Multiple sequence alignment - TraesCS5D01G112200

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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 TraesCS5D01G112200 chr5D 100.000 3202 0 0 1 3202 127885122 127888323 0.000000e+00 5914.0
1 TraesCS5D01G112200 chr5B 94.513 2661 100 22 98 2715 140823135 140825792 0.000000e+00 4063.0
2 TraesCS5D01G112200 chr5B 88.000 75 8 1 1 75 140822838 140822911 1.580000e-13 87.9
3 TraesCS5D01G112200 chr3D 93.349 436 11 3 2785 3202 573859919 573860354 2.100000e-176 628.0
4 TraesCS5D01G112200 chr4D 93.103 406 12 3 2812 3202 282203755 282204159 5.950000e-162 580.0
5 TraesCS5D01G112200 chr4D 97.778 90 2 0 2785 2874 282203656 282203745 4.280000e-34 156.0
6 TraesCS5D01G112200 chr4D 97.059 68 2 0 2717 2784 282203547 282203614 7.260000e-22 115.0
7 TraesCS5D01G112200 chr5A 95.498 311 10 3 2893 3202 691392419 691392726 7.980000e-136 494.0
8 TraesCS5D01G112200 chr6A 73.563 1044 240 28 1229 2245 613494252 613495286 1.810000e-97 366.0
9 TraesCS5D01G112200 chr6A 75.667 300 65 7 932 1225 64066129 64065832 3.330000e-30 143.0
10 TraesCS5D01G112200 chr1B 73.397 1045 246 25 1229 2248 46829698 46828661 8.440000e-96 361.0
11 TraesCS5D01G112200 chr1B 72.752 1112 270 24 1229 2316 4518368 4517266 8.500000e-91 344.0
12 TraesCS5D01G112200 chr1B 72.247 1117 270 31 1229 2316 46692577 46693682 3.100000e-80 309.0
13 TraesCS5D01G112200 chr1D 96.923 130 4 0 3068 3197 479126612 479126741 5.380000e-53 219.0
14 TraesCS5D01G112200 chr3B 80.531 226 42 2 989 1213 72922434 72922658 4.250000e-39 172.0
15 TraesCS5D01G112200 chr3A 79.741 232 40 7 985 1213 57904708 57904935 9.190000e-36 161.0
16 TraesCS5D01G112200 chr7D 83.893 149 21 3 984 1130 548231383 548231530 4.310000e-29 139.0
17 TraesCS5D01G112200 chr7B 83.893 149 21 3 984 1130 591461931 591462078 4.310000e-29 139.0
18 TraesCS5D01G112200 chr6D 76.987 239 50 5 984 1219 51068493 51068729 7.210000e-27 132.0
19 TraesCS5D01G112200 chr6D 76.016 246 52 7 984 1225 53175729 53175487 1.560000e-23 121.0
20 TraesCS5D01G112200 chr6D 75.833 240 51 7 984 1219 50956638 50956874 7.260000e-22 115.0


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 TraesCS5D01G112200 chr5D 127885122 127888323 3201 False 5914.000000 5914 100.0000 1 3202 1 chr5D.!!$F1 3201
1 TraesCS5D01G112200 chr5B 140822838 140825792 2954 False 2075.450000 4063 91.2565 1 2715 2 chr5B.!!$F1 2714
2 TraesCS5D01G112200 chr4D 282203547 282204159 612 False 283.666667 580 95.9800 2717 3202 3 chr4D.!!$F1 485
3 TraesCS5D01G112200 chr6A 613494252 613495286 1034 False 366.000000 366 73.5630 1229 2245 1 chr6A.!!$F1 1016
4 TraesCS5D01G112200 chr1B 46828661 46829698 1037 True 361.000000 361 73.3970 1229 2248 1 chr1B.!!$R2 1019
5 TraesCS5D01G112200 chr1B 4517266 4518368 1102 True 344.000000 344 72.7520 1229 2316 1 chr1B.!!$R1 1087
6 TraesCS5D01G112200 chr1B 46692577 46693682 1105 False 309.000000 309 72.2470 1229 2316 1 chr1B.!!$F1 1087

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
407 667 0.175760 TCTGGCAGATCTACGGTTGC 59.824 55.0 14.43 0.0 35.87 4.17 F
426 686 0.459489 CCGCCTCTCCTTCTCTTCTG 59.541 60.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2410 1.133976 GCATCCCAGCATCAGTTACCT 60.134 52.381 0.0 0.0 0.0 3.08 R
2407 2700 1.001860 TCAATGACAGCGACATCCACA 59.998 47.619 0.0 0.0 0.0 4.17 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
57 58 3.918977 CGTGGGTCCGTGGTGTGA 61.919 66.667 0.00 0.00 0.00 3.58
58 59 2.747686 GTGGGTCCGTGGTGTGAT 59.252 61.111 0.00 0.00 0.00 3.06
59 60 1.671054 GTGGGTCCGTGGTGTGATG 60.671 63.158 0.00 0.00 0.00 3.07
60 61 2.144078 TGGGTCCGTGGTGTGATGT 61.144 57.895 0.00 0.00 0.00 3.06
61 62 1.375523 GGGTCCGTGGTGTGATGTC 60.376 63.158 0.00 0.00 0.00 3.06
62 63 1.369692 GGTCCGTGGTGTGATGTCA 59.630 57.895 0.00 0.00 0.00 3.58
63 64 0.670546 GGTCCGTGGTGTGATGTCAG 60.671 60.000 0.00 0.00 0.00 3.51
64 65 0.670546 GTCCGTGGTGTGATGTCAGG 60.671 60.000 0.00 0.00 0.00 3.86
65 66 0.830023 TCCGTGGTGTGATGTCAGGA 60.830 55.000 0.00 0.00 0.00 3.86
66 67 0.670546 CCGTGGTGTGATGTCAGGAC 60.671 60.000 0.00 0.00 0.00 3.85
67 68 0.670546 CGTGGTGTGATGTCAGGACC 60.671 60.000 0.00 4.79 32.67 4.46
68 69 0.687354 GTGGTGTGATGTCAGGACCT 59.313 55.000 10.79 0.00 33.05 3.85
69 70 0.686789 TGGTGTGATGTCAGGACCTG 59.313 55.000 15.99 15.99 33.05 4.00
70 71 0.674895 GGTGTGATGTCAGGACCTGC 60.675 60.000 17.33 12.26 30.53 4.85
71 72 1.016130 GTGTGATGTCAGGACCTGCG 61.016 60.000 17.33 0.00 0.00 5.18
72 73 1.293498 GTGATGTCAGGACCTGCGT 59.707 57.895 17.33 12.85 0.00 5.24
73 74 1.016130 GTGATGTCAGGACCTGCGTG 61.016 60.000 17.33 0.00 0.00 5.34
74 75 1.448540 GATGTCAGGACCTGCGTGG 60.449 63.158 17.33 0.00 42.93 4.94
83 84 2.125512 CCTGCGTGGTCTGTAGGC 60.126 66.667 0.00 0.00 32.37 3.93
99 100 0.963856 AGGCGTGACGTCAGGATGTA 60.964 55.000 35.27 3.81 37.40 2.29
131 363 1.468520 GACCCAACACGTGATTGATGG 59.531 52.381 25.01 19.45 38.78 3.51
134 366 1.135603 CCAACACGTGATTGATGGCTG 60.136 52.381 25.01 5.54 33.18 4.85
197 429 9.720667 GTATTACCAAAACCATACCGAAATAAC 57.279 33.333 0.00 0.00 0.00 1.89
297 557 2.347490 CCAGTCCCCTCACAACCG 59.653 66.667 0.00 0.00 0.00 4.44
327 587 1.005037 CAAGTCCACAGCTGGCGTA 60.005 57.895 19.93 0.00 37.49 4.42
356 616 3.726557 TCACCAATCCAAGATCAAGCT 57.273 42.857 0.00 0.00 0.00 3.74
368 628 1.557269 ATCAAGCTGAGGCGGAAGGT 61.557 55.000 0.00 0.00 44.37 3.50
371 631 4.400961 GCTGAGGCGGAAGGTGCT 62.401 66.667 0.00 0.00 0.00 4.40
384 644 2.435059 GTGCTGCCCGACTTCTCC 60.435 66.667 0.00 0.00 0.00 3.71
390 650 2.355193 GCCCGACTTCTCCTGCTCT 61.355 63.158 0.00 0.00 0.00 4.09
392 652 1.515020 CCGACTTCTCCTGCTCTGG 59.485 63.158 0.00 0.00 0.00 3.86
393 653 1.153667 CGACTTCTCCTGCTCTGGC 60.154 63.158 0.00 0.00 39.26 4.85
407 667 0.175760 TCTGGCAGATCTACGGTTGC 59.824 55.000 14.43 0.00 35.87 4.17
423 683 1.194781 TTGCCGCCTCTCCTTCTCTT 61.195 55.000 0.00 0.00 0.00 2.85
426 686 0.459489 CCGCCTCTCCTTCTCTTCTG 59.541 60.000 0.00 0.00 0.00 3.02
441 701 3.698463 CTGCCGTCGCGTTTTCGT 61.698 61.111 5.77 0.00 46.03 3.85
458 718 7.462462 GCGTTTTCGTGATTCTAGGTACTAAAG 60.462 40.741 0.00 0.00 42.83 1.85
523 784 1.202758 TGTGCAACCTTGTCTACCCTG 60.203 52.381 0.00 0.00 34.36 4.45
546 807 5.420739 TGCTCTCTCTATATCTCTCGCTCTA 59.579 44.000 0.00 0.00 0.00 2.43
607 868 2.359478 CCGGCCGGTAATATGCCC 60.359 66.667 36.64 0.00 42.29 5.36
655 916 2.173569 ACCAGACCTCATATTGCCTTCC 59.826 50.000 0.00 0.00 0.00 3.46
691 952 8.049117 ACTTAATTAAGTGCTTCTGGATCATCA 58.951 33.333 26.30 0.00 44.30 3.07
738 1012 1.005215 CTCCATTCTTTCTGGCCCAGT 59.995 52.381 11.27 0.00 33.56 4.00
754 1028 3.433598 GCCCAGTTGCCTCTGAATATGTA 60.434 47.826 6.78 0.00 37.61 2.29
760 1034 7.041508 CCAGTTGCCTCTGAATATGTAAAGATC 60.042 40.741 6.78 0.00 37.61 2.75
806 1080 6.560253 AACTTGTGGCAGTTCTAGTTTATG 57.440 37.500 0.00 0.00 30.76 1.90
950 1225 9.729281 ATTTCATTAATTTCATTCCAGCACTTT 57.271 25.926 0.00 0.00 0.00 2.66
955 1230 3.731652 TTCATTCCAGCACTTTGGTTG 57.268 42.857 0.00 0.00 39.35 3.77
1011 1286 2.809665 GCATTGCTCGATGGAGGATCTT 60.810 50.000 6.88 0.00 40.57 2.40
1059 1334 2.840651 CCAGAGGATTACCAGGACAAGT 59.159 50.000 0.00 0.00 38.94 3.16
1100 1375 2.351455 TGTGTCAAAAAGTCTGTGCGA 58.649 42.857 0.00 0.00 0.00 5.10
1101 1376 2.351418 TGTGTCAAAAAGTCTGTGCGAG 59.649 45.455 0.00 0.00 0.00 5.03
1130 1405 0.535102 AATCAAAGGGCCGCTATCCG 60.535 55.000 0.00 0.00 0.00 4.18
1200 1475 3.712016 TCCCGATTCTCCAATTTGTCA 57.288 42.857 0.00 0.00 0.00 3.58
1225 1500 4.981806 ATGGAAATCAATTACACCGGTG 57.018 40.909 32.83 32.83 33.69 4.94
1299 1574 5.183904 AGCCAATTGTAAGAAGTTGATGTCC 59.816 40.000 4.43 0.00 0.00 4.02
1461 1736 3.743521 TGGATCACTGGAAGAACTTGTG 58.256 45.455 0.00 0.00 37.43 3.33
1700 1990 4.502259 GCTGAGACTTTGTCTTCTCTTGGA 60.502 45.833 1.58 0.00 43.53 3.53
1800 2090 5.284079 CACAGCTGCAACAATCTTAAAAGT 58.716 37.500 15.27 0.00 0.00 2.66
2031 2324 5.700832 TCAGATTCGTGTTCTTGTGCTTAAT 59.299 36.000 0.00 0.00 0.00 1.40
2058 2351 4.940046 GCTGACTTCTTTGATGATGAAGGA 59.060 41.667 0.00 0.00 41.47 3.36
2249 2542 4.887748 TCACAGAAGTTGGATTCTCTGAC 58.112 43.478 5.01 0.00 37.43 3.51
2259 2552 2.478831 GATTCTCTGACCATCGAAGGC 58.521 52.381 6.60 0.27 0.00 4.35
2336 2629 0.391395 CTGGAGTCAGCAAGCAGGAG 60.391 60.000 0.00 0.00 33.86 3.69
2352 2645 2.034053 CAGGAGCCGTCTCAGTAGAATC 59.966 54.545 0.00 0.00 41.13 2.52
2379 2672 8.807948 AAACATAATGCTATTGGTCAAGTAGT 57.192 30.769 0.00 0.00 0.00 2.73
2407 2700 5.010617 AGTTATTTTCGGTTGTGCCTCATTT 59.989 36.000 0.00 0.00 34.25 2.32
2421 2714 2.079158 CTCATTTGTGGATGTCGCTGT 58.921 47.619 0.00 0.00 0.00 4.40
2423 2716 1.805943 CATTTGTGGATGTCGCTGTCA 59.194 47.619 0.00 0.00 0.00 3.58
2438 2731 2.477825 CTGTCATTGACCCTGCTATCG 58.522 52.381 14.05 0.00 0.00 2.92
2453 2746 6.183360 CCCTGCTATCGTTTTCATCATTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
2473 2766 6.282199 TCTTAGAACCTGTGTCTAATGGTC 57.718 41.667 0.00 0.00 31.64 4.02
2490 2783 2.562298 TGGTCAACTTTGGATCCAATGC 59.438 45.455 30.61 19.71 35.70 3.56
2493 2786 1.545582 CAACTTTGGATCCAATGCGGT 59.454 47.619 30.61 21.73 35.70 5.68
2502 2795 2.488204 TCCAATGCGGTGAATGAAGA 57.512 45.000 0.00 0.00 35.57 2.87
2538 2831 6.014647 TCTGTTACTGGTGTACTGAACCTAT 58.985 40.000 2.84 0.00 38.60 2.57
2547 2840 7.455058 TGGTGTACTGAACCTATTTATGTTGT 58.545 34.615 2.84 0.00 38.60 3.32
2555 2848 7.946207 TGAACCTATTTATGTTGTTTTGCTCA 58.054 30.769 0.00 0.00 0.00 4.26
2578 2871 7.512130 TCATGTAGCATAATTTCTCCATGTCT 58.488 34.615 0.00 0.58 31.30 3.41
2601 2894 7.814107 GTCTGCCATCTTGAAAATTGTCATAAA 59.186 33.333 0.00 0.00 0.00 1.40
2638 2931 4.045636 ACATTTCAGGTGTTCAACTTGC 57.954 40.909 0.00 0.00 35.87 4.01
2687 2980 7.337938 TCTATGTGGTGTATGAACATGACAAT 58.662 34.615 0.00 0.00 38.08 2.71
2692 2985 7.229506 TGTGGTGTATGAACATGACAATTTGTA 59.770 33.333 0.00 0.00 38.08 2.41
2706 2999 8.574251 TGACAATTTGTATGTTATTACTGCCT 57.426 30.769 1.15 0.00 0.00 4.75
2731 3024 9.573133 CTTTATATTGGAAAATTCGATATGGCC 57.427 33.333 0.00 0.00 0.00 5.36
2753 3046 9.279233 TGGCCCATACAATCATATAGTAGTATT 57.721 33.333 0.00 0.00 0.00 1.89
2794 3128 3.066760 CCTCGGGATGCAAATTTTCTACC 59.933 47.826 0.00 0.00 0.00 3.18
2801 3135 3.573598 TGCAAATTTTCTACCGTGCATG 58.426 40.909 0.00 0.00 37.09 4.06
2925 3345 2.336809 GTGCGGGCCTATCTCTCG 59.663 66.667 0.84 0.00 0.00 4.04
2945 3365 3.866582 CCCACGCCCTCCCATCTC 61.867 72.222 0.00 0.00 0.00 2.75
3005 3426 2.174424 GCTTCTTCCTCCTCCAATCCAT 59.826 50.000 0.00 0.00 0.00 3.41
3032 3453 0.611714 TAACAACGAGCTTCTCCCCC 59.388 55.000 0.00 0.00 0.00 5.40
3062 3483 0.793861 TAATTGCGGTCGTGAAGTGC 59.206 50.000 0.00 0.00 0.00 4.40
3077 3498 4.384247 GTGAAGTGCTGAGCGACATATATC 59.616 45.833 0.00 0.00 0.00 1.63
3125 3546 6.166279 ACCGATATTACAAGTGCATCCTATG 58.834 40.000 0.00 0.00 0.00 2.23
3174 3595 2.270352 TGTGATTTGCCCGTCTTTCT 57.730 45.000 0.00 0.00 0.00 2.52
3182 3603 1.674057 CCCGTCTTTCTGCTCACCT 59.326 57.895 0.00 0.00 0.00 4.00
3190 3611 4.275936 GTCTTTCTGCTCACCTTTGCTTAA 59.724 41.667 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.279851 TTGACGTCACACCTGCGG 60.280 61.111 19.90 0.00 0.00 5.69
17 18 2.870372 GCCCACGCATGTCTTGAC 59.130 61.111 0.00 0.00 34.03 3.18
19 20 2.741985 TCGCCCACGCATGTCTTG 60.742 61.111 0.00 0.00 39.84 3.02
50 51 0.686789 CAGGTCCTGACATCACACCA 59.313 55.000 14.26 0.00 32.44 4.17
52 53 1.016130 CGCAGGTCCTGACATCACAC 61.016 60.000 23.77 0.87 32.44 3.82
53 54 1.293179 CGCAGGTCCTGACATCACA 59.707 57.895 23.77 0.00 32.44 3.58
54 55 1.016130 CACGCAGGTCCTGACATCAC 61.016 60.000 23.77 2.39 32.44 3.06
55 56 1.293179 CACGCAGGTCCTGACATCA 59.707 57.895 23.77 0.00 32.44 3.07
56 57 1.448540 CCACGCAGGTCCTGACATC 60.449 63.158 23.77 3.55 32.44 3.06
57 58 2.665000 CCACGCAGGTCCTGACAT 59.335 61.111 23.77 3.54 32.44 3.06
66 67 2.125512 GCCTACAGACCACGCAGG 60.126 66.667 0.00 0.00 45.67 4.85
67 68 2.507102 CGCCTACAGACCACGCAG 60.507 66.667 0.00 0.00 0.00 5.18
68 69 3.299977 ACGCCTACAGACCACGCA 61.300 61.111 0.00 0.00 0.00 5.24
69 70 2.809601 CACGCCTACAGACCACGC 60.810 66.667 0.00 0.00 0.00 5.34
70 71 1.443872 GTCACGCCTACAGACCACG 60.444 63.158 0.00 0.00 0.00 4.94
71 72 1.443872 CGTCACGCCTACAGACCAC 60.444 63.158 0.00 0.00 0.00 4.16
72 73 1.859427 GACGTCACGCCTACAGACCA 61.859 60.000 11.55 0.00 0.00 4.02
73 74 1.154073 GACGTCACGCCTACAGACC 60.154 63.158 11.55 0.00 0.00 3.85
74 75 0.454620 CTGACGTCACGCCTACAGAC 60.455 60.000 15.76 0.00 0.00 3.51
75 76 1.583495 CCTGACGTCACGCCTACAGA 61.583 60.000 15.76 0.00 0.00 3.41
76 77 1.154016 CCTGACGTCACGCCTACAG 60.154 63.158 15.76 1.86 0.00 2.74
77 78 0.963856 ATCCTGACGTCACGCCTACA 60.964 55.000 15.76 0.00 0.00 2.74
78 79 0.525668 CATCCTGACGTCACGCCTAC 60.526 60.000 15.76 0.00 0.00 3.18
79 80 0.963856 ACATCCTGACGTCACGCCTA 60.964 55.000 15.76 0.00 0.00 3.93
80 81 0.963856 TACATCCTGACGTCACGCCT 60.964 55.000 15.76 0.00 0.00 5.52
81 82 0.801067 GTACATCCTGACGTCACGCC 60.801 60.000 15.76 0.00 0.00 5.68
82 83 1.132199 CGTACATCCTGACGTCACGC 61.132 60.000 15.76 0.00 34.39 5.34
83 84 2.926074 CGTACATCCTGACGTCACG 58.074 57.895 15.76 11.42 34.39 4.35
131 363 1.463444 ACGTAAACGATTCTTGCCAGC 59.537 47.619 9.86 0.00 43.02 4.85
134 366 4.336532 AATGACGTAAACGATTCTTGCC 57.663 40.909 9.86 0.00 43.02 4.52
178 410 6.683715 ACCAAGTTATTTCGGTATGGTTTTG 58.316 36.000 0.00 0.00 36.32 2.44
240 473 7.457380 AGCCAGGCCATTCAGTTATATATAT 57.543 36.000 8.22 0.00 0.00 0.86
260 520 3.006677 GCTGGGGAATGGTAGCCA 58.993 61.111 0.00 0.00 38.19 4.75
291 551 3.003763 GCTCCCCTCTCCGGTTGT 61.004 66.667 0.00 0.00 0.00 3.32
297 557 2.371259 GGACTTGGCTCCCCTCTCC 61.371 68.421 0.00 0.00 0.00 3.71
356 616 4.704833 GCAGCACCTTCCGCCTCA 62.705 66.667 0.00 0.00 0.00 3.86
368 628 2.604686 AGGAGAAGTCGGGCAGCA 60.605 61.111 0.00 0.00 0.00 4.41
371 631 2.604686 AGCAGGAGAAGTCGGGCA 60.605 61.111 0.00 0.00 0.00 5.36
375 635 1.153667 GCCAGAGCAGGAGAAGTCG 60.154 63.158 0.00 0.00 39.53 4.18
377 637 4.222353 TGCCAGAGCAGGAGAAGT 57.778 55.556 0.00 0.00 46.52 3.01
390 650 4.932789 GCAACCGTAGATCTGCCA 57.067 55.556 5.18 0.00 0.00 4.92
392 652 3.706140 CGGCAACCGTAGATCTGC 58.294 61.111 5.18 2.39 42.73 4.26
402 662 2.436824 GAAGGAGAGGCGGCAACC 60.437 66.667 13.08 11.31 0.00 3.77
407 667 0.459489 CAGAAGAGAAGGAGAGGCGG 59.541 60.000 0.00 0.00 0.00 6.13
410 670 0.459489 CGGCAGAAGAGAAGGAGAGG 59.541 60.000 0.00 0.00 0.00 3.69
423 683 3.399770 CGAAAACGCGACGGCAGA 61.400 61.111 15.93 0.00 39.92 4.26
426 686 2.488852 AATCACGAAAACGCGACGGC 62.489 55.000 15.93 0.00 34.83 5.68
440 700 8.035984 AGTTGCTTCTTTAGTACCTAGAATCAC 58.964 37.037 0.00 3.34 0.00 3.06
441 701 8.135382 AGTTGCTTCTTTAGTACCTAGAATCA 57.865 34.615 0.00 0.00 0.00 2.57
442 702 8.471609 AGAGTTGCTTCTTTAGTACCTAGAATC 58.528 37.037 0.00 0.00 0.00 2.52
447 707 7.299246 ACAAGAGTTGCTTCTTTAGTACCTA 57.701 36.000 0.00 0.00 35.28 3.08
458 718 3.249559 CACAGAAGGACAAGAGTTGCTTC 59.750 47.826 0.00 0.00 33.60 3.86
509 770 1.077993 AGAGAGCAGGGTAGACAAGGT 59.922 52.381 0.00 0.00 0.00 3.50
518 779 4.323485 CGAGAGATATAGAGAGAGCAGGGT 60.323 50.000 0.00 0.00 0.00 4.34
523 784 4.759782 AGAGCGAGAGATATAGAGAGAGC 58.240 47.826 0.00 0.00 0.00 4.09
607 868 0.248580 TGCTTCAACGTTGCAGCTTG 60.249 50.000 39.03 20.00 45.63 4.01
631 892 4.423625 AGGCAATATGAGGTCTGGTTAC 57.576 45.455 0.00 0.00 0.00 2.50
719 993 1.075601 ACTGGGCCAGAAAGAATGGA 58.924 50.000 38.99 0.00 40.51 3.41
738 1012 7.496920 CACTGATCTTTACATATTCAGAGGCAA 59.503 37.037 5.33 0.00 37.75 4.52
744 1018 7.977904 TGTTGCACTGATCTTTACATATTCAG 58.022 34.615 0.00 0.00 39.70 3.02
754 1028 5.591877 AGAGAAAACTGTTGCACTGATCTTT 59.408 36.000 0.00 0.00 0.00 2.52
760 1034 3.374988 TGTGAGAGAAAACTGTTGCACTG 59.625 43.478 0.00 0.00 0.00 3.66
806 1080 5.578727 CACTCCAGCAGTAATCTACAAAGAC 59.421 44.000 0.00 0.00 31.15 3.01
869 1144 6.206634 ACACCAATGTTAATCACGAAGAACAT 59.793 34.615 0.00 4.80 42.76 2.71
955 1230 0.678048 AATCTCAAGGTTCAGCGGGC 60.678 55.000 0.00 0.00 0.00 6.13
1011 1286 3.075005 GCCAGCAGTACCTCCGGA 61.075 66.667 2.93 2.93 0.00 5.14
1025 1300 0.250234 CCTCTGGACGATTTCTGCCA 59.750 55.000 0.00 0.00 0.00 4.92
1059 1334 5.942236 CACAAGGGAAAGAGAATTCAGATCA 59.058 40.000 8.44 0.00 0.00 2.92
1100 1375 1.614317 CCCTTTGATTCGCCTCAACCT 60.614 52.381 0.00 0.00 34.96 3.50
1101 1376 0.811281 CCCTTTGATTCGCCTCAACC 59.189 55.000 0.00 0.00 34.96 3.77
1130 1405 3.192212 AGAAAACAAGCTGCATCCTAAGC 59.808 43.478 1.02 0.00 39.82 3.09
1200 1475 6.648725 CACCGGTGTAATTGATTTCCATTTTT 59.351 34.615 26.95 0.00 0.00 1.94
1225 1500 5.934625 TGTATGAGAAGAAGCTCAAGGTTTC 59.065 40.000 0.00 0.00 46.94 2.78
1299 1574 4.866508 TGGTACAGAGTTTAGTGTGAGG 57.133 45.455 0.00 0.00 0.00 3.86
1461 1736 5.393461 CCTGATTCTGTTGCAATTCCTTACC 60.393 44.000 0.59 0.00 0.00 2.85
1889 2179 4.755411 CATAGGACAACCGAGAGCTAAAA 58.245 43.478 0.00 0.00 41.83 1.52
2031 2324 4.019950 TCATCATCAAAGAAGTCAGCTCCA 60.020 41.667 0.00 0.00 0.00 3.86
2058 2351 5.044919 TGGTGAGGATGAAAGTACCATCATT 60.045 40.000 11.16 0.00 41.52 2.57
2117 2410 1.133976 GCATCCCAGCATCAGTTACCT 60.134 52.381 0.00 0.00 0.00 3.08
2157 2450 2.036475 GAGTGTCAGACTCCTCAAGCAA 59.964 50.000 13.12 0.00 44.95 3.91
2249 2542 1.798735 CAAGCACAGCCTTCGATGG 59.201 57.895 12.90 12.90 0.00 3.51
2259 2552 1.703438 GCGGAGAGATGCAAGCACAG 61.703 60.000 0.00 0.00 0.00 3.66
2336 2629 4.995124 TGTTTAGATTCTACTGAGACGGC 58.005 43.478 0.00 0.00 0.00 5.68
2379 2672 6.039493 TGAGGCACAACCGAAAATAACTTTAA 59.961 34.615 0.00 0.00 46.52 1.52
2407 2700 1.001860 TCAATGACAGCGACATCCACA 59.998 47.619 0.00 0.00 0.00 4.17
2421 2714 3.627395 AAACGATAGCAGGGTCAATGA 57.373 42.857 0.00 0.00 42.67 2.57
2423 2716 3.950397 TGAAAACGATAGCAGGGTCAAT 58.050 40.909 0.00 0.00 42.67 2.57
2438 2731 8.352942 ACACAGGTTCTAAGAAATGATGAAAAC 58.647 33.333 0.00 0.00 0.00 2.43
2453 2746 5.542635 AGTTGACCATTAGACACAGGTTCTA 59.457 40.000 0.00 0.00 33.77 2.10
2473 2766 1.545582 ACCGCATTGGATCCAAAGTTG 59.454 47.619 30.28 23.68 42.00 3.16
2490 2783 8.076178 AGACAATTTTAAAGTCTTCATTCACCG 58.924 33.333 3.42 0.00 39.45 4.94
2502 2795 8.288689 ACACCAGTAACAGACAATTTTAAAGT 57.711 30.769 0.00 0.00 0.00 2.66
2555 2848 6.206243 GCAGACATGGAGAAATTATGCTACAT 59.794 38.462 0.00 0.00 36.11 2.29
2562 2855 5.950023 AGATGGCAGACATGGAGAAATTAT 58.050 37.500 0.00 0.00 40.72 1.28
2578 2871 8.312564 TGATTTATGACAATTTTCAAGATGGCA 58.687 29.630 0.00 0.00 34.83 4.92
2601 2894 7.233348 ACCTGAAATGTTTATCTTGTGGTTGAT 59.767 33.333 0.00 0.00 0.00 2.57
2638 2931 1.205893 GAGAGGCACTGTTAGGACCTG 59.794 57.143 3.53 0.00 41.55 4.00
2706 2999 8.527810 GGGCCATATCGAATTTTCCAATATAAA 58.472 33.333 4.39 0.00 0.00 1.40
2715 3008 5.957842 TGTATGGGCCATATCGAATTTTC 57.042 39.130 27.97 12.85 0.00 2.29
2945 3365 2.554032 CAAGGCAGTGTGAGGTAAAAGG 59.446 50.000 0.00 0.00 0.00 3.11
2982 3403 0.543749 ATTGGAGGAGGAAGAAGCCG 59.456 55.000 0.00 0.00 0.00 5.52
3005 3426 3.006537 AGAAGCTCGTTGTTAACAGCCTA 59.993 43.478 15.74 4.73 36.71 3.93
3032 3453 1.705337 CCGCAATTAGGGCACGTCAG 61.705 60.000 0.00 0.00 0.00 3.51
3062 3483 4.462508 ACCATGGATATATGTCGCTCAG 57.537 45.455 21.47 0.00 0.00 3.35
3125 3546 5.925969 GGTTAGCTTCAGAGATCTTATGCTC 59.074 44.000 13.70 0.00 34.07 4.26


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

AutoCloner maintained by Alex Coulton.