Multiple sequence alignment - TraesCS3D01G394400

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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 TraesCS3D01G394400 chr3D 100.000 5566 0 0 1 5566 509257440 509251875 0.000000e+00 10279.0
1 TraesCS3D01G394400 chr3D 79.173 653 110 15 170 813 354613838 354614473 3.980000e-116 429.0
2 TraesCS3D01G394400 chr3D 72.691 747 171 28 1 732 51749021 51749749 9.390000e-53 219.0
3 TraesCS3D01G394400 chr3D 78.596 285 59 1 495 779 51766949 51767231 2.650000e-43 187.0
4 TraesCS3D01G394400 chr3D 94.118 68 3 1 1751 1817 501068192 501068259 9.860000e-18 102.0
5 TraesCS3D01G394400 chr3B 91.468 3270 162 46 2333 5566 672106352 672103164 0.000000e+00 4385.0
6 TraesCS3D01G394400 chr3B 91.774 1398 80 16 872 2245 672107751 672106365 0.000000e+00 1912.0
7 TraesCS3D01G394400 chr3A 96.808 2318 67 4 2327 4639 646857022 646854707 0.000000e+00 3864.0
8 TraesCS3D01G394400 chr3A 92.334 874 36 9 891 1755 646859861 646859010 0.000000e+00 1214.0
9 TraesCS3D01G394400 chr3A 86.968 729 51 17 4634 5346 646854758 646854058 0.000000e+00 780.0
10 TraesCS3D01G394400 chr3A 94.901 353 15 2 1895 2245 646857372 646857021 2.930000e-152 549.0
11 TraesCS3D01G394400 chr3A 91.270 126 2 3 5443 5566 646852452 646852334 4.460000e-36 163.0
12 TraesCS3D01G394400 chr6A 83.292 814 124 10 1 807 364679091 364679899 0.000000e+00 739.0
13 TraesCS3D01G394400 chr6A 73.563 783 178 25 16 782 78484046 78483277 7.110000e-69 272.0
14 TraesCS3D01G394400 chr6A 72.215 799 191 26 1 782 100486251 100485467 3.380000e-52 217.0
15 TraesCS3D01G394400 chr6A 72.000 800 191 27 1 782 616407996 616407212 7.310000e-49 206.0
16 TraesCS3D01G394400 chr6A 95.960 99 4 0 2233 2331 27342990 27342892 1.600000e-35 161.0
17 TraesCS3D01G394400 chr6B 78.024 587 111 14 1 575 129604441 129605021 2.470000e-93 353.0
18 TraesCS3D01G394400 chr5B 74.635 753 168 19 6 744 294736625 294737368 1.510000e-80 311.0
19 TraesCS3D01G394400 chr5B 88.800 125 7 6 2242 2361 406172677 406172799 4.490000e-31 147.0
20 TraesCS3D01G394400 chr5B 87.838 74 3 6 1748 1817 561916997 561917068 1.290000e-11 82.4
21 TraesCS3D01G394400 chr5D 73.585 795 187 16 1 782 449043372 449044156 3.280000e-72 283.0
22 TraesCS3D01G394400 chr2A 72.949 780 174 30 16 776 768319401 768320162 2.590000e-58 237.0
23 TraesCS3D01G394400 chr2A 95.960 99 3 1 2235 2332 568412697 568412795 5.770000e-35 159.0
24 TraesCS3D01G394400 chr6D 72.509 793 193 22 1 779 380739429 380740210 3.350000e-57 233.0
25 TraesCS3D01G394400 chr7A 72.692 780 176 31 23 782 697107675 697106913 5.610000e-55 226.0
26 TraesCS3D01G394400 chr7A 86.301 146 12 4 2211 2354 129877054 129876915 9.660000e-33 152.0
27 TraesCS3D01G394400 chr7A 98.077 52 1 0 1751 1802 443957906 443957855 2.140000e-14 91.6
28 TraesCS3D01G394400 chr5A 72.509 793 185 27 1 775 708087331 708086554 5.610000e-55 226.0
29 TraesCS3D01G394400 chr4A 72.622 778 180 27 23 782 538884790 538884028 5.610000e-55 226.0
30 TraesCS3D01G394400 chr4A 76.286 447 90 14 294 732 5194675 5195113 2.020000e-54 224.0
31 TraesCS3D01G394400 chr4A 76.201 437 88 13 353 782 602890716 602890289 3.380000e-52 217.0
32 TraesCS3D01G394400 chr7B 72.517 735 170 29 16 732 683362801 683362081 5.650000e-50 209.0
33 TraesCS3D01G394400 chr7B 90.991 111 6 4 2243 2351 551488112 551488220 4.490000e-31 147.0
34 TraesCS3D01G394400 chr7D 98.889 90 1 0 2244 2333 506141453 506141364 1.600000e-35 161.0
35 TraesCS3D01G394400 chr1B 97.826 92 2 0 2244 2335 164770366 164770457 5.770000e-35 159.0
36 TraesCS3D01G394400 chrUn 94.118 102 3 3 2244 2345 224653393 224653295 9.660000e-33 152.0
37 TraesCS3D01G394400 chr4B 92.593 108 5 3 2244 2348 586463928 586464035 9.660000e-33 152.0
38 TraesCS3D01G394400 chr4B 91.935 62 4 1 1739 1800 660460880 660460940 9.930000e-13 86.1
39 TraesCS3D01G394400 chr4B 87.838 74 3 6 1748 1817 499586389 499586460 1.290000e-11 82.4
40 TraesCS3D01G394400 chr1D 92.308 65 2 2 1751 1812 366680809 366680745 7.680000e-14 89.8
41 TraesCS3D01G394400 chr1D 87.342 79 3 5 1726 1802 437290047 437289974 3.570000e-12 84.2
42 TraesCS3D01G394400 chr1A 87.013 77 3 7 1744 1814 237513200 237513275 4.620000e-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 TraesCS3D01G394400 chr3D 509251875 509257440 5565 True 10279.0 10279 100.0000 1 5566 1 chr3D.!!$R1 5565
1 TraesCS3D01G394400 chr3D 354613838 354614473 635 False 429.0 429 79.1730 170 813 1 chr3D.!!$F3 643
2 TraesCS3D01G394400 chr3D 51749021 51749749 728 False 219.0 219 72.6910 1 732 1 chr3D.!!$F1 731
3 TraesCS3D01G394400 chr3B 672103164 672107751 4587 True 3148.5 4385 91.6210 872 5566 2 chr3B.!!$R1 4694
4 TraesCS3D01G394400 chr3A 646852334 646859861 7527 True 1314.0 3864 92.4562 891 5566 5 chr3A.!!$R1 4675
5 TraesCS3D01G394400 chr6A 364679091 364679899 808 False 739.0 739 83.2920 1 807 1 chr6A.!!$F1 806
6 TraesCS3D01G394400 chr6A 78483277 78484046 769 True 272.0 272 73.5630 16 782 1 chr6A.!!$R2 766
7 TraesCS3D01G394400 chr6A 100485467 100486251 784 True 217.0 217 72.2150 1 782 1 chr6A.!!$R3 781
8 TraesCS3D01G394400 chr6A 616407212 616407996 784 True 206.0 206 72.0000 1 782 1 chr6A.!!$R4 781
9 TraesCS3D01G394400 chr6B 129604441 129605021 580 False 353.0 353 78.0240 1 575 1 chr6B.!!$F1 574
10 TraesCS3D01G394400 chr5B 294736625 294737368 743 False 311.0 311 74.6350 6 744 1 chr5B.!!$F1 738
11 TraesCS3D01G394400 chr5D 449043372 449044156 784 False 283.0 283 73.5850 1 782 1 chr5D.!!$F1 781
12 TraesCS3D01G394400 chr2A 768319401 768320162 761 False 237.0 237 72.9490 16 776 1 chr2A.!!$F2 760
13 TraesCS3D01G394400 chr6D 380739429 380740210 781 False 233.0 233 72.5090 1 779 1 chr6D.!!$F1 778
14 TraesCS3D01G394400 chr7A 697106913 697107675 762 True 226.0 226 72.6920 23 782 1 chr7A.!!$R3 759
15 TraesCS3D01G394400 chr5A 708086554 708087331 777 True 226.0 226 72.5090 1 775 1 chr5A.!!$R1 774
16 TraesCS3D01G394400 chr4A 538884028 538884790 762 True 226.0 226 72.6220 23 782 1 chr4A.!!$R1 759
17 TraesCS3D01G394400 chr7B 683362081 683362801 720 True 209.0 209 72.5170 16 732 1 chr7B.!!$R1 716

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
911 918 0.030638 ATTCCGGCATATGCAAACGC 59.969 50.0 28.07 10.17 44.36 4.84 F
915 922 0.179140 CGGCATATGCAAACGCCTTT 60.179 50.0 28.07 0.00 42.59 3.11 F
1254 1269 0.898789 ACCTCGTCTTCATCACCGGT 60.899 55.0 0.00 0.00 0.00 5.28 F
2257 3883 0.468648 CCAAATACTCCCTCCGTCCC 59.531 60.0 0.00 0.00 0.00 4.46 F
4189 5815 0.174389 GATGGCTGCTGAGAGAACGA 59.826 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1854 0.256752 TATTCCCTCCGTCGGTCTGA 59.743 55.0 11.88 3.28 0.00 3.27 R
1823 1856 0.549950 TCTATTCCCTCCGTCGGTCT 59.450 55.0 11.88 0.00 0.00 3.85 R
2773 4399 0.749454 AACAGATGCTTCCGGCCATC 60.749 55.0 16.86 16.86 40.92 3.51 R
4200 5826 0.179150 CTGACTGCGAGAGGTAGTGC 60.179 60.0 0.00 0.00 42.06 4.40 R
5210 6880 0.511221 AAGACGATTGTTGGCGAACG 59.489 50.0 7.12 0.00 34.49 3.95 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
21 22 1.361668 CGAGTACTGCATGGCACCAC 61.362 60.000 0.00 0.00 33.79 4.16
64 65 2.671070 CAGGACGGGAGCACCATT 59.329 61.111 1.58 0.00 40.22 3.16
74 75 3.827302 CGGGAGCACCATTAGTAGTAGAT 59.173 47.826 1.58 0.00 40.22 1.98
96 97 1.557443 CTTGGCCTTCGTGTCGACAC 61.557 60.000 33.76 33.76 43.15 3.67
162 164 2.202987 CATGAGCAGACTCCCGCC 60.203 66.667 0.00 0.00 42.74 6.13
173 175 1.338136 ACTCCCGCCGATGAAGGAAT 61.338 55.000 0.00 0.00 0.00 3.01
206 208 1.436336 CCGTACCACCTCGATGTCC 59.564 63.158 0.00 0.00 0.00 4.02
210 212 0.040646 TACCACCTCGATGTCCAGGT 59.959 55.000 6.58 6.58 44.42 4.00
226 228 2.624557 CCAGGTAGTAGTGAAGAGGCCT 60.625 54.545 3.86 3.86 0.00 5.19
231 233 3.176924 AGTAGTGAAGAGGCCTCAAGA 57.823 47.619 33.90 14.24 0.00 3.02
248 250 5.752036 TCAAGACCTTGATGATGAACTCT 57.248 39.130 8.27 0.00 43.90 3.24
337 344 1.895238 GACGGGTAGGCTGTAGCAA 59.105 57.895 6.18 0.00 44.36 3.91
364 371 3.602390 ATGTGTACACAAACAACGAGC 57.398 42.857 31.01 0.00 45.41 5.03
420 427 1.291877 GAAAGGTCGTGATGCGCTGT 61.292 55.000 9.73 0.00 41.07 4.40
421 428 1.291877 AAAGGTCGTGATGCGCTGTC 61.292 55.000 9.73 7.75 41.07 3.51
425 432 3.842126 CGTGATGCGCTGTCACCG 61.842 66.667 28.29 22.04 42.25 4.94
427 434 3.690280 TGATGCGCTGTCACCGGA 61.690 61.111 9.46 0.00 0.00 5.14
462 469 1.847328 TGAGTCCATACAAGGAGCGA 58.153 50.000 0.00 0.00 38.64 4.93
474 481 1.079543 GGAGCGAGAGAGCAAGCAA 60.080 57.895 0.00 0.00 40.15 3.91
628 635 0.744414 AAGAATGGTGCGGATCGTGG 60.744 55.000 0.00 0.00 0.00 4.94
641 648 0.608035 ATCGTGGCCGGTTTGACAAT 60.608 50.000 1.90 0.00 33.95 2.71
660 667 1.180456 TCGGAGCAAAGGTGTCGGTA 61.180 55.000 0.00 0.00 0.00 4.02
688 695 4.101790 CCGCACGCTGCCGAAAAT 62.102 61.111 0.00 0.00 41.12 1.82
714 721 3.181457 GGACCACCCAGTAAGCCTTATAC 60.181 52.174 0.00 0.00 34.14 1.47
723 730 0.032267 AAGCCTTATACCGCTCGAGC 59.968 55.000 27.64 27.64 33.09 5.03
755 762 0.742990 CGGAGCTTATGCCGGAACAA 60.743 55.000 5.05 0.00 43.67 2.83
759 766 1.102978 GCTTATGCCGGAACAACCAT 58.897 50.000 5.05 0.00 38.90 3.55
762 769 3.616317 GCTTATGCCGGAACAACCATTTT 60.616 43.478 5.05 0.00 38.90 1.82
763 770 4.565022 CTTATGCCGGAACAACCATTTTT 58.435 39.130 5.05 0.00 38.90 1.94
772 779 1.139163 CAACCATTTTTGCCGCTGAC 58.861 50.000 0.00 0.00 0.00 3.51
795 802 0.180406 ATTAGCATGTGGGGGTCGAC 59.820 55.000 7.13 7.13 0.00 4.20
813 820 2.380410 CGTACAAGCTGCCACGTCC 61.380 63.158 0.00 0.00 0.00 4.79
814 821 1.004918 GTACAAGCTGCCACGTCCT 60.005 57.895 0.00 0.00 0.00 3.85
815 822 1.014564 GTACAAGCTGCCACGTCCTC 61.015 60.000 0.00 0.00 0.00 3.71
816 823 1.185618 TACAAGCTGCCACGTCCTCT 61.186 55.000 0.00 0.00 0.00 3.69
817 824 1.302033 CAAGCTGCCACGTCCTCTT 60.302 57.895 0.00 0.00 0.00 2.85
818 825 0.886490 CAAGCTGCCACGTCCTCTTT 60.886 55.000 0.00 0.00 0.00 2.52
819 826 0.179018 AAGCTGCCACGTCCTCTTTT 60.179 50.000 0.00 0.00 0.00 2.27
820 827 0.603975 AGCTGCCACGTCCTCTTTTC 60.604 55.000 0.00 0.00 0.00 2.29
821 828 0.884704 GCTGCCACGTCCTCTTTTCA 60.885 55.000 0.00 0.00 0.00 2.69
822 829 1.593196 CTGCCACGTCCTCTTTTCAA 58.407 50.000 0.00 0.00 0.00 2.69
823 830 1.264288 CTGCCACGTCCTCTTTTCAAC 59.736 52.381 0.00 0.00 0.00 3.18
824 831 1.305201 GCCACGTCCTCTTTTCAACA 58.695 50.000 0.00 0.00 0.00 3.33
825 832 1.880027 GCCACGTCCTCTTTTCAACAT 59.120 47.619 0.00 0.00 0.00 2.71
826 833 2.350772 GCCACGTCCTCTTTTCAACATG 60.351 50.000 0.00 0.00 0.00 3.21
827 834 3.138304 CCACGTCCTCTTTTCAACATGA 58.862 45.455 0.00 0.00 0.00 3.07
828 835 3.187227 CCACGTCCTCTTTTCAACATGAG 59.813 47.826 0.00 0.00 0.00 2.90
829 836 3.809832 CACGTCCTCTTTTCAACATGAGT 59.190 43.478 0.00 0.00 0.00 3.41
830 837 3.809832 ACGTCCTCTTTTCAACATGAGTG 59.190 43.478 0.00 0.00 0.00 3.51
831 838 4.058124 CGTCCTCTTTTCAACATGAGTGA 58.942 43.478 0.00 0.00 0.00 3.41
832 839 4.692625 CGTCCTCTTTTCAACATGAGTGAT 59.307 41.667 0.00 0.00 0.00 3.06
833 840 5.869344 CGTCCTCTTTTCAACATGAGTGATA 59.131 40.000 0.00 0.00 0.00 2.15
834 841 6.536582 CGTCCTCTTTTCAACATGAGTGATAT 59.463 38.462 0.00 0.00 0.00 1.63
835 842 7.465111 CGTCCTCTTTTCAACATGAGTGATATG 60.465 40.741 0.00 1.15 0.00 1.78
836 843 7.335422 GTCCTCTTTTCAACATGAGTGATATGT 59.665 37.037 0.00 0.00 40.30 2.29
837 844 8.539544 TCCTCTTTTCAACATGAGTGATATGTA 58.460 33.333 0.00 0.00 37.77 2.29
838 845 9.334947 CCTCTTTTCAACATGAGTGATATGTAT 57.665 33.333 0.00 0.00 37.77 2.29
848 855 9.574516 ACATGAGTGATATGTATAGTACTCACA 57.425 33.333 16.52 11.46 44.80 3.58
854 861 9.383462 GTGATATGTATAGTACTCACAAAGACG 57.617 37.037 12.72 0.00 34.57 4.18
855 862 9.117183 TGATATGTATAGTACTCACAAAGACGT 57.883 33.333 12.72 0.00 0.00 4.34
858 865 6.765089 TGTATAGTACTCACAAAGACGTACG 58.235 40.000 15.01 15.01 36.66 3.67
859 866 5.869753 ATAGTACTCACAAAGACGTACGT 57.130 39.130 23.04 23.04 36.66 3.57
860 867 6.968131 ATAGTACTCACAAAGACGTACGTA 57.032 37.500 22.87 2.36 36.66 3.57
861 868 5.023551 AGTACTCACAAAGACGTACGTAC 57.976 43.478 22.87 15.90 36.66 3.67
862 869 4.752101 AGTACTCACAAAGACGTACGTACT 59.248 41.667 22.87 16.69 36.66 2.73
863 870 5.926542 AGTACTCACAAAGACGTACGTACTA 59.073 40.000 22.87 4.33 36.66 1.82
864 871 5.023551 ACTCACAAAGACGTACGTACTAC 57.976 43.478 22.87 15.55 0.00 2.73
865 872 4.752101 ACTCACAAAGACGTACGTACTACT 59.248 41.667 22.87 17.34 0.00 2.57
866 873 5.237344 ACTCACAAAGACGTACGTACTACTT 59.763 40.000 22.87 21.32 0.00 2.24
867 874 6.060028 TCACAAAGACGTACGTACTACTTT 57.940 37.500 26.15 26.15 33.28 2.66
868 875 6.494842 TCACAAAGACGTACGTACTACTTTT 58.505 36.000 27.77 20.73 31.93 2.27
869 876 6.414694 TCACAAAGACGTACGTACTACTTTTG 59.585 38.462 27.77 25.97 31.93 2.44
870 877 5.687285 ACAAAGACGTACGTACTACTTTTGG 59.313 40.000 27.77 22.84 31.93 3.28
879 886 4.021981 ACGTACTACTTTTGGTGTACCCTC 60.022 45.833 0.00 0.00 33.29 4.30
896 903 0.453390 CTCGCTTGAGGGCAAATTCC 59.547 55.000 0.00 0.00 36.01 3.01
903 910 1.133513 TGAGGGCAAATTCCGGCATAT 60.134 47.619 0.00 0.00 0.00 1.78
911 918 0.030638 ATTCCGGCATATGCAAACGC 59.969 50.000 28.07 10.17 44.36 4.84
915 922 0.179140 CGGCATATGCAAACGCCTTT 60.179 50.000 28.07 0.00 42.59 3.11
930 937 1.337260 GCCTTTCGCTGTTCTCTCTGA 60.337 52.381 0.00 0.00 0.00 3.27
1195 1210 3.678717 GAGCGCGCCTACGACTTCA 62.679 63.158 30.33 0.00 43.93 3.02
1254 1269 0.898789 ACCTCGTCTTCATCACCGGT 60.899 55.000 0.00 0.00 0.00 5.28
1281 1296 1.479323 ACCGGTGCGTTGTACATATCT 59.521 47.619 6.12 0.00 0.00 1.98
1309 1325 1.559065 CGCCCCCTTCCTGTTCCTTA 61.559 60.000 0.00 0.00 0.00 2.69
1312 1328 1.560146 CCCCCTTCCTGTTCCTTACTC 59.440 57.143 0.00 0.00 0.00 2.59
1351 1368 1.949525 GTTCGGGGTGAATGGATGATG 59.050 52.381 0.00 0.00 39.21 3.07
1352 1369 1.212375 TCGGGGTGAATGGATGATGT 58.788 50.000 0.00 0.00 0.00 3.06
1367 1384 9.857656 AATGGATGATGTGATGTTTAATCTAGT 57.142 29.630 0.00 0.00 0.00 2.57
1426 1443 2.039216 TGCGTGGGGATAGTTCAGAAAA 59.961 45.455 0.00 0.00 0.00 2.29
1477 1494 4.741321 AGCAAATGTGGTAAATGGATGG 57.259 40.909 0.00 0.00 32.39 3.51
1605 1630 5.223382 AGTGTATTGCTGTATCTACGATGC 58.777 41.667 0.00 0.00 0.00 3.91
1802 1835 9.656040 TGTCTCAACTTTAGTACAACTTTGTAA 57.344 29.630 3.38 0.00 44.46 2.41
1803 1836 9.911980 GTCTCAACTTTAGTACAACTTTGTAAC 57.088 33.333 3.38 0.00 44.46 2.50
1804 1837 9.880157 TCTCAACTTTAGTACAACTTTGTAACT 57.120 29.630 3.38 6.47 44.46 2.24
1820 1853 9.603921 ACTTTGTAACTTTGTACTAACTTAGCA 57.396 29.630 0.00 0.00 0.00 3.49
1823 1856 9.767228 TTGTAACTTTGTACTAACTTAGCATCA 57.233 29.630 0.00 0.00 0.00 3.07
1824 1857 9.419297 TGTAACTTTGTACTAACTTAGCATCAG 57.581 33.333 0.00 0.00 0.00 2.90
1825 1858 9.635520 GTAACTTTGTACTAACTTAGCATCAGA 57.364 33.333 0.00 0.00 0.00 3.27
1826 1859 8.535690 AACTTTGTACTAACTTAGCATCAGAC 57.464 34.615 0.00 0.00 0.00 3.51
1838 1871 1.000019 ATCAGACCGACGGAGGGAA 60.000 57.895 23.38 1.88 35.02 3.97
1866 1899 5.073311 TCTAGCATCAGACCTGTTACAAC 57.927 43.478 0.00 0.00 0.00 3.32
1867 1900 4.772624 TCTAGCATCAGACCTGTTACAACT 59.227 41.667 0.00 0.00 0.00 3.16
1868 1901 4.357918 AGCATCAGACCTGTTACAACTT 57.642 40.909 0.00 0.00 0.00 2.66
1869 1902 5.483685 AGCATCAGACCTGTTACAACTTA 57.516 39.130 0.00 0.00 0.00 2.24
1870 1903 5.238583 AGCATCAGACCTGTTACAACTTAC 58.761 41.667 0.00 0.00 0.00 2.34
1871 1904 4.994852 GCATCAGACCTGTTACAACTTACA 59.005 41.667 0.00 0.00 0.00 2.41
1872 1905 5.468746 GCATCAGACCTGTTACAACTTACAA 59.531 40.000 0.00 0.00 0.00 2.41
1938 3562 6.695278 CCTAAAGTTCGAAGTTGCAAAAATCA 59.305 34.615 18.59 0.00 0.00 2.57
1984 3608 4.699735 AGTCATTTGTTGTCAGTTGTCACA 59.300 37.500 0.00 0.00 0.00 3.58
2041 3667 7.201384 CGGACTACTGACGAACTTAAAATAACC 60.201 40.741 0.00 0.00 0.00 2.85
2046 3672 8.161699 ACTGACGAACTTAAAATAACCAACAT 57.838 30.769 0.00 0.00 0.00 2.71
2063 3689 8.477984 AACCAACATATGATCGGAAATTTTTG 57.522 30.769 10.38 0.00 0.00 2.44
2245 3871 6.987992 TCGAAAGGTGTCCATATACCAAATAC 59.012 38.462 0.00 0.00 39.29 1.89
2247 3873 7.170998 CGAAAGGTGTCCATATACCAAATACTC 59.829 40.741 0.00 0.00 39.29 2.59
2248 3874 6.435292 AGGTGTCCATATACCAAATACTCC 57.565 41.667 0.00 0.00 39.29 3.85
2249 3875 5.309806 AGGTGTCCATATACCAAATACTCCC 59.690 44.000 0.00 0.00 39.29 4.30
2251 3877 6.465084 GTGTCCATATACCAAATACTCCCTC 58.535 44.000 0.00 0.00 0.00 4.30
2252 3878 5.546499 TGTCCATATACCAAATACTCCCTCC 59.454 44.000 0.00 0.00 0.00 4.30
2253 3879 4.775780 TCCATATACCAAATACTCCCTCCG 59.224 45.833 0.00 0.00 0.00 4.63
2255 3881 5.337330 CCATATACCAAATACTCCCTCCGTC 60.337 48.000 0.00 0.00 0.00 4.79
2256 3882 1.201424 ACCAAATACTCCCTCCGTCC 58.799 55.000 0.00 0.00 0.00 4.79
2257 3883 0.468648 CCAAATACTCCCTCCGTCCC 59.531 60.000 0.00 0.00 0.00 4.46
2258 3884 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
2259 3885 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
2260 3886 2.969950 CAAATACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
2261 3887 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2262 3888 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2263 3889 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2264 3890 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2265 3891 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2266 3892 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2267 3893 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2268 3894 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2269 3895 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2271 3897 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2272 3898 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2273 3899 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2274 3900 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2275 3901 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2319 3945 6.693315 AAAACGTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
2320 3946 5.623956 AACGTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
2321 3947 5.215252 ACGTCTTACATTATGGGATGGAG 57.785 43.478 0.00 0.00 0.00 3.86
2322 3948 4.040461 ACGTCTTACATTATGGGATGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
2323 3949 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
2324 3950 4.597507 GTCTTACATTATGGGATGGAGGGA 59.402 45.833 0.00 0.00 0.00 4.20
2325 3951 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
2335 3961 5.403512 TGGGATGGAGGGAGTAGTTTATAG 58.596 45.833 0.00 0.00 0.00 1.31
2539 4165 4.719773 ACCATGATAGCTTTGGTGTACCTA 59.280 41.667 8.90 0.00 42.09 3.08
2636 4262 2.811873 GCATCACTTTGGAGGTCAGTGT 60.812 50.000 0.00 0.00 32.84 3.55
2773 4399 2.927028 TGTGGATGGATCTGCAGAATG 58.073 47.619 22.50 0.00 40.87 2.67
2928 4554 1.876156 GACTTCAACAAGGCTCCAGTG 59.124 52.381 0.00 0.00 34.32 3.66
3057 4683 3.251004 GTGGACATCTTCACACAAGGTTC 59.749 47.826 0.00 0.00 34.16 3.62
3069 4695 3.886505 ACACAAGGTTCGGCAAGAATTTA 59.113 39.130 0.00 0.00 41.49 1.40
3447 5073 1.584308 GCGCTTGTATTCTCTCGACAC 59.416 52.381 0.00 0.00 0.00 3.67
3612 5238 4.085733 CAGATCCTTCTCCAGATCGGTAT 58.914 47.826 3.97 0.00 43.03 2.73
3759 5385 1.272490 CAGTGGGCGTCGGTATATCAT 59.728 52.381 0.00 0.00 0.00 2.45
3793 5419 2.096268 TGCGTTCTTGCTCTGATTTTCG 60.096 45.455 0.00 0.00 35.36 3.46
3862 5488 7.386059 TCAACAATCTGTGTACACATATCTGT 58.614 34.615 28.03 24.17 40.60 3.41
4131 5757 2.159226 GGTCATCGTTCTACCTCACCTG 60.159 54.545 0.00 0.00 0.00 4.00
4152 5778 3.243670 TGTGTTTCGTGGTATTACCGACA 60.244 43.478 8.32 5.37 42.58 4.35
4185 5811 2.498248 GCGATGGCTGCTGAGAGA 59.502 61.111 0.00 0.00 35.83 3.10
4188 5814 1.144565 CGATGGCTGCTGAGAGAACG 61.145 60.000 0.00 0.00 0.00 3.95
4189 5815 0.174389 GATGGCTGCTGAGAGAACGA 59.826 55.000 0.00 0.00 0.00 3.85
4200 5826 2.420372 TGAGAGAACGACATTCCGAGAG 59.580 50.000 0.00 0.00 38.16 3.20
4238 5864 6.877855 CAGTCAGGAAAGAAGAAAGATGATCA 59.122 38.462 0.00 0.00 0.00 2.92
4393 6020 1.135859 GCAAATCTTCTGTGACTGCGG 60.136 52.381 0.00 0.00 0.00 5.69
4394 6021 1.466167 CAAATCTTCTGTGACTGCGGG 59.534 52.381 0.00 0.00 0.00 6.13
4398 6029 1.134220 TCTTCTGTGACTGCGGGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
4436 6067 4.160439 TCTGAAGATACTGATGACGCCTTT 59.840 41.667 0.00 0.00 0.00 3.11
4608 6239 0.586319 CACCGTGCTATATTTGGGCG 59.414 55.000 0.00 0.00 0.00 6.13
4684 6315 2.740055 CACTGCAGACGGAGCACC 60.740 66.667 23.35 0.00 37.02 5.01
4685 6316 2.919856 ACTGCAGACGGAGCACCT 60.920 61.111 23.35 0.00 37.02 4.00
4686 6317 1.606601 ACTGCAGACGGAGCACCTA 60.607 57.895 23.35 0.00 37.02 3.08
4687 6318 1.140589 CTGCAGACGGAGCACCTAG 59.859 63.158 8.42 0.00 37.02 3.02
4688 6319 1.304134 TGCAGACGGAGCACCTAGA 60.304 57.895 0.00 0.00 37.02 2.43
4689 6320 0.898326 TGCAGACGGAGCACCTAGAA 60.898 55.000 0.00 0.00 37.02 2.10
4690 6321 0.179124 GCAGACGGAGCACCTAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
4691 6322 0.457851 CAGACGGAGCACCTAGAAGG 59.542 60.000 0.00 0.00 42.49 3.46
4692 6323 1.142097 GACGGAGCACCTAGAAGGC 59.858 63.158 0.00 0.00 39.63 4.35
4693 6324 1.305381 ACGGAGCACCTAGAAGGCT 60.305 57.895 0.00 2.93 39.63 4.58
4694 6325 0.033405 ACGGAGCACCTAGAAGGCTA 60.033 55.000 0.00 0.00 39.63 3.93
4695 6326 0.671251 CGGAGCACCTAGAAGGCTAG 59.329 60.000 0.00 0.00 39.63 3.42
4696 6327 1.751032 CGGAGCACCTAGAAGGCTAGA 60.751 57.143 0.00 0.00 45.71 2.43
4697 6328 1.960689 GGAGCACCTAGAAGGCTAGAG 59.039 57.143 0.00 0.00 45.71 2.43
4722 6367 2.099756 GCGGCTGAAGATTTTATTGGCT 59.900 45.455 0.00 0.00 0.00 4.75
4741 6386 2.426024 GCTGGGTCACTCGTCTATTACA 59.574 50.000 0.00 0.00 0.00 2.41
4768 6414 6.451064 TTTTTGTTCTTTTGGAGAGGAGAC 57.549 37.500 0.00 0.00 35.37 3.36
4847 6493 7.165812 CACATAATTTATGAAGGCTAAACACGC 59.834 37.037 20.54 0.00 39.45 5.34
4848 6494 5.637006 AATTTATGAAGGCTAAACACGCA 57.363 34.783 0.00 0.00 0.00 5.24
4873 6520 4.891992 TCTTCAGAACAGGGAGTTAAGG 57.108 45.455 0.00 0.00 41.51 2.69
4906 6553 4.768968 CACTGGATGAAATTCTTTGACCCT 59.231 41.667 0.00 0.00 0.00 4.34
4908 6555 5.478332 ACTGGATGAAATTCTTTGACCCTTC 59.522 40.000 0.00 0.00 0.00 3.46
4909 6556 5.392995 TGGATGAAATTCTTTGACCCTTCA 58.607 37.500 0.00 0.00 0.00 3.02
4910 6557 5.837979 TGGATGAAATTCTTTGACCCTTCAA 59.162 36.000 0.00 0.00 40.14 2.69
4912 6559 6.646653 GGATGAAATTCTTTGACCCTTCAAAC 59.353 38.462 0.00 0.00 45.08 2.93
4913 6560 5.587289 TGAAATTCTTTGACCCTTCAAACG 58.413 37.500 0.00 0.00 45.08 3.60
4915 6562 2.045561 TCTTTGACCCTTCAAACGCA 57.954 45.000 0.00 0.00 45.08 5.24
4916 6563 1.946768 TCTTTGACCCTTCAAACGCAG 59.053 47.619 0.00 0.00 45.08 5.18
4917 6564 0.383949 TTTGACCCTTCAAACGCAGC 59.616 50.000 0.00 0.00 45.08 5.25
4918 6565 1.781025 TTGACCCTTCAAACGCAGCG 61.781 55.000 14.82 14.82 38.87 5.18
4919 6566 2.203153 ACCCTTCAAACGCAGCGT 60.203 55.556 16.61 16.61 43.97 5.07
4951 6598 0.527565 AATGAGCAACACCATTCCGC 59.472 50.000 0.00 0.00 0.00 5.54
4955 6602 2.325082 GCAACACCATTCCGCGTCT 61.325 57.895 4.92 0.00 0.00 4.18
4974 6621 2.916269 TCTGATGTTTGGGGTGGTGATA 59.084 45.455 0.00 0.00 0.00 2.15
5020 6673 4.722220 AGCTTTAGCATGCCTATGATGAA 58.278 39.130 15.66 0.00 45.16 2.57
5097 6756 2.708216 TGTTGCACTCCTCTTGTTCA 57.292 45.000 0.00 0.00 0.00 3.18
5119 6789 2.112279 ACCTTGTCAACTGTAGGGGA 57.888 50.000 0.00 0.00 31.91 4.81
5139 6809 5.239525 GGGGAAATTATGCATGTACACTCTC 59.760 44.000 10.16 0.00 0.00 3.20
5151 6821 5.791336 TGTACACTCTCAGTTCAGTTCAT 57.209 39.130 0.00 0.00 0.00 2.57
5152 6822 5.773575 TGTACACTCTCAGTTCAGTTCATC 58.226 41.667 0.00 0.00 0.00 2.92
5153 6823 5.536538 TGTACACTCTCAGTTCAGTTCATCT 59.463 40.000 0.00 0.00 0.00 2.90
5154 6824 4.880759 ACACTCTCAGTTCAGTTCATCTG 58.119 43.478 0.00 0.00 44.85 2.90
5155 6825 4.244066 CACTCTCAGTTCAGTTCATCTGG 58.756 47.826 0.00 0.00 43.76 3.86
5156 6826 4.021632 CACTCTCAGTTCAGTTCATCTGGA 60.022 45.833 0.00 0.00 43.76 3.86
5157 6827 4.220382 ACTCTCAGTTCAGTTCATCTGGAG 59.780 45.833 0.00 0.00 43.76 3.86
5166 6836 3.705579 CAGTTCATCTGGAGTCTGGAGAT 59.294 47.826 0.00 0.00 40.23 2.75
5196 6866 3.265995 TCCTCCCAGATTACAGGTTTTCC 59.734 47.826 0.00 0.00 41.05 3.13
5209 6879 0.796927 GTTTTCCTCTGGCTGTACGC 59.203 55.000 1.72 1.72 38.13 4.42
5248 6918 4.762251 GTCTTTTGAGCAGGGATAAACTGT 59.238 41.667 0.00 0.00 38.22 3.55
5253 6923 3.010420 GAGCAGGGATAAACTGTCCAAC 58.990 50.000 0.00 0.00 38.22 3.77
5255 6925 2.290960 GCAGGGATAAACTGTCCAACCT 60.291 50.000 0.00 0.00 38.22 3.50
5290 6961 2.306805 TGTTGCACTCTCAGGGATGAAT 59.693 45.455 0.00 0.00 0.00 2.57
5293 6964 2.306805 TGCACTCTCAGGGATGAATTGT 59.693 45.455 0.00 0.00 0.00 2.71
5333 7004 2.430921 CTCTGTCCGGACACGTGC 60.431 66.667 33.23 6.89 36.21 5.34
5341 7012 0.736636 CCGGACACGTGCTAGATACA 59.263 55.000 17.22 0.00 38.78 2.29
5346 7017 3.242969 GGACACGTGCTAGATACATTCGA 60.243 47.826 17.22 0.00 0.00 3.71
5347 7018 4.348656 GACACGTGCTAGATACATTCGAA 58.651 43.478 17.22 0.00 0.00 3.71
5348 7019 4.103357 ACACGTGCTAGATACATTCGAAC 58.897 43.478 17.22 0.00 0.00 3.95
5349 7020 4.142447 ACACGTGCTAGATACATTCGAACT 60.142 41.667 17.22 0.00 0.00 3.01
5351 7022 5.969435 CACGTGCTAGATACATTCGAACTAA 59.031 40.000 0.82 0.00 0.00 2.24
5352 7023 6.471198 CACGTGCTAGATACATTCGAACTAAA 59.529 38.462 0.82 0.00 0.00 1.85
5358 7070 6.401047 AGATACATTCGAACTAAATCCGGA 57.599 37.500 6.61 6.61 0.00 5.14
5360 7072 4.196626 ACATTCGAACTAAATCCGGACA 57.803 40.909 6.12 0.00 0.00 4.02
5364 7076 2.426024 TCGAACTAAATCCGGACAGAGG 59.574 50.000 6.12 0.00 0.00 3.69
5396 7108 0.109643 TTGACGCATGTGCTTGCATC 60.110 50.000 6.08 5.30 42.91 3.91
5397 7109 1.226491 GACGCATGTGCTTGCATCC 60.226 57.895 6.08 0.00 42.91 3.51
5405 7117 0.598065 GTGCTTGCATCCGAAAACCT 59.402 50.000 0.00 0.00 0.00 3.50
5423 7135 3.139077 ACCTGATCGTCACTTTTTGGTC 58.861 45.455 0.00 0.00 0.00 4.02
5450 7162 6.275692 TGGTAATGAGACCAGGATAGACTA 57.724 41.667 0.00 0.00 44.79 2.59
5451 7163 6.307776 TGGTAATGAGACCAGGATAGACTAG 58.692 44.000 0.00 0.00 44.79 2.57
5452 7164 5.712917 GGTAATGAGACCAGGATAGACTAGG 59.287 48.000 0.00 0.00 39.51 3.02
5453 7165 5.671463 AATGAGACCAGGATAGACTAGGA 57.329 43.478 0.00 0.00 0.00 2.94
5485 8668 5.181748 AGCACTGAGTGGAAGAAATCATAC 58.818 41.667 15.24 0.00 33.64 2.39
5527 8710 1.021390 CAATGATAGATCCGCCGCCC 61.021 60.000 0.00 0.00 0.00 6.13
5528 8711 1.194781 AATGATAGATCCGCCGCCCT 61.195 55.000 0.00 0.00 0.00 5.19
5529 8712 1.892819 ATGATAGATCCGCCGCCCTG 61.893 60.000 0.00 0.00 0.00 4.45
5530 8713 3.302347 GATAGATCCGCCGCCCTGG 62.302 68.421 0.00 0.00 42.50 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.026718 GGTGGTGCCATGCAGTACTC 61.027 60.000 0.00 0.00 40.08 2.59
21 22 1.139058 CTCCTTCTACCGGTCCATTGG 59.861 57.143 12.40 8.88 0.00 3.16
48 49 0.617820 ACTAATGGTGCTCCCGTCCT 60.618 55.000 1.59 0.00 35.15 3.85
51 52 1.861982 ACTACTAATGGTGCTCCCGT 58.138 50.000 1.59 0.00 35.15 5.28
64 65 4.760715 CGAAGGCCAAGCTATCTACTACTA 59.239 45.833 5.01 0.00 0.00 1.82
74 75 1.080093 CGACACGAAGGCCAAGCTA 60.080 57.895 5.01 0.00 0.00 3.32
153 155 1.956629 TTCCTTCATCGGCGGGAGTC 61.957 60.000 7.21 0.00 0.00 3.36
157 159 1.512926 CTTATTCCTTCATCGGCGGG 58.487 55.000 7.21 0.00 0.00 6.13
162 164 3.999663 GAGGATGGCTTATTCCTTCATCG 59.000 47.826 0.00 0.00 36.15 3.84
173 175 1.038681 TACGGCGTGAGGATGGCTTA 61.039 55.000 24.86 0.00 0.00 3.09
183 185 3.740397 CGAGGTGGTACGGCGTGA 61.740 66.667 24.86 3.13 0.00 4.35
206 208 2.691011 GAGGCCTCTTCACTACTACCTG 59.309 54.545 26.25 0.00 0.00 4.00
210 212 4.017808 GTCTTGAGGCCTCTTCACTACTA 58.982 47.826 32.28 6.94 0.00 1.82
231 233 2.625737 CGCAGAGTTCATCATCAAGGT 58.374 47.619 0.00 0.00 0.00 3.50
240 242 1.079543 AGCTTCGCGCAGAGTTCAT 60.080 52.632 10.74 0.00 42.61 2.57
248 250 2.580597 CTCATCGAGCTTCGCGCA 60.581 61.111 8.75 0.00 40.21 6.09
319 326 0.459759 GTTGCTACAGCCTACCCGTC 60.460 60.000 0.00 0.00 41.18 4.79
322 329 1.814169 GCGTTGCTACAGCCTACCC 60.814 63.158 0.00 0.00 41.18 3.69
337 344 2.224329 TGTTTGTGTACACATAGGGCGT 60.224 45.455 28.35 0.00 41.52 5.68
364 371 2.415010 CTCCACTCGCTCGGATGG 59.585 66.667 6.44 6.44 0.00 3.51
462 469 2.676839 CGATCATGTTTGCTTGCTCTCT 59.323 45.455 0.00 0.00 0.00 3.10
474 481 2.246739 CGCGCATCCCGATCATGTT 61.247 57.895 8.75 0.00 40.02 2.71
628 635 1.794222 CTCCGATTGTCAAACCGGC 59.206 57.895 19.20 0.00 41.55 6.13
641 648 1.180456 TACCGACACCTTTGCTCCGA 61.180 55.000 0.00 0.00 0.00 4.55
660 667 2.830285 GCGTGCGGGTGTTGACTTT 61.830 57.895 0.00 0.00 0.00 2.66
688 695 2.601067 TTACTGGGTGGTCCGCGA 60.601 61.111 8.23 0.00 38.76 5.87
723 730 2.719979 CTCCGTCCCGATGGTACG 59.280 66.667 2.92 0.00 38.61 3.67
755 762 1.169661 TCGTCAGCGGCAAAAATGGT 61.170 50.000 1.45 0.00 38.89 3.55
772 779 0.107214 ACCCCCACATGCTAATGTCG 60.107 55.000 0.00 0.00 45.50 4.35
795 802 2.380410 GGACGTGGCAGCTTGTACG 61.380 63.158 10.74 10.74 41.86 3.67
822 829 9.574516 TGTGAGTACTATACATATCACTCATGT 57.425 33.333 8.04 0.00 42.91 3.21
828 835 9.383462 CGTCTTTGTGAGTACTATACATATCAC 57.617 37.037 11.86 6.90 38.00 3.06
829 836 9.117183 ACGTCTTTGTGAGTACTATACATATCA 57.883 33.333 11.86 0.00 0.00 2.15
832 839 8.542953 CGTACGTCTTTGTGAGTACTATACATA 58.457 37.037 7.22 7.64 37.78 2.29
833 840 7.065085 ACGTACGTCTTTGTGAGTACTATACAT 59.935 37.037 16.72 1.52 37.78 2.29
834 841 6.368791 ACGTACGTCTTTGTGAGTACTATACA 59.631 38.462 16.72 8.04 37.78 2.29
835 842 6.766084 ACGTACGTCTTTGTGAGTACTATAC 58.234 40.000 16.72 0.00 37.78 1.47
836 843 6.968131 ACGTACGTCTTTGTGAGTACTATA 57.032 37.500 16.72 0.00 37.78 1.31
837 844 5.869753 ACGTACGTCTTTGTGAGTACTAT 57.130 39.130 16.72 0.00 37.78 2.12
838 845 5.926542 AGTACGTACGTCTTTGTGAGTACTA 59.073 40.000 26.53 0.00 40.84 1.82
839 846 4.752101 AGTACGTACGTCTTTGTGAGTACT 59.248 41.667 26.53 15.29 39.39 2.73
840 847 5.023551 AGTACGTACGTCTTTGTGAGTAC 57.976 43.478 26.53 13.13 36.84 2.73
841 848 5.926542 AGTAGTACGTACGTCTTTGTGAGTA 59.073 40.000 26.53 9.76 36.66 2.59
842 849 4.752101 AGTAGTACGTACGTCTTTGTGAGT 59.248 41.667 26.53 10.82 36.66 3.41
843 850 5.274881 AGTAGTACGTACGTCTTTGTGAG 57.725 43.478 26.53 0.00 36.66 3.51
844 851 5.673337 AAGTAGTACGTACGTCTTTGTGA 57.327 39.130 26.53 1.73 36.66 3.58
845 852 6.345250 CCAAAAGTAGTACGTACGTCTTTGTG 60.345 42.308 31.13 28.07 36.66 3.33
846 853 5.687285 CCAAAAGTAGTACGTACGTCTTTGT 59.313 40.000 31.13 23.37 36.66 2.83
847 854 5.687285 ACCAAAAGTAGTACGTACGTCTTTG 59.313 40.000 31.13 27.41 36.66 2.77
848 855 5.687285 CACCAAAAGTAGTACGTACGTCTTT 59.313 40.000 28.13 28.13 36.66 2.52
849 856 5.215160 CACCAAAAGTAGTACGTACGTCTT 58.785 41.667 26.53 18.43 36.66 3.01
850 857 4.275936 ACACCAAAAGTAGTACGTACGTCT 59.724 41.667 26.53 21.99 36.66 4.18
851 858 4.537015 ACACCAAAAGTAGTACGTACGTC 58.463 43.478 26.53 16.16 36.66 4.34
852 859 4.568152 ACACCAAAAGTAGTACGTACGT 57.432 40.909 25.98 25.98 36.66 3.57
853 860 4.851558 GGTACACCAAAAGTAGTACGTACG 59.148 45.833 19.49 15.01 35.53 3.67
854 861 5.048013 AGGGTACACCAAAAGTAGTACGTAC 60.048 44.000 18.10 18.10 43.89 3.67
855 862 5.076873 AGGGTACACCAAAAGTAGTACGTA 58.923 41.667 0.00 0.00 43.89 3.57
856 863 3.897505 AGGGTACACCAAAAGTAGTACGT 59.102 43.478 0.00 0.00 43.89 3.57
857 864 4.488879 GAGGGTACACCAAAAGTAGTACG 58.511 47.826 0.00 0.00 43.89 3.67
858 865 4.488879 CGAGGGTACACCAAAAGTAGTAC 58.511 47.826 0.00 0.00 43.89 2.73
859 866 3.056607 GCGAGGGTACACCAAAAGTAGTA 60.057 47.826 0.00 0.00 43.89 1.82
860 867 2.289257 GCGAGGGTACACCAAAAGTAGT 60.289 50.000 0.00 0.00 43.89 2.73
861 868 2.028385 AGCGAGGGTACACCAAAAGTAG 60.028 50.000 0.00 0.00 43.89 2.57
862 869 1.972795 AGCGAGGGTACACCAAAAGTA 59.027 47.619 0.00 0.00 43.89 2.24
863 870 0.763035 AGCGAGGGTACACCAAAAGT 59.237 50.000 0.00 0.00 43.89 2.66
864 871 1.535462 CAAGCGAGGGTACACCAAAAG 59.465 52.381 0.00 0.00 43.89 2.27
865 872 1.141254 TCAAGCGAGGGTACACCAAAA 59.859 47.619 0.00 0.00 43.89 2.44
866 873 0.759959 TCAAGCGAGGGTACACCAAA 59.240 50.000 0.00 0.00 43.89 3.28
867 874 0.320374 CTCAAGCGAGGGTACACCAA 59.680 55.000 0.00 0.00 43.89 3.67
868 875 1.972198 CTCAAGCGAGGGTACACCA 59.028 57.895 0.00 0.00 43.89 4.17
869 876 4.913126 CTCAAGCGAGGGTACACC 57.087 61.111 0.00 0.00 35.44 4.16
879 886 1.137404 CGGAATTTGCCCTCAAGCG 59.863 57.895 0.00 0.00 33.12 4.68
890 897 2.808244 CGTTTGCATATGCCGGAATTT 58.192 42.857 24.54 0.00 41.18 1.82
911 918 2.732412 TCAGAGAGAACAGCGAAAGG 57.268 50.000 0.00 0.00 0.00 3.11
915 922 3.445096 TCAATGATCAGAGAGAACAGCGA 59.555 43.478 0.09 0.00 32.14 4.93
930 937 4.726416 CTGCAGTTTACGCTTTCAATGAT 58.274 39.130 5.25 0.00 0.00 2.45
1136 1151 4.292178 GATCCGAGAGCTGGGCCG 62.292 72.222 0.00 0.00 0.00 6.13
1281 1296 1.152312 GAAGGGGGCGATAGAGGGA 60.152 63.158 0.00 0.00 39.76 4.20
1309 1325 1.290134 GGGGAAGGATCAACAGGAGT 58.710 55.000 0.00 0.00 0.00 3.85
1312 1328 0.392998 CACGGGGAAGGATCAACAGG 60.393 60.000 0.00 0.00 0.00 4.00
1351 1368 6.879458 ACCACTCCAACTAGATTAAACATCAC 59.121 38.462 0.00 0.00 0.00 3.06
1352 1369 7.016153 ACCACTCCAACTAGATTAAACATCA 57.984 36.000 0.00 0.00 0.00 3.07
1367 1384 3.563808 CGAACATCAAAGAACCACTCCAA 59.436 43.478 0.00 0.00 0.00 3.53
1426 1443 6.715280 TGAAGCCTCATTAGTCTCTGAATTT 58.285 36.000 0.00 0.00 0.00 1.82
1477 1494 0.872388 CAGTGCCTTAACGAACCACC 59.128 55.000 0.00 0.00 0.00 4.61
1589 1614 5.705609 TCAATAGCATCGTAGATACAGCA 57.294 39.130 0.00 0.00 45.12 4.41
1802 1835 7.097834 GGTCTGATGCTAAGTTAGTACAAAGT 58.902 38.462 11.51 0.00 0.00 2.66
1803 1836 6.253727 CGGTCTGATGCTAAGTTAGTACAAAG 59.746 42.308 11.51 6.05 0.00 2.77
1804 1837 6.071784 TCGGTCTGATGCTAAGTTAGTACAAA 60.072 38.462 11.51 0.00 0.00 2.83
1805 1838 5.416639 TCGGTCTGATGCTAAGTTAGTACAA 59.583 40.000 11.51 0.00 0.00 2.41
1806 1839 4.945543 TCGGTCTGATGCTAAGTTAGTACA 59.054 41.667 11.51 8.23 0.00 2.90
1809 1842 3.181499 CGTCGGTCTGATGCTAAGTTAGT 60.181 47.826 11.51 0.00 0.00 2.24
1810 1843 3.364062 CGTCGGTCTGATGCTAAGTTAG 58.636 50.000 5.47 5.47 0.00 2.34
1811 1844 2.098607 CCGTCGGTCTGATGCTAAGTTA 59.901 50.000 2.08 0.00 31.85 2.24
1812 1845 1.135083 CCGTCGGTCTGATGCTAAGTT 60.135 52.381 2.08 0.00 31.85 2.66
1815 1848 0.738975 CTCCGTCGGTCTGATGCTAA 59.261 55.000 11.88 0.00 31.85 3.09
1819 1852 1.320344 TTCCCTCCGTCGGTCTGATG 61.320 60.000 11.88 0.00 0.00 3.07
1820 1853 0.397254 ATTCCCTCCGTCGGTCTGAT 60.397 55.000 11.88 0.00 0.00 2.90
1821 1854 0.256752 TATTCCCTCCGTCGGTCTGA 59.743 55.000 11.88 3.28 0.00 3.27
1822 1855 0.669077 CTATTCCCTCCGTCGGTCTG 59.331 60.000 11.88 3.07 0.00 3.51
1823 1856 0.549950 TCTATTCCCTCCGTCGGTCT 59.450 55.000 11.88 0.00 0.00 3.85
1824 1857 1.396653 TTCTATTCCCTCCGTCGGTC 58.603 55.000 11.88 0.00 0.00 4.79
1825 1858 1.962100 GATTCTATTCCCTCCGTCGGT 59.038 52.381 11.88 0.00 0.00 4.69
1826 1859 2.240279 AGATTCTATTCCCTCCGTCGG 58.760 52.381 4.39 4.39 0.00 4.79
1838 1871 6.992664 AACAGGTCTGATGCTAGATTCTAT 57.007 37.500 4.84 0.00 0.00 1.98
1866 1899 6.262273 AGTTACAGTTCATGTTGGGTTGTAAG 59.738 38.462 0.00 0.00 39.96 2.34
1867 1900 6.038825 CAGTTACAGTTCATGTTGGGTTGTAA 59.961 38.462 0.00 0.00 39.96 2.41
1868 1901 5.529430 CAGTTACAGTTCATGTTGGGTTGTA 59.471 40.000 0.00 0.00 39.96 2.41
1869 1902 4.338118 CAGTTACAGTTCATGTTGGGTTGT 59.662 41.667 0.00 0.00 39.96 3.32
1870 1903 4.578516 TCAGTTACAGTTCATGTTGGGTTG 59.421 41.667 0.00 0.00 39.96 3.77
1871 1904 4.787551 TCAGTTACAGTTCATGTTGGGTT 58.212 39.130 0.00 0.00 39.96 4.11
1872 1905 4.389374 CTCAGTTACAGTTCATGTTGGGT 58.611 43.478 0.00 0.00 39.96 4.51
1938 3562 7.624549 ACTATGTTGATTGTGGTTCTATGTCT 58.375 34.615 0.00 0.00 0.00 3.41
2041 3667 7.760131 AGCAAAAATTTCCGATCATATGTTG 57.240 32.000 1.90 0.00 0.00 3.33
2063 3689 3.122445 GCAAAGCAGCTGTTTATTCAAGC 59.878 43.478 16.68 9.89 0.00 4.01
2103 3729 4.083802 GCAACTGCCTAGTTACAAGTGAAG 60.084 45.833 0.00 0.00 45.12 3.02
2245 3871 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2247 3873 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2248 3874 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2249 3875 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2295 3921 6.887545 TCCATCCCATAATGTAAGACGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
2296 3922 6.419791 TCCATCCCATAATGTAAGACGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
2297 3923 5.996644 TCCATCCCATAATGTAAGACGTTT 58.003 37.500 0.00 0.00 0.00 3.60
2298 3924 5.454755 CCTCCATCCCATAATGTAAGACGTT 60.455 44.000 0.00 0.00 0.00 3.99
2299 3925 4.040461 CCTCCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
2300 3926 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
2301 3927 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
2302 3928 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
2303 3929 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
2304 3930 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
2305 3931 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
2306 3932 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
2307 3933 4.171234 ACTACTCCCTCCATCCCATAATG 58.829 47.826 0.00 0.00 0.00 1.90
2308 3934 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
2309 3935 4.295905 AACTACTCCCTCCATCCCATAA 57.704 45.455 0.00 0.00 0.00 1.90
2310 3936 4.295905 AAACTACTCCCTCCATCCCATA 57.704 45.455 0.00 0.00 0.00 2.74
2311 3937 2.897823 AACTACTCCCTCCATCCCAT 57.102 50.000 0.00 0.00 0.00 4.00
2312 3938 2.661176 AAACTACTCCCTCCATCCCA 57.339 50.000 0.00 0.00 0.00 4.37
2313 3939 5.652324 TCTATAAACTACTCCCTCCATCCC 58.348 45.833 0.00 0.00 0.00 3.85
2314 3940 6.954684 TCATCTATAAACTACTCCCTCCATCC 59.045 42.308 0.00 0.00 0.00 3.51
2315 3941 8.602472 ATCATCTATAAACTACTCCCTCCATC 57.398 38.462 0.00 0.00 0.00 3.51
2316 3942 8.980832 AATCATCTATAAACTACTCCCTCCAT 57.019 34.615 0.00 0.00 0.00 3.41
2539 4165 2.119495 GTCATAGTCCCCACCAGACAT 58.881 52.381 0.00 0.00 36.68 3.06
2729 4355 4.314961 TCTACCATATGTTATGCCAAGCG 58.685 43.478 1.24 0.00 0.00 4.68
2773 4399 0.749454 AACAGATGCTTCCGGCCATC 60.749 55.000 16.86 16.86 40.92 3.51
2856 4482 6.333416 CAGTTCTATAAGCTGCTTGTCAGTA 58.667 40.000 24.35 9.44 44.66 2.74
2928 4554 4.944048 AGTGCCCAACTGTAATTTTTGTC 58.056 39.130 0.00 0.00 37.88 3.18
3057 4683 4.719040 AGTAACGCTTTAAATTCTTGCCG 58.281 39.130 0.00 0.00 0.00 5.69
3069 4695 4.041740 TGCTCGATGATAGTAACGCTTT 57.958 40.909 0.00 0.00 0.00 3.51
3447 5073 2.680339 TGCTGAGACAGTCACTATCTCG 59.320 50.000 8.59 4.84 41.54 4.04
3456 5082 7.432869 AGTCATATATCTTTGCTGAGACAGTC 58.567 38.462 0.00 0.00 33.43 3.51
3612 5238 1.209898 CGCTTCGATTTGCAGCCAA 59.790 52.632 0.63 0.00 0.00 4.52
3862 5488 0.606130 TACTGACTACCGTCCGCACA 60.606 55.000 0.00 0.00 39.47 4.57
3897 5523 3.694566 GCCAGATAAAACCACCAAGTAGG 59.305 47.826 0.00 0.00 45.67 3.18
4131 5757 3.316283 TGTCGGTAATACCACGAAACAC 58.684 45.455 10.40 0.00 38.47 3.32
4152 5778 0.739462 TCGCGGCGAGAATCACAATT 60.739 50.000 22.69 0.00 33.17 2.32
4179 5805 2.420372 CTCTCGGAATGTCGTTCTCTCA 59.580 50.000 4.81 0.00 37.01 3.27
4185 5811 0.603569 AGTGCTCTCGGAATGTCGTT 59.396 50.000 0.00 0.00 0.00 3.85
4188 5814 1.751924 AGGTAGTGCTCTCGGAATGTC 59.248 52.381 0.00 0.00 0.00 3.06
4189 5815 1.751924 GAGGTAGTGCTCTCGGAATGT 59.248 52.381 0.00 0.00 0.00 2.71
4200 5826 0.179150 CTGACTGCGAGAGGTAGTGC 60.179 60.000 0.00 0.00 42.06 4.40
4212 5838 4.999950 TCATCTTTCTTCTTTCCTGACTGC 59.000 41.667 0.00 0.00 0.00 4.40
4238 5864 1.072965 CTCTCCTGCTCTTTTGGTGGT 59.927 52.381 0.00 0.00 0.00 4.16
4354 5980 5.801350 TTGCATCGACTGAAAGGAAATAG 57.199 39.130 0.00 0.00 39.30 1.73
4604 6235 4.056125 GCCTTTGCAACTCCGCCC 62.056 66.667 0.00 0.00 37.47 6.13
4684 6315 0.237235 CGCGAGCTCTAGCCTTCTAG 59.763 60.000 12.85 0.00 42.87 2.43
4685 6316 1.167155 CCGCGAGCTCTAGCCTTCTA 61.167 60.000 8.23 0.00 43.38 2.10
4686 6317 2.485795 CCGCGAGCTCTAGCCTTCT 61.486 63.158 8.23 0.00 43.38 2.85
4687 6318 2.026879 CCGCGAGCTCTAGCCTTC 59.973 66.667 8.23 0.00 43.38 3.46
4688 6319 4.214327 GCCGCGAGCTCTAGCCTT 62.214 66.667 8.23 0.00 43.38 4.35
4697 6328 1.006832 TAAAATCTTCAGCCGCGAGC 58.993 50.000 8.23 9.98 44.25 5.03
4722 6367 5.670792 AAATGTAATAGACGAGTGACCCA 57.329 39.130 0.00 0.00 0.00 4.51
4820 6466 8.181573 CGTGTTTAGCCTTCATAAATTATGTGT 58.818 33.333 12.18 0.00 37.45 3.72
4821 6467 7.165812 GCGTGTTTAGCCTTCATAAATTATGTG 59.834 37.037 12.18 7.17 37.45 3.21
4833 6479 4.160736 AGAAATTGCGTGTTTAGCCTTC 57.839 40.909 0.00 0.00 0.00 3.46
4834 6480 4.037446 TGAAGAAATTGCGTGTTTAGCCTT 59.963 37.500 0.00 0.00 0.00 4.35
4837 6483 4.783242 TCTGAAGAAATTGCGTGTTTAGC 58.217 39.130 0.00 0.00 0.00 3.09
4847 6493 7.308830 CCTTAACTCCCTGTTCTGAAGAAATTG 60.309 40.741 0.00 0.00 39.89 2.32
4848 6494 6.717084 CCTTAACTCCCTGTTCTGAAGAAATT 59.283 38.462 0.00 0.00 39.89 1.82
4873 6520 7.875971 AGAATTTCATCCAGTGTTAACAAGTC 58.124 34.615 10.51 0.23 0.00 3.01
4915 6562 4.437390 GCTCATTGCAAATACAGTAACGCT 60.437 41.667 1.71 0.00 42.31 5.07
4916 6563 3.786048 GCTCATTGCAAATACAGTAACGC 59.214 43.478 1.71 0.00 42.31 4.84
4951 6598 0.250727 ACCACCCCAAACATCAGACG 60.251 55.000 0.00 0.00 0.00 4.18
4955 6602 3.684130 CGATATCACCACCCCAAACATCA 60.684 47.826 3.12 0.00 0.00 3.07
4974 6621 0.611062 TGGAAGGTGAGTCGGACGAT 60.611 55.000 1.89 0.00 0.00 3.73
5040 6699 8.951243 GCTAAAATGAGGTTTCTTGACTCTATT 58.049 33.333 0.00 0.00 32.58 1.73
5119 6789 7.607607 TGAACTGAGAGTGTACATGCATAATTT 59.392 33.333 0.00 0.00 0.00 1.82
5151 6821 1.362584 TCCCAATCTCCAGACTCCAGA 59.637 52.381 0.00 0.00 0.00 3.86
5152 6822 1.871418 TCCCAATCTCCAGACTCCAG 58.129 55.000 0.00 0.00 0.00 3.86
5153 6823 2.342406 TTCCCAATCTCCAGACTCCA 57.658 50.000 0.00 0.00 0.00 3.86
5154 6824 3.434310 GGAATTCCCAATCTCCAGACTCC 60.434 52.174 14.03 0.00 34.14 3.85
5155 6825 3.457749 AGGAATTCCCAATCTCCAGACTC 59.542 47.826 21.22 0.00 37.41 3.36
5156 6826 3.457749 GAGGAATTCCCAATCTCCAGACT 59.542 47.826 21.22 0.00 37.41 3.24
5157 6827 3.434310 GGAGGAATTCCCAATCTCCAGAC 60.434 52.174 21.22 0.00 42.49 3.51
5205 6875 1.628447 GATTGTTGGCGAACGGCGTA 61.628 55.000 15.20 0.00 44.92 4.42
5206 6876 2.961669 GATTGTTGGCGAACGGCGT 61.962 57.895 6.77 6.77 44.92 5.68
5209 6879 1.131826 GACGATTGTTGGCGAACGG 59.868 57.895 7.12 0.00 34.49 4.44
5210 6880 0.511221 AAGACGATTGTTGGCGAACG 59.489 50.000 7.12 0.00 34.49 3.95
5212 6882 2.614520 TCAAAAGACGATTGTTGGCGAA 59.385 40.909 0.00 0.00 0.00 4.70
5213 6883 2.214347 TCAAAAGACGATTGTTGGCGA 58.786 42.857 0.00 0.00 0.00 5.54
5214 6884 2.574322 CTCAAAAGACGATTGTTGGCG 58.426 47.619 0.00 0.00 0.00 5.69
5218 6888 2.554032 CCCTGCTCAAAAGACGATTGTT 59.446 45.455 0.00 0.00 0.00 2.83
5248 6918 1.186200 CCAGAGACGATCAGGTTGGA 58.814 55.000 0.00 0.00 30.00 3.53
5253 6923 2.819115 CAACATCCAGAGACGATCAGG 58.181 52.381 0.00 0.00 35.92 3.86
5255 6925 1.550072 TGCAACATCCAGAGACGATCA 59.450 47.619 0.00 0.00 0.00 2.92
5290 6961 9.754382 GGGAGTATATATAAGACGTTTTGACAA 57.246 33.333 0.83 0.00 0.00 3.18
5293 6964 9.584008 AGAGGGAGTATATATAAGACGTTTTGA 57.416 33.333 0.83 0.00 0.00 2.69
5333 7004 7.537991 GTCCGGATTTAGTTCGAATGTATCTAG 59.462 40.741 7.81 2.48 0.00 2.43
5341 7012 4.441634 CCTCTGTCCGGATTTAGTTCGAAT 60.442 45.833 7.81 0.00 0.00 3.34
5346 7017 3.838903 ACTTCCTCTGTCCGGATTTAGTT 59.161 43.478 7.81 0.00 0.00 2.24
5347 7018 3.442076 ACTTCCTCTGTCCGGATTTAGT 58.558 45.455 7.81 1.95 0.00 2.24
5348 7019 5.069251 ACATACTTCCTCTGTCCGGATTTAG 59.931 44.000 7.81 7.24 0.00 1.85
5349 7020 4.960469 ACATACTTCCTCTGTCCGGATTTA 59.040 41.667 7.81 0.00 0.00 1.40
5351 7022 3.375699 ACATACTTCCTCTGTCCGGATT 58.624 45.455 7.81 0.00 0.00 3.01
5352 7023 3.033659 ACATACTTCCTCTGTCCGGAT 57.966 47.619 7.81 0.00 0.00 4.18
5384 7096 1.067635 GGTTTTCGGATGCAAGCACAT 60.068 47.619 0.00 0.00 0.00 3.21
5396 7108 2.080286 AGTGACGATCAGGTTTTCGG 57.920 50.000 0.00 0.00 39.61 4.30
5397 7109 4.468095 AAAAGTGACGATCAGGTTTTCG 57.532 40.909 0.00 0.00 41.04 3.46
5405 7117 3.057019 CGAGACCAAAAAGTGACGATCA 58.943 45.455 0.00 0.00 0.00 2.92
5423 7135 2.100197 TCCTGGTCTCATTACCACGAG 58.900 52.381 0.00 0.00 44.68 4.18
5531 8714 4.332637 GTTGCGGTGCTGCCAGTG 62.333 66.667 0.00 0.00 36.97 3.66
5532 8715 4.873810 TGTTGCGGTGCTGCCAGT 62.874 61.111 0.00 0.00 36.97 4.00


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

AutoCloner maintained by Alex Coulton.