Multiple sequence alignment - TraesCS2B01G346300

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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 TraesCS2B01G346300 chr2B 100.000 2987 0 0 1 2987 492974641 492977627 0.000000e+00 5517.0
1 TraesCS2B01G346300 chr2B 86.053 337 45 2 74 409 374434119 374434454 7.870000e-96 361.0
2 TraesCS2B01G346300 chr2B 96.296 54 2 0 2443 2496 784555323 784555376 4.100000e-14 89.8
3 TraesCS2B01G346300 chr2B 87.324 71 5 4 724 792 752824539 752824471 8.880000e-11 78.7
4 TraesCS2B01G346300 chr2B 100.000 33 0 0 2173 2205 492976767 492976735 8.940000e-06 62.1
5 TraesCS2B01G346300 chr2B 100.000 33 0 0 2095 2127 492976845 492976813 8.940000e-06 62.1
6 TraesCS2B01G346300 chr2D 93.346 1578 74 17 867 2436 420558356 420559910 0.000000e+00 2303.0
7 TraesCS2B01G346300 chr2D 81.232 341 40 15 396 719 35340600 35340933 1.370000e-63 254.0
8 TraesCS2B01G346300 chr2D 97.297 37 0 1 2092 2127 420559681 420559645 8.940000e-06 62.1
9 TraesCS2B01G346300 chr2A 92.935 1472 69 15 970 2436 569366102 569364661 0.000000e+00 2109.0
10 TraesCS2B01G346300 chr7D 91.238 719 55 7 1 718 457535865 457535154 0.000000e+00 972.0
11 TraesCS2B01G346300 chr5D 88.439 692 73 6 1 685 453230341 453229650 0.000000e+00 828.0
12 TraesCS2B01G346300 chr5D 93.151 73 4 1 2443 2514 45599090 45599018 4.070000e-19 106.0
13 TraesCS2B01G346300 chr3D 87.241 627 77 3 1 624 580118836 580119462 0.000000e+00 712.0
14 TraesCS2B01G346300 chr3D 84.848 726 84 15 1 716 560747392 560748101 0.000000e+00 708.0
15 TraesCS2B01G346300 chr3D 79.279 555 95 16 1 542 565997724 565997177 1.310000e-98 370.0
16 TraesCS2B01G346300 chr3D 89.041 73 6 2 2443 2514 17655139 17655068 4.100000e-14 89.8
17 TraesCS2B01G346300 chr6A 86.943 628 68 8 1 614 135451115 135450488 0.000000e+00 693.0
18 TraesCS2B01G346300 chr7B 83.916 572 79 10 152 716 532215716 532216281 4.380000e-148 534.0
19 TraesCS2B01G346300 chr7B 94.828 58 3 0 2444 2501 665605382 665605439 1.140000e-14 91.6
20 TraesCS2B01G346300 chr3B 77.620 706 123 27 1 686 661026951 661027641 2.160000e-106 396.0
21 TraesCS2B01G346300 chr3B 91.379 58 2 3 725 780 143264643 143264699 3.190000e-10 76.8
22 TraesCS2B01G346300 chr3B 91.071 56 4 1 725 779 739896192 739896137 1.150000e-09 75.0
23 TraesCS2B01G346300 chr7A 84.146 410 48 9 315 718 696173351 696173749 6.040000e-102 381.0
24 TraesCS2B01G346300 chr7A 84.000 300 42 4 2689 2984 721887180 721886883 1.750000e-72 283.0
25 TraesCS2B01G346300 chr7A 85.714 77 8 3 717 791 726797087 726797162 8.880000e-11 78.7
26 TraesCS2B01G346300 chr1D 80.040 496 75 19 1 481 485626696 485627182 2.200000e-91 346.0
27 TraesCS2B01G346300 chr1D 85.484 62 9 0 2716 2777 465315573 465315634 6.910000e-07 65.8
28 TraesCS2B01G346300 chr4A 75.174 576 97 31 2439 2985 543573145 543573703 2.320000e-56 230.0
29 TraesCS2B01G346300 chr4A 93.333 60 4 0 2434 2493 717421128 717421187 4.100000e-14 89.8
30 TraesCS2B01G346300 chr6B 94.737 57 3 0 2440 2496 37767385 37767329 4.100000e-14 89.8
31 TraesCS2B01G346300 chrUn 88.732 71 5 3 2427 2496 108912609 108912677 1.910000e-12 84.2
32 TraesCS2B01G346300 chr4B 88.571 70 6 2 2439 2508 568443379 568443312 1.910000e-12 84.2
33 TraesCS2B01G346300 chr4D 90.385 52 2 3 719 770 497167400 497167448 6.910000e-07 65.8


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 TraesCS2B01G346300 chr2B 492974641 492977627 2986 False 5517 5517 100.000 1 2987 1 chr2B.!!$F2 2986
1 TraesCS2B01G346300 chr2D 420558356 420559910 1554 False 2303 2303 93.346 867 2436 1 chr2D.!!$F2 1569
2 TraesCS2B01G346300 chr2A 569364661 569366102 1441 True 2109 2109 92.935 970 2436 1 chr2A.!!$R1 1466
3 TraesCS2B01G346300 chr7D 457535154 457535865 711 True 972 972 91.238 1 718 1 chr7D.!!$R1 717
4 TraesCS2B01G346300 chr5D 453229650 453230341 691 True 828 828 88.439 1 685 1 chr5D.!!$R2 684
5 TraesCS2B01G346300 chr3D 580118836 580119462 626 False 712 712 87.241 1 624 1 chr3D.!!$F2 623
6 TraesCS2B01G346300 chr3D 560747392 560748101 709 False 708 708 84.848 1 716 1 chr3D.!!$F1 715
7 TraesCS2B01G346300 chr3D 565997177 565997724 547 True 370 370 79.279 1 542 1 chr3D.!!$R2 541
8 TraesCS2B01G346300 chr6A 135450488 135451115 627 True 693 693 86.943 1 614 1 chr6A.!!$R1 613
9 TraesCS2B01G346300 chr7B 532215716 532216281 565 False 534 534 83.916 152 716 1 chr7B.!!$F1 564
10 TraesCS2B01G346300 chr3B 661026951 661027641 690 False 396 396 77.620 1 686 1 chr3B.!!$F2 685
11 TraesCS2B01G346300 chr4A 543573145 543573703 558 False 230 230 75.174 2439 2985 1 chr4A.!!$F1 546

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
545 572 0.105453 GGGATCCCAGCCTGAGTCTA 60.105 60.0 26.95 0.0 35.81 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 2537 0.108898 GTGACTGCTCAGATGCTCGT 60.109 55.0 3.6 0.0 0.0 4.18 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
43 44 6.365970 AGTGTATTATGGGCTATCTGGAAG 57.634 41.667 0.00 0.00 0.00 3.46
55 56 5.221621 GGCTATCTGGAAGCATAGAAACTCT 60.222 44.000 0.00 0.00 41.93 3.24
64 65 6.529477 GGAAGCATAGAAACTCTTGCATTTTC 59.471 38.462 0.00 0.00 34.92 2.29
150 151 2.093973 GGCTGATTCTTCTCAAGGACGA 60.094 50.000 0.00 0.00 0.00 4.20
171 172 1.227089 CTCGCGTGAAGATGGAGGG 60.227 63.158 5.77 0.00 0.00 4.30
189 190 3.395941 GAGGGATTCATGACCAGGGTTAT 59.604 47.826 0.00 0.00 0.00 1.89
221 226 0.698238 CACCCCCTTCCAGATCACAA 59.302 55.000 0.00 0.00 0.00 3.33
289 294 1.889545 GCTTCTCACCAAGCTGAACT 58.110 50.000 0.00 0.00 44.71 3.01
337 342 1.447643 GCTATGCAGTCATCCCCGT 59.552 57.895 0.00 0.00 34.22 5.28
418 423 4.285790 TCCTGGGTTCCCCTGCCT 62.286 66.667 5.34 0.00 45.70 4.75
419 424 4.052518 CCTGGGTTCCCCTGCCTG 62.053 72.222 5.34 0.00 45.70 4.85
468 479 4.120331 GCACCCGCTGGAATGTGC 62.120 66.667 0.00 6.45 46.09 4.57
481 492 3.949754 TGGAATGTGCAAGATGAAGATCC 59.050 43.478 0.00 0.00 0.00 3.36
485 496 0.811219 TGCAAGATGAAGATCCCGCG 60.811 55.000 0.00 0.00 31.65 6.46
545 572 0.105453 GGGATCCCAGCCTGAGTCTA 60.105 60.000 26.95 0.00 35.81 2.59
551 580 2.200989 CAGCCTGAGTCTAGCTGCT 58.799 57.895 18.06 7.57 46.60 4.24
552 581 0.179105 CAGCCTGAGTCTAGCTGCTG 60.179 60.000 13.43 11.81 46.60 4.41
553 582 1.143620 GCCTGAGTCTAGCTGCTGG 59.856 63.158 13.43 9.98 0.00 4.85
633 667 3.690422 TGCTTACTGAACTTGCGTTTTG 58.310 40.909 0.00 0.00 32.39 2.44
669 708 4.995487 ACCTGAACTCTGGTTTCGTTATTC 59.005 41.667 2.62 0.00 44.38 1.75
676 715 8.786826 AACTCTGGTTTCGTTATTCATAATGA 57.213 30.769 0.00 0.00 36.71 2.57
686 725 5.703592 CGTTATTCATAATGAAATCGGGGGA 59.296 40.000 0.00 0.00 40.12 4.81
691 730 3.774599 ATGAAATCGGGGGAGGCGC 62.775 63.158 0.00 0.00 0.00 6.53
710 749 2.039084 CGCTGGCCCTCCTATTATTCTT 59.961 50.000 0.00 0.00 0.00 2.52
756 795 7.525688 AGTGTTTGTTGTACTATCATGATCG 57.474 36.000 12.53 8.73 0.00 3.69
757 796 7.320399 AGTGTTTGTTGTACTATCATGATCGA 58.680 34.615 12.53 0.00 0.00 3.59
758 797 7.817478 AGTGTTTGTTGTACTATCATGATCGAA 59.183 33.333 12.53 0.00 0.00 3.71
759 798 8.110612 GTGTTTGTTGTACTATCATGATCGAAG 58.889 37.037 12.53 6.95 0.00 3.79
760 799 8.032451 TGTTTGTTGTACTATCATGATCGAAGA 58.968 33.333 12.53 0.00 45.75 2.87
761 800 9.035607 GTTTGTTGTACTATCATGATCGAAGAT 57.964 33.333 12.53 0.00 45.12 2.40
762 801 8.579682 TTGTTGTACTATCATGATCGAAGATG 57.420 34.615 12.53 0.00 45.12 2.90
763 802 7.940850 TGTTGTACTATCATGATCGAAGATGA 58.059 34.615 12.53 11.04 45.12 2.92
764 803 8.413229 TGTTGTACTATCATGATCGAAGATGAA 58.587 33.333 12.53 0.00 45.12 2.57
765 804 9.416794 GTTGTACTATCATGATCGAAGATGAAT 57.583 33.333 12.53 5.78 45.12 2.57
773 812 8.345724 TCATGATCGAAGATGAATAGATCAGA 57.654 34.615 11.30 7.02 46.98 3.27
774 813 8.800332 TCATGATCGAAGATGAATAGATCAGAA 58.200 33.333 11.30 1.25 46.98 3.02
775 814 9.078753 CATGATCGAAGATGAATAGATCAGAAG 57.921 37.037 11.30 2.38 46.98 2.85
776 815 8.175925 TGATCGAAGATGAATAGATCAGAAGT 57.824 34.615 0.00 0.00 45.12 3.01
777 816 8.637099 TGATCGAAGATGAATAGATCAGAAGTT 58.363 33.333 0.00 0.00 45.12 2.66
778 817 9.474920 GATCGAAGATGAATAGATCAGAAGTTT 57.525 33.333 0.00 0.00 45.12 2.66
810 849 6.572167 AAAAACCATGTAATGCAAAATGGG 57.428 33.333 18.81 8.20 44.97 4.00
811 850 3.910568 ACCATGTAATGCAAAATGGGG 57.089 42.857 18.81 8.62 44.97 4.96
812 851 2.504996 ACCATGTAATGCAAAATGGGGG 59.495 45.455 18.81 7.39 44.97 5.40
813 852 2.563702 CATGTAATGCAAAATGGGGGC 58.436 47.619 0.00 0.00 37.62 5.80
814 853 1.649321 TGTAATGCAAAATGGGGGCA 58.351 45.000 0.00 0.00 42.43 5.36
815 854 1.980765 TGTAATGCAAAATGGGGGCAA 59.019 42.857 0.00 0.00 41.43 4.52
816 855 2.373169 TGTAATGCAAAATGGGGGCAAA 59.627 40.909 0.00 0.00 41.43 3.68
817 856 2.671896 AATGCAAAATGGGGGCAAAA 57.328 40.000 0.00 0.00 41.43 2.44
818 857 2.671896 ATGCAAAATGGGGGCAAAAA 57.328 40.000 0.00 0.00 41.43 1.94
835 874 1.485124 AAAAATCCAATCCCCCTCGC 58.515 50.000 0.00 0.00 0.00 5.03
836 875 0.751643 AAAATCCAATCCCCCTCGCG 60.752 55.000 0.00 0.00 0.00 5.87
837 876 3.774599 AATCCAATCCCCCTCGCGC 62.775 63.158 0.00 0.00 0.00 6.86
842 881 4.889112 ATCCCCCTCGCGCGTCTA 62.889 66.667 30.98 9.98 0.00 2.59
845 884 4.253257 CCCCTCGCGCGTCTACTC 62.253 72.222 30.98 0.00 0.00 2.59
846 885 4.592936 CCCTCGCGCGTCTACTCG 62.593 72.222 30.98 9.78 0.00 4.18
847 886 3.561213 CCTCGCGCGTCTACTCGA 61.561 66.667 30.98 6.53 0.00 4.04
848 887 2.349869 CTCGCGCGTCTACTCGAC 60.350 66.667 30.98 0.00 39.33 4.20
849 888 3.079941 CTCGCGCGTCTACTCGACA 62.080 63.158 30.98 4.84 42.98 4.35
850 889 2.938002 CGCGCGTCTACTCGACAC 60.938 66.667 24.19 0.00 42.98 3.67
851 890 2.576317 GCGCGTCTACTCGACACC 60.576 66.667 8.43 0.00 42.98 4.16
852 891 2.276493 CGCGTCTACTCGACACCG 60.276 66.667 0.00 0.00 42.98 4.94
853 892 2.099831 GCGTCTACTCGACACCGG 59.900 66.667 0.00 0.00 42.98 5.28
854 893 2.789917 CGTCTACTCGACACCGGG 59.210 66.667 6.32 0.00 42.98 5.73
855 894 2.488820 GTCTACTCGACACCGGGC 59.511 66.667 6.32 0.00 40.68 6.13
856 895 2.045131 GTCTACTCGACACCGGGCT 61.045 63.158 6.32 0.00 40.68 5.19
857 896 2.044555 TCTACTCGACACCGGGCTG 61.045 63.158 6.32 0.00 40.68 4.85
858 897 3.064987 CTACTCGACACCGGGCTGG 62.065 68.421 11.83 11.83 40.68 4.85
877 916 2.590007 CCCTGCCATCGCTGTAGC 60.590 66.667 0.00 0.00 35.36 3.58
927 967 0.620556 CCCAAGCCCTCTCTGCTTAA 59.379 55.000 0.00 0.00 46.85 1.85
928 968 1.213926 CCCAAGCCCTCTCTGCTTAAT 59.786 52.381 0.00 0.00 46.85 1.40
929 969 2.357569 CCCAAGCCCTCTCTGCTTAATT 60.358 50.000 0.00 0.00 46.85 1.40
931 971 2.948315 CAAGCCCTCTCTGCTTAATTCC 59.052 50.000 0.00 0.00 46.85 3.01
932 972 1.139853 AGCCCTCTCTGCTTAATTCCG 59.860 52.381 0.00 0.00 34.87 4.30
934 974 2.224402 GCCCTCTCTGCTTAATTCCGAT 60.224 50.000 0.00 0.00 0.00 4.18
935 975 3.006967 GCCCTCTCTGCTTAATTCCGATA 59.993 47.826 0.00 0.00 0.00 2.92
937 977 5.611374 CCCTCTCTGCTTAATTCCGATAAA 58.389 41.667 0.00 0.00 0.00 1.40
938 978 6.055588 CCCTCTCTGCTTAATTCCGATAAAA 58.944 40.000 0.00 0.00 0.00 1.52
939 979 6.542370 CCCTCTCTGCTTAATTCCGATAAAAA 59.458 38.462 0.00 0.00 0.00 1.94
983 1023 1.223211 GAAGCTCCCTTCTCCCAGC 59.777 63.158 0.00 0.00 43.31 4.85
1054 1094 1.446272 CTCGCCTCAACCCTTCGAC 60.446 63.158 0.00 0.00 0.00 4.20
1098 1138 2.852075 TCCACCACCACCTCCACC 60.852 66.667 0.00 0.00 0.00 4.61
1143 1183 3.319198 GTGGCCGTCCTCTGGGAA 61.319 66.667 0.00 0.00 44.15 3.97
1188 1228 1.001282 AACTCCCCCTCTACGACTCT 58.999 55.000 0.00 0.00 0.00 3.24
1381 1421 1.078528 ACCATCCACACCCGAGAGA 59.921 57.895 0.00 0.00 0.00 3.10
1384 1424 0.608130 CATCCACACCCGAGAGAACA 59.392 55.000 0.00 0.00 0.00 3.18
1398 1438 2.357517 AACACCAAGCGCCTCGAG 60.358 61.111 2.29 5.13 0.00 4.04
1743 1783 3.357079 GCAAGGTGGGCAGACACG 61.357 66.667 0.00 0.00 42.23 4.49
1770 1810 2.685017 TGGGCAGAGGTGATCGCT 60.685 61.111 6.18 0.00 0.00 4.93
1863 1903 3.634448 AGTGGAGGTATGAAGATGACGAG 59.366 47.826 0.00 0.00 0.00 4.18
1898 1938 1.254975 TTTGAGGAGGACGGCGATGA 61.255 55.000 16.62 0.00 0.00 2.92
1923 1963 1.913262 TTCAGAAGAGCTGGCGGGA 60.913 57.895 0.00 0.00 44.98 5.14
1968 2008 0.763652 AGCTGGAATCAGATGGCGAT 59.236 50.000 0.00 0.00 43.49 4.58
1985 2028 3.065233 GGCGATGACTCATTTTGCACATA 59.935 43.478 11.62 0.00 0.00 2.29
1999 2042 5.940603 TTGCACATAAAAGTGTTTGTTCG 57.059 34.783 0.00 0.00 41.52 3.95
2009 2052 1.583404 GTGTTTGTTCGTTTGCTGCTG 59.417 47.619 0.00 0.00 0.00 4.41
2038 2081 6.295916 GGTTAGGATCCTTCAGAGTTCAGAAA 60.296 42.308 22.03 0.00 0.00 2.52
2100 2143 8.219546 TCTTTGAACAATGATCTGTTTACACA 57.780 30.769 2.22 0.00 39.63 3.72
2101 2144 8.681806 TCTTTGAACAATGATCTGTTTACACAA 58.318 29.630 2.22 0.37 39.63 3.33
2103 2146 7.566760 TGAACAATGATCTGTTTACACAAGT 57.433 32.000 2.22 0.00 39.63 3.16
2104 2147 7.995289 TGAACAATGATCTGTTTACACAAGTT 58.005 30.769 2.22 0.00 39.63 2.66
2105 2148 8.128582 TGAACAATGATCTGTTTACACAAGTTC 58.871 33.333 2.22 0.00 39.63 3.01
2106 2149 7.566760 ACAATGATCTGTTTACACAAGTTCA 57.433 32.000 0.00 0.00 30.36 3.18
2109 2152 7.664082 ATGATCTGTTTACACAAGTTCAGAG 57.336 36.000 0.00 0.00 34.70 3.35
2110 2153 6.816136 TGATCTGTTTACACAAGTTCAGAGA 58.184 36.000 0.00 0.00 34.70 3.10
2111 2154 6.925718 TGATCTGTTTACACAAGTTCAGAGAG 59.074 38.462 0.00 0.00 34.70 3.20
2112 2155 6.465439 TCTGTTTACACAAGTTCAGAGAGA 57.535 37.500 0.00 0.00 30.36 3.10
2113 2156 6.507900 TCTGTTTACACAAGTTCAGAGAGAG 58.492 40.000 0.00 0.00 30.36 3.20
2114 2157 6.096987 TCTGTTTACACAAGTTCAGAGAGAGT 59.903 38.462 0.00 0.00 30.36 3.24
2115 2158 6.640518 TGTTTACACAAGTTCAGAGAGAGTT 58.359 36.000 0.00 0.00 0.00 3.01
2116 2159 6.757010 TGTTTACACAAGTTCAGAGAGAGTTC 59.243 38.462 0.00 0.00 0.00 3.01
2117 2160 6.465439 TTACACAAGTTCAGAGAGAGTTCA 57.535 37.500 0.00 0.00 0.00 3.18
2118 2161 5.344743 ACACAAGTTCAGAGAGAGTTCAA 57.655 39.130 0.00 0.00 0.00 2.69
2119 2162 5.734720 ACACAAGTTCAGAGAGAGTTCAAA 58.265 37.500 0.00 0.00 0.00 2.69
2120 2163 6.352516 ACACAAGTTCAGAGAGAGTTCAAAT 58.647 36.000 0.00 0.00 0.00 2.32
2121 2164 6.259608 ACACAAGTTCAGAGAGAGTTCAAATG 59.740 38.462 0.00 0.00 0.00 2.32
2122 2165 6.481313 CACAAGTTCAGAGAGAGTTCAAATGA 59.519 38.462 0.00 0.00 0.00 2.57
2123 2166 7.172875 CACAAGTTCAGAGAGAGTTCAAATGAT 59.827 37.037 0.00 0.00 0.00 2.45
2124 2167 7.387397 ACAAGTTCAGAGAGAGTTCAAATGATC 59.613 37.037 0.00 0.00 0.00 2.92
2125 2168 7.243604 AGTTCAGAGAGAGTTCAAATGATCT 57.756 36.000 0.00 0.00 0.00 2.75
2126 2169 8.359875 AGTTCAGAGAGAGTTCAAATGATCTA 57.640 34.615 0.00 0.00 0.00 1.98
2127 2170 8.250332 AGTTCAGAGAGAGTTCAAATGATCTAC 58.750 37.037 0.00 0.00 0.00 2.59
2128 2171 7.709149 TCAGAGAGAGTTCAAATGATCTACA 57.291 36.000 0.00 0.00 0.00 2.74
2129 2172 7.542890 TCAGAGAGAGTTCAAATGATCTACAC 58.457 38.462 0.00 0.00 0.00 2.90
2130 2173 6.756074 CAGAGAGAGTTCAAATGATCTACACC 59.244 42.308 0.00 0.00 0.00 4.16
2140 2183 6.599244 TCAAATGATCTACACCAGTTCAATCC 59.401 38.462 0.00 0.00 36.73 3.01
2144 2187 4.974645 TCTACACCAGTTCAATCCAAGT 57.025 40.909 0.00 0.00 0.00 3.16
2145 2188 5.304686 TCTACACCAGTTCAATCCAAGTT 57.695 39.130 0.00 0.00 0.00 2.66
2169 2212 2.503895 ATGCTAGGCAGAGCTTTTGT 57.496 45.000 11.98 0.00 43.65 2.83
2237 2280 1.278238 CTGATCCCTTGCGTTCGTAC 58.722 55.000 0.00 0.00 0.00 3.67
2262 2305 2.912771 TGTGTGTCCTTTGTCGTTGAT 58.087 42.857 0.00 0.00 0.00 2.57
2266 2309 4.688879 GTGTGTCCTTTGTCGTTGATATCA 59.311 41.667 0.00 0.00 0.00 2.15
2272 2315 6.758886 GTCCTTTGTCGTTGATATCAGAGATT 59.241 38.462 5.39 0.00 0.00 2.40
2351 2396 5.084519 TGTCTAGGACAGTGGTAACTTCAT 58.915 41.667 0.00 0.00 37.67 2.57
2357 2402 7.735326 AGGACAGTGGTAACTTCATATTACT 57.265 36.000 0.00 0.00 32.98 2.24
2379 2424 7.173863 ACTGAAACGTTGTTAATACTGAGTG 57.826 36.000 0.00 0.00 0.00 3.51
2387 2432 6.456501 GTTGTTAATACTGAGTGGAGTGAGT 58.543 40.000 0.00 0.00 0.00 3.41
2411 2456 5.123820 TGACACCGAATCATCCATTTCTTTC 59.876 40.000 0.00 0.00 0.00 2.62
2414 2459 4.884164 ACCGAATCATCCATTTCTTTCCTC 59.116 41.667 0.00 0.00 0.00 3.71
2417 2462 5.277058 CGAATCATCCATTTCTTTCCTCGAC 60.277 44.000 0.00 0.00 0.00 4.20
2420 2465 2.955614 TCCATTTCTTTCCTCGACGAC 58.044 47.619 0.00 0.00 0.00 4.34
2492 2537 5.811190 TCCGATTTCCATTAGAGAAACCAA 58.189 37.500 0.00 0.00 36.13 3.67
2494 2539 5.447279 CCGATTTCCATTAGAGAAACCAACG 60.447 44.000 0.00 0.00 36.13 4.10
2501 2546 4.537135 TTAGAGAAACCAACGAGCATCT 57.463 40.909 0.00 0.00 0.00 2.90
2504 2549 2.670414 GAGAAACCAACGAGCATCTGAG 59.330 50.000 0.00 0.00 0.00 3.35
2505 2550 1.129437 GAAACCAACGAGCATCTGAGC 59.871 52.381 0.00 0.00 0.00 4.26
2506 2551 0.035317 AACCAACGAGCATCTGAGCA 59.965 50.000 0.00 0.00 36.85 4.26
2509 2554 0.997932 CAACGAGCATCTGAGCAGTC 59.002 55.000 0.00 0.00 36.85 3.51
2512 2557 0.108945 CGAGCATCTGAGCAGTCACA 60.109 55.000 0.00 0.00 36.85 3.58
2514 2559 0.391395 AGCATCTGAGCAGTCACAGC 60.391 55.000 0.00 0.00 36.85 4.40
2515 2560 1.694018 GCATCTGAGCAGTCACAGCG 61.694 60.000 0.00 0.00 37.01 5.18
2516 2561 0.389556 CATCTGAGCAGTCACAGCGT 60.390 55.000 0.00 0.00 37.01 5.07
2519 2564 1.546029 TCTGAGCAGTCACAGCGTTAT 59.454 47.619 0.00 0.00 37.01 1.89
2520 2565 2.752903 TCTGAGCAGTCACAGCGTTATA 59.247 45.455 0.00 0.00 37.01 0.98
2521 2566 3.111838 CTGAGCAGTCACAGCGTTATAG 58.888 50.000 0.00 0.00 37.01 1.31
2522 2567 2.752903 TGAGCAGTCACAGCGTTATAGA 59.247 45.455 0.00 0.00 37.01 1.98
2523 2568 3.381590 TGAGCAGTCACAGCGTTATAGAT 59.618 43.478 0.00 0.00 37.01 1.98
2524 2569 4.142160 TGAGCAGTCACAGCGTTATAGATT 60.142 41.667 0.00 0.00 37.01 2.40
2526 2571 4.098654 AGCAGTCACAGCGTTATAGATTCT 59.901 41.667 0.00 0.00 37.01 2.40
2527 2572 5.299531 AGCAGTCACAGCGTTATAGATTCTA 59.700 40.000 0.00 0.00 37.01 2.10
2529 2574 6.642950 GCAGTCACAGCGTTATAGATTCTATT 59.357 38.462 11.33 0.00 0.00 1.73
2531 2576 9.119329 CAGTCACAGCGTTATAGATTCTATTAC 57.881 37.037 11.33 11.26 0.00 1.89
2533 2578 9.627395 GTCACAGCGTTATAGATTCTATTACAT 57.373 33.333 18.11 7.36 0.00 2.29
2566 2611 2.751166 TCGAGAGAAAGCAGGGAAAG 57.249 50.000 0.00 0.00 37.03 2.62
2567 2612 2.248248 TCGAGAGAAAGCAGGGAAAGA 58.752 47.619 0.00 0.00 37.03 2.52
2568 2613 2.834549 TCGAGAGAAAGCAGGGAAAGAT 59.165 45.455 0.00 0.00 37.03 2.40
2580 2639 5.041191 CAGGGAAAGATAACACTGCCTAT 57.959 43.478 0.00 0.00 30.82 2.57
2583 2642 4.816925 GGGAAAGATAACACTGCCTATCAC 59.183 45.833 0.00 0.00 0.00 3.06
2598 2657 2.634815 ATCACCAGGCATCTAAGCAG 57.365 50.000 0.00 0.00 35.83 4.24
2599 2658 1.571955 TCACCAGGCATCTAAGCAGA 58.428 50.000 0.00 0.00 35.83 4.26
2600 2659 1.208052 TCACCAGGCATCTAAGCAGAC 59.792 52.381 0.00 0.00 35.83 3.51
2601 2660 1.209019 CACCAGGCATCTAAGCAGACT 59.791 52.381 0.00 0.00 35.83 3.24
2602 2661 2.432146 CACCAGGCATCTAAGCAGACTA 59.568 50.000 0.00 0.00 35.83 2.59
2604 2663 3.133721 ACCAGGCATCTAAGCAGACTAAG 59.866 47.826 0.00 0.00 35.83 2.18
2605 2664 3.129871 CAGGCATCTAAGCAGACTAAGC 58.870 50.000 0.00 0.00 35.83 3.09
2606 2665 3.037549 AGGCATCTAAGCAGACTAAGCT 58.962 45.455 0.00 0.00 45.97 3.74
2607 2666 4.038522 CAGGCATCTAAGCAGACTAAGCTA 59.961 45.833 0.00 0.00 42.53 3.32
2608 2667 4.837860 AGGCATCTAAGCAGACTAAGCTAT 59.162 41.667 0.00 0.00 42.53 2.97
2610 2669 5.637387 GGCATCTAAGCAGACTAAGCTATTC 59.363 44.000 0.00 0.00 42.53 1.75
2612 2671 6.873076 GCATCTAAGCAGACTAAGCTATTCAT 59.127 38.462 0.00 0.00 42.53 2.57
2613 2672 7.063308 GCATCTAAGCAGACTAAGCTATTCATC 59.937 40.741 0.00 0.00 42.53 2.92
2614 2673 7.588497 TCTAAGCAGACTAAGCTATTCATCA 57.412 36.000 0.00 0.00 42.53 3.07
2616 2675 5.212532 AGCAGACTAAGCTATTCATCAGG 57.787 43.478 0.00 0.00 41.32 3.86
2618 2677 5.130145 AGCAGACTAAGCTATTCATCAGGTT 59.870 40.000 0.00 0.00 41.32 3.50
2619 2678 5.236047 GCAGACTAAGCTATTCATCAGGTTG 59.764 44.000 0.00 0.00 35.48 3.77
2625 2684 2.421952 GCTATTCATCAGGTTGCCAGGA 60.422 50.000 0.00 0.00 0.00 3.86
2626 2685 2.905415 ATTCATCAGGTTGCCAGGAA 57.095 45.000 0.00 0.00 0.00 3.36
2633 2692 2.202395 GGTTGCCAGGAAAGCAGCA 61.202 57.895 4.24 0.00 42.57 4.41
2638 2697 2.979676 CAGGAAAGCAGCACGCCA 60.980 61.111 0.00 0.00 44.04 5.69
2641 2700 2.429739 GAAAGCAGCACGCCAAGC 60.430 61.111 0.00 0.00 44.04 4.01
2646 2705 3.818787 CAGCACGCCAAGCCATCC 61.819 66.667 0.00 0.00 0.00 3.51
2670 2729 3.484407 CCATCTATCAGCCCCAAAAGAG 58.516 50.000 0.00 0.00 0.00 2.85
2671 2730 3.137176 CCATCTATCAGCCCCAAAAGAGA 59.863 47.826 0.00 0.00 0.00 3.10
2672 2731 4.202545 CCATCTATCAGCCCCAAAAGAGAT 60.203 45.833 0.00 0.00 0.00 2.75
2673 2732 4.428294 TCTATCAGCCCCAAAAGAGATG 57.572 45.455 0.00 0.00 0.00 2.90
2674 2733 1.772836 ATCAGCCCCAAAAGAGATGC 58.227 50.000 0.00 0.00 0.00 3.91
2675 2734 0.700564 TCAGCCCCAAAAGAGATGCT 59.299 50.000 0.00 0.00 0.00 3.79
2677 2736 0.393537 AGCCCCAAAAGAGATGCTCG 60.394 55.000 0.00 0.00 35.36 5.03
2679 2738 1.826385 CCCCAAAAGAGATGCTCGTT 58.174 50.000 0.00 0.00 33.99 3.85
2680 2739 2.162681 CCCCAAAAGAGATGCTCGTTT 58.837 47.619 3.14 3.14 41.33 3.60
2681 2740 2.558359 CCCCAAAAGAGATGCTCGTTTT 59.442 45.455 5.77 3.36 39.38 2.43
2683 2742 4.229876 CCCAAAAGAGATGCTCGTTTTTC 58.770 43.478 5.77 0.00 39.38 2.29
2684 2743 4.261572 CCCAAAAGAGATGCTCGTTTTTCA 60.262 41.667 5.77 0.00 39.38 2.69
2685 2744 5.280945 CCAAAAGAGATGCTCGTTTTTCAA 58.719 37.500 5.77 0.00 39.38 2.69
2686 2745 5.922544 CCAAAAGAGATGCTCGTTTTTCAAT 59.077 36.000 5.77 0.00 39.38 2.57
2687 2746 6.088616 CCAAAAGAGATGCTCGTTTTTCAATC 59.911 38.462 5.77 0.00 39.38 2.67
2688 2747 4.954092 AGAGATGCTCGTTTTTCAATCC 57.046 40.909 0.00 0.00 35.36 3.01
2690 2749 4.394300 AGAGATGCTCGTTTTTCAATCCTG 59.606 41.667 0.00 0.00 35.36 3.86
2691 2750 4.326826 AGATGCTCGTTTTTCAATCCTGA 58.673 39.130 0.00 0.00 0.00 3.86
2692 2751 4.761739 AGATGCTCGTTTTTCAATCCTGAA 59.238 37.500 0.00 0.00 39.87 3.02
2693 2752 4.488126 TGCTCGTTTTTCAATCCTGAAG 57.512 40.909 0.00 0.00 42.48 3.02
2702 2761 2.688507 TCAATCCTGAAGTCGAAGCAC 58.311 47.619 0.00 0.00 0.00 4.40
2715 2774 3.483235 AAGCACGCCAAAACGCCAG 62.483 57.895 0.00 0.00 36.19 4.85
2733 2792 3.799755 CCTTGCGCCGCCTTGTAC 61.800 66.667 6.63 0.00 0.00 2.90
2735 2794 3.308878 CTTGCGCCGCCTTGTACAC 62.309 63.158 6.63 0.00 0.00 2.90
2736 2795 3.818121 TTGCGCCGCCTTGTACACT 62.818 57.895 6.63 0.00 0.00 3.55
2738 2797 3.023591 GCGCCGCCTTGTACACTTC 62.024 63.158 0.00 0.00 0.00 3.01
2739 2798 1.666553 CGCCGCCTTGTACACTTCA 60.667 57.895 0.00 0.00 0.00 3.02
2748 2807 4.632153 CCTTGTACACTTCACTTGCTACT 58.368 43.478 0.00 0.00 0.00 2.57
2751 2810 5.018539 TGTACACTTCACTTGCTACTTGT 57.981 39.130 0.00 0.00 0.00 3.16
2754 2813 3.555956 ACACTTCACTTGCTACTTGTTCG 59.444 43.478 0.00 0.00 0.00 3.95
2761 2820 4.449068 CACTTGCTACTTGTTCGATGAGTT 59.551 41.667 1.88 0.00 0.00 3.01
2796 2855 1.095600 GCGATTTTTCCTCTGGGTCC 58.904 55.000 0.00 0.00 0.00 4.46
2800 2859 3.826729 CGATTTTTCCTCTGGGTCCTTTT 59.173 43.478 0.00 0.00 0.00 2.27
2801 2860 4.321230 CGATTTTTCCTCTGGGTCCTTTTG 60.321 45.833 0.00 0.00 0.00 2.44
2818 2880 5.002516 CCTTTTGCAAAATAGCCCAATCAA 58.997 37.500 24.06 0.00 0.00 2.57
2835 2897 5.764192 CCAATCAAAAATCCAACCACACATT 59.236 36.000 0.00 0.00 0.00 2.71
2837 2899 7.095271 CCAATCAAAAATCCAACCACACATTAC 60.095 37.037 0.00 0.00 0.00 1.89
2841 2904 7.708752 TCAAAAATCCAACCACACATTACTTTC 59.291 33.333 0.00 0.00 0.00 2.62
2844 2907 4.787551 TCCAACCACACATTACTTTCACT 58.212 39.130 0.00 0.00 0.00 3.41
2847 2910 7.001674 TCCAACCACACATTACTTTCACTATT 58.998 34.615 0.00 0.00 0.00 1.73
2856 2919 6.607198 ACATTACTTTCACTATTCCCATTGGG 59.393 38.462 16.26 16.26 46.11 4.12
2858 2921 4.600062 ACTTTCACTATTCCCATTGGGTC 58.400 43.478 21.31 0.00 44.74 4.46
2862 2925 4.367166 TCACTATTCCCATTGGGTCAGTA 58.633 43.478 21.31 9.18 44.74 2.74
2863 2926 4.785914 TCACTATTCCCATTGGGTCAGTAA 59.214 41.667 21.31 8.38 44.74 2.24
2864 2927 4.881850 CACTATTCCCATTGGGTCAGTAAC 59.118 45.833 21.31 0.00 44.74 2.50
2865 2928 4.788617 ACTATTCCCATTGGGTCAGTAACT 59.211 41.667 21.31 0.00 44.74 2.24
2867 2930 4.463050 TTCCCATTGGGTCAGTAACTTT 57.537 40.909 21.31 0.00 44.74 2.66
2913 2976 9.349713 TCATTTCTACATTTCCATATTACCCAC 57.650 33.333 0.00 0.00 0.00 4.61
2916 2979 8.746052 TTCTACATTTCCATATTACCCACAAG 57.254 34.615 0.00 0.00 0.00 3.16
2919 2982 6.969043 ACATTTCCATATTACCCACAAGAGA 58.031 36.000 0.00 0.00 0.00 3.10
2921 2984 4.689612 TCCATATTACCCACAAGAGAGC 57.310 45.455 0.00 0.00 0.00 4.09
2922 2985 4.037222 TCCATATTACCCACAAGAGAGCA 58.963 43.478 0.00 0.00 0.00 4.26
2925 2988 3.902881 ATTACCCACAAGAGAGCAGAG 57.097 47.619 0.00 0.00 0.00 3.35
2928 2991 1.203187 ACCCACAAGAGAGCAGAGGTA 60.203 52.381 0.00 0.00 0.00 3.08
2949 3012 6.235664 GGTACCAACCAGAATCAGTTTCTTA 58.764 40.000 7.15 0.00 42.98 2.10
2955 3018 9.177608 CCAACCAGAATCAGTTTCTTATTATCA 57.822 33.333 0.00 0.00 42.15 2.15
2979 3042 8.587608 TCAGATGTGAAATTCTTTAGCCAATTT 58.412 29.630 0.00 0.00 35.38 1.82
2985 3048 7.118245 GTGAAATTCTTTAGCCAATTTCCAAGG 59.882 37.037 12.36 0.00 43.75 3.61
2986 3049 8.222883 TGAAATTCTTTAGCCAATTTCCAAGGC 61.223 37.037 12.36 0.00 43.75 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.342862 AGCCCATAATACACTAGCACAG 57.657 45.455 0.00 0.00 0.00 3.66
43 44 6.615088 TCTGAAAATGCAAGAGTTTCTATGC 58.385 36.000 13.37 0.00 39.04 3.14
64 65 9.642327 TTCAAATCAATCCACATTACATTTCTG 57.358 29.630 0.00 0.00 0.00 3.02
150 151 0.529337 CTCCATCTTCACGCGAGCAT 60.529 55.000 15.93 0.00 0.00 3.79
171 172 4.713792 AGGATAACCCTGGTCATGAATC 57.286 45.455 0.00 0.00 45.61 2.52
189 190 1.690633 GGGGTGCTCAGGATCAGGA 60.691 63.158 0.00 0.00 0.00 3.86
201 206 1.077429 GTGATCTGGAAGGGGGTGC 60.077 63.158 0.00 0.00 0.00 5.01
221 226 2.047061 TGTCAAGCTCAACTACCCTGT 58.953 47.619 0.00 0.00 0.00 4.00
262 267 1.876156 CTTGGTGAGAAGCACTTGACC 59.124 52.381 0.00 0.00 46.86 4.02
289 294 3.096092 GCAGATTTGACATTACCCCCAA 58.904 45.455 0.00 0.00 0.00 4.12
418 423 1.615116 CCTGATCTTCTTTGCTGGCCA 60.615 52.381 4.71 4.71 0.00 5.36
419 424 1.101331 CCTGATCTTCTTTGCTGGCC 58.899 55.000 0.00 0.00 0.00 5.36
468 479 1.212616 GTCGCGGGATCTTCATCTTG 58.787 55.000 6.13 0.00 0.00 3.02
485 496 0.875059 CTTGTTTTCCTCCAGCGGTC 59.125 55.000 0.00 0.00 0.00 4.79
633 667 2.618709 AGTTCAGGTAACAACAGCTTGC 59.381 45.455 0.00 0.00 40.83 4.01
669 708 2.162681 GCCTCCCCCGATTTCATTATG 58.837 52.381 0.00 0.00 0.00 1.90
676 715 4.489771 CAGCGCCTCCCCCGATTT 62.490 66.667 2.29 0.00 0.00 2.17
730 769 9.083080 CGATCATGATAGTACAACAAACACTAA 57.917 33.333 8.54 0.00 0.00 2.24
731 770 8.463607 TCGATCATGATAGTACAACAAACACTA 58.536 33.333 8.54 0.00 0.00 2.74
732 771 7.320399 TCGATCATGATAGTACAACAAACACT 58.680 34.615 8.54 0.00 0.00 3.55
733 772 7.520119 TCGATCATGATAGTACAACAAACAC 57.480 36.000 8.54 0.00 0.00 3.32
734 773 8.032451 TCTTCGATCATGATAGTACAACAAACA 58.968 33.333 8.54 0.00 0.00 2.83
735 774 8.407457 TCTTCGATCATGATAGTACAACAAAC 57.593 34.615 8.54 0.00 0.00 2.93
736 775 9.034544 CATCTTCGATCATGATAGTACAACAAA 57.965 33.333 8.54 0.00 0.00 2.83
737 776 8.413229 TCATCTTCGATCATGATAGTACAACAA 58.587 33.333 8.54 0.00 0.00 2.83
738 777 7.940850 TCATCTTCGATCATGATAGTACAACA 58.059 34.615 8.54 0.00 0.00 3.33
739 778 8.803201 TTCATCTTCGATCATGATAGTACAAC 57.197 34.615 8.54 0.00 0.00 3.32
747 786 8.968969 TCTGATCTATTCATCTTCGATCATGAT 58.031 33.333 8.25 8.25 39.53 2.45
748 787 8.345724 TCTGATCTATTCATCTTCGATCATGA 57.654 34.615 0.00 0.00 39.53 3.07
749 788 8.983307 TTCTGATCTATTCATCTTCGATCATG 57.017 34.615 0.00 0.00 39.53 3.07
750 789 8.805175 ACTTCTGATCTATTCATCTTCGATCAT 58.195 33.333 0.00 0.00 39.53 2.45
751 790 8.175925 ACTTCTGATCTATTCATCTTCGATCA 57.824 34.615 0.00 0.00 38.41 2.92
752 791 9.474920 AAACTTCTGATCTATTCATCTTCGATC 57.525 33.333 0.00 0.00 32.72 3.69
787 826 5.476254 CCCCATTTTGCATTACATGGTTTTT 59.524 36.000 0.00 0.00 35.31 1.94
788 827 5.008980 CCCCATTTTGCATTACATGGTTTT 58.991 37.500 0.00 0.00 35.31 2.43
789 828 4.567327 CCCCCATTTTGCATTACATGGTTT 60.567 41.667 0.00 0.00 35.31 3.27
790 829 3.054508 CCCCCATTTTGCATTACATGGTT 60.055 43.478 0.00 0.00 35.31 3.67
791 830 2.504996 CCCCCATTTTGCATTACATGGT 59.495 45.455 0.00 0.00 35.31 3.55
792 831 2.745812 GCCCCCATTTTGCATTACATGG 60.746 50.000 0.00 6.89 36.66 3.66
793 832 2.093075 TGCCCCCATTTTGCATTACATG 60.093 45.455 0.00 0.00 0.00 3.21
794 833 2.194859 TGCCCCCATTTTGCATTACAT 58.805 42.857 0.00 0.00 0.00 2.29
795 834 1.649321 TGCCCCCATTTTGCATTACA 58.351 45.000 0.00 0.00 0.00 2.41
796 835 2.777832 TTGCCCCCATTTTGCATTAC 57.222 45.000 0.00 0.00 34.51 1.89
797 836 3.795688 TTTTGCCCCCATTTTGCATTA 57.204 38.095 0.00 0.00 34.51 1.90
798 837 2.671896 TTTTGCCCCCATTTTGCATT 57.328 40.000 0.00 0.00 34.51 3.56
799 838 2.671896 TTTTTGCCCCCATTTTGCAT 57.328 40.000 0.00 0.00 34.51 3.96
816 855 1.485124 GCGAGGGGGATTGGATTTTT 58.515 50.000 0.00 0.00 0.00 1.94
817 856 0.751643 CGCGAGGGGGATTGGATTTT 60.752 55.000 0.00 0.00 0.00 1.82
818 857 1.152963 CGCGAGGGGGATTGGATTT 60.153 57.895 0.00 0.00 0.00 2.17
819 858 2.510906 CGCGAGGGGGATTGGATT 59.489 61.111 0.00 0.00 0.00 3.01
820 859 4.256180 GCGCGAGGGGGATTGGAT 62.256 66.667 12.10 0.00 0.00 3.41
830 869 3.561213 TCGAGTAGACGCGCGAGG 61.561 66.667 39.36 15.98 39.01 4.63
831 870 2.349869 GTCGAGTAGACGCGCGAG 60.350 66.667 39.36 10.29 40.93 5.03
839 878 2.044555 CAGCCCGGTGTCGAGTAGA 61.045 63.158 0.00 0.00 39.00 2.59
840 879 2.490217 CAGCCCGGTGTCGAGTAG 59.510 66.667 0.00 0.00 39.00 2.57
841 880 3.066190 CCAGCCCGGTGTCGAGTA 61.066 66.667 0.00 0.00 39.00 2.59
859 898 2.590007 CTACAGCGATGGCAGGGC 60.590 66.667 5.32 4.54 43.41 5.19
860 899 2.590007 GCTACAGCGATGGCAGGG 60.590 66.667 5.32 0.00 43.41 4.45
861 900 2.176273 GTGCTACAGCGATGGCAGG 61.176 63.158 5.32 0.00 45.83 4.85
862 901 1.426816 CTGTGCTACAGCGATGGCAG 61.427 60.000 5.32 2.59 45.83 4.85
863 902 1.448365 CTGTGCTACAGCGATGGCA 60.448 57.895 5.32 2.51 45.83 4.92
864 903 2.176273 CCTGTGCTACAGCGATGGC 61.176 63.158 5.32 0.00 44.63 4.40
865 904 1.522355 CCCTGTGCTACAGCGATGG 60.522 63.158 5.32 0.00 44.63 3.51
897 936 4.432741 GCTTGGGAGCTGGGGGTC 62.433 72.222 0.00 0.00 45.65 4.46
983 1023 2.423538 GACATGGGAAAGGGAAATCACG 59.576 50.000 0.00 0.00 0.00 4.35
1054 1094 3.610669 CGAGGGCGATGGGAGGAG 61.611 72.222 0.00 0.00 40.82 3.69
1170 1210 0.256464 CAGAGTCGTAGAGGGGGAGT 59.744 60.000 0.00 0.00 36.95 3.85
1269 1309 2.041819 GAGGGATCAGGGTCGGGT 60.042 66.667 0.00 0.00 0.00 5.28
1381 1421 2.357517 CTCGAGGCGCTTGGTGTT 60.358 61.111 7.64 0.00 0.00 3.32
1398 1438 2.026301 CGGGAGGACTCGATTCGC 59.974 66.667 0.00 0.00 43.41 4.70
1743 1783 3.635268 CTCTGCCCAGGTGAAGCCC 62.635 68.421 0.00 0.00 38.26 5.19
1863 1903 3.142174 CTCAAACACCACTTCTTCCTCC 58.858 50.000 0.00 0.00 0.00 4.30
1898 1938 2.617532 GCCAGCTCTTCTGAACCATCTT 60.618 50.000 0.00 0.00 45.72 2.40
1923 1963 1.039856 ATGGCTTTCCGTTTGCACTT 58.960 45.000 0.00 0.00 34.14 3.16
1968 2008 6.804677 ACACTTTTATGTGCAAAATGAGTCA 58.195 32.000 0.00 0.00 41.30 3.41
1985 2028 3.122780 GCAGCAAACGAACAAACACTTTT 59.877 39.130 0.00 0.00 0.00 2.27
2017 2060 5.832539 TTTTCTGAACTCTGAAGGATCCT 57.167 39.130 9.02 9.02 35.68 3.24
2038 2081 4.917385 TGGTGTAGCATAATCCACACTTT 58.083 39.130 3.97 0.00 40.82 2.66
2096 2139 5.344743 TTGAACTCTCTCTGAACTTGTGT 57.655 39.130 0.00 0.00 0.00 3.72
2100 2143 7.678837 AGATCATTTGAACTCTCTCTGAACTT 58.321 34.615 0.00 0.00 0.00 2.66
2101 2144 7.243604 AGATCATTTGAACTCTCTCTGAACT 57.756 36.000 0.00 0.00 0.00 3.01
2103 2146 8.031864 GTGTAGATCATTTGAACTCTCTCTGAA 58.968 37.037 0.00 0.00 0.00 3.02
2104 2147 7.363355 GGTGTAGATCATTTGAACTCTCTCTGA 60.363 40.741 0.00 0.00 0.00 3.27
2105 2148 6.756074 GGTGTAGATCATTTGAACTCTCTCTG 59.244 42.308 0.00 0.00 0.00 3.35
2106 2149 6.438741 TGGTGTAGATCATTTGAACTCTCTCT 59.561 38.462 0.00 0.00 0.00 3.10
2109 2152 6.402222 ACTGGTGTAGATCATTTGAACTCTC 58.598 40.000 0.00 0.00 0.00 3.20
2110 2153 6.365970 ACTGGTGTAGATCATTTGAACTCT 57.634 37.500 0.00 0.00 0.00 3.24
2111 2154 6.650807 TGAACTGGTGTAGATCATTTGAACTC 59.349 38.462 0.00 0.00 33.77 3.01
2112 2155 6.533730 TGAACTGGTGTAGATCATTTGAACT 58.466 36.000 0.00 0.00 33.77 3.01
2113 2156 6.801539 TGAACTGGTGTAGATCATTTGAAC 57.198 37.500 0.00 0.00 33.77 3.18
2114 2157 7.121168 GGATTGAACTGGTGTAGATCATTTGAA 59.879 37.037 0.00 0.00 37.93 2.69
2115 2158 6.599244 GGATTGAACTGGTGTAGATCATTTGA 59.401 38.462 0.00 0.00 37.93 2.69
2116 2159 6.375174 TGGATTGAACTGGTGTAGATCATTTG 59.625 38.462 0.00 0.00 37.93 2.32
2117 2160 6.484288 TGGATTGAACTGGTGTAGATCATTT 58.516 36.000 0.00 0.00 37.93 2.32
2118 2161 6.065976 TGGATTGAACTGGTGTAGATCATT 57.934 37.500 0.00 0.00 37.93 2.57
2119 2162 5.698741 TGGATTGAACTGGTGTAGATCAT 57.301 39.130 0.00 0.00 37.93 2.45
2120 2163 5.013079 ACTTGGATTGAACTGGTGTAGATCA 59.987 40.000 0.00 0.00 36.54 2.92
2121 2164 5.491982 ACTTGGATTGAACTGGTGTAGATC 58.508 41.667 0.00 0.00 0.00 2.75
2122 2165 5.505181 ACTTGGATTGAACTGGTGTAGAT 57.495 39.130 0.00 0.00 0.00 1.98
2123 2166 4.974645 ACTTGGATTGAACTGGTGTAGA 57.025 40.909 0.00 0.00 0.00 2.59
2124 2167 6.263168 AGAAAACTTGGATTGAACTGGTGTAG 59.737 38.462 0.00 0.00 0.00 2.74
2125 2168 6.126409 AGAAAACTTGGATTGAACTGGTGTA 58.874 36.000 0.00 0.00 0.00 2.90
2126 2169 4.956075 AGAAAACTTGGATTGAACTGGTGT 59.044 37.500 0.00 0.00 0.00 4.16
2127 2170 5.520376 AGAAAACTTGGATTGAACTGGTG 57.480 39.130 0.00 0.00 0.00 4.17
2128 2171 6.294731 GCATAGAAAACTTGGATTGAACTGGT 60.295 38.462 0.00 0.00 0.00 4.00
2129 2172 6.071728 AGCATAGAAAACTTGGATTGAACTGG 60.072 38.462 0.00 0.00 0.00 4.00
2130 2173 6.917533 AGCATAGAAAACTTGGATTGAACTG 58.082 36.000 0.00 0.00 0.00 3.16
2140 2183 4.034975 GCTCTGCCTAGCATAGAAAACTTG 59.965 45.833 6.19 0.00 42.77 3.16
2144 2187 4.494091 AAGCTCTGCCTAGCATAGAAAA 57.506 40.909 9.75 0.00 42.77 2.29
2145 2188 4.494091 AAAGCTCTGCCTAGCATAGAAA 57.506 40.909 9.75 0.00 42.77 2.52
2237 2280 1.660052 CGACAAAGGACACACATTGCG 60.660 52.381 0.00 0.00 0.00 4.85
2272 2315 8.362639 ACAAACGAGTACAAAGGAGTAGAAATA 58.637 33.333 0.00 0.00 0.00 1.40
2357 2402 6.282167 TCCACTCAGTATTAACAACGTTTCA 58.718 36.000 0.00 0.00 0.00 2.69
2379 2424 1.272490 TGATTCGGTGTCACTCACTCC 59.728 52.381 2.35 0.00 45.50 3.85
2387 2432 4.220693 AGAAATGGATGATTCGGTGTCA 57.779 40.909 0.00 0.00 0.00 3.58
2393 2438 4.811024 TCGAGGAAAGAAATGGATGATTCG 59.189 41.667 0.00 0.00 0.00 3.34
2411 2456 2.202362 CACGCTGAGTCGTCGAGG 60.202 66.667 10.25 0.00 41.21 4.63
2414 2459 2.872001 GCTCACGCTGAGTCGTCG 60.872 66.667 13.91 2.79 45.94 5.12
2417 2462 1.010935 ATGTTGCTCACGCTGAGTCG 61.011 55.000 13.91 0.00 45.94 4.18
2420 2465 5.663795 ATAATAATGTTGCTCACGCTGAG 57.336 39.130 9.73 9.73 46.90 3.35
2492 2537 0.108898 GTGACTGCTCAGATGCTCGT 60.109 55.000 3.60 0.00 0.00 4.18
2494 2539 1.642728 CTGTGACTGCTCAGATGCTC 58.357 55.000 3.60 0.00 37.74 4.26
2501 2546 2.752903 TCTATAACGCTGTGACTGCTCA 59.247 45.455 12.54 0.00 0.00 4.26
2504 2549 4.363999 AGAATCTATAACGCTGTGACTGC 58.636 43.478 4.22 4.22 0.00 4.40
2505 2550 9.119329 GTAATAGAATCTATAACGCTGTGACTG 57.881 37.037 2.84 0.00 0.00 3.51
2506 2551 8.847196 TGTAATAGAATCTATAACGCTGTGACT 58.153 33.333 2.84 0.00 0.00 3.41
2533 2578 8.201464 TGCTTTCTCTCGATGTAATATTGGTAA 58.799 33.333 0.00 0.00 0.00 2.85
2534 2579 7.722363 TGCTTTCTCTCGATGTAATATTGGTA 58.278 34.615 0.00 0.00 0.00 3.25
2538 2583 6.042093 TCCCTGCTTTCTCTCGATGTAATATT 59.958 38.462 0.00 0.00 0.00 1.28
2540 2585 4.893524 TCCCTGCTTTCTCTCGATGTAATA 59.106 41.667 0.00 0.00 0.00 0.98
2542 2587 3.096852 TCCCTGCTTTCTCTCGATGTAA 58.903 45.455 0.00 0.00 0.00 2.41
2543 2588 2.735151 TCCCTGCTTTCTCTCGATGTA 58.265 47.619 0.00 0.00 0.00 2.29
2544 2589 1.561643 TCCCTGCTTTCTCTCGATGT 58.438 50.000 0.00 0.00 0.00 3.06
2545 2590 2.680312 TTCCCTGCTTTCTCTCGATG 57.320 50.000 0.00 0.00 0.00 3.84
2546 2591 2.834549 TCTTTCCCTGCTTTCTCTCGAT 59.165 45.455 0.00 0.00 0.00 3.59
2548 2593 2.751166 TCTTTCCCTGCTTTCTCTCG 57.249 50.000 0.00 0.00 0.00 4.04
2549 2594 5.352846 GTGTTATCTTTCCCTGCTTTCTCTC 59.647 44.000 0.00 0.00 0.00 3.20
2551 2596 5.123027 CAGTGTTATCTTTCCCTGCTTTCTC 59.877 44.000 0.00 0.00 0.00 2.87
2552 2597 5.006386 CAGTGTTATCTTTCCCTGCTTTCT 58.994 41.667 0.00 0.00 0.00 2.52
2554 2599 3.507622 GCAGTGTTATCTTTCCCTGCTTT 59.492 43.478 0.00 0.00 41.48 3.51
2555 2600 3.084786 GCAGTGTTATCTTTCCCTGCTT 58.915 45.455 0.00 0.00 41.48 3.91
2557 2602 1.745653 GGCAGTGTTATCTTTCCCTGC 59.254 52.381 0.00 0.00 43.39 4.85
2558 2603 3.356529 AGGCAGTGTTATCTTTCCCTG 57.643 47.619 0.00 0.00 0.00 4.45
2560 2605 4.816925 GTGATAGGCAGTGTTATCTTTCCC 59.183 45.833 14.07 0.00 0.00 3.97
2561 2606 4.816925 GGTGATAGGCAGTGTTATCTTTCC 59.183 45.833 14.07 11.05 0.00 3.13
2562 2607 5.428253 TGGTGATAGGCAGTGTTATCTTTC 58.572 41.667 14.07 7.71 0.00 2.62
2563 2608 5.431765 CTGGTGATAGGCAGTGTTATCTTT 58.568 41.667 14.07 0.00 0.00 2.52
2564 2609 4.141620 CCTGGTGATAGGCAGTGTTATCTT 60.142 45.833 14.07 0.00 0.00 2.40
2566 2611 3.733337 CCTGGTGATAGGCAGTGTTATC 58.267 50.000 8.85 8.85 0.00 1.75
2567 2612 3.845781 CCTGGTGATAGGCAGTGTTAT 57.154 47.619 0.00 0.00 0.00 1.89
2580 2639 1.208052 GTCTGCTTAGATGCCTGGTGA 59.792 52.381 0.00 0.00 0.00 4.02
2583 2642 3.726607 CTTAGTCTGCTTAGATGCCTGG 58.273 50.000 0.00 0.00 0.00 4.45
2590 2649 7.255766 CCTGATGAATAGCTTAGTCTGCTTAGA 60.256 40.741 0.00 0.00 41.46 2.10
2591 2650 6.867816 CCTGATGAATAGCTTAGTCTGCTTAG 59.132 42.308 0.00 0.00 41.46 2.18
2592 2651 6.325028 ACCTGATGAATAGCTTAGTCTGCTTA 59.675 38.462 0.00 0.00 41.46 3.09
2593 2652 5.130145 ACCTGATGAATAGCTTAGTCTGCTT 59.870 40.000 0.00 0.00 41.46 3.91
2595 2654 4.954875 ACCTGATGAATAGCTTAGTCTGC 58.045 43.478 0.00 0.00 0.00 4.26
2598 2657 4.513318 GGCAACCTGATGAATAGCTTAGTC 59.487 45.833 0.00 0.00 0.00 2.59
2599 2658 4.080356 TGGCAACCTGATGAATAGCTTAGT 60.080 41.667 0.00 0.00 0.00 2.24
2600 2659 4.454678 TGGCAACCTGATGAATAGCTTAG 58.545 43.478 0.00 0.00 0.00 2.18
2601 2660 4.454678 CTGGCAACCTGATGAATAGCTTA 58.545 43.478 0.00 0.00 0.00 3.09
2602 2661 3.285484 CTGGCAACCTGATGAATAGCTT 58.715 45.455 0.00 0.00 0.00 3.74
2604 2663 1.952296 CCTGGCAACCTGATGAATAGC 59.048 52.381 0.00 0.00 0.00 2.97
2605 2664 3.565764 TCCTGGCAACCTGATGAATAG 57.434 47.619 0.00 0.00 0.00 1.73
2606 2665 4.272489 CTTTCCTGGCAACCTGATGAATA 58.728 43.478 0.00 0.00 0.00 1.75
2607 2666 2.905415 TTCCTGGCAACCTGATGAAT 57.095 45.000 0.00 0.00 0.00 2.57
2608 2667 2.517959 CTTTCCTGGCAACCTGATGAA 58.482 47.619 0.00 0.00 0.00 2.57
2610 2669 0.529378 GCTTTCCTGGCAACCTGATG 59.471 55.000 0.00 0.00 0.00 3.07
2612 2671 0.538057 CTGCTTTCCTGGCAACCTGA 60.538 55.000 0.00 0.00 39.30 3.86
2613 2672 1.962144 CTGCTTTCCTGGCAACCTG 59.038 57.895 0.00 0.00 39.30 4.00
2614 2673 1.905354 GCTGCTTTCCTGGCAACCT 60.905 57.895 0.00 0.00 39.30 3.50
2616 2675 1.006922 GTGCTGCTTTCCTGGCAAC 60.007 57.895 0.00 0.00 39.30 4.17
2618 2677 2.979676 CGTGCTGCTTTCCTGGCA 60.980 61.111 0.00 0.00 38.10 4.92
2619 2678 4.410743 GCGTGCTGCTTTCCTGGC 62.411 66.667 0.00 0.00 41.73 4.85
2625 2684 3.982241 GGCTTGGCGTGCTGCTTT 61.982 61.111 0.00 0.00 45.43 3.51
2646 2705 1.067762 TTGGGGCTGATAGATGGGGG 61.068 60.000 0.00 0.00 0.00 5.40
2647 2706 0.852842 TTTGGGGCTGATAGATGGGG 59.147 55.000 0.00 0.00 0.00 4.96
2648 2707 2.175499 TCTTTTGGGGCTGATAGATGGG 59.825 50.000 0.00 0.00 0.00 4.00
2649 2708 3.137176 TCTCTTTTGGGGCTGATAGATGG 59.863 47.826 0.00 0.00 0.00 3.51
2650 2709 4.428294 TCTCTTTTGGGGCTGATAGATG 57.572 45.455 0.00 0.00 0.00 2.90
2651 2710 4.749166 GCATCTCTTTTGGGGCTGATAGAT 60.749 45.833 0.00 0.00 0.00 1.98
2652 2711 3.434167 GCATCTCTTTTGGGGCTGATAGA 60.434 47.826 0.00 0.00 0.00 1.98
2653 2712 2.883386 GCATCTCTTTTGGGGCTGATAG 59.117 50.000 0.00 0.00 0.00 2.08
2654 2713 2.511218 AGCATCTCTTTTGGGGCTGATA 59.489 45.455 0.00 0.00 0.00 2.15
2658 2717 0.393537 CGAGCATCTCTTTTGGGGCT 60.394 55.000 0.00 0.00 0.00 5.19
2660 2719 1.826385 AACGAGCATCTCTTTTGGGG 58.174 50.000 0.00 0.00 0.00 4.96
2661 2720 3.923017 AAAACGAGCATCTCTTTTGGG 57.077 42.857 0.00 0.00 33.37 4.12
2670 2729 4.685169 TCAGGATTGAAAAACGAGCATC 57.315 40.909 0.00 0.00 0.00 3.91
2671 2730 4.520492 ACTTCAGGATTGAAAAACGAGCAT 59.480 37.500 0.00 0.00 42.48 3.79
2672 2731 3.882888 ACTTCAGGATTGAAAAACGAGCA 59.117 39.130 0.00 0.00 42.48 4.26
2673 2732 4.467735 GACTTCAGGATTGAAAAACGAGC 58.532 43.478 0.00 0.00 42.48 5.03
2674 2733 4.447724 TCGACTTCAGGATTGAAAAACGAG 59.552 41.667 0.00 0.00 42.48 4.18
2675 2734 4.373527 TCGACTTCAGGATTGAAAAACGA 58.626 39.130 0.00 0.00 42.48 3.85
2677 2736 4.912187 GCTTCGACTTCAGGATTGAAAAAC 59.088 41.667 0.00 0.00 42.48 2.43
2679 2738 4.024048 GTGCTTCGACTTCAGGATTGAAAA 60.024 41.667 0.00 0.00 42.48 2.29
2680 2739 3.498397 GTGCTTCGACTTCAGGATTGAAA 59.502 43.478 0.00 0.00 42.48 2.69
2681 2740 3.067106 GTGCTTCGACTTCAGGATTGAA 58.933 45.455 0.00 0.00 40.92 2.69
2683 2742 1.391485 CGTGCTTCGACTTCAGGATTG 59.609 52.381 0.00 0.00 42.86 2.67
2684 2743 1.714794 CGTGCTTCGACTTCAGGATT 58.285 50.000 0.00 0.00 42.86 3.01
2685 2744 0.737715 GCGTGCTTCGACTTCAGGAT 60.738 55.000 6.11 0.00 42.86 3.24
2686 2745 1.372997 GCGTGCTTCGACTTCAGGA 60.373 57.895 6.11 0.00 42.86 3.86
2687 2746 2.383527 GGCGTGCTTCGACTTCAGG 61.384 63.158 6.11 0.00 45.28 3.86
2688 2747 3.159984 GGCGTGCTTCGACTTCAG 58.840 61.111 6.11 0.00 45.28 3.02
2733 2792 3.802139 TCGAACAAGTAGCAAGTGAAGTG 59.198 43.478 0.00 0.00 0.00 3.16
2735 2794 4.686091 TCATCGAACAAGTAGCAAGTGAAG 59.314 41.667 0.00 0.00 0.00 3.02
2736 2795 4.627058 TCATCGAACAAGTAGCAAGTGAA 58.373 39.130 0.00 0.00 0.00 3.18
2738 2797 3.990469 ACTCATCGAACAAGTAGCAAGTG 59.010 43.478 0.00 0.00 0.00 3.16
2739 2798 4.258702 ACTCATCGAACAAGTAGCAAGT 57.741 40.909 0.00 0.00 0.00 3.16
2773 2832 2.025887 ACCCAGAGGAAAAATCGCTGAT 60.026 45.455 0.00 0.00 34.67 2.90
2777 2836 1.095600 GGACCCAGAGGAAAAATCGC 58.904 55.000 0.00 0.00 36.73 4.58
2779 2838 4.561530 GCAAAAGGACCCAGAGGAAAAATC 60.562 45.833 0.00 0.00 36.73 2.17
2780 2839 3.324846 GCAAAAGGACCCAGAGGAAAAAT 59.675 43.478 0.00 0.00 36.73 1.82
2782 2841 2.316108 GCAAAAGGACCCAGAGGAAAA 58.684 47.619 0.00 0.00 36.73 2.29
2796 2855 6.557291 TTTGATTGGGCTATTTTGCAAAAG 57.443 33.333 27.08 16.98 34.04 2.27
2800 2859 5.647225 GGATTTTTGATTGGGCTATTTTGCA 59.353 36.000 0.00 0.00 34.04 4.08
2801 2860 5.647225 TGGATTTTTGATTGGGCTATTTTGC 59.353 36.000 0.00 0.00 0.00 3.68
2818 2880 6.983890 GTGAAAGTAATGTGTGGTTGGATTTT 59.016 34.615 0.00 0.00 0.00 1.82
2867 2930 9.912634 GAAATGATATTGTCTTTGACAGGAAAA 57.087 29.630 0.66 0.00 43.69 2.29
2871 2934 9.166173 TGTAGAAATGATATTGTCTTTGACAGG 57.834 33.333 0.66 0.00 43.69 4.00
2899 2962 4.473196 TGCTCTCTTGTGGGTAATATGGAA 59.527 41.667 0.00 0.00 0.00 3.53
2904 2967 3.706594 CCTCTGCTCTCTTGTGGGTAATA 59.293 47.826 0.00 0.00 0.00 0.98
2906 2969 1.902508 CCTCTGCTCTCTTGTGGGTAA 59.097 52.381 0.00 0.00 0.00 2.85
2908 2971 0.472734 ACCTCTGCTCTCTTGTGGGT 60.473 55.000 0.00 0.00 0.00 4.51
2909 2972 1.205893 GTACCTCTGCTCTCTTGTGGG 59.794 57.143 0.00 0.00 0.00 4.61
2913 2976 2.354203 GGTTGGTACCTCTGCTCTCTTG 60.354 54.545 14.36 0.00 41.53 3.02
2916 2979 1.205893 CTGGTTGGTACCTCTGCTCTC 59.794 57.143 14.36 0.00 45.27 3.20
2919 2982 1.729586 TTCTGGTTGGTACCTCTGCT 58.270 50.000 14.36 0.00 45.27 4.24
2921 2984 3.261897 ACTGATTCTGGTTGGTACCTCTG 59.738 47.826 14.36 6.20 45.27 3.35
2922 2985 3.521727 ACTGATTCTGGTTGGTACCTCT 58.478 45.455 14.36 0.00 45.27 3.69
2925 2988 4.652822 AGAAACTGATTCTGGTTGGTACC 58.347 43.478 4.43 4.43 46.71 3.34
2949 3012 9.412460 TGGCTAAAGAATTTCACATCTGATAAT 57.588 29.630 0.00 0.00 40.09 1.28
2955 3018 8.037166 GGAAATTGGCTAAAGAATTTCACATCT 58.963 33.333 16.82 0.00 44.83 2.90
2957 3020 7.678837 TGGAAATTGGCTAAAGAATTTCACAT 58.321 30.769 16.82 0.00 44.83 3.21
2958 3021 7.060383 TGGAAATTGGCTAAAGAATTTCACA 57.940 32.000 16.82 11.55 44.83 3.58
2959 3022 7.118245 CCTTGGAAATTGGCTAAAGAATTTCAC 59.882 37.037 16.82 9.88 44.83 3.18
2960 3023 7.160726 CCTTGGAAATTGGCTAAAGAATTTCA 58.839 34.615 16.82 5.67 44.83 2.69
2961 3024 6.092670 GCCTTGGAAATTGGCTAAAGAATTTC 59.907 38.462 10.06 10.06 43.38 2.17
2963 3026 5.491070 GCCTTGGAAATTGGCTAAAGAATT 58.509 37.500 0.00 0.00 43.05 2.17
2964 3027 5.089970 GCCTTGGAAATTGGCTAAAGAAT 57.910 39.130 0.00 0.00 43.05 2.40


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

AutoCloner maintained by Alex Coulton.