Multiple sequence alignment - TraesCS6D01G146800

Loading Multiple Alignment...

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 TraesCS6D01G146800 chr6D 100.000 2926 0 0 1 2926 119110588 119113513 0.000000e+00 5404.0
1 TraesCS6D01G146800 chr6D 93.989 183 11 0 1909 2091 464777242 464777424 7.990000e-71 278.0
2 TraesCS6D01G146800 chr6B 90.523 1931 146 22 5 1902 210607316 210609242 0.000000e+00 2518.0
3 TraesCS6D01G146800 chr6B 95.402 174 7 1 1910 2082 42737616 42737443 2.870000e-70 276.0
4 TraesCS6D01G146800 chr6B 87.629 97 7 4 651 744 123244556 123244650 1.110000e-19 108.0
5 TraesCS6D01G146800 chr6B 88.889 90 6 3 651 737 675187912 675187824 1.110000e-19 108.0
6 TraesCS6D01G146800 chr6A 93.396 1060 65 3 844 1902 147252679 147253734 0.000000e+00 1565.0
7 TraesCS6D01G146800 chr6A 88.372 817 73 9 7 817 147250830 147251630 0.000000e+00 963.0
8 TraesCS6D01G146800 chr6A 82.988 241 28 13 2096 2329 263883911 263883677 3.820000e-49 206.0
9 TraesCS6D01G146800 chr6A 100.000 30 0 0 1250 1279 15721751 15721722 4.070000e-04 56.5
10 TraesCS6D01G146800 chr1B 84.624 852 78 24 2094 2926 390468814 390469631 0.000000e+00 798.0
11 TraesCS6D01G146800 chr1B 83.696 276 30 13 2091 2362 639920393 639920129 2.250000e-61 246.0
12 TraesCS6D01G146800 chr5B 82.874 870 98 32 2091 2926 282053710 282054562 0.000000e+00 734.0
13 TraesCS6D01G146800 chr5B 86.957 92 8 3 650 739 406061618 406061529 1.860000e-17 100.0
14 TraesCS6D01G146800 chr7D 84.959 605 62 15 2340 2926 421406493 421405900 1.170000e-163 586.0
15 TraesCS6D01G146800 chr7D 89.439 303 27 4 2624 2926 172008 172305 7.650000e-101 377.0
16 TraesCS6D01G146800 chr7D 94.444 180 7 3 1906 2082 601400933 601400754 1.030000e-69 274.0
17 TraesCS6D01G146800 chr7D 92.432 185 14 0 1912 2096 20408636 20408820 6.220000e-67 265.0
18 TraesCS6D01G146800 chr2D 79.422 865 113 44 2091 2926 621733869 621733041 4.260000e-153 551.0
19 TraesCS6D01G146800 chr2D 85.965 228 19 11 2091 2308 411263337 411263561 6.310000e-57 231.0
20 TraesCS6D01G146800 chr3D 78.971 875 110 55 2091 2926 230799661 230798822 2.000000e-146 529.0
21 TraesCS6D01G146800 chr3D 78.571 868 122 47 2096 2926 311884361 311885201 5.590000e-142 514.0
22 TraesCS6D01G146800 chr3D 76.888 887 172 29 1031 1900 529496477 529495607 3.410000e-129 472.0
23 TraesCS6D01G146800 chr3D 84.901 404 53 7 2529 2926 100140829 100141230 4.540000e-108 401.0
24 TraesCS6D01G146800 chr3D 84.938 405 41 5 2529 2915 196818124 196818526 2.730000e-105 392.0
25 TraesCS6D01G146800 chr3B 77.149 919 168 37 988 1886 700073342 700072446 2.030000e-136 496.0
26 TraesCS6D01G146800 chr3B 90.429 303 24 4 2624 2926 444836211 444836508 7.600000e-106 394.0
27 TraesCS6D01G146800 chr3B 89.562 297 26 4 2630 2926 826999699 826999408 3.560000e-99 372.0
28 TraesCS6D01G146800 chr3B 89.562 297 26 4 2630 2926 827545331 827545040 3.560000e-99 372.0
29 TraesCS6D01G146800 chr3B 73.221 773 162 30 997 1756 739572752 739573492 3.770000e-59 239.0
30 TraesCS6D01G146800 chr3B 89.773 88 6 2 651 736 273528528 273528442 3.080000e-20 110.0
31 TraesCS6D01G146800 chr3A 77.416 890 162 35 1031 1900 663441779 663440909 7.280000e-136 494.0
32 TraesCS6D01G146800 chr3A 96.273 161 6 0 1912 2072 737120050 737120210 6.220000e-67 265.0
33 TraesCS6D01G146800 chr3A 91.489 188 10 3 1912 2093 699545553 699545740 1.350000e-63 254.0
34 TraesCS6D01G146800 chr3A 90.805 87 5 3 650 734 290449161 290449076 2.380000e-21 113.0
35 TraesCS6D01G146800 chr5D 76.862 886 146 42 1016 1883 560224906 560225750 2.070000e-121 446.0
36 TraesCS6D01G146800 chr5D 95.028 181 8 1 1915 2094 542392709 542392529 1.720000e-72 283.0
37 TraesCS6D01G146800 chr5D 88.889 90 7 2 650 737 373835132 373835044 1.110000e-19 108.0
38 TraesCS6D01G146800 chr1D 77.591 772 100 52 2094 2835 252526958 252526230 1.630000e-107 399.0
39 TraesCS6D01G146800 chr1D 94.767 172 8 1 1912 2082 2853587 2853758 1.730000e-67 267.0
40 TraesCS6D01G146800 chr2A 89.644 309 27 4 2618 2926 54132479 54132782 3.540000e-104 388.0
41 TraesCS6D01G146800 chrUn 84.048 420 44 9 2525 2926 429224446 429224860 1.650000e-102 383.0
42 TraesCS6D01G146800 chrUn 93.296 179 12 0 1915 2093 161599993 161599815 6.220000e-67 265.0
43 TraesCS6D01G146800 chr5A 82.933 416 47 9 2528 2926 391757404 391757812 1.290000e-93 353.0
44 TraesCS6D01G146800 chr5A 73.868 773 146 40 1010 1755 708183058 708183801 1.040000e-64 257.0
45 TraesCS6D01G146800 chr5A 81.250 256 35 13 2096 2344 692045636 692045387 8.270000e-46 195.0
46 TraesCS6D01G146800 chr5A 89.888 89 5 2 648 734 127607905 127607991 8.570000e-21 111.0
47 TraesCS6D01G146800 chr7B 81.146 419 43 12 2525 2926 324383330 324383729 1.320000e-78 303.0
48 TraesCS6D01G146800 chr4D 74.422 778 152 33 1001 1754 3260794 3260040 1.030000e-74 291.0
49 TraesCS6D01G146800 chr4D 87.097 217 19 8 2091 2300 85826454 85826240 1.360000e-58 237.0
50 TraesCS6D01G146800 chr4D 72.868 774 160 33 1001 1754 2070985 2071728 1.370000e-53 220.0
51 TraesCS6D01G146800 chr4D 100.000 28 0 0 1256 1283 497224201 497224174 5.000000e-03 52.8
52 TraesCS6D01G146800 chr4A 74.323 775 158 28 1001 1754 602260039 602260793 1.030000e-74 291.0
53 TraesCS6D01G146800 chr4B 73.616 777 144 45 1010 1755 668873287 668874033 2.910000e-60 243.0
54 TraesCS6D01G146800 chr2B 86.916 214 20 7 2091 2299 693358490 693358280 1.750000e-57 233.0
55 TraesCS6D01G146800 chr2B 75.186 403 74 7 54 452 408314826 408314446 1.800000e-37 167.0
56 TraesCS6D01G146800 chr2B 88.298 94 5 4 649 739 211038885 211038795 1.110000e-19 108.0


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 TraesCS6D01G146800 chr6D 119110588 119113513 2925 False 5404 5404 100.000 1 2926 1 chr6D.!!$F1 2925
1 TraesCS6D01G146800 chr6B 210607316 210609242 1926 False 2518 2518 90.523 5 1902 1 chr6B.!!$F2 1897
2 TraesCS6D01G146800 chr6A 147250830 147253734 2904 False 1264 1565 90.884 7 1902 2 chr6A.!!$F1 1895
3 TraesCS6D01G146800 chr1B 390468814 390469631 817 False 798 798 84.624 2094 2926 1 chr1B.!!$F1 832
4 TraesCS6D01G146800 chr5B 282053710 282054562 852 False 734 734 82.874 2091 2926 1 chr5B.!!$F1 835
5 TraesCS6D01G146800 chr7D 421405900 421406493 593 True 586 586 84.959 2340 2926 1 chr7D.!!$R1 586
6 TraesCS6D01G146800 chr2D 621733041 621733869 828 True 551 551 79.422 2091 2926 1 chr2D.!!$R1 835
7 TraesCS6D01G146800 chr3D 230798822 230799661 839 True 529 529 78.971 2091 2926 1 chr3D.!!$R1 835
8 TraesCS6D01G146800 chr3D 311884361 311885201 840 False 514 514 78.571 2096 2926 1 chr3D.!!$F3 830
9 TraesCS6D01G146800 chr3D 529495607 529496477 870 True 472 472 76.888 1031 1900 1 chr3D.!!$R2 869
10 TraesCS6D01G146800 chr3B 700072446 700073342 896 True 496 496 77.149 988 1886 1 chr3B.!!$R2 898
11 TraesCS6D01G146800 chr3B 739572752 739573492 740 False 239 239 73.221 997 1756 1 chr3B.!!$F2 759
12 TraesCS6D01G146800 chr3A 663440909 663441779 870 True 494 494 77.416 1031 1900 1 chr3A.!!$R2 869
13 TraesCS6D01G146800 chr5D 560224906 560225750 844 False 446 446 76.862 1016 1883 1 chr5D.!!$F1 867
14 TraesCS6D01G146800 chr1D 252526230 252526958 728 True 399 399 77.591 2094 2835 1 chr1D.!!$R1 741
15 TraesCS6D01G146800 chr5A 708183058 708183801 743 False 257 257 73.868 1010 1755 1 chr5A.!!$F3 745
16 TraesCS6D01G146800 chr4D 3260040 3260794 754 True 291 291 74.422 1001 1754 1 chr4D.!!$R1 753
17 TraesCS6D01G146800 chr4D 2070985 2071728 743 False 220 220 72.868 1001 1754 1 chr4D.!!$F1 753
18 TraesCS6D01G146800 chr4A 602260039 602260793 754 False 291 291 74.323 1001 1754 1 chr4A.!!$F1 753
19 TraesCS6D01G146800 chr4B 668873287 668874033 746 False 243 243 73.616 1010 1755 1 chr4B.!!$F1 745

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
253 264 0.185416 CCTTCGCCCTCCCTAGTCTA 59.815 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 3119 0.108756 GTCCCGCGCTAAGAGTCTTT 60.109 55.0 11.4 0.0 0.0 2.52 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
26 27 2.910345 CGGGCCGAGAGCTAGTAGC 61.910 68.421 24.41 14.62 43.05 3.58
27 28 1.828660 GGGCCGAGAGCTAGTAGCA 60.829 63.158 23.77 0.00 45.56 3.49
154 155 0.464452 GATCCTTTGATCCGGTCGGT 59.536 55.000 9.36 0.00 41.37 4.69
155 156 1.684983 GATCCTTTGATCCGGTCGGTA 59.315 52.381 9.36 0.00 41.37 4.02
158 159 1.108776 CTTTGATCCGGTCGGTAGGA 58.891 55.000 9.36 0.00 41.30 2.94
163 164 0.552848 ATCCGGTCGGTAGGAAGGTA 59.447 55.000 9.36 0.00 40.32 3.08
172 173 1.211212 GGTAGGAAGGTATTTGGCGGT 59.789 52.381 0.00 0.00 0.00 5.68
253 264 0.185416 CCTTCGCCCTCCCTAGTCTA 59.815 60.000 0.00 0.00 0.00 2.59
258 269 0.828343 GCCCTCCCTAGTCTATGCGT 60.828 60.000 0.00 0.00 0.00 5.24
270 281 1.893137 TCTATGCGTTGCGGGATCTAT 59.107 47.619 0.00 0.00 0.00 1.98
323 337 4.586841 TGTAAACCCCCTTCATGAAACAAG 59.413 41.667 9.88 0.00 0.00 3.16
325 339 1.786441 ACCCCCTTCATGAAACAAGGA 59.214 47.619 9.88 0.00 41.74 3.36
366 382 1.553706 GGAAGGGTTACTCTCGACCA 58.446 55.000 0.00 0.00 37.68 4.02
385 401 5.609423 GACCATCTGATAAAGACTGCATCT 58.391 41.667 0.00 0.00 37.88 2.90
386 402 6.515696 CGACCATCTGATAAAGACTGCATCTA 60.516 42.308 0.00 0.00 37.88 1.98
388 404 7.568349 ACCATCTGATAAAGACTGCATCTAAA 58.432 34.615 0.00 0.00 37.88 1.85
511 530 3.747976 GGCGGTGGTGGTTGCATC 61.748 66.667 0.00 0.00 0.00 3.91
513 532 2.358125 CGGTGGTGGTTGCATCGA 60.358 61.111 0.00 0.00 0.00 3.59
552 571 8.119246 TCAATCCCCCTCACAAATTTAATTAGA 58.881 33.333 0.00 0.00 0.00 2.10
575 594 5.561679 ACCTAGTTCTTTGGGTGATTCTTC 58.438 41.667 0.00 0.00 0.00 2.87
578 597 4.803452 AGTTCTTTGGGTGATTCTTCCAA 58.197 39.130 7.04 7.04 38.62 3.53
600 620 6.922344 CAAAATCTTGAGAATCGGACCTCCG 61.922 48.000 7.46 7.46 46.99 4.63
614 634 0.321671 CCTCCGCCAACTTCTCTCAA 59.678 55.000 0.00 0.00 0.00 3.02
629 649 7.795047 ACTTCTCTCAAAATTTTGAACCCATT 58.205 30.769 28.49 13.23 45.61 3.16
676 697 6.960542 ACTCCCTTCGTCCCATAATATAAGAT 59.039 38.462 0.00 0.00 0.00 2.40
745 768 7.206687 GGACAGAGGAAGTAGTTATGATGAAG 58.793 42.308 0.00 0.00 0.00 3.02
750 773 8.986991 AGAGGAAGTAGTTATGATGAAGACAAT 58.013 33.333 0.00 0.00 0.00 2.71
755 778 8.894768 AGTAGTTATGATGAAGACAATTAGGC 57.105 34.615 0.00 0.00 0.00 3.93
790 813 8.930846 AAATATAGGTTCATGATTCTGGAAGG 57.069 34.615 0.00 0.00 0.00 3.46
793 816 2.948315 GGTTCATGATTCTGGAAGGAGC 59.052 50.000 0.00 0.00 0.00 4.70
795 818 4.141620 GGTTCATGATTCTGGAAGGAGCTA 60.142 45.833 0.00 0.00 0.00 3.32
820 843 8.622948 AAGTGAAGGTTCGATTCTTAAGATTT 57.377 30.769 5.89 0.00 0.00 2.17
834 1512 7.787725 TCTTAAGATTTTAGAAGAATCGGCC 57.212 36.000 0.00 0.00 38.29 6.13
839 1517 6.856895 AGATTTTAGAAGAATCGGCCAAAAG 58.143 36.000 2.24 0.00 38.29 2.27
842 1520 5.622770 TTAGAAGAATCGGCCAAAAGAAC 57.377 39.130 2.24 0.00 0.00 3.01
848 1893 5.253330 AGAATCGGCCAAAAGAACTAATGA 58.747 37.500 2.24 0.00 0.00 2.57
910 1955 2.081725 TGGACGCTGCGTTTTATACA 57.918 45.000 29.54 17.07 41.37 2.29
947 1992 1.667830 CAGCACACTGTACACCCCG 60.668 63.158 0.00 0.00 39.22 5.73
1254 2322 2.032681 GCGGAGACTGTGGGCTTT 59.967 61.111 0.00 0.00 0.00 3.51
1402 2470 1.765904 TGAGGTACCACAGCAACTTCA 59.234 47.619 15.94 2.42 0.00 3.02
1602 2695 2.360475 GTGGGTTCCTGGAGCAGC 60.360 66.667 12.78 0.90 0.00 5.25
1606 2699 2.343758 GTTCCTGGAGCAGCACGA 59.656 61.111 5.59 0.00 0.00 4.35
1607 2700 1.301716 GTTCCTGGAGCAGCACGAA 60.302 57.895 5.59 0.00 0.00 3.85
1608 2701 1.004560 TTCCTGGAGCAGCACGAAG 60.005 57.895 0.00 0.00 0.00 3.79
1701 2794 3.991051 CGTCCAGGCACACCGACT 61.991 66.667 0.00 0.00 42.76 4.18
1758 2851 1.915769 GGTCTCCAGGTGCTCCACT 60.916 63.158 7.70 0.00 34.40 4.00
1856 2949 1.283347 TCCTTCAGCTGCTCTCCAAT 58.717 50.000 9.47 0.00 0.00 3.16
1858 2951 1.339824 CCTTCAGCTGCTCTCCAATGT 60.340 52.381 9.47 0.00 0.00 2.71
1859 2952 2.434428 CTTCAGCTGCTCTCCAATGTT 58.566 47.619 9.47 0.00 0.00 2.71
1878 2971 0.251653 TAGGTTCAGGAGCGTGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
1902 2995 0.827925 TGTCCTCTCCAAGAGCGTGT 60.828 55.000 0.00 0.00 40.98 4.49
1903 2996 0.389166 GTCCTCTCCAAGAGCGTGTG 60.389 60.000 0.00 0.00 40.98 3.82
1904 2997 0.827925 TCCTCTCCAAGAGCGTGTGT 60.828 55.000 0.00 0.00 40.98 3.72
1905 2998 0.034059 CCTCTCCAAGAGCGTGTGTT 59.966 55.000 0.00 0.00 40.98 3.32
1906 2999 1.143305 CTCTCCAAGAGCGTGTGTTG 58.857 55.000 0.00 0.00 35.30 3.33
1907 3000 0.464036 TCTCCAAGAGCGTGTGTTGT 59.536 50.000 0.00 0.00 0.00 3.32
1908 3001 0.583438 CTCCAAGAGCGTGTGTTGTG 59.417 55.000 0.00 0.00 0.00 3.33
1909 3002 1.009675 CCAAGAGCGTGTGTTGTGC 60.010 57.895 0.00 0.00 0.00 4.57
1910 3003 1.713937 CCAAGAGCGTGTGTTGTGCA 61.714 55.000 0.00 0.00 0.00 4.57
1925 3018 7.608974 GTGTTGTGCACAGAGTTTTAAATAG 57.391 36.000 20.59 0.00 46.91 1.73
1926 3019 6.142320 GTGTTGTGCACAGAGTTTTAAATAGC 59.858 38.462 20.59 0.00 46.91 2.97
1927 3020 5.029650 TGTGCACAGAGTTTTAAATAGCG 57.970 39.130 17.42 0.00 0.00 4.26
1928 3021 3.846335 GTGCACAGAGTTTTAAATAGCGC 59.154 43.478 13.17 0.00 0.00 5.92
1929 3022 3.091417 GCACAGAGTTTTAAATAGCGCG 58.909 45.455 0.00 0.00 0.00 6.86
1930 3023 3.091417 CACAGAGTTTTAAATAGCGCGC 58.909 45.455 26.66 26.66 0.00 6.86
1931 3024 3.000727 ACAGAGTTTTAAATAGCGCGCT 58.999 40.909 38.01 38.01 0.00 5.92
1932 3025 4.032445 CACAGAGTTTTAAATAGCGCGCTA 59.968 41.667 39.72 39.72 0.00 4.26
1933 3026 4.628333 ACAGAGTTTTAAATAGCGCGCTAA 59.372 37.500 40.90 26.03 31.73 3.09
1934 3027 5.191059 CAGAGTTTTAAATAGCGCGCTAAG 58.809 41.667 40.90 12.87 31.73 2.18
1935 3028 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
1936 3029 3.033873 GTTTTAAATAGCGCGCTAAGCC 58.966 45.455 40.90 21.36 44.76 4.35
1937 3030 2.234300 TTAAATAGCGCGCTAAGCCT 57.766 45.000 40.90 26.65 44.76 4.58
1938 3031 1.779569 TAAATAGCGCGCTAAGCCTC 58.220 50.000 40.90 6.44 44.76 4.70
1939 3032 0.880718 AAATAGCGCGCTAAGCCTCC 60.881 55.000 40.90 5.61 44.76 4.30
1940 3033 1.749334 AATAGCGCGCTAAGCCTCCT 61.749 55.000 40.90 22.43 44.76 3.69
1941 3034 0.894184 ATAGCGCGCTAAGCCTCCTA 60.894 55.000 40.90 20.62 44.76 2.94
1942 3035 1.516365 TAGCGCGCTAAGCCTCCTAG 61.516 60.000 36.77 0.00 44.76 3.02
1943 3036 2.355244 CGCGCTAAGCCTCCTAGC 60.355 66.667 5.56 0.00 44.76 3.42
1953 3046 3.597728 CTCCTAGCGGCGGACCTC 61.598 72.222 9.78 0.00 0.00 3.85
1954 3047 4.124943 TCCTAGCGGCGGACCTCT 62.125 66.667 9.78 0.00 34.60 3.69
1955 3048 3.148279 CCTAGCGGCGGACCTCTT 61.148 66.667 9.78 0.00 31.87 2.85
1956 3049 2.722201 CCTAGCGGCGGACCTCTTT 61.722 63.158 9.78 0.00 31.87 2.52
1957 3050 1.227002 CTAGCGGCGGACCTCTTTC 60.227 63.158 9.78 0.00 31.87 2.62
1958 3051 1.945354 CTAGCGGCGGACCTCTTTCA 61.945 60.000 9.78 0.00 31.87 2.69
1959 3052 1.537814 TAGCGGCGGACCTCTTTCAA 61.538 55.000 9.78 0.00 31.87 2.69
1960 3053 1.964373 GCGGCGGACCTCTTTCAAA 60.964 57.895 9.78 0.00 0.00 2.69
1961 3054 1.305930 GCGGCGGACCTCTTTCAAAT 61.306 55.000 9.78 0.00 0.00 2.32
1962 3055 0.447801 CGGCGGACCTCTTTCAAATG 59.552 55.000 0.00 0.00 0.00 2.32
1963 3056 0.171231 GGCGGACCTCTTTCAAATGC 59.829 55.000 0.00 0.00 0.00 3.56
1964 3057 1.168714 GCGGACCTCTTTCAAATGCT 58.831 50.000 0.00 0.00 0.00 3.79
1965 3058 2.356135 GCGGACCTCTTTCAAATGCTA 58.644 47.619 0.00 0.00 0.00 3.49
1966 3059 2.945668 GCGGACCTCTTTCAAATGCTAT 59.054 45.455 0.00 0.00 0.00 2.97
1967 3060 4.127171 GCGGACCTCTTTCAAATGCTATA 58.873 43.478 0.00 0.00 0.00 1.31
1968 3061 4.212214 GCGGACCTCTTTCAAATGCTATAG 59.788 45.833 0.00 0.00 0.00 1.31
1969 3062 4.212214 CGGACCTCTTTCAAATGCTATAGC 59.788 45.833 18.18 18.18 42.50 2.97
1970 3063 4.212214 GGACCTCTTTCAAATGCTATAGCG 59.788 45.833 19.55 5.67 45.83 4.26
1971 3064 4.770795 ACCTCTTTCAAATGCTATAGCGT 58.229 39.130 19.55 16.84 45.83 5.07
1972 3065 4.572389 ACCTCTTTCAAATGCTATAGCGTG 59.428 41.667 20.02 16.47 45.83 5.34
1973 3066 4.521943 CTCTTTCAAATGCTATAGCGTGC 58.478 43.478 20.02 0.00 45.83 5.34
1974 3067 4.191544 TCTTTCAAATGCTATAGCGTGCT 58.808 39.130 20.02 7.98 45.83 4.40
1975 3068 5.356426 TCTTTCAAATGCTATAGCGTGCTA 58.644 37.500 20.02 3.73 45.83 3.49
1976 3069 5.991606 TCTTTCAAATGCTATAGCGTGCTAT 59.008 36.000 20.02 17.65 45.83 2.97
1977 3070 7.151976 TCTTTCAAATGCTATAGCGTGCTATA 58.848 34.615 20.02 17.96 45.83 1.31
2009 3102 9.107367 GCTATAGCGAGCTATTTAAAATGTTTG 57.893 33.333 20.87 0.00 39.65 2.93
2010 3103 7.914537 ATAGCGAGCTATTTAAAATGTTTGC 57.085 32.000 11.48 10.00 35.92 3.68
2011 3104 5.954335 AGCGAGCTATTTAAAATGTTTGCT 58.046 33.333 12.99 12.99 0.00 3.91
2012 3105 6.030228 AGCGAGCTATTTAAAATGTTTGCTC 58.970 36.000 12.99 11.96 41.29 4.26
2013 3106 5.799936 GCGAGCTATTTAAAATGTTTGCTCA 59.200 36.000 17.23 0.00 43.84 4.26
2014 3107 6.307800 GCGAGCTATTTAAAATGTTTGCTCAA 59.692 34.615 17.23 0.00 43.84 3.02
2015 3108 7.461938 GCGAGCTATTTAAAATGTTTGCTCAAG 60.462 37.037 17.23 7.88 43.84 3.02
2016 3109 7.538678 CGAGCTATTTAAAATGTTTGCTCAAGT 59.461 33.333 17.23 0.00 43.84 3.16
2017 3110 8.524870 AGCTATTTAAAATGTTTGCTCAAGTG 57.475 30.769 0.00 0.00 0.00 3.16
2018 3111 8.143835 AGCTATTTAAAATGTTTGCTCAAGTGT 58.856 29.630 0.00 0.00 0.00 3.55
2019 3112 8.764287 GCTATTTAAAATGTTTGCTCAAGTGTT 58.236 29.630 0.00 0.00 0.00 3.32
2022 3115 8.539770 TTTAAAATGTTTGCTCAAGTGTTTGA 57.460 26.923 0.00 0.00 40.92 2.69
2023 3116 8.539770 TTAAAATGTTTGCTCAAGTGTTTGAA 57.460 26.923 0.00 0.00 42.48 2.69
2024 3117 6.407475 AAATGTTTGCTCAAGTGTTTGAAC 57.593 33.333 0.00 0.00 42.48 3.18
2025 3118 4.511617 TGTTTGCTCAAGTGTTTGAACA 57.488 36.364 0.00 0.00 42.48 3.18
2026 3119 4.876125 TGTTTGCTCAAGTGTTTGAACAA 58.124 34.783 0.00 2.89 43.77 2.83
2030 3123 5.384063 TGCTCAAGTGTTTGAACAAAAGA 57.616 34.783 1.47 0.00 42.48 2.52
2031 3124 5.160641 TGCTCAAGTGTTTGAACAAAAGAC 58.839 37.500 1.47 2.88 42.48 3.01
2038 3131 6.786207 AGTGTTTGAACAAAAGACTCTTAGC 58.214 36.000 1.47 0.00 46.48 3.09
2039 3132 5.677178 GTGTTTGAACAAAAGACTCTTAGCG 59.323 40.000 1.47 0.00 41.21 4.26
2040 3133 4.468095 TTGAACAAAAGACTCTTAGCGC 57.532 40.909 0.00 0.00 0.00 5.92
2041 3134 2.475111 TGAACAAAAGACTCTTAGCGCG 59.525 45.455 0.00 0.00 0.00 6.86
2042 3135 1.429463 ACAAAAGACTCTTAGCGCGG 58.571 50.000 8.83 0.00 0.00 6.46
2043 3136 0.721718 CAAAAGACTCTTAGCGCGGG 59.278 55.000 8.83 0.00 0.00 6.13
2044 3137 0.606604 AAAAGACTCTTAGCGCGGGA 59.393 50.000 8.83 0.31 0.00 5.14
2045 3138 0.108756 AAAGACTCTTAGCGCGGGAC 60.109 55.000 8.83 0.00 0.00 4.46
2046 3139 1.946475 AAGACTCTTAGCGCGGGACC 61.946 60.000 8.83 0.00 0.00 4.46
2047 3140 2.362632 ACTCTTAGCGCGGGACCT 60.363 61.111 8.83 0.00 0.00 3.85
2048 3141 1.946475 GACTCTTAGCGCGGGACCTT 61.946 60.000 8.83 0.00 0.00 3.50
2049 3142 1.218316 CTCTTAGCGCGGGACCTTT 59.782 57.895 8.83 0.00 0.00 3.11
2050 3143 0.391263 CTCTTAGCGCGGGACCTTTT 60.391 55.000 8.83 0.00 0.00 2.27
2051 3144 0.672401 TCTTAGCGCGGGACCTTTTG 60.672 55.000 8.83 0.00 0.00 2.44
2052 3145 0.953960 CTTAGCGCGGGACCTTTTGT 60.954 55.000 8.83 0.00 0.00 2.83
2053 3146 0.321021 TTAGCGCGGGACCTTTTGTA 59.679 50.000 8.83 0.00 0.00 2.41
2054 3147 0.321021 TAGCGCGGGACCTTTTGTAA 59.679 50.000 8.83 0.00 0.00 2.41
2055 3148 0.535553 AGCGCGGGACCTTTTGTAAA 60.536 50.000 8.83 0.00 0.00 2.01
2056 3149 0.386352 GCGCGGGACCTTTTGTAAAC 60.386 55.000 8.83 0.00 0.00 2.01
2057 3150 0.110554 CGCGGGACCTTTTGTAAACG 60.111 55.000 0.00 0.00 0.00 3.60
2058 3151 0.386352 GCGGGACCTTTTGTAAACGC 60.386 55.000 0.00 0.00 36.66 4.84
2059 3152 1.232119 CGGGACCTTTTGTAAACGCT 58.768 50.000 0.00 0.00 0.00 5.07
2060 3153 2.415776 CGGGACCTTTTGTAAACGCTA 58.584 47.619 0.00 0.00 0.00 4.26
2061 3154 3.004862 CGGGACCTTTTGTAAACGCTAT 58.995 45.455 0.00 0.00 0.00 2.97
2062 3155 4.183101 CGGGACCTTTTGTAAACGCTATA 58.817 43.478 0.00 0.00 0.00 1.31
2063 3156 4.269363 CGGGACCTTTTGTAAACGCTATAG 59.731 45.833 0.00 0.00 0.00 1.31
2064 3157 4.034858 GGGACCTTTTGTAAACGCTATAGC 59.965 45.833 15.09 15.09 37.78 2.97
2077 3170 2.476873 CTATAGCGTGCTATAGCGGG 57.523 55.000 27.04 14.28 46.26 6.13
2078 3171 0.454600 TATAGCGTGCTATAGCGGGC 59.545 55.000 24.45 24.45 45.83 6.13
2079 3172 3.227276 AGCGTGCTATAGCGGGCT 61.227 61.111 27.28 27.28 45.83 5.19
2080 3173 0.607217 TAGCGTGCTATAGCGGGCTA 60.607 55.000 30.39 30.39 45.80 3.93
2081 3174 1.215647 GCGTGCTATAGCGGGCTAT 59.784 57.895 24.52 16.61 45.83 2.97
2082 3175 0.389948 GCGTGCTATAGCGGGCTATT 60.390 55.000 24.52 3.74 45.83 1.73
2083 3176 1.939838 GCGTGCTATAGCGGGCTATTT 60.940 52.381 24.52 0.00 45.83 1.40
2084 3177 2.673043 GCGTGCTATAGCGGGCTATTTA 60.673 50.000 24.52 1.23 45.83 1.40
2085 3178 3.581755 CGTGCTATAGCGGGCTATTTAA 58.418 45.455 19.55 0.55 45.83 1.52
2086 3179 3.991773 CGTGCTATAGCGGGCTATTTAAA 59.008 43.478 19.55 0.21 45.83 1.52
2087 3180 4.449743 CGTGCTATAGCGGGCTATTTAAAA 59.550 41.667 19.55 0.00 45.83 1.52
2088 3181 5.614013 CGTGCTATAGCGGGCTATTTAAAAC 60.614 44.000 19.55 6.59 45.83 2.43
2089 3182 4.758165 TGCTATAGCGGGCTATTTAAAACC 59.242 41.667 19.55 0.00 45.83 3.27
2090 3183 4.758165 GCTATAGCGGGCTATTTAAAACCA 59.242 41.667 17.49 0.00 39.65 3.67
2091 3184 5.414765 GCTATAGCGGGCTATTTAAAACCAT 59.585 40.000 17.49 0.00 39.65 3.55
2092 3185 5.705609 ATAGCGGGCTATTTAAAACCATG 57.294 39.130 7.36 0.00 35.92 3.66
2102 3195 6.371271 GCTATTTAAAACCATGGTTGTGCATT 59.629 34.615 30.44 21.37 38.47 3.56
2153 3246 4.382362 GCCTTGTATAGTTAAGGTCGTGGT 60.382 45.833 0.00 0.00 44.21 4.16
2181 3276 8.382875 CACCTTTGTACATCATATATACATGCG 58.617 37.037 0.00 0.00 0.00 4.73
2205 3300 4.823790 TGCACATGAGCAATACATCATC 57.176 40.909 15.81 0.00 42.46 2.92
2259 3356 1.829849 GGTTCTAACCCTAGCTTCCGT 59.170 52.381 0.00 0.00 43.43 4.69
2262 3359 0.384669 CTAACCCTAGCTTCCGTCCG 59.615 60.000 0.00 0.00 0.00 4.79
2263 3360 1.669999 TAACCCTAGCTTCCGTCCGC 61.670 60.000 0.00 0.00 0.00 5.54
2264 3361 4.222847 CCCTAGCTTCCGTCCGCC 62.223 72.222 0.00 0.00 0.00 6.13
2265 3362 4.570663 CCTAGCTTCCGTCCGCCG 62.571 72.222 0.00 0.00 0.00 6.46
2266 3363 3.823330 CTAGCTTCCGTCCGCCGT 61.823 66.667 0.00 0.00 33.66 5.68
2443 3616 4.383861 CTCAGCTGCACCCGAGCA 62.384 66.667 9.47 0.00 43.35 4.26
2512 3717 2.933834 CCGAACCCCTCCCCAAGT 60.934 66.667 0.00 0.00 0.00 3.16
2514 3719 2.526046 CGAACCCCTCCCCAAGTGT 61.526 63.158 0.00 0.00 0.00 3.55
2523 3728 2.034066 CCCAAGTGTCACCGCCAT 59.966 61.111 0.00 0.00 0.00 4.40
2576 3952 4.856801 CCTAACCCGCGCCATGCT 62.857 66.667 0.00 0.00 43.27 3.79
2704 4096 1.677966 CGGTTCGTCTCTCCCAGGA 60.678 63.158 0.00 0.00 0.00 3.86
2753 4145 1.263356 ATTTCTCCCTCGTGTTCCGA 58.737 50.000 0.00 0.00 45.00 4.55
2801 4193 1.965754 GCTCCATCGACTCCAGCCTT 61.966 60.000 0.00 0.00 0.00 4.35
2821 4213 1.272816 TGTCCCCGAGTTCCATGACTA 60.273 52.381 0.00 0.00 0.00 2.59
2822 4214 1.829222 GTCCCCGAGTTCCATGACTAA 59.171 52.381 0.00 0.00 0.00 2.24
2877 4270 2.027625 CTCACCACTTTCGCCGGAC 61.028 63.158 5.05 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.666274 ACACCACGTGCGTACATCTG 60.666 55.000 10.91 0.00 36.98 2.90
27 28 0.032952 AACACCACGTGCGTACATCT 59.967 50.000 10.91 0.00 36.98 2.90
154 155 1.210967 CCACCGCCAAATACCTTCCTA 59.789 52.381 0.00 0.00 0.00 2.94
155 156 0.034477 CCACCGCCAAATACCTTCCT 60.034 55.000 0.00 0.00 0.00 3.36
158 159 0.988832 TCTCCACCGCCAAATACCTT 59.011 50.000 0.00 0.00 0.00 3.50
163 164 1.153168 CGGATCTCCACCGCCAAAT 60.153 57.895 0.00 0.00 43.74 2.32
202 203 3.467803 GAGCACCTGCCTATAATTCGTT 58.532 45.455 0.00 0.00 43.38 3.85
205 206 2.417719 CCGAGCACCTGCCTATAATTC 58.582 52.381 0.00 0.00 43.38 2.17
208 217 1.048724 AGCCGAGCACCTGCCTATAA 61.049 55.000 0.00 0.00 43.38 0.98
211 220 3.003173 AAGCCGAGCACCTGCCTA 61.003 61.111 0.00 0.00 43.38 3.93
253 264 0.320771 GGATAGATCCCGCAACGCAT 60.321 55.000 0.00 0.00 41.20 4.73
258 269 2.437651 TGAACATGGATAGATCCCGCAA 59.562 45.455 6.09 0.00 46.59 4.85
270 281 6.568869 CCTTTTGTTACAAACTGAACATGGA 58.431 36.000 10.28 0.00 35.57 3.41
279 290 6.769134 ACAACTAGCCTTTTGTTACAAACT 57.231 33.333 10.28 7.27 31.78 2.66
323 337 4.333926 GTCTCCATGTTTCTGCAACTATCC 59.666 45.833 0.00 0.00 36.21 2.59
325 339 3.935203 CGTCTCCATGTTTCTGCAACTAT 59.065 43.478 0.00 0.00 36.21 2.12
366 382 9.757227 GTACTTTAGATGCAGTCTTTATCAGAT 57.243 33.333 0.00 0.00 38.42 2.90
385 401 0.733566 CGCCGCTTCCGTGTACTTTA 60.734 55.000 0.00 0.00 0.00 1.85
386 402 2.025418 CGCCGCTTCCGTGTACTTT 61.025 57.895 0.00 0.00 0.00 2.66
388 404 4.430765 CCGCCGCTTCCGTGTACT 62.431 66.667 0.00 0.00 0.00 2.73
429 445 5.477607 TTATGAGAACGTTTCCCTTCAGA 57.522 39.130 0.46 0.00 0.00 3.27
511 530 2.797156 GGATTGAATGTCATCCGACTCG 59.203 50.000 0.00 0.00 43.06 4.18
513 532 2.158755 GGGGATTGAATGTCATCCGACT 60.159 50.000 0.00 0.00 43.06 4.18
552 571 5.515008 GGAAGAATCACCCAAAGAACTAGGT 60.515 44.000 0.00 0.00 0.00 3.08
575 594 4.265073 AGGTCCGATTCTCAAGATTTTGG 58.735 43.478 0.00 0.00 34.97 3.28
578 597 4.143986 GGAGGTCCGATTCTCAAGATTT 57.856 45.455 0.00 0.00 0.00 2.17
600 620 6.018751 GGTTCAAAATTTTGAGAGAAGTTGGC 60.019 38.462 27.52 12.20 46.68 4.52
638 659 4.142790 CGAAGGGAGTAGCTAGGATTGTA 58.857 47.826 0.00 0.00 0.00 2.41
688 709 4.313522 GAGCATCTTTTGACACTACACG 57.686 45.455 0.00 0.00 0.00 4.49
790 813 4.749976 AGAATCGAACCTTCACTTAGCTC 58.250 43.478 0.00 0.00 0.00 4.09
793 816 8.934507 ATCTTAAGAATCGAACCTTCACTTAG 57.065 34.615 9.71 0.00 0.00 2.18
795 818 8.622948 AAATCTTAAGAATCGAACCTTCACTT 57.377 30.769 9.71 0.00 0.00 3.16
820 843 5.313712 AGTTCTTTTGGCCGATTCTTCTAA 58.686 37.500 0.00 0.00 0.00 2.10
848 1893 0.740868 CGACCGGCATCATGACAAGT 60.741 55.000 0.00 0.00 0.00 3.16
910 1955 0.400594 GCACCCTTGGGAGTACAAGT 59.599 55.000 13.39 0.00 44.89 3.16
1245 2313 0.758685 CCACCTGGAAAAAGCCCACA 60.759 55.000 0.00 0.00 37.39 4.17
1284 2352 0.179111 GCATCTCCGACATGACCGAA 60.179 55.000 0.00 0.00 0.00 4.30
1378 2446 2.034048 TTGCTGTGGTACCTCACGCA 62.034 55.000 24.55 24.55 41.45 5.24
1602 2695 2.357517 AAGGCAGCCGACTTCGTG 60.358 61.111 5.55 0.00 34.33 4.35
1606 2699 2.348998 CCTCAAGGCAGCCGACTT 59.651 61.111 5.55 0.00 43.21 3.01
1607 2700 3.710722 CCCTCAAGGCAGCCGACT 61.711 66.667 5.55 0.00 0.00 4.18
1608 2701 4.785453 CCCCTCAAGGCAGCCGAC 62.785 72.222 5.55 0.00 0.00 4.79
1701 2794 1.006571 GCACCTTCAGGAACGACGA 60.007 57.895 0.00 0.00 38.94 4.20
1706 2799 2.723501 TGGAGGAGCACCTTCAGGAAC 61.724 57.143 7.14 0.00 46.01 3.62
1742 2835 1.915266 CCAGTGGAGCACCTGGAGA 60.915 63.158 1.68 0.00 35.92 3.71
1768 2861 2.685017 AGACCGGCTGCTCATCCA 60.685 61.111 0.00 0.00 0.00 3.41
1810 2903 1.319374 CGATGTTGACGATAAACGCGT 59.681 47.619 5.58 5.58 46.94 6.01
1817 2910 0.736636 AGTCGCCGATGTTGACGATA 59.263 50.000 0.00 0.00 37.69 2.92
1827 2920 1.153549 GCTGAAGGAAGTCGCCGAT 60.154 57.895 0.00 0.00 0.00 4.18
1856 2949 0.320374 CCACGCTCCTGAACCTAACA 59.680 55.000 0.00 0.00 0.00 2.41
1858 2951 0.895530 CTCCACGCTCCTGAACCTAA 59.104 55.000 0.00 0.00 0.00 2.69
1859 2952 0.251653 ACTCCACGCTCCTGAACCTA 60.252 55.000 0.00 0.00 0.00 3.08
1878 2971 1.835494 CTCTTGGAGAGGACACGGTA 58.165 55.000 0.00 0.00 38.67 4.02
1902 2995 6.205784 GCTATTTAAAACTCTGTGCACAACA 58.794 36.000 21.98 9.47 37.22 3.33
1903 2996 5.339611 CGCTATTTAAAACTCTGTGCACAAC 59.660 40.000 21.98 0.00 0.00 3.32
1904 2997 5.448438 CGCTATTTAAAACTCTGTGCACAA 58.552 37.500 21.98 10.91 0.00 3.33
1905 2998 4.612712 GCGCTATTTAAAACTCTGTGCACA 60.613 41.667 20.37 20.37 0.00 4.57
1906 2999 3.846335 GCGCTATTTAAAACTCTGTGCAC 59.154 43.478 10.75 10.75 0.00 4.57
1907 3000 3.424302 CGCGCTATTTAAAACTCTGTGCA 60.424 43.478 5.56 0.00 0.00 4.57
1908 3001 3.091417 CGCGCTATTTAAAACTCTGTGC 58.909 45.455 5.56 0.00 0.00 4.57
1909 3002 3.091417 GCGCGCTATTTAAAACTCTGTG 58.909 45.455 26.67 0.00 0.00 3.66
1910 3003 3.000727 AGCGCGCTATTTAAAACTCTGT 58.999 40.909 35.79 1.11 0.00 3.41
1911 3004 3.658351 AGCGCGCTATTTAAAACTCTG 57.342 42.857 35.79 0.00 0.00 3.35
1912 3005 4.260253 GCTTAGCGCGCTATTTAAAACTCT 60.260 41.667 38.51 13.72 0.00 3.24
1913 3006 3.960621 GCTTAGCGCGCTATTTAAAACTC 59.039 43.478 38.51 14.58 0.00 3.01
1914 3007 3.242641 GGCTTAGCGCGCTATTTAAAACT 60.243 43.478 38.51 14.50 40.44 2.66
1915 3008 3.033873 GGCTTAGCGCGCTATTTAAAAC 58.966 45.455 38.51 21.47 40.44 2.43
1916 3009 2.940410 AGGCTTAGCGCGCTATTTAAAA 59.060 40.909 38.51 24.43 40.44 1.52
1917 3010 2.542595 GAGGCTTAGCGCGCTATTTAAA 59.457 45.455 38.51 25.16 40.44 1.52
1918 3011 2.132762 GAGGCTTAGCGCGCTATTTAA 58.867 47.619 38.51 25.53 40.44 1.52
1919 3012 1.604693 GGAGGCTTAGCGCGCTATTTA 60.605 52.381 38.51 24.25 40.44 1.40
1920 3013 0.880718 GGAGGCTTAGCGCGCTATTT 60.881 55.000 38.51 24.06 40.44 1.40
1921 3014 1.301009 GGAGGCTTAGCGCGCTATT 60.301 57.895 38.51 24.39 40.44 1.73
1922 3015 0.894184 TAGGAGGCTTAGCGCGCTAT 60.894 55.000 38.51 25.42 40.44 2.97
1923 3016 1.516365 CTAGGAGGCTTAGCGCGCTA 61.516 60.000 35.48 35.48 40.44 4.26
1924 3017 2.833582 TAGGAGGCTTAGCGCGCT 60.834 61.111 38.01 38.01 40.44 5.92
1925 3018 2.355244 CTAGGAGGCTTAGCGCGC 60.355 66.667 26.66 26.66 40.44 6.86
1926 3019 2.355244 GCTAGGAGGCTTAGCGCG 60.355 66.667 0.00 0.00 40.44 6.86
1936 3029 3.597728 GAGGTCCGCCGCTAGGAG 61.598 72.222 0.00 0.00 41.02 3.69
1937 3030 3.657038 AAGAGGTCCGCCGCTAGGA 62.657 63.158 0.00 0.00 44.34 2.94
1938 3031 2.630592 GAAAGAGGTCCGCCGCTAGG 62.631 65.000 0.00 0.00 44.34 3.02
1939 3032 1.227002 GAAAGAGGTCCGCCGCTAG 60.227 63.158 0.00 0.00 44.34 3.42
1940 3033 1.537814 TTGAAAGAGGTCCGCCGCTA 61.538 55.000 0.00 0.00 44.34 4.26
1942 3035 1.305930 ATTTGAAAGAGGTCCGCCGC 61.306 55.000 0.00 0.00 40.50 6.53
1943 3036 0.447801 CATTTGAAAGAGGTCCGCCG 59.552 55.000 0.00 0.00 40.50 6.46
1944 3037 0.171231 GCATTTGAAAGAGGTCCGCC 59.829 55.000 0.00 0.00 0.00 6.13
1945 3038 1.168714 AGCATTTGAAAGAGGTCCGC 58.831 50.000 0.00 0.00 0.00 5.54
1946 3039 4.212214 GCTATAGCATTTGAAAGAGGTCCG 59.788 45.833 20.01 0.00 41.59 4.79
1947 3040 4.212214 CGCTATAGCATTTGAAAGAGGTCC 59.788 45.833 23.99 0.00 42.21 4.46
1948 3041 4.811557 ACGCTATAGCATTTGAAAGAGGTC 59.188 41.667 23.99 0.00 42.21 3.85
1949 3042 4.572389 CACGCTATAGCATTTGAAAGAGGT 59.428 41.667 23.99 6.60 42.21 3.85
1950 3043 4.553547 GCACGCTATAGCATTTGAAAGAGG 60.554 45.833 23.99 5.98 42.21 3.69
1951 3044 4.272018 AGCACGCTATAGCATTTGAAAGAG 59.728 41.667 23.99 6.48 42.21 2.85
1952 3045 4.191544 AGCACGCTATAGCATTTGAAAGA 58.808 39.130 23.99 0.00 42.21 2.52
1953 3046 4.542662 AGCACGCTATAGCATTTGAAAG 57.457 40.909 23.99 7.87 42.21 2.62
1954 3047 7.351414 CTATAGCACGCTATAGCATTTGAAA 57.649 36.000 25.42 9.51 46.26 2.69
1955 3048 6.951256 CTATAGCACGCTATAGCATTTGAA 57.049 37.500 25.42 9.81 46.26 2.69
1983 3076 9.107367 CAAACATTTTAAATAGCTCGCTATAGC 57.893 33.333 15.09 15.09 43.11 2.97
1984 3077 9.107367 GCAAACATTTTAAATAGCTCGCTATAG 57.893 33.333 11.49 0.00 38.20 1.31
1985 3078 8.836413 AGCAAACATTTTAAATAGCTCGCTATA 58.164 29.630 11.49 0.00 38.20 1.31
1986 3079 7.707104 AGCAAACATTTTAAATAGCTCGCTAT 58.293 30.769 5.63 5.63 40.63 2.97
1987 3080 7.083875 AGCAAACATTTTAAATAGCTCGCTA 57.916 32.000 0.53 0.53 0.00 4.26
1988 3081 5.954335 AGCAAACATTTTAAATAGCTCGCT 58.046 33.333 0.00 0.00 0.00 4.93
1989 3082 6.248201 GAGCAAACATTTTAAATAGCTCGC 57.752 37.500 13.51 4.83 38.00 5.03
1991 3084 8.642020 CACTTGAGCAAACATTTTAAATAGCTC 58.358 33.333 18.09 18.09 45.40 4.09
1992 3085 8.143835 ACACTTGAGCAAACATTTTAAATAGCT 58.856 29.630 0.00 0.00 0.00 3.32
1993 3086 8.298030 ACACTTGAGCAAACATTTTAAATAGC 57.702 30.769 0.00 0.00 0.00 2.97
1996 3089 9.160496 TCAAACACTTGAGCAAACATTTTAAAT 57.840 25.926 0.00 0.00 36.62 1.40
1997 3090 8.539770 TCAAACACTTGAGCAAACATTTTAAA 57.460 26.923 0.00 0.00 36.62 1.52
1998 3091 8.439286 GTTCAAACACTTGAGCAAACATTTTAA 58.561 29.630 0.00 0.00 42.48 1.52
1999 3092 7.600375 TGTTCAAACACTTGAGCAAACATTTTA 59.400 29.630 2.42 0.00 46.13 1.52
2000 3093 6.426328 TGTTCAAACACTTGAGCAAACATTTT 59.574 30.769 2.42 0.00 46.13 1.82
2001 3094 5.931146 TGTTCAAACACTTGAGCAAACATTT 59.069 32.000 2.42 0.00 46.13 2.32
2002 3095 5.477510 TGTTCAAACACTTGAGCAAACATT 58.522 33.333 2.42 0.00 46.13 2.71
2003 3096 5.070770 TGTTCAAACACTTGAGCAAACAT 57.929 34.783 2.42 0.00 46.13 2.71
2004 3097 4.511617 TGTTCAAACACTTGAGCAAACA 57.488 36.364 2.42 0.00 46.13 2.83
2009 3102 5.402398 AGTCTTTTGTTCAAACACTTGAGC 58.598 37.500 0.00 0.00 42.48 4.26
2010 3103 6.846350 AGAGTCTTTTGTTCAAACACTTGAG 58.154 36.000 0.00 0.62 42.48 3.02
2011 3104 6.817765 AGAGTCTTTTGTTCAAACACTTGA 57.182 33.333 0.00 0.00 39.87 3.02
2012 3105 7.218963 GCTAAGAGTCTTTTGTTCAAACACTTG 59.781 37.037 11.40 0.00 38.92 3.16
2013 3106 7.251281 GCTAAGAGTCTTTTGTTCAAACACTT 58.749 34.615 11.40 6.95 38.92 3.16
2014 3107 6.456988 CGCTAAGAGTCTTTTGTTCAAACACT 60.457 38.462 11.40 8.10 38.92 3.55
2015 3108 5.677178 CGCTAAGAGTCTTTTGTTCAAACAC 59.323 40.000 11.40 0.00 38.92 3.32
2016 3109 5.729454 GCGCTAAGAGTCTTTTGTTCAAACA 60.729 40.000 11.40 0.00 37.08 2.83
2017 3110 4.671068 GCGCTAAGAGTCTTTTGTTCAAAC 59.329 41.667 11.40 0.00 0.00 2.93
2018 3111 4.551990 CGCGCTAAGAGTCTTTTGTTCAAA 60.552 41.667 11.40 0.00 0.00 2.69
2019 3112 3.059868 CGCGCTAAGAGTCTTTTGTTCAA 60.060 43.478 11.40 0.00 0.00 2.69
2020 3113 2.475111 CGCGCTAAGAGTCTTTTGTTCA 59.525 45.455 11.40 0.00 0.00 3.18
2021 3114 2.159827 CCGCGCTAAGAGTCTTTTGTTC 60.160 50.000 11.40 0.00 0.00 3.18
2022 3115 1.798813 CCGCGCTAAGAGTCTTTTGTT 59.201 47.619 11.40 0.00 0.00 2.83
2023 3116 1.429463 CCGCGCTAAGAGTCTTTTGT 58.571 50.000 11.40 0.00 0.00 2.83
2024 3117 0.721718 CCCGCGCTAAGAGTCTTTTG 59.278 55.000 11.40 6.00 0.00 2.44
2025 3118 0.606604 TCCCGCGCTAAGAGTCTTTT 59.393 50.000 11.40 0.00 0.00 2.27
2026 3119 0.108756 GTCCCGCGCTAAGAGTCTTT 60.109 55.000 11.40 0.00 0.00 2.52
2027 3120 1.511768 GTCCCGCGCTAAGAGTCTT 59.488 57.895 10.87 10.87 0.00 3.01
2028 3121 2.416432 GGTCCCGCGCTAAGAGTCT 61.416 63.158 5.56 0.00 0.00 3.24
2029 3122 1.946475 AAGGTCCCGCGCTAAGAGTC 61.946 60.000 5.56 0.00 0.00 3.36
2030 3123 1.542187 AAAGGTCCCGCGCTAAGAGT 61.542 55.000 5.56 0.00 0.00 3.24
2031 3124 0.391263 AAAAGGTCCCGCGCTAAGAG 60.391 55.000 5.56 0.00 0.00 2.85
2032 3125 0.672401 CAAAAGGTCCCGCGCTAAGA 60.672 55.000 5.56 0.00 0.00 2.10
2033 3126 0.953960 ACAAAAGGTCCCGCGCTAAG 60.954 55.000 5.56 0.00 0.00 2.18
2034 3127 0.321021 TACAAAAGGTCCCGCGCTAA 59.679 50.000 5.56 0.00 0.00 3.09
2035 3128 0.321021 TTACAAAAGGTCCCGCGCTA 59.679 50.000 5.56 0.00 0.00 4.26
2036 3129 0.535553 TTTACAAAAGGTCCCGCGCT 60.536 50.000 5.56 0.00 0.00 5.92
2037 3130 0.386352 GTTTACAAAAGGTCCCGCGC 60.386 55.000 0.00 0.00 0.00 6.86
2038 3131 0.110554 CGTTTACAAAAGGTCCCGCG 60.111 55.000 0.00 0.00 0.00 6.46
2039 3132 0.386352 GCGTTTACAAAAGGTCCCGC 60.386 55.000 0.00 0.00 34.43 6.13
2040 3133 1.232119 AGCGTTTACAAAAGGTCCCG 58.768 50.000 0.00 0.00 0.00 5.14
2041 3134 4.034858 GCTATAGCGTTTACAAAAGGTCCC 59.965 45.833 9.40 0.00 31.10 4.46
2042 3135 5.152923 GCTATAGCGTTTACAAAAGGTCC 57.847 43.478 9.40 0.00 31.10 4.46
2059 3152 0.454600 GCCCGCTATAGCACGCTATA 59.545 55.000 23.99 15.99 42.21 1.31
2060 3153 1.215647 GCCCGCTATAGCACGCTAT 59.784 57.895 23.99 15.45 42.21 2.97
2061 3154 0.607217 TAGCCCGCTATAGCACGCTA 60.607 55.000 27.03 27.03 42.62 4.26
2062 3155 1.251527 ATAGCCCGCTATAGCACGCT 61.252 55.000 28.61 28.61 44.18 5.07
2063 3156 0.389948 AATAGCCCGCTATAGCACGC 60.390 55.000 23.99 21.92 42.21 5.34
2064 3157 2.080286 AAATAGCCCGCTATAGCACG 57.920 50.000 23.99 13.71 42.21 5.34
2065 3158 5.334646 GGTTTTAAATAGCCCGCTATAGCAC 60.335 44.000 23.99 12.65 42.21 4.40
2066 3159 4.758165 GGTTTTAAATAGCCCGCTATAGCA 59.242 41.667 23.99 4.83 42.21 3.49
2067 3160 4.758165 TGGTTTTAAATAGCCCGCTATAGC 59.242 41.667 15.09 15.09 38.20 2.97
2068 3161 6.128007 CCATGGTTTTAAATAGCCCGCTATAG 60.128 42.308 9.56 0.00 38.20 1.31
2069 3162 5.708230 CCATGGTTTTAAATAGCCCGCTATA 59.292 40.000 9.56 0.00 38.20 1.31
2070 3163 4.522789 CCATGGTTTTAAATAGCCCGCTAT 59.477 41.667 2.57 3.31 40.63 2.97
2071 3164 3.886505 CCATGGTTTTAAATAGCCCGCTA 59.113 43.478 2.57 0.00 0.00 4.26
2072 3165 2.693074 CCATGGTTTTAAATAGCCCGCT 59.307 45.455 2.57 0.00 0.00 5.52
2073 3166 2.429250 ACCATGGTTTTAAATAGCCCGC 59.571 45.455 13.00 0.00 0.00 6.13
2074 3167 4.081917 ACAACCATGGTTTTAAATAGCCCG 60.082 41.667 27.82 13.72 36.00 6.13
2075 3168 5.175127 CACAACCATGGTTTTAAATAGCCC 58.825 41.667 27.82 0.00 36.00 5.19
2076 3169 4.629634 GCACAACCATGGTTTTAAATAGCC 59.370 41.667 27.82 5.97 36.00 3.93
2077 3170 5.233988 TGCACAACCATGGTTTTAAATAGC 58.766 37.500 27.82 19.36 36.00 2.97
2078 3171 7.903995 AATGCACAACCATGGTTTTAAATAG 57.096 32.000 27.82 16.37 36.00 1.73
2079 3172 8.589338 AGTAATGCACAACCATGGTTTTAAATA 58.411 29.630 27.82 13.32 36.00 1.40
2080 3173 7.387397 CAGTAATGCACAACCATGGTTTTAAAT 59.613 33.333 27.82 15.63 36.00 1.40
2081 3174 6.703607 CAGTAATGCACAACCATGGTTTTAAA 59.296 34.615 27.82 14.06 36.00 1.52
2082 3175 6.183360 ACAGTAATGCACAACCATGGTTTTAA 60.183 34.615 27.82 13.37 36.00 1.52
2083 3176 5.303078 ACAGTAATGCACAACCATGGTTTTA 59.697 36.000 27.82 19.08 36.00 1.52
2084 3177 4.100808 ACAGTAATGCACAACCATGGTTTT 59.899 37.500 27.82 19.25 36.00 2.43
2085 3178 3.640967 ACAGTAATGCACAACCATGGTTT 59.359 39.130 27.82 14.52 36.00 3.27
2086 3179 3.005684 CACAGTAATGCACAACCATGGTT 59.994 43.478 24.86 24.86 39.13 3.67
2087 3180 2.557924 CACAGTAATGCACAACCATGGT 59.442 45.455 13.00 13.00 0.00 3.55
2088 3181 2.557924 ACACAGTAATGCACAACCATGG 59.442 45.455 11.19 11.19 0.00 3.66
2089 3182 3.921119 ACACAGTAATGCACAACCATG 57.079 42.857 0.00 0.00 0.00 3.66
2090 3183 5.105797 CCAATACACAGTAATGCACAACCAT 60.106 40.000 0.00 0.00 0.00 3.55
2091 3184 4.217334 CCAATACACAGTAATGCACAACCA 59.783 41.667 0.00 0.00 0.00 3.67
2092 3185 4.380444 CCCAATACACAGTAATGCACAACC 60.380 45.833 0.00 0.00 0.00 3.77
2102 3195 2.438021 GAGATGGGCCCAATACACAGTA 59.562 50.000 32.58 0.00 0.00 2.74
2153 3246 9.942850 CATGTATATATGATGTACAAAGGTGGA 57.057 33.333 0.00 0.00 39.70 4.02
2205 3300 9.452287 TGATACCATGTATGATGTATGAATTGG 57.548 33.333 0.00 0.00 0.00 3.16
2338 3477 2.364448 GGGAGAGGAAGAGGCGGT 60.364 66.667 0.00 0.00 0.00 5.68
2364 3504 3.477346 GGTACGGAAGGGGGAGCC 61.477 72.222 0.00 0.00 0.00 4.70
2443 3616 4.643387 GAGTTGGGTGGCGGCAGT 62.643 66.667 13.91 0.00 0.00 4.40
2509 3714 2.351276 GGGATGGCGGTGACACTT 59.649 61.111 5.39 0.00 0.00 3.16
2512 3717 3.770040 CTCGGGATGGCGGTGACA 61.770 66.667 0.00 0.00 0.00 3.58
2547 3911 1.073548 GGTTAGGGTTTGGTGCGGA 59.926 57.895 0.00 0.00 0.00 5.54
2576 3952 3.138798 GCGGCTAGGGTCGTCTCA 61.139 66.667 0.00 0.00 43.14 3.27
2580 3956 3.849951 CATGGCGGCTAGGGTCGT 61.850 66.667 11.43 0.00 43.14 4.34
2723 4115 3.068307 CGAGGGAGAAATACGTCTTCCAT 59.932 47.826 0.00 0.00 44.95 3.41
2753 4145 3.500299 CGTGATCGATGAGATGGTACTCT 59.500 47.826 0.54 0.00 40.26 3.24
2801 4193 0.544357 AGTCATGGAACTCGGGGACA 60.544 55.000 0.00 0.00 0.00 4.02
2821 4213 0.391130 CGTGGTGTCGATGGTGGATT 60.391 55.000 0.00 0.00 0.00 3.01
2822 4214 1.218047 CGTGGTGTCGATGGTGGAT 59.782 57.895 0.00 0.00 0.00 3.41
2867 4259 1.004200 GAAAGAGGGTCCGGCGAAA 60.004 57.895 9.30 0.00 0.00 3.46
2868 4260 2.167398 CTGAAAGAGGGTCCGGCGAA 62.167 60.000 9.30 0.00 34.07 4.70


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

AutoCloner maintained by Alex Coulton.