Multiple sequence alignment - TraesCS1A01G153500

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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 TraesCS1A01G153500 chr1A 100.000 4235 0 0 1 4235 267172891 267168657 0.000000e+00 7821.0
1 TraesCS1A01G153500 chr1A 97.146 1051 29 1 3185 4235 267162485 267161436 0.000000e+00 1773.0
2 TraesCS1A01G153500 chr1A 95.623 1051 43 3 3185 4235 236278150 236277103 0.000000e+00 1683.0
3 TraesCS1A01G153500 chr1A 95.935 123 3 1 810 930 267157773 267157651 9.290000e-47 198.0
4 TraesCS1A01G153500 chr4A 95.913 1052 39 4 3185 4235 223098182 223099230 0.000000e+00 1701.0
5 TraesCS1A01G153500 chr3A 95.623 1051 44 2 3185 4235 247459894 247460942 0.000000e+00 1685.0
6 TraesCS1A01G153500 chr3A 95.338 1051 49 0 3185 4235 252270673 252271723 0.000000e+00 1670.0
7 TraesCS1A01G153500 chr3A 95.338 1051 47 2 3185 4235 493175190 493176238 0.000000e+00 1668.0
8 TraesCS1A01G153500 chr5A 95.351 1054 43 6 3185 4235 310834680 310835730 0.000000e+00 1670.0
9 TraesCS1A01G153500 chr5A 90.196 51 5 0 897 947 406674046 406674096 2.730000e-07 67.6
10 TraesCS1A01G153500 chr6A 95.342 1052 46 3 3185 4235 608033671 608032622 0.000000e+00 1668.0
11 TraesCS1A01G153500 chr6A 97.642 212 5 0 1721 1932 214196459 214196670 8.650000e-97 364.0
12 TraesCS1A01G153500 chr6A 82.185 421 53 14 813 1215 214195393 214195809 4.050000e-90 342.0
13 TraesCS1A01G153500 chr2A 95.347 1053 41 6 3185 4235 447023422 447022376 0.000000e+00 1666.0
14 TraesCS1A01G153500 chr2A 87.939 854 97 4 2289 3138 299771604 299770753 0.000000e+00 1002.0
15 TraesCS1A01G153500 chr2D 96.671 811 23 4 1 810 645277007 645276200 0.000000e+00 1345.0
16 TraesCS1A01G153500 chr2D 79.236 838 105 27 16 810 567621729 567620918 1.750000e-143 520.0
17 TraesCS1A01G153500 chr2D 84.722 144 16 5 670 810 645281446 645281586 5.710000e-29 139.0
18 TraesCS1A01G153500 chr6B 96.437 814 21 3 1 811 487796451 487795643 0.000000e+00 1336.0
19 TraesCS1A01G153500 chr6B 86.157 968 95 23 814 1747 94171089 94172051 0.000000e+00 1009.0
20 TraesCS1A01G153500 chr6B 91.197 727 48 6 950 1663 94144801 94145524 0.000000e+00 974.0
21 TraesCS1A01G153500 chr6B 89.706 340 22 5 950 1276 566158271 566157932 5.060000e-114 422.0
22 TraesCS1A01G153500 chr6B 93.939 231 12 2 1703 1932 94172105 94172334 8.720000e-92 348.0
23 TraesCS1A01G153500 chr6B 93.478 230 15 0 1703 1932 94145650 94145879 4.050000e-90 342.0
24 TraesCS1A01G153500 chr6B 80.417 480 69 12 1268 1735 687299319 687299785 4.050000e-90 342.0
25 TraesCS1A01G153500 chr6B 86.029 136 19 0 3049 3184 384185762 384185897 3.410000e-31 147.0
26 TraesCS1A01G153500 chr6B 85.315 143 17 4 670 810 487800320 487800460 1.230000e-30 145.0
27 TraesCS1A01G153500 chr3B 96.637 684 16 6 132 812 650049763 650049084 0.000000e+00 1129.0
28 TraesCS1A01G153500 chr3B 84.615 390 40 17 813 1191 13487529 13487149 1.860000e-98 370.0
29 TraesCS1A01G153500 chr7D 95.437 504 23 0 2681 3184 499839848 499840351 0.000000e+00 804.0
30 TraesCS1A01G153500 chr7D 79.496 834 106 24 16 810 89000047 88999240 2.240000e-147 532.0
31 TraesCS1A01G153500 chr4D 85.635 724 86 5 1961 2684 298254481 298253776 0.000000e+00 745.0
32 TraesCS1A01G153500 chr4D 87.606 355 33 7 898 1243 298525464 298525112 6.600000e-108 401.0
33 TraesCS1A01G153500 chr4D 88.026 309 36 1 1245 1553 298422592 298422285 8.650000e-97 364.0
34 TraesCS1A01G153500 chr4D 85.167 209 18 4 1549 1744 298254885 298254677 7.180000e-48 202.0
35 TraesCS1A01G153500 chr4D 83.951 162 26 0 1268 1429 228090764 228090925 5.670000e-34 156.0
36 TraesCS1A01G153500 chr2B 89.744 507 47 2 2681 3187 441491137 441490636 0.000000e+00 643.0
37 TraesCS1A01G153500 chr2B 89.688 320 27 3 172 488 227230305 227229989 1.830000e-108 403.0
38 TraesCS1A01G153500 chr2B 93.878 49 3 0 181 229 227230409 227230361 1.630000e-09 75.0
39 TraesCS1A01G153500 chr2B 100.000 37 0 0 774 810 131883403 131883439 7.600000e-08 69.4
40 TraesCS1A01G153500 chrUn 87.965 565 36 22 813 1352 64111502 64112059 4.620000e-179 638.0
41 TraesCS1A01G153500 chrUn 86.730 211 24 2 1339 1549 64112213 64112419 9.160000e-57 231.0
42 TraesCS1A01G153500 chr7B 97.674 215 5 0 1721 1935 320323316 320323102 1.860000e-98 370.0
43 TraesCS1A01G153500 chr7B 97.209 215 6 0 1721 1935 451082637 451082423 8.650000e-97 364.0
44 TraesCS1A01G153500 chr7B 82.423 421 52 16 813 1215 451083701 451083285 8.720000e-92 348.0
45 TraesCS1A01G153500 chr7B 82.831 332 42 9 897 1215 320324295 320323966 2.490000e-72 283.0
46 TraesCS1A01G153500 chr7B 89.320 206 22 0 1730 1935 611913563 611913358 4.200000e-65 259.0
47 TraesCS1A01G153500 chr7B 87.970 133 14 1 44 174 89510053 89509921 5.670000e-34 156.0
48 TraesCS1A01G153500 chr4B 97.209 215 6 0 1721 1935 140898679 140898465 8.650000e-97 364.0
49 TraesCS1A01G153500 chr4B 81.473 421 56 16 813 1215 140899745 140899329 4.080000e-85 326.0
50 TraesCS1A01G153500 chr4B 93.396 212 5 1 1721 1932 600296682 600296884 5.320000e-79 305.0
51 TraesCS1A01G153500 chr6D 84.472 161 25 0 1269 1429 298402726 298402566 4.380000e-35 159.0
52 TraesCS1A01G153500 chr6D 82.099 162 28 1 1268 1429 368744625 368744465 2.050000e-28 137.0
53 TraesCS1A01G153500 chr6D 86.567 67 5 4 897 961 212015650 212015714 2.110000e-08 71.3
54 TraesCS1A01G153500 chr3D 83.951 162 26 0 1268 1429 503732770 503732931 5.670000e-34 156.0
55 TraesCS1A01G153500 chr1D 79.832 119 17 7 697 811 67883173 67883058 3.510000e-11 80.5


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 TraesCS1A01G153500 chr1A 267168657 267172891 4234 True 7821.0 7821 100.0000 1 4235 1 chr1A.!!$R2 4234
1 TraesCS1A01G153500 chr1A 236277103 236278150 1047 True 1683.0 1683 95.6230 3185 4235 1 chr1A.!!$R1 1050
2 TraesCS1A01G153500 chr1A 267157651 267162485 4834 True 985.5 1773 96.5405 810 4235 2 chr1A.!!$R3 3425
3 TraesCS1A01G153500 chr4A 223098182 223099230 1048 False 1701.0 1701 95.9130 3185 4235 1 chr4A.!!$F1 1050
4 TraesCS1A01G153500 chr3A 247459894 247460942 1048 False 1685.0 1685 95.6230 3185 4235 1 chr3A.!!$F1 1050
5 TraesCS1A01G153500 chr3A 252270673 252271723 1050 False 1670.0 1670 95.3380 3185 4235 1 chr3A.!!$F2 1050
6 TraesCS1A01G153500 chr3A 493175190 493176238 1048 False 1668.0 1668 95.3380 3185 4235 1 chr3A.!!$F3 1050
7 TraesCS1A01G153500 chr5A 310834680 310835730 1050 False 1670.0 1670 95.3510 3185 4235 1 chr5A.!!$F1 1050
8 TraesCS1A01G153500 chr6A 608032622 608033671 1049 True 1668.0 1668 95.3420 3185 4235 1 chr6A.!!$R1 1050
9 TraesCS1A01G153500 chr6A 214195393 214196670 1277 False 353.0 364 89.9135 813 1932 2 chr6A.!!$F1 1119
10 TraesCS1A01G153500 chr2A 447022376 447023422 1046 True 1666.0 1666 95.3470 3185 4235 1 chr2A.!!$R2 1050
11 TraesCS1A01G153500 chr2A 299770753 299771604 851 True 1002.0 1002 87.9390 2289 3138 1 chr2A.!!$R1 849
12 TraesCS1A01G153500 chr2D 645276200 645277007 807 True 1345.0 1345 96.6710 1 810 1 chr2D.!!$R2 809
13 TraesCS1A01G153500 chr2D 567620918 567621729 811 True 520.0 520 79.2360 16 810 1 chr2D.!!$R1 794
14 TraesCS1A01G153500 chr6B 487795643 487796451 808 True 1336.0 1336 96.4370 1 811 1 chr6B.!!$R1 810
15 TraesCS1A01G153500 chr6B 94171089 94172334 1245 False 678.5 1009 90.0480 814 1932 2 chr6B.!!$F5 1118
16 TraesCS1A01G153500 chr6B 94144801 94145879 1078 False 658.0 974 92.3375 950 1932 2 chr6B.!!$F4 982
17 TraesCS1A01G153500 chr3B 650049084 650049763 679 True 1129.0 1129 96.6370 132 812 1 chr3B.!!$R2 680
18 TraesCS1A01G153500 chr7D 499839848 499840351 503 False 804.0 804 95.4370 2681 3184 1 chr7D.!!$F1 503
19 TraesCS1A01G153500 chr7D 88999240 89000047 807 True 532.0 532 79.4960 16 810 1 chr7D.!!$R1 794
20 TraesCS1A01G153500 chr4D 298253776 298254885 1109 True 473.5 745 85.4010 1549 2684 2 chr4D.!!$R3 1135
21 TraesCS1A01G153500 chr2B 441490636 441491137 501 True 643.0 643 89.7440 2681 3187 1 chr2B.!!$R1 506
22 TraesCS1A01G153500 chrUn 64111502 64112419 917 False 434.5 638 87.3475 813 1549 2 chrUn.!!$F1 736
23 TraesCS1A01G153500 chr7B 451082423 451083701 1278 True 356.0 364 89.8160 813 1935 2 chr7B.!!$R4 1122
24 TraesCS1A01G153500 chr7B 320323102 320324295 1193 True 326.5 370 90.2525 897 1935 2 chr7B.!!$R3 1038
25 TraesCS1A01G153500 chr4B 140898465 140899745 1280 True 345.0 364 89.3410 813 1935 2 chr4B.!!$R1 1122

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
974 1043 0.324943 CACCACCACCTCCTCGATTT 59.675 55.0 0.00 0.00 0.00 2.17 F
1502 1791 0.179234 TGCTCGAACCAGGACAACAA 59.821 50.0 0.00 0.00 0.00 2.83 F
2013 2654 0.036671 GAAACGAGGTCCGACCCATT 60.037 55.0 14.32 3.49 39.75 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2635 0.036671 AATGGGTCGGACCTCGTTTC 60.037 55.0 25.39 9.28 38.64 2.78 R
3177 3821 0.033504 CGAGGGCGTTACATATGGCT 59.966 55.0 7.80 0.00 38.35 4.75 R
3966 4618 1.072266 ATGGGCTAAGTTGGGACACA 58.928 50.0 0.00 0.00 39.29 3.72 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
339 374 7.229907 AGAGGAGATAAAGAAGAATACGAGTCC 59.770 40.741 0.00 0.00 0.00 3.85
463 498 2.543848 TCGGATCGCTTGATATTTGCAC 59.456 45.455 0.00 0.00 30.70 4.57
527 565 4.521146 GCTCCAGATTGAAATCTCTTCCA 58.479 43.478 2.50 0.00 43.65 3.53
624 665 0.610785 GGCGGACATTTTCCCTCCAA 60.611 55.000 0.00 0.00 42.27 3.53
695 736 2.363306 TACGGGAGCTCGGGTATTTA 57.637 50.000 7.83 0.00 0.00 1.40
696 737 1.713297 ACGGGAGCTCGGGTATTTAT 58.287 50.000 7.83 0.00 0.00 1.40
697 738 2.044758 ACGGGAGCTCGGGTATTTATT 58.955 47.619 7.83 0.00 0.00 1.40
698 739 2.436911 ACGGGAGCTCGGGTATTTATTT 59.563 45.455 7.83 0.00 0.00 1.40
699 740 3.642848 ACGGGAGCTCGGGTATTTATTTA 59.357 43.478 7.83 0.00 0.00 1.40
761 805 5.676079 GCTGCCGTTAGATGAAAAATTAGCA 60.676 40.000 0.00 0.00 0.00 3.49
772 818 7.615365 AGATGAAAAATTAGCAATGGGAGTACA 59.385 33.333 0.00 0.00 0.00 2.90
789 835 2.284625 AGATGGGAGCACGGGACA 60.285 61.111 0.00 0.00 0.00 4.02
815 861 3.330720 CAAGCCCCGTCCCCTCTT 61.331 66.667 0.00 0.00 0.00 2.85
816 862 2.531942 AAGCCCCGTCCCCTCTTT 60.532 61.111 0.00 0.00 0.00 2.52
817 863 2.160853 AAGCCCCGTCCCCTCTTTT 61.161 57.895 0.00 0.00 0.00 2.27
824 870 1.282382 CGTCCCCTCTTTTCCCCTTA 58.718 55.000 0.00 0.00 0.00 2.69
826 872 1.284198 GTCCCCTCTTTTCCCCTTACC 59.716 57.143 0.00 0.00 0.00 2.85
827 873 1.155745 TCCCCTCTTTTCCCCTTACCT 59.844 52.381 0.00 0.00 0.00 3.08
828 874 2.000803 CCCCTCTTTTCCCCTTACCTT 58.999 52.381 0.00 0.00 0.00 3.50
829 875 2.025226 CCCCTCTTTTCCCCTTACCTTC 60.025 54.545 0.00 0.00 0.00 3.46
831 877 2.920271 CCTCTTTTCCCCTTACCTTCCT 59.080 50.000 0.00 0.00 0.00 3.36
833 879 4.567958 CCTCTTTTCCCCTTACCTTCCTTC 60.568 50.000 0.00 0.00 0.00 3.46
835 881 2.755019 TTCCCCTTACCTTCCTTCCT 57.245 50.000 0.00 0.00 0.00 3.36
843 889 2.789409 ACCTTCCTTCCTCCAATTCG 57.211 50.000 0.00 0.00 0.00 3.34
850 896 4.030913 TCCTTCCTCCAATTCGTGTATCT 58.969 43.478 0.00 0.00 0.00 1.98
851 897 4.122776 CCTTCCTCCAATTCGTGTATCTG 58.877 47.826 0.00 0.00 0.00 2.90
852 898 4.383118 CCTTCCTCCAATTCGTGTATCTGT 60.383 45.833 0.00 0.00 0.00 3.41
853 899 4.123497 TCCTCCAATTCGTGTATCTGTG 57.877 45.455 0.00 0.00 0.00 3.66
854 900 3.767131 TCCTCCAATTCGTGTATCTGTGA 59.233 43.478 0.00 0.00 0.00 3.58
855 901 4.405680 TCCTCCAATTCGTGTATCTGTGAT 59.594 41.667 0.00 0.00 0.00 3.06
856 902 4.747108 CCTCCAATTCGTGTATCTGTGATC 59.253 45.833 0.00 0.00 0.00 2.92
866 912 5.221244 CGTGTATCTGTGATCCTGTAATCCA 60.221 44.000 0.00 0.00 0.00 3.41
867 913 5.986135 GTGTATCTGTGATCCTGTAATCCAC 59.014 44.000 0.00 0.00 0.00 4.02
868 914 4.696479 ATCTGTGATCCTGTAATCCACC 57.304 45.455 0.00 0.00 0.00 4.61
873 920 4.018506 TGTGATCCTGTAATCCACCATTGT 60.019 41.667 0.00 0.00 0.00 2.71
876 923 6.772716 GTGATCCTGTAATCCACCATTGTTAT 59.227 38.462 0.00 0.00 0.00 1.89
885 932 7.537596 AATCCACCATTGTTATTTGAGTTCA 57.462 32.000 0.00 0.00 0.00 3.18
887 934 7.156876 TCCACCATTGTTATTTGAGTTCATC 57.843 36.000 0.00 0.00 0.00 2.92
890 937 7.309377 CCACCATTGTTATTTGAGTTCATCTGT 60.309 37.037 0.00 0.00 0.00 3.41
895 943 7.425577 TGTTATTTGAGTTCATCTGTGAGTG 57.574 36.000 0.00 0.00 35.39 3.51
914 963 7.335673 TGTGAGTGATAGATCGAGGAAGATATC 59.664 40.741 0.00 0.00 0.00 1.63
924 973 4.885907 TCGAGGAAGATATCGTTAGGTTGT 59.114 41.667 0.00 0.00 39.86 3.32
974 1043 0.324943 CACCACCACCTCCTCGATTT 59.675 55.000 0.00 0.00 0.00 2.17
1032 1101 0.689623 AGCAGTCTCCTTGTTCCCTG 59.310 55.000 0.00 0.00 0.00 4.45
1219 1314 1.332375 CTGCTACTGCTACCTCGTCTC 59.668 57.143 0.00 0.00 40.48 3.36
1220 1315 1.339727 TGCTACTGCTACCTCGTCTCA 60.340 52.381 0.00 0.00 40.48 3.27
1410 1699 3.542602 ACCCCCTCCTCCACCACT 61.543 66.667 0.00 0.00 0.00 4.00
1502 1791 0.179234 TGCTCGAACCAGGACAACAA 59.821 50.000 0.00 0.00 0.00 2.83
1507 1796 1.658994 GAACCAGGACAACAACACGA 58.341 50.000 0.00 0.00 0.00 4.35
1542 1831 1.079543 AGTCATGACAGTGCCGCTC 60.080 57.895 27.02 0.00 0.00 5.03
1587 1876 2.455032 GTCACGGATCTCATTCACTCG 58.545 52.381 0.00 0.00 0.00 4.18
1735 2376 4.648626 TCCGACCGACTCCGTGGT 62.649 66.667 0.00 0.00 42.42 4.16
1781 2422 3.022287 CAATGATGTACGGCCCGC 58.978 61.111 1.23 0.00 0.00 6.13
1932 2573 2.061773 CTACCAAGTGTGCGACTGAAG 58.938 52.381 0.00 0.00 34.02 3.02
1946 2587 4.700596 GACTGAAGTCGTTTGAAGTCAG 57.299 45.455 0.00 0.00 40.56 3.51
1947 2588 4.113354 GACTGAAGTCGTTTGAAGTCAGT 58.887 43.478 3.90 3.90 45.87 3.41
1948 2589 3.865745 ACTGAAGTCGTTTGAAGTCAGTG 59.134 43.478 3.46 0.00 43.56 3.66
1949 2590 3.857052 TGAAGTCGTTTGAAGTCAGTGT 58.143 40.909 0.00 0.00 0.00 3.55
1950 2591 3.616821 TGAAGTCGTTTGAAGTCAGTGTG 59.383 43.478 0.00 0.00 0.00 3.82
1951 2592 1.933853 AGTCGTTTGAAGTCAGTGTGC 59.066 47.619 0.00 0.00 0.00 4.57
1952 2593 1.003866 GTCGTTTGAAGTCAGTGTGCC 60.004 52.381 0.00 0.00 0.00 5.01
1953 2594 1.013596 CGTTTGAAGTCAGTGTGCCA 58.986 50.000 0.00 0.00 0.00 4.92
1954 2595 1.603802 CGTTTGAAGTCAGTGTGCCAT 59.396 47.619 0.00 0.00 0.00 4.40
1955 2596 2.033299 CGTTTGAAGTCAGTGTGCCATT 59.967 45.455 0.00 0.00 0.00 3.16
1956 2597 3.249799 CGTTTGAAGTCAGTGTGCCATTA 59.750 43.478 0.00 0.00 0.00 1.90
1957 2598 4.611355 CGTTTGAAGTCAGTGTGCCATTAG 60.611 45.833 0.00 0.00 0.00 1.73
1958 2599 4.350368 TTGAAGTCAGTGTGCCATTAGA 57.650 40.909 0.00 0.00 0.00 2.10
1959 2600 3.930336 TGAAGTCAGTGTGCCATTAGAG 58.070 45.455 0.00 0.00 0.00 2.43
1960 2601 3.578282 TGAAGTCAGTGTGCCATTAGAGA 59.422 43.478 0.00 0.00 0.00 3.10
1961 2602 4.040339 TGAAGTCAGTGTGCCATTAGAGAA 59.960 41.667 0.00 0.00 0.00 2.87
1962 2603 4.199432 AGTCAGTGTGCCATTAGAGAAG 57.801 45.455 0.00 0.00 0.00 2.85
1963 2604 3.580458 AGTCAGTGTGCCATTAGAGAAGT 59.420 43.478 0.00 0.00 0.00 3.01
1964 2605 3.681897 GTCAGTGTGCCATTAGAGAAGTG 59.318 47.826 0.00 0.00 0.00 3.16
1965 2606 3.324846 TCAGTGTGCCATTAGAGAAGTGT 59.675 43.478 0.00 0.00 0.00 3.55
1966 2607 3.434641 CAGTGTGCCATTAGAGAAGTGTG 59.565 47.826 0.00 0.00 0.00 3.82
1967 2608 3.324846 AGTGTGCCATTAGAGAAGTGTGA 59.675 43.478 0.00 0.00 0.00 3.58
1968 2609 4.019860 AGTGTGCCATTAGAGAAGTGTGAT 60.020 41.667 0.00 0.00 0.00 3.06
1969 2610 4.697352 GTGTGCCATTAGAGAAGTGTGATT 59.303 41.667 0.00 0.00 0.00 2.57
1970 2611 4.696877 TGTGCCATTAGAGAAGTGTGATTG 59.303 41.667 0.00 0.00 0.00 2.67
1971 2612 4.697352 GTGCCATTAGAGAAGTGTGATTGT 59.303 41.667 0.00 0.00 0.00 2.71
1972 2613 4.696877 TGCCATTAGAGAAGTGTGATTGTG 59.303 41.667 0.00 0.00 0.00 3.33
1973 2614 4.697352 GCCATTAGAGAAGTGTGATTGTGT 59.303 41.667 0.00 0.00 0.00 3.72
1974 2615 5.391310 GCCATTAGAGAAGTGTGATTGTGTG 60.391 44.000 0.00 0.00 0.00 3.82
1975 2616 5.391310 CCATTAGAGAAGTGTGATTGTGTGC 60.391 44.000 0.00 0.00 0.00 4.57
1976 2617 3.198409 AGAGAAGTGTGATTGTGTGCA 57.802 42.857 0.00 0.00 0.00 4.57
1977 2618 3.748083 AGAGAAGTGTGATTGTGTGCAT 58.252 40.909 0.00 0.00 0.00 3.96
1978 2619 3.750130 AGAGAAGTGTGATTGTGTGCATC 59.250 43.478 0.00 0.00 0.00 3.91
1979 2620 3.748083 AGAAGTGTGATTGTGTGCATCT 58.252 40.909 0.00 0.00 0.00 2.90
1980 2621 4.139786 AGAAGTGTGATTGTGTGCATCTT 58.860 39.130 0.00 0.00 0.00 2.40
1981 2622 3.909776 AGTGTGATTGTGTGCATCTTG 57.090 42.857 0.00 0.00 0.00 3.02
1982 2623 3.216800 AGTGTGATTGTGTGCATCTTGT 58.783 40.909 0.00 0.00 0.00 3.16
1983 2624 4.388485 AGTGTGATTGTGTGCATCTTGTA 58.612 39.130 0.00 0.00 0.00 2.41
1984 2625 5.005740 AGTGTGATTGTGTGCATCTTGTAT 58.994 37.500 0.00 0.00 0.00 2.29
1985 2626 5.122869 AGTGTGATTGTGTGCATCTTGTATC 59.877 40.000 0.00 0.00 0.00 2.24
1986 2627 5.002516 TGTGATTGTGTGCATCTTGTATCA 58.997 37.500 0.00 0.00 0.00 2.15
1987 2628 5.122711 TGTGATTGTGTGCATCTTGTATCAG 59.877 40.000 0.00 0.00 0.00 2.90
1988 2629 4.095334 TGATTGTGTGCATCTTGTATCAGC 59.905 41.667 0.00 0.00 0.00 4.26
1989 2630 3.056588 TGTGTGCATCTTGTATCAGCA 57.943 42.857 0.00 0.00 0.00 4.41
1990 2631 3.004862 TGTGTGCATCTTGTATCAGCAG 58.995 45.455 0.00 0.00 35.66 4.24
1991 2632 3.264947 GTGTGCATCTTGTATCAGCAGA 58.735 45.455 0.00 0.00 35.66 4.26
1992 2633 3.063180 GTGTGCATCTTGTATCAGCAGAC 59.937 47.826 0.00 0.00 41.20 3.51
1993 2634 2.283617 GTGCATCTTGTATCAGCAGACG 59.716 50.000 0.00 0.00 35.66 4.18
1994 2635 1.863454 GCATCTTGTATCAGCAGACGG 59.137 52.381 0.00 0.00 0.00 4.79
1995 2636 2.481969 GCATCTTGTATCAGCAGACGGA 60.482 50.000 0.00 0.00 0.00 4.69
1996 2637 3.785486 CATCTTGTATCAGCAGACGGAA 58.215 45.455 0.00 0.00 0.00 4.30
1997 2638 3.953712 TCTTGTATCAGCAGACGGAAA 57.046 42.857 0.00 0.00 0.00 3.13
1998 2639 3.585862 TCTTGTATCAGCAGACGGAAAC 58.414 45.455 0.00 0.00 0.00 2.78
2010 2651 2.263852 GGAAACGAGGTCCGACCC 59.736 66.667 14.32 5.07 39.75 4.46
2011 2652 2.576832 GGAAACGAGGTCCGACCCA 61.577 63.158 14.32 0.00 39.75 4.51
2012 2653 1.595357 GAAACGAGGTCCGACCCAT 59.405 57.895 14.32 0.00 39.75 4.00
2013 2654 0.036671 GAAACGAGGTCCGACCCATT 60.037 55.000 14.32 3.49 39.75 3.16
2014 2655 0.036671 AAACGAGGTCCGACCCATTC 60.037 55.000 14.32 4.67 39.75 2.67
2015 2656 1.896122 AACGAGGTCCGACCCATTCC 61.896 60.000 14.32 0.00 39.75 3.01
2016 2657 2.355986 CGAGGTCCGACCCATTCCA 61.356 63.158 14.32 0.00 39.75 3.53
2017 2658 1.686325 CGAGGTCCGACCCATTCCAT 61.686 60.000 14.32 0.00 39.75 3.41
2018 2659 0.179045 GAGGTCCGACCCATTCCATG 60.179 60.000 14.32 0.00 39.75 3.66
2026 2667 4.585070 CCATTCCATGGCCATCGT 57.415 55.556 17.61 0.00 44.70 3.73
2027 2668 2.811307 CCATTCCATGGCCATCGTT 58.189 52.632 17.61 0.00 44.70 3.85
2028 2669 1.113788 CCATTCCATGGCCATCGTTT 58.886 50.000 17.61 0.00 44.70 3.60
2029 2670 1.067516 CCATTCCATGGCCATCGTTTC 59.932 52.381 17.61 0.00 44.70 2.78
2030 2671 2.026641 CATTCCATGGCCATCGTTTCT 58.973 47.619 17.61 0.00 0.00 2.52
2031 2672 3.213506 CATTCCATGGCCATCGTTTCTA 58.786 45.455 17.61 0.00 0.00 2.10
2032 2673 3.358111 TTCCATGGCCATCGTTTCTAA 57.642 42.857 17.61 0.00 0.00 2.10
2033 2674 3.576078 TCCATGGCCATCGTTTCTAAT 57.424 42.857 17.61 0.00 0.00 1.73
2034 2675 3.897239 TCCATGGCCATCGTTTCTAATT 58.103 40.909 17.61 0.00 0.00 1.40
2035 2676 3.631686 TCCATGGCCATCGTTTCTAATTG 59.368 43.478 17.61 0.71 0.00 2.32
2036 2677 3.243501 CCATGGCCATCGTTTCTAATTGG 60.244 47.826 17.61 7.29 0.00 3.16
2037 2678 3.358111 TGGCCATCGTTTCTAATTGGA 57.642 42.857 0.00 0.00 0.00 3.53
2064 2705 9.851686 AGGTTCATGAAGCATCTAATTATGTTA 57.148 29.630 32.68 0.00 40.96 2.41
2099 2740 7.010552 GCATGACAGTGGTTTGATTAGTAGTAG 59.989 40.741 0.00 0.00 0.00 2.57
2100 2741 7.770366 TGACAGTGGTTTGATTAGTAGTAGA 57.230 36.000 0.00 0.00 0.00 2.59
2105 2746 9.877178 CAGTGGTTTGATTAGTAGTAGATTTCT 57.123 33.333 0.00 0.00 0.00 2.52
2118 2759 9.771534 AGTAGTAGATTTCTGATGGAATTAAGC 57.228 33.333 0.00 0.00 33.53 3.09
2120 2761 7.577303 AGTAGATTTCTGATGGAATTAAGCCA 58.423 34.615 2.65 2.65 40.24 4.75
2123 2764 6.837568 AGATTTCTGATGGAATTAAGCCATGT 59.162 34.615 15.25 0.00 45.81 3.21
2124 2765 6.855763 TTTCTGATGGAATTAAGCCATGTT 57.144 33.333 15.25 0.00 45.81 2.71
2125 2766 5.840243 TCTGATGGAATTAAGCCATGTTG 57.160 39.130 15.25 7.10 45.81 3.33
2126 2767 4.646040 TCTGATGGAATTAAGCCATGTTGG 59.354 41.667 15.25 5.26 45.81 3.77
2127 2768 4.608269 TGATGGAATTAAGCCATGTTGGA 58.392 39.130 15.25 0.00 45.81 3.53
2128 2769 5.022122 TGATGGAATTAAGCCATGTTGGAA 58.978 37.500 15.25 0.00 45.81 3.53
2129 2770 5.483231 TGATGGAATTAAGCCATGTTGGAAA 59.517 36.000 15.25 0.00 45.81 3.13
2130 2771 6.156602 TGATGGAATTAAGCCATGTTGGAAAT 59.843 34.615 15.25 0.00 45.81 2.17
2131 2772 5.976458 TGGAATTAAGCCATGTTGGAAATC 58.024 37.500 0.00 0.00 40.96 2.17
2132 2773 5.721000 TGGAATTAAGCCATGTTGGAAATCT 59.279 36.000 0.00 0.00 40.96 2.40
2133 2774 6.213195 TGGAATTAAGCCATGTTGGAAATCTT 59.787 34.615 0.00 0.00 40.96 2.40
2134 2775 6.536224 GGAATTAAGCCATGTTGGAAATCTTG 59.464 38.462 0.00 0.00 40.96 3.02
2135 2776 6.610075 ATTAAGCCATGTTGGAAATCTTGT 57.390 33.333 0.00 0.00 40.96 3.16
2136 2777 3.947910 AGCCATGTTGGAAATCTTGTG 57.052 42.857 0.00 0.00 40.96 3.33
2137 2778 3.233507 AGCCATGTTGGAAATCTTGTGT 58.766 40.909 0.00 0.00 40.96 3.72
2138 2779 3.006110 AGCCATGTTGGAAATCTTGTGTG 59.994 43.478 0.00 0.00 40.96 3.82
2139 2780 3.243839 GCCATGTTGGAAATCTTGTGTGT 60.244 43.478 0.00 0.00 40.96 3.72
2140 2781 4.300803 CCATGTTGGAAATCTTGTGTGTG 58.699 43.478 0.00 0.00 40.96 3.82
2141 2782 4.300803 CATGTTGGAAATCTTGTGTGTGG 58.699 43.478 0.00 0.00 0.00 4.17
2142 2783 3.360867 TGTTGGAAATCTTGTGTGTGGT 58.639 40.909 0.00 0.00 0.00 4.16
2147 2788 4.137543 GGAAATCTTGTGTGTGGTCTTCT 58.862 43.478 0.00 0.00 0.00 2.85
2155 2796 2.031683 GTGTGTGGTCTTCTTGGAAACG 59.968 50.000 0.00 0.00 0.00 3.60
2156 2797 1.602377 GTGTGGTCTTCTTGGAAACGG 59.398 52.381 0.00 0.00 0.00 4.44
2167 2808 5.304686 TCTTGGAAACGGCATAAGGATAT 57.695 39.130 0.00 0.00 0.00 1.63
2174 2815 2.305927 ACGGCATAAGGATATTCCCAGG 59.694 50.000 0.00 0.00 37.19 4.45
2175 2816 2.305927 CGGCATAAGGATATTCCCAGGT 59.694 50.000 0.00 0.00 37.19 4.00
2182 2823 1.349357 GGATATTCCCAGGTCAGCTCC 59.651 57.143 0.00 0.00 0.00 4.70
2184 2825 3.511477 GATATTCCCAGGTCAGCTCCTA 58.489 50.000 0.00 0.00 35.87 2.94
2195 2836 3.003480 GTCAGCTCCTATGTTTGTGGTC 58.997 50.000 0.00 0.00 0.00 4.02
2213 2854 4.036734 GTGGTCTTTGCAACAAGATGAAGA 59.963 41.667 0.00 0.00 0.00 2.87
2227 2868 5.306114 AGATGAAGATGATTCATGCCTCA 57.694 39.130 3.32 4.40 39.08 3.86
2245 2886 4.511527 CCTCAATACACATGTGAAGCTCT 58.488 43.478 31.94 11.12 0.00 4.09
2271 2912 8.514330 TTCATTACAGTAAACAGTGGTTTTCT 57.486 30.769 0.00 0.00 44.63 2.52
2287 2928 5.350914 TGGTTTTCTGAACTTTGTGCATTTG 59.649 36.000 0.00 0.00 0.00 2.32
2297 2938 3.797451 TTGTGCATTTGCTGAACAAGA 57.203 38.095 3.94 0.00 46.54 3.02
2353 2997 5.745312 TTGTGGTAGTGAGATGATCTGTT 57.255 39.130 0.00 0.00 0.00 3.16
2354 2998 6.850752 TTGTGGTAGTGAGATGATCTGTTA 57.149 37.500 0.00 0.00 0.00 2.41
2367 3011 3.947196 TGATCTGTTATTGTGCACATCCC 59.053 43.478 22.39 9.68 0.00 3.85
2382 3026 3.381272 CACATCCCGGAACAAATAGCAAT 59.619 43.478 0.73 0.00 0.00 3.56
2402 3046 5.106038 GCAATGATTTCACCATTCAGTCTGA 60.106 40.000 0.00 0.00 32.40 3.27
2412 3056 4.222336 CCATTCAGTCTGATCTCCCTAGT 58.778 47.826 2.68 0.00 0.00 2.57
2461 3105 2.351157 GCATGGACTCTCAGTTTTGTGC 60.351 50.000 0.00 0.00 0.00 4.57
2474 3118 2.990514 GTTTTGTGCGGAAAACAACTGT 59.009 40.909 14.91 0.00 42.80 3.55
2478 3122 0.380378 TGCGGAAAACAACTGTCTGC 59.620 50.000 0.00 0.00 42.80 4.26
2512 3156 4.184079 AGGCATGATTTTCAGTTTCTGC 57.816 40.909 0.00 0.00 0.00 4.26
2543 3187 1.938577 CAATCCTCGAGAAGTGCATGG 59.061 52.381 15.71 0.00 0.00 3.66
2565 3209 7.867305 TGGTTTGTCTGAACTACAAATTGTA 57.133 32.000 5.66 5.66 45.62 2.41
2619 3263 0.607489 ACATCAGTGAGTTGGCTGGC 60.607 55.000 0.00 0.00 33.81 4.85
2646 3290 3.756082 TGCCTTGAGAAATTATGGGGT 57.244 42.857 0.00 0.00 0.00 4.95
2650 3294 3.382546 CCTTGAGAAATTATGGGGTGCTG 59.617 47.826 0.00 0.00 0.00 4.41
2656 3300 0.998928 ATTATGGGGTGCTGGTGACA 59.001 50.000 0.00 0.00 39.59 3.58
2712 3356 3.149196 GGAACATCACTTTCTGGAGCAA 58.851 45.455 0.00 0.00 0.00 3.91
2745 3389 7.230108 ACATGTAATATTCCTTGGCATGAGAAG 59.770 37.037 0.00 0.00 36.65 2.85
2762 3406 2.503356 AGAAGTTGCTAGGGACCATGAG 59.497 50.000 0.00 0.00 0.00 2.90
2862 3506 7.595819 TTCTAAACAAATGATTGGTGGTTCT 57.404 32.000 0.00 0.00 41.01 3.01
2906 3550 2.606378 ACTACTGGTCCCTTTCGAGTT 58.394 47.619 0.00 0.00 0.00 3.01
2914 3558 0.037232 CCCTTTCGAGTTTCGCTCCT 60.037 55.000 0.00 0.00 41.10 3.69
2954 3598 3.763360 CTGGGTGGAAATGCTTATCAACA 59.237 43.478 0.00 0.00 0.00 3.33
2967 3611 6.356556 TGCTTATCAACAGCTTATGGTACAT 58.643 36.000 0.00 0.00 40.02 2.29
3019 3663 2.536803 GCGAAGTACTTGTTTGACGACA 59.463 45.455 14.14 0.00 0.00 4.35
3116 3760 6.372381 GGGAATTATTTTGCATTGTTTCAGCT 59.628 34.615 0.00 0.00 0.00 4.24
3118 3762 6.730960 ATTATTTTGCATTGTTTCAGCTGG 57.269 33.333 15.13 0.00 0.00 4.85
3150 3794 7.147846 CCAAGGCCACTTAACATCATTATTCTT 60.148 37.037 5.01 0.00 34.49 2.52
3164 3808 7.137490 TCATTATTCTTGCTCAGTTGTCTTG 57.863 36.000 0.00 0.00 0.00 3.02
3177 3821 6.112734 TCAGTTGTCTTGCTTCAGTAAGAAA 58.887 36.000 8.72 1.49 45.71 2.52
3211 3855 1.478510 CCCTCGATGCGGCTATATCTT 59.521 52.381 0.00 0.00 0.00 2.40
3212 3856 2.093973 CCCTCGATGCGGCTATATCTTT 60.094 50.000 0.00 0.00 0.00 2.52
3291 3936 5.249622 TGAGGTAATCTTCACACAACCCATA 59.750 40.000 0.00 0.00 0.00 2.74
3443 4090 1.910580 ATGCGACAAGGTCCCCGATT 61.911 55.000 0.00 0.00 0.00 3.34
3812 4463 2.014128 CTCCAACACCGTGTTCACTTT 58.986 47.619 14.11 0.00 38.77 2.66
3921 4573 6.350949 CCGGACATTAACAAATTCCCATCTTT 60.351 38.462 0.00 0.00 0.00 2.52
3936 4588 2.819552 CTTTCCATAACCGCGGGCG 61.820 63.158 31.76 14.16 39.44 6.13
3958 4610 3.609409 GCGGCTTTCGAAAGTTCAAATCT 60.609 43.478 32.32 0.00 42.43 2.40
3966 4618 3.499918 CGAAAGTTCAAATCTCTGCAGGT 59.500 43.478 15.13 0.00 0.00 4.00
4065 4717 2.327200 GGAATCCCGGTTCTACAAGG 57.673 55.000 0.00 0.00 0.00 3.61
4191 4843 2.104451 TCCGTACAACTAAAACCAGCCA 59.896 45.455 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 6.097839 TGTTATTCTTTCGAGGCCTACTGTAT 59.902 38.462 4.42 0.00 0.00 2.29
339 374 6.426937 TCTTCAGGACCAAAAGTAAGAAATCG 59.573 38.462 0.00 0.00 0.00 3.34
527 565 6.388619 AACACAAGATCCTAAATACCAGGT 57.611 37.500 0.00 0.00 34.56 4.00
624 665 6.148811 CCTCACGTAATATCCACAACTGTTTT 59.851 38.462 0.00 0.00 0.00 2.43
695 736 4.690280 CGTGCCTTTTCTGCCAAAATAAAT 59.310 37.500 0.00 0.00 0.00 1.40
696 737 4.054671 CGTGCCTTTTCTGCCAAAATAAA 58.945 39.130 0.00 0.00 0.00 1.40
697 738 3.648009 CGTGCCTTTTCTGCCAAAATAA 58.352 40.909 0.00 0.00 0.00 1.40
698 739 2.609244 GCGTGCCTTTTCTGCCAAAATA 60.609 45.455 0.00 0.00 0.00 1.40
699 740 1.873486 GCGTGCCTTTTCTGCCAAAAT 60.873 47.619 0.00 0.00 0.00 1.82
761 805 1.771255 GCTCCCATCTGTACTCCCATT 59.229 52.381 0.00 0.00 0.00 3.16
772 818 2.284625 TGTCCCGTGCTCCCATCT 60.285 61.111 0.00 0.00 0.00 2.90
812 858 3.332783 GGAAGGAAGGTAAGGGGAAAAGA 59.667 47.826 0.00 0.00 0.00 2.52
813 859 3.333980 AGGAAGGAAGGTAAGGGGAAAAG 59.666 47.826 0.00 0.00 0.00 2.27
814 860 3.332783 GAGGAAGGAAGGTAAGGGGAAAA 59.667 47.826 0.00 0.00 0.00 2.29
815 861 2.917600 GAGGAAGGAAGGTAAGGGGAAA 59.082 50.000 0.00 0.00 0.00 3.13
816 862 2.558974 GAGGAAGGAAGGTAAGGGGAA 58.441 52.381 0.00 0.00 0.00 3.97
817 863 1.274242 GGAGGAAGGAAGGTAAGGGGA 60.274 57.143 0.00 0.00 0.00 4.81
824 870 1.985895 ACGAATTGGAGGAAGGAAGGT 59.014 47.619 0.00 0.00 0.00 3.50
826 872 3.059352 ACACGAATTGGAGGAAGGAAG 57.941 47.619 0.00 0.00 0.00 3.46
827 873 4.469945 AGATACACGAATTGGAGGAAGGAA 59.530 41.667 0.00 0.00 0.00 3.36
828 874 4.030913 AGATACACGAATTGGAGGAAGGA 58.969 43.478 0.00 0.00 0.00 3.36
829 875 4.122776 CAGATACACGAATTGGAGGAAGG 58.877 47.826 0.00 0.00 0.00 3.46
831 877 4.221924 TCACAGATACACGAATTGGAGGAA 59.778 41.667 0.00 0.00 0.00 3.36
833 879 4.123497 TCACAGATACACGAATTGGAGG 57.877 45.455 0.00 0.00 0.00 4.30
835 881 4.405680 AGGATCACAGATACACGAATTGGA 59.594 41.667 0.00 0.00 0.00 3.53
843 889 5.986135 GTGGATTACAGGATCACAGATACAC 59.014 44.000 0.00 0.00 0.00 2.90
850 896 4.018506 ACAATGGTGGATTACAGGATCACA 60.019 41.667 0.00 0.00 0.00 3.58
851 897 4.526970 ACAATGGTGGATTACAGGATCAC 58.473 43.478 0.00 0.00 0.00 3.06
852 898 4.860802 ACAATGGTGGATTACAGGATCA 57.139 40.909 0.00 0.00 0.00 2.92
853 899 7.823745 AATAACAATGGTGGATTACAGGATC 57.176 36.000 0.00 0.00 0.00 3.36
854 900 7.838696 TCAAATAACAATGGTGGATTACAGGAT 59.161 33.333 0.00 0.00 0.00 3.24
855 901 7.178573 TCAAATAACAATGGTGGATTACAGGA 58.821 34.615 0.00 0.00 0.00 3.86
856 902 7.122650 ACTCAAATAACAATGGTGGATTACAGG 59.877 37.037 0.00 0.00 0.00 4.00
866 912 7.448161 TCACAGATGAACTCAAATAACAATGGT 59.552 33.333 0.00 0.00 0.00 3.55
867 913 7.819644 TCACAGATGAACTCAAATAACAATGG 58.180 34.615 0.00 0.00 0.00 3.16
868 914 8.509690 ACTCACAGATGAACTCAAATAACAATG 58.490 33.333 0.00 0.00 33.30 2.82
873 920 9.591792 CTATCACTCACAGATGAACTCAAATAA 57.408 33.333 0.00 0.00 33.30 1.40
876 923 7.232118 TCTATCACTCACAGATGAACTCAAA 57.768 36.000 0.00 0.00 33.30 2.69
885 932 4.979335 TCCTCGATCTATCACTCACAGAT 58.021 43.478 0.00 0.00 0.00 2.90
887 934 4.819088 TCTTCCTCGATCTATCACTCACAG 59.181 45.833 0.00 0.00 0.00 3.66
890 937 6.536941 CGATATCTTCCTCGATCTATCACTCA 59.463 42.308 0.34 0.00 37.05 3.41
895 943 7.496591 ACCTAACGATATCTTCCTCGATCTATC 59.503 40.741 0.34 0.00 38.24 2.08
914 963 7.332430 TGAATACCAGATGTTAACAACCTAACG 59.668 37.037 13.23 6.57 35.00 3.18
974 1043 2.360600 CGCCGGTGGAAATTGGGA 60.361 61.111 7.26 0.00 0.00 4.37
1015 1084 1.002544 GACCAGGGAACAAGGAGACTG 59.997 57.143 0.00 0.00 42.68 3.51
1018 1087 3.375699 GATAGACCAGGGAACAAGGAGA 58.624 50.000 0.00 0.00 0.00 3.71
1054 1123 2.573869 CTCGTCTGCGGTCATGGT 59.426 61.111 0.00 0.00 38.89 3.55
1219 1314 1.141665 TGGATGCGAGGTCGATGTG 59.858 57.895 2.94 0.00 43.02 3.21
1220 1315 1.141881 GTGGATGCGAGGTCGATGT 59.858 57.895 2.94 0.00 43.02 3.06
1394 1683 3.011517 CAGTGGTGGAGGAGGGGG 61.012 72.222 0.00 0.00 0.00 5.40
1427 1716 4.873129 CCTCGGACGCATCGTGGG 62.873 72.222 0.00 1.58 41.37 4.61
1542 1831 2.743928 GGTGCGGCTGTTGAGAGG 60.744 66.667 0.00 0.00 0.00 3.69
1932 2573 1.003866 GGCACACTGACTTCAAACGAC 60.004 52.381 0.00 0.00 0.00 4.34
1948 2589 4.697352 ACAATCACACTTCTCTAATGGCAC 59.303 41.667 0.00 0.00 0.00 5.01
1949 2590 4.696877 CACAATCACACTTCTCTAATGGCA 59.303 41.667 0.00 0.00 0.00 4.92
1950 2591 4.697352 ACACAATCACACTTCTCTAATGGC 59.303 41.667 0.00 0.00 0.00 4.40
1951 2592 5.391310 GCACACAATCACACTTCTCTAATGG 60.391 44.000 0.00 0.00 0.00 3.16
1952 2593 5.179929 TGCACACAATCACACTTCTCTAATG 59.820 40.000 0.00 0.00 0.00 1.90
1953 2594 5.308014 TGCACACAATCACACTTCTCTAAT 58.692 37.500 0.00 0.00 0.00 1.73
1954 2595 4.702831 TGCACACAATCACACTTCTCTAA 58.297 39.130 0.00 0.00 0.00 2.10
1955 2596 4.335400 TGCACACAATCACACTTCTCTA 57.665 40.909 0.00 0.00 0.00 2.43
1956 2597 3.198409 TGCACACAATCACACTTCTCT 57.802 42.857 0.00 0.00 0.00 3.10
1957 2598 3.750130 AGATGCACACAATCACACTTCTC 59.250 43.478 0.00 0.00 0.00 2.87
1958 2599 3.748083 AGATGCACACAATCACACTTCT 58.252 40.909 0.00 0.00 0.00 2.85
1959 2600 4.224433 CAAGATGCACACAATCACACTTC 58.776 43.478 0.00 0.00 0.00 3.01
1960 2601 3.633525 ACAAGATGCACACAATCACACTT 59.366 39.130 0.00 0.00 0.00 3.16
1961 2602 3.216800 ACAAGATGCACACAATCACACT 58.783 40.909 0.00 0.00 0.00 3.55
1962 2603 3.631145 ACAAGATGCACACAATCACAC 57.369 42.857 0.00 0.00 0.00 3.82
1963 2604 5.002516 TGATACAAGATGCACACAATCACA 58.997 37.500 0.00 0.00 0.00 3.58
1964 2605 5.550232 TGATACAAGATGCACACAATCAC 57.450 39.130 0.00 0.00 0.00 3.06
1965 2606 4.095334 GCTGATACAAGATGCACACAATCA 59.905 41.667 0.00 0.00 0.00 2.57
1966 2607 4.095334 TGCTGATACAAGATGCACACAATC 59.905 41.667 0.00 0.00 0.00 2.67
1967 2608 4.011698 TGCTGATACAAGATGCACACAAT 58.988 39.130 0.00 0.00 0.00 2.71
1968 2609 3.410508 TGCTGATACAAGATGCACACAA 58.589 40.909 0.00 0.00 0.00 3.33
1969 2610 3.004862 CTGCTGATACAAGATGCACACA 58.995 45.455 0.00 0.00 0.00 3.72
1970 2611 3.063180 GTCTGCTGATACAAGATGCACAC 59.937 47.826 0.00 0.00 0.00 3.82
1971 2612 3.264947 GTCTGCTGATACAAGATGCACA 58.735 45.455 0.00 0.00 0.00 4.57
1972 2613 2.283617 CGTCTGCTGATACAAGATGCAC 59.716 50.000 0.00 0.00 0.00 4.57
1973 2614 2.543641 CGTCTGCTGATACAAGATGCA 58.456 47.619 0.00 0.00 0.00 3.96
1974 2615 1.863454 CCGTCTGCTGATACAAGATGC 59.137 52.381 0.00 0.00 0.00 3.91
1975 2616 3.443099 TCCGTCTGCTGATACAAGATG 57.557 47.619 0.00 0.00 0.00 2.90
1976 2617 4.184629 GTTTCCGTCTGCTGATACAAGAT 58.815 43.478 0.00 0.00 0.00 2.40
1977 2618 3.585862 GTTTCCGTCTGCTGATACAAGA 58.414 45.455 0.00 0.00 0.00 3.02
1978 2619 2.345641 CGTTTCCGTCTGCTGATACAAG 59.654 50.000 0.00 0.00 0.00 3.16
1979 2620 2.029739 TCGTTTCCGTCTGCTGATACAA 60.030 45.455 0.00 0.00 35.01 2.41
1980 2621 1.542472 TCGTTTCCGTCTGCTGATACA 59.458 47.619 0.00 0.00 35.01 2.29
1981 2622 2.186076 CTCGTTTCCGTCTGCTGATAC 58.814 52.381 0.00 0.00 35.01 2.24
1982 2623 1.134367 CCTCGTTTCCGTCTGCTGATA 59.866 52.381 0.00 0.00 35.01 2.15
1983 2624 0.108615 CCTCGTTTCCGTCTGCTGAT 60.109 55.000 0.00 0.00 35.01 2.90
1984 2625 1.289066 CCTCGTTTCCGTCTGCTGA 59.711 57.895 0.00 0.00 35.01 4.26
1985 2626 1.006102 ACCTCGTTTCCGTCTGCTG 60.006 57.895 0.00 0.00 35.01 4.41
1986 2627 1.289380 GACCTCGTTTCCGTCTGCT 59.711 57.895 0.00 0.00 35.01 4.24
1987 2628 1.737008 GGACCTCGTTTCCGTCTGC 60.737 63.158 0.00 0.00 35.01 4.26
1988 2629 4.573162 GGACCTCGTTTCCGTCTG 57.427 61.111 0.00 0.00 35.01 3.51
1993 2634 1.896122 ATGGGTCGGACCTCGTTTCC 61.896 60.000 25.39 8.58 38.64 3.13
1994 2635 0.036671 AATGGGTCGGACCTCGTTTC 60.037 55.000 25.39 9.28 38.64 2.78
1995 2636 0.036671 GAATGGGTCGGACCTCGTTT 60.037 55.000 25.39 13.92 38.64 3.60
1996 2637 1.595357 GAATGGGTCGGACCTCGTT 59.405 57.895 25.39 20.88 38.64 3.85
1997 2638 2.356780 GGAATGGGTCGGACCTCGT 61.357 63.158 25.39 14.41 38.64 4.18
1998 2639 1.686325 ATGGAATGGGTCGGACCTCG 61.686 60.000 25.39 0.00 38.64 4.63
1999 2640 0.179045 CATGGAATGGGTCGGACCTC 60.179 60.000 25.39 15.49 41.79 3.85
2000 2641 1.915228 CATGGAATGGGTCGGACCT 59.085 57.895 25.39 7.14 41.79 3.85
2001 2642 4.559502 CATGGAATGGGTCGGACC 57.440 61.111 19.06 19.06 41.79 4.46
2010 2651 2.026641 AGAAACGATGGCCATGGAATG 58.973 47.619 31.80 14.46 46.21 2.67
2011 2652 2.442236 AGAAACGATGGCCATGGAAT 57.558 45.000 31.80 19.79 0.00 3.01
2012 2653 3.358111 TTAGAAACGATGGCCATGGAA 57.642 42.857 31.80 13.90 0.00 3.53
2013 2654 3.576078 ATTAGAAACGATGGCCATGGA 57.424 42.857 31.80 10.67 0.00 3.41
2014 2655 3.243501 CCAATTAGAAACGATGGCCATGG 60.244 47.826 26.56 25.49 0.00 3.66
2015 2656 3.631686 TCCAATTAGAAACGATGGCCATG 59.368 43.478 26.56 17.71 0.00 3.66
2016 2657 3.897239 TCCAATTAGAAACGATGGCCAT 58.103 40.909 20.96 20.96 0.00 4.40
2017 2658 3.358111 TCCAATTAGAAACGATGGCCA 57.642 42.857 8.56 8.56 0.00 5.36
2018 2659 3.066760 CCTTCCAATTAGAAACGATGGCC 59.933 47.826 0.00 0.00 0.00 5.36
2019 2660 3.694566 ACCTTCCAATTAGAAACGATGGC 59.305 43.478 0.00 0.00 0.00 4.40
2020 2661 5.414454 TGAACCTTCCAATTAGAAACGATGG 59.586 40.000 0.00 0.00 0.00 3.51
2021 2662 6.494893 TGAACCTTCCAATTAGAAACGATG 57.505 37.500 0.00 0.00 0.00 3.84
2022 2663 6.884295 TCATGAACCTTCCAATTAGAAACGAT 59.116 34.615 0.00 0.00 0.00 3.73
2023 2664 6.234920 TCATGAACCTTCCAATTAGAAACGA 58.765 36.000 0.00 0.00 0.00 3.85
2024 2665 6.494893 TCATGAACCTTCCAATTAGAAACG 57.505 37.500 0.00 0.00 0.00 3.60
2025 2666 6.808704 GCTTCATGAACCTTCCAATTAGAAAC 59.191 38.462 3.38 0.00 0.00 2.78
2026 2667 6.493115 TGCTTCATGAACCTTCCAATTAGAAA 59.507 34.615 3.38 0.00 0.00 2.52
2027 2668 6.009589 TGCTTCATGAACCTTCCAATTAGAA 58.990 36.000 3.38 0.00 0.00 2.10
2028 2669 5.569355 TGCTTCATGAACCTTCCAATTAGA 58.431 37.500 3.38 0.00 0.00 2.10
2029 2670 5.902613 TGCTTCATGAACCTTCCAATTAG 57.097 39.130 3.38 0.00 0.00 1.73
2030 2671 6.189859 AGATGCTTCATGAACCTTCCAATTA 58.810 36.000 3.38 0.00 0.00 1.40
2031 2672 5.021458 AGATGCTTCATGAACCTTCCAATT 58.979 37.500 3.38 0.00 0.00 2.32
2032 2673 4.607239 AGATGCTTCATGAACCTTCCAAT 58.393 39.130 3.38 0.00 0.00 3.16
2033 2674 4.038271 AGATGCTTCATGAACCTTCCAA 57.962 40.909 3.38 0.00 0.00 3.53
2034 2675 3.726557 AGATGCTTCATGAACCTTCCA 57.273 42.857 3.38 0.00 0.00 3.53
2035 2676 6.705863 AATTAGATGCTTCATGAACCTTCC 57.294 37.500 3.38 0.00 0.00 3.46
2036 2677 8.844244 ACATAATTAGATGCTTCATGAACCTTC 58.156 33.333 3.38 6.31 0.00 3.46
2037 2678 8.757982 ACATAATTAGATGCTTCATGAACCTT 57.242 30.769 3.38 0.00 0.00 3.50
2064 2705 2.224606 CCACTGTCATGCACTTGAACT 58.775 47.619 0.00 0.00 0.00 3.01
2099 2740 7.047460 ACATGGCTTAATTCCATCAGAAATC 57.953 36.000 0.00 0.00 42.11 2.17
2100 2741 7.270047 CAACATGGCTTAATTCCATCAGAAAT 58.730 34.615 0.00 0.00 42.11 2.17
2105 2746 4.608269 TCCAACATGGCTTAATTCCATCA 58.392 39.130 0.00 0.00 42.11 3.07
2118 2759 4.300803 CACACACAAGATTTCCAACATGG 58.699 43.478 0.00 0.00 39.43 3.66
2120 2761 3.960102 ACCACACACAAGATTTCCAACAT 59.040 39.130 0.00 0.00 0.00 2.71
2121 2762 3.360867 ACCACACACAAGATTTCCAACA 58.639 40.909 0.00 0.00 0.00 3.33
2123 2764 3.897239 AGACCACACACAAGATTTCCAA 58.103 40.909 0.00 0.00 0.00 3.53
2124 2765 3.576078 AGACCACACACAAGATTTCCA 57.424 42.857 0.00 0.00 0.00 3.53
2125 2766 4.137543 AGAAGACCACACACAAGATTTCC 58.862 43.478 0.00 0.00 0.00 3.13
2126 2767 5.506317 CCAAGAAGACCACACACAAGATTTC 60.506 44.000 0.00 0.00 0.00 2.17
2127 2768 4.339247 CCAAGAAGACCACACACAAGATTT 59.661 41.667 0.00 0.00 0.00 2.17
2128 2769 3.885297 CCAAGAAGACCACACACAAGATT 59.115 43.478 0.00 0.00 0.00 2.40
2129 2770 3.136443 TCCAAGAAGACCACACACAAGAT 59.864 43.478 0.00 0.00 0.00 2.40
2130 2771 2.503765 TCCAAGAAGACCACACACAAGA 59.496 45.455 0.00 0.00 0.00 3.02
2131 2772 2.917933 TCCAAGAAGACCACACACAAG 58.082 47.619 0.00 0.00 0.00 3.16
2132 2773 3.358111 TTCCAAGAAGACCACACACAA 57.642 42.857 0.00 0.00 0.00 3.33
2133 2774 3.013921 GTTTCCAAGAAGACCACACACA 58.986 45.455 0.00 0.00 0.00 3.72
2134 2775 2.031683 CGTTTCCAAGAAGACCACACAC 59.968 50.000 0.00 0.00 0.00 3.82
2135 2776 2.285083 CGTTTCCAAGAAGACCACACA 58.715 47.619 0.00 0.00 0.00 3.72
2136 2777 1.602377 CCGTTTCCAAGAAGACCACAC 59.398 52.381 0.00 0.00 0.00 3.82
2137 2778 1.961793 CCGTTTCCAAGAAGACCACA 58.038 50.000 0.00 0.00 0.00 4.17
2138 2779 0.591659 GCCGTTTCCAAGAAGACCAC 59.408 55.000 0.00 0.00 0.00 4.16
2139 2780 0.181587 TGCCGTTTCCAAGAAGACCA 59.818 50.000 0.00 0.00 0.00 4.02
2140 2781 1.534729 ATGCCGTTTCCAAGAAGACC 58.465 50.000 0.00 0.00 0.00 3.85
2141 2782 3.127030 CCTTATGCCGTTTCCAAGAAGAC 59.873 47.826 0.00 0.00 0.00 3.01
2142 2783 3.008594 TCCTTATGCCGTTTCCAAGAAGA 59.991 43.478 0.00 0.00 0.00 2.87
2147 2788 4.825085 GGAATATCCTTATGCCGTTTCCAA 59.175 41.667 0.00 0.00 33.27 3.53
2155 2796 3.330701 TGACCTGGGAATATCCTTATGCC 59.669 47.826 0.00 0.00 36.57 4.40
2156 2797 4.583871 CTGACCTGGGAATATCCTTATGC 58.416 47.826 0.00 0.00 36.57 3.14
2167 2808 1.273838 ACATAGGAGCTGACCTGGGAA 60.274 52.381 4.21 0.00 40.81 3.97
2174 2815 3.003480 GACCACAAACATAGGAGCTGAC 58.997 50.000 0.00 0.00 0.00 3.51
2175 2816 2.906389 AGACCACAAACATAGGAGCTGA 59.094 45.455 0.00 0.00 0.00 4.26
2182 2823 4.930963 TGTTGCAAAGACCACAAACATAG 58.069 39.130 0.00 0.00 0.00 2.23
2184 2825 3.883830 TGTTGCAAAGACCACAAACAT 57.116 38.095 0.00 0.00 0.00 2.71
2195 2836 7.088272 TGAATCATCTTCATCTTGTTGCAAAG 58.912 34.615 0.00 0.00 0.00 2.77
2213 2854 5.831525 ACATGTGTATTGAGGCATGAATCAT 59.168 36.000 0.00 0.00 40.61 2.45
2227 2868 7.458409 AATGAAAGAGCTTCACATGTGTATT 57.542 32.000 24.63 6.96 46.80 1.89
2245 2886 8.962679 AGAAAACCACTGTTTACTGTAATGAAA 58.037 29.630 0.37 0.00 43.80 2.69
2271 2912 3.797451 TCAGCAAATGCACAAAGTTCA 57.203 38.095 8.28 0.00 45.16 3.18
2287 2928 2.216898 AGTGAGTTGCTCTTGTTCAGC 58.783 47.619 0.00 0.00 37.40 4.26
2297 2938 3.381590 GGAAACCAAGAAAGTGAGTTGCT 59.618 43.478 0.00 0.00 0.00 3.91
2353 2997 1.003696 TGTTCCGGGATGTGCACAATA 59.996 47.619 25.72 0.00 0.00 1.90
2354 2998 0.251121 TGTTCCGGGATGTGCACAAT 60.251 50.000 25.72 12.53 0.00 2.71
2367 3011 5.516339 GGTGAAATCATTGCTATTTGTTCCG 59.484 40.000 0.00 0.00 0.00 4.30
2382 3026 6.058553 AGATCAGACTGAATGGTGAAATCA 57.941 37.500 9.70 0.00 0.00 2.57
2402 3046 9.232473 GTAATTGTTCAAAAGAACTAGGGAGAT 57.768 33.333 9.45 0.00 36.15 2.75
2412 3056 8.474025 ACTCCACATTGTAATTGTTCAAAAGAA 58.526 29.630 0.00 0.00 0.00 2.52
2461 3105 1.002468 CCTGCAGACAGTTGTTTTCCG 60.002 52.381 17.39 0.00 42.81 4.30
2497 3141 5.415701 TGGATGGTAGCAGAAACTGAAAATC 59.584 40.000 0.00 0.00 32.44 2.17
2512 3156 3.384789 TCTCGAGGATTGTTGGATGGTAG 59.615 47.826 13.56 0.00 0.00 3.18
2619 3263 6.369615 CCCATAATTTCTCAAGGCAAAAACAG 59.630 38.462 0.00 0.00 0.00 3.16
2646 3290 0.883153 GATGCACAATGTCACCAGCA 59.117 50.000 0.00 0.00 36.34 4.41
2650 3294 2.331194 GCTTTGATGCACAATGTCACC 58.669 47.619 0.00 0.00 38.36 4.02
2656 3300 1.822990 CTCCTGGCTTTGATGCACAAT 59.177 47.619 0.00 0.00 38.36 2.71
2691 3335 2.783135 TGCTCCAGAAAGTGATGTTCC 58.217 47.619 0.00 0.00 0.00 3.62
2712 3356 6.000219 CCAAGGAATATTACATGTAGCAGCT 59.000 40.000 5.56 0.00 0.00 4.24
2745 3389 1.134371 GTCCTCATGGTCCCTAGCAAC 60.134 57.143 0.00 0.00 36.53 4.17
2762 3406 1.610522 GCCAATACATGCTCATGGTCC 59.389 52.381 13.69 0.00 42.91 4.46
2852 3496 2.024176 TCTAGCTCCAGAACCACCAA 57.976 50.000 0.00 0.00 0.00 3.67
2862 3506 3.031736 AGTAAGCGGAATTCTAGCTCCA 58.968 45.455 22.44 14.13 40.78 3.86
2906 3550 2.559698 TTCACCAAATGAGGAGCGAA 57.440 45.000 0.00 0.00 38.99 4.70
2914 3558 4.776837 ACCCAGCATTATTTCACCAAATGA 59.223 37.500 0.00 0.00 33.95 2.57
2954 3598 3.323691 TGTGGCGATATGTACCATAAGCT 59.676 43.478 11.87 0.00 35.53 3.74
2967 3611 1.558167 TTGGGAAGGCTGTGGCGATA 61.558 55.000 0.00 0.00 39.81 2.92
3019 3663 2.097110 TGGTGAACAGGTCCAGTAGT 57.903 50.000 0.00 0.00 0.00 2.73
3116 3760 3.256960 GTGGCCTTGGGGACTCCA 61.257 66.667 3.32 0.00 42.43 3.86
3118 3762 0.696501 TTAAGTGGCCTTGGGGACTC 59.303 55.000 3.32 0.00 42.43 3.36
3150 3794 2.216046 CTGAAGCAAGACAACTGAGCA 58.784 47.619 0.00 0.00 32.73 4.26
3164 3808 7.410485 GTTACATATGGCTTTCTTACTGAAGC 58.590 38.462 7.80 0.00 35.89 3.86
3177 3821 0.033504 CGAGGGCGTTACATATGGCT 59.966 55.000 7.80 0.00 38.35 4.75
3936 4588 2.113910 TTTGAACTTTCGAAAGCCGC 57.886 45.000 32.49 22.73 39.63 6.53
3958 4610 1.148273 GTTGGGACACACCTGCAGA 59.852 57.895 17.39 0.00 39.29 4.26
3966 4618 1.072266 ATGGGCTAAGTTGGGACACA 58.928 50.000 0.00 0.00 39.29 3.72
4048 4700 0.988832 TGCCTTGTAGAACCGGGATT 59.011 50.000 6.32 0.00 0.00 3.01
4065 4717 3.438781 TGTTTTACCATTGTCGAGGATGC 59.561 43.478 0.00 0.00 0.00 3.91
4191 4843 1.404315 GCCACCTCGAAGAAACTCGAT 60.404 52.381 0.00 0.00 46.14 3.59


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

AutoCloner maintained by Alex Coulton.