Multiple sequence alignment - TraesCS1A01G332300

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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 TraesCS1A01G332300 chr1A 100.000 2769 0 0 1 2769 520794934 520792166 0.000000e+00 5114.0
1 TraesCS1A01G332300 chr1A 91.328 738 61 1 4 741 331274649 331273915 0.000000e+00 1005.0
2 TraesCS1A01G332300 chr1A 94.273 454 26 0 1 454 308905427 308905880 0.000000e+00 695.0
3 TraesCS1A01G332300 chr1A 95.833 360 15 0 382 741 308905856 308906215 1.430000e-162 582.0
4 TraesCS1A01G332300 chr1D 87.177 1856 77 48 803 2559 424992579 424990786 0.000000e+00 1960.0
5 TraesCS1A01G332300 chr1D 88.966 145 10 3 2599 2742 424990389 424990250 1.020000e-39 174.0
6 TraesCS1A01G332300 chr1D 100.000 31 0 0 2738 2768 424990237 424990207 1.070000e-04 58.4
7 TraesCS1A01G332300 chr1B 88.500 1713 65 54 795 2402 574268420 574266735 0.000000e+00 1951.0
8 TraesCS1A01G332300 chr1B 89.204 741 80 0 1 741 593506698 593507438 0.000000e+00 926.0
9 TraesCS1A01G332300 chr4A 98.111 741 14 0 1 741 565428913 565429653 0.000000e+00 1291.0
10 TraesCS1A01G332300 chr5A 96.757 740 24 0 1 740 3046266 3045527 0.000000e+00 1234.0
11 TraesCS1A01G332300 chr2A 90.515 738 70 0 4 741 655515035 655514298 0.000000e+00 976.0
12 TraesCS1A01G332300 chr7B 88.934 741 82 0 1 741 740027198 740027938 0.000000e+00 915.0
13 TraesCS1A01G332300 chr4D 87.989 741 89 0 1 741 280782336 280783076 0.000000e+00 876.0
14 TraesCS1A01G332300 chr3D 85.944 747 99 2 1 741 66245764 66246510 0.000000e+00 793.0
15 TraesCS1A01G332300 chr5B 83.558 742 114 6 4 741 309668007 309667270 0.000000e+00 688.0


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 TraesCS1A01G332300 chr1A 520792166 520794934 2768 True 5114.0 5114 100.000000 1 2769 1 chr1A.!!$R2 2768
1 TraesCS1A01G332300 chr1A 331273915 331274649 734 True 1005.0 1005 91.328000 4 741 1 chr1A.!!$R1 737
2 TraesCS1A01G332300 chr1A 308905427 308906215 788 False 638.5 695 95.053000 1 741 2 chr1A.!!$F1 740
3 TraesCS1A01G332300 chr1D 424990207 424992579 2372 True 730.8 1960 92.047667 803 2768 3 chr1D.!!$R1 1965
4 TraesCS1A01G332300 chr1B 574266735 574268420 1685 True 1951.0 1951 88.500000 795 2402 1 chr1B.!!$R1 1607
5 TraesCS1A01G332300 chr1B 593506698 593507438 740 False 926.0 926 89.204000 1 741 1 chr1B.!!$F1 740
6 TraesCS1A01G332300 chr4A 565428913 565429653 740 False 1291.0 1291 98.111000 1 741 1 chr4A.!!$F1 740
7 TraesCS1A01G332300 chr5A 3045527 3046266 739 True 1234.0 1234 96.757000 1 740 1 chr5A.!!$R1 739
8 TraesCS1A01G332300 chr2A 655514298 655515035 737 True 976.0 976 90.515000 4 741 1 chr2A.!!$R1 737
9 TraesCS1A01G332300 chr7B 740027198 740027938 740 False 915.0 915 88.934000 1 741 1 chr7B.!!$F1 740
10 TraesCS1A01G332300 chr4D 280782336 280783076 740 False 876.0 876 87.989000 1 741 1 chr4D.!!$F1 740
11 TraesCS1A01G332300 chr3D 66245764 66246510 746 False 793.0 793 85.944000 1 741 1 chr3D.!!$F1 740
12 TraesCS1A01G332300 chr5B 309667270 309668007 737 True 688.0 688 83.558000 4 741 1 chr5B.!!$R1 737

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
777 832 0.391597 TGTTTTTCGAGCGAGAGGGT 59.608 50.0 0.00 0.0 0.00 4.34 F
1324 1402 0.251354 GAGGAGCTGCACCTGATCAA 59.749 55.0 23.46 0.0 37.93 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1764 0.033504 ATCTATGTTACTGGCCGCGG 59.966 55.0 24.05 24.05 0.00 6.46 R
2617 3179 0.037605 GCCTTGCTGTACCACGTACT 60.038 55.0 3.79 0.00 39.49 2.73 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
268 269 1.274703 GGTGGAGGAGCTTCCCATCA 61.275 60.000 7.68 0.00 37.19 3.07
587 642 2.456287 GAAGCGCTCCAGAAGTGGGT 62.456 60.000 12.06 0.00 45.11 4.51
728 783 3.220658 TCGCGCATCCGTCCCATA 61.221 61.111 8.75 0.00 36.67 2.74
748 803 2.990479 GGACCGGTCCTTCTGCAT 59.010 61.111 40.89 0.00 46.16 3.96
749 804 2.208527 GGACCGGTCCTTCTGCATA 58.791 57.895 40.89 0.00 46.16 3.14
750 805 0.539986 GGACCGGTCCTTCTGCATAA 59.460 55.000 40.89 0.00 46.16 1.90
751 806 1.653151 GACCGGTCCTTCTGCATAAC 58.347 55.000 24.75 0.00 0.00 1.89
752 807 1.207329 GACCGGTCCTTCTGCATAACT 59.793 52.381 24.75 0.00 0.00 2.24
753 808 1.628846 ACCGGTCCTTCTGCATAACTT 59.371 47.619 0.00 0.00 0.00 2.66
754 809 2.009774 CCGGTCCTTCTGCATAACTTG 58.990 52.381 0.00 0.00 0.00 3.16
755 810 2.615493 CCGGTCCTTCTGCATAACTTGT 60.615 50.000 0.00 0.00 0.00 3.16
756 811 3.074412 CGGTCCTTCTGCATAACTTGTT 58.926 45.455 0.00 0.00 0.00 2.83
757 812 3.502211 CGGTCCTTCTGCATAACTTGTTT 59.498 43.478 0.00 0.00 0.00 2.83
758 813 4.023193 CGGTCCTTCTGCATAACTTGTTTT 60.023 41.667 0.00 0.00 0.00 2.43
759 814 5.222631 GGTCCTTCTGCATAACTTGTTTTG 58.777 41.667 0.00 0.00 0.00 2.44
760 815 5.221244 GGTCCTTCTGCATAACTTGTTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
761 816 6.273071 GTCCTTCTGCATAACTTGTTTTGTT 58.727 36.000 0.00 0.00 0.00 2.83
762 817 6.756542 GTCCTTCTGCATAACTTGTTTTGTTT 59.243 34.615 0.00 0.00 0.00 2.83
763 818 7.277760 GTCCTTCTGCATAACTTGTTTTGTTTT 59.722 33.333 0.00 0.00 0.00 2.43
764 819 7.821846 TCCTTCTGCATAACTTGTTTTGTTTTT 59.178 29.630 0.00 0.00 0.00 1.94
765 820 8.116136 CCTTCTGCATAACTTGTTTTGTTTTTC 58.884 33.333 0.00 0.00 0.00 2.29
766 821 7.215696 TCTGCATAACTTGTTTTGTTTTTCG 57.784 32.000 0.00 0.00 0.00 3.46
767 822 7.030165 TCTGCATAACTTGTTTTGTTTTTCGA 58.970 30.769 0.00 0.00 0.00 3.71
768 823 7.215696 TGCATAACTTGTTTTGTTTTTCGAG 57.784 32.000 5.99 0.00 0.00 4.04
769 824 6.120157 GCATAACTTGTTTTGTTTTTCGAGC 58.880 36.000 5.99 0.00 0.00 5.03
770 825 4.816277 AACTTGTTTTGTTTTTCGAGCG 57.184 36.364 0.00 0.00 0.00 5.03
771 826 4.086199 ACTTGTTTTGTTTTTCGAGCGA 57.914 36.364 0.00 0.00 0.00 4.93
772 827 4.095610 ACTTGTTTTGTTTTTCGAGCGAG 58.904 39.130 0.00 0.00 0.00 5.03
773 828 4.142773 ACTTGTTTTGTTTTTCGAGCGAGA 60.143 37.500 0.00 0.00 0.00 4.04
774 829 3.935450 TGTTTTGTTTTTCGAGCGAGAG 58.065 40.909 0.00 0.00 0.00 3.20
775 830 3.242608 TGTTTTGTTTTTCGAGCGAGAGG 60.243 43.478 0.00 0.00 0.00 3.69
776 831 1.508632 TTGTTTTTCGAGCGAGAGGG 58.491 50.000 0.00 0.00 0.00 4.30
777 832 0.391597 TGTTTTTCGAGCGAGAGGGT 59.608 50.000 0.00 0.00 0.00 4.34
778 833 1.069255 GTTTTTCGAGCGAGAGGGTC 58.931 55.000 0.00 0.00 39.80 4.46
791 846 2.908015 GGGTCGCCCTTCTGCATA 59.092 61.111 7.58 0.00 41.34 3.14
792 847 1.223487 GGGTCGCCCTTCTGCATAA 59.777 57.895 7.58 0.00 41.34 1.90
793 848 1.095807 GGGTCGCCCTTCTGCATAAC 61.096 60.000 7.58 0.00 41.34 1.89
814 869 2.698855 TGCCTGCCTCTAAATCAGTC 57.301 50.000 0.00 0.00 0.00 3.51
842 897 2.291465 TCGAAATCCCCAGATACGTACG 59.709 50.000 15.01 15.01 35.42 3.67
843 898 2.033801 CGAAATCCCCAGATACGTACGT 59.966 50.000 25.98 25.98 31.92 3.57
844 899 3.250762 CGAAATCCCCAGATACGTACGTA 59.749 47.826 28.62 28.62 31.92 3.57
845 900 4.540824 GAAATCCCCAGATACGTACGTAC 58.459 47.826 28.99 21.22 33.01 3.67
1324 1402 0.251354 GAGGAGCTGCACCTGATCAA 59.749 55.000 23.46 0.00 37.93 2.57
1493 1580 2.031012 CCGCTGCACAACTGAGGA 59.969 61.111 0.00 0.00 39.15 3.71
1652 1753 4.564821 CGGAAAGGACTTACAATGGAGGAA 60.565 45.833 0.00 0.00 0.00 3.36
1661 1762 2.826428 ACAATGGAGGAACGATCGATG 58.174 47.619 24.34 8.28 0.00 3.84
1662 1763 1.528586 CAATGGAGGAACGATCGATGC 59.471 52.381 24.34 16.22 0.00 3.91
1663 1764 0.034059 ATGGAGGAACGATCGATGCC 59.966 55.000 24.34 18.43 0.00 4.40
1667 1768 3.692367 GAACGATCGATGCCCGCG 61.692 66.667 24.34 0.00 38.37 6.46
1708 1836 5.799213 AGCATATGTATAGGCCAGTTCTTC 58.201 41.667 5.01 0.00 40.64 2.87
1709 1837 5.545723 AGCATATGTATAGGCCAGTTCTTCT 59.454 40.000 5.01 0.00 40.64 2.85
1710 1838 6.043706 AGCATATGTATAGGCCAGTTCTTCTT 59.956 38.462 5.01 0.00 40.64 2.52
1711 1839 6.370166 GCATATGTATAGGCCAGTTCTTCTTC 59.630 42.308 5.01 0.00 34.26 2.87
1712 1840 7.675062 CATATGTATAGGCCAGTTCTTCTTCT 58.325 38.462 5.01 0.00 0.00 2.85
1713 1841 6.567602 ATGTATAGGCCAGTTCTTCTTCTT 57.432 37.500 5.01 0.00 0.00 2.52
1727 1855 8.704668 AGTTCTTCTTCTTCTTCTTCTTCTTCT 58.295 33.333 0.00 0.00 0.00 2.85
1732 1860 8.028652 TCTTCTTCTTCTTCTTCTTCTTCCTT 57.971 34.615 0.00 0.00 0.00 3.36
1830 1962 7.148474 CCATCAATCAATGCAAAGGAAGAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
1845 1977 2.093711 AGAAAAGCCCGCAAGTTTTTGT 60.094 40.909 2.85 0.00 36.65 2.83
1966 2098 4.337274 TCACACGTATGATGTATCCGTTCT 59.663 41.667 0.00 0.00 0.00 3.01
1967 2099 5.041287 CACACGTATGATGTATCCGTTCTT 58.959 41.667 0.00 0.00 0.00 2.52
1972 2113 7.434307 CACGTATGATGTATCCGTTCTTAAACT 59.566 37.037 0.00 0.00 32.95 2.66
1975 2116 8.969267 GTATGATGTATCCGTTCTTAAACTGAG 58.031 37.037 0.00 0.00 32.99 3.35
1983 2124 4.093556 CCGTTCTTAAACTGAGAATGAGGC 59.906 45.833 7.45 0.00 40.81 4.70
2213 2392 1.374252 ATTTCGCTCGCTCGTGGTT 60.374 52.632 0.00 0.00 0.00 3.67
2214 2393 0.108992 ATTTCGCTCGCTCGTGGTTA 60.109 50.000 0.00 0.00 0.00 2.85
2215 2394 1.005294 TTTCGCTCGCTCGTGGTTAC 61.005 55.000 0.00 0.00 0.00 2.50
2248 2427 1.135689 GCATTGCGAAGTTACAGTGGG 60.136 52.381 0.00 0.00 0.00 4.61
2252 2431 2.241160 TGCGAAGTTACAGTGGGAGTA 58.759 47.619 0.00 0.00 0.00 2.59
2272 2465 6.870439 GGAGTACGGTAGTAATTTTGACTTGT 59.130 38.462 0.00 0.00 34.16 3.16
2273 2466 7.148689 GGAGTACGGTAGTAATTTTGACTTGTG 60.149 40.741 0.00 0.00 34.16 3.33
2274 2467 7.436118 AGTACGGTAGTAATTTTGACTTGTGA 58.564 34.615 0.00 0.00 34.16 3.58
2287 2480 6.490566 TTGACTTGTGATGATGATGACTTG 57.509 37.500 0.00 0.00 0.00 3.16
2288 2481 4.939439 TGACTTGTGATGATGATGACTTGG 59.061 41.667 0.00 0.00 0.00 3.61
2313 2506 0.534203 ACTTGTGGCCGTGGTAACTG 60.534 55.000 0.00 0.00 37.61 3.16
2375 2568 0.689623 AGTGAGGCCTCTGACTTTGG 59.310 55.000 32.28 0.00 33.69 3.28
2399 2592 0.522180 AGGACAAGTCGCGAGTACTG 59.478 55.000 18.34 15.20 0.00 2.74
2406 2605 0.862283 GTCGCGAGTACTGCTACTGC 60.862 60.000 10.24 0.00 32.96 4.40
2441 2640 3.273834 CGACACCGGCACCGTTTT 61.274 61.111 0.00 0.00 37.81 2.43
2442 2641 2.635338 GACACCGGCACCGTTTTC 59.365 61.111 0.00 0.00 37.81 2.29
2443 2642 2.124653 ACACCGGCACCGTTTTCA 60.125 55.556 0.00 0.00 37.81 2.69
2444 2643 2.113131 GACACCGGCACCGTTTTCAG 62.113 60.000 0.00 0.00 37.81 3.02
2448 2647 1.234615 CCGGCACCGTTTTCAGTCAT 61.235 55.000 8.49 0.00 37.81 3.06
2454 2653 0.179250 CCGTTTTCAGTCATCGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
2456 2655 0.865769 GTTTTCAGTCATCGTGCGGT 59.134 50.000 0.00 0.00 0.00 5.68
2468 2667 0.431984 CGTGCGGTAAGTGTAACGTG 59.568 55.000 0.00 0.00 45.86 4.49
2478 2677 5.464389 GGTAAGTGTAACGTGTTCACATCTT 59.536 40.000 16.32 12.68 45.86 2.40
2515 2714 3.244875 TGCAACTCTAGAGATTGGCCAAA 60.245 43.478 26.57 4.13 0.00 3.28
2531 2736 1.069500 CCAAAATTTCTCCGTCGCGTT 60.069 47.619 5.77 0.00 0.00 4.84
2547 2752 1.070038 CGTTGCATTTACCCGTACGT 58.930 50.000 15.21 0.00 0.00 3.57
2556 2761 0.597568 TACCCGTACGTGGTGTCTTG 59.402 55.000 28.04 6.97 36.57 3.02
2559 2764 1.661480 CGTACGTGGTGTCTTGGGA 59.339 57.895 7.22 0.00 0.00 4.37
2560 2765 0.245539 CGTACGTGGTGTCTTGGGAT 59.754 55.000 7.22 0.00 0.00 3.85
2561 2766 1.722011 GTACGTGGTGTCTTGGGATG 58.278 55.000 0.00 0.00 0.00 3.51
2562 2767 1.001633 GTACGTGGTGTCTTGGGATGT 59.998 52.381 0.00 0.00 0.00 3.06
2564 2769 1.001633 ACGTGGTGTCTTGGGATGTAC 59.998 52.381 0.00 0.00 0.00 2.90
2565 2770 1.275291 CGTGGTGTCTTGGGATGTACT 59.725 52.381 0.00 0.00 0.00 2.73
2566 2771 2.494471 CGTGGTGTCTTGGGATGTACTA 59.506 50.000 0.00 0.00 0.00 1.82
2567 2772 3.428999 CGTGGTGTCTTGGGATGTACTAG 60.429 52.174 0.00 0.00 0.00 2.57
2569 2774 4.708421 GTGGTGTCTTGGGATGTACTAGTA 59.292 45.833 0.00 0.00 0.00 1.82
2585 2790 8.229253 TGTACTAGTACAGTGTCTCAAAGAAA 57.771 34.615 27.99 3.40 40.77 2.52
2586 2791 8.133627 TGTACTAGTACAGTGTCTCAAAGAAAC 58.866 37.037 27.99 2.53 40.77 2.78
2587 2792 7.349412 ACTAGTACAGTGTCTCAAAGAAACT 57.651 36.000 0.00 0.00 43.41 2.66
2589 2794 8.351461 ACTAGTACAGTGTCTCAAAGAAACTAC 58.649 37.037 0.00 0.00 40.74 2.73
2590 2795 7.108841 AGTACAGTGTCTCAAAGAAACTACA 57.891 36.000 0.00 0.00 40.74 2.74
2591 2796 7.203910 AGTACAGTGTCTCAAAGAAACTACAG 58.796 38.462 0.00 0.00 40.74 2.74
2593 2798 5.812642 ACAGTGTCTCAAAGAAACTACAGTG 59.187 40.000 0.00 0.00 40.74 3.66
2595 2800 6.019479 CAGTGTCTCAAAGAAACTACAGTGTC 60.019 42.308 0.00 0.00 40.74 3.67
2601 3163 7.987458 TCTCAAAGAAACTACAGTGTCTCAAAT 59.013 33.333 0.00 0.00 41.57 2.32
2634 3196 3.844577 ACTAGTACGTGGTACAGCAAG 57.155 47.619 0.00 3.39 41.80 4.01
2637 3199 1.017701 GTACGTGGTACAGCAAGGCC 61.018 60.000 0.00 0.00 41.80 5.19
2644 3206 2.878089 TACAGCAAGGCCGACTGCA 61.878 57.895 23.79 10.13 43.89 4.41
2677 3239 1.741145 TGCTACTCAACGAGCGATGTA 59.259 47.619 0.00 0.00 41.83 2.29
2678 3240 2.162809 TGCTACTCAACGAGCGATGTAA 59.837 45.455 0.00 0.00 41.83 2.41
2679 3241 2.784380 GCTACTCAACGAGCGATGTAAG 59.216 50.000 0.00 0.00 32.04 2.34
2680 3242 3.731264 GCTACTCAACGAGCGATGTAAGT 60.731 47.826 0.00 0.00 32.04 2.24
2721 3283 2.356313 AACTGTCTGCCGCGTGAG 60.356 61.111 4.92 0.00 0.00 3.51
2725 3287 2.004808 CTGTCTGCCGCGTGAGGATA 62.005 60.000 4.92 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
587 642 1.824329 GATCTCGACGAGGGGCTCA 60.824 63.158 23.92 4.57 0.00 4.26
741 796 7.542477 TCGAAAAACAAAACAAGTTATGCAGAA 59.458 29.630 0.00 0.00 0.00 3.02
742 797 7.030165 TCGAAAAACAAAACAAGTTATGCAGA 58.970 30.769 0.00 0.00 0.00 4.26
743 798 7.215696 TCGAAAAACAAAACAAGTTATGCAG 57.784 32.000 0.00 0.00 0.00 4.41
744 799 6.237701 GCTCGAAAAACAAAACAAGTTATGCA 60.238 34.615 0.00 0.00 0.00 3.96
745 800 6.120157 GCTCGAAAAACAAAACAAGTTATGC 58.880 36.000 0.00 0.00 0.00 3.14
746 801 6.195613 TCGCTCGAAAAACAAAACAAGTTATG 59.804 34.615 0.00 0.00 0.00 1.90
747 802 6.259638 TCGCTCGAAAAACAAAACAAGTTAT 58.740 32.000 0.00 0.00 0.00 1.89
748 803 5.629097 TCGCTCGAAAAACAAAACAAGTTA 58.371 33.333 0.00 0.00 0.00 2.24
749 804 4.477780 TCGCTCGAAAAACAAAACAAGTT 58.522 34.783 0.00 0.00 0.00 2.66
750 805 4.086199 TCGCTCGAAAAACAAAACAAGT 57.914 36.364 0.00 0.00 0.00 3.16
751 806 4.339429 TCTCGCTCGAAAAACAAAACAAG 58.661 39.130 0.00 0.00 0.00 3.16
752 807 4.339429 CTCTCGCTCGAAAAACAAAACAA 58.661 39.130 0.00 0.00 0.00 2.83
753 808 3.242608 CCTCTCGCTCGAAAAACAAAACA 60.243 43.478 0.00 0.00 0.00 2.83
754 809 3.289076 CCTCTCGCTCGAAAAACAAAAC 58.711 45.455 0.00 0.00 0.00 2.43
755 810 2.289547 CCCTCTCGCTCGAAAAACAAAA 59.710 45.455 0.00 0.00 0.00 2.44
756 811 1.871039 CCCTCTCGCTCGAAAAACAAA 59.129 47.619 0.00 0.00 0.00 2.83
757 812 1.202604 ACCCTCTCGCTCGAAAAACAA 60.203 47.619 0.00 0.00 0.00 2.83
758 813 0.391597 ACCCTCTCGCTCGAAAAACA 59.608 50.000 0.00 0.00 0.00 2.83
759 814 1.069255 GACCCTCTCGCTCGAAAAAC 58.931 55.000 0.00 0.00 0.00 2.43
760 815 0.388134 CGACCCTCTCGCTCGAAAAA 60.388 55.000 0.00 0.00 35.06 1.94
761 816 1.211969 CGACCCTCTCGCTCGAAAA 59.788 57.895 0.00 0.00 35.06 2.29
762 817 2.875485 CGACCCTCTCGCTCGAAA 59.125 61.111 0.00 0.00 35.06 3.46
776 831 1.398390 CAAGTTATGCAGAAGGGCGAC 59.602 52.381 0.00 0.00 36.28 5.19
777 832 1.737838 CAAGTTATGCAGAAGGGCGA 58.262 50.000 0.00 0.00 36.28 5.54
788 843 4.883585 TGATTTAGAGGCAGGCAAGTTATG 59.116 41.667 0.00 0.00 0.00 1.90
789 844 5.116084 TGATTTAGAGGCAGGCAAGTTAT 57.884 39.130 0.00 0.00 0.00 1.89
790 845 4.019321 ACTGATTTAGAGGCAGGCAAGTTA 60.019 41.667 0.00 0.00 34.05 2.24
791 846 3.245052 ACTGATTTAGAGGCAGGCAAGTT 60.245 43.478 0.00 0.00 34.05 2.66
792 847 2.307098 ACTGATTTAGAGGCAGGCAAGT 59.693 45.455 0.00 0.00 34.05 3.16
793 848 2.941720 GACTGATTTAGAGGCAGGCAAG 59.058 50.000 0.00 0.00 37.61 4.01
842 897 1.266466 GCGAAGTCAAGCTACGGTAC 58.734 55.000 0.00 0.00 0.00 3.34
843 898 0.171903 GGCGAAGTCAAGCTACGGTA 59.828 55.000 0.00 0.00 0.00 4.02
844 899 1.080025 GGCGAAGTCAAGCTACGGT 60.080 57.895 0.00 0.00 0.00 4.83
845 900 0.389948 AAGGCGAAGTCAAGCTACGG 60.390 55.000 0.00 0.00 0.00 4.02
937 993 2.696759 GGACGCGGTGGAAATTGGG 61.697 63.158 12.47 0.00 0.00 4.12
987 1043 3.787001 GCGAGAGGTGGAAGGGGG 61.787 72.222 0.00 0.00 0.00 5.40
1552 1643 2.125512 CTCGCTGAAGAACCCGGG 60.126 66.667 22.25 22.25 0.00 5.73
1662 1763 1.594293 CTATGTTACTGGCCGCGGG 60.594 63.158 29.38 13.36 0.00 6.13
1663 1764 0.033504 ATCTATGTTACTGGCCGCGG 59.966 55.000 24.05 24.05 0.00 6.46
1667 1768 8.424918 ACATATGCTATATCTATGTTACTGGCC 58.575 37.037 1.58 0.00 33.42 5.36
1708 1836 7.173047 CCAAGGAAGAAGAAGAAGAAGAAGAAG 59.827 40.741 0.00 0.00 0.00 2.85
1709 1837 6.995091 CCAAGGAAGAAGAAGAAGAAGAAGAA 59.005 38.462 0.00 0.00 0.00 2.52
1710 1838 6.327626 TCCAAGGAAGAAGAAGAAGAAGAAGA 59.672 38.462 0.00 0.00 0.00 2.87
1711 1839 6.529220 TCCAAGGAAGAAGAAGAAGAAGAAG 58.471 40.000 0.00 0.00 0.00 2.85
1712 1840 6.500589 TCCAAGGAAGAAGAAGAAGAAGAA 57.499 37.500 0.00 0.00 0.00 2.52
1713 1841 6.500589 TTCCAAGGAAGAAGAAGAAGAAGA 57.499 37.500 0.00 0.00 0.00 2.87
1727 1855 5.009610 CGAAAGAACCAAGAATTCCAAGGAA 59.990 40.000 13.55 3.67 38.59 3.36
1732 1860 4.204012 ACACGAAAGAACCAAGAATTCCA 58.796 39.130 0.65 0.00 0.00 3.53
1830 1962 2.243957 GGCACAAAAACTTGCGGGC 61.244 57.895 0.00 0.00 39.81 6.13
1922 2054 7.061094 GTGTGAAAGAGAAGAAAAATAATGGCG 59.939 37.037 0.00 0.00 0.00 5.69
1966 2098 3.873801 GCCTGGCCTCATTCTCAGTTTAA 60.874 47.826 7.66 0.00 0.00 1.52
1967 2099 2.356125 GCCTGGCCTCATTCTCAGTTTA 60.356 50.000 7.66 0.00 0.00 2.01
1972 2113 0.034767 CAAGCCTGGCCTCATTCTCA 60.035 55.000 16.57 0.00 0.00 3.27
1975 2116 3.930504 CCAAGCCTGGCCTCATTC 58.069 61.111 16.57 0.00 35.39 2.67
1999 2140 3.444034 CCTCGTCTTCTGGTCAGATACAA 59.556 47.826 1.16 0.00 37.29 2.41
2183 2362 0.168788 AGCGAAATGAATGCCACACG 59.831 50.000 0.00 0.00 0.00 4.49
2213 2392 5.047188 TCGCAATGCAGATCGAAATTAGTA 58.953 37.500 5.91 0.00 0.00 1.82
2214 2393 3.871006 TCGCAATGCAGATCGAAATTAGT 59.129 39.130 5.91 0.00 0.00 2.24
2215 2394 4.457433 TCGCAATGCAGATCGAAATTAG 57.543 40.909 5.91 0.00 0.00 1.73
2248 2427 7.596248 TCACAAGTCAAAATTACTACCGTACTC 59.404 37.037 0.00 0.00 0.00 2.59
2252 2431 6.932400 TCATCACAAGTCAAAATTACTACCGT 59.068 34.615 0.00 0.00 0.00 4.83
2272 2465 5.046087 AGTCAGAACCAAGTCATCATCATCA 60.046 40.000 0.00 0.00 0.00 3.07
2273 2466 5.426504 AGTCAGAACCAAGTCATCATCATC 58.573 41.667 0.00 0.00 0.00 2.92
2274 2467 5.432680 AGTCAGAACCAAGTCATCATCAT 57.567 39.130 0.00 0.00 0.00 2.45
2287 2480 1.227853 ACGGCCACAAGTCAGAACC 60.228 57.895 2.24 0.00 0.00 3.62
2288 2481 1.507141 CCACGGCCACAAGTCAGAAC 61.507 60.000 2.24 0.00 0.00 3.01
2313 2506 2.093606 GCCCAGACCAGGTAGTTAAGTC 60.094 54.545 0.00 0.00 0.00 3.01
2375 2568 0.099082 CTCGCGACTTGTCCTACTCC 59.901 60.000 3.71 0.00 0.00 3.85
2399 2592 3.636313 TACACGTGGGCGCAGTAGC 62.636 63.158 21.57 0.00 42.83 3.58
2425 2624 2.113131 CTGAAAACGGTGCCGGTGTC 62.113 60.000 11.66 11.66 43.19 3.67
2432 2631 0.865769 ACGATGACTGAAAACGGTGC 59.134 50.000 0.00 0.00 0.00 5.01
2433 2632 1.398451 GCACGATGACTGAAAACGGTG 60.398 52.381 0.00 0.00 0.00 4.94
2441 2640 0.885879 ACTTACCGCACGATGACTGA 59.114 50.000 0.00 0.00 0.00 3.41
2442 2641 0.992072 CACTTACCGCACGATGACTG 59.008 55.000 0.00 0.00 0.00 3.51
2443 2642 0.601558 ACACTTACCGCACGATGACT 59.398 50.000 0.00 0.00 0.00 3.41
2444 2643 2.267188 TACACTTACCGCACGATGAC 57.733 50.000 0.00 0.00 0.00 3.06
2448 2647 0.310543 ACGTTACACTTACCGCACGA 59.689 50.000 0.00 0.00 0.00 4.35
2454 2653 4.986659 AGATGTGAACACGTTACACTTACC 59.013 41.667 14.51 4.95 35.83 2.85
2456 2655 7.542534 AAAAGATGTGAACACGTTACACTTA 57.457 32.000 14.51 0.62 35.83 2.24
2478 2677 3.150767 AGTTGCACTATGCCCGTAAAAA 58.849 40.909 0.00 0.00 44.23 1.94
2482 2681 1.191535 AGAGTTGCACTATGCCCGTA 58.808 50.000 0.00 0.00 44.23 4.02
2483 2682 1.137086 CTAGAGTTGCACTATGCCCGT 59.863 52.381 0.00 0.00 44.23 5.28
2484 2683 1.409064 TCTAGAGTTGCACTATGCCCG 59.591 52.381 0.00 0.00 44.23 6.13
2485 2684 2.695666 TCTCTAGAGTTGCACTATGCCC 59.304 50.000 19.21 0.00 44.23 5.36
2499 2698 5.888161 GGAGAAATTTTGGCCAATCTCTAGA 59.112 40.000 31.46 12.13 34.98 2.43
2500 2699 5.220931 CGGAGAAATTTTGGCCAATCTCTAG 60.221 44.000 31.46 24.83 34.98 2.43
2507 2706 1.268352 CGACGGAGAAATTTTGGCCAA 59.732 47.619 16.05 16.05 0.00 4.52
2508 2707 0.878416 CGACGGAGAAATTTTGGCCA 59.122 50.000 0.00 0.00 0.00 5.36
2511 2710 0.515564 ACGCGACGGAGAAATTTTGG 59.484 50.000 15.93 0.00 0.00 3.28
2515 2714 1.225376 TGCAACGCGACGGAGAAATT 61.225 50.000 15.93 0.00 0.00 1.82
2531 2736 0.321021 ACCACGTACGGGTAAATGCA 59.679 50.000 21.98 0.00 36.72 3.96
2547 2752 3.786553 ACTAGTACATCCCAAGACACCA 58.213 45.455 0.00 0.00 0.00 4.17
2556 2761 5.191426 TGAGACACTGTACTAGTACATCCC 58.809 45.833 30.78 19.04 44.15 3.85
2559 2764 7.997773 TCTTTGAGACACTGTACTAGTACAT 57.002 36.000 30.78 19.34 44.15 2.29
2560 2765 7.812690 TTCTTTGAGACACTGTACTAGTACA 57.187 36.000 29.21 29.21 43.14 2.90
2561 2766 8.351461 AGTTTCTTTGAGACACTGTACTAGTAC 58.649 37.037 23.58 23.58 34.26 2.73
2562 2767 8.461249 AGTTTCTTTGAGACACTGTACTAGTA 57.539 34.615 0.00 0.00 34.26 1.82
2564 2769 8.350722 TGTAGTTTCTTTGAGACACTGTACTAG 58.649 37.037 6.94 0.00 36.10 2.57
2565 2770 8.229253 TGTAGTTTCTTTGAGACACTGTACTA 57.771 34.615 6.94 0.00 36.10 1.82
2566 2771 7.108841 TGTAGTTTCTTTGAGACACTGTACT 57.891 36.000 6.94 0.00 36.10 2.73
2567 2772 6.979238 ACTGTAGTTTCTTTGAGACACTGTAC 59.021 38.462 6.94 0.00 36.10 2.90
2569 2774 5.812642 CACTGTAGTTTCTTTGAGACACTGT 59.187 40.000 6.94 0.00 36.10 3.55
2571 2776 5.978814 ACACTGTAGTTTCTTTGAGACACT 58.021 37.500 2.72 2.72 38.63 3.55
2572 2777 6.043411 AGACACTGTAGTTTCTTTGAGACAC 58.957 40.000 0.00 0.00 31.59 3.67
2573 2778 6.127451 TGAGACACTGTAGTTTCTTTGAGACA 60.127 38.462 2.54 0.00 35.43 3.41
2574 2779 6.273825 TGAGACACTGTAGTTTCTTTGAGAC 58.726 40.000 2.54 0.00 35.43 3.36
2576 2781 7.539712 TTTGAGACACTGTAGTTTCTTTGAG 57.460 36.000 2.54 0.00 35.43 3.02
2607 3169 5.163723 GCTGTACCACGTACTAGTACATCAA 60.164 44.000 28.03 10.06 43.83 2.57
2617 3179 0.037605 GCCTTGCTGTACCACGTACT 60.038 55.000 3.79 0.00 39.49 2.73
2618 3180 1.017701 GGCCTTGCTGTACCACGTAC 61.018 60.000 0.00 0.00 39.24 3.67
2619 3181 1.294138 GGCCTTGCTGTACCACGTA 59.706 57.895 0.00 0.00 0.00 3.57
2620 3182 2.032071 GGCCTTGCTGTACCACGT 59.968 61.111 0.00 0.00 0.00 4.49
2637 3199 0.096454 CATCATGTGTGCTGCAGTCG 59.904 55.000 16.64 0.00 0.00 4.18
2659 3221 4.017380 ACTTACATCGCTCGTTGAGTAG 57.983 45.455 7.26 4.35 31.39 2.57
2677 3239 3.641437 TTAACCTGCACGTACGTACTT 57.359 42.857 22.34 11.60 0.00 2.24
2678 3240 3.191162 TCATTAACCTGCACGTACGTACT 59.809 43.478 22.34 7.87 0.00 2.73
2679 3241 3.500982 TCATTAACCTGCACGTACGTAC 58.499 45.455 22.34 16.78 0.00 3.67
2680 3242 3.427909 CCTCATTAACCTGCACGTACGTA 60.428 47.826 22.34 5.54 0.00 3.57
2721 3283 0.813210 GGAGCTGCACTGCACTATCC 60.813 60.000 0.00 4.29 36.57 2.59
2725 3287 4.341783 GGGGAGCTGCACTGCACT 62.342 66.667 7.79 2.79 37.13 4.40


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

AutoCloner maintained by Alex Coulton.