Multiple sequence alignment - TraesCS5A01G263600

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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 TraesCS5A01G263600 chr5A 100.000 3320 0 0 1 3320 476412199 476415518 0.000000e+00 6131.0
1 TraesCS5A01G263600 chr5A 83.055 897 130 18 1 884 425495147 425494260 0.000000e+00 795.0
2 TraesCS5A01G263600 chr5D 95.677 1573 51 3 884 2446 374706764 374708329 0.000000e+00 2512.0
3 TraesCS5A01G263600 chr5D 86.494 696 42 14 2658 3318 374709655 374710333 0.000000e+00 717.0
4 TraesCS5A01G263600 chr5B 94.511 1494 60 16 894 2366 447558293 447559785 0.000000e+00 2285.0
5 TraesCS5A01G263600 chr5B 92.647 204 11 3 2352 2555 447560653 447560852 1.170000e-74 291.0
6 TraesCS5A01G263600 chr5B 81.173 324 42 12 2658 2962 447560851 447561174 3.310000e-60 243.0
7 TraesCS5A01G263600 chr1A 97.624 884 20 1 1 884 366295258 366294376 0.000000e+00 1515.0
8 TraesCS5A01G263600 chr1A 83.333 894 131 15 1 883 38580080 38580966 0.000000e+00 809.0
9 TraesCS5A01G263600 chr1A 83.130 901 120 21 1 883 38633617 38634503 0.000000e+00 793.0
10 TraesCS5A01G263600 chr6D 91.236 890 69 5 1 883 186788857 186789744 0.000000e+00 1203.0
11 TraesCS5A01G263600 chr2A 91.909 791 54 4 1 791 544291987 544291207 0.000000e+00 1098.0
12 TraesCS5A01G263600 chr2A 82.886 894 133 17 1 882 617728805 617729690 0.000000e+00 785.0
13 TraesCS5A01G263600 chr7A 83.036 896 130 19 1 883 666486913 666486027 0.000000e+00 793.0
14 TraesCS5A01G263600 chr7A 81.684 475 84 2 1816 2287 222638540 222638066 3.100000e-105 392.0
15 TraesCS5A01G263600 chr7A 79.492 512 76 18 1060 1557 222639260 222638764 1.480000e-88 337.0
16 TraesCS5A01G263600 chr7A 85.185 108 12 3 2554 2659 638491446 638491341 1.260000e-19 108.0
17 TraesCS5A01G263600 chr1B 83.055 897 120 21 1 883 574255444 574256322 0.000000e+00 785.0
18 TraesCS5A01G263600 chr3A 82.682 895 135 17 1 883 707721521 707720635 0.000000e+00 776.0
19 TraesCS5A01G263600 chr3A 83.871 93 12 3 2569 2659 235826477 235826386 5.900000e-13 86.1
20 TraesCS5A01G263600 chr4A 84.786 631 87 8 259 887 580507589 580508212 2.810000e-175 625.0
21 TraesCS5A01G263600 chr4A 88.889 108 9 3 2554 2659 625486136 625486242 2.690000e-26 130.0
22 TraesCS5A01G263600 chr6A 81.085 756 124 17 133 883 608340547 608339806 1.330000e-163 586.0
23 TraesCS5A01G263600 chr7D 81.602 462 82 2 1816 2274 210022305 210021844 2.420000e-101 379.0
24 TraesCS5A01G263600 chr7D 79.102 512 78 18 1060 1557 210023025 210022529 3.190000e-85 326.0
25 TraesCS5A01G263600 chr7B 80.127 473 64 20 1060 1517 191521111 191521568 3.190000e-85 326.0
26 TraesCS5A01G263600 chr7B 83.333 108 14 3 2554 2659 644184377 644184272 2.730000e-16 97.1


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 TraesCS5A01G263600 chr5A 476412199 476415518 3319 False 6131.000000 6131 100.000000 1 3320 1 chr5A.!!$F1 3319
1 TraesCS5A01G263600 chr5A 425494260 425495147 887 True 795.000000 795 83.055000 1 884 1 chr5A.!!$R1 883
2 TraesCS5A01G263600 chr5D 374706764 374710333 3569 False 1614.500000 2512 91.085500 884 3318 2 chr5D.!!$F1 2434
3 TraesCS5A01G263600 chr5B 447558293 447561174 2881 False 939.666667 2285 89.443667 894 2962 3 chr5B.!!$F1 2068
4 TraesCS5A01G263600 chr1A 366294376 366295258 882 True 1515.000000 1515 97.624000 1 884 1 chr1A.!!$R1 883
5 TraesCS5A01G263600 chr1A 38580080 38580966 886 False 809.000000 809 83.333000 1 883 1 chr1A.!!$F1 882
6 TraesCS5A01G263600 chr1A 38633617 38634503 886 False 793.000000 793 83.130000 1 883 1 chr1A.!!$F2 882
7 TraesCS5A01G263600 chr6D 186788857 186789744 887 False 1203.000000 1203 91.236000 1 883 1 chr6D.!!$F1 882
8 TraesCS5A01G263600 chr2A 544291207 544291987 780 True 1098.000000 1098 91.909000 1 791 1 chr2A.!!$R1 790
9 TraesCS5A01G263600 chr2A 617728805 617729690 885 False 785.000000 785 82.886000 1 882 1 chr2A.!!$F1 881
10 TraesCS5A01G263600 chr7A 666486027 666486913 886 True 793.000000 793 83.036000 1 883 1 chr7A.!!$R2 882
11 TraesCS5A01G263600 chr7A 222638066 222639260 1194 True 364.500000 392 80.588000 1060 2287 2 chr7A.!!$R3 1227
12 TraesCS5A01G263600 chr1B 574255444 574256322 878 False 785.000000 785 83.055000 1 883 1 chr1B.!!$F1 882
13 TraesCS5A01G263600 chr3A 707720635 707721521 886 True 776.000000 776 82.682000 1 883 1 chr3A.!!$R2 882
14 TraesCS5A01G263600 chr4A 580507589 580508212 623 False 625.000000 625 84.786000 259 887 1 chr4A.!!$F1 628
15 TraesCS5A01G263600 chr6A 608339806 608340547 741 True 586.000000 586 81.085000 133 883 1 chr6A.!!$R1 750
16 TraesCS5A01G263600 chr7D 210021844 210023025 1181 True 352.500000 379 80.352000 1060 2274 2 chr7D.!!$R1 1214

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
931 942 0.237498 TATATGAGCACGTCCTCGCG 59.763 55.0 0.0 0.0 41.18 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2591 4828 0.508213 GCGCAAAACAACTCAATGCC 59.492 50.0 0.3 0.0 33.55 4.4 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
75 77 3.449227 CAGGAGCCCGCTGTCGTA 61.449 66.667 0.00 0.00 0.00 3.43
219 228 0.531532 AATGCCTCCTCGAGCAATCG 60.532 55.000 6.99 0.00 43.36 3.34
255 264 2.707849 CCGGACGTCCAGAATCGGT 61.708 63.158 32.80 0.00 35.14 4.69
309 318 1.095228 CACCACCGCGCCTTGATATT 61.095 55.000 0.00 0.00 0.00 1.28
722 733 1.913262 ATGTCAGCCCGACCAGTGA 60.913 57.895 0.00 0.00 44.71 3.41
799 810 4.260620 GGTGTTACGCATTAGGCACATAAG 60.261 45.833 0.00 0.00 45.17 1.73
804 815 2.489971 GCATTAGGCACATAAGCGGTA 58.510 47.619 0.00 0.00 43.97 4.02
805 816 2.875933 GCATTAGGCACATAAGCGGTAA 59.124 45.455 0.00 0.00 43.97 2.85
931 942 0.237498 TATATGAGCACGTCCTCGCG 59.763 55.000 0.00 0.00 41.18 5.87
941 952 3.849951 TCCTCGCGAGCCCATTCC 61.850 66.667 30.49 0.00 0.00 3.01
953 964 2.671070 CATTCCCAGCCCGACACT 59.329 61.111 0.00 0.00 0.00 3.55
954 965 1.450312 CATTCCCAGCCCGACACTC 60.450 63.158 0.00 0.00 0.00 3.51
955 966 1.918293 ATTCCCAGCCCGACACTCA 60.918 57.895 0.00 0.00 0.00 3.41
956 967 2.185310 ATTCCCAGCCCGACACTCAC 62.185 60.000 0.00 0.00 0.00 3.51
957 968 4.742201 CCCAGCCCGACACTCACG 62.742 72.222 0.00 0.00 0.00 4.35
958 969 3.680786 CCAGCCCGACACTCACGA 61.681 66.667 0.00 0.00 0.00 4.35
959 970 2.430921 CAGCCCGACACTCACGAC 60.431 66.667 0.00 0.00 0.00 4.34
971 982 2.130073 CTCACGACTCACGAGCCACA 62.130 60.000 0.00 0.00 45.77 4.17
1014 1050 4.802051 ATCATGCAGCCCGCGGTT 62.802 61.111 26.12 9.27 46.97 4.44
1284 1341 3.138798 GAGACGCCCGACCTGCTA 61.139 66.667 0.00 0.00 0.00 3.49
1332 1389 2.687805 CGACCTCAACGAGCTCCGA 61.688 63.158 8.47 1.41 41.76 4.55
2224 2355 1.449423 CCGGCCGATGACATTGTGA 60.449 57.895 30.73 0.00 0.00 3.58
2322 2456 1.294659 CCTTGCCAGAGTTCTGACGC 61.295 60.000 10.64 7.01 46.59 5.19
2366 3382 4.911514 ATGTCAGTTTTACCGTTTTGCT 57.088 36.364 0.00 0.00 0.00 3.91
2593 4830 8.455598 TTTTTATAATACGTTTTGAAGCTGGC 57.544 30.769 0.00 0.00 0.00 4.85
2594 4831 6.745159 TTATAATACGTTTTGAAGCTGGCA 57.255 33.333 0.00 0.00 0.00 4.92
2595 4832 5.835113 ATAATACGTTTTGAAGCTGGCAT 57.165 34.783 0.00 0.00 0.00 4.40
2596 4833 4.519540 AATACGTTTTGAAGCTGGCATT 57.480 36.364 0.00 0.00 0.00 3.56
2597 4834 2.138596 ACGTTTTGAAGCTGGCATTG 57.861 45.000 0.00 0.00 0.00 2.82
2598 4835 1.680735 ACGTTTTGAAGCTGGCATTGA 59.319 42.857 0.00 0.00 0.00 2.57
2599 4836 2.287788 ACGTTTTGAAGCTGGCATTGAG 60.288 45.455 0.00 0.00 0.00 3.02
2600 4837 2.287788 CGTTTTGAAGCTGGCATTGAGT 60.288 45.455 0.00 0.00 0.00 3.41
2601 4838 3.721035 GTTTTGAAGCTGGCATTGAGTT 58.279 40.909 0.00 0.00 0.00 3.01
2602 4839 3.374220 TTTGAAGCTGGCATTGAGTTG 57.626 42.857 0.00 0.00 0.00 3.16
2603 4840 1.985473 TGAAGCTGGCATTGAGTTGT 58.015 45.000 0.00 0.00 0.00 3.32
2604 4841 2.309613 TGAAGCTGGCATTGAGTTGTT 58.690 42.857 0.00 0.00 0.00 2.83
2605 4842 2.694628 TGAAGCTGGCATTGAGTTGTTT 59.305 40.909 0.00 0.00 0.00 2.83
2606 4843 3.132646 TGAAGCTGGCATTGAGTTGTTTT 59.867 39.130 0.00 0.00 0.00 2.43
2607 4844 3.102052 AGCTGGCATTGAGTTGTTTTG 57.898 42.857 0.00 0.00 0.00 2.44
2608 4845 1.528161 GCTGGCATTGAGTTGTTTTGC 59.472 47.619 0.00 0.00 0.00 3.68
2609 4846 1.788308 CTGGCATTGAGTTGTTTTGCG 59.212 47.619 0.00 0.00 34.17 4.85
2610 4847 0.508213 GGCATTGAGTTGTTTTGCGC 59.492 50.000 0.00 0.00 34.17 6.09
2611 4848 1.490621 GCATTGAGTTGTTTTGCGCT 58.509 45.000 9.73 0.00 0.00 5.92
2612 4849 1.453148 GCATTGAGTTGTTTTGCGCTC 59.547 47.619 9.73 0.00 0.00 5.03
2613 4850 2.859806 GCATTGAGTTGTTTTGCGCTCT 60.860 45.455 9.73 0.00 0.00 4.09
2614 4851 2.473530 TTGAGTTGTTTTGCGCTCTG 57.526 45.000 9.73 0.00 0.00 3.35
2615 4852 1.378531 TGAGTTGTTTTGCGCTCTGT 58.621 45.000 9.73 0.00 0.00 3.41
2616 4853 1.063912 TGAGTTGTTTTGCGCTCTGTG 59.936 47.619 9.73 0.00 0.00 3.66
2617 4854 1.064060 GAGTTGTTTTGCGCTCTGTGT 59.936 47.619 9.73 0.00 0.00 3.72
2618 4855 1.191096 GTTGTTTTGCGCTCTGTGTG 58.809 50.000 9.73 0.00 0.00 3.82
2619 4856 1.090728 TTGTTTTGCGCTCTGTGTGA 58.909 45.000 9.73 0.00 0.00 3.58
2620 4857 1.090728 TGTTTTGCGCTCTGTGTGAA 58.909 45.000 9.73 0.00 0.00 3.18
2621 4858 1.675483 TGTTTTGCGCTCTGTGTGAAT 59.325 42.857 9.73 0.00 0.00 2.57
2622 4859 2.098934 TGTTTTGCGCTCTGTGTGAATT 59.901 40.909 9.73 0.00 0.00 2.17
2623 4860 2.404265 TTTGCGCTCTGTGTGAATTG 57.596 45.000 9.73 0.00 0.00 2.32
2624 4861 1.308047 TTGCGCTCTGTGTGAATTGT 58.692 45.000 9.73 0.00 0.00 2.71
2625 4862 0.867746 TGCGCTCTGTGTGAATTGTC 59.132 50.000 9.73 0.00 0.00 3.18
2626 4863 1.151668 GCGCTCTGTGTGAATTGTCT 58.848 50.000 0.00 0.00 0.00 3.41
2627 4864 2.288763 TGCGCTCTGTGTGAATTGTCTA 60.289 45.455 9.73 0.00 0.00 2.59
2628 4865 2.736721 GCGCTCTGTGTGAATTGTCTAA 59.263 45.455 0.00 0.00 0.00 2.10
2629 4866 3.186409 GCGCTCTGTGTGAATTGTCTAAA 59.814 43.478 0.00 0.00 0.00 1.85
2630 4867 4.702392 CGCTCTGTGTGAATTGTCTAAAC 58.298 43.478 0.00 0.00 0.00 2.01
2631 4868 4.664139 CGCTCTGTGTGAATTGTCTAAACG 60.664 45.833 0.00 0.00 0.00 3.60
2632 4869 4.211374 GCTCTGTGTGAATTGTCTAAACGT 59.789 41.667 0.00 0.00 0.00 3.99
2633 4870 5.612709 GCTCTGTGTGAATTGTCTAAACGTC 60.613 44.000 0.00 0.00 0.00 4.34
2634 4871 5.597806 TCTGTGTGAATTGTCTAAACGTCT 58.402 37.500 0.00 0.00 0.00 4.18
2635 4872 6.046593 TCTGTGTGAATTGTCTAAACGTCTT 58.953 36.000 0.00 0.00 0.00 3.01
2636 4873 7.204604 TCTGTGTGAATTGTCTAAACGTCTTA 58.795 34.615 0.00 0.00 0.00 2.10
2637 4874 7.870954 TCTGTGTGAATTGTCTAAACGTCTTAT 59.129 33.333 0.00 0.00 0.00 1.73
2638 4875 9.135843 CTGTGTGAATTGTCTAAACGTCTTATA 57.864 33.333 0.00 0.00 0.00 0.98
2639 4876 9.478768 TGTGTGAATTGTCTAAACGTCTTATAA 57.521 29.630 0.00 0.00 0.00 0.98
2644 4881 9.983804 GAATTGTCTAAACGTCTTATAAAAGGG 57.016 33.333 0.00 0.00 33.22 3.95
2645 4882 9.729281 AATTGTCTAAACGTCTTATAAAAGGGA 57.271 29.630 0.00 0.00 33.22 4.20
2646 4883 9.729281 ATTGTCTAAACGTCTTATAAAAGGGAA 57.271 29.630 0.00 0.00 33.22 3.97
2647 4884 9.558396 TTGTCTAAACGTCTTATAAAAGGGAAA 57.442 29.630 0.00 0.00 33.22 3.13
2648 4885 9.558396 TGTCTAAACGTCTTATAAAAGGGAAAA 57.442 29.630 0.00 0.00 33.22 2.29
2682 4919 2.217429 TTTGTTCTTGGCGAAAAGGC 57.783 45.000 0.00 0.00 46.95 4.35
2734 4972 5.788531 CCTTACAAGATTTTTCTTACACGCG 59.211 40.000 3.53 3.53 0.00 6.01
2754 4992 3.421741 CGAGTCGTTGAAGTTTTTGCAA 58.578 40.909 3.82 0.00 0.00 4.08
2776 5026 1.141657 GCCTTCCCTCTGCATACATCA 59.858 52.381 0.00 0.00 0.00 3.07
2779 5029 3.370846 CCTTCCCTCTGCATACATCAACA 60.371 47.826 0.00 0.00 0.00 3.33
2795 5045 3.016031 TCAACAACACACTGTGAGCAAT 58.984 40.909 16.30 0.00 36.96 3.56
2797 5047 4.035091 TCAACAACACACTGTGAGCAATAC 59.965 41.667 16.30 0.00 36.96 1.89
2813 5063 4.341235 AGCAATACAGTTGTCGCCTCTATA 59.659 41.667 0.00 0.00 0.00 1.31
2844 5095 4.843220 AAGTGGAGCAATCTTGTTGAAG 57.157 40.909 0.00 0.00 0.00 3.02
2854 5120 3.297134 TCTTGTTGAAGCCCAGAAGTT 57.703 42.857 0.00 0.00 0.00 2.66
2855 5121 3.631250 TCTTGTTGAAGCCCAGAAGTTT 58.369 40.909 0.00 0.00 0.00 2.66
2856 5122 3.381272 TCTTGTTGAAGCCCAGAAGTTTG 59.619 43.478 0.00 0.00 0.00 2.93
2857 5123 3.011566 TGTTGAAGCCCAGAAGTTTGA 57.988 42.857 0.00 0.00 0.00 2.69
2858 5124 3.360867 TGTTGAAGCCCAGAAGTTTGAA 58.639 40.909 0.00 0.00 0.00 2.69
2859 5125 3.381272 TGTTGAAGCCCAGAAGTTTGAAG 59.619 43.478 0.00 0.00 0.00 3.02
2860 5126 3.576078 TGAAGCCCAGAAGTTTGAAGA 57.424 42.857 0.00 0.00 0.00 2.87
2861 5127 3.897239 TGAAGCCCAGAAGTTTGAAGAA 58.103 40.909 0.00 0.00 0.00 2.52
2862 5128 4.277476 TGAAGCCCAGAAGTTTGAAGAAA 58.723 39.130 0.00 0.00 0.00 2.52
2863 5129 4.097892 TGAAGCCCAGAAGTTTGAAGAAAC 59.902 41.667 0.00 0.00 41.69 2.78
2864 5130 3.631250 AGCCCAGAAGTTTGAAGAAACA 58.369 40.909 0.00 0.00 43.51 2.83
2865 5131 4.023291 AGCCCAGAAGTTTGAAGAAACAA 58.977 39.130 0.00 0.00 43.51 2.83
2866 5132 4.112634 GCCCAGAAGTTTGAAGAAACAAC 58.887 43.478 0.00 0.00 43.51 3.32
2867 5133 4.351192 CCCAGAAGTTTGAAGAAACAACG 58.649 43.478 0.00 0.00 43.51 4.10
2868 5134 4.142469 CCCAGAAGTTTGAAGAAACAACGT 60.142 41.667 0.00 0.00 43.51 3.99
2871 5137 7.024768 CCAGAAGTTTGAAGAAACAACGTAAA 58.975 34.615 0.00 0.00 43.51 2.01
2895 5161 1.816835 AGTCGTCGATGTACACACCAT 59.183 47.619 0.00 0.00 0.00 3.55
2927 5198 4.011966 TCATGATCTGGCATATCACCAC 57.988 45.455 16.62 0.00 36.24 4.16
2938 5209 1.335132 TATCACCACCCCGGAGAAGC 61.335 60.000 0.73 0.00 37.96 3.86
2945 5216 1.684049 CCCCGGAGAAGCTGAGACT 60.684 63.158 0.73 0.00 0.00 3.24
2947 5218 1.515020 CCGGAGAAGCTGAGACTGG 59.485 63.158 0.00 0.00 0.00 4.00
2982 5253 2.206576 AATCCAACTCTTGCCAGGTC 57.793 50.000 0.00 0.00 0.00 3.85
2986 5257 0.034059 CAACTCTTGCCAGGTCGAGT 59.966 55.000 0.00 2.62 38.29 4.18
2991 5262 0.970937 CTTGCCAGGTCGAGTAGGGA 60.971 60.000 0.00 0.00 0.00 4.20
3070 5341 7.254932 GGACAAGTATGCAGATCAAAATCCTAC 60.255 40.741 0.00 0.00 31.78 3.18
3075 5346 5.592104 TGCAGATCAAAATCCTACGACTA 57.408 39.130 0.00 0.00 31.78 2.59
3140 5415 2.825532 GACATGCCACCCAAATTAGTGT 59.174 45.455 0.00 0.00 31.88 3.55
3145 5420 2.166254 GCCACCCAAATTAGTGTCATGG 59.834 50.000 0.00 0.00 31.88 3.66
3186 5486 8.598075 GCATTCATTTTAATGTGACATTTCCTC 58.402 33.333 16.75 0.00 38.78 3.71
3248 5548 3.564511 CATTTGGCGAGTGTTTTACCAG 58.435 45.455 0.00 0.00 0.00 4.00
3259 5559 6.243216 AGTGTTTTACCAGTTTCTACTCCA 57.757 37.500 0.00 0.00 30.26 3.86
3260 5560 6.838382 AGTGTTTTACCAGTTTCTACTCCAT 58.162 36.000 0.00 0.00 30.26 3.41
3287 5588 4.213674 CGTAGTTTTGTTCGCTTTTACCC 58.786 43.478 0.00 0.00 0.00 3.69
3318 5619 7.727181 AGCAATCTATTATCGTCCTGTTAGTT 58.273 34.615 0.00 0.00 0.00 2.24
3319 5620 8.857098 AGCAATCTATTATCGTCCTGTTAGTTA 58.143 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 142 1.736586 GAGACTGATGGCCGACGAT 59.263 57.895 0.00 0.00 0.00 3.73
219 228 1.336125 CGGGTCCAAGTACTCCGATAC 59.664 57.143 13.25 0.67 42.94 2.24
309 318 1.796190 CGGAGATTCATCGGAGCGGA 61.796 60.000 0.00 0.00 0.00 5.54
722 733 2.024414 GTGAAACTGACAAGTTGGCCT 58.976 47.619 6.18 0.00 46.15 5.19
931 942 4.883354 CGGGCTGGGAATGGGCTC 62.883 72.222 0.00 0.00 0.00 4.70
937 948 1.918293 TGAGTGTCGGGCTGGGAAT 60.918 57.895 0.00 0.00 0.00 3.01
941 952 3.680786 TCGTGAGTGTCGGGCTGG 61.681 66.667 0.00 0.00 0.00 4.85
953 964 2.130073 CTGTGGCTCGTGAGTCGTGA 62.130 60.000 0.00 0.00 40.80 4.35
954 965 1.730902 CTGTGGCTCGTGAGTCGTG 60.731 63.158 0.00 0.00 40.80 4.35
955 966 2.645567 CTGTGGCTCGTGAGTCGT 59.354 61.111 0.00 0.00 40.80 4.34
956 967 2.807045 GCTGTGGCTCGTGAGTCG 60.807 66.667 0.00 0.00 35.37 4.18
957 968 2.807045 CGCTGTGGCTCGTGAGTC 60.807 66.667 0.00 0.00 36.09 3.36
1027 1063 1.065928 CGCCGAGGTCTATGTCCAC 59.934 63.158 0.00 0.00 0.00 4.02
1695 1823 2.991866 GTCGCTTCTGTTAAGGTACCAC 59.008 50.000 15.94 4.10 0.00 4.16
2016 2147 3.680338 GACGTCGGCCGAGAACTCC 62.680 68.421 31.97 15.12 40.70 3.85
2322 2456 3.865745 AGCAGGTGAAAATAACGATCGAG 59.134 43.478 24.34 0.00 0.00 4.04
2366 3382 9.868160 TCACAAGATATAGTGATTCTCTAAGGA 57.132 33.333 0.00 0.00 39.65 3.36
2480 4717 6.210078 TCTGAAAGAAGAAAGTTCGTCTCTC 58.790 40.000 9.47 6.65 42.31 3.20
2481 4718 6.150396 TCTGAAAGAAGAAAGTTCGTCTCT 57.850 37.500 9.47 0.00 42.31 3.10
2567 4804 9.083080 GCCAGCTTCAAAACGTATTATAAAAAT 57.917 29.630 0.00 0.00 0.00 1.82
2568 4805 8.082852 TGCCAGCTTCAAAACGTATTATAAAAA 58.917 29.630 0.00 0.00 0.00 1.94
2569 4806 7.594714 TGCCAGCTTCAAAACGTATTATAAAA 58.405 30.769 0.00 0.00 0.00 1.52
2570 4807 7.147143 TGCCAGCTTCAAAACGTATTATAAA 57.853 32.000 0.00 0.00 0.00 1.40
2571 4808 6.745159 TGCCAGCTTCAAAACGTATTATAA 57.255 33.333 0.00 0.00 0.00 0.98
2572 4809 6.935741 ATGCCAGCTTCAAAACGTATTATA 57.064 33.333 0.00 0.00 0.00 0.98
2573 4810 5.835113 ATGCCAGCTTCAAAACGTATTAT 57.165 34.783 0.00 0.00 0.00 1.28
2574 4811 5.182190 TCAATGCCAGCTTCAAAACGTATTA 59.818 36.000 0.00 0.00 0.00 0.98
2575 4812 4.022416 TCAATGCCAGCTTCAAAACGTATT 60.022 37.500 0.00 0.00 0.00 1.89
2576 4813 3.505680 TCAATGCCAGCTTCAAAACGTAT 59.494 39.130 0.00 0.00 0.00 3.06
2577 4814 2.881513 TCAATGCCAGCTTCAAAACGTA 59.118 40.909 0.00 0.00 0.00 3.57
2578 4815 1.680735 TCAATGCCAGCTTCAAAACGT 59.319 42.857 0.00 0.00 0.00 3.99
2579 4816 2.287788 ACTCAATGCCAGCTTCAAAACG 60.288 45.455 0.00 0.00 0.00 3.60
2580 4817 3.375782 ACTCAATGCCAGCTTCAAAAC 57.624 42.857 0.00 0.00 0.00 2.43
2581 4818 3.132646 ACAACTCAATGCCAGCTTCAAAA 59.867 39.130 0.00 0.00 0.00 2.44
2582 4819 2.694628 ACAACTCAATGCCAGCTTCAAA 59.305 40.909 0.00 0.00 0.00 2.69
2583 4820 2.309613 ACAACTCAATGCCAGCTTCAA 58.690 42.857 0.00 0.00 0.00 2.69
2584 4821 1.985473 ACAACTCAATGCCAGCTTCA 58.015 45.000 0.00 0.00 0.00 3.02
2585 4822 3.375782 AAACAACTCAATGCCAGCTTC 57.624 42.857 0.00 0.00 0.00 3.86
2586 4823 3.460103 CAAAACAACTCAATGCCAGCTT 58.540 40.909 0.00 0.00 0.00 3.74
2587 4824 2.804212 GCAAAACAACTCAATGCCAGCT 60.804 45.455 0.00 0.00 0.00 4.24
2588 4825 1.528161 GCAAAACAACTCAATGCCAGC 59.472 47.619 0.00 0.00 0.00 4.85
2589 4826 1.788308 CGCAAAACAACTCAATGCCAG 59.212 47.619 0.00 0.00 33.55 4.85
2590 4827 1.850377 CGCAAAACAACTCAATGCCA 58.150 45.000 0.00 0.00 33.55 4.92
2591 4828 0.508213 GCGCAAAACAACTCAATGCC 59.492 50.000 0.30 0.00 33.55 4.40
2592 4829 1.453148 GAGCGCAAAACAACTCAATGC 59.547 47.619 11.47 0.00 0.00 3.56
2593 4830 2.722629 CAGAGCGCAAAACAACTCAATG 59.277 45.455 11.47 0.00 0.00 2.82
2594 4831 2.358898 ACAGAGCGCAAAACAACTCAAT 59.641 40.909 11.47 0.00 0.00 2.57
2595 4832 1.742831 ACAGAGCGCAAAACAACTCAA 59.257 42.857 11.47 0.00 0.00 3.02
2596 4833 1.063912 CACAGAGCGCAAAACAACTCA 59.936 47.619 11.47 0.00 0.00 3.41
2597 4834 1.064060 ACACAGAGCGCAAAACAACTC 59.936 47.619 11.47 0.00 0.00 3.01
2598 4835 1.094785 ACACAGAGCGCAAAACAACT 58.905 45.000 11.47 0.00 0.00 3.16
2599 4836 1.191096 CACACAGAGCGCAAAACAAC 58.809 50.000 11.47 0.00 0.00 3.32
2600 4837 1.090728 TCACACAGAGCGCAAAACAA 58.909 45.000 11.47 0.00 0.00 2.83
2601 4838 1.090728 TTCACACAGAGCGCAAAACA 58.909 45.000 11.47 0.00 0.00 2.83
2602 4839 2.405892 ATTCACACAGAGCGCAAAAC 57.594 45.000 11.47 0.00 0.00 2.43
2603 4840 2.098934 ACAATTCACACAGAGCGCAAAA 59.901 40.909 11.47 0.00 0.00 2.44
2604 4841 1.675483 ACAATTCACACAGAGCGCAAA 59.325 42.857 11.47 0.00 0.00 3.68
2605 4842 1.264020 GACAATTCACACAGAGCGCAA 59.736 47.619 11.47 0.00 0.00 4.85
2606 4843 0.867746 GACAATTCACACAGAGCGCA 59.132 50.000 11.47 0.00 0.00 6.09
2607 4844 1.151668 AGACAATTCACACAGAGCGC 58.848 50.000 0.00 0.00 0.00 5.92
2608 4845 4.664139 CGTTTAGACAATTCACACAGAGCG 60.664 45.833 0.00 0.00 0.00 5.03
2609 4846 4.211374 ACGTTTAGACAATTCACACAGAGC 59.789 41.667 0.00 0.00 0.00 4.09
2610 4847 5.692204 AGACGTTTAGACAATTCACACAGAG 59.308 40.000 0.00 0.00 0.00 3.35
2611 4848 5.597806 AGACGTTTAGACAATTCACACAGA 58.402 37.500 0.00 0.00 0.00 3.41
2612 4849 5.907197 AGACGTTTAGACAATTCACACAG 57.093 39.130 0.00 0.00 0.00 3.66
2613 4850 7.956420 ATAAGACGTTTAGACAATTCACACA 57.044 32.000 0.00 0.00 0.00 3.72
2618 4855 9.983804 CCCTTTTATAAGACGTTTAGACAATTC 57.016 33.333 0.00 0.00 32.92 2.17
2619 4856 9.729281 TCCCTTTTATAAGACGTTTAGACAATT 57.271 29.630 0.00 0.00 32.92 2.32
2620 4857 9.729281 TTCCCTTTTATAAGACGTTTAGACAAT 57.271 29.630 0.00 0.00 32.92 2.71
2621 4858 9.558396 TTTCCCTTTTATAAGACGTTTAGACAA 57.442 29.630 0.00 0.00 32.92 3.18
2622 4859 9.558396 TTTTCCCTTTTATAAGACGTTTAGACA 57.442 29.630 0.00 0.00 32.92 3.41
2682 4919 6.033966 GGTTTTATCTACATTTGGCTTTCGG 58.966 40.000 0.00 0.00 0.00 4.30
2734 4972 4.738528 GTTGCAAAAACTTCAACGACTC 57.261 40.909 0.00 0.00 32.10 3.36
2754 4992 1.264749 TGTATGCAGAGGGAAGGCGT 61.265 55.000 0.00 0.00 0.00 5.68
2757 5007 3.209410 GTTGATGTATGCAGAGGGAAGG 58.791 50.000 0.00 0.00 0.00 3.46
2776 5026 3.944650 TGTATTGCTCACAGTGTGTTGTT 59.055 39.130 22.29 8.13 34.79 2.83
2795 5045 3.881688 GAGGTATAGAGGCGACAACTGTA 59.118 47.826 0.00 0.00 0.00 2.74
2797 5047 2.034812 GGAGGTATAGAGGCGACAACTG 59.965 54.545 0.00 0.00 0.00 3.16
2844 5095 4.112634 GTTGTTTCTTCAAACTTCTGGGC 58.887 43.478 0.00 0.00 42.29 5.36
2854 5120 6.455913 CGACTTCCTTTACGTTGTTTCTTCAA 60.456 38.462 0.00 0.00 0.00 2.69
2855 5121 5.005971 CGACTTCCTTTACGTTGTTTCTTCA 59.994 40.000 0.00 0.00 0.00 3.02
2856 5122 5.006068 ACGACTTCCTTTACGTTGTTTCTTC 59.994 40.000 0.00 0.00 35.47 2.87
2857 5123 4.872124 ACGACTTCCTTTACGTTGTTTCTT 59.128 37.500 0.00 0.00 35.47 2.52
2858 5124 4.436332 ACGACTTCCTTTACGTTGTTTCT 58.564 39.130 0.00 0.00 35.47 2.52
2859 5125 4.604697 CGACGACTTCCTTTACGTTGTTTC 60.605 45.833 0.00 0.00 39.04 2.78
2860 5126 3.243643 CGACGACTTCCTTTACGTTGTTT 59.756 43.478 0.00 0.00 39.04 2.83
2861 5127 2.791004 CGACGACTTCCTTTACGTTGTT 59.209 45.455 0.00 0.00 39.04 2.83
2862 5128 2.033299 TCGACGACTTCCTTTACGTTGT 59.967 45.455 0.00 0.00 39.92 3.32
2863 5129 2.653890 TCGACGACTTCCTTTACGTTG 58.346 47.619 0.00 0.00 39.04 4.10
2864 5130 3.240069 CATCGACGACTTCCTTTACGTT 58.760 45.455 0.00 0.00 39.04 3.99
2865 5131 2.227388 ACATCGACGACTTCCTTTACGT 59.773 45.455 0.00 0.00 41.57 3.57
2866 5132 2.860062 ACATCGACGACTTCCTTTACG 58.140 47.619 0.00 0.00 0.00 3.18
2867 5133 4.556523 GTGTACATCGACGACTTCCTTTAC 59.443 45.833 0.00 0.00 0.00 2.01
2868 5134 4.216042 TGTGTACATCGACGACTTCCTTTA 59.784 41.667 0.00 0.00 0.00 1.85
2871 5137 2.095364 GTGTGTACATCGACGACTTCCT 60.095 50.000 0.00 0.00 0.00 3.36
2895 5161 4.141959 TGCCAGATCATGATTGACGTCTTA 60.142 41.667 17.92 5.22 33.85 2.10
2927 5198 1.684049 AGTCTCAGCTTCTCCGGGG 60.684 63.158 0.00 0.00 0.00 5.73
2938 5209 0.536260 CTGGCTCTTCCCAGTCTCAG 59.464 60.000 0.10 0.00 45.87 3.35
2945 5216 4.017591 TGGATTATTTTCTGGCTCTTCCCA 60.018 41.667 0.00 0.00 0.00 4.37
2947 5218 5.654209 AGTTGGATTATTTTCTGGCTCTTCC 59.346 40.000 0.00 0.00 0.00 3.46
2982 5253 2.848691 AGGTTCGTATCTCCCTACTCG 58.151 52.381 0.00 0.00 0.00 4.18
2986 5257 2.742348 TGCAAGGTTCGTATCTCCCTA 58.258 47.619 0.00 0.00 0.00 3.53
2991 5262 3.335579 GGAACTTGCAAGGTTCGTATCT 58.664 45.455 29.18 2.92 42.58 1.98
3112 5383 0.036732 TGGGTGGCATGTCTCTTGAC 59.963 55.000 0.00 0.00 43.20 3.18
3126 5401 6.773976 ATAACCATGACACTAATTTGGGTG 57.226 37.500 0.00 2.25 39.13 4.61
3232 5532 2.876550 AGAAACTGGTAAAACACTCGCC 59.123 45.455 0.00 0.00 0.00 5.54
3248 5548 7.895975 AAACTACGGTTAATGGAGTAGAAAC 57.104 36.000 8.25 0.00 38.96 2.78
3259 5559 5.678132 AAGCGAACAAAACTACGGTTAAT 57.322 34.783 0.00 0.00 42.80 1.40
3260 5560 5.482686 AAAGCGAACAAAACTACGGTTAA 57.517 34.783 0.00 0.00 43.56 2.01
3287 5588 7.604164 ACAGGACGATAATAGATTGCTAAATGG 59.396 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.