Multiple sequence alignment - TraesCS6D01G088100

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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 TraesCS6D01G088100 chr6D 100.000 3710 0 0 1594 5303 53560246 53563955 0.000000e+00 6852.0
1 TraesCS6D01G088100 chr6D 100.000 1181 0 0 1 1181 53558653 53559833 0.000000e+00 2182.0
2 TraesCS6D01G088100 chr6D 83.412 211 29 2 248 454 144875936 144875728 1.950000e-44 191.0
3 TraesCS6D01G088100 chr6A 94.059 3737 130 44 1594 5303 61880745 61877074 0.000000e+00 5587.0
4 TraesCS6D01G088100 chr6A 98.724 392 5 0 790 1181 61881131 61880740 0.000000e+00 697.0
5 TraesCS6D01G088100 chr6A 81.392 790 128 15 7 786 61883309 61882529 1.250000e-175 627.0
6 TraesCS6D01G088100 chr6B 95.181 3154 107 21 1594 4740 118192358 118189243 0.000000e+00 4940.0
7 TraesCS6D01G088100 chr6B 87.558 643 47 16 466 1088 118193265 118192636 0.000000e+00 713.0
8 TraesCS6D01G088100 chr6B 87.703 553 22 23 4753 5303 118188896 118188388 2.110000e-168 603.0
9 TraesCS6D01G088100 chr6B 83.254 209 29 2 250 454 259078940 259078734 2.520000e-43 187.0
10 TraesCS6D01G088100 chr4A 79.355 465 71 18 1 454 130971580 130972030 2.400000e-78 303.0
11 TraesCS6D01G088100 chr3B 90.667 75 5 2 385 458 565279187 565279260 1.220000e-16 99.0
12 TraesCS6D01G088100 chr2A 84.946 93 11 2 362 454 747158899 747158988 2.030000e-14 91.6
13 TraesCS6D01G088100 chr2D 89.831 59 3 3 370 427 185399520 185399464 7.370000e-09 73.1


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 TraesCS6D01G088100 chr6D 53558653 53563955 5302 False 4517.000000 6852 100.000000 1 5303 2 chr6D.!!$F1 5302
1 TraesCS6D01G088100 chr6A 61877074 61883309 6235 True 2303.666667 5587 91.391667 7 5303 3 chr6A.!!$R1 5296
2 TraesCS6D01G088100 chr6B 118188388 118193265 4877 True 2085.333333 4940 90.147333 466 5303 3 chr6B.!!$R2 4837

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
573 583 0.036306 CCGTTGGAGTTGCCCTTAGT 59.964 55.000 0.00 0.0 34.97 2.24 F
2380 3976 0.476771 GTGGTGGGTTCCTGAGGAAA 59.523 55.000 16.79 0.0 43.86 3.13 F
2545 4141 1.880027 GAGGGCAAGTCGTTTGATGTT 59.120 47.619 6.60 0.0 39.21 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 4036 0.676184 TCTCGCTCAGCAACTCTTGT 59.324 50.000 0.0 0.0 0.0 3.16 R
3817 5413 1.280746 CACACCAGAAACAGCAGCG 59.719 57.895 0.0 0.0 0.0 5.18 R
4454 6056 0.439985 CGATGGTCAGAAAGTGCGTG 59.560 55.000 0.0 0.0 0.0 5.34 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
25 26 4.254492 GTCCACTCACTTGGGATAAGTTC 58.746 47.826 0.00 0.00 37.24 3.01
37 38 3.813724 GGGATAAGTTCCGGTTAAGCATC 59.186 47.826 0.00 0.00 46.52 3.91
39 40 4.272748 GGATAAGTTCCGGTTAAGCATCAC 59.727 45.833 0.00 0.00 33.93 3.06
47 48 2.852413 CGGTTAAGCATCACACTAGACG 59.148 50.000 5.38 0.00 0.00 4.18
70 71 8.672823 ACGAAAGTCTTAAAATACTTGAACCT 57.327 30.769 0.00 0.00 44.19 3.50
88 89 5.359009 TGAACCTCTCTTAATAGTACGGTGG 59.641 44.000 0.00 0.00 0.00 4.61
89 90 4.864726 ACCTCTCTTAATAGTACGGTGGT 58.135 43.478 0.00 0.00 0.00 4.16
90 91 4.643784 ACCTCTCTTAATAGTACGGTGGTG 59.356 45.833 0.00 0.00 0.00 4.17
91 92 4.037684 CCTCTCTTAATAGTACGGTGGTGG 59.962 50.000 0.00 0.00 0.00 4.61
99 100 1.188863 GTACGGTGGTGGTCCTATGT 58.811 55.000 0.00 0.00 34.23 2.29
104 105 1.207329 GGTGGTGGTCCTATGTCTCAC 59.793 57.143 0.00 0.00 34.23 3.51
105 106 1.135083 GTGGTGGTCCTATGTCTCACG 60.135 57.143 0.00 0.00 34.23 4.35
107 108 1.135083 GGTGGTCCTATGTCTCACGTG 60.135 57.143 9.94 9.94 0.00 4.49
116 117 5.869344 TCCTATGTCTCACGTGAAGAAAATG 59.131 40.000 20.49 6.03 0.00 2.32
119 120 6.808008 ATGTCTCACGTGAAGAAAATGAAT 57.192 33.333 20.49 5.43 0.00 2.57
120 121 6.228273 TGTCTCACGTGAAGAAAATGAATC 57.772 37.500 20.49 5.61 0.00 2.52
123 124 7.116376 TGTCTCACGTGAAGAAAATGAATCTAC 59.884 37.037 20.49 0.78 0.00 2.59
129 130 8.009974 ACGTGAAGAAAATGAATCTACGAAAAG 58.990 33.333 0.00 0.00 33.70 2.27
131 132 9.878599 GTGAAGAAAATGAATCTACGAAAAGAA 57.121 29.630 0.00 0.00 0.00 2.52
139 140 9.450807 AATGAATCTACGAAAAGAAAAACTGTG 57.549 29.630 0.00 0.00 0.00 3.66
140 141 7.981142 TGAATCTACGAAAAGAAAAACTGTGT 58.019 30.769 0.00 0.00 0.00 3.72
141 142 8.120465 TGAATCTACGAAAAGAAAAACTGTGTC 58.880 33.333 0.00 0.00 0.00 3.67
142 143 7.787725 ATCTACGAAAAGAAAAACTGTGTCT 57.212 32.000 0.00 0.00 0.00 3.41
144 145 7.681903 TCTACGAAAAGAAAAACTGTGTCTTC 58.318 34.615 0.00 0.00 31.26 2.87
145 146 6.249035 ACGAAAAGAAAAACTGTGTCTTCA 57.751 33.333 0.00 0.00 31.26 3.02
146 147 6.852664 ACGAAAAGAAAAACTGTGTCTTCAT 58.147 32.000 0.00 0.00 31.26 2.57
172 179 5.468072 TCTTCTTCACTGCAGTCAAAATCTC 59.532 40.000 18.64 0.00 0.00 2.75
173 180 4.067896 TCTTCACTGCAGTCAAAATCTCC 58.932 43.478 18.64 0.00 0.00 3.71
175 182 2.106338 TCACTGCAGTCAAAATCTCCCA 59.894 45.455 18.64 0.00 0.00 4.37
179 186 2.106338 TGCAGTCAAAATCTCCCAGACA 59.894 45.455 0.00 0.00 0.00 3.41
188 195 2.523168 TCCCAGACACGCACTCCA 60.523 61.111 0.00 0.00 0.00 3.86
192 199 0.179100 CCAGACACGCACTCCATAGG 60.179 60.000 0.00 0.00 0.00 2.57
197 204 3.704566 AGACACGCACTCCATAGGAATTA 59.295 43.478 0.00 0.00 0.00 1.40
206 213 6.258947 GCACTCCATAGGAATTACTTCACTTC 59.741 42.308 0.00 0.00 32.70 3.01
208 215 7.824289 CACTCCATAGGAATTACTTCACTTCAA 59.176 37.037 0.00 0.00 32.70 2.69
211 218 8.160765 TCCATAGGAATTACTTCACTTCAACAA 58.839 33.333 0.00 0.00 32.70 2.83
223 230 8.739972 ACTTCACTTCAACAACATTTTTAGAGT 58.260 29.630 0.00 0.00 0.00 3.24
224 231 9.226345 CTTCACTTCAACAACATTTTTAGAGTC 57.774 33.333 0.00 0.00 0.00 3.36
226 233 6.632834 CACTTCAACAACATTTTTAGAGTCCG 59.367 38.462 0.00 0.00 0.00 4.79
227 234 6.317893 ACTTCAACAACATTTTTAGAGTCCGT 59.682 34.615 0.00 0.00 0.00 4.69
231 238 4.995487 ACAACATTTTTAGAGTCCGTCTCC 59.005 41.667 2.01 0.00 43.71 3.71
232 239 3.846360 ACATTTTTAGAGTCCGTCTCCG 58.154 45.455 2.01 0.00 43.71 4.63
237 244 0.322648 TAGAGTCCGTCTCCGACACA 59.677 55.000 2.01 0.00 43.71 3.72
245 253 1.732732 CGTCTCCGACACACATCTTCC 60.733 57.143 0.00 0.00 35.63 3.46
246 254 1.546476 GTCTCCGACACACATCTTCCT 59.454 52.381 0.00 0.00 32.09 3.36
279 288 3.449018 TCCTCGAAGCTAGCAATCTTCTT 59.551 43.478 18.83 0.00 37.22 2.52
281 290 4.033817 CCTCGAAGCTAGCAATCTTCTTTG 59.966 45.833 18.83 4.55 37.22 2.77
282 291 4.569943 TCGAAGCTAGCAATCTTCTTTGT 58.430 39.130 18.83 0.00 37.22 2.83
300 309 2.766313 TGTTGCGCAGATAACACTCTT 58.234 42.857 11.31 0.00 32.76 2.85
327 336 5.801380 AGTTTATAGCAAACTTCTCCGGAA 58.199 37.500 5.23 0.00 37.18 4.30
331 340 5.819825 ATAGCAAACTTCTCCGGAAATTC 57.180 39.130 5.23 0.00 0.00 2.17
334 343 5.313712 AGCAAACTTCTCCGGAAATTCTAA 58.686 37.500 5.23 0.00 0.00 2.10
346 355 5.006746 CCGGAAATTCTAACAATCTTCTCCG 59.993 44.000 0.00 0.00 41.29 4.63
355 364 2.234908 ACAATCTTCTCCGAACTCCAGG 59.765 50.000 0.00 0.00 0.00 4.45
356 365 2.497675 CAATCTTCTCCGAACTCCAGGA 59.502 50.000 0.00 0.00 34.93 3.86
359 368 0.601558 TTCTCCGAACTCCAGGAACG 59.398 55.000 0.00 0.00 35.90 3.95
360 369 1.215647 CTCCGAACTCCAGGAACGG 59.784 63.158 18.10 18.10 44.09 4.44
362 371 1.080025 CCGAACTCCAGGAACGGTC 60.080 63.158 16.69 0.00 38.97 4.79
368 377 0.814457 CTCCAGGAACGGTCTCTCTG 59.186 60.000 0.00 0.00 0.00 3.35
372 381 1.068194 CAGGAACGGTCTCTCTGTGTC 60.068 57.143 0.00 0.00 35.59 3.67
380 389 2.558795 GGTCTCTCTGTGTCTGCACTAA 59.441 50.000 0.00 0.00 45.44 2.24
392 401 6.136071 GTGTCTGCACTAACAAACACATTAG 58.864 40.000 0.00 0.00 42.13 1.73
393 402 5.820423 TGTCTGCACTAACAAACACATTAGT 59.180 36.000 0.00 0.00 41.31 2.24
395 404 5.468746 TCTGCACTAACAAACACATTAGTCC 59.531 40.000 0.00 0.00 39.15 3.85
420 429 6.314896 CCTCACTATTTCTGTCCAACAATCTC 59.685 42.308 0.00 0.00 0.00 2.75
445 454 0.745845 CCTTCAGGGGCACTCGATTG 60.746 60.000 0.00 0.00 0.00 2.67
448 457 2.110967 CAGGGGCACTCGATTGCAG 61.111 63.158 26.37 11.17 44.94 4.41
455 464 0.587768 CACTCGATTGCAGCAACACA 59.412 50.000 10.85 0.00 0.00 3.72
458 467 0.307453 TCGATTGCAGCAACACACAC 59.693 50.000 10.85 0.00 0.00 3.82
478 487 1.371337 CTATGGACCGACGGACACGA 61.371 60.000 23.38 9.10 44.60 4.35
479 488 0.749091 TATGGACCGACGGACACGAT 60.749 55.000 23.38 15.24 44.60 3.73
542 552 2.039418 ACTAGACACACTGTGCTTCCA 58.961 47.619 9.20 0.00 36.98 3.53
553 563 1.962807 TGTGCTTCCATTTGAGTTGGG 59.037 47.619 0.00 0.00 34.85 4.12
557 567 0.178975 TTCCATTTGAGTTGGGCCGT 60.179 50.000 0.00 0.00 34.85 5.68
573 583 0.036306 CCGTTGGAGTTGCCCTTAGT 59.964 55.000 0.00 0.00 34.97 2.24
589 599 5.010213 GCCCTTAGTGTGGTGATTGTTAAAA 59.990 40.000 0.00 0.00 0.00 1.52
613 623 3.127203 ACTCTGGTAGATCGACGTTCTTG 59.873 47.826 13.30 3.53 0.00 3.02
631 641 3.440173 TCTTGACATTTCCGCATTTCTCC 59.560 43.478 0.00 0.00 0.00 3.71
637 647 1.305219 TTCCGCATTTCTCCGCCTTG 61.305 55.000 0.00 0.00 0.00 3.61
639 649 2.764314 CGCATTTCTCCGCCTTGGG 61.764 63.158 0.00 0.00 38.76 4.12
645 655 2.413310 TTCTCCGCCTTGGGTATTTC 57.587 50.000 0.00 0.00 38.76 2.17
647 657 1.436983 CTCCGCCTTGGGTATTTCGC 61.437 60.000 0.00 0.00 38.76 4.70
681 691 4.142687 CCGTTAGATTCGTTGCCATTCTTT 60.143 41.667 0.00 0.00 0.00 2.52
714 725 3.391296 GTGGCCACTAAATATCTGGGAGA 59.609 47.826 29.12 0.00 0.00 3.71
716 727 5.248477 GTGGCCACTAAATATCTGGGAGATA 59.752 44.000 29.12 0.00 41.06 1.98
777 788 4.753610 GCATGAGCTAAGAATGTGAGCATA 59.246 41.667 0.00 0.00 38.73 3.14
817 2222 5.252547 TGCATAGCATGGTTTTCTAGTGAA 58.747 37.500 1.12 0.00 31.71 3.18
1783 3379 2.053865 CCCCGTCTACAACCGCCTA 61.054 63.158 0.00 0.00 0.00 3.93
1831 3427 0.671472 TCGACCTCGTTGAGTCGCTA 60.671 55.000 7.63 0.00 40.80 4.26
2139 3735 4.404098 GGTGGAACGGATGCGGGT 62.404 66.667 12.44 0.00 38.12 5.28
2185 3781 1.303309 CGTTCAATGGCAGGATCTCC 58.697 55.000 0.00 0.00 0.00 3.71
2380 3976 0.476771 GTGGTGGGTTCCTGAGGAAA 59.523 55.000 16.79 0.00 43.86 3.13
2440 4036 2.088104 ATGGTAAGATCGGAGAGGCA 57.912 50.000 0.00 0.00 43.63 4.75
2545 4141 1.880027 GAGGGCAAGTCGTTTGATGTT 59.120 47.619 6.60 0.00 39.21 2.71
2640 4236 3.378427 GCTTATTGCTCGAAGGGAAACAT 59.622 43.478 0.00 0.00 38.95 2.71
2937 4533 6.114767 TGGGTAGTTCGTTTTCAAGTTTAGT 58.885 36.000 0.00 0.00 0.00 2.24
2949 4545 9.439537 GTTTTCAAGTTTAGTGAGTGATTCTTC 57.560 33.333 0.00 0.00 0.00 2.87
3028 4624 2.814336 GTGCAAAGAAGGAAGGTTCGAT 59.186 45.455 0.00 0.00 0.00 3.59
3085 4681 7.914346 GCAAAAGATATTTCTCCTGATTCAGTG 59.086 37.037 12.54 5.44 0.00 3.66
3151 4747 5.574188 ACATCTTCAGCCATTAAGGTTCTT 58.426 37.500 0.00 0.00 40.61 2.52
3235 4831 6.279882 GGGATTTCAAGAAAAACACATGTCA 58.720 36.000 0.00 0.00 33.56 3.58
3521 5117 4.264253 AGTGCTCTATTGCTTAATGTGCA 58.736 39.130 0.00 0.00 38.80 4.57
3626 5222 7.083062 AGTTTCCCATATAAGCAGATCATCA 57.917 36.000 0.00 0.00 0.00 3.07
3642 5238 3.285215 CATGGGGCTCTGCGATGC 61.285 66.667 0.00 0.00 0.00 3.91
3695 5291 8.773404 TCTCAAGTTGTTTATAGCTAAAGGAC 57.227 34.615 0.00 0.00 0.00 3.85
3715 5311 2.424601 ACATTCATTTGATCCAGCCACG 59.575 45.455 0.00 0.00 0.00 4.94
3817 5413 2.423538 GGCAGATGGTAATGTTGGTCAC 59.576 50.000 0.00 0.00 0.00 3.67
3943 5539 8.603242 ATCAAGTTTCTCGTTATGTGTTTACT 57.397 30.769 0.00 0.00 0.00 2.24
3985 5581 4.842531 TTGGATGCAAGGATTCTGTAGA 57.157 40.909 0.00 0.00 0.00 2.59
4033 5633 9.640952 ATTTAGTACAATAACCAAGGCATATGT 57.359 29.630 4.29 0.00 0.00 2.29
4035 5635 9.550406 TTAGTACAATAACCAAGGCATATGTAC 57.450 33.333 4.29 13.50 0.00 2.90
4036 5636 6.996282 AGTACAATAACCAAGGCATATGTACC 59.004 38.462 15.91 0.00 31.67 3.34
4037 5637 5.761205 ACAATAACCAAGGCATATGTACCA 58.239 37.500 4.29 0.00 0.00 3.25
4038 5638 6.191315 ACAATAACCAAGGCATATGTACCAA 58.809 36.000 4.29 0.00 0.00 3.67
4039 5639 6.321181 ACAATAACCAAGGCATATGTACCAAG 59.679 38.462 4.29 0.00 0.00 3.61
4040 5640 3.297134 ACCAAGGCATATGTACCAAGG 57.703 47.619 4.29 6.58 0.00 3.61
4071 5673 9.995003 TTGTTTAAAGAGTTTATTTGGATGCAT 57.005 25.926 0.00 0.00 0.00 3.96
4078 5680 5.410067 AGTTTATTTGGATGCATGGTTTCG 58.590 37.500 2.46 0.00 0.00 3.46
4105 5707 9.444600 TCTTACAAGAAACACAAACTAACTCTT 57.555 29.630 0.00 0.00 30.73 2.85
4166 5768 7.088905 GCAATGACTCTGACTTCATTTTTGAT 58.911 34.615 6.91 0.00 39.86 2.57
4287 5889 6.709397 AGCAGGATGATGACATTTATGTACTG 59.291 38.462 0.00 0.00 39.09 2.74
4323 5925 5.441500 TGAGTAAGTCTCTCATCACCCTAG 58.558 45.833 0.00 0.00 43.13 3.02
4391 5993 7.269316 TGTGACTACAAACTCACATGTTTAGA 58.731 34.615 11.13 0.00 41.46 2.10
4392 5994 7.766738 TGTGACTACAAACTCACATGTTTAGAA 59.233 33.333 11.13 0.00 41.46 2.10
4393 5995 8.609176 GTGACTACAAACTCACATGTTTAGAAA 58.391 33.333 11.13 0.00 37.98 2.52
4395 5997 7.639945 ACTACAAACTCACATGTTTAGAAAGC 58.360 34.615 11.13 0.00 37.98 3.51
4396 5998 6.699575 ACAAACTCACATGTTTAGAAAGCT 57.300 33.333 11.13 0.00 37.98 3.74
4397 5999 7.100458 ACAAACTCACATGTTTAGAAAGCTT 57.900 32.000 11.13 0.00 37.98 3.74
4398 6000 7.547227 ACAAACTCACATGTTTAGAAAGCTTT 58.453 30.769 12.53 12.53 37.98 3.51
4399 6001 8.682710 ACAAACTCACATGTTTAGAAAGCTTTA 58.317 29.630 12.68 0.00 37.98 1.85
4400 6002 9.515020 CAAACTCACATGTTTAGAAAGCTTTAA 57.485 29.630 12.68 0.35 37.98 1.52
4404 6006 9.994432 CTCACATGTTTAGAAAGCTTTAATAGG 57.006 33.333 12.68 5.91 0.00 2.57
4405 6007 9.515226 TCACATGTTTAGAAAGCTTTAATAGGT 57.485 29.630 12.68 6.55 35.72 3.08
4429 6031 5.132502 TGTGTTGATTTCTCACCACTCAAT 58.867 37.500 5.16 0.00 43.22 2.57
4451 6053 3.659786 TCTGTTTGACCGTTCTACCATG 58.340 45.455 0.00 0.00 0.00 3.66
4452 6054 2.147958 TGTTTGACCGTTCTACCATGC 58.852 47.619 0.00 0.00 0.00 4.06
4453 6055 2.224426 TGTTTGACCGTTCTACCATGCT 60.224 45.455 0.00 0.00 0.00 3.79
4454 6056 2.380084 TTGACCGTTCTACCATGCTC 57.620 50.000 0.00 0.00 0.00 4.26
4471 6074 1.800805 CTCACGCACTTTCTGACCAT 58.199 50.000 0.00 0.00 0.00 3.55
4476 6079 1.403647 CGCACTTTCTGACCATCGGTA 60.404 52.381 0.00 0.00 35.25 4.02
4489 6094 7.827236 TCTGACCATCGGTATAACTGAAAATTT 59.173 33.333 0.00 0.00 37.01 1.82
4517 6122 9.832445 AATCTAGAAGAAAATAAATAGCCACGA 57.168 29.630 0.00 0.00 0.00 4.35
4519 6124 9.832445 TCTAGAAGAAAATAAATAGCCACGATT 57.168 29.630 0.00 0.00 0.00 3.34
4544 6149 2.322355 AGAGAGACCCATTTGCATCG 57.678 50.000 0.00 0.00 0.00 3.84
4545 6150 0.659957 GAGAGACCCATTTGCATCGC 59.340 55.000 0.00 0.00 0.00 4.58
4546 6151 0.749454 AGAGACCCATTTGCATCGCC 60.749 55.000 0.00 0.00 0.00 5.54
4547 6152 1.728490 GAGACCCATTTGCATCGCCC 61.728 60.000 0.00 0.00 0.00 6.13
4548 6153 2.759560 ACCCATTTGCATCGCCCC 60.760 61.111 0.00 0.00 0.00 5.80
4549 6154 3.903282 CCCATTTGCATCGCCCCG 61.903 66.667 0.00 0.00 0.00 5.73
4574 6179 1.751927 CCTTGCCTGCCATCACCTC 60.752 63.158 0.00 0.00 0.00 3.85
4580 6185 1.153208 CTGCCATCACCTCTGCCTC 60.153 63.158 0.00 0.00 0.00 4.70
4621 6226 4.200283 CACCGCGGCCTCTCTCTC 62.200 72.222 28.58 0.00 0.00 3.20
4622 6227 4.434354 ACCGCGGCCTCTCTCTCT 62.434 66.667 28.58 0.00 0.00 3.10
4628 6233 1.152963 GGCCTCTCTCTCTCTCGCT 60.153 63.158 0.00 0.00 0.00 4.93
4686 6291 1.172180 GCTTGCTGTTGCTGGGTGTA 61.172 55.000 0.00 0.00 40.48 2.90
4692 6297 3.246112 TTGCTGGGTGTACCGCCT 61.246 61.111 3.96 0.00 44.64 5.52
4702 6307 1.215647 GTACCGCCTCTGGTGAGTG 59.784 63.158 0.00 0.00 43.68 3.51
4703 6308 2.646175 TACCGCCTCTGGTGAGTGC 61.646 63.158 0.00 0.00 43.68 4.40
4708 6313 1.676678 GCCTCTGGTGAGTGCCGATA 61.677 60.000 0.00 0.00 38.61 2.92
4713 6318 1.000283 CTGGTGAGTGCCGATATCTCC 60.000 57.143 0.34 0.00 0.00 3.71
4714 6319 0.318762 GGTGAGTGCCGATATCTCCC 59.681 60.000 0.34 0.00 0.00 4.30
4715 6320 1.333177 GTGAGTGCCGATATCTCCCT 58.667 55.000 0.34 0.00 0.00 4.20
4716 6321 1.271102 GTGAGTGCCGATATCTCCCTC 59.729 57.143 0.34 2.07 0.00 4.30
4717 6322 0.892063 GAGTGCCGATATCTCCCTCC 59.108 60.000 0.34 0.00 0.00 4.30
4729 6334 6.094881 CGATATCTCCCTCCTCTCTTTGTATC 59.905 46.154 0.34 0.00 0.00 2.24
4731 6336 5.149584 TCTCCCTCCTCTCTTTGTATCAT 57.850 43.478 0.00 0.00 0.00 2.45
4736 6341 4.657969 CCTCCTCTCTTTGTATCATCCCTT 59.342 45.833 0.00 0.00 0.00 3.95
4740 6345 5.102953 TCTCTTTGTATCATCCCTTGTGG 57.897 43.478 0.00 0.00 0.00 4.17
4786 6741 8.771920 CAAATTTGGATGAATGGATATGGATG 57.228 34.615 10.49 0.00 0.00 3.51
4858 6813 8.807948 ATGCCATTACAACTTTACAATACTCT 57.192 30.769 0.00 0.00 0.00 3.24
4859 6814 9.899661 ATGCCATTACAACTTTACAATACTCTA 57.100 29.630 0.00 0.00 0.00 2.43
4871 6826 9.888878 CTTTACAATACTCTAAATGCCATCATG 57.111 33.333 0.00 0.00 32.23 3.07
4875 6830 7.663081 ACAATACTCTAAATGCCATCATGTAGG 59.337 37.037 0.00 0.00 39.78 3.18
4919 6874 4.770010 TGTCTTCTTCCTTCTCTTCTCCTC 59.230 45.833 0.00 0.00 0.00 3.71
4934 6889 2.041405 CTCCCTCCCTCCCTCACC 60.041 72.222 0.00 0.00 0.00 4.02
4935 6890 2.540910 TCCCTCCCTCCCTCACCT 60.541 66.667 0.00 0.00 0.00 4.00
4936 6891 2.041405 CCCTCCCTCCCTCACCTC 60.041 72.222 0.00 0.00 0.00 3.85
4937 6892 2.780693 CCTCCCTCCCTCACCTCA 59.219 66.667 0.00 0.00 0.00 3.86
4938 6893 1.687493 CCTCCCTCCCTCACCTCAC 60.687 68.421 0.00 0.00 0.00 3.51
4941 6896 1.079256 CCCTCCCTCACCTCACTCA 59.921 63.158 0.00 0.00 0.00 3.41
5033 6989 4.393155 CCTGCCGCTGGTGCTGTA 62.393 66.667 8.11 0.00 36.97 2.74
5056 7012 5.026121 ACTCATGTTGTCCATCTTCCTCTA 58.974 41.667 0.00 0.00 0.00 2.43
5169 7125 1.983691 CCTCCTATGACTGCCATGGAT 59.016 52.381 18.40 1.38 35.98 3.41
5170 7126 2.290134 CCTCCTATGACTGCCATGGATG 60.290 54.545 18.40 9.52 35.98 3.51
5207 7163 0.447801 CTCCATTTTGAAGACCGCCG 59.552 55.000 0.00 0.00 0.00 6.46
5250 7206 2.517919 GAGATGGGGTCCATGGCC 59.482 66.667 6.96 11.82 45.26 5.36
5295 7252 4.202503 GCTCCATCTCAATATTCCCCTCAA 60.203 45.833 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.030027 ATCCCAAGTGAGTGGACAGA 57.970 50.000 0.00 0.00 41.65 3.41
1 2 3.261897 ACTTATCCCAAGTGAGTGGACAG 59.738 47.826 0.00 0.00 41.65 3.51
2 3 3.248024 ACTTATCCCAAGTGAGTGGACA 58.752 45.455 0.00 0.00 41.65 4.02
3 4 3.983044 ACTTATCCCAAGTGAGTGGAC 57.017 47.619 0.00 0.00 41.65 4.02
4 5 3.263425 GGAACTTATCCCAAGTGAGTGGA 59.737 47.826 0.00 0.00 43.00 4.02
5 6 3.610911 GGAACTTATCCCAAGTGAGTGG 58.389 50.000 0.00 0.00 43.00 4.00
11 12 4.840271 CTTAACCGGAACTTATCCCAAGT 58.160 43.478 9.46 0.00 46.39 3.16
25 26 3.187700 GTCTAGTGTGATGCTTAACCGG 58.812 50.000 0.00 0.00 0.00 5.28
62 63 6.973474 CACCGTACTATTAAGAGAGGTTCAAG 59.027 42.308 3.65 0.00 0.00 3.02
70 71 4.603131 ACCACCACCGTACTATTAAGAGA 58.397 43.478 3.65 0.00 0.00 3.10
83 84 0.460311 GAGACATAGGACCACCACCG 59.540 60.000 0.00 0.00 38.94 4.94
88 89 1.816835 TCACGTGAGACATAGGACCAC 59.183 52.381 15.76 0.00 0.00 4.16
89 90 2.209690 TCACGTGAGACATAGGACCA 57.790 50.000 15.76 0.00 0.00 4.02
90 91 2.753452 TCTTCACGTGAGACATAGGACC 59.247 50.000 19.11 0.00 0.00 4.46
91 92 4.436242 TTCTTCACGTGAGACATAGGAC 57.564 45.455 19.11 0.00 0.00 3.85
99 100 6.308041 CGTAGATTCATTTTCTTCACGTGAGA 59.692 38.462 19.11 14.94 0.00 3.27
104 105 8.221100 TCTTTTCGTAGATTCATTTTCTTCACG 58.779 33.333 0.00 0.00 35.04 4.35
105 106 9.878599 TTCTTTTCGTAGATTCATTTTCTTCAC 57.121 29.630 0.00 0.00 35.04 3.18
116 117 8.336080 AGACACAGTTTTTCTTTTCGTAGATTC 58.664 33.333 0.00 0.00 35.04 2.52
119 120 7.332430 TGAAGACACAGTTTTTCTTTTCGTAGA 59.668 33.333 0.00 0.00 29.54 2.59
120 121 7.461107 TGAAGACACAGTTTTTCTTTTCGTAG 58.539 34.615 0.00 0.00 29.54 3.51
123 124 7.740519 AATGAAGACACAGTTTTTCTTTTCG 57.259 32.000 0.00 0.00 29.54 3.46
129 130 8.917415 AAGAAGAAATGAAGACACAGTTTTTC 57.083 30.769 0.00 0.00 38.38 2.29
131 132 7.970614 GTGAAGAAGAAATGAAGACACAGTTTT 59.029 33.333 0.00 0.00 0.00 2.43
132 133 7.337942 AGTGAAGAAGAAATGAAGACACAGTTT 59.662 33.333 0.00 0.00 0.00 2.66
134 135 6.259608 CAGTGAAGAAGAAATGAAGACACAGT 59.740 38.462 0.00 0.00 0.00 3.55
135 136 6.656945 CAGTGAAGAAGAAATGAAGACACAG 58.343 40.000 0.00 0.00 0.00 3.66
137 138 5.008019 TGCAGTGAAGAAGAAATGAAGACAC 59.992 40.000 0.00 0.00 0.00 3.67
139 140 5.238214 ACTGCAGTGAAGAAGAAATGAAGAC 59.762 40.000 20.97 0.00 0.00 3.01
140 141 5.371526 ACTGCAGTGAAGAAGAAATGAAGA 58.628 37.500 20.97 0.00 0.00 2.87
141 142 5.237996 TGACTGCAGTGAAGAAGAAATGAAG 59.762 40.000 27.27 0.00 0.00 3.02
142 143 5.125356 TGACTGCAGTGAAGAAGAAATGAA 58.875 37.500 27.27 0.00 0.00 2.57
144 145 5.428496 TTGACTGCAGTGAAGAAGAAATG 57.572 39.130 27.27 0.00 0.00 2.32
145 146 6.455360 TTTTGACTGCAGTGAAGAAGAAAT 57.545 33.333 27.27 0.00 0.00 2.17
146 147 5.895636 TTTTGACTGCAGTGAAGAAGAAA 57.104 34.783 27.27 10.12 0.00 2.52
172 179 0.179100 CTATGGAGTGCGTGTCTGGG 60.179 60.000 0.00 0.00 0.00 4.45
173 180 0.179100 CCTATGGAGTGCGTGTCTGG 60.179 60.000 0.00 0.00 0.00 3.86
175 182 1.557099 TTCCTATGGAGTGCGTGTCT 58.443 50.000 0.00 0.00 31.21 3.41
179 186 4.161565 TGAAGTAATTCCTATGGAGTGCGT 59.838 41.667 0.00 0.00 31.21 5.24
188 195 8.918202 TGTTGTTGAAGTGAAGTAATTCCTAT 57.082 30.769 0.00 0.00 32.58 2.57
197 204 8.739972 ACTCTAAAAATGTTGTTGAAGTGAAGT 58.260 29.630 0.00 0.00 0.00 3.01
206 213 6.300354 AGACGGACTCTAAAAATGTTGTTG 57.700 37.500 0.00 0.00 0.00 3.33
208 215 4.995487 GGAGACGGACTCTAAAAATGTTGT 59.005 41.667 7.38 0.00 44.37 3.32
227 234 1.546029 CAGGAAGATGTGTGTCGGAGA 59.454 52.381 0.00 0.00 0.00 3.71
231 238 2.881074 CTACCAGGAAGATGTGTGTCG 58.119 52.381 0.00 0.00 0.00 4.35
232 239 2.028112 TGCTACCAGGAAGATGTGTGTC 60.028 50.000 0.00 0.00 0.00 3.67
237 244 3.307762 GGAGTTTGCTACCAGGAAGATGT 60.308 47.826 0.00 0.00 0.00 3.06
245 253 2.611518 CTTCGAGGAGTTTGCTACCAG 58.388 52.381 0.00 0.00 0.00 4.00
246 254 1.337823 GCTTCGAGGAGTTTGCTACCA 60.338 52.381 0.00 0.00 0.00 3.25
279 288 2.766313 AGAGTGTTATCTGCGCAACAA 58.234 42.857 13.05 2.32 36.47 2.83
281 290 4.174009 TCTAAGAGTGTTATCTGCGCAAC 58.826 43.478 13.05 7.37 0.00 4.17
282 291 4.450082 TCTAAGAGTGTTATCTGCGCAA 57.550 40.909 13.05 2.72 0.00 4.85
312 321 5.048991 TGTTAGAATTTCCGGAGAAGTTTGC 60.049 40.000 3.34 0.00 32.57 3.68
322 331 5.006746 CGGAGAAGATTGTTAGAATTTCCGG 59.993 44.000 0.00 0.00 39.94 5.14
324 333 7.334671 AGTTCGGAGAAGATTGTTAGAATTTCC 59.665 37.037 0.00 0.00 45.90 3.13
325 334 8.257830 AGTTCGGAGAAGATTGTTAGAATTTC 57.742 34.615 0.00 0.00 45.90 2.17
327 336 6.819146 GGAGTTCGGAGAAGATTGTTAGAATT 59.181 38.462 0.00 0.00 45.90 2.17
331 340 5.073311 TGGAGTTCGGAGAAGATTGTTAG 57.927 43.478 0.00 0.00 45.90 2.34
334 343 2.234908 CCTGGAGTTCGGAGAAGATTGT 59.765 50.000 0.00 0.00 45.90 2.71
346 355 1.202817 GAGAGACCGTTCCTGGAGTTC 59.797 57.143 0.00 0.00 0.00 3.01
355 364 1.667467 GCAGACACAGAGAGACCGTTC 60.667 57.143 0.00 0.00 0.00 3.95
356 365 0.315568 GCAGACACAGAGAGACCGTT 59.684 55.000 0.00 0.00 0.00 4.44
359 368 3.505808 GTGCAGACACAGAGAGACC 57.494 57.895 0.00 0.00 46.61 3.85
372 381 5.334879 GGGACTAATGTGTTTGTTAGTGCAG 60.335 44.000 15.32 0.00 45.43 4.41
380 389 4.706842 AGTGAGGGACTAATGTGTTTGT 57.293 40.909 0.00 0.00 41.55 2.83
392 401 4.254492 GTTGGACAGAAATAGTGAGGGAC 58.746 47.826 0.00 0.00 0.00 4.46
393 402 3.907474 TGTTGGACAGAAATAGTGAGGGA 59.093 43.478 0.00 0.00 0.00 4.20
395 404 6.176183 AGATTGTTGGACAGAAATAGTGAGG 58.824 40.000 0.00 0.00 0.00 3.86
420 429 0.469892 AGTGCCCCTGAAGGTTTTGG 60.470 55.000 0.00 0.00 0.00 3.28
445 454 0.523072 CCATAGGTGTGTGTTGCTGC 59.477 55.000 0.00 0.00 0.00 5.25
448 457 1.165270 GGTCCATAGGTGTGTGTTGC 58.835 55.000 0.00 0.00 0.00 4.17
455 464 1.000521 TCCGTCGGTCCATAGGTGT 60.001 57.895 11.88 0.00 0.00 4.16
458 467 1.436336 GTGTCCGTCGGTCCATAGG 59.564 63.158 11.88 0.00 0.00 2.57
523 533 2.820059 TGGAAGCACAGTGTGTCTAG 57.180 50.000 23.73 0.00 35.75 2.43
524 534 3.769739 AATGGAAGCACAGTGTGTCTA 57.230 42.857 23.73 12.97 35.75 2.59
526 536 2.618241 TCAAATGGAAGCACAGTGTGTC 59.382 45.455 23.73 14.29 35.75 3.67
532 542 2.029649 CCCAACTCAAATGGAAGCACAG 60.030 50.000 0.00 0.00 40.56 3.66
537 547 0.527565 CGGCCCAACTCAAATGGAAG 59.472 55.000 0.00 0.00 40.56 3.46
538 548 0.178975 ACGGCCCAACTCAAATGGAA 60.179 50.000 0.00 0.00 40.56 3.53
542 552 0.178975 TCCAACGGCCCAACTCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
553 563 1.302993 TAAGGGCAACTCCAACGGC 60.303 57.895 0.00 0.00 36.21 5.68
557 567 1.202879 CCACACTAAGGGCAACTCCAA 60.203 52.381 0.00 0.00 36.21 3.53
589 599 3.757493 AGAACGTCGATCTACCAGAGTTT 59.243 43.478 2.81 0.00 0.00 2.66
594 604 3.119955 TGTCAAGAACGTCGATCTACCAG 60.120 47.826 5.37 0.00 0.00 4.00
595 605 2.815503 TGTCAAGAACGTCGATCTACCA 59.184 45.455 5.37 0.76 0.00 3.25
605 615 1.588674 TGCGGAAATGTCAAGAACGT 58.411 45.000 0.00 0.00 0.00 3.99
613 623 1.531883 GCGGAGAAATGCGGAAATGTC 60.532 52.381 0.00 0.00 0.00 3.06
631 641 1.309499 TTGGCGAAATACCCAAGGCG 61.309 55.000 0.00 0.00 36.25 5.52
660 670 8.736751 TTTTAAAGAATGGCAACGAATCTAAC 57.263 30.769 0.00 0.00 42.51 2.34
687 697 6.102615 TCCCAGATATTTAGTGGCCACTATTT 59.897 38.462 39.32 30.70 42.83 1.40
690 700 4.562767 TCCCAGATATTTAGTGGCCACTA 58.437 43.478 36.63 36.63 42.54 2.74
691 701 3.392616 CTCCCAGATATTTAGTGGCCACT 59.607 47.826 38.92 38.92 45.02 4.00
693 703 3.664320 TCTCCCAGATATTTAGTGGCCA 58.336 45.455 0.00 0.00 0.00 5.36
707 718 9.807649 CAAATTACAAAGGAAATTATCTCCCAG 57.192 33.333 0.00 0.00 32.95 4.45
716 727 8.922931 AATTCTGCCAAATTACAAAGGAAATT 57.077 26.923 0.00 0.00 0.00 1.82
777 788 6.434965 TGCTATGCATATTCTACAATTGCCAT 59.565 34.615 6.92 0.00 31.71 4.40
817 2222 4.502259 GCCAAATCATCCTAGATCGTGAGT 60.502 45.833 0.00 0.00 0.00 3.41
1595 3191 3.535962 GAGGAGGCGCTGGAGGAG 61.536 72.222 7.64 0.00 0.00 3.69
1614 3210 2.447714 GGGAGGGAGAGGATGTGGC 61.448 68.421 0.00 0.00 0.00 5.01
1822 3418 3.821600 GGAGATCCTTGTATAGCGACTCA 59.178 47.826 0.00 0.00 0.00 3.41
2380 3976 1.068472 CAGCGGTTGTAACTCTCGACT 60.068 52.381 0.00 0.00 0.00 4.18
2440 4036 0.676184 TCTCGCTCAGCAACTCTTGT 59.324 50.000 0.00 0.00 0.00 3.16
2545 4141 4.425772 TCACAAAATCCTCCACTCTCCTA 58.574 43.478 0.00 0.00 0.00 2.94
2640 4236 0.955428 GATCCTGTTGGCAGCGACAA 60.955 55.000 0.00 0.00 41.26 3.18
2977 4573 7.272084 GCATTCATCAAAGTTGTGTAAGTGATC 59.728 37.037 0.00 0.00 0.00 2.92
3028 4624 6.481976 TCTCAAGTAATCGTTTCTTTGCTTCA 59.518 34.615 0.00 0.00 0.00 3.02
3151 4747 7.287061 TGAAACCTTTCTTTTCCATGTCTCTA 58.713 34.615 0.00 0.00 38.02 2.43
3235 4831 7.832685 TCACTCATCAATTCAAGGATTTCATCT 59.167 33.333 0.00 0.00 0.00 2.90
3460 5056 7.744087 TGTACTCAAAGCAACATCAAATACT 57.256 32.000 0.00 0.00 0.00 2.12
3521 5117 2.180276 AGCATAAGTGGAGAGTTCGGT 58.820 47.619 0.00 0.00 0.00 4.69
3626 5222 3.472943 GAGCATCGCAGAGCCCCAT 62.473 63.158 0.00 0.00 43.63 4.00
3642 5238 1.739562 GCTTGGTCTGCCTCACGAG 60.740 63.158 0.00 0.00 35.27 4.18
3695 5291 2.424601 ACGTGGCTGGATCAAATGAATG 59.575 45.455 0.00 0.00 0.00 2.67
3715 5311 3.003068 GTGCATCTATGACAGGCATGAAC 59.997 47.826 4.84 0.00 37.87 3.18
3817 5413 1.280746 CACACCAGAAACAGCAGCG 59.719 57.895 0.00 0.00 0.00 5.18
3882 5478 2.037144 GCAGAAGGGAATGCCAATCAT 58.963 47.619 0.00 0.00 36.41 2.45
4029 5629 9.688091 TCTTTAAACAATATGCCTTGGTACATA 57.312 29.630 0.00 0.00 39.30 2.29
4030 5630 8.588290 TCTTTAAACAATATGCCTTGGTACAT 57.412 30.769 0.00 0.00 39.30 2.29
4031 5631 7.668052 ACTCTTTAAACAATATGCCTTGGTACA 59.332 33.333 0.00 0.00 0.00 2.90
4032 5632 8.051901 ACTCTTTAAACAATATGCCTTGGTAC 57.948 34.615 0.00 0.00 0.00 3.34
4033 5633 8.644374 AACTCTTTAAACAATATGCCTTGGTA 57.356 30.769 0.00 0.00 0.00 3.25
4034 5634 7.539034 AACTCTTTAAACAATATGCCTTGGT 57.461 32.000 0.00 0.00 0.00 3.67
4071 5673 4.936411 TGTGTTTCTTGTAAGACGAAACCA 59.064 37.500 10.48 6.48 43.45 3.67
4078 5680 8.880750 AGAGTTAGTTTGTGTTTCTTGTAAGAC 58.119 33.333 0.00 0.00 34.13 3.01
4115 5717 5.527582 GCTCAACAGAGAAAGTGACCTTTAA 59.472 40.000 0.00 0.00 40.98 1.52
4121 5723 2.222911 GCAGCTCAACAGAGAAAGTGAC 59.777 50.000 0.00 0.00 0.00 3.67
4166 5768 2.223665 CGAGCACTGTCATCTCTGCATA 60.224 50.000 0.00 0.00 31.71 3.14
4287 5889 2.300437 ACTTACTCAGCCACTGTTCTCC 59.700 50.000 0.00 0.00 32.61 3.71
4323 5925 7.168219 TCCATACATGTCATTATTTAGGGCTC 58.832 38.462 0.00 0.00 0.00 4.70
4391 5993 9.476202 GAAATCAACACAACCTATTAAAGCTTT 57.524 29.630 17.30 17.30 0.00 3.51
4392 5994 8.860088 AGAAATCAACACAACCTATTAAAGCTT 58.140 29.630 0.00 0.00 0.00 3.74
4393 5995 8.409358 AGAAATCAACACAACCTATTAAAGCT 57.591 30.769 0.00 0.00 0.00 3.74
4395 5997 9.612620 GTGAGAAATCAACACAACCTATTAAAG 57.387 33.333 0.00 0.00 35.06 1.85
4396 5998 8.573035 GGTGAGAAATCAACACAACCTATTAAA 58.427 33.333 0.00 0.00 36.42 1.52
4397 5999 7.721842 TGGTGAGAAATCAACACAACCTATTAA 59.278 33.333 0.00 0.00 36.42 1.40
4398 6000 7.227873 TGGTGAGAAATCAACACAACCTATTA 58.772 34.615 0.00 0.00 36.42 0.98
4399 6001 6.068010 TGGTGAGAAATCAACACAACCTATT 58.932 36.000 0.00 0.00 36.42 1.73
4400 6002 5.630121 TGGTGAGAAATCAACACAACCTAT 58.370 37.500 0.00 0.00 36.42 2.57
4401 6003 5.042463 TGGTGAGAAATCAACACAACCTA 57.958 39.130 0.00 0.00 36.42 3.08
4402 6004 3.897239 TGGTGAGAAATCAACACAACCT 58.103 40.909 0.00 0.00 36.42 3.50
4408 6010 6.016860 CAGAATTGAGTGGTGAGAAATCAACA 60.017 38.462 0.00 0.00 34.56 3.33
4409 6011 6.016777 ACAGAATTGAGTGGTGAGAAATCAAC 60.017 38.462 0.00 0.00 33.09 3.18
4429 6031 3.823281 TGGTAGAACGGTCAAACAGAA 57.177 42.857 1.87 0.00 0.00 3.02
4452 6054 1.728971 GATGGTCAGAAAGTGCGTGAG 59.271 52.381 0.00 0.00 0.00 3.51
4453 6055 1.795768 GATGGTCAGAAAGTGCGTGA 58.204 50.000 0.00 0.00 0.00 4.35
4454 6056 0.439985 CGATGGTCAGAAAGTGCGTG 59.560 55.000 0.00 0.00 0.00 5.34
4459 6062 5.421056 TCAGTTATACCGATGGTCAGAAAGT 59.579 40.000 0.00 0.00 37.09 2.66
4517 6122 9.678260 GATGCAAATGGGTCTCTCTATATAAAT 57.322 33.333 0.00 0.00 0.00 1.40
4519 6124 7.323420 CGATGCAAATGGGTCTCTCTATATAA 58.677 38.462 0.00 0.00 0.00 0.98
4527 6132 0.749454 GGCGATGCAAATGGGTCTCT 60.749 55.000 0.00 0.00 0.00 3.10
4530 6135 2.785425 GGGGCGATGCAAATGGGTC 61.785 63.158 0.00 0.00 0.00 4.46
4546 6151 4.954970 AGGCAAGGTGTGTGCGGG 62.955 66.667 0.00 0.00 43.18 6.13
4547 6152 3.663176 CAGGCAAGGTGTGTGCGG 61.663 66.667 0.00 0.00 43.18 5.69
4548 6153 4.332637 GCAGGCAAGGTGTGTGCG 62.333 66.667 0.00 0.00 43.18 5.34
4549 6154 3.982241 GGCAGGCAAGGTGTGTGC 61.982 66.667 0.00 0.00 41.45 4.57
4580 6185 1.134753 CAGCAGAGACAGACCTAGCTG 59.865 57.143 0.00 0.00 38.30 4.24
4610 6215 0.751643 AAGCGAGAGAGAGAGAGGCC 60.752 60.000 0.00 0.00 0.00 5.19
4620 6225 1.303398 ACCACGGAGAAGCGAGAGA 60.303 57.895 0.00 0.00 0.00 3.10
4621 6226 1.153939 CACCACGGAGAAGCGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
4622 6227 2.962569 CACCACGGAGAAGCGAGA 59.037 61.111 0.00 0.00 0.00 4.04
4628 6233 2.210013 AGCTGAGCACCACGGAGAA 61.210 57.895 7.39 0.00 0.00 2.87
4686 6291 4.008933 GCACTCACCAGAGGCGGT 62.009 66.667 0.00 0.00 46.44 5.68
4692 6297 1.957177 GAGATATCGGCACTCACCAGA 59.043 52.381 0.00 0.00 0.00 3.86
4702 6307 1.005450 AGAGAGGAGGGAGATATCGGC 59.995 57.143 0.00 0.00 0.00 5.54
4703 6308 3.449746 AAGAGAGGAGGGAGATATCGG 57.550 52.381 0.00 0.00 0.00 4.18
4708 6313 5.149584 TGATACAAAGAGAGGAGGGAGAT 57.850 43.478 0.00 0.00 0.00 2.75
4713 6318 4.230455 AGGGATGATACAAAGAGAGGAGG 58.770 47.826 0.00 0.00 0.00 4.30
4714 6319 5.130145 ACAAGGGATGATACAAAGAGAGGAG 59.870 44.000 0.00 0.00 0.00 3.69
4715 6320 5.032846 ACAAGGGATGATACAAAGAGAGGA 58.967 41.667 0.00 0.00 0.00 3.71
4716 6321 5.121811 CACAAGGGATGATACAAAGAGAGG 58.878 45.833 0.00 0.00 0.00 3.69
4717 6322 5.121811 CCACAAGGGATGATACAAAGAGAG 58.878 45.833 0.00 0.00 40.01 3.20
4744 6349 7.581011 CAAATTTGGAGTATTACACAAAGCC 57.419 36.000 10.49 0.00 36.41 4.35
4786 6741 6.765989 TGGATCAATACACATTACAGCCTAAC 59.234 38.462 0.00 0.00 0.00 2.34
4850 6805 7.663081 ACCTACATGATGGCATTTAGAGTATTG 59.337 37.037 0.00 0.00 37.08 1.90
4851 6806 7.749666 ACCTACATGATGGCATTTAGAGTATT 58.250 34.615 0.00 0.00 37.08 1.89
4852 6807 7.321717 ACCTACATGATGGCATTTAGAGTAT 57.678 36.000 0.00 0.00 37.08 2.12
4853 6808 6.747414 ACCTACATGATGGCATTTAGAGTA 57.253 37.500 0.00 0.72 37.08 2.59
4854 6809 5.636903 ACCTACATGATGGCATTTAGAGT 57.363 39.130 0.00 0.00 37.08 3.24
4855 6810 6.949352 AAACCTACATGATGGCATTTAGAG 57.051 37.500 0.00 0.00 37.08 2.43
4856 6811 6.889177 TGAAAACCTACATGATGGCATTTAGA 59.111 34.615 0.00 0.00 37.08 2.10
4857 6812 7.067372 TCTGAAAACCTACATGATGGCATTTAG 59.933 37.037 0.00 6.23 35.51 1.85
4858 6813 6.889177 TCTGAAAACCTACATGATGGCATTTA 59.111 34.615 0.00 0.00 30.68 1.40
4859 6814 5.716228 TCTGAAAACCTACATGATGGCATTT 59.284 36.000 0.00 6.31 30.68 2.32
4871 6826 3.935828 GGCATCTCAGTCTGAAAACCTAC 59.064 47.826 3.67 0.00 0.00 3.18
4875 6830 4.217118 ACATTGGCATCTCAGTCTGAAAAC 59.783 41.667 3.67 0.00 0.00 2.43
4919 6874 2.041405 GAGGTGAGGGAGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
4934 6889 3.499918 GTCACTGTTGGGAAATGAGTGAG 59.500 47.826 0.00 0.00 42.73 3.51
4935 6890 3.476552 GTCACTGTTGGGAAATGAGTGA 58.523 45.455 0.00 0.00 40.50 3.41
4936 6891 2.554032 GGTCACTGTTGGGAAATGAGTG 59.446 50.000 0.00 0.00 36.23 3.51
4937 6892 2.443255 AGGTCACTGTTGGGAAATGAGT 59.557 45.455 0.00 0.00 0.00 3.41
4938 6893 2.816087 CAGGTCACTGTTGGGAAATGAG 59.184 50.000 0.00 0.00 39.92 2.90
4941 6896 1.133513 TGCAGGTCACTGTTGGGAAAT 60.134 47.619 0.00 0.00 46.62 2.17
5030 6986 4.532126 AGGAAGATGGACAACATGAGTACA 59.468 41.667 9.75 9.75 40.72 2.90
5033 6989 3.843027 AGAGGAAGATGGACAACATGAGT 59.157 43.478 0.00 0.00 40.72 3.41
5056 7012 0.550147 AGATGGTAGGTGCAAGGGGT 60.550 55.000 0.00 0.00 0.00 4.95
5154 7110 0.773014 CCCCATCCATGGCAGTCATA 59.227 55.000 6.96 0.00 46.70 2.15
5170 7126 0.849417 AGCTTCCTGATGGATTCCCC 59.151 55.000 0.00 0.00 42.81 4.81
5171 7127 1.202867 GGAGCTTCCTGATGGATTCCC 60.203 57.143 0.00 0.00 42.81 3.97
5172 7128 1.492176 TGGAGCTTCCTGATGGATTCC 59.508 52.381 0.00 0.00 42.81 3.01
5173 7129 3.505480 ATGGAGCTTCCTGATGGATTC 57.495 47.619 0.00 0.00 42.81 2.52
5174 7130 3.967467 AATGGAGCTTCCTGATGGATT 57.033 42.857 0.00 0.00 42.81 3.01
5182 7138 3.425659 GGTCTTCAAAATGGAGCTTCCT 58.574 45.455 0.00 0.00 37.46 3.36
5207 7163 2.692041 AGATAAGGCAGCAGGAATTTGC 59.308 45.455 0.00 0.00 44.41 3.68
5250 7206 2.076100 TGCTGCTGGATCAGTAAAACG 58.924 47.619 0.00 0.00 36.49 3.60


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

AutoCloner maintained by Alex Coulton.