Multiple sequence alignment - TraesCS2D01G495600

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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 TraesCS2D01G495600 chr2D 100.000 3105 0 0 1 3105 592377543 592374439 0.000000e+00 5734.0
1 TraesCS2D01G495600 chr2D 80.374 214 37 5 2347 2556 592405341 592405129 1.150000e-34 158.0
2 TraesCS2D01G495600 chr4D 97.633 845 18 2 1 843 51300779 51301623 0.000000e+00 1448.0
3 TraesCS2D01G495600 chr6D 96.209 844 29 3 1 843 278629654 278628813 0.000000e+00 1378.0
4 TraesCS2D01G495600 chr7D 95.981 846 30 3 1 843 604991540 604990696 0.000000e+00 1371.0
5 TraesCS2D01G495600 chr3D 95.858 845 31 4 1 843 395522054 395522896 0.000000e+00 1363.0
6 TraesCS2D01G495600 chr7A 95.853 844 31 3 1 843 722767094 722766254 0.000000e+00 1362.0
7 TraesCS2D01G495600 chr1A 94.793 845 39 4 1 843 118556585 118557426 0.000000e+00 1312.0
8 TraesCS2D01G495600 chr4B 90.673 847 66 11 1 843 14646333 14645496 0.000000e+00 1114.0
9 TraesCS2D01G495600 chr2B 90.599 851 64 12 1 847 245302583 245303421 0.000000e+00 1114.0
10 TraesCS2D01G495600 chr2B 90.844 841 61 9 1 835 765553929 765554759 0.000000e+00 1112.0
11 TraesCS2D01G495600 chr2B 92.979 527 20 5 889 1411 718214964 718214451 0.000000e+00 752.0
12 TraesCS2D01G495600 chr2B 88.099 605 39 16 1441 2024 718214450 718213858 0.000000e+00 688.0
13 TraesCS2D01G495600 chr2B 80.751 213 37 2 2348 2556 718391645 718391433 2.480000e-36 163.0
14 TraesCS2D01G495600 chr2B 95.833 48 2 0 2751 2798 691995329 691995282 9.230000e-11 78.7
15 TraesCS2D01G495600 chr2B 95.833 48 2 0 2751 2798 692036691 692036644 9.230000e-11 78.7
16 TraesCS2D01G495600 chr2A 89.583 912 47 23 889 1764 726954576 726953677 0.000000e+00 1114.0
17 TraesCS2D01G495600 chr2A 83.257 878 104 24 2230 3105 726953098 726952262 0.000000e+00 767.0
18 TraesCS2D01G495600 chr2A 90.741 432 32 6 1768 2197 726953522 726953097 1.250000e-158 569.0
19 TraesCS2D01G495600 chr2A 80.374 214 38 2 2347 2556 726976121 726975908 3.200000e-35 159.0
20 TraesCS2D01G495600 chr7B 83.448 145 21 3 2750 2892 718133691 718133834 6.990000e-27 132.0
21 TraesCS2D01G495600 chrUn 95.833 48 2 0 2751 2798 22219431 22219384 9.230000e-11 78.7


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 TraesCS2D01G495600 chr2D 592374439 592377543 3104 True 5734.000000 5734 100.000000 1 3105 1 chr2D.!!$R1 3104
1 TraesCS2D01G495600 chr4D 51300779 51301623 844 False 1448.000000 1448 97.633000 1 843 1 chr4D.!!$F1 842
2 TraesCS2D01G495600 chr6D 278628813 278629654 841 True 1378.000000 1378 96.209000 1 843 1 chr6D.!!$R1 842
3 TraesCS2D01G495600 chr7D 604990696 604991540 844 True 1371.000000 1371 95.981000 1 843 1 chr7D.!!$R1 842
4 TraesCS2D01G495600 chr3D 395522054 395522896 842 False 1363.000000 1363 95.858000 1 843 1 chr3D.!!$F1 842
5 TraesCS2D01G495600 chr7A 722766254 722767094 840 True 1362.000000 1362 95.853000 1 843 1 chr7A.!!$R1 842
6 TraesCS2D01G495600 chr1A 118556585 118557426 841 False 1312.000000 1312 94.793000 1 843 1 chr1A.!!$F1 842
7 TraesCS2D01G495600 chr4B 14645496 14646333 837 True 1114.000000 1114 90.673000 1 843 1 chr4B.!!$R1 842
8 TraesCS2D01G495600 chr2B 245302583 245303421 838 False 1114.000000 1114 90.599000 1 847 1 chr2B.!!$F1 846
9 TraesCS2D01G495600 chr2B 765553929 765554759 830 False 1112.000000 1112 90.844000 1 835 1 chr2B.!!$F2 834
10 TraesCS2D01G495600 chr2B 718213858 718214964 1106 True 720.000000 752 90.539000 889 2024 2 chr2B.!!$R4 1135
11 TraesCS2D01G495600 chr2A 726952262 726954576 2314 True 816.666667 1114 87.860333 889 3105 3 chr2A.!!$R2 2216

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
880 896 0.036765 GTTCCAGCATCACCGGTGTA 60.037 55.0 32.74 20.21 32.43 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2382 0.250553 CCCGTGGTGAAACAAGCCTA 60.251 55.0 0.0 0.0 39.98 3.93 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
76 79 0.531532 GCTCGTGCTCATAGCCACAT 60.532 55.000 1.41 0.00 41.51 3.21
198 202 3.815337 TGCACGCGCTAATTCTTTTTA 57.185 38.095 5.73 0.00 39.64 1.52
680 696 0.541063 TGTCTGCCTTCGGGTCACTA 60.541 55.000 0.00 0.00 37.45 2.74
719 735 3.967393 TTGGCGCGCCTAATCAGCA 62.967 57.895 45.79 24.59 36.94 4.41
829 845 1.063327 CAAAGTGACCGTTTGCGCA 59.937 52.632 5.66 5.66 36.67 6.09
832 848 0.383949 AAGTGACCGTTTGCGCAAAT 59.616 45.000 35.53 21.96 36.67 2.32
834 850 0.775861 GTGACCGTTTGCGCAAATTC 59.224 50.000 35.53 28.85 36.67 2.17
835 851 0.665835 TGACCGTTTGCGCAAATTCT 59.334 45.000 35.53 21.14 36.67 2.40
836 852 1.874231 TGACCGTTTGCGCAAATTCTA 59.126 42.857 35.53 19.31 36.67 2.10
837 853 2.290916 TGACCGTTTGCGCAAATTCTAA 59.709 40.909 35.53 19.87 36.67 2.10
838 854 2.655001 GACCGTTTGCGCAAATTCTAAC 59.345 45.455 35.53 22.27 36.67 2.34
839 855 2.033550 ACCGTTTGCGCAAATTCTAACA 59.966 40.909 35.53 10.92 36.67 2.41
840 856 2.403698 CCGTTTGCGCAAATTCTAACAC 59.596 45.455 35.53 20.87 36.67 3.32
841 857 2.403698 CGTTTGCGCAAATTCTAACACC 59.596 45.455 35.53 19.23 32.36 4.16
842 858 3.376540 GTTTGCGCAAATTCTAACACCA 58.623 40.909 35.53 8.78 32.36 4.17
843 859 3.717400 TTGCGCAAATTCTAACACCAA 57.283 38.095 22.78 0.00 0.00 3.67
844 860 3.717400 TGCGCAAATTCTAACACCAAA 57.283 38.095 8.16 0.00 0.00 3.28
845 861 3.637432 TGCGCAAATTCTAACACCAAAG 58.363 40.909 8.16 0.00 0.00 2.77
846 862 3.067461 TGCGCAAATTCTAACACCAAAGT 59.933 39.130 8.16 0.00 0.00 2.66
847 863 9.747057 GTTTGCGCAAATTCTAACACCAAAGTG 62.747 40.741 35.53 0.00 40.10 3.16
858 874 0.040425 ACCAAAGTGATCGTTTGCGC 60.040 50.000 0.00 0.00 38.14 6.09
859 875 0.040514 CCAAAGTGATCGTTTGCGCA 60.041 50.000 5.66 5.66 38.14 6.09
860 876 1.599171 CCAAAGTGATCGTTTGCGCAA 60.599 47.619 21.02 21.02 38.14 4.85
861 877 1.710249 CAAAGTGATCGTTTGCGCAAG 59.290 47.619 23.68 13.07 38.14 4.01
862 878 0.944386 AAGTGATCGTTTGCGCAAGT 59.056 45.000 23.68 10.80 41.68 3.16
863 879 0.944386 AGTGATCGTTTGCGCAAGTT 59.056 45.000 23.68 7.79 41.68 2.66
864 880 1.069906 AGTGATCGTTTGCGCAAGTTC 60.070 47.619 23.68 16.44 41.68 3.01
865 881 0.237235 TGATCGTTTGCGCAAGTTCC 59.763 50.000 23.68 12.83 41.68 3.62
866 882 0.237235 GATCGTTTGCGCAAGTTCCA 59.763 50.000 23.68 4.96 41.68 3.53
867 883 0.238289 ATCGTTTGCGCAAGTTCCAG 59.762 50.000 23.68 11.75 41.68 3.86
868 884 2.010817 CGTTTGCGCAAGTTCCAGC 61.011 57.895 23.68 1.74 41.68 4.85
869 885 1.065600 GTTTGCGCAAGTTCCAGCA 59.934 52.632 23.68 2.43 41.68 4.41
870 886 0.318955 GTTTGCGCAAGTTCCAGCAT 60.319 50.000 23.68 0.00 39.50 3.79
871 887 0.039256 TTTGCGCAAGTTCCAGCATC 60.039 50.000 23.68 0.00 39.50 3.91
872 888 1.171549 TTGCGCAAGTTCCAGCATCA 61.172 50.000 21.02 0.00 39.50 3.07
873 889 1.154150 GCGCAAGTTCCAGCATCAC 60.154 57.895 0.30 0.00 41.68 3.06
874 890 1.503542 CGCAAGTTCCAGCATCACC 59.496 57.895 0.00 0.00 0.00 4.02
875 891 1.503542 GCAAGTTCCAGCATCACCG 59.496 57.895 0.00 0.00 0.00 4.94
876 892 1.926511 GCAAGTTCCAGCATCACCGG 61.927 60.000 0.00 0.00 0.00 5.28
877 893 0.606401 CAAGTTCCAGCATCACCGGT 60.606 55.000 0.00 0.00 0.00 5.28
878 894 0.606401 AAGTTCCAGCATCACCGGTG 60.606 55.000 29.26 29.26 0.00 4.94
879 895 1.302511 GTTCCAGCATCACCGGTGT 60.303 57.895 32.74 18.15 32.43 4.16
880 896 0.036765 GTTCCAGCATCACCGGTGTA 60.037 55.000 32.74 20.21 32.43 2.90
881 897 0.687920 TTCCAGCATCACCGGTGTAA 59.312 50.000 32.74 16.65 32.43 2.41
882 898 0.908910 TCCAGCATCACCGGTGTAAT 59.091 50.000 32.74 18.27 32.43 1.89
883 899 1.280710 TCCAGCATCACCGGTGTAATT 59.719 47.619 32.74 15.39 32.43 1.40
884 900 1.401552 CCAGCATCACCGGTGTAATTG 59.598 52.381 32.74 24.35 32.43 2.32
885 901 2.355197 CAGCATCACCGGTGTAATTGA 58.645 47.619 32.74 14.26 0.00 2.57
886 902 2.095853 CAGCATCACCGGTGTAATTGAC 59.904 50.000 32.74 19.39 0.00 3.18
887 903 2.027192 AGCATCACCGGTGTAATTGACT 60.027 45.455 32.74 20.84 0.00 3.41
983 999 1.248489 CGTGTATAAACGACGCACTCG 59.752 52.381 10.01 0.00 46.49 4.18
1018 1036 1.336517 CCCGTCGCTAACAAGAACTCA 60.337 52.381 0.00 0.00 0.00 3.41
1023 1041 4.030753 CGTCGCTAACAAGAACTCAAGATC 59.969 45.833 0.00 0.00 0.00 2.75
1032 1050 4.278975 AGAACTCAAGATCCCAGAACAC 57.721 45.455 0.00 0.00 0.00 3.32
1035 1053 2.039084 ACTCAAGATCCCAGAACACCAC 59.961 50.000 0.00 0.00 0.00 4.16
1037 1055 1.073763 CAAGATCCCAGAACACCACCA 59.926 52.381 0.00 0.00 0.00 4.17
1038 1056 0.693049 AGATCCCAGAACACCACCAC 59.307 55.000 0.00 0.00 0.00 4.16
1039 1057 0.400213 GATCCCAGAACACCACCACA 59.600 55.000 0.00 0.00 0.00 4.17
1044 1062 0.376852 CAGAACACCACCACAACACG 59.623 55.000 0.00 0.00 0.00 4.49
1058 1076 2.066262 CAACACGTAGCCACCACTAAG 58.934 52.381 0.00 0.00 0.00 2.18
1215 1239 0.532573 GATGACCGACAAGCTCCAGA 59.467 55.000 0.00 0.00 0.00 3.86
1260 1284 1.675219 GTGCCGGAAGTAACTCCCA 59.325 57.895 5.05 0.00 31.03 4.37
1411 1435 3.307975 GCATGGATGTGGGAGTAGCATAT 60.308 47.826 0.00 0.00 0.00 1.78
1419 1460 1.429463 GGAGTAGCATATTTCGCCGG 58.571 55.000 0.00 0.00 0.00 6.13
1420 1461 1.429463 GAGTAGCATATTTCGCCGGG 58.571 55.000 2.18 0.00 0.00 5.73
1437 1478 0.106519 GGGATGCTGTTATGCCCTGT 60.107 55.000 0.00 0.00 35.86 4.00
1438 1479 1.027357 GGATGCTGTTATGCCCTGTG 58.973 55.000 0.00 0.00 0.00 3.66
1439 1480 0.383231 GATGCTGTTATGCCCTGTGC 59.617 55.000 0.00 0.00 41.77 4.57
1440 1481 1.039233 ATGCTGTTATGCCCTGTGCC 61.039 55.000 0.00 0.00 40.16 5.01
1441 1482 1.379044 GCTGTTATGCCCTGTGCCT 60.379 57.895 0.00 0.00 40.16 4.75
1442 1483 1.660560 GCTGTTATGCCCTGTGCCTG 61.661 60.000 0.00 0.00 40.16 4.85
1443 1484 0.322816 CTGTTATGCCCTGTGCCTGT 60.323 55.000 0.00 0.00 40.16 4.00
1580 1621 6.030228 GTGCCTTTTATGTTGAGTTCTATGC 58.970 40.000 0.00 0.00 0.00 3.14
1625 1680 1.956297 TCGCTTTCGGTTCCTTTCAA 58.044 45.000 0.00 0.00 36.13 2.69
1631 1686 4.444388 GCTTTCGGTTCCTTTCAATCAAAC 59.556 41.667 0.00 0.00 0.00 2.93
1642 1697 7.461749 TCCTTTCAATCAAACAGGAGTATCTT 58.538 34.615 0.00 0.00 33.73 2.40
1698 1757 1.967274 GCCAGAGTAGGGTGTCCTCAT 60.967 57.143 0.00 0.00 43.66 2.90
1706 1765 2.753247 AGGGTGTCCTCATTCTAGGTC 58.247 52.381 0.00 0.00 39.80 3.85
1824 2037 5.293324 GCTTTCGGTTTGTTTCCTTTCATTT 59.707 36.000 0.00 0.00 0.00 2.32
2028 2253 4.273480 ACACAATACAGAAGCAACACTCAC 59.727 41.667 0.00 0.00 0.00 3.51
2045 2270 4.445718 CACTCACATACACACAGACACTTC 59.554 45.833 0.00 0.00 0.00 3.01
2052 2277 2.286831 ACACACAGACACTTCGTAGTCG 60.287 50.000 0.00 0.00 39.67 4.18
2061 2286 3.092135 CACTTCGTAGTCGATGAGAACG 58.908 50.000 9.70 0.00 45.65 3.95
2077 2302 2.095161 AGAACGTCGTCTCATCCTGAAC 60.095 50.000 0.00 0.00 0.00 3.18
2078 2303 0.168348 ACGTCGTCTCATCCTGAACG 59.832 55.000 0.00 0.00 34.27 3.95
2079 2304 0.168348 CGTCGTCTCATCCTGAACGT 59.832 55.000 0.00 0.00 34.74 3.99
2084 2309 5.383958 GTCGTCTCATCCTGAACGTATATC 58.616 45.833 0.00 0.00 34.74 1.63
2127 2352 3.325870 TCGAGAAAATGCGAACACTCAT 58.674 40.909 0.00 0.00 33.04 2.90
2155 2380 3.441572 GTGAATGACTTGAACCTGGGATG 59.558 47.826 0.00 0.00 0.00 3.51
2156 2381 3.330405 TGAATGACTTGAACCTGGGATGA 59.670 43.478 0.00 0.00 0.00 2.92
2157 2382 4.018141 TGAATGACTTGAACCTGGGATGAT 60.018 41.667 0.00 0.00 0.00 2.45
2162 2387 2.196742 TGAACCTGGGATGATAGGCT 57.803 50.000 0.00 0.00 37.61 4.58
2174 2399 2.422597 TGATAGGCTTGTTTCACCACG 58.577 47.619 0.00 0.00 0.00 4.94
2196 2421 2.497273 GGTAACCTAACCGTCCAAGCTA 59.503 50.000 0.00 0.00 0.00 3.32
2197 2422 2.756840 AACCTAACCGTCCAAGCTAC 57.243 50.000 0.00 0.00 0.00 3.58
2198 2423 1.636148 ACCTAACCGTCCAAGCTACA 58.364 50.000 0.00 0.00 0.00 2.74
2199 2424 1.274447 ACCTAACCGTCCAAGCTACAC 59.726 52.381 0.00 0.00 0.00 2.90
2200 2425 1.549170 CCTAACCGTCCAAGCTACACT 59.451 52.381 0.00 0.00 0.00 3.55
2201 2426 2.416972 CCTAACCGTCCAAGCTACACTC 60.417 54.545 0.00 0.00 0.00 3.51
2202 2427 1.045407 AACCGTCCAAGCTACACTCA 58.955 50.000 0.00 0.00 0.00 3.41
2203 2428 1.045407 ACCGTCCAAGCTACACTCAA 58.955 50.000 0.00 0.00 0.00 3.02
2204 2429 1.623811 ACCGTCCAAGCTACACTCAAT 59.376 47.619 0.00 0.00 0.00 2.57
2205 2430 2.271800 CCGTCCAAGCTACACTCAATC 58.728 52.381 0.00 0.00 0.00 2.67
2206 2431 2.353704 CCGTCCAAGCTACACTCAATCA 60.354 50.000 0.00 0.00 0.00 2.57
2207 2432 2.668457 CGTCCAAGCTACACTCAATCAC 59.332 50.000 0.00 0.00 0.00 3.06
2208 2433 3.664107 GTCCAAGCTACACTCAATCACA 58.336 45.455 0.00 0.00 0.00 3.58
2209 2434 4.065088 GTCCAAGCTACACTCAATCACAA 58.935 43.478 0.00 0.00 0.00 3.33
2210 2435 4.697352 GTCCAAGCTACACTCAATCACAAT 59.303 41.667 0.00 0.00 0.00 2.71
2211 2436 4.937620 TCCAAGCTACACTCAATCACAATC 59.062 41.667 0.00 0.00 0.00 2.67
2212 2437 4.696877 CCAAGCTACACTCAATCACAATCA 59.303 41.667 0.00 0.00 0.00 2.57
2213 2438 5.356190 CCAAGCTACACTCAATCACAATCAT 59.644 40.000 0.00 0.00 0.00 2.45
2214 2439 6.255950 CAAGCTACACTCAATCACAATCATG 58.744 40.000 0.00 0.00 0.00 3.07
2215 2440 5.494724 AGCTACACTCAATCACAATCATGT 58.505 37.500 0.00 0.00 41.61 3.21
2216 2441 5.942236 AGCTACACTCAATCACAATCATGTT 59.058 36.000 0.00 0.00 37.82 2.71
2217 2442 6.432162 AGCTACACTCAATCACAATCATGTTT 59.568 34.615 0.00 0.00 37.82 2.83
2218 2443 7.040201 AGCTACACTCAATCACAATCATGTTTT 60.040 33.333 0.00 0.00 37.82 2.43
2219 2444 8.236586 GCTACACTCAATCACAATCATGTTTTA 58.763 33.333 0.00 0.00 37.82 1.52
2222 2447 9.814899 ACACTCAATCACAATCATGTTTTAAAA 57.185 25.926 0.00 0.00 37.82 1.52
2304 2529 6.677913 AGCGTAGAAATAAGCACACAAAAAT 58.322 32.000 0.00 0.00 0.00 1.82
2318 2543 9.539825 AGCACACAAAAATAATGACATAAAACA 57.460 25.926 0.00 0.00 0.00 2.83
2319 2544 9.796062 GCACACAAAAATAATGACATAAAACAG 57.204 29.630 0.00 0.00 0.00 3.16
2321 2546 8.987890 ACACAAAAATAATGACATAAAACAGGC 58.012 29.630 0.00 0.00 0.00 4.85
2322 2547 8.161610 CACAAAAATAATGACATAAAACAGGCG 58.838 33.333 0.00 0.00 0.00 5.52
2325 2550 3.932545 AATGACATAAAACAGGCGCAA 57.067 38.095 10.83 0.00 0.00 4.85
2326 2551 3.932545 ATGACATAAAACAGGCGCAAA 57.067 38.095 10.83 0.00 0.00 3.68
2327 2552 3.281341 TGACATAAAACAGGCGCAAAG 57.719 42.857 10.83 0.00 0.00 2.77
2338 2563 4.724697 CGCAAAGCAGCCGACACG 62.725 66.667 0.00 0.00 0.00 4.49
2339 2564 3.345808 GCAAAGCAGCCGACACGA 61.346 61.111 0.00 0.00 0.00 4.35
2340 2565 2.680913 GCAAAGCAGCCGACACGAT 61.681 57.895 0.00 0.00 0.00 3.73
2341 2566 1.868997 CAAAGCAGCCGACACGATT 59.131 52.632 0.00 0.00 0.00 3.34
2342 2567 0.238289 CAAAGCAGCCGACACGATTT 59.762 50.000 0.00 0.00 0.00 2.17
2343 2568 0.951558 AAAGCAGCCGACACGATTTT 59.048 45.000 0.00 0.00 0.00 1.82
2344 2569 0.517316 AAGCAGCCGACACGATTTTC 59.483 50.000 0.00 0.00 0.00 2.29
2345 2570 0.320771 AGCAGCCGACACGATTTTCT 60.321 50.000 0.00 0.00 0.00 2.52
2365 2590 2.586258 TTTTTAGCAAAACAGGCGCA 57.414 40.000 10.83 0.00 36.08 6.09
2385 2610 5.142635 GCAAAAAGCGTTTGACTTGAAAT 57.857 34.783 17.06 0.00 0.00 2.17
2392 2617 9.753669 AAAAGCGTTTGACTTGAAATTAAAAAG 57.246 25.926 0.00 0.00 0.00 2.27
2399 2624 6.644347 TGACTTGAAATTAAAAAGGCCACAA 58.356 32.000 5.01 0.00 0.00 3.33
2402 2627 9.267084 GACTTGAAATTAAAAAGGCCACAAATA 57.733 29.630 5.01 0.00 0.00 1.40
2454 2682 8.548880 AAAACATACTAGTATTAGAGGCCAGA 57.451 34.615 12.87 0.00 0.00 3.86
2455 2683 8.548880 AAACATACTAGTATTAGAGGCCAGAA 57.451 34.615 12.87 0.00 0.00 3.02
2456 2684 7.527568 ACATACTAGTATTAGAGGCCAGAAC 57.472 40.000 12.87 0.00 0.00 3.01
2457 2685 7.299134 ACATACTAGTATTAGAGGCCAGAACT 58.701 38.462 12.87 1.83 0.00 3.01
2458 2686 7.449086 ACATACTAGTATTAGAGGCCAGAACTC 59.551 40.741 12.87 0.00 35.20 3.01
2459 2687 5.141910 ACTAGTATTAGAGGCCAGAACTCC 58.858 45.833 5.01 0.00 35.58 3.85
2460 2688 3.995636 AGTATTAGAGGCCAGAACTCCA 58.004 45.455 5.01 0.00 35.58 3.86
2461 2689 4.362677 AGTATTAGAGGCCAGAACTCCAA 58.637 43.478 5.01 0.00 35.58 3.53
2462 2690 3.922171 ATTAGAGGCCAGAACTCCAAG 57.078 47.619 5.01 0.00 35.58 3.61
2463 2691 2.623418 TAGAGGCCAGAACTCCAAGA 57.377 50.000 5.01 0.00 35.58 3.02
2464 2692 1.274712 AGAGGCCAGAACTCCAAGAG 58.725 55.000 5.01 0.00 35.58 2.85
2465 2693 0.392327 GAGGCCAGAACTCCAAGAGC 60.392 60.000 5.01 0.00 32.04 4.09
2466 2694 0.839853 AGGCCAGAACTCCAAGAGCT 60.840 55.000 5.01 0.00 32.04 4.09
2467 2695 0.905357 GGCCAGAACTCCAAGAGCTA 59.095 55.000 0.00 0.00 32.04 3.32
2468 2696 1.279271 GGCCAGAACTCCAAGAGCTAA 59.721 52.381 0.00 0.00 32.04 3.09
2469 2697 2.092699 GGCCAGAACTCCAAGAGCTAAT 60.093 50.000 0.00 0.00 32.04 1.73
2470 2698 2.941720 GCCAGAACTCCAAGAGCTAATG 59.058 50.000 0.00 0.00 32.04 1.90
2502 2730 7.923344 AGAGCTAAATACACATAACAGTAGCAG 59.077 37.037 0.00 0.00 36.12 4.24
2505 2733 4.753516 ATACACATAACAGTAGCAGCCA 57.246 40.909 0.00 0.00 0.00 4.75
2510 2738 2.920724 TAACAGTAGCAGCCAACACA 57.079 45.000 0.00 0.00 0.00 3.72
2540 2768 2.367241 TCTTGTCCGTTGATGGAGTGAA 59.633 45.455 0.00 0.00 39.14 3.18
2546 2774 2.868583 CCGTTGATGGAGTGAATAGCTG 59.131 50.000 0.00 0.00 0.00 4.24
2557 2785 3.772025 AGTGAATAGCTGTAGTTCTGCCT 59.228 43.478 0.00 0.00 41.02 4.75
2572 2800 0.321671 TGCCTAGCTTCGCTCTTGTT 59.678 50.000 0.00 0.00 40.44 2.83
2573 2801 1.270839 TGCCTAGCTTCGCTCTTGTTT 60.271 47.619 0.00 0.00 40.44 2.83
2581 2809 2.910688 TCGCTCTTGTTTCTCCTTGT 57.089 45.000 0.00 0.00 0.00 3.16
2591 2819 3.071602 TGTTTCTCCTTGTCCTTCCTCTG 59.928 47.826 0.00 0.00 0.00 3.35
2595 2823 1.150135 TCCTTGTCCTTCCTCTGTCCT 59.850 52.381 0.00 0.00 0.00 3.85
2611 2839 1.348036 GTCCTAGAGGCAACCACAACT 59.652 52.381 0.00 0.00 34.44 3.16
2619 2847 1.754226 GGCAACCACAACTGGAAAAGA 59.246 47.619 0.00 0.00 40.55 2.52
2620 2848 2.365293 GGCAACCACAACTGGAAAAGAT 59.635 45.455 0.00 0.00 40.55 2.40
2622 2850 4.321230 GGCAACCACAACTGGAAAAGATAG 60.321 45.833 0.00 0.00 40.55 2.08
2634 2862 5.299148 TGGAAAAGATAGACCGTTCGAAAA 58.701 37.500 0.00 0.00 0.00 2.29
2641 2869 5.577164 AGATAGACCGTTCGAAAATCACTTG 59.423 40.000 0.00 0.00 0.00 3.16
2657 2885 2.940410 CACTTGTGTTTCGGTACACCTT 59.060 45.455 15.24 1.29 46.13 3.50
2658 2886 3.001939 CACTTGTGTTTCGGTACACCTTC 59.998 47.826 15.24 0.00 46.13 3.46
2659 2887 2.243602 TGTGTTTCGGTACACCTTCC 57.756 50.000 15.24 0.00 46.13 3.46
2672 2900 5.981915 GGTACACCTTCCTAAACATATCGAC 59.018 44.000 0.00 0.00 0.00 4.20
2674 2902 4.400251 ACACCTTCCTAAACATATCGACGA 59.600 41.667 0.00 0.00 0.00 4.20
2675 2903 4.738740 CACCTTCCTAAACATATCGACGAC 59.261 45.833 0.00 0.00 0.00 4.34
2676 2904 3.973135 CCTTCCTAAACATATCGACGACG 59.027 47.826 0.00 0.00 41.26 5.12
2697 2925 7.070798 CGACGACTAAGATTAACTCATACCTC 58.929 42.308 0.00 0.00 0.00 3.85
2713 2941 8.945193 ACTCATACCTCTTTATAATAAAGGGCA 58.055 33.333 11.09 0.00 0.00 5.36
2716 2944 6.841781 ACCTCTTTATAATAAAGGGCAGGA 57.158 37.500 1.68 0.00 0.00 3.86
2717 2945 7.408013 ACCTCTTTATAATAAAGGGCAGGAT 57.592 36.000 1.68 0.00 0.00 3.24
2726 2954 6.530601 AATAAAGGGCAGGATGGTAAGTAT 57.469 37.500 0.00 0.00 35.86 2.12
2727 2955 7.642094 AATAAAGGGCAGGATGGTAAGTATA 57.358 36.000 0.00 0.00 35.86 1.47
2729 2957 6.530601 AAAGGGCAGGATGGTAAGTATATT 57.469 37.500 0.00 0.00 35.86 1.28
2730 2958 5.505181 AGGGCAGGATGGTAAGTATATTG 57.495 43.478 0.00 0.00 35.86 1.90
2737 2965 7.554118 GCAGGATGGTAAGTATATTGTATGCAT 59.446 37.037 3.79 3.79 35.86 3.96
2738 2966 8.886719 CAGGATGGTAAGTATATTGTATGCATG 58.113 37.037 10.16 0.00 0.00 4.06
2739 2967 8.049117 AGGATGGTAAGTATATTGTATGCATGG 58.951 37.037 10.16 0.00 0.00 3.66
2741 2969 9.448438 GATGGTAAGTATATTGTATGCATGGAA 57.552 33.333 10.16 1.77 0.00 3.53
2744 2972 5.862924 AGTATATTGTATGCATGGAACGC 57.137 39.130 10.16 0.00 0.00 4.84
2745 2973 5.304778 AGTATATTGTATGCATGGAACGCA 58.695 37.500 10.16 0.00 44.94 5.24
2747 2975 1.819928 TTGTATGCATGGAACGCACT 58.180 45.000 10.16 0.00 43.35 4.40
2752 2980 1.368641 TGCATGGAACGCACTGATAC 58.631 50.000 0.00 0.00 33.55 2.24
2753 2981 1.338579 TGCATGGAACGCACTGATACA 60.339 47.619 0.00 0.00 33.55 2.29
2754 2982 1.942657 GCATGGAACGCACTGATACAT 59.057 47.619 0.00 0.00 0.00 2.29
2808 3036 2.943036 ACGCCCTTTTTACTCTTCCA 57.057 45.000 0.00 0.00 0.00 3.53
2854 3082 4.935808 ACAACATGATTCGAACTAAGACCC 59.064 41.667 0.00 0.00 0.00 4.46
2856 3084 3.118371 ACATGATTCGAACTAAGACCCCC 60.118 47.826 0.00 0.00 0.00 5.40
2862 3090 0.696501 GAACTAAGACCCCCAGGCAA 59.303 55.000 0.00 0.00 36.11 4.52
2866 3094 1.843851 CTAAGACCCCCAGGCAACATA 59.156 52.381 0.00 0.00 41.41 2.29
2867 3095 1.080638 AAGACCCCCAGGCAACATAA 58.919 50.000 0.00 0.00 41.41 1.90
2896 3124 5.160607 TGGTAACCAACAGGACATCTTAG 57.839 43.478 0.00 0.00 0.00 2.18
2897 3125 4.019681 TGGTAACCAACAGGACATCTTAGG 60.020 45.833 0.00 0.00 0.00 2.69
2899 3127 5.188359 GGTAACCAACAGGACATCTTAGGTA 59.812 44.000 0.00 0.00 0.00 3.08
2910 3138 7.607991 CAGGACATCTTAGGTATTGTGACTTTT 59.392 37.037 0.00 0.00 0.00 2.27
2991 3220 5.571277 TGGTTTAGTTTTCTTCGGTTTTCG 58.429 37.500 0.00 0.00 40.90 3.46
2996 3225 7.495339 TTAGTTTTCTTCGGTTTTCGTTTTG 57.505 32.000 0.00 0.00 40.32 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 7.984617 TGTTAGACATCCGAATGTAATTGATGA 59.015 33.333 4.93 0.00 46.20 2.92
575 584 3.306780 CCCTGTCAACGTGGAAAGATAGT 60.307 47.826 12.07 0.00 0.00 2.12
583 592 1.990160 AAAGGCCCTGTCAACGTGGA 61.990 55.000 0.00 0.00 0.00 4.02
585 594 0.744281 AAAAAGGCCCTGTCAACGTG 59.256 50.000 0.00 0.00 0.00 4.49
719 735 4.436998 GCTGTGTACGCCCGAGCT 62.437 66.667 3.51 0.00 36.60 4.09
754 770 2.731691 AAGTTGGCTCGGACGTGCAT 62.732 55.000 18.51 1.26 36.47 3.96
829 845 6.877611 ACGATCACTTTGGTGTTAGAATTT 57.122 33.333 0.00 0.00 43.41 1.82
832 848 5.504994 GCAAACGATCACTTTGGTGTTAGAA 60.505 40.000 12.53 0.00 43.41 2.10
834 850 4.219033 GCAAACGATCACTTTGGTGTTAG 58.781 43.478 12.53 0.00 43.41 2.34
835 851 3.303461 CGCAAACGATCACTTTGGTGTTA 60.303 43.478 12.53 0.00 43.93 2.41
836 852 2.540769 CGCAAACGATCACTTTGGTGTT 60.541 45.455 12.53 0.00 43.93 3.32
837 853 1.002900 CGCAAACGATCACTTTGGTGT 60.003 47.619 12.53 0.00 43.93 4.16
838 854 1.673760 CGCAAACGATCACTTTGGTG 58.326 50.000 12.53 0.00 43.93 4.17
839 855 0.040425 GCGCAAACGATCACTTTGGT 60.040 50.000 0.30 0.00 43.93 3.67
840 856 0.040514 TGCGCAAACGATCACTTTGG 60.041 50.000 8.16 6.19 43.93 3.28
841 857 1.710249 CTTGCGCAAACGATCACTTTG 59.290 47.619 25.01 3.64 43.93 2.77
842 858 1.333619 ACTTGCGCAAACGATCACTTT 59.666 42.857 25.01 0.00 43.93 2.66
843 859 0.944386 ACTTGCGCAAACGATCACTT 59.056 45.000 25.01 0.00 43.93 3.16
844 860 0.944386 AACTTGCGCAAACGATCACT 59.056 45.000 25.01 0.00 43.93 3.41
845 861 1.318251 GAACTTGCGCAAACGATCAC 58.682 50.000 25.01 7.69 43.93 3.06
846 862 0.237235 GGAACTTGCGCAAACGATCA 59.763 50.000 25.01 0.00 43.93 2.92
847 863 0.237235 TGGAACTTGCGCAAACGATC 59.763 50.000 25.01 16.48 43.93 3.69
848 864 0.238289 CTGGAACTTGCGCAAACGAT 59.762 50.000 25.01 8.14 43.93 3.73
849 865 1.646540 CTGGAACTTGCGCAAACGA 59.353 52.632 25.01 13.91 43.93 3.85
850 866 2.010817 GCTGGAACTTGCGCAAACG 61.011 57.895 25.01 15.92 44.07 3.60
851 867 0.318955 ATGCTGGAACTTGCGCAAAC 60.319 50.000 25.01 17.13 35.83 2.93
852 868 0.039256 GATGCTGGAACTTGCGCAAA 60.039 50.000 25.01 7.86 35.83 3.68
853 869 1.171549 TGATGCTGGAACTTGCGCAA 61.172 50.000 23.48 23.48 35.83 4.85
854 870 1.600356 TGATGCTGGAACTTGCGCA 60.600 52.632 5.66 5.66 36.75 6.09
855 871 1.154150 GTGATGCTGGAACTTGCGC 60.154 57.895 0.00 0.00 0.00 6.09
856 872 1.503542 GGTGATGCTGGAACTTGCG 59.496 57.895 0.00 0.00 0.00 4.85
857 873 1.503542 CGGTGATGCTGGAACTTGC 59.496 57.895 0.00 0.00 0.00 4.01
858 874 0.606401 ACCGGTGATGCTGGAACTTG 60.606 55.000 6.12 0.00 46.81 3.16
859 875 0.606401 CACCGGTGATGCTGGAACTT 60.606 55.000 31.31 0.00 46.81 2.66
860 876 1.003355 CACCGGTGATGCTGGAACT 60.003 57.895 31.31 0.00 46.81 3.01
861 877 0.036765 TACACCGGTGATGCTGGAAC 60.037 55.000 40.21 0.00 46.81 3.62
862 878 0.687920 TTACACCGGTGATGCTGGAA 59.312 50.000 40.21 11.67 46.81 3.53
863 879 0.908910 ATTACACCGGTGATGCTGGA 59.091 50.000 40.21 16.80 46.81 3.86
865 881 2.095853 GTCAATTACACCGGTGATGCTG 59.904 50.000 40.21 27.56 0.00 4.41
866 882 2.027192 AGTCAATTACACCGGTGATGCT 60.027 45.455 40.21 24.92 0.00 3.79
867 883 2.356135 AGTCAATTACACCGGTGATGC 58.644 47.619 40.21 23.52 0.00 3.91
868 884 5.371115 AAAAGTCAATTACACCGGTGATG 57.629 39.130 40.21 28.41 0.00 3.07
869 885 7.110155 AGATAAAAGTCAATTACACCGGTGAT 58.890 34.615 40.21 25.27 0.00 3.06
870 886 6.469410 AGATAAAAGTCAATTACACCGGTGA 58.531 36.000 40.21 20.46 0.00 4.02
871 887 6.594159 AGAGATAAAAGTCAATTACACCGGTG 59.406 38.462 32.83 32.83 0.00 4.94
872 888 6.708285 AGAGATAAAAGTCAATTACACCGGT 58.292 36.000 0.00 0.00 0.00 5.28
873 889 6.019801 CGAGAGATAAAAGTCAATTACACCGG 60.020 42.308 0.00 0.00 0.00 5.28
874 890 6.019801 CCGAGAGATAAAAGTCAATTACACCG 60.020 42.308 0.00 0.00 0.00 4.94
875 891 6.238130 GCCGAGAGATAAAAGTCAATTACACC 60.238 42.308 0.00 0.00 0.00 4.16
876 892 6.508088 CGCCGAGAGATAAAAGTCAATTACAC 60.508 42.308 0.00 0.00 0.00 2.90
877 893 5.518847 CGCCGAGAGATAAAAGTCAATTACA 59.481 40.000 0.00 0.00 0.00 2.41
878 894 5.556570 GCGCCGAGAGATAAAAGTCAATTAC 60.557 44.000 0.00 0.00 0.00 1.89
879 895 4.506654 GCGCCGAGAGATAAAAGTCAATTA 59.493 41.667 0.00 0.00 0.00 1.40
880 896 3.309954 GCGCCGAGAGATAAAAGTCAATT 59.690 43.478 0.00 0.00 0.00 2.32
881 897 2.866762 GCGCCGAGAGATAAAAGTCAAT 59.133 45.455 0.00 0.00 0.00 2.57
882 898 2.268298 GCGCCGAGAGATAAAAGTCAA 58.732 47.619 0.00 0.00 0.00 3.18
883 899 1.797713 CGCGCCGAGAGATAAAAGTCA 60.798 52.381 0.00 0.00 0.00 3.41
884 900 0.847035 CGCGCCGAGAGATAAAAGTC 59.153 55.000 0.00 0.00 0.00 3.01
885 901 1.146358 GCGCGCCGAGAGATAAAAGT 61.146 55.000 23.24 0.00 0.00 2.66
886 902 0.872021 AGCGCGCCGAGAGATAAAAG 60.872 55.000 30.33 0.00 0.00 2.27
887 903 0.382873 TAGCGCGCCGAGAGATAAAA 59.617 50.000 30.33 0.00 0.00 1.52
983 999 0.831307 ACGGGGAAGTGATAGAAGGC 59.169 55.000 0.00 0.00 0.00 4.35
1018 1036 1.073923 GTGGTGGTGTTCTGGGATCTT 59.926 52.381 0.00 0.00 0.00 2.40
1023 1041 0.395036 TGTTGTGGTGGTGTTCTGGG 60.395 55.000 0.00 0.00 0.00 4.45
1032 1050 1.227704 TGGCTACGTGTTGTGGTGG 60.228 57.895 0.00 0.00 0.00 4.61
1035 1053 1.227704 TGGTGGCTACGTGTTGTGG 60.228 57.895 0.00 0.00 0.00 4.17
1037 1055 1.042229 TAGTGGTGGCTACGTGTTGT 58.958 50.000 0.00 0.00 0.00 3.32
1038 1056 2.066262 CTTAGTGGTGGCTACGTGTTG 58.934 52.381 0.00 0.00 0.00 3.33
1039 1057 1.607251 GCTTAGTGGTGGCTACGTGTT 60.607 52.381 0.00 0.00 0.00 3.32
1044 1062 1.153429 CGGGCTTAGTGGTGGCTAC 60.153 63.158 0.00 0.00 0.00 3.58
1260 1284 2.244117 ATCATGAAGACGCCCGTGCT 62.244 55.000 0.00 0.00 34.43 4.40
1358 1382 0.322975 GCGCTCCTCCATCCATATGT 59.677 55.000 0.00 0.00 0.00 2.29
1362 1386 3.933722 CGGCGCTCCTCCATCCAT 61.934 66.667 7.64 0.00 0.00 3.41
1411 1435 0.107410 ATAACAGCATCCCGGCGAAA 60.107 50.000 9.30 0.00 39.27 3.46
1419 1460 1.027357 CACAGGGCATAACAGCATCC 58.973 55.000 0.00 0.00 35.83 3.51
1420 1461 0.383231 GCACAGGGCATAACAGCATC 59.617 55.000 0.00 0.00 43.97 3.91
1439 1480 2.036475 ACTTATCTAGATGCCGCACAGG 59.964 50.000 15.79 0.00 44.97 4.00
1440 1481 3.377346 ACTTATCTAGATGCCGCACAG 57.623 47.619 15.79 2.78 0.00 3.66
1441 1482 4.379499 CGATACTTATCTAGATGCCGCACA 60.379 45.833 15.79 0.00 0.00 4.57
1442 1483 4.099120 CGATACTTATCTAGATGCCGCAC 58.901 47.826 15.79 2.71 0.00 5.34
1443 1484 4.007659 TCGATACTTATCTAGATGCCGCA 58.992 43.478 15.79 0.00 0.00 5.69
1539 1580 2.560542 GGCACCATGGTTCAAACATACA 59.439 45.455 16.84 0.00 0.00 2.29
1625 1680 8.543774 ACACTTATCAAGATACTCCTGTTTGAT 58.456 33.333 3.84 3.84 40.47 2.57
1631 1686 6.378710 TCGACACTTATCAAGATACTCCTG 57.621 41.667 0.00 0.00 0.00 3.86
1642 1697 8.002984 TGACACCTTAATATCGACACTTATCA 57.997 34.615 0.00 0.00 0.00 2.15
1698 1757 1.897802 GGAAGGTGAACGGACCTAGAA 59.102 52.381 3.71 0.00 46.29 2.10
1706 1765 4.982916 CGAATTAGATAGGAAGGTGAACGG 59.017 45.833 0.00 0.00 0.00 4.44
1886 2110 5.888412 AGCAGCAACGAAAACAAAATAAG 57.112 34.783 0.00 0.00 0.00 1.73
1899 2123 6.959361 AGAAAATAATACCATAGCAGCAACG 58.041 36.000 0.00 0.00 0.00 4.10
1900 2124 9.586435 AAAAGAAAATAATACCATAGCAGCAAC 57.414 29.630 0.00 0.00 0.00 4.17
2001 2225 6.959361 AGTGTTGCTTCTGTATTGTGTTTAG 58.041 36.000 0.00 0.00 0.00 1.85
2015 2239 3.559655 TGTGTGTATGTGAGTGTTGCTTC 59.440 43.478 0.00 0.00 0.00 3.86
2028 2253 4.795268 ACTACGAAGTGTCTGTGTGTATG 58.205 43.478 0.00 0.00 45.73 2.39
2045 2270 1.060266 ACGACGTTCTCATCGACTACG 59.940 52.381 0.00 0.00 40.86 3.51
2078 2303 9.856488 TTTATTCTAGGCATTCTGACGATATAC 57.144 33.333 0.00 0.00 0.00 1.47
2084 2309 6.420903 TCGAATTTATTCTAGGCATTCTGACG 59.579 38.462 1.41 0.00 34.69 4.35
2088 2313 8.964476 TTTCTCGAATTTATTCTAGGCATTCT 57.036 30.769 4.71 0.00 34.69 2.40
2093 2318 6.575201 CGCATTTTCTCGAATTTATTCTAGGC 59.425 38.462 4.71 0.00 34.69 3.93
2127 2352 5.939883 CCAGGTTCAAGTCATTCACTTATCA 59.060 40.000 0.00 0.00 44.14 2.15
2155 2380 1.737793 CCGTGGTGAAACAAGCCTATC 59.262 52.381 0.00 0.00 39.98 2.08
2156 2381 1.613255 CCCGTGGTGAAACAAGCCTAT 60.613 52.381 0.00 0.00 39.98 2.57
2157 2382 0.250553 CCCGTGGTGAAACAAGCCTA 60.251 55.000 0.00 0.00 39.98 3.93
2162 2387 1.212441 AGGTTACCCGTGGTGAAACAA 59.788 47.619 0.00 0.00 36.19 2.83
2174 2399 1.676916 GCTTGGACGGTTAGGTTACCC 60.677 57.143 0.00 0.00 34.56 3.69
2187 2412 3.664107 TGTGATTGAGTGTAGCTTGGAC 58.336 45.455 0.00 0.00 0.00 4.02
2191 2416 5.942236 ACATGATTGTGATTGAGTGTAGCTT 59.058 36.000 0.00 0.00 33.85 3.74
2196 2421 9.814899 TTTTAAAACATGATTGTGATTGAGTGT 57.185 25.926 0.00 0.00 35.83 3.55
2248 2473 7.282675 AGTCATGCAAATCAAAGAGATCCTTAG 59.717 37.037 0.00 0.00 35.39 2.18
2304 2529 5.378292 TTTGCGCCTGTTTTATGTCATTA 57.622 34.783 4.18 0.00 0.00 1.90
2310 2535 1.987770 CTGCTTTGCGCCTGTTTTATG 59.012 47.619 4.18 0.00 38.05 1.90
2313 2538 1.592400 GCTGCTTTGCGCCTGTTTT 60.592 52.632 4.18 0.00 38.05 2.43
2314 2539 2.028043 GCTGCTTTGCGCCTGTTT 59.972 55.556 4.18 0.00 38.05 2.83
2315 2540 3.982241 GGCTGCTTTGCGCCTGTT 61.982 61.111 4.18 0.00 41.95 3.16
2321 2546 4.724697 CGTGTCGGCTGCTTTGCG 62.725 66.667 0.00 0.00 0.00 4.85
2322 2547 2.187599 AATCGTGTCGGCTGCTTTGC 62.188 55.000 0.00 0.00 0.00 3.68
2325 2550 0.517316 GAAAATCGTGTCGGCTGCTT 59.483 50.000 0.00 0.00 0.00 3.91
2326 2551 0.320771 AGAAAATCGTGTCGGCTGCT 60.321 50.000 0.00 0.00 0.00 4.24
2327 2552 0.517316 AAGAAAATCGTGTCGGCTGC 59.483 50.000 0.00 0.00 0.00 5.25
2328 2553 2.969443 AAAGAAAATCGTGTCGGCTG 57.031 45.000 0.00 0.00 0.00 4.85
2329 2554 3.982576 AAAAAGAAAATCGTGTCGGCT 57.017 38.095 0.00 0.00 0.00 5.52
2353 2578 3.804316 GCTTTTTGCGCCTGTTTTG 57.196 47.368 4.18 0.00 0.00 2.44
2363 2588 4.576106 TTTCAAGTCAAACGCTTTTTGC 57.424 36.364 3.39 0.45 38.57 3.68
2377 2602 9.271828 CTATTTGTGGCCTTTTTAATTTCAAGT 57.728 29.630 3.32 0.00 0.00 3.16
2402 2627 7.732025 TGTCCACCGAATTATATATTGTCACT 58.268 34.615 0.00 0.00 0.00 3.41
2419 2644 8.882415 AATACTAGTATGTTTTATGTCCACCG 57.118 34.615 16.11 0.00 0.00 4.94
2450 2678 4.081198 AGACATTAGCTCTTGGAGTTCTGG 60.081 45.833 0.00 0.00 31.39 3.86
2451 2679 5.083533 AGACATTAGCTCTTGGAGTTCTG 57.916 43.478 0.00 0.00 31.39 3.02
2452 2680 6.191315 TCTAGACATTAGCTCTTGGAGTTCT 58.809 40.000 0.00 0.00 31.39 3.01
2453 2681 6.320164 TCTCTAGACATTAGCTCTTGGAGTTC 59.680 42.308 0.00 0.00 31.39 3.01
2454 2682 6.191315 TCTCTAGACATTAGCTCTTGGAGTT 58.809 40.000 0.00 0.00 31.39 3.01
2455 2683 5.761205 TCTCTAGACATTAGCTCTTGGAGT 58.239 41.667 0.00 0.00 31.39 3.85
2456 2684 5.278463 GCTCTCTAGACATTAGCTCTTGGAG 60.278 48.000 0.00 0.00 0.00 3.86
2457 2685 4.582656 GCTCTCTAGACATTAGCTCTTGGA 59.417 45.833 0.00 0.00 0.00 3.53
2458 2686 4.584325 AGCTCTCTAGACATTAGCTCTTGG 59.416 45.833 0.00 0.00 39.23 3.61
2459 2687 5.772825 AGCTCTCTAGACATTAGCTCTTG 57.227 43.478 0.00 0.00 39.23 3.02
2460 2688 7.889873 TTTAGCTCTCTAGACATTAGCTCTT 57.110 36.000 14.28 0.00 42.33 2.85
2461 2689 9.010029 GTATTTAGCTCTCTAGACATTAGCTCT 57.990 37.037 14.28 6.84 42.33 4.09
2462 2690 8.788806 TGTATTTAGCTCTCTAGACATTAGCTC 58.211 37.037 14.28 4.78 42.33 4.09
2463 2691 8.573035 GTGTATTTAGCTCTCTAGACATTAGCT 58.427 37.037 14.93 14.93 45.14 3.32
2464 2692 8.353684 TGTGTATTTAGCTCTCTAGACATTAGC 58.646 37.037 0.00 0.00 0.00 3.09
2469 2697 9.185680 TGTTATGTGTATTTAGCTCTCTAGACA 57.814 33.333 0.00 0.00 0.00 3.41
2470 2698 9.672086 CTGTTATGTGTATTTAGCTCTCTAGAC 57.328 37.037 0.00 0.00 0.00 2.59
2502 2730 5.376854 ACAAGATACTTGATTGTGTTGGC 57.623 39.130 16.65 0.00 35.89 4.52
2505 2733 5.305585 ACGGACAAGATACTTGATTGTGTT 58.694 37.500 16.65 0.00 37.29 3.32
2510 2738 5.586243 CCATCAACGGACAAGATACTTGATT 59.414 40.000 16.65 4.57 0.00 2.57
2540 2768 3.571590 AGCTAGGCAGAACTACAGCTAT 58.428 45.455 0.00 0.00 0.00 2.97
2572 2800 2.900546 GACAGAGGAAGGACAAGGAGAA 59.099 50.000 0.00 0.00 0.00 2.87
2573 2801 2.530701 GACAGAGGAAGGACAAGGAGA 58.469 52.381 0.00 0.00 0.00 3.71
2591 2819 1.348036 AGTTGTGGTTGCCTCTAGGAC 59.652 52.381 0.00 0.00 37.39 3.85
2595 2823 1.429930 TCCAGTTGTGGTTGCCTCTA 58.570 50.000 0.00 0.00 45.28 2.43
2604 2832 3.684788 CGGTCTATCTTTTCCAGTTGTGG 59.315 47.826 0.00 0.00 46.63 4.17
2611 2839 4.524316 TTCGAACGGTCTATCTTTTCCA 57.476 40.909 0.00 0.00 0.00 3.53
2619 2847 5.120208 CACAAGTGATTTTCGAACGGTCTAT 59.880 40.000 0.00 0.00 0.00 1.98
2620 2848 4.446385 CACAAGTGATTTTCGAACGGTCTA 59.554 41.667 0.00 0.00 0.00 2.59
2622 2850 3.001939 ACACAAGTGATTTTCGAACGGTC 59.998 43.478 7.28 0.00 0.00 4.79
2641 2869 4.212004 GTTTAGGAAGGTGTACCGAAACAC 59.788 45.833 13.78 10.67 44.76 3.32
2672 2900 6.957150 AGGTATGAGTTAATCTTAGTCGTCG 58.043 40.000 0.00 0.00 0.00 5.12
2674 2902 8.522542 AAGAGGTATGAGTTAATCTTAGTCGT 57.477 34.615 0.00 0.00 0.00 4.34
2689 2917 8.383175 CCTGCCCTTTATTATAAAGAGGTATGA 58.617 37.037 22.12 9.19 0.00 2.15
2697 2925 8.934023 TTACCATCCTGCCCTTTATTATAAAG 57.066 34.615 15.62 15.62 0.00 1.85
2713 2941 8.049117 CCATGCATACAATATACTTACCATCCT 58.951 37.037 0.00 0.00 0.00 3.24
2716 2944 9.231297 GTTCCATGCATACAATATACTTACCAT 57.769 33.333 0.00 0.00 0.00 3.55
2717 2945 7.386573 CGTTCCATGCATACAATATACTTACCA 59.613 37.037 0.00 0.00 0.00 3.25
2726 2954 3.312146 CAGTGCGTTCCATGCATACAATA 59.688 43.478 0.00 0.00 42.74 1.90
2727 2955 2.097954 CAGTGCGTTCCATGCATACAAT 59.902 45.455 0.00 0.00 42.74 2.71
2729 2957 1.085893 CAGTGCGTTCCATGCATACA 58.914 50.000 0.00 0.00 42.74 2.29
2730 2958 1.368641 TCAGTGCGTTCCATGCATAC 58.631 50.000 0.00 0.00 42.74 2.39
2737 2965 2.028567 TGTCATGTATCAGTGCGTTCCA 60.029 45.455 0.00 0.00 0.00 3.53
2738 2966 2.616960 TGTCATGTATCAGTGCGTTCC 58.383 47.619 0.00 0.00 0.00 3.62
2739 2967 4.864916 AATGTCATGTATCAGTGCGTTC 57.135 40.909 0.00 0.00 0.00 3.95
2741 2969 3.623060 GGAAATGTCATGTATCAGTGCGT 59.377 43.478 0.00 0.00 0.00 5.24
2744 2972 5.188434 AGGTGGAAATGTCATGTATCAGTG 58.812 41.667 0.00 0.00 0.00 3.66
2745 2973 5.431765 GAGGTGGAAATGTCATGTATCAGT 58.568 41.667 0.00 0.00 0.00 3.41
2747 2975 4.227073 TGGAGGTGGAAATGTCATGTATCA 59.773 41.667 0.00 0.00 0.00 2.15
2752 2980 2.094675 GGTGGAGGTGGAAATGTCATG 58.905 52.381 0.00 0.00 0.00 3.07
2753 2981 1.710244 TGGTGGAGGTGGAAATGTCAT 59.290 47.619 0.00 0.00 0.00 3.06
2754 2982 1.144691 TGGTGGAGGTGGAAATGTCA 58.855 50.000 0.00 0.00 0.00 3.58
2784 3012 5.182380 TGGAAGAGTAAAAAGGGCGTAAATG 59.818 40.000 0.00 0.00 0.00 2.32
2789 3017 2.943036 TGGAAGAGTAAAAAGGGCGT 57.057 45.000 0.00 0.00 0.00 5.68
2791 3019 9.151471 GAATTTTAATGGAAGAGTAAAAAGGGC 57.849 33.333 0.00 0.00 37.57 5.19
2808 3036 8.641499 TGTTCGCAGAGTTTTTGAATTTTAAT 57.359 26.923 0.00 0.00 38.43 1.40
2823 3051 2.667969 TCGAATCATGTTGTTCGCAGAG 59.332 45.455 18.72 2.05 44.91 3.35
2826 3054 2.805671 AGTTCGAATCATGTTGTTCGCA 59.194 40.909 18.72 10.49 44.91 5.10
2851 3079 1.080638 TCTTTATGTTGCCTGGGGGT 58.919 50.000 0.00 0.00 34.45 4.95
2854 3082 3.119029 CCATTGTCTTTATGTTGCCTGGG 60.119 47.826 0.00 0.00 0.00 4.45
2856 3084 4.789012 ACCATTGTCTTTATGTTGCCTG 57.211 40.909 0.00 0.00 0.00 4.85
2862 3090 6.208599 CCTGTTGGTTACCATTGTCTTTATGT 59.791 38.462 4.38 0.00 31.53 2.29
2866 3094 4.583073 GTCCTGTTGGTTACCATTGTCTTT 59.417 41.667 4.38 0.00 31.53 2.52
2867 3095 4.142038 GTCCTGTTGGTTACCATTGTCTT 58.858 43.478 4.38 0.00 31.53 3.01


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

AutoCloner maintained by Alex Coulton.