Multiple sequence alignment - TraesCS4B01G122500

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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 TraesCS4B01G122500 chr4B 100.000 3111 0 0 1 3111 145532780 145535890 0.000000e+00 5746.0
1 TraesCS4B01G122500 chr1D 94.807 2561 85 16 561 3111 170223963 170221441 0.000000e+00 3949.0
2 TraesCS4B01G122500 chr1D 80.383 418 40 26 182 578 170224444 170224048 2.360000e-71 279.0
3 TraesCS4B01G122500 chr5B 95.315 1921 78 5 1197 3111 459433317 459435231 0.000000e+00 3038.0
4 TraesCS4B01G122500 chr5B 92.857 644 45 1 561 1203 459419198 459419841 0.000000e+00 933.0
5 TraesCS4B01G122500 chr5B 85.013 387 41 14 182 558 674662273 674662652 8.140000e-101 377.0
6 TraesCS4B01G122500 chr5B 80.340 412 44 24 182 573 459418731 459419125 8.500000e-71 278.0
7 TraesCS4B01G122500 chr5B 85.217 115 9 4 574 680 508365806 508365920 9.120000e-21 111.0
8 TraesCS4B01G122500 chr2A 95.972 1589 51 6 1530 3111 11008521 11006939 0.000000e+00 2567.0
9 TraesCS4B01G122500 chr2A 95.547 539 24 0 991 1529 11009101 11008563 0.000000e+00 863.0
10 TraesCS4B01G122500 chr7D 95.155 970 37 2 561 1529 46986459 46987419 0.000000e+00 1522.0
11 TraesCS4B01G122500 chr7D 96.995 832 20 4 1530 2361 46987470 46988296 0.000000e+00 1393.0
12 TraesCS4B01G122500 chr7D 95.801 762 26 2 2356 3111 46990007 46990768 0.000000e+00 1225.0
13 TraesCS4B01G122500 chr7D 85.370 540 43 21 724 1249 580555818 580555301 7.640000e-146 527.0
14 TraesCS4B01G122500 chr7D 94.444 180 3 3 2939 3111 508597634 508597813 1.420000e-68 270.0
15 TraesCS4B01G122500 chr7D 84.561 285 25 4 1495 1776 154630228 154629960 6.620000e-67 265.0
16 TraesCS4B01G122500 chr7D 81.849 292 28 14 1495 1776 29568430 29568154 4.040000e-54 222.0
17 TraesCS4B01G122500 chr7D 84.971 173 16 9 419 584 46986212 46986381 1.920000e-37 167.0
18 TraesCS4B01G122500 chr7D 94.737 38 2 0 3074 3111 626237653 626237616 3.350000e-05 60.2
19 TraesCS4B01G122500 chr7A 89.050 1032 79 9 1257 2259 630098607 630099633 0.000000e+00 1249.0
20 TraesCS4B01G122500 chr7A 91.614 477 37 3 2333 2808 630099629 630100103 0.000000e+00 656.0
21 TraesCS4B01G122500 chr7A 88.847 529 44 11 730 1246 672046226 672045701 1.220000e-178 636.0
22 TraesCS4B01G122500 chr7A 92.929 99 4 3 445 541 501125077 501124980 1.160000e-29 141.0
23 TraesCS4B01G122500 chr6B 96.110 437 16 1 565 1000 700093022 700093458 0.000000e+00 712.0
24 TraesCS4B01G122500 chr6B 89.623 424 23 9 179 584 700092520 700092940 1.280000e-143 520.0
25 TraesCS4B01G122500 chr6B 82.875 327 45 9 888 1207 705497219 705497541 1.830000e-72 283.0
26 TraesCS4B01G122500 chr6B 92.571 175 11 2 561 733 718357176 718357002 1.850000e-62 250.0
27 TraesCS4B01G122500 chr6B 92.771 166 11 1 561 725 646285964 646286129 4.010000e-59 239.0
28 TraesCS4B01G122500 chr7B 89.634 492 42 6 730 1213 648045127 648044637 4.410000e-173 617.0
29 TraesCS4B01G122500 chr5D 87.559 426 43 5 1780 2200 558576461 558576881 4.660000e-133 484.0
30 TraesCS4B01G122500 chr5D 84.912 285 24 9 1495 1776 558576159 558576427 1.420000e-68 270.0
31 TraesCS4B01G122500 chr5D 90.506 158 14 1 2668 2825 558576909 558577065 1.130000e-49 207.0
32 TraesCS4B01G122500 chr3B 84.197 386 42 9 2668 3046 751820277 751820650 1.060000e-94 357.0
33 TraesCS4B01G122500 chr3B 82.872 397 43 17 182 558 452563153 452562762 1.790000e-87 333.0
34 TraesCS4B01G122500 chr3B 94.857 175 7 2 561 733 436393170 436393344 3.950000e-69 272.0
35 TraesCS4B01G122500 chr3B 84.321 287 27 3 1495 1778 749153818 749153547 6.620000e-67 265.0
36 TraesCS4B01G122500 chr3B 89.447 199 20 1 2668 2866 749153067 749152870 1.850000e-62 250.0
37 TraesCS4B01G122500 chr4A 83.668 398 38 19 183 558 36004230 36003838 1.780000e-92 350.0
38 TraesCS4B01G122500 chr4D 83.038 395 41 19 182 558 462624405 462624791 4.970000e-88 335.0
39 TraesCS4B01G122500 chr4D 82.234 394 44 19 182 556 461224579 461224965 1.800000e-82 316.0
40 TraesCS4B01G122500 chr2B 82.872 397 44 17 182 558 553880196 553880588 4.970000e-88 335.0
41 TraesCS4B01G122500 chr2B 95.808 167 6 1 561 726 549375249 549375415 5.110000e-68 268.0
42 TraesCS4B01G122500 chr2B 100.000 33 0 0 526 558 351182581 351182613 9.320000e-06 62.1
43 TraesCS4B01G122500 chr5A 82.500 400 43 19 182 558 310728836 310728441 2.990000e-85 326.0
44 TraesCS4B01G122500 chr3D 82.071 396 44 20 183 558 459309830 459310218 2.330000e-81 313.0
45 TraesCS4B01G122500 chr3D 82.927 287 22 9 1495 1776 107217115 107217379 1.870000e-57 233.0
46 TraesCS4B01G122500 chr6D 82.407 324 39 11 888 1199 462701443 462701760 1.840000e-67 267.0
47 TraesCS4B01G122500 chrUn 81.985 272 24 14 1495 1756 480942145 480941889 1.130000e-49 207.0
48 TraesCS4B01G122500 chr6A 94.949 99 2 3 445 541 571279362 571279265 5.370000e-33 152.0
49 TraesCS4B01G122500 chr3A 92.929 99 4 3 445 541 91449082 91449179 1.160000e-29 141.0
50 TraesCS4B01G122500 chr3A 92.857 98 4 3 446 541 425585011 425585107 4.180000e-29 139.0


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 TraesCS4B01G122500 chr4B 145532780 145535890 3110 False 5746.000000 5746 100.0000 1 3111 1 chr4B.!!$F1 3110
1 TraesCS4B01G122500 chr1D 170221441 170224444 3003 True 2114.000000 3949 87.5950 182 3111 2 chr1D.!!$R1 2929
2 TraesCS4B01G122500 chr5B 459433317 459435231 1914 False 3038.000000 3038 95.3150 1197 3111 1 chr5B.!!$F1 1914
3 TraesCS4B01G122500 chr5B 459418731 459419841 1110 False 605.500000 933 86.5985 182 1203 2 chr5B.!!$F4 1021
4 TraesCS4B01G122500 chr2A 11006939 11009101 2162 True 1715.000000 2567 95.7595 991 3111 2 chr2A.!!$R1 2120
5 TraesCS4B01G122500 chr7D 46986212 46990768 4556 False 1076.750000 1522 93.2305 419 3111 4 chr7D.!!$F2 2692
6 TraesCS4B01G122500 chr7D 580555301 580555818 517 True 527.000000 527 85.3700 724 1249 1 chr7D.!!$R3 525
7 TraesCS4B01G122500 chr7A 630098607 630100103 1496 False 952.500000 1249 90.3320 1257 2808 2 chr7A.!!$F1 1551
8 TraesCS4B01G122500 chr7A 672045701 672046226 525 True 636.000000 636 88.8470 730 1246 1 chr7A.!!$R2 516
9 TraesCS4B01G122500 chr6B 700092520 700093458 938 False 616.000000 712 92.8665 179 1000 2 chr6B.!!$F3 821
10 TraesCS4B01G122500 chr5D 558576159 558577065 906 False 320.333333 484 87.6590 1495 2825 3 chr5D.!!$F1 1330
11 TraesCS4B01G122500 chr3B 749152870 749153818 948 True 257.500000 265 86.8840 1495 2866 2 chr3B.!!$R2 1371

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
90 91 0.037447 AGGGCAGGACAAGCTTTCTC 59.963 55.0 0.0 0.0 0.00 2.87 F
889 1047 0.320050 TACGCTTCACACAGGATGCA 59.680 50.0 0.0 0.0 42.53 3.96 F
1251 1428 0.674895 GCTCCTTCGTCTGCCACATT 60.675 55.0 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1415 0.327924 ATTCCCAATGTGGCAGACGA 59.672 50.000 0.00 0.0 35.79 4.20 R
2017 2300 1.176527 ATGGCATTCCTTGAACACCG 58.823 50.000 0.00 0.0 0.00 4.94 R
2975 4983 1.003355 ACCCATGGCTCTGTTGTCG 60.003 57.895 6.09 0.0 0.00 4.35 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
31 32 7.648039 TTGTTCAAGGGTTATTTTGTACAGT 57.352 32.000 0.00 0.00 36.44 3.55
32 33 7.266922 TGTTCAAGGGTTATTTTGTACAGTC 57.733 36.000 0.00 0.00 32.18 3.51
33 34 6.263617 TGTTCAAGGGTTATTTTGTACAGTCC 59.736 38.462 0.00 0.00 32.18 3.85
34 35 5.942961 TCAAGGGTTATTTTGTACAGTCCA 58.057 37.500 0.00 0.00 0.00 4.02
35 36 5.766174 TCAAGGGTTATTTTGTACAGTCCAC 59.234 40.000 0.00 0.00 0.00 4.02
36 37 5.578157 AGGGTTATTTTGTACAGTCCACT 57.422 39.130 0.00 0.00 0.00 4.00
37 38 6.691255 AGGGTTATTTTGTACAGTCCACTA 57.309 37.500 0.00 0.00 0.00 2.74
38 39 7.081857 AGGGTTATTTTGTACAGTCCACTAA 57.918 36.000 0.00 0.00 0.00 2.24
39 40 7.696017 AGGGTTATTTTGTACAGTCCACTAAT 58.304 34.615 0.00 0.00 0.00 1.73
40 41 8.828751 AGGGTTATTTTGTACAGTCCACTAATA 58.171 33.333 0.00 0.00 0.00 0.98
41 42 9.623000 GGGTTATTTTGTACAGTCCACTAATAT 57.377 33.333 0.00 0.00 0.00 1.28
73 74 8.191446 ACCATATCTATATGTCGATCGAAAAGG 58.809 37.037 21.31 9.66 38.73 3.11
74 75 7.649705 CCATATCTATATGTCGATCGAAAAGGG 59.350 40.741 21.31 4.72 38.73 3.95
75 76 4.806330 TCTATATGTCGATCGAAAAGGGC 58.194 43.478 21.31 6.80 0.00 5.19
76 77 2.971660 TATGTCGATCGAAAAGGGCA 57.028 45.000 21.31 12.83 0.00 5.36
77 78 1.656652 ATGTCGATCGAAAAGGGCAG 58.343 50.000 21.31 0.00 0.00 4.85
78 79 0.391130 TGTCGATCGAAAAGGGCAGG 60.391 55.000 21.31 0.00 0.00 4.85
79 80 0.108329 GTCGATCGAAAAGGGCAGGA 60.108 55.000 21.31 0.00 0.00 3.86
80 81 0.108329 TCGATCGAAAAGGGCAGGAC 60.108 55.000 16.99 0.00 0.00 3.85
81 82 0.391130 CGATCGAAAAGGGCAGGACA 60.391 55.000 10.26 0.00 0.00 4.02
82 83 1.821216 GATCGAAAAGGGCAGGACAA 58.179 50.000 0.00 0.00 0.00 3.18
83 84 1.740025 GATCGAAAAGGGCAGGACAAG 59.260 52.381 0.00 0.00 0.00 3.16
84 85 0.889186 TCGAAAAGGGCAGGACAAGC 60.889 55.000 0.00 0.00 0.00 4.01
85 86 0.890996 CGAAAAGGGCAGGACAAGCT 60.891 55.000 0.00 0.00 0.00 3.74
86 87 1.332195 GAAAAGGGCAGGACAAGCTT 58.668 50.000 0.00 0.00 0.00 3.74
87 88 1.688735 GAAAAGGGCAGGACAAGCTTT 59.311 47.619 0.00 0.00 0.00 3.51
88 89 1.332195 AAAGGGCAGGACAAGCTTTC 58.668 50.000 0.00 0.00 0.00 2.62
89 90 0.480252 AAGGGCAGGACAAGCTTTCT 59.520 50.000 0.00 0.00 0.00 2.52
90 91 0.037447 AGGGCAGGACAAGCTTTCTC 59.963 55.000 0.00 0.00 0.00 2.87
91 92 0.037447 GGGCAGGACAAGCTTTCTCT 59.963 55.000 0.00 0.00 0.00 3.10
92 93 1.546548 GGGCAGGACAAGCTTTCTCTT 60.547 52.381 0.00 0.00 0.00 2.85
93 94 2.234143 GGCAGGACAAGCTTTCTCTTT 58.766 47.619 0.00 0.00 0.00 2.52
94 95 2.030451 GGCAGGACAAGCTTTCTCTTTG 60.030 50.000 0.00 0.00 0.00 2.77
95 96 2.880890 GCAGGACAAGCTTTCTCTTTGA 59.119 45.455 0.00 0.00 0.00 2.69
96 97 3.316308 GCAGGACAAGCTTTCTCTTTGAA 59.684 43.478 0.00 0.00 0.00 2.69
97 98 4.791088 GCAGGACAAGCTTTCTCTTTGAAC 60.791 45.833 0.00 0.00 33.88 3.18
98 99 4.578105 CAGGACAAGCTTTCTCTTTGAACT 59.422 41.667 0.00 0.00 33.88 3.01
99 100 4.578105 AGGACAAGCTTTCTCTTTGAACTG 59.422 41.667 0.00 0.00 33.88 3.16
100 101 4.336713 GGACAAGCTTTCTCTTTGAACTGT 59.663 41.667 0.00 0.00 33.88 3.55
101 102 5.491635 ACAAGCTTTCTCTTTGAACTGTC 57.508 39.130 0.00 0.00 33.88 3.51
102 103 4.034510 ACAAGCTTTCTCTTTGAACTGTCG 59.965 41.667 0.00 0.00 33.88 4.35
103 104 3.134458 AGCTTTCTCTTTGAACTGTCGG 58.866 45.455 0.00 0.00 33.88 4.79
104 105 3.131396 GCTTTCTCTTTGAACTGTCGGA 58.869 45.455 0.00 0.00 33.88 4.55
105 106 3.560068 GCTTTCTCTTTGAACTGTCGGAA 59.440 43.478 0.00 0.00 33.88 4.30
106 107 4.214332 GCTTTCTCTTTGAACTGTCGGAAT 59.786 41.667 0.00 0.00 33.88 3.01
107 108 5.278022 GCTTTCTCTTTGAACTGTCGGAATT 60.278 40.000 0.00 0.00 33.88 2.17
108 109 6.693315 TTTCTCTTTGAACTGTCGGAATTT 57.307 33.333 0.00 0.00 33.88 1.82
109 110 6.693315 TTCTCTTTGAACTGTCGGAATTTT 57.307 33.333 0.00 0.00 0.00 1.82
110 111 6.060028 TCTCTTTGAACTGTCGGAATTTTG 57.940 37.500 0.00 0.00 0.00 2.44
111 112 5.008613 TCTCTTTGAACTGTCGGAATTTTGG 59.991 40.000 0.00 0.00 0.00 3.28
112 113 4.884744 TCTTTGAACTGTCGGAATTTTGGA 59.115 37.500 0.00 0.00 0.00 3.53
113 114 4.561735 TTGAACTGTCGGAATTTTGGAC 57.438 40.909 0.00 0.00 0.00 4.02
114 115 3.546724 TGAACTGTCGGAATTTTGGACA 58.453 40.909 6.89 6.89 38.29 4.02
115 116 3.948473 TGAACTGTCGGAATTTTGGACAA 59.052 39.130 8.05 0.00 39.91 3.18
116 117 4.399618 TGAACTGTCGGAATTTTGGACAAA 59.600 37.500 8.05 0.00 39.91 2.83
117 118 5.068460 TGAACTGTCGGAATTTTGGACAAAT 59.932 36.000 0.00 2.03 39.91 2.32
118 119 5.529581 ACTGTCGGAATTTTGGACAAATT 57.470 34.783 0.00 0.00 39.91 1.82
119 120 5.528870 ACTGTCGGAATTTTGGACAAATTC 58.471 37.500 10.36 10.36 42.75 2.17
120 121 5.301805 ACTGTCGGAATTTTGGACAAATTCT 59.698 36.000 15.97 0.00 42.94 2.40
121 122 6.155475 TGTCGGAATTTTGGACAAATTCTT 57.845 33.333 15.97 2.69 42.94 2.52
122 123 6.578023 TGTCGGAATTTTGGACAAATTCTTT 58.422 32.000 15.97 0.91 42.94 2.52
123 124 7.044798 TGTCGGAATTTTGGACAAATTCTTTT 58.955 30.769 15.97 0.00 42.94 2.27
124 125 7.550906 TGTCGGAATTTTGGACAAATTCTTTTT 59.449 29.630 15.97 0.00 42.94 1.94
125 126 9.036671 GTCGGAATTTTGGACAAATTCTTTTTA 57.963 29.630 15.97 0.85 42.94 1.52
126 127 9.771534 TCGGAATTTTGGACAAATTCTTTTTAT 57.228 25.926 15.97 0.00 42.94 1.40
175 176 9.959749 TTTACCTCAAATAAGATGTTGTGTTTC 57.040 29.630 0.00 0.00 0.00 2.78
176 177 7.581213 ACCTCAAATAAGATGTTGTGTTTCA 57.419 32.000 0.00 0.00 0.00 2.69
177 178 7.425606 ACCTCAAATAAGATGTTGTGTTTCAC 58.574 34.615 0.00 0.00 34.56 3.18
178 179 6.578545 CCTCAAATAAGATGTTGTGTTTCACG 59.421 38.462 0.00 0.00 37.14 4.35
179 180 6.434596 TCAAATAAGATGTTGTGTTTCACGG 58.565 36.000 0.00 0.00 37.14 4.94
180 181 2.774439 AAGATGTTGTGTTTCACGGC 57.226 45.000 0.00 0.00 37.14 5.68
213 214 5.046591 TCCTAATGTCTCAGTTGGTAGGTTG 60.047 44.000 0.00 0.00 0.00 3.77
235 236 3.122059 GCGTTTCGCGTTTTATTTTCGTT 60.122 39.130 5.77 0.00 44.55 3.85
251 252 1.019278 CGTTCCACCTCATCCGGTTG 61.019 60.000 6.15 6.15 34.29 3.77
284 285 4.660771 CCTATTTTGATACCTCCTCCCACT 59.339 45.833 0.00 0.00 0.00 4.00
355 357 2.125912 CCCACGCTCTTCAGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
682 836 2.338984 GCCGTGTCCTCGTCAAGT 59.661 61.111 0.00 0.00 0.00 3.16
747 901 1.494960 GCCTCCTTCCTCACATCTCT 58.505 55.000 0.00 0.00 0.00 3.10
759 913 3.071206 ATCTCTGGCGGCGACAGT 61.071 61.111 38.72 20.49 40.10 3.55
889 1047 0.320050 TACGCTTCACACAGGATGCA 59.680 50.000 0.00 0.00 42.53 3.96
1205 1373 1.840650 AGGTCTGTGCTCACTGCCT 60.841 57.895 13.01 13.01 42.00 4.75
1238 1415 1.496001 TGGCACCATATCATGCTCCTT 59.504 47.619 7.48 0.00 41.74 3.36
1249 1426 1.830587 ATGCTCCTTCGTCTGCCACA 61.831 55.000 0.00 0.00 0.00 4.17
1251 1428 0.674895 GCTCCTTCGTCTGCCACATT 60.675 55.000 0.00 0.00 0.00 2.71
1433 1610 5.183904 GGCACCTAAAGATGTTGAACTGATT 59.816 40.000 0.00 0.00 0.00 2.57
1672 1923 9.057089 TCTTGAATTCTGGTTCTTAGAGTTTTC 57.943 33.333 7.05 0.00 0.00 2.29
2017 2300 0.037326 TGTCAAGGAGCATCACCGTC 60.037 55.000 0.00 0.00 36.25 4.79
2116 2404 7.597288 TTCGATTATCTTGGATTGAGACCTA 57.403 36.000 0.00 0.00 0.00 3.08
2215 2505 5.599999 ATTGTACTTTCACCTCGAGCTAT 57.400 39.130 6.99 0.00 0.00 2.97
2427 4435 4.574892 TCATCGCCACTAATGTTTTCAGA 58.425 39.130 0.00 0.00 0.00 3.27
2549 4557 2.223665 GCAAATGGCCATGAGCTCTAAC 60.224 50.000 26.92 1.67 43.05 2.34
2714 4722 2.688446 GGAAAGTAGGCCAATAAGGTGC 59.312 50.000 5.01 0.00 40.61 5.01
2730 4738 5.447624 AAGGTGCTTGTATAACCAACAAC 57.552 39.130 0.00 0.00 36.37 3.32
2775 4783 8.146053 TCTTCCAAGACCATTGACTTAGATTA 57.854 34.615 0.00 0.00 0.00 1.75
2825 4833 2.094700 GTGTCAGAATGGTCGCTCTGTA 60.095 50.000 0.00 0.00 40.06 2.74
2887 4895 3.399181 CTACTTCTGGCCGGCCCA 61.399 66.667 41.75 27.59 42.79 5.36
2898 4906 1.469335 GCCGGCCCATACTACTGCTA 61.469 60.000 18.11 0.00 0.00 3.49
2958 4966 1.270305 GCTTACTGTGCTCCTGTGTCA 60.270 52.381 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.700973 ACTGTACAAAATAACCCTTGAACAATT 58.299 29.630 0.00 0.00 0.00 2.32
6 7 8.245195 ACTGTACAAAATAACCCTTGAACAAT 57.755 30.769 0.00 0.00 0.00 2.71
7 8 7.201839 GGACTGTACAAAATAACCCTTGAACAA 60.202 37.037 0.00 0.00 0.00 2.83
8 9 6.263617 GGACTGTACAAAATAACCCTTGAACA 59.736 38.462 0.00 0.00 0.00 3.18
9 10 6.263617 TGGACTGTACAAAATAACCCTTGAAC 59.736 38.462 0.00 0.00 0.00 3.18
10 11 6.263617 GTGGACTGTACAAAATAACCCTTGAA 59.736 38.462 0.00 0.00 0.00 2.69
11 12 5.766174 GTGGACTGTACAAAATAACCCTTGA 59.234 40.000 0.00 0.00 0.00 3.02
12 13 5.768164 AGTGGACTGTACAAAATAACCCTTG 59.232 40.000 0.00 0.00 0.00 3.61
13 14 5.948842 AGTGGACTGTACAAAATAACCCTT 58.051 37.500 0.00 0.00 0.00 3.95
14 15 5.578157 AGTGGACTGTACAAAATAACCCT 57.422 39.130 0.00 0.00 0.00 4.34
15 16 7.933215 ATTAGTGGACTGTACAAAATAACCC 57.067 36.000 0.00 0.00 0.00 4.11
47 48 8.191446 CCTTTTCGATCGACATATAGATATGGT 58.809 37.037 19.26 0.88 43.38 3.55
48 49 7.649705 CCCTTTTCGATCGACATATAGATATGG 59.350 40.741 19.26 5.45 43.38 2.74
49 50 7.168302 GCCCTTTTCGATCGACATATAGATATG 59.832 40.741 19.26 7.79 44.37 1.78
50 51 7.147897 TGCCCTTTTCGATCGACATATAGATAT 60.148 37.037 19.26 0.00 0.00 1.63
51 52 6.152154 TGCCCTTTTCGATCGACATATAGATA 59.848 38.462 19.26 0.00 0.00 1.98
52 53 5.047306 TGCCCTTTTCGATCGACATATAGAT 60.047 40.000 19.26 0.00 0.00 1.98
53 54 4.279922 TGCCCTTTTCGATCGACATATAGA 59.720 41.667 19.26 0.00 0.00 1.98
54 55 4.556233 TGCCCTTTTCGATCGACATATAG 58.444 43.478 19.26 7.96 0.00 1.31
55 56 4.556233 CTGCCCTTTTCGATCGACATATA 58.444 43.478 19.26 0.00 0.00 0.86
56 57 3.393800 CTGCCCTTTTCGATCGACATAT 58.606 45.455 19.26 0.00 0.00 1.78
57 58 2.483013 CCTGCCCTTTTCGATCGACATA 60.483 50.000 19.26 0.00 0.00 2.29
58 59 1.656652 CTGCCCTTTTCGATCGACAT 58.343 50.000 19.26 0.00 0.00 3.06
59 60 0.391130 CCTGCCCTTTTCGATCGACA 60.391 55.000 19.26 8.97 0.00 4.35
60 61 0.108329 TCCTGCCCTTTTCGATCGAC 60.108 55.000 19.26 5.71 0.00 4.20
61 62 0.108329 GTCCTGCCCTTTTCGATCGA 60.108 55.000 15.15 15.15 0.00 3.59
62 63 0.391130 TGTCCTGCCCTTTTCGATCG 60.391 55.000 9.36 9.36 0.00 3.69
63 64 1.740025 CTTGTCCTGCCCTTTTCGATC 59.260 52.381 0.00 0.00 0.00 3.69
64 65 1.826385 CTTGTCCTGCCCTTTTCGAT 58.174 50.000 0.00 0.00 0.00 3.59
65 66 0.889186 GCTTGTCCTGCCCTTTTCGA 60.889 55.000 0.00 0.00 0.00 3.71
66 67 0.890996 AGCTTGTCCTGCCCTTTTCG 60.891 55.000 0.00 0.00 0.00 3.46
67 68 1.332195 AAGCTTGTCCTGCCCTTTTC 58.668 50.000 0.00 0.00 0.00 2.29
68 69 1.688735 GAAAGCTTGTCCTGCCCTTTT 59.311 47.619 0.00 0.00 0.00 2.27
69 70 1.133356 AGAAAGCTTGTCCTGCCCTTT 60.133 47.619 0.00 0.00 0.00 3.11
70 71 0.480252 AGAAAGCTTGTCCTGCCCTT 59.520 50.000 0.00 0.00 0.00 3.95
71 72 0.037447 GAGAAAGCTTGTCCTGCCCT 59.963 55.000 0.00 0.00 0.00 5.19
72 73 0.037447 AGAGAAAGCTTGTCCTGCCC 59.963 55.000 0.00 0.00 0.00 5.36
73 74 1.902938 AAGAGAAAGCTTGTCCTGCC 58.097 50.000 0.00 0.00 0.00 4.85
74 75 2.880890 TCAAAGAGAAAGCTTGTCCTGC 59.119 45.455 0.00 0.00 0.00 4.85
75 76 4.578105 AGTTCAAAGAGAAAGCTTGTCCTG 59.422 41.667 0.00 1.47 38.13 3.86
76 77 4.578105 CAGTTCAAAGAGAAAGCTTGTCCT 59.422 41.667 0.00 0.00 38.13 3.85
77 78 4.336713 ACAGTTCAAAGAGAAAGCTTGTCC 59.663 41.667 0.00 0.00 38.13 4.02
78 79 5.491635 ACAGTTCAAAGAGAAAGCTTGTC 57.508 39.130 0.00 0.00 38.13 3.18
79 80 4.034510 CGACAGTTCAAAGAGAAAGCTTGT 59.965 41.667 0.00 0.00 38.13 3.16
80 81 4.521943 CGACAGTTCAAAGAGAAAGCTTG 58.478 43.478 0.00 0.00 38.13 4.01
81 82 3.561725 CCGACAGTTCAAAGAGAAAGCTT 59.438 43.478 0.00 0.00 38.13 3.74
82 83 3.134458 CCGACAGTTCAAAGAGAAAGCT 58.866 45.455 0.00 0.00 38.13 3.74
83 84 3.131396 TCCGACAGTTCAAAGAGAAAGC 58.869 45.455 0.00 0.00 38.13 3.51
84 85 5.931441 ATTCCGACAGTTCAAAGAGAAAG 57.069 39.130 0.00 0.00 38.13 2.62
85 86 6.693315 AAATTCCGACAGTTCAAAGAGAAA 57.307 33.333 0.00 0.00 38.13 2.52
86 87 6.459573 CCAAAATTCCGACAGTTCAAAGAGAA 60.460 38.462 0.00 0.00 0.00 2.87
87 88 5.008613 CCAAAATTCCGACAGTTCAAAGAGA 59.991 40.000 0.00 0.00 0.00 3.10
88 89 5.008613 TCCAAAATTCCGACAGTTCAAAGAG 59.991 40.000 0.00 0.00 0.00 2.85
89 90 4.884744 TCCAAAATTCCGACAGTTCAAAGA 59.115 37.500 0.00 0.00 0.00 2.52
90 91 4.976116 GTCCAAAATTCCGACAGTTCAAAG 59.024 41.667 0.00 0.00 0.00 2.77
91 92 4.399618 TGTCCAAAATTCCGACAGTTCAAA 59.600 37.500 0.00 0.00 32.85 2.69
92 93 3.948473 TGTCCAAAATTCCGACAGTTCAA 59.052 39.130 0.00 0.00 32.85 2.69
93 94 3.546724 TGTCCAAAATTCCGACAGTTCA 58.453 40.909 0.00 0.00 32.85 3.18
94 95 4.561735 TTGTCCAAAATTCCGACAGTTC 57.438 40.909 0.00 0.00 37.78 3.01
95 96 4.993029 TTTGTCCAAAATTCCGACAGTT 57.007 36.364 0.00 0.00 37.78 3.16
96 97 5.301805 AGAATTTGTCCAAAATTCCGACAGT 59.698 36.000 16.14 0.00 43.88 3.55
97 98 5.772521 AGAATTTGTCCAAAATTCCGACAG 58.227 37.500 16.14 0.00 43.88 3.51
98 99 5.782893 AGAATTTGTCCAAAATTCCGACA 57.217 34.783 16.14 0.00 43.88 4.35
99 100 7.477144 AAAAGAATTTGTCCAAAATTCCGAC 57.523 32.000 16.14 0.00 43.88 4.79
100 101 9.771534 ATAAAAAGAATTTGTCCAAAATTCCGA 57.228 25.926 16.14 3.03 43.88 4.55
149 150 9.959749 GAAACACAACATCTTATTTGAGGTAAA 57.040 29.630 0.00 0.00 30.38 2.01
150 151 9.126151 TGAAACACAACATCTTATTTGAGGTAA 57.874 29.630 0.00 0.00 30.38 2.85
151 152 8.564574 GTGAAACACAACATCTTATTTGAGGTA 58.435 33.333 0.00 0.00 36.32 3.08
152 153 7.425606 GTGAAACACAACATCTTATTTGAGGT 58.574 34.615 0.00 0.00 36.32 3.85
153 154 6.578545 CGTGAAACACAACATCTTATTTGAGG 59.421 38.462 0.00 0.00 35.74 3.86
154 155 6.578545 CCGTGAAACACAACATCTTATTTGAG 59.421 38.462 0.00 0.00 35.74 3.02
155 156 6.434596 CCGTGAAACACAACATCTTATTTGA 58.565 36.000 0.00 0.00 35.74 2.69
156 157 5.116983 GCCGTGAAACACAACATCTTATTTG 59.883 40.000 0.00 0.00 35.74 2.32
157 158 5.219633 GCCGTGAAACACAACATCTTATTT 58.780 37.500 0.00 0.00 35.74 1.40
158 159 4.277174 TGCCGTGAAACACAACATCTTATT 59.723 37.500 0.00 0.00 35.74 1.40
159 160 3.818210 TGCCGTGAAACACAACATCTTAT 59.182 39.130 0.00 0.00 35.74 1.73
160 161 3.206964 TGCCGTGAAACACAACATCTTA 58.793 40.909 0.00 0.00 35.74 2.10
161 162 2.020720 TGCCGTGAAACACAACATCTT 58.979 42.857 0.00 0.00 35.74 2.40
162 163 1.674359 TGCCGTGAAACACAACATCT 58.326 45.000 0.00 0.00 35.74 2.90
163 164 2.226437 AGATGCCGTGAAACACAACATC 59.774 45.455 18.07 18.07 42.00 3.06
164 165 2.226437 GAGATGCCGTGAAACACAACAT 59.774 45.455 0.00 0.00 35.74 2.71
165 166 1.601903 GAGATGCCGTGAAACACAACA 59.398 47.619 0.00 0.00 35.74 3.33
166 167 1.873591 AGAGATGCCGTGAAACACAAC 59.126 47.619 0.00 0.00 35.74 3.32
167 168 2.254546 AGAGATGCCGTGAAACACAA 57.745 45.000 0.00 0.00 35.74 3.33
168 169 2.299013 AGTAGAGATGCCGTGAAACACA 59.701 45.455 0.00 0.00 35.74 3.72
169 170 2.924290 GAGTAGAGATGCCGTGAAACAC 59.076 50.000 0.00 0.00 35.74 3.32
170 171 2.094182 GGAGTAGAGATGCCGTGAAACA 60.094 50.000 0.00 0.00 35.74 2.83
171 172 2.166664 AGGAGTAGAGATGCCGTGAAAC 59.833 50.000 0.00 0.00 0.00 2.78
172 173 2.457598 AGGAGTAGAGATGCCGTGAAA 58.542 47.619 0.00 0.00 0.00 2.69
173 174 2.145397 AGGAGTAGAGATGCCGTGAA 57.855 50.000 0.00 0.00 0.00 3.18
174 175 3.292492 TTAGGAGTAGAGATGCCGTGA 57.708 47.619 0.00 0.00 0.00 4.35
175 176 3.319405 ACATTAGGAGTAGAGATGCCGTG 59.681 47.826 0.00 0.00 0.00 4.94
176 177 3.567397 ACATTAGGAGTAGAGATGCCGT 58.433 45.455 0.00 0.00 0.00 5.68
177 178 3.823873 AGACATTAGGAGTAGAGATGCCG 59.176 47.826 0.00 0.00 0.00 5.69
178 179 4.830046 TGAGACATTAGGAGTAGAGATGCC 59.170 45.833 0.00 0.00 0.00 4.40
179 180 5.534654 ACTGAGACATTAGGAGTAGAGATGC 59.465 44.000 0.00 0.00 0.00 3.91
180 181 7.424803 CAACTGAGACATTAGGAGTAGAGATG 58.575 42.308 0.00 0.00 0.00 2.90
235 236 0.768622 AAACAACCGGATGAGGTGGA 59.231 50.000 19.77 0.00 45.21 4.02
251 252 8.464404 GGAGGTATCAAAATAGGTACCAAAAAC 58.536 37.037 15.94 0.00 39.20 2.43
284 285 4.980805 GTGGCGGGTCAGCGTGAA 62.981 66.667 0.00 0.00 38.18 3.18
355 357 3.259751 GGCGCGATCGGTGGTTAC 61.260 66.667 18.30 0.00 35.95 2.50
364 366 2.956964 CTTGTCTCGGGCGCGATC 60.957 66.667 26.78 20.98 0.00 3.69
374 376 3.854286 TTTTTCTTCGTCGCTTGTCTC 57.146 42.857 0.00 0.00 0.00 3.36
747 901 3.741830 TTTGTCACTGTCGCCGCCA 62.742 57.895 0.00 0.00 0.00 5.69
759 913 3.073678 CTCATGGTGTCGGAATTTGTCA 58.926 45.455 0.00 0.00 0.00 3.58
791 946 0.323178 GACGGGTGAGTACCTCCTCA 60.323 60.000 0.00 0.00 46.66 3.86
880 1038 3.790437 CCTCCCGCTGCATCCTGT 61.790 66.667 0.00 0.00 0.00 4.00
1095 1258 0.770499 TGGCCTTGGTGATGAAGACA 59.230 50.000 3.32 0.00 0.00 3.41
1205 1373 1.828595 TGGTGCCATAAGTAAGAGCGA 59.171 47.619 0.00 0.00 0.00 4.93
1238 1415 0.327924 ATTCCCAATGTGGCAGACGA 59.672 50.000 0.00 0.00 35.79 4.20
1249 1426 7.147408 ACAGATAAAGAGACTGCTATTCCCAAT 60.147 37.037 0.00 0.00 35.38 3.16
1251 1428 5.663106 ACAGATAAAGAGACTGCTATTCCCA 59.337 40.000 0.00 0.00 35.38 4.37
1384 1561 7.355778 CCTTTTGTGTAGAAAATCTCTCACAC 58.644 38.462 13.76 9.87 39.66 3.82
1433 1610 0.740868 GCATGAGCCTTGCAGTACGA 60.741 55.000 0.00 0.00 39.90 3.43
1456 1633 3.881089 TGTGATATCTGCATGAGCCAAAG 59.119 43.478 3.98 0.00 41.13 2.77
1837 2119 8.080417 CCCTTGCTTCATTCACATAATCATAAG 58.920 37.037 0.00 0.00 0.00 1.73
1900 2183 4.588951 ACGAGGATATGTCAAATCTGCCTA 59.411 41.667 0.00 0.00 0.00 3.93
2017 2300 1.176527 ATGGCATTCCTTGAACACCG 58.823 50.000 0.00 0.00 0.00 4.94
2059 2342 7.086376 AGAATTCAGAATCCAAATTTGTGACG 58.914 34.615 16.73 1.88 0.00 4.35
2427 4435 6.987992 ACAATTTGCAACTTGAAAGATGACAT 59.012 30.769 29.60 6.38 31.18 3.06
2699 4707 4.788925 ATACAAGCACCTTATTGGCCTA 57.211 40.909 3.32 0.00 40.22 3.93
2714 4722 7.876068 TCAAGTAGAGGTTGTTGGTTATACAAG 59.124 37.037 0.00 0.00 36.27 3.16
2730 4738 7.164803 GGAAGAATATCCCAATCAAGTAGAGG 58.835 42.308 0.00 0.00 33.05 3.69
2783 4791 8.206867 TGACACTCATAATTCTCCTAAGGATTG 58.793 37.037 0.00 0.00 32.66 2.67
2785 4793 7.786943 TCTGACACTCATAATTCTCCTAAGGAT 59.213 37.037 0.00 0.00 0.00 3.24
2795 4803 5.277058 GCGACCATTCTGACACTCATAATTC 60.277 44.000 0.00 0.00 0.00 2.17
2825 4833 1.534717 AAGCAACAGCAGGGGCATT 60.535 52.632 0.00 0.00 44.61 3.56
2887 4895 5.589192 GACCACGAACAATAGCAGTAGTAT 58.411 41.667 0.00 0.00 0.00 2.12
2975 4983 1.003355 ACCCATGGCTCTGTTGTCG 60.003 57.895 6.09 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.