Multiple sequence alignment - TraesCS2B01G524300

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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 TraesCS2B01G524300 chr2B 100.000 5154 0 0 1 5154 718608819 718603666 0.000000e+00 9518.0
1 TraesCS2B01G524300 chr2B 73.871 731 153 30 2603 3322 792954739 792955442 1.840000e-64 257.0
2 TraesCS2B01G524300 chr2B 95.161 62 2 1 119 180 683078144 683078204 4.250000e-16 97.1
3 TraesCS2B01G524300 chr2D 96.538 3957 114 14 395 4335 592639567 592635618 0.000000e+00 6527.0
4 TraesCS2B01G524300 chr2D 92.496 613 6 6 4314 4898 592635599 592634999 0.000000e+00 841.0
5 TraesCS2B01G524300 chr2D 74.399 1289 293 31 2412 3685 644170758 644169492 7.650000e-143 518.0
6 TraesCS2B01G524300 chr2D 89.268 205 4 2 4858 5058 592635084 592634894 1.850000e-59 241.0
7 TraesCS2B01G524300 chr2D 98.333 120 1 1 5035 5154 592634863 592634745 5.230000e-50 209.0
8 TraesCS2B01G524300 chr2A 95.849 3782 137 9 489 4254 727196383 727192606 0.000000e+00 6096.0
9 TraesCS2B01G524300 chr2A 90.272 257 23 2 4899 5154 727192075 727191820 8.270000e-88 335.0
10 TraesCS2B01G524300 chr2A 84.211 266 19 11 4614 4857 727192300 727192036 2.400000e-58 237.0
11 TraesCS2B01G524300 chr2A 80.866 277 24 14 194 468 727196628 727196379 1.890000e-44 191.0
12 TraesCS2B01G524300 chr2A 93.151 73 2 2 125 196 49422077 49422147 2.540000e-18 104.0
13 TraesCS2B01G524300 chr4D 72.197 2640 663 64 1077 3685 85262762 85260163 0.000000e+00 743.0
14 TraesCS2B01G524300 chr4D 95.161 62 2 1 119 180 72256252 72256192 4.250000e-16 97.1
15 TraesCS2B01G524300 chr4D 93.548 62 4 0 119 180 18207566 18207505 5.490000e-15 93.5
16 TraesCS2B01G524300 chr4A 72.174 2645 658 69 1077 3685 498988700 498986098 0.000000e+00 736.0
17 TraesCS2B01G524300 chr3A 75.527 1234 274 27 2420 3639 36301614 36302833 9.620000e-162 580.0
18 TraesCS2B01G524300 chr3D 75.000 1220 281 22 2420 3627 26302221 26303428 4.540000e-150 542.0
19 TraesCS2B01G524300 chr3D 75.542 1108 240 28 2589 3682 26292331 26293421 2.750000e-142 516.0
20 TraesCS2B01G524300 chr3D 75.181 1104 247 22 2591 3682 26282798 26283886 3.580000e-136 496.0
21 TraesCS2B01G524300 chr3D 74.387 1101 261 18 2591 3682 26220968 26219880 7.870000e-123 451.0
22 TraesCS2B01G524300 chrUn 75.567 1146 248 25 2555 3687 75443037 75444163 2.110000e-148 536.0
23 TraesCS2B01G524300 chr5A 71.948 1786 442 48 1925 3682 650280454 650282208 7.810000e-128 468.0
24 TraesCS2B01G524300 chr6D 98.276 58 1 0 123 180 319246374 319246317 9.130000e-18 102.0
25 TraesCS2B01G524300 chr6D 96.721 61 1 1 120 180 110881514 110881455 3.280000e-17 100.0
26 TraesCS2B01G524300 chr5B 96.667 60 2 0 121 180 508623266 508623325 3.280000e-17 100.0
27 TraesCS2B01G524300 chr5D 96.667 60 1 1 121 180 456088091 456088033 1.180000e-16 99.0
28 TraesCS2B01G524300 chr5D 93.846 65 3 1 116 180 519214165 519214228 4.250000e-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 TraesCS2B01G524300 chr2B 718603666 718608819 5153 True 9518.00 9518 100.00000 1 5154 1 chr2B.!!$R1 5153
1 TraesCS2B01G524300 chr2B 792954739 792955442 703 False 257.00 257 73.87100 2603 3322 1 chr2B.!!$F2 719
2 TraesCS2B01G524300 chr2D 592634745 592639567 4822 True 1954.50 6527 94.15875 395 5154 4 chr2D.!!$R2 4759
3 TraesCS2B01G524300 chr2D 644169492 644170758 1266 True 518.00 518 74.39900 2412 3685 1 chr2D.!!$R1 1273
4 TraesCS2B01G524300 chr2A 727191820 727196628 4808 True 1714.75 6096 87.79950 194 5154 4 chr2A.!!$R1 4960
5 TraesCS2B01G524300 chr4D 85260163 85262762 2599 True 743.00 743 72.19700 1077 3685 1 chr4D.!!$R3 2608
6 TraesCS2B01G524300 chr4A 498986098 498988700 2602 True 736.00 736 72.17400 1077 3685 1 chr4A.!!$R1 2608
7 TraesCS2B01G524300 chr3A 36301614 36302833 1219 False 580.00 580 75.52700 2420 3639 1 chr3A.!!$F1 1219
8 TraesCS2B01G524300 chr3D 26302221 26303428 1207 False 542.00 542 75.00000 2420 3627 1 chr3D.!!$F3 1207
9 TraesCS2B01G524300 chr3D 26292331 26293421 1090 False 516.00 516 75.54200 2589 3682 1 chr3D.!!$F2 1093
10 TraesCS2B01G524300 chr3D 26282798 26283886 1088 False 496.00 496 75.18100 2591 3682 1 chr3D.!!$F1 1091
11 TraesCS2B01G524300 chr3D 26219880 26220968 1088 True 451.00 451 74.38700 2591 3682 1 chr3D.!!$R1 1091
12 TraesCS2B01G524300 chrUn 75443037 75444163 1126 False 536.00 536 75.56700 2555 3687 1 chrUn.!!$F1 1132
13 TraesCS2B01G524300 chr5A 650280454 650282208 1754 False 468.00 468 71.94800 1925 3682 1 chr5A.!!$F1 1757

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
143 144 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.0 44.66 3.13 F
147 148 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 F
299 300 0.101579 GAAGTACGCAGGCTCTCTCC 59.898 60.000 0.00 0.0 0.00 3.71 F
1060 1101 0.322456 GGCTTGCAGTACCCATGTCA 60.322 55.000 0.00 0.0 0.00 3.58 F
2258 2299 1.067250 CTCTAGAGAGCTTGCGGGC 59.933 63.158 15.05 0.0 35.13 6.13 F
2263 2304 1.443407 GAGAGCTTGCGGGCTATCA 59.557 57.895 16.73 0.0 46.14 2.15 F
3818 3860 0.685097 TACAGAGTGGGCAACTGGTC 59.315 55.000 0.00 0.0 40.07 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1101 0.463204 CCATGTGAGGAGCAGACGAT 59.537 55.000 0.00 0.0 0.00 3.73 R
1242 1283 1.980052 CCCTTGTAAGCCTCGACCA 59.020 57.895 0.00 0.0 0.00 4.02 R
1343 1384 2.034221 GCAGGTGACCAAGGGACC 59.966 66.667 3.63 2.2 0.00 4.46 R
2383 2424 2.306847 TGCTTCAAGGGTTTTGAGGTC 58.693 47.619 1.84 0.0 0.00 3.85 R
3818 3860 1.002468 CCCAGCAACTGAAACTTCACG 60.002 52.381 0.00 0.0 32.44 4.35 R
3938 3980 3.359033 TCCCAGCAGGAAAATTCATCTG 58.641 45.455 0.00 0.0 43.78 2.90 R
4910 5075 0.332293 TTCCCCATCCGTTTAACCCC 59.668 55.000 0.00 0.0 0.00 4.95 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 4.698575 GACTGAAGAAAGAGGAACACTGT 58.301 43.478 0.00 0.00 0.00 3.55
23 24 5.104259 ACTGAAGAAAGAGGAACACTGTT 57.896 39.130 0.00 0.00 33.47 3.16
24 25 5.501156 ACTGAAGAAAGAGGAACACTGTTT 58.499 37.500 0.00 0.00 44.50 2.83
25 26 5.946377 ACTGAAGAAAGAGGAACACTGTTTT 59.054 36.000 0.00 0.00 42.17 2.43
26 27 6.127897 ACTGAAGAAAGAGGAACACTGTTTTG 60.128 38.462 0.00 0.00 42.17 2.44
27 28 5.710099 TGAAGAAAGAGGAACACTGTTTTGT 59.290 36.000 0.00 0.00 42.17 2.83
28 29 6.208599 TGAAGAAAGAGGAACACTGTTTTGTT 59.791 34.615 0.00 0.00 42.17 2.83
29 30 6.590234 AGAAAGAGGAACACTGTTTTGTTT 57.410 33.333 0.00 0.00 42.17 2.83
30 31 7.696992 AGAAAGAGGAACACTGTTTTGTTTA 57.303 32.000 0.00 0.00 42.17 2.01
31 32 7.762382 AGAAAGAGGAACACTGTTTTGTTTAG 58.238 34.615 0.00 0.00 42.17 1.85
32 33 7.610305 AGAAAGAGGAACACTGTTTTGTTTAGA 59.390 33.333 0.00 0.00 42.17 2.10
33 34 7.881775 AAGAGGAACACTGTTTTGTTTAGAT 57.118 32.000 0.00 0.00 39.88 1.98
34 35 7.264373 AGAGGAACACTGTTTTGTTTAGATG 57.736 36.000 0.00 0.00 39.88 2.90
35 36 6.828785 AGAGGAACACTGTTTTGTTTAGATGT 59.171 34.615 0.00 0.00 39.88 3.06
36 37 7.990886 AGAGGAACACTGTTTTGTTTAGATGTA 59.009 33.333 0.00 0.00 39.88 2.29
37 38 8.154649 AGGAACACTGTTTTGTTTAGATGTAG 57.845 34.615 0.00 0.00 39.88 2.74
38 39 7.773690 AGGAACACTGTTTTGTTTAGATGTAGT 59.226 33.333 0.00 0.00 39.88 2.73
39 40 9.048446 GGAACACTGTTTTGTTTAGATGTAGTA 57.952 33.333 0.00 0.00 39.88 1.82
112 113 9.841295 TTTTTACGGGAGTTGATATTATAGCTT 57.159 29.630 0.00 0.00 43.33 3.74
113 114 8.827177 TTTACGGGAGTTGATATTATAGCTTG 57.173 34.615 0.00 0.00 43.33 4.01
114 115 6.420913 ACGGGAGTTGATATTATAGCTTGT 57.579 37.500 0.00 0.00 43.33 3.16
115 116 6.456501 ACGGGAGTTGATATTATAGCTTGTC 58.543 40.000 0.00 0.00 43.33 3.18
116 117 5.573282 CGGGAGTTGATATTATAGCTTGTCG 59.427 44.000 0.00 0.00 0.00 4.35
117 118 5.869888 GGGAGTTGATATTATAGCTTGTCGG 59.130 44.000 0.00 0.00 0.00 4.79
118 119 6.456501 GGAGTTGATATTATAGCTTGTCGGT 58.543 40.000 0.00 0.00 0.00 4.69
119 120 6.366332 GGAGTTGATATTATAGCTTGTCGGTG 59.634 42.308 0.00 0.00 0.00 4.94
120 121 6.223852 AGTTGATATTATAGCTTGTCGGTGG 58.776 40.000 0.00 0.00 0.00 4.61
121 122 5.801531 TGATATTATAGCTTGTCGGTGGT 57.198 39.130 0.00 0.00 0.00 4.16
122 123 6.904463 TGATATTATAGCTTGTCGGTGGTA 57.096 37.500 0.00 0.00 0.00 3.25
123 124 6.920817 TGATATTATAGCTTGTCGGTGGTAG 58.079 40.000 0.00 0.00 0.00 3.18
124 125 6.717997 TGATATTATAGCTTGTCGGTGGTAGA 59.282 38.462 0.00 0.00 0.00 2.59
125 126 7.396339 TGATATTATAGCTTGTCGGTGGTAGAT 59.604 37.037 0.00 0.00 0.00 1.98
126 127 8.818622 ATATTATAGCTTGTCGGTGGTAGATA 57.181 34.615 0.00 0.00 0.00 1.98
127 128 4.850347 ATAGCTTGTCGGTGGTAGATAC 57.150 45.455 0.00 0.00 0.00 2.24
128 129 2.736347 AGCTTGTCGGTGGTAGATACT 58.264 47.619 0.00 0.00 0.00 2.12
129 130 2.688958 AGCTTGTCGGTGGTAGATACTC 59.311 50.000 0.00 0.00 0.00 2.59
130 131 2.223758 GCTTGTCGGTGGTAGATACTCC 60.224 54.545 0.00 0.00 0.00 3.85
131 132 2.062971 TGTCGGTGGTAGATACTCCC 57.937 55.000 0.00 0.00 0.00 4.30
132 133 1.567649 TGTCGGTGGTAGATACTCCCT 59.432 52.381 0.00 0.00 0.00 4.20
133 134 2.228925 GTCGGTGGTAGATACTCCCTC 58.771 57.143 0.00 0.00 0.00 4.30
134 135 1.144503 TCGGTGGTAGATACTCCCTCC 59.855 57.143 0.00 0.00 0.00 4.30
135 136 1.618487 GGTGGTAGATACTCCCTCCG 58.382 60.000 0.00 0.00 0.00 4.63
136 137 1.133544 GGTGGTAGATACTCCCTCCGT 60.134 57.143 0.00 0.00 0.00 4.69
137 138 2.228925 GTGGTAGATACTCCCTCCGTC 58.771 57.143 0.00 0.00 0.00 4.79
138 139 1.144503 TGGTAGATACTCCCTCCGTCC 59.855 57.143 0.00 0.00 0.00 4.79
139 140 1.521580 GTAGATACTCCCTCCGTCCG 58.478 60.000 0.00 0.00 0.00 4.79
140 141 0.399454 TAGATACTCCCTCCGTCCGG 59.601 60.000 0.00 0.00 0.00 5.14
141 142 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
142 143 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
143 144 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
144 145 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
145 146 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
146 147 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
147 148 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
148 149 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
149 150 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
150 151 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
151 152 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
152 153 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
153 154 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
154 155 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
155 156 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
156 157 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
157 158 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
158 159 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
159 160 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
160 161 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
161 162 4.630069 CGGAAATACTTGTCGGAGAAATGT 59.370 41.667 0.00 0.00 39.69 2.71
162 163 5.808540 CGGAAATACTTGTCGGAGAAATGTA 59.191 40.000 0.00 0.00 38.48 2.29
163 164 6.479001 CGGAAATACTTGTCGGAGAAATGTAT 59.521 38.462 0.00 0.00 43.96 2.29
164 165 7.650504 CGGAAATACTTGTCGGAGAAATGTATA 59.349 37.037 1.82 0.00 42.11 1.47
165 166 9.321562 GGAAATACTTGTCGGAGAAATGTATAA 57.678 33.333 1.82 0.00 42.11 0.98
171 172 8.458843 ACTTGTCGGAGAAATGTATAAAAATGG 58.541 33.333 0.00 0.00 39.69 3.16
172 173 8.568676 TTGTCGGAGAAATGTATAAAAATGGA 57.431 30.769 0.00 0.00 39.69 3.41
173 174 8.746052 TGTCGGAGAAATGTATAAAAATGGAT 57.254 30.769 0.00 0.00 39.69 3.41
174 175 8.620416 TGTCGGAGAAATGTATAAAAATGGATG 58.380 33.333 0.00 0.00 39.69 3.51
175 176 8.621286 GTCGGAGAAATGTATAAAAATGGATGT 58.379 33.333 0.00 0.00 39.69 3.06
176 177 9.839817 TCGGAGAAATGTATAAAAATGGATGTA 57.160 29.630 0.00 0.00 0.00 2.29
188 189 2.748209 TGGATGTATCTCCAGACGGA 57.252 50.000 0.00 0.00 40.43 4.69
211 212 3.577415 GGGAGTACTTGGTTCGCCTATAT 59.423 47.826 0.00 0.00 38.36 0.86
212 213 4.768968 GGGAGTACTTGGTTCGCCTATATA 59.231 45.833 0.00 0.00 38.36 0.86
213 214 5.244626 GGGAGTACTTGGTTCGCCTATATAA 59.755 44.000 0.00 0.00 38.36 0.98
214 215 6.239402 GGGAGTACTTGGTTCGCCTATATAAA 60.239 42.308 0.00 0.00 38.36 1.40
253 254 6.254804 GCTCTAAGCAGCTAGTAAAGAACTTC 59.745 42.308 0.00 0.00 41.89 3.01
280 281 0.596083 CTATCGCCGCTCTCCAACAG 60.596 60.000 0.00 0.00 0.00 3.16
299 300 0.101579 GAAGTACGCAGGCTCTCTCC 59.898 60.000 0.00 0.00 0.00 3.71
300 301 0.612174 AAGTACGCAGGCTCTCTCCA 60.612 55.000 0.00 0.00 0.00 3.86
301 302 1.139947 GTACGCAGGCTCTCTCCAC 59.860 63.158 0.00 0.00 0.00 4.02
315 318 3.283684 CCACGAGGCGGTGCAAAA 61.284 61.111 6.26 0.00 36.59 2.44
332 335 5.572896 GTGCAAAAGCATGGTAAGTTACATC 59.427 40.000 14.81 0.00 0.00 3.06
333 336 5.476599 TGCAAAAGCATGGTAAGTTACATCT 59.523 36.000 14.81 3.19 0.00 2.90
334 337 6.657117 TGCAAAAGCATGGTAAGTTACATCTA 59.343 34.615 14.81 0.00 0.00 1.98
335 338 6.967199 GCAAAAGCATGGTAAGTTACATCTAC 59.033 38.462 14.81 0.61 0.00 2.59
336 339 7.148239 GCAAAAGCATGGTAAGTTACATCTACT 60.148 37.037 14.81 2.79 0.00 2.57
337 340 9.378551 CAAAAGCATGGTAAGTTACATCTACTA 57.621 33.333 14.81 0.00 0.00 1.82
341 344 9.547753 AGCATGGTAAGTTACATCTACTATTTG 57.452 33.333 14.81 0.00 0.00 2.32
342 345 8.283291 GCATGGTAAGTTACATCTACTATTTGC 58.717 37.037 14.81 4.82 0.00 3.68
343 346 9.547753 CATGGTAAGTTACATCTACTATTTGCT 57.452 33.333 14.81 0.00 0.00 3.91
344 347 8.942338 TGGTAAGTTACATCTACTATTTGCTG 57.058 34.615 14.81 0.00 0.00 4.41
345 348 8.755028 TGGTAAGTTACATCTACTATTTGCTGA 58.245 33.333 14.81 0.00 0.00 4.26
346 349 9.595823 GGTAAGTTACATCTACTATTTGCTGAA 57.404 33.333 14.81 0.00 0.00 3.02
348 351 7.778470 AGTTACATCTACTATTTGCTGAAGC 57.222 36.000 0.00 0.00 42.50 3.86
362 365 4.907879 GCTGAAGCATATAAAGTTGGCT 57.092 40.909 0.00 0.00 41.59 4.75
363 366 5.254339 GCTGAAGCATATAAAGTTGGCTT 57.746 39.130 0.00 0.00 46.55 4.35
364 367 5.654497 GCTGAAGCATATAAAGTTGGCTTT 58.346 37.500 0.00 0.00 44.16 3.51
365 368 6.101997 GCTGAAGCATATAAAGTTGGCTTTT 58.898 36.000 0.00 0.00 44.16 2.27
366 369 6.254373 GCTGAAGCATATAAAGTTGGCTTTTC 59.746 38.462 0.00 0.00 44.16 2.29
367 370 7.466746 TGAAGCATATAAAGTTGGCTTTTCT 57.533 32.000 0.00 0.00 44.16 2.52
368 371 7.315142 TGAAGCATATAAAGTTGGCTTTTCTG 58.685 34.615 0.00 0.00 44.16 3.02
369 372 6.212888 AGCATATAAAGTTGGCTTTTCTGG 57.787 37.500 0.00 0.00 41.78 3.86
370 373 5.127682 AGCATATAAAGTTGGCTTTTCTGGG 59.872 40.000 0.00 0.00 41.78 4.45
371 374 5.105351 GCATATAAAGTTGGCTTTTCTGGGT 60.105 40.000 0.00 0.00 41.78 4.51
372 375 4.871933 ATAAAGTTGGCTTTTCTGGGTG 57.128 40.909 0.00 0.00 41.78 4.61
373 376 1.413118 AAGTTGGCTTTTCTGGGTGG 58.587 50.000 0.00 0.00 0.00 4.61
374 377 0.555769 AGTTGGCTTTTCTGGGTGGA 59.444 50.000 0.00 0.00 0.00 4.02
390 393 4.104102 TGGGTGGAGTTTCAGTGTTTCTAT 59.896 41.667 0.00 0.00 0.00 1.98
391 394 4.695928 GGGTGGAGTTTCAGTGTTTCTATC 59.304 45.833 0.00 0.00 0.00 2.08
392 395 5.513267 GGGTGGAGTTTCAGTGTTTCTATCT 60.513 44.000 0.00 0.00 0.00 1.98
393 396 5.639931 GGTGGAGTTTCAGTGTTTCTATCTC 59.360 44.000 0.00 0.00 0.00 2.75
400 418 5.728637 TCAGTGTTTCTATCTCTTGCAGA 57.271 39.130 0.00 0.00 34.78 4.26
518 536 8.940952 ACAAATGTCTAGCTTATCTTTGAGTTC 58.059 33.333 12.48 0.00 0.00 3.01
521 539 6.688578 TGTCTAGCTTATCTTTGAGTTCGTT 58.311 36.000 0.00 0.00 0.00 3.85
560 578 2.394708 TCGAGAAAGCACGAGTTTCTG 58.605 47.619 13.53 8.17 42.95 3.02
643 661 2.283617 CGCTGCTTGCTAGTTGATACAG 59.716 50.000 0.00 0.00 40.11 2.74
664 682 9.988815 ATACAGACATGTTTTCCTGATAGATAC 57.011 33.333 16.71 0.00 41.01 2.24
904 938 4.473444 ACTTCACTCACCAACAATTCCAT 58.527 39.130 0.00 0.00 0.00 3.41
1060 1101 0.322456 GGCTTGCAGTACCCATGTCA 60.322 55.000 0.00 0.00 0.00 3.58
1169 1210 2.928334 GATGTCCTGGAATGACAGCAT 58.072 47.619 0.00 0.00 45.31 3.79
1226 1267 2.209838 AAGAATCGACATCGCGTCAT 57.790 45.000 5.77 0.00 45.70 3.06
1242 1283 1.550976 GTCATTTCCCTCGACCTCAGT 59.449 52.381 0.00 0.00 0.00 3.41
1343 1384 3.164268 TGTTCATTGGACAAATCCCTGG 58.836 45.455 0.00 0.00 45.59 4.45
2258 2299 1.067250 CTCTAGAGAGCTTGCGGGC 59.933 63.158 15.05 0.00 35.13 6.13
2263 2304 1.443407 GAGAGCTTGCGGGCTATCA 59.557 57.895 16.73 0.00 46.14 2.15
2335 2376 2.074729 ATCTCTACTGGGGGAACTCG 57.925 55.000 0.00 0.00 0.00 4.18
2401 2442 3.149981 GGAGACCTCAAAACCCTTGAAG 58.850 50.000 0.00 0.00 0.00 3.02
2409 2450 4.947645 TCAAAACCCTTGAAGCATTGAAG 58.052 39.130 0.00 0.00 39.12 3.02
2514 2555 2.732619 CCTAGGCGGACCACTTCCC 61.733 68.421 0.00 0.00 42.27 3.97
2720 2761 1.661112 GTCTCACAACCGCTTATCAGC 59.339 52.381 0.00 0.00 43.41 4.26
2808 2849 2.437413 GAAGGCGAAGTCCCAGAAATT 58.563 47.619 0.00 0.00 0.00 1.82
3007 3048 6.127083 TGTGGTCATATCTGTCTTGCTATTCA 60.127 38.462 0.00 0.00 0.00 2.57
3027 3068 3.583086 TCAGGAGGAGAAAACGGAAGAAT 59.417 43.478 0.00 0.00 0.00 2.40
3396 3437 3.006967 CACTACTGTACTCAGCTTTGGGT 59.993 47.826 0.00 0.00 44.77 4.51
3494 3535 2.674796 GAGTACCTCCACCATGACAC 57.325 55.000 0.00 0.00 0.00 3.67
3818 3860 0.685097 TACAGAGTGGGCAACTGGTC 59.315 55.000 0.00 0.00 40.07 4.02
3938 3980 4.925068 ACTGAGCATCACAAACTTTGTTC 58.075 39.130 4.30 1.04 42.56 3.18
4281 4331 1.783140 GTCACTGTCGTAACCGTTCAC 59.217 52.381 0.00 0.00 35.01 3.18
4299 4349 3.362706 TCACTAGGCGAACTAACCTGAT 58.637 45.455 0.00 0.00 36.77 2.90
4300 4350 4.529897 TCACTAGGCGAACTAACCTGATA 58.470 43.478 0.00 0.00 36.77 2.15
4301 4351 4.337555 TCACTAGGCGAACTAACCTGATAC 59.662 45.833 0.00 0.00 36.77 2.24
4424 4529 1.132977 TGGTCAGGGTGTTCTCCTACA 60.133 52.381 0.00 0.00 32.49 2.74
4543 4648 3.383620 TTCATGTTGTTTGGGTGATGC 57.616 42.857 0.00 0.00 0.00 3.91
4870 5035 3.291611 GCAGGTTGATGCAAGGGG 58.708 61.111 0.00 0.00 45.77 4.79
4871 5036 2.353610 GCAGGTTGATGCAAGGGGG 61.354 63.158 0.00 0.00 45.77 5.40
4885 5050 4.670199 GGGGGTTAAACGGATGGG 57.330 61.111 0.00 0.00 0.00 4.00
4886 5051 1.076559 GGGGGTTAAACGGATGGGG 60.077 63.158 0.00 0.00 0.00 4.96
4887 5052 1.573607 GGGGGTTAAACGGATGGGGA 61.574 60.000 0.00 0.00 0.00 4.81
4888 5053 0.332293 GGGGTTAAACGGATGGGGAA 59.668 55.000 0.00 0.00 0.00 3.97
4889 5054 1.683938 GGGGTTAAACGGATGGGGAAG 60.684 57.143 0.00 0.00 0.00 3.46
4890 5055 1.282738 GGGTTAAACGGATGGGGAAGA 59.717 52.381 0.00 0.00 0.00 2.87
4891 5056 2.640184 GGTTAAACGGATGGGGAAGAG 58.360 52.381 0.00 0.00 0.00 2.85
4892 5057 2.640184 GTTAAACGGATGGGGAAGAGG 58.360 52.381 0.00 0.00 0.00 3.69
4893 5058 1.209621 TAAACGGATGGGGAAGAGGG 58.790 55.000 0.00 0.00 0.00 4.30
4894 5059 1.571773 AAACGGATGGGGAAGAGGGG 61.572 60.000 0.00 0.00 0.00 4.79
4895 5060 3.878667 CGGATGGGGAAGAGGGGC 61.879 72.222 0.00 0.00 0.00 5.80
4896 5061 2.696125 GGATGGGGAAGAGGGGCA 60.696 66.667 0.00 0.00 0.00 5.36
4897 5062 2.761465 GGATGGGGAAGAGGGGCAG 61.761 68.421 0.00 0.00 0.00 4.85
4898 5063 2.697644 ATGGGGAAGAGGGGCAGG 60.698 66.667 0.00 0.00 0.00 4.85
4899 5064 3.603330 ATGGGGAAGAGGGGCAGGT 62.603 63.158 0.00 0.00 0.00 4.00
4900 5065 2.941583 GGGGAAGAGGGGCAGGTT 60.942 66.667 0.00 0.00 0.00 3.50
4901 5066 2.356667 GGGAAGAGGGGCAGGTTG 59.643 66.667 0.00 0.00 0.00 3.77
4902 5067 2.231380 GGGAAGAGGGGCAGGTTGA 61.231 63.158 0.00 0.00 0.00 3.18
4903 5068 1.575447 GGGAAGAGGGGCAGGTTGAT 61.575 60.000 0.00 0.00 0.00 2.57
4904 5069 0.394899 GGAAGAGGGGCAGGTTGATG 60.395 60.000 0.00 0.00 0.00 3.07
4905 5070 1.000396 AAGAGGGGCAGGTTGATGC 60.000 57.895 0.00 0.00 45.74 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.698575 ACAGTGTTCCTCTTTCTTCAGTC 58.301 43.478 0.00 0.00 0.00 3.51
1 2 4.762289 ACAGTGTTCCTCTTTCTTCAGT 57.238 40.909 0.00 0.00 0.00 3.41
2 3 6.127897 ACAAAACAGTGTTCCTCTTTCTTCAG 60.128 38.462 9.40 0.00 0.00 3.02
3 4 5.710099 ACAAAACAGTGTTCCTCTTTCTTCA 59.290 36.000 9.40 0.00 0.00 3.02
4 5 6.196079 ACAAAACAGTGTTCCTCTTTCTTC 57.804 37.500 9.40 0.00 0.00 2.87
5 6 6.590234 AACAAAACAGTGTTCCTCTTTCTT 57.410 33.333 9.40 0.00 37.10 2.52
6 7 6.590234 AAACAAAACAGTGTTCCTCTTTCT 57.410 33.333 9.40 0.00 40.86 2.52
7 8 7.758495 TCTAAACAAAACAGTGTTCCTCTTTC 58.242 34.615 9.40 0.00 40.86 2.62
8 9 7.696992 TCTAAACAAAACAGTGTTCCTCTTT 57.303 32.000 9.40 7.40 40.86 2.52
9 10 7.339466 ACATCTAAACAAAACAGTGTTCCTCTT 59.661 33.333 9.40 4.08 40.86 2.85
10 11 6.828785 ACATCTAAACAAAACAGTGTTCCTCT 59.171 34.615 9.40 0.00 40.86 3.69
11 12 7.027778 ACATCTAAACAAAACAGTGTTCCTC 57.972 36.000 9.40 0.00 40.86 3.71
12 13 7.773690 ACTACATCTAAACAAAACAGTGTTCCT 59.226 33.333 9.40 0.00 40.86 3.36
13 14 7.927048 ACTACATCTAAACAAAACAGTGTTCC 58.073 34.615 9.40 0.00 40.86 3.62
86 87 9.841295 AAGCTATAATATCAACTCCCGTAAAAA 57.159 29.630 0.00 0.00 0.00 1.94
87 88 9.268268 CAAGCTATAATATCAACTCCCGTAAAA 57.732 33.333 0.00 0.00 0.00 1.52
88 89 8.426489 ACAAGCTATAATATCAACTCCCGTAAA 58.574 33.333 0.00 0.00 0.00 2.01
89 90 7.959175 ACAAGCTATAATATCAACTCCCGTAA 58.041 34.615 0.00 0.00 0.00 3.18
90 91 7.534723 ACAAGCTATAATATCAACTCCCGTA 57.465 36.000 0.00 0.00 0.00 4.02
91 92 6.420913 ACAAGCTATAATATCAACTCCCGT 57.579 37.500 0.00 0.00 0.00 5.28
92 93 5.573282 CGACAAGCTATAATATCAACTCCCG 59.427 44.000 0.00 0.00 0.00 5.14
93 94 5.869888 CCGACAAGCTATAATATCAACTCCC 59.130 44.000 0.00 0.00 0.00 4.30
94 95 6.366332 CACCGACAAGCTATAATATCAACTCC 59.634 42.308 0.00 0.00 0.00 3.85
95 96 6.366332 CCACCGACAAGCTATAATATCAACTC 59.634 42.308 0.00 0.00 0.00 3.01
96 97 6.183360 ACCACCGACAAGCTATAATATCAACT 60.183 38.462 0.00 0.00 0.00 3.16
97 98 5.989777 ACCACCGACAAGCTATAATATCAAC 59.010 40.000 0.00 0.00 0.00 3.18
98 99 6.169557 ACCACCGACAAGCTATAATATCAA 57.830 37.500 0.00 0.00 0.00 2.57
99 100 5.801531 ACCACCGACAAGCTATAATATCA 57.198 39.130 0.00 0.00 0.00 2.15
100 101 7.154435 TCTACCACCGACAAGCTATAATATC 57.846 40.000 0.00 0.00 0.00 1.63
101 102 7.719871 ATCTACCACCGACAAGCTATAATAT 57.280 36.000 0.00 0.00 0.00 1.28
102 103 7.886970 AGTATCTACCACCGACAAGCTATAATA 59.113 37.037 0.00 0.00 0.00 0.98
103 104 6.720288 AGTATCTACCACCGACAAGCTATAAT 59.280 38.462 0.00 0.00 0.00 1.28
104 105 6.066690 AGTATCTACCACCGACAAGCTATAA 58.933 40.000 0.00 0.00 0.00 0.98
105 106 5.628130 AGTATCTACCACCGACAAGCTATA 58.372 41.667 0.00 0.00 0.00 1.31
106 107 4.471548 AGTATCTACCACCGACAAGCTAT 58.528 43.478 0.00 0.00 0.00 2.97
107 108 3.881688 GAGTATCTACCACCGACAAGCTA 59.118 47.826 0.00 0.00 0.00 3.32
108 109 2.688958 GAGTATCTACCACCGACAAGCT 59.311 50.000 0.00 0.00 0.00 3.74
109 110 2.223758 GGAGTATCTACCACCGACAAGC 60.224 54.545 0.00 0.00 33.73 4.01
110 111 2.361438 GGGAGTATCTACCACCGACAAG 59.639 54.545 0.00 0.00 33.84 3.16
111 112 2.024655 AGGGAGTATCTACCACCGACAA 60.025 50.000 0.64 0.00 36.80 3.18
112 113 1.567649 AGGGAGTATCTACCACCGACA 59.432 52.381 0.64 0.00 36.80 4.35
113 114 2.228925 GAGGGAGTATCTACCACCGAC 58.771 57.143 0.64 0.00 36.80 4.79
114 115 1.144503 GGAGGGAGTATCTACCACCGA 59.855 57.143 0.64 0.00 35.59 4.69
115 116 1.618487 GGAGGGAGTATCTACCACCG 58.382 60.000 0.64 0.00 35.59 4.94
116 117 1.133544 ACGGAGGGAGTATCTACCACC 60.134 57.143 4.71 4.71 41.09 4.61
117 118 2.228925 GACGGAGGGAGTATCTACCAC 58.771 57.143 0.64 0.00 36.80 4.16
118 119 1.144503 GGACGGAGGGAGTATCTACCA 59.855 57.143 0.64 0.00 36.80 3.25
119 120 1.881498 CGGACGGAGGGAGTATCTACC 60.881 61.905 0.00 0.00 33.84 3.18
120 121 1.521580 CGGACGGAGGGAGTATCTAC 58.478 60.000 0.00 0.00 33.73 2.59
121 122 0.399454 CCGGACGGAGGGAGTATCTA 59.601 60.000 4.40 0.00 37.50 1.98
122 123 1.150992 CCGGACGGAGGGAGTATCT 59.849 63.158 4.40 0.00 37.50 1.98
123 124 0.466922 TTCCGGACGGAGGGAGTATC 60.467 60.000 13.64 0.00 46.06 2.24
124 125 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
125 126 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
126 127 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
127 128 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
128 129 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
129 130 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
130 131 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
131 132 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
132 133 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
133 134 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
134 135 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
135 136 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
136 137 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
137 138 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
138 139 4.630069 ACATTTCTCCGACAAGTATTTCCG 59.370 41.667 0.00 0.00 0.00 4.30
139 140 7.787725 ATACATTTCTCCGACAAGTATTTCC 57.212 36.000 0.00 0.00 0.00 3.13
145 146 8.458843 CCATTTTTATACATTTCTCCGACAAGT 58.541 33.333 0.00 0.00 0.00 3.16
146 147 8.673711 TCCATTTTTATACATTTCTCCGACAAG 58.326 33.333 0.00 0.00 0.00 3.16
147 148 8.568676 TCCATTTTTATACATTTCTCCGACAA 57.431 30.769 0.00 0.00 0.00 3.18
148 149 8.620416 CATCCATTTTTATACATTTCTCCGACA 58.380 33.333 0.00 0.00 0.00 4.35
149 150 8.621286 ACATCCATTTTTATACATTTCTCCGAC 58.379 33.333 0.00 0.00 0.00 4.79
150 151 8.746052 ACATCCATTTTTATACATTTCTCCGA 57.254 30.769 0.00 0.00 0.00 4.55
179 180 0.702902 AAGTACTCCCTCCGTCTGGA 59.297 55.000 0.00 0.00 43.88 3.86
180 181 0.818296 CAAGTACTCCCTCCGTCTGG 59.182 60.000 0.00 0.00 0.00 3.86
181 182 0.818296 CCAAGTACTCCCTCCGTCTG 59.182 60.000 0.00 0.00 0.00 3.51
182 183 0.408700 ACCAAGTACTCCCTCCGTCT 59.591 55.000 0.00 0.00 0.00 4.18
183 184 1.204231 GAACCAAGTACTCCCTCCGTC 59.796 57.143 0.00 0.00 0.00 4.79
184 185 1.264295 GAACCAAGTACTCCCTCCGT 58.736 55.000 0.00 0.00 0.00 4.69
185 186 0.172803 CGAACCAAGTACTCCCTCCG 59.827 60.000 0.00 0.00 0.00 4.63
186 187 0.108281 GCGAACCAAGTACTCCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
187 188 0.108281 GGCGAACCAAGTACTCCCTC 60.108 60.000 0.00 0.00 35.26 4.30
188 189 0.544595 AGGCGAACCAAGTACTCCCT 60.545 55.000 0.00 0.00 39.06 4.20
189 190 1.188863 TAGGCGAACCAAGTACTCCC 58.811 55.000 0.00 0.00 39.06 4.30
190 191 4.868314 ATATAGGCGAACCAAGTACTCC 57.132 45.455 0.00 0.00 39.06 3.85
191 192 8.086522 TCATTTATATAGGCGAACCAAGTACTC 58.913 37.037 0.00 0.00 39.06 2.59
192 193 7.959175 TCATTTATATAGGCGAACCAAGTACT 58.041 34.615 0.00 0.00 39.06 2.73
211 212 4.137116 AGAGCCATACACGCTTCATTTA 57.863 40.909 0.00 0.00 36.48 1.40
212 213 2.991250 AGAGCCATACACGCTTCATTT 58.009 42.857 0.00 0.00 36.48 2.32
213 214 2.698855 AGAGCCATACACGCTTCATT 57.301 45.000 0.00 0.00 36.48 2.57
214 215 3.722147 CTTAGAGCCATACACGCTTCAT 58.278 45.455 0.00 0.00 36.48 2.57
270 271 2.600731 CTGCGTACTTCTGTTGGAGAG 58.399 52.381 0.00 0.00 30.18 3.20
280 281 0.101579 GGAGAGAGCCTGCGTACTTC 59.898 60.000 0.00 0.00 0.00 3.01
299 300 2.252260 CTTTTGCACCGCCTCGTG 59.748 61.111 0.00 0.00 36.80 4.35
300 301 3.660111 GCTTTTGCACCGCCTCGT 61.660 61.111 0.00 0.00 46.58 4.18
315 318 9.547753 CAAATAGTAGATGTAACTTACCATGCT 57.452 33.333 0.00 0.00 0.00 3.79
337 340 7.580109 AAGCCAACTTTATATGCTTCAGCAAAT 60.580 33.333 5.40 0.00 43.95 2.32
338 341 6.295236 AAGCCAACTTTATATGCTTCAGCAAA 60.295 34.615 5.40 0.00 43.95 3.68
339 342 5.185635 AAGCCAACTTTATATGCTTCAGCAA 59.814 36.000 5.40 0.00 43.95 3.91
340 343 4.706476 AAGCCAACTTTATATGCTTCAGCA 59.294 37.500 3.45 3.45 44.56 4.41
341 344 4.907879 AGCCAACTTTATATGCTTCAGC 57.092 40.909 0.00 0.00 42.50 4.26
342 345 7.487189 CAGAAAAGCCAACTTTATATGCTTCAG 59.513 37.037 0.00 0.00 45.48 3.02
343 346 7.315142 CAGAAAAGCCAACTTTATATGCTTCA 58.685 34.615 0.00 0.00 45.48 3.02
344 347 6.753744 CCAGAAAAGCCAACTTTATATGCTTC 59.246 38.462 0.00 0.00 45.48 3.86
345 348 6.351286 CCCAGAAAAGCCAACTTTATATGCTT 60.351 38.462 0.00 0.00 45.48 3.91
346 349 5.127682 CCCAGAAAAGCCAACTTTATATGCT 59.872 40.000 0.00 0.00 45.48 3.79
347 350 5.105351 ACCCAGAAAAGCCAACTTTATATGC 60.105 40.000 0.00 0.00 45.48 3.14
348 351 6.332630 CACCCAGAAAAGCCAACTTTATATG 58.667 40.000 0.00 0.00 45.48 1.78
349 352 5.422012 CCACCCAGAAAAGCCAACTTTATAT 59.578 40.000 0.00 0.00 45.48 0.86
350 353 4.770010 CCACCCAGAAAAGCCAACTTTATA 59.230 41.667 0.00 0.00 45.48 0.98
351 354 3.578282 CCACCCAGAAAAGCCAACTTTAT 59.422 43.478 0.00 0.00 45.48 1.40
352 355 2.962421 CCACCCAGAAAAGCCAACTTTA 59.038 45.455 0.00 0.00 45.48 1.85
354 357 1.063266 TCCACCCAGAAAAGCCAACTT 60.063 47.619 0.00 0.00 37.90 2.66
355 358 0.555769 TCCACCCAGAAAAGCCAACT 59.444 50.000 0.00 0.00 0.00 3.16
356 359 0.961753 CTCCACCCAGAAAAGCCAAC 59.038 55.000 0.00 0.00 0.00 3.77
357 360 0.555769 ACTCCACCCAGAAAAGCCAA 59.444 50.000 0.00 0.00 0.00 4.52
358 361 0.555769 AACTCCACCCAGAAAAGCCA 59.444 50.000 0.00 0.00 0.00 4.75
359 362 1.613925 GAAACTCCACCCAGAAAAGCC 59.386 52.381 0.00 0.00 0.00 4.35
360 363 2.294512 CTGAAACTCCACCCAGAAAAGC 59.705 50.000 0.00 0.00 0.00 3.51
361 364 3.316308 CACTGAAACTCCACCCAGAAAAG 59.684 47.826 0.00 0.00 0.00 2.27
362 365 3.287222 CACTGAAACTCCACCCAGAAAA 58.713 45.455 0.00 0.00 0.00 2.29
363 366 2.241176 ACACTGAAACTCCACCCAGAAA 59.759 45.455 0.00 0.00 0.00 2.52
364 367 1.843851 ACACTGAAACTCCACCCAGAA 59.156 47.619 0.00 0.00 0.00 3.02
365 368 1.507140 ACACTGAAACTCCACCCAGA 58.493 50.000 0.00 0.00 0.00 3.86
366 369 2.348411 AACACTGAAACTCCACCCAG 57.652 50.000 0.00 0.00 0.00 4.45
367 370 2.241176 AGAAACACTGAAACTCCACCCA 59.759 45.455 0.00 0.00 0.00 4.51
368 371 2.932261 AGAAACACTGAAACTCCACCC 58.068 47.619 0.00 0.00 0.00 4.61
369 372 5.552178 AGATAGAAACACTGAAACTCCACC 58.448 41.667 0.00 0.00 0.00 4.61
370 373 6.459923 AGAGATAGAAACACTGAAACTCCAC 58.540 40.000 0.00 0.00 0.00 4.02
371 374 6.672266 AGAGATAGAAACACTGAAACTCCA 57.328 37.500 0.00 0.00 0.00 3.86
372 375 6.128418 GCAAGAGATAGAAACACTGAAACTCC 60.128 42.308 0.00 0.00 0.00 3.85
373 376 6.425114 TGCAAGAGATAGAAACACTGAAACTC 59.575 38.462 0.00 0.00 0.00 3.01
374 377 6.291377 TGCAAGAGATAGAAACACTGAAACT 58.709 36.000 0.00 0.00 0.00 2.66
400 418 6.406370 TGAAGTTATACAGTATGCAGCAAGT 58.594 36.000 0.00 0.00 42.53 3.16
479 497 3.319122 AGACATTTGTGCCCTTCAAGTTC 59.681 43.478 0.00 0.00 0.00 3.01
548 566 1.432514 TGCTGATCAGAAACTCGTGC 58.567 50.000 27.04 8.83 0.00 5.34
560 578 6.075205 GCATAAAATCGTGTTTCATGCTGATC 60.075 38.462 13.36 0.00 35.56 2.92
576 594 3.976942 CACAGGCTAATGCGCATAAAATC 59.023 43.478 25.61 12.40 40.82 2.17
624 642 4.498241 TGTCTGTATCAACTAGCAAGCAG 58.502 43.478 0.00 0.00 0.00 4.24
1060 1101 0.463204 CCATGTGAGGAGCAGACGAT 59.537 55.000 0.00 0.00 0.00 3.73
1169 1210 2.637872 CCTTCCCAGTTACAGAAGTCCA 59.362 50.000 8.31 0.00 36.16 4.02
1226 1267 2.362242 CCACTGAGGTCGAGGGAAA 58.638 57.895 0.00 0.00 0.00 3.13
1242 1283 1.980052 CCCTTGTAAGCCTCGACCA 59.020 57.895 0.00 0.00 0.00 4.02
1343 1384 2.034221 GCAGGTGACCAAGGGACC 59.966 66.667 3.63 2.20 0.00 4.46
2228 2269 3.506067 GCTCTCTAGAGTTCCTAGCCATC 59.494 52.174 19.21 0.00 43.60 3.51
2263 2304 7.608761 TCCTGTAAAAGCGTTGTTCCTTAATAT 59.391 33.333 0.00 0.00 0.00 1.28
2335 2376 7.312899 CCATACAACTGGTTAGAATCCAAAAC 58.687 38.462 0.00 0.00 34.35 2.43
2383 2424 2.306847 TGCTTCAAGGGTTTTGAGGTC 58.693 47.619 1.84 0.00 0.00 3.85
2401 2442 6.815142 AGAATGTTATTGGAAAGCTTCAATGC 59.185 34.615 18.78 13.30 35.50 3.56
2409 2450 6.633856 ACCATCAAGAATGTTATTGGAAAGC 58.366 36.000 0.85 0.00 33.13 3.51
2514 2555 2.813908 GCACGGCCTACTTCGGTG 60.814 66.667 0.00 0.00 37.68 4.94
2720 2761 3.997021 GCCAATAGACTTCGGTATGGATG 59.003 47.826 0.00 0.00 0.00 3.51
2808 2849 4.096833 GCAGTCACATTCTTGAATATGCCA 59.903 41.667 0.00 0.00 30.78 4.92
3007 3048 5.959583 ATATTCTTCCGTTTTCTCCTCCT 57.040 39.130 0.00 0.00 0.00 3.69
3027 3068 7.829211 CCAAAAGAAGGGAGAGACATGTAAATA 59.171 37.037 0.00 0.00 0.00 1.40
3396 3437 6.919662 GCTCTGAATTTGAAGTGTTTTCATCA 59.080 34.615 0.00 0.00 0.00 3.07
3494 3535 5.476599 TCACAATGAACAATAACTCCTTGGG 59.523 40.000 0.00 0.00 0.00 4.12
3818 3860 1.002468 CCCAGCAACTGAAACTTCACG 60.002 52.381 0.00 0.00 32.44 4.35
3938 3980 3.359033 TCCCAGCAGGAAAATTCATCTG 58.641 45.455 0.00 0.00 43.78 2.90
4281 4331 5.530171 TGTAGTATCAGGTTAGTTCGCCTAG 59.470 44.000 0.00 0.00 33.07 3.02
4390 4481 2.279918 ACCACGCCACAACTCGTC 60.280 61.111 0.00 0.00 36.73 4.20
4424 4529 4.535526 ACTCCAGCAAAAACAACTTGTT 57.464 36.364 1.00 1.00 43.41 2.83
4543 4648 5.716703 ACAAGAAATTATCCCAAACCAGAGG 59.283 40.000 0.00 0.00 0.00 3.69
4837 5002 3.878667 GCCCCTCTTCCCCATCCG 61.879 72.222 0.00 0.00 0.00 4.18
4870 5035 1.282738 TCTTCCCCATCCGTTTAACCC 59.717 52.381 0.00 0.00 0.00 4.11
4871 5036 2.640184 CTCTTCCCCATCCGTTTAACC 58.360 52.381 0.00 0.00 0.00 2.85
4872 5037 2.640184 CCTCTTCCCCATCCGTTTAAC 58.360 52.381 0.00 0.00 0.00 2.01
4873 5038 1.562475 CCCTCTTCCCCATCCGTTTAA 59.438 52.381 0.00 0.00 0.00 1.52
4874 5039 1.209621 CCCTCTTCCCCATCCGTTTA 58.790 55.000 0.00 0.00 0.00 2.01
4875 5040 1.571773 CCCCTCTTCCCCATCCGTTT 61.572 60.000 0.00 0.00 0.00 3.60
4876 5041 2.001269 CCCCTCTTCCCCATCCGTT 61.001 63.158 0.00 0.00 0.00 4.44
4877 5042 2.366972 CCCCTCTTCCCCATCCGT 60.367 66.667 0.00 0.00 0.00 4.69
4878 5043 3.878667 GCCCCTCTTCCCCATCCG 61.879 72.222 0.00 0.00 0.00 4.18
4879 5044 2.696125 TGCCCCTCTTCCCCATCC 60.696 66.667 0.00 0.00 0.00 3.51
4880 5045 2.761465 CCTGCCCCTCTTCCCCATC 61.761 68.421 0.00 0.00 0.00 3.51
4881 5046 2.697644 CCTGCCCCTCTTCCCCAT 60.698 66.667 0.00 0.00 0.00 4.00
4882 5047 3.829311 AACCTGCCCCTCTTCCCCA 62.829 63.158 0.00 0.00 0.00 4.96
4883 5048 2.941583 AACCTGCCCCTCTTCCCC 60.942 66.667 0.00 0.00 0.00 4.81
4884 5049 1.575447 ATCAACCTGCCCCTCTTCCC 61.575 60.000 0.00 0.00 0.00 3.97
4885 5050 0.394899 CATCAACCTGCCCCTCTTCC 60.395 60.000 0.00 0.00 0.00 3.46
4886 5051 1.034292 GCATCAACCTGCCCCTCTTC 61.034 60.000 0.00 0.00 36.10 2.87
4887 5052 1.000396 GCATCAACCTGCCCCTCTT 60.000 57.895 0.00 0.00 36.10 2.85
4888 5053 1.792757 TTGCATCAACCTGCCCCTCT 61.793 55.000 0.00 0.00 41.58 3.69
4889 5054 1.304381 TTGCATCAACCTGCCCCTC 60.304 57.895 0.00 0.00 41.58 4.30
4890 5055 1.304713 CTTGCATCAACCTGCCCCT 60.305 57.895 0.00 0.00 41.58 4.79
4891 5056 2.353610 CCTTGCATCAACCTGCCCC 61.354 63.158 0.00 0.00 41.58 5.80
4892 5057 2.353610 CCCTTGCATCAACCTGCCC 61.354 63.158 0.00 0.00 41.58 5.36
4893 5058 2.353610 CCCCTTGCATCAACCTGCC 61.354 63.158 0.00 0.00 41.58 4.85
4894 5059 2.353610 CCCCCTTGCATCAACCTGC 61.354 63.158 0.00 0.00 42.62 4.85
4895 5060 4.023137 CCCCCTTGCATCAACCTG 57.977 61.111 0.00 0.00 0.00 4.00
4909 5074 1.076559 CCCCATCCGTTTAACCCCC 60.077 63.158 0.00 0.00 0.00 5.40
4910 5075 0.332293 TTCCCCATCCGTTTAACCCC 59.668 55.000 0.00 0.00 0.00 4.95
4954 5119 1.284297 GCTTTCCGTTTGCCACATGC 61.284 55.000 0.00 0.00 41.77 4.06
5021 5187 2.276740 CATCCCCAGCCCTGTTCC 59.723 66.667 0.00 0.00 0.00 3.62
5022 5188 2.276740 CCATCCCCAGCCCTGTTC 59.723 66.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.