Multiple sequence alignment - TraesCS1D01G184000

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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 TraesCS1D01G184000 chr1D 100.000 3181 0 0 1 3181 254531995 254535175 0.000000e+00 5875.0
1 TraesCS1D01G184000 chr1D 91.060 481 42 1 2701 3180 253987450 253987930 0.000000e+00 649.0
2 TraesCS1D01G184000 chr1D 97.436 78 2 0 2390 2467 492056365 492056442 1.990000e-27 134.0
3 TraesCS1D01G184000 chr1D 100.000 30 0 0 2591 2620 254421463 254421492 4.430000e-04 56.5
4 TraesCS1D01G184000 chr7B 98.481 2634 37 3 1 2632 662733311 662735943 0.000000e+00 4639.0
5 TraesCS1D01G184000 chr7B 97.288 2397 60 4 240 2632 90404328 90401933 0.000000e+00 4061.0
6 TraesCS1D01G184000 chr3B 98.330 2634 41 3 1 2632 201564984 201562352 0.000000e+00 4617.0
7 TraesCS1D01G184000 chr3B 98.547 757 10 1 1 756 201545916 201546672 0.000000e+00 1336.0
8 TraesCS1D01G184000 chr3B 98.813 674 7 1 1 673 813250767 813251440 0.000000e+00 1199.0
9 TraesCS1D01G184000 chr3A 97.874 2634 53 3 1 2632 672882631 672879999 0.000000e+00 4551.0
10 TraesCS1D01G184000 chr3A 83.943 492 70 7 2691 3180 418288410 418288894 2.240000e-126 462.0
11 TraesCS1D01G184000 chr3A 84.167 480 64 12 2707 3180 458668173 458667700 3.740000e-124 455.0
12 TraesCS1D01G184000 chr3A 78.571 140 13 7 2655 2779 346646829 346646692 3.400000e-10 76.8
13 TraesCS1D01G184000 chr1B 97.798 2634 55 3 1 2632 633733073 633730441 0.000000e+00 4540.0
14 TraesCS1D01G184000 chr1B 98.966 387 4 0 1 387 421415835 421416221 0.000000e+00 693.0
15 TraesCS1D01G184000 chr1B 100.000 68 0 0 109 176 619423835 619423902 3.330000e-25 126.0
16 TraesCS1D01G184000 chr1B 100.000 60 0 0 375 434 633732640 633732699 9.330000e-21 111.0
17 TraesCS1D01G184000 chr7A 95.295 2572 106 11 67 2632 352681572 352679010 0.000000e+00 4065.0
18 TraesCS1D01G184000 chr7A 84.049 489 67 11 2698 3180 345474913 345475396 8.040000e-126 460.0
19 TraesCS1D01G184000 chr7A 83.951 486 66 12 2700 3180 415980140 415979662 3.740000e-124 455.0
20 TraesCS1D01G184000 chr6B 97.283 2392 42 12 1 2385 615601193 615598818 0.000000e+00 4036.0
21 TraesCS1D01G184000 chr6B 85.950 484 59 7 2700 3180 411263133 411262656 2.830000e-140 508.0
22 TraesCS1D01G184000 chrUn 98.291 2165 31 4 419 2579 351215174 351213012 0.000000e+00 3788.0
23 TraesCS1D01G184000 chr5D 98.486 2114 30 2 419 2530 449149178 449151291 0.000000e+00 3725.0
24 TraesCS1D01G184000 chr5D 92.000 175 14 0 2458 2632 560238033 560238207 2.450000e-61 246.0
25 TraesCS1D01G184000 chr5D 100.000 130 0 0 2503 2632 484114059 484114188 1.140000e-59 241.0
26 TraesCS1D01G184000 chr5D 75.908 523 81 30 2691 3180 262220579 262220069 3.190000e-55 226.0
27 TraesCS1D01G184000 chr5D 100.000 60 0 0 2573 2632 484117433 484117492 9.330000e-21 111.0
28 TraesCS1D01G184000 chr2A 95.455 682 22 4 1 682 706548304 706547632 0.000000e+00 1079.0
29 TraesCS1D01G184000 chr2A 84.137 498 70 7 2686 3180 304166804 304166313 1.030000e-129 473.0
30 TraesCS1D01G184000 chr2A 76.628 522 76 25 2691 3180 351303347 351302840 2.450000e-61 246.0
31 TraesCS1D01G184000 chr2A 98.529 136 2 0 1 136 651440309 651440444 1.140000e-59 241.0
32 TraesCS1D01G184000 chr2A 97.656 128 3 0 1 128 510398723 510398850 1.490000e-53 220.0
33 TraesCS1D01G184000 chr4D 88.589 482 50 5 2700 3178 46586317 46585838 5.910000e-162 580.0
34 TraesCS1D01G184000 chr4D 85.833 120 14 2 2691 2809 189984590 189984473 1.200000e-24 124.0
35 TraesCS1D01G184000 chr4D 98.387 62 1 0 2571 2632 148609088 148609027 3.350000e-20 110.0
36 TraesCS1D01G184000 chr6A 83.669 496 69 12 2691 3180 314845489 314845000 1.040000e-124 457.0
37 TraesCS1D01G184000 chr6A 96.721 122 4 0 2511 2632 157939713 157939834 1.500000e-48 204.0
38 TraesCS1D01G184000 chr7D 98.673 226 2 1 2408 2632 231598159 231597934 1.780000e-107 399.0
39 TraesCS1D01G184000 chr7D 99.020 102 1 0 2531 2632 231569333 231569434 1.950000e-42 183.0
40 TraesCS1D01G184000 chr5A 98.324 179 3 0 1 179 573591308 573591130 6.620000e-82 315.0
41 TraesCS1D01G184000 chr4A 75.348 503 97 19 2691 3180 300370559 300371047 1.920000e-52 217.0
42 TraesCS1D01G184000 chr4A 73.764 526 88 34 2691 3180 524839503 524840014 9.130000e-36 161.0
43 TraesCS1D01G184000 chr1A 100.000 65 0 0 2508 2572 446249760 446249824 1.550000e-23 121.0
44 TraesCS1D01G184000 chr1A 100.000 46 0 0 2503 2548 327269702 327269657 5.650000e-13 86.1
45 TraesCS1D01G184000 chr6D 87.209 86 11 0 2686 2771 116123301 116123386 7.260000e-17 99.0
46 TraesCS1D01G184000 chr6D 96.610 59 0 1 2574 2632 159983503 159983447 2.610000e-16 97.1


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 TraesCS1D01G184000 chr1D 254531995 254535175 3180 False 5875 5875 100.000 1 3181 1 chr1D.!!$F3 3180
1 TraesCS1D01G184000 chr7B 662733311 662735943 2632 False 4639 4639 98.481 1 2632 1 chr7B.!!$F1 2631
2 TraesCS1D01G184000 chr7B 90401933 90404328 2395 True 4061 4061 97.288 240 2632 1 chr7B.!!$R1 2392
3 TraesCS1D01G184000 chr3B 201562352 201564984 2632 True 4617 4617 98.330 1 2632 1 chr3B.!!$R1 2631
4 TraesCS1D01G184000 chr3B 201545916 201546672 756 False 1336 1336 98.547 1 756 1 chr3B.!!$F1 755
5 TraesCS1D01G184000 chr3B 813250767 813251440 673 False 1199 1199 98.813 1 673 1 chr3B.!!$F2 672
6 TraesCS1D01G184000 chr3A 672879999 672882631 2632 True 4551 4551 97.874 1 2632 1 chr3A.!!$R3 2631
7 TraesCS1D01G184000 chr1B 633730441 633733073 2632 True 4540 4540 97.798 1 2632 1 chr1B.!!$R1 2631
8 TraesCS1D01G184000 chr7A 352679010 352681572 2562 True 4065 4065 95.295 67 2632 1 chr7A.!!$R1 2565
9 TraesCS1D01G184000 chr6B 615598818 615601193 2375 True 4036 4036 97.283 1 2385 1 chr6B.!!$R2 2384
10 TraesCS1D01G184000 chrUn 351213012 351215174 2162 True 3788 3788 98.291 419 2579 1 chrUn.!!$R1 2160
11 TraesCS1D01G184000 chr5D 449149178 449151291 2113 False 3725 3725 98.486 419 2530 1 chr5D.!!$F1 2111
12 TraesCS1D01G184000 chr5D 262220069 262220579 510 True 226 226 75.908 2691 3180 1 chr5D.!!$R1 489
13 TraesCS1D01G184000 chr2A 706547632 706548304 672 True 1079 1079 95.455 1 682 1 chr2A.!!$R3 681
14 TraesCS1D01G184000 chr2A 351302840 351303347 507 True 246 246 76.628 2691 3180 1 chr2A.!!$R2 489

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
1491 1506 0.752009 TTCGCATCGGAGGAGTAGCT 60.752 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3160 3210 0.187117 TCCCACAGTGGCCAATTTGA 59.813 50.0 20.41 3.89 35.79 2.69 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
1491 1506 0.752009 TTCGCATCGGAGGAGTAGCT 60.752 55.000 0.00 0.00 0.00 3.32
1659 1676 4.249638 AGCAGTAAATTGGGGCTTATCA 57.750 40.909 0.00 0.00 0.00 2.15
1785 1802 3.184581 GGGATTCGTTAGCTCGCTATTTG 59.815 47.826 0.00 0.00 0.00 2.32
1899 1917 6.778108 ACGACGCTTTAAGAAAGAAAAGAAA 58.222 32.000 3.15 0.00 41.02 2.52
2110 2130 7.752686 GCAAATTCTTCCTCAGCTAGTTAAAAG 59.247 37.037 0.00 0.00 0.00 2.27
2146 2166 7.863375 GGCTGATATCATGACGATATTAGGTAC 59.137 40.741 5.72 0.00 45.58 3.34
2346 2366 7.334421 GTGTGGTTAGAAAGAGAAATATCTGCA 59.666 37.037 0.00 0.00 35.54 4.41
2460 2480 0.035439 TTTTGCCATCCCGAGGAGAC 60.035 55.000 0.00 0.00 34.05 3.36
2632 2652 5.046304 GGTCTTCTTATGGCAGGATATAGCA 60.046 44.000 0.00 0.00 0.00 3.49
2633 2653 6.467677 GTCTTCTTATGGCAGGATATAGCAA 58.532 40.000 0.00 0.00 0.00 3.91
2634 2654 7.108847 GTCTTCTTATGGCAGGATATAGCAAT 58.891 38.462 0.00 0.00 0.00 3.56
2635 2655 7.609532 GTCTTCTTATGGCAGGATATAGCAATT 59.390 37.037 0.00 0.00 0.00 2.32
2636 2656 7.609146 TCTTCTTATGGCAGGATATAGCAATTG 59.391 37.037 0.00 0.00 0.00 2.32
2637 2657 6.182627 TCTTATGGCAGGATATAGCAATTGG 58.817 40.000 7.72 0.00 0.00 3.16
2638 2658 3.882102 TGGCAGGATATAGCAATTGGT 57.118 42.857 15.47 15.47 0.00 3.67
2639 2659 3.489355 TGGCAGGATATAGCAATTGGTG 58.511 45.455 20.13 2.59 0.00 4.17
2640 2660 2.821969 GGCAGGATATAGCAATTGGTGG 59.178 50.000 20.13 2.50 0.00 4.61
2641 2661 3.490348 GCAGGATATAGCAATTGGTGGT 58.510 45.455 20.13 10.90 41.93 4.16
2642 2662 3.254166 GCAGGATATAGCAATTGGTGGTG 59.746 47.826 20.13 8.83 38.75 4.17
2643 2663 4.464008 CAGGATATAGCAATTGGTGGTGT 58.536 43.478 20.13 7.06 38.75 4.16
2644 2664 4.889409 CAGGATATAGCAATTGGTGGTGTT 59.111 41.667 20.13 0.70 38.75 3.32
2645 2665 5.360714 CAGGATATAGCAATTGGTGGTGTTT 59.639 40.000 20.13 0.00 38.75 2.83
2646 2666 5.957774 AGGATATAGCAATTGGTGGTGTTTT 59.042 36.000 20.13 0.00 38.75 2.43
2647 2667 6.440328 AGGATATAGCAATTGGTGGTGTTTTT 59.560 34.615 20.13 0.00 38.75 1.94
2680 2700 4.617875 GGCTTTGCCTCGAAGCTA 57.382 55.556 15.85 0.00 46.70 3.32
2681 2701 2.854522 GGCTTTGCCTCGAAGCTAA 58.145 52.632 15.85 5.13 46.70 3.09
2682 2702 0.729690 GGCTTTGCCTCGAAGCTAAG 59.270 55.000 21.16 21.16 46.70 2.18
2683 2703 1.443802 GCTTTGCCTCGAAGCTAAGT 58.556 50.000 24.38 0.00 44.79 2.24
2684 2704 1.395262 GCTTTGCCTCGAAGCTAAGTC 59.605 52.381 24.38 15.99 44.79 3.01
2685 2705 2.003301 CTTTGCCTCGAAGCTAAGTCC 58.997 52.381 18.35 0.00 39.68 3.85
2686 2706 0.249398 TTGCCTCGAAGCTAAGTCCC 59.751 55.000 7.65 0.00 0.00 4.46
2687 2707 1.144276 GCCTCGAAGCTAAGTCCCC 59.856 63.158 0.00 0.00 0.00 4.81
2688 2708 1.437986 CCTCGAAGCTAAGTCCCCG 59.562 63.158 0.00 0.00 0.00 5.73
2689 2709 1.035932 CCTCGAAGCTAAGTCCCCGA 61.036 60.000 0.00 0.00 0.00 5.14
2706 2726 1.030457 CGAGGGCTACTATCGGTGTT 58.970 55.000 0.00 0.00 32.93 3.32
2739 2759 1.841302 TACCCAGACTTGCCTGCCTG 61.841 60.000 0.00 0.00 32.97 4.85
2784 2804 0.757935 GGCCTGGTACGGTCCATCTA 60.758 60.000 0.00 0.00 36.84 1.98
2786 2806 0.666913 CCTGGTACGGTCCATCTACG 59.333 60.000 1.51 0.00 36.84 3.51
2787 2807 1.671979 CTGGTACGGTCCATCTACGA 58.328 55.000 0.00 0.00 36.84 3.43
2788 2808 2.019249 CTGGTACGGTCCATCTACGAA 58.981 52.381 0.00 0.00 36.84 3.85
2789 2809 2.019249 TGGTACGGTCCATCTACGAAG 58.981 52.381 0.00 0.00 31.96 3.79
2791 2811 2.032675 GGTACGGTCCATCTACGAAGAC 59.967 54.545 0.00 0.00 33.57 3.01
2796 2816 2.232941 GGTCCATCTACGAAGACCAACA 59.767 50.000 3.21 0.00 46.61 3.33
2798 2818 3.927142 GTCCATCTACGAAGACCAACAAG 59.073 47.826 0.00 0.00 33.57 3.16
2799 2819 3.830178 TCCATCTACGAAGACCAACAAGA 59.170 43.478 0.00 0.00 33.57 3.02
2837 2874 1.065854 GGATGACACCAAGACCTCCTG 60.066 57.143 0.00 0.00 0.00 3.86
2838 2875 1.625818 GATGACACCAAGACCTCCTGT 59.374 52.381 0.00 0.00 0.00 4.00
2842 2879 1.127567 CACCAAGACCTCCTGTGGGA 61.128 60.000 0.00 0.00 39.70 4.37
2866 2903 1.665948 CCTCCCCTGGGCTACTCCTA 61.666 65.000 7.39 0.00 34.68 2.94
2869 2906 0.264955 CCCCTGGGCTACTCCTAAGA 59.735 60.000 7.39 0.00 34.39 2.10
2890 2927 0.871057 GCGGAGATTCCTATGCAAGC 59.129 55.000 0.00 0.00 33.30 4.01
2892 2929 0.871057 GGAGATTCCTATGCAAGCGC 59.129 55.000 0.00 0.00 33.94 5.92
2894 2931 0.536006 AGATTCCTATGCAAGCGCCC 60.536 55.000 2.29 0.00 37.32 6.13
2895 2932 1.845809 GATTCCTATGCAAGCGCCCG 61.846 60.000 2.29 0.00 37.32 6.13
2896 2933 4.545706 TCCTATGCAAGCGCCCGG 62.546 66.667 2.29 0.00 37.32 5.73
2918 2955 2.742372 ACGAGGTTGCGGTGATGC 60.742 61.111 0.00 0.00 35.12 3.91
2919 2956 2.741985 CGAGGTTGCGGTGATGCA 60.742 61.111 0.00 0.00 44.61 3.96
2941 2978 2.045926 ATGACGACCAAGGCCAGC 60.046 61.111 5.01 0.00 0.00 4.85
2942 2979 3.958147 ATGACGACCAAGGCCAGCG 62.958 63.158 5.01 3.11 0.00 5.18
2955 2992 1.834378 CCAGCGGGCATAGAGGAGA 60.834 63.158 0.00 0.00 0.00 3.71
3013 3060 1.762460 GGGGCCTCGAGGAATCAGA 60.762 63.158 35.69 0.00 37.39 3.27
3027 3074 5.397360 AGGAATCAGACAAAGGTTTCCATT 58.603 37.500 0.00 0.00 36.03 3.16
3028 3075 5.478332 AGGAATCAGACAAAGGTTTCCATTC 59.522 40.000 0.00 0.00 36.03 2.67
3029 3076 5.478332 GGAATCAGACAAAGGTTTCCATTCT 59.522 40.000 0.00 0.00 34.20 2.40
3034 3081 5.182001 CAGACAAAGGTTTCCATTCTAGTGG 59.818 44.000 0.00 0.00 40.76 4.00
3051 3098 1.947456 GTGGAACAAGACCAAGACCAC 59.053 52.381 0.00 0.00 44.16 4.16
3065 3112 3.636231 CCACCAGGACGGCAGGAA 61.636 66.667 5.93 0.00 39.03 3.36
3069 3116 2.370445 CCAGGACGGCAGGAAGGAT 61.370 63.158 0.00 0.00 0.00 3.24
3078 3125 1.162800 GCAGGAAGGATGTCATCGCC 61.163 60.000 6.74 8.05 0.00 5.54
3105 3152 1.066752 CACGGTGTCACGACCAGAA 59.933 57.895 0.00 0.00 35.50 3.02
3106 3153 0.939577 CACGGTGTCACGACCAGAAG 60.940 60.000 0.00 0.00 35.50 2.85
3112 3159 1.134521 TGTCACGACCAGAAGCTTTGT 60.135 47.619 0.00 0.00 0.00 2.83
3113 3160 2.101750 TGTCACGACCAGAAGCTTTGTA 59.898 45.455 0.00 0.00 0.00 2.41
3114 3161 2.731976 GTCACGACCAGAAGCTTTGTAG 59.268 50.000 0.00 2.01 0.00 2.74
3129 3178 3.782656 TTGTAGGGAAGACCACCTTTC 57.217 47.619 0.00 0.00 43.89 2.62
3131 3180 0.611714 TAGGGAAGACCACCTTTCGC 59.388 55.000 0.00 0.00 43.89 4.70
3134 3183 0.536460 GGAAGACCACCTTTCGCCAA 60.536 55.000 0.00 0.00 34.68 4.52
3140 3189 2.678336 GACCACCTTTCGCCAAGATAAG 59.322 50.000 0.00 0.00 33.80 1.73
3141 3190 2.304761 ACCACCTTTCGCCAAGATAAGA 59.695 45.455 0.00 0.00 33.80 2.10
3149 3198 6.421202 CCTTTCGCCAAGATAAGATGTACTAC 59.579 42.308 0.00 0.00 33.80 2.73
3160 3210 7.624077 AGATAAGATGTACTACTTGTCCCCTTT 59.376 37.037 17.78 5.00 35.76 3.11
3161 3211 5.678955 AGATGTACTACTTGTCCCCTTTC 57.321 43.478 0.00 0.00 0.00 2.62
3171 3221 1.347062 GTCCCCTTTCAAATTGGCCA 58.653 50.000 0.00 0.00 0.00 5.36
3172 3222 1.001974 GTCCCCTTTCAAATTGGCCAC 59.998 52.381 3.88 0.00 0.00 5.01
3180 3230 0.318120 CAAATTGGCCACTGTGGGAC 59.682 55.000 27.02 12.02 38.19 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.420893 TGGCCTGATTTCGAAATTGTCT 58.579 40.909 23.49 2.52 0.00 3.41
747 757 4.818005 ACGTTTTCCCAAAAGTCTTCGTAT 59.182 37.500 0.00 0.00 29.59 3.06
1491 1506 2.567169 CCATCCATAAGGTAGATCGGCA 59.433 50.000 0.00 0.00 35.89 5.69
1659 1676 1.134560 GAAGCTCGTAACATCGGTCCT 59.865 52.381 0.00 0.00 0.00 3.85
1785 1802 3.377172 CCCTCATTTCACCAATTCGTACC 59.623 47.826 0.00 0.00 0.00 3.34
2030 2050 2.926329 TCTCCAGGGGAAAAGGCTATTT 59.074 45.455 0.00 0.00 0.00 1.40
2031 2051 2.573463 TCTCCAGGGGAAAAGGCTATT 58.427 47.619 0.00 0.00 0.00 1.73
2110 2130 6.800408 CGTCATGATATCAGCCAATTTCATTC 59.200 38.462 11.78 0.00 28.60 2.67
2346 2366 4.807304 GGACCAATACGTTGTTGTATCGAT 59.193 41.667 2.16 2.16 34.01 3.59
2443 2463 0.982852 ATGTCTCCTCGGGATGGCAA 60.983 55.000 0.00 0.00 0.00 4.52
2460 2480 7.785033 AGGGTCCAATGCTAAATAAAGAAATG 58.215 34.615 0.00 0.00 0.00 2.32
2665 2685 2.003301 GGACTTAGCTTCGAGGCAAAG 58.997 52.381 22.42 9.78 34.17 2.77
2666 2686 1.338769 GGGACTTAGCTTCGAGGCAAA 60.339 52.381 22.42 6.39 34.17 3.68
2667 2687 0.249398 GGGACTTAGCTTCGAGGCAA 59.751 55.000 22.42 12.36 34.17 4.52
2668 2688 1.614241 GGGGACTTAGCTTCGAGGCA 61.614 60.000 22.42 4.94 34.17 4.75
2669 2689 1.144276 GGGGACTTAGCTTCGAGGC 59.856 63.158 12.25 12.25 0.00 4.70
2670 2690 1.035932 TCGGGGACTTAGCTTCGAGG 61.036 60.000 0.00 0.00 0.00 4.63
2671 2691 0.382515 CTCGGGGACTTAGCTTCGAG 59.617 60.000 0.00 0.00 38.17 4.04
2672 2692 1.035932 CCTCGGGGACTTAGCTTCGA 61.036 60.000 0.00 0.00 33.58 3.71
2673 2693 1.437986 CCTCGGGGACTTAGCTTCG 59.562 63.158 0.00 0.00 33.58 3.79
2684 2704 1.977544 CCGATAGTAGCCCTCGGGG 60.978 68.421 3.79 0.00 46.32 5.73
2685 2705 3.682792 CCGATAGTAGCCCTCGGG 58.317 66.667 0.00 0.00 46.32 5.14
2687 2707 1.001597 GAACACCGATAGTAGCCCTCG 60.002 57.143 0.00 0.00 0.00 4.63
2688 2708 2.034812 CAGAACACCGATAGTAGCCCTC 59.965 54.545 0.00 0.00 0.00 4.30
2689 2709 2.032620 CAGAACACCGATAGTAGCCCT 58.967 52.381 0.00 0.00 0.00 5.19
2747 2767 4.451150 GTCGATGGAGCCACGCCA 62.451 66.667 0.00 0.00 37.78 5.69
2777 2797 3.830178 TCTTGTTGGTCTTCGTAGATGGA 59.170 43.478 0.00 0.00 35.04 3.41
2784 2804 3.195661 GTCTTGTCTTGTTGGTCTTCGT 58.804 45.455 0.00 0.00 0.00 3.85
2786 2806 2.879026 GGGTCTTGTCTTGTTGGTCTTC 59.121 50.000 0.00 0.00 0.00 2.87
2787 2807 2.509964 AGGGTCTTGTCTTGTTGGTCTT 59.490 45.455 0.00 0.00 0.00 3.01
2788 2808 2.104963 GAGGGTCTTGTCTTGTTGGTCT 59.895 50.000 0.00 0.00 0.00 3.85
2789 2809 2.495084 GAGGGTCTTGTCTTGTTGGTC 58.505 52.381 0.00 0.00 0.00 4.02
2791 2811 1.512926 CGAGGGTCTTGTCTTGTTGG 58.487 55.000 0.00 0.00 0.00 3.77
2796 2816 1.587054 CTCGCGAGGGTCTTGTCTT 59.413 57.895 28.40 0.00 0.00 3.01
2798 2818 2.182030 CCTCGCGAGGGTCTTGTC 59.818 66.667 41.47 0.00 44.87 3.18
2820 2857 0.758734 CACAGGAGGTCTTGGTGTCA 59.241 55.000 0.00 0.00 0.00 3.58
2848 2885 0.264955 TTAGGAGTAGCCCAGGGGAG 59.735 60.000 7.91 0.00 37.37 4.30
2850 2887 0.264955 TCTTAGGAGTAGCCCAGGGG 59.735 60.000 7.91 3.48 37.37 4.79
2852 2889 1.414550 GCTTCTTAGGAGTAGCCCAGG 59.585 57.143 0.00 0.00 39.58 4.45
2853 2890 1.067821 CGCTTCTTAGGAGTAGCCCAG 59.932 57.143 0.00 0.00 41.66 4.45
2854 2891 1.112113 CGCTTCTTAGGAGTAGCCCA 58.888 55.000 0.00 0.00 41.66 5.36
2856 2893 1.338655 CTCCGCTTCTTAGGAGTAGCC 59.661 57.143 3.49 0.00 46.68 3.93
2857 2894 2.785713 CTCCGCTTCTTAGGAGTAGC 57.214 55.000 3.49 0.00 46.68 3.58
2866 2903 2.435805 TGCATAGGAATCTCCGCTTCTT 59.564 45.455 0.00 0.00 42.75 2.52
2869 2906 2.843701 CTTGCATAGGAATCTCCGCTT 58.156 47.619 0.00 0.00 42.75 4.68
2879 2916 4.545706 CCGGGCGCTTGCATAGGA 62.546 66.667 7.64 0.00 41.71 2.94
2899 2936 1.374125 CATCACCGCAACCTCGTGA 60.374 57.895 0.00 0.00 0.00 4.35
2900 2937 3.027170 GCATCACCGCAACCTCGTG 62.027 63.158 0.00 0.00 0.00 4.35
2901 2938 2.742372 GCATCACCGCAACCTCGT 60.742 61.111 0.00 0.00 0.00 4.18
2909 2946 2.103538 CATGGCTTGCATCACCGC 59.896 61.111 0.00 0.00 0.00 5.68
2910 2947 1.430632 GTCATGGCTTGCATCACCG 59.569 57.895 0.00 0.00 0.00 4.94
2911 2948 1.026182 TCGTCATGGCTTGCATCACC 61.026 55.000 0.00 0.00 0.00 4.02
2918 2955 2.174334 CCTTGGTCGTCATGGCTTG 58.826 57.895 0.00 0.00 34.50 4.01
2919 2956 4.722193 CCTTGGTCGTCATGGCTT 57.278 55.556 0.00 0.00 34.50 4.35
2941 2978 1.115467 AACTGTCTCCTCTATGCCCG 58.885 55.000 0.00 0.00 0.00 6.13
2942 2979 2.158885 GGAAACTGTCTCCTCTATGCCC 60.159 54.545 0.00 0.00 0.00 5.36
2952 2989 2.550180 GCACCAAAGAGGAAACTGTCTC 59.450 50.000 0.00 0.00 44.43 3.36
2953 2990 2.173569 AGCACCAAAGAGGAAACTGTCT 59.826 45.455 0.00 0.00 44.43 3.41
2955 2992 2.736670 AGCACCAAAGAGGAAACTGT 57.263 45.000 0.00 0.00 44.43 3.55
2994 3041 3.154473 TGATTCCTCGAGGCCCCG 61.154 66.667 27.39 0.00 34.44 5.73
2997 3044 0.537188 TTGTCTGATTCCTCGAGGCC 59.463 55.000 27.39 17.48 34.44 5.19
2999 3046 2.234908 ACCTTTGTCTGATTCCTCGAGG 59.765 50.000 26.32 26.32 0.00 4.63
3001 3048 4.315803 GAAACCTTTGTCTGATTCCTCGA 58.684 43.478 0.00 0.00 0.00 4.04
3007 3054 7.175641 CACTAGAATGGAAACCTTTGTCTGATT 59.824 37.037 0.00 0.00 0.00 2.57
3013 3060 5.319043 TCCACTAGAATGGAAACCTTTGT 57.681 39.130 0.00 0.00 46.08 2.83
3027 3074 3.323979 GGTCTTGGTCTTGTTCCACTAGA 59.676 47.826 0.00 0.00 34.45 2.43
3028 3075 3.071023 TGGTCTTGGTCTTGTTCCACTAG 59.929 47.826 0.00 0.00 34.45 2.57
3029 3076 3.042682 TGGTCTTGGTCTTGTTCCACTA 58.957 45.455 0.00 0.00 34.45 2.74
3034 3081 2.222027 CTGGTGGTCTTGGTCTTGTTC 58.778 52.381 0.00 0.00 0.00 3.18
3051 3098 2.370445 ATCCTTCCTGCCGTCCTGG 61.370 63.158 0.00 0.00 42.50 4.45
3065 3112 2.419198 GCTCGGCGATGACATCCT 59.581 61.111 11.27 0.00 0.00 3.24
3069 3116 4.451150 GTGGGCTCGGCGATGACA 62.451 66.667 11.27 6.76 0.00 3.58
3087 3134 0.939577 CTTCTGGTCGTGACACCGTG 60.940 60.000 0.00 0.00 39.62 4.94
3091 3138 1.261619 CAAAGCTTCTGGTCGTGACAC 59.738 52.381 0.00 0.00 0.00 3.67
3098 3145 3.008049 TCTTCCCTACAAAGCTTCTGGTC 59.992 47.826 0.00 0.00 0.00 4.02
3105 3152 1.351350 GGTGGTCTTCCCTACAAAGCT 59.649 52.381 0.00 0.00 0.00 3.74
3106 3153 1.351350 AGGTGGTCTTCCCTACAAAGC 59.649 52.381 0.00 0.00 0.00 3.51
3112 3159 0.611714 GCGAAAGGTGGTCTTCCCTA 59.388 55.000 0.00 0.00 33.94 3.53
3113 3160 1.375326 GCGAAAGGTGGTCTTCCCT 59.625 57.895 0.00 0.00 33.94 4.20
3114 3161 1.674651 GGCGAAAGGTGGTCTTCCC 60.675 63.158 0.00 0.00 33.94 3.97
3129 3178 6.273825 ACAAGTAGTACATCTTATCTTGGCG 58.726 40.000 2.52 0.00 35.15 5.69
3131 3180 7.210873 GGGACAAGTAGTACATCTTATCTTGG 58.789 42.308 2.52 0.00 35.15 3.61
3134 3183 6.684538 AGGGGACAAGTAGTACATCTTATCT 58.315 40.000 2.52 0.00 30.17 1.98
3140 3189 5.416271 TGAAAGGGGACAAGTAGTACATC 57.584 43.478 2.52 0.00 30.17 3.06
3141 3190 5.836024 TTGAAAGGGGACAAGTAGTACAT 57.164 39.130 2.52 0.00 30.17 2.29
3149 3198 2.289631 GGCCAATTTGAAAGGGGACAAG 60.290 50.000 0.00 0.00 0.00 3.16
3160 3210 0.187117 TCCCACAGTGGCCAATTTGA 59.813 50.000 20.41 3.89 35.79 2.69
3161 3211 0.318120 GTCCCACAGTGGCCAATTTG 59.682 55.000 14.98 10.37 35.79 2.32


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

AutoCloner maintained by Alex Coulton.