Multiple sequence alignment - TraesCS1A01G292700

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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 TraesCS1A01G292700 chr1A 100.000 3769 0 0 1 3769 488112930 488109162 0.000000e+00 6961.0
1 TraesCS1A01G292700 chr1A 82.060 1990 223 58 994 2877 488071516 488073477 0.000000e+00 1574.0
2 TraesCS1A01G292700 chr1A 89.237 734 71 4 1 733 428998081 428997355 0.000000e+00 911.0
3 TraesCS1A01G292700 chr1A 87.250 651 61 9 97 731 494319070 494318426 0.000000e+00 723.0
4 TraesCS1A01G292700 chr1A 83.737 289 27 11 3479 3764 488073688 488073959 4.830000e-64 255.0
5 TraesCS1A01G292700 chr1A 86.087 115 13 2 1290 1404 488244185 488244296 1.840000e-23 121.0
6 TraesCS1A01G292700 chr1D 94.670 1726 65 11 763 2475 389212852 389214563 0.000000e+00 2652.0
7 TraesCS1A01G292700 chr1D 93.903 1591 72 7 781 2357 389603240 389601661 0.000000e+00 2377.0
8 TraesCS1A01G292700 chr1D 90.585 1487 74 30 2344 3769 389600371 389598890 0.000000e+00 1910.0
9 TraesCS1A01G292700 chr1D 83.299 1928 246 44 1207 3088 389555751 389553854 0.000000e+00 1707.0
10 TraesCS1A01G292700 chr1D 89.963 1365 67 36 2472 3769 389214643 389216004 0.000000e+00 1698.0
11 TraesCS1A01G292700 chr1D 83.171 1848 210 47 981 2751 388991093 388992916 0.000000e+00 1596.0
12 TraesCS1A01G292700 chr1D 93.297 731 43 5 1 729 384504730 384505456 0.000000e+00 1074.0
13 TraesCS1A01G292700 chr1D 85.695 741 84 12 1 729 424928519 424927789 0.000000e+00 761.0
14 TraesCS1A01G292700 chr1D 85.496 393 35 14 3380 3767 389553832 389553457 1.270000e-104 390.0
15 TraesCS1A01G292700 chr1D 91.549 213 14 4 3479 3687 388993290 388993502 1.320000e-74 291.0
16 TraesCS1A01G292700 chr1D 71.758 1041 183 71 838 1816 389243681 389244672 1.380000e-44 191.0
17 TraesCS1A01G292700 chr1D 75.275 364 60 24 838 1194 390581371 390581031 3.030000e-31 147.0
18 TraesCS1A01G292700 chr1D 86.607 112 12 2 1293 1404 390402018 390401910 1.840000e-23 121.0
19 TraesCS1A01G292700 chr1D 92.958 71 4 1 838 907 390855213 390855283 6.660000e-18 102.0
20 TraesCS1A01G292700 chr1D 98.246 57 1 0 841 897 389525513 389525457 2.400000e-17 100.0
21 TraesCS1A01G292700 chr1D 80.292 137 20 4 2984 3119 489715055 489714925 3.100000e-16 97.1
22 TraesCS1A01G292700 chr1D 76.220 164 32 4 2957 3119 49311733 49311890 3.120000e-11 80.5
23 TraesCS1A01G292700 chr1B 82.054 2045 241 54 948 2898 522362819 522364831 0.000000e+00 1628.0
24 TraesCS1A01G292700 chr1B 81.759 1387 173 44 970 2332 522626486 522627816 0.000000e+00 1086.0
25 TraesCS1A01G292700 chr1B 84.478 393 36 19 3380 3764 522628764 522629139 7.690000e-97 364.0
26 TraesCS1A01G292700 chr1B 82.143 392 43 12 2705 3088 522628370 522628742 1.020000e-80 311.0
27 TraesCS1A01G292700 chr1B 90.678 236 11 5 2472 2703 522628092 522628320 1.700000e-78 303.0
28 TraesCS1A01G292700 chr1B 73.948 879 159 45 1002 1833 522840979 522840124 1.320000e-74 291.0
29 TraesCS1A01G292700 chr1B 90.066 151 12 2 3616 3764 522365400 522365549 3.840000e-45 193.0
30 TraesCS1A01G292700 chr1B 71.636 966 170 66 838 1735 522739502 522740431 1.800000e-38 171.0
31 TraesCS1A01G292700 chr1B 78.431 204 36 5 995 1194 523207992 523208191 3.950000e-25 126.0
32 TraesCS1A01G292700 chr1B 81.356 118 18 3 1290 1406 523238314 523238428 4.010000e-15 93.5
33 TraesCS1A01G292700 chr5A 90.092 757 53 11 1 741 488431684 488430934 0.000000e+00 963.0
34 TraesCS1A01G292700 chr5A 92.683 41 2 1 3295 3334 168129106 168129066 1.460000e-04 58.4
35 TraesCS1A01G292700 chr4A 89.771 743 61 4 1 730 684037138 684036398 0.000000e+00 937.0
36 TraesCS1A01G292700 chr4A 89.502 743 63 4 1 730 684017348 684016608 0.000000e+00 926.0
37 TraesCS1A01G292700 chr4A 88.560 743 67 5 1 730 628845351 628846088 0.000000e+00 885.0
38 TraesCS1A01G292700 chr4A 94.595 37 1 1 3295 3331 706248726 706248691 5.260000e-04 56.5
39 TraesCS1A01G292700 chr6A 88.425 743 66 9 1 729 88126313 88125577 0.000000e+00 878.0
40 TraesCS1A01G292700 chr7A 86.968 729 82 6 1 727 657745419 657746136 0.000000e+00 808.0
41 TraesCS1A01G292700 chr7A 94.737 38 1 1 3296 3333 222704803 222704767 1.460000e-04 58.4
42 TraesCS1A01G292700 chr2A 88.227 688 59 9 1 683 728066574 728067244 0.000000e+00 802.0
43 TraesCS1A01G292700 chr2A 100.000 28 0 0 3295 3322 237219693 237219720 7.000000e-03 52.8
44 TraesCS1A01G292700 chr5B 86.333 739 77 16 1 733 587442176 587441456 0.000000e+00 784.0
45 TraesCS1A01G292700 chr5B 87.789 475 47 7 1 474 435015491 435015955 2.560000e-151 545.0
46 TraesCS1A01G292700 chr7D 84.060 734 100 9 2 730 264479505 264478784 0.000000e+00 691.0
47 TraesCS1A01G292700 chr3D 83.743 732 97 11 1 727 545418812 545418098 0.000000e+00 673.0
48 TraesCS1A01G292700 chr3D 76.220 164 32 4 2957 3119 133633893 133633736 3.120000e-11 80.5
49 TraesCS1A01G292700 chr3D 76.220 164 31 5 2957 3119 544132801 544132957 3.120000e-11 80.5
50 TraesCS1A01G292700 chr3D 75.882 170 34 4 2951 3119 546170553 546170716 3.120000e-11 80.5
51 TraesCS1A01G292700 chr3D 94.595 37 0 2 3295 3331 602056131 602056165 5.260000e-04 56.5
52 TraesCS1A01G292700 chr6B 80.597 134 18 5 2987 3119 602920076 602919950 3.100000e-16 97.1
53 TraesCS1A01G292700 chr4B 94.737 38 2 0 3295 3332 107910796 107910833 4.070000e-05 60.2
54 TraesCS1A01G292700 chr6D 97.143 35 0 1 3295 3329 289430575 289430542 1.460000e-04 58.4
55 TraesCS1A01G292700 chr7B 92.500 40 1 2 3284 3322 312666238 312666276 5.260000e-04 56.5
56 TraesCS1A01G292700 chr5D 92.105 38 3 0 3295 3332 545242857 545242820 2.000000e-03 54.7


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 TraesCS1A01G292700 chr1A 488109162 488112930 3768 True 6961.0 6961 100.0000 1 3769 1 chr1A.!!$R2 3768
1 TraesCS1A01G292700 chr1A 488071516 488073959 2443 False 914.5 1574 82.8985 994 3764 2 chr1A.!!$F2 2770
2 TraesCS1A01G292700 chr1A 428997355 428998081 726 True 911.0 911 89.2370 1 733 1 chr1A.!!$R1 732
3 TraesCS1A01G292700 chr1A 494318426 494319070 644 True 723.0 723 87.2500 97 731 1 chr1A.!!$R3 634
4 TraesCS1A01G292700 chr1D 389212852 389216004 3152 False 2175.0 2652 92.3165 763 3769 2 chr1D.!!$F6 3006
5 TraesCS1A01G292700 chr1D 389598890 389603240 4350 True 2143.5 2377 92.2440 781 3769 2 chr1D.!!$R7 2988
6 TraesCS1A01G292700 chr1D 384504730 384505456 726 False 1074.0 1074 93.2970 1 729 1 chr1D.!!$F2 728
7 TraesCS1A01G292700 chr1D 389553457 389555751 2294 True 1048.5 1707 84.3975 1207 3767 2 chr1D.!!$R6 2560
8 TraesCS1A01G292700 chr1D 388991093 388993502 2409 False 943.5 1596 87.3600 981 3687 2 chr1D.!!$F5 2706
9 TraesCS1A01G292700 chr1D 424927789 424928519 730 True 761.0 761 85.6950 1 729 1 chr1D.!!$R4 728
10 TraesCS1A01G292700 chr1B 522362819 522365549 2730 False 910.5 1628 86.0600 948 3764 2 chr1B.!!$F4 2816
11 TraesCS1A01G292700 chr1B 522626486 522629139 2653 False 516.0 1086 84.7645 970 3764 4 chr1B.!!$F5 2794
12 TraesCS1A01G292700 chr1B 522840124 522840979 855 True 291.0 291 73.9480 1002 1833 1 chr1B.!!$R1 831
13 TraesCS1A01G292700 chr5A 488430934 488431684 750 True 963.0 963 90.0920 1 741 1 chr5A.!!$R2 740
14 TraesCS1A01G292700 chr4A 684036398 684037138 740 True 937.0 937 89.7710 1 730 1 chr4A.!!$R2 729
15 TraesCS1A01G292700 chr4A 684016608 684017348 740 True 926.0 926 89.5020 1 730 1 chr4A.!!$R1 729
16 TraesCS1A01G292700 chr4A 628845351 628846088 737 False 885.0 885 88.5600 1 730 1 chr4A.!!$F1 729
17 TraesCS1A01G292700 chr6A 88125577 88126313 736 True 878.0 878 88.4250 1 729 1 chr6A.!!$R1 728
18 TraesCS1A01G292700 chr7A 657745419 657746136 717 False 808.0 808 86.9680 1 727 1 chr7A.!!$F1 726
19 TraesCS1A01G292700 chr2A 728066574 728067244 670 False 802.0 802 88.2270 1 683 1 chr2A.!!$F2 682
20 TraesCS1A01G292700 chr5B 587441456 587442176 720 True 784.0 784 86.3330 1 733 1 chr5B.!!$R1 732
21 TraesCS1A01G292700 chr7D 264478784 264479505 721 True 691.0 691 84.0600 2 730 1 chr7D.!!$R1 728
22 TraesCS1A01G292700 chr3D 545418098 545418812 714 True 673.0 673 83.7430 1 727 1 chr3D.!!$R2 726

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
756 821 0.110104 AGGTAGGCGCGGAGTACTAT 59.89 55.0 8.83 0.0 0.0 2.12 F
757 822 0.240411 GGTAGGCGCGGAGTACTATG 59.76 60.0 8.83 0.0 0.0 2.23 F
878 943 0.749649 TCCATGTGCACCAACCAAAC 59.25 50.0 15.69 0.0 0.0 2.93 F
1425 1567 1.399714 ACATGGACGCCGAGAAGATA 58.60 50.0 0.00 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1939 0.608640 CCAAGAGCCGGTACAGTTCT 59.391 55.000 1.90 0.00 0.00 3.01 R
1906 2090 0.751277 TTGTCAGGCAACACCAGGTG 60.751 55.000 18.93 18.93 43.14 4.00 R
1948 2132 0.813184 ATTGCAGAAATCCACGGCAG 59.187 50.000 0.00 0.00 39.24 4.85 R
3147 5103 1.283613 AGTGACTTGGGGTGTGTTTCA 59.716 47.619 0.00 0.00 0.00 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
18 19 1.153958 GGAAGCTGCCGTTGAATGC 60.154 57.895 0.00 0.00 0.00 3.56
66 67 3.806521 CACAAGATCTTCATCATCCGACC 59.193 47.826 4.57 0.00 0.00 4.79
190 191 2.203070 GGCCGCGATGATCACCTT 60.203 61.111 8.23 0.00 0.00 3.50
553 614 4.039357 CGTGCGTCCAGACCGTCT 62.039 66.667 0.00 0.00 0.00 4.18
689 753 5.050634 CGTCTGTTTTACCTCAAATGAACGA 60.051 40.000 0.00 0.00 0.00 3.85
708 772 1.152398 GGCCGGACAGGATAGGGTA 60.152 63.158 5.05 0.00 45.00 3.69
733 798 1.066071 GGTGGAGTTGTCCTTAGAGCC 60.066 57.143 0.00 0.00 44.30 4.70
735 800 0.460459 GGAGTTGTCCTTAGAGCCGC 60.460 60.000 0.00 0.00 40.17 6.53
736 801 0.802607 GAGTTGTCCTTAGAGCCGCG 60.803 60.000 0.00 0.00 0.00 6.46
737 802 1.214589 GTTGTCCTTAGAGCCGCGA 59.785 57.895 8.23 0.00 0.00 5.87
738 803 0.802607 GTTGTCCTTAGAGCCGCGAG 60.803 60.000 8.23 0.00 0.00 5.03
752 817 2.898840 CGAGGTAGGCGCGGAGTA 60.899 66.667 8.83 0.00 0.00 2.59
753 818 2.720605 GAGGTAGGCGCGGAGTAC 59.279 66.667 8.83 0.00 0.00 2.73
754 819 1.823041 GAGGTAGGCGCGGAGTACT 60.823 63.158 8.83 0.00 0.00 2.73
755 820 0.533755 GAGGTAGGCGCGGAGTACTA 60.534 60.000 8.83 0.00 0.00 1.82
756 821 0.110104 AGGTAGGCGCGGAGTACTAT 59.890 55.000 8.83 0.00 0.00 2.12
757 822 0.240411 GGTAGGCGCGGAGTACTATG 59.760 60.000 8.83 0.00 0.00 2.23
758 823 0.950116 GTAGGCGCGGAGTACTATGT 59.050 55.000 8.83 0.00 0.00 2.29
759 824 2.146342 GTAGGCGCGGAGTACTATGTA 58.854 52.381 8.83 0.00 0.00 2.29
760 825 1.906990 AGGCGCGGAGTACTATGTAT 58.093 50.000 8.83 0.00 0.00 2.29
761 826 2.236766 AGGCGCGGAGTACTATGTATT 58.763 47.619 8.83 0.00 0.00 1.89
786 851 6.648879 TTTGGATTTGGAAATTCGAACTCT 57.351 33.333 0.00 0.00 0.00 3.24
823 888 0.967887 TTCTCTGCGAGACCAGGGAG 60.968 60.000 7.61 0.00 42.86 4.30
824 889 2.363018 TCTGCGAGACCAGGGAGG 60.363 66.667 0.00 0.00 45.67 4.30
825 890 3.465403 CTGCGAGACCAGGGAGGG 61.465 72.222 0.00 0.00 43.89 4.30
826 891 3.965026 CTGCGAGACCAGGGAGGGA 62.965 68.421 0.00 0.00 43.89 4.20
827 892 3.462678 GCGAGACCAGGGAGGGAC 61.463 72.222 0.00 0.00 43.89 4.46
878 943 0.749649 TCCATGTGCACCAACCAAAC 59.250 50.000 15.69 0.00 0.00 2.93
935 1000 3.161450 ACCACGGCACCACAGACT 61.161 61.111 0.00 0.00 0.00 3.24
1425 1567 1.399714 ACATGGACGCCGAGAAGATA 58.600 50.000 0.00 0.00 0.00 1.98
1460 1602 3.195698 GCTCACCCAATCCGACGC 61.196 66.667 0.00 0.00 0.00 5.19
1767 1939 2.352422 GACATGGAGGTGCAGCCA 59.648 61.111 13.29 8.88 40.61 4.75
1803 1987 2.747686 GGTGTCAGCGAGGGGAAA 59.252 61.111 0.00 0.00 0.00 3.13
1906 2090 4.815308 AGCTAACACATGAGATGAGAATGC 59.185 41.667 0.00 0.00 0.00 3.56
2022 2207 6.042143 CCAACATGGTGAAATTATTAGTGCC 58.958 40.000 13.74 0.00 31.35 5.01
2068 2253 0.110486 TGGGAGGAGTGCTTTTCCAC 59.890 55.000 4.86 0.00 37.18 4.02
2069 2254 0.955919 GGGAGGAGTGCTTTTCCACG 60.956 60.000 4.86 0.00 40.59 4.94
2071 2256 1.901650 GAGGAGTGCTTTTCCACGCG 61.902 60.000 3.53 3.53 40.59 6.01
2116 2310 0.616679 TGTGCCCCTAGTACTCCCAC 60.617 60.000 0.00 1.73 31.32 4.61
2247 2486 7.270579 GCACAGGTTTTAGTCGAACATATTTTC 59.729 37.037 0.00 0.00 0.00 2.29
2273 2514 3.826524 TCATGTGCTTGGAACCTTTGTA 58.173 40.909 0.00 0.00 0.00 2.41
2288 2529 4.883585 ACCTTTGTACACAGCATGGATATG 59.116 41.667 3.35 0.00 43.62 1.78
2456 4009 6.315393 GTCTATCCTGAACTTAAATTCCGCAA 59.685 38.462 0.00 0.00 0.00 4.85
2717 4591 2.514205 AGACAACCAATTGCACAAGC 57.486 45.000 0.00 0.00 39.66 4.01
2891 4798 0.522626 TGTTCGTTCCGCGTATCTCA 59.477 50.000 4.92 0.00 42.13 3.27
3130 5086 1.055849 GGCAACCATTTTTGGAGGGT 58.944 50.000 0.00 0.00 34.43 4.34
3172 5128 2.224523 ACACACCCCAAGTCACTATGTG 60.225 50.000 0.00 0.00 41.31 3.21
3179 5135 4.380867 CCCCAAGTCACTATGTGAAATTGC 60.381 45.833 15.52 1.27 44.49 3.56
3292 5248 5.923114 CCTACGAGATAATGATGGTGTCTTG 59.077 44.000 0.00 0.00 0.00 3.02
3296 5252 5.586243 CGAGATAATGATGGTGTCTTGGTTT 59.414 40.000 0.00 0.00 0.00 3.27
3297 5253 6.457392 CGAGATAATGATGGTGTCTTGGTTTG 60.457 42.308 0.00 0.00 0.00 2.93
3299 5255 3.524095 ATGATGGTGTCTTGGTTTGGA 57.476 42.857 0.00 0.00 0.00 3.53
3300 5256 2.862541 TGATGGTGTCTTGGTTTGGAG 58.137 47.619 0.00 0.00 0.00 3.86
3302 5258 2.051334 TGGTGTCTTGGTTTGGAGTG 57.949 50.000 0.00 0.00 0.00 3.51
3304 5260 0.668535 GTGTCTTGGTTTGGAGTGGC 59.331 55.000 0.00 0.00 0.00 5.01
3305 5261 0.257328 TGTCTTGGTTTGGAGTGGCA 59.743 50.000 0.00 0.00 0.00 4.92
3306 5262 1.133513 TGTCTTGGTTTGGAGTGGCAT 60.134 47.619 0.00 0.00 0.00 4.40
3307 5263 1.963515 GTCTTGGTTTGGAGTGGCATT 59.036 47.619 0.00 0.00 0.00 3.56
3308 5264 2.365293 GTCTTGGTTTGGAGTGGCATTT 59.635 45.455 0.00 0.00 0.00 2.32
3309 5265 3.572255 GTCTTGGTTTGGAGTGGCATTTA 59.428 43.478 0.00 0.00 0.00 1.40
3310 5266 4.220602 GTCTTGGTTTGGAGTGGCATTTAT 59.779 41.667 0.00 0.00 0.00 1.40
3311 5267 4.462483 TCTTGGTTTGGAGTGGCATTTATC 59.538 41.667 0.00 0.00 0.00 1.75
3313 5269 4.155709 TGGTTTGGAGTGGCATTTATCAA 58.844 39.130 0.00 0.00 0.00 2.57
3314 5270 4.590647 TGGTTTGGAGTGGCATTTATCAAA 59.409 37.500 0.00 0.00 0.00 2.69
3317 5273 7.038729 TGGTTTGGAGTGGCATTTATCAAATTA 60.039 33.333 0.00 0.00 0.00 1.40
3318 5274 7.821846 GGTTTGGAGTGGCATTTATCAAATTAA 59.178 33.333 0.00 0.00 0.00 1.40
3319 5275 8.655970 GTTTGGAGTGGCATTTATCAAATTAAC 58.344 33.333 0.00 0.00 0.00 2.01
3320 5276 6.872920 TGGAGTGGCATTTATCAAATTAACC 58.127 36.000 0.00 0.00 0.00 2.85
3321 5277 6.127196 TGGAGTGGCATTTATCAAATTAACCC 60.127 38.462 0.00 0.00 0.00 4.11
3323 5279 7.364673 GGAGTGGCATTTATCAAATTAACCCTT 60.365 37.037 0.00 0.00 0.00 3.95
3324 5280 7.330262 AGTGGCATTTATCAAATTAACCCTTG 58.670 34.615 0.00 0.00 0.00 3.61
3326 5282 7.821846 GTGGCATTTATCAAATTAACCCTTGAA 59.178 33.333 0.00 0.00 35.31 2.69
3327 5283 8.547173 TGGCATTTATCAAATTAACCCTTGAAT 58.453 29.630 1.77 0.00 35.31 2.57
3395 5405 0.179163 GCATGCTTTTGTACGGGAGC 60.179 55.000 11.37 7.09 35.74 4.70
3610 5654 6.757897 TGTTATTACCAAATCAAGGCTGAG 57.242 37.500 0.00 0.00 34.23 3.35
3745 5967 6.052360 GGAGAAAGGTGTCCAAGAGAATATC 58.948 44.000 0.00 0.00 37.16 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.624487 TGTTCATCGGACGATTCGTG 58.376 50.000 17.75 3.14 41.37 4.35
190 191 3.050354 AACCACCCCTGTTGCGTCA 62.050 57.895 0.00 0.00 0.00 4.35
277 278 2.283966 CAGAGGGGACAGGACCGT 60.284 66.667 0.00 0.00 0.00 4.83
309 310 3.508840 GGAGGTTTGGCCATCGCG 61.509 66.667 6.09 0.00 40.61 5.87
399 448 4.593864 GGTCGCCTCCTCATCGCC 62.594 72.222 0.00 0.00 0.00 5.54
403 452 2.835431 CTCCGGTCGCCTCCTCAT 60.835 66.667 0.00 0.00 0.00 2.90
528 589 4.980805 TGGACGCACGCCCTTGTC 62.981 66.667 0.00 0.00 0.00 3.18
529 590 4.988598 CTGGACGCACGCCCTTGT 62.989 66.667 0.00 0.00 0.00 3.16
553 614 3.632107 GTGAAACGGACACGCGCA 61.632 61.111 5.73 0.00 46.04 6.09
678 741 0.672401 GTCCGGCCTCGTTCATTTGA 60.672 55.000 0.00 0.00 33.95 2.69
689 753 1.661990 TACCCTATCCTGTCCGGCCT 61.662 60.000 0.00 0.00 0.00 5.19
708 772 4.681978 GGACAACTCCACCGCGCT 62.682 66.667 5.56 0.00 36.42 5.92
735 800 2.898840 TACTCCGCGCCTACCTCG 60.899 66.667 0.00 0.00 0.00 4.63
736 801 0.533755 TAGTACTCCGCGCCTACCTC 60.534 60.000 0.00 0.00 0.00 3.85
737 802 0.110104 ATAGTACTCCGCGCCTACCT 59.890 55.000 0.00 0.00 0.00 3.08
738 803 0.240411 CATAGTACTCCGCGCCTACC 59.760 60.000 0.00 0.00 0.00 3.18
739 804 0.950116 ACATAGTACTCCGCGCCTAC 59.050 55.000 0.00 0.00 0.00 3.18
740 805 2.549064 TACATAGTACTCCGCGCCTA 57.451 50.000 0.00 0.00 0.00 3.93
741 806 1.906990 ATACATAGTACTCCGCGCCT 58.093 50.000 0.00 0.00 0.00 5.52
742 807 2.719426 AATACATAGTACTCCGCGCC 57.281 50.000 0.00 0.00 0.00 6.53
743 808 5.061808 CCAAATAATACATAGTACTCCGCGC 59.938 44.000 0.00 0.00 0.00 6.86
744 809 6.384224 TCCAAATAATACATAGTACTCCGCG 58.616 40.000 0.00 0.00 0.00 6.46
745 810 8.773404 AATCCAAATAATACATAGTACTCCGC 57.227 34.615 0.00 0.00 0.00 5.54
759 824 9.586435 GAGTTCGAATTTCCAAATCCAAATAAT 57.414 29.630 0.00 0.00 0.00 1.28
760 825 8.802267 AGAGTTCGAATTTCCAAATCCAAATAA 58.198 29.630 0.00 0.00 0.00 1.40
761 826 8.348285 AGAGTTCGAATTTCCAAATCCAAATA 57.652 30.769 0.00 0.00 0.00 1.40
772 837 4.327627 CGAGAAAGGAGAGTTCGAATTTCC 59.672 45.833 13.37 13.83 33.38 3.13
786 851 0.959553 AAGACGACAGCGAGAAAGGA 59.040 50.000 0.00 0.00 41.64 3.36
825 890 3.775654 CTGGCACGAGGAGGGGTC 61.776 72.222 0.00 0.00 0.00 4.46
826 891 4.316823 TCTGGCACGAGGAGGGGT 62.317 66.667 0.00 0.00 0.00 4.95
827 892 3.465403 CTCTGGCACGAGGAGGGG 61.465 72.222 0.00 0.00 0.00 4.79
1162 1271 4.200283 GGAGAGCTGGGAGACGCG 62.200 72.222 3.53 3.53 0.00 6.01
1242 1360 3.663815 GAGGAGGAGGAGGCCGTCA 62.664 68.421 0.00 0.00 0.00 4.35
1406 1548 1.399714 TATCTTCTCGGCGTCCATGT 58.600 50.000 6.85 0.00 0.00 3.21
1767 1939 0.608640 CCAAGAGCCGGTACAGTTCT 59.391 55.000 1.90 0.00 0.00 3.01
1803 1987 1.927174 GTCAATTCGACATAGCGCAGT 59.073 47.619 11.47 4.73 44.69 4.40
1906 2090 0.751277 TTGTCAGGCAACACCAGGTG 60.751 55.000 18.93 18.93 43.14 4.00
1948 2132 0.813184 ATTGCAGAAATCCACGGCAG 59.187 50.000 0.00 0.00 39.24 4.85
2022 2207 2.581354 CCCTCAGCCAAGTCGAGG 59.419 66.667 0.00 0.00 45.02 4.63
2068 2253 2.535984 GGTACAGAGATTTGATGTCGCG 59.464 50.000 0.00 0.00 0.00 5.87
2069 2254 3.307242 GTGGTACAGAGATTTGATGTCGC 59.693 47.826 0.00 0.00 41.80 5.19
2071 2256 3.865745 CCGTGGTACAGAGATTTGATGTC 59.134 47.826 0.00 0.00 41.80 3.06
2107 2301 1.527370 GGAGCCATGGTGGGAGTAC 59.473 63.158 14.67 0.00 38.19 2.73
2196 2409 7.275560 GCACCCTAACAATTAAAGTGCAATAAG 59.724 37.037 7.30 0.00 46.32 1.73
2247 2486 2.564062 AGGTTCCAAGCACATGAATTGG 59.436 45.455 16.96 16.96 44.00 3.16
2273 2514 6.832520 TTAACAAACATATCCATGCTGTGT 57.167 33.333 0.00 0.00 33.81 3.72
2717 4591 3.438087 CCAGTATGTCTGCCAAAGTCTTG 59.562 47.826 0.00 0.00 42.38 3.02
3012 4952 2.760092 GCAATAATCCAACCAAGAGCCA 59.240 45.455 0.00 0.00 0.00 4.75
3147 5103 1.283613 AGTGACTTGGGGTGTGTTTCA 59.716 47.619 0.00 0.00 0.00 2.69
3172 5128 6.378582 TCGGACAATTAAGACAAGCAATTTC 58.621 36.000 0.00 0.00 0.00 2.17
3179 5135 8.979574 GTATAAGGATCGGACAATTAAGACAAG 58.020 37.037 0.00 0.00 0.00 3.16
3292 5248 4.799564 TTGATAAATGCCACTCCAAACC 57.200 40.909 0.00 0.00 0.00 3.27
3296 5252 6.127196 GGGTTAATTTGATAAATGCCACTCCA 60.127 38.462 0.00 0.00 0.00 3.86
3297 5253 6.098266 AGGGTTAATTTGATAAATGCCACTCC 59.902 38.462 0.00 0.00 0.00 3.85
3299 5255 7.180051 TCAAGGGTTAATTTGATAAATGCCACT 59.820 33.333 0.00 0.00 0.00 4.00
3300 5256 7.327214 TCAAGGGTTAATTTGATAAATGCCAC 58.673 34.615 0.00 0.00 0.00 5.01
3302 5258 8.962884 ATTCAAGGGTTAATTTGATAAATGCC 57.037 30.769 0.00 0.00 33.68 4.40
3363 5340 2.757099 CATGCTTCCACCCCCAGC 60.757 66.667 0.00 0.00 0.00 4.85
3395 5405 4.624336 AGAGTACGTAGCTCAGACAATG 57.376 45.455 20.08 0.00 35.55 2.82
3610 5654 7.708752 AGATACTAGCAAGAAACATACTTCAGC 59.291 37.037 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.