Multiple sequence alignment - TraesCS6B01G251900

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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 TraesCS6B01G251900 chr6B 100.000 7486 0 0 1 7486 451934514 451927029 0.000000e+00 13825.0
1 TraesCS6B01G251900 chr6D 95.579 3958 108 27 2958 6865 291144447 291148387 0.000000e+00 6277.0
2 TraesCS6B01G251900 chr6D 94.057 1935 58 19 93 1980 291141666 291143590 0.000000e+00 2883.0
3 TraesCS6B01G251900 chr6D 90.732 874 57 11 2093 2943 291143588 291144460 0.000000e+00 1144.0
4 TraesCS6B01G251900 chr6D 90.796 402 17 7 7105 7486 291148841 291149242 3.100000e-143 520.0
5 TraesCS6B01G251900 chr6D 83.395 271 30 13 2919 3187 133475040 133475297 3.490000e-58 237.0
6 TraesCS6B01G251900 chr6D 96.899 129 4 0 6870 6998 291148426 291148554 4.550000e-52 217.0
7 TraesCS6B01G251900 chr6D 83.168 202 26 4 2987 3188 172118006 172117813 2.150000e-40 178.0
8 TraesCS6B01G251900 chr6D 87.786 131 15 1 1968 2098 147675560 147675689 1.300000e-32 152.0
9 TraesCS6B01G251900 chr6D 96.552 87 3 0 7019 7105 291148702 291148788 2.180000e-30 145.0
10 TraesCS6B01G251900 chr6A 92.445 2515 116 34 2109 4582 432524133 432521652 0.000000e+00 3524.0
11 TraesCS6B01G251900 chr6A 95.306 1342 53 5 4602 5937 432521661 432520324 0.000000e+00 2121.0
12 TraesCS6B01G251900 chr6A 92.862 1373 45 13 639 1980 432525501 432524151 0.000000e+00 1943.0
13 TraesCS6B01G251900 chr6A 96.478 937 27 4 5936 6870 432520215 432519283 0.000000e+00 1543.0
14 TraesCS6B01G251900 chr6A 88.511 470 17 16 116 576 432526215 432525774 1.110000e-147 534.0
15 TraesCS6B01G251900 chr6A 94.681 188 7 2 7105 7290 432513795 432513609 9.500000e-74 289.0
16 TraesCS6B01G251900 chr6A 89.121 239 11 4 6845 7068 432519279 432519041 4.420000e-72 283.0
17 TraesCS6B01G251900 chr6A 95.181 166 7 1 7322 7486 432513477 432513312 2.070000e-65 261.0
18 TraesCS6B01G251900 chr6A 81.754 285 35 14 2919 3199 173428855 173429126 9.780000e-54 222.0
19 TraesCS6B01G251900 chr6A 83.511 188 23 4 3001 3188 242204027 242204206 1.290000e-37 169.0
20 TraesCS6B01G251900 chr6A 97.778 45 1 0 7064 7108 432513889 432513845 2.240000e-10 78.7
21 TraesCS6B01G251900 chr6A 100.000 33 0 0 7285 7317 432513531 432513499 2.260000e-05 62.1
22 TraesCS6B01G251900 chr3D 85.036 274 29 8 2918 3189 477254340 477254077 1.240000e-67 268.0
23 TraesCS6B01G251900 chr3D 88.636 132 15 0 1974 2105 208640712 208640581 2.160000e-35 161.0
24 TraesCS6B01G251900 chr2B 84.286 280 31 8 2914 3191 774718691 774718423 2.070000e-65 261.0
25 TraesCS6B01G251900 chr2B 92.000 125 10 0 1976 2100 148871843 148871967 7.720000e-40 176.0
26 TraesCS6B01G251900 chr2B 90.385 52 4 1 7015 7066 608447062 608447112 4.850000e-07 67.6
27 TraesCS6B01G251900 chr7D 80.723 249 32 12 2957 3201 408019876 408020112 5.970000e-41 180.0
28 TraesCS6B01G251900 chr7A 89.510 143 12 3 3061 3202 467851093 467851233 2.150000e-40 178.0
29 TraesCS6B01G251900 chr5B 92.623 122 9 0 1979 2100 38365240 38365119 7.720000e-40 176.0
30 TraesCS6B01G251900 chr5A 88.889 144 15 1 3046 3188 426551291 426551434 7.720000e-40 176.0
31 TraesCS6B01G251900 chr5A 90.833 120 11 0 1979 2098 513846717 513846598 2.160000e-35 161.0
32 TraesCS6B01G251900 chr5A 91.667 48 4 0 7241 7288 667304833 667304880 4.850000e-07 67.6
33 TraesCS6B01G251900 chr5A 94.872 39 2 0 7248 7286 582384145 582384183 2.260000e-05 62.1
34 TraesCS6B01G251900 chr1B 86.076 158 20 2 3033 3188 170836509 170836352 1.290000e-37 169.0
35 TraesCS6B01G251900 chr7B 91.597 119 10 0 1977 2095 712100755 712100637 1.670000e-36 165.0
36 TraesCS6B01G251900 chr7B 88.800 125 14 0 1974 2098 3887409 3887533 3.620000e-33 154.0
37 TraesCS6B01G251900 chr4D 90.000 120 12 0 1976 2095 502404868 502404749 1.010000e-33 156.0
38 TraesCS6B01G251900 chr4D 93.333 45 3 0 7241 7285 486932169 486932213 4.850000e-07 67.6
39 TraesCS6B01G251900 chr5D 88.800 125 14 0 1979 2103 240084475 240084599 3.620000e-33 154.0
40 TraesCS6B01G251900 chr5D 94.872 39 2 0 7248 7286 462076873 462076911 2.260000e-05 62.1
41 TraesCS6B01G251900 chr2A 90.385 52 4 1 7015 7066 660512168 660512218 4.850000e-07 67.6
42 TraesCS6B01G251900 chr2D 88.462 52 5 1 7015 7066 516706782 516706832 2.260000e-05 62.1


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 TraesCS6B01G251900 chr6B 451927029 451934514 7485 True 13825.000000 13825 100.000000 1 7486 1 chr6B.!!$R1 7485
1 TraesCS6B01G251900 chr6D 291141666 291149242 7576 False 1864.333333 6277 94.102500 93 7486 6 chr6D.!!$F3 7393
2 TraesCS6B01G251900 chr6A 432519041 432526215 7174 True 1658.000000 3524 92.453833 116 7068 6 chr6A.!!$R2 6952

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
690 910 0.097325 GACCAACAACGACGCAACAA 59.903 50.000 0.00 0.00 0.00 2.83 F
697 917 0.098025 AACGACGCAACAACACAAGG 59.902 50.000 0.00 0.00 0.00 3.61 F
1312 1559 0.108585 TCGCCAACTCTTTGCTTCCT 59.891 50.000 0.00 0.00 0.00 3.36 F
2091 2356 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
2094 2359 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 F
2165 2432 0.036732 ATCTGGCTTGCCGAGTTTCA 59.963 50.000 7.18 0.00 0.00 2.69 F
2173 2440 0.242825 TGCCGAGTTTCACGACTAGG 59.757 55.000 0.00 0.00 43.04 3.02 F
2482 2750 0.319125 CGAATCTCTTAGGAGGCGGC 60.319 60.000 0.00 0.00 39.86 6.53 F
2999 3288 0.324943 ACCGCTGATGTTAGGCAAGT 59.675 50.000 0.00 0.00 0.00 3.16 F
3323 3619 0.706433 AATTCTGATGGGCCCACTGT 59.294 50.000 31.51 12.68 0.00 3.55 F
3631 3931 1.490574 ACAAGGCGGCTCTATCTTCT 58.509 50.000 13.70 0.00 0.00 2.85 F
4268 4588 1.961277 ACTTCACCGCTTTCGCTGG 60.961 57.895 0.00 0.00 36.39 4.85 F
6045 6483 0.842030 TGGGATAGCTAGGGCCCATG 60.842 60.000 27.56 17.41 45.31 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2337 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
2076 2341 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13 R
2156 2423 0.172803 CCCCTAGTCGTGAAACTCGG 59.827 60.000 0.00 0.00 33.09 4.63 R
3488 3787 0.233848 GTGCGGAAACCAGTTACGTG 59.766 55.000 0.00 0.00 0.00 4.49 R
3491 3790 1.873698 TCTGTGCGGAAACCAGTTAC 58.126 50.000 0.00 0.00 0.00 2.50 R
3492 3791 2.614983 GTTTCTGTGCGGAAACCAGTTA 59.385 45.455 20.22 0.00 45.25 2.24 R
3961 4271 3.909587 TGCAATTCATAGCAGGCCT 57.090 47.368 0.00 0.00 35.51 5.19 R
4268 4588 7.856145 AGCATACCATATAGAGCAAATAAGC 57.144 36.000 0.00 0.00 0.00 3.09 R
4979 5304 1.017387 CTCGAGCCCCAGCAATAAAC 58.983 55.000 0.00 0.00 43.56 2.01 R
5583 5910 0.750249 TGTCAGTCAAAGCTCGACCA 59.250 50.000 11.56 2.22 33.70 4.02 R
5664 5991 5.091552 AGGATTGGGTCAGTAACTCAGTAA 58.908 41.667 0.00 0.00 40.24 2.24 R
6431 6869 1.580845 CTGAGCCAACGAAGCCAAGG 61.581 60.000 0.00 0.00 0.00 3.61 R
7356 8056 0.309922 CCAGTGTGCTGAAAGTGCAG 59.690 55.000 0.00 0.00 45.28 4.41 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
21 22 4.929819 GGGCCGATGGTGTATTATTTTT 57.070 40.909 0.00 0.00 0.00 1.94
23 24 6.394025 GGGCCGATGGTGTATTATTTTTAA 57.606 37.500 0.00 0.00 0.00 1.52
24 25 6.807789 GGGCCGATGGTGTATTATTTTTAAA 58.192 36.000 0.00 0.00 0.00 1.52
25 26 7.266400 GGGCCGATGGTGTATTATTTTTAAAA 58.734 34.615 0.00 0.00 0.00 1.52
26 27 7.764901 GGGCCGATGGTGTATTATTTTTAAAAA 59.235 33.333 15.38 15.38 0.00 1.94
27 28 9.320352 GGCCGATGGTGTATTATTTTTAAAAAT 57.680 29.630 25.18 25.18 41.24 1.82
54 55 9.900710 AAAAATATCGGCGTAATATTTATGCAA 57.099 25.926 20.18 2.32 37.99 4.08
55 56 9.900710 AAAATATCGGCGTAATATTTATGCAAA 57.099 25.926 20.18 2.03 37.99 3.68
61 62 9.900710 TCGGCGTAATATTTATGCAAATTAATT 57.099 25.926 6.85 0.00 35.88 1.40
105 106 7.796958 AAAAATTTAGCTCATTTCTACACGC 57.203 32.000 0.00 0.00 0.00 5.34
106 107 6.743575 AAATTTAGCTCATTTCTACACGCT 57.256 33.333 0.00 0.00 0.00 5.07
107 108 6.743575 AATTTAGCTCATTTCTACACGCTT 57.256 33.333 0.00 0.00 0.00 4.68
108 109 7.843490 AATTTAGCTCATTTCTACACGCTTA 57.157 32.000 0.00 0.00 0.00 3.09
109 110 7.843490 ATTTAGCTCATTTCTACACGCTTAA 57.157 32.000 0.00 0.00 0.00 1.85
154 160 5.245301 GGGCCAGGTAACACTTAAATTTTCT 59.755 40.000 4.39 0.00 41.41 2.52
156 162 5.633601 GCCAGGTAACACTTAAATTTTCTGC 59.366 40.000 0.00 0.00 41.41 4.26
230 238 5.296780 CGAAATCACATTATACACCTTGCCT 59.703 40.000 0.00 0.00 0.00 4.75
241 249 4.257267 ACACCTTGCCTTTTAAGATTGC 57.743 40.909 0.00 0.00 0.00 3.56
335 344 5.647589 TGACGCCAAACATAGAACTACTAG 58.352 41.667 0.00 0.00 34.35 2.57
545 555 3.443588 ATCGATGGACCGATCGCA 58.556 55.556 10.32 2.57 45.03 5.10
549 559 4.241555 ATGGACCGATCGCAGGGC 62.242 66.667 10.32 0.00 35.57 5.19
613 623 2.509336 CGTCCACCGAGCCATGTC 60.509 66.667 0.00 0.00 39.56 3.06
615 625 4.451150 TCCACCGAGCCATGTCGC 62.451 66.667 0.38 0.00 38.69 5.19
686 906 2.518312 CGTGACCAACAACGACGCA 61.518 57.895 0.00 0.00 0.00 5.24
687 907 1.716760 GTGACCAACAACGACGCAA 59.283 52.632 0.00 0.00 0.00 4.85
690 910 0.097325 GACCAACAACGACGCAACAA 59.903 50.000 0.00 0.00 0.00 2.83
691 911 0.179184 ACCAACAACGACGCAACAAC 60.179 50.000 0.00 0.00 0.00 3.32
693 913 0.904511 CAACAACGACGCAACAACAC 59.095 50.000 0.00 0.00 0.00 3.32
694 914 0.517755 AACAACGACGCAACAACACA 59.482 45.000 0.00 0.00 0.00 3.72
695 915 0.517755 ACAACGACGCAACAACACAA 59.482 45.000 0.00 0.00 0.00 3.33
696 916 1.179332 CAACGACGCAACAACACAAG 58.821 50.000 0.00 0.00 0.00 3.16
697 917 0.098025 AACGACGCAACAACACAAGG 59.902 50.000 0.00 0.00 0.00 3.61
698 918 1.654137 CGACGCAACAACACAAGGC 60.654 57.895 0.00 0.00 0.00 4.35
889 1110 1.606737 GCCAAAAGCAGAGACGAGTCT 60.607 52.381 5.31 5.31 41.71 3.24
1172 1402 1.384989 CCGCGCCCTCTCTTTCTCTA 61.385 60.000 0.00 0.00 0.00 2.43
1303 1550 0.530744 TGCTAATCGTCGCCAACTCT 59.469 50.000 0.00 0.00 0.00 3.24
1312 1559 0.108585 TCGCCAACTCTTTGCTTCCT 59.891 50.000 0.00 0.00 0.00 3.36
1514 1761 7.291182 ACTTGGAGATGGTCTAGCATTAGTAAT 59.709 37.037 0.00 0.00 0.00 1.89
1574 1829 5.527582 GCTTCAAGGACTAACTGTCTCAAAA 59.472 40.000 0.00 0.00 44.74 2.44
1660 1915 1.140652 CCTTGATCTGCCCCTCTCTTC 59.859 57.143 0.00 0.00 0.00 2.87
1704 1959 0.657840 AGAATTGGCGCGTTATCTGC 59.342 50.000 8.43 0.00 0.00 4.26
1718 1973 2.496899 ATCTGCGTGAGTTTGGGAAT 57.503 45.000 0.00 0.00 0.00 3.01
1734 1989 0.463654 GAATGGGTAGCATGCGGTCA 60.464 55.000 13.01 10.05 0.00 4.02
1784 2039 0.680618 CTTGTTGCTTCCATTGGCCA 59.319 50.000 0.00 0.00 0.00 5.36
1911 2166 2.088950 ACGCAAAGTACATACCGCTT 57.911 45.000 0.00 0.00 0.00 4.68
1988 2253 9.742144 ATTACTACTACATATGTACTCCCTCTG 57.258 37.037 11.62 2.60 0.00 3.35
1989 2254 7.151694 ACTACTACATATGTACTCCCTCTGT 57.848 40.000 11.62 8.15 0.00 3.41
1991 2256 6.963083 ACTACATATGTACTCCCTCTGTTC 57.037 41.667 11.62 0.00 0.00 3.18
1993 2258 3.637229 ACATATGTACTCCCTCTGTTCGG 59.363 47.826 6.56 0.00 0.00 4.30
1995 2260 2.297698 TGTACTCCCTCTGTTCGGAA 57.702 50.000 0.00 0.00 0.00 4.30
1996 2261 2.816411 TGTACTCCCTCTGTTCGGAAT 58.184 47.619 0.00 0.00 0.00 3.01
1997 2262 3.170717 TGTACTCCCTCTGTTCGGAATT 58.829 45.455 0.00 0.00 0.00 2.17
1998 2263 4.346730 TGTACTCCCTCTGTTCGGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
1999 2264 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2000 2265 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2002 2267 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2004 2269 3.933332 CCCTCTGTTCGGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2005 2270 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2007 2272 2.734606 CTGTTCGGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
2008 2273 3.331150 TGTTCGGAATTACTTGTCGCAT 58.669 40.909 0.00 0.00 0.00 4.73
2009 2274 4.496360 TGTTCGGAATTACTTGTCGCATA 58.504 39.130 0.00 0.00 0.00 3.14
2010 2275 4.930405 TGTTCGGAATTACTTGTCGCATAA 59.070 37.500 0.00 0.00 0.00 1.90
2011 2276 5.408909 TGTTCGGAATTACTTGTCGCATAAA 59.591 36.000 0.00 0.00 0.00 1.40
2012 2277 6.092944 TGTTCGGAATTACTTGTCGCATAAAT 59.907 34.615 0.00 0.00 0.00 1.40
2013 2278 6.043327 TCGGAATTACTTGTCGCATAAATG 57.957 37.500 0.00 0.00 0.00 2.32
2014 2279 5.007234 TCGGAATTACTTGTCGCATAAATGG 59.993 40.000 0.00 0.00 0.00 3.16
2015 2280 5.007234 CGGAATTACTTGTCGCATAAATGGA 59.993 40.000 0.00 0.00 0.00 3.41
2016 2281 6.293407 CGGAATTACTTGTCGCATAAATGGAT 60.293 38.462 0.00 0.00 0.00 3.41
2017 2282 7.095397 CGGAATTACTTGTCGCATAAATGGATA 60.095 37.037 0.00 0.00 0.00 2.59
2018 2283 8.564574 GGAATTACTTGTCGCATAAATGGATAA 58.435 33.333 0.00 0.00 0.00 1.75
2019 2284 9.944663 GAATTACTTGTCGCATAAATGGATAAA 57.055 29.630 0.00 0.00 0.00 1.40
2024 2289 9.950680 ACTTGTCGCATAAATGGATAAAAATAG 57.049 29.630 0.00 0.00 0.00 1.73
2059 2324 9.530633 AGAACTAAAATACGTTCAGATACATCC 57.469 33.333 0.00 0.00 41.40 3.51
2060 2325 9.309516 GAACTAAAATACGTTCAGATACATCCA 57.690 33.333 0.00 0.00 39.36 3.41
2061 2326 9.832445 AACTAAAATACGTTCAGATACATCCAT 57.168 29.630 0.00 0.00 0.00 3.41
2062 2327 9.832445 ACTAAAATACGTTCAGATACATCCATT 57.168 29.630 0.00 0.00 0.00 3.16
2065 2330 8.964476 AAATACGTTCAGATACATCCATTTCT 57.036 30.769 0.00 0.00 0.00 2.52
2066 2331 8.594881 AATACGTTCAGATACATCCATTTCTC 57.405 34.615 0.00 0.00 0.00 2.87
2067 2332 6.227298 ACGTTCAGATACATCCATTTCTCT 57.773 37.500 0.00 0.00 0.00 3.10
2068 2333 7.348080 ACGTTCAGATACATCCATTTCTCTA 57.652 36.000 0.00 0.00 0.00 2.43
2069 2334 7.782049 ACGTTCAGATACATCCATTTCTCTAA 58.218 34.615 0.00 0.00 0.00 2.10
2070 2335 7.707035 ACGTTCAGATACATCCATTTCTCTAAC 59.293 37.037 0.00 0.00 0.00 2.34
2071 2336 7.706607 CGTTCAGATACATCCATTTCTCTAACA 59.293 37.037 0.00 0.00 0.00 2.41
2072 2337 9.383519 GTTCAGATACATCCATTTCTCTAACAA 57.616 33.333 0.00 0.00 0.00 2.83
2073 2338 9.605275 TTCAGATACATCCATTTCTCTAACAAG 57.395 33.333 0.00 0.00 0.00 3.16
2074 2339 8.762645 TCAGATACATCCATTTCTCTAACAAGT 58.237 33.333 0.00 0.00 0.00 3.16
2080 2345 9.178758 ACATCCATTTCTCTAACAAGTATTTCC 57.821 33.333 0.00 0.00 0.00 3.13
2081 2346 7.843490 TCCATTTCTCTAACAAGTATTTCCG 57.157 36.000 0.00 0.00 0.00 4.30
2082 2347 6.821665 TCCATTTCTCTAACAAGTATTTCCGG 59.178 38.462 0.00 0.00 0.00 5.14
2083 2348 6.821665 CCATTTCTCTAACAAGTATTTCCGGA 59.178 38.462 0.00 0.00 0.00 5.14
2084 2349 7.201617 CCATTTCTCTAACAAGTATTTCCGGAC 60.202 40.741 1.83 0.00 0.00 4.79
2085 2350 4.990257 TCTCTAACAAGTATTTCCGGACG 58.010 43.478 1.83 0.00 0.00 4.79
2086 2351 4.110482 CTCTAACAAGTATTTCCGGACGG 58.890 47.826 1.83 3.96 0.00 4.79
2087 2352 3.763360 TCTAACAAGTATTTCCGGACGGA 59.237 43.478 1.83 9.76 43.52 4.69
2088 2353 2.667473 ACAAGTATTTCCGGACGGAG 57.333 50.000 13.64 3.15 46.06 4.63
2089 2354 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2090 2355 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2091 2356 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2092 2357 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2093 2358 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2094 2359 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2095 2360 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
2096 2361 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
2097 2362 1.070604 TCCGGACGGAGGGAGTATAT 58.929 55.000 9.76 0.00 39.76 0.86
2098 2363 1.426598 TCCGGACGGAGGGAGTATATT 59.573 52.381 9.76 0.00 39.76 1.28
2099 2364 2.158415 TCCGGACGGAGGGAGTATATTT 60.158 50.000 9.76 0.00 39.76 1.40
2100 2365 2.029290 CCGGACGGAGGGAGTATATTTG 60.029 54.545 4.40 0.00 37.50 2.32
2101 2366 2.889045 CGGACGGAGGGAGTATATTTGA 59.111 50.000 0.00 0.00 0.00 2.69
2102 2367 3.057456 CGGACGGAGGGAGTATATTTGAG 60.057 52.174 0.00 0.00 0.00 3.02
2103 2368 3.896272 GGACGGAGGGAGTATATTTGAGT 59.104 47.826 0.00 0.00 0.00 3.41
2104 2369 4.262079 GGACGGAGGGAGTATATTTGAGTG 60.262 50.000 0.00 0.00 0.00 3.51
2105 2370 3.069729 ACGGAGGGAGTATATTTGAGTGC 59.930 47.826 0.00 0.00 0.00 4.40
2106 2371 3.322254 CGGAGGGAGTATATTTGAGTGCT 59.678 47.826 0.00 0.00 0.00 4.40
2107 2372 4.523173 CGGAGGGAGTATATTTGAGTGCTA 59.477 45.833 0.00 0.00 0.00 3.49
2108 2373 5.336055 CGGAGGGAGTATATTTGAGTGCTAG 60.336 48.000 0.00 0.00 0.00 3.42
2109 2374 5.474825 GAGGGAGTATATTTGAGTGCTAGC 58.525 45.833 8.10 8.10 0.00 3.42
2110 2375 5.151454 AGGGAGTATATTTGAGTGCTAGCT 58.849 41.667 17.23 0.00 0.00 3.32
2111 2376 6.315714 AGGGAGTATATTTGAGTGCTAGCTA 58.684 40.000 17.23 0.00 0.00 3.32
2112 2377 6.957020 AGGGAGTATATTTGAGTGCTAGCTAT 59.043 38.462 17.23 3.89 0.00 2.97
2113 2378 7.123547 AGGGAGTATATTTGAGTGCTAGCTATC 59.876 40.741 17.23 13.87 0.00 2.08
2114 2379 7.123547 GGGAGTATATTTGAGTGCTAGCTATCT 59.876 40.741 17.23 11.44 0.00 1.98
2115 2380 9.179909 GGAGTATATTTGAGTGCTAGCTATCTA 57.820 37.037 17.23 7.93 0.00 1.98
2140 2405 7.496529 TCTCAGAAACACAATTCAGTAAAGG 57.503 36.000 0.00 0.00 0.00 3.11
2148 2415 6.624423 ACACAATTCAGTAAAGGCAATCATC 58.376 36.000 0.00 0.00 0.00 2.92
2165 2432 0.036732 ATCTGGCTTGCCGAGTTTCA 59.963 50.000 7.18 0.00 0.00 2.69
2167 2434 2.175184 CTGGCTTGCCGAGTTTCACG 62.175 60.000 7.18 0.00 0.00 4.35
2168 2435 1.959226 GGCTTGCCGAGTTTCACGA 60.959 57.895 0.00 0.00 0.00 4.35
2173 2440 0.242825 TGCCGAGTTTCACGACTAGG 59.757 55.000 0.00 0.00 43.04 3.02
2176 2443 0.886563 CGAGTTTCACGACTAGGGGT 59.113 55.000 0.00 0.00 0.00 4.95
2182 2449 2.754658 ACGACTAGGGGTGCTCCG 60.755 66.667 0.00 0.00 36.01 4.63
2185 2452 1.380112 GACTAGGGGTGCTCCGTCT 60.380 63.158 0.00 1.93 35.00 4.18
2187 2454 1.076632 CTAGGGGTGCTCCGTCTCT 60.077 63.158 0.00 0.00 35.00 3.10
2213 2480 3.644774 GTAGGCACTAGCGAGGAAC 57.355 57.895 0.00 0.00 44.14 3.62
2298 2565 8.945195 TTCTATGAAATTGATATGCCATTCCT 57.055 30.769 0.00 0.00 0.00 3.36
2345 2613 7.759489 ATTTGGCTTGTAGTAAAGATCACAA 57.241 32.000 0.00 0.00 0.00 3.33
2461 2729 3.737774 GCTTGTTTTCTTGTCATGGCTTC 59.262 43.478 0.00 0.00 0.00 3.86
2482 2750 0.319125 CGAATCTCTTAGGAGGCGGC 60.319 60.000 0.00 0.00 39.86 6.53
2485 2753 2.930777 ATCTCTTAGGAGGCGGCGGT 62.931 60.000 9.78 0.00 39.86 5.68
2515 2783 3.350219 TTCTTCAAGGGTCCACTATGC 57.650 47.619 0.00 0.00 0.00 3.14
2524 2792 1.134280 GGTCCACTATGCTGACATGCT 60.134 52.381 0.00 0.00 37.04 3.79
2539 2807 2.045634 GCTGCAGCACCTCCATCA 60.046 61.111 33.36 0.00 41.59 3.07
2556 2824 1.557099 TCACGCTCTCCTACATGGTT 58.443 50.000 0.00 0.00 37.07 3.67
2558 2826 2.426024 TCACGCTCTCCTACATGGTTAC 59.574 50.000 0.00 0.00 37.07 2.50
2569 2837 4.451096 CCTACATGGTTACCATTGATACGC 59.549 45.833 15.07 0.00 42.23 4.42
2600 2868 7.290118 CACTTCTTTTGTCTTGTTTGGTTTTG 58.710 34.615 0.00 0.00 0.00 2.44
2603 2871 5.929415 TCTTTTGTCTTGTTTGGTTTTGGAC 59.071 36.000 0.00 0.00 0.00 4.02
2607 2875 2.231478 TCTTGTTTGGTTTTGGACGCAA 59.769 40.909 0.00 0.00 0.00 4.85
2618 2886 2.036958 TGGACGCAATTCTATGTGGG 57.963 50.000 0.00 0.00 35.13 4.61
2652 2932 1.672356 GGTGGCTCGTTCAGTGCAT 60.672 57.895 0.00 0.00 40.84 3.96
2665 2945 6.072783 TCGTTCAGTGCATTGTATGAATTTGA 60.073 34.615 9.23 4.00 34.45 2.69
2683 2969 8.956426 TGAATTTGAAGATAGAATGTTGGTACC 58.044 33.333 4.43 4.43 0.00 3.34
2707 2993 5.230942 GTCTTGTGATGTAGCACTAGTTGT 58.769 41.667 10.51 0.00 40.75 3.32
2709 2995 6.866770 GTCTTGTGATGTAGCACTAGTTGTAA 59.133 38.462 10.51 0.00 40.75 2.41
2763 3052 2.166346 TGCTTGGGGTTGGGATGGA 61.166 57.895 0.00 0.00 0.00 3.41
2821 3110 6.127786 GCAGAGCTTCAAGTAGGAATCATTTT 60.128 38.462 0.00 0.00 0.00 1.82
2886 3175 6.153510 AGGAAGAATTTTACCCTGCTTGAATC 59.846 38.462 0.00 0.00 0.00 2.52
2999 3288 0.324943 ACCGCTGATGTTAGGCAAGT 59.675 50.000 0.00 0.00 0.00 3.16
3093 3382 1.464608 GCTAAACATGTTGAGCGCTCA 59.535 47.619 35.30 35.30 37.32 4.26
3136 3425 5.647225 TCGTTGGATTGACATGAATTGATGA 59.353 36.000 12.12 0.00 0.00 2.92
3323 3619 0.706433 AATTCTGATGGGCCCACTGT 59.294 50.000 31.51 12.68 0.00 3.55
3420 3718 7.702348 GGAGTAGAATCATTGCCAAATTACAAC 59.298 37.037 0.00 0.00 0.00 3.32
3534 3834 7.939039 AGAAACTTCCTGATGACATTTCTGTTA 59.061 33.333 0.00 0.00 36.63 2.41
3535 3835 8.641498 AAACTTCCTGATGACATTTCTGTTAT 57.359 30.769 0.00 0.00 35.14 1.89
3631 3931 1.490574 ACAAGGCGGCTCTATCTTCT 58.509 50.000 13.70 0.00 0.00 2.85
3649 3949 5.189928 TCTTCTTATAAATTCCCTTGCGCA 58.810 37.500 5.66 5.66 0.00 6.09
3676 3976 3.055819 TCATTACACTCCTTCAGGTGCTC 60.056 47.826 0.00 0.00 36.99 4.26
3808 4112 2.682155 AATGTTTTGTGCCCACGTTT 57.318 40.000 0.00 0.00 0.00 3.60
3827 4131 5.137403 CGTTTTGTCCGATCAACAGTAAAG 58.863 41.667 0.00 0.00 0.00 1.85
3828 4132 5.449304 GTTTTGTCCGATCAACAGTAAAGG 58.551 41.667 0.00 0.00 0.00 3.11
3830 4134 4.819105 TGTCCGATCAACAGTAAAGGAT 57.181 40.909 0.00 0.00 0.00 3.24
3883 4189 7.921786 TGTGGTCTTTGAAAGTAATGATAGG 57.078 36.000 4.68 0.00 0.00 2.57
3911 4217 5.352569 CCAAAAGCCACATACTCTACTTCTG 59.647 44.000 0.00 0.00 0.00 3.02
3912 4218 5.746990 AAAGCCACATACTCTACTTCTGT 57.253 39.130 0.00 0.00 0.00 3.41
3961 4271 8.540388 ACTTTCTTATTGGAGCTGTAGACAATA 58.460 33.333 0.00 0.00 35.40 1.90
4010 4330 6.978659 CAGTGATATAGTTGTCGGTGTATTGT 59.021 38.462 0.00 0.00 0.00 2.71
4268 4588 1.961277 ACTTCACCGCTTTCGCTGG 60.961 57.895 0.00 0.00 36.39 4.85
4550 4870 2.684881 CAGGTAAATGTCCAGGCATGTC 59.315 50.000 0.00 0.00 0.00 3.06
4575 4895 7.066404 TCACTTTACTTTGCATTTGTACTGTCA 59.934 33.333 0.00 0.00 0.00 3.58
4604 4926 5.584649 TGTTATTCCATAGCCAAGAAACTCG 59.415 40.000 0.00 0.00 0.00 4.18
4754 5076 6.266323 TCTTTAGTTCATCAGTAGTGATCGC 58.734 40.000 10.23 0.00 41.85 4.58
4889 5211 7.761409 TCCTTGTGTTTCATTATACTGCATTC 58.239 34.615 0.00 0.00 0.00 2.67
4979 5304 2.286418 GGCTTTGATTGTATTCGGAGCG 60.286 50.000 0.00 0.00 30.97 5.03
5101 5426 3.621715 CGTATTGGTAAGCACCTTCCTTC 59.378 47.826 0.00 0.00 45.98 3.46
5407 5732 2.878406 CTGGTTTTCAGGTATATGCGGG 59.122 50.000 0.00 0.00 39.76 6.13
5466 5793 6.437793 AGGCATCTAAAGACTACAGTACTTGT 59.562 38.462 0.00 0.00 43.96 3.16
5664 5991 6.636454 TTCCTGTGATCTTACCCAATAACT 57.364 37.500 0.00 0.00 0.00 2.24
5844 6171 7.336931 TCTTCTTGGTTGCTGATTAATCTTACC 59.663 37.037 16.24 15.91 0.00 2.85
5851 6178 4.058817 GCTGATTAATCTTACCCCTGACG 58.941 47.826 16.24 0.00 0.00 4.35
6045 6483 0.842030 TGGGATAGCTAGGGCCCATG 60.842 60.000 27.56 17.41 45.31 3.66
6063 6501 5.012354 GCCCATGGGTATCAATCATTTTGAT 59.988 40.000 31.58 6.14 36.74 2.57
6259 6697 9.760077 ATTTTGAAATCTTCTTCATGATATGCC 57.240 29.630 0.00 0.00 35.31 4.40
6431 6869 1.334869 CTTAATGTCATCGGCCAAGGC 59.665 52.381 2.24 1.52 41.06 4.35
6657 7095 5.429762 TCTCCTGGGTAGAACATGAATGAAT 59.570 40.000 0.00 0.00 0.00 2.57
6841 7306 7.518161 TCAAGTAATAGCTGTGTCGATTTTTG 58.482 34.615 0.00 0.00 0.00 2.44
6845 7310 3.885484 AGCTGTGTCGATTTTTGTCTG 57.115 42.857 0.00 0.00 0.00 3.51
6891 7391 1.620323 GAAACCAGGCTCCAAAATGCT 59.380 47.619 0.00 0.00 0.00 3.79
6983 7483 0.826062 GGCCCTGTTTGGATTGGATG 59.174 55.000 0.00 0.00 38.35 3.51
7030 7657 6.428159 AACTTGAGTTAAATACTGTGGAGCAG 59.572 38.462 0.00 0.00 42.71 4.24
7050 7677 7.201652 GGAGCAGACTAATTTTACACTCAATCC 60.202 40.741 0.00 0.00 0.00 3.01
7187 7869 3.708890 TGAAATGCGCATCATCCAATTC 58.291 40.909 25.53 20.70 33.40 2.17
7189 7871 1.311859 ATGCGCATCATCCAATTCGT 58.688 45.000 19.28 0.00 0.00 3.85
7227 7909 7.451877 ACAAACAGAGAGATACTGACCTTTCTA 59.548 37.037 0.00 0.00 38.55 2.10
7235 7917 6.578023 AGATACTGACCTTTCTAACATCTGC 58.422 40.000 0.00 0.00 0.00 4.26
7239 7921 4.072131 TGACCTTTCTAACATCTGCAACC 58.928 43.478 0.00 0.00 0.00 3.77
7252 7934 6.449698 ACATCTGCAACCAAATTTGACTTAG 58.550 36.000 19.86 10.50 0.00 2.18
7254 7936 4.892934 TCTGCAACCAAATTTGACTTAGGT 59.107 37.500 19.86 4.78 0.00 3.08
7303 7985 6.832900 TGGAATGGAGTATATCAAAATGCACA 59.167 34.615 0.00 0.00 0.00 4.57
7317 7999 6.259608 TCAAAATGCACAAGTTTAACCAATGG 59.740 34.615 0.00 0.00 0.00 3.16
7320 8019 3.059166 GCACAAGTTTAACCAATGGCAG 58.941 45.455 0.00 0.00 0.00 4.85
7372 8072 4.670221 GCTTATACTGCACTTTCAGCACAC 60.670 45.833 0.00 0.00 37.02 3.82
7389 8089 3.492309 GCACACTGGAGTATCAGATCAGG 60.492 52.174 0.00 0.00 38.11 3.86
7398 8098 6.268617 TGGAGTATCAGATCAGGGAACATAAG 59.731 42.308 0.00 0.00 36.25 1.73
7409 8109 6.406370 TCAGGGAACATAAGTACTGAACATG 58.594 40.000 0.00 0.95 33.23 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.929819 AAAAATAATACACCATCGGCCC 57.070 40.909 0.00 0.00 0.00 5.80
1 2 8.705048 TTTTTAAAAATAATACACCATCGGCC 57.295 30.769 9.31 0.00 0.00 6.13
28 29 9.900710 TTGCATAAATATTACGCCGATATTTTT 57.099 25.926 8.49 4.03 39.29 1.94
29 30 9.900710 TTTGCATAAATATTACGCCGATATTTT 57.099 25.926 8.49 0.00 39.29 1.82
35 36 9.900710 AATTAATTTGCATAAATATTACGCCGA 57.099 25.926 0.00 0.00 35.50 5.54
81 82 7.593825 AGCGTGTAGAAATGAGCTAAATTTTT 58.406 30.769 7.97 5.74 32.73 1.94
82 83 7.145932 AGCGTGTAGAAATGAGCTAAATTTT 57.854 32.000 7.97 0.00 32.73 1.82
83 84 6.743575 AGCGTGTAGAAATGAGCTAAATTT 57.256 33.333 6.57 6.57 32.73 1.82
84 85 6.743575 AAGCGTGTAGAAATGAGCTAAATT 57.256 33.333 0.00 0.00 34.24 1.82
85 86 7.843490 TTAAGCGTGTAGAAATGAGCTAAAT 57.157 32.000 0.00 0.00 34.24 1.40
86 87 7.661127 TTTAAGCGTGTAGAAATGAGCTAAA 57.339 32.000 0.00 0.00 34.24 1.85
87 88 7.661127 TTTTAAGCGTGTAGAAATGAGCTAA 57.339 32.000 0.00 0.00 34.24 3.09
88 89 7.661127 TTTTTAAGCGTGTAGAAATGAGCTA 57.339 32.000 0.00 0.00 34.24 3.32
89 90 6.554334 TTTTTAAGCGTGTAGAAATGAGCT 57.446 33.333 0.00 0.00 36.40 4.09
109 110 5.054477 CCCGATATACATCCTCGTGTTTTT 58.946 41.667 0.00 0.00 33.62 1.94
230 238 3.610585 CGCGTTCAAGGGCAATCTTAAAA 60.611 43.478 0.00 0.00 0.00 1.52
241 249 0.041312 CTTGTTCACGCGTTCAAGGG 60.041 55.000 26.71 11.77 35.21 3.95
613 623 3.727258 TCCAACATGGGAGGGGCG 61.727 66.667 0.00 0.00 38.32 6.13
686 906 0.179103 GCTGCTTGCCTTGTGTTGTT 60.179 50.000 0.00 0.00 35.15 2.83
687 907 1.321805 TGCTGCTTGCCTTGTGTTGT 61.322 50.000 0.00 0.00 42.00 3.32
690 910 1.039233 ACTTGCTGCTTGCCTTGTGT 61.039 50.000 0.00 0.00 42.00 3.72
691 911 0.953727 TACTTGCTGCTTGCCTTGTG 59.046 50.000 0.00 0.00 42.00 3.33
693 913 2.229543 TGATTACTTGCTGCTTGCCTTG 59.770 45.455 0.00 0.00 42.00 3.61
694 914 2.229784 GTGATTACTTGCTGCTTGCCTT 59.770 45.455 0.00 0.00 42.00 4.35
695 915 1.815003 GTGATTACTTGCTGCTTGCCT 59.185 47.619 0.00 0.00 42.00 4.75
696 916 1.135286 GGTGATTACTTGCTGCTTGCC 60.135 52.381 0.00 0.00 42.00 4.52
697 917 1.541147 TGGTGATTACTTGCTGCTTGC 59.459 47.619 0.00 0.00 43.25 4.01
698 918 2.415090 GCTGGTGATTACTTGCTGCTTG 60.415 50.000 0.00 0.00 0.00 4.01
706 926 0.255890 ATGCCCGCTGGTGATTACTT 59.744 50.000 0.00 0.00 0.00 2.24
813 1033 4.933064 CTCGGCCGCGCTAGGAAG 62.933 72.222 23.51 5.96 0.00 3.46
889 1110 2.668212 CCGTTTGGGAGCGAGCAA 60.668 61.111 0.00 0.00 38.47 3.91
1303 1550 1.693627 TAACGGCCAAAGGAAGCAAA 58.306 45.000 2.24 0.00 0.00 3.68
1538 1787 5.564550 AGTCCTTGAAGCACTCAAATACAT 58.435 37.500 3.24 0.00 43.54 2.29
1643 1898 0.341258 AGGAAGAGAGGGGCAGATCA 59.659 55.000 0.00 0.00 0.00 2.92
1651 1906 0.965439 CCGCATAGAGGAAGAGAGGG 59.035 60.000 0.00 0.00 0.00 4.30
1660 1915 0.391661 ACAGCACAACCGCATAGAGG 60.392 55.000 0.00 0.00 0.00 3.69
1704 1959 2.356135 CTACCCATTCCCAAACTCACG 58.644 52.381 0.00 0.00 0.00 4.35
1718 1973 2.584064 CTGACCGCATGCTACCCA 59.416 61.111 17.13 7.37 0.00 4.51
1734 1989 0.698238 TAGCAACAATCACCAGGCCT 59.302 50.000 0.00 0.00 0.00 5.19
1784 2039 7.667219 CCCAAGTAGCTGAATAATGGATGTAAT 59.333 37.037 0.00 0.00 0.00 1.89
1911 2166 0.537143 ACGTACGGTGACACCCACTA 60.537 55.000 21.06 3.33 45.03 2.74
1928 2183 5.406767 ACTAGCTCTTACTGACGAATACG 57.593 43.478 0.00 0.00 45.75 3.06
1980 2245 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
1981 2246 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
1982 2247 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
1983 2248 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
1984 2249 3.060895 GCGACAAGTAATTCCGAACAGAG 59.939 47.826 0.00 0.00 0.00 3.35
1985 2250 2.991190 GCGACAAGTAATTCCGAACAGA 59.009 45.455 0.00 0.00 0.00 3.41
1986 2251 2.734606 TGCGACAAGTAATTCCGAACAG 59.265 45.455 0.00 0.00 0.00 3.16
1987 2252 2.756829 TGCGACAAGTAATTCCGAACA 58.243 42.857 0.00 0.00 0.00 3.18
1988 2253 5.459110 TTATGCGACAAGTAATTCCGAAC 57.541 39.130 0.00 0.00 0.00 3.95
1989 2254 6.457663 CCATTTATGCGACAAGTAATTCCGAA 60.458 38.462 0.00 0.00 0.00 4.30
1991 2256 5.007234 TCCATTTATGCGACAAGTAATTCCG 59.993 40.000 0.00 0.00 0.00 4.30
1993 2258 9.944663 TTTATCCATTTATGCGACAAGTAATTC 57.055 29.630 0.00 0.00 0.00 2.17
1998 2263 9.950680 CTATTTTTATCCATTTATGCGACAAGT 57.049 29.630 0.00 0.00 0.00 3.16
2033 2298 9.530633 GGATGTATCTGAACGTATTTTAGTTCT 57.469 33.333 9.30 0.00 44.95 3.01
2034 2299 9.309516 TGGATGTATCTGAACGTATTTTAGTTC 57.690 33.333 0.00 1.80 44.93 3.01
2035 2300 9.832445 ATGGATGTATCTGAACGTATTTTAGTT 57.168 29.630 0.00 0.00 0.00 2.24
2036 2301 9.832445 AATGGATGTATCTGAACGTATTTTAGT 57.168 29.630 0.00 0.00 0.00 2.24
2039 2304 9.396022 AGAAATGGATGTATCTGAACGTATTTT 57.604 29.630 0.00 0.00 0.00 1.82
2040 2305 8.964476 AGAAATGGATGTATCTGAACGTATTT 57.036 30.769 0.00 0.00 0.00 1.40
2041 2306 8.424918 AGAGAAATGGATGTATCTGAACGTATT 58.575 33.333 0.00 0.00 0.00 1.89
2042 2307 7.957002 AGAGAAATGGATGTATCTGAACGTAT 58.043 34.615 0.00 0.00 0.00 3.06
2043 2308 7.348080 AGAGAAATGGATGTATCTGAACGTA 57.652 36.000 0.00 0.00 0.00 3.57
2044 2309 6.227298 AGAGAAATGGATGTATCTGAACGT 57.773 37.500 0.00 0.00 0.00 3.99
2045 2310 7.706607 TGTTAGAGAAATGGATGTATCTGAACG 59.293 37.037 0.00 0.00 0.00 3.95
2046 2311 8.948631 TGTTAGAGAAATGGATGTATCTGAAC 57.051 34.615 0.00 0.00 0.00 3.18
2047 2312 9.605275 CTTGTTAGAGAAATGGATGTATCTGAA 57.395 33.333 0.00 0.00 0.00 3.02
2048 2313 8.762645 ACTTGTTAGAGAAATGGATGTATCTGA 58.237 33.333 0.00 0.00 0.00 3.27
2049 2314 8.954950 ACTTGTTAGAGAAATGGATGTATCTG 57.045 34.615 0.00 0.00 0.00 2.90
2054 2319 9.178758 GGAAATACTTGTTAGAGAAATGGATGT 57.821 33.333 0.00 0.00 0.00 3.06
2055 2320 8.338259 CGGAAATACTTGTTAGAGAAATGGATG 58.662 37.037 0.00 0.00 0.00 3.51
2056 2321 7.499232 CCGGAAATACTTGTTAGAGAAATGGAT 59.501 37.037 0.00 0.00 0.00 3.41
2057 2322 6.821665 CCGGAAATACTTGTTAGAGAAATGGA 59.178 38.462 0.00 0.00 0.00 3.41
2058 2323 6.821665 TCCGGAAATACTTGTTAGAGAAATGG 59.178 38.462 0.00 0.00 0.00 3.16
2059 2324 7.464178 CGTCCGGAAATACTTGTTAGAGAAATG 60.464 40.741 5.23 0.00 0.00 2.32
2060 2325 6.534079 CGTCCGGAAATACTTGTTAGAGAAAT 59.466 38.462 5.23 0.00 0.00 2.17
2061 2326 5.865552 CGTCCGGAAATACTTGTTAGAGAAA 59.134 40.000 5.23 0.00 0.00 2.52
2062 2327 5.404946 CGTCCGGAAATACTTGTTAGAGAA 58.595 41.667 5.23 0.00 0.00 2.87
2063 2328 4.142315 CCGTCCGGAAATACTTGTTAGAGA 60.142 45.833 5.23 0.00 37.50 3.10
2064 2329 4.110482 CCGTCCGGAAATACTTGTTAGAG 58.890 47.826 5.23 0.00 37.50 2.43
2065 2330 3.763360 TCCGTCCGGAAATACTTGTTAGA 59.237 43.478 5.23 0.00 42.05 2.10
2066 2331 4.110482 CTCCGTCCGGAAATACTTGTTAG 58.890 47.826 5.23 0.00 44.66 2.34
2067 2332 3.119029 CCTCCGTCCGGAAATACTTGTTA 60.119 47.826 5.23 0.00 44.66 2.41
2068 2333 2.354403 CCTCCGTCCGGAAATACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
2069 2334 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2070 2335 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2071 2336 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2072 2337 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2073 2338 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2074 2339 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2075 2340 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2076 2341 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2077 2342 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
2078 2343 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
2079 2344 1.920610 AATATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
2080 2345 2.889045 TCAAATATACTCCCTCCGTCCG 59.111 50.000 0.00 0.00 0.00 4.79
2081 2346 3.896272 ACTCAAATATACTCCCTCCGTCC 59.104 47.826 0.00 0.00 0.00 4.79
2082 2347 4.796618 GCACTCAAATATACTCCCTCCGTC 60.797 50.000 0.00 0.00 0.00 4.79
2083 2348 3.069729 GCACTCAAATATACTCCCTCCGT 59.930 47.826 0.00 0.00 0.00 4.69
2084 2349 3.322254 AGCACTCAAATATACTCCCTCCG 59.678 47.826 0.00 0.00 0.00 4.63
2085 2350 4.965200 AGCACTCAAATATACTCCCTCC 57.035 45.455 0.00 0.00 0.00 4.30
2086 2351 5.245075 AGCTAGCACTCAAATATACTCCCTC 59.755 44.000 18.83 0.00 0.00 4.30
2087 2352 5.151454 AGCTAGCACTCAAATATACTCCCT 58.849 41.667 18.83 0.00 0.00 4.20
2088 2353 5.476091 AGCTAGCACTCAAATATACTCCC 57.524 43.478 18.83 0.00 0.00 4.30
2089 2354 8.062065 AGATAGCTAGCACTCAAATATACTCC 57.938 38.462 18.83 0.00 0.00 3.85
2094 2359 9.473007 TGAGATAGATAGCTAGCACTCAAATAT 57.527 33.333 21.77 3.69 35.49 1.28
2095 2360 8.870075 TGAGATAGATAGCTAGCACTCAAATA 57.130 34.615 21.77 0.00 35.49 1.40
2096 2361 7.669304 TCTGAGATAGATAGCTAGCACTCAAAT 59.331 37.037 23.08 10.14 36.17 2.32
2097 2362 7.001073 TCTGAGATAGATAGCTAGCACTCAAA 58.999 38.462 23.08 14.48 36.17 2.69
2098 2363 6.538263 TCTGAGATAGATAGCTAGCACTCAA 58.462 40.000 23.08 15.81 36.17 3.02
2099 2364 6.120507 TCTGAGATAGATAGCTAGCACTCA 57.879 41.667 18.83 22.22 35.49 3.41
2100 2365 7.040755 TGTTTCTGAGATAGATAGCTAGCACTC 60.041 40.741 18.83 15.62 35.49 3.51
2101 2366 6.775142 TGTTTCTGAGATAGATAGCTAGCACT 59.225 38.462 18.83 14.87 35.49 4.40
2102 2367 6.861055 GTGTTTCTGAGATAGATAGCTAGCAC 59.139 42.308 18.83 7.96 35.49 4.40
2103 2368 6.547510 TGTGTTTCTGAGATAGATAGCTAGCA 59.452 38.462 18.83 3.19 35.49 3.49
2104 2369 6.976088 TGTGTTTCTGAGATAGATAGCTAGC 58.024 40.000 6.62 6.62 34.80 3.42
2105 2370 9.979578 AATTGTGTTTCTGAGATAGATAGCTAG 57.020 33.333 0.00 0.00 34.80 3.42
2106 2371 9.973450 GAATTGTGTTTCTGAGATAGATAGCTA 57.027 33.333 0.00 0.00 34.80 3.32
2107 2372 8.481314 TGAATTGTGTTTCTGAGATAGATAGCT 58.519 33.333 0.00 0.00 34.80 3.32
2108 2373 8.654230 TGAATTGTGTTTCTGAGATAGATAGC 57.346 34.615 0.00 0.00 34.80 2.97
2109 2374 9.814899 ACTGAATTGTGTTTCTGAGATAGATAG 57.185 33.333 0.00 0.00 34.80 2.08
2112 2377 9.996554 TTTACTGAATTGTGTTTCTGAGATAGA 57.003 29.630 0.00 0.00 0.00 1.98
2114 2379 9.219603 CCTTTACTGAATTGTGTTTCTGAGATA 57.780 33.333 0.00 0.00 0.00 1.98
2115 2380 7.308830 GCCTTTACTGAATTGTGTTTCTGAGAT 60.309 37.037 0.00 0.00 0.00 2.75
2140 2405 1.065273 CGGCAAGCCAGATGATTGC 59.935 57.895 12.19 6.61 46.67 3.56
2148 2415 1.576421 GTGAAACTCGGCAAGCCAG 59.424 57.895 12.19 9.96 35.37 4.85
2156 2423 0.172803 CCCCTAGTCGTGAAACTCGG 59.827 60.000 0.00 0.00 33.09 4.63
2165 2432 2.754658 CGGAGCACCCCTAGTCGT 60.755 66.667 0.00 0.00 0.00 4.34
2167 2434 1.380112 AGACGGAGCACCCCTAGTC 60.380 63.158 0.00 0.00 33.80 2.59
2168 2435 1.380112 GAGACGGAGCACCCCTAGT 60.380 63.158 0.00 0.00 0.00 2.57
2173 2440 0.173708 CTAACAGAGACGGAGCACCC 59.826 60.000 0.00 0.00 0.00 4.61
2176 2443 0.970937 CCCCTAACAGAGACGGAGCA 60.971 60.000 0.00 0.00 0.00 4.26
2182 2449 1.481363 GTGCCTACCCCTAACAGAGAC 59.519 57.143 0.00 0.00 0.00 3.36
2185 2452 2.953620 GCTAGTGCCTACCCCTAACAGA 60.954 54.545 0.00 0.00 0.00 3.41
2187 2454 1.492764 GCTAGTGCCTACCCCTAACA 58.507 55.000 0.00 0.00 0.00 2.41
2237 2504 5.507315 GCCAATTACACCATAAGGCATACAC 60.507 44.000 0.00 0.00 40.29 2.90
2319 2586 9.461312 TTGTGATCTTTACTACAAGCCAAATAT 57.539 29.630 0.00 0.00 0.00 1.28
2320 2587 8.726988 GTTGTGATCTTTACTACAAGCCAAATA 58.273 33.333 0.00 0.00 34.11 1.40
2339 2607 1.138069 TGACATATCCGGCGTTGTGAT 59.862 47.619 6.01 3.73 0.00 3.06
2345 2613 6.403049 TGATTATATTTGACATATCCGGCGT 58.597 36.000 6.01 0.00 0.00 5.68
2396 2664 3.071023 ACAAGAGCCAGCACAGTTAGTTA 59.929 43.478 0.00 0.00 0.00 2.24
2461 2729 0.661780 CGCCTCCTAAGAGATTCGCG 60.662 60.000 0.00 0.00 43.39 5.87
2482 2750 1.208614 GAAGAAAGCAGCAGCACCG 59.791 57.895 3.17 0.00 45.49 4.94
2485 2753 0.956633 CCTTGAAGAAAGCAGCAGCA 59.043 50.000 3.17 0.00 45.49 4.41
2495 2763 2.912956 AGCATAGTGGACCCTTGAAGAA 59.087 45.455 0.00 0.00 0.00 2.52
2524 2792 2.046988 CGTGATGGAGGTGCTGCA 60.047 61.111 0.00 0.00 36.05 4.41
2539 2807 1.755380 GGTAACCATGTAGGAGAGCGT 59.245 52.381 0.00 0.00 41.22 5.07
2556 2824 1.560146 TGGGTTGGCGTATCAATGGTA 59.440 47.619 0.00 0.00 0.00 3.25
2558 2826 0.738389 GTGGGTTGGCGTATCAATGG 59.262 55.000 0.00 0.00 0.00 3.16
2569 2837 3.447229 ACAAGACAAAAGAAGTGGGTTGG 59.553 43.478 0.00 0.00 0.00 3.77
2600 2868 2.325583 TCCCACATAGAATTGCGTCC 57.674 50.000 0.00 0.00 0.00 4.79
2603 2871 3.381272 ACCAAATCCCACATAGAATTGCG 59.619 43.478 0.00 0.00 0.00 4.85
2607 2875 6.017211 TGATGACCAAATCCCACATAGAAT 57.983 37.500 0.00 0.00 0.00 2.40
2618 2886 2.034124 CCACCCCATGATGACCAAATC 58.966 52.381 0.00 0.00 0.00 2.17
2665 2945 5.934402 AGACGGTACCAACATTCTATCTT 57.066 39.130 13.54 0.00 0.00 2.40
2683 2969 4.098055 ACTAGTGCTACATCACAAGACG 57.902 45.455 0.00 0.00 39.35 4.18
2709 2995 8.299570 CAGAAGTAATGCCTAACAGAAACAAAT 58.700 33.333 0.00 0.00 0.00 2.32
2763 3052 4.530161 AGATAGAAGTCAACAGACCAGCTT 59.470 41.667 0.00 0.00 32.62 3.74
2886 3175 4.868450 ACTAGTTCTCATCGAAGTCTCG 57.132 45.455 0.00 0.00 46.87 4.04
3049 3338 9.373603 AGCGTGCAATAAATATTATACGGAATA 57.626 29.630 16.31 0.00 36.04 1.75
3050 3339 8.263940 AGCGTGCAATAAATATTATACGGAAT 57.736 30.769 16.31 0.00 36.04 3.01
3051 3340 7.661127 AGCGTGCAATAAATATTATACGGAA 57.339 32.000 16.31 0.00 36.04 4.30
3052 3341 8.760103 TTAGCGTGCAATAAATATTATACGGA 57.240 30.769 16.31 0.00 36.04 4.69
3053 3342 9.257865 GTTTAGCGTGCAATAAATATTATACGG 57.742 33.333 16.31 5.67 36.04 4.02
3054 3343 9.800299 TGTTTAGCGTGCAATAAATATTATACG 57.200 29.630 12.92 12.92 37.30 3.06
3093 3382 3.055094 ACGACCTAGATTGCTTCAATGGT 60.055 43.478 0.00 0.00 33.90 3.55
3136 3425 2.103263 GGCAGATCCAACTAATCTCGGT 59.897 50.000 0.00 0.00 31.05 4.69
3261 3557 6.449698 CACTACAGCAATTTGGACAGATTTT 58.550 36.000 0.00 0.00 0.00 1.82
3484 3783 2.679450 CGGAAACCAGTTACGTGATGA 58.321 47.619 0.00 0.00 0.00 2.92
3488 3787 0.233848 GTGCGGAAACCAGTTACGTG 59.766 55.000 0.00 0.00 0.00 4.49
3491 3790 1.873698 TCTGTGCGGAAACCAGTTAC 58.126 50.000 0.00 0.00 0.00 2.50
3492 3791 2.614983 GTTTCTGTGCGGAAACCAGTTA 59.385 45.455 20.22 0.00 45.25 2.24
3535 3835 9.567776 TCAAGACTTCCACAACATAAAGAATAA 57.432 29.630 0.00 0.00 0.00 1.40
3631 3931 5.971763 ACATTTGCGCAAGGGAATTTATAA 58.028 33.333 23.68 3.89 38.28 0.98
3649 3949 5.707298 CACCTGAAGGAGTGTAATGACATTT 59.293 40.000 5.89 0.00 36.90 2.32
3676 3976 4.577693 CCAGAATATGTCCACACAGAATGG 59.422 45.833 0.00 0.00 43.62 3.16
3775 4079 8.673711 GGCACAAAACATTTATATACTCTGTCA 58.326 33.333 0.00 0.00 0.00 3.58
3808 4112 4.610605 TCCTTTACTGTTGATCGGACAA 57.389 40.909 3.70 0.00 0.00 3.18
3827 4131 6.263392 TCACAGATAGTCTAGCACAGTTATCC 59.737 42.308 0.00 0.00 0.00 2.59
3828 4132 7.136119 GTCACAGATAGTCTAGCACAGTTATC 58.864 42.308 0.00 0.00 0.00 1.75
3830 4134 5.357314 GGTCACAGATAGTCTAGCACAGTTA 59.643 44.000 0.00 0.00 0.00 2.24
3883 4189 5.705905 AGTAGAGTATGTGGCTTTTGGAAAC 59.294 40.000 0.00 0.00 0.00 2.78
3911 4217 8.778358 AGTGAACATTCTTCAACTAGATGAAAC 58.222 33.333 15.36 8.75 41.83 2.78
3912 4218 8.908786 AGTGAACATTCTTCAACTAGATGAAA 57.091 30.769 15.36 3.63 41.83 2.69
3961 4271 3.909587 TGCAATTCATAGCAGGCCT 57.090 47.368 0.00 0.00 35.51 5.19
4010 4330 9.520204 GAAAGTTAGTACATATTACGTAAGGCA 57.480 33.333 14.25 2.03 46.39 4.75
4268 4588 7.856145 AGCATACCATATAGAGCAAATAAGC 57.144 36.000 0.00 0.00 0.00 3.09
4550 4870 7.165812 GTGACAGTACAAATGCAAAGTAAAGTG 59.834 37.037 0.00 0.00 0.00 3.16
4575 4895 5.765510 TCTTGGCTATGGAATAACAATGGT 58.234 37.500 0.00 0.00 29.21 3.55
4604 4926 6.428385 AGCTAGCACATGTACTTCAATTTC 57.572 37.500 18.83 0.00 0.00 2.17
4699 5021 9.643693 ACAGGCAGTCAAAATAAAATAGAATTG 57.356 29.630 0.00 0.00 0.00 2.32
4817 5139 7.837689 ACCATACTGTCCACTAAGTTGACTATA 59.162 37.037 0.00 0.00 30.86 1.31
4818 5140 6.668283 ACCATACTGTCCACTAAGTTGACTAT 59.332 38.462 0.00 0.00 30.86 2.12
4897 5219 5.744171 TGGCAGATTGAGAAAGCAACTATA 58.256 37.500 0.00 0.00 0.00 1.31
4979 5304 1.017387 CTCGAGCCCCAGCAATAAAC 58.983 55.000 0.00 0.00 43.56 2.01
5583 5910 0.750249 TGTCAGTCAAAGCTCGACCA 59.250 50.000 11.56 2.22 33.70 4.02
5664 5991 5.091552 AGGATTGGGTCAGTAACTCAGTAA 58.908 41.667 0.00 0.00 40.24 2.24
5844 6171 6.116806 AGCATACTATAGAGATACGTCAGGG 58.883 44.000 6.78 0.00 0.00 4.45
6004 6442 6.887002 CCCAGGAAAAATATATTAGGAGGCTC 59.113 42.308 5.78 5.78 0.00 4.70
6016 6454 5.281245 GCCCTAGCTATCCCAGGAAAAATAT 60.281 44.000 0.72 0.00 35.50 1.28
6045 6483 9.696917 GGAATTACATCAAAATGATTGATACCC 57.303 33.333 3.57 0.00 34.28 3.69
6063 6501 4.461081 GCACCACCTACAAATGGAATTACA 59.539 41.667 0.00 0.00 39.46 2.41
6255 6693 3.371965 AGAAATCCTGCAGAAATGGCAT 58.628 40.909 17.39 0.00 41.06 4.40
6256 6694 2.811410 AGAAATCCTGCAGAAATGGCA 58.189 42.857 17.39 0.00 39.32 4.92
6259 6697 5.048224 ACAGTGAAGAAATCCTGCAGAAATG 60.048 40.000 17.39 0.00 28.87 2.32
6431 6869 1.580845 CTGAGCCAACGAAGCCAAGG 61.581 60.000 0.00 0.00 0.00 3.61
6508 6946 7.017551 ACTGCCCATATCAATATCTACTTTCCA 59.982 37.037 0.00 0.00 0.00 3.53
6854 7319 9.478768 GCCTGGTTTCTATAAACTATAAGTCTC 57.521 37.037 4.01 0.00 43.76 3.36
6855 7320 9.214962 AGCCTGGTTTCTATAAACTATAAGTCT 57.785 33.333 4.01 0.00 43.76 3.24
6856 7321 9.478768 GAGCCTGGTTTCTATAAACTATAAGTC 57.521 37.037 4.01 0.00 43.76 3.01
6857 7322 8.430431 GGAGCCTGGTTTCTATAAACTATAAGT 58.570 37.037 4.01 0.00 43.76 2.24
6858 7323 8.429641 TGGAGCCTGGTTTCTATAAACTATAAG 58.570 37.037 4.01 0.00 43.76 1.73
6859 7324 8.326765 TGGAGCCTGGTTTCTATAAACTATAA 57.673 34.615 4.01 0.00 43.76 0.98
6861 7326 6.824958 TGGAGCCTGGTTTCTATAAACTAT 57.175 37.500 4.01 0.00 43.76 2.12
6863 7328 5.514500 TTGGAGCCTGGTTTCTATAAACT 57.486 39.130 4.01 0.00 43.76 2.66
6864 7329 6.584185 TTTTGGAGCCTGGTTTCTATAAAC 57.416 37.500 0.00 0.00 43.58 2.01
6865 7330 6.350949 GCATTTTGGAGCCTGGTTTCTATAAA 60.351 38.462 0.00 0.00 0.00 1.40
6866 7331 5.127031 GCATTTTGGAGCCTGGTTTCTATAA 59.873 40.000 0.00 0.00 0.00 0.98
6867 7332 4.644685 GCATTTTGGAGCCTGGTTTCTATA 59.355 41.667 0.00 0.00 0.00 1.31
6868 7333 3.448660 GCATTTTGGAGCCTGGTTTCTAT 59.551 43.478 0.00 0.00 0.00 1.98
7023 7535 6.109156 TGAGTGTAAAATTAGTCTGCTCCA 57.891 37.500 0.00 0.00 0.00 3.86
7030 7657 9.612620 CTGTTTGGATTGAGTGTAAAATTAGTC 57.387 33.333 0.00 0.00 0.00 2.59
7050 7677 4.664150 TTTGAAACTAAGGCCCTGTTTG 57.336 40.909 18.87 3.59 34.55 2.93
7173 7855 3.614159 AATCACGAATTGGATGATGCG 57.386 42.857 0.00 0.00 33.37 4.73
7187 7869 6.943981 TCTCTGTTTGTGTTCTTAAATCACG 58.056 36.000 0.00 0.00 35.20 4.35
7189 7871 8.908786 ATCTCTCTGTTTGTGTTCTTAAATCA 57.091 30.769 0.00 0.00 0.00 2.57
7227 7909 5.280654 AGTCAAATTTGGTTGCAGATGTT 57.719 34.783 17.90 0.00 0.00 2.71
7235 7917 7.926018 AGCTTTTACCTAAGTCAAATTTGGTTG 59.074 33.333 17.90 5.39 38.83 3.77
7280 7962 8.408601 ACTTGTGCATTTTGATATACTCCATTC 58.591 33.333 0.00 0.00 0.00 2.67
7317 7999 5.478407 AGTTGTAAATTGGCAATAACCTGC 58.522 37.500 14.05 7.77 41.85 4.85
7320 8019 7.165460 AGGTAGTTGTAAATTGGCAATAACC 57.835 36.000 14.05 10.47 34.89 2.85
7356 8056 0.309922 CCAGTGTGCTGAAAGTGCAG 59.690 55.000 0.00 0.00 45.28 4.41
7372 8072 3.963374 TGTTCCCTGATCTGATACTCCAG 59.037 47.826 0.38 0.00 35.55 3.86
7389 8089 6.072728 TGTTGCATGTTCAGTACTTATGTTCC 60.073 38.462 0.00 0.00 0.00 3.62
7398 8098 3.904136 AAGCTGTTGCATGTTCAGTAC 57.096 42.857 12.67 0.00 42.74 2.73
7409 8109 2.969443 ACGACACAATAAGCTGTTGC 57.031 45.000 10.99 0.00 40.05 4.17


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

AutoCloner maintained by Alex Coulton.