Multiple sequence alignment - TraesCS2D01G282700

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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 TraesCS2D01G282700 chr2D 100.000 2213 0 0 1 2213 355629239 355631451 0.000000e+00 4087.0
1 TraesCS2D01G282700 chr2D 89.256 121 12 1 1682 1802 627195500 627195619 1.370000e-32 150.0
2 TraesCS2D01G282700 chr2A 95.144 1009 43 3 667 1671 475811887 475812893 0.000000e+00 1587.0
3 TraesCS2D01G282700 chr2A 93.303 433 18 4 189 610 475811314 475811746 1.440000e-176 628.0
4 TraesCS2D01G282700 chr2A 93.528 309 19 1 1804 2112 475812894 475813201 2.000000e-125 459.0
5 TraesCS2D01G282700 chr2A 96.522 115 3 1 2099 2213 475813536 475813649 2.900000e-44 189.0
6 TraesCS2D01G282700 chr2A 89.916 119 12 0 1683 1801 688769171 688769289 1.060000e-33 154.0
7 TraesCS2D01G282700 chr2B 93.428 989 42 5 696 1684 423344897 423345862 0.000000e+00 1445.0
8 TraesCS2D01G282700 chr2B 94.074 270 10 1 347 610 423342634 423342903 2.650000e-109 405.0
9 TraesCS2D01G282700 chr2B 87.097 310 39 1 1799 2108 423345861 423346169 1.260000e-92 350.0
10 TraesCS2D01G282700 chr2B 97.391 115 3 0 2099 2213 423346503 423346617 1.730000e-46 196.0
11 TraesCS2D01G282700 chr2B 87.770 139 12 3 191 325 423342419 423342556 8.180000e-35 158.0
12 TraesCS2D01G282700 chr2B 85.965 57 8 0 2010 2066 416184006 416184062 6.600000e-06 62.1
13 TraesCS2D01G282700 chr2B 87.037 54 5 2 1947 1999 725663799 725663747 2.370000e-05 60.2
14 TraesCS2D01G282700 chrUn 93.296 179 12 0 12 190 12151208 12151030 4.690000e-67 265.0
15 TraesCS2D01G282700 chrUn 93.296 179 12 0 12 190 285687358 285687180 4.690000e-67 265.0
16 TraesCS2D01G282700 chrUn 94.872 39 2 0 2011 2049 10263835 10263797 6.600000e-06 62.1
17 TraesCS2D01G282700 chr6B 92.857 182 13 0 12 193 26600278 26600097 4.690000e-67 265.0
18 TraesCS2D01G282700 chr6B 91.892 185 14 1 7 190 242221640 242221456 7.840000e-65 257.0
19 TraesCS2D01G282700 chr6B 76.389 144 19 8 1858 1987 693822794 693822652 1.830000e-06 63.9
20 TraesCS2D01G282700 chr4D 92.896 183 12 1 12 193 444466517 444466335 4.690000e-67 265.0
21 TraesCS2D01G282700 chr4D 90.678 118 11 0 1683 1800 494876029 494875912 8.180000e-35 158.0
22 TraesCS2D01G282700 chr7D 93.296 179 11 1 12 190 26501436 26501259 1.690000e-66 263.0
23 TraesCS2D01G282700 chr4B 92.737 179 13 0 12 190 655777077 655776899 2.180000e-65 259.0
24 TraesCS2D01G282700 chr4B 97.059 34 1 0 1972 2005 41557489 41557456 8.530000e-05 58.4
25 TraesCS2D01G282700 chr3A 91.935 186 14 1 12 196 713982505 713982320 2.180000e-65 259.0
26 TraesCS2D01G282700 chr4A 91.848 184 14 1 7 190 558676800 558676982 2.820000e-64 255.0
27 TraesCS2D01G282700 chr4A 90.678 118 11 0 1683 1800 590222037 590222154 8.180000e-35 158.0
28 TraesCS2D01G282700 chr7A 91.736 121 8 2 1682 1800 222941734 222941854 1.360000e-37 167.0
29 TraesCS2D01G282700 chr7A 95.000 40 2 0 2010 2049 425783236 425783275 1.830000e-06 63.9
30 TraesCS2D01G282700 chr1B 89.431 123 13 0 1683 1805 611680540 611680418 2.940000e-34 156.0
31 TraesCS2D01G282700 chr1B 89.256 121 12 1 1683 1803 8417910 8417791 1.370000e-32 150.0
32 TraesCS2D01G282700 chr1B 97.143 35 1 0 2014 2048 658472553 658472519 2.370000e-05 60.2
33 TraesCS2D01G282700 chr5B 88.372 129 14 1 1682 1810 69859 69986 1.060000e-33 154.0
34 TraesCS2D01G282700 chr5B 89.091 55 5 1 1947 2000 629950289 629950235 1.420000e-07 67.6
35 TraesCS2D01G282700 chr5A 89.167 120 13 0 1683 1802 448618752 448618633 1.370000e-32 150.0
36 TraesCS2D01G282700 chr6A 86.066 122 11 6 1881 2000 107687768 107687885 2.310000e-25 126.0
37 TraesCS2D01G282700 chr3B 86.364 66 7 2 1940 2004 766786032 766786096 1.100000e-08 71.3
38 TraesCS2D01G282700 chr1A 100.000 35 0 0 2015 2049 567927205 567927171 5.100000e-07 65.8
39 TraesCS2D01G282700 chr7B 94.872 39 2 0 2011 2049 607617957 607617995 6.600000e-06 62.1
40 TraesCS2D01G282700 chr3D 85.714 56 6 2 2021 2075 593643282 593643228 8.530000e-05 58.4


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 TraesCS2D01G282700 chr2D 355629239 355631451 2212 False 4087.00 4087 100.00000 1 2213 1 chr2D.!!$F1 2212
1 TraesCS2D01G282700 chr2A 475811314 475813649 2335 False 715.75 1587 94.62425 189 2213 4 chr2A.!!$F2 2024
2 TraesCS2D01G282700 chr2B 423342419 423346617 4198 False 510.80 1445 91.95200 191 2213 5 chr2B.!!$F2 2022

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
397 459 0.031449 GCTCTAGACGGATGTGCCTC 59.969 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3907 0.17902 CCGATGCCATCCAAAGCCTA 60.179 55.0 0.0 0.0 0.0 3.93 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 4.611310 CCACTCAGTTTCATGCATGTAG 57.389 45.455 25.43 15.56 0.00 2.74
22 23 4.005650 CCACTCAGTTTCATGCATGTAGT 58.994 43.478 25.43 14.77 0.00 2.73
23 24 4.093998 CCACTCAGTTTCATGCATGTAGTC 59.906 45.833 25.43 13.08 0.00 2.59
24 25 4.692155 CACTCAGTTTCATGCATGTAGTCA 59.308 41.667 25.43 3.60 0.00 3.41
25 26 5.353400 CACTCAGTTTCATGCATGTAGTCAT 59.647 40.000 25.43 6.35 34.21 3.06
26 27 6.536224 CACTCAGTTTCATGCATGTAGTCATA 59.464 38.462 25.43 2.03 32.47 2.15
27 28 7.064966 CACTCAGTTTCATGCATGTAGTCATAA 59.935 37.037 25.43 8.51 32.47 1.90
28 29 7.772292 ACTCAGTTTCATGCATGTAGTCATAAT 59.228 33.333 25.43 4.26 32.47 1.28
29 30 7.922837 TCAGTTTCATGCATGTAGTCATAATG 58.077 34.615 25.43 10.66 32.87 1.90
30 31 7.769970 TCAGTTTCATGCATGTAGTCATAATGA 59.230 33.333 25.43 12.68 35.96 2.57
46 47 8.894768 GTCATAATGACAATTAGCTACTTCCT 57.105 34.615 0.00 0.00 46.22 3.36
47 48 8.983724 GTCATAATGACAATTAGCTACTTCCTC 58.016 37.037 0.00 0.00 46.22 3.71
48 49 8.150945 TCATAATGACAATTAGCTACTTCCTCC 58.849 37.037 0.00 0.00 31.81 4.30
49 50 5.957771 ATGACAATTAGCTACTTCCTCCA 57.042 39.130 0.00 0.00 0.00 3.86
50 51 5.086104 TGACAATTAGCTACTTCCTCCAC 57.914 43.478 0.00 0.00 0.00 4.02
51 52 4.777896 TGACAATTAGCTACTTCCTCCACT 59.222 41.667 0.00 0.00 0.00 4.00
52 53 5.105310 TGACAATTAGCTACTTCCTCCACTC 60.105 44.000 0.00 0.00 0.00 3.51
53 54 4.777896 ACAATTAGCTACTTCCTCCACTCA 59.222 41.667 0.00 0.00 0.00 3.41
54 55 5.105146 ACAATTAGCTACTTCCTCCACTCAG 60.105 44.000 0.00 0.00 0.00 3.35
55 56 2.614134 AGCTACTTCCTCCACTCAGT 57.386 50.000 0.00 0.00 0.00 3.41
56 57 2.896039 AGCTACTTCCTCCACTCAGTT 58.104 47.619 0.00 0.00 0.00 3.16
57 58 3.243724 AGCTACTTCCTCCACTCAGTTT 58.756 45.455 0.00 0.00 0.00 2.66
58 59 3.259625 AGCTACTTCCTCCACTCAGTTTC 59.740 47.826 0.00 0.00 0.00 2.78
59 60 3.259625 GCTACTTCCTCCACTCAGTTTCT 59.740 47.826 0.00 0.00 0.00 2.52
60 61 4.262678 GCTACTTCCTCCACTCAGTTTCTT 60.263 45.833 0.00 0.00 0.00 2.52
61 62 4.779993 ACTTCCTCCACTCAGTTTCTTT 57.220 40.909 0.00 0.00 0.00 2.52
62 63 4.455606 ACTTCCTCCACTCAGTTTCTTTG 58.544 43.478 0.00 0.00 0.00 2.77
63 64 2.851195 TCCTCCACTCAGTTTCTTTGC 58.149 47.619 0.00 0.00 0.00 3.68
64 65 2.172505 TCCTCCACTCAGTTTCTTTGCA 59.827 45.455 0.00 0.00 0.00 4.08
65 66 3.152341 CCTCCACTCAGTTTCTTTGCAT 58.848 45.455 0.00 0.00 0.00 3.96
66 67 3.057736 CCTCCACTCAGTTTCTTTGCATG 60.058 47.826 0.00 0.00 0.00 4.06
67 68 2.294233 TCCACTCAGTTTCTTTGCATGC 59.706 45.455 11.82 11.82 0.00 4.06
68 69 2.034939 CCACTCAGTTTCTTTGCATGCA 59.965 45.455 18.46 18.46 0.00 3.96
69 70 3.305813 CCACTCAGTTTCTTTGCATGCAT 60.306 43.478 23.37 0.58 0.00 3.96
70 71 3.673338 CACTCAGTTTCTTTGCATGCATG 59.327 43.478 23.37 22.70 0.00 4.06
82 83 3.837213 GCATGCATGCGGAGTATTAAT 57.163 42.857 33.99 0.00 44.67 1.40
83 84 3.495193 GCATGCATGCGGAGTATTAATG 58.505 45.455 33.99 8.73 44.67 1.90
84 85 3.189080 GCATGCATGCGGAGTATTAATGA 59.811 43.478 33.99 0.00 44.67 2.57
85 86 4.142534 GCATGCATGCGGAGTATTAATGAT 60.143 41.667 33.99 0.00 44.67 2.45
86 87 5.566623 CATGCATGCGGAGTATTAATGATC 58.433 41.667 14.93 0.00 28.75 2.92
87 88 4.002982 TGCATGCGGAGTATTAATGATCC 58.997 43.478 14.09 9.63 0.00 3.36
88 89 3.375299 GCATGCGGAGTATTAATGATCCC 59.625 47.826 0.00 8.00 0.00 3.85
89 90 4.578871 CATGCGGAGTATTAATGATCCCA 58.421 43.478 12.66 11.79 0.00 4.37
90 91 4.271696 TGCGGAGTATTAATGATCCCAG 57.728 45.455 12.66 4.27 0.00 4.45
91 92 3.646162 TGCGGAGTATTAATGATCCCAGT 59.354 43.478 12.66 0.00 0.00 4.00
92 93 4.836175 TGCGGAGTATTAATGATCCCAGTA 59.164 41.667 12.66 1.05 0.00 2.74
93 94 5.305902 TGCGGAGTATTAATGATCCCAGTAA 59.694 40.000 12.66 0.00 37.27 2.24
94 95 6.183361 TGCGGAGTATTAATGATCCCAGTAAA 60.183 38.462 12.66 0.00 36.58 2.01
95 96 6.147328 GCGGAGTATTAATGATCCCAGTAAAC 59.853 42.308 12.66 0.00 36.58 2.01
96 97 7.214381 CGGAGTATTAATGATCCCAGTAAACA 58.786 38.462 12.66 0.00 36.58 2.83
97 98 7.713507 CGGAGTATTAATGATCCCAGTAAACAA 59.286 37.037 12.66 0.00 36.58 2.83
98 99 9.057089 GGAGTATTAATGATCCCAGTAAACAAG 57.943 37.037 8.81 0.00 36.58 3.16
99 100 9.832445 GAGTATTAATGATCCCAGTAAACAAGA 57.168 33.333 0.00 0.00 36.58 3.02
103 104 9.753674 ATTAATGATCCCAGTAAACAAGAAGAA 57.246 29.630 0.00 0.00 36.58 2.52
104 105 9.581289 TTAATGATCCCAGTAAACAAGAAGAAA 57.419 29.630 0.00 0.00 30.92 2.52
105 106 8.477419 AATGATCCCAGTAAACAAGAAGAAAA 57.523 30.769 0.00 0.00 0.00 2.29
106 107 7.510549 TGATCCCAGTAAACAAGAAGAAAAG 57.489 36.000 0.00 0.00 0.00 2.27
107 108 7.060421 TGATCCCAGTAAACAAGAAGAAAAGT 58.940 34.615 0.00 0.00 0.00 2.66
108 109 7.559897 TGATCCCAGTAAACAAGAAGAAAAGTT 59.440 33.333 0.00 0.00 0.00 2.66
109 110 8.990163 ATCCCAGTAAACAAGAAGAAAAGTTA 57.010 30.769 0.00 0.00 0.00 2.24
110 111 8.810990 TCCCAGTAAACAAGAAGAAAAGTTAA 57.189 30.769 0.00 0.00 0.00 2.01
111 112 8.680001 TCCCAGTAAACAAGAAGAAAAGTTAAC 58.320 33.333 0.00 0.00 0.00 2.01
112 113 8.683615 CCCAGTAAACAAGAAGAAAAGTTAACT 58.316 33.333 1.12 1.12 0.00 2.24
137 138 9.202273 CTTGTAAAGCAGGCATTAAATTTTACA 57.798 29.630 0.00 7.99 36.98 2.41
138 139 9.717942 TTGTAAAGCAGGCATTAAATTTTACAT 57.282 25.926 11.15 0.00 38.52 2.29
139 140 9.717942 TGTAAAGCAGGCATTAAATTTTACATT 57.282 25.926 0.00 0.00 35.70 2.71
140 141 9.971744 GTAAAGCAGGCATTAAATTTTACATTG 57.028 29.630 0.00 0.00 32.60 2.82
141 142 8.620116 AAAGCAGGCATTAAATTTTACATTGT 57.380 26.923 0.00 0.00 0.00 2.71
142 143 8.620116 AAGCAGGCATTAAATTTTACATTGTT 57.380 26.923 0.00 0.00 0.00 2.83
143 144 9.717942 AAGCAGGCATTAAATTTTACATTGTTA 57.282 25.926 0.00 0.00 0.00 2.41
144 145 9.150348 AGCAGGCATTAAATTTTACATTGTTAC 57.850 29.630 0.00 0.00 0.00 2.50
145 146 8.930760 GCAGGCATTAAATTTTACATTGTTACA 58.069 29.630 0.00 0.00 0.00 2.41
163 164 8.864069 TTGTTACATGTAATTCAAGTTTGTGG 57.136 30.769 20.72 0.00 0.00 4.17
164 165 8.001881 TGTTACATGTAATTCAAGTTTGTGGT 57.998 30.769 20.72 0.00 0.00 4.16
165 166 8.132362 TGTTACATGTAATTCAAGTTTGTGGTC 58.868 33.333 20.72 3.61 0.00 4.02
166 167 6.959639 ACATGTAATTCAAGTTTGTGGTCT 57.040 33.333 0.00 0.00 0.00 3.85
167 168 7.346751 ACATGTAATTCAAGTTTGTGGTCTT 57.653 32.000 0.00 0.00 0.00 3.01
168 169 7.202526 ACATGTAATTCAAGTTTGTGGTCTTG 58.797 34.615 0.00 0.00 41.36 3.02
169 170 6.767524 TGTAATTCAAGTTTGTGGTCTTGT 57.232 33.333 0.00 0.00 40.97 3.16
170 171 7.867305 TGTAATTCAAGTTTGTGGTCTTGTA 57.133 32.000 0.00 0.00 40.97 2.41
171 172 8.458573 TGTAATTCAAGTTTGTGGTCTTGTAT 57.541 30.769 0.00 0.00 40.97 2.29
172 173 9.562408 TGTAATTCAAGTTTGTGGTCTTGTATA 57.438 29.630 0.00 0.00 40.97 1.47
184 185 8.746052 TGTGGTCTTGTATATAAAAATGGAGG 57.254 34.615 0.00 0.00 0.00 4.30
185 186 8.553153 TGTGGTCTTGTATATAAAAATGGAGGA 58.447 33.333 0.00 0.00 0.00 3.71
186 187 9.403583 GTGGTCTTGTATATAAAAATGGAGGAA 57.596 33.333 0.00 0.00 0.00 3.36
187 188 9.627123 TGGTCTTGTATATAAAAATGGAGGAAG 57.373 33.333 0.00 0.00 0.00 3.46
244 249 5.632347 GCTGGAACATGATTGAAAAGAACAG 59.368 40.000 0.00 0.00 38.20 3.16
326 332 8.832521 ACGAACATAAATGTAGAAAAACAGTCA 58.167 29.630 0.00 0.00 40.80 3.41
334 340 7.621428 ATGTAGAAAAACAGTCATGATCCAG 57.379 36.000 0.00 0.00 31.70 3.86
355 417 5.005586 CCAGAAACGTACACGAACAAGTTTA 59.994 40.000 9.04 0.00 43.02 2.01
397 459 0.031449 GCTCTAGACGGATGTGCCTC 59.969 60.000 0.00 0.00 0.00 4.70
610 682 7.010183 CCGGTTAATGTGTCTACATCAAAGTAG 59.990 40.741 0.00 0.00 46.54 2.57
611 683 7.758076 CGGTTAATGTGTCTACATCAAAGTAGA 59.242 37.037 0.00 0.00 46.54 2.59
633 2711 6.483687 AGACATCAACGTTTAACACTTTGAC 58.516 36.000 0.00 0.00 44.15 3.18
639 2717 7.140048 TCAACGTTTAACACTTTGACAACTTT 58.860 30.769 0.00 0.00 38.42 2.66
647 2725 3.192422 CACTTTGACAACTTTCACCACCA 59.808 43.478 0.00 0.00 0.00 4.17
649 2727 1.757682 TGACAACTTTCACCACCACC 58.242 50.000 0.00 0.00 0.00 4.61
651 2729 0.396556 ACAACTTTCACCACCACCCC 60.397 55.000 0.00 0.00 0.00 4.95
652 2730 1.152839 AACTTTCACCACCACCCCG 60.153 57.895 0.00 0.00 0.00 5.73
653 2731 2.983592 CTTTCACCACCACCCCGC 60.984 66.667 0.00 0.00 0.00 6.13
654 2732 3.783362 CTTTCACCACCACCCCGCA 62.783 63.158 0.00 0.00 0.00 5.69
655 2733 3.360423 TTTCACCACCACCCCGCAA 62.360 57.895 0.00 0.00 0.00 4.85
656 2734 2.856039 TTTCACCACCACCCCGCAAA 62.856 55.000 0.00 0.00 0.00 3.68
657 2735 2.835431 CACCACCACCCCGCAAAA 60.835 61.111 0.00 0.00 0.00 2.44
658 2736 2.042843 ACCACCACCCCGCAAAAA 60.043 55.556 0.00 0.00 0.00 1.94
679 2757 2.765689 AAAAATCACCACCCCACTCA 57.234 45.000 0.00 0.00 0.00 3.41
680 2758 2.292828 AAAATCACCACCCCACTCAG 57.707 50.000 0.00 0.00 0.00 3.35
681 2759 1.149101 AAATCACCACCCCACTCAGT 58.851 50.000 0.00 0.00 0.00 3.41
748 2826 5.461032 TTGGCTTTTGATTTTACGTCCAT 57.539 34.783 0.00 0.00 0.00 3.41
784 2862 5.369404 ACACCACAATGATATACCCTCATCA 59.631 40.000 0.00 0.00 35.72 3.07
888 2968 0.811281 CCTTTCCACATTCCTTCGCC 59.189 55.000 0.00 0.00 0.00 5.54
894 2974 1.683011 CCACATTCCTTCGCCCTCATT 60.683 52.381 0.00 0.00 0.00 2.57
955 3035 1.078426 GGCAGCCGGTAAGACACAT 60.078 57.895 1.90 0.00 0.00 3.21
971 3051 1.303888 CATTGGCCAGCAGGACTGT 60.304 57.895 5.11 0.00 46.30 3.55
1326 3408 7.793927 TCATATGCGTGTGGTTAATTGATTA 57.206 32.000 2.56 0.00 0.00 1.75
1341 3423 1.338674 TGATTAGTCAAGGTGGGCACG 60.339 52.381 0.00 0.00 0.00 5.34
1346 3428 0.604578 GTCAAGGTGGGCACGTACTA 59.395 55.000 0.00 0.00 0.00 1.82
1365 3447 5.952347 ACTACCTCCGATCCAAAATAGTT 57.048 39.130 0.00 0.00 0.00 2.24
1375 3457 3.896122 TCCAAAATAGTTGCGCAGTTTC 58.104 40.909 11.31 2.92 0.00 2.78
1504 3586 6.579666 ACGTGGATACTGTAAAGTAGTTCA 57.420 37.500 0.00 0.00 37.61 3.18
1506 3588 5.515626 CGTGGATACTGTAAAGTAGTTCAGC 59.484 44.000 0.00 0.00 37.61 4.26
1540 3622 0.472044 TGTTCAGCCTGTACCAAGCA 59.528 50.000 0.00 0.00 0.00 3.91
1674 3756 3.198068 ACGATCCATTTTGATGACCTCG 58.802 45.455 0.00 0.00 0.00 4.63
1682 3764 5.590259 CCATTTTGATGACCTCGGACTTTAT 59.410 40.000 0.00 0.00 0.00 1.40
1683 3765 6.765989 CCATTTTGATGACCTCGGACTTTATA 59.234 38.462 0.00 0.00 0.00 0.98
1684 3766 7.254795 CCATTTTGATGACCTCGGACTTTATAC 60.255 40.741 0.00 0.00 0.00 1.47
1685 3767 6.540438 TTTGATGACCTCGGACTTTATACT 57.460 37.500 0.00 0.00 0.00 2.12
1686 3768 5.769484 TGATGACCTCGGACTTTATACTC 57.231 43.478 0.00 0.00 0.00 2.59
1687 3769 4.583489 TGATGACCTCGGACTTTATACTCC 59.417 45.833 0.00 0.00 0.00 3.85
1688 3770 3.972133 TGACCTCGGACTTTATACTCCA 58.028 45.455 0.00 0.00 0.00 3.86
1689 3771 4.543689 TGACCTCGGACTTTATACTCCAT 58.456 43.478 0.00 0.00 0.00 3.41
1690 3772 4.583489 TGACCTCGGACTTTATACTCCATC 59.417 45.833 0.00 0.00 0.00 3.51
1691 3773 3.896272 ACCTCGGACTTTATACTCCATCC 59.104 47.826 0.00 0.00 0.00 3.51
1694 3776 3.898529 CGGACTTTATACTCCATCCGTC 58.101 50.000 2.37 0.00 43.19 4.79
1695 3777 3.305199 CGGACTTTATACTCCATCCGTCC 60.305 52.174 2.37 0.00 43.19 4.79
1696 3778 3.640029 GGACTTTATACTCCATCCGTCCA 59.360 47.826 0.00 0.00 39.47 4.02
1697 3779 4.100498 GGACTTTATACTCCATCCGTCCAA 59.900 45.833 0.00 0.00 39.47 3.53
1698 3780 5.395990 GGACTTTATACTCCATCCGTCCAAA 60.396 44.000 0.00 0.00 39.47 3.28
1699 3781 6.057321 ACTTTATACTCCATCCGTCCAAAA 57.943 37.500 0.00 0.00 0.00 2.44
1700 3782 6.478129 ACTTTATACTCCATCCGTCCAAAAA 58.522 36.000 0.00 0.00 0.00 1.94
1721 3803 6.966534 AAAAGCTTGTCCCTTATATGGATG 57.033 37.500 0.00 0.00 33.65 3.51
1722 3804 5.653255 AAGCTTGTCCCTTATATGGATGT 57.347 39.130 0.00 0.00 33.65 3.06
1723 3805 6.763715 AAGCTTGTCCCTTATATGGATGTA 57.236 37.500 0.00 0.00 33.65 2.29
1724 3806 6.959606 AGCTTGTCCCTTATATGGATGTAT 57.040 37.500 6.23 0.00 33.65 2.29
1725 3807 6.951971 AGCTTGTCCCTTATATGGATGTATC 58.048 40.000 6.23 0.00 33.65 2.24
1726 3808 6.732862 AGCTTGTCCCTTATATGGATGTATCT 59.267 38.462 6.23 0.00 33.65 1.98
1727 3809 7.901322 AGCTTGTCCCTTATATGGATGTATCTA 59.099 37.037 6.23 0.00 33.65 1.98
1728 3810 8.540388 GCTTGTCCCTTATATGGATGTATCTAA 58.460 37.037 6.23 0.00 33.65 2.10
1729 3811 9.877178 CTTGTCCCTTATATGGATGTATCTAAC 57.123 37.037 6.23 0.00 33.65 2.34
1730 3812 8.966155 TGTCCCTTATATGGATGTATCTAACA 57.034 34.615 6.23 0.00 43.86 2.41
1753 3835 8.839310 ACATCAAATTAGTGCTAGATACATCC 57.161 34.615 0.00 0.00 0.00 3.51
1754 3836 8.432013 ACATCAAATTAGTGCTAGATACATCCA 58.568 33.333 0.00 0.00 0.00 3.41
1755 3837 9.445878 CATCAAATTAGTGCTAGATACATCCAT 57.554 33.333 0.00 0.00 0.00 3.41
1757 3839 9.494271 TCAAATTAGTGCTAGATACATCCATTC 57.506 33.333 0.00 0.00 0.00 2.67
1758 3840 8.438513 CAAATTAGTGCTAGATACATCCATTCG 58.561 37.037 0.00 0.00 0.00 3.34
1759 3841 6.894339 TTAGTGCTAGATACATCCATTCGA 57.106 37.500 0.00 0.00 0.00 3.71
1760 3842 5.384063 AGTGCTAGATACATCCATTCGAG 57.616 43.478 0.00 0.00 0.00 4.04
1761 3843 5.073428 AGTGCTAGATACATCCATTCGAGA 58.927 41.667 0.00 0.00 0.00 4.04
1762 3844 5.536538 AGTGCTAGATACATCCATTCGAGAA 59.463 40.000 0.00 0.00 0.00 2.87
1763 3845 6.040955 AGTGCTAGATACATCCATTCGAGAAA 59.959 38.462 0.00 0.00 0.00 2.52
1764 3846 6.144724 GTGCTAGATACATCCATTCGAGAAAC 59.855 42.308 0.00 0.00 0.00 2.78
1765 3847 6.183360 TGCTAGATACATCCATTCGAGAAACA 60.183 38.462 0.00 0.00 0.00 2.83
1766 3848 6.701841 GCTAGATACATCCATTCGAGAAACAA 59.298 38.462 0.00 0.00 0.00 2.83
1767 3849 7.095857 GCTAGATACATCCATTCGAGAAACAAG 60.096 40.741 0.00 0.00 0.00 3.16
1768 3850 5.525378 AGATACATCCATTCGAGAAACAAGC 59.475 40.000 0.00 0.00 0.00 4.01
1769 3851 3.679389 ACATCCATTCGAGAAACAAGCT 58.321 40.909 0.00 0.00 0.00 3.74
1770 3852 4.074970 ACATCCATTCGAGAAACAAGCTT 58.925 39.130 0.00 0.00 0.00 3.74
1771 3853 4.083110 ACATCCATTCGAGAAACAAGCTTG 60.083 41.667 24.84 24.84 0.00 4.01
1772 3854 2.813754 TCCATTCGAGAAACAAGCTTGG 59.186 45.455 29.18 11.25 0.00 3.61
1773 3855 2.095059 CCATTCGAGAAACAAGCTTGGG 60.095 50.000 29.18 13.19 0.00 4.12
1774 3856 2.631160 TTCGAGAAACAAGCTTGGGA 57.369 45.000 29.18 13.44 0.00 4.37
1775 3857 1.878953 TCGAGAAACAAGCTTGGGAC 58.121 50.000 29.18 18.46 0.00 4.46
1776 3858 1.140052 TCGAGAAACAAGCTTGGGACA 59.860 47.619 29.18 4.66 0.00 4.02
1789 3871 1.981256 TGGGACAAGCTTTTCCAGAC 58.019 50.000 28.35 14.71 31.92 3.51
1790 3872 0.875059 GGGACAAGCTTTTCCAGACG 59.125 55.000 28.35 4.42 33.01 4.18
1791 3873 0.875059 GGACAAGCTTTTCCAGACGG 59.125 55.000 23.89 0.04 0.00 4.79
1792 3874 1.542547 GGACAAGCTTTTCCAGACGGA 60.543 52.381 23.89 0.00 40.60 4.69
1793 3875 1.801178 GACAAGCTTTTCCAGACGGAG 59.199 52.381 0.00 0.00 44.10 4.63
1794 3876 1.160137 CAAGCTTTTCCAGACGGAGG 58.840 55.000 0.00 0.00 44.10 4.30
1795 3877 1.056660 AAGCTTTTCCAGACGGAGGA 58.943 50.000 0.00 0.00 44.10 3.71
1796 3878 1.056660 AGCTTTTCCAGACGGAGGAA 58.943 50.000 1.90 1.90 44.10 3.36
1797 3879 1.002544 AGCTTTTCCAGACGGAGGAAG 59.997 52.381 5.77 0.00 45.25 3.46
1825 3907 8.630054 TTTATGTAAGTTGTTTCATAGGTGCT 57.370 30.769 0.00 0.00 0.00 4.40
1835 3917 2.477245 TCATAGGTGCTAGGCTTTGGA 58.523 47.619 0.00 0.00 0.00 3.53
1939 4021 6.685657 TCATAAGATCTGACATTGAGATCCG 58.314 40.000 0.00 1.18 44.82 4.18
1945 4027 3.384467 TCTGACATTGAGATCCGTGCATA 59.616 43.478 0.00 0.00 0.00 3.14
2167 4597 6.085849 GGCGTTATTTTTCTAAAACACTCACG 59.914 38.462 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.005650 ACTACATGCATGAAACTGAGTGG 58.994 43.478 32.75 12.09 0.00 4.00
1 2 4.692155 TGACTACATGCATGAAACTGAGTG 59.308 41.667 32.75 12.64 0.00 3.51
2 3 4.898320 TGACTACATGCATGAAACTGAGT 58.102 39.130 32.75 21.55 0.00 3.41
3 4 7.543947 TTATGACTACATGCATGAAACTGAG 57.456 36.000 32.75 18.96 37.87 3.35
4 5 7.769970 TCATTATGACTACATGCATGAAACTGA 59.230 33.333 32.75 17.01 36.00 3.41
5 6 7.854422 GTCATTATGACTACATGCATGAAACTG 59.146 37.037 32.75 17.72 43.73 3.16
6 7 7.923888 GTCATTATGACTACATGCATGAAACT 58.076 34.615 32.75 13.10 43.73 2.66
22 23 8.150945 GGAGGAAGTAGCTAATTGTCATTATGA 58.849 37.037 11.80 0.00 0.00 2.15
23 24 7.933577 TGGAGGAAGTAGCTAATTGTCATTATG 59.066 37.037 11.80 0.00 0.00 1.90
24 25 7.934120 GTGGAGGAAGTAGCTAATTGTCATTAT 59.066 37.037 11.80 0.00 0.00 1.28
25 26 7.125811 AGTGGAGGAAGTAGCTAATTGTCATTA 59.874 37.037 11.80 0.00 0.00 1.90
26 27 6.069963 AGTGGAGGAAGTAGCTAATTGTCATT 60.070 38.462 11.80 0.00 0.00 2.57
27 28 5.426833 AGTGGAGGAAGTAGCTAATTGTCAT 59.573 40.000 11.80 0.00 0.00 3.06
28 29 4.777896 AGTGGAGGAAGTAGCTAATTGTCA 59.222 41.667 11.80 1.60 0.00 3.58
29 30 5.105310 TGAGTGGAGGAAGTAGCTAATTGTC 60.105 44.000 11.80 7.65 0.00 3.18
30 31 4.777896 TGAGTGGAGGAAGTAGCTAATTGT 59.222 41.667 11.80 0.00 0.00 2.71
31 32 5.105146 ACTGAGTGGAGGAAGTAGCTAATTG 60.105 44.000 11.80 0.00 0.00 2.32
32 33 5.026790 ACTGAGTGGAGGAAGTAGCTAATT 58.973 41.667 6.06 6.06 0.00 1.40
33 34 4.615513 ACTGAGTGGAGGAAGTAGCTAAT 58.384 43.478 0.00 0.00 0.00 1.73
34 35 4.048970 ACTGAGTGGAGGAAGTAGCTAA 57.951 45.455 0.00 0.00 0.00 3.09
35 36 3.741245 ACTGAGTGGAGGAAGTAGCTA 57.259 47.619 0.00 0.00 0.00 3.32
36 37 2.614134 ACTGAGTGGAGGAAGTAGCT 57.386 50.000 0.00 0.00 0.00 3.32
37 38 3.259625 AGAAACTGAGTGGAGGAAGTAGC 59.740 47.826 0.00 0.00 0.00 3.58
38 39 5.476091 AAGAAACTGAGTGGAGGAAGTAG 57.524 43.478 0.00 0.00 0.00 2.57
39 40 5.611374 CAAAGAAACTGAGTGGAGGAAGTA 58.389 41.667 0.00 0.00 0.00 2.24
40 41 4.455606 CAAAGAAACTGAGTGGAGGAAGT 58.544 43.478 0.00 0.00 0.00 3.01
41 42 3.251972 GCAAAGAAACTGAGTGGAGGAAG 59.748 47.826 0.00 0.00 0.00 3.46
42 43 3.214328 GCAAAGAAACTGAGTGGAGGAA 58.786 45.455 0.00 0.00 0.00 3.36
43 44 2.172505 TGCAAAGAAACTGAGTGGAGGA 59.827 45.455 0.00 0.00 0.00 3.71
44 45 2.575532 TGCAAAGAAACTGAGTGGAGG 58.424 47.619 0.00 0.00 0.00 4.30
45 46 3.611057 GCATGCAAAGAAACTGAGTGGAG 60.611 47.826 14.21 0.00 0.00 3.86
46 47 2.294233 GCATGCAAAGAAACTGAGTGGA 59.706 45.455 14.21 0.00 0.00 4.02
47 48 2.034939 TGCATGCAAAGAAACTGAGTGG 59.965 45.455 20.30 0.00 0.00 4.00
48 49 3.358707 TGCATGCAAAGAAACTGAGTG 57.641 42.857 20.30 0.00 0.00 3.51
49 50 3.909430 CATGCATGCAAAGAAACTGAGT 58.091 40.909 26.68 0.00 0.00 3.41
63 64 5.448225 GGATCATTAATACTCCGCATGCATG 60.448 44.000 22.70 22.70 0.00 4.06
64 65 4.637534 GGATCATTAATACTCCGCATGCAT 59.362 41.667 19.57 0.00 0.00 3.96
65 66 4.002982 GGATCATTAATACTCCGCATGCA 58.997 43.478 19.57 0.00 0.00 3.96
66 67 3.375299 GGGATCATTAATACTCCGCATGC 59.625 47.826 7.91 7.91 0.00 4.06
67 68 4.578871 TGGGATCATTAATACTCCGCATG 58.421 43.478 0.00 0.00 0.00 4.06
68 69 4.287067 ACTGGGATCATTAATACTCCGCAT 59.713 41.667 0.00 0.00 0.00 4.73
69 70 3.646162 ACTGGGATCATTAATACTCCGCA 59.354 43.478 0.00 7.45 0.00 5.69
70 71 4.273148 ACTGGGATCATTAATACTCCGC 57.727 45.455 0.00 4.35 0.00 5.54
71 72 7.214381 TGTTTACTGGGATCATTAATACTCCG 58.786 38.462 0.00 1.34 0.00 4.63
72 73 8.974060 TTGTTTACTGGGATCATTAATACTCC 57.026 34.615 6.85 6.85 0.00 3.85
73 74 9.832445 TCTTGTTTACTGGGATCATTAATACTC 57.168 33.333 0.00 0.00 0.00 2.59
77 78 9.753674 TTCTTCTTGTTTACTGGGATCATTAAT 57.246 29.630 0.00 0.00 0.00 1.40
78 79 9.581289 TTTCTTCTTGTTTACTGGGATCATTAA 57.419 29.630 0.00 0.00 0.00 1.40
79 80 9.581289 TTTTCTTCTTGTTTACTGGGATCATTA 57.419 29.630 0.00 0.00 0.00 1.90
80 81 8.477419 TTTTCTTCTTGTTTACTGGGATCATT 57.523 30.769 0.00 0.00 0.00 2.57
81 82 7.725844 ACTTTTCTTCTTGTTTACTGGGATCAT 59.274 33.333 0.00 0.00 0.00 2.45
82 83 7.060421 ACTTTTCTTCTTGTTTACTGGGATCA 58.940 34.615 0.00 0.00 0.00 2.92
83 84 7.511959 ACTTTTCTTCTTGTTTACTGGGATC 57.488 36.000 0.00 0.00 0.00 3.36
84 85 7.898014 AACTTTTCTTCTTGTTTACTGGGAT 57.102 32.000 0.00 0.00 0.00 3.85
85 86 8.680001 GTTAACTTTTCTTCTTGTTTACTGGGA 58.320 33.333 0.00 0.00 0.00 4.37
86 87 8.683615 AGTTAACTTTTCTTCTTGTTTACTGGG 58.316 33.333 1.12 0.00 33.14 4.45
94 95 9.569167 GCTTTACAAGTTAACTTTTCTTCTTGT 57.431 29.630 18.25 13.23 44.51 3.16
95 96 9.567848 TGCTTTACAAGTTAACTTTTCTTCTTG 57.432 29.630 18.25 8.00 38.40 3.02
96 97 9.788960 CTGCTTTACAAGTTAACTTTTCTTCTT 57.211 29.630 18.25 0.00 33.11 2.52
97 98 8.406297 CCTGCTTTACAAGTTAACTTTTCTTCT 58.594 33.333 18.25 0.00 33.11 2.85
98 99 7.167635 GCCTGCTTTACAAGTTAACTTTTCTTC 59.832 37.037 18.25 7.11 33.11 2.87
99 100 6.978659 GCCTGCTTTACAAGTTAACTTTTCTT 59.021 34.615 18.25 6.03 33.11 2.52
100 101 6.096282 TGCCTGCTTTACAAGTTAACTTTTCT 59.904 34.615 18.25 6.65 33.11 2.52
101 102 6.270064 TGCCTGCTTTACAAGTTAACTTTTC 58.730 36.000 18.25 1.50 33.11 2.29
102 103 6.215495 TGCCTGCTTTACAAGTTAACTTTT 57.785 33.333 18.25 14.64 33.11 2.27
103 104 5.845391 TGCCTGCTTTACAAGTTAACTTT 57.155 34.783 18.25 12.01 33.11 2.66
104 105 6.405278 AATGCCTGCTTTACAAGTTAACTT 57.595 33.333 15.22 15.22 36.45 2.66
105 106 7.519032 TTAATGCCTGCTTTACAAGTTAACT 57.481 32.000 1.12 1.12 0.00 2.24
106 107 8.757164 ATTTAATGCCTGCTTTACAAGTTAAC 57.243 30.769 0.00 0.00 0.00 2.01
107 108 9.771534 AAATTTAATGCCTGCTTTACAAGTTAA 57.228 25.926 0.00 0.00 0.00 2.01
108 109 9.771534 AAAATTTAATGCCTGCTTTACAAGTTA 57.228 25.926 0.00 0.00 0.00 2.24
109 110 8.675705 AAAATTTAATGCCTGCTTTACAAGTT 57.324 26.923 0.00 0.81 0.00 2.66
110 111 9.203421 GTAAAATTTAATGCCTGCTTTACAAGT 57.797 29.630 0.00 0.00 31.32 3.16
111 112 9.202273 TGTAAAATTTAATGCCTGCTTTACAAG 57.798 29.630 7.50 0.00 35.79 3.16
112 113 9.717942 ATGTAAAATTTAATGCCTGCTTTACAA 57.282 25.926 11.74 5.45 39.70 2.41
113 114 9.717942 AATGTAAAATTTAATGCCTGCTTTACA 57.282 25.926 10.71 10.71 40.23 2.41
114 115 9.971744 CAATGTAAAATTTAATGCCTGCTTTAC 57.028 29.630 0.00 0.00 0.00 2.01
115 116 9.717942 ACAATGTAAAATTTAATGCCTGCTTTA 57.282 25.926 0.00 0.00 0.00 1.85
116 117 8.620116 ACAATGTAAAATTTAATGCCTGCTTT 57.380 26.923 0.00 0.00 0.00 3.51
117 118 8.620116 AACAATGTAAAATTTAATGCCTGCTT 57.380 26.923 0.00 0.00 0.00 3.91
118 119 9.150348 GTAACAATGTAAAATTTAATGCCTGCT 57.850 29.630 0.00 0.00 0.00 4.24
119 120 8.930760 TGTAACAATGTAAAATTTAATGCCTGC 58.069 29.630 0.00 0.00 0.00 4.85
137 138 9.474920 CCACAAACTTGAATTACATGTAACAAT 57.525 29.630 20.26 9.90 36.16 2.71
138 139 8.470805 ACCACAAACTTGAATTACATGTAACAA 58.529 29.630 20.26 17.98 36.16 2.83
139 140 8.001881 ACCACAAACTTGAATTACATGTAACA 57.998 30.769 20.26 12.04 36.16 2.41
140 141 8.349983 AGACCACAAACTTGAATTACATGTAAC 58.650 33.333 20.26 9.57 36.16 2.50
141 142 8.458573 AGACCACAAACTTGAATTACATGTAA 57.541 30.769 20.14 20.14 36.16 2.41
142 143 8.349245 CAAGACCACAAACTTGAATTACATGTA 58.651 33.333 0.08 0.08 43.98 2.29
143 144 6.959639 AGACCACAAACTTGAATTACATGT 57.040 33.333 2.69 2.69 38.28 3.21
144 145 7.202526 ACAAGACCACAAACTTGAATTACATG 58.797 34.615 12.69 0.00 43.98 3.21
145 146 7.346751 ACAAGACCACAAACTTGAATTACAT 57.653 32.000 12.69 0.00 43.98 2.29
146 147 6.767524 ACAAGACCACAAACTTGAATTACA 57.232 33.333 12.69 0.00 43.98 2.41
158 159 9.184523 CCTCCATTTTTATATACAAGACCACAA 57.815 33.333 0.00 0.00 0.00 3.33
159 160 8.553153 TCCTCCATTTTTATATACAAGACCACA 58.447 33.333 0.00 0.00 0.00 4.17
160 161 8.974060 TCCTCCATTTTTATATACAAGACCAC 57.026 34.615 0.00 0.00 0.00 4.16
161 162 9.627123 CTTCCTCCATTTTTATATACAAGACCA 57.373 33.333 0.00 0.00 0.00 4.02
162 163 9.628500 ACTTCCTCCATTTTTATATACAAGACC 57.372 33.333 0.00 0.00 0.00 3.85
173 174 9.672673 CTTCTTCATCTACTTCCTCCATTTTTA 57.327 33.333 0.00 0.00 0.00 1.52
174 175 7.613411 CCTTCTTCATCTACTTCCTCCATTTTT 59.387 37.037 0.00 0.00 0.00 1.94
175 176 7.115414 CCTTCTTCATCTACTTCCTCCATTTT 58.885 38.462 0.00 0.00 0.00 1.82
176 177 6.216456 ACCTTCTTCATCTACTTCCTCCATTT 59.784 38.462 0.00 0.00 0.00 2.32
177 178 5.728741 ACCTTCTTCATCTACTTCCTCCATT 59.271 40.000 0.00 0.00 0.00 3.16
178 179 5.130145 CACCTTCTTCATCTACTTCCTCCAT 59.870 44.000 0.00 0.00 0.00 3.41
179 180 4.467795 CACCTTCTTCATCTACTTCCTCCA 59.532 45.833 0.00 0.00 0.00 3.86
180 181 4.712337 TCACCTTCTTCATCTACTTCCTCC 59.288 45.833 0.00 0.00 0.00 4.30
181 182 5.923733 TCACCTTCTTCATCTACTTCCTC 57.076 43.478 0.00 0.00 0.00 3.71
182 183 5.544176 TGTTCACCTTCTTCATCTACTTCCT 59.456 40.000 0.00 0.00 0.00 3.36
183 184 5.794894 TGTTCACCTTCTTCATCTACTTCC 58.205 41.667 0.00 0.00 0.00 3.46
184 185 6.459923 ACTGTTCACCTTCTTCATCTACTTC 58.540 40.000 0.00 0.00 0.00 3.01
185 186 6.426646 ACTGTTCACCTTCTTCATCTACTT 57.573 37.500 0.00 0.00 0.00 2.24
186 187 7.015292 TGTTACTGTTCACCTTCTTCATCTACT 59.985 37.037 0.00 0.00 0.00 2.57
187 188 7.152645 TGTTACTGTTCACCTTCTTCATCTAC 58.847 38.462 0.00 0.00 0.00 2.59
244 249 6.678540 TTCGTTCTTTATTTTTAAAGCGGC 57.321 33.333 0.00 0.00 37.07 6.53
326 332 3.861276 TCGTGTACGTTTCTGGATCAT 57.139 42.857 0.00 0.00 40.80 2.45
329 335 3.374220 TGTTCGTGTACGTTTCTGGAT 57.626 42.857 0.00 0.00 40.80 3.41
334 340 4.886779 CGTAAACTTGTTCGTGTACGTTTC 59.113 41.667 0.00 0.00 42.96 2.78
355 417 0.597568 TGGTTTACGTCGTGATCCGT 59.402 50.000 8.47 0.55 40.87 4.69
368 430 1.203052 CCGTCTAGAGCCGTTGGTTTA 59.797 52.381 0.00 0.00 0.00 2.01
372 434 0.249073 CATCCGTCTAGAGCCGTTGG 60.249 60.000 0.00 0.00 0.00 3.77
397 459 5.885230 TGATACAAGCCAGAAATTCACAG 57.115 39.130 0.00 0.00 0.00 3.66
464 530 6.480763 TCATTGCTAATTAACCAACTGAGGA 58.519 36.000 1.56 0.00 0.00 3.71
577 649 0.955905 ACACATTAACCGGCACAACC 59.044 50.000 0.00 0.00 0.00 3.77
615 687 6.921332 AAGTTGTCAAAGTGTTAAACGTTG 57.079 33.333 0.00 0.00 46.10 4.10
633 2711 1.452145 CGGGGTGGTGGTGAAAGTTG 61.452 60.000 0.00 0.00 0.00 3.16
639 2717 2.856039 TTTTTGCGGGGTGGTGGTGA 62.856 55.000 0.00 0.00 0.00 4.02
660 2738 2.091333 ACTGAGTGGGGTGGTGATTTTT 60.091 45.455 0.00 0.00 0.00 1.94
661 2739 1.499007 ACTGAGTGGGGTGGTGATTTT 59.501 47.619 0.00 0.00 0.00 1.82
662 2740 1.149101 ACTGAGTGGGGTGGTGATTT 58.851 50.000 0.00 0.00 0.00 2.17
663 2741 0.401738 CACTGAGTGGGGTGGTGATT 59.598 55.000 4.28 0.00 0.00 2.57
664 2742 2.069776 CACTGAGTGGGGTGGTGAT 58.930 57.895 4.28 0.00 0.00 3.06
665 2743 3.562250 CACTGAGTGGGGTGGTGA 58.438 61.111 4.28 0.00 0.00 4.02
674 2752 0.951040 GTCGGGAAAGCCACTGAGTG 60.951 60.000 5.42 5.42 35.15 3.51
675 2753 1.371558 GTCGGGAAAGCCACTGAGT 59.628 57.895 0.00 0.00 35.15 3.41
676 2754 0.951040 GTGTCGGGAAAGCCACTGAG 60.951 60.000 0.00 0.00 35.15 3.35
677 2755 1.070786 GTGTCGGGAAAGCCACTGA 59.929 57.895 0.00 0.00 35.15 3.41
678 2756 0.606401 ATGTGTCGGGAAAGCCACTG 60.606 55.000 0.00 0.00 35.15 3.66
679 2757 0.606401 CATGTGTCGGGAAAGCCACT 60.606 55.000 0.00 0.00 35.15 4.00
680 2758 0.605319 TCATGTGTCGGGAAAGCCAC 60.605 55.000 0.00 0.00 35.15 5.01
681 2759 0.327924 ATCATGTGTCGGGAAAGCCA 59.672 50.000 0.00 0.00 35.15 4.75
800 2878 6.293845 GCTCTGATGCTGAAAGAAGAAGAAAA 60.294 38.462 0.00 0.00 34.07 2.29
804 2882 4.001652 TGCTCTGATGCTGAAAGAAGAAG 58.998 43.478 0.00 0.00 34.07 2.85
888 2968 6.016860 TGTTTGTGTTGATGAGAAGAATGAGG 60.017 38.462 0.00 0.00 0.00 3.86
894 2974 6.057533 AGATGTGTTTGTGTTGATGAGAAGA 58.942 36.000 0.00 0.00 0.00 2.87
1119 3199 0.744771 GGACGAAGATGGACTTGCCC 60.745 60.000 0.00 0.00 39.13 5.36
1326 3408 1.119574 AGTACGTGCCCACCTTGACT 61.120 55.000 0.00 0.00 0.00 3.41
1341 3423 6.402456 ACTATTTTGGATCGGAGGTAGTAC 57.598 41.667 0.00 0.00 0.00 2.73
1346 3428 3.279434 GCAACTATTTTGGATCGGAGGT 58.721 45.455 0.00 0.00 0.00 3.85
1365 3447 2.147958 ACCTTAATTCGAAACTGCGCA 58.852 42.857 10.98 10.98 0.00 6.09
1504 3586 4.002982 TGAACAATAAGATGCAGTTCGCT 58.997 39.130 7.86 0.00 40.95 4.93
1506 3588 4.337763 GCTGAACAATAAGATGCAGTTCG 58.662 43.478 7.86 4.97 40.95 3.95
1515 3597 4.901197 TGGTACAGGCTGAACAATAAGA 57.099 40.909 23.66 0.00 0.00 2.10
1561 3643 2.037772 ACGAAAGGTCATGAGAAGCTGT 59.962 45.455 0.00 0.00 0.00 4.40
1674 3756 3.640029 TGGACGGATGGAGTATAAAGTCC 59.360 47.826 4.52 4.52 44.51 3.85
1697 3779 6.897413 ACATCCATATAAGGGACAAGCTTTTT 59.103 34.615 0.00 0.00 37.23 1.94
1698 3780 6.435164 ACATCCATATAAGGGACAAGCTTTT 58.565 36.000 0.00 0.00 37.23 2.27
1699 3781 6.018433 ACATCCATATAAGGGACAAGCTTT 57.982 37.500 0.00 0.00 37.23 3.51
1700 3782 5.653255 ACATCCATATAAGGGACAAGCTT 57.347 39.130 0.00 0.00 37.23 3.74
1701 3783 6.732862 AGATACATCCATATAAGGGACAAGCT 59.267 38.462 0.00 0.00 37.23 3.74
1702 3784 6.951971 AGATACATCCATATAAGGGACAAGC 58.048 40.000 0.00 0.00 37.23 4.01
1703 3785 9.877178 GTTAGATACATCCATATAAGGGACAAG 57.123 37.037 0.00 0.00 37.23 3.16
1704 3786 9.387397 TGTTAGATACATCCATATAAGGGACAA 57.613 33.333 0.00 0.00 37.23 3.18
1705 3787 8.966155 TGTTAGATACATCCATATAAGGGACA 57.034 34.615 0.00 0.00 37.23 4.02
1727 3809 9.277783 GGATGTATCTAGCACTAATTTGATGTT 57.722 33.333 0.00 0.00 0.00 2.71
1728 3810 8.432013 TGGATGTATCTAGCACTAATTTGATGT 58.568 33.333 0.00 0.00 0.00 3.06
1729 3811 8.837788 TGGATGTATCTAGCACTAATTTGATG 57.162 34.615 0.00 0.00 0.00 3.07
1731 3813 9.494271 GAATGGATGTATCTAGCACTAATTTGA 57.506 33.333 0.00 0.00 0.00 2.69
1732 3814 8.438513 CGAATGGATGTATCTAGCACTAATTTG 58.561 37.037 0.00 0.00 0.00 2.32
1733 3815 8.367911 TCGAATGGATGTATCTAGCACTAATTT 58.632 33.333 0.00 0.00 0.00 1.82
1734 3816 7.896811 TCGAATGGATGTATCTAGCACTAATT 58.103 34.615 0.00 0.00 0.00 1.40
1735 3817 7.394641 TCTCGAATGGATGTATCTAGCACTAAT 59.605 37.037 0.00 0.00 0.00 1.73
1736 3818 6.715264 TCTCGAATGGATGTATCTAGCACTAA 59.285 38.462 0.00 0.00 0.00 2.24
1737 3819 6.238648 TCTCGAATGGATGTATCTAGCACTA 58.761 40.000 0.00 0.00 0.00 2.74
1738 3820 5.073428 TCTCGAATGGATGTATCTAGCACT 58.927 41.667 0.00 0.00 0.00 4.40
1739 3821 5.378292 TCTCGAATGGATGTATCTAGCAC 57.622 43.478 0.00 0.00 0.00 4.40
1740 3822 6.183360 TGTTTCTCGAATGGATGTATCTAGCA 60.183 38.462 0.00 0.00 0.00 3.49
1741 3823 6.216569 TGTTTCTCGAATGGATGTATCTAGC 58.783 40.000 0.00 0.00 0.00 3.42
1742 3824 7.095857 GCTTGTTTCTCGAATGGATGTATCTAG 60.096 40.741 0.00 0.00 0.00 2.43
1743 3825 6.701841 GCTTGTTTCTCGAATGGATGTATCTA 59.298 38.462 0.00 0.00 0.00 1.98
1744 3826 5.525378 GCTTGTTTCTCGAATGGATGTATCT 59.475 40.000 0.00 0.00 0.00 1.98
1745 3827 5.525378 AGCTTGTTTCTCGAATGGATGTATC 59.475 40.000 0.00 0.00 0.00 2.24
1746 3828 5.431765 AGCTTGTTTCTCGAATGGATGTAT 58.568 37.500 0.00 0.00 0.00 2.29
1747 3829 4.832248 AGCTTGTTTCTCGAATGGATGTA 58.168 39.130 0.00 0.00 0.00 2.29
1748 3830 3.679389 AGCTTGTTTCTCGAATGGATGT 58.321 40.909 0.00 0.00 0.00 3.06
1749 3831 4.409570 CAAGCTTGTTTCTCGAATGGATG 58.590 43.478 18.65 0.00 0.00 3.51
1750 3832 3.441572 CCAAGCTTGTTTCTCGAATGGAT 59.558 43.478 24.35 0.00 0.00 3.41
1751 3833 2.813754 CCAAGCTTGTTTCTCGAATGGA 59.186 45.455 24.35 0.00 0.00 3.41
1752 3834 2.095059 CCCAAGCTTGTTTCTCGAATGG 60.095 50.000 24.35 10.71 0.00 3.16
1753 3835 2.813754 TCCCAAGCTTGTTTCTCGAATG 59.186 45.455 24.35 5.47 0.00 2.67
1754 3836 2.814336 GTCCCAAGCTTGTTTCTCGAAT 59.186 45.455 24.35 0.00 0.00 3.34
1755 3837 2.218603 GTCCCAAGCTTGTTTCTCGAA 58.781 47.619 24.35 0.00 0.00 3.71
1756 3838 1.140052 TGTCCCAAGCTTGTTTCTCGA 59.860 47.619 24.35 7.45 0.00 4.04
1757 3839 1.593196 TGTCCCAAGCTTGTTTCTCG 58.407 50.000 24.35 8.31 0.00 4.04
1758 3840 2.287849 GCTTGTCCCAAGCTTGTTTCTC 60.288 50.000 24.35 10.65 40.01 2.87
1759 3841 1.683385 GCTTGTCCCAAGCTTGTTTCT 59.317 47.619 24.35 0.00 40.01 2.52
1760 3842 2.140065 GCTTGTCCCAAGCTTGTTTC 57.860 50.000 24.35 13.85 40.01 2.78
1767 3849 1.000171 CTGGAAAAGCTTGTCCCAAGC 60.000 52.381 29.33 18.69 43.31 4.01
1768 3850 2.294512 GTCTGGAAAAGCTTGTCCCAAG 59.705 50.000 29.33 21.49 32.48 3.61
1769 3851 2.306847 GTCTGGAAAAGCTTGTCCCAA 58.693 47.619 29.33 16.45 32.48 4.12
1770 3852 1.813862 CGTCTGGAAAAGCTTGTCCCA 60.814 52.381 29.33 20.18 32.48 4.37
1771 3853 0.875059 CGTCTGGAAAAGCTTGTCCC 59.125 55.000 29.33 15.25 32.48 4.46
1772 3854 0.875059 CCGTCTGGAAAAGCTTGTCC 59.125 55.000 26.56 26.56 37.49 4.02
1773 3855 1.801178 CTCCGTCTGGAAAAGCTTGTC 59.199 52.381 8.23 8.23 45.87 3.18
1774 3856 1.543429 CCTCCGTCTGGAAAAGCTTGT 60.543 52.381 0.00 0.00 45.87 3.16
1775 3857 1.160137 CCTCCGTCTGGAAAAGCTTG 58.840 55.000 0.00 0.00 45.87 4.01
1776 3858 1.056660 TCCTCCGTCTGGAAAAGCTT 58.943 50.000 0.00 0.00 45.87 3.74
1777 3859 1.002544 CTTCCTCCGTCTGGAAAAGCT 59.997 52.381 0.00 0.00 45.87 3.74
1778 3860 1.270893 ACTTCCTCCGTCTGGAAAAGC 60.271 52.381 0.00 0.00 45.87 3.51
1779 3861 2.841442 ACTTCCTCCGTCTGGAAAAG 57.159 50.000 0.00 5.16 45.87 2.27
1780 3862 4.903045 AATACTTCCTCCGTCTGGAAAA 57.097 40.909 0.00 0.00 45.87 2.29
1781 3863 4.903045 AAATACTTCCTCCGTCTGGAAA 57.097 40.909 0.00 0.00 45.87 3.13
1782 3864 5.424252 ACATAAATACTTCCTCCGTCTGGAA 59.576 40.000 0.00 0.00 45.87 3.53
1783 3865 4.960469 ACATAAATACTTCCTCCGTCTGGA 59.040 41.667 0.00 0.00 43.88 3.86
1784 3866 5.277857 ACATAAATACTTCCTCCGTCTGG 57.722 43.478 0.00 0.00 0.00 3.86
1785 3867 7.490000 ACTTACATAAATACTTCCTCCGTCTG 58.510 38.462 0.00 0.00 0.00 3.51
1786 3868 7.657023 ACTTACATAAATACTTCCTCCGTCT 57.343 36.000 0.00 0.00 0.00 4.18
1787 3869 7.763071 ACAACTTACATAAATACTTCCTCCGTC 59.237 37.037 0.00 0.00 0.00 4.79
1788 3870 7.618137 ACAACTTACATAAATACTTCCTCCGT 58.382 34.615 0.00 0.00 0.00 4.69
1789 3871 8.488651 AACAACTTACATAAATACTTCCTCCG 57.511 34.615 0.00 0.00 0.00 4.63
1825 3907 0.179020 CCGATGCCATCCAAAGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
1926 4008 5.679734 AAATATGCACGGATCTCAATGTC 57.320 39.130 0.00 0.00 0.00 3.06
2167 4597 9.190858 CTCTCTATGACTGTATATTTGAGTTGC 57.809 37.037 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.