Multiple sequence alignment - TraesCS5A01G200200

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 TraesCS5A01G200200 chr5A 100.000 2688 0 0 630 3317 405019652 405016965 0.000000e+00 4964
1 TraesCS5A01G200200 chr5A 100.000 440 0 0 1 440 405020281 405019842 0.000000e+00 813
2 TraesCS5A01G200200 chr5A 75.537 605 131 17 1601 2198 406483376 406482782 7.010000e-72 281
3 TraesCS5A01G200200 chr5A 80.693 202 31 7 2863 3060 405039395 405039198 2.060000e-32 150
4 TraesCS5A01G200200 chr5A 95.349 86 4 0 726 811 405019471 405019556 1.600000e-28 137
5 TraesCS5A01G200200 chr5B 95.219 2510 114 5 813 3317 358382441 358379933 0.000000e+00 3965
6 TraesCS5A01G200200 chr5B 94.508 437 23 1 4 440 358383054 358382619 0.000000e+00 673
7 TraesCS5A01G200200 chr5B 75.702 605 130 17 1601 2198 358637871 358637277 1.510000e-73 287
8 TraesCS5A01G200200 chr5B 90.789 76 7 0 652 727 358382518 358382443 5.850000e-18 102
9 TraesCS5A01G200200 chr5D 94.783 2511 113 5 810 3317 312063256 312060761 0.000000e+00 3895
10 TraesCS5A01G200200 chr5D 95.195 333 8 2 116 440 312063770 312063438 1.360000e-143 520
11 TraesCS5A01G200200 chr5D 75.537 605 131 17 1601 2198 312369962 312369368 7.010000e-72 281
12 TraesCS5A01G200200 chr5D 98.425 127 2 0 4 130 312063911 312063785 1.200000e-54 224
13 TraesCS5A01G200200 chr5D 86.806 144 15 3 2863 3004 312067860 312067719 1.230000e-34 158
14 TraesCS5A01G200200 chr5D 100.000 79 0 0 649 727 312063333 312063255 2.670000e-31 147
15 TraesCS5A01G200200 chr5D 94.505 91 5 0 721 811 7053402 7053492 1.240000e-29 141
16 TraesCS5A01G200200 chr1B 96.512 86 3 0 726 811 479429938 479430023 3.450000e-30 143
17 TraesCS5A01G200200 chr1B 94.382 89 5 0 723 811 479430026 479429938 1.600000e-28 137
18 TraesCS5A01G200200 chr1B 94.253 87 5 0 725 811 61951690 61951776 2.080000e-27 134
19 TraesCS5A01G200200 chr1B 94.186 86 5 0 726 811 61951776 61951691 7.470000e-27 132
20 TraesCS5A01G200200 chr1B 92.308 91 7 0 726 816 666066018 666066108 2.690000e-26 130
21 TraesCS5A01G200200 chr6B 95.349 86 4 0 726 811 676296536 676296621 1.600000e-28 137
22 TraesCS5A01G200200 chr4B 95.349 86 4 0 726 811 599830305 599830390 1.600000e-28 137


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 TraesCS5A01G200200 chr5A 405016965 405020281 3316 True 2888.5 4964 100.000000 1 3317 2 chr5A.!!$R3 3316
1 TraesCS5A01G200200 chr5A 406482782 406483376 594 True 281.0 281 75.537000 1601 2198 1 chr5A.!!$R2 597
2 TraesCS5A01G200200 chr5B 358379933 358383054 3121 True 1580.0 3965 93.505333 4 3317 3 chr5B.!!$R2 3313
3 TraesCS5A01G200200 chr5B 358637277 358637871 594 True 287.0 287 75.702000 1601 2198 1 chr5B.!!$R1 597
4 TraesCS5A01G200200 chr5D 312060761 312067860 7099 True 988.8 3895 95.041800 4 3317 5 chr5D.!!$R2 3313
5 TraesCS5A01G200200 chr5D 312369368 312369962 594 True 281.0 281 75.537000 1601 2198 1 chr5D.!!$R1 597

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
174 4154 0.252513 TTGGTCTCATCCTCCCCGAA 60.253 55.0 0.00 0.0 0.00 4.30 F
265 4245 1.168714 GCGCCTTCTGGAATTCTTGT 58.831 50.0 5.23 0.0 34.57 3.16 F
1488 5484 0.038744 CCTTGCCTGATGTTCCCACT 59.961 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 5430 0.250234 CAGGCGATCCAAGTTCCTCA 59.750 55.0 0.0 0.0 33.74 3.86 R
1926 5922 0.457851 AGAAAGCCGAGACTGGATCG 59.542 55.0 0.0 0.0 39.86 3.69 R
2743 6739 0.107945 GACCCAGAAGTGCAGCTAGG 60.108 60.0 0.0 0.0 0.00 3.02 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
20 3967 1.985895 GGTAAGCCCAGTAGCCCATAT 59.014 52.381 0.00 0.00 0.00 1.78
174 4154 0.252513 TTGGTCTCATCCTCCCCGAA 60.253 55.000 0.00 0.00 0.00 4.30
265 4245 1.168714 GCGCCTTCTGGAATTCTTGT 58.831 50.000 5.23 0.00 34.57 3.16
433 4417 7.254898 CCTGTGTACATATGGATCAACAATGTC 60.255 40.741 7.80 0.00 33.15 3.06
727 4719 1.666189 GCGCTCCCATTGTTCTTCTAC 59.334 52.381 0.00 0.00 0.00 2.59
728 4720 2.678190 GCGCTCCCATTGTTCTTCTACT 60.678 50.000 0.00 0.00 0.00 2.57
729 4721 3.190874 CGCTCCCATTGTTCTTCTACTC 58.809 50.000 0.00 0.00 0.00 2.59
730 4722 3.536570 GCTCCCATTGTTCTTCTACTCC 58.463 50.000 0.00 0.00 0.00 3.85
731 4723 3.682999 GCTCCCATTGTTCTTCTACTCCC 60.683 52.174 0.00 0.00 0.00 4.30
732 4724 3.777522 CTCCCATTGTTCTTCTACTCCCT 59.222 47.826 0.00 0.00 0.00 4.20
733 4725 3.775316 TCCCATTGTTCTTCTACTCCCTC 59.225 47.826 0.00 0.00 0.00 4.30
734 4726 3.118223 CCCATTGTTCTTCTACTCCCTCC 60.118 52.174 0.00 0.00 0.00 4.30
735 4727 3.430929 CCATTGTTCTTCTACTCCCTCCG 60.431 52.174 0.00 0.00 0.00 4.63
736 4728 2.599408 TGTTCTTCTACTCCCTCCGT 57.401 50.000 0.00 0.00 0.00 4.69
737 4729 2.885616 TGTTCTTCTACTCCCTCCGTT 58.114 47.619 0.00 0.00 0.00 4.44
738 4730 2.824341 TGTTCTTCTACTCCCTCCGTTC 59.176 50.000 0.00 0.00 0.00 3.95
739 4731 3.090790 GTTCTTCTACTCCCTCCGTTCT 58.909 50.000 0.00 0.00 0.00 3.01
740 4732 2.724454 TCTTCTACTCCCTCCGTTCTG 58.276 52.381 0.00 0.00 0.00 3.02
741 4733 2.307980 TCTTCTACTCCCTCCGTTCTGA 59.692 50.000 0.00 0.00 0.00 3.27
742 4734 3.053544 TCTTCTACTCCCTCCGTTCTGAT 60.054 47.826 0.00 0.00 0.00 2.90
743 4735 3.383698 TCTACTCCCTCCGTTCTGATT 57.616 47.619 0.00 0.00 0.00 2.57
744 4736 3.709587 TCTACTCCCTCCGTTCTGATTT 58.290 45.455 0.00 0.00 0.00 2.17
745 4737 4.863548 TCTACTCCCTCCGTTCTGATTTA 58.136 43.478 0.00 0.00 0.00 1.40
746 4738 3.889520 ACTCCCTCCGTTCTGATTTAC 57.110 47.619 0.00 0.00 0.00 2.01
747 4739 3.442076 ACTCCCTCCGTTCTGATTTACT 58.558 45.455 0.00 0.00 0.00 2.24
748 4740 3.838903 ACTCCCTCCGTTCTGATTTACTT 59.161 43.478 0.00 0.00 0.00 2.24
749 4741 4.184629 CTCCCTCCGTTCTGATTTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
750 4742 3.581332 TCCCTCCGTTCTGATTTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
751 4743 3.933332 CCCTCCGTTCTGATTTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
752 4744 3.612860 CCTCCGTTCTGATTTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
753 4745 4.235360 CTCCGTTCTGATTTACTTGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
754 4746 3.985279 TCCGTTCTGATTTACTTGTCGTG 59.015 43.478 0.00 0.00 0.00 4.35
755 4747 3.985279 CCGTTCTGATTTACTTGTCGTGA 59.015 43.478 0.00 0.00 0.00 4.35
756 4748 4.625742 CCGTTCTGATTTACTTGTCGTGAT 59.374 41.667 0.00 0.00 0.00 3.06
757 4749 5.120208 CCGTTCTGATTTACTTGTCGTGATT 59.880 40.000 0.00 0.00 0.00 2.57
758 4750 6.347402 CCGTTCTGATTTACTTGTCGTGATTT 60.347 38.462 0.00 0.00 0.00 2.17
759 4751 7.069569 CGTTCTGATTTACTTGTCGTGATTTT 58.930 34.615 0.00 0.00 0.00 1.82
760 4752 8.218441 CGTTCTGATTTACTTGTCGTGATTTTA 58.782 33.333 0.00 0.00 0.00 1.52
761 4753 9.530129 GTTCTGATTTACTTGTCGTGATTTTAG 57.470 33.333 0.00 0.00 0.00 1.85
762 4754 8.827177 TCTGATTTACTTGTCGTGATTTTAGT 57.173 30.769 0.00 0.00 0.00 2.24
763 4755 9.268268 TCTGATTTACTTGTCGTGATTTTAGTT 57.732 29.630 0.00 0.00 0.00 2.24
764 4756 9.530129 CTGATTTACTTGTCGTGATTTTAGTTC 57.470 33.333 0.00 0.00 0.00 3.01
765 4757 9.047371 TGATTTACTTGTCGTGATTTTAGTTCA 57.953 29.630 0.00 0.00 0.00 3.18
766 4758 9.872757 GATTTACTTGTCGTGATTTTAGTTCAA 57.127 29.630 0.00 0.00 0.00 2.69
771 4763 9.019764 ACTTGTCGTGATTTTAGTTCAAATTTG 57.980 29.630 12.15 12.15 0.00 2.32
772 4764 9.232082 CTTGTCGTGATTTTAGTTCAAATTTGA 57.768 29.630 16.91 16.91 34.92 2.69
773 4765 9.574458 TTGTCGTGATTTTAGTTCAAATTTGAA 57.426 25.926 26.01 26.01 44.31 2.69
788 4780 9.574458 TTCAAATTTGAACTAAAATCACGACAA 57.426 25.926 26.01 1.80 41.88 3.18
789 4781 9.743057 TCAAATTTGAACTAAAATCACGACAAT 57.257 25.926 18.45 0.00 33.55 2.71
796 4788 9.536558 TGAACTAAAATCACGACAATTAAATCG 57.463 29.630 0.00 5.80 43.97 3.34
797 4789 8.889849 AACTAAAATCACGACAATTAAATCGG 57.110 30.769 10.66 2.44 42.67 4.18
798 4790 8.259049 ACTAAAATCACGACAATTAAATCGGA 57.741 30.769 10.66 6.49 42.67 4.55
799 4791 8.723311 ACTAAAATCACGACAATTAAATCGGAA 58.277 29.630 10.66 1.14 42.67 4.30
800 4792 7.790861 AAAATCACGACAATTAAATCGGAAC 57.209 32.000 10.66 0.00 42.67 3.62
848 4841 1.472878 CCAAACTCGGTCTCTCGATCA 59.527 52.381 0.00 0.00 38.55 2.92
856 4849 6.395629 ACTCGGTCTCTCGATCAATTTTTAA 58.604 36.000 0.00 0.00 38.55 1.52
859 4852 6.872020 TCGGTCTCTCGATCAATTTTTAAAGT 59.128 34.615 0.00 0.00 33.92 2.66
884 4877 6.949578 ATCGACCATTTGCTAATTTGTTTG 57.050 33.333 0.00 0.00 0.00 2.93
923 4916 9.846248 CAGAGAACTTGTTCAAAATTATAAGGG 57.154 33.333 14.80 0.00 0.00 3.95
943 4936 4.336433 AGGGAATGCTGAAATATCAACACG 59.664 41.667 0.00 0.00 34.66 4.49
977 4973 9.620259 TTTCAAATGGCTAAATTTTTACTGGTT 57.380 25.926 0.00 0.00 0.00 3.67
1015 5011 3.199946 CCTAGGCATGGAACAGGAAGTTA 59.800 47.826 0.00 0.00 46.40 2.24
1016 5012 3.356529 AGGCATGGAACAGGAAGTTAG 57.643 47.619 0.00 0.00 46.40 2.34
1018 5014 2.436417 GCATGGAACAGGAAGTTAGCA 58.564 47.619 0.00 0.00 46.40 3.49
1022 5018 2.703536 TGGAACAGGAAGTTAGCAGTGA 59.296 45.455 0.00 0.00 41.51 3.41
1044 5040 2.865551 CAAAAACATGGTGGCACAAGAC 59.134 45.455 20.82 1.98 44.16 3.01
1061 5057 1.457267 ACCACAACAATGGCAGCCA 60.457 52.632 18.99 18.99 44.33 4.75
1254 5250 2.436109 GCCCAGAAGAGGCCAACA 59.564 61.111 5.01 0.00 45.16 3.33
1273 5269 2.061773 CACAACGGAAGAGTACAGCAG 58.938 52.381 0.00 0.00 0.00 4.24
1320 5316 3.515901 AGAAGCTATCGTTCTTTCCCACT 59.484 43.478 0.00 0.00 29.57 4.00
1324 5320 3.430374 GCTATCGTTCTTTCCCACTAGCA 60.430 47.826 0.00 0.00 32.58 3.49
1385 5381 5.829924 AGAAGAAGGATCTTGTTTTGCTTCA 59.170 36.000 0.00 0.00 45.91 3.02
1434 5430 4.310740 AGGGTAATCAGAATGGGTCTCAT 58.689 43.478 0.00 0.00 37.79 2.90
1488 5484 0.038744 CCTTGCCTGATGTTCCCACT 59.961 55.000 0.00 0.00 0.00 4.00
1493 5489 1.947678 GCCTGATGTTCCCACTGACAG 60.948 57.143 0.00 0.00 0.00 3.51
1494 5490 1.625315 CCTGATGTTCCCACTGACAGA 59.375 52.381 10.08 0.00 0.00 3.41
1497 5493 4.330250 CTGATGTTCCCACTGACAGAAAT 58.670 43.478 10.08 0.00 0.00 2.17
1639 5635 0.311790 ACTTGCATTGCCTGAACACG 59.688 50.000 6.12 0.00 0.00 4.49
1659 5655 1.819753 AGGCCATTCCTACTGCCATA 58.180 50.000 5.01 0.00 45.41 2.74
1664 5660 3.954258 GCCATTCCTACTGCCATAAAACT 59.046 43.478 0.00 0.00 0.00 2.66
1701 5697 1.143813 GTCAGGATGGATCCCATGGT 58.856 55.000 11.73 0.00 45.26 3.55
1876 5872 1.311651 GGCCAAGCTGAAGGAGAAGC 61.312 60.000 0.00 0.00 39.82 3.86
1933 5929 0.999406 CGTTTGGCACTACGATCCAG 59.001 55.000 14.22 0.00 38.83 3.86
1941 5937 0.107116 ACTACGATCCAGTCTCGGCT 60.107 55.000 0.00 0.00 40.37 5.52
2315 6311 7.598248 TCTAAACCTATGATGGGTCCTAAGTA 58.402 38.462 0.00 0.00 35.83 2.24
2375 6371 1.229209 AGGAAGACTGGGGCGAAGA 60.229 57.895 0.00 0.00 0.00 2.87
2427 6423 3.599343 TCATCAGTACATGGACACAAGC 58.401 45.455 11.55 0.00 0.00 4.01
2428 6424 3.007831 TCATCAGTACATGGACACAAGCA 59.992 43.478 11.55 0.00 0.00 3.91
2448 6444 0.962489 AGAGTCTTCGTGGTCCAGTG 59.038 55.000 0.00 0.00 0.00 3.66
2463 6459 1.401530 CAGTGCACTTGTTTGATGCG 58.598 50.000 18.94 0.00 42.44 4.73
2480 6476 1.209261 TGCGATTAGGGATGTGAAGCA 59.791 47.619 0.00 0.00 0.00 3.91
2496 6492 1.226379 GCATGATTTGCGTCGTGGG 60.226 57.895 0.00 0.00 42.54 4.61
2510 6506 2.167900 GTCGTGGGGTTAAGAGCTATGT 59.832 50.000 0.00 0.00 0.00 2.29
2560 6556 3.413846 AGATGCAGCAGAAGTTCAAGA 57.586 42.857 4.07 0.00 0.00 3.02
2667 6663 5.310451 AGCGGTTACCTCTGTAAAAATGAA 58.690 37.500 0.00 0.00 38.62 2.57
2706 6702 4.649692 AGGATGTCCATGATACATTGCTC 58.350 43.478 12.98 3.98 37.69 4.26
2763 6759 0.107945 CTAGCTGCACTTCTGGGTCC 60.108 60.000 1.02 0.00 0.00 4.46
2865 6861 4.448210 GAGACAAATGTAATAAGGGGCGA 58.552 43.478 0.00 0.00 0.00 5.54
2958 6954 3.009143 GGTGGAAGGAACATAACCTGACT 59.991 47.826 0.00 0.00 37.85 3.41
2985 6981 2.764314 AATTGCTCGGATGGCACGC 61.764 57.895 0.00 0.00 39.55 5.34
3100 7096 2.992543 GAGCAGCTTGTCTGTACTCAAG 59.007 50.000 16.00 16.00 44.66 3.02
3114 7110 0.539051 CTCAAGATTGGCTCGGACCT 59.461 55.000 0.00 0.00 0.00 3.85
3115 7111 1.757118 CTCAAGATTGGCTCGGACCTA 59.243 52.381 0.00 0.00 0.00 3.08
3127 7123 0.804989 CGGACCTAACCGTACGTTCT 59.195 55.000 15.21 0.23 46.70 3.01
3147 7143 5.906113 TCTACTCTCTCGCTTTTCTCATT 57.094 39.130 0.00 0.00 0.00 2.57
3151 7147 4.869297 ACTCTCTCGCTTTTCTCATTGATG 59.131 41.667 0.00 0.00 0.00 3.07
3161 7157 3.236632 TCTCATTGATGTCCTGTCACG 57.763 47.619 0.00 0.00 0.00 4.35
3210 7206 1.271597 CCTAGGTTCTGCAAGCAAGGT 60.272 52.381 0.00 0.00 31.93 3.50
3229 7225 3.555059 GGTCTCAACCAGCGATCTTTCG 61.555 54.545 0.00 0.00 45.68 3.46
3301 7297 2.127271 ACACATGGCAATCCGATTCA 57.873 45.000 0.00 0.00 34.14 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.290323 CCATATGGGCTACTGGGCTTAC 60.290 54.545 14.52 0.00 40.65 2.34
2 3 1.985159 CCATATGGGCTACTGGGCTTA 59.015 52.381 14.52 0.00 40.65 3.09
174 4154 1.961277 CCGTGTTTCTTCTGCGCCT 60.961 57.895 4.18 0.00 0.00 5.52
265 4245 6.757010 GCATTATCTACAGAGAAGAAACGGAA 59.243 38.462 0.00 0.00 34.61 4.30
629 4613 1.423584 TCTGATGCCATCGGTACCAT 58.576 50.000 13.54 1.74 36.98 3.55
630 4614 1.423584 ATCTGATGCCATCGGTACCA 58.576 50.000 13.54 0.00 36.98 3.25
631 4615 2.550830 AATCTGATGCCATCGGTACC 57.449 50.000 13.08 0.16 36.98 3.34
632 4616 4.521130 TCTAATCTGATGCCATCGGTAC 57.479 45.455 13.08 0.00 36.98 3.34
633 4617 4.561530 GCTTCTAATCTGATGCCATCGGTA 60.562 45.833 13.08 1.31 36.98 4.02
634 4618 3.805108 GCTTCTAATCTGATGCCATCGGT 60.805 47.826 13.08 0.00 36.98 4.69
635 4619 2.740981 GCTTCTAATCTGATGCCATCGG 59.259 50.000 7.22 7.22 36.99 4.18
636 4620 3.396560 TGCTTCTAATCTGATGCCATCG 58.603 45.455 0.00 0.00 36.62 3.84
637 4621 3.188873 GCTGCTTCTAATCTGATGCCATC 59.811 47.826 0.00 0.00 36.62 3.51
727 4719 4.184629 CAAGTAAATCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
728 4720 3.581332 ACAAGTAAATCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
729 4721 3.933332 GACAAGTAAATCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
730 4722 3.612860 CGACAAGTAAATCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
731 4723 4.090066 CACGACAAGTAAATCAGAACGGAG 59.910 45.833 0.00 0.00 0.00 4.63
732 4724 3.985279 CACGACAAGTAAATCAGAACGGA 59.015 43.478 0.00 0.00 0.00 4.69
733 4725 3.985279 TCACGACAAGTAAATCAGAACGG 59.015 43.478 0.00 0.00 0.00 4.44
734 4726 5.763444 ATCACGACAAGTAAATCAGAACG 57.237 39.130 0.00 0.00 0.00 3.95
735 4727 9.530129 CTAAAATCACGACAAGTAAATCAGAAC 57.470 33.333 0.00 0.00 0.00 3.01
736 4728 9.268268 ACTAAAATCACGACAAGTAAATCAGAA 57.732 29.630 0.00 0.00 0.00 3.02
737 4729 8.827177 ACTAAAATCACGACAAGTAAATCAGA 57.173 30.769 0.00 0.00 0.00 3.27
738 4730 9.530129 GAACTAAAATCACGACAAGTAAATCAG 57.470 33.333 0.00 0.00 0.00 2.90
739 4731 9.047371 TGAACTAAAATCACGACAAGTAAATCA 57.953 29.630 0.00 0.00 0.00 2.57
740 4732 9.872757 TTGAACTAAAATCACGACAAGTAAATC 57.127 29.630 0.00 0.00 0.00 2.17
745 4737 9.019764 CAAATTTGAACTAAAATCACGACAAGT 57.980 29.630 13.08 0.00 0.00 3.16
746 4738 9.232082 TCAAATTTGAACTAAAATCACGACAAG 57.768 29.630 18.45 0.00 33.55 3.16
747 4739 9.574458 TTCAAATTTGAACTAAAATCACGACAA 57.426 25.926 26.01 1.80 41.88 3.18
762 4754 9.574458 TTGTCGTGATTTTAGTTCAAATTTGAA 57.426 25.926 26.01 26.01 44.31 2.69
763 4755 9.743057 ATTGTCGTGATTTTAGTTCAAATTTGA 57.257 25.926 16.91 16.91 34.92 2.69
770 4762 9.536558 CGATTTAATTGTCGTGATTTTAGTTCA 57.463 29.630 0.00 0.00 33.42 3.18
771 4763 8.995906 CCGATTTAATTGTCGTGATTTTAGTTC 58.004 33.333 8.30 0.00 36.17 3.01
772 4764 8.723311 TCCGATTTAATTGTCGTGATTTTAGTT 58.277 29.630 8.30 0.00 36.17 2.24
773 4765 8.259049 TCCGATTTAATTGTCGTGATTTTAGT 57.741 30.769 8.30 0.00 36.17 2.24
774 4766 8.995906 GTTCCGATTTAATTGTCGTGATTTTAG 58.004 33.333 8.30 0.00 36.17 1.85
775 4767 7.688989 CGTTCCGATTTAATTGTCGTGATTTTA 59.311 33.333 8.30 0.00 36.17 1.52
776 4768 6.521821 CGTTCCGATTTAATTGTCGTGATTTT 59.478 34.615 8.30 0.00 36.17 1.82
777 4769 6.019152 CGTTCCGATTTAATTGTCGTGATTT 58.981 36.000 8.30 0.00 36.17 2.17
778 4770 5.446741 CCGTTCCGATTTAATTGTCGTGATT 60.447 40.000 8.30 0.00 36.17 2.57
779 4771 4.033587 CCGTTCCGATTTAATTGTCGTGAT 59.966 41.667 8.30 0.00 36.17 3.06
780 4772 3.368539 CCGTTCCGATTTAATTGTCGTGA 59.631 43.478 8.30 4.12 36.17 4.35
781 4773 3.368539 TCCGTTCCGATTTAATTGTCGTG 59.631 43.478 8.30 2.41 36.17 4.35
782 4774 3.587923 TCCGTTCCGATTTAATTGTCGT 58.412 40.909 8.30 0.00 36.17 4.34
783 4775 3.000925 CCTCCGTTCCGATTTAATTGTCG 59.999 47.826 0.00 0.00 37.58 4.35
784 4776 3.311596 CCCTCCGTTCCGATTTAATTGTC 59.688 47.826 0.00 0.00 0.00 3.18
785 4777 3.054948 TCCCTCCGTTCCGATTTAATTGT 60.055 43.478 0.00 0.00 0.00 2.71
786 4778 3.537580 TCCCTCCGTTCCGATTTAATTG 58.462 45.455 0.00 0.00 0.00 2.32
787 4779 3.199289 ACTCCCTCCGTTCCGATTTAATT 59.801 43.478 0.00 0.00 0.00 1.40
788 4780 2.770232 ACTCCCTCCGTTCCGATTTAAT 59.230 45.455 0.00 0.00 0.00 1.40
789 4781 2.181975 ACTCCCTCCGTTCCGATTTAA 58.818 47.619 0.00 0.00 0.00 1.52
790 4782 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
791 4783 1.856629 TACTCCCTCCGTTCCGATTT 58.143 50.000 0.00 0.00 0.00 2.17
792 4784 1.479730 GTTACTCCCTCCGTTCCGATT 59.520 52.381 0.00 0.00 0.00 3.34
793 4785 1.109609 GTTACTCCCTCCGTTCCGAT 58.890 55.000 0.00 0.00 0.00 4.18
794 4786 0.038744 AGTTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
795 4787 0.172803 CAGTTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
796 4788 1.264295 ACAGTTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
797 4789 4.441217 GGATAACAGTTACTCCCTCCGTTC 60.441 50.000 0.00 0.00 0.00 3.95
798 4790 3.450096 GGATAACAGTTACTCCCTCCGTT 59.550 47.826 0.00 0.00 0.00 4.44
799 4791 3.029570 GGATAACAGTTACTCCCTCCGT 58.970 50.000 0.00 0.00 0.00 4.69
800 4792 2.364647 GGGATAACAGTTACTCCCTCCG 59.635 54.545 22.03 0.00 43.45 4.63
801 4793 2.704596 GGGGATAACAGTTACTCCCTCC 59.295 54.545 25.17 16.02 45.65 4.30
802 4794 3.655384 AGGGGATAACAGTTACTCCCTC 58.345 50.000 25.17 19.34 45.65 4.30
803 4795 3.797671 AGGGGATAACAGTTACTCCCT 57.202 47.619 25.17 23.51 45.65 4.20
804 4796 4.967442 ACTTAGGGGATAACAGTTACTCCC 59.033 45.833 21.59 21.59 45.64 4.30
805 4797 5.070180 GGACTTAGGGGATAACAGTTACTCC 59.930 48.000 0.00 4.52 0.00 3.85
806 4798 5.659971 TGGACTTAGGGGATAACAGTTACTC 59.340 44.000 0.00 0.00 0.00 2.59
807 4799 5.596763 TGGACTTAGGGGATAACAGTTACT 58.403 41.667 0.00 0.00 0.00 2.24
808 4800 5.945144 TGGACTTAGGGGATAACAGTTAC 57.055 43.478 0.00 0.00 0.00 2.50
809 4801 6.502863 AGTTTGGACTTAGGGGATAACAGTTA 59.497 38.462 0.00 0.00 29.87 2.24
810 4802 5.312443 AGTTTGGACTTAGGGGATAACAGTT 59.688 40.000 0.00 0.00 29.87 3.16
848 4841 9.705290 AGCAAATGGTCGATTACTTTAAAAATT 57.295 25.926 0.00 0.00 0.00 1.82
856 4849 7.826690 ACAAATTAGCAAATGGTCGATTACTT 58.173 30.769 0.00 0.00 0.00 2.24
859 4852 7.062839 GCAAACAAATTAGCAAATGGTCGATTA 59.937 33.333 0.00 0.00 0.00 1.75
923 4916 4.661125 TGCGTGTTGATATTTCAGCATTC 58.339 39.130 6.03 2.83 43.69 2.67
951 4947 9.620259 AACCAGTAAAAATTTAGCCATTTGAAA 57.380 25.926 0.00 0.00 0.00 2.69
977 4973 5.291905 GCCTAGGCATAAGAAAAGGTAGA 57.708 43.478 29.33 0.00 41.49 2.59
1015 5011 2.101249 CCACCATGTTTTTGTCACTGCT 59.899 45.455 0.00 0.00 0.00 4.24
1016 5012 2.472816 CCACCATGTTTTTGTCACTGC 58.527 47.619 0.00 0.00 0.00 4.40
1018 5014 2.106566 TGCCACCATGTTTTTGTCACT 58.893 42.857 0.00 0.00 0.00 3.41
1022 5018 2.499289 TCTTGTGCCACCATGTTTTTGT 59.501 40.909 0.00 0.00 0.00 2.83
1044 5040 1.005867 GTGGCTGCCATTGTTGTGG 60.006 57.895 26.22 0.00 42.35 4.17
1212 5208 3.063704 CCGCACATGGCATGGTGT 61.064 61.111 29.49 9.49 45.17 4.16
1254 5250 1.605712 GCTGCTGTACTCTTCCGTTGT 60.606 52.381 0.00 0.00 0.00 3.32
1273 5269 2.588314 CGGATCAGAGCCAGCTGC 60.588 66.667 8.66 3.91 41.71 5.25
1385 5381 4.184629 GCTCTTCCGATTAGTGTCATTGT 58.815 43.478 0.00 0.00 0.00 2.71
1410 5406 3.711704 GAGACCCATTCTGATTACCCTCA 59.288 47.826 0.00 0.00 33.22 3.86
1434 5430 0.250234 CAGGCGATCCAAGTTCCTCA 59.750 55.000 0.00 0.00 33.74 3.86
1488 5484 7.552687 ACTTGTTGACTCTTTGTATTTCTGTCA 59.447 33.333 0.00 0.00 0.00 3.58
1493 5489 9.387123 GATCAACTTGTTGACTCTTTGTATTTC 57.613 33.333 17.02 4.47 33.23 2.17
1494 5490 8.902806 TGATCAACTTGTTGACTCTTTGTATTT 58.097 29.630 17.02 0.00 33.23 1.40
1497 5493 7.857734 TTGATCAACTTGTTGACTCTTTGTA 57.142 32.000 17.02 0.00 33.23 2.41
1560 5556 2.905415 TGTCAGGGAAGGCATCATTT 57.095 45.000 0.00 0.00 0.00 2.32
1639 5635 0.475906 ATGGCAGTAGGAATGGCCTC 59.524 55.000 3.32 0.00 46.97 4.70
1659 5655 5.835280 ACCAACATCCTGATTCTTCAGTTTT 59.165 36.000 2.61 0.00 46.71 2.43
1664 5660 4.566278 CCTGACCAACATCCTGATTCTTCA 60.566 45.833 0.00 0.00 0.00 3.02
1701 5697 2.825532 GGCCAATTTCCTAACAAGCTCA 59.174 45.455 0.00 0.00 0.00 4.26
1876 5872 2.670934 ACTGCGAAGGGCTGCAAG 60.671 61.111 0.50 0.00 43.74 4.01
1926 5922 0.457851 AGAAAGCCGAGACTGGATCG 59.542 55.000 0.00 0.00 39.86 3.69
1933 5929 1.069636 CAAGCACAAGAAAGCCGAGAC 60.070 52.381 0.00 0.00 0.00 3.36
1941 5937 5.581126 AATGAACACTCAAGCACAAGAAA 57.419 34.783 0.00 0.00 34.49 2.52
2064 6060 2.292267 CAAAGACCCCAATCTCGGATG 58.708 52.381 0.00 0.00 0.00 3.51
2283 6279 6.790319 ACCCATCATAGGTTTAGAACAGTTT 58.210 36.000 0.00 0.00 32.05 2.66
2315 6311 1.517832 GGATACCGCACTGCAGACT 59.482 57.895 23.35 0.00 0.00 3.24
2375 6371 2.171840 AGGTCTCACACATCTTACGCT 58.828 47.619 0.00 0.00 0.00 5.07
2427 6423 1.341531 ACTGGACCACGAAGACTCTTG 59.658 52.381 0.00 0.00 0.00 3.02
2428 6424 1.341531 CACTGGACCACGAAGACTCTT 59.658 52.381 0.00 0.00 0.00 2.85
2448 6444 3.429085 CCTAATCGCATCAAACAAGTGC 58.571 45.455 0.00 0.00 35.59 4.40
2463 6459 6.444633 CAAATCATGCTTCACATCCCTAATC 58.555 40.000 0.00 0.00 36.64 1.75
2480 6476 0.608035 AACCCCACGACGCAAATCAT 60.608 50.000 0.00 0.00 0.00 2.45
2496 6492 4.689612 TCCATCCACATAGCTCTTAACC 57.310 45.455 0.00 0.00 0.00 2.85
2560 6556 8.177119 TGTAAGCAACAGAGTTTCCAATATTT 57.823 30.769 0.00 0.00 33.01 1.40
2667 6663 7.619302 TGGACATCCTTTTTATAGCCATCTTTT 59.381 33.333 0.00 0.00 36.82 2.27
2706 6702 8.637099 TGACCAGAATATTCATAGAAGAGACTG 58.363 37.037 17.56 2.62 0.00 3.51
2743 6739 0.107945 GACCCAGAAGTGCAGCTAGG 60.108 60.000 0.00 0.00 0.00 3.02
2763 6759 7.648142 TGATAACAGTTTCCTTGCTAGTTTTG 58.352 34.615 0.00 0.00 0.00 2.44
2859 6855 0.319641 GTTCTATCATCGGTCGCCCC 60.320 60.000 0.00 0.00 0.00 5.80
2865 6861 3.769844 ACTGGTCAAGTTCTATCATCGGT 59.230 43.478 0.00 0.00 34.57 4.69
2958 6954 4.641396 CCATCCGAGCAATTGTAGGATAA 58.359 43.478 22.07 5.29 39.47 1.75
3100 7096 3.381370 GGTTAGGTCCGAGCCAATC 57.619 57.895 0.00 0.00 0.00 2.67
3114 7110 3.859961 CGAGAGAGTAGAACGTACGGTTA 59.140 47.826 21.06 5.70 39.50 2.85
3115 7111 2.670414 CGAGAGAGTAGAACGTACGGTT 59.330 50.000 21.06 11.28 42.96 4.44
3127 7123 5.644977 TCAATGAGAAAAGCGAGAGAGTA 57.355 39.130 0.00 0.00 0.00 2.59
3147 7143 1.068541 CGAGAACGTGACAGGACATCA 60.069 52.381 1.39 0.00 34.56 3.07
3161 7157 8.193250 ACACAATGTATGGTTAATACGAGAAC 57.807 34.615 0.00 0.00 43.66 3.01
3210 7206 1.996292 CGAAAGATCGCTGGTTGAGA 58.004 50.000 0.00 0.00 42.96 3.27
3229 7225 0.984995 AAGGCCCAAGTACTCAGTCC 59.015 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.