Multiple sequence alignment - TraesCS5A01G457900

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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 TraesCS5A01G457900 chr5A 100.000 3497 0 0 1 3497 638070918 638067422 0.000000e+00 6458.0
1 TraesCS5A01G457900 chr5A 99.336 904 6 0 1 904 453524947 453524044 0.000000e+00 1637.0
2 TraesCS5A01G457900 chr5D 90.296 1927 98 44 903 2786 510058076 510059956 0.000000e+00 2440.0
3 TraesCS5A01G457900 chr5D 81.500 200 37 0 2033 2232 565785706 565785507 7.770000e-37 165.0
4 TraesCS5A01G457900 chr5B 90.934 1798 98 34 903 2672 641042463 641044223 0.000000e+00 2357.0
5 TraesCS5A01G457900 chr5B 81.553 206 36 2 2028 2232 707359592 707359388 6.000000e-38 169.0
6 TraesCS5A01G457900 chr5B 81.773 203 35 2 2028 2229 707391279 707391480 6.000000e-38 169.0
7 TraesCS5A01G457900 chr5B 97.959 49 1 0 2741 2789 641046402 641046450 6.220000e-13 86.1
8 TraesCS5A01G457900 chr6A 99.339 908 5 1 1 907 598919783 598918876 0.000000e+00 1642.0
9 TraesCS5A01G457900 chr3B 99.447 904 4 1 1 903 816312154 816313057 0.000000e+00 1640.0
10 TraesCS5A01G457900 chr3B 99.336 904 4 2 1 903 794880818 794881720 0.000000e+00 1635.0
11 TraesCS5A01G457900 chr3B 91.518 224 19 0 3014 3237 126480552 126480329 3.390000e-80 309.0
12 TraesCS5A01G457900 chr3A 99.447 904 4 1 1 903 484646191 484645288 0.000000e+00 1640.0
13 TraesCS5A01G457900 chr1B 99.336 904 5 1 1 903 675329338 675330241 0.000000e+00 1635.0
14 TraesCS5A01G457900 chr1B 99.226 904 6 1 1 903 101276061 101276964 0.000000e+00 1629.0
15 TraesCS5A01G457900 chr1B 78.510 349 72 2 2018 2363 675790255 675789907 3.510000e-55 226.0
16 TraesCS5A01G457900 chr7B 99.011 910 8 1 1 909 658894136 658895045 0.000000e+00 1629.0
17 TraesCS5A01G457900 chr7B 88.263 213 20 5 3021 3229 672648515 672648726 2.080000e-62 250.0
18 TraesCS5A01G457900 chr7B 90.857 175 16 0 3249 3423 684384362 684384188 5.840000e-58 235.0
19 TraesCS5A01G457900 chr2B 98.904 912 7 3 1 911 733170318 733169409 0.000000e+00 1626.0
20 TraesCS5A01G457900 chr2B 96.484 256 9 0 3242 3497 146970883 146970628 1.160000e-114 424.0
21 TraesCS5A01G457900 chr2B 92.166 217 17 0 3021 3237 146971191 146970975 1.220000e-79 307.0
22 TraesCS5A01G457900 chr1D 80.176 908 159 16 1478 2368 485544258 485545161 0.000000e+00 660.0
23 TraesCS5A01G457900 chr1D 78.289 1064 194 30 1330 2368 485538770 485539821 0.000000e+00 651.0
24 TraesCS5A01G457900 chr1D 81.271 299 53 2 2018 2313 485489017 485488719 4.510000e-59 239.0
25 TraesCS5A01G457900 chr4D 98.828 256 2 1 3242 3497 487272322 487272068 4.110000e-124 455.0
26 TraesCS5A01G457900 chr4D 92.857 238 16 1 3000 3237 487281177 487280941 9.290000e-91 344.0
27 TraesCS5A01G457900 chr3D 95.720 257 9 2 3242 3497 49441785 49441530 2.510000e-111 412.0
28 TraesCS5A01G457900 chr3D 91.213 239 19 2 3000 3237 49442108 49441871 1.210000e-84 324.0
29 TraesCS5A01G457900 chr1A 75.028 909 183 25 1064 1959 582841229 582842106 7.080000e-102 381.0
30 TraesCS5A01G457900 chr1A 79.959 489 89 8 1478 1959 582845034 582845520 5.550000e-93 351.0
31 TraesCS5A01G457900 chr1A 81.271 299 53 2 2018 2313 582694191 582693893 4.510000e-59 239.0
32 TraesCS5A01G457900 chr7A 92.969 256 16 2 3242 3497 45164163 45163910 4.260000e-99 372.0
33 TraesCS5A01G457900 chr7A 90.476 231 20 2 3009 3238 45164477 45164248 1.580000e-78 303.0
34 TraesCS5A01G457900 chr7A 86.266 233 27 5 3000 3229 44859448 44859678 7.500000e-62 248.0
35 TraesCS5A01G457900 chr7A 85.837 233 28 5 3000 3229 44970866 44971096 3.490000e-60 243.0
36 TraesCS5A01G457900 chr7A 85.837 233 27 5 3001 3229 169316562 169316792 3.490000e-60 243.0
37 TraesCS5A01G457900 chr7A 93.836 146 9 0 3348 3493 44929283 44929428 1.630000e-53 220.0
38 TraesCS5A01G457900 chr7A 79.426 209 39 2 1751 1957 616219872 616219666 1.010000e-30 145.0
39 TraesCS5A01G457900 chr4A 90.873 252 20 2 3246 3497 28557433 28557681 5.590000e-88 335.0
40 TraesCS5A01G457900 chr2D 90.873 252 20 2 3246 3497 544575477 544575725 5.590000e-88 335.0
41 TraesCS5A01G457900 chr4B 90.476 252 21 2 3246 3497 602235736 602235984 2.600000e-86 329.0
42 TraesCS5A01G457900 chrUn 81.553 206 36 2 2028 2232 67469582 67469378 6.000000e-38 169.0
43 TraesCS5A01G457900 chr7D 79.426 209 39 2 1751 1957 536765442 536765648 1.010000e-30 145.0


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 TraesCS5A01G457900 chr5A 638067422 638070918 3496 True 6458.00 6458 100.0000 1 3497 1 chr5A.!!$R2 3496
1 TraesCS5A01G457900 chr5A 453524044 453524947 903 True 1637.00 1637 99.3360 1 904 1 chr5A.!!$R1 903
2 TraesCS5A01G457900 chr5D 510058076 510059956 1880 False 2440.00 2440 90.2960 903 2786 1 chr5D.!!$F1 1883
3 TraesCS5A01G457900 chr5B 641042463 641046450 3987 False 1221.55 2357 94.4465 903 2789 2 chr5B.!!$F2 1886
4 TraesCS5A01G457900 chr6A 598918876 598919783 907 True 1642.00 1642 99.3390 1 907 1 chr6A.!!$R1 906
5 TraesCS5A01G457900 chr3B 816312154 816313057 903 False 1640.00 1640 99.4470 1 903 1 chr3B.!!$F2 902
6 TraesCS5A01G457900 chr3B 794880818 794881720 902 False 1635.00 1635 99.3360 1 903 1 chr3B.!!$F1 902
7 TraesCS5A01G457900 chr3A 484645288 484646191 903 True 1640.00 1640 99.4470 1 903 1 chr3A.!!$R1 902
8 TraesCS5A01G457900 chr1B 675329338 675330241 903 False 1635.00 1635 99.3360 1 903 1 chr1B.!!$F2 902
9 TraesCS5A01G457900 chr1B 101276061 101276964 903 False 1629.00 1629 99.2260 1 903 1 chr1B.!!$F1 902
10 TraesCS5A01G457900 chr7B 658894136 658895045 909 False 1629.00 1629 99.0110 1 909 1 chr7B.!!$F1 908
11 TraesCS5A01G457900 chr2B 733169409 733170318 909 True 1626.00 1626 98.9040 1 911 1 chr2B.!!$R1 910
12 TraesCS5A01G457900 chr2B 146970628 146971191 563 True 365.50 424 94.3250 3021 3497 2 chr2B.!!$R2 476
13 TraesCS5A01G457900 chr1D 485544258 485545161 903 False 660.00 660 80.1760 1478 2368 1 chr1D.!!$F2 890
14 TraesCS5A01G457900 chr1D 485538770 485539821 1051 False 651.00 651 78.2890 1330 2368 1 chr1D.!!$F1 1038
15 TraesCS5A01G457900 chr3D 49441530 49442108 578 True 368.00 412 93.4665 3000 3497 2 chr3D.!!$R1 497
16 TraesCS5A01G457900 chr1A 582841229 582845520 4291 False 366.00 381 77.4935 1064 1959 2 chr1A.!!$F1 895
17 TraesCS5A01G457900 chr7A 45163910 45164477 567 True 337.50 372 91.7225 3009 3497 2 chr7A.!!$R2 488

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
964 966 0.820074 TTCGCCGGCCTTTTTCAAGA 60.82 50.0 23.46 5.72 30.57 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2816 5576 0.038166 GGGCATGAGGGACTTGTTCA 59.962 55.0 0.0 0.0 41.55 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
867 869 5.607171 AGGAGTTTGAGTAGGAGAAGGAAAA 59.393 40.000 0.00 0.00 0.00 2.29
961 963 2.557372 GGTTCGCCGGCCTTTTTCA 61.557 57.895 23.46 0.00 0.00 2.69
964 966 0.820074 TTCGCCGGCCTTTTTCAAGA 60.820 50.000 23.46 5.72 30.57 3.02
969 971 2.862530 GCCGGCCTTTTTCAAGAAGAAC 60.863 50.000 18.11 0.00 35.56 3.01
970 972 2.604614 CCGGCCTTTTTCAAGAAGAACG 60.605 50.000 0.00 0.00 35.56 3.95
971 973 2.289547 CGGCCTTTTTCAAGAAGAACGA 59.710 45.455 0.00 0.00 35.56 3.85
972 974 3.629058 GGCCTTTTTCAAGAAGAACGAC 58.371 45.455 0.00 0.00 35.56 4.34
973 975 3.550233 GGCCTTTTTCAAGAAGAACGACC 60.550 47.826 0.00 0.00 35.56 4.79
974 976 3.066203 GCCTTTTTCAAGAAGAACGACCA 59.934 43.478 0.00 0.00 35.56 4.02
975 977 4.789802 GCCTTTTTCAAGAAGAACGACCAG 60.790 45.833 0.00 0.00 35.56 4.00
976 978 4.574828 CCTTTTTCAAGAAGAACGACCAGA 59.425 41.667 0.00 0.00 35.56 3.86
977 979 5.239525 CCTTTTTCAAGAAGAACGACCAGAT 59.760 40.000 0.00 0.00 35.56 2.90
978 980 5.924475 TTTTCAAGAAGAACGACCAGATC 57.076 39.130 0.00 0.00 35.56 2.75
981 983 3.119814 TCAAGAAGAACGACCAGATCTCG 60.120 47.826 0.00 0.00 37.17 4.04
982 984 2.712709 AGAAGAACGACCAGATCTCGA 58.287 47.619 9.56 0.00 35.08 4.04
983 985 3.283751 AGAAGAACGACCAGATCTCGAT 58.716 45.455 9.56 0.00 35.08 3.59
985 987 1.600013 AGAACGACCAGATCTCGATCG 59.400 52.381 9.36 9.36 42.48 3.69
986 988 1.598132 GAACGACCAGATCTCGATCGA 59.402 52.381 18.32 18.32 42.48 3.59
987 989 1.222300 ACGACCAGATCTCGATCGAG 58.778 55.000 34.20 34.20 42.48 4.04
1006 1011 3.136123 CCCAAGTCGCCATGCCTG 61.136 66.667 0.00 0.00 0.00 4.85
1007 1012 3.136123 CCAAGTCGCCATGCCTGG 61.136 66.667 3.22 3.22 46.17 4.45
1008 1013 2.360350 CAAGTCGCCATGCCTGGT 60.360 61.111 9.95 0.00 45.10 4.00
1009 1014 1.973281 CAAGTCGCCATGCCTGGTT 60.973 57.895 9.95 0.00 45.10 3.67
1010 1015 1.675641 AAGTCGCCATGCCTGGTTC 60.676 57.895 9.95 1.20 45.10 3.62
1011 1016 3.499737 GTCGCCATGCCTGGTTCG 61.500 66.667 9.95 5.85 45.10 3.95
1012 1017 4.015406 TCGCCATGCCTGGTTCGT 62.015 61.111 9.95 0.00 45.10 3.85
1013 1018 3.499737 CGCCATGCCTGGTTCGTC 61.500 66.667 9.95 0.00 45.10 4.20
1014 1019 3.499737 GCCATGCCTGGTTCGTCG 61.500 66.667 9.95 0.00 45.10 5.12
1021 1026 2.501222 CTGGTTCGTCGTCGTCGG 60.501 66.667 11.74 0.00 38.33 4.79
1038 1043 1.591863 GGCGTCATACGAGAAGGCC 60.592 63.158 3.22 0.00 46.05 5.19
1149 1154 1.821936 CCTGCTCTCCTACTGCCTG 59.178 63.158 0.00 0.00 0.00 4.85
1818 1833 3.233980 AGCCTCATCGCCGCCATA 61.234 61.111 0.00 0.00 0.00 2.74
1987 2002 8.001881 ACGAGATGATGATAGTAACACTTCTT 57.998 34.615 0.00 0.00 0.00 2.52
1994 2009 8.191446 TGATGATAGTAACACTTCTTCTAGCAC 58.809 37.037 0.00 0.00 31.59 4.40
2007 2022 0.389948 CTAGCACCACCAAGGACGAC 60.390 60.000 0.00 0.00 41.22 4.34
2211 2366 5.661056 TCAGGATTCTCGTCAACAACTAT 57.339 39.130 0.00 0.00 0.00 2.12
2254 2409 0.955178 CTATCCACAGATCGAGGCGT 59.045 55.000 0.00 0.00 33.67 5.68
2319 2477 1.266178 TGATGAGGAGCGAAGAACCA 58.734 50.000 0.00 0.00 0.00 3.67
2396 2554 3.786635 CAGAATCTGCCACTACCAGTAC 58.213 50.000 0.00 0.00 0.00 2.73
2399 2557 0.038599 TCTGCCACTACCAGTACGGA 59.961 55.000 10.17 0.00 38.63 4.69
2400 2558 1.112113 CTGCCACTACCAGTACGGAT 58.888 55.000 10.17 0.00 38.63 4.18
2401 2559 1.067212 CTGCCACTACCAGTACGGATC 59.933 57.143 10.17 0.00 38.63 3.36
2410 2568 1.323412 CAGTACGGATCAGGAGGAGG 58.677 60.000 0.00 0.00 0.00 4.30
2413 2571 2.178106 AGTACGGATCAGGAGGAGGATT 59.822 50.000 0.00 0.00 0.00 3.01
2419 2577 3.007831 GGATCAGGAGGAGGATTGTGATC 59.992 52.174 0.00 0.00 39.62 2.92
2420 2578 2.034878 TCAGGAGGAGGATTGTGATCG 58.965 52.381 0.00 0.00 32.84 3.69
2433 2591 1.476891 TGTGATCGTGCTAAGGAGGAC 59.523 52.381 0.00 0.00 40.49 3.85
2444 2602 1.783071 AAGGAGGACGAGGAGGATTC 58.217 55.000 0.00 0.00 0.00 2.52
2454 2612 3.239861 GGAGGATTCCGATGATGCC 57.760 57.895 0.00 0.00 32.79 4.40
2466 2624 4.532126 TCCGATGATGCCAAGGATAATAGT 59.468 41.667 0.00 0.00 31.29 2.12
2468 2626 4.633126 CGATGATGCCAAGGATAATAGTGG 59.367 45.833 0.00 0.00 0.00 4.00
2486 2662 2.096713 GTGGCGATGATGATAACGAAGC 60.097 50.000 0.00 0.00 0.00 3.86
2532 2709 7.706607 TGATCGAGTGGTCTAACAATGATAAAG 59.293 37.037 0.00 0.00 0.00 1.85
2537 2714 9.606631 GAGTGGTCTAACAATGATAAAGAATCT 57.393 33.333 0.00 0.00 35.45 2.40
2538 2715 9.388506 AGTGGTCTAACAATGATAAAGAATCTG 57.611 33.333 0.00 0.00 35.45 2.90
2558 2737 2.002586 GTACGTGTGCCTACGAGAGTA 58.997 52.381 15.48 0.00 46.46 2.59
2575 2754 4.491676 AGAGTAATTTTTCTACTGCGCGA 58.508 39.130 12.10 0.00 29.62 5.87
2609 2793 1.142262 TGCATGATCCACTCTCCATGG 59.858 52.381 4.97 4.97 37.46 3.66
2610 2794 1.142465 GCATGATCCACTCTCCATGGT 59.858 52.381 12.58 0.00 38.47 3.55
2611 2795 2.809665 GCATGATCCACTCTCCATGGTC 60.810 54.545 12.58 0.00 38.47 4.02
2612 2796 2.252535 TGATCCACTCTCCATGGTCA 57.747 50.000 12.58 2.19 38.47 4.02
2614 2798 1.139853 GATCCACTCTCCATGGTCACC 59.860 57.143 12.58 0.00 38.47 4.02
2615 2799 0.117140 TCCACTCTCCATGGTCACCT 59.883 55.000 12.58 0.00 38.47 4.00
2616 2800 0.987294 CCACTCTCCATGGTCACCTT 59.013 55.000 12.58 0.00 32.08 3.50
2617 2801 1.339438 CCACTCTCCATGGTCACCTTG 60.339 57.143 12.58 2.52 32.08 3.61
2619 2803 1.905215 ACTCTCCATGGTCACCTTGAG 59.095 52.381 12.58 6.41 31.33 3.02
2621 2805 2.770802 CTCTCCATGGTCACCTTGAGAT 59.229 50.000 12.58 0.00 31.33 2.75
2622 2806 3.184628 TCTCCATGGTCACCTTGAGATT 58.815 45.455 12.58 0.00 31.33 2.40
2623 2807 3.198635 TCTCCATGGTCACCTTGAGATTC 59.801 47.826 12.58 0.00 31.33 2.52
2625 2809 3.054875 TCCATGGTCACCTTGAGATTCAG 60.055 47.826 12.58 0.00 31.33 3.02
2626 2810 3.276857 CATGGTCACCTTGAGATTCAGG 58.723 50.000 3.48 0.00 31.33 3.86
2627 2811 1.003580 TGGTCACCTTGAGATTCAGGC 59.996 52.381 0.00 0.00 0.00 4.85
2628 2812 1.280421 GGTCACCTTGAGATTCAGGCT 59.720 52.381 0.00 0.00 0.00 4.58
2629 2813 2.290577 GGTCACCTTGAGATTCAGGCTT 60.291 50.000 0.00 0.00 0.00 4.35
2630 2814 3.416156 GTCACCTTGAGATTCAGGCTTT 58.584 45.455 0.00 0.00 0.00 3.51
2645 2829 6.420913 TCAGGCTTTGTTTTCTACTAGTCT 57.579 37.500 0.00 0.00 0.00 3.24
2662 2846 7.399245 ACTAGTCTTGCCAAAGTTTGTTTTA 57.601 32.000 14.36 0.00 34.78 1.52
2671 2855 9.660180 TTGCCAAAGTTTGTTTTATTTTAGAGT 57.340 25.926 14.36 0.00 0.00 3.24
2686 2870 9.748708 TTATTTTAGAGTACGTGTTGTTACAGT 57.251 29.630 0.00 0.00 34.24 3.55
2687 2871 8.652810 ATTTTAGAGTACGTGTTGTTACAGTT 57.347 30.769 0.00 0.00 34.24 3.16
2688 2872 7.684062 TTTAGAGTACGTGTTGTTACAGTTC 57.316 36.000 0.00 0.00 34.24 3.01
2689 2873 5.511234 AGAGTACGTGTTGTTACAGTTCT 57.489 39.130 0.00 0.00 34.24 3.01
2692 2876 6.474751 AGAGTACGTGTTGTTACAGTTCTTTC 59.525 38.462 0.00 0.00 34.24 2.62
2693 2877 4.509915 ACGTGTTGTTACAGTTCTTTCG 57.490 40.909 0.00 0.00 34.24 3.46
2696 2880 4.584394 GTGTTGTTACAGTTCTTTCGGTG 58.416 43.478 0.00 0.00 34.24 4.94
2698 2882 3.188159 TGTTACAGTTCTTTCGGTGCT 57.812 42.857 0.00 0.00 0.00 4.40
2707 2906 1.796459 TCTTTCGGTGCTAAAGAACGC 59.204 47.619 0.00 0.00 39.40 4.84
2717 2916 2.540101 GCTAAAGAACGCATGTATCGCT 59.460 45.455 0.00 0.00 0.00 4.93
2718 2917 3.734231 GCTAAAGAACGCATGTATCGCTA 59.266 43.478 0.00 0.00 0.00 4.26
2719 2918 4.375105 GCTAAAGAACGCATGTATCGCTAC 60.375 45.833 0.00 0.00 0.00 3.58
2720 2919 2.135664 AGAACGCATGTATCGCTACC 57.864 50.000 0.00 0.00 0.00 3.18
2722 2921 2.882761 AGAACGCATGTATCGCTACCTA 59.117 45.455 0.00 0.00 0.00 3.08
2724 2923 4.698780 AGAACGCATGTATCGCTACCTATA 59.301 41.667 0.00 0.00 0.00 1.31
2789 5549 9.575783 GGTTTATCAGTTCTCTTCTTACTACTG 57.424 37.037 0.00 0.00 35.51 2.74
2795 5555 9.434420 TCAGTTCTCTTCTTACTACTGTACTAC 57.566 37.037 0.00 0.00 35.64 2.73
2796 5556 9.439500 CAGTTCTCTTCTTACTACTGTACTACT 57.561 37.037 0.00 0.00 0.00 2.57
2800 5560 9.598517 TCTCTTCTTACTACTGTACTACTTAGC 57.401 37.037 0.00 0.00 0.00 3.09
2801 5561 8.417780 TCTTCTTACTACTGTACTACTTAGCG 57.582 38.462 0.00 0.00 0.00 4.26
2802 5562 6.595772 TCTTACTACTGTACTACTTAGCGC 57.404 41.667 0.00 0.00 0.00 5.92
2803 5563 6.108687 TCTTACTACTGTACTACTTAGCGCA 58.891 40.000 11.47 0.00 0.00 6.09
2804 5564 6.765036 TCTTACTACTGTACTACTTAGCGCAT 59.235 38.462 11.47 0.00 0.00 4.73
2805 5565 5.421212 ACTACTGTACTACTTAGCGCATC 57.579 43.478 11.47 0.00 0.00 3.91
2806 5566 4.880120 ACTACTGTACTACTTAGCGCATCA 59.120 41.667 11.47 0.00 0.00 3.07
2807 5567 4.030134 ACTGTACTACTTAGCGCATCAC 57.970 45.455 11.47 0.00 0.00 3.06
2808 5568 3.442625 ACTGTACTACTTAGCGCATCACA 59.557 43.478 11.47 0.82 0.00 3.58
2809 5569 4.082408 ACTGTACTACTTAGCGCATCACAA 60.082 41.667 11.47 0.00 0.00 3.33
2810 5570 4.171005 TGTACTACTTAGCGCATCACAAC 58.829 43.478 11.47 0.00 0.00 3.32
2811 5571 2.618053 ACTACTTAGCGCATCACAACC 58.382 47.619 11.47 0.00 0.00 3.77
2812 5572 2.233922 ACTACTTAGCGCATCACAACCT 59.766 45.455 11.47 0.00 0.00 3.50
2813 5573 3.446161 ACTACTTAGCGCATCACAACCTA 59.554 43.478 11.47 0.00 0.00 3.08
2814 5574 3.543680 ACTTAGCGCATCACAACCTAT 57.456 42.857 11.47 0.00 0.00 2.57
2815 5575 4.665833 ACTTAGCGCATCACAACCTATA 57.334 40.909 11.47 0.00 0.00 1.31
2816 5576 5.215252 ACTTAGCGCATCACAACCTATAT 57.785 39.130 11.47 0.00 0.00 0.86
2817 5577 4.991056 ACTTAGCGCATCACAACCTATATG 59.009 41.667 11.47 0.00 0.00 1.78
2818 5578 3.751479 AGCGCATCACAACCTATATGA 57.249 42.857 11.47 0.00 0.00 2.15
2819 5579 4.071961 AGCGCATCACAACCTATATGAA 57.928 40.909 11.47 0.00 0.00 2.57
2820 5580 3.809832 AGCGCATCACAACCTATATGAAC 59.190 43.478 11.47 0.00 0.00 3.18
2821 5581 3.559655 GCGCATCACAACCTATATGAACA 59.440 43.478 0.30 0.00 0.00 3.18
2822 5582 4.035091 GCGCATCACAACCTATATGAACAA 59.965 41.667 0.30 0.00 0.00 2.83
2823 5583 5.741425 CGCATCACAACCTATATGAACAAG 58.259 41.667 0.00 0.00 0.00 3.16
2824 5584 5.294306 CGCATCACAACCTATATGAACAAGT 59.706 40.000 0.00 0.00 0.00 3.16
2825 5585 6.510157 CGCATCACAACCTATATGAACAAGTC 60.510 42.308 0.00 0.00 0.00 3.01
2826 5586 6.238484 GCATCACAACCTATATGAACAAGTCC 60.238 42.308 0.00 0.00 0.00 3.85
2827 5587 5.741011 TCACAACCTATATGAACAAGTCCC 58.259 41.667 0.00 0.00 0.00 4.46
2828 5588 5.487488 TCACAACCTATATGAACAAGTCCCT 59.513 40.000 0.00 0.00 0.00 4.20
2829 5589 5.817816 CACAACCTATATGAACAAGTCCCTC 59.182 44.000 0.00 0.00 0.00 4.30
2830 5590 5.487488 ACAACCTATATGAACAAGTCCCTCA 59.513 40.000 0.00 0.00 0.00 3.86
2831 5591 6.158695 ACAACCTATATGAACAAGTCCCTCAT 59.841 38.462 0.00 0.00 34.29 2.90
2832 5592 6.179906 ACCTATATGAACAAGTCCCTCATG 57.820 41.667 0.00 0.00 32.22 3.07
2833 5593 4.999950 CCTATATGAACAAGTCCCTCATGC 59.000 45.833 0.00 0.00 32.22 4.06
2834 5594 2.134789 ATGAACAAGTCCCTCATGCC 57.865 50.000 0.00 0.00 0.00 4.40
2835 5595 0.038166 TGAACAAGTCCCTCATGCCC 59.962 55.000 0.00 0.00 0.00 5.36
2836 5596 0.681243 GAACAAGTCCCTCATGCCCC 60.681 60.000 0.00 0.00 0.00 5.80
2837 5597 2.124570 CAAGTCCCTCATGCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
2838 5598 2.285368 AAGTCCCTCATGCCCCGA 60.285 61.111 0.00 0.00 0.00 5.14
2839 5599 1.923395 AAGTCCCTCATGCCCCGAA 60.923 57.895 0.00 0.00 0.00 4.30
2840 5600 1.281925 AAGTCCCTCATGCCCCGAAT 61.282 55.000 0.00 0.00 0.00 3.34
2841 5601 1.227973 GTCCCTCATGCCCCGAATC 60.228 63.158 0.00 0.00 0.00 2.52
2842 5602 1.384502 TCCCTCATGCCCCGAATCT 60.385 57.895 0.00 0.00 0.00 2.40
2843 5603 1.072159 CCCTCATGCCCCGAATCTC 59.928 63.158 0.00 0.00 0.00 2.75
2844 5604 1.301244 CCTCATGCCCCGAATCTCG 60.301 63.158 0.00 0.00 40.07 4.04
2845 5605 1.742146 CTCATGCCCCGAATCTCGA 59.258 57.895 0.00 0.00 43.74 4.04
2846 5606 0.104855 CTCATGCCCCGAATCTCGAA 59.895 55.000 0.00 0.00 43.74 3.71
2847 5607 0.539518 TCATGCCCCGAATCTCGAAA 59.460 50.000 0.00 0.00 43.74 3.46
2848 5608 0.940126 CATGCCCCGAATCTCGAAAG 59.060 55.000 0.00 0.00 43.74 2.62
2849 5609 0.830648 ATGCCCCGAATCTCGAAAGA 59.169 50.000 0.00 0.00 43.74 2.52
2850 5610 0.611200 TGCCCCGAATCTCGAAAGAA 59.389 50.000 0.00 0.00 43.74 2.52
2851 5611 1.007580 GCCCCGAATCTCGAAAGAAC 58.992 55.000 0.00 0.00 43.74 3.01
2852 5612 1.278238 CCCCGAATCTCGAAAGAACG 58.722 55.000 0.00 0.00 43.74 3.95
2853 5613 1.135199 CCCCGAATCTCGAAAGAACGA 60.135 52.381 0.00 0.00 43.74 3.85
2854 5614 2.481449 CCCCGAATCTCGAAAGAACGAT 60.481 50.000 0.00 0.00 43.74 3.73
2855 5615 3.243301 CCCCGAATCTCGAAAGAACGATA 60.243 47.826 0.00 0.00 43.74 2.92
2856 5616 4.357142 CCCGAATCTCGAAAGAACGATAA 58.643 43.478 0.00 0.00 43.74 1.75
2857 5617 4.982916 CCCGAATCTCGAAAGAACGATAAT 59.017 41.667 0.00 0.00 43.74 1.28
2858 5618 6.147581 CCCGAATCTCGAAAGAACGATAATA 58.852 40.000 0.00 0.00 43.74 0.98
2859 5619 6.807230 CCCGAATCTCGAAAGAACGATAATAT 59.193 38.462 0.00 0.00 43.74 1.28
2860 5620 7.328737 CCCGAATCTCGAAAGAACGATAATATT 59.671 37.037 0.00 0.00 43.74 1.28
2861 5621 8.700644 CCGAATCTCGAAAGAACGATAATATTT 58.299 33.333 0.00 0.00 43.74 1.40
2888 5648 4.210832 CTCGAATATGCACGAGTCTACA 57.789 45.455 14.41 0.00 46.90 2.74
2889 5649 4.788690 CTCGAATATGCACGAGTCTACAT 58.211 43.478 14.41 0.00 46.90 2.29
2890 5650 5.928153 CTCGAATATGCACGAGTCTACATA 58.072 41.667 14.41 0.00 46.90 2.29
2891 5651 6.496338 TCGAATATGCACGAGTCTACATAT 57.504 37.500 0.00 4.47 37.32 1.78
2892 5652 6.543736 TCGAATATGCACGAGTCTACATATC 58.456 40.000 0.00 4.50 35.26 1.63
2893 5653 6.148811 TCGAATATGCACGAGTCTACATATCA 59.851 38.462 0.00 0.00 35.26 2.15
2894 5654 6.969473 CGAATATGCACGAGTCTACATATCAT 59.031 38.462 0.00 0.00 35.26 2.45
2895 5655 8.122952 CGAATATGCACGAGTCTACATATCATA 58.877 37.037 0.00 0.00 35.26 2.15
2896 5656 9.958234 GAATATGCACGAGTCTACATATCATAT 57.042 33.333 0.00 0.00 35.26 1.78
2927 5687 2.037941 GCAAAGAAAGCCTTCACGAC 57.962 50.000 0.00 0.00 33.02 4.34
2928 5688 1.333619 GCAAAGAAAGCCTTCACGACA 59.666 47.619 0.00 0.00 33.02 4.35
2929 5689 2.223479 GCAAAGAAAGCCTTCACGACAA 60.223 45.455 0.00 0.00 33.02 3.18
2930 5690 3.621794 CAAAGAAAGCCTTCACGACAAG 58.378 45.455 0.00 0.00 33.02 3.16
2931 5691 2.622064 AGAAAGCCTTCACGACAAGT 57.378 45.000 0.00 0.00 33.64 3.16
2932 5692 2.919228 AGAAAGCCTTCACGACAAGTT 58.081 42.857 0.00 0.00 33.64 2.66
2933 5693 4.067972 AGAAAGCCTTCACGACAAGTTA 57.932 40.909 0.00 0.00 33.64 2.24
2934 5694 3.808174 AGAAAGCCTTCACGACAAGTTAC 59.192 43.478 0.00 0.00 33.64 2.50
2935 5695 2.902705 AGCCTTCACGACAAGTTACA 57.097 45.000 0.00 0.00 0.00 2.41
2936 5696 3.402628 AGCCTTCACGACAAGTTACAT 57.597 42.857 0.00 0.00 0.00 2.29
2937 5697 3.067106 AGCCTTCACGACAAGTTACATG 58.933 45.455 0.00 0.00 0.00 3.21
2938 5698 2.806244 GCCTTCACGACAAGTTACATGT 59.194 45.455 2.69 2.69 0.00 3.21
2939 5699 3.991773 GCCTTCACGACAAGTTACATGTA 59.008 43.478 0.08 0.08 0.00 2.29
2940 5700 4.143179 GCCTTCACGACAAGTTACATGTAC 60.143 45.833 4.68 1.30 0.00 2.90
2941 5701 4.986034 CCTTCACGACAAGTTACATGTACA 59.014 41.667 4.68 0.00 0.00 2.90
2942 5702 5.637810 CCTTCACGACAAGTTACATGTACAT 59.362 40.000 4.68 1.41 0.00 2.29
2943 5703 6.809689 CCTTCACGACAAGTTACATGTACATA 59.190 38.462 8.32 0.00 0.00 2.29
2944 5704 7.491372 CCTTCACGACAAGTTACATGTACATAT 59.509 37.037 8.32 0.00 0.00 1.78
2945 5705 7.980742 TCACGACAAGTTACATGTACATATC 57.019 36.000 8.32 0.00 0.00 1.63
2946 5706 6.976349 TCACGACAAGTTACATGTACATATCC 59.024 38.462 8.32 0.00 0.00 2.59
2947 5707 5.975344 ACGACAAGTTACATGTACATATCCG 59.025 40.000 8.32 8.41 0.00 4.18
2948 5708 5.975344 CGACAAGTTACATGTACATATCCGT 59.025 40.000 8.32 4.93 0.00 4.69
2949 5709 6.075046 CGACAAGTTACATGTACATATCCGTG 60.075 42.308 8.32 7.93 0.00 4.94
2950 5710 5.522460 ACAAGTTACATGTACATATCCGTGC 59.478 40.000 8.32 1.07 0.00 5.34
2951 5711 4.295870 AGTTACATGTACATATCCGTGCG 58.704 43.478 8.32 0.00 0.00 5.34
2952 5712 2.148916 ACATGTACATATCCGTGCGG 57.851 50.000 8.32 3.94 0.00 5.69
2953 5713 0.790207 CATGTACATATCCGTGCGGC 59.210 55.000 8.32 0.00 34.68 6.53
2954 5714 0.679505 ATGTACATATCCGTGCGGCT 59.320 50.000 6.56 0.00 34.68 5.52
2955 5715 0.462375 TGTACATATCCGTGCGGCTT 59.538 50.000 5.64 0.00 34.68 4.35
2956 5716 1.134640 TGTACATATCCGTGCGGCTTT 60.135 47.619 5.64 0.00 34.68 3.51
2957 5717 1.937899 GTACATATCCGTGCGGCTTTT 59.062 47.619 5.64 0.00 34.68 2.27
2958 5718 2.319136 ACATATCCGTGCGGCTTTTA 57.681 45.000 5.64 0.00 34.68 1.52
2959 5719 2.210116 ACATATCCGTGCGGCTTTTAG 58.790 47.619 5.64 0.00 34.68 1.85
2960 5720 1.069906 CATATCCGTGCGGCTTTTAGC 60.070 52.381 5.64 0.00 41.46 3.09
2961 5721 0.177141 TATCCGTGCGGCTTTTAGCT 59.823 50.000 5.64 0.00 41.99 3.32
2962 5722 1.090052 ATCCGTGCGGCTTTTAGCTC 61.090 55.000 5.64 0.00 41.99 4.09
2963 5723 2.395690 CGTGCGGCTTTTAGCTCG 59.604 61.111 0.00 2.49 41.99 5.03
2967 5727 2.785258 CGGCTTTTAGCTCGCACC 59.215 61.111 0.00 0.00 41.99 5.01
2968 5728 2.750888 CGGCTTTTAGCTCGCACCC 61.751 63.158 0.00 0.00 41.99 4.61
2969 5729 1.674322 GGCTTTTAGCTCGCACCCA 60.674 57.895 0.00 0.00 41.99 4.51
2970 5730 1.502190 GCTTTTAGCTCGCACCCAC 59.498 57.895 0.00 0.00 38.45 4.61
2971 5731 1.787847 CTTTTAGCTCGCACCCACG 59.212 57.895 0.00 0.00 0.00 4.94
2972 5732 2.240612 CTTTTAGCTCGCACCCACGC 62.241 60.000 0.00 0.00 0.00 5.34
2973 5733 4.752879 TTAGCTCGCACCCACGCC 62.753 66.667 0.00 0.00 0.00 5.68
2977 5737 4.988598 CTCGCACCCACGCCACTT 62.989 66.667 0.00 0.00 0.00 3.16
2978 5738 3.583276 CTCGCACCCACGCCACTTA 62.583 63.158 0.00 0.00 0.00 2.24
2982 5742 1.852067 GCACCCACGCCACTTACAAG 61.852 60.000 0.00 0.00 0.00 3.16
2987 5747 0.944386 CACGCCACTTACAAGCAAGT 59.056 50.000 0.00 0.00 39.34 3.16
2992 5752 2.552373 GCCACTTACAAGCAAGTACCCT 60.552 50.000 0.00 0.00 36.61 4.34
2993 5753 3.307199 GCCACTTACAAGCAAGTACCCTA 60.307 47.826 0.00 0.00 36.61 3.53
2994 5754 4.251268 CCACTTACAAGCAAGTACCCTAC 58.749 47.826 0.00 0.00 36.61 3.18
2995 5755 4.020485 CCACTTACAAGCAAGTACCCTACT 60.020 45.833 0.00 0.00 41.73 2.57
3015 5775 3.844211 ACTCCAGGGAGCAACTACAATAA 59.156 43.478 15.18 0.00 45.54 1.40
3016 5776 4.288626 ACTCCAGGGAGCAACTACAATAAA 59.711 41.667 15.18 0.00 45.54 1.40
3074 5834 1.053424 GGGCCATTGGATCGTAGGTA 58.947 55.000 6.95 0.00 0.00 3.08
3104 5864 3.647113 CAGATTCAGGTGGATGGATCTCT 59.353 47.826 0.00 0.00 42.58 3.10
3141 5902 8.998377 GTACATTTTACGAAAAACCCCTACTAA 58.002 33.333 0.00 0.00 37.41 2.24
3145 5906 7.495135 TTTACGAAAAACCCCTACTAACAAG 57.505 36.000 0.00 0.00 0.00 3.16
3206 5967 3.827008 TTTCATCTCCCTCTCCATTCG 57.173 47.619 0.00 0.00 0.00 3.34
3320 6168 7.307493 TGTCAGTGCAAAGTATGTCAATATC 57.693 36.000 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
867 869 4.246458 GTTTCCGTAGCATCTCAAACTCT 58.754 43.478 0.00 0.00 0.00 3.24
955 957 6.055588 AGATCTGGTCGTTCTTCTTGAAAAA 58.944 36.000 0.00 0.00 36.30 1.94
961 963 3.082548 TCGAGATCTGGTCGTTCTTCTT 58.917 45.455 0.00 0.00 38.60 2.52
964 966 2.032302 CGATCGAGATCTGGTCGTTCTT 59.968 50.000 10.26 0.00 38.60 2.52
969 971 1.503294 TCTCGATCGAGATCTGGTCG 58.497 55.000 37.31 15.22 45.26 4.79
978 980 0.028242 CGACTTGGGTCTCGATCGAG 59.972 60.000 34.20 34.20 43.21 4.04
981 983 1.227002 GGCGACTTGGGTCTCGATC 60.227 63.158 0.00 0.00 40.10 3.69
982 984 1.330655 ATGGCGACTTGGGTCTCGAT 61.331 55.000 0.00 0.00 40.10 3.59
983 985 1.982395 ATGGCGACTTGGGTCTCGA 60.982 57.895 0.00 0.00 40.10 4.04
985 987 2.109126 GCATGGCGACTTGGGTCTC 61.109 63.158 6.25 0.00 40.10 3.36
986 988 2.045926 GCATGGCGACTTGGGTCT 60.046 61.111 6.25 0.00 40.10 3.85
987 989 3.134127 GGCATGGCGACTTGGGTC 61.134 66.667 2.41 0.00 38.97 4.46
989 991 3.136123 CAGGCATGGCGACTTGGG 61.136 66.667 14.30 0.00 36.09 4.12
1011 1016 1.931612 GTATGACGCCGACGACGAC 60.932 63.158 11.37 4.59 43.93 4.34
1012 1017 2.400798 GTATGACGCCGACGACGA 59.599 61.111 11.37 0.00 43.93 4.20
1013 1018 3.009599 CGTATGACGCCGACGACG 61.010 66.667 0.85 0.85 43.93 5.12
1014 1019 1.650536 CTCGTATGACGCCGACGAC 60.651 63.158 0.00 0.00 42.21 4.34
1021 1026 0.459585 TTGGCCTTCTCGTATGACGC 60.460 55.000 3.32 0.00 42.21 5.19
1026 1031 2.168728 GACCTCTTTGGCCTTCTCGTAT 59.831 50.000 3.32 0.00 40.22 3.06
1038 1043 1.108776 CCATGGCCATGACCTCTTTG 58.891 55.000 41.32 21.30 41.20 2.77
1188 1193 1.864862 GTCGGTCTTCTCGACGACA 59.135 57.895 16.26 0.00 45.53 4.35
1319 1325 3.691342 CCTCGTCGTCCAGGCCAA 61.691 66.667 5.01 0.00 0.00 4.52
1320 1326 4.671590 TCCTCGTCGTCCAGGCCA 62.672 66.667 5.01 0.00 0.00 5.36
1321 1327 4.131088 GTCCTCGTCGTCCAGGCC 62.131 72.222 0.00 0.00 0.00 5.19
1322 1328 4.477975 CGTCCTCGTCGTCCAGGC 62.478 72.222 0.00 0.00 0.00 4.85
1323 1329 2.745100 TCGTCCTCGTCGTCCAGG 60.745 66.667 0.00 0.00 38.33 4.45
1324 1330 2.479650 GTCGTCCTCGTCGTCCAG 59.520 66.667 0.00 0.00 38.33 3.86
1356 1365 1.457831 GCCCTCCTCCATACCGAGT 60.458 63.158 0.00 0.00 0.00 4.18
1362 1371 1.153989 CTCCTCGCCCTCCTCCATA 59.846 63.158 0.00 0.00 0.00 2.74
1987 2002 0.541063 TCGTCCTTGGTGGTGCTAGA 60.541 55.000 0.00 0.00 37.07 2.43
1991 2006 1.525077 TTGTCGTCCTTGGTGGTGC 60.525 57.895 0.00 0.00 37.07 5.01
1994 2009 0.661020 GTTGTTGTCGTCCTTGGTGG 59.339 55.000 0.00 0.00 37.10 4.61
2007 2022 3.130340 ACAAGGTTACCTGCTTGTTGTTG 59.870 43.478 3.99 0.00 36.76 3.33
2211 2366 1.409064 GCATGGTAGTCGATGGAGTGA 59.591 52.381 0.00 0.00 31.86 3.41
2254 2409 1.630369 CACTTCCACCTCCTCCATCAA 59.370 52.381 0.00 0.00 0.00 2.57
2316 2474 1.690633 ATGGAGGGCGACATCTGGT 60.691 57.895 1.57 0.00 41.91 4.00
2319 2477 2.037620 GAGCATGGAGGGCGACATCT 62.038 60.000 1.57 0.00 41.91 2.90
2389 2547 0.629596 TCCTCCTGATCCGTACTGGT 59.370 55.000 4.11 0.00 39.52 4.00
2396 2554 1.069823 CACAATCCTCCTCCTGATCCG 59.930 57.143 0.00 0.00 0.00 4.18
2399 2557 2.632028 CGATCACAATCCTCCTCCTGAT 59.368 50.000 0.00 0.00 0.00 2.90
2400 2558 2.034878 CGATCACAATCCTCCTCCTGA 58.965 52.381 0.00 0.00 0.00 3.86
2401 2559 1.759445 ACGATCACAATCCTCCTCCTG 59.241 52.381 0.00 0.00 0.00 3.86
2410 2568 3.126831 CCTCCTTAGCACGATCACAATC 58.873 50.000 0.00 0.00 0.00 2.67
2413 2571 1.476891 GTCCTCCTTAGCACGATCACA 59.523 52.381 0.00 0.00 0.00 3.58
2419 2577 1.030488 TCCTCGTCCTCCTTAGCACG 61.030 60.000 0.00 0.00 0.00 5.34
2420 2578 0.741915 CTCCTCGTCCTCCTTAGCAC 59.258 60.000 0.00 0.00 0.00 4.40
2433 2591 1.671261 GCATCATCGGAATCCTCCTCG 60.671 57.143 0.00 0.00 39.93 4.63
2444 2602 4.633126 CACTATTATCCTTGGCATCATCGG 59.367 45.833 0.00 0.00 0.00 4.18
2454 2612 5.482006 TCATCATCGCCACTATTATCCTTG 58.518 41.667 0.00 0.00 0.00 3.61
2466 2624 2.135139 GCTTCGTTATCATCATCGCCA 58.865 47.619 0.00 0.00 0.00 5.69
2468 2626 3.052745 TCAGCTTCGTTATCATCATCGC 58.947 45.455 0.00 0.00 0.00 4.58
2486 2662 8.775527 TCGATCATTACTACTACTAGCTTTCAG 58.224 37.037 0.00 0.00 0.00 3.02
2497 2674 7.989170 TGTTAGACCACTCGATCATTACTACTA 59.011 37.037 0.00 0.00 0.00 1.82
2504 2681 5.977635 TCATTGTTAGACCACTCGATCATT 58.022 37.500 0.00 0.00 0.00 2.57
2505 2682 5.598416 TCATTGTTAGACCACTCGATCAT 57.402 39.130 0.00 0.00 0.00 2.45
2532 2709 2.159476 TCGTAGGCACACGTACAGATTC 60.159 50.000 10.76 0.00 42.51 2.52
2537 2714 0.800631 CTCTCGTAGGCACACGTACA 59.199 55.000 10.76 0.00 42.51 2.90
2538 2715 0.801251 ACTCTCGTAGGCACACGTAC 59.199 55.000 10.76 0.00 42.51 3.67
2540 2717 1.527034 TTACTCTCGTAGGCACACGT 58.473 50.000 10.76 0.00 42.51 4.49
2541 2718 2.846039 ATTACTCTCGTAGGCACACG 57.154 50.000 5.42 5.42 43.28 4.49
2558 2737 1.804151 TGCTCGCGCAGTAGAAAAATT 59.196 42.857 8.75 0.00 42.25 1.82
2575 2754 4.882427 GGATCATGCATGCTATAAGATGCT 59.118 41.667 22.25 4.35 44.46 3.79
2578 2757 6.063496 AGTGGATCATGCATGCTATAAGAT 57.937 37.500 22.25 13.80 0.00 2.40
2580 2759 5.489249 AGAGTGGATCATGCATGCTATAAG 58.511 41.667 22.25 4.26 0.00 1.73
2609 2793 2.777832 AGCCTGAATCTCAAGGTGAC 57.222 50.000 0.00 0.00 0.00 3.67
2610 2794 3.181440 ACAAAGCCTGAATCTCAAGGTGA 60.181 43.478 0.00 0.00 0.00 4.02
2611 2795 3.152341 ACAAAGCCTGAATCTCAAGGTG 58.848 45.455 0.00 0.00 0.00 4.00
2612 2796 3.515602 ACAAAGCCTGAATCTCAAGGT 57.484 42.857 0.00 0.00 0.00 3.50
2614 2798 6.081872 AGAAAACAAAGCCTGAATCTCAAG 57.918 37.500 0.00 0.00 0.00 3.02
2615 2799 6.772716 AGTAGAAAACAAAGCCTGAATCTCAA 59.227 34.615 0.00 0.00 0.00 3.02
2616 2800 6.299141 AGTAGAAAACAAAGCCTGAATCTCA 58.701 36.000 0.00 0.00 0.00 3.27
2617 2801 6.809630 AGTAGAAAACAAAGCCTGAATCTC 57.190 37.500 0.00 0.00 0.00 2.75
2619 2803 7.604545 AGACTAGTAGAAAACAAAGCCTGAATC 59.395 37.037 3.59 0.00 0.00 2.52
2621 2805 6.827727 AGACTAGTAGAAAACAAAGCCTGAA 58.172 36.000 3.59 0.00 0.00 3.02
2622 2806 6.420913 AGACTAGTAGAAAACAAAGCCTGA 57.579 37.500 3.59 0.00 0.00 3.86
2623 2807 6.566753 GCAAGACTAGTAGAAAACAAAGCCTG 60.567 42.308 3.59 0.00 0.00 4.85
2625 2809 5.334957 GGCAAGACTAGTAGAAAACAAAGCC 60.335 44.000 3.59 2.86 0.00 4.35
2626 2810 5.238650 TGGCAAGACTAGTAGAAAACAAAGC 59.761 40.000 3.59 0.00 0.00 3.51
2627 2811 6.861065 TGGCAAGACTAGTAGAAAACAAAG 57.139 37.500 3.59 0.00 0.00 2.77
2628 2812 7.338449 ACTTTGGCAAGACTAGTAGAAAACAAA 59.662 33.333 3.59 3.47 33.72 2.83
2629 2813 6.826741 ACTTTGGCAAGACTAGTAGAAAACAA 59.173 34.615 3.59 0.00 33.72 2.83
2630 2814 6.354130 ACTTTGGCAAGACTAGTAGAAAACA 58.646 36.000 3.59 0.00 33.72 2.83
2645 2829 9.660180 ACTCTAAAATAAAACAAACTTTGGCAA 57.340 25.926 6.47 0.00 34.12 4.52
2662 2846 8.652810 AACTGTAACAACACGTACTCTAAAAT 57.347 30.769 0.00 0.00 0.00 1.82
2671 2855 4.503734 CCGAAAGAACTGTAACAACACGTA 59.496 41.667 0.00 0.00 0.00 3.57
2672 2856 3.307782 CCGAAAGAACTGTAACAACACGT 59.692 43.478 0.00 0.00 0.00 4.49
2673 2857 3.307782 ACCGAAAGAACTGTAACAACACG 59.692 43.478 0.00 0.00 0.00 4.49
2674 2858 4.584394 CACCGAAAGAACTGTAACAACAC 58.416 43.478 0.00 0.00 0.00 3.32
2686 2870 2.222445 GCGTTCTTTAGCACCGAAAGAA 59.778 45.455 6.49 6.49 45.91 2.52
2687 2871 1.796459 GCGTTCTTTAGCACCGAAAGA 59.204 47.619 0.00 0.00 40.35 2.52
2688 2872 1.529438 TGCGTTCTTTAGCACCGAAAG 59.471 47.619 0.00 0.00 38.59 2.62
2689 2873 1.584175 TGCGTTCTTTAGCACCGAAA 58.416 45.000 0.00 0.00 38.59 3.46
2692 2876 0.796312 ACATGCGTTCTTTAGCACCG 59.204 50.000 0.00 0.00 46.83 4.94
2693 2877 3.302480 CGATACATGCGTTCTTTAGCACC 60.302 47.826 0.00 0.00 46.83 5.01
2696 2880 2.540101 AGCGATACATGCGTTCTTTAGC 59.460 45.455 0.00 0.00 37.44 3.09
2698 2882 4.046462 GGTAGCGATACATGCGTTCTTTA 58.954 43.478 13.56 0.00 37.44 1.85
2748 5508 9.762381 AACTGATAAACCTGGATAAAATAACCA 57.238 29.630 0.00 0.00 0.00 3.67
2789 5549 3.550678 GGTTGTGATGCGCTAAGTAGTAC 59.449 47.826 9.73 0.00 0.00 2.73
2790 5550 3.446161 AGGTTGTGATGCGCTAAGTAGTA 59.554 43.478 9.73 0.00 0.00 1.82
2791 5551 2.233922 AGGTTGTGATGCGCTAAGTAGT 59.766 45.455 9.73 0.00 0.00 2.73
2792 5552 2.893637 AGGTTGTGATGCGCTAAGTAG 58.106 47.619 9.73 0.00 0.00 2.57
2793 5553 4.665833 ATAGGTTGTGATGCGCTAAGTA 57.334 40.909 9.73 0.00 0.00 2.24
2794 5554 3.543680 ATAGGTTGTGATGCGCTAAGT 57.456 42.857 9.73 0.00 0.00 2.24
2795 5555 5.230182 TCATATAGGTTGTGATGCGCTAAG 58.770 41.667 9.73 0.00 0.00 2.18
2796 5556 5.208463 TCATATAGGTTGTGATGCGCTAA 57.792 39.130 9.73 0.00 0.00 3.09
2797 5557 4.864704 TCATATAGGTTGTGATGCGCTA 57.135 40.909 9.73 0.00 0.00 4.26
2798 5558 3.751479 TCATATAGGTTGTGATGCGCT 57.249 42.857 9.73 0.00 0.00 5.92
2799 5559 3.559655 TGTTCATATAGGTTGTGATGCGC 59.440 43.478 0.00 0.00 0.00 6.09
2800 5560 5.294306 ACTTGTTCATATAGGTTGTGATGCG 59.706 40.000 0.00 0.00 0.00 4.73
2801 5561 6.238484 GGACTTGTTCATATAGGTTGTGATGC 60.238 42.308 0.00 0.00 0.00 3.91
2802 5562 6.260936 GGGACTTGTTCATATAGGTTGTGATG 59.739 42.308 0.00 0.00 0.00 3.07
2803 5563 6.158695 AGGGACTTGTTCATATAGGTTGTGAT 59.841 38.462 0.00 0.00 27.25 3.06
2804 5564 5.487488 AGGGACTTGTTCATATAGGTTGTGA 59.513 40.000 0.00 0.00 27.25 3.58
2805 5565 5.745227 AGGGACTTGTTCATATAGGTTGTG 58.255 41.667 0.00 0.00 27.25 3.33
2806 5566 5.487488 TGAGGGACTTGTTCATATAGGTTGT 59.513 40.000 0.00 0.00 41.55 3.32
2807 5567 5.989477 TGAGGGACTTGTTCATATAGGTTG 58.011 41.667 0.00 0.00 41.55 3.77
2808 5568 6.595682 CATGAGGGACTTGTTCATATAGGTT 58.404 40.000 0.00 0.00 41.55 3.50
2809 5569 5.455326 GCATGAGGGACTTGTTCATATAGGT 60.455 44.000 0.00 0.00 41.55 3.08
2810 5570 4.999950 GCATGAGGGACTTGTTCATATAGG 59.000 45.833 0.00 0.00 41.55 2.57
2811 5571 4.999950 GGCATGAGGGACTTGTTCATATAG 59.000 45.833 0.00 0.00 41.55 1.31
2812 5572 4.202461 GGGCATGAGGGACTTGTTCATATA 60.202 45.833 0.00 0.00 41.55 0.86
2813 5573 3.435601 GGGCATGAGGGACTTGTTCATAT 60.436 47.826 0.00 0.00 41.55 1.78
2814 5574 2.092429 GGGCATGAGGGACTTGTTCATA 60.092 50.000 0.00 0.00 41.55 2.15
2815 5575 1.341383 GGGCATGAGGGACTTGTTCAT 60.341 52.381 0.00 0.00 41.55 2.57
2816 5576 0.038166 GGGCATGAGGGACTTGTTCA 59.962 55.000 0.00 0.00 41.55 3.18
2817 5577 0.681243 GGGGCATGAGGGACTTGTTC 60.681 60.000 0.00 0.00 41.55 3.18
2818 5578 1.384191 GGGGCATGAGGGACTTGTT 59.616 57.895 0.00 0.00 41.55 2.83
2819 5579 2.971598 CGGGGCATGAGGGACTTGT 61.972 63.158 0.00 0.00 41.55 3.16
2820 5580 2.124570 CGGGGCATGAGGGACTTG 60.125 66.667 0.00 0.00 41.55 3.16
2821 5581 1.281925 ATTCGGGGCATGAGGGACTT 61.282 55.000 0.00 0.00 41.55 3.01
2823 5583 1.227973 GATTCGGGGCATGAGGGAC 60.228 63.158 0.00 0.00 0.00 4.46
2824 5584 1.384502 AGATTCGGGGCATGAGGGA 60.385 57.895 0.00 0.00 0.00 4.20
2825 5585 1.072159 GAGATTCGGGGCATGAGGG 59.928 63.158 0.00 0.00 0.00 4.30
2826 5586 1.301244 CGAGATTCGGGGCATGAGG 60.301 63.158 0.00 0.00 36.00 3.86
2827 5587 0.104855 TTCGAGATTCGGGGCATGAG 59.895 55.000 0.00 0.00 40.88 2.90
2828 5588 0.539518 TTTCGAGATTCGGGGCATGA 59.460 50.000 0.00 0.00 40.88 3.07
2829 5589 0.940126 CTTTCGAGATTCGGGGCATG 59.060 55.000 0.00 0.00 40.88 4.06
2830 5590 0.830648 TCTTTCGAGATTCGGGGCAT 59.169 50.000 0.00 0.00 40.88 4.40
2831 5591 0.611200 TTCTTTCGAGATTCGGGGCA 59.389 50.000 0.00 0.00 40.88 5.36
2832 5592 1.007580 GTTCTTTCGAGATTCGGGGC 58.992 55.000 0.00 0.00 40.88 5.80
2833 5593 1.135199 TCGTTCTTTCGAGATTCGGGG 60.135 52.381 0.00 0.00 40.88 5.73
2834 5594 2.273370 TCGTTCTTTCGAGATTCGGG 57.727 50.000 0.00 0.00 40.88 5.14
2835 5595 7.798486 ATATTATCGTTCTTTCGAGATTCGG 57.202 36.000 0.00 0.00 43.00 4.30
2868 5628 4.830826 ATGTAGACTCGTGCATATTCGA 57.169 40.909 0.00 0.00 34.88 3.71
2869 5629 6.314784 TGATATGTAGACTCGTGCATATTCG 58.685 40.000 0.00 0.00 35.45 3.34
2870 5630 9.958234 ATATGATATGTAGACTCGTGCATATTC 57.042 33.333 0.00 0.00 35.45 1.75
2908 5668 1.333619 TGTCGTGAAGGCTTTCTTTGC 59.666 47.619 10.19 0.00 35.50 3.68
2909 5669 3.065371 ACTTGTCGTGAAGGCTTTCTTTG 59.935 43.478 10.19 0.03 35.50 2.77
2910 5670 3.279434 ACTTGTCGTGAAGGCTTTCTTT 58.721 40.909 10.19 0.00 35.50 2.52
2911 5671 2.919228 ACTTGTCGTGAAGGCTTTCTT 58.081 42.857 10.19 0.00 38.65 2.52
2912 5672 2.622064 ACTTGTCGTGAAGGCTTTCT 57.378 45.000 10.19 0.00 34.31 2.52
2913 5673 3.558418 TGTAACTTGTCGTGAAGGCTTTC 59.442 43.478 0.00 0.77 0.00 2.62
2914 5674 3.537580 TGTAACTTGTCGTGAAGGCTTT 58.462 40.909 0.00 0.00 0.00 3.51
2915 5675 3.188159 TGTAACTTGTCGTGAAGGCTT 57.812 42.857 0.00 0.00 0.00 4.35
2916 5676 2.902705 TGTAACTTGTCGTGAAGGCT 57.097 45.000 0.00 0.00 0.00 4.58
2917 5677 2.806244 ACATGTAACTTGTCGTGAAGGC 59.194 45.455 0.00 0.00 0.00 4.35
2918 5678 4.986034 TGTACATGTAACTTGTCGTGAAGG 59.014 41.667 7.25 0.00 0.00 3.46
2919 5679 6.706055 ATGTACATGTAACTTGTCGTGAAG 57.294 37.500 7.78 0.00 0.00 3.02
2920 5680 7.490079 GGATATGTACATGTAACTTGTCGTGAA 59.510 37.037 18.81 0.00 0.00 3.18
2921 5681 6.976349 GGATATGTACATGTAACTTGTCGTGA 59.024 38.462 18.81 0.00 0.00 4.35
2922 5682 6.075046 CGGATATGTACATGTAACTTGTCGTG 60.075 42.308 18.81 2.42 0.00 4.35
2923 5683 5.975344 CGGATATGTACATGTAACTTGTCGT 59.025 40.000 18.81 0.00 0.00 4.34
2924 5684 5.975344 ACGGATATGTACATGTAACTTGTCG 59.025 40.000 18.81 10.51 0.00 4.35
2925 5685 6.292168 GCACGGATATGTACATGTAACTTGTC 60.292 42.308 18.81 7.95 0.00 3.18
2926 5686 5.522460 GCACGGATATGTACATGTAACTTGT 59.478 40.000 18.81 5.06 0.00 3.16
2927 5687 5.332280 CGCACGGATATGTACATGTAACTTG 60.332 44.000 18.81 12.27 0.00 3.16
2928 5688 4.743151 CGCACGGATATGTACATGTAACTT 59.257 41.667 18.81 3.59 0.00 2.66
2929 5689 4.295870 CGCACGGATATGTACATGTAACT 58.704 43.478 18.81 0.33 0.00 2.24
2930 5690 3.427528 CCGCACGGATATGTACATGTAAC 59.572 47.826 18.81 7.54 37.50 2.50
2931 5691 3.644823 CCGCACGGATATGTACATGTAA 58.355 45.455 18.81 0.00 37.50 2.41
2932 5692 2.608506 GCCGCACGGATATGTACATGTA 60.609 50.000 18.81 0.08 37.50 2.29
2933 5693 1.872237 GCCGCACGGATATGTACATGT 60.872 52.381 18.81 12.06 37.50 3.21
2934 5694 0.790207 GCCGCACGGATATGTACATG 59.210 55.000 18.81 4.00 37.50 3.21
2935 5695 0.679505 AGCCGCACGGATATGTACAT 59.320 50.000 14.43 13.93 37.50 2.29
2936 5696 0.462375 AAGCCGCACGGATATGTACA 59.538 50.000 14.43 0.00 37.50 2.90
2937 5697 1.578583 AAAGCCGCACGGATATGTAC 58.421 50.000 14.43 0.00 37.50 2.90
2938 5698 2.319136 AAAAGCCGCACGGATATGTA 57.681 45.000 14.43 0.00 37.50 2.29
2939 5699 2.210116 CTAAAAGCCGCACGGATATGT 58.790 47.619 14.43 0.00 37.50 2.29
2940 5700 1.069906 GCTAAAAGCCGCACGGATATG 60.070 52.381 14.43 0.00 34.48 1.78
2941 5701 1.202651 AGCTAAAAGCCGCACGGATAT 60.203 47.619 14.43 1.83 43.77 1.63
2942 5702 0.177141 AGCTAAAAGCCGCACGGATA 59.823 50.000 14.43 0.00 43.77 2.59
2943 5703 1.078426 AGCTAAAAGCCGCACGGAT 60.078 52.632 14.43 2.72 43.77 4.18
2944 5704 1.740296 GAGCTAAAAGCCGCACGGA 60.740 57.895 14.43 0.00 43.77 4.69
2945 5705 2.785258 GAGCTAAAAGCCGCACGG 59.215 61.111 4.30 4.30 43.77 4.94
2946 5706 2.395690 CGAGCTAAAAGCCGCACG 59.604 61.111 0.00 0.00 43.77 5.34
2950 5710 2.750888 GGGTGCGAGCTAAAAGCCG 61.751 63.158 0.00 0.83 43.77 5.52
2951 5711 1.674322 TGGGTGCGAGCTAAAAGCC 60.674 57.895 0.00 0.00 43.77 4.35
2952 5712 1.502190 GTGGGTGCGAGCTAAAAGC 59.498 57.895 0.00 0.00 42.84 3.51
2953 5713 1.787847 CGTGGGTGCGAGCTAAAAG 59.212 57.895 0.00 0.00 0.00 2.27
2954 5714 2.322081 GCGTGGGTGCGAGCTAAAA 61.322 57.895 0.00 0.00 0.00 1.52
2955 5715 2.740826 GCGTGGGTGCGAGCTAAA 60.741 61.111 0.00 0.00 0.00 1.85
2956 5716 4.752879 GGCGTGGGTGCGAGCTAA 62.753 66.667 0.00 0.00 35.06 3.09
2960 5720 3.583276 TAAGTGGCGTGGGTGCGAG 62.583 63.158 0.00 0.00 35.06 5.03
2961 5721 3.617735 TAAGTGGCGTGGGTGCGA 61.618 61.111 0.00 0.00 35.06 5.10
2962 5722 3.419759 GTAAGTGGCGTGGGTGCG 61.420 66.667 0.00 0.00 35.06 5.34
2963 5723 1.852067 CTTGTAAGTGGCGTGGGTGC 61.852 60.000 0.00 0.00 0.00 5.01
2964 5724 1.852067 GCTTGTAAGTGGCGTGGGTG 61.852 60.000 0.00 0.00 0.00 4.61
2965 5725 1.599797 GCTTGTAAGTGGCGTGGGT 60.600 57.895 0.00 0.00 0.00 4.51
2966 5726 1.169661 TTGCTTGTAAGTGGCGTGGG 61.170 55.000 0.00 0.00 0.00 4.61
2967 5727 0.238289 CTTGCTTGTAAGTGGCGTGG 59.762 55.000 0.00 0.00 0.00 4.94
2968 5728 0.944386 ACTTGCTTGTAAGTGGCGTG 59.056 50.000 3.44 0.00 39.33 5.34
2969 5729 2.140717 GTACTTGCTTGTAAGTGGCGT 58.859 47.619 13.01 0.00 40.85 5.68
2970 5730 1.463444 GGTACTTGCTTGTAAGTGGCG 59.537 52.381 13.01 0.00 40.85 5.69
2971 5731 1.810755 GGGTACTTGCTTGTAAGTGGC 59.189 52.381 13.01 6.83 40.85 5.01
2972 5732 3.418684 AGGGTACTTGCTTGTAAGTGG 57.581 47.619 13.01 0.00 40.85 4.00
2973 5733 5.148651 AGTAGGGTACTTGCTTGTAAGTG 57.851 43.478 13.01 0.00 40.85 3.16
2974 5734 4.222366 GGAGTAGGGTACTTGCTTGTAAGT 59.778 45.833 8.92 8.92 43.03 2.24
2975 5735 4.222145 TGGAGTAGGGTACTTGCTTGTAAG 59.778 45.833 0.00 0.00 39.59 2.34
2976 5736 4.161876 TGGAGTAGGGTACTTGCTTGTAA 58.838 43.478 0.00 0.00 39.59 2.41
2977 5737 3.767673 CTGGAGTAGGGTACTTGCTTGTA 59.232 47.826 0.00 0.00 39.59 2.41
2978 5738 2.567615 CTGGAGTAGGGTACTTGCTTGT 59.432 50.000 0.00 0.00 39.59 3.16
2992 5752 2.615986 TGTAGTTGCTCCCTGGAGTA 57.384 50.000 14.45 7.48 43.70 2.59
2993 5753 1.729586 TTGTAGTTGCTCCCTGGAGT 58.270 50.000 14.45 0.00 43.70 3.85
2994 5754 4.487714 TTATTGTAGTTGCTCCCTGGAG 57.512 45.455 8.91 8.91 44.56 3.86
2995 5755 4.919774 TTTATTGTAGTTGCTCCCTGGA 57.080 40.909 0.00 0.00 0.00 3.86
3019 5779 1.394618 TTTTGCACACGTAGCCCTTT 58.605 45.000 9.36 0.00 0.00 3.11
3029 5789 6.761242 AGGTTCCTTTTTCTATTTTTGCACAC 59.239 34.615 0.00 0.00 0.00 3.82
3030 5790 6.760770 CAGGTTCCTTTTTCTATTTTTGCACA 59.239 34.615 0.00 0.00 0.00 4.57
3074 5834 1.064906 CCACCTGAATCTGTGCCATCT 60.065 52.381 0.00 0.00 0.00 2.90
3104 5864 9.692749 TTTTCGTAAAATGTACATTAAATGGCA 57.307 25.926 21.07 6.35 33.60 4.92
3109 5869 9.473640 GGGGTTTTTCGTAAAATGTACATTAAA 57.526 29.630 21.07 14.05 35.80 1.52
3145 5906 8.850452 GCTGCAAATGTTCTGTTTTATAACTAC 58.150 33.333 0.00 0.00 35.24 2.73
3170 5931 4.702131 AGATGAAATACTTGAGGTGGTTGC 59.298 41.667 0.00 0.00 0.00 4.17
3206 5967 3.057806 CCATAAGGGTCGTTGGACAAAAC 60.058 47.826 0.00 0.00 45.28 2.43


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

AutoCloner maintained by Alex Coulton.