Multiple sequence alignment - TraesCS6B01G156000

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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 TraesCS6B01G156000 chr6B 100.000 3075 0 0 1 3075 158857585 158860659 0.000000e+00 5679.0
1 TraesCS6B01G156000 chr6B 91.477 176 4 2 2191 2359 158896459 158896630 6.630000e-57 231.0
2 TraesCS6B01G156000 chr6B 96.364 55 2 0 2970 3024 158860501 158860555 1.170000e-14 91.6
3 TraesCS6B01G156000 chr6B 96.364 55 2 0 2917 2971 158860554 158860608 1.170000e-14 91.6
4 TraesCS6B01G156000 chr6A 97.101 1242 35 1 950 2191 88605235 88606475 0.000000e+00 2093.0
5 TraesCS6B01G156000 chr6A 95.641 390 15 1 1 388 88604790 88605179 2.600000e-175 625.0
6 TraesCS6B01G156000 chr6A 91.216 296 15 2 2368 2663 428682000 428682284 2.870000e-105 392.0
7 TraesCS6B01G156000 chr6A 82.564 195 21 9 2191 2374 428681591 428681783 3.170000e-35 159.0
8 TraesCS6B01G156000 chr6A 94.521 73 3 1 2896 2968 428682487 428682558 9.010000e-21 111.0
9 TraesCS6B01G156000 chr7A 91.075 549 34 4 385 918 180243367 180242819 0.000000e+00 728.0
10 TraesCS6B01G156000 chr7A 93.011 186 10 2 3 185 83784834 83785019 5.050000e-68 268.0
11 TraesCS6B01G156000 chr1A 91.075 549 33 6 387 920 113250050 113250597 0.000000e+00 728.0
12 TraesCS6B01G156000 chr1A 86.286 175 13 3 2191 2356 462770794 462770966 2.440000e-41 180.0
13 TraesCS6B01G156000 chr3B 86.201 558 58 5 388 928 744595754 744596309 1.230000e-163 586.0
14 TraesCS6B01G156000 chr3B 92.308 182 13 1 3 183 352239842 352239661 1.090000e-64 257.0
15 TraesCS6B01G156000 chr1B 88.326 454 51 2 385 837 655420522 655420974 7.500000e-151 544.0
16 TraesCS6B01G156000 chr1B 85.941 505 54 4 428 916 398050491 398049988 9.770000e-145 523.0
17 TraesCS6B01G156000 chr1B 84.226 336 24 8 2636 2971 583418438 583418132 1.790000e-77 300.0
18 TraesCS6B01G156000 chr1B 90.972 144 11 1 2498 2641 583422525 583422384 3.130000e-45 193.0
19 TraesCS6B01G156000 chr5A 90.698 344 24 2 2498 2841 616087845 616088180 4.680000e-123 451.0
20 TraesCS6B01G156000 chr5A 88.150 346 25 4 2498 2843 262338911 262339240 6.180000e-107 398.0
21 TraesCS6B01G156000 chr5A 81.093 439 59 12 494 913 11265879 11266312 2.290000e-86 329.0
22 TraesCS6B01G156000 chr2D 93.411 258 16 1 2498 2755 645261792 645261536 6.220000e-102 381.0
23 TraesCS6B01G156000 chr2D 82.000 150 12 7 2191 2333 566269347 566269206 2.510000e-21 113.0
24 TraesCS6B01G156000 chr2D 91.803 61 4 1 2784 2843 645261547 645261487 1.960000e-12 84.2
25 TraesCS6B01G156000 chr7D 90.714 280 24 2 388 666 421788853 421788575 3.740000e-99 372.0
26 TraesCS6B01G156000 chr7D 85.252 278 26 1 654 916 421782891 421782614 3.910000e-69 272.0
27 TraesCS6B01G156000 chr7D 93.011 186 11 2 1 185 567733250 567733434 1.410000e-68 270.0
28 TraesCS6B01G156000 chr4B 82.720 353 43 5 584 919 108374501 108374150 6.450000e-77 298.0
29 TraesCS6B01G156000 chr4B 82.418 182 18 7 2191 2363 437092474 437092298 2.470000e-31 147.0
30 TraesCS6B01G156000 chr4D 92.473 186 13 1 3 187 482703625 482703440 6.540000e-67 265.0
31 TraesCS6B01G156000 chr4D 84.354 147 7 4 2212 2348 353541314 353541454 2.490000e-26 130.0
32 TraesCS6B01G156000 chr3D 92.896 183 11 2 2 183 422517794 422517613 6.540000e-67 265.0
33 TraesCS6B01G156000 chr3D 82.386 176 17 5 2191 2356 604770729 604770900 1.150000e-29 141.0
34 TraesCS6B01G156000 chr4A 92.350 183 13 1 2 183 681712913 681713095 3.040000e-65 259.0
35 TraesCS6B01G156000 chr4A 85.795 176 12 3 2191 2357 548052884 548053055 1.130000e-39 174.0
36 TraesCS6B01G156000 chr1D 92.308 182 13 1 3 183 86918686 86918505 1.090000e-64 257.0
37 TraesCS6B01G156000 chr5B 91.758 182 14 1 2 182 574956444 574956625 5.090000e-63 252.0
38 TraesCS6B01G156000 chrUn 87.324 142 11 1 2191 2325 134517123 134517264 4.110000e-34 156.0
39 TraesCS6B01G156000 chrUn 83.333 150 10 5 2191 2325 196638326 196638475 1.160000e-24 124.0
40 TraesCS6B01G156000 chr6D 86.620 142 8 2 2191 2325 335038949 335039086 2.470000e-31 147.0
41 TraesCS6B01G156000 chr2B 82.184 174 18 8 2191 2355 696087362 696087531 1.490000e-28 137.0
42 TraesCS6B01G156000 chr2B 80.513 195 21 6 2191 2372 154925384 154925194 1.920000e-27 134.0


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 TraesCS6B01G156000 chr6B 158857585 158860659 3074 False 1954.066667 5679 97.576000 1 3075 3 chr6B.!!$F2 3074
1 TraesCS6B01G156000 chr6A 88604790 88606475 1685 False 1359.000000 2093 96.371000 1 2191 2 chr6A.!!$F1 2190
2 TraesCS6B01G156000 chr6A 428681591 428682558 967 False 220.666667 392 89.433667 2191 2968 3 chr6A.!!$F2 777
3 TraesCS6B01G156000 chr7A 180242819 180243367 548 True 728.000000 728 91.075000 385 918 1 chr7A.!!$R1 533
4 TraesCS6B01G156000 chr1A 113250050 113250597 547 False 728.000000 728 91.075000 387 920 1 chr1A.!!$F1 533
5 TraesCS6B01G156000 chr3B 744595754 744596309 555 False 586.000000 586 86.201000 388 928 1 chr3B.!!$F1 540
6 TraesCS6B01G156000 chr1B 398049988 398050491 503 True 523.000000 523 85.941000 428 916 1 chr1B.!!$R1 488
7 TraesCS6B01G156000 chr1B 583418132 583422525 4393 True 246.500000 300 87.599000 2498 2971 2 chr1B.!!$R2 473

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
703 707 0.610232 CCTTCTGAACTGGGCCAAGG 60.61 60.0 13.11 5.62 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2380 0.456995 GAAACGAGCGAGGGAGACAG 60.457 60.0 0.0 0.0 0.0 3.51 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
69 70 1.420138 GAAGGGTCTGACCACTTTGGA 59.580 52.381 26.94 0.00 40.96 3.53
92 93 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
124 125 3.121929 AGAGGCTATTTCCAGGACTCA 57.878 47.619 5.52 0.00 37.56 3.41
128 129 3.017442 GGCTATTTCCAGGACTCAAACC 58.983 50.000 0.00 0.00 0.00 3.27
139 140 2.069273 GACTCAAACCGTGACCTCATG 58.931 52.381 0.00 0.00 31.13 3.07
194 195 1.074566 CTCCCCTTCTTGCCAGTTCTT 59.925 52.381 0.00 0.00 0.00 2.52
251 254 1.490574 CGAGATCTGGAAGGAGGGTT 58.509 55.000 0.00 0.00 0.00 4.11
252 255 1.834263 CGAGATCTGGAAGGAGGGTTT 59.166 52.381 0.00 0.00 0.00 3.27
253 256 2.159028 CGAGATCTGGAAGGAGGGTTTC 60.159 54.545 0.00 0.00 0.00 2.78
399 402 0.899720 ATCGTTAAGGGCCTGTTCGA 59.100 50.000 22.38 22.38 0.00 3.71
422 425 1.633915 CCTGCCAGCTCCCAGATTCT 61.634 60.000 10.89 0.00 0.00 2.40
470 473 2.361737 GCCCACCTCCAAGAAGCC 60.362 66.667 0.00 0.00 0.00 4.35
633 637 0.744281 GCCTTCTCTCTCCCTTCTCG 59.256 60.000 0.00 0.00 0.00 4.04
648 652 3.865745 CCTTCTCGCGTCATGTTCTATTT 59.134 43.478 5.77 0.00 0.00 1.40
703 707 0.610232 CCTTCTGAACTGGGCCAAGG 60.610 60.000 13.11 5.62 0.00 3.61
767 771 1.516110 ATCTATTGAGCTGGCTGGGT 58.484 50.000 0.00 0.00 0.00 4.51
851 870 5.387547 CGAACAGTTTTCGTAGAAGAAGCTC 60.388 44.000 3.24 0.00 45.90 4.09
877 896 4.594970 TCCGGAAATTGAAGCTGGATTTA 58.405 39.130 0.00 0.00 32.32 1.40
989 1032 9.474313 AACTAGTCTCTCTGAATGATCTTAAGT 57.526 33.333 1.63 0.00 0.00 2.24
1014 1057 6.142818 TGTATTTTTATGCTTGCCGCTTAT 57.857 33.333 0.00 0.00 40.11 1.73
1130 1173 7.074653 TGATTCCACTTAAAGAACTACTGGT 57.925 36.000 0.00 0.00 0.00 4.00
1238 1281 1.986575 GCGATCCAGAAGGCTGCAAC 61.987 60.000 0.50 0.00 40.91 4.17
1263 1306 3.382278 TCAGAGCCTCTTCATCCAGAAT 58.618 45.455 0.00 0.00 35.25 2.40
1453 1496 8.773404 AGACAATTTAGTGTATGTGACTTACC 57.227 34.615 6.23 0.00 0.00 2.85
1454 1497 8.372459 AGACAATTTAGTGTATGTGACTTACCA 58.628 33.333 6.23 0.00 0.00 3.25
1622 1665 9.425893 CGTCATAATCACATTTTTCTGATGTAC 57.574 33.333 0.00 0.00 36.04 2.90
1624 1667 9.685276 TCATAATCACATTTTTCTGATGTACCT 57.315 29.630 0.00 0.00 36.04 3.08
1625 1668 9.941664 CATAATCACATTTTTCTGATGTACCTC 57.058 33.333 0.00 0.00 36.04 3.85
1699 1742 4.751060 CGAGGTAACCAGTACAGCAATAA 58.249 43.478 0.00 0.00 34.01 1.40
1700 1743 5.357257 CGAGGTAACCAGTACAGCAATAAT 58.643 41.667 0.00 0.00 34.01 1.28
1724 1767 2.039084 CCTCTCCTTGTACTTGCACCTT 59.961 50.000 0.00 0.00 0.00 3.50
1731 1774 1.073763 TGTACTTGCACCTTGATGGCT 59.926 47.619 0.00 0.00 40.22 4.75
1736 1779 0.035725 TGCACCTTGATGGCTCAGAG 60.036 55.000 0.00 0.00 40.22 3.35
1737 1780 0.251354 GCACCTTGATGGCTCAGAGA 59.749 55.000 0.00 0.00 40.22 3.10
1757 1800 3.906846 AGAAGCTCCCTCATAAGTATGGG 59.093 47.826 0.00 0.00 40.95 4.00
1847 1890 4.220821 CCAGGTTCAGTTCTACTTAGCTGA 59.779 45.833 14.54 0.00 37.70 4.26
1851 1894 7.865385 CAGGTTCAGTTCTACTTAGCTGATATC 59.135 40.741 0.00 0.00 37.70 1.63
1854 1897 7.278461 TCAGTTCTACTTAGCTGATATCACC 57.722 40.000 0.00 0.00 33.62 4.02
1859 1902 2.224066 ACTTAGCTGATATCACCGCACC 60.224 50.000 16.66 0.00 0.00 5.01
1880 1923 4.641989 ACCATAAATTGACTGCCATGTCTC 59.358 41.667 0.00 0.00 37.79 3.36
1963 2006 1.351017 GGGTGGTCTGACTTCATTCCA 59.649 52.381 7.85 0.00 0.00 3.53
1967 2010 3.499918 GTGGTCTGACTTCATTCCACTTG 59.500 47.826 18.07 0.00 41.62 3.16
1984 2027 4.945543 CCACTTGAGACATTCATGAATCCA 59.054 41.667 18.16 10.74 35.27 3.41
2076 2119 0.897621 TGTCGTCTGATGGCATGAGT 59.102 50.000 13.69 0.00 0.00 3.41
2162 2205 6.096987 TGAATAAGAGAGGGTTGTAGTAGCTG 59.903 42.308 0.00 0.00 0.00 4.24
2173 2216 4.785511 TGTAGTAGCTGTTCTCAGAACC 57.214 45.455 15.20 0.28 43.76 3.62
2232 2275 7.945109 GTCCTATTAATCCCTGCTTTTCCTAAT 59.055 37.037 0.00 0.00 0.00 1.73
2244 2287 0.899720 TTCCTAATCGAGGCGGTTGT 59.100 50.000 0.00 0.00 46.25 3.32
2246 2289 0.529992 CCTAATCGAGGCGGTTGTCC 60.530 60.000 0.00 0.00 38.96 4.02
2248 2291 0.974010 TAATCGAGGCGGTTGTCCCT 60.974 55.000 0.00 0.00 30.88 4.20
2249 2292 1.838073 AATCGAGGCGGTTGTCCCTT 61.838 55.000 0.00 0.00 0.00 3.95
2250 2293 2.240162 ATCGAGGCGGTTGTCCCTTC 62.240 60.000 0.00 0.00 0.00 3.46
2253 2303 4.011517 GGCGGTTGTCCCTTCGGA 62.012 66.667 0.00 0.00 35.01 4.55
2289 2339 9.106070 TCGCGGGCTATATATATATATGTGTAG 57.894 37.037 20.93 14.89 31.69 2.74
2290 2340 8.890718 CGCGGGCTATATATATATATGTGTAGT 58.109 37.037 20.93 1.36 31.69 2.73
2337 2388 6.937436 TTCACTTTTACTTTTCTGTCTCCC 57.063 37.500 0.00 0.00 0.00 4.30
2339 2390 6.289064 TCACTTTTACTTTTCTGTCTCCCTC 58.711 40.000 0.00 0.00 0.00 4.30
2340 2391 5.177696 CACTTTTACTTTTCTGTCTCCCTCG 59.822 44.000 0.00 0.00 0.00 4.63
2343 2394 1.273886 ACTTTTCTGTCTCCCTCGCTC 59.726 52.381 0.00 0.00 0.00 5.03
2344 2395 0.243907 TTTTCTGTCTCCCTCGCTCG 59.756 55.000 0.00 0.00 0.00 5.03
2345 2396 0.894184 TTTCTGTCTCCCTCGCTCGT 60.894 55.000 0.00 0.00 0.00 4.18
2348 2400 0.456995 CTGTCTCCCTCGCTCGTTTC 60.457 60.000 0.00 0.00 0.00 2.78
2353 2405 1.727335 CTCCCTCGCTCGTTTCTTTTC 59.273 52.381 0.00 0.00 0.00 2.29
2354 2406 1.069513 TCCCTCGCTCGTTTCTTTTCA 59.930 47.619 0.00 0.00 0.00 2.69
2359 2411 4.527564 CTCGCTCGTTTCTTTTCAAACAT 58.472 39.130 0.00 0.00 36.23 2.71
2360 2412 4.278858 TCGCTCGTTTCTTTTCAAACATG 58.721 39.130 0.00 0.00 36.23 3.21
2445 2720 1.439353 CGGATCCGCACTTGATTGGG 61.439 60.000 23.37 0.00 0.00 4.12
2453 2728 1.670811 GCACTTGATTGGGGTACATCG 59.329 52.381 0.00 0.00 0.00 3.84
2467 2742 2.115343 ACATCGAGAGGAAAAAGGGC 57.885 50.000 0.00 0.00 0.00 5.19
2485 2760 1.447838 CGAGGCGGCAGTTACACAT 60.448 57.895 13.08 0.00 0.00 3.21
2551 2826 3.133542 TCACAGAGATGCGGAATCAGATT 59.866 43.478 0.00 0.00 37.81 2.40
2558 2833 2.905075 TGCGGAATCAGATTCGTCAAT 58.095 42.857 15.65 0.00 40.17 2.57
2564 2839 5.008019 CGGAATCAGATTCGTCAATTGGATT 59.992 40.000 15.65 3.99 40.17 3.01
2565 2840 6.433766 GGAATCAGATTCGTCAATTGGATTC 58.566 40.000 15.65 15.63 38.96 2.52
2568 2843 7.578310 ATCAGATTCGTCAATTGGATTCATT 57.422 32.000 5.42 0.00 0.00 2.57
2569 2844 6.788243 TCAGATTCGTCAATTGGATTCATTG 58.212 36.000 5.42 0.00 0.00 2.82
2574 2849 9.520204 GATTCGTCAATTGGATTCATTGTTATT 57.480 29.630 5.42 0.00 0.00 1.40
2643 6869 5.971895 TTTGACCACGTACTAGTTTTGAC 57.028 39.130 0.00 0.00 0.00 3.18
2663 6889 1.676006 CCGGATGAACTAACCATTGCC 59.324 52.381 0.00 0.00 0.00 4.52
2666 6998 3.560068 CGGATGAACTAACCATTGCCTAC 59.440 47.826 0.00 0.00 0.00 3.18
2736 7068 0.525029 GCTACCGTAAGCAGGTCGTC 60.525 60.000 1.64 0.00 42.81 4.20
2761 7093 4.368808 CGGCCTCAACGCAACGTG 62.369 66.667 0.00 0.00 39.99 4.49
2762 7094 4.683334 GGCCTCAACGCAACGTGC 62.683 66.667 0.00 0.00 39.99 5.34
2831 7163 0.034896 GCAAACTCGTCCTCCCAGAA 59.965 55.000 0.00 0.00 0.00 3.02
2832 7164 1.941668 GCAAACTCGTCCTCCCAGAAG 60.942 57.143 0.00 0.00 0.00 2.85
2841 7173 3.068691 TCCCAGAAGGAGGCGACG 61.069 66.667 0.00 0.00 40.93 5.12
2842 7174 4.148825 CCCAGAAGGAGGCGACGG 62.149 72.222 0.00 0.00 38.24 4.79
2843 7175 4.821589 CCAGAAGGAGGCGACGGC 62.822 72.222 14.41 14.41 36.89 5.68
2844 7176 3.764466 CAGAAGGAGGCGACGGCT 61.764 66.667 25.29 25.29 42.48 5.52
2845 7177 3.764466 AGAAGGAGGCGACGGCTG 61.764 66.667 30.01 0.00 38.98 4.85
2846 7178 4.070552 GAAGGAGGCGACGGCTGT 62.071 66.667 30.01 12.91 38.98 4.40
2847 7179 4.379243 AAGGAGGCGACGGCTGTG 62.379 66.667 30.01 0.00 38.98 3.66
3008 7340 2.044551 GGCTTGGCCTTCCCAGAG 60.045 66.667 3.32 0.00 46.39 3.35
3009 7341 2.759795 GCTTGGCCTTCCCAGAGT 59.240 61.111 3.32 0.00 46.39 3.24
3010 7342 1.075659 GCTTGGCCTTCCCAGAGTT 59.924 57.895 3.32 0.00 46.39 3.01
3011 7343 0.962855 GCTTGGCCTTCCCAGAGTTC 60.963 60.000 3.32 0.00 46.39 3.01
3012 7344 0.322906 CTTGGCCTTCCCAGAGTTCC 60.323 60.000 3.32 0.00 46.39 3.62
3013 7345 1.065410 TTGGCCTTCCCAGAGTTCCA 61.065 55.000 3.32 0.00 46.39 3.53
3014 7346 1.002011 GGCCTTCCCAGAGTTCCAC 60.002 63.158 0.00 0.00 0.00 4.02
3015 7347 1.492993 GGCCTTCCCAGAGTTCCACT 61.493 60.000 0.00 0.00 0.00 4.00
3016 7348 0.322008 GCCTTCCCAGAGTTCCACTG 60.322 60.000 0.00 0.00 35.43 3.66
3017 7349 0.322008 CCTTCCCAGAGTTCCACTGC 60.322 60.000 0.00 0.00 34.47 4.40
3018 7350 0.671781 CTTCCCAGAGTTCCACTGCG 60.672 60.000 0.00 0.00 34.47 5.18
3019 7351 2.731691 TTCCCAGAGTTCCACTGCGC 62.732 60.000 0.00 0.00 34.47 6.09
3020 7352 2.031012 CCAGAGTTCCACTGCGCA 59.969 61.111 10.98 10.98 34.47 6.09
3021 7353 2.320587 CCAGAGTTCCACTGCGCAC 61.321 63.158 5.66 0.00 34.47 5.34
3022 7354 2.356313 AGAGTTCCACTGCGCACG 60.356 61.111 5.66 5.54 0.00 5.34
3023 7355 4.077188 GAGTTCCACTGCGCACGC 62.077 66.667 5.66 8.33 42.35 5.34
3043 7375 4.147449 CAGATGGTCGCCTCGGCA 62.147 66.667 8.87 0.00 42.06 5.69
3044 7376 3.390521 AGATGGTCGCCTCGGCAA 61.391 61.111 8.87 0.00 42.06 4.52
3045 7377 3.195698 GATGGTCGCCTCGGCAAC 61.196 66.667 8.87 0.00 42.06 4.17
3068 7400 2.277858 AGGACTGCCTCCAACTACG 58.722 57.895 0.59 0.00 42.19 3.51
3069 7401 0.251653 AGGACTGCCTCCAACTACGA 60.252 55.000 0.00 0.00 42.19 3.43
3070 7402 0.824759 GGACTGCCTCCAACTACGAT 59.175 55.000 0.00 0.00 39.21 3.73
3071 7403 1.471676 GGACTGCCTCCAACTACGATG 60.472 57.143 0.00 0.00 39.21 3.84
3072 7404 0.108138 ACTGCCTCCAACTACGATGC 60.108 55.000 0.00 0.00 0.00 3.91
3073 7405 1.148157 CTGCCTCCAACTACGATGCG 61.148 60.000 0.00 0.00 0.00 4.73
3074 7406 1.883084 GCCTCCAACTACGATGCGG 60.883 63.158 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.286725 ACCCTTCCCCGGACCCTA 61.287 66.667 0.73 0.00 0.00 3.53
42 43 2.284405 TCAGACCCTTCCCCGGAC 60.284 66.667 0.73 0.00 0.00 4.79
69 70 3.258622 GGGAAAGGCTGCGTACTATAGAT 59.741 47.826 6.78 0.00 0.00 1.98
92 93 2.495155 TAGCCTCTTGCAGAAATGCA 57.505 45.000 0.00 0.00 44.83 3.96
139 140 0.746659 AAAGCTGTTGCCTTGTGACC 59.253 50.000 0.00 0.00 40.80 4.02
227 230 2.031120 CTCCTTCCAGATCTCGCTCTT 58.969 52.381 0.00 0.00 0.00 2.85
399 402 2.367377 TGGGAGCTGGCAGGCTAT 60.367 61.111 17.64 0.00 43.20 2.97
422 425 1.789751 CTTCGCTCGCTGATTTGCA 59.210 52.632 0.00 0.00 0.00 4.08
458 461 1.746991 GAAGCCGGCTTCTTGGAGG 60.747 63.158 46.69 2.05 46.38 4.30
470 473 1.300233 GCTACGATCCTGGAAGCCG 60.300 63.158 0.00 7.69 0.00 5.52
616 620 0.380378 CGCGAGAAGGGAGAGAGAAG 59.620 60.000 0.00 0.00 34.27 2.85
648 652 0.242825 CCACGTAGCCTCGTCAAGAA 59.757 55.000 0.82 0.00 42.27 2.52
703 707 3.005539 TGGAGGAGAGTGGCTGGC 61.006 66.667 0.00 0.00 0.00 4.85
797 801 2.109126 CCAGCTTCTTGTAGGCGCC 61.109 63.158 21.89 21.89 0.00 6.53
851 870 0.734889 AGCTTCAATTTCCGGATGCG 59.265 50.000 4.15 0.00 38.70 4.73
887 906 1.153745 CGGAAGTCCTCCAGCTTCG 60.154 63.158 0.00 0.00 45.74 3.79
899 918 4.635699 AATTTAGGGTCTGTTCGGAAGT 57.364 40.909 0.00 0.00 0.00 3.01
939 958 1.949525 GCAACAAGCACGGGATCATAT 59.050 47.619 0.00 0.00 44.79 1.78
940 959 1.378531 GCAACAAGCACGGGATCATA 58.621 50.000 0.00 0.00 44.79 2.15
941 960 2.183409 GCAACAAGCACGGGATCAT 58.817 52.632 0.00 0.00 44.79 2.45
942 961 3.667087 GCAACAAGCACGGGATCA 58.333 55.556 0.00 0.00 44.79 2.92
1006 1049 8.549338 AGATAAAAAGGACTTATATAAGCGGC 57.451 34.615 20.24 11.03 36.79 6.53
1238 1281 3.878103 CTGGATGAAGAGGCTCTGAATTG 59.122 47.826 19.53 5.99 0.00 2.32
1263 1306 7.838884 TGCAGGTCAATTTGATGAAATTATCA 58.161 30.769 2.40 0.00 39.34 2.15
1324 1367 8.870160 TCAAATCTTGAACAAACGAATTTCAT 57.130 26.923 0.00 0.00 36.59 2.57
1444 1487 8.662781 TGCTTTTATATGATCTGGTAAGTCAC 57.337 34.615 0.00 0.00 0.00 3.67
1451 1494 6.488006 GGTCACATGCTTTTATATGATCTGGT 59.512 38.462 0.00 0.00 0.00 4.00
1453 1496 7.500720 TGGTCACATGCTTTTATATGATCTG 57.499 36.000 0.00 0.00 0.00 2.90
1454 1497 8.408601 GTTTGGTCACATGCTTTTATATGATCT 58.591 33.333 0.00 0.00 0.00 2.75
1622 1665 7.651027 ATGAGAGGAAAACAAATAATGGAGG 57.349 36.000 0.00 0.00 0.00 4.30
1624 1667 8.869109 ACAAATGAGAGGAAAACAAATAATGGA 58.131 29.630 0.00 0.00 0.00 3.41
1625 1668 9.492973 AACAAATGAGAGGAAAACAAATAATGG 57.507 29.630 0.00 0.00 0.00 3.16
1634 1677 6.039829 ACCTGAAGAACAAATGAGAGGAAAAC 59.960 38.462 0.00 0.00 0.00 2.43
1678 1721 7.016361 CAATTATTGCTGTACTGGTTACCTC 57.984 40.000 2.07 0.00 0.00 3.85
1699 1742 2.040278 TGCAAGTACAAGGAGAGGCAAT 59.960 45.455 0.00 0.00 0.00 3.56
1700 1743 1.419762 TGCAAGTACAAGGAGAGGCAA 59.580 47.619 0.00 0.00 0.00 4.52
1724 1767 0.829333 GGAGCTTCTCTGAGCCATCA 59.171 55.000 0.00 0.00 43.74 3.07
1731 1774 3.987745 ACTTATGAGGGAGCTTCTCTGA 58.012 45.455 15.83 0.00 32.78 3.27
1736 1779 3.904339 TCCCATACTTATGAGGGAGCTTC 59.096 47.826 0.00 0.00 45.15 3.86
1737 1780 3.941629 TCCCATACTTATGAGGGAGCTT 58.058 45.455 0.00 0.00 45.15 3.74
1847 1890 5.239306 CAGTCAATTTATGGTGCGGTGATAT 59.761 40.000 0.00 0.00 0.00 1.63
1851 1894 2.731968 GCAGTCAATTTATGGTGCGGTG 60.732 50.000 0.00 0.00 32.23 4.94
1854 1897 1.472082 TGGCAGTCAATTTATGGTGCG 59.528 47.619 0.00 0.00 39.16 5.34
1859 1902 4.333649 ACGAGACATGGCAGTCAATTTATG 59.666 41.667 0.00 0.00 40.98 1.90
1880 1923 3.603857 CGACAAGGTAAGAACAGCAAACG 60.604 47.826 0.00 0.00 0.00 3.60
1963 2006 6.058553 TCTGGATTCATGAATGTCTCAAGT 57.941 37.500 25.37 0.00 37.67 3.16
1967 2010 6.159299 TCTCTCTGGATTCATGAATGTCTC 57.841 41.667 25.37 11.62 0.00 3.36
1984 2027 5.705441 CGATTCTACAAGATAGCCTCTCTCT 59.295 44.000 0.00 0.00 31.03 3.10
2076 2119 1.696884 TGTGGCGGGCATTCTATATCA 59.303 47.619 7.75 0.00 0.00 2.15
2141 2184 4.931914 ACAGCTACTACAACCCTCTCTTA 58.068 43.478 0.00 0.00 0.00 2.10
2173 2216 6.816136 TCCTAACATATACATCACCACACAG 58.184 40.000 0.00 0.00 0.00 3.66
2206 2249 5.696030 AGGAAAAGCAGGGATTAATAGGAC 58.304 41.667 0.00 0.00 0.00 3.85
2208 2251 7.119846 CGATTAGGAAAAGCAGGGATTAATAGG 59.880 40.741 0.00 0.00 0.00 2.57
2232 2275 2.920912 AAGGGACAACCGCCTCGA 60.921 61.111 0.00 0.00 46.96 4.04
2248 2291 4.367023 CGAAGGGGTGCGTCCGAA 62.367 66.667 0.00 0.00 37.00 4.30
2260 2310 7.915923 CACATATATATATATAGCCCGCGAAGG 59.084 40.741 8.23 1.15 40.63 3.46
2282 2332 9.265901 GTTCTCATTGATAATGCTACTACACAT 57.734 33.333 0.00 0.00 38.77 3.21
2291 2341 9.399797 TGAATAGTTGTTCTCATTGATAATGCT 57.600 29.630 0.00 0.00 38.77 3.79
2327 2378 0.894184 AACGAGCGAGGGAGACAGAA 60.894 55.000 0.00 0.00 0.00 3.02
2329 2380 0.456995 GAAACGAGCGAGGGAGACAG 60.457 60.000 0.00 0.00 0.00 3.51
2337 2388 3.935450 TGTTTGAAAAGAAACGAGCGAG 58.065 40.909 0.00 0.00 38.46 5.03
2339 2390 4.035017 ACATGTTTGAAAAGAAACGAGCG 58.965 39.130 0.00 0.00 38.46 5.03
2340 2391 5.949233 AACATGTTTGAAAAGAAACGAGC 57.051 34.783 4.92 0.00 38.46 5.03
2343 2394 7.990499 CGTTGATAACATGTTTGAAAAGAAACG 59.010 33.333 17.78 15.90 38.46 3.60
2344 2395 7.787480 GCGTTGATAACATGTTTGAAAAGAAAC 59.213 33.333 17.78 9.25 36.53 2.78
2345 2396 7.305705 CGCGTTGATAACATGTTTGAAAAGAAA 60.306 33.333 17.78 0.00 0.00 2.52
2348 2400 5.662815 GCGCGTTGATAACATGTTTGAAAAG 60.663 40.000 17.78 11.37 0.00 2.27
2353 2405 2.589407 CAGCGCGTTGATAACATGTTTG 59.411 45.455 18.92 0.60 0.00 2.93
2354 2406 2.414029 CCAGCGCGTTGATAACATGTTT 60.414 45.455 25.28 4.68 0.00 2.83
2359 2411 2.395360 GCCCAGCGCGTTGATAACA 61.395 57.895 25.28 0.00 0.00 2.41
2360 2412 2.403586 GCCCAGCGCGTTGATAAC 59.596 61.111 25.28 6.62 0.00 1.89
2429 2704 0.916086 TACCCCAATCAAGTGCGGAT 59.084 50.000 0.00 0.00 0.00 4.18
2434 2709 3.118775 TCTCGATGTACCCCAATCAAGTG 60.119 47.826 0.00 0.00 0.00 3.16
2438 2713 2.039418 CCTCTCGATGTACCCCAATCA 58.961 52.381 0.00 0.00 0.00 2.57
2442 2717 2.241281 TTTCCTCTCGATGTACCCCA 57.759 50.000 0.00 0.00 0.00 4.96
2445 2720 3.532542 CCCTTTTTCCTCTCGATGTACC 58.467 50.000 0.00 0.00 0.00 3.34
2453 2728 1.027255 GCCTCGCCCTTTTTCCTCTC 61.027 60.000 0.00 0.00 0.00 3.20
2467 2742 1.421410 GATGTGTAACTGCCGCCTCG 61.421 60.000 0.00 0.00 38.04 4.63
2485 2760 0.539518 TCGCCGATTCCCAAATCTGA 59.460 50.000 0.00 0.00 39.36 3.27
2551 2826 7.479980 GGAATAACAATGAATCCAATTGACGA 58.520 34.615 7.12 0.00 0.00 4.20
2558 2833 6.393990 CAAACCGGAATAACAATGAATCCAA 58.606 36.000 9.46 0.00 0.00 3.53
2564 2839 6.238897 GGATATGCAAACCGGAATAACAATGA 60.239 38.462 9.46 0.00 0.00 2.57
2565 2840 5.920273 GGATATGCAAACCGGAATAACAATG 59.080 40.000 9.46 0.00 0.00 2.82
2568 2843 4.336993 GTGGATATGCAAACCGGAATAACA 59.663 41.667 9.46 0.00 0.00 2.41
2569 2844 4.578928 AGTGGATATGCAAACCGGAATAAC 59.421 41.667 9.46 0.00 0.00 1.89
2574 2849 1.557371 TGAGTGGATATGCAAACCGGA 59.443 47.619 9.46 0.00 0.00 5.14
2643 6869 1.676006 GGCAATGGTTAGTTCATCCGG 59.324 52.381 0.00 0.00 0.00 5.14
2663 6889 4.213482 GGCAAACAACCAAGACTAGTGTAG 59.787 45.833 0.00 0.00 0.00 2.74
2666 6998 2.032030 CGGCAAACAACCAAGACTAGTG 60.032 50.000 0.00 0.00 0.00 2.74
2817 7149 4.766272 TCCTTCTGGGAGGACGAG 57.234 61.111 0.00 0.00 40.87 4.18
2842 7174 3.702048 TAGGGGTCGGTGCACAGC 61.702 66.667 20.43 8.58 0.00 4.40
2843 7175 2.264794 GTAGGGGTCGGTGCACAG 59.735 66.667 20.43 15.76 0.00 3.66
2844 7176 3.687102 CGTAGGGGTCGGTGCACA 61.687 66.667 20.43 0.00 0.00 4.57
2857 7189 4.301027 GATGCCCCGGCTCCGTAG 62.301 72.222 7.35 0.00 42.51 3.51
2992 7324 0.962855 GAACTCTGGGAAGGCCAAGC 60.963 60.000 5.01 0.00 34.95 4.01
2993 7325 0.322906 GGAACTCTGGGAAGGCCAAG 60.323 60.000 5.01 0.00 36.46 3.61
2994 7326 1.065410 TGGAACTCTGGGAAGGCCAA 61.065 55.000 5.01 0.00 35.15 4.52
2995 7327 1.463214 TGGAACTCTGGGAAGGCCA 60.463 57.895 5.01 0.00 35.15 5.36
2996 7328 1.002011 GTGGAACTCTGGGAAGGCC 60.002 63.158 0.00 0.00 0.00 5.19
2997 7329 4.724262 GTGGAACTCTGGGAAGGC 57.276 61.111 0.00 0.00 0.00 4.35
3026 7358 3.664025 TTGCCGAGGCGACCATCTG 62.664 63.158 9.78 0.00 45.51 2.90
3027 7359 3.390521 TTGCCGAGGCGACCATCT 61.391 61.111 9.78 0.00 45.51 2.90
3028 7360 3.195698 GTTGCCGAGGCGACCATC 61.196 66.667 21.00 0.00 46.77 3.51
3040 7372 3.050275 GCAGTCCTCACGGTTGCC 61.050 66.667 0.00 0.00 36.58 4.52
3041 7373 3.050275 GGCAGTCCTCACGGTTGC 61.050 66.667 0.00 0.00 39.54 4.17
3042 7374 2.743718 AGGCAGTCCTCACGGTTG 59.256 61.111 0.00 0.00 38.72 3.77
3052 7384 1.927895 CATCGTAGTTGGAGGCAGTC 58.072 55.000 0.00 0.00 0.00 3.51
3053 7385 0.108138 GCATCGTAGTTGGAGGCAGT 60.108 55.000 0.00 0.00 40.64 4.40
3054 7386 1.148157 CGCATCGTAGTTGGAGGCAG 61.148 60.000 0.00 0.00 40.96 4.85
3055 7387 1.153647 CGCATCGTAGTTGGAGGCA 60.154 57.895 0.00 0.00 40.96 4.75
3056 7388 1.883084 CCGCATCGTAGTTGGAGGC 60.883 63.158 0.00 0.00 37.81 4.70
3057 7389 4.420143 CCGCATCGTAGTTGGAGG 57.580 61.111 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.