Multiple sequence alignment - TraesCS5D01G164300

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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 TraesCS5D01G164300 chr5D 100.000 6827 0 0 1 6827 255697903 255691077 0.000000e+00 12608.0
1 TraesCS5D01G164300 chr5D 100.000 1806 0 0 7182 8987 255690722 255688917 0.000000e+00 3336.0
2 TraesCS5D01G164300 chr5D 97.122 139 4 0 1 139 258001598 258001460 1.510000e-57 235.0
3 TraesCS5D01G164300 chr5D 91.912 136 11 0 1 136 37077828 37077963 3.310000e-44 191.0
4 TraesCS5D01G164300 chr5D 89.630 135 13 1 1 134 458690207 458690073 4.310000e-38 171.0
5 TraesCS5D01G164300 chr5D 100.000 75 0 0 4490 4564 255693340 255693266 1.220000e-28 139.0
6 TraesCS5D01G164300 chr5D 100.000 75 0 0 4564 4638 255693414 255693340 1.220000e-28 139.0
7 TraesCS5D01G164300 chr5D 89.855 69 2 5 730 794 107792632 107792565 5.780000e-12 84.2
8 TraesCS5D01G164300 chr5A 94.379 3825 104 33 821 4564 339749220 339745426 0.000000e+00 5770.0
9 TraesCS5D01G164300 chr5A 96.387 1965 61 6 4564 6522 339745500 339743540 0.000000e+00 3227.0
10 TraesCS5D01G164300 chr5A 93.654 1828 75 25 7187 8985 339742978 339741163 0.000000e+00 2695.0
11 TraesCS5D01G164300 chr5A 89.815 216 11 5 6622 6827 339743234 339743020 5.350000e-67 267.0
12 TraesCS5D01G164300 chr5A 93.519 108 2 3 6534 6639 339743403 339743507 1.210000e-33 156.0
13 TraesCS5D01G164300 chr5A 95.652 46 1 1 3526 3570 339746475 339746520 1.250000e-08 73.1
14 TraesCS5D01G164300 chr5A 84.932 73 5 5 716 785 520115243 520115174 1.620000e-07 69.4
15 TraesCS5D01G164300 chr5B 91.198 1227 66 15 821 2036 289584600 289583405 0.000000e+00 1629.0
16 TraesCS5D01G164300 chr5B 95.682 741 30 1 7407 8145 289574818 289574078 0.000000e+00 1190.0
17 TraesCS5D01G164300 chr5B 94.694 735 25 4 8251 8985 289567351 289566631 0.000000e+00 1129.0
18 TraesCS5D01G164300 chr5B 92.145 802 52 9 3568 4362 289582269 289581472 0.000000e+00 1122.0
19 TraesCS5D01G164300 chr5B 91.644 742 44 11 2302 3031 289583409 289582674 0.000000e+00 1011.0
20 TraesCS5D01G164300 chr5B 86.873 777 45 13 4570 5294 289581389 289580618 0.000000e+00 817.0
21 TraesCS5D01G164300 chr5B 88.615 650 55 7 5291 5926 289580514 289579870 0.000000e+00 773.0
22 TraesCS5D01G164300 chr5B 93.443 366 14 8 5921 6281 289575177 289574817 1.330000e-147 534.0
23 TraesCS5D01G164300 chr5B 83.247 579 80 6 131 699 211148389 211148960 4.810000e-142 516.0
24 TraesCS5D01G164300 chr5B 89.048 420 21 4 3058 3475 289582675 289582279 1.740000e-136 497.0
25 TraesCS5D01G164300 chr5B 89.950 199 14 4 2108 2302 575815956 575816152 1.500000e-62 252.0
26 TraesCS5D01G164300 chr5B 97.794 136 3 0 1 136 96780044 96779909 1.510000e-57 235.0
27 TraesCS5D01G164300 chr5B 93.496 123 5 2 6705 6827 665744608 665744489 7.170000e-41 180.0
28 TraesCS5D01G164300 chr5B 92.661 109 6 2 8144 8252 289567617 289567511 1.210000e-33 156.0
29 TraesCS5D01G164300 chr5B 83.721 86 11 3 3484 3568 580983186 580983269 2.690000e-10 78.7
30 TraesCS5D01G164300 chr5B 90.909 55 4 1 732 786 8523621 8523674 1.250000e-08 73.1
31 TraesCS5D01G164300 chr3B 89.072 668 59 4 131 792 151200456 151199797 0.000000e+00 817.0
32 TraesCS5D01G164300 chr3B 88.372 86 9 1 3484 3568 738379778 738379693 1.600000e-17 102.0
33 TraesCS5D01G164300 chr3B 87.342 79 5 5 717 791 486384948 486385025 1.610000e-12 86.1
34 TraesCS5D01G164300 chr3B 93.182 44 2 1 7186 7228 458336468 458336425 7.530000e-06 63.9
35 TraesCS5D01G164300 chr3A 88.946 579 55 5 131 708 99482286 99482856 0.000000e+00 706.0
36 TraesCS5D01G164300 chr6B 88.446 502 57 1 198 699 31224544 31225044 9.980000e-169 604.0
37 TraesCS5D01G164300 chr6B 87.649 502 61 1 198 699 31162028 31162528 4.680000e-162 582.0
38 TraesCS5D01G164300 chr6B 93.548 124 7 1 6704 6827 468734608 468734486 5.540000e-42 183.0
39 TraesCS5D01G164300 chr6B 97.059 34 1 0 747 780 281617633 281617600 3.500000e-04 58.4
40 TraesCS5D01G164300 chr6B 94.118 34 2 0 7195 7228 502300400 502300433 1.600000e-02 52.8
41 TraesCS5D01G164300 chr1A 91.837 196 14 2 2108 2302 208883936 208884130 1.150000e-68 272.0
42 TraesCS5D01G164300 chr1A 88.525 61 5 2 3510 3569 10070689 10070748 1.250000e-08 73.1
43 TraesCS5D01G164300 chr4D 90.816 196 15 3 2108 2301 408335434 408335240 8.950000e-65 259.0
44 TraesCS5D01G164300 chr4D 93.496 123 8 0 6703 6825 74079495 74079373 5.540000e-42 183.0
45 TraesCS5D01G164300 chr4D 91.765 85 7 0 3484 3568 493948218 493948302 1.590000e-22 119.0
46 TraesCS5D01G164300 chr2D 90.722 194 16 2 2110 2302 298287615 298287807 3.220000e-64 257.0
47 TraesCS5D01G164300 chr1D 90.256 195 17 2 2108 2301 150941575 150941768 4.160000e-63 254.0
48 TraesCS5D01G164300 chr2B 90.206 194 17 2 2110 2302 363924720 363924528 1.500000e-62 252.0
49 TraesCS5D01G164300 chr2B 89.500 200 18 3 2108 2306 331019016 331018819 5.390000e-62 250.0
50 TraesCS5D01G164300 chr2B 97.059 34 1 0 747 780 396925036 396925069 3.500000e-04 58.4
51 TraesCS5D01G164300 chr1B 89.796 196 17 3 2108 2302 586290693 586290500 1.940000e-61 248.0
52 TraesCS5D01G164300 chr1B 97.059 136 4 0 1 136 558229947 558230082 7.020000e-56 230.0
53 TraesCS5D01G164300 chr4A 96.454 141 5 0 1 141 584226363 584226223 5.430000e-57 233.0
54 TraesCS5D01G164300 chr4B 97.015 134 4 0 1 134 633304247 633304114 9.080000e-55 226.0
55 TraesCS5D01G164300 chr4B 94.074 135 2 1 1 135 633301263 633301135 5.500000e-47 200.0
56 TraesCS5D01G164300 chr4B 92.800 125 8 1 6703 6827 146469359 146469236 7.170000e-41 180.0
57 TraesCS5D01G164300 chr7D 93.600 125 7 1 6703 6827 34756875 34756998 1.540000e-42 185.0
58 TraesCS5D01G164300 chr2A 92.857 126 8 1 6702 6827 141506326 141506450 1.990000e-41 182.0
59 TraesCS5D01G164300 chr2A 89.655 58 2 3 731 786 744906371 744906316 4.500000e-08 71.3
60 TraesCS5D01G164300 chr7B 92.742 124 9 0 6704 6827 437669576 437669699 7.170000e-41 180.0
61 TraesCS5D01G164300 chr7B 90.076 131 13 0 6 136 208843991 208843861 4.310000e-38 171.0
62 TraesCS5D01G164300 chr7B 88.889 72 6 2 3500 3570 588875306 588875236 4.470000e-13 87.9
63 TraesCS5D01G164300 chr6A 92.742 124 8 1 6703 6826 538097822 538097700 2.580000e-40 178.0
64 TraesCS5D01G164300 chr3D 91.954 87 7 0 3484 3570 66406689 66406775 1.230000e-23 122.0
65 TraesCS5D01G164300 chr3D 86.842 76 3 6 718 789 447611996 447612068 2.690000e-10 78.7
66 TraesCS5D01G164300 chr3D 97.059 34 0 1 7196 7228 357103968 357103935 1.000000e-03 56.5


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 TraesCS5D01G164300 chr5D 255688917 255697903 8986 True 7972.000000 12608 100.00000 1 8987 2 chr5D.!!$R4 8986
1 TraesCS5D01G164300 chr5A 339741163 339749220 8057 True 2989.750000 5770 93.55875 821 8985 4 chr5A.!!$R2 8164
2 TraesCS5D01G164300 chr5B 289579870 289584600 4730 True 974.833333 1629 89.92050 821 5926 6 chr5B.!!$R5 5105
3 TraesCS5D01G164300 chr5B 289574078 289575177 1099 True 862.000000 1190 94.56250 5921 8145 2 chr5B.!!$R4 2224
4 TraesCS5D01G164300 chr5B 289566631 289567617 986 True 642.500000 1129 93.67750 8144 8985 2 chr5B.!!$R3 841
5 TraesCS5D01G164300 chr5B 211148389 211148960 571 False 516.000000 516 83.24700 131 699 1 chr5B.!!$F2 568
6 TraesCS5D01G164300 chr3B 151199797 151200456 659 True 817.000000 817 89.07200 131 792 1 chr3B.!!$R1 661
7 TraesCS5D01G164300 chr3A 99482286 99482856 570 False 706.000000 706 88.94600 131 708 1 chr3A.!!$F1 577
8 TraesCS5D01G164300 chr6B 31224544 31225044 500 False 604.000000 604 88.44600 198 699 1 chr6B.!!$F2 501
9 TraesCS5D01G164300 chr6B 31162028 31162528 500 False 582.000000 582 87.64900 198 699 1 chr6B.!!$F1 501
10 TraesCS5D01G164300 chr4B 633301135 633304247 3112 True 213.000000 226 95.54450 1 135 2 chr4B.!!$R2 134

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
804 824 0.034896 GAAAGTGTTCGGGCTCCTGA 59.965 55.000 0.00 0.00 0.00 3.86 F
807 827 0.036010 AGTGTTCGGGCTCCTGATTG 60.036 55.000 0.00 0.00 0.00 2.67 F
2107 2149 0.106519 GGCTAGGCAATCCACACCAT 60.107 55.000 12.16 0.00 33.74 3.55 F
3345 4388 0.391597 TCGTTGAGCCTCGGTTTTCT 59.608 50.000 0.00 0.00 0.00 2.52 F
4891 5996 0.870393 ACTGTGCTTGTCAATGCTCG 59.130 50.000 8.01 0.00 0.00 5.03 F
5730 7193 1.178534 AGTTTGTTCCCCATGCGTGG 61.179 55.000 18.73 18.73 45.61 4.94 F
6522 8002 1.075536 CAGTTAAAAGGCACTCCCCCT 59.924 52.381 0.00 0.00 38.49 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2185 0.686789 AAAATTGCTGTTGCCCCCTC 59.313 50.000 0.00 0.0 38.71 4.30 R
2170 2213 1.270550 CAAGTCCTGGCTTTCGCAATT 59.729 47.619 1.37 0.0 38.10 2.32 R
3520 4604 1.064825 ACTGGGGGAACTTGTACTGG 58.935 55.000 0.00 0.0 0.00 4.00 R
5025 6156 2.048222 TTCGCAAGTGGAGCCGAG 60.048 61.111 0.00 0.0 39.48 4.63 R
6522 8002 1.889829 CCGCACCTTACATTTTGGGAA 59.110 47.619 0.00 0.0 0.00 3.97 R
7518 9205 1.089920 CCTGATGCTTTCTTCCGGTG 58.910 55.000 0.00 0.0 0.00 4.94 R
8171 9970 0.250727 AGCGTTAAGGCTCCAAGCAA 60.251 50.000 16.67 0.0 44.75 3.91 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
69 70 3.742369 ACAACCGTACACCGAATAAACAG 59.258 43.478 0.00 0.00 39.56 3.16
82 83 6.833839 CCGAATAAACAGACAAATCGGTTAA 58.166 36.000 3.30 0.00 41.68 2.01
181 182 3.917760 CGACCTCCATCTCCCGCC 61.918 72.222 0.00 0.00 0.00 6.13
196 198 2.962569 GCCCGGCCAAGAAAAGAC 59.037 61.111 2.24 0.00 0.00 3.01
360 362 2.367202 GCCATCTCCCAACTCCGGA 61.367 63.158 2.93 2.93 0.00 5.14
560 572 2.443016 CCTCCGCTGCTACTCCCT 60.443 66.667 0.00 0.00 0.00 4.20
565 577 2.671070 GCTGCTACTCCCTTGCCA 59.329 61.111 0.00 0.00 0.00 4.92
617 629 1.896660 GCCGCCACACCAGAAGAAA 60.897 57.895 0.00 0.00 0.00 2.52
722 742 0.909610 CTGGGGTAGCACAAGGAGGA 60.910 60.000 0.00 0.00 0.00 3.71
792 812 1.489560 CGGGAGGAAGGGGAAAGTGT 61.490 60.000 0.00 0.00 0.00 3.55
793 813 0.778083 GGGAGGAAGGGGAAAGTGTT 59.222 55.000 0.00 0.00 0.00 3.32
794 814 1.271982 GGGAGGAAGGGGAAAGTGTTC 60.272 57.143 0.00 0.00 0.00 3.18
795 815 1.610886 GGAGGAAGGGGAAAGTGTTCG 60.611 57.143 0.00 0.00 34.28 3.95
796 816 0.400594 AGGAAGGGGAAAGTGTTCGG 59.599 55.000 0.00 0.00 34.28 4.30
797 817 0.608308 GGAAGGGGAAAGTGTTCGGG 60.608 60.000 0.00 0.00 34.28 5.14
798 818 1.228459 AAGGGGAAAGTGTTCGGGC 60.228 57.895 0.00 0.00 34.28 6.13
799 819 1.716028 AAGGGGAAAGTGTTCGGGCT 61.716 55.000 0.00 0.00 34.28 5.19
800 820 1.674651 GGGGAAAGTGTTCGGGCTC 60.675 63.158 0.00 0.00 34.28 4.70
801 821 1.674651 GGGAAAGTGTTCGGGCTCC 60.675 63.158 0.00 0.00 34.28 4.70
802 822 1.375326 GGAAAGTGTTCGGGCTCCT 59.625 57.895 0.00 0.00 34.28 3.69
803 823 0.955919 GGAAAGTGTTCGGGCTCCTG 60.956 60.000 0.00 0.00 34.28 3.86
804 824 0.034896 GAAAGTGTTCGGGCTCCTGA 59.965 55.000 0.00 0.00 0.00 3.86
805 825 0.693049 AAAGTGTTCGGGCTCCTGAT 59.307 50.000 0.00 0.00 0.00 2.90
806 826 0.693049 AAGTGTTCGGGCTCCTGATT 59.307 50.000 0.00 0.00 0.00 2.57
807 827 0.036010 AGTGTTCGGGCTCCTGATTG 60.036 55.000 0.00 0.00 0.00 2.67
808 828 1.377202 TGTTCGGGCTCCTGATTGC 60.377 57.895 0.00 0.00 0.00 3.56
809 829 2.125147 TTCGGGCTCCTGATTGCG 60.125 61.111 0.00 0.00 0.00 4.85
810 830 2.954684 TTCGGGCTCCTGATTGCGT 61.955 57.895 0.00 0.00 0.00 5.24
811 831 3.197790 CGGGCTCCTGATTGCGTG 61.198 66.667 0.00 0.00 0.00 5.34
812 832 2.045926 GGGCTCCTGATTGCGTGT 60.046 61.111 0.00 0.00 0.00 4.49
813 833 2.401766 GGGCTCCTGATTGCGTGTG 61.402 63.158 0.00 0.00 0.00 3.82
814 834 2.401766 GGCTCCTGATTGCGTGTGG 61.402 63.158 0.00 0.00 0.00 4.17
815 835 1.375908 GCTCCTGATTGCGTGTGGA 60.376 57.895 0.00 0.00 0.00 4.02
816 836 0.955428 GCTCCTGATTGCGTGTGGAA 60.955 55.000 0.00 0.00 0.00 3.53
817 837 1.081892 CTCCTGATTGCGTGTGGAAG 58.918 55.000 0.00 0.00 0.00 3.46
818 838 0.321564 TCCTGATTGCGTGTGGAAGG 60.322 55.000 0.00 0.00 0.00 3.46
819 839 0.606401 CCTGATTGCGTGTGGAAGGT 60.606 55.000 0.00 0.00 0.00 3.50
948 975 0.179067 TACAAATGGATCCGACGGCC 60.179 55.000 9.66 6.28 0.00 6.13
988 1015 2.554462 GGAGAAAAGGCACCAAGTCTTC 59.446 50.000 0.00 0.00 42.53 2.87
1262 1289 4.449968 GGGAGGAGATGAGATAGAAGGGAA 60.450 50.000 0.00 0.00 0.00 3.97
1344 1371 1.257750 TGCAGAAGCTCTTCCGCCTA 61.258 55.000 13.43 0.00 41.09 3.93
1428 1457 4.497291 AGGATTTGGTTGACGCCTAATA 57.503 40.909 0.00 0.00 34.90 0.98
1432 1461 5.977129 GGATTTGGTTGACGCCTAATATTTG 59.023 40.000 0.00 0.00 34.90 2.32
1548 1577 4.072131 GGCTACTGAAGGAAACACAATCA 58.928 43.478 0.00 0.00 0.00 2.57
1595 1624 7.325725 ACCCTACTTACTGTACCTCAAAATT 57.674 36.000 0.00 0.00 0.00 1.82
1725 1754 4.635765 GGTGTGCTATGTCTTCTTTGCATA 59.364 41.667 0.00 0.00 33.90 3.14
1802 1831 6.126409 AGGTTTCACTTGGTAGTTCATGAAA 58.874 36.000 10.35 0.00 30.26 2.69
1901 1931 7.360113 TGCACTCATAAACTACCAGATGATA 57.640 36.000 0.00 0.00 0.00 2.15
1902 1932 7.791029 TGCACTCATAAACTACCAGATGATAA 58.209 34.615 0.00 0.00 0.00 1.75
1903 1933 8.432013 TGCACTCATAAACTACCAGATGATAAT 58.568 33.333 0.00 0.00 0.00 1.28
2051 2091 6.946340 TGAGAGATTTGTTAAGCTCCATACA 58.054 36.000 0.00 0.00 45.68 2.29
2062 2102 2.169352 AGCTCCATACACTAGCCAACAG 59.831 50.000 0.00 0.00 36.92 3.16
2099 2141 0.258774 TGGGAAAGGGCTAGGCAATC 59.741 55.000 19.14 11.99 0.00 2.67
2107 2149 0.106519 GGCTAGGCAATCCACACCAT 60.107 55.000 12.16 0.00 33.74 3.55
2143 2185 2.968574 AGAGGCCTATACATGGACACAG 59.031 50.000 4.42 0.00 34.31 3.66
2151 2193 2.204136 ATGGACACAGAGGGGGCA 60.204 61.111 0.00 0.00 0.00 5.36
2226 2269 1.086696 CCCTGACACCATGTTAAGCG 58.913 55.000 0.00 0.00 0.00 4.68
2256 2299 1.480545 AGCCAACACAACCAAAAGTCC 59.519 47.619 0.00 0.00 0.00 3.85
2278 2321 3.744530 CGAACTTATGGAAAGGGCTAGGG 60.745 52.174 0.00 0.00 0.00 3.53
2448 3459 3.139850 TCATGCACAAATTTGCCAAAGG 58.860 40.909 18.12 9.49 42.25 3.11
2474 3485 1.267533 GCGTTCCCGTTTTGTTACCAT 59.732 47.619 0.00 0.00 36.15 3.55
2836 3866 1.436600 AGAAGAATGCTGTGACTGCG 58.563 50.000 9.85 0.00 0.00 5.18
3010 4040 3.615937 CAGACACATACACACTCATCAGC 59.384 47.826 0.00 0.00 0.00 4.26
3279 4322 8.993121 GTCATTACTGGAACCAGACATATAATG 58.007 37.037 25.03 23.01 46.30 1.90
3345 4388 0.391597 TCGTTGAGCCTCGGTTTTCT 59.608 50.000 0.00 0.00 0.00 2.52
3502 4586 8.475331 AAAAACACTCCGTCTGTACTATAATG 57.525 34.615 0.00 0.00 0.00 1.90
3520 4604 2.626780 GCTTGTCGCTGGGGGAAAC 61.627 63.158 0.00 0.00 35.14 2.78
3538 4622 1.064825 ACCAGTACAAGTTCCCCCAG 58.935 55.000 0.00 0.00 0.00 4.45
3539 4623 1.064825 CCAGTACAAGTTCCCCCAGT 58.935 55.000 0.00 0.00 0.00 4.00
3717 4804 2.302260 TCATTGTTGAAGGTTTCGGCA 58.698 42.857 0.00 0.00 0.00 5.69
4059 5146 6.868339 ACAGTGCATAATAAAGGTTTTCTTGC 59.132 34.615 0.00 0.00 35.55 4.01
4121 5208 1.315257 ATGTGCTTGCCCCGATGTTC 61.315 55.000 0.00 0.00 0.00 3.18
4494 5582 7.234384 GTCTCTGTTGGTAATTCATGTTTACG 58.766 38.462 12.15 0.00 31.66 3.18
4891 5996 0.870393 ACTGTGCTTGTCAATGCTCG 59.130 50.000 8.01 0.00 0.00 5.03
5025 6156 4.141688 CCTAGACATCCCAAGGGTTTACTC 60.142 50.000 4.80 0.00 36.47 2.59
5295 6435 9.817809 TGTAGACAGGTGATTCAATTATAGAAC 57.182 33.333 0.00 0.00 0.00 3.01
5459 6851 5.601662 ACTCTTTGTTCTTTCTCATGTCGA 58.398 37.500 0.00 0.00 0.00 4.20
5518 6972 8.795842 TTGTATCCCTTCGTTTATTTGTATGT 57.204 30.769 0.00 0.00 0.00 2.29
5730 7193 1.178534 AGTTTGTTCCCCATGCGTGG 61.179 55.000 18.73 18.73 45.61 4.94
5743 7206 1.307355 TGCGTGGCAGATCACCAATG 61.307 55.000 8.91 6.51 39.39 2.82
6070 7535 5.482526 TGTTAGAGCTGGTCCAAATACTACA 59.517 40.000 2.76 0.00 0.00 2.74
6128 7593 2.547123 ATCTTGCCCCCGAGGTAGGT 62.547 60.000 0.00 0.00 38.26 3.08
6164 7629 9.134734 TCTTGTCTGTTGAAAAACAAACATTAC 57.865 29.630 0.00 0.00 40.36 1.89
6290 7760 5.106555 CCAGTAGTGTAAGAATGCCAAACAG 60.107 44.000 0.00 0.00 0.00 3.16
6301 7771 2.992593 TGCCAAACAGTACAAGTCACA 58.007 42.857 0.00 0.00 0.00 3.58
6339 7809 4.103153 ACTGATGAGAAACAGACTTTCCCA 59.897 41.667 0.00 0.00 37.54 4.37
6344 7814 5.065914 TGAGAAACAGACTTTCCCAGATTG 58.934 41.667 0.00 0.00 0.00 2.67
6362 7832 6.294342 CCAGATTGAGTTTCAACATGACACAT 60.294 38.462 0.00 0.00 39.45 3.21
6385 7855 9.106070 ACATTTTTATATGAGGACGTTACCTTC 57.894 33.333 0.00 0.00 40.73 3.46
6454 7924 3.940209 TGACATCAATTTGCAGTTCCC 57.060 42.857 0.00 0.00 0.00 3.97
6477 7947 6.093404 CCCTGCGTCACAATATACTGTATAG 58.907 44.000 12.61 3.70 0.00 1.31
6522 8002 1.075536 CAGTTAAAAGGCACTCCCCCT 59.924 52.381 0.00 0.00 38.49 4.79
6532 8012 1.560505 CACTCCCCCTTCCCAAAATG 58.439 55.000 0.00 0.00 0.00 2.32
6542 8022 1.540267 TCCCAAAATGTAAGGTGCGG 58.460 50.000 0.00 0.00 0.00 5.69
6546 8026 3.119637 CCCAAAATGTAAGGTGCGGTTAG 60.120 47.826 0.00 0.00 0.00 2.34
6558 8038 2.544480 GCGGTTAGCTTTTGATGGTC 57.456 50.000 0.00 0.00 44.04 4.02
6560 8040 2.488153 GCGGTTAGCTTTTGATGGTCTT 59.512 45.455 0.00 0.00 44.04 3.01
6561 8041 3.687698 GCGGTTAGCTTTTGATGGTCTTA 59.312 43.478 0.00 0.00 44.04 2.10
6562 8042 4.155280 GCGGTTAGCTTTTGATGGTCTTAA 59.845 41.667 0.00 0.00 44.04 1.85
6563 8043 5.673818 GCGGTTAGCTTTTGATGGTCTTAAG 60.674 44.000 0.00 0.00 44.04 1.85
6566 8046 6.655425 GGTTAGCTTTTGATGGTCTTAAGTCT 59.345 38.462 1.63 0.00 0.00 3.24
6567 8047 7.822822 GGTTAGCTTTTGATGGTCTTAAGTCTA 59.177 37.037 1.63 0.00 0.00 2.59
6568 8048 9.384764 GTTAGCTTTTGATGGTCTTAAGTCTAT 57.615 33.333 1.63 0.00 0.00 1.98
6569 8049 7.856145 AGCTTTTGATGGTCTTAAGTCTATG 57.144 36.000 3.45 0.00 0.00 2.23
6570 8050 7.624549 AGCTTTTGATGGTCTTAAGTCTATGA 58.375 34.615 3.45 0.00 0.00 2.15
6571 8051 8.270744 AGCTTTTGATGGTCTTAAGTCTATGAT 58.729 33.333 3.45 0.00 0.00 2.45
6572 8052 8.897752 GCTTTTGATGGTCTTAAGTCTATGATT 58.102 33.333 3.45 0.00 0.00 2.57
6576 8056 9.958180 TTGATGGTCTTAAGTCTATGATTTTGA 57.042 29.630 3.45 0.00 0.00 2.69
6577 8057 9.383519 TGATGGTCTTAAGTCTATGATTTTGAC 57.616 33.333 3.45 0.00 0.00 3.18
6579 8059 9.606631 ATGGTCTTAAGTCTATGATTTTGACTC 57.393 33.333 1.63 0.00 39.78 3.36
6580 8060 7.759886 TGGTCTTAAGTCTATGATTTTGACTCG 59.240 37.037 1.63 0.00 39.78 4.18
6582 8062 9.522804 GTCTTAAGTCTATGATTTTGACTCGAT 57.477 33.333 1.63 0.00 39.78 3.59
6681 8359 8.169977 ACAACACCATTCATATATGTCCAATC 57.830 34.615 12.42 0.00 0.00 2.67
6793 8479 7.982371 AGCACACTAAAACGTGTCTATATAC 57.018 36.000 0.00 0.00 45.74 1.47
6815 8501 8.786826 ATACATCCGATTCACAAAAAGAGTTA 57.213 30.769 0.00 0.00 0.00 2.24
7226 8912 2.423538 CGCCTTACATTTTGGGAAGGAG 59.576 50.000 8.35 0.92 36.98 3.69
7248 8934 3.551485 GGTGCATCAAACAAGTGTGAAAC 59.449 43.478 0.00 0.00 37.35 2.78
7263 8949 5.236478 AGTGTGAAACGTTATGTGGAGAAAG 59.764 40.000 0.00 0.00 42.39 2.62
7266 8952 6.485313 TGTGAAACGTTATGTGGAGAAAGAAT 59.515 34.615 0.00 0.00 42.39 2.40
7267 8953 7.012894 TGTGAAACGTTATGTGGAGAAAGAATT 59.987 33.333 0.00 0.00 42.39 2.17
7292 8978 6.014584 TCAGTTAGTGAAAACCAGAGCATAGA 60.015 38.462 0.00 0.00 29.64 1.98
7378 9065 7.492524 TCTAGCATTACAGTGTGATCTTTAGG 58.507 38.462 5.88 0.00 0.00 2.69
7399 9086 3.201290 GTTGCCCTGAGTGATGAGTATG 58.799 50.000 0.00 0.00 0.00 2.39
7487 9174 3.608316 TTGGGGTTTGCTAATGATTGC 57.392 42.857 0.00 0.00 0.00 3.56
7618 9307 3.140144 ACCTGATTTCTCCTGAAAACCCA 59.860 43.478 0.00 0.00 44.22 4.51
7782 9580 0.895559 CCTTTGGTCTTGTCCTGGGC 60.896 60.000 0.00 0.00 0.00 5.36
8028 9827 1.226323 CTGTTCTCTACGCCGACCG 60.226 63.158 0.00 0.00 44.21 4.79
8058 9857 2.079158 CGGATGATGTGTTGCTCAAGT 58.921 47.619 0.00 0.00 0.00 3.16
8171 9970 7.961351 TCACTATCCACCACATTTTCATTTTT 58.039 30.769 0.00 0.00 0.00 1.94
8205 10004 2.674796 ACGCTCAAGGGATGTACTTC 57.325 50.000 0.59 0.10 0.00 3.01
8237 10036 6.206395 ACATTGTTTTCAATCGGCATCATA 57.794 33.333 0.00 0.00 46.18 2.15
8243 10042 7.639039 TGTTTTCAATCGGCATCATAGAATAC 58.361 34.615 0.00 0.00 0.00 1.89
8249 10048 5.060662 TCGGCATCATAGAATACACTAGC 57.939 43.478 0.00 0.00 0.00 3.42
8354 10313 6.528537 ACATGGTCAAAATGCAGCTTATTA 57.471 33.333 0.00 0.00 0.00 0.98
8355 10314 7.116075 ACATGGTCAAAATGCAGCTTATTAT 57.884 32.000 0.00 0.00 0.00 1.28
8356 10315 7.558604 ACATGGTCAAAATGCAGCTTATTATT 58.441 30.769 0.00 0.00 0.00 1.40
8357 10316 7.707893 ACATGGTCAAAATGCAGCTTATTATTC 59.292 33.333 0.00 0.00 0.00 1.75
8388 10347 3.016031 TCTTGGCACGATTATTGCACAT 58.984 40.909 0.00 0.00 42.12 3.21
8499 10458 1.556911 TCTCCTTCATCAGCCTTCACC 59.443 52.381 0.00 0.00 0.00 4.02
8500 10459 1.280133 CTCCTTCATCAGCCTTCACCA 59.720 52.381 0.00 0.00 0.00 4.17
8504 10463 2.408271 TCATCAGCCTTCACCATGTC 57.592 50.000 0.00 0.00 0.00 3.06
8555 10516 2.260822 AGGTAGAGCCAGAAAAGCAGA 58.739 47.619 0.00 0.00 40.61 4.26
8709 10670 0.600255 GTCCCAACCCTATCGATGCG 60.600 60.000 8.54 0.00 0.00 4.73
8820 10784 1.075970 CTCCTCCCTCGGACCATCA 60.076 63.158 0.00 0.00 0.00 3.07
8985 10949 4.731853 TCCCTGCCATCCCGGTCA 62.732 66.667 0.00 0.00 36.97 4.02
8986 10950 4.489771 CCCTGCCATCCCGGTCAC 62.490 72.222 0.00 0.00 36.97 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 0.383368 CGAAAAACCGAACCGAACCG 60.383 55.000 0.00 0.00 0.00 4.44
100 101 1.202166 ACACCGAAAACCGAAAAACCG 60.202 47.619 0.00 0.00 41.76 4.44
147 148 4.660938 GGGTTGCTTGCCCTCGGT 62.661 66.667 3.98 0.00 42.81 4.69
181 182 2.978018 GCGGTCTTTTCTTGGCCGG 61.978 63.158 8.81 0.00 42.34 6.13
196 198 1.372087 GAGATGGACCAAAGCTGCGG 61.372 60.000 0.00 0.06 0.00 5.69
290 292 2.440980 GGTCCTTGGGCCATCTGC 60.441 66.667 7.26 0.00 40.16 4.26
467 479 4.329545 GCGGCTGGGTCAAGGTGA 62.330 66.667 0.00 0.00 0.00 4.02
709 729 0.615331 CAAGCCTCCTCCTTGTGCTA 59.385 55.000 0.00 0.00 35.97 3.49
715 735 3.721706 CCCGCAAGCCTCCTCCTT 61.722 66.667 0.00 0.00 0.00 3.36
773 793 1.299976 CACTTTCCCCTTCCTCCCG 59.700 63.158 0.00 0.00 0.00 5.14
792 812 2.125147 CGCAATCAGGAGCCCGAA 60.125 61.111 0.00 0.00 0.00 4.30
793 813 3.390521 ACGCAATCAGGAGCCCGA 61.391 61.111 0.00 0.00 0.00 5.14
794 814 3.197790 CACGCAATCAGGAGCCCG 61.198 66.667 0.00 0.00 0.00 6.13
795 815 2.045926 ACACGCAATCAGGAGCCC 60.046 61.111 0.00 0.00 0.00 5.19
796 816 2.401766 CCACACGCAATCAGGAGCC 61.402 63.158 0.00 0.00 0.00 4.70
797 817 0.955428 TTCCACACGCAATCAGGAGC 60.955 55.000 0.00 0.00 0.00 4.70
798 818 1.081892 CTTCCACACGCAATCAGGAG 58.918 55.000 0.00 0.00 0.00 3.69
799 819 0.321564 CCTTCCACACGCAATCAGGA 60.322 55.000 0.00 0.00 0.00 3.86
800 820 0.606401 ACCTTCCACACGCAATCAGG 60.606 55.000 0.00 0.00 0.00 3.86
801 821 2.093306 TACCTTCCACACGCAATCAG 57.907 50.000 0.00 0.00 0.00 2.90
802 822 2.027653 TGATACCTTCCACACGCAATCA 60.028 45.455 0.00 0.00 0.00 2.57
803 823 2.609459 CTGATACCTTCCACACGCAATC 59.391 50.000 0.00 0.00 0.00 2.67
804 824 2.632377 CTGATACCTTCCACACGCAAT 58.368 47.619 0.00 0.00 0.00 3.56
805 825 1.338674 CCTGATACCTTCCACACGCAA 60.339 52.381 0.00 0.00 0.00 4.85
806 826 0.249120 CCTGATACCTTCCACACGCA 59.751 55.000 0.00 0.00 0.00 5.24
807 827 0.462047 CCCTGATACCTTCCACACGC 60.462 60.000 0.00 0.00 0.00 5.34
808 828 1.137086 CTCCCTGATACCTTCCACACG 59.863 57.143 0.00 0.00 0.00 4.49
809 829 1.134371 GCTCCCTGATACCTTCCACAC 60.134 57.143 0.00 0.00 0.00 3.82
810 830 1.204146 GCTCCCTGATACCTTCCACA 58.796 55.000 0.00 0.00 0.00 4.17
811 831 1.204146 TGCTCCCTGATACCTTCCAC 58.796 55.000 0.00 0.00 0.00 4.02
812 832 1.965414 TTGCTCCCTGATACCTTCCA 58.035 50.000 0.00 0.00 0.00 3.53
813 833 3.117888 TGAATTGCTCCCTGATACCTTCC 60.118 47.826 0.00 0.00 0.00 3.46
814 834 4.156455 TGAATTGCTCCCTGATACCTTC 57.844 45.455 0.00 0.00 0.00 3.46
815 835 4.591321 TTGAATTGCTCCCTGATACCTT 57.409 40.909 0.00 0.00 0.00 3.50
816 836 4.166725 TGATTGAATTGCTCCCTGATACCT 59.833 41.667 0.00 0.00 0.00 3.08
817 837 4.276926 GTGATTGAATTGCTCCCTGATACC 59.723 45.833 0.00 0.00 0.00 2.73
818 838 5.128919 AGTGATTGAATTGCTCCCTGATAC 58.871 41.667 0.00 0.00 0.00 2.24
819 839 5.378230 AGTGATTGAATTGCTCCCTGATA 57.622 39.130 0.00 0.00 0.00 2.15
948 975 0.179073 CTTGTCTGCGGGTATCCCTG 60.179 60.000 3.25 0.00 42.67 4.45
952 979 1.112113 TCTCCTTGTCTGCGGGTATC 58.888 55.000 0.00 0.00 0.00 2.24
959 986 1.268079 GTGCCTTTTCTCCTTGTCTGC 59.732 52.381 0.00 0.00 0.00 4.26
961 988 1.494721 TGGTGCCTTTTCTCCTTGTCT 59.505 47.619 0.00 0.00 0.00 3.41
988 1015 1.363744 GTTGTCATTCAGAGCCGAGG 58.636 55.000 0.00 0.00 0.00 4.63
1060 1087 2.674563 TACGGTTGCTGCAGCCTTGT 62.675 55.000 34.64 26.90 41.18 3.16
1262 1289 2.185310 GATGGCGGTGGAGTTGGAGT 62.185 60.000 0.00 0.00 0.00 3.85
1411 1440 4.218635 TGCAAATATTAGGCGTCAACCAAA 59.781 37.500 7.33 0.00 0.00 3.28
1418 1447 4.468095 AATCGTGCAAATATTAGGCGTC 57.532 40.909 0.00 0.00 0.00 5.19
1428 1457 6.365839 CGAGCAATTAGATAATCGTGCAAAT 58.634 36.000 10.37 0.00 33.84 2.32
1432 1461 3.430218 AGCGAGCAATTAGATAATCGTGC 59.570 43.478 0.00 2.41 32.38 5.34
1548 1577 9.574516 GGGTATTCTATTGACAATAACTCCAAT 57.425 33.333 9.14 0.00 34.16 3.16
1582 1611 9.436957 GATTAGAGAACTGAATTTTGAGGTACA 57.563 33.333 0.00 0.00 0.00 2.90
1595 1624 3.621558 TCAGCTCCGATTAGAGAACTGA 58.378 45.455 0.00 0.00 35.82 3.41
1734 1763 9.407380 TGGAAGTGCAACAATATATAGAACAAT 57.593 29.630 0.00 0.00 41.43 2.71
1735 1764 8.800370 TGGAAGTGCAACAATATATAGAACAA 57.200 30.769 0.00 0.00 41.43 2.83
1736 1765 8.800370 TTGGAAGTGCAACAATATATAGAACA 57.200 30.769 0.00 0.00 41.43 3.18
1846 1876 0.850784 ACAAGGGCCAAACCTACACT 59.149 50.000 6.18 0.00 40.87 3.55
1852 1882 1.757423 ATGCACACAAGGGCCAAACC 61.757 55.000 6.18 0.00 37.93 3.27
1924 1962 6.152492 TGCAGTGTATTATTTCAAGAATGCCA 59.848 34.615 0.00 0.00 0.00 4.92
1925 1963 6.473455 GTGCAGTGTATTATTTCAAGAATGCC 59.527 38.462 0.00 0.00 0.00 4.40
2051 2091 4.278310 ACTTTTTGGTTCTGTTGGCTAGT 58.722 39.130 0.00 0.00 0.00 2.57
2062 2102 1.266989 CCAGCTCGGACTTTTTGGTTC 59.733 52.381 0.00 0.00 36.56 3.62
2107 2149 2.700897 GGCCTCTTGAGCTATACCTTGA 59.299 50.000 0.00 0.00 0.00 3.02
2143 2185 0.686789 AAAATTGCTGTTGCCCCCTC 59.313 50.000 0.00 0.00 38.71 4.30
2165 2208 3.128589 GTCCTGGCTTTCGCAATTTATCA 59.871 43.478 0.00 0.00 38.10 2.15
2170 2213 1.270550 CAAGTCCTGGCTTTCGCAATT 59.729 47.619 1.37 0.00 38.10 2.32
2226 2269 1.522668 TGTGTTGGCTAGTGCATGAC 58.477 50.000 0.00 0.00 41.91 3.06
2256 2299 3.467803 CCTAGCCCTTTCCATAAGTTCG 58.532 50.000 0.00 0.00 0.00 3.95
2278 2321 6.316140 TCTTGTTGAAGTGTATATGTGGATGC 59.684 38.462 0.00 0.00 0.00 3.91
2474 3485 7.684317 TTCCACCACCTCAAGTATATATTGA 57.316 36.000 0.00 4.00 35.45 2.57
3083 4113 7.970102 ACCAGGTTTCTCAGTTAAGTATTACA 58.030 34.615 0.00 0.00 0.00 2.41
3279 4322 5.186198 ACCATACAGCAAAGAGTATGAACC 58.814 41.667 12.66 0.00 46.55 3.62
3345 4388 1.523758 GAGAAGGCAGGCGAAAAAGA 58.476 50.000 0.00 0.00 0.00 2.52
3520 4604 1.064825 ACTGGGGGAACTTGTACTGG 58.935 55.000 0.00 0.00 0.00 4.00
3538 4622 4.929808 CCTCTGTACCACAATACTTGTCAC 59.070 45.833 0.00 0.00 43.23 3.67
3539 4623 4.020573 CCCTCTGTACCACAATACTTGTCA 60.021 45.833 0.00 0.00 43.23 3.58
3902 4989 9.233232 GAATTCCAAACACCAACGAATATTATC 57.767 33.333 0.00 0.00 0.00 1.75
4059 5146 3.264450 ACACCACCCTCCAAATAGAGAAG 59.736 47.826 0.00 0.00 35.82 2.85
4372 5460 4.126437 TCAATCTTGTGCTCGTCTCAAAA 58.874 39.130 0.00 0.00 0.00 2.44
4373 5461 3.727726 TCAATCTTGTGCTCGTCTCAAA 58.272 40.909 0.00 0.00 0.00 2.69
4374 5462 3.385193 TCAATCTTGTGCTCGTCTCAA 57.615 42.857 0.00 0.00 0.00 3.02
4375 5463 3.385193 TTCAATCTTGTGCTCGTCTCA 57.615 42.857 0.00 0.00 0.00 3.27
4380 5468 7.326789 ACAAATACAAATTCAATCTTGTGCTCG 59.673 33.333 7.71 0.00 36.47 5.03
4468 5556 6.575162 AAACATGAATTACCAACAGAGACC 57.425 37.500 0.00 0.00 0.00 3.85
4878 5983 5.967674 GGAATTCAATACGAGCATTGACAAG 59.032 40.000 7.93 0.00 42.99 3.16
4881 5986 4.518217 CGGAATTCAATACGAGCATTGAC 58.482 43.478 7.93 2.44 42.99 3.18
5025 6156 2.048222 TTCGCAAGTGGAGCCGAG 60.048 61.111 0.00 0.00 39.48 4.63
5112 6244 3.873361 TCTCTTGTCAGTGAAGTTGCTTG 59.127 43.478 0.00 0.00 0.00 4.01
5114 6246 3.827008 TCTCTTGTCAGTGAAGTTGCT 57.173 42.857 0.00 0.00 0.00 3.91
5295 6435 7.489113 GCAATTCAGTAAATACCCAATGTGAAG 59.511 37.037 0.00 0.00 0.00 3.02
5314 6561 2.354303 CCCACCTACAGTACGCAATTCA 60.354 50.000 0.00 0.00 0.00 2.57
5367 6614 1.202818 GCGGATAGAGGAAATTGCCCT 60.203 52.381 0.00 0.00 36.57 5.19
5454 6846 5.097742 AGGTATTGGATGAACAATCGACA 57.902 39.130 0.00 0.00 41.12 4.35
5459 6851 8.543293 AATGATCAAGGTATTGGATGAACAAT 57.457 30.769 0.00 0.00 43.13 2.71
5730 7193 2.410469 GCGCCATTGGTGATCTGC 59.590 61.111 20.37 3.77 34.74 4.26
5787 7250 4.262592 CCTGAAGGCATTGCTTTTTAGGTT 60.263 41.667 20.26 0.00 32.25 3.50
5891 7356 4.165950 ACAATGTCCCCAGCAATGTATAGA 59.834 41.667 0.00 0.00 29.27 1.98
6070 7535 4.008330 CTGTCAAAGCATCCTGAACAGAT 58.992 43.478 3.19 0.00 0.00 2.90
6301 7771 7.536159 TCTCATCAGTATCATAAGTCTGCAT 57.464 36.000 0.00 0.00 0.00 3.96
6317 7787 4.645535 TGGGAAAGTCTGTTTCTCATCAG 58.354 43.478 0.00 0.00 34.27 2.90
6335 7805 4.761739 GTCATGTTGAAACTCAATCTGGGA 59.238 41.667 0.00 0.00 38.79 4.37
6339 7809 6.889301 ATGTGTCATGTTGAAACTCAATCT 57.111 33.333 0.00 0.00 38.79 2.40
6374 7844 7.559590 TTATCTACTGGTAGAAGGTAACGTC 57.440 40.000 13.45 0.00 44.44 4.34
6454 7924 6.909909 TCTATACAGTATATTGTGACGCAGG 58.090 40.000 10.90 0.00 32.56 4.85
6490 7960 7.174426 AGTGCCTTTTAACTGGAGTAACATAAC 59.826 37.037 0.00 0.00 0.00 1.89
6522 8002 1.889829 CCGCACCTTACATTTTGGGAA 59.110 47.619 0.00 0.00 0.00 3.97
6532 8012 2.809696 TCAAAAGCTAACCGCACCTTAC 59.190 45.455 0.00 0.00 42.61 2.34
6542 8022 7.674471 AGACTTAAGACCATCAAAAGCTAAC 57.326 36.000 10.09 0.00 0.00 2.34
6546 8026 7.849804 TCATAGACTTAAGACCATCAAAAGC 57.150 36.000 10.09 0.00 0.00 3.51
6551 8031 9.383519 GTCAAAATCATAGACTTAAGACCATCA 57.616 33.333 10.09 0.00 0.00 3.07
6552 8032 9.606631 AGTCAAAATCATAGACTTAAGACCATC 57.393 33.333 10.09 0.00 39.45 3.51
6553 8033 9.606631 GAGTCAAAATCATAGACTTAAGACCAT 57.393 33.333 10.09 0.00 42.29 3.55
6554 8034 7.759886 CGAGTCAAAATCATAGACTTAAGACCA 59.240 37.037 10.09 0.00 42.29 4.02
6555 8035 7.974501 TCGAGTCAAAATCATAGACTTAAGACC 59.025 37.037 10.09 0.40 42.29 3.85
6556 8036 8.912787 TCGAGTCAAAATCATAGACTTAAGAC 57.087 34.615 10.09 2.62 42.29 3.01
6602 8082 9.573166 CCCCATGTCTTCATACTAATTTCATAA 57.427 33.333 0.00 0.00 32.47 1.90
6603 8083 7.665559 GCCCCATGTCTTCATACTAATTTCATA 59.334 37.037 0.00 0.00 32.47 2.15
6604 8084 6.491403 GCCCCATGTCTTCATACTAATTTCAT 59.509 38.462 0.00 0.00 32.47 2.57
6606 8086 5.827797 TGCCCCATGTCTTCATACTAATTTC 59.172 40.000 0.00 0.00 32.47 2.17
6610 8090 6.508030 TTATGCCCCATGTCTTCATACTAA 57.492 37.500 0.00 0.00 32.47 2.24
6612 8092 5.387113 TTTATGCCCCATGTCTTCATACT 57.613 39.130 0.00 0.00 32.47 2.12
6613 8093 6.655078 ATTTTATGCCCCATGTCTTCATAC 57.345 37.500 0.00 0.00 32.47 2.39
6616 8096 7.673641 AATAATTTTATGCCCCATGTCTTCA 57.326 32.000 0.00 0.00 0.00 3.02
6617 8097 7.041848 GCAAATAATTTTATGCCCCATGTCTTC 60.042 37.037 0.00 0.00 32.73 2.87
6618 8098 6.767423 GCAAATAATTTTATGCCCCATGTCTT 59.233 34.615 0.00 0.00 32.73 3.01
6619 8099 6.126825 TGCAAATAATTTTATGCCCCATGTCT 60.127 34.615 6.58 0.00 38.00 3.41
6620 8100 6.054295 TGCAAATAATTTTATGCCCCATGTC 58.946 36.000 6.58 0.00 38.00 3.06
6625 8301 5.289083 TCCTGCAAATAATTTTATGCCCC 57.711 39.130 6.58 0.00 38.00 5.80
6660 8337 7.991084 ACAGATTGGACATATATGAATGGTG 57.009 36.000 19.63 10.11 0.00 4.17
6701 8379 7.226918 TCCAAAACAACATATACTTGTGAACGA 59.773 33.333 0.00 0.00 32.07 3.85
6716 8402 9.149225 GTGCATATTGAAATATCCAAAACAACA 57.851 29.630 0.00 0.00 29.35 3.33
6793 8479 7.364522 TCTAACTCTTTTTGTGAATCGGATG 57.635 36.000 0.00 0.00 0.00 3.51
7181 8867 5.239525 GCACTTACTTTTCATGGTCTCAAGT 59.760 40.000 0.00 0.00 0.00 3.16
7182 8868 5.615544 CGCACTTACTTTTCATGGTCTCAAG 60.616 44.000 0.00 0.00 0.00 3.02
7183 8869 4.213270 CGCACTTACTTTTCATGGTCTCAA 59.787 41.667 0.00 0.00 0.00 3.02
7184 8870 3.745975 CGCACTTACTTTTCATGGTCTCA 59.254 43.478 0.00 0.00 0.00 3.27
7185 8871 3.424962 GCGCACTTACTTTTCATGGTCTC 60.425 47.826 0.30 0.00 0.00 3.36
7186 8872 2.484264 GCGCACTTACTTTTCATGGTCT 59.516 45.455 0.30 0.00 0.00 3.85
7187 8873 2.414161 GGCGCACTTACTTTTCATGGTC 60.414 50.000 10.83 0.00 0.00 4.02
7188 8874 1.539827 GGCGCACTTACTTTTCATGGT 59.460 47.619 10.83 0.00 0.00 3.55
7189 8875 1.812571 AGGCGCACTTACTTTTCATGG 59.187 47.619 10.83 0.00 0.00 3.66
7190 8876 3.559238 AAGGCGCACTTACTTTTCATG 57.441 42.857 10.83 0.00 37.74 3.07
7199 8885 2.490115 CCCAAAATGTAAGGCGCACTTA 59.510 45.455 10.83 11.90 40.64 2.24
7226 8912 3.435105 TTCACACTTGTTTGATGCACC 57.565 42.857 0.00 0.00 0.00 5.01
7248 8934 6.727824 ACTGAATTCTTTCTCCACATAACG 57.272 37.500 7.05 0.00 32.78 3.18
7263 8949 6.017109 TGCTCTGGTTTTCACTAACTGAATTC 60.017 38.462 0.00 0.00 38.74 2.17
7266 8952 4.776349 TGCTCTGGTTTTCACTAACTGAA 58.224 39.130 0.00 0.00 37.08 3.02
7267 8953 4.415881 TGCTCTGGTTTTCACTAACTGA 57.584 40.909 0.00 0.00 0.00 3.41
7292 8978 6.099125 ACTTTTAACCCATTTTACCTTGCTGT 59.901 34.615 0.00 0.00 0.00 4.40
7339 9025 6.697455 TGTAATGCTAGAAAACATAGAGAGCG 59.303 38.462 0.00 0.00 0.00 5.03
7378 9065 3.201290 CATACTCATCACTCAGGGCAAC 58.799 50.000 0.00 0.00 0.00 4.17
7399 9086 3.876320 TGGCATTCTTTTTCTTGGTTTGC 59.124 39.130 0.00 0.00 0.00 3.68
7454 9141 5.776716 AGCAAACCCCAATGATATAGAATGG 59.223 40.000 0.00 0.00 0.00 3.16
7487 9174 1.681264 GTTCCAACCAAGTGAACCCTG 59.319 52.381 0.00 0.00 33.85 4.45
7518 9205 1.089920 CCTGATGCTTTCTTCCGGTG 58.910 55.000 0.00 0.00 0.00 4.94
7618 9307 2.997897 GTGGACTCGGAGCTGGGT 60.998 66.667 4.58 0.00 0.00 4.51
7755 9553 1.217942 ACAAGACCAAAGGGAAGCCTT 59.782 47.619 0.00 0.00 38.05 4.35
8028 9827 4.046938 ACACATCATCCGTATCACAGTC 57.953 45.455 0.00 0.00 0.00 3.51
8058 9857 1.970640 TGAAGCTTCTGTGGCTGTAGA 59.029 47.619 26.09 0.00 40.19 2.59
8131 9930 7.148069 GGTGGATAGTGAATTCCCTAACAAAAG 60.148 40.741 2.27 0.00 0.00 2.27
8171 9970 0.250727 AGCGTTAAGGCTCCAAGCAA 60.251 50.000 16.67 0.00 44.75 3.91
8205 10004 7.009174 GCCGATTGAAAACAATGTAACCATTAG 59.991 37.037 0.00 0.00 39.28 1.73
8237 10036 7.721842 TCATACTTAGCTGAGCTAGTGTATTCT 59.278 37.037 25.44 13.25 42.34 2.40
8243 10042 4.981674 GCTTCATACTTAGCTGAGCTAGTG 59.018 45.833 14.49 13.44 42.34 2.74
8249 10048 7.226128 TCAATGATTGCTTCATACTTAGCTGAG 59.774 37.037 3.53 3.53 44.51 3.35
8354 10313 3.285484 GTGCCAAGATGAGATGTGGAAT 58.715 45.455 0.00 0.00 32.54 3.01
8355 10314 2.715046 GTGCCAAGATGAGATGTGGAA 58.285 47.619 0.00 0.00 32.54 3.53
8356 10315 1.405933 CGTGCCAAGATGAGATGTGGA 60.406 52.381 0.00 0.00 32.54 4.02
8357 10316 1.012086 CGTGCCAAGATGAGATGTGG 58.988 55.000 0.00 0.00 0.00 4.17
8479 10438 1.556911 GGTGAAGGCTGATGAAGGAGA 59.443 52.381 0.00 0.00 0.00 3.71
8480 10439 1.280133 TGGTGAAGGCTGATGAAGGAG 59.720 52.381 0.00 0.00 0.00 3.69
8499 10458 7.703298 TTTTGCATTTTTCTTGAGAGACATG 57.297 32.000 0.00 0.00 0.00 3.21
8531 10492 2.877708 GCTTTTCTGGCTCTACCTTGCT 60.878 50.000 0.00 0.00 40.22 3.91
8533 10494 2.746362 CTGCTTTTCTGGCTCTACCTTG 59.254 50.000 0.00 0.00 40.22 3.61
8555 10516 1.765230 TGTAACTTTGGCGGTTTGGT 58.235 45.000 0.00 0.00 0.00 3.67
8591 10552 7.665561 TTTTTCTTTTAACACTGCAAGCTTT 57.334 28.000 0.00 0.00 37.60 3.51
8625 10586 5.049828 CCAAGCTTAAAACCAACAAAGGAG 58.950 41.667 0.00 0.00 0.00 3.69
8679 10640 2.943036 GGTTGGGACCACTGAAGTAA 57.057 50.000 0.00 0.00 45.77 2.24
8709 10670 1.645034 TAGAGATGAACAAGCTGCGC 58.355 50.000 0.00 0.00 0.00 6.09
8757 10718 1.746991 GAAGAAGGGCAGCGGGAAG 60.747 63.158 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.