Multiple sequence alignment - TraesCS7D01G251000

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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 TraesCS7D01G251000 chr7D 100.000 3570 0 0 1 3570 223750974 223754543 0.000000e+00 6593.0
1 TraesCS7D01G251000 chr7D 91.304 69 4 2 3279 3346 58135200 58135267 3.790000e-15 93.5
2 TraesCS7D01G251000 chr7A 91.779 1861 92 31 1081 2892 234352039 234353887 0.000000e+00 2532.0
3 TraesCS7D01G251000 chr7A 91.982 1085 61 15 16 1089 234350926 234351995 0.000000e+00 1498.0
4 TraesCS7D01G251000 chr7A 86.592 537 52 15 3045 3570 234353940 234354467 3.090000e-160 575.0
5 TraesCS7D01G251000 chr7B 94.950 1505 59 12 1081 2579 176359339 176357846 0.000000e+00 2342.0
6 TraesCS7D01G251000 chr7B 95.431 985 32 7 1081 2060 176399411 176398435 0.000000e+00 1557.0
7 TraesCS7D01G251000 chr7B 89.416 1096 79 19 1 1089 176360448 176359383 0.000000e+00 1347.0
8 TraesCS7D01G251000 chr7B 89.152 1097 81 20 1 1089 176400521 176399455 0.000000e+00 1332.0
9 TraesCS7D01G251000 chr2B 92.233 103 7 1 2897 2999 488043925 488043824 1.030000e-30 145.0
10 TraesCS7D01G251000 chr2A 88.136 118 11 3 360 476 630462535 630462420 1.730000e-28 137.0
11 TraesCS7D01G251000 chr5B 86.842 114 13 2 364 477 345867010 345866899 3.740000e-25 126.0
12 TraesCS7D01G251000 chr4A 82.407 108 16 3 3462 3567 501900382 501900488 1.360000e-14 91.6
13 TraesCS7D01G251000 chr6D 97.561 41 1 0 3521 3561 32384304 32384344 1.780000e-08 71.3
14 TraesCS7D01G251000 chr6D 73.043 230 44 16 3348 3567 461626351 461626572 8.270000e-07 65.8
15 TraesCS7D01G251000 chr6B 91.489 47 4 0 3521 3567 68203366 68203412 8.270000e-07 65.8
16 TraesCS7D01G251000 chr6B 94.737 38 1 1 3530 3567 703446750 703446786 1.380000e-04 58.4
17 TraesCS7D01G251000 chr6B 92.105 38 3 0 3269 3306 134830508 134830545 2.000000e-03 54.7
18 TraesCS7D01G251000 chr5A 97.222 36 1 0 3521 3556 19244237 19244272 1.070000e-05 62.1
19 TraesCS7D01G251000 chr1B 85.000 60 8 1 3279 3338 535711337 535711279 3.850000e-05 60.2
20 TraesCS7D01G251000 chr2D 100.000 30 0 0 3279 3308 476799176 476799205 4.980000e-04 56.5


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 TraesCS7D01G251000 chr7D 223750974 223754543 3569 False 6593.0 6593 100.000000 1 3570 1 chr7D.!!$F2 3569
1 TraesCS7D01G251000 chr7A 234350926 234354467 3541 False 1535.0 2532 90.117667 16 3570 3 chr7A.!!$F1 3554
2 TraesCS7D01G251000 chr7B 176357846 176360448 2602 True 1844.5 2342 92.183000 1 2579 2 chr7B.!!$R1 2578
3 TraesCS7D01G251000 chr7B 176398435 176400521 2086 True 1444.5 1557 92.291500 1 2060 2 chr7B.!!$R2 2059

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
631 640 0.17910 CAGTAGACCAGTCCATGCCG 60.179 60.0 0.0 0.0 0.00 5.69 F
814 828 0.95104 CGAGCCTTTCCAGCTTCGTT 60.951 55.0 0.0 0.0 41.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2010 0.895530 ACACATGGTGGTACTCTCCG 59.104 55.0 0.0 0.0 37.94 4.63 R
2734 2851 0.176219 ACCACCTTTCGTTCGTGTGA 59.824 50.0 0.0 0.0 0.00 3.58 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
25 26 4.108778 AGAATAGAGGCAGGAGGATAGGAA 59.891 45.833 0.00 0.00 0.00 3.36
55 56 1.873591 GTGGTGATTTTCTGTGCGAGT 59.126 47.619 0.00 0.00 0.00 4.18
64 65 0.744281 TCTGTGCGAGTGAAGTGACA 59.256 50.000 0.00 0.00 0.00 3.58
91 93 0.482446 AATGCAGTGGGGGAAAGACA 59.518 50.000 0.00 0.00 0.00 3.41
99 101 1.292546 TGGGGGAAAGACAAGGGTTTT 59.707 47.619 0.00 0.00 0.00 2.43
262 264 0.319555 CTTTCGCCCGAGTTGAGTCA 60.320 55.000 0.00 0.00 0.00 3.41
264 266 1.461091 TTCGCCCGAGTTGAGTCAGT 61.461 55.000 0.00 0.00 0.00 3.41
271 273 1.068885 CGAGTTGAGTCAGTCGCTTCT 60.069 52.381 12.43 0.00 0.00 2.85
277 279 0.952280 AGTCAGTCGCTTCTGAACGA 59.048 50.000 8.81 9.78 44.48 3.85
309 311 1.358402 CTAGCAGCGCATCGTCTCT 59.642 57.895 11.47 0.00 0.00 3.10
419 421 6.681178 CAGTACAAAGTGTCACGTTTTGTAAG 59.319 38.462 22.39 16.96 44.29 2.34
476 478 5.995897 GTGGTGGTTCTGTGTATTTTACTCT 59.004 40.000 0.00 0.00 0.00 3.24
477 479 5.995282 TGGTGGTTCTGTGTATTTTACTCTG 59.005 40.000 0.00 0.00 0.00 3.35
478 480 6.183361 TGGTGGTTCTGTGTATTTTACTCTGA 60.183 38.462 0.00 0.00 0.00 3.27
479 481 6.369065 GGTGGTTCTGTGTATTTTACTCTGAG 59.631 42.308 2.45 2.45 33.71 3.35
520 522 7.227512 CCTGAACTTCTGAAGATTTTACACTGT 59.772 37.037 23.36 0.00 0.00 3.55
631 640 0.179100 CAGTAGACCAGTCCATGCCG 60.179 60.000 0.00 0.00 0.00 5.69
714 728 2.030451 ACCAAGAACTACTCCGTTCGTC 60.030 50.000 0.00 0.00 46.00 4.20
814 828 0.951040 CGAGCCTTTCCAGCTTCGTT 60.951 55.000 0.00 0.00 41.75 3.85
832 846 2.661979 CGTTTCTGCACGTAGCTTTTCC 60.662 50.000 10.54 0.00 45.94 3.13
834 848 1.795768 TCTGCACGTAGCTTTTCCAG 58.204 50.000 10.54 0.00 45.94 3.86
912 926 4.779733 TCACGAGCTCCCCTCCCC 62.780 72.222 8.47 0.00 37.27 4.81
926 940 4.840005 CCCCGCGCCTCTCCTTTC 62.840 72.222 0.00 0.00 0.00 2.62
944 958 3.151906 CCCCCGTCCATCCATCTC 58.848 66.667 0.00 0.00 0.00 2.75
946 960 2.737180 CCCGTCCATCCATCTCCG 59.263 66.667 0.00 0.00 0.00 4.63
947 961 2.737180 CCGTCCATCCATCTCCGG 59.263 66.667 0.00 0.00 0.00 5.14
948 962 2.029666 CGTCCATCCATCTCCGGC 59.970 66.667 0.00 0.00 0.00 6.13
949 963 2.427753 GTCCATCCATCTCCGGCC 59.572 66.667 0.00 0.00 0.00 6.13
950 964 2.143419 GTCCATCCATCTCCGGCCT 61.143 63.158 0.00 0.00 0.00 5.19
951 965 1.838846 TCCATCCATCTCCGGCCTC 60.839 63.158 0.00 0.00 0.00 4.70
952 966 1.840650 CCATCCATCTCCGGCCTCT 60.841 63.158 0.00 0.00 0.00 3.69
953 967 1.670590 CATCCATCTCCGGCCTCTC 59.329 63.158 0.00 0.00 0.00 3.20
955 969 2.029892 ATCCATCTCCGGCCTCTCCT 62.030 60.000 0.00 0.00 0.00 3.69
958 972 1.152830 ATCTCCGGCCTCTCCTCTC 59.847 63.158 0.00 0.00 0.00 3.20
960 974 4.507916 TCCGGCCTCTCCTCTCCG 62.508 72.222 0.00 0.00 41.41 4.63
962 976 2.904866 CGGCCTCTCCTCTCCGAG 60.905 72.222 0.00 0.00 44.23 4.63
963 977 3.223589 GGCCTCTCCTCTCCGAGC 61.224 72.222 0.00 0.00 0.00 5.03
964 978 3.591835 GCCTCTCCTCTCCGAGCG 61.592 72.222 0.00 0.00 0.00 5.03
965 979 3.591835 CCTCTCCTCTCCGAGCGC 61.592 72.222 0.00 0.00 0.00 5.92
966 980 2.515991 CTCTCCTCTCCGAGCGCT 60.516 66.667 11.27 11.27 0.00 5.92
967 981 2.826287 TCTCCTCTCCGAGCGCTG 60.826 66.667 18.48 7.34 0.00 5.18
971 985 2.560119 CCTCTCCGAGCGCTGCTAT 61.560 63.158 18.48 0.00 39.88 2.97
1008 1022 4.154613 CTGCGAGTCAACGGAGTC 57.845 61.111 0.00 0.00 45.00 3.36
1067 1081 2.883730 CCCGTACACATGGCGTCG 60.884 66.667 0.00 0.00 0.00 5.12
1418 1483 3.429141 CGGCAGCTGCTGTTCCTG 61.429 66.667 34.82 14.62 42.29 3.86
1425 1490 2.525629 TGCTGTTCCTGGACGGGA 60.526 61.111 0.00 0.00 0.00 5.14
1937 2002 2.603776 AACTCCGGCGACCTCCTT 60.604 61.111 9.30 0.00 0.00 3.36
1945 2010 0.179153 GGCGACCTCCTTGTACGTAC 60.179 60.000 18.90 18.90 0.00 3.67
1946 2011 0.522076 GCGACCTCCTTGTACGTACG 60.522 60.000 20.18 15.01 0.00 3.67
1947 2012 0.097674 CGACCTCCTTGTACGTACGG 59.902 60.000 21.06 15.87 0.00 4.02
1948 2013 1.453155 GACCTCCTTGTACGTACGGA 58.547 55.000 21.06 18.91 0.00 4.69
1950 2015 1.003580 ACCTCCTTGTACGTACGGAGA 59.996 52.381 33.67 22.91 44.56 3.71
1951 2016 1.669779 CCTCCTTGTACGTACGGAGAG 59.330 57.143 33.67 28.01 44.56 3.20
1952 2017 2.354259 CTCCTTGTACGTACGGAGAGT 58.646 52.381 30.74 0.00 44.56 3.24
1969 2041 2.237143 AGAGTACCACCATGTGTCCATG 59.763 50.000 0.00 0.00 46.65 3.66
2162 2250 3.215568 CTGCACCACGGCAAACCA 61.216 61.111 0.00 0.00 44.40 3.67
2234 2322 2.765807 CTCCCCGGAGCAGGATGT 60.766 66.667 0.73 0.00 39.31 3.06
2319 2407 6.205464 GGAATAATGGAGCAATCGATTTCTGA 59.795 38.462 15.17 2.11 0.00 3.27
2356 2444 8.289618 TCTAACAATCTAACTTTGTTGATGTGC 58.710 33.333 11.03 0.00 44.63 4.57
2360 2462 4.858935 TCTAACTTTGTTGATGTGCTTGC 58.141 39.130 0.00 0.00 0.00 4.01
2513 2615 3.566742 GCTGTAGTTCTCTCCTAGCTACC 59.433 52.174 0.00 0.00 33.20 3.18
2531 2633 2.443416 ACCAGTACATCGACTACTGCA 58.557 47.619 19.94 0.00 39.83 4.41
2621 2723 7.829211 AGTAAATTCAGCTAGTTATTGCTTCCA 59.171 33.333 0.00 0.00 37.44 3.53
2639 2741 7.112122 TGCTTCCAGAATAATTACACATCAGT 58.888 34.615 0.00 0.00 0.00 3.41
2658 2760 5.034152 TCAGTTTTGCGTTTTGAGTTCATC 58.966 37.500 0.00 0.00 0.00 2.92
2660 2762 2.679355 TTGCGTTTTGAGTTCATCCG 57.321 45.000 0.00 0.00 0.00 4.18
2661 2763 1.588674 TGCGTTTTGAGTTCATCCGT 58.411 45.000 0.00 0.00 0.00 4.69
2662 2764 1.262950 TGCGTTTTGAGTTCATCCGTG 59.737 47.619 0.00 0.00 0.00 4.94
2663 2765 1.950472 CGTTTTGAGTTCATCCGTGC 58.050 50.000 0.00 0.00 0.00 5.34
2668 2785 2.740714 GAGTTCATCCGTGCCACGC 61.741 63.158 12.68 0.00 40.91 5.34
2672 2789 1.448119 TTCATCCGTGCCACGCAAAA 61.448 50.000 12.68 0.10 41.47 2.44
2673 2790 1.007964 CATCCGTGCCACGCAAAAA 60.008 52.632 12.68 0.00 41.47 1.94
2694 2811 9.340695 CAAAAACTGCGTATCTTTTCATTGATA 57.659 29.630 0.00 0.00 0.00 2.15
2699 2816 7.766278 ACTGCGTATCTTTTCATTGATAGAAGT 59.234 33.333 3.88 1.24 0.00 3.01
2703 2820 9.307121 CGTATCTTTTCATTGATAGAAGTGAGT 57.693 33.333 3.88 0.00 0.00 3.41
2707 2824 9.559732 TCTTTTCATTGATAGAAGTGAGTGAAA 57.440 29.630 0.00 0.00 33.88 2.69
2710 2827 9.506018 TTTCATTGATAGAAGTGAGTGAAATGA 57.494 29.630 0.00 0.00 31.62 2.57
2711 2828 8.713737 TCATTGATAGAAGTGAGTGAAATGAG 57.286 34.615 0.00 0.00 30.38 2.90
2712 2829 8.316946 TCATTGATAGAAGTGAGTGAAATGAGT 58.683 33.333 0.00 0.00 30.38 3.41
2713 2830 9.591792 CATTGATAGAAGTGAGTGAAATGAGTA 57.408 33.333 0.00 0.00 0.00 2.59
2714 2831 8.988064 TTGATAGAAGTGAGTGAAATGAGTAC 57.012 34.615 0.00 0.00 0.00 2.73
2718 2835 7.721286 AGAAGTGAGTGAAATGAGTACAAAG 57.279 36.000 0.00 0.00 0.00 2.77
2720 2837 7.655328 AGAAGTGAGTGAAATGAGTACAAAGAG 59.345 37.037 0.00 0.00 0.00 2.85
2724 2841 5.308825 AGTGAAATGAGTACAAAGAGGTGG 58.691 41.667 0.00 0.00 0.00 4.61
2730 2847 5.818678 TGAGTACAAAGAGGTGGTACAAT 57.181 39.130 0.00 0.00 44.16 2.71
2734 2851 7.038587 TGAGTACAAAGAGGTGGTACAATACAT 60.039 37.037 0.00 0.00 44.16 2.29
2735 2852 7.328737 AGTACAAAGAGGTGGTACAATACATC 58.671 38.462 0.00 0.00 44.16 3.06
2740 2857 3.857052 AGGTGGTACAATACATCACACG 58.143 45.455 0.00 0.00 44.16 4.49
2743 2860 4.092383 GGTGGTACAATACATCACACGAAC 59.908 45.833 0.00 0.00 44.16 3.95
2753 2870 0.176219 TCACACGAACGAAAGGTGGT 59.824 50.000 0.14 0.00 41.85 4.16
2759 2876 3.682858 CACGAACGAAAGGTGGTATGAAT 59.317 43.478 0.14 0.00 37.80 2.57
2760 2877 3.682858 ACGAACGAAAGGTGGTATGAATG 59.317 43.478 0.14 0.00 38.25 2.67
2761 2878 3.930229 CGAACGAAAGGTGGTATGAATGA 59.070 43.478 0.00 0.00 0.00 2.57
2762 2879 4.570772 CGAACGAAAGGTGGTATGAATGAT 59.429 41.667 0.00 0.00 0.00 2.45
2763 2880 5.502382 CGAACGAAAGGTGGTATGAATGATG 60.502 44.000 0.00 0.00 0.00 3.07
2764 2881 3.627577 ACGAAAGGTGGTATGAATGATGC 59.372 43.478 0.00 0.00 0.00 3.91
2765 2882 3.003689 CGAAAGGTGGTATGAATGATGCC 59.996 47.826 0.00 0.00 37.34 4.40
2787 2906 1.558756 AGAGCAGAAGGTCAAGGGATG 59.441 52.381 0.00 0.00 44.60 3.51
2806 2925 1.244019 GCTCAGCCCCAAACAACGAT 61.244 55.000 0.00 0.00 0.00 3.73
2807 2926 1.948611 GCTCAGCCCCAAACAACGATA 60.949 52.381 0.00 0.00 0.00 2.92
2808 2927 2.643551 CTCAGCCCCAAACAACGATAT 58.356 47.619 0.00 0.00 0.00 1.63
2809 2928 3.804036 CTCAGCCCCAAACAACGATATA 58.196 45.455 0.00 0.00 0.00 0.86
2811 2930 3.942748 TCAGCCCCAAACAACGATATAAC 59.057 43.478 0.00 0.00 0.00 1.89
2812 2931 3.692101 CAGCCCCAAACAACGATATAACA 59.308 43.478 0.00 0.00 0.00 2.41
2813 2932 3.692593 AGCCCCAAACAACGATATAACAC 59.307 43.478 0.00 0.00 0.00 3.32
2814 2933 3.440872 GCCCCAAACAACGATATAACACA 59.559 43.478 0.00 0.00 0.00 3.72
2815 2934 4.438200 GCCCCAAACAACGATATAACACAG 60.438 45.833 0.00 0.00 0.00 3.66
2825 2945 7.764443 ACAACGATATAACACAGCTAAACTCAT 59.236 33.333 0.00 0.00 0.00 2.90
2838 2958 7.229306 ACAGCTAAACTCATGATTGTCTGAAAA 59.771 33.333 14.18 0.00 0.00 2.29
2860 2980 9.818796 GAAAATTCTAGCACTTTAGCTATATGC 57.181 33.333 13.72 13.72 45.32 3.14
2862 2982 9.512588 AAATTCTAGCACTTTAGCTATATGCAT 57.487 29.630 20.32 3.79 45.32 3.96
2866 2986 5.614308 AGCACTTTAGCTATATGCATGTCA 58.386 37.500 20.32 0.00 44.50 3.58
2867 2987 5.468072 AGCACTTTAGCTATATGCATGTCAC 59.532 40.000 20.32 0.00 44.50 3.67
2868 2988 5.334414 GCACTTTAGCTATATGCATGTCACC 60.334 44.000 10.16 0.00 45.94 4.02
2870 2990 5.994054 ACTTTAGCTATATGCATGTCACCTG 59.006 40.000 10.16 0.00 45.94 4.00
2873 2993 5.039920 AGCTATATGCATGTCACCTGAAA 57.960 39.130 10.16 0.00 45.94 2.69
2876 2996 6.548622 AGCTATATGCATGTCACCTGAAAATT 59.451 34.615 10.16 0.00 45.94 1.82
2880 3000 5.471556 TGCATGTCACCTGAAAATTGATT 57.528 34.783 0.00 0.00 0.00 2.57
2883 3003 7.440198 TGCATGTCACCTGAAAATTGATTTTA 58.560 30.769 1.93 0.00 39.86 1.52
2893 3013 9.626045 CCTGAAAATTGATTTTAGGTAAGTCAC 57.374 33.333 1.93 0.00 45.33 3.67
2894 3014 9.329913 CTGAAAATTGATTTTAGGTAAGTCACG 57.670 33.333 1.93 0.00 39.86 4.35
2895 3015 7.806014 TGAAAATTGATTTTAGGTAAGTCACGC 59.194 33.333 1.93 0.00 39.86 5.34
2896 3016 6.811253 AATTGATTTTAGGTAAGTCACGCA 57.189 33.333 0.00 0.00 32.85 5.24
2898 3018 6.811253 TTGATTTTAGGTAAGTCACGCATT 57.189 33.333 0.00 0.00 32.85 3.56
2899 3019 7.908827 TTGATTTTAGGTAAGTCACGCATTA 57.091 32.000 0.00 0.00 32.85 1.90
2900 3020 7.908827 TGATTTTAGGTAAGTCACGCATTAA 57.091 32.000 0.00 0.00 28.62 1.40
2901 3021 7.970384 TGATTTTAGGTAAGTCACGCATTAAG 58.030 34.615 0.00 0.00 28.62 1.85
2903 3023 3.611766 AGGTAAGTCACGCATTAAGCT 57.388 42.857 0.00 0.00 42.61 3.74
2904 3024 4.730949 AGGTAAGTCACGCATTAAGCTA 57.269 40.909 0.00 0.00 42.61 3.32
2905 3025 5.080969 AGGTAAGTCACGCATTAAGCTAA 57.919 39.130 0.00 0.00 42.61 3.09
2906 3026 5.671493 AGGTAAGTCACGCATTAAGCTAAT 58.329 37.500 0.00 0.00 42.61 1.73
2907 3027 6.113411 AGGTAAGTCACGCATTAAGCTAATT 58.887 36.000 0.00 0.00 42.61 1.40
2911 3031 9.763465 GTAAGTCACGCATTAAGCTAATTTTTA 57.237 29.630 0.00 0.00 42.61 1.52
2913 3033 9.685828 AAGTCACGCATTAAGCTAATTTTTAAA 57.314 25.926 0.00 0.00 42.61 1.52
2914 3034 9.341899 AGTCACGCATTAAGCTAATTTTTAAAG 57.658 29.630 0.00 0.00 42.61 1.85
2916 3036 9.900710 TCACGCATTAAGCTAATTTTTAAAGAA 57.099 25.926 0.00 0.00 42.61 2.52
2933 3053 9.555727 TTTTAAAGAAGATATTCTACCATCCCG 57.444 33.333 2.40 0.00 0.00 5.14
2934 3054 5.746990 AAGAAGATATTCTACCATCCCGG 57.253 43.478 2.40 0.00 42.50 5.73
2935 3055 4.097418 AGAAGATATTCTACCATCCCGGG 58.903 47.826 16.85 16.85 40.22 5.73
2936 3056 3.847042 AGATATTCTACCATCCCGGGA 57.153 47.619 29.18 29.18 40.22 5.14
2937 3057 4.141990 AGATATTCTACCATCCCGGGAA 57.858 45.455 30.84 10.38 40.22 3.97
2938 3058 4.097418 AGATATTCTACCATCCCGGGAAG 58.903 47.826 30.84 24.59 40.22 3.46
2939 3059 2.489528 ATTCTACCATCCCGGGAAGA 57.510 50.000 30.84 23.02 40.22 2.87
2940 3060 2.489528 TTCTACCATCCCGGGAAGAT 57.510 50.000 30.84 14.08 40.22 2.40
2941 3061 3.623466 TTCTACCATCCCGGGAAGATA 57.377 47.619 30.84 14.58 40.22 1.98
2942 3062 2.885616 TCTACCATCCCGGGAAGATAC 58.114 52.381 30.84 0.00 40.22 2.24
2943 3063 2.449730 TCTACCATCCCGGGAAGATACT 59.550 50.000 30.84 6.77 40.22 2.12
2944 3064 2.191981 ACCATCCCGGGAAGATACTT 57.808 50.000 30.84 5.84 40.22 2.24
2945 3065 2.047830 ACCATCCCGGGAAGATACTTC 58.952 52.381 30.84 0.00 40.22 3.01
2946 3066 2.330216 CCATCCCGGGAAGATACTTCT 58.670 52.381 30.84 3.97 0.00 2.85
2947 3067 2.706190 CCATCCCGGGAAGATACTTCTT 59.294 50.000 30.84 3.04 44.99 2.52
2948 3068 3.136626 CCATCCCGGGAAGATACTTCTTT 59.863 47.826 30.84 2.38 42.34 2.52
2949 3069 4.347000 CCATCCCGGGAAGATACTTCTTTA 59.653 45.833 30.84 0.00 42.34 1.85
2950 3070 5.013183 CCATCCCGGGAAGATACTTCTTTAT 59.987 44.000 30.84 1.57 42.34 1.40
2951 3071 6.465894 CCATCCCGGGAAGATACTTCTTTATT 60.466 42.308 30.84 0.76 42.34 1.40
2952 3072 6.570654 TCCCGGGAAGATACTTCTTTATTT 57.429 37.500 24.50 0.00 42.34 1.40
2953 3073 7.679732 TCCCGGGAAGATACTTCTTTATTTA 57.320 36.000 24.50 0.00 42.34 1.40
2954 3074 7.732996 TCCCGGGAAGATACTTCTTTATTTAG 58.267 38.462 24.50 0.00 42.34 1.85
2955 3075 6.427242 CCCGGGAAGATACTTCTTTATTTAGC 59.573 42.308 18.48 0.00 42.34 3.09
2956 3076 6.990349 CCGGGAAGATACTTCTTTATTTAGCA 59.010 38.462 10.58 0.00 42.34 3.49
2957 3077 7.661847 CCGGGAAGATACTTCTTTATTTAGCAT 59.338 37.037 10.58 0.00 42.34 3.79
2958 3078 9.057089 CGGGAAGATACTTCTTTATTTAGCATT 57.943 33.333 10.58 0.00 42.34 3.56
2963 3083 9.343539 AGATACTTCTTTATTTAGCATTGGACC 57.656 33.333 0.00 0.00 0.00 4.46
2964 3084 6.775594 ACTTCTTTATTTAGCATTGGACCC 57.224 37.500 0.00 0.00 0.00 4.46
2965 3085 6.494059 ACTTCTTTATTTAGCATTGGACCCT 58.506 36.000 0.00 0.00 0.00 4.34
2966 3086 6.603599 ACTTCTTTATTTAGCATTGGACCCTC 59.396 38.462 0.00 0.00 0.00 4.30
2967 3087 6.327386 TCTTTATTTAGCATTGGACCCTCT 57.673 37.500 0.00 0.00 0.00 3.69
2968 3088 7.446106 TCTTTATTTAGCATTGGACCCTCTA 57.554 36.000 0.00 0.00 0.00 2.43
2969 3089 8.045720 TCTTTATTTAGCATTGGACCCTCTAT 57.954 34.615 0.00 0.00 0.00 1.98
2970 3090 7.939039 TCTTTATTTAGCATTGGACCCTCTATG 59.061 37.037 0.00 0.00 0.00 2.23
2971 3091 4.437682 TTTAGCATTGGACCCTCTATGG 57.562 45.455 0.00 0.00 0.00 2.74
2972 3092 0.475906 AGCATTGGACCCTCTATGGC 59.524 55.000 0.00 0.00 0.00 4.40
2973 3093 0.183492 GCATTGGACCCTCTATGGCA 59.817 55.000 0.00 0.00 0.00 4.92
2974 3094 1.816961 GCATTGGACCCTCTATGGCAG 60.817 57.143 0.00 0.00 0.00 4.85
2975 3095 1.492176 CATTGGACCCTCTATGGCAGT 59.508 52.381 0.00 0.00 0.00 4.40
2976 3096 1.204146 TTGGACCCTCTATGGCAGTC 58.796 55.000 0.00 0.00 0.00 3.51
2977 3097 0.042581 TGGACCCTCTATGGCAGTCA 59.957 55.000 0.00 0.00 31.29 3.41
2978 3098 1.344393 TGGACCCTCTATGGCAGTCAT 60.344 52.381 0.00 0.00 39.78 3.06
2979 3099 2.090775 TGGACCCTCTATGGCAGTCATA 60.091 50.000 0.00 0.00 37.30 2.15
2980 3100 3.177228 GGACCCTCTATGGCAGTCATAT 58.823 50.000 0.00 0.00 37.67 1.78
2981 3101 3.584848 GGACCCTCTATGGCAGTCATATT 59.415 47.826 0.00 0.00 37.67 1.28
2982 3102 4.777896 GGACCCTCTATGGCAGTCATATTA 59.222 45.833 0.00 0.00 37.67 0.98
2983 3103 5.105146 GGACCCTCTATGGCAGTCATATTAG 60.105 48.000 0.00 0.00 37.67 1.73
2984 3104 5.407049 ACCCTCTATGGCAGTCATATTAGT 58.593 41.667 0.00 0.00 37.67 2.24
2985 3105 5.846714 ACCCTCTATGGCAGTCATATTAGTT 59.153 40.000 0.00 0.00 37.67 2.24
2986 3106 6.330250 ACCCTCTATGGCAGTCATATTAGTTT 59.670 38.462 0.00 0.00 37.67 2.66
2987 3107 7.147302 ACCCTCTATGGCAGTCATATTAGTTTT 60.147 37.037 0.00 0.00 37.67 2.43
2988 3108 8.375506 CCCTCTATGGCAGTCATATTAGTTTTA 58.624 37.037 0.00 0.00 37.67 1.52
2989 3109 9.950496 CCTCTATGGCAGTCATATTAGTTTTAT 57.050 33.333 0.00 0.00 37.67 1.40
3053 3173 7.610865 TCTTTTTGGACTGTTCTGAATTGTTT 58.389 30.769 0.00 0.00 0.00 2.83
3054 3174 8.093927 TCTTTTTGGACTGTTCTGAATTGTTTT 58.906 29.630 0.00 0.00 0.00 2.43
3058 3178 4.051237 GACTGTTCTGAATTGTTTTGGGC 58.949 43.478 0.00 0.00 0.00 5.36
3071 3191 3.194861 GTTTTGGGCTGGTTCTTTTGAC 58.805 45.455 0.00 0.00 0.00 3.18
3087 3208 3.304911 TTGACTGACACCAATTTGGGA 57.695 42.857 19.39 0.19 43.37 4.37
3091 3212 2.091885 ACTGACACCAATTTGGGACAGT 60.092 45.455 24.72 24.72 43.37 3.55
3101 3222 5.232463 CAATTTGGGACAGTCAATTCCTTG 58.768 41.667 2.17 0.00 42.39 3.61
3111 3232 3.525199 AGTCAATTCCTTGATGGGCTAGT 59.475 43.478 0.00 0.00 43.08 2.57
3113 3234 5.191722 AGTCAATTCCTTGATGGGCTAGTTA 59.808 40.000 0.00 0.00 43.08 2.24
3135 3256 2.414785 CCCATTACTTGTGCGGCCC 61.415 63.158 0.00 0.00 0.00 5.80
3136 3257 1.677300 CCATTACTTGTGCGGCCCA 60.677 57.895 0.00 0.00 0.00 5.36
3139 3260 4.715523 TACTTGTGCGGCCCAGCC 62.716 66.667 0.00 0.00 46.75 4.85
3153 3274 1.304464 CAGCCAACCCCTTTCTCCC 60.304 63.158 0.00 0.00 0.00 4.30
3163 3284 4.566837 ACCCCTTTCTCCCTTTGATTTTT 58.433 39.130 0.00 0.00 0.00 1.94
3217 3338 9.167311 TGCTCTTGATCTTTTCTTTATTAGTCC 57.833 33.333 0.00 0.00 0.00 3.85
3241 3363 6.407979 CCTTTTGGGTATATTTGGGATGTTGG 60.408 42.308 0.00 0.00 35.46 3.77
3242 3364 3.571590 TGGGTATATTTGGGATGTTGGC 58.428 45.455 0.00 0.00 0.00 4.52
3339 3462 2.797330 TGCAAGGTTGTGTGCACG 59.203 55.556 13.13 0.00 45.52 5.34
3340 3463 2.655044 GCAAGGTTGTGTGCACGC 60.655 61.111 23.40 23.40 40.58 5.34
3352 3475 2.783832 GTGTGCACGCTTTTTCTTCTTC 59.216 45.455 22.93 0.00 0.00 2.87
3362 3485 9.072294 CACGCTTTTTCTTCTTCTTTTAAAAGA 57.928 29.630 23.65 23.65 42.91 2.52
3527 3656 8.854614 ATACCAATGCTAGTAATCCATTCTTC 57.145 34.615 0.00 0.00 0.00 2.87
3533 3663 7.914427 TGCTAGTAATCCATTCTTCCTTAGA 57.086 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.616374 CGCTCCTCTTTCCTATCCTCC 59.384 57.143 0.00 0.00 0.00 4.30
25 26 0.693049 AAATCACCACCGCTCCTCTT 59.307 50.000 0.00 0.00 0.00 2.85
55 56 3.070878 TGCATTCAGTACCTGTCACTTCA 59.929 43.478 0.00 0.00 32.61 3.02
77 78 0.701310 ACCCTTGTCTTTCCCCCACT 60.701 55.000 0.00 0.00 0.00 4.00
81 82 3.035363 TCAAAAACCCTTGTCTTTCCCC 58.965 45.455 0.00 0.00 0.00 4.81
84 85 7.841915 TTGAATTCAAAAACCCTTGTCTTTC 57.158 32.000 18.45 0.00 32.11 2.62
85 86 7.828717 ACATTGAATTCAAAAACCCTTGTCTTT 59.171 29.630 23.91 0.35 39.55 2.52
91 93 7.609532 TGTTTCACATTGAATTCAAAAACCCTT 59.390 29.630 27.42 11.28 39.55 3.95
99 101 5.976534 CCGTTCTGTTTCACATTGAATTCAA 59.023 36.000 22.52 22.52 36.11 2.69
139 141 2.202531 GGTAGCCGTCGGTCGTTC 60.203 66.667 13.94 0.00 37.94 3.95
178 180 3.066190 CCGTAGCCAGTCGGTCCA 61.066 66.667 0.00 0.00 41.58 4.02
179 181 3.834799 CCCGTAGCCAGTCGGTCC 61.835 72.222 0.00 0.00 44.51 4.46
249 251 1.444553 GCGACTGACTCAACTCGGG 60.445 63.158 7.55 0.00 0.00 5.14
264 266 2.602878 GTAATGGTCGTTCAGAAGCGA 58.397 47.619 4.37 4.37 34.54 4.93
271 273 0.390603 CGGCTGGTAATGGTCGTTCA 60.391 55.000 0.00 0.00 0.00 3.18
277 279 1.146263 GCTAGCGGCTGGTAATGGT 59.854 57.895 13.86 0.00 38.06 3.55
302 304 3.749064 GGCCGACAGCAGAGACGA 61.749 66.667 0.00 0.00 46.50 4.20
419 421 1.797025 CTCTCGGAAAACCACCACTC 58.203 55.000 0.00 0.00 0.00 3.51
476 478 8.974060 AGTTCAGGTTTGTAGAAAATAACTCA 57.026 30.769 0.00 0.00 0.00 3.41
477 479 9.880064 GAAGTTCAGGTTTGTAGAAAATAACTC 57.120 33.333 0.00 0.00 0.00 3.01
478 480 9.628500 AGAAGTTCAGGTTTGTAGAAAATAACT 57.372 29.630 5.50 0.00 0.00 2.24
479 481 9.665264 CAGAAGTTCAGGTTTGTAGAAAATAAC 57.335 33.333 5.50 0.00 0.00 1.89
491 493 8.406297 GTGTAAAATCTTCAGAAGTTCAGGTTT 58.594 33.333 10.09 0.06 0.00 3.27
631 640 0.947244 CAACAGTGTTGGAGCACCTC 59.053 55.000 25.45 0.00 40.04 3.85
661 675 2.177580 AAGTGTCAACGTGTGGCGG 61.178 57.895 0.00 0.00 46.52 6.13
663 677 0.027586 GTCAAGTGTCAACGTGTGGC 59.972 55.000 0.00 0.00 37.13 5.01
664 678 1.062002 GTGTCAAGTGTCAACGTGTGG 59.938 52.381 0.00 0.00 37.13 4.17
665 679 1.729517 TGTGTCAAGTGTCAACGTGTG 59.270 47.619 0.00 0.00 37.13 3.82
814 828 2.143122 CTGGAAAAGCTACGTGCAGAA 58.857 47.619 0.00 0.00 45.94 3.02
832 846 1.499056 GCGGCAAGATGTGTGACTG 59.501 57.895 0.00 0.00 0.00 3.51
834 848 2.476051 CGCGGCAAGATGTGTGAC 59.524 61.111 0.00 0.00 0.00 3.67
912 926 4.840005 GGGGAAAGGAGAGGCGCG 62.840 72.222 0.00 0.00 0.00 6.86
939 953 1.152567 AGAGGAGAGGCCGGAGATG 60.153 63.158 5.05 0.00 43.43 2.90
940 954 1.152830 GAGAGGAGAGGCCGGAGAT 59.847 63.158 5.05 0.00 43.43 2.75
941 955 2.598467 GAGAGGAGAGGCCGGAGA 59.402 66.667 5.05 0.00 43.43 3.71
942 956 2.520741 GGAGAGGAGAGGCCGGAG 60.521 72.222 5.05 0.00 43.43 4.63
943 957 4.507916 CGGAGAGGAGAGGCCGGA 62.508 72.222 5.05 0.00 43.43 5.14
944 958 4.507916 TCGGAGAGGAGAGGCCGG 62.508 72.222 0.00 0.00 43.71 6.13
955 969 1.738350 GTATATAGCAGCGCTCGGAGA 59.262 52.381 7.13 0.00 40.44 3.71
958 972 2.188524 CATGTATATAGCAGCGCTCGG 58.811 52.381 7.13 0.00 40.44 4.63
960 974 1.929836 GCCATGTATATAGCAGCGCTC 59.070 52.381 7.13 2.24 40.44 5.03
962 976 0.647410 CGCCATGTATATAGCAGCGC 59.353 55.000 0.00 0.00 35.33 5.92
963 977 0.647410 GCGCCATGTATATAGCAGCG 59.353 55.000 0.00 10.44 44.54 5.18
964 978 0.647410 CGCGCCATGTATATAGCAGC 59.353 55.000 0.00 0.00 0.00 5.25
965 979 1.280982 CCGCGCCATGTATATAGCAG 58.719 55.000 0.00 0.00 0.00 4.24
966 980 0.108377 CCCGCGCCATGTATATAGCA 60.108 55.000 0.00 0.00 0.00 3.49
967 981 1.429148 GCCCGCGCCATGTATATAGC 61.429 60.000 0.00 0.00 0.00 2.97
990 1004 1.286260 GACTCCGTTGACTCGCAGT 59.714 57.895 0.00 0.00 34.39 4.40
1277 1342 4.821589 GAAGCCGGGGACAGCGAG 62.822 72.222 2.18 0.00 34.20 5.03
1945 2010 0.895530 ACACATGGTGGTACTCTCCG 59.104 55.000 0.00 0.00 37.94 4.63
1946 2011 1.207329 GGACACATGGTGGTACTCTCC 59.793 57.143 0.00 0.00 37.94 3.71
1947 2012 1.899814 TGGACACATGGTGGTACTCTC 59.100 52.381 0.00 0.00 37.94 3.20
1948 2013 2.024176 TGGACACATGGTGGTACTCT 57.976 50.000 0.00 0.00 37.94 3.24
1959 2031 1.202302 CGTACTCGCTCATGGACACAT 60.202 52.381 0.00 0.00 37.99 3.21
1969 2041 2.202623 CCAGGCACGTACTCGCTC 60.203 66.667 0.00 0.00 41.18 5.03
2234 2322 3.808728 AGCTTGTCTGCTTTTGTAGTCA 58.191 40.909 0.00 0.00 40.93 3.41
2288 2376 9.739276 AATCGATTGCTCCATTATTCCTTTATA 57.261 29.630 10.50 0.00 0.00 0.98
2341 2429 3.119029 ACAGCAAGCACATCAACAAAGTT 60.119 39.130 0.00 0.00 0.00 2.66
2350 2438 1.334556 TGAACACACAGCAAGCACATC 59.665 47.619 0.00 0.00 0.00 3.06
2351 2439 1.335810 CTGAACACACAGCAAGCACAT 59.664 47.619 0.00 0.00 0.00 3.21
2356 2444 1.004610 CGTCACTGAACACACAGCAAG 60.005 52.381 0.00 0.00 41.06 4.01
2360 2462 2.124903 GGTACGTCACTGAACACACAG 58.875 52.381 0.00 0.00 42.78 3.66
2513 2615 4.025145 TCGTATGCAGTAGTCGATGTACTG 60.025 45.833 23.77 23.77 46.92 2.74
2531 2633 5.916661 ACTAACAATCACTGGTCTCGTAT 57.083 39.130 0.00 0.00 0.00 3.06
2579 2681 7.339207 TGAATTTACTTACACTTTCGTCAACG 58.661 34.615 0.00 0.00 41.45 4.10
2621 2723 7.816640 ACGCAAAACTGATGTGTAATTATTCT 58.183 30.769 0.00 0.00 39.58 2.40
2631 2733 4.104776 ACTCAAAACGCAAAACTGATGTG 58.895 39.130 0.00 0.00 0.00 3.21
2632 2734 4.370364 ACTCAAAACGCAAAACTGATGT 57.630 36.364 0.00 0.00 0.00 3.06
2639 2741 3.181495 ACGGATGAACTCAAAACGCAAAA 60.181 39.130 0.00 0.00 0.00 2.44
2642 2744 1.262950 CACGGATGAACTCAAAACGCA 59.737 47.619 0.00 0.00 0.00 5.24
2658 2760 1.943693 CAGTTTTTGCGTGGCACGG 60.944 57.895 37.33 21.23 42.82 4.94
2660 2762 3.308660 GCAGTTTTTGCGTGGCAC 58.691 55.556 7.79 7.79 44.09 5.01
2668 2785 7.621832 TCAATGAAAAGATACGCAGTTTTTG 57.378 32.000 0.00 0.00 37.78 2.44
2672 2789 8.492673 TTCTATCAATGAAAAGATACGCAGTT 57.507 30.769 0.44 0.00 37.78 3.16
2694 2811 7.500992 TCTTTGTACTCATTTCACTCACTTCT 58.499 34.615 0.00 0.00 0.00 2.85
2699 2816 5.991606 CACCTCTTTGTACTCATTTCACTCA 59.008 40.000 0.00 0.00 0.00 3.41
2703 2820 5.304686 ACCACCTCTTTGTACTCATTTCA 57.695 39.130 0.00 0.00 0.00 2.69
2707 2824 5.818678 TTGTACCACCTCTTTGTACTCAT 57.181 39.130 0.00 0.00 36.63 2.90
2708 2825 5.818678 ATTGTACCACCTCTTTGTACTCA 57.181 39.130 0.00 0.00 36.63 3.41
2709 2826 6.694447 TGTATTGTACCACCTCTTTGTACTC 58.306 40.000 0.00 0.00 36.63 2.59
2710 2827 6.675413 TGTATTGTACCACCTCTTTGTACT 57.325 37.500 0.00 0.00 36.63 2.73
2711 2828 7.064253 GTGATGTATTGTACCACCTCTTTGTAC 59.936 40.741 0.00 0.00 36.30 2.90
2712 2829 7.101054 GTGATGTATTGTACCACCTCTTTGTA 58.899 38.462 0.00 0.00 0.00 2.41
2713 2830 5.938125 GTGATGTATTGTACCACCTCTTTGT 59.062 40.000 0.00 0.00 0.00 2.83
2714 2831 5.937540 TGTGATGTATTGTACCACCTCTTTG 59.062 40.000 0.00 0.00 0.00 2.77
2718 2835 3.863424 CGTGTGATGTATTGTACCACCTC 59.137 47.826 0.00 0.00 0.00 3.85
2720 2837 3.852286 TCGTGTGATGTATTGTACCACC 58.148 45.455 0.00 0.00 0.00 4.61
2724 2841 5.750484 TTCGTTCGTGTGATGTATTGTAC 57.250 39.130 0.00 0.00 0.00 2.90
2730 2847 3.054166 CACCTTTCGTTCGTGTGATGTA 58.946 45.455 0.00 0.00 0.00 2.29
2734 2851 0.176219 ACCACCTTTCGTTCGTGTGA 59.824 50.000 0.00 0.00 0.00 3.58
2735 2852 1.855513 TACCACCTTTCGTTCGTGTG 58.144 50.000 0.00 0.00 0.00 3.82
2740 2857 5.730568 GCATCATTCATACCACCTTTCGTTC 60.731 44.000 0.00 0.00 0.00 3.95
2743 2860 3.003689 GGCATCATTCATACCACCTTTCG 59.996 47.826 0.00 0.00 0.00 3.46
2763 2880 1.134551 CCTTGACCTTCTGCTCTAGGC 60.135 57.143 0.00 0.00 42.22 3.93
2764 2881 1.484240 CCCTTGACCTTCTGCTCTAGG 59.516 57.143 0.00 0.00 37.56 3.02
2765 2882 2.461695 TCCCTTGACCTTCTGCTCTAG 58.538 52.381 0.00 0.00 0.00 2.43
2775 2894 1.606531 GCTGAGCATCCCTTGACCT 59.393 57.895 0.00 0.00 0.00 3.85
2787 2906 1.244019 ATCGTTGTTTGGGGCTGAGC 61.244 55.000 0.00 0.00 0.00 4.26
2806 2925 9.098355 GACAATCATGAGTTTAGCTGTGTTATA 57.902 33.333 0.09 0.00 0.00 0.98
2807 2926 7.826252 AGACAATCATGAGTTTAGCTGTGTTAT 59.174 33.333 0.09 0.00 0.00 1.89
2808 2927 7.118245 CAGACAATCATGAGTTTAGCTGTGTTA 59.882 37.037 0.09 0.00 0.00 2.41
2809 2928 6.000219 AGACAATCATGAGTTTAGCTGTGTT 59.000 36.000 0.09 0.00 0.00 3.32
2811 2930 5.640783 TCAGACAATCATGAGTTTAGCTGTG 59.359 40.000 0.09 0.00 0.00 3.66
2812 2931 5.798132 TCAGACAATCATGAGTTTAGCTGT 58.202 37.500 0.09 0.00 0.00 4.40
2813 2932 6.732531 TTCAGACAATCATGAGTTTAGCTG 57.267 37.500 0.09 3.57 0.00 4.24
2814 2933 7.750229 TTTTCAGACAATCATGAGTTTAGCT 57.250 32.000 0.09 0.00 0.00 3.32
2815 2934 8.976986 AATTTTCAGACAATCATGAGTTTAGC 57.023 30.769 0.09 0.00 0.00 3.09
2825 2945 7.750229 AAGTGCTAGAATTTTCAGACAATCA 57.250 32.000 0.00 0.00 0.00 2.57
2838 2958 8.099537 ACATGCATATAGCTAAAGTGCTAGAAT 58.900 33.333 21.40 9.81 46.89 2.40
2860 2980 8.090214 ACCTAAAATCAATTTTCAGGTGACATG 58.910 33.333 18.36 0.00 39.47 3.21
2862 2982 7.595819 ACCTAAAATCAATTTTCAGGTGACA 57.404 32.000 18.36 0.00 39.47 3.58
2866 2986 9.362151 TGACTTACCTAAAATCAATTTTCAGGT 57.638 29.630 20.55 20.55 41.32 4.00
2867 2987 9.626045 GTGACTTACCTAAAATCAATTTTCAGG 57.374 33.333 4.07 11.10 40.24 3.86
2868 2988 9.329913 CGTGACTTACCTAAAATCAATTTTCAG 57.670 33.333 4.07 1.11 40.24 3.02
2870 2990 7.806014 TGCGTGACTTACCTAAAATCAATTTTC 59.194 33.333 4.07 0.00 40.24 2.29
2873 2993 6.811253 TGCGTGACTTACCTAAAATCAATT 57.189 33.333 0.00 0.00 0.00 2.32
2876 2996 7.413657 GCTTAATGCGTGACTTACCTAAAATCA 60.414 37.037 0.00 0.00 0.00 2.57
2880 3000 5.789710 GCTTAATGCGTGACTTACCTAAA 57.210 39.130 0.00 0.00 0.00 1.85
2907 3027 9.555727 CGGGATGGTAGAATATCTTCTTTAAAA 57.444 33.333 0.00 0.00 41.91 1.52
2911 3031 5.013183 CCCGGGATGGTAGAATATCTTCTTT 59.987 44.000 18.48 0.00 37.64 2.52
2912 3032 4.532521 CCCGGGATGGTAGAATATCTTCTT 59.467 45.833 18.48 0.00 37.64 2.52
2913 3033 4.097418 CCCGGGATGGTAGAATATCTTCT 58.903 47.826 18.48 0.00 39.01 2.85
2914 3034 4.094476 TCCCGGGATGGTAGAATATCTTC 58.906 47.826 22.63 0.00 35.15 2.87
2916 3036 3.847042 TCCCGGGATGGTAGAATATCT 57.153 47.619 22.63 0.00 35.15 1.98
2917 3037 4.094476 TCTTCCCGGGATGGTAGAATATC 58.906 47.826 30.44 0.00 35.15 1.63
2919 3039 3.623466 TCTTCCCGGGATGGTAGAATA 57.377 47.619 30.44 10.74 35.15 1.75
2921 3041 2.489528 ATCTTCCCGGGATGGTAGAA 57.510 50.000 30.44 15.26 32.24 2.10
2923 3043 2.890814 AGTATCTTCCCGGGATGGTAG 58.109 52.381 30.44 22.34 35.15 3.18
2924 3044 3.116862 AGAAGTATCTTCCCGGGATGGTA 60.117 47.826 30.44 26.52 30.06 3.25
2925 3045 2.047830 GAAGTATCTTCCCGGGATGGT 58.952 52.381 30.44 27.53 35.15 3.55
2926 3046 2.330216 AGAAGTATCTTCCCGGGATGG 58.670 52.381 30.44 22.99 29.15 3.51
2927 3047 4.423625 AAAGAAGTATCTTCCCGGGATG 57.576 45.455 27.48 27.08 45.19 3.51
2928 3048 6.765355 AATAAAGAAGTATCTTCCCGGGAT 57.235 37.500 27.48 12.94 45.19 3.85
2930 3050 6.427242 GCTAAATAAAGAAGTATCTTCCCGGG 59.573 42.308 16.85 16.85 45.19 5.73
2931 3051 6.990349 TGCTAAATAAAGAAGTATCTTCCCGG 59.010 38.462 0.00 0.00 45.19 5.73
2932 3052 8.608844 ATGCTAAATAAAGAAGTATCTTCCCG 57.391 34.615 5.97 0.00 45.19 5.14
2937 3057 9.343539 GGTCCAATGCTAAATAAAGAAGTATCT 57.656 33.333 0.00 0.00 37.57 1.98
2938 3058 8.568794 GGGTCCAATGCTAAATAAAGAAGTATC 58.431 37.037 0.00 0.00 0.00 2.24
2939 3059 8.282256 AGGGTCCAATGCTAAATAAAGAAGTAT 58.718 33.333 0.00 0.00 0.00 2.12
2940 3060 7.639378 AGGGTCCAATGCTAAATAAAGAAGTA 58.361 34.615 0.00 0.00 0.00 2.24
2941 3061 6.494059 AGGGTCCAATGCTAAATAAAGAAGT 58.506 36.000 0.00 0.00 0.00 3.01
2942 3062 6.830838 AGAGGGTCCAATGCTAAATAAAGAAG 59.169 38.462 0.00 0.00 0.00 2.85
2943 3063 6.731467 AGAGGGTCCAATGCTAAATAAAGAA 58.269 36.000 0.00 0.00 0.00 2.52
2944 3064 6.327386 AGAGGGTCCAATGCTAAATAAAGA 57.673 37.500 0.00 0.00 0.00 2.52
2945 3065 7.175641 CCATAGAGGGTCCAATGCTAAATAAAG 59.824 40.741 0.00 0.00 0.00 1.85
2946 3066 7.004086 CCATAGAGGGTCCAATGCTAAATAAA 58.996 38.462 0.00 0.00 0.00 1.40
2947 3067 6.542821 CCATAGAGGGTCCAATGCTAAATAA 58.457 40.000 0.00 0.00 0.00 1.40
2948 3068 5.514834 GCCATAGAGGGTCCAATGCTAAATA 60.515 44.000 0.00 0.00 38.09 1.40
2949 3069 4.751028 GCCATAGAGGGTCCAATGCTAAAT 60.751 45.833 0.00 0.00 38.09 1.40
2950 3070 3.435026 GCCATAGAGGGTCCAATGCTAAA 60.435 47.826 0.00 0.00 38.09 1.85
2951 3071 2.106511 GCCATAGAGGGTCCAATGCTAA 59.893 50.000 0.00 0.00 38.09 3.09
2952 3072 1.699634 GCCATAGAGGGTCCAATGCTA 59.300 52.381 0.00 0.00 38.09 3.49
2953 3073 0.475906 GCCATAGAGGGTCCAATGCT 59.524 55.000 0.00 0.00 38.09 3.79
2954 3074 0.183492 TGCCATAGAGGGTCCAATGC 59.817 55.000 0.00 0.00 38.09 3.56
2955 3075 1.492176 ACTGCCATAGAGGGTCCAATG 59.508 52.381 0.00 0.00 38.09 2.82
2956 3076 1.771255 GACTGCCATAGAGGGTCCAAT 59.229 52.381 0.00 0.00 38.09 3.16
2957 3077 1.204146 GACTGCCATAGAGGGTCCAA 58.796 55.000 0.00 0.00 38.09 3.53
2958 3078 0.042581 TGACTGCCATAGAGGGTCCA 59.957 55.000 0.00 0.00 38.09 4.02
2959 3079 1.428869 ATGACTGCCATAGAGGGTCC 58.571 55.000 0.00 0.00 38.09 4.46
2960 3080 4.899352 AATATGACTGCCATAGAGGGTC 57.101 45.455 0.00 0.00 40.75 4.46
2961 3081 5.407049 ACTAATATGACTGCCATAGAGGGT 58.593 41.667 0.00 0.00 40.75 4.34
2962 3082 6.365970 AACTAATATGACTGCCATAGAGGG 57.634 41.667 0.00 0.00 40.75 4.30
2963 3083 9.950496 ATAAAACTAATATGACTGCCATAGAGG 57.050 33.333 0.00 0.00 40.75 3.69
3018 3138 9.300681 AGAACAGTCCAAAAAGAATATGAATGA 57.699 29.630 0.00 0.00 0.00 2.57
3019 3139 9.350357 CAGAACAGTCCAAAAAGAATATGAATG 57.650 33.333 0.00 0.00 0.00 2.67
3020 3140 9.300681 TCAGAACAGTCCAAAAAGAATATGAAT 57.699 29.630 0.00 0.00 0.00 2.57
3021 3141 8.690203 TCAGAACAGTCCAAAAAGAATATGAA 57.310 30.769 0.00 0.00 0.00 2.57
3022 3142 8.690203 TTCAGAACAGTCCAAAAAGAATATGA 57.310 30.769 0.00 0.00 0.00 2.15
3023 3143 9.918630 AATTCAGAACAGTCCAAAAAGAATATG 57.081 29.630 0.00 0.00 0.00 1.78
3024 3144 9.918630 CAATTCAGAACAGTCCAAAAAGAATAT 57.081 29.630 0.00 0.00 0.00 1.28
3025 3145 8.912988 ACAATTCAGAACAGTCCAAAAAGAATA 58.087 29.630 0.00 0.00 0.00 1.75
3026 3146 7.785033 ACAATTCAGAACAGTCCAAAAAGAAT 58.215 30.769 0.00 0.00 0.00 2.40
3027 3147 7.169158 ACAATTCAGAACAGTCCAAAAAGAA 57.831 32.000 0.00 0.00 0.00 2.52
3028 3148 6.773976 ACAATTCAGAACAGTCCAAAAAGA 57.226 33.333 0.00 0.00 0.00 2.52
3029 3149 7.832503 AAACAATTCAGAACAGTCCAAAAAG 57.167 32.000 0.00 0.00 0.00 2.27
3030 3150 7.118971 CCAAAACAATTCAGAACAGTCCAAAAA 59.881 33.333 0.00 0.00 0.00 1.94
3031 3151 6.593382 CCAAAACAATTCAGAACAGTCCAAAA 59.407 34.615 0.00 0.00 0.00 2.44
3032 3152 6.105333 CCAAAACAATTCAGAACAGTCCAAA 58.895 36.000 0.00 0.00 0.00 3.28
3033 3153 5.395103 CCCAAAACAATTCAGAACAGTCCAA 60.395 40.000 0.00 0.00 0.00 3.53
3034 3154 4.099266 CCCAAAACAATTCAGAACAGTCCA 59.901 41.667 0.00 0.00 0.00 4.02
3035 3155 4.620982 CCCAAAACAATTCAGAACAGTCC 58.379 43.478 0.00 0.00 0.00 3.85
3036 3156 4.051237 GCCCAAAACAATTCAGAACAGTC 58.949 43.478 0.00 0.00 0.00 3.51
3039 3159 3.181467 CCAGCCCAAAACAATTCAGAACA 60.181 43.478 0.00 0.00 0.00 3.18
3042 3162 2.676748 ACCAGCCCAAAACAATTCAGA 58.323 42.857 0.00 0.00 0.00 3.27
3043 3163 3.070015 AGAACCAGCCCAAAACAATTCAG 59.930 43.478 0.00 0.00 0.00 3.02
3053 3173 2.031120 CAGTCAAAAGAACCAGCCCAA 58.969 47.619 0.00 0.00 0.00 4.12
3054 3174 1.214175 TCAGTCAAAAGAACCAGCCCA 59.786 47.619 0.00 0.00 0.00 5.36
3058 3178 3.278574 TGGTGTCAGTCAAAAGAACCAG 58.721 45.455 0.00 0.00 32.62 4.00
3071 3191 2.554032 GACTGTCCCAAATTGGTGTCAG 59.446 50.000 19.01 19.01 35.17 3.51
3087 3208 2.042162 AGCCCATCAAGGAATTGACTGT 59.958 45.455 0.00 0.00 41.22 3.55
3091 3212 4.591321 AACTAGCCCATCAAGGAATTGA 57.409 40.909 0.00 0.00 41.22 2.57
3135 3256 1.304464 GGGAGAAAGGGGTTGGCTG 60.304 63.158 0.00 0.00 0.00 4.85
3136 3257 1.074296 AAGGGAGAAAGGGGTTGGCT 61.074 55.000 0.00 0.00 0.00 4.75
3139 3260 2.675658 TCAAAGGGAGAAAGGGGTTG 57.324 50.000 0.00 0.00 0.00 3.77
3163 3284 7.493367 ACACATAAAAATGAGAAAACGGGAAA 58.507 30.769 0.00 0.00 0.00 3.13
3166 3287 7.707774 AAACACATAAAAATGAGAAAACGGG 57.292 32.000 0.00 0.00 0.00 5.28
3167 3288 7.582319 GCAAAACACATAAAAATGAGAAAACGG 59.418 33.333 0.00 0.00 0.00 4.44
3169 3290 9.636965 GAGCAAAACACATAAAAATGAGAAAAC 57.363 29.630 0.00 0.00 0.00 2.43
3173 3294 8.412456 TCAAGAGCAAAACACATAAAAATGAGA 58.588 29.630 0.00 0.00 0.00 3.27
3174 3295 8.578308 TCAAGAGCAAAACACATAAAAATGAG 57.422 30.769 0.00 0.00 0.00 2.90
3175 3296 9.195411 GATCAAGAGCAAAACACATAAAAATGA 57.805 29.630 0.00 0.00 0.00 2.57
3176 3297 9.199982 AGATCAAGAGCAAAACACATAAAAATG 57.800 29.630 0.00 0.00 0.00 2.32
3177 3298 9.768662 AAGATCAAGAGCAAAACACATAAAAAT 57.231 25.926 0.00 0.00 0.00 1.82
3217 3338 6.581712 CCAACATCCCAAATATACCCAAAAG 58.418 40.000 0.00 0.00 0.00 2.27
3313 3436 3.552699 CACACAACCTTGCACTGAAATTG 59.447 43.478 0.00 0.00 0.00 2.32
3326 3449 0.530288 AAAAAGCGTGCACACAACCT 59.470 45.000 18.64 1.44 0.00 3.50
3440 3566 9.936759 AAACAAAACACCAAATTAGAGAAGAAA 57.063 25.926 0.00 0.00 0.00 2.52
3486 3615 9.646522 AGCATTGGTATTATGTTTAGGAAGAAT 57.353 29.630 0.00 0.00 0.00 2.40
3489 3618 9.561069 ACTAGCATTGGTATTATGTTTAGGAAG 57.439 33.333 0.00 0.00 0.00 3.46
3519 3648 7.751768 AGTGAAGTTTTCTAAGGAAGAATGG 57.248 36.000 0.00 0.00 43.75 3.16


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

AutoCloner maintained by Alex Coulton.