Multiple sequence alignment - TraesCS7A01G418100

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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 TraesCS7A01G418100 chr7A 100.000 2804 0 0 1 2804 609432680 609429877 0.000000e+00 5179.0
1 TraesCS7A01G418100 chr7B 91.484 1867 81 38 703 2517 568107898 568106058 0.000000e+00 2495.0
2 TraesCS7A01G418100 chr7B 88.298 188 12 2 2506 2693 568100951 568100774 1.690000e-52 217.0
3 TraesCS7A01G418100 chr7B 100.000 45 0 0 104 148 568107965 568107921 1.790000e-12 84.2
4 TraesCS7A01G418100 chr7D 94.494 1126 30 13 703 1811 529956925 529955815 0.000000e+00 1707.0
5 TraesCS7A01G418100 chr7D 92.754 828 43 7 1876 2693 529955722 529954902 0.000000e+00 1181.0
6 TraesCS7A01G418100 chr7D 89.971 688 59 7 2 687 529957591 529956912 0.000000e+00 880.0
7 TraesCS7A01G418100 chr1D 78.898 635 85 29 1186 1796 14986302 14985693 4.380000e-103 385.0
8 TraesCS7A01G418100 chr6A 80.912 351 49 13 1086 1424 85586837 85586493 7.700000e-66 261.0
9 TraesCS7A01G418100 chr6B 80.516 349 51 12 1086 1424 143200178 143199837 4.640000e-63 252.0
10 TraesCS7A01G418100 chr2D 82.609 207 35 1 1203 1408 539895940 539895734 6.170000e-42 182.0
11 TraesCS7A01G418100 chr5D 80.000 200 33 6 1204 1399 330078610 330078806 1.050000e-29 141.0
12 TraesCS7A01G418100 chr5B 80.100 201 31 8 1204 1399 383036035 383036231 1.050000e-29 141.0
13 TraesCS7A01G418100 chr5A 79.000 200 35 6 1204 1399 426730435 426730239 2.270000e-26 130.0
14 TraesCS7A01G418100 chr4A 78.014 141 28 2 500 640 728849890 728850027 4.980000e-13 86.1


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 TraesCS7A01G418100 chr7A 609429877 609432680 2803 True 5179.0 5179 100.000000 1 2804 1 chr7A.!!$R1 2803
1 TraesCS7A01G418100 chr7B 568106058 568107965 1907 True 1289.6 2495 95.742000 104 2517 2 chr7B.!!$R2 2413
2 TraesCS7A01G418100 chr7D 529954902 529957591 2689 True 1256.0 1707 92.406333 2 2693 3 chr7D.!!$R1 2691
3 TraesCS7A01G418100 chr1D 14985693 14986302 609 True 385.0 385 78.898000 1186 1796 1 chr1D.!!$R1 610

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
280 282 0.036952 CCATCGACAACCTGCTGACT 60.037 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1883 0.038166 GGGGGCATCTGAACTGTGAA 59.962 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
28 29 8.212995 AGTCCAACCTCATTGAAAATTTTCATT 58.787 29.630 29.13 23.39 45.65 2.57
65 66 3.521947 ATTGACAAGTAGGGCGTCTAC 57.478 47.619 9.16 9.16 46.63 2.59
78 79 4.338682 AGGGCGTCTACTTATAACACTCTG 59.661 45.833 0.00 0.00 0.00 3.35
176 178 0.099082 CCTGCTAAGTCTCGGTCGAC 59.901 60.000 7.13 7.13 0.00 4.20
178 180 2.277969 CTGCTAAGTCTCGGTCGACTA 58.722 52.381 16.46 3.17 43.14 2.59
226 228 2.744202 CGCTTGGTTGCTCTAGAAACAT 59.256 45.455 9.06 0.00 35.23 2.71
227 229 3.189287 CGCTTGGTTGCTCTAGAAACATT 59.811 43.478 9.06 0.00 35.23 2.71
232 234 7.575720 GCTTGGTTGCTCTAGAAACATTGTAAT 60.576 37.037 9.06 0.00 35.23 1.89
241 243 9.401058 CTCTAGAAACATTGTAATGGGAAGATT 57.599 33.333 9.22 0.00 40.70 2.40
247 249 7.645058 ACATTGTAATGGGAAGATTTTCGAT 57.355 32.000 9.22 0.00 40.70 3.59
249 251 7.339212 ACATTGTAATGGGAAGATTTTCGATGA 59.661 33.333 9.22 0.00 40.70 2.92
250 252 7.880160 TTGTAATGGGAAGATTTTCGATGAT 57.120 32.000 0.00 0.00 33.98 2.45
260 262 3.829886 TTTTCGATGATGCACAAGTCC 57.170 42.857 0.00 0.00 0.00 3.85
280 282 0.036952 CCATCGACAACCTGCTGACT 60.037 55.000 0.00 0.00 0.00 3.41
282 284 2.146342 CATCGACAACCTGCTGACTTT 58.854 47.619 0.00 0.00 0.00 2.66
306 308 3.131396 TCAAAGACGAGGCAAGACTTTC 58.869 45.455 0.00 0.00 32.95 2.62
358 360 6.939163 AGAGCATCATTCCTGTAATATGAACC 59.061 38.462 0.00 0.00 37.82 3.62
384 386 2.361737 GGCTGAGCAACCCCTTCC 60.362 66.667 6.82 0.00 0.00 3.46
398 400 0.534412 CCTTCCGATGCTCACTCTGT 59.466 55.000 0.00 0.00 0.00 3.41
404 406 2.613977 CCGATGCTCACTCTGTTTTCCT 60.614 50.000 0.00 0.00 0.00 3.36
411 413 4.363138 CTCACTCTGTTTTCCTTTTTGCC 58.637 43.478 0.00 0.00 0.00 4.52
412 414 4.023291 TCACTCTGTTTTCCTTTTTGCCT 58.977 39.130 0.00 0.00 0.00 4.75
459 461 2.043801 AGCTCTTCTGTTACTCTCCCCT 59.956 50.000 0.00 0.00 0.00 4.79
476 478 6.759272 TCTCCCCTATCAATGAAAAGATACG 58.241 40.000 0.00 0.00 0.00 3.06
477 479 5.305585 TCCCCTATCAATGAAAAGATACGC 58.694 41.667 0.00 0.00 0.00 4.42
485 487 1.300481 GAAAAGATACGCCCCTGAGC 58.700 55.000 0.00 0.00 0.00 4.26
494 496 2.993539 GCCCCTGAGCGTATTTCTC 58.006 57.895 0.00 0.00 0.00 2.87
533 536 5.220951 CGATGCTATAGCCGTGAGATCTTAT 60.221 44.000 21.84 3.98 41.18 1.73
598 601 6.000891 TCTTGCATGTTAATGTCACTTGAC 57.999 37.500 2.19 2.19 44.97 3.18
615 618 9.736023 GTCACTTGACTGAAACTTGATTAAATT 57.264 29.630 1.92 0.00 41.65 1.82
635 638 9.595823 TTAAATTTCAATCGACTAAGACCTAGG 57.404 33.333 7.41 7.41 31.14 3.02
653 656 5.850028 ACCTAGGCACACCCATTTACTATAT 59.150 40.000 9.30 0.00 36.11 0.86
687 690 5.305585 TCTCAGTTCTTGCGGAATTTAACT 58.694 37.500 6.43 6.43 36.24 2.24
688 691 5.408604 TCTCAGTTCTTGCGGAATTTAACTC 59.591 40.000 8.54 0.00 36.24 3.01
689 692 5.305585 TCAGTTCTTGCGGAATTTAACTCT 58.694 37.500 8.54 0.00 36.24 3.24
690 693 5.763204 TCAGTTCTTGCGGAATTTAACTCTT 59.237 36.000 8.54 0.00 36.24 2.85
691 694 6.262273 TCAGTTCTTGCGGAATTTAACTCTTT 59.738 34.615 8.54 0.00 36.24 2.52
692 695 6.918022 CAGTTCTTGCGGAATTTAACTCTTTT 59.082 34.615 8.54 0.00 36.24 2.27
693 696 7.435192 CAGTTCTTGCGGAATTTAACTCTTTTT 59.565 33.333 8.54 0.00 36.24 1.94
708 711 2.833582 TTTTTGCGGGGTTGCGGA 60.834 55.556 0.00 0.00 37.81 5.54
709 712 2.423898 TTTTTGCGGGGTTGCGGAA 61.424 52.632 0.00 0.00 37.81 4.30
710 713 2.356818 TTTTTGCGGGGTTGCGGAAG 62.357 55.000 0.00 0.00 37.81 3.46
711 714 4.572571 TTGCGGGGTTGCGGAAGT 62.573 61.111 0.00 0.00 37.81 3.01
712 715 4.572571 TGCGGGGTTGCGGAAGTT 62.573 61.111 0.00 0.00 37.81 2.66
713 716 2.358984 GCGGGGTTGCGGAAGTTA 60.359 61.111 0.00 0.00 0.00 2.24
714 717 1.967494 GCGGGGTTGCGGAAGTTAA 60.967 57.895 0.00 0.00 0.00 2.01
715 718 1.871077 CGGGGTTGCGGAAGTTAAC 59.129 57.895 0.00 0.00 0.00 2.01
758 765 7.437748 TCCTAAGTGATCTTTTATGCTCTAGC 58.562 38.462 0.00 0.00 37.04 3.42
760 767 7.712639 CCTAAGTGATCTTTTATGCTCTAGCAA 59.287 37.037 9.01 0.00 43.29 3.91
1017 1036 1.528309 ACCAGCCAAACCAACCGAG 60.528 57.895 0.00 0.00 0.00 4.63
1502 1546 4.819761 TGCAGATGAGGCGACGGC 62.820 66.667 14.41 14.41 38.90 5.68
1549 1603 1.949847 ATGAGTTCAGACGGGGAGCG 61.950 60.000 0.00 0.00 0.00 5.03
1551 1605 4.452733 GTTCAGACGGGGAGCGGG 62.453 72.222 0.00 0.00 0.00 6.13
1716 1781 6.730960 ATGCAAAAACTTAGGCATTTGATG 57.269 33.333 0.00 0.00 43.97 3.07
1728 1793 1.125384 CATTTGATGCTGTTTGTGCGC 59.875 47.619 0.00 0.00 0.00 6.09
1747 1812 1.491670 CGCCATTATCCGTGTCTCTG 58.508 55.000 0.00 0.00 0.00 3.35
1824 1889 4.987832 CAGTAGCCTGTAGTACTTCACAG 58.012 47.826 15.99 15.99 41.51 3.66
1825 1890 4.459685 CAGTAGCCTGTAGTACTTCACAGT 59.540 45.833 19.67 8.79 40.47 3.55
1826 1891 5.047943 CAGTAGCCTGTAGTACTTCACAGTT 60.048 44.000 19.67 12.39 40.47 3.16
1827 1892 4.522722 AGCCTGTAGTACTTCACAGTTC 57.477 45.455 19.67 13.01 40.47 3.01
1828 1893 3.895656 AGCCTGTAGTACTTCACAGTTCA 59.104 43.478 19.67 1.31 40.47 3.18
1829 1894 4.021894 AGCCTGTAGTACTTCACAGTTCAG 60.022 45.833 19.67 9.18 40.47 3.02
1830 1895 4.022242 GCCTGTAGTACTTCACAGTTCAGA 60.022 45.833 19.67 0.00 40.47 3.27
1831 1896 5.336849 GCCTGTAGTACTTCACAGTTCAGAT 60.337 44.000 19.67 0.00 40.47 2.90
1832 1897 6.096036 CCTGTAGTACTTCACAGTTCAGATG 58.904 44.000 19.67 4.18 40.47 2.90
1833 1898 5.470368 TGTAGTACTTCACAGTTCAGATGC 58.530 41.667 0.00 0.00 34.06 3.91
1834 1899 3.931578 AGTACTTCACAGTTCAGATGCC 58.068 45.455 0.00 0.00 34.06 4.40
1835 1900 2.191128 ACTTCACAGTTCAGATGCCC 57.809 50.000 0.00 0.00 0.00 5.36
1861 1926 1.871039 GCTTAACAGTTCAGCAACCGA 59.129 47.619 13.65 0.00 33.45 4.69
1865 1930 2.038387 ACAGTTCAGCAACCGAAACT 57.962 45.000 0.00 0.00 32.22 2.66
1869 1987 2.354821 AGTTCAGCAACCGAAACTGTTC 59.645 45.455 0.00 0.00 32.22 3.18
1873 1991 0.310854 GCAACCGAAACTGTTCCAGG 59.689 55.000 0.00 0.54 35.51 4.45
1874 1992 0.310854 CAACCGAAACTGTTCCAGGC 59.689 55.000 0.00 0.00 35.51 4.85
1922 2040 1.202627 TGTTGGGGAAAATGCAACTGC 60.203 47.619 0.00 0.00 42.50 4.40
1927 2045 1.067354 GGGAAAATGCAACTGCTCTGG 60.067 52.381 2.95 0.00 42.66 3.86
2017 2135 5.645497 ACTCCATTGACAAGAGTTGCTTATC 59.355 40.000 4.65 0.00 37.60 1.75
2154 2276 6.321945 TCCATTCTTCATTGTCAATACATGGG 59.678 38.462 14.60 6.32 34.97 4.00
2194 2316 3.939740 ATCATGTTGCCACTACCTCAT 57.060 42.857 0.00 0.00 0.00 2.90
2221 2343 6.352516 AGTGTCAAGGCATTAATAAGAGAGG 58.647 40.000 0.00 0.00 0.00 3.69
2244 2366 3.956848 AGCCAGATAAAAAGGGAGATTGC 59.043 43.478 0.00 0.00 0.00 3.56
2375 2507 2.437449 TGCAATGGAGCAGCAGGT 59.563 55.556 0.00 0.00 40.11 4.00
2376 2508 1.974875 TGCAATGGAGCAGCAGGTG 60.975 57.895 0.00 0.00 40.11 4.00
2377 2509 1.975407 GCAATGGAGCAGCAGGTGT 60.975 57.895 0.66 0.00 0.00 4.16
2378 2510 1.880894 CAATGGAGCAGCAGGTGTG 59.119 57.895 0.66 0.00 0.00 3.82
2379 2511 0.892358 CAATGGAGCAGCAGGTGTGT 60.892 55.000 0.66 0.00 0.00 3.72
2380 2512 0.892358 AATGGAGCAGCAGGTGTGTG 60.892 55.000 0.66 0.00 0.00 3.82
2381 2513 2.060567 ATGGAGCAGCAGGTGTGTGT 62.061 55.000 0.66 0.00 0.00 3.72
2382 2514 2.256591 GGAGCAGCAGGTGTGTGTG 61.257 63.158 0.66 0.00 0.00 3.82
2390 2522 2.358247 GGTGTGTGTGGGTAGCCG 60.358 66.667 6.45 0.00 0.00 5.52
2421 2553 3.120041 CGGTTTCATTTGTTTGGTGTCC 58.880 45.455 0.00 0.00 0.00 4.02
2447 2579 5.067023 AGCTCTTGATTTTGGAATCGGAATC 59.933 40.000 0.00 0.00 43.75 2.52
2467 2599 7.439356 CGGAATCATAATCTCTACTTGCTTTGA 59.561 37.037 0.00 0.00 0.00 2.69
2504 2637 4.468868 TGCCATCATAGGATCTGATGTAGG 59.531 45.833 17.48 14.51 45.52 3.18
2523 2656 1.160870 TCTTCCTCCAGGGCAGGAA 59.839 57.895 8.96 8.96 46.05 3.36
2524 2657 3.826282 TTCCTCCAGGGCAGGAAG 58.174 61.111 5.64 0.00 43.84 3.46
2527 2660 2.373707 CCTCCAGGGCAGGAAGGAG 61.374 68.421 0.00 0.00 45.68 3.69
2532 2665 3.334054 GGGCAGGAAGGAGGCAGT 61.334 66.667 0.00 0.00 0.00 4.40
2580 2713 3.002791 GCACATCGAGGACAAGAAATCA 58.997 45.455 3.06 0.00 0.00 2.57
2609 2742 2.092753 GTGATGCTCTCCTTGATCCCAA 60.093 50.000 0.00 0.00 0.00 4.12
2610 2743 2.092753 TGATGCTCTCCTTGATCCCAAC 60.093 50.000 0.00 0.00 0.00 3.77
2611 2744 1.361204 TGCTCTCCTTGATCCCAACA 58.639 50.000 0.00 0.00 0.00 3.33
2612 2745 1.003580 TGCTCTCCTTGATCCCAACAC 59.996 52.381 0.00 0.00 0.00 3.32
2613 2746 1.680249 GCTCTCCTTGATCCCAACACC 60.680 57.143 0.00 0.00 0.00 4.16
2614 2747 1.630369 CTCTCCTTGATCCCAACACCA 59.370 52.381 0.00 0.00 0.00 4.17
2615 2748 2.040278 CTCTCCTTGATCCCAACACCAA 59.960 50.000 0.00 0.00 0.00 3.67
2655 2793 2.097954 TGATTGATCAATGTTCCAGCGC 59.902 45.455 25.37 0.00 33.08 5.92
2659 2797 0.806868 ATCAATGTTCCAGCGCACTG 59.193 50.000 11.47 0.00 44.05 3.66
2693 2831 2.299867 AGGTAAAAATGTTGCAGGGCAG 59.700 45.455 0.00 0.00 40.61 4.85
2694 2832 2.037121 GGTAAAAATGTTGCAGGGCAGT 59.963 45.455 0.00 0.00 40.61 4.40
2695 2833 3.257127 GGTAAAAATGTTGCAGGGCAGTA 59.743 43.478 0.00 0.00 40.61 2.74
2696 2834 3.665745 AAAAATGTTGCAGGGCAGTAG 57.334 42.857 0.00 0.00 40.61 2.57
2697 2835 1.549203 AAATGTTGCAGGGCAGTAGG 58.451 50.000 0.00 0.00 40.61 3.18
2698 2836 0.698238 AATGTTGCAGGGCAGTAGGA 59.302 50.000 0.00 0.00 40.61 2.94
2699 2837 0.035056 ATGTTGCAGGGCAGTAGGAC 60.035 55.000 0.00 0.00 40.61 3.85
2700 2838 1.374947 GTTGCAGGGCAGTAGGACA 59.625 57.895 0.00 0.00 40.61 4.02
2701 2839 0.955919 GTTGCAGGGCAGTAGGACAC 60.956 60.000 0.00 0.00 40.61 3.67
2702 2840 1.127567 TTGCAGGGCAGTAGGACACT 61.128 55.000 0.00 0.00 40.61 3.55
2703 2841 0.252057 TGCAGGGCAGTAGGACACTA 60.252 55.000 0.00 0.00 34.98 2.74
2704 2842 1.123928 GCAGGGCAGTAGGACACTAT 58.876 55.000 0.00 0.00 34.98 2.12
2705 2843 1.202580 GCAGGGCAGTAGGACACTATG 60.203 57.143 0.00 0.00 34.98 2.23
2706 2844 1.123928 AGGGCAGTAGGACACTATGC 58.876 55.000 0.00 0.00 34.98 3.14
2707 2845 0.106894 GGGCAGTAGGACACTATGCC 59.893 60.000 5.96 5.96 44.40 4.40
2708 2846 0.106894 GGCAGTAGGACACTATGCCC 59.893 60.000 3.11 0.00 42.14 5.36
2709 2847 0.249489 GCAGTAGGACACTATGCCCG 60.249 60.000 0.00 0.00 34.98 6.13
2710 2848 1.399714 CAGTAGGACACTATGCCCGA 58.600 55.000 0.00 0.00 34.98 5.14
2711 2849 1.754803 CAGTAGGACACTATGCCCGAA 59.245 52.381 0.00 0.00 34.98 4.30
2712 2850 2.365617 CAGTAGGACACTATGCCCGAAT 59.634 50.000 0.00 0.00 34.98 3.34
2713 2851 2.628657 AGTAGGACACTATGCCCGAATC 59.371 50.000 0.00 0.00 34.98 2.52
2714 2852 0.759346 AGGACACTATGCCCGAATCC 59.241 55.000 0.00 0.00 0.00 3.01
2715 2853 0.468226 GGACACTATGCCCGAATCCA 59.532 55.000 0.00 0.00 0.00 3.41
2716 2854 1.541233 GGACACTATGCCCGAATCCAG 60.541 57.143 0.00 0.00 0.00 3.86
2717 2855 1.139058 GACACTATGCCCGAATCCAGT 59.861 52.381 0.00 0.00 0.00 4.00
2718 2856 2.364324 GACACTATGCCCGAATCCAGTA 59.636 50.000 0.00 0.00 0.00 2.74
2719 2857 2.769663 ACACTATGCCCGAATCCAGTAA 59.230 45.455 0.00 0.00 0.00 2.24
2720 2858 3.391296 ACACTATGCCCGAATCCAGTAAT 59.609 43.478 0.00 0.00 0.00 1.89
2721 2859 4.591498 ACACTATGCCCGAATCCAGTAATA 59.409 41.667 0.00 0.00 0.00 0.98
2722 2860 4.929808 CACTATGCCCGAATCCAGTAATAC 59.070 45.833 0.00 0.00 0.00 1.89
2723 2861 2.922740 TGCCCGAATCCAGTAATACC 57.077 50.000 0.00 0.00 0.00 2.73
2724 2862 1.418637 TGCCCGAATCCAGTAATACCC 59.581 52.381 0.00 0.00 0.00 3.69
2725 2863 1.418637 GCCCGAATCCAGTAATACCCA 59.581 52.381 0.00 0.00 0.00 4.51
2726 2864 2.158726 GCCCGAATCCAGTAATACCCAA 60.159 50.000 0.00 0.00 0.00 4.12
2727 2865 3.473625 CCCGAATCCAGTAATACCCAAC 58.526 50.000 0.00 0.00 0.00 3.77
2728 2866 3.118186 CCCGAATCCAGTAATACCCAACA 60.118 47.826 0.00 0.00 0.00 3.33
2729 2867 4.519213 CCGAATCCAGTAATACCCAACAA 58.481 43.478 0.00 0.00 0.00 2.83
2730 2868 4.944930 CCGAATCCAGTAATACCCAACAAA 59.055 41.667 0.00 0.00 0.00 2.83
2731 2869 5.592688 CCGAATCCAGTAATACCCAACAAAT 59.407 40.000 0.00 0.00 0.00 2.32
2732 2870 6.238648 CCGAATCCAGTAATACCCAACAAATC 60.239 42.308 0.00 0.00 0.00 2.17
2733 2871 6.317642 CGAATCCAGTAATACCCAACAAATCA 59.682 38.462 0.00 0.00 0.00 2.57
2734 2872 7.467267 CGAATCCAGTAATACCCAACAAATCAG 60.467 40.741 0.00 0.00 0.00 2.90
2735 2873 5.505780 TCCAGTAATACCCAACAAATCAGG 58.494 41.667 0.00 0.00 0.00 3.86
2736 2874 5.014755 TCCAGTAATACCCAACAAATCAGGT 59.985 40.000 0.00 0.00 36.36 4.00
2737 2875 5.125417 CCAGTAATACCCAACAAATCAGGTG 59.875 44.000 0.00 0.00 33.70 4.00
2738 2876 5.943416 CAGTAATACCCAACAAATCAGGTGA 59.057 40.000 0.00 0.00 33.70 4.02
2739 2877 6.432783 CAGTAATACCCAACAAATCAGGTGAA 59.567 38.462 0.00 0.00 33.70 3.18
2740 2878 7.007723 AGTAATACCCAACAAATCAGGTGAAA 58.992 34.615 0.00 0.00 33.70 2.69
2741 2879 5.982890 ATACCCAACAAATCAGGTGAAAG 57.017 39.130 0.00 0.00 33.70 2.62
2742 2880 3.642141 ACCCAACAAATCAGGTGAAAGT 58.358 40.909 0.00 0.00 0.00 2.66
2743 2881 3.384467 ACCCAACAAATCAGGTGAAAGTG 59.616 43.478 0.00 0.00 0.00 3.16
2744 2882 3.636300 CCCAACAAATCAGGTGAAAGTGA 59.364 43.478 0.00 0.00 0.00 3.41
2745 2883 4.281688 CCCAACAAATCAGGTGAAAGTGAT 59.718 41.667 0.00 0.00 34.79 3.06
2746 2884 5.224888 CCAACAAATCAGGTGAAAGTGATG 58.775 41.667 0.00 0.00 33.58 3.07
2747 2885 4.510038 ACAAATCAGGTGAAAGTGATGC 57.490 40.909 0.00 0.00 33.58 3.91
2748 2886 4.147321 ACAAATCAGGTGAAAGTGATGCT 58.853 39.130 0.00 0.00 33.58 3.79
2749 2887 4.586001 ACAAATCAGGTGAAAGTGATGCTT 59.414 37.500 0.00 0.00 39.52 3.91
2760 2898 5.921962 AAAGTGATGCTTTCCTTAATCCC 57.078 39.130 0.00 0.00 43.42 3.85
2761 2899 4.591321 AGTGATGCTTTCCTTAATCCCA 57.409 40.909 0.00 0.00 0.00 4.37
2762 2900 4.530875 AGTGATGCTTTCCTTAATCCCAG 58.469 43.478 0.00 0.00 0.00 4.45
2763 2901 3.067320 GTGATGCTTTCCTTAATCCCAGC 59.933 47.826 0.00 0.00 0.00 4.85
2764 2902 2.897271 TGCTTTCCTTAATCCCAGCA 57.103 45.000 0.00 0.00 34.92 4.41
2765 2903 2.726821 TGCTTTCCTTAATCCCAGCAG 58.273 47.619 0.00 0.00 32.38 4.24
2766 2904 1.406898 GCTTTCCTTAATCCCAGCAGC 59.593 52.381 0.00 0.00 0.00 5.25
2767 2905 2.947695 GCTTTCCTTAATCCCAGCAGCT 60.948 50.000 0.00 0.00 0.00 4.24
2768 2906 3.685550 GCTTTCCTTAATCCCAGCAGCTA 60.686 47.826 0.00 0.00 0.00 3.32
2769 2907 4.526970 CTTTCCTTAATCCCAGCAGCTAA 58.473 43.478 0.00 0.00 0.00 3.09
2770 2908 3.560636 TCCTTAATCCCAGCAGCTAAC 57.439 47.619 0.00 0.00 0.00 2.34
2771 2909 2.158957 TCCTTAATCCCAGCAGCTAACG 60.159 50.000 0.00 0.00 0.00 3.18
2772 2910 2.213499 CTTAATCCCAGCAGCTAACGG 58.787 52.381 0.00 0.00 0.00 4.44
2773 2911 1.491668 TAATCCCAGCAGCTAACGGA 58.508 50.000 7.36 7.36 0.00 4.69
2774 2912 0.618458 AATCCCAGCAGCTAACGGAA 59.382 50.000 8.70 0.00 0.00 4.30
2775 2913 0.618458 ATCCCAGCAGCTAACGGAAA 59.382 50.000 8.70 0.00 0.00 3.13
2776 2914 0.618458 TCCCAGCAGCTAACGGAAAT 59.382 50.000 0.00 0.00 0.00 2.17
2777 2915 0.734889 CCCAGCAGCTAACGGAAATG 59.265 55.000 0.00 0.00 0.00 2.32
2778 2916 0.099436 CCAGCAGCTAACGGAAATGC 59.901 55.000 0.00 0.00 37.15 3.56
2779 2917 0.804364 CAGCAGCTAACGGAAATGCA 59.196 50.000 0.00 0.00 39.34 3.96
2780 2918 1.089920 AGCAGCTAACGGAAATGCAG 58.910 50.000 0.00 0.00 39.34 4.41
2781 2919 0.804989 GCAGCTAACGGAAATGCAGT 59.195 50.000 0.00 0.00 36.88 4.40
2782 2920 1.466360 GCAGCTAACGGAAATGCAGTG 60.466 52.381 0.00 0.00 36.88 3.66
2783 2921 2.076100 CAGCTAACGGAAATGCAGTGA 58.924 47.619 0.00 0.00 0.00 3.41
2784 2922 2.679837 CAGCTAACGGAAATGCAGTGAT 59.320 45.455 0.00 0.00 0.00 3.06
2785 2923 2.679837 AGCTAACGGAAATGCAGTGATG 59.320 45.455 0.00 0.00 0.00 3.07
2786 2924 2.223340 GCTAACGGAAATGCAGTGATGG 60.223 50.000 0.00 0.00 0.00 3.51
2787 2925 2.198827 AACGGAAATGCAGTGATGGA 57.801 45.000 0.00 0.00 0.00 3.41
2788 2926 2.425143 ACGGAAATGCAGTGATGGAT 57.575 45.000 0.00 0.00 0.00 3.41
2789 2927 2.292267 ACGGAAATGCAGTGATGGATC 58.708 47.619 0.00 0.00 0.00 3.36
2790 2928 2.291365 CGGAAATGCAGTGATGGATCA 58.709 47.619 0.00 0.00 0.00 2.92
2791 2929 2.684374 CGGAAATGCAGTGATGGATCAA 59.316 45.455 0.00 0.00 38.75 2.57
2792 2930 3.488047 CGGAAATGCAGTGATGGATCAAC 60.488 47.826 0.00 0.00 38.75 3.18
2793 2931 3.488047 GGAAATGCAGTGATGGATCAACG 60.488 47.826 0.00 0.00 38.75 4.10
2794 2932 1.019673 ATGCAGTGATGGATCAACGC 58.980 50.000 0.00 5.10 38.75 4.84
2795 2933 0.036105 TGCAGTGATGGATCAACGCT 60.036 50.000 0.00 0.00 38.75 5.07
2796 2934 0.376152 GCAGTGATGGATCAACGCTG 59.624 55.000 16.59 16.59 43.99 5.18
2797 2935 0.376152 CAGTGATGGATCAACGCTGC 59.624 55.000 11.48 0.00 37.78 5.25
2798 2936 0.036105 AGTGATGGATCAACGCTGCA 60.036 50.000 0.00 0.00 38.75 4.41
2799 2937 0.376152 GTGATGGATCAACGCTGCAG 59.624 55.000 10.11 10.11 38.75 4.41
2800 2938 1.354506 GATGGATCAACGCTGCAGC 59.645 57.895 29.12 29.12 37.78 5.25
2801 2939 1.371337 GATGGATCAACGCTGCAGCA 61.371 55.000 36.03 18.99 42.21 4.41
2802 2940 1.651240 ATGGATCAACGCTGCAGCAC 61.651 55.000 36.03 18.90 42.21 4.40
2803 2941 2.327343 GGATCAACGCTGCAGCACA 61.327 57.895 36.03 17.78 42.21 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.376854 AATTTTCAATGAGGTTGGACTCG 57.623 39.130 0.00 0.00 40.39 4.18
36 37 4.142600 GCCCTACTTGTCAATTGTCATGAC 60.143 45.833 19.27 19.27 45.82 3.06
40 41 2.224426 ACGCCCTACTTGTCAATTGTCA 60.224 45.455 5.13 2.96 0.00 3.58
41 42 2.415512 GACGCCCTACTTGTCAATTGTC 59.584 50.000 5.13 0.00 32.91 3.18
42 43 2.038557 AGACGCCCTACTTGTCAATTGT 59.961 45.455 5.13 0.00 35.09 2.71
43 44 2.699954 AGACGCCCTACTTGTCAATTG 58.300 47.619 0.00 0.00 35.09 2.32
44 45 3.858247 GTAGACGCCCTACTTGTCAATT 58.142 45.455 7.97 0.00 43.42 2.32
45 46 3.521947 GTAGACGCCCTACTTGTCAAT 57.478 47.619 7.97 0.00 43.42 2.57
56 57 4.499357 CCAGAGTGTTATAAGTAGACGCCC 60.499 50.000 0.00 0.00 0.00 6.13
176 178 4.362932 TGATGAGCGAGTGAAGTCTTAG 57.637 45.455 0.00 0.00 0.00 2.18
178 180 3.883830 ATGATGAGCGAGTGAAGTCTT 57.116 42.857 0.00 0.00 0.00 3.01
213 215 6.061022 TCCCATTACAATGTTTCTAGAGCA 57.939 37.500 0.00 0.00 34.60 4.26
219 221 8.028938 CGAAAATCTTCCCATTACAATGTTTCT 58.971 33.333 0.00 0.00 34.60 2.52
226 228 7.681782 GCATCATCGAAAATCTTCCCATTACAA 60.682 37.037 0.00 0.00 0.00 2.41
227 229 6.238731 GCATCATCGAAAATCTTCCCATTACA 60.239 38.462 0.00 0.00 0.00 2.41
232 234 3.378112 GTGCATCATCGAAAATCTTCCCA 59.622 43.478 0.00 0.00 0.00 4.37
241 243 2.083774 GGGACTTGTGCATCATCGAAA 58.916 47.619 0.00 0.00 0.00 3.46
247 249 0.392863 CGATGGGGACTTGTGCATCA 60.393 55.000 0.00 0.00 0.00 3.07
249 251 0.392998 GTCGATGGGGACTTGTGCAT 60.393 55.000 0.00 0.00 34.09 3.96
250 252 1.003839 GTCGATGGGGACTTGTGCA 60.004 57.895 0.00 0.00 34.09 4.57
260 262 1.021390 GTCAGCAGGTTGTCGATGGG 61.021 60.000 0.00 0.00 0.00 4.00
280 282 5.305585 AGTCTTGCCTCGTCTTTGATTAAA 58.694 37.500 0.00 0.00 0.00 1.52
282 284 4.537135 AGTCTTGCCTCGTCTTTGATTA 57.463 40.909 0.00 0.00 0.00 1.75
331 333 6.393171 TCATATTACAGGAATGATGCTCTCG 58.607 40.000 0.00 0.00 0.00 4.04
347 349 4.593634 AGCCCCTACAGAGGTTCATATTAC 59.406 45.833 0.00 0.00 41.95 1.89
358 360 0.107945 GTTGCTCAGCCCCTACAGAG 60.108 60.000 0.00 0.00 0.00 3.35
384 386 2.693069 AGGAAAACAGAGTGAGCATCG 58.307 47.619 0.00 0.00 38.61 3.84
398 400 2.908688 GCTGGAGGCAAAAAGGAAAA 57.091 45.000 0.00 0.00 41.35 2.29
411 413 1.815421 GGCCGTACACATGCTGGAG 60.815 63.158 0.00 0.00 0.00 3.86
412 414 2.118233 TTGGCCGTACACATGCTGGA 62.118 55.000 0.00 0.00 0.00 3.86
421 423 1.373435 CTTGTCCCTTGGCCGTACA 59.627 57.895 0.00 0.00 0.00 2.90
459 461 5.063204 CAGGGGCGTATCTTTTCATTGATA 58.937 41.667 0.00 0.00 0.00 2.15
476 478 0.178068 TGAGAAATACGCTCAGGGGC 59.822 55.000 0.00 0.00 37.46 5.80
477 479 2.691409 TTGAGAAATACGCTCAGGGG 57.309 50.000 0.00 0.00 42.74 4.79
508 511 1.892209 TCTCACGGCTATAGCATCGA 58.108 50.000 25.53 16.02 44.36 3.59
510 513 4.448537 AAGATCTCACGGCTATAGCATC 57.551 45.455 25.53 17.40 44.36 3.91
519 522 9.209175 ACAGATTTTAATATAAGATCTCACGGC 57.791 33.333 0.00 0.00 0.00 5.68
570 573 3.010027 TGACATTAACATGCAAGAGGGGA 59.990 43.478 0.00 0.00 33.05 4.81
571 574 3.129287 GTGACATTAACATGCAAGAGGGG 59.871 47.826 0.00 0.00 33.05 4.79
573 576 5.181811 TCAAGTGACATTAACATGCAAGAGG 59.818 40.000 0.00 0.00 33.05 3.69
615 618 4.021229 TGCCTAGGTCTTAGTCGATTGAA 58.979 43.478 11.31 0.00 0.00 2.69
618 621 3.130693 GTGTGCCTAGGTCTTAGTCGATT 59.869 47.826 11.31 0.00 0.00 3.34
626 629 1.372501 AATGGGTGTGCCTAGGTCTT 58.627 50.000 11.31 0.00 34.45 3.01
635 638 9.284968 AGAATTACATATAGTAAATGGGTGTGC 57.715 33.333 0.00 0.00 45.25 4.57
653 656 5.177511 CGCAAGAACTGAGAACAGAATTACA 59.822 40.000 0.00 0.00 43.36 2.41
691 694 2.356818 CTTCCGCAACCCCGCAAAAA 62.357 55.000 0.00 0.00 0.00 1.94
692 695 2.833582 TTCCGCAACCCCGCAAAA 60.834 55.556 0.00 0.00 0.00 2.44
693 696 3.291383 CTTCCGCAACCCCGCAAA 61.291 61.111 0.00 0.00 0.00 3.68
694 697 2.677765 TAACTTCCGCAACCCCGCAA 62.678 55.000 0.00 0.00 0.00 4.85
695 698 2.677765 TTAACTTCCGCAACCCCGCA 62.678 55.000 0.00 0.00 0.00 5.69
696 699 1.967494 TTAACTTCCGCAACCCCGC 60.967 57.895 0.00 0.00 0.00 6.13
697 700 0.885596 TGTTAACTTCCGCAACCCCG 60.886 55.000 7.22 0.00 0.00 5.73
698 701 1.541379 ATGTTAACTTCCGCAACCCC 58.459 50.000 7.22 0.00 0.00 4.95
699 702 2.924880 GCAATGTTAACTTCCGCAACCC 60.925 50.000 7.22 0.00 0.00 4.11
700 703 2.324860 GCAATGTTAACTTCCGCAACC 58.675 47.619 7.22 0.00 0.00 3.77
701 704 2.287909 TGGCAATGTTAACTTCCGCAAC 60.288 45.455 7.22 0.00 0.00 4.17
702 705 1.957177 TGGCAATGTTAACTTCCGCAA 59.043 42.857 7.22 0.00 0.00 4.85
703 706 1.610363 TGGCAATGTTAACTTCCGCA 58.390 45.000 7.22 0.00 0.00 5.69
704 707 2.163412 TCATGGCAATGTTAACTTCCGC 59.837 45.455 7.22 7.15 35.15 5.54
705 708 3.190327 TGTCATGGCAATGTTAACTTCCG 59.810 43.478 0.00 0.00 35.15 4.30
706 709 4.218417 ACTGTCATGGCAATGTTAACTTCC 59.782 41.667 0.00 3.50 35.15 3.46
707 710 5.376854 ACTGTCATGGCAATGTTAACTTC 57.623 39.130 0.00 0.00 35.15 3.01
708 711 5.068987 ACAACTGTCATGGCAATGTTAACTT 59.931 36.000 11.50 0.00 35.15 2.66
709 712 4.584325 ACAACTGTCATGGCAATGTTAACT 59.416 37.500 11.50 0.00 35.15 2.24
710 713 4.870363 ACAACTGTCATGGCAATGTTAAC 58.130 39.130 11.50 0.00 35.15 2.01
711 714 5.508825 GGAACAACTGTCATGGCAATGTTAA 60.509 40.000 23.47 0.00 35.15 2.01
712 715 4.022416 GGAACAACTGTCATGGCAATGTTA 60.022 41.667 23.47 0.00 35.15 2.41
713 716 3.243839 GGAACAACTGTCATGGCAATGTT 60.244 43.478 23.58 23.58 35.15 2.71
714 717 2.297033 GGAACAACTGTCATGGCAATGT 59.703 45.455 11.50 11.50 35.15 2.71
715 718 2.559668 AGGAACAACTGTCATGGCAATG 59.440 45.455 0.00 6.33 34.88 2.82
758 765 4.865776 TGTTTAGCAGGGTTTCGAAATTG 58.134 39.130 14.69 13.50 0.00 2.32
760 767 5.163499 TGTTTGTTTAGCAGGGTTTCGAAAT 60.163 36.000 14.69 0.00 0.00 2.17
858 873 1.753930 TGCTCAAATCGATGCACCAT 58.246 45.000 0.00 0.00 0.00 3.55
932 951 2.743928 CCTCTCGTGGTTGCCTGC 60.744 66.667 0.00 0.00 0.00 4.85
957 976 5.141910 GGGTGTATATATAGAGGAGGGAGC 58.858 50.000 0.00 0.00 0.00 4.70
1017 1036 1.880819 CTGCTGGTTGATGGTTGGCC 61.881 60.000 0.00 0.00 0.00 5.36
1111 1131 1.084370 GTCCCGGATCTTGTTGCTCG 61.084 60.000 0.73 0.00 0.00 5.03
1154 1174 2.040544 CATCCGCTTCCACCGCTTT 61.041 57.895 0.00 0.00 0.00 3.51
1442 1486 3.545481 GAGCGGTCGCACATGTCG 61.545 66.667 17.71 3.20 44.88 4.35
1443 1487 3.188786 GGAGCGGTCGCACATGTC 61.189 66.667 17.71 5.64 44.88 3.06
1716 1781 2.794627 TAATGGCGCGCACAAACAGC 62.795 55.000 34.42 13.35 0.00 4.40
1728 1793 1.491670 CAGAGACACGGATAATGGCG 58.508 55.000 0.00 0.00 0.00 5.69
1747 1812 1.075748 AATGGAGGCAGGGGAATGC 60.076 57.895 0.00 0.00 45.74 3.56
1811 1876 4.865365 GGCATCTGAACTGTGAAGTACTAC 59.135 45.833 0.00 0.00 0.00 2.73
1812 1877 4.081642 GGGCATCTGAACTGTGAAGTACTA 60.082 45.833 0.00 0.00 0.00 1.82
1813 1878 3.307059 GGGCATCTGAACTGTGAAGTACT 60.307 47.826 0.00 0.00 0.00 2.73
1814 1879 3.003480 GGGCATCTGAACTGTGAAGTAC 58.997 50.000 0.00 0.00 0.00 2.73
1815 1880 2.027192 GGGGCATCTGAACTGTGAAGTA 60.027 50.000 0.00 0.00 0.00 2.24
1816 1881 1.271597 GGGGCATCTGAACTGTGAAGT 60.272 52.381 0.00 0.00 0.00 3.01
1817 1882 1.457346 GGGGCATCTGAACTGTGAAG 58.543 55.000 0.00 0.00 0.00 3.02
1818 1883 0.038166 GGGGGCATCTGAACTGTGAA 59.962 55.000 0.00 0.00 0.00 3.18
1819 1884 0.842030 AGGGGGCATCTGAACTGTGA 60.842 55.000 0.00 0.00 0.00 3.58
1820 1885 0.038744 AAGGGGGCATCTGAACTGTG 59.961 55.000 0.00 0.00 0.00 3.66
1821 1886 0.779997 AAAGGGGGCATCTGAACTGT 59.220 50.000 0.00 0.00 0.00 3.55
1822 1887 1.180029 CAAAGGGGGCATCTGAACTG 58.820 55.000 0.00 0.00 0.00 3.16
1823 1888 0.613012 GCAAAGGGGGCATCTGAACT 60.613 55.000 0.00 0.00 0.00 3.01
1824 1889 0.613012 AGCAAAGGGGGCATCTGAAC 60.613 55.000 0.00 0.00 0.00 3.18
1825 1890 0.114954 AAGCAAAGGGGGCATCTGAA 59.885 50.000 0.00 0.00 0.00 3.02
1826 1891 0.998928 TAAGCAAAGGGGGCATCTGA 59.001 50.000 0.00 0.00 0.00 3.27
1827 1892 1.478105 GTTAAGCAAAGGGGGCATCTG 59.522 52.381 0.00 0.00 0.00 2.90
1828 1893 1.077005 TGTTAAGCAAAGGGGGCATCT 59.923 47.619 0.00 0.00 0.00 2.90
1829 1894 1.478105 CTGTTAAGCAAAGGGGGCATC 59.522 52.381 0.00 0.00 0.00 3.91
1830 1895 1.203174 ACTGTTAAGCAAAGGGGGCAT 60.203 47.619 0.00 0.00 0.00 4.40
1831 1896 0.187361 ACTGTTAAGCAAAGGGGGCA 59.813 50.000 0.00 0.00 0.00 5.36
1832 1897 1.272490 GAACTGTTAAGCAAAGGGGGC 59.728 52.381 0.00 0.00 0.00 5.80
1833 1898 2.558359 CTGAACTGTTAAGCAAAGGGGG 59.442 50.000 0.00 0.00 0.00 5.40
1834 1899 2.029918 GCTGAACTGTTAAGCAAAGGGG 60.030 50.000 22.26 0.00 36.91 4.79
1835 1900 2.622942 TGCTGAACTGTTAAGCAAAGGG 59.377 45.455 26.44 0.00 43.65 3.95
1865 1930 2.203480 GTGCCTTGGCCTGGAACA 60.203 61.111 18.09 6.59 33.32 3.18
1953 2071 1.167781 TGCGTATGCCATGAGCCATG 61.168 55.000 4.05 7.88 42.71 3.66
2066 2184 0.906756 ATGGGGCCGATCGATCATCT 60.907 55.000 24.40 0.00 0.00 2.90
2154 2276 4.880120 TGATTCAGAAGATGCTGATTCCAC 59.120 41.667 9.28 0.00 43.84 4.02
2221 2343 4.037327 GCAATCTCCCTTTTTATCTGGCTC 59.963 45.833 0.00 0.00 0.00 4.70
2373 2505 2.358247 CGGCTACCCACACACACC 60.358 66.667 0.00 0.00 0.00 4.16
2374 2506 2.358247 CCGGCTACCCACACACAC 60.358 66.667 0.00 0.00 0.00 3.82
2375 2507 3.632080 CCCGGCTACCCACACACA 61.632 66.667 0.00 0.00 0.00 3.72
2376 2508 4.404098 CCCCGGCTACCCACACAC 62.404 72.222 0.00 0.00 0.00 3.82
2377 2509 3.935456 ATCCCCGGCTACCCACACA 62.935 63.158 0.00 0.00 0.00 3.72
2378 2510 3.087906 ATCCCCGGCTACCCACAC 61.088 66.667 0.00 0.00 0.00 3.82
2379 2511 2.766651 GATCCCCGGCTACCCACA 60.767 66.667 0.00 0.00 0.00 4.17
2380 2512 3.925090 CGATCCCCGGCTACCCAC 61.925 72.222 0.00 0.00 33.91 4.61
2381 2513 3.462056 ATCGATCCCCGGCTACCCA 62.462 63.158 0.00 0.00 39.14 4.51
2382 2514 2.603776 ATCGATCCCCGGCTACCC 60.604 66.667 0.00 0.00 39.14 3.69
2390 2522 2.256117 AATGAAACCGATCGATCCCC 57.744 50.000 18.66 5.24 0.00 4.81
2421 2553 3.242543 CCGATTCCAAAATCAAGAGCTCG 60.243 47.826 8.37 0.00 41.22 5.03
2447 2579 8.484641 TCAGTTCAAAGCAAGTAGAGATTATG 57.515 34.615 0.00 0.00 0.00 1.90
2467 2599 3.030291 TGATGGCACCAAAAACTCAGTT 58.970 40.909 0.00 0.00 0.00 3.16
2504 2637 1.201429 TTCCTGCCCTGGAGGAAGAC 61.201 60.000 12.38 0.00 45.94 3.01
2580 2713 2.264455 AGGAGAGCATCACTTTCACCT 58.736 47.619 0.00 0.00 37.82 4.00
2609 2742 3.577805 ACTTTCCTTAGCTGTTGGTGT 57.422 42.857 0.00 0.00 0.00 4.16
2610 2743 4.385825 TGTACTTTCCTTAGCTGTTGGTG 58.614 43.478 0.00 0.00 0.00 4.17
2611 2744 4.102681 ACTGTACTTTCCTTAGCTGTTGGT 59.897 41.667 0.00 0.00 0.00 3.67
2612 2745 4.452455 CACTGTACTTTCCTTAGCTGTTGG 59.548 45.833 0.00 0.00 0.00 3.77
2613 2746 5.297547 TCACTGTACTTTCCTTAGCTGTTG 58.702 41.667 0.00 0.00 0.00 3.33
2614 2747 5.546621 TCACTGTACTTTCCTTAGCTGTT 57.453 39.130 0.00 0.00 0.00 3.16
2615 2748 5.746990 ATCACTGTACTTTCCTTAGCTGT 57.253 39.130 0.00 0.00 0.00 4.40
2649 2782 0.592637 TTTGATGTTCAGTGCGCTGG 59.407 50.000 26.23 8.76 42.78 4.85
2671 2809 2.703007 TGCCCTGCAACATTTTTACCTT 59.297 40.909 0.00 0.00 34.76 3.50
2673 2811 2.037121 ACTGCCCTGCAACATTTTTACC 59.963 45.455 0.00 0.00 38.41 2.85
2674 2812 3.385193 ACTGCCCTGCAACATTTTTAC 57.615 42.857 0.00 0.00 38.41 2.01
2675 2813 3.509575 CCTACTGCCCTGCAACATTTTTA 59.490 43.478 0.00 0.00 38.41 1.52
2677 2815 1.895131 CCTACTGCCCTGCAACATTTT 59.105 47.619 0.00 0.00 38.41 1.82
2690 2828 0.249489 CGGGCATAGTGTCCTACTGC 60.249 60.000 0.00 0.00 40.79 4.40
2693 2831 2.288886 GGATTCGGGCATAGTGTCCTAC 60.289 54.545 0.00 0.00 40.79 3.18
2694 2832 1.968493 GGATTCGGGCATAGTGTCCTA 59.032 52.381 0.00 0.00 40.79 2.94
2695 2833 0.759346 GGATTCGGGCATAGTGTCCT 59.241 55.000 0.00 0.00 40.79 3.85
2696 2834 0.468226 TGGATTCGGGCATAGTGTCC 59.532 55.000 0.00 0.00 39.19 4.02
2697 2835 1.139058 ACTGGATTCGGGCATAGTGTC 59.861 52.381 0.00 0.00 0.00 3.67
2698 2836 1.204146 ACTGGATTCGGGCATAGTGT 58.796 50.000 0.00 0.00 0.00 3.55
2699 2837 3.469008 TTACTGGATTCGGGCATAGTG 57.531 47.619 0.00 0.00 0.00 2.74
2700 2838 4.020485 GGTATTACTGGATTCGGGCATAGT 60.020 45.833 0.00 0.00 0.00 2.12
2701 2839 4.504858 GGTATTACTGGATTCGGGCATAG 58.495 47.826 0.00 0.00 0.00 2.23
2702 2840 3.262405 GGGTATTACTGGATTCGGGCATA 59.738 47.826 0.00 0.00 0.00 3.14
2703 2841 2.039879 GGGTATTACTGGATTCGGGCAT 59.960 50.000 0.00 0.00 0.00 4.40
2704 2842 1.418637 GGGTATTACTGGATTCGGGCA 59.581 52.381 0.00 0.00 0.00 5.36
2705 2843 1.418637 TGGGTATTACTGGATTCGGGC 59.581 52.381 0.00 0.00 0.00 6.13
2706 2844 3.118186 TGTTGGGTATTACTGGATTCGGG 60.118 47.826 0.00 0.00 0.00 5.14
2707 2845 4.145365 TGTTGGGTATTACTGGATTCGG 57.855 45.455 0.00 0.00 0.00 4.30
2708 2846 6.317642 TGATTTGTTGGGTATTACTGGATTCG 59.682 38.462 0.00 0.00 0.00 3.34
2709 2847 7.201821 CCTGATTTGTTGGGTATTACTGGATTC 60.202 40.741 0.00 0.00 0.00 2.52
2710 2848 6.607198 CCTGATTTGTTGGGTATTACTGGATT 59.393 38.462 0.00 0.00 0.00 3.01
2711 2849 6.129179 CCTGATTTGTTGGGTATTACTGGAT 58.871 40.000 0.00 0.00 0.00 3.41
2712 2850 5.014755 ACCTGATTTGTTGGGTATTACTGGA 59.985 40.000 0.00 0.00 0.00 3.86
2713 2851 5.125417 CACCTGATTTGTTGGGTATTACTGG 59.875 44.000 0.00 0.00 0.00 4.00
2714 2852 5.943416 TCACCTGATTTGTTGGGTATTACTG 59.057 40.000 0.00 0.00 0.00 2.74
2715 2853 6.134535 TCACCTGATTTGTTGGGTATTACT 57.865 37.500 0.00 0.00 0.00 2.24
2716 2854 6.827586 TTCACCTGATTTGTTGGGTATTAC 57.172 37.500 0.00 0.00 0.00 1.89
2717 2855 7.007723 ACTTTCACCTGATTTGTTGGGTATTA 58.992 34.615 0.00 0.00 0.00 0.98
2718 2856 5.838521 ACTTTCACCTGATTTGTTGGGTATT 59.161 36.000 0.00 0.00 0.00 1.89
2719 2857 5.243730 CACTTTCACCTGATTTGTTGGGTAT 59.756 40.000 0.00 0.00 0.00 2.73
2720 2858 4.582656 CACTTTCACCTGATTTGTTGGGTA 59.417 41.667 0.00 0.00 0.00 3.69
2721 2859 3.384467 CACTTTCACCTGATTTGTTGGGT 59.616 43.478 0.00 0.00 0.00 4.51
2722 2860 3.636300 TCACTTTCACCTGATTTGTTGGG 59.364 43.478 0.00 0.00 0.00 4.12
2723 2861 4.916983 TCACTTTCACCTGATTTGTTGG 57.083 40.909 0.00 0.00 0.00 3.77
2724 2862 4.682860 GCATCACTTTCACCTGATTTGTTG 59.317 41.667 0.00 0.00 0.00 3.33
2725 2863 4.586001 AGCATCACTTTCACCTGATTTGTT 59.414 37.500 0.00 0.00 0.00 2.83
2726 2864 4.147321 AGCATCACTTTCACCTGATTTGT 58.853 39.130 0.00 0.00 0.00 2.83
2727 2865 4.778534 AGCATCACTTTCACCTGATTTG 57.221 40.909 0.00 0.00 0.00 2.32
2728 2866 5.796424 AAAGCATCACTTTCACCTGATTT 57.204 34.783 0.00 0.00 45.78 2.17
2739 2877 4.934356 TGGGATTAAGGAAAGCATCACTT 58.066 39.130 0.00 0.00 41.70 3.16
2740 2878 4.530875 CTGGGATTAAGGAAAGCATCACT 58.469 43.478 0.00 0.00 0.00 3.41
2741 2879 3.067320 GCTGGGATTAAGGAAAGCATCAC 59.933 47.826 0.00 0.00 0.00 3.06
2742 2880 3.290710 GCTGGGATTAAGGAAAGCATCA 58.709 45.455 0.00 0.00 0.00 3.07
2743 2881 3.290710 TGCTGGGATTAAGGAAAGCATC 58.709 45.455 0.00 0.00 35.84 3.91
2744 2882 3.294214 CTGCTGGGATTAAGGAAAGCAT 58.706 45.455 6.25 0.00 39.70 3.79
2745 2883 2.726821 CTGCTGGGATTAAGGAAAGCA 58.273 47.619 5.80 5.80 38.27 3.91
2746 2884 1.406898 GCTGCTGGGATTAAGGAAAGC 59.593 52.381 0.00 0.00 0.00 3.51
2747 2885 3.010200 AGCTGCTGGGATTAAGGAAAG 57.990 47.619 0.00 0.00 0.00 2.62
2748 2886 4.270008 GTTAGCTGCTGGGATTAAGGAAA 58.730 43.478 13.43 0.00 0.00 3.13
2749 2887 3.681594 CGTTAGCTGCTGGGATTAAGGAA 60.682 47.826 13.43 0.00 0.00 3.36
2750 2888 2.158957 CGTTAGCTGCTGGGATTAAGGA 60.159 50.000 13.43 0.00 0.00 3.36
2751 2889 2.213499 CGTTAGCTGCTGGGATTAAGG 58.787 52.381 13.43 0.00 0.00 2.69
2752 2890 2.158957 TCCGTTAGCTGCTGGGATTAAG 60.159 50.000 13.43 0.00 0.00 1.85
2753 2891 1.834896 TCCGTTAGCTGCTGGGATTAA 59.165 47.619 13.43 0.00 0.00 1.40
2754 2892 1.491668 TCCGTTAGCTGCTGGGATTA 58.508 50.000 13.43 0.00 0.00 1.75
2755 2893 0.618458 TTCCGTTAGCTGCTGGGATT 59.382 50.000 13.43 0.00 0.00 3.01
2756 2894 0.618458 TTTCCGTTAGCTGCTGGGAT 59.382 50.000 13.43 0.00 0.00 3.85
2757 2895 0.618458 ATTTCCGTTAGCTGCTGGGA 59.382 50.000 13.43 13.10 0.00 4.37
2758 2896 0.734889 CATTTCCGTTAGCTGCTGGG 59.265 55.000 13.43 10.90 0.00 4.45
2759 2897 0.099436 GCATTTCCGTTAGCTGCTGG 59.901 55.000 13.43 5.20 0.00 4.85
2760 2898 0.804364 TGCATTTCCGTTAGCTGCTG 59.196 50.000 13.43 0.00 34.02 4.41
2761 2899 1.089920 CTGCATTTCCGTTAGCTGCT 58.910 50.000 7.57 7.57 34.02 4.24
2762 2900 0.804989 ACTGCATTTCCGTTAGCTGC 59.195 50.000 0.00 0.00 0.00 5.25
2763 2901 2.076100 TCACTGCATTTCCGTTAGCTG 58.924 47.619 0.00 0.00 0.00 4.24
2764 2902 2.472695 TCACTGCATTTCCGTTAGCT 57.527 45.000 0.00 0.00 0.00 3.32
2765 2903 2.223340 CCATCACTGCATTTCCGTTAGC 60.223 50.000 0.00 0.00 0.00 3.09
2766 2904 3.270027 TCCATCACTGCATTTCCGTTAG 58.730 45.455 0.00 0.00 0.00 2.34
2767 2905 3.342377 TCCATCACTGCATTTCCGTTA 57.658 42.857 0.00 0.00 0.00 3.18
2768 2906 2.198827 TCCATCACTGCATTTCCGTT 57.801 45.000 0.00 0.00 0.00 4.44
2769 2907 2.292267 GATCCATCACTGCATTTCCGT 58.708 47.619 0.00 0.00 0.00 4.69
2770 2908 2.291365 TGATCCATCACTGCATTTCCG 58.709 47.619 0.00 0.00 0.00 4.30
2771 2909 3.488047 CGTTGATCCATCACTGCATTTCC 60.488 47.826 0.00 0.00 36.36 3.13
2772 2910 3.688272 CGTTGATCCATCACTGCATTTC 58.312 45.455 0.00 0.00 36.36 2.17
2773 2911 2.159338 GCGTTGATCCATCACTGCATTT 60.159 45.455 7.14 0.00 37.22 2.32
2774 2912 1.402968 GCGTTGATCCATCACTGCATT 59.597 47.619 7.14 0.00 37.22 3.56
2775 2913 1.019673 GCGTTGATCCATCACTGCAT 58.980 50.000 7.14 0.00 37.22 3.96
2776 2914 0.036105 AGCGTTGATCCATCACTGCA 60.036 50.000 12.41 0.00 38.77 4.41
2777 2915 0.376152 CAGCGTTGATCCATCACTGC 59.624 55.000 0.00 4.68 36.36 4.40
2778 2916 0.376152 GCAGCGTTGATCCATCACTG 59.624 55.000 2.38 2.65 36.36 3.66
2779 2917 0.036105 TGCAGCGTTGATCCATCACT 60.036 50.000 2.38 0.00 36.36 3.41
2780 2918 0.376152 CTGCAGCGTTGATCCATCAC 59.624 55.000 2.38 0.00 36.36 3.06
2781 2919 1.371337 GCTGCAGCGTTGATCCATCA 61.371 55.000 25.23 0.00 34.44 3.07
2782 2920 1.354506 GCTGCAGCGTTGATCCATC 59.645 57.895 25.23 0.00 0.00 3.51
2783 2921 1.377594 TGCTGCAGCGTTGATCCAT 60.378 52.632 32.11 0.00 45.83 3.41
2784 2922 2.032376 TGCTGCAGCGTTGATCCA 59.968 55.556 32.11 10.70 45.83 3.41
2785 2923 2.327343 TGTGCTGCAGCGTTGATCC 61.327 57.895 32.11 14.31 45.83 3.36
2786 2924 3.256936 TGTGCTGCAGCGTTGATC 58.743 55.556 32.11 17.73 45.83 2.92


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

AutoCloner maintained by Alex Coulton.