Multiple sequence alignment - TraesCS5B01G210500

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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 TraesCS5B01G210500 chr5B 100.000 4168 0 0 1 4168 381045454 381041287 0.000000e+00 7697.0
1 TraesCS5B01G210500 chr5B 81.569 510 63 15 2 482 58572966 58572459 3.910000e-105 392.0
2 TraesCS5B01G210500 chr5D 92.420 2269 95 36 1665 3918 327633237 327631031 0.000000e+00 3166.0
3 TraesCS5B01G210500 chr5D 92.418 1187 60 16 503 1668 327634443 327633266 0.000000e+00 1666.0
4 TraesCS5B01G210500 chr5D 94.064 219 13 0 3905 4123 327629084 327628866 2.400000e-87 333.0
5 TraesCS5B01G210500 chr5D 97.959 49 1 0 4120 4168 395941507 395941555 7.420000e-13 86.1
6 TraesCS5B01G210500 chr5A 90.157 2164 156 33 1780 3927 428995751 428997873 0.000000e+00 2763.0
7 TraesCS5B01G210500 chr5A 82.515 1018 97 46 593 1556 428994397 428995387 0.000000e+00 819.0
8 TraesCS5B01G210500 chr5A 82.353 119 21 0 3978 4096 606309831 606309949 2.050000e-18 104.0
9 TraesCS5B01G210500 chr3D 83.301 509 72 8 1 497 475883979 475883472 1.370000e-124 457.0
10 TraesCS5B01G210500 chr3D 84.030 263 36 5 2 263 478124410 478124667 8.950000e-62 248.0
11 TraesCS5B01G210500 chr3D 94.545 55 3 0 4114 4168 23677567 23677513 7.420000e-13 86.1
12 TraesCS5B01G210500 chr3D 97.872 47 1 0 4122 4168 443631906 443631952 9.600000e-12 82.4
13 TraesCS5B01G210500 chr4D 83.499 503 67 11 1 487 8941745 8942247 4.910000e-124 455.0
14 TraesCS5B01G210500 chr4D 80.421 475 59 15 1 444 305151309 305150838 8.640000e-87 331.0
15 TraesCS5B01G210500 chr4D 83.395 271 40 3 231 497 381113258 381113527 3.220000e-61 246.0
16 TraesCS5B01G210500 chr4D 97.872 47 1 0 4122 4168 341032559 341032605 9.600000e-12 82.4
17 TraesCS5B01G210500 chr7B 79.804 510 57 24 1 485 46977567 46977079 3.110000e-86 329.0
18 TraesCS5B01G210500 chr7B 82.927 246 37 4 231 471 675051115 675051360 2.520000e-52 217.0
19 TraesCS5B01G210500 chr7D 82.961 358 52 7 147 497 124028432 124028077 8.700000e-82 315.0
20 TraesCS5B01G210500 chr1A 88.186 237 26 2 1 237 544061583 544061817 8.820000e-72 281.0
21 TraesCS5B01G210500 chrUn 86.752 234 28 3 1 233 48507676 48507907 1.490000e-64 257.0
22 TraesCS5B01G210500 chrUn 80.515 272 43 7 231 497 65978982 65979248 2.540000e-47 200.0
23 TraesCS5B01G210500 chr6A 81.703 317 51 7 8 319 178084169 178084483 1.490000e-64 257.0
24 TraesCS5B01G210500 chr2D 86.580 231 29 2 1 230 624373450 624373221 1.920000e-63 254.0
25 TraesCS5B01G210500 chr2D 83.019 265 36 8 232 491 486486272 486486012 9.010000e-57 231.0
26 TraesCS5B01G210500 chr2D 97.872 47 1 0 4122 4168 566833001 566833047 9.600000e-12 82.4
27 TraesCS5B01G210500 chr2A 83.026 271 40 6 231 497 679983558 679983290 1.500000e-59 241.0
28 TraesCS5B01G210500 chr4B 83.761 234 36 2 1 233 578048155 578047923 1.950000e-53 220.0
29 TraesCS5B01G210500 chr4B 89.394 66 6 1 4101 4166 177852930 177852994 9.600000e-12 82.4
30 TraesCS5B01G210500 chr1B 98.077 52 0 1 4118 4168 414777684 414777633 5.740000e-14 89.8
31 TraesCS5B01G210500 chr1B 97.872 47 1 0 4122 4168 48620329 48620375 9.600000e-12 82.4
32 TraesCS5B01G210500 chr6B 97.959 49 1 0 4120 4168 435581826 435581874 7.420000e-13 86.1


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 TraesCS5B01G210500 chr5B 381041287 381045454 4167 True 7697.000000 7697 100.000000 1 4168 1 chr5B.!!$R2 4167
1 TraesCS5B01G210500 chr5B 58572459 58572966 507 True 392.000000 392 81.569000 2 482 1 chr5B.!!$R1 480
2 TraesCS5B01G210500 chr5D 327628866 327634443 5577 True 1721.666667 3166 92.967333 503 4123 3 chr5D.!!$R1 3620
3 TraesCS5B01G210500 chr5A 428994397 428997873 3476 False 1791.000000 2763 86.336000 593 3927 2 chr5A.!!$F2 3334
4 TraesCS5B01G210500 chr3D 475883472 475883979 507 True 457.000000 457 83.301000 1 497 1 chr3D.!!$R2 496
5 TraesCS5B01G210500 chr4D 8941745 8942247 502 False 455.000000 455 83.499000 1 487 1 chr4D.!!$F1 486

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
490 534 0.174845 GGTAAAATTTGAGGCCCGCC 59.825 55.0 0.00 0.00 0.0 6.13 F
1264 1356 0.179018 AGTGCGCTTGGGAAGAACTT 60.179 50.0 9.73 0.00 0.0 2.66 F
1265 1357 0.238553 GTGCGCTTGGGAAGAACTTC 59.761 55.0 9.73 6.06 38.8 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1605 0.252239 GGGGGAGGGACAAGCAAAAT 60.252 55.000 0.00 0.0 0.00 1.82 R
2528 2820 0.530431 CATCATCGTGCGGGTCATGA 60.530 55.000 0.00 0.0 44.18 3.07 R
3191 3488 1.077212 GATGCACACCTGGCCTCAT 60.077 57.895 3.32 0.0 0.00 2.90 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
30 31 5.053811 TCTCGCTGTTTGAACAAGATAACA 58.946 37.500 0.00 0.00 38.66 2.41
60 61 7.493645 CACTAGACTGCATTTCATCAACTGATA 59.506 37.037 0.00 0.00 32.72 2.15
99 100 3.909776 AGTTCGTCTCGTTCATGTACA 57.090 42.857 0.00 0.00 0.00 2.90
105 108 4.798387 TCGTCTCGTTCATGTACATTGATG 59.202 41.667 5.37 3.52 0.00 3.07
121 124 4.422073 TTGATGCCCCTACTACAATGAG 57.578 45.455 0.00 0.00 0.00 2.90
166 172 6.344572 TCGATTTTTATCGACAGATTGTGG 57.655 37.500 6.17 0.00 46.64 4.17
299 338 2.306512 TGGACAACCCGGCTATTTAAGT 59.693 45.455 0.00 0.00 37.93 2.24
319 358 3.374745 GTCGGTCGACTAGTTTTTCACA 58.625 45.455 16.46 0.00 41.57 3.58
324 363 1.862201 CGACTAGTTTTTCACACGGCA 59.138 47.619 0.00 0.00 0.00 5.69
341 380 3.244284 ACGGCAAGGTGTGACTAATACAA 60.244 43.478 0.00 0.00 30.19 2.41
384 424 7.159437 TGAGCAATTTTTGTATGTTTTGACG 57.841 32.000 0.00 0.00 0.00 4.35
386 426 6.045955 AGCAATTTTTGTATGTTTTGACGGT 58.954 32.000 0.00 0.00 0.00 4.83
418 459 0.815734 AGACGGACGGAATGATCGTT 59.184 50.000 0.00 0.00 41.22 3.85
428 469 1.402968 GAATGATCGTTGTGCATGGCT 59.597 47.619 4.51 0.00 0.00 4.75
438 482 4.201901 CGTTGTGCATGGCTCATGTAATAA 60.202 41.667 14.21 7.92 43.10 1.40
444 488 6.418819 GTGCATGGCTCATGTAATAAATGTTC 59.581 38.462 14.21 0.00 43.10 3.18
466 510 9.344772 TGTTCTAAAAATAGTGTATGTGGTTGT 57.655 29.630 0.00 0.00 0.00 3.32
487 531 6.043854 TGTAAATGGTAAAATTTGAGGCCC 57.956 37.500 0.00 0.00 32.16 5.80
490 534 0.174845 GGTAAAATTTGAGGCCCGCC 59.825 55.000 0.00 0.00 0.00 6.13
516 560 1.277326 CGCGGACAGATCATTTCGAA 58.723 50.000 0.00 0.00 0.00 3.71
519 563 2.600792 GCGGACAGATCATTTCGAATGC 60.601 50.000 0.00 0.00 0.00 3.56
521 565 3.249320 CGGACAGATCATTTCGAATGCAT 59.751 43.478 0.00 0.00 0.00 3.96
528 572 8.288208 ACAGATCATTTCGAATGCATATTTCTC 58.712 33.333 0.00 0.00 0.00 2.87
529 573 8.504815 CAGATCATTTCGAATGCATATTTCTCT 58.495 33.333 0.00 0.00 0.00 3.10
534 578 5.535753 TCGAATGCATATTTCTCTGGAGA 57.464 39.130 0.00 0.00 35.27 3.71
535 579 5.917462 TCGAATGCATATTTCTCTGGAGAA 58.083 37.500 0.00 8.74 44.94 2.87
552 596 3.057174 GGAGAAATATCGATCGACCAGCT 60.057 47.826 22.06 13.89 0.00 4.24
562 606 2.822399 GACCAGCTGATACGGGGG 59.178 66.667 17.39 0.00 0.00 5.40
576 620 1.282157 ACGGGGGAGATTTTCTTGAGG 59.718 52.381 0.00 0.00 0.00 3.86
697 746 3.817084 TGCCAGATGAAGCATGTATAAGC 59.183 43.478 0.00 0.00 33.08 3.09
698 747 4.070716 GCCAGATGAAGCATGTATAAGCT 58.929 43.478 0.00 0.00 44.31 3.74
744 799 1.541588 CTACAAAGCCTTGGGACTTGC 59.458 52.381 0.00 0.00 36.82 4.01
780 845 1.089481 CGCTCCAATAAGCAAGCCGA 61.089 55.000 0.00 0.00 42.62 5.54
1059 1132 6.469275 GCGATCTTTATTTTGCAGTAGGTTTC 59.531 38.462 0.00 0.00 0.00 2.78
1071 1144 4.261572 GCAGTAGGTTTCATGTGCTTGAAA 60.262 41.667 8.54 8.54 41.92 2.69
1072 1145 5.735922 GCAGTAGGTTTCATGTGCTTGAAAA 60.736 40.000 12.67 0.00 44.71 2.29
1091 1164 2.033448 GTGCGGATGGGTGGTTGA 59.967 61.111 0.00 0.00 0.00 3.18
1102 1189 1.244019 GGTGGTTGACTGGTGATGGC 61.244 60.000 0.00 0.00 0.00 4.40
1142 1229 1.226746 GGCGCTATGGTAATGTGACC 58.773 55.000 7.64 0.00 40.21 4.02
1250 1342 2.811317 GGCCTTCTCGTGAGTGCG 60.811 66.667 0.00 0.00 0.00 5.34
1260 1352 1.301716 GTGAGTGCGCTTGGGAAGA 60.302 57.895 9.73 0.00 0.00 2.87
1261 1353 0.884704 GTGAGTGCGCTTGGGAAGAA 60.885 55.000 9.73 0.00 0.00 2.52
1262 1354 0.884704 TGAGTGCGCTTGGGAAGAAC 60.885 55.000 9.73 0.00 0.00 3.01
1263 1355 0.603975 GAGTGCGCTTGGGAAGAACT 60.604 55.000 9.73 0.00 0.00 3.01
1264 1356 0.179018 AGTGCGCTTGGGAAGAACTT 60.179 50.000 9.73 0.00 0.00 2.66
1265 1357 0.238553 GTGCGCTTGGGAAGAACTTC 59.761 55.000 9.73 6.06 38.80 3.01
1280 1372 4.137543 AGAACTTCCGCTTTCTTGTTCAT 58.862 39.130 0.00 0.00 37.03 2.57
1317 1409 5.823570 GTGTGCTATAGACTAGTCCAGAAGA 59.176 44.000 19.38 5.02 0.00 2.87
1319 1411 6.319152 TGTGCTATAGACTAGTCCAGAAGAAC 59.681 42.308 19.38 15.46 0.00 3.01
1338 1433 4.517832 AGAACGACCACCATTTCCTTTAAC 59.482 41.667 0.00 0.00 0.00 2.01
1400 1497 7.651808 TCTCTGCTTTTACTCCTTGAAAAATG 58.348 34.615 0.00 0.00 0.00 2.32
1472 1576 5.768317 TCAAAGTTATTTTTGCTTCCTCGG 58.232 37.500 0.00 0.00 37.83 4.63
1620 1822 4.864916 GCGATGAAGCTAACTTTGATGA 57.135 40.909 0.00 0.00 35.82 2.92
1621 1823 4.582459 GCGATGAAGCTAACTTTGATGAC 58.418 43.478 0.00 0.00 35.82 3.06
1673 1945 5.014123 ACATTCCCTGACTTGTTCTCCATTA 59.986 40.000 0.00 0.00 0.00 1.90
1697 1969 9.595823 TTATTTTCTATCCCTAACTCTGTTTCG 57.404 33.333 0.00 0.00 0.00 3.46
1700 1972 2.450609 TCCCTAACTCTGTTTCGTGC 57.549 50.000 0.00 0.00 0.00 5.34
1707 1979 2.515854 ACTCTGTTTCGTGCTCTCCTA 58.484 47.619 0.00 0.00 0.00 2.94
1758 2037 7.231317 TCAAAGTCTCAACTAATGGAAGCAAAT 59.769 33.333 0.00 0.00 33.48 2.32
1760 2039 7.617041 AGTCTCAACTAATGGAAGCAAATAC 57.383 36.000 0.00 0.00 32.59 1.89
1762 2041 7.665559 AGTCTCAACTAATGGAAGCAAATACAA 59.334 33.333 0.00 0.00 32.59 2.41
1827 2107 7.149128 GCATACTTTGATTTTCTCGTGTTTGTC 60.149 37.037 0.00 0.00 0.00 3.18
1956 2245 9.387123 GTTTTGTTCTATTGATCTGAAGTCAAC 57.613 33.333 0.00 0.00 38.31 3.18
1963 2252 8.424918 TCTATTGATCTGAAGTCAACTAATCCC 58.575 37.037 0.00 0.00 38.31 3.85
1971 2260 4.457834 AGTCAACTAATCCCGTCTGAAG 57.542 45.455 0.00 0.00 0.00 3.02
1972 2261 3.833070 AGTCAACTAATCCCGTCTGAAGT 59.167 43.478 0.00 0.00 0.00 3.01
1974 2263 5.479375 AGTCAACTAATCCCGTCTGAAGTTA 59.521 40.000 0.00 0.00 0.00 2.24
1975 2264 5.575995 GTCAACTAATCCCGTCTGAAGTTAC 59.424 44.000 0.00 0.00 0.00 2.50
1976 2265 5.244402 TCAACTAATCCCGTCTGAAGTTACA 59.756 40.000 0.00 0.00 0.00 2.41
1977 2266 5.069501 ACTAATCCCGTCTGAAGTTACAC 57.930 43.478 0.00 0.00 0.00 2.90
1978 2267 4.771054 ACTAATCCCGTCTGAAGTTACACT 59.229 41.667 0.00 0.00 0.00 3.55
1979 2268 3.594603 ATCCCGTCTGAAGTTACACTG 57.405 47.619 0.00 0.00 0.00 3.66
1980 2269 1.616865 TCCCGTCTGAAGTTACACTGG 59.383 52.381 0.00 0.00 0.00 4.00
1981 2270 1.343465 CCCGTCTGAAGTTACACTGGT 59.657 52.381 0.00 0.00 0.00 4.00
1982 2271 2.559668 CCCGTCTGAAGTTACACTGGTA 59.440 50.000 0.00 0.00 0.00 3.25
1983 2272 3.194968 CCCGTCTGAAGTTACACTGGTAT 59.805 47.826 0.00 0.00 0.00 2.73
1985 2274 5.105635 CCCGTCTGAAGTTACACTGGTATTA 60.106 44.000 0.00 0.00 0.00 0.98
1989 2278 7.921214 CGTCTGAAGTTACACTGGTATTATCAT 59.079 37.037 0.00 0.00 0.00 2.45
1997 2286 9.477484 GTTACACTGGTATTATCATAAGTCAGG 57.523 37.037 8.42 2.77 0.00 3.86
1998 2287 6.525629 ACACTGGTATTATCATAAGTCAGGC 58.474 40.000 8.42 0.00 0.00 4.85
1999 2288 6.327626 ACACTGGTATTATCATAAGTCAGGCT 59.672 38.462 8.42 0.00 0.00 4.58
2000 2289 6.648310 CACTGGTATTATCATAAGTCAGGCTG 59.352 42.308 8.58 8.58 0.00 4.85
2001 2290 6.327626 ACTGGTATTATCATAAGTCAGGCTGT 59.672 38.462 15.27 0.00 0.00 4.40
2002 2291 6.759272 TGGTATTATCATAAGTCAGGCTGTC 58.241 40.000 15.27 9.24 0.00 3.51
2005 2294 7.171678 GGTATTATCATAAGTCAGGCTGTCAAC 59.828 40.741 15.27 5.50 0.00 3.18
2006 2295 4.833478 ATCATAAGTCAGGCTGTCAACT 57.167 40.909 15.27 7.99 0.00 3.16
2007 2296 5.939764 ATCATAAGTCAGGCTGTCAACTA 57.060 39.130 15.27 2.88 0.00 2.24
2008 2297 5.738619 TCATAAGTCAGGCTGTCAACTAA 57.261 39.130 15.27 0.00 0.00 2.24
2009 2298 5.724328 TCATAAGTCAGGCTGTCAACTAAG 58.276 41.667 15.27 4.89 0.00 2.18
2010 2299 2.464157 AGTCAGGCTGTCAACTAAGC 57.536 50.000 15.27 0.00 38.76 3.09
2018 2307 4.406001 GCTGTCAACTAAGCCTGTTAAC 57.594 45.455 0.00 0.00 33.12 2.01
2019 2308 3.813166 GCTGTCAACTAAGCCTGTTAACA 59.187 43.478 8.28 8.28 33.12 2.41
2020 2309 4.274950 GCTGTCAACTAAGCCTGTTAACAA 59.725 41.667 10.03 0.00 33.12 2.83
2021 2310 5.220970 GCTGTCAACTAAGCCTGTTAACAAA 60.221 40.000 10.03 0.00 33.12 2.83
2022 2311 6.126568 TGTCAACTAAGCCTGTTAACAAAC 57.873 37.500 10.03 4.64 0.00 2.93
2023 2312 5.648526 TGTCAACTAAGCCTGTTAACAAACA 59.351 36.000 10.03 0.00 0.00 2.83
2091 2381 2.238942 TCAAGCGATTGCCGACATAT 57.761 45.000 8.91 0.00 44.31 1.78
2234 2526 4.273480 CCGGACATCCAATTTAAGCTAGTG 59.727 45.833 0.00 0.00 35.14 2.74
2258 2550 8.480501 GTGTGAACTTAGGACCATACCTTTATA 58.519 37.037 0.00 0.00 41.00 0.98
2293 2585 8.999431 TGGAACTAGCAACTTAATTTAGTTCTG 58.001 33.333 17.28 7.55 44.67 3.02
2294 2586 8.451748 GGAACTAGCAACTTAATTTAGTTCTGG 58.548 37.037 17.28 15.21 44.67 3.86
2309 2601 3.118038 AGTTCTGGTGTGCAGGTTCTAAA 60.118 43.478 0.00 0.00 0.00 1.85
2318 2610 1.439679 CAGGTTCTAAAGTGCCGGAC 58.560 55.000 5.05 0.00 0.00 4.79
2476 2768 6.075984 AGTTTACAGAGGAGGAAGTAGACAA 58.924 40.000 0.00 0.00 0.00 3.18
2477 2769 6.553852 AGTTTACAGAGGAGGAAGTAGACAAA 59.446 38.462 0.00 0.00 0.00 2.83
2520 2812 5.312895 TGATACTAGCAAGCAAAGACCAAA 58.687 37.500 0.00 0.00 0.00 3.28
2526 2818 2.737039 GCAAGCAAAGACCAAACGGAAA 60.737 45.455 0.00 0.00 0.00 3.13
2528 2820 2.375146 AGCAAAGACCAAACGGAAACT 58.625 42.857 0.00 0.00 0.00 2.66
2535 2827 2.225727 GACCAAACGGAAACTCATGACC 59.774 50.000 0.00 0.00 0.00 4.02
2549 2841 0.530650 ATGACCCGCACGATGATGAC 60.531 55.000 0.00 0.00 0.00 3.06
2556 2848 1.858091 GCACGATGATGACCAGGTAG 58.142 55.000 0.00 0.00 0.00 3.18
2568 2860 3.211045 GACCAGGTAGCTTCACACAAAA 58.789 45.455 0.00 0.00 0.00 2.44
2610 2902 2.403132 GAAGCACAGGGACCAGCTGT 62.403 60.000 13.81 0.11 37.41 4.40
2612 2904 1.529244 GCACAGGGACCAGCTGTTT 60.529 57.895 13.81 0.00 0.00 2.83
2615 2910 1.880027 CACAGGGACCAGCTGTTTAAC 59.120 52.381 13.81 0.00 0.00 2.01
2619 2914 2.441750 AGGGACCAGCTGTTTAACAAGA 59.558 45.455 13.81 0.00 0.00 3.02
2647 2942 7.251281 GTCATAAGTAAGGCAAAAGATTCACC 58.749 38.462 0.00 0.00 0.00 4.02
2669 2964 3.075148 GGGGAAGAAAGCAAGTACACTC 58.925 50.000 0.00 0.00 0.00 3.51
2678 2973 1.336887 GCAAGTACACTCAAGCCGAGA 60.337 52.381 7.71 0.00 45.45 4.04
2681 2976 2.447443 AGTACACTCAAGCCGAGATCA 58.553 47.619 7.71 0.00 45.45 2.92
2694 2989 1.285578 GAGATCAGTTGCTTCGCTCC 58.714 55.000 0.00 0.00 0.00 4.70
2710 3005 2.284190 GCTCCTCAAACTACTCATGCC 58.716 52.381 0.00 0.00 0.00 4.40
2711 3006 2.093235 GCTCCTCAAACTACTCATGCCT 60.093 50.000 0.00 0.00 0.00 4.75
2749 3044 1.704628 TGCTGTTCCAGATCCAAGGAA 59.295 47.619 7.57 7.57 41.41 3.36
2950 3247 1.425066 AGACATTTGGACTGGAAGCCA 59.575 47.619 0.00 0.00 38.15 4.75
3191 3488 6.662865 ACATGGGTGAATACATTTGTTCAA 57.337 33.333 0.00 0.00 34.91 2.69
3348 3649 1.046472 AGGGATCCGCGGTGTTATGA 61.046 55.000 27.15 3.40 0.00 2.15
3349 3650 0.034896 GGGATCCGCGGTGTTATGAT 59.965 55.000 27.15 9.30 0.00 2.45
3350 3651 1.274167 GGGATCCGCGGTGTTATGATA 59.726 52.381 27.15 1.58 0.00 2.15
3351 3652 2.093658 GGGATCCGCGGTGTTATGATAT 60.094 50.000 27.15 7.57 0.00 1.63
3571 3874 7.965718 TCACATATGAACAGTGATGATGGATA 58.034 34.615 10.38 0.00 37.36 2.59
3587 3890 6.776744 TGATGGATATTTCTGATCCTCCTTG 58.223 40.000 3.49 0.00 43.00 3.61
3685 3989 3.451178 TGCCTAGTAGATCTGGGTTTCAC 59.549 47.826 5.18 0.00 45.14 3.18
3704 4008 1.413077 ACGCCAGATAGTTAAGAGCCC 59.587 52.381 0.00 0.00 0.00 5.19
3729 4033 7.148171 CCCTTTGATCTGTAGGATTTGAAGAAC 60.148 40.741 9.15 0.00 34.33 3.01
3730 4034 7.148171 CCTTTGATCTGTAGGATTTGAAGAACC 60.148 40.741 0.00 0.00 34.33 3.62
3733 4037 5.165961 TCTGTAGGATTTGAAGAACCCAG 57.834 43.478 0.00 0.00 0.00 4.45
3737 4041 6.235664 TGTAGGATTTGAAGAACCCAGTAAC 58.764 40.000 0.00 0.00 0.00 2.50
3930 6195 6.382869 ACTTGAACTTCTGAAACCATCTTG 57.617 37.500 0.00 0.00 0.00 3.02
3938 6203 4.978099 TCTGAAACCATCTTGAGAAAGCT 58.022 39.130 0.00 0.00 0.00 3.74
3996 6261 1.633561 GGGCTCTTCCGTTTACGTAC 58.366 55.000 0.00 0.00 37.74 3.67
4007 6272 2.354510 CGTTTACGTACCTCGGGATACA 59.645 50.000 0.00 0.00 44.69 2.29
4053 6318 8.482128 ACCAACAAGGAGTGAAAAATAATTGAA 58.518 29.630 0.00 0.00 41.22 2.69
4054 6319 9.323985 CCAACAAGGAGTGAAAAATAATTGAAA 57.676 29.630 0.00 0.00 41.22 2.69
4072 6337 4.668289 TGAAAACCAGTTCGAAAAGAAGC 58.332 39.130 0.00 0.00 39.95 3.86
4075 6340 2.135933 ACCAGTTCGAAAAGAAGCTCG 58.864 47.619 0.00 0.00 39.95 5.03
4106 6371 7.703058 AAAAGGGTAAACTCATGTCTTATGG 57.297 36.000 0.00 0.00 0.00 2.74
4123 6388 6.755607 GTCTTATGGAGGACGGTTAACTTTAG 59.244 42.308 5.42 0.00 0.00 1.85
4124 6389 3.967332 TGGAGGACGGTTAACTTTAGG 57.033 47.619 5.42 0.00 0.00 2.69
4125 6390 3.509442 TGGAGGACGGTTAACTTTAGGA 58.491 45.455 5.42 0.00 0.00 2.94
4126 6391 3.903090 TGGAGGACGGTTAACTTTAGGAA 59.097 43.478 5.42 0.00 0.00 3.36
4127 6392 4.533311 TGGAGGACGGTTAACTTTAGGAAT 59.467 41.667 5.42 0.00 0.00 3.01
4128 6393 5.114780 GGAGGACGGTTAACTTTAGGAATC 58.885 45.833 5.42 0.00 0.00 2.52
4129 6394 5.105023 GGAGGACGGTTAACTTTAGGAATCT 60.105 44.000 5.42 0.00 0.00 2.40
4130 6395 6.097412 GGAGGACGGTTAACTTTAGGAATCTA 59.903 42.308 5.42 0.00 0.00 1.98
4131 6396 7.364144 GGAGGACGGTTAACTTTAGGAATCTAA 60.364 40.741 5.42 0.00 33.97 2.10
4132 6397 8.087303 AGGACGGTTAACTTTAGGAATCTAAT 57.913 34.615 5.42 0.00 35.61 1.73
4133 6398 9.205513 AGGACGGTTAACTTTAGGAATCTAATA 57.794 33.333 5.42 0.00 35.61 0.98
4134 6399 9.822185 GGACGGTTAACTTTAGGAATCTAATAA 57.178 33.333 5.42 0.00 35.61 1.40
4141 6406 7.909485 ACTTTAGGAATCTAATAACTCCCGA 57.091 36.000 0.00 0.00 35.61 5.14
4142 6407 8.315220 ACTTTAGGAATCTAATAACTCCCGAA 57.685 34.615 0.00 0.00 35.61 4.30
4143 6408 8.202811 ACTTTAGGAATCTAATAACTCCCGAAC 58.797 37.037 0.00 0.00 35.61 3.95
4144 6409 5.197682 AGGAATCTAATAACTCCCGAACG 57.802 43.478 0.00 0.00 0.00 3.95
4145 6410 4.648307 AGGAATCTAATAACTCCCGAACGT 59.352 41.667 0.00 0.00 0.00 3.99
4146 6411 5.128335 AGGAATCTAATAACTCCCGAACGTT 59.872 40.000 0.00 0.00 0.00 3.99
4147 6412 5.461407 GGAATCTAATAACTCCCGAACGTTC 59.539 44.000 18.47 18.47 0.00 3.95
4158 6423 1.865725 CGAACGTTCGGATTTTGAGC 58.134 50.000 36.53 4.05 46.30 4.26
4159 6424 1.193650 CGAACGTTCGGATTTTGAGCA 59.806 47.619 36.53 0.00 46.30 4.26
4160 6425 2.159707 CGAACGTTCGGATTTTGAGCAT 60.160 45.455 36.53 0.00 46.30 3.79
4161 6426 3.666902 CGAACGTTCGGATTTTGAGCATT 60.667 43.478 36.53 0.00 46.30 3.56
4162 6427 3.915437 ACGTTCGGATTTTGAGCATTT 57.085 38.095 0.00 0.00 0.00 2.32
4163 6428 3.821841 ACGTTCGGATTTTGAGCATTTC 58.178 40.909 0.00 0.00 0.00 2.17
4164 6429 2.840176 CGTTCGGATTTTGAGCATTTCG 59.160 45.455 0.00 0.00 0.00 3.46
4165 6430 3.666902 CGTTCGGATTTTGAGCATTTCGT 60.667 43.478 0.00 0.00 0.00 3.85
4166 6431 3.740044 TCGGATTTTGAGCATTTCGTC 57.260 42.857 0.00 0.00 0.00 4.20
4167 6432 2.418628 TCGGATTTTGAGCATTTCGTCC 59.581 45.455 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.367911 AGTCTAGTGTCATGTTATCTTGTTCAA 58.632 33.333 0.00 0.00 0.00 2.69
22 23 6.286240 TGCAGTCTAGTGTCATGTTATCTT 57.714 37.500 0.00 0.00 0.00 2.40
30 31 5.737860 TGATGAAATGCAGTCTAGTGTCAT 58.262 37.500 0.00 0.00 0.00 3.06
60 61 5.333339 CGAACTTGACACTCGATGAACAATT 60.333 40.000 0.00 0.00 34.52 2.32
99 100 4.660303 TCTCATTGTAGTAGGGGCATCAAT 59.340 41.667 0.00 0.00 0.00 2.57
105 108 4.471548 TCTACTCTCATTGTAGTAGGGGC 58.528 47.826 19.54 0.00 43.51 5.80
177 183 9.334947 CAAGAGAACCATTCATGTCAATACTAT 57.665 33.333 0.00 0.00 0.00 2.12
178 184 8.321353 ACAAGAGAACCATTCATGTCAATACTA 58.679 33.333 0.00 0.00 0.00 1.82
183 189 5.375773 TGACAAGAGAACCATTCATGTCAA 58.624 37.500 16.04 6.43 42.04 3.18
195 201 5.394773 GGGTCTATCTCCTTGACAAGAGAAC 60.395 48.000 16.99 12.59 32.03 3.01
277 316 3.244981 ACTTAAATAGCCGGGTTGTCCAA 60.245 43.478 13.43 0.00 34.36 3.53
283 322 2.320745 CCGACTTAAATAGCCGGGTT 57.679 50.000 13.43 0.00 45.17 4.11
299 338 3.374745 GTGTGAAAAACTAGTCGACCGA 58.625 45.455 13.01 0.00 0.00 4.69
311 350 1.178276 ACACCTTGCCGTGTGAAAAA 58.822 45.000 3.91 0.00 45.19 1.94
313 352 4.647825 ACACCTTGCCGTGTGAAA 57.352 50.000 3.91 0.00 45.19 2.69
319 358 2.300723 TGTATTAGTCACACCTTGCCGT 59.699 45.455 0.00 0.00 0.00 5.68
324 363 6.169557 TCACACTTGTATTAGTCACACCTT 57.830 37.500 0.00 0.00 0.00 3.50
341 380 8.621532 TTGCTCATACTTAAGATTTTCACACT 57.378 30.769 10.09 0.00 0.00 3.55
374 414 2.641197 GGCTGGACCGTCAAAACAT 58.359 52.632 0.00 0.00 0.00 2.71
409 450 1.402968 GAGCCATGCACAACGATCATT 59.597 47.619 0.00 0.00 0.00 2.57
418 459 5.360429 ACATTTATTACATGAGCCATGCACA 59.640 36.000 13.19 0.00 44.80 4.57
466 510 4.382147 GCGGGCCTCAAATTTTACCATTTA 60.382 41.667 0.84 0.00 0.00 1.40
494 538 0.931005 GAAATGATCTGTCCGCGGAC 59.069 55.000 43.88 43.88 44.77 4.79
495 539 0.527600 CGAAATGATCTGTCCGCGGA 60.528 55.000 27.28 27.28 0.00 5.54
496 540 0.527600 TCGAAATGATCTGTCCGCGG 60.528 55.000 22.12 22.12 0.00 6.46
497 541 1.277326 TTCGAAATGATCTGTCCGCG 58.723 50.000 0.00 0.00 0.00 6.46
498 542 2.600792 GCATTCGAAATGATCTGTCCGC 60.601 50.000 0.00 0.00 0.00 5.54
499 543 2.609002 TGCATTCGAAATGATCTGTCCG 59.391 45.455 0.00 0.00 0.00 4.79
500 544 4.825546 ATGCATTCGAAATGATCTGTCC 57.174 40.909 0.00 0.00 0.00 4.02
501 545 8.288208 AGAAATATGCATTCGAAATGATCTGTC 58.712 33.333 3.54 0.00 32.04 3.51
528 572 4.480541 CTGGTCGATCGATATTTCTCCAG 58.519 47.826 25.13 25.13 34.91 3.86
529 573 3.305403 GCTGGTCGATCGATATTTCTCCA 60.305 47.826 22.50 19.39 0.00 3.86
534 578 4.527509 ATCAGCTGGTCGATCGATATTT 57.472 40.909 22.50 3.75 0.00 1.40
535 579 4.437524 CGTATCAGCTGGTCGATCGATATT 60.438 45.833 22.50 3.01 0.00 1.28
552 596 3.778075 TCAAGAAAATCTCCCCCGTATCA 59.222 43.478 0.00 0.00 0.00 2.15
562 606 6.382608 GGTTTTAGCACCTCAAGAAAATCTC 58.617 40.000 0.00 0.00 33.50 2.75
576 620 0.872388 CCAGACGTGGGTTTTAGCAC 59.128 55.000 0.00 0.00 40.67 4.40
614 659 1.065418 TCCCTTTTCGGAGGAGCATTC 60.065 52.381 2.51 0.00 39.25 2.67
697 746 1.685517 TGATGAGGTGCTGCTAGCTAG 59.314 52.381 16.84 16.84 42.97 3.42
698 747 1.685517 CTGATGAGGTGCTGCTAGCTA 59.314 52.381 17.23 1.31 42.97 3.32
744 799 2.406616 CGATTTGAAGGGGGTGGCG 61.407 63.158 0.00 0.00 0.00 5.69
861 926 0.892814 AGAGGCCTTGCACTTGAAGC 60.893 55.000 6.77 0.00 0.00 3.86
1032 1104 5.590259 ACCTACTGCAAAATAAAGATCGCAT 59.410 36.000 0.00 0.00 0.00 4.73
1035 1107 7.526608 TGAAACCTACTGCAAAATAAAGATCG 58.473 34.615 0.00 0.00 0.00 3.69
1059 1132 1.411394 CGCACCTTTTCAAGCACATG 58.589 50.000 0.00 0.00 0.00 3.21
1071 1144 2.840753 AACCACCCATCCGCACCTT 61.841 57.895 0.00 0.00 0.00 3.50
1072 1145 3.256960 AACCACCCATCCGCACCT 61.257 61.111 0.00 0.00 0.00 4.00
1091 1164 2.185310 GAGGTTCCGCCATCACCAGT 62.185 60.000 0.00 0.00 40.61 4.00
1102 1189 2.357517 ACGCAAGCAGAGGTTCCG 60.358 61.111 0.00 0.00 45.62 4.30
1142 1229 4.637483 TCTGCAAGAAAAACAGAGGTTG 57.363 40.909 0.00 0.00 42.31 3.77
1250 1342 0.606673 AGCGGAAGTTCTTCCCAAGC 60.607 55.000 21.33 18.72 37.84 4.01
1260 1352 3.882888 TGATGAACAAGAAAGCGGAAGTT 59.117 39.130 0.00 0.00 0.00 2.66
1261 1353 3.476552 TGATGAACAAGAAAGCGGAAGT 58.523 40.909 0.00 0.00 0.00 3.01
1262 1354 4.488126 TTGATGAACAAGAAAGCGGAAG 57.512 40.909 0.00 0.00 34.20 3.46
1263 1355 4.909696 TTTGATGAACAAGAAAGCGGAA 57.090 36.364 0.00 0.00 39.77 4.30
1264 1356 6.206634 ACTTATTTGATGAACAAGAAAGCGGA 59.793 34.615 0.00 0.00 39.77 5.54
1265 1357 6.381801 ACTTATTTGATGAACAAGAAAGCGG 58.618 36.000 0.00 0.00 39.77 5.52
1280 1372 8.967918 AGTCTATAGCACACAGTACTTATTTGA 58.032 33.333 0.00 0.00 0.00 2.69
1317 1409 3.570975 GGTTAAAGGAAATGGTGGTCGTT 59.429 43.478 0.00 0.00 0.00 3.85
1319 1411 2.160813 CGGTTAAAGGAAATGGTGGTCG 59.839 50.000 0.00 0.00 0.00 4.79
1338 1433 3.641437 TTTCCTCATGTTTTCAAGCGG 57.359 42.857 0.00 0.00 0.00 5.52
1400 1497 3.335579 ACTTCGGAGCAAAGATGTAACC 58.664 45.455 0.00 0.00 0.00 2.85
1501 1605 0.252239 GGGGGAGGGACAAGCAAAAT 60.252 55.000 0.00 0.00 0.00 1.82
1552 1660 2.618053 ACGGAGTGCGGAAAATTAGAG 58.382 47.619 9.43 0.00 42.51 2.43
1618 1820 7.655521 ACTAAGTACACTGGCATTATAGTCA 57.344 36.000 0.00 0.00 0.00 3.41
1619 1821 8.943909 AAACTAAGTACACTGGCATTATAGTC 57.056 34.615 0.00 0.00 0.00 2.59
1673 1945 7.549488 CACGAAACAGAGTTAGGGATAGAAAAT 59.451 37.037 0.00 0.00 0.00 1.82
1687 1959 1.333177 AGGAGAGCACGAAACAGAGT 58.667 50.000 0.00 0.00 0.00 3.24
1697 1969 3.130693 AGTTGTACGGAATAGGAGAGCAC 59.869 47.826 0.00 0.00 0.00 4.40
1700 1972 5.050227 CGACTAGTTGTACGGAATAGGAGAG 60.050 48.000 0.00 0.00 0.00 3.20
1707 1979 1.820519 TGCCGACTAGTTGTACGGAAT 59.179 47.619 21.30 0.00 46.94 3.01
1798 2077 5.700832 ACACGAGAAAATCAAAGTATGCAGA 59.299 36.000 0.00 0.00 0.00 4.26
1801 2080 6.636850 ACAAACACGAGAAAATCAAAGTATGC 59.363 34.615 0.00 0.00 0.00 3.14
1861 2141 2.045536 GGCTGAGAGTTGGGGCTG 60.046 66.667 0.00 0.00 0.00 4.85
1971 2260 9.477484 CCTGACTTATGATAATACCAGTGTAAC 57.523 37.037 0.00 0.00 0.00 2.50
1972 2261 8.148351 GCCTGACTTATGATAATACCAGTGTAA 58.852 37.037 0.00 0.00 0.00 2.41
1974 2263 6.327626 AGCCTGACTTATGATAATACCAGTGT 59.672 38.462 0.00 0.00 0.00 3.55
1975 2264 6.648310 CAGCCTGACTTATGATAATACCAGTG 59.352 42.308 0.00 0.00 0.00 3.66
1976 2265 6.327626 ACAGCCTGACTTATGATAATACCAGT 59.672 38.462 0.00 0.00 0.00 4.00
1977 2266 6.763355 ACAGCCTGACTTATGATAATACCAG 58.237 40.000 0.00 0.00 0.00 4.00
1978 2267 6.326323 TGACAGCCTGACTTATGATAATACCA 59.674 38.462 0.00 0.00 0.00 3.25
1979 2268 6.759272 TGACAGCCTGACTTATGATAATACC 58.241 40.000 0.00 0.00 0.00 2.73
1980 2269 7.928706 AGTTGACAGCCTGACTTATGATAATAC 59.071 37.037 0.00 0.00 0.00 1.89
1981 2270 8.023021 AGTTGACAGCCTGACTTATGATAATA 57.977 34.615 0.00 0.00 0.00 0.98
1982 2271 6.893583 AGTTGACAGCCTGACTTATGATAAT 58.106 36.000 0.00 0.00 0.00 1.28
1983 2272 6.299805 AGTTGACAGCCTGACTTATGATAA 57.700 37.500 0.00 0.00 0.00 1.75
1985 2274 4.833478 AGTTGACAGCCTGACTTATGAT 57.167 40.909 0.00 0.00 0.00 2.45
1989 2278 3.926616 GCTTAGTTGACAGCCTGACTTA 58.073 45.455 0.00 0.00 0.00 2.24
1990 2279 2.772287 GCTTAGTTGACAGCCTGACTT 58.228 47.619 0.00 0.00 0.00 3.01
1997 2286 3.813166 TGTTAACAGGCTTAGTTGACAGC 59.187 43.478 3.59 0.00 39.54 4.40
1998 2287 6.183360 TGTTTGTTAACAGGCTTAGTTGACAG 60.183 38.462 8.56 0.00 43.35 3.51
1999 2288 5.648526 TGTTTGTTAACAGGCTTAGTTGACA 59.351 36.000 8.56 10.12 41.69 3.58
2000 2289 6.126568 TGTTTGTTAACAGGCTTAGTTGAC 57.873 37.500 8.56 5.89 39.29 3.18
2012 2301 6.939730 TCCAATATGAGCTCTGTTTGTTAACA 59.060 34.615 16.19 3.59 41.82 2.41
2013 2302 7.334421 TCTCCAATATGAGCTCTGTTTGTTAAC 59.666 37.037 16.19 0.00 32.22 2.01
2014 2303 7.394016 TCTCCAATATGAGCTCTGTTTGTTAA 58.606 34.615 16.19 0.00 32.22 2.01
2015 2304 6.946340 TCTCCAATATGAGCTCTGTTTGTTA 58.054 36.000 16.19 5.54 32.22 2.41
2016 2305 5.809001 TCTCCAATATGAGCTCTGTTTGTT 58.191 37.500 16.19 0.00 32.22 2.83
2017 2306 5.426689 TCTCCAATATGAGCTCTGTTTGT 57.573 39.130 16.19 0.00 32.22 2.83
2018 2307 6.238676 CCATTCTCCAATATGAGCTCTGTTTG 60.239 42.308 16.19 14.22 32.22 2.93
2019 2308 5.826737 CCATTCTCCAATATGAGCTCTGTTT 59.173 40.000 16.19 2.58 32.22 2.83
2020 2309 5.131642 TCCATTCTCCAATATGAGCTCTGTT 59.868 40.000 16.19 4.19 32.22 3.16
2021 2310 4.657504 TCCATTCTCCAATATGAGCTCTGT 59.342 41.667 16.19 6.35 32.22 3.41
2022 2311 5.224821 TCCATTCTCCAATATGAGCTCTG 57.775 43.478 16.19 4.39 32.22 3.35
2023 2312 5.803795 GCATCCATTCTCCAATATGAGCTCT 60.804 44.000 16.19 3.04 32.22 4.09
2024 2313 4.395542 GCATCCATTCTCCAATATGAGCTC 59.604 45.833 6.82 6.82 32.22 4.09
2025 2314 4.202535 TGCATCCATTCTCCAATATGAGCT 60.203 41.667 0.00 0.00 32.22 4.09
2026 2315 4.077108 TGCATCCATTCTCCAATATGAGC 58.923 43.478 0.00 0.00 32.22 4.26
2059 2349 7.254556 CGGCAATCGCTTGATCACATATATAAT 60.255 37.037 2.58 0.00 38.60 1.28
2077 2367 3.279950 CGTTTTCATATGTCGGCAATCG 58.720 45.455 0.00 0.00 40.90 3.34
2091 2381 4.515191 CCTGATGTTCTCTTTCCGTTTTCA 59.485 41.667 0.00 0.00 0.00 2.69
2234 2526 9.708092 GATATAAAGGTATGGTCCTAAGTTCAC 57.292 37.037 0.00 0.00 36.74 3.18
2258 2550 8.635765 TTAAGTTGCTAGTTCCATGAAAAGAT 57.364 30.769 0.00 0.00 0.00 2.40
2293 2585 1.266989 GCACTTTAGAACCTGCACACC 59.733 52.381 0.00 0.00 0.00 4.16
2294 2586 1.266989 GGCACTTTAGAACCTGCACAC 59.733 52.381 0.00 0.00 0.00 3.82
2309 2601 3.923864 TTGCGACAGTCCGGCACT 61.924 61.111 0.00 0.00 36.23 4.40
2414 2706 3.008517 TGCCCATCCTCGGAAGCA 61.009 61.111 5.02 5.02 0.00 3.91
2415 2707 2.203126 CTGCCCATCCTCGGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
2476 2768 9.846248 GTATCATTGCAAACTCTTTCTGTATTT 57.154 29.630 1.71 0.00 0.00 1.40
2477 2769 9.236006 AGTATCATTGCAAACTCTTTCTGTATT 57.764 29.630 1.71 0.00 0.00 1.89
2520 2812 1.375523 GCGGGTCATGAGTTTCCGT 60.376 57.895 20.43 0.00 42.35 4.69
2526 2818 1.153568 CATCGTGCGGGTCATGAGT 60.154 57.895 0.00 0.00 43.39 3.41
2528 2820 0.530431 CATCATCGTGCGGGTCATGA 60.530 55.000 0.00 0.00 44.18 3.07
2535 2827 1.884464 CCTGGTCATCATCGTGCGG 60.884 63.158 0.00 0.00 0.00 5.69
2549 2841 4.037923 ACATTTTTGTGTGAAGCTACCTGG 59.962 41.667 0.00 0.00 0.00 4.45
2556 2848 4.536065 TCATCGACATTTTTGTGTGAAGC 58.464 39.130 0.00 0.00 31.16 3.86
2568 2860 6.519382 TCTCATTTATGCTCTCATCGACATT 58.481 36.000 0.00 0.00 34.22 2.71
2610 2902 7.820386 TGCCTTACTTATGACGATCTTGTTAAA 59.180 33.333 0.00 0.00 0.00 1.52
2612 2904 6.869695 TGCCTTACTTATGACGATCTTGTTA 58.130 36.000 0.00 0.00 0.00 2.41
2615 2910 6.662414 TTTGCCTTACTTATGACGATCTTG 57.338 37.500 0.00 0.00 0.00 3.02
2619 2914 7.552687 TGAATCTTTTGCCTTACTTATGACGAT 59.447 33.333 0.00 0.00 0.00 3.73
2647 2942 1.804748 GTGTACTTGCTTTCTTCCCCG 59.195 52.381 0.00 0.00 0.00 5.73
2669 2964 1.396301 GAAGCAACTGATCTCGGCTTG 59.604 52.381 15.61 2.88 44.16 4.01
2694 2989 4.080863 ACCCTTAGGCATGAGTAGTTTGAG 60.081 45.833 0.00 0.00 36.11 3.02
2749 3044 5.014544 TCCATTCTTGATTGAGGGAAAGAGT 59.985 40.000 0.00 0.00 30.77 3.24
2950 3247 5.239744 GCATTCATTGATCTCTTGCTCATCT 59.760 40.000 0.00 0.00 0.00 2.90
3191 3488 1.077212 GATGCACACCTGGCCTCAT 60.077 57.895 3.32 0.00 0.00 2.90
3226 3527 2.368221 GCCATGAGTTCTCCTGATAGCT 59.632 50.000 0.00 0.00 0.00 3.32
3396 3699 4.630644 ACAGAGGGGCATTACATCATAG 57.369 45.455 0.00 0.00 0.00 2.23
3471 3774 3.140814 GGAATGGCTTGTCCCGGC 61.141 66.667 0.00 0.00 0.00 6.13
3571 3874 8.605325 AAATTCATTCAAGGAGGATCAGAAAT 57.395 30.769 0.00 0.00 36.25 2.17
3685 3989 1.270358 GGGGCTCTTAACTATCTGGCG 60.270 57.143 0.00 0.00 0.00 5.69
3704 4008 7.148171 GGTTCTTCAAATCCTACAGATCAAAGG 60.148 40.741 0.00 0.00 32.47 3.11
3779 4083 8.459521 TTTTTATGTTTTCTAATCGTGCATGG 57.540 30.769 5.98 0.00 0.00 3.66
3952 6217 3.821033 ACCTCCGAAAAGACAAAGGATTG 59.179 43.478 0.00 0.00 42.46 2.67
3953 6218 3.821033 CACCTCCGAAAAGACAAAGGATT 59.179 43.478 0.00 0.00 0.00 3.01
3961 6226 1.002502 CCCCCACCTCCGAAAAGAC 60.003 63.158 0.00 0.00 0.00 3.01
4007 6272 1.271325 TGAGTTTGCGGTGATGGATGT 60.271 47.619 0.00 0.00 0.00 3.06
4053 6318 3.002348 CGAGCTTCTTTTCGAACTGGTTT 59.998 43.478 0.00 0.00 39.06 3.27
4054 6319 2.544267 CGAGCTTCTTTTCGAACTGGTT 59.456 45.455 0.00 0.00 39.06 3.67
4072 6337 6.458210 TGAGTTTACCCTTTTAACTACCGAG 58.542 40.000 0.00 0.00 32.58 4.63
4075 6340 7.881751 AGACATGAGTTTACCCTTTTAACTACC 59.118 37.037 0.00 0.00 32.58 3.18
4106 6371 5.975282 AGATTCCTAAAGTTAACCGTCCTC 58.025 41.667 0.88 0.00 0.00 3.71
4123 6388 4.941657 ACGTTCGGGAGTTATTAGATTCC 58.058 43.478 0.00 0.00 0.00 3.01
4124 6389 5.172771 CGAACGTTCGGGAGTTATTAGATTC 59.827 44.000 36.53 2.01 46.30 2.52
4125 6390 5.039333 CGAACGTTCGGGAGTTATTAGATT 58.961 41.667 36.53 0.00 46.30 2.40
4126 6391 4.604976 CGAACGTTCGGGAGTTATTAGAT 58.395 43.478 36.53 0.00 46.30 1.98
4127 6392 4.019919 CGAACGTTCGGGAGTTATTAGA 57.980 45.455 36.53 0.00 46.30 2.10
4140 6405 2.961522 TGCTCAAAATCCGAACGTTC 57.038 45.000 18.47 18.47 0.00 3.95
4141 6406 3.915437 AATGCTCAAAATCCGAACGTT 57.085 38.095 0.00 0.00 0.00 3.99
4142 6407 3.666902 CGAAATGCTCAAAATCCGAACGT 60.667 43.478 0.00 0.00 0.00 3.99
4143 6408 2.840176 CGAAATGCTCAAAATCCGAACG 59.160 45.455 0.00 0.00 0.00 3.95
4144 6409 3.821841 ACGAAATGCTCAAAATCCGAAC 58.178 40.909 0.00 0.00 0.00 3.95
4145 6410 3.119990 GGACGAAATGCTCAAAATCCGAA 60.120 43.478 0.00 0.00 0.00 4.30
4146 6411 2.418628 GGACGAAATGCTCAAAATCCGA 59.581 45.455 0.00 0.00 0.00 4.55
4147 6412 2.785679 GGACGAAATGCTCAAAATCCG 58.214 47.619 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.