Multiple sequence alignment - TraesCS2B01G099600

Loading Multiple Alignment...

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 TraesCS2B01G099600 chr2B 100.000 5294 0 0 1 5294 58974929 58980222 0.000000e+00 9777.0
1 TraesCS2B01G099600 chr2B 95.897 195 8 0 1989 2183 58976728 58976922 3.080000e-82 316.0
2 TraesCS2B01G099600 chr2B 95.897 195 8 0 1800 1994 58976917 58977111 3.080000e-82 316.0
3 TraesCS2B01G099600 chr2A 96.828 4792 138 6 1 4788 38964045 38968826 0.000000e+00 7995.0
4 TraesCS2B01G099600 chr2A 97.949 195 4 0 1800 1994 38966030 38966224 6.570000e-89 339.0
5 TraesCS2B01G099600 chr2A 96.410 195 7 0 1989 2183 38965841 38966035 6.610000e-84 322.0
6 TraesCS2B01G099600 chr2A 90.438 251 10 3 4808 5058 38968811 38969047 8.560000e-83 318.0
7 TraesCS2B01G099600 chr2A 91.667 96 6 2 4379 4473 161948591 161948685 1.200000e-26 132.0
8 TraesCS2B01G099600 chr2D 96.663 4105 121 7 278 4375 35780356 35784451 0.000000e+00 6807.0
9 TraesCS2B01G099600 chr2D 94.883 469 16 4 4808 5275 35784757 35785218 0.000000e+00 726.0
10 TraesCS2B01G099600 chr2D 96.605 324 9 2 4466 4788 35784450 35784772 2.170000e-148 536.0
11 TraesCS2B01G099600 chr2D 97.627 295 7 0 3 297 35779992 35780286 1.700000e-139 507.0
12 TraesCS2B01G099600 chr2D 97.949 195 4 0 1800 1994 35782062 35782256 6.570000e-89 339.0
13 TraesCS2B01G099600 chr2D 96.410 195 7 0 1989 2183 35781873 35782067 6.610000e-84 322.0
14 TraesCS2B01G099600 chr2D 100.000 30 0 0 836 865 35780301 35780330 7.410000e-04 56.5
15 TraesCS2B01G099600 chr4B 72.929 676 155 23 2795 3450 107237198 107237865 5.370000e-50 209.0
16 TraesCS2B01G099600 chr4A 71.917 673 159 23 2799 3450 512580706 512580043 9.120000e-38 169.0
17 TraesCS2B01G099600 chr7A 95.294 85 4 0 4379 4463 82512318 82512402 9.250000e-28 135.0
18 TraesCS2B01G099600 chr6B 94.253 87 5 0 4379 4465 472612145 472612059 3.330000e-27 134.0
19 TraesCS2B01G099600 chr6B 91.579 95 7 1 4375 4468 76149744 76149838 4.300000e-26 130.0
20 TraesCS2B01G099600 chr5B 94.253 87 5 0 4378 4464 62940322 62940408 3.330000e-27 134.0
21 TraesCS2B01G099600 chr5B 91.579 95 7 1 4377 4471 140965928 140966021 4.300000e-26 130.0
22 TraesCS2B01G099600 chr5D 91.579 95 7 1 4377 4471 128577586 128577679 4.300000e-26 130.0
23 TraesCS2B01G099600 chr5A 91.579 95 7 1 4377 4471 450750794 450750701 4.300000e-26 130.0


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 TraesCS2B01G099600 chr2B 58974929 58980222 5293 False 3469.666667 9777 97.264667 1 5294 3 chr2B.!!$F1 5293
1 TraesCS2B01G099600 chr2A 38964045 38969047 5002 False 2243.500000 7995 95.406250 1 5058 4 chr2A.!!$F2 5057
2 TraesCS2B01G099600 chr2D 35779992 35785218 5226 False 1327.642857 6807 97.162429 3 5275 7 chr2D.!!$F1 5272
3 TraesCS2B01G099600 chr4B 107237198 107237865 667 False 209.000000 209 72.929000 2795 3450 1 chr4B.!!$F1 655

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
923 1020 2.030946 GCATCCGTTATCTGCTGTGAAC 59.969 50.000 0.00 0.0 33.15 3.18 F
1723 1820 0.465460 TGCACAGGAAACCACAGGTC 60.465 55.000 0.00 0.0 33.12 3.85 F
2024 2121 0.598065 ACAAGCGGGCAAAGTCAATC 59.402 50.000 0.00 0.0 0.00 2.67 F
2607 2704 1.276421 ACTAACGCTGACAGGCAATCT 59.724 47.619 4.26 0.0 0.00 2.40 F
4032 4144 1.220206 CTCGAGCCCTCATGCTTGT 59.780 57.895 0.00 0.0 42.95 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2544 1.073125 TCCTAGCTGATCTCCGGAGAG 59.927 57.143 35.72 24.46 41.33 3.20 R
3494 3606 0.036952 TCCTCTACTGCTTGCACTGC 60.037 55.000 4.10 4.10 0.00 4.40 R
3991 4103 0.318762 GTCCAGTCAGGTGTCCAGTC 59.681 60.000 0.00 0.00 39.02 3.51 R
4040 4152 1.402194 GCTCGATGATCTCACCGATCC 60.402 57.143 0.00 0.00 41.66 3.36 R
4982 5095 0.261991 AGGGACCAGCGAAGGAGATA 59.738 55.000 0.16 0.00 0.00 1.98 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
140 141 6.092259 GTCGAGAATGGCACTGTATTTACTTT 59.908 38.462 0.00 0.00 0.00 2.66
141 142 6.092122 TCGAGAATGGCACTGTATTTACTTTG 59.908 38.462 0.00 0.00 0.00 2.77
179 180 8.773404 TTACTTCTCTATTTGTTTCTAGTGGC 57.227 34.615 0.00 0.00 0.00 5.01
350 444 2.176273 GCTGGCCACGTAGCTGATG 61.176 63.158 0.00 0.00 36.99 3.07
438 535 6.698008 TGTCAATCTTGTTCACATGTCTTT 57.302 33.333 0.00 0.00 0.00 2.52
700 797 7.775120 AGGAAACTATCTATTTACGAACGGAA 58.225 34.615 0.00 0.00 40.61 4.30
780 877 9.034800 ACTTATTGTTATGGAATCCACAAATGT 57.965 29.630 3.09 3.22 35.80 2.71
867 964 5.098211 GTCCTGATGCAGTAAATTTTCAGC 58.902 41.667 9.01 7.34 31.45 4.26
923 1020 2.030946 GCATCCGTTATCTGCTGTGAAC 59.969 50.000 0.00 0.00 33.15 3.18
985 1082 2.186076 CGTGAGAGCTTCGTGGTATTC 58.814 52.381 0.00 0.00 0.00 1.75
1474 1571 1.750193 CAAATGCGATGTACCTGGGT 58.250 50.000 0.00 0.00 0.00 4.51
1478 1575 1.783071 TGCGATGTACCTGGGTATGA 58.217 50.000 2.63 0.00 32.82 2.15
1533 1630 6.810676 GTCAGATGCGATATCAGTATCACAAT 59.189 38.462 19.37 4.87 37.20 2.71
1616 1713 6.542370 AAGTACAACTTGCAAGAACAGTATGT 59.458 34.615 32.50 22.24 45.11 2.29
1629 1726 2.892374 CAGTATGTGCCGACTTCATCA 58.108 47.619 0.00 0.00 0.00 3.07
1659 1756 5.070001 CCCACTAATTCTCAAGTTCCAACA 58.930 41.667 0.00 0.00 0.00 3.33
1723 1820 0.465460 TGCACAGGAAACCACAGGTC 60.465 55.000 0.00 0.00 33.12 3.85
1740 1837 2.092914 AGGTCCGAATCCAAGGATGAAC 60.093 50.000 1.66 0.00 38.97 3.18
1742 1839 0.657840 CCGAATCCAAGGATGAACGC 59.342 55.000 1.66 0.00 34.70 4.84
1749 1846 3.976701 AAGGATGAACGCGGCCCAG 62.977 63.158 12.47 0.00 0.00 4.45
1750 1847 4.778143 GGATGAACGCGGCCCAGT 62.778 66.667 12.47 0.00 0.00 4.00
1821 1918 3.802948 AGTCAGTCAAGAACGACAAGT 57.197 42.857 0.00 0.00 38.43 3.16
1869 1966 3.892284 TCAAGAAAAACCTGCTGTACCA 58.108 40.909 0.00 0.00 0.00 3.25
2024 2121 0.598065 ACAAGCGGGCAAAGTCAATC 59.402 50.000 0.00 0.00 0.00 2.67
2036 2133 4.857588 GCAAAGTCAATCTTCAGCAATGAG 59.142 41.667 0.00 0.00 37.19 2.90
2120 2217 3.434596 CCTCCTGATCCAAGCATCATTGA 60.435 47.826 0.00 0.00 32.21 2.57
2166 2263 1.545759 CATCTGCAGCTTCAAATGCG 58.454 50.000 9.47 0.00 45.54 4.73
2187 2284 1.450312 GAATGTCCCTGGTCCTGCG 60.450 63.158 0.00 0.00 0.00 5.18
2245 2342 7.492344 CCAAAATAAGGATAAATGTGGCAGAAC 59.508 37.037 0.00 0.00 0.00 3.01
2268 2365 4.537015 GCGATATAAAAGGGCATGACAAC 58.463 43.478 0.00 0.00 0.00 3.32
2303 2400 4.809815 AGGAAGCTAACGAGTCGTATAC 57.190 45.455 20.23 10.92 39.99 1.47
2320 2417 7.397192 AGTCGTATACTACAAAGGGGAAAGTTA 59.603 37.037 9.91 0.00 36.36 2.24
2338 2435 7.169813 GGAAAGTTAAAATTCCAGCAAAGACTG 59.830 37.037 13.20 0.00 43.73 3.51
2373 2470 4.278170 TCTGCCCAAACTGTAAACATGAAG 59.722 41.667 0.00 0.00 0.00 3.02
2446 2543 1.877672 AAATGCTGCAGGATCCCCCA 61.878 55.000 21.89 5.76 37.41 4.96
2447 2544 2.578586 AATGCTGCAGGATCCCCCAC 62.579 60.000 21.89 0.00 37.41 4.61
2534 2631 6.858478 AGCAAAAAGAAGCGAAGAAAGAATAC 59.142 34.615 0.00 0.00 35.48 1.89
2542 2639 6.487689 AGCGAAGAAAGAATACTTTTCCAG 57.512 37.500 0.00 0.00 44.97 3.86
2544 2641 5.316770 CGAAGAAAGAATACTTTTCCAGCG 58.683 41.667 0.00 0.00 44.97 5.18
2607 2704 1.276421 ACTAACGCTGACAGGCAATCT 59.724 47.619 4.26 0.00 0.00 2.40
2619 2716 2.681848 CAGGCAATCTGTTCCATCTGAC 59.318 50.000 0.00 0.00 38.64 3.51
2717 2814 6.274157 AGTTACAGATACTGTTGGTCAGAG 57.726 41.667 9.63 0.00 42.59 3.35
2760 2857 2.704572 CTTTCTTTCCCTGACGCAGAT 58.295 47.619 8.20 0.00 32.44 2.90
2880 2977 6.321717 TGCTAGAATAAAAAGTTTGGATGCG 58.678 36.000 0.00 0.00 0.00 4.73
3244 3356 3.416156 GTCAGGATTGAAGGCTTTGTCT 58.584 45.455 0.00 0.00 34.49 3.41
3494 3606 3.446161 ACATCCATTGATTTGAGCACTGG 59.554 43.478 0.00 0.00 37.41 4.00
3523 3635 5.693814 CAAGCAGTAGAGGAAAACATGAAC 58.306 41.667 0.00 0.00 0.00 3.18
3537 3649 9.912634 GGAAAACATGAACATATTTCTTCTGAA 57.087 29.630 0.00 0.00 31.71 3.02
3557 3669 3.228188 ACCAAAGACATCCTTGCAGAA 57.772 42.857 0.00 0.00 34.79 3.02
3762 3874 3.440228 GGTAAGCAAAGTCGAGCTAGAG 58.560 50.000 0.00 0.00 40.90 2.43
3897 4009 4.580995 TGGACAACCATGTACGAAACAAAT 59.419 37.500 0.00 0.00 43.92 2.32
3939 4051 1.586154 GCACCGGACATGACCCAAAG 61.586 60.000 9.46 0.00 0.00 2.77
3955 4067 4.202388 ACCCAAAGCAGCAGATTGAAATTT 60.202 37.500 0.00 0.00 0.00 1.82
3991 4103 4.818546 GTGAGATTTGGGTCATCTACATGG 59.181 45.833 0.00 0.00 30.70 3.66
4032 4144 1.220206 CTCGAGCCCTCATGCTTGT 59.780 57.895 0.00 0.00 42.95 3.16
4040 4152 1.479323 CCCTCATGCTTGTGGATTTGG 59.521 52.381 19.26 1.90 38.53 3.28
4285 4397 4.579869 TCCAGATGTCTTCCTTTACAAGC 58.420 43.478 0.00 0.00 0.00 4.01
4291 4403 3.084786 GTCTTCCTTTACAAGCATGCCT 58.915 45.455 15.66 0.00 0.00 4.75
4292 4404 3.084039 TCTTCCTTTACAAGCATGCCTG 58.916 45.455 15.66 15.20 0.00 4.85
4360 4472 5.542779 ACTAGAATCATGTCTTATTCCGCC 58.457 41.667 0.00 0.00 33.44 6.13
4389 4501 1.760192 TTCTACAGTACTCCCTCCGC 58.240 55.000 0.00 0.00 0.00 5.54
4418 4530 9.469807 AGAAATATAAGAGCGTTTAGATCACTG 57.530 33.333 0.00 0.00 37.82 3.66
4421 4533 2.886081 AGAGCGTTTAGATCACTGCTG 58.114 47.619 0.00 0.00 37.82 4.41
4422 4534 2.232452 AGAGCGTTTAGATCACTGCTGT 59.768 45.455 0.00 0.00 37.82 4.40
4683 4796 2.832129 AGTTTGCTCGGGATAGAGTTGA 59.168 45.455 0.00 0.00 40.26 3.18
4751 4864 1.816835 AGCACATCCGTTCTACTCGAA 59.183 47.619 0.00 0.00 0.00 3.71
4753 4866 2.535984 GCACATCCGTTCTACTCGAATG 59.464 50.000 0.00 0.00 38.18 2.67
4772 4885 4.675063 ATGGTTCTTTACTGGGATTGGT 57.325 40.909 0.00 0.00 0.00 3.67
4773 4886 4.463050 TGGTTCTTTACTGGGATTGGTT 57.537 40.909 0.00 0.00 0.00 3.67
4774 4887 4.403734 TGGTTCTTTACTGGGATTGGTTC 58.596 43.478 0.00 0.00 0.00 3.62
4775 4888 3.439129 GGTTCTTTACTGGGATTGGTTCG 59.561 47.826 0.00 0.00 0.00 3.95
4776 4889 4.070009 GTTCTTTACTGGGATTGGTTCGT 58.930 43.478 0.00 0.00 0.00 3.85
4777 4890 3.670625 TCTTTACTGGGATTGGTTCGTG 58.329 45.455 0.00 0.00 0.00 4.35
4778 4891 1.816074 TTACTGGGATTGGTTCGTGC 58.184 50.000 0.00 0.00 0.00 5.34
4779 4892 0.035820 TACTGGGATTGGTTCGTGCC 60.036 55.000 0.00 0.00 0.00 5.01
4780 4893 2.034999 TGGGATTGGTTCGTGCCC 59.965 61.111 0.00 0.00 39.29 5.36
4781 4894 2.355115 GGGATTGGTTCGTGCCCT 59.645 61.111 0.00 0.00 35.86 5.19
4782 4895 1.202099 TGGGATTGGTTCGTGCCCTA 61.202 55.000 0.00 0.00 39.57 3.53
4783 4896 0.463833 GGGATTGGTTCGTGCCCTAG 60.464 60.000 0.00 0.00 35.86 3.02
4784 4897 0.252197 GGATTGGTTCGTGCCCTAGT 59.748 55.000 0.00 0.00 0.00 2.57
4785 4898 1.339727 GGATTGGTTCGTGCCCTAGTT 60.340 52.381 0.00 0.00 0.00 2.24
4786 4899 2.433436 GATTGGTTCGTGCCCTAGTTT 58.567 47.619 0.00 0.00 0.00 2.66
4787 4900 2.351706 TTGGTTCGTGCCCTAGTTTT 57.648 45.000 0.00 0.00 0.00 2.43
4788 4901 2.351706 TGGTTCGTGCCCTAGTTTTT 57.648 45.000 0.00 0.00 0.00 1.94
4882 4995 5.764686 TGCATTCTTAGTACCCAGCAATATG 59.235 40.000 0.00 0.00 0.00 1.78
4927 5040 4.378874 GCAGGAAGCAACATCTTCAACTAC 60.379 45.833 5.96 0.00 43.14 2.73
4939 5052 7.418840 CATCTTCAACTACCATAAGATGCTC 57.581 40.000 10.07 0.00 44.76 4.26
5007 5120 0.035458 CTTCGCTGGTCCCTGAAACT 59.965 55.000 0.00 0.00 0.00 2.66
5009 5122 0.895530 TCGCTGGTCCCTGAAACTAG 59.104 55.000 0.00 0.00 0.00 2.57
5100 5213 8.552865 CATGGTTGGTGCATTTTGATATAATTG 58.447 33.333 0.00 0.00 0.00 2.32
5153 5267 2.751259 CTGTAGCAGCATCATTGTTGGT 59.249 45.455 0.00 0.54 45.17 3.67
5154 5268 3.156293 TGTAGCAGCATCATTGTTGGTT 58.844 40.909 0.00 0.00 41.25 3.67
5155 5269 3.573538 TGTAGCAGCATCATTGTTGGTTT 59.426 39.130 0.00 0.00 41.25 3.27
5184 5298 0.958876 TTCTGGAGTAGCTGCGTCGA 60.959 55.000 0.00 0.00 0.00 4.20
5275 5389 8.983724 GTAGGAAAAATCTGCTACATCTCATAC 58.016 37.037 0.00 0.00 39.37 2.39
5276 5390 7.568349 AGGAAAAATCTGCTACATCTCATACA 58.432 34.615 0.00 0.00 0.00 2.29
5277 5391 7.497249 AGGAAAAATCTGCTACATCTCATACAC 59.503 37.037 0.00 0.00 0.00 2.90
5278 5392 6.834959 AAAATCTGCTACATCTCATACACG 57.165 37.500 0.00 0.00 0.00 4.49
5279 5393 5.521906 AATCTGCTACATCTCATACACGT 57.478 39.130 0.00 0.00 0.00 4.49
5280 5394 4.292977 TCTGCTACATCTCATACACGTG 57.707 45.455 15.48 15.48 0.00 4.49
5281 5395 3.066760 TCTGCTACATCTCATACACGTGG 59.933 47.826 21.57 1.74 0.00 4.94
5282 5396 2.128035 GCTACATCTCATACACGTGGC 58.872 52.381 21.57 4.84 0.00 5.01
5283 5397 2.385315 CTACATCTCATACACGTGGCG 58.615 52.381 21.57 7.66 0.00 5.69
5284 5398 0.806102 ACATCTCATACACGTGGCGC 60.806 55.000 21.57 0.00 0.00 6.53
5285 5399 0.528466 CATCTCATACACGTGGCGCT 60.528 55.000 21.57 0.32 0.00 5.92
5286 5400 0.175760 ATCTCATACACGTGGCGCTT 59.824 50.000 21.57 0.00 0.00 4.68
5287 5401 0.735978 TCTCATACACGTGGCGCTTG 60.736 55.000 21.57 9.50 0.00 4.01
5288 5402 2.098298 CATACACGTGGCGCTTGC 59.902 61.111 21.57 0.00 38.11 4.01
5289 5403 2.047274 ATACACGTGGCGCTTGCT 60.047 55.556 21.57 0.00 39.13 3.91
5290 5404 1.081556 CATACACGTGGCGCTTGCTA 61.082 55.000 21.57 0.17 39.13 3.49
5291 5405 1.082117 ATACACGTGGCGCTTGCTAC 61.082 55.000 21.57 0.00 45.70 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.683876 TGGGTTGTTCAAGGAAAATTTGA 57.316 34.783 0.00 0.00 33.00 2.69
179 180 0.254747 TGACCGGAAAGGGGCATAAG 59.745 55.000 9.46 0.00 41.26 1.73
350 444 9.865484 GTAAGGAAGAGCGAATTGTTATTTATC 57.135 33.333 0.00 0.00 0.00 1.75
438 535 3.873952 GGCAATACCAGCAACAACAAAAA 59.126 39.130 0.00 0.00 38.86 1.94
443 540 3.317150 GAAAGGCAATACCAGCAACAAC 58.683 45.455 0.00 0.00 43.14 3.32
445 542 1.539388 CGAAAGGCAATACCAGCAACA 59.461 47.619 0.00 0.00 43.14 3.33
446 543 1.810151 TCGAAAGGCAATACCAGCAAC 59.190 47.619 0.00 0.00 43.14 4.17
700 797 7.962995 ACGAGACCACATATGATATATTCCT 57.037 36.000 10.38 0.00 0.00 3.36
826 923 9.014297 CATCAGGACCTACAAATTTAAGAAGTT 57.986 33.333 0.00 0.00 0.00 2.66
827 924 7.121315 GCATCAGGACCTACAAATTTAAGAAGT 59.879 37.037 0.00 0.00 0.00 3.01
867 964 9.090692 GGATCAATTTCTCAAACAACAATATGG 57.909 33.333 0.00 0.00 0.00 2.74
985 1082 5.359009 ACTCCATCATAATCACTGCCAAAAG 59.641 40.000 0.00 0.00 0.00 2.27
1474 1571 7.888021 ACATATGGTCCAAAAAGTCAGTTCATA 59.112 33.333 7.80 0.00 0.00 2.15
1478 1575 5.243730 CCACATATGGTCCAAAAAGTCAGTT 59.756 40.000 7.80 0.00 41.64 3.16
1502 1599 4.987285 ACTGATATCGCATCTGACAATGAC 59.013 41.667 0.00 0.00 0.00 3.06
1533 1630 4.142160 CGGATCAGAGTGTTTAGGACATGA 60.142 45.833 0.00 0.00 41.10 3.07
1602 1699 1.128692 GTCGGCACATACTGTTCTTGC 59.871 52.381 0.00 0.00 0.00 4.01
1616 1713 2.611971 GGTACACTTGATGAAGTCGGCA 60.612 50.000 0.00 0.00 40.68 5.69
1659 1756 4.142469 CCTTGTTGACTTGGAAACGTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
1723 1820 0.657840 GCGTTCATCCTTGGATTCGG 59.342 55.000 15.05 1.72 0.00 4.30
1742 1839 3.229156 TAACCGTCACACTGGGCCG 62.229 63.158 0.00 0.00 0.00 6.13
1749 1846 2.482721 CCCTTTCATGTAACCGTCACAC 59.517 50.000 0.00 0.00 0.00 3.82
1750 1847 2.105134 ACCCTTTCATGTAACCGTCACA 59.895 45.455 0.00 0.00 0.00 3.58
1821 1918 2.433604 TGCTGAAAATTGACTTTGCCCA 59.566 40.909 0.00 0.00 0.00 5.36
1869 1966 4.081531 CCACCCATATGTTCATTTGCAGTT 60.082 41.667 1.24 0.00 0.00 3.16
2024 2121 5.689068 GGTTTTTCTTGACTCATTGCTGAAG 59.311 40.000 0.00 0.00 0.00 3.02
2036 2133 3.303791 CGGTACAGCAGGTTTTTCTTGAC 60.304 47.826 0.00 0.00 0.00 3.18
2095 2192 2.781757 TGATGCTTGGATCAGGAGGATT 59.218 45.455 0.68 0.00 36.00 3.01
2120 2217 2.300437 GCTCTACCTGACTTTGGTCTGT 59.700 50.000 0.00 0.00 42.54 3.41
2166 2263 1.748591 GCAGGACCAGGGACATTCATC 60.749 57.143 0.00 0.00 0.00 2.92
2187 2284 7.798982 GTGTTTACACTTGTAGATGAAAGCTTC 59.201 37.037 0.00 0.00 43.25 3.86
2203 2300 8.250332 CCTTATTTTGGCATATGTGTTTACACT 58.750 33.333 13.61 3.14 46.55 3.55
2245 2342 2.805671 TGTCATGCCCTTTTATATCGCG 59.194 45.455 0.00 0.00 0.00 5.87
2268 2365 1.208293 GCTTCCTTCTCACCACTAGGG 59.792 57.143 0.00 0.00 44.81 3.53
2277 2374 2.161808 CGACTCGTTAGCTTCCTTCTCA 59.838 50.000 0.00 0.00 0.00 3.27
2303 2400 7.958088 TGGAATTTTAACTTTCCCCTTTGTAG 58.042 34.615 11.35 0.00 40.61 2.74
2320 2417 6.225981 ACTTTCAGTCTTTGCTGGAATTTT 57.774 33.333 0.00 0.00 33.86 1.82
2338 2435 6.152379 CAGTTTGGGCAGAAGATTTACTTTC 58.848 40.000 0.00 0.00 39.13 2.62
2373 2470 5.560966 TCTTTCTGTCAAAAACACCTGTC 57.439 39.130 0.00 0.00 33.24 3.51
2446 2543 1.202879 CCTAGCTGATCTCCGGAGAGT 60.203 57.143 35.72 24.31 41.33 3.24
2447 2544 1.073125 TCCTAGCTGATCTCCGGAGAG 59.927 57.143 35.72 24.46 41.33 3.20
2542 2639 1.202222 CCCATTCAAGTCAGCATTCGC 60.202 52.381 0.00 0.00 38.99 4.70
2544 2641 3.428589 GCTTCCCATTCAAGTCAGCATTC 60.429 47.826 0.00 0.00 0.00 2.67
2553 2650 7.982919 TCATCAAATATTTGCTTCCCATTCAAG 59.017 33.333 21.15 0.35 38.05 3.02
2619 2716 2.148916 TGTCTACTTTGCCAGACACG 57.851 50.000 0.44 0.00 44.70 4.49
2717 2814 4.378874 GCTTCACAGAATAGCAAGGTTGAC 60.379 45.833 0.00 0.00 35.05 3.18
3093 3205 3.652869 TCCATCCCTTATAAAGAGCCCAG 59.347 47.826 0.00 0.00 0.00 4.45
3244 3356 5.992829 TCTCCTTAACTGTCGCAAATAAACA 59.007 36.000 0.00 0.00 0.00 2.83
3494 3606 0.036952 TCCTCTACTGCTTGCACTGC 60.037 55.000 4.10 4.10 0.00 4.40
3523 3635 8.186821 GGATGTCTTTGGTTCAGAAGAAATATG 58.813 37.037 0.00 0.00 31.57 1.78
3537 3649 2.957402 TCTGCAAGGATGTCTTTGGT 57.043 45.000 6.94 0.00 34.05 3.67
3557 3669 4.623863 AGCATTAGGACCATTGGGATTTT 58.376 39.130 7.78 0.00 38.05 1.82
3762 3874 5.696270 CCAGGTCAAATAAACTTTGAAAGGC 59.304 40.000 10.02 0.00 39.76 4.35
3806 3918 0.671781 CCACTGTTTCTCCTGCTCCG 60.672 60.000 0.00 0.00 0.00 4.63
3897 4009 9.534565 GTGCATACTAAATGAGAGAAAGTATCA 57.465 33.333 0.00 0.00 32.44 2.15
3939 4051 3.181527 GCGGAAAAATTTCAATCTGCTGC 60.182 43.478 18.15 4.58 40.27 5.25
3955 4067 3.695830 AATCTCACCTACTTGCGGAAA 57.304 42.857 0.00 0.00 0.00 3.13
3991 4103 0.318762 GTCCAGTCAGGTGTCCAGTC 59.681 60.000 0.00 0.00 39.02 3.51
4032 4144 1.578897 TCTCACCGATCCCAAATCCA 58.421 50.000 0.00 0.00 0.00 3.41
4040 4152 1.402194 GCTCGATGATCTCACCGATCC 60.402 57.143 0.00 0.00 41.66 3.36
4056 4168 2.512301 GCTAGCTTCAGTGCGCTCG 61.512 63.158 9.73 1.74 37.68 5.03
4291 4403 2.416680 TTTCCATCGGCATGTCATCA 57.583 45.000 0.00 0.00 0.00 3.07
4292 4404 2.542411 GCTTTTCCATCGGCATGTCATC 60.542 50.000 0.00 0.00 0.00 2.92
4418 4530 4.522722 AGAGTGTTTAGGTCACTACAGC 57.477 45.455 0.00 0.00 44.68 4.40
4598 4711 2.126228 CTTTACTGACGGGCGCGA 60.126 61.111 30.98 7.34 0.00 5.87
4683 4796 3.804036 TGATCAAGAACTTTCACACCGT 58.196 40.909 0.00 0.00 0.00 4.83
4751 4864 4.675063 ACCAATCCCAGTAAAGAACCAT 57.325 40.909 0.00 0.00 0.00 3.55
4753 4866 3.439129 CGAACCAATCCCAGTAAAGAACC 59.561 47.826 0.00 0.00 0.00 3.62
4795 4908 4.674281 AGGGCACAAATCCGTTTAAAAA 57.326 36.364 0.00 0.00 0.00 1.94
4796 4909 4.828387 ACTAGGGCACAAATCCGTTTAAAA 59.172 37.500 0.00 0.00 0.00 1.52
4797 4910 4.400120 ACTAGGGCACAAATCCGTTTAAA 58.600 39.130 0.00 0.00 0.00 1.52
4798 4911 4.023726 ACTAGGGCACAAATCCGTTTAA 57.976 40.909 0.00 0.00 0.00 1.52
4799 4912 3.706600 ACTAGGGCACAAATCCGTTTA 57.293 42.857 0.00 0.00 0.00 2.01
4800 4913 2.579410 ACTAGGGCACAAATCCGTTT 57.421 45.000 0.00 0.00 0.00 3.60
4801 4914 2.579410 AACTAGGGCACAAATCCGTT 57.421 45.000 0.00 0.00 0.00 4.44
4802 4915 2.556622 CAAAACTAGGGCACAAATCCGT 59.443 45.455 0.00 0.00 0.00 4.69
4803 4916 2.094752 CCAAAACTAGGGCACAAATCCG 60.095 50.000 0.00 0.00 0.00 4.18
4804 4917 3.592898 CCAAAACTAGGGCACAAATCC 57.407 47.619 0.00 0.00 0.00 3.01
4891 5004 2.419324 GCTTCCTGCTCTGCATATATGC 59.581 50.000 27.45 27.45 45.50 3.14
4904 5017 2.555757 AGTTGAAGATGTTGCTTCCTGC 59.444 45.455 0.00 0.00 42.79 4.85
4919 5032 5.592104 TCGAGCATCTTATGGTAGTTGAA 57.408 39.130 0.00 0.00 41.77 2.69
4927 5040 5.967674 GTGTTTCAAATCGAGCATCTTATGG 59.032 40.000 0.00 0.00 0.00 2.74
4982 5095 0.261991 AGGGACCAGCGAAGGAGATA 59.738 55.000 0.16 0.00 0.00 1.98
4983 5096 1.002274 AGGGACCAGCGAAGGAGAT 59.998 57.895 0.16 0.00 0.00 2.75
4984 5097 1.984570 CAGGGACCAGCGAAGGAGA 60.985 63.158 0.16 0.00 0.00 3.71
4985 5098 1.544825 TTCAGGGACCAGCGAAGGAG 61.545 60.000 0.16 0.00 0.00 3.69
4986 5099 1.125093 TTTCAGGGACCAGCGAAGGA 61.125 55.000 0.16 0.00 0.00 3.36
5058 5171 1.816835 CCATGCCATGCCTAATAGCTG 59.183 52.381 0.00 0.00 0.00 4.24
5072 5185 1.158434 CAAAATGCACCAACCATGCC 58.842 50.000 0.00 0.00 42.69 4.40
5215 5329 9.114952 TCGTTCATATTTGGTTTTGCTCATATA 57.885 29.630 0.00 0.00 0.00 0.86
5275 5389 2.603247 TTGTAGCAAGCGCCACGTG 61.603 57.895 9.08 9.08 39.83 4.49
5276 5390 2.280524 TTGTAGCAAGCGCCACGT 60.281 55.556 2.29 0.00 39.83 4.49


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

AutoCloner maintained by Alex Coulton.