Multiple sequence alignment - TraesCS6A01G302400

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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 TraesCS6A01G302400 chr6A 100.000 4611 0 0 1 4611 535986613 535982003 0.000000e+00 8516
1 TraesCS6A01G302400 chr6A 92.958 71 4 1 4251 4321 535982329 535982260 8.160000e-18 102
2 TraesCS6A01G302400 chr6A 92.958 71 4 1 4285 4354 535982363 535982293 8.160000e-18 102
3 TraesCS6A01G302400 chr6D 92.892 1829 79 23 997 2795 389593132 389591325 0.000000e+00 2610
4 TraesCS6A01G302400 chr6D 94.512 1312 57 7 2787 4096 389590038 389588740 0.000000e+00 2010
5 TraesCS6A01G302400 chr6D 83.602 805 102 15 6 783 287032123 287031322 0.000000e+00 728
6 TraesCS6A01G302400 chr6D 86.070 402 53 2 346 744 84636573 84636172 3.300000e-116 429
7 TraesCS6A01G302400 chr6D 90.741 324 16 12 4285 4603 389588494 389588180 1.980000e-113 420
8 TraesCS6A01G302400 chr6D 90.708 226 13 3 4096 4315 389588653 389588430 1.250000e-75 294
9 TraesCS6A01G302400 chr6D 86.239 109 12 3 807 914 10715186 10715292 1.050000e-21 115
10 TraesCS6A01G302400 chr6B 94.417 1612 56 11 2498 4096 582866942 582865352 0.000000e+00 2447
11 TraesCS6A01G302400 chr6B 92.203 1539 73 18 980 2499 582868576 582867066 0.000000e+00 2134
12 TraesCS6A01G302400 chr6B 82.152 818 110 10 2 783 447897370 447896553 0.000000e+00 669
13 TraesCS6A01G302400 chr6B 93.478 322 12 7 4285 4603 582829653 582829338 1.940000e-128 470
14 TraesCS6A01G302400 chr6B 90.840 131 3 3 4094 4216 582865277 582865148 2.850000e-37 167
15 TraesCS6A01G302400 chr2D 82.939 803 114 8 2 783 540168272 540167472 0.000000e+00 702
16 TraesCS6A01G302400 chr2D 82.598 793 108 12 2 777 139531360 139530581 0.000000e+00 673
17 TraesCS6A01G302400 chr2D 82.331 798 116 12 2 777 8475552 8476346 0.000000e+00 669
18 TraesCS6A01G302400 chr2D 92.593 81 4 2 807 886 518838880 518838959 1.050000e-21 115
19 TraesCS6A01G302400 chr2D 86.111 108 11 4 807 913 638288612 638288508 3.770000e-21 113
20 TraesCS6A01G302400 chrUn 82.826 821 101 14 2 783 86618308 86619127 0.000000e+00 699
21 TraesCS6A01G302400 chrUn 82.955 792 102 11 2 777 94848781 94849555 0.000000e+00 684
22 TraesCS6A01G302400 chrUn 83.558 371 45 4 2 356 129566683 129566313 2.660000e-87 333
23 TraesCS6A01G302400 chr1D 82.346 793 108 12 1 777 288838067 288838843 0.000000e+00 660
24 TraesCS6A01G302400 chr1D 82.809 413 56 7 2 399 401017179 401016767 5.670000e-94 355
25 TraesCS6A01G302400 chr7B 81.796 813 109 16 2 777 18214248 18215058 0.000000e+00 645
26 TraesCS6A01G302400 chr7B 82.609 230 40 0 1970 2199 100031520 100031291 2.170000e-48 204
27 TraesCS6A01G302400 chr5D 82.078 770 122 9 17 772 54095553 54096320 1.080000e-180 643
28 TraesCS6A01G302400 chr5D 90.361 83 7 1 807 889 360752226 360752145 1.750000e-19 108
29 TraesCS6A01G302400 chr2B 81.515 779 120 11 2 758 11219849 11220625 1.820000e-173 619
30 TraesCS6A01G302400 chr7D 80.952 798 134 7 2 783 571188019 571187224 2.360000e-172 616
31 TraesCS6A01G302400 chr7D 80.958 814 100 19 2 777 446366250 446365454 1.100000e-165 593
32 TraesCS6A01G302400 chr7D 83.262 233 39 0 1971 2203 136591883 136591651 1.000000e-51 215
33 TraesCS6A01G302400 chr7D 95.775 71 1 2 807 876 623704317 623704386 3.770000e-21 113
34 TraesCS6A01G302400 chr7D 91.463 82 5 2 807 886 500813127 500813208 1.360000e-20 111
35 TraesCS6A01G302400 chr7D 91.358 81 5 2 807 886 623691571 623691650 4.880000e-20 110
36 TraesCS6A01G302400 chr3A 80.929 818 114 20 6 783 174277494 174276679 3.940000e-170 608
37 TraesCS6A01G302400 chr7A 79.543 787 138 11 14 777 412723426 412724212 1.460000e-149 540
38 TraesCS6A01G302400 chr7A 91.228 171 15 0 2521 2691 136350083 136349913 2.770000e-57 233
39 TraesCS6A01G302400 chr7A 84.977 213 32 0 1987 2199 136350599 136350387 2.790000e-52 217
40 TraesCS6A01G302400 chr7A 86.207 145 18 2 1971 2114 136393523 136393380 6.180000e-34 156
41 TraesCS6A01G302400 chr3B 77.650 698 109 22 117 783 526077479 526076798 9.360000e-102 381
42 TraesCS6A01G302400 chr5A 92.208 77 4 2 810 885 37961458 37961533 1.750000e-19 108
43 TraesCS6A01G302400 chr5B 89.286 84 7 2 807 889 555126223 555126141 2.270000e-18 104


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 TraesCS6A01G302400 chr6A 535982003 535986613 4610 True 8516.000000 8516 100.000000 1 4611 1 chr6A.!!$R1 4610
1 TraesCS6A01G302400 chr6D 389588180 389593132 4952 True 1333.500000 2610 92.213250 997 4603 4 chr6D.!!$R3 3606
2 TraesCS6A01G302400 chr6D 287031322 287032123 801 True 728.000000 728 83.602000 6 783 1 chr6D.!!$R2 777
3 TraesCS6A01G302400 chr6B 582865148 582868576 3428 True 1582.666667 2447 92.486667 980 4216 3 chr6B.!!$R3 3236
4 TraesCS6A01G302400 chr6B 447896553 447897370 817 True 669.000000 669 82.152000 2 783 1 chr6B.!!$R1 781
5 TraesCS6A01G302400 chr2D 540167472 540168272 800 True 702.000000 702 82.939000 2 783 1 chr2D.!!$R2 781
6 TraesCS6A01G302400 chr2D 139530581 139531360 779 True 673.000000 673 82.598000 2 777 1 chr2D.!!$R1 775
7 TraesCS6A01G302400 chr2D 8475552 8476346 794 False 669.000000 669 82.331000 2 777 1 chr2D.!!$F1 775
8 TraesCS6A01G302400 chrUn 86618308 86619127 819 False 699.000000 699 82.826000 2 783 1 chrUn.!!$F1 781
9 TraesCS6A01G302400 chrUn 94848781 94849555 774 False 684.000000 684 82.955000 2 777 1 chrUn.!!$F2 775
10 TraesCS6A01G302400 chr1D 288838067 288838843 776 False 660.000000 660 82.346000 1 777 1 chr1D.!!$F1 776
11 TraesCS6A01G302400 chr7B 18214248 18215058 810 False 645.000000 645 81.796000 2 777 1 chr7B.!!$F1 775
12 TraesCS6A01G302400 chr5D 54095553 54096320 767 False 643.000000 643 82.078000 17 772 1 chr5D.!!$F1 755
13 TraesCS6A01G302400 chr2B 11219849 11220625 776 False 619.000000 619 81.515000 2 758 1 chr2B.!!$F1 756
14 TraesCS6A01G302400 chr7D 571187224 571188019 795 True 616.000000 616 80.952000 2 783 1 chr7D.!!$R3 781
15 TraesCS6A01G302400 chr7D 446365454 446366250 796 True 593.000000 593 80.958000 2 777 1 chr7D.!!$R2 775
16 TraesCS6A01G302400 chr3A 174276679 174277494 815 True 608.000000 608 80.929000 6 783 1 chr3A.!!$R1 777
17 TraesCS6A01G302400 chr7A 412723426 412724212 786 False 540.000000 540 79.543000 14 777 1 chr7A.!!$F1 763
18 TraesCS6A01G302400 chr7A 136349913 136350599 686 True 225.000000 233 88.102500 1987 2691 2 chr7A.!!$R2 704
19 TraesCS6A01G302400 chr3B 526076798 526077479 681 True 381.000000 381 77.650000 117 783 1 chr3B.!!$R1 666

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
924 991 0.034337 GTTTGTGGGACGGCTGTAGA 59.966 55.0 0.0 0.0 0.00 2.59 F
1620 1720 0.107703 TCAATCGACCATGTGAGGGC 60.108 55.0 0.0 0.0 0.00 5.19 F
1774 1874 1.123655 GCTTTGTTTCAGCAACGAGC 58.876 50.0 0.0 0.0 46.19 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1849 0.525242 TGCTGAAACAAAGCGCACAC 60.525 50.000 11.47 0.00 43.88 3.82 R
2579 2811 1.791555 CGACGCCATTCATGAACTTGC 60.792 52.381 11.07 12.33 0.00 4.01 R
3758 5300 1.078759 GCATGTTCGACGAGTGAGGG 61.079 60.000 0.00 0.00 0.00 4.30 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
115 116 3.136123 GTCCGGATCCGTCGACCA 61.136 66.667 31.22 6.25 37.81 4.02
144 145 2.342279 CGTGCGGGTTGGAGAAGA 59.658 61.111 0.00 0.00 0.00 2.87
152 161 2.437413 GGGTTGGAGAAGACAATGGTC 58.563 52.381 0.00 0.00 44.66 4.02
190 201 2.283529 GCTCCTGGGAGGACAACGA 61.284 63.158 17.16 0.00 40.06 3.85
366 409 1.226262 GAAAGGATAAGGGCCGCCA 59.774 57.895 12.58 0.00 0.00 5.69
370 413 2.595655 GATAAGGGCCGCCAAGGT 59.404 61.111 12.58 0.00 43.70 3.50
433 497 2.812499 GGAAGCCATCCGCGTCTA 59.188 61.111 4.92 0.00 44.50 2.59
439 503 1.934463 CCATCCGCGTCTACATTGC 59.066 57.895 4.92 0.00 0.00 3.56
457 521 0.788391 GCGAAGAAACGACAACGGAT 59.212 50.000 0.00 0.00 44.46 4.18
458 522 1.193874 GCGAAGAAACGACAACGGATT 59.806 47.619 0.00 0.00 44.46 3.01
498 562 1.817099 GAGCAGAATGGGGCTGTCG 60.817 63.158 0.00 0.00 41.22 4.35
580 645 2.024871 CGACGAGCAGATCCGACC 59.975 66.667 0.00 0.00 0.00 4.79
635 700 1.179814 AGAAGGACGACAAGGACGCT 61.180 55.000 0.00 0.00 0.00 5.07
668 733 1.450312 CAGCCGTGGATGAACTCCC 60.450 63.158 0.00 0.00 44.23 4.30
676 741 1.488812 TGGATGAACTCCCCCATAACG 59.511 52.381 0.00 0.00 44.23 3.18
678 743 2.224305 GGATGAACTCCCCCATAACGAG 60.224 54.545 0.00 0.00 38.19 4.18
692 758 4.799949 CCATAACGAGACATGCCAAATTTG 59.200 41.667 11.40 11.40 0.00 2.32
730 797 6.018669 GCATGTTTAGTTAGTAGTGATGGAGC 60.019 42.308 0.00 0.00 0.00 4.70
736 803 0.684479 AGTAGTGATGGAGCAGCCGA 60.684 55.000 0.00 0.00 40.66 5.54
765 832 9.119056 GATGTATGTGCATCGACGTAGTTGTAC 62.119 44.444 16.86 16.86 43.74 2.90
783 850 7.208080 AGTTGTACGAGTTTCTATGAGTTTGT 58.792 34.615 0.00 0.00 0.00 2.83
784 851 7.709613 AGTTGTACGAGTTTCTATGAGTTTGTT 59.290 33.333 0.00 0.00 0.00 2.83
785 852 7.402811 TGTACGAGTTTCTATGAGTTTGTTG 57.597 36.000 0.00 0.00 0.00 3.33
786 853 5.924475 ACGAGTTTCTATGAGTTTGTTGG 57.076 39.130 0.00 0.00 0.00 3.77
787 854 5.607477 ACGAGTTTCTATGAGTTTGTTGGA 58.393 37.500 0.00 0.00 0.00 3.53
788 855 6.231211 ACGAGTTTCTATGAGTTTGTTGGAT 58.769 36.000 0.00 0.00 0.00 3.41
789 856 6.710744 ACGAGTTTCTATGAGTTTGTTGGATT 59.289 34.615 0.00 0.00 0.00 3.01
790 857 7.228706 ACGAGTTTCTATGAGTTTGTTGGATTT 59.771 33.333 0.00 0.00 0.00 2.17
791 858 8.076178 CGAGTTTCTATGAGTTTGTTGGATTTT 58.924 33.333 0.00 0.00 0.00 1.82
792 859 9.750125 GAGTTTCTATGAGTTTGTTGGATTTTT 57.250 29.630 0.00 0.00 0.00 1.94
829 896 9.958180 TTAGAGTTTGTTGGATTTGAGATATGA 57.042 29.630 0.00 0.00 0.00 2.15
844 911 7.631717 TGAGATATGATAATAGAGGTGTCCG 57.368 40.000 0.00 0.00 0.00 4.79
845 912 6.603599 TGAGATATGATAATAGAGGTGTCCGG 59.396 42.308 0.00 0.00 0.00 5.14
846 913 6.732487 AGATATGATAATAGAGGTGTCCGGA 58.268 40.000 0.00 0.00 0.00 5.14
847 914 7.358263 AGATATGATAATAGAGGTGTCCGGAT 58.642 38.462 7.81 0.00 0.00 4.18
848 915 5.667539 ATGATAATAGAGGTGTCCGGATG 57.332 43.478 7.81 0.00 0.00 3.51
849 916 4.480115 TGATAATAGAGGTGTCCGGATGT 58.520 43.478 7.81 0.00 0.00 3.06
850 917 4.280929 TGATAATAGAGGTGTCCGGATGTG 59.719 45.833 7.81 0.00 0.00 3.21
851 918 1.414158 ATAGAGGTGTCCGGATGTGG 58.586 55.000 7.81 0.00 0.00 4.17
852 919 0.333652 TAGAGGTGTCCGGATGTGGA 59.666 55.000 7.81 0.00 35.04 4.02
853 920 0.325671 AGAGGTGTCCGGATGTGGAT 60.326 55.000 7.81 0.00 40.91 3.41
854 921 0.541863 GAGGTGTCCGGATGTGGATT 59.458 55.000 7.81 0.00 40.91 3.01
855 922 1.760613 GAGGTGTCCGGATGTGGATTA 59.239 52.381 7.81 0.00 40.91 1.75
856 923 1.485066 AGGTGTCCGGATGTGGATTAC 59.515 52.381 7.81 0.00 40.91 1.89
857 924 1.208535 GGTGTCCGGATGTGGATTACA 59.791 52.381 7.81 0.00 44.87 2.41
871 938 6.987557 TGTGGATTACATTATTTAAGGGGGT 58.012 36.000 0.00 0.00 33.42 4.95
872 939 6.836527 TGTGGATTACATTATTTAAGGGGGTG 59.163 38.462 0.00 0.00 33.42 4.61
873 940 6.837048 GTGGATTACATTATTTAAGGGGGTGT 59.163 38.462 0.00 0.00 0.00 4.16
874 941 7.013942 GTGGATTACATTATTTAAGGGGGTGTC 59.986 40.741 0.00 0.00 0.00 3.67
875 942 6.492429 GGATTACATTATTTAAGGGGGTGTCC 59.508 42.308 0.00 0.00 0.00 4.02
876 943 3.893521 ACATTATTTAAGGGGGTGTCCG 58.106 45.455 0.00 0.00 36.01 4.79
877 944 3.219281 CATTATTTAAGGGGGTGTCCGG 58.781 50.000 0.00 0.00 36.01 5.14
878 945 1.969713 TATTTAAGGGGGTGTCCGGT 58.030 50.000 0.00 0.00 36.01 5.28
879 946 0.622136 ATTTAAGGGGGTGTCCGGTC 59.378 55.000 0.00 0.00 36.01 4.79
880 947 1.829523 TTTAAGGGGGTGTCCGGTCG 61.830 60.000 0.00 0.00 36.01 4.79
908 975 3.788766 GTGCATCCGCGAGCGTTT 61.789 61.111 8.23 0.17 42.97 3.60
909 976 3.787676 TGCATCCGCGAGCGTTTG 61.788 61.111 8.23 13.36 42.97 2.93
910 977 3.788766 GCATCCGCGAGCGTTTGT 61.789 61.111 8.23 0.00 37.81 2.83
911 978 2.096406 CATCCGCGAGCGTTTGTG 59.904 61.111 8.23 5.65 37.81 3.33
912 979 3.118454 ATCCGCGAGCGTTTGTGG 61.118 61.111 8.23 12.62 39.38 4.17
915 982 4.072088 CGCGAGCGTTTGTGGGAC 62.072 66.667 0.00 0.00 34.35 4.46
916 983 4.072088 GCGAGCGTTTGTGGGACG 62.072 66.667 0.00 0.00 43.04 4.79
917 984 3.411351 CGAGCGTTTGTGGGACGG 61.411 66.667 0.00 0.00 40.66 4.79
918 985 3.723348 GAGCGTTTGTGGGACGGC 61.723 66.667 0.00 0.00 40.66 5.68
919 986 4.250305 AGCGTTTGTGGGACGGCT 62.250 61.111 0.00 0.00 40.66 5.52
920 987 4.025401 GCGTTTGTGGGACGGCTG 62.025 66.667 0.00 0.00 40.66 4.85
921 988 2.590575 CGTTTGTGGGACGGCTGT 60.591 61.111 0.00 0.00 36.90 4.40
922 989 1.301087 CGTTTGTGGGACGGCTGTA 60.301 57.895 0.00 0.00 36.90 2.74
923 990 1.289109 CGTTTGTGGGACGGCTGTAG 61.289 60.000 0.00 0.00 36.90 2.74
924 991 0.034337 GTTTGTGGGACGGCTGTAGA 59.966 55.000 0.00 0.00 0.00 2.59
925 992 0.981183 TTTGTGGGACGGCTGTAGAT 59.019 50.000 0.00 0.00 0.00 1.98
926 993 0.249120 TTGTGGGACGGCTGTAGATG 59.751 55.000 0.00 0.00 0.00 2.90
927 994 1.521681 GTGGGACGGCTGTAGATGC 60.522 63.158 0.00 0.00 0.00 3.91
928 995 1.685765 TGGGACGGCTGTAGATGCT 60.686 57.895 0.00 0.00 0.00 3.79
929 996 1.227380 GGGACGGCTGTAGATGCTG 60.227 63.158 0.00 0.00 42.11 4.41
933 1000 2.586258 ACGGCTGTAGATGCTGTAAG 57.414 50.000 0.00 0.00 46.77 2.34
950 1017 6.880822 CTGTAAGCTACGTTATGTTAGCAA 57.119 37.500 8.35 0.00 37.97 3.91
951 1018 6.880822 TGTAAGCTACGTTATGTTAGCAAG 57.119 37.500 8.35 0.00 37.97 4.01
952 1019 6.392354 TGTAAGCTACGTTATGTTAGCAAGT 58.608 36.000 8.35 0.00 37.97 3.16
953 1020 6.869913 TGTAAGCTACGTTATGTTAGCAAGTT 59.130 34.615 8.35 0.00 37.97 2.66
954 1021 6.796705 AAGCTACGTTATGTTAGCAAGTTT 57.203 33.333 8.35 0.00 37.97 2.66
955 1022 7.894376 AAGCTACGTTATGTTAGCAAGTTTA 57.106 32.000 8.35 0.00 37.97 2.01
956 1023 8.488651 AAGCTACGTTATGTTAGCAAGTTTAT 57.511 30.769 8.35 0.00 37.97 1.40
957 1024 9.590451 AAGCTACGTTATGTTAGCAAGTTTATA 57.410 29.630 8.35 0.00 37.97 0.98
958 1025 9.590451 AGCTACGTTATGTTAGCAAGTTTATAA 57.410 29.630 8.35 0.00 37.97 0.98
959 1026 9.845305 GCTACGTTATGTTAGCAAGTTTATAAG 57.155 33.333 0.00 0.00 35.76 1.73
962 1029 8.601476 ACGTTATGTTAGCAAGTTTATAAGAGC 58.399 33.333 0.00 0.00 0.00 4.09
963 1030 8.600625 CGTTATGTTAGCAAGTTTATAAGAGCA 58.399 33.333 0.00 0.00 0.00 4.26
967 1034 8.560355 TGTTAGCAAGTTTATAAGAGCAATCA 57.440 30.769 0.00 0.00 0.00 2.57
968 1035 8.450964 TGTTAGCAAGTTTATAAGAGCAATCAC 58.549 33.333 0.00 0.00 0.00 3.06
969 1036 6.442513 AGCAAGTTTATAAGAGCAATCACC 57.557 37.500 0.00 0.00 0.00 4.02
970 1037 6.183347 AGCAAGTTTATAAGAGCAATCACCT 58.817 36.000 0.00 0.00 0.00 4.00
971 1038 6.317391 AGCAAGTTTATAAGAGCAATCACCTC 59.683 38.462 0.00 0.00 0.00 3.85
972 1039 6.458888 GCAAGTTTATAAGAGCAATCACCTCC 60.459 42.308 0.00 0.00 0.00 4.30
973 1040 5.685728 AGTTTATAAGAGCAATCACCTCCC 58.314 41.667 0.00 0.00 0.00 4.30
974 1041 4.706842 TTATAAGAGCAATCACCTCCCC 57.293 45.455 0.00 0.00 0.00 4.81
975 1042 1.965414 TAAGAGCAATCACCTCCCCA 58.035 50.000 0.00 0.00 0.00 4.96
976 1043 1.075601 AAGAGCAATCACCTCCCCAA 58.924 50.000 0.00 0.00 0.00 4.12
977 1044 1.075601 AGAGCAATCACCTCCCCAAA 58.924 50.000 0.00 0.00 0.00 3.28
978 1045 1.428912 AGAGCAATCACCTCCCCAAAA 59.571 47.619 0.00 0.00 0.00 2.44
979 1046 2.158325 AGAGCAATCACCTCCCCAAAAA 60.158 45.455 0.00 0.00 0.00 1.94
1016 1083 3.317744 TCGCATGAATTTACGCACATC 57.682 42.857 0.00 0.00 0.00 3.06
1018 1085 3.031126 CGCATGAATTTACGCACATCTG 58.969 45.455 0.00 0.00 0.00 2.90
1064 1134 0.538584 CTAAGACCGGTACCAACCCC 59.461 60.000 7.34 0.00 43.54 4.95
1075 1150 2.357034 CAACCCCTGTCACGGTCG 60.357 66.667 0.00 0.00 0.00 4.79
1169 1256 3.208383 CGCAACCACACCTGCACA 61.208 61.111 0.00 0.00 38.52 4.57
1170 1257 2.769539 CGCAACCACACCTGCACAA 61.770 57.895 0.00 0.00 38.52 3.33
1172 1259 1.383456 GCAACCACACCTGCACAAGA 61.383 55.000 0.00 0.00 38.48 3.02
1175 1262 1.095228 ACCACACCTGCACAAGAACG 61.095 55.000 0.00 0.00 0.00 3.95
1176 1263 1.648720 CACACCTGCACAAGAACGG 59.351 57.895 0.00 0.00 0.00 4.44
1177 1264 2.186826 ACACCTGCACAAGAACGGC 61.187 57.895 0.00 0.00 0.00 5.68
1178 1265 2.594592 ACCTGCACAAGAACGGCC 60.595 61.111 0.00 0.00 0.00 6.13
1179 1266 3.365265 CCTGCACAAGAACGGCCC 61.365 66.667 0.00 0.00 0.00 5.80
1180 1267 3.365265 CTGCACAAGAACGGCCCC 61.365 66.667 0.00 0.00 0.00 5.80
1183 1270 2.281208 CACAAGAACGGCCCCGAA 60.281 61.111 14.44 0.00 42.83 4.30
1184 1271 1.894756 CACAAGAACGGCCCCGAAA 60.895 57.895 14.44 0.00 42.83 3.46
1185 1272 1.152922 ACAAGAACGGCCCCGAAAA 60.153 52.632 14.44 0.00 42.83 2.29
1186 1273 1.170290 ACAAGAACGGCCCCGAAAAG 61.170 55.000 14.44 2.04 42.83 2.27
1552 1652 1.743252 CGCTCCCTGTTGCTCTTCC 60.743 63.158 0.00 0.00 0.00 3.46
1567 1667 4.009002 GCTCTTCCTTGATCTCTTTTGCT 58.991 43.478 0.00 0.00 0.00 3.91
1591 1691 4.142708 TGCTTATTTTGATTCGATGCGTGT 60.143 37.500 0.00 0.00 0.00 4.49
1620 1720 0.107703 TCAATCGACCATGTGAGGGC 60.108 55.000 0.00 0.00 0.00 5.19
1623 1723 1.496060 ATCGACCATGTGAGGGCTTA 58.504 50.000 0.00 0.00 33.12 3.09
1640 1740 3.751698 GGCTTACTAACCTTGGTGTTCTG 59.248 47.826 0.00 0.00 0.00 3.02
1646 1746 2.052782 ACCTTGGTGTTCTGTTGTCC 57.947 50.000 0.00 0.00 0.00 4.02
1684 1784 3.771491 GCGTGCACGTCTCAGCAG 61.771 66.667 36.80 9.58 42.14 4.24
1774 1874 1.123655 GCTTTGTTTCAGCAACGAGC 58.876 50.000 0.00 0.00 46.19 5.03
1831 1931 1.978624 CGTCGAATTCGCAATCTTCG 58.021 50.000 22.90 13.10 42.24 3.79
2162 2267 2.887568 CGTGCTCAGATGACCGCC 60.888 66.667 0.00 0.00 0.00 6.13
2300 2407 6.611613 ATTTAGAGGTCTTCATGTCTGTGA 57.388 37.500 0.00 0.00 0.00 3.58
2302 2409 7.718334 TTTAGAGGTCTTCATGTCTGTGATA 57.282 36.000 0.00 0.00 0.00 2.15
2303 2410 7.718334 TTAGAGGTCTTCATGTCTGTGATAA 57.282 36.000 0.00 0.00 0.00 1.75
2304 2411 6.805016 AGAGGTCTTCATGTCTGTGATAAT 57.195 37.500 0.00 0.00 0.00 1.28
2305 2412 7.904558 AGAGGTCTTCATGTCTGTGATAATA 57.095 36.000 0.00 0.00 0.00 0.98
2579 2811 2.094854 GGCTGATCTGTTTGGCAAAGAG 60.095 50.000 26.25 26.25 33.39 2.85
2725 2958 8.364142 TGTTAATTTAGTTGGATCTTTGGTTGG 58.636 33.333 0.00 0.00 0.00 3.77
2738 2971 3.806949 TTGGTTGGAGATGGTTTAGCT 57.193 42.857 0.00 0.00 0.00 3.32
2751 2985 3.149981 GGTTTAGCTTGTCTCTTGGCTT 58.850 45.455 0.00 0.00 36.40 4.35
3059 4588 5.359009 CCAATCAGCCATGTTTTAGTGAGAT 59.641 40.000 0.00 0.00 0.00 2.75
3060 4589 6.543465 CCAATCAGCCATGTTTTAGTGAGATA 59.457 38.462 0.00 0.00 0.00 1.98
3061 4590 7.412853 CAATCAGCCATGTTTTAGTGAGATAC 58.587 38.462 0.00 0.00 0.00 2.24
3062 4591 6.299805 TCAGCCATGTTTTAGTGAGATACT 57.700 37.500 0.00 0.00 43.56 2.12
3063 4592 6.108687 TCAGCCATGTTTTAGTGAGATACTG 58.891 40.000 0.00 0.00 40.65 2.74
3086 4615 7.595502 ACTGTAGATACTAATGCATTAAGACGC 59.404 37.037 19.32 8.72 0.00 5.19
3087 4616 6.866770 TGTAGATACTAATGCATTAAGACGCC 59.133 38.462 19.32 7.60 0.00 5.68
3090 4619 6.647067 AGATACTAATGCATTAAGACGCCTTC 59.353 38.462 19.32 8.49 33.94 3.46
3119 4648 2.450609 TAAGCCTTGAGTTGTCGACC 57.549 50.000 14.12 0.00 0.00 4.79
3246 4777 9.377312 GAGTCTTCTCTATTTTCTAACTGCAAT 57.623 33.333 0.00 0.00 37.68 3.56
3282 4813 7.287950 CAACAAAATGCTGATTTCATGTTCAG 58.712 34.615 14.60 14.60 41.84 3.02
3364 4895 2.742589 AGAAGCTAAAGCAACTAACGGC 59.257 45.455 4.54 0.00 45.16 5.68
3405 4936 6.346838 CCAAGCAAAACTATAAAACAGCAAGC 60.347 38.462 0.00 0.00 0.00 4.01
3466 5005 9.264719 TCTTATATGTGTGCAGATCAATACTTG 57.735 33.333 0.00 0.00 0.00 3.16
3622 5161 3.194116 TGGATCAGTAAGACGGTAACCAC 59.806 47.826 0.00 0.00 0.00 4.16
3747 5289 0.519519 TTATTTTGCAGCGGTGGTCG 59.480 50.000 17.54 0.00 42.76 4.79
3748 5290 0.320858 TATTTTGCAGCGGTGGTCGA 60.321 50.000 17.54 0.00 42.43 4.20
3749 5291 1.852067 ATTTTGCAGCGGTGGTCGAC 61.852 55.000 17.54 7.13 42.43 4.20
3750 5292 2.933878 TTTTGCAGCGGTGGTCGACT 62.934 55.000 17.54 0.00 42.43 4.18
3751 5293 3.858868 TTGCAGCGGTGGTCGACTC 62.859 63.158 17.54 8.99 42.43 3.36
3758 5300 2.126424 GTGGTCGACTCGAGGCAC 60.126 66.667 20.47 15.04 36.23 5.01
3787 5329 2.083774 GTCGAACATGCATTTCTCCCA 58.916 47.619 0.00 0.00 0.00 4.37
3832 5374 7.713750 TCACATACTATTGAGCACTAGTAACC 58.286 38.462 10.48 0.00 34.27 2.85
3874 5416 2.634940 TGCAGTTTGTAGCTTCTCCTCT 59.365 45.455 0.00 0.00 0.00 3.69
3908 5450 2.161855 CCATTGCAGCTTGTAACAGGA 58.838 47.619 0.00 0.00 0.00 3.86
3922 5464 7.519032 TTGTAACAGGAAAATGTAGGGAAAG 57.481 36.000 0.00 0.00 31.70 2.62
3931 5473 6.486993 GGAAAATGTAGGGAAAGTATAGGCTG 59.513 42.308 0.00 0.00 0.00 4.85
3969 5511 6.796785 AAATGGGGATAAAATTCTGGTCAG 57.203 37.500 0.00 0.00 0.00 3.51
3974 5516 5.437060 GGGATAAAATTCTGGTCAGCAGTA 58.563 41.667 3.23 0.00 0.00 2.74
4004 5546 4.105697 ACTCCTTTTGTTCCCCACATTCTA 59.894 41.667 0.00 0.00 34.43 2.10
4023 5565 5.996669 TCTATAGATGCGACTTTACGACA 57.003 39.130 0.00 0.00 35.09 4.35
4027 5569 3.650139 AGATGCGACTTTACGACAACTT 58.350 40.909 0.00 0.00 35.09 2.66
4083 5625 5.580691 GTCAGAAATGATACCGTGTGATCAA 59.419 40.000 0.00 0.00 35.76 2.57
4092 5634 6.315144 TGATACCGTGTGATCAAAACAATAGG 59.685 38.462 0.00 0.00 0.00 2.57
4149 5784 1.091537 TATAAGCAACACAAGCGCCC 58.908 50.000 2.29 0.00 37.01 6.13
4162 5797 4.864334 CGCCCAGCCCAGATCACC 62.864 72.222 0.00 0.00 0.00 4.02
4217 5854 1.466025 TTTTGGCCCAGCTTCAGCAG 61.466 55.000 0.00 0.00 45.16 4.24
4245 5882 2.544277 GGCCGGGTTACAGAAAACAAAC 60.544 50.000 2.18 0.00 0.00 2.93
4249 5886 4.036971 CCGGGTTACAGAAAACAAACATGA 59.963 41.667 0.00 0.00 0.00 3.07
4285 5922 5.712152 AAAAACTGTTAGCCTTGATCCAG 57.288 39.130 0.00 0.00 0.00 3.86
4286 5923 4.640771 AAACTGTTAGCCTTGATCCAGA 57.359 40.909 0.00 0.00 0.00 3.86
4287 5924 3.902881 ACTGTTAGCCTTGATCCAGAG 57.097 47.619 0.00 0.00 0.00 3.35
4288 5925 3.445008 ACTGTTAGCCTTGATCCAGAGA 58.555 45.455 0.00 0.00 0.00 3.10
4289 5926 3.840666 ACTGTTAGCCTTGATCCAGAGAA 59.159 43.478 0.00 0.00 0.00 2.87
4290 5927 4.287067 ACTGTTAGCCTTGATCCAGAGAAA 59.713 41.667 0.00 0.00 0.00 2.52
4291 5928 4.836825 TGTTAGCCTTGATCCAGAGAAAG 58.163 43.478 0.00 0.00 0.00 2.62
4292 5929 4.532126 TGTTAGCCTTGATCCAGAGAAAGA 59.468 41.667 0.00 0.00 0.00 2.52
4293 5930 5.190528 TGTTAGCCTTGATCCAGAGAAAGAT 59.809 40.000 0.00 0.00 0.00 2.40
4294 5931 4.858965 AGCCTTGATCCAGAGAAAGATT 57.141 40.909 0.00 0.00 0.00 2.40
4295 5932 5.965033 AGCCTTGATCCAGAGAAAGATTA 57.035 39.130 0.00 0.00 0.00 1.75
4296 5933 5.927819 AGCCTTGATCCAGAGAAAGATTAG 58.072 41.667 0.00 0.00 0.00 1.73
4297 5934 5.664908 AGCCTTGATCCAGAGAAAGATTAGA 59.335 40.000 0.00 0.00 0.00 2.10
4298 5935 6.157645 AGCCTTGATCCAGAGAAAGATTAGAA 59.842 38.462 0.00 0.00 0.00 2.10
4299 5936 6.825721 GCCTTGATCCAGAGAAAGATTAGAAA 59.174 38.462 0.00 0.00 0.00 2.52
4300 5937 7.337942 GCCTTGATCCAGAGAAAGATTAGAAAA 59.662 37.037 0.00 0.00 0.00 2.29
4301 5938 8.672815 CCTTGATCCAGAGAAAGATTAGAAAAC 58.327 37.037 0.00 0.00 0.00 2.43
4302 5939 9.447157 CTTGATCCAGAGAAAGATTAGAAAACT 57.553 33.333 0.00 0.00 0.00 2.66
4303 5940 8.783833 TGATCCAGAGAAAGATTAGAAAACTG 57.216 34.615 0.00 0.00 0.00 3.16
4304 5941 8.378565 TGATCCAGAGAAAGATTAGAAAACTGT 58.621 33.333 0.00 0.00 0.00 3.55
4305 5942 9.225436 GATCCAGAGAAAGATTAGAAAACTGTT 57.775 33.333 0.00 0.00 0.00 3.16
4332 5969 6.825721 GCCTTGATCCAGAGAAAGATTAGAAA 59.174 38.462 0.00 0.00 0.00 2.52
4351 5990 3.904136 AAACTGTTTGCCTCGATTCAG 57.096 42.857 4.73 0.00 0.00 3.02
4403 6042 2.354821 GCGTCTGAAGTTGGAAAAGTGT 59.645 45.455 0.00 0.00 0.00 3.55
4404 6043 3.788797 GCGTCTGAAGTTGGAAAAGTGTG 60.789 47.826 0.00 0.00 0.00 3.82
4451 6090 0.753867 TGAGGTCAACGTTGGCACTA 59.246 50.000 31.79 15.43 33.59 2.74
4455 6094 1.732259 GGTCAACGTTGGCACTAGATG 59.268 52.381 31.79 2.56 33.59 2.90
4461 6100 3.686016 ACGTTGGCACTAGATGGAAAAT 58.314 40.909 0.00 0.00 0.00 1.82
4480 6119 0.610687 TATGCACCGTCCACATGTGA 59.389 50.000 27.46 10.46 31.66 3.58
4512 6151 3.070159 TGAGCTGGCACATCTTATCTACC 59.930 47.826 0.00 0.00 33.65 3.18
4516 6155 4.214971 GCTGGCACATCTTATCTACCAATG 59.785 45.833 0.00 0.00 38.20 2.82
4518 6157 3.503748 GGCACATCTTATCTACCAATGCC 59.496 47.826 0.00 0.00 42.93 4.40
4531 6170 0.667184 CAATGCCCGCTGTTTTGACC 60.667 55.000 0.00 0.00 0.00 4.02
4533 6172 1.526575 ATGCCCGCTGTTTTGACCTG 61.527 55.000 0.00 0.00 0.00 4.00
4534 6173 2.193536 GCCCGCTGTTTTGACCTGT 61.194 57.895 0.00 0.00 0.00 4.00
4536 6175 0.310854 CCCGCTGTTTTGACCTGTTC 59.689 55.000 0.00 0.00 0.00 3.18
4537 6176 1.021202 CCGCTGTTTTGACCTGTTCA 58.979 50.000 0.00 0.00 0.00 3.18
4539 6178 2.034558 CCGCTGTTTTGACCTGTTCATT 59.965 45.455 0.00 0.00 32.84 2.57
4540 6179 3.300009 CGCTGTTTTGACCTGTTCATTC 58.700 45.455 0.00 0.00 32.84 2.67
4603 6244 3.181503 GCATGCATCTCTTCGTGACATTT 60.182 43.478 14.21 0.00 0.00 2.32
4604 6245 4.673580 GCATGCATCTCTTCGTGACATTTT 60.674 41.667 14.21 0.00 0.00 1.82
4605 6246 5.396484 CATGCATCTCTTCGTGACATTTTT 58.604 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 0.036388 ATGCGGACGACCATTGTCTT 60.036 50.000 4.48 0.00 39.47 3.01
144 145 1.922135 GCAATGCGGACGACCATTGT 61.922 55.000 18.96 0.00 46.15 2.71
152 161 3.853330 CGGAGTGCAATGCGGACG 61.853 66.667 20.64 0.00 41.69 4.79
335 377 3.431725 CTTTCTTCCCACGGCGGC 61.432 66.667 13.24 0.00 0.00 6.53
349 391 0.395724 CTTGGCGGCCCTTATCCTTT 60.396 55.000 17.97 0.00 0.00 3.11
411 475 1.327690 ACGCGGATGGCTTCCTCTTA 61.328 55.000 12.47 0.00 42.99 2.10
413 477 3.077556 ACGCGGATGGCTTCCTCT 61.078 61.111 12.47 0.00 42.99 3.69
433 497 2.598907 CGTTGTCGTTTCTTCGCAATGT 60.599 45.455 0.00 0.00 33.67 2.71
439 503 4.084952 TGTTAATCCGTTGTCGTTTCTTCG 60.085 41.667 0.00 0.00 35.01 3.79
457 521 1.957186 GCGAGGGCACACGTGTTAA 60.957 57.895 20.79 0.00 39.62 2.01
458 522 2.356553 GCGAGGGCACACGTGTTA 60.357 61.111 20.79 0.00 39.62 2.41
635 700 2.679092 CTGCTCATGCCCTTCCCA 59.321 61.111 0.00 0.00 38.71 4.37
668 733 2.036958 TTGGCATGTCTCGTTATGGG 57.963 50.000 0.00 0.00 0.00 4.00
692 758 2.717639 AACATGCCATCAGACTACCC 57.282 50.000 0.00 0.00 0.00 3.69
730 797 0.301687 GCACATACATCGTTCGGCTG 59.698 55.000 0.00 0.00 0.00 4.85
765 832 6.727824 ATCCAACAAACTCATAGAAACTCG 57.272 37.500 0.00 0.00 0.00 4.18
803 870 9.958180 TCATATCTCAAATCCAACAAACTCTAA 57.042 29.630 0.00 0.00 0.00 2.10
818 885 8.523658 CGGACACCTCTATTATCATATCTCAAA 58.476 37.037 0.00 0.00 0.00 2.69
819 886 7.122799 CCGGACACCTCTATTATCATATCTCAA 59.877 40.741 0.00 0.00 0.00 3.02
820 887 6.603599 CCGGACACCTCTATTATCATATCTCA 59.396 42.308 0.00 0.00 0.00 3.27
821 888 6.829298 TCCGGACACCTCTATTATCATATCTC 59.171 42.308 0.00 0.00 0.00 2.75
822 889 6.732487 TCCGGACACCTCTATTATCATATCT 58.268 40.000 0.00 0.00 0.00 1.98
823 890 7.068839 ACATCCGGACACCTCTATTATCATATC 59.931 40.741 6.12 0.00 0.00 1.63
824 891 6.897966 ACATCCGGACACCTCTATTATCATAT 59.102 38.462 6.12 0.00 0.00 1.78
825 892 6.152831 CACATCCGGACACCTCTATTATCATA 59.847 42.308 6.12 0.00 0.00 2.15
826 893 5.047021 CACATCCGGACACCTCTATTATCAT 60.047 44.000 6.12 0.00 0.00 2.45
827 894 4.280929 CACATCCGGACACCTCTATTATCA 59.719 45.833 6.12 0.00 0.00 2.15
828 895 4.322049 CCACATCCGGACACCTCTATTATC 60.322 50.000 6.12 0.00 0.00 1.75
829 896 3.578716 CCACATCCGGACACCTCTATTAT 59.421 47.826 6.12 0.00 0.00 1.28
830 897 2.963101 CCACATCCGGACACCTCTATTA 59.037 50.000 6.12 0.00 0.00 0.98
831 898 1.762957 CCACATCCGGACACCTCTATT 59.237 52.381 6.12 0.00 0.00 1.73
832 899 1.063190 TCCACATCCGGACACCTCTAT 60.063 52.381 6.12 0.00 0.00 1.98
833 900 0.333652 TCCACATCCGGACACCTCTA 59.666 55.000 6.12 0.00 0.00 2.43
834 901 0.325671 ATCCACATCCGGACACCTCT 60.326 55.000 6.12 0.00 38.07 3.69
835 902 0.541863 AATCCACATCCGGACACCTC 59.458 55.000 6.12 0.00 38.07 3.85
836 903 1.485066 GTAATCCACATCCGGACACCT 59.515 52.381 6.12 0.00 38.07 4.00
837 904 1.208535 TGTAATCCACATCCGGACACC 59.791 52.381 6.12 0.00 38.07 4.16
838 905 2.684001 TGTAATCCACATCCGGACAC 57.316 50.000 6.12 0.00 38.07 3.67
847 914 6.836527 CACCCCCTTAAATAATGTAATCCACA 59.163 38.462 0.00 0.00 42.69 4.17
848 915 6.837048 ACACCCCCTTAAATAATGTAATCCAC 59.163 38.462 0.00 0.00 0.00 4.02
849 916 6.987557 ACACCCCCTTAAATAATGTAATCCA 58.012 36.000 0.00 0.00 0.00 3.41
850 917 6.492429 GGACACCCCCTTAAATAATGTAATCC 59.508 42.308 0.00 0.00 0.00 3.01
851 918 6.206048 CGGACACCCCCTTAAATAATGTAATC 59.794 42.308 0.00 0.00 0.00 1.75
852 919 6.066032 CGGACACCCCCTTAAATAATGTAAT 58.934 40.000 0.00 0.00 0.00 1.89
853 920 5.438833 CGGACACCCCCTTAAATAATGTAA 58.561 41.667 0.00 0.00 0.00 2.41
854 921 4.141436 CCGGACACCCCCTTAAATAATGTA 60.141 45.833 0.00 0.00 0.00 2.29
855 922 3.372241 CCGGACACCCCCTTAAATAATGT 60.372 47.826 0.00 0.00 0.00 2.71
856 923 3.219281 CCGGACACCCCCTTAAATAATG 58.781 50.000 0.00 0.00 0.00 1.90
857 924 2.854337 ACCGGACACCCCCTTAAATAAT 59.146 45.455 9.46 0.00 0.00 1.28
858 925 2.239402 GACCGGACACCCCCTTAAATAA 59.761 50.000 9.46 0.00 0.00 1.40
859 926 1.839354 GACCGGACACCCCCTTAAATA 59.161 52.381 9.46 0.00 0.00 1.40
860 927 0.622136 GACCGGACACCCCCTTAAAT 59.378 55.000 9.46 0.00 0.00 1.40
861 928 1.829523 CGACCGGACACCCCCTTAAA 61.830 60.000 9.46 0.00 0.00 1.52
862 929 2.285024 CGACCGGACACCCCCTTAA 61.285 63.158 9.46 0.00 0.00 1.85
863 930 2.681064 CGACCGGACACCCCCTTA 60.681 66.667 9.46 0.00 0.00 2.69
891 958 3.788766 AAACGCTCGCGGATGCAC 61.789 61.111 16.18 0.00 44.69 4.57
892 959 3.787676 CAAACGCTCGCGGATGCA 61.788 61.111 16.18 0.00 44.69 3.96
893 960 3.788766 ACAAACGCTCGCGGATGC 61.789 61.111 16.18 7.97 44.69 3.91
894 961 2.096406 CACAAACGCTCGCGGATG 59.904 61.111 16.18 15.03 44.69 3.51
895 962 3.118454 CCACAAACGCTCGCGGAT 61.118 61.111 16.18 1.09 44.69 4.18
898 965 4.072088 GTCCCACAAACGCTCGCG 62.072 66.667 10.06 10.06 46.03 5.87
899 966 4.072088 CGTCCCACAAACGCTCGC 62.072 66.667 0.00 0.00 32.84 5.03
900 967 3.411351 CCGTCCCACAAACGCTCG 61.411 66.667 0.00 0.00 38.77 5.03
901 968 3.723348 GCCGTCCCACAAACGCTC 61.723 66.667 0.00 0.00 38.77 5.03
902 969 4.250305 AGCCGTCCCACAAACGCT 62.250 61.111 0.00 0.00 38.77 5.07
903 970 4.025401 CAGCCGTCCCACAAACGC 62.025 66.667 0.00 0.00 38.77 4.84
904 971 1.289109 CTACAGCCGTCCCACAAACG 61.289 60.000 0.00 0.00 39.78 3.60
905 972 0.034337 TCTACAGCCGTCCCACAAAC 59.966 55.000 0.00 0.00 0.00 2.93
906 973 0.981183 ATCTACAGCCGTCCCACAAA 59.019 50.000 0.00 0.00 0.00 2.83
907 974 0.249120 CATCTACAGCCGTCCCACAA 59.751 55.000 0.00 0.00 0.00 3.33
908 975 1.897423 CATCTACAGCCGTCCCACA 59.103 57.895 0.00 0.00 0.00 4.17
909 976 1.521681 GCATCTACAGCCGTCCCAC 60.522 63.158 0.00 0.00 0.00 4.61
910 977 1.685765 AGCATCTACAGCCGTCCCA 60.686 57.895 0.00 0.00 0.00 4.37
911 978 1.227380 CAGCATCTACAGCCGTCCC 60.227 63.158 0.00 0.00 0.00 4.46
912 979 0.744874 TACAGCATCTACAGCCGTCC 59.255 55.000 0.00 0.00 0.00 4.79
913 980 2.464865 CTTACAGCATCTACAGCCGTC 58.535 52.381 0.00 0.00 0.00 4.79
914 981 1.471676 GCTTACAGCATCTACAGCCGT 60.472 52.381 0.00 0.00 41.89 5.68
915 982 1.202463 AGCTTACAGCATCTACAGCCG 60.202 52.381 0.00 0.00 45.56 5.52
916 983 2.611225 AGCTTACAGCATCTACAGCC 57.389 50.000 0.00 0.00 45.56 4.85
917 984 3.046390 CGTAGCTTACAGCATCTACAGC 58.954 50.000 0.00 0.00 45.56 4.40
918 985 4.294416 ACGTAGCTTACAGCATCTACAG 57.706 45.455 0.00 0.00 45.56 2.74
919 986 4.713824 AACGTAGCTTACAGCATCTACA 57.286 40.909 0.00 0.00 45.56 2.74
920 987 6.207213 ACATAACGTAGCTTACAGCATCTAC 58.793 40.000 0.00 0.00 45.56 2.59
921 988 6.387041 ACATAACGTAGCTTACAGCATCTA 57.613 37.500 0.00 0.00 45.56 1.98
922 989 5.263968 ACATAACGTAGCTTACAGCATCT 57.736 39.130 0.00 0.00 45.56 2.90
923 990 5.968387 AACATAACGTAGCTTACAGCATC 57.032 39.130 0.00 0.00 45.56 3.91
924 991 5.462398 GCTAACATAACGTAGCTTACAGCAT 59.538 40.000 0.00 0.00 45.56 3.79
925 992 4.802039 GCTAACATAACGTAGCTTACAGCA 59.198 41.667 0.00 0.00 45.56 4.41
926 993 4.802039 TGCTAACATAACGTAGCTTACAGC 59.198 41.667 7.23 3.67 42.84 4.40
927 994 6.530534 ACTTGCTAACATAACGTAGCTTACAG 59.469 38.462 7.23 1.76 36.58 2.74
928 995 6.392354 ACTTGCTAACATAACGTAGCTTACA 58.608 36.000 7.23 0.00 36.58 2.41
929 996 6.882458 ACTTGCTAACATAACGTAGCTTAC 57.118 37.500 7.23 0.00 36.58 2.34
930 997 7.894376 AAACTTGCTAACATAACGTAGCTTA 57.106 32.000 7.23 0.00 36.58 3.09
931 998 6.796705 AAACTTGCTAACATAACGTAGCTT 57.203 33.333 7.23 0.00 36.58 3.74
932 999 9.590451 TTATAAACTTGCTAACATAACGTAGCT 57.410 29.630 7.23 0.00 36.58 3.32
933 1000 9.845305 CTTATAAACTTGCTAACATAACGTAGC 57.155 33.333 0.00 0.00 36.20 3.58
936 1003 8.601476 GCTCTTATAAACTTGCTAACATAACGT 58.399 33.333 0.00 0.00 0.00 3.99
937 1004 8.600625 TGCTCTTATAAACTTGCTAACATAACG 58.399 33.333 0.00 0.00 0.00 3.18
941 1008 9.177608 TGATTGCTCTTATAAACTTGCTAACAT 57.822 29.630 0.00 0.00 0.00 2.71
942 1009 8.450964 GTGATTGCTCTTATAAACTTGCTAACA 58.549 33.333 0.00 0.00 0.00 2.41
943 1010 7.910683 GGTGATTGCTCTTATAAACTTGCTAAC 59.089 37.037 0.00 0.00 0.00 2.34
944 1011 7.829211 AGGTGATTGCTCTTATAAACTTGCTAA 59.171 33.333 0.00 0.00 0.00 3.09
945 1012 7.338710 AGGTGATTGCTCTTATAAACTTGCTA 58.661 34.615 0.00 0.00 0.00 3.49
946 1013 6.183347 AGGTGATTGCTCTTATAAACTTGCT 58.817 36.000 0.00 0.00 0.00 3.91
947 1014 6.442513 AGGTGATTGCTCTTATAAACTTGC 57.557 37.500 0.00 0.00 0.00 4.01
948 1015 6.038714 GGGAGGTGATTGCTCTTATAAACTTG 59.961 42.308 0.00 0.00 0.00 3.16
949 1016 6.122964 GGGAGGTGATTGCTCTTATAAACTT 58.877 40.000 0.00 0.00 0.00 2.66
950 1017 5.398012 GGGGAGGTGATTGCTCTTATAAACT 60.398 44.000 0.00 0.00 0.00 2.66
951 1018 4.822350 GGGGAGGTGATTGCTCTTATAAAC 59.178 45.833 0.00 0.00 0.00 2.01
952 1019 4.476846 TGGGGAGGTGATTGCTCTTATAAA 59.523 41.667 0.00 0.00 0.00 1.40
953 1020 4.044308 TGGGGAGGTGATTGCTCTTATAA 58.956 43.478 0.00 0.00 0.00 0.98
954 1021 3.664320 TGGGGAGGTGATTGCTCTTATA 58.336 45.455 0.00 0.00 0.00 0.98
955 1022 2.492025 TGGGGAGGTGATTGCTCTTAT 58.508 47.619 0.00 0.00 0.00 1.73
956 1023 1.965414 TGGGGAGGTGATTGCTCTTA 58.035 50.000 0.00 0.00 0.00 2.10
957 1024 1.075601 TTGGGGAGGTGATTGCTCTT 58.924 50.000 0.00 0.00 0.00 2.85
958 1025 1.075601 TTTGGGGAGGTGATTGCTCT 58.924 50.000 0.00 0.00 0.00 4.09
959 1026 1.923356 TTTTGGGGAGGTGATTGCTC 58.077 50.000 0.00 0.00 0.00 4.26
960 1027 2.397044 TTTTTGGGGAGGTGATTGCT 57.603 45.000 0.00 0.00 0.00 3.91
977 1044 9.202273 TCATGCGATTGCTTTTATAAACTTTTT 57.798 25.926 6.47 0.00 43.34 1.94
978 1045 8.755696 TCATGCGATTGCTTTTATAAACTTTT 57.244 26.923 6.47 0.00 43.34 2.27
979 1046 8.755696 TTCATGCGATTGCTTTTATAAACTTT 57.244 26.923 6.47 0.00 43.34 2.66
980 1047 8.931385 ATTCATGCGATTGCTTTTATAAACTT 57.069 26.923 6.47 0.00 43.34 2.66
981 1048 8.931385 AATTCATGCGATTGCTTTTATAAACT 57.069 26.923 6.47 0.00 43.34 2.66
1064 1134 1.007271 AAGCAGACGACCGTGACAG 60.007 57.895 0.00 0.00 0.00 3.51
1075 1150 4.898607 TGGTTGGTCCAAGCAGAC 57.101 55.556 28.52 7.23 45.03 3.51
1105 1186 3.376234 GGTCGGAGGCAGGTTTTATAAAC 59.624 47.826 0.00 0.00 0.00 2.01
1163 1250 3.365265 GGGGCCGTTCTTGTGCAG 61.365 66.667 0.00 0.00 0.00 4.41
1169 1256 0.605589 CTCTTTTCGGGGCCGTTCTT 60.606 55.000 0.00 0.00 40.74 2.52
1170 1257 1.003718 CTCTTTTCGGGGCCGTTCT 60.004 57.895 0.00 0.00 40.74 3.01
1172 1259 0.887836 GTTCTCTTTTCGGGGCCGTT 60.888 55.000 0.00 0.00 40.74 4.44
1175 1262 2.038837 CCGTTCTCTTTTCGGGGCC 61.039 63.158 0.00 0.00 40.49 5.80
1176 1263 2.687805 GCCGTTCTCTTTTCGGGGC 61.688 63.158 5.06 0.00 43.77 5.80
1177 1264 2.038837 GGCCGTTCTCTTTTCGGGG 61.039 63.158 5.06 0.00 43.77 5.73
1178 1265 2.038837 GGGCCGTTCTCTTTTCGGG 61.039 63.158 0.00 0.00 43.77 5.14
1179 1266 2.388232 CGGGCCGTTCTCTTTTCGG 61.388 63.158 19.97 0.00 45.94 4.30
1180 1267 0.947180 TTCGGGCCGTTCTCTTTTCG 60.947 55.000 27.32 0.00 0.00 3.46
1181 1268 0.516001 GTTCGGGCCGTTCTCTTTTC 59.484 55.000 27.32 3.39 0.00 2.29
1182 1269 0.179040 TGTTCGGGCCGTTCTCTTTT 60.179 50.000 27.32 0.00 0.00 2.27
1183 1270 0.179040 TTGTTCGGGCCGTTCTCTTT 60.179 50.000 27.32 0.00 0.00 2.52
1184 1271 0.179040 TTTGTTCGGGCCGTTCTCTT 60.179 50.000 27.32 0.00 0.00 2.85
1185 1272 0.179040 TTTTGTTCGGGCCGTTCTCT 60.179 50.000 27.32 0.00 0.00 3.10
1186 1273 0.664224 TTTTTGTTCGGGCCGTTCTC 59.336 50.000 27.32 14.57 0.00 2.87
1502 1594 0.525668 ATTGCGTTCCGAGCTACGAG 60.526 55.000 10.83 0.56 45.77 4.18
1504 1596 1.631072 CATTGCGTTCCGAGCTACG 59.369 57.895 2.36 2.36 40.55 3.51
1506 1598 0.179111 CTCCATTGCGTTCCGAGCTA 60.179 55.000 0.00 0.00 35.28 3.32
1542 1642 5.697826 CAAAAGAGATCAAGGAAGAGCAAC 58.302 41.667 0.00 0.00 0.00 4.17
1552 1652 8.433126 CAAAATAAGCAAGCAAAAGAGATCAAG 58.567 33.333 0.00 0.00 0.00 3.02
1567 1667 4.792702 CACGCATCGAATCAAAATAAGCAA 59.207 37.500 0.00 0.00 0.00 3.91
1614 1714 2.304761 CACCAAGGTTAGTAAGCCCTCA 59.695 50.000 8.46 0.00 0.00 3.86
1620 1720 5.820947 ACAACAGAACACCAAGGTTAGTAAG 59.179 40.000 0.00 0.00 0.00 2.34
1623 1723 4.196971 GACAACAGAACACCAAGGTTAGT 58.803 43.478 0.00 0.00 0.00 2.24
1640 1740 3.050275 GCTCCGCACCAGGACAAC 61.050 66.667 0.00 0.00 36.14 3.32
1646 1746 2.110967 CCATTCTGCTCCGCACCAG 61.111 63.158 0.00 0.00 33.79 4.00
1684 1784 1.447838 TTTGACGGAGATGAGCGCC 60.448 57.895 2.29 0.00 0.00 6.53
1749 1849 0.525242 TGCTGAAACAAAGCGCACAC 60.525 50.000 11.47 0.00 43.88 3.82
1831 1931 1.440145 GCTTAGCCGGCTCAATCACC 61.440 60.000 36.73 11.73 0.00 4.02
1928 2032 7.734924 TGATATTATAGCAGGCAAAACAGAG 57.265 36.000 0.00 0.00 0.00 3.35
1936 2040 8.953313 CATGAAGAATTGATATTATAGCAGGCA 58.047 33.333 0.00 0.00 0.00 4.75
1968 2073 1.279496 ATCAGTGCAGCCTCACCTAA 58.721 50.000 0.00 0.00 37.68 2.69
2162 2267 0.875908 GCTGCATCATGGCAAGCATG 60.876 55.000 7.54 4.06 44.40 4.06
2302 2409 8.421002 GCACAATAATTGGAACCTGGTATTATT 58.579 33.333 15.02 15.02 33.79 1.40
2303 2410 7.563188 TGCACAATAATTGGAACCTGGTATTAT 59.437 33.333 0.00 3.29 34.12 1.28
2304 2411 6.892456 TGCACAATAATTGGAACCTGGTATTA 59.108 34.615 0.00 0.72 34.12 0.98
2305 2412 5.719085 TGCACAATAATTGGAACCTGGTATT 59.281 36.000 0.00 0.00 34.12 1.89
2579 2811 1.791555 CGACGCCATTCATGAACTTGC 60.792 52.381 11.07 12.33 0.00 4.01
2725 2958 4.633565 CCAAGAGACAAGCTAAACCATCTC 59.366 45.833 0.00 0.00 34.14 2.75
2738 2971 7.828717 TGATATGTATTCAAAGCCAAGAGACAA 59.171 33.333 0.00 0.00 0.00 3.18
2872 4401 7.013559 TCTGCAGGTCAAAATATATGATGGTTG 59.986 37.037 15.13 0.00 0.00 3.77
3026 4555 2.192664 TGGCTGATTGGAAAGCGTAA 57.807 45.000 0.00 0.00 40.46 3.18
3060 4589 7.595502 GCGTCTTAATGCATTAGTATCTACAGT 59.404 37.037 18.13 0.00 37.37 3.55
3061 4590 7.062371 GGCGTCTTAATGCATTAGTATCTACAG 59.938 40.741 18.13 10.85 39.30 2.74
3062 4591 6.866770 GGCGTCTTAATGCATTAGTATCTACA 59.133 38.462 18.13 1.60 39.30 2.74
3063 4592 7.091443 AGGCGTCTTAATGCATTAGTATCTAC 58.909 38.462 18.13 10.59 39.30 2.59
3087 4616 6.890293 ACTCAAGGCTTATTACCTAAGGAAG 58.110 40.000 0.00 0.00 37.82 3.46
3090 4619 6.415573 ACAACTCAAGGCTTATTACCTAAGG 58.584 40.000 0.00 0.00 37.82 2.69
3242 4773 2.166821 TGTTGCACCCAATTCATTGC 57.833 45.000 0.00 0.00 36.48 3.56
3243 4774 5.453648 CATTTTGTTGCACCCAATTCATTG 58.546 37.500 0.00 0.00 37.52 2.82
3246 4777 2.877168 GCATTTTGTTGCACCCAATTCA 59.123 40.909 0.00 0.00 42.31 2.57
3282 4813 7.928167 TGTCAGATGATGGTCAAGATATGTTAC 59.072 37.037 0.00 0.00 0.00 2.50
3364 4895 8.542953 GTTTTGCTTGGAGTAAAAGAAAAGATG 58.457 33.333 4.54 0.00 39.74 2.90
3405 4936 3.250040 CCCACTTCACCTCAAAAACTACG 59.750 47.826 0.00 0.00 0.00 3.51
3491 5030 8.915057 AAGCTAGCATGTTCATCTATACAAAT 57.085 30.769 18.83 0.00 0.00 2.32
3667 5207 4.960938 AGCAGTATCTTCGGAATAATGCA 58.039 39.130 19.64 0.00 33.69 3.96
3695 5237 6.192970 ACCCATTCAAGATAAAGGATCGAT 57.807 37.500 0.00 0.00 39.80 3.59
3758 5300 1.078759 GCATGTTCGACGAGTGAGGG 61.079 60.000 0.00 0.00 0.00 4.30
3832 5374 4.142730 GCAGCAAACTCCTTACATCTCAAG 60.143 45.833 0.00 0.00 0.00 3.02
3908 5450 5.828328 GCAGCCTATACTTTCCCTACATTTT 59.172 40.000 0.00 0.00 0.00 1.82
3931 5473 2.223805 CCCATTTAATCTTTCAGGCCGC 60.224 50.000 0.00 0.00 0.00 6.53
3969 5511 3.821033 ACAAAAGGAGTGGAACATACTGC 59.179 43.478 0.00 0.00 44.52 4.40
3974 5516 3.230976 GGGAACAAAAGGAGTGGAACAT 58.769 45.455 0.00 0.00 44.52 2.71
4004 5546 4.995124 AGTTGTCGTAAAGTCGCATCTAT 58.005 39.130 0.00 0.00 0.00 1.98
4023 5565 7.920160 ACACAAAAACATTCAATTCCAAGTT 57.080 28.000 0.00 0.00 0.00 2.66
4027 5569 7.361542 CCAACAACACAAAAACATTCAATTCCA 60.362 33.333 0.00 0.00 0.00 3.53
4083 5625 7.806680 AATGGTGGATTAAACCCTATTGTTT 57.193 32.000 0.00 0.00 41.18 2.83
4149 5784 1.856539 AACAGGGGTGATCTGGGCTG 61.857 60.000 0.00 0.00 36.62 4.85
4192 5829 1.412343 GAAGCTGGGCCAAAAGACAAA 59.588 47.619 8.04 0.00 0.00 2.83
4273 5910 4.858965 AATCTTTCTCTGGATCAAGGCT 57.141 40.909 0.00 0.00 0.00 4.58
4274 5911 5.923204 TCTAATCTTTCTCTGGATCAAGGC 58.077 41.667 0.00 0.00 0.00 4.35
4275 5912 8.672815 GTTTTCTAATCTTTCTCTGGATCAAGG 58.327 37.037 0.00 0.00 0.00 3.61
4276 5913 9.447157 AGTTTTCTAATCTTTCTCTGGATCAAG 57.553 33.333 0.00 0.00 0.00 3.02
4277 5914 9.224267 CAGTTTTCTAATCTTTCTCTGGATCAA 57.776 33.333 0.00 0.00 0.00 2.57
4278 5915 8.378565 ACAGTTTTCTAATCTTTCTCTGGATCA 58.621 33.333 0.00 0.00 0.00 2.92
4279 5916 8.785329 ACAGTTTTCTAATCTTTCTCTGGATC 57.215 34.615 0.00 0.00 0.00 3.36
4280 5917 9.579932 AAACAGTTTTCTAATCTTTCTCTGGAT 57.420 29.630 0.00 0.00 0.00 3.41
4281 5918 8.840321 CAAACAGTTTTCTAATCTTTCTCTGGA 58.160 33.333 0.00 0.00 0.00 3.86
4282 5919 7.592903 GCAAACAGTTTTCTAATCTTTCTCTGG 59.407 37.037 0.00 0.00 0.00 3.86
4283 5920 7.592903 GGCAAACAGTTTTCTAATCTTTCTCTG 59.407 37.037 0.00 0.00 0.00 3.35
4284 5921 7.503902 AGGCAAACAGTTTTCTAATCTTTCTCT 59.496 33.333 0.00 0.00 0.00 3.10
4285 5922 7.652727 AGGCAAACAGTTTTCTAATCTTTCTC 58.347 34.615 0.00 0.00 0.00 2.87
4286 5923 7.588497 AGGCAAACAGTTTTCTAATCTTTCT 57.412 32.000 0.00 0.00 0.00 2.52
4287 5924 7.920682 TCAAGGCAAACAGTTTTCTAATCTTTC 59.079 33.333 0.00 0.00 0.00 2.62
4288 5925 7.781056 TCAAGGCAAACAGTTTTCTAATCTTT 58.219 30.769 0.00 0.00 0.00 2.52
4289 5926 7.346751 TCAAGGCAAACAGTTTTCTAATCTT 57.653 32.000 0.00 0.00 0.00 2.40
4290 5927 6.959639 TCAAGGCAAACAGTTTTCTAATCT 57.040 33.333 0.00 0.00 0.00 2.40
4291 5928 6.808704 GGATCAAGGCAAACAGTTTTCTAATC 59.191 38.462 0.00 4.91 0.00 1.75
4292 5929 6.267471 TGGATCAAGGCAAACAGTTTTCTAAT 59.733 34.615 0.00 0.00 0.00 1.73
4293 5930 5.596361 TGGATCAAGGCAAACAGTTTTCTAA 59.404 36.000 0.00 0.00 0.00 2.10
4294 5931 5.136828 TGGATCAAGGCAAACAGTTTTCTA 58.863 37.500 0.00 0.00 0.00 2.10
4295 5932 3.960102 TGGATCAAGGCAAACAGTTTTCT 59.040 39.130 0.00 0.00 0.00 2.52
4296 5933 4.037923 TCTGGATCAAGGCAAACAGTTTTC 59.962 41.667 0.00 0.00 0.00 2.29
4297 5934 3.960102 TCTGGATCAAGGCAAACAGTTTT 59.040 39.130 0.00 0.00 0.00 2.43
4298 5935 3.565307 TCTGGATCAAGGCAAACAGTTT 58.435 40.909 0.00 0.00 0.00 2.66
4299 5936 3.152341 CTCTGGATCAAGGCAAACAGTT 58.848 45.455 0.00 0.00 0.00 3.16
4300 5937 2.373169 TCTCTGGATCAAGGCAAACAGT 59.627 45.455 0.00 0.00 0.00 3.55
4301 5938 3.063510 TCTCTGGATCAAGGCAAACAG 57.936 47.619 0.00 0.00 0.00 3.16
4302 5939 3.507162 TTCTCTGGATCAAGGCAAACA 57.493 42.857 0.00 0.00 0.00 2.83
4303 5940 4.074970 TCTTTCTCTGGATCAAGGCAAAC 58.925 43.478 0.00 0.00 0.00 2.93
4304 5941 4.371624 TCTTTCTCTGGATCAAGGCAAA 57.628 40.909 0.00 0.00 0.00 3.68
4305 5942 4.581309 ATCTTTCTCTGGATCAAGGCAA 57.419 40.909 0.00 0.00 0.00 4.52
4332 5969 3.070018 CTCTGAATCGAGGCAAACAGTT 58.930 45.455 0.00 0.00 0.00 3.16
4351 5990 1.982073 CTGGTTGATTTCCGCGCCTC 61.982 60.000 0.00 0.00 0.00 4.70
4403 6042 2.983192 TCCACAGGTTTTCTATCACCCA 59.017 45.455 0.00 0.00 32.92 4.51
4404 6043 3.713826 TCCACAGGTTTTCTATCACCC 57.286 47.619 0.00 0.00 32.92 4.61
4451 6090 3.214328 GGACGGTGCATATTTTCCATCT 58.786 45.455 0.00 0.00 0.00 2.90
4455 6094 2.088423 TGTGGACGGTGCATATTTTCC 58.912 47.619 5.42 0.00 0.00 3.13
4461 6100 0.610687 TCACATGTGGACGGTGCATA 59.389 50.000 25.16 3.13 32.69 3.14
4480 6119 0.183492 TGCCAGCTCAAGTTTCTGGT 59.817 50.000 13.91 0.00 46.82 4.00
4512 6151 0.667184 GGTCAAAACAGCGGGCATTG 60.667 55.000 0.00 0.00 0.00 2.82
4516 6155 1.734388 AACAGGTCAAAACAGCGGGC 61.734 55.000 0.00 0.00 0.00 6.13
4518 6157 1.021202 TGAACAGGTCAAAACAGCGG 58.979 50.000 0.00 0.00 31.51 5.52
4531 6170 9.180678 GGCGGTAAATAAAATATGAATGAACAG 57.819 33.333 0.00 0.00 0.00 3.16
4533 6172 7.597369 GGGGCGGTAAATAAAATATGAATGAAC 59.403 37.037 0.00 0.00 0.00 3.18
4534 6173 7.287927 TGGGGCGGTAAATAAAATATGAATGAA 59.712 33.333 0.00 0.00 0.00 2.57
4536 6175 6.866248 GTGGGGCGGTAAATAAAATATGAATG 59.134 38.462 0.00 0.00 0.00 2.67
4537 6176 6.780522 AGTGGGGCGGTAAATAAAATATGAAT 59.219 34.615 0.00 0.00 0.00 2.57
4539 6178 5.697067 AGTGGGGCGGTAAATAAAATATGA 58.303 37.500 0.00 0.00 0.00 2.15
4540 6179 5.048294 GGAGTGGGGCGGTAAATAAAATATG 60.048 44.000 0.00 0.00 0.00 1.78
4568 6209 3.028130 CATGCCATGCCGTGCTAG 58.972 61.111 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.