Multiple sequence alignment - TraesCS6A01G020600

Loading Multiple Alignment...

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 TraesCS6A01G020600 chr6A 100.000 4149 0 0 1 4149 9580529 9576381 0.000000e+00 7662.0
1 TraesCS6A01G020600 chr6B 96.056 1293 46 5 2858 4149 16507686 16508974 0.000000e+00 2100.0
2 TraesCS6A01G020600 chr2A 90.043 934 69 8 6 926 776210062 776210984 0.000000e+00 1188.0
3 TraesCS6A01G020600 chr1B 88.984 935 76 12 6 926 321709149 321710070 0.000000e+00 1131.0
4 TraesCS6A01G020600 chr1B 90.017 591 55 3 340 926 278021073 278021663 0.000000e+00 761.0
5 TraesCS6A01G020600 chr1B 72.787 757 187 17 2635 3380 577925891 577925143 5.360000e-59 239.0
6 TraesCS6A01G020600 chr4D 79.230 1507 288 18 2353 3850 1697577 1699067 0.000000e+00 1026.0
7 TraesCS6A01G020600 chr4D 81.559 1052 183 10 994 2037 1696156 1697204 0.000000e+00 857.0
8 TraesCS6A01G020600 chr4D 85.870 736 63 9 206 929 454853793 454853087 0.000000e+00 745.0
9 TraesCS6A01G020600 chr4D 79.075 865 166 10 2565 3426 2130783 2129931 7.730000e-162 580.0
10 TraesCS6A01G020600 chr3D 78.490 1576 304 28 2585 4148 13179916 13178364 0.000000e+00 1000.0
11 TraesCS6A01G020600 chr3D 80.209 1051 195 13 1001 2043 13181569 13180524 0.000000e+00 776.0
12 TraesCS6A01G020600 chr3A 78.426 1576 306 26 2585 4148 24012214 24013767 0.000000e+00 996.0
13 TraesCS6A01G020600 chr3A 80.057 1048 196 13 998 2037 24010590 24011632 0.000000e+00 765.0
14 TraesCS6A01G020600 chr3A 88.435 588 61 5 341 926 348681108 348681690 0.000000e+00 702.0
15 TraesCS6A01G020600 chr3A 86.230 610 56 15 341 926 620781255 620780650 1.630000e-178 636.0
16 TraesCS6A01G020600 chr3A 81.818 121 12 5 6 126 535552492 535552382 4.420000e-15 93.5
17 TraesCS6A01G020600 chr3A 87.324 71 2 1 7 70 348680992 348681062 1.600000e-09 75.0
18 TraesCS6A01G020600 chr4A 78.481 1501 302 19 2539 4029 603045259 603046748 0.000000e+00 963.0
19 TraesCS6A01G020600 chr4A 77.557 1056 215 15 994 2038 602870803 602871847 5.890000e-173 617.0
20 TraesCS6A01G020600 chr4A 80.662 574 104 6 1185 1753 603053643 603053072 4.920000e-119 438.0
21 TraesCS6A01G020600 chr4A 89.062 128 7 1 6 126 67422281 67422154 7.180000e-33 152.0
22 TraesCS6A01G020600 chr3B 77.947 1578 310 33 2585 4148 18861139 18859586 0.000000e+00 952.0
23 TraesCS6A01G020600 chr3B 79.353 1051 204 13 1001 2043 18862746 18861701 0.000000e+00 726.0
24 TraesCS6A01G020600 chr6D 85.539 733 64 20 206 926 27003629 27004331 0.000000e+00 728.0
25 TraesCS6A01G020600 chr6D 96.117 103 4 0 7 109 24851061 24851163 7.130000e-38 169.0
26 TraesCS6A01G020600 chr1A 88.494 591 64 2 340 926 59052017 59051427 0.000000e+00 712.0
27 TraesCS6A01G020600 chr1A 88.764 445 46 2 485 926 54142037 54142480 3.650000e-150 542.0
28 TraesCS6A01G020600 chr2D 84.741 734 66 10 206 926 213737225 213737925 0.000000e+00 693.0
29 TraesCS6A01G020600 chr2D 89.844 128 6 1 6 126 648397587 648397460 1.540000e-34 158.0
30 TraesCS6A01G020600 chr4B 87.986 591 63 3 340 926 271538599 271539185 0.000000e+00 691.0
31 TraesCS6A01G020600 chr4B 84.720 733 66 16 206 926 330849204 330848506 0.000000e+00 691.0
32 TraesCS6A01G020600 chr4B 79.331 987 176 18 1210 2175 3714553 3713574 0.000000e+00 667.0
33 TraesCS6A01G020600 chr4B 85.774 478 64 3 2552 3028 3305728 3305254 1.720000e-138 503.0
34 TraesCS6A01G020600 chrUn 78.437 1062 198 20 994 2041 47450830 47451874 0.000000e+00 664.0
35 TraesCS6A01G020600 chrUn 75.212 827 181 16 1223 2037 47658280 47659094 1.820000e-98 370.0
36 TraesCS6A01G020600 chr5D 86.116 605 59 12 341 922 309715193 309714591 2.720000e-176 628.0
37 TraesCS6A01G020600 chr7B 72.632 760 183 21 2635 3380 747525981 747525233 1.160000e-55 228.0
38 TraesCS6A01G020600 chr7B 80.488 123 22 2 1916 2037 743998325 743998204 4.420000e-15 93.5
39 TraesCS6A01G020600 chr7B 80.488 123 22 2 1916 2037 744006425 744006304 4.420000e-15 93.5
40 TraesCS6A01G020600 chr7B 80.488 123 22 2 1916 2037 744294151 744294030 4.420000e-15 93.5
41 TraesCS6A01G020600 chr7B 80.488 123 22 2 1916 2037 745231086 745231207 4.420000e-15 93.5
42 TraesCS6A01G020600 chr5A 89.062 128 7 1 6 126 104948271 104948144 7.180000e-33 152.0
43 TraesCS6A01G020600 chr7D 71.664 547 134 20 2635 3169 555049628 555050165 9.360000e-27 132.0
44 TraesCS6A01G020600 chr7A 78.571 154 31 2 1576 1728 735845119 735844967 2.640000e-17 100.0
45 TraesCS6A01G020600 chr7A 79.528 127 24 2 1916 2041 736002613 736002488 5.710000e-14 89.8


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 TraesCS6A01G020600 chr6A 9576381 9580529 4148 True 7662.0 7662 100.0000 1 4149 1 chr6A.!!$R1 4148
1 TraesCS6A01G020600 chr6B 16507686 16508974 1288 False 2100.0 2100 96.0560 2858 4149 1 chr6B.!!$F1 1291
2 TraesCS6A01G020600 chr2A 776210062 776210984 922 False 1188.0 1188 90.0430 6 926 1 chr2A.!!$F1 920
3 TraesCS6A01G020600 chr1B 321709149 321710070 921 False 1131.0 1131 88.9840 6 926 1 chr1B.!!$F2 920
4 TraesCS6A01G020600 chr1B 278021073 278021663 590 False 761.0 761 90.0170 340 926 1 chr1B.!!$F1 586
5 TraesCS6A01G020600 chr1B 577925143 577925891 748 True 239.0 239 72.7870 2635 3380 1 chr1B.!!$R1 745
6 TraesCS6A01G020600 chr4D 1696156 1699067 2911 False 941.5 1026 80.3945 994 3850 2 chr4D.!!$F1 2856
7 TraesCS6A01G020600 chr4D 454853087 454853793 706 True 745.0 745 85.8700 206 929 1 chr4D.!!$R2 723
8 TraesCS6A01G020600 chr4D 2129931 2130783 852 True 580.0 580 79.0750 2565 3426 1 chr4D.!!$R1 861
9 TraesCS6A01G020600 chr3D 13178364 13181569 3205 True 888.0 1000 79.3495 1001 4148 2 chr3D.!!$R1 3147
10 TraesCS6A01G020600 chr3A 24010590 24013767 3177 False 880.5 996 79.2415 998 4148 2 chr3A.!!$F1 3150
11 TraesCS6A01G020600 chr3A 620780650 620781255 605 True 636.0 636 86.2300 341 926 1 chr3A.!!$R2 585
12 TraesCS6A01G020600 chr3A 348680992 348681690 698 False 388.5 702 87.8795 7 926 2 chr3A.!!$F2 919
13 TraesCS6A01G020600 chr4A 603045259 603046748 1489 False 963.0 963 78.4810 2539 4029 1 chr4A.!!$F2 1490
14 TraesCS6A01G020600 chr4A 602870803 602871847 1044 False 617.0 617 77.5570 994 2038 1 chr4A.!!$F1 1044
15 TraesCS6A01G020600 chr4A 603053072 603053643 571 True 438.0 438 80.6620 1185 1753 1 chr4A.!!$R2 568
16 TraesCS6A01G020600 chr3B 18859586 18862746 3160 True 839.0 952 78.6500 1001 4148 2 chr3B.!!$R1 3147
17 TraesCS6A01G020600 chr6D 27003629 27004331 702 False 728.0 728 85.5390 206 926 1 chr6D.!!$F2 720
18 TraesCS6A01G020600 chr1A 59051427 59052017 590 True 712.0 712 88.4940 340 926 1 chr1A.!!$R1 586
19 TraesCS6A01G020600 chr2D 213737225 213737925 700 False 693.0 693 84.7410 206 926 1 chr2D.!!$F1 720
20 TraesCS6A01G020600 chr4B 271538599 271539185 586 False 691.0 691 87.9860 340 926 1 chr4B.!!$F1 586
21 TraesCS6A01G020600 chr4B 330848506 330849204 698 True 691.0 691 84.7200 206 926 1 chr4B.!!$R3 720
22 TraesCS6A01G020600 chr4B 3713574 3714553 979 True 667.0 667 79.3310 1210 2175 1 chr4B.!!$R2 965
23 TraesCS6A01G020600 chrUn 47450830 47451874 1044 False 664.0 664 78.4370 994 2041 1 chrUn.!!$F1 1047
24 TraesCS6A01G020600 chrUn 47658280 47659094 814 False 370.0 370 75.2120 1223 2037 1 chrUn.!!$F2 814
25 TraesCS6A01G020600 chr5D 309714591 309715193 602 True 628.0 628 86.1160 341 922 1 chr5D.!!$R1 581
26 TraesCS6A01G020600 chr7B 747525233 747525981 748 True 228.0 228 72.6320 2635 3380 1 chr7B.!!$R4 745

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
858 905 0.184211 ACGTGGGGTTAGTTTGGCTT 59.816 50.0 0.0 0.0 0.00 4.35 F
2044 2099 0.031178 CAAGAAGCAGGTTGGTGTGC 59.969 55.0 0.0 0.0 40.17 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2352 0.105709 TGGAGTGGAGTGTGGAGACA 60.106 55.0 0.00 0.0 38.70 3.41 R
3900 4120 0.321564 CATCTTGGGAGTTGACGCCA 60.322 55.0 6.25 0.0 37.57 5.69 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
87 95 9.753674 ATAAACCTGAGATTTTATCAAACCTGA 57.246 29.630 0.00 0.00 35.56 3.86
111 119 1.153025 GCTGGAGCATGGCATGAGA 60.153 57.895 30.69 9.48 41.59 3.27
125 133 4.125703 GGCATGAGAAACTAGTGATCCAG 58.874 47.826 0.00 0.00 0.00 3.86
126 134 3.559242 GCATGAGAAACTAGTGATCCAGC 59.441 47.826 0.00 0.00 0.00 4.85
127 135 4.682859 GCATGAGAAACTAGTGATCCAGCT 60.683 45.833 0.00 0.00 0.00 4.24
128 136 5.426504 CATGAGAAACTAGTGATCCAGCTT 58.573 41.667 0.00 0.00 0.00 3.74
181 191 4.082300 TGGTACACTGCAATGCCTTATTTG 60.082 41.667 1.53 0.00 0.00 2.32
213 223 8.921670 GGAAACAATGTACACCATATTTGTTTC 58.078 33.333 31.80 31.80 46.33 2.78
217 227 4.328536 TGTACACCATATTTGTTTCGGCT 58.671 39.130 0.00 0.00 0.00 5.52
224 234 5.123979 ACCATATTTGTTTCGGCTTCTTCTC 59.876 40.000 0.00 0.00 0.00 2.87
297 315 5.255687 TGACTTGCCATATTGTGAATGAGT 58.744 37.500 0.00 0.00 0.00 3.41
298 316 5.124297 TGACTTGCCATATTGTGAATGAGTG 59.876 40.000 0.00 0.00 0.00 3.51
299 317 5.255687 ACTTGCCATATTGTGAATGAGTGA 58.744 37.500 0.00 0.00 0.00 3.41
300 318 5.711506 ACTTGCCATATTGTGAATGAGTGAA 59.288 36.000 0.00 0.00 0.00 3.18
301 319 6.209192 ACTTGCCATATTGTGAATGAGTGAAA 59.791 34.615 0.00 0.00 0.00 2.69
302 320 6.778834 TGCCATATTGTGAATGAGTGAAAT 57.221 33.333 0.00 0.00 0.00 2.17
303 321 7.172868 TGCCATATTGTGAATGAGTGAAATT 57.827 32.000 0.00 0.00 0.00 1.82
304 322 7.613585 TGCCATATTGTGAATGAGTGAAATTT 58.386 30.769 0.00 0.00 0.00 1.82
305 323 7.760794 TGCCATATTGTGAATGAGTGAAATTTC 59.239 33.333 11.41 11.41 0.00 2.17
306 324 7.760794 GCCATATTGTGAATGAGTGAAATTTCA 59.239 33.333 16.91 16.91 34.20 2.69
307 325 9.297586 CCATATTGTGAATGAGTGAAATTTCAG 57.702 33.333 21.05 3.86 37.98 3.02
376 395 7.724305 TGTGTCTTTTCAGATAAAGGTACAC 57.276 36.000 14.79 14.79 40.11 2.90
384 403 3.859961 CAGATAAAGGTACACGCTGACTG 59.140 47.826 0.00 0.00 0.00 3.51
476 495 7.345691 TCAATTATCACCCTTAATTCAGCTCA 58.654 34.615 0.00 0.00 29.07 4.26
504 523 9.485206 TTTGTTATTACCTCTGTACTTCAAGTC 57.515 33.333 0.00 0.00 0.00 3.01
506 525 8.521176 TGTTATTACCTCTGTACTTCAAGTCTC 58.479 37.037 0.00 0.00 0.00 3.36
543 562 4.199310 TGTAAGCTGTCAAGGGCAATATC 58.801 43.478 0.00 0.00 0.00 1.63
547 566 3.455910 AGCTGTCAAGGGCAATATCTGTA 59.544 43.478 0.00 0.00 0.00 2.74
567 610 6.500684 TGTACTTCAGAATCTGGATTTTGC 57.499 37.500 10.71 0.00 34.15 3.68
568 611 6.003326 TGTACTTCAGAATCTGGATTTTGCA 58.997 36.000 10.71 0.00 34.15 4.08
569 612 5.382618 ACTTCAGAATCTGGATTTTGCAC 57.617 39.130 10.71 0.00 34.15 4.57
577 620 5.824904 ATCTGGATTTTGCACTACATGTC 57.175 39.130 0.00 0.00 0.00 3.06
596 639 3.947196 TGTCATGAAGCTGTCAAGTGTTT 59.053 39.130 0.00 0.00 40.50 2.83
600 643 6.148480 GTCATGAAGCTGTCAAGTGTTTATCT 59.852 38.462 0.00 0.00 40.50 1.98
633 676 6.816640 TGTTGGTAGTGCAGAATATGTAAGTC 59.183 38.462 0.00 0.00 0.00 3.01
646 689 7.979537 AGAATATGTAAGTCGTCAAGTGCAATA 59.020 33.333 0.00 0.00 0.00 1.90
654 697 4.027621 GTCGTCAAGTGCAATATCTGTACG 60.028 45.833 0.00 0.00 44.70 3.67
740 787 3.117888 ACATGTATGGTGGGGAACTGATC 60.118 47.826 0.00 0.00 0.00 2.92
753 800 4.902448 GGGAACTGATCTAGAACCATAGGT 59.098 45.833 0.00 0.00 37.65 3.08
782 829 5.968167 ACCATAGTTCCTACAATGGGTTAGA 59.032 40.000 5.29 0.00 42.66 2.10
784 831 7.162082 CCATAGTTCCTACAATGGGTTAGATC 58.838 42.308 0.00 0.00 36.12 2.75
793 840 3.732048 ATGGGTTAGATCGGTTTTGGT 57.268 42.857 0.00 0.00 0.00 3.67
796 843 3.007635 GGGTTAGATCGGTTTTGGTGAG 58.992 50.000 0.00 0.00 0.00 3.51
797 844 3.007635 GGTTAGATCGGTTTTGGTGAGG 58.992 50.000 0.00 0.00 0.00 3.86
825 872 0.830023 TGGTTTAGTTTGGGCTGGGC 60.830 55.000 0.00 0.00 0.00 5.36
856 903 1.894881 TTACGTGGGGTTAGTTTGGC 58.105 50.000 0.00 0.00 0.00 4.52
858 905 0.184211 ACGTGGGGTTAGTTTGGCTT 59.816 50.000 0.00 0.00 0.00 4.35
859 906 0.596082 CGTGGGGTTAGTTTGGCTTG 59.404 55.000 0.00 0.00 0.00 4.01
871 918 3.990959 TTTGGCTTGGTTTCCAAAACT 57.009 38.095 4.17 0.00 46.03 2.66
891 938 2.631160 TCATCACGTGGGTTCAGTTT 57.369 45.000 17.00 0.00 0.00 2.66
896 943 2.964464 TCACGTGGGTTCAGTTTAGGTA 59.036 45.455 17.00 0.00 0.00 3.08
904 951 4.322953 GGGTTCAGTTTAGGTATGGTTCGA 60.323 45.833 0.00 0.00 0.00 3.71
907 954 6.183360 GGTTCAGTTTAGGTATGGTTCGATTG 60.183 42.308 0.00 0.00 0.00 2.67
912 959 1.283613 AGGTATGGTTCGATTGCCCAA 59.716 47.619 0.00 0.00 0.00 4.12
926 973 2.449464 TGCCCAACCATTCTCAGATTG 58.551 47.619 0.00 0.00 0.00 2.67
929 976 3.129988 GCCCAACCATTCTCAGATTGAAG 59.870 47.826 0.00 0.00 0.00 3.02
930 977 4.338879 CCCAACCATTCTCAGATTGAAGT 58.661 43.478 0.00 0.00 0.00 3.01
931 978 5.500234 CCCAACCATTCTCAGATTGAAGTA 58.500 41.667 0.00 0.00 0.00 2.24
932 979 5.355350 CCCAACCATTCTCAGATTGAAGTAC 59.645 44.000 0.00 0.00 0.00 2.73
933 980 5.939883 CCAACCATTCTCAGATTGAAGTACA 59.060 40.000 0.00 0.00 0.00 2.90
934 981 6.430925 CCAACCATTCTCAGATTGAAGTACAA 59.569 38.462 0.00 0.00 42.95 2.41
935 982 7.361542 CCAACCATTCTCAGATTGAAGTACAAG 60.362 40.741 0.00 0.00 42.02 3.16
936 983 7.009179 ACCATTCTCAGATTGAAGTACAAGA 57.991 36.000 0.00 0.00 42.02 3.02
937 984 7.628234 ACCATTCTCAGATTGAAGTACAAGAT 58.372 34.615 0.00 0.00 42.02 2.40
938 985 7.768120 ACCATTCTCAGATTGAAGTACAAGATC 59.232 37.037 0.00 0.00 42.02 2.75
939 986 7.986320 CCATTCTCAGATTGAAGTACAAGATCT 59.014 37.037 0.00 0.00 42.02 2.75
940 987 9.381033 CATTCTCAGATTGAAGTACAAGATCTT 57.619 33.333 0.88 0.88 42.02 2.40
941 988 8.768957 TTCTCAGATTGAAGTACAAGATCTTG 57.231 34.615 29.74 29.74 45.58 3.02
942 989 8.127150 TCTCAGATTGAAGTACAAGATCTTGA 57.873 34.615 36.15 19.74 42.93 3.02
943 990 8.756927 TCTCAGATTGAAGTACAAGATCTTGAT 58.243 33.333 36.15 23.50 42.93 2.57
972 1019 9.533831 AGATAACTAATTTTCTTTGACCCATGT 57.466 29.630 0.00 0.00 0.00 3.21
976 1023 9.679661 AACTAATTTTCTTTGACCCATGTTTTT 57.320 25.926 0.00 0.00 0.00 1.94
977 1024 9.108284 ACTAATTTTCTTTGACCCATGTTTTTG 57.892 29.630 0.00 0.00 0.00 2.44
978 1025 6.940831 ATTTTCTTTGACCCATGTTTTTGG 57.059 33.333 0.00 0.00 36.46 3.28
979 1026 3.467374 TCTTTGACCCATGTTTTTGGC 57.533 42.857 0.00 0.00 35.29 4.52
980 1027 2.768527 TCTTTGACCCATGTTTTTGGCA 59.231 40.909 0.00 0.00 35.29 4.92
981 1028 2.906691 TTGACCCATGTTTTTGGCAG 57.093 45.000 0.00 0.00 35.29 4.85
982 1029 0.392336 TGACCCATGTTTTTGGCAGC 59.608 50.000 0.00 0.00 35.29 5.25
983 1030 0.392336 GACCCATGTTTTTGGCAGCA 59.608 50.000 0.00 0.00 35.29 4.41
984 1031 0.393820 ACCCATGTTTTTGGCAGCAG 59.606 50.000 0.00 0.00 35.29 4.24
985 1032 0.952010 CCCATGTTTTTGGCAGCAGC 60.952 55.000 0.00 0.00 41.10 5.25
986 1033 0.249953 CCATGTTTTTGGCAGCAGCA 60.250 50.000 2.65 0.00 44.61 4.41
987 1034 1.144969 CATGTTTTTGGCAGCAGCAG 58.855 50.000 2.65 0.00 44.61 4.24
988 1035 0.601841 ATGTTTTTGGCAGCAGCAGC 60.602 50.000 2.65 0.00 44.61 5.25
1015 1062 1.668826 ACTAATGGCAGGGGTTCTGA 58.331 50.000 0.00 0.00 46.18 3.27
1020 1067 3.608432 GCAGGGGTTCTGAATGCC 58.392 61.111 2.99 0.00 46.18 4.40
1043 1090 1.058404 GCGTCTTACGTGACCAAGAC 58.942 55.000 15.80 15.80 44.73 3.01
1044 1091 1.335689 GCGTCTTACGTGACCAAGACT 60.336 52.381 20.82 0.00 45.50 3.24
1134 1181 4.018050 AGCATCAAACTTAGGGACCTCAAT 60.018 41.667 0.00 0.00 0.00 2.57
1170 1217 3.378512 TGCAGATAGGAGGAACATCACT 58.621 45.455 0.00 0.00 0.00 3.41
1197 1244 3.343421 GTTCGTGCGTGGGTGGAC 61.343 66.667 0.00 0.00 0.00 4.02
1230 1277 1.441729 CATGTACCTCGCCACCGAT 59.558 57.895 0.00 0.00 43.47 4.18
1262 1309 1.527034 TGTCAGCTCAAGTTCATGGC 58.473 50.000 0.00 0.00 0.00 4.40
1270 1317 3.334691 CTCAAGTTCATGGCGAAAGGTA 58.665 45.455 0.00 0.00 34.69 3.08
1319 1366 0.374063 CTGCTCTTCTGCATGCGAAG 59.626 55.000 29.94 29.94 42.48 3.79
1341 1388 1.212375 CCCTCCACACCCATGACATA 58.788 55.000 0.00 0.00 0.00 2.29
1356 1403 0.034574 ACATAGGCACCCGCATCAAA 60.035 50.000 0.00 0.00 41.24 2.69
1428 1475 5.184892 ACTTCATCAAGTTGGAAGCCTAT 57.815 39.130 17.05 1.30 40.16 2.57
1444 1491 3.320541 AGCCTATCAAGACCAGAAGATCG 59.679 47.826 0.00 0.00 0.00 3.69
1457 1504 2.029666 GATCGCCCGACCTCATGG 59.970 66.667 0.00 0.00 39.83 3.66
1485 1532 1.135859 CGCAAGACACATCCTTTGCTC 60.136 52.381 6.50 0.00 43.02 4.26
1519 1566 3.496331 GTGGTTGGGGAGAAGATTGAAA 58.504 45.455 0.00 0.00 0.00 2.69
1520 1567 3.507622 GTGGTTGGGGAGAAGATTGAAAG 59.492 47.826 0.00 0.00 0.00 2.62
1534 1581 4.883585 AGATTGAAAGTGACACAAGAGCAA 59.116 37.500 8.59 5.28 0.00 3.91
1559 1612 2.906389 TGGAGATGCTCACAAAGGTAGT 59.094 45.455 0.00 0.00 31.08 2.73
1587 1640 5.876651 AGAGTGATAGCATCATGGTGTTA 57.123 39.130 8.00 6.39 42.04 2.41
1605 1658 4.359475 GCCATTGTTGGTGTTGGC 57.641 55.556 0.00 0.00 46.94 4.52
1629 1682 2.862780 TGGCAAGACCACCCTTAGT 58.137 52.632 0.00 0.00 46.36 2.24
1631 1684 1.906574 TGGCAAGACCACCCTTAGTAG 59.093 52.381 0.00 0.00 46.36 2.57
1635 1688 3.200165 GCAAGACCACCCTTAGTAGGAAT 59.800 47.826 0.00 0.00 45.05 3.01
1640 1693 7.417811 AGACCACCCTTAGTAGGAATATCTA 57.582 40.000 0.00 0.00 45.05 1.98
1669 1722 4.811908 TGATGTCATCCAATGCAAGTTTG 58.188 39.130 10.36 0.00 0.00 2.93
1704 1757 4.887071 TGGTTAAGCATCACACAAGAGTTT 59.113 37.500 2.54 0.00 0.00 2.66
1725 1778 0.319900 GCGAGGTTGAGCTGTTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
1758 1811 0.954452 CCGCTAATGGAGAATTGCCC 59.046 55.000 0.00 0.00 0.00 5.36
1762 1815 2.687914 GCTAATGGAGAATTGCCCAGGT 60.688 50.000 2.37 0.00 35.67 4.00
1792 1845 5.119694 GTGGGTCTCAAGATAAAGCCTTAG 58.880 45.833 0.00 0.00 0.00 2.18
1863 1918 1.034356 TGGACGACATATGGGGTACG 58.966 55.000 7.80 7.21 0.00 3.67
1866 1921 1.268899 GACGACATATGGGGTACGGAG 59.731 57.143 7.80 0.00 0.00 4.63
1875 1930 1.137697 GGGGTACGGAGGAATGGAAT 58.862 55.000 0.00 0.00 0.00 3.01
1876 1931 1.202770 GGGGTACGGAGGAATGGAATG 60.203 57.143 0.00 0.00 0.00 2.67
1906 1961 2.270858 TGACACCCTTTAGCCATGGTA 58.729 47.619 14.67 1.63 0.00 3.25
1987 2042 1.471851 CGATGCAACCGTACCACCATA 60.472 52.381 0.00 0.00 0.00 2.74
1992 2047 2.612212 GCAACCGTACCACCATATTGAG 59.388 50.000 0.00 0.00 0.00 3.02
1998 2053 5.588648 ACCGTACCACCATATTGAGAAATTG 59.411 40.000 0.00 0.00 0.00 2.32
2002 2057 5.203528 ACCACCATATTGAGAAATTGGGAG 58.796 41.667 0.00 0.00 0.00 4.30
2042 2097 1.972872 CTCAAGAAGCAGGTTGGTGT 58.027 50.000 0.00 0.00 0.00 4.16
2044 2099 0.031178 CAAGAAGCAGGTTGGTGTGC 59.969 55.000 0.00 0.00 40.17 4.57
2056 2117 2.536761 TGGTGTGCAACTACCAGTAC 57.463 50.000 13.10 0.00 41.07 2.73
2061 2145 4.390909 GGTGTGCAACTACCAGTACAATAC 59.609 45.833 10.29 0.00 37.75 1.89
2062 2146 5.235516 GTGTGCAACTACCAGTACAATACT 58.764 41.667 0.00 0.00 37.31 2.12
2063 2147 5.347907 GTGTGCAACTACCAGTACAATACTC 59.652 44.000 0.00 0.00 35.33 2.59
2064 2148 5.245301 TGTGCAACTACCAGTACAATACTCT 59.755 40.000 0.00 0.00 35.33 3.24
2065 2149 6.434965 TGTGCAACTACCAGTACAATACTCTA 59.565 38.462 0.00 0.00 35.33 2.43
2069 2153 8.414778 GCAACTACCAGTACAATACTCTATCTT 58.585 37.037 0.00 0.00 36.76 2.40
2133 2257 3.391296 CCCTACCTTAATTGCTCCTGCTA 59.609 47.826 0.00 0.00 40.48 3.49
2139 2263 7.751768 ACCTTAATTGCTCCTGCTATTTATC 57.248 36.000 3.48 0.00 40.62 1.75
2149 2273 4.511454 TCCTGCTATTTATCGTGTCAATGC 59.489 41.667 0.00 0.00 0.00 3.56
2161 2303 3.609879 CGTGTCAATGCTGCTTGATGAAA 60.610 43.478 14.46 1.96 37.47 2.69
2175 2317 8.718102 TGCTTGATGAAAATTACTAGTACTCC 57.282 34.615 0.91 0.00 0.00 3.85
2176 2318 8.318412 TGCTTGATGAAAATTACTAGTACTCCA 58.682 33.333 0.91 0.00 0.00 3.86
2195 2337 9.875675 GTACTCCAAAACTATATACTCACTACG 57.124 37.037 0.00 0.00 0.00 3.51
2205 2347 9.373603 ACTATATACTCACTACGAATAGCAGAG 57.626 37.037 0.00 0.00 38.72 3.35
2206 2348 3.701532 ACTCACTACGAATAGCAGAGC 57.298 47.619 0.00 0.00 37.37 4.09
2207 2349 3.017442 ACTCACTACGAATAGCAGAGCA 58.983 45.455 0.00 0.00 37.37 4.26
2208 2350 3.444034 ACTCACTACGAATAGCAGAGCAA 59.556 43.478 0.00 0.00 37.37 3.91
2209 2351 4.033990 TCACTACGAATAGCAGAGCAAG 57.966 45.455 0.00 0.00 30.75 4.01
2210 2352 3.444034 TCACTACGAATAGCAGAGCAAGT 59.556 43.478 0.00 0.00 30.75 3.16
2211 2353 3.549471 CACTACGAATAGCAGAGCAAGTG 59.451 47.826 0.00 0.00 30.75 3.16
2212 2354 2.751166 ACGAATAGCAGAGCAAGTGT 57.249 45.000 0.00 0.00 0.00 3.55
2213 2355 2.611518 ACGAATAGCAGAGCAAGTGTC 58.388 47.619 0.00 0.00 0.00 3.67
2214 2356 2.232452 ACGAATAGCAGAGCAAGTGTCT 59.768 45.455 0.00 0.00 0.00 3.41
2215 2357 2.857152 CGAATAGCAGAGCAAGTGTCTC 59.143 50.000 0.00 0.00 0.00 3.36
2216 2358 2.977772 ATAGCAGAGCAAGTGTCTCC 57.022 50.000 0.00 0.00 0.00 3.71
2217 2359 1.632589 TAGCAGAGCAAGTGTCTCCA 58.367 50.000 0.00 0.00 0.00 3.86
2218 2360 0.034616 AGCAGAGCAAGTGTCTCCAC 59.965 55.000 0.00 0.00 42.17 4.02
2219 2361 0.250038 GCAGAGCAAGTGTCTCCACA 60.250 55.000 0.00 0.00 44.39 4.17
2228 2370 2.746697 TGTCTCCACACTCCACTCC 58.253 57.895 0.00 0.00 0.00 3.85
2229 2371 0.105709 TGTCTCCACACTCCACTCCA 60.106 55.000 0.00 0.00 0.00 3.86
2230 2372 1.048601 GTCTCCACACTCCACTCCAA 58.951 55.000 0.00 0.00 0.00 3.53
2231 2373 1.001406 GTCTCCACACTCCACTCCAAG 59.999 57.143 0.00 0.00 0.00 3.61
2254 2396 3.439857 AACTGCTTGTATGTCCACCAT 57.560 42.857 0.00 0.00 37.58 3.55
2258 2400 2.224992 TGCTTGTATGTCCACCATGGTT 60.225 45.455 16.84 2.33 39.03 3.67
2259 2401 2.164219 GCTTGTATGTCCACCATGGTTG 59.836 50.000 16.84 12.93 39.03 3.77
2261 2403 3.797559 TGTATGTCCACCATGGTTGAA 57.202 42.857 19.65 10.87 39.03 2.69
2266 2448 2.092158 TGTCCACCATGGTTGAAGTTCA 60.092 45.455 19.65 10.95 39.03 3.18
2268 2450 4.202514 TGTCCACCATGGTTGAAGTTCATA 60.203 41.667 19.65 0.00 39.03 2.15
2275 2457 6.891908 ACCATGGTTGAAGTTCATATTAGCTT 59.108 34.615 13.00 0.00 0.00 3.74
2315 2498 9.125026 ACTATGCCTTTACTATTCAATTCTTGG 57.875 33.333 0.00 0.00 0.00 3.61
2317 2500 8.593945 ATGCCTTTACTATTCAATTCTTGGAA 57.406 30.769 0.00 0.00 0.00 3.53
2320 2503 9.140286 GCCTTTACTATTCAATTCTTGGAAAAC 57.860 33.333 0.00 0.00 0.00 2.43
2344 2527 4.944962 TTACATGCATGTACTTGCTGTC 57.055 40.909 33.74 6.29 42.48 3.51
2345 2528 3.063510 ACATGCATGTACTTGCTGTCT 57.936 42.857 30.50 12.07 43.18 3.41
2348 2531 5.003160 ACATGCATGTACTTGCTGTCTAAA 58.997 37.500 30.50 11.47 43.18 1.85
2350 2533 5.801350 TGCATGTACTTGCTGTCTAAATC 57.199 39.130 27.83 2.91 43.18 2.17
2351 2534 5.244755 TGCATGTACTTGCTGTCTAAATCA 58.755 37.500 27.83 7.04 43.18 2.57
2355 2543 5.237815 TGTACTTGCTGTCTAAATCACCAG 58.762 41.667 0.00 0.00 0.00 4.00
2357 2545 5.483685 ACTTGCTGTCTAAATCACCAGTA 57.516 39.130 0.00 0.00 0.00 2.74
2362 2550 6.941857 TGCTGTCTAAATCACCAGTATGTAA 58.058 36.000 0.00 0.00 0.00 2.41
2378 2567 8.768955 CCAGTATGTAAATTTATGCTGAGAGTC 58.231 37.037 16.29 0.00 38.71 3.36
2387 2576 6.384258 TTTATGCTGAGAGTCACTAGCTAG 57.616 41.667 19.44 19.44 37.10 3.42
2391 2580 4.878971 TGCTGAGAGTCACTAGCTAGTTAG 59.121 45.833 23.94 13.79 37.10 2.34
2399 2592 8.846211 AGAGTCACTAGCTAGTTAGATCATTTC 58.154 37.037 23.94 11.91 33.46 2.17
2436 2642 8.717717 AGAATTACAAGGACATCAATCCATCTA 58.282 33.333 0.00 0.00 41.73 1.98
2440 2646 6.590068 ACAAGGACATCAATCCATCTAGAAG 58.410 40.000 0.00 0.00 41.73 2.85
2443 2649 6.142498 AGGACATCAATCCATCTAGAAGTCT 58.858 40.000 0.00 0.00 41.73 3.24
2444 2650 6.041865 AGGACATCAATCCATCTAGAAGTCTG 59.958 42.308 0.00 0.00 41.73 3.51
2445 2651 6.172136 ACATCAATCCATCTAGAAGTCTGG 57.828 41.667 0.00 0.00 0.00 3.86
2446 2652 5.901853 ACATCAATCCATCTAGAAGTCTGGA 59.098 40.000 13.84 13.84 41.76 3.86
2447 2653 6.385176 ACATCAATCCATCTAGAAGTCTGGAA 59.615 38.462 15.14 2.02 40.94 3.53
2448 2654 6.874278 TCAATCCATCTAGAAGTCTGGAAA 57.126 37.500 15.14 3.81 40.94 3.13
2449 2655 7.257790 TCAATCCATCTAGAAGTCTGGAAAA 57.742 36.000 15.14 3.52 40.94 2.29
2453 2659 6.837312 TCCATCTAGAAGTCTGGAAAAACAA 58.163 36.000 9.87 0.00 37.03 2.83
2461 2667 6.551227 AGAAGTCTGGAAAAACAAGGCTTTAT 59.449 34.615 0.00 0.00 0.00 1.40
2462 2668 6.332735 AGTCTGGAAAAACAAGGCTTTATC 57.667 37.500 0.00 0.00 0.00 1.75
2463 2669 6.071320 AGTCTGGAAAAACAAGGCTTTATCT 58.929 36.000 0.00 0.00 0.00 1.98
2465 2671 6.642540 GTCTGGAAAAACAAGGCTTTATCTTG 59.357 38.462 0.00 0.00 45.03 3.02
2467 2673 7.069331 TCTGGAAAAACAAGGCTTTATCTTGAA 59.931 33.333 10.30 0.00 42.94 2.69
2468 2674 7.560368 TGGAAAAACAAGGCTTTATCTTGAAA 58.440 30.769 10.30 0.00 42.94 2.69
2469 2675 7.710475 TGGAAAAACAAGGCTTTATCTTGAAAG 59.290 33.333 10.30 0.00 42.94 2.62
2530 2736 8.823220 ATTCTTGCCAACCTAATTTATGTAGT 57.177 30.769 0.00 0.00 0.00 2.73
2537 2743 8.827677 GCCAACCTAATTTATGTAGTAGACTTG 58.172 37.037 0.00 0.00 0.00 3.16
2541 2749 8.714906 ACCTAATTTATGTAGTAGACTTGCCAT 58.285 33.333 0.00 0.00 0.00 4.40
2552 2760 2.012673 GACTTGCCATTAGCCACTCAG 58.987 52.381 0.00 0.00 42.71 3.35
2576 2791 8.783093 CAGAAATGTTAGTGTTCCTTATTGACA 58.217 33.333 0.00 0.00 0.00 3.58
2577 2792 9.003658 AGAAATGTTAGTGTTCCTTATTGACAG 57.996 33.333 0.00 0.00 0.00 3.51
2710 2925 3.295973 TGCCATAAAAGTAATGGGAGGC 58.704 45.455 4.40 0.00 43.53 4.70
2770 2985 5.869344 GGAAAAGGTTTTGAATGATGCTACC 59.131 40.000 0.00 0.00 0.00 3.18
2791 3006 2.868583 CTGGTCAGTATCTCAAATGCCG 59.131 50.000 0.00 0.00 0.00 5.69
2794 3009 3.495100 GGTCAGTATCTCAAATGCCGGAT 60.495 47.826 5.05 0.00 0.00 4.18
2800 3015 0.661552 CTCAAATGCCGGATGAGCTG 59.338 55.000 5.05 0.00 34.72 4.24
2836 3051 3.682696 TCTTAGCTACGAGGACTTGTCA 58.317 45.455 0.00 0.00 0.00 3.58
3019 3235 4.750021 AAGGAACCTTATAGAACCGGAC 57.250 45.455 9.46 0.99 34.05 4.79
3175 3394 8.033626 AGGTTTCTTAGGTTGTCTATAGAAACG 58.966 37.037 3.40 0.60 44.22 3.60
3283 3502 0.035439 TTCAGCCCGGTGATTCCTTC 60.035 55.000 0.00 0.00 0.00 3.46
3381 3601 4.576463 GCTCATACACTTGAGGTATTTGGG 59.424 45.833 3.85 0.00 42.78 4.12
3492 3712 2.638480 TCTTGTGGAACTTCCTGGTG 57.362 50.000 9.31 0.00 37.46 4.17
3578 3798 3.542969 AGGGGTTTTGGTGCTCTAAAT 57.457 42.857 0.00 0.00 0.00 1.40
3705 3925 2.868583 CTGGAGAATGTAACTGATGCCG 59.131 50.000 0.00 0.00 0.00 5.69
3742 3962 2.403252 AGGCTCGGTGAAAAGGTATG 57.597 50.000 0.00 0.00 0.00 2.39
3773 3993 2.762535 TGACCTTAAGCTGTAGCACC 57.237 50.000 6.65 0.00 45.16 5.01
4041 4262 2.229784 CCATGTTTGGAGTTCTTGGAGC 59.770 50.000 0.00 0.00 46.92 4.70
4048 4269 0.603569 GAGTTCTTGGAGCTCCGACA 59.396 55.000 27.43 11.38 34.57 4.35
4056 4277 3.392228 AGCTCCGACATGCTCCAA 58.608 55.556 0.00 0.00 33.90 3.53
4099 4320 2.655364 CGTGCAGGGCTACGATCG 60.655 66.667 14.88 14.88 42.54 3.69
4128 4349 0.842030 TGCTTCATCCCAGGAGGTGT 60.842 55.000 0.00 0.00 36.75 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.995636 AGTAGGTGGGTATGACATCTGT 58.004 45.455 0.00 0.00 30.63 3.41
4 5 6.824958 ATGTAAAGTAGGTGGGTATGACAT 57.175 37.500 0.00 0.00 0.00 3.06
77 85 2.909006 TCCAGCTTCTCTCAGGTTTGAT 59.091 45.455 0.00 0.00 31.68 2.57
87 95 1.224039 GCCATGCTCCAGCTTCTCT 59.776 57.895 0.00 0.00 42.66 3.10
111 119 4.284490 TGAGTCAAGCTGGATCACTAGTTT 59.716 41.667 0.00 0.00 0.00 2.66
174 184 9.226606 TGTACATTGTTTCCTAGGTCAAATAAG 57.773 33.333 9.08 4.99 0.00 1.73
181 191 4.901868 TGGTGTACATTGTTTCCTAGGTC 58.098 43.478 9.08 1.69 0.00 3.85
213 223 0.324943 TTTCCCCTGAGAAGAAGCCG 59.675 55.000 0.00 0.00 0.00 5.52
297 315 9.734620 CTTTACATTGACACTTCTGAAATTTCA 57.265 29.630 19.45 19.45 35.57 2.69
298 316 9.950680 TCTTTACATTGACACTTCTGAAATTTC 57.049 29.630 11.41 11.41 0.00 2.17
367 386 2.914379 GCAGTCAGCGTGTACCTTT 58.086 52.632 0.00 0.00 0.00 3.11
384 403 0.175760 TGAGTTCTCATGGCGGTAGC 59.824 55.000 0.00 0.00 44.18 3.58
476 495 9.490379 CTTGAAGTACAGAGGTAATAACAAACT 57.510 33.333 0.00 0.00 30.23 2.66
504 523 4.681942 GCTTACATATTCTGCACTACCGAG 59.318 45.833 0.00 0.00 0.00 4.63
506 525 4.445718 CAGCTTACATATTCTGCACTACCG 59.554 45.833 0.00 0.00 0.00 4.02
543 562 6.149973 TGCAAAATCCAGATTCTGAAGTACAG 59.850 38.462 15.36 0.00 46.97 2.74
547 566 5.075493 AGTGCAAAATCCAGATTCTGAAGT 58.925 37.500 15.36 0.00 32.44 3.01
560 579 5.514204 GCTTCATGACATGTAGTGCAAAATC 59.486 40.000 19.53 1.54 31.22 2.17
567 610 4.248058 TGACAGCTTCATGACATGTAGTG 58.752 43.478 19.53 17.52 31.22 2.74
568 611 4.541973 TGACAGCTTCATGACATGTAGT 57.458 40.909 19.53 10.75 31.22 2.73
569 612 4.934001 ACTTGACAGCTTCATGACATGTAG 59.066 41.667 15.63 15.63 33.73 2.74
577 620 6.492007 AGATAAACACTTGACAGCTTCATG 57.508 37.500 0.00 0.00 32.84 3.07
596 639 8.755028 TCTGCACTACCAACACTTAAATAGATA 58.245 33.333 0.00 0.00 0.00 1.98
600 643 9.899661 ATATTCTGCACTACCAACACTTAAATA 57.100 29.630 0.00 0.00 0.00 1.40
633 676 3.857665 ACGTACAGATATTGCACTTGACG 59.142 43.478 0.00 0.00 0.00 4.35
646 689 5.810587 CACCAGCTTAATAACACGTACAGAT 59.189 40.000 0.00 0.00 0.00 2.90
771 818 3.761752 ACCAAAACCGATCTAACCCATTG 59.238 43.478 0.00 0.00 0.00 2.82
782 829 2.227194 GACAACCTCACCAAAACCGAT 58.773 47.619 0.00 0.00 0.00 4.18
784 831 1.384525 TGACAACCTCACCAAAACCG 58.615 50.000 0.00 0.00 0.00 4.44
793 840 4.431416 ACTAAACCACATGACAACCTCA 57.569 40.909 0.00 0.00 0.00 3.86
796 843 4.500716 CCCAAACTAAACCACATGACAACC 60.501 45.833 0.00 0.00 0.00 3.77
797 844 4.616953 CCCAAACTAAACCACATGACAAC 58.383 43.478 0.00 0.00 0.00 3.32
825 872 0.525242 CCACGTAATTGGCATTGGCG 60.525 55.000 5.68 0.00 42.47 5.69
856 903 4.739716 CGTGATGAAGTTTTGGAAACCAAG 59.260 41.667 3.49 0.00 44.84 3.61
858 905 3.697045 ACGTGATGAAGTTTTGGAAACCA 59.303 39.130 0.00 0.00 0.00 3.67
859 906 4.041723 CACGTGATGAAGTTTTGGAAACC 58.958 43.478 10.90 0.00 0.00 3.27
871 918 2.631160 AACTGAACCCACGTGATGAA 57.369 45.000 19.30 0.00 0.00 2.57
891 938 2.120312 TGGGCAATCGAACCATACCTA 58.880 47.619 0.00 0.00 0.00 3.08
904 951 2.905415 TCTGAGAATGGTTGGGCAAT 57.095 45.000 0.00 0.00 0.00 3.56
907 954 2.726821 TCAATCTGAGAATGGTTGGGC 58.273 47.619 0.00 0.00 0.00 5.36
912 959 7.009179 TCTTGTACTTCAATCTGAGAATGGT 57.991 36.000 0.00 0.00 35.35 3.55
946 993 9.533831 ACATGGGTCAAAGAAAATTAGTTATCT 57.466 29.630 0.00 0.00 0.00 1.98
950 997 9.679661 AAAAACATGGGTCAAAGAAAATTAGTT 57.320 25.926 0.00 0.00 0.00 2.24
951 998 9.108284 CAAAAACATGGGTCAAAGAAAATTAGT 57.892 29.630 0.00 0.00 0.00 2.24
952 999 8.558700 CCAAAAACATGGGTCAAAGAAAATTAG 58.441 33.333 0.00 0.00 36.79 1.73
953 1000 7.012799 GCCAAAAACATGGGTCAAAGAAAATTA 59.987 33.333 0.00 0.00 41.01 1.40
954 1001 6.183360 GCCAAAAACATGGGTCAAAGAAAATT 60.183 34.615 0.00 0.00 41.01 1.82
955 1002 5.299028 GCCAAAAACATGGGTCAAAGAAAAT 59.701 36.000 0.00 0.00 41.01 1.82
956 1003 4.637977 GCCAAAAACATGGGTCAAAGAAAA 59.362 37.500 0.00 0.00 41.01 2.29
957 1004 4.195416 GCCAAAAACATGGGTCAAAGAAA 58.805 39.130 0.00 0.00 41.01 2.52
958 1005 3.198635 TGCCAAAAACATGGGTCAAAGAA 59.801 39.130 0.00 0.00 41.01 2.52
959 1006 2.768527 TGCCAAAAACATGGGTCAAAGA 59.231 40.909 0.00 0.00 41.01 2.52
960 1007 3.132925 CTGCCAAAAACATGGGTCAAAG 58.867 45.455 0.00 0.00 41.01 2.77
961 1008 2.744494 GCTGCCAAAAACATGGGTCAAA 60.744 45.455 0.00 0.00 41.01 2.69
962 1009 1.202627 GCTGCCAAAAACATGGGTCAA 60.203 47.619 0.00 0.00 41.01 3.18
963 1010 0.392336 GCTGCCAAAAACATGGGTCA 59.608 50.000 0.00 0.00 41.01 4.02
964 1011 0.392336 TGCTGCCAAAAACATGGGTC 59.608 50.000 0.00 0.00 41.01 4.46
965 1012 0.393820 CTGCTGCCAAAAACATGGGT 59.606 50.000 0.00 0.00 41.01 4.51
966 1013 0.952010 GCTGCTGCCAAAAACATGGG 60.952 55.000 3.85 0.00 41.01 4.00
967 1014 0.249953 TGCTGCTGCCAAAAACATGG 60.250 50.000 13.47 0.00 43.70 3.66
968 1015 1.144969 CTGCTGCTGCCAAAAACATG 58.855 50.000 13.47 0.00 38.71 3.21
969 1016 0.601841 GCTGCTGCTGCCAAAAACAT 60.602 50.000 19.30 0.00 38.71 2.71
970 1017 1.227321 GCTGCTGCTGCCAAAAACA 60.227 52.632 19.30 0.00 38.71 2.83
971 1018 3.633951 GCTGCTGCTGCCAAAAAC 58.366 55.556 19.30 0.00 38.71 2.43
981 1028 1.016130 TTAGTTGCTCGAGCTGCTGC 61.016 55.000 35.27 20.38 42.66 5.25
982 1029 1.326852 CATTAGTTGCTCGAGCTGCTG 59.673 52.381 35.27 19.96 42.66 4.41
983 1030 1.649664 CATTAGTTGCTCGAGCTGCT 58.350 50.000 35.27 30.86 42.66 4.24
984 1031 0.654683 CCATTAGTTGCTCGAGCTGC 59.345 55.000 35.27 26.52 42.66 5.25
985 1032 0.654683 GCCATTAGTTGCTCGAGCTG 59.345 55.000 35.27 23.91 42.66 4.24
986 1033 0.250234 TGCCATTAGTTGCTCGAGCT 59.750 50.000 35.27 19.88 42.66 4.09
987 1034 0.654683 CTGCCATTAGTTGCTCGAGC 59.345 55.000 30.42 30.42 42.50 5.03
988 1035 1.293924 CCTGCCATTAGTTGCTCGAG 58.706 55.000 8.45 8.45 0.00 4.04
989 1036 0.107703 CCCTGCCATTAGTTGCTCGA 60.108 55.000 0.00 0.00 0.00 4.04
990 1037 1.097547 CCCCTGCCATTAGTTGCTCG 61.098 60.000 0.00 0.00 0.00 5.03
991 1038 0.034089 ACCCCTGCCATTAGTTGCTC 60.034 55.000 0.00 0.00 0.00 4.26
992 1039 0.409484 AACCCCTGCCATTAGTTGCT 59.591 50.000 0.00 0.00 0.00 3.91
1015 1062 2.466867 CGTAAGACGCCAAGGCATT 58.533 52.632 12.19 5.28 40.12 3.56
1065 1112 1.225426 GATCAGCATGGCCACCTCA 59.775 57.895 8.16 0.00 36.16 3.86
1152 1199 3.634448 CGTCAGTGATGTTCCTCCTATCT 59.366 47.826 4.02 0.00 0.00 1.98
1197 1244 0.806868 ACATGGCATGCTTCAGTTCG 59.193 50.000 26.70 0.00 0.00 3.95
1255 1302 2.026729 TGGATGTACCTTTCGCCATGAA 60.027 45.455 0.00 0.00 39.86 2.57
1262 1309 3.328382 TGTCCTTGGATGTACCTTTCG 57.672 47.619 0.00 0.00 39.86 3.46
1270 1317 0.332632 CACCCCATGTCCTTGGATGT 59.667 55.000 1.00 0.00 39.25 3.06
1319 1366 1.923395 TCATGGGTGTGGAGGGGAC 60.923 63.158 0.00 0.00 0.00 4.46
1341 1388 3.064324 GCTTTGATGCGGGTGCCT 61.064 61.111 0.00 0.00 41.78 4.75
1417 1464 3.181329 TCTGGTCTTGATAGGCTTCCAA 58.819 45.455 0.00 0.00 0.00 3.53
1428 1475 0.537188 GGGCGATCTTCTGGTCTTGA 59.463 55.000 0.00 0.00 0.00 3.02
1457 1504 1.993370 GATGTGTCTTGCGGTCACTAC 59.007 52.381 7.91 0.00 33.82 2.73
1460 1507 0.320771 AGGATGTGTCTTGCGGTCAC 60.321 55.000 0.00 0.00 0.00 3.67
1497 1544 1.354368 TCAATCTTCTCCCCAACCACC 59.646 52.381 0.00 0.00 0.00 4.61
1519 1566 3.976793 CACAATTGCTCTTGTGTCACT 57.023 42.857 18.22 0.00 46.97 3.41
1534 1581 3.087031 CCTTTGTGAGCATCTCCACAAT 58.913 45.455 8.47 0.00 34.37 2.71
1559 1612 5.121105 CCATGATGCTATCACTCTTGTCAA 58.879 41.667 0.00 0.00 43.01 3.18
1669 1722 4.893424 TGCTTAACCATATCTTTTCCGC 57.107 40.909 0.00 0.00 0.00 5.54
1671 1724 7.148086 TGTGTGATGCTTAACCATATCTTTTCC 60.148 37.037 0.00 0.00 0.00 3.13
1672 1725 7.761409 TGTGTGATGCTTAACCATATCTTTTC 58.239 34.615 0.00 0.00 0.00 2.29
1704 1757 0.966179 TCAACAGCTCAACCTCGCTA 59.034 50.000 0.00 0.00 34.58 4.26
1736 1789 1.405105 GCAATTCTCCATTAGCGGCAA 59.595 47.619 1.45 0.00 0.00 4.52
1758 1811 3.330720 GACCCACCCCCAGACCTG 61.331 72.222 0.00 0.00 0.00 4.00
1762 1815 1.538876 CTTGAGACCCACCCCCAGA 60.539 63.158 0.00 0.00 0.00 3.86
1863 1918 4.335416 TCAACAAGTCATTCCATTCCTCC 58.665 43.478 0.00 0.00 0.00 4.30
1866 1921 5.183713 TGTCATCAACAAGTCATTCCATTCC 59.816 40.000 0.00 0.00 34.03 3.01
1875 1930 3.576078 AAGGGTGTCATCAACAAGTCA 57.424 42.857 0.00 0.00 40.31 3.41
1876 1931 4.083271 GCTAAAGGGTGTCATCAACAAGTC 60.083 45.833 0.00 0.00 40.31 3.01
1968 2023 2.319136 TATGGTGGTACGGTTGCATC 57.681 50.000 0.00 0.00 0.00 3.91
1987 2042 2.806945 TCGGCTCCCAATTTCTCAAT 57.193 45.000 0.00 0.00 0.00 2.57
1992 2047 1.066152 GCATCTTCGGCTCCCAATTTC 59.934 52.381 0.00 0.00 0.00 2.17
1998 2053 1.821332 CCAAGCATCTTCGGCTCCC 60.821 63.158 0.00 0.00 41.66 4.30
2002 2057 1.098050 AATGACCAAGCATCTTCGGC 58.902 50.000 0.00 0.00 0.00 5.54
2042 2097 5.995565 AGAGTATTGTACTGGTAGTTGCA 57.004 39.130 0.00 0.00 39.59 4.08
2087 2171 9.482627 GGGAACACAAAATACATGAAAATGTAA 57.517 29.630 0.00 0.00 40.04 2.41
2088 2172 8.865090 AGGGAACACAAAATACATGAAAATGTA 58.135 29.630 0.00 1.33 40.79 2.29
2089 2173 7.734942 AGGGAACACAAAATACATGAAAATGT 58.265 30.769 0.00 0.00 38.49 2.71
2090 2174 9.139174 GTAGGGAACACAAAATACATGAAAATG 57.861 33.333 0.00 0.00 0.00 2.32
2096 2187 6.834168 AAGGTAGGGAACACAAAATACATG 57.166 37.500 0.00 0.00 0.00 3.21
2101 2192 6.496911 AGCAATTAAGGTAGGGAACACAAAAT 59.503 34.615 0.00 0.00 0.00 1.82
2108 2199 4.200092 CAGGAGCAATTAAGGTAGGGAAC 58.800 47.826 0.00 0.00 0.00 3.62
2112 2219 3.567478 AGCAGGAGCAATTAAGGTAGG 57.433 47.619 0.00 0.00 45.49 3.18
2133 2257 4.395854 TCAAGCAGCATTGACACGATAAAT 59.604 37.500 0.00 0.00 34.31 1.40
2139 2263 1.465777 TCATCAAGCAGCATTGACACG 59.534 47.619 8.82 3.27 41.76 4.49
2149 2273 8.821894 GGAGTACTAGTAATTTTCATCAAGCAG 58.178 37.037 3.61 0.00 0.00 4.24
2180 2322 8.332464 GCTCTGCTATTCGTAGTGAGTATATAG 58.668 40.741 0.00 0.00 0.00 1.31
2181 2323 7.822822 TGCTCTGCTATTCGTAGTGAGTATATA 59.177 37.037 0.00 0.00 0.00 0.86
2185 2327 4.196971 TGCTCTGCTATTCGTAGTGAGTA 58.803 43.478 0.00 0.00 0.00 2.59
2186 2328 3.017442 TGCTCTGCTATTCGTAGTGAGT 58.983 45.455 0.00 0.00 0.00 3.41
2187 2329 3.699779 TGCTCTGCTATTCGTAGTGAG 57.300 47.619 0.00 0.00 0.00 3.51
2188 2330 3.444034 ACTTGCTCTGCTATTCGTAGTGA 59.556 43.478 0.00 0.00 0.00 3.41
2189 2331 3.549471 CACTTGCTCTGCTATTCGTAGTG 59.451 47.826 0.00 0.00 0.00 2.74
2190 2332 3.193691 ACACTTGCTCTGCTATTCGTAGT 59.806 43.478 0.00 0.00 0.00 2.73
2191 2333 3.775202 ACACTTGCTCTGCTATTCGTAG 58.225 45.455 0.00 0.00 0.00 3.51
2192 2334 3.444034 AGACACTTGCTCTGCTATTCGTA 59.556 43.478 0.00 0.00 0.00 3.43
2193 2335 2.232452 AGACACTTGCTCTGCTATTCGT 59.768 45.455 0.00 0.00 0.00 3.85
2194 2336 2.857152 GAGACACTTGCTCTGCTATTCG 59.143 50.000 0.00 0.00 0.00 3.34
2195 2337 3.194062 GGAGACACTTGCTCTGCTATTC 58.806 50.000 0.00 0.00 32.98 1.75
2198 2340 1.632589 TGGAGACACTTGCTCTGCTA 58.367 50.000 0.00 0.00 33.40 3.49
2199 2341 2.445396 TGGAGACACTTGCTCTGCT 58.555 52.632 0.00 0.00 33.40 4.24
2210 2352 0.105709 TGGAGTGGAGTGTGGAGACA 60.106 55.000 0.00 0.00 38.70 3.41
2211 2353 1.001406 CTTGGAGTGGAGTGTGGAGAC 59.999 57.143 0.00 0.00 0.00 3.36
2212 2354 1.342074 CTTGGAGTGGAGTGTGGAGA 58.658 55.000 0.00 0.00 0.00 3.71
2213 2355 0.321122 GCTTGGAGTGGAGTGTGGAG 60.321 60.000 0.00 0.00 0.00 3.86
2214 2356 1.053835 TGCTTGGAGTGGAGTGTGGA 61.054 55.000 0.00 0.00 0.00 4.02
2215 2357 0.179020 TTGCTTGGAGTGGAGTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
2216 2358 1.334869 GTTTGCTTGGAGTGGAGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
2217 2359 1.212935 AGTTTGCTTGGAGTGGAGTGT 59.787 47.619 0.00 0.00 0.00 3.55
2218 2360 1.605710 CAGTTTGCTTGGAGTGGAGTG 59.394 52.381 0.00 0.00 0.00 3.51
2219 2361 1.972872 CAGTTTGCTTGGAGTGGAGT 58.027 50.000 0.00 0.00 0.00 3.85
2220 2362 0.595095 GCAGTTTGCTTGGAGTGGAG 59.405 55.000 0.00 0.00 40.96 3.86
2221 2363 2.719376 GCAGTTTGCTTGGAGTGGA 58.281 52.632 0.00 0.00 40.96 4.02
2231 2373 2.351738 GGTGGACATACAAGCAGTTTGC 60.352 50.000 0.00 0.00 45.46 3.68
2275 2457 9.649167 GTAAAGGCATAGTCTAGTAGTTTTTGA 57.351 33.333 0.00 0.00 0.00 2.69
2281 2463 9.863650 TGAATAGTAAAGGCATAGTCTAGTAGT 57.136 33.333 0.00 0.00 0.00 2.73
2348 2531 8.978874 TCAGCATAAATTTACATACTGGTGAT 57.021 30.769 19.30 2.51 35.47 3.06
2350 2533 8.437360 TCTCAGCATAAATTTACATACTGGTG 57.563 34.615 16.43 16.43 33.29 4.17
2351 2534 8.267894 ACTCTCAGCATAAATTTACATACTGGT 58.732 33.333 0.00 0.00 0.00 4.00
2355 2543 9.319143 AGTGACTCTCAGCATAAATTTACATAC 57.681 33.333 0.00 0.00 0.00 2.39
2357 2545 9.539825 CTAGTGACTCTCAGCATAAATTTACAT 57.460 33.333 0.00 0.00 0.00 2.29
2362 2550 6.232581 AGCTAGTGACTCTCAGCATAAATT 57.767 37.500 8.40 0.00 36.47 1.82
2399 2592 8.322906 TGTCCTTGTAATTCTTCTAACACATG 57.677 34.615 0.00 0.00 0.00 3.21
2412 2605 8.717717 TCTAGATGGATTGATGTCCTTGTAATT 58.282 33.333 0.00 0.00 39.12 1.40
2436 2642 3.903467 AGCCTTGTTTTTCCAGACTTCT 58.097 40.909 0.00 0.00 0.00 2.85
2440 2646 6.332735 AGATAAAGCCTTGTTTTTCCAGAC 57.667 37.500 0.00 0.00 0.00 3.51
2443 2649 6.723298 TCAAGATAAAGCCTTGTTTTTCCA 57.277 33.333 0.00 0.00 41.18 3.53
2444 2650 7.926018 TCTTTCAAGATAAAGCCTTGTTTTTCC 59.074 33.333 0.00 0.00 41.18 3.13
2445 2651 8.871686 TCTTTCAAGATAAAGCCTTGTTTTTC 57.128 30.769 0.00 0.00 41.18 2.29
2446 2652 9.836864 AATCTTTCAAGATAAAGCCTTGTTTTT 57.163 25.926 2.41 0.00 44.67 1.94
2493 2699 7.154656 AGGTTGGCAAGAATCAAATAAAGAAC 58.845 34.615 0.00 0.00 0.00 3.01
2495 2701 6.916360 AGGTTGGCAAGAATCAAATAAAGA 57.084 33.333 0.00 0.00 0.00 2.52
2500 2706 9.603921 CATAAATTAGGTTGGCAAGAATCAAAT 57.396 29.630 0.00 0.00 0.00 2.32
2501 2707 8.592809 ACATAAATTAGGTTGGCAAGAATCAAA 58.407 29.630 0.00 0.00 0.00 2.69
2504 2710 8.903820 ACTACATAAATTAGGTTGGCAAGAATC 58.096 33.333 0.00 0.00 0.00 2.52
2505 2711 8.823220 ACTACATAAATTAGGTTGGCAAGAAT 57.177 30.769 0.00 0.00 0.00 2.40
2506 2712 9.391006 CTACTACATAAATTAGGTTGGCAAGAA 57.609 33.333 0.00 0.00 0.00 2.52
2525 2731 3.772572 TGGCTAATGGCAAGTCTACTACA 59.227 43.478 0.00 0.00 46.03 2.74
2537 2743 3.019564 ACATTTCTGAGTGGCTAATGGC 58.980 45.455 0.00 0.00 40.90 4.40
2541 2749 5.865085 ACACTAACATTTCTGAGTGGCTAA 58.135 37.500 5.91 0.00 42.93 3.09
2552 2760 8.784043 ACTGTCAATAAGGAACACTAACATTTC 58.216 33.333 0.00 0.00 0.00 2.17
2576 2791 3.010138 TGCAAGGAGTTTAAGGCCATACT 59.990 43.478 5.01 1.60 0.00 2.12
2577 2792 3.352648 TGCAAGGAGTTTAAGGCCATAC 58.647 45.455 5.01 0.00 0.00 2.39
2583 2798 5.163713 GCAAGTATCTGCAAGGAGTTTAAGG 60.164 44.000 0.00 0.00 42.17 2.69
2683 2898 2.931512 TTACTTTTATGGCAAGCGGC 57.068 45.000 0.00 0.00 43.74 6.53
2743 2958 4.452114 GCATCATTCAAAACCTTTTCCCAC 59.548 41.667 0.00 0.00 0.00 4.61
2770 2985 2.868583 CGGCATTTGAGATACTGACCAG 59.131 50.000 0.00 0.00 0.00 4.00
2791 3006 7.986320 AGATATATTGCATAGTTCAGCTCATCC 59.014 37.037 0.00 0.00 0.00 3.51
2794 3009 9.866798 CTAAGATATATTGCATAGTTCAGCTCA 57.133 33.333 0.00 0.00 0.00 4.26
2957 3173 7.872138 TGGTAATCAAATCCTAGTTCTTCCAT 58.128 34.615 0.00 0.00 0.00 3.41
3019 3235 8.340443 CAAACATATTGACCAGAGTATGATGTG 58.660 37.037 0.00 0.00 0.00 3.21
3175 3394 8.090214 TCAAATTCATCCAATTCAACTCCTTTC 58.910 33.333 0.00 0.00 33.16 2.62
3283 3502 6.183360 GGGTTCGTAGACTTGAAATGGTAATG 60.183 42.308 0.00 0.00 34.32 1.90
3492 3712 6.966021 TCAGTTCTTGTAACTTTGCAATACC 58.034 36.000 0.00 0.00 32.46 2.73
3542 3762 5.500546 AACCCCTAGGCATACTAATTAGC 57.499 43.478 12.54 0.00 36.11 3.09
3742 3962 5.065731 CAGCTTAAGGTCATGATGGAAAGAC 59.934 44.000 3.68 0.00 0.00 3.01
3811 4031 7.127801 TCTCAATTATTCCTTGATCCTTCTCCA 59.872 37.037 0.00 0.00 32.50 3.86
3854 4074 0.461548 CTATGCGAGCTGGAGGACAA 59.538 55.000 0.00 0.00 0.00 3.18
3867 4087 8.633561 TCCAGTTATATGGATATCTTCTATGCG 58.366 37.037 2.05 0.00 44.56 4.73
3900 4120 0.321564 CATCTTGGGAGTTGACGCCA 60.322 55.000 6.25 0.00 37.57 5.69
4041 4262 1.667724 GATTGTTGGAGCATGTCGGAG 59.332 52.381 0.00 0.00 0.00 4.63
4048 4269 3.225104 ACACACTTGATTGTTGGAGCAT 58.775 40.909 0.00 0.00 0.00 3.79
4056 4277 1.039856 GGCCCAACACACTTGATTGT 58.960 50.000 0.00 0.00 0.00 2.71
4099 4320 0.654683 GGATGAAGCATGACGACAGC 59.345 55.000 0.00 0.00 0.00 4.40
4128 4349 1.949525 GTGCAGTCTTGGAAAAGCAGA 59.050 47.619 0.00 0.00 32.03 4.26


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

AutoCloner maintained by Alex Coulton.