Multiple sequence alignment - TraesCS2D01G302300

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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 TraesCS2D01G302300 chr2D 100.000 7366 0 0 1 7366 385392302 385384937 0.000000e+00 13603.0
1 TraesCS2D01G302300 chr2D 81.261 1110 162 19 2812 3887 385388388 385387291 0.000000e+00 856.0
2 TraesCS2D01G302300 chr2D 81.261 1110 162 19 3915 5012 385389491 385388416 0.000000e+00 856.0
3 TraesCS2D01G302300 chr2D 91.186 295 23 2 2525 2816 385389490 385389196 1.490000e-106 398.0
4 TraesCS2D01G302300 chr2D 91.186 295 23 2 2813 3107 385389778 385389487 1.490000e-106 398.0
5 TraesCS2D01G302300 chr2A 97.242 4314 60 9 2184 6474 520993397 520989120 0.000000e+00 7252.0
6 TraesCS2D01G302300 chr2A 97.081 925 25 2 6442 7366 520989089 520988167 0.000000e+00 1557.0
7 TraesCS2D01G302300 chr2A 97.666 857 16 4 1304 2158 520994233 520993379 0.000000e+00 1469.0
8 TraesCS2D01G302300 chr2A 82.793 1110 163 11 3915 5012 520992765 520991672 0.000000e+00 966.0
9 TraesCS2D01G302300 chr2A 81.532 1110 159 19 2812 3887 520991644 520990547 0.000000e+00 872.0
10 TraesCS2D01G302300 chr2A 92.203 295 23 0 2813 3107 520993055 520992761 1.140000e-112 418.0
11 TraesCS2D01G302300 chr2A 89.552 335 11 5 864 1198 520994851 520994541 3.200000e-108 403.0
12 TraesCS2D01G302300 chr2A 90.476 294 25 2 2525 2815 520992764 520992471 1.160000e-102 385.0
13 TraesCS2D01G302300 chr2B 94.245 3875 165 15 2083 5915 456344287 456340429 0.000000e+00 5867.0
14 TraesCS2D01G302300 chr2B 91.966 1170 49 16 885 2026 456345437 456344285 0.000000e+00 1598.0
15 TraesCS2D01G302300 chr2B 93.711 636 29 6 6734 7366 456339191 456338564 0.000000e+00 942.0
16 TraesCS2D01G302300 chr2B 81.558 1117 167 12 3915 5012 456343551 456342455 0.000000e+00 885.0
17 TraesCS2D01G302300 chr2B 88.114 387 25 9 5928 6306 456340389 456340016 2.440000e-119 440.0
18 TraesCS2D01G302300 chr2B 93.220 295 20 0 2813 3107 456343841 456343547 1.130000e-117 435.0
19 TraesCS2D01G302300 chr2B 76.238 808 183 8 7 809 109990665 109989862 3.180000e-113 420.0
20 TraesCS2D01G302300 chr2B 91.525 295 22 1 2525 2816 456343550 456343256 3.200000e-108 403.0
21 TraesCS2D01G302300 chr2B 92.115 279 13 4 6442 6717 456339726 456339454 1.160000e-102 385.0
22 TraesCS2D01G302300 chr4D 77.833 803 171 7 1 800 374629272 374630070 2.390000e-134 490.0
23 TraesCS2D01G302300 chr4D 76.125 800 185 6 1 797 417379179 417379975 1.480000e-111 414.0
24 TraesCS2D01G302300 chr5D 77.387 796 175 4 7 800 545820565 545821357 1.120000e-127 468.0
25 TraesCS2D01G302300 chr5D 76.413 814 180 12 1 808 214600813 214601620 5.280000e-116 429.0
26 TraesCS2D01G302300 chr5B 77.256 809 168 14 1 801 369623642 369624442 1.870000e-125 460.0
27 TraesCS2D01G302300 chr5B 75.342 803 189 9 1 800 396397396 396398192 1.940000e-100 377.0
28 TraesCS2D01G302300 chr7D 77.171 806 172 11 7 806 454926844 454926045 6.730000e-125 459.0
29 TraesCS2D01G302300 chr7D 80.059 341 50 12 1399 1729 413449088 413448756 3.440000e-58 237.0
30 TraesCS2D01G302300 chr6D 76.578 824 189 3 7 828 88681335 88682156 4.050000e-122 449.0
31 TraesCS2D01G302300 chr6D 93.878 49 3 0 1965 2013 237070210 237070162 2.850000e-09 75.0
32 TraesCS2D01G302300 chr1B 89.855 207 18 3 3681 3885 684001084 684000879 5.670000e-66 263.0
33 TraesCS2D01G302300 chr1B 85.784 204 28 1 4808 5010 684001082 684000879 1.610000e-51 215.0
34 TraesCS2D01G302300 chr1D 85.306 245 27 6 1348 1591 47848843 47849079 2.050000e-60 244.0
35 TraesCS2D01G302300 chr1D 90.909 55 5 0 1959 2013 47849115 47849169 2.850000e-09 75.0
36 TraesCS2D01G302300 chr3D 84.490 245 29 6 1348 1591 523247108 523247344 4.440000e-57 233.0
37 TraesCS2D01G302300 chr3D 89.091 55 6 0 1959 2013 523247380 523247434 1.330000e-07 69.4
38 TraesCS2D01G302300 chr7A 84.158 202 24 6 1394 1594 475191277 475191083 9.760000e-44 189.0
39 TraesCS2D01G302300 chr7B 85.795 176 23 2 1422 1596 427833611 427833437 1.260000e-42 185.0


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 TraesCS2D01G302300 chr2D 385384937 385392302 7365 True 13603.000 13603 100.000000 1 7366 1 chr2D.!!$R1 7365
1 TraesCS2D01G302300 chr2D 385387291 385389778 2487 True 627.000 856 86.223500 2525 5012 4 chr2D.!!$R2 2487
2 TraesCS2D01G302300 chr2A 520988167 520994851 6684 True 1665.250 7252 91.068125 864 7366 8 chr2A.!!$R1 6502
3 TraesCS2D01G302300 chr2B 456338564 456345437 6873 True 1369.375 5867 90.806750 885 7366 8 chr2B.!!$R2 6481
4 TraesCS2D01G302300 chr2B 109989862 109990665 803 True 420.000 420 76.238000 7 809 1 chr2B.!!$R1 802
5 TraesCS2D01G302300 chr4D 374629272 374630070 798 False 490.000 490 77.833000 1 800 1 chr4D.!!$F1 799
6 TraesCS2D01G302300 chr4D 417379179 417379975 796 False 414.000 414 76.125000 1 797 1 chr4D.!!$F2 796
7 TraesCS2D01G302300 chr5D 545820565 545821357 792 False 468.000 468 77.387000 7 800 1 chr5D.!!$F2 793
8 TraesCS2D01G302300 chr5D 214600813 214601620 807 False 429.000 429 76.413000 1 808 1 chr5D.!!$F1 807
9 TraesCS2D01G302300 chr5B 369623642 369624442 800 False 460.000 460 77.256000 1 801 1 chr5B.!!$F1 800
10 TraesCS2D01G302300 chr5B 396397396 396398192 796 False 377.000 377 75.342000 1 800 1 chr5B.!!$F2 799
11 TraesCS2D01G302300 chr7D 454926045 454926844 799 True 459.000 459 77.171000 7 806 1 chr7D.!!$R2 799
12 TraesCS2D01G302300 chr6D 88681335 88682156 821 False 449.000 449 76.578000 7 828 1 chr6D.!!$F1 821


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
860 862 0.035630 GCTCCCTGTGATGTTGCTCT 60.036 55.0 0.00 0.00 0.00 4.09 F
862 864 0.247460 TCCCTGTGATGTTGCTCTCG 59.753 55.0 0.00 0.00 0.00 4.04 F
1176 1187 0.318784 CGGCTATTGACTACTCGGCC 60.319 60.0 0.00 0.00 35.33 6.13 F
5228 5503 1.019673 GTGGTCAGTATGCTGCATGG 58.980 55.0 24.59 13.74 42.29 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 2756 1.988107 AGATTCTTTCCTGGGCTGTCA 59.012 47.619 0.00 0.00 0.00 3.58 R
5228 5503 5.041191 TCCAGAGATCATAAAAGGGAAGC 57.959 43.478 0.00 0.00 0.00 3.86 R
5445 5720 5.794894 TGAATTTCAGAACTGAGGGTCTAC 58.205 41.667 4.72 0.00 41.13 2.59 R
6882 7616 0.105593 ATCTTGAGTGCGCATCGGAT 59.894 50.000 15.91 15.36 0.00 4.18 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
59 60 3.517296 TTGAACCCCAGTTTGAGCATA 57.483 42.857 0.00 0.00 35.94 3.14
68 69 4.178540 CCAGTTTGAGCATAATGGCTTTG 58.821 43.478 0.00 0.00 45.99 2.77
74 75 7.504911 AGTTTGAGCATAATGGCTTTGAGATAT 59.495 33.333 0.00 0.00 45.99 1.63
82 83 2.025037 TGGCTTTGAGATATGGCCACTT 60.025 45.455 8.16 0.00 46.35 3.16
134 135 2.408271 TGAGGGCACATGACTGATTC 57.592 50.000 0.00 0.00 0.00 2.52
176 177 5.871465 TCATAAAATGCAAGCACTCGTAA 57.129 34.783 0.00 0.00 0.00 3.18
298 299 9.209175 GATAACCTTCGAAGCAATCTTATACAT 57.791 33.333 19.99 0.00 31.48 2.29
311 312 9.976255 GCAATCTTATACATTACGTTACACAAA 57.024 29.630 0.00 0.00 0.00 2.83
328 329 3.252215 CACAAACTGATTGGGCGAAACTA 59.748 43.478 2.69 0.00 43.66 2.24
342 344 3.305964 CGAAACTAAGACAGAAGCGTGA 58.694 45.455 0.00 0.00 0.00 4.35
423 425 4.946157 CAGTGCCTTCTACAATCCTCAAAT 59.054 41.667 0.00 0.00 0.00 2.32
437 439 1.466167 CTCAAATCTGCCTTGGTGACG 59.534 52.381 0.00 0.00 0.00 4.35
446 448 1.447838 CTTGGTGACGTCATCCCCG 60.448 63.158 25.41 14.67 0.00 5.73
452 454 1.324005 TGACGTCATCCCCGCATGTA 61.324 55.000 15.76 0.00 0.00 2.29
566 568 3.195610 TCTGACTGTACGGAGCATTCAAT 59.804 43.478 9.17 0.00 0.00 2.57
569 571 4.081917 TGACTGTACGGAGCATTCAATGTA 60.082 41.667 9.17 0.00 0.00 2.29
611 613 1.079750 GGTCGGGACTGTCTCAAGC 60.080 63.158 8.63 0.00 0.00 4.01
629 631 2.556144 GCACCTGCTCCATATCATGA 57.444 50.000 0.00 0.00 38.21 3.07
632 634 3.812262 CACCTGCTCCATATCATGAACA 58.188 45.455 0.00 0.00 0.00 3.18
638 640 3.181451 GCTCCATATCATGAACACCCTCA 60.181 47.826 0.00 0.00 0.00 3.86
673 675 4.825085 GTCCTGATAAAAGGTTGTGGTCAA 59.175 41.667 0.00 0.00 38.58 3.18
675 677 5.894393 TCCTGATAAAAGGTTGTGGTCAAAA 59.106 36.000 0.00 0.00 38.58 2.44
676 678 5.983118 CCTGATAAAAGGTTGTGGTCAAAAC 59.017 40.000 0.00 0.00 35.20 2.43
683 685 2.698274 GGTTGTGGTCAAAACCTCCATT 59.302 45.455 14.17 0.00 46.60 3.16
691 693 3.564225 GTCAAAACCTCCATTTCTGACGT 59.436 43.478 0.00 0.00 0.00 4.34
694 696 5.642063 TCAAAACCTCCATTTCTGACGTATC 59.358 40.000 0.00 0.00 0.00 2.24
701 703 4.466370 TCCATTTCTGACGTATCCTCAGTT 59.534 41.667 0.00 0.00 37.12 3.16
706 708 7.692460 TTTCTGACGTATCCTCAGTTAACTA 57.308 36.000 8.04 0.00 37.12 2.24
745 747 6.374333 TGGAGAGATTTTATTTGGTTCTTCCG 59.626 38.462 0.00 0.00 39.52 4.30
801 803 0.247814 GTTCTTGTCGCCATGCATCG 60.248 55.000 0.00 0.00 0.00 3.84
809 811 0.101040 CGCCATGCATCGACCATTTT 59.899 50.000 0.00 0.00 0.00 1.82
811 813 2.602933 CGCCATGCATCGACCATTTTAG 60.603 50.000 0.00 0.00 0.00 1.85
812 814 2.618241 GCCATGCATCGACCATTTTAGA 59.382 45.455 0.00 0.00 0.00 2.10
813 815 3.254166 GCCATGCATCGACCATTTTAGAT 59.746 43.478 0.00 0.00 0.00 1.98
821 823 1.604278 GACCATTTTAGATGGGCTCGC 59.396 52.381 6.72 0.00 43.87 5.03
835 837 4.435436 TCGCTGGCGCTCGTCAAT 62.435 61.111 7.64 0.00 39.59 2.57
836 838 3.490759 CGCTGGCGCTCGTCAATT 61.491 61.111 7.64 0.00 0.00 2.32
837 839 2.164663 CGCTGGCGCTCGTCAATTA 61.165 57.895 7.64 0.00 0.00 1.40
838 840 1.638467 GCTGGCGCTCGTCAATTAG 59.362 57.895 7.64 0.00 0.00 1.73
839 841 1.084370 GCTGGCGCTCGTCAATTAGT 61.084 55.000 7.64 0.00 0.00 2.24
840 842 1.359848 CTGGCGCTCGTCAATTAGTT 58.640 50.000 7.64 0.00 0.00 2.24
841 843 1.061131 CTGGCGCTCGTCAATTAGTTG 59.939 52.381 7.64 0.00 36.65 3.16
842 844 0.247695 GGCGCTCGTCAATTAGTTGC 60.248 55.000 7.64 0.00 35.26 4.17
843 845 0.721718 GCGCTCGTCAATTAGTTGCT 59.278 50.000 0.00 0.00 35.26 3.91
844 846 1.267087 GCGCTCGTCAATTAGTTGCTC 60.267 52.381 0.00 0.00 35.26 4.26
845 847 1.324736 CGCTCGTCAATTAGTTGCTCC 59.675 52.381 0.00 0.00 35.26 4.70
846 848 1.666189 GCTCGTCAATTAGTTGCTCCC 59.334 52.381 0.00 0.00 35.26 4.30
847 849 2.678190 GCTCGTCAATTAGTTGCTCCCT 60.678 50.000 0.00 0.00 35.26 4.20
848 850 2.932614 CTCGTCAATTAGTTGCTCCCTG 59.067 50.000 0.00 0.00 35.26 4.45
849 851 2.301870 TCGTCAATTAGTTGCTCCCTGT 59.698 45.455 0.00 0.00 35.26 4.00
850 852 2.416547 CGTCAATTAGTTGCTCCCTGTG 59.583 50.000 0.00 0.00 35.26 3.66
851 853 3.674997 GTCAATTAGTTGCTCCCTGTGA 58.325 45.455 0.00 0.00 35.26 3.58
852 854 4.265073 GTCAATTAGTTGCTCCCTGTGAT 58.735 43.478 0.00 0.00 35.26 3.06
853 855 4.095483 GTCAATTAGTTGCTCCCTGTGATG 59.905 45.833 0.00 0.00 35.26 3.07
854 856 4.012374 CAATTAGTTGCTCCCTGTGATGT 58.988 43.478 0.00 0.00 0.00 3.06
855 857 3.788227 TTAGTTGCTCCCTGTGATGTT 57.212 42.857 0.00 0.00 0.00 2.71
856 858 1.901591 AGTTGCTCCCTGTGATGTTG 58.098 50.000 0.00 0.00 0.00 3.33
857 859 0.242017 GTTGCTCCCTGTGATGTTGC 59.758 55.000 0.00 0.00 0.00 4.17
858 860 0.111061 TTGCTCCCTGTGATGTTGCT 59.889 50.000 0.00 0.00 0.00 3.91
859 861 0.321919 TGCTCCCTGTGATGTTGCTC 60.322 55.000 0.00 0.00 0.00 4.26
860 862 0.035630 GCTCCCTGTGATGTTGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
861 863 2.011046 GCTCCCTGTGATGTTGCTCTC 61.011 57.143 0.00 0.00 0.00 3.20
862 864 0.247460 TCCCTGTGATGTTGCTCTCG 59.753 55.000 0.00 0.00 0.00 4.04
869 871 1.639298 GATGTTGCTCTCGTGGCACC 61.639 60.000 12.86 0.00 39.55 5.01
871 873 1.598130 GTTGCTCTCGTGGCACCTT 60.598 57.895 12.86 0.00 39.55 3.50
943 945 2.103153 TTAGAATCAGCCCGGGATCT 57.897 50.000 29.31 19.91 0.00 2.75
944 946 1.342074 TAGAATCAGCCCGGGATCTG 58.658 55.000 29.31 23.24 0.00 2.90
945 947 1.599240 GAATCAGCCCGGGATCTGC 60.599 63.158 29.31 8.41 0.00 4.26
950 952 4.256180 GCCCGGGATCTGCCGAAT 62.256 66.667 29.31 0.00 37.63 3.34
951 953 2.879233 GCCCGGGATCTGCCGAATA 61.879 63.158 29.31 0.00 37.63 1.75
952 954 1.983224 CCCGGGATCTGCCGAATAT 59.017 57.895 18.48 0.00 37.63 1.28
1176 1187 0.318784 CGGCTATTGACTACTCGGCC 60.319 60.000 0.00 0.00 35.33 6.13
1199 1210 1.543941 GGCGCTGATTCAGACGATCG 61.544 60.000 24.65 14.88 34.71 3.69
1201 1212 1.543941 CGCTGATTCAGACGATCGCC 61.544 60.000 16.60 3.44 34.71 5.54
1252 1263 3.665825 TACCGGCTGTTACGCGTCG 62.666 63.158 18.63 12.49 0.00 5.12
1266 1277 2.926242 GTCGTTCCCCTCCCCACA 60.926 66.667 0.00 0.00 0.00 4.17
2347 2586 1.768275 TGTCTGCCTCAGAAAACCAGA 59.232 47.619 0.00 0.00 42.46 3.86
5228 5503 1.019673 GTGGTCAGTATGCTGCATGG 58.980 55.000 24.59 13.74 42.29 3.66
5347 5622 1.118356 AAAATTTCGCTGGGTGGGCA 61.118 50.000 0.00 0.00 0.00 5.36
5445 5720 8.872845 GCACTAATTGAGGTAAAATCCATTTTG 58.127 33.333 7.42 0.00 40.00 2.44
5559 5834 5.831525 TGGATTTATGCAAGCATTCTCTGAT 59.168 36.000 13.32 0.00 37.82 2.90
5769 6044 5.163652 GGCTGAATATTAACGGTGCTCTTTT 60.164 40.000 0.00 0.00 0.00 2.27
6152 6462 3.809832 CCAGTTTTTGAGTGTCGATGTCT 59.190 43.478 0.00 0.00 0.00 3.41
6251 6561 1.892338 GCAATTTGCAGGCCTAGCA 59.108 52.632 21.35 21.35 44.26 3.49
6255 6565 0.394899 ATTTGCAGGCCTAGCAGGAC 60.395 55.000 23.11 3.35 46.64 3.85
6265 6575 1.075536 CCTAGCAGGACCCCAACTTTT 59.924 52.381 0.00 0.00 37.67 2.27
6346 6656 2.871096 TAGGACCGTGGCTTGAATTT 57.129 45.000 0.00 0.00 0.00 1.82
6384 6789 6.272324 TCCTGGAAAATTCTCCTGTCTTTCTA 59.728 38.462 0.00 0.00 36.35 2.10
6414 6819 1.067283 CAGCATAGCAGGGATAGTCCG 60.067 57.143 0.00 0.00 37.43 4.79
6749 7481 5.599999 TGAGGTCCTTAAGATGCTCTAAC 57.400 43.478 3.36 0.00 0.00 2.34
6771 7503 6.156748 ACATGTTGGTTAAAGGAGAAAACC 57.843 37.500 0.00 0.00 42.49 3.27
6778 7510 7.483580 TGGTTAAAGGAGAAAACCTGAAAAA 57.516 32.000 5.19 0.00 42.60 1.94
6831 7565 4.383649 TGTGTCGCTTCAAACGATTAGTAC 59.616 41.667 0.00 0.00 42.26 2.73
6850 7584 1.001406 ACGCTGGACAAGAAGAGAAGG 59.999 52.381 0.00 0.00 0.00 3.46
6882 7616 5.244755 TCATCATCAAGGTCAAAATCGTCA 58.755 37.500 0.00 0.00 0.00 4.35
6897 7631 1.519234 GTCATCCGATGCGCACTCA 60.519 57.895 14.90 0.00 0.00 3.41
6911 7645 3.485877 GCGCACTCAAGATATGAACCAAC 60.486 47.826 0.30 0.00 37.67 3.77
6920 7654 2.552599 TATGAACCAACCGACTTGCA 57.447 45.000 0.00 0.00 0.00 4.08
7153 7887 3.038280 TCTCTGAGAAGGTGTCACCAAA 58.962 45.455 24.02 3.67 41.95 3.28
7323 8057 4.021807 TGTGAGAATAGGTCTGCGTAACAA 60.022 41.667 0.00 0.00 36.41 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.367937 AGATATTGTCATGAGCCTGGTTACT 59.632 40.000 0.00 0.00 0.00 2.24
39 40 2.380064 ATGCTCAAACTGGGGTTCAA 57.620 45.000 0.00 0.00 34.14 2.69
53 54 5.392811 GCCATATCTCAAAGCCATTATGCTC 60.393 44.000 0.00 0.00 41.80 4.26
68 69 1.771255 AGGGTGAAGTGGCCATATCTC 59.229 52.381 9.72 11.30 0.00 2.75
74 75 1.426251 ATGACAGGGTGAAGTGGCCA 61.426 55.000 0.00 0.00 0.00 5.36
82 83 4.019411 TGATGAAAGCTTATGACAGGGTGA 60.019 41.667 0.00 0.00 0.00 4.02
134 135 2.575805 AGAGGAACAAGGCCAAGAAG 57.424 50.000 5.01 0.00 0.00 2.85
176 177 7.503549 TGATCACAGATAACATCATAACAGCT 58.496 34.615 0.00 0.00 0.00 4.24
206 207 2.301346 CAGTCAGCTTTTGTTCCAGGT 58.699 47.619 0.00 0.00 0.00 4.00
298 299 4.023878 GCCCAATCAGTTTGTGTAACGTAA 60.024 41.667 0.00 0.00 42.39 3.18
311 312 3.244422 TGTCTTAGTTTCGCCCAATCAGT 60.244 43.478 0.00 0.00 0.00 3.41
359 361 9.847224 ATAAATGAGACGGTCTTGGTATTAATT 57.153 29.630 12.67 0.99 0.00 1.40
423 425 0.037326 GATGACGTCACCAAGGCAGA 60.037 55.000 22.71 0.00 0.00 4.26
437 439 0.321653 GGGATACATGCGGGGATGAC 60.322 60.000 7.19 0.00 39.74 3.06
446 448 1.338973 CAGCACCATTGGGATACATGC 59.661 52.381 7.78 6.62 38.05 4.06
494 496 1.677633 CCCAACTAAAGCACCCGGG 60.678 63.158 22.25 22.25 0.00 5.73
566 568 6.179756 AGTAACACCAGCAATGAATGATACA 58.820 36.000 0.00 0.00 0.00 2.29
569 571 6.392354 CAAAGTAACACCAGCAATGAATGAT 58.608 36.000 0.00 0.00 0.00 2.45
611 613 3.562973 GTGTTCATGATATGGAGCAGGTG 59.437 47.826 0.00 0.00 0.00 4.00
629 631 4.362677 ACCTGTATACATCTGAGGGTGTT 58.637 43.478 5.91 0.00 0.00 3.32
632 634 3.207777 AGGACCTGTATACATCTGAGGGT 59.792 47.826 5.91 8.91 0.00 4.34
638 640 7.569111 ACCTTTTATCAGGACCTGTATACATCT 59.431 37.037 21.06 0.00 37.39 2.90
673 675 4.225267 AGGATACGTCAGAAATGGAGGTTT 59.775 41.667 0.00 0.00 46.39 3.27
675 677 3.375699 AGGATACGTCAGAAATGGAGGT 58.624 45.455 0.00 0.00 46.39 3.85
676 678 3.384789 TGAGGATACGTCAGAAATGGAGG 59.615 47.826 0.00 0.00 46.39 4.30
683 685 6.094603 GGTAGTTAACTGAGGATACGTCAGAA 59.905 42.308 18.56 10.88 41.50 3.02
691 693 4.210331 GGACGGGTAGTTAACTGAGGATA 58.790 47.826 18.56 0.00 0.00 2.59
694 696 1.133790 CGGACGGGTAGTTAACTGAGG 59.866 57.143 18.56 7.22 0.00 3.86
728 730 4.320641 CGAAGGCGGAAGAACCAAATAAAA 60.321 41.667 0.00 0.00 38.90 1.52
801 803 1.604278 GCGAGCCCATCTAAAATGGTC 59.396 52.381 3.54 0.00 37.48 4.02
809 811 3.916544 CGCCAGCGAGCCCATCTA 61.917 66.667 6.06 0.00 42.83 1.98
821 823 1.061131 CAACTAATTGACGAGCGCCAG 59.939 52.381 2.29 0.00 38.15 4.85
828 830 2.301870 ACAGGGAGCAACTAATTGACGA 59.698 45.455 0.00 0.00 38.15 4.20
829 831 2.416547 CACAGGGAGCAACTAATTGACG 59.583 50.000 0.00 0.00 38.15 4.35
830 832 3.674997 TCACAGGGAGCAACTAATTGAC 58.325 45.455 0.00 0.00 38.15 3.18
831 833 4.263462 ACATCACAGGGAGCAACTAATTGA 60.263 41.667 0.00 0.00 38.15 2.57
832 834 4.012374 ACATCACAGGGAGCAACTAATTG 58.988 43.478 0.00 0.00 38.99 2.32
833 835 4.307032 ACATCACAGGGAGCAACTAATT 57.693 40.909 0.00 0.00 0.00 1.40
834 836 4.012374 CAACATCACAGGGAGCAACTAAT 58.988 43.478 0.00 0.00 0.00 1.73
835 837 3.411446 CAACATCACAGGGAGCAACTAA 58.589 45.455 0.00 0.00 0.00 2.24
836 838 2.875672 GCAACATCACAGGGAGCAACTA 60.876 50.000 0.00 0.00 0.00 2.24
837 839 1.901591 CAACATCACAGGGAGCAACT 58.098 50.000 0.00 0.00 0.00 3.16
838 840 0.242017 GCAACATCACAGGGAGCAAC 59.758 55.000 0.00 0.00 0.00 4.17
839 841 0.111061 AGCAACATCACAGGGAGCAA 59.889 50.000 0.00 0.00 0.00 3.91
840 842 0.321919 GAGCAACATCACAGGGAGCA 60.322 55.000 0.00 0.00 0.00 4.26
841 843 0.035630 AGAGCAACATCACAGGGAGC 60.036 55.000 0.00 0.00 0.00 4.70
842 844 1.738365 CGAGAGCAACATCACAGGGAG 60.738 57.143 0.00 0.00 0.00 4.30
843 845 0.247460 CGAGAGCAACATCACAGGGA 59.753 55.000 0.00 0.00 0.00 4.20
844 846 0.036952 ACGAGAGCAACATCACAGGG 60.037 55.000 0.00 0.00 0.00 4.45
845 847 1.073964 CACGAGAGCAACATCACAGG 58.926 55.000 0.00 0.00 0.00 4.00
846 848 1.073964 CCACGAGAGCAACATCACAG 58.926 55.000 0.00 0.00 0.00 3.66
847 849 0.950555 GCCACGAGAGCAACATCACA 60.951 55.000 0.00 0.00 0.00 3.58
848 850 0.950555 TGCCACGAGAGCAACATCAC 60.951 55.000 0.00 0.00 37.28 3.06
849 851 0.950555 GTGCCACGAGAGCAACATCA 60.951 55.000 0.00 0.00 43.02 3.07
850 852 1.790387 GTGCCACGAGAGCAACATC 59.210 57.895 0.00 0.00 43.02 3.06
851 853 3.972227 GTGCCACGAGAGCAACAT 58.028 55.556 0.00 0.00 43.02 2.71
854 856 1.597854 CAAGGTGCCACGAGAGCAA 60.598 57.895 0.00 0.00 43.02 3.91
855 857 2.031012 CAAGGTGCCACGAGAGCA 59.969 61.111 0.00 0.00 38.08 4.26
856 858 2.743928 CCAAGGTGCCACGAGAGC 60.744 66.667 0.00 0.00 0.00 4.09
857 859 2.046892 CCCAAGGTGCCACGAGAG 60.047 66.667 0.00 0.00 0.00 3.20
858 860 4.329545 GCCCAAGGTGCCACGAGA 62.330 66.667 0.00 0.00 0.00 4.04
943 945 1.570813 CTTCGCAGTGATATTCGGCA 58.429 50.000 0.00 0.00 0.00 5.69
944 946 0.861837 CCTTCGCAGTGATATTCGGC 59.138 55.000 0.00 0.00 0.00 5.54
945 947 0.861837 GCCTTCGCAGTGATATTCGG 59.138 55.000 0.00 0.00 34.03 4.30
1176 1187 1.880340 GTCTGAATCAGCGCCGGAG 60.880 63.158 5.05 1.55 0.00 4.63
1252 1263 3.007542 GGATGTGGGGAGGGGAAC 58.992 66.667 0.00 0.00 0.00 3.62
1660 1884 3.367498 GCCCGGTTGCACAATAAATGTAA 60.367 43.478 0.00 0.00 41.46 2.41
2229 2467 9.223099 CTTATAACATCATATGCTGACCATTCA 57.777 33.333 13.32 0.00 36.48 2.57
2517 2756 1.988107 AGATTCTTTCCTGGGCTGTCA 59.012 47.619 0.00 0.00 0.00 3.58
5228 5503 5.041191 TCCAGAGATCATAAAAGGGAAGC 57.959 43.478 0.00 0.00 0.00 3.86
5347 5622 8.495160 AGAATCTCATAATCAGGATCTCTGTT 57.505 34.615 9.98 7.31 43.76 3.16
5445 5720 5.794894 TGAATTTCAGAACTGAGGGTCTAC 58.205 41.667 4.72 0.00 41.13 2.59
5559 5834 4.339814 ACAAGGTCCGAAAAACAATAAGCA 59.660 37.500 0.00 0.00 0.00 3.91
5644 5919 0.321564 TGGTCTCCAACATCTTGCGG 60.322 55.000 0.00 0.00 0.00 5.69
5769 6044 2.242047 TTAGTACCAACGCTGTGCAA 57.758 45.000 0.00 0.00 0.00 4.08
6024 6333 9.311916 CTGTAACATGATCAAAAGAACCAAAAA 57.688 29.630 0.00 0.00 0.00 1.94
6037 6346 5.178061 AGATTTGTCGCTGTAACATGATCA 58.822 37.500 0.00 0.00 0.00 2.92
6127 6437 4.638421 ACATCGACACTCAAAAACTGGAAA 59.362 37.500 0.00 0.00 0.00 3.13
6152 6462 7.661536 AGCACTAAACTCCTCATATGTCTTA 57.338 36.000 1.90 0.00 0.00 2.10
6248 6558 3.181423 TGATAAAAAGTTGGGGTCCTGCT 60.181 43.478 0.00 0.00 0.00 4.24
6251 6561 4.741928 AGTGATAAAAAGTTGGGGTCCT 57.258 40.909 0.00 0.00 0.00 3.85
6255 6565 9.869757 CCTAAAATTAGTGATAAAAAGTTGGGG 57.130 33.333 0.00 0.00 0.00 4.96
6384 6789 2.486727 CCTGCTATGCTGACACATCCAT 60.487 50.000 0.00 0.00 0.00 3.41
6549 7030 4.705023 GCCCCAGATTTAAAACTAGCTTCA 59.295 41.667 0.00 0.00 0.00 3.02
6668 7151 2.154567 AGGTACATTGCCTCGGACTA 57.845 50.000 0.00 0.00 0.00 2.59
6749 7481 6.040391 TCAGGTTTTCTCCTTTAACCAACATG 59.960 38.462 0.00 0.00 42.96 3.21
6831 7565 1.273606 TCCTTCTCTTCTTGTCCAGCG 59.726 52.381 0.00 0.00 0.00 5.18
6850 7584 2.200067 CCTTGATGATGAGTGACGCTC 58.800 52.381 9.16 9.16 44.36 5.03
6882 7616 0.105593 ATCTTGAGTGCGCATCGGAT 59.894 50.000 15.91 15.36 0.00 4.18
6897 7631 3.689649 GCAAGTCGGTTGGTTCATATCTT 59.310 43.478 1.37 0.00 36.56 2.40
6911 7645 2.897436 TCATCATCTTCTGCAAGTCGG 58.103 47.619 0.00 0.00 33.76 4.79
6920 7654 6.822676 GGATGACAAGTCTTTCATCATCTTCT 59.177 38.462 23.98 2.63 46.82 2.85
7153 7887 3.430929 GGAGACGGCTACATTGTCTGAAT 60.431 47.826 0.00 0.00 42.71 2.57
7323 8057 8.515414 GGCTCTTATTTGACTTGTTAAATGTCT 58.485 33.333 11.95 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.