Multiple sequence alignment - TraesCS5D01G474800

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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 TraesCS5D01G474800 chr5D 100.000 2541 0 0 1 2541 514925090 514922550 0.000000e+00 4693.0
1 TraesCS5D01G474800 chr5A 88.197 1830 145 46 1 1803 642920355 642918570 0.000000e+00 2117.0
2 TraesCS5D01G474800 chr5B 94.407 1198 40 10 703 1877 647387624 647386431 0.000000e+00 1816.0
3 TraesCS5D01G474800 chr5B 97.238 362 8 2 1922 2283 647386431 647386072 1.670000e-171 612.0
4 TraesCS5D01G474800 chr5B 81.408 355 42 10 376 720 647388114 647387774 4.170000e-68 268.0
5 TraesCS5D01G474800 chr5B 89.080 174 14 3 119 292 647388617 647388449 7.120000e-51 211.0
6 TraesCS5D01G474800 chr5B 88.957 163 15 1 175 337 647388449 647388290 5.540000e-47 198.0
7 TraesCS5D01G474800 chr5B 97.321 112 3 0 2278 2389 647385841 647385730 9.280000e-45 191.0
8 TraesCS5D01G474800 chr5B 87.234 141 6 2 1 130 647390281 647390142 1.570000e-32 150.0
9 TraesCS5D01G474800 chr6D 86.928 918 91 16 633 1541 16502553 16503450 0.000000e+00 1003.0
10 TraesCS5D01G474800 chr6D 87.337 845 65 25 740 1556 16523452 16522622 0.000000e+00 929.0
11 TraesCS5D01G474800 chr6D 89.108 762 54 18 815 1556 16307432 16306680 0.000000e+00 920.0
12 TraesCS5D01G474800 chr6D 86.085 848 80 23 730 1557 16510497 16511326 0.000000e+00 878.0
13 TraesCS5D01G474800 chr6D 88.742 151 15 2 2391 2540 46457478 46457329 1.550000e-42 183.0
14 TraesCS5D01G474800 chr6D 87.273 55 7 0 1604 1658 16522566 16522512 2.110000e-06 63.9
15 TraesCS5D01G474800 chr6A 89.323 768 52 18 809 1557 16593984 16593228 0.000000e+00 937.0
16 TraesCS5D01G474800 chr6A 88.263 639 45 18 937 1550 33010751 33011384 0.000000e+00 737.0
17 TraesCS5D01G474800 chr6B 88.598 763 60 15 814 1557 28925844 28926598 0.000000e+00 902.0
18 TraesCS5D01G474800 chr6B 89.590 634 51 9 933 1557 58812333 58812960 0.000000e+00 791.0
19 TraesCS5D01G474800 chr6B 89.542 153 12 3 2391 2541 60119816 60119666 9.280000e-45 191.0
20 TraesCS5D01G474800 chr6B 87.742 155 19 0 2387 2541 59748039 59747885 5.580000e-42 182.0
21 TraesCS5D01G474800 chr2D 93.377 151 10 0 2391 2541 158625146 158625296 9.150000e-55 224.0
22 TraesCS5D01G474800 chr4D 91.667 156 13 0 2386 2541 487635561 487635716 1.530000e-52 217.0
23 TraesCS5D01G474800 chr1D 88.889 162 16 2 2380 2540 289609889 289609729 5.540000e-47 198.0
24 TraesCS5D01G474800 chr4A 87.742 155 19 0 2387 2541 158515915 158515761 5.580000e-42 182.0
25 TraesCS5D01G474800 chr4A 86.420 162 21 1 2380 2541 731262146 731261986 2.600000e-40 176.0
26 TraesCS5D01G474800 chr2B 87.742 155 19 0 2387 2541 758670657 758670503 5.580000e-42 182.0


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 TraesCS5D01G474800 chr5D 514922550 514925090 2540 True 4693.000000 4693 100.000000 1 2541 1 chr5D.!!$R1 2540
1 TraesCS5D01G474800 chr5A 642918570 642920355 1785 True 2117.000000 2117 88.197000 1 1803 1 chr5A.!!$R1 1802
2 TraesCS5D01G474800 chr5B 647385730 647390281 4551 True 492.285714 1816 90.806429 1 2389 7 chr5B.!!$R1 2388
3 TraesCS5D01G474800 chr6D 16502553 16503450 897 False 1003.000000 1003 86.928000 633 1541 1 chr6D.!!$F1 908
4 TraesCS5D01G474800 chr6D 16306680 16307432 752 True 920.000000 920 89.108000 815 1556 1 chr6D.!!$R1 741
5 TraesCS5D01G474800 chr6D 16510497 16511326 829 False 878.000000 878 86.085000 730 1557 1 chr6D.!!$F2 827
6 TraesCS5D01G474800 chr6D 16522512 16523452 940 True 496.450000 929 87.305000 740 1658 2 chr6D.!!$R3 918
7 TraesCS5D01G474800 chr6A 16593228 16593984 756 True 937.000000 937 89.323000 809 1557 1 chr6A.!!$R1 748
8 TraesCS5D01G474800 chr6A 33010751 33011384 633 False 737.000000 737 88.263000 937 1550 1 chr6A.!!$F1 613
9 TraesCS5D01G474800 chr6B 28925844 28926598 754 False 902.000000 902 88.598000 814 1557 1 chr6B.!!$F1 743
10 TraesCS5D01G474800 chr6B 58812333 58812960 627 False 791.000000 791 89.590000 933 1557 1 chr6B.!!$F2 624

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
372 2184 0.312102 AAAGCTCTTTGTTGCTCCGC 59.688 50.000 0.0 0.0 38.75 5.54 F
728 2719 1.001860 GCAGAGAGAGAACCAAGTGCT 59.998 52.381 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 3316 0.881118 GGACCTGCGATTCAAAAGCA 59.119 50.0 0.00 0.0 39.25 3.91 R
2484 4838 0.037697 GCACCGTATATGGATGCCGA 60.038 55.0 18.22 0.0 0.00 5.54 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
85 97 5.300034 AGTTTGAGCAACATGAACAATGAGA 59.700 36.000 0.00 0.00 38.72 3.27
137 1685 7.775729 AAACGAAAACTATTATGAAAGCACG 57.224 32.000 0.00 0.00 0.00 5.34
262 1922 3.393106 GGCCACAAATGCAGGGGG 61.393 66.667 0.00 0.00 0.00 5.40
276 1936 1.226945 GGGGGCAAAAATCGATGCG 60.227 57.895 0.00 0.00 43.47 4.73
278 1938 0.525455 GGGGCAAAAATCGATGCGAC 60.525 55.000 0.00 0.00 43.47 5.19
279 1939 0.861450 GGGCAAAAATCGATGCGACG 60.861 55.000 0.00 0.00 43.47 5.12
327 1987 7.174253 TGGAGAAACGAAGCAAGTAAAATATGT 59.826 33.333 0.00 0.00 0.00 2.29
360 2172 6.431198 TTTGTTGAACGTAAAGAAAGCTCT 57.569 33.333 0.00 0.00 0.00 4.09
361 2173 6.431198 TTGTTGAACGTAAAGAAAGCTCTT 57.569 33.333 0.00 0.00 44.11 2.85
370 2182 3.998099 AAGAAAGCTCTTTGTTGCTCC 57.002 42.857 4.27 0.00 38.89 4.70
371 2183 1.876156 AGAAAGCTCTTTGTTGCTCCG 59.124 47.619 0.00 0.00 38.75 4.63
372 2184 0.312102 AAAGCTCTTTGTTGCTCCGC 59.688 50.000 0.00 0.00 38.75 5.54
373 2185 1.518903 AAGCTCTTTGTTGCTCCGCC 61.519 55.000 0.00 0.00 38.75 6.13
374 2186 2.982744 GCTCTTTGTTGCTCCGCCC 61.983 63.158 0.00 0.00 0.00 6.13
380 2192 3.056328 GTTGCTCCGCCCCTTGTC 61.056 66.667 0.00 0.00 0.00 3.18
390 2202 4.473520 CCCTTGTCGCTCCGCCAT 62.474 66.667 0.00 0.00 0.00 4.40
398 2210 2.559231 TGTCGCTCCGCCATGTATTATA 59.441 45.455 0.00 0.00 0.00 0.98
415 2227 8.856153 TGTATTATACACATGGTGAGTTTTGT 57.144 30.769 0.29 0.00 36.96 2.83
461 2274 4.157105 ACTTTTGTTTGCGTCTTGGTAGTT 59.843 37.500 0.00 0.00 0.00 2.24
471 2284 2.804527 GTCTTGGTAGTTTTGGACGTCC 59.195 50.000 28.17 28.17 0.00 4.79
520 2333 7.966753 TCGTTAGACACTGATGTACTTTATCAC 59.033 37.037 0.00 0.00 39.95 3.06
534 2347 7.613801 TGTACTTTATCACCCACTTATGCAAAT 59.386 33.333 0.00 0.00 0.00 2.32
540 2354 6.357579 TCACCCACTTATGCAAATTTGATT 57.642 33.333 22.31 10.07 0.00 2.57
545 2359 9.566432 ACCCACTTATGCAAATTTGATTAAAAA 57.434 25.926 22.31 5.70 0.00 1.94
571 2385 9.765295 AAAACCTAATACTACTCCTCTAAGTGA 57.235 33.333 0.00 0.00 0.00 3.41
573 2387 9.577222 AACCTAATACTACTCCTCTAAGTGATC 57.423 37.037 0.00 0.00 0.00 2.92
574 2388 7.879160 ACCTAATACTACTCCTCTAAGTGATCG 59.121 40.741 0.00 0.00 0.00 3.69
575 2389 6.563222 AATACTACTCCTCTAAGTGATCGC 57.437 41.667 0.00 0.00 0.00 4.58
577 2391 3.880490 ACTACTCCTCTAAGTGATCGCTG 59.120 47.826 10.09 0.00 0.00 5.18
578 2392 2.028130 ACTCCTCTAAGTGATCGCTGG 58.972 52.381 10.09 6.79 0.00 4.85
638 2460 3.450096 GGGAACGGAGGAAGTGTATAACT 59.550 47.826 0.00 0.00 42.60 2.24
687 2509 6.647334 TGGATGCAAGATAAGTGTGAAAAA 57.353 33.333 0.00 0.00 0.00 1.94
728 2719 1.001860 GCAGAGAGAGAACCAAGTGCT 59.998 52.381 0.00 0.00 0.00 4.40
799 2791 4.652131 ATCGCCGCCACCCAAACA 62.652 61.111 0.00 0.00 0.00 2.83
902 2904 1.297598 CTCCAATAAAAGCCGCGCG 60.298 57.895 25.67 25.67 0.00 6.86
1261 3316 6.432162 ACAGATAACTGATTTTGCATCTGTGT 59.568 34.615 12.78 0.00 46.55 3.72
1408 3470 4.388499 GTGACCATCGCCCACGGT 62.388 66.667 0.00 0.00 40.63 4.83
1459 3524 4.697756 CCCAAGAAGTCCGCCGCA 62.698 66.667 0.00 0.00 0.00 5.69
1569 3662 5.181748 CCATAGCCTAGTTCCATAATCAGC 58.818 45.833 0.00 0.00 0.00 4.26
1641 3739 0.382515 GCCTAGTCTGTAGTGGCTCG 59.617 60.000 0.00 0.00 40.36 5.03
1782 3894 2.173569 AGAAAGTGTGCATCTATCCCCC 59.826 50.000 0.00 0.00 0.00 5.40
1803 3915 5.455612 CCCCTTGTACCTTCTGTCAGTTTAA 60.456 44.000 0.00 0.00 0.00 1.52
1877 3995 3.016031 ACCATGCTTAATCATGCGTCAA 58.984 40.909 12.79 0.00 41.77 3.18
1878 3996 3.065786 ACCATGCTTAATCATGCGTCAAG 59.934 43.478 12.79 2.53 41.77 3.02
1879 3997 3.065786 CCATGCTTAATCATGCGTCAAGT 59.934 43.478 12.79 0.00 41.77 3.16
1880 3998 4.277258 CATGCTTAATCATGCGTCAAGTC 58.723 43.478 6.37 0.00 37.60 3.01
1881 3999 3.599343 TGCTTAATCATGCGTCAAGTCT 58.401 40.909 0.00 0.00 0.00 3.24
1882 4000 4.002982 TGCTTAATCATGCGTCAAGTCTT 58.997 39.130 0.00 0.00 0.00 3.01
1883 4001 4.142838 TGCTTAATCATGCGTCAAGTCTTG 60.143 41.667 6.21 6.21 0.00 3.02
1884 4002 4.142816 GCTTAATCATGCGTCAAGTCTTGT 60.143 41.667 12.30 0.00 0.00 3.16
1885 4003 5.063438 GCTTAATCATGCGTCAAGTCTTGTA 59.937 40.000 12.30 0.00 0.00 2.41
1886 4004 4.928661 AATCATGCGTCAAGTCTTGTAC 57.071 40.909 12.30 8.38 0.00 2.90
1887 4005 2.324860 TCATGCGTCAAGTCTTGTACG 58.675 47.619 22.44 22.44 37.30 3.67
1888 4006 2.058798 CATGCGTCAAGTCTTGTACGT 58.941 47.619 24.94 12.96 36.91 3.57
1889 4007 3.058085 TCATGCGTCAAGTCTTGTACGTA 60.058 43.478 24.94 22.98 36.91 3.57
1890 4008 2.924903 TGCGTCAAGTCTTGTACGTAG 58.075 47.619 24.94 10.82 36.91 3.51
1891 4009 2.549329 TGCGTCAAGTCTTGTACGTAGA 59.451 45.455 24.94 14.50 36.91 2.59
1892 4010 3.189910 TGCGTCAAGTCTTGTACGTAGAT 59.810 43.478 24.94 0.00 36.91 1.98
1893 4011 4.164294 GCGTCAAGTCTTGTACGTAGATT 58.836 43.478 24.94 0.00 36.91 2.40
1894 4012 5.106594 TGCGTCAAGTCTTGTACGTAGATTA 60.107 40.000 24.94 11.73 36.91 1.75
1895 4013 5.970023 GCGTCAAGTCTTGTACGTAGATTAT 59.030 40.000 24.94 0.00 36.91 1.28
1896 4014 6.471519 GCGTCAAGTCTTGTACGTAGATTATT 59.528 38.462 24.94 0.00 36.91 1.40
1897 4015 7.008992 GCGTCAAGTCTTGTACGTAGATTATTT 59.991 37.037 24.94 0.00 36.91 1.40
1898 4016 8.521860 CGTCAAGTCTTGTACGTAGATTATTTC 58.478 37.037 20.24 0.00 33.04 2.17
1899 4017 9.350357 GTCAAGTCTTGTACGTAGATTATTTCA 57.650 33.333 12.30 0.00 0.00 2.69
1900 4018 9.569167 TCAAGTCTTGTACGTAGATTATTTCAG 57.431 33.333 12.30 0.00 0.00 3.02
1901 4019 9.569167 CAAGTCTTGTACGTAGATTATTTCAGA 57.431 33.333 4.27 0.00 0.00 3.27
1902 4020 9.570488 AAGTCTTGTACGTAGATTATTTCAGAC 57.430 33.333 9.33 9.33 0.00 3.51
1903 4021 8.737175 AGTCTTGTACGTAGATTATTTCAGACA 58.263 33.333 16.24 0.00 0.00 3.41
1904 4022 9.517609 GTCTTGTACGTAGATTATTTCAGACAT 57.482 33.333 11.48 0.00 0.00 3.06
1905 4023 9.516314 TCTTGTACGTAGATTATTTCAGACATG 57.484 33.333 0.00 0.00 0.00 3.21
1906 4024 7.694388 TGTACGTAGATTATTTCAGACATGC 57.306 36.000 0.00 0.00 0.00 4.06
1907 4025 6.700081 TGTACGTAGATTATTTCAGACATGCC 59.300 38.462 0.00 0.00 0.00 4.40
1908 4026 5.670485 ACGTAGATTATTTCAGACATGCCA 58.330 37.500 0.00 0.00 0.00 4.92
1909 4027 6.112734 ACGTAGATTATTTCAGACATGCCAA 58.887 36.000 0.00 0.00 0.00 4.52
1910 4028 6.597672 ACGTAGATTATTTCAGACATGCCAAA 59.402 34.615 0.00 0.00 0.00 3.28
1911 4029 7.120579 ACGTAGATTATTTCAGACATGCCAAAA 59.879 33.333 0.00 0.00 0.00 2.44
1912 4030 7.429340 CGTAGATTATTTCAGACATGCCAAAAC 59.571 37.037 0.00 0.00 0.00 2.43
1913 4031 7.230849 AGATTATTTCAGACATGCCAAAACA 57.769 32.000 0.00 0.00 0.00 2.83
1914 4032 7.844009 AGATTATTTCAGACATGCCAAAACAT 58.156 30.769 0.00 0.00 0.00 2.71
1982 4100 8.321353 AGACAATTTAAATTTGATCTTTCCCCC 58.679 33.333 10.77 0.00 0.00 5.40
1995 4113 0.118346 TTCCCCCTCCAGCTGAGTTA 59.882 55.000 17.39 0.00 39.65 2.24
2016 4134 8.281212 AGTTAGTTGTAGATTATTTTGGCCAG 57.719 34.615 5.11 0.00 0.00 4.85
2027 4145 6.543430 TTATTTTGGCCAGTCATAAGCAAT 57.457 33.333 5.11 0.00 0.00 3.56
2088 4206 8.828688 AGTACTACATACAACAAACTTCTTCC 57.171 34.615 0.00 0.00 36.09 3.46
2179 4297 8.867097 ACTATTGGACTGAACTACTAAAACAGA 58.133 33.333 0.00 0.00 33.53 3.41
2292 4646 8.660295 TCCAAATGAGGTACTAGTAGAAGAAA 57.340 34.615 1.87 0.00 41.55 2.52
2293 4647 9.268282 TCCAAATGAGGTACTAGTAGAAGAAAT 57.732 33.333 1.87 0.00 41.55 2.17
2389 4743 7.491048 TCAGTAAAAAGCACCATTTTCAGAAAC 59.509 33.333 0.00 0.00 31.25 2.78
2390 4744 7.277539 CAGTAAAAAGCACCATTTTCAGAAACA 59.722 33.333 0.00 0.00 31.25 2.83
2391 4745 6.667007 AAAAAGCACCATTTTCAGAAACAG 57.333 33.333 0.00 0.00 31.25 3.16
2392 4746 5.343307 AAAGCACCATTTTCAGAAACAGT 57.657 34.783 0.00 0.00 0.00 3.55
2393 4747 4.574599 AGCACCATTTTCAGAAACAGTC 57.425 40.909 0.00 0.00 0.00 3.51
2394 4748 3.953612 AGCACCATTTTCAGAAACAGTCA 59.046 39.130 0.00 0.00 0.00 3.41
2395 4749 4.402155 AGCACCATTTTCAGAAACAGTCAA 59.598 37.500 0.00 0.00 0.00 3.18
2396 4750 5.069516 AGCACCATTTTCAGAAACAGTCAAT 59.930 36.000 0.00 0.00 0.00 2.57
2397 4751 5.754890 GCACCATTTTCAGAAACAGTCAATT 59.245 36.000 0.00 0.00 0.00 2.32
2398 4752 6.922957 GCACCATTTTCAGAAACAGTCAATTA 59.077 34.615 0.00 0.00 0.00 1.40
2399 4753 7.096065 GCACCATTTTCAGAAACAGTCAATTAC 60.096 37.037 0.00 0.00 0.00 1.89
2400 4754 7.920151 CACCATTTTCAGAAACAGTCAATTACA 59.080 33.333 0.00 0.00 0.00 2.41
2401 4755 7.920682 ACCATTTTCAGAAACAGTCAATTACAC 59.079 33.333 0.00 0.00 0.00 2.90
2402 4756 7.382218 CCATTTTCAGAAACAGTCAATTACACC 59.618 37.037 0.00 0.00 0.00 4.16
2403 4757 7.397892 TTTTCAGAAACAGTCAATTACACCA 57.602 32.000 0.00 0.00 0.00 4.17
2404 4758 6.371809 TTCAGAAACAGTCAATTACACCAC 57.628 37.500 0.00 0.00 0.00 4.16
2405 4759 5.680619 TCAGAAACAGTCAATTACACCACT 58.319 37.500 0.00 0.00 0.00 4.00
2406 4760 6.822442 TCAGAAACAGTCAATTACACCACTA 58.178 36.000 0.00 0.00 0.00 2.74
2407 4761 6.929049 TCAGAAACAGTCAATTACACCACTAG 59.071 38.462 0.00 0.00 0.00 2.57
2408 4762 6.706270 CAGAAACAGTCAATTACACCACTAGT 59.294 38.462 0.00 0.00 0.00 2.57
2417 4771 3.706055 CACCACTAGTGCCACAACT 57.294 52.632 17.86 0.00 40.28 3.16
2418 4772 1.967319 CACCACTAGTGCCACAACTT 58.033 50.000 17.86 0.00 40.28 2.66
2419 4773 1.603802 CACCACTAGTGCCACAACTTG 59.396 52.381 17.86 3.01 40.28 3.16
2430 4784 3.525268 CCACAACTTGGCAAGAAAAGT 57.475 42.857 32.50 20.05 39.07 2.66
2431 4785 3.447742 CCACAACTTGGCAAGAAAAGTC 58.552 45.455 32.50 0.00 39.07 3.01
2432 4786 3.119173 CCACAACTTGGCAAGAAAAGTCA 60.119 43.478 32.50 0.00 39.07 3.41
2433 4787 4.107622 CACAACTTGGCAAGAAAAGTCAG 58.892 43.478 32.50 14.18 35.60 3.51
2434 4788 3.763897 ACAACTTGGCAAGAAAAGTCAGT 59.236 39.130 32.50 14.74 35.60 3.41
2435 4789 4.220602 ACAACTTGGCAAGAAAAGTCAGTT 59.779 37.500 32.50 11.68 35.60 3.16
2436 4790 5.170748 CAACTTGGCAAGAAAAGTCAGTTT 58.829 37.500 32.50 10.14 35.60 2.66
2437 4791 6.071616 ACAACTTGGCAAGAAAAGTCAGTTTA 60.072 34.615 32.50 0.00 35.60 2.01
2438 4792 6.136541 ACTTGGCAAGAAAAGTCAGTTTAG 57.863 37.500 32.50 2.02 30.87 1.85
2439 4793 5.652452 ACTTGGCAAGAAAAGTCAGTTTAGT 59.348 36.000 32.50 2.72 30.87 2.24
2440 4794 5.499139 TGGCAAGAAAAGTCAGTTTAGTG 57.501 39.130 0.00 0.00 0.00 2.74
2441 4795 4.202010 TGGCAAGAAAAGTCAGTTTAGTGC 60.202 41.667 0.00 0.00 33.03 4.40
2442 4796 4.036852 GGCAAGAAAAGTCAGTTTAGTGCT 59.963 41.667 7.15 0.00 33.74 4.40
2443 4797 5.238650 GGCAAGAAAAGTCAGTTTAGTGCTA 59.761 40.000 7.15 0.00 33.74 3.49
2444 4798 6.238648 GGCAAGAAAAGTCAGTTTAGTGCTAA 60.239 38.462 7.15 0.00 33.74 3.09
2445 4799 7.193595 GCAAGAAAAGTCAGTTTAGTGCTAAA 58.806 34.615 0.68 0.68 31.95 1.85
2446 4800 7.700656 GCAAGAAAAGTCAGTTTAGTGCTAAAA 59.299 33.333 6.02 0.00 36.86 1.52
2447 4801 9.010366 CAAGAAAAGTCAGTTTAGTGCTAAAAC 57.990 33.333 6.02 2.43 36.86 2.43
2448 4802 8.507524 AGAAAAGTCAGTTTAGTGCTAAAACT 57.492 30.769 6.02 4.40 36.86 2.66
2449 4803 8.957466 AGAAAAGTCAGTTTAGTGCTAAAACTT 58.043 29.630 11.47 11.47 36.21 2.66
2450 4804 8.911247 AAAAGTCAGTTTAGTGCTAAAACTTG 57.089 30.769 15.29 10.72 35.50 3.16
2451 4805 6.061231 AGTCAGTTTAGTGCTAAAACTTGC 57.939 37.500 6.02 5.71 36.86 4.01
2452 4806 4.904154 GTCAGTTTAGTGCTAAAACTTGCG 59.096 41.667 6.02 1.04 36.86 4.85
2453 4807 4.812091 TCAGTTTAGTGCTAAAACTTGCGA 59.188 37.500 6.02 2.85 36.86 5.10
2454 4808 4.904154 CAGTTTAGTGCTAAAACTTGCGAC 59.096 41.667 6.02 0.00 36.86 5.19
2455 4809 4.573201 AGTTTAGTGCTAAAACTTGCGACA 59.427 37.500 6.02 0.00 36.86 4.35
2456 4810 5.238650 AGTTTAGTGCTAAAACTTGCGACAT 59.761 36.000 6.02 0.00 36.86 3.06
2457 4811 6.425721 AGTTTAGTGCTAAAACTTGCGACATA 59.574 34.615 6.02 0.00 36.86 2.29
2458 4812 4.663636 AGTGCTAAAACTTGCGACATAC 57.336 40.909 0.00 0.00 0.00 2.39
2459 4813 4.062293 AGTGCTAAAACTTGCGACATACA 58.938 39.130 0.00 0.00 0.00 2.29
2460 4814 4.695455 AGTGCTAAAACTTGCGACATACAT 59.305 37.500 0.00 0.00 0.00 2.29
2461 4815 5.181245 AGTGCTAAAACTTGCGACATACATT 59.819 36.000 0.00 0.00 0.00 2.71
2462 4816 5.283717 GTGCTAAAACTTGCGACATACATTG 59.716 40.000 0.00 0.00 0.00 2.82
2463 4817 5.180304 TGCTAAAACTTGCGACATACATTGA 59.820 36.000 0.00 0.00 0.00 2.57
2464 4818 6.083630 GCTAAAACTTGCGACATACATTGAA 58.916 36.000 0.00 0.00 0.00 2.69
2465 4819 6.032460 GCTAAAACTTGCGACATACATTGAAC 59.968 38.462 0.00 0.00 0.00 3.18
2466 4820 5.689383 AAACTTGCGACATACATTGAACT 57.311 34.783 0.00 0.00 0.00 3.01
2467 4821 4.668576 ACTTGCGACATACATTGAACTG 57.331 40.909 0.00 0.00 0.00 3.16
2468 4822 3.436704 ACTTGCGACATACATTGAACTGG 59.563 43.478 0.00 0.00 0.00 4.00
2469 4823 3.052455 TGCGACATACATTGAACTGGT 57.948 42.857 0.00 0.00 0.00 4.00
2470 4824 2.741517 TGCGACATACATTGAACTGGTG 59.258 45.455 0.00 0.00 0.00 4.17
2471 4825 2.476185 GCGACATACATTGAACTGGTGC 60.476 50.000 0.00 0.00 0.00 5.01
2472 4826 2.095853 CGACATACATTGAACTGGTGCC 59.904 50.000 0.00 0.00 0.00 5.01
2473 4827 3.081061 GACATACATTGAACTGGTGCCA 58.919 45.455 0.00 0.00 0.00 4.92
2474 4828 2.819608 ACATACATTGAACTGGTGCCAC 59.180 45.455 0.00 0.00 0.00 5.01
2475 4829 2.647683 TACATTGAACTGGTGCCACA 57.352 45.000 0.00 0.00 0.00 4.17
2476 4830 1.774110 ACATTGAACTGGTGCCACAA 58.226 45.000 0.00 0.00 0.00 3.33
2477 4831 1.408702 ACATTGAACTGGTGCCACAAC 59.591 47.619 0.00 0.00 0.00 3.32
2478 4832 1.682854 CATTGAACTGGTGCCACAACT 59.317 47.619 0.00 0.00 0.00 3.16
2479 4833 1.846007 TTGAACTGGTGCCACAACTT 58.154 45.000 0.00 0.00 0.00 2.66
2480 4834 1.102154 TGAACTGGTGCCACAACTTG 58.898 50.000 0.00 0.00 0.00 3.16
2488 4842 2.644992 CCACAACTTGGCTTCGGC 59.355 61.111 0.00 0.00 39.07 5.54
2489 4843 2.192861 CCACAACTTGGCTTCGGCA 61.193 57.895 0.00 0.00 43.96 5.69
2490 4844 1.526575 CCACAACTTGGCTTCGGCAT 61.527 55.000 0.00 0.00 43.96 4.40
2491 4845 0.109597 CACAACTTGGCTTCGGCATC 60.110 55.000 0.00 0.00 43.96 3.91
2492 4846 1.244019 ACAACTTGGCTTCGGCATCC 61.244 55.000 0.00 0.00 43.96 3.51
2493 4847 1.074775 AACTTGGCTTCGGCATCCA 59.925 52.632 0.00 0.00 43.96 3.41
2494 4848 0.323725 AACTTGGCTTCGGCATCCAT 60.324 50.000 0.00 0.00 43.96 3.41
2495 4849 0.546122 ACTTGGCTTCGGCATCCATA 59.454 50.000 0.00 0.00 43.96 2.74
2496 4850 1.143684 ACTTGGCTTCGGCATCCATAT 59.856 47.619 0.00 0.00 43.96 1.78
2497 4851 2.371841 ACTTGGCTTCGGCATCCATATA 59.628 45.455 0.00 0.00 43.96 0.86
2498 4852 2.472695 TGGCTTCGGCATCCATATAC 57.527 50.000 0.00 0.00 43.96 1.47
2499 4853 1.337728 TGGCTTCGGCATCCATATACG 60.338 52.381 0.00 0.00 43.96 3.06
2500 4854 1.359848 GCTTCGGCATCCATATACGG 58.640 55.000 0.00 0.00 41.33 4.02
2501 4855 1.337823 GCTTCGGCATCCATATACGGT 60.338 52.381 0.00 0.00 41.33 4.83
2502 4856 2.337583 CTTCGGCATCCATATACGGTG 58.662 52.381 0.00 0.00 0.00 4.94
2503 4857 0.037697 TCGGCATCCATATACGGTGC 60.038 55.000 4.47 4.47 34.37 5.01
2504 4858 0.320334 CGGCATCCATATACGGTGCA 60.320 55.000 12.31 0.00 35.83 4.57
2505 4859 1.875996 CGGCATCCATATACGGTGCAA 60.876 52.381 12.31 0.00 35.83 4.08
2506 4860 2.226330 GGCATCCATATACGGTGCAAA 58.774 47.619 12.31 0.00 35.83 3.68
2507 4861 2.819608 GGCATCCATATACGGTGCAAAT 59.180 45.455 12.31 0.00 35.83 2.32
2508 4862 3.119849 GGCATCCATATACGGTGCAAATC 60.120 47.826 12.31 0.00 35.83 2.17
2509 4863 3.501828 GCATCCATATACGGTGCAAATCA 59.498 43.478 7.30 0.00 34.89 2.57
2510 4864 4.613622 GCATCCATATACGGTGCAAATCAC 60.614 45.833 7.30 0.00 44.90 3.06
2511 4865 3.127589 TCCATATACGGTGCAAATCACG 58.872 45.455 0.00 0.00 46.56 4.35
2512 4866 2.869801 CCATATACGGTGCAAATCACGT 59.130 45.455 0.00 0.00 46.56 4.49
2513 4867 3.311322 CCATATACGGTGCAAATCACGTT 59.689 43.478 6.90 0.57 46.56 3.99
2514 4868 4.508492 CCATATACGGTGCAAATCACGTTA 59.492 41.667 6.90 0.00 46.56 3.18
2515 4869 5.178623 CCATATACGGTGCAAATCACGTTAT 59.821 40.000 6.90 0.00 46.56 1.89
2516 4870 6.293190 CCATATACGGTGCAAATCACGTTATT 60.293 38.462 6.90 0.00 46.56 1.40
2517 4871 3.196007 ACGGTGCAAATCACGTTATTG 57.804 42.857 0.00 0.00 46.56 1.90
2518 4872 1.910819 CGGTGCAAATCACGTTATTGC 59.089 47.619 18.05 18.05 46.56 3.56
2521 4875 0.561141 GCAAATCACGTTATTGCGCG 59.439 50.000 0.00 0.00 39.89 6.86
2522 4876 1.788699 GCAAATCACGTTATTGCGCGA 60.789 47.619 12.10 0.00 39.89 5.87
2523 4877 2.500888 CAAATCACGTTATTGCGCGAA 58.499 42.857 12.10 0.00 34.88 4.70
2524 4878 2.153680 AATCACGTTATTGCGCGAAC 57.846 45.000 12.10 3.93 34.88 3.95
2525 4879 1.072391 ATCACGTTATTGCGCGAACA 58.928 45.000 12.10 0.00 34.88 3.18
2526 4880 0.162082 TCACGTTATTGCGCGAACAC 59.838 50.000 12.10 9.29 34.88 3.32
2527 4881 0.111045 CACGTTATTGCGCGAACACA 60.111 50.000 12.10 0.00 34.88 3.72
2528 4882 0.162933 ACGTTATTGCGCGAACACAG 59.837 50.000 12.10 9.06 34.88 3.66
2529 4883 0.162933 CGTTATTGCGCGAACACAGT 59.837 50.000 12.10 0.00 0.00 3.55
2530 4884 1.591248 GTTATTGCGCGAACACAGTG 58.409 50.000 12.10 0.00 0.00 3.66
2531 4885 0.110419 TTATTGCGCGAACACAGTGC 60.110 50.000 12.10 0.00 44.57 4.40
2532 4886 0.948623 TATTGCGCGAACACAGTGCT 60.949 50.000 12.10 0.00 44.60 4.40
2533 4887 2.448153 ATTGCGCGAACACAGTGCTG 62.448 55.000 12.10 0.00 44.60 4.41
2534 4888 3.337889 GCGCGAACACAGTGCTGA 61.338 61.111 12.10 0.00 41.45 4.26
2535 4889 2.671177 GCGCGAACACAGTGCTGAT 61.671 57.895 12.10 0.00 41.45 2.90
2536 4890 1.862123 CGCGAACACAGTGCTGATT 59.138 52.632 0.00 0.15 0.00 2.57
2537 4891 1.067693 CGCGAACACAGTGCTGATTA 58.932 50.000 0.00 0.00 0.00 1.75
2538 4892 1.059692 CGCGAACACAGTGCTGATTAG 59.940 52.381 0.00 2.35 0.00 1.73
2539 4893 1.394917 GCGAACACAGTGCTGATTAGG 59.605 52.381 6.17 0.00 0.00 2.69
2540 4894 1.394917 CGAACACAGTGCTGATTAGGC 59.605 52.381 6.17 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.336993 CACGCCTAGTCTTATCAAGAGTCT 59.663 45.833 0.00 0.00 41.33 3.24
117 129 6.961554 CACTCCGTGCTTTCATAATAGTTTTC 59.038 38.462 0.00 0.00 0.00 2.29
137 1685 1.071605 GCTTGTCGTGACATCACTCC 58.928 55.000 10.18 1.43 44.34 3.85
204 1752 6.280643 AGATACTACATGCATTACTCGCAAA 58.719 36.000 0.00 0.00 43.84 3.68
205 1753 5.842907 AGATACTACATGCATTACTCGCAA 58.157 37.500 0.00 0.00 43.84 4.85
206 1754 5.009610 TGAGATACTACATGCATTACTCGCA 59.990 40.000 0.00 0.00 44.94 5.10
218 1766 6.836527 AGTTCAACCTAGCTGAGATACTACAT 59.163 38.462 0.00 0.00 0.00 2.29
262 1922 2.091409 GTACGTCGCATCGATTTTTGC 58.909 47.619 0.00 0.00 38.42 3.68
276 1936 6.101332 TGTTATAGGACATGTTTGGTACGTC 58.899 40.000 0.00 0.00 0.00 4.34
327 1987 6.879276 TTACGTTCAACAAATACATGGGAA 57.121 33.333 0.00 0.00 0.00 3.97
341 2153 6.431198 ACAAAGAGCTTTCTTTACGTTCAA 57.569 33.333 0.00 0.00 37.80 2.69
344 2156 5.034797 GCAACAAAGAGCTTTCTTTACGTT 58.965 37.500 0.00 0.90 37.80 3.99
367 2179 4.821589 GAGCGACAAGGGGCGGAG 62.822 72.222 0.00 0.00 0.00 4.63
380 2192 2.954316 TGTATAATACATGGCGGAGCG 58.046 47.619 0.00 0.00 45.20 5.03
390 2202 8.856153 ACAAAACTCACCATGTGTATAATACA 57.144 30.769 0.00 0.00 34.79 2.29
398 2210 1.946768 CCGACAAAACTCACCATGTGT 59.053 47.619 0.00 0.00 34.79 3.72
461 2274 6.939132 TTTACAATTTACAGGACGTCCAAA 57.061 33.333 35.00 25.70 38.89 3.28
471 2284 7.646130 ACGACACAAACCATTTACAATTTACAG 59.354 33.333 0.00 0.00 0.00 2.74
545 2359 9.765295 TCACTTAGAGGAGTAGTATTAGGTTTT 57.235 33.333 0.00 0.00 0.00 2.43
549 2363 7.148373 GCGATCACTTAGAGGAGTAGTATTAGG 60.148 44.444 0.00 0.00 0.00 2.69
560 2374 2.437085 TCCAGCGATCACTTAGAGGA 57.563 50.000 0.00 0.00 0.00 3.71
561 2375 4.279671 ACTTATCCAGCGATCACTTAGAGG 59.720 45.833 0.00 0.00 0.00 3.69
563 2377 5.048643 GCTACTTATCCAGCGATCACTTAGA 60.049 44.000 0.00 0.00 0.00 2.10
564 2378 5.157781 GCTACTTATCCAGCGATCACTTAG 58.842 45.833 0.00 0.00 0.00 2.18
565 2379 5.122512 GCTACTTATCCAGCGATCACTTA 57.877 43.478 0.00 0.00 0.00 2.24
567 2381 3.651803 GCTACTTATCCAGCGATCACT 57.348 47.619 0.00 0.00 0.00 3.41
574 2388 1.341606 GCGATCGCTACTTATCCAGC 58.658 55.000 31.94 0.00 38.26 4.85
638 2460 7.698506 TCGACTTTTCACTTAGAGGAATCTA 57.301 36.000 0.00 0.00 0.00 1.98
728 2719 4.288626 AGCAGGGATCTTGTTTTACCACTA 59.711 41.667 0.00 0.00 0.00 2.74
1050 3084 3.569200 GAACTGGAGCCCGGCCTTT 62.569 63.158 5.55 0.00 32.02 3.11
1261 3316 0.881118 GGACCTGCGATTCAAAAGCA 59.119 50.000 0.00 0.00 39.25 3.91
1459 3524 2.607750 TTGGCCTCCTTCTCGGCT 60.608 61.111 3.32 0.00 45.57 5.52
1569 3662 2.285827 AAAGGCTCGTCATCTTCTCG 57.714 50.000 0.00 0.00 0.00 4.04
1678 3781 8.664798 CATTCTCGACATTAATCAGGTACAAAA 58.335 33.333 0.00 0.00 0.00 2.44
1679 3782 7.279981 CCATTCTCGACATTAATCAGGTACAAA 59.720 37.037 0.00 0.00 0.00 2.83
1782 3894 8.836413 TCAATTTAAACTGACAGAAGGTACAAG 58.164 33.333 10.08 0.00 0.00 3.16
1877 3995 8.737175 TGTCTGAAATAATCTACGTACAAGACT 58.263 33.333 0.00 0.00 0.00 3.24
1878 3996 8.906636 TGTCTGAAATAATCTACGTACAAGAC 57.093 34.615 0.00 0.00 0.00 3.01
1879 3997 9.516314 CATGTCTGAAATAATCTACGTACAAGA 57.484 33.333 0.00 0.00 0.00 3.02
1880 3998 8.269424 GCATGTCTGAAATAATCTACGTACAAG 58.731 37.037 0.00 0.00 0.00 3.16
1881 3999 7.223971 GGCATGTCTGAAATAATCTACGTACAA 59.776 37.037 0.00 0.00 0.00 2.41
1882 4000 6.700081 GGCATGTCTGAAATAATCTACGTACA 59.300 38.462 0.00 0.00 0.00 2.90
1883 4001 6.700081 TGGCATGTCTGAAATAATCTACGTAC 59.300 38.462 0.00 0.00 0.00 3.67
1884 4002 6.811954 TGGCATGTCTGAAATAATCTACGTA 58.188 36.000 0.00 0.00 0.00 3.57
1885 4003 5.670485 TGGCATGTCTGAAATAATCTACGT 58.330 37.500 0.00 0.00 0.00 3.57
1886 4004 6.603237 TTGGCATGTCTGAAATAATCTACG 57.397 37.500 0.00 0.00 0.00 3.51
1887 4005 8.243426 TGTTTTGGCATGTCTGAAATAATCTAC 58.757 33.333 0.00 0.00 0.00 2.59
1888 4006 8.347004 TGTTTTGGCATGTCTGAAATAATCTA 57.653 30.769 0.00 0.00 0.00 1.98
1889 4007 7.230849 TGTTTTGGCATGTCTGAAATAATCT 57.769 32.000 0.00 0.00 0.00 2.40
1890 4008 7.464977 GCATGTTTTGGCATGTCTGAAATAATC 60.465 37.037 0.00 0.00 45.75 1.75
1891 4009 6.314400 GCATGTTTTGGCATGTCTGAAATAAT 59.686 34.615 0.00 0.00 45.75 1.28
1892 4010 5.638657 GCATGTTTTGGCATGTCTGAAATAA 59.361 36.000 0.00 0.00 45.75 1.40
1893 4011 5.170021 GCATGTTTTGGCATGTCTGAAATA 58.830 37.500 0.00 0.00 45.75 1.40
1894 4012 3.998341 GCATGTTTTGGCATGTCTGAAAT 59.002 39.130 0.00 0.00 45.75 2.17
1895 4013 3.391965 GCATGTTTTGGCATGTCTGAAA 58.608 40.909 0.00 0.00 45.75 2.69
1896 4014 3.029320 GCATGTTTTGGCATGTCTGAA 57.971 42.857 0.00 0.00 45.75 3.02
1897 4015 2.728690 GCATGTTTTGGCATGTCTGA 57.271 45.000 0.00 0.00 45.75 3.27
1906 4024 5.771153 AATTTCCTTTTGGCATGTTTTGG 57.229 34.783 0.00 0.00 40.12 3.28
1907 4025 7.256756 TGTAATTTCCTTTTGGCATGTTTTG 57.743 32.000 0.00 0.00 40.12 2.44
1908 4026 7.872113 TTGTAATTTCCTTTTGGCATGTTTT 57.128 28.000 0.00 0.00 40.12 2.43
1909 4027 7.872113 TTTGTAATTTCCTTTTGGCATGTTT 57.128 28.000 0.00 0.00 40.12 2.83
1910 4028 7.872113 TTTTGTAATTTCCTTTTGGCATGTT 57.128 28.000 0.00 0.00 40.12 2.71
1911 4029 7.872113 TTTTTGTAATTTCCTTTTGGCATGT 57.128 28.000 0.00 0.00 40.12 3.21
1995 4113 6.245408 TGACTGGCCAAAATAATCTACAACT 58.755 36.000 7.01 0.00 0.00 3.16
2179 4297 8.573035 TCTTAATTTTTCAGTAAGCATCCGTTT 58.427 29.630 0.00 0.00 0.00 3.60
2237 4355 1.145819 CTCCTAGCTCTGCCCTTGC 59.854 63.158 0.00 0.00 38.26 4.01
2244 4362 1.953686 GCCTGACTACTCCTAGCTCTG 59.046 57.143 0.00 0.00 0.00 3.35
2292 4646 8.168058 ACTGTATTTACCCTCCTGTTACAAAAT 58.832 33.333 0.00 0.00 0.00 1.82
2293 4647 7.519927 ACTGTATTTACCCTCCTGTTACAAAA 58.480 34.615 0.00 0.00 0.00 2.44
2303 4657 5.295152 CCGACAATACTGTATTTACCCTCC 58.705 45.833 10.25 0.00 35.30 4.30
2389 4743 3.684788 GGCACTAGTGGTGTAATTGACTG 59.315 47.826 23.95 0.00 46.86 3.51
2390 4744 3.326588 TGGCACTAGTGGTGTAATTGACT 59.673 43.478 23.95 0.00 46.86 3.41
2391 4745 3.435671 GTGGCACTAGTGGTGTAATTGAC 59.564 47.826 23.95 3.33 46.86 3.18
2392 4746 3.071747 TGTGGCACTAGTGGTGTAATTGA 59.928 43.478 23.95 0.00 46.86 2.57
2393 4747 3.407698 TGTGGCACTAGTGGTGTAATTG 58.592 45.455 23.95 0.00 46.86 2.32
2394 4748 3.780804 TGTGGCACTAGTGGTGTAATT 57.219 42.857 23.95 0.00 46.86 1.40
2395 4749 3.072476 AGTTGTGGCACTAGTGGTGTAAT 59.928 43.478 23.95 0.00 46.86 1.89
2396 4750 2.436542 AGTTGTGGCACTAGTGGTGTAA 59.563 45.455 23.95 0.00 46.86 2.41
2397 4751 2.043992 AGTTGTGGCACTAGTGGTGTA 58.956 47.619 23.95 0.00 46.86 2.90
2398 4752 0.837272 AGTTGTGGCACTAGTGGTGT 59.163 50.000 23.95 0.00 46.86 4.16
2400 4754 1.476833 CCAAGTTGTGGCACTAGTGGT 60.477 52.381 23.95 0.00 41.72 4.16
2401 4755 1.238439 CCAAGTTGTGGCACTAGTGG 58.762 55.000 23.95 16.57 41.72 4.00
2411 4765 4.107622 CTGACTTTTCTTGCCAAGTTGTG 58.892 43.478 4.04 0.00 33.22 3.33
2412 4766 3.763897 ACTGACTTTTCTTGCCAAGTTGT 59.236 39.130 4.04 0.00 33.22 3.32
2413 4767 4.376340 ACTGACTTTTCTTGCCAAGTTG 57.624 40.909 4.04 0.00 33.22 3.16
2414 4768 5.405935 AAACTGACTTTTCTTGCCAAGTT 57.594 34.783 4.04 0.00 33.22 2.66
2415 4769 5.652452 ACTAAACTGACTTTTCTTGCCAAGT 59.348 36.000 4.04 0.00 35.88 3.16
2416 4770 5.973565 CACTAAACTGACTTTTCTTGCCAAG 59.026 40.000 0.00 0.00 0.00 3.61
2417 4771 5.678616 GCACTAAACTGACTTTTCTTGCCAA 60.679 40.000 0.00 0.00 0.00 4.52
2418 4772 4.202010 GCACTAAACTGACTTTTCTTGCCA 60.202 41.667 0.00 0.00 0.00 4.92
2419 4773 4.036852 AGCACTAAACTGACTTTTCTTGCC 59.963 41.667 0.00 0.00 31.25 4.52
2420 4774 5.175090 AGCACTAAACTGACTTTTCTTGC 57.825 39.130 0.00 0.00 31.14 4.01
2421 4775 9.010366 GTTTTAGCACTAAACTGACTTTTCTTG 57.990 33.333 2.36 0.00 35.05 3.02
2422 4776 8.957466 AGTTTTAGCACTAAACTGACTTTTCTT 58.043 29.630 9.24 0.00 35.05 2.52
2423 4777 8.507524 AGTTTTAGCACTAAACTGACTTTTCT 57.492 30.769 9.24 0.00 35.05 2.52
2424 4778 9.010366 CAAGTTTTAGCACTAAACTGACTTTTC 57.990 33.333 12.68 0.00 34.22 2.29
2425 4779 7.488150 GCAAGTTTTAGCACTAAACTGACTTTT 59.512 33.333 12.68 0.00 34.22 2.27
2426 4780 6.972901 GCAAGTTTTAGCACTAAACTGACTTT 59.027 34.615 12.68 1.93 34.22 2.66
2427 4781 6.495706 GCAAGTTTTAGCACTAAACTGACTT 58.504 36.000 10.70 10.70 35.60 3.01
2428 4782 5.277345 CGCAAGTTTTAGCACTAAACTGACT 60.277 40.000 10.38 2.04 35.05 3.41
2429 4783 4.904154 CGCAAGTTTTAGCACTAAACTGAC 59.096 41.667 10.38 0.00 35.05 3.51
2430 4784 4.812091 TCGCAAGTTTTAGCACTAAACTGA 59.188 37.500 10.38 3.50 35.05 3.41
2431 4785 4.904154 GTCGCAAGTTTTAGCACTAAACTG 59.096 41.667 10.38 2.99 35.05 3.16
2432 4786 4.573201 TGTCGCAAGTTTTAGCACTAAACT 59.427 37.500 2.36 5.38 35.05 2.66
2433 4787 4.839796 TGTCGCAAGTTTTAGCACTAAAC 58.160 39.130 2.36 0.00 35.05 2.01
2434 4788 5.682943 ATGTCGCAAGTTTTAGCACTAAA 57.317 34.783 0.00 0.00 39.48 1.85
2435 4789 5.697178 TGTATGTCGCAAGTTTTAGCACTAA 59.303 36.000 0.00 0.00 39.48 2.24
2436 4790 5.231702 TGTATGTCGCAAGTTTTAGCACTA 58.768 37.500 0.00 0.00 39.48 2.74
2437 4791 4.062293 TGTATGTCGCAAGTTTTAGCACT 58.938 39.130 0.00 0.00 39.48 4.40
2438 4792 4.398549 TGTATGTCGCAAGTTTTAGCAC 57.601 40.909 0.00 0.00 39.48 4.40
2439 4793 5.180304 TCAATGTATGTCGCAAGTTTTAGCA 59.820 36.000 0.00 0.00 39.48 3.49
2440 4794 5.627172 TCAATGTATGTCGCAAGTTTTAGC 58.373 37.500 0.00 0.00 39.48 3.09
2441 4795 7.269084 CAGTTCAATGTATGTCGCAAGTTTTAG 59.731 37.037 0.00 0.00 39.48 1.85
2442 4796 7.075121 CAGTTCAATGTATGTCGCAAGTTTTA 58.925 34.615 0.00 0.00 39.48 1.52
2443 4797 5.914635 CAGTTCAATGTATGTCGCAAGTTTT 59.085 36.000 0.00 0.00 39.48 2.43
2444 4798 5.451908 CAGTTCAATGTATGTCGCAAGTTT 58.548 37.500 0.00 0.00 39.48 2.66
2445 4799 4.083324 CCAGTTCAATGTATGTCGCAAGTT 60.083 41.667 0.00 0.00 39.48 2.66
2446 4800 3.436704 CCAGTTCAATGTATGTCGCAAGT 59.563 43.478 0.00 0.00 39.48 3.16
2447 4801 3.436704 ACCAGTTCAATGTATGTCGCAAG 59.563 43.478 0.00 0.00 0.00 4.01
2448 4802 3.188254 CACCAGTTCAATGTATGTCGCAA 59.812 43.478 0.00 0.00 0.00 4.85
2449 4803 2.741517 CACCAGTTCAATGTATGTCGCA 59.258 45.455 0.00 0.00 0.00 5.10
2450 4804 2.476185 GCACCAGTTCAATGTATGTCGC 60.476 50.000 0.00 0.00 0.00 5.19
2451 4805 2.095853 GGCACCAGTTCAATGTATGTCG 59.904 50.000 0.00 0.00 0.00 4.35
2452 4806 3.081061 TGGCACCAGTTCAATGTATGTC 58.919 45.455 0.00 0.00 0.00 3.06
2453 4807 2.819608 GTGGCACCAGTTCAATGTATGT 59.180 45.455 6.29 0.00 0.00 2.29
2454 4808 2.819019 TGTGGCACCAGTTCAATGTATG 59.181 45.455 16.26 0.00 0.00 2.39
2455 4809 3.153369 TGTGGCACCAGTTCAATGTAT 57.847 42.857 16.26 0.00 0.00 2.29
2456 4810 2.621055 GTTGTGGCACCAGTTCAATGTA 59.379 45.455 16.26 0.00 0.00 2.29
2457 4811 1.408702 GTTGTGGCACCAGTTCAATGT 59.591 47.619 16.26 0.00 0.00 2.71
2458 4812 1.682854 AGTTGTGGCACCAGTTCAATG 59.317 47.619 16.26 0.00 0.00 2.82
2459 4813 2.071778 AGTTGTGGCACCAGTTCAAT 57.928 45.000 16.26 0.00 0.00 2.57
2460 4814 1.476085 CAAGTTGTGGCACCAGTTCAA 59.524 47.619 16.26 0.00 0.00 2.69
2461 4815 1.102154 CAAGTTGTGGCACCAGTTCA 58.898 50.000 16.26 0.00 0.00 3.18
2462 4816 0.385390 CCAAGTTGTGGCACCAGTTC 59.615 55.000 16.26 1.07 41.72 3.01
2463 4817 2.503775 CCAAGTTGTGGCACCAGTT 58.496 52.632 16.26 10.70 41.72 3.16
2464 4818 4.258206 CCAAGTTGTGGCACCAGT 57.742 55.556 16.26 3.84 41.72 4.00
2472 4826 0.109597 GATGCCGAAGCCAAGTTGTG 60.110 55.000 1.45 0.00 38.69 3.33
2473 4827 1.244019 GGATGCCGAAGCCAAGTTGT 61.244 55.000 1.45 0.00 38.69 3.32
2474 4828 1.243342 TGGATGCCGAAGCCAAGTTG 61.243 55.000 0.00 0.00 38.69 3.16
2475 4829 0.323725 ATGGATGCCGAAGCCAAGTT 60.324 50.000 0.00 0.00 38.69 2.66
2476 4830 0.546122 TATGGATGCCGAAGCCAAGT 59.454 50.000 0.00 0.00 38.69 3.16
2477 4831 1.901591 ATATGGATGCCGAAGCCAAG 58.098 50.000 0.00 0.00 38.69 3.61
2478 4832 2.778299 GTATATGGATGCCGAAGCCAA 58.222 47.619 0.00 0.00 38.69 4.52
2479 4833 1.337728 CGTATATGGATGCCGAAGCCA 60.338 52.381 0.00 0.00 38.69 4.75
2480 4834 1.359848 CGTATATGGATGCCGAAGCC 58.640 55.000 0.00 0.00 38.69 4.35
2481 4835 1.337823 ACCGTATATGGATGCCGAAGC 60.338 52.381 18.22 0.00 40.48 3.86
2482 4836 2.337583 CACCGTATATGGATGCCGAAG 58.662 52.381 18.22 0.00 0.00 3.79
2483 4837 1.606994 GCACCGTATATGGATGCCGAA 60.607 52.381 18.22 0.00 0.00 4.30
2484 4838 0.037697 GCACCGTATATGGATGCCGA 60.038 55.000 18.22 0.00 0.00 5.54
2485 4839 0.320334 TGCACCGTATATGGATGCCG 60.320 55.000 23.98 9.13 35.37 5.69
2486 4840 1.890876 TTGCACCGTATATGGATGCC 58.109 50.000 23.98 13.56 35.37 4.40
2487 4841 3.501828 TGATTTGCACCGTATATGGATGC 59.498 43.478 18.22 20.52 36.81 3.91
2488 4842 4.377328 CGTGATTTGCACCGTATATGGATG 60.377 45.833 18.22 12.42 44.85 3.51
2489 4843 3.745975 CGTGATTTGCACCGTATATGGAT 59.254 43.478 18.22 0.00 44.85 3.41
2490 4844 3.127589 CGTGATTTGCACCGTATATGGA 58.872 45.455 18.22 0.00 44.85 3.41
2491 4845 2.869801 ACGTGATTTGCACCGTATATGG 59.130 45.455 9.60 9.60 44.85 2.74
2492 4846 4.530094 AACGTGATTTGCACCGTATATG 57.470 40.909 0.00 0.00 44.85 1.78
2493 4847 6.655062 CAATAACGTGATTTGCACCGTATAT 58.345 36.000 0.00 0.00 44.85 0.86
2494 4848 5.502706 GCAATAACGTGATTTGCACCGTATA 60.503 40.000 19.52 0.00 44.85 1.47
2495 4849 4.729458 GCAATAACGTGATTTGCACCGTAT 60.729 41.667 19.52 0.00 44.85 3.06
2496 4850 3.425094 GCAATAACGTGATTTGCACCGTA 60.425 43.478 19.52 0.00 44.85 4.02
2497 4851 2.667171 GCAATAACGTGATTTGCACCGT 60.667 45.455 19.52 0.00 44.85 4.83
2498 4852 1.910819 GCAATAACGTGATTTGCACCG 59.089 47.619 19.52 0.96 44.85 4.94
2499 4853 1.910819 CGCAATAACGTGATTTGCACC 59.089 47.619 22.32 2.89 44.58 5.01
2500 4854 1.317319 GCGCAATAACGTGATTTGCAC 59.683 47.619 22.32 13.72 44.58 4.57
2501 4855 1.612156 GCGCAATAACGTGATTTGCA 58.388 45.000 22.32 0.00 44.58 4.08
2502 4856 0.561141 CGCGCAATAACGTGATTTGC 59.439 50.000 8.75 16.22 46.13 3.68
2503 4857 2.152237 TCGCGCAATAACGTGATTTG 57.848 45.000 8.75 0.00 46.67 2.32
2508 4862 0.111045 TGTGTTCGCGCAATAACGTG 60.111 50.000 8.75 0.00 44.65 4.49
2509 4863 0.162933 CTGTGTTCGCGCAATAACGT 59.837 50.000 8.75 0.00 37.15 3.99
2510 4864 0.162933 ACTGTGTTCGCGCAATAACG 59.837 50.000 8.75 0.00 37.15 3.18
2511 4865 1.591248 CACTGTGTTCGCGCAATAAC 58.409 50.000 8.75 9.28 37.15 1.89
2512 4866 0.110419 GCACTGTGTTCGCGCAATAA 60.110 50.000 8.75 0.00 37.15 1.40
2513 4867 0.948623 AGCACTGTGTTCGCGCAATA 60.949 50.000 8.75 0.00 37.15 1.90
2514 4868 2.252260 GCACTGTGTTCGCGCAAT 59.748 55.556 8.75 0.00 37.15 3.56
2515 4869 2.894879 AGCACTGTGTTCGCGCAA 60.895 55.556 8.75 0.00 37.15 4.85
2516 4870 3.639008 CAGCACTGTGTTCGCGCA 61.639 61.111 8.75 0.00 36.08 6.09
2517 4871 2.175184 AATCAGCACTGTGTTCGCGC 62.175 55.000 9.86 0.00 0.00 6.86
2518 4872 1.059692 CTAATCAGCACTGTGTTCGCG 59.940 52.381 9.86 0.00 0.00 5.87
2519 4873 1.394917 CCTAATCAGCACTGTGTTCGC 59.605 52.381 9.86 0.00 0.00 4.70
2520 4874 1.394917 GCCTAATCAGCACTGTGTTCG 59.605 52.381 9.86 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.