Multiple sequence alignment - TraesCS5D01G357900

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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 TraesCS5D01G357900 chr5D 100.000 2867 0 0 1 2867 438436819 438433953 0.000000e+00 5295.0
1 TraesCS5D01G357900 chr5D 97.436 312 6 2 2333 2642 514940010 514940321 5.440000e-147 531.0
2 TraesCS5D01G357900 chr5D 98.649 148 2 0 2720 2867 514940320 514940467 2.190000e-66 263.0
3 TraesCS5D01G357900 chr5D 90.173 173 15 2 723 894 447821911 447821740 1.030000e-54 224.0
4 TraesCS5D01G357900 chr5A 94.989 938 43 2 893 1827 553487839 553486903 0.000000e+00 1469.0
5 TraesCS5D01G357900 chr5A 89.122 524 25 8 209 731 553488337 553487845 8.720000e-175 623.0
6 TraesCS5D01G357900 chr5A 88.386 508 55 2 2364 2867 13506787 13507294 2.440000e-170 608.0
7 TraesCS5D01G357900 chr5A 89.560 182 19 0 1841 2022 553480822 553480641 6.180000e-57 231.0
8 TraesCS5D01G357900 chr5A 73.768 629 135 22 1061 1671 554085261 554084645 1.340000e-53 220.0
9 TraesCS5D01G357900 chr7D 99.239 394 3 0 2474 2867 4654092 4653699 0.000000e+00 712.0
10 TraesCS5D01G357900 chr7D 90.795 478 26 5 2399 2867 154642842 154643310 8.720000e-175 623.0
11 TraesCS5D01G357900 chr7D 94.152 171 10 0 730 900 5033801 5033971 7.880000e-66 261.0
12 TraesCS5D01G357900 chr7D 94.611 167 9 0 730 896 54541055 54541221 2.830000e-65 259.0
13 TraesCS5D01G357900 chr7D 85.792 183 24 2 713 895 459386790 459386970 2.920000e-45 193.0
14 TraesCS5D01G357900 chr7D 85.165 182 22 3 716 895 2093811 2093989 6.310000e-42 182.0
15 TraesCS5D01G357900 chr7D 85.000 180 20 5 717 894 508895771 508895597 2.940000e-40 176.0
16 TraesCS5D01G357900 chr7D 88.462 78 5 4 153 227 325333873 325333949 1.090000e-14 91.6
17 TraesCS5D01G357900 chr5B 92.672 464 32 2 1364 1827 533020514 533020053 0.000000e+00 667.0
18 TraesCS5D01G357900 chr5B 90.147 477 43 2 893 1366 533032751 533032276 4.060000e-173 617.0
19 TraesCS5D01G357900 chr5B 84.516 465 48 12 2343 2792 15074336 15073881 3.390000e-119 438.0
20 TraesCS5D01G357900 chr5B 90.244 287 19 5 2061 2339 533019144 533018859 1.620000e-97 366.0
21 TraesCS5D01G357900 chr5B 85.027 374 39 9 2505 2866 15127990 15127622 5.840000e-97 364.0
22 TraesCS5D01G357900 chr5B 84.054 370 41 12 2505 2866 15094027 15093668 9.840000e-90 340.0
23 TraesCS5D01G357900 chr5B 86.254 291 33 4 443 728 533033045 533032757 2.770000e-80 309.0
24 TraesCS5D01G357900 chr5B 89.674 184 11 5 208 391 533033217 533033042 7.990000e-56 228.0
25 TraesCS5D01G357900 chr5B 82.119 151 7 10 1 150 533033361 533033230 8.400000e-21 111.0
26 TraesCS5D01G357900 chr3A 89.507 467 38 3 2364 2820 588948359 588948824 5.320000e-162 580.0
27 TraesCS5D01G357900 chr1A 85.000 540 49 17 2334 2867 4638787 4639300 1.180000e-143 520.0
28 TraesCS5D01G357900 chr1A 83.957 187 28 2 709 895 507257398 507257214 8.160000e-41 178.0
29 TraesCS5D01G357900 chr1A 95.238 63 1 2 153 213 543651782 543651844 6.540000e-17 99.0
30 TraesCS5D01G357900 chr6D 88.177 406 23 9 2468 2867 71121751 71122137 7.240000e-126 460.0
31 TraesCS5D01G357900 chr6D 85.000 180 19 6 2349 2521 327348962 327349140 2.940000e-40 176.0
32 TraesCS5D01G357900 chr6D 88.608 79 5 4 153 228 193466589 193466666 3.040000e-15 93.5
33 TraesCS5D01G357900 chr6D 87.342 79 6 4 153 228 309794079 309794156 1.420000e-13 87.9
34 TraesCS5D01G357900 chr7B 91.718 326 16 3 2544 2867 117021608 117021292 2.620000e-120 442.0
35 TraesCS5D01G357900 chr7B 92.537 67 3 2 157 221 275202836 275202902 8.460000e-16 95.3
36 TraesCS5D01G357900 chr2B 75.431 871 166 33 986 1823 65045458 65046313 2.080000e-101 379.0
37 TraesCS5D01G357900 chr2B 95.495 111 5 0 2343 2453 24922183 24922073 8.160000e-41 178.0
38 TraesCS5D01G357900 chr2D 75.235 852 170 32 986 1813 37277834 37278668 1.620000e-97 366.0
39 TraesCS5D01G357900 chr2D 96.407 167 6 0 730 896 613424402 613424236 2.810000e-70 276.0
40 TraesCS5D01G357900 chr2D 96.364 165 6 0 730 894 288620474 288620638 3.640000e-69 272.0
41 TraesCS5D01G357900 chr2D 91.892 74 5 1 574 647 12629342 12629270 5.050000e-18 102.0
42 TraesCS5D01G357900 chr2D 86.458 96 8 2 574 665 12635012 12634918 1.820000e-17 100.0
43 TraesCS5D01G357900 chr2D 93.939 66 3 1 153 217 179127649 179127584 6.540000e-17 99.0
44 TraesCS5D01G357900 chr2D 93.750 64 3 1 153 215 155510449 155510512 8.460000e-16 95.3
45 TraesCS5D01G357900 chr2D 87.342 79 6 4 153 228 268205381 268205304 1.420000e-13 87.9
46 TraesCS5D01G357900 chr2A 74.938 806 167 22 1040 1823 14723347 14722555 1.270000e-88 337.0
47 TraesCS5D01G357900 chr2A 85.484 186 22 5 713 897 755112028 755112209 3.770000e-44 189.0
48 TraesCS5D01G357900 chr2A 87.500 96 7 3 574 665 14733250 14733156 3.910000e-19 106.0
49 TraesCS5D01G357900 chr2A 91.892 74 5 1 574 647 14693692 14693620 5.050000e-18 102.0
50 TraesCS5D01G357900 chr2A 90.541 74 6 1 574 647 14714660 14714588 2.350000e-16 97.1
51 TraesCS5D01G357900 chr2A 86.517 89 7 2 583 667 14723688 14723601 3.040000e-15 93.5
52 TraesCS5D01G357900 chr2A 84.375 96 10 2 574 665 14725134 14725040 3.930000e-14 89.8
53 TraesCS5D01G357900 chr6B 88.703 239 19 3 2371 2603 145885029 145885265 4.680000e-73 285.0
54 TraesCS5D01G357900 chr6B 87.709 179 22 0 716 894 25247821 25247999 2.890000e-50 209.0
55 TraesCS5D01G357900 chr4D 94.944 178 8 1 723 899 109243695 109243872 7.820000e-71 278.0
56 TraesCS5D01G357900 chr4D 95.152 165 8 0 735 899 83291762 83291598 7.880000e-66 261.0
57 TraesCS5D01G357900 chr3D 95.758 165 7 0 730 894 6669553 6669717 1.690000e-67 267.0
58 TraesCS5D01G357900 chr3D 93.678 174 9 2 723 894 95568169 95568342 2.830000e-65 259.0
59 TraesCS5D01G357900 chr3D 85.556 180 18 6 2349 2521 436251412 436251590 6.310000e-42 182.0
60 TraesCS5D01G357900 chr1D 94.578 166 9 0 729 894 404282252 404282087 1.020000e-64 257.0
61 TraesCS5D01G357900 chr4B 87.778 180 19 3 716 894 654706596 654706773 1.040000e-49 207.0
62 TraesCS5D01G357900 chr4A 86.740 181 21 3 716 895 627753285 627753107 6.270000e-47 198.0
63 TraesCS5D01G357900 chr1B 88.235 102 12 0 2766 2867 645353362 645353261 3.880000e-24 122.0
64 TraesCS5D01G357900 chr1B 90.278 72 4 3 153 222 348397254 348397184 1.090000e-14 91.6


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 TraesCS5D01G357900 chr5D 438433953 438436819 2866 True 5295.00 5295 100.0000 1 2867 1 chr5D.!!$R1 2866
1 TraesCS5D01G357900 chr5A 553486903 553488337 1434 True 1046.00 1469 92.0555 209 1827 2 chr5A.!!$R3 1618
2 TraesCS5D01G357900 chr5A 13506787 13507294 507 False 608.00 608 88.3860 2364 2867 1 chr5A.!!$F1 503
3 TraesCS5D01G357900 chr5A 554084645 554085261 616 True 220.00 220 73.7680 1061 1671 1 chr5A.!!$R2 610
4 TraesCS5D01G357900 chr5B 533018859 533020514 1655 True 516.50 667 91.4580 1364 2339 2 chr5B.!!$R4 975
5 TraesCS5D01G357900 chr5B 533032276 533033361 1085 True 316.25 617 87.0485 1 1366 4 chr5B.!!$R5 1365
6 TraesCS5D01G357900 chr1A 4638787 4639300 513 False 520.00 520 85.0000 2334 2867 1 chr1A.!!$F1 533
7 TraesCS5D01G357900 chr2B 65045458 65046313 855 False 379.00 379 75.4310 986 1823 1 chr2B.!!$F1 837
8 TraesCS5D01G357900 chr2D 37277834 37278668 834 False 366.00 366 75.2350 986 1813 1 chr2D.!!$F1 827

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
42 43 0.179094 AACGTGTGCGGTTTCTCTCA 60.179 50.0 0.0 0.0 43.45 3.27 F
43 44 0.179094 ACGTGTGCGGTTTCTCTCAA 60.179 50.0 0.0 0.0 43.45 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1523 0.255318 AGCTTCATGCCAGGAAGGAG 59.745 55.0 19.53 0.00 44.23 3.69 R
2028 2779 0.391130 TGATGTACCGAAGCTGGTGC 60.391 55.0 5.99 5.25 43.68 5.01 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
31 32 4.477302 ACTTGGTTAATGTAACGTGTGC 57.523 40.909 0.00 0.00 39.54 4.57
42 43 0.179094 AACGTGTGCGGTTTCTCTCA 60.179 50.000 0.00 0.00 43.45 3.27
43 44 0.179094 ACGTGTGCGGTTTCTCTCAA 60.179 50.000 0.00 0.00 43.45 3.02
44 45 0.232303 CGTGTGCGGTTTCTCTCAAC 59.768 55.000 0.00 0.00 0.00 3.18
45 46 1.295792 GTGTGCGGTTTCTCTCAACA 58.704 50.000 0.00 0.00 0.00 3.33
53 54 6.640907 GTGCGGTTTCTCTCAACAAAATAAAT 59.359 34.615 0.00 0.00 0.00 1.40
56 57 9.187455 GCGGTTTCTCTCAACAAAATAAATAAA 57.813 29.630 0.00 0.00 0.00 1.40
68 69 9.757227 AACAAAATAAATAAACAGCTAACAGCA 57.243 25.926 0.38 0.00 45.56 4.41
69 70 9.757227 ACAAAATAAATAAACAGCTAACAGCAA 57.243 25.926 0.38 0.00 45.56 3.91
73 74 6.769608 AAATAAACAGCTAACAGCAAAAGC 57.230 33.333 0.38 0.00 45.56 3.51
74 75 2.800881 AACAGCTAACAGCAAAAGCC 57.199 45.000 0.38 0.00 45.56 4.35
75 76 1.986882 ACAGCTAACAGCAAAAGCCT 58.013 45.000 0.38 0.00 45.56 4.58
76 77 3.140325 ACAGCTAACAGCAAAAGCCTA 57.860 42.857 0.38 0.00 45.56 3.93
77 78 3.486383 ACAGCTAACAGCAAAAGCCTAA 58.514 40.909 0.38 0.00 45.56 2.69
78 79 3.253432 ACAGCTAACAGCAAAAGCCTAAC 59.747 43.478 0.38 0.00 45.56 2.34
108 109 4.703897 ACAAACGATGAACTGAAAGAGGA 58.296 39.130 0.00 0.00 37.43 3.71
109 110 4.752101 ACAAACGATGAACTGAAAGAGGAG 59.248 41.667 0.00 0.00 37.43 3.69
110 111 2.966050 ACGATGAACTGAAAGAGGAGC 58.034 47.619 0.00 0.00 37.43 4.70
116 117 0.839853 ACTGAAAGAGGAGCCTGCCT 60.840 55.000 0.00 0.00 42.17 4.75
138 139 5.882000 CCTCCATCATTGTACAGTTTGATCA 59.118 40.000 12.49 0.00 0.00 2.92
150 151 9.725019 TGTACAGTTTGATCATTTTCTCAGTAT 57.275 29.630 0.00 0.00 0.00 2.12
153 154 9.512588 ACAGTTTGATCATTTTCTCAGTATTCT 57.487 29.630 0.00 0.00 0.00 2.40
154 155 9.985318 CAGTTTGATCATTTTCTCAGTATTCTC 57.015 33.333 0.00 0.00 0.00 2.87
155 156 9.956640 AGTTTGATCATTTTCTCAGTATTCTCT 57.043 29.630 0.00 0.00 0.00 3.10
161 162 9.612066 ATCATTTTCTCAGTATTCTCTTTCTCC 57.388 33.333 0.00 0.00 0.00 3.71
162 163 8.820831 TCATTTTCTCAGTATTCTCTTTCTCCT 58.179 33.333 0.00 0.00 0.00 3.69
163 164 9.097257 CATTTTCTCAGTATTCTCTTTCTCCTC 57.903 37.037 0.00 0.00 0.00 3.71
164 165 8.429237 TTTTCTCAGTATTCTCTTTCTCCTCT 57.571 34.615 0.00 0.00 0.00 3.69
165 166 8.429237 TTTCTCAGTATTCTCTTTCTCCTCTT 57.571 34.615 0.00 0.00 0.00 2.85
166 167 9.535170 TTTCTCAGTATTCTCTTTCTCCTCTTA 57.465 33.333 0.00 0.00 0.00 2.10
167 168 9.707957 TTCTCAGTATTCTCTTTCTCCTCTTAT 57.292 33.333 0.00 0.00 0.00 1.73
168 169 9.707957 TCTCAGTATTCTCTTTCTCCTCTTATT 57.292 33.333 0.00 0.00 0.00 1.40
180 181 9.282569 CTTTCTCCTCTTATTTAATGGATGAGG 57.717 37.037 0.00 0.00 40.47 3.86
181 182 6.773638 TCTCCTCTTATTTAATGGATGAGGC 58.226 40.000 0.00 0.00 39.36 4.70
182 183 6.329986 TCTCCTCTTATTTAATGGATGAGGCA 59.670 38.462 0.00 0.00 39.36 4.75
183 184 6.910191 TCCTCTTATTTAATGGATGAGGCAA 58.090 36.000 0.00 0.00 39.36 4.52
184 185 7.353525 TCCTCTTATTTAATGGATGAGGCAAA 58.646 34.615 0.00 0.00 39.36 3.68
185 186 8.006564 TCCTCTTATTTAATGGATGAGGCAAAT 58.993 33.333 0.00 0.00 39.36 2.32
186 187 8.645110 CCTCTTATTTAATGGATGAGGCAAATT 58.355 33.333 0.00 0.00 34.16 1.82
188 189 9.820725 TCTTATTTAATGGATGAGGCAAATTTG 57.179 29.630 14.03 14.03 0.00 2.32
189 190 9.603921 CTTATTTAATGGATGAGGCAAATTTGT 57.396 29.630 19.03 0.26 0.00 2.83
190 191 9.956640 TTATTTAATGGATGAGGCAAATTTGTT 57.043 25.926 19.03 8.37 0.00 2.83
191 192 7.670009 TTTAATGGATGAGGCAAATTTGTTG 57.330 32.000 19.03 0.00 0.00 3.33
192 193 3.042871 TGGATGAGGCAAATTTGTTGC 57.957 42.857 19.03 6.05 44.22 4.17
198 199 3.586430 GCAAATTTGTTGCCTCCGT 57.414 47.368 19.03 0.00 39.38 4.69
199 200 1.864565 GCAAATTTGTTGCCTCCGTT 58.135 45.000 19.03 0.00 39.38 4.44
200 201 2.209273 GCAAATTTGTTGCCTCCGTTT 58.791 42.857 19.03 0.00 39.38 3.60
203 204 1.600023 ATTTGTTGCCTCCGTTTCGA 58.400 45.000 0.00 0.00 0.00 3.71
206 207 1.380524 TGTTGCCTCCGTTTCGAAAA 58.619 45.000 13.10 0.00 0.00 2.29
420 421 6.774673 TCAAGGTGATTTACTATGGTTCACA 58.225 36.000 12.75 0.00 38.71 3.58
444 445 4.497100 CGCGAACGATCTCAGAAATAAAC 58.503 43.478 0.00 0.00 43.93 2.01
534 535 6.536941 TGGTTTTATTTTCAAACAAGGTCTGC 59.463 34.615 0.00 0.00 36.07 4.26
535 536 6.761242 GGTTTTATTTTCAAACAAGGTCTGCT 59.239 34.615 0.00 0.00 36.07 4.24
536 537 7.923878 GGTTTTATTTTCAAACAAGGTCTGCTA 59.076 33.333 0.00 0.00 36.07 3.49
566 567 0.818040 CCAGGCCGGTATTGCTTACC 60.818 60.000 1.90 6.41 46.10 2.85
731 744 8.449085 TCGCAATCGAACAAGATAGATAATAC 57.551 34.615 0.00 0.00 42.44 1.89
732 745 8.297426 TCGCAATCGAACAAGATAGATAATACT 58.703 33.333 0.00 0.00 42.44 2.12
733 746 8.916654 CGCAATCGAACAAGATAGATAATACTT 58.083 33.333 0.00 0.00 38.10 2.24
738 751 8.794553 TCGAACAAGATAGATAATACTTCCTCC 58.205 37.037 0.00 0.00 0.00 4.30
739 752 7.751348 CGAACAAGATAGATAATACTTCCTCCG 59.249 40.741 0.00 0.00 0.00 4.63
740 753 8.480133 AACAAGATAGATAATACTTCCTCCGT 57.520 34.615 0.00 0.00 0.00 4.69
741 754 8.480133 ACAAGATAGATAATACTTCCTCCGTT 57.520 34.615 0.00 0.00 0.00 4.44
742 755 8.578151 ACAAGATAGATAATACTTCCTCCGTTC 58.422 37.037 0.00 0.00 0.00 3.95
743 756 7.706100 AGATAGATAATACTTCCTCCGTTCC 57.294 40.000 0.00 0.00 0.00 3.62
744 757 4.850347 AGATAATACTTCCTCCGTTCCG 57.150 45.455 0.00 0.00 0.00 4.30
745 758 4.467769 AGATAATACTTCCTCCGTTCCGA 58.532 43.478 0.00 0.00 0.00 4.55
746 759 4.891756 AGATAATACTTCCTCCGTTCCGAA 59.108 41.667 0.00 0.00 0.00 4.30
747 760 3.967332 AATACTTCCTCCGTTCCGAAA 57.033 42.857 0.00 0.00 0.00 3.46
748 761 4.482952 AATACTTCCTCCGTTCCGAAAT 57.517 40.909 0.00 0.00 0.00 2.17
749 762 5.603170 AATACTTCCTCCGTTCCGAAATA 57.397 39.130 0.00 0.00 0.00 1.40
750 763 5.803237 ATACTTCCTCCGTTCCGAAATAT 57.197 39.130 0.00 0.00 0.00 1.28
751 764 6.906157 ATACTTCCTCCGTTCCGAAATATA 57.094 37.500 0.00 0.00 0.00 0.86
752 765 5.603170 ACTTCCTCCGTTCCGAAATATAA 57.397 39.130 0.00 0.00 0.00 0.98
753 766 5.598769 ACTTCCTCCGTTCCGAAATATAAG 58.401 41.667 0.00 0.00 0.00 1.73
754 767 5.128335 ACTTCCTCCGTTCCGAAATATAAGT 59.872 40.000 0.00 0.00 0.00 2.24
755 768 5.192327 TCCTCCGTTCCGAAATATAAGTC 57.808 43.478 0.00 0.00 0.00 3.01
756 769 4.891756 TCCTCCGTTCCGAAATATAAGTCT 59.108 41.667 0.00 0.00 0.00 3.24
757 770 5.361857 TCCTCCGTTCCGAAATATAAGTCTT 59.638 40.000 0.00 0.00 0.00 3.01
758 771 6.047231 CCTCCGTTCCGAAATATAAGTCTTT 58.953 40.000 0.00 0.00 0.00 2.52
759 772 6.537660 CCTCCGTTCCGAAATATAAGTCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
760 773 7.065443 CCTCCGTTCCGAAATATAAGTCTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
761 774 9.090692 CTCCGTTCCGAAATATAAGTCTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
762 775 9.090692 TCCGTTCCGAAATATAAGTCTTTTTAG 57.909 33.333 0.00 0.00 0.00 1.85
763 776 9.090692 CCGTTCCGAAATATAAGTCTTTTTAGA 57.909 33.333 0.00 0.00 0.00 2.10
764 777 9.897349 CGTTCCGAAATATAAGTCTTTTTAGAC 57.103 33.333 0.00 0.00 39.00 2.59
777 790 9.750125 AAGTCTTTTTAGACATTTCAAATGGTC 57.250 29.630 14.70 9.26 41.02 4.02
778 791 9.136323 AGTCTTTTTAGACATTTCAAATGGTCT 57.864 29.630 14.70 15.05 42.76 3.85
783 796 9.959749 TTTTAGACATTTCAAATGGTCTACAAC 57.040 29.630 14.70 0.00 41.21 3.32
784 797 8.684386 TTAGACATTTCAAATGGTCTACAACA 57.316 30.769 14.70 2.66 41.21 3.33
785 798 7.765695 AGACATTTCAAATGGTCTACAACAT 57.234 32.000 14.70 0.00 38.74 2.71
786 799 8.862325 AGACATTTCAAATGGTCTACAACATA 57.138 30.769 14.70 0.00 38.74 2.29
787 800 8.730680 AGACATTTCAAATGGTCTACAACATAC 58.269 33.333 14.70 0.00 38.74 2.39
788 801 7.526608 ACATTTCAAATGGTCTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
789 802 6.489127 TTTCAAATGGTCTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
790 803 5.408880 TCAAATGGTCTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
791 804 5.984725 TCAAATGGTCTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
792 805 7.114866 TCAAATGGTCTACAACATACGGATA 57.885 36.000 0.00 0.00 0.00 2.59
793 806 7.732025 TCAAATGGTCTACAACATACGGATAT 58.268 34.615 0.00 0.00 0.00 1.63
794 807 8.862085 TCAAATGGTCTACAACATACGGATATA 58.138 33.333 0.00 0.00 0.00 0.86
795 808 9.653287 CAAATGGTCTACAACATACGGATATAT 57.347 33.333 0.00 0.00 0.00 0.86
796 809 9.653287 AAATGGTCTACAACATACGGATATATG 57.347 33.333 0.00 0.00 38.34 1.78
797 810 7.770366 TGGTCTACAACATACGGATATATGT 57.230 36.000 0.00 0.00 45.69 2.29
798 811 8.866970 TGGTCTACAACATACGGATATATGTA 57.133 34.615 0.00 0.00 43.50 2.29
799 812 8.953313 TGGTCTACAACATACGGATATATGTAG 58.047 37.037 15.50 15.50 43.50 2.74
800 813 9.170734 GGTCTACAACATACGGATATATGTAGA 57.829 37.037 18.38 18.38 43.50 2.59
801 814 9.985318 GTCTACAACATACGGATATATGTAGAC 57.015 37.037 26.97 26.97 46.82 2.59
802 815 9.729281 TCTACAACATACGGATATATGTAGACA 57.271 33.333 18.38 5.27 43.50 3.41
837 850 9.328845 AGTGTAAATTCATTCATTTTGCTTTGT 57.671 25.926 0.00 0.00 0.00 2.83
845 858 9.624697 TTCATTCATTTTGCTTTGTATGTAGTC 57.375 29.630 0.00 0.00 0.00 2.59
846 859 8.791675 TCATTCATTTTGCTTTGTATGTAGTCA 58.208 29.630 0.00 0.00 0.00 3.41
847 860 8.853345 CATTCATTTTGCTTTGTATGTAGTCAC 58.147 33.333 0.00 0.00 0.00 3.67
848 861 6.598525 TCATTTTGCTTTGTATGTAGTCACG 58.401 36.000 0.00 0.00 0.00 4.35
849 862 5.994887 TTTTGCTTTGTATGTAGTCACGT 57.005 34.783 0.00 0.00 0.00 4.49
850 863 7.385478 TCATTTTGCTTTGTATGTAGTCACGTA 59.615 33.333 0.00 0.00 0.00 3.57
851 864 7.661127 TTTTGCTTTGTATGTAGTCACGTAT 57.339 32.000 0.00 0.00 0.00 3.06
852 865 7.661127 TTTGCTTTGTATGTAGTCACGTATT 57.339 32.000 0.00 0.00 0.00 1.89
853 866 8.760103 TTTGCTTTGTATGTAGTCACGTATTA 57.240 30.769 0.00 0.00 0.00 0.98
854 867 8.760103 TTGCTTTGTATGTAGTCACGTATTAA 57.240 30.769 0.00 0.00 0.00 1.40
855 868 8.760103 TGCTTTGTATGTAGTCACGTATTAAA 57.240 30.769 0.00 0.00 0.00 1.52
856 869 9.205719 TGCTTTGTATGTAGTCACGTATTAAAA 57.794 29.630 0.00 0.00 0.00 1.52
885 898 9.595823 TCTAGAAAGACTTATATTTTGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
886 899 9.595823 CTAGAAAGACTTATATTTTGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
887 900 8.494016 AGAAAGACTTATATTTTGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
888 901 7.553044 AGAAAGACTTATATTTTGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
889 902 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
890 903 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
891 904 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
938 951 4.358851 CTTCGTCAAACCATTTTCTTGCA 58.641 39.130 0.00 0.00 0.00 4.08
1027 1040 1.379044 CCGGCTTTCCCATGCTTCT 60.379 57.895 0.00 0.00 0.00 2.85
1132 1157 4.148825 GCGCCACCATCGTCTCCT 62.149 66.667 0.00 0.00 0.00 3.69
1148 1173 1.561542 CTCCTATGGAGGTGCCTTTGT 59.438 52.381 5.75 0.00 45.43 2.83
1230 1255 2.664402 ACAACAACATCCCTGAGCTT 57.336 45.000 0.00 0.00 0.00 3.74
1247 1272 0.887387 CTTACCGTGGTGTGGGTTGG 60.887 60.000 0.72 0.00 37.75 3.77
1634 1677 5.605069 TCCCTCAAATATTCTTATGGGACGA 59.395 40.000 9.28 0.00 37.56 4.20
1813 1856 0.963962 CCCACACACTAGGTACGTGT 59.036 55.000 0.00 0.00 45.80 4.49
1829 2579 3.660865 ACGTGTTGACCTACTTTGGATC 58.339 45.455 0.00 0.00 0.00 3.36
1834 2584 4.825085 TGTTGACCTACTTTGGATCCAAAC 59.175 41.667 31.75 21.92 40.51 2.93
1836 2586 2.418976 GACCTACTTTGGATCCAAACGC 59.581 50.000 31.75 15.32 40.51 4.84
1838 2588 2.161609 CCTACTTTGGATCCAAACGCAC 59.838 50.000 31.75 0.00 40.51 5.34
1839 2589 0.958822 ACTTTGGATCCAAACGCACC 59.041 50.000 31.75 0.00 40.51 5.01
1861 2612 7.674414 CACCCTTAGTGTTTGTCCAGTACAAG 61.674 46.154 0.00 0.00 42.45 3.16
1884 2635 3.191371 GGTAGTTCACATTTGCTTCCCTG 59.809 47.826 0.00 0.00 0.00 4.45
1892 2643 2.888834 TTTGCTTCCCTGAGTTTTGC 57.111 45.000 0.00 0.00 0.00 3.68
1893 2644 1.774110 TTGCTTCCCTGAGTTTTGCA 58.226 45.000 0.00 0.00 0.00 4.08
1919 2670 6.535865 TGTACTATTGTAATGTACCTTTGGCG 59.464 38.462 0.00 0.00 36.63 5.69
1936 2687 6.380095 TTTGGCGTACAAATATTGATACCC 57.620 37.500 3.77 0.59 43.81 3.69
1938 2689 5.626142 TGGCGTACAAATATTGATACCCAT 58.374 37.500 11.52 0.00 0.00 4.00
1970 2721 0.179108 AGCGAATAACTGCCTCGTCC 60.179 55.000 0.00 0.00 35.06 4.79
1971 2722 1.480219 GCGAATAACTGCCTCGTCCG 61.480 60.000 0.00 0.00 35.06 4.79
1981 2732 4.615834 CTCGTCCGAGCCTAGCGC 62.616 72.222 0.00 0.00 35.31 5.92
2000 2751 3.852205 GCGCTGTTTTTAACCTTGGACTC 60.852 47.826 0.00 0.00 0.00 3.36
2018 2769 7.873719 TGGACTCAAGTGTAAGATTGAAAAA 57.126 32.000 0.00 0.00 35.14 1.94
2020 2771 8.912988 TGGACTCAAGTGTAAGATTGAAAAATT 58.087 29.630 0.00 0.00 35.14 1.82
2035 2786 8.707938 ATTGAAAAATTATTCTTAGCACCAGC 57.292 30.769 0.00 0.00 42.56 4.85
2045 2796 4.617875 GCACCAGCTTCGGTACAT 57.382 55.556 0.00 0.00 37.07 2.29
2046 2797 2.384203 GCACCAGCTTCGGTACATC 58.616 57.895 0.00 0.00 37.07 3.06
2047 2798 0.391130 GCACCAGCTTCGGTACATCA 60.391 55.000 0.00 0.00 37.07 3.07
2048 2799 1.743772 GCACCAGCTTCGGTACATCAT 60.744 52.381 0.00 0.00 37.07 2.45
2049 2800 2.632377 CACCAGCTTCGGTACATCATT 58.368 47.619 0.00 0.00 37.07 2.57
2050 2801 2.352651 CACCAGCTTCGGTACATCATTG 59.647 50.000 0.00 0.00 37.07 2.82
2051 2802 2.236146 ACCAGCTTCGGTACATCATTGA 59.764 45.455 0.00 0.00 37.57 2.57
2052 2803 2.868583 CCAGCTTCGGTACATCATTGAG 59.131 50.000 0.00 0.00 0.00 3.02
2053 2804 2.286294 CAGCTTCGGTACATCATTGAGC 59.714 50.000 0.00 0.00 0.00 4.26
2054 2805 2.093500 AGCTTCGGTACATCATTGAGCA 60.093 45.455 0.00 0.00 0.00 4.26
2055 2806 2.030946 GCTTCGGTACATCATTGAGCAC 59.969 50.000 0.00 0.00 0.00 4.40
2056 2807 3.261580 CTTCGGTACATCATTGAGCACA 58.738 45.455 0.00 0.00 0.00 4.57
2057 2808 2.616960 TCGGTACATCATTGAGCACAC 58.383 47.619 0.00 0.00 0.00 3.82
2058 2809 1.665679 CGGTACATCATTGAGCACACC 59.334 52.381 0.00 0.00 0.00 4.16
2059 2810 2.017049 GGTACATCATTGAGCACACCC 58.983 52.381 0.00 0.00 0.00 4.61
2078 2829 4.896482 CACCCTATGCTAGAGAAACCTACT 59.104 45.833 0.00 0.00 0.00 2.57
2081 2832 5.598830 CCCTATGCTAGAGAAACCTACTCAA 59.401 44.000 0.00 0.00 36.91 3.02
2087 2838 3.944087 AGAGAAACCTACTCAACATGGC 58.056 45.455 0.00 0.00 36.91 4.40
2095 2846 1.538047 ACTCAACATGGCGATGCTTT 58.462 45.000 8.81 0.00 32.14 3.51
2096 2847 1.200716 ACTCAACATGGCGATGCTTTG 59.799 47.619 8.81 7.12 32.14 2.77
2098 2849 0.527113 CAACATGGCGATGCTTTGGA 59.473 50.000 8.81 0.00 32.14 3.53
2102 2853 2.234414 ACATGGCGATGCTTTGGAAAAT 59.766 40.909 8.81 0.00 32.14 1.82
2103 2854 2.367030 TGGCGATGCTTTGGAAAATG 57.633 45.000 0.00 0.00 0.00 2.32
2145 2897 7.492669 CACAGTACTATGGACTCGAAAATTGAT 59.507 37.037 0.00 0.00 0.00 2.57
2156 2908 8.237267 GGACTCGAAAATTGATGTGTTTAATCT 58.763 33.333 0.00 0.00 0.00 2.40
2185 2937 8.131731 GGAGAAATTATGTTTCCTCTAACATGC 58.868 37.037 11.18 0.00 45.63 4.06
2208 2960 9.982651 ATGCGTACTTTATCTTATATGTCAAGT 57.017 29.630 0.00 0.00 0.00 3.16
2231 2983 5.885912 GTGGTGACCATATTGTTAACTCCAT 59.114 40.000 7.94 0.00 35.28 3.41
2261 3013 5.105187 TCCACAATGAGAGAAGTAGACCATG 60.105 44.000 0.00 0.00 0.00 3.66
2262 3014 4.569966 CACAATGAGAGAAGTAGACCATGC 59.430 45.833 0.00 0.00 0.00 4.06
2271 3023 8.814038 AGAGAAGTAGACCATGCATTATTTTT 57.186 30.769 0.00 0.00 0.00 1.94
2301 3060 8.586570 AATTTTCTGAGCAGAGATAATAGACG 57.413 34.615 0.00 0.00 38.88 4.18
2306 3065 5.073428 TGAGCAGAGATAATAGACGGACAT 58.927 41.667 0.00 0.00 0.00 3.06
2339 3098 4.548669 AGGGGTAAAGCAACCTGTTTTTA 58.451 39.130 3.31 0.00 39.65 1.52
2340 3099 5.152193 AGGGGTAAAGCAACCTGTTTTTAT 58.848 37.500 3.31 0.00 39.65 1.40
2341 3100 6.316513 AGGGGTAAAGCAACCTGTTTTTATA 58.683 36.000 3.31 0.00 39.65 0.98
2355 3114 9.462606 ACCTGTTTTTATAGGGAGATTTTACTG 57.537 33.333 0.00 0.00 38.42 2.74
2427 3186 2.167693 AGCATGAGACGGTCGGATTTTA 59.832 45.455 0.00 0.00 0.00 1.52
2428 3187 2.933906 GCATGAGACGGTCGGATTTTAA 59.066 45.455 0.00 0.00 0.00 1.52
2483 3242 8.076714 TCTAATTAATTAGACTGATTGCAGCG 57.923 34.615 26.90 4.87 42.66 5.18
2587 3346 4.783621 GGCCATCCAGACGCTGCA 62.784 66.667 0.00 0.00 0.00 4.41
2628 3396 1.673993 CCCAACACCGCATGCACTA 60.674 57.895 19.57 0.00 0.00 2.74
2641 3409 2.973899 CACTACTCCCAGCGCACT 59.026 61.111 11.47 0.00 0.00 4.40
2651 3419 1.672030 CAGCGCACTGTCATCCCAA 60.672 57.895 11.47 0.00 39.22 4.12
2666 3434 0.033228 CCCAACGCTGCCAAAAATCA 59.967 50.000 0.00 0.00 0.00 2.57
2685 3453 2.435586 AGCCTACGCTGCTTGCAG 60.436 61.111 17.34 17.34 46.19 4.41
2689 3457 4.328025 TACGCTGCTTGCAGGCCA 62.328 61.111 19.11 5.59 43.06 5.36
2770 3538 4.194640 TGGCATGATGTAAAGAAGAGAGC 58.805 43.478 0.00 0.00 0.00 4.09
2787 3555 4.832266 AGAGAGCTCGATGGAGTTGAATAT 59.168 41.667 8.37 0.00 42.53 1.28
2823 3591 3.243569 GCCTCGTATTCTAGTGTCTGCAT 60.244 47.826 0.00 0.00 0.00 3.96
2854 3622 2.847234 ACGGGCTGGACAAGGTCA 60.847 61.111 0.00 0.00 33.68 4.02
2858 3626 2.529744 GGCTGGACAAGGTCAGGGT 61.530 63.158 0.00 0.00 33.68 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.475242 CGCACACGTTACATTAACCAAG 58.525 45.455 0.00 0.00 35.27 3.61
25 26 0.232303 GTTGAGAGAAACCGCACACG 59.768 55.000 0.00 0.00 39.67 4.49
42 43 9.757227 TGCTGTTAGCTGTTTATTTATTTTGTT 57.243 25.926 0.00 0.00 42.97 2.83
43 44 9.757227 TTGCTGTTAGCTGTTTATTTATTTTGT 57.243 25.926 0.00 0.00 42.97 2.83
53 54 3.888930 AGGCTTTTGCTGTTAGCTGTTTA 59.111 39.130 0.00 0.00 46.54 2.01
56 57 1.986882 AGGCTTTTGCTGTTAGCTGT 58.013 45.000 0.00 0.00 46.54 4.40
57 58 3.503748 AGTTAGGCTTTTGCTGTTAGCTG 59.496 43.478 0.00 0.00 46.54 4.24
63 64 3.287222 TGTTCAGTTAGGCTTTTGCTGT 58.713 40.909 0.00 0.00 46.54 4.40
64 65 3.988379 TGTTCAGTTAGGCTTTTGCTG 57.012 42.857 0.00 0.00 46.54 4.41
65 66 4.159506 TGTTTGTTCAGTTAGGCTTTTGCT 59.840 37.500 0.00 0.00 46.54 3.91
66 67 4.429108 TGTTTGTTCAGTTAGGCTTTTGC 58.571 39.130 0.00 0.00 46.64 3.68
67 68 6.453659 CGTTTGTTTGTTCAGTTAGGCTTTTG 60.454 38.462 0.00 0.00 0.00 2.44
68 69 5.575218 CGTTTGTTTGTTCAGTTAGGCTTTT 59.425 36.000 0.00 0.00 0.00 2.27
69 70 5.099575 CGTTTGTTTGTTCAGTTAGGCTTT 58.900 37.500 0.00 0.00 0.00 3.51
70 71 4.396790 TCGTTTGTTTGTTCAGTTAGGCTT 59.603 37.500 0.00 0.00 0.00 4.35
71 72 3.942748 TCGTTTGTTTGTTCAGTTAGGCT 59.057 39.130 0.00 0.00 0.00 4.58
72 73 4.281525 TCGTTTGTTTGTTCAGTTAGGC 57.718 40.909 0.00 0.00 0.00 3.93
73 74 6.055231 TCATCGTTTGTTTGTTCAGTTAGG 57.945 37.500 0.00 0.00 0.00 2.69
74 75 7.164171 CAGTTCATCGTTTGTTTGTTCAGTTAG 59.836 37.037 0.00 0.00 0.00 2.34
75 76 6.964370 CAGTTCATCGTTTGTTTGTTCAGTTA 59.036 34.615 0.00 0.00 0.00 2.24
76 77 5.799936 CAGTTCATCGTTTGTTTGTTCAGTT 59.200 36.000 0.00 0.00 0.00 3.16
77 78 5.123186 TCAGTTCATCGTTTGTTTGTTCAGT 59.877 36.000 0.00 0.00 0.00 3.41
78 79 5.568482 TCAGTTCATCGTTTGTTTGTTCAG 58.432 37.500 0.00 0.00 0.00 3.02
108 109 1.133976 GTACAATGATGGAGGCAGGCT 60.134 52.381 0.00 0.00 0.00 4.58
109 110 1.312815 GTACAATGATGGAGGCAGGC 58.687 55.000 0.00 0.00 0.00 4.85
110 111 2.092753 ACTGTACAATGATGGAGGCAGG 60.093 50.000 0.00 0.00 0.00 4.85
116 117 7.943079 AATGATCAAACTGTACAATGATGGA 57.057 32.000 18.13 8.81 32.90 3.41
138 139 9.045745 AGAGGAGAAAGAGAATACTGAGAAAAT 57.954 33.333 0.00 0.00 0.00 1.82
154 155 9.282569 CCTCATCCATTAAATAAGAGGAGAAAG 57.717 37.037 0.00 2.41 42.87 2.62
155 156 7.721399 GCCTCATCCATTAAATAAGAGGAGAAA 59.279 37.037 9.57 0.00 42.87 2.52
156 157 7.147320 TGCCTCATCCATTAAATAAGAGGAGAA 60.147 37.037 9.57 1.85 42.87 2.87
157 158 6.329986 TGCCTCATCCATTAAATAAGAGGAGA 59.670 38.462 9.57 0.00 42.87 3.71
158 159 6.537355 TGCCTCATCCATTAAATAAGAGGAG 58.463 40.000 9.57 9.14 42.87 3.69
159 160 6.514012 TGCCTCATCCATTAAATAAGAGGA 57.486 37.500 9.57 5.13 42.87 3.71
160 161 7.587037 TTTGCCTCATCCATTAAATAAGAGG 57.413 36.000 0.00 0.00 43.04 3.69
162 163 9.820725 CAAATTTGCCTCATCCATTAAATAAGA 57.179 29.630 5.01 0.00 0.00 2.10
163 164 9.603921 ACAAATTTGCCTCATCCATTAAATAAG 57.396 29.630 18.12 0.00 0.00 1.73
164 165 9.956640 AACAAATTTGCCTCATCCATTAAATAA 57.043 25.926 18.12 0.00 0.00 1.40
165 166 9.381033 CAACAAATTTGCCTCATCCATTAAATA 57.619 29.630 18.12 0.00 0.00 1.40
166 167 7.148205 GCAACAAATTTGCCTCATCCATTAAAT 60.148 33.333 18.12 0.00 39.38 1.40
167 168 6.149142 GCAACAAATTTGCCTCATCCATTAAA 59.851 34.615 18.12 0.00 39.38 1.52
168 169 5.642919 GCAACAAATTTGCCTCATCCATTAA 59.357 36.000 18.12 0.00 39.38 1.40
169 170 5.177326 GCAACAAATTTGCCTCATCCATTA 58.823 37.500 18.12 0.00 39.38 1.90
170 171 4.004982 GCAACAAATTTGCCTCATCCATT 58.995 39.130 18.12 0.00 39.38 3.16
171 172 3.602483 GCAACAAATTTGCCTCATCCAT 58.398 40.909 18.12 0.00 39.38 3.41
172 173 3.042871 GCAACAAATTTGCCTCATCCA 57.957 42.857 18.12 0.00 39.38 3.41
180 181 1.864565 AACGGAGGCAACAAATTTGC 58.135 45.000 18.12 5.02 44.22 3.68
181 182 2.470999 CGAAACGGAGGCAACAAATTTG 59.529 45.455 16.67 16.67 41.41 2.32
182 183 2.359531 TCGAAACGGAGGCAACAAATTT 59.640 40.909 0.00 0.00 41.41 1.82
183 184 1.950909 TCGAAACGGAGGCAACAAATT 59.049 42.857 0.00 0.00 41.41 1.82
184 185 1.600023 TCGAAACGGAGGCAACAAAT 58.400 45.000 0.00 0.00 41.41 2.32
185 186 1.380524 TTCGAAACGGAGGCAACAAA 58.619 45.000 0.00 0.00 41.41 2.83
186 187 1.380524 TTTCGAAACGGAGGCAACAA 58.619 45.000 6.47 0.00 41.41 2.83
187 188 1.380524 TTTTCGAAACGGAGGCAACA 58.619 45.000 10.79 0.00 41.41 3.33
188 189 2.478547 TTTTTCGAAACGGAGGCAAC 57.521 45.000 10.79 0.00 0.00 4.17
420 421 0.242825 TTTCTGAGATCGTTCGCGGT 59.757 50.000 6.13 0.00 41.70 5.68
522 523 1.699634 TCCAGCTAGCAGACCTTGTTT 59.300 47.619 18.83 0.00 0.00 2.83
566 567 2.093973 AGTCAGGCTAGTGACCGAAATG 60.094 50.000 9.29 0.00 46.94 2.32
706 712 8.297426 AGTATTATCTATCTTGTTCGATTGCGA 58.703 33.333 0.00 0.00 46.33 5.10
738 751 9.897349 GTCTAAAAAGACTTATATTTCGGAACG 57.103 33.333 0.00 0.00 44.07 3.95
751 764 9.750125 GACCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
752 765 9.136323 AGACCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 2.38 39.41 3.24
757 770 9.959749 GTTGTAGACCATTTGAAATGTCTAAAA 57.040 29.630 20.91 19.69 0.00 1.52
758 771 9.126151 TGTTGTAGACCATTTGAAATGTCTAAA 57.874 29.630 20.91 16.73 0.00 1.85
759 772 8.684386 TGTTGTAGACCATTTGAAATGTCTAA 57.316 30.769 20.91 12.44 0.00 2.10
760 773 8.862325 ATGTTGTAGACCATTTGAAATGTCTA 57.138 30.769 15.93 17.14 0.00 2.59
761 774 7.765695 ATGTTGTAGACCATTTGAAATGTCT 57.234 32.000 15.93 17.95 0.00 3.41
762 775 7.692291 CGTATGTTGTAGACCATTTGAAATGTC 59.308 37.037 15.93 12.82 0.00 3.06
763 776 7.361713 CCGTATGTTGTAGACCATTTGAAATGT 60.362 37.037 15.93 5.15 0.00 2.71
764 777 6.966632 CCGTATGTTGTAGACCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
765 778 6.882140 TCCGTATGTTGTAGACCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
766 779 6.231951 TCCGTATGTTGTAGACCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
767 780 5.795972 TCCGTATGTTGTAGACCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
768 781 5.408880 TCCGTATGTTGTAGACCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
769 782 7.962964 ATATCCGTATGTTGTAGACCATTTG 57.037 36.000 0.00 0.00 0.00 2.32
770 783 9.653287 CATATATCCGTATGTTGTAGACCATTT 57.347 33.333 0.00 0.00 0.00 2.32
771 784 8.812972 ACATATATCCGTATGTTGTAGACCATT 58.187 33.333 0.00 0.00 41.29 3.16
772 785 8.362464 ACATATATCCGTATGTTGTAGACCAT 57.638 34.615 0.00 0.00 41.29 3.55
773 786 7.770366 ACATATATCCGTATGTTGTAGACCA 57.230 36.000 0.00 0.00 41.29 4.02
774 787 9.170734 TCTACATATATCCGTATGTTGTAGACC 57.829 37.037 5.04 0.00 41.29 3.85
775 788 9.985318 GTCTACATATATCCGTATGTTGTAGAC 57.015 37.037 18.79 18.79 45.73 2.59
776 789 9.729281 TGTCTACATATATCCGTATGTTGTAGA 57.271 33.333 5.04 5.93 41.29 2.59
811 824 9.328845 ACAAAGCAAAATGAATGAATTTACACT 57.671 25.926 0.00 0.00 0.00 3.55
819 832 9.624697 GACTACATACAAAGCAAAATGAATGAA 57.375 29.630 0.00 0.00 0.00 2.57
820 833 8.791675 TGACTACATACAAAGCAAAATGAATGA 58.208 29.630 0.00 0.00 0.00 2.57
821 834 8.853345 GTGACTACATACAAAGCAAAATGAATG 58.147 33.333 0.00 0.00 0.00 2.67
822 835 7.750458 CGTGACTACATACAAAGCAAAATGAAT 59.250 33.333 0.00 0.00 0.00 2.57
823 836 7.075121 CGTGACTACATACAAAGCAAAATGAA 58.925 34.615 0.00 0.00 0.00 2.57
824 837 6.203915 ACGTGACTACATACAAAGCAAAATGA 59.796 34.615 0.00 0.00 0.00 2.57
825 838 6.370593 ACGTGACTACATACAAAGCAAAATG 58.629 36.000 0.00 0.00 0.00 2.32
826 839 6.554334 ACGTGACTACATACAAAGCAAAAT 57.446 33.333 0.00 0.00 0.00 1.82
827 840 5.994887 ACGTGACTACATACAAAGCAAAA 57.005 34.783 0.00 0.00 0.00 2.44
828 841 7.661127 AATACGTGACTACATACAAAGCAAA 57.339 32.000 0.00 0.00 0.00 3.68
829 842 8.760103 TTAATACGTGACTACATACAAAGCAA 57.240 30.769 0.00 0.00 0.00 3.91
830 843 8.760103 TTTAATACGTGACTACATACAAAGCA 57.240 30.769 0.00 0.00 0.00 3.91
859 872 9.595823 CCGTTCCAAAATATAAGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
860 873 9.595823 TCCGTTCCAAAATATAAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
861 874 9.595823 CTCCGTTCCAAAATATAAGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
862 875 7.553044 CCTCCGTTCCAAAATATAAGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
863 876 7.201705 CCCTCCGTTCCAAAATATAAGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
864 877 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
865 878 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
866 879 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
867 880 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
868 881 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
869 882 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
870 883 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
871 884 6.138263 TCTACTCCCTCCGTTCCAAAATATA 58.862 40.000 0.00 0.00 0.00 0.86
872 885 4.966805 TCTACTCCCTCCGTTCCAAAATAT 59.033 41.667 0.00 0.00 0.00 1.28
873 886 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
874 887 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
875 888 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
876 889 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
877 890 2.108168 CATCTACTCCCTCCGTTCCAA 58.892 52.381 0.00 0.00 0.00 3.53
878 891 1.776662 CATCTACTCCCTCCGTTCCA 58.223 55.000 0.00 0.00 0.00 3.53
879 892 0.389757 GCATCTACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
880 893 1.067821 CAGCATCTACTCCCTCCGTTC 59.932 57.143 0.00 0.00 0.00 3.95
881 894 1.115467 CAGCATCTACTCCCTCCGTT 58.885 55.000 0.00 0.00 0.00 4.44
882 895 0.757188 CCAGCATCTACTCCCTCCGT 60.757 60.000 0.00 0.00 0.00 4.69
883 896 0.468214 TCCAGCATCTACTCCCTCCG 60.468 60.000 0.00 0.00 0.00 4.63
884 897 1.414550 GTTCCAGCATCTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
885 898 2.393646 AGTTCCAGCATCTACTCCCTC 58.606 52.381 0.00 0.00 0.00 4.30
886 899 2.503356 CAAGTTCCAGCATCTACTCCCT 59.497 50.000 0.00 0.00 0.00 4.20
887 900 2.237392 ACAAGTTCCAGCATCTACTCCC 59.763 50.000 0.00 0.00 0.00 4.30
888 901 3.526534 GACAAGTTCCAGCATCTACTCC 58.473 50.000 0.00 0.00 0.00 3.85
889 902 3.182967 CGACAAGTTCCAGCATCTACTC 58.817 50.000 0.00 0.00 0.00 2.59
890 903 2.563179 ACGACAAGTTCCAGCATCTACT 59.437 45.455 0.00 0.00 0.00 2.57
891 904 2.960819 ACGACAAGTTCCAGCATCTAC 58.039 47.619 0.00 0.00 0.00 2.59
938 951 4.768448 TCTTGCATTGAGGTTTGATCACAT 59.232 37.500 0.00 0.00 0.00 3.21
1027 1040 7.013750 CAGAAGTATCAACACTGCTATCCTAGA 59.986 40.741 0.00 0.00 32.22 2.43
1132 1157 5.304686 CCTAATACAAAGGCACCTCCATA 57.695 43.478 0.00 0.00 37.29 2.74
1148 1173 3.967987 GGACAGGGAGAAGAAGCCTAATA 59.032 47.826 0.00 0.00 0.00 0.98
1198 1223 1.463444 GTTGTTGTACCAGATGCCGAC 59.537 52.381 0.00 0.00 0.00 4.79
1230 1255 2.830317 CCAACCCACACCACGGTA 59.170 61.111 0.00 0.00 0.00 4.02
1247 1272 3.053896 CCGGGTTTCCTCGGTTGC 61.054 66.667 0.00 0.00 41.23 4.17
1256 1281 2.909965 TGTTGCTGGCCGGGTTTC 60.910 61.111 15.02 0.00 0.00 2.78
1390 1430 0.394938 TTTAGAAGCACTGCCACGGA 59.605 50.000 0.00 0.00 0.00 4.69
1483 1523 0.255318 AGCTTCATGCCAGGAAGGAG 59.745 55.000 19.53 0.00 44.23 3.69
1530 1570 1.077716 GGATACCAGGCGGTTGCTT 60.078 57.895 6.35 0.00 46.31 3.91
1534 1577 0.912487 TTCCAGGATACCAGGCGGTT 60.912 55.000 6.35 0.00 46.31 4.44
1634 1677 3.063084 GAGACACCGGACGCTCCT 61.063 66.667 9.46 0.00 33.30 3.69
1813 1856 4.069304 CGTTTGGATCCAAAGTAGGTCAA 58.931 43.478 35.06 12.46 45.16 3.18
1836 2586 4.443739 TGTACTGGACAAACACTAAGGGTG 60.444 45.833 0.00 0.00 42.62 4.61
1838 2588 4.345859 TGTACTGGACAAACACTAAGGG 57.654 45.455 0.00 0.00 34.15 3.95
1850 2600 3.322828 TGTGAACTACCCTTGTACTGGAC 59.677 47.826 6.99 0.00 0.00 4.02
1855 2606 4.760204 AGCAAATGTGAACTACCCTTGTAC 59.240 41.667 0.00 0.00 0.00 2.90
1861 2612 2.492088 GGGAAGCAAATGTGAACTACCC 59.508 50.000 0.00 0.00 0.00 3.69
1866 2617 2.887152 ACTCAGGGAAGCAAATGTGAAC 59.113 45.455 0.00 0.00 0.00 3.18
1892 2643 8.342634 GCCAAAGGTACATTACAATAGTACATG 58.657 37.037 0.00 0.00 39.78 3.21
1893 2644 7.225931 CGCCAAAGGTACATTACAATAGTACAT 59.774 37.037 0.00 0.00 39.78 2.29
1934 2685 5.940192 TTCGCTATAGTTTTATGCATGGG 57.060 39.130 10.16 0.00 0.00 4.00
1936 2687 9.533983 CAGTTATTCGCTATAGTTTTATGCATG 57.466 33.333 10.16 0.00 0.00 4.06
1938 2689 7.307751 GGCAGTTATTCGCTATAGTTTTATGCA 60.308 37.037 0.84 0.00 0.00 3.96
1950 2701 1.066605 GGACGAGGCAGTTATTCGCTA 59.933 52.381 0.00 0.00 37.84 4.26
2028 2779 0.391130 TGATGTACCGAAGCTGGTGC 60.391 55.000 5.99 5.25 43.68 5.01
2029 2780 2.315925 ATGATGTACCGAAGCTGGTG 57.684 50.000 5.99 0.00 43.68 4.17
2030 2781 2.236146 TCAATGATGTACCGAAGCTGGT 59.764 45.455 0.82 0.82 46.26 4.00
2031 2782 2.868583 CTCAATGATGTACCGAAGCTGG 59.131 50.000 0.00 0.00 0.00 4.85
2032 2783 2.286294 GCTCAATGATGTACCGAAGCTG 59.714 50.000 0.00 0.00 0.00 4.24
2033 2784 2.093500 TGCTCAATGATGTACCGAAGCT 60.093 45.455 0.00 0.00 0.00 3.74
2034 2785 2.030946 GTGCTCAATGATGTACCGAAGC 59.969 50.000 0.00 0.00 0.00 3.86
2035 2786 3.062639 GTGTGCTCAATGATGTACCGAAG 59.937 47.826 0.00 0.00 0.00 3.79
2036 2787 3.000041 GTGTGCTCAATGATGTACCGAA 59.000 45.455 0.00 0.00 0.00 4.30
2037 2788 2.616960 GTGTGCTCAATGATGTACCGA 58.383 47.619 0.00 0.00 0.00 4.69
2038 2789 1.665679 GGTGTGCTCAATGATGTACCG 59.334 52.381 0.00 0.00 0.00 4.02
2039 2790 2.017049 GGGTGTGCTCAATGATGTACC 58.983 52.381 0.00 0.00 0.00 3.34
2040 2791 2.991250 AGGGTGTGCTCAATGATGTAC 58.009 47.619 0.00 0.00 0.00 2.90
2041 2792 4.707105 CATAGGGTGTGCTCAATGATGTA 58.293 43.478 0.00 0.00 0.00 2.29
2042 2793 3.548770 CATAGGGTGTGCTCAATGATGT 58.451 45.455 0.00 0.00 0.00 3.06
2043 2794 2.292569 GCATAGGGTGTGCTCAATGATG 59.707 50.000 3.05 1.21 39.45 3.07
2044 2795 2.579873 GCATAGGGTGTGCTCAATGAT 58.420 47.619 3.05 0.00 39.45 2.45
2045 2796 2.042686 GCATAGGGTGTGCTCAATGA 57.957 50.000 3.05 0.00 39.45 2.57
2052 2803 3.198872 GTTTCTCTAGCATAGGGTGTGC 58.801 50.000 0.00 0.00 41.03 4.57
2053 2804 3.452627 AGGTTTCTCTAGCATAGGGTGTG 59.547 47.826 0.00 0.00 41.03 3.82
2054 2805 3.725634 AGGTTTCTCTAGCATAGGGTGT 58.274 45.455 0.00 0.00 41.03 4.16
2055 2806 4.896482 AGTAGGTTTCTCTAGCATAGGGTG 59.104 45.833 0.00 0.00 41.03 4.61
2056 2807 5.141910 GAGTAGGTTTCTCTAGCATAGGGT 58.858 45.833 0.00 0.00 41.03 4.34
2057 2808 5.141182 TGAGTAGGTTTCTCTAGCATAGGG 58.859 45.833 0.00 0.00 41.83 3.53
2058 2809 6.096987 TGTTGAGTAGGTTTCTCTAGCATAGG 59.903 42.308 0.00 0.00 39.78 2.57
2059 2810 7.101652 TGTTGAGTAGGTTTCTCTAGCATAG 57.898 40.000 0.00 0.00 41.04 2.23
2067 2818 2.673368 CGCCATGTTGAGTAGGTTTCTC 59.327 50.000 0.00 0.00 0.00 2.87
2078 2829 0.527113 CCAAAGCATCGCCATGTTGA 59.473 50.000 0.00 0.00 31.86 3.18
2081 2832 1.255882 TTTCCAAAGCATCGCCATGT 58.744 45.000 0.00 0.00 31.86 3.21
2087 2838 3.916172 CACACTCATTTTCCAAAGCATCG 59.084 43.478 0.00 0.00 0.00 3.84
2095 2846 3.569277 CCACACATCACACTCATTTTCCA 59.431 43.478 0.00 0.00 0.00 3.53
2096 2847 3.612479 GCCACACATCACACTCATTTTCC 60.612 47.826 0.00 0.00 0.00 3.13
2098 2849 2.297033 GGCCACACATCACACTCATTTT 59.703 45.455 0.00 0.00 0.00 1.82
2102 2853 0.534877 GTGGCCACACATCACACTCA 60.535 55.000 31.23 0.00 46.90 3.41
2103 2854 2.247790 GTGGCCACACATCACACTC 58.752 57.895 31.23 0.00 46.90 3.51
2126 2878 6.668541 ACACATCAATTTTCGAGTCCATAG 57.331 37.500 0.00 0.00 0.00 2.23
2156 2908 9.053472 TGTTAGAGGAAACATAATTTCTCCCTA 57.947 33.333 0.00 0.00 34.50 3.53
2185 2937 9.745880 ACCACTTGACATATAAGATAAAGTACG 57.254 33.333 0.00 0.00 0.00 3.67
2208 2960 5.506730 TGGAGTTAACAATATGGTCACCA 57.493 39.130 0.00 0.00 38.19 4.17
2231 2983 4.792068 ACTTCTCTCATTGTGGAAACCAA 58.208 39.130 0.00 0.00 34.18 3.67
2301 3060 7.201794 GCTTTACCCCTAAAATCACTTATGTCC 60.202 40.741 0.00 0.00 0.00 4.02
2306 3065 6.434965 GGTTGCTTTACCCCTAAAATCACTTA 59.565 38.462 0.00 0.00 31.71 2.24
2340 3099 9.656323 AGTATGATGTACAGTAAAATCTCCCTA 57.344 33.333 0.33 0.00 0.00 3.53
2341 3100 8.554490 AGTATGATGTACAGTAAAATCTCCCT 57.446 34.615 0.33 0.00 0.00 4.20
2355 3114 9.464714 CCTGTTATGTTGAGTAGTATGATGTAC 57.535 37.037 0.00 0.00 0.00 2.90
2408 3167 4.181578 AGTTAAAATCCGACCGTCTCATG 58.818 43.478 0.00 0.00 0.00 3.07
2416 3175 6.997239 ATGTCCTTAAGTTAAAATCCGACC 57.003 37.500 0.97 0.00 0.00 4.79
2599 3358 1.928567 GTGTTGGGATGGAGGGGGA 60.929 63.158 0.00 0.00 0.00 4.81
2628 3396 2.513026 GATGACAGTGCGCTGGGAGT 62.513 60.000 29.60 13.44 46.62 3.85
2641 3409 2.359850 GGCAGCGTTGGGATGACA 60.360 61.111 0.16 0.00 40.77 3.58
2651 3419 0.318955 GCTGTGATTTTTGGCAGCGT 60.319 50.000 0.00 0.00 43.60 5.07
2698 3466 6.761714 GCTAGCTAATTAAGTTAGTTCCTGCA 59.238 38.462 7.70 0.00 40.25 4.41
2728 3496 4.456566 GCCATGTGCATTCTTTTCCAAAAT 59.543 37.500 0.00 0.00 40.77 1.82
2759 3527 3.096092 ACTCCATCGAGCTCTCTTCTTT 58.904 45.455 12.85 0.00 40.03 2.52
2770 3538 7.657354 TCATGGTAAATATTCAACTCCATCGAG 59.343 37.037 0.00 0.00 42.32 4.04
2823 3591 1.607071 CCCGTCCCATGAATGACCA 59.393 57.895 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.