Multiple sequence alignment - TraesCS3A01G470900

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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 TraesCS3A01G470900 chr3A 100.000 2232 0 0 1 2232 702575985 702578216 0.000000e+00 4122.0
1 TraesCS3A01G470900 chr3D 92.128 813 27 13 189 974 570036212 570037014 0.000000e+00 1112.0
2 TraesCS3A01G470900 chr3D 95.026 583 23 5 968 1547 570037589 570038168 0.000000e+00 911.0
3 TraesCS3A01G470900 chr3D 91.058 548 27 8 1706 2231 570041162 570041709 0.000000e+00 721.0
4 TraesCS3A01G470900 chr3D 97.917 96 2 0 1543 1638 570038941 570039036 1.370000e-37 167.0
5 TraesCS3A01G470900 chr3D 100.000 50 0 0 1662 1711 570037421 570037470 2.360000e-15 93.5
6 TraesCS3A01G470900 chr3B 85.060 830 79 15 189 975 756671811 756672638 0.000000e+00 804.0
7 TraesCS3A01G470900 chr3B 87.968 507 54 4 972 1472 756673151 756673656 1.910000e-165 592.0
8 TraesCS3A01G470900 chr2B 80.588 170 18 8 189 347 553976711 553976876 1.400000e-22 117.0
9 TraesCS3A01G470900 chr2A 79.641 167 18 12 188 347 615520603 615520760 3.030000e-19 106.0
10 TraesCS3A01G470900 chrUn 79.845 129 15 4 188 306 75463522 75463395 1.420000e-12 84.2
11 TraesCS3A01G470900 chr7A 100.000 28 0 0 1766 1793 183834678 183834651 4.000000e-03 52.8


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 TraesCS3A01G470900 chr3A 702575985 702578216 2231 False 4122.0 4122 100.0000 1 2232 1 chr3A.!!$F1 2231
1 TraesCS3A01G470900 chr3D 570036212 570041709 5497 False 600.9 1112 95.2258 189 2231 5 chr3D.!!$F1 2042
2 TraesCS3A01G470900 chr3B 756671811 756673656 1845 False 698.0 804 86.5140 189 1472 2 chr3B.!!$F1 1283

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
180 181 0.534203 GCTTCCTCGTGGTTGTTGGA 60.534 55.0 2.99 0.0 34.23 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 5277 0.752658 AACTTCAAAAGCACCCCAGC 59.247 50.0 0.0 0.0 0.0 4.85 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
17 18 4.181010 CAGGGAGGCGACATGGGG 62.181 72.222 0.00 0.00 0.00 4.96
32 33 2.767073 GGGGGTACGAGGGGAAGG 60.767 72.222 0.00 0.00 0.00 3.46
33 34 2.767073 GGGGTACGAGGGGAAGGG 60.767 72.222 0.00 0.00 0.00 3.95
34 35 2.767073 GGGTACGAGGGGAAGGGG 60.767 72.222 0.00 0.00 0.00 4.79
35 36 2.767073 GGTACGAGGGGAAGGGGG 60.767 72.222 0.00 0.00 0.00 5.40
36 37 2.365764 GTACGAGGGGAAGGGGGA 59.634 66.667 0.00 0.00 0.00 4.81
37 38 1.306397 GTACGAGGGGAAGGGGGAA 60.306 63.158 0.00 0.00 0.00 3.97
38 39 1.002533 TACGAGGGGAAGGGGGAAG 59.997 63.158 0.00 0.00 0.00 3.46
39 40 2.540842 TACGAGGGGAAGGGGGAAGG 62.541 65.000 0.00 0.00 0.00 3.46
40 41 2.127528 GAGGGGAAGGGGGAAGGT 59.872 66.667 0.00 0.00 0.00 3.50
41 42 2.204306 AGGGGAAGGGGGAAGGTG 60.204 66.667 0.00 0.00 0.00 4.00
42 43 3.347590 GGGGAAGGGGGAAGGTGG 61.348 72.222 0.00 0.00 0.00 4.61
43 44 2.204244 GGGAAGGGGGAAGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
44 45 2.309504 GGGAAGGGGGAAGGTGGAG 61.310 68.421 0.00 0.00 0.00 3.86
45 46 2.309504 GGAAGGGGGAAGGTGGAGG 61.310 68.421 0.00 0.00 0.00 4.30
46 47 2.204306 AAGGGGGAAGGTGGAGGG 60.204 66.667 0.00 0.00 0.00 4.30
47 48 2.782997 GAAGGGGGAAGGTGGAGGGA 62.783 65.000 0.00 0.00 0.00 4.20
48 49 2.692741 GGGGGAAGGTGGAGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
49 50 2.692741 GGGGAAGGTGGAGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
50 51 2.692741 GGGAAGGTGGAGGGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
51 52 2.692741 GGAAGGTGGAGGGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
52 53 3.412408 GAAGGTGGAGGGAGGGGC 61.412 72.222 0.00 0.00 0.00 5.80
150 151 3.777910 GCGGAAACCCTAGGCGGA 61.778 66.667 2.05 0.00 33.16 5.54
151 152 2.983791 CGGAAACCCTAGGCGGAA 59.016 61.111 2.05 0.00 33.16 4.30
152 153 1.153429 CGGAAACCCTAGGCGGAAG 60.153 63.158 2.05 0.00 33.16 3.46
153 154 1.223763 GGAAACCCTAGGCGGAAGG 59.776 63.158 2.05 0.00 33.16 3.46
167 168 3.626924 AAGGGTCGCACGCTTCCT 61.627 61.111 11.10 0.00 46.59 3.36
168 169 3.591254 AAGGGTCGCACGCTTCCTC 62.591 63.158 11.10 0.00 46.59 3.71
170 171 4.719369 GGTCGCACGCTTCCTCGT 62.719 66.667 0.00 0.00 44.35 4.18
176 177 2.819550 ACGCTTCCTCGTGGTTGT 59.180 55.556 2.99 0.00 41.62 3.32
177 178 1.145377 ACGCTTCCTCGTGGTTGTT 59.855 52.632 2.99 0.00 41.62 2.83
178 179 1.157870 ACGCTTCCTCGTGGTTGTTG 61.158 55.000 2.99 0.00 41.62 3.33
179 180 1.841663 CGCTTCCTCGTGGTTGTTGG 61.842 60.000 2.99 0.00 34.23 3.77
180 181 0.534203 GCTTCCTCGTGGTTGTTGGA 60.534 55.000 2.99 0.00 34.23 3.53
181 182 1.512926 CTTCCTCGTGGTTGTTGGAG 58.487 55.000 2.99 0.00 34.23 3.86
182 183 0.834612 TTCCTCGTGGTTGTTGGAGT 59.165 50.000 2.99 0.00 34.23 3.85
183 184 0.834612 TCCTCGTGGTTGTTGGAGTT 59.165 50.000 2.99 0.00 34.23 3.01
184 185 2.040939 TCCTCGTGGTTGTTGGAGTTA 58.959 47.619 2.99 0.00 34.23 2.24
185 186 2.140717 CCTCGTGGTTGTTGGAGTTAC 58.859 52.381 0.00 0.00 0.00 2.50
186 187 2.224209 CCTCGTGGTTGTTGGAGTTACT 60.224 50.000 0.00 0.00 0.00 2.24
187 188 3.463944 CTCGTGGTTGTTGGAGTTACTT 58.536 45.455 0.00 0.00 0.00 2.24
239 243 7.700322 TGCTATTGATATCAAGAACGAGTTC 57.300 36.000 21.97 7.83 39.47 3.01
293 298 4.025647 GCGAGTATAGTTCCACAGCATTTC 60.026 45.833 0.00 0.00 0.00 2.17
298 303 7.820648 AGTATAGTTCCACAGCATTTCTTTTG 58.179 34.615 0.00 0.00 0.00 2.44
316 321 8.633075 TTCTTTTGCTTGTTTAACATGAAGAG 57.367 30.769 13.97 2.70 0.00 2.85
343 348 4.502259 GCAGTAGGCTATGTGCTGATTACT 60.502 45.833 19.27 0.00 42.39 2.24
382 387 6.649557 GGTACTGCCCACTGATATTATTACAC 59.350 42.308 0.00 0.00 0.00 2.90
433 444 6.090483 TGGCCGAAATCAGATTTGTTTTTA 57.910 33.333 13.38 0.00 31.47 1.52
477 505 0.801251 GCTGTTCAGGATGTGTCTGC 59.199 55.000 1.97 0.00 37.40 4.26
525 553 0.746659 GGGCAGTAATCATGTTGGGC 59.253 55.000 0.00 0.00 0.00 5.36
586 614 1.294138 GGCGCCCTACTGTGTACAA 59.706 57.895 18.11 0.00 0.00 2.41
589 617 1.065358 CGCCCTACTGTGTACAAACG 58.935 55.000 0.00 0.00 0.00 3.60
669 698 4.278956 GTGGTTGGCTAGTCCACG 57.721 61.111 9.81 0.00 46.55 4.94
735 764 4.499357 CCCTAACTTGATAGTAGGTGACGC 60.499 50.000 0.00 0.00 33.17 5.19
736 765 3.521947 AACTTGATAGTAGGTGACGCC 57.478 47.619 0.00 0.00 33.17 5.68
737 766 1.404391 ACTTGATAGTAGGTGACGCCG 59.596 52.381 0.00 0.00 43.70 6.46
738 767 1.404391 CTTGATAGTAGGTGACGCCGT 59.596 52.381 0.00 0.00 43.70 5.68
739 768 0.736636 TGATAGTAGGTGACGCCGTG 59.263 55.000 0.00 0.00 43.70 4.94
740 769 1.019673 GATAGTAGGTGACGCCGTGA 58.980 55.000 0.00 0.00 43.70 4.35
741 770 0.737219 ATAGTAGGTGACGCCGTGAC 59.263 55.000 0.00 0.00 43.70 3.67
742 771 1.638388 TAGTAGGTGACGCCGTGACG 61.638 60.000 0.00 0.00 43.70 4.35
870 927 6.258727 GGTATGATGTAGATCCTTTGTGTGTG 59.741 42.308 0.00 0.00 0.00 3.82
873 930 4.019792 TGTAGATCCTTTGTGTGTGCAT 57.980 40.909 0.00 0.00 0.00 3.96
997 1644 5.963176 TTCTGTTGATGCATTTGCTCTTA 57.037 34.783 0.00 0.00 42.66 2.10
998 1645 5.963176 TCTGTTGATGCATTTGCTCTTAA 57.037 34.783 0.00 0.00 42.66 1.85
1072 1722 6.045106 ACCTCCCAAAGTAAATAAGGACAAGA 59.955 38.462 0.00 0.00 0.00 3.02
1083 1733 0.543749 AGGACAAGATAGGCAGCACC 59.456 55.000 0.00 0.00 39.61 5.01
1206 1858 7.814264 ATCAGCATAAGGATAAGGAGTTTTG 57.186 36.000 0.00 0.00 0.00 2.44
1211 1863 7.834181 AGCATAAGGATAAGGAGTTTTGCTTTA 59.166 33.333 0.00 0.00 36.32 1.85
1355 2007 9.850628 TTTTCAATCTTCTGAAAATCTGCATAG 57.149 29.630 7.27 0.00 45.71 2.23
1360 2012 6.656902 TCTTCTGAAAATCTGCATAGTGGAT 58.343 36.000 0.00 0.00 0.00 3.41
1372 2024 3.464907 CATAGTGGATGTCTTGGCTCTG 58.535 50.000 0.00 0.00 0.00 3.35
1384 2036 2.462456 TGGCTCTGTGTGAACTCATC 57.538 50.000 0.00 0.00 0.00 2.92
1446 2098 7.987649 TCCAGTTTACAAATAAGTGACGTTTT 58.012 30.769 0.00 0.00 0.00 2.43
1454 2106 7.921787 ACAAATAAGTGACGTTTTGACATACA 58.078 30.769 13.50 0.00 34.13 2.29
1516 2169 9.748708 CTTGTTTTTGATATGGAAACTTGAAGA 57.251 29.630 0.00 0.00 35.04 2.87
1578 3010 4.905269 CATGTATATCATGCTCATTGGCG 58.095 43.478 0.00 0.00 45.69 5.69
1620 3052 5.192927 TCACTTCATTTGTGAACCACTTCT 58.807 37.500 0.00 0.00 40.89 2.85
1640 5165 5.932619 TCTTACCTGAAGTAGCAGCAATA 57.067 39.130 0.00 0.00 36.45 1.90
1646 5171 4.641989 CCTGAAGTAGCAGCAATATGGTTT 59.358 41.667 0.00 0.00 34.56 3.27
1647 5172 5.822519 CCTGAAGTAGCAGCAATATGGTTTA 59.177 40.000 0.00 0.00 34.56 2.01
1650 5175 6.538742 TGAAGTAGCAGCAATATGGTTTAGTC 59.461 38.462 0.00 0.00 32.19 2.59
1654 5179 2.290641 CAGCAATATGGTTTAGTCGGGC 59.709 50.000 0.00 0.00 0.00 6.13
1665 5190 0.602638 TAGTCGGGCACAACTGCAAG 60.603 55.000 0.00 0.00 46.28 4.01
1684 5209 8.398491 CTGCAAGTGTTTAATATGAAATGGTC 57.602 34.615 0.00 0.00 0.00 4.02
1685 5210 8.121305 TGCAAGTGTTTAATATGAAATGGTCT 57.879 30.769 0.00 0.00 0.00 3.85
1686 5211 8.584157 TGCAAGTGTTTAATATGAAATGGTCTT 58.416 29.630 0.00 0.00 0.00 3.01
1687 5212 8.863049 GCAAGTGTTTAATATGAAATGGTCTTG 58.137 33.333 12.49 12.49 0.00 3.02
1688 5213 9.912634 CAAGTGTTTAATATGAAATGGTCTTGT 57.087 29.630 0.00 0.00 0.00 3.16
1692 5217 9.202273 TGTTTAATATGAAATGGTCTTGTTTGC 57.798 29.630 0.00 0.00 0.00 3.68
1693 5218 9.202273 GTTTAATATGAAATGGTCTTGTTTGCA 57.798 29.630 0.00 0.00 0.00 4.08
1694 5219 8.755696 TTAATATGAAATGGTCTTGTTTGCAC 57.244 30.769 0.00 0.00 0.00 4.57
1695 5220 4.669206 ATGAAATGGTCTTGTTTGCACA 57.331 36.364 0.00 0.00 0.00 4.57
1696 5221 4.669206 TGAAATGGTCTTGTTTGCACAT 57.331 36.364 0.00 0.00 31.06 3.21
1697 5222 5.781210 TGAAATGGTCTTGTTTGCACATA 57.219 34.783 0.00 0.00 31.06 2.29
1698 5223 6.154203 TGAAATGGTCTTGTTTGCACATAA 57.846 33.333 0.00 0.00 31.06 1.90
1699 5224 5.982516 TGAAATGGTCTTGTTTGCACATAAC 59.017 36.000 0.00 0.00 31.06 1.89
1700 5225 4.519540 ATGGTCTTGTTTGCACATAACC 57.480 40.909 0.00 0.00 37.93 2.85
1701 5226 3.561143 TGGTCTTGTTTGCACATAACCT 58.439 40.909 0.00 0.00 38.13 3.50
1702 5227 3.568007 TGGTCTTGTTTGCACATAACCTC 59.432 43.478 0.00 0.00 38.13 3.85
1703 5228 3.057526 GGTCTTGTTTGCACATAACCTCC 60.058 47.826 0.00 0.00 35.97 4.30
1704 5229 3.057526 GTCTTGTTTGCACATAACCTCCC 60.058 47.826 0.00 0.00 31.06 4.30
1705 5230 2.666272 TGTTTGCACATAACCTCCCA 57.334 45.000 0.00 0.00 0.00 4.37
1706 5231 3.168035 TGTTTGCACATAACCTCCCAT 57.832 42.857 0.00 0.00 0.00 4.00
1707 5232 3.505386 TGTTTGCACATAACCTCCCATT 58.495 40.909 0.00 0.00 0.00 3.16
1708 5233 3.509575 TGTTTGCACATAACCTCCCATTC 59.490 43.478 0.00 0.00 0.00 2.67
1709 5234 3.737559 TTGCACATAACCTCCCATTCT 57.262 42.857 0.00 0.00 0.00 2.40
1710 5235 3.737559 TGCACATAACCTCCCATTCTT 57.262 42.857 0.00 0.00 0.00 2.52
1711 5236 4.046286 TGCACATAACCTCCCATTCTTT 57.954 40.909 0.00 0.00 0.00 2.52
1752 5277 2.876079 GCTAACCACTTGAACTGGGAGG 60.876 54.545 0.00 0.00 32.45 4.30
1753 5278 0.178990 AACCACTTGAACTGGGAGGC 60.179 55.000 0.00 0.00 32.45 4.70
1764 5298 3.984732 GGGAGGCTGGGGTGCTTT 61.985 66.667 0.00 0.00 0.00 3.51
1785 5319 7.080724 GCTTTTGAAGTTCATCTCTTAGTTGG 58.919 38.462 6.36 0.00 0.00 3.77
1845 5379 6.822667 ACATTTGATGAGTGCTTATGTTGA 57.177 33.333 0.00 0.00 0.00 3.18
1851 5385 2.224744 TGAGTGCTTATGTTGAGGCCAA 60.225 45.455 5.01 0.00 0.00 4.52
1870 5404 7.349598 AGGCCAACTAAGATATGAACTTCAAT 58.650 34.615 5.01 0.00 0.00 2.57
1911 5445 2.362077 ACACAGGATGCCAAGTTGAAAC 59.638 45.455 3.87 0.00 42.53 2.78
2012 5558 6.482898 TTGCAACCATAAAGATGCCAATAT 57.517 33.333 0.00 0.00 38.00 1.28
2050 5596 0.447801 CACTCGAAATGAAAGCCCCG 59.552 55.000 0.00 0.00 0.00 5.73
2054 5600 1.861542 CGAAATGAAAGCCCCGCACA 61.862 55.000 0.00 0.00 0.00 4.57
2076 5622 6.748658 CACAAGCAGTGTTTGACAATATATGG 59.251 38.462 24.39 0.00 43.40 2.74
2214 5761 8.565896 ACATGTAGAATTACACACACATCATT 57.434 30.769 0.00 0.00 42.29 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.181010 CCCCATGTCGCCTCCCTG 62.181 72.222 0.00 0.00 0.00 4.45
15 16 2.767073 CCTTCCCCTCGTACCCCC 60.767 72.222 0.00 0.00 0.00 5.40
16 17 2.767073 CCCTTCCCCTCGTACCCC 60.767 72.222 0.00 0.00 0.00 4.95
17 18 2.767073 CCCCTTCCCCTCGTACCC 60.767 72.222 0.00 0.00 0.00 3.69
18 19 2.767073 CCCCCTTCCCCTCGTACC 60.767 72.222 0.00 0.00 0.00 3.34
19 20 1.306397 TTCCCCCTTCCCCTCGTAC 60.306 63.158 0.00 0.00 0.00 3.67
20 21 1.002533 CTTCCCCCTTCCCCTCGTA 59.997 63.158 0.00 0.00 0.00 3.43
21 22 2.285442 CTTCCCCCTTCCCCTCGT 60.285 66.667 0.00 0.00 0.00 4.18
22 23 3.090532 CCTTCCCCCTTCCCCTCG 61.091 72.222 0.00 0.00 0.00 4.63
23 24 2.127528 ACCTTCCCCCTTCCCCTC 59.872 66.667 0.00 0.00 0.00 4.30
24 25 2.204306 CACCTTCCCCCTTCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
25 26 3.347590 CCACCTTCCCCCTTCCCC 61.348 72.222 0.00 0.00 0.00 4.81
26 27 2.204244 TCCACCTTCCCCCTTCCC 60.204 66.667 0.00 0.00 0.00 3.97
27 28 2.309504 CCTCCACCTTCCCCCTTCC 61.310 68.421 0.00 0.00 0.00 3.46
28 29 2.309504 CCCTCCACCTTCCCCCTTC 61.310 68.421 0.00 0.00 0.00 3.46
29 30 2.204306 CCCTCCACCTTCCCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
30 31 3.216371 TCCCTCCACCTTCCCCCT 61.216 66.667 0.00 0.00 0.00 4.79
31 32 2.692741 CTCCCTCCACCTTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
32 33 2.692741 CCTCCCTCCACCTTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
33 34 2.692741 CCCTCCCTCCACCTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
34 35 2.692741 CCCCTCCCTCCACCTTCC 60.693 72.222 0.00 0.00 0.00 3.46
35 36 3.412408 GCCCCTCCCTCCACCTTC 61.412 72.222 0.00 0.00 0.00 3.46
133 134 3.319441 TTCCGCCTAGGGTTTCCGC 62.319 63.158 11.72 0.00 41.52 5.54
134 135 1.153429 CTTCCGCCTAGGGTTTCCG 60.153 63.158 11.72 4.75 41.52 4.30
135 136 1.223763 CCTTCCGCCTAGGGTTTCC 59.776 63.158 11.72 0.00 41.52 3.13
136 137 1.223763 CCCTTCCGCCTAGGGTTTC 59.776 63.158 11.72 0.00 46.16 2.78
137 138 3.411700 CCCTTCCGCCTAGGGTTT 58.588 61.111 11.72 0.00 46.16 3.27
141 142 4.222847 GCGACCCTTCCGCCTAGG 62.223 72.222 3.67 3.67 46.22 3.02
148 149 3.119096 GAAGCGTGCGACCCTTCC 61.119 66.667 0.00 0.00 31.16 3.46
149 150 3.119096 GGAAGCGTGCGACCCTTC 61.119 66.667 0.00 0.00 35.42 3.46
150 151 3.591254 GAGGAAGCGTGCGACCCTT 62.591 63.158 0.00 0.00 0.00 3.95
151 152 4.070552 GAGGAAGCGTGCGACCCT 62.071 66.667 0.00 4.97 0.00 4.34
153 154 4.719369 ACGAGGAAGCGTGCGACC 62.719 66.667 0.00 2.98 43.79 4.79
159 160 1.145377 AACAACCACGAGGAAGCGT 59.855 52.632 5.68 0.00 46.88 5.07
160 161 1.569493 CAACAACCACGAGGAAGCG 59.431 57.895 5.68 0.00 38.69 4.68
161 162 0.534203 TCCAACAACCACGAGGAAGC 60.534 55.000 5.68 0.00 38.69 3.86
162 163 1.202651 ACTCCAACAACCACGAGGAAG 60.203 52.381 5.68 0.00 38.69 3.46
163 164 0.834612 ACTCCAACAACCACGAGGAA 59.165 50.000 5.68 0.00 38.69 3.36
164 165 0.834612 AACTCCAACAACCACGAGGA 59.165 50.000 5.68 0.00 38.69 3.71
165 166 2.140717 GTAACTCCAACAACCACGAGG 58.859 52.381 0.00 0.00 42.21 4.63
166 167 3.107642 AGTAACTCCAACAACCACGAG 57.892 47.619 0.00 0.00 0.00 4.18
167 168 3.547054 AAGTAACTCCAACAACCACGA 57.453 42.857 0.00 0.00 0.00 4.35
168 169 4.625972 AAAAGTAACTCCAACAACCACG 57.374 40.909 0.00 0.00 0.00 4.94
169 170 5.126545 AGGAAAAAGTAACTCCAACAACCAC 59.873 40.000 0.00 0.00 0.00 4.16
170 171 5.265989 AGGAAAAAGTAACTCCAACAACCA 58.734 37.500 0.00 0.00 0.00 3.67
171 172 5.847111 AGGAAAAAGTAACTCCAACAACC 57.153 39.130 0.00 0.00 0.00 3.77
172 173 7.423199 CCTAAGGAAAAAGTAACTCCAACAAC 58.577 38.462 0.00 0.00 0.00 3.32
173 174 6.040054 GCCTAAGGAAAAAGTAACTCCAACAA 59.960 38.462 0.00 0.00 0.00 2.83
174 175 5.533528 GCCTAAGGAAAAAGTAACTCCAACA 59.466 40.000 0.00 0.00 0.00 3.33
175 176 5.533528 TGCCTAAGGAAAAAGTAACTCCAAC 59.466 40.000 0.00 0.00 0.00 3.77
176 177 5.533528 GTGCCTAAGGAAAAAGTAACTCCAA 59.466 40.000 0.00 0.00 0.00 3.53
177 178 5.067954 GTGCCTAAGGAAAAAGTAACTCCA 58.932 41.667 0.00 0.00 0.00 3.86
178 179 5.314529 AGTGCCTAAGGAAAAAGTAACTCC 58.685 41.667 0.00 0.00 0.00 3.85
179 180 6.879276 AAGTGCCTAAGGAAAAAGTAACTC 57.121 37.500 0.00 0.00 0.00 3.01
180 181 7.489160 CAAAAGTGCCTAAGGAAAAAGTAACT 58.511 34.615 0.00 0.00 0.00 2.24
181 182 6.200286 GCAAAAGTGCCTAAGGAAAAAGTAAC 59.800 38.462 0.00 0.00 45.68 2.50
182 183 6.277605 GCAAAAGTGCCTAAGGAAAAAGTAA 58.722 36.000 0.00 0.00 45.68 2.24
183 184 5.838529 GCAAAAGTGCCTAAGGAAAAAGTA 58.161 37.500 0.00 0.00 45.68 2.24
184 185 4.693283 GCAAAAGTGCCTAAGGAAAAAGT 58.307 39.130 0.00 0.00 45.68 2.66
293 298 7.202526 TCCTCTTCATGTTAAACAAGCAAAAG 58.797 34.615 0.00 0.00 0.00 2.27
298 303 5.157067 GCTTCCTCTTCATGTTAAACAAGC 58.843 41.667 0.00 0.00 0.00 4.01
343 348 0.034380 AGTACCAGACCAGCGCTAGA 60.034 55.000 10.99 0.00 0.00 2.43
382 387 2.507471 AGAAAGGCATCTAGTCCCTTGG 59.493 50.000 10.56 0.00 38.87 3.61
433 444 7.013655 GCATTTTGTATCTGATGATGGTAACCT 59.986 37.037 0.00 0.00 34.32 3.50
525 553 4.082787 AGACGTGCTGAAAAATTACCATGG 60.083 41.667 11.19 11.19 0.00 3.66
586 614 5.916661 ATTGTGATACCAGTCTAGTCGTT 57.083 39.130 0.00 0.00 0.00 3.85
589 617 8.035394 TCAAGAAATTGTGATACCAGTCTAGTC 58.965 37.037 0.00 0.00 0.00 2.59
669 698 8.807581 CCTGAAAAACATGTTTACAAGAACTTC 58.192 33.333 23.53 19.04 31.63 3.01
736 765 2.444624 CCATCTTCACGCCGTCACG 61.445 63.158 0.00 0.00 39.50 4.35
737 766 1.374252 ACCATCTTCACGCCGTCAC 60.374 57.895 0.00 0.00 0.00 3.67
738 767 1.374125 CACCATCTTCACGCCGTCA 60.374 57.895 0.00 0.00 0.00 4.35
739 768 1.078759 CTCACCATCTTCACGCCGTC 61.079 60.000 0.00 0.00 0.00 4.79
740 769 1.079819 CTCACCATCTTCACGCCGT 60.080 57.895 0.00 0.00 0.00 5.68
741 770 1.079819 ACTCACCATCTTCACGCCG 60.080 57.895 0.00 0.00 0.00 6.46
742 771 1.639298 GCACTCACCATCTTCACGCC 61.639 60.000 0.00 0.00 0.00 5.68
997 1644 6.211515 GTGAAGCATCTGAGAAACACATTTT 58.788 36.000 0.00 0.00 0.00 1.82
998 1645 5.278660 GGTGAAGCATCTGAGAAACACATTT 60.279 40.000 0.00 0.00 0.00 2.32
1072 1722 3.435601 CCTTCCTTATTGGTGCTGCCTAT 60.436 47.826 0.00 0.81 38.35 2.57
1083 1733 4.079787 TCCTTGGATGGTCCTTCCTTATTG 60.080 45.833 21.39 8.49 37.46 1.90
1137 1787 2.753055 TGATCGACCGGAATTTGACA 57.247 45.000 9.46 0.00 0.00 3.58
1138 1788 3.621268 TCATTGATCGACCGGAATTTGAC 59.379 43.478 9.46 0.00 0.00 3.18
1206 1858 9.788960 CTTACATTCTATTTGAAGGGTTAAAGC 57.211 33.333 0.00 0.00 40.40 3.51
1211 1863 8.336235 TCATCCTTACATTCTATTTGAAGGGTT 58.664 33.333 0.00 0.00 40.40 4.11
1304 1956 8.729805 ATTCAGAAAGAGATGATAAGAACCAC 57.270 34.615 0.00 0.00 0.00 4.16
1342 1994 6.459298 CCAAGACATCCACTATGCAGATTTTC 60.459 42.308 0.00 0.00 39.39 2.29
1355 2007 1.271054 ACACAGAGCCAAGACATCCAC 60.271 52.381 0.00 0.00 0.00 4.02
1360 2012 1.486310 AGTTCACACAGAGCCAAGACA 59.514 47.619 0.00 0.00 0.00 3.41
1372 2024 6.893958 AGATATTGTTCGATGAGTTCACAC 57.106 37.500 0.00 0.00 0.00 3.82
1384 2036 8.717821 TGTTTCTCAGGTTTTAGATATTGTTCG 58.282 33.333 0.00 0.00 0.00 3.95
1483 2136 6.855763 TCCATATCAAAAACAAGAATGGCT 57.144 33.333 0.00 0.00 33.87 4.75
1578 3010 5.965922 AGTGAATTTAATTAGCTTGTGGCC 58.034 37.500 0.00 0.00 43.05 5.36
1620 3052 5.104527 ACCATATTGCTGCTACTTCAGGTAA 60.105 40.000 0.00 0.00 34.74 2.85
1640 5165 1.073284 AGTTGTGCCCGACTAAACCAT 59.927 47.619 0.00 0.00 33.31 3.55
1654 5179 8.572828 TTTCATATTAAACACTTGCAGTTGTG 57.427 30.769 12.81 12.81 39.80 3.33
1666 5191 9.202273 GCAAACAAGACCATTTCATATTAAACA 57.798 29.630 0.00 0.00 0.00 2.83
1668 5193 9.202273 GTGCAAACAAGACCATTTCATATTAAA 57.798 29.630 0.00 0.00 0.00 1.52
1669 5194 8.363390 TGTGCAAACAAGACCATTTCATATTAA 58.637 29.630 0.00 0.00 0.00 1.40
1670 5195 7.890515 TGTGCAAACAAGACCATTTCATATTA 58.109 30.769 0.00 0.00 0.00 0.98
1671 5196 6.757237 TGTGCAAACAAGACCATTTCATATT 58.243 32.000 0.00 0.00 0.00 1.28
1672 5197 6.343716 TGTGCAAACAAGACCATTTCATAT 57.656 33.333 0.00 0.00 0.00 1.78
1673 5198 5.781210 TGTGCAAACAAGACCATTTCATA 57.219 34.783 0.00 0.00 0.00 2.15
1674 5199 4.669206 TGTGCAAACAAGACCATTTCAT 57.331 36.364 0.00 0.00 0.00 2.57
1675 5200 4.669206 ATGTGCAAACAAGACCATTTCA 57.331 36.364 0.00 0.00 0.00 2.69
1676 5201 5.405269 GGTTATGTGCAAACAAGACCATTTC 59.595 40.000 2.40 0.00 32.43 2.17
1677 5202 5.070313 AGGTTATGTGCAAACAAGACCATTT 59.930 36.000 13.23 0.00 33.69 2.32
1678 5203 4.588528 AGGTTATGTGCAAACAAGACCATT 59.411 37.500 13.23 0.00 33.69 3.16
1679 5204 4.151883 AGGTTATGTGCAAACAAGACCAT 58.848 39.130 13.23 2.50 33.69 3.55
1680 5205 3.561143 AGGTTATGTGCAAACAAGACCA 58.439 40.909 13.23 0.00 33.69 4.02
1681 5206 3.057526 GGAGGTTATGTGCAAACAAGACC 60.058 47.826 2.40 3.89 0.00 3.85
1682 5207 3.057526 GGGAGGTTATGTGCAAACAAGAC 60.058 47.826 2.40 0.00 0.00 3.01
1683 5208 3.153919 GGGAGGTTATGTGCAAACAAGA 58.846 45.455 2.40 0.00 0.00 3.02
1684 5209 2.890311 TGGGAGGTTATGTGCAAACAAG 59.110 45.455 2.40 0.00 0.00 3.16
1685 5210 2.950781 TGGGAGGTTATGTGCAAACAA 58.049 42.857 2.40 0.00 0.00 2.83
1686 5211 2.666272 TGGGAGGTTATGTGCAAACA 57.334 45.000 2.40 0.00 0.00 2.83
1687 5212 3.763897 AGAATGGGAGGTTATGTGCAAAC 59.236 43.478 0.00 0.00 0.00 2.93
1688 5213 4.046286 AGAATGGGAGGTTATGTGCAAA 57.954 40.909 0.00 0.00 0.00 3.68
1689 5214 3.737559 AGAATGGGAGGTTATGTGCAA 57.262 42.857 0.00 0.00 0.00 4.08
1690 5215 3.737559 AAGAATGGGAGGTTATGTGCA 57.262 42.857 0.00 0.00 0.00 4.57
1691 5216 4.036852 GCTAAAGAATGGGAGGTTATGTGC 59.963 45.833 0.00 0.00 0.00 4.57
1692 5217 5.440610 AGCTAAAGAATGGGAGGTTATGTG 58.559 41.667 0.00 0.00 0.00 3.21
1693 5218 5.191722 TGAGCTAAAGAATGGGAGGTTATGT 59.808 40.000 0.00 0.00 0.00 2.29
1694 5219 5.684704 TGAGCTAAAGAATGGGAGGTTATG 58.315 41.667 0.00 0.00 0.00 1.90
1695 5220 5.975988 TGAGCTAAAGAATGGGAGGTTAT 57.024 39.130 0.00 0.00 0.00 1.89
1696 5221 5.453339 CGATGAGCTAAAGAATGGGAGGTTA 60.453 44.000 0.00 0.00 0.00 2.85
1697 5222 4.684485 CGATGAGCTAAAGAATGGGAGGTT 60.684 45.833 0.00 0.00 0.00 3.50
1698 5223 3.181461 CGATGAGCTAAAGAATGGGAGGT 60.181 47.826 0.00 0.00 0.00 3.85
1699 5224 3.070159 TCGATGAGCTAAAGAATGGGAGG 59.930 47.826 0.00 0.00 0.00 4.30
1700 5225 4.054671 GTCGATGAGCTAAAGAATGGGAG 58.945 47.826 0.00 0.00 0.00 4.30
1701 5226 3.706594 AGTCGATGAGCTAAAGAATGGGA 59.293 43.478 0.00 0.00 0.00 4.37
1702 5227 4.065321 AGTCGATGAGCTAAAGAATGGG 57.935 45.455 0.00 0.00 0.00 4.00
1703 5228 4.260538 GCAAGTCGATGAGCTAAAGAATGG 60.261 45.833 0.00 0.00 0.00 3.16
1704 5229 4.569966 AGCAAGTCGATGAGCTAAAGAATG 59.430 41.667 6.66 0.00 35.19 2.67
1705 5230 4.764172 AGCAAGTCGATGAGCTAAAGAAT 58.236 39.130 6.66 0.00 35.19 2.40
1706 5231 4.177026 GAGCAAGTCGATGAGCTAAAGAA 58.823 43.478 8.18 0.00 37.48 2.52
1707 5232 3.775202 GAGCAAGTCGATGAGCTAAAGA 58.225 45.455 8.18 0.00 37.48 2.52
1752 5277 0.752658 AACTTCAAAAGCACCCCAGC 59.247 50.000 0.00 0.00 0.00 4.85
1753 5278 2.031120 TGAACTTCAAAAGCACCCCAG 58.969 47.619 0.00 0.00 0.00 4.45
1764 5298 5.003804 GGCCAACTAAGAGATGAACTTCAA 58.996 41.667 0.00 0.00 0.00 2.69
1799 5333 2.744202 GTCAGCACCTGGTTCTAATGTG 59.256 50.000 0.00 0.00 31.51 3.21
1804 5338 1.765904 TGTTGTCAGCACCTGGTTCTA 59.234 47.619 0.00 0.00 31.51 2.10
1845 5379 6.313519 TGAAGTTCATATCTTAGTTGGCCT 57.686 37.500 3.32 0.00 0.00 5.19
1942 5476 8.430063 CAATTTTTGCATCTCTGTATGTTTCAC 58.570 33.333 0.00 0.00 0.00 3.18
1973 5507 5.047448 TGGTTGCAATTGCTAGCATTCTTTA 60.047 36.000 32.69 15.54 45.88 1.85
1981 5520 4.997565 TCTTTATGGTTGCAATTGCTAGC 58.002 39.130 29.05 29.05 42.80 3.42
1982 5521 5.461078 GCATCTTTATGGTTGCAATTGCTAG 59.539 40.000 29.37 9.88 36.39 3.42
2012 5558 3.450457 AGTGTTTTCATTGGTCCAAGCAA 59.550 39.130 10.72 2.30 40.12 3.91
2054 5600 5.418524 TGCCATATATTGTCAAACACTGCTT 59.581 36.000 0.00 0.00 0.00 3.91
2076 5622 7.910162 CCATTGTGTACAACTATTGACTATTGC 59.090 37.037 0.00 0.00 38.86 3.56
2170 5716 6.240894 ACATGTACTTTCCAATGATGTCTGT 58.759 36.000 0.00 0.00 0.00 3.41
2171 5717 6.748333 ACATGTACTTTCCAATGATGTCTG 57.252 37.500 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.