Multiple sequence alignment - TraesCS5D01G263600

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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 TraesCS5D01G263600 chr5D 100.000 3060 0 0 1 3060 369066872 369063813 0.000000e+00 5651.0
1 TraesCS5D01G263600 chr5D 74.886 438 96 12 2506 2932 410902533 410902099 1.450000e-43 187.0
2 TraesCS5D01G263600 chr5D 79.310 116 16 6 2112 2219 449275862 449275977 1.180000e-09 75.0
3 TraesCS5D01G263600 chr5A 86.429 2557 202 67 588 3060 471467760 471465265 0.000000e+00 2665.0
4 TraesCS5D01G263600 chr5A 89.972 359 30 3 1 358 471468628 471468275 2.780000e-125 459.0
5 TraesCS5D01G263600 chr5A 87.603 121 13 1 344 462 471467911 471467791 4.110000e-29 139.0
6 TraesCS5D01G263600 chr5A 78.481 158 21 10 2112 2256 568160737 568160894 1.170000e-14 91.6
7 TraesCS5D01G263600 chr5B 90.713 1669 98 27 577 2210 437563861 437562215 0.000000e+00 2170.0
8 TraesCS5D01G263600 chr5B 94.147 803 42 4 2051 2849 437555476 437554675 0.000000e+00 1218.0
9 TraesCS5D01G263600 chr5B 89.633 463 42 5 4 462 437564332 437563872 4.400000e-163 584.0
10 TraesCS5D01G263600 chr5B 76.832 505 86 23 2443 2929 18693507 18693016 3.920000e-64 255.0
11 TraesCS5D01G263600 chr5B 95.122 123 6 0 2938 3060 437554383 437554261 8.660000e-46 195.0
12 TraesCS5D01G263600 chr5B 72.893 439 66 31 2184 2589 548724309 548723891 5.400000e-18 102.0
13 TraesCS5D01G263600 chr5B 100.000 28 0 0 2014 2041 437555532 437555505 6.000000e-03 52.8
14 TraesCS5D01G263600 chr4D 77.273 660 122 25 2270 2914 18476885 18476239 2.240000e-96 363.0
15 TraesCS5D01G263600 chr4D 74.900 498 91 22 2444 2928 144865649 144866125 2.410000e-46 196.0
16 TraesCS5D01G263600 chr6D 81.347 386 36 18 1611 1978 441894979 441895346 6.460000e-72 281.0
17 TraesCS5D01G263600 chr3D 73.944 852 149 45 2109 2922 467498964 467498148 3.010000e-70 276.0
18 TraesCS5D01G263600 chr2D 75.158 632 119 24 2444 3051 526809439 526810056 2.340000e-66 263.0
19 TraesCS5D01G263600 chr2D 100.000 30 0 0 2114 2143 48613595 48613566 4.260000e-04 56.5
20 TraesCS5D01G263600 chr6B 79.381 388 49 19 1617 1994 667895403 667895769 8.480000e-61 244.0
21 TraesCS5D01G263600 chr4B 74.458 646 125 26 2270 2906 30373696 30373082 3.050000e-60 243.0
22 TraesCS5D01G263600 chr6A 79.420 345 60 10 2500 2841 445609909 445610245 1.830000e-57 233.0
23 TraesCS5D01G263600 chr6A 90.000 170 17 0 1617 1786 591263103 591263272 1.430000e-53 220.0
24 TraesCS5D01G263600 chr6A 81.871 171 17 8 1831 1991 591263561 591263727 6.880000e-27 132.0
25 TraesCS5D01G263600 chr3B 74.950 499 98 16 2443 2925 403243930 403243443 1.440000e-48 204.0
26 TraesCS5D01G263600 chr3B 80.303 132 19 5 2108 2233 780771802 780771932 3.250000e-15 93.5
27 TraesCS5D01G263600 chr3B 80.303 132 19 5 2108 2233 780794025 780794155 3.250000e-15 93.5
28 TraesCS5D01G263600 chr2A 74.888 446 82 20 2443 2867 677522449 677522013 3.140000e-40 176.0
29 TraesCS5D01G263600 chr7A 79.130 230 45 3 2701 2929 556313644 556313871 4.090000e-34 156.0
30 TraesCS5D01G263600 chr2B 89.855 69 3 4 2184 2248 27941847 27941779 5.440000e-13 86.1
31 TraesCS5D01G263600 chr2B 96.970 33 1 0 2110 2142 362250887 362250855 4.260000e-04 56.5
32 TraesCS5D01G263600 chr4A 83.871 93 5 9 2163 2248 576057416 576057505 2.530000e-11 80.5
33 TraesCS5D01G263600 chr3A 78.814 118 19 4 2110 2224 610061502 610061388 1.180000e-09 75.0
34 TraesCS5D01G263600 chr7D 86.154 65 8 1 2931 2995 603841308 603841371 5.470000e-08 69.4


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 TraesCS5D01G263600 chr5D 369063813 369066872 3059 True 5651.000000 5651 100.000000 1 3060 1 chr5D.!!$R1 3059
1 TraesCS5D01G263600 chr5A 471465265 471468628 3363 True 1087.666667 2665 88.001333 1 3060 3 chr5A.!!$R1 3059
2 TraesCS5D01G263600 chr5B 437562215 437564332 2117 True 1377.000000 2170 90.173000 4 2210 2 chr5B.!!$R4 2206
3 TraesCS5D01G263600 chr5B 437554261 437555532 1271 True 488.600000 1218 96.423000 2014 3060 3 chr5B.!!$R3 1046
4 TraesCS5D01G263600 chr4D 18476239 18476885 646 True 363.000000 363 77.273000 2270 2914 1 chr4D.!!$R1 644
5 TraesCS5D01G263600 chr3D 467498148 467498964 816 True 276.000000 276 73.944000 2109 2922 1 chr3D.!!$R1 813
6 TraesCS5D01G263600 chr2D 526809439 526810056 617 False 263.000000 263 75.158000 2444 3051 1 chr2D.!!$F1 607
7 TraesCS5D01G263600 chr4B 30373082 30373696 614 True 243.000000 243 74.458000 2270 2906 1 chr4B.!!$R1 636

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
843 1238 0.604578 TTCTTGTCTTACCCCCGTCG 59.395 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2890 0.032952 GATTGTATAGCCCGGACGCA 59.967 55.0 0.73 0.0 0.0 5.24 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
227 229 6.480524 TGAAGTTGATACAAAACATCGAGG 57.519 37.500 0.00 0.00 29.93 4.63
260 262 9.737427 CAAGATATGAATATACCATCTACGACC 57.263 37.037 0.00 0.00 0.00 4.79
301 303 3.140325 ACAAGGACGACAATGTTCCAT 57.860 42.857 6.85 0.00 0.00 3.41
302 304 2.813754 ACAAGGACGACAATGTTCCATG 59.186 45.455 6.85 7.22 0.00 3.66
377 757 3.242608 TGACTTGTTTCAAGCTTGTACGC 60.243 43.478 25.19 14.33 0.00 4.42
391 771 4.416620 CTTGTACGCACCTTTGTTTCAAA 58.583 39.130 0.00 0.00 0.00 2.69
392 772 4.436242 TGTACGCACCTTTGTTTCAAAA 57.564 36.364 0.00 0.00 0.00 2.44
393 773 4.806330 TGTACGCACCTTTGTTTCAAAAA 58.194 34.783 0.00 0.00 0.00 1.94
425 808 5.733676 AGTGGAACATTTGTTTCAAGCTTT 58.266 33.333 6.00 0.00 44.42 3.51
426 809 5.812127 AGTGGAACATTTGTTTCAAGCTTTC 59.188 36.000 6.00 0.00 44.42 2.62
462 845 6.880529 TGATGCATAGCTAGCAATGCTAAATA 59.119 34.615 18.83 11.65 46.87 1.40
463 846 7.391275 TGATGCATAGCTAGCAATGCTAAATAA 59.609 33.333 18.83 2.91 46.87 1.40
465 848 6.712095 TGCATAGCTAGCAATGCTAAATAACT 59.288 34.615 18.83 10.55 46.87 2.24
466 849 7.877612 TGCATAGCTAGCAATGCTAAATAACTA 59.122 33.333 18.83 12.14 46.87 2.24
467 850 8.721478 GCATAGCTAGCAATGCTAAATAACTAA 58.279 33.333 18.83 0.00 44.73 2.24
470 853 8.908786 AGCTAGCAATGCTAAATAACTAATGA 57.091 30.769 18.83 0.00 40.82 2.57
471 854 9.342308 AGCTAGCAATGCTAAATAACTAATGAA 57.658 29.630 18.83 0.00 40.82 2.57
472 855 9.950680 GCTAGCAATGCTAAATAACTAATGAAA 57.049 29.630 16.35 0.00 40.82 2.69
552 935 9.880157 AGTACGTACCTATTGATACATTTGTTT 57.120 29.630 21.80 0.00 0.00 2.83
554 937 8.780846 ACGTACCTATTGATACATTTGTTTCA 57.219 30.769 0.00 0.49 34.91 2.69
555 938 9.221933 ACGTACCTATTGATACATTTGTTTCAA 57.778 29.630 15.62 15.62 45.24 2.69
556 939 9.702726 CGTACCTATTGATACATTTGTTTCAAG 57.297 33.333 17.43 9.76 44.70 3.02
557 940 9.503427 GTACCTATTGATACATTTGTTTCAAGC 57.497 33.333 17.43 5.09 44.70 4.01
558 941 8.353423 ACCTATTGATACATTTGTTTCAAGCT 57.647 30.769 17.43 8.22 44.70 3.74
559 942 8.806146 ACCTATTGATACATTTGTTTCAAGCTT 58.194 29.630 17.43 0.00 44.70 3.74
560 943 9.079833 CCTATTGATACATTTGTTTCAAGCTTG 57.920 33.333 20.81 20.81 44.70 4.01
561 944 9.630098 CTATTGATACATTTGTTTCAAGCTTGT 57.370 29.630 25.19 6.74 44.70 3.16
563 946 8.795786 TTGATACATTTGTTTCAAGCTTGTAC 57.204 30.769 25.19 22.30 39.73 2.90
564 947 7.075121 TGATACATTTGTTTCAAGCTTGTACG 58.925 34.615 25.19 13.50 34.05 3.67
565 948 5.243426 ACATTTGTTTCAAGCTTGTACGT 57.757 34.783 25.19 14.02 0.00 3.57
566 949 6.366315 ACATTTGTTTCAAGCTTGTACGTA 57.634 33.333 25.19 15.36 0.00 3.57
567 950 6.196571 ACATTTGTTTCAAGCTTGTACGTAC 58.803 36.000 25.19 18.90 0.00 3.67
568 951 4.799419 TTGTTTCAAGCTTGTACGTACC 57.201 40.909 25.19 7.75 0.00 3.34
569 952 4.062677 TGTTTCAAGCTTGTACGTACCT 57.937 40.909 25.19 9.97 0.00 3.08
570 953 4.444536 TGTTTCAAGCTTGTACGTACCTT 58.555 39.130 25.19 15.15 0.00 3.50
571 954 4.877251 TGTTTCAAGCTTGTACGTACCTTT 59.123 37.500 25.19 8.88 0.00 3.11
572 955 5.202640 GTTTCAAGCTTGTACGTACCTTTG 58.797 41.667 25.19 18.60 0.00 2.77
573 956 4.062677 TCAAGCTTGTACGTACCTTTGT 57.937 40.909 25.19 3.07 0.00 2.83
574 957 4.444536 TCAAGCTTGTACGTACCTTTGTT 58.555 39.130 25.19 7.33 0.00 2.83
575 958 4.508861 TCAAGCTTGTACGTACCTTTGTTC 59.491 41.667 25.19 5.40 0.00 3.18
682 1075 5.242434 AGTACGTCAATGTGAAGCCAAATA 58.758 37.500 0.00 0.00 28.70 1.40
720 1113 3.508793 GCTTGTGGCTCCGTACCTATATA 59.491 47.826 0.00 0.00 38.06 0.86
721 1114 4.159879 GCTTGTGGCTCCGTACCTATATAT 59.840 45.833 0.00 0.00 38.06 0.86
722 1115 5.359009 GCTTGTGGCTCCGTACCTATATATA 59.641 44.000 0.00 0.00 38.06 0.86
723 1116 6.040616 GCTTGTGGCTCCGTACCTATATATAT 59.959 42.308 0.00 0.00 38.06 0.86
731 1124 8.995220 GCTCCGTACCTATATATATCTTGAGAG 58.005 40.741 0.00 0.73 0.00 3.20
809 1204 6.178507 CGCTAAACACAGATCACTTATTTCG 58.821 40.000 0.00 0.00 0.00 3.46
843 1238 0.604578 TTCTTGTCTTACCCCCGTCG 59.395 55.000 0.00 0.00 0.00 5.12
872 1267 2.953466 TTCTATCGACCGAAACCCAG 57.047 50.000 0.00 0.00 0.00 4.45
1061 1457 1.742761 AACAAGCACATCCTGATCCG 58.257 50.000 0.00 0.00 0.00 4.18
1067 1463 1.804372 GCACATCCTGATCCGTCTGAC 60.804 57.143 0.00 0.00 0.00 3.51
1074 1470 0.748367 TGATCCGTCTGACCTCCTCG 60.748 60.000 1.55 0.00 0.00 4.63
1334 1742 1.953138 GCGCTGGACTGGATGATCG 60.953 63.158 0.00 0.00 0.00 3.69
1820 2249 3.375610 CAGAGTAAGCTTAGCTCGACAGA 59.624 47.826 20.60 0.00 38.25 3.41
1829 2260 6.289834 AGCTTAGCTCGACAGATAGTTAGTA 58.710 40.000 0.00 0.00 30.62 1.82
1830 2261 6.425721 AGCTTAGCTCGACAGATAGTTAGTAG 59.574 42.308 0.00 0.00 30.62 2.57
1831 2262 6.203338 GCTTAGCTCGACAGATAGTTAGTAGT 59.797 42.308 0.00 0.00 0.00 2.73
1833 2264 8.503458 TTAGCTCGACAGATAGTTAGTAGTTT 57.497 34.615 0.00 0.00 0.00 2.66
1834 2265 7.018635 AGCTCGACAGATAGTTAGTAGTTTC 57.981 40.000 0.00 0.00 0.00 2.78
1998 2433 1.731720 AGCTGAACGAATGCTTCTCC 58.268 50.000 0.00 0.00 32.61 3.71
2000 2435 0.371645 CTGAACGAATGCTTCTCCGC 59.628 55.000 0.00 0.00 0.00 5.54
2012 2447 3.267860 CTCCGCCGAATGCTCTGC 61.268 66.667 0.00 0.00 38.05 4.26
2078 2532 3.067106 AGGTCTTCACTGTAACATTGCG 58.933 45.455 0.00 0.00 0.00 4.85
2102 2559 6.362283 CGACTTACATTGTTGGGAAAATTGAC 59.638 38.462 0.00 0.00 0.00 3.18
2103 2560 6.521162 ACTTACATTGTTGGGAAAATTGACC 58.479 36.000 0.00 0.00 0.00 4.02
2149 2607 1.898574 GCCATCTAACCATGCCCCG 60.899 63.158 0.00 0.00 0.00 5.73
2248 2712 9.855021 AAAATGCAAATGTCCTTAGTATAACAC 57.145 29.630 0.00 0.00 0.00 3.32
2330 2813 1.086696 GACACATGTCATTCCACCCG 58.913 55.000 7.15 0.00 44.18 5.28
2349 2832 2.520979 CGTAGTTCCTCTTGAGCTTCG 58.479 52.381 0.00 0.00 38.35 3.79
2406 2890 2.093658 CCTTGTAGTACAGGGCGACAAT 60.094 50.000 17.62 0.00 38.55 2.71
2437 2921 6.703607 CGGGCTATACAATCTGATGATTATCC 59.296 42.308 0.00 0.00 40.61 2.59
2459 2943 4.383649 CCAGTTGCAAAATTGAGTGAATCG 59.616 41.667 0.00 0.00 0.00 3.34
2477 2961 8.184192 AGTGAATCGATAAAATTGACCAACATC 58.816 33.333 0.00 0.00 0.00 3.06
2772 3298 2.283298 CAACTCATCCTCAATCACCGG 58.717 52.381 0.00 0.00 0.00 5.28
2819 3347 6.036735 TCCAGAAAACAACAAGAAGTTCTACG 59.963 38.462 5.65 3.26 38.74 3.51
2854 3385 2.921754 GACATTTGACGGAAGACCTACG 59.078 50.000 0.00 0.00 0.00 3.51
2857 3388 0.251297 TTGACGGAAGACCTACGGGA 60.251 55.000 0.00 0.00 36.25 5.14
2858 3389 0.679002 TGACGGAAGACCTACGGGAG 60.679 60.000 0.00 0.00 36.25 4.30
2919 3450 3.801997 CCTGGCTGCGGAGGGATT 61.802 66.667 5.93 0.00 0.00 3.01
2929 3461 0.978146 CGGAGGGATTCTGGTGGACT 60.978 60.000 0.00 0.00 0.00 3.85
3040 3786 4.315264 GGGGGAGCAGGGGCAAAA 62.315 66.667 0.00 0.00 44.61 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.261040 AGTGCTATATAATTGGTGCCCAT 57.739 39.130 0.00 0.00 31.53 4.00
110 111 2.660612 GGTGTCGTTACCGCAACCG 61.661 63.158 0.00 0.00 33.19 4.44
166 167 3.950087 GCACATTGATGCGTAGATCAA 57.050 42.857 8.47 8.47 44.47 2.57
205 207 5.324697 GCCTCGATGTTTTGTATCAACTTC 58.675 41.667 0.00 0.00 0.00 3.01
219 221 3.845781 ATCTTGTAATGGCCTCGATGT 57.154 42.857 3.32 0.00 0.00 3.06
275 277 1.872952 CATTGTCGTCCTTGTTGCAGA 59.127 47.619 0.00 0.00 0.00 4.26
277 279 1.674359 ACATTGTCGTCCTTGTTGCA 58.326 45.000 0.00 0.00 0.00 4.08
334 336 2.426522 CCATGTTCATGGTGTCGTCTT 58.573 47.619 20.05 0.00 36.95 3.01
398 778 8.353423 AGCTTGAAACAAATGTTCCACTATAT 57.647 30.769 0.00 0.00 37.25 0.86
400 780 6.655078 AGCTTGAAACAAATGTTCCACTAT 57.345 33.333 0.00 0.00 37.25 2.12
425 808 4.280929 AGCTATGCATCAATAGGTACGTGA 59.719 41.667 0.19 0.00 38.71 4.35
426 809 4.560128 AGCTATGCATCAATAGGTACGTG 58.440 43.478 0.19 0.00 38.71 4.49
526 909 9.880157 AAACAAATGTATCAATAGGTACGTACT 57.120 29.630 24.07 13.10 0.00 2.73
528 911 9.872721 TGAAACAAATGTATCAATAGGTACGTA 57.127 29.630 0.00 0.00 0.00 3.57
529 912 8.780846 TGAAACAAATGTATCAATAGGTACGT 57.219 30.769 0.00 0.00 0.00 3.57
530 913 9.702726 CTTGAAACAAATGTATCAATAGGTACG 57.297 33.333 0.00 0.00 31.92 3.67
531 914 9.503427 GCTTGAAACAAATGTATCAATAGGTAC 57.497 33.333 0.00 0.00 31.92 3.34
532 915 9.461312 AGCTTGAAACAAATGTATCAATAGGTA 57.539 29.630 0.00 0.00 31.92 3.08
533 916 8.353423 AGCTTGAAACAAATGTATCAATAGGT 57.647 30.769 0.00 0.00 31.92 3.08
534 917 9.079833 CAAGCTTGAAACAAATGTATCAATAGG 57.920 33.333 22.31 0.00 31.92 2.57
535 918 9.630098 ACAAGCTTGAAACAAATGTATCAATAG 57.370 29.630 32.50 0.00 31.92 1.73
537 920 9.410556 GTACAAGCTTGAAACAAATGTATCAAT 57.589 29.630 32.50 6.48 31.92 2.57
538 921 7.589587 CGTACAAGCTTGAAACAAATGTATCAA 59.410 33.333 32.50 0.00 0.00 2.57
539 922 7.075121 CGTACAAGCTTGAAACAAATGTATCA 58.925 34.615 32.50 0.00 0.00 2.15
540 923 7.075741 ACGTACAAGCTTGAAACAAATGTATC 58.924 34.615 32.50 6.27 0.00 2.24
541 924 6.966021 ACGTACAAGCTTGAAACAAATGTAT 58.034 32.000 32.50 8.18 0.00 2.29
542 925 6.366315 ACGTACAAGCTTGAAACAAATGTA 57.634 33.333 32.50 9.20 0.00 2.29
543 926 5.243426 ACGTACAAGCTTGAAACAAATGT 57.757 34.783 32.50 17.63 0.00 2.71
544 927 5.623673 GGTACGTACAAGCTTGAAACAAATG 59.376 40.000 32.50 17.09 0.00 2.32
545 928 5.529800 AGGTACGTACAAGCTTGAAACAAAT 59.470 36.000 32.50 17.73 0.00 2.32
546 929 4.877251 AGGTACGTACAAGCTTGAAACAAA 59.123 37.500 32.50 15.94 0.00 2.83
547 930 4.444536 AGGTACGTACAAGCTTGAAACAA 58.555 39.130 32.50 16.25 0.00 2.83
548 931 4.062677 AGGTACGTACAAGCTTGAAACA 57.937 40.909 32.50 11.55 0.00 2.83
549 932 5.202640 CAAAGGTACGTACAAGCTTGAAAC 58.797 41.667 32.50 25.08 35.02 2.78
550 933 4.877251 ACAAAGGTACGTACAAGCTTGAAA 59.123 37.500 32.50 16.87 35.02 2.69
551 934 4.444536 ACAAAGGTACGTACAAGCTTGAA 58.555 39.130 32.50 9.44 35.02 2.69
552 935 4.062677 ACAAAGGTACGTACAAGCTTGA 57.937 40.909 32.50 13.49 35.02 3.02
553 936 4.319261 GGAACAAAGGTACGTACAAGCTTG 60.319 45.833 26.02 24.84 35.02 4.01
554 937 3.811497 GGAACAAAGGTACGTACAAGCTT 59.189 43.478 26.02 16.97 36.28 3.74
555 938 3.181463 TGGAACAAAGGTACGTACAAGCT 60.181 43.478 26.02 12.08 31.92 3.74
556 939 3.132925 TGGAACAAAGGTACGTACAAGC 58.867 45.455 26.02 9.95 31.92 4.01
568 951 8.379476 AAGGAAAACTTGCATGATGGAACAAAG 61.379 37.037 6.60 0.00 39.47 2.77
569 952 6.632219 AAGGAAAACTTGCATGATGGAACAAA 60.632 34.615 6.60 0.00 39.47 2.83
570 953 5.163322 AAGGAAAACTTGCATGATGGAACAA 60.163 36.000 6.60 0.00 39.47 2.83
571 954 4.344679 AAGGAAAACTTGCATGATGGAACA 59.655 37.500 6.60 0.00 40.18 3.18
572 955 4.525912 AGGAAAACTTGCATGATGGAAC 57.474 40.909 6.60 0.00 0.00 3.62
573 956 5.549742 AAAGGAAAACTTGCATGATGGAA 57.450 34.783 6.60 0.00 39.96 3.53
574 957 5.070180 TCAAAAGGAAAACTTGCATGATGGA 59.930 36.000 6.60 0.00 39.96 3.41
575 958 5.178067 GTCAAAAGGAAAACTTGCATGATGG 59.822 40.000 6.60 0.00 39.96 3.51
644 1036 8.691727 CATTGACGTACTACTAAAGCATATGTC 58.308 37.037 4.29 0.00 34.00 3.06
650 1042 6.016213 TCACATTGACGTACTACTAAAGCA 57.984 37.500 0.00 0.00 0.00 3.91
651 1043 6.453922 GCTTCACATTGACGTACTACTAAAGC 60.454 42.308 0.00 0.00 0.00 3.51
652 1044 6.034683 GGCTTCACATTGACGTACTACTAAAG 59.965 42.308 0.00 0.00 0.00 1.85
654 1046 5.047872 TGGCTTCACATTGACGTACTACTAA 60.048 40.000 0.00 0.00 0.00 2.24
655 1047 4.460034 TGGCTTCACATTGACGTACTACTA 59.540 41.667 0.00 0.00 0.00 1.82
656 1048 3.257375 TGGCTTCACATTGACGTACTACT 59.743 43.478 0.00 0.00 0.00 2.57
657 1049 3.581755 TGGCTTCACATTGACGTACTAC 58.418 45.455 0.00 0.00 0.00 2.73
682 1075 3.436704 CACAAGCAATAGGTTCACGATGT 59.563 43.478 0.00 0.00 32.07 3.06
720 1113 4.526262 CCGATCAAGGGACTCTCAAGATAT 59.474 45.833 0.00 0.00 38.49 1.63
721 1114 3.891977 CCGATCAAGGGACTCTCAAGATA 59.108 47.826 0.00 0.00 38.49 1.98
722 1115 2.697751 CCGATCAAGGGACTCTCAAGAT 59.302 50.000 0.00 0.00 38.49 2.40
723 1116 2.103373 CCGATCAAGGGACTCTCAAGA 58.897 52.381 0.00 0.00 38.49 3.02
731 1124 3.134081 TCCATTAACTCCGATCAAGGGAC 59.866 47.826 0.00 0.00 0.00 4.46
872 1267 2.094417 GCGCGATGCTAAGGAATAATCC 59.906 50.000 12.10 0.00 43.00 3.01
942 1337 4.510386 GGGTTGGGAAGTAAAAGGAAGGAT 60.510 45.833 0.00 0.00 0.00 3.24
1061 1457 0.966920 TTTGGACGAGGAGGTCAGAC 59.033 55.000 0.00 0.00 38.70 3.51
1067 1463 0.175989 GGTAGCTTTGGACGAGGAGG 59.824 60.000 0.00 0.00 0.00 4.30
1074 1470 1.449778 GCCTCGGGTAGCTTTGGAC 60.450 63.158 0.00 0.00 0.00 4.02
1166 1565 3.173240 GACGACGAACAGCGCCTC 61.173 66.667 2.29 0.00 46.04 4.70
1478 1907 3.816920 CGTCGTCTTGCGCGTGAG 61.817 66.667 8.43 6.23 41.07 3.51
1795 2224 1.537135 CGAGCTAAGCTTACTCTGCCC 60.537 57.143 22.49 9.48 39.88 5.36
1820 2249 7.719871 TTGCTCAGGAGAAACTACTAACTAT 57.280 36.000 0.00 0.00 0.00 2.12
1944 2375 1.404391 TCGCAACTAGCTACAGCCTAC 59.596 52.381 0.00 0.00 43.38 3.18
1951 2382 4.566759 TGTCAATGAATCGCAACTAGCTAC 59.433 41.667 0.00 0.00 42.61 3.58
1952 2383 4.754322 TGTCAATGAATCGCAACTAGCTA 58.246 39.130 0.00 0.00 42.61 3.32
2000 2435 1.063174 GCTTTACAGCAGAGCATTCGG 59.937 52.381 0.00 0.00 46.49 4.30
2012 2447 4.391830 TGAGAAGTATTTGCCGCTTTACAG 59.608 41.667 0.00 0.00 0.00 2.74
2078 2532 6.645003 GGTCAATTTTCCCAACAATGTAAGTC 59.355 38.462 0.00 0.00 0.00 3.01
2103 2560 4.082523 ATCAGTGTCCACGGGCCG 62.083 66.667 27.06 27.06 36.20 6.13
2224 2688 8.807948 AGTGTTATACTAAGGACATTTGCATT 57.192 30.769 0.00 0.00 38.04 3.56
2248 2712 7.678947 ATTCTTGTTGAACATCCTGAACTAG 57.321 36.000 0.00 0.00 37.52 2.57
2349 2832 2.579207 TACGCTCATACTTGTGAGGC 57.421 50.000 5.28 0.00 44.55 4.70
2406 2890 0.032952 GATTGTATAGCCCGGACGCA 59.967 55.000 0.73 0.00 0.00 5.24
2437 2921 5.214417 TCGATTCACTCAATTTTGCAACTG 58.786 37.500 0.00 0.00 0.00 3.16
2477 2961 9.736023 ATAAGTTTTGCTTTCTTGTTGTTCTAG 57.264 29.630 0.00 0.00 38.57 2.43
2772 3298 0.751643 AAGCATGATGGCGGGGTAAC 60.752 55.000 0.00 0.00 39.27 2.50
2854 3385 2.606587 ATGGCAGACACCACCTCCC 61.607 63.158 0.00 0.00 44.17 4.30
2857 3388 1.847506 TCCATGGCAGACACCACCT 60.848 57.895 6.96 0.00 44.17 4.00
2858 3389 1.675641 GTCCATGGCAGACACCACC 60.676 63.158 6.96 0.00 44.17 4.61


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

AutoCloner maintained by Alex Coulton.