Multiple sequence alignment - TraesCS6A01G305700

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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 TraesCS6A01G305700 chr6A 100.000 3178 0 0 1 3178 538539859 538543036 0.000000e+00 5869.0
1 TraesCS6A01G305700 chr6A 88.235 102 5 4 2190 2285 127215415 127215315 7.200000e-22 115.0
2 TraesCS6A01G305700 chr6D 91.597 2142 123 23 92 2201 392585340 392587456 0.000000e+00 2905.0
3 TraesCS6A01G305700 chr6D 89.037 301 25 6 698 992 392583911 392584209 1.800000e-97 366.0
4 TraesCS6A01G305700 chr6D 90.196 153 10 2 458 610 392583430 392583577 8.990000e-46 195.0
5 TraesCS6A01G305700 chr6D 95.098 102 1 2 983 1084 392584358 392584455 1.180000e-34 158.0
6 TraesCS6A01G305700 chr6D 92.632 95 7 0 1 95 392585216 392585310 1.540000e-28 137.0
7 TraesCS6A01G305700 chr6D 89.362 94 7 3 2192 2284 428262263 428262354 7.200000e-22 115.0
8 TraesCS6A01G305700 chr6B 90.676 1405 88 17 816 2202 586076187 586074808 0.000000e+00 1829.0
9 TraesCS6A01G305700 chr6B 90.816 98 7 2 95 192 586077606 586077511 2.570000e-26 130.0
10 TraesCS6A01G305700 chr7D 88.613 887 79 6 2314 3178 206065885 206066771 0.000000e+00 1059.0
11 TraesCS6A01G305700 chr7D 88.626 888 77 12 2314 3178 412678214 412677328 0.000000e+00 1059.0
12 TraesCS6A01G305700 chr7D 88.162 887 83 4 2314 3178 371841663 371842549 0.000000e+00 1037.0
13 TraesCS6A01G305700 chr7D 89.205 667 50 6 2534 3178 66870363 66871029 0.000000e+00 813.0
14 TraesCS6A01G305700 chr7D 77.551 735 96 41 978 1677 542825882 542826582 2.310000e-101 379.0
15 TraesCS6A01G305700 chr7D 86.916 107 6 6 2201 2302 514661127 514661024 2.590000e-21 113.0
16 TraesCS6A01G305700 chr2D 88.613 887 76 5 2314 3178 306491958 306491075 0.000000e+00 1055.0
17 TraesCS6A01G305700 chr5D 88.462 884 78 7 2314 3175 432501314 432502195 0.000000e+00 1046.0
18 TraesCS6A01G305700 chr5D 87.797 885 86 4 2316 3178 225747898 225747014 0.000000e+00 1016.0
19 TraesCS6A01G305700 chr5D 87.739 889 82 10 2314 3178 476692387 476691502 0.000000e+00 1013.0
20 TraesCS6A01G305700 chr4D 88.462 884 79 7 2314 3175 464985932 464986814 0.000000e+00 1046.0
21 TraesCS6A01G305700 chr4D 80.788 203 27 6 227 423 43624537 43624341 7.100000e-32 148.0
22 TraesCS6A01G305700 chr1D 88.275 887 82 6 2314 3178 162719895 162720781 0.000000e+00 1042.0
23 TraesCS6A01G305700 chr1D 86.916 107 7 5 2196 2296 43004579 43004474 2.590000e-21 113.0
24 TraesCS6A01G305700 chr1A 88.275 887 82 9 2314 3178 553954896 553955782 0.000000e+00 1042.0
25 TraesCS6A01G305700 chr1A 87.486 887 88 10 2314 3178 48775805 48776690 0.000000e+00 1002.0
26 TraesCS6A01G305700 chr1A 87.379 103 7 4 2194 2290 56623715 56623817 2.590000e-21 113.0
27 TraesCS6A01G305700 chr4A 88.162 887 83 6 2314 3178 159497869 159496983 0.000000e+00 1037.0
28 TraesCS6A01G305700 chr3B 88.162 887 83 10 2314 3178 101643736 101644622 0.000000e+00 1037.0
29 TraesCS6A01G305700 chr2A 88.162 887 83 9 2314 3178 59991837 59990951 0.000000e+00 1037.0
30 TraesCS6A01G305700 chr2A 82.707 133 14 4 218 342 727165740 727165609 3.350000e-20 110.0
31 TraesCS6A01G305700 chrUn 87.937 887 85 10 2314 3178 55787459 55786573 0.000000e+00 1026.0
32 TraesCS6A01G305700 chrUn 85.155 485 50 10 2314 2776 421864374 421864858 7.980000e-131 477.0
33 TraesCS6A01G305700 chrUn 88.119 101 5 3 2193 2287 97273195 97273096 2.590000e-21 113.0
34 TraesCS6A01G305700 chr1B 87.148 887 92 6 2314 3178 51286328 51285442 0.000000e+00 987.0
35 TraesCS6A01G305700 chr7B 79.454 623 80 22 1076 1677 586240688 586241283 6.390000e-107 398.0
36 TraesCS6A01G305700 chr7B 77.105 760 108 37 950 1677 585944426 585945151 2.310000e-101 379.0
37 TraesCS6A01G305700 chr7B 76.711 760 111 35 950 1677 586067196 586067921 2.330000e-96 363.0
38 TraesCS6A01G305700 chr7B 75.730 651 97 40 950 1573 585991675 585992291 1.450000e-68 270.0
39 TraesCS6A01G305700 chr7B 85.915 71 3 6 98 164 77428648 77428715 5.690000e-08 69.4
40 TraesCS6A01G305700 chr7A 76.380 779 107 45 950 1689 624840614 624841354 6.520000e-92 348.0
41 TraesCS6A01G305700 chr7A 75.778 739 100 42 1036 1729 624957671 624958375 1.850000e-77 300.0
42 TraesCS6A01G305700 chr5B 86.441 118 15 1 227 344 88210394 88210278 9.250000e-26 128.0
43 TraesCS6A01G305700 chr5A 90.426 94 4 1 2199 2287 635512569 635512476 5.570000e-23 119.0
44 TraesCS6A01G305700 chr4B 90.323 93 5 2 2199 2287 11912310 11912402 5.570000e-23 119.0
45 TraesCS6A01G305700 chr4B 90.110 91 9 0 2199 2289 90729623 90729533 5.570000e-23 119.0
46 TraesCS6A01G305700 chr3D 81.356 118 18 4 227 342 526990407 526990522 3.380000e-15 93.5


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 TraesCS6A01G305700 chr6A 538539859 538543036 3177 False 5869.0 5869 100.000 1 3178 1 chr6A.!!$F1 3177
1 TraesCS6A01G305700 chr6D 392583430 392587456 4026 False 752.2 2905 91.712 1 2201 5 chr6D.!!$F2 2200
2 TraesCS6A01G305700 chr6B 586074808 586077606 2798 True 979.5 1829 90.746 95 2202 2 chr6B.!!$R1 2107
3 TraesCS6A01G305700 chr7D 206065885 206066771 886 False 1059.0 1059 88.613 2314 3178 1 chr7D.!!$F2 864
4 TraesCS6A01G305700 chr7D 412677328 412678214 886 True 1059.0 1059 88.626 2314 3178 1 chr7D.!!$R1 864
5 TraesCS6A01G305700 chr7D 371841663 371842549 886 False 1037.0 1037 88.162 2314 3178 1 chr7D.!!$F3 864
6 TraesCS6A01G305700 chr7D 66870363 66871029 666 False 813.0 813 89.205 2534 3178 1 chr7D.!!$F1 644
7 TraesCS6A01G305700 chr7D 542825882 542826582 700 False 379.0 379 77.551 978 1677 1 chr7D.!!$F4 699
8 TraesCS6A01G305700 chr2D 306491075 306491958 883 True 1055.0 1055 88.613 2314 3178 1 chr2D.!!$R1 864
9 TraesCS6A01G305700 chr5D 432501314 432502195 881 False 1046.0 1046 88.462 2314 3175 1 chr5D.!!$F1 861
10 TraesCS6A01G305700 chr5D 225747014 225747898 884 True 1016.0 1016 87.797 2316 3178 1 chr5D.!!$R1 862
11 TraesCS6A01G305700 chr5D 476691502 476692387 885 True 1013.0 1013 87.739 2314 3178 1 chr5D.!!$R2 864
12 TraesCS6A01G305700 chr4D 464985932 464986814 882 False 1046.0 1046 88.462 2314 3175 1 chr4D.!!$F1 861
13 TraesCS6A01G305700 chr1D 162719895 162720781 886 False 1042.0 1042 88.275 2314 3178 1 chr1D.!!$F1 864
14 TraesCS6A01G305700 chr1A 553954896 553955782 886 False 1042.0 1042 88.275 2314 3178 1 chr1A.!!$F3 864
15 TraesCS6A01G305700 chr1A 48775805 48776690 885 False 1002.0 1002 87.486 2314 3178 1 chr1A.!!$F1 864
16 TraesCS6A01G305700 chr4A 159496983 159497869 886 True 1037.0 1037 88.162 2314 3178 1 chr4A.!!$R1 864
17 TraesCS6A01G305700 chr3B 101643736 101644622 886 False 1037.0 1037 88.162 2314 3178 1 chr3B.!!$F1 864
18 TraesCS6A01G305700 chr2A 59990951 59991837 886 True 1037.0 1037 88.162 2314 3178 1 chr2A.!!$R1 864
19 TraesCS6A01G305700 chrUn 55786573 55787459 886 True 1026.0 1026 87.937 2314 3178 1 chrUn.!!$R1 864
20 TraesCS6A01G305700 chr1B 51285442 51286328 886 True 987.0 987 87.148 2314 3178 1 chr1B.!!$R1 864
21 TraesCS6A01G305700 chr7B 586240688 586241283 595 False 398.0 398 79.454 1076 1677 1 chr7B.!!$F5 601
22 TraesCS6A01G305700 chr7B 585944426 585945151 725 False 379.0 379 77.105 950 1677 1 chr7B.!!$F2 727
23 TraesCS6A01G305700 chr7B 586067196 586067921 725 False 363.0 363 76.711 950 1677 1 chr7B.!!$F4 727
24 TraesCS6A01G305700 chr7B 585991675 585992291 616 False 270.0 270 75.730 950 1573 1 chr7B.!!$F3 623
25 TraesCS6A01G305700 chr7A 624840614 624841354 740 False 348.0 348 76.380 950 1689 1 chr7A.!!$F1 739
26 TraesCS6A01G305700 chr7A 624957671 624958375 704 False 300.0 300 75.778 1036 1729 1 chr7A.!!$F2 693

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
676 3100 0.108567 GCCGGAGAAGAGTCTGAACC 60.109 60.0 5.05 0.0 32.80 3.62 F
754 3178 0.172803 CCGACGTTGGGTAGGAAGAG 59.827 60.0 14.66 0.0 43.54 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 4632 0.176910 TCAGCACCTCAACACGTTGA 59.823 50.0 11.85 11.85 46.27 3.18 R
2303 4933 0.329931 TGCCGAGGAGAGAGAGACTT 59.670 55.0 0.00 0.00 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 1818 7.206687 GGACCTAAGTGAGATCTACAAATCTG 58.793 42.308 0.00 0.00 36.13 2.90
64 1851 9.936759 TGTCTTATTCTTCCTTTTTGTTTTTGT 57.063 25.926 0.00 0.00 0.00 2.83
124 1944 8.122472 TCTTTCTGACTGAACATGTCTATGTA 57.878 34.615 0.00 0.00 46.54 2.29
170 1990 8.510243 TGATGTCTGATGTTGTATGCTTATTT 57.490 30.769 0.00 0.00 0.00 1.40
227 2061 7.039270 GGCTTAGCTTCTCTATAATTCTAGCC 58.961 42.308 3.59 0.00 35.44 3.93
250 2084 2.078849 TGATAAGTGCCACACGTCAG 57.921 50.000 0.00 0.00 39.64 3.51
251 2085 1.343142 TGATAAGTGCCACACGTCAGT 59.657 47.619 0.00 0.00 39.64 3.41
308 2195 1.904287 TTTAAGCCACGCAAGGATGT 58.096 45.000 0.00 0.00 46.39 3.06
312 2199 0.957395 AGCCACGCAAGGATGTCAAG 60.957 55.000 0.00 0.00 46.39 3.02
316 2412 1.197721 CACGCAAGGATGTCAAGTTCC 59.802 52.381 0.00 0.00 46.39 3.62
322 2418 3.409026 AGGATGTCAAGTTCCAGTGAC 57.591 47.619 0.00 0.00 43.66 3.67
344 2440 2.146342 CACGGCAAGTTTCTGTCAGAT 58.854 47.619 2.68 0.00 0.00 2.90
346 2442 2.549754 ACGGCAAGTTTCTGTCAGATTG 59.450 45.455 2.68 6.82 0.00 2.67
352 2448 5.564259 GCAAGTTTCTGTCAGATTGAAGCAT 60.564 40.000 15.72 0.00 0.00 3.79
360 2456 6.936335 TCTGTCAGATTGAAGCATGAAAGTTA 59.064 34.615 0.00 0.00 30.48 2.24
366 2462 5.643379 TTGAAGCATGAAAGTTACCATCC 57.357 39.130 0.00 0.00 0.00 3.51
370 2466 3.445096 AGCATGAAAGTTACCATCCTTGC 59.555 43.478 0.00 0.00 0.00 4.01
383 2479 4.250464 CCATCCTTGCGTCACTAAACTTA 58.750 43.478 0.00 0.00 0.00 2.24
384 2480 4.876107 CCATCCTTGCGTCACTAAACTTAT 59.124 41.667 0.00 0.00 0.00 1.73
424 2520 2.749776 TGACACATGTGTTCGTACCTG 58.250 47.619 31.03 1.89 45.05 4.00
426 2522 2.729882 GACACATGTGTTCGTACCTGAC 59.270 50.000 31.03 11.60 45.05 3.51
445 2543 4.659115 TGACTGTGGCACTTACTAGAGTA 58.341 43.478 19.83 0.00 0.00 2.59
507 2605 3.287222 GGCATAGCCCACAATTTAGACA 58.713 45.455 0.00 0.00 44.06 3.41
509 2607 4.261741 GGCATAGCCCACAATTTAGACATG 60.262 45.833 0.00 0.00 44.06 3.21
587 3011 2.668550 GACGACCTGGTTGGCCAC 60.669 66.667 18.18 0.00 40.46 5.01
606 3030 4.736896 GCGTCACCGGTGGAGGAC 62.737 72.222 33.40 22.47 34.73 3.85
676 3100 0.108567 GCCGGAGAAGAGTCTGAACC 60.109 60.000 5.05 0.00 32.80 3.62
682 3106 3.951680 GGAGAAGAGTCTGAACCTAGAGG 59.048 52.174 0.00 0.00 36.13 3.69
687 3111 4.285863 AGAGTCTGAACCTAGAGGAATGG 58.714 47.826 1.60 0.00 38.94 3.16
720 3144 2.361104 GGCAATGAAGGTGGCGGA 60.361 61.111 0.00 0.00 0.00 5.54
754 3178 0.172803 CCGACGTTGGGTAGGAAGAG 59.827 60.000 14.66 0.00 43.54 2.85
779 3204 1.398692 GCAGGAGGAAGAGAGACGAT 58.601 55.000 0.00 0.00 0.00 3.73
782 3207 2.357637 CAGGAGGAAGAGAGACGATGAC 59.642 54.545 0.00 0.00 0.00 3.06
786 3211 1.474478 GGAAGAGAGACGATGACAGCA 59.526 52.381 0.00 0.00 0.00 4.41
790 3215 0.814457 AGAGACGATGACAGCAGGAC 59.186 55.000 0.00 0.00 0.00 3.85
853 3377 2.426522 TCAGCCAACTTGCATGTAGTC 58.573 47.619 5.56 0.00 0.00 2.59
855 3379 1.001974 AGCCAACTTGCATGTAGTCGA 59.998 47.619 5.56 0.00 0.00 4.20
859 3383 3.553511 CCAACTTGCATGTAGTCGATCTC 59.446 47.826 5.56 0.00 0.00 2.75
879 3403 9.613957 CGATCTCGATTTTTGTCTATACATACT 57.386 33.333 0.00 0.00 43.02 2.12
1024 3558 1.885887 GCTCCAAACAATACAGGCACA 59.114 47.619 0.00 0.00 0.00 4.57
1025 3559 2.351738 GCTCCAAACAATACAGGCACAC 60.352 50.000 0.00 0.00 0.00 3.82
1094 3655 4.704833 TCAAGCTCCCGGCAGCAC 62.705 66.667 21.97 0.00 42.40 4.40
1354 3921 0.955919 CTTCACCGTTTCAGAGGGCC 60.956 60.000 0.00 0.00 36.75 5.80
1364 3943 0.337773 TCAGAGGGCCAGATCAGTCT 59.662 55.000 6.18 0.00 34.14 3.24
1412 3997 1.146041 GATCATGCGGTACCTGCCA 59.854 57.895 20.88 11.48 0.00 4.92
1516 4102 1.134848 GCGAGCATCTTCTTCCTCAGT 60.135 52.381 0.00 0.00 0.00 3.41
1549 4138 4.200283 CGAGCCAGCGGAGAGGAC 62.200 72.222 0.00 0.00 0.00 3.85
1640 4256 2.058595 ACGGAGAGGTTCATCGGGG 61.059 63.158 0.00 0.00 0.00 5.73
1647 4263 0.546747 AGGTTCATCGGGGACTTCCA 60.547 55.000 0.00 0.00 37.91 3.53
1720 4341 6.759272 ACTTAATTTGGCTTTCCTTTTCCTC 58.241 36.000 0.00 0.00 0.00 3.71
1775 4401 3.044305 GCGCCGGTGATATCAGGC 61.044 66.667 21.76 20.86 43.31 4.85
1781 4407 1.414181 CCGGTGATATCAGGCTTGTCT 59.586 52.381 5.42 0.00 0.00 3.41
1782 4408 2.158900 CCGGTGATATCAGGCTTGTCTT 60.159 50.000 5.42 0.00 0.00 3.01
1788 4414 4.397103 TGATATCAGGCTTGTCTTTTGCTG 59.603 41.667 0.00 0.00 0.00 4.41
1926 4552 3.616956 TCAGCTTCCAGGTTACATCTG 57.383 47.619 0.00 0.00 0.00 2.90
1937 4563 3.389329 AGGTTACATCTGGACCTGCTATG 59.611 47.826 6.70 0.00 42.04 2.23
1989 4619 6.942976 TGTTTATTTCTACAGGACCGAGAAT 58.057 36.000 7.19 2.66 0.00 2.40
2005 4635 3.060138 CGAGAATTTCGTTGTTCGGTCAA 60.060 43.478 2.97 0.00 44.27 3.18
2039 4669 3.509740 CTGAGATGCAGTGTCAGTACAG 58.490 50.000 12.48 0.00 41.90 2.74
2048 4678 4.419280 CAGTGTCAGTACAGTCTGCTATG 58.581 47.826 0.00 0.00 37.15 2.23
2091 4721 1.301677 GCTAGCCACAGGAGCAACAC 61.302 60.000 2.29 0.00 36.20 3.32
2124 4754 5.784177 ACAACACGAGTATCAAAGATGAGT 58.216 37.500 0.00 0.00 39.39 3.41
2135 4765 9.606631 AGTATCAAAGATGAGTGGAGAAATAAC 57.393 33.333 0.00 0.00 39.39 1.89
2174 4804 9.087424 GAAGTTCTACAAAAGTTCTTGCAAAAT 57.913 29.630 0.00 0.00 36.22 1.82
2202 4832 6.506661 AGAGGAGAAGGGCATGTCATATATA 58.493 40.000 0.00 0.00 0.00 0.86
2203 4833 7.138250 AGAGGAGAAGGGCATGTCATATATAT 58.862 38.462 0.00 0.00 0.00 0.86
2204 4834 8.292480 AGAGGAGAAGGGCATGTCATATATATA 58.708 37.037 0.00 0.00 0.00 0.86
2205 4835 8.256356 AGGAGAAGGGCATGTCATATATATAC 57.744 38.462 0.00 0.00 0.00 1.47
2206 4836 8.070604 AGGAGAAGGGCATGTCATATATATACT 58.929 37.037 0.00 0.00 0.00 2.12
2207 4837 8.364142 GGAGAAGGGCATGTCATATATATACTC 58.636 40.741 0.00 0.00 0.00 2.59
2208 4838 8.256356 AGAAGGGCATGTCATATATATACTCC 57.744 38.462 0.00 0.00 0.00 3.85
2209 4839 7.291182 AGAAGGGCATGTCATATATATACTCCC 59.709 40.741 0.00 7.11 0.00 4.30
2210 4840 6.697654 AGGGCATGTCATATATATACTCCCT 58.302 40.000 0.00 13.53 34.59 4.20
2211 4841 6.784969 AGGGCATGTCATATATATACTCCCTC 59.215 42.308 0.00 0.00 34.32 4.30
2212 4842 6.014156 GGGCATGTCATATATATACTCCCTCC 60.014 46.154 0.00 0.00 0.00 4.30
2213 4843 6.294787 GGCATGTCATATATATACTCCCTCCG 60.295 46.154 0.00 0.00 0.00 4.63
2214 4844 6.265649 GCATGTCATATATATACTCCCTCCGT 59.734 42.308 0.00 0.00 0.00 4.69
2215 4845 7.201920 GCATGTCATATATATACTCCCTCCGTT 60.202 40.741 0.00 0.00 0.00 4.44
2216 4846 7.876936 TGTCATATATATACTCCCTCCGTTC 57.123 40.000 0.00 0.00 0.00 3.95
2217 4847 6.832384 TGTCATATATATACTCCCTCCGTTCC 59.168 42.308 0.00 0.00 0.00 3.62
2218 4848 6.832384 GTCATATATATACTCCCTCCGTTCCA 59.168 42.308 0.00 0.00 0.00 3.53
2219 4849 7.341256 GTCATATATATACTCCCTCCGTTCCAA 59.659 40.741 0.00 0.00 0.00 3.53
2220 4850 7.897030 TCATATATATACTCCCTCCGTTCCAAA 59.103 37.037 0.00 0.00 0.00 3.28
2221 4851 8.537016 CATATATATACTCCCTCCGTTCCAAAA 58.463 37.037 0.00 0.00 0.00 2.44
2222 4852 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
2223 4853 8.674925 ATATATACTCCCTCCGTTCCAAAATA 57.325 34.615 0.00 0.00 0.00 1.40
2224 4854 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2225 4855 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2226 4856 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2227 4857 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2228 4858 3.118038 TCCCTCCGTTCCAAAATAGATGG 60.118 47.826 0.00 0.00 39.41 3.51
2229 4859 2.618709 CCTCCGTTCCAAAATAGATGGC 59.381 50.000 0.00 0.00 37.88 4.40
2230 4860 3.545703 CTCCGTTCCAAAATAGATGGCT 58.454 45.455 0.00 0.00 37.88 4.75
2231 4861 3.541632 TCCGTTCCAAAATAGATGGCTC 58.458 45.455 0.00 0.00 37.88 4.70
2232 4862 3.054728 TCCGTTCCAAAATAGATGGCTCA 60.055 43.478 0.00 0.00 37.88 4.26
2233 4863 3.694072 CCGTTCCAAAATAGATGGCTCAA 59.306 43.478 0.00 0.00 37.88 3.02
2234 4864 4.438744 CCGTTCCAAAATAGATGGCTCAAC 60.439 45.833 0.00 0.00 37.88 3.18
2235 4865 4.396166 CGTTCCAAAATAGATGGCTCAACT 59.604 41.667 0.00 0.00 37.88 3.16
2236 4866 5.106157 CGTTCCAAAATAGATGGCTCAACTT 60.106 40.000 0.00 0.00 37.88 2.66
2237 4867 6.570378 CGTTCCAAAATAGATGGCTCAACTTT 60.570 38.462 0.00 0.00 37.88 2.66
2238 4868 7.361713 CGTTCCAAAATAGATGGCTCAACTTTA 60.362 37.037 0.00 0.00 37.88 1.85
2239 4869 8.303876 GTTCCAAAATAGATGGCTCAACTTTAA 58.696 33.333 0.00 0.00 37.88 1.52
2240 4870 8.415950 TCCAAAATAGATGGCTCAACTTTAAA 57.584 30.769 0.00 0.00 37.88 1.52
2241 4871 8.522830 TCCAAAATAGATGGCTCAACTTTAAAG 58.477 33.333 13.76 13.76 37.88 1.85
2242 4872 8.306761 CCAAAATAGATGGCTCAACTTTAAAGT 58.693 33.333 15.22 15.22 42.04 2.66
2275 4905 7.611213 AGTTAAGTCATCTATTTTGGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
2276 4906 7.391620 AGTTAAGTCATCTATTTTGGAACGGA 58.608 34.615 0.00 0.00 0.00 4.69
2277 4907 7.549488 AGTTAAGTCATCTATTTTGGAACGGAG 59.451 37.037 0.00 0.00 0.00 4.63
2278 4908 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2279 4909 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2280 4910 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2281 4911 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2282 4912 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2283 4913 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2284 4914 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2285 4915 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2286 4916 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
2287 4917 1.191535 TGGAACGGAGGGAGTACATG 58.808 55.000 0.00 0.00 0.00 3.21
2288 4918 1.192428 GGAACGGAGGGAGTACATGT 58.808 55.000 2.69 2.69 0.00 3.21
2289 4919 1.134788 GGAACGGAGGGAGTACATGTG 60.135 57.143 9.11 0.00 0.00 3.21
2290 4920 1.549170 GAACGGAGGGAGTACATGTGT 59.451 52.381 9.11 0.00 0.00 3.72
2291 4921 0.895530 ACGGAGGGAGTACATGTGTG 59.104 55.000 9.11 0.00 0.00 3.82
2292 4922 1.182667 CGGAGGGAGTACATGTGTGA 58.817 55.000 9.11 0.00 0.00 3.58
2293 4923 1.548719 CGGAGGGAGTACATGTGTGAA 59.451 52.381 9.11 0.00 0.00 3.18
2294 4924 2.028476 CGGAGGGAGTACATGTGTGAAA 60.028 50.000 9.11 0.00 0.00 2.69
2295 4925 3.369471 CGGAGGGAGTACATGTGTGAAAT 60.369 47.826 9.11 0.00 0.00 2.17
2296 4926 4.192317 GGAGGGAGTACATGTGTGAAATC 58.808 47.826 9.11 0.00 0.00 2.17
2297 4927 4.080863 GGAGGGAGTACATGTGTGAAATCT 60.081 45.833 9.11 0.00 0.00 2.40
2298 4928 4.836825 AGGGAGTACATGTGTGAAATCTG 58.163 43.478 9.11 0.00 0.00 2.90
2299 4929 3.375299 GGGAGTACATGTGTGAAATCTGC 59.625 47.826 9.11 1.19 0.00 4.26
2300 4930 4.002982 GGAGTACATGTGTGAAATCTGCA 58.997 43.478 9.11 0.00 0.00 4.41
2301 4931 4.637534 GGAGTACATGTGTGAAATCTGCAT 59.362 41.667 9.11 0.00 0.00 3.96
2302 4932 5.124457 GGAGTACATGTGTGAAATCTGCATT 59.876 40.000 9.11 0.00 0.00 3.56
2303 4933 6.316140 GGAGTACATGTGTGAAATCTGCATTA 59.684 38.462 9.11 0.00 0.00 1.90
2304 4934 7.148255 GGAGTACATGTGTGAAATCTGCATTAA 60.148 37.037 9.11 0.00 0.00 1.40
2305 4935 7.755591 AGTACATGTGTGAAATCTGCATTAAG 58.244 34.615 9.11 0.00 0.00 1.85
2306 4936 6.579666 ACATGTGTGAAATCTGCATTAAGT 57.420 33.333 0.00 0.00 0.00 2.24
2307 4937 6.615088 ACATGTGTGAAATCTGCATTAAGTC 58.385 36.000 0.00 0.00 0.00 3.01
2308 4938 6.432162 ACATGTGTGAAATCTGCATTAAGTCT 59.568 34.615 0.00 0.00 0.00 3.24
2309 4939 6.486253 TGTGTGAAATCTGCATTAAGTCTC 57.514 37.500 0.00 0.00 0.00 3.36
2310 4940 6.233434 TGTGTGAAATCTGCATTAAGTCTCT 58.767 36.000 0.00 0.00 0.00 3.10
2311 4941 6.369890 TGTGTGAAATCTGCATTAAGTCTCTC 59.630 38.462 0.00 0.00 0.00 3.20
2312 4942 6.593382 GTGTGAAATCTGCATTAAGTCTCTCT 59.407 38.462 0.00 0.00 0.00 3.10
2356 4989 7.766219 TTAAATTACTGACGGAAGATAGTGC 57.234 36.000 0.00 0.00 34.06 4.40
2383 5016 6.152379 GGCAAACACTCTTAAGGAGAAAATG 58.848 40.000 1.85 0.00 44.45 2.32
2384 5017 5.631096 GCAAACACTCTTAAGGAGAAAATGC 59.369 40.000 1.85 2.89 44.45 3.56
2387 5020 5.790593 ACACTCTTAAGGAGAAAATGCGTA 58.209 37.500 1.85 0.00 44.45 4.42
2392 5025 6.235664 TCTTAAGGAGAAAATGCGTAGGTTT 58.764 36.000 1.85 0.00 0.00 3.27
2417 5050 4.726583 AGGCGGTATCTCAAGTATACTGA 58.273 43.478 6.06 5.61 38.09 3.41
2453 5086 3.589735 TCCACTTTTGGGCAGGTCTAATA 59.410 43.478 0.00 0.00 44.11 0.98
2522 5155 5.760253 GGATGGCTCGAAAATTAGATTCTGA 59.240 40.000 0.00 0.00 0.00 3.27
2616 5249 1.856597 GTGATACAATCGCCACGGTAC 59.143 52.381 0.00 0.00 33.78 3.34
2619 5252 1.175654 TACAATCGCCACGGTACTGA 58.824 50.000 9.17 0.00 0.00 3.41
2686 5341 2.743718 CTCCAGCGGTTGTCCACT 59.256 61.111 0.00 0.00 0.00 4.00
2766 5421 5.752892 TTCTCAGTGGAGTCGATGTATAC 57.247 43.478 0.00 0.00 42.05 1.47
2789 5444 3.055819 AGCGTTAATCCAGTCTGATGTGT 60.056 43.478 0.00 0.00 0.00 3.72
2790 5445 3.062639 GCGTTAATCCAGTCTGATGTGTG 59.937 47.826 0.00 0.00 0.00 3.82
2876 5531 2.572191 TATTCGTCGCGGAGTCATTT 57.428 45.000 6.13 0.00 0.00 2.32
2957 5613 7.757941 TGTCACCATGATGAGACAATAAAAA 57.242 32.000 15.06 0.00 37.99 1.94
2988 5644 2.036992 TCCATTGCAAATTGGCTCGTTT 59.963 40.909 13.33 0.00 32.80 3.60
2996 5652 4.209080 GCAAATTGGCTCGTTTTATATGGC 59.791 41.667 0.00 0.00 0.00 4.40
3012 5668 3.959495 ATGGCCAGTCATCCAAATAGT 57.041 42.857 13.05 0.00 35.75 2.12
3024 5680 5.183713 TCATCCAAATAGTTTCTGGCTTGTG 59.816 40.000 0.00 0.00 0.00 3.33
3042 5698 2.769663 TGTGTCCTCCTTGTAGTGTTGT 59.230 45.455 0.00 0.00 0.00 3.32
3048 5704 5.001232 TCCTCCTTGTAGTGTTGTTAATGC 58.999 41.667 0.00 0.00 0.00 3.56
3077 5733 4.887071 GCAACTGGTTACATGGGATTGATA 59.113 41.667 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.830651 TCTCACTTAGGTCCCTCCTC 57.169 55.000 0.00 0.00 44.42 3.71
2 3 3.322191 AGATCTCACTTAGGTCCCTCC 57.678 52.381 0.00 0.00 35.77 4.30
3 4 4.794334 TGTAGATCTCACTTAGGTCCCTC 58.206 47.826 0.00 0.00 35.77 4.30
4 5 4.883021 TGTAGATCTCACTTAGGTCCCT 57.117 45.455 0.00 0.00 35.77 4.20
95 1915 7.630242 AGACATGTTCAGTCAGAAAGAAAAA 57.370 32.000 0.00 0.00 38.13 1.94
100 1920 8.763049 TTACATAGACATGTTCAGTCAGAAAG 57.237 34.615 0.00 0.00 42.98 2.62
227 2061 3.188254 TGACGTGTGGCACTTATCATTTG 59.812 43.478 19.83 0.77 31.34 2.32
308 2195 1.472552 CCGTGTGTCACTGGAACTTGA 60.473 52.381 4.27 0.00 32.71 3.02
312 2199 1.092921 TTGCCGTGTGTCACTGGAAC 61.093 55.000 16.21 0.83 32.71 3.62
316 2412 0.732571 AAACTTGCCGTGTGTCACTG 59.267 50.000 4.27 0.00 31.34 3.66
322 2418 1.003545 CTGACAGAAACTTGCCGTGTG 60.004 52.381 0.00 0.00 0.00 3.82
344 2440 5.324409 AGGATGGTAACTTTCATGCTTCAA 58.676 37.500 0.00 0.00 38.59 2.69
346 2442 5.644644 CAAGGATGGTAACTTTCATGCTTC 58.355 41.667 7.01 0.00 44.73 3.86
352 2448 3.071479 GACGCAAGGATGGTAACTTTCA 58.929 45.455 0.00 0.00 46.39 2.69
360 2456 2.038557 AGTTTAGTGACGCAAGGATGGT 59.961 45.455 0.00 0.00 46.39 3.55
399 2495 3.179443 ACGAACACATGTGTCAACTCT 57.821 42.857 30.64 14.93 44.13 3.24
402 2498 3.059868 CAGGTACGAACACATGTGTCAAC 60.060 47.826 30.64 22.89 44.13 3.18
407 2503 2.731451 CAGTCAGGTACGAACACATGTG 59.269 50.000 24.25 24.25 32.24 3.21
424 2520 4.701171 AGTACTCTAGTAAGTGCCACAGTC 59.299 45.833 0.00 0.00 32.88 3.51
426 2522 6.754702 TTAGTACTCTAGTAAGTGCCACAG 57.245 41.667 0.00 0.00 32.88 3.66
457 2555 5.746952 AGCCATGCTTTGCTCATAAGCTATA 60.747 40.000 8.78 0.00 46.30 1.31
534 2958 6.149474 AGTTACATTCTCGCTAACTTGCAATT 59.851 34.615 0.00 0.00 28.24 2.32
535 2959 5.643777 AGTTACATTCTCGCTAACTTGCAAT 59.356 36.000 0.00 0.00 28.24 3.56
536 2960 4.994852 AGTTACATTCTCGCTAACTTGCAA 59.005 37.500 0.00 0.00 28.24 4.08
537 2961 4.566004 AGTTACATTCTCGCTAACTTGCA 58.434 39.130 0.00 0.00 28.24 4.08
606 3030 0.798776 GCACCATCAACTTCCGAGTG 59.201 55.000 0.00 0.00 35.91 3.51
676 3100 3.151906 CCCCCGCCATTCCTCTAG 58.848 66.667 0.00 0.00 0.00 2.43
742 3166 1.710341 CCCCTCCTCTTCCTACCCA 59.290 63.158 0.00 0.00 0.00 4.51
744 3168 1.003051 TGCCCCTCCTCTTCCTACC 59.997 63.158 0.00 0.00 0.00 3.18
747 3171 2.041928 CCTGCCCCTCCTCTTCCT 59.958 66.667 0.00 0.00 0.00 3.36
754 3178 2.041265 TCTTCCTCCTGCCCCTCC 59.959 66.667 0.00 0.00 0.00 4.30
779 3204 1.040646 ACTTCTTCGTCCTGCTGTCA 58.959 50.000 0.00 0.00 0.00 3.58
782 3207 2.611518 CCTAACTTCTTCGTCCTGCTG 58.388 52.381 0.00 0.00 0.00 4.41
786 3211 1.640917 TGCCCTAACTTCTTCGTCCT 58.359 50.000 0.00 0.00 0.00 3.85
790 3215 4.201724 CGATCTTTTGCCCTAACTTCTTCG 60.202 45.833 0.00 0.00 0.00 3.79
837 3361 3.525537 AGATCGACTACATGCAAGTTGG 58.474 45.455 0.00 0.00 0.00 3.77
853 3377 9.613957 AGTATGTATAGACAAAAATCGAGATCG 57.386 33.333 0.00 0.00 39.59 3.69
859 3383 7.011950 TGGCCAAGTATGTATAGACAAAAATCG 59.988 37.037 0.61 0.00 39.59 3.34
870 3394 2.637872 GCTCCCTGGCCAAGTATGTATA 59.362 50.000 7.01 0.00 0.00 1.47
879 3403 1.980765 CATATCTAGCTCCCTGGCCAA 59.019 52.381 7.01 0.00 0.00 4.52
948 3472 7.154656 TGCATATATAGGCAACATCGGATATC 58.845 38.462 19.09 0.00 40.30 1.63
1024 3558 3.685550 GCCAATATAGCTGGTGGTTCAGT 60.686 47.826 0.00 0.00 37.12 3.41
1025 3559 2.880890 GCCAATATAGCTGGTGGTTCAG 59.119 50.000 0.00 0.00 36.24 3.02
1094 3655 2.370445 CCACCTGGGGGAGCAGTAG 61.370 68.421 10.26 0.00 36.25 2.57
1103 3664 3.338250 TAGCTTGGCCACCTGGGG 61.338 66.667 3.88 0.00 37.04 4.96
1354 3921 3.243569 GGTCGTTGGGATAGACTGATCTG 60.244 52.174 0.00 0.00 36.29 2.90
1364 3943 1.952102 GCCGTCTGGTCGTTGGGATA 61.952 60.000 0.00 0.00 37.67 2.59
1412 3997 5.648092 GGTCAACTATGTTACTTGCTCCAAT 59.352 40.000 0.00 0.00 0.00 3.16
1549 4138 3.582148 TGCTCTTCGCATGCCTTG 58.418 55.556 13.15 1.94 45.47 3.61
1565 4154 2.338500 GAGTTTACGGTCTTCCTGCTG 58.662 52.381 0.00 0.00 0.00 4.41
1640 4256 1.338579 CCTGAGCTCCTTGTGGAAGTC 60.339 57.143 12.15 0.00 42.66 3.01
1647 4263 0.252479 CTGCATCCTGAGCTCCTTGT 59.748 55.000 12.15 0.00 0.00 3.16
1689 4310 9.674068 AAAGGAAAGCCAAATTAAGTTTTTGTA 57.326 25.926 0.00 0.00 36.29 2.41
1698 4319 6.994421 AGAGGAAAAGGAAAGCCAAATTAA 57.006 33.333 0.00 0.00 36.29 1.40
1775 4401 6.311200 ACAAAAAGTTAGCAGCAAAAGACAAG 59.689 34.615 0.00 0.00 0.00 3.16
1781 4407 5.698545 ACACAACAAAAAGTTAGCAGCAAAA 59.301 32.000 0.00 0.00 38.74 2.44
1782 4408 5.233988 ACACAACAAAAAGTTAGCAGCAAA 58.766 33.333 0.00 0.00 38.74 3.68
1788 4414 3.610677 ACGCAACACAACAAAAAGTTAGC 59.389 39.130 0.00 0.00 38.74 3.09
1819 4445 1.134877 CACATCTCGCTCACCTCATGT 60.135 52.381 0.00 0.00 0.00 3.21
1926 4552 2.103771 TCTCAGATTGCATAGCAGGTCC 59.896 50.000 0.00 0.00 40.61 4.46
1937 4563 8.887717 AGTTGAACTTTATACATCTCAGATTGC 58.112 33.333 0.00 0.00 0.00 3.56
2000 4630 0.814010 AGCACCTCAACACGTTGACC 60.814 55.000 8.51 0.00 43.90 4.02
2002 4632 0.176910 TCAGCACCTCAACACGTTGA 59.823 50.000 11.85 11.85 46.27 3.18
2005 4635 0.681733 ATCTCAGCACCTCAACACGT 59.318 50.000 0.00 0.00 0.00 4.49
2007 4637 0.801251 GCATCTCAGCACCTCAACAC 59.199 55.000 0.00 0.00 0.00 3.32
2039 4669 4.335874 TCGAAGAGGTTACTCATAGCAGAC 59.664 45.833 0.00 0.00 46.44 3.51
2048 4678 6.196168 GCTAAAACGTATCGAAGAGGTTACTC 59.804 42.308 8.61 0.00 43.63 2.59
2091 4721 6.260377 TGATACTCGTGTTGTCCTATTTACG 58.740 40.000 0.00 0.00 0.00 3.18
2166 4796 5.279456 GCCCTTCTCCTCTTTTATTTTGCAA 60.279 40.000 0.00 0.00 0.00 4.08
2174 4804 3.587061 TGACATGCCCTTCTCCTCTTTTA 59.413 43.478 0.00 0.00 0.00 1.52
2202 4832 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
2203 4833 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2204 4834 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2205 4835 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2206 4836 3.118038 CCATCTATTTTGGAACGGAGGGA 60.118 47.826 0.00 0.00 36.26 4.20
2207 4837 3.214328 CCATCTATTTTGGAACGGAGGG 58.786 50.000 0.00 0.00 36.26 4.30
2208 4838 2.618709 GCCATCTATTTTGGAACGGAGG 59.381 50.000 0.00 0.00 36.26 4.30
2209 4839 3.545703 AGCCATCTATTTTGGAACGGAG 58.454 45.455 0.00 0.00 36.26 4.63
2210 4840 3.054728 TGAGCCATCTATTTTGGAACGGA 60.055 43.478 0.00 0.00 36.26 4.69
2211 4841 3.278574 TGAGCCATCTATTTTGGAACGG 58.721 45.455 0.00 0.00 36.26 4.44
2212 4842 4.396166 AGTTGAGCCATCTATTTTGGAACG 59.604 41.667 0.00 0.00 36.26 3.95
2213 4843 5.904362 AGTTGAGCCATCTATTTTGGAAC 57.096 39.130 0.00 0.00 36.26 3.62
2214 4844 6.916360 AAAGTTGAGCCATCTATTTTGGAA 57.084 33.333 0.00 0.00 36.26 3.53
2215 4845 8.415950 TTTAAAGTTGAGCCATCTATTTTGGA 57.584 30.769 0.00 0.00 36.26 3.53
2216 4846 8.306761 ACTTTAAAGTTGAGCCATCTATTTTGG 58.693 33.333 15.22 0.00 35.21 3.28
2217 4847 9.696917 AACTTTAAAGTTGAGCCATCTATTTTG 57.303 29.630 28.38 0.00 46.80 2.44
2249 4879 8.512138 CCGTTCCAAAATAGATGACTTAACTTT 58.488 33.333 0.00 0.00 0.00 2.66
2250 4880 7.881232 TCCGTTCCAAAATAGATGACTTAACTT 59.119 33.333 0.00 0.00 0.00 2.66
2251 4881 7.391620 TCCGTTCCAAAATAGATGACTTAACT 58.608 34.615 0.00 0.00 0.00 2.24
2252 4882 7.201617 CCTCCGTTCCAAAATAGATGACTTAAC 60.202 40.741 0.00 0.00 0.00 2.01
2253 4883 6.821665 CCTCCGTTCCAAAATAGATGACTTAA 59.178 38.462 0.00 0.00 0.00 1.85
2254 4884 6.346096 CCTCCGTTCCAAAATAGATGACTTA 58.654 40.000 0.00 0.00 0.00 2.24
2255 4885 5.186198 CCTCCGTTCCAAAATAGATGACTT 58.814 41.667 0.00 0.00 0.00 3.01
2256 4886 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2257 4887 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2258 4888 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2259 4889 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2260 4890 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2261 4891 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2262 4892 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2263 4893 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2264 4894 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2265 4895 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2266 4896 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2267 4897 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2268 4898 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2269 4899 1.134788 CACATGTACTCCCTCCGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
2270 4900 1.549170 ACACATGTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
2271 4901 1.275291 CACACATGTACTCCCTCCGTT 59.725 52.381 0.00 0.00 0.00 4.44
2272 4902 0.895530 CACACATGTACTCCCTCCGT 59.104 55.000 0.00 0.00 0.00 4.69
2273 4903 1.182667 TCACACATGTACTCCCTCCG 58.817 55.000 0.00 0.00 0.00 4.63
2274 4904 3.695830 TTTCACACATGTACTCCCTCC 57.304 47.619 0.00 0.00 0.00 4.30
2275 4905 4.872691 CAGATTTCACACATGTACTCCCTC 59.127 45.833 0.00 0.00 0.00 4.30
2276 4906 4.836825 CAGATTTCACACATGTACTCCCT 58.163 43.478 0.00 0.00 0.00 4.20
2277 4907 3.375299 GCAGATTTCACACATGTACTCCC 59.625 47.826 0.00 0.00 0.00 4.30
2278 4908 4.002982 TGCAGATTTCACACATGTACTCC 58.997 43.478 0.00 0.00 0.00 3.85
2279 4909 5.808042 ATGCAGATTTCACACATGTACTC 57.192 39.130 0.00 0.00 0.00 2.59
2280 4910 7.391554 ACTTAATGCAGATTTCACACATGTACT 59.608 33.333 0.00 0.00 0.00 2.73
2281 4911 7.530010 ACTTAATGCAGATTTCACACATGTAC 58.470 34.615 0.00 0.00 0.00 2.90
2282 4912 7.607607 AGACTTAATGCAGATTTCACACATGTA 59.392 33.333 0.00 0.00 0.00 2.29
2283 4913 6.432162 AGACTTAATGCAGATTTCACACATGT 59.568 34.615 0.00 0.00 0.00 3.21
2284 4914 6.849502 AGACTTAATGCAGATTTCACACATG 58.150 36.000 0.00 0.00 0.00 3.21
2285 4915 6.883217 AGAGACTTAATGCAGATTTCACACAT 59.117 34.615 0.00 0.00 0.00 3.21
2286 4916 6.233434 AGAGACTTAATGCAGATTTCACACA 58.767 36.000 0.00 0.00 0.00 3.72
2287 4917 6.593382 AGAGAGACTTAATGCAGATTTCACAC 59.407 38.462 0.00 0.00 0.00 3.82
2288 4918 6.705302 AGAGAGACTTAATGCAGATTTCACA 58.295 36.000 0.00 0.00 0.00 3.58
2289 4919 7.041107 AGAGAGAGACTTAATGCAGATTTCAC 58.959 38.462 0.00 0.00 0.00 3.18
2290 4920 7.180322 AGAGAGAGACTTAATGCAGATTTCA 57.820 36.000 0.00 0.00 0.00 2.69
2291 4921 6.701400 GGAGAGAGAGACTTAATGCAGATTTC 59.299 42.308 0.00 0.00 0.00 2.17
2292 4922 6.383726 AGGAGAGAGAGACTTAATGCAGATTT 59.616 38.462 0.00 0.00 0.00 2.17
2293 4923 5.898972 AGGAGAGAGAGACTTAATGCAGATT 59.101 40.000 0.00 0.00 0.00 2.40
2294 4924 5.457686 AGGAGAGAGAGACTTAATGCAGAT 58.542 41.667 0.00 0.00 0.00 2.90
2295 4925 4.865905 AGGAGAGAGAGACTTAATGCAGA 58.134 43.478 0.00 0.00 0.00 4.26
2296 4926 4.261155 CGAGGAGAGAGAGACTTAATGCAG 60.261 50.000 0.00 0.00 0.00 4.41
2297 4927 3.629855 CGAGGAGAGAGAGACTTAATGCA 59.370 47.826 0.00 0.00 0.00 3.96
2298 4928 3.004315 CCGAGGAGAGAGAGACTTAATGC 59.996 52.174 0.00 0.00 0.00 3.56
2299 4929 3.004315 GCCGAGGAGAGAGAGACTTAATG 59.996 52.174 0.00 0.00 0.00 1.90
2300 4930 3.219281 GCCGAGGAGAGAGAGACTTAAT 58.781 50.000 0.00 0.00 0.00 1.40
2301 4931 2.026169 TGCCGAGGAGAGAGAGACTTAA 60.026 50.000 0.00 0.00 0.00 1.85
2302 4932 1.560146 TGCCGAGGAGAGAGAGACTTA 59.440 52.381 0.00 0.00 0.00 2.24
2303 4933 0.329931 TGCCGAGGAGAGAGAGACTT 59.670 55.000 0.00 0.00 0.00 3.01
2304 4934 0.329931 TTGCCGAGGAGAGAGAGACT 59.670 55.000 0.00 0.00 0.00 3.24
2305 4935 1.178276 TTTGCCGAGGAGAGAGAGAC 58.822 55.000 0.00 0.00 0.00 3.36
2306 4936 1.753649 CATTTGCCGAGGAGAGAGAGA 59.246 52.381 0.00 0.00 0.00 3.10
2307 4937 1.753649 TCATTTGCCGAGGAGAGAGAG 59.246 52.381 0.00 0.00 0.00 3.20
2308 4938 1.852633 TCATTTGCCGAGGAGAGAGA 58.147 50.000 0.00 0.00 0.00 3.10
2309 4939 2.871022 CAATCATTTGCCGAGGAGAGAG 59.129 50.000 0.00 0.00 0.00 3.20
2310 4940 2.237143 ACAATCATTTGCCGAGGAGAGA 59.763 45.455 0.00 0.00 36.22 3.10
2311 4941 2.636830 ACAATCATTTGCCGAGGAGAG 58.363 47.619 0.00 0.00 36.22 3.20
2312 4942 2.787473 ACAATCATTTGCCGAGGAGA 57.213 45.000 0.00 0.00 36.22 3.71
2352 4982 1.696063 AAGAGTGTTTGCCATGCACT 58.304 45.000 2.96 2.96 44.97 4.40
2356 4989 4.326826 TCTCCTTAAGAGTGTTTGCCATG 58.673 43.478 3.36 0.00 43.71 3.66
2383 5016 0.390209 TACCGCCTTGAAACCTACGC 60.390 55.000 0.00 0.00 0.00 4.42
2384 5017 2.159142 AGATACCGCCTTGAAACCTACG 60.159 50.000 0.00 0.00 0.00 3.51
2387 5020 1.906574 TGAGATACCGCCTTGAAACCT 59.093 47.619 0.00 0.00 0.00 3.50
2392 5025 5.009710 CAGTATACTTGAGATACCGCCTTGA 59.990 44.000 1.56 0.00 31.27 3.02
2481 5114 5.762218 AGCCATCCTTAATTGAGAAAGATCG 59.238 40.000 0.00 0.00 0.00 3.69
2486 5119 5.097742 TCGAGCCATCCTTAATTGAGAAA 57.902 39.130 0.00 0.00 0.00 2.52
2522 5155 1.359474 TCTCCTAGCCACTTGTCCTCT 59.641 52.381 0.00 0.00 0.00 3.69
2603 5236 2.277084 GATTTCAGTACCGTGGCGATT 58.723 47.619 0.00 0.00 0.00 3.34
2640 5273 1.640428 TCATGATTGGAGTCGAACGC 58.360 50.000 0.00 0.00 0.00 4.84
2766 5421 3.308053 CACATCAGACTGGATTAACGCTG 59.692 47.826 1.81 0.00 0.00 5.18
2843 5498 4.025229 GCGACGAATATACCATGCAAAGAA 60.025 41.667 0.00 0.00 0.00 2.52
2858 5513 1.722011 AAAATGACTCCGCGACGAAT 58.278 45.000 8.23 0.00 0.00 3.34
2957 5613 7.612633 AGCCAATTTGCAATGGAAGAATAAATT 59.387 29.630 20.88 1.44 39.12 1.82
2971 5627 5.809562 CCATATAAAACGAGCCAATTTGCAA 59.190 36.000 4.12 0.00 0.00 4.08
2988 5644 7.090319 ACTATTTGGATGACTGGCCATATAA 57.910 36.000 5.51 0.00 33.46 0.98
2996 5652 4.096984 GCCAGAAACTATTTGGATGACTGG 59.903 45.833 0.00 0.00 43.26 4.00
3012 5668 1.140312 AGGAGGACACAAGCCAGAAA 58.860 50.000 0.00 0.00 0.00 2.52
3024 5680 5.106673 GCATTAACAACACTACAAGGAGGAC 60.107 44.000 0.00 0.00 0.00 3.85
3048 5704 3.500982 CCATGTAACCAGTTGCGAAATG 58.499 45.455 0.00 0.00 0.00 2.32
3077 5733 4.202367 CCTGAGGAGTGTTCTAAACCTGTT 60.202 45.833 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.