Multiple sequence alignment - TraesCS5B01G382200

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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 TraesCS5B01G382200 chr5B 100.000 3747 0 0 1 3747 560440269 560444015 0.000000e+00 6920.0
1 TraesCS5B01G382200 chr5B 87.618 1696 161 31 1043 2735 677818618 677820267 0.000000e+00 1923.0
2 TraesCS5B01G382200 chr5B 86.812 781 103 0 1168 1948 561061780 561062560 0.000000e+00 872.0
3 TraesCS5B01G382200 chr5B 85.756 688 96 2 2048 2734 561062657 561063343 0.000000e+00 726.0
4 TraesCS5B01G382200 chr5B 83.133 830 90 37 2938 3747 561063611 561064410 0.000000e+00 712.0
5 TraesCS5B01G382200 chr5B 86.495 659 69 14 2935 3590 560731101 560731742 0.000000e+00 706.0
6 TraesCS5B01G382200 chr5B 76.736 864 116 46 2938 3747 677820616 677821448 1.620000e-108 403.0
7 TraesCS5B01G382200 chr5B 93.506 77 5 0 3671 3747 560731902 560731978 8.500000e-22 115.0
8 TraesCS5B01G382200 chr5B 93.182 44 3 0 672 715 249579723 249579766 8.690000e-07 65.8
9 TraesCS5B01G382200 chr5D 93.354 2934 94 40 868 3747 458094472 458097358 0.000000e+00 4244.0
10 TraesCS5B01G382200 chr5D 87.170 1707 163 30 1033 2738 537221905 537223556 0.000000e+00 1888.0
11 TraesCS5B01G382200 chr5D 88.633 783 87 2 1168 1949 458180050 458180831 0.000000e+00 952.0
12 TraesCS5B01G382200 chr5D 83.053 832 89 42 2938 3747 458181900 458182701 0.000000e+00 708.0
13 TraesCS5B01G382200 chr5D 78.049 820 106 47 2985 3747 537223963 537224765 2.050000e-122 449.0
14 TraesCS5B01G382200 chr5D 86.095 338 24 6 340 661 458093951 458094281 3.580000e-90 342.0
15 TraesCS5B01G382200 chr5D 87.097 248 18 3 1 248 458091292 458091525 6.170000e-68 268.0
16 TraesCS5B01G382200 chr5D 90.909 99 7 1 758 856 458094337 458094433 8.440000e-27 132.0
17 TraesCS5B01G382200 chr5D 91.358 81 6 1 247 327 458091828 458091907 3.960000e-20 110.0
18 TraesCS5B01G382200 chr5A 92.716 2732 108 41 1033 3747 575705920 575708577 0.000000e+00 3858.0
19 TraesCS5B01G382200 chr5A 87.356 783 95 4 1168 1948 576084873 576085653 0.000000e+00 894.0
20 TraesCS5B01G382200 chr5A 87.356 783 95 4 1168 1948 576272558 576271778 0.000000e+00 894.0
21 TraesCS5B01G382200 chr5A 85.465 688 98 2 2048 2734 576085738 576086424 0.000000e+00 715.0
22 TraesCS5B01G382200 chr5A 85.465 688 98 2 2048 2734 576271693 576271007 0.000000e+00 715.0
23 TraesCS5B01G382200 chr5A 86.364 660 71 13 2938 3591 576086820 576087466 0.000000e+00 702.0
24 TraesCS5B01G382200 chr5A 85.051 689 99 4 2048 2734 575901893 575902579 0.000000e+00 699.0
25 TraesCS5B01G382200 chr5A 82.460 821 108 26 2938 3747 575902890 575903685 0.000000e+00 686.0
26 TraesCS5B01G382200 chr5A 90.099 404 27 8 246 639 575700613 575701013 2.580000e-141 512.0
27 TraesCS5B01G382200 chr5A 92.661 327 24 0 2938 3264 576270611 576270285 4.380000e-129 472.0
28 TraesCS5B01G382200 chr5A 93.976 249 14 1 1 248 575700084 575700332 3.530000e-100 375.0
29 TraesCS5B01G382200 chr5A 85.926 135 16 2 722 856 575701026 575701157 1.400000e-29 141.0
30 TraesCS5B01G382200 chr4A 88.663 1720 156 26 1033 2744 632943851 632945539 0.000000e+00 2060.0
31 TraesCS5B01G382200 chr4A 80.316 696 79 29 2936 3590 632949256 632949934 1.220000e-129 473.0
32 TraesCS5B01G382200 chr4A 92.045 88 7 0 2845 2932 632945638 632945725 1.410000e-24 124.0
33 TraesCS5B01G382200 chr4B 83.175 422 68 2 2842 3263 27521135 27521553 2.110000e-102 383.0
34 TraesCS5B01G382200 chr4B 88.532 218 25 0 3374 3591 27521575 27521792 7.980000e-67 265.0
35 TraesCS5B01G382200 chr4B 87.615 218 27 0 3374 3591 27249905 27249688 1.730000e-63 254.0
36 TraesCS5B01G382200 chr7A 91.071 56 5 0 673 728 641955189 641955134 4.010000e-10 76.8


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 TraesCS5B01G382200 chr5B 560440269 560444015 3746 False 6920.000000 6920 100.000000 1 3747 1 chr5B.!!$F2 3746
1 TraesCS5B01G382200 chr5B 677818618 677821448 2830 False 1163.000000 1923 82.177000 1043 3747 2 chr5B.!!$F5 2704
2 TraesCS5B01G382200 chr5B 561061780 561064410 2630 False 770.000000 872 85.233667 1168 3747 3 chr5B.!!$F4 2579
3 TraesCS5B01G382200 chr5B 560731101 560731978 877 False 410.500000 706 90.000500 2935 3747 2 chr5B.!!$F3 812
4 TraesCS5B01G382200 chr5D 537221905 537224765 2860 False 1168.500000 1888 82.609500 1033 3747 2 chr5D.!!$F3 2714
5 TraesCS5B01G382200 chr5D 458091292 458097358 6066 False 1019.200000 4244 89.762600 1 3747 5 chr5D.!!$F1 3746
6 TraesCS5B01G382200 chr5D 458180050 458182701 2651 False 830.000000 952 85.843000 1168 3747 2 chr5D.!!$F2 2579
7 TraesCS5B01G382200 chr5A 575705920 575708577 2657 False 3858.000000 3858 92.716000 1033 3747 1 chr5A.!!$F1 2714
8 TraesCS5B01G382200 chr5A 576084873 576087466 2593 False 770.333333 894 86.395000 1168 3591 3 chr5A.!!$F4 2423
9 TraesCS5B01G382200 chr5A 576270285 576272558 2273 True 693.666667 894 88.494000 1168 3264 3 chr5A.!!$R1 2096
10 TraesCS5B01G382200 chr5A 575901893 575903685 1792 False 692.500000 699 83.755500 2048 3747 2 chr5A.!!$F3 1699
11 TraesCS5B01G382200 chr5A 575700084 575701157 1073 False 342.666667 512 90.000333 1 856 3 chr5A.!!$F2 855
12 TraesCS5B01G382200 chr4A 632943851 632949934 6083 False 885.666667 2060 87.008000 1033 3590 3 chr4A.!!$F1 2557
13 TraesCS5B01G382200 chr4B 27521135 27521792 657 False 324.000000 383 85.853500 2842 3591 2 chr4B.!!$F1 749

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
661 3016 0.037303 CCTCAGGCTGCTGGAAAGAA 59.963 55.0 17.64 0.00 0.00 2.52 F
665 3020 0.037447 AGGCTGCTGGAAAGAAGTCC 59.963 55.0 0.00 0.00 38.27 3.85 F
1897 4312 0.465824 ACGGGTAGTCCTCGATCAGG 60.466 60.0 5.18 5.18 45.15 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 3919 2.955881 CGACCCGGAGAAGGCCTTT 61.956 63.158 21.54 9.74 0.00 3.11 R
2518 5001 3.177249 GCTTCGTGTACGCGACCC 61.177 66.667 29.62 19.23 40.85 4.46 R
3585 9836 0.948623 TGATTGGAACGTGACGCAGG 60.949 55.000 4.25 0.00 0.00 4.85 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
77 78 3.670625 TCGGTTGGACTCAAATAGGTTG 58.329 45.455 0.00 0.00 38.71 3.77
106 107 2.233566 TCCAGCAGAAGCCATGGGT 61.234 57.895 11.62 11.62 43.56 4.51
125 126 5.080337 TGGGTAGTTTATGCAAATGGTCAA 58.920 37.500 0.00 0.00 0.00 3.18
128 129 7.102993 GGGTAGTTTATGCAAATGGTCAATTT 58.897 34.615 0.00 0.00 39.13 1.82
203 205 6.124340 TGAACCTGCATGATTGTATGAGATT 58.876 36.000 0.00 0.00 0.00 2.40
224 226 9.547753 GAGATTAAGTCATTAGGCTTTACATGA 57.452 33.333 0.00 0.00 0.00 3.07
238 240 8.302438 AGGCTTTACATGAAATTTTCTTCAGAG 58.698 33.333 10.33 3.61 38.66 3.35
239 241 7.062722 GGCTTTACATGAAATTTTCTTCAGAGC 59.937 37.037 10.33 11.19 38.66 4.09
253 561 2.121948 TCAGAGCCCTGCAGTATGAAT 58.878 47.619 13.81 0.00 40.20 2.57
361 2700 5.552870 AACAGAGAAACACCTACTGATGT 57.447 39.130 0.00 0.00 33.53 3.06
374 2713 1.270839 ACTGATGTTTGGTGTCTCGGG 60.271 52.381 0.00 0.00 0.00 5.14
379 2718 1.340211 TGTTTGGTGTCTCGGGTGTTT 60.340 47.619 0.00 0.00 0.00 2.83
401 2740 4.725556 TTCTCGACAATTTGGAAGTTCG 57.274 40.909 0.78 1.03 0.00 3.95
404 2743 3.459145 TCGACAATTTGGAAGTTCGACA 58.541 40.909 0.78 0.00 0.00 4.35
422 2761 3.183574 CGACAGAATAGTGCGTGTTTTGA 59.816 43.478 0.00 0.00 0.00 2.69
592 2946 1.207089 TGTGTATGGCTGACACTAGGC 59.793 52.381 18.77 0.00 46.05 3.93
636 2990 5.047802 GCAACCCTGAAGATGAAAGATGAAA 60.048 40.000 0.00 0.00 0.00 2.69
643 2998 7.255520 CCTGAAGATGAAAGATGAAATGATCCC 60.256 40.741 0.00 0.00 0.00 3.85
661 3016 0.037303 CCTCAGGCTGCTGGAAAGAA 59.963 55.000 17.64 0.00 0.00 2.52
662 3017 1.451067 CTCAGGCTGCTGGAAAGAAG 58.549 55.000 10.34 0.00 0.00 2.85
665 3020 0.037447 AGGCTGCTGGAAAGAAGTCC 59.963 55.000 0.00 0.00 38.27 3.85
668 3023 2.290323 GGCTGCTGGAAAGAAGTCCTTA 60.290 50.000 0.00 0.00 38.62 2.69
670 3025 4.013050 GCTGCTGGAAAGAAGTCCTTAAT 58.987 43.478 0.00 0.00 38.62 1.40
671 3026 5.186198 GCTGCTGGAAAGAAGTCCTTAATA 58.814 41.667 0.00 0.00 38.62 0.98
672 3027 5.648092 GCTGCTGGAAAGAAGTCCTTAATAA 59.352 40.000 0.00 0.00 38.62 1.40
674 3029 7.148000 GCTGCTGGAAAGAAGTCCTTAATAAAT 60.148 37.037 0.00 0.00 38.62 1.40
675 3030 8.650143 TGCTGGAAAGAAGTCCTTAATAAATT 57.350 30.769 0.00 0.00 38.62 1.82
676 3031 9.747898 TGCTGGAAAGAAGTCCTTAATAAATTA 57.252 29.630 0.00 0.00 38.62 1.40
685 3040 9.465985 GAAGTCCTTAATAAATTACTCTCTCCG 57.534 37.037 0.00 0.00 0.00 4.63
686 3041 8.536340 AGTCCTTAATAAATTACTCTCTCCGT 57.464 34.615 0.00 0.00 0.00 4.69
687 3042 8.631797 AGTCCTTAATAAATTACTCTCTCCGTC 58.368 37.037 0.00 0.00 0.00 4.79
688 3043 7.866898 GTCCTTAATAAATTACTCTCTCCGTCC 59.133 40.741 0.00 0.00 0.00 4.79
689 3044 7.015001 TCCTTAATAAATTACTCTCTCCGTCCC 59.985 40.741 0.00 0.00 0.00 4.46
690 3045 7.201974 CCTTAATAAATTACTCTCTCCGTCCCA 60.202 40.741 0.00 0.00 0.00 4.37
691 3046 6.749036 AATAAATTACTCTCTCCGTCCCAT 57.251 37.500 0.00 0.00 0.00 4.00
692 3047 7.850935 AATAAATTACTCTCTCCGTCCCATA 57.149 36.000 0.00 0.00 0.00 2.74
693 3048 7.850935 ATAAATTACTCTCTCCGTCCCATAA 57.149 36.000 0.00 0.00 0.00 1.90
694 3049 6.749036 AAATTACTCTCTCCGTCCCATAAT 57.251 37.500 0.00 0.00 0.00 1.28
695 3050 7.850935 AAATTACTCTCTCCGTCCCATAATA 57.149 36.000 0.00 0.00 0.00 0.98
696 3051 8.437274 AAATTACTCTCTCCGTCCCATAATAT 57.563 34.615 0.00 0.00 0.00 1.28
697 3052 9.543231 AAATTACTCTCTCCGTCCCATAATATA 57.457 33.333 0.00 0.00 0.00 0.86
698 3053 9.543231 AATTACTCTCTCCGTCCCATAATATAA 57.457 33.333 0.00 0.00 0.00 0.98
699 3054 8.945195 TTACTCTCTCCGTCCCATAATATAAA 57.055 34.615 0.00 0.00 0.00 1.40
700 3055 9.543231 TTACTCTCTCCGTCCCATAATATAAAT 57.457 33.333 0.00 0.00 0.00 1.40
701 3056 7.841956 ACTCTCTCCGTCCCATAATATAAATG 58.158 38.462 0.00 0.00 0.00 2.32
702 3057 6.640518 TCTCTCCGTCCCATAATATAAATGC 58.359 40.000 0.00 0.00 0.00 3.56
703 3058 6.440647 TCTCTCCGTCCCATAATATAAATGCT 59.559 38.462 0.00 0.00 0.00 3.79
704 3059 7.016153 TCTCCGTCCCATAATATAAATGCTT 57.984 36.000 0.00 0.00 0.00 3.91
705 3060 7.458397 TCTCCGTCCCATAATATAAATGCTTT 58.542 34.615 0.00 0.00 0.00 3.51
706 3061 7.942341 TCTCCGTCCCATAATATAAATGCTTTT 59.058 33.333 2.86 2.86 0.00 2.27
707 3062 8.472007 TCCGTCCCATAATATAAATGCTTTTT 57.528 30.769 2.59 0.00 0.00 1.94
797 3158 2.033299 CGTGTGCAAAGTCCTTGATTGT 59.967 45.455 0.00 0.00 37.17 2.71
856 3217 8.564574 TCGTTTAGACTTCATGCTACAAAAATT 58.435 29.630 0.00 0.00 0.00 1.82
857 3218 8.629986 CGTTTAGACTTCATGCTACAAAAATTG 58.370 33.333 0.00 0.00 0.00 2.32
858 3219 8.915654 GTTTAGACTTCATGCTACAAAAATTGG 58.084 33.333 0.00 0.00 34.12 3.16
859 3220 6.899393 AGACTTCATGCTACAAAAATTGGA 57.101 33.333 0.00 0.00 34.12 3.53
861 3222 6.029346 ACTTCATGCTACAAAAATTGGAGG 57.971 37.500 4.59 0.00 42.10 4.30
862 3223 5.047092 ACTTCATGCTACAAAAATTGGAGGG 60.047 40.000 4.59 0.00 42.10 4.30
864 3225 2.534990 TGCTACAAAAATTGGAGGGGG 58.465 47.619 4.59 0.00 42.10 5.40
865 3226 2.110899 TGCTACAAAAATTGGAGGGGGA 59.889 45.455 4.59 0.00 42.10 4.81
866 3227 2.760650 GCTACAAAAATTGGAGGGGGAG 59.239 50.000 4.59 0.00 42.10 4.30
867 3228 1.644509 ACAAAAATTGGAGGGGGAGC 58.355 50.000 0.00 0.00 34.12 4.70
868 3229 1.149923 ACAAAAATTGGAGGGGGAGCT 59.850 47.619 0.00 0.00 34.12 4.09
921 3310 4.472691 TTGAGCAACTTGAACTTGATCG 57.527 40.909 0.00 0.00 36.94 3.69
952 3341 2.878406 GCAAACAGAGGAGCTTACAACA 59.122 45.455 0.00 0.00 0.00 3.33
956 3345 1.347707 CAGAGGAGCTTACAACACCCA 59.652 52.381 0.00 0.00 0.00 4.51
976 3365 2.886523 CAAAGCAGAGGGAACATCACAA 59.113 45.455 0.00 0.00 0.00 3.33
1017 3406 4.696877 GGGCAAATGAAGGGAATTTTTCTG 59.303 41.667 0.00 0.00 0.00 3.02
1108 3508 1.137282 CATGGCAAAGCATATGCACCA 59.863 47.619 28.62 26.32 45.60 4.17
1159 3570 0.944311 CAAGCAAGCAAGCAAGCAGG 60.944 55.000 10.52 0.00 36.85 4.85
1504 3919 2.505407 CTGGTTGGTGATGGTGAGGATA 59.495 50.000 0.00 0.00 0.00 2.59
1897 4312 0.465824 ACGGGTAGTCCTCGATCAGG 60.466 60.000 5.18 5.18 45.15 3.86
1970 4385 8.234546 TGCATCATCAAGATCGATTAATCATTG 58.765 33.333 15.57 12.83 33.72 2.82
1973 4388 7.803724 TCATCAAGATCGATTAATCATTGCTG 58.196 34.615 15.57 13.72 0.00 4.41
2013 4474 6.416750 CGTCATTTGTCATTGATTGATCCATG 59.583 38.462 0.00 0.00 36.54 3.66
2014 4475 6.700081 GTCATTTGTCATTGATTGATCCATGG 59.300 38.462 4.97 4.97 36.54 3.66
2015 4476 6.608002 TCATTTGTCATTGATTGATCCATGGA 59.392 34.615 18.88 18.88 36.54 3.41
2297 4780 1.191489 TGACGAAGGGCTCCATCACA 61.191 55.000 0.00 0.00 0.00 3.58
2518 5001 2.581354 CAGGAAGAGCAGGGTCCG 59.419 66.667 0.00 0.00 36.49 4.79
2755 5238 3.615496 ACGCAGTCAAATAATGGTACGAC 59.385 43.478 0.00 0.00 29.74 4.34
2767 5250 2.156917 TGGTACGACCAGTGAGTGTAG 58.843 52.381 3.02 0.00 44.79 2.74
2769 5252 2.555757 GGTACGACCAGTGAGTGTAGTT 59.444 50.000 0.00 0.00 38.42 2.24
2771 5254 3.814005 ACGACCAGTGAGTGTAGTTTT 57.186 42.857 0.00 0.00 0.00 2.43
2825 5311 3.916761 TGCTTGAATTTGCTCAATGGTC 58.083 40.909 0.00 0.00 34.86 4.02
3325 9558 0.304705 GACCAAGTGCACAGACGTTG 59.695 55.000 21.04 13.79 0.00 4.10
3541 9792 3.437795 TTCCGGAGCTCGTCGTCC 61.438 66.667 3.34 0.00 37.11 4.79
3601 9852 2.970324 GCCTGCGTCACGTTCCAA 60.970 61.111 0.00 0.00 0.00 3.53
3602 9853 2.325082 GCCTGCGTCACGTTCCAAT 61.325 57.895 0.00 0.00 0.00 3.16
3633 10035 3.244976 CCGATCAGCAAACAAAATCCAC 58.755 45.455 0.00 0.00 0.00 4.02
3634 10036 3.057315 CCGATCAGCAAACAAAATCCACT 60.057 43.478 0.00 0.00 0.00 4.00
3638 10040 3.068024 TCAGCAAACAAAATCCACTGGAC 59.932 43.478 0.00 0.00 32.98 4.02
3643 10045 2.306847 ACAAAATCCACTGGACCACAC 58.693 47.619 0.00 0.00 32.98 3.82
3645 10047 3.137544 ACAAAATCCACTGGACCACACTA 59.862 43.478 0.00 0.00 32.98 2.74
3646 10048 3.703001 AAATCCACTGGACCACACTAG 57.297 47.619 0.00 0.00 32.98 2.57
3663 10065 6.584184 CCACACTAGTACATCGATGATTGATC 59.416 42.308 31.33 13.45 0.00 2.92
3664 10066 7.366513 CACACTAGTACATCGATGATTGATCT 58.633 38.462 31.33 18.70 0.00 2.75
3665 10067 7.536964 CACACTAGTACATCGATGATTGATCTC 59.463 40.741 31.33 11.30 0.00 2.75
3666 10068 6.740453 CACTAGTACATCGATGATTGATCTCG 59.260 42.308 31.33 15.60 0.00 4.04
3667 10069 4.480541 AGTACATCGATGATTGATCTCGC 58.519 43.478 31.33 8.37 31.90 5.03
3668 10070 2.323059 ACATCGATGATTGATCTCGCG 58.677 47.619 31.33 0.00 31.90 5.87
3669 10071 2.287849 ACATCGATGATTGATCTCGCGT 60.288 45.455 31.33 1.24 31.90 6.01
3675 10080 3.249013 TGATTGATCTCGCGTAGTACG 57.751 47.619 18.37 18.37 45.88 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.251354 TCTGCTGGACAATGAGCCTC 59.749 55.000 0.00 0.00 34.04 4.70
83 84 1.134367 CATGGCTTCTGCTGGACAATG 59.866 52.381 0.00 0.00 39.59 2.82
125 126 6.841030 AAGGTCCCCTCATTGGTATCCAAAT 61.841 44.000 5.31 0.00 39.04 2.32
128 129 1.010793 AGGTCCCCTCATTGGTATCCA 59.989 52.381 0.00 0.00 0.00 3.41
129 130 1.821088 AGGTCCCCTCATTGGTATCC 58.179 55.000 0.00 0.00 0.00 2.59
224 226 3.233507 TGCAGGGCTCTGAAGAAAATTT 58.766 40.909 20.53 0.00 43.49 1.82
238 240 1.873591 CCGTTATTCATACTGCAGGGC 59.126 52.381 19.93 0.00 0.00 5.19
239 241 1.873591 GCCGTTATTCATACTGCAGGG 59.126 52.381 19.93 7.33 0.00 4.45
253 561 5.110940 GTTAAAACCACATTCAGCCGTTA 57.889 39.130 0.00 0.00 0.00 3.18
277 585 7.888424 TGCACATTATCAGGAATATCCAAATG 58.112 34.615 0.00 5.90 39.61 2.32
336 644 6.483640 ACATCAGTAGGTGTTTCTCTGTTTTC 59.516 38.462 0.00 0.00 0.00 2.29
361 2700 2.131776 AAAACACCCGAGACACCAAA 57.868 45.000 0.00 0.00 0.00 3.28
374 2713 6.033966 ACTTCCAAATTGTCGAGAAAAACAC 58.966 36.000 0.00 0.00 0.00 3.32
379 2718 4.812091 TCGAACTTCCAAATTGTCGAGAAA 59.188 37.500 0.00 0.00 0.00 2.52
401 2740 4.725556 TCAAAACACGCACTATTCTGTC 57.274 40.909 0.00 0.00 0.00 3.51
404 2743 5.885881 TGTTTTCAAAACACGCACTATTCT 58.114 33.333 11.83 0.00 0.00 2.40
422 2761 4.154942 AGGATCATCCACTTGCTTGTTTT 58.845 39.130 6.42 0.00 39.61 2.43
511 2857 1.811266 CCCCGCGTCAGAACATCTG 60.811 63.158 4.92 0.88 45.59 2.90
523 2869 1.269309 TGAACATTTTTGTTCCCCGCG 60.269 47.619 14.37 0.00 45.41 6.46
563 2909 3.735746 GTCAGCCATACACAAAACAAAGC 59.264 43.478 0.00 0.00 0.00 3.51
592 2946 1.468565 CCATCAGTCGGCTGCAATTTG 60.469 52.381 13.43 4.60 42.29 2.32
636 2990 1.706995 CCAGCAGCCTGAGGGATCAT 61.707 60.000 0.00 0.00 41.77 2.45
643 2998 1.271271 ACTTCTTTCCAGCAGCCTGAG 60.271 52.381 0.00 0.00 41.77 3.35
661 3016 8.536340 ACGGAGAGAGTAATTTATTAAGGACT 57.464 34.615 0.00 0.00 0.00 3.85
662 3017 7.866898 GGACGGAGAGAGTAATTTATTAAGGAC 59.133 40.741 0.00 0.00 0.00 3.85
665 3020 7.723324 TGGGACGGAGAGAGTAATTTATTAAG 58.277 38.462 0.00 0.00 0.00 1.85
668 3023 6.749036 ATGGGACGGAGAGAGTAATTTATT 57.251 37.500 0.00 0.00 0.00 1.40
670 3025 7.850935 ATTATGGGACGGAGAGAGTAATTTA 57.149 36.000 0.00 0.00 0.00 1.40
671 3026 6.749036 ATTATGGGACGGAGAGAGTAATTT 57.251 37.500 0.00 0.00 0.00 1.82
672 3027 9.543231 TTATATTATGGGACGGAGAGAGTAATT 57.457 33.333 0.00 0.00 0.00 1.40
674 3029 8.945195 TTTATATTATGGGACGGAGAGAGTAA 57.055 34.615 0.00 0.00 0.00 2.24
675 3030 8.967918 CATTTATATTATGGGACGGAGAGAGTA 58.032 37.037 0.00 0.00 0.00 2.59
676 3031 7.579723 GCATTTATATTATGGGACGGAGAGAGT 60.580 40.741 0.00 0.00 0.00 3.24
677 3032 6.758886 GCATTTATATTATGGGACGGAGAGAG 59.241 42.308 0.00 0.00 0.00 3.20
678 3033 6.440647 AGCATTTATATTATGGGACGGAGAGA 59.559 38.462 0.00 0.00 0.00 3.10
679 3034 6.644347 AGCATTTATATTATGGGACGGAGAG 58.356 40.000 0.00 0.00 0.00 3.20
680 3035 6.620877 AGCATTTATATTATGGGACGGAGA 57.379 37.500 0.00 0.00 0.00 3.71
681 3036 7.687941 AAAGCATTTATATTATGGGACGGAG 57.312 36.000 0.00 0.00 35.86 4.63
682 3037 8.472007 AAAAAGCATTTATATTATGGGACGGA 57.528 30.769 0.00 0.00 37.28 4.69
706 3061 9.554395 TCAAGAAACATAATACTCAGTGTCAAA 57.446 29.630 0.00 0.00 0.00 2.69
707 3062 9.554395 TTCAAGAAACATAATACTCAGTGTCAA 57.446 29.630 0.00 0.00 0.00 3.18
708 3063 9.554395 TTTCAAGAAACATAATACTCAGTGTCA 57.446 29.630 0.00 0.00 0.00 3.58
748 3109 8.642432 CCTCAAGACTTCTACCATATATGACAA 58.358 37.037 14.54 0.77 0.00 3.18
752 3113 7.040340 ACGACCTCAAGACTTCTACCATATATG 60.040 40.741 5.68 5.68 0.00 1.78
755 3116 5.067936 CACGACCTCAAGACTTCTACCATAT 59.932 44.000 0.00 0.00 0.00 1.78
756 3117 4.398358 CACGACCTCAAGACTTCTACCATA 59.602 45.833 0.00 0.00 0.00 2.74
760 3121 3.566523 CACACGACCTCAAGACTTCTAC 58.433 50.000 0.00 0.00 0.00 2.59
856 3217 1.158007 AAAAGAAAGCTCCCCCTCCA 58.842 50.000 0.00 0.00 0.00 3.86
857 3218 2.310779 AAAAAGAAAGCTCCCCCTCC 57.689 50.000 0.00 0.00 0.00 4.30
921 3310 3.214328 TCCTCTGTTTGCTCTGTTTTCC 58.786 45.455 0.00 0.00 0.00 3.13
952 3341 0.779997 ATGTTCCCTCTGCTTTGGGT 59.220 50.000 8.02 0.00 43.74 4.51
956 3345 2.957402 TGTGATGTTCCCTCTGCTTT 57.043 45.000 0.00 0.00 0.00 3.51
976 3365 6.767524 TTGCCCAATAATAAAGTCGATGTT 57.232 33.333 0.00 0.00 0.00 2.71
1017 3406 3.161405 CGGTGCGTCGTCGTGTAC 61.161 66.667 3.66 1.39 39.49 2.90
1108 3508 0.035458 GCTAGTGTGGGTGTTCTGCT 59.965 55.000 0.00 0.00 0.00 4.24
1159 3570 0.686224 CCATCTGAGGAGCTCCATCC 59.314 60.000 33.90 21.65 39.89 3.51
1504 3919 2.955881 CGACCCGGAGAAGGCCTTT 61.956 63.158 21.54 9.74 0.00 3.11
1970 4385 4.367023 TGGACCGTACGTGGCAGC 62.367 66.667 15.21 0.00 0.00 5.25
2297 4780 4.908687 TGGCTCAACACGCACGCT 62.909 61.111 0.00 0.00 0.00 5.07
2518 5001 3.177249 GCTTCGTGTACGCGACCC 61.177 66.667 29.62 19.23 40.85 4.46
2775 5258 5.881923 ACTACACTCACTACCCTCAAAAA 57.118 39.130 0.00 0.00 0.00 1.94
2777 5260 5.881923 AAACTACACTCACTACCCTCAAA 57.118 39.130 0.00 0.00 0.00 2.69
2778 5261 5.364446 TCAAAACTACACTCACTACCCTCAA 59.636 40.000 0.00 0.00 0.00 3.02
2779 5262 4.897076 TCAAAACTACACTCACTACCCTCA 59.103 41.667 0.00 0.00 0.00 3.86
2780 5263 5.464030 TCAAAACTACACTCACTACCCTC 57.536 43.478 0.00 0.00 0.00 4.30
2781 5264 5.881923 TTCAAAACTACACTCACTACCCT 57.118 39.130 0.00 0.00 0.00 4.34
2782 5265 5.106673 GCATTCAAAACTACACTCACTACCC 60.107 44.000 0.00 0.00 0.00 3.69
2783 5266 5.701290 AGCATTCAAAACTACACTCACTACC 59.299 40.000 0.00 0.00 0.00 3.18
2784 5267 6.787085 AGCATTCAAAACTACACTCACTAC 57.213 37.500 0.00 0.00 0.00 2.73
2785 5268 6.989759 TCAAGCATTCAAAACTACACTCACTA 59.010 34.615 0.00 0.00 0.00 2.74
2786 5269 5.822519 TCAAGCATTCAAAACTACACTCACT 59.177 36.000 0.00 0.00 0.00 3.41
2787 5270 6.060028 TCAAGCATTCAAAACTACACTCAC 57.940 37.500 0.00 0.00 0.00 3.51
2788 5271 6.691754 TTCAAGCATTCAAAACTACACTCA 57.308 33.333 0.00 0.00 0.00 3.41
2789 5272 8.482429 CAAATTCAAGCATTCAAAACTACACTC 58.518 33.333 0.00 0.00 0.00 3.51
2790 5273 7.042523 GCAAATTCAAGCATTCAAAACTACACT 60.043 33.333 0.00 0.00 0.00 3.55
2796 5279 6.289745 TGAGCAAATTCAAGCATTCAAAAC 57.710 33.333 0.00 0.00 0.00 2.43
2825 5311 1.930908 GACACCCACTCCGTCTACCG 61.931 65.000 0.00 0.00 0.00 4.02
2843 5429 1.300620 CAAACGCCTCACGGTCAGA 60.301 57.895 0.00 0.00 44.78 3.27
3325 9558 4.015084 TCCGATCTAATCTCCCCGTAATC 58.985 47.826 0.00 0.00 0.00 1.75
3585 9836 0.948623 TGATTGGAACGTGACGCAGG 60.949 55.000 4.25 0.00 0.00 4.85
3592 9843 1.209127 GCCCGTTGATTGGAACGTG 59.791 57.895 0.00 0.00 45.82 4.49
3593 9844 1.228003 TGCCCGTTGATTGGAACGT 60.228 52.632 0.00 0.00 45.82 3.99
3595 9846 1.584495 GGTGCCCGTTGATTGGAAC 59.416 57.895 0.00 0.00 0.00 3.62
3596 9847 1.969064 CGGTGCCCGTTGATTGGAA 60.969 57.895 5.56 0.00 42.73 3.53
3597 9848 2.359354 CGGTGCCCGTTGATTGGA 60.359 61.111 5.56 0.00 42.73 3.53
3609 9860 2.132740 TTTTGTTTGCTGATCGGTGC 57.867 45.000 2.89 0.79 0.00 5.01
3617 9995 3.383761 GTCCAGTGGATTTTGTTTGCTG 58.616 45.455 16.67 0.00 32.73 4.41
3623 10025 2.091885 AGTGTGGTCCAGTGGATTTTGT 60.092 45.455 16.67 0.00 32.73 2.83
3633 10035 3.014623 TCGATGTACTAGTGTGGTCCAG 58.985 50.000 5.39 0.00 0.00 3.86
3634 10036 3.076079 TCGATGTACTAGTGTGGTCCA 57.924 47.619 5.39 0.00 0.00 4.02
3638 10040 5.831997 TCAATCATCGATGTACTAGTGTGG 58.168 41.667 24.09 4.85 0.00 4.17
3643 10045 5.736824 GCGAGATCAATCATCGATGTACTAG 59.263 44.000 24.09 14.95 38.72 2.57
3645 10047 4.480541 GCGAGATCAATCATCGATGTACT 58.519 43.478 24.09 14.47 38.72 2.73
3646 10048 3.299281 CGCGAGATCAATCATCGATGTAC 59.701 47.826 24.09 10.60 38.72 2.90


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

AutoCloner maintained by Alex Coulton.