Multiple sequence alignment - TraesCS3B01G113100

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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 TraesCS3B01G113100 chr3B 100.000 3231 0 0 1 3231 79271310 79274540 0.000000e+00 5967.0
1 TraesCS3B01G113100 chr3D 87.379 1347 84 54 622 1945 49779778 49781061 0.000000e+00 1467.0
2 TraesCS3B01G113100 chr3D 91.176 612 49 5 14 622 49774191 49774800 0.000000e+00 826.0
3 TraesCS3B01G113100 chr3D 87.838 592 45 14 2661 3231 49781674 49782259 0.000000e+00 669.0
4 TraesCS3B01G113100 chr3D 86.111 576 38 22 2117 2676 49781105 49781654 1.670000e-162 582.0
5 TraesCS3B01G113100 chr3A 85.623 1092 72 47 879 1946 63130833 63131863 0.000000e+00 1068.0
6 TraesCS3B01G113100 chr3A 80.731 1204 97 62 2117 3231 63168240 63169397 0.000000e+00 813.0
7 TraesCS3B01G113100 chr3A 82.370 692 101 16 14 693 742043153 742042471 1.670000e-162 582.0
8 TraesCS3B01G113100 chr3A 89.831 413 31 9 2117 2521 63131956 63132365 1.330000e-143 520.0
9 TraesCS3B01G113100 chr3A 86.667 210 19 4 2925 3132 63134874 63135076 1.170000e-54 224.0
10 TraesCS3B01G113100 chr3A 94.656 131 7 0 743 873 63130417 63130547 1.520000e-48 204.0
11 TraesCS3B01G113100 chr3A 77.209 215 31 10 2634 2834 63134479 63134689 3.410000e-20 110.0
12 TraesCS3B01G113100 chr3A 97.619 42 1 0 2585 2626 63134410 63134451 4.470000e-09 73.1
13 TraesCS3B01G113100 chr2B 86.637 666 80 9 3 664 780011979 780012639 0.000000e+00 728.0
14 TraesCS3B01G113100 chr2B 86.164 159 16 4 1071 1229 627723982 627724134 1.990000e-37 167.0
15 TraesCS3B01G113100 chr1B 88.430 605 64 5 14 615 48056747 48056146 0.000000e+00 725.0
16 TraesCS3B01G113100 chr1B 82.336 685 106 11 14 693 675464436 675463762 6.010000e-162 580.0
17 TraesCS3B01G113100 chr2D 85.756 688 89 9 3 685 651067229 651067912 0.000000e+00 719.0
18 TraesCS3B01G113100 chr5B 85.888 659 85 7 14 667 158909710 158909055 0.000000e+00 695.0
19 TraesCS3B01G113100 chr2A 84.726 694 95 10 3 690 776604697 776604009 0.000000e+00 684.0
20 TraesCS3B01G113100 chr5D 83.285 688 100 11 7 686 396812705 396813385 1.270000e-173 619.0
21 TraesCS3B01G113100 chr5D 91.011 89 8 0 1196 1284 436205627 436205539 1.570000e-23 121.0
22 TraesCS3B01G113100 chr1D 85.526 152 22 0 1196 1347 109578831 109578680 3.340000e-35 159.0
23 TraesCS3B01G113100 chr1A 81.347 193 32 3 1157 1347 113252069 113251879 1.550000e-33 154.0


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 TraesCS3B01G113100 chr3B 79271310 79274540 3230 False 5967.000000 5967 100.000000 1 3231 1 chr3B.!!$F1 3230
1 TraesCS3B01G113100 chr3D 49779778 49782259 2481 False 906.000000 1467 87.109333 622 3231 3 chr3D.!!$F2 2609
2 TraesCS3B01G113100 chr3D 49774191 49774800 609 False 826.000000 826 91.176000 14 622 1 chr3D.!!$F1 608
3 TraesCS3B01G113100 chr3A 63168240 63169397 1157 False 813.000000 813 80.731000 2117 3231 1 chr3A.!!$F1 1114
4 TraesCS3B01G113100 chr3A 742042471 742043153 682 True 582.000000 582 82.370000 14 693 1 chr3A.!!$R1 679
5 TraesCS3B01G113100 chr3A 63130417 63135076 4659 False 366.516667 1068 88.600833 743 3132 6 chr3A.!!$F2 2389
6 TraesCS3B01G113100 chr2B 780011979 780012639 660 False 728.000000 728 86.637000 3 664 1 chr2B.!!$F2 661
7 TraesCS3B01G113100 chr1B 48056146 48056747 601 True 725.000000 725 88.430000 14 615 1 chr1B.!!$R1 601
8 TraesCS3B01G113100 chr1B 675463762 675464436 674 True 580.000000 580 82.336000 14 693 1 chr1B.!!$R2 679
9 TraesCS3B01G113100 chr2D 651067229 651067912 683 False 719.000000 719 85.756000 3 685 1 chr2D.!!$F1 682
10 TraesCS3B01G113100 chr5B 158909055 158909710 655 True 695.000000 695 85.888000 14 667 1 chr5B.!!$R1 653
11 TraesCS3B01G113100 chr2A 776604009 776604697 688 True 684.000000 684 84.726000 3 690 1 chr2A.!!$R1 687
12 TraesCS3B01G113100 chr5D 396812705 396813385 680 False 619.000000 619 83.285000 7 686 1 chr5D.!!$F1 679

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
394 400 0.034477 GGTGTTACCCATCCCCACTG 60.034 60.0 0.0 0.0 30.04 3.66 F
1051 1362 0.108615 CACGATCCCTCTGTTTCGCT 60.109 55.0 0.0 0.0 35.08 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2307 0.034059 ACAGCAAGGTCTTCGGTCTG 59.966 55.0 0.0 0.0 0.00 3.51 R
2967 5546 0.107848 GCACCAGCTTACCGTACCAT 60.108 55.0 0.0 0.0 37.91 3.55 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
52 53 3.479203 CCCCTACTGCGGCATCCA 61.479 66.667 1.75 0.00 0.00 3.41
156 157 2.592993 CCCCTCTCGTTTCCTGGCA 61.593 63.158 0.00 0.00 0.00 4.92
298 301 1.546773 GGTAGTGGTGTTTGGGATGCA 60.547 52.381 0.00 0.00 0.00 3.96
335 338 1.659622 TTCATCCGGCTCTAACGCGA 61.660 55.000 15.93 0.00 0.00 5.87
394 400 0.034477 GGTGTTACCCATCCCCACTG 60.034 60.000 0.00 0.00 30.04 3.66
433 439 6.329530 GGGAAACCCTAGGATATGTCCAGC 62.330 54.167 11.48 0.00 46.38 4.85
483 491 1.136828 TGGAGGTGTTGCTTGGTACT 58.863 50.000 0.00 0.00 0.00 2.73
485 493 2.706723 TGGAGGTGTTGCTTGGTACTTA 59.293 45.455 0.00 0.00 0.00 2.24
499 507 2.097825 GTACTTAGAGGTTCGGAGCCA 58.902 52.381 13.62 0.00 0.00 4.75
506 517 3.414700 GTTCGGAGCCACAGTGCG 61.415 66.667 0.00 0.00 36.02 5.34
558 570 1.202114 TGGCGGATCATTTGTGCTTTC 59.798 47.619 0.00 0.00 0.00 2.62
565 577 1.806542 TCATTTGTGCTTTCTCGAGCC 59.193 47.619 7.81 0.00 42.01 4.70
593 606 6.616774 TTGTTGGCATTTTCAATTCTTTCC 57.383 33.333 0.00 0.00 0.00 3.13
616 630 4.320608 TTTCTTTTGGGCTTGATGTGTC 57.679 40.909 0.00 0.00 0.00 3.67
646 660 0.727398 GCAGTTATCTTGTGGTCGGC 59.273 55.000 0.00 0.00 0.00 5.54
658 672 0.320858 TGGTCGGCGAATGTTGCTTA 60.321 50.000 12.92 0.00 0.00 3.09
677 695 7.817418 TGCTTAATAATCTAAAGCGGGAAAT 57.183 32.000 0.00 0.00 46.78 2.17
746 764 7.879962 TTTTGATACAACGTCGTAAGTTTTG 57.120 32.000 0.00 0.00 39.48 2.44
760 778 2.871453 AGTTTTGGCAACGGGTAGAAT 58.129 42.857 0.00 0.00 42.51 2.40
767 785 6.627395 TTGGCAACGGGTAGAATATAAATG 57.373 37.500 0.00 0.00 42.51 2.32
799 817 2.040813 AGCTCATGGATCCAAACAGTGT 59.959 45.455 20.67 0.00 0.00 3.55
825 843 0.737715 AAAGGTCGTCTCTGCATCGC 60.738 55.000 0.00 0.00 0.00 4.58
866 884 7.176075 CGAGCAGTAACAAAAGTAATCAGATG 58.824 38.462 0.00 0.00 0.00 2.90
931 1229 6.258727 AGCACACTTCTCATTATTAATCCACG 59.741 38.462 0.00 0.00 0.00 4.94
932 1230 6.257849 GCACACTTCTCATTATTAATCCACGA 59.742 38.462 0.00 0.00 0.00 4.35
933 1231 7.517417 GCACACTTCTCATTATTAATCCACGAG 60.517 40.741 0.00 0.00 0.00 4.18
934 1232 7.706607 CACACTTCTCATTATTAATCCACGAGA 59.293 37.037 0.00 0.00 0.00 4.04
935 1233 8.258007 ACACTTCTCATTATTAATCCACGAGAA 58.742 33.333 14.10 14.10 36.76 2.87
936 1234 9.265901 CACTTCTCATTATTAATCCACGAGAAT 57.734 33.333 14.74 7.38 37.39 2.40
937 1235 9.482627 ACTTCTCATTATTAATCCACGAGAATC 57.517 33.333 14.74 0.00 37.39 2.52
938 1236 8.833231 TTCTCATTATTAATCCACGAGAATCC 57.167 34.615 12.15 0.00 34.14 3.01
939 1237 7.962441 TCTCATTATTAATCCACGAGAATCCA 58.038 34.615 0.00 0.00 0.00 3.41
940 1238 7.872993 TCTCATTATTAATCCACGAGAATCCAC 59.127 37.037 0.00 0.00 0.00 4.02
1010 1310 2.836981 CCTCAGTGATCACTTCCTCCTT 59.163 50.000 25.84 0.00 40.20 3.36
1049 1360 1.630148 GACACGATCCCTCTGTTTCG 58.370 55.000 0.00 0.00 37.60 3.46
1051 1362 0.108615 CACGATCCCTCTGTTTCGCT 60.109 55.000 0.00 0.00 35.08 4.93
1072 1388 0.796927 TACAGAGCAGAGACACGTCG 59.203 55.000 0.00 0.00 34.09 5.12
1081 1397 0.738975 GAGACACGTCGATCCATCCA 59.261 55.000 0.00 0.00 34.09 3.41
1192 1508 4.010575 CTGACGAGGGACAGCTCT 57.989 61.111 0.00 0.00 0.00 4.09
1298 1614 2.558286 AAGAACGCCGTCTCCGACA 61.558 57.895 0.00 0.00 35.63 4.35
1300 1616 4.695231 AACGCCGTCTCCGACACG 62.695 66.667 0.00 5.28 37.63 4.49
1502 1839 3.132139 CCTTCTCCTCCGCGTCGA 61.132 66.667 4.92 0.00 0.00 4.20
1511 1848 4.175489 CCGCGTCGACCTCGTCAT 62.175 66.667 19.14 0.00 40.80 3.06
1512 1849 2.648102 CGCGTCGACCTCGTCATC 60.648 66.667 10.58 0.00 40.80 2.92
1513 1850 2.648102 GCGTCGACCTCGTCATCG 60.648 66.667 10.58 0.00 40.80 3.84
1514 1851 2.783275 CGTCGACCTCGTCATCGT 59.217 61.111 10.58 0.00 39.38 3.73
1515 1852 1.296722 CGTCGACCTCGTCATCGTC 60.297 63.158 10.58 0.00 39.38 4.20
1516 1853 1.792301 GTCGACCTCGTCATCGTCA 59.208 57.895 3.51 0.00 39.38 4.35
1517 1854 0.377554 GTCGACCTCGTCATCGTCAT 59.622 55.000 3.51 0.00 39.38 3.06
1518 1855 0.656259 TCGACCTCGTCATCGTCATC 59.344 55.000 0.00 0.00 39.38 2.92
1519 1856 0.317103 CGACCTCGTCATCGTCATCC 60.317 60.000 0.00 0.00 38.33 3.51
1520 1857 1.025812 GACCTCGTCATCGTCATCCT 58.974 55.000 0.00 0.00 38.33 3.24
1521 1858 1.002251 GACCTCGTCATCGTCATCCTC 60.002 57.143 0.00 0.00 38.33 3.71
1524 1861 2.495084 CTCGTCATCGTCATCCTCCTA 58.505 52.381 0.00 0.00 38.33 2.94
1529 1866 1.537638 CATCGTCATCCTCCTACTCGG 59.462 57.143 0.00 0.00 0.00 4.63
1531 1868 1.101635 CGTCATCCTCCTACTCGGCA 61.102 60.000 0.00 0.00 0.00 5.69
1534 1871 1.145945 TCATCCTCCTACTCGGCATCT 59.854 52.381 0.00 0.00 0.00 2.90
1537 1874 0.312416 CCTCCTACTCGGCATCTTCG 59.688 60.000 0.00 0.00 0.00 3.79
1546 1883 2.813908 GCATCTTCGTTCCGCCGT 60.814 61.111 0.00 0.00 0.00 5.68
1549 1886 1.140375 ATCTTCGTTCCGCCGTACC 59.860 57.895 0.00 0.00 0.00 3.34
1550 1887 1.597797 ATCTTCGTTCCGCCGTACCA 61.598 55.000 0.00 0.00 0.00 3.25
1551 1888 2.049248 TTCGTTCCGCCGTACCAC 60.049 61.111 0.00 0.00 0.00 4.16
1552 1889 3.895102 TTCGTTCCGCCGTACCACG 62.895 63.158 0.00 0.00 42.11 4.94
1555 1892 4.728102 TTCCGCCGTACCACGCAG 62.728 66.667 0.00 0.00 40.91 5.18
1562 1899 4.409218 GTACCACGCAGTCGCCGA 62.409 66.667 0.00 0.00 41.61 5.54
1563 1900 3.445687 TACCACGCAGTCGCCGAT 61.446 61.111 0.00 0.00 41.61 4.18
1564 1901 3.693382 TACCACGCAGTCGCCGATG 62.693 63.158 0.00 0.00 41.61 3.84
1769 2109 2.707849 GCGCAGAGGGTCTAACCGA 61.708 63.158 0.30 0.00 39.83 4.69
1770 2110 1.888018 CGCAGAGGGTCTAACCGAA 59.112 57.895 0.00 0.00 39.83 4.30
1771 2111 0.458025 CGCAGAGGGTCTAACCGAAC 60.458 60.000 0.00 0.00 39.83 3.95
1772 2112 0.896226 GCAGAGGGTCTAACCGAACT 59.104 55.000 0.00 0.00 39.83 3.01
1773 2113 2.097825 GCAGAGGGTCTAACCGAACTA 58.902 52.381 0.00 0.00 39.83 2.24
1778 2118 4.018960 AGAGGGTCTAACCGAACTACACTA 60.019 45.833 0.00 0.00 39.83 2.74
1786 2126 1.909532 CCGAACTACACTAAACTCGCG 59.090 52.381 0.00 0.00 0.00 5.87
1813 2161 1.214367 AGGACGTGCGTTGTTACTTG 58.786 50.000 0.00 0.00 0.00 3.16
1848 2197 0.533308 TACCCAAGTCGTGTGTTGGC 60.533 55.000 0.00 0.00 41.77 4.52
1937 2289 5.410746 GCATGTTCAGAACTTCAGATCAGAA 59.589 40.000 14.51 0.22 0.00 3.02
1946 2298 6.436847 AGAACTTCAGATCAGAACTCTCATCA 59.563 38.462 0.00 0.00 0.00 3.07
1947 2299 6.795144 ACTTCAGATCAGAACTCTCATCAT 57.205 37.500 0.00 0.00 0.00 2.45
1949 2301 6.608405 ACTTCAGATCAGAACTCTCATCATCT 59.392 38.462 0.00 0.00 0.00 2.90
1951 2303 5.535783 TCAGATCAGAACTCTCATCATCTCC 59.464 44.000 0.00 0.00 0.00 3.71
1952 2304 5.537295 CAGATCAGAACTCTCATCATCTCCT 59.463 44.000 0.00 0.00 0.00 3.69
1953 2305 6.041182 CAGATCAGAACTCTCATCATCTCCTT 59.959 42.308 0.00 0.00 0.00 3.36
1954 2306 5.595257 TCAGAACTCTCATCATCTCCTTG 57.405 43.478 0.00 0.00 0.00 3.61
1955 2307 4.121317 CAGAACTCTCATCATCTCCTTGC 58.879 47.826 0.00 0.00 0.00 4.01
1956 2308 3.773667 AGAACTCTCATCATCTCCTTGCA 59.226 43.478 0.00 0.00 0.00 4.08
1959 2311 3.132646 ACTCTCATCATCTCCTTGCAGAC 59.867 47.826 0.00 0.00 0.00 3.51
1960 2312 2.433604 TCTCATCATCTCCTTGCAGACC 59.566 50.000 0.00 0.00 0.00 3.85
1961 2313 1.137675 TCATCATCTCCTTGCAGACCG 59.862 52.381 0.00 0.00 0.00 4.79
1962 2314 1.137675 CATCATCTCCTTGCAGACCGA 59.862 52.381 0.00 0.00 0.00 4.69
1963 2315 1.266178 TCATCTCCTTGCAGACCGAA 58.734 50.000 0.00 0.00 0.00 4.30
1964 2316 1.205655 TCATCTCCTTGCAGACCGAAG 59.794 52.381 0.00 0.00 0.00 3.79
1965 2317 1.205655 CATCTCCTTGCAGACCGAAGA 59.794 52.381 0.00 0.00 0.00 2.87
1966 2318 0.603569 TCTCCTTGCAGACCGAAGAC 59.396 55.000 0.00 0.00 0.00 3.01
1967 2319 0.390472 CTCCTTGCAGACCGAAGACC 60.390 60.000 0.00 0.00 0.00 3.85
1968 2320 0.832135 TCCTTGCAGACCGAAGACCT 60.832 55.000 0.00 0.00 0.00 3.85
1969 2321 0.035458 CCTTGCAGACCGAAGACCTT 59.965 55.000 0.00 0.00 0.00 3.50
1970 2322 1.151668 CTTGCAGACCGAAGACCTTG 58.848 55.000 0.00 0.00 0.00 3.61
1971 2323 0.884704 TTGCAGACCGAAGACCTTGC 60.885 55.000 0.00 0.00 0.00 4.01
1972 2324 1.004440 GCAGACCGAAGACCTTGCT 60.004 57.895 0.00 0.00 0.00 3.91
1973 2325 1.294659 GCAGACCGAAGACCTTGCTG 61.295 60.000 0.00 0.00 0.00 4.41
1974 2326 0.034059 CAGACCGAAGACCTTGCTGT 59.966 55.000 0.00 0.00 0.00 4.40
1975 2327 1.272490 CAGACCGAAGACCTTGCTGTA 59.728 52.381 0.00 0.00 0.00 2.74
1976 2328 1.546476 AGACCGAAGACCTTGCTGTAG 59.454 52.381 0.00 0.00 0.00 2.74
1977 2329 1.272769 GACCGAAGACCTTGCTGTAGT 59.727 52.381 0.00 0.00 0.00 2.73
1978 2330 1.000955 ACCGAAGACCTTGCTGTAGTG 59.999 52.381 0.00 0.00 0.00 2.74
1979 2331 1.071605 CGAAGACCTTGCTGTAGTGC 58.928 55.000 0.00 0.00 0.00 4.40
1980 2332 1.443802 GAAGACCTTGCTGTAGTGCC 58.556 55.000 0.00 0.00 0.00 5.01
1981 2333 0.764890 AAGACCTTGCTGTAGTGCCA 59.235 50.000 0.00 0.00 0.00 4.92
1984 2336 1.740025 GACCTTGCTGTAGTGCCAATC 59.260 52.381 0.00 0.00 0.00 2.67
1992 2344 3.201290 CTGTAGTGCCAATCTGACCATC 58.799 50.000 0.00 0.00 0.00 3.51
1997 2349 3.009916 AGTGCCAATCTGACCATCTTTCT 59.990 43.478 0.00 0.00 0.00 2.52
2000 2352 4.263639 TGCCAATCTGACCATCTTTCTTCT 60.264 41.667 0.00 0.00 0.00 2.85
2001 2353 4.335037 GCCAATCTGACCATCTTTCTTCTC 59.665 45.833 0.00 0.00 0.00 2.87
2003 2355 5.585445 CCAATCTGACCATCTTTCTTCTCTG 59.415 44.000 0.00 0.00 0.00 3.35
2004 2356 4.815533 TCTGACCATCTTTCTTCTCTGG 57.184 45.455 0.00 0.00 0.00 3.86
2005 2357 4.420206 TCTGACCATCTTTCTTCTCTGGA 58.580 43.478 0.00 0.00 0.00 3.86
2006 2358 4.465660 TCTGACCATCTTTCTTCTCTGGAG 59.534 45.833 0.00 0.00 0.00 3.86
2007 2359 3.055530 TGACCATCTTTCTTCTCTGGAGC 60.056 47.826 0.00 0.00 0.00 4.70
2008 2360 2.909006 ACCATCTTTCTTCTCTGGAGCA 59.091 45.455 0.00 0.00 0.00 4.26
2009 2361 3.328931 ACCATCTTTCTTCTCTGGAGCAA 59.671 43.478 0.00 0.00 0.00 3.91
2010 2362 3.940221 CCATCTTTCTTCTCTGGAGCAAG 59.060 47.826 0.00 0.00 0.00 4.01
2011 2363 4.565236 CCATCTTTCTTCTCTGGAGCAAGT 60.565 45.833 0.00 0.00 0.00 3.16
2012 2364 4.000331 TCTTTCTTCTCTGGAGCAAGTG 58.000 45.455 0.00 0.00 0.00 3.16
2013 2365 2.175878 TTCTTCTCTGGAGCAAGTGC 57.824 50.000 0.00 0.00 42.49 4.40
2018 2370 2.867624 TCTCTGGAGCAAGTGCATTTT 58.132 42.857 6.00 0.00 45.16 1.82
2019 2371 4.019792 TCTCTGGAGCAAGTGCATTTTA 57.980 40.909 6.00 0.00 45.16 1.52
2020 2372 4.397420 TCTCTGGAGCAAGTGCATTTTAA 58.603 39.130 6.00 0.00 45.16 1.52
2034 2386 7.909267 AGTGCATTTTAAGTTTTCTTTTCTGC 58.091 30.769 0.00 0.00 40.91 4.26
2035 2387 7.011389 AGTGCATTTTAAGTTTTCTTTTCTGCC 59.989 33.333 0.00 0.00 40.91 4.85
2036 2388 6.019156 TGCATTTTAAGTTTTCTTTTCTGCCG 60.019 34.615 0.00 0.00 40.91 5.69
2037 2389 6.200097 GCATTTTAAGTTTTCTTTTCTGCCGA 59.800 34.615 0.00 0.00 40.91 5.54
2038 2390 7.254286 GCATTTTAAGTTTTCTTTTCTGCCGAA 60.254 33.333 0.00 0.00 40.91 4.30
2041 2393 8.535690 TTTAAGTTTTCTTTTCTGCCGAAAAA 57.464 26.923 15.57 6.00 45.57 1.94
2042 2394 6.647212 AAGTTTTCTTTTCTGCCGAAAAAG 57.353 33.333 15.57 11.69 45.57 2.27
2043 2395 5.720202 AGTTTTCTTTTCTGCCGAAAAAGT 58.280 33.333 15.57 3.16 45.57 2.66
2044 2396 5.576774 AGTTTTCTTTTCTGCCGAAAAAGTG 59.423 36.000 15.57 6.21 45.57 3.16
2045 2397 4.712122 TTCTTTTCTGCCGAAAAAGTGT 57.288 36.364 15.57 0.00 45.57 3.55
2046 2398 4.712122 TCTTTTCTGCCGAAAAAGTGTT 57.288 36.364 15.57 0.00 45.57 3.32
2047 2399 5.066968 TCTTTTCTGCCGAAAAAGTGTTT 57.933 34.783 15.57 0.00 45.57 2.83
2048 2400 4.862018 TCTTTTCTGCCGAAAAAGTGTTTG 59.138 37.500 15.57 4.39 45.57 2.93
2056 2408 5.096849 GCCGAAAAAGTGTTTGAGTGTTAA 58.903 37.500 0.00 0.00 0.00 2.01
2066 2418 7.781056 AGTGTTTGAGTGTTAATCCATGTTTT 58.219 30.769 0.00 0.00 0.00 2.43
2067 2419 7.920682 AGTGTTTGAGTGTTAATCCATGTTTTC 59.079 33.333 0.00 0.00 0.00 2.29
2068 2420 7.920682 GTGTTTGAGTGTTAATCCATGTTTTCT 59.079 33.333 0.00 0.00 0.00 2.52
2070 2422 8.968242 GTTTGAGTGTTAATCCATGTTTTCTTC 58.032 33.333 0.00 0.00 0.00 2.87
2071 2423 8.463930 TTGAGTGTTAATCCATGTTTTCTTCT 57.536 30.769 0.00 0.00 0.00 2.85
2072 2424 8.099364 TGAGTGTTAATCCATGTTTTCTTCTC 57.901 34.615 0.00 0.00 0.00 2.87
2073 2425 7.939039 TGAGTGTTAATCCATGTTTTCTTCTCT 59.061 33.333 0.00 0.00 0.00 3.10
2074 2426 8.103948 AGTGTTAATCCATGTTTTCTTCTCTG 57.896 34.615 0.00 0.00 0.00 3.35
2075 2427 7.175641 AGTGTTAATCCATGTTTTCTTCTCTGG 59.824 37.037 0.00 0.00 0.00 3.86
2077 2429 7.391554 TGTTAATCCATGTTTTCTTCTCTGGAG 59.608 37.037 0.00 0.00 36.31 3.86
2078 2430 3.679389 TCCATGTTTTCTTCTCTGGAGC 58.321 45.455 0.00 0.00 0.00 4.70
2079 2431 3.072915 TCCATGTTTTCTTCTCTGGAGCA 59.927 43.478 0.00 0.00 0.00 4.26
2081 2433 4.082895 CCATGTTTTCTTCTCTGGAGCAAG 60.083 45.833 0.00 0.00 0.00 4.01
2083 2435 3.879295 TGTTTTCTTCTCTGGAGCAAGTG 59.121 43.478 0.00 0.00 0.00 3.16
2084 2436 2.175878 TTCTTCTCTGGAGCAAGTGC 57.824 50.000 0.00 0.00 42.49 4.40
2085 2437 1.051008 TCTTCTCTGGAGCAAGTGCA 58.949 50.000 6.00 0.00 45.16 4.57
2087 2439 2.039480 TCTTCTCTGGAGCAAGTGCATT 59.961 45.455 6.00 0.00 45.16 3.56
2088 2440 2.574006 TCTCTGGAGCAAGTGCATTT 57.426 45.000 6.00 0.00 45.16 2.32
2089 2441 2.867624 TCTCTGGAGCAAGTGCATTTT 58.132 42.857 6.00 0.00 45.16 1.82
2090 2442 4.019792 TCTCTGGAGCAAGTGCATTTTA 57.980 40.909 6.00 0.00 45.16 1.52
2091 2443 4.005650 TCTCTGGAGCAAGTGCATTTTAG 58.994 43.478 6.00 0.00 45.16 1.85
2092 2444 3.084039 TCTGGAGCAAGTGCATTTTAGG 58.916 45.455 6.00 0.00 45.16 2.69
2093 2445 2.821969 CTGGAGCAAGTGCATTTTAGGT 59.178 45.455 6.00 0.00 45.16 3.08
2094 2446 3.230134 TGGAGCAAGTGCATTTTAGGTT 58.770 40.909 6.00 0.00 45.16 3.50
2095 2447 3.640967 TGGAGCAAGTGCATTTTAGGTTT 59.359 39.130 6.00 0.00 45.16 3.27
2096 2448 4.100808 TGGAGCAAGTGCATTTTAGGTTTT 59.899 37.500 6.00 0.00 45.16 2.43
2097 2449 4.686091 GGAGCAAGTGCATTTTAGGTTTTC 59.314 41.667 6.00 0.00 45.16 2.29
2098 2450 5.509670 GGAGCAAGTGCATTTTAGGTTTTCT 60.510 40.000 6.00 0.00 45.16 2.52
2099 2451 5.917462 AGCAAGTGCATTTTAGGTTTTCTT 58.083 33.333 6.00 0.00 45.16 2.52
2100 2452 6.348498 AGCAAGTGCATTTTAGGTTTTCTTT 58.652 32.000 6.00 0.00 45.16 2.52
2101 2453 6.823182 AGCAAGTGCATTTTAGGTTTTCTTTT 59.177 30.769 6.00 0.00 45.16 2.27
2102 2454 6.906678 GCAAGTGCATTTTAGGTTTTCTTTTG 59.093 34.615 0.00 0.00 41.59 2.44
2103 2455 7.413988 GCAAGTGCATTTTAGGTTTTCTTTTGT 60.414 33.333 0.00 0.00 41.59 2.83
2104 2456 8.450180 CAAGTGCATTTTAGGTTTTCTTTTGTT 58.550 29.630 0.00 0.00 0.00 2.83
2105 2457 9.660180 AAGTGCATTTTAGGTTTTCTTTTGTTA 57.340 25.926 0.00 0.00 0.00 2.41
2106 2458 9.660180 AGTGCATTTTAGGTTTTCTTTTGTTAA 57.340 25.926 0.00 0.00 0.00 2.01
2139 2491 6.173339 TGAGTGTTATCCTGGAAAGTTGATC 58.827 40.000 0.00 0.00 0.00 2.92
2147 2499 4.019860 TCCTGGAAAGTTGATCTCTTCCTG 60.020 45.833 0.00 12.54 35.91 3.86
2235 2594 7.389053 GGAATAAAGAATGTCTATCAGCCGAAT 59.611 37.037 0.00 0.00 0.00 3.34
2316 2676 5.587289 TGAATTATATTTTTGGCGCTGTCC 58.413 37.500 7.64 0.00 0.00 4.02
2332 2692 1.339535 TGTCCAACAACTGTGTGAGCA 60.340 47.619 0.00 0.00 38.27 4.26
2466 2831 0.665835 TGCACACACGGGAATTGTTC 59.334 50.000 0.00 0.00 0.00 3.18
2583 2960 7.782168 AGAAGAAGAAGAAGAAGAAAAATGGGT 59.218 33.333 0.00 0.00 0.00 4.51
2628 4995 1.545136 TGAATGCACATGACCGCAATT 59.455 42.857 11.96 7.97 42.37 2.32
2648 5036 0.829333 CATGCTGAGCCCTGAGTAGT 59.171 55.000 0.23 0.00 0.00 2.73
2743 5184 8.099364 AGTAGAACCAAAATGTTCACTATGTG 57.901 34.615 6.67 0.00 45.62 3.21
2803 5253 0.031716 TATGCTGAGGAGTGAGGGCT 60.032 55.000 0.00 0.00 0.00 5.19
2945 5524 0.107456 ACCAGCTCACACTCACCAAG 59.893 55.000 0.00 0.00 0.00 3.61
2959 5538 5.721232 ACTCACCAAGTGCAAGTATAGTAC 58.279 41.667 0.00 0.00 36.65 2.73
2967 5546 5.262009 AGTGCAAGTATAGTACTGGACTGA 58.738 41.667 5.39 0.00 39.39 3.41
2974 5553 5.996513 AGTATAGTACTGGACTGATGGTACG 59.003 44.000 5.39 0.00 39.39 3.67
3063 5643 3.255725 TCCATGATTCGTTGACGGTAAC 58.744 45.455 3.48 0.00 40.29 2.50
3081 5661 4.982295 GGTAACAAGATGGTGAAAACTTGC 59.018 41.667 0.00 0.00 42.00 4.01
3133 5732 1.024579 ACGTGAATGTGAATCCCCGC 61.025 55.000 0.00 0.00 0.00 6.13
3148 5747 2.202610 CGCACGCTTCAGATCCGA 60.203 61.111 0.00 0.00 0.00 4.55
3149 5748 2.508891 CGCACGCTTCAGATCCGAC 61.509 63.158 0.00 0.00 0.00 4.79
3166 5765 1.335597 CGACTTGGAGTACTGTCGCAA 60.336 52.381 17.24 4.10 44.00 4.85
3183 5792 1.336755 GCAACGACATGGTTTTGTCCT 59.663 47.619 0.00 0.00 42.46 3.85
3187 5796 3.020984 ACGACATGGTTTTGTCCTTTGT 58.979 40.909 0.00 0.00 42.46 2.83
3199 5808 7.412891 GGTTTTGTCCTTTGTTGAGATGTTTTG 60.413 37.037 0.00 0.00 0.00 2.44
3201 5810 7.397892 TTGTCCTTTGTTGAGATGTTTTGTA 57.602 32.000 0.00 0.00 0.00 2.41
3203 5812 6.601613 TGTCCTTTGTTGAGATGTTTTGTACT 59.398 34.615 0.00 0.00 0.00 2.73
3204 5813 6.912591 GTCCTTTGTTGAGATGTTTTGTACTG 59.087 38.462 0.00 0.00 0.00 2.74
3226 5840 7.824672 ACTGTACTATACTACAACTGTTGACC 58.175 38.462 26.00 3.10 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.790962 CCAGCTGGATGCCGCAGT 62.791 66.667 29.88 0.00 44.23 4.40
48 49 4.227134 CGCGGTAGCCAGCTGGAT 62.227 66.667 37.21 33.17 41.18 3.41
156 157 1.702957 CTAGAGGACGGAGAGAGGGAT 59.297 57.143 0.00 0.00 0.00 3.85
256 258 1.386525 CCAATCCGGAGCCAACCATG 61.387 60.000 11.34 0.00 36.56 3.66
298 301 1.208165 AACCGGCAGGGATTTCTCCT 61.208 55.000 8.08 0.00 43.47 3.69
409 415 3.599348 GGACATATCCTAGGGTTTCCCT 58.401 50.000 9.46 12.22 46.02 4.20
433 439 3.767230 CGTTGACGACGCTGCTGG 61.767 66.667 1.51 0.00 45.86 4.85
483 491 0.895530 CTGTGGCTCCGAACCTCTAA 59.104 55.000 0.00 0.00 0.00 2.10
485 493 1.534235 ACTGTGGCTCCGAACCTCT 60.534 57.895 0.00 0.00 0.00 3.69
506 517 3.279875 GGATTCATCCCACCGCGC 61.280 66.667 0.00 0.00 41.20 6.86
507 518 2.967076 CGGATTCATCCCACCGCG 60.967 66.667 0.00 0.00 44.24 6.46
530 541 2.482796 AATGATCCGCCACCACTGCA 62.483 55.000 0.00 0.00 0.00 4.41
535 546 1.594194 GCACAAATGATCCGCCACCA 61.594 55.000 0.00 0.00 0.00 4.17
558 570 2.753966 CCAACAATGGCGGCTCGAG 61.754 63.158 11.43 8.45 40.58 4.04
583 595 6.057533 AGCCCAAAAGAAAAGGAAAGAATTG 58.942 36.000 0.00 0.00 0.00 2.32
584 596 6.252599 AGCCCAAAAGAAAAGGAAAGAATT 57.747 33.333 0.00 0.00 0.00 2.17
585 597 5.894298 AGCCCAAAAGAAAAGGAAAGAAT 57.106 34.783 0.00 0.00 0.00 2.40
593 606 4.696455 ACACATCAAGCCCAAAAGAAAAG 58.304 39.130 0.00 0.00 0.00 2.27
646 660 7.321271 CCGCTTTAGATTATTAAGCAACATTCG 59.679 37.037 0.00 0.00 43.34 3.34
746 764 6.870971 TTCATTTATATTCTACCCGTTGCC 57.129 37.500 0.00 0.00 0.00 4.52
760 778 7.609146 CCATGAGCTAAGCAGGATTCATTTATA 59.391 37.037 0.00 0.00 0.00 0.98
767 785 3.482156 TCCATGAGCTAAGCAGGATTC 57.518 47.619 0.00 0.00 0.00 2.52
799 817 1.613925 CAGAGACGACCTTTGACCTCA 59.386 52.381 0.00 0.00 0.00 3.86
825 843 0.807667 CTCGGCTGTCCAAGATTCCG 60.808 60.000 0.00 0.00 38.34 4.30
866 884 0.318784 CCCGCTGCCGTTAGTATCTC 60.319 60.000 0.00 0.00 0.00 2.75
931 1229 2.958355 CAGAGAGAGAGGGTGGATTCTC 59.042 54.545 0.00 0.00 40.07 2.87
932 1230 2.954539 GCAGAGAGAGAGGGTGGATTCT 60.955 54.545 0.00 0.00 0.00 2.40
933 1231 1.412343 GCAGAGAGAGAGGGTGGATTC 59.588 57.143 0.00 0.00 0.00 2.52
934 1232 1.008206 AGCAGAGAGAGAGGGTGGATT 59.992 52.381 0.00 0.00 0.00 3.01
935 1233 0.636101 AGCAGAGAGAGAGGGTGGAT 59.364 55.000 0.00 0.00 0.00 3.41
936 1234 0.324183 CAGCAGAGAGAGAGGGTGGA 60.324 60.000 0.00 0.00 0.00 4.02
937 1235 1.958902 GCAGCAGAGAGAGAGGGTGG 61.959 65.000 0.00 0.00 0.00 4.61
938 1236 1.516892 GCAGCAGAGAGAGAGGGTG 59.483 63.158 0.00 0.00 0.00 4.61
939 1237 1.685421 GGCAGCAGAGAGAGAGGGT 60.685 63.158 0.00 0.00 0.00 4.34
940 1238 2.784356 CGGCAGCAGAGAGAGAGGG 61.784 68.421 0.00 0.00 0.00 4.30
989 1289 2.465813 AGGAGGAAGTGATCACTGAGG 58.534 52.381 28.52 0.00 41.58 3.86
1033 1344 0.108615 CAGCGAAACAGAGGGATCGT 60.109 55.000 0.00 0.00 37.60 3.73
1046 1357 1.200252 GTCTCTGCTCTGTACAGCGAA 59.800 52.381 18.45 5.59 42.92 4.70
1049 1360 1.730772 CGTGTCTCTGCTCTGTACAGC 60.731 57.143 18.45 9.10 40.13 4.40
1051 1362 1.535896 GACGTGTCTCTGCTCTGTACA 59.464 52.381 0.00 0.00 0.00 2.90
1099 1415 3.726517 CTGTCCTTGCCGTTGCCG 61.727 66.667 0.00 0.00 36.33 5.69
1100 1416 3.365265 CCTGTCCTTGCCGTTGCC 61.365 66.667 0.00 0.00 36.33 4.52
1101 1417 3.365265 CCCTGTCCTTGCCGTTGC 61.365 66.667 0.00 0.00 38.26 4.17
1102 1418 1.672356 CTCCCTGTCCTTGCCGTTG 60.672 63.158 0.00 0.00 0.00 4.10
1103 1419 2.750350 CTCCCTGTCCTTGCCGTT 59.250 61.111 0.00 0.00 0.00 4.44
1104 1420 3.322466 CCTCCCTGTCCTTGCCGT 61.322 66.667 0.00 0.00 0.00 5.68
1211 1527 1.751927 CCACGCCGTAGTAGACCCT 60.752 63.158 0.00 0.00 0.00 4.34
1391 1713 2.281761 CGGCCTGAACCTGTTGCT 60.282 61.111 0.00 0.00 0.00 3.91
1502 1839 1.025812 GAGGATGACGATGACGAGGT 58.974 55.000 0.00 0.00 42.66 3.85
1510 1847 1.898902 CCGAGTAGGAGGATGACGAT 58.101 55.000 0.00 0.00 45.00 3.73
1511 1848 0.818445 GCCGAGTAGGAGGATGACGA 60.818 60.000 0.00 0.00 45.00 4.20
1512 1849 1.101635 TGCCGAGTAGGAGGATGACG 61.102 60.000 0.00 0.00 45.00 4.35
1513 1850 1.271102 GATGCCGAGTAGGAGGATGAC 59.729 57.143 0.00 0.00 45.00 3.06
1514 1851 1.145945 AGATGCCGAGTAGGAGGATGA 59.854 52.381 0.00 0.00 45.00 2.92
1515 1852 1.626686 AGATGCCGAGTAGGAGGATG 58.373 55.000 0.00 0.00 45.00 3.51
1516 1853 2.243810 GAAGATGCCGAGTAGGAGGAT 58.756 52.381 0.00 0.00 45.00 3.24
1517 1854 1.693627 GAAGATGCCGAGTAGGAGGA 58.306 55.000 0.00 0.00 45.00 3.71
1518 1855 0.312416 CGAAGATGCCGAGTAGGAGG 59.688 60.000 0.00 0.00 45.00 4.30
1519 1856 1.025812 ACGAAGATGCCGAGTAGGAG 58.974 55.000 0.00 0.00 45.00 3.69
1520 1857 1.404391 GAACGAAGATGCCGAGTAGGA 59.596 52.381 0.00 0.00 45.00 2.94
1521 1858 1.536284 GGAACGAAGATGCCGAGTAGG 60.536 57.143 0.00 0.00 44.97 3.18
1524 1861 4.913126 GGAACGAAGATGCCGAGT 57.087 55.556 0.00 0.00 0.00 4.18
1546 1883 3.445687 ATCGGCGACTGCGTGGTA 61.446 61.111 13.76 0.00 44.10 3.25
1624 1964 4.554036 GCCATGGCCGTCTCCTCC 62.554 72.222 27.24 0.00 34.56 4.30
1744 2084 4.479993 ACCCTCTGCGCCTGATGC 62.480 66.667 4.18 0.00 0.00 3.91
1745 2085 1.395045 TAGACCCTCTGCGCCTGATG 61.395 60.000 4.18 0.06 0.00 3.07
1746 2086 0.687757 TTAGACCCTCTGCGCCTGAT 60.688 55.000 4.18 0.00 0.00 2.90
1747 2087 1.304962 TTAGACCCTCTGCGCCTGA 60.305 57.895 4.18 1.91 0.00 3.86
1748 2088 1.153549 GTTAGACCCTCTGCGCCTG 60.154 63.158 4.18 0.00 0.00 4.85
1749 2089 2.359967 GGTTAGACCCTCTGCGCCT 61.360 63.158 4.18 0.00 30.04 5.52
1752 2092 0.458025 GTTCGGTTAGACCCTCTGCG 60.458 60.000 0.00 0.00 33.75 5.18
1769 2109 2.035066 ACACCGCGAGTTTAGTGTAGTT 59.965 45.455 8.23 0.00 41.48 2.24
1770 2110 1.610522 ACACCGCGAGTTTAGTGTAGT 59.389 47.619 8.23 0.00 41.48 2.73
1771 2111 1.983605 CACACCGCGAGTTTAGTGTAG 59.016 52.381 8.23 3.66 41.35 2.74
1772 2112 1.931709 GCACACCGCGAGTTTAGTGTA 60.932 52.381 8.23 0.00 41.35 2.90
1773 2113 1.219522 GCACACCGCGAGTTTAGTGT 61.220 55.000 8.23 9.49 43.99 3.55
1778 2118 3.022287 CTTGCACACCGCGAGTTT 58.978 55.556 8.23 0.00 45.87 2.66
1786 2126 4.012895 CGCACGTCCTTGCACACC 62.013 66.667 0.00 0.00 43.15 4.16
1807 2147 4.866508 AACTCCACTCGACATCAAGTAA 57.133 40.909 0.00 0.00 0.00 2.24
1813 2161 2.232941 TGGGTAAACTCCACTCGACATC 59.767 50.000 0.00 0.00 0.00 3.06
1848 2197 6.192234 AGCATTACAGAAGCTCAATCAAAG 57.808 37.500 0.00 0.00 32.05 2.77
1937 2289 3.132646 GTCTGCAAGGAGATGATGAGAGT 59.867 47.826 0.00 0.00 0.00 3.24
1946 2298 1.205893 GTCTTCGGTCTGCAAGGAGAT 59.794 52.381 0.00 0.00 0.00 2.75
1947 2299 0.603569 GTCTTCGGTCTGCAAGGAGA 59.396 55.000 0.00 0.00 0.00 3.71
1949 2301 0.832135 AGGTCTTCGGTCTGCAAGGA 60.832 55.000 0.00 0.00 0.00 3.36
1951 2303 1.151668 CAAGGTCTTCGGTCTGCAAG 58.848 55.000 0.00 0.00 0.00 4.01
1952 2304 0.884704 GCAAGGTCTTCGGTCTGCAA 60.885 55.000 0.00 0.00 0.00 4.08
1953 2305 1.301716 GCAAGGTCTTCGGTCTGCA 60.302 57.895 0.00 0.00 0.00 4.41
1954 2306 1.004440 AGCAAGGTCTTCGGTCTGC 60.004 57.895 0.00 0.00 0.00 4.26
1955 2307 0.034059 ACAGCAAGGTCTTCGGTCTG 59.966 55.000 0.00 0.00 0.00 3.51
1956 2308 1.546476 CTACAGCAAGGTCTTCGGTCT 59.454 52.381 0.00 0.00 0.00 3.85
1959 2311 1.714794 CACTACAGCAAGGTCTTCGG 58.285 55.000 0.00 0.00 0.00 4.30
1960 2312 1.071605 GCACTACAGCAAGGTCTTCG 58.928 55.000 0.00 0.00 0.00 3.79
1961 2313 1.270839 TGGCACTACAGCAAGGTCTTC 60.271 52.381 0.00 0.00 35.83 2.87
1962 2314 0.764890 TGGCACTACAGCAAGGTCTT 59.235 50.000 0.00 0.00 35.83 3.01
1963 2315 0.764890 TTGGCACTACAGCAAGGTCT 59.235 50.000 0.00 0.00 35.83 3.85
1964 2316 1.740025 GATTGGCACTACAGCAAGGTC 59.260 52.381 0.00 0.00 35.83 3.85
1965 2317 1.352352 AGATTGGCACTACAGCAAGGT 59.648 47.619 0.00 0.00 35.83 3.50
1966 2318 1.741706 CAGATTGGCACTACAGCAAGG 59.258 52.381 0.00 0.00 35.83 3.61
1967 2319 2.417933 GTCAGATTGGCACTACAGCAAG 59.582 50.000 0.00 0.00 35.83 4.01
1968 2320 2.426522 GTCAGATTGGCACTACAGCAA 58.573 47.619 0.00 0.00 35.83 3.91
1969 2321 1.339055 GGTCAGATTGGCACTACAGCA 60.339 52.381 0.00 0.00 35.83 4.41
1970 2322 1.339055 TGGTCAGATTGGCACTACAGC 60.339 52.381 0.00 0.00 0.00 4.40
1971 2323 2.768253 TGGTCAGATTGGCACTACAG 57.232 50.000 0.00 0.00 0.00 2.74
1972 2324 2.840038 AGATGGTCAGATTGGCACTACA 59.160 45.455 0.00 0.00 0.00 2.74
1973 2325 3.550437 AGATGGTCAGATTGGCACTAC 57.450 47.619 0.00 0.00 0.00 2.73
1974 2326 4.225942 AGAAAGATGGTCAGATTGGCACTA 59.774 41.667 0.00 0.00 0.00 2.74
1975 2327 3.009916 AGAAAGATGGTCAGATTGGCACT 59.990 43.478 0.00 0.00 0.00 4.40
1976 2328 3.350833 AGAAAGATGGTCAGATTGGCAC 58.649 45.455 0.00 0.00 0.00 5.01
1977 2329 3.726557 AGAAAGATGGTCAGATTGGCA 57.273 42.857 0.00 0.00 0.00 4.92
1978 2330 4.268359 AGAAGAAAGATGGTCAGATTGGC 58.732 43.478 0.00 0.00 0.00 4.52
1979 2331 5.585445 CAGAGAAGAAAGATGGTCAGATTGG 59.415 44.000 0.00 0.00 0.00 3.16
1980 2332 5.585445 CCAGAGAAGAAAGATGGTCAGATTG 59.415 44.000 0.00 0.00 0.00 2.67
1981 2333 5.486775 TCCAGAGAAGAAAGATGGTCAGATT 59.513 40.000 0.00 0.00 32.68 2.40
1984 2336 4.757594 CTCCAGAGAAGAAAGATGGTCAG 58.242 47.826 0.00 0.00 32.68 3.51
1992 2344 2.483491 GCACTTGCTCCAGAGAAGAAAG 59.517 50.000 0.00 0.00 38.21 2.62
1997 2349 2.574006 AATGCACTTGCTCCAGAGAA 57.426 45.000 2.33 0.00 42.66 2.87
2000 2352 4.144297 ACTTAAAATGCACTTGCTCCAGA 58.856 39.130 2.33 0.00 42.66 3.86
2001 2353 4.510038 ACTTAAAATGCACTTGCTCCAG 57.490 40.909 2.33 0.00 42.66 3.86
2003 2355 5.985530 AGAAAACTTAAAATGCACTTGCTCC 59.014 36.000 2.33 0.00 42.66 4.70
2004 2356 7.468922 AAGAAAACTTAAAATGCACTTGCTC 57.531 32.000 2.33 0.00 42.66 4.26
2005 2357 7.848223 AAAGAAAACTTAAAATGCACTTGCT 57.152 28.000 2.33 0.00 42.66 3.91
2006 2358 8.390354 AGAAAAGAAAACTTAAAATGCACTTGC 58.610 29.630 0.00 0.00 42.50 4.01
2007 2359 9.693157 CAGAAAAGAAAACTTAAAATGCACTTG 57.307 29.630 0.00 0.00 0.00 3.16
2008 2360 8.390354 GCAGAAAAGAAAACTTAAAATGCACTT 58.610 29.630 0.00 0.00 0.00 3.16
2009 2361 7.011389 GGCAGAAAAGAAAACTTAAAATGCACT 59.989 33.333 0.00 0.00 0.00 4.40
2010 2362 7.125755 GGCAGAAAAGAAAACTTAAAATGCAC 58.874 34.615 0.00 0.00 0.00 4.57
2011 2363 6.019156 CGGCAGAAAAGAAAACTTAAAATGCA 60.019 34.615 0.00 0.00 0.00 3.96
2012 2364 6.200097 TCGGCAGAAAAGAAAACTTAAAATGC 59.800 34.615 0.00 0.00 0.00 3.56
2013 2365 7.692908 TCGGCAGAAAAGAAAACTTAAAATG 57.307 32.000 0.00 0.00 0.00 2.32
2034 2386 6.416750 GGATTAACACTCAAACACTTTTTCGG 59.583 38.462 0.00 0.00 0.00 4.30
2035 2387 6.970043 TGGATTAACACTCAAACACTTTTTCG 59.030 34.615 0.00 0.00 0.00 3.46
2036 2388 8.755018 CATGGATTAACACTCAAACACTTTTTC 58.245 33.333 0.00 0.00 0.00 2.29
2037 2389 8.257306 ACATGGATTAACACTCAAACACTTTTT 58.743 29.630 0.00 0.00 0.00 1.94
2038 2390 7.781056 ACATGGATTAACACTCAAACACTTTT 58.219 30.769 0.00 0.00 0.00 2.27
2041 2393 6.959639 AACATGGATTAACACTCAAACACT 57.040 33.333 0.00 0.00 0.00 3.55
2042 2394 7.920682 AGAAAACATGGATTAACACTCAAACAC 59.079 33.333 0.00 0.00 0.00 3.32
2043 2395 8.006298 AGAAAACATGGATTAACACTCAAACA 57.994 30.769 0.00 0.00 0.00 2.83
2044 2396 8.871686 AAGAAAACATGGATTAACACTCAAAC 57.128 30.769 0.00 0.00 0.00 2.93
2045 2397 8.912988 AGAAGAAAACATGGATTAACACTCAAA 58.087 29.630 0.00 0.00 0.00 2.69
2046 2398 8.463930 AGAAGAAAACATGGATTAACACTCAA 57.536 30.769 0.00 0.00 0.00 3.02
2047 2399 7.939039 AGAGAAGAAAACATGGATTAACACTCA 59.061 33.333 0.00 0.00 0.00 3.41
2048 2400 8.233190 CAGAGAAGAAAACATGGATTAACACTC 58.767 37.037 0.00 0.00 0.00 3.51
2056 2408 4.263639 TGCTCCAGAGAAGAAAACATGGAT 60.264 41.667 0.00 0.00 36.31 3.41
2066 2418 1.051008 TGCACTTGCTCCAGAGAAGA 58.949 50.000 2.33 0.00 42.66 2.87
2067 2419 2.110901 ATGCACTTGCTCCAGAGAAG 57.889 50.000 2.33 2.66 42.66 2.85
2068 2420 2.574006 AATGCACTTGCTCCAGAGAA 57.426 45.000 2.33 0.00 42.66 2.87
2070 2422 3.128242 CCTAAAATGCACTTGCTCCAGAG 59.872 47.826 2.33 0.00 42.66 3.35
2071 2423 3.084039 CCTAAAATGCACTTGCTCCAGA 58.916 45.455 2.33 0.00 42.66 3.86
2072 2424 2.821969 ACCTAAAATGCACTTGCTCCAG 59.178 45.455 2.33 0.00 42.66 3.86
2073 2425 2.875296 ACCTAAAATGCACTTGCTCCA 58.125 42.857 2.33 0.00 42.66 3.86
2074 2426 3.942130 AACCTAAAATGCACTTGCTCC 57.058 42.857 2.33 0.00 42.66 4.70
2075 2427 5.532557 AGAAAACCTAAAATGCACTTGCTC 58.467 37.500 2.33 0.00 42.66 4.26
2077 2429 6.603237 AAAGAAAACCTAAAATGCACTTGC 57.397 33.333 0.00 0.00 42.50 4.01
2078 2430 7.973601 ACAAAAGAAAACCTAAAATGCACTTG 58.026 30.769 0.00 0.00 0.00 3.16
2079 2431 8.560355 AACAAAAGAAAACCTAAAATGCACTT 57.440 26.923 0.00 0.00 0.00 3.16
2090 2442 9.108284 CAAACATGGATTAACAAAAGAAAACCT 57.892 29.630 0.00 0.00 0.00 3.50
2091 2443 9.103861 TCAAACATGGATTAACAAAAGAAAACC 57.896 29.630 0.00 0.00 0.00 3.27
2093 2445 9.883142 ACTCAAACATGGATTAACAAAAGAAAA 57.117 25.926 0.00 0.00 0.00 2.29
2094 2446 9.311916 CACTCAAACATGGATTAACAAAAGAAA 57.688 29.630 0.00 0.00 0.00 2.52
2095 2447 8.474025 ACACTCAAACATGGATTAACAAAAGAA 58.526 29.630 0.00 0.00 0.00 2.52
2096 2448 8.006298 ACACTCAAACATGGATTAACAAAAGA 57.994 30.769 0.00 0.00 0.00 2.52
2097 2449 8.647143 AACACTCAAACATGGATTAACAAAAG 57.353 30.769 0.00 0.00 0.00 2.27
2099 2451 9.906660 GATAACACTCAAACATGGATTAACAAA 57.093 29.630 0.00 0.00 0.00 2.83
2100 2452 8.519526 GGATAACACTCAAACATGGATTAACAA 58.480 33.333 0.00 0.00 0.00 2.83
2101 2453 7.888021 AGGATAACACTCAAACATGGATTAACA 59.112 33.333 0.00 0.00 0.00 2.41
2102 2454 8.184192 CAGGATAACACTCAAACATGGATTAAC 58.816 37.037 0.00 0.00 0.00 2.01
2103 2455 7.339212 CCAGGATAACACTCAAACATGGATTAA 59.661 37.037 0.00 0.00 0.00 1.40
2104 2456 6.828273 CCAGGATAACACTCAAACATGGATTA 59.172 38.462 0.00 0.00 0.00 1.75
2105 2457 5.653769 CCAGGATAACACTCAAACATGGATT 59.346 40.000 0.00 0.00 0.00 3.01
2106 2458 5.044919 TCCAGGATAACACTCAAACATGGAT 60.045 40.000 0.00 0.00 0.00 3.41
2107 2459 4.288366 TCCAGGATAACACTCAAACATGGA 59.712 41.667 0.00 0.00 0.00 3.41
2108 2460 4.588899 TCCAGGATAACACTCAAACATGG 58.411 43.478 0.00 0.00 0.00 3.66
2109 2461 6.207417 ACTTTCCAGGATAACACTCAAACATG 59.793 38.462 0.00 0.00 0.00 3.21
2110 2462 6.306987 ACTTTCCAGGATAACACTCAAACAT 58.693 36.000 0.00 0.00 0.00 2.71
2111 2463 5.690865 ACTTTCCAGGATAACACTCAAACA 58.309 37.500 0.00 0.00 0.00 2.83
2112 2464 6.262273 TCAACTTTCCAGGATAACACTCAAAC 59.738 38.462 0.00 0.00 0.00 2.93
2113 2465 6.361433 TCAACTTTCCAGGATAACACTCAAA 58.639 36.000 0.00 0.00 0.00 2.69
2114 2466 5.935945 TCAACTTTCCAGGATAACACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2115 2467 5.560722 TCAACTTTCCAGGATAACACTCA 57.439 39.130 0.00 0.00 0.00 3.41
2139 2491 3.499918 CCAACTAACACAAGCAGGAAGAG 59.500 47.826 0.00 0.00 0.00 2.85
2147 2499 4.846779 TCATTTCCCAACTAACACAAGC 57.153 40.909 0.00 0.00 0.00 4.01
2235 2594 7.289084 AGGCTGAAAGGGTTGTTTAATCTTTTA 59.711 33.333 0.00 0.00 27.70 1.52
2316 2676 3.763097 TTTCTGCTCACACAGTTGTTG 57.237 42.857 0.00 0.00 38.84 3.33
2390 2753 4.634443 ACATCCCGCAAAAGTACAGAATAC 59.366 41.667 0.00 0.00 0.00 1.89
2406 2771 1.466167 CAGTCTGCAGAAAACATCCCG 59.534 52.381 20.19 0.00 0.00 5.14
2435 2800 1.956477 GTGTGTGCAGGGAAAATGACT 59.044 47.619 0.00 0.00 0.00 3.41
2466 2831 2.169789 CAACTGCGAGGATGCCGAG 61.170 63.158 0.00 0.00 0.00 4.63
2497 2862 1.633852 CTTGTGCGCTTGAGAGAGCC 61.634 60.000 9.73 0.00 46.67 4.70
2555 2932 9.676195 CCATTTTTCTTCTTCTTCTTCTTCTTC 57.324 33.333 0.00 0.00 0.00 2.87
2557 2934 7.782168 ACCCATTTTTCTTCTTCTTCTTCTTCT 59.218 33.333 0.00 0.00 0.00 2.85
2558 2935 7.946207 ACCCATTTTTCTTCTTCTTCTTCTTC 58.054 34.615 0.00 0.00 0.00 2.87
2559 2936 7.904558 ACCCATTTTTCTTCTTCTTCTTCTT 57.095 32.000 0.00 0.00 0.00 2.52
2583 2960 1.343142 ACCATCGCACTTGACACAGTA 59.657 47.619 0.00 0.00 0.00 2.74
2648 5036 2.200373 TCACTCCTCACGATCTCACA 57.800 50.000 0.00 0.00 0.00 3.58
2862 5429 8.405531 ACATATTTATTTTGTTGGGTCTCATCG 58.594 33.333 0.00 0.00 0.00 3.84
2894 5465 4.762251 AGAAAGAGCCATTAACCAGTGAAC 59.238 41.667 0.00 0.00 0.00 3.18
2945 5524 5.578005 TCAGTCCAGTACTATACTTGCAC 57.422 43.478 6.57 0.00 35.76 4.57
2959 5538 2.481449 GCTTACCGTACCATCAGTCCAG 60.481 54.545 0.00 0.00 0.00 3.86
2967 5546 0.107848 GCACCAGCTTACCGTACCAT 60.108 55.000 0.00 0.00 37.91 3.55
2974 5553 0.676782 ATGAACCGCACCAGCTTACC 60.677 55.000 0.00 0.00 39.10 2.85
3044 5624 4.387559 TCTTGTTACCGTCAACGAATCATG 59.612 41.667 3.71 0.00 43.02 3.07
3081 5661 3.231324 GAAACCCGTCCGTTGCACG 62.231 63.158 0.00 0.00 42.11 5.34
3110 5690 2.615493 GGGGATTCACATTCACGTGACT 60.615 50.000 19.90 10.75 45.36 3.41
3133 5732 0.994995 CAAGTCGGATCTGAAGCGTG 59.005 55.000 5.62 0.00 0.00 5.34
3148 5747 1.602165 CGTTGCGACAGTACTCCAAGT 60.602 52.381 4.64 0.00 0.00 3.16
3149 5748 1.060713 CGTTGCGACAGTACTCCAAG 58.939 55.000 4.64 0.00 0.00 3.61
3171 5780 5.363580 ACATCTCAACAAAGGACAAAACCAT 59.636 36.000 0.00 0.00 0.00 3.55
3183 5792 8.500753 AGTACAGTACAAAACATCTCAACAAA 57.499 30.769 13.37 0.00 0.00 2.83
3199 5808 9.766277 GTCAACAGTTGTAGTATAGTACAGTAC 57.234 37.037 17.69 14.66 34.41 2.73
3201 5810 7.094032 GGGTCAACAGTTGTAGTATAGTACAGT 60.094 40.741 17.69 11.41 34.41 3.55
3203 5812 6.127925 CGGGTCAACAGTTGTAGTATAGTACA 60.128 42.308 15.13 15.13 0.00 2.90
3204 5813 6.261118 CGGGTCAACAGTTGTAGTATAGTAC 58.739 44.000 13.14 10.34 0.00 2.73


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

AutoCloner maintained by Alex Coulton.