Multiple sequence alignment - TraesCS6A01G224300

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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 TraesCS6A01G224300 chr6A 100.000 2941 0 0 1 2941 421366806 421369746 0.000000e+00 5432.0
1 TraesCS6A01G224300 chr6A 88.016 1018 75 22 846 1829 421225821 421226825 0.000000e+00 1160.0
2 TraesCS6A01G224300 chr6A 90.920 826 48 17 1028 1829 420973657 420974479 0.000000e+00 1085.0
3 TraesCS6A01G224300 chr6A 90.085 827 54 18 1029 1830 421102716 421103539 0.000000e+00 1048.0
4 TraesCS6A01G224300 chr6A 97.481 397 9 1 590 985 421463281 421463677 0.000000e+00 676.0
5 TraesCS6A01G224300 chr6A 90.123 81 6 2 2145 2225 421254921 421254999 1.440000e-18 104.0
6 TraesCS6A01G224300 chr6D 89.625 1041 57 20 820 1829 298207546 298206526 0.000000e+00 1277.0
7 TraesCS6A01G224300 chr6D 89.235 994 60 13 1074 2059 297407378 297406424 0.000000e+00 1199.0
8 TraesCS6A01G224300 chr6D 90.090 888 47 9 982 1863 297489994 297489142 0.000000e+00 1114.0
9 TraesCS6A01G224300 chr6D 91.925 805 46 8 1040 1830 298444843 298444044 0.000000e+00 1109.0
10 TraesCS6A01G224300 chr6D 92.598 635 26 6 2233 2854 297488818 297488192 0.000000e+00 893.0
11 TraesCS6A01G224300 chr6D 87.092 674 73 9 2258 2926 297405096 297404432 0.000000e+00 750.0
12 TraesCS6A01G224300 chr6D 88.952 525 36 9 259 767 297514564 297514046 1.920000e-176 628.0
13 TraesCS6A01G224300 chr6D 93.197 294 18 2 513 804 296994337 296994044 5.820000e-117 431.0
14 TraesCS6A01G224300 chr6D 91.830 306 17 4 687 985 297407826 297407522 1.260000e-113 420.0
15 TraesCS6A01G224300 chr6D 94.421 233 11 2 755 985 297490279 297490047 1.000000e-94 357.0
16 TraesCS6A01G224300 chr6D 93.421 228 12 3 424 650 297429255 297429030 4.700000e-88 335.0
17 TraesCS6A01G224300 chr6D 93.583 187 11 1 800 985 296993844 296993658 8.030000e-71 278.0
18 TraesCS6A01G224300 chr6D 95.783 166 6 1 259 424 297430907 297430743 1.740000e-67 267.0
19 TraesCS6A01G224300 chr6D 82.528 269 16 10 1895 2160 297489144 297488904 1.070000e-49 207.0
20 TraesCS6A01G224300 chr6D 94.444 36 2 0 2906 2941 297404431 297404396 4.090000e-04 56.5
21 TraesCS6A01G224300 chr6B 88.496 1017 76 21 846 1830 461848509 461847502 0.000000e+00 1192.0
22 TraesCS6A01G224300 chr6B 93.257 786 43 5 1074 1850 461961868 461961084 0.000000e+00 1149.0
23 TraesCS6A01G224300 chr6B 90.552 815 60 8 1028 1830 461903715 461902906 0.000000e+00 1062.0
24 TraesCS6A01G224300 chr6B 93.008 472 22 5 516 985 461395289 461394827 0.000000e+00 678.0
25 TraesCS6A01G224300 chr6B 82.591 718 103 11 2233 2941 461846112 461845408 5.390000e-172 614.0
26 TraesCS6A01G224300 chr6B 92.537 268 18 2 259 525 461402886 461402620 1.650000e-102 383.0
27 TraesCS6A01G224300 chr6B 88.235 272 26 5 2235 2504 461432139 461431872 1.320000e-83 320.0
28 TraesCS6A01G224300 chr6B 92.810 153 11 0 259 411 461589038 461588886 3.820000e-54 222.0
29 TraesCS6A01G224300 chr7D 93.609 266 14 3 1 266 568325187 568324925 7.640000e-106 394.0
30 TraesCS6A01G224300 chr1D 93.798 258 14 2 1 258 415157333 415157588 1.280000e-103 387.0
31 TraesCS6A01G224300 chr5A 92.720 261 13 5 1 258 28647941 28648198 3.580000e-99 372.0
32 TraesCS6A01G224300 chr1A 91.954 261 15 5 1 258 555103558 555103815 7.750000e-96 361.0
33 TraesCS6A01G224300 chr1A 91.255 263 16 6 1 260 251142255 251141997 4.660000e-93 351.0
34 TraesCS6A01G224300 chr7A 91.698 265 13 4 1 265 641109820 641109565 2.790000e-95 359.0
35 TraesCS6A01G224300 chr7A 91.045 268 18 5 1 265 86148903 86149167 1.000000e-94 357.0
36 TraesCS6A01G224300 chr3B 91.221 262 20 3 4 265 199644350 199644092 1.300000e-93 353.0
37 TraesCS6A01G224300 chr3B 91.473 258 16 6 3 258 772757426 772757679 1.680000e-92 350.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G224300 chr6A 421366806 421369746 2940 False 5432.000 5432 100.00000 1 2941 1 chr6A.!!$F5 2940
1 TraesCS6A01G224300 chr6A 421225821 421226825 1004 False 1160.000 1160 88.01600 846 1829 1 chr6A.!!$F3 983
2 TraesCS6A01G224300 chr6A 420973657 420974479 822 False 1085.000 1085 90.92000 1028 1829 1 chr6A.!!$F1 801
3 TraesCS6A01G224300 chr6A 421102716 421103539 823 False 1048.000 1048 90.08500 1029 1830 1 chr6A.!!$F2 801
4 TraesCS6A01G224300 chr6D 298206526 298207546 1020 True 1277.000 1277 89.62500 820 1829 1 chr6D.!!$R2 1009
5 TraesCS6A01G224300 chr6D 298444044 298444843 799 True 1109.000 1109 91.92500 1040 1830 1 chr6D.!!$R3 790
6 TraesCS6A01G224300 chr6D 297488192 297490279 2087 True 642.750 1114 89.90925 755 2854 4 chr6D.!!$R7 2099
7 TraesCS6A01G224300 chr6D 297514046 297514564 518 True 628.000 628 88.95200 259 767 1 chr6D.!!$R1 508
8 TraesCS6A01G224300 chr6D 297404396 297407826 3430 True 606.375 1199 90.65025 687 2941 4 chr6D.!!$R5 2254
9 TraesCS6A01G224300 chr6D 296993658 296994337 679 True 354.500 431 93.39000 513 985 2 chr6D.!!$R4 472
10 TraesCS6A01G224300 chr6D 297429030 297430907 1877 True 301.000 335 94.60200 259 650 2 chr6D.!!$R6 391
11 TraesCS6A01G224300 chr6B 461961084 461961868 784 True 1149.000 1149 93.25700 1074 1850 1 chr6B.!!$R6 776
12 TraesCS6A01G224300 chr6B 461902906 461903715 809 True 1062.000 1062 90.55200 1028 1830 1 chr6B.!!$R5 802
13 TraesCS6A01G224300 chr6B 461845408 461848509 3101 True 903.000 1192 85.54350 846 2941 2 chr6B.!!$R7 2095

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
141 142 0.100146 AACCCGTGCGCGTTTAAAAA 59.900 45.0 19.61 0.00 36.15 1.94 F
169 170 0.108377 ATCTGATAACACGTGGCGCA 60.108 50.0 21.57 11.06 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1009 2787 0.309922 TTCTCGGTCGAGTGTGTGAC 59.690 55.000 18.18 0.0 42.49 3.67 R
2063 4847 1.197264 ACAAGAGTCGTCGTCTAGTGC 59.803 52.381 0.00 0.0 0.00 4.40 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
27 28 4.959596 GCCGCCGCTCCTGATCTC 62.960 72.222 0.00 0.00 0.00 2.75
28 29 4.292178 CCGCCGCTCCTGATCTCC 62.292 72.222 0.00 0.00 0.00 3.71
29 30 3.531207 CGCCGCTCCTGATCTCCA 61.531 66.667 0.00 0.00 0.00 3.86
30 31 2.420890 GCCGCTCCTGATCTCCAG 59.579 66.667 0.00 0.00 42.55 3.86
37 38 2.586245 CTGATCTCCAGGCGCCAA 59.414 61.111 31.54 12.89 39.23 4.52
38 39 1.817099 CTGATCTCCAGGCGCCAAC 60.817 63.158 31.54 6.62 39.23 3.77
39 40 2.268920 GATCTCCAGGCGCCAACA 59.731 61.111 31.54 10.38 0.00 3.33
40 41 1.377202 GATCTCCAGGCGCCAACAA 60.377 57.895 31.54 10.31 0.00 2.83
41 42 1.372087 GATCTCCAGGCGCCAACAAG 61.372 60.000 31.54 19.51 0.00 3.16
42 43 3.741476 CTCCAGGCGCCAACAAGC 61.741 66.667 31.54 0.00 0.00 4.01
71 72 4.785453 CGGTTGCCCTGCCTCCTC 62.785 72.222 0.00 0.00 0.00 3.71
72 73 4.785453 GGTTGCCCTGCCTCCTCG 62.785 72.222 0.00 0.00 0.00 4.63
77 78 4.463879 CCCTGCCTCCTCGCACTG 62.464 72.222 0.00 0.00 34.35 3.66
78 79 3.385384 CCTGCCTCCTCGCACTGA 61.385 66.667 0.00 0.00 34.35 3.41
79 80 2.659016 CTGCCTCCTCGCACTGAA 59.341 61.111 0.00 0.00 34.35 3.02
80 81 1.004560 CTGCCTCCTCGCACTGAAA 60.005 57.895 0.00 0.00 34.35 2.69
81 82 0.392193 CTGCCTCCTCGCACTGAAAT 60.392 55.000 0.00 0.00 34.35 2.17
82 83 0.674581 TGCCTCCTCGCACTGAAATG 60.675 55.000 0.00 0.00 32.62 2.32
83 84 0.391661 GCCTCCTCGCACTGAAATGA 60.392 55.000 0.00 0.00 0.00 2.57
84 85 1.363744 CCTCCTCGCACTGAAATGAC 58.636 55.000 0.00 0.00 0.00 3.06
85 86 1.338105 CCTCCTCGCACTGAAATGACA 60.338 52.381 0.00 0.00 0.00 3.58
86 87 1.728971 CTCCTCGCACTGAAATGACAC 59.271 52.381 0.00 0.00 0.00 3.67
87 88 0.798776 CCTCGCACTGAAATGACACC 59.201 55.000 0.00 0.00 0.00 4.16
88 89 0.798776 CTCGCACTGAAATGACACCC 59.201 55.000 0.00 0.00 0.00 4.61
89 90 0.605319 TCGCACTGAAATGACACCCC 60.605 55.000 0.00 0.00 0.00 4.95
90 91 1.586154 CGCACTGAAATGACACCCCC 61.586 60.000 0.00 0.00 0.00 5.40
91 92 1.586154 GCACTGAAATGACACCCCCG 61.586 60.000 0.00 0.00 0.00 5.73
92 93 0.250727 CACTGAAATGACACCCCCGT 60.251 55.000 0.00 0.00 0.00 5.28
93 94 0.250727 ACTGAAATGACACCCCCGTG 60.251 55.000 0.00 0.00 46.11 4.94
94 95 1.586154 CTGAAATGACACCCCCGTGC 61.586 60.000 0.00 0.00 44.40 5.34
95 96 2.671619 AAATGACACCCCCGTGCG 60.672 61.111 0.00 0.00 44.40 5.34
96 97 4.715523 AATGACACCCCCGTGCGG 62.716 66.667 3.25 3.25 44.40 5.69
110 111 4.418337 GCGGTTGCAGCAAAAACT 57.582 50.000 10.11 0.00 42.15 2.66
111 112 1.926490 GCGGTTGCAGCAAAAACTG 59.074 52.632 10.11 4.67 42.15 3.16
112 113 1.489881 GCGGTTGCAGCAAAAACTGG 61.490 55.000 10.11 0.00 42.15 4.00
113 114 0.875474 CGGTTGCAGCAAAAACTGGG 60.875 55.000 10.11 0.00 38.16 4.45
114 115 0.463620 GGTTGCAGCAAAAACTGGGA 59.536 50.000 10.11 0.00 38.16 4.37
115 116 1.134551 GGTTGCAGCAAAAACTGGGAA 60.135 47.619 10.11 0.00 38.16 3.97
116 117 2.626840 GTTGCAGCAAAAACTGGGAAA 58.373 42.857 10.11 0.00 38.16 3.13
117 118 2.600470 TGCAGCAAAAACTGGGAAAG 57.400 45.000 0.00 0.00 38.16 2.62
118 119 1.138661 TGCAGCAAAAACTGGGAAAGG 59.861 47.619 0.00 0.00 38.16 3.11
119 120 1.541015 GCAGCAAAAACTGGGAAAGGG 60.541 52.381 0.00 0.00 38.16 3.95
120 121 2.038659 CAGCAAAAACTGGGAAAGGGA 58.961 47.619 0.00 0.00 33.85 4.20
121 122 2.634453 CAGCAAAAACTGGGAAAGGGAT 59.366 45.455 0.00 0.00 33.85 3.85
122 123 3.831911 CAGCAAAAACTGGGAAAGGGATA 59.168 43.478 0.00 0.00 33.85 2.59
123 124 4.283212 CAGCAAAAACTGGGAAAGGGATAA 59.717 41.667 0.00 0.00 33.85 1.75
124 125 4.283467 AGCAAAAACTGGGAAAGGGATAAC 59.717 41.667 0.00 0.00 0.00 1.89
125 126 4.562757 GCAAAAACTGGGAAAGGGATAACC 60.563 45.833 0.00 0.00 40.67 2.85
135 136 2.816520 GGATAACCCGTGCGCGTT 60.817 61.111 19.61 9.82 36.15 4.84
136 137 2.392974 GGATAACCCGTGCGCGTTT 61.393 57.895 19.61 13.41 36.15 3.60
137 138 1.083242 GGATAACCCGTGCGCGTTTA 61.083 55.000 19.61 15.14 36.15 2.01
138 139 0.720590 GATAACCCGTGCGCGTTTAA 59.279 50.000 19.61 1.53 36.15 1.52
139 140 1.128321 GATAACCCGTGCGCGTTTAAA 59.872 47.619 19.61 0.00 36.15 1.52
140 141 0.940126 TAACCCGTGCGCGTTTAAAA 59.060 45.000 19.61 0.00 36.15 1.52
141 142 0.100146 AACCCGTGCGCGTTTAAAAA 59.900 45.000 19.61 0.00 36.15 1.94
165 166 7.496529 AAAATATGGATCTGATAACACGTGG 57.503 36.000 21.57 0.08 0.00 4.94
166 167 2.309528 TGGATCTGATAACACGTGGC 57.690 50.000 21.57 6.76 0.00 5.01
167 168 1.209128 GGATCTGATAACACGTGGCG 58.791 55.000 21.57 0.00 0.00 5.69
168 169 0.577269 GATCTGATAACACGTGGCGC 59.423 55.000 21.57 0.00 0.00 6.53
169 170 0.108377 ATCTGATAACACGTGGCGCA 60.108 50.000 21.57 11.06 0.00 6.09
170 171 0.735978 TCTGATAACACGTGGCGCAG 60.736 55.000 21.57 19.38 0.00 5.18
171 172 0.735978 CTGATAACACGTGGCGCAGA 60.736 55.000 21.57 0.00 0.00 4.26
172 173 1.011968 TGATAACACGTGGCGCAGAC 61.012 55.000 21.57 3.89 0.00 3.51
184 185 2.343758 GCAGACAGCGTCCTTGGA 59.656 61.111 5.29 0.00 32.18 3.53
185 186 1.078848 GCAGACAGCGTCCTTGGAT 60.079 57.895 5.29 0.00 32.18 3.41
186 187 1.086634 GCAGACAGCGTCCTTGGATC 61.087 60.000 5.29 0.00 32.18 3.36
187 188 0.247460 CAGACAGCGTCCTTGGATCA 59.753 55.000 0.00 0.00 32.18 2.92
188 189 0.976641 AGACAGCGTCCTTGGATCAA 59.023 50.000 0.00 0.00 32.18 2.57
189 190 1.347707 AGACAGCGTCCTTGGATCAAA 59.652 47.619 0.00 0.00 32.18 2.69
190 191 1.734465 GACAGCGTCCTTGGATCAAAG 59.266 52.381 2.48 2.48 0.00 2.77
191 192 1.089920 CAGCGTCCTTGGATCAAAGG 58.910 55.000 21.55 21.55 46.99 3.11
203 204 2.632377 GATCAAAGGAGATCCAACGCA 58.368 47.619 0.92 0.00 38.75 5.24
204 205 1.808411 TCAAAGGAGATCCAACGCAC 58.192 50.000 0.92 0.00 38.89 5.34
205 206 0.443869 CAAAGGAGATCCAACGCACG 59.556 55.000 0.92 0.00 38.89 5.34
206 207 0.673644 AAAGGAGATCCAACGCACGG 60.674 55.000 0.92 0.00 38.89 4.94
207 208 1.541310 AAGGAGATCCAACGCACGGA 61.541 55.000 0.92 0.00 38.89 4.69
208 209 1.079405 GGAGATCCAACGCACGGAA 60.079 57.895 0.00 0.00 35.77 4.30
209 210 1.359459 GGAGATCCAACGCACGGAAC 61.359 60.000 0.00 0.00 35.77 3.62
252 253 3.977244 CGCCCCAGCCACAAACAC 61.977 66.667 0.00 0.00 34.57 3.32
253 254 2.521708 GCCCCAGCCACAAACACT 60.522 61.111 0.00 0.00 0.00 3.55
254 255 2.133641 GCCCCAGCCACAAACACTT 61.134 57.895 0.00 0.00 0.00 3.16
255 256 2.041153 CCCCAGCCACAAACACTTC 58.959 57.895 0.00 0.00 0.00 3.01
256 257 1.463553 CCCCAGCCACAAACACTTCC 61.464 60.000 0.00 0.00 0.00 3.46
257 258 1.463553 CCCAGCCACAAACACTTCCC 61.464 60.000 0.00 0.00 0.00 3.97
370 371 6.279882 TCGGAAACTTTCAATTCTTGCATTT 58.720 32.000 3.93 0.00 0.00 2.32
393 394 3.684788 AGTAATTCGGATGTGCACACTTC 59.315 43.478 24.37 16.91 35.48 3.01
413 425 7.607991 ACACTTCCTATTGGTGAAACTATCAAG 59.392 37.037 0.00 0.00 40.50 3.02
608 2111 5.107109 CAGTAGTATGCTGCTCTCTAGTG 57.893 47.826 0.00 9.42 43.16 2.74
650 2156 3.677596 CACCAATAACCGGAAACAATTGC 59.322 43.478 9.46 0.00 0.00 3.56
685 2192 6.548321 TGTAGATAACCATGGAACCAAAAGT 58.452 36.000 21.47 0.00 0.00 2.66
694 2201 4.171878 TGGAACCAAAAGTACATCACCA 57.828 40.909 0.00 0.00 0.00 4.17
740 2249 4.409218 GCACACACGCATGCCTGG 62.409 66.667 18.94 11.19 35.73 4.45
787 2297 1.204704 AGAAGCCGGGCAATAAAAAGC 59.795 47.619 23.09 0.00 0.00 3.51
903 2624 3.064324 AATGGCCGCAACTGCTCC 61.064 61.111 0.00 1.92 39.32 4.70
931 2652 2.293399 GCTCCAATTGACCACGTTTTCT 59.707 45.455 7.12 0.00 0.00 2.52
1008 2786 4.275689 GTCAACACACTGAACAATCCATCA 59.724 41.667 0.00 0.00 0.00 3.07
1009 2787 4.516321 TCAACACACTGAACAATCCATCAG 59.484 41.667 1.46 1.46 46.69 2.90
1060 2853 1.123861 AGGTGCAGAGGAGTGAGCAA 61.124 55.000 0.00 0.00 38.91 3.91
1063 2862 0.604780 TGCAGAGGAGTGAGCAAAGC 60.605 55.000 0.00 0.00 33.48 3.51
1066 2865 1.534595 CAGAGGAGTGAGCAAAGCAAC 59.465 52.381 0.00 0.00 0.00 4.17
1067 2866 1.419387 AGAGGAGTGAGCAAAGCAACT 59.581 47.619 0.00 0.00 32.00 3.16
1072 2871 2.549754 GAGTGAGCAAAGCAACTAAGCA 59.450 45.455 0.00 0.00 36.85 3.91
1085 2884 3.146104 ACTAAGCAAGCAATGGTGAGT 57.854 42.857 6.03 6.03 44.79 3.41
1151 2950 0.978146 CGGAGGAGGACATGACCCTT 60.978 60.000 10.77 0.00 33.36 3.95
1181 2980 4.996434 GAGCAGCACGGGCACAGT 62.996 66.667 14.57 0.00 44.61 3.55
1192 2991 2.032071 GCACAGTAACTGGCGGGT 59.968 61.111 0.00 0.00 35.51 5.28
1322 3121 2.512896 AGAAGCCATCATCCAACTCCAT 59.487 45.455 0.00 0.00 0.00 3.41
1409 3208 0.530650 AGAACGTCTGGCACACACAG 60.531 55.000 0.00 0.00 37.30 3.66
1440 3242 0.822532 ACTCCAGTCGTCGTCCAAGT 60.823 55.000 0.00 0.00 0.00 3.16
1689 3512 0.666274 GACACTTGCGATGTCGGTGA 60.666 55.000 14.24 0.00 37.34 4.02
1923 4688 2.545742 GGAAACGAGGCAAGCAAACAAT 60.546 45.455 0.00 0.00 0.00 2.71
1925 4690 4.295051 GAAACGAGGCAAGCAAACAATAA 58.705 39.130 0.00 0.00 0.00 1.40
2023 4807 3.814504 ATGAACAGGGAAGTGACCAAT 57.185 42.857 0.00 0.00 0.00 3.16
2036 4820 4.432712 AGTGACCAATCAAGCAAAACAAC 58.567 39.130 0.00 0.00 36.31 3.32
2037 4821 4.081752 AGTGACCAATCAAGCAAAACAACA 60.082 37.500 0.00 0.00 36.31 3.33
2038 4822 4.810491 GTGACCAATCAAGCAAAACAACAT 59.190 37.500 0.00 0.00 36.31 2.71
2039 4823 5.982516 GTGACCAATCAAGCAAAACAACATA 59.017 36.000 0.00 0.00 36.31 2.29
2040 4824 6.478344 GTGACCAATCAAGCAAAACAACATAA 59.522 34.615 0.00 0.00 36.31 1.90
2041 4825 6.478344 TGACCAATCAAGCAAAACAACATAAC 59.522 34.615 0.00 0.00 0.00 1.89
2042 4826 6.344500 ACCAATCAAGCAAAACAACATAACA 58.656 32.000 0.00 0.00 0.00 2.41
2043 4827 6.257630 ACCAATCAAGCAAAACAACATAACAC 59.742 34.615 0.00 0.00 0.00 3.32
2044 4828 6.292811 CCAATCAAGCAAAACAACATAACACC 60.293 38.462 0.00 0.00 0.00 4.16
2045 4829 5.590530 TCAAGCAAAACAACATAACACCT 57.409 34.783 0.00 0.00 0.00 4.00
2046 4830 6.701145 TCAAGCAAAACAACATAACACCTA 57.299 33.333 0.00 0.00 0.00 3.08
2047 4831 6.500041 TCAAGCAAAACAACATAACACCTAC 58.500 36.000 0.00 0.00 0.00 3.18
2048 4832 6.095580 TCAAGCAAAACAACATAACACCTACA 59.904 34.615 0.00 0.00 0.00 2.74
2049 4833 6.648879 AGCAAAACAACATAACACCTACAT 57.351 33.333 0.00 0.00 0.00 2.29
2050 4834 6.446318 AGCAAAACAACATAACACCTACATG 58.554 36.000 0.00 0.00 0.00 3.21
2051 4835 6.040391 AGCAAAACAACATAACACCTACATGT 59.960 34.615 2.69 2.69 34.42 3.21
2052 4836 6.362283 GCAAAACAACATAACACCTACATGTC 59.638 38.462 0.00 0.00 31.82 3.06
2053 4837 7.421599 CAAAACAACATAACACCTACATGTCA 58.578 34.615 0.00 0.00 31.82 3.58
2054 4838 6.801539 AACAACATAACACCTACATGTCAG 57.198 37.500 0.00 0.00 31.82 3.51
2055 4839 6.109156 ACAACATAACACCTACATGTCAGA 57.891 37.500 0.00 0.00 31.82 3.27
2056 4840 5.932303 ACAACATAACACCTACATGTCAGAC 59.068 40.000 0.00 0.00 31.82 3.51
2057 4841 5.738619 ACATAACACCTACATGTCAGACA 57.261 39.130 5.50 5.50 30.55 3.41
2058 4842 6.299805 ACATAACACCTACATGTCAGACAT 57.700 37.500 10.53 10.53 39.91 3.06
2059 4843 7.418337 ACATAACACCTACATGTCAGACATA 57.582 36.000 15.98 0.71 36.53 2.29
2060 4844 7.847096 ACATAACACCTACATGTCAGACATAA 58.153 34.615 15.98 6.65 36.53 1.90
2061 4845 8.486210 ACATAACACCTACATGTCAGACATAAT 58.514 33.333 15.98 9.82 36.53 1.28
2062 4846 9.981114 CATAACACCTACATGTCAGACATAATA 57.019 33.333 15.98 10.41 36.53 0.98
2070 5978 7.588497 ACATGTCAGACATAATAGCACTAGA 57.412 36.000 15.98 0.00 36.53 2.43
2165 6100 0.814010 GTGAGGAAACAGGCGTGTGT 60.814 55.000 13.63 7.51 36.84 3.72
2166 6101 0.813610 TGAGGAAACAGGCGTGTGTG 60.814 55.000 13.63 0.00 36.84 3.82
2167 6102 0.814010 GAGGAAACAGGCGTGTGTGT 60.814 55.000 13.63 1.42 36.84 3.72
2227 6162 7.936496 TGGTTACTCATGATGAATTTGCTTA 57.064 32.000 0.00 0.00 0.00 3.09
2231 6166 8.668353 GTTACTCATGATGAATTTGCTTACTCA 58.332 33.333 0.00 0.00 0.00 3.41
2289 6268 6.655078 ATTTTTGGCACTCAATAAGTCACT 57.345 33.333 0.00 0.00 35.45 3.41
2488 6472 0.943673 GTGCAAATGGGTGGCAAAAC 59.056 50.000 0.00 0.00 39.57 2.43
2519 6503 6.212955 GTGTATGTGTGTTAGTTGCCAAAAT 58.787 36.000 0.00 0.00 0.00 1.82
2736 6726 2.952310 TGATCGTGATGTAGAGGTCAGG 59.048 50.000 0.00 0.00 0.00 3.86
2750 6740 3.378512 AGGTCAGGCATGATGAAGAGTA 58.621 45.455 3.55 0.00 37.87 2.59
2754 6744 3.969312 TCAGGCATGATGAAGAGTATGGA 59.031 43.478 0.00 0.00 0.00 3.41
2790 6780 0.586319 AAGCGGACACAACAATCACG 59.414 50.000 0.00 0.00 0.00 4.35
2791 6781 0.249699 AGCGGACACAACAATCACGA 60.250 50.000 0.00 0.00 0.00 4.35
2807 6808 2.747686 GAGGGGCTTGTTGGACGA 59.252 61.111 0.00 0.00 0.00 4.20
2825 6826 1.544917 AAATGGCCCAGGACCCTCT 60.545 57.895 0.00 0.00 0.00 3.69
2826 6827 1.149133 AAATGGCCCAGGACCCTCTT 61.149 55.000 0.00 0.00 0.00 2.85
2827 6828 0.253630 AATGGCCCAGGACCCTCTTA 60.254 55.000 0.00 0.00 0.00 2.10
2828 6829 0.028642 ATGGCCCAGGACCCTCTTAT 60.029 55.000 0.00 0.00 0.00 1.73
2829 6830 0.253630 TGGCCCAGGACCCTCTTATT 60.254 55.000 0.00 0.00 0.00 1.40
2873 6874 5.845391 AAGTGACTACTAATGAGAGAGGC 57.155 43.478 0.00 0.00 35.69 4.70
2898 6899 3.230976 TGTAGAGAGGCTGTCAAACTGA 58.769 45.455 14.66 0.00 0.00 3.41
2934 6956 6.403866 AACACTCAAAAACTCCATTGCATA 57.596 33.333 0.00 0.00 0.00 3.14
2935 6957 6.594788 ACACTCAAAAACTCCATTGCATAT 57.405 33.333 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.959596 GAGATCAGGAGCGGCGGC 62.960 72.222 9.78 8.43 40.37 6.53
11 12 4.292178 GGAGATCAGGAGCGGCGG 62.292 72.222 9.78 0.00 0.00 6.13
12 13 3.496875 CTGGAGATCAGGAGCGGCG 62.497 68.421 0.51 0.51 39.76 6.46
13 14 2.420890 CTGGAGATCAGGAGCGGC 59.579 66.667 0.00 0.00 39.76 6.53
20 21 1.817099 GTTGGCGCCTGGAGATCAG 60.817 63.158 29.70 0.00 43.00 2.90
21 22 2.123248 TTGTTGGCGCCTGGAGATCA 62.123 55.000 29.70 9.25 0.00 2.92
22 23 1.372087 CTTGTTGGCGCCTGGAGATC 61.372 60.000 29.70 6.41 0.00 2.75
23 24 1.377725 CTTGTTGGCGCCTGGAGAT 60.378 57.895 29.70 0.00 0.00 2.75
24 25 2.032528 CTTGTTGGCGCCTGGAGA 59.967 61.111 29.70 9.46 0.00 3.71
25 26 3.741476 GCTTGTTGGCGCCTGGAG 61.741 66.667 29.70 19.83 0.00 3.86
60 61 4.463879 CAGTGCGAGGAGGCAGGG 62.464 72.222 0.00 0.00 44.93 4.45
61 62 2.454832 TTTCAGTGCGAGGAGGCAGG 62.455 60.000 0.00 0.00 44.93 4.85
62 63 0.392193 ATTTCAGTGCGAGGAGGCAG 60.392 55.000 0.00 0.00 44.93 4.85
63 64 0.674581 CATTTCAGTGCGAGGAGGCA 60.675 55.000 0.00 0.00 41.45 4.75
64 65 0.391661 TCATTTCAGTGCGAGGAGGC 60.392 55.000 0.00 0.00 0.00 4.70
65 66 1.338105 TGTCATTTCAGTGCGAGGAGG 60.338 52.381 0.00 0.00 0.00 4.30
66 67 1.728971 GTGTCATTTCAGTGCGAGGAG 59.271 52.381 0.00 0.00 0.00 3.69
67 68 1.608025 GGTGTCATTTCAGTGCGAGGA 60.608 52.381 0.00 0.00 0.00 3.71
68 69 0.798776 GGTGTCATTTCAGTGCGAGG 59.201 55.000 0.00 0.00 0.00 4.63
69 70 0.798776 GGGTGTCATTTCAGTGCGAG 59.201 55.000 0.00 0.00 0.00 5.03
70 71 0.605319 GGGGTGTCATTTCAGTGCGA 60.605 55.000 0.00 0.00 0.00 5.10
71 72 1.586154 GGGGGTGTCATTTCAGTGCG 61.586 60.000 0.00 0.00 0.00 5.34
72 73 1.586154 CGGGGGTGTCATTTCAGTGC 61.586 60.000 0.00 0.00 0.00 4.40
73 74 0.250727 ACGGGGGTGTCATTTCAGTG 60.251 55.000 0.00 0.00 0.00 3.66
74 75 0.250727 CACGGGGGTGTCATTTCAGT 60.251 55.000 0.00 0.00 0.00 3.41
75 76 1.586154 GCACGGGGGTGTCATTTCAG 61.586 60.000 0.00 0.00 0.00 3.02
76 77 1.602323 GCACGGGGGTGTCATTTCA 60.602 57.895 0.00 0.00 0.00 2.69
77 78 2.686816 CGCACGGGGGTGTCATTTC 61.687 63.158 0.00 0.00 0.00 2.17
78 79 2.671619 CGCACGGGGGTGTCATTT 60.672 61.111 0.00 0.00 0.00 2.32
79 80 4.715523 CCGCACGGGGGTGTCATT 62.716 66.667 0.00 0.00 0.00 2.57
89 90 3.764810 TTTTGCTGCAACCGCACGG 62.765 57.895 15.72 7.71 45.36 4.94
90 91 1.875813 TTTTTGCTGCAACCGCACG 60.876 52.632 15.72 0.00 45.36 5.34
91 92 0.805711 AGTTTTTGCTGCAACCGCAC 60.806 50.000 15.72 9.14 45.36 5.34
93 94 1.489881 CCAGTTTTTGCTGCAACCGC 61.490 55.000 15.72 7.77 35.28 5.68
94 95 0.875474 CCCAGTTTTTGCTGCAACCG 60.875 55.000 15.72 0.00 35.28 4.44
95 96 0.463620 TCCCAGTTTTTGCTGCAACC 59.536 50.000 15.72 6.19 35.28 3.77
96 97 2.307934 TTCCCAGTTTTTGCTGCAAC 57.692 45.000 15.72 4.55 35.28 4.17
97 98 2.419851 CCTTTCCCAGTTTTTGCTGCAA 60.420 45.455 11.69 11.69 35.28 4.08
98 99 1.138661 CCTTTCCCAGTTTTTGCTGCA 59.861 47.619 0.00 0.00 35.28 4.41
99 100 1.541015 CCCTTTCCCAGTTTTTGCTGC 60.541 52.381 0.00 0.00 35.28 5.25
100 101 2.038659 TCCCTTTCCCAGTTTTTGCTG 58.961 47.619 0.00 0.00 36.31 4.41
101 102 2.470057 TCCCTTTCCCAGTTTTTGCT 57.530 45.000 0.00 0.00 0.00 3.91
102 103 4.562757 GGTTATCCCTTTCCCAGTTTTTGC 60.563 45.833 0.00 0.00 0.00 3.68
103 104 5.147330 GGTTATCCCTTTCCCAGTTTTTG 57.853 43.478 0.00 0.00 0.00 2.44
118 119 2.816520 AACGCGCACGGGTTATCC 60.817 61.111 21.70 0.00 46.88 2.59
123 124 1.726265 TTTTTAAACGCGCACGGGT 59.274 47.368 5.73 6.95 46.04 5.28
124 125 4.610844 TTTTTAAACGCGCACGGG 57.389 50.000 5.73 5.49 46.04 5.28
140 141 7.468631 GCCACGTGTTATCAGATCCATATTTTT 60.469 37.037 15.65 0.00 0.00 1.94
141 142 6.017109 GCCACGTGTTATCAGATCCATATTTT 60.017 38.462 15.65 0.00 0.00 1.82
142 143 5.470098 GCCACGTGTTATCAGATCCATATTT 59.530 40.000 15.65 0.00 0.00 1.40
143 144 4.997395 GCCACGTGTTATCAGATCCATATT 59.003 41.667 15.65 0.00 0.00 1.28
144 145 4.569943 GCCACGTGTTATCAGATCCATAT 58.430 43.478 15.65 0.00 0.00 1.78
145 146 3.552068 CGCCACGTGTTATCAGATCCATA 60.552 47.826 15.65 0.00 0.00 2.74
146 147 2.803133 CGCCACGTGTTATCAGATCCAT 60.803 50.000 15.65 0.00 0.00 3.41
147 148 1.470805 CGCCACGTGTTATCAGATCCA 60.471 52.381 15.65 0.00 0.00 3.41
148 149 1.209128 CGCCACGTGTTATCAGATCC 58.791 55.000 15.65 0.00 0.00 3.36
149 150 0.577269 GCGCCACGTGTTATCAGATC 59.423 55.000 15.65 0.00 0.00 2.75
150 151 0.108377 TGCGCCACGTGTTATCAGAT 60.108 50.000 15.65 0.00 0.00 2.90
151 152 0.735978 CTGCGCCACGTGTTATCAGA 60.736 55.000 15.65 0.00 0.00 3.27
152 153 0.735978 TCTGCGCCACGTGTTATCAG 60.736 55.000 15.65 14.81 0.00 2.90
153 154 1.011968 GTCTGCGCCACGTGTTATCA 61.012 55.000 15.65 5.89 0.00 2.15
154 155 1.011968 TGTCTGCGCCACGTGTTATC 61.012 55.000 15.65 1.18 0.00 1.75
155 156 1.005512 TGTCTGCGCCACGTGTTAT 60.006 52.632 15.65 0.00 0.00 1.89
156 157 1.663388 CTGTCTGCGCCACGTGTTA 60.663 57.895 15.65 0.00 0.00 2.41
157 158 2.967076 CTGTCTGCGCCACGTGTT 60.967 61.111 15.65 0.00 0.00 3.32
167 168 1.078848 ATCCAAGGACGCTGTCTGC 60.079 57.895 8.26 0.00 38.57 4.26
168 169 0.247460 TGATCCAAGGACGCTGTCTG 59.753 55.000 8.26 1.35 32.47 3.51
169 170 0.976641 TTGATCCAAGGACGCTGTCT 59.023 50.000 8.26 0.00 32.47 3.41
170 171 1.734465 CTTTGATCCAAGGACGCTGTC 59.266 52.381 0.00 0.79 0.00 3.51
171 172 1.611673 CCTTTGATCCAAGGACGCTGT 60.612 52.381 18.73 0.00 0.00 4.40
172 173 1.089920 CCTTTGATCCAAGGACGCTG 58.910 55.000 18.73 0.00 0.00 5.18
173 174 0.984230 TCCTTTGATCCAAGGACGCT 59.016 50.000 21.43 0.00 0.00 5.07
174 175 1.066143 TCTCCTTTGATCCAAGGACGC 60.066 52.381 21.43 0.00 0.00 5.19
175 176 3.462021 GATCTCCTTTGATCCAAGGACG 58.538 50.000 21.43 17.15 37.47 4.79
183 184 2.352960 GTGCGTTGGATCTCCTTTGATC 59.647 50.000 0.00 0.00 41.39 2.92
184 185 2.359900 GTGCGTTGGATCTCCTTTGAT 58.640 47.619 0.00 0.00 36.82 2.57
185 186 1.808411 GTGCGTTGGATCTCCTTTGA 58.192 50.000 0.00 0.00 36.82 2.69
186 187 0.443869 CGTGCGTTGGATCTCCTTTG 59.556 55.000 0.00 0.00 36.82 2.77
187 188 0.673644 CCGTGCGTTGGATCTCCTTT 60.674 55.000 0.00 0.00 36.82 3.11
188 189 1.079127 CCGTGCGTTGGATCTCCTT 60.079 57.895 0.00 0.00 36.82 3.36
189 190 1.541310 TTCCGTGCGTTGGATCTCCT 61.541 55.000 0.00 0.00 34.91 3.69
190 191 1.079405 TTCCGTGCGTTGGATCTCC 60.079 57.895 0.00 0.00 34.91 3.71
191 192 1.683790 CGTTCCGTGCGTTGGATCTC 61.684 60.000 0.00 0.00 34.91 2.75
192 193 1.736645 CGTTCCGTGCGTTGGATCT 60.737 57.895 0.00 0.00 34.91 2.75
193 194 2.776072 CGTTCCGTGCGTTGGATC 59.224 61.111 0.00 0.00 34.91 3.36
194 195 3.419759 GCGTTCCGTGCGTTGGAT 61.420 61.111 0.00 0.00 34.91 3.41
235 236 3.977244 GTGTTTGTGGCTGGGGCG 61.977 66.667 0.00 0.00 39.81 6.13
236 237 2.087462 GAAGTGTTTGTGGCTGGGGC 62.087 60.000 0.00 0.00 37.82 5.80
237 238 1.463553 GGAAGTGTTTGTGGCTGGGG 61.464 60.000 0.00 0.00 0.00 4.96
238 239 1.463553 GGGAAGTGTTTGTGGCTGGG 61.464 60.000 0.00 0.00 0.00 4.45
239 240 0.754957 TGGGAAGTGTTTGTGGCTGG 60.755 55.000 0.00 0.00 0.00 4.85
240 241 1.331214 ATGGGAAGTGTTTGTGGCTG 58.669 50.000 0.00 0.00 0.00 4.85
241 242 2.969821 TATGGGAAGTGTTTGTGGCT 57.030 45.000 0.00 0.00 0.00 4.75
242 243 5.652994 TTATTATGGGAAGTGTTTGTGGC 57.347 39.130 0.00 0.00 0.00 5.01
243 244 7.835822 TGAATTATTATGGGAAGTGTTTGTGG 58.164 34.615 0.00 0.00 0.00 4.17
244 245 9.357652 CTTGAATTATTATGGGAAGTGTTTGTG 57.642 33.333 0.00 0.00 0.00 3.33
245 246 8.034804 GCTTGAATTATTATGGGAAGTGTTTGT 58.965 33.333 0.00 0.00 0.00 2.83
246 247 8.034215 TGCTTGAATTATTATGGGAAGTGTTTG 58.966 33.333 0.00 0.00 0.00 2.93
247 248 8.133024 TGCTTGAATTATTATGGGAAGTGTTT 57.867 30.769 0.00 0.00 0.00 2.83
248 249 7.716799 TGCTTGAATTATTATGGGAAGTGTT 57.283 32.000 0.00 0.00 0.00 3.32
249 250 7.902920 ATGCTTGAATTATTATGGGAAGTGT 57.097 32.000 0.00 0.00 0.00 3.55
250 251 7.654520 CCAATGCTTGAATTATTATGGGAAGTG 59.345 37.037 0.00 0.00 0.00 3.16
251 252 7.202029 CCCAATGCTTGAATTATTATGGGAAGT 60.202 37.037 0.67 0.00 46.32 3.01
252 253 7.156673 CCCAATGCTTGAATTATTATGGGAAG 58.843 38.462 0.67 0.00 46.32 3.46
253 254 6.614906 ACCCAATGCTTGAATTATTATGGGAA 59.385 34.615 13.59 0.00 46.32 3.97
254 255 6.041865 CACCCAATGCTTGAATTATTATGGGA 59.958 38.462 13.59 0.00 46.32 4.37
256 257 6.819284 ACACCCAATGCTTGAATTATTATGG 58.181 36.000 0.00 0.00 0.00 2.74
257 258 7.439056 GGAACACCCAATGCTTGAATTATTATG 59.561 37.037 0.00 0.00 34.14 1.90
277 278 9.330063 TGAAAGTATCATCATCATTAGGAACAC 57.670 33.333 0.00 0.00 31.50 3.32
370 371 4.465632 AGTGTGCACATCCGAATTACTA 57.534 40.909 24.69 0.00 0.00 1.82
447 1947 4.928615 ACATACCGTTTCCGTCGAAAAATA 59.071 37.500 0.00 0.00 39.66 1.40
448 1948 3.747529 ACATACCGTTTCCGTCGAAAAAT 59.252 39.130 0.00 0.00 39.66 1.82
449 1949 3.129871 ACATACCGTTTCCGTCGAAAAA 58.870 40.909 0.00 0.00 39.66 1.94
606 2109 6.205658 GGTGAATAAAATCATCCTCTAGCCAC 59.794 42.308 0.00 0.00 0.00 5.01
607 2110 6.126507 TGGTGAATAAAATCATCCTCTAGCCA 60.127 38.462 0.00 0.00 28.94 4.75
608 2111 6.299141 TGGTGAATAAAATCATCCTCTAGCC 58.701 40.000 0.00 0.00 28.94 3.93
650 2156 7.762615 TCCATGGTTATCTACAGTAAGTTTTCG 59.237 37.037 12.58 0.00 0.00 3.46
656 2163 6.884832 TGGTTCCATGGTTATCTACAGTAAG 58.115 40.000 12.58 0.00 0.00 2.34
685 2192 7.175990 GGTTTGAAAAAGTAGGATGGTGATGTA 59.824 37.037 0.00 0.00 0.00 2.29
694 2201 6.702716 TTTGTCGGTTTGAAAAAGTAGGAT 57.297 33.333 0.00 0.00 30.17 3.24
787 2297 3.424829 CCATGTAGTACGTTGCTTGCTTG 60.425 47.826 0.00 0.00 0.00 4.01
852 2567 2.614057 GAGGGAGAATTGTGGCGTTATG 59.386 50.000 0.00 0.00 0.00 1.90
903 2624 0.804989 GGTCAATTGGAGCAGGTTCG 59.195 55.000 5.42 0.00 43.54 3.95
1008 2786 0.534427 TCTCGGTCGAGTGTGTGACT 60.534 55.000 18.18 0.00 42.49 3.41
1009 2787 0.309922 TTCTCGGTCGAGTGTGTGAC 59.690 55.000 18.18 0.00 42.49 3.67
1060 2853 2.629617 ACCATTGCTTGCTTAGTTGCTT 59.370 40.909 0.00 0.00 0.00 3.91
1063 2862 3.254166 ACTCACCATTGCTTGCTTAGTTG 59.746 43.478 0.00 0.00 0.00 3.16
1066 2865 2.415090 GCACTCACCATTGCTTGCTTAG 60.415 50.000 0.00 0.00 35.74 2.18
1067 2866 1.541147 GCACTCACCATTGCTTGCTTA 59.459 47.619 0.00 0.00 35.74 3.09
1430 3232 2.126580 CCGGACGACTTGGACGAC 60.127 66.667 0.00 0.00 34.70 4.34
1475 3277 1.965930 CGCAGCCACAGCAGGTTTA 60.966 57.895 0.00 0.00 43.56 2.01
1534 3348 3.069980 GACATCGCGAGGGACTGCT 62.070 63.158 25.76 1.77 41.55 4.24
1736 3559 3.545481 GACGACGGCGATGCACTG 61.545 66.667 22.49 0.00 41.64 3.66
1861 4626 5.104693 GGGAAACCCCTTTTCTTCAAAAGAA 60.105 40.000 8.48 0.00 46.99 2.52
1862 4627 4.407621 GGGAAACCCCTTTTCTTCAAAAGA 59.592 41.667 8.48 0.00 46.99 2.52
2007 4791 2.815589 GCTTGATTGGTCACTTCCCTGT 60.816 50.000 0.00 0.00 33.11 4.00
2023 4807 5.590530 AGGTGTTATGTTGTTTTGCTTGA 57.409 34.783 0.00 0.00 0.00 3.02
2036 4820 8.893219 ATTATGTCTGACATGTAGGTGTTATG 57.107 34.615 28.67 0.00 39.53 1.90
2038 4822 8.141909 GCTATTATGTCTGACATGTAGGTGTTA 58.858 37.037 28.67 6.76 39.53 2.41
2039 4823 6.986817 GCTATTATGTCTGACATGTAGGTGTT 59.013 38.462 28.67 6.75 39.53 3.32
2040 4824 6.098266 TGCTATTATGTCTGACATGTAGGTGT 59.902 38.462 28.67 7.43 39.53 4.16
2041 4825 6.422100 GTGCTATTATGTCTGACATGTAGGTG 59.578 42.308 28.67 15.98 39.53 4.00
2042 4826 6.325028 AGTGCTATTATGTCTGACATGTAGGT 59.675 38.462 28.67 14.20 39.53 3.08
2043 4827 6.753180 AGTGCTATTATGTCTGACATGTAGG 58.247 40.000 28.67 17.88 39.53 3.18
2044 4828 8.787852 TCTAGTGCTATTATGTCTGACATGTAG 58.212 37.037 28.67 26.55 39.53 2.74
2045 4829 8.568794 GTCTAGTGCTATTATGTCTGACATGTA 58.431 37.037 28.67 20.10 39.53 2.29
2046 4830 7.429633 GTCTAGTGCTATTATGTCTGACATGT 58.570 38.462 28.67 20.06 39.53 3.21
2047 4831 6.580416 CGTCTAGTGCTATTATGTCTGACATG 59.420 42.308 28.67 15.50 39.53 3.21
2048 4832 6.486993 TCGTCTAGTGCTATTATGTCTGACAT 59.513 38.462 25.01 25.01 42.35 3.06
2049 4833 5.820947 TCGTCTAGTGCTATTATGTCTGACA 59.179 40.000 13.60 13.60 0.00 3.58
2050 4834 6.137415 GTCGTCTAGTGCTATTATGTCTGAC 58.863 44.000 0.00 0.00 0.00 3.51
2051 4835 5.050295 CGTCGTCTAGTGCTATTATGTCTGA 60.050 44.000 0.00 0.00 0.00 3.27
2052 4836 5.050295 TCGTCGTCTAGTGCTATTATGTCTG 60.050 44.000 0.00 0.00 0.00 3.51
2053 4837 5.050227 GTCGTCGTCTAGTGCTATTATGTCT 60.050 44.000 0.00 0.00 0.00 3.41
2054 4838 5.050227 AGTCGTCGTCTAGTGCTATTATGTC 60.050 44.000 0.00 0.00 0.00 3.06
2055 4839 4.815308 AGTCGTCGTCTAGTGCTATTATGT 59.185 41.667 0.00 0.00 0.00 2.29
2056 4840 5.177881 AGAGTCGTCGTCTAGTGCTATTATG 59.822 44.000 0.00 0.00 0.00 1.90
2057 4841 5.299148 AGAGTCGTCGTCTAGTGCTATTAT 58.701 41.667 0.00 0.00 0.00 1.28
2058 4842 4.691175 AGAGTCGTCGTCTAGTGCTATTA 58.309 43.478 0.00 0.00 0.00 0.98
2059 4843 3.533547 AGAGTCGTCGTCTAGTGCTATT 58.466 45.455 0.00 0.00 0.00 1.73
2060 4844 3.182341 AGAGTCGTCGTCTAGTGCTAT 57.818 47.619 0.00 0.00 0.00 2.97
2061 4845 2.669300 AGAGTCGTCGTCTAGTGCTA 57.331 50.000 0.00 0.00 0.00 3.49
2062 4846 1.465387 CAAGAGTCGTCGTCTAGTGCT 59.535 52.381 0.00 0.00 0.00 4.40
2063 4847 1.197264 ACAAGAGTCGTCGTCTAGTGC 59.803 52.381 0.00 0.00 0.00 4.40
2135 6043 5.745227 CCTGTTTCCTCACACATATTACCT 58.255 41.667 0.00 0.00 0.00 3.08
2141 6049 1.346395 ACGCCTGTTTCCTCACACATA 59.654 47.619 0.00 0.00 0.00 2.29
2165 6100 4.116585 ACCGGCACCAACACCACA 62.117 61.111 0.00 0.00 0.00 4.17
2166 6101 3.284449 GACCGGCACCAACACCAC 61.284 66.667 0.00 0.00 0.00 4.16
2167 6102 3.126703 ATGACCGGCACCAACACCA 62.127 57.895 0.00 0.00 0.00 4.17
2256 6235 6.998968 TGAGTGCCAAAAATTTGACAAAAT 57.001 29.167 4.41 0.00 40.55 1.82
2358 6337 8.011844 TCGATGCATGCCTATAAGATATAGTT 57.988 34.615 16.68 0.00 0.00 2.24
2359 6338 7.286546 ACTCGATGCATGCCTATAAGATATAGT 59.713 37.037 16.68 4.34 0.00 2.12
2374 6353 8.501580 AGATTTATACATTCAACTCGATGCATG 58.498 33.333 2.46 0.00 31.41 4.06
2473 6457 4.042684 ACCATATTGTTTTGCCACCCATTT 59.957 37.500 0.00 0.00 0.00 2.32
2488 6472 6.966632 GCAACTAACACACATACACCATATTG 59.033 38.462 0.00 0.00 0.00 1.90
2736 6726 6.441093 TGTTTTCCATACTCTTCATCATGC 57.559 37.500 0.00 0.00 0.00 4.06
2750 6740 3.173953 TGGCCTCTTCATGTTTTCCAT 57.826 42.857 3.32 0.00 0.00 3.41
2754 6744 2.288395 CGCTTTGGCCTCTTCATGTTTT 60.288 45.455 3.32 0.00 34.44 2.43
2790 6780 0.536460 TTTCGTCCAACAAGCCCCTC 60.536 55.000 0.00 0.00 0.00 4.30
2791 6781 0.112412 ATTTCGTCCAACAAGCCCCT 59.888 50.000 0.00 0.00 0.00 4.79
2807 6808 1.149133 AAGAGGGTCCTGGGCCATTT 61.149 55.000 20.86 3.94 0.00 2.32
2825 6826 8.791327 TGAGAATCAACTCTTGCACATAATAA 57.209 30.769 0.00 0.00 45.97 1.40
2873 6874 0.528017 TGACAGCCTCTCTACAAGCG 59.472 55.000 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.