Multiple sequence alignment - TraesCS6B01G054000

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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 TraesCS6B01G054000 chr6B 100.000 2949 0 0 1 2949 34092442 34095390 0.000000e+00 5446.0
1 TraesCS6B01G054000 chr6D 93.309 1614 79 12 577 2171 20120388 20121991 0.000000e+00 2355.0
2 TraesCS6B01G054000 chr6D 85.739 568 79 2 1 566 20135024 20134457 1.510000e-167 599.0
3 TraesCS6B01G054000 chr6D 84.800 500 45 15 2457 2949 20122561 20123036 9.570000e-130 473.0
4 TraesCS6B01G054000 chr6D 92.899 169 11 1 2169 2336 97856420 97856588 8.160000e-61 244.0
5 TraesCS6B01G054000 chr6A 92.716 1112 64 7 579 1680 20162967 20164071 0.000000e+00 1589.0
6 TraesCS6B01G054000 chr6A 91.495 388 28 5 1791 2175 20164299 20164684 2.010000e-146 529.0
7 TraesCS6B01G054000 chr6A 85.425 494 52 2 2457 2949 20171546 20172020 2.040000e-136 496.0
8 TraesCS6B01G054000 chr7B 88.007 567 65 3 1 565 104298404 104298969 0.000000e+00 667.0
9 TraesCS6B01G054000 chr7B 86.796 568 73 2 1 566 748331164 748331731 1.490000e-177 632.0
10 TraesCS6B01G054000 chr7D 87.302 567 70 2 1 565 136414845 136414279 0.000000e+00 647.0
11 TraesCS6B01G054000 chr7D 86.243 567 75 3 1 565 628134568 628135133 1.940000e-171 612.0
12 TraesCS6B01G054000 chr2A 86.243 567 76 2 1 566 66767270 66767835 5.400000e-172 614.0
13 TraesCS6B01G054000 chr5D 85.989 571 75 5 1 568 76030595 76031163 9.040000e-170 606.0
14 TraesCS6B01G054000 chr5D 89.785 186 14 4 2153 2335 25039964 25040147 1.770000e-57 233.0
15 TraesCS6B01G054000 chr5D 86.667 75 9 1 2093 2167 563904914 563904841 6.770000e-12 82.4
16 TraesCS6B01G054000 chr5D 87.302 63 7 1 2112 2174 339987817 339987756 1.470000e-08 71.3
17 TraesCS6B01G054000 chr5D 84.286 70 11 0 2098 2167 520654351 520654420 5.270000e-08 69.4
18 TraesCS6B01G054000 chr3D 85.915 568 78 2 1 566 562514541 562513974 3.250000e-169 604.0
19 TraesCS6B01G054000 chr3D 83.571 140 22 1 2690 2829 373330841 373330703 2.390000e-26 130.0
20 TraesCS6B01G054000 chr4A 85.789 570 79 2 1 568 607312012 607312581 1.170000e-168 603.0
21 TraesCS6B01G054000 chr4A 86.893 206 21 6 2138 2339 26539971 26539768 2.960000e-55 226.0
22 TraesCS6B01G054000 chr4A 84.810 79 12 0 2092 2170 547311774 547311696 2.440000e-11 80.5
23 TraesCS6B01G054000 chr5B 92.353 170 12 1 2164 2332 663232334 663232165 1.060000e-59 241.0
24 TraesCS6B01G054000 chr4B 90.556 180 15 2 2168 2346 448983216 448983394 1.370000e-58 237.0
25 TraesCS6B01G054000 chr1D 90.556 180 15 2 2168 2346 235806437 235806259 1.370000e-58 237.0
26 TraesCS6B01G054000 chr1D 90.556 180 15 2 2168 2346 244450879 244450701 1.370000e-58 237.0
27 TraesCS6B01G054000 chr1D 87.379 206 23 3 2164 2367 206955706 206955502 1.770000e-57 233.0
28 TraesCS6B01G054000 chr1D 84.507 71 11 0 2096 2166 370207284 370207214 1.470000e-08 71.3
29 TraesCS6B01G054000 chr2B 88.601 193 17 4 2169 2357 174794822 174795013 2.290000e-56 230.0
30 TraesCS6B01G054000 chr2B 81.944 72 13 0 2090 2161 60122575 60122646 8.830000e-06 62.1
31 TraesCS6B01G054000 chr4D 88.710 62 7 0 2105 2166 10475430 10475491 3.150000e-10 76.8
32 TraesCS6B01G054000 chr4D 77.778 144 19 8 2704 2845 427943173 427943305 3.150000e-10 76.8


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 TraesCS6B01G054000 chr6B 34092442 34095390 2948 False 5446 5446 100.0000 1 2949 1 chr6B.!!$F1 2948
1 TraesCS6B01G054000 chr6D 20120388 20123036 2648 False 1414 2355 89.0545 577 2949 2 chr6D.!!$F2 2372
2 TraesCS6B01G054000 chr6D 20134457 20135024 567 True 599 599 85.7390 1 566 1 chr6D.!!$R1 565
3 TraesCS6B01G054000 chr6A 20162967 20164684 1717 False 1059 1589 92.1055 579 2175 2 chr6A.!!$F2 1596
4 TraesCS6B01G054000 chr7B 104298404 104298969 565 False 667 667 88.0070 1 565 1 chr7B.!!$F1 564
5 TraesCS6B01G054000 chr7B 748331164 748331731 567 False 632 632 86.7960 1 566 1 chr7B.!!$F2 565
6 TraesCS6B01G054000 chr7D 136414279 136414845 566 True 647 647 87.3020 1 565 1 chr7D.!!$R1 564
7 TraesCS6B01G054000 chr7D 628134568 628135133 565 False 612 612 86.2430 1 565 1 chr7D.!!$F1 564
8 TraesCS6B01G054000 chr2A 66767270 66767835 565 False 614 614 86.2430 1 566 1 chr2A.!!$F1 565
9 TraesCS6B01G054000 chr5D 76030595 76031163 568 False 606 606 85.9890 1 568 1 chr5D.!!$F2 567
10 TraesCS6B01G054000 chr3D 562513974 562514541 567 True 604 604 85.9150 1 566 1 chr3D.!!$R2 565
11 TraesCS6B01G054000 chr4A 607312012 607312581 569 False 603 603 85.7890 1 568 1 chr4A.!!$F1 567

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
229 231 0.379316 ACCGGAAGAAACACAAACGC 59.621 50.0 9.46 0.0 0.00 4.84 F
1615 1638 0.179243 GTTTTACGCTTACGCCACGG 60.179 55.0 0.00 0.0 45.53 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1673 0.257328 TGCTGTTGGGTGTCCTTTCA 59.743 50.0 0.0 0.0 0.0 2.69 R
2633 3262 0.248907 CGATAGGTGTGTACTGGCGG 60.249 60.0 0.0 0.0 0.0 6.13 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
43 44 0.876399 TAGCGACGACTACAAGCACA 59.124 50.000 0.00 0.00 0.00 4.57
45 46 0.663568 GCGACGACTACAAGCACAGT 60.664 55.000 0.00 0.00 0.00 3.55
50 51 1.401148 CGACTACAAGCACAGTAGCGT 60.401 52.381 9.33 0.00 42.04 5.07
77 78 4.819761 GAGCTGCCGTCATCGCCA 62.820 66.667 0.00 0.00 35.54 5.69
131 133 4.618920 AGTAGACAGTCGGGAAATTGTT 57.381 40.909 0.00 0.00 0.00 2.83
140 142 2.227865 TCGGGAAATTGTTGTGCTAAGC 59.772 45.455 0.00 0.00 0.00 3.09
157 159 0.617820 AGCTCCCATAGGACCAACGT 60.618 55.000 0.00 0.00 37.19 3.99
176 178 1.067071 GTAGTAGAACAGCAACCGCCT 60.067 52.381 0.00 0.00 39.83 5.52
207 209 6.436738 AGAGTAGTGTAGATCGGAAGGATA 57.563 41.667 0.00 0.00 34.82 2.59
229 231 0.379316 ACCGGAAGAAACACAAACGC 59.621 50.000 9.46 0.00 0.00 4.84
292 294 3.680786 CGCCGGAGACACACCTCA 61.681 66.667 5.05 0.00 34.94 3.86
293 295 2.262915 GCCGGAGACACACCTCAG 59.737 66.667 5.05 0.00 34.94 3.35
302 304 1.379443 CACACCTCAGCATGCCCAT 60.379 57.895 15.66 0.00 34.76 4.00
308 310 3.274586 CAGCATGCCCATCGACGG 61.275 66.667 15.66 0.00 0.00 4.79
344 347 4.810184 AACGGGGATAGGCGGGGT 62.810 66.667 0.00 0.00 0.00 4.95
415 418 7.342284 TGAATAGGACACAAACCCTAACAAAAA 59.658 33.333 0.00 0.00 38.42 1.94
425 428 9.679661 ACAAACCCTAACAAAAATTGAAGAAAT 57.320 25.926 0.00 0.00 0.00 2.17
426 429 9.934190 CAAACCCTAACAAAAATTGAAGAAATG 57.066 29.630 0.00 0.00 0.00 2.32
447 450 3.008049 TGTCTAAAAACAGAGCCCTCCTC 59.992 47.826 0.00 0.00 41.07 3.71
449 452 1.450360 AAAAACAGAGCCCTCCTCCT 58.550 50.000 0.00 0.00 41.74 3.69
469 472 2.835431 CGAGGGCCGAGATCCACT 60.835 66.667 0.00 0.00 41.76 4.00
506 509 3.695606 GCCACCAGAGACGAGGCA 61.696 66.667 0.00 0.00 44.59 4.75
547 550 1.341089 GGAGGCAAAGGAACCCTAAGG 60.341 57.143 0.00 0.00 40.04 2.69
568 572 2.142292 TTTCTTGGGAGGAGGCTGCC 62.142 60.000 11.65 11.65 35.23 4.85
569 573 4.120755 CTTGGGAGGAGGCTGCCC 62.121 72.222 16.57 6.85 42.38 5.36
573 577 4.785453 GGAGGAGGCTGCCCGTTG 62.785 72.222 16.57 0.00 35.76 4.10
574 578 3.706373 GAGGAGGCTGCCCGTTGA 61.706 66.667 16.57 0.00 35.76 3.18
575 579 3.249189 AGGAGGCTGCCCGTTGAA 61.249 61.111 16.57 0.00 35.76 2.69
644 654 5.627499 TGACACTGGTGCTTAATCAATTC 57.373 39.130 0.17 0.00 0.00 2.17
668 678 1.843421 TGTTGGCCTAACAGGTGCT 59.157 52.632 14.38 0.00 44.07 4.40
724 736 3.055094 TCCAACTGCCCTCTATTCAGAAC 60.055 47.826 0.00 0.00 0.00 3.01
783 795 4.261072 CCGACAACTACGACAGCATACTAT 60.261 45.833 0.00 0.00 0.00 2.12
839 859 4.261801 AGAAGTGTACCATTGGCATGTAC 58.738 43.478 1.54 12.77 0.00 2.90
840 860 4.019321 AGAAGTGTACCATTGGCATGTACT 60.019 41.667 17.67 0.00 0.00 2.73
841 861 5.188948 AGAAGTGTACCATTGGCATGTACTA 59.811 40.000 17.67 7.04 0.00 1.82
842 862 5.630415 AGTGTACCATTGGCATGTACTAT 57.370 39.130 17.67 8.20 0.00 2.12
861 881 9.884636 TGTACTATTATATGTTTGCTGTTGAGT 57.115 29.630 0.00 0.00 0.00 3.41
901 921 7.497909 TGACATTATAGTCGAGACATGTCTACA 59.502 37.037 27.95 14.62 39.61 2.74
984 1004 1.003839 TACTGAGCCTTGGTTGCCG 60.004 57.895 0.00 0.00 0.00 5.69
1066 1086 2.434185 GCCTCGTGTTCCGCATCA 60.434 61.111 0.00 0.00 36.19 3.07
1198 1218 5.529800 GGCAACTACAACTCCTTCAAGTAAA 59.470 40.000 0.00 0.00 0.00 2.01
1216 1236 7.559590 AAGTAAATCAGCATACTTGTCCATC 57.440 36.000 0.00 0.00 40.04 3.51
1227 1247 0.392863 TTGTCCATCGACCAGGCATG 60.393 55.000 0.00 0.00 38.32 4.06
1367 1390 2.743718 CAGCCAAGGTCGTGGAGT 59.256 61.111 7.11 0.00 41.65 3.85
1615 1638 0.179243 GTTTTACGCTTACGCCACGG 60.179 55.000 0.00 0.00 45.53 4.94
1616 1639 1.899521 TTTTACGCTTACGCCACGGC 61.900 55.000 0.00 0.00 45.53 5.68
1617 1640 2.768503 TTTACGCTTACGCCACGGCT 62.769 55.000 6.48 0.00 45.53 5.52
1618 1641 1.932011 TTACGCTTACGCCACGGCTA 61.932 55.000 6.48 0.00 45.53 3.93
1619 1642 2.597117 TACGCTTACGCCACGGCTAC 62.597 60.000 6.48 0.00 45.53 3.58
1622 1645 4.132441 TTACGCCACGGCTACGGG 62.132 66.667 6.48 0.00 46.48 5.28
1650 1673 1.870064 CCAGCCAGGGAAATTCCAAT 58.130 50.000 14.68 0.00 38.64 3.16
1654 1677 3.261390 CAGCCAGGGAAATTCCAATGAAA 59.739 43.478 14.68 0.00 38.64 2.69
1658 1681 4.081476 CCAGGGAAATTCCAATGAAAGGAC 60.081 45.833 14.68 0.00 38.64 3.85
1661 1774 4.322725 GGGAAATTCCAATGAAAGGACACC 60.323 45.833 14.68 0.00 38.64 4.16
1743 1904 2.498167 CAAGTGTGGAGAAGAACCAGG 58.502 52.381 0.00 0.00 38.14 4.45
1747 1908 2.269241 GGAGAAGAACCAGGGCCG 59.731 66.667 0.00 0.00 0.00 6.13
1756 1923 4.415150 CCAGGGCCGTGCACAGAT 62.415 66.667 20.20 0.00 32.33 2.90
1950 2124 8.192774 AGCATGTGTTTATGTCCATGAATAAAG 58.807 33.333 0.00 0.00 37.47 1.85
2080 2255 7.316640 TGTACCAATTAAATGACCGATTTTGG 58.683 34.615 0.00 0.00 36.26 3.28
2090 2265 2.667969 GACCGATTTTGGATTTGCTTGC 59.332 45.455 0.00 0.00 0.00 4.01
2116 2291 6.849085 TGTACTCCCTACGGTACATTTTAA 57.151 37.500 0.00 0.00 41.90 1.52
2184 2360 9.993454 TGATCAAATATACTCTCTCCATTCTTG 57.007 33.333 0.00 0.00 0.00 3.02
2217 2393 7.639162 TTTTCTAGAGATTTCGACAAGTGAC 57.361 36.000 0.00 0.00 0.00 3.67
2218 2394 6.576662 TTCTAGAGATTTCGACAAGTGACT 57.423 37.500 0.00 0.00 0.00 3.41
2219 2395 7.683437 TTCTAGAGATTTCGACAAGTGACTA 57.317 36.000 0.00 0.00 0.00 2.59
2220 2396 7.074507 TCTAGAGATTTCGACAAGTGACTAC 57.925 40.000 0.00 0.00 0.00 2.73
2221 2397 5.707242 AGAGATTTCGACAAGTGACTACA 57.293 39.130 0.00 0.00 0.00 2.74
2222 2398 6.274157 AGAGATTTCGACAAGTGACTACAT 57.726 37.500 0.00 0.00 0.00 2.29
2223 2399 7.392494 AGAGATTTCGACAAGTGACTACATA 57.608 36.000 0.00 0.00 0.00 2.29
2224 2400 7.251994 AGAGATTTCGACAAGTGACTACATAC 58.748 38.462 0.00 0.00 0.00 2.39
2225 2401 6.028368 AGATTTCGACAAGTGACTACATACG 58.972 40.000 0.00 0.00 0.00 3.06
2226 2402 5.361135 TTTCGACAAGTGACTACATACGA 57.639 39.130 0.00 0.00 0.00 3.43
2227 2403 5.361135 TTCGACAAGTGACTACATACGAA 57.639 39.130 0.00 0.00 35.49 3.85
2228 2404 4.966249 TCGACAAGTGACTACATACGAAG 58.034 43.478 0.00 0.00 0.00 3.79
2229 2405 3.542704 CGACAAGTGACTACATACGAAGC 59.457 47.826 0.00 0.00 0.00 3.86
2230 2406 4.482386 GACAAGTGACTACATACGAAGCA 58.518 43.478 0.00 0.00 0.00 3.91
2231 2407 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2232 2408 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2233 2409 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2234 2410 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2235 2411 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2236 2412 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2237 2413 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2238 2414 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2239 2415 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2240 2416 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2241 2417 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2242 2418 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2243 2419 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2244 2420 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2245 2421 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2246 2422 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2247 2423 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2248 2424 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2296 2472 9.653287 TCCGTATATGATAGTCCATTTGAAATC 57.347 33.333 0.00 0.00 0.00 2.17
2297 2473 9.658799 CCGTATATGATAGTCCATTTGAAATCT 57.341 33.333 0.00 0.00 0.00 2.40
2303 2479 9.690913 ATGATAGTCCATTTGAAATCTCTGAAA 57.309 29.630 0.00 0.00 0.00 2.69
2304 2480 9.519191 TGATAGTCCATTTGAAATCTCTGAAAA 57.481 29.630 0.00 0.00 0.00 2.29
2306 2482 9.745018 ATAGTCCATTTGAAATCTCTGAAAAGA 57.255 29.630 0.00 0.00 0.00 2.52
2307 2483 7.880105 AGTCCATTTGAAATCTCTGAAAAGAC 58.120 34.615 0.00 0.00 0.00 3.01
2308 2484 7.503566 AGTCCATTTGAAATCTCTGAAAAGACA 59.496 33.333 0.00 0.00 0.00 3.41
2309 2485 8.137437 GTCCATTTGAAATCTCTGAAAAGACAA 58.863 33.333 0.00 0.00 0.00 3.18
2310 2486 8.694540 TCCATTTGAAATCTCTGAAAAGACAAA 58.305 29.630 0.00 0.00 0.00 2.83
2311 2487 9.485206 CCATTTGAAATCTCTGAAAAGACAAAT 57.515 29.630 0.00 0.00 33.34 2.32
2322 2498 9.760660 CTCTGAAAAGACAAATATTTAGGAACG 57.239 33.333 0.00 0.00 0.00 3.95
2323 2499 8.726988 TCTGAAAAGACAAATATTTAGGAACGG 58.273 33.333 0.00 0.00 0.00 4.44
2324 2500 8.624367 TGAAAAGACAAATATTTAGGAACGGA 57.376 30.769 0.00 0.00 0.00 4.69
2325 2501 8.726988 TGAAAAGACAAATATTTAGGAACGGAG 58.273 33.333 0.00 0.00 0.00 4.63
2326 2502 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2327 2503 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
2328 2504 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
2329 2505 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
2330 2506 6.718294 ACAAATATTTAGGAACGGAGGAAGT 58.282 36.000 0.00 0.00 0.00 3.01
2331 2507 7.854337 ACAAATATTTAGGAACGGAGGAAGTA 58.146 34.615 0.00 0.00 0.00 2.24
2332 2508 8.491958 ACAAATATTTAGGAACGGAGGAAGTAT 58.508 33.333 0.00 0.00 0.00 2.12
2341 2517 7.574607 AGGAACGGAGGAAGTATATTGAAATT 58.425 34.615 0.00 0.00 0.00 1.82
2394 2572 5.598416 AAAAAGTAAATGCAGATAGGCCC 57.402 39.130 0.00 0.00 0.00 5.80
2395 2573 3.951563 AAGTAAATGCAGATAGGCCCA 57.048 42.857 0.00 0.00 0.00 5.36
2396 2574 3.214696 AGTAAATGCAGATAGGCCCAC 57.785 47.619 0.00 0.00 0.00 4.61
2400 2578 1.422161 ATGCAGATAGGCCCACTCCC 61.422 60.000 0.00 0.00 0.00 4.30
2405 2583 0.846693 GATAGGCCCACTCCCAATGT 59.153 55.000 0.00 0.00 0.00 2.71
2413 2591 1.153524 ACTCCCAATGTGGCTTGCA 59.846 52.632 0.00 0.00 35.79 4.08
2421 2599 0.957395 ATGTGGCTTGCAGAGTTCCG 60.957 55.000 0.00 0.00 0.00 4.30
2429 2607 2.607892 GCAGAGTTCCGTGTGCACC 61.608 63.158 15.69 4.74 35.91 5.01
2449 2627 5.931724 GCACCCATTACTAAATTTGCAAGTT 59.068 36.000 0.65 0.65 0.00 2.66
2461 3083 7.472334 AAATTTGCAAGTTGGAGATACATCT 57.528 32.000 8.06 0.00 40.50 2.90
2483 3105 0.178947 GACCCATCCAAAACCCCACA 60.179 55.000 0.00 0.00 0.00 4.17
2487 3109 1.906333 ATCCAAAACCCCACACGGC 60.906 57.895 0.00 0.00 0.00 5.68
2503 3126 4.815108 GCCCCGTGTTCCCATCCC 62.815 72.222 0.00 0.00 0.00 3.85
2511 3134 0.253583 TGTTCCCATCCCATCCCTCA 60.254 55.000 0.00 0.00 0.00 3.86
2516 3139 2.184339 TCCCATCCCATCCCTCATTCTA 59.816 50.000 0.00 0.00 0.00 2.10
2518 3141 4.048440 TCCCATCCCATCCCTCATTCTATA 59.952 45.833 0.00 0.00 0.00 1.31
2524 3147 5.017757 TCCCATCCCTCATTCTATAGATCCA 59.982 44.000 2.58 0.00 0.00 3.41
2528 3151 7.364585 CCATCCCTCATTCTATAGATCCACTTC 60.365 44.444 2.58 0.00 0.00 3.01
2529 3152 6.019748 TCCCTCATTCTATAGATCCACTTCC 58.980 44.000 2.58 0.00 0.00 3.46
2534 3157 5.688220 TTCTATAGATCCACTTCCTCCCT 57.312 43.478 2.58 0.00 0.00 4.20
2537 3160 2.885388 AGATCCACTTCCTCCCTCAT 57.115 50.000 0.00 0.00 0.00 2.90
2556 3185 4.221422 GCCGCCGCTCTACCATCA 62.221 66.667 0.00 0.00 0.00 3.07
2557 3186 2.499205 CCGCCGCTCTACCATCAA 59.501 61.111 0.00 0.00 0.00 2.57
2561 3190 1.227674 CCGCTCTACCATCAAGGCC 60.228 63.158 0.00 0.00 43.14 5.19
2578 3207 2.892425 CGCCTGCTAAGCCCTTCG 60.892 66.667 0.00 0.00 0.00 3.79
2579 3208 2.584608 GCCTGCTAAGCCCTTCGA 59.415 61.111 0.00 0.00 0.00 3.71
2582 3211 0.755686 CCTGCTAAGCCCTTCGAGAT 59.244 55.000 0.00 0.00 0.00 2.75
2587 3216 1.686052 CTAAGCCCTTCGAGATGCTCT 59.314 52.381 5.31 0.00 32.62 4.09
2598 3227 0.969917 AGATGCTCTGCGACCTCTGT 60.970 55.000 0.00 0.00 0.00 3.41
2608 3237 2.997897 ACCTCTGTCGCTCCACCC 60.998 66.667 0.00 0.00 0.00 4.61
2613 3242 3.633094 CTGTCGCTCCACCCAGTCG 62.633 68.421 0.00 0.00 0.00 4.18
2619 3248 3.302347 CTCCACCCAGTCGCCTCAC 62.302 68.421 0.00 0.00 0.00 3.51
2632 3261 2.100631 CCTCACCGCTTTGCCTACG 61.101 63.158 0.00 0.00 0.00 3.51
2633 3262 2.740714 CTCACCGCTTTGCCTACGC 61.741 63.158 0.00 0.00 0.00 4.42
2654 3283 1.135199 CGCCAGTACACACCTATCGTT 60.135 52.381 0.00 0.00 0.00 3.85
2665 3294 1.138036 CTATCGTTCGTCCGCCACA 59.862 57.895 0.00 0.00 0.00 4.17
2679 3308 1.980052 CCACACAGGTACCATCCGT 59.020 57.895 15.94 2.41 0.00 4.69
2680 3309 1.187974 CCACACAGGTACCATCCGTA 58.812 55.000 15.94 0.00 0.00 4.02
2709 3338 1.589803 GTCAACACGCCCTACAAGTT 58.410 50.000 0.00 0.00 0.00 2.66
2711 3340 2.032290 GTCAACACGCCCTACAAGTTTC 60.032 50.000 0.00 0.00 0.00 2.78
2721 3350 4.581868 CCCTACAAGTTTCCGGTGAAATA 58.418 43.478 0.00 0.00 42.20 1.40
2724 3353 2.224784 ACAAGTTTCCGGTGAAATACGC 59.775 45.455 0.00 0.00 42.20 4.42
2764 3393 5.649782 TCCTTCTTTGAAGCAATGGATTC 57.350 39.130 0.00 0.00 39.83 2.52
2772 3401 4.009002 TGAAGCAATGGATTCGAACATGA 58.991 39.130 0.00 0.00 42.27 3.07
2796 3425 5.535333 AGTACATGTACAAGCACTACGTTT 58.465 37.500 32.02 8.89 38.48 3.60
2797 3426 6.680810 AGTACATGTACAAGCACTACGTTTA 58.319 36.000 32.02 0.00 38.48 2.01
2799 3428 5.535333 ACATGTACAAGCACTACGTTTAGT 58.465 37.500 0.00 0.00 39.30 2.24
2800 3429 7.410087 GTACATGTACAAGCACTACGTTTAGTG 60.410 40.741 27.37 13.10 44.40 2.74
2807 3436 2.997485 ACTACGTTTAGTGGTCCGAC 57.003 50.000 0.00 0.00 40.80 4.79
2821 3450 0.387929 TCCGACGTGGAGGATTATGC 59.612 55.000 0.00 0.00 43.74 3.14
2822 3451 0.939577 CCGACGTGGAGGATTATGCG 60.940 60.000 0.00 0.00 42.00 4.73
2823 3452 0.939577 CGACGTGGAGGATTATGCGG 60.940 60.000 0.00 0.00 0.00 5.69
2824 3453 0.387929 GACGTGGAGGATTATGCGGA 59.612 55.000 0.00 0.00 0.00 5.54
2825 3454 1.000955 GACGTGGAGGATTATGCGGAT 59.999 52.381 0.00 0.00 0.00 4.18
2826 3455 1.270305 ACGTGGAGGATTATGCGGATG 60.270 52.381 0.00 0.00 0.00 3.51
2827 3456 1.000843 CGTGGAGGATTATGCGGATGA 59.999 52.381 0.00 0.00 0.00 2.92
2828 3457 2.547855 CGTGGAGGATTATGCGGATGAA 60.548 50.000 0.00 0.00 0.00 2.57
2829 3458 3.679389 GTGGAGGATTATGCGGATGAAT 58.321 45.455 0.00 0.00 0.00 2.57
2830 3459 4.074970 GTGGAGGATTATGCGGATGAATT 58.925 43.478 0.00 0.00 0.00 2.17
2831 3460 4.074259 TGGAGGATTATGCGGATGAATTG 58.926 43.478 0.00 0.00 0.00 2.32
2832 3461 3.441572 GGAGGATTATGCGGATGAATTGG 59.558 47.826 0.00 0.00 0.00 3.16
2833 3462 4.074970 GAGGATTATGCGGATGAATTGGT 58.925 43.478 0.00 0.00 0.00 3.67
2834 3463 3.822735 AGGATTATGCGGATGAATTGGTG 59.177 43.478 0.00 0.00 0.00 4.17
2835 3464 3.820467 GGATTATGCGGATGAATTGGTGA 59.180 43.478 0.00 0.00 0.00 4.02
2850 3479 0.966875 GGTGATGATGCAGGCAACCA 60.967 55.000 7.10 5.02 37.17 3.67
2852 3481 1.479323 GTGATGATGCAGGCAACCAAT 59.521 47.619 0.00 0.00 37.17 3.16
2877 3506 5.629079 AATGGAAAACAACAGCTAGCTAC 57.371 39.130 18.86 0.00 0.00 3.58
2918 3547 4.749099 GGAGCATGACAAGAGTAGCAATAG 59.251 45.833 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 0.443088 CTCGTCTTCGACACGCTACT 59.557 55.000 10.58 0.00 41.35 2.57
45 46 1.134075 GCTCGTCTTCGACACGCTA 59.866 57.895 10.58 0.00 41.35 4.26
50 51 2.258591 GGCAGCTCGTCTTCGACA 59.741 61.111 0.00 0.00 41.35 4.35
52 53 3.362797 ACGGCAGCTCGTCTTCGA 61.363 61.111 3.38 0.00 44.12 3.71
106 108 7.040473 ACAATTTCCCGACTGTCTACTATAG 57.960 40.000 6.21 0.00 0.00 1.31
108 110 5.934402 ACAATTTCCCGACTGTCTACTAT 57.066 39.130 6.21 0.00 0.00 2.12
131 133 1.762957 GTCCTATGGGAGCTTAGCACA 59.237 52.381 7.07 2.69 43.12 4.57
140 142 2.385803 ACTACGTTGGTCCTATGGGAG 58.614 52.381 0.00 0.00 43.12 4.30
157 159 1.203994 GAGGCGGTTGCTGTTCTACTA 59.796 52.381 0.00 0.00 42.25 1.82
176 178 6.602009 TCCGATCTACACTACTCTTCATTTGA 59.398 38.462 0.00 0.00 0.00 2.69
207 209 2.159490 CGTTTGTGTTTCTTCCGGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
213 215 2.716398 GTCTGCGTTTGTGTTTCTTCC 58.284 47.619 0.00 0.00 0.00 3.46
229 231 2.223294 GGATCTGGTCGTAGTTCGTCTG 60.223 54.545 0.00 0.00 40.80 3.51
292 294 3.785859 ACCGTCGATGGGCATGCT 61.786 61.111 27.02 2.29 0.00 3.79
293 295 3.576356 CACCGTCGATGGGCATGC 61.576 66.667 27.02 9.90 0.00 4.06
308 310 1.171308 TCCGGTAGTGTGTCTAGCAC 58.829 55.000 0.00 9.52 44.54 4.40
344 347 4.788075 TCCCTGAAGATGGAATAAGGTTCA 59.212 41.667 0.00 0.00 0.00 3.18
415 418 8.084684 GGCTCTGTTTTTAGACATTTCTTCAAT 58.915 33.333 0.00 0.00 32.75 2.57
425 428 2.979678 AGGAGGGCTCTGTTTTTAGACA 59.020 45.455 0.00 0.00 0.00 3.41
426 429 3.601435 GAGGAGGGCTCTGTTTTTAGAC 58.399 50.000 0.00 0.00 0.00 2.59
453 456 2.818132 CAGTGGATCTCGGCCCTC 59.182 66.667 0.00 0.00 0.00 4.30
481 484 1.306997 TCTCTGGTGGCCTTAGGGG 60.307 63.158 3.32 0.00 38.36 4.79
547 550 1.539157 CAGCCTCCTCCCAAGAAAAC 58.461 55.000 0.00 0.00 0.00 2.43
568 572 1.529226 TGCATAACACCCTTCAACGG 58.471 50.000 0.00 0.00 0.00 4.44
569 573 3.243234 TGTTTGCATAACACCCTTCAACG 60.243 43.478 9.46 0.00 0.00 4.10
570 574 4.314740 TGTTTGCATAACACCCTTCAAC 57.685 40.909 9.46 0.00 0.00 3.18
571 575 5.112686 GTTTGTTTGCATAACACCCTTCAA 58.887 37.500 12.14 3.40 0.00 2.69
572 576 4.442192 GGTTTGTTTGCATAACACCCTTCA 60.442 41.667 12.14 0.00 0.00 3.02
573 577 4.055360 GGTTTGTTTGCATAACACCCTTC 58.945 43.478 12.14 4.39 0.00 3.46
574 578 3.181459 GGGTTTGTTTGCATAACACCCTT 60.181 43.478 20.80 0.00 35.02 3.95
575 579 2.367241 GGGTTTGTTTGCATAACACCCT 59.633 45.455 20.80 0.00 35.02 4.34
585 589 6.484977 TCCAATGATTTTTAGGGTTTGTTTGC 59.515 34.615 0.00 0.00 0.00 3.68
644 654 3.381272 CACCTGTTAGGCCAACAATATGG 59.619 47.826 17.65 16.71 46.37 2.74
709 721 6.765915 AAAGAAATGTTCTGAATAGAGGGC 57.234 37.500 0.00 0.00 40.59 5.19
724 736 7.973601 AGTTTGGTAGCAAACAAAAAGAAATG 58.026 30.769 37.82 0.00 44.86 2.32
783 795 5.565592 TTTAACGGCACTTCTATCGACTA 57.434 39.130 0.00 0.00 0.00 2.59
842 862 9.237187 TCCATTAACTCAACAGCAAACATATAA 57.763 29.630 0.00 0.00 0.00 0.98
861 881 8.190326 ACTATAATGTCATCGACCTCCATTAA 57.810 34.615 10.70 0.00 33.24 1.40
901 921 3.923425 AGGGGGTCAAAGAATCCTAAACT 59.077 43.478 0.00 0.00 0.00 2.66
945 965 0.832626 ATCGAGGATGGATGTGCACA 59.167 50.000 24.08 24.08 30.11 4.57
984 1004 4.384056 CTCCCATGTATGAGTGATTGGAC 58.616 47.826 0.00 0.00 0.00 4.02
1198 1218 3.493350 GGTCGATGGACAAGTATGCTGAT 60.493 47.826 10.22 0.00 45.28 2.90
1227 1247 2.835027 ACTTGAGAAGTGAAACGACCC 58.165 47.619 0.00 0.00 45.86 4.46
1367 1390 3.143675 GCAGGAGCTTGTCGATGAA 57.856 52.632 0.00 0.00 37.91 2.57
1631 1654 1.483415 CATTGGAATTTCCCTGGCTGG 59.517 52.381 12.90 2.96 35.03 4.85
1637 1660 4.528206 GTGTCCTTTCATTGGAATTTCCCT 59.472 41.667 12.90 0.00 35.03 4.20
1638 1661 4.322725 GGTGTCCTTTCATTGGAATTTCCC 60.323 45.833 12.90 0.00 35.03 3.97
1641 1664 4.230455 TGGGTGTCCTTTCATTGGAATTT 58.770 39.130 0.00 0.00 35.10 1.82
1645 1668 2.091610 TGTTGGGTGTCCTTTCATTGGA 60.092 45.455 0.00 0.00 0.00 3.53
1650 1673 0.257328 TGCTGTTGGGTGTCCTTTCA 59.743 50.000 0.00 0.00 0.00 2.69
1654 1677 2.515901 GGTGCTGTTGGGTGTCCT 59.484 61.111 0.00 0.00 0.00 3.85
1706 1819 0.906775 TTGGGTCCGGTAGGTGATTC 59.093 55.000 0.00 0.00 39.05 2.52
1707 1820 0.909623 CTTGGGTCCGGTAGGTGATT 59.090 55.000 0.00 0.00 39.05 2.57
1709 1822 1.156803 ACTTGGGTCCGGTAGGTGA 59.843 57.895 0.00 0.00 39.05 4.02
1721 1882 1.142870 TGGTTCTTCTCCACACTTGGG 59.857 52.381 0.00 0.00 44.11 4.12
1740 1901 0.464373 AATATCTGTGCACGGCCCTG 60.464 55.000 21.33 0.00 0.00 4.45
1742 1903 1.447317 CCAATATCTGTGCACGGCCC 61.447 60.000 21.33 0.00 0.00 5.80
1743 1904 1.447317 CCCAATATCTGTGCACGGCC 61.447 60.000 21.33 0.00 0.00 6.13
1747 1908 1.680338 GGGTCCCAATATCTGTGCAC 58.320 55.000 10.75 10.75 0.00 4.57
1813 1986 2.639327 GCAGCCTTGCGGGATTGTT 61.639 57.895 0.00 0.00 41.13 2.83
2010 2185 8.090214 CACACATTCCCATTGTATCTTTTTCTT 58.910 33.333 0.00 0.00 0.00 2.52
2018 2193 3.023119 TGCCACACATTCCCATTGTATC 58.977 45.455 0.00 0.00 0.00 2.24
2022 2197 4.141892 ACATAATGCCACACATTCCCATTG 60.142 41.667 0.00 0.00 46.28 2.82
2068 2243 3.860378 GCAAGCAAATCCAAAATCGGTCA 60.860 43.478 0.00 0.00 0.00 4.02
2080 2255 3.507622 AGGGAGTACAAAGCAAGCAAATC 59.492 43.478 0.00 0.00 0.00 2.17
2116 2291 7.103641 ACTTGACACAAATCTAATACGTGGAT 58.896 34.615 0.00 0.00 31.83 3.41
2192 2368 7.926555 AGTCACTTGTCGAAATCTCTAGAAAAA 59.073 33.333 0.00 0.00 0.00 1.94
2193 2369 7.434492 AGTCACTTGTCGAAATCTCTAGAAAA 58.566 34.615 0.00 0.00 0.00 2.29
2194 2370 6.982852 AGTCACTTGTCGAAATCTCTAGAAA 58.017 36.000 0.00 0.00 0.00 2.52
2195 2371 6.576662 AGTCACTTGTCGAAATCTCTAGAA 57.423 37.500 0.00 0.00 0.00 2.10
2196 2372 6.653740 TGTAGTCACTTGTCGAAATCTCTAGA 59.346 38.462 0.00 0.00 0.00 2.43
2197 2373 6.843208 TGTAGTCACTTGTCGAAATCTCTAG 58.157 40.000 0.00 0.00 0.00 2.43
2198 2374 6.812879 TGTAGTCACTTGTCGAAATCTCTA 57.187 37.500 0.00 0.00 0.00 2.43
2199 2375 5.707242 TGTAGTCACTTGTCGAAATCTCT 57.293 39.130 0.00 0.00 0.00 3.10
2200 2376 6.194876 CGTATGTAGTCACTTGTCGAAATCTC 59.805 42.308 0.00 0.00 0.00 2.75
2201 2377 6.028368 CGTATGTAGTCACTTGTCGAAATCT 58.972 40.000 0.00 0.00 0.00 2.40
2202 2378 6.025896 TCGTATGTAGTCACTTGTCGAAATC 58.974 40.000 0.00 0.00 0.00 2.17
2203 2379 5.946298 TCGTATGTAGTCACTTGTCGAAAT 58.054 37.500 0.00 0.00 0.00 2.17
2204 2380 5.361135 TCGTATGTAGTCACTTGTCGAAA 57.639 39.130 0.00 0.00 0.00 3.46
2205 2381 5.361135 TTCGTATGTAGTCACTTGTCGAA 57.639 39.130 0.00 0.00 32.74 3.71
2206 2382 4.670992 GCTTCGTATGTAGTCACTTGTCGA 60.671 45.833 0.00 0.00 0.00 4.20
2207 2383 3.542704 GCTTCGTATGTAGTCACTTGTCG 59.457 47.826 0.00 0.00 0.00 4.35
2208 2384 4.482386 TGCTTCGTATGTAGTCACTTGTC 58.518 43.478 0.00 0.00 0.00 3.18
2209 2385 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2210 2386 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2211 2387 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2212 2388 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2213 2389 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2214 2390 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2215 2391 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2216 2392 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2217 2393 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2218 2394 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2219 2395 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2220 2396 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2221 2397 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2222 2398 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2223 2399 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2224 2400 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2225 2401 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2270 2446 9.653287 GATTTCAAATGGACTATCATATACGGA 57.347 33.333 0.00 0.00 0.00 4.69
2271 2447 9.658799 AGATTTCAAATGGACTATCATATACGG 57.341 33.333 0.00 0.00 0.00 4.02
2277 2453 9.690913 TTTCAGAGATTTCAAATGGACTATCAT 57.309 29.630 0.00 0.00 0.00 2.45
2278 2454 9.519191 TTTTCAGAGATTTCAAATGGACTATCA 57.481 29.630 0.00 0.00 0.00 2.15
2280 2456 9.745018 TCTTTTCAGAGATTTCAAATGGACTAT 57.255 29.630 0.00 0.00 0.00 2.12
2281 2457 9.003658 GTCTTTTCAGAGATTTCAAATGGACTA 57.996 33.333 0.00 0.00 0.00 2.59
2282 2458 7.503566 TGTCTTTTCAGAGATTTCAAATGGACT 59.496 33.333 0.00 0.00 0.00 3.85
2283 2459 7.651808 TGTCTTTTCAGAGATTTCAAATGGAC 58.348 34.615 0.00 0.00 0.00 4.02
2284 2460 7.822161 TGTCTTTTCAGAGATTTCAAATGGA 57.178 32.000 0.00 0.00 0.00 3.41
2285 2461 8.876275 TTTGTCTTTTCAGAGATTTCAAATGG 57.124 30.769 0.00 0.00 0.00 3.16
2296 2472 9.760660 CGTTCCTAAATATTTGTCTTTTCAGAG 57.239 33.333 11.05 0.00 0.00 3.35
2297 2473 8.726988 CCGTTCCTAAATATTTGTCTTTTCAGA 58.273 33.333 11.05 0.00 0.00 3.27
2298 2474 8.726988 TCCGTTCCTAAATATTTGTCTTTTCAG 58.273 33.333 11.05 0.00 0.00 3.02
2299 2475 8.624367 TCCGTTCCTAAATATTTGTCTTTTCA 57.376 30.769 11.05 0.00 0.00 2.69
2300 2476 8.182227 CCTCCGTTCCTAAATATTTGTCTTTTC 58.818 37.037 11.05 0.00 0.00 2.29
2301 2477 7.886446 TCCTCCGTTCCTAAATATTTGTCTTTT 59.114 33.333 11.05 0.00 0.00 2.27
2302 2478 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
2303 2479 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
2304 2480 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
2305 2481 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2306 2482 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2307 2483 8.904099 ATACTTCCTCCGTTCCTAAATATTTG 57.096 34.615 11.05 1.40 0.00 2.32
2311 2487 9.370930 TCAATATACTTCCTCCGTTCCTAAATA 57.629 33.333 0.00 0.00 0.00 1.40
2312 2488 8.258850 TCAATATACTTCCTCCGTTCCTAAAT 57.741 34.615 0.00 0.00 0.00 1.40
2313 2489 7.664552 TCAATATACTTCCTCCGTTCCTAAA 57.335 36.000 0.00 0.00 0.00 1.85
2314 2490 7.664552 TTCAATATACTTCCTCCGTTCCTAA 57.335 36.000 0.00 0.00 0.00 2.69
2315 2491 7.664552 TTTCAATATACTTCCTCCGTTCCTA 57.335 36.000 0.00 0.00 0.00 2.94
2316 2492 6.555463 TTTCAATATACTTCCTCCGTTCCT 57.445 37.500 0.00 0.00 0.00 3.36
2317 2493 7.803279 AATTTCAATATACTTCCTCCGTTCC 57.197 36.000 0.00 0.00 0.00 3.62
2341 2517 5.241662 TGACGTCATTGTGGATGTTCATAA 58.758 37.500 15.76 0.00 37.16 1.90
2345 2521 4.685169 AATGACGTCATTGTGGATGTTC 57.315 40.909 36.26 0.00 44.22 3.18
2375 2553 3.203040 AGTGGGCCTATCTGCATTTACTT 59.797 43.478 4.53 0.00 0.00 2.24
2379 2557 1.133668 GGAGTGGGCCTATCTGCATTT 60.134 52.381 4.53 0.00 0.00 2.32
2394 2572 1.180456 TGCAAGCCACATTGGGAGTG 61.180 55.000 0.00 0.00 38.19 3.51
2395 2573 0.896940 CTGCAAGCCACATTGGGAGT 60.897 55.000 0.00 0.00 38.19 3.85
2396 2574 0.609957 TCTGCAAGCCACATTGGGAG 60.610 55.000 0.00 0.00 38.19 4.30
2400 2578 1.068055 GGAACTCTGCAAGCCACATTG 60.068 52.381 0.00 0.00 0.00 2.82
2405 2583 1.597854 CACGGAACTCTGCAAGCCA 60.598 57.895 0.00 0.00 0.00 4.75
2413 2591 1.768684 ATGGGTGCACACGGAACTCT 61.769 55.000 20.43 0.00 0.00 3.24
2421 2599 4.625311 GCAAATTTAGTAATGGGTGCACAC 59.375 41.667 20.43 17.25 31.85 3.82
2429 2607 7.601856 TCTCCAACTTGCAAATTTAGTAATGG 58.398 34.615 0.00 0.26 0.00 3.16
2461 3083 1.381076 GGGTTTTGGATGGGTCGGA 59.619 57.895 0.00 0.00 0.00 4.55
2497 3120 5.283763 TCTATAGAATGAGGGATGGGATGG 58.716 45.833 0.00 0.00 0.00 3.51
2503 3126 7.364585 GGAAGTGGATCTATAGAATGAGGGATG 60.365 44.444 6.52 0.00 0.00 3.51
2511 3134 6.183361 TGAGGGAGGAAGTGGATCTATAGAAT 60.183 42.308 6.52 0.00 0.00 2.40
2516 3139 4.424842 GATGAGGGAGGAAGTGGATCTAT 58.575 47.826 0.00 0.00 0.00 1.98
2518 3141 2.688477 GATGAGGGAGGAAGTGGATCT 58.312 52.381 0.00 0.00 0.00 2.75
2524 3147 2.427245 CGGCGATGAGGGAGGAAGT 61.427 63.158 0.00 0.00 0.00 3.01
2534 3157 4.266070 GTAGAGCGGCGGCGATGA 62.266 66.667 36.87 16.64 46.35 2.92
2544 3173 1.592669 CGGCCTTGATGGTAGAGCG 60.593 63.158 0.00 0.00 38.35 5.03
2556 3185 4.803908 GGCTTAGCAGGCGGCCTT 62.804 66.667 21.26 8.86 46.50 4.35
2561 3190 2.892425 CGAAGGGCTTAGCAGGCG 60.892 66.667 6.53 0.00 46.96 5.52
2608 3237 2.357517 AAAGCGGTGAGGCGACTG 60.358 61.111 0.00 0.00 44.43 3.51
2613 3242 2.046314 TAGGCAAAGCGGTGAGGC 60.046 61.111 5.17 5.17 0.00 4.70
2632 3261 0.529992 GATAGGTGTGTACTGGCGGC 60.530 60.000 0.00 0.00 0.00 6.53
2633 3262 0.248907 CGATAGGTGTGTACTGGCGG 60.249 60.000 0.00 0.00 0.00 6.13
2654 3283 2.598099 TACCTGTGTGGCGGACGA 60.598 61.111 0.00 0.00 40.22 4.20
2679 3308 1.135315 GCGTGTTGACCATCGTAGGTA 60.135 52.381 1.63 0.00 43.38 3.08
2680 3309 0.389426 GCGTGTTGACCATCGTAGGT 60.389 55.000 1.22 1.22 46.82 3.08
2709 3338 1.628447 GCACGCGTATTTCACCGGAA 61.628 55.000 13.44 0.00 0.00 4.30
2711 3340 0.802994 TAGCACGCGTATTTCACCGG 60.803 55.000 13.44 0.00 0.00 5.28
2721 3350 3.073144 ACACAAAAATTTAGCACGCGT 57.927 38.095 5.58 5.58 0.00 6.01
2724 3353 5.977129 AGAAGGAACACAAAAATTTAGCACG 59.023 36.000 0.00 0.00 0.00 5.34
2772 3401 5.130292 ACGTAGTGCTTGTACATGTACTT 57.870 39.130 30.69 14.45 42.51 2.24
2792 3421 1.005294 CCACGTCGGACCACTAAACG 61.005 60.000 1.91 0.00 36.56 3.60
2796 3425 1.676635 CCTCCACGTCGGACCACTA 60.677 63.158 1.91 0.00 39.64 2.74
2797 3426 2.783122 ATCCTCCACGTCGGACCACT 62.783 60.000 1.91 0.00 39.64 4.00
2799 3428 0.323633 TAATCCTCCACGTCGGACCA 60.324 55.000 1.91 0.00 39.64 4.02
2800 3429 1.038280 ATAATCCTCCACGTCGGACC 58.962 55.000 1.91 0.00 39.64 4.46
2801 3430 1.868519 GCATAATCCTCCACGTCGGAC 60.869 57.143 0.00 0.00 39.64 4.79
2803 3432 0.939577 CGCATAATCCTCCACGTCGG 60.940 60.000 0.00 0.00 0.00 4.79
2804 3433 0.939577 CCGCATAATCCTCCACGTCG 60.940 60.000 0.00 0.00 0.00 5.12
2805 3434 0.387929 TCCGCATAATCCTCCACGTC 59.612 55.000 0.00 0.00 0.00 4.34
2806 3435 1.048601 ATCCGCATAATCCTCCACGT 58.951 50.000 0.00 0.00 0.00 4.49
2807 3436 1.000843 TCATCCGCATAATCCTCCACG 59.999 52.381 0.00 0.00 0.00 4.94
2812 3441 3.822735 CACCAATTCATCCGCATAATCCT 59.177 43.478 0.00 0.00 0.00 3.24
2813 3442 3.820467 TCACCAATTCATCCGCATAATCC 59.180 43.478 0.00 0.00 0.00 3.01
2814 3443 5.181811 TCATCACCAATTCATCCGCATAATC 59.818 40.000 0.00 0.00 0.00 1.75
2815 3444 5.072055 TCATCACCAATTCATCCGCATAAT 58.928 37.500 0.00 0.00 0.00 1.28
2816 3445 4.459330 TCATCACCAATTCATCCGCATAA 58.541 39.130 0.00 0.00 0.00 1.90
2817 3446 4.084011 TCATCACCAATTCATCCGCATA 57.916 40.909 0.00 0.00 0.00 3.14
2818 3447 2.934887 TCATCACCAATTCATCCGCAT 58.065 42.857 0.00 0.00 0.00 4.73
2819 3448 2.416680 TCATCACCAATTCATCCGCA 57.583 45.000 0.00 0.00 0.00 5.69
2820 3449 2.606308 GCATCATCACCAATTCATCCGC 60.606 50.000 0.00 0.00 0.00 5.54
2821 3450 2.619646 TGCATCATCACCAATTCATCCG 59.380 45.455 0.00 0.00 0.00 4.18
2822 3451 3.005472 CCTGCATCATCACCAATTCATCC 59.995 47.826 0.00 0.00 0.00 3.51
2823 3452 3.552273 GCCTGCATCATCACCAATTCATC 60.552 47.826 0.00 0.00 0.00 2.92
2824 3453 2.364324 GCCTGCATCATCACCAATTCAT 59.636 45.455 0.00 0.00 0.00 2.57
2825 3454 1.752498 GCCTGCATCATCACCAATTCA 59.248 47.619 0.00 0.00 0.00 2.57
2826 3455 1.752498 TGCCTGCATCATCACCAATTC 59.248 47.619 0.00 0.00 0.00 2.17
2827 3456 1.855295 TGCCTGCATCATCACCAATT 58.145 45.000 0.00 0.00 0.00 2.32
2828 3457 1.479323 GTTGCCTGCATCATCACCAAT 59.521 47.619 0.00 0.00 0.00 3.16
2829 3458 0.889994 GTTGCCTGCATCATCACCAA 59.110 50.000 0.00 0.00 0.00 3.67
2830 3459 0.966875 GGTTGCCTGCATCATCACCA 60.967 55.000 5.31 0.00 0.00 4.17
2831 3460 0.966875 TGGTTGCCTGCATCATCACC 60.967 55.000 3.52 3.52 0.00 4.02
2832 3461 0.889994 TTGGTTGCCTGCATCATCAC 59.110 50.000 0.00 0.00 0.00 3.06
2833 3462 1.855295 ATTGGTTGCCTGCATCATCA 58.145 45.000 0.00 0.00 0.00 3.07
2834 3463 4.389890 TTTATTGGTTGCCTGCATCATC 57.610 40.909 0.00 0.00 0.00 2.92
2835 3464 4.822685 TTTTATTGGTTGCCTGCATCAT 57.177 36.364 0.00 0.00 0.00 2.45
2850 3479 7.670364 AGCTAGCTGTTGTTTTCCATTTTATT 58.330 30.769 18.57 0.00 0.00 1.40
2852 3481 6.648879 AGCTAGCTGTTGTTTTCCATTTTA 57.351 33.333 18.57 0.00 0.00 1.52
2877 3506 3.318017 CTCCTTTGTCGAGTACTTGTGG 58.682 50.000 10.00 6.34 0.00 4.17
2918 3547 2.991866 CGAGGTCGGTCTTTAAAAGGTC 59.008 50.000 0.00 0.00 35.37 3.85


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

AutoCloner maintained by Alex Coulton.