Multiple sequence alignment - TraesCS2D01G572300

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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 TraesCS2D01G572300 chr2D 100.000 2435 0 0 1 2435 638311137 638308703 0.000000e+00 4497.0
1 TraesCS2D01G572300 chr2D 77.339 684 104 32 42 679 147115744 147116422 8.280000e-95 357.0
2 TraesCS2D01G572300 chr2D 76.724 696 97 44 1 678 650771843 650771195 6.490000e-86 327.0
3 TraesCS2D01G572300 chr2D 82.682 358 37 14 1297 1638 638256574 638256226 6.580000e-76 294.0
4 TraesCS2D01G572300 chr2D 100.000 28 0 0 2106 2133 638308924 638308897 4.000000e-03 52.8
5 TraesCS2D01G572300 chr2D 100.000 28 0 0 2214 2241 638309032 638309005 4.000000e-03 52.8
6 TraesCS2D01G572300 chr2A 92.888 1392 55 18 852 2222 764008789 764010157 0.000000e+00 1982.0
7 TraesCS2D01G572300 chr2A 77.182 653 110 23 54 680 699604356 699604995 6.450000e-91 344.0
8 TraesCS2D01G572300 chr2B 86.930 834 52 32 852 1662 797127143 797126344 0.000000e+00 883.0
9 TraesCS2D01G572300 chr2B 80.372 698 107 16 1 675 148049002 148048312 1.000000e-138 503.0
10 TraesCS2D01G572300 chr2B 85.027 187 20 2 1923 2105 797125972 797125790 1.490000e-42 183.0
11 TraesCS2D01G572300 chr3D 81.924 686 96 18 1 665 296159054 296159732 2.740000e-154 555.0
12 TraesCS2D01G572300 chr5A 79.161 715 103 27 1 677 479654723 479655429 1.030000e-123 453.0
13 TraesCS2D01G572300 chr5A 78.764 631 109 17 52 665 47776584 47777206 1.360000e-107 399.0
14 TraesCS2D01G572300 chr5A 83.824 408 41 15 284 679 640320007 640319613 4.950000e-97 364.0
15 TraesCS2D01G572300 chr5A 77.507 698 86 40 1 677 401506778 401506131 1.070000e-93 353.0
16 TraesCS2D01G572300 chr5A 77.119 708 101 36 1 675 585211646 585212325 1.070000e-93 353.0
17 TraesCS2D01G572300 chr5A 75.246 711 100 36 1 678 482492002 482491335 3.990000e-68 268.0
18 TraesCS2D01G572300 chr5A 90.265 113 9 2 713 825 631515918 631516028 1.950000e-31 147.0
19 TraesCS2D01G572300 chr5A 81.818 99 11 6 707 803 3872651 3872558 2.600000e-10 76.8
20 TraesCS2D01G572300 chr3B 79.196 721 90 36 1 677 530607890 530608594 1.720000e-121 446.0
21 TraesCS2D01G572300 chr4B 78.622 711 108 22 2 675 184232111 184231408 4.810000e-117 431.0
22 TraesCS2D01G572300 chr1A 76.250 720 104 43 1 685 461057538 461056851 1.090000e-83 320.0
23 TraesCS2D01G572300 chr7A 77.250 611 74 37 1 579 539397088 539397665 5.090000e-77 298.0
24 TraesCS2D01G572300 chr7A 79.211 380 61 12 304 677 84708778 84708411 5.200000e-62 248.0
25 TraesCS2D01G572300 chr7D 80.366 382 54 15 7 375 494963945 494963572 1.110000e-68 270.0
26 TraesCS2D01G572300 chr5D 80.925 346 50 10 339 678 493275857 493275522 2.400000e-65 259.0
27 TraesCS2D01G572300 chr3A 75.276 635 107 31 71 675 666011817 666011203 8.640000e-65 257.0


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 TraesCS2D01G572300 chr2D 638308703 638311137 2434 True 1534.2 4497 100.0000 1 2435 3 chr2D.!!$R3 2434
1 TraesCS2D01G572300 chr2D 147115744 147116422 678 False 357.0 357 77.3390 42 679 1 chr2D.!!$F1 637
2 TraesCS2D01G572300 chr2D 650771195 650771843 648 True 327.0 327 76.7240 1 678 1 chr2D.!!$R2 677
3 TraesCS2D01G572300 chr2A 764008789 764010157 1368 False 1982.0 1982 92.8880 852 2222 1 chr2A.!!$F2 1370
4 TraesCS2D01G572300 chr2A 699604356 699604995 639 False 344.0 344 77.1820 54 680 1 chr2A.!!$F1 626
5 TraesCS2D01G572300 chr2B 797125790 797127143 1353 True 533.0 883 85.9785 852 2105 2 chr2B.!!$R2 1253
6 TraesCS2D01G572300 chr2B 148048312 148049002 690 True 503.0 503 80.3720 1 675 1 chr2B.!!$R1 674
7 TraesCS2D01G572300 chr3D 296159054 296159732 678 False 555.0 555 81.9240 1 665 1 chr3D.!!$F1 664
8 TraesCS2D01G572300 chr5A 479654723 479655429 706 False 453.0 453 79.1610 1 677 1 chr5A.!!$F2 676
9 TraesCS2D01G572300 chr5A 47776584 47777206 622 False 399.0 399 78.7640 52 665 1 chr5A.!!$F1 613
10 TraesCS2D01G572300 chr5A 401506131 401506778 647 True 353.0 353 77.5070 1 677 1 chr5A.!!$R2 676
11 TraesCS2D01G572300 chr5A 585211646 585212325 679 False 353.0 353 77.1190 1 675 1 chr5A.!!$F3 674
12 TraesCS2D01G572300 chr5A 482491335 482492002 667 True 268.0 268 75.2460 1 678 1 chr5A.!!$R3 677
13 TraesCS2D01G572300 chr3B 530607890 530608594 704 False 446.0 446 79.1960 1 677 1 chr3B.!!$F1 676
14 TraesCS2D01G572300 chr4B 184231408 184232111 703 True 431.0 431 78.6220 2 675 1 chr4B.!!$R1 673
15 TraesCS2D01G572300 chr1A 461056851 461057538 687 True 320.0 320 76.2500 1 685 1 chr1A.!!$R1 684
16 TraesCS2D01G572300 chr7A 539397088 539397665 577 False 298.0 298 77.2500 1 579 1 chr7A.!!$F1 578
17 TraesCS2D01G572300 chr3A 666011203 666011817 614 True 257.0 257 75.2760 71 675 1 chr3A.!!$R1 604

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
596 734 0.110373 AAAGCGGAATCGAACGTTGC 60.11 50.0 5.0 0.0 39.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2012 0.040157 TGCAGTGCAAACAATCTCGC 60.04 50.0 17.26 0.0 34.76 5.03 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
98 116 2.506438 GACCGGAGTAGTGCGTGC 60.506 66.667 9.46 0.00 35.36 5.34
212 235 3.123620 CTGGCAAGCACCTCGAGC 61.124 66.667 6.99 0.00 0.00 5.03
412 511 4.322385 GCGCCGCCTCGTTGTTTT 62.322 61.111 0.00 0.00 0.00 2.43
413 512 2.957052 GCGCCGCCTCGTTGTTTTA 61.957 57.895 0.00 0.00 0.00 1.52
414 513 1.570475 CGCCGCCTCGTTGTTTTAA 59.430 52.632 0.00 0.00 0.00 1.52
415 514 0.452122 CGCCGCCTCGTTGTTTTAAG 60.452 55.000 0.00 0.00 0.00 1.85
416 515 0.589708 GCCGCCTCGTTGTTTTAAGT 59.410 50.000 0.00 0.00 0.00 2.24
424 523 6.687958 CGCCTCGTTGTTTTAAGTTTCTTTTA 59.312 34.615 0.00 0.00 0.00 1.52
579 717 4.049640 GCATGCGCCGACCCAAAA 62.050 61.111 4.18 0.00 0.00 2.44
596 734 0.110373 AAAGCGGAATCGAACGTTGC 60.110 50.000 5.00 0.00 39.00 4.17
628 770 2.888414 ACCGACCGAAATGGACAAAAAT 59.112 40.909 0.00 0.00 42.00 1.82
686 828 4.529109 GAGTTGCTCTTAGAACTCCTGT 57.471 45.455 0.00 0.00 41.47 4.00
687 829 4.888917 GAGTTGCTCTTAGAACTCCTGTT 58.111 43.478 0.00 0.00 41.47 3.16
688 830 5.297569 AGTTGCTCTTAGAACTCCTGTTT 57.702 39.130 0.00 0.00 36.39 2.83
689 831 5.685728 AGTTGCTCTTAGAACTCCTGTTTT 58.314 37.500 0.00 0.00 36.39 2.43
690 832 5.760743 AGTTGCTCTTAGAACTCCTGTTTTC 59.239 40.000 0.00 0.00 36.39 2.29
691 833 5.552870 TGCTCTTAGAACTCCTGTTTTCT 57.447 39.130 0.00 0.00 36.39 2.52
692 834 5.542779 TGCTCTTAGAACTCCTGTTTTCTC 58.457 41.667 0.00 0.00 36.39 2.87
693 835 4.932799 GCTCTTAGAACTCCTGTTTTCTCC 59.067 45.833 0.00 0.00 36.39 3.71
694 836 5.279758 GCTCTTAGAACTCCTGTTTTCTCCT 60.280 44.000 0.00 0.00 36.39 3.69
695 837 6.742926 GCTCTTAGAACTCCTGTTTTCTCCTT 60.743 42.308 0.00 0.00 36.39 3.36
696 838 7.138054 TCTTAGAACTCCTGTTTTCTCCTTT 57.862 36.000 0.00 0.00 36.39 3.11
697 839 7.574607 TCTTAGAACTCCTGTTTTCTCCTTTT 58.425 34.615 0.00 0.00 36.39 2.27
698 840 8.053355 TCTTAGAACTCCTGTTTTCTCCTTTTT 58.947 33.333 0.00 0.00 36.39 1.94
720 862 8.641499 TTTTTCGCTGATTTTTGTTATCAGTT 57.359 26.923 12.78 0.00 46.84 3.16
721 863 8.641499 TTTTCGCTGATTTTTGTTATCAGTTT 57.359 26.923 12.78 0.00 46.84 2.66
722 864 7.621832 TTCGCTGATTTTTGTTATCAGTTTG 57.378 32.000 12.78 5.56 46.84 2.93
723 865 6.734137 TCGCTGATTTTTGTTATCAGTTTGT 58.266 32.000 12.78 0.00 46.84 2.83
724 866 6.855914 TCGCTGATTTTTGTTATCAGTTTGTC 59.144 34.615 12.78 0.00 46.84 3.18
725 867 6.857964 CGCTGATTTTTGTTATCAGTTTGTCT 59.142 34.615 12.78 0.00 46.84 3.41
726 868 8.015087 CGCTGATTTTTGTTATCAGTTTGTCTA 58.985 33.333 12.78 0.00 46.84 2.59
727 869 9.677567 GCTGATTTTTGTTATCAGTTTGTCTAA 57.322 29.630 12.78 0.00 46.84 2.10
769 911 7.936950 TTGAAGAATATCACATCTAAGCTCG 57.063 36.000 0.00 0.00 0.00 5.03
770 912 7.043961 TGAAGAATATCACATCTAAGCTCGT 57.956 36.000 0.00 0.00 0.00 4.18
771 913 7.492524 TGAAGAATATCACATCTAAGCTCGTT 58.507 34.615 0.00 0.00 0.00 3.85
772 914 7.649705 TGAAGAATATCACATCTAAGCTCGTTC 59.350 37.037 0.00 0.00 0.00 3.95
773 915 7.043961 AGAATATCACATCTAAGCTCGTTCA 57.956 36.000 0.00 0.00 0.00 3.18
774 916 7.492524 AGAATATCACATCTAAGCTCGTTCAA 58.507 34.615 0.00 0.00 0.00 2.69
775 917 7.981789 AGAATATCACATCTAAGCTCGTTCAAA 59.018 33.333 0.00 0.00 0.00 2.69
776 918 8.668510 AATATCACATCTAAGCTCGTTCAAAT 57.331 30.769 0.00 0.00 0.00 2.32
777 919 9.764363 AATATCACATCTAAGCTCGTTCAAATA 57.236 29.630 0.00 0.00 0.00 1.40
778 920 9.935241 ATATCACATCTAAGCTCGTTCAAATAT 57.065 29.630 0.00 0.00 0.00 1.28
780 922 9.935241 ATCACATCTAAGCTCGTTCAAATATAT 57.065 29.630 0.00 0.00 0.00 0.86
789 931 9.489084 AAGCTCGTTCAAATATATAATACAGCA 57.511 29.630 0.00 0.00 0.00 4.41
790 932 9.144747 AGCTCGTTCAAATATATAATACAGCAG 57.855 33.333 0.00 0.00 0.00 4.24
791 933 7.900352 GCTCGTTCAAATATATAATACAGCAGC 59.100 37.037 0.00 0.00 0.00 5.25
792 934 8.825667 TCGTTCAAATATATAATACAGCAGCA 57.174 30.769 0.00 0.00 0.00 4.41
793 935 9.267084 TCGTTCAAATATATAATACAGCAGCAA 57.733 29.630 0.00 0.00 0.00 3.91
794 936 9.533983 CGTTCAAATATATAATACAGCAGCAAG 57.466 33.333 0.00 0.00 0.00 4.01
795 937 9.831737 GTTCAAATATATAATACAGCAGCAAGG 57.168 33.333 0.00 0.00 0.00 3.61
796 938 9.791801 TTCAAATATATAATACAGCAGCAAGGA 57.208 29.630 0.00 0.00 0.00 3.36
797 939 9.791801 TCAAATATATAATACAGCAGCAAGGAA 57.208 29.630 0.00 0.00 0.00 3.36
838 980 9.673454 AAAAATAGACCACGAATAAAACACTTC 57.327 29.630 0.00 0.00 0.00 3.01
839 981 7.972832 AATAGACCACGAATAAAACACTTCA 57.027 32.000 0.00 0.00 0.00 3.02
840 982 8.561738 AATAGACCACGAATAAAACACTTCAT 57.438 30.769 0.00 0.00 0.00 2.57
841 983 6.481954 AGACCACGAATAAAACACTTCATC 57.518 37.500 0.00 0.00 0.00 2.92
842 984 6.231211 AGACCACGAATAAAACACTTCATCT 58.769 36.000 0.00 0.00 0.00 2.90
843 985 6.147821 AGACCACGAATAAAACACTTCATCTG 59.852 38.462 0.00 0.00 0.00 2.90
844 986 5.763204 ACCACGAATAAAACACTTCATCTGT 59.237 36.000 0.00 0.00 0.00 3.41
845 987 6.073222 ACCACGAATAAAACACTTCATCTGTC 60.073 38.462 0.00 0.00 0.00 3.51
846 988 6.147821 CCACGAATAAAACACTTCATCTGTCT 59.852 38.462 0.00 0.00 0.00 3.41
847 989 7.307989 CCACGAATAAAACACTTCATCTGTCTT 60.308 37.037 0.00 0.00 0.00 3.01
848 990 7.531871 CACGAATAAAACACTTCATCTGTCTTG 59.468 37.037 0.00 0.00 0.00 3.02
849 991 7.226720 ACGAATAAAACACTTCATCTGTCTTGT 59.773 33.333 0.00 0.00 0.00 3.16
850 992 8.708742 CGAATAAAACACTTCATCTGTCTTGTA 58.291 33.333 0.00 0.00 0.00 2.41
895 1037 3.374042 AAGTAGAGTGGAGAGCTAGCA 57.626 47.619 18.83 0.00 0.00 3.49
896 1038 2.930950 AGTAGAGTGGAGAGCTAGCAG 58.069 52.381 18.83 0.00 0.00 4.24
897 1039 1.336755 GTAGAGTGGAGAGCTAGCAGC 59.663 57.143 18.83 8.57 42.84 5.25
1026 1181 4.516195 GGCTCCTCCTTCGCGTCC 62.516 72.222 5.77 0.00 0.00 4.79
1428 1592 4.443266 GCCGAAGAGACCGCTGCT 62.443 66.667 0.00 0.00 0.00 4.24
1499 1667 2.754946 AATCGTCGTTCCCTTTGCTA 57.245 45.000 0.00 0.00 0.00 3.49
1500 1668 2.981859 ATCGTCGTTCCCTTTGCTAT 57.018 45.000 0.00 0.00 0.00 2.97
1506 1674 1.812571 CGTTCCCTTTGCTATTGCTGT 59.187 47.619 0.00 0.00 40.48 4.40
1576 1744 5.703130 ACTTGGCTCTGAAATCTGTACTTTC 59.297 40.000 0.00 0.00 34.02 2.62
1589 1757 4.588951 TCTGTACTTTCTCTTCTTCCTGCA 59.411 41.667 0.00 0.00 0.00 4.41
1702 1873 5.522460 TGAACAACCAAACAAACGAACAAAA 59.478 32.000 0.00 0.00 0.00 2.44
1718 1889 8.090250 ACGAACAAAATATTACACACTTGCTA 57.910 30.769 0.00 0.00 0.00 3.49
1733 1904 5.403246 CACTTGCTAGTGTTACAGAGTAGG 58.597 45.833 18.65 0.00 45.46 3.18
1734 1905 5.047943 CACTTGCTAGTGTTACAGAGTAGGT 60.048 44.000 18.65 0.00 45.46 3.08
1735 1906 6.150641 CACTTGCTAGTGTTACAGAGTAGGTA 59.849 42.308 18.65 0.00 45.46 3.08
1737 1908 4.633126 TGCTAGTGTTACAGAGTAGGTACG 59.367 45.833 0.00 0.00 0.00 3.67
1839 2012 6.660949 AGAGTTGAATCAGAGTTTAAATGGGG 59.339 38.462 0.00 0.00 0.00 4.96
1842 2015 3.644966 ATCAGAGTTTAAATGGGGCGA 57.355 42.857 0.00 0.00 0.00 5.54
1860 2077 1.694639 GAGATTGTTTGCACTGCAGC 58.305 50.000 15.27 1.39 40.61 5.25
1877 2094 1.022735 AGCAGTACATCCGTCCTACG 58.977 55.000 0.00 0.00 42.11 3.51
1890 2107 0.178533 TCCTACGGGTAATTTGCGGG 59.821 55.000 0.00 0.00 0.00 6.13
1902 2119 1.028905 TTTGCGGGGACAGTTTCTTG 58.971 50.000 0.00 0.00 0.00 3.02
1979 2289 1.180029 ATGCCTGACATGAACTTGCC 58.820 50.000 0.00 0.00 37.70 4.52
2021 2331 0.950836 GCTCTCTAGCTCGCATCTGA 59.049 55.000 0.00 0.00 45.85 3.27
2024 2334 1.885233 TCTCTAGCTCGCATCTGATGG 59.115 52.381 18.60 9.30 0.00 3.51
2029 2339 0.603172 GCTCGCATCTGATGGCTCAT 60.603 55.000 18.60 0.00 0.00 2.90
2031 2341 1.001068 CTCGCATCTGATGGCTCATCT 59.999 52.381 18.60 0.00 41.06 2.90
2075 2385 2.040145 TCATGAGCATTCTGGGACACAA 59.960 45.455 0.00 0.00 0.00 3.33
2080 2390 3.087031 AGCATTCTGGGACACAATCTTG 58.913 45.455 0.00 0.00 0.00 3.02
2107 2417 5.351465 TGAACTTGTTTGTCTGAACTCTCAC 59.649 40.000 0.00 0.00 0.00 3.51
2215 2525 5.537300 TTCATAAGAGATCCCTAGCACAC 57.463 43.478 0.00 0.00 0.00 3.82
2219 2529 3.326946 AGAGATCCCTAGCACACTGAT 57.673 47.619 0.00 0.00 0.00 2.90
2220 2530 2.964464 AGAGATCCCTAGCACACTGATG 59.036 50.000 0.00 0.00 0.00 3.07
2221 2531 2.961741 GAGATCCCTAGCACACTGATGA 59.038 50.000 0.00 0.00 0.00 2.92
2222 2532 3.577848 GAGATCCCTAGCACACTGATGAT 59.422 47.826 0.00 0.00 0.00 2.45
2223 2533 3.324268 AGATCCCTAGCACACTGATGATG 59.676 47.826 0.00 0.00 0.00 3.07
2224 2534 1.764723 TCCCTAGCACACTGATGATGG 59.235 52.381 0.00 0.00 0.00 3.51
2225 2535 1.487976 CCCTAGCACACTGATGATGGT 59.512 52.381 0.00 0.00 0.00 3.55
2226 2536 2.558378 CCTAGCACACTGATGATGGTG 58.442 52.381 0.00 0.00 39.13 4.17
2227 2537 2.169144 CCTAGCACACTGATGATGGTGA 59.831 50.000 0.00 0.00 37.22 4.02
2228 2538 2.865119 AGCACACTGATGATGGTGAA 57.135 45.000 0.00 0.00 37.22 3.18
2229 2539 2.430465 AGCACACTGATGATGGTGAAC 58.570 47.619 0.00 0.00 37.22 3.18
2230 2540 2.153645 GCACACTGATGATGGTGAACA 58.846 47.619 0.00 0.00 37.22 3.18
2231 2541 2.553602 GCACACTGATGATGGTGAACAA 59.446 45.455 0.00 0.00 37.22 2.83
2232 2542 3.610114 GCACACTGATGATGGTGAACAAC 60.610 47.826 0.00 0.00 37.22 3.32
2250 2560 9.204792 GTGAACAACCAAACAAAATAAAAATCG 57.795 29.630 0.00 0.00 0.00 3.34
2251 2561 9.151471 TGAACAACCAAACAAAATAAAAATCGA 57.849 25.926 0.00 0.00 0.00 3.59
2252 2562 9.631639 GAACAACCAAACAAAATAAAAATCGAG 57.368 29.630 0.00 0.00 0.00 4.04
2253 2563 8.710835 ACAACCAAACAAAATAAAAATCGAGT 57.289 26.923 0.00 0.00 0.00 4.18
2254 2564 8.599774 ACAACCAAACAAAATAAAAATCGAGTG 58.400 29.630 0.00 0.00 0.00 3.51
2255 2565 7.172654 ACCAAACAAAATAAAAATCGAGTGC 57.827 32.000 0.00 0.00 0.00 4.40
2256 2566 6.074569 ACCAAACAAAATAAAAATCGAGTGCG 60.075 34.615 0.00 0.00 39.35 5.34
2257 2567 5.494863 AACAAAATAAAAATCGAGTGCGC 57.505 34.783 0.00 0.00 37.46 6.09
2258 2568 4.794169 ACAAAATAAAAATCGAGTGCGCT 58.206 34.783 9.73 0.00 37.46 5.92
2259 2569 5.219633 ACAAAATAAAAATCGAGTGCGCTT 58.780 33.333 9.73 0.00 37.46 4.68
2260 2570 5.689961 ACAAAATAAAAATCGAGTGCGCTTT 59.310 32.000 9.73 0.00 37.43 3.51
2261 2571 6.200097 ACAAAATAAAAATCGAGTGCGCTTTT 59.800 30.769 9.73 7.73 44.66 2.27
2262 2572 5.745653 AATAAAAATCGAGTGCGCTTTTG 57.254 34.783 9.73 0.22 42.76 2.44
2263 2573 1.408422 AAAATCGAGTGCGCTTTTGC 58.592 45.000 9.73 0.00 42.21 3.68
2264 2574 0.593128 AAATCGAGTGCGCTTTTGCT 59.407 45.000 9.73 0.00 44.80 3.91
2265 2575 1.438651 AATCGAGTGCGCTTTTGCTA 58.561 45.000 9.73 0.00 44.80 3.49
2266 2576 1.002366 ATCGAGTGCGCTTTTGCTAG 58.998 50.000 9.73 0.00 44.80 3.42
2267 2577 0.319555 TCGAGTGCGCTTTTGCTAGT 60.320 50.000 9.73 0.00 44.80 2.57
2268 2578 1.068125 TCGAGTGCGCTTTTGCTAGTA 60.068 47.619 9.73 0.00 44.80 1.82
2269 2579 1.724623 CGAGTGCGCTTTTGCTAGTAA 59.275 47.619 9.73 0.00 44.80 2.24
2270 2580 2.348666 CGAGTGCGCTTTTGCTAGTAAT 59.651 45.455 9.73 0.00 44.80 1.89
2271 2581 3.674423 GAGTGCGCTTTTGCTAGTAATG 58.326 45.455 9.73 0.00 44.80 1.90
2272 2582 3.074412 AGTGCGCTTTTGCTAGTAATGT 58.926 40.909 9.73 0.00 44.80 2.71
2273 2583 4.250464 AGTGCGCTTTTGCTAGTAATGTA 58.750 39.130 9.73 0.00 44.80 2.29
2274 2584 4.693566 AGTGCGCTTTTGCTAGTAATGTAA 59.306 37.500 9.73 0.00 44.80 2.41
2275 2585 5.354234 AGTGCGCTTTTGCTAGTAATGTAAT 59.646 36.000 9.73 0.00 44.80 1.89
2276 2586 5.452302 GTGCGCTTTTGCTAGTAATGTAATG 59.548 40.000 9.73 0.00 44.80 1.90
2277 2587 5.123186 TGCGCTTTTGCTAGTAATGTAATGT 59.877 36.000 9.73 0.00 44.80 2.71
2278 2588 5.452302 GCGCTTTTGCTAGTAATGTAATGTG 59.548 40.000 0.00 0.00 44.80 3.21
2279 2589 5.965334 CGCTTTTGCTAGTAATGTAATGTGG 59.035 40.000 0.00 0.00 44.80 4.17
2280 2590 6.183360 CGCTTTTGCTAGTAATGTAATGTGGA 60.183 38.462 0.00 0.00 44.80 4.02
2281 2591 7.189512 GCTTTTGCTAGTAATGTAATGTGGAG 58.810 38.462 0.00 0.00 43.35 3.86
2282 2592 7.065803 GCTTTTGCTAGTAATGTAATGTGGAGA 59.934 37.037 0.00 0.00 43.35 3.71
2283 2593 7.843490 TTTGCTAGTAATGTAATGTGGAGAC 57.157 36.000 0.00 0.00 0.00 3.36
2284 2594 6.538945 TGCTAGTAATGTAATGTGGAGACA 57.461 37.500 0.00 0.00 36.22 3.41
2285 2595 7.124573 TGCTAGTAATGTAATGTGGAGACAT 57.875 36.000 0.00 0.00 45.24 3.06
2297 2607 6.910536 ATGTGGAGACATTTCTTCGTATTC 57.089 37.500 0.00 0.00 46.14 1.75
2298 2608 5.789521 TGTGGAGACATTTCTTCGTATTCA 58.210 37.500 0.00 0.00 46.14 2.57
2299 2609 5.869344 TGTGGAGACATTTCTTCGTATTCAG 59.131 40.000 0.00 0.00 46.14 3.02
2300 2610 5.869888 GTGGAGACATTTCTTCGTATTCAGT 59.130 40.000 0.00 0.00 46.14 3.41
2301 2611 6.035112 GTGGAGACATTTCTTCGTATTCAGTC 59.965 42.308 0.00 0.00 46.14 3.51
2302 2612 5.520649 GGAGACATTTCTTCGTATTCAGTCC 59.479 44.000 0.00 0.00 29.47 3.85
2303 2613 6.037786 AGACATTTCTTCGTATTCAGTCCA 57.962 37.500 0.00 0.00 0.00 4.02
2304 2614 6.464222 AGACATTTCTTCGTATTCAGTCCAA 58.536 36.000 0.00 0.00 0.00 3.53
2305 2615 7.106239 AGACATTTCTTCGTATTCAGTCCAAT 58.894 34.615 0.00 0.00 0.00 3.16
2306 2616 8.258007 AGACATTTCTTCGTATTCAGTCCAATA 58.742 33.333 0.00 0.00 0.00 1.90
2307 2617 8.197988 ACATTTCTTCGTATTCAGTCCAATAC 57.802 34.615 0.00 0.00 36.33 1.89
2308 2618 7.822334 ACATTTCTTCGTATTCAGTCCAATACA 59.178 33.333 4.65 0.00 38.63 2.29
2309 2619 8.830580 CATTTCTTCGTATTCAGTCCAATACAT 58.169 33.333 4.65 0.00 38.63 2.29
2312 2622 9.692749 TTCTTCGTATTCAGTCCAATACATATC 57.307 33.333 4.65 0.00 38.63 1.63
2313 2623 8.304596 TCTTCGTATTCAGTCCAATACATATCC 58.695 37.037 4.65 0.00 38.63 2.59
2314 2624 7.776618 TCGTATTCAGTCCAATACATATCCT 57.223 36.000 4.65 0.00 38.63 3.24
2315 2625 8.873186 TCGTATTCAGTCCAATACATATCCTA 57.127 34.615 4.65 0.00 38.63 2.94
2316 2626 8.737175 TCGTATTCAGTCCAATACATATCCTAC 58.263 37.037 4.65 0.00 38.63 3.18
2317 2627 8.740906 CGTATTCAGTCCAATACATATCCTACT 58.259 37.037 4.65 0.00 38.63 2.57
2320 2630 9.830186 ATTCAGTCCAATACATATCCTACTAGT 57.170 33.333 0.00 0.00 0.00 2.57
2322 2632 9.736414 TCAGTCCAATACATATCCTACTAGTAC 57.264 37.037 0.00 0.00 0.00 2.73
2323 2633 8.958506 CAGTCCAATACATATCCTACTAGTACC 58.041 40.741 0.00 0.00 0.00 3.34
2324 2634 8.676020 AGTCCAATACATATCCTACTAGTACCA 58.324 37.037 0.00 0.00 0.00 3.25
2325 2635 8.958506 GTCCAATACATATCCTACTAGTACCAG 58.041 40.741 0.00 0.00 0.00 4.00
2326 2636 7.614583 TCCAATACATATCCTACTAGTACCAGC 59.385 40.741 0.00 0.00 0.00 4.85
2327 2637 7.396339 CCAATACATATCCTACTAGTACCAGCA 59.604 40.741 0.00 0.00 0.00 4.41
2328 2638 8.462811 CAATACATATCCTACTAGTACCAGCAG 58.537 40.741 0.00 0.00 0.00 4.24
2329 2639 6.202202 ACATATCCTACTAGTACCAGCAGA 57.798 41.667 0.00 0.00 0.00 4.26
2330 2640 6.611785 ACATATCCTACTAGTACCAGCAGAA 58.388 40.000 0.00 0.00 0.00 3.02
2331 2641 6.717540 ACATATCCTACTAGTACCAGCAGAAG 59.282 42.308 0.00 0.00 0.00 2.85
2332 2642 3.288964 TCCTACTAGTACCAGCAGAAGC 58.711 50.000 0.00 0.00 42.56 3.86
2359 2669 7.513190 CAGTAGTAGACTAATGTGAACTTGC 57.487 40.000 8.61 0.00 39.07 4.01
2360 2670 7.316640 CAGTAGTAGACTAATGTGAACTTGCT 58.683 38.462 8.61 0.00 39.07 3.91
2361 2671 7.274468 CAGTAGTAGACTAATGTGAACTTGCTG 59.726 40.741 8.61 0.00 39.07 4.41
2362 2672 6.102897 AGTAGACTAATGTGAACTTGCTGT 57.897 37.500 0.00 0.00 0.00 4.40
2363 2673 6.525629 AGTAGACTAATGTGAACTTGCTGTT 58.474 36.000 0.00 0.00 42.38 3.16
2364 2674 6.992715 AGTAGACTAATGTGAACTTGCTGTTT 59.007 34.615 0.00 0.00 39.30 2.83
2365 2675 6.064846 AGACTAATGTGAACTTGCTGTTTG 57.935 37.500 0.00 0.00 39.30 2.93
2366 2676 5.590259 AGACTAATGTGAACTTGCTGTTTGT 59.410 36.000 0.00 0.00 39.30 2.83
2367 2677 5.821204 ACTAATGTGAACTTGCTGTTTGTC 58.179 37.500 0.00 0.00 39.30 3.18
2368 2678 4.989279 AATGTGAACTTGCTGTTTGTCT 57.011 36.364 0.00 0.00 39.30 3.41
2369 2679 6.765989 ACTAATGTGAACTTGCTGTTTGTCTA 59.234 34.615 0.00 0.00 39.30 2.59
2370 2680 6.449635 AATGTGAACTTGCTGTTTGTCTAA 57.550 33.333 0.00 0.00 39.30 2.10
2371 2681 5.888691 TGTGAACTTGCTGTTTGTCTAAA 57.111 34.783 0.00 0.00 39.30 1.85
2372 2682 6.449635 TGTGAACTTGCTGTTTGTCTAAAT 57.550 33.333 0.00 0.00 39.30 1.40
2373 2683 6.862209 TGTGAACTTGCTGTTTGTCTAAATT 58.138 32.000 0.00 0.00 39.30 1.82
2374 2684 6.751425 TGTGAACTTGCTGTTTGTCTAAATTG 59.249 34.615 0.00 0.00 39.30 2.32
2375 2685 6.972328 GTGAACTTGCTGTTTGTCTAAATTGA 59.028 34.615 0.00 0.00 39.30 2.57
2376 2686 7.166473 GTGAACTTGCTGTTTGTCTAAATTGAG 59.834 37.037 0.00 0.00 39.30 3.02
2377 2687 6.699575 ACTTGCTGTTTGTCTAAATTGAGT 57.300 33.333 0.00 0.00 0.00 3.41
2378 2688 7.100458 ACTTGCTGTTTGTCTAAATTGAGTT 57.900 32.000 0.00 0.00 0.00 3.01
2379 2689 6.974622 ACTTGCTGTTTGTCTAAATTGAGTTG 59.025 34.615 0.00 0.00 0.00 3.16
2380 2690 5.280945 TGCTGTTTGTCTAAATTGAGTTGC 58.719 37.500 0.00 0.00 0.00 4.17
2381 2691 5.067674 TGCTGTTTGTCTAAATTGAGTTGCT 59.932 36.000 0.00 0.00 0.00 3.91
2382 2692 5.626955 GCTGTTTGTCTAAATTGAGTTGCTC 59.373 40.000 0.00 0.00 0.00 4.26
2383 2693 6.514048 GCTGTTTGTCTAAATTGAGTTGCTCT 60.514 38.462 0.00 0.00 0.00 4.09
2384 2694 7.307989 GCTGTTTGTCTAAATTGAGTTGCTCTA 60.308 37.037 0.00 0.00 0.00 2.43
2385 2695 8.087982 TGTTTGTCTAAATTGAGTTGCTCTAG 57.912 34.615 0.00 0.00 0.00 2.43
2386 2696 6.727824 TTGTCTAAATTGAGTTGCTCTAGC 57.272 37.500 0.00 0.00 42.50 3.42
2387 2697 6.042638 TGTCTAAATTGAGTTGCTCTAGCT 57.957 37.500 3.26 0.00 42.66 3.32
2388 2698 6.102663 TGTCTAAATTGAGTTGCTCTAGCTC 58.897 40.000 3.26 0.00 42.66 4.09
2389 2699 5.231147 GTCTAAATTGAGTTGCTCTAGCTCG 59.769 44.000 3.26 0.00 39.29 5.03
2390 2700 1.933247 ATTGAGTTGCTCTAGCTCGC 58.067 50.000 3.26 0.00 39.29 5.03
2391 2701 0.603065 TTGAGTTGCTCTAGCTCGCA 59.397 50.000 3.26 0.00 39.29 5.10
2392 2702 0.820226 TGAGTTGCTCTAGCTCGCAT 59.180 50.000 3.26 0.00 39.29 4.73
2393 2703 1.202348 TGAGTTGCTCTAGCTCGCATC 60.202 52.381 3.26 5.98 39.29 3.91
2394 2704 1.066908 GAGTTGCTCTAGCTCGCATCT 59.933 52.381 12.99 12.99 42.66 2.90
2395 2705 1.202394 AGTTGCTCTAGCTCGCATCTG 60.202 52.381 12.58 0.00 42.66 2.90
2396 2706 1.106285 TTGCTCTAGCTCGCATCTGA 58.894 50.000 3.26 0.00 42.66 3.27
2397 2707 1.326328 TGCTCTAGCTCGCATCTGAT 58.674 50.000 3.26 0.00 42.66 2.90
2398 2708 1.000496 TGCTCTAGCTCGCATCTGATG 60.000 52.381 13.26 13.26 42.66 3.07
2399 2709 2.260550 GCTCTAGCTCGCATCTGATGC 61.261 57.143 28.28 28.28 44.58 3.91
2408 2718 3.309052 CATCTGATGCCTCCAGCTC 57.691 57.895 4.47 0.00 44.23 4.09
2409 2719 0.468648 CATCTGATGCCTCCAGCTCA 59.531 55.000 4.47 0.00 44.23 4.26
2410 2720 1.134189 CATCTGATGCCTCCAGCTCAA 60.134 52.381 4.47 0.00 44.23 3.02
2411 2721 0.986527 TCTGATGCCTCCAGCTCAAA 59.013 50.000 0.00 0.00 44.23 2.69
2412 2722 1.093159 CTGATGCCTCCAGCTCAAAC 58.907 55.000 0.00 0.00 44.23 2.93
2413 2723 0.401356 TGATGCCTCCAGCTCAAACA 59.599 50.000 0.00 0.00 44.23 2.83
2414 2724 1.005097 TGATGCCTCCAGCTCAAACAT 59.995 47.619 0.00 0.00 44.23 2.71
2415 2725 1.674962 GATGCCTCCAGCTCAAACATC 59.325 52.381 0.00 0.00 44.23 3.06
2416 2726 0.694771 TGCCTCCAGCTCAAACATCT 59.305 50.000 0.00 0.00 44.23 2.90
2417 2727 1.074405 TGCCTCCAGCTCAAACATCTT 59.926 47.619 0.00 0.00 44.23 2.40
2418 2728 1.471684 GCCTCCAGCTCAAACATCTTG 59.528 52.381 0.00 0.00 38.99 3.02
2419 2729 2.089980 CCTCCAGCTCAAACATCTTGG 58.910 52.381 0.00 0.00 0.00 3.61
2420 2730 2.290514 CCTCCAGCTCAAACATCTTGGA 60.291 50.000 0.00 0.00 0.00 3.53
2421 2731 3.618351 CTCCAGCTCAAACATCTTGGAT 58.382 45.455 0.00 0.00 0.00 3.41
2422 2732 3.349927 TCCAGCTCAAACATCTTGGATG 58.650 45.455 6.04 6.04 0.00 3.51
2423 2733 2.426024 CCAGCTCAAACATCTTGGATGG 59.574 50.000 11.46 0.00 0.00 3.51
2424 2734 2.097825 AGCTCAAACATCTTGGATGGC 58.902 47.619 11.46 5.38 0.00 4.40
2425 2735 1.202222 GCTCAAACATCTTGGATGGCG 60.202 52.381 11.46 1.10 0.00 5.69
2426 2736 0.810648 TCAAACATCTTGGATGGCGC 59.189 50.000 0.00 0.00 0.00 6.53
2427 2737 0.527113 CAAACATCTTGGATGGCGCA 59.473 50.000 10.83 0.00 0.00 6.09
2428 2738 0.813184 AAACATCTTGGATGGCGCAG 59.187 50.000 10.83 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.379044 CTTGACTGTGGATGGGGGC 60.379 63.158 0.00 0.00 0.00 5.80
27 28 1.379044 GGCCTTGACTGTGGATGGG 60.379 63.158 0.00 0.00 0.00 4.00
36 37 1.684049 CTCCTCCTCGGCCTTGACT 60.684 63.158 0.00 0.00 0.00 3.41
196 214 3.630013 AGCTCGAGGTGCTTGCCA 61.630 61.111 17.85 0.00 37.52 4.92
369 438 1.153309 TAGGCGTCCTCATCGTCGA 60.153 57.895 0.00 0.00 37.99 4.20
424 523 7.487829 GCGTCCACATTACATTAATTCAACATT 59.512 33.333 0.00 0.00 0.00 2.71
430 531 5.914635 CCATGCGTCCACATTACATTAATTC 59.085 40.000 0.00 0.00 0.00 2.17
432 533 5.008613 GTCCATGCGTCCACATTACATTAAT 59.991 40.000 0.00 0.00 0.00 1.40
436 537 2.092968 AGTCCATGCGTCCACATTACAT 60.093 45.455 0.00 0.00 0.00 2.29
438 541 1.933853 GAGTCCATGCGTCCACATTAC 59.066 52.381 0.00 0.00 0.00 1.89
579 717 1.374252 AGCAACGTTCGATTCCGCT 60.374 52.632 0.00 0.00 35.37 5.52
614 752 6.836577 TTTTGTCCGATTTTTGTCCATTTC 57.163 33.333 0.00 0.00 0.00 2.17
628 770 2.679450 ACGAACGATGATTTTGTCCGA 58.321 42.857 0.14 0.00 0.00 4.55
743 885 8.820933 CGAGCTTAGATGTGATATTCTTCAAAA 58.179 33.333 0.00 0.00 0.00 2.44
744 886 7.981789 ACGAGCTTAGATGTGATATTCTTCAAA 59.018 33.333 0.00 0.00 0.00 2.69
745 887 7.492524 ACGAGCTTAGATGTGATATTCTTCAA 58.507 34.615 0.00 0.00 0.00 2.69
746 888 7.043961 ACGAGCTTAGATGTGATATTCTTCA 57.956 36.000 0.00 0.00 0.00 3.02
747 889 7.649705 TGAACGAGCTTAGATGTGATATTCTTC 59.350 37.037 0.00 0.00 0.00 2.87
748 890 7.492524 TGAACGAGCTTAGATGTGATATTCTT 58.507 34.615 0.00 0.00 0.00 2.52
749 891 7.043961 TGAACGAGCTTAGATGTGATATTCT 57.956 36.000 0.00 0.00 0.00 2.40
750 892 7.700322 TTGAACGAGCTTAGATGTGATATTC 57.300 36.000 0.00 0.00 0.00 1.75
751 893 8.668510 ATTTGAACGAGCTTAGATGTGATATT 57.331 30.769 0.00 0.00 0.00 1.28
752 894 9.935241 ATATTTGAACGAGCTTAGATGTGATAT 57.065 29.630 0.00 0.00 0.00 1.63
754 896 9.935241 ATATATTTGAACGAGCTTAGATGTGAT 57.065 29.630 0.00 0.00 0.00 3.06
763 905 9.489084 TGCTGTATTATATATTTGAACGAGCTT 57.511 29.630 0.00 0.00 0.00 3.74
764 906 9.144747 CTGCTGTATTATATATTTGAACGAGCT 57.855 33.333 0.00 0.00 0.00 4.09
765 907 7.900352 GCTGCTGTATTATATATTTGAACGAGC 59.100 37.037 0.00 0.00 0.00 5.03
766 908 8.925700 TGCTGCTGTATTATATATTTGAACGAG 58.074 33.333 0.00 0.00 0.00 4.18
767 909 8.825667 TGCTGCTGTATTATATATTTGAACGA 57.174 30.769 0.00 0.00 0.00 3.85
768 910 9.533983 CTTGCTGCTGTATTATATATTTGAACG 57.466 33.333 0.00 0.00 0.00 3.95
769 911 9.831737 CCTTGCTGCTGTATTATATATTTGAAC 57.168 33.333 0.00 0.00 0.00 3.18
770 912 9.791801 TCCTTGCTGCTGTATTATATATTTGAA 57.208 29.630 0.00 0.00 0.00 2.69
771 913 9.791801 TTCCTTGCTGCTGTATTATATATTTGA 57.208 29.630 0.00 0.00 0.00 2.69
812 954 9.673454 GAAGTGTTTTATTCGTGGTCTATTTTT 57.327 29.630 0.00 0.00 0.00 1.94
813 955 8.842280 TGAAGTGTTTTATTCGTGGTCTATTTT 58.158 29.630 0.00 0.00 0.00 1.82
814 956 8.385898 TGAAGTGTTTTATTCGTGGTCTATTT 57.614 30.769 0.00 0.00 0.00 1.40
815 957 7.972832 TGAAGTGTTTTATTCGTGGTCTATT 57.027 32.000 0.00 0.00 0.00 1.73
816 958 8.041323 AGATGAAGTGTTTTATTCGTGGTCTAT 58.959 33.333 0.00 0.00 0.00 1.98
817 959 7.330946 CAGATGAAGTGTTTTATTCGTGGTCTA 59.669 37.037 0.00 0.00 0.00 2.59
818 960 6.147821 CAGATGAAGTGTTTTATTCGTGGTCT 59.852 38.462 0.00 0.00 0.00 3.85
819 961 6.073222 ACAGATGAAGTGTTTTATTCGTGGTC 60.073 38.462 0.00 0.00 0.00 4.02
820 962 5.763204 ACAGATGAAGTGTTTTATTCGTGGT 59.237 36.000 0.00 0.00 0.00 4.16
821 963 6.147821 AGACAGATGAAGTGTTTTATTCGTGG 59.852 38.462 0.00 0.00 0.00 4.94
822 964 7.121974 AGACAGATGAAGTGTTTTATTCGTG 57.878 36.000 0.00 0.00 0.00 4.35
823 965 7.226720 ACAAGACAGATGAAGTGTTTTATTCGT 59.773 33.333 0.00 0.00 0.00 3.85
824 966 7.576236 ACAAGACAGATGAAGTGTTTTATTCG 58.424 34.615 0.00 0.00 0.00 3.34
825 967 9.813080 GTACAAGACAGATGAAGTGTTTTATTC 57.187 33.333 0.00 0.00 0.00 1.75
826 968 9.337396 TGTACAAGACAGATGAAGTGTTTTATT 57.663 29.630 0.00 0.00 32.86 1.40
827 969 8.774586 GTGTACAAGACAGATGAAGTGTTTTAT 58.225 33.333 0.00 0.00 39.29 1.40
828 970 7.042992 CGTGTACAAGACAGATGAAGTGTTTTA 60.043 37.037 2.23 0.00 39.29 1.52
829 971 6.238103 CGTGTACAAGACAGATGAAGTGTTTT 60.238 38.462 2.23 0.00 39.29 2.43
830 972 5.234329 CGTGTACAAGACAGATGAAGTGTTT 59.766 40.000 2.23 0.00 39.29 2.83
831 973 4.745125 CGTGTACAAGACAGATGAAGTGTT 59.255 41.667 2.23 0.00 39.29 3.32
832 974 4.202121 ACGTGTACAAGACAGATGAAGTGT 60.202 41.667 16.00 0.00 39.29 3.55
833 975 4.148871 CACGTGTACAAGACAGATGAAGTG 59.851 45.833 16.00 0.00 39.29 3.16
834 976 4.202121 ACACGTGTACAAGACAGATGAAGT 60.202 41.667 21.98 0.00 39.29 3.01
835 977 4.299155 ACACGTGTACAAGACAGATGAAG 58.701 43.478 21.98 0.00 39.29 3.02
836 978 4.316205 ACACGTGTACAAGACAGATGAA 57.684 40.909 21.98 0.00 39.29 2.57
849 991 2.689785 CGCCTCCGGTACACGTGTA 61.690 63.158 24.10 24.10 42.24 2.90
850 992 4.047059 CGCCTCCGGTACACGTGT 62.047 66.667 26.52 26.52 42.24 4.49
860 1002 3.909430 TCTACTTATATTTGCGCCTCCG 58.091 45.455 4.18 0.00 37.57 4.63
861 1003 4.686554 CACTCTACTTATATTTGCGCCTCC 59.313 45.833 4.18 0.00 0.00 4.30
867 1009 6.754193 AGCTCTCCACTCTACTTATATTTGC 58.246 40.000 0.00 0.00 0.00 3.68
904 1049 1.465172 GGGGTTTCTTTCCAGGCCT 59.535 57.895 0.00 0.00 0.00 5.19
933 1078 7.184753 GGGATGGGATAGGATAAAGATAAGGTT 59.815 40.741 0.00 0.00 0.00 3.50
982 1135 2.933260 GCATCTTCTTCGTCTTCCTTCC 59.067 50.000 0.00 0.00 0.00 3.46
1026 1181 3.636231 TGGAGCTGGGTGAACGGG 61.636 66.667 0.00 0.00 0.00 5.28
1197 1355 3.659089 CTCCCGGCGGTGGTACTTG 62.659 68.421 26.32 6.71 0.00 3.16
1374 1532 3.827898 GACTGGGACTCGAGCGGG 61.828 72.222 13.61 1.16 0.00 6.13
1377 1535 3.827898 CCGGACTGGGACTCGAGC 61.828 72.222 13.61 5.26 0.00 5.03
1423 1587 0.747283 AAGCATCACTAGGCAGCAGC 60.747 55.000 0.00 0.00 33.96 5.25
1424 1588 1.134461 AGAAGCATCACTAGGCAGCAG 60.134 52.381 0.00 0.00 33.96 4.24
1425 1589 0.907486 AGAAGCATCACTAGGCAGCA 59.093 50.000 0.00 0.00 33.96 4.41
1428 1592 1.742761 GCAAGAAGCATCACTAGGCA 58.257 50.000 0.00 0.00 44.79 4.75
1499 1667 1.615392 GGGAGCAAGAACAACAGCAAT 59.385 47.619 0.00 0.00 0.00 3.56
1500 1668 1.032014 GGGAGCAAGAACAACAGCAA 58.968 50.000 0.00 0.00 0.00 3.91
1506 1674 2.038557 GTCTACAGGGGAGCAAGAACAA 59.961 50.000 0.00 0.00 0.00 2.83
1576 1744 2.469274 TCTTGCTGCAGGAAGAAGAG 57.531 50.000 38.70 20.59 46.95 2.85
1718 1889 4.627467 CGTACGTACCTACTCTGTAACACT 59.373 45.833 19.67 0.00 0.00 3.55
1734 1905 7.011763 AGCATTCTTCAGATAAGTACGTACGTA 59.988 37.037 23.60 23.60 0.00 3.57
1735 1906 5.970023 GCATTCTTCAGATAAGTACGTACGT 59.030 40.000 25.98 25.98 0.00 3.57
1737 1908 7.377397 CAGAGCATTCTTCAGATAAGTACGTAC 59.623 40.741 18.10 18.10 0.00 3.67
1839 2012 0.040157 TGCAGTGCAAACAATCTCGC 60.040 50.000 17.26 0.00 34.76 5.03
1842 2015 1.000607 CTGCTGCAGTGCAAACAATCT 60.001 47.619 20.22 0.00 42.83 2.40
1877 2094 0.323087 ACTGTCCCCGCAAATTACCC 60.323 55.000 0.00 0.00 0.00 3.69
1890 2107 3.753797 GACTGAATCCCAAGAAACTGTCC 59.246 47.826 0.00 0.00 31.05 4.02
1979 2289 4.361451 ACTGCACTTGAAACAAACTGAG 57.639 40.909 0.00 0.00 0.00 3.35
2021 2331 3.552875 CAGGATGTTTGAGATGAGCCAT 58.447 45.455 0.00 0.00 0.00 4.40
2024 2334 3.272574 TCCAGGATGTTTGAGATGAGC 57.727 47.619 0.00 0.00 0.00 4.26
2029 2339 1.407299 CGGCATCCAGGATGTTTGAGA 60.407 52.381 27.36 0.00 41.60 3.27
2031 2341 1.031571 GCGGCATCCAGGATGTTTGA 61.032 55.000 27.36 0.00 41.60 2.69
2075 2385 5.300034 TCAGACAAACAAGTTCATGCAAGAT 59.700 36.000 0.00 0.00 0.00 2.40
2080 2390 4.925068 AGTTCAGACAAACAAGTTCATGC 58.075 39.130 0.00 0.00 0.00 4.06
2224 2534 9.204792 CGATTTTTATTTTGTTTGGTTGTTCAC 57.795 29.630 0.00 0.00 0.00 3.18
2225 2535 9.151471 TCGATTTTTATTTTGTTTGGTTGTTCA 57.849 25.926 0.00 0.00 0.00 3.18
2226 2536 9.631639 CTCGATTTTTATTTTGTTTGGTTGTTC 57.368 29.630 0.00 0.00 0.00 3.18
2227 2537 9.157104 ACTCGATTTTTATTTTGTTTGGTTGTT 57.843 25.926 0.00 0.00 0.00 2.83
2228 2538 8.599774 CACTCGATTTTTATTTTGTTTGGTTGT 58.400 29.630 0.00 0.00 0.00 3.32
2229 2539 7.582319 GCACTCGATTTTTATTTTGTTTGGTTG 59.418 33.333 0.00 0.00 0.00 3.77
2230 2540 7.515998 CGCACTCGATTTTTATTTTGTTTGGTT 60.516 33.333 0.00 0.00 38.10 3.67
2231 2541 6.074569 CGCACTCGATTTTTATTTTGTTTGGT 60.075 34.615 0.00 0.00 38.10 3.67
2232 2542 6.288419 CGCACTCGATTTTTATTTTGTTTGG 58.712 36.000 0.00 0.00 38.10 3.28
2233 2543 5.778345 GCGCACTCGATTTTTATTTTGTTTG 59.222 36.000 0.30 0.00 38.10 2.93
2234 2544 5.689961 AGCGCACTCGATTTTTATTTTGTTT 59.310 32.000 11.47 0.00 38.10 2.83
2235 2545 5.219633 AGCGCACTCGATTTTTATTTTGTT 58.780 33.333 11.47 0.00 38.10 2.83
2236 2546 4.794169 AGCGCACTCGATTTTTATTTTGT 58.206 34.783 11.47 0.00 38.10 2.83
2237 2547 5.745653 AAGCGCACTCGATTTTTATTTTG 57.254 34.783 11.47 0.00 42.08 2.44
2247 2557 1.002366 CTAGCAAAAGCGCACTCGAT 58.998 50.000 11.47 0.00 38.10 3.59
2248 2558 0.319555 ACTAGCAAAAGCGCACTCGA 60.320 50.000 11.47 0.00 38.10 4.04
2249 2559 1.346365 TACTAGCAAAAGCGCACTCG 58.654 50.000 11.47 0.00 39.07 4.18
2250 2560 3.125316 ACATTACTAGCAAAAGCGCACTC 59.875 43.478 11.47 0.00 0.00 3.51
2251 2561 3.074412 ACATTACTAGCAAAAGCGCACT 58.926 40.909 11.47 0.70 0.00 4.40
2252 2562 3.471495 ACATTACTAGCAAAAGCGCAC 57.529 42.857 11.47 0.00 0.00 5.34
2253 2563 5.123186 ACATTACATTACTAGCAAAAGCGCA 59.877 36.000 11.47 0.00 0.00 6.09
2254 2564 5.452302 CACATTACATTACTAGCAAAAGCGC 59.548 40.000 0.00 0.00 0.00 5.92
2255 2565 5.965334 CCACATTACATTACTAGCAAAAGCG 59.035 40.000 0.00 0.00 0.00 4.68
2256 2566 7.065803 TCTCCACATTACATTACTAGCAAAAGC 59.934 37.037 0.00 0.00 0.00 3.51
2257 2567 8.391106 GTCTCCACATTACATTACTAGCAAAAG 58.609 37.037 0.00 0.00 0.00 2.27
2258 2568 7.880713 TGTCTCCACATTACATTACTAGCAAAA 59.119 33.333 0.00 0.00 0.00 2.44
2259 2569 7.390823 TGTCTCCACATTACATTACTAGCAAA 58.609 34.615 0.00 0.00 0.00 3.68
2260 2570 6.941857 TGTCTCCACATTACATTACTAGCAA 58.058 36.000 0.00 0.00 0.00 3.91
2261 2571 6.538945 TGTCTCCACATTACATTACTAGCA 57.461 37.500 0.00 0.00 0.00 3.49
2274 2584 6.406370 TGAATACGAAGAAATGTCTCCACAT 58.594 36.000 0.00 0.00 45.89 3.21
2275 2585 5.789521 TGAATACGAAGAAATGTCTCCACA 58.210 37.500 0.00 0.00 36.78 4.17
2276 2586 5.869888 ACTGAATACGAAGAAATGTCTCCAC 59.130 40.000 0.00 0.00 30.70 4.02
2277 2587 6.037786 ACTGAATACGAAGAAATGTCTCCA 57.962 37.500 0.00 0.00 30.70 3.86
2278 2588 5.520649 GGACTGAATACGAAGAAATGTCTCC 59.479 44.000 0.00 0.00 30.70 3.71
2279 2589 6.100004 TGGACTGAATACGAAGAAATGTCTC 58.900 40.000 0.00 0.00 30.70 3.36
2280 2590 6.037786 TGGACTGAATACGAAGAAATGTCT 57.962 37.500 0.00 0.00 34.72 3.41
2281 2591 6.721571 TTGGACTGAATACGAAGAAATGTC 57.278 37.500 0.00 0.00 0.00 3.06
2282 2592 7.822334 TGTATTGGACTGAATACGAAGAAATGT 59.178 33.333 0.00 0.00 40.36 2.71
2283 2593 8.196802 TGTATTGGACTGAATACGAAGAAATG 57.803 34.615 0.00 0.00 40.36 2.32
2284 2594 8.964476 ATGTATTGGACTGAATACGAAGAAAT 57.036 30.769 0.00 0.00 40.36 2.17
2286 2596 9.692749 GATATGTATTGGACTGAATACGAAGAA 57.307 33.333 0.00 0.00 40.36 2.52
2287 2597 8.304596 GGATATGTATTGGACTGAATACGAAGA 58.695 37.037 0.00 0.00 40.36 2.87
2288 2598 8.307483 AGGATATGTATTGGACTGAATACGAAG 58.693 37.037 0.00 0.00 40.36 3.79
2289 2599 8.190326 AGGATATGTATTGGACTGAATACGAA 57.810 34.615 0.00 0.00 40.36 3.85
2290 2600 7.776618 AGGATATGTATTGGACTGAATACGA 57.223 36.000 0.00 0.00 40.36 3.43
2291 2601 8.740906 AGTAGGATATGTATTGGACTGAATACG 58.259 37.037 0.00 0.00 40.36 3.06
2294 2604 9.830186 ACTAGTAGGATATGTATTGGACTGAAT 57.170 33.333 1.45 0.00 0.00 2.57
2296 2606 9.736414 GTACTAGTAGGATATGTATTGGACTGA 57.264 37.037 1.87 0.00 0.00 3.41
2297 2607 8.958506 GGTACTAGTAGGATATGTATTGGACTG 58.041 40.741 1.87 0.00 0.00 3.51
2298 2608 8.676020 TGGTACTAGTAGGATATGTATTGGACT 58.324 37.037 1.87 0.00 0.00 3.85
2299 2609 8.874744 TGGTACTAGTAGGATATGTATTGGAC 57.125 38.462 1.87 0.00 0.00 4.02
2300 2610 7.614583 GCTGGTACTAGTAGGATATGTATTGGA 59.385 40.741 8.16 0.00 0.00 3.53
2301 2611 7.396339 TGCTGGTACTAGTAGGATATGTATTGG 59.604 40.741 8.16 0.00 0.00 3.16
2302 2612 8.349568 TGCTGGTACTAGTAGGATATGTATTG 57.650 38.462 8.16 0.00 0.00 1.90
2303 2613 8.391699 TCTGCTGGTACTAGTAGGATATGTATT 58.608 37.037 21.12 0.00 32.13 1.89
2304 2614 7.929959 TCTGCTGGTACTAGTAGGATATGTAT 58.070 38.462 21.12 0.00 32.13 2.29
2305 2615 7.325725 TCTGCTGGTACTAGTAGGATATGTA 57.674 40.000 21.12 0.80 32.13 2.29
2306 2616 6.202202 TCTGCTGGTACTAGTAGGATATGT 57.798 41.667 21.12 0.00 32.13 2.29
2307 2617 6.349777 GCTTCTGCTGGTACTAGTAGGATATG 60.350 46.154 21.12 5.47 36.03 1.78
2308 2618 5.712917 GCTTCTGCTGGTACTAGTAGGATAT 59.287 44.000 21.12 0.00 36.03 1.63
2309 2619 5.071370 GCTTCTGCTGGTACTAGTAGGATA 58.929 45.833 21.12 8.80 36.03 2.59
2310 2620 3.892588 GCTTCTGCTGGTACTAGTAGGAT 59.107 47.826 21.12 0.00 36.03 3.24
2311 2621 3.288964 GCTTCTGCTGGTACTAGTAGGA 58.711 50.000 21.12 13.78 36.03 2.94
2312 2622 3.719173 GCTTCTGCTGGTACTAGTAGG 57.281 52.381 21.12 9.64 36.03 3.18
2320 2630 9.428336 AGTCTACTACTGTAGCTTCTGCTGGTA 62.428 44.444 14.55 0.00 43.10 3.25
2321 2631 8.717573 AGTCTACTACTGTAGCTTCTGCTGGT 62.718 46.154 14.55 0.00 43.10 4.00
2322 2632 6.379317 AGTCTACTACTGTAGCTTCTGCTGG 61.379 48.000 14.55 0.00 43.10 4.85
2323 2633 4.638421 AGTCTACTACTGTAGCTTCTGCTG 59.362 45.833 14.55 0.00 43.10 4.41
2324 2634 4.850680 AGTCTACTACTGTAGCTTCTGCT 58.149 43.478 14.55 3.64 44.51 4.24
2325 2635 6.680874 TTAGTCTACTACTGTAGCTTCTGC 57.319 41.667 14.55 1.54 44.26 4.26
2326 2636 8.126074 CACATTAGTCTACTACTGTAGCTTCTG 58.874 40.741 14.55 0.00 44.26 3.02
2327 2637 8.047911 TCACATTAGTCTACTACTGTAGCTTCT 58.952 37.037 14.55 10.17 44.26 2.85
2328 2638 8.211116 TCACATTAGTCTACTACTGTAGCTTC 57.789 38.462 14.55 3.79 44.26 3.86
2329 2639 8.460428 GTTCACATTAGTCTACTACTGTAGCTT 58.540 37.037 14.55 0.00 44.26 3.74
2330 2640 7.830201 AGTTCACATTAGTCTACTACTGTAGCT 59.170 37.037 14.55 6.37 44.26 3.32
2331 2641 7.987649 AGTTCACATTAGTCTACTACTGTAGC 58.012 38.462 14.55 0.00 44.26 3.58
2332 2642 9.776158 CAAGTTCACATTAGTCTACTACTGTAG 57.224 37.037 13.13 13.13 45.56 2.74
2333 2643 8.242053 GCAAGTTCACATTAGTCTACTACTGTA 58.758 37.037 11.42 0.00 39.38 2.74
2334 2644 7.039644 AGCAAGTTCACATTAGTCTACTACTGT 60.040 37.037 7.18 7.18 41.22 3.55
2335 2645 7.274468 CAGCAAGTTCACATTAGTCTACTACTG 59.726 40.741 6.08 6.08 39.39 2.74
2336 2646 7.039644 ACAGCAAGTTCACATTAGTCTACTACT 60.040 37.037 0.00 0.00 42.62 2.57
2337 2647 7.091443 ACAGCAAGTTCACATTAGTCTACTAC 58.909 38.462 0.00 0.00 0.00 2.73
2338 2648 7.228314 ACAGCAAGTTCACATTAGTCTACTA 57.772 36.000 0.00 0.00 0.00 1.82
2339 2649 6.102897 ACAGCAAGTTCACATTAGTCTACT 57.897 37.500 0.00 0.00 0.00 2.57
2340 2650 6.787085 AACAGCAAGTTCACATTAGTCTAC 57.213 37.500 0.00 0.00 34.74 2.59
2341 2651 6.765989 ACAAACAGCAAGTTCACATTAGTCTA 59.234 34.615 0.00 0.00 40.26 2.59
2342 2652 5.590259 ACAAACAGCAAGTTCACATTAGTCT 59.410 36.000 0.00 0.00 40.26 3.24
2343 2653 5.821204 ACAAACAGCAAGTTCACATTAGTC 58.179 37.500 0.00 0.00 40.26 2.59
2344 2654 5.590259 AGACAAACAGCAAGTTCACATTAGT 59.410 36.000 0.00 0.00 40.26 2.24
2345 2655 6.064846 AGACAAACAGCAAGTTCACATTAG 57.935 37.500 0.00 0.00 40.26 1.73
2346 2656 7.561021 TTAGACAAACAGCAAGTTCACATTA 57.439 32.000 0.00 0.00 40.26 1.90
2347 2657 4.989279 AGACAAACAGCAAGTTCACATT 57.011 36.364 0.00 0.00 40.26 2.71
2348 2658 6.449635 TTTAGACAAACAGCAAGTTCACAT 57.550 33.333 0.00 0.00 40.26 3.21
2349 2659 5.888691 TTTAGACAAACAGCAAGTTCACA 57.111 34.783 0.00 0.00 40.26 3.58
2350 2660 6.972328 TCAATTTAGACAAACAGCAAGTTCAC 59.028 34.615 0.00 0.00 40.26 3.18
2351 2661 7.094508 TCAATTTAGACAAACAGCAAGTTCA 57.905 32.000 0.00 0.00 40.26 3.18
2352 2662 7.196331 ACTCAATTTAGACAAACAGCAAGTTC 58.804 34.615 0.00 0.00 40.26 3.01
2353 2663 7.100458 ACTCAATTTAGACAAACAGCAAGTT 57.900 32.000 0.00 0.00 43.89 2.66
2354 2664 6.699575 ACTCAATTTAGACAAACAGCAAGT 57.300 33.333 0.00 0.00 0.00 3.16
2355 2665 6.074676 GCAACTCAATTTAGACAAACAGCAAG 60.075 38.462 0.00 0.00 0.00 4.01
2356 2666 5.748152 GCAACTCAATTTAGACAAACAGCAA 59.252 36.000 0.00 0.00 0.00 3.91
2357 2667 5.067674 AGCAACTCAATTTAGACAAACAGCA 59.932 36.000 0.00 0.00 0.00 4.41
2358 2668 5.523369 AGCAACTCAATTTAGACAAACAGC 58.477 37.500 0.00 0.00 0.00 4.40
2359 2669 6.963796 AGAGCAACTCAATTTAGACAAACAG 58.036 36.000 0.00 0.00 32.06 3.16
2360 2670 6.942532 AGAGCAACTCAATTTAGACAAACA 57.057 33.333 0.00 0.00 32.06 2.83
2361 2671 7.018235 GCTAGAGCAACTCAATTTAGACAAAC 58.982 38.462 0.00 0.00 41.59 2.93
2362 2672 6.936900 AGCTAGAGCAACTCAATTTAGACAAA 59.063 34.615 4.01 0.00 45.16 2.83
2363 2673 6.467677 AGCTAGAGCAACTCAATTTAGACAA 58.532 36.000 4.01 0.00 45.16 3.18
2364 2674 6.042638 AGCTAGAGCAACTCAATTTAGACA 57.957 37.500 4.01 0.00 45.16 3.41
2365 2675 5.231147 CGAGCTAGAGCAACTCAATTTAGAC 59.769 44.000 4.01 0.00 45.16 2.59
2366 2676 5.344066 CGAGCTAGAGCAACTCAATTTAGA 58.656 41.667 4.01 0.00 45.16 2.10
2367 2677 4.026145 GCGAGCTAGAGCAACTCAATTTAG 60.026 45.833 4.01 0.00 45.16 1.85
2368 2678 3.865745 GCGAGCTAGAGCAACTCAATTTA 59.134 43.478 4.01 0.00 45.16 1.40
2369 2679 2.675348 GCGAGCTAGAGCAACTCAATTT 59.325 45.455 4.01 0.00 45.16 1.82
2370 2680 2.275318 GCGAGCTAGAGCAACTCAATT 58.725 47.619 4.01 0.00 45.16 2.32
2371 2681 1.205655 TGCGAGCTAGAGCAACTCAAT 59.794 47.619 8.32 0.00 45.16 2.57
2372 2682 0.603065 TGCGAGCTAGAGCAACTCAA 59.397 50.000 8.32 0.00 45.16 3.02
2373 2683 2.267045 TGCGAGCTAGAGCAACTCA 58.733 52.632 8.32 0.00 45.16 3.41
2379 2689 1.700523 CATCAGATGCGAGCTAGAGC 58.299 55.000 0.00 0.00 42.49 4.09
2390 2700 0.468648 TGAGCTGGAGGCATCAGATG 59.531 55.000 5.98 5.98 44.79 2.90
2391 2701 1.210538 TTGAGCTGGAGGCATCAGAT 58.789 50.000 0.00 4.62 44.79 2.90
2392 2702 0.986527 TTTGAGCTGGAGGCATCAGA 59.013 50.000 0.00 0.00 44.79 3.27
2393 2703 1.093159 GTTTGAGCTGGAGGCATCAG 58.907 55.000 0.00 0.00 44.79 2.90
2394 2704 0.401356 TGTTTGAGCTGGAGGCATCA 59.599 50.000 0.00 0.00 44.79 3.07
2395 2705 1.674962 GATGTTTGAGCTGGAGGCATC 59.325 52.381 0.00 0.00 44.79 3.91
2396 2706 1.284198 AGATGTTTGAGCTGGAGGCAT 59.716 47.619 0.00 0.00 44.79 4.40
2397 2707 0.694771 AGATGTTTGAGCTGGAGGCA 59.305 50.000 0.00 0.00 44.79 4.75
2398 2708 1.471684 CAAGATGTTTGAGCTGGAGGC 59.528 52.381 0.00 0.00 42.19 4.70
2399 2709 2.089980 CCAAGATGTTTGAGCTGGAGG 58.910 52.381 0.00 0.00 0.00 4.30
2400 2710 3.063510 TCCAAGATGTTTGAGCTGGAG 57.936 47.619 0.00 0.00 0.00 3.86
2401 2711 3.349927 CATCCAAGATGTTTGAGCTGGA 58.650 45.455 0.00 0.00 0.00 3.86
2402 2712 2.426024 CCATCCAAGATGTTTGAGCTGG 59.574 50.000 0.00 0.00 0.00 4.85
2403 2713 2.159282 GCCATCCAAGATGTTTGAGCTG 60.159 50.000 0.00 0.00 0.00 4.24
2404 2714 2.097825 GCCATCCAAGATGTTTGAGCT 58.902 47.619 4.04 0.00 0.00 4.09
2405 2715 1.202222 CGCCATCCAAGATGTTTGAGC 60.202 52.381 4.04 0.00 0.00 4.26
2406 2716 1.202222 GCGCCATCCAAGATGTTTGAG 60.202 52.381 0.00 0.00 0.00 3.02
2407 2717 0.810648 GCGCCATCCAAGATGTTTGA 59.189 50.000 0.00 0.00 0.00 2.69
2408 2718 0.527113 TGCGCCATCCAAGATGTTTG 59.473 50.000 4.18 0.00 0.00 2.93
2409 2719 0.813184 CTGCGCCATCCAAGATGTTT 59.187 50.000 4.18 0.00 0.00 2.83
2410 2720 1.660560 GCTGCGCCATCCAAGATGTT 61.661 55.000 4.18 0.00 0.00 2.71
2411 2721 2.117156 GCTGCGCCATCCAAGATGT 61.117 57.895 4.18 0.00 0.00 3.06
2412 2722 1.783031 GAGCTGCGCCATCCAAGATG 61.783 60.000 4.18 0.00 0.00 2.90
2413 2723 1.525535 GAGCTGCGCCATCCAAGAT 60.526 57.895 4.18 0.00 0.00 2.40
2414 2724 2.124983 GAGCTGCGCCATCCAAGA 60.125 61.111 4.18 0.00 0.00 3.02
2415 2725 1.822613 ATGAGCTGCGCCATCCAAG 60.823 57.895 4.18 0.00 0.00 3.61
2416 2726 2.116533 CATGAGCTGCGCCATCCAA 61.117 57.895 4.18 0.00 0.00 3.53
2417 2727 2.515290 CATGAGCTGCGCCATCCA 60.515 61.111 4.18 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.