Multiple sequence alignment - TraesCS2D01G514400

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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 TraesCS2D01G514400 chr2D 100.000 3131 0 0 1 3131 606215702 606212572 0.000000e+00 5782.0
1 TraesCS2D01G514400 chr2D 90.697 2268 154 26 890 3131 606188757 606186521 0.000000e+00 2966.0
2 TraesCS2D01G514400 chr2D 86.844 2364 207 44 844 3131 606156543 606154208 0.000000e+00 2547.0
3 TraesCS2D01G514400 chr2D 87.007 1216 109 24 1780 2962 606162004 606160805 0.000000e+00 1325.0
4 TraesCS2D01G514400 chr2D 83.363 565 61 17 1965 2512 606149661 606149113 2.810000e-135 492.0
5 TraesCS2D01G514400 chr2D 98.276 58 1 0 1 58 536640863 536640806 5.520000e-18 102.0
6 TraesCS2D01G514400 chr2A 86.343 2160 208 39 844 2965 737735358 737733248 0.000000e+00 2274.0
7 TraesCS2D01G514400 chr2A 91.148 1672 102 21 766 2414 738007080 738005432 0.000000e+00 2226.0
8 TraesCS2D01G514400 chr2A 86.536 1894 173 27 844 2672 737880517 737878641 0.000000e+00 2010.0
9 TraesCS2D01G514400 chr2A 83.578 1023 113 22 1981 2965 737837320 737836315 0.000000e+00 907.0
10 TraesCS2D01G514400 chr2A 87.639 720 84 4 2410 3124 738003091 738002372 0.000000e+00 832.0
11 TraesCS2D01G514400 chr2A 87.162 740 68 9 844 1559 737838454 737837718 0.000000e+00 815.0
12 TraesCS2D01G514400 chr2A 87.832 452 35 6 334 780 738007533 738007097 2.150000e-141 512.0
13 TraesCS2D01G514400 chr2A 86.400 125 15 1 3009 3131 737836238 737836114 5.450000e-28 135.0
14 TraesCS2D01G514400 chr2A 85.600 125 16 1 3009 3131 737733171 737733047 2.530000e-26 130.0
15 TraesCS2D01G514400 chrUn 87.423 1614 139 19 1090 2656 386125594 386123998 0.000000e+00 1797.0
16 TraesCS2D01G514400 chrUn 89.242 567 60 1 2566 3131 334698582 334698016 0.000000e+00 708.0
17 TraesCS2D01G514400 chrUn 88.679 106 6 3 844 943 30267023 30266918 1.180000e-24 124.0
18 TraesCS2D01G514400 chrUn 98.246 57 1 0 1 57 11243156 11243100 1.990000e-17 100.0
19 TraesCS2D01G514400 chrUn 98.246 57 1 0 1 57 11249554 11249498 1.990000e-17 100.0
20 TraesCS2D01G514400 chrUn 98.246 57 1 0 1 57 330796805 330796861 1.990000e-17 100.0
21 TraesCS2D01G514400 chr2B 88.584 1419 129 17 844 2242 737097279 737095874 0.000000e+00 1692.0
22 TraesCS2D01G514400 chr2B 88.998 1327 101 21 748 2054 737272475 737271174 0.000000e+00 1600.0
23 TraesCS2D01G514400 chr2B 85.696 1573 145 27 844 2382 737108539 737107013 0.000000e+00 1585.0
24 TraesCS2D01G514400 chr2B 86.034 1475 135 32 844 2290 737160701 737159270 0.000000e+00 1517.0
25 TraesCS2D01G514400 chr2B 87.454 1092 102 13 844 1909 737246133 737245051 0.000000e+00 1225.0
26 TraesCS2D01G514400 chr2B 89.242 567 60 1 2566 3131 737219181 737218615 0.000000e+00 708.0
27 TraesCS2D01G514400 chr2B 89.242 567 60 1 2566 3131 737238565 737237999 0.000000e+00 708.0
28 TraesCS2D01G514400 chr2B 89.250 400 29 6 359 758 737272898 737272513 3.630000e-134 488.0
29 TraesCS2D01G514400 chr2B 86.329 395 31 11 1907 2288 737225892 737225508 2.910000e-110 409.0
30 TraesCS2D01G514400 chr2B 86.329 395 31 8 1907 2288 737244948 737244564 2.910000e-110 409.0
31 TraesCS2D01G514400 chr2B 90.400 125 10 1 3009 3131 737094702 737094578 2.500000e-36 163.0
32 TraesCS2D01G514400 chr5D 83.004 253 32 8 154 400 117260656 117260409 5.260000e-53 219.0
33 TraesCS2D01G514400 chr5D 96.774 62 2 0 1 62 351123327 351123266 1.540000e-18 104.0
34 TraesCS2D01G514400 chr5D 98.276 58 1 0 1 58 169089671 169089728 5.520000e-18 102.0
35 TraesCS2D01G514400 chr5B 85.204 196 29 0 68 263 527260014 527259819 5.290000e-48 202.0
36 TraesCS2D01G514400 chr7D 98.276 58 1 0 1 58 532156907 532156964 5.520000e-18 102.0
37 TraesCS2D01G514400 chr6D 98.246 57 1 0 1 57 64060461 64060405 1.990000e-17 100.0
38 TraesCS2D01G514400 chr1D 93.846 65 3 1 1 64 226023811 226023875 2.570000e-16 97.1


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 TraesCS2D01G514400 chr2D 606212572 606215702 3130 True 5782.0 5782 100.000000 1 3131 1 chr2D.!!$R6 3130
1 TraesCS2D01G514400 chr2D 606186521 606188757 2236 True 2966.0 2966 90.697000 890 3131 1 chr2D.!!$R5 2241
2 TraesCS2D01G514400 chr2D 606154208 606156543 2335 True 2547.0 2547 86.844000 844 3131 1 chr2D.!!$R3 2287
3 TraesCS2D01G514400 chr2D 606160805 606162004 1199 True 1325.0 1325 87.007000 1780 2962 1 chr2D.!!$R4 1182
4 TraesCS2D01G514400 chr2D 606149113 606149661 548 True 492.0 492 83.363000 1965 2512 1 chr2D.!!$R2 547
5 TraesCS2D01G514400 chr2A 737878641 737880517 1876 True 2010.0 2010 86.536000 844 2672 1 chr2A.!!$R1 1828
6 TraesCS2D01G514400 chr2A 737733047 737735358 2311 True 1202.0 2274 85.971500 844 3131 2 chr2A.!!$R2 2287
7 TraesCS2D01G514400 chr2A 738002372 738007533 5161 True 1190.0 2226 88.873000 334 3124 3 chr2A.!!$R4 2790
8 TraesCS2D01G514400 chr2A 737836114 737838454 2340 True 619.0 907 85.713333 844 3131 3 chr2A.!!$R3 2287
9 TraesCS2D01G514400 chrUn 386123998 386125594 1596 True 1797.0 1797 87.423000 1090 2656 1 chrUn.!!$R5 1566
10 TraesCS2D01G514400 chrUn 334698016 334698582 566 True 708.0 708 89.242000 2566 3131 1 chrUn.!!$R4 565
11 TraesCS2D01G514400 chr2B 737107013 737108539 1526 True 1585.0 1585 85.696000 844 2382 1 chr2B.!!$R1 1538
12 TraesCS2D01G514400 chr2B 737159270 737160701 1431 True 1517.0 1517 86.034000 844 2290 1 chr2B.!!$R2 1446
13 TraesCS2D01G514400 chr2B 737271174 737272898 1724 True 1044.0 1600 89.124000 359 2054 2 chr2B.!!$R8 1695
14 TraesCS2D01G514400 chr2B 737094578 737097279 2701 True 927.5 1692 89.492000 844 3131 2 chr2B.!!$R6 2287
15 TraesCS2D01G514400 chr2B 737244564 737246133 1569 True 817.0 1225 86.891500 844 2288 2 chr2B.!!$R7 1444
16 TraesCS2D01G514400 chr2B 737218615 737219181 566 True 708.0 708 89.242000 2566 3131 1 chr2B.!!$R3 565
17 TraesCS2D01G514400 chr2B 737237999 737238565 566 True 708.0 708 89.242000 2566 3131 1 chr2B.!!$R5 565

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
53 54 0.035820 TCCCGAAAAATCCGGTCCTG 60.036 55.0 0.0 0.0 45.14 3.86 F
54 55 0.035820 CCCGAAAAATCCGGTCCTGA 60.036 55.0 0.0 0.0 45.14 3.86 F
71 72 0.036732 TGACATGGAGTGGCAAGGTC 59.963 55.0 0.0 0.0 44.83 3.85 F
1706 1855 0.032952 GCTTCAGTGTGGGTGACGTA 59.967 55.0 0.0 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1292 1.218047 CATCCGCCGAGAGTTTGGA 59.782 57.895 0.0 0.0 0.0 3.53 R
1706 1855 1.661463 TGAAAGCCCAGATCTCCACT 58.339 50.000 0.0 0.0 0.0 4.00 R
2026 2312 2.614057 CACTCAGACAAACACAAGGACC 59.386 50.000 0.0 0.0 0.0 4.46 R
2905 5864 0.031449 GAGGAGATACGTGAGCTGGC 59.969 60.000 0.0 0.0 0.0 4.85 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
22 23 3.726557 TGAGCACAGGGATCATTTTCT 57.273 42.857 0.00 0.00 36.91 2.52
23 24 3.349927 TGAGCACAGGGATCATTTTCTG 58.650 45.455 0.00 0.00 36.91 3.02
24 25 2.686915 GAGCACAGGGATCATTTTCTGG 59.313 50.000 0.00 0.00 0.00 3.86
25 26 1.753073 GCACAGGGATCATTTTCTGGG 59.247 52.381 0.00 0.00 34.07 4.45
26 27 2.621407 GCACAGGGATCATTTTCTGGGA 60.621 50.000 0.00 0.00 32.79 4.37
27 28 3.700538 CACAGGGATCATTTTCTGGGAA 58.299 45.455 0.00 0.00 32.79 3.97
28 29 4.088634 CACAGGGATCATTTTCTGGGAAA 58.911 43.478 0.00 0.00 32.79 3.13
29 30 4.527816 CACAGGGATCATTTTCTGGGAAAA 59.472 41.667 7.71 7.71 32.79 2.29
30 31 5.188359 CACAGGGATCATTTTCTGGGAAAAT 59.812 40.000 11.10 11.10 32.79 1.82
31 32 6.380846 CACAGGGATCATTTTCTGGGAAAATA 59.619 38.462 15.03 7.30 32.79 1.40
32 33 7.070322 CACAGGGATCATTTTCTGGGAAAATAT 59.930 37.037 15.03 10.48 32.79 1.28
33 34 8.288812 ACAGGGATCATTTTCTGGGAAAATATA 58.711 33.333 15.03 9.06 0.00 0.86
34 35 9.317827 CAGGGATCATTTTCTGGGAAAATATAT 57.682 33.333 15.03 12.27 0.00 0.86
35 36 9.539194 AGGGATCATTTTCTGGGAAAATATATC 57.461 33.333 15.03 17.43 0.00 1.63
36 37 8.753133 GGGATCATTTTCTGGGAAAATATATCC 58.247 37.037 26.71 26.71 38.72 2.59
47 48 6.617879 GGGAAAATATATCCCGAAAAATCCG 58.382 40.000 10.03 0.00 46.76 4.18
48 49 6.349860 GGGAAAATATATCCCGAAAAATCCGG 60.350 42.308 10.03 0.00 46.76 5.14
49 50 6.208007 GGAAAATATATCCCGAAAAATCCGGT 59.792 38.462 0.00 0.00 45.14 5.28
50 51 6.812879 AAATATATCCCGAAAAATCCGGTC 57.187 37.500 0.00 0.00 45.14 4.79
51 52 2.625695 TATCCCGAAAAATCCGGTCC 57.374 50.000 0.00 0.00 45.14 4.46
52 53 0.916809 ATCCCGAAAAATCCGGTCCT 59.083 50.000 0.00 0.00 45.14 3.85
53 54 0.035820 TCCCGAAAAATCCGGTCCTG 60.036 55.000 0.00 0.00 45.14 3.86
54 55 0.035820 CCCGAAAAATCCGGTCCTGA 60.036 55.000 0.00 0.00 45.14 3.86
55 56 1.084289 CCGAAAAATCCGGTCCTGAC 58.916 55.000 0.00 0.00 41.91 3.51
56 57 1.609580 CCGAAAAATCCGGTCCTGACA 60.610 52.381 0.00 0.00 41.91 3.58
57 58 2.356135 CGAAAAATCCGGTCCTGACAT 58.644 47.619 0.00 0.00 0.00 3.06
58 59 2.095853 CGAAAAATCCGGTCCTGACATG 59.904 50.000 0.00 0.00 0.00 3.21
59 60 2.128771 AAAATCCGGTCCTGACATGG 57.871 50.000 0.00 0.92 0.00 3.66
60 61 1.285280 AAATCCGGTCCTGACATGGA 58.715 50.000 0.00 11.43 40.22 3.41
61 62 0.833287 AATCCGGTCCTGACATGGAG 59.167 55.000 0.00 0.00 39.60 3.86
62 63 0.325671 ATCCGGTCCTGACATGGAGT 60.326 55.000 0.00 3.37 39.60 3.85
63 64 1.219124 CCGGTCCTGACATGGAGTG 59.781 63.158 0.00 0.00 36.69 3.51
64 65 1.219124 CGGTCCTGACATGGAGTGG 59.781 63.158 0.00 0.00 36.69 4.00
65 66 1.078143 GGTCCTGACATGGAGTGGC 60.078 63.158 0.00 0.00 36.69 5.01
66 67 1.679311 GTCCTGACATGGAGTGGCA 59.321 57.895 0.00 0.00 45.90 4.92
70 71 2.154139 TGACATGGAGTGGCAAGGT 58.846 52.632 0.00 0.00 44.83 3.50
71 72 0.036732 TGACATGGAGTGGCAAGGTC 59.963 55.000 0.00 0.00 44.83 3.85
72 73 0.326264 GACATGGAGTGGCAAGGTCT 59.674 55.000 0.00 0.00 35.22 3.85
73 74 0.326264 ACATGGAGTGGCAAGGTCTC 59.674 55.000 0.00 0.00 0.00 3.36
74 75 0.742281 CATGGAGTGGCAAGGTCTCG 60.742 60.000 0.00 0.00 0.00 4.04
75 76 2.435059 GGAGTGGCAAGGTCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
80 81 4.821589 GGCAAGGTCTCGCCGGAG 62.822 72.222 5.05 0.00 43.70 4.63
81 82 3.760035 GCAAGGTCTCGCCGGAGA 61.760 66.667 5.05 6.70 46.90 3.71
105 106 3.730761 GCACCGGTCTGCTGCAAG 61.731 66.667 2.59 0.00 34.06 4.01
131 132 3.770040 TCCCGCCGGAGTCACATG 61.770 66.667 5.05 0.00 32.86 3.21
132 133 4.838152 CCCGCCGGAGTCACATGG 62.838 72.222 5.05 0.00 0.00 3.66
135 136 4.451150 GCCGGAGTCACATGGCGA 62.451 66.667 5.05 0.00 37.81 5.54
136 137 2.202797 CCGGAGTCACATGGCGAG 60.203 66.667 0.00 0.00 0.00 5.03
137 138 2.573869 CGGAGTCACATGGCGAGT 59.426 61.111 0.00 0.00 0.00 4.18
138 139 1.807165 CGGAGTCACATGGCGAGTG 60.807 63.158 0.00 3.04 38.32 3.51
139 140 1.293498 GGAGTCACATGGCGAGTGT 59.707 57.895 8.65 0.00 38.16 3.55
140 141 0.737715 GGAGTCACATGGCGAGTGTC 60.738 60.000 8.65 4.13 38.16 3.67
141 142 1.073216 GAGTCACATGGCGAGTGTCG 61.073 60.000 8.65 0.00 43.89 4.35
142 143 2.094659 GTCACATGGCGAGTGTCGG 61.095 63.158 8.65 0.00 40.84 4.79
143 144 2.048222 CACATGGCGAGTGTCGGT 60.048 61.111 0.00 0.00 40.84 4.69
144 145 2.048222 ACATGGCGAGTGTCGGTG 60.048 61.111 0.00 0.00 40.84 4.94
145 146 2.815211 CATGGCGAGTGTCGGTGG 60.815 66.667 0.00 0.00 40.84 4.61
146 147 4.760047 ATGGCGAGTGTCGGTGGC 62.760 66.667 0.00 0.00 40.84 5.01
150 151 3.103911 CGAGTGTCGGTGGCGAAC 61.104 66.667 0.00 0.00 36.00 3.95
151 152 2.737376 GAGTGTCGGTGGCGAACC 60.737 66.667 0.00 0.00 46.60 3.62
158 159 2.029964 GGTGGCGAACCTTGACGA 59.970 61.111 0.00 0.00 46.55 4.20
159 160 2.315386 GGTGGCGAACCTTGACGAC 61.315 63.158 0.00 0.00 46.55 4.34
160 161 2.355363 TGGCGAACCTTGACGACG 60.355 61.111 0.00 0.00 40.70 5.12
161 162 2.049802 GGCGAACCTTGACGACGA 60.050 61.111 0.00 0.00 0.00 4.20
162 163 2.087009 GGCGAACCTTGACGACGAG 61.087 63.158 0.00 0.00 0.00 4.18
163 164 2.717809 GCGAACCTTGACGACGAGC 61.718 63.158 0.00 0.00 0.00 5.03
181 182 4.415332 GTCGCGAGGACGAGGCAA 62.415 66.667 10.24 0.00 43.89 4.52
182 183 4.116328 TCGCGAGGACGAGGCAAG 62.116 66.667 3.71 0.00 42.66 4.01
184 185 3.760035 GCGAGGACGAGGCAAGGA 61.760 66.667 0.00 0.00 42.66 3.36
185 186 2.492090 CGAGGACGAGGCAAGGAG 59.508 66.667 0.00 0.00 42.66 3.69
186 187 2.896443 GAGGACGAGGCAAGGAGG 59.104 66.667 0.00 0.00 0.00 4.30
187 188 1.682684 GAGGACGAGGCAAGGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
188 189 1.671901 GAGGACGAGGCAAGGAGGAG 61.672 65.000 0.00 0.00 0.00 3.69
189 190 1.682684 GGACGAGGCAAGGAGGAGA 60.683 63.158 0.00 0.00 0.00 3.71
190 191 1.671901 GGACGAGGCAAGGAGGAGAG 61.672 65.000 0.00 0.00 0.00 3.20
191 192 1.671901 GACGAGGCAAGGAGGAGAGG 61.672 65.000 0.00 0.00 0.00 3.69
192 193 2.430610 CGAGGCAAGGAGGAGAGGG 61.431 68.421 0.00 0.00 0.00 4.30
193 194 2.690510 AGGCAAGGAGGAGAGGGC 60.691 66.667 0.00 0.00 0.00 5.19
194 195 4.168291 GGCAAGGAGGAGAGGGCG 62.168 72.222 0.00 0.00 0.00 6.13
195 196 4.168291 GCAAGGAGGAGAGGGCGG 62.168 72.222 0.00 0.00 0.00 6.13
196 197 3.474570 CAAGGAGGAGAGGGCGGG 61.475 72.222 0.00 0.00 0.00 6.13
197 198 3.684628 AAGGAGGAGAGGGCGGGA 61.685 66.667 0.00 0.00 0.00 5.14
198 199 3.254035 AAGGAGGAGAGGGCGGGAA 62.254 63.158 0.00 0.00 0.00 3.97
199 200 3.471806 GGAGGAGAGGGCGGGAAC 61.472 72.222 0.00 0.00 0.00 3.62
226 227 4.883354 GGGGCGCATGGGAGAAGG 62.883 72.222 14.90 0.00 0.00 3.46
227 228 4.883354 GGGCGCATGGGAGAAGGG 62.883 72.222 14.90 0.00 0.00 3.95
228 229 4.115199 GGCGCATGGGAGAAGGGT 62.115 66.667 14.90 0.00 0.00 4.34
229 230 2.825836 GCGCATGGGAGAAGGGTG 60.826 66.667 14.90 0.00 0.00 4.61
230 231 2.989639 CGCATGGGAGAAGGGTGA 59.010 61.111 3.11 0.00 0.00 4.02
231 232 1.299648 CGCATGGGAGAAGGGTGAA 59.700 57.895 3.11 0.00 0.00 3.18
232 233 0.107017 CGCATGGGAGAAGGGTGAAT 60.107 55.000 3.11 0.00 0.00 2.57
233 234 1.396653 GCATGGGAGAAGGGTGAATG 58.603 55.000 0.00 0.00 0.00 2.67
234 235 1.396653 CATGGGAGAAGGGTGAATGC 58.603 55.000 0.00 0.00 0.00 3.56
235 236 0.259938 ATGGGAGAAGGGTGAATGCC 59.740 55.000 0.00 0.00 0.00 4.40
236 237 1.139498 TGGGAGAAGGGTGAATGCCA 61.139 55.000 0.00 0.00 0.00 4.92
237 238 0.259938 GGGAGAAGGGTGAATGCCAT 59.740 55.000 0.00 0.00 0.00 4.40
238 239 1.396653 GGAGAAGGGTGAATGCCATG 58.603 55.000 0.00 0.00 0.00 3.66
239 240 0.743097 GAGAAGGGTGAATGCCATGC 59.257 55.000 0.00 0.00 0.00 4.06
240 241 1.033746 AGAAGGGTGAATGCCATGCG 61.034 55.000 0.00 0.00 0.00 4.73
241 242 2.008268 GAAGGGTGAATGCCATGCGG 62.008 60.000 0.00 0.00 0.00 5.69
263 264 2.278013 CTACGCGCGGAGGAGAAC 60.278 66.667 34.28 0.00 0.00 3.01
264 265 3.047718 CTACGCGCGGAGGAGAACA 62.048 63.158 34.28 5.71 0.00 3.18
265 266 2.537792 CTACGCGCGGAGGAGAACAA 62.538 60.000 34.28 4.48 0.00 2.83
266 267 2.537792 TACGCGCGGAGGAGAACAAG 62.538 60.000 35.22 0.99 0.00 3.16
267 268 2.815647 GCGCGGAGGAGAACAAGG 60.816 66.667 8.83 0.00 0.00 3.61
268 269 2.970639 CGCGGAGGAGAACAAGGA 59.029 61.111 0.00 0.00 0.00 3.36
269 270 1.292223 CGCGGAGGAGAACAAGGAA 59.708 57.895 0.00 0.00 0.00 3.36
270 271 0.108138 CGCGGAGGAGAACAAGGAAT 60.108 55.000 0.00 0.00 0.00 3.01
271 272 1.136305 CGCGGAGGAGAACAAGGAATA 59.864 52.381 0.00 0.00 0.00 1.75
272 273 2.799917 CGCGGAGGAGAACAAGGAATAG 60.800 54.545 0.00 0.00 0.00 1.73
273 274 2.168728 GCGGAGGAGAACAAGGAATAGT 59.831 50.000 0.00 0.00 0.00 2.12
274 275 3.738590 GCGGAGGAGAACAAGGAATAGTC 60.739 52.174 0.00 0.00 0.00 2.59
275 276 3.489398 CGGAGGAGAACAAGGAATAGTCG 60.489 52.174 0.00 0.00 0.00 4.18
276 277 3.449632 GAGGAGAACAAGGAATAGTCGC 58.550 50.000 0.00 0.00 0.00 5.19
277 278 2.159226 AGGAGAACAAGGAATAGTCGCG 60.159 50.000 0.00 0.00 0.00 5.87
278 279 2.159282 GGAGAACAAGGAATAGTCGCGA 60.159 50.000 3.71 3.71 0.00 5.87
279 280 3.109619 GAGAACAAGGAATAGTCGCGAG 58.890 50.000 10.24 0.00 0.00 5.03
280 281 2.753452 AGAACAAGGAATAGTCGCGAGA 59.247 45.455 10.24 0.00 38.16 4.04
281 282 2.853731 ACAAGGAATAGTCGCGAGAG 57.146 50.000 10.24 0.00 43.49 3.20
282 283 1.405821 ACAAGGAATAGTCGCGAGAGG 59.594 52.381 10.24 0.00 43.49 3.69
283 284 1.033574 AAGGAATAGTCGCGAGAGGG 58.966 55.000 10.24 0.00 43.49 4.30
292 293 3.157949 GCGAGAGGGAAGGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
293 294 2.444895 CGAGAGGGAAGGAGGGGG 60.445 72.222 0.00 0.00 0.00 5.40
311 312 1.780503 GGGGGAGAAAATGACATGGG 58.219 55.000 0.00 0.00 0.00 4.00
312 313 1.007118 GGGGGAGAAAATGACATGGGT 59.993 52.381 0.00 0.00 0.00 4.51
313 314 2.102578 GGGGAGAAAATGACATGGGTG 58.897 52.381 0.00 0.00 0.00 4.61
314 315 2.291540 GGGGAGAAAATGACATGGGTGA 60.292 50.000 0.00 0.00 0.00 4.02
315 316 3.430453 GGGAGAAAATGACATGGGTGAA 58.570 45.455 0.00 0.00 0.00 3.18
316 317 4.026052 GGGAGAAAATGACATGGGTGAAT 58.974 43.478 0.00 0.00 0.00 2.57
317 318 5.200483 GGGAGAAAATGACATGGGTGAATA 58.800 41.667 0.00 0.00 0.00 1.75
318 319 5.656416 GGGAGAAAATGACATGGGTGAATAA 59.344 40.000 0.00 0.00 0.00 1.40
319 320 6.183360 GGGAGAAAATGACATGGGTGAATAAG 60.183 42.308 0.00 0.00 0.00 1.73
320 321 6.183360 GGAGAAAATGACATGGGTGAATAAGG 60.183 42.308 0.00 0.00 0.00 2.69
321 322 6.493166 AGAAAATGACATGGGTGAATAAGGA 58.507 36.000 0.00 0.00 0.00 3.36
322 323 7.128077 AGAAAATGACATGGGTGAATAAGGAT 58.872 34.615 0.00 0.00 0.00 3.24
323 324 6.966534 AAATGACATGGGTGAATAAGGATC 57.033 37.500 0.00 0.00 0.00 3.36
324 325 4.437682 TGACATGGGTGAATAAGGATCC 57.562 45.455 2.48 2.48 0.00 3.36
325 326 4.047166 TGACATGGGTGAATAAGGATCCT 58.953 43.478 9.02 9.02 0.00 3.24
326 327 5.223655 TGACATGGGTGAATAAGGATCCTA 58.776 41.667 16.55 3.95 0.00 2.94
327 328 5.851693 TGACATGGGTGAATAAGGATCCTAT 59.148 40.000 16.55 8.15 0.00 2.57
328 329 6.131972 ACATGGGTGAATAAGGATCCTATG 57.868 41.667 16.55 13.71 40.99 2.23
329 330 5.014544 ACATGGGTGAATAAGGATCCTATGG 59.985 44.000 16.55 0.00 40.03 2.74
330 331 3.330701 TGGGTGAATAAGGATCCTATGGC 59.669 47.826 16.55 6.18 0.00 4.40
331 332 3.589288 GGGTGAATAAGGATCCTATGGCT 59.411 47.826 16.55 0.57 0.00 4.75
332 333 4.043435 GGGTGAATAAGGATCCTATGGCTT 59.957 45.833 16.55 0.00 0.00 4.35
412 413 4.339247 CCTACCATTGGCCATAGAAAAGTG 59.661 45.833 6.09 0.00 0.00 3.16
460 461 7.148440 GCAATAATGAAAACCAAATTAGCAGCA 60.148 33.333 0.00 0.00 0.00 4.41
465 466 4.605640 AAACCAAATTAGCAGCATGTGT 57.394 36.364 0.00 0.00 39.31 3.72
479 480 5.615544 GCAGCATGTGTAGTTTCTAGTGTTG 60.616 44.000 0.00 0.00 39.31 3.33
480 481 5.466728 CAGCATGTGTAGTTTCTAGTGTTGT 59.533 40.000 0.00 0.00 0.00 3.32
481 482 6.645003 CAGCATGTGTAGTTTCTAGTGTTGTA 59.355 38.462 0.00 0.00 0.00 2.41
510 511 9.448587 AGAATTATTTCTACCAGTACCAGGTAT 57.551 33.333 13.49 4.83 40.47 2.73
674 675 4.871557 CCATCCAAGTGCATTTGGTTTATG 59.128 41.667 32.58 27.56 46.23 1.90
721 722 6.071952 AGTGCATTTGGAAAACGATACTGAAT 60.072 34.615 0.00 0.00 0.00 2.57
749 750 1.035139 GGCTGGATTCGGATTGCATT 58.965 50.000 0.00 0.00 0.00 3.56
782 862 2.776312 TCATCTGGTATTCGAGTCGC 57.224 50.000 7.92 0.00 0.00 5.19
788 868 1.749063 TGGTATTCGAGTCGCAGTCAT 59.251 47.619 7.92 0.00 0.00 3.06
804 887 7.539710 GTCGCAGTCATATACCGTAAATTATCA 59.460 37.037 0.00 0.00 0.00 2.15
805 888 7.539710 TCGCAGTCATATACCGTAAATTATCAC 59.460 37.037 0.00 0.00 0.00 3.06
1029 1151 1.705337 CCTATTTGCGCGACACAGGG 61.705 60.000 12.10 0.00 0.00 4.45
1706 1855 0.032952 GCTTCAGTGTGGGTGACGTA 59.967 55.000 0.00 0.00 0.00 3.57
1752 1901 2.718731 CCTTGCGTTTGTTCGGCA 59.281 55.556 0.00 0.00 0.00 5.69
1889 2053 4.465512 GCACAAGACCATGCGCCG 62.466 66.667 4.18 0.00 30.97 6.46
2018 2304 0.871722 TGCATGTAACCTGCGTTGAC 59.128 50.000 0.00 0.00 42.62 3.18
2026 2312 4.563580 TGTAACCTGCGTTGACATAATACG 59.436 41.667 0.00 0.00 38.26 3.06
2035 2321 4.032445 CGTTGACATAATACGGTCCTTGTG 59.968 45.833 0.00 0.00 33.09 3.33
2039 2325 5.410132 TGACATAATACGGTCCTTGTGTTTG 59.590 40.000 7.03 0.00 33.09 2.93
2042 2328 3.764237 ATACGGTCCTTGTGTTTGTCT 57.236 42.857 0.00 0.00 0.00 3.41
2066 2353 9.942850 TCTGAGTGACAAAATTACATATCTCAA 57.057 29.630 0.00 0.00 0.00 3.02
2240 2718 1.306568 AGGACCAGCTTCCTCCTCC 60.307 63.158 0.72 0.00 42.98 4.30
2241 2719 1.306568 GGACCAGCTTCCTCCTCCT 60.307 63.158 0.00 0.00 32.24 3.69
2242 2720 1.621672 GGACCAGCTTCCTCCTCCTG 61.622 65.000 0.00 0.00 32.24 3.86
2243 2721 3.318191 CCAGCTTCCTCCTCCTGG 58.682 66.667 0.00 0.00 38.93 4.45
2244 2722 1.614824 CCAGCTTCCTCCTCCTGGT 60.615 63.158 0.00 0.00 39.93 4.00
2245 2723 1.621672 CCAGCTTCCTCCTCCTGGTC 61.622 65.000 0.00 0.00 39.93 4.02
2246 2724 1.306568 AGCTTCCTCCTCCTGGTCC 60.307 63.158 0.00 0.00 34.23 4.46
2247 2725 1.306568 GCTTCCTCCTCCTGGTCCT 60.307 63.158 0.00 0.00 34.23 3.85
2248 2726 1.334384 GCTTCCTCCTCCTGGTCCTC 61.334 65.000 0.00 0.00 34.23 3.71
2280 2759 6.551385 AGATTAAACCTCAATCATCGCATC 57.449 37.500 0.00 0.00 35.30 3.91
2384 2875 6.348458 CGGACTCTTTGAACATTGCTAATTCA 60.348 38.462 0.00 0.00 0.00 2.57
2387 2878 7.542025 ACTCTTTGAACATTGCTAATTCATCC 58.458 34.615 0.39 0.00 32.61 3.51
2453 5292 7.172532 AGTTTAGTGATTGCGATACAAAGTCAA 59.827 33.333 0.00 0.00 42.86 3.18
2471 5310 0.913205 AATATGGGGTGTGTACGGCA 59.087 50.000 0.00 0.00 0.00 5.69
2476 5315 1.080025 GGGTGTGTACGGCAGTCTC 60.080 63.158 0.00 0.00 0.00 3.36
2592 5543 2.234908 AGAAGTGTCGAGGGAAGATTGG 59.765 50.000 0.00 0.00 0.00 3.16
2710 5664 6.500751 ACCCTAGGTTTTCAGATTAGTCTTGA 59.499 38.462 8.29 0.00 27.29 3.02
2783 5737 8.864087 ACATGCACATGAGAAACTATATCTAGA 58.136 33.333 17.19 0.00 41.20 2.43
2826 5781 6.553100 TGATCAATGTTTCCCTTAAAGTGGTT 59.447 34.615 0.00 0.00 0.00 3.67
2861 5820 2.213499 CTGCCATAATCTTCGTCCACC 58.787 52.381 0.00 0.00 0.00 4.61
2872 5831 2.153034 TCGTCCACCAGTCCATGATA 57.847 50.000 0.00 0.00 0.00 2.15
2878 5837 4.649674 GTCCACCAGTCCATGATAGACTAA 59.350 45.833 0.00 0.00 42.69 2.24
2922 5881 1.068250 GGCCAGCTCACGTATCTCC 59.932 63.158 0.00 0.00 0.00 3.71
2985 6101 3.750371 ACAATAGCTAGTGGTTTGCACA 58.250 40.909 23.81 0.00 0.00 4.57
2988 6104 1.826385 AGCTAGTGGTTTGCACATCC 58.174 50.000 0.00 0.00 0.00 3.51
3117 6235 4.657013 TGTTTGGCTATGGATAACACACA 58.343 39.130 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.036498 CAGAAAATGATCCCTGTGCTCATC 59.964 45.833 0.00 0.00 0.00 2.92
1 2 3.952323 CAGAAAATGATCCCTGTGCTCAT 59.048 43.478 0.00 0.00 0.00 2.90
2 3 3.349927 CAGAAAATGATCCCTGTGCTCA 58.650 45.455 0.00 0.00 0.00 4.26
3 4 2.686915 CCAGAAAATGATCCCTGTGCTC 59.313 50.000 0.00 0.00 0.00 4.26
4 5 2.622452 CCCAGAAAATGATCCCTGTGCT 60.622 50.000 0.00 0.00 0.00 4.40
5 6 1.753073 CCCAGAAAATGATCCCTGTGC 59.247 52.381 0.00 0.00 0.00 4.57
6 7 3.370840 TCCCAGAAAATGATCCCTGTG 57.629 47.619 0.00 0.00 0.00 3.66
7 8 4.402616 TTTCCCAGAAAATGATCCCTGT 57.597 40.909 0.00 0.00 0.00 4.00
8 9 5.945144 ATTTTCCCAGAAAATGATCCCTG 57.055 39.130 13.10 0.00 0.00 4.45
9 10 9.539194 GATATATTTTCCCAGAAAATGATCCCT 57.461 33.333 20.28 1.67 32.64 4.20
10 11 8.753133 GGATATATTTTCCCAGAAAATGATCCC 58.247 37.037 26.13 18.16 37.41 3.85
24 25 6.617879 CCGGATTTTTCGGGATATATTTTCC 58.382 40.000 0.00 0.00 43.45 3.13
37 38 1.803334 TGTCAGGACCGGATTTTTCG 58.197 50.000 9.46 0.00 0.00 3.46
38 39 2.423538 CCATGTCAGGACCGGATTTTTC 59.576 50.000 9.46 0.00 0.00 2.29
39 40 2.041081 TCCATGTCAGGACCGGATTTTT 59.959 45.455 9.46 0.00 31.23 1.94
40 41 1.633432 TCCATGTCAGGACCGGATTTT 59.367 47.619 9.46 0.00 31.23 1.82
41 42 1.210478 CTCCATGTCAGGACCGGATTT 59.790 52.381 9.46 0.00 33.26 2.17
42 43 0.833287 CTCCATGTCAGGACCGGATT 59.167 55.000 9.46 0.00 33.26 3.01
43 44 0.325671 ACTCCATGTCAGGACCGGAT 60.326 55.000 9.46 0.00 33.26 4.18
44 45 1.078528 ACTCCATGTCAGGACCGGA 59.921 57.895 9.46 7.28 33.19 5.14
45 46 1.219124 CACTCCATGTCAGGACCGG 59.781 63.158 0.00 0.00 33.19 5.28
46 47 1.219124 CCACTCCATGTCAGGACCG 59.781 63.158 0.00 0.00 33.19 4.79
47 48 1.078143 GCCACTCCATGTCAGGACC 60.078 63.158 0.00 0.00 33.19 4.46
48 49 0.036732 TTGCCACTCCATGTCAGGAC 59.963 55.000 0.00 0.00 33.19 3.85
49 50 0.325933 CTTGCCACTCCATGTCAGGA 59.674 55.000 0.00 0.00 36.00 3.86
50 51 0.679002 CCTTGCCACTCCATGTCAGG 60.679 60.000 0.00 0.00 0.00 3.86
51 52 0.037303 ACCTTGCCACTCCATGTCAG 59.963 55.000 0.00 0.00 0.00 3.51
52 53 0.036732 GACCTTGCCACTCCATGTCA 59.963 55.000 0.00 0.00 0.00 3.58
53 54 0.326264 AGACCTTGCCACTCCATGTC 59.674 55.000 0.00 0.00 0.00 3.06
54 55 0.326264 GAGACCTTGCCACTCCATGT 59.674 55.000 0.00 0.00 0.00 3.21
55 56 0.742281 CGAGACCTTGCCACTCCATG 60.742 60.000 0.00 0.00 0.00 3.66
56 57 1.599047 CGAGACCTTGCCACTCCAT 59.401 57.895 0.00 0.00 0.00 3.41
57 58 3.059982 CGAGACCTTGCCACTCCA 58.940 61.111 0.00 0.00 0.00 3.86
58 59 2.435059 GCGAGACCTTGCCACTCC 60.435 66.667 0.00 0.00 33.90 3.85
64 65 3.760035 TCTCCGGCGAGACCTTGC 61.760 66.667 9.30 0.61 40.34 4.01
89 90 3.730761 GCTTGCAGCAGACCGGTG 61.731 66.667 14.63 0.00 46.27 4.94
90 91 3.946201 AGCTTGCAGCAGACCGGT 61.946 61.111 6.92 6.92 45.56 5.28
91 92 3.429141 CAGCTTGCAGCAGACCGG 61.429 66.667 0.00 0.00 45.56 5.28
92 93 4.099170 GCAGCTTGCAGCAGACCG 62.099 66.667 5.14 0.00 45.56 4.79
93 94 4.099170 CGCAGCTTGCAGCAGACC 62.099 66.667 10.37 0.00 45.36 3.85
94 95 3.024782 CTCGCAGCTTGCAGCAGAC 62.025 63.158 10.37 0.00 45.36 3.51
95 96 2.741211 CTCGCAGCTTGCAGCAGA 60.741 61.111 10.37 7.36 45.36 4.26
96 97 4.462417 GCTCGCAGCTTGCAGCAG 62.462 66.667 18.14 7.63 45.36 4.24
114 115 3.770040 CATGTGACTCCGGCGGGA 61.770 66.667 27.98 13.04 41.08 5.14
115 116 4.838152 CCATGTGACTCCGGCGGG 62.838 72.222 27.98 19.08 0.00 6.13
118 119 4.451150 TCGCCATGTGACTCCGGC 62.451 66.667 0.00 0.00 41.30 6.13
119 120 2.202797 CTCGCCATGTGACTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
120 121 1.807165 CACTCGCCATGTGACTCCG 60.807 63.158 0.00 0.00 37.60 4.63
121 122 0.737715 GACACTCGCCATGTGACTCC 60.738 60.000 5.56 0.00 38.65 3.85
122 123 1.073216 CGACACTCGCCATGTGACTC 61.073 60.000 5.56 0.00 38.65 3.36
123 124 1.080501 CGACACTCGCCATGTGACT 60.081 57.895 5.56 0.00 38.65 3.41
124 125 2.094659 CCGACACTCGCCATGTGAC 61.095 63.158 5.56 0.00 38.82 3.67
125 126 2.261361 CCGACACTCGCCATGTGA 59.739 61.111 5.56 0.00 38.82 3.58
126 127 2.048222 ACCGACACTCGCCATGTG 60.048 61.111 0.00 0.00 38.82 3.21
127 128 2.048222 CACCGACACTCGCCATGT 60.048 61.111 0.00 0.00 38.82 3.21
128 129 2.815211 CCACCGACACTCGCCATG 60.815 66.667 0.00 0.00 38.82 3.66
129 130 4.760047 GCCACCGACACTCGCCAT 62.760 66.667 0.00 0.00 38.82 4.40
133 134 3.103911 GTTCGCCACCGACACTCG 61.104 66.667 0.00 0.00 44.30 4.18
134 135 2.737376 GGTTCGCCACCGACACTC 60.737 66.667 0.00 0.00 44.30 3.51
142 143 2.654912 CGTCGTCAAGGTTCGCCAC 61.655 63.158 0.00 0.00 40.60 5.01
143 144 2.355363 CGTCGTCAAGGTTCGCCA 60.355 61.111 0.00 0.00 40.60 5.69
144 145 2.049802 TCGTCGTCAAGGTTCGCC 60.050 61.111 0.00 0.00 37.60 5.54
145 146 2.717809 GCTCGTCGTCAAGGTTCGC 61.718 63.158 0.00 0.00 0.00 4.70
146 147 2.426183 CGCTCGTCGTCAAGGTTCG 61.426 63.158 0.00 0.00 0.00 3.95
147 148 3.449042 CGCTCGTCGTCAAGGTTC 58.551 61.111 0.00 0.00 0.00 3.62
164 165 4.415332 TTGCCTCGTCCTCGCGAC 62.415 66.667 3.71 0.00 36.80 5.19
165 166 4.116328 CTTGCCTCGTCCTCGCGA 62.116 66.667 9.26 9.26 39.22 5.87
167 168 3.708220 CTCCTTGCCTCGTCCTCGC 62.708 68.421 0.00 0.00 36.96 5.03
168 169 2.492090 CTCCTTGCCTCGTCCTCG 59.508 66.667 0.00 0.00 38.55 4.63
169 170 1.671901 CTCCTCCTTGCCTCGTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
170 171 1.684049 CTCCTCCTTGCCTCGTCCT 60.684 63.158 0.00 0.00 0.00 3.85
171 172 1.671901 CTCTCCTCCTTGCCTCGTCC 61.672 65.000 0.00 0.00 0.00 4.79
172 173 1.671901 CCTCTCCTCCTTGCCTCGTC 61.672 65.000 0.00 0.00 0.00 4.20
173 174 1.684049 CCTCTCCTCCTTGCCTCGT 60.684 63.158 0.00 0.00 0.00 4.18
174 175 2.430610 CCCTCTCCTCCTTGCCTCG 61.431 68.421 0.00 0.00 0.00 4.63
175 176 2.741055 GCCCTCTCCTCCTTGCCTC 61.741 68.421 0.00 0.00 0.00 4.70
176 177 2.690510 GCCCTCTCCTCCTTGCCT 60.691 66.667 0.00 0.00 0.00 4.75
177 178 4.168291 CGCCCTCTCCTCCTTGCC 62.168 72.222 0.00 0.00 0.00 4.52
178 179 4.168291 CCGCCCTCTCCTCCTTGC 62.168 72.222 0.00 0.00 0.00 4.01
179 180 3.474570 CCCGCCCTCTCCTCCTTG 61.475 72.222 0.00 0.00 0.00 3.61
180 181 3.254035 TTCCCGCCCTCTCCTCCTT 62.254 63.158 0.00 0.00 0.00 3.36
181 182 3.684628 TTCCCGCCCTCTCCTCCT 61.685 66.667 0.00 0.00 0.00 3.69
182 183 3.471806 GTTCCCGCCCTCTCCTCC 61.472 72.222 0.00 0.00 0.00 4.30
183 184 3.839432 CGTTCCCGCCCTCTCCTC 61.839 72.222 0.00 0.00 0.00 3.71
209 210 4.883354 CCTTCTCCCATGCGCCCC 62.883 72.222 4.18 0.00 0.00 5.80
210 211 4.883354 CCCTTCTCCCATGCGCCC 62.883 72.222 4.18 0.00 0.00 6.13
211 212 4.115199 ACCCTTCTCCCATGCGCC 62.115 66.667 4.18 0.00 0.00 6.53
212 213 2.819984 TTCACCCTTCTCCCATGCGC 62.820 60.000 0.00 0.00 0.00 6.09
213 214 0.107017 ATTCACCCTTCTCCCATGCG 60.107 55.000 0.00 0.00 0.00 4.73
214 215 1.396653 CATTCACCCTTCTCCCATGC 58.603 55.000 0.00 0.00 0.00 4.06
215 216 1.396653 GCATTCACCCTTCTCCCATG 58.603 55.000 0.00 0.00 0.00 3.66
216 217 0.259938 GGCATTCACCCTTCTCCCAT 59.740 55.000 0.00 0.00 0.00 4.00
217 218 1.139498 TGGCATTCACCCTTCTCCCA 61.139 55.000 0.00 0.00 0.00 4.37
218 219 0.259938 ATGGCATTCACCCTTCTCCC 59.740 55.000 0.00 0.00 0.00 4.30
219 220 1.396653 CATGGCATTCACCCTTCTCC 58.603 55.000 0.00 0.00 0.00 3.71
220 221 0.743097 GCATGGCATTCACCCTTCTC 59.257 55.000 0.00 0.00 0.00 2.87
221 222 1.033746 CGCATGGCATTCACCCTTCT 61.034 55.000 0.00 0.00 0.00 2.85
222 223 1.434696 CGCATGGCATTCACCCTTC 59.565 57.895 0.00 0.00 0.00 3.46
223 224 2.053865 CCGCATGGCATTCACCCTT 61.054 57.895 0.00 0.00 0.00 3.95
224 225 2.440796 CCGCATGGCATTCACCCT 60.441 61.111 0.00 0.00 0.00 4.34
242 243 4.124351 TCCTCCGCGCGTAGGTTG 62.124 66.667 35.76 17.53 34.30 3.77
243 244 3.823330 CTCCTCCGCGCGTAGGTT 61.823 66.667 35.76 0.00 34.30 3.50
244 245 4.790962 TCTCCTCCGCGCGTAGGT 62.791 66.667 35.76 0.00 34.30 3.08
245 246 3.515286 TTCTCCTCCGCGCGTAGG 61.515 66.667 32.99 32.99 0.00 3.18
246 247 2.278013 GTTCTCCTCCGCGCGTAG 60.278 66.667 29.95 23.22 0.00 3.51
247 248 2.537792 CTTGTTCTCCTCCGCGCGTA 62.538 60.000 29.95 13.14 0.00 4.42
248 249 3.916392 CTTGTTCTCCTCCGCGCGT 62.916 63.158 29.95 0.00 0.00 6.01
249 250 3.181967 CTTGTTCTCCTCCGCGCG 61.182 66.667 25.67 25.67 0.00 6.86
250 251 2.781595 TTCCTTGTTCTCCTCCGCGC 62.782 60.000 0.00 0.00 0.00 6.86
251 252 0.108138 ATTCCTTGTTCTCCTCCGCG 60.108 55.000 0.00 0.00 0.00 6.46
252 253 2.168728 ACTATTCCTTGTTCTCCTCCGC 59.831 50.000 0.00 0.00 0.00 5.54
253 254 3.489398 CGACTATTCCTTGTTCTCCTCCG 60.489 52.174 0.00 0.00 0.00 4.63
254 255 3.738590 GCGACTATTCCTTGTTCTCCTCC 60.739 52.174 0.00 0.00 0.00 4.30
255 256 3.449632 GCGACTATTCCTTGTTCTCCTC 58.550 50.000 0.00 0.00 0.00 3.71
256 257 2.159226 CGCGACTATTCCTTGTTCTCCT 60.159 50.000 0.00 0.00 0.00 3.69
257 258 2.159282 TCGCGACTATTCCTTGTTCTCC 60.159 50.000 3.71 0.00 0.00 3.71
258 259 3.109619 CTCGCGACTATTCCTTGTTCTC 58.890 50.000 3.71 0.00 0.00 2.87
259 260 2.753452 TCTCGCGACTATTCCTTGTTCT 59.247 45.455 3.71 0.00 0.00 3.01
260 261 3.109619 CTCTCGCGACTATTCCTTGTTC 58.890 50.000 3.71 0.00 0.00 3.18
261 262 2.159226 CCTCTCGCGACTATTCCTTGTT 60.159 50.000 3.71 0.00 0.00 2.83
262 263 1.405821 CCTCTCGCGACTATTCCTTGT 59.594 52.381 3.71 0.00 0.00 3.16
263 264 1.269309 CCCTCTCGCGACTATTCCTTG 60.269 57.143 3.71 0.00 0.00 3.61
264 265 1.033574 CCCTCTCGCGACTATTCCTT 58.966 55.000 3.71 0.00 0.00 3.36
265 266 0.183014 TCCCTCTCGCGACTATTCCT 59.817 55.000 3.71 0.00 0.00 3.36
266 267 1.001158 CTTCCCTCTCGCGACTATTCC 60.001 57.143 3.71 0.00 0.00 3.01
267 268 1.001158 CCTTCCCTCTCGCGACTATTC 60.001 57.143 3.71 0.00 0.00 1.75
268 269 1.033574 CCTTCCCTCTCGCGACTATT 58.966 55.000 3.71 0.00 0.00 1.73
269 270 0.183014 TCCTTCCCTCTCGCGACTAT 59.817 55.000 3.71 0.00 0.00 2.12
270 271 0.464013 CTCCTTCCCTCTCGCGACTA 60.464 60.000 3.71 0.00 0.00 2.59
271 272 1.751162 CTCCTTCCCTCTCGCGACT 60.751 63.158 3.71 0.00 0.00 4.18
272 273 2.776913 CCTCCTTCCCTCTCGCGAC 61.777 68.421 3.71 0.00 0.00 5.19
273 274 2.440430 CCTCCTTCCCTCTCGCGA 60.440 66.667 9.26 9.26 0.00 5.87
274 275 3.532155 CCCTCCTTCCCTCTCGCG 61.532 72.222 0.00 0.00 0.00 5.87
275 276 3.157949 CCCCTCCTTCCCTCTCGC 61.158 72.222 0.00 0.00 0.00 5.03
276 277 2.444895 CCCCCTCCTTCCCTCTCG 60.445 72.222 0.00 0.00 0.00 4.04
292 293 1.007118 ACCCATGTCATTTTCTCCCCC 59.993 52.381 0.00 0.00 0.00 5.40
293 294 2.102578 CACCCATGTCATTTTCTCCCC 58.897 52.381 0.00 0.00 0.00 4.81
294 295 3.085952 TCACCCATGTCATTTTCTCCC 57.914 47.619 0.00 0.00 0.00 4.30
295 296 6.183360 CCTTATTCACCCATGTCATTTTCTCC 60.183 42.308 0.00 0.00 0.00 3.71
296 297 6.603201 TCCTTATTCACCCATGTCATTTTCTC 59.397 38.462 0.00 0.00 0.00 2.87
297 298 6.493166 TCCTTATTCACCCATGTCATTTTCT 58.507 36.000 0.00 0.00 0.00 2.52
298 299 6.773976 TCCTTATTCACCCATGTCATTTTC 57.226 37.500 0.00 0.00 0.00 2.29
299 300 6.324770 GGATCCTTATTCACCCATGTCATTTT 59.675 38.462 3.84 0.00 0.00 1.82
300 301 5.835280 GGATCCTTATTCACCCATGTCATTT 59.165 40.000 3.84 0.00 0.00 2.32
301 302 5.135020 AGGATCCTTATTCACCCATGTCATT 59.865 40.000 9.02 0.00 0.00 2.57
302 303 4.666907 AGGATCCTTATTCACCCATGTCAT 59.333 41.667 9.02 0.00 0.00 3.06
303 304 4.047166 AGGATCCTTATTCACCCATGTCA 58.953 43.478 9.02 0.00 0.00 3.58
304 305 4.713792 AGGATCCTTATTCACCCATGTC 57.286 45.455 9.02 0.00 0.00 3.06
305 306 5.014544 CCATAGGATCCTTATTCACCCATGT 59.985 44.000 22.03 0.00 0.00 3.21
306 307 5.503927 CCATAGGATCCTTATTCACCCATG 58.496 45.833 22.03 13.49 0.00 3.66
307 308 4.018050 GCCATAGGATCCTTATTCACCCAT 60.018 45.833 22.03 0.10 0.00 4.00
308 309 3.330701 GCCATAGGATCCTTATTCACCCA 59.669 47.826 22.03 0.00 0.00 4.51
309 310 3.589288 AGCCATAGGATCCTTATTCACCC 59.411 47.826 22.03 0.96 0.00 4.61
310 311 4.917906 AGCCATAGGATCCTTATTCACC 57.082 45.455 22.03 2.60 0.00 4.02
311 312 5.006386 CCAAGCCATAGGATCCTTATTCAC 58.994 45.833 22.03 5.35 0.00 3.18
312 313 4.043310 CCCAAGCCATAGGATCCTTATTCA 59.957 45.833 22.03 0.52 0.00 2.57
313 314 4.593956 CCCAAGCCATAGGATCCTTATTC 58.406 47.826 22.03 7.59 0.00 1.75
314 315 3.245407 GCCCAAGCCATAGGATCCTTATT 60.245 47.826 22.03 2.34 0.00 1.40
315 316 2.310052 GCCCAAGCCATAGGATCCTTAT 59.690 50.000 22.03 8.66 0.00 1.73
316 317 1.705186 GCCCAAGCCATAGGATCCTTA 59.295 52.381 22.03 6.48 0.00 2.69
317 318 0.480252 GCCCAAGCCATAGGATCCTT 59.520 55.000 22.03 5.03 0.00 3.36
318 319 2.158780 GCCCAAGCCATAGGATCCT 58.841 57.895 20.48 20.48 0.00 3.24
319 320 4.830573 GCCCAAGCCATAGGATCC 57.169 61.111 2.48 2.48 0.00 3.36
330 331 4.891727 CCGTCGGATCGGCCCAAG 62.892 72.222 4.91 0.00 43.96 3.61
393 394 2.431782 CCCACTTTTCTATGGCCAATGG 59.568 50.000 10.96 7.55 34.37 3.16
412 413 1.705997 AATGGATACGTGGGCCTCCC 61.706 60.000 4.53 0.00 42.51 4.30
423 424 6.640907 GGTTTTCATTATTGCGGAATGGATAC 59.359 38.462 12.93 8.17 35.42 2.24
424 425 6.322456 TGGTTTTCATTATTGCGGAATGGATA 59.678 34.615 12.93 0.35 35.42 2.59
460 461 9.293404 TCTACTACAACACTAGAAACTACACAT 57.707 33.333 0.00 0.00 0.00 3.21
510 511 1.215382 CGTAGCCTGTGTAGCTGCA 59.785 57.895 0.00 0.00 42.38 4.41
627 628 3.062639 CGATCGTGTTGCTAATTCTTGCT 59.937 43.478 7.03 0.00 0.00 3.91
721 722 0.463654 CGAATCCAGCCCAAATCCGA 60.464 55.000 0.00 0.00 0.00 4.55
782 862 7.274904 CGGGTGATAATTTACGGTATATGACTG 59.725 40.741 0.00 0.00 40.66 3.51
788 868 7.465353 TCATCGGGTGATAATTTACGGTATA 57.535 36.000 0.00 0.00 32.18 1.47
842 925 0.319900 CCGCCTCGAATACCAGATGG 60.320 60.000 0.00 0.00 42.17 3.51
998 1109 2.861935 CGCAAATAGGTTACGGTGGTAG 59.138 50.000 0.00 0.00 0.00 3.18
1029 1151 1.643810 GCACATCGTGAATTTGTTCGC 59.356 47.619 0.00 0.00 35.23 4.70
1167 1292 1.218047 CATCCGCCGAGAGTTTGGA 59.782 57.895 0.00 0.00 0.00 3.53
1241 1372 1.978617 CTTGGGAGCGGTGGCATTT 60.979 57.895 0.00 0.00 43.41 2.32
1243 1374 4.431131 CCTTGGGAGCGGTGGCAT 62.431 66.667 0.00 0.00 43.41 4.40
1706 1855 1.661463 TGAAAGCCCAGATCTCCACT 58.339 50.000 0.00 0.00 0.00 4.00
1752 1901 2.735906 ACCCCTCCTGGTAGATATCCAT 59.264 50.000 0.00 0.00 36.67 3.41
1889 2053 5.855740 ACAACTAGGGAACTATCTAGCAC 57.144 43.478 0.00 0.00 43.39 4.40
2018 2304 5.642063 AGACAAACACAAGGACCGTATTATG 59.358 40.000 0.00 0.00 0.00 1.90
2026 2312 2.614057 CACTCAGACAAACACAAGGACC 59.386 50.000 0.00 0.00 0.00 4.46
2066 2353 4.320870 TCTTTCGCCGGAGAAAAACTAAT 58.679 39.130 29.40 0.00 39.33 1.73
2162 2460 3.071479 GGAGTGTTAACATTTGCTCCGA 58.929 45.455 20.89 0.00 34.09 4.55
2240 2718 0.637195 TCTTCCCCTAGGAGGACCAG 59.363 60.000 11.48 10.44 43.04 4.00
2241 2719 2.829267 TCTTCCCCTAGGAGGACCA 58.171 57.895 11.48 1.60 43.04 4.02
2245 2723 4.308128 AGGTTTAATCTTCCCCTAGGAGG 58.692 47.826 11.48 10.25 45.19 4.30
2246 2724 4.969359 TGAGGTTTAATCTTCCCCTAGGAG 59.031 45.833 11.48 0.00 45.19 3.69
2247 2725 4.967871 TGAGGTTTAATCTTCCCCTAGGA 58.032 43.478 11.48 0.00 41.88 2.94
2248 2726 5.710409 TTGAGGTTTAATCTTCCCCTAGG 57.290 43.478 0.06 0.06 0.00 3.02
2280 2759 0.825010 AAACAAGGGAGCTGGTGCAG 60.825 55.000 0.00 0.00 42.74 4.41
2420 5257 9.063615 TGTATCGCAATCACTAAACTAGAGATA 57.936 33.333 0.00 0.00 35.50 1.98
2453 5292 0.468226 CTGCCGTACACACCCCATAT 59.532 55.000 0.00 0.00 0.00 1.78
2471 5310 5.965033 ATGGTGATCTTTGGTATGAGACT 57.035 39.130 0.00 0.00 0.00 3.24
2476 5315 5.463392 CGAGTGTATGGTGATCTTTGGTATG 59.537 44.000 0.00 0.00 0.00 2.39
2710 5664 3.969976 TCAAGGATAGAGGCACATAGCTT 59.030 43.478 0.00 0.00 44.79 3.74
2783 5737 3.788227 TCATTTGTCAAGGCCACTAGT 57.212 42.857 5.01 0.00 0.00 2.57
2826 5781 1.198759 GGCAGTTGTCCCTCCTACCA 61.199 60.000 0.00 0.00 0.00 3.25
2861 5820 6.907853 TCATCCTTAGTCTATCATGGACTG 57.092 41.667 13.77 0.00 42.98 3.51
2872 5831 3.327172 CCATGCTCCATCATCCTTAGTCT 59.673 47.826 0.00 0.00 0.00 3.24
2878 5837 0.769873 GGACCATGCTCCATCATCCT 59.230 55.000 1.90 0.00 0.00 3.24
2905 5864 0.031449 GAGGAGATACGTGAGCTGGC 59.969 60.000 0.00 0.00 0.00 4.85
2915 5874 6.418057 AAGATCAAGATGGTGAGGAGATAC 57.582 41.667 0.00 0.00 0.00 2.24
2922 5881 7.854557 TGTGAAATAAGATCAAGATGGTGAG 57.145 36.000 0.00 0.00 0.00 3.51
2985 6101 4.939509 CGTCAAAGGTAAATCAACGGAT 57.060 40.909 0.00 0.00 34.43 4.18
2988 6104 4.477302 AACCGTCAAAGGTAAATCAACG 57.523 40.909 0.00 0.00 45.21 4.10


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

AutoCloner maintained by Alex Coulton.