Multiple sequence alignment - TraesCS6B01G366000

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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 TraesCS6B01G366000 chr6B 100.000 2786 0 0 1 2786 638512136 638509351 0.000000e+00 5145.0
1 TraesCS6B01G366000 chr6B 90.274 730 66 3 1 729 638545573 638544848 0.000000e+00 950.0
2 TraesCS6B01G366000 chr6D 92.935 1741 110 9 1054 2786 423557500 423555765 0.000000e+00 2521.0
3 TraesCS6B01G366000 chr6D 90.881 329 27 3 727 1052 423558195 423557867 3.290000e-119 438.0
4 TraesCS6B01G366000 chr6D 87.500 216 26 1 727 941 10022397 10022612 5.960000e-62 248.0
5 TraesCS6B01G366000 chr4B 88.707 735 67 4 3 726 559392380 559393109 0.000000e+00 883.0
6 TraesCS6B01G366000 chr4B 87.884 619 58 8 126 729 100199331 100198715 0.000000e+00 712.0
7 TraesCS6B01G366000 chr4B 87.963 216 25 1 727 941 300785294 300785509 1.280000e-63 254.0
8 TraesCS6B01G366000 chr5B 88.394 741 71 6 1 729 219578591 219577854 0.000000e+00 878.0
9 TraesCS6B01G366000 chr5B 87.963 216 25 1 727 941 367470192 367470407 1.280000e-63 254.0
10 TraesCS6B01G366000 chr5B 100.000 29 0 0 2059 2087 41972425 41972397 1.000000e-03 54.7
11 TraesCS6B01G366000 chr1B 88.115 732 76 7 3 726 238759273 238760001 0.000000e+00 859.0
12 TraesCS6B01G366000 chr1B 87.534 738 75 8 3 726 238812596 238813330 0.000000e+00 837.0
13 TraesCS6B01G366000 chr1B 87.123 730 83 9 3 726 47267093 47266369 0.000000e+00 817.0
14 TraesCS6B01G366000 chr1B 85.970 727 86 12 9 728 411577111 411576394 0.000000e+00 763.0
15 TraesCS6B01G366000 chr1B 88.273 631 58 7 108 726 360061764 360062390 0.000000e+00 741.0
16 TraesCS6B01G366000 chr1B 86.749 566 69 4 168 730 373626622 373627184 2.360000e-175 625.0
17 TraesCS6B01G366000 chr1B 84.343 396 60 2 1 394 338026436 338026041 1.210000e-103 387.0
18 TraesCS6B01G366000 chr1B 88.837 215 22 2 727 939 585666847 585667061 2.130000e-66 263.0
19 TraesCS6B01G366000 chr3D 84.828 725 90 19 9 724 344008753 344009466 0.000000e+00 712.0
20 TraesCS6B01G366000 chr3D 100.000 28 0 0 2059 2086 604262606 604262579 5.000000e-03 52.8
21 TraesCS6B01G366000 chr4D 84.024 676 81 20 1 660 53043659 53042995 2.360000e-175 625.0
22 TraesCS6B01G366000 chr4D 81.976 749 106 24 3 729 476826974 476826233 2.370000e-170 608.0
23 TraesCS6B01G366000 chr4D 89.401 217 22 1 727 942 58656377 58656593 3.540000e-69 272.0
24 TraesCS6B01G366000 chr2B 84.288 611 82 12 3 605 449582629 449582025 4.000000e-163 584.0
25 TraesCS6B01G366000 chr4A 88.426 216 24 1 727 941 229508475 229508260 2.750000e-65 259.0
26 TraesCS6B01G366000 chr4A 100.000 28 0 0 2060 2087 577983092 577983119 5.000000e-03 52.8
27 TraesCS6B01G366000 chr7D 88.372 215 24 1 727 940 489998670 489998884 9.900000e-65 257.0
28 TraesCS6B01G366000 chr3A 87.037 216 24 2 727 941 709474030 709474242 9.970000e-60 241.0
29 TraesCS6B01G366000 chr6A 85.799 169 21 3 2341 2508 567806195 567806029 2.850000e-40 176.0
30 TraesCS6B01G366000 chr2A 80.741 135 17 6 2646 2776 541775139 541775268 2.280000e-16 97.1
31 TraesCS6B01G366000 chr7A 95.000 40 2 0 2685 2724 498594842 498594803 2.320000e-06 63.9
32 TraesCS6B01G366000 chr7A 100.000 30 0 0 2057 2086 261705559 261705530 3.880000e-04 56.5
33 TraesCS6B01G366000 chr7B 100.000 29 0 0 2058 2086 626062102 626062074 1.000000e-03 54.7
34 TraesCS6B01G366000 chr1A 96.970 33 0 1 2059 2091 259202264 259202233 1.000000e-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 TraesCS6B01G366000 chr6B 638509351 638512136 2785 True 5145.0 5145 100.000 1 2786 1 chr6B.!!$R1 2785
1 TraesCS6B01G366000 chr6B 638544848 638545573 725 True 950.0 950 90.274 1 729 1 chr6B.!!$R2 728
2 TraesCS6B01G366000 chr6D 423555765 423558195 2430 True 1479.5 2521 91.908 727 2786 2 chr6D.!!$R1 2059
3 TraesCS6B01G366000 chr4B 559392380 559393109 729 False 883.0 883 88.707 3 726 1 chr4B.!!$F2 723
4 TraesCS6B01G366000 chr4B 100198715 100199331 616 True 712.0 712 87.884 126 729 1 chr4B.!!$R1 603
5 TraesCS6B01G366000 chr5B 219577854 219578591 737 True 878.0 878 88.394 1 729 1 chr5B.!!$R2 728
6 TraesCS6B01G366000 chr1B 238759273 238760001 728 False 859.0 859 88.115 3 726 1 chr1B.!!$F1 723
7 TraesCS6B01G366000 chr1B 238812596 238813330 734 False 837.0 837 87.534 3 726 1 chr1B.!!$F2 723
8 TraesCS6B01G366000 chr1B 47266369 47267093 724 True 817.0 817 87.123 3 726 1 chr1B.!!$R1 723
9 TraesCS6B01G366000 chr1B 411576394 411577111 717 True 763.0 763 85.970 9 728 1 chr1B.!!$R3 719
10 TraesCS6B01G366000 chr1B 360061764 360062390 626 False 741.0 741 88.273 108 726 1 chr1B.!!$F3 618
11 TraesCS6B01G366000 chr1B 373626622 373627184 562 False 625.0 625 86.749 168 730 1 chr1B.!!$F4 562
12 TraesCS6B01G366000 chr3D 344008753 344009466 713 False 712.0 712 84.828 9 724 1 chr3D.!!$F1 715
13 TraesCS6B01G366000 chr4D 53042995 53043659 664 True 625.0 625 84.024 1 660 1 chr4D.!!$R1 659
14 TraesCS6B01G366000 chr4D 476826233 476826974 741 True 608.0 608 81.976 3 729 1 chr4D.!!$R2 726
15 TraesCS6B01G366000 chr2B 449582025 449582629 604 True 584.0 584 84.288 3 605 1 chr2B.!!$R1 602

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
57 58 0.731417 ATGGGACGAGTCTACGTTCG 59.269 55.0 5.86 5.86 46.52 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2311 0.321298 GCGTGCTTCCAAGGGAGTAA 60.321 55.0 0.0 0.0 31.21 2.24 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
57 58 0.731417 ATGGGACGAGTCTACGTTCG 59.269 55.000 5.86 5.86 46.52 3.95
342 367 2.919043 GGCTCCCCGGACAATGAT 59.081 61.111 0.73 0.00 0.00 2.45
505 571 2.717639 CCTAAGCCTTGGCATGTACT 57.282 50.000 14.54 0.00 0.00 2.73
523 590 2.136026 ACTCCTTCTTCCCCAAACAGT 58.864 47.619 0.00 0.00 0.00 3.55
664 731 2.363795 CTCTGGAGCCCACCGGTA 60.364 66.667 6.87 0.00 37.55 4.02
770 837 9.994432 CTAACTAAGAAATAGCAAACTGGAATG 57.006 33.333 0.00 0.00 34.78 2.67
774 841 9.383519 CTAAGAAATAGCAAACTGGAATGTCTA 57.616 33.333 0.00 0.00 0.00 2.59
780 847 3.873910 CAAACTGGAATGTCTATCCCGT 58.126 45.455 0.00 0.00 36.14 5.28
818 885 9.594478 ACCTAAAATTTTCTTAACAACACCAAG 57.406 29.630 6.72 0.00 0.00 3.61
846 913 8.816894 TCCTTCATCTCAAACTCACTACTTAAT 58.183 33.333 0.00 0.00 0.00 1.40
901 969 6.675026 CCCTTGCAGTAATCAACATATCATG 58.325 40.000 0.00 0.00 0.00 3.07
942 1010 8.046708 AGTGTATAGCTAATCCATCAACAAACA 58.953 33.333 0.00 0.00 0.00 2.83
943 1011 8.338259 GTGTATAGCTAATCCATCAACAAACAG 58.662 37.037 0.00 0.00 0.00 3.16
946 1014 5.316167 AGCTAATCCATCAACAAACAGTCA 58.684 37.500 0.00 0.00 0.00 3.41
950 1020 4.422073 TCCATCAACAAACAGTCAGTCT 57.578 40.909 0.00 0.00 0.00 3.24
962 1032 2.489722 CAGTCAGTCTCAGAATCGACCA 59.510 50.000 0.00 0.00 0.00 4.02
976 1046 1.068474 CGACCACGTTGACCTTCATC 58.932 55.000 0.00 0.00 34.56 2.92
1002 1072 4.955811 AGTGACCAACTGATCTGTTGTA 57.044 40.909 31.38 20.17 44.01 2.41
1008 1078 8.391106 GTGACCAACTGATCTGTTGTATTAATC 58.609 37.037 31.38 21.62 44.01 1.75
1020 1090 7.606456 TCTGTTGTATTAATCGAAGCCTTTTCT 59.394 33.333 0.00 0.00 0.00 2.52
1022 1092 7.606456 TGTTGTATTAATCGAAGCCTTTTCTCT 59.394 33.333 0.00 0.00 0.00 3.10
1023 1093 8.451748 GTTGTATTAATCGAAGCCTTTTCTCTT 58.548 33.333 0.00 0.00 0.00 2.85
1024 1094 8.561738 TGTATTAATCGAAGCCTTTTCTCTTT 57.438 30.769 0.00 0.00 0.00 2.52
1041 1111 2.102578 CTTTGGAGGGTTAGCAATGGG 58.897 52.381 0.00 0.00 0.00 4.00
1052 1122 1.668826 AGCAATGGGTGGAGGTTAGA 58.331 50.000 0.00 0.00 0.00 2.10
1062 1497 5.788533 TGGGTGGAGGTTAGAAGATTAGAAA 59.211 40.000 0.00 0.00 0.00 2.52
1109 1544 9.469097 TTTACATACAACCTTAATGCCACTATT 57.531 29.630 0.00 0.00 0.00 1.73
1263 1699 3.489355 CCATATCTGGCCAATACAAGCA 58.511 45.455 7.01 0.00 35.23 3.91
1264 1700 4.084287 CCATATCTGGCCAATACAAGCAT 58.916 43.478 7.01 0.00 35.23 3.79
1288 1724 4.508662 AGATAGCAACTTACTGAGCAACC 58.491 43.478 0.00 0.00 0.00 3.77
1296 1732 3.782244 CTGAGCAACCACGAGCGC 61.782 66.667 0.00 0.00 35.48 5.92
1321 1757 1.496060 ATTCCACTAGCCATGACGGA 58.504 50.000 0.00 0.00 36.56 4.69
1349 1785 3.323979 ACGGGATATTACCACTCACCATC 59.676 47.826 0.00 0.00 0.00 3.51
1353 1789 4.038763 GGATATTACCACTCACCATCGTCA 59.961 45.833 0.00 0.00 0.00 4.35
1359 1795 2.430694 CCACTCACCATCGTCATCCTTA 59.569 50.000 0.00 0.00 0.00 2.69
1370 1806 9.035890 ACCATCGTCATCCTTATTCTATTATCA 57.964 33.333 0.00 0.00 0.00 2.15
1371 1807 9.307121 CCATCGTCATCCTTATTCTATTATCAC 57.693 37.037 0.00 0.00 0.00 3.06
1383 1819 6.742559 TTCTATTATCACCAGGTAGTTCCC 57.257 41.667 0.00 0.00 36.75 3.97
1389 1825 0.974383 ACCAGGTAGTTCCCGTTCTG 59.026 55.000 0.00 0.00 36.75 3.02
1398 1834 4.184079 AGTTCCCGTTCTGTACATGTAC 57.816 45.455 25.99 25.99 36.63 2.90
1412 1848 8.343366 TCTGTACATGTACGATTAACATCTCTC 58.657 37.037 26.59 2.38 38.85 3.20
1415 1851 9.517609 GTACATGTACGATTAACATCTCTCTTT 57.482 33.333 19.71 0.00 35.39 2.52
1440 1876 4.658063 TGTTGGTAAAGTTGATTCGGGAT 58.342 39.130 0.00 0.00 0.00 3.85
1459 1895 5.414454 CGGGATGGAAGAACAATTGAACTAA 59.586 40.000 13.59 1.71 0.00 2.24
1494 1930 2.785562 TGTATGTGGTTGTGGCCTTAC 58.214 47.619 3.32 0.00 0.00 2.34
1499 1935 1.136828 TGGTTGTGGCCTTACAGACT 58.863 50.000 3.32 0.00 0.00 3.24
1503 1939 0.320374 TGTGGCCTTACAGACTTCCG 59.680 55.000 3.32 0.00 0.00 4.30
1540 1976 2.363147 AGGGAGGAGGCTGACGTC 60.363 66.667 9.11 9.11 0.00 4.34
1587 2023 2.676121 CAAGGTCATTGGCCGCCA 60.676 61.111 8.43 8.43 35.08 5.69
1633 2069 3.453717 ACTCATGCCATAAGAAGCTCAGA 59.546 43.478 0.00 0.00 0.00 3.27
1642 2078 4.443266 AAGCTCAGAGGCGTCGGC 62.443 66.667 11.43 11.43 37.29 5.54
1648 2084 3.616721 AGAGGCGTCGGCAACTGT 61.617 61.111 21.79 0.00 42.47 3.55
1698 2134 0.553819 TACTGCAACACACCCCCTTT 59.446 50.000 0.00 0.00 0.00 3.11
1700 2136 1.063567 ACTGCAACACACCCCCTTTTA 60.064 47.619 0.00 0.00 0.00 1.52
1701 2137 1.339929 CTGCAACACACCCCCTTTTAC 59.660 52.381 0.00 0.00 0.00 2.01
1742 2181 1.202687 TCCATTGAAGGGCTAGATGCG 60.203 52.381 0.00 0.00 44.05 4.73
1769 2208 8.964420 ACACCGATAAAATTTTGTGTTATGAG 57.036 30.769 13.76 0.00 33.47 2.90
1803 2242 9.283768 TGTTCATCAATAAACTACATGACTTGT 57.716 29.630 0.00 0.00 42.62 3.16
1829 2268 4.002982 TGCAAGCAACTAGTACCAATCAG 58.997 43.478 0.00 0.00 0.00 2.90
1834 2273 7.308348 GCAAGCAACTAGTACCAATCAGTTTAA 60.308 37.037 0.00 0.00 0.00 1.52
1837 2276 7.883311 AGCAACTAGTACCAATCAGTTTAACAT 59.117 33.333 0.00 0.00 0.00 2.71
1879 2318 7.991084 AGTGTTACCTTGTTATTTTACTCCC 57.009 36.000 0.00 0.00 0.00 4.30
1889 2328 5.475564 TGTTATTTTACTCCCTTGGAAGCAC 59.524 40.000 0.00 0.00 0.00 4.40
1896 2335 1.635663 CCCTTGGAAGCACGCGTTAG 61.636 60.000 10.22 0.00 0.00 2.34
1912 2351 6.140895 CACGCGTTAGTAGTAATCTCTCATTG 59.859 42.308 10.22 0.00 0.00 2.82
1917 2356 7.435488 CGTTAGTAGTAATCTCTCATTGGTTGG 59.565 40.741 0.00 0.00 0.00 3.77
1927 2366 4.984295 TCTCATTGGTTGGTCTTTCATCA 58.016 39.130 0.00 0.00 0.00 3.07
1941 2380 7.139392 GGTCTTTCATCAGTCAAAGTTAAACC 58.861 38.462 0.00 0.00 32.37 3.27
1955 2394 9.015367 TCAAAGTTAAACCGATTCCATGATTTA 57.985 29.630 0.00 0.00 0.00 1.40
2006 2445 6.989155 ACCTTAAAATCATCCATGCATCAT 57.011 33.333 0.00 0.00 0.00 2.45
2017 2456 1.478916 CATGCATCATTTGGTCCAGCA 59.521 47.619 0.00 3.91 34.78 4.41
2033 2472 0.811616 AGCATGGTCGCGAGAATTCC 60.812 55.000 10.24 7.54 45.01 3.01
2146 2585 3.455849 TCCATACAATAGGACCACCACA 58.544 45.455 0.00 0.00 38.94 4.17
2147 2586 3.199071 TCCATACAATAGGACCACCACAC 59.801 47.826 0.00 0.00 38.94 3.82
2160 2599 0.700564 ACCACACTGGCCATGAGAAT 59.299 50.000 5.51 0.00 42.67 2.40
2173 2612 4.153117 GCCATGAGAATTATAGCCACGAAG 59.847 45.833 0.00 0.00 0.00 3.79
2182 2621 2.167398 TAGCCACGAAGCACCTCACC 62.167 60.000 0.00 0.00 34.23 4.02
2184 2623 2.029073 CACGAAGCACCTCACCGT 59.971 61.111 0.00 0.00 0.00 4.83
2193 2632 1.937108 GCACCTCACCGTTTCTCTCTG 60.937 57.143 0.00 0.00 0.00 3.35
2212 2651 3.580458 TCTGGACAAGAGAGGAAAGGAAG 59.420 47.826 0.00 0.00 0.00 3.46
2228 2667 0.259065 GAAGGGGAAGCTTTAGGGGG 59.741 60.000 0.00 0.00 0.00 5.40
2232 2671 0.991893 GGGAAGCTTTAGGGGGCCTA 60.992 60.000 0.84 0.00 34.61 3.93
2234 2673 0.183014 GAAGCTTTAGGGGGCCTACC 59.817 60.000 0.84 5.69 35.63 3.18
2265 2704 3.111484 TCCATTACCACTGCTACCATCA 58.889 45.455 0.00 0.00 0.00 3.07
2266 2705 3.134623 TCCATTACCACTGCTACCATCAG 59.865 47.826 0.00 0.00 37.56 2.90
2290 2729 2.350738 GCCCAAAGCCTAAGCACAA 58.649 52.632 0.00 0.00 43.56 3.33
2347 2786 5.528690 GCCATCTACATGCACTATTTCAGAA 59.471 40.000 0.00 0.00 0.00 3.02
2359 2798 8.147058 TGCACTATTTCAGAAGGATCTAGAATC 58.853 37.037 0.00 0.00 33.50 2.52
2372 2811 8.388484 AGGATCTAGAATCACATTATGTTTGC 57.612 34.615 0.00 0.00 0.00 3.68
2392 2831 8.865001 TGTTTGCAAGTTTTACACTTAACAATC 58.135 29.630 0.00 0.70 44.60 2.67
2409 2848 9.916397 CTTAACAATCATCGTCTATGGTTAAAC 57.084 33.333 0.00 0.00 36.76 2.01
2432 2871 7.849804 ACTATTAAGTGCATCTACAAAGGTG 57.150 36.000 0.00 0.00 36.87 4.00
2437 2876 4.324267 AGTGCATCTACAAAGGTGTTACC 58.676 43.478 0.00 0.00 39.30 2.85
2483 2922 0.253327 GGAGGGAGAATGACACACCC 59.747 60.000 0.00 0.00 40.71 4.61
2511 2950 4.541973 AAGATTGGGCTCACATTTTTCC 57.458 40.909 0.00 0.00 0.00 3.13
2529 2968 4.464069 TTCCCGCAAAATAAAGATTGGG 57.536 40.909 0.00 0.00 38.70 4.12
2530 2969 3.436243 TCCCGCAAAATAAAGATTGGGT 58.564 40.909 0.00 0.00 37.67 4.51
2547 2986 7.433680 AGATTGGGTTCACATTTAAAAGTCAC 58.566 34.615 0.00 0.00 0.00 3.67
2561 3000 5.834239 AAAAGTCACGTTAATAGTGGACG 57.166 39.130 12.20 0.00 39.86 4.79
2566 3005 5.575606 AGTCACGTTAATAGTGGACGATTTG 59.424 40.000 12.20 0.00 39.86 2.32
2571 3010 6.090358 ACGTTAATAGTGGACGATTTGTTCTG 59.910 38.462 7.71 0.00 39.85 3.02
2587 3026 3.501828 TGTTCTGATCCCGTGTTGAAATG 59.498 43.478 0.00 0.00 0.00 2.32
2683 3124 7.651027 ACATTGCTTATATTTCCTTTCTGCT 57.349 32.000 0.00 0.00 0.00 4.24
2685 3126 7.977853 ACATTGCTTATATTTCCTTTCTGCTTG 59.022 33.333 0.00 0.00 0.00 4.01
2759 3200 5.987347 AGAATCAACACTCCAAAATGCTTTG 59.013 36.000 0.00 0.00 41.45 2.77
2768 3210 7.665559 ACACTCCAAAATGCTTTGAAGATAGTA 59.334 33.333 0.22 0.00 44.03 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.824425 GCTGGGATGGGATGGGCA 61.824 66.667 0.00 0.00 0.00 5.36
57 58 2.877168 CACTATTGCCTTGCTCATCTCC 59.123 50.000 0.00 0.00 0.00 3.71
504 570 2.959465 ACTGTTTGGGGAAGAAGGAG 57.041 50.000 0.00 0.00 0.00 3.69
505 571 2.158519 GGAACTGTTTGGGGAAGAAGGA 60.159 50.000 0.00 0.00 0.00 3.36
523 590 2.609747 AGTACAGAGTTGCTCCTGGAA 58.390 47.619 0.00 0.00 0.00 3.53
564 631 4.016479 AGAGATAACACCCCTAGTCCTTCA 60.016 45.833 0.00 0.00 0.00 3.02
764 831 4.899457 AGATTACACGGGATAGACATTCCA 59.101 41.667 0.00 0.00 34.77 3.53
770 837 5.105837 GGTATGGAGATTACACGGGATAGAC 60.106 48.000 0.00 0.00 0.00 2.59
774 841 3.858135 AGGTATGGAGATTACACGGGAT 58.142 45.455 0.00 0.00 0.00 3.85
811 878 4.916041 TTGAGATGAAGGATCTTGGTGT 57.084 40.909 0.00 0.00 41.91 4.16
818 885 6.872920 AGTAGTGAGTTTGAGATGAAGGATC 58.127 40.000 0.00 0.00 0.00 3.36
860 927 6.396829 GCAAGGGCAATAAATAGATCACTT 57.603 37.500 0.00 0.00 40.72 3.16
919 987 8.438676 ACTGTTTGTTGATGGATTAGCTATAC 57.561 34.615 0.00 0.00 0.00 1.47
925 993 6.652481 AGACTGACTGTTTGTTGATGGATTAG 59.348 38.462 0.00 0.00 0.00 1.73
927 995 5.380043 AGACTGACTGTTTGTTGATGGATT 58.620 37.500 0.00 0.00 0.00 3.01
942 1010 2.490115 GTGGTCGATTCTGAGACTGACT 59.510 50.000 7.54 0.00 37.52 3.41
943 1011 2.729467 CGTGGTCGATTCTGAGACTGAC 60.729 54.545 0.00 0.68 39.71 3.51
946 1014 1.535833 ACGTGGTCGATTCTGAGACT 58.464 50.000 0.00 0.00 40.62 3.24
950 1020 1.336517 GGTCAACGTGGTCGATTCTGA 60.337 52.381 0.00 0.00 40.62 3.27
962 1032 2.563179 ACTGCTAGATGAAGGTCAACGT 59.437 45.455 0.00 0.00 0.00 3.99
1000 1070 7.910683 CCAAAGAGAAAAGGCTTCGATTAATAC 59.089 37.037 0.00 0.00 0.00 1.89
1002 1072 6.659242 TCCAAAGAGAAAAGGCTTCGATTAAT 59.341 34.615 0.00 0.00 0.00 1.40
1008 1078 2.485814 CCTCCAAAGAGAAAAGGCTTCG 59.514 50.000 0.00 0.00 43.39 3.79
1020 1090 2.291540 CCCATTGCTAACCCTCCAAAGA 60.292 50.000 0.00 0.00 0.00 2.52
1022 1092 1.431243 ACCCATTGCTAACCCTCCAAA 59.569 47.619 0.00 0.00 0.00 3.28
1023 1093 1.080638 ACCCATTGCTAACCCTCCAA 58.919 50.000 0.00 0.00 0.00 3.53
1024 1094 0.331278 CACCCATTGCTAACCCTCCA 59.669 55.000 0.00 0.00 0.00 3.86
1041 1111 8.483758 TGGTATTTCTAATCTTCTAACCTCCAC 58.516 37.037 0.00 0.00 0.00 4.02
1187 1622 7.452501 GGTTTAGGGGTTTATAGTTGTTTTCCT 59.547 37.037 0.00 0.00 0.00 3.36
1253 1689 9.869844 GTAAGTTGCTATCTTATGCTTGTATTG 57.130 33.333 0.00 0.00 31.47 1.90
1258 1694 7.518052 GCTCAGTAAGTTGCTATCTTATGCTTG 60.518 40.741 0.00 0.00 31.47 4.01
1260 1696 5.988561 GCTCAGTAAGTTGCTATCTTATGCT 59.011 40.000 0.00 0.00 31.47 3.79
1263 1699 6.763610 GGTTGCTCAGTAAGTTGCTATCTTAT 59.236 38.462 0.00 0.00 31.47 1.73
1264 1700 6.106673 GGTTGCTCAGTAAGTTGCTATCTTA 58.893 40.000 0.00 0.00 0.00 2.10
1288 1724 1.944676 GGAATACCTCGCGCTCGTG 60.945 63.158 5.56 0.00 36.96 4.35
1296 1732 2.628178 TCATGGCTAGTGGAATACCTCG 59.372 50.000 0.00 0.00 37.04 4.63
1321 1757 1.140252 GTGGTAATATCCCGTGGCTGT 59.860 52.381 0.00 0.00 0.00 4.40
1349 1785 7.761704 CCTGGTGATAATAGAATAAGGATGACG 59.238 40.741 0.00 0.00 0.00 4.35
1353 1789 9.845214 ACTACCTGGTGATAATAGAATAAGGAT 57.155 33.333 10.23 0.00 0.00 3.24
1359 1795 6.014499 CGGGAACTACCTGGTGATAATAGAAT 60.014 42.308 10.23 0.00 41.14 2.40
1383 1819 6.858104 TGTTAATCGTACATGTACAGAACG 57.142 37.500 30.17 21.07 35.87 3.95
1389 1825 9.517609 AAAGAGAGATGTTAATCGTACATGTAC 57.482 33.333 23.53 23.53 36.41 2.90
1415 1851 5.360144 TCCCGAATCAACTTTACCAACAAAA 59.640 36.000 0.00 0.00 0.00 2.44
1424 1860 5.429681 TCTTCCATCCCGAATCAACTTTA 57.570 39.130 0.00 0.00 0.00 1.85
1425 1861 4.301072 TCTTCCATCCCGAATCAACTTT 57.699 40.909 0.00 0.00 0.00 2.66
1435 1871 3.758554 AGTTCAATTGTTCTTCCATCCCG 59.241 43.478 5.13 0.00 0.00 5.14
1440 1876 6.959639 AAGCTTAGTTCAATTGTTCTTCCA 57.040 33.333 5.13 0.00 0.00 3.53
1459 1895 8.677300 CAACCACATACAACAAGAATATAAGCT 58.323 33.333 0.00 0.00 0.00 3.74
1494 1930 2.670414 GCTCTGACATTTCGGAAGTCTG 59.330 50.000 10.35 9.83 36.65 3.51
1499 1935 1.798223 CAACGCTCTGACATTTCGGAA 59.202 47.619 0.00 0.00 36.65 4.30
1503 1939 2.143122 TCACCAACGCTCTGACATTTC 58.857 47.619 0.00 0.00 0.00 2.17
1540 1976 5.471797 TGTGTAATGGTTGTAATCTGTGGTG 59.528 40.000 0.00 0.00 0.00 4.17
1587 2023 4.314440 ACGTGCGGATGGTGCAGT 62.314 61.111 0.00 0.00 44.21 4.40
1633 2069 3.165160 AAGACAGTTGCCGACGCCT 62.165 57.895 0.00 0.00 0.00 5.52
1666 2102 3.940852 TGTTGCAGTAATATGAGCACCTG 59.059 43.478 0.00 0.00 36.62 4.00
1712 2151 2.103094 CCCTTCAATGGAGCGTCTCATA 59.897 50.000 8.71 0.00 31.08 2.15
1742 2181 8.024285 TCATAACACAAAATTTTATCGGTGTCC 58.976 33.333 19.25 0.00 38.42 4.02
1769 2208 8.236586 TGTAGTTTATTGATGAACAAGATGTGC 58.763 33.333 2.16 0.00 42.02 4.57
1803 2242 4.610605 TGGTACTAGTTGCTTGCAGTAA 57.389 40.909 0.00 0.00 0.00 2.24
1806 2245 4.002982 TGATTGGTACTAGTTGCTTGCAG 58.997 43.478 0.00 0.00 0.00 4.41
1856 2295 7.991084 AGGGAGTAAAATAACAAGGTAACAC 57.009 36.000 0.00 0.00 41.41 3.32
1857 2296 7.449086 CCAAGGGAGTAAAATAACAAGGTAACA 59.551 37.037 0.00 0.00 41.41 2.41
1872 2311 0.321298 GCGTGCTTCCAAGGGAGTAA 60.321 55.000 0.00 0.00 31.21 2.24
1879 2318 1.654105 CTACTAACGCGTGCTTCCAAG 59.346 52.381 14.98 4.61 0.00 3.61
1889 2328 5.625721 CCAATGAGAGATTACTACTAACGCG 59.374 44.000 3.53 3.53 0.00 6.01
1896 2335 6.879400 AGACCAACCAATGAGAGATTACTAC 58.121 40.000 0.00 0.00 0.00 2.73
1912 2351 4.580580 ACTTTGACTGATGAAAGACCAACC 59.419 41.667 0.00 0.00 34.02 3.77
1917 2356 6.851330 CGGTTTAACTTTGACTGATGAAAGAC 59.149 38.462 0.00 0.00 34.02 3.01
1927 2366 6.001460 TCATGGAATCGGTTTAACTTTGACT 58.999 36.000 0.00 0.00 0.00 3.41
1955 2394 3.055891 GGCCATGGCAGTTGTTTAGAAAT 60.056 43.478 36.56 0.00 44.11 2.17
2006 2445 1.971167 GCGACCATGCTGGACCAAA 60.971 57.895 8.91 0.00 40.96 3.28
2017 2456 1.338674 TGTTGGAATTCTCGCGACCAT 60.339 47.619 15.20 2.97 0.00 3.55
2146 2585 4.026356 GGCTATAATTCTCATGGCCAGT 57.974 45.455 13.05 0.00 46.31 4.00
2160 2599 1.828595 TGAGGTGCTTCGTGGCTATAA 59.171 47.619 4.36 0.00 0.00 0.98
2173 2612 0.318762 AGAGAGAAACGGTGAGGTGC 59.681 55.000 0.00 0.00 0.00 5.01
2193 2632 2.026729 CCCTTCCTTTCCTCTCTTGTCC 60.027 54.545 0.00 0.00 0.00 4.02
2212 2651 2.279073 GCCCCCTAAAGCTTCCCC 59.721 66.667 0.00 0.00 0.00 4.81
2232 2671 0.252197 GTAATGGAGGCCTTGTCGGT 59.748 55.000 6.77 0.00 34.25 4.69
2234 2673 0.251916 TGGTAATGGAGGCCTTGTCG 59.748 55.000 6.77 0.00 0.00 4.35
2242 2681 1.837439 TGGTAGCAGTGGTAATGGAGG 59.163 52.381 3.06 0.00 0.00 4.30
2290 2729 1.078709 CCAATGACGCGACTTGATGT 58.921 50.000 15.93 0.00 0.00 3.06
2347 2786 7.994911 TGCAAACATAATGTGATTCTAGATCCT 59.005 33.333 0.00 0.00 0.00 3.24
2359 2798 8.351495 AGTGTAAAACTTGCAAACATAATGTG 57.649 30.769 0.00 0.00 34.57 3.21
2409 2848 7.849804 ACACCTTTGTAGATGCACTTAATAG 57.150 36.000 0.00 0.00 32.60 1.73
2414 2853 4.760204 GGTAACACCTTTGTAGATGCACTT 59.240 41.667 0.00 0.00 33.55 3.16
2432 2871 7.122138 AGTATTAAGGGTCAGCTTAGGTAAC 57.878 40.000 0.00 0.00 0.00 2.50
2437 2876 7.069578 TCCTGTTAGTATTAAGGGTCAGCTTAG 59.930 40.741 0.00 0.00 0.00 2.18
2483 2922 5.649782 ATGTGAGCCCAATCTTAACAAAG 57.350 39.130 0.00 0.00 0.00 2.77
2511 2950 4.625311 GTGAACCCAATCTTTATTTTGCGG 59.375 41.667 0.00 0.00 0.00 5.69
2547 2986 6.309494 TCAGAACAAATCGTCCACTATTAACG 59.691 38.462 0.00 0.00 37.74 3.18
2561 3000 3.751175 TCAACACGGGATCAGAACAAATC 59.249 43.478 0.00 0.00 0.00 2.17
2566 3005 3.119849 CCATTTCAACACGGGATCAGAAC 60.120 47.826 0.00 0.00 0.00 3.01
2571 3010 1.743394 GGACCATTTCAACACGGGATC 59.257 52.381 0.00 0.00 0.00 3.36
2587 3026 8.044908 TGGATTTTTACTGTTCATAGTAGGACC 58.955 37.037 0.00 0.00 34.84 4.46
2660 3100 7.977853 ACAAGCAGAAAGGAAATATAAGCAATG 59.022 33.333 0.00 0.00 0.00 2.82
2674 3115 8.653338 CATCATGAAAATTTACAAGCAGAAAGG 58.347 33.333 0.00 0.00 0.00 3.11
2712 3153 2.808906 ATTTTAGCCCAGACCTCCAC 57.191 50.000 0.00 0.00 0.00 4.02
2759 3200 7.875041 TGCTCATGCTCCTAAAATACTATCTTC 59.125 37.037 0.00 0.00 40.48 2.87


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

AutoCloner maintained by Alex Coulton.