Multiple sequence alignment - TraesCS2A01G336100

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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 TraesCS2A01G336100 chr2A 100.000 4328 0 0 1 4328 570006284 570010611 0.000000e+00 7993.0
1 TraesCS2A01G336100 chr2D 96.395 3495 106 11 846 4328 420172362 420168876 0.000000e+00 5738.0
2 TraesCS2A01G336100 chr2D 78.726 785 138 23 8 779 135314905 135314137 8.360000e-137 497.0
3 TraesCS2A01G336100 chr2B 96.919 2921 83 7 846 3763 492622599 492619683 0.000000e+00 4889.0
4 TraesCS2A01G336100 chr2B 93.333 405 19 1 3757 4153 492619563 492619159 3.730000e-165 592.0
5 TraesCS2A01G336100 chr2B 97.765 179 4 0 4150 4328 492619037 492618859 4.200000e-80 309.0
6 TraesCS2A01G336100 chr2B 91.743 218 18 0 1070 1287 492624118 492623901 1.960000e-78 303.0
7 TraesCS2A01G336100 chr2B 90.179 224 12 6 845 1066 492705124 492704909 2.550000e-72 283.0
8 TraesCS2A01G336100 chr7B 92.621 786 42 4 1 779 638225395 638224619 0.000000e+00 1116.0
9 TraesCS2A01G336100 chr7B 77.922 308 59 4 472 779 632259426 632259724 2.660000e-42 183.0
10 TraesCS2A01G336100 chr7D 78.454 789 141 22 5 779 573441164 573441937 5.030000e-134 488.0
11 TraesCS2A01G336100 chr7D 75.125 599 129 16 185 777 422202470 422201886 3.320000e-66 263.0
12 TraesCS2A01G336100 chr7A 77.481 786 152 19 5 779 663385140 663385911 8.540000e-122 448.0
13 TraesCS2A01G336100 chr7A 88.095 84 8 2 3717 3799 573432806 573432724 9.910000e-17 99.0
14 TraesCS2A01G336100 chr4D 75.080 626 134 18 161 779 64744393 64745003 5.520000e-69 272.0
15 TraesCS2A01G336100 chr6D 75.000 620 133 18 167 779 81942084 81941480 2.570000e-67 267.0
16 TraesCS2A01G336100 chr6D 83.099 71 9 3 3732 3799 1814260 1814190 1.300000e-05 62.1
17 TraesCS2A01G336100 chr5D 74.682 628 133 21 161 779 440377829 440378439 5.550000e-64 255.0
18 TraesCS2A01G336100 chr5D 87.805 82 10 0 3718 3799 1866852 1866933 3.560000e-16 97.1
19 TraesCS2A01G336100 chr5B 88.000 75 9 0 3725 3799 652934280 652934354 5.960000e-14 89.8
20 TraesCS2A01G336100 chr5B 81.579 76 12 2 3725 3799 8376909 8376983 1.300000e-05 62.1
21 TraesCS2A01G336100 chr5B 81.818 77 10 4 3725 3799 652934373 652934299 1.300000e-05 62.1
22 TraesCS2A01G336100 chr1A 97.917 48 1 0 3723 3770 518695330 518695377 2.770000e-12 84.2


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 TraesCS2A01G336100 chr2A 570006284 570010611 4327 False 7993.00 7993 100.000 1 4328 1 chr2A.!!$F1 4327
1 TraesCS2A01G336100 chr2D 420168876 420172362 3486 True 5738.00 5738 96.395 846 4328 1 chr2D.!!$R2 3482
2 TraesCS2A01G336100 chr2D 135314137 135314905 768 True 497.00 497 78.726 8 779 1 chr2D.!!$R1 771
3 TraesCS2A01G336100 chr2B 492618859 492624118 5259 True 1523.25 4889 94.940 846 4328 4 chr2B.!!$R2 3482
4 TraesCS2A01G336100 chr7B 638224619 638225395 776 True 1116.00 1116 92.621 1 779 1 chr7B.!!$R1 778
5 TraesCS2A01G336100 chr7D 573441164 573441937 773 False 488.00 488 78.454 5 779 1 chr7D.!!$F1 774
6 TraesCS2A01G336100 chr7D 422201886 422202470 584 True 263.00 263 75.125 185 777 1 chr7D.!!$R1 592
7 TraesCS2A01G336100 chr7A 663385140 663385911 771 False 448.00 448 77.481 5 779 1 chr7A.!!$F1 774
8 TraesCS2A01G336100 chr4D 64744393 64745003 610 False 272.00 272 75.080 161 779 1 chr4D.!!$F1 618
9 TraesCS2A01G336100 chr6D 81941480 81942084 604 True 267.00 267 75.000 167 779 1 chr6D.!!$R2 612
10 TraesCS2A01G336100 chr5D 440377829 440378439 610 False 255.00 255 74.682 161 779 1 chr5D.!!$F2 618

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
809 819 0.111061 TCCTTCAGCCTGTGCAATGT 59.889 50.0 0.00 0.0 41.13 2.71 F
1594 2268 0.035820 TGGGTGCGTTAGGAATGACC 60.036 55.0 0.00 0.0 39.35 4.02 F
2826 3500 0.111832 CAGGCTATGGGATGCATGGT 59.888 55.0 2.46 0.0 37.33 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2911 1.741706 CTCTGCAATGCATTTCTCGGT 59.258 47.619 8.91 0.0 38.13 4.69 R
2977 3651 2.076863 CTTCAGGTTAGGTTCAAGGCG 58.923 52.381 0.00 0.0 0.00 5.52 R
3897 4707 0.658536 GTTGCAGTGCGAACTTGAGC 60.659 55.000 6.63 0.0 0.00 4.26 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
61 68 4.764050 TTGATAAATTCCCTACTCGGCA 57.236 40.909 0.00 0.00 0.00 5.69
413 420 2.421073 CCTCAACGCACATGATGAACAT 59.579 45.455 0.00 0.00 40.17 2.71
494 503 9.086336 GAGAGATTTCTATTCACTTTCACTCTG 57.914 37.037 0.00 0.00 32.53 3.35
511 520 7.482169 TCACTCTGTACTTTATTGTCCTCAT 57.518 36.000 0.00 0.00 0.00 2.90
519 528 5.883661 ACTTTATTGTCCTCATGCATTTCG 58.116 37.500 0.00 0.00 0.00 3.46
571 580 3.491964 CCCATCTTTCGCATCATGCATTT 60.492 43.478 11.00 0.00 45.36 2.32
592 601 6.729690 TTTCAGAAATTCCCATTCAACACT 57.270 33.333 0.00 0.00 0.00 3.55
606 615 6.319658 CCATTCAACACTGTCATAGGCTTTAT 59.680 38.462 0.00 0.00 0.00 1.40
634 643 0.663153 AGTTTGACCGCAACAAGAGC 59.337 50.000 0.00 0.00 32.79 4.09
637 646 0.380378 TTGACCGCAACAAGAGCAAC 59.620 50.000 0.00 0.00 0.00 4.17
638 647 0.746204 TGACCGCAACAAGAGCAACA 60.746 50.000 0.00 0.00 0.00 3.33
639 648 0.380378 GACCGCAACAAGAGCAACAA 59.620 50.000 0.00 0.00 0.00 2.83
641 650 0.662619 CCGCAACAAGAGCAACAAGA 59.337 50.000 0.00 0.00 0.00 3.02
642 651 1.267806 CCGCAACAAGAGCAACAAGAT 59.732 47.619 0.00 0.00 0.00 2.40
672 682 2.227194 CCCCCTTACGTTTATGCATCC 58.773 52.381 0.19 0.00 0.00 3.51
739 749 0.472471 TCAGGAACAAAGGCGGACTT 59.528 50.000 0.00 0.00 42.52 3.01
784 794 7.693969 GAAGAATTTCCTTCAATCTCAGGAA 57.306 36.000 0.00 0.00 45.74 3.36
791 801 7.693969 TTCCTTCAATCTCAGGAAGAATTTC 57.306 36.000 0.00 0.00 43.11 2.17
807 817 1.999648 TTTCCTTCAGCCTGTGCAAT 58.000 45.000 0.00 0.00 41.13 3.56
808 818 1.250328 TTCCTTCAGCCTGTGCAATG 58.750 50.000 0.00 0.00 41.13 2.82
809 819 0.111061 TCCTTCAGCCTGTGCAATGT 59.889 50.000 0.00 0.00 41.13 2.71
810 820 0.963962 CCTTCAGCCTGTGCAATGTT 59.036 50.000 0.00 0.00 41.13 2.71
811 821 1.068055 CCTTCAGCCTGTGCAATGTTC 60.068 52.381 0.00 0.00 41.13 3.18
814 824 1.072806 TCAGCCTGTGCAATGTTCTCT 59.927 47.619 0.00 0.00 41.13 3.10
815 825 2.302733 TCAGCCTGTGCAATGTTCTCTA 59.697 45.455 0.00 0.00 41.13 2.43
817 827 2.038952 AGCCTGTGCAATGTTCTCTACA 59.961 45.455 0.00 0.00 39.87 2.74
818 828 2.813754 GCCTGTGCAATGTTCTCTACAA 59.186 45.455 0.00 0.00 37.64 2.41
819 829 3.120060 GCCTGTGCAATGTTCTCTACAAG 60.120 47.826 0.00 0.00 37.64 3.16
820 830 3.120060 CCTGTGCAATGTTCTCTACAAGC 60.120 47.826 0.00 0.00 40.89 4.01
821 831 3.743521 TGTGCAATGTTCTCTACAAGCT 58.256 40.909 0.00 0.00 40.89 3.74
822 832 3.499537 TGTGCAATGTTCTCTACAAGCTG 59.500 43.478 0.00 0.00 40.89 4.24
823 833 3.748048 GTGCAATGTTCTCTACAAGCTGA 59.252 43.478 0.00 0.00 40.89 4.26
824 834 4.394300 GTGCAATGTTCTCTACAAGCTGAT 59.606 41.667 0.00 0.00 40.89 2.90
825 835 4.633126 TGCAATGTTCTCTACAAGCTGATC 59.367 41.667 0.00 0.00 40.89 2.92
827 837 5.006552 GCAATGTTCTCTACAAGCTGATCTC 59.993 44.000 0.00 0.00 40.89 2.75
828 838 5.929058 ATGTTCTCTACAAGCTGATCTCA 57.071 39.130 0.00 0.00 40.89 3.27
829 839 5.728637 TGTTCTCTACAAGCTGATCTCAA 57.271 39.130 0.00 0.00 32.64 3.02
830 840 6.101650 TGTTCTCTACAAGCTGATCTCAAA 57.898 37.500 0.00 0.00 32.64 2.69
831 841 6.162079 TGTTCTCTACAAGCTGATCTCAAAG 58.838 40.000 0.00 0.00 32.64 2.77
832 842 5.991933 TCTCTACAAGCTGATCTCAAAGT 57.008 39.130 0.00 0.00 0.00 2.66
835 845 2.787994 ACAAGCTGATCTCAAAGTGGG 58.212 47.619 0.00 0.00 0.00 4.61
836 846 1.471684 CAAGCTGATCTCAAAGTGGGC 59.528 52.381 0.00 0.00 0.00 5.36
837 847 0.990374 AGCTGATCTCAAAGTGGGCT 59.010 50.000 0.00 0.00 0.00 5.19
840 850 2.787994 CTGATCTCAAAGTGGGCTTGT 58.212 47.619 0.00 0.00 34.71 3.16
843 853 1.032014 TCTCAAAGTGGGCTTGTTGC 58.968 50.000 0.00 0.00 41.94 4.17
844 854 1.035139 CTCAAAGTGGGCTTGTTGCT 58.965 50.000 0.00 0.00 42.39 3.91
845 855 1.410153 CTCAAAGTGGGCTTGTTGCTT 59.590 47.619 0.00 0.00 42.39 3.91
846 856 1.830477 TCAAAGTGGGCTTGTTGCTTT 59.170 42.857 0.00 0.00 42.39 3.51
847 857 1.935199 CAAAGTGGGCTTGTTGCTTTG 59.065 47.619 0.00 0.00 42.39 2.77
848 858 0.179076 AAGTGGGCTTGTTGCTTTGC 60.179 50.000 0.00 0.00 42.39 3.68
849 859 1.595109 GTGGGCTTGTTGCTTTGCC 60.595 57.895 0.00 0.00 44.22 4.52
851 861 3.141449 GGCTTGTTGCTTTGCCCT 58.859 55.556 0.00 0.00 42.39 5.19
852 862 2.350738 GGCTTGTTGCTTTGCCCTA 58.649 52.632 0.00 0.00 42.39 3.53
854 864 1.337167 GGCTTGTTGCTTTGCCCTAAG 60.337 52.381 0.00 0.00 42.39 2.18
930 1603 4.321230 GGTTCAGCCAAATCGATTGAGTTT 60.321 41.667 12.25 0.00 41.85 2.66
1044 1718 3.382832 CCGACGAGTCTGGGCCTT 61.383 66.667 4.53 0.00 0.00 4.35
1066 1740 2.362632 ACCGCTTCCTAGCCTCGT 60.363 61.111 0.00 0.00 44.86 4.18
1128 1802 4.074526 GCTCTCGCTGCCACCTCA 62.075 66.667 0.00 0.00 0.00 3.86
1287 1961 2.040544 CCATTGCGCCTCCGACTTT 61.041 57.895 4.18 0.00 36.29 2.66
1437 2111 3.302347 CTCCGTCAAGCTCGGCCTT 62.302 63.158 7.44 0.00 46.49 4.35
1538 2212 1.128692 GAAGCTGTTCGACGAAATGGG 59.871 52.381 12.67 4.18 0.00 4.00
1594 2268 0.035820 TGGGTGCGTTAGGAATGACC 60.036 55.000 0.00 0.00 39.35 4.02
1597 2271 1.369625 GTGCGTTAGGAATGACCAGG 58.630 55.000 0.00 0.00 42.04 4.45
1608 2282 0.119155 ATGACCAGGGTGAGAAGGGA 59.881 55.000 0.00 0.00 0.00 4.20
1698 2372 1.973812 GAGTGGGTTGGAGGCTTGC 60.974 63.158 0.00 0.00 0.00 4.01
1702 2376 3.056328 GGTTGGAGGCTTGCGGAC 61.056 66.667 0.00 0.00 0.00 4.79
1710 2384 2.266055 GCTTGCGGACTGCTAGGT 59.734 61.111 17.67 0.00 45.14 3.08
1844 2518 5.263599 TGAGGATGCATGTGTTTTATTCCT 58.736 37.500 2.46 0.00 0.00 3.36
2237 2911 5.069318 TGATGTCAAATGCTTGGAGTTGTA 58.931 37.500 2.68 0.00 33.01 2.41
2326 3000 2.029290 TCTTCTTGTTCACGGCTAGGAC 60.029 50.000 0.00 0.00 0.00 3.85
2355 3029 3.065925 GGTTAGGTCAATCAGCTCATTGC 59.934 47.826 5.29 0.99 43.29 3.56
2826 3500 0.111832 CAGGCTATGGGATGCATGGT 59.888 55.000 2.46 0.00 37.33 3.55
2971 3645 1.918262 AGCTGTTCATCAGAATGGGGA 59.082 47.619 0.00 0.00 46.27 4.81
2977 3651 5.200483 TGTTCATCAGAATGGGGAAATACC 58.800 41.667 0.00 0.00 35.92 2.73
3321 3995 1.742831 TGGAGTGCGGTTGATATTTGC 59.257 47.619 0.00 0.00 0.00 3.68
3392 4066 7.340999 AGGGTAAATAACTAATTGACCGCATTT 59.659 33.333 0.00 0.00 46.83 2.32
3415 4089 8.579850 TTTGCTCATTTACATAAACTCTGGAT 57.420 30.769 0.00 0.00 0.00 3.41
3416 4090 7.792374 TGCTCATTTACATAAACTCTGGATC 57.208 36.000 0.00 0.00 0.00 3.36
3417 4091 7.337938 TGCTCATTTACATAAACTCTGGATCA 58.662 34.615 0.00 0.00 0.00 2.92
3418 4092 7.496920 TGCTCATTTACATAAACTCTGGATCAG 59.503 37.037 0.00 0.00 0.00 2.90
3419 4093 7.519649 GCTCATTTACATAAACTCTGGATCAGC 60.520 40.741 0.00 0.00 0.00 4.26
3420 4094 7.568349 TCATTTACATAAACTCTGGATCAGCT 58.432 34.615 0.00 0.00 0.00 4.24
3512 4188 5.301045 AGTCTGTGAATTATGCATCCATTGG 59.699 40.000 0.19 0.00 32.85 3.16
3600 4276 4.934001 AGATGATGTTGCTAATATCGGCAG 59.066 41.667 3.42 0.00 39.68 4.85
3751 4428 5.428783 CCCCTCCGTCCCATAATATAAGATT 59.571 44.000 0.00 0.00 0.00 2.40
3784 4586 6.298361 TCCAATATGTGAGTATGTTGGATGG 58.702 40.000 11.39 0.00 46.68 3.51
3806 4616 6.005823 TGGAATAAGATCTTATACGGACGGA 58.994 40.000 24.81 0.00 34.90 4.69
3808 4618 3.919223 AAGATCTTATACGGACGGAGC 57.081 47.619 6.06 0.00 0.00 4.70
3897 4707 5.092105 TGTTTGTCTGTTTTGTGAATGTCG 58.908 37.500 0.00 0.00 0.00 4.35
3898 4708 3.332761 TGTCTGTTTTGTGAATGTCGC 57.667 42.857 0.00 0.00 0.00 5.19
3928 4738 2.351157 GCACTGCAACTTCTCATTCACC 60.351 50.000 0.00 0.00 0.00 4.02
3944 4754 6.614657 TCATTCACCTCTCCATGTATCTAGA 58.385 40.000 0.00 0.00 0.00 2.43
3966 4776 0.954452 CTCCTGGCTGTTTTGGACAC 59.046 55.000 0.00 0.00 33.82 3.67
4063 4873 2.997986 CCATTTGGATGAGCAAAAGTGC 59.002 45.455 0.00 0.00 44.42 4.40
4209 5144 1.447489 CCTCCTCAAGCAGCTCGTG 60.447 63.158 0.00 0.00 0.00 4.35
4309 5244 6.430007 AGACTTCATTTGCCTCAGGATTATT 58.570 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 68 3.695830 ACCAGTTCATGTTGGTATCGT 57.304 42.857 14.66 0.00 45.58 3.73
494 503 6.907212 CGAAATGCATGAGGACAATAAAGTAC 59.093 38.462 0.00 0.00 0.00 2.73
511 520 4.142491 GGATCAACACCATTACGAAATGCA 60.142 41.667 0.00 0.00 41.06 3.96
519 528 4.157840 GGAGGTTTGGATCAACACCATTAC 59.842 45.833 8.17 0.00 37.26 1.89
571 580 5.139727 ACAGTGTTGAATGGGAATTTCTGA 58.860 37.500 0.00 0.00 0.00 3.27
592 601 9.851686 AACTTGATATGAATAAAGCCTATGACA 57.148 29.630 0.00 0.00 27.42 3.58
606 615 4.517075 TGTTGCGGTCAAACTTGATATGAA 59.483 37.500 0.00 0.00 39.73 2.57
634 643 2.555199 GGGGACGAGATGATCTTGTTG 58.445 52.381 16.07 0.74 41.04 3.33
637 646 3.997672 GGGGGACGAGATGATCTTG 57.002 57.895 8.14 8.14 34.04 3.02
662 672 7.340122 TGAAATAAACCATCGGATGCATAAA 57.660 32.000 12.54 0.00 0.00 1.40
672 682 6.502652 TGTTGGCATATGAAATAAACCATCG 58.497 36.000 6.97 0.00 37.58 3.84
720 730 0.472471 AAGTCCGCCTTTGTTCCTGA 59.528 50.000 0.00 0.00 0.00 3.86
781 791 6.403318 GCACAGGCTGAAGGAAATTCTTCC 62.403 50.000 23.66 0.00 43.52 3.46
782 792 3.366781 GCACAGGCTGAAGGAAATTCTTC 60.367 47.826 23.66 0.94 42.43 2.87
783 793 2.560105 GCACAGGCTGAAGGAAATTCTT 59.440 45.455 23.66 0.00 38.83 2.52
784 794 2.165998 GCACAGGCTGAAGGAAATTCT 58.834 47.619 23.66 0.00 38.83 2.40
785 795 1.888512 TGCACAGGCTGAAGGAAATTC 59.111 47.619 23.66 0.20 41.91 2.17
786 796 1.999648 TGCACAGGCTGAAGGAAATT 58.000 45.000 23.66 0.00 41.91 1.82
788 798 1.614903 CATTGCACAGGCTGAAGGAAA 59.385 47.619 23.66 11.22 41.91 3.13
789 799 1.250328 CATTGCACAGGCTGAAGGAA 58.750 50.000 23.66 19.62 41.91 3.36
790 800 0.111061 ACATTGCACAGGCTGAAGGA 59.889 50.000 23.66 11.66 41.91 3.36
791 801 0.963962 AACATTGCACAGGCTGAAGG 59.036 50.000 23.66 9.54 41.91 3.46
792 802 1.884579 AGAACATTGCACAGGCTGAAG 59.115 47.619 23.66 14.16 41.91 3.02
793 803 1.881973 GAGAACATTGCACAGGCTGAA 59.118 47.619 23.66 5.42 41.91 3.02
794 804 1.072806 AGAGAACATTGCACAGGCTGA 59.927 47.619 23.66 0.00 41.91 4.26
795 805 1.531423 AGAGAACATTGCACAGGCTG 58.469 50.000 14.16 14.16 41.91 4.85
799 809 3.750130 AGCTTGTAGAGAACATTGCACAG 59.250 43.478 0.00 0.00 39.16 3.66
800 810 3.499537 CAGCTTGTAGAGAACATTGCACA 59.500 43.478 0.00 0.00 39.16 4.57
801 811 3.748048 TCAGCTTGTAGAGAACATTGCAC 59.252 43.478 0.00 0.00 39.16 4.57
802 812 4.006780 TCAGCTTGTAGAGAACATTGCA 57.993 40.909 0.00 0.00 39.16 4.08
807 817 5.728637 TTGAGATCAGCTTGTAGAGAACA 57.271 39.130 0.00 0.00 35.88 3.18
808 818 6.090628 CACTTTGAGATCAGCTTGTAGAGAAC 59.909 42.308 0.00 0.00 0.00 3.01
809 819 6.162079 CACTTTGAGATCAGCTTGTAGAGAA 58.838 40.000 0.00 0.00 0.00 2.87
810 820 5.337089 CCACTTTGAGATCAGCTTGTAGAGA 60.337 44.000 0.00 0.00 0.00 3.10
811 821 4.869297 CCACTTTGAGATCAGCTTGTAGAG 59.131 45.833 0.00 0.00 0.00 2.43
814 824 3.869912 GCCCACTTTGAGATCAGCTTGTA 60.870 47.826 0.00 0.00 0.00 2.41
815 825 2.787994 CCCACTTTGAGATCAGCTTGT 58.212 47.619 0.00 0.00 0.00 3.16
817 827 1.353694 AGCCCACTTTGAGATCAGCTT 59.646 47.619 0.00 0.00 0.00 3.74
818 828 0.990374 AGCCCACTTTGAGATCAGCT 59.010 50.000 0.00 0.00 0.00 4.24
819 829 1.471684 CAAGCCCACTTTGAGATCAGC 59.528 52.381 0.00 0.00 32.29 4.26
820 830 2.787994 ACAAGCCCACTTTGAGATCAG 58.212 47.619 0.00 0.00 32.29 2.90
821 831 2.886523 CAACAAGCCCACTTTGAGATCA 59.113 45.455 0.00 0.00 32.29 2.92
822 832 2.352127 GCAACAAGCCCACTTTGAGATC 60.352 50.000 0.00 0.00 37.23 2.75
823 833 1.615392 GCAACAAGCCCACTTTGAGAT 59.385 47.619 0.00 0.00 37.23 2.75
824 834 1.032014 GCAACAAGCCCACTTTGAGA 58.968 50.000 0.00 0.00 37.23 3.27
825 835 3.575399 GCAACAAGCCCACTTTGAG 57.425 52.632 0.00 0.00 37.23 3.02
835 845 1.337167 CCTTAGGGCAAAGCAACAAGC 60.337 52.381 0.00 0.00 46.19 4.01
836 846 2.238521 TCCTTAGGGCAAAGCAACAAG 58.761 47.619 0.00 0.00 0.00 3.16
837 847 2.373335 TCCTTAGGGCAAAGCAACAA 57.627 45.000 0.00 0.00 0.00 2.83
840 850 2.375174 TCTCTTCCTTAGGGCAAAGCAA 59.625 45.455 0.00 0.00 0.00 3.91
843 853 2.238395 AGCTCTCTTCCTTAGGGCAAAG 59.762 50.000 0.00 0.00 0.00 2.77
844 854 2.237392 GAGCTCTCTTCCTTAGGGCAAA 59.763 50.000 6.43 0.00 0.00 3.68
845 855 1.834263 GAGCTCTCTTCCTTAGGGCAA 59.166 52.381 6.43 0.00 0.00 4.52
846 856 1.007721 AGAGCTCTCTTCCTTAGGGCA 59.992 52.381 11.45 0.00 36.31 5.36
847 857 1.412343 CAGAGCTCTCTTCCTTAGGGC 59.588 57.143 14.96 0.00 37.98 5.19
848 858 2.038659 CCAGAGCTCTCTTCCTTAGGG 58.961 57.143 14.96 4.80 37.98 3.53
849 859 2.430332 CACCAGAGCTCTCTTCCTTAGG 59.570 54.545 14.96 12.06 37.98 2.69
850 860 3.360867 TCACCAGAGCTCTCTTCCTTAG 58.639 50.000 14.96 0.00 37.98 2.18
851 861 3.245443 ACTCACCAGAGCTCTCTTCCTTA 60.245 47.826 14.96 0.00 46.09 2.69
852 862 2.178580 CTCACCAGAGCTCTCTTCCTT 58.821 52.381 14.96 0.00 37.98 3.36
854 864 1.204467 CACTCACCAGAGCTCTCTTCC 59.796 57.143 14.96 0.00 46.09 3.46
930 1603 3.795150 GCAGTCGCCTGAAAATTTGTTCA 60.795 43.478 0.00 0.00 41.50 3.18
958 1631 5.155509 TCAAACACGTTGATCAGTTGAAG 57.844 39.130 0.00 0.00 41.47 3.02
1044 1718 3.617368 GCTAGGAAGCGGTGGAGA 58.383 61.111 0.00 0.00 39.39 3.71
1233 1907 1.276705 GAGTTCCAGAGGAAGGTGTCC 59.723 57.143 0.00 0.00 42.88 4.02
1437 2111 2.208527 GGAACCATCGCCTACCAGA 58.791 57.895 0.00 0.00 0.00 3.86
1476 2150 1.933181 CACCTGGCATACATGTACACG 59.067 52.381 7.96 0.00 0.00 4.49
1538 2212 0.179161 CGTGATGACGTCCCTCTCAC 60.179 60.000 14.12 17.61 40.91 3.51
1594 2268 2.191400 TCTCATTCCCTTCTCACCCTG 58.809 52.381 0.00 0.00 0.00 4.45
1597 2271 5.363939 CAAGTATCTCATTCCCTTCTCACC 58.636 45.833 0.00 0.00 0.00 4.02
1608 2282 4.080129 ACCATCTGCACCAAGTATCTCATT 60.080 41.667 0.00 0.00 0.00 2.57
1844 2518 3.318839 CACATCTTTTTCTGGCAACTCCA 59.681 43.478 0.00 0.00 44.18 3.86
1946 2620 2.427320 GCTGCAGACCAGACACCA 59.573 61.111 20.43 0.00 44.64 4.17
2051 2725 7.793927 AAACTGTCTCCAAAGTTTCTCTTAG 57.206 36.000 0.00 0.00 41.61 2.18
2076 2750 7.895594 TTGAAATCAAAGCATTGGCAACCAAG 61.896 38.462 0.00 0.00 44.61 3.61
2237 2911 1.741706 CTCTGCAATGCATTTCTCGGT 59.258 47.619 8.91 0.00 38.13 4.69
2326 3000 2.416547 CTGATTGACCTAACCGCAGTTG 59.583 50.000 0.00 0.00 36.68 3.16
2355 3029 3.549299 AGCAAGCACTTGATCGAAAAG 57.451 42.857 14.44 9.11 42.93 2.27
2971 3645 3.009805 AGGTTAGGTTCAAGGCGGTATTT 59.990 43.478 0.00 0.00 0.00 1.40
2977 3651 2.076863 CTTCAGGTTAGGTTCAAGGCG 58.923 52.381 0.00 0.00 0.00 5.52
3225 3899 5.241403 TCTCTTCCCATTTTTCAGCACTA 57.759 39.130 0.00 0.00 0.00 2.74
3321 3995 3.743911 TGCCATAACTGTTAACTCACACG 59.256 43.478 7.22 0.00 0.00 4.49
3392 4066 7.337938 TGATCCAGAGTTTATGTAAATGAGCA 58.662 34.615 0.00 0.00 0.00 4.26
3415 4089 6.572509 GCCGGTCATTATATCTCTAAAGCTGA 60.573 42.308 1.90 0.00 0.00 4.26
3416 4090 5.578727 GCCGGTCATTATATCTCTAAAGCTG 59.421 44.000 1.90 0.00 0.00 4.24
3417 4091 5.482175 AGCCGGTCATTATATCTCTAAAGCT 59.518 40.000 1.90 0.00 0.00 3.74
3418 4092 5.578727 CAGCCGGTCATTATATCTCTAAAGC 59.421 44.000 1.90 0.00 0.00 3.51
3419 4093 6.809196 GTCAGCCGGTCATTATATCTCTAAAG 59.191 42.308 1.90 0.00 0.00 1.85
3420 4094 6.493802 AGTCAGCCGGTCATTATATCTCTAAA 59.506 38.462 1.90 0.00 0.00 1.85
3512 4188 8.443953 ACAGACTATTGAAGAAGATAAATGCC 57.556 34.615 0.00 0.00 0.00 4.40
3547 4223 3.284449 GGACTTTTGCCGCCACGT 61.284 61.111 0.00 0.00 0.00 4.49
3667 4344 9.630098 GCTTTTCAATAACTCAAAGAATCATGA 57.370 29.630 0.00 0.00 0.00 3.07
3776 4578 8.311836 TCCGTATAAGATCTTATTCCATCCAAC 58.688 37.037 28.39 17.92 37.07 3.77
3784 4586 6.028987 GCTCCGTCCGTATAAGATCTTATTC 58.971 44.000 28.39 22.69 37.07 1.75
3897 4707 0.658536 GTTGCAGTGCGAACTTGAGC 60.659 55.000 6.63 0.00 0.00 4.26
3898 4708 0.940126 AGTTGCAGTGCGAACTTGAG 59.060 50.000 20.35 0.00 30.35 3.02
3928 4738 5.887598 CAGGAGGATCTAGATACATGGAGAG 59.112 48.000 17.47 0.00 33.73 3.20
3944 4754 1.075601 TCCAAAACAGCCAGGAGGAT 58.924 50.000 0.00 0.00 36.89 3.24
3966 4776 9.836076 CATGTCATGTATTAGAAAATAGCATGG 57.164 33.333 4.53 0.00 37.49 3.66
4024 4834 5.633830 AATGGCCTATATGAAATTCGCTG 57.366 39.130 3.32 0.00 0.00 5.18
4063 4873 5.693104 CCAGTGGTTCTGAACATTTTTCATG 59.307 40.000 21.01 8.27 46.27 3.07
4138 4948 7.886629 AGTTCCAGATGTACATATTTGCAAT 57.113 32.000 8.71 0.00 0.00 3.56
4170 5105 1.067974 CGGGGAGTAATGTCGTATGCA 59.932 52.381 0.00 0.00 0.00 3.96
4209 5144 4.704057 AGATCCAGGATTTTCAGCTCAAAC 59.296 41.667 2.53 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.