Multiple sequence alignment - TraesCS3A01G364300

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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 TraesCS3A01G364300 chr3A 100.000 2447 0 0 1 2447 613172851 613170405 0.000000e+00 4519
1 TraesCS3A01G364300 chr3A 76.407 551 65 31 1918 2447 35435725 35435219 1.130000e-58 237
2 TraesCS3A01G364300 chr3B 87.998 1758 118 43 694 2416 625333775 625332076 0.000000e+00 1991
3 TraesCS3A01G364300 chr3B 91.629 657 42 7 1 655 625334417 625333772 0.000000e+00 896
4 TraesCS3A01G364300 chr3D 89.082 1035 49 19 1450 2447 470888720 470887713 0.000000e+00 1227
5 TraesCS3A01G364300 chr3D 86.770 771 66 22 694 1449 470889505 470888756 0.000000e+00 826
6 TraesCS3A01G364300 chr3D 87.764 662 44 11 1 655 470890133 470889502 0.000000e+00 739
7 TraesCS3A01G364300 chr3D 87.903 620 39 10 1 613 470892275 470891685 0.000000e+00 697
8 TraesCS3A01G364300 chr3D 87.237 619 42 11 2 613 470891202 470890614 0.000000e+00 671
9 TraesCS3A01G364300 chr4D 90.026 391 27 6 1067 1449 307236498 307236112 1.690000e-136 496
10 TraesCS3A01G364300 chr7D 76.155 541 76 26 1918 2447 69088430 69088928 4.070000e-58 235
11 TraesCS3A01G364300 chr2A 77.091 275 56 5 1064 1332 511095296 511095569 4.210000e-33 152


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 TraesCS3A01G364300 chr3A 613170405 613172851 2446 True 4519.0 4519 100.0000 1 2447 1 chr3A.!!$R2 2446
1 TraesCS3A01G364300 chr3A 35435219 35435725 506 True 237.0 237 76.4070 1918 2447 1 chr3A.!!$R1 529
2 TraesCS3A01G364300 chr3B 625332076 625334417 2341 True 1443.5 1991 89.8135 1 2416 2 chr3B.!!$R1 2415
3 TraesCS3A01G364300 chr3D 470887713 470892275 4562 True 832.0 1227 87.7512 1 2447 5 chr3D.!!$R1 2446

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
667 2800 0.03831 TCTCCAGAGACCGCAGAGAA 59.962 55.0 0.0 0.0 30.88 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 3932 0.400594 AACCTGTCCTGCTTGTACCC 59.599 55.0 0.0 0.0 0.0 3.69 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
139 140 1.153489 CCACGGATCTGTGAGGCTG 60.153 63.158 32.02 13.82 42.55 4.85
168 169 4.827481 GGCTCGTAGAATTGCCGA 57.173 55.556 0.00 0.00 35.71 5.54
219 1277 3.290710 AGTGTGTCCTTCATTTGTGCTT 58.709 40.909 0.00 0.00 0.00 3.91
268 1326 2.361438 GTGCTTAGCTATGGAGTACCGT 59.639 50.000 5.60 0.00 39.42 4.83
273 1331 2.311124 GCTATGGAGTACCGTTGCTT 57.689 50.000 0.00 0.00 45.54 3.91
309 1367 6.292061 CGAGAAGAAGCTGCTATGTATTGTTC 60.292 42.308 0.90 0.34 0.00 3.18
311 1369 4.122776 AGAAGCTGCTATGTATTGTTCCG 58.877 43.478 0.90 0.00 0.00 4.30
316 1374 2.285083 GCTATGTATTGTTCCGTGCCA 58.715 47.619 0.00 0.00 0.00 4.92
317 1375 2.680841 GCTATGTATTGTTCCGTGCCAA 59.319 45.455 0.00 0.00 0.00 4.52
446 1509 9.547753 TCTTCAGATAATTACCTGCATTAGTTC 57.452 33.333 1.47 0.00 0.00 3.01
506 2639 2.143122 CAGCTTCTACTGCCGTTTTCA 58.857 47.619 0.00 0.00 0.00 2.69
513 2646 0.763035 ACTGCCGTTTTCAGGTACCT 59.237 50.000 9.21 9.21 35.94 3.08
514 2647 1.156736 CTGCCGTTTTCAGGTACCTG 58.843 55.000 32.61 32.61 44.86 4.00
619 2752 0.107456 AATGATGGCGAGCCGAATCT 59.893 50.000 9.78 0.00 39.42 2.40
665 2798 4.328041 TCTCCAGAGACCGCAGAG 57.672 61.111 0.00 0.00 31.41 3.35
666 2799 1.685820 TCTCCAGAGACCGCAGAGA 59.314 57.895 0.00 0.00 31.41 3.10
667 2800 0.038310 TCTCCAGAGACCGCAGAGAA 59.962 55.000 0.00 0.00 30.88 2.87
668 2801 0.891373 CTCCAGAGACCGCAGAGAAA 59.109 55.000 0.00 0.00 0.00 2.52
669 2802 1.480137 CTCCAGAGACCGCAGAGAAAT 59.520 52.381 0.00 0.00 0.00 2.17
670 2803 1.902508 TCCAGAGACCGCAGAGAAATT 59.097 47.619 0.00 0.00 0.00 1.82
671 2804 2.303022 TCCAGAGACCGCAGAGAAATTT 59.697 45.455 0.00 0.00 0.00 1.82
672 2805 2.675348 CCAGAGACCGCAGAGAAATTTC 59.325 50.000 10.33 10.33 0.00 2.17
673 2806 2.675348 CAGAGACCGCAGAGAAATTTCC 59.325 50.000 14.61 6.57 0.00 3.13
674 2807 2.303022 AGAGACCGCAGAGAAATTTCCA 59.697 45.455 14.61 0.00 0.00 3.53
675 2808 3.054802 AGAGACCGCAGAGAAATTTCCAT 60.055 43.478 14.61 0.71 0.00 3.41
676 2809 3.012518 AGACCGCAGAGAAATTTCCATG 58.987 45.455 14.61 13.89 0.00 3.66
677 2810 2.094675 ACCGCAGAGAAATTTCCATGG 58.905 47.619 14.61 4.97 0.00 3.66
678 2811 1.202336 CCGCAGAGAAATTTCCATGGC 60.202 52.381 14.61 11.97 0.00 4.40
679 2812 1.202336 CGCAGAGAAATTTCCATGGCC 60.202 52.381 14.61 0.00 0.00 5.36
680 2813 1.202336 GCAGAGAAATTTCCATGGCCG 60.202 52.381 14.61 0.00 0.00 6.13
681 2814 2.094675 CAGAGAAATTTCCATGGCCGT 58.905 47.619 14.61 0.00 0.00 5.68
682 2815 2.493278 CAGAGAAATTTCCATGGCCGTT 59.507 45.455 14.61 0.00 0.00 4.44
683 2816 2.755103 AGAGAAATTTCCATGGCCGTTC 59.245 45.455 14.61 7.92 0.00 3.95
684 2817 2.491693 GAGAAATTTCCATGGCCGTTCA 59.508 45.455 14.61 0.00 0.00 3.18
685 2818 3.099141 AGAAATTTCCATGGCCGTTCAT 58.901 40.909 14.61 0.00 0.00 2.57
686 2819 3.131046 AGAAATTTCCATGGCCGTTCATC 59.869 43.478 14.61 0.00 0.00 2.92
687 2820 1.402787 ATTTCCATGGCCGTTCATCC 58.597 50.000 6.96 0.00 0.00 3.51
688 2821 0.331278 TTTCCATGGCCGTTCATCCT 59.669 50.000 6.96 0.00 0.00 3.24
689 2822 0.394216 TTCCATGGCCGTTCATCCTG 60.394 55.000 6.96 0.00 0.00 3.86
690 2823 2.484062 CCATGGCCGTTCATCCTGC 61.484 63.158 0.00 0.00 0.00 4.85
691 2824 2.124151 ATGGCCGTTCATCCTGCC 60.124 61.111 0.00 0.00 44.27 4.85
693 2826 3.134127 GGCCGTTCATCCTGCCAC 61.134 66.667 0.00 0.00 43.46 5.01
694 2827 3.134127 GCCGTTCATCCTGCCACC 61.134 66.667 0.00 0.00 0.00 4.61
695 2828 2.350895 CCGTTCATCCTGCCACCA 59.649 61.111 0.00 0.00 0.00 4.17
696 2829 1.746615 CCGTTCATCCTGCCACCAG 60.747 63.158 0.00 0.00 38.85 4.00
697 2830 1.003355 CGTTCATCCTGCCACCAGT 60.003 57.895 0.00 0.00 37.38 4.00
731 2864 2.159085 AGTAGGTAGTGCTCGAAATGGC 60.159 50.000 0.00 0.00 0.00 4.40
733 2866 1.210478 AGGTAGTGCTCGAAATGGCAT 59.790 47.619 0.00 0.00 40.66 4.40
734 2867 1.599542 GGTAGTGCTCGAAATGGCATC 59.400 52.381 0.00 0.00 40.66 3.91
735 2868 1.258982 GTAGTGCTCGAAATGGCATCG 59.741 52.381 0.00 1.53 40.66 3.84
738 2871 2.628106 CTCGAAATGGCATCGCGG 59.372 61.111 17.90 8.34 40.04 6.46
739 2872 1.882625 CTCGAAATGGCATCGCGGA 60.883 57.895 17.90 6.29 40.04 5.54
743 2876 0.530650 GAAATGGCATCGCGGAGAGA 60.531 55.000 6.13 0.00 42.88 3.10
754 2887 1.815196 CGGAGAGAGCTCAGTGCAT 59.185 57.895 17.77 0.00 45.94 3.96
775 2908 1.303317 GCGGGGCCAAAAGAGAAGA 60.303 57.895 4.39 0.00 0.00 2.87
778 2911 1.065126 CGGGGCCAAAAGAGAAGAGAT 60.065 52.381 4.39 0.00 0.00 2.75
779 2912 2.170607 CGGGGCCAAAAGAGAAGAGATA 59.829 50.000 4.39 0.00 0.00 1.98
780 2913 3.370527 CGGGGCCAAAAGAGAAGAGATAA 60.371 47.826 4.39 0.00 0.00 1.75
781 2914 4.600062 GGGGCCAAAAGAGAAGAGATAAA 58.400 43.478 4.39 0.00 0.00 1.40
782 2915 4.399618 GGGGCCAAAAGAGAAGAGATAAAC 59.600 45.833 4.39 0.00 0.00 2.01
784 2917 4.095036 GGCCAAAAGAGAAGAGATAAACGG 59.905 45.833 0.00 0.00 0.00 4.44
785 2918 4.695928 GCCAAAAGAGAAGAGATAAACGGT 59.304 41.667 0.00 0.00 0.00 4.83
786 2919 5.873164 GCCAAAAGAGAAGAGATAAACGGTA 59.127 40.000 0.00 0.00 0.00 4.02
787 2920 6.036191 GCCAAAAGAGAAGAGATAAACGGTAG 59.964 42.308 0.00 0.00 0.00 3.18
788 2921 7.097834 CCAAAAGAGAAGAGATAAACGGTAGT 58.902 38.462 0.00 0.00 0.00 2.73
789 2922 7.063544 CCAAAAGAGAAGAGATAAACGGTAGTG 59.936 40.741 0.00 0.00 0.00 2.74
790 2923 5.838531 AGAGAAGAGATAAACGGTAGTGG 57.161 43.478 0.00 0.00 0.00 4.00
791 2924 5.507637 AGAGAAGAGATAAACGGTAGTGGA 58.492 41.667 0.00 0.00 0.00 4.02
796 2929 2.159282 AGATAAACGGTAGTGGAGTGCG 60.159 50.000 0.00 0.00 0.00 5.34
797 2930 0.961019 TAAACGGTAGTGGAGTGCGT 59.039 50.000 0.00 0.00 0.00 5.24
815 2948 1.846124 TCCTCCACTTCGGGCCTTT 60.846 57.895 0.84 0.00 34.36 3.11
825 2958 2.342650 CGGGCCTTTCACACCATGG 61.343 63.158 11.19 11.19 0.00 3.66
826 2959 2.649129 GGGCCTTTCACACCATGGC 61.649 63.158 13.04 0.00 42.56 4.40
827 2960 2.973082 GCCTTTCACACCATGGCC 59.027 61.111 13.04 0.00 37.81 5.36
828 2961 2.993471 GCCTTTCACACCATGGCCG 61.993 63.158 13.04 5.85 37.81 6.13
829 2962 1.603455 CCTTTCACACCATGGCCGT 60.603 57.895 13.04 6.62 0.00 5.68
846 2981 0.516877 CGTGGCGAAATCTTCAAGCA 59.483 50.000 0.00 0.00 0.00 3.91
848 2983 1.806542 GTGGCGAAATCTTCAAGCAGA 59.193 47.619 0.00 0.00 0.00 4.26
849 2984 2.079158 TGGCGAAATCTTCAAGCAGAG 58.921 47.619 0.00 0.00 0.00 3.35
860 2995 1.886313 AAGCAGAGCATCGATGGCG 60.886 57.895 26.00 1.96 42.67 5.69
864 2999 2.663188 GAGCATCGATGGCGTCCC 60.663 66.667 26.00 8.80 38.98 4.46
867 3002 2.355126 CATCGATGGCGTCCCTCG 60.355 66.667 17.96 14.14 43.12 4.63
897 3038 3.792459 GCACCGGAGCGCTGTATATATAG 60.792 52.174 18.48 2.25 0.00 1.31
900 3041 2.287668 CGGAGCGCTGTATATATAGCCC 60.288 54.545 18.48 16.66 37.16 5.19
903 3044 1.679680 GCGCTGTATATATAGCCCGGA 59.320 52.381 21.62 0.00 37.16 5.14
906 3047 2.034305 GCTGTATATATAGCCCGGACGG 59.966 54.545 18.10 3.25 34.79 4.79
923 3072 2.181584 GGGACGTCGAGACAGACAT 58.818 57.895 9.92 0.00 40.98 3.06
936 3085 0.873312 CAGACATCATCGGAGTGCGG 60.873 60.000 3.57 0.00 0.00 5.69
937 3086 2.202932 ACATCATCGGAGTGCGGC 60.203 61.111 3.57 0.00 0.00 6.53
938 3087 2.202919 CATCATCGGAGTGCGGCA 60.203 61.111 3.57 0.00 0.00 5.69
939 3088 2.202932 ATCATCGGAGTGCGGCAC 60.203 61.111 25.00 25.00 34.10 5.01
955 3104 3.352447 CACGGGTGCATACAGAGAG 57.648 57.895 0.00 0.00 0.00 3.20
957 3106 1.227380 CGGGTGCATACAGAGAGGC 60.227 63.158 0.00 0.00 0.00 4.70
958 3107 1.680522 CGGGTGCATACAGAGAGGCT 61.681 60.000 0.00 0.00 0.00 4.58
959 3108 1.414158 GGGTGCATACAGAGAGGCTA 58.586 55.000 0.00 0.00 0.00 3.93
960 3109 1.342819 GGGTGCATACAGAGAGGCTAG 59.657 57.143 0.00 0.00 0.00 3.42
961 3110 2.311463 GGTGCATACAGAGAGGCTAGA 58.689 52.381 0.00 0.00 0.00 2.43
962 3111 2.295909 GGTGCATACAGAGAGGCTAGAG 59.704 54.545 0.00 0.00 0.00 2.43
972 3121 4.818546 CAGAGAGGCTAGAGAAGAAGAGAG 59.181 50.000 0.00 0.00 0.00 3.20
984 3133 1.203112 AGAAGAGAGGAGTGAGGTGCA 60.203 52.381 0.00 0.00 0.00 4.57
1006 3155 3.843027 AGCCAAGAGAAAAGAGATGGAGA 59.157 43.478 0.00 0.00 0.00 3.71
1017 3166 3.329542 GATGGAGACCAAGGCGGCA 62.330 63.158 13.08 0.00 36.95 5.69
1346 3495 0.519519 TGCGGCCGTAAGTTCATTTG 59.480 50.000 28.70 0.00 0.00 2.32
1355 3507 5.088739 CCGTAAGTTCATTTGTTCTGATGC 58.911 41.667 0.00 0.00 0.00 3.91
1359 3511 3.438087 AGTTCATTTGTTCTGATGCTCGG 59.562 43.478 0.00 0.00 0.00 4.63
1400 3555 1.002069 TGTCCCTTGGAGCCATCATT 58.998 50.000 0.00 0.00 29.39 2.57
1407 3562 0.896923 TGGAGCCATCATTGTTTGCC 59.103 50.000 0.00 0.00 0.00 4.52
1416 3571 1.000060 TCATTGTTTGCCTTGCTCTGC 60.000 47.619 0.00 0.00 0.00 4.26
1421 3582 1.862827 GTTTGCCTTGCTCTGCTTTTG 59.137 47.619 0.00 0.00 0.00 2.44
1497 3693 1.135199 CACACCTGATGCCATCTTTGC 60.135 52.381 6.21 0.00 0.00 3.68
1667 3867 8.691661 ATATGAAGTTCCAACAGTACAGTTTT 57.308 30.769 0.16 0.00 0.00 2.43
1668 3868 9.787435 ATATGAAGTTCCAACAGTACAGTTTTA 57.213 29.630 0.16 0.00 0.00 1.52
1669 3869 7.925043 TGAAGTTCCAACAGTACAGTTTTAA 57.075 32.000 0.16 0.00 0.00 1.52
1732 3932 2.091939 TGGTCTGGAGAGAGGATCAGAG 60.092 54.545 0.00 0.00 37.00 3.35
1852 4055 6.073314 ACACCAAGTTCTAGGTACTTGTAGA 58.927 40.000 24.46 0.00 46.98 2.59
1968 4173 1.610624 CGTCCAAATACTGCCACCACT 60.611 52.381 0.00 0.00 0.00 4.00
1984 4190 3.058016 CACCACTGATGAGCGAATGTTTT 60.058 43.478 0.00 0.00 0.00 2.43
2103 4320 5.106197 TGAGGAAACGATCAAACCAATGATG 60.106 40.000 0.00 0.00 40.08 3.07
2109 4348 3.799963 CGATCAAACCAATGATGCAATGG 59.200 43.478 9.00 9.00 40.08 3.16
2111 4350 1.661617 CAAACCAATGATGCAATGGCG 59.338 47.619 10.15 0.00 45.35 5.69
2167 4406 5.067674 AGACACAAAACATTCTGCAGCTTAA 59.932 36.000 9.47 0.00 0.00 1.85
2171 4410 6.580041 CACAAAACATTCTGCAGCTTAACTAG 59.420 38.462 9.47 0.00 0.00 2.57
2259 4505 7.014615 AGGATTCACAAGTTGCTTAAAATGTCT 59.985 33.333 1.81 0.00 0.00 3.41
2340 4589 3.196039 TGATTTACACTACGGCCTAAGCA 59.804 43.478 0.00 0.00 42.56 3.91
2407 4663 6.435430 TGGTATAGCAAGCAATACAACTTG 57.565 37.500 1.19 0.00 44.88 3.16
2417 4673 6.869913 CAAGCAATACAACTTGATGGAACATT 59.130 34.615 0.00 0.00 44.89 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 1326 4.630894 TTCTCGCAAAAAGAAGAAGCAA 57.369 36.364 0.00 0.00 0.00 3.91
317 1375 9.855021 TCGTTTCTCTTTTTCATTCTTCTTTTT 57.145 25.926 0.00 0.00 0.00 1.94
337 1396 2.156343 AGAGCAGGACACTTCGTTTC 57.844 50.000 0.00 0.00 0.00 2.78
355 1414 1.998315 CTGATCACGAGGTCTGCAAAG 59.002 52.381 0.00 0.00 0.00 2.77
446 1509 0.304098 GAGTCTGTCCGTACCGATCG 59.696 60.000 8.51 8.51 0.00 3.69
460 1523 6.318900 CAGGTTTTCACTTTTAACTGGAGTCT 59.681 38.462 0.00 0.00 0.00 3.24
513 2646 2.486548 CCTTTCCGGTTCTTCACCTTCA 60.487 50.000 0.00 0.00 44.69 3.02
514 2647 2.152016 CCTTTCCGGTTCTTCACCTTC 58.848 52.381 0.00 0.00 44.69 3.46
515 2648 1.818131 GCCTTTCCGGTTCTTCACCTT 60.818 52.381 0.00 0.00 44.69 3.50
516 2649 0.250770 GCCTTTCCGGTTCTTCACCT 60.251 55.000 0.00 0.00 44.69 4.00
517 2650 0.536460 TGCCTTTCCGGTTCTTCACC 60.536 55.000 0.00 0.00 43.16 4.02
518 2651 0.875059 CTGCCTTTCCGGTTCTTCAC 59.125 55.000 0.00 0.00 34.25 3.18
619 2752 1.748493 GTATGGCCTTGCGATGGAAAA 59.252 47.619 3.32 0.00 0.00 2.29
655 2788 2.859165 TGGAAATTTCTCTGCGGTCT 57.141 45.000 17.42 0.00 0.00 3.85
656 2789 2.098117 CCATGGAAATTTCTCTGCGGTC 59.902 50.000 17.42 0.00 0.00 4.79
657 2790 2.094675 CCATGGAAATTTCTCTGCGGT 58.905 47.619 17.42 0.00 0.00 5.68
658 2791 1.202336 GCCATGGAAATTTCTCTGCGG 60.202 52.381 18.40 11.76 0.00 5.69
659 2792 1.202336 GGCCATGGAAATTTCTCTGCG 60.202 52.381 18.40 9.99 0.00 5.18
660 2793 1.202336 CGGCCATGGAAATTTCTCTGC 60.202 52.381 18.40 13.92 0.00 4.26
661 2794 2.094675 ACGGCCATGGAAATTTCTCTG 58.905 47.619 18.40 13.90 0.00 3.35
662 2795 2.514458 ACGGCCATGGAAATTTCTCT 57.486 45.000 18.40 2.99 0.00 3.10
663 2796 2.491693 TGAACGGCCATGGAAATTTCTC 59.508 45.455 18.40 8.61 0.00 2.87
664 2797 2.524306 TGAACGGCCATGGAAATTTCT 58.476 42.857 18.40 0.00 0.00 2.52
665 2798 3.447742 GATGAACGGCCATGGAAATTTC 58.552 45.455 18.40 9.83 0.00 2.17
666 2799 2.168313 GGATGAACGGCCATGGAAATTT 59.832 45.455 18.40 1.54 0.00 1.82
667 2800 1.756538 GGATGAACGGCCATGGAAATT 59.243 47.619 18.40 5.09 0.00 1.82
668 2801 1.063717 AGGATGAACGGCCATGGAAAT 60.064 47.619 18.40 0.00 0.00 2.17
669 2802 0.331278 AGGATGAACGGCCATGGAAA 59.669 50.000 18.40 0.00 0.00 3.13
670 2803 0.394216 CAGGATGAACGGCCATGGAA 60.394 55.000 18.40 0.00 39.69 3.53
671 2804 1.224315 CAGGATGAACGGCCATGGA 59.776 57.895 18.40 0.00 39.69 3.41
672 2805 2.484062 GCAGGATGAACGGCCATGG 61.484 63.158 7.63 7.63 39.69 3.66
673 2806 2.484062 GGCAGGATGAACGGCCATG 61.484 63.158 2.24 0.00 45.70 3.66
674 2807 2.124151 GGCAGGATGAACGGCCAT 60.124 61.111 2.24 0.00 45.70 4.40
676 2809 3.134127 GTGGCAGGATGAACGGCC 61.134 66.667 0.00 0.00 46.58 6.13
677 2810 3.134127 GGTGGCAGGATGAACGGC 61.134 66.667 0.00 0.00 39.69 5.68
678 2811 1.746615 CTGGTGGCAGGATGAACGG 60.747 63.158 0.00 0.00 39.69 4.44
679 2812 1.003355 ACTGGTGGCAGGATGAACG 60.003 57.895 0.00 0.00 39.69 3.95
680 2813 0.250901 ACACTGGTGGCAGGATGAAC 60.251 55.000 5.70 0.00 38.34 3.18
681 2814 1.278985 CTACACTGGTGGCAGGATGAA 59.721 52.381 5.70 0.00 38.34 2.57
682 2815 0.904649 CTACACTGGTGGCAGGATGA 59.095 55.000 5.70 0.00 38.34 2.92
683 2816 0.615331 ACTACACTGGTGGCAGGATG 59.385 55.000 5.70 0.00 40.87 3.51
684 2817 0.615331 CACTACACTGGTGGCAGGAT 59.385 55.000 5.70 0.00 34.19 3.24
685 2818 1.480212 CCACTACACTGGTGGCAGGA 61.480 60.000 5.70 0.00 45.97 3.86
686 2819 1.003355 CCACTACACTGGTGGCAGG 60.003 63.158 5.70 0.00 45.97 4.85
687 2820 4.701663 CCACTACACTGGTGGCAG 57.298 61.111 5.70 4.73 45.97 4.85
691 2824 0.392706 TGCACTCCACTACACTGGTG 59.607 55.000 0.00 0.00 32.50 4.17
692 2825 0.681733 CTGCACTCCACTACACTGGT 59.318 55.000 0.00 0.00 32.50 4.00
693 2826 0.681733 ACTGCACTCCACTACACTGG 59.318 55.000 0.00 0.00 0.00 4.00
694 2827 2.094494 CCTACTGCACTCCACTACACTG 60.094 54.545 0.00 0.00 0.00 3.66
695 2828 2.171840 CCTACTGCACTCCACTACACT 58.828 52.381 0.00 0.00 0.00 3.55
696 2829 1.893801 ACCTACTGCACTCCACTACAC 59.106 52.381 0.00 0.00 0.00 2.90
697 2830 2.304221 ACCTACTGCACTCCACTACA 57.696 50.000 0.00 0.00 0.00 2.74
707 2840 1.541379 TTCGAGCACTACCTACTGCA 58.459 50.000 0.00 0.00 35.73 4.41
731 2864 1.008652 CTGAGCTCTCTCCGCGATG 60.009 63.158 16.19 0.00 38.58 3.84
733 2866 2.045829 ACTGAGCTCTCTCCGCGA 60.046 61.111 16.19 0.00 38.58 5.87
734 2867 2.101965 CACTGAGCTCTCTCCGCG 59.898 66.667 16.19 0.00 38.58 6.46
735 2868 2.202730 GCACTGAGCTCTCTCCGC 60.203 66.667 16.19 6.84 41.15 5.54
738 2871 1.146957 CGCATGCACTGAGCTCTCTC 61.147 60.000 19.57 2.26 45.94 3.20
739 2872 1.153608 CGCATGCACTGAGCTCTCT 60.154 57.895 19.57 0.00 45.94 3.10
760 2893 4.095036 CGTTTATCTCTTCTCTTTTGGCCC 59.905 45.833 0.00 0.00 0.00 5.80
763 2896 7.063544 CACTACCGTTTATCTCTTCTCTTTTGG 59.936 40.741 0.00 0.00 0.00 3.28
775 2908 2.159282 CGCACTCCACTACCGTTTATCT 60.159 50.000 0.00 0.00 0.00 1.98
778 2911 0.961019 ACGCACTCCACTACCGTTTA 59.039 50.000 0.00 0.00 0.00 2.01
779 2912 0.319297 GACGCACTCCACTACCGTTT 60.319 55.000 0.00 0.00 31.65 3.60
780 2913 1.288127 GACGCACTCCACTACCGTT 59.712 57.895 0.00 0.00 31.65 4.44
781 2914 2.633509 GGACGCACTCCACTACCGT 61.634 63.158 0.00 0.00 39.21 4.83
782 2915 2.181021 GGACGCACTCCACTACCG 59.819 66.667 0.00 0.00 39.21 4.02
790 2923 1.444553 CGAAGTGGAGGACGCACTC 60.445 63.158 0.00 0.00 36.76 3.51
791 2924 2.651361 CGAAGTGGAGGACGCACT 59.349 61.111 0.00 0.00 32.11 4.40
796 2929 2.125766 AAAGGCCCGAAGTGGAGGAC 62.126 60.000 0.00 0.00 42.00 3.85
797 2930 1.838073 GAAAGGCCCGAAGTGGAGGA 61.838 60.000 0.00 0.00 42.00 3.71
806 2939 1.303236 CATGGTGTGAAAGGCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
825 2958 0.179189 CTTGAAGATTTCGCCACGGC 60.179 55.000 0.00 0.00 37.85 5.68
826 2959 0.179189 GCTTGAAGATTTCGCCACGG 60.179 55.000 0.00 0.00 0.00 4.94
827 2960 0.516877 TGCTTGAAGATTTCGCCACG 59.483 50.000 0.00 0.00 0.00 4.94
828 2961 1.806542 TCTGCTTGAAGATTTCGCCAC 59.193 47.619 0.00 0.00 0.00 5.01
829 2962 2.079158 CTCTGCTTGAAGATTTCGCCA 58.921 47.619 0.00 0.00 0.00 5.69
846 2981 2.419198 GGACGCCATCGATGCTCT 59.581 61.111 20.25 3.29 39.41 4.09
848 2983 3.157217 GAGGGACGCCATCGATGCT 62.157 63.158 20.25 10.14 39.41 3.79
849 2984 2.663188 GAGGGACGCCATCGATGC 60.663 66.667 20.25 13.87 39.41 3.91
877 3012 2.358267 GCTATATATACAGCGCTCCGGT 59.642 50.000 7.13 5.31 38.40 5.28
884 3025 2.286831 CGTCCGGGCTATATATACAGCG 60.287 54.545 3.66 0.00 38.73 5.18
903 3044 2.031616 TCTGTCTCGACGTCCCGT 59.968 61.111 10.58 0.00 45.10 5.28
906 3047 0.803117 TGATGTCTGTCTCGACGTCC 59.197 55.000 10.58 0.00 45.16 4.79
908 3049 1.062733 CGATGATGTCTGTCTCGACGT 59.937 52.381 0.00 0.00 36.71 4.34
910 3051 1.671328 TCCGATGATGTCTGTCTCGAC 59.329 52.381 0.00 0.00 34.52 4.20
911 3052 1.943340 CTCCGATGATGTCTGTCTCGA 59.057 52.381 0.00 0.00 0.00 4.04
918 3059 1.439228 CCGCACTCCGATGATGTCT 59.561 57.895 0.00 0.00 40.02 3.41
919 3060 2.240500 GCCGCACTCCGATGATGTC 61.241 63.158 0.00 0.00 40.02 3.06
920 3061 2.202932 GCCGCACTCCGATGATGT 60.203 61.111 0.00 0.00 40.02 3.06
923 3072 4.794439 CGTGCCGCACTCCGATGA 62.794 66.667 20.87 0.00 40.02 2.92
937 3086 0.179100 CCTCTCTGTATGCACCCGTG 60.179 60.000 0.00 0.00 0.00 4.94
938 3087 1.961180 GCCTCTCTGTATGCACCCGT 61.961 60.000 0.00 0.00 0.00 5.28
939 3088 1.227380 GCCTCTCTGTATGCACCCG 60.227 63.158 0.00 0.00 0.00 5.28
941 3090 2.295909 CTCTAGCCTCTCTGTATGCACC 59.704 54.545 0.00 0.00 0.00 5.01
942 3091 3.218453 TCTCTAGCCTCTCTGTATGCAC 58.782 50.000 0.00 0.00 0.00 4.57
943 3092 3.584733 TCTCTAGCCTCTCTGTATGCA 57.415 47.619 0.00 0.00 0.00 3.96
944 3093 4.141287 TCTTCTCTAGCCTCTCTGTATGC 58.859 47.826 0.00 0.00 0.00 3.14
945 3094 6.061441 TCTTCTTCTCTAGCCTCTCTGTATG 58.939 44.000 0.00 0.00 0.00 2.39
947 3096 5.427157 TCTCTTCTTCTCTAGCCTCTCTGTA 59.573 44.000 0.00 0.00 0.00 2.74
949 3098 4.780815 TCTCTTCTTCTCTAGCCTCTCTG 58.219 47.826 0.00 0.00 0.00 3.35
951 3100 4.137543 CCTCTCTTCTTCTCTAGCCTCTC 58.862 52.174 0.00 0.00 0.00 3.20
952 3101 3.785887 TCCTCTCTTCTTCTCTAGCCTCT 59.214 47.826 0.00 0.00 0.00 3.69
953 3102 4.137543 CTCCTCTCTTCTTCTCTAGCCTC 58.862 52.174 0.00 0.00 0.00 4.70
954 3103 3.527665 ACTCCTCTCTTCTTCTCTAGCCT 59.472 47.826 0.00 0.00 0.00 4.58
955 3104 3.632145 CACTCCTCTCTTCTTCTCTAGCC 59.368 52.174 0.00 0.00 0.00 3.93
957 3106 5.126067 CCTCACTCCTCTCTTCTTCTCTAG 58.874 50.000 0.00 0.00 0.00 2.43
958 3107 4.538490 ACCTCACTCCTCTCTTCTTCTCTA 59.462 45.833 0.00 0.00 0.00 2.43
959 3108 3.333680 ACCTCACTCCTCTCTTCTTCTCT 59.666 47.826 0.00 0.00 0.00 3.10
960 3109 3.443681 CACCTCACTCCTCTCTTCTTCTC 59.556 52.174 0.00 0.00 0.00 2.87
961 3110 3.430453 CACCTCACTCCTCTCTTCTTCT 58.570 50.000 0.00 0.00 0.00 2.85
962 3111 2.094234 GCACCTCACTCCTCTCTTCTTC 60.094 54.545 0.00 0.00 0.00 2.87
972 3121 1.673665 CTTGGCTGCACCTCACTCC 60.674 63.158 0.50 0.00 40.22 3.85
984 3133 3.843027 TCTCCATCTCTTTTCTCTTGGCT 59.157 43.478 0.00 0.00 0.00 4.75
1017 3166 1.602888 CAGCAAGCAGAGGCACCTT 60.603 57.895 0.00 0.00 44.61 3.50
1312 3461 0.813610 CCGCATTTGTAGCCGATGGA 60.814 55.000 0.00 0.00 0.00 3.41
1346 3495 1.390463 GAAACGACCGAGCATCAGAAC 59.610 52.381 0.00 0.00 33.17 3.01
1355 3507 1.467713 GCTACAGAGGAAACGACCGAG 60.468 57.143 0.00 0.00 34.73 4.63
1359 3511 3.690628 AGAGTAGCTACAGAGGAAACGAC 59.309 47.826 25.28 0.00 0.00 4.34
1400 3555 1.113788 AAAGCAGAGCAAGGCAAACA 58.886 45.000 0.00 0.00 0.00 2.83
1407 3562 1.767289 CACAGCAAAAGCAGAGCAAG 58.233 50.000 0.00 0.00 0.00 4.01
1477 3673 1.135199 GCAAAGATGGCATCAGGTGTG 60.135 52.381 27.93 14.45 0.00 3.82
1497 3693 7.219484 AGATTCAAGTAAAAGTTCCACATGG 57.781 36.000 0.00 0.00 0.00 3.66
1533 3729 9.911788 ACCACATTGTTTATTGAGATCTCTTAT 57.088 29.630 22.95 17.37 0.00 1.73
1534 3730 9.739276 AACCACATTGTTTATTGAGATCTCTTA 57.261 29.630 22.95 11.79 0.00 2.10
1535 3731 8.517878 CAACCACATTGTTTATTGAGATCTCTT 58.482 33.333 22.95 13.07 33.20 2.85
1536 3732 8.048534 CAACCACATTGTTTATTGAGATCTCT 57.951 34.615 22.95 6.99 33.20 3.10
1551 3747 3.507233 ACAGAGGCATTACAACCACATTG 59.493 43.478 0.00 0.00 44.60 2.82
1625 3823 8.706322 ACTTCATATAAGTTTGGGAAGTGTTT 57.294 30.769 0.00 0.00 42.22 2.83
1732 3932 0.400594 AACCTGTCCTGCTTGTACCC 59.599 55.000 0.00 0.00 0.00 3.69
1799 4002 1.213296 TAAAGGGTCCTGAGGCCATC 58.787 55.000 5.01 0.00 0.00 3.51
1808 4011 1.992557 TCAGGTTGCATAAAGGGTCCT 59.007 47.619 0.00 0.00 0.00 3.85
1852 4055 7.756722 GTGCTTTAGCTGTGAAATGTAATGAAT 59.243 33.333 0.00 0.00 42.66 2.57
1968 4173 3.436704 GTGGAGAAAACATTCGCTCATCA 59.563 43.478 0.00 0.00 0.00 3.07
1984 4190 9.021807 GCAGTTATATACCTTACATAGTGGAGA 57.978 37.037 0.00 0.00 0.00 3.71
2035 4241 1.139853 CAGGAAATCGAAGGGGGAGAG 59.860 57.143 0.00 0.00 0.00 3.20
2036 4242 1.204146 CAGGAAATCGAAGGGGGAGA 58.796 55.000 0.00 0.00 0.00 3.71
2103 4320 4.829064 TTACCTAAATCATCGCCATTGC 57.171 40.909 0.00 0.00 0.00 3.56
2167 4406 5.459982 AGTCAGAACCTATCAGACCTAGT 57.540 43.478 0.00 0.00 43.56 2.57
2171 4410 6.276847 CAACATAGTCAGAACCTATCAGACC 58.723 44.000 0.00 0.00 43.56 3.85
2226 4469 5.535333 AGCAACTTGTGAATCCTGATTTTG 58.465 37.500 0.00 0.00 0.00 2.44
2232 4475 6.925165 ACATTTTAAGCAACTTGTGAATCCTG 59.075 34.615 0.00 0.00 0.00 3.86
2370 4622 7.201617 GCTTGCTATACCATTACTTTCGTCTTT 60.202 37.037 0.00 0.00 0.00 2.52
2407 4663 0.447801 ACTTGCGCGAATGTTCCATC 59.552 50.000 12.10 0.00 0.00 3.51
2417 4673 2.499756 TATGCTCACCACTTGCGCGA 62.500 55.000 12.10 0.00 38.92 5.87
2421 4677 2.907910 CAAGTATGCTCACCACTTGC 57.092 50.000 11.05 0.00 41.75 4.01


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

AutoCloner maintained by Alex Coulton.