Multiple sequence alignment - TraesCS6A01G051400

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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 TraesCS6A01G051400 chr6A 100.000 3434 0 0 1 3434 26766417 26762984 0.000000e+00 6342.0
1 TraesCS6A01G051400 chrUn 95.281 2225 103 2 775 2997 95396598 95394374 0.000000e+00 3526.0
2 TraesCS6A01G051400 chrUn 93.043 345 19 3 3011 3354 95394327 95393987 1.840000e-137 499.0
3 TraesCS6A01G051400 chrUn 85.375 506 43 8 265 767 95397129 95396652 2.380000e-136 496.0
4 TraesCS6A01G051400 chrUn 96.552 58 1 1 3377 3434 95393988 95393932 1.010000e-15 95.3
5 TraesCS6A01G051400 chr6B 93.904 1706 85 13 775 2478 46440736 46439048 0.000000e+00 2556.0
6 TraesCS6A01G051400 chr6B 89.320 515 38 10 256 767 46441290 46440790 6.250000e-177 630.0
7 TraesCS6A01G051400 chr6B 93.427 426 23 4 3011 3434 46436736 46436314 8.090000e-176 627.0
8 TraesCS6A01G051400 chr6B 93.029 373 20 2 2475 2846 46438910 46438543 1.080000e-149 540.0
9 TraesCS6A01G051400 chr6B 91.765 170 9 4 2831 2997 46436952 46436785 7.410000e-57 231.0
10 TraesCS6A01G051400 chr4A 89.232 1718 168 6 769 2478 595382914 595384622 0.000000e+00 2132.0
11 TraesCS6A01G051400 chr4A 90.217 92 5 2 656 744 595382742 595382832 2.170000e-22 117.0


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 TraesCS6A01G051400 chr6A 26762984 26766417 3433 True 6342.000 6342 100.00000 1 3434 1 chr6A.!!$R1 3433
1 TraesCS6A01G051400 chrUn 95393932 95397129 3197 True 1154.075 3526 92.56275 265 3434 4 chrUn.!!$R1 3169
2 TraesCS6A01G051400 chr6B 46436314 46441290 4976 True 916.800 2556 92.28900 256 3434 5 chr6B.!!$R1 3178
3 TraesCS6A01G051400 chr4A 595382742 595384622 1880 False 1124.500 2132 89.72450 656 2478 2 chr4A.!!$F1 1822

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
997 1074 0.322636 AGGAGAGAGTTCTTCGCCGA 60.323 55.0 0.0 0.0 33.82 5.54 F
1482 1565 0.179034 GGATTGCCAAGGAGATCGCT 60.179 55.0 0.0 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2330 0.108424 CAGCCTCCTTCAACCTCGAG 60.108 60.000 5.13 5.13 0.00 4.04 R
3365 5238 1.520666 CACTACCAAGCCTACGGGG 59.479 63.158 0.00 0.00 38.36 5.73 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
20 21 3.529634 CGATTAAAAAGGTGTGCGTGA 57.470 42.857 0.00 0.00 0.00 4.35
21 22 3.223157 CGATTAAAAAGGTGTGCGTGAC 58.777 45.455 0.00 0.00 0.00 3.67
22 23 3.303461 CGATTAAAAAGGTGTGCGTGACA 60.303 43.478 0.00 0.00 0.00 3.58
23 24 4.612712 CGATTAAAAAGGTGTGCGTGACAT 60.613 41.667 0.00 0.00 36.78 3.06
24 25 4.640789 TTAAAAAGGTGTGCGTGACATT 57.359 36.364 0.00 0.00 36.78 2.71
25 26 5.752892 TTAAAAAGGTGTGCGTGACATTA 57.247 34.783 0.00 0.00 36.78 1.90
26 27 4.640789 AAAAAGGTGTGCGTGACATTAA 57.359 36.364 0.00 0.00 36.78 1.40
27 28 4.640789 AAAAGGTGTGCGTGACATTAAA 57.359 36.364 0.00 0.00 36.78 1.52
28 29 4.640789 AAAGGTGTGCGTGACATTAAAA 57.359 36.364 0.00 0.00 36.78 1.52
29 30 4.640789 AAGGTGTGCGTGACATTAAAAA 57.359 36.364 0.00 0.00 36.78 1.94
51 52 7.840342 AAAAACTGTTCACATATTTGCACAA 57.160 28.000 0.00 0.00 0.00 3.33
52 53 8.436046 AAAAACTGTTCACATATTTGCACAAT 57.564 26.923 0.00 0.00 0.00 2.71
53 54 9.539825 AAAAACTGTTCACATATTTGCACAATA 57.460 25.926 0.00 0.00 0.00 1.90
54 55 9.709495 AAAACTGTTCACATATTTGCACAATAT 57.291 25.926 0.00 0.00 0.00 1.28
55 56 8.692110 AACTGTTCACATATTTGCACAATATG 57.308 30.769 24.56 24.56 43.03 1.78
57 58 8.955388 ACTGTTCACATATTTGCACAATATGTA 58.045 29.630 27.77 19.17 46.40 2.29
58 59 9.955208 CTGTTCACATATTTGCACAATATGTAT 57.045 29.630 27.77 15.69 46.40 2.29
59 60 9.733219 TGTTCACATATTTGCACAATATGTATG 57.267 29.630 27.77 21.73 46.40 2.39
60 61 9.184062 GTTCACATATTTGCACAATATGTATGG 57.816 33.333 27.77 21.30 46.40 2.74
61 62 8.462589 TCACATATTTGCACAATATGTATGGT 57.537 30.769 27.77 14.82 46.40 3.55
62 63 8.351461 TCACATATTTGCACAATATGTATGGTG 58.649 33.333 27.77 20.91 46.40 4.17
63 64 7.595875 CACATATTTGCACAATATGTATGGTGG 59.404 37.037 27.77 18.73 46.40 4.61
64 65 4.383850 TTTGCACAATATGTATGGTGGC 57.616 40.909 9.07 3.46 37.94 5.01
65 66 3.010200 TGCACAATATGTATGGTGGCA 57.990 42.857 9.07 5.52 37.94 4.92
66 67 3.564264 TGCACAATATGTATGGTGGCAT 58.436 40.909 9.07 0.00 37.94 4.40
67 68 3.959449 TGCACAATATGTATGGTGGCATT 59.041 39.130 9.07 0.00 37.94 3.56
68 69 4.405036 TGCACAATATGTATGGTGGCATTT 59.595 37.500 9.07 0.00 37.94 2.32
69 70 5.105023 TGCACAATATGTATGGTGGCATTTT 60.105 36.000 9.07 0.00 37.94 1.82
70 71 5.816777 GCACAATATGTATGGTGGCATTTTT 59.183 36.000 9.07 0.00 37.94 1.94
71 72 6.983307 GCACAATATGTATGGTGGCATTTTTA 59.017 34.615 9.07 0.00 37.94 1.52
72 73 7.169645 GCACAATATGTATGGTGGCATTTTTAG 59.830 37.037 9.07 0.00 37.94 1.85
73 74 8.412456 CACAATATGTATGGTGGCATTTTTAGA 58.588 33.333 0.00 0.00 34.64 2.10
74 75 8.976353 ACAATATGTATGGTGGCATTTTTAGAA 58.024 29.630 0.00 0.00 0.00 2.10
75 76 9.814899 CAATATGTATGGTGGCATTTTTAGAAA 57.185 29.630 0.00 0.00 0.00 2.52
186 187 9.935682 ATATTATCGCACTTCATAAAAACTGTG 57.064 29.630 0.00 0.00 0.00 3.66
187 188 5.940192 ATCGCACTTCATAAAAACTGTGA 57.060 34.783 0.00 0.00 0.00 3.58
188 189 5.090652 TCGCACTTCATAAAAACTGTGAC 57.909 39.130 0.00 0.00 0.00 3.67
189 190 4.572795 TCGCACTTCATAAAAACTGTGACA 59.427 37.500 0.00 0.00 0.00 3.58
190 191 5.238432 TCGCACTTCATAAAAACTGTGACAT 59.762 36.000 0.00 0.00 0.00 3.06
191 192 5.914635 CGCACTTCATAAAAACTGTGACATT 59.085 36.000 0.00 0.00 0.00 2.71
192 193 6.417635 CGCACTTCATAAAAACTGTGACATTT 59.582 34.615 0.00 0.00 0.00 2.32
193 194 7.043458 CGCACTTCATAAAAACTGTGACATTTT 60.043 33.333 2.89 2.89 0.00 1.82
194 195 8.603181 GCACTTCATAAAAACTGTGACATTTTT 58.397 29.630 7.69 7.69 40.28 1.94
223 224 6.853279 ATTGAATGTAAGAAAATGTTCGCG 57.147 33.333 0.00 0.00 38.90 5.87
224 225 5.351233 TGAATGTAAGAAAATGTTCGCGT 57.649 34.783 5.77 0.00 38.90 6.01
225 226 5.143660 TGAATGTAAGAAAATGTTCGCGTG 58.856 37.500 5.77 0.00 38.90 5.34
226 227 2.911120 TGTAAGAAAATGTTCGCGTGC 58.089 42.857 5.77 0.15 38.90 5.34
227 228 2.546368 TGTAAGAAAATGTTCGCGTGCT 59.454 40.909 5.77 0.00 38.90 4.40
228 229 2.316119 AAGAAAATGTTCGCGTGCTC 57.684 45.000 5.77 0.00 38.90 4.26
229 230 1.512926 AGAAAATGTTCGCGTGCTCT 58.487 45.000 5.77 0.00 38.90 4.09
230 231 2.683968 AGAAAATGTTCGCGTGCTCTA 58.316 42.857 5.77 0.00 38.90 2.43
231 232 3.064207 AGAAAATGTTCGCGTGCTCTAA 58.936 40.909 5.77 0.00 38.90 2.10
232 233 2.875080 AAATGTTCGCGTGCTCTAAC 57.125 45.000 5.77 2.11 0.00 2.34
233 234 1.790755 AATGTTCGCGTGCTCTAACA 58.209 45.000 5.77 8.76 36.37 2.41
234 235 2.010145 ATGTTCGCGTGCTCTAACAT 57.990 45.000 13.83 13.83 37.65 2.71
235 236 2.640346 TGTTCGCGTGCTCTAACATA 57.360 45.000 5.77 0.00 0.00 2.29
236 237 2.949142 TGTTCGCGTGCTCTAACATAA 58.051 42.857 5.77 0.00 0.00 1.90
237 238 3.318886 TGTTCGCGTGCTCTAACATAAA 58.681 40.909 5.77 0.00 0.00 1.40
238 239 3.930229 TGTTCGCGTGCTCTAACATAAAT 59.070 39.130 5.77 0.00 0.00 1.40
239 240 4.201676 TGTTCGCGTGCTCTAACATAAATG 60.202 41.667 5.77 0.00 0.00 2.32
240 241 3.517602 TCGCGTGCTCTAACATAAATGT 58.482 40.909 5.77 0.00 44.20 2.71
316 317 9.549078 TGTGTATAAGAAAATATTCCGCATGTA 57.451 29.630 0.00 0.00 36.12 2.29
343 344 7.881643 TGAATAATGCACAATGTGGTTTAAC 57.118 32.000 15.78 0.00 33.64 2.01
351 355 6.095580 TGCACAATGTGGTTTAACTTAGACAA 59.904 34.615 15.78 0.00 33.64 3.18
421 425 8.751302 ATAAACGCCAAATAAAAACGAAGATT 57.249 26.923 0.00 0.00 0.00 2.40
449 453 5.702349 AGAAACTGATGAAGAAAAGCAGG 57.298 39.130 0.00 0.00 0.00 4.85
454 458 5.836347 ACTGATGAAGAAAAGCAGGAAAAC 58.164 37.500 0.00 0.00 0.00 2.43
457 461 6.042143 TGATGAAGAAAAGCAGGAAAACAAC 58.958 36.000 0.00 0.00 0.00 3.32
469 473 4.343814 CAGGAAAACAACAGTAACCCCAAT 59.656 41.667 0.00 0.00 0.00 3.16
483 487 5.801531 AACCCCAATAAACTGAAGAAACC 57.198 39.130 0.00 0.00 0.00 3.27
498 502 5.048782 TGAAGAAACCCGATGAAGAAATGTG 60.049 40.000 0.00 0.00 0.00 3.21
500 504 4.697352 AGAAACCCGATGAAGAAATGTGAG 59.303 41.667 0.00 0.00 0.00 3.51
502 506 4.819105 ACCCGATGAAGAAATGTGAGTA 57.181 40.909 0.00 0.00 0.00 2.59
508 512 5.446473 CGATGAAGAAATGTGAGTAACCAGC 60.446 44.000 0.00 0.00 0.00 4.85
523 527 3.159353 ACCAGCCAAAAACGAAGAAAC 57.841 42.857 0.00 0.00 0.00 2.78
581 585 3.507233 TCGAAGGTGTACATCCGTTACTT 59.493 43.478 1.47 0.00 0.00 2.24
598 602 3.433984 TTGGACTGGGCTGCTTGCA 62.434 57.895 0.00 0.00 45.15 4.08
843 918 3.483869 GGCTGAGGGAGGCCGATT 61.484 66.667 0.00 0.00 41.56 3.34
926 1002 2.030562 CTTCCTCCGTGCCACGTT 59.969 61.111 16.99 0.00 40.58 3.99
997 1074 0.322636 AGGAGAGAGTTCTTCGCCGA 60.323 55.000 0.00 0.00 33.82 5.54
1010 1087 1.592669 CGCCGACCATGTCATCTCC 60.593 63.158 0.00 0.00 32.09 3.71
1021 1098 3.842923 CATCTCCGGCGAGCTGGT 61.843 66.667 21.05 0.83 42.88 4.00
1077 1157 0.446222 CACCGGCATTGGTTAAGACG 59.554 55.000 0.00 0.00 41.38 4.18
1084 1164 0.611714 ATTGGTTAAGACGGACGGCT 59.388 50.000 0.00 0.00 32.88 5.52
1103 1183 2.350522 CTCCAAGTTACTTCGCAGCAT 58.649 47.619 0.00 0.00 0.00 3.79
1125 1208 0.735287 GCTTTGGTCGTCGGTCTACC 60.735 60.000 0.00 0.00 33.17 3.18
1126 1209 0.886563 CTTTGGTCGTCGGTCTACCT 59.113 55.000 2.89 0.00 33.65 3.08
1141 1224 4.026300 CCTCTCGGGTCTCTTGCT 57.974 61.111 0.00 0.00 0.00 3.91
1162 1245 1.299976 GGGTCATCCAGCGGAAGTT 59.700 57.895 1.44 0.00 34.34 2.66
1164 1247 1.534729 GGTCATCCAGCGGAAGTTTT 58.465 50.000 1.44 0.00 34.34 2.43
1177 1260 2.328473 GAAGTTTTGCCAAGGAATCGC 58.672 47.619 0.00 0.00 0.00 4.58
1192 1275 3.557054 GGAATCGCCATATGGTAAGCAGA 60.557 47.826 22.79 12.59 37.57 4.26
1197 1280 2.749466 GCCATATGGTAAGCAGAAGGCA 60.749 50.000 22.79 0.00 40.81 4.75
1213 1296 1.591863 GCATACGAAGAGGACGCCC 60.592 63.158 0.00 0.00 0.00 6.13
1228 1311 1.226262 GCCCCTGCGGATAAGGAAA 59.774 57.895 0.00 0.00 36.91 3.13
1333 1416 4.351938 CGAACCCGGCGACACAGA 62.352 66.667 9.30 0.00 0.00 3.41
1413 1496 4.680237 CACGTCCGGCTGGCTTCA 62.680 66.667 6.73 0.00 34.14 3.02
1482 1565 0.179034 GGATTGCCAAGGAGATCGCT 60.179 55.000 0.00 0.00 0.00 4.93
1524 1607 3.286751 TGCAAAGTGCTGGACCGC 61.287 61.111 1.43 0.00 45.31 5.68
1711 1794 1.442857 CGCTTCGACGAGCTGAAGT 60.443 57.895 11.82 0.21 42.77 3.01
1791 1874 2.003548 GAGGGGGTTCATCAGGGCT 61.004 63.158 0.00 0.00 0.00 5.19
1857 1940 1.344953 ACAAGAGGACACTGCACCCA 61.345 55.000 0.00 0.00 0.00 4.51
1929 2012 3.048475 CTCGCTGCTGCACTGCTT 61.048 61.111 16.29 0.00 40.84 3.91
1953 2036 2.430610 GCTCGGTGAGAGGCCAGAT 61.431 63.158 5.01 0.00 46.91 2.90
2247 2330 2.082231 GAAAGGGCTTTTCGGTACCTC 58.918 52.381 10.90 0.00 36.16 3.85
2382 2465 0.037697 AGTCAATCGGCGTGTTGCTA 60.038 50.000 18.11 4.66 45.43 3.49
2397 2480 3.194062 GTTGCTAGACAAGAGGCTGATC 58.806 50.000 0.00 0.00 39.50 2.92
2487 2712 9.352191 GTGTAATTATCTAGAGGAGGTAAGACA 57.648 37.037 0.00 0.00 34.14 3.41
2502 2728 6.296803 AGGTAAGACAAGTGGGTTTCTTTAG 58.703 40.000 0.00 0.00 30.89 1.85
2536 2762 1.227263 CGGTTCCATGCTAGACGGG 60.227 63.158 0.00 0.00 0.00 5.28
2554 2780 2.097466 CGGGTGTATTTGTGATGCTTCC 59.903 50.000 0.00 0.00 0.00 3.46
2565 2791 5.426689 TGTGATGCTTCCTACTGAAATCT 57.573 39.130 0.00 0.00 31.06 2.40
2569 2795 5.877012 TGATGCTTCCTACTGAAATCTGTTC 59.123 40.000 0.00 0.00 31.06 3.18
2572 2798 2.876091 TCCTACTGAAATCTGTTCGCG 58.124 47.619 0.00 0.00 0.00 5.87
2579 2805 2.092055 TGAAATCTGTTCGCGTGAATCG 59.908 45.455 15.45 9.07 43.12 3.34
2601 2827 4.693566 CGCTTTAACCTGTAAGATTGTGGA 59.306 41.667 0.00 0.00 34.07 4.02
2636 2862 7.466746 TGCTAGCAGTTCCAAATATTTCTTT 57.533 32.000 14.93 0.00 0.00 2.52
2669 2895 6.983307 TGAACAGTTTGTTAACAAATCCATGG 59.017 34.615 30.65 19.62 46.12 3.66
2675 2901 7.656948 AGTTTGTTAACAAATCCATGGACATTG 59.343 33.333 30.65 28.25 46.12 2.82
2719 2945 3.325870 TCTGAACAGATAACTTGGCGTG 58.674 45.455 0.00 0.00 31.41 5.34
2858 4690 7.308589 GGGCACACTTATGTAATAGGCTTAATG 60.309 40.741 0.00 0.00 36.72 1.90
2948 4783 9.607285 GTTAGTGTTCATCGTGAAATTTTATGT 57.393 29.630 2.47 0.00 38.22 2.29
2999 4834 8.721133 TGCTCCTACCTGTATATATTTTCAGA 57.279 34.615 11.33 0.00 0.00 3.27
3000 4835 8.807118 TGCTCCTACCTGTATATATTTTCAGAG 58.193 37.037 11.33 0.00 0.00 3.35
3001 4836 7.762159 GCTCCTACCTGTATATATTTTCAGAGC 59.238 40.741 11.33 0.00 0.00 4.09
3002 4837 8.721133 TCCTACCTGTATATATTTTCAGAGCA 57.279 34.615 11.33 0.00 0.00 4.26
3008 4843 9.512588 CCTGTATATATTTTCAGAGCAAAGGAT 57.487 33.333 11.33 0.00 0.00 3.24
3019 4889 3.137533 GAGCAAAGGATAAGCTAGCTGG 58.862 50.000 20.16 0.00 39.02 4.85
3068 4939 6.488006 ACAACTAACAAGCTTGATTGTGATCT 59.512 34.615 32.50 10.03 42.49 2.75
3159 5031 3.572604 ACCGTCTAAGTTTTCTCCTCG 57.427 47.619 0.00 0.00 0.00 4.63
3180 5052 6.540189 CCTCGGAATTTTCAGATAATGTCAGT 59.460 38.462 0.00 0.00 31.23 3.41
3361 5234 4.560128 TGTCATTTAGCAGTGAGTCACTC 58.440 43.478 23.08 16.69 43.43 3.51
3365 5238 2.991434 TAGCAGTGAGTCACTCGAAC 57.009 50.000 23.08 12.50 43.43 3.95
3369 5242 1.080705 GTGAGTCACTCGAACCCCG 60.081 63.158 16.26 0.00 40.25 5.73
3372 5245 0.450983 GAGTCACTCGAACCCCGTAG 59.549 60.000 0.00 0.00 39.75 3.51
3423 5296 3.290710 GGGCTTAATCATGAGCAAGGAA 58.709 45.455 16.66 0.00 39.81 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.223157 GTCACGCACACCTTTTTAATCG 58.777 45.455 0.00 0.00 0.00 3.34
1 2 4.217754 TGTCACGCACACCTTTTTAATC 57.782 40.909 0.00 0.00 0.00 1.75
3 4 4.640789 AATGTCACGCACACCTTTTTAA 57.359 36.364 0.00 0.00 38.04 1.52
5 6 4.640789 TTAATGTCACGCACACCTTTTT 57.359 36.364 0.00 0.00 38.04 1.94
6 7 4.640789 TTTAATGTCACGCACACCTTTT 57.359 36.364 0.00 0.00 38.04 2.27
27 28 7.840342 TTGTGCAAATATGTGAACAGTTTTT 57.160 28.000 6.80 0.00 0.00 1.94
28 29 9.709495 ATATTGTGCAAATATGTGAACAGTTTT 57.291 25.926 7.30 0.00 0.00 2.43
29 30 9.142515 CATATTGTGCAAATATGTGAACAGTTT 57.857 29.630 21.28 0.00 36.40 2.66
30 31 8.306038 ACATATTGTGCAAATATGTGAACAGTT 58.694 29.630 27.73 2.71 46.36 3.16
31 32 7.829725 ACATATTGTGCAAATATGTGAACAGT 58.170 30.769 27.73 7.00 46.36 3.55
39 40 6.587226 GCCACCATACATATTGTGCAAATATG 59.413 38.462 24.56 24.56 43.03 1.78
40 41 6.267242 TGCCACCATACATATTGTGCAAATAT 59.733 34.615 0.00 0.00 30.43 1.28
41 42 5.595952 TGCCACCATACATATTGTGCAAATA 59.404 36.000 0.00 0.00 30.43 1.40
42 43 4.405036 TGCCACCATACATATTGTGCAAAT 59.595 37.500 0.00 0.00 30.43 2.32
43 44 3.766051 TGCCACCATACATATTGTGCAAA 59.234 39.130 0.00 0.00 30.43 3.68
44 45 3.359950 TGCCACCATACATATTGTGCAA 58.640 40.909 0.00 0.00 30.43 4.08
45 46 3.010200 TGCCACCATACATATTGTGCA 57.990 42.857 0.00 0.00 30.43 4.57
46 47 4.589216 AATGCCACCATACATATTGTGC 57.411 40.909 0.00 0.00 30.43 4.57
47 48 8.412456 TCTAAAAATGCCACCATACATATTGTG 58.588 33.333 0.00 0.00 0.00 3.33
48 49 8.532186 TCTAAAAATGCCACCATACATATTGT 57.468 30.769 0.00 0.00 0.00 2.71
49 50 9.814899 TTTCTAAAAATGCCACCATACATATTG 57.185 29.630 0.00 0.00 0.00 1.90
160 161 9.935682 CACAGTTTTTATGAAGTGCGATAATAT 57.064 29.630 0.00 0.00 34.10 1.28
161 162 9.157104 TCACAGTTTTTATGAAGTGCGATAATA 57.843 29.630 0.00 0.00 34.10 0.98
162 163 7.962918 GTCACAGTTTTTATGAAGTGCGATAAT 59.037 33.333 0.00 0.00 34.10 1.28
163 164 7.041712 TGTCACAGTTTTTATGAAGTGCGATAA 60.042 33.333 0.00 0.00 34.10 1.75
164 165 6.425417 TGTCACAGTTTTTATGAAGTGCGATA 59.575 34.615 0.00 0.00 34.10 2.92
165 166 5.238432 TGTCACAGTTTTTATGAAGTGCGAT 59.762 36.000 0.00 0.00 34.10 4.58
166 167 4.572795 TGTCACAGTTTTTATGAAGTGCGA 59.427 37.500 0.00 0.00 34.10 5.10
167 168 4.843147 TGTCACAGTTTTTATGAAGTGCG 58.157 39.130 0.00 0.00 34.10 5.34
168 169 7.698836 AAATGTCACAGTTTTTATGAAGTGC 57.301 32.000 0.00 0.00 34.10 4.40
197 198 9.009327 CGCGAACATTTTCTTACATTCAATATT 57.991 29.630 0.00 0.00 0.00 1.28
198 199 8.181573 ACGCGAACATTTTCTTACATTCAATAT 58.818 29.630 15.93 0.00 0.00 1.28
199 200 7.480229 CACGCGAACATTTTCTTACATTCAATA 59.520 33.333 15.93 0.00 0.00 1.90
200 201 6.305399 CACGCGAACATTTTCTTACATTCAAT 59.695 34.615 15.93 0.00 0.00 2.57
201 202 5.623264 CACGCGAACATTTTCTTACATTCAA 59.377 36.000 15.93 0.00 0.00 2.69
202 203 5.143660 CACGCGAACATTTTCTTACATTCA 58.856 37.500 15.93 0.00 0.00 2.57
203 204 4.029087 GCACGCGAACATTTTCTTACATTC 59.971 41.667 15.93 0.00 0.00 2.67
204 205 3.911964 GCACGCGAACATTTTCTTACATT 59.088 39.130 15.93 0.00 0.00 2.71
205 206 3.188460 AGCACGCGAACATTTTCTTACAT 59.812 39.130 15.93 0.00 0.00 2.29
206 207 2.546368 AGCACGCGAACATTTTCTTACA 59.454 40.909 15.93 0.00 0.00 2.41
207 208 3.120649 AGAGCACGCGAACATTTTCTTAC 60.121 43.478 15.93 0.00 0.00 2.34
208 209 3.064207 AGAGCACGCGAACATTTTCTTA 58.936 40.909 15.93 0.00 0.00 2.10
209 210 1.873591 AGAGCACGCGAACATTTTCTT 59.126 42.857 15.93 0.00 0.00 2.52
210 211 1.512926 AGAGCACGCGAACATTTTCT 58.487 45.000 15.93 2.61 0.00 2.52
211 212 3.153735 GTTAGAGCACGCGAACATTTTC 58.846 45.455 15.93 0.04 0.00 2.29
212 213 2.546368 TGTTAGAGCACGCGAACATTTT 59.454 40.909 15.93 0.00 0.00 1.82
213 214 2.139917 TGTTAGAGCACGCGAACATTT 58.860 42.857 15.93 0.00 0.00 2.32
214 215 1.790755 TGTTAGAGCACGCGAACATT 58.209 45.000 15.93 0.00 0.00 2.71
215 216 2.010145 ATGTTAGAGCACGCGAACAT 57.990 45.000 15.93 14.57 37.62 2.71
216 217 2.640346 TATGTTAGAGCACGCGAACA 57.360 45.000 15.93 12.63 36.32 3.18
217 218 3.984018 TTTATGTTAGAGCACGCGAAC 57.016 42.857 15.93 6.07 0.00 3.95
218 219 3.930229 ACATTTATGTTAGAGCACGCGAA 59.070 39.130 15.93 0.00 37.90 4.70
219 220 3.517602 ACATTTATGTTAGAGCACGCGA 58.482 40.909 15.93 0.00 37.90 5.87
220 221 3.925688 ACATTTATGTTAGAGCACGCG 57.074 42.857 3.53 3.53 37.90 6.01
224 225 7.525194 ATGGCACAAAACATTTATGTTAGAGCA 60.525 33.333 20.46 12.97 46.27 4.26
225 226 6.813152 ATGGCACAAAACATTTATGTTAGAGC 59.187 34.615 8.41 12.71 46.27 4.09
226 227 8.761575 AATGGCACAAAACATTTATGTTAGAG 57.238 30.769 8.41 5.22 46.27 2.43
310 311 8.856247 CACATTGTGCATTATTCATATACATGC 58.144 33.333 3.43 0.00 40.61 4.06
323 324 8.293867 GTCTAAGTTAAACCACATTGTGCATTA 58.706 33.333 11.41 9.29 31.34 1.90
371 375 2.353579 CCGGTCTTCTTCGTGTGTTTTT 59.646 45.455 0.00 0.00 0.00 1.94
372 376 1.937899 CCGGTCTTCTTCGTGTGTTTT 59.062 47.619 0.00 0.00 0.00 2.43
373 377 1.134610 ACCGGTCTTCTTCGTGTGTTT 60.135 47.619 0.00 0.00 0.00 2.83
387 391 1.158434 TTGGCGTTTATTCACCGGTC 58.842 50.000 2.59 0.00 0.00 4.79
421 425 4.617253 TTCTTCATCAGTTTCTTCGGGA 57.383 40.909 0.00 0.00 0.00 5.14
449 453 7.436970 CAGTTTATTGGGGTTACTGTTGTTTTC 59.563 37.037 0.00 0.00 33.34 2.29
454 458 6.488683 TCTTCAGTTTATTGGGGTTACTGTTG 59.511 38.462 0.00 0.00 37.90 3.33
457 461 7.368059 GTTTCTTCAGTTTATTGGGGTTACTG 58.632 38.462 0.00 0.00 38.00 2.74
469 473 5.860611 TCTTCATCGGGTTTCTTCAGTTTA 58.139 37.500 0.00 0.00 0.00 2.01
483 487 4.935205 TGGTTACTCACATTTCTTCATCGG 59.065 41.667 0.00 0.00 0.00 4.18
498 502 3.562557 TCTTCGTTTTTGGCTGGTTACTC 59.437 43.478 0.00 0.00 0.00 2.59
500 504 3.974871 TCTTCGTTTTTGGCTGGTTAC 57.025 42.857 0.00 0.00 0.00 2.50
502 506 3.517602 GTTTCTTCGTTTTTGGCTGGTT 58.482 40.909 0.00 0.00 0.00 3.67
508 512 3.423996 TTCGGGTTTCTTCGTTTTTGG 57.576 42.857 0.00 0.00 0.00 3.28
533 537 3.190953 TCCGTTTGTTTCTTTTGGTTCGT 59.809 39.130 0.00 0.00 0.00 3.85
581 585 3.855503 CTGCAAGCAGCCCAGTCCA 62.856 63.158 9.36 0.00 44.83 4.02
695 699 7.124147 GTGAGAGGATTTGGGGATTGATTTTTA 59.876 37.037 0.00 0.00 0.00 1.52
966 1043 0.333312 TCTCTCCTCGCCTCTTCCTT 59.667 55.000 0.00 0.00 0.00 3.36
967 1044 0.106719 CTCTCTCCTCGCCTCTTCCT 60.107 60.000 0.00 0.00 0.00 3.36
997 1074 2.021068 CTCGCCGGAGATGACATGGT 62.021 60.000 8.83 0.00 43.27 3.55
1049 1126 4.740822 ATGCCGGTGCCAGGGAAC 62.741 66.667 1.90 0.00 36.33 3.62
1077 1157 1.723220 GAAGTAACTTGGAGCCGTCC 58.277 55.000 0.00 0.00 44.24 4.79
1084 1164 2.472695 ATGCTGCGAAGTAACTTGGA 57.527 45.000 0.00 0.00 0.00 3.53
1103 1183 0.963962 AGACCGACGACCAAAGCTTA 59.036 50.000 0.00 0.00 0.00 3.09
1125 1208 0.455410 CAGAGCAAGAGACCCGAGAG 59.545 60.000 0.00 0.00 0.00 3.20
1126 1209 0.967887 CCAGAGCAAGAGACCCGAGA 60.968 60.000 0.00 0.00 0.00 4.04
1162 1245 2.136298 TATGGCGATTCCTTGGCAAA 57.864 45.000 0.00 0.00 43.92 3.68
1164 1247 1.608055 CATATGGCGATTCCTTGGCA 58.392 50.000 0.00 0.00 44.74 4.92
1177 1260 3.213206 TGCCTTCTGCTTACCATATGG 57.787 47.619 20.68 20.68 42.00 2.74
1192 1275 0.179108 GCGTCCTCTTCGTATGCCTT 60.179 55.000 0.00 0.00 0.00 4.35
1197 1280 1.076192 AGGGGCGTCCTCTTCGTAT 60.076 57.895 5.77 0.00 44.06 3.06
1228 1311 1.272147 GCTCCATTCTGAACCACCCTT 60.272 52.381 0.00 0.00 0.00 3.95
1461 1544 0.181114 CGATCTCCTTGGCAATCCCA 59.819 55.000 0.00 0.00 43.51 4.37
1711 1794 1.004560 CCTCAAGCGCAGACTCCAA 60.005 57.895 11.47 0.00 0.00 3.53
1807 1890 0.179045 AGTTCAAGGAGCTTGCGTGT 60.179 50.000 0.00 0.00 40.84 4.49
1830 1913 3.055819 GCAGTGTCCTCTTGTTCATCCTA 60.056 47.826 0.00 0.00 0.00 2.94
1929 2012 1.670949 GCCTCTCACCGAGCTCATCA 61.671 60.000 15.40 0.00 38.49 3.07
1953 2036 4.549793 TGCTGTCGCAGGTCAAAA 57.450 50.000 8.57 0.00 42.25 2.44
2247 2330 0.108424 CAGCCTCCTTCAACCTCGAG 60.108 60.000 5.13 5.13 0.00 4.04
2317 2400 3.415087 GGCCATCCTCCCTGCTGT 61.415 66.667 0.00 0.00 0.00 4.40
2382 2465 2.093553 GCTTGAGATCAGCCTCTTGTCT 60.094 50.000 0.00 0.00 34.38 3.41
2397 2480 2.027377 ACCCATCTCAGACAAGCTTGAG 60.027 50.000 32.50 19.20 0.00 3.02
2487 2712 5.125367 AGAACACCTAAAGAAACCCACTT 57.875 39.130 0.00 0.00 0.00 3.16
2502 2728 3.058432 GGAACCGCTAAGAAAAGAACACC 60.058 47.826 0.00 0.00 0.00 4.16
2536 2762 5.874810 TCAGTAGGAAGCATCACAAATACAC 59.125 40.000 0.00 0.00 0.00 2.90
2554 2780 3.242518 TCACGCGAACAGATTTCAGTAG 58.757 45.455 15.93 0.00 0.00 2.57
2572 2798 6.663944 ATCTTACAGGTTAAAGCGATTCAC 57.336 37.500 0.00 0.00 0.00 3.18
2579 2805 6.759497 ATCCACAATCTTACAGGTTAAAGC 57.241 37.500 0.00 0.00 0.00 3.51
2601 2827 7.938140 TGGAACTGCTAGCAATTTAAACTAT 57.062 32.000 19.86 0.00 0.00 2.12
2636 2862 7.915293 TGTTAACAAACTGTTCAGAGAAAGA 57.085 32.000 5.64 0.00 40.22 2.52
2669 2895 7.766278 AGTCCTGATATCTACAAACACAATGTC 59.234 37.037 3.98 0.00 32.27 3.06
2675 2901 9.469807 CAGATTAGTCCTGATATCTACAAACAC 57.530 37.037 3.98 0.00 33.65 3.32
2719 2945 4.602340 TGGACCTCACTAAACTCAGAAC 57.398 45.455 0.00 0.00 0.00 3.01
2948 4783 2.066700 TTGCTCTGCATGGACCCACA 62.067 55.000 0.00 0.00 38.76 4.17
2981 4816 8.494433 TCCTTTGCTCTGAAAATATATACAGGT 58.506 33.333 11.75 0.00 0.00 4.00
2997 4832 3.181456 CCAGCTAGCTTATCCTTTGCTCT 60.181 47.826 16.46 0.00 38.15 4.09
2999 4834 2.507471 ACCAGCTAGCTTATCCTTTGCT 59.493 45.455 16.46 0.00 40.43 3.91
3000 4835 2.924421 ACCAGCTAGCTTATCCTTTGC 58.076 47.619 16.46 0.00 0.00 3.68
3001 4836 5.918608 TCTTACCAGCTAGCTTATCCTTTG 58.081 41.667 16.46 1.49 0.00 2.77
3002 4837 6.755542 ATCTTACCAGCTAGCTTATCCTTT 57.244 37.500 16.46 0.00 0.00 3.11
3005 4840 7.616313 ACAATATCTTACCAGCTAGCTTATCC 58.384 38.462 16.46 0.00 0.00 2.59
3008 4843 8.920174 TGTAACAATATCTTACCAGCTAGCTTA 58.080 33.333 16.46 2.79 0.00 3.09
3009 4844 7.792032 TGTAACAATATCTTACCAGCTAGCTT 58.208 34.615 16.46 3.98 0.00 3.74
3068 4939 3.132824 AGCATCGTGGTGATCATCAACTA 59.867 43.478 11.02 0.00 34.53 2.24
3153 5025 6.763135 TGACATTATCTGAAAATTCCGAGGAG 59.237 38.462 0.00 0.00 0.00 3.69
3187 5059 5.163163 CCAATATCATGGACCTTTCCTGAGA 60.163 44.000 0.00 0.00 43.54 3.27
3365 5238 1.520666 CACTACCAAGCCTACGGGG 59.479 63.158 0.00 0.00 38.36 5.73
3369 5242 2.474410 AAGTGCACTACCAAGCCTAC 57.526 50.000 22.01 0.00 0.00 3.18
3372 5245 2.076863 CTGTAAGTGCACTACCAAGCC 58.923 52.381 22.01 3.75 0.00 4.35


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

AutoCloner maintained by Alex Coulton.