Multiple sequence alignment - TraesCS3D01G426800

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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 TraesCS3D01G426800 chr3D 100.000 5776 0 0 1 5776 540089886 540084111 0.000000e+00 10667.0
1 TraesCS3D01G426800 chr3D 100.000 36 0 0 3559 3594 540086263 540086228 3.740000e-07 67.6
2 TraesCS3D01G426800 chr3D 100.000 36 0 0 3624 3659 540086328 540086293 3.740000e-07 67.6
3 TraesCS3D01G426800 chr3B 94.959 3432 137 21 1569 4983 716148934 716145522 0.000000e+00 5347.0
4 TraesCS3D01G426800 chr3B 92.108 925 35 21 631 1545 716150011 716149115 0.000000e+00 1269.0
5 TraesCS3D01G426800 chr3B 86.334 622 69 11 1 619 716151078 716150470 0.000000e+00 664.0
6 TraesCS3D01G426800 chr3B 88.636 264 15 4 5513 5776 716144635 716144387 2.020000e-79 307.0
7 TraesCS3D01G426800 chr3B 89.474 171 16 2 3963 4132 59234276 59234445 1.260000e-51 215.0
8 TraesCS3D01G426800 chr3A 91.546 3395 168 52 239 3591 674985315 674981998 0.000000e+00 4569.0
9 TraesCS3D01G426800 chr3A 93.145 1488 64 22 3617 5079 674982037 674980563 0.000000e+00 2148.0
10 TraesCS3D01G426800 chr3A 86.221 479 25 16 5297 5774 674979923 674979485 1.130000e-131 481.0
11 TraesCS3D01G426800 chr2B 86.413 920 81 18 2640 3548 434720918 434721804 0.000000e+00 966.0
12 TraesCS3D01G426800 chr2B 84.161 846 106 11 3613 4454 434721809 434722630 0.000000e+00 795.0
13 TraesCS3D01G426800 chr2B 87.799 418 38 8 2195 2603 434720505 434720918 1.460000e-130 477.0
14 TraesCS3D01G426800 chr4A 83.826 575 76 10 3626 4200 713739573 713739016 1.100000e-146 531.0
15 TraesCS3D01G426800 chr5B 88.889 171 17 2 3963 4132 17605512 17605681 5.860000e-50 209.0
16 TraesCS3D01G426800 chr1B 88.889 171 17 2 3963 4132 46948542 46948711 5.860000e-50 209.0
17 TraesCS3D01G426800 chr1B 88.889 171 17 2 3963 4132 80966164 80966333 5.860000e-50 209.0
18 TraesCS3D01G426800 chr2D 82.927 123 19 2 5 127 50118578 50118698 6.120000e-20 110.0
19 TraesCS3D01G426800 chr6D 97.222 36 0 1 1539 1573 450559153 450559188 6.250000e-05 60.2


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 TraesCS3D01G426800 chr3D 540084111 540089886 5775 True 3600.733333 10667 100.000000 1 5776 3 chr3D.!!$R1 5775
1 TraesCS3D01G426800 chr3B 716144387 716151078 6691 True 1896.750000 5347 90.509250 1 5776 4 chr3B.!!$R1 5775
2 TraesCS3D01G426800 chr3A 674979485 674985315 5830 True 2399.333333 4569 90.304000 239 5774 3 chr3A.!!$R1 5535
3 TraesCS3D01G426800 chr2B 434720505 434722630 2125 False 746.000000 966 86.124333 2195 4454 3 chr2B.!!$F1 2259
4 TraesCS3D01G426800 chr4A 713739016 713739573 557 True 531.000000 531 83.826000 3626 4200 1 chr4A.!!$R1 574

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
538 540 0.040157 TGGTCGTGACTTCGTAACCG 60.040 55.0 0.00 0.0 32.71 4.44 F
1252 1715 0.311790 TCGTACGTGATTATCCCCGC 59.688 55.0 16.05 0.0 0.00 6.13 F
1258 1721 0.321996 GTGATTATCCCCGCCCTCTC 59.678 60.0 0.00 0.0 0.00 3.20 F
1881 2510 0.829333 TCTCTTCATCTGCTCCAGGC 59.171 55.0 0.00 0.0 42.22 4.85 F
2463 3100 1.101049 ACTTTGCAGGTCCCAACACG 61.101 55.0 0.00 0.0 0.00 4.49 F
3001 3638 1.207488 TGGGCCCTAACTGTCATGCT 61.207 55.0 25.70 0.0 0.00 3.79 F
4515 5179 0.179034 GGTCCTCACATCCATGCTCC 60.179 60.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 2205 1.153628 GTGCCGCCGTCTTACAGAT 60.154 57.895 0.00 0.00 0.00 2.90 R
2983 3620 0.837272 TAGCATGACAGTTAGGGCCC 59.163 55.000 16.46 16.46 0.00 5.80 R
3221 3858 2.028476 CGGTTACAACACTCCCATCTGA 60.028 50.000 0.00 0.00 0.00 3.27 R
3731 4378 1.679139 CTGTTGCTCCACTGTTTCCA 58.321 50.000 0.00 0.00 0.00 3.53 R
4403 5057 0.464036 CCACAGCCGCTATAAGGTCA 59.536 55.000 0.00 0.00 0.00 4.02 R
4520 5184 0.039708 GCAACCTCAAGCTCTGCAAC 60.040 55.000 0.00 0.00 33.19 4.17 R
5436 6621 0.026803 GGTCCGTGCTAGTACGTACG 59.973 60.000 27.80 15.01 42.24 3.67 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
38 39 4.892934 AGAACCAAGAAGGCACACATAAAA 59.107 37.500 0.00 0.00 43.14 1.52
44 45 6.183360 CCAAGAAGGCACACATAAAAGGATAG 60.183 42.308 0.00 0.00 0.00 2.08
47 48 6.599638 AGAAGGCACACATAAAAGGATAGAAC 59.400 38.462 0.00 0.00 0.00 3.01
52 53 6.180472 CACACATAAAAGGATAGAACCCACT 58.820 40.000 0.00 0.00 0.00 4.00
68 69 6.992715 AGAACCCACTTTAGTATATGTGATGC 59.007 38.462 0.00 0.00 30.37 3.91
70 71 4.690748 CCCACTTTAGTATATGTGATGCGG 59.309 45.833 0.00 0.00 30.37 5.69
91 92 1.000396 GTCCCTTGGCAATGGAGCT 60.000 57.895 22.44 0.00 34.17 4.09
152 154 1.536922 CGGACTGAGATCCAATGACCG 60.537 57.143 0.00 0.00 38.87 4.79
153 155 1.482593 GGACTGAGATCCAATGACCGT 59.517 52.381 0.00 0.00 38.77 4.83
154 156 2.544685 GACTGAGATCCAATGACCGTG 58.455 52.381 0.00 0.00 0.00 4.94
155 157 1.208052 ACTGAGATCCAATGACCGTGG 59.792 52.381 0.00 0.00 37.51 4.94
157 159 0.830648 GAGATCCAATGACCGTGGGA 59.169 55.000 0.00 0.00 36.73 4.37
164 166 2.504367 CAATGACCGTGGGAAAAGAGT 58.496 47.619 0.00 0.00 0.00 3.24
185 187 1.433064 GTGTGGCCATGCGGTATTG 59.567 57.895 9.72 0.00 33.28 1.90
190 192 1.752694 GCCATGCGGTATTGGGTGT 60.753 57.895 0.00 0.00 33.28 4.16
214 216 4.940046 ACACCATGAACTCATCATCTTGAC 59.060 41.667 0.00 0.00 45.91 3.18
218 220 5.220548 CCATGAACTCATCATCTTGACGTTC 60.221 44.000 0.00 0.00 45.91 3.95
223 225 7.915923 TGAACTCATCATCTTGACGTTCTATAC 59.084 37.037 0.00 0.00 36.20 1.47
231 233 6.179504 TCTTGACGTTCTATACAGTCACTC 57.820 41.667 0.00 0.00 38.80 3.51
247 249 4.841246 AGTCACTCTCCAATGTTAGTCCTT 59.159 41.667 0.00 0.00 0.00 3.36
292 294 6.868339 GCAAATAGCAAGTAGGAAACAACAAT 59.132 34.615 0.00 0.00 44.79 2.71
301 303 9.097257 CAAGTAGGAAACAACAATGAAAATGTT 57.903 29.630 0.00 0.00 41.50 2.71
322 324 7.015226 TGTTGCCGATTCATTAAACTCATAG 57.985 36.000 0.00 0.00 0.00 2.23
330 332 8.554528 CGATTCATTAAACTCATAGCAAGATGT 58.445 33.333 0.00 0.00 0.00 3.06
333 335 8.429493 TCATTAAACTCATAGCAAGATGTCTG 57.571 34.615 0.00 0.00 0.00 3.51
339 341 6.647229 ACTCATAGCAAGATGTCTGAAATGA 58.353 36.000 0.00 0.00 0.00 2.57
340 342 7.108194 ACTCATAGCAAGATGTCTGAAATGAA 58.892 34.615 0.00 0.00 0.00 2.57
341 343 7.609146 ACTCATAGCAAGATGTCTGAAATGAAA 59.391 33.333 0.00 0.00 0.00 2.69
414 416 2.631160 ATGTTGTGTCTCCGGAAACA 57.369 45.000 18.35 18.35 37.87 2.83
415 417 2.631160 TGTTGTGTCTCCGGAAACAT 57.369 45.000 14.94 0.00 39.21 2.71
445 447 7.773224 CCTAATGATGGTATCACCTTGTGTTTA 59.227 37.037 0.00 0.00 43.01 2.01
504 506 4.452733 GGAGCCTCCCACCGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
514 516 0.661020 CCACCGTTCGAAAGCACTTT 59.339 50.000 0.00 0.00 35.14 2.66
538 540 0.040157 TGGTCGTGACTTCGTAACCG 60.040 55.000 0.00 0.00 32.71 4.44
585 587 1.366366 CTCCCACCGTTCTCGTTGT 59.634 57.895 0.00 0.00 35.01 3.32
598 600 5.684626 CGTTCTCGTTGTACTTCTTTGTACT 59.315 40.000 6.41 0.00 42.22 2.73
604 606 9.669353 CTCGTTGTACTTCTTTGTACTAGTTTA 57.331 33.333 0.00 0.00 42.22 2.01
607 609 8.706936 GTTGTACTTCTTTGTACTAGTTTAGGC 58.293 37.037 0.00 0.00 42.22 3.93
745 1202 0.608130 GGTCAACCCAAGGAAATGGC 59.392 55.000 0.00 0.00 39.26 4.40
752 1209 1.005215 CCCAAGGAAATGGCAGAGACT 59.995 52.381 0.00 0.00 39.26 3.24
753 1210 2.089980 CCAAGGAAATGGCAGAGACTG 58.910 52.381 0.00 0.00 32.78 3.51
876 1334 3.873805 GAGCAGCTCCAACCAAAAC 57.126 52.632 11.84 0.00 0.00 2.43
885 1343 0.390860 CCAACCAAAACAATCCGGCA 59.609 50.000 0.00 0.00 0.00 5.69
1029 1487 4.841617 TCTCCCCGGATCAGCGCT 62.842 66.667 2.64 2.64 0.00 5.92
1251 1714 1.068748 CCTCGTACGTGATTATCCCCG 60.069 57.143 18.29 0.87 0.00 5.73
1252 1715 0.311790 TCGTACGTGATTATCCCCGC 59.688 55.000 16.05 0.00 0.00 6.13
1255 1718 0.470456 TACGTGATTATCCCCGCCCT 60.470 55.000 0.00 0.00 0.00 5.19
1256 1719 1.004918 CGTGATTATCCCCGCCCTC 60.005 63.158 0.00 0.00 0.00 4.30
1258 1721 0.321996 GTGATTATCCCCGCCCTCTC 59.678 60.000 0.00 0.00 0.00 3.20
1261 1724 1.002544 GATTATCCCCGCCCTCTCTTG 59.997 57.143 0.00 0.00 0.00 3.02
1265 1728 2.045926 CCCGCCCTCTCTTGTTGG 60.046 66.667 0.00 0.00 0.00 3.77
1267 1730 1.376037 CCGCCCTCTCTTGTTGGTC 60.376 63.158 0.00 0.00 0.00 4.02
1268 1731 1.376037 CGCCCTCTCTTGTTGGTCC 60.376 63.158 0.00 0.00 0.00 4.46
1269 1732 1.002011 GCCCTCTCTTGTTGGTCCC 60.002 63.158 0.00 0.00 0.00 4.46
1270 1733 1.296715 CCCTCTCTTGTTGGTCCCG 59.703 63.158 0.00 0.00 0.00 5.14
1271 1734 1.296715 CCTCTCTTGTTGGTCCCGG 59.703 63.158 0.00 0.00 0.00 5.73
1280 1743 3.818121 TTGGTCCCGGTCGTTGCTG 62.818 63.158 0.00 0.00 0.00 4.41
1299 1762 1.014044 GCGAGTCATTTCCACGCTGA 61.014 55.000 0.00 0.00 44.67 4.26
1301 1764 2.002586 CGAGTCATTTCCACGCTGATT 58.997 47.619 0.00 0.00 0.00 2.57
1302 1765 2.416547 CGAGTCATTTCCACGCTGATTT 59.583 45.455 0.00 0.00 0.00 2.17
1303 1766 3.120199 CGAGTCATTTCCACGCTGATTTT 60.120 43.478 0.00 0.00 0.00 1.82
1304 1767 4.613622 CGAGTCATTTCCACGCTGATTTTT 60.614 41.667 0.00 0.00 0.00 1.94
1390 1853 2.734673 GCTTTCTGGTCGAGCGCTG 61.735 63.158 18.48 7.71 0.00 5.18
1484 1948 1.061411 CGCAGCGACATGATTGGTG 59.939 57.895 9.98 5.58 42.35 4.17
1552 2020 8.874744 ATCTATTATGATGATCTGAATCTGCG 57.125 34.615 0.00 0.00 32.75 5.18
1553 2021 7.834803 TCTATTATGATGATCTGAATCTGCGT 58.165 34.615 0.00 0.00 32.75 5.24
1554 2022 8.960591 TCTATTATGATGATCTGAATCTGCGTA 58.039 33.333 0.00 0.00 32.75 4.42
1555 2023 9.747293 CTATTATGATGATCTGAATCTGCGTAT 57.253 33.333 0.00 0.00 32.75 3.06
1556 2024 7.823149 TTATGATGATCTGAATCTGCGTATG 57.177 36.000 0.00 0.00 32.75 2.39
1576 2205 4.886496 TGCATGATTGTGGAATTTGGAA 57.114 36.364 0.00 0.00 0.00 3.53
1617 2246 4.921515 CCAGATGTTTCTTGATGCAAAGTG 59.078 41.667 0.00 0.00 0.00 3.16
1760 2389 1.374252 CACCACTGTGTACGAGGCC 60.374 63.158 7.08 0.00 37.72 5.19
1835 2464 2.420890 CTGCTCTGCGGGATCCTC 59.579 66.667 12.58 4.64 0.00 3.71
1881 2510 0.829333 TCTCTTCATCTGCTCCAGGC 59.171 55.000 0.00 0.00 42.22 4.85
1929 2558 1.535028 CTATGTGCTGTGTTTTGCGGA 59.465 47.619 0.00 0.00 0.00 5.54
1996 2625 3.643792 AGCTAGAAGACACACCAGTTTCT 59.356 43.478 0.00 0.00 36.37 2.52
2029 2658 6.099845 TGACTAGAAACCCTCTCTTTGTTCTT 59.900 38.462 0.00 0.00 35.41 2.52
2082 2711 2.888834 ATGGTGCAAGGTTTGTGAAC 57.111 45.000 0.00 0.00 34.96 3.18
2263 2892 1.678970 ACGAATGGAAAGGGCAGCC 60.679 57.895 1.26 1.26 0.00 4.85
2299 2928 3.745803 GCTGCTGCTGTTGAGGGC 61.746 66.667 8.53 0.00 36.03 5.19
2327 2956 3.287867 AGCATTGGGGAACATCTGTAG 57.712 47.619 0.00 0.00 0.00 2.74
2432 3062 5.226194 TCAGCAATTTGCCCTTTTAATGT 57.774 34.783 17.51 0.00 46.52 2.71
2463 3100 1.101049 ACTTTGCAGGTCCCAACACG 61.101 55.000 0.00 0.00 0.00 4.49
2605 3242 9.679661 TCCAGAATAAATGCTGTTACAGAATAA 57.320 29.630 17.40 3.71 28.08 1.40
2647 3284 2.094700 TCTTAGAGTGGCTACTGTTGCG 60.095 50.000 7.76 0.00 37.25 4.85
2921 3558 5.904362 AGGTAAGCAAAGCCAAAATAGAG 57.096 39.130 0.00 0.00 0.00 2.43
2925 3562 7.067494 AGGTAAGCAAAGCCAAAATAGAGTATG 59.933 37.037 0.00 0.00 0.00 2.39
2983 3620 8.777413 TCTGTATTTTCTCTTCAACTGTCATTG 58.223 33.333 0.00 0.00 0.00 2.82
3001 3638 1.207488 TGGGCCCTAACTGTCATGCT 61.207 55.000 25.70 0.00 0.00 3.79
3253 3890 4.032355 GTGTTGTAACCGTTGTTGATGTG 58.968 43.478 0.00 0.00 35.87 3.21
3363 4010 8.073467 ACTTTCAGGTTTTGAACTGGAAAATA 57.927 30.769 0.00 0.00 45.22 1.40
3438 4085 6.539826 TGGATGCTGTAATCTGTATCTTGTTG 59.460 38.462 0.00 0.00 35.91 3.33
3513 4160 9.793259 AATATACAAGTTGTATGGACCATTAGG 57.207 33.333 30.37 0.00 42.93 2.69
3575 4222 5.652744 AAACTTGTCAGTGTCGTGTATTC 57.347 39.130 0.00 0.00 31.60 1.75
3659 4306 8.533153 GTGTATTCTTCGCTTTCATTACTCTAC 58.467 37.037 0.00 0.00 0.00 2.59
3731 4378 6.274157 TGTTTGTGTTGTTGTATTCAGGTT 57.726 33.333 0.00 0.00 0.00 3.50
3809 4456 3.084039 GGATTCAGCAATGTCAAGTGGA 58.916 45.455 0.00 0.00 0.00 4.02
3851 4498 4.478206 TTCCAGAAGGTTAGCATCTCTG 57.522 45.455 0.00 0.00 35.89 3.35
3945 4593 1.276622 ACTAAAGTGGCATCCGAGGT 58.723 50.000 0.00 0.00 0.00 3.85
4063 4712 2.751166 ACTGTGGTATGCACTCTCAC 57.249 50.000 0.00 0.00 0.00 3.51
4095 4744 5.071250 TCACGCTAACTGGGATTATACCATT 59.929 40.000 0.00 0.00 37.38 3.16
4403 5057 6.849085 AAAGTCATACTCTCATCAGACACT 57.151 37.500 0.00 0.00 0.00 3.55
4509 5173 3.541242 AAAAATGGGTCCTCACATCCA 57.459 42.857 0.00 0.00 36.59 3.41
4511 5175 2.742428 AATGGGTCCTCACATCCATG 57.258 50.000 0.00 0.00 39.66 3.66
4512 5176 0.184451 ATGGGTCCTCACATCCATGC 59.816 55.000 0.00 0.00 38.45 4.06
4513 5177 0.915872 TGGGTCCTCACATCCATGCT 60.916 55.000 0.00 0.00 0.00 3.79
4515 5179 0.179034 GGTCCTCACATCCATGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
4516 5180 0.835941 GTCCTCACATCCATGCTCCT 59.164 55.000 0.00 0.00 0.00 3.69
4517 5181 1.126488 TCCTCACATCCATGCTCCTC 58.874 55.000 0.00 0.00 0.00 3.71
4519 5183 1.489649 CCTCACATCCATGCTCCTCTT 59.510 52.381 0.00 0.00 0.00 2.85
4520 5184 2.562635 CTCACATCCATGCTCCTCTTG 58.437 52.381 0.00 0.00 0.00 3.02
4522 5186 2.306805 TCACATCCATGCTCCTCTTGTT 59.693 45.455 0.00 0.00 0.00 2.83
4598 5264 0.516001 CCGTCTCGTCAGACTTCGAA 59.484 55.000 0.00 0.00 46.31 3.71
4601 5267 3.002451 CCGTCTCGTCAGACTTCGAATAT 59.998 47.826 0.00 0.00 46.31 1.28
4697 5363 1.808411 TGGCTTACCTGAAAAGAGCG 58.192 50.000 0.00 0.00 36.63 5.03
4938 5614 2.880268 GGTTGTACACCCTAAACACCAC 59.120 50.000 1.44 0.00 40.19 4.16
4940 5616 2.125233 TGTACACCCTAAACACCACCA 58.875 47.619 0.00 0.00 0.00 4.17
4941 5617 2.158784 TGTACACCCTAAACACCACCAC 60.159 50.000 0.00 0.00 0.00 4.16
4994 5672 3.853355 ATTGGCCATTTGTTTGGAACA 57.147 38.095 6.09 0.00 39.25 3.18
5014 5692 1.284715 CACGCCGTCAGTGTAGTGA 59.715 57.895 0.00 0.00 36.98 3.41
5018 5696 1.795525 CGCCGTCAGTGTAGTGAGATG 60.796 57.143 0.00 0.00 0.00 2.90
5020 5698 1.819288 CCGTCAGTGTAGTGAGATGGT 59.181 52.381 0.00 0.00 33.49 3.55
5068 5789 0.106708 TGTGTGCTTGTCTGACCCTC 59.893 55.000 5.17 0.00 0.00 4.30
5079 5800 0.752054 CTGACCCTCTCATCCTCTGC 59.248 60.000 0.00 0.00 0.00 4.26
5081 5802 0.752054 GACCCTCTCATCCTCTGCAG 59.248 60.000 7.63 7.63 0.00 4.41
5084 5805 1.688942 CCCTCTCATCCTCTGCAGTCT 60.689 57.143 14.67 0.00 0.00 3.24
5085 5806 1.409790 CCTCTCATCCTCTGCAGTCTG 59.590 57.143 14.67 7.35 0.00 3.51
5086 5807 0.822811 TCTCATCCTCTGCAGTCTGC 59.177 55.000 18.32 18.32 45.29 4.26
5105 5826 3.258971 GCACTATCTGCTTTCCACTCT 57.741 47.619 0.00 0.00 43.33 3.24
5106 5827 3.194062 GCACTATCTGCTTTCCACTCTC 58.806 50.000 0.00 0.00 43.33 3.20
5107 5828 3.791245 CACTATCTGCTTTCCACTCTCC 58.209 50.000 0.00 0.00 0.00 3.71
5108 5829 2.769095 ACTATCTGCTTTCCACTCTCCC 59.231 50.000 0.00 0.00 0.00 4.30
5109 5830 0.915364 ATCTGCTTTCCACTCTCCCC 59.085 55.000 0.00 0.00 0.00 4.81
5110 5831 0.178891 TCTGCTTTCCACTCTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
5111 5832 0.035630 CTGCTTTCCACTCTCCCCTG 60.036 60.000 0.00 0.00 0.00 4.45
5112 5833 1.377856 GCTTTCCACTCTCCCCTGC 60.378 63.158 0.00 0.00 0.00 4.85
5113 5834 1.846712 GCTTTCCACTCTCCCCTGCT 61.847 60.000 0.00 0.00 0.00 4.24
5114 5835 0.035630 CTTTCCACTCTCCCCTGCTG 60.036 60.000 0.00 0.00 0.00 4.41
5115 5836 0.473694 TTTCCACTCTCCCCTGCTGA 60.474 55.000 0.00 0.00 0.00 4.26
5116 5837 0.252881 TTCCACTCTCCCCTGCTGAT 60.253 55.000 0.00 0.00 0.00 2.90
5117 5838 0.689080 TCCACTCTCCCCTGCTGATC 60.689 60.000 0.00 0.00 0.00 2.92
5118 5839 1.694133 CCACTCTCCCCTGCTGATCC 61.694 65.000 0.00 0.00 0.00 3.36
5119 5840 0.690411 CACTCTCCCCTGCTGATCCT 60.690 60.000 0.00 0.00 0.00 3.24
5120 5841 0.398381 ACTCTCCCCTGCTGATCCTC 60.398 60.000 0.00 0.00 0.00 3.71
5121 5842 1.074926 TCTCCCCTGCTGATCCTCC 60.075 63.158 0.00 0.00 0.00 4.30
5122 5843 2.444706 TCCCCTGCTGATCCTCCG 60.445 66.667 0.00 0.00 0.00 4.63
5158 5879 2.480555 GTCGAGCCGTTGCCAATG 59.519 61.111 0.00 0.00 38.69 2.82
5160 5881 3.055719 CGAGCCGTTGCCAATGGT 61.056 61.111 16.78 4.23 39.84 3.55
5161 5882 2.625823 CGAGCCGTTGCCAATGGTT 61.626 57.895 16.78 11.20 39.84 3.67
5162 5883 1.302383 CGAGCCGTTGCCAATGGTTA 61.302 55.000 16.78 0.00 39.84 2.85
5163 5884 0.170339 GAGCCGTTGCCAATGGTTAC 59.830 55.000 16.78 5.54 39.84 2.50
5203 6138 4.678509 TCACACGGATTAAATTGTCAGC 57.321 40.909 0.00 0.00 0.00 4.26
5260 6196 1.656818 AACAATTCATCCCCGCGCAG 61.657 55.000 8.75 0.00 0.00 5.18
5298 6241 3.501458 GACCGCCCTATCTGGTCGC 62.501 68.421 0.00 0.00 42.42 5.19
5303 6246 2.125326 CCCTATCTGGTCGCGGTCA 61.125 63.158 6.13 4.00 0.00 4.02
5304 6247 1.065928 CCTATCTGGTCGCGGTCAC 59.934 63.158 6.13 0.00 0.00 3.67
5305 6248 1.384989 CCTATCTGGTCGCGGTCACT 61.385 60.000 6.13 0.00 0.00 3.41
5306 6249 0.248661 CTATCTGGTCGCGGTCACTG 60.249 60.000 6.13 0.00 0.00 3.66
5307 6250 0.963856 TATCTGGTCGCGGTCACTGT 60.964 55.000 6.13 0.00 0.00 3.55
5310 6253 2.137425 CTGGTCGCGGTCACTGTACA 62.137 60.000 6.13 0.00 0.00 2.90
5313 6256 1.372499 TCGCGGTCACTGTACAAGC 60.372 57.895 6.13 0.00 0.00 4.01
5316 6495 1.736645 CGGTCACTGTACAAGCCGG 60.737 63.158 15.09 0.00 36.05 6.13
5340 6519 1.771783 ATCCATCCATGCTGCCGCTA 61.772 55.000 0.70 0.00 36.97 4.26
5341 6520 1.964891 CCATCCATGCTGCCGCTAG 60.965 63.158 0.70 0.00 36.97 3.42
5419 6603 4.096003 CAGGACGGGCCGGACAAT 62.096 66.667 31.78 8.61 43.43 2.71
5420 6604 2.364579 AGGACGGGCCGGACAATA 60.365 61.111 31.78 0.00 43.43 1.90
5436 6621 6.701841 CCGGACAATATCATGGCATATACTAC 59.298 42.308 0.00 0.00 0.00 2.73
5437 6622 6.417930 CGGACAATATCATGGCATATACTACG 59.582 42.308 0.00 0.00 0.00 3.51
5438 6623 7.265673 GGACAATATCATGGCATATACTACGT 58.734 38.462 0.00 0.00 0.00 3.57
5439 6624 8.410912 GGACAATATCATGGCATATACTACGTA 58.589 37.037 0.00 0.00 0.00 3.57
5440 6625 9.234384 GACAATATCATGGCATATACTACGTAC 57.766 37.037 0.00 0.00 0.00 3.67
5442 6627 5.892160 ATCATGGCATATACTACGTACGT 57.108 39.130 25.98 25.98 0.00 3.57
5443 6628 6.990341 ATCATGGCATATACTACGTACGTA 57.010 37.500 25.41 25.41 0.00 3.57
5444 6629 6.169419 TCATGGCATATACTACGTACGTAC 57.831 41.667 23.60 15.90 0.00 3.67
5445 6630 5.934043 TCATGGCATATACTACGTACGTACT 59.066 40.000 23.60 16.88 0.00 2.73
5446 6631 7.096551 TCATGGCATATACTACGTACGTACTA 58.903 38.462 23.60 18.40 0.00 1.82
5447 6632 6.951256 TGGCATATACTACGTACGTACTAG 57.049 41.667 23.60 18.27 0.00 2.57
5449 6634 5.348724 GGCATATACTACGTACGTACTAGCA 59.651 44.000 23.60 8.00 0.00 3.49
5450 6635 6.237073 GCATATACTACGTACGTACTAGCAC 58.763 44.000 23.60 7.70 0.00 4.40
5452 6637 1.927174 ACTACGTACGTACTAGCACGG 59.073 52.381 23.60 13.68 46.12 4.94
5453 6638 2.193447 CTACGTACGTACTAGCACGGA 58.807 52.381 23.60 8.52 46.12 4.69
5456 6641 2.383170 TACGTACTAGCACGGACCG 58.617 57.895 19.25 13.61 46.12 4.79
5457 6642 0.391130 TACGTACTAGCACGGACCGT 60.391 55.000 15.37 15.37 46.12 4.83
5458 6643 1.237285 ACGTACTAGCACGGACCGTT 61.237 55.000 19.02 6.63 46.12 4.44
5459 6644 0.109597 CGTACTAGCACGGACCGTTT 60.110 55.000 19.02 11.45 38.32 3.60
5460 6645 1.666888 CGTACTAGCACGGACCGTTTT 60.667 52.381 19.02 11.06 38.32 2.43
5493 6678 1.804151 TCACTGCGCCAAACTGATTAC 59.196 47.619 4.18 0.00 0.00 1.89
5504 6689 5.588648 GCCAAACTGATTACAAGCCATACTA 59.411 40.000 0.00 0.00 0.00 1.82
5505 6690 6.238484 GCCAAACTGATTACAAGCCATACTAG 60.238 42.308 0.00 0.00 0.00 2.57
5515 6700 6.918067 ACAAGCCATACTAGTATATCAGCA 57.082 37.500 15.03 0.00 0.00 4.41
5606 6791 4.889995 CCTTCTTCTTCCTCAACCTTTTGT 59.110 41.667 0.00 0.00 34.02 2.83
5613 6798 3.815809 TCCTCAACCTTTTGTACCACTG 58.184 45.455 0.00 0.00 34.02 3.66
5614 6799 3.201266 TCCTCAACCTTTTGTACCACTGT 59.799 43.478 0.00 0.00 34.02 3.55
5615 6800 4.409574 TCCTCAACCTTTTGTACCACTGTA 59.590 41.667 0.00 0.00 34.02 2.74
5616 6801 4.755123 CCTCAACCTTTTGTACCACTGTAG 59.245 45.833 0.00 0.00 34.02 2.74
5617 6802 4.710324 TCAACCTTTTGTACCACTGTAGG 58.290 43.478 0.00 0.00 34.02 3.18
5618 6803 4.409574 TCAACCTTTTGTACCACTGTAGGA 59.590 41.667 0.00 0.00 34.02 2.94
5665 6850 2.189594 TCAGTTCAAGCACTGATGGG 57.810 50.000 0.69 0.00 46.76 4.00
5669 6854 2.639839 AGTTCAAGCACTGATGGGTAGT 59.360 45.455 0.00 0.00 32.78 2.73
5682 6867 1.273724 TGGGTAGTGGATTCCCGGTAA 60.274 52.381 0.00 0.00 43.75 2.85
5683 6868 1.839354 GGGTAGTGGATTCCCGGTAAA 59.161 52.381 0.00 0.00 34.29 2.01
5684 6869 2.420547 GGGTAGTGGATTCCCGGTAAAC 60.421 54.545 0.00 0.00 34.29 2.01
5685 6870 2.543641 GTAGTGGATTCCCGGTAAACG 58.456 52.381 0.00 0.00 43.80 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.871125 CACATATACTAAAGTGGGTTCTATCCT 58.129 37.037 0.00 0.00 0.00 3.24
44 45 6.073765 CGCATCACATATACTAAAGTGGGTTC 60.074 42.308 0.00 0.00 33.01 3.62
47 48 4.690748 CCGCATCACATATACTAAAGTGGG 59.309 45.833 0.00 0.00 33.01 4.61
52 53 5.284861 ACACCCGCATCACATATACTAAA 57.715 39.130 0.00 0.00 0.00 1.85
70 71 0.967380 CTCCATTGCCAAGGGACACC 60.967 60.000 6.75 0.00 36.24 4.16
91 92 6.320518 CCCTAGGGTATTCACTATGGACTTA 58.679 44.000 20.88 0.00 37.48 2.24
137 139 0.541392 CCCACGGTCATTGGATCTCA 59.459 55.000 0.00 0.00 36.02 3.27
145 147 2.884639 CAACTCTTTTCCCACGGTCATT 59.115 45.455 0.00 0.00 0.00 2.57
147 149 1.476110 CCAACTCTTTTCCCACGGTCA 60.476 52.381 0.00 0.00 0.00 4.02
148 150 1.235724 CCAACTCTTTTCCCACGGTC 58.764 55.000 0.00 0.00 0.00 4.79
149 151 0.549469 ACCAACTCTTTTCCCACGGT 59.451 50.000 0.00 0.00 0.00 4.83
150 152 0.951558 CACCAACTCTTTTCCCACGG 59.048 55.000 0.00 0.00 0.00 4.94
152 154 1.681264 CCACACCAACTCTTTTCCCAC 59.319 52.381 0.00 0.00 0.00 4.61
153 155 2.026905 GCCACACCAACTCTTTTCCCA 61.027 52.381 0.00 0.00 0.00 4.37
154 156 0.673985 GCCACACCAACTCTTTTCCC 59.326 55.000 0.00 0.00 0.00 3.97
155 157 0.673985 GGCCACACCAACTCTTTTCC 59.326 55.000 0.00 0.00 38.86 3.13
175 177 1.407712 GGTGTACACCCAATACCGCAT 60.408 52.381 31.39 0.00 45.68 4.73
185 187 4.626287 ATGATGAGTTCATGGTGTACACCC 60.626 45.833 36.26 22.88 43.60 4.61
190 192 6.108687 GTCAAGATGATGAGTTCATGGTGTA 58.891 40.000 0.00 0.00 45.29 2.90
206 208 6.556212 AGTGACTGTATAGAACGTCAAGATG 58.444 40.000 0.00 0.00 40.62 2.90
214 216 5.562506 TTGGAGAGTGACTGTATAGAACG 57.437 43.478 0.00 0.00 0.00 3.95
218 220 8.001881 ACTAACATTGGAGAGTGACTGTATAG 57.998 38.462 0.00 0.00 0.00 1.31
223 225 4.221703 AGGACTAACATTGGAGAGTGACTG 59.778 45.833 0.00 0.00 0.00 3.51
231 233 5.102953 TGGATGAAGGACTAACATTGGAG 57.897 43.478 0.00 0.00 0.00 3.86
292 294 7.151308 AGTTTAATGAATCGGCAACATTTTCA 58.849 30.769 0.00 0.00 36.06 2.69
301 303 5.122519 TGCTATGAGTTTAATGAATCGGCA 58.877 37.500 0.00 0.00 0.00 5.69
414 416 6.898171 AGGTGATACCATCATTAGGCATAT 57.102 37.500 0.28 0.00 41.95 1.78
415 417 6.044287 ACAAGGTGATACCATCATTAGGCATA 59.956 38.462 0.28 0.00 41.95 3.14
445 447 5.105752 TGTTGCGTTTGCTCATTTTAAAGT 58.894 33.333 0.00 0.00 43.34 2.66
504 506 4.451096 TCACGACCATAAGAAAGTGCTTTC 59.549 41.667 14.80 14.80 46.85 2.62
514 516 4.379813 GGTTACGAAGTCACGACCATAAGA 60.380 45.833 0.00 0.00 43.93 2.10
538 540 7.475840 ACTTCTCTGAACAAAATGTTTCAGAC 58.524 34.615 9.44 0.00 41.28 3.51
585 587 7.452880 TCGCCTAAACTAGTACAAAGAAGTA 57.547 36.000 0.00 0.00 0.00 2.24
598 600 4.513442 AGCATGTGAAATCGCCTAAACTA 58.487 39.130 0.00 0.00 0.00 2.24
604 606 2.119801 AAGAGCATGTGAAATCGCCT 57.880 45.000 0.00 0.00 0.00 5.52
607 609 5.698832 TGGTTAAAAGAGCATGTGAAATCG 58.301 37.500 0.00 0.00 0.00 3.34
711 1168 2.430694 GTTGACCCAACCTGCTTTCTTT 59.569 45.455 0.00 0.00 38.30 2.52
775 1232 0.944311 CGTACACTTGGCTCGTGCTT 60.944 55.000 9.61 0.00 39.59 3.91
785 1242 2.716828 CCGACGCAGCGTACACTTG 61.717 63.158 23.04 6.61 41.37 3.16
876 1334 1.202290 CGGAAGGAAAATGCCGGATTG 60.202 52.381 5.05 0.00 40.08 2.67
1251 1714 1.002011 GGGACCAACAAGAGAGGGC 60.002 63.158 0.00 0.00 0.00 5.19
1252 1715 1.296715 CGGGACCAACAAGAGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
1255 1718 1.812686 CGACCGGGACCAACAAGAGA 61.813 60.000 6.32 0.00 0.00 3.10
1256 1719 1.374252 CGACCGGGACCAACAAGAG 60.374 63.158 6.32 0.00 0.00 2.85
1258 1721 1.227734 AACGACCGGGACCAACAAG 60.228 57.895 6.32 0.00 0.00 3.16
1261 1724 3.351416 GCAACGACCGGGACCAAC 61.351 66.667 6.32 0.00 0.00 3.77
1269 1732 3.470567 GACTCGCAGCAACGACCG 61.471 66.667 0.00 0.00 37.09 4.79
1270 1733 1.291877 AATGACTCGCAGCAACGACC 61.292 55.000 0.00 0.00 37.09 4.79
1271 1734 0.512952 AAATGACTCGCAGCAACGAC 59.487 50.000 0.00 0.00 37.09 4.34
1280 1743 1.014044 TCAGCGTGGAAATGACTCGC 61.014 55.000 0.00 0.00 45.82 5.03
1301 1764 2.614983 GACCCAACAGCGACAGTAAAAA 59.385 45.455 0.00 0.00 0.00 1.94
1302 1765 2.215196 GACCCAACAGCGACAGTAAAA 58.785 47.619 0.00 0.00 0.00 1.52
1303 1766 1.870580 CGACCCAACAGCGACAGTAAA 60.871 52.381 0.00 0.00 0.00 2.01
1304 1767 0.319211 CGACCCAACAGCGACAGTAA 60.319 55.000 0.00 0.00 0.00 2.24
1305 1768 1.287815 CGACCCAACAGCGACAGTA 59.712 57.895 0.00 0.00 0.00 2.74
1306 1769 2.029073 CGACCCAACAGCGACAGT 59.971 61.111 0.00 0.00 0.00 3.55
1307 1770 3.414700 GCGACCCAACAGCGACAG 61.415 66.667 0.00 0.00 0.00 3.51
1444 1908 5.567915 GCGCTGACTAAAAGTAAAATGTTCC 59.432 40.000 0.00 0.00 0.00 3.62
1495 1959 9.368416 ACTGAGATTTACTACTGGCTAATCATA 57.632 33.333 0.00 0.00 0.00 2.15
1497 1961 7.661536 ACTGAGATTTACTACTGGCTAATCA 57.338 36.000 0.00 0.00 0.00 2.57
1500 1964 9.422681 AGATAACTGAGATTTACTACTGGCTAA 57.577 33.333 0.00 0.00 0.00 3.09
1502 1966 7.906199 AGATAACTGAGATTTACTACTGGCT 57.094 36.000 0.00 0.00 0.00 4.75
1503 1967 9.849166 GATAGATAACTGAGATTTACTACTGGC 57.151 37.037 0.00 0.00 0.00 4.85
1552 2020 5.904941 TCCAAATTCCACAATCATGCATAC 58.095 37.500 0.00 0.00 0.00 2.39
1553 2021 6.541934 TTCCAAATTCCACAATCATGCATA 57.458 33.333 0.00 0.00 0.00 3.14
1554 2022 5.423704 TTCCAAATTCCACAATCATGCAT 57.576 34.783 0.00 0.00 0.00 3.96
1555 2023 4.886496 TTCCAAATTCCACAATCATGCA 57.114 36.364 0.00 0.00 0.00 3.96
1556 2024 5.522460 CAGATTCCAAATTCCACAATCATGC 59.478 40.000 0.00 0.00 0.00 4.06
1561 2029 7.362056 CGTCTTACAGATTCCAAATTCCACAAT 60.362 37.037 0.00 0.00 0.00 2.71
1566 2034 4.201920 GCCGTCTTACAGATTCCAAATTCC 60.202 45.833 0.00 0.00 0.00 3.01
1567 2196 4.494199 CGCCGTCTTACAGATTCCAAATTC 60.494 45.833 0.00 0.00 0.00 2.17
1576 2205 1.153628 GTGCCGCCGTCTTACAGAT 60.154 57.895 0.00 0.00 0.00 2.90
1617 2246 1.295792 TGCGATTTCGGCTGTATTCC 58.704 50.000 1.75 0.00 40.23 3.01
1818 2447 2.420890 GAGGATCCCGCAGAGCAG 59.579 66.667 8.55 0.00 30.22 4.24
1835 2464 3.766591 AGATCTACCTCACCTTGTCAGTG 59.233 47.826 0.00 0.00 36.54 3.66
1929 2558 4.021229 TGTGGTTATGTCCTGATACGAGT 58.979 43.478 0.00 0.00 0.00 4.18
1996 2625 5.590818 AGAGGGTTTCTAGTCATGACCTTA 58.409 41.667 22.21 8.33 33.23 2.69
2029 2658 4.988716 ACCGCGAGAGTGTCCCCA 62.989 66.667 8.23 0.00 40.80 4.96
2082 2711 2.158755 AGCCCAAATATCAGGAGGAACG 60.159 50.000 0.00 0.00 0.00 3.95
2263 2892 1.325943 GCGATTGCTCTTCCTTTCTCG 59.674 52.381 0.00 0.00 38.39 4.04
2299 2928 1.200020 GTTCCCCAATGCTTCTCAACG 59.800 52.381 0.00 0.00 0.00 4.10
2327 2956 4.993029 ACATAAGAGACTACAGACCAGC 57.007 45.455 0.00 0.00 0.00 4.85
2432 3062 5.010617 GGACCTGCAAAGTAAATGGAGAAAA 59.989 40.000 0.00 0.00 38.38 2.29
2463 3100 4.340263 GTTCACGAAGAGTTTCCACAAAC 58.660 43.478 0.00 0.00 42.14 2.93
2469 3106 2.144482 TCCGTTCACGAAGAGTTTCC 57.856 50.000 0.00 0.00 43.02 3.13
2647 3284 1.064060 GTCAACACAGTGTCAGTTGGC 59.936 52.381 20.37 17.08 42.08 4.52
2830 3467 5.042593 GCATCAATATATCTCTCGAGCTGG 58.957 45.833 7.81 0.00 0.00 4.85
2983 3620 0.837272 TAGCATGACAGTTAGGGCCC 59.163 55.000 16.46 16.46 0.00 5.80
3001 3638 4.081142 TCGAAAAGAGTTCCAGGCATGATA 60.081 41.667 0.00 0.00 0.00 2.15
3221 3858 2.028476 CGGTTACAACACTCCCATCTGA 60.028 50.000 0.00 0.00 0.00 3.27
3253 3890 2.421073 TGCAGCATGAGTTATGTGAAGC 59.579 45.455 0.00 0.00 39.69 3.86
3438 4085 6.743575 AGTAACTTCCATCATGCAACTTAC 57.256 37.500 0.00 0.00 0.00 2.34
3513 4160 5.524284 CAGACCAGATAGCACATACACTAC 58.476 45.833 0.00 0.00 0.00 2.73
3548 4195 2.806244 ACGACACTGACAAGTTTATGGC 59.194 45.455 0.00 0.00 32.98 4.40
3575 4222 9.065871 CCAATTTTTAGAGTAATGAAAGCGAAG 57.934 33.333 0.00 0.00 0.00 3.79
3606 4253 5.010933 ACTGACAGTAAGCTTGCTCTAGTA 58.989 41.667 14.73 0.00 0.00 1.82
3607 4254 3.829601 ACTGACAGTAAGCTTGCTCTAGT 59.170 43.478 14.73 14.80 0.00 2.57
3608 4255 4.172505 CACTGACAGTAAGCTTGCTCTAG 58.827 47.826 14.73 14.21 0.00 2.43
3609 4256 3.574396 ACACTGACAGTAAGCTTGCTCTA 59.426 43.478 14.73 3.20 0.00 2.43
3611 4258 2.734079 GACACTGACAGTAAGCTTGCTC 59.266 50.000 14.73 5.49 0.00 4.26
3659 4306 9.077674 GGCATGATATCTCTAAACTTATACACG 57.922 37.037 3.98 0.00 0.00 4.49
3731 4378 1.679139 CTGTTGCTCCACTGTTTCCA 58.321 50.000 0.00 0.00 0.00 3.53
3809 4456 6.183361 TGGAATCATCATCATCATCAAGAGGT 60.183 38.462 0.00 0.00 0.00 3.85
3851 4498 9.079833 CATGTCATCAAAATGATAGGTTGAAAC 57.920 33.333 0.00 0.00 43.62 2.78
3945 4593 3.517100 GGCTGATCTTCCCATATCTGCTA 59.483 47.826 12.04 0.00 43.00 3.49
4063 4712 1.139989 CAGTTAGCGTGACACCACAG 58.860 55.000 0.00 0.00 43.34 3.66
4095 4744 6.482973 GGCATGAAATGGAAAAAGAAAGAACA 59.517 34.615 0.00 0.00 46.86 3.18
4403 5057 0.464036 CCACAGCCGCTATAAGGTCA 59.536 55.000 0.00 0.00 0.00 4.02
4494 5158 0.915872 AGCATGGATGTGAGGACCCA 60.916 55.000 0.00 0.00 0.00 4.51
4499 5163 1.129917 AGAGGAGCATGGATGTGAGG 58.870 55.000 0.00 0.00 0.00 3.86
4505 5169 1.005097 TGCAACAAGAGGAGCATGGAT 59.995 47.619 0.00 0.00 31.05 3.41
4507 5171 0.809385 CTGCAACAAGAGGAGCATGG 59.191 55.000 0.00 0.00 36.28 3.66
4509 5173 1.949547 GCTCTGCAACAAGAGGAGCAT 60.950 52.381 14.85 0.00 45.79 3.79
4511 5175 0.321475 AGCTCTGCAACAAGAGGAGC 60.321 55.000 12.54 12.54 46.54 4.70
4512 5176 1.805345 CAAGCTCTGCAACAAGAGGAG 59.195 52.381 3.19 0.00 43.37 3.69
4513 5177 1.417517 TCAAGCTCTGCAACAAGAGGA 59.582 47.619 3.19 0.00 43.37 3.71
4515 5179 1.805345 CCTCAAGCTCTGCAACAAGAG 59.195 52.381 0.00 0.00 45.52 2.85
4516 5180 1.141657 ACCTCAAGCTCTGCAACAAGA 59.858 47.619 0.00 0.00 0.00 3.02
4517 5181 1.602311 ACCTCAAGCTCTGCAACAAG 58.398 50.000 0.00 0.00 0.00 3.16
4519 5183 1.311859 CAACCTCAAGCTCTGCAACA 58.688 50.000 0.00 0.00 0.00 3.33
4520 5184 0.039708 GCAACCTCAAGCTCTGCAAC 60.040 55.000 0.00 0.00 33.19 4.17
4522 5186 1.148949 TGCAACCTCAAGCTCTGCA 59.851 52.632 0.00 0.00 40.54 4.41
4589 5255 2.224066 CCTTCCGGCATATTCGAAGTCT 60.224 50.000 3.35 0.00 0.00 3.24
4598 5264 2.426023 GCGTCCCTTCCGGCATAT 59.574 61.111 0.00 0.00 0.00 1.78
4682 5348 0.690762 AGCCCGCTCTTTTCAGGTAA 59.309 50.000 0.00 0.00 0.00 2.85
4938 5614 5.879777 TGTACAAAGGTGATGATGTATGTGG 59.120 40.000 0.00 0.00 31.57 4.17
4940 5616 7.828717 TCATTGTACAAAGGTGATGATGTATGT 59.171 33.333 13.23 0.00 31.57 2.29
4941 5617 8.212317 TCATTGTACAAAGGTGATGATGTATG 57.788 34.615 13.23 1.16 31.57 2.39
4994 5672 0.596600 CACTACACTGACGGCGTGTT 60.597 55.000 21.19 0.00 42.56 3.32
5004 5682 4.725790 TCATCACCATCTCACTACACTG 57.274 45.455 0.00 0.00 0.00 3.66
5014 5692 2.022195 GCAGCACATTCATCACCATCT 58.978 47.619 0.00 0.00 0.00 2.90
5018 5696 1.171308 ACTGCAGCACATTCATCACC 58.829 50.000 15.27 0.00 0.00 4.02
5020 5698 1.068125 GCAACTGCAGCACATTCATCA 60.068 47.619 15.27 0.00 41.59 3.07
5068 5789 3.365976 GCAGACTGCAGAGGATGAG 57.634 57.895 23.35 3.82 44.26 2.90
5086 5807 3.431486 GGGAGAGTGGAAAGCAGATAGTG 60.431 52.174 0.00 0.00 0.00 2.74
5087 5808 2.769095 GGGAGAGTGGAAAGCAGATAGT 59.231 50.000 0.00 0.00 0.00 2.12
5088 5809 2.103941 GGGGAGAGTGGAAAGCAGATAG 59.896 54.545 0.00 0.00 0.00 2.08
5089 5810 2.119495 GGGGAGAGTGGAAAGCAGATA 58.881 52.381 0.00 0.00 0.00 1.98
5104 5825 2.506061 CGGAGGATCAGCAGGGGAG 61.506 68.421 0.00 0.00 36.25 4.30
5105 5826 2.444706 CGGAGGATCAGCAGGGGA 60.445 66.667 0.00 0.00 36.25 4.81
5118 5839 1.227674 GCCATGCCTACTTCCGGAG 60.228 63.158 3.34 1.34 0.00 4.63
5119 5840 1.344953 ATGCCATGCCTACTTCCGGA 61.345 55.000 0.00 0.00 0.00 5.14
5120 5841 1.149174 ATGCCATGCCTACTTCCGG 59.851 57.895 0.00 0.00 0.00 5.14
5121 5842 2.324215 CATGCCATGCCTACTTCCG 58.676 57.895 0.00 0.00 0.00 4.30
5141 5862 2.480555 CATTGGCAACGGCTCGAC 59.519 61.111 0.00 0.00 40.87 4.20
5143 5864 1.302383 TAACCATTGGCAACGGCTCG 61.302 55.000 13.04 0.00 40.87 5.03
5158 5879 2.851263 TGGTGATGGTGTCAGTAACC 57.149 50.000 0.00 0.00 37.56 2.85
5160 5881 4.632327 TGAATGGTGATGGTGTCAGTAA 57.368 40.909 0.00 0.00 37.56 2.24
5161 5882 4.224818 TGATGAATGGTGATGGTGTCAGTA 59.775 41.667 0.00 0.00 37.56 2.74
5162 5883 3.009363 TGATGAATGGTGATGGTGTCAGT 59.991 43.478 0.00 0.00 37.56 3.41
5163 5884 3.376234 GTGATGAATGGTGATGGTGTCAG 59.624 47.826 0.00 0.00 37.56 3.51
5174 6109 6.152661 ACAATTTAATCCGTGTGATGAATGGT 59.847 34.615 0.00 0.00 32.68 3.55
5175 6110 6.563422 ACAATTTAATCCGTGTGATGAATGG 58.437 36.000 0.00 0.00 32.68 3.16
5219 6154 0.322816 TGGCCACCTTCTGAATCTGC 60.323 55.000 0.00 0.00 0.00 4.26
5284 6227 3.501458 GACCGCGACCAGATAGGGC 62.501 68.421 8.23 0.00 44.64 5.19
5298 6241 1.736645 CCGGCTTGTACAGTGACCG 60.737 63.158 16.46 16.46 40.30 4.79
5313 6256 4.648626 ATGGATGGATGCCGCCGG 62.649 66.667 0.00 0.00 0.00 6.13
5340 6519 2.095978 AACAACGGGACTAGCGCACT 62.096 55.000 11.47 0.00 0.00 4.40
5341 6520 1.226030 AAACAACGGGACTAGCGCAC 61.226 55.000 11.47 0.00 0.00 5.34
5345 6524 0.796927 GCTGAAACAACGGGACTAGC 59.203 55.000 0.00 0.00 0.00 3.42
5436 6621 0.026803 GGTCCGTGCTAGTACGTACG 59.973 60.000 27.80 15.01 42.24 3.67
5437 6622 0.026803 CGGTCCGTGCTAGTACGTAC 59.973 60.000 27.80 23.18 42.24 3.67
5438 6623 0.391130 ACGGTCCGTGCTAGTACGTA 60.391 55.000 27.80 13.36 42.24 3.57
5439 6624 1.237285 AACGGTCCGTGCTAGTACGT 61.237 55.000 27.80 9.77 39.99 3.57
5440 6625 0.109597 AAACGGTCCGTGCTAGTACG 60.110 55.000 24.32 24.32 39.99 3.67
5442 6627 1.936203 GCAAAACGGTCCGTGCTAGTA 60.936 52.381 19.67 0.00 39.99 1.82
5443 6628 1.226030 GCAAAACGGTCCGTGCTAGT 61.226 55.000 19.67 0.00 39.99 2.57
5444 6629 0.949105 AGCAAAACGGTCCGTGCTAG 60.949 55.000 22.36 12.59 39.99 3.42
5445 6630 0.947180 GAGCAAAACGGTCCGTGCTA 60.947 55.000 23.35 0.00 39.99 3.49
5446 6631 2.203153 AGCAAAACGGTCCGTGCT 60.203 55.556 19.67 19.37 39.99 4.40
5447 6632 2.251371 GAGCAAAACGGTCCGTGC 59.749 61.111 19.67 17.27 39.99 5.34
5452 6637 1.216941 TTCGACGGAGCAAAACGGTC 61.217 55.000 0.00 0.00 41.64 4.79
5453 6638 0.601841 ATTCGACGGAGCAAAACGGT 60.602 50.000 0.00 0.00 0.00 4.83
5454 6639 0.515564 AATTCGACGGAGCAAAACGG 59.484 50.000 0.00 0.00 0.00 4.44
5456 6641 2.223377 AGTGAATTCGACGGAGCAAAAC 59.777 45.455 0.04 0.00 0.00 2.43
5457 6642 2.223144 CAGTGAATTCGACGGAGCAAAA 59.777 45.455 0.04 0.00 0.00 2.44
5458 6643 1.798223 CAGTGAATTCGACGGAGCAAA 59.202 47.619 0.04 0.00 0.00 3.68
5459 6644 1.428448 CAGTGAATTCGACGGAGCAA 58.572 50.000 0.04 0.00 0.00 3.91
5460 6645 1.014044 GCAGTGAATTCGACGGAGCA 61.014 55.000 0.04 0.00 0.00 4.26
5493 6678 6.587990 GTGTGCTGATATACTAGTATGGCTTG 59.412 42.308 23.09 11.41 0.00 4.01
5515 6700 0.537188 GGATCGACCCATGTCAGTGT 59.463 55.000 0.00 0.00 41.85 3.55
5527 6712 0.947244 GTGGCATTGGATGGATCGAC 59.053 55.000 0.00 0.00 0.00 4.20
5606 6791 5.252586 ACAGAGTTACTCCTACAGTGGTA 57.747 43.478 8.96 0.00 36.43 3.25
5613 6798 5.415077 TGCAGTCTTACAGAGTTACTCCTAC 59.585 44.000 8.96 0.00 0.00 3.18
5614 6799 5.567430 TGCAGTCTTACAGAGTTACTCCTA 58.433 41.667 8.96 0.00 0.00 2.94
5615 6800 4.408276 TGCAGTCTTACAGAGTTACTCCT 58.592 43.478 8.96 0.00 0.00 3.69
5616 6801 4.785511 TGCAGTCTTACAGAGTTACTCC 57.214 45.455 8.96 0.00 0.00 3.85
5617 6802 6.015027 TCTTGCAGTCTTACAGAGTTACTC 57.985 41.667 3.85 3.85 0.00 2.59
5618 6803 6.406692 TTCTTGCAGTCTTACAGAGTTACT 57.593 37.500 0.00 0.00 0.00 2.24
5665 6850 2.543641 CGTTTACCGGGAATCCACTAC 58.456 52.381 6.32 0.00 0.00 2.73
5682 6867 4.018490 ACACCTGTTTTTCTTTACCCGTT 58.982 39.130 0.00 0.00 0.00 4.44
5683 6868 3.379057 CACACCTGTTTTTCTTTACCCGT 59.621 43.478 0.00 0.00 0.00 5.28
5684 6869 3.628487 TCACACCTGTTTTTCTTTACCCG 59.372 43.478 0.00 0.00 0.00 5.28
5685 6870 5.585820 TTCACACCTGTTTTTCTTTACCC 57.414 39.130 0.00 0.00 0.00 3.69
5686 6871 5.983118 CCATTCACACCTGTTTTTCTTTACC 59.017 40.000 0.00 0.00 0.00 2.85
5687 6872 5.462068 GCCATTCACACCTGTTTTTCTTTAC 59.538 40.000 0.00 0.00 0.00 2.01
5688 6873 5.452636 GGCCATTCACACCTGTTTTTCTTTA 60.453 40.000 0.00 0.00 0.00 1.85
5689 6874 4.441792 GCCATTCACACCTGTTTTTCTTT 58.558 39.130 0.00 0.00 0.00 2.52
5721 6906 2.733026 GCAACAAAGCAAAGCGATTGAT 59.267 40.909 14.38 0.09 41.85 2.57


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

AutoCloner maintained by Alex Coulton.