Multiple sequence alignment - TraesCS3A01G160600

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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 TraesCS3A01G160600 chr3A 100.000 4024 0 0 1 4024 161442766 161446789 0.000000e+00 7432
1 TraesCS3A01G160600 chr3A 97.273 110 3 0 1 110 430781716 430781825 1.910000e-43 187
2 TraesCS3A01G160600 chr3A 87.778 90 11 0 1044 1133 523334098 523334009 5.500000e-19 106
3 TraesCS3A01G160600 chr3B 90.909 2354 122 40 1739 4024 204280055 204282384 0.000000e+00 3077
4 TraesCS3A01G160600 chr3B 93.097 1014 35 8 747 1739 204279031 204280030 0.000000e+00 1452
5 TraesCS3A01G160600 chr3B 90.068 735 51 10 1 729 521703164 521703882 0.000000e+00 933
6 TraesCS3A01G160600 chr3B 89.331 703 50 12 1 680 141738990 141739690 0.000000e+00 859
7 TraesCS3A01G160600 chr3D 90.238 2356 116 42 1739 4024 142474691 142477002 0.000000e+00 2972
8 TraesCS3A01G160600 chr3D 95.115 1003 20 10 761 1739 142473669 142474666 0.000000e+00 1554
9 TraesCS3A01G160600 chr3D 89.110 753 51 12 1 725 21324682 21323933 0.000000e+00 907
10 TraesCS3A01G160600 chr3D 90.106 566 39 8 1 549 454525822 454525257 0.000000e+00 719
11 TraesCS3A01G160600 chr3D 96.364 110 4 0 1 110 580544000 580544109 8.880000e-42 182
12 TraesCS3A01G160600 chr3D 79.343 213 36 8 1044 1252 402494127 402493919 4.190000e-30 143
13 TraesCS3A01G160600 chr2D 89.523 754 54 12 1 732 117239328 117238578 0.000000e+00 931
14 TraesCS3A01G160600 chr2D 92.012 338 18 6 1775 2106 392545318 392544984 2.190000e-127 466
15 TraesCS3A01G160600 chr7D 88.755 747 60 8 1 724 404745609 404746354 0.000000e+00 893
16 TraesCS3A01G160600 chr7D 92.012 338 18 6 1775 2106 474076516 474076850 2.190000e-127 466
17 TraesCS3A01G160600 chr7B 88.173 761 62 8 1 735 65252634 65253392 0.000000e+00 881
18 TraesCS3A01G160600 chr2A 87.834 748 66 5 1 725 722684002 722683257 0.000000e+00 854
19 TraesCS3A01G160600 chr2A 92.059 340 17 7 1775 2105 130808767 130809105 1.690000e-128 470
20 TraesCS3A01G160600 chr2B 87.433 748 68 7 1 725 195061038 195060294 0.000000e+00 837
21 TraesCS3A01G160600 chr2B 92.560 336 16 4 1778 2107 136170537 136170205 1.310000e-129 473
22 TraesCS3A01G160600 chrUn 87.084 751 48 13 1 726 48560019 48560745 0.000000e+00 804
23 TraesCS3A01G160600 chr6A 92.793 333 20 4 1775 2106 258137514 258137843 2.810000e-131 479
24 TraesCS3A01G160600 chr6B 87.356 435 32 9 1 412 14310367 14309933 1.010000e-130 477
25 TraesCS3A01G160600 chr6B 94.545 110 6 0 1 110 88325328 88325437 1.920000e-38 171
26 TraesCS3A01G160600 chr1A 92.308 338 17 6 1775 2106 396446021 396445687 4.710000e-129 472
27 TraesCS3A01G160600 chr7A 92.012 338 18 6 1775 2106 319591665 319591999 2.190000e-127 466
28 TraesCS3A01G160600 chr4A 84.956 339 25 11 1 317 382432215 382431881 1.800000e-83 320


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 TraesCS3A01G160600 chr3A 161442766 161446789 4023 False 7432.0 7432 100.0000 1 4024 1 chr3A.!!$F1 4023
1 TraesCS3A01G160600 chr3B 204279031 204282384 3353 False 2264.5 3077 92.0030 747 4024 2 chr3B.!!$F3 3277
2 TraesCS3A01G160600 chr3B 521703164 521703882 718 False 933.0 933 90.0680 1 729 1 chr3B.!!$F2 728
3 TraesCS3A01G160600 chr3B 141738990 141739690 700 False 859.0 859 89.3310 1 680 1 chr3B.!!$F1 679
4 TraesCS3A01G160600 chr3D 142473669 142477002 3333 False 2263.0 2972 92.6765 761 4024 2 chr3D.!!$F2 3263
5 TraesCS3A01G160600 chr3D 21323933 21324682 749 True 907.0 907 89.1100 1 725 1 chr3D.!!$R1 724
6 TraesCS3A01G160600 chr3D 454525257 454525822 565 True 719.0 719 90.1060 1 549 1 chr3D.!!$R3 548
7 TraesCS3A01G160600 chr2D 117238578 117239328 750 True 931.0 931 89.5230 1 732 1 chr2D.!!$R1 731
8 TraesCS3A01G160600 chr7D 404745609 404746354 745 False 893.0 893 88.7550 1 724 1 chr7D.!!$F1 723
9 TraesCS3A01G160600 chr7B 65252634 65253392 758 False 881.0 881 88.1730 1 735 1 chr7B.!!$F1 734
10 TraesCS3A01G160600 chr2A 722683257 722684002 745 True 854.0 854 87.8340 1 725 1 chr2A.!!$R1 724
11 TraesCS3A01G160600 chr2B 195060294 195061038 744 True 837.0 837 87.4330 1 725 1 chr2B.!!$R2 724
12 TraesCS3A01G160600 chrUn 48560019 48560745 726 False 804.0 804 87.0840 1 726 1 chrUn.!!$F1 725

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
122 148 0.250338 AGCTTTTCCTGTCACCGGTC 60.250 55.0 2.59 0.0 0.00 4.79 F
984 1039 0.320946 TCGATCCGAAAACCACCACC 60.321 55.0 0.00 0.0 31.06 4.61 F
1699 1776 0.168788 CACAAAATGCGGCGATCAGT 59.831 50.0 12.98 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1719 0.033504 GTCTCAGGTCGTGCAGGAAA 59.966 55.0 11.28 0.0 0.00 3.13 R
1995 2103 0.321021 TCATGGTTTTGGCACATGGC 59.679 50.0 13.76 0.0 41.64 4.40 R
3351 3504 0.396435 ATTCTGTTCTGGACACGGCA 59.604 50.0 0.00 0.0 33.82 5.69 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
38 39 8.987890 GGTTGTAACTTTTATAACTGTCGGTTA 58.012 33.333 6.72 6.72 43.49 2.85
67 68 1.265635 CGTTTTTCGTCCATGGCTTCA 59.734 47.619 6.96 0.00 34.52 3.02
89 92 5.578727 TCATTTCCACGGTTGAAACTTTTTG 59.421 36.000 9.27 4.69 34.77 2.44
110 113 6.903883 TTGTATAGTCGGATGAAGCTTTTC 57.096 37.500 0.00 0.73 0.00 2.29
122 148 0.250338 AGCTTTTCCTGTCACCGGTC 60.250 55.000 2.59 0.00 0.00 4.79
123 149 0.534203 GCTTTTCCTGTCACCGGTCA 60.534 55.000 2.59 0.00 0.00 4.02
334 366 1.371267 CTTCAGTCGTCGCAACCGA 60.371 57.895 0.00 0.00 42.01 4.69
447 479 3.479203 CTAGGATGGTGGCCGGCA 61.479 66.667 30.85 12.04 0.00 5.69
483 515 2.994995 TGCGATGAGGACGGTGGT 60.995 61.111 0.00 0.00 0.00 4.16
573 607 0.753848 TGGCGTATGGGAGATCACGA 60.754 55.000 5.31 0.00 36.53 4.35
575 609 0.952280 GCGTATGGGAGATCACGAGA 59.048 55.000 5.31 0.00 36.53 4.04
643 694 3.644966 ATTGGGGAAGAAGCAATCGTA 57.355 42.857 0.00 0.00 0.00 3.43
696 747 1.153706 CGACCGGCCGTATTGTTCT 60.154 57.895 26.12 0.00 0.00 3.01
706 757 1.451207 TATTGTTCTGCCGGCGCAT 60.451 52.632 23.90 9.35 46.11 4.73
732 783 3.855689 CACATCAGTGCCCCTAAAAAG 57.144 47.619 0.00 0.00 39.21 2.27
734 785 3.191371 CACATCAGTGCCCCTAAAAAGAC 59.809 47.826 0.00 0.00 39.21 3.01
735 786 2.579410 TCAGTGCCCCTAAAAAGACC 57.421 50.000 0.00 0.00 0.00 3.85
737 788 1.075536 CAGTGCCCCTAAAAAGACCCT 59.924 52.381 0.00 0.00 0.00 4.34
738 789 1.354705 AGTGCCCCTAAAAAGACCCTC 59.645 52.381 0.00 0.00 0.00 4.30
739 790 1.354705 GTGCCCCTAAAAAGACCCTCT 59.645 52.381 0.00 0.00 0.00 3.69
740 791 2.574824 GTGCCCCTAAAAAGACCCTCTA 59.425 50.000 0.00 0.00 0.00 2.43
741 792 2.844348 TGCCCCTAAAAAGACCCTCTAG 59.156 50.000 0.00 0.00 0.00 2.43
742 793 3.113043 GCCCCTAAAAAGACCCTCTAGA 58.887 50.000 0.00 0.00 0.00 2.43
743 794 3.717392 GCCCCTAAAAAGACCCTCTAGAT 59.283 47.826 0.00 0.00 0.00 1.98
744 795 4.202377 GCCCCTAAAAAGACCCTCTAGATC 60.202 50.000 0.00 0.00 0.00 2.75
745 796 5.220521 CCCCTAAAAAGACCCTCTAGATCT 58.779 45.833 0.00 0.00 0.00 2.75
982 1037 0.682852 ACTCGATCCGAAAACCACCA 59.317 50.000 0.00 0.00 34.74 4.17
984 1039 0.320946 TCGATCCGAAAACCACCACC 60.321 55.000 0.00 0.00 31.06 4.61
1307 1365 4.640647 GTGCCTTTGGTAGATTTCTTAGGG 59.359 45.833 0.00 0.00 0.00 3.53
1357 1425 5.010719 TGGATTCGTAGATGATGGTTAGGTC 59.989 44.000 0.00 0.00 35.04 3.85
1362 1430 4.556898 CGTAGATGATGGTTAGGTCCTTCG 60.557 50.000 0.00 0.00 35.32 3.79
1465 1534 5.395682 CCATCTGGCCATATGTTTTATGG 57.604 43.478 24.85 14.88 45.50 2.74
1608 1685 1.839424 AGGCACTACAATTTCCCAGC 58.161 50.000 0.00 0.00 36.02 4.85
1634 1711 4.631377 TGCGAATCAGATTACAAGTTCCTG 59.369 41.667 0.00 0.00 0.00 3.86
1697 1774 1.505807 CCACAAAATGCGGCGATCA 59.494 52.632 12.98 0.00 0.00 2.92
1699 1776 0.168788 CACAAAATGCGGCGATCAGT 59.831 50.000 12.98 0.00 0.00 3.41
1715 1792 5.300752 CGATCAGTATCTGCCCAGTAATTT 58.699 41.667 0.00 0.00 0.00 1.82
1810 1912 2.868044 GCTTGTCCAACATCGTCTGAGT 60.868 50.000 0.00 0.00 0.00 3.41
1849 1951 3.080121 AGGCCTCCAGAAGCTCCG 61.080 66.667 0.00 0.00 0.00 4.63
1858 1960 1.144936 AGAAGCTCCGGTGCATAGC 59.855 57.895 28.68 17.08 36.48 2.97
1960 2062 6.051717 AGATTTGAAGGATTGGAGTATCACG 58.948 40.000 0.00 0.00 36.25 4.35
1995 2103 1.639298 GGTGCGTGGAAGCTTGCTAG 61.639 60.000 19.34 13.27 38.13 3.42
2006 2114 1.597797 GCTTGCTAGCCATGTGCCAA 61.598 55.000 13.29 0.00 41.74 4.52
2051 2159 0.919710 ATGGGTTTCACCTCTAGCCC 59.080 55.000 0.00 0.00 38.64 5.19
2091 2199 6.406065 GGGACTAAAGGCTTTGTTGTTGTTTA 60.406 38.462 22.32 0.00 0.00 2.01
2122 2230 5.606348 TTGTTGGCCTGTACAGAAAATTT 57.394 34.783 24.68 0.00 0.00 1.82
2132 2240 9.569167 GCCTGTACAGAAAATTTATTAGGTTTC 57.431 33.333 24.68 0.00 0.00 2.78
2215 2323 2.753296 GCTGCATGCCAAACAAAAGTA 58.247 42.857 16.68 0.00 35.15 2.24
2238 2346 4.018415 AGTTCACTACCATTACCTGCCATT 60.018 41.667 0.00 0.00 0.00 3.16
2291 2399 3.490348 CAGTTGGATTGACTTGGACCTT 58.510 45.455 0.00 0.00 0.00 3.50
2302 2410 9.788960 GATTGACTTGGACCTTATATTGTTTTC 57.211 33.333 0.00 0.00 0.00 2.29
2323 2431 2.223923 CCCAATTTCCGAAACAGCACAA 60.224 45.455 0.00 0.00 0.00 3.33
2370 2478 8.984891 TGTGCTATTGTTTATTTGAATCCAAG 57.015 30.769 0.00 0.00 33.23 3.61
2402 2510 9.587772 GTACTATATTTCTATATGTGCAGGTGG 57.412 37.037 0.00 0.00 0.00 4.61
2424 2532 4.044426 GTGCATTCTTTTTCAGTGTCCAC 58.956 43.478 0.00 0.00 0.00 4.02
2446 2554 8.439971 TCCACTTGAGCTATTATTTCACCATAT 58.560 33.333 0.00 0.00 0.00 1.78
2518 2626 4.136796 CTCCATGTCTTCAACTGGAAACA 58.863 43.478 0.00 0.00 35.85 2.83
2520 2628 4.338118 TCCATGTCTTCAACTGGAAACAAC 59.662 41.667 0.00 0.00 42.06 3.32
2598 2706 7.307870 GCATCACAGAGAAAAGCATCCTAATAG 60.308 40.741 0.00 0.00 0.00 1.73
2599 2707 6.051717 TCACAGAGAAAAGCATCCTAATAGC 58.948 40.000 0.00 0.00 0.00 2.97
2600 2708 6.054295 CACAGAGAAAAGCATCCTAATAGCT 58.946 40.000 0.00 0.00 41.03 3.32
2602 2710 6.765512 ACAGAGAAAAGCATCCTAATAGCTTC 59.234 38.462 0.00 0.00 46.95 3.86
2603 2711 6.765036 CAGAGAAAAGCATCCTAATAGCTTCA 59.235 38.462 0.00 0.00 46.95 3.02
2613 2745 7.228308 GCATCCTAATAGCTTCACTTCTTTCAT 59.772 37.037 0.00 0.00 0.00 2.57
2651 2786 2.228822 GCATGGTGAACTTACAACCCAG 59.771 50.000 0.00 0.00 0.00 4.45
2657 2792 2.706723 TGAACTTACAACCCAGTGGCTA 59.293 45.455 2.61 0.00 33.59 3.93
2666 2801 4.080015 ACAACCCAGTGGCTATTATAAGCA 60.080 41.667 2.61 0.00 44.64 3.91
2674 2809 4.932200 GTGGCTATTATAAGCAGCAGTAGG 59.068 45.833 18.52 0.00 44.64 3.18
2704 2839 6.461927 CCACCTTTTGATGTTATGCATGCTAT 60.462 38.462 20.33 12.94 38.06 2.97
2705 2840 6.639686 CACCTTTTGATGTTATGCATGCTATC 59.360 38.462 20.33 14.09 38.06 2.08
2749 2902 5.164620 TCTTAGTTGCTCATGGTCATTGA 57.835 39.130 0.00 0.00 0.00 2.57
2751 2904 5.645067 TCTTAGTTGCTCATGGTCATTGAAG 59.355 40.000 0.00 0.00 0.00 3.02
2764 2917 5.307976 TGGTCATTGAAGAGTATAGGGGATG 59.692 44.000 0.00 0.00 0.00 3.51
2765 2918 5.280215 GGTCATTGAAGAGTATAGGGGATGG 60.280 48.000 0.00 0.00 0.00 3.51
2766 2919 4.846367 TCATTGAAGAGTATAGGGGATGGG 59.154 45.833 0.00 0.00 0.00 4.00
2767 2920 3.275848 TGAAGAGTATAGGGGATGGGG 57.724 52.381 0.00 0.00 0.00 4.96
2769 2922 3.174779 GAAGAGTATAGGGGATGGGGTC 58.825 54.545 0.00 0.00 0.00 4.46
2770 2923 2.161624 AGAGTATAGGGGATGGGGTCA 58.838 52.381 0.00 0.00 0.00 4.02
2771 2924 2.735906 AGAGTATAGGGGATGGGGTCAT 59.264 50.000 0.00 0.00 36.09 3.06
2772 2925 2.840651 GAGTATAGGGGATGGGGTCATG 59.159 54.545 0.00 0.00 32.98 3.07
2773 2926 2.458706 AGTATAGGGGATGGGGTCATGA 59.541 50.000 0.00 0.00 32.98 3.07
2774 2927 2.769011 ATAGGGGATGGGGTCATGAT 57.231 50.000 0.00 0.00 32.98 2.45
2775 2928 2.531177 TAGGGGATGGGGTCATGATT 57.469 50.000 0.00 0.00 32.98 2.57
2776 2929 1.152649 AGGGGATGGGGTCATGATTC 58.847 55.000 0.00 0.00 32.98 2.52
2777 2930 0.113190 GGGGATGGGGTCATGATTCC 59.887 60.000 0.00 4.46 32.98 3.01
2778 2931 1.152649 GGGATGGGGTCATGATTCCT 58.847 55.000 15.38 4.67 32.98 3.36
2779 2932 2.348472 GGGATGGGGTCATGATTCCTA 58.652 52.381 15.38 11.24 32.98 2.94
2780 2933 2.040412 GGGATGGGGTCATGATTCCTAC 59.960 54.545 15.38 10.31 32.98 3.18
2781 2934 2.982488 GGATGGGGTCATGATTCCTACT 59.018 50.000 15.38 4.10 32.98 2.57
2782 2935 3.008485 GGATGGGGTCATGATTCCTACTC 59.992 52.174 15.38 10.47 32.98 2.59
2783 2936 3.421394 TGGGGTCATGATTCCTACTCT 57.579 47.619 15.38 0.00 0.00 3.24
2784 2937 4.552883 TGGGGTCATGATTCCTACTCTA 57.447 45.455 15.38 0.00 0.00 2.43
2785 2938 5.093236 TGGGGTCATGATTCCTACTCTAT 57.907 43.478 15.38 0.00 0.00 1.98
2786 2939 5.476983 TGGGGTCATGATTCCTACTCTATT 58.523 41.667 15.38 0.00 0.00 1.73
2787 2940 5.911178 TGGGGTCATGATTCCTACTCTATTT 59.089 40.000 15.38 0.00 0.00 1.40
2788 2941 6.043243 TGGGGTCATGATTCCTACTCTATTTC 59.957 42.308 15.38 0.25 0.00 2.17
2789 2942 6.043243 GGGGTCATGATTCCTACTCTATTTCA 59.957 42.308 14.95 0.00 0.00 2.69
2790 2943 7.256835 GGGGTCATGATTCCTACTCTATTTCAT 60.257 40.741 14.95 0.00 0.00 2.57
2791 2944 7.605691 GGGTCATGATTCCTACTCTATTTCATG 59.394 40.741 0.00 0.00 40.01 3.07
2826 2979 4.904251 ACTATGGACTGATGGTATGCTCTT 59.096 41.667 0.00 0.00 0.00 2.85
2827 2980 3.827008 TGGACTGATGGTATGCTCTTC 57.173 47.619 0.00 0.00 0.00 2.87
2830 2983 3.494048 GGACTGATGGTATGCTCTTCCTG 60.494 52.174 0.00 0.00 0.00 3.86
3017 3170 2.388232 CGAGCTGGTTAACGTGGCC 61.388 63.158 0.00 0.00 0.00 5.36
3083 3236 9.507280 AAAACGAAGCACTATGAATGAATATTG 57.493 29.630 0.00 0.00 0.00 1.90
3091 3244 7.073883 CACTATGAATGAATATTGTCAAGCCG 58.926 38.462 0.00 0.00 0.00 5.52
3290 3443 3.242252 GCGCTGAGCTTTAGAGATCAAAC 60.242 47.826 1.78 0.00 46.70 2.93
3311 3464 3.378112 ACGGAATGAACTGCCATTACATG 59.622 43.478 0.00 0.00 37.24 3.21
3332 3485 4.346970 TGTTGTGTTGAATTGCTGTTACG 58.653 39.130 0.00 0.00 0.00 3.18
3351 3504 9.820229 CTGTTACGTTGTGTTGATGTTATATTT 57.180 29.630 0.00 0.00 0.00 1.40
3377 3530 4.527564 GTGTCCAGAACAGAATTTTCGTG 58.472 43.478 0.00 0.00 38.97 4.35
3395 3548 2.414138 CGTGGAGATCCGGTAAAACAAC 59.586 50.000 0.00 0.00 39.43 3.32
3544 3711 3.254024 AAACATGGCTCCCGTCGCT 62.254 57.895 0.00 0.00 0.00 4.93
3582 3752 0.537188 TCATCGGAGGAGGCAGAAAC 59.463 55.000 0.00 0.00 0.00 2.78
3930 4100 2.424523 CCACCCTCTCCTTCTACGGTAT 60.425 54.545 0.00 0.00 0.00 2.73
4000 4183 4.474846 CCGGCGGCCGTGATTTTG 62.475 66.667 36.22 17.86 46.80 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.422546 TGGACGAAAAACGAAAACTTGT 57.577 36.364 0.00 0.00 45.77 3.16
67 68 5.483811 ACAAAAAGTTTCAACCGTGGAAAT 58.516 33.333 4.36 0.00 36.71 2.17
89 92 5.463724 CAGGAAAAGCTTCATCCGACTATAC 59.536 44.000 19.90 1.11 38.31 1.47
110 113 2.762535 AAGTTATGACCGGTGACAGG 57.237 50.000 14.63 0.00 0.00 4.00
227 258 1.498865 GATGCCCGATGCTACAACCG 61.499 60.000 0.00 0.00 42.00 4.44
299 331 2.584261 AAGCTCATCGGCATGCTCGT 62.584 55.000 18.92 7.58 34.38 4.18
312 344 0.939577 GTTGCGACGACTGAAGCTCA 60.940 55.000 0.00 0.00 0.00 4.26
334 366 2.902705 TGTTGAGACCGTTGTAGCTT 57.097 45.000 0.00 0.00 0.00 3.74
489 521 4.680537 AGCCGTCCACCCTCGTCT 62.681 66.667 0.00 0.00 0.00 4.18
573 607 2.289072 CGTCTGTTCATTCCCACTGTCT 60.289 50.000 0.00 0.00 0.00 3.41
575 609 1.691976 TCGTCTGTTCATTCCCACTGT 59.308 47.619 0.00 0.00 0.00 3.55
643 694 3.254166 ACGATACGTTCCATAATAGCCGT 59.746 43.478 0.00 0.00 36.35 5.68
688 739 2.046796 TGCGCCGGCAGAACAATA 60.047 55.556 28.98 0.00 46.21 1.90
714 765 2.755103 GGTCTTTTTAGGGGCACTGATG 59.245 50.000 0.00 0.00 0.00 3.07
732 783 5.831702 TTGAACGTTAGATCTAGAGGGTC 57.168 43.478 0.00 8.59 0.00 4.46
734 785 9.765795 ATAATTTTGAACGTTAGATCTAGAGGG 57.234 33.333 0.00 0.00 0.00 4.30
958 1013 0.989890 GTTTTCGGATCGAGTCGTGG 59.010 55.000 13.12 0.72 37.14 4.94
1215 1270 1.869767 GCAGTAAAGATGATGGAGCCG 59.130 52.381 0.00 0.00 0.00 5.52
1357 1425 8.665685 ACTATAAAGCTACACAAATTTCGAAGG 58.334 33.333 0.00 0.00 0.00 3.46
1362 1430 6.687105 CGCCACTATAAAGCTACACAAATTTC 59.313 38.462 0.00 0.00 0.00 2.17
1465 1534 7.823745 AATACCAACCATCCAGATAATTCAC 57.176 36.000 0.00 0.00 0.00 3.18
1510 1587 5.562890 GCCTCCGTTCCAAAATATAATCTGC 60.563 44.000 0.00 0.00 0.00 4.26
1561 1638 3.125520 AAAGGCGCTTTCCCTTTCA 57.874 47.368 4.81 0.00 46.88 2.69
1608 1685 4.584029 ACTTGTAATCTGATTCGCAACG 57.416 40.909 6.10 9.56 0.00 4.10
1634 1711 1.155424 TCGTGCAGGAAACGTTCACC 61.155 55.000 6.64 14.15 41.70 4.02
1642 1719 0.033504 GTCTCAGGTCGTGCAGGAAA 59.966 55.000 11.28 0.00 0.00 3.13
1697 1774 6.763715 TGGATAAATTACTGGGCAGATACT 57.236 37.500 0.00 0.00 0.00 2.12
1699 1776 7.829211 GCTATTGGATAAATTACTGGGCAGATA 59.171 37.037 0.00 0.00 0.00 1.98
1810 1912 1.476085 CGCTGAATATGCCCAAACCAA 59.524 47.619 0.00 0.00 0.00 3.67
1858 1960 3.255379 GCTCGCTTTAGCCGTCCG 61.255 66.667 0.00 0.00 36.45 4.79
1873 1975 3.172339 ACCTCTCTTGACATTCTCAGCT 58.828 45.455 0.00 0.00 0.00 4.24
1879 1981 2.040412 ACCCCAACCTCTCTTGACATTC 59.960 50.000 0.00 0.00 0.00 2.67
1960 2062 1.897560 CACCCCTGTCCAGTTCTTTC 58.102 55.000 0.00 0.00 0.00 2.62
1995 2103 0.321021 TCATGGTTTTGGCACATGGC 59.679 50.000 13.76 0.00 41.64 4.40
2021 2129 3.531538 GTGAAACCCATAAGATCTCGCA 58.468 45.455 0.00 0.00 0.00 5.10
2073 2181 7.174080 ACAAACAATAAACAACAACAAAGCCTT 59.826 29.630 0.00 0.00 0.00 4.35
2091 2199 3.625649 ACAGGCCAACAAACAAACAAT 57.374 38.095 5.01 0.00 0.00 2.71
2201 2309 5.066764 GGTAGTGAACTACTTTTGTTTGGCA 59.933 40.000 17.71 0.00 46.06 4.92
2215 2323 2.910319 TGGCAGGTAATGGTAGTGAACT 59.090 45.455 0.00 0.00 0.00 3.01
2238 2346 0.610174 CTGGCCAGCAGAACTGTAGA 59.390 55.000 22.33 0.00 45.68 2.59
2269 2377 1.541588 GGTCCAAGTCAATCCAACTGC 59.458 52.381 0.00 0.00 0.00 4.40
2291 2399 8.585881 TGTTTCGGAAATTGGGAAAACAATATA 58.414 29.630 6.43 0.00 40.01 0.86
2302 2410 1.339610 TGTGCTGTTTCGGAAATTGGG 59.660 47.619 6.43 0.00 0.00 4.12
2323 2431 7.651808 CACAATACAAGATTGGAAAAGAGTGT 58.348 34.615 2.62 0.00 33.56 3.55
2370 2478 9.804758 GCACATATAGAAATATAGTACCCTCAC 57.195 37.037 0.00 0.00 0.00 3.51
2402 2510 4.044426 GTGGACACTGAAAAAGAATGCAC 58.956 43.478 0.00 0.00 32.09 4.57
2411 2519 3.281727 AGCTCAAGTGGACACTGAAAA 57.718 42.857 5.63 0.00 41.58 2.29
2492 2600 5.631245 TTTCCAGTTGAAGACATGGAGACAA 60.631 40.000 0.00 0.00 42.54 3.18
2518 2626 8.928448 ACTATCAATATGGTATGACAGACTGTT 58.072 33.333 10.01 0.00 0.00 3.16
2520 2628 9.847706 GTACTATCAATATGGTATGACAGACTG 57.152 37.037 0.00 0.00 32.41 3.51
2557 2665 5.945191 TCTGTGATGCATGACATTAAAGGAA 59.055 36.000 19.53 0.00 39.84 3.36
2564 2672 5.621555 GCTTTTCTCTGTGATGCATGACATT 60.622 40.000 19.53 0.00 39.84 2.71
2572 2680 3.015327 AGGATGCTTTTCTCTGTGATGC 58.985 45.455 0.00 0.00 0.00 3.91
2624 2756 6.451393 GGTTGTAAGTTCACCATGCAATTTA 58.549 36.000 0.00 0.00 0.00 1.40
2625 2757 5.296748 GGTTGTAAGTTCACCATGCAATTT 58.703 37.500 0.00 0.00 0.00 1.82
2626 2758 4.262420 GGGTTGTAAGTTCACCATGCAATT 60.262 41.667 0.00 0.00 0.00 2.32
2642 2777 5.131308 TGCTTATAATAGCCACTGGGTTGTA 59.869 40.000 4.78 0.00 40.49 2.41
2651 2786 4.932200 CCTACTGCTGCTTATAATAGCCAC 59.068 45.833 15.34 0.91 40.49 5.01
2657 2792 5.839063 TGGTAGTCCTACTGCTGCTTATAAT 59.161 40.000 0.00 0.00 36.36 1.28
2666 2801 2.625282 AAGGTGGTAGTCCTACTGCT 57.375 50.000 4.58 0.00 36.36 4.24
2674 2809 5.414454 TGCATAACATCAAAAGGTGGTAGTC 59.586 40.000 0.00 0.00 0.00 2.59
2728 2881 5.645067 TCTTCAATGACCATGAGCAACTAAG 59.355 40.000 0.00 0.00 0.00 2.18
2749 2902 2.527057 TGACCCCATCCCCTATACTCTT 59.473 50.000 0.00 0.00 0.00 2.85
2751 2904 2.715763 TGACCCCATCCCCTATACTC 57.284 55.000 0.00 0.00 0.00 2.59
2764 2917 6.043243 TGAAATAGAGTAGGAATCATGACCCC 59.957 42.308 11.28 9.21 0.00 4.95
2765 2918 7.067496 TGAAATAGAGTAGGAATCATGACCC 57.933 40.000 0.00 2.27 0.00 4.46
2766 2919 8.370940 TCATGAAATAGAGTAGGAATCATGACC 58.629 37.037 10.52 0.00 43.82 4.02
2769 2922 9.939802 TCATCATGAAATAGAGTAGGAATCATG 57.060 33.333 0.00 6.53 42.35 3.07
2771 2924 9.939802 CATCATCATGAAATAGAGTAGGAATCA 57.060 33.333 0.00 0.00 30.57 2.57
2772 2925 8.881743 GCATCATCATGAAATAGAGTAGGAATC 58.118 37.037 0.00 0.00 30.57 2.52
2773 2926 8.380867 TGCATCATCATGAAATAGAGTAGGAAT 58.619 33.333 0.00 0.00 30.57 3.01
2774 2927 7.738847 TGCATCATCATGAAATAGAGTAGGAA 58.261 34.615 0.00 0.00 30.57 3.36
2775 2928 7.307131 TGCATCATCATGAAATAGAGTAGGA 57.693 36.000 0.00 0.00 30.57 2.94
2776 2929 7.606839 ACATGCATCATCATGAAATAGAGTAGG 59.393 37.037 0.00 0.00 44.94 3.18
2777 2930 8.549338 ACATGCATCATCATGAAATAGAGTAG 57.451 34.615 0.00 0.00 44.94 2.57
2778 2931 9.428097 GTACATGCATCATCATGAAATAGAGTA 57.572 33.333 0.00 0.00 44.94 2.59
2779 2932 8.155510 AGTACATGCATCATCATGAAATAGAGT 58.844 33.333 0.00 0.00 44.94 3.24
2780 2933 8.549338 AGTACATGCATCATCATGAAATAGAG 57.451 34.615 0.00 0.00 44.94 2.43
2783 2936 9.169592 CCATAGTACATGCATCATCATGAAATA 57.830 33.333 0.00 0.00 44.94 1.40
2784 2937 7.886446 TCCATAGTACATGCATCATCATGAAAT 59.114 33.333 0.00 0.00 44.94 2.17
2785 2938 7.173735 GTCCATAGTACATGCATCATCATGAAA 59.826 37.037 0.00 0.00 44.94 2.69
2786 2939 6.652062 GTCCATAGTACATGCATCATCATGAA 59.348 38.462 0.00 0.00 44.94 2.57
2787 2940 6.013984 AGTCCATAGTACATGCATCATCATGA 60.014 38.462 10.31 0.00 44.94 3.07
2788 2941 6.092259 CAGTCCATAGTACATGCATCATCATG 59.908 42.308 0.00 2.54 46.86 3.07
2789 2942 6.013984 TCAGTCCATAGTACATGCATCATCAT 60.014 38.462 0.00 0.00 0.00 2.45
2790 2943 5.305128 TCAGTCCATAGTACATGCATCATCA 59.695 40.000 0.00 0.00 0.00 3.07
2791 2944 5.787380 TCAGTCCATAGTACATGCATCATC 58.213 41.667 0.00 0.00 0.00 2.92
3017 3170 5.689819 CAGGGAAACTTCAACAATTACTCG 58.310 41.667 0.00 0.00 0.00 4.18
3083 3236 1.235724 AAGCTTACCAACGGCTTGAC 58.764 50.000 0.00 0.00 43.44 3.18
3091 3244 9.353999 CCATAAGAAATAAACAAGCTTACCAAC 57.646 33.333 0.00 0.00 0.00 3.77
3290 3443 3.956233 CATGTAATGGCAGTTCATTCCG 58.044 45.455 4.26 0.00 41.79 4.30
3311 3464 4.347813 ACGTAACAGCAATTCAACACAAC 58.652 39.130 0.00 0.00 0.00 3.32
3332 3485 6.033407 CACGGCAAATATAACATCAACACAAC 59.967 38.462 0.00 0.00 0.00 3.32
3351 3504 0.396435 ATTCTGTTCTGGACACGGCA 59.604 50.000 0.00 0.00 33.82 5.69
3377 3530 3.671716 ACTGTTGTTTTACCGGATCTCC 58.328 45.455 9.46 0.00 0.00 3.71
3544 3711 4.386951 CGTGGATGCCGGTGACCA 62.387 66.667 1.90 7.45 0.00 4.02
3563 3730 0.537188 GTTTCTGCCTCCTCCGATGA 59.463 55.000 0.00 0.00 0.00 2.92
3564 3731 0.539051 AGTTTCTGCCTCCTCCGATG 59.461 55.000 0.00 0.00 0.00 3.84
3565 3732 0.539051 CAGTTTCTGCCTCCTCCGAT 59.461 55.000 0.00 0.00 0.00 4.18
3616 3786 1.694133 CCTCCACTGATGGCTCCTCC 61.694 65.000 0.00 0.00 46.80 4.30
3628 3798 4.681978 GCGAACGCCACCTCCACT 62.682 66.667 8.03 0.00 34.56 4.00
4000 4183 1.501169 GTGAAACCACCTGCAAATGC 58.499 50.000 0.00 0.00 42.50 3.56


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

AutoCloner maintained by Alex Coulton.