Multiple sequence alignment - TraesCS3B01G099000

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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 TraesCS3B01G099000 chr3B 100.000 2555 0 0 1 2555 66472136 66469582 0.000000e+00 4719.0
1 TraesCS3B01G099000 chr3B 82.627 967 113 23 1356 2280 66478604 66477651 0.000000e+00 804.0
2 TraesCS3B01G099000 chr3B 79.200 875 138 25 1397 2245 143509976 143510832 4.520000e-158 568.0
3 TraesCS3B01G099000 chr3B 77.047 928 155 32 1359 2258 143604241 143605138 6.060000e-132 481.0
4 TraesCS3B01G099000 chr3B 100.000 210 0 0 2914 3123 66469223 66469014 3.780000e-104 388.0
5 TraesCS3B01G099000 chr3B 84.615 104 15 1 487 590 66479295 66479193 5.510000e-18 102.0
6 TraesCS3B01G099000 chr3A 94.118 1054 54 6 1329 2381 54232937 54231891 0.000000e+00 1596.0
7 TraesCS3B01G099000 chr3A 89.327 862 57 16 483 1327 54233728 54232885 0.000000e+00 1050.0
8 TraesCS3B01G099000 chr3A 82.103 894 117 24 1398 2257 54284868 54283984 0.000000e+00 725.0
9 TraesCS3B01G099000 chr3A 77.962 903 149 28 1397 2268 547182357 547183240 1.280000e-143 520.0
10 TraesCS3B01G099000 chr3A 88.636 264 21 6 943 1202 54285195 54284937 2.340000e-81 313.0
11 TraesCS3B01G099000 chr3A 87.907 215 17 7 2914 3123 54231752 54231542 8.650000e-61 244.0
12 TraesCS3B01G099000 chr3A 97.059 34 1 0 1 34 149077764 149077797 1.210000e-04 58.4
13 TraesCS3B01G099000 chr3D 92.986 1055 60 8 1328 2381 42679909 42678868 0.000000e+00 1526.0
14 TraesCS3B01G099000 chr3D 89.777 851 59 13 483 1325 42680688 42679858 0.000000e+00 1064.0
15 TraesCS3B01G099000 chr3D 84.308 701 99 9 1584 2280 42687197 42686504 0.000000e+00 675.0
16 TraesCS3B01G099000 chr3D 77.840 898 146 33 1397 2268 92896048 92895178 9.990000e-140 507.0
17 TraesCS3B01G099000 chr3D 76.700 691 116 27 1584 2257 92813676 92813014 2.980000e-90 342.0
18 TraesCS3B01G099000 chr3D 88.940 217 12 8 2915 3123 42678690 42678478 1.110000e-64 257.0
19 TraesCS3B01G099000 chr3D 89.677 155 7 7 2401 2555 42678888 42678743 4.110000e-44 189.0
20 TraesCS3B01G099000 chr3D 85.185 162 20 1 1359 1520 42687516 42687359 2.490000e-36 163.0
21 TraesCS3B01G099000 chr3D 86.538 104 13 1 487 590 42688211 42688109 2.550000e-21 113.0
22 TraesCS3B01G099000 chr2B 92.562 484 30 4 1 482 604325967 604326446 0.000000e+00 689.0
23 TraesCS3B01G099000 chr6D 92.541 429 28 3 59 485 389969846 389969420 2.060000e-171 612.0
24 TraesCS3B01G099000 chr6D 95.890 73 3 0 1 73 389969934 389969862 5.470000e-23 119.0
25 TraesCS3B01G099000 chr7B 89.938 487 26 9 1 483 135983091 135983558 9.580000e-170 606.0
26 TraesCS3B01G099000 chr7B 81.724 290 40 12 200 485 135981994 135981714 2.420000e-56 230.0
27 TraesCS3B01G099000 chr7B 87.402 127 14 2 1 127 703268765 703268641 9.030000e-31 145.0
28 TraesCS3B01G099000 chr2A 91.705 434 29 6 57 487 181844832 181845261 2.070000e-166 595.0
29 TraesCS3B01G099000 chr2A 97.183 71 2 0 1 71 181837431 181837501 1.520000e-23 121.0
30 TraesCS3B01G099000 chr2D 90.736 421 27 3 57 477 498319573 498319981 4.550000e-153 551.0
31 TraesCS3B01G099000 chr2D 95.890 73 3 0 1 73 498319482 498319554 5.470000e-23 119.0
32 TraesCS3B01G099000 chr5A 84.562 434 58 8 57 485 469134530 469134959 3.720000e-114 422.0
33 TraesCS3B01G099000 chr4D 78.899 327 58 9 158 479 340093579 340093259 8.770000e-51 211.0
34 TraesCS3B01G099000 chr5D 78.659 328 52 14 165 482 25302292 25301973 5.280000e-48 202.0
35 TraesCS3B01G099000 chr6B 100.000 31 0 0 4 34 720008308 720008338 1.210000e-04 58.4
36 TraesCS3B01G099000 chr7D 96.774 31 1 0 1 31 45762388 45762418 6.000000e-03 52.8


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 TraesCS3B01G099000 chr3B 66469014 66472136 3122 True 2553.500000 4719 100.000000 1 3123 2 chr3B.!!$R1 3122
1 TraesCS3B01G099000 chr3B 143509976 143510832 856 False 568.000000 568 79.200000 1397 2245 1 chr3B.!!$F1 848
2 TraesCS3B01G099000 chr3B 143604241 143605138 897 False 481.000000 481 77.047000 1359 2258 1 chr3B.!!$F2 899
3 TraesCS3B01G099000 chr3B 66477651 66479295 1644 True 453.000000 804 83.621000 487 2280 2 chr3B.!!$R2 1793
4 TraesCS3B01G099000 chr3A 54231542 54233728 2186 True 963.333333 1596 90.450667 483 3123 3 chr3A.!!$R1 2640
5 TraesCS3B01G099000 chr3A 547182357 547183240 883 False 520.000000 520 77.962000 1397 2268 1 chr3A.!!$F2 871
6 TraesCS3B01G099000 chr3A 54283984 54285195 1211 True 519.000000 725 85.369500 943 2257 2 chr3A.!!$R2 1314
7 TraesCS3B01G099000 chr3D 42678478 42680688 2210 True 759.000000 1526 90.345000 483 3123 4 chr3D.!!$R3 2640
8 TraesCS3B01G099000 chr3D 92895178 92896048 870 True 507.000000 507 77.840000 1397 2268 1 chr3D.!!$R2 871
9 TraesCS3B01G099000 chr3D 92813014 92813676 662 True 342.000000 342 76.700000 1584 2257 1 chr3D.!!$R1 673
10 TraesCS3B01G099000 chr3D 42686504 42688211 1707 True 317.000000 675 85.343667 487 2280 3 chr3D.!!$R4 1793
11 TraesCS3B01G099000 chr6D 389969420 389969934 514 True 365.500000 612 94.215500 1 485 2 chr6D.!!$R1 484

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
259 290 0.248012 TATGGCGCTCGGTCTTTTCA 59.752 50.0 7.64 0.0 0.00 2.69 F
309 342 0.378257 AAATATGCGTTGGCTGAGCG 59.622 50.0 0.00 0.0 40.82 5.03 F
1790 2008 0.175073 CCCCTACCAGCTCGTGTAAC 59.825 60.0 0.00 0.0 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1544 0.037590 TTTGGATCCACCCTGAACCG 59.962 55.0 15.91 0.00 38.0 4.44 R
1863 2088 0.804364 GCGATCAATCAAGGTGCACA 59.196 50.0 20.43 0.00 0.0 4.57 R
2917 3178 0.532115 GTGGAAGGATGCGGCAAATT 59.468 50.0 6.82 1.69 0.0 1.82 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 4.825546 CAGTATCTGCAGCCCATTTAAG 57.174 45.455 9.47 0.00 0.00 1.85
98 129 2.513204 CACGAGCTCAGCATGGGG 60.513 66.667 15.40 0.00 36.76 4.96
121 152 2.648059 GAGTGGCTGTAATGGCTGAAT 58.352 47.619 0.00 0.00 0.00 2.57
179 210 5.983118 CCTTTTTGGCGTTAATTTTCTCAGT 59.017 36.000 0.00 0.00 0.00 3.41
183 214 5.600908 TGGCGTTAATTTTCTCAGTGTAC 57.399 39.130 0.00 0.00 0.00 2.90
184 215 4.150980 TGGCGTTAATTTTCTCAGTGTACG 59.849 41.667 0.00 0.00 0.00 3.67
198 229 4.810491 TCAGTGTACGGTGGTTAGTTTTTC 59.190 41.667 0.00 0.00 0.00 2.29
200 231 4.812626 AGTGTACGGTGGTTAGTTTTTCTG 59.187 41.667 0.00 0.00 0.00 3.02
208 239 6.362283 CGGTGGTTAGTTTTTCTGCAAATAAG 59.638 38.462 0.00 0.00 0.00 1.73
258 289 1.062148 GTTATGGCGCTCGGTCTTTTC 59.938 52.381 7.64 0.00 0.00 2.29
259 290 0.248012 TATGGCGCTCGGTCTTTTCA 59.752 50.000 7.64 0.00 0.00 2.69
309 342 0.378257 AAATATGCGTTGGCTGAGCG 59.622 50.000 0.00 0.00 40.82 5.03
339 372 0.762418 TTGATAGGTGGGCCCATACG 59.238 55.000 31.45 0.00 34.66 3.06
362 395 3.120321 TGGATACACCCGCAACATATC 57.880 47.619 0.00 0.00 46.17 1.63
366 399 4.578928 GGATACACCCGCAACATATCTTTT 59.421 41.667 0.00 0.00 0.00 2.27
367 400 3.848272 ACACCCGCAACATATCTTTTG 57.152 42.857 0.00 0.00 0.00 2.44
368 401 2.491693 ACACCCGCAACATATCTTTTGG 59.508 45.455 0.00 0.00 0.00 3.28
412 445 6.494842 GTCAAGTTAAGTGACTGCAATTTCA 58.505 36.000 10.62 0.00 41.80 2.69
413 446 6.634436 GTCAAGTTAAGTGACTGCAATTTCAG 59.366 38.462 3.36 3.36 41.80 3.02
419 452 8.482429 GTTAAGTGACTGCAATTTCAGATTTTG 58.518 33.333 12.25 0.00 37.51 2.44
446 479 6.296026 AGTTCTAGCACCAAACTGAACATTA 58.704 36.000 0.00 0.00 37.03 1.90
450 483 3.636300 AGCACCAAACTGAACATTAAGCA 59.364 39.130 0.00 0.00 0.00 3.91
457 490 6.198966 CCAAACTGAACATTAAGCACAAGTTC 59.801 38.462 0.00 0.00 39.11 3.01
463 496 8.565896 TGAACATTAAGCACAAGTTCTATGAT 57.434 30.769 0.00 0.00 39.33 2.45
469 502 5.339008 AGCACAAGTTCTATGATTACCGA 57.661 39.130 0.00 0.00 0.00 4.69
552 585 9.739276 TGGTCCAGATATTAAAATTATAGGCAG 57.261 33.333 0.00 0.00 0.00 4.85
692 733 2.662520 GCGTGCCAAAAATGCAATGTTC 60.663 45.455 0.00 0.00 41.06 3.18
780 821 4.201637 GCAATTAACCGTTTTAAATGCCCG 60.202 41.667 12.56 0.00 35.73 6.13
788 829 4.327627 CCGTTTTAAATGCCCGGTAATTTG 59.672 41.667 17.52 4.82 34.10 2.32
795 836 3.409026 TGCCCGGTAATTTGCATTTTT 57.591 38.095 0.00 0.00 0.00 1.94
799 840 2.093467 CCGGTAATTTGCATTTTTGCCG 59.907 45.455 19.34 19.34 36.82 5.69
801 842 3.060628 CGGTAATTTGCATTTTTGCCGAG 59.939 43.478 20.74 1.43 39.05 4.63
862 947 8.781067 TTCAAAATAGCGTACAAATATGCATC 57.219 30.769 0.19 0.00 44.58 3.91
873 962 1.527034 ATATGCATCCATGGCGTGAC 58.473 50.000 17.93 10.94 32.85 3.67
874 963 0.879839 TATGCATCCATGGCGTGACG 60.880 55.000 17.93 0.00 32.85 4.35
925 1018 0.867746 GCGTGAGTGAAGCATTGTGA 59.132 50.000 0.00 0.00 0.00 3.58
929 1022 3.120752 CGTGAGTGAAGCATTGTGAGAAG 60.121 47.826 0.00 0.00 0.00 2.85
968 1064 2.094659 CAGGAAGCACGCACGTAGG 61.095 63.158 0.00 0.00 0.00 3.18
975 1071 0.928908 GCACGCACGTAGGTAGATCG 60.929 60.000 0.00 0.00 0.00 3.69
976 1072 0.654160 CACGCACGTAGGTAGATCGA 59.346 55.000 0.00 0.00 0.00 3.59
977 1073 1.263484 CACGCACGTAGGTAGATCGAT 59.737 52.381 0.00 0.00 0.00 3.59
978 1074 1.530293 ACGCACGTAGGTAGATCGATC 59.470 52.381 17.91 17.91 0.00 3.69
988 1084 3.634448 AGGTAGATCGATCTGTTGTCCAG 59.366 47.826 33.22 0.00 42.97 3.86
1184 1280 2.091499 TCTTGGATAGGAGCTCCGGTAA 60.091 50.000 26.95 16.64 42.08 2.85
1209 1309 7.275920 AGTATCATCTTTTTCTCCTACGCATT 58.724 34.615 0.00 0.00 0.00 3.56
1213 1313 4.637276 TCTTTTTCTCCTACGCATTGACA 58.363 39.130 0.00 0.00 0.00 3.58
1238 1338 9.011095 CAATCAGGAGATTATGCTAATCATGTT 57.989 33.333 14.38 0.00 42.46 2.71
1269 1373 6.786122 AGTAGACTAAATTAAGTGGCCCAAA 58.214 36.000 0.00 0.00 0.00 3.28
1270 1374 7.235804 AGTAGACTAAATTAAGTGGCCCAAAA 58.764 34.615 0.00 0.00 0.00 2.44
1274 1378 9.095700 AGACTAAATTAAGTGGCCCAAAAATAA 57.904 29.630 0.00 0.00 0.00 1.40
1279 1383 6.809630 TTAAGTGGCCCAAAAATAAATTGC 57.190 33.333 0.00 0.00 0.00 3.56
1280 1384 3.333804 AGTGGCCCAAAAATAAATTGCG 58.666 40.909 0.00 0.00 0.00 4.85
1281 1385 3.007398 AGTGGCCCAAAAATAAATTGCGA 59.993 39.130 0.00 0.00 0.00 5.10
1283 1387 3.937706 TGGCCCAAAAATAAATTGCGATG 59.062 39.130 0.00 0.00 0.00 3.84
1284 1388 3.938334 GGCCCAAAAATAAATTGCGATGT 59.062 39.130 0.00 0.00 0.00 3.06
1286 1390 5.006261 GGCCCAAAAATAAATTGCGATGTAC 59.994 40.000 0.00 0.00 0.00 2.90
1287 1391 5.276161 GCCCAAAAATAAATTGCGATGTACG 60.276 40.000 0.00 0.00 45.66 3.67
1288 1392 5.231147 CCCAAAAATAAATTGCGATGTACGG 59.769 40.000 0.00 0.00 42.83 4.02
1289 1393 6.030849 CCAAAAATAAATTGCGATGTACGGA 58.969 36.000 0.00 0.00 42.83 4.69
1297 1401 2.756829 TGCGATGTACGGAAAAGTTCA 58.243 42.857 0.00 0.00 39.76 3.18
1298 1402 3.331150 TGCGATGTACGGAAAAGTTCAT 58.669 40.909 0.00 0.00 39.76 2.57
1299 1403 3.124466 TGCGATGTACGGAAAAGTTCATG 59.876 43.478 0.00 0.00 39.76 3.07
1300 1404 3.670203 CGATGTACGGAAAAGTTCATGC 58.330 45.455 0.00 0.00 33.32 4.06
1301 1405 3.124466 CGATGTACGGAAAAGTTCATGCA 59.876 43.478 0.00 0.00 33.32 3.96
1302 1406 4.651994 GATGTACGGAAAAGTTCATGCAG 58.348 43.478 0.00 0.00 33.32 4.41
1303 1407 3.472652 TGTACGGAAAAGTTCATGCAGT 58.527 40.909 0.00 0.00 0.00 4.40
1304 1408 3.880490 TGTACGGAAAAGTTCATGCAGTT 59.120 39.130 0.00 0.00 0.00 3.16
1305 1409 3.626028 ACGGAAAAGTTCATGCAGTTC 57.374 42.857 0.00 0.00 0.00 3.01
1315 1419 6.017400 AGTTCATGCAGTTCGATTGAATTT 57.983 33.333 0.00 0.00 36.29 1.82
1319 1423 4.159377 TGCAGTTCGATTGAATTTGACC 57.841 40.909 12.10 0.00 36.29 4.02
1320 1424 3.057596 TGCAGTTCGATTGAATTTGACCC 60.058 43.478 12.10 0.00 36.29 4.46
1325 1429 6.646240 CAGTTCGATTGAATTTGACCCAAAAT 59.354 34.615 0.00 0.00 36.90 1.82
1326 1430 7.171337 CAGTTCGATTGAATTTGACCCAAAATT 59.829 33.333 0.00 0.00 41.34 1.82
1431 1544 2.460757 TTAGTTCCAAGGTGGCGTAC 57.539 50.000 0.00 0.00 37.47 3.67
1654 1872 3.172106 TTGGGCAACGTGGAGGGA 61.172 61.111 0.00 0.00 37.60 4.20
1684 1902 2.613977 CGCTCTCCAGACCAACATCTTT 60.614 50.000 0.00 0.00 0.00 2.52
1790 2008 0.175073 CCCCTACCAGCTCGTGTAAC 59.825 60.000 0.00 0.00 0.00 2.50
1852 2077 4.835678 TGCGGATCAATGCATATATCTGT 58.164 39.130 21.97 0.00 35.90 3.41
1929 2154 0.036010 CGGGTGCTCAAGAACCTCAT 60.036 55.000 7.12 0.00 43.60 2.90
2062 2299 1.167781 CCGCCGTGTTACAGGGTTTT 61.168 55.000 22.65 0.00 40.97 2.43
2122 2359 1.959848 CTCACTGAGCCTGTCGTGA 59.040 57.895 0.00 0.00 36.79 4.35
2143 2380 4.593864 GCGATCCGGAGCCTGACC 62.594 72.222 15.35 0.00 0.00 4.02
2346 2587 9.799106 AAAGAAGGTCTGAATTCATAAGAAAGA 57.201 29.630 8.96 0.00 37.29 2.52
2381 2623 7.343316 TCTTTTTGTGGGAAAGAGGAAAACATA 59.657 33.333 0.00 0.00 38.00 2.29
2382 2624 7.425224 TTTTGTGGGAAAGAGGAAAACATAA 57.575 32.000 0.00 0.00 0.00 1.90
2383 2625 6.648879 TTGTGGGAAAGAGGAAAACATAAG 57.351 37.500 0.00 0.00 0.00 1.73
2384 2626 5.947663 TGTGGGAAAGAGGAAAACATAAGA 58.052 37.500 0.00 0.00 0.00 2.10
2385 2627 6.369629 TGTGGGAAAGAGGAAAACATAAGAA 58.630 36.000 0.00 0.00 0.00 2.52
2386 2628 6.836527 TGTGGGAAAGAGGAAAACATAAGAAA 59.163 34.615 0.00 0.00 0.00 2.52
2387 2629 7.014230 TGTGGGAAAGAGGAAAACATAAGAAAG 59.986 37.037 0.00 0.00 0.00 2.62
2388 2630 7.230712 GTGGGAAAGAGGAAAACATAAGAAAGA 59.769 37.037 0.00 0.00 0.00 2.52
2389 2631 7.782644 TGGGAAAGAGGAAAACATAAGAAAGAA 59.217 33.333 0.00 0.00 0.00 2.52
2390 2632 8.300286 GGGAAAGAGGAAAACATAAGAAAGAAG 58.700 37.037 0.00 0.00 0.00 2.85
2391 2633 9.067986 GGAAAGAGGAAAACATAAGAAAGAAGA 57.932 33.333 0.00 0.00 0.00 2.87
2416 2658 4.681074 AAAAATTGCGGGAAAGAGGAAA 57.319 36.364 0.00 0.00 0.00 3.13
2417 2659 4.681074 AAAATTGCGGGAAAGAGGAAAA 57.319 36.364 0.00 0.00 0.00 2.29
2418 2660 3.660501 AATTGCGGGAAAGAGGAAAAC 57.339 42.857 0.00 0.00 0.00 2.43
2419 2661 2.060050 TTGCGGGAAAGAGGAAAACA 57.940 45.000 0.00 0.00 0.00 2.83
2420 2662 2.286365 TGCGGGAAAGAGGAAAACAT 57.714 45.000 0.00 0.00 0.00 2.71
2518 2779 1.804326 CGTACGACCGGCTTTCCAG 60.804 63.158 10.44 0.00 0.00 3.86
2549 2810 5.389411 GCTGTGCCCGTCAAAATTTTATTTC 60.389 40.000 2.44 0.00 0.00 2.17
3064 3332 7.174599 GGAAATCAACCTCTAATCATCATCAGG 59.825 40.741 0.00 0.00 0.00 3.86
3072 3341 6.149640 CCTCTAATCATCATCAGGCAATCTTG 59.850 42.308 0.00 0.00 0.00 3.02
3121 3390 8.831715 ACAAATTTATGGAAAGAATTGACCAC 57.168 30.769 0.00 0.00 37.97 4.16
3122 3391 7.598493 ACAAATTTATGGAAAGAATTGACCACG 59.402 33.333 0.00 0.00 37.97 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.004106 GCTTAAATGGGCTGCAGATACTG 59.996 47.826 20.43 0.00 34.12 2.74
31 32 4.424061 TGAACAGTAATGCATGTCAAGC 57.576 40.909 0.00 0.00 0.00 4.01
80 111 2.267006 CCCATGCTGAGCTCGTGT 59.733 61.111 9.64 0.00 0.00 4.49
98 129 0.035056 AGCCATTACAGCCACTCCAC 60.035 55.000 0.00 0.00 0.00 4.02
121 152 2.112928 ACACGCCATGTTCAGCCA 59.887 55.556 0.00 0.00 38.98 4.75
179 210 3.560896 GCAGAAAAACTAACCACCGTACA 59.439 43.478 0.00 0.00 0.00 2.90
183 214 3.701532 TTGCAGAAAAACTAACCACCG 57.298 42.857 0.00 0.00 0.00 4.94
184 215 7.207383 ACTTATTTGCAGAAAAACTAACCACC 58.793 34.615 0.00 0.00 0.00 4.61
198 229 7.865706 ACCTCCTTGTATTACTTATTTGCAG 57.134 36.000 0.00 0.00 0.00 4.41
247 278 4.921470 TTTATTCGCTGAAAAGACCGAG 57.079 40.909 0.00 0.00 0.00 4.63
309 342 3.144506 CCACCTATCAATGACTGATGGC 58.855 50.000 0.00 0.00 44.84 4.40
324 357 1.344065 CATACGTATGGGCCCACCTA 58.656 55.000 31.51 14.94 41.11 3.08
339 372 2.319136 TGTTGCGGGTGTATCCATAC 57.681 50.000 0.00 0.00 38.11 2.39
362 395 1.136085 CGTGCACATACGGTCCAAAAG 60.136 52.381 18.64 0.00 40.22 2.27
366 399 2.433491 GCGTGCACATACGGTCCA 60.433 61.111 18.64 0.00 43.87 4.02
410 443 6.061441 TGGTGCTAGAACTTTCAAAATCTGA 58.939 36.000 0.00 0.00 0.00 3.27
412 445 6.959639 TTGGTGCTAGAACTTTCAAAATCT 57.040 33.333 0.00 0.00 0.00 2.40
413 446 7.168135 CAGTTTGGTGCTAGAACTTTCAAAATC 59.832 37.037 0.00 0.00 31.63 2.17
419 452 5.065988 TGTTCAGTTTGGTGCTAGAACTTTC 59.934 40.000 0.00 0.00 37.03 2.62
432 465 5.591099 ACTTGTGCTTAATGTTCAGTTTGG 58.409 37.500 0.00 0.00 0.00 3.28
446 479 5.730550 TCGGTAATCATAGAACTTGTGCTT 58.269 37.500 0.00 0.00 0.00 3.91
653 690 6.585702 TGGCACGCAATAAATTAATGATATGC 59.414 34.615 0.00 0.00 0.00 3.14
780 821 3.993736 ACTCGGCAAAAATGCAAATTACC 59.006 39.130 2.97 0.00 36.33 2.85
788 829 8.628882 AGTAAATAAATACTCGGCAAAAATGC 57.371 30.769 0.00 0.00 30.26 3.56
795 836 8.967664 AAATGGTAGTAAATAAATACTCGGCA 57.032 30.769 0.00 0.00 37.34 5.69
834 911 9.579768 TGCATATTTGTACGCTATTTTGAAATT 57.420 25.926 0.00 0.00 0.00 1.82
835 912 9.748708 ATGCATATTTGTACGCTATTTTGAAAT 57.251 25.926 0.00 0.00 0.00 2.17
855 940 0.879839 CGTCACGCCATGGATGCATA 60.880 55.000 18.40 0.00 0.00 3.14
873 962 0.828022 TAAGGGTAGATGTGCCACCG 59.172 55.000 0.00 0.00 32.84 4.94
874 963 4.910458 ATATAAGGGTAGATGTGCCACC 57.090 45.455 0.00 0.00 0.00 4.61
925 1018 1.274712 CCAGGTTCTGAGCTCCTTCT 58.725 55.000 12.15 0.00 32.44 2.85
929 1022 2.937433 GCTTAACCAGGTTCTGAGCTCC 60.937 54.545 20.34 0.00 32.44 4.70
988 1084 1.135286 GGAAGCCATTGTTAGCTGCAC 60.135 52.381 1.02 0.00 39.87 4.57
1029 1125 1.669927 GGAGGGGGAGGATGAGGAGA 61.670 65.000 0.00 0.00 0.00 3.71
1184 1280 6.222038 TGCGTAGGAGAAAAAGATGATACT 57.778 37.500 0.00 0.00 0.00 2.12
1209 1309 7.738847 TGATTAGCATAATCTCCTGATTGTCA 58.261 34.615 10.09 0.00 42.34 3.58
1213 1313 9.011095 CAACATGATTAGCATAATCTCCTGATT 57.989 33.333 0.00 0.00 44.32 2.57
1262 1366 3.938334 ACATCGCAATTTATTTTTGGGCC 59.062 39.130 0.00 0.00 37.06 5.80
1269 1373 7.309920 ACTTTTCCGTACATCGCAATTTATTT 58.690 30.769 0.00 0.00 38.35 1.40
1270 1374 6.848451 ACTTTTCCGTACATCGCAATTTATT 58.152 32.000 0.00 0.00 38.35 1.40
1274 1378 4.214545 TGAACTTTTCCGTACATCGCAATT 59.785 37.500 0.00 0.00 38.35 2.32
1279 1383 3.124466 TGCATGAACTTTTCCGTACATCG 59.876 43.478 0.00 0.00 39.52 3.84
1280 1384 4.154195 ACTGCATGAACTTTTCCGTACATC 59.846 41.667 0.00 0.00 0.00 3.06
1281 1385 4.072131 ACTGCATGAACTTTTCCGTACAT 58.928 39.130 0.00 0.00 0.00 2.29
1283 1387 4.464112 GAACTGCATGAACTTTTCCGTAC 58.536 43.478 0.00 0.00 0.00 3.67
1284 1388 3.185594 CGAACTGCATGAACTTTTCCGTA 59.814 43.478 0.00 0.00 0.00 4.02
1286 1390 2.223144 TCGAACTGCATGAACTTTTCCG 59.777 45.455 0.00 0.00 0.00 4.30
1287 1391 3.896648 TCGAACTGCATGAACTTTTCC 57.103 42.857 0.00 0.00 0.00 3.13
1288 1392 5.451908 TCAATCGAACTGCATGAACTTTTC 58.548 37.500 0.00 0.00 0.00 2.29
1289 1393 5.437289 TCAATCGAACTGCATGAACTTTT 57.563 34.783 0.00 0.00 0.00 2.27
1290 1394 5.437289 TTCAATCGAACTGCATGAACTTT 57.563 34.783 0.00 0.00 0.00 2.66
1291 1395 5.633830 ATTCAATCGAACTGCATGAACTT 57.366 34.783 0.00 0.00 33.29 2.66
1292 1396 5.633830 AATTCAATCGAACTGCATGAACT 57.366 34.783 0.00 0.00 33.29 3.01
1293 1397 5.858049 TCAAATTCAATCGAACTGCATGAAC 59.142 36.000 0.00 0.00 33.29 3.18
1294 1398 5.858049 GTCAAATTCAATCGAACTGCATGAA 59.142 36.000 0.00 0.00 32.81 2.57
1295 1399 5.393124 GTCAAATTCAATCGAACTGCATGA 58.607 37.500 0.00 0.00 32.81 3.07
1296 1400 4.560035 GGTCAAATTCAATCGAACTGCATG 59.440 41.667 0.00 0.00 32.81 4.06
1297 1401 4.380867 GGGTCAAATTCAATCGAACTGCAT 60.381 41.667 0.00 0.00 32.81 3.96
1298 1402 3.057596 GGGTCAAATTCAATCGAACTGCA 60.058 43.478 0.00 0.00 32.81 4.41
1299 1403 3.057596 TGGGTCAAATTCAATCGAACTGC 60.058 43.478 0.00 0.00 32.81 4.40
1300 1404 4.764679 TGGGTCAAATTCAATCGAACTG 57.235 40.909 0.00 0.00 32.81 3.16
1301 1405 5.782893 TTTGGGTCAAATTCAATCGAACT 57.217 34.783 0.00 0.00 32.81 3.01
1302 1406 7.420184 AATTTTGGGTCAAATTCAATCGAAC 57.580 32.000 0.00 0.00 33.19 3.95
1303 1407 9.547753 TTTAATTTTGGGTCAAATTCAATCGAA 57.452 25.926 0.00 0.00 33.19 3.71
1304 1408 9.717942 ATTTAATTTTGGGTCAAATTCAATCGA 57.282 25.926 0.00 0.00 33.19 3.59
1315 1419 5.788450 ACATCGCAATTTAATTTTGGGTCA 58.212 33.333 12.46 0.41 38.00 4.02
1319 1423 8.417780 TTCCATACATCGCAATTTAATTTTGG 57.582 30.769 0.00 0.00 0.00 3.28
1325 1429 8.300286 TCAACTTTTCCATACATCGCAATTTAA 58.700 29.630 0.00 0.00 0.00 1.52
1326 1430 7.821652 TCAACTTTTCCATACATCGCAATTTA 58.178 30.769 0.00 0.00 0.00 1.40
1431 1544 0.037590 TTTGGATCCACCCTGAACCG 59.962 55.000 15.91 0.00 38.00 4.44
1482 1595 1.131928 AGAAGGCCGTTACAACCCCT 61.132 55.000 0.00 0.00 0.00 4.79
1573 1788 2.222976 CGACGTGAGCTACAAGATACGT 60.223 50.000 0.00 0.00 45.92 3.57
1575 1790 2.353889 TCCGACGTGAGCTACAAGATAC 59.646 50.000 0.00 0.00 0.00 2.24
1577 1792 1.402259 CTCCGACGTGAGCTACAAGAT 59.598 52.381 0.00 0.00 0.00 2.40
1684 1902 1.667830 CTCGCCTTTGCCGTTCAGA 60.668 57.895 0.00 0.00 0.00 3.27
1790 2008 2.911636 AGCTAGGGGATGATTGATGGAG 59.088 50.000 0.00 0.00 0.00 3.86
1863 2088 0.804364 GCGATCAATCAAGGTGCACA 59.196 50.000 20.43 0.00 0.00 4.57
2062 2299 2.731571 GGGGCAGCCATAGACGTCA 61.732 63.158 19.50 4.13 0.00 4.35
2122 2359 3.771160 AGGCTCCGGATCGCGTTT 61.771 61.111 3.57 0.00 0.00 3.60
2395 2637 4.681074 TTTCCTCTTTCCCGCAATTTTT 57.319 36.364 0.00 0.00 0.00 1.94
2396 2638 4.141824 TGTTTTCCTCTTTCCCGCAATTTT 60.142 37.500 0.00 0.00 0.00 1.82
2397 2639 3.386402 TGTTTTCCTCTTTCCCGCAATTT 59.614 39.130 0.00 0.00 0.00 1.82
2398 2640 2.962421 TGTTTTCCTCTTTCCCGCAATT 59.038 40.909 0.00 0.00 0.00 2.32
2399 2641 2.593026 TGTTTTCCTCTTTCCCGCAAT 58.407 42.857 0.00 0.00 0.00 3.56
2400 2642 2.060050 TGTTTTCCTCTTTCCCGCAA 57.940 45.000 0.00 0.00 0.00 4.85
2401 2643 2.286365 ATGTTTTCCTCTTTCCCGCA 57.714 45.000 0.00 0.00 0.00 5.69
2402 2644 3.317150 CAAATGTTTTCCTCTTTCCCGC 58.683 45.455 0.00 0.00 0.00 6.13
2403 2645 3.320826 ACCAAATGTTTTCCTCTTTCCCG 59.679 43.478 0.00 0.00 0.00 5.14
2404 2646 4.955811 ACCAAATGTTTTCCTCTTTCCC 57.044 40.909 0.00 0.00 0.00 3.97
2405 2647 6.264518 TCACTACCAAATGTTTTCCTCTTTCC 59.735 38.462 0.00 0.00 0.00 3.13
2406 2648 7.272037 TCACTACCAAATGTTTTCCTCTTTC 57.728 36.000 0.00 0.00 0.00 2.62
2407 2649 7.039714 GGATCACTACCAAATGTTTTCCTCTTT 60.040 37.037 0.00 0.00 0.00 2.52
2408 2650 6.434340 GGATCACTACCAAATGTTTTCCTCTT 59.566 38.462 0.00 0.00 0.00 2.85
2409 2651 5.946377 GGATCACTACCAAATGTTTTCCTCT 59.054 40.000 0.00 0.00 0.00 3.69
2410 2652 5.125578 GGGATCACTACCAAATGTTTTCCTC 59.874 44.000 0.00 0.00 0.00 3.71
2411 2653 5.016831 GGGATCACTACCAAATGTTTTCCT 58.983 41.667 0.00 0.00 0.00 3.36
2412 2654 4.770010 TGGGATCACTACCAAATGTTTTCC 59.230 41.667 0.00 0.00 32.89 3.13
2413 2655 5.975693 TGGGATCACTACCAAATGTTTTC 57.024 39.130 0.00 0.00 32.89 2.29
2472 2714 6.293462 GGAGAACGAACAAATAAGCTGAAACT 60.293 38.462 0.00 0.00 0.00 2.66
2917 3178 0.532115 GTGGAAGGATGCGGCAAATT 59.468 50.000 6.82 1.69 0.00 1.82
2962 3228 2.363306 TTGGTCTGATTTGGCAGTGT 57.637 45.000 0.00 0.00 37.20 3.55
2963 3229 3.087031 AGATTGGTCTGATTTGGCAGTG 58.913 45.455 0.00 0.00 37.20 3.66
3030 3296 2.025887 AGAGGTTGATTTCCGGCTGATT 60.026 45.455 0.00 0.00 0.00 2.57
3095 3364 9.271828 GTGGTCAATTCTTTCCATAAATTTGTT 57.728 29.630 0.00 0.00 32.45 2.83


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

AutoCloner maintained by Alex Coulton.