Multiple sequence alignment - TraesCS2D01G434600

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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 TraesCS2D01G434600 chr2D 100.000 3991 0 0 1 3991 545854530 545850540 0.000000e+00 7371
1 TraesCS2D01G434600 chr2D 86.224 392 21 8 272 662 451008810 451009169 1.040000e-105 394
2 TraesCS2D01G434600 chr2A 89.362 2209 148 35 252 2424 689200885 689203042 0.000000e+00 2697
3 TraesCS2D01G434600 chr2A 86.874 1059 73 23 2528 3528 689203188 689204238 0.000000e+00 1125
4 TraesCS2D01G434600 chr2A 90.019 521 21 8 3487 3991 689204240 689204745 0.000000e+00 645
5 TraesCS2D01G434600 chr2A 80.124 161 19 6 3 162 689200742 689200890 1.520000e-19 108
6 TraesCS2D01G434600 chr2B 84.955 2200 199 61 1827 3939 652411305 652409151 0.000000e+00 2108
7 TraesCS2D01G434600 chr2B 88.935 1446 105 18 255 1660 652413064 652411634 0.000000e+00 1733
8 TraesCS2D01G434600 chr2B 83.766 154 17 3 1 150 652413227 652413078 5.380000e-29 139
9 TraesCS2D01G434600 chrUn 83.548 620 85 9 1906 2519 407129514 407128906 7.490000e-157 564
10 TraesCS2D01G434600 chrUn 83.226 620 86 10 1906 2519 299704292 299704899 1.620000e-153 553
11 TraesCS2D01G434600 chrUn 83.226 620 87 9 1906 2519 352728859 352729467 1.620000e-153 553
12 TraesCS2D01G434600 chrUn 86.364 176 13 1 1740 1904 299704007 299704182 8.810000e-42 182
13 TraesCS2D01G434600 chr3D 83.387 620 86 9 1906 2519 29476258 29475650 3.480000e-155 558
14 TraesCS2D01G434600 chr3D 83.387 620 85 10 1906 2519 29510370 29509763 3.480000e-155 558
15 TraesCS2D01G434600 chr3D 83.387 620 86 9 1906 2519 29549792 29549184 3.480000e-155 558
16 TraesCS2D01G434600 chr3D 86.364 176 13 1 1740 1904 29476520 29476345 8.810000e-42 182
17 TraesCS2D01G434600 chr3D 86.364 176 13 1 1740 1904 29510632 29510457 8.810000e-42 182
18 TraesCS2D01G434600 chr3D 86.364 176 13 1 1740 1904 29550054 29549879 8.810000e-42 182
19 TraesCS2D01G434600 chr3D 96.117 103 4 0 155 257 48070907 48071009 6.860000e-38 169
20 TraesCS2D01G434600 chr3D 92.035 113 9 0 158 270 24129012 24128900 4.130000e-35 159
21 TraesCS2D01G434600 chr7B 86.000 500 53 8 264 762 60368330 60368813 1.640000e-143 520
22 TraesCS2D01G434600 chr7B 84.436 514 49 14 264 762 486731313 486730816 1.000000e-130 477
23 TraesCS2D01G434600 chr4B 85.800 500 54 7 264 762 59871949 59871466 7.650000e-142 514
24 TraesCS2D01G434600 chr6D 86.026 458 47 7 264 720 14448208 14447767 3.610000e-130 475
25 TraesCS2D01G434600 chr6D 94.340 159 9 0 1177 1335 2958040 2957882 1.110000e-60 244
26 TraesCS2D01G434600 chr6D 95.192 104 5 0 156 259 389999798 389999695 8.870000e-37 165
27 TraesCS2D01G434600 chr5B 85.014 347 31 10 422 762 42945550 42945219 2.300000e-87 333
28 TraesCS2D01G434600 chr5B 95.192 104 5 0 154 257 475312591 475312694 8.870000e-37 165
29 TraesCS2D01G434600 chr7A 96.104 154 6 0 1181 1334 23331925 23331772 6.620000e-63 252
30 TraesCS2D01G434600 chr7A 97.059 102 3 0 155 256 629780016 629780117 5.300000e-39 172
31 TraesCS2D01G434600 chr7A 95.370 108 4 1 154 261 641450199 641450305 1.910000e-38 171
32 TraesCS2D01G434600 chr7D 88.018 217 18 5 1122 1334 22782268 22782056 2.380000e-62 250
33 TraesCS2D01G434600 chr4A 94.268 157 9 0 1178 1334 707036929 707037085 1.430000e-59 241
34 TraesCS2D01G434600 chr4A 92.793 111 5 3 146 256 543742069 543742176 1.480000e-34 158
35 TraesCS2D01G434600 chr6A 92.308 169 11 1 1167 1335 1985426 1985592 5.150000e-59 239
36 TraesCS2D01G434600 chr6B 93.038 158 11 0 1178 1335 6168628 6168471 8.630000e-57 231
37 TraesCS2D01G434600 chr3A 85.915 213 25 4 1128 1335 707465770 707465558 5.190000e-54 222
38 TraesCS2D01G434600 chr3A 97.170 106 3 0 158 263 692869668 692869563 3.170000e-41 180
39 TraesCS2D01G434600 chr3B 93.519 108 7 0 149 256 803625622 803625729 1.150000e-35 161


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 TraesCS2D01G434600 chr2D 545850540 545854530 3990 True 7371.000000 7371 100.000000 1 3991 1 chr2D.!!$R1 3990
1 TraesCS2D01G434600 chr2A 689200742 689204745 4003 False 1143.750000 2697 86.594750 3 3991 4 chr2A.!!$F1 3988
2 TraesCS2D01G434600 chr2B 652409151 652413227 4076 True 1326.666667 2108 85.885333 1 3939 3 chr2B.!!$R1 3938
3 TraesCS2D01G434600 chrUn 407128906 407129514 608 True 564.000000 564 83.548000 1906 2519 1 chrUn.!!$R1 613
4 TraesCS2D01G434600 chrUn 352728859 352729467 608 False 553.000000 553 83.226000 1906 2519 1 chrUn.!!$F1 613
5 TraesCS2D01G434600 chrUn 299704007 299704899 892 False 367.500000 553 84.795000 1740 2519 2 chrUn.!!$F2 779
6 TraesCS2D01G434600 chr3D 29475650 29476520 870 True 370.000000 558 84.875500 1740 2519 2 chr3D.!!$R2 779
7 TraesCS2D01G434600 chr3D 29509763 29510632 869 True 370.000000 558 84.875500 1740 2519 2 chr3D.!!$R3 779
8 TraesCS2D01G434600 chr3D 29549184 29550054 870 True 370.000000 558 84.875500 1740 2519 2 chr3D.!!$R4 779

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
168 176 0.033306 AGGACCGAACTACTCCCTCC 60.033 60.0 0.0 0.00 0.00 4.30 F
431 443 0.103755 TCAGCTAAGATCCAGCAGCG 59.896 55.0 16.8 7.03 41.66 5.18 F
1539 1587 0.400594 GCTGGAAGGTACAACCCTGT 59.599 55.0 0.0 0.00 39.75 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1973 0.037046 CTTGGACCTTGGCAATTGGC 60.037 55.0 24.20 24.20 43.74 4.52 R
1734 1974 0.609662 CCTTGGACCTTGGCAATTGG 59.390 55.0 7.72 1.55 0.00 3.16 R
3254 3754 0.038166 AGGGCGAATGGAGCTGAAAA 59.962 50.0 0.00 0.00 34.52 2.29 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
30 31 7.234577 AGCTGGAATTAAAATCCCACAAAACTA 59.765 33.333 7.89 0.00 36.04 2.24
33 34 9.589461 TGGAATTAAAATCCCACAAAACTACTA 57.411 29.630 7.89 0.00 36.04 1.82
45 46 6.591834 CCACAAAACTACTACTCCTCAGAATG 59.408 42.308 0.00 0.00 37.54 2.67
49 50 3.957497 ACTACTACTCCTCAGAATGCCAG 59.043 47.826 0.00 0.00 34.76 4.85
54 55 5.843421 ACTACTCCTCAGAATGCCAGATATT 59.157 40.000 0.00 0.00 34.76 1.28
60 61 7.164122 TCCTCAGAATGCCAGATATTAACATC 58.836 38.462 0.00 0.00 34.76 3.06
73 74 1.344065 TAACATCACCTCCACACGGT 58.656 50.000 0.00 0.00 34.38 4.83
80 81 1.079819 CCTCCACACGGTGTAGCTG 60.080 63.158 14.30 1.29 0.00 4.24
89 90 2.157668 CACGGTGTAGCTGCAAAACTAG 59.842 50.000 5.91 0.00 0.00 2.57
94 95 3.189287 GTGTAGCTGCAAAACTAGCACAT 59.811 43.478 5.91 0.00 42.29 3.21
141 145 5.288232 GCTTAAACATTCATACGCAATTGCA 59.712 36.000 28.77 12.04 42.21 4.08
155 163 1.683943 ATTGCATGATTCCAGGACCG 58.316 50.000 0.00 0.00 0.00 4.79
162 170 2.816411 TGATTCCAGGACCGAACTACT 58.184 47.619 0.00 0.00 0.00 2.57
163 171 2.758979 TGATTCCAGGACCGAACTACTC 59.241 50.000 0.00 0.00 0.00 2.59
164 172 1.553706 TTCCAGGACCGAACTACTCC 58.446 55.000 0.00 0.00 0.00 3.85
165 173 0.324091 TCCAGGACCGAACTACTCCC 60.324 60.000 0.00 0.00 0.00 4.30
166 174 0.324460 CCAGGACCGAACTACTCCCT 60.324 60.000 0.00 0.00 0.00 4.20
167 175 1.104630 CAGGACCGAACTACTCCCTC 58.895 60.000 0.00 0.00 0.00 4.30
168 176 0.033306 AGGACCGAACTACTCCCTCC 60.033 60.000 0.00 0.00 0.00 4.30
169 177 1.382692 GGACCGAACTACTCCCTCCG 61.383 65.000 0.00 0.00 0.00 4.63
170 178 0.679321 GACCGAACTACTCCCTCCGT 60.679 60.000 0.00 0.00 0.00 4.69
171 179 0.251519 ACCGAACTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
172 180 0.455005 CCGAACTACTCCCTCCGTTC 59.545 60.000 0.00 0.00 34.07 3.95
173 181 0.455005 CGAACTACTCCCTCCGTTCC 59.545 60.000 0.00 0.00 33.92 3.62
174 182 1.553706 GAACTACTCCCTCCGTTCCA 58.446 55.000 0.00 0.00 31.89 3.53
175 183 1.897802 GAACTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 31.89 3.53
176 184 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
177 185 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
178 186 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
179 187 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
180 188 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
181 189 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
182 190 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
183 191 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
184 192 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
185 193 4.226394 TCCCTCCGTTCCAAAATAGATGAA 59.774 41.667 0.00 0.00 0.00 2.57
186 194 4.335594 CCCTCCGTTCCAAAATAGATGAAC 59.664 45.833 0.00 0.00 35.03 3.18
187 195 4.335594 CCTCCGTTCCAAAATAGATGAACC 59.664 45.833 0.00 0.00 34.93 3.62
188 196 4.912586 TCCGTTCCAAAATAGATGAACCA 58.087 39.130 0.00 0.00 34.93 3.67
189 197 5.317808 TCCGTTCCAAAATAGATGAACCAA 58.682 37.500 0.00 0.00 34.93 3.67
190 198 5.182380 TCCGTTCCAAAATAGATGAACCAAC 59.818 40.000 0.00 0.00 34.93 3.77
191 199 5.183140 CCGTTCCAAAATAGATGAACCAACT 59.817 40.000 0.00 0.00 34.93 3.16
192 200 6.294508 CCGTTCCAAAATAGATGAACCAACTT 60.295 38.462 0.00 0.00 34.93 2.66
193 201 7.145323 CGTTCCAAAATAGATGAACCAACTTT 58.855 34.615 0.00 0.00 34.93 2.66
194 202 7.114811 CGTTCCAAAATAGATGAACCAACTTTG 59.885 37.037 0.00 0.00 34.93 2.77
195 203 7.595819 TCCAAAATAGATGAACCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
196 204 8.698973 TCCAAAATAGATGAACCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
197 205 8.573035 TCCAAAATAGATGAACCAACTTTGTAC 58.427 33.333 0.00 0.00 0.00 2.90
198 206 8.576442 CCAAAATAGATGAACCAACTTTGTACT 58.424 33.333 0.00 0.00 0.00 2.73
205 213 9.965824 AGATGAACCAACTTTGTACTAATTTTG 57.034 29.630 0.00 0.11 0.00 2.44
206 214 9.744468 GATGAACCAACTTTGTACTAATTTTGT 57.256 29.630 0.00 0.00 0.00 2.83
242 250 9.003658 AGTACAAACTTGAGTCATCTATTTTGG 57.996 33.333 9.57 0.00 36.13 3.28
243 251 8.999431 GTACAAACTTGAGTCATCTATTTTGGA 58.001 33.333 9.57 0.96 36.13 3.53
244 252 8.463930 ACAAACTTGAGTCATCTATTTTGGAA 57.536 30.769 9.57 0.00 36.13 3.53
245 253 8.352942 ACAAACTTGAGTCATCTATTTTGGAAC 58.647 33.333 9.57 0.00 36.13 3.62
246 254 6.727824 ACTTGAGTCATCTATTTTGGAACG 57.272 37.500 0.00 0.00 0.00 3.95
247 255 5.643777 ACTTGAGTCATCTATTTTGGAACGG 59.356 40.000 0.00 0.00 0.00 4.44
248 256 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
249 257 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
250 258 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
251 259 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
252 260 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
253 261 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
254 262 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
255 263 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
256 264 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
304 312 8.953313 GGTTAATTTAGCTTACATACCAACAGT 58.047 33.333 0.00 0.00 0.00 3.55
308 316 3.939066 AGCTTACATACCAACAGTCACC 58.061 45.455 0.00 0.00 0.00 4.02
383 391 1.747745 GCCCACACATTACGGACCC 60.748 63.158 0.00 0.00 0.00 4.46
429 441 3.321396 TCAGATCAGCTAAGATCCAGCAG 59.679 47.826 16.80 10.37 44.32 4.24
431 443 0.103755 TCAGCTAAGATCCAGCAGCG 59.896 55.000 16.80 7.03 41.66 5.18
446 458 2.202946 GCGGAGGCCAGCTACTTC 60.203 66.667 5.01 0.00 0.00 3.01
448 460 1.596934 CGGAGGCCAGCTACTTCAA 59.403 57.895 5.01 0.00 0.00 2.69
455 467 4.151883 AGGCCAGCTACTTCAAAAATCAA 58.848 39.130 5.01 0.00 0.00 2.57
466 478 2.745281 TCAAAAATCAACGATCCCCGAC 59.255 45.455 0.00 0.00 41.76 4.79
482 495 0.465642 CGACCCCCTTTGCTTATCCC 60.466 60.000 0.00 0.00 0.00 3.85
506 519 2.616960 TCGACCGGATCATCAAACAAG 58.383 47.619 9.46 0.00 0.00 3.16
521 534 1.289694 CAAGCAGCGCCCAAATTGA 59.710 52.632 2.29 0.00 0.00 2.57
531 544 1.202521 GCCCAAATTGAAATAGCGGGG 60.203 52.381 0.00 0.00 37.39 5.73
630 643 1.268625 ACGGGAAAAGAAATCAACGGC 59.731 47.619 0.00 0.00 0.00 5.68
846 869 2.125106 GCCGGCCGTTTCAGATCT 60.125 61.111 26.12 0.00 0.00 2.75
858 885 5.231568 CCGTTTCAGATCTGGTTACGAATAC 59.768 44.000 29.59 13.96 33.96 1.89
861 888 3.949754 TCAGATCTGGTTACGAATACGGT 59.050 43.478 22.42 0.00 44.46 4.83
863 890 3.317430 AGATCTGGTTACGAATACGGTCC 59.683 47.826 0.00 0.00 44.46 4.46
956 1004 0.546598 ATCCATTCCGGTTCCACCTC 59.453 55.000 0.00 0.00 35.66 3.85
957 1005 1.077716 CCATTCCGGTTCCACCTCC 60.078 63.158 0.00 0.00 35.66 4.30
958 1006 1.562672 CCATTCCGGTTCCACCTCCT 61.563 60.000 0.00 0.00 35.66 3.69
963 1011 2.711922 CGGTTCCACCTCCTCCTCG 61.712 68.421 0.00 0.00 35.66 4.63
982 1030 4.856607 CCGCTCGTCTCCTTCCGC 62.857 72.222 0.00 0.00 0.00 5.54
1337 1385 1.280998 CAAGGTCGTGGGGAGGTAATT 59.719 52.381 0.00 0.00 0.00 1.40
1340 1388 0.533951 GTCGTGGGGAGGTAATTCGT 59.466 55.000 0.00 0.00 0.00 3.85
1345 1393 1.448893 GGGAGGTAATTCGTGCGCA 60.449 57.895 5.66 5.66 0.00 6.09
1361 1409 1.818850 CGCATTTGGCTCGATTTCTG 58.181 50.000 0.00 0.00 41.67 3.02
1366 1414 1.019278 TTGGCTCGATTTCTGTCCGC 61.019 55.000 0.00 0.00 0.00 5.54
1384 1432 1.377229 CCCCGACCTTGGTTGCTTA 59.623 57.895 1.52 0.00 0.00 3.09
1408 1456 4.423732 CGGAATGAGGCTAATTTTGGTTG 58.576 43.478 0.00 0.00 0.00 3.77
1410 1458 5.566627 CGGAATGAGGCTAATTTTGGTTGTT 60.567 40.000 0.00 0.00 0.00 2.83
1539 1587 0.400594 GCTGGAAGGTACAACCCTGT 59.599 55.000 0.00 0.00 39.75 4.00
1547 1595 2.108250 AGGTACAACCCTGTGAAATGCT 59.892 45.455 0.00 0.00 39.75 3.79
1548 1596 2.890945 GGTACAACCCTGTGAAATGCTT 59.109 45.455 0.00 0.00 36.96 3.91
1565 1613 7.224362 TGAAATGCTTACTTGTTTCCATGTTTG 59.776 33.333 0.00 0.00 31.92 2.93
1568 1616 6.039616 TGCTTACTTGTTTCCATGTTTGAAC 58.960 36.000 0.00 0.00 31.92 3.18
1569 1617 6.127479 TGCTTACTTGTTTCCATGTTTGAACT 60.127 34.615 0.00 0.00 31.92 3.01
1570 1618 6.756542 GCTTACTTGTTTCCATGTTTGAACTT 59.243 34.615 0.00 0.00 31.92 2.66
1571 1619 7.277760 GCTTACTTGTTTCCATGTTTGAACTTT 59.722 33.333 0.00 0.00 31.92 2.66
1604 1652 6.493115 ACATTGCGATAATGGGATTTGGATAA 59.507 34.615 14.65 0.00 32.14 1.75
1606 1654 4.454161 TGCGATAATGGGATTTGGATAACG 59.546 41.667 0.00 0.00 0.00 3.18
1607 1655 4.142687 GCGATAATGGGATTTGGATAACGG 60.143 45.833 0.00 0.00 0.00 4.44
1609 1657 2.746279 ATGGGATTTGGATAACGGCA 57.254 45.000 0.00 0.00 0.00 5.69
1614 1662 3.081804 GGATTTGGATAACGGCATAGGG 58.918 50.000 0.00 0.00 0.00 3.53
1642 1692 7.025365 CAGTTTCCAATTGATACAGTCATGTG 58.975 38.462 7.12 0.00 40.79 3.21
1652 1891 3.541996 ACAGTCATGTGTCAGTGTTCA 57.458 42.857 0.00 0.00 38.57 3.18
1656 1895 5.049828 CAGTCATGTGTCAGTGTTCAGTTA 58.950 41.667 0.00 0.00 0.00 2.24
1660 1899 5.928264 TCATGTGTCAGTGTTCAGTTATCTG 59.072 40.000 0.00 0.00 42.54 2.90
1666 1905 5.406780 GTCAGTGTTCAGTTATCTGGTTGAG 59.593 44.000 1.00 0.00 41.59 3.02
1708 1948 3.602390 TTGCTAACTGCGAGTCAAAAC 57.398 42.857 0.00 0.00 46.63 2.43
1726 1966 6.249050 GTCAAAACTTTTCAAGTGCAAAATGC 59.751 34.615 0.00 0.00 41.91 3.56
1735 1975 3.846754 GCAAAATGCGTGAGTGCC 58.153 55.556 0.00 0.00 31.71 5.01
1736 1976 1.007502 GCAAAATGCGTGAGTGCCA 60.008 52.632 0.00 0.00 31.71 4.92
1737 1977 0.597118 GCAAAATGCGTGAGTGCCAA 60.597 50.000 0.00 0.00 31.71 4.52
1738 1978 1.936203 GCAAAATGCGTGAGTGCCAAT 60.936 47.619 0.00 0.00 31.71 3.16
1767 2007 7.998964 CCAAGGTCCAAGGATTACATAATACTT 59.001 37.037 3.62 3.62 45.35 2.24
1860 2111 7.884877 GTGATCCTTTGGTGATGGATATATTGA 59.115 37.037 0.00 0.00 41.15 2.57
1904 2155 2.489938 TCTCACTTGGGTTGTATGGC 57.510 50.000 0.00 0.00 0.00 4.40
1921 2280 5.943416 TGTATGGCATGCTACTACACTTTTT 59.057 36.000 18.92 0.00 0.00 1.94
1948 2307 3.809832 CGTTGATGGTGTATCAGGGATTC 59.190 47.826 0.00 0.00 46.01 2.52
1949 2308 4.683129 CGTTGATGGTGTATCAGGGATTCA 60.683 45.833 0.00 0.00 46.01 2.57
1956 2315 7.206789 TGGTGTATCAGGGATTCAATTTCTA 57.793 36.000 0.00 0.00 0.00 2.10
1996 2355 8.121305 AGAAGGTTTATTATGTGAAATGTGCA 57.879 30.769 0.00 0.00 0.00 4.57
2052 2414 7.329588 TGTCGAATGTTCAGTAGCTAATCTA 57.670 36.000 0.00 0.00 0.00 1.98
2315 2687 6.860023 GCTTATGTGCTCATTATTCCATTGTC 59.140 38.462 6.57 0.00 35.70 3.18
2341 2713 7.810766 TGTCGAATTCTTTGAATTTTATGGC 57.189 32.000 3.52 1.86 0.00 4.40
2445 2818 8.483758 TGACTATTCCCTTCCAGTTATTCTTAC 58.516 37.037 0.00 0.00 0.00 2.34
2446 2819 7.498443 ACTATTCCCTTCCAGTTATTCTTACG 58.502 38.462 0.00 0.00 0.00 3.18
2452 2825 6.127253 CCCTTCCAGTTATTCTTACGGACTTA 60.127 42.308 0.00 0.00 0.00 2.24
2472 2845 8.890718 GGACTTAATTCTACTTAATGAACCACC 58.109 37.037 0.00 0.00 0.00 4.61
2560 3003 5.429130 AGGAAGCCTTATTTAGTAGCACAC 58.571 41.667 0.00 0.00 0.00 3.82
2580 3024 5.404968 CACACGGTGCATCAATTTGTTAATT 59.595 36.000 8.30 0.00 34.29 1.40
2599 3045 2.543777 TAGTGTTGGTTGCAGTCCTC 57.456 50.000 10.56 5.60 0.00 3.71
2643 3089 5.856156 CTGATCCTTCAGTTATGATCTGCT 58.144 41.667 0.00 0.00 43.73 4.24
2658 3104 4.880120 TGATCTGCTTGGCTTTCTATTCAG 59.120 41.667 0.00 0.00 0.00 3.02
2671 3117 6.831868 GCTTTCTATTCAGGGGTTTATACCAA 59.168 38.462 4.65 0.00 46.96 3.67
2672 3118 7.505923 GCTTTCTATTCAGGGGTTTATACCAAT 59.494 37.037 4.65 0.00 46.96 3.16
2705 3151 3.069586 TCATATGCCTCCTGAACCGTTAG 59.930 47.826 0.00 0.00 0.00 2.34
2728 3184 7.054491 AGTTACAACTGCAATTGATCCTTTT 57.946 32.000 15.88 0.00 37.98 2.27
2734 3190 5.324409 ACTGCAATTGATCCTTTTAGACCA 58.676 37.500 10.34 0.00 0.00 4.02
2735 3191 5.774690 ACTGCAATTGATCCTTTTAGACCAA 59.225 36.000 10.34 0.00 0.00 3.67
2740 3196 7.657354 GCAATTGATCCTTTTAGACCAAAACTT 59.343 33.333 10.34 0.00 32.65 2.66
2779 3239 6.638610 ACATACTTCTGTTCTCCATCAAGAG 58.361 40.000 0.00 0.00 35.04 2.85
2786 3246 4.654915 TGTTCTCCATCAAGAGCATTTCA 58.345 39.130 0.00 0.00 32.38 2.69
2787 3247 5.258841 TGTTCTCCATCAAGAGCATTTCAT 58.741 37.500 0.00 0.00 32.38 2.57
2789 3249 6.541278 TGTTCTCCATCAAGAGCATTTCATAG 59.459 38.462 0.00 0.00 32.38 2.23
2791 3251 6.522946 TCTCCATCAAGAGCATTTCATAGAG 58.477 40.000 0.00 0.00 33.66 2.43
2792 3252 6.099413 TCTCCATCAAGAGCATTTCATAGAGT 59.901 38.462 0.00 0.00 33.66 3.24
2809 3271 7.629157 TCATAGAGTGTGATAATTTTGTCCCA 58.371 34.615 0.00 0.00 0.00 4.37
2832 3294 1.477553 TTTCATCATGCTGCCCTTCC 58.522 50.000 0.00 0.00 0.00 3.46
2915 3377 4.154347 GAGCCGGTGCCTCAGAGG 62.154 72.222 12.81 12.81 38.69 3.69
2992 3454 2.046604 GGCCTACCAACGGTGACC 60.047 66.667 0.00 0.00 36.19 4.02
2993 3455 2.046604 GCCTACCAACGGTGACCC 60.047 66.667 0.00 0.00 36.19 4.46
3003 3465 4.876652 GGTGACCCGTCGTTCTAC 57.123 61.111 0.00 0.00 0.00 2.59
3004 3466 2.261215 GGTGACCCGTCGTTCTACT 58.739 57.895 0.00 0.00 0.00 2.57
3017 3487 2.124570 CTACTGCAAGCGCCCCAT 60.125 61.111 2.29 0.00 37.60 4.00
3029 3500 1.968540 GCCCCATTGCTATCGCTCC 60.969 63.158 0.00 0.00 36.97 4.70
3040 3511 1.476085 CTATCGCTCCTGCCCTAGATG 59.524 57.143 0.00 0.00 35.36 2.90
3045 3516 0.972883 CTCCTGCCCTAGATGTAGCC 59.027 60.000 0.00 0.00 0.00 3.93
3072 3543 4.794648 CGCCCGAAATGCCCCTCA 62.795 66.667 0.00 0.00 0.00 3.86
3254 3754 2.121506 TGAACCCTCCCTGCCCTT 60.122 61.111 0.00 0.00 0.00 3.95
3279 3783 0.530870 GCTCCATTCGCCCTCTGTAC 60.531 60.000 0.00 0.00 0.00 2.90
3286 3790 1.140375 CGCCCTCTGTACGTAACCC 59.860 63.158 0.00 0.00 0.00 4.11
3333 3858 3.366781 GCAGGGAGCTCATTTTCAGAAAC 60.367 47.826 17.19 0.00 41.15 2.78
3335 3860 2.162408 GGGAGCTCATTTTCAGAAACCG 59.838 50.000 17.19 0.00 0.00 4.44
3371 3896 2.409055 GCACGAGCCATGATGCCAA 61.409 57.895 0.00 0.00 33.58 4.52
3386 3914 2.671070 CAATGACCACGGGAGGCT 59.329 61.111 0.00 0.00 0.00 4.58
3471 4007 3.820590 CAGCAAACGTGTGGTGGA 58.179 55.556 26.72 0.00 42.11 4.02
3474 4010 0.814010 AGCAAACGTGTGGTGGAGAC 60.814 55.000 10.19 0.00 0.00 3.36
3475 4011 1.092921 GCAAACGTGTGGTGGAGACA 61.093 55.000 8.05 0.00 38.70 3.41
3477 4013 0.179056 AAACGTGTGGTGGAGACAGG 60.179 55.000 0.00 0.00 44.46 4.00
3716 4321 2.536365 CACACGTACGTATGCTTCCAT 58.464 47.619 22.34 0.00 35.44 3.41
3728 4333 1.209261 TGCTTCCATATTCCGACTGCA 59.791 47.619 0.00 0.00 0.00 4.41
3759 4364 4.973168 ACTCTGATGCAAGTTAACAGGAA 58.027 39.130 8.61 0.00 0.00 3.36
3760 4365 5.564550 ACTCTGATGCAAGTTAACAGGAAT 58.435 37.500 8.61 0.00 0.00 3.01
3761 4366 5.413833 ACTCTGATGCAAGTTAACAGGAATG 59.586 40.000 8.61 0.25 0.00 2.67
3777 4382 2.420372 GGAATGTTTCTCGCTTTCTCCC 59.580 50.000 0.00 0.00 0.00 4.30
3872 4477 4.821589 CGGCTCCGCAGAAGGGAC 62.822 72.222 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.107402 TCTGGCATTCTGAGGAGTAGT 57.893 47.619 0.00 0.00 0.00 2.73
33 34 6.100279 TGTTAATATCTGGCATTCTGAGGAGT 59.900 38.462 0.00 0.00 0.00 3.85
36 37 6.938596 TGATGTTAATATCTGGCATTCTGAGG 59.061 38.462 12.72 0.00 0.00 3.86
45 46 4.757149 GTGGAGGTGATGTTAATATCTGGC 59.243 45.833 12.72 4.29 0.00 4.85
49 50 4.750098 CCGTGTGGAGGTGATGTTAATATC 59.250 45.833 5.31 5.31 37.49 1.63
54 55 1.344065 ACCGTGTGGAGGTGATGTTA 58.656 50.000 0.00 0.00 41.10 2.41
73 74 2.844946 TGTGCTAGTTTTGCAGCTACA 58.155 42.857 0.00 0.00 41.41 2.74
74 75 5.122396 ACTTATGTGCTAGTTTTGCAGCTAC 59.878 40.000 0.00 0.00 41.41 3.58
75 76 5.122239 CACTTATGTGCTAGTTTTGCAGCTA 59.878 40.000 0.00 0.00 41.41 3.32
80 81 4.766404 ACCACTTATGTGCTAGTTTTGC 57.234 40.909 3.24 0.00 42.54 3.68
89 90 4.094294 TGAAGCGAAATACCACTTATGTGC 59.906 41.667 3.24 0.00 42.54 4.57
94 95 4.939509 GCTTGAAGCGAAATACCACTTA 57.060 40.909 0.00 0.00 0.00 2.24
141 145 3.375699 AGTAGTTCGGTCCTGGAATCAT 58.624 45.455 0.00 0.00 0.00 2.45
155 163 1.553706 TGGAACGGAGGGAGTAGTTC 58.446 55.000 0.00 0.00 41.40 3.01
162 170 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
163 171 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
164 172 4.335594 GGTTCATCTATTTTGGAACGGAGG 59.664 45.833 0.00 0.00 40.30 4.30
165 173 4.941263 TGGTTCATCTATTTTGGAACGGAG 59.059 41.667 0.00 0.00 40.30 4.63
166 174 4.912586 TGGTTCATCTATTTTGGAACGGA 58.087 39.130 0.00 0.00 40.30 4.69
167 175 5.183140 AGTTGGTTCATCTATTTTGGAACGG 59.817 40.000 0.00 0.00 40.30 4.44
168 176 6.254281 AGTTGGTTCATCTATTTTGGAACG 57.746 37.500 0.00 0.00 40.30 3.95
169 177 7.926018 ACAAAGTTGGTTCATCTATTTTGGAAC 59.074 33.333 0.00 0.00 39.04 3.62
170 178 8.017418 ACAAAGTTGGTTCATCTATTTTGGAA 57.983 30.769 0.00 0.00 0.00 3.53
171 179 7.595819 ACAAAGTTGGTTCATCTATTTTGGA 57.404 32.000 0.00 0.00 0.00 3.53
172 180 8.576442 AGTACAAAGTTGGTTCATCTATTTTGG 58.424 33.333 0.00 0.00 0.00 3.28
179 187 9.965824 CAAAATTAGTACAAAGTTGGTTCATCT 57.034 29.630 0.00 0.00 0.00 2.90
180 188 9.744468 ACAAAATTAGTACAAAGTTGGTTCATC 57.256 29.630 0.00 0.00 0.00 2.92
216 224 9.003658 CCAAAATAGATGACTCAAGTTTGTACT 57.996 33.333 0.00 0.00 35.68 2.73
217 225 8.999431 TCCAAAATAGATGACTCAAGTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
218 226 9.567776 TTCCAAAATAGATGACTCAAGTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
219 227 8.352942 GTTCCAAAATAGATGACTCAAGTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
220 228 7.535258 CGTTCCAAAATAGATGACTCAAGTTTG 59.465 37.037 0.00 0.00 0.00 2.93
221 229 7.308589 CCGTTCCAAAATAGATGACTCAAGTTT 60.309 37.037 0.00 0.00 0.00 2.66
222 230 6.149474 CCGTTCCAAAATAGATGACTCAAGTT 59.851 38.462 0.00 0.00 0.00 2.66
223 231 5.643777 CCGTTCCAAAATAGATGACTCAAGT 59.356 40.000 0.00 0.00 0.00 3.16
224 232 5.874810 TCCGTTCCAAAATAGATGACTCAAG 59.125 40.000 0.00 0.00 0.00 3.02
225 233 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
226 234 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
227 235 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
228 236 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
229 237 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
230 238 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
231 239 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
232 240 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
233 241 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
234 242 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
235 243 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
236 244 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
237 245 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
238 246 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
239 247 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
240 248 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
241 249 0.535797 CAAGGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 45.47 3.62
242 250 0.535797 CCAAGGTACTCCCTCCGTTC 59.464 60.000 0.00 0.00 45.47 3.95
243 251 0.115745 TCCAAGGTACTCCCTCCGTT 59.884 55.000 0.00 0.00 45.47 4.44
244 252 0.115745 TTCCAAGGTACTCCCTCCGT 59.884 55.000 0.00 0.00 45.47 4.69
245 253 0.535797 GTTCCAAGGTACTCCCTCCG 59.464 60.000 0.00 0.00 45.47 4.63
246 254 1.555533 CTGTTCCAAGGTACTCCCTCC 59.444 57.143 0.00 0.00 45.47 4.30
247 255 1.066071 GCTGTTCCAAGGTACTCCCTC 60.066 57.143 0.00 0.00 45.47 4.30
249 257 0.690762 TGCTGTTCCAAGGTACTCCC 59.309 55.000 0.00 0.00 38.49 4.30
250 258 2.427506 CTTGCTGTTCCAAGGTACTCC 58.572 52.381 0.00 0.00 38.49 3.85
251 259 1.807142 GCTTGCTGTTCCAAGGTACTC 59.193 52.381 4.33 0.00 41.88 2.59
252 260 1.897560 GCTTGCTGTTCCAAGGTACT 58.102 50.000 4.33 0.00 41.88 2.73
256 264 2.096496 CGATTAGCTTGCTGTTCCAAGG 59.904 50.000 5.26 0.00 41.88 3.61
290 298 4.345547 TCTGTGGTGACTGTTGGTATGTAA 59.654 41.667 0.00 0.00 0.00 2.41
297 305 4.008074 ACTATTCTGTGGTGACTGTTGG 57.992 45.455 0.00 0.00 0.00 3.77
304 312 5.128827 GGTAGATCCAACTATTCTGTGGTGA 59.871 44.000 0.00 0.00 35.97 4.02
308 316 5.453903 CCTGGGTAGATCCAACTATTCTGTG 60.454 48.000 0.00 0.00 36.21 3.66
383 391 0.449388 GATTTGCAGCTTGAGGTCGG 59.551 55.000 0.00 0.00 0.00 4.79
385 397 1.471684 CTGGATTTGCAGCTTGAGGTC 59.528 52.381 0.00 0.00 0.00 3.85
393 405 3.211865 TGATCTGATCTGGATTTGCAGC 58.788 45.455 17.82 0.00 0.00 5.25
429 441 2.202946 GAAGTAGCTGGCCTCCGC 60.203 66.667 3.32 3.97 0.00 5.54
431 443 2.200373 TTTTGAAGTAGCTGGCCTCC 57.800 50.000 3.32 0.00 0.00 4.30
446 458 2.159435 GGTCGGGGATCGTTGATTTTTG 60.159 50.000 0.00 0.00 40.32 2.44
448 460 1.680860 GGGTCGGGGATCGTTGATTTT 60.681 52.381 0.00 0.00 40.32 1.82
455 467 3.937372 AAAGGGGGTCGGGGATCGT 62.937 63.158 0.00 0.00 40.32 3.73
466 478 0.338120 TTGGGGATAAGCAAAGGGGG 59.662 55.000 0.00 0.00 0.00 5.40
482 495 2.238942 TTGATGATCCGGTCGATTGG 57.761 50.000 0.00 0.00 0.00 3.16
506 519 2.195922 CTATTTCAATTTGGGCGCTGC 58.804 47.619 7.64 0.00 0.00 5.25
521 534 3.757248 CTGCTCGCCCCCGCTATTT 62.757 63.158 0.00 0.00 0.00 1.40
531 544 2.517450 CGATTCGAACCTGCTCGCC 61.517 63.158 0.00 0.00 38.73 5.54
541 554 0.795735 GGTCGCTTCGTCGATTCGAA 60.796 55.000 10.87 10.04 45.46 3.71
555 568 3.869272 CGCTTGATGCTGGGTCGC 61.869 66.667 0.00 0.00 40.11 5.19
675 688 1.403679 CTCTTGATTCGAGTCGCCTCT 59.596 52.381 7.92 0.00 35.43 3.69
692 711 2.661718 GGATCCTTCTCGTCTTCCTCT 58.338 52.381 3.84 0.00 0.00 3.69
694 713 1.341187 ACGGATCCTTCTCGTCTTCCT 60.341 52.381 10.75 0.00 30.89 3.36
762 781 7.288672 CGGCCGTAATAAATAGTCTTGAAATC 58.711 38.462 19.50 0.00 0.00 2.17
763 782 6.293244 GCGGCCGTAATAAATAGTCTTGAAAT 60.293 38.462 28.70 0.00 0.00 2.17
846 869 1.173043 ACGGACCGTATTCGTAACCA 58.827 50.000 20.23 0.00 38.73 3.67
858 885 0.804933 GCCTTAGTGCTAACGGACCG 60.805 60.000 13.61 13.61 30.87 4.79
861 888 0.905809 TGGGCCTTAGTGCTAACGGA 60.906 55.000 4.53 0.00 0.00 4.69
863 890 0.535335 TCTGGGCCTTAGTGCTAACG 59.465 55.000 4.53 0.00 0.00 3.18
956 1004 3.878519 GACGAGCGGACGAGGAGG 61.879 72.222 7.83 0.00 37.03 4.30
957 1005 2.815298 GAGACGAGCGGACGAGGAG 61.815 68.421 7.83 0.00 37.03 3.69
958 1006 2.818714 GAGACGAGCGGACGAGGA 60.819 66.667 7.83 0.00 37.03 3.71
963 1011 2.490685 GGAAGGAGACGAGCGGAC 59.509 66.667 0.00 0.00 0.00 4.79
1345 1393 2.009774 CGGACAGAAATCGAGCCAAAT 58.990 47.619 0.00 0.00 0.00 2.32
1366 1414 0.676782 CTAAGCAACCAAGGTCGGGG 60.677 60.000 0.00 0.00 0.00 5.73
1374 1422 2.083774 CTCATTCCGCTAAGCAACCAA 58.916 47.619 0.00 0.00 0.00 3.67
1378 1426 0.253044 AGCCTCATTCCGCTAAGCAA 59.747 50.000 0.00 0.00 32.26 3.91
1384 1432 2.689983 CCAAAATTAGCCTCATTCCGCT 59.310 45.455 0.00 0.00 39.17 5.52
1408 1456 1.298788 CACCGGCGACCAACAAAAC 60.299 57.895 9.30 0.00 0.00 2.43
1410 1458 0.881159 CTACACCGGCGACCAACAAA 60.881 55.000 9.30 0.00 0.00 2.83
1531 1579 4.037923 ACAAGTAAGCATTTCACAGGGTTG 59.962 41.667 0.00 0.00 0.00 3.77
1533 1581 3.832527 ACAAGTAAGCATTTCACAGGGT 58.167 40.909 0.00 0.00 0.00 4.34
1534 1582 4.853924 AACAAGTAAGCATTTCACAGGG 57.146 40.909 0.00 0.00 0.00 4.45
1535 1583 5.221224 TGGAAACAAGTAAGCATTTCACAGG 60.221 40.000 0.00 0.00 37.44 4.00
1537 1585 5.843673 TGGAAACAAGTAAGCATTTCACA 57.156 34.783 0.00 0.00 37.44 3.58
1585 1633 4.142687 GCCGTTATCCAAATCCCATTATCG 60.143 45.833 0.00 0.00 0.00 2.92
1592 1640 3.081804 CCTATGCCGTTATCCAAATCCC 58.918 50.000 0.00 0.00 0.00 3.85
1604 1652 1.339727 GGAAACTGAACCCTATGCCGT 60.340 52.381 0.00 0.00 0.00 5.68
1606 1654 2.507407 TGGAAACTGAACCCTATGCC 57.493 50.000 0.00 0.00 0.00 4.40
1607 1655 4.462483 TCAATTGGAAACTGAACCCTATGC 59.538 41.667 5.42 0.00 0.00 3.14
1609 1657 7.410174 TGTATCAATTGGAAACTGAACCCTAT 58.590 34.615 5.42 0.00 0.00 2.57
1614 1662 7.202016 TGACTGTATCAATTGGAAACTGAAC 57.798 36.000 5.42 6.61 33.02 3.18
1642 1692 5.297547 TCAACCAGATAACTGAACACTGAC 58.702 41.667 0.79 0.00 46.03 3.51
1648 1887 7.602644 TCATGTTACTCAACCAGATAACTGAAC 59.397 37.037 0.79 0.00 43.23 3.18
1656 1895 7.882791 TGTGTTAATCATGTTACTCAACCAGAT 59.117 33.333 0.00 0.00 33.41 2.90
1660 1899 7.336931 AGGATGTGTTAATCATGTTACTCAACC 59.663 37.037 0.00 3.32 33.41 3.77
1666 1905 8.028938 AGCAAAAGGATGTGTTAATCATGTTAC 58.971 33.333 0.00 0.00 0.00 2.50
1708 1948 3.551082 TCACGCATTTTGCACTTGAAAAG 59.449 39.130 0.00 0.00 45.36 2.27
1726 1966 3.353600 TGGCAATTGGCACTCACG 58.646 55.556 29.00 0.00 46.12 4.35
1733 1973 0.037046 CTTGGACCTTGGCAATTGGC 60.037 55.000 24.20 24.20 43.74 4.52
1734 1974 0.609662 CCTTGGACCTTGGCAATTGG 59.390 55.000 7.72 1.55 0.00 3.16
1735 1975 1.631405 TCCTTGGACCTTGGCAATTG 58.369 50.000 0.00 0.00 0.00 2.32
1736 1976 2.629017 ATCCTTGGACCTTGGCAATT 57.371 45.000 0.00 0.00 0.00 2.32
1737 1977 2.629017 AATCCTTGGACCTTGGCAAT 57.371 45.000 0.00 0.00 0.00 3.56
1738 1978 2.109128 TGTAATCCTTGGACCTTGGCAA 59.891 45.455 0.00 0.00 0.00 4.52
1767 2007 6.325919 CATGTTACAACTTGCCCTTTTCTA 57.674 37.500 0.00 0.00 0.00 2.10
1803 2043 8.478066 TGCACAATTCAGTCTCTACTAATATGT 58.522 33.333 0.00 0.00 33.48 2.29
1895 2146 4.442706 AGTGTAGTAGCATGCCATACAAC 58.557 43.478 21.83 17.01 0.00 3.32
1904 2155 5.408604 ACGAAGGAAAAAGTGTAGTAGCATG 59.591 40.000 0.00 0.00 0.00 4.06
1921 2280 3.118775 CCTGATACACCATCAACGAAGGA 60.119 47.826 0.00 0.00 43.15 3.36
2152 2521 6.148976 CACCAGATATCCAACAGCAAGATATG 59.851 42.308 0.00 0.00 34.20 1.78
2157 2526 2.947652 CCACCAGATATCCAACAGCAAG 59.052 50.000 0.00 0.00 0.00 4.01
2302 2674 8.511604 AGAATTCGACAAGACAATGGAATAAT 57.488 30.769 0.00 0.00 0.00 1.28
2315 2687 8.375465 GCCATAAAATTCAAAGAATTCGACAAG 58.625 33.333 5.54 0.00 0.00 3.16
2341 2713 1.556911 AGTATGGTCTCCCAACAGCTG 59.443 52.381 13.48 13.48 46.04 4.24
2382 2755 8.902806 GGTATCACAAATCTGATTGACCAATTA 58.097 33.333 3.22 0.00 32.61 1.40
2445 2818 8.601476 GTGGTTCATTAAGTAGAATTAAGTCCG 58.399 37.037 0.00 0.00 0.00 4.79
2446 2819 8.890718 GGTGGTTCATTAAGTAGAATTAAGTCC 58.109 37.037 0.00 0.00 0.00 3.85
2452 2825 8.109634 ACTGATGGTGGTTCATTAAGTAGAATT 58.890 33.333 0.00 0.00 0.00 2.17
2472 2845 7.821595 ATACATCATTTGCACAAAACTGATG 57.178 32.000 24.57 24.57 42.27 3.07
2542 2985 3.308866 CACCGTGTGCTACTAAATAAGGC 59.691 47.826 0.00 0.00 0.00 4.35
2560 3003 6.806249 ACACTAATTAACAAATTGATGCACCG 59.194 34.615 0.00 0.00 0.00 4.94
2568 3012 8.136057 TGCAACCAACACTAATTAACAAATTG 57.864 30.769 0.00 0.00 0.00 2.32
2574 3018 5.240844 AGGACTGCAACCAACACTAATTAAC 59.759 40.000 11.38 0.00 0.00 2.01
2580 3024 1.765904 TGAGGACTGCAACCAACACTA 59.234 47.619 11.38 0.00 0.00 2.74
2599 3045 6.985117 TCAGTCTTTCCAAAAGGATCATTTG 58.015 36.000 6.05 10.61 37.48 2.32
2631 3077 6.874288 ATAGAAAGCCAAGCAGATCATAAC 57.126 37.500 0.00 0.00 0.00 1.89
2633 3079 6.594744 TGAATAGAAAGCCAAGCAGATCATA 58.405 36.000 0.00 0.00 0.00 2.15
2639 3085 2.686915 CCCTGAATAGAAAGCCAAGCAG 59.313 50.000 0.00 0.00 0.00 4.24
2643 3089 3.825908 AACCCCTGAATAGAAAGCCAA 57.174 42.857 0.00 0.00 0.00 4.52
2658 3104 6.838382 ACAGTCTGATATTGGTATAAACCCC 58.162 40.000 6.91 0.00 46.16 4.95
2671 3117 5.784390 AGGAGGCATATGAACAGTCTGATAT 59.216 40.000 6.97 0.00 0.00 1.63
2672 3118 5.011431 CAGGAGGCATATGAACAGTCTGATA 59.989 44.000 6.97 0.00 0.00 2.15
2673 3119 3.972638 AGGAGGCATATGAACAGTCTGAT 59.027 43.478 6.97 0.00 0.00 2.90
2705 3151 8.296713 TCTAAAAGGATCAATTGCAGTTGTAAC 58.703 33.333 19.91 11.67 0.00 2.50
2745 3201 9.036980 GGAGAACAGAAGTATGTATATGGGTAT 57.963 37.037 0.00 0.00 31.70 2.73
2749 3205 8.588472 TGATGGAGAACAGAAGTATGTATATGG 58.412 37.037 0.00 0.00 31.70 2.74
2755 3211 6.611613 TCTTGATGGAGAACAGAAGTATGT 57.388 37.500 0.00 0.00 33.96 2.29
2779 3239 9.793252 ACAAAATTATCACACTCTATGAAATGC 57.207 29.630 0.00 0.00 0.00 3.56
2786 3246 7.861629 TCTGGGACAAAATTATCACACTCTAT 58.138 34.615 0.00 0.00 38.70 1.98
2787 3247 7.252612 TCTGGGACAAAATTATCACACTCTA 57.747 36.000 0.00 0.00 38.70 2.43
2789 3249 7.396540 AATCTGGGACAAAATTATCACACTC 57.603 36.000 0.00 0.00 38.70 3.51
2791 3251 8.087750 TGAAAATCTGGGACAAAATTATCACAC 58.912 33.333 0.00 0.00 38.70 3.82
2792 3252 8.187913 TGAAAATCTGGGACAAAATTATCACA 57.812 30.769 0.00 0.00 38.70 3.58
2809 3271 3.028094 AGGGCAGCATGATGAAAATCT 57.972 42.857 16.67 0.79 39.69 2.40
2832 3294 2.483877 TCACAAATAACTCGGCTGCAAG 59.516 45.455 0.50 0.41 0.00 4.01
2915 3377 0.179108 AACGCGGTCTATCTTGAGCC 60.179 55.000 12.47 0.00 0.00 4.70
2992 3454 1.674611 CGCTTGCAGTAGAACGACGG 61.675 60.000 0.00 0.00 0.00 4.79
2993 3455 1.696644 CGCTTGCAGTAGAACGACG 59.303 57.895 0.00 0.00 0.00 5.12
2997 3459 2.399356 GGGGCGCTTGCAGTAGAAC 61.399 63.158 7.64 0.00 41.71 3.01
2998 3460 2.046314 GGGGCGCTTGCAGTAGAA 60.046 61.111 7.64 0.00 41.71 2.10
2999 3461 2.196997 AATGGGGCGCTTGCAGTAGA 62.197 55.000 7.64 0.00 41.71 2.59
3000 3462 1.750399 AATGGGGCGCTTGCAGTAG 60.750 57.895 7.64 0.00 41.71 2.57
3002 3464 3.376078 CAATGGGGCGCTTGCAGT 61.376 61.111 7.64 0.00 41.71 4.40
3003 3465 4.807039 GCAATGGGGCGCTTGCAG 62.807 66.667 22.63 4.85 45.50 4.41
3029 3500 1.069823 CAGTGGCTACATCTAGGGCAG 59.930 57.143 2.02 0.00 36.26 4.85
3072 3543 2.096496 GCTACAATGCAGCAAAGACGAT 59.904 45.455 0.00 0.00 38.93 3.73
3254 3754 0.038166 AGGGCGAATGGAGCTGAAAA 59.962 50.000 0.00 0.00 34.52 2.29
3279 3783 1.356624 CTACCTACGCCGGGTTACG 59.643 63.158 2.18 0.00 43.80 3.18
3286 3790 1.008767 GCTGCTACTACCTACGCCG 60.009 63.158 0.00 0.00 0.00 6.46
3333 3858 1.468224 CGAGAACACAGAGATGGACGG 60.468 57.143 0.00 0.00 0.00 4.79
3335 3860 1.067565 TGCGAGAACACAGAGATGGAC 60.068 52.381 0.00 0.00 0.00 4.02
3371 3896 3.402681 CCAGCCTCCCGTGGTCAT 61.403 66.667 0.00 0.00 0.00 3.06
3386 3914 0.687920 TCCACATTGTTACCGAGCCA 59.312 50.000 0.00 0.00 0.00 4.75
3413 3946 3.136123 TAGTTCCTCCGCGTCCCG 61.136 66.667 4.92 0.00 0.00 5.14
3471 4007 1.194781 ACGTGCATTCTCCCCTGTCT 61.195 55.000 0.00 0.00 0.00 3.41
3474 4010 2.401766 GCACGTGCATTCTCCCCTG 61.402 63.158 34.52 0.00 41.59 4.45
3475 4011 2.045926 GCACGTGCATTCTCCCCT 60.046 61.111 34.52 0.00 41.59 4.79
3498 4082 1.539065 CGGATAAGGCAGCGAATCACT 60.539 52.381 0.00 0.00 0.00 3.41
3704 4309 3.675225 CAGTCGGAATATGGAAGCATACG 59.325 47.826 0.00 0.00 0.00 3.06
3728 4333 3.072184 ACTTGCATCAGAGTTGGAGACTT 59.928 43.478 0.00 0.00 39.19 3.01
3735 4340 4.756642 TCCTGTTAACTTGCATCAGAGTTG 59.243 41.667 11.01 0.00 36.79 3.16
3736 4341 4.973168 TCCTGTTAACTTGCATCAGAGTT 58.027 39.130 7.22 6.73 39.32 3.01
3737 4342 4.623932 TCCTGTTAACTTGCATCAGAGT 57.376 40.909 7.22 0.00 0.00 3.24
3759 4364 2.704572 CAGGGAGAAAGCGAGAAACAT 58.295 47.619 0.00 0.00 0.00 2.71
3760 4365 1.878102 GCAGGGAGAAAGCGAGAAACA 60.878 52.381 0.00 0.00 0.00 2.83
3761 4366 0.799393 GCAGGGAGAAAGCGAGAAAC 59.201 55.000 0.00 0.00 0.00 2.78
3777 4382 0.803117 CAGCACACCTGAATCTGCAG 59.197 55.000 7.63 7.63 44.64 4.41
3872 4477 3.764160 GAAGCAGCCCCCGATCAGG 62.764 68.421 0.00 0.00 40.63 3.86


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

AutoCloner maintained by Alex Coulton.