Multiple sequence alignment - TraesCS4D01G073200

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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 TraesCS4D01G073200 chr4D 100.000 5522 0 0 1 5522 47849007 47854528 0.000000e+00 10198.0
1 TraesCS4D01G073200 chr4B 95.310 3369 97 19 1555 4888 70253528 70256870 0.000000e+00 5289.0
2 TraesCS4D01G073200 chr4B 94.290 683 28 8 894 1573 70252716 70253390 0.000000e+00 1035.0
3 TraesCS4D01G073200 chr4B 88.308 650 48 3 1 647 70251518 70252142 0.000000e+00 754.0
4 TraesCS4D01G073200 chr4B 94.964 139 6 1 4941 5078 70256864 70257002 3.350000e-52 217.0
5 TraesCS4D01G073200 chr4A 94.003 1951 81 13 3213 5155 549880481 549878559 0.000000e+00 2922.0
6 TraesCS4D01G073200 chr4A 92.439 1640 70 27 1605 3216 549882174 549880561 0.000000e+00 2292.0
7 TraesCS4D01G073200 chr4A 87.685 877 86 9 1 863 549888337 549887469 0.000000e+00 1002.0
8 TraesCS4D01G073200 chr4A 94.163 651 30 5 926 1575 549882816 549882173 0.000000e+00 985.0
9 TraesCS4D01G073200 chr4A 79.121 364 43 18 5174 5515 549878509 549878157 2.590000e-53 220.0
10 TraesCS4D01G073200 chr1D 80.000 180 25 10 1926 2099 158104769 158104943 7.510000e-24 122.0
11 TraesCS4D01G073200 chr1A 79.888 179 27 8 1926 2099 224812532 224812358 7.510000e-24 122.0
12 TraesCS4D01G073200 chr1B 80.380 158 22 8 1947 2099 222304083 222303930 1.630000e-20 111.0
13 TraesCS4D01G073200 chr7D 90.909 55 4 1 4629 4683 5333458 5333511 7.670000e-09 73.1
14 TraesCS4D01G073200 chr5D 93.333 45 3 0 4641 4685 381914490 381914446 3.570000e-07 67.6
15 TraesCS4D01G073200 chr5D 93.182 44 3 0 4643 4686 69354263 69354220 1.280000e-06 65.8
16 TraesCS4D01G073200 chr5D 88.000 50 4 1 4641 4690 56125637 56125684 2.150000e-04 58.4
17 TraesCS4D01G073200 chr5B 93.023 43 3 0 4643 4685 1739568 1739526 4.620000e-06 63.9
18 TraesCS4D01G073200 chr5A 93.023 43 3 0 4643 4685 10906 10864 4.620000e-06 63.9
19 TraesCS4D01G073200 chr7A 92.857 42 3 0 4642 4683 120981908 120981949 1.660000e-05 62.1


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 TraesCS4D01G073200 chr4D 47849007 47854528 5521 False 10198.00 10198 100.0000 1 5522 1 chr4D.!!$F1 5521
1 TraesCS4D01G073200 chr4B 70251518 70257002 5484 False 1823.75 5289 93.2180 1 5078 4 chr4B.!!$F1 5077
2 TraesCS4D01G073200 chr4A 549878157 549882816 4659 True 1604.75 2922 89.9315 926 5515 4 chr4A.!!$R2 4589
3 TraesCS4D01G073200 chr4A 549887469 549888337 868 True 1002.00 1002 87.6850 1 863 1 chr4A.!!$R1 862

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
158 160 0.323725 ACATGTGTCTCCATTGCCCC 60.324 55.0 0.0 0.0 0.00 5.80 F
828 1090 0.536460 ACACGCCCTAAGTTTGTGGG 60.536 55.0 0.0 0.0 43.62 4.61 F
1637 2178 0.255890 TGAGGGCTATTCCTTGGTGC 59.744 55.0 0.0 0.0 37.25 5.01 F
3144 3740 0.261696 AACCCAGAAGTTTGGTGCCT 59.738 50.0 0.0 0.0 36.45 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1756 1.050204 AATTGGCCAGCTTCTTTGCA 58.950 45.000 5.11 0.0 34.99 4.08 R
1906 2449 4.189231 GGCAGTCCATAAGTCGTATTTGT 58.811 43.478 0.00 0.0 0.00 2.83 R
3266 3945 3.018856 CCATGCATGCTTTCAGACCTAA 58.981 45.455 21.69 0.0 0.00 2.69 R
4992 5676 0.037975 CTTCATTGGCGCAAAGGCTT 60.038 50.000 10.83 0.0 46.88 4.35 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
70 71 0.666374 GTAAGCAGGCAACCAAACGT 59.334 50.000 0.00 0.00 37.17 3.99
120 122 3.499737 GGCCATGACAACGCCTCG 61.500 66.667 0.00 0.00 39.70 4.63
142 144 1.690219 GGAGGAGATGGCGTCCACAT 61.690 60.000 2.37 0.00 41.33 3.21
158 160 0.323725 ACATGTGTCTCCATTGCCCC 60.324 55.000 0.00 0.00 0.00 5.80
191 193 0.537188 GCCAGATTTCTCCTCGACCA 59.463 55.000 0.00 0.00 0.00 4.02
216 218 1.080501 TCACTTCTTCGGAGCGCAG 60.081 57.895 11.47 0.00 0.00 5.18
269 278 3.316573 CTCACCGTGAAGAGGGGGC 62.317 68.421 2.19 0.00 29.81 5.80
285 294 3.017314 GCGTCGGATGTCGCTACG 61.017 66.667 4.47 0.00 46.69 3.51
413 424 1.959226 CCACGCGCTACAACCTTGT 60.959 57.895 5.73 0.00 44.86 3.16
423 434 2.030562 AACCTTGTCGCCCTCACG 59.969 61.111 0.00 0.00 0.00 4.35
540 551 4.767255 GACTCCACCGCAGCCTGG 62.767 72.222 0.00 0.00 0.00 4.45
561 573 2.514592 CGCCACCCAGCATACCAG 60.515 66.667 0.00 0.00 0.00 4.00
564 576 1.750399 CCACCCAGCATACCAGCAC 60.750 63.158 0.00 0.00 36.85 4.40
579 591 1.302511 GCACTGGACCAACACCGAT 60.303 57.895 0.00 0.00 0.00 4.18
699 960 3.817647 GCCCTATGATAAAGGTTGAGCTG 59.182 47.826 0.00 0.00 31.70 4.24
760 1022 1.681793 GCATCTACTCAGCCCGTCTTA 59.318 52.381 0.00 0.00 0.00 2.10
776 1038 4.504461 CCGTCTTAGACACATATGCAAGAC 59.496 45.833 13.14 16.74 38.85 3.01
777 1039 5.102313 CGTCTTAGACACATATGCAAGACA 58.898 41.667 21.66 1.10 41.09 3.41
778 1040 5.230936 CGTCTTAGACACATATGCAAGACAG 59.769 44.000 21.66 15.35 41.09 3.51
779 1041 5.006165 GTCTTAGACACATATGCAAGACAGC 59.994 44.000 19.38 0.00 40.85 4.40
780 1042 7.341342 GTCTTAGACACATATGCAAGACAGCA 61.341 42.308 19.38 0.00 40.85 4.41
781 1043 8.742440 GTCTTAGACACATATGCAAGACAGCAA 61.742 40.741 19.38 1.00 40.85 3.91
813 1075 4.520743 ACGATGCAAGATATCAAACACG 57.479 40.909 5.32 6.16 0.00 4.49
828 1090 0.536460 ACACGCCCTAAGTTTGTGGG 60.536 55.000 0.00 0.00 43.62 4.61
847 1109 3.054287 TGGGCGGTGTATCTTTATTTGGA 60.054 43.478 0.00 0.00 0.00 3.53
868 1130 9.950496 TTTGGAATTAAATAAAGCCAAATAGCA 57.050 25.926 14.01 0.14 37.44 3.49
1037 1423 2.436646 CGCACCCTACCTTGCCTG 60.437 66.667 0.00 0.00 35.14 4.85
1176 1562 2.717639 AGATGCCGGTGCTCTTATTT 57.282 45.000 1.90 0.00 38.71 1.40
1213 1599 3.136123 TCCGCGACCCCTTCTACG 61.136 66.667 8.23 0.00 0.00 3.51
1291 1677 4.083271 GCTTGGTTTATCGCTATCCATTCC 60.083 45.833 0.00 0.00 0.00 3.01
1295 1681 5.305902 TGGTTTATCGCTATCCATTCCTGTA 59.694 40.000 0.00 0.00 0.00 2.74
1353 1740 1.908066 GACGGAATGCGTGGTTGGTC 61.908 60.000 3.60 0.00 0.00 4.02
1369 1756 1.145377 GTCCTTGGTGGTGACGTGT 59.855 57.895 0.00 0.00 37.07 4.49
1470 1857 0.459899 TGTGCTGTATCCGCTACTGG 59.540 55.000 0.00 0.00 31.74 4.00
1474 1861 2.224042 TGCTGTATCCGCTACTGGATTG 60.224 50.000 0.00 0.00 46.74 2.67
1579 2120 6.058833 TCAGTACTGCAGAATAGAGTAGAGG 58.941 44.000 23.35 0.00 0.00 3.69
1592 2133 4.615513 AGAGTAGAGGCCTGTGAAATAGT 58.384 43.478 12.00 0.00 0.00 2.12
1603 2144 4.446371 CTGTGAAATAGTAGAAGGCTGGG 58.554 47.826 0.00 0.00 0.00 4.45
1633 2174 2.755103 GGTTGTTGAGGGCTATTCCTTG 59.245 50.000 0.00 0.00 37.25 3.61
1637 2178 0.255890 TGAGGGCTATTCCTTGGTGC 59.744 55.000 0.00 0.00 37.25 5.01
1647 2188 6.459710 GGCTATTCCTTGGTGCTGTTTTATAC 60.460 42.308 0.00 0.00 0.00 1.47
1767 2308 4.627611 TTCCGTTCTAGTTGATCCTACG 57.372 45.455 0.00 0.00 0.00 3.51
2043 2612 1.143073 GTGGGAGGAAGACAAGGTTGT 59.857 52.381 0.00 0.00 45.65 3.32
2077 2646 8.709386 ATTATATCTTGGCTAGTTTATGCTCG 57.291 34.615 0.00 0.00 0.00 5.03
2456 3051 1.134128 TGTTTGAAGAGCAGCACTGGA 60.134 47.619 0.00 0.00 0.00 3.86
2582 3178 6.370718 AGCCCTACTACGTCTTAATTTTTGTG 59.629 38.462 0.00 0.00 0.00 3.33
2586 3182 3.653539 ACGTCTTAATTTTTGTGGGGC 57.346 42.857 0.00 0.00 0.00 5.80
2587 3183 3.227614 ACGTCTTAATTTTTGTGGGGCT 58.772 40.909 0.00 0.00 0.00 5.19
2626 3222 4.835615 TGTGGGGCTTATGTTTGTTTGTAT 59.164 37.500 0.00 0.00 0.00 2.29
2633 3229 6.813152 GGCTTATGTTTGTTTGTATGCATTCT 59.187 34.615 3.54 0.00 0.00 2.40
2641 3237 7.697352 TTGTTTGTATGCATTCTTGAAACAG 57.303 32.000 3.54 0.00 34.37 3.16
2865 3461 6.378280 TGATCTGCTCTTGATACTGTCACTTA 59.622 38.462 0.00 0.00 36.32 2.24
3144 3740 0.261696 AACCCAGAAGTTTGGTGCCT 59.738 50.000 0.00 0.00 36.45 4.75
3266 3945 5.986501 TTGTAATCCATTTTTACGCCCTT 57.013 34.783 0.00 0.00 33.23 3.95
3617 4296 8.291191 TCATATGAACTCCATTTTGTTATGCA 57.709 30.769 1.98 0.00 36.71 3.96
3740 4420 6.023603 TGTTTACCCTTGAGAGGATAAGAGT 58.976 40.000 0.00 0.00 46.74 3.24
3758 4438 4.770795 AGAGTGTCTAAAAACTGCACAGT 58.229 39.130 0.00 0.00 44.94 3.55
3778 4458 7.596494 CACAGTATTTGACACTCCATCAATTT 58.404 34.615 0.00 0.00 36.02 1.82
3790 4470 8.109634 ACACTCCATCAATTTGACCTTATAGTT 58.890 33.333 0.15 0.00 0.00 2.24
3791 4471 8.960591 CACTCCATCAATTTGACCTTATAGTTT 58.039 33.333 0.15 0.00 0.00 2.66
3792 4472 9.178758 ACTCCATCAATTTGACCTTATAGTTTC 57.821 33.333 0.15 0.00 0.00 2.78
3925 4605 4.826274 ACAGAGCAAATAGAAGGCTGTA 57.174 40.909 0.00 0.00 38.15 2.74
3995 4676 7.450074 ACCTGAGATGTTTGAACTGTATGTAA 58.550 34.615 0.00 0.00 0.00 2.41
4111 4792 5.355350 ACTTGCTATGTTTTCATGCTAGGTC 59.645 40.000 0.00 0.00 41.09 3.85
4123 4804 4.036852 TCATGCTAGGTCATTCTCGTACTG 59.963 45.833 0.00 0.00 0.00 2.74
4130 4811 4.106197 GGTCATTCTCGTACTGTGTGATC 58.894 47.826 0.00 0.00 0.00 2.92
4171 4852 4.685169 TCGAATAAAAAGGCTGCTTCTG 57.315 40.909 0.00 0.00 0.00 3.02
4187 4868 3.604582 CTTCTGATCTTGGACTTGGACC 58.395 50.000 0.00 0.00 0.00 4.46
4228 4909 1.129811 GGAATACGCAAACCTTCACCG 59.870 52.381 0.00 0.00 0.00 4.94
4468 5149 6.327934 GCACTAAAGAATGATTTGTGCTCAT 58.672 36.000 15.17 0.00 40.29 2.90
4754 5435 6.469782 AAACATAATTTACATGCCTCCAGG 57.530 37.500 0.00 0.00 38.53 4.45
4755 5436 7.947284 GTAAACATAATTTACATGCCTCCAGGC 60.947 40.741 10.97 10.97 45.14 4.85
4870 5551 9.801873 AGGATGAAAATAAATCATGTTTAACCG 57.198 29.630 0.00 0.00 37.64 4.44
4885 5566 5.647225 TGTTTAACCGAGTTTAAGTGTGGTT 59.353 36.000 9.88 9.88 42.08 3.67
4886 5567 6.820656 TGTTTAACCGAGTTTAAGTGTGGTTA 59.179 34.615 8.37 8.37 40.08 2.85
4887 5568 7.011295 TGTTTAACCGAGTTTAAGTGTGGTTAG 59.989 37.037 10.93 0.00 41.46 2.34
4889 5570 4.625028 ACCGAGTTTAAGTGTGGTTAGTC 58.375 43.478 0.00 0.00 0.00 2.59
4902 5586 7.031975 AGTGTGGTTAGTCGCTTAACTTATAC 58.968 38.462 8.23 6.94 34.65 1.47
4903 5587 6.808212 GTGTGGTTAGTCGCTTAACTTATACA 59.192 38.462 8.23 6.72 34.65 2.29
4917 5601 5.422214 ACTTATACACAACTAAGCCAGCT 57.578 39.130 0.00 0.00 0.00 4.24
4928 5612 1.089920 AAGCCAGCTAAACATGAGCG 58.910 50.000 0.00 0.00 44.98 5.03
4929 5613 0.745845 AGCCAGCTAAACATGAGCGG 60.746 55.000 0.00 5.64 44.98 5.52
4931 5615 2.397751 CAGCTAAACATGAGCGGGG 58.602 57.895 0.00 0.00 44.98 5.73
4988 5672 7.624549 TCAGTACTTCCATCTATCAAAGCTTT 58.375 34.615 5.69 5.69 0.00 3.51
5094 5778 8.135529 TGTATTCAGATGGTAGTAAATCAGTCG 58.864 37.037 0.00 0.00 0.00 4.18
5108 5792 4.500116 GTCGCGAGGCAGGGTCTC 62.500 72.222 10.24 0.00 34.40 3.36
5119 5803 1.616628 AGGGTCTCCGCCAATTCCT 60.617 57.895 0.00 0.00 38.33 3.36
5121 5805 0.323451 GGGTCTCCGCCAATTCCTTT 60.323 55.000 0.00 0.00 0.00 3.11
5122 5806 1.545841 GGTCTCCGCCAATTCCTTTT 58.454 50.000 0.00 0.00 0.00 2.27
5147 5835 0.319555 TGAGTTGAAGTCTTCGCCGG 60.320 55.000 8.06 0.00 0.00 6.13
5155 5843 1.192428 AGTCTTCGCCGGTTCCTATT 58.808 50.000 1.90 0.00 0.00 1.73
5156 5844 1.553704 AGTCTTCGCCGGTTCCTATTT 59.446 47.619 1.90 0.00 0.00 1.40
5157 5845 1.664151 GTCTTCGCCGGTTCCTATTTG 59.336 52.381 1.90 0.00 0.00 2.32
5159 5847 1.027792 TTCGCCGGTTCCTATTTGGC 61.028 55.000 1.90 0.00 42.29 4.52
5161 5849 3.107447 CCGGTTCCTATTTGGCGC 58.893 61.111 0.00 0.00 35.26 6.53
5169 5857 1.974957 TCCTATTTGGCGCCTATAGCA 59.025 47.619 28.94 19.90 37.28 3.49
5172 5860 0.537371 ATTTGGCGCCTATAGCACCC 60.537 55.000 29.70 0.00 43.59 4.61
5179 5898 2.132762 CGCCTATAGCACCCGTTAAAG 58.867 52.381 0.00 0.00 44.04 1.85
5188 5907 2.734893 CCCGTTAAAGGGCAAACCA 58.265 52.632 13.90 0.00 45.72 3.67
5191 5910 2.164827 CCCGTTAAAGGGCAAACCATAC 59.835 50.000 13.90 0.00 45.72 2.39
5192 5911 2.820787 CCGTTAAAGGGCAAACCATACA 59.179 45.455 0.00 0.00 43.89 2.29
5194 5913 4.481463 CGTTAAAGGGCAAACCATACAAG 58.519 43.478 0.00 0.00 43.89 3.16
5195 5914 4.242475 GTTAAAGGGCAAACCATACAAGC 58.758 43.478 0.00 0.00 43.89 4.01
5196 5915 2.008242 AAGGGCAAACCATACAAGCA 57.992 45.000 0.00 0.00 43.89 3.91
5198 5917 2.539302 AGGGCAAACCATACAAGCAAT 58.461 42.857 0.00 0.00 43.89 3.56
5199 5918 2.497273 AGGGCAAACCATACAAGCAATC 59.503 45.455 0.00 0.00 43.89 2.67
5200 5919 2.233431 GGGCAAACCATACAAGCAATCA 59.767 45.455 0.00 0.00 39.85 2.57
5202 5921 3.679502 GGCAAACCATACAAGCAATCAAC 59.320 43.478 0.00 0.00 35.26 3.18
5203 5922 3.364621 GCAAACCATACAAGCAATCAACG 59.635 43.478 0.00 0.00 0.00 4.10
5204 5923 2.919666 ACCATACAAGCAATCAACGC 57.080 45.000 0.00 0.00 0.00 4.84
5205 5924 2.158559 ACCATACAAGCAATCAACGCA 58.841 42.857 0.00 0.00 0.00 5.24
5261 5982 2.319136 TCTGGTTTGTGTGTAGCGTT 57.681 45.000 0.00 0.00 0.00 4.84
5283 6004 2.984871 CCGGTTTTGGCCAGTTTTG 58.015 52.632 5.11 0.00 0.00 2.44
5435 6164 9.982291 TTAGTGAACATTTTCAAATATACGAGC 57.018 29.630 0.00 0.00 43.52 5.03
5436 6165 8.268850 AGTGAACATTTTCAAATATACGAGCT 57.731 30.769 0.00 0.00 43.52 4.09
5437 6166 8.730680 AGTGAACATTTTCAAATATACGAGCTT 58.269 29.630 0.00 0.00 43.52 3.74
5438 6167 9.982291 GTGAACATTTTCAAATATACGAGCTTA 57.018 29.630 0.00 0.00 43.52 3.09
5460 6210 7.410835 GCTTATTCTGAAATCCGCAAACTTTTC 60.411 37.037 0.00 0.00 0.00 2.29
5474 6224 6.896088 CGCAAACTTTTCTCAAATTCACAAAG 59.104 34.615 0.00 0.00 0.00 2.77
5479 6229 8.831715 ACTTTTCTCAAATTCACAAAGTTGTT 57.168 26.923 0.00 0.00 40.44 2.83
5480 6230 9.271828 ACTTTTCTCAAATTCACAAAGTTGTTT 57.728 25.926 0.00 0.00 40.44 2.83
5483 6233 8.824159 TTCTCAAATTCACAAAGTTGTTTTCA 57.176 26.923 0.00 0.00 40.44 2.69
5484 6234 8.824159 TCTCAAATTCACAAAGTTGTTTTCAA 57.176 26.923 0.00 0.00 40.44 2.69
5485 6235 9.265901 TCTCAAATTCACAAAGTTGTTTTCAAA 57.734 25.926 0.00 0.00 40.44 2.69
5486 6236 9.875675 CTCAAATTCACAAAGTTGTTTTCAAAA 57.124 25.926 0.00 0.00 40.44 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.480320 GCATGATGTTTGGTAGGTCTACTTAG 59.520 42.308 0.00 0.00 36.36 2.18
13 14 4.225042 ACTGCATGATGTTTGGTAGGTCTA 59.775 41.667 0.00 0.00 0.00 2.59
76 77 0.404040 TCCCCTTTTCTTGCACCGAT 59.596 50.000 0.00 0.00 0.00 4.18
120 122 2.503382 GGACGCCATCTCCTCCCTC 61.503 68.421 0.00 0.00 0.00 4.30
237 246 1.218316 GTGAGGACCCAAGGTAGCG 59.782 63.158 0.00 0.00 35.25 4.26
423 434 2.550101 GGCGCTGCATTCCCTCATC 61.550 63.158 7.64 0.00 0.00 2.92
514 525 2.266055 GGTGGAGTCGCCCTCTTG 59.734 66.667 2.59 0.00 40.30 3.02
540 551 3.792736 TATGCTGGGTGGCGGTCC 61.793 66.667 0.00 0.00 34.52 4.46
542 553 4.109675 GGTATGCTGGGTGGCGGT 62.110 66.667 0.00 0.00 34.52 5.68
561 573 1.302511 ATCGGTGTTGGTCCAGTGC 60.303 57.895 0.00 0.00 0.00 4.40
564 576 1.377202 CCCATCGGTGTTGGTCCAG 60.377 63.158 0.00 0.00 31.99 3.86
670 682 1.420138 CTTTATCATAGGGCACGGGGT 59.580 52.381 0.00 0.00 0.00 4.95
676 690 3.459598 AGCTCAACCTTTATCATAGGGCA 59.540 43.478 0.00 0.00 37.09 5.36
699 960 2.874701 ACATCGTTTGATAGGCTGCATC 59.125 45.455 0.50 0.00 32.18 3.91
716 977 6.957077 GCAATTGAAAATATGTTGTGCACATC 59.043 34.615 22.39 20.44 43.17 3.06
737 998 0.833287 ACGGGCTGAGTAGATGCAAT 59.167 50.000 0.00 0.00 0.00 3.56
760 1022 3.339253 TGCTGTCTTGCATATGTGTCT 57.661 42.857 4.29 0.00 38.12 3.41
828 1090 9.744468 ATTTAATTCCAAATAAAGATACACCGC 57.256 29.630 0.00 0.00 0.00 5.68
1176 1562 3.450507 ACGGTGTCCATGACGTCA 58.549 55.556 22.48 22.48 33.92 4.35
1213 1599 1.210722 GAAGAAGGAGGGGATGTGGTC 59.789 57.143 0.00 0.00 0.00 4.02
1291 1677 2.165641 TGCCTAGACCACACGAATACAG 59.834 50.000 0.00 0.00 0.00 2.74
1295 1681 1.743772 GCATGCCTAGACCACACGAAT 60.744 52.381 6.36 0.00 0.00 3.34
1353 1740 2.542907 GCACACGTCACCACCAAGG 61.543 63.158 0.00 0.00 45.67 3.61
1369 1756 1.050204 AATTGGCCAGCTTCTTTGCA 58.950 45.000 5.11 0.00 34.99 4.08
1470 1857 9.305925 CAATTCCTAAGTAAAATTCCAGCAATC 57.694 33.333 0.00 0.00 0.00 2.67
1474 1861 6.867550 AGCAATTCCTAAGTAAAATTCCAGC 58.132 36.000 0.00 0.00 0.00 4.85
1579 2120 3.873952 CAGCCTTCTACTATTTCACAGGC 59.126 47.826 0.00 0.00 44.88 4.85
1592 2133 1.843851 CCATAACACCCCAGCCTTCTA 59.156 52.381 0.00 0.00 0.00 2.10
1603 2144 2.167662 CCCTCAACAACCCATAACACC 58.832 52.381 0.00 0.00 0.00 4.16
1633 2174 5.121221 AGTGCAAAGTATAAAACAGCACC 57.879 39.130 10.58 0.00 46.24 5.01
1637 2178 8.801715 AAACATGAGTGCAAAGTATAAAACAG 57.198 30.769 0.00 0.00 0.00 3.16
1647 2188 4.611355 CGGTACTGAAACATGAGTGCAAAG 60.611 45.833 0.00 0.00 0.00 2.77
1767 2308 7.174946 TCCTTCATGGACATTCTACAAAAGAAC 59.825 37.037 0.00 0.00 42.66 3.01
1904 2447 5.813672 GGCAGTCCATAAGTCGTATTTGTAA 59.186 40.000 0.00 0.00 0.00 2.41
1906 2449 4.189231 GGCAGTCCATAAGTCGTATTTGT 58.811 43.478 0.00 0.00 0.00 2.83
1908 2451 4.442706 CTGGCAGTCCATAAGTCGTATTT 58.557 43.478 6.28 0.00 42.51 1.40
2043 2612 4.242811 AGCCAAGATATAATCCCTGTCCA 58.757 43.478 0.00 0.00 0.00 4.02
2626 3222 9.979578 AAATAAACATACTGTTTCAAGAATGCA 57.020 25.926 8.41 0.00 46.61 3.96
2865 3461 9.515226 AACATAATGGTGTTTAACTCACAGTAT 57.485 29.630 10.72 0.07 39.15 2.12
2917 3513 8.529424 AGATCTGCCATCATTGAAGAATTTTA 57.471 30.769 0.00 0.00 0.00 1.52
3266 3945 3.018856 CCATGCATGCTTTCAGACCTAA 58.981 45.455 21.69 0.00 0.00 2.69
3460 4139 3.739300 TCGACAGCTTTAACTTTTCCTCG 59.261 43.478 0.00 0.00 0.00 4.63
3609 4288 5.834742 AGCTATCCATTCCATTTGCATAACA 59.165 36.000 0.00 0.00 0.00 2.41
3740 4420 7.066404 TGTCAAATACTGTGCAGTTTTTAGACA 59.934 33.333 25.42 25.42 41.10 3.41
3758 4438 6.947733 AGGTCAAATTGATGGAGTGTCAAATA 59.052 34.615 0.00 0.00 38.89 1.40
3833 4513 8.988934 GGCGAAACTATTGTCTATCATTATCAA 58.011 33.333 0.00 0.00 0.00 2.57
3839 4519 7.807977 AAATGGCGAAACTATTGTCTATCAT 57.192 32.000 0.00 0.00 28.53 2.45
3846 4526 4.618227 GCTCCAAAATGGCGAAACTATTGT 60.618 41.667 0.00 0.00 37.47 2.71
3856 4536 1.000385 TGACAAAGCTCCAAAATGGCG 60.000 47.619 0.00 0.00 37.47 5.69
4080 4761 3.004629 TGAAAACATAGCAAGTGCAGTGG 59.995 43.478 6.00 0.00 45.16 4.00
4111 4792 2.531912 GCGATCACACAGTACGAGAATG 59.468 50.000 0.00 0.00 0.00 2.67
4123 4804 1.797046 CAGCCTATGATGCGATCACAC 59.203 52.381 0.00 0.00 43.01 3.82
4130 4811 3.795639 CGATAGATTCAGCCTATGATGCG 59.204 47.826 0.00 0.00 36.29 4.73
4171 4852 3.990959 AGAAGGTCCAAGTCCAAGATC 57.009 47.619 0.00 0.00 0.00 2.75
4187 4868 7.946655 TTCCTGCGTAACATTATGATAGAAG 57.053 36.000 0.00 0.00 0.00 2.85
4228 4909 3.428862 CCACGGCATGAAGGTAAAAATCC 60.429 47.826 0.00 0.00 0.00 3.01
4446 5127 7.318141 CCAATGAGCACAAATCATTCTTTAGT 58.682 34.615 0.00 0.00 43.74 2.24
4468 5149 1.133199 AGGTGCCAATTCAACTCCCAA 60.133 47.619 0.00 0.00 24.50 4.12
4749 5430 6.409234 CCTTTAATAACATACTGGAGCCTGGA 60.409 42.308 0.00 0.00 0.00 3.86
4787 5468 1.970640 ACAACTCCCCAAAAGCCATTC 59.029 47.619 0.00 0.00 0.00 2.67
4791 5472 1.408969 TTCACAACTCCCCAAAAGCC 58.591 50.000 0.00 0.00 0.00 4.35
4870 5551 4.304939 AGCGACTAACCACACTTAAACTC 58.695 43.478 0.00 0.00 0.00 3.01
4885 5566 9.778993 CTTAGTTGTGTATAAGTTAAGCGACTA 57.221 33.333 0.00 0.00 0.00 2.59
4886 5567 7.275123 GCTTAGTTGTGTATAAGTTAAGCGACT 59.725 37.037 0.00 0.00 32.64 4.18
4887 5568 7.389479 GCTTAGTTGTGTATAAGTTAAGCGAC 58.611 38.462 0.00 0.00 32.64 5.19
4889 5570 6.311935 TGGCTTAGTTGTGTATAAGTTAAGCG 59.688 38.462 7.10 0.00 38.48 4.68
4902 5586 4.455533 TCATGTTTAGCTGGCTTAGTTGTG 59.544 41.667 0.00 0.00 0.00 3.33
4903 5587 4.651778 TCATGTTTAGCTGGCTTAGTTGT 58.348 39.130 0.00 0.00 0.00 3.32
4928 5612 0.105039 CTCTACCATTGTCGAGCCCC 59.895 60.000 0.00 0.00 28.86 5.80
4929 5613 3.669354 CTCTACCATTGTCGAGCCC 57.331 57.895 0.00 0.00 28.86 5.19
4988 5672 1.134753 CATTGGCGCAAAGGCTTATCA 59.865 47.619 10.83 0.00 46.88 2.15
4992 5676 0.037975 CTTCATTGGCGCAAAGGCTT 60.038 50.000 10.83 0.00 46.88 4.35
5125 5809 2.286833 CGGCGAAGACTTCAACTCAAAA 59.713 45.455 15.36 0.00 0.00 2.44
5126 5810 1.864711 CGGCGAAGACTTCAACTCAAA 59.135 47.619 15.36 0.00 0.00 2.69
5136 5824 1.192428 AATAGGAACCGGCGAAGACT 58.808 50.000 9.30 3.75 0.00 3.24
5147 5835 2.742589 GCTATAGGCGCCAAATAGGAAC 59.257 50.000 32.87 21.02 41.22 3.62
5159 5847 2.132762 CTTTAACGGGTGCTATAGGCG 58.867 52.381 1.04 0.00 45.43 5.52
5161 5849 2.809299 GCCCTTTAACGGGTGCTATAGG 60.809 54.545 17.80 0.00 46.47 2.57
5169 5857 0.106116 TGGTTTGCCCTTTAACGGGT 60.106 50.000 17.80 0.00 46.47 5.28
5172 5860 4.481463 CTTGTATGGTTTGCCCTTTAACG 58.519 43.478 0.00 0.00 0.00 3.18
5179 5898 2.233431 TGATTGCTTGTATGGTTTGCCC 59.767 45.455 0.00 0.00 0.00 5.36
5188 5907 4.906065 ATCATGCGTTGATTGCTTGTAT 57.094 36.364 0.00 0.00 42.62 2.29
5191 5910 5.004061 CACTTTATCATGCGTTGATTGCTTG 59.996 40.000 7.21 0.00 42.62 4.01
5192 5911 5.097529 CACTTTATCATGCGTTGATTGCTT 58.902 37.500 7.21 0.00 42.62 3.91
5194 5913 3.792956 CCACTTTATCATGCGTTGATTGC 59.207 43.478 7.21 0.00 42.62 3.56
5195 5914 4.353737 CCCACTTTATCATGCGTTGATTG 58.646 43.478 7.21 0.93 42.62 2.67
5196 5915 3.181487 GCCCACTTTATCATGCGTTGATT 60.181 43.478 7.21 0.00 42.62 2.57
5198 5917 1.742831 GCCCACTTTATCATGCGTTGA 59.257 47.619 0.00 0.00 39.12 3.18
5199 5918 1.202290 GGCCCACTTTATCATGCGTTG 60.202 52.381 0.00 0.00 0.00 4.10
5200 5919 1.102978 GGCCCACTTTATCATGCGTT 58.897 50.000 0.00 0.00 0.00 4.84
5202 5921 1.648720 CGGCCCACTTTATCATGCG 59.351 57.895 0.00 0.00 0.00 4.73
5203 5922 2.032981 CCGGCCCACTTTATCATGC 58.967 57.895 0.00 0.00 0.00 4.06
5204 5923 1.455383 GGCCGGCCCACTTTATCATG 61.455 60.000 36.64 0.00 0.00 3.07
5205 5924 1.152756 GGCCGGCCCACTTTATCAT 60.153 57.895 36.64 0.00 0.00 2.45
5243 5963 3.606153 GCTAAACGCTACACACAAACCAG 60.606 47.826 0.00 0.00 35.14 4.00
5254 5975 1.135888 CCAAAACCGGCTAAACGCTAC 60.136 52.381 0.00 0.00 39.13 3.58
5266 5987 2.017138 AACAAAACTGGCCAAAACCG 57.983 45.000 7.01 0.00 0.00 4.44
5411 6140 8.268850 AGCTCGTATATTTGAAAATGTTCACT 57.731 30.769 0.00 0.00 43.52 3.41
5412 6141 8.895932 AAGCTCGTATATTTGAAAATGTTCAC 57.104 30.769 0.00 0.00 43.52 3.18
5424 6153 8.926710 CGGATTTCAGAATAAGCTCGTATATTT 58.073 33.333 0.00 0.00 0.00 1.40
5427 6156 5.862323 GCGGATTTCAGAATAAGCTCGTATA 59.138 40.000 0.00 0.00 0.00 1.47
5430 6159 2.866762 GCGGATTTCAGAATAAGCTCGT 59.133 45.455 0.00 0.00 0.00 4.18
5431 6160 2.866156 TGCGGATTTCAGAATAAGCTCG 59.134 45.455 0.00 0.00 32.35 5.03
5432 6161 4.882671 TTGCGGATTTCAGAATAAGCTC 57.117 40.909 0.00 0.00 32.35 4.09
5434 6163 4.986622 AGTTTGCGGATTTCAGAATAAGC 58.013 39.130 0.00 0.00 0.00 3.09
5435 6164 7.809806 AGAAAAGTTTGCGGATTTCAGAATAAG 59.190 33.333 3.99 0.00 34.91 1.73
5436 6165 7.657336 AGAAAAGTTTGCGGATTTCAGAATAA 58.343 30.769 3.99 0.00 34.91 1.40
5437 6166 7.040755 TGAGAAAAGTTTGCGGATTTCAGAATA 60.041 33.333 3.99 0.00 34.91 1.75
5438 6167 6.089249 AGAAAAGTTTGCGGATTTCAGAAT 57.911 33.333 3.99 0.00 34.91 2.40
5441 6170 4.858935 TGAGAAAAGTTTGCGGATTTCAG 58.141 39.130 3.99 0.00 34.91 3.02
5443 6172 6.769608 ATTTGAGAAAAGTTTGCGGATTTC 57.230 33.333 0.00 0.00 33.13 2.17
5460 6210 9.875675 TTTTGAAAACAACTTTGTGAATTTGAG 57.124 25.926 0.00 0.00 41.31 3.02
5474 6224 9.891828 AAAAACTTCAGGAATTTTGAAAACAAC 57.108 25.926 0.00 0.00 34.41 3.32


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

AutoCloner maintained by Alex Coulton.