Multiple sequence alignment - TraesCS5A01G201700

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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 TraesCS5A01G201700 chr5A 100.000 4987 0 0 1 4987 408179729 408184715 0.000000e+00 9210.0
1 TraesCS5A01G201700 chr5D 95.635 4124 108 20 886 4987 314382457 314386530 0.000000e+00 6553.0
2 TraesCS5A01G201700 chr5D 91.422 886 68 5 1 885 314381544 314382422 0.000000e+00 1208.0
3 TraesCS5A01G201700 chr5D 81.402 742 131 7 39 777 230031310 230030573 2.570000e-167 599.0
4 TraesCS5A01G201700 chr5D 88.626 211 18 4 4565 4773 58532674 58532880 8.290000e-63 252.0
5 TraesCS5A01G201700 chr5B 95.049 4120 108 29 904 4987 362117357 362121416 0.000000e+00 6390.0
6 TraesCS5A01G201700 chr5B 81.586 706 122 8 2 703 680615990 680615289 1.200000e-160 577.0
7 TraesCS5A01G201700 chr2B 81.020 843 142 17 1 835 45782569 45783401 0.000000e+00 654.0
8 TraesCS5A01G201700 chr4A 83.405 693 105 9 1 689 593824526 593825212 7.040000e-178 634.0
9 TraesCS5A01G201700 chr4A 81.445 706 126 5 1 703 629465532 629466235 1.560000e-159 573.0
10 TraesCS5A01G201700 chr4A 93.182 44 3 0 3080 3123 356556160 356556117 1.160000e-06 65.8
11 TraesCS5A01G201700 chr4D 80.476 799 150 6 2 796 346146367 346145571 1.540000e-169 606.0
12 TraesCS5A01G201700 chr4D 93.182 44 3 0 3080 3123 241795771 241795814 1.160000e-06 65.8
13 TraesCS5A01G201700 chr6B 86.232 552 65 8 3153 3698 36045522 36044976 5.560000e-164 588.0
14 TraesCS5A01G201700 chr6B 79.373 766 150 8 6 769 262278460 262277701 2.640000e-147 532.0
15 TraesCS5A01G201700 chr6B 87.838 222 19 6 4563 4781 648789793 648790009 2.300000e-63 254.0
16 TraesCS5A01G201700 chr2D 86.642 539 59 8 3153 3686 24677703 24677173 7.190000e-163 584.0
17 TraesCS5A01G201700 chr2D 80.127 785 134 15 1 771 83046743 83045967 2.610000e-157 566.0
18 TraesCS5A01G201700 chr2D 88.182 220 20 3 4563 4780 78385415 78385630 1.780000e-64 257.0
19 TraesCS5A01G201700 chr2D 87.037 54 7 0 3081 3134 625243613 625243560 1.500000e-05 62.1
20 TraesCS5A01G201700 chr6D 86.271 539 64 7 3153 3686 21364506 21363973 1.200000e-160 577.0
21 TraesCS5A01G201700 chr6D 87.470 423 45 5 3153 3570 21059438 21059019 9.710000e-132 481.0
22 TraesCS5A01G201700 chr6D 86.824 425 46 7 3153 3570 21820565 21820144 2.720000e-127 466.0
23 TraesCS5A01G201700 chr6D 100.000 39 0 0 3153 3191 20961189 20961227 6.930000e-09 73.1
24 TraesCS5A01G201700 chr6A 85.926 540 66 5 3153 3686 21392570 21392035 7.250000e-158 568.0
25 TraesCS5A01G201700 chr3B 88.584 219 19 3 4563 4779 353997211 353997425 1.380000e-65 261.0
26 TraesCS5A01G201700 chrUn 87.838 222 19 6 4563 4781 392798416 392798632 2.300000e-63 254.0
27 TraesCS5A01G201700 chrUn 87.727 220 20 4 4563 4780 91756569 91756355 2.980000e-62 250.0
28 TraesCS5A01G201700 chr7D 87.727 220 20 4 4563 4780 137681818 137681604 2.980000e-62 250.0
29 TraesCS5A01G201700 chr1A 84.795 171 20 3 4596 4764 15428513 15428347 3.090000e-37 167.0
30 TraesCS5A01G201700 chr2A 89.362 47 4 1 4516 4562 634878335 634878380 1.940000e-04 58.4


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 TraesCS5A01G201700 chr5A 408179729 408184715 4986 False 9210.0 9210 100.0000 1 4987 1 chr5A.!!$F1 4986
1 TraesCS5A01G201700 chr5D 314381544 314386530 4986 False 3880.5 6553 93.5285 1 4987 2 chr5D.!!$F2 4986
2 TraesCS5A01G201700 chr5D 230030573 230031310 737 True 599.0 599 81.4020 39 777 1 chr5D.!!$R1 738
3 TraesCS5A01G201700 chr5B 362117357 362121416 4059 False 6390.0 6390 95.0490 904 4987 1 chr5B.!!$F1 4083
4 TraesCS5A01G201700 chr5B 680615289 680615990 701 True 577.0 577 81.5860 2 703 1 chr5B.!!$R1 701
5 TraesCS5A01G201700 chr2B 45782569 45783401 832 False 654.0 654 81.0200 1 835 1 chr2B.!!$F1 834
6 TraesCS5A01G201700 chr4A 593824526 593825212 686 False 634.0 634 83.4050 1 689 1 chr4A.!!$F1 688
7 TraesCS5A01G201700 chr4A 629465532 629466235 703 False 573.0 573 81.4450 1 703 1 chr4A.!!$F2 702
8 TraesCS5A01G201700 chr4D 346145571 346146367 796 True 606.0 606 80.4760 2 796 1 chr4D.!!$R1 794
9 TraesCS5A01G201700 chr6B 36044976 36045522 546 True 588.0 588 86.2320 3153 3698 1 chr6B.!!$R1 545
10 TraesCS5A01G201700 chr6B 262277701 262278460 759 True 532.0 532 79.3730 6 769 1 chr6B.!!$R2 763
11 TraesCS5A01G201700 chr2D 24677173 24677703 530 True 584.0 584 86.6420 3153 3686 1 chr2D.!!$R1 533
12 TraesCS5A01G201700 chr2D 83045967 83046743 776 True 566.0 566 80.1270 1 771 1 chr2D.!!$R2 770
13 TraesCS5A01G201700 chr6D 21363973 21364506 533 True 577.0 577 86.2710 3153 3686 1 chr6D.!!$R2 533
14 TraesCS5A01G201700 chr6A 21392035 21392570 535 True 568.0 568 85.9260 3153 3686 1 chr6A.!!$R1 533

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
865 883 0.531090 CAAACCGACGTGAGGGTCAA 60.531 55.0 10.92 0.00 36.73 3.18 F
1306 1368 0.107606 CTCTCCTTGATGCTGCTGCT 60.108 55.0 17.00 2.26 40.48 4.24 F
1307 1369 0.392595 TCTCCTTGATGCTGCTGCTG 60.393 55.0 17.00 0.77 40.48 4.41 F
2310 2373 0.737715 CGAAAGGGCCGTCTCTCTTG 60.738 60.0 0.00 0.00 0.00 3.02 F
3266 3339 2.600470 TTGAGCAGGCCAAAAAGTTG 57.400 45.0 5.01 0.00 34.25 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2663 0.031043 TGAATGCTGTGCTTGTGTGC 59.969 50.000 0.00 0.0 0.00 4.57 R
2704 2777 1.062488 AGGTGCTCCTTGGTCCTTGT 61.062 55.000 0.18 0.0 42.12 3.16 R
2715 2788 2.832733 ACTTCTGTAGGTAAGGTGCTCC 59.167 50.000 0.00 0.0 0.00 4.70 R
3816 3900 1.064003 TGGGTGACAATAGCCTGTGT 58.936 50.000 0.00 0.0 38.99 3.72 R
4258 4366 1.418264 TCATTCACACAGGAAACGGGA 59.582 47.619 0.00 0.0 0.00 5.14 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
183 185 0.906282 GGGGGTTCCGACCTACTTGA 60.906 60.000 0.00 0.00 45.75 3.02
235 237 2.770589 GCCATGGCGCCGTTTGTAT 61.771 57.895 23.48 3.02 0.00 2.29
305 307 4.742201 CTGCCACGACCTCCACGG 62.742 72.222 0.00 0.00 39.35 4.94
331 333 2.039831 ACCACCAGACCCACCAGT 60.040 61.111 0.00 0.00 0.00 4.00
487 490 3.162666 ACAGGTTCTCTGACGTTCCATA 58.837 45.455 0.00 0.00 46.18 2.74
506 509 2.031465 GTCGGTGGCGGAAGGAAA 59.969 61.111 0.00 0.00 0.00 3.13
643 646 2.166907 TTTCTTTTGGGTTGGCCAGA 57.833 45.000 5.11 0.00 36.17 3.86
644 647 1.408969 TTCTTTTGGGTTGGCCAGAC 58.591 50.000 5.11 7.55 36.17 3.51
647 652 2.285889 TTTTGGGTTGGCCAGACGGA 62.286 55.000 5.11 0.00 36.17 4.69
666 673 4.021719 ACGGATAAAGAAGGACGTTTCTCA 60.022 41.667 3.07 0.00 36.42 3.27
710 725 4.763793 CCTCCACATTTGTCTCTGATTTGT 59.236 41.667 0.00 0.00 0.00 2.83
712 727 5.375773 TCCACATTTGTCTCTGATTTGTGA 58.624 37.500 0.00 0.00 36.06 3.58
715 730 6.016860 CCACATTTGTCTCTGATTTGTGAGAA 60.017 38.462 0.00 0.00 40.47 2.87
777 792 4.527944 TCACTAGATGACTTCCACGATCT 58.472 43.478 0.00 0.00 29.99 2.75
790 805 0.615331 ACGATCTGGACAGCATGGTT 59.385 50.000 0.00 0.00 43.62 3.67
801 816 2.474266 CATGGTTCGAACGCACGG 59.526 61.111 21.34 12.26 0.00 4.94
819 834 1.676303 GGGGAAATTTGCGGGTCGA 60.676 57.895 3.43 0.00 0.00 4.20
865 883 0.531090 CAAACCGACGTGAGGGTCAA 60.531 55.000 10.92 0.00 36.73 3.18
971 1023 0.599204 TGACGGAGAAGACGCCAAAC 60.599 55.000 0.00 0.00 35.72 2.93
1065 1125 2.680370 GCTCCCCCACGAAATCCCT 61.680 63.158 0.00 0.00 0.00 4.20
1135 1197 4.678743 GGCCAACCACACCCCTCC 62.679 72.222 0.00 0.00 35.26 4.30
1306 1368 0.107606 CTCTCCTTGATGCTGCTGCT 60.108 55.000 17.00 2.26 40.48 4.24
1307 1369 0.392595 TCTCCTTGATGCTGCTGCTG 60.393 55.000 17.00 0.77 40.48 4.41
1308 1370 1.994507 CTCCTTGATGCTGCTGCTGC 61.995 60.000 22.51 22.51 40.48 5.25
1375 1437 1.443407 CTGATGCGAAGTCGGGGAT 59.557 57.895 2.47 0.00 40.23 3.85
1895 1957 5.809001 TGCAAAGACTGGTAAATCTCTGAT 58.191 37.500 0.00 0.00 0.00 2.90
2240 2303 5.845985 AGTTTACACTGATGTCACATTCG 57.154 39.130 0.00 0.00 40.48 3.34
2244 2307 3.849911 ACACTGATGTCACATTCGTAGG 58.150 45.455 0.00 0.00 31.55 3.18
2258 2321 9.476202 TCACATTCGTAGGTTTCATAAGATATG 57.524 33.333 0.00 0.00 0.00 1.78
2291 2354 4.274459 AGAACAGTTTTGTCTCATGTCTGC 59.726 41.667 0.00 0.00 36.23 4.26
2310 2373 0.737715 CGAAAGGGCCGTCTCTCTTG 60.738 60.000 0.00 0.00 0.00 3.02
2550 2619 9.769093 AAAGATGTTTGAACTACATAAATACGC 57.231 29.630 0.00 0.00 36.41 4.42
2594 2663 7.439157 TGTCAGAGTTTGGAAATCAGTATTG 57.561 36.000 0.00 0.00 0.00 1.90
2633 2703 8.497554 GCATTCATTGTTTTGATTTTTAGAGCA 58.502 29.630 0.00 0.00 0.00 4.26
2711 2784 9.832445 TCTCATCCTTATATTTGTTACAAGGAC 57.168 33.333 3.64 0.00 45.56 3.85
2712 2785 8.974060 TCATCCTTATATTTGTTACAAGGACC 57.026 34.615 3.64 0.00 45.56 4.46
2713 2786 8.553153 TCATCCTTATATTTGTTACAAGGACCA 58.447 33.333 3.64 0.00 45.56 4.02
2714 2787 9.184523 CATCCTTATATTTGTTACAAGGACCAA 57.815 33.333 3.64 0.00 45.56 3.67
2715 2788 8.801882 TCCTTATATTTGTTACAAGGACCAAG 57.198 34.615 0.00 0.80 39.80 3.61
2716 2789 7.832187 TCCTTATATTTGTTACAAGGACCAAGG 59.168 37.037 15.23 15.23 39.80 3.61
2905 2978 5.823861 AAAGGTTGCCTGTTTTGGATTAT 57.176 34.783 0.00 0.00 32.13 1.28
2973 3046 5.759273 GCATTGCAGTTCTCTCTTATCTGAT 59.241 40.000 3.15 0.00 0.00 2.90
3089 3162 3.420893 CAACAAATTGCTACTCCCTCCA 58.579 45.455 0.00 0.00 0.00 3.86
3101 3174 6.174049 GCTACTCCCTCCATTCCATAATAAC 58.826 44.000 0.00 0.00 0.00 1.89
3123 3196 4.696402 ACTGTCGTGGTTTTAGTTCAAACA 59.304 37.500 0.00 0.00 38.25 2.83
3266 3339 2.600470 TTGAGCAGGCCAAAAAGTTG 57.400 45.000 5.01 0.00 34.25 3.16
3314 3387 4.925646 GCTAAAGAAAATGGTGCAAAGAGG 59.074 41.667 0.00 0.00 0.00 3.69
3689 3773 2.958355 TGCTGGCAATCTTAAATAGGCC 59.042 45.455 0.00 0.00 41.70 5.19
3811 3895 6.229733 GCTATCAGCAGTGATTAGGATCTTT 58.770 40.000 0.00 0.00 40.84 2.52
3812 3896 6.147492 GCTATCAGCAGTGATTAGGATCTTTG 59.853 42.308 0.00 0.00 40.84 2.77
3814 3898 5.181009 TCAGCAGTGATTAGGATCTTTGTG 58.819 41.667 0.00 0.00 33.28 3.33
3815 3899 5.046376 TCAGCAGTGATTAGGATCTTTGTGA 60.046 40.000 0.00 0.00 33.28 3.58
3816 3900 5.645067 CAGCAGTGATTAGGATCTTTGTGAA 59.355 40.000 0.00 0.00 33.28 3.18
3817 3901 5.645497 AGCAGTGATTAGGATCTTTGTGAAC 59.355 40.000 0.00 0.00 33.28 3.18
3818 3902 5.412594 GCAGTGATTAGGATCTTTGTGAACA 59.587 40.000 0.00 0.00 33.28 3.18
3819 3903 6.621596 GCAGTGATTAGGATCTTTGTGAACAC 60.622 42.308 0.00 0.00 33.28 3.32
3820 3904 6.427853 CAGTGATTAGGATCTTTGTGAACACA 59.572 38.462 3.39 3.39 34.91 3.72
3821 3905 6.652481 AGTGATTAGGATCTTTGTGAACACAG 59.348 38.462 7.67 0.00 36.61 3.66
3822 3906 5.939883 TGATTAGGATCTTTGTGAACACAGG 59.060 40.000 7.67 5.88 36.61 4.00
3823 3907 2.508526 AGGATCTTTGTGAACACAGGC 58.491 47.619 7.67 0.00 42.94 4.85
4138 4244 7.707893 GGATTGAAATTATGTTTGCTGCTGTAT 59.292 33.333 0.00 0.00 0.00 2.29
4139 4245 8.638685 ATTGAAATTATGTTTGCTGCTGTATC 57.361 30.769 0.00 0.00 0.00 2.24
4259 4367 4.792087 TCCCTGCAGGAAACGTTC 57.208 55.556 34.91 0.00 43.78 3.95
4478 4586 7.552687 AGCCTTCATAAATCGTTAGATCAACAA 59.447 33.333 0.00 0.00 36.92 2.83
4479 4587 8.345565 GCCTTCATAAATCGTTAGATCAACAAT 58.654 33.333 0.00 0.00 36.92 2.71
4641 4749 5.351948 TGCAAGTTACATAGAGCATACCA 57.648 39.130 0.00 0.00 0.00 3.25
4663 4771 6.432783 ACCATCAAATTCATACGTGAAAGGAA 59.567 34.615 0.00 0.00 46.67 3.36
4665 4773 6.869315 TCAAATTCATACGTGAAAGGAACA 57.131 33.333 0.00 0.00 46.67 3.18
4826 4938 9.044150 CACATTCAACATTAAACTTTGTGGATT 57.956 29.630 0.00 0.00 0.00 3.01
4868 4980 7.899648 TTTCTATGAGGGAAGGAACTACTAG 57.100 40.000 0.00 0.00 38.49 2.57
4871 4985 7.420029 TCTATGAGGGAAGGAACTACTAGTTT 58.580 38.462 0.00 0.00 38.80 2.66
4959 5073 2.820059 TGCTATTATGCGAGGGTGAG 57.180 50.000 0.00 0.00 35.36 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 177 2.012673 ACTACTACGCCGTCAAGTAGG 58.987 52.381 23.72 11.28 44.53 3.18
183 185 1.602311 CCTCCATACTACTACGCCGT 58.398 55.000 0.00 0.00 0.00 5.68
305 307 4.408821 TCTGGTGGTGGCGATGGC 62.409 66.667 0.00 0.00 38.90 4.40
331 333 1.600636 CTCAAGAAGCGGTTGGCCA 60.601 57.895 3.70 0.00 45.17 5.36
430 432 0.750911 GGAGGTGTCGGAGGATACGT 60.751 60.000 0.00 0.00 46.39 3.57
433 435 1.826921 GCGGAGGTGTCGGAGGATA 60.827 63.158 0.00 0.00 0.00 2.59
481 483 2.182284 CGCCACCGACGTATGGAA 59.818 61.111 17.21 0.00 38.34 3.53
506 509 4.227073 CCTCTCTTTTCTCCCATCCTCTTT 59.773 45.833 0.00 0.00 0.00 2.52
616 619 2.067365 ACCCAAAAGAAAAGCGGAGT 57.933 45.000 0.00 0.00 0.00 3.85
623 626 2.169561 GTCTGGCCAACCCAAAAGAAAA 59.830 45.455 7.01 0.00 44.81 2.29
643 646 4.021719 TGAGAAACGTCCTTCTTTATCCGT 60.022 41.667 4.09 0.00 35.76 4.69
644 647 4.491676 TGAGAAACGTCCTTCTTTATCCG 58.508 43.478 4.09 0.00 35.76 4.18
647 652 5.875359 GGACATGAGAAACGTCCTTCTTTAT 59.125 40.000 0.00 0.80 44.82 1.40
710 725 4.377021 CGGTCCGGATATGATTTTTCTCA 58.623 43.478 7.81 0.00 0.00 3.27
712 727 3.139077 GCGGTCCGGATATGATTTTTCT 58.861 45.455 14.38 0.00 0.00 2.52
715 730 1.202604 ACGCGGTCCGGATATGATTTT 60.203 47.619 14.38 0.00 42.52 1.82
777 792 0.948623 CGTTCGAACCATGCTGTCCA 60.949 55.000 22.07 0.00 0.00 4.02
790 805 2.734948 AATTTCCCCCGTGCGTTCGA 62.735 55.000 0.00 0.00 0.00 3.71
801 816 1.676303 TCGACCCGCAAATTTCCCC 60.676 57.895 0.00 0.00 0.00 4.81
852 869 2.022129 CACGCTTGACCCTCACGTC 61.022 63.158 0.00 0.00 28.57 4.34
971 1023 0.322456 TCCGATTGGAGCAGGTTTGG 60.322 55.000 0.00 0.00 40.17 3.28
1065 1125 1.624753 GGAGGGCAGGGGTAGTCTA 59.375 63.158 0.00 0.00 0.00 2.59
1306 1368 3.517140 GGCGGAAATGGCGATGCA 61.517 61.111 0.00 0.00 0.00 3.96
1307 1369 2.941964 CTTGGCGGAAATGGCGATGC 62.942 60.000 0.00 0.00 37.19 3.91
1308 1370 1.064621 CTTGGCGGAAATGGCGATG 59.935 57.895 0.00 0.00 37.19 3.84
1645 1707 1.135083 TCGAATCGGCAGAAGAAGTCC 60.135 52.381 1.76 0.00 0.00 3.85
2046 2109 6.143278 CCAAACGCAAGGTAAACTAATTTGTC 59.857 38.462 0.00 0.00 46.39 3.18
2217 2280 5.177511 ACGAATGTGACATCAGTGTAAACTG 59.822 40.000 6.72 6.72 39.09 3.16
2258 2321 7.754924 TGAGACAAAACTGTTCTTTTGAATCAC 59.245 33.333 10.55 0.58 41.72 3.06
2291 2354 0.737715 CAAGAGAGACGGCCCTTTCG 60.738 60.000 0.00 0.00 0.00 3.46
2310 2373 7.115947 CAGAACAAAGAGATTGCTGAATTTTCC 59.884 37.037 0.00 0.00 43.13 3.13
2594 2663 0.031043 TGAATGCTGTGCTTGTGTGC 59.969 50.000 0.00 0.00 0.00 4.57
2668 2738 7.293073 AGGATGAGATACAATGCTTTAACCAT 58.707 34.615 0.00 0.00 0.00 3.55
2704 2777 1.062488 AGGTGCTCCTTGGTCCTTGT 61.062 55.000 0.18 0.00 42.12 3.16
2715 2788 2.832733 ACTTCTGTAGGTAAGGTGCTCC 59.167 50.000 0.00 0.00 0.00 4.70
2716 2789 4.461781 TGTACTTCTGTAGGTAAGGTGCTC 59.538 45.833 0.00 0.00 0.00 4.26
2843 2916 5.183904 AGGAAAGGACAAACATATGTTCTGC 59.816 40.000 21.02 14.00 38.22 4.26
2905 2978 7.691993 ACTCTTATAGGAGGCAAGGAATTAA 57.308 36.000 15.60 0.00 37.63 1.40
2973 3046 9.513906 TTAAGAGACATTTAACATGATTGGTGA 57.486 29.630 0.00 0.00 0.00 4.02
3089 3162 7.696992 AAAACCACGACAGTTATTATGGAAT 57.303 32.000 0.00 0.00 0.00 3.01
3101 3174 5.064198 TCTGTTTGAACTAAAACCACGACAG 59.936 40.000 0.00 0.00 38.93 3.51
3123 3196 5.361285 CAGCACAGTACTAAATACTCCCTCT 59.639 44.000 0.00 0.00 42.62 3.69
3281 3354 4.484236 CATTTTCTTTAGCACAATCCGCA 58.516 39.130 0.00 0.00 0.00 5.69
3314 3387 3.279434 ACTCGGGTATGAATTTGAAGGC 58.721 45.455 0.00 0.00 0.00 4.35
3478 3558 2.318908 TGAAGGAACAAAGGCAAGCAT 58.681 42.857 0.00 0.00 0.00 3.79
3480 3560 2.888834 TTGAAGGAACAAAGGCAAGC 57.111 45.000 0.00 0.00 0.00 4.01
3764 3848 3.246226 AGCTTAGCGCATTCAGTTATTCG 59.754 43.478 11.47 0.00 42.61 3.34
3811 3895 3.138304 GTGACAATAGCCTGTGTTCACA 58.862 45.455 5.52 5.52 31.66 3.58
3812 3896 2.484264 GGTGACAATAGCCTGTGTTCAC 59.516 50.000 0.00 0.00 0.00 3.18
3814 3898 2.084546 GGGTGACAATAGCCTGTGTTC 58.915 52.381 0.00 0.00 35.37 3.18
3815 3899 1.423541 TGGGTGACAATAGCCTGTGTT 59.576 47.619 0.00 0.00 38.99 3.32
3816 3900 1.064003 TGGGTGACAATAGCCTGTGT 58.936 50.000 0.00 0.00 38.99 3.72
3817 3901 2.425143 ATGGGTGACAATAGCCTGTG 57.575 50.000 0.00 0.00 38.99 3.66
3818 3902 4.156455 CTAATGGGTGACAATAGCCTGT 57.844 45.455 0.00 0.00 38.99 4.00
3823 3907 6.236409 AGATCATGCTAATGGGTGACAATAG 58.764 40.000 0.00 0.00 35.97 1.73
3980 4084 5.221342 TGGTTTTTGTTGAAGCGATTACCAT 60.221 36.000 0.00 0.00 0.00 3.55
3981 4085 4.098044 TGGTTTTTGTTGAAGCGATTACCA 59.902 37.500 0.00 0.00 0.00 3.25
4138 4244 2.970639 CAGGAAACGCTCCCGAGA 59.029 61.111 0.56 0.00 46.81 4.04
4139 4245 2.815647 GCAGGAAACGCTCCCGAG 60.816 66.667 0.56 0.00 46.81 4.63
4257 4365 2.158740 TCATTCACACAGGAAACGGGAA 60.159 45.455 0.00 0.00 0.00 3.97
4258 4366 1.418264 TCATTCACACAGGAAACGGGA 59.582 47.619 0.00 0.00 0.00 5.14
4259 4367 1.890876 TCATTCACACAGGAAACGGG 58.109 50.000 0.00 0.00 0.00 5.28
4260 4368 3.073678 TCATCATTCACACAGGAAACGG 58.926 45.455 0.00 0.00 0.00 4.44
4446 4554 7.208080 TCTAACGATTTATGAAGGCTCCTAAC 58.792 38.462 0.00 0.00 0.00 2.34
4478 4586 8.032045 TGGGGCATTTACAATGATGATTTAAT 57.968 30.769 0.49 0.00 0.00 1.40
4479 4587 7.429374 TGGGGCATTTACAATGATGATTTAA 57.571 32.000 0.49 0.00 0.00 1.52
4491 4599 6.719370 GGAGTATATGAAATGGGGCATTTACA 59.281 38.462 0.00 0.00 43.05 2.41
4641 4749 7.447374 TGTTCCTTTCACGTATGAATTTGAT 57.553 32.000 0.00 0.00 44.36 2.57
4715 4823 7.013750 TCGAGACTGCTCTTTGACTATTGATAT 59.986 37.037 0.00 0.00 39.06 1.63
4731 4839 2.457366 ATCCGTTTTTCGAGACTGCT 57.543 45.000 0.00 0.00 42.86 4.24
4826 4938 3.880490 AGAAAACTACGCACACAATTCCA 59.120 39.130 0.00 0.00 0.00 3.53
4871 4985 8.764558 AGTAACCCAGAATTATGTGTGTACATA 58.235 33.333 0.00 0.00 45.45 2.29
4959 5073 3.717707 TCTTGTGCGCATACTATCTTCC 58.282 45.455 15.91 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.