Multiple sequence alignment - TraesCS6A01G394300

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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 TraesCS6A01G394300 chr6A 100.000 6750 0 0 1 6750 607950828 607957577 0.000000e+00 12429.0
1 TraesCS6A01G394300 chr6A 94.309 123 7 0 1914 2036 607952699 607952821 8.940000e-44 189.0
2 TraesCS6A01G394300 chr6A 94.309 123 7 0 1872 1994 607952741 607952863 8.940000e-44 189.0
3 TraesCS6A01G394300 chr6A 94.253 87 5 0 1956 2042 607952699 607952785 4.250000e-27 134.0
4 TraesCS6A01G394300 chr6A 94.253 87 5 0 1872 1958 607952783 607952869 4.250000e-27 134.0
5 TraesCS6A01G394300 chr6A 94.545 55 2 1 6250 6304 607957023 607957076 4.340000e-12 84.2
6 TraesCS6A01G394300 chr6A 94.545 55 2 1 6196 6249 607957077 607957131 4.340000e-12 84.2
7 TraesCS6A01G394300 chr6B 94.165 4182 171 36 380 4531 702824547 702828685 0.000000e+00 6303.0
8 TraesCS6A01G394300 chr6B 94.110 1545 58 15 4735 6258 702829026 702830558 0.000000e+00 2318.0
9 TraesCS6A01G394300 chr6B 89.610 308 19 7 6250 6555 702830496 702830792 4.940000e-101 379.0
10 TraesCS6A01G394300 chr6B 89.153 295 16 9 39 330 702823914 702824195 2.990000e-93 353.0
11 TraesCS6A01G394300 chr6B 96.124 129 5 0 1914 2042 702826041 702826169 1.910000e-50 211.0
12 TraesCS6A01G394300 chr6B 95.122 123 6 0 1872 1994 702826083 702826205 1.920000e-45 195.0
13 TraesCS6A01G394300 chr6B 91.743 109 8 1 6581 6689 702830959 702831066 4.220000e-32 150.0
14 TraesCS6A01G394300 chr6B 96.552 87 3 0 1872 1958 702826125 702826211 1.960000e-30 145.0
15 TraesCS6A01G394300 chr6B 93.103 87 6 0 1956 2042 702826041 702826127 1.980000e-25 128.0
16 TraesCS6A01G394300 chr6D 96.467 3510 90 16 2817 6304 461356414 461359911 0.000000e+00 5764.0
17 TraesCS6A01G394300 chr6D 92.063 2016 87 33 3 1994 461353624 461355590 0.000000e+00 2769.0
18 TraesCS6A01G394300 chr6D 98.037 917 15 1 1914 2830 461355468 461356381 0.000000e+00 1591.0
19 TraesCS6A01G394300 chr6D 89.703 437 27 12 6306 6737 461360464 461360887 5.950000e-150 542.0
20 TraesCS6A01G394300 chr6D 92.683 82 6 0 3402 3483 471973108 471973189 1.190000e-22 119.0
21 TraesCS6A01G394300 chr6D 92.683 82 6 0 3402 3483 472033447 472033528 1.190000e-22 119.0
22 TraesCS6A01G394300 chr1B 83.786 1289 121 40 2973 4225 655101572 655100336 0.000000e+00 1142.0
23 TraesCS6A01G394300 chr1D 82.099 905 108 23 3420 4314 471433021 471433881 0.000000e+00 725.0
24 TraesCS6A01G394300 chr1D 84.767 709 65 13 2966 3674 471300325 471299660 0.000000e+00 671.0
25 TraesCS6A01G394300 chr1D 81.675 764 87 36 4735 5478 471295169 471294439 2.710000e-163 586.0
26 TraesCS6A01G394300 chr1D 82.432 518 71 12 4945 5448 471299652 471299141 1.040000e-117 435.0
27 TraesCS6A01G394300 chr1D 83.004 506 58 19 4988 5477 471297174 471296681 3.740000e-117 433.0
28 TraesCS6A01G394300 chr7A 82.898 421 50 14 4986 5404 704893498 704893098 6.440000e-95 359.0
29 TraesCS6A01G394300 chr7A 76.712 146 30 4 4069 4212 237519436 237519293 2.020000e-10 78.7
30 TraesCS6A01G394300 chr7D 82.506 423 52 14 4986 5404 613449717 613449313 1.080000e-92 351.0
31 TraesCS6A01G394300 chr7D 85.000 260 28 8 4986 5239 29534949 29534695 3.120000e-63 254.0
32 TraesCS6A01G394300 chr7D 76.712 146 30 4 4069 4212 224055477 224055620 2.020000e-10 78.7
33 TraesCS6A01G394300 chr3D 84.942 259 31 5 4986 5239 461201987 461202242 8.690000e-64 255.0
34 TraesCS6A01G394300 chr3B 82.591 247 23 14 5900 6146 611679465 611679691 4.130000e-47 200.0
35 TraesCS6A01G394300 chr7B 76.027 146 31 4 4069 4212 173864858 173865001 9.390000e-09 73.1
36 TraesCS6A01G394300 chr5D 89.091 55 6 0 4073 4127 40994882 40994828 1.210000e-07 69.4
37 TraesCS6A01G394300 chr2B 100.000 37 0 0 4073 4109 31624450 31624486 1.210000e-07 69.4
38 TraesCS6A01G394300 chr2A 89.091 55 6 0 4073 4127 20822252 20822198 1.210000e-07 69.4
39 TraesCS6A01G394300 chr5B 100.000 29 0 0 176 204 41980409 41980381 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G394300 chr6A 607950828 607957577 6749 False 12429.000000 12429 100.0000 1 6750 1 chr6A.!!$F1 6749
1 TraesCS6A01G394300 chr6B 702823914 702831066 7152 False 1131.333333 6303 93.2980 39 6689 9 chr6B.!!$F1 6650
2 TraesCS6A01G394300 chr6D 461353624 461360887 7263 False 2666.500000 5764 94.0675 3 6737 4 chr6D.!!$F3 6734
3 TraesCS6A01G394300 chr1B 655100336 655101572 1236 True 1142.000000 1142 83.7860 2973 4225 1 chr1B.!!$R1 1252
4 TraesCS6A01G394300 chr1D 471433021 471433881 860 False 725.000000 725 82.0990 3420 4314 1 chr1D.!!$F1 894
5 TraesCS6A01G394300 chr1D 471294439 471300325 5886 True 531.250000 671 82.9695 2966 5478 4 chr1D.!!$R1 2512

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
784 1107 0.249868 GTTTGGTTTCTTGGCCCTGC 60.250 55.000 0.00 0.0 0.00 4.85 F
785 1108 0.398381 TTTGGTTTCTTGGCCCTGCT 60.398 50.000 0.00 0.0 0.00 4.24 F
1909 2252 0.453390 CCGGAATGCTTTTGAGAGCC 59.547 55.000 0.00 0.0 42.01 4.70 F
1950 2293 0.179153 GCCGGAATGCTTTTGAGAGC 60.179 55.000 5.05 0.0 43.00 4.09 F
1994 2379 1.250154 CGGAATGCTTTTGAGGGCCA 61.250 55.000 6.18 0.0 0.00 5.36 F
2212 2597 1.923204 CTTCGATCTCAAGAAGCACCG 59.077 52.381 0.00 0.0 37.62 4.94 F
3284 3724 0.768221 CCAGGCAAGGGGATAGGCTA 60.768 60.000 0.00 0.0 36.31 3.93 F
3285 3725 1.140312 CAGGCAAGGGGATAGGCTAA 58.860 55.000 0.00 0.0 36.31 3.09 F
3286 3726 1.141185 AGGCAAGGGGATAGGCTAAC 58.859 55.000 0.00 0.0 36.31 2.34 F
4007 4473 1.911057 AGGCTTTAGAAGTGGTTGGC 58.089 50.000 0.00 0.0 0.00 4.52 F
5160 5812 1.012841 GCTCTTATGTGCTGTGGCTC 58.987 55.000 0.00 0.0 39.59 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2274 0.179153 GCTCTCAAAAGCATTCCGGC 60.179 55.000 0.00 0.00 42.05 6.13 R
1932 2275 0.453390 GGCTCTCAAAAGCATTCCGG 59.547 55.000 0.00 0.00 44.35 5.14 R
2830 3218 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82 R
3275 3715 4.748600 GGAATACGTGTTGTTAGCCTATCC 59.251 45.833 0.91 0.00 0.00 2.59 R
3284 3724 4.963276 CATGGATGGAATACGTGTTGTT 57.037 40.909 0.91 0.00 39.42 2.83 R
4067 4543 1.737838 TGCCATTCTGATCACGAACC 58.262 50.000 9.00 3.83 0.00 3.62 R
4451 4930 1.425066 AGGCCTGAGTGAAATTGTCCA 59.575 47.619 3.11 0.00 0.00 4.02 R
4452 4931 2.206576 AGGCCTGAGTGAAATTGTCC 57.793 50.000 3.11 0.00 0.00 4.02 R
4519 4998 3.419943 TGATATGCAACTGCCAACTTGA 58.580 40.909 0.00 0.00 41.18 3.02 R
5657 7018 1.134250 TGGAAAAGGGTTTGCAAAGGC 60.134 47.619 13.26 1.18 41.52 4.35 R
6265 7862 0.614812 TACTTCCAGAGCTGCATGCA 59.385 50.000 21.29 21.29 45.94 3.96 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 32 8.419442 AGCAATCATCTCAAAGATATTTTTCCC 58.581 33.333 0.00 0.00 32.12 3.97
36 37 9.989296 TCATCTCAAAGATATTTTTCCCCTAAA 57.011 29.630 0.00 0.00 32.12 1.85
45 47 8.972127 AGATATTTTTCCCCTAAAAGAAAGAGC 58.028 33.333 0.00 0.00 38.29 4.09
62 64 7.869800 AGAAAGAGCACATAACAAGAAAAGAG 58.130 34.615 0.00 0.00 0.00 2.85
69 71 6.681777 CACATAACAAGAAAAGAGAAAGGGG 58.318 40.000 0.00 0.00 0.00 4.79
111 113 7.413438 GCATTGCATTGCATAGGACTAGTATAC 60.413 40.741 24.71 0.00 42.31 1.47
132 134 0.983378 TAGCCAGGAGGAGGAAAGCC 60.983 60.000 0.00 0.00 36.89 4.35
151 153 2.573340 CACCAAATCCGCCAAGGC 59.427 61.111 0.00 0.00 40.77 4.35
204 206 1.344114 CTTTGCCTTTGCCTTTGCCTA 59.656 47.619 0.00 0.00 36.33 3.93
211 214 0.991920 TTGCCTTTGCCTAGCCTAGT 59.008 50.000 0.00 0.00 36.33 2.57
230 233 3.743132 AGTCTAGGAGAGGAGAGGAGAA 58.257 50.000 0.00 0.00 0.00 2.87
584 898 1.783416 CGATTTGTTCGCTGCTTCGAC 60.783 52.381 0.00 0.00 41.69 4.20
611 925 1.070601 GCCAGTGGGTTTGCTGATTTT 59.929 47.619 12.15 0.00 34.87 1.82
680 994 2.108168 GCCCCTAAAAGGTGGGATTTC 58.892 52.381 0.00 0.00 46.15 2.17
685 999 5.046591 CCCCTAAAAGGTGGGATTTCTTTTC 60.047 44.000 0.00 0.00 46.15 2.29
762 1082 1.227380 AGCCGATTCCATGTCGCTC 60.227 57.895 0.00 0.00 37.75 5.03
784 1107 0.249868 GTTTGGTTTCTTGGCCCTGC 60.250 55.000 0.00 0.00 0.00 4.85
785 1108 0.398381 TTTGGTTTCTTGGCCCTGCT 60.398 50.000 0.00 0.00 0.00 4.24
816 1139 4.489810 TCTGCTTCTGATCGTTTTCTCTC 58.510 43.478 0.00 0.00 0.00 3.20
840 1163 3.009584 AGTTCATCCAGTTCTTCTTCCCC 59.990 47.826 0.00 0.00 0.00 4.81
851 1174 0.889186 TTCTTCCCCAAGCTTCGTGC 60.889 55.000 0.00 0.00 43.29 5.34
861 1184 3.479269 CTTCGTGCGCGTTCCTCC 61.479 66.667 20.50 0.00 39.49 4.30
901 1224 1.749634 CGGAGTTCTAATCACCGTCCT 59.250 52.381 0.00 0.00 38.97 3.85
903 1226 2.758979 GGAGTTCTAATCACCGTCCTGA 59.241 50.000 0.00 0.00 0.00 3.86
906 1229 3.769844 AGTTCTAATCACCGTCCTGATGT 59.230 43.478 0.00 0.00 30.92 3.06
909 1232 5.160607 TCTAATCACCGTCCTGATGTTTT 57.839 39.130 0.00 0.00 30.92 2.43
912 1235 3.040147 TCACCGTCCTGATGTTTTCTC 57.960 47.619 0.00 0.00 0.00 2.87
983 1308 3.712907 GGCCGGCTAGGTGACCAA 61.713 66.667 28.56 0.00 43.70 3.67
1533 1867 1.737735 CCTCGCACGTCAGCAATCA 60.738 57.895 0.00 0.00 0.00 2.57
1681 2024 8.046708 TGCTCTGCAATAGATTCTTTAACCTTA 58.953 33.333 0.00 0.00 34.76 2.69
1747 2090 4.098044 TGCACTTATACTGACAGGCTACTC 59.902 45.833 7.51 0.00 0.00 2.59
1764 2107 4.272018 GCTACTCCTACAATGCATCACTTG 59.728 45.833 0.00 0.00 0.00 3.16
1779 2122 8.840833 TGCATCACTTGTAAGACTATTTTGTA 57.159 30.769 0.00 0.00 0.00 2.41
1780 2123 8.717821 TGCATCACTTGTAAGACTATTTTGTAC 58.282 33.333 0.00 0.00 0.00 2.90
1781 2124 8.936864 GCATCACTTGTAAGACTATTTTGTACT 58.063 33.333 0.00 0.00 0.00 2.73
1794 2137 8.943909 ACTATTTTGTACTAGCATGTAAGTCC 57.056 34.615 5.50 0.00 0.00 3.85
1850 2193 6.012337 TCCATGACAGGAAAATATTAGCCA 57.988 37.500 0.00 0.00 33.93 4.75
1909 2252 0.453390 CCGGAATGCTTTTGAGAGCC 59.547 55.000 0.00 0.00 42.01 4.70
1910 2253 0.453390 CGGAATGCTTTTGAGAGCCC 59.547 55.000 0.00 0.00 42.01 5.19
1911 2254 1.549203 GGAATGCTTTTGAGAGCCCA 58.451 50.000 0.00 0.00 42.01 5.36
1912 2255 1.895131 GGAATGCTTTTGAGAGCCCAA 59.105 47.619 0.00 0.00 42.01 4.12
1913 2256 2.299867 GGAATGCTTTTGAGAGCCCAAA 59.700 45.455 0.00 0.00 42.01 3.28
1914 2257 3.055602 GGAATGCTTTTGAGAGCCCAAAT 60.056 43.478 0.00 0.00 42.01 2.32
1915 2258 3.881937 ATGCTTTTGAGAGCCCAAATC 57.118 42.857 0.00 0.00 42.01 2.17
1916 2259 1.895131 TGCTTTTGAGAGCCCAAATCC 59.105 47.619 0.00 0.00 42.01 3.01
1917 2260 2.174360 GCTTTTGAGAGCCCAAATCCT 58.826 47.619 0.00 0.00 36.12 3.24
1918 2261 2.564504 GCTTTTGAGAGCCCAAATCCTT 59.435 45.455 0.00 0.00 36.12 3.36
1919 2262 3.367806 GCTTTTGAGAGCCCAAATCCTTC 60.368 47.826 0.00 0.00 36.12 3.46
1920 2263 3.524095 TTTGAGAGCCCAAATCCTTCA 57.476 42.857 0.00 0.00 31.73 3.02
1921 2264 2.496899 TGAGAGCCCAAATCCTTCAC 57.503 50.000 0.00 0.00 0.00 3.18
1922 2265 1.339055 TGAGAGCCCAAATCCTTCACG 60.339 52.381 0.00 0.00 0.00 4.35
1923 2266 0.678048 AGAGCCCAAATCCTTCACGC 60.678 55.000 0.00 0.00 0.00 5.34
1924 2267 0.678048 GAGCCCAAATCCTTCACGCT 60.678 55.000 0.00 0.00 0.00 5.07
1925 2268 0.678048 AGCCCAAATCCTTCACGCTC 60.678 55.000 0.00 0.00 0.00 5.03
1926 2269 0.678048 GCCCAAATCCTTCACGCTCT 60.678 55.000 0.00 0.00 0.00 4.09
1927 2270 1.406887 GCCCAAATCCTTCACGCTCTA 60.407 52.381 0.00 0.00 0.00 2.43
1928 2271 2.939640 GCCCAAATCCTTCACGCTCTAA 60.940 50.000 0.00 0.00 0.00 2.10
1929 2272 3.545703 CCCAAATCCTTCACGCTCTAAT 58.454 45.455 0.00 0.00 0.00 1.73
1930 2273 4.703897 CCCAAATCCTTCACGCTCTAATA 58.296 43.478 0.00 0.00 0.00 0.98
1931 2274 4.752101 CCCAAATCCTTCACGCTCTAATAG 59.248 45.833 0.00 0.00 0.00 1.73
1941 2284 2.464157 GCTCTAATAGCCGGAATGCT 57.536 50.000 5.05 0.00 46.25 3.79
1942 2285 2.772287 GCTCTAATAGCCGGAATGCTT 58.228 47.619 5.05 0.00 46.25 3.91
1943 2286 3.142174 GCTCTAATAGCCGGAATGCTTT 58.858 45.455 5.05 0.00 46.25 3.51
1944 2287 3.565902 GCTCTAATAGCCGGAATGCTTTT 59.434 43.478 5.05 0.00 46.25 2.27
1945 2288 4.555511 GCTCTAATAGCCGGAATGCTTTTG 60.556 45.833 5.05 0.00 46.25 2.44
1946 2289 4.776349 TCTAATAGCCGGAATGCTTTTGA 58.224 39.130 5.05 0.00 42.75 2.69
1947 2290 4.816385 TCTAATAGCCGGAATGCTTTTGAG 59.184 41.667 5.05 0.00 42.75 3.02
1948 2291 2.779755 TAGCCGGAATGCTTTTGAGA 57.220 45.000 5.05 0.00 42.75 3.27
1949 2292 1.457346 AGCCGGAATGCTTTTGAGAG 58.543 50.000 5.05 0.00 38.85 3.20
1950 2293 0.179153 GCCGGAATGCTTTTGAGAGC 60.179 55.000 5.05 0.00 43.00 4.09
1994 2379 1.250154 CGGAATGCTTTTGAGGGCCA 61.250 55.000 6.18 0.00 0.00 5.36
2212 2597 1.923204 CTTCGATCTCAAGAAGCACCG 59.077 52.381 0.00 0.00 37.62 4.94
2478 2866 7.251704 AGATGTGCTCTTTAATAATGTTCCG 57.748 36.000 0.00 0.00 0.00 4.30
2578 2966 5.245531 CAGTCTTTCCAAATGGTAGCAGTA 58.754 41.667 0.00 0.00 36.34 2.74
2830 3218 2.241176 ACTGGTACTCTCTCTCTCCCTG 59.759 54.545 0.00 0.00 0.00 4.45
3002 3436 2.574018 GCAGGCAAACCCCAACTCC 61.574 63.158 0.00 0.00 36.11 3.85
3275 3715 2.757099 GGTCATGCCAGGCAAGGG 60.757 66.667 20.84 11.56 43.62 3.95
3284 3724 0.768221 CCAGGCAAGGGGATAGGCTA 60.768 60.000 0.00 0.00 36.31 3.93
3285 3725 1.140312 CAGGCAAGGGGATAGGCTAA 58.860 55.000 0.00 0.00 36.31 3.09
3286 3726 1.141185 AGGCAAGGGGATAGGCTAAC 58.859 55.000 0.00 0.00 36.31 2.34
4007 4473 1.911057 AGGCTTTAGAAGTGGTTGGC 58.089 50.000 0.00 0.00 0.00 4.52
4059 4535 5.003804 AGCTTGACGGAAACACAATTATCT 58.996 37.500 0.00 0.00 0.00 1.98
4067 4543 8.519492 ACGGAAACACAATTATCTTGAAATTG 57.481 30.769 6.93 6.93 45.59 2.32
4259 4738 4.095410 TGGATGCGTTTCATTCACAATC 57.905 40.909 0.00 0.00 35.77 2.67
4410 4889 6.508030 TGGCAATTATGTTATCCAGGTAGA 57.492 37.500 0.00 0.00 0.00 2.59
4423 4902 9.289782 GTTATCCAGGTAGATGCTTATTCATTT 57.710 33.333 0.00 0.00 0.00 2.32
4425 4904 8.854614 ATCCAGGTAGATGCTTATTCATTTAC 57.145 34.615 0.00 0.00 34.89 2.01
4426 4905 8.034313 TCCAGGTAGATGCTTATTCATTTACT 57.966 34.615 0.00 0.00 35.55 2.24
4427 4906 8.150945 TCCAGGTAGATGCTTATTCATTTACTC 58.849 37.037 0.00 0.00 35.55 2.59
4428 4907 7.389053 CCAGGTAGATGCTTATTCATTTACTCC 59.611 40.741 0.00 0.00 35.55 3.85
4499 4978 7.663501 ATATTAAATTAGTGGGAGGGATGGT 57.336 36.000 0.00 0.00 0.00 3.55
4519 4998 9.136323 GGATGGTTTATGTTGGATTTCTTCTAT 57.864 33.333 0.00 0.00 0.00 1.98
4533 5080 5.947228 TTCTTCTATCAAGTTGGCAGTTG 57.053 39.130 2.34 5.53 34.94 3.16
4559 5106 9.212641 GCATATCATGTAAATGCTCTTTCTCTA 57.787 33.333 16.90 0.00 42.15 2.43
4616 5164 4.219033 CCGAATGTGCTTGTACTGTTTTC 58.781 43.478 0.00 0.00 0.00 2.29
4641 5189 1.136828 ACTTTCTGCCCAGTACCACA 58.863 50.000 0.00 0.00 0.00 4.17
5056 5701 4.588528 AGCCATTACAGGTGTGTTTTCAAT 59.411 37.500 0.00 0.00 38.19 2.57
5093 5738 3.356290 ACTGGTTCTTTGTTGCAGAACT 58.644 40.909 13.51 0.00 46.46 3.01
5115 5760 9.334693 GAACTTGCTCTGTGTAGAAATAAAATG 57.665 33.333 0.00 0.00 31.21 2.32
5154 5806 7.902387 ACATGAATATAGCTCTTATGTGCTG 57.098 36.000 13.68 0.76 42.20 4.41
5160 5812 1.012841 GCTCTTATGTGCTGTGGCTC 58.987 55.000 0.00 0.00 39.59 4.70
5222 5875 6.353323 TGTTTTGTCTATGTCTTGAGGAACA 58.647 36.000 0.00 0.00 0.00 3.18
5226 5879 6.611613 TGTCTATGTCTTGAGGAACAGAAT 57.388 37.500 0.00 0.00 0.00 2.40
5397 6055 3.837213 ATGATGAAAGACCAGTTTGCG 57.163 42.857 0.00 0.00 0.00 4.85
5573 6934 2.097825 CAGATTCCAAAGCCCCTCTTG 58.902 52.381 0.00 0.00 34.67 3.02
5646 7007 1.885887 AGGCGTTTGCTTATTGCTTCA 59.114 42.857 0.00 0.00 43.37 3.02
5657 7018 6.443792 TGCTTATTGCTTCATAATCTGCATG 58.556 36.000 0.00 0.00 43.37 4.06
5715 7077 4.669206 TTTTCTCATTTGCAGAAAGGCA 57.331 36.364 0.00 0.00 40.22 4.75
6160 7756 5.566774 CGCAGAAATCAAATGTTTCAGTCTC 59.433 40.000 0.00 0.00 37.89 3.36
6168 7764 7.496529 TCAAATGTTTCAGTCTCTGTAAAGG 57.503 36.000 0.00 0.00 32.61 3.11
6181 7777 5.544176 TCTCTGTAAAGGAGGTTTCACAGAT 59.456 40.000 2.98 0.00 37.70 2.90
6191 7787 7.052873 AGGAGGTTTCACAGATATCAAATGAG 58.947 38.462 5.32 0.00 0.00 2.90
6272 7869 4.263435 TGTCTATGAAATGTCTGCATGCA 58.737 39.130 21.29 21.29 35.15 3.96
6316 8464 8.911662 GTTTTTATTATGTTGTCATGTGTGGTC 58.088 33.333 0.00 0.00 35.70 4.02
6340 8488 9.278734 GTCGATGTATCTTTTTCCATCTTTTTC 57.721 33.333 0.00 0.00 33.24 2.29
6341 8489 8.458843 TCGATGTATCTTTTTCCATCTTTTTCC 58.541 33.333 0.00 0.00 33.24 3.13
6345 8493 5.195001 TCTTTTTCCATCTTTTTCCGTGG 57.805 39.130 0.00 0.00 0.00 4.94
6348 8496 2.649531 TCCATCTTTTTCCGTGGTGT 57.350 45.000 0.00 0.00 33.47 4.16
6350 8498 3.292460 TCCATCTTTTTCCGTGGTGTTT 58.708 40.909 0.00 0.00 33.47 2.83
6351 8499 3.067461 TCCATCTTTTTCCGTGGTGTTTG 59.933 43.478 0.00 0.00 33.47 2.93
6352 8500 3.067461 CCATCTTTTTCCGTGGTGTTTGA 59.933 43.478 0.00 0.00 0.00 2.69
6354 8502 5.048364 CCATCTTTTTCCGTGGTGTTTGATA 60.048 40.000 0.00 0.00 0.00 2.15
6356 8504 6.249035 TCTTTTTCCGTGGTGTTTGATATC 57.751 37.500 0.00 0.00 0.00 1.63
6357 8505 6.001460 TCTTTTTCCGTGGTGTTTGATATCT 58.999 36.000 3.98 0.00 0.00 1.98
6358 8506 5.873179 TTTTCCGTGGTGTTTGATATCTC 57.127 39.130 3.98 0.00 0.00 2.75
6359 8507 3.536956 TCCGTGGTGTTTGATATCTCC 57.463 47.619 3.98 0.34 0.00 3.71
6406 8554 2.683362 TGTCTCTCGACTTGCGACATAT 59.317 45.455 0.00 0.00 45.59 1.78
6470 8618 9.897744 TTTCATTGAGAGTTCACATTATTTGAC 57.102 29.630 0.00 0.00 31.71 3.18
6471 8619 8.853077 TCATTGAGAGTTCACATTATTTGACT 57.147 30.769 0.00 0.00 31.71 3.41
6472 8620 9.942850 TCATTGAGAGTTCACATTATTTGACTA 57.057 29.630 0.00 0.00 31.71 2.59
6505 8656 3.921119 TCATCACAGGAACATTTGCAC 57.079 42.857 0.00 0.00 0.00 4.57
6529 8681 4.319118 GCTCATAATAGCCGTTGAAAGAGC 60.319 45.833 0.00 0.00 38.09 4.09
6557 8709 2.223782 GGCTGAATTTGTTGCACTGACA 60.224 45.455 0.00 0.00 0.00 3.58
6558 8710 3.047796 GCTGAATTTGTTGCACTGACAG 58.952 45.455 0.00 0.00 0.00 3.51
6559 8711 3.243168 GCTGAATTTGTTGCACTGACAGA 60.243 43.478 10.08 0.00 0.00 3.41
6560 8712 4.558095 GCTGAATTTGTTGCACTGACAGAT 60.558 41.667 10.08 0.00 0.00 2.90
6561 8713 5.335113 GCTGAATTTGTTGCACTGACAGATA 60.335 40.000 10.08 0.00 0.00 1.98
6563 8715 5.764686 TGAATTTGTTGCACTGACAGATAGT 59.235 36.000 10.08 0.00 0.00 2.12
6564 8716 5.618056 ATTTGTTGCACTGACAGATAGTG 57.382 39.130 10.08 0.00 46.37 2.74
6565 8717 4.335400 TTGTTGCACTGACAGATAGTGA 57.665 40.909 10.08 0.00 46.52 3.41
6608 8901 2.500229 CCAGTTGCCTCGGTTAGAAAA 58.500 47.619 0.00 0.00 0.00 2.29
6647 8940 9.764870 CACAACTCATAACTGATCTAAAATGTG 57.235 33.333 0.00 0.00 0.00 3.21
6737 10548 3.367288 TGGAGTATGTGTCCACCGA 57.633 52.632 0.00 0.00 39.28 4.69
6738 10549 0.892755 TGGAGTATGTGTCCACCGAC 59.107 55.000 0.00 0.00 39.28 4.79
6739 10550 1.183549 GGAGTATGTGTCCACCGACT 58.816 55.000 2.09 2.09 39.94 4.18
6740 10551 1.549170 GGAGTATGTGTCCACCGACTT 59.451 52.381 0.00 0.00 39.94 3.01
6742 10553 2.492484 GAGTATGTGTCCACCGACTTCT 59.508 50.000 0.00 0.00 39.94 2.85
6743 10554 2.231478 AGTATGTGTCCACCGACTTCTG 59.769 50.000 0.00 0.00 39.94 3.02
6744 10555 1.338107 ATGTGTCCACCGACTTCTGA 58.662 50.000 0.00 0.00 39.94 3.27
6747 10558 0.673985 TGTCCACCGACTTCTGACAG 59.326 55.000 0.00 0.00 39.94 3.51
6749 10560 1.340248 GTCCACCGACTTCTGACAGAA 59.660 52.381 16.86 16.86 35.99 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.492494 TCTTTGAGATGATTGCTAGGCA 57.508 40.909 0.00 0.00 36.47 4.75
1 2 7.684937 AATATCTTTGAGATGATTGCTAGGC 57.315 36.000 0.82 0.00 35.37 3.93
29 30 5.710099 TGTTATGTGCTCTTTCTTTTAGGGG 59.290 40.000 0.00 0.00 0.00 4.79
30 31 6.817765 TGTTATGTGCTCTTTCTTTTAGGG 57.182 37.500 0.00 0.00 0.00 3.53
31 32 8.099364 TCTTGTTATGTGCTCTTTCTTTTAGG 57.901 34.615 0.00 0.00 0.00 2.69
34 35 9.305925 CTTTTCTTGTTATGTGCTCTTTCTTTT 57.694 29.630 0.00 0.00 0.00 2.27
35 36 8.686334 TCTTTTCTTGTTATGTGCTCTTTCTTT 58.314 29.630 0.00 0.00 0.00 2.52
36 37 8.225603 TCTTTTCTTGTTATGTGCTCTTTCTT 57.774 30.769 0.00 0.00 0.00 2.52
37 38 7.716998 TCTCTTTTCTTGTTATGTGCTCTTTCT 59.283 33.333 0.00 0.00 0.00 2.52
38 39 7.865707 TCTCTTTTCTTGTTATGTGCTCTTTC 58.134 34.615 0.00 0.00 0.00 2.62
41 42 7.040823 CCTTTCTCTTTTCTTGTTATGTGCTCT 60.041 37.037 0.00 0.00 0.00 4.09
42 43 7.080724 CCTTTCTCTTTTCTTGTTATGTGCTC 58.919 38.462 0.00 0.00 0.00 4.26
45 47 6.490040 TCCCCTTTCTCTTTTCTTGTTATGTG 59.510 38.462 0.00 0.00 0.00 3.21
62 64 3.165875 CCCTTTTCTTTCCTCCCCTTTC 58.834 50.000 0.00 0.00 0.00 2.62
69 71 3.862264 GCAATGCACCCTTTTCTTTCCTC 60.862 47.826 0.00 0.00 0.00 3.71
111 113 1.127343 CTTTCCTCCTCCTGGCTAGG 58.873 60.000 10.47 10.47 46.06 3.02
132 134 2.179018 CTTGGCGGATTTGGTGCG 59.821 61.111 0.00 0.00 45.31 5.34
204 206 2.979678 CTCTCCTCTCCTAGACTAGGCT 59.020 54.545 22.04 2.16 45.82 4.58
211 214 3.973973 CTCTTCTCCTCTCCTCTCCTAGA 59.026 52.174 0.00 0.00 0.00 2.43
230 233 3.485463 TGGTTTTGTTGGTCGATCTCT 57.515 42.857 0.00 0.00 0.00 3.10
584 898 0.673644 CAAACCCACTGGCTACTCCG 60.674 60.000 0.00 0.00 37.80 4.63
611 925 5.162925 TGAACCCCTAATTTCCTTGGAGAAA 60.163 40.000 0.00 0.00 39.92 2.52
614 928 4.263949 ACTGAACCCCTAATTTCCTTGGAG 60.264 45.833 0.00 0.00 0.00 3.86
615 929 3.660669 ACTGAACCCCTAATTTCCTTGGA 59.339 43.478 0.00 0.00 0.00 3.53
617 931 4.321974 GCAACTGAACCCCTAATTTCCTTG 60.322 45.833 0.00 0.00 0.00 3.61
618 932 3.832490 GCAACTGAACCCCTAATTTCCTT 59.168 43.478 0.00 0.00 0.00 3.36
620 934 3.431415 AGCAACTGAACCCCTAATTTCC 58.569 45.455 0.00 0.00 0.00 3.13
621 935 4.522789 TCAAGCAACTGAACCCCTAATTTC 59.477 41.667 0.00 0.00 0.00 2.17
622 936 4.479158 TCAAGCAACTGAACCCCTAATTT 58.521 39.130 0.00 0.00 0.00 1.82
680 994 2.297315 GCAAGAGGAACCCCAAGAAAAG 59.703 50.000 0.00 0.00 33.88 2.27
685 999 1.246737 GCAGCAAGAGGAACCCCAAG 61.247 60.000 0.00 0.00 33.88 3.61
754 1074 1.263217 GAAACCAAACACGAGCGACAT 59.737 47.619 0.00 0.00 0.00 3.06
762 1082 0.249280 GGGCCAAGAAACCAAACACG 60.249 55.000 4.39 0.00 0.00 4.49
784 1107 3.316071 TCAGAAGCAGAGAAGCAGAAG 57.684 47.619 0.00 0.00 36.85 2.85
785 1108 3.675502 CGATCAGAAGCAGAGAAGCAGAA 60.676 47.826 0.00 0.00 36.85 3.02
816 1139 5.423886 GGGAAGAAGAACTGGATGAACTAG 58.576 45.833 0.00 0.00 0.00 2.57
840 1163 2.497628 GAACGCGCACGAAGCTTG 60.498 61.111 5.73 0.00 43.93 4.01
851 1174 1.571919 CCAGATTAAGGAGGAACGCG 58.428 55.000 3.53 3.53 0.00 6.01
853 1176 2.236395 ACACCCAGATTAAGGAGGAACG 59.764 50.000 0.00 0.00 0.00 3.95
861 1184 4.941263 TCCGAATTTCACACCCAGATTAAG 59.059 41.667 0.00 0.00 0.00 1.85
901 1224 5.503357 CGAAACCTGAAACGAGAAAACATCA 60.503 40.000 0.00 0.00 0.00 3.07
903 1226 4.334481 ACGAAACCTGAAACGAGAAAACAT 59.666 37.500 0.00 0.00 0.00 2.71
906 1229 3.685756 ACACGAAACCTGAAACGAGAAAA 59.314 39.130 0.00 0.00 0.00 2.29
909 1232 2.198406 CACACGAAACCTGAAACGAGA 58.802 47.619 0.00 0.00 0.00 4.04
912 1235 0.306533 CCCACACGAAACCTGAAACG 59.693 55.000 0.00 0.00 0.00 3.60
975 1300 2.908073 CGCAGCCTTGTTGGTCACC 61.908 63.158 0.00 0.00 38.35 4.02
1167 1498 1.974343 AGAGAAGAGCGTGCCGACT 60.974 57.895 0.00 0.00 0.00 4.18
1353 1687 2.753029 GCAGCCTGGAACCTCTGT 59.247 61.111 0.00 0.00 0.00 3.41
1419 1753 0.967887 CCGAGAACAGAGAGCTCCCA 60.968 60.000 10.93 0.00 0.00 4.37
1460 1794 1.409427 GGAGATAGTCCACTCCGTTGG 59.591 57.143 0.00 0.00 46.10 3.77
1530 1864 1.528824 CCCAAGCCACTCCGATGAT 59.471 57.895 0.00 0.00 0.00 2.45
1533 1867 2.826777 CTTGCCCAAGCCACTCCGAT 62.827 60.000 0.00 0.00 38.69 4.18
1747 2090 5.877012 AGTCTTACAAGTGATGCATTGTAGG 59.123 40.000 11.72 11.72 41.50 3.18
1779 2122 1.861982 ACCGGGACTTACATGCTAGT 58.138 50.000 6.32 0.00 0.00 2.57
1780 2123 2.936498 CAAACCGGGACTTACATGCTAG 59.064 50.000 6.32 0.00 0.00 3.42
1781 2124 2.303600 ACAAACCGGGACTTACATGCTA 59.696 45.455 6.32 0.00 0.00 3.49
1794 2137 9.680315 TGTAAATTAGATAACAAAACAAACCGG 57.320 29.630 0.00 0.00 0.00 5.28
1909 2252 4.212214 GCTATTAGAGCGTGAAGGATTTGG 59.788 45.833 0.00 0.00 42.62 3.28
1910 2253 5.335827 GCTATTAGAGCGTGAAGGATTTG 57.664 43.478 0.00 0.00 42.62 2.32
1923 2266 4.816385 TCAAAAGCATTCCGGCTATTAGAG 59.184 41.667 0.00 0.00 45.07 2.43
1924 2267 4.776349 TCAAAAGCATTCCGGCTATTAGA 58.224 39.130 0.00 0.00 45.07 2.10
1925 2268 4.816385 TCTCAAAAGCATTCCGGCTATTAG 59.184 41.667 0.00 0.00 45.07 1.73
1926 2269 4.776349 TCTCAAAAGCATTCCGGCTATTA 58.224 39.130 0.00 0.00 45.07 0.98
1927 2270 3.620488 TCTCAAAAGCATTCCGGCTATT 58.380 40.909 0.00 0.00 45.07 1.73
1928 2271 3.209410 CTCTCAAAAGCATTCCGGCTAT 58.791 45.455 0.00 0.00 45.07 2.97
1929 2272 2.632377 CTCTCAAAAGCATTCCGGCTA 58.368 47.619 0.00 0.00 45.07 3.93
1931 2274 0.179153 GCTCTCAAAAGCATTCCGGC 60.179 55.000 0.00 0.00 42.05 6.13
1932 2275 0.453390 GGCTCTCAAAAGCATTCCGG 59.547 55.000 0.00 0.00 44.35 5.14
1933 2276 0.453390 GGGCTCTCAAAAGCATTCCG 59.547 55.000 0.00 0.00 44.35 4.30
1934 2277 1.549203 TGGGCTCTCAAAAGCATTCC 58.451 50.000 0.00 0.00 44.35 3.01
1935 2278 3.665745 TTTGGGCTCTCAAAAGCATTC 57.334 42.857 0.00 0.00 44.35 2.67
1936 2279 3.836562 AGATTTGGGCTCTCAAAAGCATT 59.163 39.130 0.00 0.00 44.35 3.56
1937 2280 3.438183 AGATTTGGGCTCTCAAAAGCAT 58.562 40.909 0.00 0.00 44.35 3.79
1938 2281 2.880443 AGATTTGGGCTCTCAAAAGCA 58.120 42.857 0.00 0.00 44.35 3.91
1939 2282 3.949842 AAGATTTGGGCTCTCAAAAGC 57.050 42.857 0.00 0.00 39.64 3.51
1940 2283 5.225642 GTGAAAGATTTGGGCTCTCAAAAG 58.774 41.667 0.00 0.00 39.64 2.27
1941 2284 4.261572 CGTGAAAGATTTGGGCTCTCAAAA 60.262 41.667 0.00 0.00 39.64 2.44
1942 2285 3.253188 CGTGAAAGATTTGGGCTCTCAAA 59.747 43.478 0.00 0.00 40.37 2.69
1943 2286 2.813754 CGTGAAAGATTTGGGCTCTCAA 59.186 45.455 0.00 0.00 0.00 3.02
1944 2287 2.426522 CGTGAAAGATTTGGGCTCTCA 58.573 47.619 0.00 0.00 0.00 3.27
1945 2288 1.131315 GCGTGAAAGATTTGGGCTCTC 59.869 52.381 0.00 0.00 0.00 3.20
1946 2289 1.168714 GCGTGAAAGATTTGGGCTCT 58.831 50.000 0.00 0.00 0.00 4.09
1947 2290 1.131315 GAGCGTGAAAGATTTGGGCTC 59.869 52.381 0.00 0.00 38.65 4.70
1948 2291 1.168714 GAGCGTGAAAGATTTGGGCT 58.831 50.000 0.00 0.00 0.00 5.19
1949 2292 1.168714 AGAGCGTGAAAGATTTGGGC 58.831 50.000 0.00 0.00 0.00 5.36
1950 2293 5.277538 GCTATTAGAGCGTGAAAGATTTGGG 60.278 44.000 0.00 0.00 42.62 4.12
2470 2858 3.197766 TGTCTATGCTCCTTCGGAACATT 59.802 43.478 4.32 0.00 39.05 2.71
2471 2859 2.766263 TGTCTATGCTCCTTCGGAACAT 59.234 45.455 4.42 4.42 40.91 2.71
2472 2860 2.166459 CTGTCTATGCTCCTTCGGAACA 59.834 50.000 0.00 0.00 32.07 3.18
2478 2866 4.873259 GGAGAAAACTGTCTATGCTCCTTC 59.127 45.833 0.00 0.00 37.91 3.46
2532 2920 4.335416 CATATTCCAGGGCATTTATCGGT 58.665 43.478 0.00 0.00 0.00 4.69
2830 3218 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3275 3715 4.748600 GGAATACGTGTTGTTAGCCTATCC 59.251 45.833 0.91 0.00 0.00 2.59
3284 3724 4.963276 CATGGATGGAATACGTGTTGTT 57.037 40.909 0.91 0.00 39.42 2.83
3773 4235 6.507023 AGAACTGCCAAGAACAACAAATTAG 58.493 36.000 0.00 0.00 0.00 1.73
4007 4473 2.270275 TTTGTGTTTGTTGCTCCACG 57.730 45.000 0.00 0.00 0.00 4.94
4059 4535 6.380995 CATTCTGATCACGAACCAATTTCAA 58.619 36.000 9.00 0.00 33.24 2.69
4067 4543 1.737838 TGCCATTCTGATCACGAACC 58.262 50.000 9.00 3.83 0.00 3.62
4410 4889 9.686683 AACAAGTAGGAGTAAATGAATAAGCAT 57.313 29.630 0.00 0.00 0.00 3.79
4424 4903 9.498176 AACGACAAATATTTAACAAGTAGGAGT 57.502 29.630 0.00 0.00 0.00 3.85
4427 4906 9.337091 CCAAACGACAAATATTTAACAAGTAGG 57.663 33.333 0.00 1.11 0.00 3.18
4451 4930 1.425066 AGGCCTGAGTGAAATTGTCCA 59.575 47.619 3.11 0.00 0.00 4.02
4452 4931 2.206576 AGGCCTGAGTGAAATTGTCC 57.793 50.000 3.11 0.00 0.00 4.02
4465 4944 8.822805 TCCCACTAATTTAATATACTAGGCCTG 58.177 37.037 17.99 8.18 0.00 4.85
4519 4998 3.419943 TGATATGCAACTGCCAACTTGA 58.580 40.909 0.00 0.00 41.18 3.02
4533 5080 8.097078 AGAGAAAGAGCATTTACATGATATGC 57.903 34.615 17.56 17.56 43.78 3.14
4559 5106 9.939802 AACTACTTCCAACGAGATATAAAAACT 57.060 29.630 0.00 0.00 0.00 2.66
4616 5164 4.192317 GGTACTGGGCAGAAAGTATGAAG 58.808 47.826 0.00 0.00 31.83 3.02
4641 5189 4.082463 ACACCGAACAAATCAACACACTTT 60.082 37.500 0.00 0.00 0.00 2.66
4648 5196 4.749245 AGATCACACCGAACAAATCAAC 57.251 40.909 0.00 0.00 0.00 3.18
5093 5738 7.994425 TCCATTTTATTTCTACACAGAGCAA 57.006 32.000 0.00 0.00 30.73 3.91
5154 5806 6.715347 ATTATACCAAAATTCAGGAGCCAC 57.285 37.500 3.35 0.00 0.00 5.01
5160 5812 9.260002 GTGCCAATAATTATACCAAAATTCAGG 57.740 33.333 0.00 0.00 0.00 3.86
5222 5875 7.067859 ACACATATAGCATGCTGAACAAATTCT 59.932 33.333 30.42 1.31 35.69 2.40
5226 5879 5.647225 TCACACATATAGCATGCTGAACAAA 59.353 36.000 30.42 9.47 0.00 2.83
5313 5967 6.220201 TGCCCAAAAATACAAGCTTTAGAAC 58.780 36.000 0.00 0.00 0.00 3.01
5397 6055 6.640907 CCAAAACCTTTTGCACTACATAGTTC 59.359 38.462 5.16 0.00 44.62 3.01
5478 6136 3.762288 AGGTGTATCTCTTCAGTGCGTTA 59.238 43.478 0.00 0.00 0.00 3.18
5573 6934 4.276926 GGATGAATTGCAGTAAGGATGACC 59.723 45.833 0.00 0.00 0.00 4.02
5657 7018 1.134250 TGGAAAAGGGTTTGCAAAGGC 60.134 47.619 13.26 1.18 41.52 4.35
5715 7077 1.516365 CTGCGACGAGACCCCGATAT 61.516 60.000 0.00 0.00 0.00 1.63
5836 7413 1.197721 ACAATCAAAGGCTTTCGCGAG 59.802 47.619 10.08 0.00 36.88 5.03
5837 7414 1.234821 ACAATCAAAGGCTTTCGCGA 58.765 45.000 10.08 3.71 36.88 5.87
5838 7415 2.892373 TACAATCAAAGGCTTTCGCG 57.108 45.000 10.08 0.00 36.88 5.87
5839 7416 7.201435 CCTTTATTTACAATCAAAGGCTTTCGC 60.201 37.037 10.08 0.00 40.29 4.70
5840 7417 8.026607 TCCTTTATTTACAATCAAAGGCTTTCG 58.973 33.333 10.08 6.32 44.38 3.46
5905 7495 5.946377 ACAACTTCTCTCCTTTTGAACAAGT 59.054 36.000 0.00 0.00 0.00 3.16
6160 7756 7.331026 TGATATCTGTGAAACCTCCTTTACAG 58.669 38.462 3.98 0.00 37.47 2.74
6168 7764 7.678218 GCACTCATTTGATATCTGTGAAACCTC 60.678 40.741 3.98 0.00 34.36 3.85
6181 7777 6.484364 TCATAGACAGGCACTCATTTGATA 57.516 37.500 0.00 0.00 34.60 2.15
6191 7787 4.096833 TGCATTCATTTCATAGACAGGCAC 59.903 41.667 0.00 0.00 0.00 5.01
6249 7846 4.334481 TGCATGCAGACATTTCATAGACAG 59.666 41.667 18.46 0.00 32.87 3.51
6250 7847 4.263435 TGCATGCAGACATTTCATAGACA 58.737 39.130 18.46 0.00 32.87 3.41
6265 7862 0.614812 TACTTCCAGAGCTGCATGCA 59.385 50.000 21.29 21.29 45.94 3.96
6316 8464 7.429340 CGGAAAAAGATGGAAAAAGATACATCG 59.571 37.037 0.00 0.00 43.29 3.84
6340 8488 2.936498 GTGGAGATATCAAACACCACGG 59.064 50.000 5.32 0.00 37.81 4.94
6345 8493 3.878778 AGCTGGTGGAGATATCAAACAC 58.121 45.455 5.32 10.16 0.00 3.32
6348 8496 9.120538 GTAAAATTAGCTGGTGGAGATATCAAA 57.879 33.333 5.32 0.00 0.00 2.69
6350 8498 8.034313 AGTAAAATTAGCTGGTGGAGATATCA 57.966 34.615 5.32 0.00 0.00 2.15
6351 8499 8.371699 AGAGTAAAATTAGCTGGTGGAGATATC 58.628 37.037 0.00 0.00 0.00 1.63
6352 8500 8.268878 AGAGTAAAATTAGCTGGTGGAGATAT 57.731 34.615 0.00 0.00 0.00 1.63
6354 8502 6.567602 AGAGTAAAATTAGCTGGTGGAGAT 57.432 37.500 0.00 0.00 0.00 2.75
6356 8504 6.655003 TGAAAGAGTAAAATTAGCTGGTGGAG 59.345 38.462 0.00 0.00 0.00 3.86
6357 8505 6.539173 TGAAAGAGTAAAATTAGCTGGTGGA 58.461 36.000 0.00 0.00 0.00 4.02
6358 8506 6.817765 TGAAAGAGTAAAATTAGCTGGTGG 57.182 37.500 0.00 0.00 0.00 4.61
6359 8507 6.803807 GCTTGAAAGAGTAAAATTAGCTGGTG 59.196 38.462 0.00 0.00 0.00 4.17
6363 8511 7.663493 AGACAGCTTGAAAGAGTAAAATTAGCT 59.337 33.333 0.00 0.00 36.94 3.32
6406 8554 9.681062 ATCGTTATGAGGAAATAAGAGGAAAAA 57.319 29.630 0.00 0.00 0.00 1.94
6446 8594 8.853077 AGTCAAATAATGTGAACTCTCAATGA 57.147 30.769 0.00 0.00 31.88 2.57
6472 8620 9.739276 TGTTCCTGTGATGAAACTAAGAATATT 57.261 29.630 0.00 0.00 0.00 1.28
6473 8621 9.911788 ATGTTCCTGTGATGAAACTAAGAATAT 57.088 29.630 0.00 0.00 0.00 1.28
6505 8656 3.802139 TCTTTCAACGGCTATTATGAGCG 59.198 43.478 0.00 0.00 43.83 5.03
6529 8681 2.412770 GCAACAAATTCAGCCAATTCCG 59.587 45.455 0.00 0.00 33.16 4.30
6557 8709 8.322091 AGTTAACATTAAGTTGCCTCACTATCT 58.678 33.333 8.61 0.00 41.50 1.98
6558 8710 8.494016 AGTTAACATTAAGTTGCCTCACTATC 57.506 34.615 8.61 0.00 41.50 2.08
6559 8711 9.379791 GTAGTTAACATTAAGTTGCCTCACTAT 57.620 33.333 8.61 0.00 41.50 2.12
6560 8712 8.369424 TGTAGTTAACATTAAGTTGCCTCACTA 58.631 33.333 8.61 0.00 41.50 2.74
6561 8713 7.172703 GTGTAGTTAACATTAAGTTGCCTCACT 59.827 37.037 8.61 0.00 41.10 3.41
6563 8715 6.428771 GGTGTAGTTAACATTAAGTTGCCTCA 59.571 38.462 8.61 0.00 41.10 3.86
6564 8716 6.128090 GGGTGTAGTTAACATTAAGTTGCCTC 60.128 42.308 8.61 0.00 41.10 4.70
6565 8717 5.708697 GGGTGTAGTTAACATTAAGTTGCCT 59.291 40.000 8.61 0.00 41.10 4.75
6573 8725 5.005094 GGCAACTGGGTGTAGTTAACATTA 58.995 41.667 8.61 0.00 41.10 1.90
6575 8727 3.418047 GGCAACTGGGTGTAGTTAACAT 58.582 45.455 8.61 0.00 41.10 2.71
6576 8728 2.853705 GGCAACTGGGTGTAGTTAACA 58.146 47.619 8.61 0.00 38.78 2.41
6647 8940 8.746922 TGCTTTGAACAACAATTCATCTAATC 57.253 30.769 0.00 0.00 38.37 1.75


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

AutoCloner maintained by Alex Coulton.