Multiple sequence alignment - TraesCS6D01G198400

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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 TraesCS6D01G198400 chr6D 100.000 2646 0 0 1 2646 276457887 276455242 0.000000e+00 4887.0
1 TraesCS6D01G198400 chr6D 93.961 414 23 2 2234 2646 175236835 175236423 2.550000e-175 625.0
2 TraesCS6D01G198400 chr6D 100.000 67 0 0 2948 3014 276454940 276454874 1.130000e-24 124.0
3 TraesCS6D01G198400 chr6D 97.015 67 2 0 2948 3014 144893653 144893587 2.460000e-21 113.0
4 TraesCS6D01G198400 chr6D 97.015 67 2 0 2948 3014 176866716 176866650 2.460000e-21 113.0
5 TraesCS6D01G198400 chr6B 93.232 1980 76 23 253 2192 438387675 438385714 0.000000e+00 2861.0
6 TraesCS6D01G198400 chr6A 94.698 1207 50 8 993 2192 399721984 399723183 0.000000e+00 1862.0
7 TraesCS6D01G198400 chr6A 94.876 605 22 5 360 956 399721375 399721978 0.000000e+00 937.0
8 TraesCS6D01G198400 chr6A 94.118 102 5 1 92 192 399720980 399721081 1.450000e-33 154.0
9 TraesCS6D01G198400 chr6A 86.184 152 8 6 189 340 399721120 399721258 5.200000e-33 152.0
10 TraesCS6D01G198400 chr3D 86.084 927 79 27 1145 2060 575726031 575726918 0.000000e+00 952.0
11 TraesCS6D01G198400 chr3D 81.913 1056 133 28 993 2011 577255877 577254843 0.000000e+00 839.0
12 TraesCS6D01G198400 chr3D 94.699 415 16 4 2235 2646 262984772 262984361 9.110000e-180 640.0
13 TraesCS6D01G198400 chr3D 91.411 326 22 1 1477 1796 577264186 577263861 2.760000e-120 442.0
14 TraesCS6D01G198400 chr3D 79.412 238 24 12 1917 2130 577263863 577263627 8.710000e-31 145.0
15 TraesCS6D01G198400 chr3D 77.215 237 30 16 856 1075 577264653 577264424 1.900000e-22 117.0
16 TraesCS6D01G198400 chr3B 85.976 927 81 26 1145 2061 766631424 766632311 0.000000e+00 946.0
17 TraesCS6D01G198400 chr3B 81.741 1183 143 39 913 2060 769056466 769055322 0.000000e+00 920.0
18 TraesCS6D01G198400 chr3A 85.514 925 82 23 1145 2060 711218001 711218882 0.000000e+00 918.0
19 TraesCS6D01G198400 chr3A 84.504 897 85 28 1176 2060 711203149 711204003 0.000000e+00 837.0
20 TraesCS6D01G198400 chr3A 87.067 549 49 8 1473 2011 712571789 712571253 4.300000e-168 601.0
21 TraesCS6D01G198400 chr3A 82.819 518 57 19 1179 1676 712572297 712571792 4.610000e-118 435.0
22 TraesCS6D01G198400 chr3A 74.704 423 49 27 697 1075 711217460 711217868 5.240000e-28 135.0
23 TraesCS6D01G198400 chr5D 95.377 411 18 1 2236 2646 163840138 163839729 0.000000e+00 652.0
24 TraesCS6D01G198400 chr5D 87.246 345 38 4 1670 2011 91405841 91405500 3.640000e-104 388.0
25 TraesCS6D01G198400 chr5D 97.015 67 2 0 2948 3014 163839270 163839204 2.460000e-21 113.0
26 TraesCS6D01G198400 chr5D 97.015 67 2 0 2948 3014 168028619 168028553 2.460000e-21 113.0
27 TraesCS6D01G198400 chr5D 89.583 48 5 0 31 78 92441226 92441179 9.020000e-06 62.1
28 TraesCS6D01G198400 chr7D 95.086 407 16 2 2243 2646 564182449 564182854 3.280000e-179 638.0
29 TraesCS6D01G198400 chr7D 94.621 409 17 5 2238 2646 601702729 601703132 1.970000e-176 628.0
30 TraesCS6D01G198400 chr7D 94.132 409 20 3 2238 2646 420786479 420786883 1.190000e-173 619.0
31 TraesCS6D01G198400 chr7D 97.015 67 2 0 2948 3014 564182856 564182922 2.460000e-21 113.0
32 TraesCS6D01G198400 chr7D 97.015 67 2 0 2948 3014 601703134 601703200 2.460000e-21 113.0
33 TraesCS6D01G198400 chr7D 84.615 104 10 5 2 102 393099277 393099377 6.880000e-17 99.0
34 TraesCS6D01G198400 chr2D 94.660 412 17 4 2235 2646 109018602 109018196 4.240000e-178 634.0
35 TraesCS6D01G198400 chr2D 93.917 411 21 4 2238 2646 460879177 460879585 4.270000e-173 617.0
36 TraesCS6D01G198400 chr2D 97.015 67 2 0 2948 3014 69922234 69922300 2.460000e-21 113.0
37 TraesCS6D01G198400 chr2D 92.683 41 3 0 32 72 24429824 24429864 3.240000e-05 60.2
38 TraesCS6D01G198400 chr1D 94.132 409 20 4 2238 2646 328407203 328406799 1.190000e-173 619.0
39 TraesCS6D01G198400 chr5A 87.536 345 37 4 1670 2011 85164426 85164085 7.830000e-106 394.0
40 TraesCS6D01G198400 chr5B 86.667 345 40 4 1670 2011 96764631 96764290 7.890000e-101 377.0
41 TraesCS6D01G198400 chr5B 86.420 81 6 4 2 80 227955985 227955908 1.930000e-12 84.2
42 TraesCS6D01G198400 chr4D 78.426 343 65 8 1670 2006 508501908 508502247 6.540000e-52 215.0
43 TraesCS6D01G198400 chr4D 97.015 67 2 0 2948 3014 504366601 504366667 2.460000e-21 113.0
44 TraesCS6D01G198400 chr4D 97.015 67 2 0 2948 3014 504392791 504392857 2.460000e-21 113.0
45 TraesCS6D01G198400 chr1B 77.745 337 66 6 1670 2006 406037241 406037568 6.590000e-47 198.0
46 TraesCS6D01G198400 chrUn 83.516 91 12 3 2 91 49175991 49176079 6.930000e-12 82.4
47 TraesCS6D01G198400 chrUn 83.516 91 12 3 2 91 252592861 252592949 6.930000e-12 82.4
48 TraesCS6D01G198400 chr7B 86.364 66 7 1 2 65 339218599 339218534 1.500000e-08 71.3
49 TraesCS6D01G198400 chr4B 83.562 73 10 1 2 72 367941061 367940989 1.940000e-07 67.6
50 TraesCS6D01G198400 chr7A 94.595 37 2 0 32 68 422471883 422471847 1.170000e-04 58.4


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 TraesCS6D01G198400 chr6D 276454874 276457887 3013 True 2505.500000 4887 100.000000 1 3014 2 chr6D.!!$R4 3013
1 TraesCS6D01G198400 chr6B 438385714 438387675 1961 True 2861.000000 2861 93.232000 253 2192 1 chr6B.!!$R1 1939
2 TraesCS6D01G198400 chr6A 399720980 399723183 2203 False 776.250000 1862 92.469000 92 2192 4 chr6A.!!$F1 2100
3 TraesCS6D01G198400 chr3D 575726031 575726918 887 False 952.000000 952 86.084000 1145 2060 1 chr3D.!!$F1 915
4 TraesCS6D01G198400 chr3D 577254843 577255877 1034 True 839.000000 839 81.913000 993 2011 1 chr3D.!!$R2 1018
5 TraesCS6D01G198400 chr3D 577263627 577264653 1026 True 234.666667 442 82.679333 856 2130 3 chr3D.!!$R3 1274
6 TraesCS6D01G198400 chr3B 766631424 766632311 887 False 946.000000 946 85.976000 1145 2061 1 chr3B.!!$F1 916
7 TraesCS6D01G198400 chr3B 769055322 769056466 1144 True 920.000000 920 81.741000 913 2060 1 chr3B.!!$R1 1147
8 TraesCS6D01G198400 chr3A 711203149 711204003 854 False 837.000000 837 84.504000 1176 2060 1 chr3A.!!$F1 884
9 TraesCS6D01G198400 chr3A 711217460 711218882 1422 False 526.500000 918 80.109000 697 2060 2 chr3A.!!$F2 1363
10 TraesCS6D01G198400 chr3A 712571253 712572297 1044 True 518.000000 601 84.943000 1179 2011 2 chr3A.!!$R1 832
11 TraesCS6D01G198400 chr5D 163839204 163840138 934 True 382.500000 652 96.196000 2236 3014 2 chr5D.!!$R4 778

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
61 62 0.035439 AGAGCCACACCCGTATTTGG 60.035 55.0 0.0 0.0 0.0 3.28 F
71 72 0.390603 CCGTATTTGGGTGTCGAGCA 60.391 55.0 0.0 0.0 0.0 4.26 F
1744 2276 0.101939 GAACCCGAACTACCTAGCGG 59.898 60.0 0.0 0.0 43.2 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 2276 1.201880 GTTCTCGTACTCCACCAGGAC 59.798 57.143 0.0 0.0 39.61 3.85 R
1842 2374 2.903357 CCCCACGACTCCCTCATG 59.097 66.667 0.0 0.0 0.00 3.07 R
2606 3178 1.668419 CTGGTATTCTTTGGAGGGCG 58.332 55.000 0.0 0.0 0.00 6.13 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
27 28 6.911484 ATTGTACTTGTACGTACGTTGTAC 57.089 37.500 27.92 28.70 42.00 2.90
28 29 4.778904 TGTACTTGTACGTACGTTGTACC 58.221 43.478 30.27 21.21 42.00 3.34
29 30 4.513692 TGTACTTGTACGTACGTTGTACCT 59.486 41.667 30.27 7.73 42.00 3.08
30 31 4.568152 ACTTGTACGTACGTTGTACCTT 57.432 40.909 27.92 0.45 41.13 3.50
31 32 4.932146 ACTTGTACGTACGTTGTACCTTT 58.068 39.130 27.92 0.00 41.13 3.11
32 33 6.067263 ACTTGTACGTACGTTGTACCTTTA 57.933 37.500 27.92 1.29 41.13 1.85
33 34 6.677913 ACTTGTACGTACGTTGTACCTTTAT 58.322 36.000 27.92 0.00 41.13 1.40
34 35 7.812648 ACTTGTACGTACGTTGTACCTTTATA 58.187 34.615 27.92 0.00 41.13 0.98
35 36 8.458843 ACTTGTACGTACGTTGTACCTTTATAT 58.541 33.333 27.92 0.00 41.13 0.86
36 37 9.929722 CTTGTACGTACGTTGTACCTTTATATA 57.070 33.333 27.92 0.00 41.13 0.86
55 56 6.869206 ATATATATAAAGAGCCACACCCGT 57.131 37.500 0.00 0.00 0.00 5.28
56 57 7.966339 ATATATATAAAGAGCCACACCCGTA 57.034 36.000 0.00 0.00 0.00 4.02
57 58 6.869206 ATATATAAAGAGCCACACCCGTAT 57.131 37.500 0.00 0.00 0.00 3.06
58 59 3.926058 ATAAAGAGCCACACCCGTATT 57.074 42.857 0.00 0.00 0.00 1.89
59 60 2.579410 AAAGAGCCACACCCGTATTT 57.421 45.000 0.00 0.00 0.00 1.40
60 61 1.821216 AAGAGCCACACCCGTATTTG 58.179 50.000 0.00 0.00 0.00 2.32
61 62 0.035439 AGAGCCACACCCGTATTTGG 60.035 55.000 0.00 0.00 0.00 3.28
69 70 3.059603 CCCGTATTTGGGTGTCGAG 57.940 57.895 0.00 0.00 44.76 4.04
70 71 1.087771 CCCGTATTTGGGTGTCGAGC 61.088 60.000 0.00 0.00 44.76 5.03
71 72 0.390603 CCGTATTTGGGTGTCGAGCA 60.391 55.000 0.00 0.00 0.00 4.26
72 73 1.651987 CGTATTTGGGTGTCGAGCAT 58.348 50.000 0.00 0.00 0.00 3.79
73 74 2.006888 CGTATTTGGGTGTCGAGCATT 58.993 47.619 0.00 0.00 0.00 3.56
74 75 3.191669 CGTATTTGGGTGTCGAGCATTA 58.808 45.455 0.00 0.00 0.00 1.90
75 76 3.807622 CGTATTTGGGTGTCGAGCATTAT 59.192 43.478 0.00 0.00 0.00 1.28
76 77 4.272504 CGTATTTGGGTGTCGAGCATTATT 59.727 41.667 0.00 0.00 0.00 1.40
77 78 4.900635 ATTTGGGTGTCGAGCATTATTC 57.099 40.909 0.00 0.00 0.00 1.75
78 79 3.627395 TTGGGTGTCGAGCATTATTCT 57.373 42.857 0.00 0.00 0.00 2.40
79 80 3.179443 TGGGTGTCGAGCATTATTCTC 57.821 47.619 0.00 0.00 0.00 2.87
80 81 2.766263 TGGGTGTCGAGCATTATTCTCT 59.234 45.455 0.00 0.00 0.00 3.10
81 82 3.958147 TGGGTGTCGAGCATTATTCTCTA 59.042 43.478 0.00 0.00 0.00 2.43
82 83 4.404394 TGGGTGTCGAGCATTATTCTCTAA 59.596 41.667 0.00 0.00 0.00 2.10
83 84 5.070446 TGGGTGTCGAGCATTATTCTCTAAT 59.930 40.000 0.00 0.00 0.00 1.73
84 85 5.635700 GGGTGTCGAGCATTATTCTCTAATC 59.364 44.000 0.00 0.00 0.00 1.75
85 86 6.451393 GGTGTCGAGCATTATTCTCTAATCT 58.549 40.000 0.00 0.00 0.00 2.40
86 87 6.926272 GGTGTCGAGCATTATTCTCTAATCTT 59.074 38.462 0.00 0.00 0.00 2.40
87 88 8.082852 GGTGTCGAGCATTATTCTCTAATCTTA 58.917 37.037 0.00 0.00 0.00 2.10
88 89 9.464714 GTGTCGAGCATTATTCTCTAATCTTAA 57.535 33.333 0.00 0.00 0.00 1.85
89 90 9.464714 TGTCGAGCATTATTCTCTAATCTTAAC 57.535 33.333 0.00 0.00 0.00 2.01
90 91 9.464714 GTCGAGCATTATTCTCTAATCTTAACA 57.535 33.333 0.00 0.00 0.00 2.41
128 130 3.303495 CGTTCGTCGCTTATGACTTTCAT 59.697 43.478 0.00 0.00 40.72 2.57
136 138 6.524586 GTCGCTTATGACTTTCATCTTTTTGG 59.475 38.462 0.00 0.00 38.26 3.28
138 140 7.121168 TCGCTTATGACTTTCATCTTTTTGGAT 59.879 33.333 0.00 0.00 38.26 3.41
186 188 7.713764 AGTTTTATTGCATTTCACCTTCAAC 57.286 32.000 0.00 0.00 0.00 3.18
258 302 9.988815 ATCCAGATCATTACACTTGTACTATTC 57.011 33.333 0.00 0.00 0.00 1.75
340 384 6.228616 TCCAACATTGTATCTTCCGATGTA 57.771 37.500 0.00 0.00 31.24 2.29
343 387 6.018751 CCAACATTGTATCTTCCGATGTACTG 60.019 42.308 0.00 0.00 31.24 2.74
347 391 6.961359 TTGTATCTTCCGATGTACTGTTTG 57.039 37.500 0.00 0.00 0.00 2.93
349 393 7.160547 TGTATCTTCCGATGTACTGTTTGTA 57.839 36.000 0.00 0.00 0.00 2.41
350 394 7.778083 TGTATCTTCCGATGTACTGTTTGTAT 58.222 34.615 0.00 0.00 33.23 2.29
351 395 7.919091 TGTATCTTCCGATGTACTGTTTGTATC 59.081 37.037 0.00 0.00 33.23 2.24
352 396 6.525578 TCTTCCGATGTACTGTTTGTATCT 57.474 37.500 0.00 0.00 33.23 1.98
362 421 8.289440 TGTACTGTTTGTATCTTTCGTTAGTG 57.711 34.615 0.00 0.00 33.23 2.74
403 545 5.768662 TGTTTTCATACCATTTCACCGGTAA 59.231 36.000 6.87 0.00 41.03 2.85
423 565 6.403636 CGGTAACTTGTACGTAACCACTATCT 60.404 42.308 11.38 0.00 0.00 1.98
424 566 6.749118 GGTAACTTGTACGTAACCACTATCTG 59.251 42.308 0.00 0.00 0.00 2.90
444 586 3.879295 CTGATTTTCGTATCATGCCCTGT 59.121 43.478 0.00 0.00 34.24 4.00
509 651 7.324935 TCATAGCACTAGTTTGGTATTTTCGA 58.675 34.615 0.00 0.00 37.95 3.71
520 662 8.724229 AGTTTGGTATTTTCGAGGTACATAAAC 58.276 33.333 16.83 16.83 32.81 2.01
695 844 7.990314 TGTAATGCAGTATGTATGTATGGTTGT 59.010 33.333 0.00 0.00 41.90 3.32
974 1168 1.132643 CACCAGAGTACGGTAGTCAGC 59.867 57.143 21.62 0.00 34.02 4.26
991 1185 3.257561 CAACCGGCGAGATCAGCG 61.258 66.667 9.30 5.52 35.00 5.18
1108 1312 1.075050 CTGCCATATTCTGCCCTGGAT 59.925 52.381 0.00 0.00 0.00 3.41
1537 2069 1.817209 GTCCCTGAGACGGTGATCC 59.183 63.158 0.00 0.00 35.30 3.36
1744 2276 0.101939 GAACCCGAACTACCTAGCGG 59.898 60.000 0.00 0.00 43.20 5.52
2217 2789 9.634163 CATTATAACTAAACACTTTTCCAACCC 57.366 33.333 0.00 0.00 0.00 4.11
2218 2790 8.999905 TTATAACTAAACACTTTTCCAACCCT 57.000 30.769 0.00 0.00 0.00 4.34
2219 2791 5.847111 AACTAAACACTTTTCCAACCCTC 57.153 39.130 0.00 0.00 0.00 4.30
2220 2792 5.125367 ACTAAACACTTTTCCAACCCTCT 57.875 39.130 0.00 0.00 0.00 3.69
2221 2793 5.131067 ACTAAACACTTTTCCAACCCTCTC 58.869 41.667 0.00 0.00 0.00 3.20
2222 2794 3.662759 AACACTTTTCCAACCCTCTCA 57.337 42.857 0.00 0.00 0.00 3.27
2223 2795 3.214696 ACACTTTTCCAACCCTCTCAG 57.785 47.619 0.00 0.00 0.00 3.35
2224 2796 2.777692 ACACTTTTCCAACCCTCTCAGA 59.222 45.455 0.00 0.00 0.00 3.27
2225 2797 3.142174 CACTTTTCCAACCCTCTCAGAC 58.858 50.000 0.00 0.00 0.00 3.51
2226 2798 3.049344 ACTTTTCCAACCCTCTCAGACT 58.951 45.455 0.00 0.00 0.00 3.24
2227 2799 4.040461 CACTTTTCCAACCCTCTCAGACTA 59.960 45.833 0.00 0.00 0.00 2.59
2228 2800 4.846940 ACTTTTCCAACCCTCTCAGACTAT 59.153 41.667 0.00 0.00 0.00 2.12
2229 2801 5.310857 ACTTTTCCAACCCTCTCAGACTATT 59.689 40.000 0.00 0.00 0.00 1.73
2230 2802 6.500751 ACTTTTCCAACCCTCTCAGACTATTA 59.499 38.462 0.00 0.00 0.00 0.98
2231 2803 6.546428 TTTCCAACCCTCTCAGACTATTAG 57.454 41.667 0.00 0.00 0.00 1.73
2232 2804 3.961408 TCCAACCCTCTCAGACTATTAGC 59.039 47.826 0.00 0.00 0.00 3.09
2233 2805 3.706594 CCAACCCTCTCAGACTATTAGCA 59.293 47.826 0.00 0.00 0.00 3.49
2234 2806 4.346418 CCAACCCTCTCAGACTATTAGCAT 59.654 45.833 0.00 0.00 0.00 3.79
2241 2813 6.313519 TCTCAGACTATTAGCATTTGGGTT 57.686 37.500 0.00 0.00 0.00 4.11
2254 2826 0.391927 TTGGGTTCCGATAACTGCCG 60.392 55.000 0.00 0.00 0.00 5.69
2355 2927 4.047059 CAAAGCCACAGCCCGCAG 62.047 66.667 0.00 0.00 41.25 5.18
2375 2947 3.601685 CCGGTGTGTGGCAAACCC 61.602 66.667 5.12 5.35 38.47 4.11
2470 3042 3.069980 GACTGCCGCCATCGTCTCT 62.070 63.158 0.00 0.00 0.00 3.10
2483 3055 1.483004 TCGTCTCTCACCTCTCGATCT 59.517 52.381 0.00 0.00 0.00 2.75
2507 3079 3.798954 CTCCATCGCCGGCCTTCTC 62.799 68.421 23.46 0.00 0.00 2.87
2539 3111 1.405526 GCAACCAGAGCAGATCCGTAA 60.406 52.381 0.00 0.00 0.00 3.18
2562 3134 0.953960 CTTCCCACCGCTAACCACAC 60.954 60.000 0.00 0.00 0.00 3.82
2619 3191 2.466186 AACCCCGCCCTCCAAAGAA 61.466 57.895 0.00 0.00 0.00 2.52
2620 3192 1.800229 AACCCCGCCCTCCAAAGAAT 61.800 55.000 0.00 0.00 0.00 2.40
2996 4025 5.933463 TCTGGGCAGAAAATTGCAAATTTAG 59.067 36.000 12.35 9.42 45.86 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.697250 GTACAACGTACGTACAAGTACAATATA 57.303 33.333 28.66 6.09 45.25 0.86
2 3 7.696453 GGTACAACGTACGTACAAGTACAATAT 59.304 37.037 31.32 12.61 45.25 1.28
3 4 7.018826 GGTACAACGTACGTACAAGTACAATA 58.981 38.462 31.32 13.43 45.25 1.90
4 5 5.856455 GGTACAACGTACGTACAAGTACAAT 59.144 40.000 31.32 13.16 45.25 2.71
5 6 5.008217 AGGTACAACGTACGTACAAGTACAA 59.992 40.000 31.32 13.03 45.25 2.41
6 7 4.513692 AGGTACAACGTACGTACAAGTACA 59.486 41.667 31.32 13.34 45.25 2.90
7 8 5.030874 AGGTACAACGTACGTACAAGTAC 57.969 43.478 27.21 27.21 40.84 2.73
8 9 5.682943 AAGGTACAACGTACGTACAAGTA 57.317 39.130 23.12 17.86 40.84 2.24
9 10 4.568152 AAGGTACAACGTACGTACAAGT 57.432 40.909 23.12 18.83 40.84 3.16
10 11 8.841444 ATATAAAGGTACAACGTACGTACAAG 57.159 34.615 23.12 14.11 40.84 3.16
29 30 8.818860 ACGGGTGTGGCTCTTTATATATATAAA 58.181 33.333 21.30 21.30 36.85 1.40
30 31 8.370266 ACGGGTGTGGCTCTTTATATATATAA 57.630 34.615 10.55 10.55 0.00 0.98
31 32 7.966339 ACGGGTGTGGCTCTTTATATATATA 57.034 36.000 0.00 0.00 0.00 0.86
32 33 6.869206 ACGGGTGTGGCTCTTTATATATAT 57.131 37.500 0.00 0.00 0.00 0.86
33 34 7.966339 ATACGGGTGTGGCTCTTTATATATA 57.034 36.000 0.00 0.00 0.00 0.86
34 35 6.869206 ATACGGGTGTGGCTCTTTATATAT 57.131 37.500 0.00 0.00 0.00 0.86
35 36 6.675413 AATACGGGTGTGGCTCTTTATATA 57.325 37.500 0.00 0.00 0.00 0.86
36 37 5.562298 AATACGGGTGTGGCTCTTTATAT 57.438 39.130 0.00 0.00 0.00 0.86
37 38 5.120399 CAAATACGGGTGTGGCTCTTTATA 58.880 41.667 0.00 0.00 0.00 0.98
38 39 3.926058 AATACGGGTGTGGCTCTTTAT 57.074 42.857 0.00 0.00 0.00 1.40
39 40 3.340034 CAAATACGGGTGTGGCTCTTTA 58.660 45.455 0.00 0.00 0.00 1.85
40 41 2.159382 CAAATACGGGTGTGGCTCTTT 58.841 47.619 0.00 0.00 0.00 2.52
41 42 1.613255 CCAAATACGGGTGTGGCTCTT 60.613 52.381 0.00 0.00 0.00 2.85
42 43 0.035439 CCAAATACGGGTGTGGCTCT 60.035 55.000 0.00 0.00 0.00 4.09
43 44 1.029947 CCCAAATACGGGTGTGGCTC 61.030 60.000 0.00 0.00 41.83 4.70
44 45 1.001393 CCCAAATACGGGTGTGGCT 60.001 57.895 0.00 0.00 41.83 4.75
45 46 3.598327 CCCAAATACGGGTGTGGC 58.402 61.111 0.00 0.00 41.83 5.01
52 53 0.390603 TGCTCGACACCCAAATACGG 60.391 55.000 0.00 0.00 0.00 4.02
53 54 1.651987 ATGCTCGACACCCAAATACG 58.348 50.000 0.00 0.00 0.00 3.06
54 55 5.527582 AGAATAATGCTCGACACCCAAATAC 59.472 40.000 0.00 0.00 0.00 1.89
55 56 5.680619 AGAATAATGCTCGACACCCAAATA 58.319 37.500 0.00 0.00 0.00 1.40
56 57 4.526970 AGAATAATGCTCGACACCCAAAT 58.473 39.130 0.00 0.00 0.00 2.32
57 58 3.938963 GAGAATAATGCTCGACACCCAAA 59.061 43.478 0.00 0.00 0.00 3.28
58 59 3.197766 AGAGAATAATGCTCGACACCCAA 59.802 43.478 0.00 0.00 37.46 4.12
59 60 2.766263 AGAGAATAATGCTCGACACCCA 59.234 45.455 0.00 0.00 37.46 4.51
60 61 3.460857 AGAGAATAATGCTCGACACCC 57.539 47.619 0.00 0.00 37.46 4.61
61 62 6.451393 AGATTAGAGAATAATGCTCGACACC 58.549 40.000 0.00 0.00 37.46 4.16
62 63 7.938563 AAGATTAGAGAATAATGCTCGACAC 57.061 36.000 0.00 0.00 37.46 3.67
63 64 9.464714 GTTAAGATTAGAGAATAATGCTCGACA 57.535 33.333 0.00 0.00 37.46 4.35
64 65 9.464714 TGTTAAGATTAGAGAATAATGCTCGAC 57.535 33.333 0.00 0.00 37.46 4.20
65 66 9.464714 GTGTTAAGATTAGAGAATAATGCTCGA 57.535 33.333 0.00 0.00 37.46 4.04
66 67 9.249457 TGTGTTAAGATTAGAGAATAATGCTCG 57.751 33.333 0.00 0.00 37.46 5.03
75 76 9.035890 TGAGGAAGATGTGTTAAGATTAGAGAA 57.964 33.333 0.00 0.00 0.00 2.87
76 77 8.595362 TGAGGAAGATGTGTTAAGATTAGAGA 57.405 34.615 0.00 0.00 0.00 3.10
77 78 9.658799 TTTGAGGAAGATGTGTTAAGATTAGAG 57.341 33.333 0.00 0.00 0.00 2.43
81 82 8.883731 CGTATTTGAGGAAGATGTGTTAAGATT 58.116 33.333 0.00 0.00 0.00 2.40
82 83 8.041323 ACGTATTTGAGGAAGATGTGTTAAGAT 58.959 33.333 0.00 0.00 28.00 2.40
83 84 7.383687 ACGTATTTGAGGAAGATGTGTTAAGA 58.616 34.615 0.00 0.00 28.00 2.10
84 85 7.596749 ACGTATTTGAGGAAGATGTGTTAAG 57.403 36.000 0.00 0.00 28.00 1.85
85 86 7.148705 CGAACGTATTTGAGGAAGATGTGTTAA 60.149 37.037 0.00 0.00 29.56 2.01
86 87 6.309494 CGAACGTATTTGAGGAAGATGTGTTA 59.691 38.462 0.00 0.00 29.56 2.41
87 88 5.120208 CGAACGTATTTGAGGAAGATGTGTT 59.880 40.000 0.00 0.00 29.56 3.32
88 89 4.625742 CGAACGTATTTGAGGAAGATGTGT 59.374 41.667 0.00 0.00 29.56 3.72
89 90 4.625742 ACGAACGTATTTGAGGAAGATGTG 59.374 41.667 0.00 0.00 29.56 3.21
90 91 4.817517 ACGAACGTATTTGAGGAAGATGT 58.182 39.130 0.00 0.00 30.24 3.06
128 130 5.065914 CCTTGAGTCACTCATCCAAAAAGA 58.934 41.667 8.74 0.00 40.39 2.52
136 138 2.777832 AAGCCCTTGAGTCACTCATC 57.222 50.000 8.74 0.00 40.39 2.92
138 140 1.270305 CGAAAGCCCTTGAGTCACTCA 60.270 52.381 2.36 2.36 38.87 3.41
145 147 1.897560 ACTTTCCGAAAGCCCTTGAG 58.102 50.000 18.92 0.00 42.27 3.02
186 188 7.470289 AAGTAGCTCTTGCATTTAGTAATCG 57.530 36.000 0.00 0.00 42.74 3.34
228 272 8.758829 AGTACAAGTGTAATGATCTGGATACAA 58.241 33.333 0.00 0.00 38.13 2.41
240 284 5.742453 ACTCGCGAATAGTACAAGTGTAATG 59.258 40.000 11.33 0.00 30.89 1.90
247 291 4.187594 TCGTACTCGCGAATAGTACAAG 57.812 45.455 26.66 16.55 46.32 3.16
258 302 5.228635 ACATGTAACTTTATTCGTACTCGCG 59.771 40.000 0.00 0.00 36.96 5.87
309 353 7.442364 CGGAAGATACAATGTTGGATGTAATCT 59.558 37.037 0.00 0.00 44.71 2.40
311 355 7.279615 TCGGAAGATACAATGTTGGATGTAAT 58.720 34.615 0.00 0.00 35.79 1.89
333 377 5.575606 ACGAAAGATACAAACAGTACATCGG 59.424 40.000 0.00 0.00 35.05 4.18
340 384 6.759827 ACACACTAACGAAAGATACAAACAGT 59.240 34.615 0.00 0.00 0.00 3.55
343 387 7.042925 AGTGACACACTAACGAAAGATACAAAC 60.043 37.037 8.59 0.00 43.46 2.93
347 391 5.345202 CCAGTGACACACTAACGAAAGATAC 59.655 44.000 8.59 0.00 43.43 2.24
349 393 4.038763 TCCAGTGACACACTAACGAAAGAT 59.961 41.667 8.59 0.00 43.43 2.40
350 394 3.382227 TCCAGTGACACACTAACGAAAGA 59.618 43.478 8.59 0.00 43.43 2.52
351 395 3.713288 TCCAGTGACACACTAACGAAAG 58.287 45.455 8.59 0.00 43.43 2.62
352 396 3.804786 TCCAGTGACACACTAACGAAA 57.195 42.857 8.59 0.00 43.43 3.46
362 421 3.299340 AACACGAGTATCCAGTGACAC 57.701 47.619 0.00 0.00 39.04 3.67
403 545 6.770746 ATCAGATAGTGGTTACGTACAAGT 57.229 37.500 0.00 0.00 0.00 3.16
423 565 3.884895 ACAGGGCATGATACGAAAATCA 58.115 40.909 5.99 0.00 40.07 2.57
424 566 4.261197 GGAACAGGGCATGATACGAAAATC 60.261 45.833 5.99 0.00 0.00 2.17
509 651 3.994392 CGAGCTTGTGTGTTTATGTACCT 59.006 43.478 0.00 0.00 0.00 3.08
520 662 1.788258 ATCAGTGACGAGCTTGTGTG 58.212 50.000 12.53 6.35 0.00 3.82
582 731 3.184379 GGCATCTTTTTCTTGGCGTTTTC 59.816 43.478 0.00 0.00 0.00 2.29
659 808 0.729116 CTGCATTACAGGTGCTTCCG 59.271 55.000 0.00 0.00 43.19 4.30
695 844 8.981647 GCATTTCTCTCTGCTTTTAAAAATCAA 58.018 29.630 1.66 0.00 35.49 2.57
739 888 2.615447 CAACTGGCTGCTATACACCATG 59.385 50.000 0.00 0.00 31.69 3.66
778 930 3.443045 CAGGGCCGGTTCACATGC 61.443 66.667 1.90 0.00 0.00 4.06
974 1168 3.257561 CGCTGATCTCGCCGGTTG 61.258 66.667 1.90 0.00 0.00 3.77
979 1173 4.257510 TCGCTCGCTGATCTCGCC 62.258 66.667 0.00 0.00 0.00 5.54
986 1180 3.114650 CCATCTCTCGCTCGCTGA 58.885 61.111 0.00 0.00 0.00 4.26
991 1185 2.279120 CGGTGCCATCTCTCGCTC 60.279 66.667 0.00 0.00 0.00 5.03
1035 1239 1.968540 GGCGAGCAGGCAGAAAAGT 60.969 57.895 0.00 0.00 45.92 2.66
1108 1312 1.683365 GTGTAGGCGTGGGGGAGTA 60.683 63.158 0.00 0.00 0.00 2.59
1537 2069 3.181489 GGGTAGTAGTTCATGTCGGTGAG 60.181 52.174 0.00 0.00 0.00 3.51
1744 2276 1.201880 GTTCTCGTACTCCACCAGGAC 59.798 57.143 0.00 0.00 39.61 3.85
1842 2374 2.903357 CCCCACGACTCCCTCATG 59.097 66.667 0.00 0.00 0.00 3.07
2191 2763 9.634163 GGGTTGGAAAAGTGTTTAGTTATAATG 57.366 33.333 0.00 0.00 0.00 1.90
2192 2764 9.596308 AGGGTTGGAAAAGTGTTTAGTTATAAT 57.404 29.630 0.00 0.00 0.00 1.28
2193 2765 8.999905 AGGGTTGGAAAAGTGTTTAGTTATAA 57.000 30.769 0.00 0.00 0.00 0.98
2194 2766 8.442374 AGAGGGTTGGAAAAGTGTTTAGTTATA 58.558 33.333 0.00 0.00 0.00 0.98
2195 2767 7.295340 AGAGGGTTGGAAAAGTGTTTAGTTAT 58.705 34.615 0.00 0.00 0.00 1.89
2196 2768 6.665695 AGAGGGTTGGAAAAGTGTTTAGTTA 58.334 36.000 0.00 0.00 0.00 2.24
2197 2769 5.516044 AGAGGGTTGGAAAAGTGTTTAGTT 58.484 37.500 0.00 0.00 0.00 2.24
2198 2770 5.125367 AGAGGGTTGGAAAAGTGTTTAGT 57.875 39.130 0.00 0.00 0.00 2.24
2199 2771 5.130350 TGAGAGGGTTGGAAAAGTGTTTAG 58.870 41.667 0.00 0.00 0.00 1.85
2200 2772 5.104277 TCTGAGAGGGTTGGAAAAGTGTTTA 60.104 40.000 0.00 0.00 0.00 2.01
2201 2773 3.954258 CTGAGAGGGTTGGAAAAGTGTTT 59.046 43.478 0.00 0.00 0.00 2.83
2202 2774 3.202151 TCTGAGAGGGTTGGAAAAGTGTT 59.798 43.478 0.00 0.00 0.00 3.32
2203 2775 2.777692 TCTGAGAGGGTTGGAAAAGTGT 59.222 45.455 0.00 0.00 0.00 3.55
2204 2776 3.142174 GTCTGAGAGGGTTGGAAAAGTG 58.858 50.000 0.00 0.00 0.00 3.16
2205 2777 3.049344 AGTCTGAGAGGGTTGGAAAAGT 58.951 45.455 0.00 0.00 0.00 2.66
2206 2778 3.778954 AGTCTGAGAGGGTTGGAAAAG 57.221 47.619 0.00 0.00 0.00 2.27
2207 2779 5.843019 AATAGTCTGAGAGGGTTGGAAAA 57.157 39.130 0.00 0.00 0.00 2.29
2208 2780 5.104900 GCTAATAGTCTGAGAGGGTTGGAAA 60.105 44.000 0.00 0.00 0.00 3.13
2209 2781 4.406003 GCTAATAGTCTGAGAGGGTTGGAA 59.594 45.833 0.00 0.00 0.00 3.53
2210 2782 3.961408 GCTAATAGTCTGAGAGGGTTGGA 59.039 47.826 0.00 0.00 0.00 3.53
2211 2783 3.706594 TGCTAATAGTCTGAGAGGGTTGG 59.293 47.826 0.00 0.00 0.00 3.77
2212 2784 5.543507 ATGCTAATAGTCTGAGAGGGTTG 57.456 43.478 0.00 0.00 0.00 3.77
2213 2785 6.352516 CAAATGCTAATAGTCTGAGAGGGTT 58.647 40.000 0.00 0.00 0.00 4.11
2214 2786 5.163258 CCAAATGCTAATAGTCTGAGAGGGT 60.163 44.000 0.00 0.00 0.00 4.34
2215 2787 5.303971 CCAAATGCTAATAGTCTGAGAGGG 58.696 45.833 0.00 0.00 0.00 4.30
2216 2788 5.163258 ACCCAAATGCTAATAGTCTGAGAGG 60.163 44.000 0.00 0.00 0.00 3.69
2217 2789 5.923204 ACCCAAATGCTAATAGTCTGAGAG 58.077 41.667 0.00 0.00 0.00 3.20
2218 2790 5.957771 ACCCAAATGCTAATAGTCTGAGA 57.042 39.130 0.00 0.00 0.00 3.27
2219 2791 5.529060 GGAACCCAAATGCTAATAGTCTGAG 59.471 44.000 0.00 0.00 0.00 3.35
2220 2792 5.437060 GGAACCCAAATGCTAATAGTCTGA 58.563 41.667 0.00 0.00 0.00 3.27
2221 2793 4.273480 CGGAACCCAAATGCTAATAGTCTG 59.727 45.833 0.00 0.00 0.00 3.51
2222 2794 4.163458 TCGGAACCCAAATGCTAATAGTCT 59.837 41.667 0.00 0.00 0.00 3.24
2223 2795 4.448210 TCGGAACCCAAATGCTAATAGTC 58.552 43.478 0.00 0.00 0.00 2.59
2224 2796 4.497291 TCGGAACCCAAATGCTAATAGT 57.503 40.909 0.00 0.00 0.00 2.12
2225 2797 6.710744 AGTTATCGGAACCCAAATGCTAATAG 59.289 38.462 0.00 0.00 0.00 1.73
2226 2798 6.485313 CAGTTATCGGAACCCAAATGCTAATA 59.515 38.462 0.00 0.00 0.00 0.98
2227 2799 5.299279 CAGTTATCGGAACCCAAATGCTAAT 59.701 40.000 0.00 0.00 0.00 1.73
2228 2800 4.638421 CAGTTATCGGAACCCAAATGCTAA 59.362 41.667 0.00 0.00 0.00 3.09
2229 2801 4.196193 CAGTTATCGGAACCCAAATGCTA 58.804 43.478 0.00 0.00 0.00 3.49
2230 2802 3.016736 CAGTTATCGGAACCCAAATGCT 58.983 45.455 0.00 0.00 0.00 3.79
2231 2803 2.479560 GCAGTTATCGGAACCCAAATGC 60.480 50.000 0.00 0.00 35.25 3.56
2232 2804 2.099098 GGCAGTTATCGGAACCCAAATG 59.901 50.000 0.00 0.00 0.00 2.32
2233 2805 2.375146 GGCAGTTATCGGAACCCAAAT 58.625 47.619 0.00 0.00 0.00 2.32
2234 2806 1.828979 GGCAGTTATCGGAACCCAAA 58.171 50.000 0.00 0.00 0.00 3.28
2241 2813 2.202690 CGTGCGGCAGTTATCGGA 60.203 61.111 1.18 0.00 0.00 4.55
2263 2835 0.601057 GGCACAACCACCCAATACAC 59.399 55.000 0.00 0.00 38.86 2.90
2355 2927 2.517402 TTTGCCACACACCGGACC 60.517 61.111 9.46 0.00 0.00 4.46
2358 2930 3.601685 GGGTTTGCCACACACCGG 61.602 66.667 0.00 0.00 35.27 5.28
2391 2963 4.664677 GGCAGCGTGGTCGTCTGT 62.665 66.667 11.20 0.00 40.46 3.41
2470 3042 2.105134 GAGGTAGGAGATCGAGAGGTGA 59.895 54.545 0.00 0.00 0.00 4.02
2483 3055 2.520982 CCGGCGATGGAGGTAGGA 60.521 66.667 9.30 0.00 0.00 2.94
2539 3111 2.609610 TTAGCGGTGGGAAGGCCT 60.610 61.111 0.00 0.00 0.00 5.19
2606 3178 1.668419 CTGGTATTCTTTGGAGGGCG 58.332 55.000 0.00 0.00 0.00 6.13
2954 3983 2.937799 CAGAAGAAGGATGAGAAGCAGC 59.062 50.000 0.00 0.00 0.00 5.25
2996 4025 2.665185 AGTCGCCACCTTCGTTGC 60.665 61.111 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.