Multiple sequence alignment - TraesCS1B01G102000

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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 TraesCS1B01G102000 chr1B 100.000 2384 0 0 1 2384 111973690 111971307 0.000000e+00 4403.0
1 TraesCS1B01G102000 chr1B 93.243 74 5 0 2311 2384 593510951 593511024 2.510000e-20 110.0
2 TraesCS1B01G102000 chr1B 96.610 59 2 0 2314 2372 565805589 565805647 5.420000e-17 99.0
3 TraesCS1B01G102000 chr1D 92.288 2308 114 31 36 2316 70566046 70563776 0.000000e+00 3217.0
4 TraesCS1B01G102000 chr1A 90.000 740 59 6 851 1576 71060430 71059692 0.000000e+00 942.0
5 TraesCS1B01G102000 chr1A 84.726 694 41 31 1 669 71070054 71069401 3.340000e-178 634.0
6 TraesCS1B01G102000 chr1A 94.330 194 7 3 667 859 71068992 71068802 6.440000e-76 294.0
7 TraesCS1B01G102000 chr7B 94.595 74 4 0 2311 2384 649294367 649294440 5.380000e-22 115.0
8 TraesCS1B01G102000 chr4B 94.366 71 4 0 2314 2384 517625642 517625572 2.510000e-20 110.0
9 TraesCS1B01G102000 chr7D 91.892 74 6 0 2311 2384 564217019 564217092 1.170000e-18 104.0
10 TraesCS1B01G102000 chr5B 92.958 71 5 0 2314 2384 394697870 394697800 1.170000e-18 104.0
11 TraesCS1B01G102000 chr6D 92.683 41 3 0 2311 2351 119999470 119999430 2.560000e-05 60.2
12 TraesCS1B01G102000 chr3A 96.970 33 0 1 2319 2351 676216959 676216990 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G102000 chr1B 111971307 111973690 2383 True 4403 4403 100.000 1 2384 1 chr1B.!!$R1 2383
1 TraesCS1B01G102000 chr1D 70563776 70566046 2270 True 3217 3217 92.288 36 2316 1 chr1D.!!$R1 2280
2 TraesCS1B01G102000 chr1A 71059692 71060430 738 True 942 942 90.000 851 1576 1 chr1A.!!$R1 725
3 TraesCS1B01G102000 chr1A 71068802 71070054 1252 True 464 634 89.528 1 859 2 chr1A.!!$R2 858

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
440 460 0.738389 CGGATGGCGGTTTAGCAATT 59.262 50.0 0.0 0.0 39.27 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2808 1.069358 GCCAGAGAGGTTTATCCGAGG 59.931 57.143 0.0 0.0 41.99 4.63 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
23 24 4.563140 GGACAACCCTGATACCTTTACA 57.437 45.455 0.00 0.00 0.00 2.41
25 26 4.941873 GGACAACCCTGATACCTTTACAAG 59.058 45.833 0.00 0.00 0.00 3.16
102 106 4.778904 GCGTGTTACATGCTTACTTTTCA 58.221 39.130 20.86 0.00 42.44 2.69
104 108 5.333798 GCGTGTTACATGCTTACTTTTCAGA 60.334 40.000 20.86 0.00 42.44 3.27
108 112 7.798982 GTGTTACATGCTTACTTTTCAGAACTC 59.201 37.037 0.00 0.00 0.00 3.01
111 115 7.333528 ACATGCTTACTTTTCAGAACTCAAA 57.666 32.000 0.00 0.00 0.00 2.69
115 119 7.598278 TGCTTACTTTTCAGAACTCAAAAACA 58.402 30.769 0.00 0.00 0.00 2.83
143 147 2.679837 CCAATCAACCCGATCACTTCTG 59.320 50.000 0.00 0.00 31.11 3.02
177 194 4.098914 TCTGACAAATGCAGGTTAGGTT 57.901 40.909 0.00 0.00 34.20 3.50
193 210 6.389869 AGGTTAGGTTGGGATTCTAATCATGA 59.610 38.462 0.00 0.00 37.15 3.07
198 215 8.223378 AGGTTGGGATTCTAATCATGATATGA 57.777 34.615 9.04 7.50 44.55 2.15
210 227 4.383173 TCATGATATGATGCCAGACACAC 58.617 43.478 0.00 0.00 33.59 3.82
245 262 2.030363 TGCCAAACTGAATGTAAAGCCG 60.030 45.455 0.00 0.00 0.00 5.52
279 296 6.305272 TCCATTAATTTGCAATTGCCCTTA 57.695 33.333 26.94 17.50 41.18 2.69
292 309 7.069702 TGCAATTGCCCTTATCTTTATCATCAA 59.930 33.333 26.94 0.00 41.18 2.57
297 314 8.218423 TGCCCTTATCTTTATCATCAAGGATA 57.782 34.615 0.00 0.00 35.58 2.59
308 325 2.570415 TCAAGGATACGGTTTTGCCA 57.430 45.000 0.00 0.00 46.39 4.92
316 333 2.840066 CGGTTTTGCCAGCGGTCAA 61.840 57.895 0.00 0.00 36.97 3.18
327 344 3.953775 CGGTCAACCAGGGCCAGT 61.954 66.667 6.18 0.00 35.14 4.00
328 345 2.282462 GGTCAACCAGGGCCAGTG 60.282 66.667 6.18 0.09 35.64 3.66
329 346 2.282462 GTCAACCAGGGCCAGTGG 60.282 66.667 19.56 19.56 41.30 4.00
333 350 2.122144 ACCAGGGCCAGTGGTACA 60.122 61.111 24.17 0.00 46.96 2.90
361 378 5.914033 TGACTAGTGTAGTGCAGTTTCTTT 58.086 37.500 0.00 0.00 39.59 2.52
384 404 5.692115 TTTCTGATCTATGGGTGCAACTA 57.308 39.130 0.00 0.00 36.74 2.24
385 405 5.894298 TTCTGATCTATGGGTGCAACTAT 57.106 39.130 5.71 5.71 36.74 2.12
399 419 2.369394 CAACTATTTGGAGCTGGTCCC 58.631 52.381 22.16 5.98 46.31 4.46
428 448 7.875971 AGATTTATTTAACTGATTCGGATGGC 58.124 34.615 0.00 0.00 0.00 4.40
440 460 0.738389 CGGATGGCGGTTTAGCAATT 59.262 50.000 0.00 0.00 39.27 2.32
441 461 1.268539 CGGATGGCGGTTTAGCAATTC 60.269 52.381 0.00 0.00 39.27 2.17
511 531 5.473504 GGCAGAGTCCTTTGTGATTTCTTTA 59.526 40.000 0.00 0.00 0.00 1.85
512 532 6.151817 GGCAGAGTCCTTTGTGATTTCTTTAT 59.848 38.462 0.00 0.00 0.00 1.40
513 533 7.309438 GGCAGAGTCCTTTGTGATTTCTTTATT 60.309 37.037 0.00 0.00 0.00 1.40
557 577 3.995048 TGCAATAAAATGGTGTGTGCATG 59.005 39.130 0.00 0.00 35.72 4.06
636 658 5.534654 AGGTCATCAATCTCTGTAGTCTAGC 59.465 44.000 0.00 0.00 0.00 3.42
653 675 2.457366 AGCCTCTTCCTTTACACACG 57.543 50.000 0.00 0.00 0.00 4.49
654 676 1.968493 AGCCTCTTCCTTTACACACGA 59.032 47.619 0.00 0.00 0.00 4.35
656 678 2.029290 GCCTCTTCCTTTACACACGAGA 60.029 50.000 0.00 0.00 0.00 4.04
658 680 3.367498 CCTCTTCCTTTACACACGAGAGG 60.367 52.174 0.00 0.00 41.81 3.69
799 1232 5.242434 TGATAAGTAACCGCAATCACTTGT 58.758 37.500 0.00 0.00 34.69 3.16
822 1255 6.095300 TGTTCATTTTCCATAGCATGTACCAG 59.905 38.462 0.00 0.00 0.00 4.00
921 1354 0.813610 ATAATGCCACTTGCGCGCTA 60.814 50.000 33.29 24.65 45.60 4.26
966 1401 3.816523 TGAAAAATCCTACCACACCGAAC 59.183 43.478 0.00 0.00 0.00 3.95
989 1424 1.739338 TTCCAGCCTAGCTAGCGCTC 61.739 60.000 25.09 0.00 45.15 5.03
1008 1443 3.326297 GCTCTGGCCTATAAATGGAGACT 59.674 47.826 3.32 0.00 0.00 3.24
1024 1459 0.036010 GACTATCCGGCATCCATGGG 60.036 60.000 13.02 0.00 0.00 4.00
1046 1481 0.178998 AGCCATCATAGCCCAAGCAG 60.179 55.000 0.00 0.00 43.56 4.24
1128 1563 2.815684 TAGCCACACCACCCTCCGAT 62.816 60.000 0.00 0.00 0.00 4.18
1161 1596 3.432326 GGGTGCATAAGGTCGAGAAGATT 60.432 47.826 0.00 0.00 0.00 2.40
1176 1611 2.119801 AGATTGAGCTTGTCCGCAAT 57.880 45.000 0.00 0.00 33.65 3.56
1179 1614 1.442769 TTGAGCTTGTCCGCAATCTC 58.557 50.000 0.00 4.76 44.01 2.75
1197 1632 2.158959 CGTGACCAAGCCGTCGATC 61.159 63.158 0.00 0.00 35.40 3.69
1284 1719 0.611714 CCAACACCGGTAAGGCTACT 59.388 55.000 6.87 0.00 46.52 2.57
1444 1887 4.034394 TCACGTCTACATATACACACCGAC 59.966 45.833 0.00 0.00 0.00 4.79
1484 1927 2.135189 TGGAATTTCCCCTCGATGGAT 58.865 47.619 12.90 0.00 35.03 3.41
1561 2010 6.150976 TGCAATTAATTGTGTGTCCTCTTAGG 59.849 38.462 25.15 0.00 39.88 2.69
1598 2047 6.980416 AGTCCTCTTAGAAAGTGTGTAGTT 57.020 37.500 0.00 0.00 0.00 2.24
1600 2049 8.474710 AGTCCTCTTAGAAAGTGTGTAGTTAA 57.525 34.615 0.00 0.00 0.00 2.01
1613 2062 8.976986 AGTGTGTAGTTAAATCTTTACTACCG 57.023 34.615 11.22 0.00 32.51 4.02
1616 2065 9.577110 TGTGTAGTTAAATCTTTACTACCGATG 57.423 33.333 11.22 0.00 32.51 3.84
1702 2151 5.940192 TTGGTTTGTTCACTGCTATACTG 57.060 39.130 0.00 0.00 0.00 2.74
1703 2152 5.222079 TGGTTTGTTCACTGCTATACTGA 57.778 39.130 0.00 0.00 0.00 3.41
1713 2162 9.265901 GTTCACTGCTATACTGATATGTGAAAT 57.734 33.333 0.00 0.00 42.29 2.17
1857 2309 6.872020 AGGCAAATGTCTTTCAAATCATCAAG 59.128 34.615 0.00 0.00 0.00 3.02
1885 2337 7.781324 ATGGTTTTCTTGGATGTAATCTTGT 57.219 32.000 0.00 0.00 44.71 3.16
1968 2420 2.417933 GCTTGATGTTGTGAGTAGCCTG 59.582 50.000 0.00 0.00 0.00 4.85
2036 2488 7.038154 TGACTCCTTTCCATAGTTTGTTTTG 57.962 36.000 0.00 0.00 0.00 2.44
2226 2678 8.088981 ACTGTCGACAGACTTAAATATCAGTTT 58.911 33.333 43.55 18.14 46.59 2.66
2304 2756 9.843334 GTGAGGTAGTTAGACATATATAGTTGC 57.157 37.037 0.00 0.00 0.00 4.17
2339 2791 2.495155 TGATCATCAAGTGGTGGTGG 57.505 50.000 0.00 0.00 39.03 4.61
2340 2792 1.984424 TGATCATCAAGTGGTGGTGGA 59.016 47.619 0.00 0.00 39.03 4.02
2341 2793 2.374839 TGATCATCAAGTGGTGGTGGAA 59.625 45.455 0.00 0.00 39.03 3.53
2342 2794 3.181435 TGATCATCAAGTGGTGGTGGAAA 60.181 43.478 0.00 0.00 39.03 3.13
2343 2795 3.304911 TCATCAAGTGGTGGTGGAAAA 57.695 42.857 0.00 0.00 39.03 2.29
2344 2796 3.843422 TCATCAAGTGGTGGTGGAAAAT 58.157 40.909 0.00 0.00 39.03 1.82
2345 2797 3.826157 TCATCAAGTGGTGGTGGAAAATC 59.174 43.478 0.00 0.00 39.03 2.17
2346 2798 3.304911 TCAAGTGGTGGTGGAAAATCA 57.695 42.857 0.00 0.00 0.00 2.57
2347 2799 3.843422 TCAAGTGGTGGTGGAAAATCAT 58.157 40.909 0.00 0.00 0.00 2.45
2348 2800 3.573538 TCAAGTGGTGGTGGAAAATCATG 59.426 43.478 0.00 0.00 0.00 3.07
2349 2801 3.524095 AGTGGTGGTGGAAAATCATGA 57.476 42.857 0.00 0.00 0.00 3.07
2350 2802 3.157087 AGTGGTGGTGGAAAATCATGAC 58.843 45.455 0.00 0.00 0.00 3.06
2351 2803 2.231235 GTGGTGGTGGAAAATCATGACC 59.769 50.000 0.00 0.00 0.00 4.02
2352 2804 2.158400 TGGTGGTGGAAAATCATGACCA 60.158 45.455 0.00 0.00 34.26 4.02
2353 2805 3.099141 GGTGGTGGAAAATCATGACCAT 58.901 45.455 0.00 0.00 38.90 3.55
2354 2806 3.131046 GGTGGTGGAAAATCATGACCATC 59.869 47.826 0.00 1.46 38.90 3.51
2355 2807 3.763360 GTGGTGGAAAATCATGACCATCA 59.237 43.478 11.08 11.08 40.57 3.07
2356 2808 3.763360 TGGTGGAAAATCATGACCATCAC 59.237 43.478 11.08 9.70 38.40 3.06
2357 2809 3.131046 GGTGGAAAATCATGACCATCACC 59.869 47.826 16.15 16.15 34.14 4.02
2358 2810 4.019174 GTGGAAAATCATGACCATCACCT 58.981 43.478 0.00 0.00 34.87 4.00
2359 2811 4.096984 GTGGAAAATCATGACCATCACCTC 59.903 45.833 0.00 0.00 34.87 3.85
2360 2812 3.313526 GGAAAATCATGACCATCACCTCG 59.686 47.826 0.00 0.00 0.00 4.63
2361 2813 2.627515 AATCATGACCATCACCTCGG 57.372 50.000 0.00 0.00 0.00 4.63
2362 2814 1.793414 ATCATGACCATCACCTCGGA 58.207 50.000 0.00 0.00 0.00 4.55
2363 2815 1.793414 TCATGACCATCACCTCGGAT 58.207 50.000 0.00 0.00 0.00 4.18
2364 2816 2.957474 TCATGACCATCACCTCGGATA 58.043 47.619 0.00 0.00 0.00 2.59
2365 2817 3.304829 TCATGACCATCACCTCGGATAA 58.695 45.455 0.00 0.00 0.00 1.75
2366 2818 3.709141 TCATGACCATCACCTCGGATAAA 59.291 43.478 0.00 0.00 0.00 1.40
2367 2819 3.536956 TGACCATCACCTCGGATAAAC 57.463 47.619 0.00 0.00 0.00 2.01
2368 2820 2.169769 TGACCATCACCTCGGATAAACC 59.830 50.000 0.00 0.00 0.00 3.27
2369 2821 2.434702 GACCATCACCTCGGATAAACCT 59.565 50.000 0.00 0.00 36.31 3.50
2370 2822 2.434702 ACCATCACCTCGGATAAACCTC 59.565 50.000 0.00 0.00 36.31 3.85
2371 2823 2.700897 CCATCACCTCGGATAAACCTCT 59.299 50.000 0.00 0.00 36.31 3.69
2372 2824 3.243907 CCATCACCTCGGATAAACCTCTC 60.244 52.174 0.00 0.00 36.31 3.20
2373 2825 3.383698 TCACCTCGGATAAACCTCTCT 57.616 47.619 0.00 0.00 36.31 3.10
2374 2826 3.024547 TCACCTCGGATAAACCTCTCTG 58.975 50.000 0.00 0.00 36.31 3.35
2375 2827 2.101582 CACCTCGGATAAACCTCTCTGG 59.898 54.545 0.00 0.00 42.93 3.86
2376 2828 1.069358 CCTCGGATAAACCTCTCTGGC 59.931 57.143 0.00 0.00 40.22 4.85
2377 2829 2.035632 CTCGGATAAACCTCTCTGGCT 58.964 52.381 0.00 0.00 40.22 4.75
2378 2830 2.032620 TCGGATAAACCTCTCTGGCTC 58.967 52.381 0.00 0.00 40.22 4.70
2379 2831 1.757118 CGGATAAACCTCTCTGGCTCA 59.243 52.381 0.00 0.00 40.22 4.26
2380 2832 2.168521 CGGATAAACCTCTCTGGCTCAA 59.831 50.000 0.00 0.00 40.22 3.02
2381 2833 3.536570 GGATAAACCTCTCTGGCTCAAC 58.463 50.000 0.00 0.00 40.22 3.18
2382 2834 3.055094 GGATAAACCTCTCTGGCTCAACA 60.055 47.826 0.00 0.00 40.22 3.33
2383 2835 4.384647 GGATAAACCTCTCTGGCTCAACAT 60.385 45.833 0.00 0.00 40.22 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.014966 TCTCTGTAACCTACTCCTACCTTGT 59.985 44.000 0.00 0.00 0.00 3.16
22 23 5.507637 TCTCTGTAACCTACTCCTACCTTG 58.492 45.833 0.00 0.00 0.00 3.61
23 24 5.793034 TCTCTGTAACCTACTCCTACCTT 57.207 43.478 0.00 0.00 0.00 3.50
25 26 4.278919 GCATCTCTGTAACCTACTCCTACC 59.721 50.000 0.00 0.00 0.00 3.18
27 28 5.390087 AGCATCTCTGTAACCTACTCCTA 57.610 43.478 0.00 0.00 0.00 2.94
28 29 4.258457 AGCATCTCTGTAACCTACTCCT 57.742 45.455 0.00 0.00 0.00 3.69
29 30 4.278919 GGTAGCATCTCTGTAACCTACTCC 59.721 50.000 0.00 0.00 0.00 3.85
30 31 5.134661 AGGTAGCATCTCTGTAACCTACTC 58.865 45.833 0.00 0.00 37.66 2.59
31 32 5.132043 AGGTAGCATCTCTGTAACCTACT 57.868 43.478 0.00 0.00 37.66 2.57
101 105 5.350633 TGGCTTCATTGTTTTTGAGTTCTG 58.649 37.500 0.00 0.00 0.00 3.02
102 106 5.596836 TGGCTTCATTGTTTTTGAGTTCT 57.403 34.783 0.00 0.00 0.00 3.01
104 108 6.347696 TGATTGGCTTCATTGTTTTTGAGTT 58.652 32.000 0.00 0.00 0.00 3.01
108 112 5.277925 GGGTTGATTGGCTTCATTGTTTTTG 60.278 40.000 0.00 0.00 0.00 2.44
111 115 3.554752 CGGGTTGATTGGCTTCATTGTTT 60.555 43.478 0.00 0.00 0.00 2.83
115 119 2.214376 TCGGGTTGATTGGCTTCATT 57.786 45.000 0.00 0.00 0.00 2.57
143 147 5.220228 GCATTTGTCAGATACAGTACGTGTC 60.220 44.000 0.00 4.42 40.94 3.67
193 210 4.701651 ATCAGTGTGTCTGGCATCATAT 57.298 40.909 0.00 0.00 43.76 1.78
198 215 7.776969 AGATTAATTAATCAGTGTGTCTGGCAT 59.223 33.333 30.52 9.89 43.43 4.40
199 216 7.066163 CAGATTAATTAATCAGTGTGTCTGGCA 59.934 37.037 30.52 0.00 43.43 4.92
200 217 7.412853 CAGATTAATTAATCAGTGTGTCTGGC 58.587 38.462 30.52 8.27 43.43 4.85
201 218 7.412853 GCAGATTAATTAATCAGTGTGTCTGG 58.587 38.462 30.52 13.20 43.43 3.86
202 219 7.066163 TGGCAGATTAATTAATCAGTGTGTCTG 59.934 37.037 30.52 21.63 43.43 3.51
203 220 7.112122 TGGCAGATTAATTAATCAGTGTGTCT 58.888 34.615 30.52 12.64 43.43 3.41
204 221 7.320443 TGGCAGATTAATTAATCAGTGTGTC 57.680 36.000 30.52 23.35 43.43 3.67
205 222 7.701539 TTGGCAGATTAATTAATCAGTGTGT 57.298 32.000 30.52 13.18 43.43 3.72
206 223 8.246180 AGTTTGGCAGATTAATTAATCAGTGTG 58.754 33.333 30.52 22.79 43.43 3.82
279 296 8.840321 CAAAACCGTATCCTTGATGATAAAGAT 58.160 33.333 0.00 0.00 0.00 2.40
292 309 1.024579 CGCTGGCAAAACCGTATCCT 61.025 55.000 0.00 0.00 43.94 3.24
297 314 3.284449 GACCGCTGGCAAAACCGT 61.284 61.111 0.00 0.00 43.94 4.83
316 333 2.122144 TGTACCACTGGCCCTGGT 60.122 61.111 22.51 22.51 44.59 4.00
323 340 4.333690 ACTAGTCAGTAGTGTACCACTGG 58.666 47.826 15.41 0.00 45.01 4.00
334 351 5.630661 AACTGCACTACACTAGTCAGTAG 57.369 43.478 15.43 15.43 41.66 2.57
335 352 5.768662 AGAAACTGCACTACACTAGTCAGTA 59.231 40.000 11.73 3.56 41.66 2.74
336 353 4.585162 AGAAACTGCACTACACTAGTCAGT 59.415 41.667 6.79 6.79 42.95 3.41
337 354 5.127693 AGAAACTGCACTACACTAGTCAG 57.872 43.478 0.00 0.00 36.76 3.51
338 355 5.531122 AAGAAACTGCACTACACTAGTCA 57.469 39.130 0.00 0.00 36.76 3.41
339 356 6.846325 AAAAGAAACTGCACTACACTAGTC 57.154 37.500 0.00 0.00 36.76 2.59
361 378 4.922206 AGTTGCACCCATAGATCAGAAAA 58.078 39.130 0.00 0.00 0.00 2.29
364 381 5.894298 AATAGTTGCACCCATAGATCAGA 57.106 39.130 0.00 0.00 0.00 3.27
365 382 5.240183 CCAAATAGTTGCACCCATAGATCAG 59.760 44.000 0.00 0.00 33.01 2.90
366 383 5.104151 TCCAAATAGTTGCACCCATAGATCA 60.104 40.000 0.00 0.00 33.01 2.92
367 384 5.376625 TCCAAATAGTTGCACCCATAGATC 58.623 41.667 0.00 0.00 33.01 2.75
368 385 5.380043 CTCCAAATAGTTGCACCCATAGAT 58.620 41.667 0.00 0.00 33.01 1.98
369 386 4.780815 CTCCAAATAGTTGCACCCATAGA 58.219 43.478 0.00 0.00 33.01 1.98
370 387 3.316308 GCTCCAAATAGTTGCACCCATAG 59.684 47.826 0.00 0.00 33.01 2.23
384 404 1.002069 TCATGGGACCAGCTCCAAAT 58.998 50.000 0.00 0.00 41.63 2.32
385 405 0.329261 CTCATGGGACCAGCTCCAAA 59.671 55.000 0.00 0.00 41.63 3.28
428 448 7.587757 GCATTACTAATCTGAATTGCTAAACCG 59.412 37.037 0.00 0.00 0.00 4.44
471 491 6.183360 GGACTCTGCCAACAAGAATAAAGATC 60.183 42.308 0.00 0.00 0.00 2.75
557 577 1.363744 CTCAACCTCTGCATCGGTTC 58.636 55.000 14.82 0.00 41.37 3.62
606 628 9.606631 GACTACAGAGATTGATGACCTAATTTT 57.393 33.333 0.00 0.00 0.00 1.82
625 647 5.652891 TGTAAAGGAAGAGGCTAGACTACAG 59.347 44.000 0.00 0.00 0.00 2.74
636 658 3.367498 CCTCTCGTGTGTAAAGGAAGAGG 60.367 52.174 0.00 0.00 35.17 3.69
656 678 2.787994 TCGACTACGAGGAGAAAACCT 58.212 47.619 0.00 0.00 43.81 3.50
669 1102 5.956642 AGAACCAGAAAAGATCTCGACTAC 58.043 41.667 0.00 0.00 35.73 2.73
747 1180 0.607489 CTTTGTGGAGCCTCTGGTGG 60.607 60.000 0.00 0.00 0.00 4.61
799 1232 6.318648 GTCTGGTACATGCTATGGAAAATGAA 59.681 38.462 0.00 0.00 38.20 2.57
822 1255 4.489679 AAACTTCTTGCCTGAATTCGTC 57.510 40.909 0.04 0.00 0.00 4.20
868 1301 8.141268 TGGTTTATGTTTGTTCTGAAATTCTCC 58.859 33.333 0.00 0.00 0.00 3.71
966 1401 0.105778 GCTAGCTAGGCTGGAAGTGG 59.894 60.000 22.10 0.00 39.54 4.00
989 1424 5.394663 CGGATAGTCTCCATTTATAGGCCAG 60.395 48.000 5.01 0.00 45.24 4.85
1008 1443 1.714011 TTGCCCATGGATGCCGGATA 61.714 55.000 15.22 0.00 0.00 2.59
1024 1459 0.672342 CTTGGGCTATGATGGCTTGC 59.328 55.000 0.00 0.00 0.00 4.01
1046 1481 4.165779 CTGCCGGTTTTGATATGTGTTTC 58.834 43.478 1.90 0.00 0.00 2.78
1105 1540 1.612442 AGGGTGGTGTGGCTATCGT 60.612 57.895 0.00 0.00 0.00 3.73
1167 1602 1.080093 GGTCACGAGATTGCGGACA 60.080 57.895 0.00 0.00 35.00 4.02
1176 1611 2.649034 GACGGCTTGGTCACGAGA 59.351 61.111 0.00 0.00 36.91 4.04
1179 1614 2.126071 ATCGACGGCTTGGTCACG 60.126 61.111 0.00 0.00 36.73 4.35
1197 1632 2.202837 GGGTTGGCGCCGTAGTAG 60.203 66.667 23.90 0.00 0.00 2.57
1227 1662 2.512515 GCACCTCGCCTCATGGTC 60.513 66.667 0.00 0.00 35.27 4.02
1436 1879 3.494626 GCATACATCCATTAGTCGGTGTG 59.505 47.826 0.00 0.00 0.00 3.82
1444 1887 5.065235 TCCACACATGCATACATCCATTAG 58.935 41.667 0.00 0.00 32.87 1.73
1484 1927 7.977293 ACACGTTTACATAGCACATCTTACATA 59.023 33.333 0.00 0.00 0.00 2.29
1561 2010 2.630580 AGAGGACTTGACTCCACACTTC 59.369 50.000 0.00 0.00 35.58 3.01
1569 2018 5.923684 CACACTTTCTAAGAGGACTTGACTC 59.076 44.000 0.00 0.00 37.53 3.36
1662 2111 6.382869 AACCAAAACAATCTGAAGTCTGAG 57.617 37.500 0.00 0.00 0.00 3.35
1722 2171 8.424133 ACTGGCAAGATCTTTGAAATAAAACTT 58.576 29.630 4.86 0.00 0.00 2.66
1862 2314 6.775142 TCACAAGATTACATCCAAGAAAACCA 59.225 34.615 0.00 0.00 0.00 3.67
1885 2337 3.744238 TGACGATTTGAAGGACACTCA 57.256 42.857 0.00 0.00 0.00 3.41
1968 2420 1.226030 GGGTACTCACAACACGCACC 61.226 60.000 0.00 0.00 0.00 5.01
2014 2466 7.505585 TGATCAAAACAAACTATGGAAAGGAGT 59.494 33.333 0.00 0.00 0.00 3.85
2200 2652 7.159322 ACTGATATTTAAGTCTGTCGACAGT 57.841 36.000 37.21 24.62 44.12 3.55
2232 2684 9.936329 AACTGATAGTTAATTGGGGTAATTCAT 57.064 29.630 0.00 0.00 36.52 2.57
2279 2731 9.582648 TGCAACTATATATGTCTAACTACCTCA 57.417 33.333 0.00 0.00 0.00 3.86
2283 2735 9.141400 GCCTTGCAACTATATATGTCTAACTAC 57.859 37.037 0.00 0.00 0.00 2.73
2319 2771 2.374839 TCCACCACCACTTGATGATCAA 59.625 45.455 7.73 7.73 34.79 2.57
2320 2772 1.984424 TCCACCACCACTTGATGATCA 59.016 47.619 0.00 0.00 0.00 2.92
2321 2773 2.787473 TCCACCACCACTTGATGATC 57.213 50.000 0.00 0.00 0.00 2.92
2322 2774 3.524095 TTTCCACCACCACTTGATGAT 57.476 42.857 0.00 0.00 0.00 2.45
2323 2775 3.304911 TTTTCCACCACCACTTGATGA 57.695 42.857 0.00 0.00 0.00 2.92
2324 2776 3.573538 TGATTTTCCACCACCACTTGATG 59.426 43.478 0.00 0.00 0.00 3.07
2325 2777 3.843422 TGATTTTCCACCACCACTTGAT 58.157 40.909 0.00 0.00 0.00 2.57
2326 2778 3.304911 TGATTTTCCACCACCACTTGA 57.695 42.857 0.00 0.00 0.00 3.02
2327 2779 3.573538 TCATGATTTTCCACCACCACTTG 59.426 43.478 0.00 0.00 0.00 3.16
2328 2780 3.573967 GTCATGATTTTCCACCACCACTT 59.426 43.478 0.00 0.00 0.00 3.16
2329 2781 3.157087 GTCATGATTTTCCACCACCACT 58.843 45.455 0.00 0.00 0.00 4.00
2330 2782 2.231235 GGTCATGATTTTCCACCACCAC 59.769 50.000 0.00 0.00 0.00 4.16
2331 2783 2.158400 TGGTCATGATTTTCCACCACCA 60.158 45.455 0.00 0.00 31.99 4.17
2332 2784 2.524306 TGGTCATGATTTTCCACCACC 58.476 47.619 0.00 0.00 31.99 4.61
2333 2785 3.763360 TGATGGTCATGATTTTCCACCAC 59.237 43.478 4.99 2.13 39.94 4.16
2334 2786 3.763360 GTGATGGTCATGATTTTCCACCA 59.237 43.478 4.99 3.95 41.36 4.17
2335 2787 3.131046 GGTGATGGTCATGATTTTCCACC 59.869 47.826 16.09 16.09 35.41 4.61
2336 2788 4.019174 AGGTGATGGTCATGATTTTCCAC 58.981 43.478 4.99 7.15 32.60 4.02
2337 2789 4.272489 GAGGTGATGGTCATGATTTTCCA 58.728 43.478 0.00 1.30 0.00 3.53
2338 2790 3.313526 CGAGGTGATGGTCATGATTTTCC 59.686 47.826 0.00 0.00 0.00 3.13
2339 2791 3.313526 CCGAGGTGATGGTCATGATTTTC 59.686 47.826 0.00 0.00 0.00 2.29
2340 2792 3.054434 TCCGAGGTGATGGTCATGATTTT 60.054 43.478 0.00 0.00 0.00 1.82
2341 2793 2.505407 TCCGAGGTGATGGTCATGATTT 59.495 45.455 0.00 0.00 0.00 2.17
2342 2794 2.118679 TCCGAGGTGATGGTCATGATT 58.881 47.619 0.00 0.00 0.00 2.57
2343 2795 1.793414 TCCGAGGTGATGGTCATGAT 58.207 50.000 0.00 0.00 0.00 2.45
2344 2796 1.793414 ATCCGAGGTGATGGTCATGA 58.207 50.000 0.00 0.00 0.00 3.07
2345 2797 3.751479 TTATCCGAGGTGATGGTCATG 57.249 47.619 0.00 0.00 0.00 3.07
2346 2798 3.181454 GGTTTATCCGAGGTGATGGTCAT 60.181 47.826 0.00 0.00 0.00 3.06
2347 2799 2.169769 GGTTTATCCGAGGTGATGGTCA 59.830 50.000 0.00 0.00 0.00 4.02
2348 2800 2.434702 AGGTTTATCCGAGGTGATGGTC 59.565 50.000 0.00 0.00 41.99 4.02
2349 2801 2.434702 GAGGTTTATCCGAGGTGATGGT 59.565 50.000 0.00 0.00 41.99 3.55
2350 2802 2.700897 AGAGGTTTATCCGAGGTGATGG 59.299 50.000 0.00 0.00 41.99 3.51
2351 2803 3.639094 AGAGAGGTTTATCCGAGGTGATG 59.361 47.826 0.00 0.00 41.99 3.07
2352 2804 3.639094 CAGAGAGGTTTATCCGAGGTGAT 59.361 47.826 0.00 0.00 41.99 3.06
2353 2805 3.024547 CAGAGAGGTTTATCCGAGGTGA 58.975 50.000 0.00 0.00 41.99 4.02
2354 2806 2.101582 CCAGAGAGGTTTATCCGAGGTG 59.898 54.545 0.00 0.00 41.99 4.00
2355 2807 2.389715 CCAGAGAGGTTTATCCGAGGT 58.610 52.381 0.00 0.00 41.99 3.85
2356 2808 1.069358 GCCAGAGAGGTTTATCCGAGG 59.931 57.143 0.00 0.00 41.99 4.63
2357 2809 2.035321 GAGCCAGAGAGGTTTATCCGAG 59.965 54.545 0.00 0.00 41.99 4.63
2358 2810 2.032620 GAGCCAGAGAGGTTTATCCGA 58.967 52.381 0.00 0.00 41.99 4.55
2359 2811 1.757118 TGAGCCAGAGAGGTTTATCCG 59.243 52.381 0.00 0.00 41.99 4.18
2360 2812 3.055094 TGTTGAGCCAGAGAGGTTTATCC 60.055 47.826 0.00 0.00 40.61 2.59
2361 2813 4.207891 TGTTGAGCCAGAGAGGTTTATC 57.792 45.455 0.00 0.00 40.61 1.75
2362 2814 4.851639 ATGTTGAGCCAGAGAGGTTTAT 57.148 40.909 0.00 0.00 40.61 1.40


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

AutoCloner maintained by Alex Coulton.