Multiple sequence alignment - TraesCS5B01G476400

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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 TraesCS5B01G476400 chr5B 100.000 3566 0 0 1549 5114 648751845 648755410 0.000000e+00 6586.0
1 TraesCS5B01G476400 chr5B 100.000 1231 0 0 1 1231 648750297 648751527 0.000000e+00 2274.0
2 TraesCS5B01G476400 chr5B 98.261 460 8 0 330 789 394968238 394967779 0.000000e+00 806.0
3 TraesCS5B01G476400 chr5B 91.334 577 42 4 3474 4042 648361373 648361949 0.000000e+00 782.0
4 TraesCS5B01G476400 chr5B 82.609 460 48 16 4473 4905 648354726 648354272 1.340000e-100 377.0
5 TraesCS5B01G476400 chr5B 90.155 193 14 3 4263 4454 648356130 648355942 3.950000e-61 246.0
6 TraesCS5B01G476400 chr5B 75.499 551 107 19 3581 4114 647875640 647876179 1.420000e-60 244.0
7 TraesCS5B01G476400 chr5B 90.351 114 11 0 4991 5104 648344880 648344767 3.190000e-32 150.0
8 TraesCS5B01G476400 chr5B 72.927 410 83 22 3689 4090 648854399 648854788 3.240000e-22 117.0
9 TraesCS5B01G476400 chr1D 96.782 1243 35 4 2234 3475 441202430 441201192 0.000000e+00 2069.0
10 TraesCS5B01G476400 chr1D 96.541 1243 39 2 2234 3476 423629410 423628172 0.000000e+00 2054.0
11 TraesCS5B01G476400 chr1D 93.140 379 16 2 1562 1939 441204743 441204374 9.680000e-152 547.0
12 TraesCS5B01G476400 chr1D 91.270 378 17 2 1562 1939 423631689 423631328 7.640000e-138 501.0
13 TraesCS5B01G476400 chr1D 96.970 264 8 0 1972 2235 441204265 441204002 1.310000e-120 444.0
14 TraesCS5B01G476400 chr1D 96.591 264 9 0 1972 2235 423631252 423630989 6.080000e-119 438.0
15 TraesCS5B01G476400 chr1D 98.413 63 1 0 1168 1230 441204827 441204765 1.510000e-20 111.0
16 TraesCS5B01G476400 chr1D 96.923 65 1 1 1167 1230 423631776 423631712 1.950000e-19 108.0
17 TraesCS5B01G476400 chr4D 96.527 1238 40 2 2234 3471 154232798 154234032 0.000000e+00 2045.0
18 TraesCS5B01G476400 chr4D 91.557 379 22 2 1562 1939 154230515 154230884 9.820000e-142 514.0
19 TraesCS5B01G476400 chr4D 96.212 264 10 0 1972 2235 154230993 154231256 2.830000e-117 433.0
20 TraesCS5B01G476400 chr7A 96.515 1234 41 1 2234 3467 616999563 617000794 0.000000e+00 2039.0
21 TraesCS5B01G476400 chr7A 98.715 778 10 0 12 789 618474545 618475322 0.000000e+00 1382.0
22 TraesCS5B01G476400 chr7A 100.000 538 0 0 13 550 671092328 671092865 0.000000e+00 994.0
23 TraesCS5B01G476400 chr7A 91.691 698 44 5 1551 2235 176983492 176984188 0.000000e+00 955.0
24 TraesCS5B01G476400 chr7A 97.835 462 10 0 330 791 656036414 656035953 0.000000e+00 798.0
25 TraesCS5B01G476400 chr7A 92.479 359 25 2 1581 1939 616997235 616997591 3.530000e-141 512.0
26 TraesCS5B01G476400 chr7A 98.333 60 1 0 1171 1230 616997109 616997168 7.000000e-19 106.0
27 TraesCS5B01G476400 chr7B 96.513 1233 41 1 2234 3466 133320143 133318913 0.000000e+00 2037.0
28 TraesCS5B01G476400 chr7B 91.029 379 24 2 1562 1939 133321284 133320915 2.130000e-138 503.0
29 TraesCS5B01G476400 chr7B 98.333 60 1 0 1171 1230 133321365 133321306 7.000000e-19 106.0
30 TraesCS5B01G476400 chr2A 96.353 1234 43 1 2234 3467 708290776 708292007 0.000000e+00 2028.0
31 TraesCS5B01G476400 chr2A 95.833 264 11 0 1972 2235 708288932 708289195 1.320000e-115 427.0
32 TraesCS5B01G476400 chr2A 85.432 405 29 9 1562 1939 708288422 708288823 1.330000e-105 394.0
33 TraesCS5B01G476400 chr2A 100.000 59 0 0 1172 1230 708288342 708288400 5.410000e-20 110.0
34 TraesCS5B01G476400 chr2B 95.951 1235 47 3 2234 3467 728935400 728934168 0.000000e+00 2001.0
35 TraesCS5B01G476400 chr2B 98.344 785 12 1 5 788 496144494 496143710 0.000000e+00 1376.0
36 TraesCS5B01G476400 chr2B 93.153 701 31 6 1551 2235 25262481 25261782 0.000000e+00 1013.0
37 TraesCS5B01G476400 chr2B 100.000 60 0 0 1171 1230 728937058 728936999 1.510000e-20 111.0
38 TraesCS5B01G476400 chr2B 95.161 62 3 0 1170 1231 25262586 25262525 1.170000e-16 99.0
39 TraesCS5B01G476400 chr3B 94.809 1233 62 2 2234 3466 400330799 400332029 0.000000e+00 1921.0
40 TraesCS5B01G476400 chr3B 97.835 462 10 0 330 791 425725039 425724578 0.000000e+00 798.0
41 TraesCS5B01G476400 chr6A 94.165 1234 70 2 2234 3466 176995499 176994267 0.000000e+00 1879.0
42 TraesCS5B01G476400 chr5D 92.381 1260 70 12 3466 4718 515678504 515679744 0.000000e+00 1772.0
43 TraesCS5B01G476400 chr5D 76.748 615 129 12 3505 4114 515862467 515861862 1.060000e-86 331.0
44 TraesCS5B01G476400 chr5D 92.558 215 11 5 927 1136 515678287 515678501 2.310000e-78 303.0
45 TraesCS5B01G476400 chr5D 89.474 190 20 0 4804 4993 515679787 515679976 1.840000e-59 241.0
46 TraesCS5B01G476400 chr5D 75.059 425 94 9 3674 4095 515690333 515690748 2.430000e-43 187.0
47 TraesCS5B01G476400 chr5D 94.828 58 3 0 804 861 515678231 515678288 1.960000e-14 91.6
48 TraesCS5B01G476400 chr3A 98.968 775 8 0 9 783 492203414 492204188 0.000000e+00 1387.0
49 TraesCS5B01G476400 chr3A 98.118 744 12 2 4 747 218320851 218320110 0.000000e+00 1295.0
50 TraesCS5B01G476400 chr3A 91.985 811 44 9 3 796 702188505 702189311 0.000000e+00 1118.0
51 TraesCS5B01G476400 chr3A 91.105 697 41 8 1551 2234 626009447 626008759 0.000000e+00 924.0
52 TraesCS5B01G476400 chr3A 98.462 65 0 1 1167 1230 626009526 626009462 4.180000e-21 113.0
53 TraesCS5B01G476400 chr5A 93.278 848 41 8 3466 4311 643930480 643931313 0.000000e+00 1236.0
54 TraesCS5B01G476400 chr5A 90.260 308 29 1 4684 4991 643949646 643949952 7.980000e-108 401.0
55 TraesCS5B01G476400 chr5A 89.212 241 14 6 4458 4695 643935698 643935929 1.800000e-74 291.0
56 TraesCS5B01G476400 chr5A 75.418 598 109 26 3526 4106 643300069 643299493 6.570000e-64 255.0
57 TraesCS5B01G476400 chr5A 92.025 163 13 0 1010 1172 643930328 643930490 3.980000e-56 230.0
58 TraesCS5B01G476400 chr5A 92.982 114 8 0 4991 5104 643949997 643950110 3.170000e-37 167.0
59 TraesCS5B01G476400 chr4B 93.590 780 31 9 5 767 662085157 662084380 0.000000e+00 1146.0
60 TraesCS5B01G476400 chrUn 95.075 670 29 1 1570 2235 21293158 21293827 0.000000e+00 1051.0
61 TraesCS5B01G476400 chrUn 98.438 64 1 0 1168 1231 21293099 21293162 4.180000e-21 113.0
62 TraesCS5B01G476400 chr6B 93.123 698 33 6 1551 2235 715594159 715593464 0.000000e+00 1009.0
63 TraesCS5B01G476400 chr1A 99.448 543 1 2 9 550 581537051 581536510 0.000000e+00 985.0
64 TraesCS5B01G476400 chr4A 99.439 535 2 1 16 550 741966743 741966210 0.000000e+00 970.0
65 TraesCS5B01G476400 chr7D 100.000 30 0 0 4369 4398 497343151 497343122 7.150000e-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 TraesCS5B01G476400 chr5B 648750297 648755410 5113 False 4430.000000 6586 100.000000 1 5114 2 chr5B.!!$F4 5113
1 TraesCS5B01G476400 chr5B 648361373 648361949 576 False 782.000000 782 91.334000 3474 4042 1 chr5B.!!$F2 568
2 TraesCS5B01G476400 chr5B 648354272 648356130 1858 True 311.500000 377 86.382000 4263 4905 2 chr5B.!!$R3 642
3 TraesCS5B01G476400 chr5B 647875640 647876179 539 False 244.000000 244 75.499000 3581 4114 1 chr5B.!!$F1 533
4 TraesCS5B01G476400 chr1D 441201192 441204827 3635 True 792.750000 2069 96.326250 1168 3475 4 chr1D.!!$R2 2307
5 TraesCS5B01G476400 chr1D 423628172 423631776 3604 True 775.250000 2054 95.331250 1167 3476 4 chr1D.!!$R1 2309
6 TraesCS5B01G476400 chr4D 154230515 154234032 3517 False 997.333333 2045 94.765333 1562 3471 3 chr4D.!!$F1 1909
7 TraesCS5B01G476400 chr7A 618474545 618475322 777 False 1382.000000 1382 98.715000 12 789 1 chr7A.!!$F2 777
8 TraesCS5B01G476400 chr7A 671092328 671092865 537 False 994.000000 994 100.000000 13 550 1 chr7A.!!$F3 537
9 TraesCS5B01G476400 chr7A 176983492 176984188 696 False 955.000000 955 91.691000 1551 2235 1 chr7A.!!$F1 684
10 TraesCS5B01G476400 chr7A 616997109 617000794 3685 False 885.666667 2039 95.775667 1171 3467 3 chr7A.!!$F4 2296
11 TraesCS5B01G476400 chr7B 133318913 133321365 2452 True 882.000000 2037 95.291667 1171 3466 3 chr7B.!!$R1 2295
12 TraesCS5B01G476400 chr2A 708288342 708292007 3665 False 739.750000 2028 94.404500 1172 3467 4 chr2A.!!$F1 2295
13 TraesCS5B01G476400 chr2B 496143710 496144494 784 True 1376.000000 1376 98.344000 5 788 1 chr2B.!!$R1 783
14 TraesCS5B01G476400 chr2B 728934168 728937058 2890 True 1056.000000 2001 97.975500 1171 3467 2 chr2B.!!$R3 2296
15 TraesCS5B01G476400 chr2B 25261782 25262586 804 True 556.000000 1013 94.157000 1170 2235 2 chr2B.!!$R2 1065
16 TraesCS5B01G476400 chr3B 400330799 400332029 1230 False 1921.000000 1921 94.809000 2234 3466 1 chr3B.!!$F1 1232
17 TraesCS5B01G476400 chr6A 176994267 176995499 1232 True 1879.000000 1879 94.165000 2234 3466 1 chr6A.!!$R1 1232
18 TraesCS5B01G476400 chr5D 515678231 515679976 1745 False 601.900000 1772 92.310250 804 4993 4 chr5D.!!$F2 4189
19 TraesCS5B01G476400 chr5D 515861862 515862467 605 True 331.000000 331 76.748000 3505 4114 1 chr5D.!!$R1 609
20 TraesCS5B01G476400 chr3A 492203414 492204188 774 False 1387.000000 1387 98.968000 9 783 1 chr3A.!!$F1 774
21 TraesCS5B01G476400 chr3A 218320110 218320851 741 True 1295.000000 1295 98.118000 4 747 1 chr3A.!!$R1 743
22 TraesCS5B01G476400 chr3A 702188505 702189311 806 False 1118.000000 1118 91.985000 3 796 1 chr3A.!!$F2 793
23 TraesCS5B01G476400 chr3A 626008759 626009526 767 True 518.500000 924 94.783500 1167 2234 2 chr3A.!!$R2 1067
24 TraesCS5B01G476400 chr5A 643930328 643931313 985 False 733.000000 1236 92.651500 1010 4311 2 chr5A.!!$F2 3301
25 TraesCS5B01G476400 chr5A 643299493 643300069 576 True 255.000000 255 75.418000 3526 4106 1 chr5A.!!$R1 580
26 TraesCS5B01G476400 chr4B 662084380 662085157 777 True 1146.000000 1146 93.590000 5 767 1 chr4B.!!$R1 762
27 TraesCS5B01G476400 chrUn 21293099 21293827 728 False 582.000000 1051 96.756500 1168 2235 2 chrUn.!!$F1 1067
28 TraesCS5B01G476400 chr6B 715593464 715594159 695 True 1009.000000 1009 93.123000 1551 2235 1 chr6B.!!$R1 684
29 TraesCS5B01G476400 chr1A 581536510 581537051 541 True 985.000000 985 99.448000 9 550 1 chr1A.!!$R1 541
30 TraesCS5B01G476400 chr4A 741966210 741966743 533 True 970.000000 970 99.439000 16 550 1 chr4A.!!$R1 534

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
884 903 0.037605 CAATATCTCCCCGGCCGTAC 60.038 60.0 26.12 0.0 0.00 3.67 F
913 932 0.044855 ACCTACCTCATCAGCCCCTT 59.955 55.0 0.00 0.0 0.00 3.95 F
915 934 0.179034 CTACCTCATCAGCCCCTTGC 60.179 60.0 0.00 0.0 41.71 4.01 F
1779 1878 0.252513 TCCTTCGGTCCTTCCCATCA 60.253 55.0 0.00 0.0 0.00 3.07 F
2669 4543 0.179111 TCATGGAAGATCACGTCGGC 60.179 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1875 0.740868 CGACAGTTGATGGCCGTGAT 60.741 55.000 0.00 0.00 30.50 3.06 R
1779 1878 2.742372 GCGACAGTTGATGGCCGT 60.742 61.111 0.00 0.00 30.50 5.68 R
2469 4343 3.573967 TCTCTTTGGCAAAGATTTGGACC 59.426 43.478 35.33 1.97 45.75 4.46 R
3625 5518 0.234884 GGCGTTTCGAGTTCCAGTTG 59.765 55.000 0.00 0.00 0.00 3.16 R
4499 7606 0.321996 GGGATTCGGTGGCTAGGATC 59.678 60.000 0.00 0.00 0.00 3.36 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
561 569 4.350816 TGAAAAGGAGAGAACCAGGAATCA 59.649 41.667 0.00 0.00 0.00 2.57
605 613 1.206132 CGTGAGGCTAATACCACCACA 59.794 52.381 0.00 0.00 36.14 4.17
664 672 6.181908 ACCTTAAATAAACATAAGCCGTCCA 58.818 36.000 0.00 0.00 0.00 4.02
678 697 2.676342 GCCGTCCACGATTTAAGTGAAT 59.324 45.455 0.00 0.00 41.83 2.57
727 746 7.068226 GCATGGTGGGTAATTATTTACAACTCT 59.932 37.037 9.17 0.00 39.62 3.24
799 818 7.669089 AGTAGGGAAAGATTAGAGAAAGAGG 57.331 40.000 0.00 0.00 0.00 3.69
800 819 5.966853 AGGGAAAGATTAGAGAAAGAGGG 57.033 43.478 0.00 0.00 0.00 4.30
801 820 5.604752 AGGGAAAGATTAGAGAAAGAGGGA 58.395 41.667 0.00 0.00 0.00 4.20
802 821 6.032693 AGGGAAAGATTAGAGAAAGAGGGAA 58.967 40.000 0.00 0.00 0.00 3.97
839 858 1.002201 TCGTTCGTTAGCCCAAATCCA 59.998 47.619 0.00 0.00 0.00 3.41
842 861 1.444836 TCGTTAGCCCAAATCCAACG 58.555 50.000 0.00 0.00 42.38 4.10
844 863 2.014128 CGTTAGCCCAAATCCAACGAT 58.986 47.619 0.00 0.00 43.37 3.73
862 881 4.527157 GCACGCCGCATTCAGCTC 62.527 66.667 0.00 0.00 42.61 4.09
863 882 4.214383 CACGCCGCATTCAGCTCG 62.214 66.667 0.00 0.00 42.61 5.03
864 883 4.435436 ACGCCGCATTCAGCTCGA 62.435 61.111 0.00 0.00 42.61 4.04
865 884 3.918220 CGCCGCATTCAGCTCGAC 61.918 66.667 0.00 0.00 42.61 4.20
866 885 2.815211 GCCGCATTCAGCTCGACA 60.815 61.111 0.00 0.00 42.61 4.35
867 886 2.390599 GCCGCATTCAGCTCGACAA 61.391 57.895 0.00 0.00 42.61 3.18
868 887 1.709147 GCCGCATTCAGCTCGACAAT 61.709 55.000 0.00 0.00 42.61 2.71
869 888 1.570813 CCGCATTCAGCTCGACAATA 58.429 50.000 0.00 0.00 42.61 1.90
870 889 2.138320 CCGCATTCAGCTCGACAATAT 58.862 47.619 0.00 0.00 42.61 1.28
871 890 2.156504 CCGCATTCAGCTCGACAATATC 59.843 50.000 0.00 0.00 42.61 1.63
872 891 3.055591 CGCATTCAGCTCGACAATATCT 58.944 45.455 0.00 0.00 42.61 1.98
873 892 3.120947 CGCATTCAGCTCGACAATATCTC 59.879 47.826 0.00 0.00 42.61 2.75
874 893 3.431572 GCATTCAGCTCGACAATATCTCC 59.568 47.826 0.00 0.00 41.15 3.71
875 894 3.735237 TTCAGCTCGACAATATCTCCC 57.265 47.619 0.00 0.00 0.00 4.30
876 895 1.964223 TCAGCTCGACAATATCTCCCC 59.036 52.381 0.00 0.00 0.00 4.81
877 896 0.962489 AGCTCGACAATATCTCCCCG 59.038 55.000 0.00 0.00 0.00 5.73
878 897 0.038159 GCTCGACAATATCTCCCCGG 60.038 60.000 0.00 0.00 0.00 5.73
879 898 0.038159 CTCGACAATATCTCCCCGGC 60.038 60.000 0.00 0.00 0.00 6.13
880 899 1.004918 CGACAATATCTCCCCGGCC 60.005 63.158 0.00 0.00 0.00 6.13
881 900 1.004918 GACAATATCTCCCCGGCCG 60.005 63.158 21.04 21.04 0.00 6.13
882 901 1.755393 GACAATATCTCCCCGGCCGT 61.755 60.000 26.12 6.67 0.00 5.68
883 902 0.470456 ACAATATCTCCCCGGCCGTA 60.470 55.000 26.12 9.08 0.00 4.02
884 903 0.037605 CAATATCTCCCCGGCCGTAC 60.038 60.000 26.12 0.00 0.00 3.67
885 904 1.530013 AATATCTCCCCGGCCGTACG 61.530 60.000 26.12 8.69 0.00 3.67
895 914 3.110178 GCCGTACGCCTGTGTCAC 61.110 66.667 10.49 0.00 0.00 3.67
896 915 2.431942 CCGTACGCCTGTGTCACC 60.432 66.667 10.49 0.00 0.00 4.02
897 916 2.649034 CGTACGCCTGTGTCACCT 59.351 61.111 0.52 0.00 0.00 4.00
898 917 1.588824 CCGTACGCCTGTGTCACCTA 61.589 60.000 10.49 0.00 0.00 3.08
899 918 0.455633 CGTACGCCTGTGTCACCTAC 60.456 60.000 0.52 0.00 0.00 3.18
900 919 0.108945 GTACGCCTGTGTCACCTACC 60.109 60.000 0.00 0.00 0.00 3.18
901 920 0.251474 TACGCCTGTGTCACCTACCT 60.251 55.000 0.00 0.00 0.00 3.08
902 921 1.215647 CGCCTGTGTCACCTACCTC 59.784 63.158 0.00 0.00 0.00 3.85
903 922 1.532604 CGCCTGTGTCACCTACCTCA 61.533 60.000 0.00 0.00 0.00 3.86
904 923 0.905357 GCCTGTGTCACCTACCTCAT 59.095 55.000 0.00 0.00 0.00 2.90
905 924 1.134670 GCCTGTGTCACCTACCTCATC 60.135 57.143 0.00 0.00 0.00 2.92
906 925 2.179427 CCTGTGTCACCTACCTCATCA 58.821 52.381 0.00 0.00 0.00 3.07
907 926 2.167281 CCTGTGTCACCTACCTCATCAG 59.833 54.545 0.00 0.00 0.00 2.90
908 927 1.550524 TGTGTCACCTACCTCATCAGC 59.449 52.381 0.00 0.00 0.00 4.26
909 928 1.134670 GTGTCACCTACCTCATCAGCC 60.135 57.143 0.00 0.00 0.00 4.85
910 929 0.466124 GTCACCTACCTCATCAGCCC 59.534 60.000 0.00 0.00 0.00 5.19
911 930 0.691078 TCACCTACCTCATCAGCCCC 60.691 60.000 0.00 0.00 0.00 5.80
912 931 0.692419 CACCTACCTCATCAGCCCCT 60.692 60.000 0.00 0.00 0.00 4.79
913 932 0.044855 ACCTACCTCATCAGCCCCTT 59.955 55.000 0.00 0.00 0.00 3.95
914 933 0.471617 CCTACCTCATCAGCCCCTTG 59.528 60.000 0.00 0.00 0.00 3.61
915 934 0.179034 CTACCTCATCAGCCCCTTGC 60.179 60.000 0.00 0.00 41.71 4.01
916 935 1.635817 TACCTCATCAGCCCCTTGCC 61.636 60.000 0.00 0.00 42.71 4.52
917 936 2.679092 CTCATCAGCCCCTTGCCA 59.321 61.111 0.00 0.00 42.71 4.92
918 937 1.751927 CTCATCAGCCCCTTGCCAC 60.752 63.158 0.00 0.00 42.71 5.01
919 938 3.136123 CATCAGCCCCTTGCCACG 61.136 66.667 0.00 0.00 42.71 4.94
936 955 2.269529 CGCCCCGTGCCCTTTAAAA 61.270 57.895 0.00 0.00 36.24 1.52
948 967 0.598065 CTTTAAAAGGCAGCGCACCT 59.402 50.000 15.64 15.64 40.02 4.00
996 1015 3.684908 TGATTTCTCCATCGCCAAAGAA 58.315 40.909 0.00 0.00 0.00 2.52
1007 1027 2.159531 TCGCCAAAGAAAAGATGATGCG 60.160 45.455 0.00 0.00 40.72 4.73
1008 1028 1.922545 GCCAAAGAAAAGATGATGCGC 59.077 47.619 0.00 0.00 0.00 6.09
1056 1076 2.041819 GAGATCCCCTCCCACGGT 60.042 66.667 0.00 0.00 35.87 4.83
1776 1875 2.291043 GCTCCTTCGGTCCTTCCCA 61.291 63.158 0.00 0.00 0.00 4.37
1779 1878 0.252513 TCCTTCGGTCCTTCCCATCA 60.253 55.000 0.00 0.00 0.00 3.07
1788 1887 1.224315 CTTCCCATCACGGCCATCA 59.776 57.895 2.24 0.00 0.00 3.07
1912 2011 3.959329 CTCCTCCGGTCCTTCCCGT 62.959 68.421 0.00 0.00 46.66 5.28
1958 2065 0.452784 GTGAGTTTTGACGATGCCGC 60.453 55.000 0.00 0.00 39.95 6.53
1960 2067 2.202298 GTTTTGACGATGCCGCCG 60.202 61.111 0.00 0.00 39.95 6.46
2123 2368 2.019249 TGCTCTGAACATATGCTTGCC 58.981 47.619 1.58 0.00 0.00 4.52
2469 4343 8.892723 TGTTATTCTTGGCTATACAAATGAGTG 58.107 33.333 0.00 0.00 0.00 3.51
2484 4358 2.238521 TGAGTGGTCCAAATCTTTGCC 58.761 47.619 0.00 0.00 36.86 4.52
2669 4543 0.179111 TCATGGAAGATCACGTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
2681 4555 4.316205 TCACGTCGGCATTATGAAGTAT 57.684 40.909 0.00 0.00 0.00 2.12
2806 4680 2.132740 TTTGCATGTCGGCTTTGAAC 57.867 45.000 0.00 0.00 34.04 3.18
2873 4747 3.136443 ACTTGCCGAATTCTATCCCATGA 59.864 43.478 3.52 0.00 0.00 3.07
3097 4971 6.319141 AGTGTTGAAAGAGTATTTTCAGCC 57.681 37.500 11.13 5.04 45.00 4.85
3408 5283 8.739039 CCATATTTTGTCTGACACTTGGATTAA 58.261 33.333 10.56 0.00 0.00 1.40
3414 5289 8.777865 TTGTCTGACACTTGGATTAATAGAAG 57.222 34.615 10.56 4.94 0.00 2.85
3516 5392 1.713830 GGCAATGTCGTACTTCGCC 59.286 57.895 0.00 0.00 39.67 5.54
3627 5520 4.680237 CCGGACCTGTCGCAGCAA 62.680 66.667 0.00 0.00 0.00 3.91
3633 5526 1.597854 CCTGTCGCAGCAACTGGAA 60.598 57.895 3.25 0.00 37.80 3.53
3637 5530 1.664649 TCGCAGCAACTGGAACTCG 60.665 57.895 0.00 0.00 31.21 4.18
3807 5709 3.092511 ATGGAGTGCCTCGCCCAT 61.093 61.111 0.00 0.00 35.07 4.00
3905 5807 3.692406 GGAGGTCGACCGTGCCTT 61.692 66.667 28.26 10.43 42.08 4.35
3937 5839 2.915659 ACCTCGCCACCGTCTTCA 60.916 61.111 0.00 0.00 35.54 3.02
4071 5976 3.781307 TCCCTCGACGCCAATGGG 61.781 66.667 0.00 0.00 39.22 4.00
4074 5979 2.267642 CTCGACGCCAATGGGGAA 59.732 61.111 23.60 6.96 40.01 3.97
4084 5989 1.152830 AATGGGGAACACGTGCCTT 59.847 52.632 17.22 2.70 37.99 4.35
4095 6000 1.302832 CGTGCCTTTCTTCCAGCCT 60.303 57.895 0.00 0.00 0.00 4.58
4116 6021 4.120331 GCTGCGGCGGCTTGATTT 62.120 61.111 25.88 0.00 40.82 2.17
4138 6044 1.945394 GGTATCATCAGTTGGCTGCTG 59.055 52.381 0.00 3.14 42.29 4.41
4235 6141 2.633199 AGTCGGCTTTAGTCTCGTTC 57.367 50.000 0.00 0.00 0.00 3.95
4245 6151 6.073440 GGCTTTAGTCTCGTTCATGTTTGTTA 60.073 38.462 0.00 0.00 0.00 2.41
4246 6152 7.349711 GCTTTAGTCTCGTTCATGTTTGTTAA 58.650 34.615 0.00 0.00 0.00 2.01
4247 6153 8.015658 GCTTTAGTCTCGTTCATGTTTGTTAAT 58.984 33.333 0.00 0.00 0.00 1.40
4248 6154 9.878599 CTTTAGTCTCGTTCATGTTTGTTAATT 57.121 29.630 0.00 0.00 0.00 1.40
4326 6232 6.355747 TGATGATGTAGATGGTTACATTGCA 58.644 36.000 0.75 0.00 42.68 4.08
4363 6269 7.949434 ACTTATTATTACTCCCTTCGTTCGAT 58.051 34.615 0.00 0.00 0.00 3.59
4364 6270 8.081025 ACTTATTATTACTCCCTTCGTTCGATC 58.919 37.037 0.00 0.00 0.00 3.69
4365 6271 2.838386 TTACTCCCTTCGTTCGATCG 57.162 50.000 9.36 9.36 0.00 3.69
4366 6272 2.028420 TACTCCCTTCGTTCGATCGA 57.972 50.000 15.15 15.15 38.08 3.59
4433 6340 7.618502 TTGAAACTGTTGAGTACTTGCTTTA 57.381 32.000 0.00 0.00 0.00 1.85
4448 6355 1.405661 GCTTTAGTCGCTAGGTGCCTT 60.406 52.381 0.00 0.00 38.78 4.35
4512 7619 0.249073 CAAGTCGATCCTAGCCACCG 60.249 60.000 0.00 0.00 0.00 4.94
4524 7634 4.506255 CCACCGAATCCCCCTGCC 62.506 72.222 0.00 0.00 0.00 4.85
4525 7635 3.727258 CACCGAATCCCCCTGCCA 61.727 66.667 0.00 0.00 0.00 4.92
4526 7636 3.728373 ACCGAATCCCCCTGCCAC 61.728 66.667 0.00 0.00 0.00 5.01
4552 7662 3.134792 GAGGCAGACTCTCGGCGA 61.135 66.667 10.14 10.14 43.14 5.54
4620 7730 1.789576 GCCTCTTCTCCAACCCCCAA 61.790 60.000 0.00 0.00 0.00 4.12
4629 7739 2.933834 AACCCCCAACCCTCCTCG 60.934 66.667 0.00 0.00 0.00 4.63
4634 7744 3.411517 CCAACCCTCCTCGCCCAT 61.412 66.667 0.00 0.00 0.00 4.00
4635 7745 2.190578 CAACCCTCCTCGCCCATC 59.809 66.667 0.00 0.00 0.00 3.51
4636 7746 2.285368 AACCCTCCTCGCCCATCA 60.285 61.111 0.00 0.00 0.00 3.07
4637 7747 2.370445 AACCCTCCTCGCCCATCAG 61.370 63.158 0.00 0.00 0.00 2.90
4638 7748 4.247380 CCCTCCTCGCCCATCAGC 62.247 72.222 0.00 0.00 0.00 4.26
4639 7749 3.160047 CCTCCTCGCCCATCAGCT 61.160 66.667 0.00 0.00 0.00 4.24
4640 7750 1.834378 CCTCCTCGCCCATCAGCTA 60.834 63.158 0.00 0.00 0.00 3.32
4643 7754 2.434843 CCTCGCCCATCAGCTACCA 61.435 63.158 0.00 0.00 0.00 3.25
4673 7785 3.512516 GTTGGGATGCTCCAGCGC 61.513 66.667 0.00 0.00 45.83 5.92
4722 7834 1.078759 GACCGTGGCGTCAGATTCAG 61.079 60.000 0.00 0.00 32.74 3.02
4725 7837 1.354337 CGTGGCGTCAGATTCAGTGG 61.354 60.000 0.00 0.00 0.00 4.00
4726 7838 0.320771 GTGGCGTCAGATTCAGTGGT 60.321 55.000 0.00 0.00 0.00 4.16
4728 7840 0.798776 GGCGTCAGATTCAGTGGTTG 59.201 55.000 0.00 0.00 0.00 3.77
4737 7849 0.836606 TTCAGTGGTTGGCTGTCTGA 59.163 50.000 0.00 0.00 35.60 3.27
4750 7862 2.289565 CTGTCTGATCTGCATGCATGT 58.710 47.619 26.79 12.95 0.00 3.21
4753 7865 1.137479 TCTGATCTGCATGCATGTCGA 59.863 47.619 26.79 21.90 0.00 4.20
4757 7869 0.741927 TCTGCATGCATGTCGACCTG 60.742 55.000 26.79 14.94 0.00 4.00
4767 7879 0.904865 TGTCGACCTGAGGCTTGGAT 60.905 55.000 14.12 0.00 0.00 3.41
4779 7891 0.038892 GCTTGGATGTGGCACAACAG 60.039 55.000 25.95 16.51 44.16 3.16
4831 7965 1.450848 CAGATGCAGCGGTGGATGT 60.451 57.895 26.61 19.74 34.30 3.06
4842 7976 1.886222 CGGTGGATGTTTGGGTGATGT 60.886 52.381 0.00 0.00 0.00 3.06
4845 7979 0.532115 GGATGTTTGGGTGATGTGCC 59.468 55.000 0.00 0.00 0.00 5.01
4848 7982 2.282816 TTTGGGTGATGTGCCGGG 60.283 61.111 2.18 0.00 0.00 5.73
4882 8016 1.698506 CCGGTCTCTAGCCAGATTCT 58.301 55.000 0.00 0.00 0.00 2.40
4885 8019 3.829601 CCGGTCTCTAGCCAGATTCTATT 59.170 47.826 0.00 0.00 0.00 1.73
4910 8044 4.309950 GCGTCGGGACCTTGGTGT 62.310 66.667 0.00 0.00 0.00 4.16
4914 8048 4.619227 CGGGACCTTGGTGTGCGT 62.619 66.667 0.00 0.00 0.00 5.24
4944 8078 1.820906 CTGGATGTGGACCATGGCG 60.821 63.158 13.04 0.00 36.79 5.69
4947 8081 3.993614 GATGTGGACCATGGCGGCA 62.994 63.158 16.34 16.34 39.03 5.69
4995 8129 4.301027 GGCTAGCCGCGCTATGGT 62.301 66.667 20.16 1.75 40.54 3.55
4996 8130 3.038417 GCTAGCCGCGCTATGGTG 61.038 66.667 5.56 0.00 40.54 4.17
4997 8131 2.728180 CTAGCCGCGCTATGGTGA 59.272 61.111 5.56 0.00 40.54 4.02
4998 8132 1.290324 CTAGCCGCGCTATGGTGAT 59.710 57.895 5.56 0.00 40.54 3.06
4999 8133 1.006220 TAGCCGCGCTATGGTGATG 60.006 57.895 5.56 0.00 40.44 3.07
5000 8134 1.460273 TAGCCGCGCTATGGTGATGA 61.460 55.000 5.56 0.00 40.44 2.92
5001 8135 2.598632 GCCGCGCTATGGTGATGAC 61.599 63.158 5.56 0.00 0.00 3.06
5002 8136 1.068083 CCGCGCTATGGTGATGACT 59.932 57.895 5.56 0.00 0.00 3.41
5003 8137 0.313987 CCGCGCTATGGTGATGACTA 59.686 55.000 5.56 0.00 0.00 2.59
5004 8138 1.409412 CGCGCTATGGTGATGACTAC 58.591 55.000 5.56 0.00 0.00 2.73
5005 8139 1.269051 CGCGCTATGGTGATGACTACA 60.269 52.381 5.56 0.00 0.00 2.74
5006 8140 2.798145 CGCGCTATGGTGATGACTACAA 60.798 50.000 5.56 0.00 0.00 2.41
5007 8141 3.194861 GCGCTATGGTGATGACTACAAA 58.805 45.455 0.00 0.00 0.00 2.83
5008 8142 3.246226 GCGCTATGGTGATGACTACAAAG 59.754 47.826 0.00 0.00 0.00 2.77
5009 8143 4.433615 CGCTATGGTGATGACTACAAAGT 58.566 43.478 0.00 0.00 39.21 2.66
5010 8144 5.588240 CGCTATGGTGATGACTACAAAGTA 58.412 41.667 0.00 0.00 35.56 2.24
5011 8145 6.216569 CGCTATGGTGATGACTACAAAGTAT 58.783 40.000 0.00 0.00 35.56 2.12
5012 8146 6.701841 CGCTATGGTGATGACTACAAAGTATT 59.298 38.462 0.00 0.00 35.56 1.89
5013 8147 7.306807 CGCTATGGTGATGACTACAAAGTATTG 60.307 40.741 0.00 0.00 42.46 1.90
5014 8148 6.683974 ATGGTGATGACTACAAAGTATTGC 57.316 37.500 0.00 0.00 40.34 3.56
5015 8149 4.629634 TGGTGATGACTACAAAGTATTGCG 59.370 41.667 0.00 0.00 40.34 4.85
5016 8150 4.034048 GGTGATGACTACAAAGTATTGCGG 59.966 45.833 0.00 0.00 40.34 5.69
5017 8151 3.621268 TGATGACTACAAAGTATTGCGGC 59.379 43.478 0.00 0.00 40.34 6.53
5018 8152 1.996898 TGACTACAAAGTATTGCGGCG 59.003 47.619 0.51 0.51 40.34 6.46
5019 8153 2.264813 GACTACAAAGTATTGCGGCGA 58.735 47.619 12.98 0.00 40.34 5.54
5020 8154 1.997606 ACTACAAAGTATTGCGGCGAC 59.002 47.619 12.98 2.02 40.34 5.19
5021 8155 2.268298 CTACAAAGTATTGCGGCGACT 58.732 47.619 12.98 1.02 40.34 4.18
5022 8156 1.519408 ACAAAGTATTGCGGCGACTT 58.481 45.000 12.98 8.69 40.34 3.01
5023 8157 1.463444 ACAAAGTATTGCGGCGACTTC 59.537 47.619 12.98 0.00 40.34 3.01
5024 8158 1.084289 AAAGTATTGCGGCGACTTCC 58.916 50.000 12.98 0.00 32.27 3.46
5034 8168 3.744719 CGACTTCCGACCGCTCCA 61.745 66.667 0.00 0.00 41.76 3.86
5035 8169 2.126031 GACTTCCGACCGCTCCAC 60.126 66.667 0.00 0.00 0.00 4.02
5036 8170 3.966026 GACTTCCGACCGCTCCACG 62.966 68.421 0.00 0.00 43.15 4.94
5046 8180 2.105128 GCTCCACGACGAGGATGG 59.895 66.667 14.59 5.17 33.99 3.51
5047 8181 2.711922 GCTCCACGACGAGGATGGT 61.712 63.158 14.59 0.00 33.99 3.55
5048 8182 1.433879 CTCCACGACGAGGATGGTC 59.566 63.158 14.59 0.00 40.74 4.02
5049 8183 1.303806 TCCACGACGAGGATGGTCA 60.304 57.895 10.16 0.00 44.74 4.02
5050 8184 0.683179 TCCACGACGAGGATGGTCAT 60.683 55.000 10.16 0.00 44.74 3.06
5051 8185 0.249073 CCACGACGAGGATGGTCATC 60.249 60.000 5.25 2.52 44.74 2.92
5058 8192 2.990066 GAGGATGGTCATCGAAAGGT 57.010 50.000 5.05 0.00 38.69 3.50
5059 8193 3.268023 GAGGATGGTCATCGAAAGGTT 57.732 47.619 5.05 0.00 38.69 3.50
5060 8194 2.939103 GAGGATGGTCATCGAAAGGTTG 59.061 50.000 5.05 0.00 38.69 3.77
5061 8195 2.017049 GGATGGTCATCGAAAGGTTGG 58.983 52.381 5.05 0.00 38.69 3.77
5062 8196 2.017049 GATGGTCATCGAAAGGTTGGG 58.983 52.381 0.00 0.00 0.00 4.12
5063 8197 1.060729 TGGTCATCGAAAGGTTGGGA 58.939 50.000 0.00 0.00 0.00 4.37
5064 8198 1.003118 TGGTCATCGAAAGGTTGGGAG 59.997 52.381 0.00 0.00 0.00 4.30
5065 8199 1.679032 GGTCATCGAAAGGTTGGGAGG 60.679 57.143 0.00 0.00 0.00 4.30
5066 8200 0.618458 TCATCGAAAGGTTGGGAGGG 59.382 55.000 0.00 0.00 0.00 4.30
5067 8201 0.394352 CATCGAAAGGTTGGGAGGGG 60.394 60.000 0.00 0.00 0.00 4.79
5068 8202 0.845102 ATCGAAAGGTTGGGAGGGGT 60.845 55.000 0.00 0.00 0.00 4.95
5069 8203 1.063654 TCGAAAGGTTGGGAGGGGTT 61.064 55.000 0.00 0.00 0.00 4.11
5070 8204 0.694196 CGAAAGGTTGGGAGGGGTTA 59.306 55.000 0.00 0.00 0.00 2.85
5071 8205 1.283905 CGAAAGGTTGGGAGGGGTTAT 59.716 52.381 0.00 0.00 0.00 1.89
5072 8206 2.682858 CGAAAGGTTGGGAGGGGTTATC 60.683 54.545 0.00 0.00 0.00 1.75
5073 8207 2.378308 AAGGTTGGGAGGGGTTATCT 57.622 50.000 0.00 0.00 0.00 1.98
5074 8208 1.894699 AGGTTGGGAGGGGTTATCTC 58.105 55.000 0.00 0.00 0.00 2.75
5075 8209 1.369983 AGGTTGGGAGGGGTTATCTCT 59.630 52.381 0.00 0.00 0.00 3.10
5076 8210 1.769465 GGTTGGGAGGGGTTATCTCTC 59.231 57.143 0.00 0.00 32.57 3.20
5077 8211 1.769465 GTTGGGAGGGGTTATCTCTCC 59.231 57.143 1.98 1.98 44.64 3.71
5078 8212 1.330155 TGGGAGGGGTTATCTCTCCT 58.670 55.000 11.68 0.00 44.72 3.69
5079 8213 1.062121 TGGGAGGGGTTATCTCTCCTG 60.062 57.143 11.68 0.00 44.72 3.86
5080 8214 1.220750 GGGAGGGGTTATCTCTCCTGA 59.779 57.143 11.68 0.00 44.72 3.86
5081 8215 2.158081 GGGAGGGGTTATCTCTCCTGAT 60.158 54.545 11.68 0.00 44.72 2.90
5082 8216 3.592865 GGAGGGGTTATCTCTCCTGATT 58.407 50.000 3.70 0.00 42.70 2.57
5083 8217 3.977326 GGAGGGGTTATCTCTCCTGATTT 59.023 47.826 3.70 0.00 42.70 2.17
5084 8218 4.202409 GGAGGGGTTATCTCTCCTGATTTG 60.202 50.000 3.70 0.00 42.70 2.32
5085 8219 3.718956 AGGGGTTATCTCTCCTGATTTGG 59.281 47.826 0.00 0.00 0.00 3.28
5086 8220 3.459969 GGGGTTATCTCTCCTGATTTGGT 59.540 47.826 0.00 0.00 0.00 3.67
5087 8221 4.455606 GGGTTATCTCTCCTGATTTGGTG 58.544 47.826 0.00 0.00 0.00 4.17
5088 8222 4.455606 GGTTATCTCTCCTGATTTGGTGG 58.544 47.826 0.00 0.00 0.00 4.61
5089 8223 4.080299 GGTTATCTCTCCTGATTTGGTGGT 60.080 45.833 0.00 0.00 0.00 4.16
5090 8224 5.501156 GTTATCTCTCCTGATTTGGTGGTT 58.499 41.667 0.00 0.00 0.00 3.67
5091 8225 3.423539 TCTCTCCTGATTTGGTGGTTG 57.576 47.619 0.00 0.00 0.00 3.77
5092 8226 2.978978 TCTCTCCTGATTTGGTGGTTGA 59.021 45.455 0.00 0.00 0.00 3.18
5093 8227 3.077359 CTCTCCTGATTTGGTGGTTGAC 58.923 50.000 0.00 0.00 0.00 3.18
5094 8228 2.711009 TCTCCTGATTTGGTGGTTGACT 59.289 45.455 0.00 0.00 0.00 3.41
5095 8229 3.138283 TCTCCTGATTTGGTGGTTGACTT 59.862 43.478 0.00 0.00 0.00 3.01
5096 8230 3.486383 TCCTGATTTGGTGGTTGACTTC 58.514 45.455 0.00 0.00 0.00 3.01
5097 8231 3.117701 TCCTGATTTGGTGGTTGACTTCA 60.118 43.478 0.00 0.00 0.00 3.02
5098 8232 3.636300 CCTGATTTGGTGGTTGACTTCAA 59.364 43.478 0.00 0.00 0.00 2.69
5099 8233 4.281688 CCTGATTTGGTGGTTGACTTCAAT 59.718 41.667 0.00 0.00 38.24 2.57
5100 8234 5.199024 TGATTTGGTGGTTGACTTCAATG 57.801 39.130 0.00 0.00 38.24 2.82
5101 8235 4.039004 TGATTTGGTGGTTGACTTCAATGG 59.961 41.667 0.00 0.00 38.24 3.16
5102 8236 2.746279 TGGTGGTTGACTTCAATGGT 57.254 45.000 0.00 0.00 38.24 3.55
5103 8237 2.305928 TGGTGGTTGACTTCAATGGTG 58.694 47.619 0.00 0.00 38.24 4.17
5104 8238 1.000274 GGTGGTTGACTTCAATGGTGC 60.000 52.381 0.00 0.00 38.24 5.01
5105 8239 1.956477 GTGGTTGACTTCAATGGTGCT 59.044 47.619 0.00 0.00 38.24 4.40
5106 8240 2.362077 GTGGTTGACTTCAATGGTGCTT 59.638 45.455 0.00 0.00 38.24 3.91
5107 8241 2.361757 TGGTTGACTTCAATGGTGCTTG 59.638 45.455 0.00 0.00 38.24 4.01
5108 8242 2.622942 GGTTGACTTCAATGGTGCTTGA 59.377 45.455 0.00 0.00 38.24 3.02
5109 8243 3.256631 GGTTGACTTCAATGGTGCTTGAT 59.743 43.478 0.00 0.00 38.24 2.57
5110 8244 4.232221 GTTGACTTCAATGGTGCTTGATG 58.768 43.478 0.00 0.00 38.24 3.07
5111 8245 2.229543 TGACTTCAATGGTGCTTGATGC 59.770 45.455 0.00 0.00 43.25 3.91
5112 8246 7.732976 GTTGACTTCAATGGTGCTTGATGCA 62.733 44.000 0.00 0.00 43.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
605 613 1.404391 CATAACGCGAGGTAGAGTGGT 59.596 52.381 15.93 0.00 36.25 4.16
727 746 7.027161 GTCGTACGTCACTAAAATTACCCTTA 58.973 38.462 16.05 0.00 0.00 2.69
789 808 6.133356 AGATCGTATCTTTCCCTCTTTCTCT 58.867 40.000 0.00 0.00 35.76 3.10
790 809 6.399639 AGATCGTATCTTTCCCTCTTTCTC 57.600 41.667 0.00 0.00 35.76 2.87
794 813 6.843752 TCTCTAGATCGTATCTTTCCCTCTT 58.156 40.000 0.00 0.00 40.76 2.85
796 815 7.316544 GATCTCTAGATCGTATCTTTCCCTC 57.683 44.000 4.29 0.00 41.15 4.30
861 880 1.469335 GGCCGGGGAGATATTGTCGA 61.469 60.000 2.18 0.00 0.00 4.20
862 881 1.004918 GGCCGGGGAGATATTGTCG 60.005 63.158 2.18 0.00 0.00 4.35
863 882 1.004918 CGGCCGGGGAGATATTGTC 60.005 63.158 20.10 0.00 0.00 3.18
864 883 0.470456 TACGGCCGGGGAGATATTGT 60.470 55.000 31.76 5.83 0.00 2.71
865 884 0.037605 GTACGGCCGGGGAGATATTG 60.038 60.000 31.76 0.00 0.00 1.90
866 885 1.530013 CGTACGGCCGGGGAGATATT 61.530 60.000 31.76 7.29 0.00 1.28
867 886 1.975407 CGTACGGCCGGGGAGATAT 60.975 63.158 31.76 8.14 0.00 1.63
868 887 2.595463 CGTACGGCCGGGGAGATA 60.595 66.667 31.76 8.66 0.00 1.98
878 897 3.110178 GTGACACAGGCGTACGGC 61.110 66.667 32.18 32.18 42.51 5.68
879 898 1.588824 TAGGTGACACAGGCGTACGG 61.589 60.000 18.39 2.64 0.00 4.02
880 899 0.455633 GTAGGTGACACAGGCGTACG 60.456 60.000 11.84 11.84 0.00 3.67
881 900 0.108945 GGTAGGTGACACAGGCGTAC 60.109 60.000 8.08 1.10 0.00 3.67
882 901 0.251474 AGGTAGGTGACACAGGCGTA 60.251 55.000 8.08 0.00 0.00 4.42
883 902 1.533273 AGGTAGGTGACACAGGCGT 60.533 57.895 8.08 0.00 0.00 5.68
884 903 1.215647 GAGGTAGGTGACACAGGCG 59.784 63.158 8.08 0.00 0.00 5.52
885 904 0.905357 ATGAGGTAGGTGACACAGGC 59.095 55.000 8.08 0.00 0.00 4.85
886 905 2.167281 CTGATGAGGTAGGTGACACAGG 59.833 54.545 8.08 0.00 0.00 4.00
887 906 2.417924 GCTGATGAGGTAGGTGACACAG 60.418 54.545 8.08 0.00 0.00 3.66
888 907 1.550524 GCTGATGAGGTAGGTGACACA 59.449 52.381 8.08 0.00 0.00 3.72
889 908 1.134670 GGCTGATGAGGTAGGTGACAC 60.135 57.143 0.00 0.00 0.00 3.67
890 909 1.195115 GGCTGATGAGGTAGGTGACA 58.805 55.000 0.00 0.00 0.00 3.58
891 910 0.466124 GGGCTGATGAGGTAGGTGAC 59.534 60.000 0.00 0.00 0.00 3.67
892 911 0.691078 GGGGCTGATGAGGTAGGTGA 60.691 60.000 0.00 0.00 0.00 4.02
893 912 0.692419 AGGGGCTGATGAGGTAGGTG 60.692 60.000 0.00 0.00 0.00 4.00
894 913 0.044855 AAGGGGCTGATGAGGTAGGT 59.955 55.000 0.00 0.00 0.00 3.08
895 914 0.471617 CAAGGGGCTGATGAGGTAGG 59.528 60.000 0.00 0.00 0.00 3.18
896 915 0.179034 GCAAGGGGCTGATGAGGTAG 60.179 60.000 0.00 0.00 40.25 3.18
897 916 1.635817 GGCAAGGGGCTGATGAGGTA 61.636 60.000 0.00 0.00 44.01 3.08
898 917 2.679716 GCAAGGGGCTGATGAGGT 59.320 61.111 0.00 0.00 40.25 3.85
899 918 2.123982 GGCAAGGGGCTGATGAGG 60.124 66.667 0.00 0.00 44.01 3.86
900 919 1.751927 GTGGCAAGGGGCTGATGAG 60.752 63.158 0.00 0.00 44.01 2.90
901 920 2.356278 GTGGCAAGGGGCTGATGA 59.644 61.111 0.00 0.00 44.01 2.92
902 921 3.136123 CGTGGCAAGGGGCTGATG 61.136 66.667 0.00 0.00 44.01 3.07
917 936 2.980105 TTTTAAAGGGCACGGGGCGT 62.980 55.000 4.64 1.53 46.16 5.68
918 937 2.207788 CTTTTAAAGGGCACGGGGCG 62.208 60.000 4.64 0.00 46.16 6.13
919 938 1.589630 CTTTTAAAGGGCACGGGGC 59.410 57.895 0.65 0.65 43.74 5.80
920 939 2.272923 CCTTTTAAAGGGCACGGGG 58.727 57.895 15.55 0.00 45.27 5.73
929 948 0.598065 AGGTGCGCTGCCTTTTAAAG 59.402 50.000 16.43 0.00 31.04 1.85
932 951 1.674322 GGAGGTGCGCTGCCTTTTA 60.674 57.895 21.51 0.00 36.29 1.52
948 967 0.668535 ATGCTCGTGATCGAATCGGA 59.331 50.000 1.76 0.00 45.61 4.55
996 1015 1.647545 CGTGGGTGCGCATCATCTTT 61.648 55.000 24.30 0.00 0.00 2.52
1158 1178 2.348998 CCACTGGTGCAGGACTCC 59.651 66.667 0.00 0.00 35.51 3.85
1163 1183 4.641645 TTCCGCCACTGGTGCAGG 62.642 66.667 2.75 0.00 35.51 4.85
1164 1184 3.357079 GTTCCGCCACTGGTGCAG 61.357 66.667 2.75 0.00 37.52 4.41
1165 1185 4.947147 GGTTCCGCCACTGGTGCA 62.947 66.667 2.75 0.00 37.17 4.57
1166 1186 4.947147 TGGTTCCGCCACTGGTGC 62.947 66.667 2.75 0.00 43.61 5.01
1564 1586 2.879756 GCCTGGGCTCAATAGTCAACAA 60.880 50.000 4.12 0.00 38.26 2.83
1776 1875 0.740868 CGACAGTTGATGGCCGTGAT 60.741 55.000 0.00 0.00 30.50 3.06
1779 1878 2.742372 GCGACAGTTGATGGCCGT 60.742 61.111 0.00 0.00 30.50 5.68
2041 2225 4.730035 GCATATGTTCAGAGCAGAAGCAAC 60.730 45.833 4.29 0.00 45.49 4.17
2123 2368 7.565450 TCAGTTTGCAAACATATGATTTTCG 57.435 32.000 36.46 14.20 41.30 3.46
2469 4343 3.573967 TCTCTTTGGCAAAGATTTGGACC 59.426 43.478 35.33 1.97 45.75 4.46
2720 4594 6.264970 TCTTGAATGGTTTGATCAATGACACA 59.735 34.615 9.40 6.47 33.03 3.72
2806 4680 4.796038 AGAAGCAAATGAGTTGATTGGG 57.204 40.909 0.00 0.00 45.68 4.12
2873 4747 8.627403 CCTTATCAAATCTGTGCTTGATATGTT 58.373 33.333 5.58 0.00 41.69 2.71
3046 4920 9.692749 GTCGTCTCCATCAGTAAAATCAATATA 57.307 33.333 0.00 0.00 0.00 0.86
3062 4936 1.244816 TCAACACTCGTCGTCTCCAT 58.755 50.000 0.00 0.00 0.00 3.41
3066 4940 2.358267 ACTCTTTCAACACTCGTCGTCT 59.642 45.455 0.00 0.00 0.00 4.18
3374 5249 8.028938 AGTGTCAGACAAAATATGGCAAAATAC 58.971 33.333 4.32 0.00 40.75 1.89
3625 5518 0.234884 GGCGTTTCGAGTTCCAGTTG 59.765 55.000 0.00 0.00 0.00 3.16
3627 5520 1.663702 CGGCGTTTCGAGTTCCAGT 60.664 57.895 0.00 0.00 0.00 4.00
3637 5530 2.476499 GAAGCAGCTCGGCGTTTC 59.524 61.111 6.85 0.00 39.27 2.78
3774 5673 1.676968 CATCGGGGTGAAGGTGACA 59.323 57.895 0.00 0.00 0.00 3.58
3807 5709 3.457263 TAGCGATGCAGGGCGACA 61.457 61.111 10.12 0.00 0.00 4.35
3937 5839 2.420129 GGTGCTCCATGTTAAGGACGAT 60.420 50.000 0.00 0.00 34.96 3.73
4071 5976 0.591659 GGAAGAAAGGCACGTGTTCC 59.408 55.000 18.38 16.47 34.69 3.62
4074 5979 1.166531 GCTGGAAGAAAGGCACGTGT 61.167 55.000 18.38 0.00 34.07 4.49
4246 6152 9.249053 ACTGACATAGTAGCTATGCATACTAAT 57.751 33.333 10.34 13.33 45.33 1.73
4247 6153 8.515414 CACTGACATAGTAGCTATGCATACTAA 58.485 37.037 10.34 2.22 45.33 2.24
4248 6154 7.362142 GCACTGACATAGTAGCTATGCATACTA 60.362 40.741 14.06 5.92 45.33 1.82
4359 6265 4.325204 CCAACGACACTTATTTTCGATCGA 59.675 41.667 15.15 15.15 36.58 3.59
4363 6269 5.738118 AAACCAACGACACTTATTTTCGA 57.262 34.783 0.00 0.00 36.58 3.71
4364 6270 6.652245 ACTAAACCAACGACACTTATTTTCG 58.348 36.000 0.00 0.00 38.73 3.46
4419 6325 3.936372 AGCGACTAAAGCAAGTACTCA 57.064 42.857 0.00 0.00 37.01 3.41
4448 6355 3.706373 GCTTGGGAGCGACCTGGA 61.706 66.667 0.00 0.00 39.48 3.86
4499 7606 0.321996 GGGATTCGGTGGCTAGGATC 59.678 60.000 0.00 0.00 0.00 3.36
4512 7619 2.003548 AGGAGTGGCAGGGGGATTC 61.004 63.158 0.00 0.00 0.00 2.52
4620 7730 2.765807 CTGATGGGCGAGGAGGGT 60.766 66.667 0.00 0.00 0.00 4.34
4629 7739 1.525535 CTGCTGGTAGCTGATGGGC 60.526 63.158 0.00 0.00 41.94 5.36
4630 7740 1.147824 CCTGCTGGTAGCTGATGGG 59.852 63.158 8.95 0.00 41.94 4.00
4643 7754 4.335647 CCAACGCTGGGACCTGCT 62.336 66.667 16.53 3.24 39.30 4.24
4722 7834 1.446907 CAGATCAGACAGCCAACCAC 58.553 55.000 0.00 0.00 0.00 4.16
4725 7837 1.400846 CATGCAGATCAGACAGCCAAC 59.599 52.381 0.00 0.00 0.00 3.77
4726 7838 1.746470 CATGCAGATCAGACAGCCAA 58.254 50.000 0.00 0.00 0.00 4.52
4728 7840 0.746923 TGCATGCAGATCAGACAGCC 60.747 55.000 18.46 0.00 0.00 4.85
4737 7849 0.179702 AGGTCGACATGCATGCAGAT 59.820 50.000 26.69 16.32 0.00 2.90
4750 7862 0.904865 ACATCCAAGCCTCAGGTCGA 60.905 55.000 0.00 0.00 0.00 4.20
4753 7865 1.687612 CCACATCCAAGCCTCAGGT 59.312 57.895 0.00 0.00 0.00 4.00
4757 7869 0.895100 TTGTGCCACATCCAAGCCTC 60.895 55.000 0.00 0.00 0.00 4.70
4767 7879 0.254462 TTGTCTCCTGTTGTGCCACA 59.746 50.000 0.00 0.00 0.00 4.17
4831 7965 2.282816 CCCGGCACATCACCCAAA 60.283 61.111 0.00 0.00 0.00 3.28
4882 8016 0.542333 TCCCGACGCCAAATCCAATA 59.458 50.000 0.00 0.00 0.00 1.90
4885 8019 2.046700 GTCCCGACGCCAAATCCA 60.047 61.111 0.00 0.00 0.00 3.41
4926 8060 1.820906 CGCCATGGTCCACATCCAG 60.821 63.158 14.67 0.00 37.84 3.86
4929 8063 3.211963 GCCGCCATGGTCCACATC 61.212 66.667 14.67 0.00 37.84 3.06
4978 8112 4.301027 ACCATAGCGCGGCTAGCC 62.301 66.667 24.75 24.75 44.66 3.93
4993 8127 4.034048 CCGCAATACTTTGTAGTCATCACC 59.966 45.833 0.00 0.00 35.78 4.02
4994 8128 4.494199 GCCGCAATACTTTGTAGTCATCAC 60.494 45.833 0.00 0.00 35.78 3.06
4995 8129 3.621268 GCCGCAATACTTTGTAGTCATCA 59.379 43.478 0.00 0.00 35.78 3.07
4996 8130 3.302480 CGCCGCAATACTTTGTAGTCATC 60.302 47.826 0.00 0.00 35.78 2.92
4997 8131 2.607635 CGCCGCAATACTTTGTAGTCAT 59.392 45.455 0.00 0.00 35.78 3.06
4998 8132 1.996898 CGCCGCAATACTTTGTAGTCA 59.003 47.619 0.00 0.00 35.78 3.41
4999 8133 2.028883 GTCGCCGCAATACTTTGTAGTC 59.971 50.000 0.00 0.00 35.78 2.59
5000 8134 1.997606 GTCGCCGCAATACTTTGTAGT 59.002 47.619 0.00 0.00 38.44 2.73
5001 8135 2.268298 AGTCGCCGCAATACTTTGTAG 58.732 47.619 0.00 0.00 35.17 2.74
5002 8136 2.373540 AGTCGCCGCAATACTTTGTA 57.626 45.000 0.00 0.00 35.17 2.41
5003 8137 1.463444 GAAGTCGCCGCAATACTTTGT 59.537 47.619 4.73 0.00 33.72 2.83
5004 8138 1.202031 GGAAGTCGCCGCAATACTTTG 60.202 52.381 4.73 0.00 33.72 2.77
5005 8139 1.084289 GGAAGTCGCCGCAATACTTT 58.916 50.000 4.73 0.00 33.72 2.66
5006 8140 1.082117 CGGAAGTCGCCGCAATACTT 61.082 55.000 3.17 3.17 45.38 2.24
5007 8141 1.518572 CGGAAGTCGCCGCAATACT 60.519 57.895 0.00 0.00 45.38 2.12
5008 8142 3.003478 CGGAAGTCGCCGCAATAC 58.997 61.111 0.00 0.00 45.38 1.89
5017 8151 3.744719 TGGAGCGGTCGGAAGTCG 61.745 66.667 8.77 0.00 40.90 4.18
5018 8152 2.126031 GTGGAGCGGTCGGAAGTC 60.126 66.667 8.77 0.00 0.00 3.01
5019 8153 4.052229 CGTGGAGCGGTCGGAAGT 62.052 66.667 8.77 0.00 36.85 3.01
5020 8154 3.744719 TCGTGGAGCGGTCGGAAG 61.745 66.667 8.77 0.30 41.72 3.46
5021 8155 4.047059 GTCGTGGAGCGGTCGGAA 62.047 66.667 8.77 0.00 41.72 4.30
5024 8158 4.813526 CTCGTCGTGGAGCGGTCG 62.814 72.222 8.77 0.00 41.72 4.79
5025 8159 4.477975 CCTCGTCGTGGAGCGGTC 62.478 72.222 7.59 5.93 41.72 4.79
5027 8161 3.518998 ATCCTCGTCGTGGAGCGG 61.519 66.667 19.77 0.76 41.72 5.52
5028 8162 2.278206 CATCCTCGTCGTGGAGCG 60.278 66.667 19.77 10.74 43.01 5.03
5029 8163 2.105128 CCATCCTCGTCGTGGAGC 59.895 66.667 19.77 0.00 36.99 4.70
5030 8164 1.313091 TGACCATCCTCGTCGTGGAG 61.313 60.000 19.77 10.75 36.99 3.86
5031 8165 0.683179 ATGACCATCCTCGTCGTGGA 60.683 55.000 17.70 17.70 36.82 4.02
5032 8166 0.249073 GATGACCATCCTCGTCGTGG 60.249 60.000 7.02 7.02 38.96 4.94
5033 8167 0.592500 CGATGACCATCCTCGTCGTG 60.593 60.000 4.58 0.00 42.37 4.35
5034 8168 0.746923 TCGATGACCATCCTCGTCGT 60.747 55.000 9.86 0.00 45.82 4.34
5035 8169 0.380733 TTCGATGACCATCCTCGTCG 59.619 55.000 4.58 4.74 46.65 5.12
5036 8170 2.464865 CTTTCGATGACCATCCTCGTC 58.535 52.381 4.58 0.00 36.23 4.20
5037 8171 1.137086 CCTTTCGATGACCATCCTCGT 59.863 52.381 4.58 0.00 36.23 4.18
5038 8172 1.137086 ACCTTTCGATGACCATCCTCG 59.863 52.381 4.58 0.00 36.16 4.63
5039 8173 2.939103 CAACCTTTCGATGACCATCCTC 59.061 50.000 4.58 0.00 34.40 3.71
5040 8174 2.356125 CCAACCTTTCGATGACCATCCT 60.356 50.000 4.58 0.00 34.40 3.24
5041 8175 2.017049 CCAACCTTTCGATGACCATCC 58.983 52.381 4.58 0.00 34.40 3.51
5042 8176 2.017049 CCCAACCTTTCGATGACCATC 58.983 52.381 0.04 0.04 34.56 3.51
5043 8177 1.633432 TCCCAACCTTTCGATGACCAT 59.367 47.619 0.00 0.00 0.00 3.55
5044 8178 1.003118 CTCCCAACCTTTCGATGACCA 59.997 52.381 0.00 0.00 0.00 4.02
5045 8179 1.679032 CCTCCCAACCTTTCGATGACC 60.679 57.143 0.00 0.00 0.00 4.02
5046 8180 1.679032 CCCTCCCAACCTTTCGATGAC 60.679 57.143 0.00 0.00 0.00 3.06
5047 8181 0.618458 CCCTCCCAACCTTTCGATGA 59.382 55.000 0.00 0.00 0.00 2.92
5048 8182 0.394352 CCCCTCCCAACCTTTCGATG 60.394 60.000 0.00 0.00 0.00 3.84
5049 8183 0.845102 ACCCCTCCCAACCTTTCGAT 60.845 55.000 0.00 0.00 0.00 3.59
5050 8184 1.063654 AACCCCTCCCAACCTTTCGA 61.064 55.000 0.00 0.00 0.00 3.71
5051 8185 0.694196 TAACCCCTCCCAACCTTTCG 59.306 55.000 0.00 0.00 0.00 3.46
5052 8186 2.581246 AGATAACCCCTCCCAACCTTTC 59.419 50.000 0.00 0.00 0.00 2.62
5053 8187 2.581246 GAGATAACCCCTCCCAACCTTT 59.419 50.000 0.00 0.00 0.00 3.11
5054 8188 2.206223 GAGATAACCCCTCCCAACCTT 58.794 52.381 0.00 0.00 0.00 3.50
5055 8189 1.369983 AGAGATAACCCCTCCCAACCT 59.630 52.381 0.00 0.00 0.00 3.50
5056 8190 1.769465 GAGAGATAACCCCTCCCAACC 59.231 57.143 0.00 0.00 0.00 3.77
5057 8191 1.769465 GGAGAGATAACCCCTCCCAAC 59.231 57.143 0.00 0.00 40.35 3.77
5058 8192 1.657162 AGGAGAGATAACCCCTCCCAA 59.343 52.381 0.00 0.00 45.77 4.12
5059 8193 1.062121 CAGGAGAGATAACCCCTCCCA 60.062 57.143 0.00 0.00 45.77 4.37
5060 8194 1.220750 TCAGGAGAGATAACCCCTCCC 59.779 57.143 0.00 0.00 45.77 4.30
5061 8195 2.777459 TCAGGAGAGATAACCCCTCC 57.223 55.000 0.00 0.00 45.16 4.30
5062 8196 4.202409 CCAAATCAGGAGAGATAACCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
5063 8197 3.718956 CCAAATCAGGAGAGATAACCCCT 59.281 47.826 0.00 0.00 0.00 4.79
5064 8198 3.459969 ACCAAATCAGGAGAGATAACCCC 59.540 47.826 0.00 0.00 0.00 4.95
5065 8199 4.455606 CACCAAATCAGGAGAGATAACCC 58.544 47.826 0.00 0.00 0.00 4.11
5066 8200 4.080299 ACCACCAAATCAGGAGAGATAACC 60.080 45.833 0.00 0.00 0.00 2.85
5067 8201 5.104259 ACCACCAAATCAGGAGAGATAAC 57.896 43.478 0.00 0.00 0.00 1.89
5068 8202 5.250543 TCAACCACCAAATCAGGAGAGATAA 59.749 40.000 0.00 0.00 0.00 1.75
5069 8203 4.782691 TCAACCACCAAATCAGGAGAGATA 59.217 41.667 0.00 0.00 0.00 1.98
5070 8204 3.588842 TCAACCACCAAATCAGGAGAGAT 59.411 43.478 0.00 0.00 0.00 2.75
5071 8205 2.978978 TCAACCACCAAATCAGGAGAGA 59.021 45.455 0.00 0.00 0.00 3.10
5072 8206 3.077359 GTCAACCACCAAATCAGGAGAG 58.923 50.000 0.00 0.00 0.00 3.20
5073 8207 2.711009 AGTCAACCACCAAATCAGGAGA 59.289 45.455 0.00 0.00 0.00 3.71
5074 8208 3.146104 AGTCAACCACCAAATCAGGAG 57.854 47.619 0.00 0.00 0.00 3.69
5075 8209 3.117701 TGAAGTCAACCACCAAATCAGGA 60.118 43.478 0.00 0.00 0.00 3.86
5076 8210 3.221771 TGAAGTCAACCACCAAATCAGG 58.778 45.455 0.00 0.00 0.00 3.86
5077 8211 4.916983 TTGAAGTCAACCACCAAATCAG 57.083 40.909 0.00 0.00 0.00 2.90
5078 8212 4.039004 CCATTGAAGTCAACCACCAAATCA 59.961 41.667 0.00 0.00 38.86 2.57
5079 8213 4.039124 ACCATTGAAGTCAACCACCAAATC 59.961 41.667 0.00 0.00 38.86 2.17
5080 8214 3.966665 ACCATTGAAGTCAACCACCAAAT 59.033 39.130 0.00 0.00 38.86 2.32
5081 8215 3.131933 CACCATTGAAGTCAACCACCAAA 59.868 43.478 0.00 0.00 38.86 3.28
5082 8216 2.692557 CACCATTGAAGTCAACCACCAA 59.307 45.455 0.00 0.00 38.86 3.67
5083 8217 2.305928 CACCATTGAAGTCAACCACCA 58.694 47.619 0.00 0.00 38.86 4.17
5084 8218 1.000274 GCACCATTGAAGTCAACCACC 60.000 52.381 0.00 0.00 38.86 4.61
5085 8219 1.956477 AGCACCATTGAAGTCAACCAC 59.044 47.619 0.00 0.00 38.86 4.16
5086 8220 2.361757 CAAGCACCATTGAAGTCAACCA 59.638 45.455 0.00 0.00 38.86 3.67
5087 8221 2.622942 TCAAGCACCATTGAAGTCAACC 59.377 45.455 0.00 0.00 38.86 3.77
5088 8222 3.988379 TCAAGCACCATTGAAGTCAAC 57.012 42.857 0.00 0.00 38.86 3.18
5089 8223 3.305539 GCATCAAGCACCATTGAAGTCAA 60.306 43.478 0.00 0.00 42.21 3.18
5090 8224 2.229543 GCATCAAGCACCATTGAAGTCA 59.770 45.455 0.00 0.00 42.21 3.41
5091 8225 2.872370 GCATCAAGCACCATTGAAGTC 58.128 47.619 0.00 0.00 42.21 3.01


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

AutoCloner maintained by Alex Coulton.