Multiple sequence alignment - TraesCS1D01G364300

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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 TraesCS1D01G364300 chr1D 100.000 1929 0 0 1 1929 445326517 445324589 0.000000e+00 3563.0
1 TraesCS1D01G364300 chr1D 82.785 1429 160 42 211 1584 445286225 445287622 0.000000e+00 1197.0
2 TraesCS1D01G364300 chr1D 100.000 383 0 0 2188 2570 445324330 445323948 0.000000e+00 708.0
3 TraesCS1D01G364300 chr1D 81.602 799 105 17 824 1584 445246767 445247561 7.810000e-175 623.0
4 TraesCS1D01G364300 chr1D 93.668 379 23 1 2188 2565 408413062 408412684 1.330000e-157 566.0
5 TraesCS1D01G364300 chr1D 93.785 177 8 3 211 387 445246543 445246716 1.960000e-66 263.0
6 TraesCS1D01G364300 chr1D 82.787 122 10 3 1 122 445286028 445286138 5.850000e-17 99.0
7 TraesCS1D01G364300 chr1A 95.206 1335 47 10 1 1321 541400081 541398750 0.000000e+00 2095.0
8 TraesCS1D01G364300 chr1A 82.547 1633 188 48 22 1584 541146285 541147890 0.000000e+00 1347.0
9 TraesCS1D01G364300 chr1A 83.879 794 85 26 824 1584 541163995 541164778 0.000000e+00 717.0
10 TraesCS1D01G364300 chr1A 92.913 254 16 2 1320 1573 541395936 541395685 4.040000e-98 368.0
11 TraesCS1D01G364300 chr1A 90.385 156 13 2 626 780 542180796 542180642 1.210000e-48 204.0
12 TraesCS1D01G364300 chr1A 83.673 196 19 11 1580 1774 541389175 541388992 3.400000e-39 172.0
13 TraesCS1D01G364300 chr1B 93.016 988 47 11 620 1585 606849609 606848622 0.000000e+00 1423.0
14 TraesCS1D01G364300 chr1B 83.958 1147 119 34 480 1584 608421245 608422368 0.000000e+00 1038.0
15 TraesCS1D01G364300 chr1B 83.871 1147 120 34 480 1584 608403097 608404220 0.000000e+00 1033.0
16 TraesCS1D01G364300 chr1B 83.435 1147 119 37 480 1584 608439744 608440861 0.000000e+00 1000.0
17 TraesCS1D01G364300 chr1B 89.037 301 26 3 184 477 606849910 606849610 1.450000e-97 366.0
18 TraesCS1D01G364300 chr1B 96.241 133 5 0 1 133 606850041 606849909 4.310000e-53 219.0
19 TraesCS1D01G364300 chr1B 88.043 92 3 3 1827 1914 606846141 606846054 4.520000e-18 102.0
20 TraesCS1D01G364300 chr1B 89.552 67 4 2 1591 1657 606848510 606848447 5.890000e-12 82.4
21 TraesCS1D01G364300 chr7D 94.531 384 20 1 2188 2570 23556877 23557260 2.200000e-165 592.0
22 TraesCS1D01G364300 chr7D 80.814 172 33 0 618 789 181008775 181008946 4.460000e-28 135.0
23 TraesCS1D01G364300 chr4D 93.506 385 22 3 2188 2570 451695005 451694622 1.030000e-158 569.0
24 TraesCS1D01G364300 chr4D 93.438 381 24 1 2188 2567 502490822 502491202 4.800000e-157 564.0
25 TraesCS1D01G364300 chr3D 93.701 381 23 1 2188 2567 506000209 506000589 1.030000e-158 569.0
26 TraesCS1D01G364300 chr3D 92.727 385 24 4 2188 2570 572191346 572191728 1.040000e-153 553.0
27 TraesCS1D01G364300 chr2D 92.969 384 24 2 2188 2570 607136116 607135735 8.030000e-155 556.0
28 TraesCS1D01G364300 chr2D 92.708 384 26 2 2188 2570 645447202 645447584 1.040000e-153 553.0
29 TraesCS1D01G364300 chr5D 92.708 384 27 1 2188 2570 374655893 374655510 1.040000e-153 553.0


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 TraesCS1D01G364300 chr1D 445323948 445326517 2569 True 2135.50 3563 100.0000 1 2570 2 chr1D.!!$R2 2569
1 TraesCS1D01G364300 chr1D 445286028 445287622 1594 False 648.00 1197 82.7860 1 1584 2 chr1D.!!$F2 1583
2 TraesCS1D01G364300 chr1D 445246543 445247561 1018 False 443.00 623 87.6935 211 1584 2 chr1D.!!$F1 1373
3 TraesCS1D01G364300 chr1A 541146285 541147890 1605 False 1347.00 1347 82.5470 22 1584 1 chr1A.!!$F1 1562
4 TraesCS1D01G364300 chr1A 541395685 541400081 4396 True 1231.50 2095 94.0595 1 1573 2 chr1A.!!$R3 1572
5 TraesCS1D01G364300 chr1A 541163995 541164778 783 False 717.00 717 83.8790 824 1584 1 chr1A.!!$F2 760
6 TraesCS1D01G364300 chr1B 608421245 608422368 1123 False 1038.00 1038 83.9580 480 1584 1 chr1B.!!$F2 1104
7 TraesCS1D01G364300 chr1B 608403097 608404220 1123 False 1033.00 1033 83.8710 480 1584 1 chr1B.!!$F1 1104
8 TraesCS1D01G364300 chr1B 608439744 608440861 1117 False 1000.00 1000 83.4350 480 1584 1 chr1B.!!$F3 1104
9 TraesCS1D01G364300 chr1B 606846054 606850041 3987 True 438.48 1423 91.1778 1 1914 5 chr1B.!!$R1 1913

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
381 414 0.171231 CAGAGACGACTTCCGCATCA 59.829 55.0 0.0 0.0 43.32 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 4708 0.460311 ACTTCCCGATCCTGCTTACG 59.54 55.0 0.0 0.0 0.0 3.18 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
149 150 3.276857 CGGTGGCTGAGAGTAGTTACTA 58.723 50.000 0.00 0.00 36.50 1.82
225 249 2.350895 CGATGGGTGGTTCCAGCA 59.649 61.111 20.20 8.88 42.88 4.41
298 325 3.738246 CCACAGCAGCAGCAGCAG 61.738 66.667 12.92 6.60 45.49 4.24
381 414 0.171231 CAGAGACGACTTCCGCATCA 59.829 55.000 0.00 0.00 43.32 3.07
387 420 1.643832 GACTTCCGCATCATTCGGC 59.356 57.895 0.00 0.00 46.05 5.54
539 615 3.003689 GCGGAAATTGATGTATGAGTGGG 59.996 47.826 0.00 0.00 0.00 4.61
917 1003 1.623311 TGGCAAAGCACTGCTAGACTA 59.377 47.619 3.33 0.00 42.25 2.59
1059 1146 1.442769 CAAAGCTGTCGCAGTATGGT 58.557 50.000 8.32 0.00 39.10 3.55
1066 1153 0.878416 GTCGCAGTATGGTTTGGCAA 59.122 50.000 0.00 0.00 35.86 4.52
1097 1187 1.202405 GCTAGCTGCAGAGGAAGAGAC 60.202 57.143 20.43 0.00 42.31 3.36
1321 1442 6.756299 ATTTGCTGGTTTTTGTTGATTTGT 57.244 29.167 0.00 0.00 0.00 2.83
1322 1443 6.566197 TTTGCTGGTTTTTGTTGATTTGTT 57.434 29.167 0.00 0.00 0.00 2.83
1323 1444 6.566197 TTGCTGGTTTTTGTTGATTTGTTT 57.434 29.167 0.00 0.00 0.00 2.83
1324 1445 5.936054 TGCTGGTTTTTGTTGATTTGTTTG 58.064 33.333 0.00 0.00 0.00 2.93
1326 1447 5.302357 TGGTTTTTGTTGATTTGTTTGGC 57.698 34.783 0.00 0.00 0.00 4.52
1426 4365 0.037447 TCCGTCCATGGATTTGCACA 59.963 50.000 19.62 0.00 31.53 4.57
1575 4515 1.881709 GGCGCCTCGTTAACCTAGC 60.882 63.158 22.15 0.00 0.00 3.42
1585 4525 1.062258 TTAACCTAGCGCGAAACGTG 58.938 50.000 12.10 0.00 46.11 4.49
1594 4640 1.782807 GCGAAACGTGCGGATGTTA 59.217 52.632 15.26 0.00 30.69 2.41
1605 4651 1.956297 CGGATGTTAATTGGCCCGTA 58.044 50.000 0.00 0.00 33.02 4.02
1611 4657 6.372103 CGGATGTTAATTGGCCCGTATTAATA 59.628 38.462 14.28 12.76 31.18 0.98
1612 4658 7.094720 CGGATGTTAATTGGCCCGTATTAATAA 60.095 37.037 14.28 9.03 31.18 1.40
1613 4659 8.745590 GGATGTTAATTGGCCCGTATTAATAAT 58.254 33.333 14.28 11.95 31.18 1.28
1614 4660 9.567848 GATGTTAATTGGCCCGTATTAATAATG 57.432 33.333 14.28 0.00 31.18 1.90
1615 4661 7.887381 TGTTAATTGGCCCGTATTAATAATGG 58.113 34.615 14.28 2.65 31.18 3.16
1616 4662 7.724506 TGTTAATTGGCCCGTATTAATAATGGA 59.275 33.333 13.96 0.00 31.18 3.41
1617 4663 6.584185 AATTGGCCCGTATTAATAATGGAC 57.416 37.500 13.96 11.77 0.00 4.02
1657 4703 3.802418 GAGGTGGAACGGTGTGCGT 62.802 63.158 0.00 0.00 38.12 5.24
1658 4704 2.029369 GGTGGAACGGTGTGCGTA 59.971 61.111 0.00 0.00 38.12 4.42
1659 4705 2.312436 GGTGGAACGGTGTGCGTAC 61.312 63.158 0.00 0.00 38.12 3.67
1660 4706 2.354891 TGGAACGGTGTGCGTACG 60.355 61.111 11.84 11.84 0.00 3.67
1661 4707 3.107661 GGAACGGTGTGCGTACGG 61.108 66.667 18.39 1.02 0.00 4.02
1662 4708 3.770424 GAACGGTGTGCGTACGGC 61.770 66.667 18.39 9.98 43.96 5.68
1711 4757 3.111853 TGAACCGATCCATGCTGATAC 57.888 47.619 0.00 0.00 0.00 2.24
1712 4758 2.224281 TGAACCGATCCATGCTGATACC 60.224 50.000 0.00 0.00 0.00 2.73
1725 4892 4.973168 TGCTGATACCCTACATTCATTCC 58.027 43.478 0.00 0.00 0.00 3.01
1730 4897 1.134098 ACCCTACATTCATTCCGCTGG 60.134 52.381 0.00 0.00 0.00 4.85
1763 4938 2.281761 CGGCTCAAGGCTTGTGGT 60.282 61.111 25.39 0.00 41.46 4.16
1764 4939 1.003839 CGGCTCAAGGCTTGTGGTA 60.004 57.895 25.39 6.66 41.46 3.25
1765 4940 1.021390 CGGCTCAAGGCTTGTGGTAG 61.021 60.000 25.39 16.62 41.46 3.18
1766 4941 0.324943 GGCTCAAGGCTTGTGGTAGA 59.675 55.000 25.39 5.55 41.46 2.59
1767 4942 1.065126 GGCTCAAGGCTTGTGGTAGAT 60.065 52.381 25.39 0.00 41.46 1.98
1768 4943 2.170607 GGCTCAAGGCTTGTGGTAGATA 59.829 50.000 25.39 4.09 41.46 1.98
1769 4944 3.198872 GCTCAAGGCTTGTGGTAGATAC 58.801 50.000 25.39 6.17 38.06 2.24
1770 4945 3.118592 GCTCAAGGCTTGTGGTAGATACT 60.119 47.826 25.39 0.00 38.06 2.12
1771 4946 4.099573 GCTCAAGGCTTGTGGTAGATACTA 59.900 45.833 25.39 2.13 38.06 1.82
1772 4947 5.593010 CTCAAGGCTTGTGGTAGATACTAC 58.407 45.833 25.39 0.00 38.06 2.73
1773 4948 5.269991 TCAAGGCTTGTGGTAGATACTACT 58.730 41.667 25.39 0.00 38.35 2.57
1793 4970 1.583556 ATGTCCCTGTGATGCCTGTA 58.416 50.000 0.00 0.00 0.00 2.74
1800 4977 2.027745 CCTGTGATGCCTGTACTTCAGT 60.028 50.000 0.00 0.00 42.19 3.41
1803 4980 1.204704 TGATGCCTGTACTTCAGTCGG 59.795 52.381 0.00 0.00 42.19 4.79
1818 4995 1.135199 AGTCGGCGTTGTCGTTATGAT 60.135 47.619 6.85 0.00 39.49 2.45
1819 4996 2.097954 AGTCGGCGTTGTCGTTATGATA 59.902 45.455 6.85 0.00 39.49 2.15
1822 4999 2.466571 CGGCGTTGTCGTTATGATAGTC 59.533 50.000 0.00 0.00 39.49 2.59
1863 7065 1.213296 GGGGCTGGGTTCAGATCTTA 58.787 55.000 0.00 0.00 43.49 2.10
1876 7082 6.039382 GGTTCAGATCTTACAGTGGTTTGTTT 59.961 38.462 0.00 0.00 32.56 2.83
1879 7085 7.479980 TCAGATCTTACAGTGGTTTGTTTTTG 58.520 34.615 0.00 0.00 32.56 2.44
1893 7099 6.374578 GTTTGTTTTTGCTTTTTGCCTTGTA 58.625 32.000 0.00 0.00 42.00 2.41
1894 7100 6.749923 TTGTTTTTGCTTTTTGCCTTGTAT 57.250 29.167 0.00 0.00 42.00 2.29
1895 7101 7.849804 TTGTTTTTGCTTTTTGCCTTGTATA 57.150 28.000 0.00 0.00 42.00 1.47
1896 7102 7.240414 TGTTTTTGCTTTTTGCCTTGTATAC 57.760 32.000 0.00 0.00 42.00 1.47
1903 7109 5.793457 GCTTTTTGCCTTGTATACGTAGTTG 59.207 40.000 0.08 0.00 37.62 3.16
1914 7120 8.900511 TTGTATACGTAGTTGTGTTGTATCTC 57.099 34.615 0.08 0.00 37.78 2.75
1915 7121 8.272545 TGTATACGTAGTTGTGTTGTATCTCT 57.727 34.615 0.08 0.00 37.78 3.10
1916 7122 9.382275 TGTATACGTAGTTGTGTTGTATCTCTA 57.618 33.333 0.08 0.00 37.78 2.43
1917 7123 9.861138 GTATACGTAGTTGTGTTGTATCTCTAG 57.139 37.037 0.08 0.00 37.78 2.43
1918 7124 5.638783 ACGTAGTTGTGTTGTATCTCTAGC 58.361 41.667 0.00 0.00 37.78 3.42
1919 7125 5.035443 CGTAGTTGTGTTGTATCTCTAGCC 58.965 45.833 0.00 0.00 0.00 3.93
1920 7126 4.111375 AGTTGTGTTGTATCTCTAGCCG 57.889 45.455 0.00 0.00 0.00 5.52
1921 7127 2.579207 TGTGTTGTATCTCTAGCCGC 57.421 50.000 0.00 0.00 0.00 6.53
1922 7128 1.136305 TGTGTTGTATCTCTAGCCGCC 59.864 52.381 0.00 0.00 0.00 6.13
1923 7129 0.750850 TGTTGTATCTCTAGCCGCCC 59.249 55.000 0.00 0.00 0.00 6.13
1924 7130 0.033642 GTTGTATCTCTAGCCGCCCC 59.966 60.000 0.00 0.00 0.00 5.80
1925 7131 0.105658 TTGTATCTCTAGCCGCCCCT 60.106 55.000 0.00 0.00 0.00 4.79
1926 7132 0.539901 TGTATCTCTAGCCGCCCCTC 60.540 60.000 0.00 0.00 0.00 4.30
1927 7133 1.076906 TATCTCTAGCCGCCCCTCC 59.923 63.158 0.00 0.00 0.00 4.30
1928 7134 1.436179 TATCTCTAGCCGCCCCTCCT 61.436 60.000 0.00 0.00 0.00 3.69
2235 7441 4.357279 GCCTCAGTTGCCCTGCCT 62.357 66.667 0.00 0.00 41.25 4.75
2236 7442 2.045536 CCTCAGTTGCCCTGCCTC 60.046 66.667 0.00 0.00 41.25 4.70
2237 7443 2.600729 CCTCAGTTGCCCTGCCTCT 61.601 63.158 0.00 0.00 41.25 3.69
2238 7444 1.376942 CTCAGTTGCCCTGCCTCTG 60.377 63.158 0.00 0.00 41.25 3.35
2239 7445 3.060615 CAGTTGCCCTGCCTCTGC 61.061 66.667 0.00 0.00 33.59 4.26
2240 7446 4.711949 AGTTGCCCTGCCTCTGCG 62.712 66.667 0.00 0.00 41.78 5.18
2247 7453 4.020617 CTGCCTCTGCGTGGGGAA 62.021 66.667 0.00 0.00 41.78 3.97
2248 7454 4.329545 TGCCTCTGCGTGGGGAAC 62.330 66.667 0.00 0.00 41.78 3.62
2261 7467 3.231298 GGAACCCCGGATCTGGAG 58.769 66.667 23.02 11.90 0.00 3.86
2262 7468 2.506472 GAACCCCGGATCTGGAGC 59.494 66.667 23.02 4.29 0.00 4.70
2263 7469 3.447025 GAACCCCGGATCTGGAGCG 62.447 68.421 23.02 11.04 0.00 5.03
2279 7485 3.746889 CGGCGGCTTCATTGGCAA 61.747 61.111 7.61 0.68 0.00 4.52
2280 7486 2.182537 GGCGGCTTCATTGGCAAG 59.817 61.111 5.96 0.00 0.00 4.01
2281 7487 2.182537 GCGGCTTCATTGGCAAGG 59.817 61.111 5.35 5.35 0.00 3.61
2282 7488 2.182537 CGGCTTCATTGGCAAGGC 59.817 61.111 7.07 3.57 41.81 4.35
2283 7489 2.638354 CGGCTTCATTGGCAAGGCA 61.638 57.895 7.07 0.00 44.68 4.75
2284 7490 1.079612 GGCTTCATTGGCAAGGCAC 60.080 57.895 7.07 0.00 44.04 5.01
2285 7491 1.444895 GCTTCATTGGCAAGGCACG 60.445 57.895 7.07 0.00 0.00 5.34
2286 7492 1.213537 CTTCATTGGCAAGGCACGG 59.786 57.895 7.07 0.00 0.00 4.94
2287 7493 2.824071 CTTCATTGGCAAGGCACGGC 62.824 60.000 7.07 0.00 0.00 5.68
2316 7522 4.457496 CGTGCTGGCGGTGGATCT 62.457 66.667 0.00 0.00 0.00 2.75
2317 7523 2.821366 GTGCTGGCGGTGGATCTG 60.821 66.667 0.00 0.00 0.00 2.90
2318 7524 4.100084 TGCTGGCGGTGGATCTGG 62.100 66.667 0.00 0.00 0.00 3.86
2350 7556 4.996434 GGGCGGCGGGATCTGATG 62.996 72.222 9.78 0.00 0.00 3.07
2351 7557 4.996434 GGCGGCGGGATCTGATGG 62.996 72.222 9.78 0.00 0.00 3.51
2352 7558 4.241555 GCGGCGGGATCTGATGGT 62.242 66.667 9.78 0.00 0.00 3.55
2353 7559 2.029666 CGGCGGGATCTGATGGTC 59.970 66.667 0.00 0.00 0.00 4.02
2354 7560 2.029666 GGCGGGATCTGATGGTCG 59.970 66.667 0.00 0.00 0.00 4.79
2355 7561 2.797278 GGCGGGATCTGATGGTCGT 61.797 63.158 0.00 0.00 0.00 4.34
2356 7562 1.144057 GCGGGATCTGATGGTCGTT 59.856 57.895 0.00 0.00 0.00 3.85
2357 7563 1.154205 GCGGGATCTGATGGTCGTTG 61.154 60.000 0.00 0.00 0.00 4.10
2358 7564 0.530650 CGGGATCTGATGGTCGTTGG 60.531 60.000 0.00 0.00 0.00 3.77
2359 7565 0.815615 GGGATCTGATGGTCGTTGGC 60.816 60.000 0.00 0.00 0.00 4.52
2360 7566 1.154205 GGATCTGATGGTCGTTGGCG 61.154 60.000 0.00 0.00 39.92 5.69
2361 7567 1.153369 ATCTGATGGTCGTTGGCGG 60.153 57.895 0.00 0.00 38.89 6.13
2362 7568 3.499737 CTGATGGTCGTTGGCGGC 61.500 66.667 0.00 0.00 42.81 6.53
2363 7569 3.958147 CTGATGGTCGTTGGCGGCT 62.958 63.158 11.43 0.00 43.14 5.52
2364 7570 3.499737 GATGGTCGTTGGCGGCTG 61.500 66.667 11.43 0.00 43.14 4.85
2385 7591 2.886124 GCGGCTTCTACGGCAGTC 60.886 66.667 0.00 0.00 36.05 3.51
2386 7592 2.579787 CGGCTTCTACGGCAGTCG 60.580 66.667 0.00 0.00 45.88 4.18
2387 7593 2.202756 GGCTTCTACGGCAGTCGG 60.203 66.667 0.00 0.00 44.45 4.79
2388 7594 2.572284 GCTTCTACGGCAGTCGGT 59.428 61.111 0.00 0.00 44.45 4.69
2389 7595 1.805945 GCTTCTACGGCAGTCGGTG 60.806 63.158 0.00 0.00 44.45 4.94
2412 7618 3.934962 GATCTGGCGCCTCCCCTC 61.935 72.222 29.70 13.15 0.00 4.30
2419 7625 4.150454 CGCCTCCCCTCCTCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
2420 7626 2.445654 GCCTCCCCTCCTCTCCTG 60.446 72.222 0.00 0.00 0.00 3.86
2421 7627 3.114390 CCTCCCCTCCTCTCCTGT 58.886 66.667 0.00 0.00 0.00 4.00
2422 7628 1.394151 CCTCCCCTCCTCTCCTGTT 59.606 63.158 0.00 0.00 0.00 3.16
2423 7629 0.689412 CCTCCCCTCCTCTCCTGTTC 60.689 65.000 0.00 0.00 0.00 3.18
2424 7630 1.000486 TCCCCTCCTCTCCTGTTCG 60.000 63.158 0.00 0.00 0.00 3.95
2425 7631 1.000486 CCCCTCCTCTCCTGTTCGA 60.000 63.158 0.00 0.00 0.00 3.71
2426 7632 1.324005 CCCCTCCTCTCCTGTTCGAC 61.324 65.000 0.00 0.00 0.00 4.20
2427 7633 1.658686 CCCTCCTCTCCTGTTCGACG 61.659 65.000 0.00 0.00 0.00 5.12
2428 7634 0.961358 CCTCCTCTCCTGTTCGACGT 60.961 60.000 0.00 0.00 0.00 4.34
2429 7635 0.169230 CTCCTCTCCTGTTCGACGTG 59.831 60.000 0.00 0.00 0.00 4.49
2430 7636 1.444553 CCTCTCCTGTTCGACGTGC 60.445 63.158 0.00 0.00 0.00 5.34
2431 7637 1.797933 CTCTCCTGTTCGACGTGCG 60.798 63.158 0.00 0.00 42.69 5.34
2432 7638 2.805353 CTCCTGTTCGACGTGCGG 60.805 66.667 0.00 0.00 41.33 5.69
2433 7639 4.351938 TCCTGTTCGACGTGCGGG 62.352 66.667 0.00 11.27 41.33 6.13
2464 7670 2.815647 CCGCGCTTCCTCTTGGTC 60.816 66.667 5.56 0.00 34.23 4.02
2465 7671 3.181967 CGCGCTTCCTCTTGGTCG 61.182 66.667 5.56 0.00 34.23 4.79
2466 7672 3.491652 GCGCTTCCTCTTGGTCGC 61.492 66.667 0.00 0.00 39.03 5.19
2467 7673 2.815647 CGCTTCCTCTTGGTCGCC 60.816 66.667 0.00 0.00 34.23 5.54
2468 7674 2.815647 GCTTCCTCTTGGTCGCCG 60.816 66.667 0.00 0.00 34.23 6.46
2469 7675 2.125512 CTTCCTCTTGGTCGCCGG 60.126 66.667 0.00 0.00 34.23 6.13
2470 7676 2.920912 TTCCTCTTGGTCGCCGGT 60.921 61.111 1.90 0.00 34.23 5.28
2471 7677 2.450479 CTTCCTCTTGGTCGCCGGTT 62.450 60.000 1.90 0.00 34.23 4.44
2472 7678 2.434359 CCTCTTGGTCGCCGGTTC 60.434 66.667 1.90 0.00 0.00 3.62
2473 7679 2.657237 CTCTTGGTCGCCGGTTCT 59.343 61.111 1.90 0.00 0.00 3.01
2474 7680 1.738099 CTCTTGGTCGCCGGTTCTG 60.738 63.158 1.90 0.00 0.00 3.02
2475 7681 2.030562 CTTGGTCGCCGGTTCTGT 59.969 61.111 1.90 0.00 0.00 3.41
2476 7682 1.180456 TCTTGGTCGCCGGTTCTGTA 61.180 55.000 1.90 0.00 0.00 2.74
2477 7683 1.005867 TTGGTCGCCGGTTCTGTAC 60.006 57.895 1.90 0.00 0.00 2.90
2478 7684 1.746322 TTGGTCGCCGGTTCTGTACA 61.746 55.000 1.90 0.00 0.00 2.90
2479 7685 1.445582 GGTCGCCGGTTCTGTACAG 60.446 63.158 17.17 17.17 0.00 2.74
2480 7686 1.445582 GTCGCCGGTTCTGTACAGG 60.446 63.158 22.48 8.35 44.10 4.00
2481 7687 1.604308 TCGCCGGTTCTGTACAGGA 60.604 57.895 22.48 11.97 44.02 3.86
2482 7688 1.153823 CGCCGGTTCTGTACAGGAG 60.154 63.158 22.48 11.05 44.02 3.69
2483 7689 1.218316 GCCGGTTCTGTACAGGAGG 59.782 63.158 22.48 19.11 44.02 4.30
2484 7690 1.218316 CCGGTTCTGTACAGGAGGC 59.782 63.158 22.48 10.03 44.02 4.70
2485 7691 1.153823 CGGTTCTGTACAGGAGGCG 60.154 63.158 22.48 0.00 0.00 5.52
2486 7692 1.448013 GGTTCTGTACAGGAGGCGC 60.448 63.158 22.48 0.00 0.00 6.53
2487 7693 1.592223 GTTCTGTACAGGAGGCGCT 59.408 57.895 22.48 0.00 0.00 5.92
2488 7694 0.737715 GTTCTGTACAGGAGGCGCTG 60.738 60.000 22.48 0.00 0.00 5.18
2489 7695 2.507110 TTCTGTACAGGAGGCGCTGC 62.507 60.000 22.48 0.00 0.00 5.25
2490 7696 2.997315 TGTACAGGAGGCGCTGCT 60.997 61.111 7.64 0.48 30.68 4.24
2505 7711 3.647367 GCTGGTGGCAGGGATCTA 58.353 61.111 0.00 0.00 41.35 1.98
2506 7712 1.449353 GCTGGTGGCAGGGATCTAG 59.551 63.158 0.00 0.00 41.35 2.43
2507 7713 1.341156 GCTGGTGGCAGGGATCTAGT 61.341 60.000 0.00 0.00 41.35 2.57
2508 7714 1.207791 CTGGTGGCAGGGATCTAGTT 58.792 55.000 0.00 0.00 0.00 2.24
2509 7715 1.139853 CTGGTGGCAGGGATCTAGTTC 59.860 57.143 0.00 0.00 0.00 3.01
2510 7716 0.105039 GGTGGCAGGGATCTAGTTCG 59.895 60.000 0.00 0.00 0.00 3.95
2511 7717 0.105039 GTGGCAGGGATCTAGTTCGG 59.895 60.000 0.00 0.00 0.00 4.30
2512 7718 1.048724 TGGCAGGGATCTAGTTCGGG 61.049 60.000 0.00 0.00 0.00 5.14
2513 7719 1.069935 GCAGGGATCTAGTTCGGGC 59.930 63.158 0.00 0.00 0.00 6.13
2514 7720 1.364171 CAGGGATCTAGTTCGGGCG 59.636 63.158 0.00 0.00 0.00 6.13
2515 7721 1.107538 CAGGGATCTAGTTCGGGCGA 61.108 60.000 0.00 0.00 0.00 5.54
2516 7722 0.178958 AGGGATCTAGTTCGGGCGAT 60.179 55.000 0.00 0.00 0.00 4.58
2517 7723 1.075050 AGGGATCTAGTTCGGGCGATA 59.925 52.381 0.00 0.00 0.00 2.92
2518 7724 2.100989 GGGATCTAGTTCGGGCGATAT 58.899 52.381 0.00 0.00 0.00 1.63
2519 7725 2.099427 GGGATCTAGTTCGGGCGATATC 59.901 54.545 0.00 0.00 0.00 1.63
2520 7726 2.099427 GGATCTAGTTCGGGCGATATCC 59.901 54.545 0.00 0.00 0.00 2.59
2521 7727 1.542492 TCTAGTTCGGGCGATATCCC 58.458 55.000 0.00 0.00 43.02 3.85
2522 7728 1.075050 TCTAGTTCGGGCGATATCCCT 59.925 52.381 9.32 0.00 44.30 4.20
2523 7729 1.202582 CTAGTTCGGGCGATATCCCTG 59.797 57.143 11.09 11.09 44.30 4.45
2524 7730 1.004918 GTTCGGGCGATATCCCTGG 60.005 63.158 15.25 7.11 44.30 4.45
2525 7731 2.879233 TTCGGGCGATATCCCTGGC 61.879 63.158 15.25 6.65 44.30 4.85
2526 7732 4.394712 CGGGCGATATCCCTGGCC 62.395 72.222 10.07 10.07 44.30 5.36
2527 7733 4.394712 GGGCGATATCCCTGGCCG 62.395 72.222 11.72 0.00 46.50 6.13
2528 7734 4.394712 GGCGATATCCCTGGCCGG 62.395 72.222 3.88 3.88 35.59 6.13
2530 7736 4.394712 CGATATCCCTGGCCGGCC 62.395 72.222 39.40 39.40 0.00 6.13
2531 7737 3.249189 GATATCCCTGGCCGGCCA 61.249 66.667 44.03 44.03 45.02 5.36
2532 7738 2.532715 ATATCCCTGGCCGGCCAT 60.533 61.111 46.65 33.97 46.15 4.40
2533 7739 2.826777 GATATCCCTGGCCGGCCATG 62.827 65.000 46.65 40.94 46.15 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 150 2.371658 AAGTTTGCAAGGAAGGAGCT 57.628 45.000 0.00 0.00 0.00 4.09
238 262 2.044946 CTTCCTTCCTTGCCCCCG 60.045 66.667 0.00 0.00 0.00 5.73
275 302 1.676635 GCTGCTGCTGTGGGAATCA 60.677 57.895 8.53 0.00 36.03 2.57
381 414 0.752009 TAGAGACTCGCCTGCCGAAT 60.752 55.000 0.00 0.00 46.81 3.34
387 420 1.737363 GCCTTTGTAGAGACTCGCCTG 60.737 57.143 0.00 0.00 0.00 4.85
478 542 5.934921 CATGACATCATGCATGGTACATAC 58.065 41.667 25.97 11.70 45.16 2.39
612 690 5.291905 TGAGTTGCTCTGATGATGATGAT 57.708 39.130 0.00 0.00 0.00 2.45
613 691 4.748277 TGAGTTGCTCTGATGATGATGA 57.252 40.909 0.00 0.00 0.00 2.92
614 692 4.634443 TGTTGAGTTGCTCTGATGATGATG 59.366 41.667 0.00 0.00 0.00 3.07
844 928 3.123959 CCGGTGGTTAGTTAATCAACACG 59.876 47.826 0.00 1.15 33.66 4.49
917 1003 5.355350 GCAGCTATGTTTATCCTTGTGTTCT 59.645 40.000 0.00 0.00 0.00 3.01
1097 1187 6.145696 GGCAATATTAGTACTTAGCGTGAAGG 59.854 42.308 0.00 0.00 0.00 3.46
1106 1211 5.396485 TCTCGGGGGCAATATTAGTACTTA 58.604 41.667 0.00 0.00 0.00 2.24
1256 1365 7.391620 TGGCTATAGTTAACTTACCCATATGC 58.608 38.462 14.49 9.80 0.00 3.14
1426 4365 1.683385 GGAAGCAACTTTCAGTGCCTT 59.317 47.619 0.00 0.00 0.00 4.35
1497 4436 2.577772 AAGGCGAGACAGAGCTGCA 61.578 57.895 1.02 0.00 0.00 4.41
1585 4525 1.358759 CGGGCCAATTAACATCCGC 59.641 57.895 4.39 0.00 0.00 5.54
1586 4526 1.956297 TACGGGCCAATTAACATCCG 58.044 50.000 4.39 0.00 42.69 4.18
1589 4635 8.527810 CCATTATTAATACGGGCCAATTAACAT 58.472 33.333 18.31 12.70 32.08 2.71
1594 4640 6.311735 AGTCCATTATTAATACGGGCCAATT 58.688 36.000 4.39 5.28 0.00 2.32
1611 4657 5.941788 ACCAAGTCAACTTCTAAGTCCATT 58.058 37.500 0.00 0.00 38.57 3.16
1612 4658 5.568620 ACCAAGTCAACTTCTAAGTCCAT 57.431 39.130 0.00 0.00 38.57 3.41
1613 4659 5.130477 AGAACCAAGTCAACTTCTAAGTCCA 59.870 40.000 0.00 0.00 38.57 4.02
1614 4660 5.612351 AGAACCAAGTCAACTTCTAAGTCC 58.388 41.667 0.00 0.00 38.57 3.85
1615 4661 7.659186 TCTAGAACCAAGTCAACTTCTAAGTC 58.341 38.462 0.00 0.00 38.57 3.01
1616 4662 7.256012 CCTCTAGAACCAAGTCAACTTCTAAGT 60.256 40.741 0.00 0.00 42.04 2.24
1617 4663 7.093992 CCTCTAGAACCAAGTCAACTTCTAAG 58.906 42.308 0.00 0.00 33.11 2.18
1657 4703 1.357690 CGATCCTGCTTACGCCGTA 59.642 57.895 0.00 0.00 34.43 4.02
1658 4704 2.104331 CGATCCTGCTTACGCCGT 59.896 61.111 0.00 0.00 34.43 5.68
1659 4705 2.658593 CCGATCCTGCTTACGCCG 60.659 66.667 0.00 0.00 34.43 6.46
1660 4706 2.280186 CCCGATCCTGCTTACGCC 60.280 66.667 0.00 0.00 34.43 5.68
1661 4707 0.876342 CTTCCCGATCCTGCTTACGC 60.876 60.000 0.00 0.00 0.00 4.42
1662 4708 0.460311 ACTTCCCGATCCTGCTTACG 59.540 55.000 0.00 0.00 0.00 3.18
1663 4709 2.693267 AACTTCCCGATCCTGCTTAC 57.307 50.000 0.00 0.00 0.00 2.34
1664 4710 2.569853 TGAAACTTCCCGATCCTGCTTA 59.430 45.455 0.00 0.00 0.00 3.09
1665 4711 1.351017 TGAAACTTCCCGATCCTGCTT 59.649 47.619 0.00 0.00 0.00 3.91
1666 4712 0.984230 TGAAACTTCCCGATCCTGCT 59.016 50.000 0.00 0.00 0.00 4.24
1667 4713 1.373570 CTGAAACTTCCCGATCCTGC 58.626 55.000 0.00 0.00 0.00 4.85
1668 4714 1.065854 AGCTGAAACTTCCCGATCCTG 60.066 52.381 0.00 0.00 0.00 3.86
1669 4715 1.065854 CAGCTGAAACTTCCCGATCCT 60.066 52.381 8.42 0.00 0.00 3.24
1670 4716 1.066143 TCAGCTGAAACTTCCCGATCC 60.066 52.381 15.67 0.00 0.00 3.36
1671 4717 2.386661 TCAGCTGAAACTTCCCGATC 57.613 50.000 15.67 0.00 0.00 3.69
1672 4718 2.237143 TCATCAGCTGAAACTTCCCGAT 59.763 45.455 22.50 0.00 0.00 4.18
1673 4719 1.623311 TCATCAGCTGAAACTTCCCGA 59.377 47.619 22.50 4.61 0.00 5.14
1674 4720 2.099141 TCATCAGCTGAAACTTCCCG 57.901 50.000 22.50 2.26 0.00 5.14
1675 4721 2.489722 GGTTCATCAGCTGAAACTTCCC 59.510 50.000 22.50 12.09 46.29 3.97
1676 4722 3.839051 GGTTCATCAGCTGAAACTTCC 57.161 47.619 22.50 15.24 46.29 3.46
1700 4746 4.356405 TGAATGTAGGGTATCAGCATGG 57.644 45.455 0.00 0.00 36.16 3.66
1711 4757 1.134098 ACCAGCGGAATGAATGTAGGG 60.134 52.381 1.50 0.00 0.00 3.53
1712 4758 1.942657 CACCAGCGGAATGAATGTAGG 59.057 52.381 1.50 0.00 0.00 3.18
1725 4892 4.124351 CCCTTGCATGCACCAGCG 62.124 66.667 22.58 4.62 46.23 5.18
1730 4897 1.080569 CCGAAACCCTTGCATGCAC 60.081 57.895 22.58 5.96 0.00 4.57
1763 4938 6.659668 GCATCACAGGGACATAGTAGTATCTA 59.340 42.308 0.00 0.00 0.00 1.98
1764 4939 5.478679 GCATCACAGGGACATAGTAGTATCT 59.521 44.000 0.00 0.00 0.00 1.98
1765 4940 5.336849 GGCATCACAGGGACATAGTAGTATC 60.337 48.000 0.00 0.00 0.00 2.24
1766 4941 4.528596 GGCATCACAGGGACATAGTAGTAT 59.471 45.833 0.00 0.00 0.00 2.12
1767 4942 3.895656 GGCATCACAGGGACATAGTAGTA 59.104 47.826 0.00 0.00 0.00 1.82
1768 4943 2.700897 GGCATCACAGGGACATAGTAGT 59.299 50.000 0.00 0.00 0.00 2.73
1769 4944 2.968574 AGGCATCACAGGGACATAGTAG 59.031 50.000 0.00 0.00 0.00 2.57
1770 4945 2.700371 CAGGCATCACAGGGACATAGTA 59.300 50.000 0.00 0.00 0.00 1.82
1771 4946 1.487976 CAGGCATCACAGGGACATAGT 59.512 52.381 0.00 0.00 0.00 2.12
1772 4947 1.487976 ACAGGCATCACAGGGACATAG 59.512 52.381 0.00 0.00 0.00 2.23
1773 4948 1.583556 ACAGGCATCACAGGGACATA 58.416 50.000 0.00 0.00 0.00 2.29
1793 4970 1.660575 CGACAACGCCGACTGAAGT 60.661 57.895 0.00 0.00 0.00 3.01
1800 4977 2.097954 ACTATCATAACGACAACGCCGA 59.902 45.455 0.00 0.00 43.96 5.54
1803 4980 3.357021 TCGACTATCATAACGACAACGC 58.643 45.455 0.00 0.00 43.96 4.84
1818 4995 3.341823 AGAAACGACCTAAGCTCGACTA 58.658 45.455 0.00 0.00 35.08 2.59
1819 4996 2.161030 AGAAACGACCTAAGCTCGACT 58.839 47.619 0.00 0.00 35.08 4.18
1822 4999 2.923605 AGAGAAACGACCTAAGCTCG 57.076 50.000 0.00 0.00 37.17 5.03
1863 7065 5.756849 CAAAAAGCAAAAACAAACCACTGT 58.243 33.333 0.00 0.00 0.00 3.55
1879 7085 5.541098 ACTACGTATACAAGGCAAAAAGC 57.459 39.130 3.32 0.00 44.65 3.51
1893 7099 7.416022 GCTAGAGATACAACACAACTACGTAT 58.584 38.462 0.00 0.00 0.00 3.06
1894 7100 6.183360 GGCTAGAGATACAACACAACTACGTA 60.183 42.308 0.00 0.00 0.00 3.57
1895 7101 5.392811 GGCTAGAGATACAACACAACTACGT 60.393 44.000 0.00 0.00 0.00 3.57
1896 7102 5.035443 GGCTAGAGATACAACACAACTACG 58.965 45.833 0.00 0.00 0.00 3.51
1903 7109 1.538419 GGGCGGCTAGAGATACAACAC 60.538 57.143 9.56 0.00 0.00 3.32
2223 7429 4.711949 CGCAGAGGCAGGGCAACT 62.712 66.667 0.00 0.00 41.24 3.16
2230 7436 4.020617 TTCCCCACGCAGAGGCAG 62.021 66.667 0.00 0.00 41.24 4.85
2231 7437 4.329545 GTTCCCCACGCAGAGGCA 62.330 66.667 0.00 0.00 41.24 4.75
2233 7439 4.410400 GGGTTCCCCACGCAGAGG 62.410 72.222 0.00 0.00 44.65 3.69
2242 7448 3.489513 CCAGATCCGGGGTTCCCC 61.490 72.222 16.52 16.52 41.57 4.81
2243 7449 2.366435 TCCAGATCCGGGGTTCCC 60.366 66.667 0.00 0.00 41.09 3.97
2244 7450 3.108288 GCTCCAGATCCGGGGTTCC 62.108 68.421 0.00 0.00 0.00 3.62
2245 7451 2.506472 GCTCCAGATCCGGGGTTC 59.494 66.667 0.00 0.00 0.00 3.62
2246 7452 3.470888 CGCTCCAGATCCGGGGTT 61.471 66.667 0.00 0.00 0.00 4.11
2262 7468 3.688475 CTTGCCAATGAAGCCGCCG 62.688 63.158 0.00 0.00 0.00 6.46
2263 7469 2.182537 CTTGCCAATGAAGCCGCC 59.817 61.111 0.00 0.00 0.00 6.13
2264 7470 2.182537 CCTTGCCAATGAAGCCGC 59.817 61.111 0.00 0.00 0.00 6.53
2265 7471 2.182537 GCCTTGCCAATGAAGCCG 59.817 61.111 0.00 0.00 0.00 5.52
2266 7472 1.079612 GTGCCTTGCCAATGAAGCC 60.080 57.895 0.00 0.00 0.00 4.35
2267 7473 1.444895 CGTGCCTTGCCAATGAAGC 60.445 57.895 0.00 0.00 0.00 3.86
2268 7474 1.213537 CCGTGCCTTGCCAATGAAG 59.786 57.895 0.00 0.00 0.00 3.02
2269 7475 2.929903 GCCGTGCCTTGCCAATGAA 61.930 57.895 0.00 0.00 0.00 2.57
2270 7476 3.372730 GCCGTGCCTTGCCAATGA 61.373 61.111 0.00 0.00 0.00 2.57
2271 7477 4.440127 GGCCGTGCCTTGCCAATG 62.440 66.667 7.58 0.00 46.69 2.82
2299 7505 4.457496 AGATCCACCGCCAGCACG 62.457 66.667 0.00 0.00 0.00 5.34
2300 7506 2.821366 CAGATCCACCGCCAGCAC 60.821 66.667 0.00 0.00 0.00 4.40
2301 7507 4.100084 CCAGATCCACCGCCAGCA 62.100 66.667 0.00 0.00 0.00 4.41
2333 7539 4.996434 CATCAGATCCCGCCGCCC 62.996 72.222 0.00 0.00 0.00 6.13
2334 7540 4.996434 CCATCAGATCCCGCCGCC 62.996 72.222 0.00 0.00 0.00 6.13
2335 7541 4.241555 ACCATCAGATCCCGCCGC 62.242 66.667 0.00 0.00 0.00 6.53
2336 7542 2.029666 GACCATCAGATCCCGCCG 59.970 66.667 0.00 0.00 0.00 6.46
2337 7543 2.029666 CGACCATCAGATCCCGCC 59.970 66.667 0.00 0.00 0.00 6.13
2338 7544 1.144057 AACGACCATCAGATCCCGC 59.856 57.895 0.00 0.00 0.00 6.13
2339 7545 0.530650 CCAACGACCATCAGATCCCG 60.531 60.000 0.00 0.00 0.00 5.14
2340 7546 0.815615 GCCAACGACCATCAGATCCC 60.816 60.000 0.00 0.00 0.00 3.85
2341 7547 1.154205 CGCCAACGACCATCAGATCC 61.154 60.000 0.00 0.00 43.93 3.36
2342 7548 1.154205 CCGCCAACGACCATCAGATC 61.154 60.000 0.00 0.00 43.93 2.75
2343 7549 1.153369 CCGCCAACGACCATCAGAT 60.153 57.895 0.00 0.00 43.93 2.90
2344 7550 2.264480 CCGCCAACGACCATCAGA 59.736 61.111 0.00 0.00 43.93 3.27
2345 7551 3.499737 GCCGCCAACGACCATCAG 61.500 66.667 0.00 0.00 43.93 2.90
2346 7552 4.015406 AGCCGCCAACGACCATCA 62.015 61.111 0.00 0.00 43.93 3.07
2347 7553 3.499737 CAGCCGCCAACGACCATC 61.500 66.667 0.00 0.00 43.93 3.51
2367 7573 4.452733 ACTGCCGTAGAAGCCGCC 62.453 66.667 0.00 0.00 0.00 6.13
2368 7574 2.886124 GACTGCCGTAGAAGCCGC 60.886 66.667 0.00 0.00 0.00 6.53
2369 7575 2.579787 CGACTGCCGTAGAAGCCG 60.580 66.667 0.00 0.00 0.00 5.52
2370 7576 2.202756 CCGACTGCCGTAGAAGCC 60.203 66.667 0.00 0.00 36.31 4.35
2371 7577 1.805945 CACCGACTGCCGTAGAAGC 60.806 63.158 0.00 0.00 36.31 3.86
2372 7578 1.805945 GCACCGACTGCCGTAGAAG 60.806 63.158 0.00 0.00 40.42 2.85
2373 7579 2.260434 GCACCGACTGCCGTAGAA 59.740 61.111 0.00 0.00 40.42 2.10
2374 7580 4.111016 CGCACCGACTGCCGTAGA 62.111 66.667 0.00 0.00 43.84 2.59
2395 7601 3.934962 GAGGGGAGGCGCCAGATC 61.935 72.222 31.54 17.95 39.05 2.75
2402 7608 4.150454 AGGAGAGGAGGGGAGGCG 62.150 72.222 0.00 0.00 0.00 5.52
2403 7609 2.445654 CAGGAGAGGAGGGGAGGC 60.446 72.222 0.00 0.00 0.00 4.70
2404 7610 0.689412 GAACAGGAGAGGAGGGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
2405 7611 1.040339 CGAACAGGAGAGGAGGGGAG 61.040 65.000 0.00 0.00 0.00 4.30
2406 7612 1.000486 CGAACAGGAGAGGAGGGGA 60.000 63.158 0.00 0.00 0.00 4.81
2407 7613 1.000486 TCGAACAGGAGAGGAGGGG 60.000 63.158 0.00 0.00 0.00 4.79
2408 7614 1.658686 CGTCGAACAGGAGAGGAGGG 61.659 65.000 0.00 0.00 0.00 4.30
2409 7615 0.961358 ACGTCGAACAGGAGAGGAGG 60.961 60.000 0.00 0.00 0.00 4.30
2410 7616 0.169230 CACGTCGAACAGGAGAGGAG 59.831 60.000 0.00 0.00 0.00 3.69
2411 7617 1.863662 GCACGTCGAACAGGAGAGGA 61.864 60.000 0.00 0.00 0.00 3.71
2412 7618 1.444553 GCACGTCGAACAGGAGAGG 60.445 63.158 0.00 0.00 0.00 3.69
2413 7619 1.797933 CGCACGTCGAACAGGAGAG 60.798 63.158 0.00 0.00 41.67 3.20
2414 7620 2.254350 CGCACGTCGAACAGGAGA 59.746 61.111 0.00 0.00 41.67 3.71
2415 7621 2.805353 CCGCACGTCGAACAGGAG 60.805 66.667 0.00 0.00 41.67 3.69
2416 7622 4.351938 CCCGCACGTCGAACAGGA 62.352 66.667 0.00 0.00 41.67 3.86
2447 7653 2.815647 GACCAAGAGGAAGCGCGG 60.816 66.667 8.83 0.00 38.69 6.46
2448 7654 3.181967 CGACCAAGAGGAAGCGCG 61.182 66.667 0.00 0.00 38.69 6.86
2449 7655 3.491652 GCGACCAAGAGGAAGCGC 61.492 66.667 0.00 0.00 42.39 5.92
2450 7656 2.815647 GGCGACCAAGAGGAAGCG 60.816 66.667 0.00 0.00 40.09 4.68
2451 7657 2.815647 CGGCGACCAAGAGGAAGC 60.816 66.667 0.00 0.00 39.08 3.86
2452 7658 2.125512 CCGGCGACCAAGAGGAAG 60.126 66.667 9.30 0.00 38.69 3.46
2453 7659 2.444700 GAACCGGCGACCAAGAGGAA 62.445 60.000 9.30 0.00 38.69 3.36
2454 7660 2.920912 AACCGGCGACCAAGAGGA 60.921 61.111 9.30 0.00 38.69 3.71
2455 7661 2.434359 GAACCGGCGACCAAGAGG 60.434 66.667 9.30 0.00 42.21 3.69
2456 7662 1.738099 CAGAACCGGCGACCAAGAG 60.738 63.158 9.30 0.00 0.00 2.85
2457 7663 1.180456 TACAGAACCGGCGACCAAGA 61.180 55.000 9.30 0.00 0.00 3.02
2458 7664 1.012486 GTACAGAACCGGCGACCAAG 61.012 60.000 9.30 0.00 0.00 3.61
2459 7665 1.005867 GTACAGAACCGGCGACCAA 60.006 57.895 9.30 0.00 0.00 3.67
2460 7666 2.149803 CTGTACAGAACCGGCGACCA 62.150 60.000 18.45 0.00 0.00 4.02
2461 7667 1.445582 CTGTACAGAACCGGCGACC 60.446 63.158 18.45 0.00 0.00 4.79
2462 7668 1.445582 CCTGTACAGAACCGGCGAC 60.446 63.158 24.68 0.00 0.00 5.19
2463 7669 1.592400 CTCCTGTACAGAACCGGCGA 61.592 60.000 24.68 9.72 32.70 5.54
2464 7670 1.153823 CTCCTGTACAGAACCGGCG 60.154 63.158 24.68 0.00 32.70 6.46
2465 7671 1.218316 CCTCCTGTACAGAACCGGC 59.782 63.158 24.68 0.00 32.70 6.13
2466 7672 1.218316 GCCTCCTGTACAGAACCGG 59.782 63.158 24.68 17.34 33.90 5.28
2467 7673 1.153823 CGCCTCCTGTACAGAACCG 60.154 63.158 24.68 15.72 0.00 4.44
2468 7674 1.448013 GCGCCTCCTGTACAGAACC 60.448 63.158 24.68 8.34 0.00 3.62
2469 7675 0.737715 CAGCGCCTCCTGTACAGAAC 60.738 60.000 24.68 9.07 0.00 3.01
2470 7676 1.591703 CAGCGCCTCCTGTACAGAA 59.408 57.895 24.68 2.15 0.00 3.02
2471 7677 3.006756 GCAGCGCCTCCTGTACAGA 62.007 63.158 24.68 9.38 35.28 3.41
2472 7678 2.510238 GCAGCGCCTCCTGTACAG 60.510 66.667 16.34 16.34 35.28 2.74
2473 7679 2.997315 AGCAGCGCCTCCTGTACA 60.997 61.111 2.29 0.00 35.28 2.90
2474 7680 2.510238 CAGCAGCGCCTCCTGTAC 60.510 66.667 2.29 0.00 35.28 2.90
2475 7681 3.774528 CCAGCAGCGCCTCCTGTA 61.775 66.667 2.29 0.00 35.28 2.74
2488 7694 1.341156 ACTAGATCCCTGCCACCAGC 61.341 60.000 0.00 0.00 44.14 4.85
2489 7695 1.139853 GAACTAGATCCCTGCCACCAG 59.860 57.143 0.00 0.00 38.85 4.00
2490 7696 1.204146 GAACTAGATCCCTGCCACCA 58.796 55.000 0.00 0.00 0.00 4.17
2491 7697 0.105039 CGAACTAGATCCCTGCCACC 59.895 60.000 0.00 0.00 0.00 4.61
2492 7698 0.105039 CCGAACTAGATCCCTGCCAC 59.895 60.000 0.00 0.00 0.00 5.01
2493 7699 1.048724 CCCGAACTAGATCCCTGCCA 61.049 60.000 0.00 0.00 0.00 4.92
2494 7700 1.749033 CCCGAACTAGATCCCTGCC 59.251 63.158 0.00 0.00 0.00 4.85
2495 7701 1.069935 GCCCGAACTAGATCCCTGC 59.930 63.158 0.00 0.00 0.00 4.85
2496 7702 1.107538 TCGCCCGAACTAGATCCCTG 61.108 60.000 0.00 0.00 0.00 4.45
2497 7703 0.178958 ATCGCCCGAACTAGATCCCT 60.179 55.000 0.00 0.00 0.00 4.20
2498 7704 1.542492 TATCGCCCGAACTAGATCCC 58.458 55.000 0.00 0.00 0.00 3.85
2499 7705 2.099427 GGATATCGCCCGAACTAGATCC 59.901 54.545 0.00 0.00 0.00 3.36
2500 7706 2.099427 GGGATATCGCCCGAACTAGATC 59.901 54.545 8.56 0.00 38.58 2.75
2501 7707 2.100989 GGGATATCGCCCGAACTAGAT 58.899 52.381 8.56 0.00 38.58 1.98
2502 7708 1.542492 GGGATATCGCCCGAACTAGA 58.458 55.000 8.56 0.00 38.58 2.43
2511 7717 4.394712 CCGGCCAGGGATATCGCC 62.395 72.222 15.62 11.97 38.07 5.54
2513 7719 4.394712 GGCCGGCCAGGGATATCG 62.395 72.222 40.73 0.00 41.48 2.92
2514 7720 3.249189 TGGCCGGCCAGGGATATC 61.249 66.667 44.23 15.73 41.89 1.63


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

AutoCloner maintained by Alex Coulton.