Multiple sequence alignment - TraesCS5B01G100300

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 TraesCS5B01G100300 chr5B 100.000 3449 0 0 1 3449 133420005 133416557 0.000000e+00 6370.0
1 TraesCS5B01G100300 chr5B 97.064 613 17 1 138 749 371299870 371300482 0.000000e+00 1031.0
2 TraesCS5B01G100300 chr5B 97.857 140 3 0 1 140 371292469 371292608 3.440000e-60 243.0
3 TraesCS5B01G100300 chr5B 97.143 140 4 0 1 140 63291579 63291440 1.600000e-58 237.0
4 TraesCS5B01G100300 chr5B 97.143 140 4 0 1 140 264914770 264914909 1.600000e-58 237.0
5 TraesCS5B01G100300 chr5A 90.733 2223 105 34 807 2962 130287013 130284825 0.000000e+00 2870.0
6 TraesCS5B01G100300 chr5A 88.294 504 31 8 2970 3449 130284662 130284163 2.310000e-161 579.0
7 TraesCS5B01G100300 chr5D 93.251 1941 81 20 789 2697 119915653 119913731 0.000000e+00 2813.0
8 TraesCS5B01G100300 chr5D 87.968 507 31 13 2970 3449 119911507 119911004 3.860000e-159 571.0
9 TraesCS5B01G100300 chr3A 98.206 613 10 1 138 749 684721458 684720846 0.000000e+00 1070.0
10 TraesCS5B01G100300 chr3A 98.571 140 2 0 1 140 684728857 684728718 7.390000e-62 248.0
11 TraesCS5B01G100300 chr2A 98.042 613 11 1 138 749 61502485 61503097 0.000000e+00 1064.0
12 TraesCS5B01G100300 chr2A 97.857 140 3 0 1 140 61495581 61495720 3.440000e-60 243.0
13 TraesCS5B01G100300 chr2A 75.526 523 89 22 1335 1830 120461666 120462176 1.610000e-53 220.0
14 TraesCS5B01G100300 chr6B 97.883 614 11 2 138 749 195195710 195196323 0.000000e+00 1061.0
15 TraesCS5B01G100300 chr6B 96.900 613 18 1 138 749 18574019 18573407 0.000000e+00 1026.0
16 TraesCS5B01G100300 chr6B 97.857 140 3 0 1 140 52028581 52028442 3.440000e-60 243.0
17 TraesCS5B01G100300 chr6B 97.857 140 3 0 1 140 195188342 195188481 3.440000e-60 243.0
18 TraesCS5B01G100300 chr4B 97.716 613 13 1 138 749 644582114 644582726 0.000000e+00 1053.0
19 TraesCS5B01G100300 chr4B 98.571 140 2 0 1 140 644578900 644579039 7.390000e-62 248.0
20 TraesCS5B01G100300 chr4B 89.474 76 8 0 1353 1428 653720290 653720365 2.830000e-16 97.1
21 TraesCS5B01G100300 chr3B 97.363 531 13 1 138 667 591477409 591477939 0.000000e+00 902.0
22 TraesCS5B01G100300 chr3B 94.845 485 23 2 267 749 2429713 2430197 0.000000e+00 756.0
23 TraesCS5B01G100300 chr1B 96.998 533 15 1 138 669 7059144 7058612 0.000000e+00 894.0
24 TraesCS5B01G100300 chr2B 90.431 209 19 1 138 345 154849346 154849554 1.220000e-69 274.0
25 TraesCS5B01G100300 chr1A 97.143 140 4 0 1 140 542851841 542851980 1.600000e-58 237.0


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 TraesCS5B01G100300 chr5B 133416557 133420005 3448 True 6370.0 6370 100.0000 1 3449 1 chr5B.!!$R2 3448
1 TraesCS5B01G100300 chr5B 371299870 371300482 612 False 1031.0 1031 97.0640 138 749 1 chr5B.!!$F3 611
2 TraesCS5B01G100300 chr5A 130284163 130287013 2850 True 1724.5 2870 89.5135 807 3449 2 chr5A.!!$R1 2642
3 TraesCS5B01G100300 chr5D 119911004 119915653 4649 True 1692.0 2813 90.6095 789 3449 2 chr5D.!!$R1 2660
4 TraesCS5B01G100300 chr3A 684720846 684721458 612 True 1070.0 1070 98.2060 138 749 1 chr3A.!!$R1 611
5 TraesCS5B01G100300 chr2A 61502485 61503097 612 False 1064.0 1064 98.0420 138 749 1 chr2A.!!$F2 611
6 TraesCS5B01G100300 chr2A 120461666 120462176 510 False 220.0 220 75.5260 1335 1830 1 chr2A.!!$F3 495
7 TraesCS5B01G100300 chr6B 195195710 195196323 613 False 1061.0 1061 97.8830 138 749 1 chr6B.!!$F2 611
8 TraesCS5B01G100300 chr6B 18573407 18574019 612 True 1026.0 1026 96.9000 138 749 1 chr6B.!!$R1 611
9 TraesCS5B01G100300 chr4B 644578900 644582726 3826 False 650.5 1053 98.1435 1 749 2 chr4B.!!$F2 748
10 TraesCS5B01G100300 chr3B 591477409 591477939 530 False 902.0 902 97.3630 138 667 1 chr3B.!!$F2 529
11 TraesCS5B01G100300 chr1B 7058612 7059144 532 True 894.0 894 96.9980 138 669 1 chr1B.!!$R1 531

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
298 3376 0.323999 GGTTGGCGGGGAAATAAGGT 60.324 55.0 0.0 0.0 0.0 3.50 F
2154 5295 0.036105 TCGTGCTGTCGGAGTACCTA 60.036 55.0 0.0 0.0 33.9 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 5367 0.249699 CATAGAACCCGTGCGCCATA 60.250 55.000 4.18 0.0 0.0 2.74 R
3011 8181 1.403679 CAGAAGCGTTGTTTCACCCAA 59.596 47.619 0.00 0.0 0.0 4.12 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
90 91 2.978010 CGTTTTCGGCCAGCCTGT 60.978 61.111 2.24 0.00 39.94 4.00
260 3338 5.450550 GGAGAAAATGGCGGGAAAGAATAAG 60.451 44.000 0.00 0.00 0.00 1.73
298 3376 0.323999 GGTTGGCGGGGAAATAAGGT 60.324 55.000 0.00 0.00 0.00 3.50
423 3502 2.257371 CGAGAAACGAGTGGCGGA 59.743 61.111 0.00 0.00 46.49 5.54
492 3571 1.382522 CATGCAACTTCGGCCTACAT 58.617 50.000 0.00 0.00 0.00 2.29
758 3838 8.934023 TCATAGTTTTGAAAAATGTACCTCCT 57.066 30.769 0.35 0.00 0.00 3.69
759 3839 9.362151 TCATAGTTTTGAAAAATGTACCTCCTT 57.638 29.630 0.35 0.00 0.00 3.36
760 3840 9.410556 CATAGTTTTGAAAAATGTACCTCCTTG 57.589 33.333 0.35 0.00 0.00 3.61
761 3841 7.418337 AGTTTTGAAAAATGTACCTCCTTGT 57.582 32.000 0.00 0.00 0.00 3.16
762 3842 7.847096 AGTTTTGAAAAATGTACCTCCTTGTT 58.153 30.769 0.00 0.00 0.00 2.83
763 3843 7.763985 AGTTTTGAAAAATGTACCTCCTTGTTG 59.236 33.333 0.00 0.00 0.00 3.33
764 3844 5.195001 TGAAAAATGTACCTCCTTGTTGC 57.805 39.130 0.00 0.00 0.00 4.17
765 3845 4.892934 TGAAAAATGTACCTCCTTGTTGCT 59.107 37.500 0.00 0.00 0.00 3.91
766 3846 5.009610 TGAAAAATGTACCTCCTTGTTGCTC 59.990 40.000 0.00 0.00 0.00 4.26
767 3847 2.789409 ATGTACCTCCTTGTTGCTCC 57.211 50.000 0.00 0.00 0.00 4.70
768 3848 1.729586 TGTACCTCCTTGTTGCTCCT 58.270 50.000 0.00 0.00 0.00 3.69
769 3849 1.623811 TGTACCTCCTTGTTGCTCCTC 59.376 52.381 0.00 0.00 0.00 3.71
770 3850 0.895530 TACCTCCTTGTTGCTCCTCG 59.104 55.000 0.00 0.00 0.00 4.63
771 3851 1.743252 CCTCCTTGTTGCTCCTCGC 60.743 63.158 0.00 0.00 39.77 5.03
787 3867 4.820744 GCACCACGCCCCATCCAT 62.821 66.667 0.00 0.00 32.94 3.41
804 3884 1.645034 CATACCTTGCGTCCACTCAG 58.355 55.000 0.00 0.00 0.00 3.35
805 3885 1.204704 CATACCTTGCGTCCACTCAGA 59.795 52.381 0.00 0.00 0.00 3.27
806 3886 0.888619 TACCTTGCGTCCACTCAGAG 59.111 55.000 0.00 0.00 0.00 3.35
842 3922 2.352915 GGCACTCGATCGCTCTCG 60.353 66.667 11.09 0.00 39.99 4.04
968 4048 1.137404 CGCAAGGGCAAAGATTCCG 59.863 57.895 0.00 0.00 41.24 4.30
1032 4113 2.224967 ACCAGCTTCTGATTCTTGGCTT 60.225 45.455 0.00 0.00 32.44 4.35
1033 4114 2.422832 CCAGCTTCTGATTCTTGGCTTC 59.577 50.000 0.00 0.00 32.44 3.86
1257 4374 1.033746 AATGCAGTGGCCGAATGGAG 61.034 55.000 0.00 0.00 40.13 3.86
1495 4612 1.097547 CCCGTGGTTCATCATGCTCC 61.098 60.000 0.00 0.00 0.00 4.70
1821 4962 3.151022 GAGGGCTCGTGGGAGGAG 61.151 72.222 0.00 0.00 40.80 3.69
1893 5034 4.955774 GGTGGCGACGACACGGTT 62.956 66.667 26.55 0.00 43.55 4.44
1902 5043 2.403037 CGACGACACGGTTTACTTTCTC 59.597 50.000 0.00 0.00 0.00 2.87
1908 5049 3.942748 ACACGGTTTACTTTCTCAGCAAA 59.057 39.130 0.00 0.00 0.00 3.68
2154 5295 0.036105 TCGTGCTGTCGGAGTACCTA 60.036 55.000 0.00 0.00 33.90 3.08
2244 5385 0.249741 GTATGGCGCACGGGTTCTAT 60.250 55.000 10.83 0.00 0.00 1.98
2268 5409 0.687354 AGAAGGCCGACATCAACTGT 59.313 50.000 0.00 0.00 42.15 3.55
2421 5562 2.352805 CTGGCCGCCTTCTCCTTT 59.647 61.111 11.61 0.00 0.00 3.11
2459 5600 3.904571 TCAACGTCTAAGTGCGTGTATT 58.095 40.909 0.00 0.00 41.42 1.89
2460 5601 3.671459 TCAACGTCTAAGTGCGTGTATTG 59.329 43.478 0.00 0.00 41.42 1.90
2461 5602 3.293311 ACGTCTAAGTGCGTGTATTGT 57.707 42.857 0.00 0.00 40.03 2.71
2462 5603 2.984471 ACGTCTAAGTGCGTGTATTGTG 59.016 45.455 0.00 0.00 40.03 3.33
2463 5604 2.984471 CGTCTAAGTGCGTGTATTGTGT 59.016 45.455 0.00 0.00 0.00 3.72
2464 5605 3.181544 CGTCTAAGTGCGTGTATTGTGTG 60.182 47.826 0.00 0.00 0.00 3.82
2465 5606 3.739300 GTCTAAGTGCGTGTATTGTGTGT 59.261 43.478 0.00 0.00 0.00 3.72
2498 5639 4.389576 CTTTGCACCAGCGCCGTC 62.390 66.667 2.29 0.00 46.23 4.79
2519 5672 4.929211 GTCAAGGAGCACTGTTTTGTTTTT 59.071 37.500 0.00 0.00 0.00 1.94
2522 5675 6.151985 TCAAGGAGCACTGTTTTGTTTTTCTA 59.848 34.615 0.00 0.00 0.00 2.10
2606 5763 7.961326 AAGTTAGATATTTGGGTGCTTCATT 57.039 32.000 0.00 0.00 0.00 2.57
2607 5764 7.961326 AGTTAGATATTTGGGTGCTTCATTT 57.039 32.000 0.00 0.00 0.00 2.32
2608 5765 7.775120 AGTTAGATATTTGGGTGCTTCATTTG 58.225 34.615 0.00 0.00 0.00 2.32
2697 7675 5.120674 CACTTCTTAATTGATCAGTGCGTCA 59.879 40.000 0.00 0.00 0.00 4.35
2698 7676 5.700832 ACTTCTTAATTGATCAGTGCGTCAA 59.299 36.000 11.54 11.54 38.57 3.18
2699 7677 5.784750 TCTTAATTGATCAGTGCGTCAAG 57.215 39.130 13.70 3.86 37.72 3.02
2700 7678 5.237815 TCTTAATTGATCAGTGCGTCAAGT 58.762 37.500 13.70 13.38 37.72 3.16
2701 7679 5.348724 TCTTAATTGATCAGTGCGTCAAGTC 59.651 40.000 12.24 0.00 37.72 3.01
2702 7680 2.820059 TTGATCAGTGCGTCAAGTCT 57.180 45.000 0.00 0.00 31.24 3.24
2703 7681 3.934457 TTGATCAGTGCGTCAAGTCTA 57.066 42.857 0.00 0.00 31.24 2.59
2704 7682 3.217599 TGATCAGTGCGTCAAGTCTAC 57.782 47.619 0.00 0.00 0.00 2.59
2705 7683 2.177977 GATCAGTGCGTCAAGTCTACG 58.822 52.381 0.00 0.00 43.12 3.51
2706 7684 0.240145 TCAGTGCGTCAAGTCTACGG 59.760 55.000 0.00 0.00 40.64 4.02
2707 7685 0.240145 CAGTGCGTCAAGTCTACGGA 59.760 55.000 0.00 0.00 40.64 4.69
2708 7686 0.522180 AGTGCGTCAAGTCTACGGAG 59.478 55.000 0.00 0.00 41.42 4.63
2717 7695 5.752472 CGTCAAGTCTACGGAGAAGTCTATA 59.248 44.000 0.00 0.00 36.71 1.31
2726 7704 5.991861 ACGGAGAAGTCTATAGAGAAGTCA 58.008 41.667 1.64 0.00 31.96 3.41
2754 7732 1.980765 TGGCTTGAGGAGAAGTGATGT 59.019 47.619 0.00 0.00 0.00 3.06
2771 7750 8.627208 AAGTGATGTTGATGACTTTGTAGAAT 57.373 30.769 0.00 0.00 32.66 2.40
2798 7777 1.682257 GGTGCTCCTCTTCTTGGCT 59.318 57.895 0.00 0.00 0.00 4.75
2811 7798 2.551270 TCTTGGCTTGGGATAGTCAGT 58.449 47.619 0.00 0.00 30.28 3.41
2866 7853 3.649073 GGCTTTCCGCAAATTAACAAGT 58.351 40.909 0.00 0.00 41.67 3.16
2874 7861 5.298276 TCCGCAAATTAACAAGTCAAGTCTT 59.702 36.000 0.00 0.00 0.00 3.01
2903 7890 7.597288 AACTTTTTAGCCCTAAGAACACAAT 57.403 32.000 0.00 0.00 0.00 2.71
2906 7893 7.505923 ACTTTTTAGCCCTAAGAACACAATTCT 59.494 33.333 0.00 0.00 0.00 2.40
2911 7898 7.454260 AGCCCTAAGAACACAATTCTAAAAG 57.546 36.000 0.00 0.00 0.00 2.27
2923 7910 8.803235 ACACAATTCTAAAAGAAAATAGGACCC 58.197 33.333 0.00 0.00 37.82 4.46
2925 7912 7.122204 ACAATTCTAAAAGAAAATAGGACCCCG 59.878 37.037 0.00 0.00 37.82 5.73
2938 7925 2.502538 AGGACCCCGATAAATCACGAAA 59.497 45.455 0.00 0.00 0.00 3.46
2942 7929 4.329392 ACCCCGATAAATCACGAAAGTTT 58.671 39.130 0.00 0.00 46.40 2.66
2963 7950 5.798125 TTGGATTTTAAGCATGTCAACCA 57.202 34.783 0.00 0.00 0.00 3.67
2964 7951 5.798125 TGGATTTTAAGCATGTCAACCAA 57.202 34.783 0.00 0.00 0.00 3.67
2968 8138 6.366061 GGATTTTAAGCATGTCAACCAAAGTC 59.634 38.462 0.00 0.00 0.00 3.01
2984 8154 5.068460 ACCAAAGTCAAAATCCGAACATTCA 59.932 36.000 0.00 0.00 0.00 2.57
2986 8156 6.437928 CAAAGTCAAAATCCGAACATTCAGA 58.562 36.000 0.00 0.00 0.00 3.27
3052 8224 7.122138 TCTGATCCCATATAATCATCTCAGC 57.878 40.000 0.00 0.00 31.79 4.26
3053 8225 5.910614 TGATCCCATATAATCATCTCAGCG 58.089 41.667 0.00 0.00 0.00 5.18
3061 8233 9.029243 CCATATAATCATCTCAGCGAATAGTTC 57.971 37.037 0.00 0.00 0.00 3.01
3070 8242 4.009675 TCAGCGAATAGTTCTTGCCATTT 58.990 39.130 0.00 0.00 0.00 2.32
3079 8252 5.200368 AGTTCTTGCCATTTAACCACAAG 57.800 39.130 0.00 0.00 39.22 3.16
3084 8257 5.594725 TCTTGCCATTTAACCACAAGTGTTA 59.405 36.000 0.00 0.00 38.99 2.41
3121 8294 9.638300 CAATTCTTACAATGTACGCTAAATCTC 57.362 33.333 0.00 0.00 0.00 2.75
3160 8346 1.036707 CTCTCTGGTCGGGAAGATCC 58.963 60.000 0.00 0.00 35.23 3.36
3179 8365 9.927668 GAAGATCCCATTTGTTCAATCTTTTTA 57.072 29.630 0.00 0.00 34.52 1.52
3203 8389 0.537188 AGGCCCACATCGTAGTTCTG 59.463 55.000 0.00 0.00 0.00 3.02
3204 8390 0.462047 GGCCCACATCGTAGTTCTGG 60.462 60.000 0.00 0.00 0.00 3.86
3206 8392 0.902531 CCCACATCGTAGTTCTGGGT 59.097 55.000 0.00 0.00 37.39 4.51
3375 8564 7.987750 AACTTTCTTGATCTACCTTTCTTCC 57.012 36.000 0.00 0.00 0.00 3.46
3376 8565 7.323052 ACTTTCTTGATCTACCTTTCTTCCT 57.677 36.000 0.00 0.00 0.00 3.36
3377 8566 7.750655 ACTTTCTTGATCTACCTTTCTTCCTT 58.249 34.615 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 3338 1.427819 CTTTCCCGCCATAACGCAC 59.572 57.895 0.00 0.00 0.00 5.34
298 3376 3.738481 CCCGCCAATCCCTTCCCA 61.738 66.667 0.00 0.00 0.00 4.37
423 3502 1.835267 GTTTCCCGCCAACCCCTTT 60.835 57.895 0.00 0.00 0.00 3.11
492 3571 5.039480 CGAAAAGTACTACTTCGGTCTCA 57.961 43.478 23.01 0.00 37.47 3.27
749 3829 1.623811 GAGGAGCAACAAGGAGGTACA 59.376 52.381 0.00 0.00 0.00 2.90
750 3830 1.404315 CGAGGAGCAACAAGGAGGTAC 60.404 57.143 0.00 0.00 0.00 3.34
751 3831 0.895530 CGAGGAGCAACAAGGAGGTA 59.104 55.000 0.00 0.00 0.00 3.08
752 3832 1.674057 CGAGGAGCAACAAGGAGGT 59.326 57.895 0.00 0.00 0.00 3.85
753 3833 4.606071 CGAGGAGCAACAAGGAGG 57.394 61.111 0.00 0.00 0.00 4.30
770 3850 3.414136 TATGGATGGGGCGTGGTGC 62.414 63.158 0.00 0.00 45.38 5.01
771 3851 1.525995 GTATGGATGGGGCGTGGTG 60.526 63.158 0.00 0.00 0.00 4.17
772 3852 2.752807 GGTATGGATGGGGCGTGGT 61.753 63.158 0.00 0.00 0.00 4.16
773 3853 1.994885 AAGGTATGGATGGGGCGTGG 61.995 60.000 0.00 0.00 0.00 4.94
774 3854 0.819259 CAAGGTATGGATGGGGCGTG 60.819 60.000 0.00 0.00 0.00 5.34
775 3855 1.531748 CAAGGTATGGATGGGGCGT 59.468 57.895 0.00 0.00 0.00 5.68
776 3856 1.898574 GCAAGGTATGGATGGGGCG 60.899 63.158 0.00 0.00 0.00 6.13
777 3857 1.898574 CGCAAGGTATGGATGGGGC 60.899 63.158 0.00 0.00 0.00 5.80
778 3858 0.535102 GACGCAAGGTATGGATGGGG 60.535 60.000 0.00 0.00 46.39 4.96
779 3859 0.535102 GGACGCAAGGTATGGATGGG 60.535 60.000 0.00 0.00 46.39 4.00
780 3860 0.180171 TGGACGCAAGGTATGGATGG 59.820 55.000 0.00 0.00 46.39 3.51
781 3861 1.134401 AGTGGACGCAAGGTATGGATG 60.134 52.381 0.00 0.00 46.39 3.51
782 3862 1.139058 GAGTGGACGCAAGGTATGGAT 59.861 52.381 0.00 0.00 46.39 3.41
783 3863 0.535335 GAGTGGACGCAAGGTATGGA 59.465 55.000 0.00 0.00 46.39 3.41
784 3864 0.249120 TGAGTGGACGCAAGGTATGG 59.751 55.000 0.00 0.00 46.39 2.74
785 3865 1.204704 TCTGAGTGGACGCAAGGTATG 59.795 52.381 0.00 0.00 46.39 2.39
786 3866 1.478510 CTCTGAGTGGACGCAAGGTAT 59.521 52.381 0.00 0.00 46.39 2.73
787 3867 0.888619 CTCTGAGTGGACGCAAGGTA 59.111 55.000 0.00 0.00 46.39 3.08
804 3884 1.181786 CTCCACTCCACTCCACTCTC 58.818 60.000 0.00 0.00 0.00 3.20
805 3885 0.485099 ACTCCACTCCACTCCACTCT 59.515 55.000 0.00 0.00 0.00 3.24
806 3886 0.605589 CACTCCACTCCACTCCACTC 59.394 60.000 0.00 0.00 0.00 3.51
842 3922 1.948508 TGCGTTGACATGCAAGGAC 59.051 52.632 19.64 13.59 42.25 3.85
912 3992 1.609841 CCCTTTGTTACGTCTGGGGTC 60.610 57.143 0.00 0.00 0.00 4.46
968 4048 1.066787 GCTCAGGTAGGGTGTGTTCTC 60.067 57.143 0.00 0.00 0.00 2.87
1032 4113 4.879545 AGACAAAACTTGGTTAGAAAGCGA 59.120 37.500 0.00 0.00 34.12 4.93
1033 4114 5.169836 AGACAAAACTTGGTTAGAAAGCG 57.830 39.130 0.00 0.00 34.12 4.68
1257 4374 3.922893 GACATCTGCGCGCTCAGC 61.923 66.667 33.29 10.79 43.95 4.26
1433 4550 2.577785 GCGTCGAGGAATGTAGCGC 61.578 63.158 9.75 0.00 36.75 5.92
1486 4603 2.505982 CCGTTCGGGGAGCATGAT 59.494 61.111 0.00 0.00 0.00 2.45
1893 5034 2.747446 GCCGGATTTGCTGAGAAAGTAA 59.253 45.455 5.05 0.00 0.00 2.24
1902 5043 3.118454 ACGTCGCCGGATTTGCTG 61.118 61.111 5.05 0.00 38.78 4.41
1908 5049 4.203076 GCTACCACGTCGCCGGAT 62.203 66.667 5.05 0.00 38.78 4.18
1923 5064 1.106351 TGCGTTTCATGTTGGTGGCT 61.106 50.000 0.00 0.00 0.00 4.75
2070 5211 1.439353 CGAAATGCACGGGGAGGATG 61.439 60.000 0.00 0.00 0.00 3.51
2226 5367 0.249699 CATAGAACCCGTGCGCCATA 60.250 55.000 4.18 0.00 0.00 2.74
2244 5385 0.690192 TGATGTCGGCCTTCTTTCCA 59.310 50.000 0.00 0.00 0.00 3.53
2369 5510 2.108514 CCGTCGCCATTGATGCACT 61.109 57.895 0.00 0.00 0.00 4.40
2421 5562 2.946329 GTTGATCTCTACTCTCGGCTCA 59.054 50.000 0.00 0.00 0.00 4.26
2459 5600 1.335415 GCAAACACACACACACACACA 60.335 47.619 0.00 0.00 0.00 3.72
2460 5601 1.335415 TGCAAACACACACACACACAC 60.335 47.619 0.00 0.00 0.00 3.82
2461 5602 0.954452 TGCAAACACACACACACACA 59.046 45.000 0.00 0.00 0.00 3.72
2462 5603 1.335935 GTGCAAACACACACACACAC 58.664 50.000 0.00 0.00 46.61 3.82
2463 5604 3.782884 GTGCAAACACACACACACA 57.217 47.368 0.00 0.00 46.61 3.72
2497 5638 4.799564 AAAACAAAACAGTGCTCCTTGA 57.200 36.364 0.00 0.00 0.00 3.02
2498 5639 5.170748 AGAAAAACAAAACAGTGCTCCTTG 58.829 37.500 0.00 0.00 0.00 3.61
2519 5672 8.792830 AATAATCAAACAAGCAAGCTAGTAGA 57.207 30.769 0.00 0.00 0.00 2.59
2562 5719 0.806868 AGACCATGCGATGCAACAAG 59.193 50.000 0.00 0.00 43.62 3.16
2606 5763 4.079980 TCAAGGACTCGAATTGGTTCAA 57.920 40.909 0.00 0.00 33.86 2.69
2607 5764 3.762407 TCAAGGACTCGAATTGGTTCA 57.238 42.857 0.00 0.00 33.86 3.18
2608 5765 5.642063 TGTAATCAAGGACTCGAATTGGTTC 59.358 40.000 2.28 0.00 30.32 3.62
2685 5846 2.177977 CGTAGACTTGACGCACTGATC 58.822 52.381 0.00 0.00 32.89 2.92
2697 7675 7.364149 TCTCTATAGACTTCTCCGTAGACTT 57.636 40.000 0.00 0.00 0.00 3.01
2698 7676 6.982160 TCTCTATAGACTTCTCCGTAGACT 57.018 41.667 0.00 0.00 0.00 3.24
2699 7677 7.212274 ACTTCTCTATAGACTTCTCCGTAGAC 58.788 42.308 0.00 0.00 0.00 2.59
2700 7678 7.069702 TGACTTCTCTATAGACTTCTCCGTAGA 59.930 40.741 0.00 0.00 0.00 2.59
2701 7679 7.211573 TGACTTCTCTATAGACTTCTCCGTAG 58.788 42.308 0.00 0.00 0.00 3.51
2702 7680 7.069702 TCTGACTTCTCTATAGACTTCTCCGTA 59.930 40.741 0.00 0.00 0.00 4.02
2703 7681 5.991861 TGACTTCTCTATAGACTTCTCCGT 58.008 41.667 0.00 0.00 0.00 4.69
2704 7682 6.285224 TCTGACTTCTCTATAGACTTCTCCG 58.715 44.000 0.00 0.00 0.00 4.63
2705 7683 7.280356 ACTCTGACTTCTCTATAGACTTCTCC 58.720 42.308 0.00 0.00 0.00 3.71
2706 7684 7.169308 CGACTCTGACTTCTCTATAGACTTCTC 59.831 44.444 0.00 0.00 0.00 2.87
2707 7685 6.984474 CGACTCTGACTTCTCTATAGACTTCT 59.016 42.308 0.00 0.00 0.00 2.85
2708 7686 6.292703 GCGACTCTGACTTCTCTATAGACTTC 60.293 46.154 0.00 0.00 0.00 3.01
2717 7695 1.173043 CCAGCGACTCTGACTTCTCT 58.827 55.000 0.00 0.00 45.72 3.10
2726 7704 1.603236 CTCCTCAAGCCAGCGACTCT 61.603 60.000 0.00 0.00 0.00 3.24
2754 7732 7.033791 GTCGAGGTATTCTACAAAGTCATCAA 58.966 38.462 0.00 0.00 0.00 2.57
2798 7777 0.539986 GGCCGAACTGACTATCCCAA 59.460 55.000 0.00 0.00 0.00 4.12
2864 7851 8.622157 GGCTAAAAAGTTAGAAAAGACTTGACT 58.378 33.333 0.00 0.00 39.36 3.41
2866 7853 7.778382 AGGGCTAAAAAGTTAGAAAAGACTTGA 59.222 33.333 0.00 0.00 39.36 3.02
2874 7861 8.843262 GTGTTCTTAGGGCTAAAAAGTTAGAAA 58.157 33.333 0.00 0.00 39.36 2.52
2903 7890 6.377245 TCGGGGTCCTATTTTCTTTTAGAA 57.623 37.500 0.00 0.00 31.28 2.10
2906 7893 9.346005 GATTTATCGGGGTCCTATTTTCTTTTA 57.654 33.333 0.00 0.00 0.00 1.52
2911 7898 5.178809 CGTGATTTATCGGGGTCCTATTTTC 59.821 44.000 0.00 0.00 0.00 2.29
2923 7910 5.539582 TCCAAACTTTCGTGATTTATCGG 57.460 39.130 0.00 0.00 0.00 4.18
2938 7925 6.183360 TGGTTGACATGCTTAAAATCCAAACT 60.183 34.615 0.00 0.00 0.00 2.66
2942 7929 5.798125 TTGGTTGACATGCTTAAAATCCA 57.202 34.783 0.00 0.00 0.00 3.41
2963 7950 6.633500 TCTGAATGTTCGGATTTTGACTTT 57.367 33.333 0.21 0.00 37.65 2.66
2964 7951 6.633500 TTCTGAATGTTCGGATTTTGACTT 57.367 33.333 5.19 0.00 41.85 3.01
2968 8138 9.571810 TGATAAATTCTGAATGTTCGGATTTTG 57.428 29.630 22.39 0.00 41.98 2.44
3006 8176 4.010667 AGCGTTGTTTCACCCAAGTATA 57.989 40.909 0.00 0.00 0.00 1.47
3007 8177 2.858745 AGCGTTGTTTCACCCAAGTAT 58.141 42.857 0.00 0.00 0.00 2.12
3008 8178 2.335316 AGCGTTGTTTCACCCAAGTA 57.665 45.000 0.00 0.00 0.00 2.24
3009 8179 1.404035 GAAGCGTTGTTTCACCCAAGT 59.596 47.619 0.00 0.00 0.00 3.16
3010 8180 1.676006 AGAAGCGTTGTTTCACCCAAG 59.324 47.619 0.00 0.00 0.00 3.61
3011 8181 1.403679 CAGAAGCGTTGTTTCACCCAA 59.596 47.619 0.00 0.00 0.00 4.12
3052 8224 6.027749 GTGGTTAAATGGCAAGAACTATTCG 58.972 40.000 0.00 0.00 34.02 3.34
3053 8225 6.919721 TGTGGTTAAATGGCAAGAACTATTC 58.080 36.000 0.00 0.00 0.00 1.75
3061 8233 4.320608 ACACTTGTGGTTAAATGGCAAG 57.679 40.909 5.72 0.00 41.40 4.01
3063 8235 5.854010 TTAACACTTGTGGTTAAATGGCA 57.146 34.783 5.72 0.00 37.67 4.92
3070 8242 6.127675 GGAAGTTGGTTTAACACTTGTGGTTA 60.128 38.462 5.70 0.02 41.88 2.85
3079 8252 8.192110 TGTAAGAATTGGAAGTTGGTTTAACAC 58.808 33.333 0.00 0.00 41.88 3.32
3084 8257 7.791029 ACATTGTAAGAATTGGAAGTTGGTTT 58.209 30.769 0.00 0.00 0.00 3.27
3121 8294 5.403246 AGAGCAGTACAAAATAGTGACTCG 58.597 41.667 0.00 0.00 32.02 4.18
3179 8365 4.838986 AGAACTACGATGTGGGCCTAATAT 59.161 41.667 4.53 0.00 0.00 1.28
3181 8367 3.039011 AGAACTACGATGTGGGCCTAAT 58.961 45.455 4.53 0.00 0.00 1.73
3374 8563 1.603802 TGCACTTGCGAGAAAGAAAGG 59.396 47.619 8.31 0.00 45.83 3.11
3375 8564 2.289002 ACTGCACTTGCGAGAAAGAAAG 59.711 45.455 8.31 0.00 45.83 2.62
3376 8565 2.032054 CACTGCACTTGCGAGAAAGAAA 59.968 45.455 8.31 0.00 45.83 2.52
3377 8566 1.599071 CACTGCACTTGCGAGAAAGAA 59.401 47.619 8.31 0.00 45.83 2.52


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

AutoCloner maintained by Alex Coulton.