Multiple sequence alignment - TraesCS5D01G223100

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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 TraesCS5D01G223100 chr5D 100.000 2848 0 0 1 2848 330718189 330721036 0.000000e+00 5260.0
1 TraesCS5D01G223100 chr5D 93.790 628 35 3 1 627 111942958 111943582 0.000000e+00 941.0
2 TraesCS5D01G223100 chr5B 92.395 1052 54 7 782 1814 386558976 386557932 0.000000e+00 1476.0
3 TraesCS5D01G223100 chr5B 90.079 252 25 0 2156 2407 513661419 513661168 7.610000e-86 327.0
4 TraesCS5D01G223100 chr5B 87.218 266 23 4 2403 2657 513653577 513653312 2.780000e-75 292.0
5 TraesCS5D01G223100 chr5B 91.667 192 15 1 2655 2845 513653223 513653032 6.050000e-67 265.0
6 TraesCS5D01G223100 chr7D 95.122 615 26 4 1 614 413996850 413996239 0.000000e+00 966.0
7 TraesCS5D01G223100 chr7D 93.333 75 4 1 712 785 80321818 80321744 3.000000e-20 110.0
8 TraesCS5D01G223100 chr7D 91.566 83 2 4 712 790 80466414 80466333 3.000000e-20 110.0
9 TraesCS5D01G223100 chr7D 92.958 71 5 0 627 697 616551097 616551027 1.400000e-18 104.0
10 TraesCS5D01G223100 chr2D 94.108 628 33 3 1 628 333498186 333497563 0.000000e+00 952.0
11 TraesCS5D01G223100 chr2D 89.691 194 20 0 2655 2848 562711335 562711142 6.090000e-62 248.0
12 TraesCS5D01G223100 chr1D 93.829 632 34 4 1 630 463931239 463930611 0.000000e+00 946.0
13 TraesCS5D01G223100 chr1D 76.496 468 84 19 1200 1660 435144948 435145396 6.140000e-57 231.0
14 TraesCS5D01G223100 chr1D 73.554 484 90 26 1204 1668 424453092 424453556 1.770000e-32 150.0
15 TraesCS5D01G223100 chr3D 93.810 630 33 4 1 628 592991610 592990985 0.000000e+00 942.0
16 TraesCS5D01G223100 chr3D 94.444 612 33 1 3 614 15914480 15913870 0.000000e+00 941.0
17 TraesCS5D01G223100 chr3D 94.309 615 34 1 1 614 596773393 596772779 0.000000e+00 941.0
18 TraesCS5D01G223100 chr3D 92.438 648 43 5 1 647 448746822 448746180 0.000000e+00 920.0
19 TraesCS5D01G223100 chr6B 93.492 630 33 5 1 628 682935944 682936567 0.000000e+00 929.0
20 TraesCS5D01G223100 chr6B 81.187 691 101 24 999 1668 161353393 161352711 1.940000e-146 529.0
21 TraesCS5D01G223100 chr6B 85.083 181 27 0 2668 2848 710957726 710957546 4.850000e-43 185.0
22 TraesCS5D01G223100 chr6B 93.506 77 1 3 714 787 720181832 720181907 8.340000e-21 111.0
23 TraesCS5D01G223100 chr6A 86.627 845 100 7 1820 2657 155220126 155219288 0.000000e+00 922.0
24 TraesCS5D01G223100 chr6A 85.806 465 66 0 1204 1668 101932639 101932175 7.090000e-136 494.0
25 TraesCS5D01G223100 chr6A 89.560 182 19 0 2655 2836 155219199 155219018 6.140000e-57 231.0
26 TraesCS5D01G223100 chr6A 94.366 71 2 2 712 781 471880918 471880987 1.080000e-19 108.0
27 TraesCS5D01G223100 chr6A 84.337 83 13 0 2427 2509 475080671 475080589 6.540000e-12 82.4
28 TraesCS5D01G223100 chr3A 86.277 838 112 2 1821 2657 178200780 178199945 0.000000e+00 907.0
29 TraesCS5D01G223100 chr3A 89.535 86 3 5 712 793 23307359 23307276 1.400000e-18 104.0
30 TraesCS5D01G223100 chr3A 83.333 96 14 2 2415 2509 81106795 81106701 1.410000e-13 87.9
31 TraesCS5D01G223100 chr3A 86.441 59 8 0 1878 1936 430764065 430764123 6.590000e-07 65.8
32 TraesCS5D01G223100 chr4A 86.277 838 110 3 1821 2657 15119379 15120212 0.000000e+00 905.0
33 TraesCS5D01G223100 chr4D 83.393 843 132 4 1817 2657 394953068 394953904 0.000000e+00 774.0
34 TraesCS5D01G223100 chr4D 89.412 85 5 3 712 793 48708842 48708925 1.400000e-18 104.0
35 TraesCS5D01G223100 chr5A 84.405 622 33 23 805 1382 426312008 426312609 1.150000e-153 553.0
36 TraesCS5D01G223100 chr6D 87.309 457 56 2 1213 1668 84685622 84685167 3.250000e-144 521.0
37 TraesCS5D01G223100 chr6D 86.695 466 60 2 1204 1668 85504848 85505312 1.510000e-142 516.0
38 TraesCS5D01G223100 chr6D 91.237 194 17 0 2655 2848 134263710 134263903 6.050000e-67 265.0
39 TraesCS5D01G223100 chr6D 90.588 85 4 3 712 793 82943797 82943714 3.000000e-20 110.0
40 TraesCS5D01G223100 chr1A 88.083 193 23 0 2656 2848 257405709 257405901 2.210000e-56 230.0
41 TraesCS5D01G223100 chr3B 84.530 181 28 0 2668 2848 78602121 78601941 2.250000e-41 180.0
42 TraesCS5D01G223100 chr3B 95.775 71 1 2 712 781 553091797 553091866 2.320000e-21 113.0
43 TraesCS5D01G223100 chr4B 83.158 190 32 0 2659 2848 413160537 413160726 1.050000e-39 174.0
44 TraesCS5D01G223100 chr4B 90.141 71 7 0 627 697 416168323 416168393 3.020000e-15 93.5
45 TraesCS5D01G223100 chr4B 86.441 59 8 0 1878 1936 10774982 10775040 6.590000e-07 65.8
46 TraesCS5D01G223100 chr2B 77.064 218 46 4 2297 2512 333083724 333083939 3.850000e-24 122.0
47 TraesCS5D01G223100 chr2A 92.500 80 2 3 712 788 1882156 1882078 8.340000e-21 111.0
48 TraesCS5D01G223100 chr7B 88.889 90 7 3 712 799 307381052 307380964 1.080000e-19 108.0
49 TraesCS5D01G223100 chr7A 95.000 60 3 0 627 686 511508299 511508358 8.400000e-16 95.3


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 TraesCS5D01G223100 chr5D 330718189 330721036 2847 False 5260.0 5260 100.0000 1 2848 1 chr5D.!!$F2 2847
1 TraesCS5D01G223100 chr5D 111942958 111943582 624 False 941.0 941 93.7900 1 627 1 chr5D.!!$F1 626
2 TraesCS5D01G223100 chr5B 386557932 386558976 1044 True 1476.0 1476 92.3950 782 1814 1 chr5B.!!$R1 1032
3 TraesCS5D01G223100 chr5B 513653032 513653577 545 True 278.5 292 89.4425 2403 2845 2 chr5B.!!$R3 442
4 TraesCS5D01G223100 chr7D 413996239 413996850 611 True 966.0 966 95.1220 1 614 1 chr7D.!!$R3 613
5 TraesCS5D01G223100 chr2D 333497563 333498186 623 True 952.0 952 94.1080 1 628 1 chr2D.!!$R1 627
6 TraesCS5D01G223100 chr1D 463930611 463931239 628 True 946.0 946 93.8290 1 630 1 chr1D.!!$R1 629
7 TraesCS5D01G223100 chr3D 592990985 592991610 625 True 942.0 942 93.8100 1 628 1 chr3D.!!$R3 627
8 TraesCS5D01G223100 chr3D 15913870 15914480 610 True 941.0 941 94.4440 3 614 1 chr3D.!!$R1 611
9 TraesCS5D01G223100 chr3D 596772779 596773393 614 True 941.0 941 94.3090 1 614 1 chr3D.!!$R4 613
10 TraesCS5D01G223100 chr3D 448746180 448746822 642 True 920.0 920 92.4380 1 647 1 chr3D.!!$R2 646
11 TraesCS5D01G223100 chr6B 682935944 682936567 623 False 929.0 929 93.4920 1 628 1 chr6B.!!$F1 627
12 TraesCS5D01G223100 chr6B 161352711 161353393 682 True 529.0 529 81.1870 999 1668 1 chr6B.!!$R1 669
13 TraesCS5D01G223100 chr6A 155219018 155220126 1108 True 576.5 922 88.0935 1820 2836 2 chr6A.!!$R3 1016
14 TraesCS5D01G223100 chr3A 178199945 178200780 835 True 907.0 907 86.2770 1821 2657 1 chr3A.!!$R3 836
15 TraesCS5D01G223100 chr4A 15119379 15120212 833 False 905.0 905 86.2770 1821 2657 1 chr4A.!!$F1 836
16 TraesCS5D01G223100 chr4D 394953068 394953904 836 False 774.0 774 83.3930 1817 2657 1 chr4D.!!$F2 840
17 TraesCS5D01G223100 chr5A 426312008 426312609 601 False 553.0 553 84.4050 805 1382 1 chr5A.!!$F1 577

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
110 112 0.096976 AGAAAAATGGATCGTGCGCG 59.903 50.0 14.79 14.79 39.92 6.86 F
993 1014 0.245266 TAAGCGCTGAATGGACACGA 59.755 50.0 12.58 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1377 0.034337 TTGTAGTTCTGGCCGGTGTC 59.966 55.0 12.43 3.43 0.0 3.67 R
2497 2628 0.036010 ATGTCGAGTCCCAAGCAAGG 60.036 55.0 0.00 0.00 0.0 3.61 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
26 27 5.050490 GGTATGCATGTGTAGTTCTCGATT 58.950 41.667 10.16 0.00 0.00 3.34
110 112 0.096976 AGAAAAATGGATCGTGCGCG 59.903 50.000 14.79 14.79 39.92 6.86
416 418 9.106070 GAGTTACGGTTTAAAAGATATGGATGT 57.894 33.333 0.00 0.00 0.00 3.06
527 530 3.319755 GTTCGGTGTGACTTAAATCCGA 58.680 45.455 0.00 0.00 43.93 4.55
588 592 2.515996 AAATGATGCGACGGACGGGT 62.516 55.000 1.66 0.00 42.83 5.28
652 656 9.847224 AAATTTCTTATTAGGAGGATTAGCGAA 57.153 29.630 0.00 0.00 0.00 4.70
653 657 8.834749 ATTTCTTATTAGGAGGATTAGCGAAC 57.165 34.615 0.00 0.00 0.00 3.95
654 658 6.010294 TCTTATTAGGAGGATTAGCGAACG 57.990 41.667 0.00 0.00 0.00 3.95
655 659 5.766670 TCTTATTAGGAGGATTAGCGAACGA 59.233 40.000 0.00 0.00 0.00 3.85
656 660 6.433404 TCTTATTAGGAGGATTAGCGAACGAT 59.567 38.462 0.00 0.00 0.00 3.73
657 661 2.802787 AGGAGGATTAGCGAACGATG 57.197 50.000 0.00 0.00 0.00 3.84
658 662 2.032620 AGGAGGATTAGCGAACGATGT 58.967 47.619 0.00 0.00 0.00 3.06
659 663 3.220110 AGGAGGATTAGCGAACGATGTA 58.780 45.455 0.00 0.00 0.00 2.29
660 664 3.635373 AGGAGGATTAGCGAACGATGTAA 59.365 43.478 0.00 0.00 0.00 2.41
661 665 4.281182 AGGAGGATTAGCGAACGATGTAAT 59.719 41.667 0.00 0.00 0.00 1.89
662 666 4.621886 GGAGGATTAGCGAACGATGTAATC 59.378 45.833 0.00 7.02 40.89 1.75
685 689 9.744468 AATCGTTGTTTGAGTTTAATAAAGCTT 57.256 25.926 0.00 0.00 0.00 3.74
687 691 9.654417 TCGTTGTTTGAGTTTAATAAAGCTTAC 57.346 29.630 0.00 0.00 0.00 2.34
688 692 9.659830 CGTTGTTTGAGTTTAATAAAGCTTACT 57.340 29.630 0.00 0.00 0.00 2.24
697 701 9.627123 AGTTTAATAAAGCTTACTATGATGGCA 57.373 29.630 0.00 0.00 0.00 4.92
761 765 6.503616 GACTTCAGTCAACTCTAATATGCG 57.496 41.667 1.86 0.00 44.18 4.73
762 766 5.352284 ACTTCAGTCAACTCTAATATGCGG 58.648 41.667 0.00 0.00 0.00 5.69
763 767 5.127194 ACTTCAGTCAACTCTAATATGCGGA 59.873 40.000 0.00 0.00 0.00 5.54
764 768 5.188327 TCAGTCAACTCTAATATGCGGAG 57.812 43.478 0.00 0.00 0.00 4.63
765 769 4.645136 TCAGTCAACTCTAATATGCGGAGT 59.355 41.667 0.00 0.00 41.37 3.85
766 770 5.826208 TCAGTCAACTCTAATATGCGGAGTA 59.174 40.000 6.10 0.00 39.09 2.59
767 771 6.320418 TCAGTCAACTCTAATATGCGGAGTAA 59.680 38.462 6.10 0.00 39.09 2.24
768 772 6.978659 CAGTCAACTCTAATATGCGGAGTAAA 59.021 38.462 6.10 0.00 39.09 2.01
769 773 7.653713 CAGTCAACTCTAATATGCGGAGTAAAT 59.346 37.037 6.10 0.00 39.09 1.40
770 774 8.857098 AGTCAACTCTAATATGCGGAGTAAATA 58.143 33.333 6.10 0.00 39.09 1.40
771 775 9.472361 GTCAACTCTAATATGCGGAGTAAATAA 57.528 33.333 6.10 0.00 39.09 1.40
928 946 5.222048 TGGATACCTGGTGAATAATTAGGCC 60.222 44.000 10.23 0.00 31.69 5.19
963 981 2.352651 CGTTCATTGGTGAGCATGGTAG 59.647 50.000 0.00 0.00 35.53 3.18
970 990 2.187946 GAGCATGGTAGCGTGGCT 59.812 61.111 15.57 12.37 43.41 4.75
991 1012 2.742053 TCTTTAAGCGCTGAATGGACAC 59.258 45.455 12.58 0.00 0.00 3.67
993 1014 0.245266 TAAGCGCTGAATGGACACGA 59.755 50.000 12.58 0.00 0.00 4.35
996 1017 1.361668 GCGCTGAATGGACACGATGT 61.362 55.000 0.00 0.00 0.00 3.06
1030 1054 2.343475 CTGTGGTTGTGGGCTGGAGT 62.343 60.000 0.00 0.00 0.00 3.85
1200 1279 2.049248 GTGTGGTTTGGGCATGCG 60.049 61.111 12.44 0.00 0.00 4.73
1201 1280 2.520500 TGTGGTTTGGGCATGCGT 60.521 55.556 12.44 0.00 0.00 5.24
1202 1281 2.049248 GTGGTTTGGGCATGCGTG 60.049 61.111 12.44 0.09 0.00 5.34
1287 1366 4.874977 GCCCTACAGCTCGGACGC 62.875 72.222 0.00 0.00 0.00 5.19
1288 1367 4.208686 CCCTACAGCTCGGACGCC 62.209 72.222 0.00 0.00 0.00 5.68
1375 1484 3.699894 CACCGGCAGCTCCTCACT 61.700 66.667 0.00 0.00 0.00 3.41
1558 1667 1.275291 TGGAAGACGGTCAACATCTCC 59.725 52.381 11.27 6.67 0.00 3.71
1668 1777 1.513158 CCTTCATCTCGTCGCTGGT 59.487 57.895 0.00 0.00 0.00 4.00
1670 1779 0.171231 CTTCATCTCGTCGCTGGTGA 59.829 55.000 0.00 0.00 0.00 4.02
1699 1823 1.480212 ATCCGCTGGTGAACTGGACA 61.480 55.000 0.00 0.00 0.00 4.02
1717 1841 1.997874 ACAGGGGCTGGTCCTCATC 60.998 63.158 0.00 0.00 38.00 2.92
1731 1855 3.869272 CATCGGCAGGCGCAACTC 61.869 66.667 12.43 0.00 41.24 3.01
1746 1870 4.379243 CTCCGGCGCCACAGAGTT 62.379 66.667 28.98 0.00 0.00 3.01
1779 1903 6.128090 TGAGCATTCATGTAAAGCTTCTTCAG 60.128 38.462 0.00 0.00 42.01 3.02
1780 1904 5.942236 AGCATTCATGTAAAGCTTCTTCAGA 59.058 36.000 0.00 0.00 38.99 3.27
1818 1944 8.811017 TCTTTCCATAACAAAATATTTGCTCCA 58.189 29.630 0.39 0.00 0.00 3.86
1876 2002 2.202096 GCGATCGCATATGCACGC 60.202 61.111 33.89 31.51 44.54 5.34
1882 2008 1.657822 TCGCATATGCACGCCTAAAA 58.342 45.000 26.52 0.00 42.21 1.52
1917 2043 0.179034 ATCATCAAGAAGCTCGCCCC 60.179 55.000 0.00 0.00 0.00 5.80
1918 2044 1.078214 CATCAAGAAGCTCGCCCCA 60.078 57.895 0.00 0.00 0.00 4.96
1936 2062 2.147387 ACCCCTGCTCCACGAAGTT 61.147 57.895 0.00 0.00 41.61 2.66
1940 2066 1.291877 CCTGCTCCACGAAGTTTCCG 61.292 60.000 0.00 0.00 41.61 4.30
1968 2094 0.749091 CCGGATGCAGAGCCATTCAA 60.749 55.000 0.00 0.00 0.00 2.69
2045 2171 1.308998 CAGCAAGGTGGAAAACGTCT 58.691 50.000 0.00 0.00 0.00 4.18
2098 2224 1.003839 GGTGGTTGATGACGAGGCA 60.004 57.895 0.00 0.00 0.00 4.75
2191 2317 1.805428 GCAAGTGCGTCCCCAACAAT 61.805 55.000 0.00 0.00 0.00 2.71
2201 2327 2.169769 GTCCCCAACAATATCGACCTCA 59.830 50.000 0.00 0.00 0.00 3.86
2215 2341 1.052124 ACCTCACCGGTGGTTCTGAA 61.052 55.000 33.40 12.19 46.80 3.02
2233 2359 1.724582 AAGTTGCGGTTGGTGTGCTC 61.725 55.000 0.00 0.00 0.00 4.26
2239 2365 2.320587 GGTTGGTGTGCTCTGAGCG 61.321 63.158 23.35 0.00 46.26 5.03
2261 2387 2.203280 CGTTGGTGCTGGGGTTGA 60.203 61.111 0.00 0.00 0.00 3.18
2262 2388 2.551912 CGTTGGTGCTGGGGTTGAC 61.552 63.158 0.00 0.00 0.00 3.18
2277 2404 3.552890 GGGTTGACTGTTTTCTTCATGGC 60.553 47.826 0.00 0.00 0.00 4.40
2306 2433 3.257873 CCCACAAATTGTATGCTGGAACA 59.742 43.478 0.00 0.00 0.00 3.18
2375 2502 5.538118 TCTTTGCTTCGTTGAGAGTCAATA 58.462 37.500 0.00 0.00 38.79 1.90
2377 2504 5.784750 TTGCTTCGTTGAGAGTCAATATG 57.215 39.130 0.00 0.00 38.79 1.78
2497 2628 1.392510 GAGACGCGTGGTGGTATTTTC 59.607 52.381 20.70 0.00 0.00 2.29
2524 2665 2.152699 GGACTCGACATGCGTGACG 61.153 63.158 22.03 22.03 43.22 4.35
2648 2790 8.077991 TGATGAGCTAAAAACACAATTTCTCAG 58.922 33.333 0.00 0.00 32.51 3.35
2657 2799 9.736023 AAAAACACAATTTCTCAGTGACTTATC 57.264 29.630 0.00 0.00 37.05 1.75
2658 2800 8.450578 AAACACAATTTCTCAGTGACTTATCA 57.549 30.769 0.00 0.00 37.05 2.15
2659 2801 8.450578 AACACAATTTCTCAGTGACTTATCAA 57.549 30.769 0.00 0.00 36.31 2.57
2702 2935 6.980397 AGTTCCAAAACTTTGTTGATGATCAC 59.020 34.615 0.00 0.00 43.28 3.06
2822 3055 1.494721 GAATGGGAGTTGGCCTATCCA 59.505 52.381 19.11 13.99 44.85 3.41
2841 3074 2.939103 CCAGACTACCTTATGCAAGCAC 59.061 50.000 0.00 0.00 0.00 4.40
2842 3075 3.369892 CCAGACTACCTTATGCAAGCACT 60.370 47.826 0.00 0.00 0.00 4.40
2843 3076 3.868077 CAGACTACCTTATGCAAGCACTC 59.132 47.826 0.00 0.00 0.00 3.51
2844 3077 3.772025 AGACTACCTTATGCAAGCACTCT 59.228 43.478 0.00 0.00 0.00 3.24
2845 3078 4.116238 GACTACCTTATGCAAGCACTCTC 58.884 47.826 0.00 0.00 0.00 3.20
2846 3079 2.409948 ACCTTATGCAAGCACTCTCC 57.590 50.000 0.00 0.00 0.00 3.71
2847 3080 1.630369 ACCTTATGCAAGCACTCTCCA 59.370 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 428 9.787532 CGGATCATATTTAAGTCAAACAAATGT 57.212 29.630 0.00 0.00 0.00 2.71
496 499 3.249080 AGTCACACCGAACCGTTATTTTG 59.751 43.478 0.00 0.00 0.00 2.44
527 530 6.642707 TTTTCATGAAATCAACCCGTAGTT 57.357 33.333 21.10 0.00 40.16 2.24
626 630 9.847224 TTCGCTAATCCTCCTAATAAGAAATTT 57.153 29.630 0.00 0.00 0.00 1.82
627 631 9.274206 GTTCGCTAATCCTCCTAATAAGAAATT 57.726 33.333 0.00 0.00 0.00 1.82
628 632 7.599245 CGTTCGCTAATCCTCCTAATAAGAAAT 59.401 37.037 0.00 0.00 0.00 2.17
629 633 6.921857 CGTTCGCTAATCCTCCTAATAAGAAA 59.078 38.462 0.00 0.00 0.00 2.52
630 634 6.263842 TCGTTCGCTAATCCTCCTAATAAGAA 59.736 38.462 0.00 0.00 0.00 2.52
631 635 5.766670 TCGTTCGCTAATCCTCCTAATAAGA 59.233 40.000 0.00 0.00 0.00 2.10
632 636 6.010294 TCGTTCGCTAATCCTCCTAATAAG 57.990 41.667 0.00 0.00 0.00 1.73
633 637 6.015688 ACATCGTTCGCTAATCCTCCTAATAA 60.016 38.462 0.00 0.00 0.00 1.40
634 638 5.475909 ACATCGTTCGCTAATCCTCCTAATA 59.524 40.000 0.00 0.00 0.00 0.98
635 639 4.281182 ACATCGTTCGCTAATCCTCCTAAT 59.719 41.667 0.00 0.00 0.00 1.73
636 640 3.635373 ACATCGTTCGCTAATCCTCCTAA 59.365 43.478 0.00 0.00 0.00 2.69
637 641 3.220110 ACATCGTTCGCTAATCCTCCTA 58.780 45.455 0.00 0.00 0.00 2.94
638 642 2.032620 ACATCGTTCGCTAATCCTCCT 58.967 47.619 0.00 0.00 0.00 3.69
639 643 2.510768 ACATCGTTCGCTAATCCTCC 57.489 50.000 0.00 0.00 0.00 4.30
640 644 5.748872 GATTACATCGTTCGCTAATCCTC 57.251 43.478 0.00 0.00 0.00 3.71
659 663 9.744468 AAGCTTTATTAAACTCAAACAACGATT 57.256 25.926 0.00 0.00 0.00 3.34
661 665 9.654417 GTAAGCTTTATTAAACTCAAACAACGA 57.346 29.630 3.20 0.00 0.00 3.85
662 666 9.659830 AGTAAGCTTTATTAAACTCAAACAACG 57.340 29.630 3.20 0.00 0.00 4.10
671 675 9.627123 TGCCATCATAGTAAGCTTTATTAAACT 57.373 29.630 3.20 3.09 0.00 2.66
738 742 5.460419 CCGCATATTAGAGTTGACTGAAGTC 59.540 44.000 3.41 3.41 44.97 3.01
739 743 5.127194 TCCGCATATTAGAGTTGACTGAAGT 59.873 40.000 0.00 0.00 0.00 3.01
740 744 5.592054 TCCGCATATTAGAGTTGACTGAAG 58.408 41.667 0.00 0.00 0.00 3.02
741 745 5.127194 ACTCCGCATATTAGAGTTGACTGAA 59.873 40.000 0.00 0.00 37.60 3.02
742 746 4.645136 ACTCCGCATATTAGAGTTGACTGA 59.355 41.667 0.00 0.00 37.60 3.41
743 747 4.938080 ACTCCGCATATTAGAGTTGACTG 58.062 43.478 0.00 0.00 37.60 3.51
744 748 6.710597 TTACTCCGCATATTAGAGTTGACT 57.289 37.500 4.78 0.00 41.09 3.41
745 749 7.948278 ATTTACTCCGCATATTAGAGTTGAC 57.052 36.000 4.78 0.00 41.09 3.18
778 782 9.089601 GCAGAGAAAACCTTATAAAGTACTCTC 57.910 37.037 13.09 13.09 0.00 3.20
779 783 8.817876 AGCAGAGAAAACCTTATAAAGTACTCT 58.182 33.333 0.00 10.23 0.00 3.24
780 784 9.438228 AAGCAGAGAAAACCTTATAAAGTACTC 57.562 33.333 0.00 0.00 0.00 2.59
784 788 8.352942 CACAAAGCAGAGAAAACCTTATAAAGT 58.647 33.333 0.00 0.00 0.00 2.66
788 792 7.284489 ACAACACAAAGCAGAGAAAACCTTATA 59.716 33.333 0.00 0.00 0.00 0.98
794 798 4.732784 TGACAACACAAAGCAGAGAAAAC 58.267 39.130 0.00 0.00 0.00 2.43
798 802 1.942657 GCTGACAACACAAAGCAGAGA 59.057 47.619 0.00 0.00 35.69 3.10
900 915 8.826765 CCTAATTATTCACCAGGTATCCAGTAT 58.173 37.037 0.00 0.00 0.00 2.12
970 990 2.742053 GTGTCCATTCAGCGCTTAAAGA 59.258 45.455 7.50 5.17 0.00 2.52
991 1012 2.819154 TGCGGACATGCCACATCG 60.819 61.111 0.00 0.00 35.94 3.84
993 1014 3.126879 CGTGCGGACATGCCACAT 61.127 61.111 8.11 0.00 35.94 3.21
1064 1088 2.031516 CAGAGCAGGAGCAACCACG 61.032 63.158 2.96 0.00 45.49 4.94
1065 1089 0.952984 GACAGAGCAGGAGCAACCAC 60.953 60.000 2.96 0.00 45.49 4.16
1066 1090 1.123861 AGACAGAGCAGGAGCAACCA 61.124 55.000 2.96 0.00 45.49 3.67
1141 1165 8.027771 ACGTACGAGAGATCTTAAAACTTGATT 58.972 33.333 24.41 0.00 0.00 2.57
1200 1279 2.159272 GACGCTGACGAAACCTGCAC 62.159 60.000 0.00 0.00 43.93 4.57
1201 1280 1.954146 GACGCTGACGAAACCTGCA 60.954 57.895 0.00 0.00 43.93 4.41
1202 1281 2.853914 GACGCTGACGAAACCTGC 59.146 61.111 0.00 0.00 43.93 4.85
1203 1282 1.371267 TCGACGCTGACGAAACCTG 60.371 57.895 0.00 0.00 43.93 4.00
1297 1376 1.445582 GTAGTTCTGGCCGGTGTCG 60.446 63.158 12.43 0.00 0.00 4.35
1298 1377 0.034337 TTGTAGTTCTGGCCGGTGTC 59.966 55.000 12.43 3.43 0.00 3.67
1299 1378 0.250166 GTTGTAGTTCTGGCCGGTGT 60.250 55.000 12.43 0.00 0.00 4.16
1300 1379 1.289109 CGTTGTAGTTCTGGCCGGTG 61.289 60.000 12.43 0.00 0.00 4.94
1301 1380 1.005394 CGTTGTAGTTCTGGCCGGT 60.005 57.895 12.43 0.00 0.00 5.28
1456 1565 2.933287 ATGAAGGTGGCCCGGACA 60.933 61.111 0.73 0.00 35.12 4.02
1509 1618 1.677637 GCCGAGGTAGAGGTCCAAGG 61.678 65.000 0.00 0.00 0.00 3.61
1513 1622 2.439883 ACGCCGAGGTAGAGGTCC 60.440 66.667 0.00 0.00 0.00 4.46
1549 1658 0.742281 CGTCAGGCCTGGAGATGTTG 60.742 60.000 32.23 4.54 0.00 3.33
1558 1667 4.994471 TGCACTGCGTCAGGCCTG 62.994 66.667 27.87 27.87 42.61 4.85
1668 1777 1.470805 CCAGCGGATACATCGTGTTCA 60.471 52.381 0.00 0.00 0.00 3.18
1670 1779 0.535335 ACCAGCGGATACATCGTGTT 59.465 50.000 1.50 0.00 0.00 3.32
1699 1823 1.997874 GATGAGGACCAGCCCCTGT 60.998 63.158 0.00 0.00 37.37 4.00
1731 1855 3.958147 ATCAACTCTGTGGCGCCGG 62.958 63.158 23.90 14.68 0.00 6.13
1741 1865 5.426689 TGAATGCTCACCTAATCAACTCT 57.573 39.130 0.00 0.00 0.00 3.24
1746 1870 6.038603 GCTTTACATGAATGCTCACCTAATCA 59.961 38.462 0.00 0.00 35.75 2.57
1779 1903 7.717568 TGTTATGGAAAGAGTAGTCTATGCTC 58.282 38.462 0.00 0.00 40.70 4.26
1780 1904 7.661536 TGTTATGGAAAGAGTAGTCTATGCT 57.338 36.000 0.00 0.00 30.45 3.79
1827 1953 0.374758 CATGCCATCTGTCGTTTCCG 59.625 55.000 0.00 0.00 0.00 4.30
1837 1963 2.898920 CTTGCGGGGTCATGCCATCT 62.899 60.000 8.20 0.00 39.65 2.90
1917 2043 2.046892 CTTCGTGGAGCAGGGGTG 60.047 66.667 0.00 0.00 0.00 4.61
1918 2044 1.705997 AAACTTCGTGGAGCAGGGGT 61.706 55.000 0.00 0.00 0.00 4.95
1929 2055 3.241177 GAAGCGCGGAAACTTCGT 58.759 55.556 8.83 0.00 33.56 3.85
1987 2113 0.252479 CAGCAGCTCTCTTGGTGGAT 59.748 55.000 0.00 0.00 36.12 3.41
2017 2143 0.038744 CCACCTTGCTGGACTTGGAT 59.961 55.000 3.40 0.00 39.71 3.41
2098 2224 5.248380 ACAAATCCTGAAGCTCCTTAACT 57.752 39.130 0.00 0.00 0.00 2.24
2201 2327 0.818040 GCAACTTCAGAACCACCGGT 60.818 55.000 0.00 0.00 37.65 5.28
2215 2341 2.124320 AGCACACCAACCGCAACT 60.124 55.556 0.00 0.00 0.00 3.16
2261 2387 3.554934 TGTGAGCCATGAAGAAAACAGT 58.445 40.909 0.00 0.00 0.00 3.55
2262 2388 4.293415 GTTGTGAGCCATGAAGAAAACAG 58.707 43.478 0.00 0.00 0.00 3.16
2277 2404 4.022068 AGCATACAATTTGTGGGTTGTGAG 60.022 41.667 12.30 0.00 38.84 3.51
2497 2628 0.036010 ATGTCGAGTCCCAAGCAAGG 60.036 55.000 0.00 0.00 0.00 3.61
2657 2799 7.770433 TGGAACTTGGTCATCATAGTTCTATTG 59.230 37.037 12.04 0.00 39.95 1.90
2658 2800 7.861629 TGGAACTTGGTCATCATAGTTCTATT 58.138 34.615 12.04 0.00 39.95 1.73
2659 2801 7.437713 TGGAACTTGGTCATCATAGTTCTAT 57.562 36.000 12.04 0.00 39.95 1.98
2699 2932 4.014406 TGTATAGTTCCTTGAGCTCGTGA 58.986 43.478 9.64 2.24 0.00 4.35
2702 2935 3.738282 GCATGTATAGTTCCTTGAGCTCG 59.262 47.826 9.64 0.00 0.00 5.03
2822 3055 3.772025 AGAGTGCTTGCATAAGGTAGTCT 59.228 43.478 0.00 0.00 34.40 3.24


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

AutoCloner maintained by Alex Coulton.