Multiple sequence alignment - TraesCS3A01G475300

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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 TraesCS3A01G475300 chr3A 100.000 2751 0 0 1 2751 706910367 706913117 0.000000e+00 5081.0
1 TraesCS3A01G475300 chr3A 88.498 939 83 13 842 1762 706899495 706900426 0.000000e+00 1112.0
2 TraesCS3A01G475300 chr3A 81.978 738 112 14 975 1703 706850167 706850892 8.430000e-170 606.0
3 TraesCS3A01G475300 chr3A 87.121 132 11 4 653 783 706899221 706899347 7.940000e-31 145.0
4 TraesCS3A01G475300 chr3D 96.082 1123 36 5 646 1766 572049739 572048623 0.000000e+00 1823.0
5 TraesCS3A01G475300 chr3D 88.939 886 81 8 889 1762 572088785 572087905 0.000000e+00 1077.0
6 TraesCS3A01G475300 chr3D 94.720 644 29 3 5 647 572050459 572049820 0.000000e+00 996.0
7 TraesCS3A01G475300 chr3D 89.841 502 38 7 117 610 572096245 572095749 1.390000e-177 632.0
8 TraesCS3A01G475300 chr3D 81.316 760 119 16 966 1711 572103041 572102291 1.820000e-166 595.0
9 TraesCS3A01G475300 chr3D 91.813 171 14 0 1842 2012 572048325 572048155 3.540000e-59 239.0
10 TraesCS3A01G475300 chr3D 90.076 131 10 2 654 783 572090878 572090750 1.690000e-37 167.0
11 TraesCS3A01G475300 chr3D 100.000 37 0 0 842 878 572090661 572090625 4.920000e-08 69.4
12 TraesCS3A01G475300 chr3B 95.212 1107 41 6 646 1749 761932905 761934002 0.000000e+00 1740.0
13 TraesCS3A01G475300 chr3B 88.095 546 44 8 117 647 761932276 761932815 1.800000e-176 628.0
14 TraesCS3A01G475300 chr3B 82.008 717 110 12 1001 1708 761901025 761901731 2.360000e-165 592.0
15 TraesCS3A01G475300 chr3B 86.159 289 15 10 1748 2012 761934061 761934348 3.470000e-74 289.0
16 TraesCS3A01G475300 chr6B 85.240 542 43 12 2225 2751 43069305 43068786 8.730000e-145 523.0
17 TraesCS3A01G475300 chr6B 91.453 117 10 0 1 117 58846438 58846322 7.880000e-36 161.0
18 TraesCS3A01G475300 chr2D 93.162 117 8 0 1 117 522908738 522908854 3.640000e-39 172.0
19 TraesCS3A01G475300 chr4D 92.308 117 9 0 1 117 321978324 321978440 1.690000e-37 167.0
20 TraesCS3A01G475300 chr4D 93.043 115 6 2 1 115 478273465 478273577 1.690000e-37 167.0
21 TraesCS3A01G475300 chr4A 92.308 117 9 0 1 117 744492373 744492489 1.690000e-37 167.0
22 TraesCS3A01G475300 chr7D 92.241 116 9 0 2 117 381351332 381351447 6.090000e-37 165.0
23 TraesCS3A01G475300 chr7D 92.241 116 9 0 2 117 381352069 381352184 6.090000e-37 165.0
24 TraesCS3A01G475300 chr1D 88.148 135 12 4 1 133 184302390 184302522 1.020000e-34 158.0


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 TraesCS3A01G475300 chr3A 706910367 706913117 2750 False 5081.000000 5081 100.0000 1 2751 1 chr3A.!!$F2 2750
1 TraesCS3A01G475300 chr3A 706899221 706900426 1205 False 628.500000 1112 87.8095 653 1762 2 chr3A.!!$F3 1109
2 TraesCS3A01G475300 chr3A 706850167 706850892 725 False 606.000000 606 81.9780 975 1703 1 chr3A.!!$F1 728
3 TraesCS3A01G475300 chr3D 572048155 572050459 2304 True 1019.333333 1823 94.2050 5 2012 3 chr3D.!!$R3 2007
4 TraesCS3A01G475300 chr3D 572102291 572103041 750 True 595.000000 595 81.3160 966 1711 1 chr3D.!!$R2 745
5 TraesCS3A01G475300 chr3D 572087905 572090878 2973 True 437.800000 1077 93.0050 654 1762 3 chr3D.!!$R4 1108
6 TraesCS3A01G475300 chr3B 761932276 761934348 2072 False 885.666667 1740 89.8220 117 2012 3 chr3B.!!$F2 1895
7 TraesCS3A01G475300 chr3B 761901025 761901731 706 False 592.000000 592 82.0080 1001 1708 1 chr3B.!!$F1 707
8 TraesCS3A01G475300 chr6B 43068786 43069305 519 True 523.000000 523 85.2400 2225 2751 1 chr6B.!!$R1 526

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
566 582 0.034896 ACCCAAACGCTGGTCACTAG 59.965 55.0 3.63 0.0 44.76 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 3963 0.034089 GTGGGGAGGGATCAAAGTGG 60.034 60.0 0.0 0.0 0.0 4.0 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
32 33 0.839477 CTTTTTCACGTGCGCACAAG 59.161 50.000 37.03 28.04 0.00 3.16
101 102 3.853330 CTCCCGTTGCATCGCACG 61.853 66.667 11.68 6.67 38.71 5.34
210 213 5.423886 TGCCTTATATCACACGATCAAACA 58.576 37.500 0.00 0.00 32.73 2.83
213 216 6.705782 CCTTATATCACACGATCAAACACAC 58.294 40.000 0.00 0.00 32.73 3.82
215 218 2.613026 TCACACGATCAAACACACCT 57.387 45.000 0.00 0.00 0.00 4.00
226 229 5.545063 TCAAACACACCTTGATCTAGTCA 57.455 39.130 3.47 0.00 34.25 3.41
354 359 9.249457 GAGTTTGTTCCCAGAAAATTAAGAAAG 57.751 33.333 0.00 0.00 0.00 2.62
381 386 5.881923 AAATAGGGTTGTAGATCGGCTAA 57.118 39.130 0.00 0.00 0.00 3.09
436 441 3.674528 ATTGATGCATAGAGGTCCTCG 57.325 47.619 13.41 0.53 35.36 4.63
526 542 8.301002 CCCTGAAAAATAAAAATCACCTAACGA 58.699 33.333 0.00 0.00 0.00 3.85
565 581 0.250124 CACCCAAACGCTGGTCACTA 60.250 55.000 3.63 0.00 44.76 2.74
566 582 0.034896 ACCCAAACGCTGGTCACTAG 59.965 55.000 3.63 0.00 44.76 2.57
567 583 0.034896 CCCAAACGCTGGTCACTAGT 59.965 55.000 3.63 0.00 44.76 2.57
727 835 1.382629 GGTGCATACCTTGGTGGGT 59.617 57.895 2.03 0.00 43.97 4.51
784 1020 5.147162 CAACTATTGGAAAGAGAAACACGC 58.853 41.667 0.00 0.00 37.32 5.34
828 1064 0.336737 TTTTGACCAACCCACCACCT 59.663 50.000 0.00 0.00 0.00 4.00
831 1067 1.451449 TGACCAACCCACCACCTATT 58.549 50.000 0.00 0.00 0.00 1.73
834 1070 1.501604 ACCAACCCACCACCTATTTGT 59.498 47.619 0.00 0.00 0.00 2.83
835 1071 1.892474 CCAACCCACCACCTATTTGTG 59.108 52.381 0.00 0.00 35.98 3.33
836 1072 2.489985 CCAACCCACCACCTATTTGTGA 60.490 50.000 0.00 0.00 38.55 3.58
837 1073 2.556622 CAACCCACCACCTATTTGTGAC 59.443 50.000 0.00 0.00 38.55 3.67
878 1116 3.510388 TCGTCTGTGGAATAAGCAGAG 57.490 47.619 0.00 0.00 39.56 3.35
941 3008 6.376864 CCCGGCATTATATATTCAACATTGGA 59.623 38.462 0.00 0.00 0.00 3.53
994 3070 3.577848 GTCCATCCATAGCTCTGATCAGT 59.422 47.826 21.92 6.09 0.00 3.41
1051 3127 1.384222 CGGAAAGCAATACCCTGGCC 61.384 60.000 0.00 0.00 0.00 5.36
1158 3234 1.131303 TGACGTCCATGGACCCCTTT 61.131 55.000 34.05 16.39 41.76 3.11
1460 3536 0.035820 GGGTTCGCCAATCAGGTACA 60.036 55.000 0.00 0.00 40.61 2.90
1685 3797 4.590850 AGTCCAAGCAAGAAATTTCCAC 57.409 40.909 14.61 4.73 0.00 4.02
1711 3823 5.296748 AGTTTGACTGCTTTGTTGTTTTGT 58.703 33.333 0.00 0.00 0.00 2.83
1713 3825 6.259829 AGTTTGACTGCTTTGTTGTTTTGTTT 59.740 30.769 0.00 0.00 0.00 2.83
1725 3837 3.976169 TGTTTTGTTTGCATCACTAGGC 58.024 40.909 0.00 0.00 0.00 3.93
1726 3838 3.636300 TGTTTTGTTTGCATCACTAGGCT 59.364 39.130 0.00 0.00 32.35 4.58
1729 3841 2.153645 TGTTTGCATCACTAGGCTGTG 58.846 47.619 0.00 3.91 39.15 3.66
1730 3842 1.135575 GTTTGCATCACTAGGCTGTGC 60.136 52.381 0.00 0.46 37.81 4.57
1745 3860 4.874970 GGCTGTGCCCTTGATTATTATTG 58.125 43.478 0.00 0.00 44.06 1.90
1787 3962 1.691976 GGCAAGCCCCACTTTACTTTT 59.308 47.619 0.00 0.00 36.04 2.27
1788 3963 2.288825 GGCAAGCCCCACTTTACTTTTC 60.289 50.000 0.00 0.00 36.04 2.29
1789 3964 2.288825 GCAAGCCCCACTTTACTTTTCC 60.289 50.000 0.00 0.00 36.04 3.13
1790 3965 2.962421 CAAGCCCCACTTTACTTTTCCA 59.038 45.455 0.00 0.00 36.04 3.53
1791 3966 2.594131 AGCCCCACTTTACTTTTCCAC 58.406 47.619 0.00 0.00 0.00 4.02
1794 3969 3.386726 GCCCCACTTTACTTTTCCACTTT 59.613 43.478 0.00 0.00 0.00 2.66
1795 3970 4.739436 GCCCCACTTTACTTTTCCACTTTG 60.739 45.833 0.00 0.00 0.00 2.77
1796 3971 4.647399 CCCCACTTTACTTTTCCACTTTGA 59.353 41.667 0.00 0.00 0.00 2.69
1797 3972 5.304357 CCCCACTTTACTTTTCCACTTTGAT 59.696 40.000 0.00 0.00 0.00 2.57
1801 3979 6.265422 CACTTTACTTTTCCACTTTGATCCCT 59.735 38.462 0.00 0.00 0.00 4.20
1803 3981 3.767711 ACTTTTCCACTTTGATCCCTCC 58.232 45.455 0.00 0.00 0.00 4.30
1806 3984 0.178846 TCCACTTTGATCCCTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
1851 4262 1.269517 TGCAGGAACCGCAAACAATTC 60.270 47.619 7.60 0.00 36.17 2.17
1866 4277 7.293018 GCAAACAATTCAAGCTAATGGAAAAG 58.707 34.615 0.00 0.00 0.00 2.27
2012 4423 9.015577 TCTTTAACAAAAATGTGAAGCGTAAAG 57.984 29.630 0.00 0.00 0.00 1.85
2013 4424 8.912787 TTTAACAAAAATGTGAAGCGTAAAGA 57.087 26.923 0.00 0.00 0.00 2.52
2014 4425 9.522804 TTTAACAAAAATGTGAAGCGTAAAGAT 57.477 25.926 0.00 0.00 0.00 2.40
2015 4426 6.991485 ACAAAAATGTGAAGCGTAAAGATG 57.009 33.333 0.00 0.00 0.00 2.90
2016 4427 6.503524 ACAAAAATGTGAAGCGTAAAGATGT 58.496 32.000 0.00 0.00 0.00 3.06
2017 4428 6.978080 ACAAAAATGTGAAGCGTAAAGATGTT 59.022 30.769 0.00 0.00 0.00 2.71
2018 4429 6.991485 AAAATGTGAAGCGTAAAGATGTTG 57.009 33.333 0.00 0.00 0.00 3.33
2019 4430 5.940192 AATGTGAAGCGTAAAGATGTTGA 57.060 34.783 0.00 0.00 0.00 3.18
2020 4431 4.725556 TGTGAAGCGTAAAGATGTTGAC 57.274 40.909 0.00 0.00 0.00 3.18
2021 4432 3.496884 TGTGAAGCGTAAAGATGTTGACC 59.503 43.478 0.00 0.00 0.00 4.02
2022 4433 3.496884 GTGAAGCGTAAAGATGTTGACCA 59.503 43.478 0.00 0.00 0.00 4.02
2023 4434 4.154195 GTGAAGCGTAAAGATGTTGACCAT 59.846 41.667 0.00 0.00 36.13 3.55
2024 4435 5.350365 GTGAAGCGTAAAGATGTTGACCATA 59.650 40.000 0.00 0.00 32.56 2.74
2025 4436 6.037172 GTGAAGCGTAAAGATGTTGACCATAT 59.963 38.462 0.00 0.00 32.56 1.78
2026 4437 6.257849 TGAAGCGTAAAGATGTTGACCATATC 59.742 38.462 0.00 0.00 32.56 1.63
2027 4438 5.918608 AGCGTAAAGATGTTGACCATATCT 58.081 37.500 0.00 0.00 32.56 1.98
2028 4439 6.349300 AGCGTAAAGATGTTGACCATATCTT 58.651 36.000 0.00 0.00 41.53 2.40
2029 4440 6.823689 AGCGTAAAGATGTTGACCATATCTTT 59.176 34.615 13.45 13.45 46.82 2.52
2030 4441 7.985184 AGCGTAAAGATGTTGACCATATCTTTA 59.015 33.333 11.92 11.92 44.75 1.85
2034 4445 8.511604 AAAGATGTTGACCATATCTTTACCTG 57.488 34.615 8.84 0.00 44.75 4.00
2035 4446 7.437713 AGATGTTGACCATATCTTTACCTGA 57.562 36.000 0.00 0.00 32.56 3.86
2036 4447 8.038862 AGATGTTGACCATATCTTTACCTGAT 57.961 34.615 0.00 0.00 32.56 2.90
2037 4448 7.935755 AGATGTTGACCATATCTTTACCTGATG 59.064 37.037 0.00 0.00 32.56 3.07
2038 4449 6.957631 TGTTGACCATATCTTTACCTGATGT 58.042 36.000 0.00 0.00 0.00 3.06
2039 4450 7.402054 TGTTGACCATATCTTTACCTGATGTT 58.598 34.615 0.00 0.00 0.00 2.71
2040 4451 8.544622 TGTTGACCATATCTTTACCTGATGTTA 58.455 33.333 0.00 0.00 0.00 2.41
2041 4452 9.391006 GTTGACCATATCTTTACCTGATGTTAA 57.609 33.333 0.00 0.00 0.00 2.01
2042 4453 9.967451 TTGACCATATCTTTACCTGATGTTAAA 57.033 29.630 0.00 0.00 0.00 1.52
2043 4454 9.613428 TGACCATATCTTTACCTGATGTTAAAG 57.387 33.333 0.00 0.00 0.00 1.85
2044 4455 8.980481 ACCATATCTTTACCTGATGTTAAAGG 57.020 34.615 0.00 0.00 39.65 3.11
2045 4456 8.778059 ACCATATCTTTACCTGATGTTAAAGGA 58.222 33.333 0.00 0.00 37.01 3.36
2046 4457 9.057089 CCATATCTTTACCTGATGTTAAAGGAC 57.943 37.037 0.00 0.00 37.01 3.85
2047 4458 8.765219 CATATCTTTACCTGATGTTAAAGGACG 58.235 37.037 0.00 0.00 37.01 4.79
2048 4459 5.484715 TCTTTACCTGATGTTAAAGGACGG 58.515 41.667 0.00 0.00 37.01 4.79
2049 4460 5.246656 TCTTTACCTGATGTTAAAGGACGGA 59.753 40.000 0.00 0.00 37.01 4.69
2050 4461 3.611766 ACCTGATGTTAAAGGACGGAG 57.388 47.619 0.00 0.00 37.01 4.63
2051 4462 3.170717 ACCTGATGTTAAAGGACGGAGA 58.829 45.455 0.00 0.00 37.01 3.71
2052 4463 3.056035 ACCTGATGTTAAAGGACGGAGAC 60.056 47.826 0.00 0.00 37.01 3.36
2053 4464 3.195825 CCTGATGTTAAAGGACGGAGACT 59.804 47.826 0.00 0.00 35.40 3.24
2054 4465 4.322801 CCTGATGTTAAAGGACGGAGACTT 60.323 45.833 0.00 0.00 35.40 3.01
2055 4466 5.223449 TGATGTTAAAGGACGGAGACTTT 57.777 39.130 0.00 0.00 40.09 2.66
2056 4467 5.235516 TGATGTTAAAGGACGGAGACTTTC 58.764 41.667 0.00 0.00 38.58 2.62
2057 4468 4.675976 TGTTAAAGGACGGAGACTTTCA 57.324 40.909 0.00 0.00 38.58 2.69
2058 4469 5.223449 TGTTAAAGGACGGAGACTTTCAT 57.777 39.130 0.00 0.00 38.58 2.57
2059 4470 4.994852 TGTTAAAGGACGGAGACTTTCATG 59.005 41.667 0.00 0.00 38.58 3.07
2060 4471 2.770164 AAGGACGGAGACTTTCATGG 57.230 50.000 0.00 0.00 0.00 3.66
2061 4472 1.645710 AGGACGGAGACTTTCATGGT 58.354 50.000 0.00 0.00 0.00 3.55
2062 4473 1.978580 AGGACGGAGACTTTCATGGTT 59.021 47.619 0.00 0.00 0.00 3.67
2063 4474 2.028020 AGGACGGAGACTTTCATGGTTC 60.028 50.000 0.00 0.00 0.00 3.62
2064 4475 2.028020 GGACGGAGACTTTCATGGTTCT 60.028 50.000 0.00 0.00 0.00 3.01
2065 4476 3.557264 GGACGGAGACTTTCATGGTTCTT 60.557 47.826 0.00 0.00 0.00 2.52
2066 4477 3.665190 ACGGAGACTTTCATGGTTCTTC 58.335 45.455 0.00 0.00 0.00 2.87
2067 4478 3.071023 ACGGAGACTTTCATGGTTCTTCA 59.929 43.478 0.00 0.00 0.00 3.02
2068 4479 4.256920 CGGAGACTTTCATGGTTCTTCAT 58.743 43.478 0.00 0.00 0.00 2.57
2069 4480 5.046591 ACGGAGACTTTCATGGTTCTTCATA 60.047 40.000 0.00 0.00 0.00 2.15
2070 4481 5.292101 CGGAGACTTTCATGGTTCTTCATAC 59.708 44.000 0.00 0.00 0.00 2.39
2071 4482 5.292101 GGAGACTTTCATGGTTCTTCATACG 59.708 44.000 0.00 0.00 0.00 3.06
2072 4483 5.794894 AGACTTTCATGGTTCTTCATACGT 58.205 37.500 0.00 0.00 0.00 3.57
2073 4484 6.231211 AGACTTTCATGGTTCTTCATACGTT 58.769 36.000 0.00 0.00 0.00 3.99
2074 4485 6.710744 AGACTTTCATGGTTCTTCATACGTTT 59.289 34.615 0.00 0.00 0.00 3.60
2075 4486 7.228706 AGACTTTCATGGTTCTTCATACGTTTT 59.771 33.333 0.00 0.00 0.00 2.43
2076 4487 7.712797 ACTTTCATGGTTCTTCATACGTTTTT 58.287 30.769 0.00 0.00 0.00 1.94
2077 4488 7.860872 ACTTTCATGGTTCTTCATACGTTTTTC 59.139 33.333 0.00 0.00 0.00 2.29
2078 4489 7.504924 TTCATGGTTCTTCATACGTTTTTCT 57.495 32.000 0.00 0.00 0.00 2.52
2079 4490 7.504924 TCATGGTTCTTCATACGTTTTTCTT 57.495 32.000 0.00 0.00 0.00 2.52
2080 4491 8.610248 TCATGGTTCTTCATACGTTTTTCTTA 57.390 30.769 0.00 0.00 0.00 2.10
2081 4492 8.717821 TCATGGTTCTTCATACGTTTTTCTTAG 58.282 33.333 0.00 0.00 0.00 2.18
2082 4493 8.504005 CATGGTTCTTCATACGTTTTTCTTAGT 58.496 33.333 0.00 0.00 0.00 2.24
2083 4494 8.441312 TGGTTCTTCATACGTTTTTCTTAGTT 57.559 30.769 0.00 0.00 0.00 2.24
2084 4495 8.895737 TGGTTCTTCATACGTTTTTCTTAGTTT 58.104 29.630 0.00 0.00 0.00 2.66
2085 4496 9.726232 GGTTCTTCATACGTTTTTCTTAGTTTT 57.274 29.630 0.00 0.00 0.00 2.43
2087 4498 9.940166 TTCTTCATACGTTTTTCTTAGTTTTCC 57.060 29.630 0.00 0.00 0.00 3.13
2088 4499 9.111613 TCTTCATACGTTTTTCTTAGTTTTCCA 57.888 29.630 0.00 0.00 0.00 3.53
2089 4500 9.893305 CTTCATACGTTTTTCTTAGTTTTCCAT 57.107 29.630 0.00 0.00 0.00 3.41
2090 4501 9.672086 TTCATACGTTTTTCTTAGTTTTCCATG 57.328 29.630 0.00 0.00 0.00 3.66
2091 4502 7.806014 TCATACGTTTTTCTTAGTTTTCCATGC 59.194 33.333 0.00 0.00 0.00 4.06
2092 4503 4.973663 ACGTTTTTCTTAGTTTTCCATGCG 59.026 37.500 0.00 0.00 0.00 4.73
2093 4504 4.381566 CGTTTTTCTTAGTTTTCCATGCGG 59.618 41.667 0.00 0.00 0.00 5.69
2094 4505 5.525199 GTTTTTCTTAGTTTTCCATGCGGA 58.475 37.500 0.00 0.00 40.60 5.54
2101 4512 3.614806 TTCCATGCGGAATTGGCC 58.385 55.556 0.00 0.00 46.79 5.36
2102 4513 1.304796 TTCCATGCGGAATTGGCCA 60.305 52.632 0.00 0.00 46.79 5.36
2103 4514 0.687098 TTCCATGCGGAATTGGCCAT 60.687 50.000 6.09 0.00 46.79 4.40
2104 4515 1.108727 TCCATGCGGAATTGGCCATC 61.109 55.000 6.09 0.75 38.83 3.51
2105 4516 1.111116 CCATGCGGAATTGGCCATCT 61.111 55.000 6.09 0.00 0.00 2.90
2106 4517 1.608055 CATGCGGAATTGGCCATCTA 58.392 50.000 6.09 0.00 0.00 1.98
2107 4518 1.538512 CATGCGGAATTGGCCATCTAG 59.461 52.381 6.09 2.09 0.00 2.43
2108 4519 0.179020 TGCGGAATTGGCCATCTAGG 60.179 55.000 6.09 0.00 41.84 3.02
2118 4529 1.447643 CCATCTAGGCCGAGTTGGG 59.552 63.158 27.11 16.86 38.63 4.12
2126 4537 3.267974 CCGAGTTGGGCTTGCTTC 58.732 61.111 0.00 0.00 0.00 3.86
2127 4538 1.600636 CCGAGTTGGGCTTGCTTCA 60.601 57.895 0.00 0.00 0.00 3.02
2128 4539 0.962356 CCGAGTTGGGCTTGCTTCAT 60.962 55.000 0.00 0.00 0.00 2.57
2129 4540 0.169672 CGAGTTGGGCTTGCTTCATG 59.830 55.000 0.00 0.00 0.00 3.07
2130 4541 0.108945 GAGTTGGGCTTGCTTCATGC 60.109 55.000 0.00 0.00 43.25 4.06
2142 4553 3.122937 GCTTCATGCAGTTTTCGGTAG 57.877 47.619 0.00 0.00 42.31 3.18
2143 4554 2.742053 GCTTCATGCAGTTTTCGGTAGA 59.258 45.455 0.00 0.00 42.31 2.59
2144 4555 3.424962 GCTTCATGCAGTTTTCGGTAGAC 60.425 47.826 0.00 0.00 42.31 2.59
2145 4556 3.678056 TCATGCAGTTTTCGGTAGACT 57.322 42.857 0.00 0.00 0.00 3.24
2146 4557 4.794278 TCATGCAGTTTTCGGTAGACTA 57.206 40.909 0.00 0.00 0.00 2.59
2147 4558 4.744570 TCATGCAGTTTTCGGTAGACTAG 58.255 43.478 0.00 0.00 0.00 2.57
2148 4559 2.955614 TGCAGTTTTCGGTAGACTAGC 58.044 47.619 1.37 1.37 0.00 3.42
2149 4560 2.297880 TGCAGTTTTCGGTAGACTAGCA 59.702 45.455 11.99 0.00 0.00 3.49
2150 4561 3.243941 TGCAGTTTTCGGTAGACTAGCAA 60.244 43.478 11.99 3.15 30.40 3.91
2151 4562 3.744426 GCAGTTTTCGGTAGACTAGCAAA 59.256 43.478 11.99 8.34 0.00 3.68
2152 4563 4.212636 GCAGTTTTCGGTAGACTAGCAAAA 59.787 41.667 11.99 12.80 0.00 2.44
2153 4564 5.277634 GCAGTTTTCGGTAGACTAGCAAAAA 60.278 40.000 11.99 9.12 0.00 1.94
2170 4581 1.710816 AAAAATTGCTTCCGTGGGGA 58.289 45.000 0.00 0.00 41.83 4.81
2171 4582 1.937191 AAAATTGCTTCCGTGGGGAT 58.063 45.000 0.00 0.00 43.41 3.85
2172 4583 1.937191 AAATTGCTTCCGTGGGGATT 58.063 45.000 0.00 0.00 43.41 3.01
2173 4584 1.474330 AATTGCTTCCGTGGGGATTC 58.526 50.000 0.00 0.00 43.41 2.52
2174 4585 0.331278 ATTGCTTCCGTGGGGATTCA 59.669 50.000 0.00 0.00 43.41 2.57
2175 4586 0.111446 TTGCTTCCGTGGGGATTCAA 59.889 50.000 0.00 0.00 43.41 2.69
2176 4587 0.111446 TGCTTCCGTGGGGATTCAAA 59.889 50.000 0.00 0.00 43.41 2.69
2177 4588 1.272425 TGCTTCCGTGGGGATTCAAAT 60.272 47.619 0.00 0.00 43.41 2.32
2178 4589 1.824852 GCTTCCGTGGGGATTCAAATT 59.175 47.619 0.00 0.00 43.41 1.82
2179 4590 2.417243 GCTTCCGTGGGGATTCAAATTG 60.417 50.000 0.00 0.00 43.41 2.32
2180 4591 1.846007 TCCGTGGGGATTCAAATTGG 58.154 50.000 0.00 0.00 37.43 3.16
2181 4592 0.175531 CCGTGGGGATTCAAATTGGC 59.824 55.000 0.00 0.00 34.06 4.52
2182 4593 0.894141 CGTGGGGATTCAAATTGGCA 59.106 50.000 0.00 0.00 0.00 4.92
2183 4594 1.274728 CGTGGGGATTCAAATTGGCAA 59.725 47.619 0.68 0.68 0.00 4.52
2184 4595 2.698803 GTGGGGATTCAAATTGGCAAC 58.301 47.619 0.00 0.00 0.00 4.17
2199 4610 3.620488 TGGCAACATCTTCCTTATGACC 58.380 45.455 0.00 0.00 46.17 4.02
2200 4611 3.010027 TGGCAACATCTTCCTTATGACCA 59.990 43.478 0.00 0.00 46.17 4.02
2201 4612 3.378427 GGCAACATCTTCCTTATGACCAC 59.622 47.826 0.00 0.00 0.00 4.16
2202 4613 4.009675 GCAACATCTTCCTTATGACCACA 58.990 43.478 0.00 0.00 0.00 4.17
2203 4614 4.458989 GCAACATCTTCCTTATGACCACAA 59.541 41.667 0.00 0.00 0.00 3.33
2204 4615 5.392380 GCAACATCTTCCTTATGACCACAAG 60.392 44.000 0.00 0.00 0.00 3.16
2205 4616 4.848357 ACATCTTCCTTATGACCACAAGG 58.152 43.478 0.75 0.75 42.34 3.61
2206 4617 4.536090 ACATCTTCCTTATGACCACAAGGA 59.464 41.667 5.71 5.71 46.75 3.36
2209 4620 3.931907 TCCTTATGACCACAAGGATGG 57.068 47.619 5.71 0.00 44.24 3.51
2210 4621 3.459828 TCCTTATGACCACAAGGATGGA 58.540 45.455 5.71 0.00 44.24 3.41
2211 4622 3.455910 TCCTTATGACCACAAGGATGGAG 59.544 47.826 5.71 0.00 44.24 3.86
2212 4623 3.209410 CTTATGACCACAAGGATGGAGC 58.791 50.000 0.00 0.00 43.02 4.70
2213 4624 0.257039 ATGACCACAAGGATGGAGCC 59.743 55.000 0.00 0.00 43.02 4.70
2214 4625 1.133181 TGACCACAAGGATGGAGCCA 61.133 55.000 0.00 0.00 43.02 4.75
2215 4626 0.038166 GACCACAAGGATGGAGCCAA 59.962 55.000 0.00 0.00 43.02 4.52
2216 4627 0.251341 ACCACAAGGATGGAGCCAAC 60.251 55.000 0.00 0.00 43.02 3.77
2217 4628 0.967380 CCACAAGGATGGAGCCAACC 60.967 60.000 7.68 7.68 43.02 3.77
2218 4629 0.251297 CACAAGGATGGAGCCAACCA 60.251 55.000 16.86 0.00 40.76 3.67
2219 4630 0.482446 ACAAGGATGGAGCCAACCAA 59.518 50.000 16.86 0.00 43.47 3.67
2220 4631 1.180029 CAAGGATGGAGCCAACCAAG 58.820 55.000 16.86 5.98 43.47 3.61
2221 4632 0.613012 AAGGATGGAGCCAACCAAGC 60.613 55.000 16.86 0.00 43.47 4.01
2222 4633 1.000396 GGATGGAGCCAACCAAGCT 60.000 57.895 10.61 0.00 43.47 3.74
2223 4634 0.255890 GGATGGAGCCAACCAAGCTA 59.744 55.000 10.61 0.00 43.47 3.32
2224 4635 1.340991 GGATGGAGCCAACCAAGCTAA 60.341 52.381 10.61 0.00 43.47 3.09
2225 4636 1.745653 GATGGAGCCAACCAAGCTAAC 59.254 52.381 0.00 0.00 43.47 2.34
2226 4637 0.251165 TGGAGCCAACCAAGCTAACC 60.251 55.000 0.00 0.00 41.75 2.85
2227 4638 0.038310 GGAGCCAACCAAGCTAACCT 59.962 55.000 0.00 0.00 41.75 3.50
2228 4639 1.547901 GGAGCCAACCAAGCTAACCTT 60.548 52.381 0.00 0.00 41.75 3.50
2229 4640 1.813178 GAGCCAACCAAGCTAACCTTC 59.187 52.381 0.00 0.00 41.75 3.46
2230 4641 1.425448 AGCCAACCAAGCTAACCTTCT 59.575 47.619 0.00 0.00 39.29 2.85
2239 4650 4.023707 CCAAGCTAACCTTCTCTTGTTGTG 60.024 45.833 0.00 0.00 35.42 3.33
2244 4655 5.989777 GCTAACCTTCTCTTGTTGTGTAAGA 59.010 40.000 0.00 0.00 33.44 2.10
2250 4661 6.346919 CCTTCTCTTGTTGTGTAAGATGTTCG 60.347 42.308 0.00 0.00 33.99 3.95
2276 4687 8.852135 GCTATACAGATTATATAGTCCCACCTC 58.148 40.741 1.84 0.00 35.75 3.85
2278 4689 5.977533 ACAGATTATATAGTCCCACCTCCA 58.022 41.667 1.84 0.00 0.00 3.86
2283 4694 1.705873 ATAGTCCCACCTCCATCGTC 58.294 55.000 0.00 0.00 0.00 4.20
2292 4703 1.482593 ACCTCCATCGTCTTCATCACC 59.517 52.381 0.00 0.00 0.00 4.02
2298 4709 4.002982 CCATCGTCTTCATCACCTTTCAA 58.997 43.478 0.00 0.00 0.00 2.69
2339 4750 3.424703 AGTTGTGTGGGGAATCATGAAG 58.575 45.455 0.00 0.00 0.00 3.02
2346 4757 3.091545 TGGGGAATCATGAAGCTGTTTC 58.908 45.455 0.00 0.00 36.29 2.78
2362 4773 3.492337 TGTTTCGGGAATTAACTTGCCT 58.508 40.909 6.61 0.00 42.94 4.75
2363 4774 3.892588 TGTTTCGGGAATTAACTTGCCTT 59.107 39.130 6.61 0.00 42.94 4.35
2364 4775 4.234574 GTTTCGGGAATTAACTTGCCTTG 58.765 43.478 6.61 0.00 42.94 3.61
2365 4776 3.426787 TCGGGAATTAACTTGCCTTGA 57.573 42.857 6.61 0.00 42.94 3.02
2366 4777 3.343617 TCGGGAATTAACTTGCCTTGAG 58.656 45.455 6.61 0.00 42.94 3.02
2367 4778 3.008594 TCGGGAATTAACTTGCCTTGAGA 59.991 43.478 6.61 0.00 42.94 3.27
2368 4779 3.127030 CGGGAATTAACTTGCCTTGAGAC 59.873 47.826 6.61 0.00 42.94 3.36
2369 4780 3.444034 GGGAATTAACTTGCCTTGAGACC 59.556 47.826 0.00 0.00 41.91 3.85
2370 4781 4.336280 GGAATTAACTTGCCTTGAGACCT 58.664 43.478 0.00 0.00 0.00 3.85
2371 4782 5.497474 GGAATTAACTTGCCTTGAGACCTA 58.503 41.667 0.00 0.00 0.00 3.08
2372 4783 5.944007 GGAATTAACTTGCCTTGAGACCTAA 59.056 40.000 0.00 0.00 0.00 2.69
2373 4784 6.433093 GGAATTAACTTGCCTTGAGACCTAAA 59.567 38.462 0.00 0.00 0.00 1.85
2374 4785 7.362142 GGAATTAACTTGCCTTGAGACCTAAAG 60.362 40.741 0.00 0.00 0.00 1.85
2375 4786 4.706842 AACTTGCCTTGAGACCTAAAGA 57.293 40.909 0.00 0.00 0.00 2.52
2385 4796 1.557371 AGACCTAAAGAGAGGCCAAGC 59.443 52.381 5.01 0.00 40.65 4.01
2403 4814 1.278985 AGCGGGAGACATGATTTGTGA 59.721 47.619 0.00 0.00 39.18 3.58
2440 4858 1.830477 GAGAGAAGAGAGTGCCATGGT 59.170 52.381 14.67 0.00 0.00 3.55
2451 4869 2.582636 AGTGCCATGGTAGGAAGGAATT 59.417 45.455 14.67 0.00 0.00 2.17
2468 4886 4.603610 AGGAATTGGAGAAGAAGAAGGGAA 59.396 41.667 0.00 0.00 0.00 3.97
2526 4944 1.078918 CGGTGATGCAGCAGGAGAA 60.079 57.895 4.06 0.00 0.00 2.87
2530 4948 0.540454 TGATGCAGCAGGAGAAGAGG 59.460 55.000 0.00 0.00 0.00 3.69
2553 4971 2.743928 GGGTCGAAGTGCAGGCAG 60.744 66.667 0.00 0.00 0.00 4.85
2563 4981 3.842923 GCAGGCAGCCGAGCTCTA 61.843 66.667 20.88 0.00 36.40 2.43
2578 4996 1.748244 GCTCTATGCTTGGTGCCATGA 60.748 52.381 8.11 0.00 42.00 3.07
2614 5032 1.965754 CTCGGGGGAGAAGAAGGCAG 61.966 65.000 0.00 0.00 0.00 4.85
2622 5040 1.204113 AGAAGAAGGCAGGGGGACAG 61.204 60.000 0.00 0.00 0.00 3.51
2623 5041 2.203549 GAAGAAGGCAGGGGGACAGG 62.204 65.000 0.00 0.00 0.00 4.00
2662 5080 2.756283 AGGAGACCCGCGGAGAAG 60.756 66.667 30.73 12.89 37.58 2.85
2680 5098 1.682684 GGGGTCGAGGCAGAGAGAA 60.683 63.158 0.00 0.00 0.00 2.87
2683 5101 1.671901 GGTCGAGGCAGAGAGAAGGG 61.672 65.000 0.00 0.00 0.00 3.95
2685 5103 0.967887 TCGAGGCAGAGAGAAGGGTG 60.968 60.000 0.00 0.00 0.00 4.61
2713 5131 3.426568 GCGAGGAACACCTGCTGC 61.427 66.667 0.00 0.00 33.73 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.607359 CGCACGTGAAAAAGAAACATTTAGC 60.607 40.000 22.23 0.00 0.00 3.09
5 6 3.000177 GCGCACGTGAAAAAGAAACATTT 60.000 39.130 22.23 0.00 0.00 2.32
6 7 2.533942 GCGCACGTGAAAAAGAAACATT 59.466 40.909 22.23 0.00 0.00 2.71
7 8 2.116366 GCGCACGTGAAAAAGAAACAT 58.884 42.857 22.23 0.00 0.00 2.71
8 9 1.135660 TGCGCACGTGAAAAAGAAACA 60.136 42.857 22.23 0.00 0.00 2.83
9 10 1.251762 GTGCGCACGTGAAAAAGAAAC 59.748 47.619 26.77 0.00 0.00 2.78
10 11 1.135660 TGTGCGCACGTGAAAAAGAAA 60.136 42.857 33.22 10.34 0.00 2.52
11 12 0.448197 TGTGCGCACGTGAAAAAGAA 59.552 45.000 33.22 10.88 0.00 2.52
12 13 0.448197 TTGTGCGCACGTGAAAAAGA 59.552 45.000 33.22 11.66 0.00 2.52
13 14 0.839477 CTTGTGCGCACGTGAAAAAG 59.161 50.000 33.22 24.93 0.00 2.27
32 33 7.009540 GTGAGAATTATATGTGCAAGCAAAACC 59.990 37.037 0.00 0.00 0.00 3.27
81 82 1.078497 TGCGATGCAACGGGAGAAT 60.078 52.632 18.44 0.00 34.76 2.40
187 190 5.293324 GTGTTTGATCGTGTGATATAAGGCA 59.707 40.000 0.00 0.00 34.09 4.75
210 213 4.929479 AGAGTCTGACTAGATCAAGGTGT 58.071 43.478 10.86 0.00 36.69 4.16
226 229 7.344352 AGAATAAATAGTGCCTCAGAAGAGTCT 59.656 37.037 0.00 0.00 40.40 3.24
354 359 5.220796 GCCGATCTACAACCCTATTTTGTTC 60.221 44.000 0.00 0.00 38.21 3.18
370 375 6.484643 ACGACTGTATTTAGTTAGCCGATCTA 59.515 38.462 0.00 0.00 0.00 1.98
403 408 9.920133 CTCTATGCATCAATACAACAGTAGTAT 57.080 33.333 0.19 0.00 33.79 2.12
436 441 2.415512 GGCACAAGTTTCTCGATACACC 59.584 50.000 0.00 0.00 0.00 4.16
565 581 7.991460 GGTGATGGGTACTTTAATTAAGCTACT 59.009 37.037 0.00 0.00 37.37 2.57
566 582 7.042254 CGGTGATGGGTACTTTAATTAAGCTAC 60.042 40.741 0.00 2.68 37.37 3.58
567 583 6.987992 CGGTGATGGGTACTTTAATTAAGCTA 59.012 38.462 0.00 0.00 37.37 3.32
727 835 5.812286 TGTCAGGAGTATGTAGTCAGTACA 58.188 41.667 0.00 0.00 45.93 2.90
1051 3127 1.154016 CGACGTACAGGGTGAGCTG 60.154 63.158 0.00 0.00 0.00 4.24
1137 3213 2.267961 GGGTCCATGGACGTCACC 59.732 66.667 33.24 25.67 45.41 4.02
1158 3234 3.496160 CCTCCGGGAAAAACTTCAAGAGA 60.496 47.826 0.00 0.00 33.58 3.10
1203 3279 1.802960 CAGTACTGGTTGCTCTTGCTG 59.197 52.381 15.49 0.00 40.48 4.41
1386 3462 2.031919 ATCGCAACGTTCTGGGCA 59.968 55.556 0.00 0.00 0.00 5.36
1460 3536 3.637998 ATCAACGTAGTGAACAGTCGT 57.362 42.857 0.00 0.00 45.00 4.34
1685 3797 3.758300 ACAACAAAGCAGTCAAACTTCG 58.242 40.909 0.00 0.00 0.00 3.79
1711 3823 1.167851 GCACAGCCTAGTGATGCAAA 58.832 50.000 5.80 0.00 42.05 3.68
1713 3825 1.078214 GGCACAGCCTAGTGATGCA 60.078 57.895 0.00 0.00 46.69 3.96
1725 3837 9.683069 GTTAATCAATAATAATCAAGGGCACAG 57.317 33.333 0.00 0.00 0.00 3.66
1726 3838 8.637986 GGTTAATCAATAATAATCAAGGGCACA 58.362 33.333 0.00 0.00 0.00 4.57
1729 3841 9.077885 TCTGGTTAATCAATAATAATCAAGGGC 57.922 33.333 0.00 0.00 0.00 5.19
1745 3860 3.496130 CGCAGGACATCATCTGGTTAATC 59.504 47.826 0.00 0.00 0.00 1.75
1787 3962 0.178846 TGGGGAGGGATCAAAGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
1788 3963 0.034089 GTGGGGAGGGATCAAAGTGG 60.034 60.000 0.00 0.00 0.00 4.00
1789 3964 0.034089 GGTGGGGAGGGATCAAAGTG 60.034 60.000 0.00 0.00 0.00 3.16
1790 3965 1.214992 GGGTGGGGAGGGATCAAAGT 61.215 60.000 0.00 0.00 0.00 2.66
1791 3966 1.615262 GGGTGGGGAGGGATCAAAG 59.385 63.158 0.00 0.00 0.00 2.77
1794 3969 3.632049 TGGGGTGGGGAGGGATCA 61.632 66.667 0.00 0.00 0.00 2.92
1795 3970 3.097162 GTGGGGTGGGGAGGGATC 61.097 72.222 0.00 0.00 0.00 3.36
1796 3971 4.779486 GGTGGGGTGGGGAGGGAT 62.779 72.222 0.00 0.00 0.00 3.85
1801 3979 4.885449 TTTGGGGTGGGGTGGGGA 62.885 66.667 0.00 0.00 0.00 4.81
1803 3981 1.151921 AATTTTGGGGTGGGGTGGG 60.152 57.895 0.00 0.00 0.00 4.61
1806 3984 4.658427 CCAATTTTGGGGTGGGGT 57.342 55.556 1.14 0.00 44.70 4.95
1817 3995 3.291101 CTGCAGCAGCCGCCAATTT 62.291 57.895 10.14 0.00 41.13 1.82
1851 4262 5.927689 TGCATTTGTCTTTTCCATTAGCTTG 59.072 36.000 0.00 0.00 0.00 4.01
1945 4356 8.401709 AGTTCTGTTTGAATGACTTTCTCTTTC 58.598 33.333 3.08 0.00 36.99 2.62
1955 4366 6.918022 CCCTTGTTAAGTTCTGTTTGAATGAC 59.082 38.462 0.00 0.00 36.99 3.06
1961 4372 5.124776 TGACACCCTTGTTAAGTTCTGTTTG 59.875 40.000 0.00 0.00 35.47 2.93
1966 4377 5.568620 AGATGACACCCTTGTTAAGTTCT 57.431 39.130 0.00 0.00 35.47 3.01
2012 4423 7.716998 ACATCAGGTAAAGATATGGTCAACATC 59.283 37.037 0.00 0.00 41.03 3.06
2013 4424 7.577303 ACATCAGGTAAAGATATGGTCAACAT 58.423 34.615 0.00 0.00 43.68 2.71
2014 4425 6.957631 ACATCAGGTAAAGATATGGTCAACA 58.042 36.000 0.00 0.00 0.00 3.33
2015 4426 7.865706 AACATCAGGTAAAGATATGGTCAAC 57.134 36.000 0.00 0.00 0.00 3.18
2016 4427 9.967451 TTTAACATCAGGTAAAGATATGGTCAA 57.033 29.630 0.00 0.00 0.00 3.18
2017 4428 9.613428 CTTTAACATCAGGTAAAGATATGGTCA 57.387 33.333 7.12 0.00 32.85 4.02
2018 4429 9.057089 CCTTTAACATCAGGTAAAGATATGGTC 57.943 37.037 13.10 0.00 32.85 4.02
2019 4430 8.778059 TCCTTTAACATCAGGTAAAGATATGGT 58.222 33.333 13.10 0.00 32.85 3.55
2020 4431 9.057089 GTCCTTTAACATCAGGTAAAGATATGG 57.943 37.037 13.10 0.00 32.85 2.74
2021 4432 8.765219 CGTCCTTTAACATCAGGTAAAGATATG 58.235 37.037 13.10 4.64 32.85 1.78
2022 4433 7.931948 CCGTCCTTTAACATCAGGTAAAGATAT 59.068 37.037 13.10 0.00 32.85 1.63
2023 4434 7.124599 TCCGTCCTTTAACATCAGGTAAAGATA 59.875 37.037 13.10 0.83 32.85 1.98
2024 4435 6.070424 TCCGTCCTTTAACATCAGGTAAAGAT 60.070 38.462 13.10 0.00 32.85 2.40
2025 4436 5.246656 TCCGTCCTTTAACATCAGGTAAAGA 59.753 40.000 13.10 0.00 32.85 2.52
2026 4437 5.484715 TCCGTCCTTTAACATCAGGTAAAG 58.515 41.667 6.15 6.15 0.00 1.85
2027 4438 5.246656 TCTCCGTCCTTTAACATCAGGTAAA 59.753 40.000 0.00 0.00 0.00 2.01
2028 4439 4.773674 TCTCCGTCCTTTAACATCAGGTAA 59.226 41.667 0.00 0.00 0.00 2.85
2029 4440 4.159135 GTCTCCGTCCTTTAACATCAGGTA 59.841 45.833 0.00 0.00 0.00 3.08
2030 4441 3.056035 GTCTCCGTCCTTTAACATCAGGT 60.056 47.826 0.00 0.00 0.00 4.00
2031 4442 3.195825 AGTCTCCGTCCTTTAACATCAGG 59.804 47.826 0.00 0.00 0.00 3.86
2032 4443 4.457834 AGTCTCCGTCCTTTAACATCAG 57.542 45.455 0.00 0.00 0.00 2.90
2033 4444 4.884668 AAGTCTCCGTCCTTTAACATCA 57.115 40.909 0.00 0.00 0.00 3.07
2034 4445 5.235516 TGAAAGTCTCCGTCCTTTAACATC 58.764 41.667 0.00 0.00 31.30 3.06
2035 4446 5.223449 TGAAAGTCTCCGTCCTTTAACAT 57.777 39.130 0.00 0.00 31.30 2.71
2036 4447 4.675976 TGAAAGTCTCCGTCCTTTAACA 57.324 40.909 0.00 0.00 31.30 2.41
2037 4448 4.392138 CCATGAAAGTCTCCGTCCTTTAAC 59.608 45.833 0.00 0.00 31.30 2.01
2038 4449 4.041198 ACCATGAAAGTCTCCGTCCTTTAA 59.959 41.667 0.00 0.00 31.30 1.52
2039 4450 3.581332 ACCATGAAAGTCTCCGTCCTTTA 59.419 43.478 0.00 0.00 31.30 1.85
2040 4451 2.372172 ACCATGAAAGTCTCCGTCCTTT 59.628 45.455 0.00 0.00 33.74 3.11
2041 4452 1.978580 ACCATGAAAGTCTCCGTCCTT 59.021 47.619 0.00 0.00 0.00 3.36
2042 4453 1.645710 ACCATGAAAGTCTCCGTCCT 58.354 50.000 0.00 0.00 0.00 3.85
2043 4454 2.028020 AGAACCATGAAAGTCTCCGTCC 60.028 50.000 0.00 0.00 0.00 4.79
2044 4455 3.320673 AGAACCATGAAAGTCTCCGTC 57.679 47.619 0.00 0.00 0.00 4.79
2045 4456 3.071023 TGAAGAACCATGAAAGTCTCCGT 59.929 43.478 0.00 0.00 0.00 4.69
2046 4457 3.664107 TGAAGAACCATGAAAGTCTCCG 58.336 45.455 0.00 0.00 0.00 4.63
2047 4458 5.292101 CGTATGAAGAACCATGAAAGTCTCC 59.708 44.000 0.00 0.00 0.00 3.71
2048 4459 5.869888 ACGTATGAAGAACCATGAAAGTCTC 59.130 40.000 0.00 0.00 0.00 3.36
2049 4460 5.794894 ACGTATGAAGAACCATGAAAGTCT 58.205 37.500 0.00 0.00 0.00 3.24
2050 4461 6.481954 AACGTATGAAGAACCATGAAAGTC 57.518 37.500 0.00 0.00 0.00 3.01
2051 4462 6.877611 AAACGTATGAAGAACCATGAAAGT 57.122 33.333 0.00 0.00 0.00 2.66
2052 4463 8.076178 AGAAAAACGTATGAAGAACCATGAAAG 58.924 33.333 0.00 0.00 0.00 2.62
2053 4464 7.936584 AGAAAAACGTATGAAGAACCATGAAA 58.063 30.769 0.00 0.00 0.00 2.69
2054 4465 7.504924 AGAAAAACGTATGAAGAACCATGAA 57.495 32.000 0.00 0.00 0.00 2.57
2055 4466 7.504924 AAGAAAAACGTATGAAGAACCATGA 57.495 32.000 0.00 0.00 0.00 3.07
2056 4467 8.504005 ACTAAGAAAAACGTATGAAGAACCATG 58.496 33.333 0.00 0.00 0.00 3.66
2057 4468 8.617290 ACTAAGAAAAACGTATGAAGAACCAT 57.383 30.769 0.00 0.00 0.00 3.55
2058 4469 8.441312 AACTAAGAAAAACGTATGAAGAACCA 57.559 30.769 0.00 0.00 0.00 3.67
2059 4470 9.726232 AAAACTAAGAAAAACGTATGAAGAACC 57.274 29.630 0.00 0.00 0.00 3.62
2061 4472 9.940166 GGAAAACTAAGAAAAACGTATGAAGAA 57.060 29.630 0.00 0.00 0.00 2.52
2062 4473 9.111613 TGGAAAACTAAGAAAAACGTATGAAGA 57.888 29.630 0.00 0.00 0.00 2.87
2063 4474 9.893305 ATGGAAAACTAAGAAAAACGTATGAAG 57.107 29.630 0.00 0.00 0.00 3.02
2064 4475 9.672086 CATGGAAAACTAAGAAAAACGTATGAA 57.328 29.630 0.00 0.00 0.00 2.57
2065 4476 7.806014 GCATGGAAAACTAAGAAAAACGTATGA 59.194 33.333 0.00 0.00 0.00 2.15
2066 4477 7.201232 CGCATGGAAAACTAAGAAAAACGTATG 60.201 37.037 0.00 0.00 0.00 2.39
2067 4478 6.799925 CGCATGGAAAACTAAGAAAAACGTAT 59.200 34.615 0.00 0.00 0.00 3.06
2068 4479 6.137415 CGCATGGAAAACTAAGAAAAACGTA 58.863 36.000 0.00 0.00 0.00 3.57
2069 4480 4.973663 CGCATGGAAAACTAAGAAAAACGT 59.026 37.500 0.00 0.00 0.00 3.99
2070 4481 4.381566 CCGCATGGAAAACTAAGAAAAACG 59.618 41.667 0.00 0.00 37.49 3.60
2071 4482 5.525199 TCCGCATGGAAAACTAAGAAAAAC 58.475 37.500 0.00 0.00 42.85 2.43
2072 4483 5.776173 TCCGCATGGAAAACTAAGAAAAA 57.224 34.783 0.00 0.00 42.85 1.94
2085 4496 1.076118 ATGGCCAATTCCGCATGGA 60.076 52.632 10.96 0.00 44.61 3.41
2086 4497 1.111116 AGATGGCCAATTCCGCATGG 61.111 55.000 10.96 0.00 39.80 3.66
2087 4498 1.538512 CTAGATGGCCAATTCCGCATG 59.461 52.381 10.96 0.00 0.00 4.06
2088 4499 1.546323 CCTAGATGGCCAATTCCGCAT 60.546 52.381 10.96 0.00 0.00 4.73
2089 4500 0.179020 CCTAGATGGCCAATTCCGCA 60.179 55.000 10.96 0.00 0.00 5.69
2090 4501 2.633860 CCTAGATGGCCAATTCCGC 58.366 57.895 10.96 0.00 0.00 5.54
2100 4511 1.447643 CCCAACTCGGCCTAGATGG 59.552 63.158 22.65 22.65 38.74 3.51
2101 4512 1.227674 GCCCAACTCGGCCTAGATG 60.228 63.158 11.98 9.51 43.66 2.90
2102 4513 3.231298 GCCCAACTCGGCCTAGAT 58.769 61.111 11.98 0.00 43.66 1.98
2109 4520 0.962356 ATGAAGCAAGCCCAACTCGG 60.962 55.000 0.00 0.00 0.00 4.63
2110 4521 0.169672 CATGAAGCAAGCCCAACTCG 59.830 55.000 0.00 0.00 0.00 4.18
2111 4522 0.108945 GCATGAAGCAAGCCCAACTC 60.109 55.000 0.00 0.00 44.79 3.01
2112 4523 1.969862 GCATGAAGCAAGCCCAACT 59.030 52.632 0.00 0.00 44.79 3.16
2113 4524 4.584688 GCATGAAGCAAGCCCAAC 57.415 55.556 0.00 0.00 44.79 3.77
2122 4533 2.742053 TCTACCGAAAACTGCATGAAGC 59.258 45.455 0.00 0.00 45.96 3.86
2123 4534 3.997021 AGTCTACCGAAAACTGCATGAAG 59.003 43.478 0.00 0.00 0.00 3.02
2124 4535 4.002906 AGTCTACCGAAAACTGCATGAA 57.997 40.909 0.00 0.00 0.00 2.57
2125 4536 3.678056 AGTCTACCGAAAACTGCATGA 57.322 42.857 0.00 0.00 0.00 3.07
2126 4537 3.307242 GCTAGTCTACCGAAAACTGCATG 59.693 47.826 0.00 0.00 0.00 4.06
2127 4538 3.056107 TGCTAGTCTACCGAAAACTGCAT 60.056 43.478 0.00 0.00 0.00 3.96
2128 4539 2.297880 TGCTAGTCTACCGAAAACTGCA 59.702 45.455 0.00 0.00 0.00 4.41
2129 4540 2.955614 TGCTAGTCTACCGAAAACTGC 58.044 47.619 0.00 0.00 0.00 4.40
2130 4541 5.917541 TTTTGCTAGTCTACCGAAAACTG 57.082 39.130 0.00 0.00 0.00 3.16
2151 4562 1.710816 TCCCCACGGAAGCAATTTTT 58.289 45.000 0.00 0.00 34.19 1.94
2152 4563 1.937191 ATCCCCACGGAAGCAATTTT 58.063 45.000 0.00 0.00 43.10 1.82
2153 4564 1.824852 GAATCCCCACGGAAGCAATTT 59.175 47.619 0.00 0.00 43.10 1.82
2154 4565 1.272425 TGAATCCCCACGGAAGCAATT 60.272 47.619 0.00 0.00 43.10 2.32
2155 4566 0.331278 TGAATCCCCACGGAAGCAAT 59.669 50.000 0.00 0.00 43.10 3.56
2156 4567 0.111446 TTGAATCCCCACGGAAGCAA 59.889 50.000 0.00 0.00 43.10 3.91
2157 4568 0.111446 TTTGAATCCCCACGGAAGCA 59.889 50.000 0.00 0.00 43.10 3.91
2158 4569 1.474330 ATTTGAATCCCCACGGAAGC 58.526 50.000 0.00 0.00 43.10 3.86
2159 4570 2.166254 CCAATTTGAATCCCCACGGAAG 59.834 50.000 0.00 0.00 43.10 3.46
2160 4571 2.175202 CCAATTTGAATCCCCACGGAA 58.825 47.619 0.00 0.00 43.10 4.30
2161 4572 1.846007 CCAATTTGAATCCCCACGGA 58.154 50.000 0.00 0.00 44.33 4.69
2162 4573 0.175531 GCCAATTTGAATCCCCACGG 59.824 55.000 0.00 0.00 0.00 4.94
2163 4574 0.894141 TGCCAATTTGAATCCCCACG 59.106 50.000 0.00 0.00 0.00 4.94
2164 4575 2.038295 TGTTGCCAATTTGAATCCCCAC 59.962 45.455 0.00 0.00 0.00 4.61
2165 4576 2.333069 TGTTGCCAATTTGAATCCCCA 58.667 42.857 0.00 0.00 0.00 4.96
2166 4577 3.198417 AGATGTTGCCAATTTGAATCCCC 59.802 43.478 0.00 0.00 0.00 4.81
2167 4578 4.476628 AGATGTTGCCAATTTGAATCCC 57.523 40.909 0.00 0.00 0.00 3.85
2168 4579 4.872124 GGAAGATGTTGCCAATTTGAATCC 59.128 41.667 0.00 0.00 0.00 3.01
2169 4580 5.727434 AGGAAGATGTTGCCAATTTGAATC 58.273 37.500 0.00 0.00 0.00 2.52
2170 4581 5.750352 AGGAAGATGTTGCCAATTTGAAT 57.250 34.783 0.00 0.00 0.00 2.57
2171 4582 5.549742 AAGGAAGATGTTGCCAATTTGAA 57.450 34.783 0.00 0.00 0.00 2.69
2172 4583 6.436847 TCATAAGGAAGATGTTGCCAATTTGA 59.563 34.615 0.00 0.00 0.00 2.69
2173 4584 6.532657 GTCATAAGGAAGATGTTGCCAATTTG 59.467 38.462 0.00 0.00 0.00 2.32
2174 4585 6.351286 GGTCATAAGGAAGATGTTGCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
2175 4586 5.127682 GGTCATAAGGAAGATGTTGCCAATT 59.872 40.000 0.00 0.00 0.00 2.32
2176 4587 4.646492 GGTCATAAGGAAGATGTTGCCAAT 59.354 41.667 0.00 0.00 0.00 3.16
2177 4588 4.016444 GGTCATAAGGAAGATGTTGCCAA 58.984 43.478 0.00 0.00 0.00 4.52
2178 4589 3.010027 TGGTCATAAGGAAGATGTTGCCA 59.990 43.478 0.00 0.00 0.00 4.92
2179 4590 3.378427 GTGGTCATAAGGAAGATGTTGCC 59.622 47.826 0.00 0.00 0.00 4.52
2180 4591 4.009675 TGTGGTCATAAGGAAGATGTTGC 58.990 43.478 0.00 0.00 0.00 4.17
2181 4592 6.187125 CTTGTGGTCATAAGGAAGATGTTG 57.813 41.667 0.34 0.00 0.00 3.33
2191 4602 3.209410 GCTCCATCCTTGTGGTCATAAG 58.791 50.000 1.22 1.22 40.27 1.73
2192 4603 2.092429 GGCTCCATCCTTGTGGTCATAA 60.092 50.000 0.00 0.00 40.27 1.90
2193 4604 1.490490 GGCTCCATCCTTGTGGTCATA 59.510 52.381 0.00 0.00 40.27 2.15
2194 4605 0.257039 GGCTCCATCCTTGTGGTCAT 59.743 55.000 0.00 0.00 40.27 3.06
2195 4606 1.133181 TGGCTCCATCCTTGTGGTCA 61.133 55.000 0.00 0.00 40.27 4.02
2196 4607 0.038166 TTGGCTCCATCCTTGTGGTC 59.962 55.000 0.00 0.00 40.27 4.02
2197 4608 0.251341 GTTGGCTCCATCCTTGTGGT 60.251 55.000 0.00 0.00 40.27 4.16
2198 4609 0.967380 GGTTGGCTCCATCCTTGTGG 60.967 60.000 8.43 0.00 40.76 4.17
2199 4610 0.251297 TGGTTGGCTCCATCCTTGTG 60.251 55.000 15.02 0.00 36.89 3.33
2200 4611 0.482446 TTGGTTGGCTCCATCCTTGT 59.518 50.000 15.02 0.00 37.33 3.16
2201 4612 1.180029 CTTGGTTGGCTCCATCCTTG 58.820 55.000 15.02 6.17 37.33 3.61
2202 4613 0.613012 GCTTGGTTGGCTCCATCCTT 60.613 55.000 15.02 0.00 37.33 3.36
2203 4614 1.000396 GCTTGGTTGGCTCCATCCT 60.000 57.895 15.02 0.00 37.33 3.24
2204 4615 0.255890 TAGCTTGGTTGGCTCCATCC 59.744 55.000 8.70 8.70 40.74 3.51
2205 4616 1.745653 GTTAGCTTGGTTGGCTCCATC 59.254 52.381 0.00 0.00 40.74 3.51
2206 4617 1.616994 GGTTAGCTTGGTTGGCTCCAT 60.617 52.381 0.00 0.00 40.74 3.41
2207 4618 0.251165 GGTTAGCTTGGTTGGCTCCA 60.251 55.000 0.00 0.00 40.74 3.86
2208 4619 0.038310 AGGTTAGCTTGGTTGGCTCC 59.962 55.000 0.00 0.00 40.74 4.70
2209 4620 1.813178 GAAGGTTAGCTTGGTTGGCTC 59.187 52.381 0.00 0.00 40.74 4.70
2210 4621 1.425448 AGAAGGTTAGCTTGGTTGGCT 59.575 47.619 0.00 0.00 43.02 4.75
2211 4622 1.813178 GAGAAGGTTAGCTTGGTTGGC 59.187 52.381 0.00 0.00 0.00 4.52
2212 4623 3.425162 AGAGAAGGTTAGCTTGGTTGG 57.575 47.619 0.00 0.00 0.00 3.77
2213 4624 4.137543 ACAAGAGAAGGTTAGCTTGGTTG 58.862 43.478 0.00 5.01 41.41 3.77
2214 4625 4.439253 ACAAGAGAAGGTTAGCTTGGTT 57.561 40.909 0.00 0.00 41.41 3.67
2215 4626 4.137543 CAACAAGAGAAGGTTAGCTTGGT 58.862 43.478 0.00 0.00 41.41 3.67
2216 4627 4.023707 CACAACAAGAGAAGGTTAGCTTGG 60.024 45.833 0.00 0.00 41.41 3.61
2217 4628 4.576463 ACACAACAAGAGAAGGTTAGCTTG 59.424 41.667 0.00 0.00 42.46 4.01
2218 4629 4.781934 ACACAACAAGAGAAGGTTAGCTT 58.218 39.130 0.00 0.00 0.00 3.74
2219 4630 4.423625 ACACAACAAGAGAAGGTTAGCT 57.576 40.909 0.00 0.00 0.00 3.32
2220 4631 5.989777 TCTTACACAACAAGAGAAGGTTAGC 59.010 40.000 0.00 0.00 0.00 3.09
2221 4632 7.657761 ACATCTTACACAACAAGAGAAGGTTAG 59.342 37.037 0.00 0.00 35.57 2.34
2222 4633 7.506114 ACATCTTACACAACAAGAGAAGGTTA 58.494 34.615 0.00 0.00 35.57 2.85
2223 4634 6.357367 ACATCTTACACAACAAGAGAAGGTT 58.643 36.000 0.00 0.00 35.57 3.50
2224 4635 5.930135 ACATCTTACACAACAAGAGAAGGT 58.070 37.500 0.00 0.00 35.57 3.50
2225 4636 6.346919 CGAACATCTTACACAACAAGAGAAGG 60.347 42.308 0.00 0.00 35.57 3.46
2226 4637 6.584954 CGAACATCTTACACAACAAGAGAAG 58.415 40.000 0.00 0.00 35.57 2.85
2227 4638 5.050363 GCGAACATCTTACACAACAAGAGAA 60.050 40.000 0.00 0.00 35.57 2.87
2228 4639 4.447724 GCGAACATCTTACACAACAAGAGA 59.552 41.667 0.00 0.00 35.57 3.10
2229 4640 4.449068 AGCGAACATCTTACACAACAAGAG 59.551 41.667 0.00 0.00 35.57 2.85
2230 4641 4.377021 AGCGAACATCTTACACAACAAGA 58.623 39.130 0.00 0.00 36.50 3.02
2250 4661 8.770010 AGGTGGGACTATATAATCTGTATAGC 57.230 38.462 0.00 0.00 36.18 2.97
2276 4687 3.599343 TGAAAGGTGATGAAGACGATGG 58.401 45.455 0.00 0.00 0.00 3.51
2278 4689 4.641396 TGTTGAAAGGTGATGAAGACGAT 58.359 39.130 0.00 0.00 0.00 3.73
2309 4720 1.474879 CCCCACACAACTTTTGAACGT 59.525 47.619 0.00 0.00 0.00 3.99
2313 4724 3.636679 TGATTCCCCACACAACTTTTGA 58.363 40.909 0.00 0.00 0.00 2.69
2314 4725 4.039004 TCATGATTCCCCACACAACTTTTG 59.961 41.667 0.00 0.00 0.00 2.44
2315 4726 4.222336 TCATGATTCCCCACACAACTTTT 58.778 39.130 0.00 0.00 0.00 2.27
2316 4727 3.843422 TCATGATTCCCCACACAACTTT 58.157 40.909 0.00 0.00 0.00 2.66
2318 4729 3.424703 CTTCATGATTCCCCACACAACT 58.575 45.455 0.00 0.00 0.00 3.16
2319 4730 2.094545 GCTTCATGATTCCCCACACAAC 60.095 50.000 0.00 0.00 0.00 3.32
2320 4731 2.170166 GCTTCATGATTCCCCACACAA 58.830 47.619 0.00 0.00 0.00 3.33
2321 4732 1.355381 AGCTTCATGATTCCCCACACA 59.645 47.619 0.00 0.00 0.00 3.72
2322 4733 1.747355 CAGCTTCATGATTCCCCACAC 59.253 52.381 0.00 0.00 0.00 3.82
2339 4750 3.242518 GCAAGTTAATTCCCGAAACAGC 58.757 45.455 0.00 0.00 0.00 4.40
2346 4757 3.127030 GTCTCAAGGCAAGTTAATTCCCG 59.873 47.826 0.00 0.00 0.00 5.14
2362 4773 2.902608 TGGCCTCTCTTTAGGTCTCAA 58.097 47.619 3.32 0.00 42.10 3.02
2363 4774 2.623418 TGGCCTCTCTTTAGGTCTCA 57.377 50.000 3.32 0.00 42.10 3.27
2364 4775 2.419436 GCTTGGCCTCTCTTTAGGTCTC 60.419 54.545 3.32 0.00 42.10 3.36
2365 4776 1.557371 GCTTGGCCTCTCTTTAGGTCT 59.443 52.381 3.32 0.00 42.10 3.85
2366 4777 1.740718 CGCTTGGCCTCTCTTTAGGTC 60.741 57.143 3.32 0.00 41.94 3.85
2367 4778 0.250513 CGCTTGGCCTCTCTTTAGGT 59.749 55.000 3.32 0.00 39.02 3.08
2368 4779 0.462759 CCGCTTGGCCTCTCTTTAGG 60.463 60.000 3.32 0.00 39.87 2.69
2369 4780 0.462759 CCCGCTTGGCCTCTCTTTAG 60.463 60.000 3.32 0.00 0.00 1.85
2370 4781 0.907704 TCCCGCTTGGCCTCTCTTTA 60.908 55.000 3.32 0.00 0.00 1.85
2371 4782 2.190488 CTCCCGCTTGGCCTCTCTTT 62.190 60.000 3.32 0.00 0.00 2.52
2372 4783 2.607750 TCCCGCTTGGCCTCTCTT 60.608 61.111 3.32 0.00 0.00 2.85
2373 4784 3.080121 CTCCCGCTTGGCCTCTCT 61.080 66.667 3.32 0.00 0.00 3.10
2374 4785 3.077556 TCTCCCGCTTGGCCTCTC 61.078 66.667 3.32 0.00 0.00 3.20
2375 4786 3.394836 GTCTCCCGCTTGGCCTCT 61.395 66.667 3.32 0.00 0.00 3.69
2385 4796 1.667724 GCTCACAAATCATGTCTCCCG 59.332 52.381 0.00 0.00 41.46 5.14
2421 4832 1.949799 ACCATGGCACTCTCTTCTCT 58.050 50.000 13.04 0.00 0.00 3.10
2440 4858 6.069963 CCTTCTTCTTCTCCAATTCCTTCCTA 60.070 42.308 0.00 0.00 0.00 2.94
2451 4869 1.630878 GGCTTCCCTTCTTCTTCTCCA 59.369 52.381 0.00 0.00 0.00 3.86
2468 4886 4.722535 TCTGCCCTCCCTTCGGCT 62.723 66.667 0.00 0.00 45.90 5.52
2520 4938 0.498685 ACCCCTTTCCCTCTTCTCCT 59.501 55.000 0.00 0.00 0.00 3.69
2526 4944 0.178900 ACTTCGACCCCTTTCCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
2530 4948 0.955919 CTGCACTTCGACCCCTTTCC 60.956 60.000 0.00 0.00 0.00 3.13
2588 5006 1.229209 TTCTCCCCCGAGCTTGACT 60.229 57.895 1.22 0.00 35.94 3.41
2630 5048 4.864334 CCTCTGCCCGCCATGGAC 62.864 72.222 18.40 5.97 42.00 4.02
2654 5072 3.839432 CCTCGACCCCTTCTCCGC 61.839 72.222 0.00 0.00 0.00 5.54
2655 5073 3.839432 GCCTCGACCCCTTCTCCG 61.839 72.222 0.00 0.00 0.00 4.63
2662 5080 1.671901 CTTCTCTCTGCCTCGACCCC 61.672 65.000 0.00 0.00 0.00 4.95
2720 5146 1.812922 CATCTGGCGGCTCAGTGAC 60.813 63.158 11.43 0.00 36.25 3.67
2723 5149 2.581354 GTCATCTGGCGGCTCAGT 59.419 61.111 11.43 4.09 36.25 3.41
2732 5158 1.983224 ACCCTTCACCGTCATCTGG 59.017 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.