Multiple sequence alignment - TraesCS5A01G173800

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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 TraesCS5A01G173800 chr5A 100.000 3727 0 0 1 3727 367101177 367097451 0.000000e+00 6883
1 TraesCS5A01G173800 chr5B 95.307 2898 91 15 845 3727 315910045 315907178 0.000000e+00 4556
2 TraesCS5A01G173800 chr5B 93.003 586 34 6 1 582 315918820 315918238 0.000000e+00 848
3 TraesCS5A01G173800 chr5D 91.546 2626 123 32 845 3447 277728014 277725465 0.000000e+00 3528
4 TraesCS5A01G173800 chr5D 87.944 788 59 20 1 768 277728805 277728034 0.000000e+00 896
5 TraesCS5A01G173800 chr5D 89.888 89 4 4 3451 3538 277725310 277725226 3.940000e-20 110


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 TraesCS5A01G173800 chr5A 367097451 367101177 3726 True 6883.000000 6883 100.000000 1 3727 1 chr5A.!!$R1 3726
1 TraesCS5A01G173800 chr5B 315907178 315910045 2867 True 4556.000000 4556 95.307000 845 3727 1 chr5B.!!$R1 2882
2 TraesCS5A01G173800 chr5B 315918238 315918820 582 True 848.000000 848 93.003000 1 582 1 chr5B.!!$R2 581
3 TraesCS5A01G173800 chr5D 277725226 277728805 3579 True 1511.333333 3528 89.792667 1 3538 3 chr5D.!!$R1 3537

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
806 829 0.251608 TAAGGGGGCTGTTTTCTGGC 60.252 55.000 0.00 0.00 42.01 4.85 F
826 849 0.537143 TGGAAGCACCGTGAGCAATT 60.537 50.000 1.65 0.00 42.61 2.32 F
827 850 0.598065 GGAAGCACCGTGAGCAATTT 59.402 50.000 1.65 0.00 0.00 1.82 F
873 896 1.153862 GAGAGCAGAGCACGTCCTG 60.154 63.158 0.00 5.12 0.00 3.86 F
2251 2293 1.266989 GCTAGTGTGCAGTTGTTTCCC 59.733 52.381 0.00 0.00 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1857 1.183549 ACGACGGGATGAAGCTTACT 58.816 50.000 0.0 0.0 0.00 2.24 R
2347 2391 1.331214 ACATGCAAAGTTGGTCCTGG 58.669 50.000 0.0 0.0 0.00 4.45 R
2502 2546 1.542915 GCGGTCTACCACTACACTTGA 59.457 52.381 0.0 0.0 35.14 3.02 R
2503 2547 1.544691 AGCGGTCTACCACTACACTTG 59.455 52.381 0.0 0.0 35.14 3.16 R
3108 3155 0.951558 AATTCGGAGCAGCAAAACGT 59.048 45.000 0.0 0.0 0.00 3.99 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
196 197 2.726351 CCAGGCCTCGTCTCCCTTC 61.726 68.421 0.00 0.00 0.00 3.46
211 212 2.420058 CCTTCATAAGGTGGGACCAC 57.580 55.000 13.03 13.03 43.95 4.16
341 342 6.693315 AAAGCATGCGTAACATATTACCTT 57.307 33.333 13.01 0.00 37.94 3.50
360 362 0.991920 TCAGAAAAGAGGGCCCGAAT 59.008 50.000 18.44 2.76 0.00 3.34
381 383 6.526674 CGAATCTGGGTAAAAACTTTATGTGC 59.473 38.462 0.00 0.00 0.00 4.57
382 384 6.909550 ATCTGGGTAAAAACTTTATGTGCA 57.090 33.333 0.00 0.00 0.00 4.57
386 388 8.207545 TCTGGGTAAAAACTTTATGTGCATTTT 58.792 29.630 0.00 0.00 0.00 1.82
387 389 9.482627 CTGGGTAAAAACTTTATGTGCATTTTA 57.517 29.630 0.00 0.00 0.00 1.52
404 406 8.448615 GTGCATTTTATTCGAGTACTTTAGGTT 58.551 33.333 0.00 0.00 0.00 3.50
445 447 3.057806 GCTTTAATGCGGGTTTGTACACT 60.058 43.478 0.00 0.00 0.00 3.55
549 553 9.108284 CACAAAATTCAAAATTCAACCTAGGTT 57.892 29.630 21.96 21.96 39.13 3.50
557 561 5.914898 AATTCAACCTAGGTTTACATGCC 57.085 39.130 24.99 0.00 36.00 4.40
586 608 6.393171 AGCAAAAGGATAAAAATCAGAGTGC 58.607 36.000 0.00 0.00 0.00 4.40
623 645 0.451783 GGTGGCGTGTGAAATCATCC 59.548 55.000 0.00 0.00 0.00 3.51
628 650 3.320541 TGGCGTGTGAAATCATCCTTTTT 59.679 39.130 0.00 0.00 0.00 1.94
642 664 5.989777 TCATCCTTTTTAGATAGCTAACCGC 59.010 40.000 0.00 0.00 36.37 5.68
673 695 1.967319 AGTGCCTGAAATCACACGTT 58.033 45.000 0.00 0.00 38.08 3.99
683 705 7.753132 GCCTGAAATCACACGTTAATATTCAAA 59.247 33.333 0.00 0.00 0.00 2.69
708 730 2.230750 AGATTTGCTCCTTTTCAGCTGC 59.769 45.455 9.47 0.00 37.79 5.25
745 768 9.553418 TTGACATGAATTTTGTGATATTGTACG 57.447 29.630 0.00 0.00 0.00 3.67
762 785 5.001237 TGTACGTACATACCCAATGACTG 57.999 43.478 24.10 0.00 39.07 3.51
765 788 4.901868 ACGTACATACCCAATGACTGTTT 58.098 39.130 0.00 0.00 39.07 2.83
766 789 4.693566 ACGTACATACCCAATGACTGTTTG 59.306 41.667 0.00 0.00 39.07 2.93
767 790 4.693566 CGTACATACCCAATGACTGTTTGT 59.306 41.667 0.00 0.00 39.07 2.83
770 793 7.095144 CGTACATACCCAATGACTGTTTGTTTA 60.095 37.037 0.00 0.00 39.07 2.01
771 794 7.589958 ACATACCCAATGACTGTTTGTTTAA 57.410 32.000 0.00 0.00 39.07 1.52
772 795 7.657336 ACATACCCAATGACTGTTTGTTTAAG 58.343 34.615 0.00 0.00 39.07 1.85
773 796 7.504238 ACATACCCAATGACTGTTTGTTTAAGA 59.496 33.333 0.00 0.00 39.07 2.10
774 797 6.783708 ACCCAATGACTGTTTGTTTAAGAA 57.216 33.333 0.00 0.00 0.00 2.52
778 801 8.387354 CCCAATGACTGTTTGTTTAAGAAAAAC 58.613 33.333 0.00 0.00 34.97 2.43
782 805 9.868277 ATGACTGTTTGTTTAAGAAAAACATGA 57.132 25.926 0.00 0.00 41.52 3.07
794 817 9.785982 TTAAGAAAAACATGATTTTTAAGGGGG 57.214 29.630 14.06 0.00 32.85 5.40
795 818 6.237901 AGAAAAACATGATTTTTAAGGGGGC 58.762 36.000 14.06 0.81 32.85 5.80
796 819 5.841267 AAAACATGATTTTTAAGGGGGCT 57.159 34.783 0.00 0.00 0.00 5.19
797 820 4.824479 AACATGATTTTTAAGGGGGCTG 57.176 40.909 0.00 0.00 0.00 4.85
798 821 3.790126 ACATGATTTTTAAGGGGGCTGT 58.210 40.909 0.00 0.00 0.00 4.40
799 822 4.167319 ACATGATTTTTAAGGGGGCTGTT 58.833 39.130 0.00 0.00 0.00 3.16
800 823 4.597075 ACATGATTTTTAAGGGGGCTGTTT 59.403 37.500 0.00 0.00 0.00 2.83
801 824 5.073008 ACATGATTTTTAAGGGGGCTGTTTT 59.927 36.000 0.00 0.00 0.00 2.43
802 825 5.222079 TGATTTTTAAGGGGGCTGTTTTC 57.778 39.130 0.00 0.00 0.00 2.29
803 826 4.904853 TGATTTTTAAGGGGGCTGTTTTCT 59.095 37.500 0.00 0.00 0.00 2.52
804 827 4.681074 TTTTTAAGGGGGCTGTTTTCTG 57.319 40.909 0.00 0.00 0.00 3.02
805 828 2.302587 TTAAGGGGGCTGTTTTCTGG 57.697 50.000 0.00 0.00 0.00 3.86
806 829 0.251608 TAAGGGGGCTGTTTTCTGGC 60.252 55.000 0.00 0.00 42.01 4.85
823 846 2.031012 CTGGAAGCACCGTGAGCA 59.969 61.111 1.65 0.00 42.61 4.26
824 847 1.597854 CTGGAAGCACCGTGAGCAA 60.598 57.895 1.65 0.00 42.61 3.91
825 848 0.957395 CTGGAAGCACCGTGAGCAAT 60.957 55.000 1.65 0.00 42.61 3.56
826 849 0.537143 TGGAAGCACCGTGAGCAATT 60.537 50.000 1.65 0.00 42.61 2.32
827 850 0.598065 GGAAGCACCGTGAGCAATTT 59.402 50.000 1.65 0.00 0.00 1.82
828 851 1.810151 GGAAGCACCGTGAGCAATTTA 59.190 47.619 1.65 0.00 0.00 1.40
829 852 2.423538 GGAAGCACCGTGAGCAATTTAT 59.576 45.455 1.65 0.00 0.00 1.40
830 853 3.119495 GGAAGCACCGTGAGCAATTTATT 60.119 43.478 1.65 0.00 0.00 1.40
831 854 4.485163 GAAGCACCGTGAGCAATTTATTT 58.515 39.130 1.65 0.00 0.00 1.40
832 855 4.519540 AGCACCGTGAGCAATTTATTTT 57.480 36.364 1.65 0.00 0.00 1.82
833 856 4.485163 AGCACCGTGAGCAATTTATTTTC 58.515 39.130 1.65 0.00 0.00 2.29
834 857 4.218417 AGCACCGTGAGCAATTTATTTTCT 59.782 37.500 1.65 0.00 0.00 2.52
835 858 4.923281 GCACCGTGAGCAATTTATTTTCTT 59.077 37.500 1.65 0.00 0.00 2.52
836 859 5.405269 GCACCGTGAGCAATTTATTTTCTTT 59.595 36.000 1.65 0.00 0.00 2.52
837 860 6.073819 GCACCGTGAGCAATTTATTTTCTTTT 60.074 34.615 1.65 0.00 0.00 2.27
838 861 7.282916 CACCGTGAGCAATTTATTTTCTTTTG 58.717 34.615 0.00 0.00 0.00 2.44
839 862 7.168972 CACCGTGAGCAATTTATTTTCTTTTGA 59.831 33.333 0.00 0.00 0.00 2.69
840 863 7.382218 ACCGTGAGCAATTTATTTTCTTTTGAG 59.618 33.333 0.00 0.00 0.00 3.02
841 864 7.222654 CGTGAGCAATTTATTTTCTTTTGAGC 58.777 34.615 0.00 0.00 0.00 4.26
842 865 7.222654 GTGAGCAATTTATTTTCTTTTGAGCG 58.777 34.615 0.00 0.00 0.00 5.03
843 866 7.114811 GTGAGCAATTTATTTTCTTTTGAGCGA 59.885 33.333 0.00 0.00 0.00 4.93
853 876 1.227999 TTTTGAGCGAGGAAGCACCG 61.228 55.000 0.00 0.00 44.74 4.94
854 877 2.377628 TTTGAGCGAGGAAGCACCGT 62.378 55.000 0.00 0.00 44.74 4.83
855 878 2.811317 GAGCGAGGAAGCACCGTG 60.811 66.667 0.00 0.00 44.74 4.94
856 879 3.282745 GAGCGAGGAAGCACCGTGA 62.283 63.158 1.65 0.00 44.74 4.35
873 896 1.153862 GAGAGCAGAGCACGTCCTG 60.154 63.158 0.00 5.12 0.00 3.86
900 923 2.811101 CACAGCGGCCCAACAAAA 59.189 55.556 0.00 0.00 0.00 2.44
967 995 2.616893 CCACCCCATTCCTCCCCA 60.617 66.667 0.00 0.00 0.00 4.96
978 1006 4.394712 CTCCCCACACCCGTGCTC 62.395 72.222 0.00 0.00 42.17 4.26
979 1007 4.954118 TCCCCACACCCGTGCTCT 62.954 66.667 0.00 0.00 42.17 4.09
981 1009 3.314331 CCCACACCCGTGCTCTCT 61.314 66.667 0.00 0.00 42.17 3.10
982 1010 2.262915 CCACACCCGTGCTCTCTC 59.737 66.667 0.00 0.00 42.17 3.20
984 1012 2.203640 ACACCCGTGCTCTCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
985 1013 2.279069 ACACCCGTGCTCTCTCCAG 61.279 63.158 0.00 0.00 0.00 3.86
986 1014 2.681778 ACCCGTGCTCTCTCCAGG 60.682 66.667 0.00 0.00 0.00 4.45
1328 1362 2.422479 AGTGCAATGTAATGCTGCTCTG 59.578 45.455 0.00 0.00 46.54 3.35
1338 1372 2.028190 CTGCTCTGGTATCGGCGG 59.972 66.667 7.21 0.00 0.00 6.13
1391 1425 1.607148 TCATCTGGTCGCGATAACGAT 59.393 47.619 14.06 9.60 45.06 3.73
1466 1500 8.999431 GTCCTTATCATGTTCTTGTTCTTGTTA 58.001 33.333 0.00 0.00 0.00 2.41
1467 1501 9.739276 TCCTTATCATGTTCTTGTTCTTGTTAT 57.261 29.630 0.00 0.00 0.00 1.89
1630 1664 7.035612 CCTGCCAATTTTACAAGATAGAAACC 58.964 38.462 0.00 0.00 0.00 3.27
1632 1666 7.375053 TGCCAATTTTACAAGATAGAAACCAC 58.625 34.615 0.00 0.00 0.00 4.16
1816 1857 3.340928 CATTGAGAGCCTGAATGACACA 58.659 45.455 8.09 0.00 37.27 3.72
2194 2236 3.412386 AGCTGCGGTTTCTACTTTCAAT 58.588 40.909 0.00 0.00 0.00 2.57
2251 2293 1.266989 GCTAGTGTGCAGTTGTTTCCC 59.733 52.381 0.00 0.00 0.00 3.97
2252 2294 2.571212 CTAGTGTGCAGTTGTTTCCCA 58.429 47.619 0.00 0.00 0.00 4.37
2274 2316 6.403964 CCCAATCACATTACATCACTTGACAG 60.404 42.308 0.00 0.00 0.00 3.51
2276 2318 7.334171 CCAATCACATTACATCACTTGACAGTA 59.666 37.037 0.00 0.00 0.00 2.74
2277 2319 8.720562 CAATCACATTACATCACTTGACAGTAA 58.279 33.333 7.97 7.97 34.55 2.24
2289 2333 6.479001 TCACTTGACAGTAAAAAGCAGACTAC 59.521 38.462 0.00 0.00 0.00 2.73
2318 2362 5.817296 TCAAAACTTGATATGCGACAGCTAT 59.183 36.000 0.00 0.00 38.40 2.97
2509 2553 4.881273 TGTAAGCAACATCTGTTCAAGTGT 59.119 37.500 0.00 0.00 35.83 3.55
2743 2789 4.214971 AGCATAGGCATAGCAGAAATTTCG 59.785 41.667 12.42 8.75 44.61 3.46
2752 2798 2.165030 AGCAGAAATTTCGCATTGGAGG 59.835 45.455 25.73 7.96 32.08 4.30
2854 2900 5.393461 CCTTTGATGTAATTTCACTCTGGCC 60.393 44.000 0.00 0.00 0.00 5.36
2862 2908 1.289160 TTCACTCTGGCCCTAAGCAT 58.711 50.000 0.00 0.00 46.50 3.79
2967 3013 6.420903 CAGCATTTCTAAATGATTGCTCATGG 59.579 38.462 17.46 0.00 46.72 3.66
3047 3094 3.788775 GCTTTCAGCAAGAGCAAGG 57.211 52.632 0.00 0.00 45.49 3.61
3108 3155 4.686091 CGTCAGAAACATAGACAGCAAGAA 59.314 41.667 0.00 0.00 32.68 2.52
3148 3195 9.512435 CGAATTCATGATTTAGCTTTTGAATCT 57.488 29.630 6.22 0.00 33.85 2.40
3172 3219 4.142227 GCCTGATGAGATGCTTTCAAATGT 60.142 41.667 0.00 0.00 0.00 2.71
3308 3359 4.758674 TCTGTCCTTTCTTCTGAAATGCTG 59.241 41.667 0.00 0.00 40.85 4.41
3363 3414 0.338814 AGTTATCGACCAGAGGGGGT 59.661 55.000 0.00 0.00 46.02 4.95
3381 3432 3.782443 GGGGCGTGAACGGGAGAT 61.782 66.667 4.84 0.00 40.23 2.75
3385 3436 0.879090 GGCGTGAACGGGAGATTTTT 59.121 50.000 4.84 0.00 40.23 1.94
3386 3437 1.135774 GGCGTGAACGGGAGATTTTTC 60.136 52.381 4.84 0.00 40.23 2.29
3410 3461 7.324178 TCTTTTTGACCATTTCTTCGGAAAAA 58.676 30.769 0.00 0.00 45.52 1.94
3424 3476 3.817148 GGAAAAACACGCTATCCGAAA 57.183 42.857 0.00 0.00 41.02 3.46
3526 3729 0.814457 AGAGTCAGAAGCACGCTAGG 59.186 55.000 0.00 0.00 0.00 3.02
3538 3741 5.189659 AGCACGCTAGGTAGAAGAAATAG 57.810 43.478 0.00 0.00 0.00 1.73
3543 3746 7.577979 CACGCTAGGTAGAAGAAATAGAGTAG 58.422 42.308 0.00 0.00 0.00 2.57
3598 3801 7.823745 ATGGAAAATACTCACACAAGTCTTT 57.176 32.000 0.00 0.00 29.70 2.52
3715 3918 5.063944 CGAAGGCACATAGATATGTTATGCC 59.936 44.000 18.43 18.43 45.90 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 0.690762 TCTTGGGCCTCACCTTGTAC 59.309 55.000 4.53 0.00 39.10 2.90
196 197 1.451387 GCCGTGGTCCCACCTTATG 60.451 63.158 10.77 0.00 43.49 1.90
341 342 0.991920 ATTCGGGCCCTCTTTTCTGA 59.008 50.000 22.43 3.53 0.00 3.27
360 362 6.909550 ATGCACATAAAGTTTTTACCCAGA 57.090 33.333 0.00 0.00 0.00 3.86
376 378 8.612619 CCTAAAGTACTCGAATAAAATGCACAT 58.387 33.333 0.00 0.00 0.00 3.21
386 388 5.916883 GCGCATAACCTAAAGTACTCGAATA 59.083 40.000 0.30 0.00 0.00 1.75
387 389 4.743644 GCGCATAACCTAAAGTACTCGAAT 59.256 41.667 0.30 0.00 0.00 3.34
392 394 4.809426 GTGATGCGCATAACCTAAAGTACT 59.191 41.667 25.14 0.00 0.00 2.73
400 402 2.928801 TATGGTGATGCGCATAACCT 57.071 45.000 42.75 32.80 41.99 3.50
404 406 2.006552 GCCGATATGGTGATGCGCATA 61.007 52.381 25.40 8.16 41.21 3.14
533 537 6.496911 AGGCATGTAAACCTAGGTTGAATTTT 59.503 34.615 27.75 13.31 38.47 1.82
549 553 4.854173 TCCTTTTGCTCATAGGCATGTAA 58.146 39.130 0.00 0.00 42.09 2.41
557 561 9.947669 CTCTGATTTTTATCCTTTTGCTCATAG 57.052 33.333 0.00 0.00 0.00 2.23
576 598 2.957402 TTGTCTTGGGCACTCTGATT 57.043 45.000 0.00 0.00 0.00 2.57
600 622 1.539388 TGATTTCACACGCCACCATTC 59.461 47.619 0.00 0.00 0.00 2.67
601 623 1.614996 TGATTTCACACGCCACCATT 58.385 45.000 0.00 0.00 0.00 3.16
608 630 5.938322 TCTAAAAAGGATGATTTCACACGC 58.062 37.500 0.00 0.00 0.00 5.34
642 664 2.809601 GGCACTACACCGCACGAG 60.810 66.667 0.00 0.00 0.00 4.18
649 671 2.484264 GTGTGATTTCAGGCACTACACC 59.516 50.000 0.00 0.00 36.02 4.16
651 673 2.224185 ACGTGTGATTTCAGGCACTACA 60.224 45.455 0.00 0.00 36.02 2.74
652 674 2.413837 ACGTGTGATTTCAGGCACTAC 58.586 47.619 0.00 0.00 36.02 2.73
653 675 2.831685 ACGTGTGATTTCAGGCACTA 57.168 45.000 0.00 0.00 36.02 2.74
654 676 1.967319 AACGTGTGATTTCAGGCACT 58.033 45.000 0.00 0.00 43.88 4.40
655 677 3.889196 TTAACGTGTGATTTCAGGCAC 57.111 42.857 0.00 0.00 35.63 5.01
656 678 6.372937 TGAATATTAACGTGTGATTTCAGGCA 59.627 34.615 0.00 0.00 0.00 4.75
657 679 6.781138 TGAATATTAACGTGTGATTTCAGGC 58.219 36.000 0.00 0.00 0.00 4.85
683 705 5.182760 CAGCTGAAAAGGAGCAAATCTAAGT 59.817 40.000 8.42 0.00 39.05 2.24
694 716 0.731417 CATCCGCAGCTGAAAAGGAG 59.269 55.000 20.43 9.68 34.14 3.69
708 730 2.014335 TCATGTCAAGACTGCATCCG 57.986 50.000 1.53 0.00 0.00 4.18
745 768 6.569179 AACAAACAGTCATTGGGTATGTAC 57.431 37.500 0.00 0.00 35.64 2.90
752 775 8.387354 GTTTTTCTTAAACAAACAGTCATTGGG 58.613 33.333 0.00 0.00 31.81 4.12
753 776 8.930760 TGTTTTTCTTAAACAAACAGTCATTGG 58.069 29.630 0.92 0.00 35.88 3.16
770 793 6.714810 GCCCCCTTAAAAATCATGTTTTTCTT 59.285 34.615 13.48 3.88 34.01 2.52
771 794 6.044287 AGCCCCCTTAAAAATCATGTTTTTCT 59.956 34.615 13.48 7.89 34.01 2.52
772 795 6.149308 CAGCCCCCTTAAAAATCATGTTTTTC 59.851 38.462 13.48 1.42 34.01 2.29
773 796 6.003326 CAGCCCCCTTAAAAATCATGTTTTT 58.997 36.000 17.10 17.10 35.91 1.94
774 797 5.073008 ACAGCCCCCTTAAAAATCATGTTTT 59.927 36.000 0.00 0.00 35.02 2.43
778 801 4.824479 AACAGCCCCCTTAAAAATCATG 57.176 40.909 0.00 0.00 0.00 3.07
780 803 4.904853 AGAAAACAGCCCCCTTAAAAATCA 59.095 37.500 0.00 0.00 0.00 2.57
781 804 5.237815 CAGAAAACAGCCCCCTTAAAAATC 58.762 41.667 0.00 0.00 0.00 2.17
782 805 4.041567 CCAGAAAACAGCCCCCTTAAAAAT 59.958 41.667 0.00 0.00 0.00 1.82
784 807 2.969262 CCAGAAAACAGCCCCCTTAAAA 59.031 45.455 0.00 0.00 0.00 1.52
785 808 2.604139 CCAGAAAACAGCCCCCTTAAA 58.396 47.619 0.00 0.00 0.00 1.52
786 809 1.825641 GCCAGAAAACAGCCCCCTTAA 60.826 52.381 0.00 0.00 0.00 1.85
787 810 0.251608 GCCAGAAAACAGCCCCCTTA 60.252 55.000 0.00 0.00 0.00 2.69
788 811 1.533994 GCCAGAAAACAGCCCCCTT 60.534 57.895 0.00 0.00 0.00 3.95
789 812 2.118294 GCCAGAAAACAGCCCCCT 59.882 61.111 0.00 0.00 0.00 4.79
790 813 2.118294 AGCCAGAAAACAGCCCCC 59.882 61.111 0.00 0.00 0.00 5.40
791 814 2.278330 CCAGCCAGAAAACAGCCCC 61.278 63.158 0.00 0.00 0.00 5.80
792 815 0.827507 TTCCAGCCAGAAAACAGCCC 60.828 55.000 0.00 0.00 0.00 5.19
793 816 0.600057 CTTCCAGCCAGAAAACAGCC 59.400 55.000 0.00 0.00 0.00 4.85
794 817 0.038801 GCTTCCAGCCAGAAAACAGC 60.039 55.000 0.00 0.00 34.48 4.40
795 818 1.000938 GTGCTTCCAGCCAGAAAACAG 60.001 52.381 0.00 0.00 41.51 3.16
796 819 1.032014 GTGCTTCCAGCCAGAAAACA 58.968 50.000 0.00 0.00 41.51 2.83
797 820 0.315251 GGTGCTTCCAGCCAGAAAAC 59.685 55.000 0.00 0.00 41.51 2.43
798 821 1.172180 CGGTGCTTCCAGCCAGAAAA 61.172 55.000 0.00 0.00 41.51 2.29
799 822 1.600636 CGGTGCTTCCAGCCAGAAA 60.601 57.895 0.00 0.00 41.51 2.52
800 823 2.032528 CGGTGCTTCCAGCCAGAA 59.967 61.111 0.00 0.00 41.51 3.02
801 824 3.241530 ACGGTGCTTCCAGCCAGA 61.242 61.111 0.00 0.00 41.51 3.86
802 825 3.052082 CACGGTGCTTCCAGCCAG 61.052 66.667 0.00 0.00 41.51 4.85
803 826 3.535629 CTCACGGTGCTTCCAGCCA 62.536 63.158 2.51 0.00 41.51 4.75
804 827 2.743928 CTCACGGTGCTTCCAGCC 60.744 66.667 2.51 0.00 41.51 4.85
805 828 3.426568 GCTCACGGTGCTTCCAGC 61.427 66.667 2.51 3.05 42.82 4.85
806 829 0.957395 ATTGCTCACGGTGCTTCCAG 60.957 55.000 2.51 0.00 35.57 3.86
814 837 7.206687 TCAAAAGAAAATAAATTGCTCACGGT 58.793 30.769 0.00 0.00 0.00 4.83
821 844 6.586082 TCCTCGCTCAAAAGAAAATAAATTGC 59.414 34.615 0.00 0.00 0.00 3.56
822 845 8.519492 TTCCTCGCTCAAAAGAAAATAAATTG 57.481 30.769 0.00 0.00 0.00 2.32
823 846 7.329471 GCTTCCTCGCTCAAAAGAAAATAAATT 59.671 33.333 0.00 0.00 0.00 1.82
824 847 6.808704 GCTTCCTCGCTCAAAAGAAAATAAAT 59.191 34.615 0.00 0.00 0.00 1.40
825 848 6.149633 GCTTCCTCGCTCAAAAGAAAATAAA 58.850 36.000 0.00 0.00 0.00 1.40
826 849 5.240623 TGCTTCCTCGCTCAAAAGAAAATAA 59.759 36.000 0.00 0.00 0.00 1.40
827 850 4.759693 TGCTTCCTCGCTCAAAAGAAAATA 59.240 37.500 0.00 0.00 0.00 1.40
828 851 3.569701 TGCTTCCTCGCTCAAAAGAAAAT 59.430 39.130 0.00 0.00 0.00 1.82
829 852 2.948979 TGCTTCCTCGCTCAAAAGAAAA 59.051 40.909 0.00 0.00 0.00 2.29
830 853 2.290641 GTGCTTCCTCGCTCAAAAGAAA 59.709 45.455 0.00 0.00 0.00 2.52
831 854 1.873591 GTGCTTCCTCGCTCAAAAGAA 59.126 47.619 0.00 0.00 0.00 2.52
832 855 1.512926 GTGCTTCCTCGCTCAAAAGA 58.487 50.000 0.00 0.00 0.00 2.52
833 856 0.519077 GGTGCTTCCTCGCTCAAAAG 59.481 55.000 0.00 0.00 0.00 2.27
834 857 1.227999 CGGTGCTTCCTCGCTCAAAA 61.228 55.000 0.00 0.00 0.00 2.44
835 858 1.667830 CGGTGCTTCCTCGCTCAAA 60.668 57.895 0.00 0.00 0.00 2.69
836 859 2.048222 CGGTGCTTCCTCGCTCAA 60.048 61.111 0.00 0.00 0.00 3.02
837 860 3.303135 ACGGTGCTTCCTCGCTCA 61.303 61.111 0.00 0.00 0.00 4.26
838 861 2.811317 CACGGTGCTTCCTCGCTC 60.811 66.667 0.00 0.00 0.00 5.03
839 862 3.288308 CTCACGGTGCTTCCTCGCT 62.288 63.158 2.51 0.00 0.00 4.93
840 863 2.811317 CTCACGGTGCTTCCTCGC 60.811 66.667 2.51 0.00 0.00 5.03
841 864 1.153939 CTCTCACGGTGCTTCCTCG 60.154 63.158 2.51 0.00 0.00 4.63
842 865 1.446966 GCTCTCACGGTGCTTCCTC 60.447 63.158 2.51 0.00 0.00 3.71
843 866 2.164865 CTGCTCTCACGGTGCTTCCT 62.165 60.000 2.51 0.00 35.67 3.36
853 876 1.445238 GGACGTGCTCTGCTCTCAC 60.445 63.158 0.00 0.00 0.00 3.51
854 877 1.604879 AGGACGTGCTCTGCTCTCA 60.605 57.895 2.68 0.00 0.00 3.27
855 878 1.153862 CAGGACGTGCTCTGCTCTC 60.154 63.158 6.61 0.00 0.00 3.20
856 879 2.969016 CAGGACGTGCTCTGCTCT 59.031 61.111 6.61 0.00 0.00 4.09
967 995 2.203640 TGGAGAGAGCACGGGTGT 60.204 61.111 0.25 0.00 0.00 4.16
977 1005 2.757508 CTGGAGCGCCTGGAGAGA 60.758 66.667 8.34 0.00 34.31 3.10
978 1006 4.527583 GCTGGAGCGCCTGGAGAG 62.528 72.222 14.91 0.94 33.99 3.20
1630 1664 5.045215 CCATAGCCATTTGCATGTTAAGTG 58.955 41.667 0.00 0.00 44.83 3.16
1632 1666 5.045215 CACCATAGCCATTTGCATGTTAAG 58.955 41.667 0.00 0.00 44.83 1.85
1792 1833 1.282738 TCATTCAGGCTCTCAATGGCA 59.717 47.619 9.40 0.00 0.00 4.92
1816 1857 1.183549 ACGACGGGATGAAGCTTACT 58.816 50.000 0.00 0.00 0.00 2.24
2194 2236 5.009510 TGTGCAAAAGAAGCTTACTGCATTA 59.990 36.000 20.48 13.37 45.94 1.90
2251 2293 7.137490 ACTGTCAAGTGATGTAATGTGATTG 57.863 36.000 0.00 0.00 34.48 2.67
2252 2294 8.846943 TTACTGTCAAGTGATGTAATGTGATT 57.153 30.769 6.05 0.00 37.19 2.57
2274 2316 5.662211 TGAAACCGTAGTCTGCTTTTTAC 57.338 39.130 0.00 0.00 0.00 2.01
2276 2318 5.570234 TTTGAAACCGTAGTCTGCTTTTT 57.430 34.783 0.00 0.00 0.00 1.94
2277 2319 5.124936 AGTTTTGAAACCGTAGTCTGCTTTT 59.875 36.000 3.14 0.00 39.71 2.27
2289 2333 4.553429 GTCGCATATCAAGTTTTGAAACCG 59.447 41.667 3.14 0.00 43.95 4.44
2347 2391 1.331214 ACATGCAAAGTTGGTCCTGG 58.669 50.000 0.00 0.00 0.00 4.45
2493 2537 5.036117 ACCACTACACTTGAACAGATGTT 57.964 39.130 0.00 0.00 41.64 2.71
2502 2546 1.542915 GCGGTCTACCACTACACTTGA 59.457 52.381 0.00 0.00 35.14 3.02
2503 2547 1.544691 AGCGGTCTACCACTACACTTG 59.455 52.381 0.00 0.00 35.14 3.16
2509 2553 1.693034 TGGGAGCGGTCTACCACTA 59.307 57.895 15.18 0.00 46.34 2.74
2538 2582 6.894339 ATGGTTTACTGGGTACAAGAAAAG 57.106 37.500 0.00 0.00 0.00 2.27
2743 2789 1.755783 CTCCCCTTGCCTCCAATGC 60.756 63.158 0.00 0.00 0.00 3.56
2752 2798 3.392616 TCTCCAAGATATTCTCCCCTTGC 59.607 47.826 0.00 0.00 35.83 4.01
2967 3013 3.874392 AAGTGAATAAACCATGCTGCC 57.126 42.857 0.00 0.00 0.00 4.85
3042 3089 4.084066 CCTTGAAAAATAAAACGGCCTTGC 60.084 41.667 0.00 0.00 0.00 4.01
3043 3090 5.293560 TCCTTGAAAAATAAAACGGCCTTG 58.706 37.500 0.00 0.00 0.00 3.61
3044 3091 5.538849 TCCTTGAAAAATAAAACGGCCTT 57.461 34.783 0.00 0.00 0.00 4.35
3045 3092 5.738619 ATCCTTGAAAAATAAAACGGCCT 57.261 34.783 0.00 0.00 0.00 5.19
3046 3093 6.391537 TGTATCCTTGAAAAATAAAACGGCC 58.608 36.000 0.00 0.00 0.00 6.13
3047 3094 7.222031 GGATGTATCCTTGAAAAATAAAACGGC 59.778 37.037 3.63 0.00 43.73 5.68
3086 3133 5.388890 CGTTCTTGCTGTCTATGTTTCTGAC 60.389 44.000 0.00 0.00 0.00 3.51
3108 3155 0.951558 AATTCGGAGCAGCAAAACGT 59.048 45.000 0.00 0.00 0.00 3.99
3148 3195 2.793288 TGAAAGCATCTCATCAGGCA 57.207 45.000 0.00 0.00 0.00 4.75
3172 3219 4.955811 AACCTATGATATCCGCTGAACA 57.044 40.909 0.00 0.00 0.00 3.18
3308 3359 4.023107 GCCTTTGGAGAGGTGTCTTTTTAC 60.023 45.833 0.00 0.00 39.11 2.01
3381 3432 7.324178 TCCGAAGAAATGGTCAAAAAGAAAAA 58.676 30.769 0.00 0.00 0.00 1.94
3385 3436 6.458232 TTTCCGAAGAAATGGTCAAAAAGA 57.542 33.333 0.00 0.00 37.07 2.52
3386 3437 7.064016 TGTTTTTCCGAAGAAATGGTCAAAAAG 59.936 33.333 0.00 0.00 41.55 2.27
3424 3476 8.579006 TGCATAGTTCTGTTCAATCTCATTTTT 58.421 29.630 0.00 0.00 0.00 1.94
3434 3486 7.977789 TCAGTATTTGCATAGTTCTGTTCAA 57.022 32.000 0.00 0.00 0.00 2.69
3538 3741 9.418045 CCTAGCTTTATGATTAGCTTTCTACTC 57.582 37.037 7.00 0.00 45.03 2.59
3543 3746 6.867662 TGCCTAGCTTTATGATTAGCTTTC 57.132 37.500 7.00 0.00 45.03 2.62
3565 3768 7.148323 TGTGTGAGTATTTTCCATTATCCGTTG 60.148 37.037 0.00 0.00 0.00 4.10
3567 3770 6.411376 TGTGTGAGTATTTTCCATTATCCGT 58.589 36.000 0.00 0.00 0.00 4.69
3598 3801 2.030371 TCATTCTTTGTGGCTGTTGCA 58.970 42.857 0.00 0.00 41.91 4.08
3635 3838 9.239551 ACCTTTACTTTTTGTACTTTCTTCTGT 57.760 29.630 0.00 0.00 0.00 3.41
3645 3848 7.716560 TCTTCCCACTACCTTTACTTTTTGTAC 59.283 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.