Multiple sequence alignment - TraesCS5D01G048900

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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 TraesCS5D01G048900 chr5D 100.000 3752 0 0 748 4499 46610719 46614470 0.000000e+00 6929.0
1 TraesCS5D01G048900 chr5D 80.807 1339 186 31 1120 2400 48656700 48658025 0.000000e+00 983.0
2 TraesCS5D01G048900 chr5D 92.690 342 21 4 3868 4205 46336049 46335708 1.450000e-134 490.0
3 TraesCS5D01G048900 chr5D 83.883 273 27 11 4219 4476 46329819 46329549 1.250000e-60 244.0
4 TraesCS5D01G048900 chr5D 86.624 157 12 6 4339 4491 46335568 46335417 1.000000e-36 165.0
5 TraesCS5D01G048900 chr5D 100.000 73 0 0 1 73 46609972 46610044 7.850000e-28 135.0
6 TraesCS5D01G048900 chr5D 98.182 55 1 0 2451 2505 48659887 48659941 3.700000e-16 97.1
7 TraesCS5D01G048900 chr5D 94.444 36 2 0 2860 2895 48660456 48660491 6.290000e-04 56.5
8 TraesCS5D01G048900 chr5B 93.135 2185 88 35 1524 3694 48873819 48871683 0.000000e+00 3147.0
9 TraesCS5D01G048900 chr5B 92.925 735 25 7 795 1527 48874558 48873849 0.000000e+00 1044.0
10 TraesCS5D01G048900 chr5B 91.954 522 34 6 3690 4205 48871507 48870988 0.000000e+00 725.0
11 TraesCS5D01G048900 chr5B 92.969 256 14 3 4196 4448 48870959 48870705 1.980000e-98 370.0
12 TraesCS5D01G048900 chr5B 81.818 264 31 11 4228 4476 47567188 47567449 5.900000e-49 206.0
13 TraesCS5D01G048900 chr5A 91.452 1088 50 15 1524 2596 37641228 37640169 0.000000e+00 1454.0
14 TraesCS5D01G048900 chr5A 79.798 1386 197 40 1216 2538 38118654 38120019 0.000000e+00 931.0
15 TraesCS5D01G048900 chr5A 91.340 485 25 10 2834 3305 37638230 37637750 0.000000e+00 647.0
16 TraesCS5D01G048900 chr5A 89.159 452 38 8 3763 4205 37637160 37636711 1.830000e-153 553.0
17 TraesCS5D01G048900 chr5A 89.277 401 32 7 3379 3770 37637754 37637356 4.040000e-135 492.0
18 TraesCS5D01G048900 chr5A 95.985 274 9 2 1255 1527 37641530 37641258 1.150000e-120 444.0
19 TraesCS5D01G048900 chr5A 93.644 236 13 2 2608 2842 37640189 37639955 7.160000e-93 351.0
20 TraesCS5D01G048900 chr5A 87.938 257 23 6 4195 4448 37636685 37636434 3.400000e-76 296.0
21 TraesCS5D01G048900 chr1D 82.609 230 29 6 2185 2409 328156911 328156688 4.590000e-45 193.0
22 TraesCS5D01G048900 chr1D 79.130 115 21 2 3436 3548 328881704 328881817 4.830000e-10 76.8
23 TraesCS5D01G048900 chr6B 83.028 218 29 6 2195 2409 334886593 334886381 1.650000e-44 191.0
24 TraesCS5D01G048900 chr1B 82.805 221 30 7 2192 2409 345543604 345543389 1.650000e-44 191.0
25 TraesCS5D01G048900 chr3A 81.223 229 32 5 2185 2409 196001980 196001759 1.660000e-39 174.0
26 TraesCS5D01G048900 chr7A 81.991 211 30 6 2193 2400 586470695 586470900 5.980000e-39 172.0
27 TraesCS5D01G048900 chr2A 92.982 57 4 0 2697 2753 24282221 24282165 2.880000e-12 84.2
28 TraesCS5D01G048900 chr2A 92.982 57 4 0 2701 2757 113408484 113408428 2.880000e-12 84.2
29 TraesCS5D01G048900 chr2B 97.872 47 1 0 2707 2753 39306796 39306842 1.040000e-11 82.4
30 TraesCS5D01G048900 chr6D 90.000 60 5 1 2697 2756 23010289 23010347 4.830000e-10 76.8
31 TraesCS5D01G048900 chr1A 80.612 98 19 0 3436 3533 425717265 425717362 4.830000e-10 76.8


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 TraesCS5D01G048900 chr5D 46609972 46614470 4498 False 3532.000000 6929 100.000000 1 4499 2 chr5D.!!$F1 4498
1 TraesCS5D01G048900 chr5D 48656700 48660491 3791 False 378.866667 983 91.144333 1120 2895 3 chr5D.!!$F2 1775
2 TraesCS5D01G048900 chr5D 46335417 46336049 632 True 327.500000 490 89.657000 3868 4491 2 chr5D.!!$R2 623
3 TraesCS5D01G048900 chr5B 48870705 48874558 3853 True 1321.500000 3147 92.745750 795 4448 4 chr5B.!!$R1 3653
4 TraesCS5D01G048900 chr5A 38118654 38120019 1365 False 931.000000 931 79.798000 1216 2538 1 chr5A.!!$F1 1322
5 TraesCS5D01G048900 chr5A 37636434 37641530 5096 True 605.285714 1454 91.256429 1255 4448 7 chr5A.!!$R1 3193

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
961 962 0.605083 CCAAGAGCAAAAAGGAGGGC 59.395 55.0 0.00 0.0 0.00 5.19 F
1306 1349 0.104855 ACCATGGGTCATCATCGACG 59.895 55.0 18.09 0.0 36.73 5.12 F
2618 4532 0.480252 AGAAAAGGGCTTGCTCCTGT 59.520 50.0 3.98 0.0 34.34 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 4513 0.480252 ACAGGAGCAAGCCCTTTTCT 59.520 50.0 0.16 0.0 0.00 2.52 R
3004 6707 0.251354 ACATAGCCTGTGACCAGCAG 59.749 55.0 0.00 0.0 36.48 4.24 R
3799 7898 0.249741 AATATGCGGTCTACGGGTGC 60.250 55.0 0.00 0.0 44.51 5.01 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
47 48 8.647256 TTCTATATTCCTAACTACCTAGTGCC 57.353 38.462 0.00 0.00 36.50 5.01
48 49 7.997915 TCTATATTCCTAACTACCTAGTGCCT 58.002 38.462 0.00 0.00 36.50 4.75
49 50 9.120658 TCTATATTCCTAACTACCTAGTGCCTA 57.879 37.037 0.00 0.00 36.50 3.93
50 51 9.750783 CTATATTCCTAACTACCTAGTGCCTAA 57.249 37.037 0.00 0.00 36.50 2.69
51 52 6.980416 ATTCCTAACTACCTAGTGCCTAAG 57.020 41.667 0.00 0.00 36.50 2.18
52 53 4.213513 TCCTAACTACCTAGTGCCTAAGC 58.786 47.826 0.00 0.00 36.50 3.09
53 54 4.079327 TCCTAACTACCTAGTGCCTAAGCT 60.079 45.833 0.00 0.00 40.80 3.74
54 55 4.650131 CCTAACTACCTAGTGCCTAAGCTT 59.350 45.833 3.48 3.48 40.80 3.74
55 56 4.739587 AACTACCTAGTGCCTAAGCTTC 57.260 45.455 0.00 0.00 40.80 3.86
56 57 3.709587 ACTACCTAGTGCCTAAGCTTCA 58.290 45.455 0.00 0.00 40.80 3.02
57 58 4.094476 ACTACCTAGTGCCTAAGCTTCAA 58.906 43.478 0.00 0.00 40.80 2.69
58 59 3.336138 ACCTAGTGCCTAAGCTTCAAC 57.664 47.619 0.00 0.00 40.80 3.18
59 60 2.637872 ACCTAGTGCCTAAGCTTCAACA 59.362 45.455 0.00 0.00 40.80 3.33
60 61 3.003480 CCTAGTGCCTAAGCTTCAACAC 58.997 50.000 0.00 9.85 40.80 3.32
61 62 2.638480 AGTGCCTAAGCTTCAACACA 57.362 45.000 20.98 6.10 40.80 3.72
62 63 2.930950 AGTGCCTAAGCTTCAACACAA 58.069 42.857 20.98 0.00 40.80 3.33
63 64 3.287222 AGTGCCTAAGCTTCAACACAAA 58.713 40.909 20.98 0.00 40.80 2.83
64 65 3.891366 AGTGCCTAAGCTTCAACACAAAT 59.109 39.130 20.98 4.92 40.80 2.32
65 66 5.070001 AGTGCCTAAGCTTCAACACAAATA 58.930 37.500 20.98 0.00 40.80 1.40
66 67 5.048713 AGTGCCTAAGCTTCAACACAAATAC 60.049 40.000 20.98 3.96 40.80 1.89
67 68 5.048713 GTGCCTAAGCTTCAACACAAATACT 60.049 40.000 0.00 0.00 40.80 2.12
68 69 6.148811 GTGCCTAAGCTTCAACACAAATACTA 59.851 38.462 0.00 0.00 40.80 1.82
69 70 6.884295 TGCCTAAGCTTCAACACAAATACTAT 59.116 34.615 0.00 0.00 40.80 2.12
70 71 7.148255 TGCCTAAGCTTCAACACAAATACTATG 60.148 37.037 0.00 0.00 40.80 2.23
71 72 7.679638 GCCTAAGCTTCAACACAAATACTATGG 60.680 40.741 0.00 0.00 35.50 2.74
72 73 5.567138 AGCTTCAACACAAATACTATGGC 57.433 39.130 0.00 0.00 0.00 4.40
764 765 4.436998 CCACAGAGCGGACGGTCC 62.437 72.222 17.38 17.38 42.97 4.46
765 766 3.680786 CACAGAGCGGACGGTCCA 61.681 66.667 25.80 0.00 42.97 4.02
766 767 2.915659 ACAGAGCGGACGGTCCAA 60.916 61.111 25.80 0.00 42.97 3.53
767 768 2.342279 CAGAGCGGACGGTCCAAA 59.658 61.111 25.80 0.00 42.97 3.28
768 769 2.027625 CAGAGCGGACGGTCCAAAC 61.028 63.158 25.80 14.64 42.97 2.93
769 770 3.110178 GAGCGGACGGTCCAAACG 61.110 66.667 25.80 13.21 35.91 3.60
770 771 3.562779 GAGCGGACGGTCCAAACGA 62.563 63.158 25.80 0.00 35.91 3.85
771 772 3.110178 GCGGACGGTCCAAACGAG 61.110 66.667 25.80 10.19 35.91 4.18
772 773 3.110178 CGGACGGTCCAAACGAGC 61.110 66.667 25.80 0.00 35.91 5.03
773 774 2.342648 GGACGGTCCAAACGAGCT 59.657 61.111 22.10 0.00 36.28 4.09
774 775 1.737008 GGACGGTCCAAACGAGCTC 60.737 63.158 22.10 2.73 36.28 4.09
775 776 2.049433 ACGGTCCAAACGAGCTCG 60.049 61.111 33.45 33.45 46.33 5.03
776 777 2.257371 CGGTCCAAACGAGCTCGA 59.743 61.111 40.58 17.00 43.02 4.04
777 778 1.801913 CGGTCCAAACGAGCTCGAG 60.802 63.158 40.58 27.13 43.02 4.04
778 779 2.095252 GGTCCAAACGAGCTCGAGC 61.095 63.158 40.58 30.01 43.02 5.03
789 790 4.056125 CTCGAGCGGAGTGGCACA 62.056 66.667 21.41 0.00 38.02 4.57
790 791 3.573772 CTCGAGCGGAGTGGCACAA 62.574 63.158 21.41 0.00 44.16 3.33
791 792 3.414700 CGAGCGGAGTGGCACAAC 61.415 66.667 21.41 12.98 44.16 3.32
792 793 2.280797 GAGCGGAGTGGCACAACA 60.281 61.111 21.41 0.00 44.16 3.33
793 794 1.891919 GAGCGGAGTGGCACAACAA 60.892 57.895 21.41 0.00 44.16 2.83
799 800 1.469079 GGAGTGGCACAACAACACAAC 60.469 52.381 21.41 0.00 44.16 3.32
803 804 2.602660 GTGGCACAACAACACAACAATC 59.397 45.455 13.86 0.00 44.16 2.67
824 825 1.027357 ATTCATGGCTTGCATCGACC 58.973 50.000 0.00 0.00 0.00 4.79
831 832 1.401539 GGCTTGCATCGACCTGTTTTC 60.402 52.381 0.00 0.00 0.00 2.29
848 849 6.006275 TGTTTTCAAATTGGAAAATGGGGA 57.994 33.333 20.89 0.00 45.43 4.81
852 853 3.643792 TCAAATTGGAAAATGGGGAACGT 59.356 39.130 0.00 0.00 0.00 3.99
863 864 2.667470 TGGGGAACGTTTTTGGATTCA 58.333 42.857 0.46 0.00 0.00 2.57
890 891 8.489990 AATTTCAAATTGACACAATTCACACA 57.510 26.923 9.60 0.00 0.00 3.72
891 892 6.884096 TTCAAATTGACACAATTCACACAC 57.116 33.333 9.60 0.00 0.00 3.82
892 893 5.958955 TCAAATTGACACAATTCACACACA 58.041 33.333 9.60 0.00 0.00 3.72
893 894 5.804473 TCAAATTGACACAATTCACACACAC 59.196 36.000 9.60 0.00 0.00 3.82
894 895 4.979943 ATTGACACAATTCACACACACA 57.020 36.364 0.00 0.00 0.00 3.72
895 896 3.755965 TGACACAATTCACACACACAC 57.244 42.857 0.00 0.00 0.00 3.82
896 897 3.077359 TGACACAATTCACACACACACA 58.923 40.909 0.00 0.00 0.00 3.72
897 898 3.120025 TGACACAATTCACACACACACAC 60.120 43.478 0.00 0.00 0.00 3.82
898 899 2.816672 ACACAATTCACACACACACACA 59.183 40.909 0.00 0.00 0.00 3.72
899 900 3.170505 CACAATTCACACACACACACAC 58.829 45.455 0.00 0.00 0.00 3.82
940 941 4.649218 TCAAAAAGGAGGGAAAAGACCAAG 59.351 41.667 0.00 0.00 0.00 3.61
941 942 4.536295 AAAAGGAGGGAAAAGACCAAGA 57.464 40.909 0.00 0.00 0.00 3.02
942 943 3.510531 AAGGAGGGAAAAGACCAAGAC 57.489 47.619 0.00 0.00 0.00 3.01
943 944 1.705745 AGGAGGGAAAAGACCAAGACC 59.294 52.381 0.00 0.00 0.00 3.85
944 945 1.423921 GGAGGGAAAAGACCAAGACCA 59.576 52.381 0.00 0.00 0.00 4.02
945 946 2.158519 GGAGGGAAAAGACCAAGACCAA 60.159 50.000 0.00 0.00 0.00 3.67
947 948 2.783510 AGGGAAAAGACCAAGACCAAGA 59.216 45.455 0.00 0.00 0.00 3.02
948 949 3.149981 GGGAAAAGACCAAGACCAAGAG 58.850 50.000 0.00 0.00 0.00 2.85
949 950 2.554462 GGAAAAGACCAAGACCAAGAGC 59.446 50.000 0.00 0.00 0.00 4.09
950 951 3.214328 GAAAAGACCAAGACCAAGAGCA 58.786 45.455 0.00 0.00 0.00 4.26
951 952 3.297134 AAAGACCAAGACCAAGAGCAA 57.703 42.857 0.00 0.00 0.00 3.91
952 953 3.297134 AAGACCAAGACCAAGAGCAAA 57.703 42.857 0.00 0.00 0.00 3.68
954 955 3.631250 AGACCAAGACCAAGAGCAAAAA 58.369 40.909 0.00 0.00 0.00 1.94
955 956 3.633986 AGACCAAGACCAAGAGCAAAAAG 59.366 43.478 0.00 0.00 0.00 2.27
956 957 2.695147 ACCAAGACCAAGAGCAAAAAGG 59.305 45.455 0.00 0.00 0.00 3.11
957 958 2.958355 CCAAGACCAAGAGCAAAAAGGA 59.042 45.455 0.00 0.00 0.00 3.36
958 959 3.005155 CCAAGACCAAGAGCAAAAAGGAG 59.995 47.826 0.00 0.00 0.00 3.69
959 960 2.868899 AGACCAAGAGCAAAAAGGAGG 58.131 47.619 0.00 0.00 0.00 4.30
960 961 1.889170 GACCAAGAGCAAAAAGGAGGG 59.111 52.381 0.00 0.00 0.00 4.30
961 962 0.605083 CCAAGAGCAAAAAGGAGGGC 59.395 55.000 0.00 0.00 0.00 5.19
962 963 1.331214 CAAGAGCAAAAAGGAGGGCA 58.669 50.000 0.00 0.00 0.00 5.36
963 964 1.000171 CAAGAGCAAAAAGGAGGGCAC 60.000 52.381 0.00 0.00 0.00 5.01
964 965 0.890996 AGAGCAAAAAGGAGGGCACG 60.891 55.000 0.00 0.00 0.00 5.34
965 966 2.049156 GCAAAAAGGAGGGCACGC 60.049 61.111 0.00 0.00 0.00 5.34
1028 1029 0.321653 CAACCTCTACACCCCTGCAC 60.322 60.000 0.00 0.00 0.00 4.57
1306 1349 0.104855 ACCATGGGTCATCATCGACG 59.895 55.000 18.09 0.00 36.73 5.12
1310 1353 1.592669 GGGTCATCATCGACGGCAG 60.593 63.158 0.00 0.00 36.73 4.85
1569 1645 3.585428 AACCCCATCACCGGCCAA 61.585 61.111 0.00 0.00 0.00 4.52
1647 1732 1.763770 CCTCCTCACCAAAGCAGGT 59.236 57.895 0.00 0.00 44.48 4.00
1779 1867 3.604667 CTTGGCCTGCCGTGCAAA 61.605 61.111 3.32 0.00 38.41 3.68
1797 1885 4.077184 CCGCCGCTCAAGTGGGTA 62.077 66.667 11.41 0.00 45.52 3.69
1815 1903 3.202151 GGGTAATGGAGATGAACCAGGAA 59.798 47.826 0.00 0.00 40.89 3.36
2505 4416 5.717078 ACACCGTCTTACTGTAGATTGAA 57.283 39.130 0.00 0.00 0.00 2.69
2506 4417 6.092955 ACACCGTCTTACTGTAGATTGAAA 57.907 37.500 0.00 0.00 0.00 2.69
2507 4418 6.698380 ACACCGTCTTACTGTAGATTGAAAT 58.302 36.000 0.00 0.00 0.00 2.17
2508 4419 7.159372 ACACCGTCTTACTGTAGATTGAAATT 58.841 34.615 0.00 0.00 0.00 1.82
2509 4420 8.308931 ACACCGTCTTACTGTAGATTGAAATTA 58.691 33.333 0.00 0.00 0.00 1.40
2591 4505 2.057137 TGTGCTTGCTCCTGTTCTTT 57.943 45.000 0.00 0.00 0.00 2.52
2615 4529 4.600692 TTTTTAGAAAAGGGCTTGCTCC 57.399 40.909 0.00 0.00 0.00 4.70
2616 4530 3.525800 TTTAGAAAAGGGCTTGCTCCT 57.474 42.857 0.00 0.00 35.88 3.69
2617 4531 2.496899 TAGAAAAGGGCTTGCTCCTG 57.503 50.000 3.98 0.00 34.34 3.86
2618 4532 0.480252 AGAAAAGGGCTTGCTCCTGT 59.520 50.000 3.98 0.00 34.34 4.00
2619 4533 1.133356 AGAAAAGGGCTTGCTCCTGTT 60.133 47.619 5.60 5.60 34.68 3.16
2620 4534 1.270826 GAAAAGGGCTTGCTCCTGTTC 59.729 52.381 13.39 13.39 40.29 3.18
2621 4535 0.480252 AAAGGGCTTGCTCCTGTTCT 59.520 50.000 3.98 0.00 34.34 3.01
2622 4536 0.480252 AAGGGCTTGCTCCTGTTCTT 59.520 50.000 3.98 0.00 34.34 2.52
2623 4537 1.362224 AGGGCTTGCTCCTGTTCTTA 58.638 50.000 2.63 0.00 32.53 2.10
2624 4538 1.918957 AGGGCTTGCTCCTGTTCTTAT 59.081 47.619 2.63 0.00 32.53 1.73
2625 4539 2.310052 AGGGCTTGCTCCTGTTCTTATT 59.690 45.455 2.63 0.00 32.53 1.40
2626 4540 3.092301 GGGCTTGCTCCTGTTCTTATTT 58.908 45.455 0.00 0.00 0.00 1.40
2627 4541 3.511540 GGGCTTGCTCCTGTTCTTATTTT 59.488 43.478 0.00 0.00 0.00 1.82
2628 4542 4.380973 GGGCTTGCTCCTGTTCTTATTTTC 60.381 45.833 0.00 0.00 0.00 2.29
2629 4543 4.460731 GGCTTGCTCCTGTTCTTATTTTCT 59.539 41.667 0.00 0.00 0.00 2.52
2792 4710 1.064060 GCGCCCATGAACTATGTTCAC 59.936 52.381 14.23 2.82 34.87 3.18
2799 4720 5.482006 CCATGAACTATGTTCACTCACAGA 58.518 41.667 14.23 0.00 34.87 3.41
2803 4724 4.848562 ACTATGTTCACTCACAGAACGA 57.151 40.909 0.00 0.00 46.34 3.85
2804 4725 4.547532 ACTATGTTCACTCACAGAACGAC 58.452 43.478 0.00 0.00 46.34 4.34
2805 4726 2.951457 TGTTCACTCACAGAACGACA 57.049 45.000 0.00 0.00 46.34 4.35
3004 6707 8.533569 TTGTCCTCTGAATAAATTAAATCCCC 57.466 34.615 0.00 0.00 0.00 4.81
3005 6708 7.882755 TGTCCTCTGAATAAATTAAATCCCCT 58.117 34.615 0.00 0.00 0.00 4.79
3034 6737 2.632377 CAGGCTATGTGTTACCTGTGG 58.368 52.381 0.00 0.00 43.86 4.17
3066 6769 9.337396 TCTTCATGTTCTGTTGTAGTATGTTTT 57.663 29.630 0.00 0.00 0.00 2.43
3091 6794 0.764890 CTGTTCCCTTCCCTGTCACA 59.235 55.000 0.00 0.00 0.00 3.58
3185 6889 2.503895 AAGGAAGGGCATCTGAAGTG 57.496 50.000 0.00 0.00 0.00 3.16
3242 6946 9.251792 CAAATCATGTTAATGTTATGATGGTGG 57.748 33.333 0.00 0.00 39.82 4.61
3291 7001 2.758130 TGGTCTGGACATATGCTACCA 58.242 47.619 1.58 9.34 32.92 3.25
3347 7057 1.127567 ACCAGTCTAAGGCAGCACCA 61.128 55.000 0.00 0.00 43.14 4.17
3393 7103 7.870826 TGTTGATATATCTAATTGCCCAAACG 58.129 34.615 13.79 0.00 0.00 3.60
3394 7104 7.500892 TGTTGATATATCTAATTGCCCAAACGT 59.499 33.333 13.79 0.00 0.00 3.99
3535 7245 8.524487 TCTGAGAAAGTACTCAAGGTATTTCTC 58.476 37.037 17.17 17.17 44.62 2.87
3548 7258 8.855110 TCAAGGTATTTCTCATCAGAGTAGATC 58.145 37.037 0.00 0.00 42.66 2.75
3620 7331 9.831737 CTGTTCAAGAAATGTAATAGTCTTTGG 57.168 33.333 0.00 0.00 30.79 3.28
3644 7355 6.036408 GGGAGCATGCTAAAATGAAAACAATC 59.964 38.462 22.74 1.76 0.00 2.67
3645 7356 6.815142 GGAGCATGCTAAAATGAAAACAATCT 59.185 34.615 22.74 0.00 0.00 2.40
3646 7357 7.975616 GGAGCATGCTAAAATGAAAACAATCTA 59.024 33.333 22.74 0.00 0.00 1.98
3647 7358 9.525409 GAGCATGCTAAAATGAAAACAATCTAT 57.475 29.630 22.74 0.00 0.00 1.98
3648 7359 9.880157 AGCATGCTAAAATGAAAACAATCTATT 57.120 25.926 21.21 0.00 0.00 1.73
3679 7395 7.260387 TGGATATTTACTCTGGTGTTGGTAA 57.740 36.000 0.00 0.00 0.00 2.85
3696 7592 6.017440 TGTTGGTAATGTTGAAGAGTGTTAGC 60.017 38.462 0.00 0.00 0.00 3.09
3712 7608 1.823169 TAGCAAAACCTCGGCCTCGT 61.823 55.000 0.00 0.00 37.69 4.18
3757 7655 6.477033 GTCAAGTGACTACAGCTTATATGTGG 59.523 42.308 4.15 0.00 41.65 4.17
3799 7898 0.887836 CATGATGATGGTCCTGCCCG 60.888 60.000 0.00 0.00 36.04 6.13
3844 7948 2.623502 GGTACAGTAGAGGAAGGGAGCA 60.624 54.545 0.00 0.00 0.00 4.26
3848 7952 2.058595 TAGAGGAAGGGAGCACCGC 61.059 63.158 0.00 0.00 46.96 5.68
3864 7969 1.580893 CGCCGACGTGATTTGCATG 60.581 57.895 0.00 0.00 39.48 4.06
3865 7970 1.793581 GCCGACGTGATTTGCATGA 59.206 52.632 0.00 0.00 36.97 3.07
3866 7971 0.167908 GCCGACGTGATTTGCATGAA 59.832 50.000 0.00 0.00 36.97 2.57
3871 7976 3.093574 GACGTGATTTGCATGAATGTCG 58.906 45.455 0.00 0.00 36.97 4.35
3895 8000 0.103026 TCTGGAAGACGATGCCGATG 59.897 55.000 0.00 0.00 38.67 3.84
3956 8061 2.860735 ACTTATTCTTCGCTCATCACGC 59.139 45.455 0.00 0.00 0.00 5.34
3988 8094 0.252057 TGGTACTGCTGCTAGTCCCA 60.252 55.000 10.74 10.74 34.70 4.37
4052 8159 4.348863 AGAAGATGCAAACACAGACTCT 57.651 40.909 0.00 0.00 0.00 3.24
4053 8160 4.063689 AGAAGATGCAAACACAGACTCTG 58.936 43.478 4.36 4.36 37.52 3.35
4054 8161 3.482156 AGATGCAAACACAGACTCTGT 57.518 42.857 5.82 5.82 46.51 3.41
4055 8162 4.607293 AGATGCAAACACAGACTCTGTA 57.393 40.909 11.47 0.00 43.43 2.74
4056 8163 4.310769 AGATGCAAACACAGACTCTGTAC 58.689 43.478 11.47 0.89 43.43 2.90
4057 8164 3.535280 TGCAAACACAGACTCTGTACA 57.465 42.857 11.47 0.00 43.43 2.90
4171 8283 2.944129 TGTTCCAAGAGGTCCTTTTGG 58.056 47.619 28.16 28.16 44.12 3.28
4198 8310 7.064253 GGTGTATATATTGCTCGGGTAATTGAC 59.936 40.741 3.26 0.00 0.00 3.18
4238 8388 1.001293 TGACTGCACTGTGAGGCTTAG 59.999 52.381 12.86 2.09 0.00 2.18
4247 8397 5.057149 CACTGTGAGGCTTAGTAGTTTGTT 58.943 41.667 0.32 0.00 0.00 2.83
4352 8505 4.389992 CACTGAGACGCACATTCAGTTATT 59.610 41.667 3.79 0.00 46.89 1.40
4353 8506 4.997395 ACTGAGACGCACATTCAGTTATTT 59.003 37.500 0.81 0.00 46.89 1.40
4450 8607 7.199167 TGGTGATGCAACTGGCTATATATAT 57.801 36.000 0.00 0.00 45.15 0.86
4451 8608 8.317776 TGGTGATGCAACTGGCTATATATATA 57.682 34.615 2.49 2.49 45.15 0.86
4476 8633 4.679639 GCCGTACTGTATTGGTGATGAAGA 60.680 45.833 9.79 0.00 0.00 2.87
4478 8635 5.163550 CCGTACTGTATTGGTGATGAAGAGA 60.164 44.000 0.00 0.00 0.00 3.10
4481 8638 5.121811 ACTGTATTGGTGATGAAGAGATGC 58.878 41.667 0.00 0.00 0.00 3.91
4487 8644 2.611292 GGTGATGAAGAGATGCGAAAGG 59.389 50.000 0.00 0.00 0.00 3.11
4491 8648 4.393062 TGATGAAGAGATGCGAAAGGAAAC 59.607 41.667 0.00 0.00 32.68 2.78
4493 8650 5.147330 TGAAGAGATGCGAAAGGAAACTA 57.853 39.130 0.00 0.00 42.68 2.24
4494 8651 5.171476 TGAAGAGATGCGAAAGGAAACTAG 58.829 41.667 0.00 0.00 42.68 2.57
4495 8652 5.047306 TGAAGAGATGCGAAAGGAAACTAGA 60.047 40.000 0.00 0.00 42.68 2.43
4496 8653 5.407407 AGAGATGCGAAAGGAAACTAGAA 57.593 39.130 0.00 0.00 42.68 2.10
4497 8654 5.794894 AGAGATGCGAAAGGAAACTAGAAA 58.205 37.500 0.00 0.00 42.68 2.52
4498 8655 5.872070 AGAGATGCGAAAGGAAACTAGAAAG 59.128 40.000 0.00 0.00 42.68 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.086758 GGCACTAGGTAGTTAGGAATATAGAAA 57.913 37.037 0.00 0.00 33.46 2.52
22 23 8.454494 AGGCACTAGGTAGTTAGGAATATAGAA 58.546 37.037 0.00 0.00 36.02 2.10
23 24 7.997915 AGGCACTAGGTAGTTAGGAATATAGA 58.002 38.462 0.00 0.00 36.02 1.98
24 25 9.750783 TTAGGCACTAGGTAGTTAGGAATATAG 57.249 37.037 0.00 0.00 44.25 1.31
25 26 9.750783 CTTAGGCACTAGGTAGTTAGGAATATA 57.249 37.037 0.00 0.00 44.25 0.86
26 27 7.178805 GCTTAGGCACTAGGTAGTTAGGAATAT 59.821 40.741 0.00 0.00 44.25 1.28
27 28 6.492772 GCTTAGGCACTAGGTAGTTAGGAATA 59.507 42.308 0.00 0.00 44.25 1.75
28 29 5.304871 GCTTAGGCACTAGGTAGTTAGGAAT 59.695 44.000 0.00 0.00 44.25 3.01
29 30 4.648307 GCTTAGGCACTAGGTAGTTAGGAA 59.352 45.833 0.00 0.00 44.25 3.36
30 31 4.079327 AGCTTAGGCACTAGGTAGTTAGGA 60.079 45.833 0.00 0.00 44.25 2.94
31 32 4.216708 AGCTTAGGCACTAGGTAGTTAGG 58.783 47.826 0.00 0.00 44.25 2.69
32 33 5.360144 TGAAGCTTAGGCACTAGGTAGTTAG 59.640 44.000 0.00 0.00 44.25 2.34
33 34 5.266788 TGAAGCTTAGGCACTAGGTAGTTA 58.733 41.667 0.00 0.00 44.25 2.24
34 35 4.094476 TGAAGCTTAGGCACTAGGTAGTT 58.906 43.478 0.00 0.00 44.25 2.24
35 36 3.709587 TGAAGCTTAGGCACTAGGTAGT 58.290 45.455 0.00 0.00 44.25 2.73
36 37 4.081642 TGTTGAAGCTTAGGCACTAGGTAG 60.082 45.833 0.00 0.00 44.25 3.18
37 38 3.835978 TGTTGAAGCTTAGGCACTAGGTA 59.164 43.478 0.00 0.00 44.25 3.08
38 39 2.637872 TGTTGAAGCTTAGGCACTAGGT 59.362 45.455 0.00 0.00 44.25 3.08
39 40 3.003480 GTGTTGAAGCTTAGGCACTAGG 58.997 50.000 15.30 0.00 44.25 3.02
40 41 3.664107 TGTGTTGAAGCTTAGGCACTAG 58.336 45.455 20.17 0.00 44.25 2.57
41 42 3.762407 TGTGTTGAAGCTTAGGCACTA 57.238 42.857 20.17 9.69 41.75 2.74
42 43 2.638480 TGTGTTGAAGCTTAGGCACT 57.362 45.000 20.17 0.00 46.37 4.40
43 44 3.708563 TTTGTGTTGAAGCTTAGGCAC 57.291 42.857 15.57 15.57 41.70 5.01
44 45 5.070001 AGTATTTGTGTTGAAGCTTAGGCA 58.930 37.500 0.00 0.00 41.70 4.75
45 46 5.629079 AGTATTTGTGTTGAAGCTTAGGC 57.371 39.130 0.00 0.00 39.06 3.93
46 47 7.679638 GCCATAGTATTTGTGTTGAAGCTTAGG 60.680 40.741 0.00 0.00 0.00 2.69
47 48 7.189512 GCCATAGTATTTGTGTTGAAGCTTAG 58.810 38.462 0.00 0.00 0.00 2.18
48 49 7.083875 GCCATAGTATTTGTGTTGAAGCTTA 57.916 36.000 0.00 0.00 0.00 3.09
49 50 5.954335 GCCATAGTATTTGTGTTGAAGCTT 58.046 37.500 0.00 0.00 0.00 3.74
50 51 5.567138 GCCATAGTATTTGTGTTGAAGCT 57.433 39.130 0.00 0.00 0.00 3.74
747 748 4.436998 GGACCGTCCGCTCTGTGG 62.437 72.222 0.65 0.00 33.99 4.17
748 749 2.709125 TTTGGACCGTCCGCTCTGTG 62.709 60.000 13.02 0.00 40.17 3.66
749 750 2.504274 TTTGGACCGTCCGCTCTGT 61.504 57.895 13.02 0.00 40.17 3.41
750 751 2.027625 GTTTGGACCGTCCGCTCTG 61.028 63.158 13.02 0.00 40.17 3.35
751 752 2.342648 GTTTGGACCGTCCGCTCT 59.657 61.111 13.02 0.00 40.17 4.09
752 753 3.110178 CGTTTGGACCGTCCGCTC 61.110 66.667 13.02 4.64 40.17 5.03
753 754 3.569049 CTCGTTTGGACCGTCCGCT 62.569 63.158 13.02 0.00 40.17 5.52
754 755 3.110178 CTCGTTTGGACCGTCCGC 61.110 66.667 13.02 5.00 40.17 5.54
755 756 3.110178 GCTCGTTTGGACCGTCCG 61.110 66.667 13.02 1.00 40.17 4.79
756 757 1.737008 GAGCTCGTTTGGACCGTCC 60.737 63.158 10.96 10.96 36.96 4.79
757 758 2.087009 CGAGCTCGTTTGGACCGTC 61.087 63.158 27.79 0.00 34.11 4.79
758 759 2.049433 CGAGCTCGTTTGGACCGT 60.049 61.111 27.79 0.00 34.11 4.83
759 760 1.801913 CTCGAGCTCGTTTGGACCG 60.802 63.158 33.33 7.70 40.80 4.79
760 761 2.095252 GCTCGAGCTCGTTTGGACC 61.095 63.158 33.33 12.50 40.80 4.46
761 762 2.437343 CGCTCGAGCTCGTTTGGAC 61.437 63.158 33.33 16.79 40.80 4.02
762 763 2.126463 CGCTCGAGCTCGTTTGGA 60.126 61.111 33.33 14.80 40.80 3.53
763 764 3.181967 CCGCTCGAGCTCGTTTGG 61.182 66.667 33.33 26.85 40.80 3.28
764 765 2.126463 TCCGCTCGAGCTCGTTTG 60.126 61.111 33.33 24.18 40.80 2.93
765 766 2.179517 CTCCGCTCGAGCTCGTTT 59.820 61.111 33.33 0.00 40.80 3.60
766 767 3.056938 ACTCCGCTCGAGCTCGTT 61.057 61.111 33.33 13.61 43.01 3.85
767 768 3.805307 CACTCCGCTCGAGCTCGT 61.805 66.667 33.33 22.98 43.01 4.18
768 769 4.544689 CCACTCCGCTCGAGCTCG 62.545 72.222 32.88 30.03 43.01 5.03
769 770 4.863925 GCCACTCCGCTCGAGCTC 62.864 72.222 32.88 2.73 43.01 4.09
772 773 3.573772 TTGTGCCACTCCGCTCGAG 62.574 63.158 8.45 8.45 44.95 4.04
773 774 3.611674 TTGTGCCACTCCGCTCGA 61.612 61.111 0.00 0.00 0.00 4.04
774 775 3.414700 GTTGTGCCACTCCGCTCG 61.415 66.667 0.00 0.00 0.00 5.03
775 776 1.891919 TTGTTGTGCCACTCCGCTC 60.892 57.895 0.00 0.00 0.00 5.03
776 777 2.186826 GTTGTTGTGCCACTCCGCT 61.187 57.895 0.00 0.00 0.00 5.52
777 778 2.331451 GTTGTTGTGCCACTCCGC 59.669 61.111 0.00 0.00 0.00 5.54
778 779 1.355210 GTGTTGTTGTGCCACTCCG 59.645 57.895 0.00 0.00 0.00 4.63
779 780 0.814457 TTGTGTTGTTGTGCCACTCC 59.186 50.000 0.00 0.00 0.00 3.85
780 781 1.201181 TGTTGTGTTGTTGTGCCACTC 59.799 47.619 0.00 0.00 0.00 3.51
781 782 1.252175 TGTTGTGTTGTTGTGCCACT 58.748 45.000 0.00 0.00 0.00 4.00
782 783 2.071688 TTGTTGTGTTGTTGTGCCAC 57.928 45.000 0.00 0.00 0.00 5.01
783 784 2.417924 GGATTGTTGTGTTGTTGTGCCA 60.418 45.455 0.00 0.00 0.00 4.92
784 785 2.200899 GGATTGTTGTGTTGTTGTGCC 58.799 47.619 0.00 0.00 0.00 5.01
785 786 2.886081 TGGATTGTTGTGTTGTTGTGC 58.114 42.857 0.00 0.00 0.00 4.57
786 787 5.107824 TGAATGGATTGTTGTGTTGTTGTG 58.892 37.500 0.00 0.00 0.00 3.33
787 788 5.336150 TGAATGGATTGTTGTGTTGTTGT 57.664 34.783 0.00 0.00 0.00 3.32
788 789 6.218025 CATGAATGGATTGTTGTGTTGTTG 57.782 37.500 0.00 0.00 0.00 3.33
789 790 8.368602 AGCCATGAATGGATTGTTGTGTTGTT 62.369 38.462 13.65 0.00 45.90 2.83
790 791 6.969768 AGCCATGAATGGATTGTTGTGTTGT 61.970 40.000 13.65 0.00 45.90 3.32
791 792 4.561938 AGCCATGAATGGATTGTTGTGTTG 60.562 41.667 13.65 0.00 45.90 3.33
792 793 3.579586 AGCCATGAATGGATTGTTGTGTT 59.420 39.130 13.65 0.00 45.90 3.32
793 794 3.167485 AGCCATGAATGGATTGTTGTGT 58.833 40.909 13.65 0.00 45.90 3.72
824 825 6.060788 TCCCCATTTTCCAATTTGAAAACAG 58.939 36.000 17.01 13.07 44.46 3.16
831 832 4.001618 ACGTTCCCCATTTTCCAATTTG 57.998 40.909 0.00 0.00 0.00 2.32
863 864 9.771915 GTGTGAATTGTGTCAATTTGAAATTTT 57.228 25.926 0.00 0.00 0.00 1.82
883 884 1.533299 GTGTGTGTGTGTGTGTGTGAA 59.467 47.619 0.00 0.00 0.00 3.18
890 891 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
891 892 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
892 893 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
893 894 0.179192 GCTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
894 895 1.305219 GGCTGTGTGTGTGTGTGTGT 61.305 55.000 0.00 0.00 0.00 3.72
895 896 1.026182 AGGCTGTGTGTGTGTGTGTG 61.026 55.000 0.00 0.00 0.00 3.82
896 897 1.026182 CAGGCTGTGTGTGTGTGTGT 61.026 55.000 6.28 0.00 0.00 3.72
897 898 1.717791 CCAGGCTGTGTGTGTGTGTG 61.718 60.000 14.43 0.00 0.00 3.82
898 899 1.451927 CCAGGCTGTGTGTGTGTGT 60.452 57.895 14.43 0.00 0.00 3.72
899 900 1.439353 GACCAGGCTGTGTGTGTGTG 61.439 60.000 14.43 0.00 0.00 3.82
940 941 1.889170 CCCTCCTTTTTGCTCTTGGTC 59.111 52.381 0.00 0.00 0.00 4.02
941 942 2.001076 CCCTCCTTTTTGCTCTTGGT 57.999 50.000 0.00 0.00 0.00 3.67
942 943 0.605083 GCCCTCCTTTTTGCTCTTGG 59.395 55.000 0.00 0.00 0.00 3.61
943 944 1.000171 GTGCCCTCCTTTTTGCTCTTG 60.000 52.381 0.00 0.00 0.00 3.02
944 945 1.332195 GTGCCCTCCTTTTTGCTCTT 58.668 50.000 0.00 0.00 0.00 2.85
945 946 0.890996 CGTGCCCTCCTTTTTGCTCT 60.891 55.000 0.00 0.00 0.00 4.09
947 948 2.564721 GCGTGCCCTCCTTTTTGCT 61.565 57.895 0.00 0.00 0.00 3.91
948 949 2.049156 GCGTGCCCTCCTTTTTGC 60.049 61.111 0.00 0.00 0.00 3.68
949 950 0.318955 CTTGCGTGCCCTCCTTTTTG 60.319 55.000 0.00 0.00 0.00 2.44
950 951 0.755327 ACTTGCGTGCCCTCCTTTTT 60.755 50.000 0.00 0.00 0.00 1.94
951 952 1.152756 ACTTGCGTGCCCTCCTTTT 60.153 52.632 0.00 0.00 0.00 2.27
952 953 1.600916 GACTTGCGTGCCCTCCTTT 60.601 57.895 0.00 0.00 0.00 3.11
954 955 4.379243 CGACTTGCGTGCCCTCCT 62.379 66.667 0.00 0.00 34.64 3.69
964 965 0.243907 TAGACCTGTCTGCGACTTGC 59.756 55.000 10.02 0.00 46.70 4.01
965 966 1.269723 TGTAGACCTGTCTGCGACTTG 59.730 52.381 10.02 4.24 43.87 3.16
981 982 1.561643 TTGGCTCCTGGAGACTGTAG 58.438 55.000 28.95 1.67 38.75 2.74
1028 1029 1.078759 GTAGCCTGTACGCTGCAGTG 61.079 60.000 25.37 25.37 40.76 3.66
1796 1884 4.513442 CGTTTCCTGGTTCATCTCCATTA 58.487 43.478 0.00 0.00 34.26 1.90
1797 1885 3.347216 CGTTTCCTGGTTCATCTCCATT 58.653 45.455 0.00 0.00 34.26 3.16
2505 4416 6.592994 GCTACTACCAAACGGAGAACTTAATT 59.407 38.462 0.00 0.00 0.00 1.40
2506 4417 6.104665 GCTACTACCAAACGGAGAACTTAAT 58.895 40.000 0.00 0.00 0.00 1.40
2507 4418 5.473039 GCTACTACCAAACGGAGAACTTAA 58.527 41.667 0.00 0.00 0.00 1.85
2508 4419 4.379813 CGCTACTACCAAACGGAGAACTTA 60.380 45.833 0.00 0.00 0.00 2.24
2509 4420 3.613432 CGCTACTACCAAACGGAGAACTT 60.613 47.826 0.00 0.00 0.00 2.66
2517 4428 2.660236 GAGTGAACGCTACTACCAAACG 59.340 50.000 0.00 0.00 0.00 3.60
2596 4510 3.157087 CAGGAGCAAGCCCTTTTCTAAA 58.843 45.455 0.16 0.00 0.00 1.85
2597 4511 2.108250 ACAGGAGCAAGCCCTTTTCTAA 59.892 45.455 0.16 0.00 0.00 2.10
2598 4512 1.705186 ACAGGAGCAAGCCCTTTTCTA 59.295 47.619 0.16 0.00 0.00 2.10
2599 4513 0.480252 ACAGGAGCAAGCCCTTTTCT 59.520 50.000 0.16 0.00 0.00 2.52
2600 4514 1.270826 GAACAGGAGCAAGCCCTTTTC 59.729 52.381 10.52 10.52 34.54 2.29
2601 4515 1.133356 AGAACAGGAGCAAGCCCTTTT 60.133 47.619 0.16 1.22 0.00 2.27
2602 4516 0.480252 AGAACAGGAGCAAGCCCTTT 59.520 50.000 0.16 0.37 0.00 3.11
2603 4517 0.480252 AAGAACAGGAGCAAGCCCTT 59.520 50.000 0.16 0.00 0.00 3.95
2604 4518 1.362224 TAAGAACAGGAGCAAGCCCT 58.638 50.000 0.00 0.00 0.00 5.19
2605 4519 2.426842 ATAAGAACAGGAGCAAGCCC 57.573 50.000 0.00 0.00 0.00 5.19
2606 4520 4.460731 AGAAAATAAGAACAGGAGCAAGCC 59.539 41.667 0.00 0.00 0.00 4.35
2607 4521 5.182001 TGAGAAAATAAGAACAGGAGCAAGC 59.818 40.000 0.00 0.00 0.00 4.01
2608 4522 6.652481 TCTGAGAAAATAAGAACAGGAGCAAG 59.348 38.462 0.00 0.00 0.00 4.01
2609 4523 6.533730 TCTGAGAAAATAAGAACAGGAGCAA 58.466 36.000 0.00 0.00 0.00 3.91
2610 4524 6.114187 TCTGAGAAAATAAGAACAGGAGCA 57.886 37.500 0.00 0.00 0.00 4.26
2611 4525 7.120432 ACAATCTGAGAAAATAAGAACAGGAGC 59.880 37.037 0.00 0.00 0.00 4.70
2612 4526 8.558973 ACAATCTGAGAAAATAAGAACAGGAG 57.441 34.615 0.00 0.00 0.00 3.69
2613 4527 8.924511 AACAATCTGAGAAAATAAGAACAGGA 57.075 30.769 0.00 0.00 0.00 3.86
2614 4528 9.971922 AAAACAATCTGAGAAAATAAGAACAGG 57.028 29.630 0.00 0.00 0.00 4.00
2616 4530 9.663904 CGAAAACAATCTGAGAAAATAAGAACA 57.336 29.630 0.00 0.00 0.00 3.18
2617 4531 9.878599 TCGAAAACAATCTGAGAAAATAAGAAC 57.121 29.630 0.00 0.00 0.00 3.01
2624 4538 9.923143 TCTAGTATCGAAAACAATCTGAGAAAA 57.077 29.630 0.00 0.00 0.00 2.29
2626 4540 9.521503 CATCTAGTATCGAAAACAATCTGAGAA 57.478 33.333 0.00 0.00 0.00 2.87
2627 4541 8.903820 TCATCTAGTATCGAAAACAATCTGAGA 58.096 33.333 0.00 0.00 0.00 3.27
2628 4542 9.689976 ATCATCTAGTATCGAAAACAATCTGAG 57.310 33.333 0.00 0.00 0.00 3.35
2629 4543 9.684448 GATCATCTAGTATCGAAAACAATCTGA 57.316 33.333 0.00 0.00 0.00 3.27
2699 4617 3.393800 TGAGCTCCTTCTGTCGAAAAAG 58.606 45.455 12.15 0.00 0.00 2.27
2705 4623 1.074752 GCTTTGAGCTCCTTCTGTCG 58.925 55.000 12.15 0.00 38.45 4.35
2792 4710 5.523369 TGCATAGATATGTCGTTCTGTGAG 58.477 41.667 2.03 0.00 34.18 3.51
2799 4720 9.271828 TGAAATAACATGCATAGATATGTCGTT 57.728 29.630 0.00 0.00 36.56 3.85
2953 6655 7.081857 ACTTGGGTGGTCAGTTAACTAAATA 57.918 36.000 8.04 0.00 0.00 1.40
3004 6707 0.251354 ACATAGCCTGTGACCAGCAG 59.749 55.000 0.00 0.00 36.48 4.24
3005 6708 2.376063 ACATAGCCTGTGACCAGCA 58.624 52.632 0.00 0.00 36.48 4.41
3034 6737 5.741388 ACAACAGAACATGAAGAGTTCAC 57.259 39.130 0.00 0.00 45.93 3.18
3066 6769 1.699634 CAGGGAAGGGAACAGAACTGA 59.300 52.381 8.87 0.00 0.00 3.41
3185 6889 8.655651 TTTGTCAAAGTGGGATTAATTGTTTC 57.344 30.769 0.00 0.00 0.00 2.78
3263 6973 0.322816 ATGTCCAGACCATGCACCAC 60.323 55.000 0.00 0.00 0.00 4.16
3374 7084 7.445707 TGCATTACGTTTGGGCAATTAGATATA 59.554 33.333 0.00 0.00 0.00 0.86
3535 7245 9.814899 AAAACTACATCAAGATCTACTCTGATG 57.185 33.333 24.20 24.20 42.55 3.07
3599 7310 7.121168 TGCTCCCAAAGACTATTACATTTCTTG 59.879 37.037 0.00 0.00 0.00 3.02
3609 7320 3.659183 AGCATGCTCCCAAAGACTATT 57.341 42.857 16.30 0.00 0.00 1.73
3618 7329 4.282957 TGTTTTCATTTTAGCATGCTCCCA 59.717 37.500 26.57 9.42 0.00 4.37
3620 7331 6.815142 AGATTGTTTTCATTTTAGCATGCTCC 59.185 34.615 26.57 1.13 0.00 4.70
3646 7357 9.838339 CACCAGAGTAAATATCCAAAGAGTAAT 57.162 33.333 0.00 0.00 0.00 1.89
3647 7358 8.822805 ACACCAGAGTAAATATCCAAAGAGTAA 58.177 33.333 0.00 0.00 0.00 2.24
3648 7359 8.375493 ACACCAGAGTAAATATCCAAAGAGTA 57.625 34.615 0.00 0.00 0.00 2.59
3649 7360 7.259088 ACACCAGAGTAAATATCCAAAGAGT 57.741 36.000 0.00 0.00 0.00 3.24
3650 7361 7.066284 CCAACACCAGAGTAAATATCCAAAGAG 59.934 40.741 0.00 0.00 0.00 2.85
3652 7363 6.659242 ACCAACACCAGAGTAAATATCCAAAG 59.341 38.462 0.00 0.00 0.00 2.77
3653 7364 6.548321 ACCAACACCAGAGTAAATATCCAAA 58.452 36.000 0.00 0.00 0.00 3.28
3654 7365 6.134535 ACCAACACCAGAGTAAATATCCAA 57.865 37.500 0.00 0.00 0.00 3.53
3655 7366 5.772393 ACCAACACCAGAGTAAATATCCA 57.228 39.130 0.00 0.00 0.00 3.41
3656 7367 7.773690 ACATTACCAACACCAGAGTAAATATCC 59.226 37.037 0.00 0.00 0.00 2.59
3657 7368 8.732746 ACATTACCAACACCAGAGTAAATATC 57.267 34.615 0.00 0.00 0.00 1.63
3660 7376 7.001674 TCAACATTACCAACACCAGAGTAAAT 58.998 34.615 0.00 0.00 0.00 1.40
3662 7378 5.931294 TCAACATTACCAACACCAGAGTAA 58.069 37.500 0.00 0.00 0.00 2.24
3664 7380 4.431416 TCAACATTACCAACACCAGAGT 57.569 40.909 0.00 0.00 0.00 3.24
3667 7383 4.821805 ACTCTTCAACATTACCAACACCAG 59.178 41.667 0.00 0.00 0.00 4.00
3679 7395 5.594317 AGGTTTTGCTAACACTCTTCAACAT 59.406 36.000 4.98 0.00 0.00 2.71
3696 7592 1.164041 AACACGAGGCCGAGGTTTTG 61.164 55.000 0.00 0.00 39.50 2.44
3799 7898 0.249741 AATATGCGGTCTACGGGTGC 60.250 55.000 0.00 0.00 44.51 5.01
3844 7948 3.419759 GCAAATCACGTCGGCGGT 61.420 61.111 16.39 0.00 43.45 5.68
3848 7952 2.159531 ACATTCATGCAAATCACGTCGG 60.160 45.455 0.00 0.00 0.00 4.79
3850 7954 3.093574 CGACATTCATGCAAATCACGTC 58.906 45.455 0.00 0.00 0.00 4.34
3853 7957 4.094887 AGGTACGACATTCATGCAAATCAC 59.905 41.667 0.00 0.00 0.00 3.06
3854 7958 4.260985 AGGTACGACATTCATGCAAATCA 58.739 39.130 0.00 0.00 0.00 2.57
3855 7959 4.572389 AGAGGTACGACATTCATGCAAATC 59.428 41.667 0.00 0.00 0.00 2.17
3864 7969 3.731264 CGTCTTCCAGAGGTACGACATTC 60.731 52.174 0.00 0.00 35.66 2.67
3865 7970 2.163815 CGTCTTCCAGAGGTACGACATT 59.836 50.000 0.00 0.00 35.66 2.71
3866 7971 1.743958 CGTCTTCCAGAGGTACGACAT 59.256 52.381 0.00 0.00 35.66 3.06
3871 7976 1.202428 GGCATCGTCTTCCAGAGGTAC 60.202 57.143 0.00 0.00 32.36 3.34
3895 8000 7.141363 AGTTCAAGTGTTTCAGATGCAAATAC 58.859 34.615 0.00 0.00 0.00 1.89
4030 8136 4.514441 CAGAGTCTGTGTTTGCATCTTCTT 59.486 41.667 12.28 0.00 0.00 2.52
4057 8164 9.908152 GGATGTACTAAAACAATGTAAAGCTTT 57.092 29.630 17.30 17.30 32.02 3.51
4171 8283 3.975168 ACCCGAGCAATATATACACCC 57.025 47.619 0.00 0.00 0.00 4.61
4352 8505 5.590818 ACTGAATGTAGACTCCTCCCTTAA 58.409 41.667 0.00 0.00 0.00 1.85
4353 8506 5.202004 GACTGAATGTAGACTCCTCCCTTA 58.798 45.833 0.00 0.00 0.00 2.69
4450 8607 4.403113 TCATCACCAATACAGTACGGCTTA 59.597 41.667 0.00 0.00 0.00 3.09
4451 8608 3.196901 TCATCACCAATACAGTACGGCTT 59.803 43.478 0.00 0.00 0.00 4.35
4462 8619 4.670896 TCGCATCTCTTCATCACCAATA 57.329 40.909 0.00 0.00 0.00 1.90
4463 8620 3.548745 TCGCATCTCTTCATCACCAAT 57.451 42.857 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.