGAGGATGTAC 58.941 47.826 0.00 0.00 0.00 2.90
401 411 3.709653 ACGAGCCCAATTAAGAGGATGTA 59.290 43.478 0.00 0.00 0.00 2.29
429 439 4.517815 GCAATGGCATGGCGGGTG 62.518 66.667 11.79 12.80 40.72 4.61
465 475 4.729918 CCAGAGCCACCCACCTGC 62.730 72.222 0.00 0.00 0.00 4.85
504 514 3.822167 TCCATGCATGCAACAGTATATGG 59.178 43.478 26.68 23.51 36.13 2.74
527 537 4.103103 CGACTCGCTGCCGACTCA 62.103 66.667 0.00 0.00 38.82 3.41
540 553 2.645567 CTGTGGCACGAGACGACT 59.354 61.111 13.77 0.00 0.00 4.18
567 593 3.055167 CCATCCACTGTGTAGATTCCACA 60.055 47.826 7.08 0.00 40.35 4.17
570 600 3.181461 CCTCCATCCACTGTGTAGATTCC 60.181 52.174 7.08 0.00 0.00 3.01
615 646 0.037232 GCTCCCACTCCACTGTACAC 60.037 60.000 0.00 0.00 0.00 2.90
617 648 0.247736 CAGCTCCCACTCCACTGTAC 59.752 60.000 0.00 0.00 0.00 2.90
639 670 2.663188 GACCGGCCTCATCGCATC 60.663 66.667 0.00 0.00 0.00 3.91
761 807 2.807045 GGAGACGAGCTGTGCGTG 60.807 66.667 3.40 0.00 42.77 5.34
762 808 2.549611 GATGGAGACGAGCTGTGCGT 62.550 60.000 0.00 0.00 45.79 5.24
774 822 1.306397 TGGCAGCAGGAGATGGAGA 60.306 57.895 0.00 0.00 0.00 3.71
775 823 1.153208 GTGGCAGCAGGAGATGGAG 60.153 63.158 0.00 0.00 0.00 3.86
786 834 1.814169 GGCTAACCTACGTGGCAGC 60.814 63.158 16.22 16.22 42.97 5.25
868 916 8.843262 ACGTAGTGTGTGTGTGTGTATATATAT 58.157 33.333 0.00 0.00 42.51 0.86
869 917 8.212317 ACGTAGTGTGTGTGTGTGTATATATA 57.788 34.615 0.00 0.00 42.51 0.86
870 918 7.092137 ACGTAGTGTGTGTGTGTGTATATAT 57.908 36.000 0.00 0.00 42.51 0.86
871 919 6.499234 ACGTAGTGTGTGTGTGTGTATATA 57.501 37.500 0.00 0.00 42.51 0.86
872 920 5.381174 ACGTAGTGTGTGTGTGTGTATAT 57.619 39.130 0.00 0.00 42.51 0.86
873 921 4.834357 ACGTAGTGTGTGTGTGTGTATA 57.166 40.909 0.00 0.00 42.51 1.47
874 922 3.720949 ACGTAGTGTGTGTGTGTGTAT 57.279 42.857 0.00 0.00 42.51 2.29
911 959 1.880340 GCTCACTTGATCGAGGGCG 60.880 63.158 14.65 6.37 39.35 6.13
934 982 6.207810 TGAATGTGATGGTAGGTACAAAAACC 59.792 38.462 0.00 0.00 40.06 3.27
939 987 5.491323 TGTGAATGTGATGGTAGGTACAA 57.509 39.130 0.00 0.00 0.00 2.41
940 988 5.188751 TGATGTGAATGTGATGGTAGGTACA 59.811 40.000 0.00 0.00 0.00 2.90
941 989 5.523916 GTGATGTGAATGTGATGGTAGGTAC 59.476 44.000 0.00 0.00 0.00 3.34
942 990 5.188751 TGTGATGTGAATGTGATGGTAGGTA 59.811 40.000 0.00 0.00 0.00 3.08
943 991 4.019411 TGTGATGTGAATGTGATGGTAGGT 60.019 41.667 0.00 0.00 0.00 3.08
945 993 6.426025 CCTATGTGATGTGAATGTGATGGTAG 59.574 42.308 0.00 0.00 0.00 3.18
946 994 6.290605 CCTATGTGATGTGAATGTGATGGTA 58.709 40.000 0.00 0.00 0.00 3.25
948 996 4.023450 GCCTATGTGATGTGAATGTGATGG 60.023 45.833 0.00 0.00 0.00 3.51
949 997 4.023450 GGCCTATGTGATGTGAATGTGATG 60.023 45.833 0.00 0.00 0.00 3.07
951 999 3.544684 GGCCTATGTGATGTGAATGTGA 58.455 45.455 0.00 0.00 0.00 3.58
952 1000 2.620115 GGGCCTATGTGATGTGAATGTG 59.380 50.000 0.84 0.00 0.00 3.21
953 1001 2.746142 CGGGCCTATGTGATGTGAATGT 60.746 50.000 0.84 0.00 0.00 2.71
957 1005 1.829456 CCGGGCCTATGTGATGTGA 59.171 57.895 0.84 0.00 0.00 3.58
958 1006 1.893808 GCCGGGCCTATGTGATGTG 60.894 63.158 8.12 0.00 0.00 3.21
959 1007 2.510906 GCCGGGCCTATGTGATGT 59.489 61.111 8.12 0.00 0.00 3.06
1164 1229 2.124653 TCGAGGGAGACGAGAGCC 60.125 66.667 0.00 0.00 34.85 4.70
1167 1232 1.221293 GAGGTCGAGGGAGACGAGA 59.779 63.158 0.00 0.00 41.81 4.04
1222 1287 2.039624 GGTGCAGGAGGAGGAGGA 59.960 66.667 0.00 0.00 0.00 3.71
1223 1288 3.465403 CGGTGCAGGAGGAGGAGG 61.465 72.222 0.00 0.00 0.00 4.30
1231 1296 4.467084 GATTCGCCCGGTGCAGGA 62.467 66.667 14.17 2.81 41.33 3.86
1232 1297 4.776322 TGATTCGCCCGGTGCAGG 62.776 66.667 14.17 0.00 41.33 4.85
1262 1345 4.717629 TCAGCTCGACAACGGCGG 62.718 66.667 13.24 0.00 39.38 6.13
1565 1662 1.507141 GGAAGGTCAACAGCCGTGTG 61.507 60.000 0.00 0.00 36.84 3.82
1583 1702 2.040544 AAATTGACCTGCTCGCCGG 61.041 57.895 0.00 0.00 0.00 6.13
1588 1707 5.048504 TCTGAAATCACAAATTGACCTGCTC 60.049 40.000 0.00 0.00 36.92 4.26
1590 1709 5.125100 TCTGAAATCACAAATTGACCTGC 57.875 39.130 0.00 0.00 36.92 4.85
1623 1743 1.714794 GGTGACCACGAACTGAGATG 58.285 55.000 0.00 0.00 0.00 2.90
1626 1774 1.372997 CCGGTGACCACGAACTGAG 60.373 63.158 1.11 0.00 0.00 3.35
1764 2240 6.408858 TTCAAAGCTCGTTTGCTATAGAAG 57.591 37.500 3.21 0.00 44.67 2.85
1765 2241 6.985188 ATTCAAAGCTCGTTTGCTATAGAA 57.015 33.333 3.21 0.00 44.67 2.10
1766 2242 7.265673 ACTATTCAAAGCTCGTTTGCTATAGA 58.734 34.615 3.21 8.17 44.67 1.98
1801 2284 7.931578 ATTATTGTAATTGACAGTCGGGAAA 57.068 32.000 0.00 0.00 39.88 3.13
1816 2299 8.941977 ACAAAAGTCGTGCAGATATTATTGTAA 58.058 29.630 0.00 0.00 0.00 2.41
1822 2305 6.037062 CCATCACAAAAGTCGTGCAGATATTA 59.963 38.462 0.00 0.00 34.27 0.98
1825 2310 3.684305 CCATCACAAAAGTCGTGCAGATA 59.316 43.478 0.00 0.00 34.27 1.98
1832 2317 1.697432 TCCCTCCATCACAAAAGTCGT 59.303 47.619 0.00 0.00 0.00 4.34
1840 2325 0.824109 GTCATCGTCCCTCCATCACA 59.176 55.000 0.00 0.00 0.00 3.58
1880 2365 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
1914 2399 7.281100 CCAGAAGTAAAGATTACATCCAAGTCC 59.719 40.741 3.37 0.00 0.00 3.85
1915 2400 7.824779 ACCAGAAGTAAAGATTACATCCAAGTC 59.175 37.037 3.37 0.00 0.00 3.01
1921 2406 8.779354 AGAACACCAGAAGTAAAGATTACATC 57.221 34.615 3.37 1.02 0.00 3.06
1922 2407 9.574516 AAAGAACACCAGAAGTAAAGATTACAT 57.425 29.630 3.37 0.00 0.00 2.29
1923 2408 8.836413 CAAAGAACACCAGAAGTAAAGATTACA 58.164 33.333 3.37 0.00 0.00 2.41
1924 2409 8.837389 ACAAAGAACACCAGAAGTAAAGATTAC 58.163 33.333 0.00 0.00 0.00 1.89
1925 2410 8.974060 ACAAAGAACACCAGAAGTAAAGATTA 57.026 30.769 0.00 0.00 0.00 1.75
1927 2412 8.974060 TTACAAAGAACACCAGAAGTAAAGAT 57.026 30.769 0.00 0.00 0.00 2.40
1980 2506 8.617290 AACACGAAAGTTACTATCCAAATCTT 57.383 30.769 0.00 0.00 46.40 2.40
1988 2514 7.088905 TCCAGAAGAACACGAAAGTTACTATC 58.911 38.462 0.00 0.00 46.40 2.08
1990 2516 6.395426 TCCAGAAGAACACGAAAGTTACTA 57.605 37.500 0.00 0.00 46.40 1.82
1991 2517 5.272283 TCCAGAAGAACACGAAAGTTACT 57.728 39.130 0.00 0.00 46.40 2.24
2034 2560 8.636843 GTGTTACTATTCTAGTTGTCGAAGTTG 58.363 37.037 0.00 0.00 40.14 3.16
2120 2646 8.793592 GGTGAAATGACTTCTATGGTAGTTTTT 58.206 33.333 0.00 0.00 34.86 1.94
2121 2647 7.119262 CGGTGAAATGACTTCTATGGTAGTTTT 59.881 37.037 0.00 0.00 34.86 2.43
2122 2648 6.594159 CGGTGAAATGACTTCTATGGTAGTTT 59.406 38.462 0.00 0.00 34.86 2.66
2123 2649 6.106673 CGGTGAAATGACTTCTATGGTAGTT 58.893 40.000 0.00 0.00 34.86 2.24
2124 2650 5.661458 CGGTGAAATGACTTCTATGGTAGT 58.339 41.667 0.00 0.00 34.86 2.73
2125 2651 4.508124 GCGGTGAAATGACTTCTATGGTAG 59.492 45.833 0.00 0.00 34.86 3.18
2171 2697 1.822371 TGTAACGAGCATGGTCTAGCA 59.178 47.619 21.73 12.37 0.00 3.49
2183 2709 6.049263 AGCTCTGAAACTTTTTGTAACGAG 57.951 37.500 0.00 0.00 0.00 4.18
2241 2767 8.450964 CGAAAATACACAATGAAACCTAGTCAT 58.549 33.333 0.00 0.00 37.31 3.06
2242 2768 7.442969 ACGAAAATACACAATGAAACCTAGTCA 59.557 33.333 0.00 0.00 0.00 3.41
2253 2785 9.478019 GAGAAACATAGACGAAAATACACAATG 57.522 33.333 0.00 0.00 0.00 2.82
2254 2786 9.214957 TGAGAAACATAGACGAAAATACACAAT 57.785 29.630 0.00 0.00 0.00 2.71
2284 2831 9.696917 GAAAAATGAAAGATAACATGGAAGTGT 57.303 29.630 0.00 0.00 0.00 3.55
2309 2856 6.523840 CCAATCCAATCAAAAGGTTTCTTGA 58.476 36.000 0.00 0.00 36.08 3.02
2334 2881 2.092995 CCGCAACATTTTCATGCATGTG 59.907 45.455 25.43 18.30 40.04 3.21
2355 2902 0.807667 AGCGGTTCTGATGATGACGC 60.808 55.000 0.00 0.00 45.15 5.19
2360 2907 2.947652 CAATGGAAGCGGTTCTGATGAT 59.052 45.455 25.05 8.47 32.72 2.45
2367 2914 5.560966 TTTTATCTCAATGGAAGCGGTTC 57.439 39.130 18.86 18.86 0.00 3.62
2421 2968 6.786122 TGGGGTATATTATAAGGGTTTGCTC 58.214 40.000 0.00 0.00 0.00 4.26
2492 3039 6.151985 TGCGGGTATTTGTCTAATTGATTGTT 59.848 34.615 0.00 0.00 0.00 2.83
2524 3087 5.968528 TTTGCGGGTATTTGTCTAATTGT 57.031 34.783 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.