Multiple sequence alignment - TraesCS3B01G456900

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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 TraesCS3B01G456900 chr3B 100.000 2624 0 0 1 2624 698231306 698233929 0.000000e+00 4846
1 TraesCS3B01G456900 chr3D 92.335 1996 74 29 2 1949 528131341 528133305 0.000000e+00 2765
2 TraesCS3B01G456900 chr3D 91.349 289 22 3 2336 2624 433443317 433443602 2.450000e-105 392
3 TraesCS3B01G456900 chr3D 90.625 288 24 1 2337 2624 380179897 380180181 1.910000e-101 379
4 TraesCS3B01G456900 chr3A 90.657 974 57 15 295 1248 662561973 662562932 0.000000e+00 1264
5 TraesCS3B01G456900 chr3A 93.298 746 23 15 1214 1949 662562868 662563596 0.000000e+00 1075
6 TraesCS3B01G456900 chr3A 95.053 283 10 3 27 305 662561671 662561953 2.400000e-120 442
7 TraesCS3B01G456900 chr3A 87.632 380 45 2 1954 2333 662563958 662564335 8.620000e-120 440
8 TraesCS3B01G456900 chr7B 91.349 289 22 1 2336 2624 640720357 640720642 2.450000e-105 392
9 TraesCS3B01G456900 chr7B 90.311 289 26 1 2336 2624 582275332 582275046 6.860000e-101 377
10 TraesCS3B01G456900 chr7D 90.909 286 25 1 2338 2623 101411205 101410921 1.470000e-102 383
11 TraesCS3B01G456900 chr5B 89.251 307 27 4 2318 2624 356369170 356369470 1.910000e-101 379
12 TraesCS3B01G456900 chr2D 90.034 291 25 2 2334 2624 23303666 23303380 8.870000e-100 374
13 TraesCS3B01G456900 chr2D 89.796 294 23 4 2333 2624 106335184 106334896 1.150000e-98 370
14 TraesCS3B01G456900 chr6D 90.244 287 24 2 2338 2624 452936571 452936289 3.190000e-99 372


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 TraesCS3B01G456900 chr3B 698231306 698233929 2623 False 4846.00 4846 100.000 1 2624 1 chr3B.!!$F1 2623
1 TraesCS3B01G456900 chr3D 528131341 528133305 1964 False 2765.00 2765 92.335 2 1949 1 chr3D.!!$F3 1947
2 TraesCS3B01G456900 chr3A 662561671 662564335 2664 False 805.25 1264 91.660 27 2333 4 chr3A.!!$F1 2306

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
274 279 0.034574 TGACATACACCACCCATGCC 60.035 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1810 0.104855 AGACACACATCACAGCACGT 59.895 50.0 0.0 0.0 0.0 4.49 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
115 116 7.324178 AGTATTCTTTTACTGCTGGAGTAGTG 58.676 38.462 9.03 4.54 41.09 2.74
185 186 4.229123 CCTGGCTAATGGGATAAGGATGAT 59.771 45.833 0.00 0.00 0.00 2.45
191 192 7.398024 GCTAATGGGATAAGGATGATTGTAGT 58.602 38.462 0.00 0.00 0.00 2.73
192 197 7.885399 GCTAATGGGATAAGGATGATTGTAGTT 59.115 37.037 0.00 0.00 0.00 2.24
194 199 5.376625 TGGGATAAGGATGATTGTAGTTGC 58.623 41.667 0.00 0.00 0.00 4.17
200 205 2.351726 GGATGATTGTAGTTGCGGTCAC 59.648 50.000 0.00 0.00 0.00 3.67
274 279 0.034574 TGACATACACCACCCATGCC 60.035 55.000 0.00 0.00 0.00 4.40
502 537 1.062002 GACGTCATTAACCCACATGCG 59.938 52.381 11.55 0.00 0.00 4.73
562 597 7.041098 TGAGGAAGTAATCAAAAGAGCACTTTC 60.041 37.037 9.66 0.00 44.32 2.62
576 611 6.752168 AGAGCACTTTCTTTATTGCACAAAT 58.248 32.000 0.00 0.00 37.44 2.32
683 718 1.321474 CTTGAGAAGTGCAAGGCCAA 58.679 50.000 5.01 0.00 39.18 4.52
848 885 9.255304 CTTCAGTAATTAGAAGTCCTAAGATGC 57.745 37.037 6.39 0.00 40.40 3.91
853 890 9.465985 GTAATTAGAAGTCCTAAGATGCAGTAC 57.534 37.037 0.00 0.00 40.40 2.73
854 891 7.906199 ATTAGAAGTCCTAAGATGCAGTACT 57.094 36.000 0.00 0.00 40.40 2.73
855 892 8.998277 ATTAGAAGTCCTAAGATGCAGTACTA 57.002 34.615 0.00 0.00 40.40 1.82
856 893 6.952773 AGAAGTCCTAAGATGCAGTACTAG 57.047 41.667 0.00 0.00 0.00 2.57
857 894 6.664714 AGAAGTCCTAAGATGCAGTACTAGA 58.335 40.000 0.00 0.00 0.00 2.43
858 895 6.770785 AGAAGTCCTAAGATGCAGTACTAGAG 59.229 42.308 0.00 0.00 0.00 2.43
859 896 6.008696 AGTCCTAAGATGCAGTACTAGAGT 57.991 41.667 0.00 0.00 0.00 3.24
860 897 6.428295 AGTCCTAAGATGCAGTACTAGAGTT 58.572 40.000 0.00 0.00 0.00 3.01
920 977 1.730612 CCGATCGATGCATGATTCCTG 59.269 52.381 18.66 0.48 0.00 3.86
922 979 2.082231 GATCGATGCATGATTCCTGGG 58.918 52.381 2.46 0.00 0.00 4.45
928 985 3.281727 TGCATGATTCCTGGGTCTAAC 57.718 47.619 0.00 0.00 0.00 2.34
936 993 5.783360 TGATTCCTGGGTCTAACTGAAGTTA 59.217 40.000 3.06 3.06 39.31 2.24
941 998 6.940298 TCCTGGGTCTAACTGAAGTTAATTTG 59.060 38.462 4.57 0.00 39.70 2.32
944 1001 5.105877 GGGTCTAACTGAAGTTAATTTGGGC 60.106 44.000 4.57 0.00 39.70 5.36
965 1022 3.990092 CGTAGCATAAGCATACAGGGAA 58.010 45.455 0.00 0.00 45.49 3.97
983 1040 5.948758 CAGGGAAAAGAAGAGGAATTAAGCT 59.051 40.000 0.00 0.00 0.00 3.74
990 1047 5.739959 AGAAGAGGAATTAAGCTCCAAGAC 58.260 41.667 8.66 0.00 35.20 3.01
1368 1434 1.607148 GGTGGCTACAACAACAACTCC 59.393 52.381 1.52 0.00 33.38 3.85
1488 1557 4.155733 CACGTCTATGGGGCGCCA 62.156 66.667 30.85 26.32 0.00 5.69
1659 1731 0.179009 ATATGGCTGAATGCGCTGGT 60.179 50.000 9.73 0.00 44.05 4.00
1689 1761 2.202919 CATGGATGCTGGCGACGA 60.203 61.111 0.00 0.00 0.00 4.20
1690 1762 1.596203 CATGGATGCTGGCGACGAT 60.596 57.895 0.00 0.00 0.00 3.73
1716 1803 7.227711 TCGATCGAGTACTACACTACTACTACT 59.772 40.741 15.15 0.00 37.72 2.57
1717 1804 8.499967 CGATCGAGTACTACACTACTACTACTA 58.500 40.741 10.26 0.00 37.72 1.82
1718 1805 9.607285 GATCGAGTACTACACTACTACTACTAC 57.393 40.741 0.00 0.00 37.72 2.73
1719 1806 8.740123 TCGAGTACTACACTACTACTACTACT 57.260 38.462 0.00 0.00 37.72 2.57
1720 1807 9.833917 TCGAGTACTACACTACTACTACTACTA 57.166 37.037 0.00 0.00 37.72 1.82
1721 1808 9.872757 CGAGTACTACACTACTACTACTACTAC 57.127 40.741 0.00 0.00 37.72 2.73
1726 1813 9.398538 ACTACACTACTACTACTACTACTACGT 57.601 37.037 0.00 0.00 0.00 3.57
1727 1814 9.658475 CTACACTACTACTACTACTACTACGTG 57.342 40.741 0.00 0.00 0.00 4.49
1728 1815 6.975772 ACACTACTACTACTACTACTACGTGC 59.024 42.308 0.00 0.00 0.00 5.34
1729 1816 7.147983 ACACTACTACTACTACTACTACGTGCT 60.148 40.741 0.00 0.00 0.00 4.40
1730 1817 7.167302 CACTACTACTACTACTACTACGTGCTG 59.833 44.444 0.00 0.00 0.00 4.41
1731 1818 5.971763 ACTACTACTACTACTACGTGCTGT 58.028 41.667 0.00 0.00 0.00 4.40
1732 1819 5.809562 ACTACTACTACTACTACGTGCTGTG 59.190 44.000 0.00 0.00 0.00 3.66
1733 1820 4.825422 ACTACTACTACTACGTGCTGTGA 58.175 43.478 0.00 0.00 0.00 3.58
1734 1821 5.426504 ACTACTACTACTACGTGCTGTGAT 58.573 41.667 0.00 0.00 0.00 3.06
1735 1822 4.617808 ACTACTACTACGTGCTGTGATG 57.382 45.455 0.00 0.00 0.00 3.07
1770 1857 4.164981 AGTTTCCAGGTGTACCAGTGATA 58.835 43.478 3.56 0.00 38.89 2.15
1801 1891 1.094650 TGCGCAGTGATGTGTGTGTT 61.095 50.000 5.66 0.00 0.00 3.32
1934 2031 6.122850 TCTTGTAATTGCATGCAGATACAC 57.877 37.500 31.12 21.67 32.52 2.90
1935 2032 4.534794 TGTAATTGCATGCAGATACACG 57.465 40.909 29.14 0.00 29.88 4.49
1936 2033 3.312146 TGTAATTGCATGCAGATACACGG 59.688 43.478 29.14 0.00 29.88 4.94
1937 2034 0.664761 ATTGCATGCAGATACACGGC 59.335 50.000 21.50 0.00 39.97 5.68
1944 2041 2.549926 TGCAGATACACGGCAACTATG 58.450 47.619 0.00 0.00 45.55 2.23
1947 2044 3.809832 GCAGATACACGGCAACTATGATT 59.190 43.478 0.00 0.00 39.38 2.57
1948 2045 4.273480 GCAGATACACGGCAACTATGATTT 59.727 41.667 0.00 0.00 39.38 2.17
1949 2046 5.559035 GCAGATACACGGCAACTATGATTTC 60.559 44.000 0.00 0.00 39.38 2.17
1950 2047 5.523552 CAGATACACGGCAACTATGATTTCA 59.476 40.000 0.00 0.00 0.00 2.69
1951 2048 5.523916 AGATACACGGCAACTATGATTTCAC 59.476 40.000 0.00 0.00 0.00 3.18
1960 2417 6.767902 GGCAACTATGATTTCACTCTCCAATA 59.232 38.462 0.00 0.00 0.00 1.90
1965 2422 8.543774 ACTATGATTTCACTCTCCAATAGTTGT 58.456 33.333 0.00 0.00 0.00 3.32
1983 2440 4.275936 AGTTGTTTCCATGCTGAGTGTAAC 59.724 41.667 0.00 0.00 0.00 2.50
2012 2469 5.579904 GTGTCCTTCGTAAAAATCCTACTCC 59.420 44.000 0.00 0.00 0.00 3.85
2020 2477 7.673180 TCGTAAAAATCCTACTCCTTTGAGAA 58.327 34.615 0.00 0.00 41.42 2.87
2025 2482 4.891992 TCCTACTCCTTTGAGAACCAAG 57.108 45.455 0.00 0.00 41.42 3.61
2033 2490 2.359230 GAGAACCAAGCGCTGCCT 60.359 61.111 12.58 3.58 0.00 4.75
2039 2496 2.488355 CAAGCGCTGCCTTGGATG 59.512 61.111 12.58 0.00 38.78 3.51
2051 2508 3.498774 CCTTGGATGGCTACAGCTTAT 57.501 47.619 0.54 0.00 41.70 1.73
2062 2519 1.026718 ACAGCTTATCGGGTGCAAGC 61.027 55.000 0.00 0.00 43.97 4.01
2083 2540 2.785425 GCCCGCCCATGTTTGATCC 61.785 63.158 0.00 0.00 0.00 3.36
2112 2569 5.811100 GGAGGTCTCATTTCTACCTTTAACG 59.189 44.000 0.00 0.00 43.69 3.18
2154 2611 8.980596 TCATAGACAAGCAAAATATCCCAAAAT 58.019 29.630 0.00 0.00 0.00 1.82
2185 2642 9.681692 TGGAAAATTCATCGATATTAGCAAATG 57.318 29.630 0.00 0.00 0.00 2.32
2193 2650 4.346709 TCGATATTAGCAAATGACTCCCCA 59.653 41.667 0.00 0.00 0.00 4.96
2202 2659 3.393426 AATGACTCCCCATCAATTGCT 57.607 42.857 0.00 0.00 0.00 3.91
2215 2672 7.383687 CCCATCAATTGCTGCAAGATATAAAT 58.616 34.615 20.72 0.00 34.07 1.40
2265 2722 7.224362 CAGTCCTCAAGATGTAATTCTGATGAC 59.776 40.741 0.00 0.00 0.00 3.06
2274 2731 8.043113 AGATGTAATTCTGATGACTGCTTTACA 58.957 33.333 0.00 0.00 0.00 2.41
2313 2770 6.885735 AAGTGCAATACAAAGAAACACAAC 57.114 33.333 0.00 0.00 0.00 3.32
2316 2773 6.697019 AGTGCAATACAAAGAAACACAACATC 59.303 34.615 0.00 0.00 0.00 3.06
2317 2774 6.475076 GTGCAATACAAAGAAACACAACATCA 59.525 34.615 0.00 0.00 0.00 3.07
2360 2817 5.997732 TTTTGCGTAGTAATACGTGTCTC 57.002 39.130 22.09 7.36 44.53 3.36
2361 2818 4.683501 TTGCGTAGTAATACGTGTCTCA 57.316 40.909 22.09 9.73 44.53 3.27
2362 2819 4.888038 TGCGTAGTAATACGTGTCTCAT 57.112 40.909 22.09 0.00 44.53 2.90
2363 2820 5.239359 TGCGTAGTAATACGTGTCTCATT 57.761 39.130 22.09 0.00 44.53 2.57
2364 2821 6.362210 TGCGTAGTAATACGTGTCTCATTA 57.638 37.500 22.09 0.00 44.53 1.90
2365 2822 6.784176 TGCGTAGTAATACGTGTCTCATTAA 58.216 36.000 22.09 0.00 44.53 1.40
2366 2823 7.420002 TGCGTAGTAATACGTGTCTCATTAAT 58.580 34.615 22.09 0.00 44.53 1.40
2367 2824 8.558700 TGCGTAGTAATACGTGTCTCATTAATA 58.441 33.333 22.09 0.00 44.53 0.98
2368 2825 9.385902 GCGTAGTAATACGTGTCTCATTAATAA 57.614 33.333 22.09 0.00 44.53 1.40
2393 2850 7.759489 AATAAAGATTCACTTACAAGCCACA 57.241 32.000 0.00 0.00 37.93 4.17
2394 2851 7.944729 ATAAAGATTCACTTACAAGCCACAT 57.055 32.000 0.00 0.00 37.93 3.21
2395 2852 9.461312 AATAAAGATTCACTTACAAGCCACATA 57.539 29.630 0.00 0.00 37.93 2.29
2396 2853 7.759489 AAAGATTCACTTACAAGCCACATAA 57.241 32.000 0.00 0.00 37.93 1.90
2397 2854 7.759489 AAGATTCACTTACAAGCCACATAAA 57.241 32.000 0.00 0.00 37.03 1.40
2398 2855 7.145932 AGATTCACTTACAAGCCACATAAAC 57.854 36.000 0.00 0.00 0.00 2.01
2399 2856 6.714810 AGATTCACTTACAAGCCACATAAACA 59.285 34.615 0.00 0.00 0.00 2.83
2400 2857 6.892658 TTCACTTACAAGCCACATAAACAT 57.107 33.333 0.00 0.00 0.00 2.71
2401 2858 6.494893 TCACTTACAAGCCACATAAACATC 57.505 37.500 0.00 0.00 0.00 3.06
2402 2859 5.414454 TCACTTACAAGCCACATAAACATCC 59.586 40.000 0.00 0.00 0.00 3.51
2403 2860 5.182950 CACTTACAAGCCACATAAACATCCA 59.817 40.000 0.00 0.00 0.00 3.41
2404 2861 5.183140 ACTTACAAGCCACATAAACATCCAC 59.817 40.000 0.00 0.00 0.00 4.02
2405 2862 2.487762 ACAAGCCACATAAACATCCACG 59.512 45.455 0.00 0.00 0.00 4.94
2406 2863 2.487762 CAAGCCACATAAACATCCACGT 59.512 45.455 0.00 0.00 0.00 4.49
2407 2864 2.790433 AGCCACATAAACATCCACGTT 58.210 42.857 0.00 0.00 0.00 3.99
2408 2865 3.945346 AGCCACATAAACATCCACGTTA 58.055 40.909 0.00 0.00 0.00 3.18
2409 2866 3.687698 AGCCACATAAACATCCACGTTAC 59.312 43.478 0.00 0.00 0.00 2.50
2410 2867 3.437395 GCCACATAAACATCCACGTTACA 59.563 43.478 0.00 0.00 0.00 2.41
2411 2868 4.095782 GCCACATAAACATCCACGTTACAT 59.904 41.667 0.00 0.00 0.00 2.29
2412 2869 5.568482 CCACATAAACATCCACGTTACATG 58.432 41.667 0.00 0.00 32.07 3.21
2413 2870 5.352846 CCACATAAACATCCACGTTACATGA 59.647 40.000 0.00 0.00 31.09 3.07
2414 2871 6.038161 CCACATAAACATCCACGTTACATGAT 59.962 38.462 0.00 0.00 31.09 2.45
2415 2872 7.415095 CCACATAAACATCCACGTTACATGATT 60.415 37.037 0.00 3.04 31.09 2.57
2416 2873 7.429051 CACATAAACATCCACGTTACATGATTG 59.571 37.037 0.00 0.00 31.09 2.67
2417 2874 7.335673 ACATAAACATCCACGTTACATGATTGA 59.664 33.333 0.00 0.00 31.09 2.57
2418 2875 6.567687 AAACATCCACGTTACATGATTGAA 57.432 33.333 0.00 0.00 0.00 2.69
2419 2876 6.567687 AACATCCACGTTACATGATTGAAA 57.432 33.333 0.00 0.00 0.00 2.69
2420 2877 6.567687 ACATCCACGTTACATGATTGAAAA 57.432 33.333 0.00 0.00 0.00 2.29
2421 2878 6.611381 ACATCCACGTTACATGATTGAAAAG 58.389 36.000 0.00 0.00 0.00 2.27
2422 2879 6.429692 ACATCCACGTTACATGATTGAAAAGA 59.570 34.615 0.00 0.00 0.00 2.52
2423 2880 7.121168 ACATCCACGTTACATGATTGAAAAGAT 59.879 33.333 0.00 0.00 0.00 2.40
2424 2881 8.611757 CATCCACGTTACATGATTGAAAAGATA 58.388 33.333 0.00 0.00 0.00 1.98
2425 2882 8.196802 TCCACGTTACATGATTGAAAAGATAG 57.803 34.615 0.00 0.00 0.00 2.08
2426 2883 7.279981 TCCACGTTACATGATTGAAAAGATAGG 59.720 37.037 0.00 0.00 0.00 2.57
2427 2884 7.279981 CCACGTTACATGATTGAAAAGATAGGA 59.720 37.037 0.00 0.00 0.00 2.94
2428 2885 8.830580 CACGTTACATGATTGAAAAGATAGGAT 58.169 33.333 0.00 0.00 0.00 3.24
2462 2919 3.800826 AAAAACAGCGTCTGTCCCT 57.199 47.368 11.92 0.00 44.62 4.20
2463 2920 1.594331 AAAAACAGCGTCTGTCCCTC 58.406 50.000 11.92 0.00 44.62 4.30
2464 2921 0.759346 AAAACAGCGTCTGTCCCTCT 59.241 50.000 11.92 0.00 44.62 3.69
2465 2922 0.318762 AAACAGCGTCTGTCCCTCTC 59.681 55.000 11.92 0.00 44.62 3.20
2466 2923 1.536943 AACAGCGTCTGTCCCTCTCC 61.537 60.000 11.92 0.00 44.62 3.71
2467 2924 1.979155 CAGCGTCTGTCCCTCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
2468 2925 1.979693 AGCGTCTGTCCCTCTCCAC 60.980 63.158 0.00 0.00 0.00 4.02
2469 2926 1.979693 GCGTCTGTCCCTCTCCACT 60.980 63.158 0.00 0.00 0.00 4.00
2470 2927 0.680280 GCGTCTGTCCCTCTCCACTA 60.680 60.000 0.00 0.00 0.00 2.74
2471 2928 1.835494 CGTCTGTCCCTCTCCACTAA 58.165 55.000 0.00 0.00 0.00 2.24
2472 2929 1.746220 CGTCTGTCCCTCTCCACTAAG 59.254 57.143 0.00 0.00 0.00 2.18
2473 2930 2.104170 GTCTGTCCCTCTCCACTAAGG 58.896 57.143 0.00 0.00 39.47 2.69
2474 2931 2.000803 TCTGTCCCTCTCCACTAAGGA 58.999 52.381 0.00 0.00 46.75 3.36
2489 2946 8.089625 TCCACTAAGGAAAATGAGACATATCA 57.910 34.615 0.00 0.00 45.65 2.15
2490 2947 7.987458 TCCACTAAGGAAAATGAGACATATCAC 59.013 37.037 0.00 0.00 45.65 3.06
2491 2948 7.227512 CCACTAAGGAAAATGAGACATATCACC 59.772 40.741 0.00 0.00 41.22 4.02
2492 2949 7.989741 CACTAAGGAAAATGAGACATATCACCT 59.010 37.037 0.00 0.00 30.46 4.00
2493 2950 8.207545 ACTAAGGAAAATGAGACATATCACCTC 58.792 37.037 0.00 0.00 30.46 3.85
2494 2951 6.821616 AGGAAAATGAGACATATCACCTCT 57.178 37.500 0.00 0.00 30.46 3.69
2495 2952 7.205515 AGGAAAATGAGACATATCACCTCTT 57.794 36.000 0.00 0.00 30.46 2.85
2496 2953 7.278875 AGGAAAATGAGACATATCACCTCTTC 58.721 38.462 0.00 0.00 30.46 2.87
2497 2954 7.050377 GGAAAATGAGACATATCACCTCTTCA 58.950 38.462 0.00 0.00 30.46 3.02
2498 2955 7.011857 GGAAAATGAGACATATCACCTCTTCAC 59.988 40.741 0.00 0.00 30.46 3.18
2499 2956 5.543507 ATGAGACATATCACCTCTTCACC 57.456 43.478 0.00 0.00 30.46 4.02
2500 2957 4.352893 TGAGACATATCACCTCTTCACCA 58.647 43.478 0.00 0.00 0.00 4.17
2501 2958 4.403752 TGAGACATATCACCTCTTCACCAG 59.596 45.833 0.00 0.00 0.00 4.00
2502 2959 4.614475 AGACATATCACCTCTTCACCAGA 58.386 43.478 0.00 0.00 0.00 3.86
2509 2966 3.712020 CTCTTCACCAGAGCTCGAC 57.288 57.895 8.37 0.00 42.96 4.20
2510 2967 0.179176 CTCTTCACCAGAGCTCGACG 60.179 60.000 8.37 1.99 42.96 5.12
2511 2968 1.803519 CTTCACCAGAGCTCGACGC 60.804 63.158 8.37 0.00 39.57 5.19
2512 2969 3.610791 TTCACCAGAGCTCGACGCG 62.611 63.158 8.37 3.53 45.59 6.01
2521 2978 4.193334 CTCGACGCGGCTCCATCA 62.193 66.667 11.76 0.00 0.00 3.07
2522 2979 3.490793 CTCGACGCGGCTCCATCAT 62.491 63.158 11.76 0.00 0.00 2.45
2523 2980 2.586079 CGACGCGGCTCCATCATT 60.586 61.111 11.76 0.00 0.00 2.57
2524 2981 2.874694 CGACGCGGCTCCATCATTG 61.875 63.158 11.76 0.00 0.00 2.82
2525 2982 1.521457 GACGCGGCTCCATCATTGA 60.521 57.895 12.47 0.00 0.00 2.57
2526 2983 0.882042 GACGCGGCTCCATCATTGAT 60.882 55.000 12.47 0.00 0.00 2.57
2527 2984 0.882042 ACGCGGCTCCATCATTGATC 60.882 55.000 12.47 0.00 0.00 2.92
2528 2985 0.881600 CGCGGCTCCATCATTGATCA 60.882 55.000 0.00 0.00 0.00 2.92
2529 2986 0.873054 GCGGCTCCATCATTGATCAG 59.127 55.000 0.00 0.00 0.00 2.90
2530 2987 0.873054 CGGCTCCATCATTGATCAGC 59.127 55.000 14.84 14.84 0.00 4.26
2531 2988 1.812708 CGGCTCCATCATTGATCAGCA 60.813 52.381 20.94 0.00 30.61 4.41
2532 2989 1.880675 GGCTCCATCATTGATCAGCAG 59.119 52.381 20.94 7.48 30.61 4.24
2533 2990 1.267261 GCTCCATCATTGATCAGCAGC 59.733 52.381 17.02 9.68 29.89 5.25
2534 2991 2.852449 CTCCATCATTGATCAGCAGCT 58.148 47.619 0.00 0.00 0.00 4.24
2535 2992 3.215151 CTCCATCATTGATCAGCAGCTT 58.785 45.455 0.00 0.00 0.00 3.74
2536 2993 3.628008 TCCATCATTGATCAGCAGCTTT 58.372 40.909 0.00 0.00 0.00 3.51
2537 2994 4.784177 TCCATCATTGATCAGCAGCTTTA 58.216 39.130 0.00 0.00 0.00 1.85
2538 2995 4.577693 TCCATCATTGATCAGCAGCTTTAC 59.422 41.667 0.00 0.00 0.00 2.01
2539 2996 4.524749 CATCATTGATCAGCAGCTTTACG 58.475 43.478 0.00 0.00 0.00 3.18
2540 2997 2.938451 TCATTGATCAGCAGCTTTACGG 59.062 45.455 0.00 0.00 0.00 4.02
2541 2998 2.760634 TTGATCAGCAGCTTTACGGA 57.239 45.000 0.00 0.00 0.00 4.69
2542 2999 2.010145 TGATCAGCAGCTTTACGGAC 57.990 50.000 0.00 0.00 0.00 4.79
2543 3000 1.291132 GATCAGCAGCTTTACGGACC 58.709 55.000 0.00 0.00 0.00 4.46
2544 3001 0.905357 ATCAGCAGCTTTACGGACCT 59.095 50.000 0.00 0.00 0.00 3.85
2545 3002 0.246635 TCAGCAGCTTTACGGACCTC 59.753 55.000 0.00 0.00 0.00 3.85
2546 3003 0.741221 CAGCAGCTTTACGGACCTCC 60.741 60.000 0.00 0.00 0.00 4.30
2547 3004 1.192146 AGCAGCTTTACGGACCTCCA 61.192 55.000 0.00 0.00 35.14 3.86
2548 3005 0.321298 GCAGCTTTACGGACCTCCAA 60.321 55.000 0.00 0.00 35.14 3.53
2549 3006 1.880646 GCAGCTTTACGGACCTCCAAA 60.881 52.381 0.00 0.00 35.14 3.28
2550 3007 2.076863 CAGCTTTACGGACCTCCAAAG 58.923 52.381 0.00 5.42 34.15 2.77
2551 3008 1.697982 AGCTTTACGGACCTCCAAAGT 59.302 47.619 9.66 0.00 33.78 2.66
2552 3009 2.901839 AGCTTTACGGACCTCCAAAGTA 59.098 45.455 9.66 0.00 33.78 2.24
2553 3010 3.056035 AGCTTTACGGACCTCCAAAGTAG 60.056 47.826 9.66 0.00 33.78 2.57
2554 3011 3.306571 GCTTTACGGACCTCCAAAGTAGT 60.307 47.826 9.66 0.00 33.78 2.73
2555 3012 4.801914 GCTTTACGGACCTCCAAAGTAGTT 60.802 45.833 9.66 0.00 33.78 2.24
2556 3013 4.961438 TTACGGACCTCCAAAGTAGTTT 57.039 40.909 0.00 0.00 35.14 2.66
2557 3014 3.121738 ACGGACCTCCAAAGTAGTTTG 57.878 47.619 14.97 14.97 42.49 2.93
2558 3015 1.804748 CGGACCTCCAAAGTAGTTTGC 59.195 52.381 16.26 3.76 41.64 3.68
2559 3016 2.160205 GGACCTCCAAAGTAGTTTGCC 58.840 52.381 16.26 8.74 41.64 4.52
2560 3017 2.224793 GGACCTCCAAAGTAGTTTGCCT 60.225 50.000 16.26 0.00 41.64 4.75
2561 3018 2.814336 GACCTCCAAAGTAGTTTGCCTG 59.186 50.000 16.26 9.19 41.64 4.85
2562 3019 2.441750 ACCTCCAAAGTAGTTTGCCTGA 59.558 45.455 16.26 8.45 41.64 3.86
2563 3020 3.117663 ACCTCCAAAGTAGTTTGCCTGAA 60.118 43.478 16.26 0.40 41.64 3.02
2564 3021 3.503748 CCTCCAAAGTAGTTTGCCTGAAG 59.496 47.826 16.26 8.40 41.64 3.02
2565 3022 2.884639 TCCAAAGTAGTTTGCCTGAAGC 59.115 45.455 16.26 0.00 41.64 3.86
2576 3033 2.531522 GCCTGAAGCAAAACCATTGT 57.468 45.000 0.00 0.00 42.97 2.71
2577 3034 2.837498 GCCTGAAGCAAAACCATTGTT 58.163 42.857 0.00 0.00 42.97 2.83
2578 3035 2.545106 GCCTGAAGCAAAACCATTGTTG 59.455 45.455 0.00 0.00 42.97 3.33
2579 3036 3.795877 CCTGAAGCAAAACCATTGTTGT 58.204 40.909 0.00 0.00 34.13 3.32
2580 3037 4.190772 CCTGAAGCAAAACCATTGTTGTT 58.809 39.130 0.00 0.00 34.13 2.83
2581 3038 4.034279 CCTGAAGCAAAACCATTGTTGTTG 59.966 41.667 0.00 0.00 34.13 3.33
2582 3039 4.825422 TGAAGCAAAACCATTGTTGTTGA 58.175 34.783 8.01 0.00 34.13 3.18
2583 3040 5.240891 TGAAGCAAAACCATTGTTGTTGAA 58.759 33.333 8.01 0.00 34.13 2.69
2584 3041 5.702670 TGAAGCAAAACCATTGTTGTTGAAA 59.297 32.000 8.01 0.00 34.13 2.69
2585 3042 5.799681 AGCAAAACCATTGTTGTTGAAAG 57.200 34.783 8.01 0.00 34.13 2.62
2586 3043 5.486526 AGCAAAACCATTGTTGTTGAAAGA 58.513 33.333 8.01 0.00 34.13 2.52
2587 3044 5.936956 AGCAAAACCATTGTTGTTGAAAGAA 59.063 32.000 8.01 0.00 34.13 2.52
2588 3045 6.598850 AGCAAAACCATTGTTGTTGAAAGAAT 59.401 30.769 8.01 0.00 34.13 2.40
2589 3046 6.906678 GCAAAACCATTGTTGTTGAAAGAATC 59.093 34.615 8.01 0.00 34.13 2.52
2590 3047 7.413877 GCAAAACCATTGTTGTTGAAAGAATCA 60.414 33.333 8.01 0.00 34.13 2.57
2591 3048 7.775397 AAACCATTGTTGTTGAAAGAATCAG 57.225 32.000 0.00 0.00 35.43 2.90
2592 3049 6.713762 ACCATTGTTGTTGAAAGAATCAGA 57.286 33.333 0.00 0.00 39.77 3.27
2593 3050 7.294017 ACCATTGTTGTTGAAAGAATCAGAT 57.706 32.000 0.00 0.00 39.77 2.90
2594 3051 7.373493 ACCATTGTTGTTGAAAGAATCAGATC 58.627 34.615 0.00 0.00 39.77 2.75
2595 3052 6.525628 CCATTGTTGTTGAAAGAATCAGATCG 59.474 38.462 0.00 0.00 39.77 3.69
2596 3053 5.611796 TGTTGTTGAAAGAATCAGATCGG 57.388 39.130 0.00 0.00 39.77 4.18
2597 3054 4.455533 TGTTGTTGAAAGAATCAGATCGGG 59.544 41.667 0.00 0.00 39.77 5.14
2598 3055 4.551702 TGTTGAAAGAATCAGATCGGGA 57.448 40.909 0.00 0.00 39.77 5.14
2599 3056 4.253685 TGTTGAAAGAATCAGATCGGGAC 58.746 43.478 0.00 0.00 39.77 4.46
2600 3057 4.253685 GTTGAAAGAATCAGATCGGGACA 58.746 43.478 0.00 0.00 39.77 4.02
2601 3058 4.551702 TGAAAGAATCAGATCGGGACAA 57.448 40.909 0.00 0.00 33.04 3.18
2602 3059 4.253685 TGAAAGAATCAGATCGGGACAAC 58.746 43.478 0.00 0.00 33.04 3.32
2603 3060 2.586258 AGAATCAGATCGGGACAACG 57.414 50.000 0.00 0.00 0.00 4.10
2604 3061 1.825474 AGAATCAGATCGGGACAACGT 59.175 47.619 0.00 0.00 34.94 3.99
2605 3062 1.927174 GAATCAGATCGGGACAACGTG 59.073 52.381 0.00 0.00 34.94 4.49
2606 3063 0.895530 ATCAGATCGGGACAACGTGT 59.104 50.000 0.00 0.00 34.94 4.49
2607 3064 0.242825 TCAGATCGGGACAACGTGTC 59.757 55.000 8.94 8.94 46.23 3.67
2614 3071 2.356673 GACAACGTGTCCCCGGAC 60.357 66.667 0.73 6.95 41.37 4.79
2622 3079 2.203209 GTCCCCGGACATGCCATC 60.203 66.667 0.73 0.00 44.02 3.51
2623 3080 3.860605 TCCCCGGACATGCCATCG 61.861 66.667 0.73 0.00 35.94 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.944007 GGGGTCAACTTACTCACATTACATT 59.056 40.000 0.00 0.00 0.00 2.71
164 165 5.074929 ACAATCATCCTTATCCCATTAGCCA 59.925 40.000 0.00 0.00 0.00 4.75
185 186 1.539496 GGTCAGTGACCGCAACTACAA 60.539 52.381 26.12 0.00 43.14 2.41
200 205 5.028549 AGTTGCAACCTATCTATGGTCAG 57.971 43.478 25.62 0.00 36.69 3.51
274 279 2.510691 GGACCGGTATGTGTGGCG 60.511 66.667 7.34 0.00 0.00 5.69
502 537 2.227865 TCATTTTCCCTTGTAACTGCGC 59.772 45.455 0.00 0.00 0.00 6.09
562 597 6.750501 CAGAGGTCATCATTTGTGCAATAAAG 59.249 38.462 0.00 0.00 27.97 1.85
576 611 4.160439 GTGTCTATCCAACAGAGGTCATCA 59.840 45.833 0.00 0.00 0.00 3.07
683 718 5.183140 GCATACCAGACAATAAAGTGGTTGT 59.817 40.000 0.00 0.00 40.54 3.32
816 853 8.368962 AGGACTTCTAATTACTGAAGCTAACT 57.631 34.615 12.20 5.35 42.27 2.24
875 917 5.040635 CGGAAAACACATAAAACTTGTGCT 58.959 37.500 3.85 0.00 46.65 4.40
876 918 5.038033 TCGGAAAACACATAAAACTTGTGC 58.962 37.500 3.85 0.00 46.65 4.57
879 921 4.673311 CGGTCGGAAAACACATAAAACTTG 59.327 41.667 0.00 0.00 0.00 3.16
887 929 1.355971 CGATCGGTCGGAAAACACAT 58.644 50.000 11.03 0.00 44.00 3.21
899 956 1.345741 AGGAATCATGCATCGATCGGT 59.654 47.619 16.41 4.70 0.00 4.69
920 977 5.105877 GCCCAAATTAACTTCAGTTAGACCC 60.106 44.000 0.00 0.00 41.03 4.46
922 979 5.180680 ACGCCCAAATTAACTTCAGTTAGAC 59.819 40.000 0.00 0.00 41.03 2.59
928 985 3.438781 TGCTACGCCCAAATTAACTTCAG 59.561 43.478 0.00 0.00 0.00 3.02
936 993 2.374184 TGCTTATGCTACGCCCAAATT 58.626 42.857 1.96 0.00 40.48 1.82
941 998 2.069273 CTGTATGCTTATGCTACGCCC 58.931 52.381 1.96 0.00 40.48 6.13
944 1001 3.660501 TCCCTGTATGCTTATGCTACG 57.339 47.619 1.96 0.00 40.48 3.51
953 1010 3.846588 TCCTCTTCTTTTCCCTGTATGCT 59.153 43.478 0.00 0.00 0.00 3.79
954 1011 4.222124 TCCTCTTCTTTTCCCTGTATGC 57.778 45.455 0.00 0.00 0.00 3.14
955 1012 8.807948 TTAATTCCTCTTCTTTTCCCTGTATG 57.192 34.615 0.00 0.00 0.00 2.39
956 1013 7.558081 GCTTAATTCCTCTTCTTTTCCCTGTAT 59.442 37.037 0.00 0.00 0.00 2.29
957 1014 6.884836 GCTTAATTCCTCTTCTTTTCCCTGTA 59.115 38.462 0.00 0.00 0.00 2.74
958 1015 5.712446 GCTTAATTCCTCTTCTTTTCCCTGT 59.288 40.000 0.00 0.00 0.00 4.00
965 1022 6.657117 GTCTTGGAGCTTAATTCCTCTTCTTT 59.343 38.462 7.45 0.00 35.67 2.52
990 1047 1.811266 CCACGACATCGCCTCCAAG 60.811 63.158 0.14 0.00 44.43 3.61
1443 1512 3.118555 CCCTGGTGTTTATGTACATCGGA 60.119 47.826 12.68 0.00 37.66 4.55
1488 1557 1.220529 TGTAGTCGTCGTCGTTCTGT 58.779 50.000 1.33 0.00 38.33 3.41
1575 1647 1.488261 GATCGACGAAATGGCCGACC 61.488 60.000 0.00 0.00 33.69 4.79
1650 1722 0.107268 TATCTGCATGACCAGCGCAT 59.893 50.000 11.47 0.00 34.63 4.73
1687 1759 8.044175 AGTAGTAGTGTAGTACTCGATCGATCG 61.044 44.444 35.91 35.91 40.04 3.69
1688 1760 7.083858 AGTAGTAGTGTAGTACTCGATCGATC 58.916 42.308 19.78 15.68 40.04 3.69
1689 1761 6.980593 AGTAGTAGTGTAGTACTCGATCGAT 58.019 40.000 19.78 11.36 40.04 3.59
1690 1762 6.384258 AGTAGTAGTGTAGTACTCGATCGA 57.616 41.667 18.32 18.32 40.04 3.59
1716 1803 3.754850 ACACATCACAGCACGTAGTAGTA 59.245 43.478 0.00 0.00 41.61 1.82
1717 1804 2.557056 ACACATCACAGCACGTAGTAGT 59.443 45.455 0.00 0.00 41.61 2.73
1718 1805 2.917343 CACACATCACAGCACGTAGTAG 59.083 50.000 0.00 0.00 41.61 2.57
1719 1806 2.295070 ACACACATCACAGCACGTAGTA 59.705 45.455 0.00 0.00 41.61 1.82
1721 1808 1.721389 GACACACATCACAGCACGTAG 59.279 52.381 0.00 0.00 0.00 3.51
1723 1810 0.104855 AGACACACATCACAGCACGT 59.895 50.000 0.00 0.00 0.00 4.49
1724 1811 1.070376 CAAGACACACATCACAGCACG 60.070 52.381 0.00 0.00 0.00 5.34
1725 1812 1.265095 CCAAGACACACATCACAGCAC 59.735 52.381 0.00 0.00 0.00 4.40
1726 1813 1.140652 TCCAAGACACACATCACAGCA 59.859 47.619 0.00 0.00 0.00 4.41
1727 1814 1.882912 TCCAAGACACACATCACAGC 58.117 50.000 0.00 0.00 0.00 4.40
1728 1815 4.825422 ACTATCCAAGACACACATCACAG 58.175 43.478 0.00 0.00 0.00 3.66
1729 1816 4.890158 ACTATCCAAGACACACATCACA 57.110 40.909 0.00 0.00 0.00 3.58
1730 1817 6.170675 GAAACTATCCAAGACACACATCAC 57.829 41.667 0.00 0.00 0.00 3.06
1756 1843 4.122776 CTGAAGCATATCACTGGTACACC 58.877 47.826 0.00 0.00 0.00 4.16
1770 1857 0.604780 ACTGCGCAGAACTGAAGCAT 60.605 50.000 42.03 14.36 41.90 3.79
1801 1891 2.678336 TGTACACGATGCAACACAAACA 59.322 40.909 0.00 0.00 0.00 2.83
1900 1997 7.698130 GCATGCAATTACAAGAAGTAACCTAAG 59.302 37.037 14.21 0.00 44.95 2.18
1901 1998 7.175816 TGCATGCAATTACAAGAAGTAACCTAA 59.824 33.333 20.30 0.00 44.95 2.69
1903 2000 5.476599 TGCATGCAATTACAAGAAGTAACCT 59.523 36.000 20.30 0.00 44.95 3.50
1934 2031 3.557595 GGAGAGTGAAATCATAGTTGCCG 59.442 47.826 0.00 0.00 0.00 5.69
1935 2032 4.517285 TGGAGAGTGAAATCATAGTTGCC 58.483 43.478 0.00 0.00 0.00 4.52
1936 2033 6.690194 ATTGGAGAGTGAAATCATAGTTGC 57.310 37.500 0.00 0.00 0.00 4.17
1937 2034 8.954950 ACTATTGGAGAGTGAAATCATAGTTG 57.045 34.615 0.00 0.00 0.00 3.16
1938 2035 9.388506 CAACTATTGGAGAGTGAAATCATAGTT 57.611 33.333 0.00 0.00 33.13 2.24
1939 2036 8.543774 ACAACTATTGGAGAGTGAAATCATAGT 58.456 33.333 0.00 0.00 34.12 2.12
1940 2037 8.954950 ACAACTATTGGAGAGTGAAATCATAG 57.045 34.615 0.00 0.00 34.12 2.23
1941 2038 9.739276 AAACAACTATTGGAGAGTGAAATCATA 57.261 29.630 0.00 0.00 34.12 2.15
1942 2039 8.641498 AAACAACTATTGGAGAGTGAAATCAT 57.359 30.769 0.00 0.00 34.12 2.45
1944 2041 7.174946 TGGAAACAACTATTGGAGAGTGAAATC 59.825 37.037 0.00 0.00 37.44 2.17
1947 2044 5.935945 TGGAAACAACTATTGGAGAGTGAA 58.064 37.500 0.00 0.00 37.44 3.18
1948 2045 5.560722 TGGAAACAACTATTGGAGAGTGA 57.439 39.130 0.00 0.00 37.44 3.41
1960 2417 7.677384 GAGTTACACTCAGCATGGAAACAACT 61.677 42.308 0.00 0.00 44.29 3.16
1983 2440 5.643777 AGGATTTTTACGAAGGACACATGAG 59.356 40.000 0.00 0.00 0.00 2.90
1987 2444 6.105397 AGTAGGATTTTTACGAAGGACACA 57.895 37.500 0.00 0.00 0.00 3.72
1988 2445 5.579904 GGAGTAGGATTTTTACGAAGGACAC 59.420 44.000 0.00 0.00 0.00 3.67
1989 2446 5.482878 AGGAGTAGGATTTTTACGAAGGACA 59.517 40.000 0.00 0.00 0.00 4.02
1990 2447 5.975282 AGGAGTAGGATTTTTACGAAGGAC 58.025 41.667 0.00 0.00 0.00 3.85
1992 2449 6.877322 TCAAAGGAGTAGGATTTTTACGAAGG 59.123 38.462 0.00 0.00 0.00 3.46
1997 2454 7.664318 TGGTTCTCAAAGGAGTAGGATTTTTAC 59.336 37.037 0.00 0.00 42.05 2.01
2012 2469 0.386478 GCAGCGCTTGGTTCTCAAAG 60.386 55.000 7.50 0.00 34.56 2.77
2033 2490 2.224281 CCGATAAGCTGTAGCCATCCAA 60.224 50.000 0.00 0.00 43.38 3.53
2039 2496 0.880718 GCACCCGATAAGCTGTAGCC 60.881 60.000 0.00 0.00 43.38 3.93
2044 2501 1.723870 GCTTGCACCCGATAAGCTG 59.276 57.895 0.00 0.00 42.55 4.24
2062 2519 3.814268 CAAACATGGGCGGGCGAG 61.814 66.667 0.00 0.00 0.00 5.03
2069 2526 2.408835 CGCGGATCAAACATGGGC 59.591 61.111 0.00 0.00 0.00 5.36
2072 2529 1.439353 CTCCCCGCGGATCAAACATG 61.439 60.000 30.73 5.91 37.60 3.21
2073 2530 1.153168 CTCCCCGCGGATCAAACAT 60.153 57.895 30.73 0.00 37.60 2.71
2083 2540 1.521681 GAAATGAGACCTCCCCGCG 60.522 63.158 0.00 0.00 0.00 6.46
2092 2549 7.829378 ATGTCGTTAAAGGTAGAAATGAGAC 57.171 36.000 0.00 0.00 0.00 3.36
2146 2603 9.160496 CGATGAATTTTCCAATAAATTTTGGGA 57.840 29.630 8.69 5.33 45.21 4.37
2166 2623 6.650807 GGGAGTCATTTGCTAATATCGATGAA 59.349 38.462 8.54 0.00 0.00 2.57
2172 2629 6.240894 TGATGGGGAGTCATTTGCTAATATC 58.759 40.000 0.00 0.00 0.00 1.63
2184 2641 1.956636 GCAGCAATTGATGGGGAGTCA 60.957 52.381 24.02 0.00 31.02 3.41
2185 2642 0.743097 GCAGCAATTGATGGGGAGTC 59.257 55.000 24.02 3.55 31.02 3.36
2215 2672 9.594478 CTGTAACATGTCTAAACACCATGTATA 57.406 33.333 0.00 0.00 46.20 1.47
2220 2677 5.938125 GGACTGTAACATGTCTAAACACCAT 59.062 40.000 0.00 0.00 38.48 3.55
2221 2678 5.071250 AGGACTGTAACATGTCTAAACACCA 59.929 40.000 0.00 0.00 38.48 4.17
2240 2697 7.125507 AGTCATCAGAATTACATCTTGAGGACT 59.874 37.037 12.57 12.57 40.08 3.85
2367 2824 8.637986 TGTGGCTTGTAAGTGAATCTTTATTTT 58.362 29.630 0.00 0.00 37.56 1.82
2368 2825 8.177119 TGTGGCTTGTAAGTGAATCTTTATTT 57.823 30.769 0.00 0.00 37.56 1.40
2369 2826 7.759489 TGTGGCTTGTAAGTGAATCTTTATT 57.241 32.000 0.00 0.00 37.56 1.40
2370 2827 7.944729 ATGTGGCTTGTAAGTGAATCTTTAT 57.055 32.000 0.00 0.00 37.56 1.40
2371 2828 8.856153 TTATGTGGCTTGTAAGTGAATCTTTA 57.144 30.769 0.00 0.00 37.56 1.85
2372 2829 7.759489 TTATGTGGCTTGTAAGTGAATCTTT 57.241 32.000 0.00 0.00 37.56 2.52
2373 2830 7.230510 TGTTTATGTGGCTTGTAAGTGAATCTT 59.769 33.333 0.00 0.00 39.89 2.40
2374 2831 6.714810 TGTTTATGTGGCTTGTAAGTGAATCT 59.285 34.615 0.00 0.00 0.00 2.40
2375 2832 6.908825 TGTTTATGTGGCTTGTAAGTGAATC 58.091 36.000 0.00 0.00 0.00 2.52
2376 2833 6.892658 TGTTTATGTGGCTTGTAAGTGAAT 57.107 33.333 0.00 0.00 0.00 2.57
2377 2834 6.072175 GGATGTTTATGTGGCTTGTAAGTGAA 60.072 38.462 0.00 0.00 0.00 3.18
2378 2835 5.414454 GGATGTTTATGTGGCTTGTAAGTGA 59.586 40.000 0.00 0.00 0.00 3.41
2379 2836 5.182950 TGGATGTTTATGTGGCTTGTAAGTG 59.817 40.000 0.00 0.00 0.00 3.16
2380 2837 5.183140 GTGGATGTTTATGTGGCTTGTAAGT 59.817 40.000 0.00 0.00 0.00 2.24
2381 2838 5.640732 GTGGATGTTTATGTGGCTTGTAAG 58.359 41.667 0.00 0.00 0.00 2.34
2382 2839 4.155099 CGTGGATGTTTATGTGGCTTGTAA 59.845 41.667 0.00 0.00 0.00 2.41
2383 2840 3.687212 CGTGGATGTTTATGTGGCTTGTA 59.313 43.478 0.00 0.00 0.00 2.41
2384 2841 2.487762 CGTGGATGTTTATGTGGCTTGT 59.512 45.455 0.00 0.00 0.00 3.16
2385 2842 2.487762 ACGTGGATGTTTATGTGGCTTG 59.512 45.455 0.00 0.00 0.00 4.01
2386 2843 2.790433 ACGTGGATGTTTATGTGGCTT 58.210 42.857 0.00 0.00 0.00 4.35
2387 2844 2.489938 ACGTGGATGTTTATGTGGCT 57.510 45.000 0.00 0.00 0.00 4.75
2388 2845 3.437395 TGTAACGTGGATGTTTATGTGGC 59.563 43.478 0.00 0.00 33.32 5.01
2389 2846 5.352846 TCATGTAACGTGGATGTTTATGTGG 59.647 40.000 0.00 0.00 33.32 4.17
2390 2847 6.415798 TCATGTAACGTGGATGTTTATGTG 57.584 37.500 0.00 0.00 33.32 3.21
2391 2848 7.335673 TCAATCATGTAACGTGGATGTTTATGT 59.664 33.333 0.00 0.00 33.32 2.29
2392 2849 7.693020 TCAATCATGTAACGTGGATGTTTATG 58.307 34.615 0.00 0.00 33.32 1.90
2393 2850 7.857734 TCAATCATGTAACGTGGATGTTTAT 57.142 32.000 0.00 0.00 33.32 1.40
2394 2851 7.674471 TTCAATCATGTAACGTGGATGTTTA 57.326 32.000 0.00 0.00 33.32 2.01
2395 2852 6.567687 TTCAATCATGTAACGTGGATGTTT 57.432 33.333 0.00 0.00 33.32 2.83
2396 2853 6.567687 TTTCAATCATGTAACGTGGATGTT 57.432 33.333 0.00 0.00 35.86 2.71
2397 2854 6.429692 TCTTTTCAATCATGTAACGTGGATGT 59.570 34.615 0.00 0.00 0.00 3.06
2398 2855 6.841119 TCTTTTCAATCATGTAACGTGGATG 58.159 36.000 0.00 0.00 0.00 3.51
2399 2856 7.630242 ATCTTTTCAATCATGTAACGTGGAT 57.370 32.000 0.00 0.00 0.00 3.41
2400 2857 7.279981 CCTATCTTTTCAATCATGTAACGTGGA 59.720 37.037 0.00 0.00 0.00 4.02
2401 2858 7.279981 TCCTATCTTTTCAATCATGTAACGTGG 59.720 37.037 0.00 0.00 0.00 4.94
2402 2859 8.196802 TCCTATCTTTTCAATCATGTAACGTG 57.803 34.615 0.00 0.00 0.00 4.49
2403 2860 8.964476 ATCCTATCTTTTCAATCATGTAACGT 57.036 30.769 0.00 0.00 0.00 3.99
2444 2901 1.141053 AGAGGGACAGACGCTGTTTTT 59.859 47.619 12.63 3.40 45.44 1.94
2445 2902 0.759346 AGAGGGACAGACGCTGTTTT 59.241 50.000 12.63 3.69 45.44 2.43
2446 2903 0.318762 GAGAGGGACAGACGCTGTTT 59.681 55.000 12.63 3.98 45.44 2.83
2447 2904 1.536943 GGAGAGGGACAGACGCTGTT 61.537 60.000 12.63 0.00 45.44 3.16
2449 2906 1.979155 TGGAGAGGGACAGACGCTG 60.979 63.158 5.47 5.47 41.84 5.18
2450 2907 1.979693 GTGGAGAGGGACAGACGCT 60.980 63.158 0.00 0.00 44.45 5.07
2451 2908 0.680280 TAGTGGAGAGGGACAGACGC 60.680 60.000 0.00 0.00 0.00 5.19
2452 2909 1.746220 CTTAGTGGAGAGGGACAGACG 59.254 57.143 0.00 0.00 0.00 4.18
2453 2910 2.104170 CCTTAGTGGAGAGGGACAGAC 58.896 57.143 0.00 0.00 38.35 3.51
2454 2911 2.000803 TCCTTAGTGGAGAGGGACAGA 58.999 52.381 0.00 0.00 40.56 3.41
2455 2912 2.534042 TCCTTAGTGGAGAGGGACAG 57.466 55.000 0.00 0.00 40.56 3.51
2464 2921 7.987458 GTGATATGTCTCATTTTCCTTAGTGGA 59.013 37.037 0.00 0.00 44.51 4.02
2465 2922 7.227512 GGTGATATGTCTCATTTTCCTTAGTGG 59.772 40.741 0.00 0.00 37.10 4.00
2466 2923 7.989741 AGGTGATATGTCTCATTTTCCTTAGTG 59.010 37.037 0.00 0.00 0.00 2.74
2467 2924 8.095452 AGGTGATATGTCTCATTTTCCTTAGT 57.905 34.615 0.00 0.00 0.00 2.24
2468 2925 8.428063 AGAGGTGATATGTCTCATTTTCCTTAG 58.572 37.037 0.00 0.00 0.00 2.18
2469 2926 8.324191 AGAGGTGATATGTCTCATTTTCCTTA 57.676 34.615 0.00 0.00 0.00 2.69
2470 2927 7.205515 AGAGGTGATATGTCTCATTTTCCTT 57.794 36.000 0.00 0.00 0.00 3.36
2471 2928 6.821616 AGAGGTGATATGTCTCATTTTCCT 57.178 37.500 0.00 0.00 0.00 3.36
2472 2929 7.011857 GTGAAGAGGTGATATGTCTCATTTTCC 59.988 40.741 6.88 0.00 28.04 3.13
2473 2930 7.011857 GGTGAAGAGGTGATATGTCTCATTTTC 59.988 40.741 3.58 3.58 0.00 2.29
2474 2931 6.825721 GGTGAAGAGGTGATATGTCTCATTTT 59.174 38.462 0.00 0.00 0.00 1.82
2475 2932 6.070021 TGGTGAAGAGGTGATATGTCTCATTT 60.070 38.462 0.00 0.00 0.00 2.32
2476 2933 5.426509 TGGTGAAGAGGTGATATGTCTCATT 59.573 40.000 0.00 0.00 0.00 2.57
2477 2934 4.964897 TGGTGAAGAGGTGATATGTCTCAT 59.035 41.667 0.00 0.00 0.00 2.90
2478 2935 4.352893 TGGTGAAGAGGTGATATGTCTCA 58.647 43.478 0.00 0.00 0.00 3.27
2479 2936 4.646945 TCTGGTGAAGAGGTGATATGTCTC 59.353 45.833 0.00 0.00 0.00 3.36
2480 2937 4.614475 TCTGGTGAAGAGGTGATATGTCT 58.386 43.478 0.00 0.00 0.00 3.41
2492 2949 1.876664 CGTCGAGCTCTGGTGAAGA 59.123 57.895 12.85 0.00 0.00 2.87
2493 2950 1.803519 GCGTCGAGCTCTGGTGAAG 60.804 63.158 12.85 5.10 44.04 3.02
2494 2951 2.258591 GCGTCGAGCTCTGGTGAA 59.741 61.111 12.85 0.00 44.04 3.18
2495 2952 4.103103 CGCGTCGAGCTCTGGTGA 62.103 66.667 12.85 0.00 45.59 4.02
2504 2961 2.960957 AATGATGGAGCCGCGTCGAG 62.961 60.000 4.92 0.00 0.00 4.04
2505 2962 3.076258 AATGATGGAGCCGCGTCGA 62.076 57.895 4.92 0.00 0.00 4.20
2506 2963 2.586079 AATGATGGAGCCGCGTCG 60.586 61.111 4.92 0.00 0.00 5.12
2507 2964 0.882042 ATCAATGATGGAGCCGCGTC 60.882 55.000 4.92 0.00 0.00 5.19
2508 2965 0.882042 GATCAATGATGGAGCCGCGT 60.882 55.000 4.92 0.00 0.00 6.01
2509 2966 0.881600 TGATCAATGATGGAGCCGCG 60.882 55.000 0.00 0.00 0.00 6.46
2510 2967 0.873054 CTGATCAATGATGGAGCCGC 59.127 55.000 0.00 0.00 0.00 6.53
2511 2968 0.873054 GCTGATCAATGATGGAGCCG 59.127 55.000 0.00 0.00 0.00 5.52
2512 2969 1.880675 CTGCTGATCAATGATGGAGCC 59.119 52.381 16.74 0.00 0.00 4.70
2513 2970 1.267261 GCTGCTGATCAATGATGGAGC 59.733 52.381 10.32 10.32 0.00 4.70
2514 2971 2.852449 AGCTGCTGATCAATGATGGAG 58.148 47.619 0.00 0.00 0.00 3.86
2515 2972 3.292492 AAGCTGCTGATCAATGATGGA 57.708 42.857 1.35 0.00 0.00 3.41
2516 2973 4.554134 CGTAAAGCTGCTGATCAATGATGG 60.554 45.833 1.35 0.00 0.00 3.51
2517 2974 4.524749 CGTAAAGCTGCTGATCAATGATG 58.475 43.478 1.35 0.00 0.00 3.07
2518 2975 3.562973 CCGTAAAGCTGCTGATCAATGAT 59.437 43.478 1.35 0.00 0.00 2.45
2519 2976 2.938451 CCGTAAAGCTGCTGATCAATGA 59.062 45.455 1.35 0.00 0.00 2.57
2520 2977 2.938451 TCCGTAAAGCTGCTGATCAATG 59.062 45.455 1.35 0.00 0.00 2.82
2521 2978 2.939103 GTCCGTAAAGCTGCTGATCAAT 59.061 45.455 1.35 0.00 0.00 2.57
2522 2979 2.346803 GTCCGTAAAGCTGCTGATCAA 58.653 47.619 1.35 0.00 0.00 2.57
2523 2980 1.405526 GGTCCGTAAAGCTGCTGATCA 60.406 52.381 1.35 0.00 0.00 2.92
2524 2981 1.134670 AGGTCCGTAAAGCTGCTGATC 60.135 52.381 1.35 0.00 0.00 2.92
2525 2982 0.905357 AGGTCCGTAAAGCTGCTGAT 59.095 50.000 1.35 0.00 0.00 2.90
2526 2983 0.246635 GAGGTCCGTAAAGCTGCTGA 59.753 55.000 1.35 0.00 0.00 4.26
2527 2984 0.741221 GGAGGTCCGTAAAGCTGCTG 60.741 60.000 1.35 0.00 32.97 4.41
2528 2985 1.192146 TGGAGGTCCGTAAAGCTGCT 61.192 55.000 0.00 0.00 39.43 4.24
2529 2986 0.321298 TTGGAGGTCCGTAAAGCTGC 60.321 55.000 0.00 0.00 39.43 5.25
2530 2987 2.076863 CTTTGGAGGTCCGTAAAGCTG 58.923 52.381 0.00 0.00 39.43 4.24
2531 2988 1.697982 ACTTTGGAGGTCCGTAAAGCT 59.302 47.619 12.57 0.00 39.43 3.74
2532 2989 2.180432 ACTTTGGAGGTCCGTAAAGC 57.820 50.000 12.57 0.00 39.43 3.51
2533 2990 4.532314 ACTACTTTGGAGGTCCGTAAAG 57.468 45.455 11.59 11.59 39.43 1.85
2534 2991 4.961438 AACTACTTTGGAGGTCCGTAAA 57.039 40.909 0.00 0.00 39.43 2.01
2535 2992 4.634199 CAAACTACTTTGGAGGTCCGTAA 58.366 43.478 0.00 0.00 39.43 3.18
2536 2993 3.555586 GCAAACTACTTTGGAGGTCCGTA 60.556 47.826 0.00 0.00 37.78 4.02
2537 2994 2.809299 GCAAACTACTTTGGAGGTCCGT 60.809 50.000 0.00 0.00 37.78 4.69
2538 2995 1.804748 GCAAACTACTTTGGAGGTCCG 59.195 52.381 0.00 0.00 37.78 4.79
2539 2996 2.160205 GGCAAACTACTTTGGAGGTCC 58.840 52.381 0.00 0.00 37.78 4.46
2540 2997 2.814336 CAGGCAAACTACTTTGGAGGTC 59.186 50.000 0.00 0.00 37.78 3.85
2541 2998 2.441750 TCAGGCAAACTACTTTGGAGGT 59.558 45.455 0.00 0.00 37.78 3.85
2542 2999 3.140325 TCAGGCAAACTACTTTGGAGG 57.860 47.619 0.00 0.00 37.78 4.30
2543 3000 3.057946 GCTTCAGGCAAACTACTTTGGAG 60.058 47.826 0.00 0.00 37.78 3.86
2544 3001 2.884639 GCTTCAGGCAAACTACTTTGGA 59.115 45.455 0.00 0.00 37.78 3.53
2545 3002 3.288809 GCTTCAGGCAAACTACTTTGG 57.711 47.619 0.00 0.00 37.78 3.28
2556 3013 3.988582 CAACAATGGTTTTGCTTCAGGCA 60.989 43.478 0.00 0.00 41.74 4.75
2557 3014 2.531522 ACAATGGTTTTGCTTCAGGC 57.468 45.000 0.00 0.00 42.22 4.85
2558 3015 3.795877 ACAACAATGGTTTTGCTTCAGG 58.204 40.909 0.00 0.00 34.21 3.86
2559 3016 4.869297 TCAACAACAATGGTTTTGCTTCAG 59.131 37.500 0.00 0.00 34.21 3.02
2560 3017 4.825422 TCAACAACAATGGTTTTGCTTCA 58.175 34.783 0.00 0.00 34.21 3.02
2561 3018 5.793026 TTCAACAACAATGGTTTTGCTTC 57.207 34.783 0.00 0.00 34.21 3.86
2562 3019 5.936956 TCTTTCAACAACAATGGTTTTGCTT 59.063 32.000 0.00 0.00 34.21 3.91
2563 3020 5.486526 TCTTTCAACAACAATGGTTTTGCT 58.513 33.333 0.00 0.00 34.21 3.91
2564 3021 5.793026 TCTTTCAACAACAATGGTTTTGC 57.207 34.783 0.00 0.00 34.21 3.68
2565 3022 7.972527 TGATTCTTTCAACAACAATGGTTTTG 58.027 30.769 0.00 0.00 34.21 2.44
2566 3023 8.040132 TCTGATTCTTTCAACAACAATGGTTTT 58.960 29.630 0.00 0.00 31.74 2.43
2567 3024 7.555087 TCTGATTCTTTCAACAACAATGGTTT 58.445 30.769 0.00 0.00 31.74 3.27
2568 3025 7.111247 TCTGATTCTTTCAACAACAATGGTT 57.889 32.000 0.00 0.00 33.47 3.67
2569 3026 6.713762 TCTGATTCTTTCAACAACAATGGT 57.286 33.333 0.00 0.00 32.78 3.55
2570 3027 6.525628 CGATCTGATTCTTTCAACAACAATGG 59.474 38.462 0.00 0.00 32.78 3.16
2571 3028 6.525628 CCGATCTGATTCTTTCAACAACAATG 59.474 38.462 0.00 0.00 32.78 2.82
2572 3029 6.349611 CCCGATCTGATTCTTTCAACAACAAT 60.350 38.462 0.00 0.00 32.78 2.71
2573 3030 5.048782 CCCGATCTGATTCTTTCAACAACAA 60.049 40.000 0.00 0.00 32.78 2.83
2574 3031 4.455533 CCCGATCTGATTCTTTCAACAACA 59.544 41.667 0.00 0.00 32.78 3.33
2575 3032 4.695455 TCCCGATCTGATTCTTTCAACAAC 59.305 41.667 0.00 0.00 32.78 3.32
2576 3033 4.695455 GTCCCGATCTGATTCTTTCAACAA 59.305 41.667 0.00 0.00 32.78 2.83
2577 3034 4.253685 GTCCCGATCTGATTCTTTCAACA 58.746 43.478 0.00 0.00 32.78 3.33
2578 3035 4.253685 TGTCCCGATCTGATTCTTTCAAC 58.746 43.478 0.00 0.00 32.78 3.18
2579 3036 4.551702 TGTCCCGATCTGATTCTTTCAA 57.448 40.909 0.00 0.00 32.78 2.69
2580 3037 4.253685 GTTGTCCCGATCTGATTCTTTCA 58.746 43.478 0.00 0.00 0.00 2.69
2581 3038 3.307242 CGTTGTCCCGATCTGATTCTTTC 59.693 47.826 0.00 0.00 0.00 2.62
2582 3039 3.262420 CGTTGTCCCGATCTGATTCTTT 58.738 45.455 0.00 0.00 0.00 2.52
2583 3040 2.233922 ACGTTGTCCCGATCTGATTCTT 59.766 45.455 0.00 0.00 0.00 2.52
2584 3041 1.825474 ACGTTGTCCCGATCTGATTCT 59.175 47.619 0.00 0.00 0.00 2.40
2585 3042 1.927174 CACGTTGTCCCGATCTGATTC 59.073 52.381 0.00 0.00 0.00 2.52
2586 3043 1.275291 ACACGTTGTCCCGATCTGATT 59.725 47.619 0.00 0.00 0.00 2.57
2587 3044 0.895530 ACACGTTGTCCCGATCTGAT 59.104 50.000 0.00 0.00 0.00 2.90
2588 3045 0.242825 GACACGTTGTCCCGATCTGA 59.757 55.000 6.82 0.00 41.37 3.27
2589 3046 2.738147 GACACGTTGTCCCGATCTG 58.262 57.895 6.82 0.00 41.37 2.90
2597 3054 2.356673 GTCCGGGGACACGTTGTC 60.357 66.667 12.90 8.94 46.23 3.18
2605 3062 2.203209 GATGGCATGTCCGGGGAC 60.203 66.667 3.81 10.95 44.77 4.46
2606 3063 3.860605 CGATGGCATGTCCGGGGA 61.861 66.667 3.81 0.00 37.80 4.81


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

AutoCloner maintained by Alex Coulton.