Multiple sequence alignment - TraesCS4B01G096500

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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 TraesCS4B01G096500 chr4B 100.000 2944 0 0 1 2944 100575173 100578116 0.000000e+00 5437
1 TraesCS4B01G096500 chr4B 100.000 209 0 0 3147 3355 100578319 100578527 1.460000e-103 387
2 TraesCS4B01G096500 chr4B 87.113 194 16 7 2 190 450698031 450698220 9.430000e-51 211
3 TraesCS4B01G096500 chr4A 89.516 2709 138 65 211 2852 517883333 517885962 0.000000e+00 3295
4 TraesCS4B01G096500 chr4A 93.478 138 3 3 3147 3278 517886123 517885986 2.040000e-47 200
5 TraesCS4B01G096500 chr4A 92.086 139 4 3 2813 2944 517886288 517886150 4.420000e-44 189
6 TraesCS4B01G096500 chr4D 93.171 1933 61 27 1049 2944 68052976 68054874 0.000000e+00 2772
7 TraesCS4B01G096500 chr4D 79.873 631 72 31 211 815 68052118 68052719 8.660000e-111 411
8 TraesCS4B01G096500 chr4D 94.860 214 4 3 3147 3353 68054904 68055117 8.980000e-86 327
9 TraesCS4B01G096500 chr5B 78.873 639 86 37 1261 1868 211146022 211146642 1.460000e-103 387
10 TraesCS4B01G096500 chr5B 85.185 135 18 2 1491 1624 514279495 514279362 1.620000e-28 137
11 TraesCS4B01G096500 chr5D 78.717 639 89 36 1261 1868 200501049 200501671 1.890000e-102 383
12 TraesCS4B01G096500 chr5D 90.299 134 13 0 1268 1401 425077485 425077352 3.440000e-40 176
13 TraesCS4B01G096500 chr5D 74.619 394 74 22 1491 1865 425077353 425076967 2.090000e-32 150
14 TraesCS4B01G096500 chr5A 78.261 644 87 43 1261 1868 214166396 214167022 6.840000e-97 364
15 TraesCS4B01G096500 chr5A 90.299 134 13 0 1268 1401 539093485 539093352 3.440000e-40 176
16 TraesCS4B01G096500 chr5A 74.611 386 75 21 1491 1865 539093353 539092980 7.500000e-32 148
17 TraesCS4B01G096500 chr1D 88.021 192 19 3 2 190 15303692 15303502 1.210000e-54 224
18 TraesCS4B01G096500 chr1D 87.931 174 20 1 2 175 350298300 350298472 1.580000e-48 204
19 TraesCS4B01G096500 chr1D 89.116 147 14 2 1738 1883 364624919 364624774 7.390000e-42 182
20 TraesCS4B01G096500 chr2A 91.304 161 9 4 2 162 382274179 382274334 7.290000e-52 215
21 TraesCS4B01G096500 chr2A 91.304 161 8 4 2 162 382312545 382312391 7.290000e-52 215
22 TraesCS4B01G096500 chr2A 84.848 198 23 6 2 194 754045567 754045372 3.420000e-45 193
23 TraesCS4B01G096500 chr1B 89.634 164 14 3 1737 1898 487951128 487950966 4.390000e-49 206
24 TraesCS4B01G096500 chr1B 85.938 192 23 3 2 190 22107069 22107259 5.680000e-48 202
25 TraesCS4B01G096500 chr3A 88.068 176 16 4 2 175 328930785 328930957 1.580000e-48 204
26 TraesCS4B01G096500 chr3A 90.580 138 13 0 1261 1398 633922094 633922231 2.060000e-42 183
27 TraesCS4B01G096500 chr1A 85.859 198 16 10 2 193 561622926 561623117 2.040000e-47 200
28 TraesCS4B01G096500 chr1A 89.865 148 13 2 1738 1884 463461337 463461191 4.420000e-44 189
29 TraesCS4B01G096500 chr3B 89.130 138 15 0 1261 1398 653152044 653152181 4.450000e-39 172
30 TraesCS4B01G096500 chr3D 90.244 123 12 0 1737 1859 492131788 492131910 9.630000e-36 161
31 TraesCS4B01G096500 chr3D 80.925 173 30 3 1454 1625 352367978 352367808 2.100000e-27 134


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 TraesCS4B01G096500 chr4B 100575173 100578527 3354 False 2912 5437 100.000000 1 3355 2 chr4B.!!$F2 3354
1 TraesCS4B01G096500 chr4A 517883333 517885962 2629 False 3295 3295 89.516000 211 2852 1 chr4A.!!$F1 2641
2 TraesCS4B01G096500 chr4D 68052118 68055117 2999 False 1170 2772 89.301333 211 3353 3 chr4D.!!$F1 3142
3 TraesCS4B01G096500 chr5B 211146022 211146642 620 False 387 387 78.873000 1261 1868 1 chr5B.!!$F1 607
4 TraesCS4B01G096500 chr5D 200501049 200501671 622 False 383 383 78.717000 1261 1868 1 chr5D.!!$F1 607
5 TraesCS4B01G096500 chr5A 214166396 214167022 626 False 364 364 78.261000 1261 1868 1 chr5A.!!$F1 607

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
177 178 0.030504 CAACATCACGGCAAAGCACA 59.969 50.0 0.0 0.0 0.00 4.57 F
565 596 0.108585 TCTGACCAACTGCCAAGGAC 59.891 55.0 0.0 0.0 0.00 3.85 F
1120 1184 0.319900 TCTCAAAAAGCTCGCTCGCT 60.320 50.0 0.0 0.0 43.31 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1639 0.533032 CCTCCTCCTCGGTGAAGTTC 59.467 60.0 0.00 0.0 0.0 3.01 R
2333 2435 0.644937 ATTGGCCTCCTCCCTCTAGT 59.355 55.0 3.32 0.0 0.0 2.57 R
2731 2858 0.844661 TCCCATAACCACCACCAGCT 60.845 55.0 0.00 0.0 0.0 4.24 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
158 159 6.976636 TTTTTCAAGAAATCCAACAACACC 57.023 33.333 0.00 0.00 0.00 4.16
159 160 5.667539 TTTCAAGAAATCCAACAACACCA 57.332 34.783 0.00 0.00 0.00 4.17
160 161 5.667539 TTCAAGAAATCCAACAACACCAA 57.332 34.783 0.00 0.00 0.00 3.67
161 162 5.004922 TCAAGAAATCCAACAACACCAAC 57.995 39.130 0.00 0.00 0.00 3.77
162 163 4.464244 TCAAGAAATCCAACAACACCAACA 59.536 37.500 0.00 0.00 0.00 3.33
163 164 5.128499 TCAAGAAATCCAACAACACCAACAT 59.872 36.000 0.00 0.00 0.00 2.71
164 165 5.200368 AGAAATCCAACAACACCAACATC 57.800 39.130 0.00 0.00 0.00 3.06
165 166 4.648762 AGAAATCCAACAACACCAACATCA 59.351 37.500 0.00 0.00 0.00 3.07
166 167 4.320608 AATCCAACAACACCAACATCAC 57.679 40.909 0.00 0.00 0.00 3.06
167 168 1.673400 TCCAACAACACCAACATCACG 59.327 47.619 0.00 0.00 0.00 4.35
168 169 1.268999 CCAACAACACCAACATCACGG 60.269 52.381 0.00 0.00 0.00 4.94
169 170 0.383949 AACAACACCAACATCACGGC 59.616 50.000 0.00 0.00 0.00 5.68
170 171 0.749818 ACAACACCAACATCACGGCA 60.750 50.000 0.00 0.00 0.00 5.69
171 172 0.383590 CAACACCAACATCACGGCAA 59.616 50.000 0.00 0.00 0.00 4.52
172 173 1.107114 AACACCAACATCACGGCAAA 58.893 45.000 0.00 0.00 0.00 3.68
173 174 0.667993 ACACCAACATCACGGCAAAG 59.332 50.000 0.00 0.00 0.00 2.77
174 175 0.664166 CACCAACATCACGGCAAAGC 60.664 55.000 0.00 0.00 0.00 3.51
175 176 1.106351 ACCAACATCACGGCAAAGCA 61.106 50.000 0.00 0.00 0.00 3.91
176 177 0.664166 CCAACATCACGGCAAAGCAC 60.664 55.000 0.00 0.00 0.00 4.40
177 178 0.030504 CAACATCACGGCAAAGCACA 59.969 50.000 0.00 0.00 0.00 4.57
178 179 0.961019 AACATCACGGCAAAGCACAT 59.039 45.000 0.00 0.00 0.00 3.21
179 180 0.523072 ACATCACGGCAAAGCACATC 59.477 50.000 0.00 0.00 0.00 3.06
180 181 0.179156 CATCACGGCAAAGCACATCC 60.179 55.000 0.00 0.00 0.00 3.51
181 182 0.608856 ATCACGGCAAAGCACATCCA 60.609 50.000 0.00 0.00 0.00 3.41
182 183 1.081242 CACGGCAAAGCACATCCAC 60.081 57.895 0.00 0.00 0.00 4.02
183 184 1.228245 ACGGCAAAGCACATCCACT 60.228 52.632 0.00 0.00 0.00 4.00
184 185 0.823356 ACGGCAAAGCACATCCACTT 60.823 50.000 0.00 0.00 0.00 3.16
185 186 0.109597 CGGCAAAGCACATCCACTTC 60.110 55.000 0.00 0.00 0.00 3.01
186 187 1.251251 GGCAAAGCACATCCACTTCT 58.749 50.000 0.00 0.00 0.00 2.85
187 188 2.436417 GGCAAAGCACATCCACTTCTA 58.564 47.619 0.00 0.00 0.00 2.10
188 189 2.421424 GGCAAAGCACATCCACTTCTAG 59.579 50.000 0.00 0.00 0.00 2.43
189 190 3.077359 GCAAAGCACATCCACTTCTAGT 58.923 45.455 0.00 0.00 0.00 2.57
190 191 4.253685 GCAAAGCACATCCACTTCTAGTA 58.746 43.478 0.00 0.00 0.00 1.82
191 192 4.878397 GCAAAGCACATCCACTTCTAGTAT 59.122 41.667 0.00 0.00 0.00 2.12
192 193 6.049149 GCAAAGCACATCCACTTCTAGTATA 58.951 40.000 0.00 0.00 0.00 1.47
193 194 6.708054 GCAAAGCACATCCACTTCTAGTATAT 59.292 38.462 0.00 0.00 0.00 0.86
194 195 7.227512 GCAAAGCACATCCACTTCTAGTATATT 59.772 37.037 0.00 0.00 0.00 1.28
195 196 9.764363 CAAAGCACATCCACTTCTAGTATATTA 57.236 33.333 0.00 0.00 0.00 0.98
224 225 2.385803 GGGACTTCATCGTTAGAGGGA 58.614 52.381 0.00 0.00 0.00 4.20
244 245 7.554476 AGAGGGATGCTAGATTTGAGTTAAAAC 59.446 37.037 0.00 0.00 0.00 2.43
245 246 7.175104 AGGGATGCTAGATTTGAGTTAAAACA 58.825 34.615 0.00 0.00 0.00 2.83
273 275 7.443272 TCAATAACTCTTGTGAGATATGCCATG 59.557 37.037 0.00 0.00 42.73 3.66
274 276 4.767578 ACTCTTGTGAGATATGCCATGT 57.232 40.909 0.00 0.00 42.73 3.21
275 277 4.701765 ACTCTTGTGAGATATGCCATGTC 58.298 43.478 0.00 0.00 42.73 3.06
276 278 4.063689 CTCTTGTGAGATATGCCATGTCC 58.936 47.826 0.00 0.00 42.73 4.02
277 279 3.455543 TCTTGTGAGATATGCCATGTCCA 59.544 43.478 0.00 0.00 0.00 4.02
278 280 3.929955 TGTGAGATATGCCATGTCCAA 57.070 42.857 0.00 0.00 0.00 3.53
282 284 6.363882 TGTGAGATATGCCATGTCCAATAAA 58.636 36.000 0.00 0.00 0.00 1.40
285 287 7.864379 GTGAGATATGCCATGTCCAATAAAAAG 59.136 37.037 0.00 0.00 0.00 2.27
338 340 2.008242 TAAAGTGCATGCCCAAAGGT 57.992 45.000 16.68 0.00 34.57 3.50
339 341 1.130777 AAAGTGCATGCCCAAAGGTT 58.869 45.000 16.68 0.00 34.57 3.50
347 349 0.827507 TGCCCAAAGGTTTCTGCCTC 60.828 55.000 0.00 0.00 38.03 4.70
390 417 3.357504 TGCATCTCTCGTGCATCAG 57.642 52.632 0.00 0.00 46.76 2.90
399 426 4.056740 CTCTCGTGCATCAGCTCAATATT 58.943 43.478 0.00 0.00 42.74 1.28
401 428 4.271776 TCTCGTGCATCAGCTCAATATTTG 59.728 41.667 0.00 0.00 42.74 2.32
402 429 4.190772 TCGTGCATCAGCTCAATATTTGA 58.809 39.130 0.00 0.00 42.74 2.69
425 453 3.488778 AAAATGAAGGGCATGCAACAA 57.511 38.095 21.36 0.51 37.28 2.83
451 479 2.472059 GCTCATCGAAATGGCCGCA 61.472 57.895 0.00 0.00 33.42 5.69
455 484 0.451383 CATCGAAATGGCCGCAAAGA 59.549 50.000 0.00 0.00 0.00 2.52
467 496 4.338118 TGGCCGCAAAGATAAGAAATAAGG 59.662 41.667 0.00 0.00 0.00 2.69
468 497 4.290969 GCCGCAAAGATAAGAAATAAGGC 58.709 43.478 0.00 0.00 0.00 4.35
473 502 7.126398 CGCAAAGATAAGAAATAAGGCAGTAC 58.874 38.462 0.00 0.00 0.00 2.73
484 513 3.266240 GGCAGTACCTCCCCTTTTG 57.734 57.895 0.00 0.00 34.51 2.44
488 517 1.000019 GTACCTCCCCTTTTGCCCC 60.000 63.158 0.00 0.00 0.00 5.80
489 518 1.466386 TACCTCCCCTTTTGCCCCA 60.466 57.895 0.00 0.00 0.00 4.96
490 519 1.506028 TACCTCCCCTTTTGCCCCAG 61.506 60.000 0.00 0.00 0.00 4.45
491 520 2.854076 CTCCCCTTTTGCCCCAGT 59.146 61.111 0.00 0.00 0.00 4.00
492 521 1.304464 CTCCCCTTTTGCCCCAGTC 60.304 63.158 0.00 0.00 0.00 3.51
493 522 2.676471 CCCCTTTTGCCCCAGTCG 60.676 66.667 0.00 0.00 0.00 4.18
494 523 2.434331 CCCTTTTGCCCCAGTCGA 59.566 61.111 0.00 0.00 0.00 4.20
495 524 1.971695 CCCTTTTGCCCCAGTCGAC 60.972 63.158 7.70 7.70 0.00 4.20
497 526 1.301401 CTTTTGCCCCAGTCGACGA 60.301 57.895 10.46 0.00 0.00 4.20
498 527 0.673644 CTTTTGCCCCAGTCGACGAT 60.674 55.000 10.46 0.00 0.00 3.73
499 528 0.609151 TTTTGCCCCAGTCGACGATA 59.391 50.000 10.46 0.00 0.00 2.92
500 529 0.174845 TTTGCCCCAGTCGACGATAG 59.825 55.000 10.46 2.08 46.19 2.08
502 531 1.101635 TGCCCCAGTCGACGATAGAG 61.102 60.000 10.46 0.00 41.38 2.43
503 532 0.818445 GCCCCAGTCGACGATAGAGA 60.818 60.000 10.46 0.00 41.38 3.10
512 541 2.096496 TCGACGATAGAGACGGAAAACC 59.904 50.000 0.00 0.00 41.38 3.27
519 548 7.144000 ACGATAGAGACGGAAAACCAATATAC 58.856 38.462 0.00 0.00 41.38 1.47
563 594 2.787473 TATCTGACCAACTGCCAAGG 57.213 50.000 0.00 0.00 0.00 3.61
565 596 0.108585 TCTGACCAACTGCCAAGGAC 59.891 55.000 0.00 0.00 0.00 3.85
566 597 0.890996 CTGACCAACTGCCAAGGACC 60.891 60.000 0.00 0.00 0.00 4.46
567 598 1.603739 GACCAACTGCCAAGGACCC 60.604 63.158 0.00 0.00 0.00 4.46
568 599 2.351924 GACCAACTGCCAAGGACCCA 62.352 60.000 0.00 0.00 0.00 4.51
569 600 1.152567 CCAACTGCCAAGGACCCAA 60.153 57.895 0.00 0.00 0.00 4.12
570 601 1.181098 CCAACTGCCAAGGACCCAAG 61.181 60.000 0.00 0.00 0.00 3.61
571 602 1.153756 AACTGCCAAGGACCCAAGG 59.846 57.895 0.00 0.00 0.00 3.61
572 603 1.655114 AACTGCCAAGGACCCAAGGT 61.655 55.000 0.00 0.00 39.44 3.50
573 604 0.770557 ACTGCCAAGGACCCAAGGTA 60.771 55.000 0.00 0.00 35.25 3.08
574 605 0.625849 CTGCCAAGGACCCAAGGTAT 59.374 55.000 0.00 0.00 35.25 2.73
575 606 0.331278 TGCCAAGGACCCAAGGTATG 59.669 55.000 0.00 0.00 35.25 2.39
598 629 5.163457 TGGAATTTTTCTTTTCGAGGCAAGT 60.163 36.000 0.00 0.00 0.00 3.16
611 642 5.060506 TCGAGGCAAGTGTAGAATTTTCAA 58.939 37.500 0.00 0.00 0.00 2.69
662 693 1.507742 ACCCTCCCTCCAAAAACCAAT 59.492 47.619 0.00 0.00 0.00 3.16
664 695 3.245622 ACCCTCCCTCCAAAAACCAATAG 60.246 47.826 0.00 0.00 0.00 1.73
666 697 2.760650 CTCCCTCCAAAAACCAATAGCC 59.239 50.000 0.00 0.00 0.00 3.93
667 698 2.381961 TCCCTCCAAAAACCAATAGCCT 59.618 45.455 0.00 0.00 0.00 4.58
668 699 2.760650 CCCTCCAAAAACCAATAGCCTC 59.239 50.000 0.00 0.00 0.00 4.70
669 700 3.564352 CCCTCCAAAAACCAATAGCCTCT 60.564 47.826 0.00 0.00 0.00 3.69
709 740 0.385390 CCCGTTGCATTCATTAGGCC 59.615 55.000 0.00 0.00 0.00 5.19
777 808 1.545430 CCCCCTCCTACCCCCAAAA 60.545 63.158 0.00 0.00 0.00 2.44
778 809 1.580994 CCCCCTCCTACCCCCAAAAG 61.581 65.000 0.00 0.00 0.00 2.27
783 814 3.438816 CCCTCCTACCCCCAAAAGAAAAA 60.439 47.826 0.00 0.00 0.00 1.94
825 860 9.843334 AAAACCACGAAGCGAATAATAATTAAA 57.157 25.926 0.00 0.00 0.00 1.52
827 863 9.843334 AACCACGAAGCGAATAATAATTAAAAA 57.157 25.926 0.00 0.00 0.00 1.94
1040 1078 2.122189 CCCATCCTCCTCCTCCCC 60.122 72.222 0.00 0.00 0.00 4.81
1041 1079 2.731461 CCCATCCTCCTCCTCCCCT 61.731 68.421 0.00 0.00 0.00 4.79
1042 1080 1.152139 CCATCCTCCTCCTCCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
1043 1081 1.152139 CATCCTCCTCCTCCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
1044 1082 1.311371 ATCCTCCTCCTCCCCTCCT 60.311 63.158 0.00 0.00 0.00 3.69
1045 1083 1.376249 ATCCTCCTCCTCCCCTCCTC 61.376 65.000 0.00 0.00 0.00 3.71
1046 1084 2.612251 CTCCTCCTCCCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1047 1085 3.036959 TCCTCCTCCCCTCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
1099 1163 0.469917 CTCTCTCTCCTCCTCGCTCT 59.530 60.000 0.00 0.00 0.00 4.09
1116 1180 2.930455 GCTCTCTCTCAAAAAGCTCGCT 60.930 50.000 0.00 0.00 0.00 4.93
1120 1184 0.319900 TCTCAAAAAGCTCGCTCGCT 60.320 50.000 0.00 0.00 43.31 4.93
1140 1204 2.826287 CACGCACCACCAACACCA 60.826 61.111 0.00 0.00 0.00 4.17
1174 1238 2.153401 CCCTCAGACCCACCCACAA 61.153 63.158 0.00 0.00 0.00 3.33
1235 1299 4.598894 CGGCGGCATCTCCTCCTG 62.599 72.222 10.53 0.00 37.58 3.86
1236 1300 3.474570 GGCGGCATCTCCTCCTGT 61.475 66.667 3.07 0.00 36.76 4.00
1238 1302 2.430610 GCGGCATCTCCTCCTGTCT 61.431 63.158 0.00 0.00 0.00 3.41
1239 1303 1.109920 GCGGCATCTCCTCCTGTCTA 61.110 60.000 0.00 0.00 0.00 2.59
1240 1304 0.671251 CGGCATCTCCTCCTGTCTAC 59.329 60.000 0.00 0.00 0.00 2.59
1241 1305 0.671251 GGCATCTCCTCCTGTCTACG 59.329 60.000 0.00 0.00 0.00 3.51
1242 1306 1.394618 GCATCTCCTCCTGTCTACGT 58.605 55.000 0.00 0.00 0.00 3.57
1243 1307 2.573369 GCATCTCCTCCTGTCTACGTA 58.427 52.381 0.00 0.00 0.00 3.57
1244 1308 2.550606 GCATCTCCTCCTGTCTACGTAG 59.449 54.545 16.73 16.73 0.00 3.51
1245 1309 3.142951 CATCTCCTCCTGTCTACGTAGG 58.857 54.545 22.01 9.30 35.34 3.18
1246 1310 2.194859 TCTCCTCCTGTCTACGTAGGT 58.805 52.381 22.01 0.00 35.54 3.08
1247 1311 3.378512 TCTCCTCCTGTCTACGTAGGTA 58.621 50.000 22.01 10.57 35.54 3.08
1248 1312 3.972638 TCTCCTCCTGTCTACGTAGGTAT 59.027 47.826 22.01 0.00 35.54 2.73
1250 1314 3.065655 CCTCCTGTCTACGTAGGTATCG 58.934 54.545 22.01 6.95 35.54 2.92
1251 1315 3.494048 CCTCCTGTCTACGTAGGTATCGT 60.494 52.174 22.01 0.00 43.86 3.73
1252 1316 4.262207 CCTCCTGTCTACGTAGGTATCGTA 60.262 50.000 22.01 0.00 41.72 3.43
1253 1317 5.474578 TCCTGTCTACGTAGGTATCGTAT 57.525 43.478 22.01 0.00 41.69 3.06
1254 1318 6.350528 CCTCCTGTCTACGTAGGTATCGTATA 60.351 46.154 22.01 0.00 41.69 1.47
1255 1319 6.390721 TCCTGTCTACGTAGGTATCGTATAC 58.609 44.000 22.01 10.05 41.69 1.47
1256 1320 5.287274 CCTGTCTACGTAGGTATCGTATACG 59.713 48.000 22.01 19.23 45.81 3.06
1437 1503 1.868251 GCGACCAAGACGCGTCTAG 60.868 63.158 39.33 32.95 46.05 2.43
1561 1639 4.404098 CCGGACCTCAAACGGGGG 62.404 72.222 0.00 0.00 43.69 5.40
1633 1711 4.854399 TCGGCAACAAGTAACAATTCTTG 58.146 39.130 3.69 3.69 44.29 3.02
2012 2111 1.304464 TCTCTCCAGCTCAGCCGAA 60.304 57.895 0.00 0.00 0.00 4.30
2117 2216 1.138661 CTCAACCTCTCCATCAGCCTC 59.861 57.143 0.00 0.00 0.00 4.70
2333 2435 3.065233 GCATGTTTAGATTCATCGCACCA 59.935 43.478 0.00 0.00 0.00 4.17
2342 2444 0.033503 TCATCGCACCACTAGAGGGA 60.034 55.000 11.20 5.07 0.00 4.20
2346 2448 1.388065 CGCACCACTAGAGGGAGGAG 61.388 65.000 11.20 0.00 0.00 3.69
2516 2632 2.273179 ATCGGGCCATGCATGCATC 61.273 57.895 30.07 19.38 33.90 3.91
2517 2633 2.987355 ATCGGGCCATGCATGCATCA 62.987 55.000 30.07 4.08 33.90 3.07
2518 2634 2.570284 CGGGCCATGCATGCATCAT 61.570 57.895 30.07 8.53 33.90 2.45
2555 2682 7.823310 ACATAGTTCATGAATAGATCATCAGCC 59.177 37.037 12.12 0.00 45.91 4.85
2580 2707 3.261897 CAGCTCCTACCTTCTTTCCTTCA 59.738 47.826 0.00 0.00 0.00 3.02
2645 2772 7.271511 CACTAGATCTAATCAAGCATATCCCC 58.728 42.308 3.57 0.00 0.00 4.81
2690 2817 3.037851 TCTAGGGAGTGAGTGATGCAT 57.962 47.619 0.00 0.00 0.00 3.96
2691 2818 4.184649 TCTAGGGAGTGAGTGATGCATA 57.815 45.455 0.00 0.00 0.00 3.14
2692 2819 4.148079 TCTAGGGAGTGAGTGATGCATAG 58.852 47.826 0.00 0.00 0.00 2.23
2693 2820 2.756907 AGGGAGTGAGTGATGCATAGT 58.243 47.619 0.00 0.00 0.00 2.12
2694 2821 2.433604 AGGGAGTGAGTGATGCATAGTG 59.566 50.000 0.00 0.00 0.00 2.74
2695 2822 2.432146 GGGAGTGAGTGATGCATAGTGA 59.568 50.000 0.00 0.00 0.00 3.41
2696 2823 3.070734 GGGAGTGAGTGATGCATAGTGAT 59.929 47.826 0.00 0.00 0.00 3.06
2731 2858 1.136305 GGAGTGAGCGTTATGGTGCTA 59.864 52.381 0.00 0.00 42.60 3.49
2778 2905 0.251354 TCTTGGATGTCTGCAGGCTC 59.749 55.000 20.86 13.84 0.00 4.70
2861 2993 5.148502 AGGTTTGTCTTGTAGAGAGGAGAA 58.851 41.667 0.00 0.00 34.31 2.87
2906 3044 5.718801 TGCCCATATTTTCTGGTTAGGTA 57.281 39.130 0.00 0.00 31.44 3.08
3206 3344 0.392193 AATGGTCAGAGAGCTTGGCG 60.392 55.000 0.00 0.00 0.00 5.69
3234 3372 1.162329 TCTGGCCTTCTTGGGGGTA 59.838 57.895 3.32 0.00 36.00 3.69
3291 3433 8.598202 TTTAATCATGGACCAGTACTACAGTA 57.402 34.615 0.00 0.00 0.00 2.74
3353 3498 6.231211 CAGTCAGGGTATCAGTAGTTTGTTT 58.769 40.000 0.00 0.00 0.00 2.83
3354 3499 6.147821 CAGTCAGGGTATCAGTAGTTTGTTTG 59.852 42.308 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 6.467677 TGGTGTTGTTGGATTTCTTGAAAAA 58.532 32.000 0.00 0.00 0.00 1.94
136 137 6.042638 TGGTGTTGTTGGATTTCTTGAAAA 57.957 33.333 0.00 0.00 0.00 2.29
137 138 5.667539 TGGTGTTGTTGGATTTCTTGAAA 57.332 34.783 0.00 0.00 0.00 2.69
138 139 5.047021 TGTTGGTGTTGTTGGATTTCTTGAA 60.047 36.000 0.00 0.00 0.00 2.69
139 140 4.464244 TGTTGGTGTTGTTGGATTTCTTGA 59.536 37.500 0.00 0.00 0.00 3.02
140 141 4.753233 TGTTGGTGTTGTTGGATTTCTTG 58.247 39.130 0.00 0.00 0.00 3.02
141 142 5.128499 TGATGTTGGTGTTGTTGGATTTCTT 59.872 36.000 0.00 0.00 0.00 2.52
142 143 4.648762 TGATGTTGGTGTTGTTGGATTTCT 59.351 37.500 0.00 0.00 0.00 2.52
143 144 4.744631 GTGATGTTGGTGTTGTTGGATTTC 59.255 41.667 0.00 0.00 0.00 2.17
144 145 4.692228 GTGATGTTGGTGTTGTTGGATTT 58.308 39.130 0.00 0.00 0.00 2.17
145 146 3.243367 CGTGATGTTGGTGTTGTTGGATT 60.243 43.478 0.00 0.00 0.00 3.01
146 147 2.293122 CGTGATGTTGGTGTTGTTGGAT 59.707 45.455 0.00 0.00 0.00 3.41
147 148 1.673400 CGTGATGTTGGTGTTGTTGGA 59.327 47.619 0.00 0.00 0.00 3.53
148 149 1.268999 CCGTGATGTTGGTGTTGTTGG 60.269 52.381 0.00 0.00 0.00 3.77
149 150 1.863624 GCCGTGATGTTGGTGTTGTTG 60.864 52.381 0.00 0.00 0.00 3.33
150 151 0.383949 GCCGTGATGTTGGTGTTGTT 59.616 50.000 0.00 0.00 0.00 2.83
151 152 0.749818 TGCCGTGATGTTGGTGTTGT 60.750 50.000 0.00 0.00 0.00 3.32
152 153 0.383590 TTGCCGTGATGTTGGTGTTG 59.616 50.000 0.00 0.00 0.00 3.33
153 154 1.066908 CTTTGCCGTGATGTTGGTGTT 59.933 47.619 0.00 0.00 0.00 3.32
154 155 0.667993 CTTTGCCGTGATGTTGGTGT 59.332 50.000 0.00 0.00 0.00 4.16
155 156 0.664166 GCTTTGCCGTGATGTTGGTG 60.664 55.000 0.00 0.00 0.00 4.17
156 157 1.106351 TGCTTTGCCGTGATGTTGGT 61.106 50.000 0.00 0.00 0.00 3.67
157 158 0.664166 GTGCTTTGCCGTGATGTTGG 60.664 55.000 0.00 0.00 0.00 3.77
158 159 0.030504 TGTGCTTTGCCGTGATGTTG 59.969 50.000 0.00 0.00 0.00 3.33
159 160 0.961019 ATGTGCTTTGCCGTGATGTT 59.039 45.000 0.00 0.00 0.00 2.71
160 161 0.523072 GATGTGCTTTGCCGTGATGT 59.477 50.000 0.00 0.00 0.00 3.06
161 162 0.179156 GGATGTGCTTTGCCGTGATG 60.179 55.000 0.00 0.00 0.00 3.07
162 163 0.608856 TGGATGTGCTTTGCCGTGAT 60.609 50.000 0.00 0.00 0.00 3.06
163 164 1.228094 TGGATGTGCTTTGCCGTGA 60.228 52.632 0.00 0.00 0.00 4.35
164 165 1.081242 GTGGATGTGCTTTGCCGTG 60.081 57.895 0.00 0.00 0.00 4.94
165 166 0.823356 AAGTGGATGTGCTTTGCCGT 60.823 50.000 0.00 0.00 0.00 5.68
166 167 0.109597 GAAGTGGATGTGCTTTGCCG 60.110 55.000 0.00 0.00 0.00 5.69
167 168 1.251251 AGAAGTGGATGTGCTTTGCC 58.749 50.000 0.00 0.00 0.00 4.52
168 169 3.077359 ACTAGAAGTGGATGTGCTTTGC 58.923 45.455 0.00 0.00 0.00 3.68
169 170 8.668510 AATATACTAGAAGTGGATGTGCTTTG 57.331 34.615 0.00 0.00 0.00 2.77
189 190 9.899661 CGATGAAGTCCCCCAAATAATAATATA 57.100 33.333 0.00 0.00 0.00 0.86
190 191 8.390921 ACGATGAAGTCCCCCAAATAATAATAT 58.609 33.333 0.00 0.00 0.00 1.28
191 192 7.751646 ACGATGAAGTCCCCCAAATAATAATA 58.248 34.615 0.00 0.00 0.00 0.98
192 193 6.610830 ACGATGAAGTCCCCCAAATAATAAT 58.389 36.000 0.00 0.00 0.00 1.28
193 194 6.008696 ACGATGAAGTCCCCCAAATAATAA 57.991 37.500 0.00 0.00 0.00 1.40
194 195 5.640158 ACGATGAAGTCCCCCAAATAATA 57.360 39.130 0.00 0.00 0.00 0.98
195 196 4.519906 ACGATGAAGTCCCCCAAATAAT 57.480 40.909 0.00 0.00 0.00 1.28
196 197 4.310022 AACGATGAAGTCCCCCAAATAA 57.690 40.909 0.00 0.00 0.00 1.40
197 198 4.717778 TCTAACGATGAAGTCCCCCAAATA 59.282 41.667 0.00 0.00 0.00 1.40
198 199 2.899303 AACGATGAAGTCCCCCAAAT 57.101 45.000 0.00 0.00 0.00 2.32
199 200 2.907696 TCTAACGATGAAGTCCCCCAAA 59.092 45.455 0.00 0.00 0.00 3.28
200 201 2.500098 CTCTAACGATGAAGTCCCCCAA 59.500 50.000 0.00 0.00 0.00 4.12
201 202 2.108168 CTCTAACGATGAAGTCCCCCA 58.892 52.381 0.00 0.00 0.00 4.96
202 203 1.413077 CCTCTAACGATGAAGTCCCCC 59.587 57.143 0.00 0.00 0.00 5.40
203 204 1.413077 CCCTCTAACGATGAAGTCCCC 59.587 57.143 0.00 0.00 0.00 4.81
204 205 2.385803 TCCCTCTAACGATGAAGTCCC 58.614 52.381 0.00 0.00 0.00 4.46
205 206 3.800604 GCATCCCTCTAACGATGAAGTCC 60.801 52.174 1.34 0.00 38.53 3.85
206 207 3.068873 AGCATCCCTCTAACGATGAAGTC 59.931 47.826 1.34 0.00 38.53 3.01
207 208 3.034635 AGCATCCCTCTAACGATGAAGT 58.965 45.455 1.34 0.00 38.53 3.01
208 209 3.742433 AGCATCCCTCTAACGATGAAG 57.258 47.619 1.34 0.00 38.53 3.02
209 210 4.470602 TCTAGCATCCCTCTAACGATGAA 58.529 43.478 1.34 0.00 38.53 2.57
244 245 8.288208 GGCATATCTCACAAGAGTTATTGAATG 58.712 37.037 0.00 0.00 42.66 2.67
245 246 7.994911 TGGCATATCTCACAAGAGTTATTGAAT 59.005 33.333 0.00 0.00 42.66 2.57
312 314 4.613925 TGGGCATGCACTTTAATTTGAA 57.386 36.364 22.81 0.00 0.00 2.69
313 315 4.613925 TTGGGCATGCACTTTAATTTGA 57.386 36.364 22.81 0.00 0.00 2.69
326 328 0.037046 GGCAGAAACCTTTGGGCATG 60.037 55.000 0.00 0.00 35.63 4.06
354 356 3.325870 TGCAAGGTATATAGCGATGTGC 58.674 45.455 18.08 18.08 46.98 4.57
355 357 5.414360 AGATGCAAGGTATATAGCGATGTG 58.586 41.667 16.74 10.86 0.00 3.21
357 359 5.900425 AGAGATGCAAGGTATATAGCGATG 58.100 41.667 13.27 13.27 0.00 3.84
363 365 5.060662 GCACGAGAGATGCAAGGTATATA 57.939 43.478 0.00 0.00 42.88 0.86
373 400 0.530211 AGCTGATGCACGAGAGATGC 60.530 55.000 0.00 0.00 43.68 3.91
407 435 1.276989 CCTTGTTGCATGCCCTTCATT 59.723 47.619 16.68 0.00 31.79 2.57
408 436 0.899720 CCTTGTTGCATGCCCTTCAT 59.100 50.000 16.68 0.00 35.31 2.57
419 447 0.316204 ATGAGCAGTTGCCTTGTTGC 59.684 50.000 0.00 0.00 43.38 4.17
421 449 0.877071 CGATGAGCAGTTGCCTTGTT 59.123 50.000 0.00 0.00 43.38 2.83
425 453 1.741706 CATTTCGATGAGCAGTTGCCT 59.258 47.619 0.00 0.00 43.38 4.75
431 459 1.645455 CGGCCATTTCGATGAGCAG 59.355 57.895 2.24 0.00 0.00 4.24
444 472 4.338118 CCTTATTTCTTATCTTTGCGGCCA 59.662 41.667 2.24 0.00 0.00 5.36
468 497 0.323451 GGGCAAAAGGGGAGGTACTG 60.323 60.000 0.00 0.00 41.55 2.74
473 502 2.037847 CTGGGGCAAAAGGGGAGG 59.962 66.667 0.00 0.00 0.00 4.30
475 504 2.851045 GACTGGGGCAAAAGGGGA 59.149 61.111 0.00 0.00 0.00 4.81
479 508 0.673644 ATCGTCGACTGGGGCAAAAG 60.674 55.000 14.70 0.00 0.00 2.27
483 512 1.077285 TCTATCGTCGACTGGGGCA 60.077 57.895 14.70 0.00 0.00 5.36
484 513 0.818445 TCTCTATCGTCGACTGGGGC 60.818 60.000 14.70 0.00 0.00 5.80
488 517 1.568606 TCCGTCTCTATCGTCGACTG 58.431 55.000 14.70 7.51 0.00 3.51
489 518 2.306341 TTCCGTCTCTATCGTCGACT 57.694 50.000 14.70 0.00 0.00 4.18
490 519 3.097185 GTTTTCCGTCTCTATCGTCGAC 58.903 50.000 5.18 5.18 0.00 4.20
491 520 2.096496 GGTTTTCCGTCTCTATCGTCGA 59.904 50.000 0.00 0.00 0.00 4.20
492 521 2.159476 TGGTTTTCCGTCTCTATCGTCG 60.159 50.000 0.00 0.00 44.36 5.12
493 522 3.498927 TGGTTTTCCGTCTCTATCGTC 57.501 47.619 0.00 0.00 44.36 4.20
494 523 3.947910 TTGGTTTTCCGTCTCTATCGT 57.052 42.857 0.00 0.00 44.36 3.73
495 524 7.368833 AGTATATTGGTTTTCCGTCTCTATCG 58.631 38.462 0.00 0.00 44.36 2.92
497 526 7.441458 GCAAGTATATTGGTTTTCCGTCTCTAT 59.559 37.037 0.00 0.00 44.36 1.98
498 527 6.759827 GCAAGTATATTGGTTTTCCGTCTCTA 59.240 38.462 0.00 0.00 44.36 2.43
499 528 5.585047 GCAAGTATATTGGTTTTCCGTCTCT 59.415 40.000 0.00 0.00 44.36 3.10
500 529 5.353123 TGCAAGTATATTGGTTTTCCGTCTC 59.647 40.000 0.00 0.00 44.36 3.36
502 531 5.554822 TGCAAGTATATTGGTTTTCCGTC 57.445 39.130 0.00 0.00 44.36 4.79
503 532 6.524101 AATGCAAGTATATTGGTTTTCCGT 57.476 33.333 0.00 0.00 44.36 4.69
536 565 5.897250 TGGCAGTTGGTCAGATATCTTACTA 59.103 40.000 15.03 7.84 0.00 1.82
537 566 4.716784 TGGCAGTTGGTCAGATATCTTACT 59.283 41.667 15.03 6.30 0.00 2.24
547 576 0.890996 GGTCCTTGGCAGTTGGTCAG 60.891 60.000 0.00 0.00 29.11 3.51
556 587 0.331278 CATACCTTGGGTCCTTGGCA 59.669 55.000 0.00 0.00 37.09 4.92
563 594 6.605471 AAGAAAAATTCCATACCTTGGGTC 57.395 37.500 0.00 0.00 46.45 4.46
565 596 6.589907 CGAAAAGAAAAATTCCATACCTTGGG 59.410 38.462 0.00 0.00 46.45 4.12
567 598 7.542130 CCTCGAAAAGAAAAATTCCATACCTTG 59.458 37.037 0.00 0.00 0.00 3.61
568 599 7.602753 CCTCGAAAAGAAAAATTCCATACCTT 58.397 34.615 0.00 0.00 0.00 3.50
569 600 6.350194 GCCTCGAAAAGAAAAATTCCATACCT 60.350 38.462 0.00 0.00 0.00 3.08
570 601 5.805486 GCCTCGAAAAGAAAAATTCCATACC 59.195 40.000 0.00 0.00 0.00 2.73
571 602 6.386654 TGCCTCGAAAAGAAAAATTCCATAC 58.613 36.000 0.00 0.00 0.00 2.39
572 603 6.582677 TGCCTCGAAAAGAAAAATTCCATA 57.417 33.333 0.00 0.00 0.00 2.74
573 604 5.467035 TGCCTCGAAAAGAAAAATTCCAT 57.533 34.783 0.00 0.00 0.00 3.41
574 605 4.927978 TGCCTCGAAAAGAAAAATTCCA 57.072 36.364 0.00 0.00 0.00 3.53
575 606 5.175673 CACTTGCCTCGAAAAGAAAAATTCC 59.824 40.000 8.66 0.00 0.00 3.01
576 607 5.748630 ACACTTGCCTCGAAAAGAAAAATTC 59.251 36.000 8.66 0.00 0.00 2.17
577 608 5.660460 ACACTTGCCTCGAAAAGAAAAATT 58.340 33.333 8.66 0.00 0.00 1.82
578 609 5.262588 ACACTTGCCTCGAAAAGAAAAAT 57.737 34.783 8.66 0.00 0.00 1.82
579 610 4.712122 ACACTTGCCTCGAAAAGAAAAA 57.288 36.364 8.66 0.00 0.00 1.94
580 611 5.120399 TCTACACTTGCCTCGAAAAGAAAA 58.880 37.500 8.66 0.00 0.00 2.29
581 612 4.699637 TCTACACTTGCCTCGAAAAGAAA 58.300 39.130 8.66 0.00 0.00 2.52
582 613 4.330944 TCTACACTTGCCTCGAAAAGAA 57.669 40.909 8.66 0.00 0.00 2.52
583 614 4.330944 TTCTACACTTGCCTCGAAAAGA 57.669 40.909 8.66 0.00 0.00 2.52
584 615 5.613358 AATTCTACACTTGCCTCGAAAAG 57.387 39.130 0.00 0.00 0.00 2.27
588 619 4.637276 TGAAAATTCTACACTTGCCTCGA 58.363 39.130 0.00 0.00 0.00 4.04
591 622 7.817418 TTACTTGAAAATTCTACACTTGCCT 57.183 32.000 0.00 0.00 0.00 4.75
611 642 8.299570 CAACATCAAATGGCTAGTTCTTTTACT 58.700 33.333 0.00 0.00 33.60 2.24
625 656 4.399303 GGAGGGTAGTTCAACATCAAATGG 59.601 45.833 0.00 0.00 33.60 3.16
662 693 2.365635 GGGGTGAGGCAGAGGCTA 60.366 66.667 0.00 0.00 38.98 3.93
664 695 2.713531 TTTTGGGGTGAGGCAGAGGC 62.714 60.000 0.00 0.00 40.13 4.70
666 697 0.895559 GGTTTTGGGGTGAGGCAGAG 60.896 60.000 0.00 0.00 0.00 3.35
667 698 1.152830 GGTTTTGGGGTGAGGCAGA 59.847 57.895 0.00 0.00 0.00 4.26
668 699 1.908299 GGGTTTTGGGGTGAGGCAG 60.908 63.158 0.00 0.00 0.00 4.85
669 700 2.200092 GGGTTTTGGGGTGAGGCA 59.800 61.111 0.00 0.00 0.00 4.75
709 740 0.458543 CACCAGCAGTAGTAGGTGCG 60.459 60.000 0.00 0.00 44.25 5.34
844 880 2.158740 GCTTGTCCTATTCCCTTCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
847 883 1.475213 CCGCTTGTCCTATTCCCTTCC 60.475 57.143 0.00 0.00 0.00 3.46
849 885 0.107165 GCCGCTTGTCCTATTCCCTT 60.107 55.000 0.00 0.00 0.00 3.95
851 887 0.815615 CTGCCGCTTGTCCTATTCCC 60.816 60.000 0.00 0.00 0.00 3.97
1040 1078 3.199289 AGTTGGTTTTATACGGGGAGGAG 59.801 47.826 0.00 0.00 0.00 3.69
1041 1079 3.183801 AGTTGGTTTTATACGGGGAGGA 58.816 45.455 0.00 0.00 0.00 3.71
1042 1080 3.639672 AGTTGGTTTTATACGGGGAGG 57.360 47.619 0.00 0.00 0.00 4.30
1043 1081 4.445453 GGTAGTTGGTTTTATACGGGGAG 58.555 47.826 0.00 0.00 0.00 4.30
1044 1082 3.199727 GGGTAGTTGGTTTTATACGGGGA 59.800 47.826 0.00 0.00 0.00 4.81
1045 1083 3.054508 TGGGTAGTTGGTTTTATACGGGG 60.055 47.826 0.00 0.00 0.00 5.73
1046 1084 3.940852 GTGGGTAGTTGGTTTTATACGGG 59.059 47.826 0.00 0.00 0.00 5.28
1047 1085 3.940852 GGTGGGTAGTTGGTTTTATACGG 59.059 47.826 0.00 0.00 0.00 4.02
1099 1163 1.702886 CGAGCGAGCTTTTTGAGAGA 58.297 50.000 0.00 0.00 0.00 3.10
1120 1184 4.840005 TGTTGGTGGTGCGTGCGA 62.840 61.111 0.00 0.00 0.00 5.10
1140 1204 2.593956 GGGAAAGGAGGAGCGGTGT 61.594 63.158 0.00 0.00 0.00 4.16
1174 1238 5.933617 ACTGATGATATATGCTGTTGTGGT 58.066 37.500 0.00 0.00 0.00 4.16
1225 1289 2.778850 ACCTACGTAGACAGGAGGAGAT 59.221 50.000 24.15 0.00 36.89 2.75
1226 1290 2.194859 ACCTACGTAGACAGGAGGAGA 58.805 52.381 24.15 0.00 36.89 3.71
1229 1293 3.065655 CGATACCTACGTAGACAGGAGG 58.934 54.545 24.15 10.48 36.89 4.30
1230 1294 3.726607 ACGATACCTACGTAGACAGGAG 58.273 50.000 24.15 12.15 42.17 3.69
1231 1295 3.827008 ACGATACCTACGTAGACAGGA 57.173 47.619 24.15 4.36 42.17 3.86
1235 1299 5.443431 GCACGTATACGATACCTACGTAGAC 60.443 48.000 30.77 9.38 46.85 2.59
1236 1300 4.621460 GCACGTATACGATACCTACGTAGA 59.379 45.833 30.77 5.23 46.85 2.59
1238 1302 3.678072 GGCACGTATACGATACCTACGTA 59.322 47.826 30.77 0.00 46.85 3.57
1240 1304 3.109230 GGCACGTATACGATACCTACG 57.891 52.381 30.77 4.71 42.84 3.51
1434 1500 2.406401 CCGTCGCCGTACACCTAG 59.594 66.667 0.00 0.00 0.00 3.02
1561 1639 0.533032 CCTCCTCCTCGGTGAAGTTC 59.467 60.000 0.00 0.00 0.00 3.01
1923 2022 3.044305 AGCAGCGAAGTGGCGTTC 61.044 61.111 0.00 0.00 38.18 3.95
1931 2030 3.730761 GGTGTGGCAGCAGCGAAG 61.731 66.667 0.00 0.00 43.41 3.79
2132 2231 2.504274 TTTCACCGCTGGGTCGTCT 61.504 57.895 0.00 0.00 46.01 4.18
2170 2272 0.961019 TGTTGCATTGTTCTGGCTCC 59.039 50.000 0.00 0.00 0.00 4.70
2177 2279 2.116366 GTGGACGTTGTTGCATTGTTC 58.884 47.619 0.00 0.00 0.00 3.18
2206 2308 1.653667 CGGTTCAAGCACATGCACA 59.346 52.632 6.64 0.00 45.16 4.57
2311 2413 3.065233 TGGTGCGATGAATCTAAACATGC 59.935 43.478 0.00 0.00 0.00 4.06
2333 2435 0.644937 ATTGGCCTCCTCCCTCTAGT 59.355 55.000 3.32 0.00 0.00 2.57
2342 2444 2.182516 AGTGCTACTATTGGCCTCCT 57.817 50.000 3.32 0.00 0.00 3.69
2346 2448 5.163437 ACTGTTACTAGTGCTACTATTGGCC 60.163 44.000 5.39 0.00 29.08 5.36
2425 2527 4.259356 TGTTACAGAGAGCTAGCGAGTTA 58.741 43.478 9.55 0.00 0.00 2.24
2430 2532 3.428746 ACATGTTACAGAGAGCTAGCG 57.571 47.619 9.55 0.00 0.00 4.26
2516 2632 7.664758 TCATGAACTATGTCACCTAGATGATG 58.335 38.462 0.00 0.00 38.01 3.07
2517 2633 7.846101 TCATGAACTATGTCACCTAGATGAT 57.154 36.000 0.00 0.00 38.01 2.45
2518 2634 7.660030 TTCATGAACTATGTCACCTAGATGA 57.340 36.000 3.38 0.00 38.01 2.92
2555 2682 2.626840 GAAAGAAGGTAGGAGCTGCTG 58.373 52.381 19.25 0.00 30.55 4.41
2645 2772 7.938140 TGATGAACCTAACTTCCCTAAATTG 57.062 36.000 0.00 0.00 0.00 2.32
2655 2782 6.098982 CACTCCCTAGATGATGAACCTAACTT 59.901 42.308 0.00 0.00 0.00 2.66
2690 2817 3.956848 CCCACTCTCATCAGTCATCACTA 59.043 47.826 0.00 0.00 0.00 2.74
2691 2818 2.765135 CCCACTCTCATCAGTCATCACT 59.235 50.000 0.00 0.00 0.00 3.41
2692 2819 2.762887 TCCCACTCTCATCAGTCATCAC 59.237 50.000 0.00 0.00 0.00 3.06
2693 2820 3.029570 CTCCCACTCTCATCAGTCATCA 58.970 50.000 0.00 0.00 0.00 3.07
2694 2821 3.030291 ACTCCCACTCTCATCAGTCATC 58.970 50.000 0.00 0.00 0.00 2.92
2695 2822 2.765135 CACTCCCACTCTCATCAGTCAT 59.235 50.000 0.00 0.00 0.00 3.06
2696 2823 2.174360 CACTCCCACTCTCATCAGTCA 58.826 52.381 0.00 0.00 0.00 3.41
2731 2858 0.844661 TCCCATAACCACCACCAGCT 60.845 55.000 0.00 0.00 0.00 4.24
2778 2905 1.357690 GATGGCCATGTCATGTGCG 59.642 57.895 26.56 0.00 0.00 5.34
2841 2968 4.528596 CCCTTCTCCTCTCTACAAGACAAA 59.471 45.833 0.00 0.00 0.00 2.83
2844 2971 3.028130 CCCCTTCTCCTCTCTACAAGAC 58.972 54.545 0.00 0.00 0.00 3.01
2845 2972 2.927007 TCCCCTTCTCCTCTCTACAAGA 59.073 50.000 0.00 0.00 0.00 3.02
2861 2993 3.736224 CATGCTGCCCACTCCCCT 61.736 66.667 0.00 0.00 0.00 4.79
2906 3044 4.060192 TCTCCCATACCTTCTACCTACCT 58.940 47.826 0.00 0.00 0.00 3.08
3206 3344 1.510480 GAAGGCCAGACACAGCACAC 61.510 60.000 5.01 0.00 0.00 3.82
3234 3372 1.077501 CACCAACTCCGGCATCCAT 60.078 57.895 0.00 0.00 0.00 3.41
3278 3420 7.108841 TGGCTTTAGATTACTGTAGTACTGG 57.891 40.000 5.39 0.00 0.00 4.00
3285 3427 6.049955 ACAAGCTGGCTTTAGATTACTGTA 57.950 37.500 4.98 0.00 33.42 2.74


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

AutoCloner maintained by Alex Coulton.