Multiple sequence alignment - TraesCS5A01G298500

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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 TraesCS5A01G298500 chr5A 100.000 5090 0 0 1 5090 505614309 505609220 0.000000e+00 9400.0
1 TraesCS5A01G298500 chr5A 98.837 86 1 0 4630 4715 215479586 215479501 2.450000e-33 154.0
2 TraesCS5A01G298500 chr5D 93.336 3031 129 30 672 3645 400281922 400278908 0.000000e+00 4410.0
3 TraesCS5A01G298500 chr5D 93.148 1080 45 10 3530 4580 400278931 400277852 0.000000e+00 1557.0
4 TraesCS5A01G298500 chr5D 87.324 497 42 13 171 652 400282397 400281907 2.680000e-152 549.0
5 TraesCS5A01G298500 chr5D 88.270 341 15 10 4713 5050 400277617 400277299 7.990000e-103 385.0
6 TraesCS5A01G298500 chr5B 91.928 2775 135 49 4 2727 480295831 480293095 0.000000e+00 3801.0
7 TraesCS5A01G298500 chr5B 92.622 1613 68 16 3009 4580 480293102 480291500 0.000000e+00 2272.0
8 TraesCS5A01G298500 chr5B 94.220 346 11 2 4713 5050 480291265 480290921 2.100000e-143 520.0
9 TraesCS5A01G298500 chr5B 94.000 100 3 3 4630 4729 664024234 664024330 1.140000e-31 148.0
10 TraesCS5A01G298500 chr5B 96.364 55 2 0 4577 4631 480291318 480291264 1.950000e-14 91.6
11 TraesCS5A01G298500 chr3D 95.026 764 28 3 971 1731 554063307 554064063 0.000000e+00 1192.0
12 TraesCS5A01G298500 chr3D 79.837 491 75 17 1225 1709 457018913 457019385 2.270000e-88 337.0
13 TraesCS5A01G298500 chr7D 94.156 770 35 4 965 1731 77074675 77075437 0.000000e+00 1164.0
14 TraesCS5A01G298500 chr7D 81.481 270 50 0 1576 1845 251374733 251374464 6.630000e-54 222.0
15 TraesCS5A01G298500 chr7D 97.753 89 2 0 4627 4715 177106857 177106945 2.450000e-33 154.0
16 TraesCS5A01G298500 chr7D 97.727 88 2 0 4630 4717 49381898 49381985 8.830000e-33 152.0
17 TraesCS5A01G298500 chr7D 92.079 101 7 1 4625 4724 185552875 185552775 1.910000e-29 141.0
18 TraesCS5A01G298500 chr6B 94.862 545 24 2 977 1518 513612794 513612251 0.000000e+00 848.0
19 TraesCS5A01G298500 chr6B 83.784 185 28 2 1661 1844 717076325 717076142 1.880000e-39 174.0
20 TraesCS5A01G298500 chr3B 94.555 551 26 2 971 1518 576333409 576333958 0.000000e+00 848.0
21 TraesCS5A01G298500 chr3B 91.906 556 32 3 965 1518 82299966 82300510 0.000000e+00 765.0
22 TraesCS5A01G298500 chr3B 89.574 470 30 8 971 1440 464613627 464613177 3.420000e-161 579.0
23 TraesCS5A01G298500 chr2A 90.893 549 29 11 971 1518 66913738 66913210 0.000000e+00 717.0
24 TraesCS5A01G298500 chr2B 90.710 549 30 10 971 1518 698085628 698085100 0.000000e+00 712.0
25 TraesCS5A01G298500 chr3A 79.218 486 77 17 1225 1704 599861200 599861667 2.960000e-82 316.0
26 TraesCS5A01G298500 chr1D 78.947 475 78 16 1240 1709 388651032 388650575 2.300000e-78 303.0
27 TraesCS5A01G298500 chr1A 78.947 475 78 16 1240 1709 487741407 487740950 2.300000e-78 303.0
28 TraesCS5A01G298500 chr1B 78.826 477 75 18 1240 1709 522061084 522060627 1.070000e-76 298.0
29 TraesCS5A01G298500 chr7A 81.481 270 50 0 1576 1845 270042937 270043206 6.630000e-54 222.0
30 TraesCS5A01G298500 chr7B 81.111 270 51 0 1576 1845 228363472 228363203 3.090000e-52 217.0
31 TraesCS5A01G298500 chr6A 82.703 185 30 2 1661 1844 617657601 617657784 4.080000e-36 163.0
32 TraesCS5A01G298500 chr6D 96.703 91 2 1 4626 4715 17316716 17316626 3.170000e-32 150.0
33 TraesCS5A01G298500 chr6D 81.383 188 27 5 1661 1844 472358413 472358230 4.110000e-31 147.0
34 TraesCS5A01G298500 chr4D 84.507 142 22 0 1703 1844 12410755 12410896 1.910000e-29 141.0
35 TraesCS5A01G298500 chr4B 90.566 106 9 1 4628 4732 491017639 491017744 6.870000e-29 139.0
36 TraesCS5A01G298500 chr4A 88.235 119 11 3 4630 4747 107422484 107422600 6.870000e-29 139.0
37 TraesCS5A01G298500 chr4A 87.395 119 12 3 4630 4747 107368847 107368963 3.200000e-27 134.0


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 TraesCS5A01G298500 chr5A 505609220 505614309 5089 True 9400.00 9400 100.0000 1 5090 1 chr5A.!!$R2 5089
1 TraesCS5A01G298500 chr5D 400277299 400282397 5098 True 1725.25 4410 90.5195 171 5050 4 chr5D.!!$R1 4879
2 TraesCS5A01G298500 chr5B 480290921 480295831 4910 True 1671.15 3801 93.7835 4 5050 4 chr5B.!!$R1 5046
3 TraesCS5A01G298500 chr3D 554063307 554064063 756 False 1192.00 1192 95.0260 971 1731 1 chr3D.!!$F2 760
4 TraesCS5A01G298500 chr7D 77074675 77075437 762 False 1164.00 1164 94.1560 965 1731 1 chr7D.!!$F2 766
5 TraesCS5A01G298500 chr6B 513612251 513612794 543 True 848.00 848 94.8620 977 1518 1 chr6B.!!$R1 541
6 TraesCS5A01G298500 chr3B 576333409 576333958 549 False 848.00 848 94.5550 971 1518 1 chr3B.!!$F2 547
7 TraesCS5A01G298500 chr3B 82299966 82300510 544 False 765.00 765 91.9060 965 1518 1 chr3B.!!$F1 553
8 TraesCS5A01G298500 chr2A 66913210 66913738 528 True 717.00 717 90.8930 971 1518 1 chr2A.!!$R1 547
9 TraesCS5A01G298500 chr2B 698085100 698085628 528 True 712.00 712 90.7100 971 1518 1 chr2B.!!$R1 547

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
386 402 0.321346 TGCTTCAACGCAGGATCTGA 59.679 50.000 0.0 0.0 34.44 3.27 F
647 675 0.321919 TCCAGAATGCCACTGCTGTC 60.322 55.000 0.0 0.0 38.71 3.51 F
648 676 0.322277 CCAGAATGCCACTGCTGTCT 60.322 55.000 0.0 0.0 38.71 3.41 F
650 678 0.689055 AGAATGCCACTGCTGTCTGA 59.311 50.000 0.0 0.0 38.71 3.27 F
2554 2639 1.198178 TCGTTGCCAAGAATTTACCGC 59.802 47.619 0.0 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2405 0.178767 TTGATCCACGGATGCTCTGG 59.821 55.000 2.54 0.00 34.60 3.86 R
2595 2680 0.971386 TACCGTCCTTGTCCTTGTCC 59.029 55.000 0.00 0.00 0.00 4.02 R
2724 2809 3.795561 AAGAGAGCAATGAAAACGTCG 57.204 42.857 0.00 0.00 0.00 5.12 R
2748 2833 7.779326 TCCCAATCATCATAGCTATTTTGTTCA 59.221 33.333 2.64 0.00 0.00 3.18 R
4440 4656 0.038343 TGCTCCTTTTGGCAATTCGC 60.038 50.000 0.00 0.76 40.12 4.70 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
21 22 4.357947 GACGGCAGGCGTGACTGA 62.358 66.667 28.83 0.00 40.97 3.41
30 31 1.040339 GGCGTGACTGATCCCTCTCT 61.040 60.000 0.00 0.00 0.00 3.10
44 45 0.524392 CTCTCTGGCACGATGTCGAC 60.524 60.000 9.11 9.11 43.02 4.20
101 102 1.063327 CGAGGCACTACGAGAGCAG 59.937 63.158 0.00 0.00 41.55 4.24
104 105 2.485582 GCACTACGAGAGCAGCGA 59.514 61.111 0.00 0.00 31.92 4.93
122 123 2.202298 CGGCGACCGCATTGTTTC 60.202 61.111 16.47 0.00 41.17 2.78
127 128 0.789383 CGACCGCATTGTTTCGCTTC 60.789 55.000 0.00 0.00 0.00 3.86
140 141 1.328279 TCGCTTCTGGTCAGTCTGAA 58.672 50.000 3.51 0.00 0.00 3.02
145 146 2.533266 TCTGGTCAGTCTGAAACAGC 57.467 50.000 22.22 6.31 35.14 4.40
168 169 8.610896 CAGCAAAATCACAAATTAGGTTGAAAA 58.389 29.630 0.00 0.00 32.59 2.29
189 190 4.689612 ACCATAGTACATCCCACATCAC 57.310 45.455 0.00 0.00 0.00 3.06
260 261 4.830600 GGAATAGAGGGGAGAACAGAGTAG 59.169 50.000 0.00 0.00 0.00 2.57
266 267 2.427812 GGGGAGAACAGAGTAGCTACAC 59.572 54.545 25.28 19.11 0.00 2.90
283 293 4.603535 CCGCCCCCAATCCCCATC 62.604 72.222 0.00 0.00 0.00 3.51
335 346 0.376152 CAAGTGCTAGCATCGCAAGG 59.624 55.000 22.51 3.04 39.39 3.61
347 358 2.704725 TCGCAAGGCAAGATCAAAAC 57.295 45.000 0.00 0.00 38.47 2.43
353 365 2.863809 AGGCAAGATCAAAACGAAGGT 58.136 42.857 0.00 0.00 0.00 3.50
386 402 0.321346 TGCTTCAACGCAGGATCTGA 59.679 50.000 0.00 0.00 34.44 3.27
391 407 3.019003 AACGCAGGATCTGACCCCG 62.019 63.158 0.00 0.00 32.44 5.73
393 409 4.554036 GCAGGATCTGACCCCGGC 62.554 72.222 0.00 7.14 36.56 6.13
402 418 4.646877 GACCCCGGCGGAAAACCA 62.647 66.667 30.79 0.00 34.64 3.67
521 540 0.383737 GATGTTCGCGCGTGTGAAAA 60.384 50.000 30.98 20.99 45.53 2.29
522 541 0.384230 ATGTTCGCGCGTGTGAAAAG 60.384 50.000 30.98 0.00 45.53 2.27
523 542 1.011574 GTTCGCGCGTGTGAAAAGT 60.012 52.632 30.98 0.00 45.53 2.66
524 543 1.011684 TTCGCGCGTGTGAAAAGTG 60.012 52.632 30.98 0.00 41.42 3.16
525 544 1.422179 TTCGCGCGTGTGAAAAGTGA 61.422 50.000 30.98 1.78 41.42 3.41
526 545 1.011684 CGCGCGTGTGAAAAGTGAA 60.012 52.632 24.19 0.00 0.00 3.18
527 546 0.587737 CGCGCGTGTGAAAAGTGAAA 60.588 50.000 24.19 0.00 0.00 2.69
528 547 0.837605 GCGCGTGTGAAAAGTGAAAC 59.162 50.000 8.43 0.00 0.00 2.78
529 548 1.792273 GCGCGTGTGAAAAGTGAAACA 60.792 47.619 8.43 0.00 41.43 2.83
535 554 3.725740 GTGTGAAAAGTGAAACAGATGCG 59.274 43.478 0.00 0.00 41.43 4.73
538 557 3.250762 TGAAAAGTGAAACAGATGCGGAG 59.749 43.478 0.00 0.00 41.43 4.63
543 562 1.303309 GAAACAGATGCGGAGATGGG 58.697 55.000 0.00 0.00 0.00 4.00
621 649 3.744719 CCGGCGAGTTCGTCTCCA 61.745 66.667 9.30 0.00 42.59 3.86
646 674 0.322277 CTCCAGAATGCCACTGCTGT 60.322 55.000 0.00 0.00 38.71 4.40
647 675 0.321919 TCCAGAATGCCACTGCTGTC 60.322 55.000 0.00 0.00 38.71 3.51
648 676 0.322277 CCAGAATGCCACTGCTGTCT 60.322 55.000 0.00 0.00 38.71 3.41
649 677 0.803117 CAGAATGCCACTGCTGTCTG 59.197 55.000 0.00 0.00 40.33 3.51
650 678 0.689055 AGAATGCCACTGCTGTCTGA 59.311 50.000 0.00 0.00 38.71 3.27
844 880 2.278661 GCGCAGACCGGTAGCTAC 60.279 66.667 24.05 15.88 37.44 3.58
845 881 2.412112 CGCAGACCGGTAGCTACC 59.588 66.667 29.96 29.96 42.98 3.18
916 952 4.946266 TGGAACGCGCGAACGGAA 62.946 61.111 39.36 13.68 40.57 4.30
1233 1287 4.151582 GCCAAGCGGTACCGGCTA 62.152 66.667 33.98 0.00 41.50 3.93
1818 1872 2.515854 GGCGTCATCCTCTACATCCTA 58.484 52.381 0.00 0.00 0.00 2.94
1883 1937 4.536765 TCCTTGCTTCTTTCTTCACCTTT 58.463 39.130 0.00 0.00 0.00 3.11
1884 1938 4.580580 TCCTTGCTTCTTTCTTCACCTTTC 59.419 41.667 0.00 0.00 0.00 2.62
1885 1939 4.339247 CCTTGCTTCTTTCTTCACCTTTCA 59.661 41.667 0.00 0.00 0.00 2.69
1886 1940 5.010415 CCTTGCTTCTTTCTTCACCTTTCAT 59.990 40.000 0.00 0.00 0.00 2.57
1889 1943 4.378874 GCTTCTTTCTTCACCTTTCATCGG 60.379 45.833 0.00 0.00 0.00 4.18
1890 1944 3.074412 TCTTTCTTCACCTTTCATCGGC 58.926 45.455 0.00 0.00 0.00 5.54
1891 1945 2.559698 TTCTTCACCTTTCATCGGCA 57.440 45.000 0.00 0.00 0.00 5.69
1892 1946 2.787473 TCTTCACCTTTCATCGGCAT 57.213 45.000 0.00 0.00 0.00 4.40
1893 1947 2.358957 TCTTCACCTTTCATCGGCATG 58.641 47.619 0.00 0.00 0.00 4.06
1894 1948 2.027285 TCTTCACCTTTCATCGGCATGA 60.027 45.455 0.00 0.00 37.24 3.07
1929 1983 3.453717 CCATTCCTCCTCTCATGACTGAA 59.546 47.826 0.00 0.00 0.00 3.02
1930 1984 4.440880 CATTCCTCCTCTCATGACTGAAC 58.559 47.826 0.00 0.00 0.00 3.18
1957 2011 4.333649 AGTGCTCATGTGATTTTATGTCCG 59.666 41.667 0.00 0.00 0.00 4.79
1977 2031 3.545124 ATGAACCGGGCGCAGACAA 62.545 57.895 10.83 0.00 37.00 3.18
2020 2074 3.250040 CGATAATCCGGGGTGAAATCAAC 59.750 47.826 0.00 0.00 0.00 3.18
2110 2164 2.298158 ATCCTGCTACCCGCTTGACG 62.298 60.000 0.00 0.00 40.11 4.35
2164 2218 1.629043 TGGTCTAGTTTCCAGCTCGT 58.371 50.000 0.00 0.00 0.00 4.18
2192 2246 6.513066 GCAAACCAAACAAACACAATATGCAT 60.513 34.615 3.79 3.79 0.00 3.96
2273 2355 2.750166 CGGAGGTCTAGCGATACATGAT 59.250 50.000 0.00 0.00 0.00 2.45
2278 2360 6.095580 GGAGGTCTAGCGATACATGATGAATA 59.904 42.308 0.00 0.00 0.00 1.75
2302 2384 3.926527 TGTTATGCACTGAACTAAGAGCG 59.073 43.478 8.84 0.00 36.66 5.03
2309 2394 4.448060 GCACTGAACTAAGAGCGTTAACTT 59.552 41.667 3.71 0.00 0.00 2.66
2320 2405 3.831112 AGCGTTAACTTCTCCTACGAAC 58.169 45.455 3.71 0.00 34.36 3.95
2335 2420 1.596934 GAACCAGAGCATCCGTGGA 59.403 57.895 0.00 0.00 35.17 4.02
2375 2460 1.421485 CGAATGTGTCGCTTGGAGC 59.579 57.895 0.00 0.00 44.14 4.70
2406 2491 2.632377 TCCAGGCTTAAGCAATTCTCG 58.368 47.619 27.83 9.41 44.36 4.04
2451 2536 1.872237 GCACTCGGAGTAAGTTGCACA 60.872 52.381 10.87 0.00 0.00 4.57
2461 2546 2.594592 GTTGCACAGAACCGGGCT 60.595 61.111 6.32 0.00 0.00 5.19
2503 2588 9.958180 TTTCTTCCAGTGTGATATATTCTTTGA 57.042 29.630 0.00 0.00 0.00 2.69
2504 2589 8.948631 TCTTCCAGTGTGATATATTCTTTGAC 57.051 34.615 0.00 0.00 0.00 3.18
2554 2639 1.198178 TCGTTGCCAAGAATTTACCGC 59.802 47.619 0.00 0.00 0.00 5.68
2556 2641 1.271102 GTTGCCAAGAATTTACCGCCA 59.729 47.619 0.00 0.00 0.00 5.69
2578 2663 4.876679 CAGAGGACATCGAGAACTACACTA 59.123 45.833 0.00 0.00 0.00 2.74
2748 2833 6.978659 TCGACGTTTTCATTGCTCTCTTATAT 59.021 34.615 0.00 0.00 0.00 0.86
2824 2909 3.499918 AGTGAGAGCTGTACAAATGCAAC 59.500 43.478 8.15 2.55 0.00 4.17
2839 2924 3.090952 TGCAACGAAAAATGTTCTGGG 57.909 42.857 0.00 0.00 0.00 4.45
2849 2934 7.447238 ACGAAAAATGTTCTGGGAAATCTAGAA 59.553 33.333 0.00 0.00 0.00 2.10
2877 2962 4.439974 GCCATTGCAAAGTATTCGATTCCA 60.440 41.667 1.71 0.00 37.47 3.53
2885 2970 7.498900 TGCAAAGTATTCGATTCCAAGATATGT 59.501 33.333 0.00 0.00 0.00 2.29
2893 2978 4.982295 CGATTCCAAGATATGTCGCTACAA 59.018 41.667 0.00 0.00 39.58 2.41
2904 2989 7.916450 AGATATGTCGCTACAAAGTTCTACTTC 59.084 37.037 0.00 0.00 37.47 3.01
2908 2993 5.919141 GTCGCTACAAAGTTCTACTTCTGAA 59.081 40.000 0.00 0.00 37.47 3.02
2912 2997 7.042658 CGCTACAAAGTTCTACTTCTGAAAACT 60.043 37.037 0.54 0.54 37.47 2.66
2918 3003 6.517605 AGTTCTACTTCTGAAAACTGACTCC 58.482 40.000 4.81 0.00 0.00 3.85
2921 3006 2.158957 ACTTCTGAAAACTGACTCCGCA 60.159 45.455 0.00 0.00 0.00 5.69
2970 3055 4.998671 TTGTGAGGCATGAAAAGACAAA 57.001 36.364 0.00 0.00 0.00 2.83
2971 3056 5.534207 TTGTGAGGCATGAAAAGACAAAT 57.466 34.783 0.00 0.00 0.00 2.32
3024 3110 7.201705 CGTTTTCTTCCATTTAGAGGGGTATTC 60.202 40.741 0.00 0.00 0.00 1.75
3028 3114 2.709397 CCATTTAGAGGGGTATTCCGGT 59.291 50.000 0.00 0.00 36.01 5.28
3070 3156 9.685828 AAAAATAAAGTTAGCAGCGTCATTTTA 57.314 25.926 0.00 0.00 0.00 1.52
3143 3230 6.994496 CACATATCTAGCTTTCCCAATTCTGA 59.006 38.462 0.00 0.00 0.00 3.27
3156 3243 4.389077 CCCAATTCTGACACGAGTCTAAAC 59.611 45.833 14.15 0.00 45.20 2.01
3176 3263 8.784994 TCTAAACGCAATTGAAACCAAGTATTA 58.215 29.630 10.34 0.00 0.00 0.98
3392 3479 3.718434 TGATGGAGGCTTTAGGTGATGAT 59.282 43.478 0.00 0.00 0.00 2.45
3417 3504 1.751927 GGCCCAGATGAGCAAGTGG 60.752 63.158 0.00 0.00 0.00 4.00
3419 3506 0.610232 GCCCAGATGAGCAAGTGGTT 60.610 55.000 0.00 0.00 0.00 3.67
3507 3602 7.067859 ACATTGATCACTTAATGCTGCTGTATT 59.932 33.333 11.37 11.37 37.71 1.89
3511 3606 6.426980 TCACTTAATGCTGCTGTATTTCAG 57.573 37.500 11.83 10.68 46.12 3.02
3518 3613 3.503363 TGCTGCTGTATTTCAGGAAAGTG 59.497 43.478 0.00 0.00 43.54 3.16
3575 3762 9.645128 AGACACCATTTATCCATATCAAATGAA 57.355 29.630 7.62 0.00 40.49 2.57
3620 3807 3.401683 TGGATTGTTTACCCTAAACCCCA 59.598 43.478 3.10 5.14 45.63 4.96
3679 3869 1.425066 TCCAGTGAAAAGGGCACATCT 59.575 47.619 0.00 0.00 38.70 2.90
3685 3875 4.051237 GTGAAAAGGGCACATCTGAAAAC 58.949 43.478 0.00 0.00 36.31 2.43
3690 3880 2.092323 GGGCACATCTGAAAACTACCC 58.908 52.381 0.00 0.00 0.00 3.69
3701 3891 1.428718 AAACTACCCGCTTTCCCCCA 61.429 55.000 0.00 0.00 0.00 4.96
3710 3900 1.090052 GCTTTCCCCCATCGTTCTCG 61.090 60.000 0.00 0.00 38.55 4.04
3754 3944 7.504924 TGACAAAAGGAAATTACTACACCTG 57.495 36.000 0.00 0.00 0.00 4.00
3910 4100 4.764050 TTCCAGTCCAAGAGTACACAAA 57.236 40.909 0.00 0.00 0.00 2.83
3985 4175 4.210120 GTCGCATTAGCTATCAGGAGTTTG 59.790 45.833 0.00 0.00 39.10 2.93
4040 4230 1.077089 GCTTCTCGGCGGTACTCAAC 61.077 60.000 7.21 0.00 0.00 3.18
4065 4255 4.543692 CAAATTTCAGCAACCTCAGTCAG 58.456 43.478 0.00 0.00 0.00 3.51
4072 4280 1.155042 CAACCTCAGTCAGAAGCTGC 58.845 55.000 0.00 0.00 34.21 5.25
4078 4286 1.670406 AGTCAGAAGCTGCGCCAAG 60.670 57.895 4.18 0.00 0.00 3.61
4081 4289 2.046507 AGAAGCTGCGCCAAGGAG 60.047 61.111 4.18 0.00 41.69 3.69
4089 4297 0.901827 TGCGCCAAGGAGTTCTATGA 59.098 50.000 4.18 0.00 0.00 2.15
4097 4305 5.649831 GCCAAGGAGTTCTATGAAACAAGAT 59.350 40.000 0.00 0.00 0.00 2.40
4173 4381 8.777865 TCAGTAGATGACCTAAAACTCAAATG 57.222 34.615 0.00 0.00 31.12 2.32
4205 4413 3.445096 GGTTTGGAGGACATCAGGATTTG 59.555 47.826 0.00 0.00 0.00 2.32
4206 4414 2.425143 TGGAGGACATCAGGATTTGC 57.575 50.000 0.00 0.00 0.00 3.68
4207 4415 1.064463 TGGAGGACATCAGGATTTGCC 60.064 52.381 0.00 0.00 0.00 4.52
4240 4456 2.003301 GCTCGGATGACAAAGTTCCTC 58.997 52.381 0.00 0.00 0.00 3.71
4264 4480 2.611224 GCAGAAGCAGAAAACCCAATGG 60.611 50.000 0.00 0.00 41.58 3.16
4270 4486 1.545582 CAGAAAACCCAATGGCATCGT 59.454 47.619 0.00 0.00 33.59 3.73
4461 4677 2.533266 CGAATTGCCAAAAGGAGCATC 58.467 47.619 0.00 0.00 39.11 3.91
4481 4700 5.703130 GCATCCTTTCCATCCAGTATACTTC 59.297 44.000 1.56 0.00 0.00 3.01
4557 4776 4.576463 TGGAGAAGTTCAGAAGAAAACTGC 59.424 41.667 5.50 0.00 35.93 4.40
4609 5013 5.450412 CCATACCAGCAATTTAGTCGCAAAT 60.450 40.000 0.00 0.00 0.00 2.32
4621 5025 3.541632 AGTCGCAAATAGGTTACCATGG 58.458 45.455 11.19 11.19 0.00 3.66
4629 5033 7.552459 GCAAATAGGTTACCATGGTGTTTATT 58.448 34.615 28.17 19.76 0.00 1.40
4630 5034 8.688151 GCAAATAGGTTACCATGGTGTTTATTA 58.312 33.333 28.17 12.01 0.00 0.98
4632 5036 9.984590 AAATAGGTTACCATGGTGTTTATTACT 57.015 29.630 28.17 14.81 0.00 2.24
4633 5037 9.623000 AATAGGTTACCATGGTGTTTATTACTC 57.377 33.333 28.17 5.06 0.00 2.59
4634 5038 6.420638 AGGTTACCATGGTGTTTATTACTCC 58.579 40.000 28.17 10.13 40.18 3.85
4635 5039 5.591472 GGTTACCATGGTGTTTATTACTCCC 59.409 44.000 28.17 6.41 39.23 4.30
4636 5040 6.420638 GTTACCATGGTGTTTATTACTCCCT 58.579 40.000 28.17 0.00 39.23 4.20
4637 5041 5.112129 ACCATGGTGTTTATTACTCCCTC 57.888 43.478 18.99 0.00 39.23 4.30
4638 5042 4.079958 ACCATGGTGTTTATTACTCCCTCC 60.080 45.833 18.99 0.00 39.23 4.30
4639 5043 3.899052 TGGTGTTTATTACTCCCTCCG 57.101 47.619 0.00 0.00 39.23 4.63
4640 5044 3.175594 TGGTGTTTATTACTCCCTCCGT 58.824 45.455 0.00 0.00 39.23 4.69
4641 5045 3.196254 TGGTGTTTATTACTCCCTCCGTC 59.804 47.826 0.00 0.00 39.23 4.79
4642 5046 3.431346 GGTGTTTATTACTCCCTCCGTCC 60.431 52.174 0.00 0.00 34.91 4.79
4643 5047 2.767960 TGTTTATTACTCCCTCCGTCCC 59.232 50.000 0.00 0.00 0.00 4.46
4644 5048 2.767960 GTTTATTACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
4645 5049 2.077687 TATTACTCCCTCCGTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
4646 5050 0.042131 ATTACTCCCTCCGTCCCACA 59.958 55.000 0.00 0.00 0.00 4.17
4647 5051 0.178926 TTACTCCCTCCGTCCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
4648 5052 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
4649 5053 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
4650 5054 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
4651 5055 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
4652 5056 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
4653 5057 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
4654 5058 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4655 5059 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
4656 5060 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
4657 5061 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
4658 5062 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
4659 5063 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
4660 5064 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
4661 5065 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
4662 5066 5.501897 CGTCCCACAATATAAGAGCGTTTTC 60.502 44.000 0.00 0.00 0.00 2.29
4704 5108 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4705 5109 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4706 5110 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4707 5111 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4708 5112 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4709 5113 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4710 5114 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4711 5115 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4787 5191 4.478317 TCCAGGGTCACCAAGAATCATATT 59.522 41.667 0.00 0.00 40.13 1.28
4788 5192 4.823989 CCAGGGTCACCAAGAATCATATTC 59.176 45.833 0.00 0.00 40.13 1.75
4826 5230 3.629142 ACCTAGCGCCTGAAGTAAAAT 57.371 42.857 2.29 0.00 0.00 1.82
4828 5232 5.093849 ACCTAGCGCCTGAAGTAAAATTA 57.906 39.130 2.29 0.00 0.00 1.40
4829 5233 5.493809 ACCTAGCGCCTGAAGTAAAATTAA 58.506 37.500 2.29 0.00 0.00 1.40
4914 5318 8.608185 ATCCCAACCATTAAGAATGTGTAAAT 57.392 30.769 0.00 0.00 37.18 1.40
5050 5463 7.587757 GTCAACAATGTTTTGAGCTACTTGTAG 59.412 37.037 0.00 3.60 33.63 2.74
5051 5464 6.560253 ACAATGTTTTGAGCTACTTGTAGG 57.440 37.500 9.49 0.00 36.64 3.18
5052 5465 6.062095 ACAATGTTTTGAGCTACTTGTAGGT 58.938 36.000 11.64 11.64 36.64 3.08
5053 5466 7.221450 ACAATGTTTTGAGCTACTTGTAGGTA 58.779 34.615 11.76 0.00 36.64 3.08
5054 5467 7.387948 ACAATGTTTTGAGCTACTTGTAGGTAG 59.612 37.037 11.76 0.00 38.22 3.18
5055 5468 6.659745 TGTTTTGAGCTACTTGTAGGTAGA 57.340 37.500 11.76 2.53 40.98 2.59
5056 5469 7.241042 TGTTTTGAGCTACTTGTAGGTAGAT 57.759 36.000 11.76 0.00 40.98 1.98
5057 5470 7.097192 TGTTTTGAGCTACTTGTAGGTAGATG 58.903 38.462 11.76 0.00 40.98 2.90
5058 5471 5.854010 TTGAGCTACTTGTAGGTAGATGG 57.146 43.478 11.76 0.00 40.98 3.51
5059 5472 4.215908 TGAGCTACTTGTAGGTAGATGGG 58.784 47.826 11.76 0.00 40.98 4.00
5060 5473 4.216708 GAGCTACTTGTAGGTAGATGGGT 58.783 47.826 11.76 0.00 40.98 4.51
5061 5474 4.621769 AGCTACTTGTAGGTAGATGGGTT 58.378 43.478 10.32 0.00 40.98 4.11
5062 5475 4.650131 AGCTACTTGTAGGTAGATGGGTTC 59.350 45.833 10.32 0.00 40.98 3.62
5063 5476 4.404715 GCTACTTGTAGGTAGATGGGTTCA 59.595 45.833 9.49 0.00 40.98 3.18
5064 5477 5.452077 GCTACTTGTAGGTAGATGGGTTCAG 60.452 48.000 9.49 0.00 40.98 3.02
5065 5478 4.684724 ACTTGTAGGTAGATGGGTTCAGA 58.315 43.478 0.00 0.00 0.00 3.27
5066 5479 5.091552 ACTTGTAGGTAGATGGGTTCAGAA 58.908 41.667 0.00 0.00 0.00 3.02
5067 5480 5.726793 ACTTGTAGGTAGATGGGTTCAGAAT 59.273 40.000 0.00 0.00 0.00 2.40
5068 5481 5.614324 TGTAGGTAGATGGGTTCAGAATG 57.386 43.478 0.00 0.00 37.54 2.67
5069 5482 3.567478 AGGTAGATGGGTTCAGAATGC 57.433 47.619 0.00 0.00 34.76 3.56
5070 5483 2.173569 AGGTAGATGGGTTCAGAATGCC 59.826 50.000 0.00 0.00 34.76 4.40
5071 5484 2.092429 GGTAGATGGGTTCAGAATGCCA 60.092 50.000 0.00 0.00 34.76 4.92
5072 5485 2.905415 AGATGGGTTCAGAATGCCAA 57.095 45.000 0.00 0.00 34.76 4.52
5073 5486 3.393426 AGATGGGTTCAGAATGCCAAT 57.607 42.857 0.00 0.00 34.76 3.16
5074 5487 4.524802 AGATGGGTTCAGAATGCCAATA 57.475 40.909 0.00 0.00 34.76 1.90
5075 5488 5.070823 AGATGGGTTCAGAATGCCAATAT 57.929 39.130 0.00 0.00 34.76 1.28
5076 5489 5.461327 AGATGGGTTCAGAATGCCAATATT 58.539 37.500 0.00 0.00 34.76 1.28
5077 5490 6.613699 AGATGGGTTCAGAATGCCAATATTA 58.386 36.000 0.00 0.00 34.76 0.98
5078 5491 6.718454 AGATGGGTTCAGAATGCCAATATTAG 59.282 38.462 0.00 0.00 34.76 1.73
5079 5492 4.584325 TGGGTTCAGAATGCCAATATTAGC 59.416 41.667 0.00 0.00 34.76 3.09
5080 5493 4.584325 GGGTTCAGAATGCCAATATTAGCA 59.416 41.667 11.01 11.01 44.45 3.49
5081 5494 5.068987 GGGTTCAGAATGCCAATATTAGCAA 59.931 40.000 12.58 0.00 43.36 3.91
5082 5495 6.211515 GGTTCAGAATGCCAATATTAGCAAG 58.788 40.000 12.58 4.13 43.36 4.01
5083 5496 6.183360 GGTTCAGAATGCCAATATTAGCAAGT 60.183 38.462 12.58 4.10 43.36 3.16
5084 5497 7.013274 GGTTCAGAATGCCAATATTAGCAAGTA 59.987 37.037 12.58 0.00 43.36 2.24
5085 5498 8.405531 GTTCAGAATGCCAATATTAGCAAGTAA 58.594 33.333 12.58 1.57 43.36 2.24
5086 5499 8.518430 TCAGAATGCCAATATTAGCAAGTAAA 57.482 30.769 12.58 0.00 43.36 2.01
5087 5500 8.405531 TCAGAATGCCAATATTAGCAAGTAAAC 58.594 33.333 12.58 2.10 43.36 2.01
5088 5501 7.376866 CAGAATGCCAATATTAGCAAGTAAACG 59.623 37.037 12.58 0.00 43.36 3.60
5089 5502 6.935741 ATGCCAATATTAGCAAGTAAACGA 57.064 33.333 12.58 0.00 43.36 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.041684 TGCCAGAGAGGGATCAGTCA 59.958 55.000 0.00 0.00 38.09 3.41
21 22 0.689080 ACATCGTGCCAGAGAGGGAT 60.689 55.000 0.00 0.00 41.14 3.85
30 31 4.350441 TGCGTCGACATCGTGCCA 62.350 61.111 17.16 0.00 39.60 4.92
53 54 1.160137 GTCTCATGACAAGGCCACAC 58.840 55.000 5.01 0.00 42.48 3.82
119 120 1.686587 TCAGACTGACCAGAAGCGAAA 59.313 47.619 0.00 0.00 0.00 3.46
120 121 1.328279 TCAGACTGACCAGAAGCGAA 58.672 50.000 0.00 0.00 0.00 4.70
122 123 1.795286 GTTTCAGACTGACCAGAAGCG 59.205 52.381 4.15 0.00 0.00 4.68
127 128 2.245159 TGCTGTTTCAGACTGACCAG 57.755 50.000 19.99 19.99 32.44 4.00
140 141 7.271511 TCAACCTAATTTGTGATTTTGCTGTT 58.728 30.769 0.00 0.00 0.00 3.16
168 169 3.391296 GGTGATGTGGGATGTACTATGGT 59.609 47.826 0.00 0.00 0.00 3.55
189 190 7.502060 AGATGAGATAATAATGGGGTACTGG 57.498 40.000 0.00 0.00 0.00 4.00
218 219 4.546829 TCCGGCTACTGTTAATGTCTTT 57.453 40.909 0.00 0.00 0.00 2.52
237 238 3.648739 ACTCTGTTCTCCCCTCTATTCC 58.351 50.000 0.00 0.00 0.00 3.01
260 261 2.516225 GATTGGGGGCGGTGTAGC 60.516 66.667 0.00 0.00 0.00 3.58
266 267 4.603535 GATGGGGATTGGGGGCGG 62.604 72.222 0.00 0.00 0.00 6.13
283 293 9.350357 CTTGGTTATGTTTTCTTGATTCATGAG 57.650 33.333 0.00 0.00 0.00 2.90
335 346 2.552315 TCCACCTTCGTTTTGATCTTGC 59.448 45.455 0.00 0.00 0.00 4.01
386 402 4.653888 CTGGTTTTCCGCCGGGGT 62.654 66.667 18.27 0.00 44.36 4.95
391 407 1.000843 AGATTTTGCTGGTTTTCCGCC 59.999 47.619 0.00 0.00 44.36 6.13
393 409 2.584791 CGAGATTTTGCTGGTTTTCCG 58.415 47.619 0.00 0.00 44.36 4.30
396 412 1.335872 CGGCGAGATTTTGCTGGTTTT 60.336 47.619 0.00 0.00 36.58 2.43
402 418 2.100631 CGTCCGGCGAGATTTTGCT 61.101 57.895 9.30 0.00 44.77 3.91
405 421 2.818274 GGCGTCCGGCGAGATTTT 60.818 61.111 20.06 0.00 44.92 1.82
497 513 2.202623 ACGCGCGAACATCTCTCC 60.203 61.111 39.36 0.00 0.00 3.71
500 516 1.614227 TTCACACGCGCGAACATCTC 61.614 55.000 39.36 0.00 0.00 2.75
521 540 2.625737 CATCTCCGCATCTGTTTCACT 58.374 47.619 0.00 0.00 0.00 3.41
522 541 1.667724 CCATCTCCGCATCTGTTTCAC 59.332 52.381 0.00 0.00 0.00 3.18
523 542 1.407299 CCCATCTCCGCATCTGTTTCA 60.407 52.381 0.00 0.00 0.00 2.69
524 543 1.303309 CCCATCTCCGCATCTGTTTC 58.697 55.000 0.00 0.00 0.00 2.78
525 544 0.749454 GCCCATCTCCGCATCTGTTT 60.749 55.000 0.00 0.00 0.00 2.83
526 545 1.153086 GCCCATCTCCGCATCTGTT 60.153 57.895 0.00 0.00 0.00 3.16
527 546 2.507944 GCCCATCTCCGCATCTGT 59.492 61.111 0.00 0.00 0.00 3.41
528 547 2.664185 CGCCCATCTCCGCATCTG 60.664 66.667 0.00 0.00 0.00 2.90
529 548 2.839632 TCGCCCATCTCCGCATCT 60.840 61.111 0.00 0.00 0.00 2.90
535 554 1.005630 CGGATTCTCGCCCATCTCC 60.006 63.158 0.00 0.00 0.00 3.71
538 557 1.666234 GCTCGGATTCTCGCCCATC 60.666 63.158 0.00 0.00 0.00 3.51
543 562 3.326210 CAGCGCTCGGATTCTCGC 61.326 66.667 7.13 0.00 46.95 5.03
604 629 2.558554 AATGGAGACGAACTCGCCGG 62.559 60.000 0.00 0.00 45.76 6.13
621 649 3.887716 GCAGTGGCATTCTGGAGATTAAT 59.112 43.478 7.17 0.00 40.72 1.40
749 783 2.722201 GGCCTGTGTACGGGAGGAG 61.722 68.421 13.97 0.00 45.36 3.69
823 859 4.430765 CTACCGGTCTGCGCGGTT 62.431 66.667 12.40 0.00 40.40 4.44
1566 1620 3.705638 CACAGCTGCACGACGTGG 61.706 66.667 27.86 14.23 33.64 4.94
1836 1890 2.358737 CACGCACCTCCCCAGAAC 60.359 66.667 0.00 0.00 0.00 3.01
1890 1944 4.441079 GGAATGGACCTGCATTCTTTCATG 60.441 45.833 16.32 0.00 37.79 3.07
1891 1945 3.703052 GGAATGGACCTGCATTCTTTCAT 59.297 43.478 16.32 0.00 37.79 2.57
1892 1946 3.091545 GGAATGGACCTGCATTCTTTCA 58.908 45.455 16.32 0.00 37.79 2.69
1893 1947 3.359950 AGGAATGGACCTGCATTCTTTC 58.640 45.455 16.32 3.71 39.01 2.62
1894 1948 3.359950 GAGGAATGGACCTGCATTCTTT 58.640 45.455 16.32 7.74 40.73 2.52
1929 1983 0.700564 AATCACATGAGCACTGGGGT 59.299 50.000 0.00 0.00 0.00 4.95
1930 1984 1.843368 AAATCACATGAGCACTGGGG 58.157 50.000 0.00 0.00 0.00 4.96
1957 2011 4.467084 TCTGCGCCCGGTTCATCC 62.467 66.667 4.18 0.00 0.00 3.51
2020 2074 1.445095 CCATGGCTCCCTCTCGAAG 59.555 63.158 0.00 0.00 0.00 3.79
2164 2218 1.347707 TGTGTTTGTTTGGTTTGCCCA 59.652 42.857 0.00 0.00 43.27 5.36
2167 2221 5.204101 GCATATTGTGTTTGTTTGGTTTGC 58.796 37.500 0.00 0.00 0.00 3.68
2170 2224 6.765036 TGAATGCATATTGTGTTTGTTTGGTT 59.235 30.769 0.00 0.00 0.00 3.67
2171 2225 6.202570 GTGAATGCATATTGTGTTTGTTTGGT 59.797 34.615 0.00 0.00 0.00 3.67
2192 2246 6.625362 TGTGAACTTGTAGCAAATTTGTGAA 58.375 32.000 19.03 6.59 0.00 3.18
2302 2384 5.382618 TCTGGTTCGTAGGAGAAGTTAAC 57.617 43.478 0.00 0.00 0.00 2.01
2309 2394 2.025155 GATGCTCTGGTTCGTAGGAGA 58.975 52.381 0.00 0.00 0.00 3.71
2320 2405 0.178767 TTGATCCACGGATGCTCTGG 59.821 55.000 2.54 0.00 34.60 3.86
2335 2420 2.840974 CCTTGTCGGCGTTCTTGAT 58.159 52.632 6.85 0.00 0.00 2.57
2367 2452 1.639298 ATCGAACAAGCGCTCCAAGC 61.639 55.000 12.06 0.00 38.02 4.01
2375 2460 1.021390 AAGCCTGGATCGAACAAGCG 61.021 55.000 0.00 0.00 30.81 4.68
2406 2491 6.476706 CCTTCTTTTTGAACTTGTTCATGGAC 59.523 38.462 15.67 0.00 0.00 4.02
2451 2536 1.628846 AGAACAATGTAGCCCGGTTCT 59.371 47.619 0.00 0.00 42.29 3.01
2461 2546 8.912988 ACTGGAAGAAAAATCAAGAACAATGTA 58.087 29.630 0.00 0.00 37.43 2.29
2501 2586 5.956068 TCATTGGAAAATGATTCACGTCA 57.044 34.783 0.00 0.00 34.50 4.35
2554 2639 3.017442 TGTAGTTCTCGATGTCCTCTGG 58.983 50.000 0.00 0.00 0.00 3.86
2556 2641 3.958018 AGTGTAGTTCTCGATGTCCTCT 58.042 45.455 0.00 0.00 0.00 3.69
2578 2663 6.494491 TCCTTGTCCATCATTTGAAACATCTT 59.506 34.615 0.00 0.00 0.00 2.40
2595 2680 0.971386 TACCGTCCTTGTCCTTGTCC 59.029 55.000 0.00 0.00 0.00 4.02
2724 2809 3.795561 AAGAGAGCAATGAAAACGTCG 57.204 42.857 0.00 0.00 0.00 5.12
2748 2833 7.779326 TCCCAATCATCATAGCTATTTTGTTCA 59.221 33.333 2.64 0.00 0.00 3.18
2756 2841 6.905215 TCCACTATCCCAATCATCATAGCTAT 59.095 38.462 0.00 0.00 0.00 2.97
2760 2845 5.879223 GCTTCCACTATCCCAATCATCATAG 59.121 44.000 0.00 0.00 0.00 2.23
2763 2848 3.718434 AGCTTCCACTATCCCAATCATCA 59.282 43.478 0.00 0.00 0.00 3.07
2806 2891 2.766313 TCGTTGCATTTGTACAGCTCT 58.234 42.857 7.07 0.00 0.00 4.09
2807 2892 3.536158 TTCGTTGCATTTGTACAGCTC 57.464 42.857 7.07 0.88 0.00 4.09
2824 2909 7.377766 TCTAGATTTCCCAGAACATTTTTCG 57.622 36.000 0.00 0.00 0.00 3.46
2866 2951 6.025749 AGCGACATATCTTGGAATCGAATA 57.974 37.500 0.00 0.00 0.00 1.75
2868 2953 4.322080 AGCGACATATCTTGGAATCGAA 57.678 40.909 0.00 0.00 0.00 3.71
2877 2962 7.773149 AGTAGAACTTTGTAGCGACATATCTT 58.227 34.615 0.00 0.00 34.86 2.40
2885 2970 5.700722 TCAGAAGTAGAACTTTGTAGCGA 57.299 39.130 0.00 0.00 38.80 4.93
2893 2978 6.987404 GGAGTCAGTTTTCAGAAGTAGAACTT 59.013 38.462 0.00 0.00 41.95 2.66
2904 2989 2.614057 AGTTTGCGGAGTCAGTTTTCAG 59.386 45.455 0.00 0.00 0.00 3.02
2908 2993 1.065551 GCAAGTTTGCGGAGTCAGTTT 59.934 47.619 0.53 0.00 45.11 2.66
2921 3006 7.649306 GTCATCTGAAACAATTACAGCAAGTTT 59.351 33.333 0.00 0.00 35.33 2.66
2933 3018 5.336213 GCCTCACAATGTCATCTGAAACAAT 60.336 40.000 1.12 0.00 0.00 2.71
2999 3085 7.068348 GGAATACCCCTCTAAATGGAAGAAAAC 59.932 40.741 0.00 0.00 0.00 2.43
3070 3156 0.178975 TGCCCCACGAATTCCACTTT 60.179 50.000 0.00 0.00 0.00 2.66
3111 3198 4.446371 GAAAGCTAGATATGTGCCACTGT 58.554 43.478 0.00 0.00 0.00 3.55
3143 3230 3.386486 TCAATTGCGTTTAGACTCGTGT 58.614 40.909 0.00 0.00 0.00 4.49
3156 3243 7.253288 CGTGATTAATACTTGGTTTCAATTGCG 60.253 37.037 0.00 0.00 31.75 4.85
3176 3263 7.979537 TGTTAGAACATAATGTAGCTCGTGATT 59.020 33.333 0.00 0.00 33.17 2.57
3303 3390 4.537135 TGAAAGCTTCAGGTAGGTACTG 57.463 45.455 0.00 0.00 34.75 2.74
3392 3479 0.833287 GCTCATCTGGGCCTAGTTCA 59.167 55.000 16.69 0.00 0.00 3.18
3417 3504 7.889712 GTCAACGTCACGTATAATGTCTTTAAC 59.110 37.037 1.57 0.00 39.99 2.01
3419 3506 7.060979 GTGTCAACGTCACGTATAATGTCTTTA 59.939 37.037 1.57 0.00 39.99 1.85
3507 3602 1.494721 AGCAAGGTCCACTTTCCTGAA 59.505 47.619 0.00 0.00 37.29 3.02
3511 3606 2.206576 ATCAGCAAGGTCCACTTTCC 57.793 50.000 0.00 0.00 37.29 3.13
3518 3613 3.766051 AGGATTCAAAATCAGCAAGGTCC 59.234 43.478 2.42 0.00 0.00 4.46
3575 3762 7.779798 TCCAGCTAGCTTAAAATTACATTGGAT 59.220 33.333 16.46 0.00 0.00 3.41
3581 3768 7.938140 ACAATCCAGCTAGCTTAAAATTACA 57.062 32.000 16.46 0.00 0.00 2.41
3620 3807 8.512138 CCGTCTACAGTTTCAGGATTTAAAATT 58.488 33.333 0.00 0.00 0.00 1.82
3685 3875 1.148498 GATGGGGGAAAGCGGGTAG 59.852 63.158 0.00 0.00 0.00 3.18
3690 3880 1.078426 AGAACGATGGGGGAAAGCG 60.078 57.895 0.00 0.00 0.00 4.68
3701 3891 1.218316 GGCACTTCCCGAGAACGAT 59.782 57.895 0.00 0.00 42.66 3.73
3710 3900 3.572255 TCAAACATTAGTTGGCACTTCCC 59.428 43.478 0.00 0.00 38.17 3.97
3754 3944 5.516090 TGTTGTTGATTTACGCTTCTTTCC 58.484 37.500 0.00 0.00 0.00 3.13
3863 4053 2.696707 CCATGGATGGCAGCAATAAGTT 59.303 45.455 5.56 0.00 41.75 2.66
3866 4056 1.707106 CCCATGGATGGCAGCAATAA 58.293 50.000 15.22 0.00 46.70 1.40
3910 4100 9.201989 TGTCAGTTATCCTATAGAAGAATGTGT 57.798 33.333 0.00 0.00 0.00 3.72
3985 4175 4.202233 TGAGCCAGATCTCATCATCACTTC 60.202 45.833 0.00 0.00 38.11 3.01
4040 4230 3.243636 ACTGAGGTTGCTGAAATTTGCTG 60.244 43.478 0.00 0.00 0.00 4.41
4072 4280 3.334691 TGTTTCATAGAACTCCTTGGCG 58.665 45.455 0.00 0.00 0.00 5.69
4078 4286 6.422400 GGATCGATCTTGTTTCATAGAACTCC 59.578 42.308 23.96 0.00 0.00 3.85
4081 4289 7.539712 TTGGATCGATCTTGTTTCATAGAAC 57.460 36.000 23.96 3.75 0.00 3.01
4089 4297 2.421424 GCTGCTTGGATCGATCTTGTTT 59.579 45.455 23.96 0.00 0.00 2.83
4173 4381 1.920351 TCCTCCAAACCCAGTAATCCC 59.080 52.381 0.00 0.00 0.00 3.85
4205 4413 1.376609 CGAGCAACTGGGTTATGGGC 61.377 60.000 0.00 0.00 0.00 5.36
4206 4414 0.748005 CCGAGCAACTGGGTTATGGG 60.748 60.000 0.00 0.00 0.00 4.00
4207 4415 0.251916 TCCGAGCAACTGGGTTATGG 59.748 55.000 0.00 0.00 31.18 2.74
4240 4456 1.682854 TGGGTTTTCTGCTTCTGCTTG 59.317 47.619 0.00 0.00 40.48 4.01
4264 4480 3.120304 GGTTTCAGTACAAAGGACGATGC 60.120 47.826 0.00 0.00 0.00 3.91
4270 4486 9.974980 GAAATATTTTGGTTTCAGTACAAAGGA 57.025 29.630 1.43 0.00 35.74 3.36
4328 4544 5.560724 CTTTTCTTCCCTTACATCTGTCCA 58.439 41.667 0.00 0.00 0.00 4.02
4417 4633 7.816513 TCGCAATGTTGATCCATGAAATTTTTA 59.183 29.630 0.00 0.00 0.00 1.52
4418 4634 6.649973 TCGCAATGTTGATCCATGAAATTTTT 59.350 30.769 0.00 0.00 0.00 1.94
4440 4656 0.038343 TGCTCCTTTTGGCAATTCGC 60.038 50.000 0.00 0.76 40.12 4.70
4461 4677 5.050490 CACGAAGTATACTGGATGGAAAGG 58.950 45.833 6.06 0.00 41.61 3.11
4481 4700 1.589731 CGCGTATCAGTTCATTGCACG 60.590 52.381 0.00 0.00 32.76 5.34
4609 5013 7.365831 GGGAGTAATAAACACCATGGTAACCTA 60.366 40.741 19.28 7.32 40.39 3.08
4621 5025 3.431346 GGGACGGAGGGAGTAATAAACAC 60.431 52.174 0.00 0.00 0.00 3.32
4629 5033 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
4630 5034 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
4631 5035 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4632 5036 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4633 5037 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4634 5038 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
4635 5039 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
4636 5040 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
4637 5041 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
4638 5042 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
4639 5043 5.501897 CGAAAACGCTCTTATATTGTGGGAC 60.502 44.000 0.00 0.00 0.00 4.46
4640 5044 4.569162 CGAAAACGCTCTTATATTGTGGGA 59.431 41.667 0.00 0.00 0.00 4.37
4641 5045 4.569162 TCGAAAACGCTCTTATATTGTGGG 59.431 41.667 0.00 0.00 0.00 4.61
4642 5046 5.062934 TGTCGAAAACGCTCTTATATTGTGG 59.937 40.000 0.00 0.00 0.00 4.17
4643 5047 5.952064 GTGTCGAAAACGCTCTTATATTGTG 59.048 40.000 0.00 0.00 35.42 3.33
4644 5048 5.867716 AGTGTCGAAAACGCTCTTATATTGT 59.132 36.000 0.00 0.00 45.69 2.71
4645 5049 6.332504 AGTGTCGAAAACGCTCTTATATTG 57.667 37.500 0.00 0.00 45.69 1.90
4646 5050 7.220300 CAGTAGTGTCGAAAACGCTCTTATATT 59.780 37.037 0.00 0.00 45.69 1.28
4647 5051 6.691818 CAGTAGTGTCGAAAACGCTCTTATAT 59.308 38.462 0.00 0.00 45.69 0.86
4648 5052 6.025896 CAGTAGTGTCGAAAACGCTCTTATA 58.974 40.000 0.00 0.00 45.69 0.98
4649 5053 4.857588 CAGTAGTGTCGAAAACGCTCTTAT 59.142 41.667 0.00 0.00 45.69 1.73
4650 5054 4.224433 CAGTAGTGTCGAAAACGCTCTTA 58.776 43.478 0.00 0.00 45.69 2.10
4651 5055 3.050619 CAGTAGTGTCGAAAACGCTCTT 58.949 45.455 0.00 0.00 45.69 2.85
4652 5056 2.034305 ACAGTAGTGTCGAAAACGCTCT 59.966 45.455 0.00 0.00 45.69 4.09
4653 5057 2.391879 ACAGTAGTGTCGAAAACGCTC 58.608 47.619 0.00 0.00 45.69 5.03
4655 5059 3.303406 ACTACAGTAGTGTCGAAAACGC 58.697 45.455 12.75 0.00 37.69 4.84
4680 5084 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4681 5085 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4682 5086 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4683 5087 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4684 5088 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4685 5089 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4686 5090 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4687 5091 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4688 5092 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4689 5093 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4690 5094 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4691 5095 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4692 5096 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4693 5097 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
4694 5098 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
4695 5099 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
4696 5100 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
4697 5101 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
4698 5102 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
4699 5103 1.790818 AATTCTACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
4700 5104 2.627221 GGTAATTCTACTCCCTCCGTCC 59.373 54.545 0.00 0.00 0.00 4.79
4701 5105 3.318557 CAGGTAATTCTACTCCCTCCGTC 59.681 52.174 0.00 0.00 0.00 4.79
4702 5106 3.053095 TCAGGTAATTCTACTCCCTCCGT 60.053 47.826 0.00 0.00 0.00 4.69
4703 5107 3.563223 TCAGGTAATTCTACTCCCTCCG 58.437 50.000 0.00 0.00 0.00 4.63
4704 5108 5.952347 TTTCAGGTAATTCTACTCCCTCC 57.048 43.478 0.00 0.00 0.00 4.30
4705 5109 7.797062 AGATTTTCAGGTAATTCTACTCCCTC 58.203 38.462 0.00 0.00 0.00 4.30
4706 5110 7.757242 AGATTTTCAGGTAATTCTACTCCCT 57.243 36.000 0.00 0.00 0.00 4.20
4787 5191 2.611971 GGTACTGCTGAAATGGTGACGA 60.612 50.000 0.00 0.00 0.00 4.20
4788 5192 1.732259 GGTACTGCTGAAATGGTGACG 59.268 52.381 0.00 0.00 0.00 4.35
4934 5338 4.144297 ACACACAGTTGCTTGATATGGTT 58.856 39.130 0.00 0.00 0.00 3.67
5050 5463 2.092429 TGGCATTCTGAACCCATCTACC 60.092 50.000 7.35 0.00 0.00 3.18
5051 5464 3.281727 TGGCATTCTGAACCCATCTAC 57.718 47.619 7.35 0.00 0.00 2.59
5052 5465 4.524802 ATTGGCATTCTGAACCCATCTA 57.475 40.909 11.12 0.18 0.00 1.98
5053 5466 2.905415 TTGGCATTCTGAACCCATCT 57.095 45.000 11.12 0.00 0.00 2.90
5054 5467 5.796424 AATATTGGCATTCTGAACCCATC 57.204 39.130 11.12 0.00 0.00 3.51
5055 5468 5.244626 GCTAATATTGGCATTCTGAACCCAT 59.755 40.000 17.98 1.89 34.50 4.00
5056 5469 4.584325 GCTAATATTGGCATTCTGAACCCA 59.416 41.667 17.98 7.35 34.50 4.51
5057 5470 4.584325 TGCTAATATTGGCATTCTGAACCC 59.416 41.667 21.19 0.00 39.85 4.11
5058 5471 5.772825 TGCTAATATTGGCATTCTGAACC 57.227 39.130 21.19 0.00 39.85 3.62
5059 5472 6.799512 ACTTGCTAATATTGGCATTCTGAAC 58.200 36.000 24.82 0.00 44.25 3.18
5060 5473 8.518430 TTACTTGCTAATATTGGCATTCTGAA 57.482 30.769 24.82 13.05 44.25 3.02
5061 5474 8.405531 GTTTACTTGCTAATATTGGCATTCTGA 58.594 33.333 24.82 10.53 44.25 3.27
5062 5475 7.376866 CGTTTACTTGCTAATATTGGCATTCTG 59.623 37.037 24.82 17.17 44.25 3.02
5063 5476 7.282224 TCGTTTACTTGCTAATATTGGCATTCT 59.718 33.333 24.82 13.50 44.25 2.40
5064 5477 7.414436 TCGTTTACTTGCTAATATTGGCATTC 58.586 34.615 24.82 11.79 44.25 2.67
5065 5478 7.328277 TCGTTTACTTGCTAATATTGGCATT 57.672 32.000 24.82 17.46 44.25 3.56
5066 5479 6.935741 TCGTTTACTTGCTAATATTGGCAT 57.064 33.333 24.82 14.77 44.25 4.40


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

AutoCloner maintained by Alex Coulton.