Multiple sequence alignment - TraesCS2B01G226000

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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 TraesCS2B01G226000 chr2B 100.000 2353 0 0 2399 4751 216854894 216852542 0.000000e+00 4346.0
1 TraesCS2B01G226000 chr2B 100.000 1931 0 0 1 1931 216857292 216855362 0.000000e+00 3567.0
2 TraesCS2B01G226000 chr2B 91.033 513 18 3 1171 1682 239996956 239996471 0.000000e+00 667.0
3 TraesCS2B01G226000 chr2B 90.476 84 8 0 1842 1925 9739421 9739504 1.400000e-20 111.0
4 TraesCS2B01G226000 chr2D 93.327 2053 89 26 2733 4751 159688299 159686261 0.000000e+00 2988.0
5 TraesCS2B01G226000 chr2D 89.134 681 40 8 674 1333 159690171 159689504 0.000000e+00 817.0
6 TraesCS2B01G226000 chr2D 84.334 383 43 14 1379 1751 159689414 159689039 4.520000e-95 359.0
7 TraesCS2B01G226000 chr2D 91.765 85 7 0 1841 1925 557267267 557267183 8.350000e-23 119.0
8 TraesCS2B01G226000 chr2A 96.505 1545 47 6 2733 4272 170933824 170932282 0.000000e+00 2547.0
9 TraesCS2B01G226000 chr2A 92.110 621 33 2 746 1350 170935518 170934898 0.000000e+00 861.0
10 TraesCS2B01G226000 chr2A 85.567 388 40 8 1379 1751 170934811 170934425 4.460000e-105 392.0
11 TraesCS2B01G226000 chr2A 83.434 332 39 11 4355 4670 170915309 170914978 1.290000e-75 294.0
12 TraesCS2B01G226000 chr2A 81.416 226 27 9 4539 4750 170914972 170914748 2.270000e-38 171.0
13 TraesCS2B01G226000 chr2A 93.814 97 4 2 2641 2736 678421970 678422065 1.380000e-30 145.0
14 TraesCS2B01G226000 chr2A 95.000 80 4 0 4271 4350 170932121 170932042 4.990000e-25 126.0
15 TraesCS2B01G226000 chr2A 89.773 88 8 1 1839 1925 593655906 593655993 1.400000e-20 111.0
16 TraesCS2B01G226000 chr7B 93.478 690 23 5 1 669 586332788 586332100 0.000000e+00 1005.0
17 TraesCS2B01G226000 chr7B 92.814 668 44 3 1 666 585911694 585911029 0.000000e+00 965.0
18 TraesCS2B01G226000 chr7B 89.820 668 63 4 1 666 224052864 224053528 0.000000e+00 852.0
19 TraesCS2B01G226000 chr7B 91.033 513 18 9 1171 1682 712761274 712760789 0.000000e+00 667.0
20 TraesCS2B01G226000 chr3B 93.103 667 41 3 1 665 693650681 693650018 0.000000e+00 972.0
21 TraesCS2B01G226000 chr3B 92.665 668 34 7 1 666 30496251 30495597 0.000000e+00 948.0
22 TraesCS2B01G226000 chr3B 90.891 516 19 3 1171 1685 272587888 272587400 0.000000e+00 667.0
23 TraesCS2B01G226000 chr3B 96.231 398 11 2 1280 1677 233224726 233225119 0.000000e+00 649.0
24 TraesCS2B01G226000 chr3B 93.506 77 5 0 1854 1930 680423370 680423294 1.080000e-21 115.0
25 TraesCS2B01G226000 chr3B 90.476 84 8 0 1842 1925 113517657 113517574 1.400000e-20 111.0
26 TraesCS2B01G226000 chr3B 84.404 109 11 5 1825 1928 1611936 1612043 8.410000e-18 102.0
27 TraesCS2B01G226000 chr6B 92.708 672 40 5 1 670 701622380 701623044 0.000000e+00 961.0
28 TraesCS2B01G226000 chr6B 90.419 668 58 5 1 666 645517849 645518512 0.000000e+00 874.0
29 TraesCS2B01G226000 chr6B 95.736 516 17 3 1168 1682 664806123 664806634 0.000000e+00 826.0
30 TraesCS2B01G226000 chr1B 90.120 668 60 4 1 666 441495288 441495951 0.000000e+00 863.0
31 TraesCS2B01G226000 chr5B 88.840 681 66 7 1 677 509474100 509474774 0.000000e+00 828.0
32 TraesCS2B01G226000 chr5B 96.020 402 13 1 1280 1681 619683559 619683161 0.000000e+00 651.0
33 TraesCS2B01G226000 chr5B 89.720 107 7 3 2649 2752 227839161 227839056 2.980000e-27 134.0
34 TraesCS2B01G226000 chr6A 95.814 215 9 0 1280 1494 567628236 567628450 9.790000e-92 348.0
35 TraesCS2B01G226000 chr6A 86.890 328 18 7 1168 1494 580784826 580785129 1.270000e-90 344.0
36 TraesCS2B01G226000 chr6A 92.000 100 6 2 2640 2737 134179292 134179193 6.410000e-29 139.0
37 TraesCS2B01G226000 chr4B 91.975 162 10 2 3110 3268 628631680 628631841 1.720000e-54 224.0
38 TraesCS2B01G226000 chr4B 91.589 107 8 1 2643 2748 91298307 91298413 3.830000e-31 147.0
39 TraesCS2B01G226000 chr4B 88.182 110 11 2 2640 2748 432817386 432817278 3.860000e-26 130.0
40 TraesCS2B01G226000 chr5A 91.358 162 11 1 3110 3268 672417019 672417180 8.010000e-53 219.0
41 TraesCS2B01G226000 chr5A 92.784 97 4 3 2640 2734 659866868 659866963 2.310000e-28 137.0
42 TraesCS2B01G226000 chr4D 90.741 162 12 1 3110 3268 491692364 491692203 3.720000e-51 213.0
43 TraesCS2B01G226000 chr4D 96.032 126 5 0 3143 3268 490602926 490602801 6.230000e-49 206.0
44 TraesCS2B01G226000 chr4D 95.604 91 3 1 2646 2735 28237898 28237808 1.380000e-30 145.0
45 TraesCS2B01G226000 chr4D 95.082 61 3 0 1625 1685 448037494 448037434 3.910000e-16 97.1
46 TraesCS2B01G226000 chr7A 92.929 99 6 1 2638 2735 184126727 184126825 4.960000e-30 143.0
47 TraesCS2B01G226000 chr7A 92.857 84 6 0 1842 1925 398924516 398924433 6.460000e-24 122.0
48 TraesCS2B01G226000 chr4A 93.684 95 4 2 2648 2741 570916240 570916147 1.780000e-29 141.0
49 TraesCS2B01G226000 chr4A 90.361 83 8 0 1842 1924 590111631 590111549 5.030000e-20 110.0
50 TraesCS2B01G226000 chr1D 90.476 84 8 0 1842 1925 332935612 332935695 1.400000e-20 111.0


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 TraesCS2B01G226000 chr2B 216852542 216857292 4750 True 3956.5 4346 100.000000 1 4751 2 chr2B.!!$R2 4750
1 TraesCS2B01G226000 chr2D 159686261 159690171 3910 True 1388.0 2988 88.931667 674 4751 3 chr2D.!!$R2 4077
2 TraesCS2B01G226000 chr2A 170932042 170935518 3476 True 981.5 2547 92.295500 746 4350 4 chr2A.!!$R2 3604
3 TraesCS2B01G226000 chr2A 170914748 170915309 561 True 232.5 294 82.425000 4355 4750 2 chr2A.!!$R1 395
4 TraesCS2B01G226000 chr7B 586332100 586332788 688 True 1005.0 1005 93.478000 1 669 1 chr7B.!!$R2 668
5 TraesCS2B01G226000 chr7B 585911029 585911694 665 True 965.0 965 92.814000 1 666 1 chr7B.!!$R1 665
6 TraesCS2B01G226000 chr7B 224052864 224053528 664 False 852.0 852 89.820000 1 666 1 chr7B.!!$F1 665
7 TraesCS2B01G226000 chr3B 693650018 693650681 663 True 972.0 972 93.103000 1 665 1 chr3B.!!$R5 664
8 TraesCS2B01G226000 chr3B 30495597 30496251 654 True 948.0 948 92.665000 1 666 1 chr3B.!!$R1 665
9 TraesCS2B01G226000 chr6B 701622380 701623044 664 False 961.0 961 92.708000 1 670 1 chr6B.!!$F3 669
10 TraesCS2B01G226000 chr6B 645517849 645518512 663 False 874.0 874 90.419000 1 666 1 chr6B.!!$F1 665
11 TraesCS2B01G226000 chr6B 664806123 664806634 511 False 826.0 826 95.736000 1168 1682 1 chr6B.!!$F2 514
12 TraesCS2B01G226000 chr1B 441495288 441495951 663 False 863.0 863 90.120000 1 666 1 chr1B.!!$F1 665
13 TraesCS2B01G226000 chr5B 509474100 509474774 674 False 828.0 828 88.840000 1 677 1 chr5B.!!$F1 676

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
727 753 0.178926 TTCCCGTTACCCTCTCACCA 60.179 55.0 0.0 0.0 0.00 4.17 F
741 767 0.178955 TCACCACCGACTCCACCTTA 60.179 55.0 0.0 0.0 0.00 2.69 F
2492 2742 0.107654 GACCTGCCGATGCTTACCTT 60.108 55.0 0.0 0.0 38.71 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2722 0.107654 AAGGTAAGCATCGGCAGGTC 60.108 55.000 0.0 0.0 44.61 3.85 R
2709 2960 1.562475 CCCTCCGTCCCAAAATAAGGA 59.438 52.381 0.0 0.0 0.00 3.36 R
4426 4868 0.036952 ATCACTGCCAAGACCGACAG 60.037 55.000 0.0 0.0 36.22 3.51 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 77 2.045438 CCACACCGCCATGGCTTA 60.045 61.111 33.07 0.00 43.94 3.09
276 279 3.716195 CCATCCTGGGCGGTGTCA 61.716 66.667 0.00 0.00 32.67 3.58
283 286 1.076632 TGGGCGGTGTCAAAGGTTT 60.077 52.632 0.00 0.00 0.00 3.27
478 481 1.199789 CAGATGGCGCTGCAGTTTTAA 59.800 47.619 16.64 0.00 0.00 1.52
632 658 1.301423 AAAGCACTTTTACCGCGTGA 58.699 45.000 4.92 0.00 0.00 4.35
711 737 1.142474 CCGTACGGTGACACTTTTCC 58.858 55.000 26.39 0.00 0.00 3.13
720 746 1.770061 TGACACTTTTCCCGTTACCCT 59.230 47.619 0.00 0.00 0.00 4.34
727 753 0.178926 TTCCCGTTACCCTCTCACCA 60.179 55.000 0.00 0.00 0.00 4.17
728 754 0.901580 TCCCGTTACCCTCTCACCAC 60.902 60.000 0.00 0.00 0.00 4.16
737 763 1.587054 CTCTCACCACCGACTCCAC 59.413 63.158 0.00 0.00 0.00 4.02
740 766 1.458777 TCACCACCGACTCCACCTT 60.459 57.895 0.00 0.00 0.00 3.50
741 767 0.178955 TCACCACCGACTCCACCTTA 60.179 55.000 0.00 0.00 0.00 2.69
761 787 1.943693 CCCACAAACAAAGCGCGTG 60.944 57.895 8.43 11.94 0.00 5.34
768 794 1.440938 AACAAAGCGCGTGCCAACTA 61.441 50.000 19.02 0.00 44.31 2.24
770 796 0.794229 CAAAGCGCGTGCCAACTATG 60.794 55.000 19.02 4.17 44.31 2.23
799 825 1.442526 CCGCGGTCATACGAGTACCT 61.443 60.000 19.50 0.00 35.47 3.08
831 857 3.959991 GACAAGTCCGAGGGCCTGC 62.960 68.421 12.95 1.12 0.00 4.85
1116 1160 2.658422 GTACGTTTCCGCCTCCCA 59.342 61.111 0.00 0.00 37.70 4.37
1134 1178 1.539929 CCATGTCCCTCTGATTCGCTC 60.540 57.143 0.00 0.00 0.00 5.03
1151 1195 0.859232 CTCTTGTGTTCGTTGACCGG 59.141 55.000 0.00 0.00 37.11 5.28
1162 1206 3.517602 TCGTTGACCGGATTTGACTATG 58.482 45.455 9.46 0.00 37.11 2.23
1181 1225 1.274728 TGGATTGGCGTGAAAATTGGG 59.725 47.619 0.00 0.00 0.00 4.12
1198 1242 2.432444 TGGGTCAATTGCGTTTAGAGG 58.568 47.619 0.00 0.00 0.00 3.69
1399 1509 2.045536 CTGGGCAGCAGGGAAGAC 60.046 66.667 0.00 0.00 0.00 3.01
1655 1773 4.215613 GGACTCGAATGTAAAACCTGCTTT 59.784 41.667 0.00 0.00 0.00 3.51
1687 1820 5.257262 TGCCATTGCCATGTACTAAAGTAA 58.743 37.500 0.00 0.00 36.33 2.24
1738 1871 5.978919 TGAAGAAACATCAAGCAAACATGTC 59.021 36.000 0.00 0.00 30.22 3.06
1740 1873 6.882610 AGAAACATCAAGCAAACATGTCTA 57.117 33.333 0.00 0.00 30.22 2.59
1761 1894 8.908903 TGTCTACATGGTTTAACTGAAAAACAT 58.091 29.630 0.00 7.91 45.42 2.71
1765 1898 5.606348 TGGTTTAACTGAAAAACATGCCT 57.394 34.783 0.00 0.00 38.34 4.75
1768 1901 6.045955 GGTTTAACTGAAAAACATGCCTTCA 58.954 36.000 0.00 0.00 38.34 3.02
1769 1902 6.705825 GGTTTAACTGAAAAACATGCCTTCAT 59.294 34.615 0.00 0.00 38.34 2.57
1780 2003 4.191033 CATGCCTTCATGTGCCTTTTTA 57.809 40.909 0.00 0.00 43.85 1.52
1784 2007 5.719173 TGCCTTCATGTGCCTTTTTATAAC 58.281 37.500 0.00 0.00 0.00 1.89
1787 2010 6.818142 GCCTTCATGTGCCTTTTTATAACATT 59.182 34.615 0.00 0.00 29.20 2.71
1788 2011 7.978975 GCCTTCATGTGCCTTTTTATAACATTA 59.021 33.333 0.00 0.00 29.20 1.90
1827 2057 2.047061 TGTCCTGGAGCACACTACTTT 58.953 47.619 0.00 0.00 0.00 2.66
1837 2067 5.584649 GGAGCACACTACTTTATGCATTACA 59.415 40.000 3.54 0.00 40.63 2.41
1838 2068 6.260936 GGAGCACACTACTTTATGCATTACAT 59.739 38.462 3.54 0.00 40.63 2.29
1839 2069 7.441157 GGAGCACACTACTTTATGCATTACATA 59.559 37.037 3.54 0.00 40.63 2.29
1852 2082 5.849510 TGCATTACATAATACTGCCTACGT 58.150 37.500 0.00 0.00 0.00 3.57
1853 2083 6.983984 TGCATTACATAATACTGCCTACGTA 58.016 36.000 0.00 0.00 0.00 3.57
1855 2085 7.383029 TGCATTACATAATACTGCCTACGTAAC 59.617 37.037 0.00 0.00 0.00 2.50
1858 2088 6.475596 ACATAATACTGCCTACGTAACCTT 57.524 37.500 0.00 0.00 0.00 3.50
1861 2091 8.477256 ACATAATACTGCCTACGTAACCTTTTA 58.523 33.333 0.00 0.00 0.00 1.52
1862 2092 9.485206 CATAATACTGCCTACGTAACCTTTTAT 57.515 33.333 0.00 0.00 0.00 1.40
1865 2095 9.538508 AATACTGCCTACGTAACCTTTTATAAG 57.461 33.333 0.00 0.00 0.00 1.73
1867 2097 7.038048 ACTGCCTACGTAACCTTTTATAAGAC 58.962 38.462 0.00 0.00 32.92 3.01
1868 2098 6.035843 TGCCTACGTAACCTTTTATAAGACG 58.964 40.000 0.00 4.77 36.05 4.18
1869 2099 6.036470 GCCTACGTAACCTTTTATAAGACGT 58.964 40.000 13.10 13.10 41.90 4.34
1870 2100 6.531594 GCCTACGTAACCTTTTATAAGACGTT 59.468 38.462 13.55 5.24 40.55 3.99
1871 2101 7.063426 GCCTACGTAACCTTTTATAAGACGTTT 59.937 37.037 13.55 0.00 40.55 3.60
1872 2102 8.925700 CCTACGTAACCTTTTATAAGACGTTTT 58.074 33.333 13.55 0.00 40.55 2.43
1873 2103 9.731519 CTACGTAACCTTTTATAAGACGTTTTG 57.268 33.333 13.55 5.08 40.55 2.44
1880 2110 9.939802 ACCTTTTATAAGACGTTTTGATAGTCT 57.060 29.630 0.83 0.00 46.01 3.24
1887 2117 9.737427 ATAAGACGTTTTGATAGTCTATGACAG 57.263 33.333 0.83 0.00 43.60 3.51
1888 2118 7.159322 AGACGTTTTGATAGTCTATGACAGT 57.841 36.000 0.00 0.00 42.71 3.55
1889 2119 7.030165 AGACGTTTTGATAGTCTATGACAGTG 58.970 38.462 0.00 0.00 42.71 3.66
1890 2120 6.688578 ACGTTTTGATAGTCTATGACAGTGT 58.311 36.000 0.00 0.00 34.60 3.55
1891 2121 6.807230 ACGTTTTGATAGTCTATGACAGTGTC 59.193 38.462 16.68 16.68 34.60 3.67
1893 2123 7.328493 CGTTTTGATAGTCTATGACAGTGTCAA 59.672 37.037 28.70 16.69 45.96 3.18
1894 2124 8.988934 GTTTTGATAGTCTATGACAGTGTCAAA 58.011 33.333 28.70 14.94 45.96 2.69
1895 2125 9.554395 TTTTGATAGTCTATGACAGTGTCAAAA 57.446 29.630 28.70 17.57 45.96 2.44
1896 2126 9.554395 TTTGATAGTCTATGACAGTGTCAAAAA 57.446 29.630 28.70 16.19 45.96 1.94
1923 2153 8.848182 ACGTCTTATATTAAGTTACAGAGGGAG 58.152 37.037 0.00 0.00 0.00 4.30
1924 2154 8.848182 CGTCTTATATTAAGTTACAGAGGGAGT 58.152 37.037 0.00 0.00 0.00 3.85
2420 2650 4.833126 CGGCATAACAGTGTTGTATTAGC 58.167 43.478 18.90 10.93 36.23 3.09
2433 2663 1.211949 GTATTAGCTGCACCCCCTGAA 59.788 52.381 1.02 0.00 0.00 3.02
2434 2664 0.257039 ATTAGCTGCACCCCCTGAAG 59.743 55.000 1.02 0.00 0.00 3.02
2439 2669 3.984732 GCACCCCCTGAAGCCCTT 61.985 66.667 0.00 0.00 0.00 3.95
2448 2697 1.661341 CTGAAGCCCTTCCATTCTCG 58.339 55.000 5.64 0.00 38.77 4.04
2473 2722 4.852138 GCAACATGCAGTTCCTACATATG 58.148 43.478 0.00 0.00 44.26 1.78
2477 2726 4.410228 ACATGCAGTTCCTACATATGACCT 59.590 41.667 10.38 0.00 0.00 3.85
2492 2742 0.107654 GACCTGCCGATGCTTACCTT 60.108 55.000 0.00 0.00 38.71 3.50
2495 2745 2.172717 ACCTGCCGATGCTTACCTTAAT 59.827 45.455 0.00 0.00 38.71 1.40
2524 2775 5.515270 GTCTAAAAACTTTGAAGTGTGGCAC 59.485 40.000 11.55 11.55 39.66 5.01
2527 2778 3.951775 AACTTTGAAGTGTGGCACAAA 57.048 38.095 23.90 10.32 38.27 2.83
2538 2789 4.462508 TGTGGCACAAACAGATTTTGAA 57.537 36.364 19.74 0.00 44.16 2.69
2539 2790 5.021033 TGTGGCACAAACAGATTTTGAAT 57.979 34.783 19.74 0.00 44.16 2.57
2540 2791 4.809958 TGTGGCACAAACAGATTTTGAATG 59.190 37.500 19.74 0.00 44.16 2.67
2541 2792 3.808726 TGGCACAAACAGATTTTGAATGC 59.191 39.130 3.81 4.24 33.40 3.56
2542 2793 3.187022 GGCACAAACAGATTTTGAATGCC 59.813 43.478 12.78 12.78 41.25 4.40
2543 2794 3.808726 GCACAAACAGATTTTGAATGCCA 59.191 39.130 3.81 0.00 33.83 4.92
2544 2795 4.453136 GCACAAACAGATTTTGAATGCCAT 59.547 37.500 3.81 0.00 33.83 4.40
2545 2796 5.638657 GCACAAACAGATTTTGAATGCCATA 59.361 36.000 3.81 0.00 33.83 2.74
2546 2797 6.314400 GCACAAACAGATTTTGAATGCCATAT 59.686 34.615 3.81 0.00 33.83 1.78
2547 2798 7.464977 GCACAAACAGATTTTGAATGCCATATC 60.465 37.037 3.81 0.00 33.83 1.63
2548 2799 7.010738 CACAAACAGATTTTGAATGCCATATCC 59.989 37.037 3.81 0.00 33.83 2.59
2549 2800 7.093201 ACAAACAGATTTTGAATGCCATATCCT 60.093 33.333 3.81 0.00 33.83 3.24
2550 2801 7.427989 AACAGATTTTGAATGCCATATCCTT 57.572 32.000 0.00 0.00 0.00 3.36
2551 2802 8.537728 AACAGATTTTGAATGCCATATCCTTA 57.462 30.769 0.00 0.00 0.00 2.69
2552 2803 8.716674 ACAGATTTTGAATGCCATATCCTTAT 57.283 30.769 0.00 0.00 0.00 1.73
2553 2804 9.151177 ACAGATTTTGAATGCCATATCCTTATT 57.849 29.630 0.00 0.00 0.00 1.40
2554 2805 9.991906 CAGATTTTGAATGCCATATCCTTATTT 57.008 29.630 0.00 0.00 0.00 1.40
2560 2811 9.812347 TTGAATGCCATATCCTTATTTATCACT 57.188 29.630 0.00 0.00 0.00 3.41
2561 2812 9.234827 TGAATGCCATATCCTTATTTATCACTG 57.765 33.333 0.00 0.00 0.00 3.66
2562 2813 7.636150 ATGCCATATCCTTATTTATCACTGC 57.364 36.000 0.00 0.00 0.00 4.40
2563 2814 6.541907 TGCCATATCCTTATTTATCACTGCA 58.458 36.000 0.00 0.00 0.00 4.41
2564 2815 6.430925 TGCCATATCCTTATTTATCACTGCAC 59.569 38.462 0.00 0.00 0.00 4.57
2565 2816 6.656693 GCCATATCCTTATTTATCACTGCACT 59.343 38.462 0.00 0.00 0.00 4.40
2566 2817 7.361542 GCCATATCCTTATTTATCACTGCACTG 60.362 40.741 0.00 0.00 0.00 3.66
2584 2835 9.914834 ACTGCACTGTAAATATAAGGGATAAAA 57.085 29.630 0.00 0.00 0.00 1.52
2609 2860 5.081315 TCCCTTCCTTTTCACCCAAAATA 57.919 39.130 0.00 0.00 33.34 1.40
2635 2886 3.909995 TCAATCCTTCTGGACTTCCTGAA 59.090 43.478 14.77 14.77 46.51 3.02
2663 2914 8.302515 TCTTAATATAATACTCCATCCGTCCC 57.697 38.462 0.00 0.00 0.00 4.46
2664 2915 7.897030 TCTTAATATAATACTCCATCCGTCCCA 59.103 37.037 0.00 0.00 0.00 4.37
2665 2916 6.945636 AATATAATACTCCATCCGTCCCAA 57.054 37.500 0.00 0.00 0.00 4.12
2666 2917 6.945636 ATATAATACTCCATCCGTCCCAAA 57.054 37.500 0.00 0.00 0.00 3.28
2667 2918 5.640158 ATAATACTCCATCCGTCCCAAAA 57.360 39.130 0.00 0.00 0.00 2.44
2668 2919 4.519906 AATACTCCATCCGTCCCAAAAT 57.480 40.909 0.00 0.00 0.00 1.82
2669 2920 5.640158 AATACTCCATCCGTCCCAAAATA 57.360 39.130 0.00 0.00 0.00 1.40
2670 2921 5.640158 ATACTCCATCCGTCCCAAAATAA 57.360 39.130 0.00 0.00 0.00 1.40
2671 2922 3.886123 ACTCCATCCGTCCCAAAATAAG 58.114 45.455 0.00 0.00 0.00 1.73
2672 2923 3.265995 ACTCCATCCGTCCCAAAATAAGT 59.734 43.478 0.00 0.00 0.00 2.24
2673 2924 3.616219 TCCATCCGTCCCAAAATAAGTG 58.384 45.455 0.00 0.00 0.00 3.16
2674 2925 3.264706 TCCATCCGTCCCAAAATAAGTGA 59.735 43.478 0.00 0.00 0.00 3.41
2675 2926 3.377172 CCATCCGTCCCAAAATAAGTGAC 59.623 47.826 0.00 0.00 0.00 3.67
2676 2927 4.261801 CATCCGTCCCAAAATAAGTGACT 58.738 43.478 0.00 0.00 0.00 3.41
2677 2928 3.934068 TCCGTCCCAAAATAAGTGACTC 58.066 45.455 0.00 0.00 0.00 3.36
2678 2929 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2679 2930 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2680 2931 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2681 2932 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2682 2933 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2683 2934 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2684 2935 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2685 2936 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2686 2937 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2687 2938 8.410141 CCCAAAATAAGTGACTCAACTTTGTAA 58.590 33.333 0.00 0.00 40.77 2.41
2688 2939 9.965824 CCAAAATAAGTGACTCAACTTTGTAAT 57.034 29.630 0.00 0.00 40.77 1.89
2720 2971 8.166422 AGTACAAAGTTGAGTCCTTATTTTGG 57.834 34.615 0.00 0.00 0.00 3.28
2721 2972 6.405278 ACAAAGTTGAGTCCTTATTTTGGG 57.595 37.500 0.00 0.00 0.00 4.12
2722 2973 6.133356 ACAAAGTTGAGTCCTTATTTTGGGA 58.867 36.000 0.00 0.00 0.00 4.37
2728 2979 2.640184 GTCCTTATTTTGGGACGGAGG 58.360 52.381 0.00 0.00 41.82 4.30
2729 2980 1.562475 TCCTTATTTTGGGACGGAGGG 59.438 52.381 0.00 0.00 0.00 4.30
2730 2981 1.562475 CCTTATTTTGGGACGGAGGGA 59.438 52.381 0.00 0.00 0.00 4.20
2731 2982 2.421529 CCTTATTTTGGGACGGAGGGAG 60.422 54.545 0.00 0.00 0.00 4.30
2744 2995 3.322254 ACGGAGGGAGTATAAGATTGCAG 59.678 47.826 0.00 0.00 0.00 4.41
2746 2997 4.039245 CGGAGGGAGTATAAGATTGCAGAA 59.961 45.833 0.00 0.00 0.00 3.02
2938 3191 7.526142 AGTCTAAACAGTTCTGTCATCACTA 57.474 36.000 5.91 0.00 0.00 2.74
3057 3310 5.648092 GGCTAATAACAAGGATGTCACTGTT 59.352 40.000 0.00 0.00 39.40 3.16
3090 3343 4.495422 CACTATGTGCTAAAGGAGTTCGT 58.505 43.478 0.00 0.00 0.00 3.85
3140 3393 5.905331 TCACCTGGGAGTCTCATGTTAATAT 59.095 40.000 0.00 0.00 0.00 1.28
3141 3394 6.042093 TCACCTGGGAGTCTCATGTTAATATC 59.958 42.308 0.00 0.00 0.00 1.63
3213 3466 0.843309 TTCCTGGGTGCAGAGAACAA 59.157 50.000 0.00 0.00 0.00 2.83
3375 3628 3.911155 GAAAGTTGAGCCACGCGCG 62.911 63.158 30.96 30.96 44.76 6.86
3543 3796 3.501911 AGCAGTGGTGGTGGCCTT 61.502 61.111 3.32 0.00 31.51 4.35
3795 4054 8.090831 TCACATGAGTATGTTATAAGCCTGATC 58.909 37.037 0.00 0.00 45.01 2.92
3907 4166 1.081094 GCCAAGCCATTGTCAATTGC 58.919 50.000 12.58 12.58 34.39 3.56
3913 4172 3.857052 AGCCATTGTCAATTGCATGAAG 58.143 40.909 20.33 0.00 32.34 3.02
3943 4202 5.217978 TGGACACCAGAAACTAAACGTAT 57.782 39.130 0.00 0.00 0.00 3.06
4026 4287 1.956802 CAAGGACAAAACGGCTCCC 59.043 57.895 0.00 0.00 0.00 4.30
4088 4367 6.016443 TCTGTGATGTACAATGCACAAATGAA 60.016 34.615 21.90 9.40 40.34 2.57
4089 4368 6.689554 TGTGATGTACAATGCACAAATGAAT 58.310 32.000 20.39 0.00 38.21 2.57
4090 4369 7.153315 TGTGATGTACAATGCACAAATGAATT 58.847 30.769 20.39 0.00 38.21 2.17
4091 4370 7.656542 TGTGATGTACAATGCACAAATGAATTT 59.343 29.630 20.39 0.00 38.21 1.82
4092 4371 8.497554 GTGATGTACAATGCACAAATGAATTTT 58.502 29.630 17.03 0.00 30.87 1.82
4093 4372 9.053840 TGATGTACAATGCACAAATGAATTTTT 57.946 25.926 0.00 0.00 30.87 1.94
4094 4373 9.320406 GATGTACAATGCACAAATGAATTTTTG 57.680 29.630 0.00 1.82 41.37 2.44
4096 4375 9.317936 TGTACAATGCACAAATGAATTTTTGTA 57.682 25.926 7.71 0.00 45.54 2.41
4099 4378 9.053840 ACAATGCACAAATGAATTTTTGTATGA 57.946 25.926 7.71 0.00 45.54 2.15
4370 4812 1.622811 ACTCAGCTACTCTTGCTTGCT 59.377 47.619 0.00 0.00 38.92 3.91
4426 4868 2.033194 CGCCAACGGAGAAGGTTCC 61.033 63.158 0.00 0.00 34.97 3.62
4442 4884 1.407656 TTCCTGTCGGTCTTGGCAGT 61.408 55.000 0.00 0.00 0.00 4.40
4507 4949 1.336240 GCATTTGAAGGCGTGCTTCTT 60.336 47.619 0.00 0.00 34.85 2.52
4519 4964 1.048601 TGCTTCTTCACTTCCTCGGT 58.951 50.000 0.00 0.00 0.00 4.69
4593 5188 4.609018 CGATCTTGGCGGGGCGAT 62.609 66.667 0.00 0.00 0.00 4.58
4595 5190 3.460672 GATCTTGGCGGGGCGATCA 62.461 63.158 0.00 0.00 34.04 2.92
4597 5192 3.282157 CTTGGCGGGGCGATCATG 61.282 66.667 0.00 0.00 0.00 3.07
4599 5194 4.545706 TGGCGGGGCGATCATGTC 62.546 66.667 0.00 0.00 0.00 3.06
4601 5196 4.545706 GCGGGGCGATCATGTCCA 62.546 66.667 0.00 0.00 34.42 4.02
4602 5197 2.189257 CGGGGCGATCATGTCCAA 59.811 61.111 0.00 0.00 34.42 3.53
4603 5198 1.889105 CGGGGCGATCATGTCCAAG 60.889 63.158 0.00 0.00 34.42 3.61
4604 5199 1.224592 GGGGCGATCATGTCCAAGT 59.775 57.895 0.00 0.00 34.42 3.16
4606 5201 0.179000 GGGCGATCATGTCCAAGTCT 59.821 55.000 0.00 0.00 32.44 3.24
4607 5202 1.576356 GGCGATCATGTCCAAGTCTC 58.424 55.000 0.00 0.00 0.00 3.36
4608 5203 1.134699 GGCGATCATGTCCAAGTCTCA 60.135 52.381 0.00 0.00 0.00 3.27
4609 5204 2.484417 GGCGATCATGTCCAAGTCTCAT 60.484 50.000 0.00 0.00 0.00 2.90
4610 5205 2.799412 GCGATCATGTCCAAGTCTCATC 59.201 50.000 0.00 0.00 0.00 2.92
4611 5206 3.388308 CGATCATGTCCAAGTCTCATCC 58.612 50.000 0.00 0.00 0.00 3.51
4612 5207 3.181472 CGATCATGTCCAAGTCTCATCCA 60.181 47.826 0.00 0.00 0.00 3.41
4619 5228 3.632604 GTCCAAGTCTCATCCATACGAGA 59.367 47.826 0.00 0.00 35.93 4.04
4629 5238 0.102300 CCATACGAGACGACATGGCA 59.898 55.000 0.00 0.00 36.70 4.92
4635 5244 1.009829 GAGACGACATGGCATTGTCC 58.990 55.000 18.14 9.66 42.46 4.02
4654 5263 2.090719 TCCGATGGATTAGGGAAGGAGT 60.091 50.000 0.00 0.00 0.00 3.85
4695 5304 5.473162 TGAGATGACCGAACAACATGATTTT 59.527 36.000 0.00 0.00 0.00 1.82
4723 5332 0.608856 TTGGAGACCGCATGTGCATT 60.609 50.000 0.00 0.00 42.21 3.56
4740 5349 1.197721 CATTCGCGGAATTAGGATGGC 59.802 52.381 6.13 0.00 28.87 4.40
4746 5355 1.680338 GGAATTAGGATGGCGTTGCT 58.320 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
276 279 1.003718 CCTCGGCCTCGAAACCTTT 60.004 57.895 0.00 0.00 45.47 3.11
562 588 2.926420 GCGGTGGCGGGAAACAAAT 61.926 57.895 0.00 0.00 0.00 2.32
666 692 2.047830 GTAGTCAATCCCCCACCCTAG 58.952 57.143 0.00 0.00 0.00 3.02
701 727 2.038164 AGAGGGTAACGGGAAAAGTGTC 59.962 50.000 0.00 0.00 37.60 3.67
711 737 1.595357 GGTGGTGAGAGGGTAACGG 59.405 63.158 0.00 0.00 37.60 4.44
720 746 1.906824 GGTGGAGTCGGTGGTGAGA 60.907 63.158 0.00 0.00 0.00 3.27
727 753 1.611556 GGGGTAAGGTGGAGTCGGT 60.612 63.158 0.00 0.00 0.00 4.69
728 754 1.611261 TGGGGTAAGGTGGAGTCGG 60.611 63.158 0.00 0.00 0.00 4.79
737 763 1.000717 CGCTTTGTTTGTGGGGTAAGG 60.001 52.381 0.00 0.00 0.00 2.69
740 766 1.787057 CGCGCTTTGTTTGTGGGGTA 61.787 55.000 5.56 0.00 0.00 3.69
741 767 2.811799 GCGCTTTGTTTGTGGGGT 59.188 55.556 0.00 0.00 0.00 4.95
761 787 1.654023 GGCCCGTGTTCATAGTTGGC 61.654 60.000 0.00 0.00 36.68 4.52
813 839 2.266055 CAGGCCCTCGGACTTGTC 59.734 66.667 0.00 0.00 38.30 3.18
831 857 0.733729 TTTGACGGTGTGTTTTCGGG 59.266 50.000 0.00 0.00 0.00 5.14
954 998 2.582436 GGATCCGGGCAAACTCGA 59.418 61.111 0.00 0.00 0.00 4.04
1116 1160 1.786937 AGAGCGAATCAGAGGGACAT 58.213 50.000 0.00 0.00 0.00 3.06
1151 1195 3.876914 TCACGCCAATCCATAGTCAAATC 59.123 43.478 0.00 0.00 0.00 2.17
1162 1206 1.275010 ACCCAATTTTCACGCCAATCC 59.725 47.619 0.00 0.00 0.00 3.01
1181 1225 3.365969 CCCAACCTCTAAACGCAATTGAC 60.366 47.826 10.34 0.00 0.00 3.18
1198 1242 4.489306 AGAATACTTAGACAGGCCCAAC 57.511 45.455 0.00 0.00 0.00 3.77
1399 1509 3.817647 CACAGAACTGGAGAAAGAAAGGG 59.182 47.826 6.76 0.00 34.19 3.95
1596 1714 7.120579 TGTCCATAAACTATTAACCAAGCACAG 59.879 37.037 0.00 0.00 0.00 3.66
1655 1773 3.117550 ACATGGCAATGGCAGTTAGGATA 60.118 43.478 16.10 0.00 42.43 2.59
1738 1871 7.116233 GGCATGTTTTTCAGTTAAACCATGTAG 59.884 37.037 0.00 0.00 38.14 2.74
1740 1873 5.757808 GGCATGTTTTTCAGTTAAACCATGT 59.242 36.000 0.00 0.00 38.14 3.21
1761 1894 5.244851 TGTTATAAAAAGGCACATGAAGGCA 59.755 36.000 16.01 0.00 0.00 4.75
1762 1895 5.719173 TGTTATAAAAAGGCACATGAAGGC 58.281 37.500 0.00 3.83 0.00 4.35
1801 2024 2.655090 TGTGCTCCAGGACAAAATCA 57.345 45.000 0.00 0.00 43.38 2.57
1814 2044 6.662414 TGTAATGCATAAAGTAGTGTGCTC 57.338 37.500 0.00 0.00 38.37 4.26
1827 2057 7.608153 ACGTAGGCAGTATTATGTAATGCATA 58.392 34.615 0.00 8.12 39.91 3.14
1839 2069 9.538508 CTTATAAAAGGTTACGTAGGCAGTATT 57.461 33.333 0.00 0.00 0.00 1.89
1841 2071 8.190784 GTCTTATAAAAGGTTACGTAGGCAGTA 58.809 37.037 0.00 0.00 33.22 2.74
1842 2072 7.038048 GTCTTATAAAAGGTTACGTAGGCAGT 58.962 38.462 0.00 0.00 33.22 4.40
1843 2073 6.197842 CGTCTTATAAAAGGTTACGTAGGCAG 59.802 42.308 0.00 0.00 33.22 4.85
1844 2074 6.035843 CGTCTTATAAAAGGTTACGTAGGCA 58.964 40.000 0.00 0.00 33.22 4.75
1845 2075 6.036470 ACGTCTTATAAAAGGTTACGTAGGC 58.964 40.000 0.00 0.00 40.09 3.93
1846 2076 8.466086 AAACGTCTTATAAAAGGTTACGTAGG 57.534 34.615 0.00 0.00 40.63 3.18
1847 2077 9.731519 CAAAACGTCTTATAAAAGGTTACGTAG 57.268 33.333 0.00 0.00 40.63 3.51
1848 2078 9.469807 TCAAAACGTCTTATAAAAGGTTACGTA 57.530 29.630 0.00 0.00 40.63 3.57
1849 2079 8.364129 TCAAAACGTCTTATAAAAGGTTACGT 57.636 30.769 0.00 0.00 42.24 3.57
1861 2091 9.737427 CTGTCATAGACTATCAAAACGTCTTAT 57.263 33.333 0.00 0.00 38.77 1.73
1862 2092 8.737175 ACTGTCATAGACTATCAAAACGTCTTA 58.263 33.333 0.00 0.00 38.77 2.10
1863 2093 7.542477 CACTGTCATAGACTATCAAAACGTCTT 59.458 37.037 0.00 0.00 38.77 3.01
1864 2094 7.030165 CACTGTCATAGACTATCAAAACGTCT 58.970 38.462 0.00 0.00 40.74 4.18
1865 2095 6.807230 ACACTGTCATAGACTATCAAAACGTC 59.193 38.462 0.00 0.00 33.15 4.34
1867 2097 6.806739 TGACACTGTCATAGACTATCAAAACG 59.193 38.462 7.84 0.00 37.67 3.60
1868 2098 8.534333 TTGACACTGTCATAGACTATCAAAAC 57.466 34.615 12.71 0.00 42.40 2.43
1869 2099 9.554395 TTTTGACACTGTCATAGACTATCAAAA 57.446 29.630 12.71 17.22 42.40 2.44
1870 2100 9.554395 TTTTTGACACTGTCATAGACTATCAAA 57.446 29.630 12.71 4.58 42.40 2.69
1895 2125 9.813446 CCCTCTGTAACTTAATATAAGACGTTT 57.187 33.333 4.24 0.00 0.00 3.60
1896 2126 9.193806 TCCCTCTGTAACTTAATATAAGACGTT 57.806 33.333 4.24 0.00 0.00 3.99
1898 2128 8.848182 ACTCCCTCTGTAACTTAATATAAGACG 58.152 37.037 4.24 0.00 0.00 4.18
2398 2628 4.570772 AGCTAATACAACACTGTTATGCCG 59.429 41.667 0.00 0.00 36.96 5.69
2399 2629 5.730568 GCAGCTAATACAACACTGTTATGCC 60.731 44.000 0.00 0.00 36.96 4.40
2400 2630 5.163764 TGCAGCTAATACAACACTGTTATGC 60.164 40.000 0.00 0.00 36.96 3.14
2401 2631 6.250819 GTGCAGCTAATACAACACTGTTATG 58.749 40.000 0.00 0.00 36.96 1.90
2402 2632 5.354234 GGTGCAGCTAATACAACACTGTTAT 59.646 40.000 9.07 0.00 36.96 1.89
2403 2633 4.693566 GGTGCAGCTAATACAACACTGTTA 59.306 41.667 9.07 0.00 36.96 2.41
2404 2634 3.502211 GGTGCAGCTAATACAACACTGTT 59.498 43.478 9.07 0.00 36.96 3.16
2405 2635 3.074412 GGTGCAGCTAATACAACACTGT 58.926 45.455 9.07 0.00 39.75 3.55
2406 2636 2.420022 GGGTGCAGCTAATACAACACTG 59.580 50.000 16.65 0.00 0.00 3.66
2407 2637 2.618045 GGGGTGCAGCTAATACAACACT 60.618 50.000 16.65 0.00 0.00 3.55
2408 2638 1.743394 GGGGTGCAGCTAATACAACAC 59.257 52.381 16.65 0.00 0.00 3.32
2409 2639 1.340600 GGGGGTGCAGCTAATACAACA 60.341 52.381 16.65 0.00 0.00 3.33
2410 2640 1.064685 AGGGGGTGCAGCTAATACAAC 60.065 52.381 16.65 0.00 0.00 3.32
2411 2641 1.064758 CAGGGGGTGCAGCTAATACAA 60.065 52.381 16.65 0.00 0.00 2.41
2412 2642 0.546122 CAGGGGGTGCAGCTAATACA 59.454 55.000 16.65 0.00 0.00 2.29
2413 2643 0.837272 TCAGGGGGTGCAGCTAATAC 59.163 55.000 16.65 0.00 0.00 1.89
2415 2645 0.257039 CTTCAGGGGGTGCAGCTAAT 59.743 55.000 16.65 0.00 0.00 1.73
2417 2647 2.971598 GCTTCAGGGGGTGCAGCTA 61.972 63.158 16.65 0.00 41.78 3.32
2420 2650 4.748144 GGGCTTCAGGGGGTGCAG 62.748 72.222 0.00 0.00 0.00 4.41
2433 2663 0.678048 GCAACGAGAATGGAAGGGCT 60.678 55.000 0.00 0.00 0.00 5.19
2434 2664 0.960364 TGCAACGAGAATGGAAGGGC 60.960 55.000 0.00 0.00 0.00 5.19
2438 2668 2.351641 GCATGTTGCAACGAGAATGGAA 60.352 45.455 23.79 4.02 44.26 3.53
2439 2669 1.199789 GCATGTTGCAACGAGAATGGA 59.800 47.619 23.79 4.77 44.26 3.41
2463 2712 2.375014 TCGGCAGGTCATATGTAGGA 57.625 50.000 1.90 0.00 0.00 2.94
2468 2717 1.888215 AAGCATCGGCAGGTCATATG 58.112 50.000 0.00 0.00 44.61 1.78
2473 2722 0.107654 AAGGTAAGCATCGGCAGGTC 60.108 55.000 0.00 0.00 44.61 3.85
2477 2726 5.047660 ACAAAAATTAAGGTAAGCATCGGCA 60.048 36.000 0.00 0.00 44.61 5.69
2495 2745 8.983724 CCACACTTCAAAGTTTTTAGACAAAAA 58.016 29.630 0.00 0.00 40.47 1.94
2524 2775 7.270047 AGGATATGGCATTCAAAATCTGTTTG 58.730 34.615 4.78 0.00 0.00 2.93
2527 2778 8.716674 ATAAGGATATGGCATTCAAAATCTGT 57.283 30.769 4.78 0.00 0.00 3.41
2528 2779 9.991906 AAATAAGGATATGGCATTCAAAATCTG 57.008 29.630 4.78 0.00 0.00 2.90
2535 2786 9.234827 CAGTGATAAATAAGGATATGGCATTCA 57.765 33.333 4.78 0.00 0.00 2.57
2536 2787 8.186821 GCAGTGATAAATAAGGATATGGCATTC 58.813 37.037 4.78 3.20 0.00 2.67
2537 2788 7.670979 TGCAGTGATAAATAAGGATATGGCATT 59.329 33.333 4.78 0.00 0.00 3.56
2538 2789 7.121759 GTGCAGTGATAAATAAGGATATGGCAT 59.878 37.037 4.88 4.88 0.00 4.40
2539 2790 6.430925 GTGCAGTGATAAATAAGGATATGGCA 59.569 38.462 0.00 0.00 0.00 4.92
2540 2791 6.656693 AGTGCAGTGATAAATAAGGATATGGC 59.343 38.462 0.00 0.00 0.00 4.40
2541 2792 7.663081 ACAGTGCAGTGATAAATAAGGATATGG 59.337 37.037 28.02 0.00 0.00 2.74
2542 2793 8.613060 ACAGTGCAGTGATAAATAAGGATATG 57.387 34.615 28.02 0.00 0.00 1.78
2545 2796 9.632638 ATTTACAGTGCAGTGATAAATAAGGAT 57.367 29.630 28.02 9.47 0.00 3.24
2552 2803 9.337396 CCCTTATATTTACAGTGCAGTGATAAA 57.663 33.333 28.02 23.71 0.00 1.40
2553 2804 8.710239 TCCCTTATATTTACAGTGCAGTGATAA 58.290 33.333 28.02 19.26 0.00 1.75
2554 2805 8.257602 TCCCTTATATTTACAGTGCAGTGATA 57.742 34.615 28.02 15.06 0.00 2.15
2555 2806 7.136822 TCCCTTATATTTACAGTGCAGTGAT 57.863 36.000 28.02 13.35 0.00 3.06
2556 2807 6.553953 TCCCTTATATTTACAGTGCAGTGA 57.446 37.500 28.02 6.19 0.00 3.41
2557 2808 8.902540 TTATCCCTTATATTTACAGTGCAGTG 57.097 34.615 20.11 20.11 0.00 3.66
2558 2809 9.914834 TTTTATCCCTTATATTTACAGTGCAGT 57.085 29.630 0.00 0.00 0.00 4.40
2584 2835 3.628832 TGGGTGAAAAGGAAGGGATTT 57.371 42.857 0.00 0.00 0.00 2.17
2590 2841 7.441017 TGAACATATTTTGGGTGAAAAGGAAG 58.559 34.615 0.00 0.00 36.97 3.46
2593 2844 7.334171 GGATTGAACATATTTTGGGTGAAAAGG 59.666 37.037 0.00 0.00 36.97 3.11
2649 2900 4.472108 ACTTATTTTGGGACGGATGGAGTA 59.528 41.667 0.00 0.00 0.00 2.59
2650 2901 3.265995 ACTTATTTTGGGACGGATGGAGT 59.734 43.478 0.00 0.00 0.00 3.85
2651 2902 3.627577 CACTTATTTTGGGACGGATGGAG 59.372 47.826 0.00 0.00 0.00 3.86
2652 2903 3.264706 TCACTTATTTTGGGACGGATGGA 59.735 43.478 0.00 0.00 0.00 3.41
2653 2904 3.377172 GTCACTTATTTTGGGACGGATGG 59.623 47.826 0.00 0.00 0.00 3.51
2654 2905 4.261801 AGTCACTTATTTTGGGACGGATG 58.738 43.478 0.00 0.00 33.84 3.51
2655 2906 4.019681 TGAGTCACTTATTTTGGGACGGAT 60.020 41.667 0.00 0.00 33.84 4.18
2656 2907 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2657 2908 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2658 2909 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2659 2910 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2660 2911 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2661 2912 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2662 2913 9.965824 ATTACAAAGTTGAGTCACTTATTTTGG 57.034 29.630 12.94 0.78 35.87 3.28
2694 2945 9.280174 CCAAAATAAGGACTCAACTTTGTACTA 57.720 33.333 0.00 0.00 0.00 1.82
2695 2946 7.230712 CCCAAAATAAGGACTCAACTTTGTACT 59.769 37.037 0.00 0.00 0.00 2.73
2696 2947 7.229907 TCCCAAAATAAGGACTCAACTTTGTAC 59.770 37.037 0.00 0.00 0.00 2.90
2697 2948 7.291566 TCCCAAAATAAGGACTCAACTTTGTA 58.708 34.615 0.00 0.00 0.00 2.41
2698 2949 6.133356 TCCCAAAATAAGGACTCAACTTTGT 58.867 36.000 0.00 0.00 0.00 2.83
2699 2950 6.648879 TCCCAAAATAAGGACTCAACTTTG 57.351 37.500 0.00 0.00 0.00 2.77
2709 2960 1.562475 CCCTCCGTCCCAAAATAAGGA 59.438 52.381 0.00 0.00 0.00 3.36
2710 2961 1.562475 TCCCTCCGTCCCAAAATAAGG 59.438 52.381 0.00 0.00 0.00 2.69
2711 2962 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2712 2963 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2713 2964 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2714 2965 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2715 2966 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2716 2967 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2717 2968 2.245546 TCTTATACTCCCTCCGTCCCAA 59.754 50.000 0.00 0.00 0.00 4.12
2718 2969 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
2719 2970 2.671896 TCTTATACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
2720 2971 3.306156 GCAATCTTATACTCCCTCCGTCC 60.306 52.174 0.00 0.00 0.00 4.79
2721 2972 3.321111 TGCAATCTTATACTCCCTCCGTC 59.679 47.826 0.00 0.00 0.00 4.79
2722 2973 3.305720 TGCAATCTTATACTCCCTCCGT 58.694 45.455 0.00 0.00 0.00 4.69
2723 2974 3.574396 TCTGCAATCTTATACTCCCTCCG 59.426 47.826 0.00 0.00 0.00 4.63
2724 2975 5.552870 TTCTGCAATCTTATACTCCCTCC 57.447 43.478 0.00 0.00 0.00 4.30
2725 2976 7.432350 CAATTCTGCAATCTTATACTCCCTC 57.568 40.000 0.00 0.00 0.00 4.30
2744 2995 6.039047 ACATGACTACATCCTCAATGCAATTC 59.961 38.462 0.00 0.00 39.12 2.17
2746 2997 5.443283 ACATGACTACATCCTCAATGCAAT 58.557 37.500 0.00 0.00 39.12 3.56
2868 3121 8.570068 AAAGGCAAATAATTTCAGAATGCAAT 57.430 26.923 6.52 0.00 31.94 3.56
2938 3191 1.532316 ACAATGGCTGGCTGCACTT 60.532 52.632 18.32 7.66 45.15 3.16
3057 3310 2.696989 CACATAGTGGGCAGATGACA 57.303 50.000 0.00 0.00 0.00 3.58
3090 3343 6.015265 TGTTTGCATCTTCATTTGGATTCAGA 60.015 34.615 0.00 0.00 0.00 3.27
3141 3394 4.024133 TGGTAATTTGATGGATCGCAATCG 60.024 41.667 0.00 0.00 32.24 3.34
3213 3466 5.749596 TGATTGTGTTCGAAAATGTCAGT 57.250 34.783 0.00 0.00 0.00 3.41
3249 3502 0.887836 TGAGGCAGTGCTCTTTGCTG 60.888 55.000 16.11 0.00 43.37 4.41
3375 3628 1.103398 AACCACTGCCACTGCTGTTC 61.103 55.000 0.00 0.00 46.11 3.18
3492 3745 1.839994 CCATCCTTAGCCTTCTGGACA 59.160 52.381 0.00 0.00 34.57 4.02
3543 3796 1.948834 CACTGAACACATTGCTCCACA 59.051 47.619 0.00 0.00 0.00 4.17
3787 4046 2.698855 AATTACACAGCGATCAGGCT 57.301 45.000 0.00 0.00 46.13 4.58
3795 4054 6.422776 AAATGAGGAGTAAATTACACAGCG 57.577 37.500 5.89 0.00 0.00 5.18
3859 4118 3.885484 AGACTTTCTTTCATGTGCACG 57.115 42.857 13.13 0.00 0.00 5.34
3907 4166 0.249120 TGTCCAGTACGGGCTTCATG 59.751 55.000 7.24 0.00 41.50 3.07
3913 4172 2.264794 CTGGTGTCCAGTACGGGC 59.735 66.667 7.24 4.30 45.82 6.13
3939 4198 5.957796 GTCTCGCAATTTAGTTTGGAATACG 59.042 40.000 0.00 0.00 0.00 3.06
3943 4202 3.504520 GGGTCTCGCAATTTAGTTTGGAA 59.495 43.478 0.00 0.00 0.00 3.53
4044 4305 5.399596 CACAGAAATAGACGACGTATGGATG 59.600 44.000 5.18 0.15 0.00 3.51
4096 4375 9.912634 ACAAGTGACGATTTTTCATATTTTCAT 57.087 25.926 0.00 0.00 0.00 2.57
4097 4376 9.179552 CACAAGTGACGATTTTTCATATTTTCA 57.820 29.630 0.00 0.00 0.00 2.69
4098 4377 9.180678 ACACAAGTGACGATTTTTCATATTTTC 57.819 29.630 7.28 0.00 0.00 2.29
4142 4421 3.120649 GCGACTTGCAAGAAACGAACTAT 60.121 43.478 32.50 5.99 45.45 2.12
4353 4795 1.467734 CCAAGCAAGCAAGAGTAGCTG 59.532 52.381 0.00 0.00 42.53 4.24
4386 4828 2.361104 GAATTGGCGGCCTCCACA 60.361 61.111 15.82 6.53 35.50 4.17
4426 4868 0.036952 ATCACTGCCAAGACCGACAG 60.037 55.000 0.00 0.00 36.22 3.51
4507 4949 1.272490 CTACAAGCACCGAGGAAGTGA 59.728 52.381 0.00 0.00 37.42 3.41
4579 5174 3.479203 ATGATCGCCCCGCCAAGA 61.479 61.111 0.00 0.00 0.00 3.02
4593 5188 4.202151 CGTATGGATGAGACTTGGACATGA 60.202 45.833 0.00 0.00 0.00 3.07
4595 5190 3.960755 TCGTATGGATGAGACTTGGACAT 59.039 43.478 0.00 0.00 0.00 3.06
4597 5192 3.632604 TCTCGTATGGATGAGACTTGGAC 59.367 47.826 0.00 0.00 41.85 4.02
4604 5199 2.914059 TGTCGTCTCGTATGGATGAGA 58.086 47.619 0.00 0.00 44.02 3.27
4606 5201 2.293399 CCATGTCGTCTCGTATGGATGA 59.707 50.000 16.39 0.00 41.32 2.92
4607 5202 2.666026 CCATGTCGTCTCGTATGGATG 58.334 52.381 16.39 0.00 41.32 3.51
4608 5203 1.000163 GCCATGTCGTCTCGTATGGAT 60.000 52.381 21.52 0.00 41.32 3.41
4609 5204 0.384309 GCCATGTCGTCTCGTATGGA 59.616 55.000 21.52 0.00 41.32 3.41
4610 5205 0.102300 TGCCATGTCGTCTCGTATGG 59.898 55.000 16.76 16.76 41.52 2.74
4611 5206 2.140065 ATGCCATGTCGTCTCGTATG 57.860 50.000 0.00 0.00 0.00 2.39
4612 5207 2.159099 ACAATGCCATGTCGTCTCGTAT 60.159 45.455 0.00 0.00 0.00 3.06
4629 5238 3.073062 CCTTCCCTAATCCATCGGACAAT 59.927 47.826 0.00 0.00 32.98 2.71
4635 5244 4.408276 TCTACTCCTTCCCTAATCCATCG 58.592 47.826 0.00 0.00 0.00 3.84
4654 5263 2.421197 TCATGCCCCATGATCCTCTA 57.579 50.000 3.91 0.00 44.60 2.43
4695 5304 3.552132 TGCGGTCTCCAATGCTATAAA 57.448 42.857 0.00 0.00 0.00 1.40
4703 5312 0.394762 ATGCACATGCGGTCTCCAAT 60.395 50.000 0.00 0.00 45.83 3.16
4723 5332 1.300620 CGCCATCCTAATTCCGCGA 60.301 57.895 8.23 0.00 42.03 5.87


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

AutoCloner maintained by Alex Coulton.