Multiple sequence alignment - TraesCS6A01G155100

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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 TraesCS6A01G155100 chr6A 100.000 2243 0 0 1 2243 143753766 143751524 0.000000e+00 4143.0
1 TraesCS6A01G155100 chr6A 87.379 412 32 17 1434 1838 586409002 586408604 2.630000e-124 455.0
2 TraesCS6A01G155100 chr6A 87.317 410 30 17 1439 1838 166932980 166933377 1.220000e-122 449.0
3 TraesCS6A01G155100 chr6A 87.786 393 35 9 1454 1838 541106289 541106676 4.390000e-122 448.0
4 TraesCS6A01G155100 chr6A 87.918 389 28 12 1457 1838 432508809 432509185 7.350000e-120 440.0
5 TraesCS6A01G155100 chr6A 86.829 410 29 17 1439 1840 225206388 225206780 3.420000e-118 435.0
6 TraesCS6A01G155100 chr6A 86.634 404 38 10 1438 1840 327492891 327492503 1.230000e-117 433.0
7 TraesCS6A01G155100 chr6A 82.451 359 44 15 1271 1623 426630366 426630021 1.680000e-76 296.0
8 TraesCS6A01G155100 chr6A 82.622 328 41 13 1268 1584 595895519 595895841 2.190000e-70 276.0
9 TraesCS6A01G155100 chr6A 82.196 337 42 15 1271 1597 506418904 506419232 7.890000e-70 274.0
10 TraesCS6A01G155100 chr6A 100.000 49 0 0 2183 2231 601937824 601937872 8.530000e-15 91.6
11 TraesCS6A01G155100 chr6D 92.689 1272 46 7 1 1269 115332010 115330783 0.000000e+00 1790.0
12 TraesCS6A01G155100 chr6D 88.673 309 29 3 1839 2144 115330790 115330485 2.720000e-99 372.0
13 TraesCS6A01G155100 chr6D 95.122 41 2 0 130 170 325600871 325600831 5.170000e-07 65.8
14 TraesCS6A01G155100 chr6B 84.916 895 54 29 1 841 204662089 204661222 0.000000e+00 830.0
15 TraesCS6A01G155100 chr6B 90.572 647 27 15 627 1269 204661440 204660824 0.000000e+00 826.0
16 TraesCS6A01G155100 chr6B 88.669 353 33 4 1839 2187 204660831 204660482 7.410000e-115 424.0
17 TraesCS6A01G155100 chr6B 97.436 39 1 0 132 170 694112829 694112791 1.440000e-07 67.6
18 TraesCS6A01G155100 chr3A 88.101 395 33 10 1453 1838 126128172 126128561 7.300000e-125 457.0
19 TraesCS6A01G155100 chr3A 82.584 356 48 11 1271 1616 678000632 678000983 3.620000e-78 302.0
20 TraesCS6A01G155100 chr4D 87.286 409 37 10 1438 1841 304574032 304574430 9.440000e-124 453.0
21 TraesCS6A01G155100 chr4D 83.041 342 47 11 1267 1603 304573690 304574025 1.300000e-77 300.0
22 TraesCS6A01G155100 chr7D 86.486 407 39 14 1439 1838 599729276 599729673 1.230000e-117 433.0
23 TraesCS6A01G155100 chr7A 82.796 372 34 20 1271 1616 536602265 536601898 2.800000e-79 305.0
24 TraesCS6A01G155100 chr7A 82.436 353 49 11 1271 1623 596658599 596658260 1.680000e-76 296.0
25 TraesCS6A01G155100 chr2A 83.929 336 33 14 1261 1581 654680714 654681043 3.620000e-78 302.0
26 TraesCS6A01G155100 chr7B 100.000 51 0 0 2181 2231 217620503 217620553 6.590000e-16 95.3
27 TraesCS6A01G155100 chr7B 100.000 49 0 0 2183 2231 427825147 427825195 8.530000e-15 91.6
28 TraesCS6A01G155100 chr7B 97.561 41 1 0 130 170 367017100 367017140 1.110000e-08 71.3
29 TraesCS6A01G155100 chr7B 95.455 44 2 0 127 170 570465369 570465326 1.110000e-08 71.3
30 TraesCS6A01G155100 chr7B 97.436 39 1 0 132 170 367017208 367017170 1.440000e-07 67.6
31 TraesCS6A01G155100 chr1A 100.000 51 0 0 2181 2231 427568595 427568545 6.590000e-16 95.3
32 TraesCS6A01G155100 chr1A 98.113 53 0 1 2180 2231 186733816 186733868 8.530000e-15 91.6
33 TraesCS6A01G155100 chr1A 90.698 43 4 0 88 130 363050585 363050543 8.650000e-05 58.4
34 TraesCS6A01G155100 chr4B 100.000 49 0 0 2183 2231 31657863 31657911 8.530000e-15 91.6
35 TraesCS6A01G155100 chr3B 92.308 65 3 2 2168 2230 37966905 37966841 8.530000e-15 91.6
36 TraesCS6A01G155100 chr5B 100.000 48 0 0 2184 2231 402872053 402872100 3.070000e-14 89.8
37 TraesCS6A01G155100 chr5B 100.000 48 0 0 2184 2231 419524173 419524126 3.070000e-14 89.8
38 TraesCS6A01G155100 chr5B 95.745 47 2 0 124 170 580688936 580688890 2.390000e-10 76.8
39 TraesCS6A01G155100 chr5B 95.238 42 2 0 129 170 707007634 707007675 1.440000e-07 67.6
40 TraesCS6A01G155100 chr2B 97.368 38 1 0 38 75 11146085 11146122 5.170000e-07 65.8
41 TraesCS6A01G155100 chr5A 95.000 40 2 0 131 170 657987084 657987045 1.860000e-06 63.9


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 TraesCS6A01G155100 chr6A 143751524 143753766 2242 True 4143.000000 4143 100.000000 1 2243 1 chr6A.!!$R1 2242
1 TraesCS6A01G155100 chr6D 115330485 115332010 1525 True 1081.000000 1790 90.681000 1 2144 2 chr6D.!!$R2 2143
2 TraesCS6A01G155100 chr6B 204660482 204662089 1607 True 693.333333 830 88.052333 1 2187 3 chr6B.!!$R2 2186
3 TraesCS6A01G155100 chr4D 304573690 304574430 740 False 376.500000 453 85.163500 1267 1841 2 chr4D.!!$F1 574

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
367 396 0.506932 AACATGTTGAACGCTCGTCG 59.493 50.0 11.07 0.0 45.38 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1504 0.179217 CAACATCACACACGGATGCG 60.179 55.0 4.58 4.58 44.68 4.73 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
145 146 0.614134 AGTTGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
158 159 1.894466 TCCGTCCCGAATTACTTGTCA 59.106 47.619 0.00 0.00 0.00 3.58
234 245 7.931578 ATTAAATCACGGACACTTATTTGGA 57.068 32.000 0.00 0.00 0.00 3.53
235 246 5.622770 AAATCACGGACACTTATTTGGAC 57.377 39.130 0.00 0.00 0.00 4.02
236 247 3.755112 TCACGGACACTTATTTGGACA 57.245 42.857 0.00 0.00 0.00 4.02
279 291 7.993183 AGGGATATTTGACAGAACATTAATCGT 59.007 33.333 0.00 0.00 0.00 3.73
367 396 0.506932 AACATGTTGAACGCTCGTCG 59.493 50.000 11.07 0.00 45.38 5.12
410 439 8.196771 TGCTAAATTGACATGAATTAATGGTCC 58.803 33.333 7.72 0.00 31.46 4.46
417 446 8.450578 TGACATGAATTAATGGTCCAGAATAC 57.549 34.615 7.72 0.00 31.46 1.89
436 465 2.547990 ACTTGGATCTACCCCTTTCGT 58.452 47.619 0.00 0.00 38.00 3.85
437 466 3.716431 ACTTGGATCTACCCCTTTCGTA 58.284 45.455 0.00 0.00 38.00 3.43
545 599 4.808077 ATCTCTTTTACTGCATGCATCG 57.192 40.909 22.97 13.40 0.00 3.84
613 668 5.539955 AGGCAACAACTAAATGAGGTTCATT 59.460 36.000 0.00 0.00 44.40 2.57
622 677 3.420893 AATGAGGTTCATTTTCCTCGCA 58.579 40.909 6.71 0.00 44.03 5.10
623 678 3.826157 AATGAGGTTCATTTTCCTCGCAA 59.174 39.130 6.71 0.00 44.03 4.85
624 679 3.915437 GAGGTTCATTTTCCTCGCAAA 57.085 42.857 0.00 0.00 40.36 3.68
625 680 3.565516 GAGGTTCATTTTCCTCGCAAAC 58.434 45.455 0.00 0.00 40.36 2.93
626 681 3.222603 AGGTTCATTTTCCTCGCAAACT 58.777 40.909 0.00 0.00 0.00 2.66
627 682 4.394729 AGGTTCATTTTCCTCGCAAACTA 58.605 39.130 0.00 0.00 0.00 2.24
628 683 4.825085 AGGTTCATTTTCCTCGCAAACTAA 59.175 37.500 0.00 0.00 0.00 2.24
629 684 5.300792 AGGTTCATTTTCCTCGCAAACTAAA 59.699 36.000 0.00 0.00 0.00 1.85
630 685 6.015434 AGGTTCATTTTCCTCGCAAACTAAAT 60.015 34.615 0.00 0.00 0.00 1.40
631 686 6.089417 GGTTCATTTTCCTCGCAAACTAAATG 59.911 38.462 0.00 0.00 35.42 2.32
632 687 6.567687 TCATTTTCCTCGCAAACTAAATGA 57.432 33.333 0.00 0.00 38.77 2.57
633 688 6.611381 TCATTTTCCTCGCAAACTAAATGAG 58.389 36.000 0.00 0.00 37.19 2.90
634 689 5.371115 TTTTCCTCGCAAACTAAATGAGG 57.629 39.130 0.12 0.12 46.06 3.86
635 690 3.695830 TCCTCGCAAACTAAATGAGGT 57.304 42.857 6.48 0.00 45.15 3.85
636 691 4.015872 TCCTCGCAAACTAAATGAGGTT 57.984 40.909 6.48 0.00 45.15 3.50
637 692 4.000988 TCCTCGCAAACTAAATGAGGTTC 58.999 43.478 6.48 0.00 45.15 3.62
638 693 3.751175 CCTCGCAAACTAAATGAGGTTCA 59.249 43.478 0.00 0.00 41.04 3.18
639 694 4.396166 CCTCGCAAACTAAATGAGGTTCAT 59.604 41.667 0.00 0.00 41.04 2.57
640 695 5.295431 TCGCAAACTAAATGAGGTTCATG 57.705 39.130 0.00 0.00 37.15 3.07
641 696 4.759693 TCGCAAACTAAATGAGGTTCATGT 59.240 37.500 0.00 0.00 37.15 3.21
642 697 5.240623 TCGCAAACTAAATGAGGTTCATGTT 59.759 36.000 0.00 0.00 37.15 2.71
691 749 6.197364 TGGAAACAAGTACAAACGTGAATT 57.803 33.333 0.00 0.00 38.33 2.17
1221 1279 1.929836 GATGAGAACGTGATGCACCTC 59.070 52.381 0.00 0.00 0.00 3.85
1262 1320 0.466543 ACAGACCCAACGCAGTGTAA 59.533 50.000 0.00 0.00 45.00 2.41
1263 1321 1.071699 ACAGACCCAACGCAGTGTAAT 59.928 47.619 0.00 0.00 45.00 1.89
1264 1322 1.732259 CAGACCCAACGCAGTGTAATC 59.268 52.381 0.00 0.00 45.00 1.75
1265 1323 1.623811 AGACCCAACGCAGTGTAATCT 59.376 47.619 0.00 0.00 45.00 2.40
1266 1324 2.000447 GACCCAACGCAGTGTAATCTC 59.000 52.381 0.00 0.00 45.00 2.75
1267 1325 1.346395 ACCCAACGCAGTGTAATCTCA 59.654 47.619 0.00 0.00 45.00 3.27
1268 1326 2.224426 ACCCAACGCAGTGTAATCTCAA 60.224 45.455 0.00 0.00 45.00 3.02
1269 1327 2.159627 CCCAACGCAGTGTAATCTCAAC 59.840 50.000 0.00 0.00 45.00 3.18
1270 1328 2.159841 CCAACGCAGTGTAATCTCAACG 60.160 50.000 0.00 0.00 45.00 4.10
1271 1329 2.717580 ACGCAGTGTAATCTCAACGA 57.282 45.000 0.00 0.00 42.51 3.85
1295 1353 9.450807 CGAGAAAATTCTTTATTTGACACTGTT 57.549 29.630 0.00 0.00 37.73 3.16
1351 1409 8.942338 AAAGTTTTTCTTCCTTATTTGACACC 57.058 30.769 0.00 0.00 35.02 4.16
1355 1413 8.626526 GTTTTTCTTCCTTATTTGACACCAGTA 58.373 33.333 0.00 0.00 0.00 2.74
1361 1419 9.280174 CTTCCTTATTTGACACCAGTACTAAAA 57.720 33.333 0.00 0.00 0.00 1.52
1404 1462 6.657541 ACTTCCGTTCATTTTGAGCCTAAATA 59.342 34.615 0.00 0.00 0.00 1.40
1438 1496 1.305213 ATTTTGCCCCTCATGCGGT 60.305 52.632 0.13 0.00 0.00 5.68
1446 1504 1.439353 CCCTCATGCGGTATGTGTGC 61.439 60.000 5.97 0.00 38.01 4.57
1447 1505 1.637934 CTCATGCGGTATGTGTGCG 59.362 57.895 5.97 0.00 38.01 5.34
1449 1507 2.435762 ATGCGGTATGTGTGCGCA 60.436 55.556 5.66 5.66 39.89 6.09
1450 1508 1.819208 ATGCGGTATGTGTGCGCAT 60.819 52.632 15.91 0.00 40.77 4.73
1451 1509 1.775039 ATGCGGTATGTGTGCGCATC 61.775 55.000 15.91 11.19 41.60 3.91
1460 1520 3.041351 GTGCGCATCCGTGTGTGA 61.041 61.111 15.91 0.00 38.13 3.58
1469 1529 1.204062 CCGTGTGTGATGTTGCGTC 59.796 57.895 0.00 0.00 0.00 5.19
1545 1646 4.854924 TGCCTGCGTGTGTGCTGT 62.855 61.111 0.00 0.00 35.36 4.40
1556 1707 2.037702 TGTGCTGTTGCGTGTGTGT 61.038 52.632 0.00 0.00 43.34 3.72
1607 1832 2.746904 GGTGCATGTGTATGTGTTGCTA 59.253 45.455 0.00 0.00 36.65 3.49
1612 1837 2.409012 TGTGTATGTGTTGCTACGTGG 58.591 47.619 0.00 0.00 0.00 4.94
1636 1861 2.267006 CTGCCCTCGCACTGATGT 59.733 61.111 0.00 0.00 41.12 3.06
1647 1872 0.658244 CACTGATGTTGCGTGTGTGC 60.658 55.000 0.00 0.00 0.00 4.57
1648 1873 1.094650 ACTGATGTTGCGTGTGTGCA 61.095 50.000 0.00 0.00 44.61 4.57
1702 1927 3.375642 GCAAAAGAGTCTTTTCAGGTGC 58.624 45.455 24.77 21.36 0.00 5.01
1727 1952 5.975693 TTTAGGCTCAAAATGAACGGAAT 57.024 34.783 0.00 0.00 0.00 3.01
1730 1955 3.573967 AGGCTCAAAATGAACGGAATTGT 59.426 39.130 0.00 0.00 0.00 2.71
1776 2001 8.606830 AGAACTAGTGTCAAATAGGGAAGAAAT 58.393 33.333 0.00 0.00 0.00 2.17
1777 2002 9.232473 GAACTAGTGTCAAATAGGGAAGAAATT 57.768 33.333 0.00 0.00 0.00 1.82
1778 2003 8.567285 ACTAGTGTCAAATAGGGAAGAAATTG 57.433 34.615 0.00 0.00 0.00 2.32
1783 2008 9.325198 GTGTCAAATAGGGAAGAAATTGTTTTT 57.675 29.630 0.00 0.00 0.00 1.94
1879 2106 8.080083 TGTTTGAATAACTAGTCTTCGAAACC 57.920 34.615 22.61 14.57 0.00 3.27
1880 2107 7.711772 TGTTTGAATAACTAGTCTTCGAAACCA 59.288 33.333 22.61 15.88 0.00 3.67
1881 2108 8.718734 GTTTGAATAACTAGTCTTCGAAACCAT 58.281 33.333 16.64 0.00 0.00 3.55
1882 2109 8.842358 TTGAATAACTAGTCTTCGAAACCATT 57.158 30.769 0.00 0.00 0.00 3.16
1922 2149 9.914131 CCAGTTTTAGGAGGATTTTTAGAAAAG 57.086 33.333 0.00 0.00 0.00 2.27
1958 2188 7.642586 AGTTGTTTTTGTTAAAGCTAGCTTACG 59.357 33.333 29.52 0.00 34.84 3.18
1964 2194 8.726870 TTTGTTAAAGCTAGCTTACGGAATAT 57.273 30.769 29.52 14.13 34.84 1.28
2014 2244 5.750484 TTCGACATTGATACACGTACAAC 57.250 39.130 0.00 0.00 0.00 3.32
2043 2273 5.301805 CCTTTTTGAAGGCTTTGTCTAGGAA 59.698 40.000 0.00 0.00 32.43 3.36
2086 2316 4.575885 GCATGTAGTAGGGTTTGTGAAGA 58.424 43.478 0.00 0.00 0.00 2.87
2093 2323 3.884037 AGGGTTTGTGAAGATCCTGTT 57.116 42.857 0.00 0.00 0.00 3.16
2105 2335 3.034635 AGATCCTGTTGCGAGGTAGATT 58.965 45.455 0.00 0.00 34.36 2.40
2112 2342 5.584649 CCTGTTGCGAGGTAGATTCAATTTA 59.415 40.000 0.00 0.00 0.00 1.40
2115 2345 7.047891 TGTTGCGAGGTAGATTCAATTTAGAT 58.952 34.615 0.00 0.00 0.00 1.98
2138 2368 5.977635 TGTCGATATTGGACTTTGTCTCAT 58.022 37.500 8.69 0.00 35.45 2.90
2169 2399 0.543277 ATCTCAATGCAGAGGCCGAA 59.457 50.000 0.00 0.00 40.13 4.30
2171 2401 0.107993 CTCAATGCAGAGGCCGAAGA 60.108 55.000 0.00 0.00 40.13 2.87
2181 2411 1.153147 GGCCGAAGACATTCCCCTC 60.153 63.158 0.00 0.00 31.21 4.30
2186 2416 3.421844 CCGAAGACATTCCCCTCTTTTT 58.578 45.455 0.00 0.00 31.21 1.94
2205 2435 2.727103 TTTTTGAGGAACCGGCAGG 58.273 52.632 0.00 0.00 45.13 4.85
2206 2436 0.183971 TTTTTGAGGAACCGGCAGGA 59.816 50.000 10.86 0.00 41.02 3.86
2207 2437 0.250727 TTTTGAGGAACCGGCAGGAG 60.251 55.000 10.86 0.00 41.02 3.69
2208 2438 2.748058 TTTGAGGAACCGGCAGGAGC 62.748 60.000 10.86 0.05 41.02 4.70
2209 2439 3.706373 GAGGAACCGGCAGGAGCA 61.706 66.667 10.86 0.00 44.61 4.26
2210 2440 3.959991 GAGGAACCGGCAGGAGCAC 62.960 68.421 10.86 0.00 44.61 4.40
2211 2441 4.021925 GGAACCGGCAGGAGCACT 62.022 66.667 10.86 0.00 44.61 4.40
2220 2450 3.025924 CAGGAGCACTGCCTTTTCA 57.974 52.632 0.00 0.00 40.97 2.69
2221 2451 1.542492 CAGGAGCACTGCCTTTTCAT 58.458 50.000 0.00 0.00 40.97 2.57
2222 2452 2.715046 CAGGAGCACTGCCTTTTCATA 58.285 47.619 0.00 0.00 40.97 2.15
2223 2453 3.285484 CAGGAGCACTGCCTTTTCATAT 58.715 45.455 0.00 0.00 40.97 1.78
2224 2454 4.454678 CAGGAGCACTGCCTTTTCATATA 58.545 43.478 0.00 0.00 40.97 0.86
2225 2455 4.883585 CAGGAGCACTGCCTTTTCATATAA 59.116 41.667 0.00 0.00 40.97 0.98
2226 2456 5.008415 CAGGAGCACTGCCTTTTCATATAAG 59.992 44.000 0.00 0.00 40.97 1.73
2227 2457 5.104360 AGGAGCACTGCCTTTTCATATAAGA 60.104 40.000 0.00 0.00 29.44 2.10
2228 2458 5.590259 GGAGCACTGCCTTTTCATATAAGAA 59.410 40.000 0.00 0.00 0.00 2.52
2229 2459 6.238593 GGAGCACTGCCTTTTCATATAAGAAG 60.239 42.308 0.00 0.00 0.00 2.85
2230 2460 5.591877 AGCACTGCCTTTTCATATAAGAAGG 59.408 40.000 0.00 0.00 41.23 3.46
2231 2461 5.358160 GCACTGCCTTTTCATATAAGAAGGT 59.642 40.000 0.00 0.00 40.57 3.50
2232 2462 6.542370 GCACTGCCTTTTCATATAAGAAGGTA 59.458 38.462 0.00 0.00 40.57 3.08
2235 2465 8.738645 CTGCCTTTTCATATAAGAAGGTAGTT 57.261 34.615 5.40 0.00 43.04 2.24
2236 2466 9.178758 CTGCCTTTTCATATAAGAAGGTAGTTT 57.821 33.333 5.40 0.00 43.04 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 2.827921 GGACGGAGGGAGTACAACTTTA 59.172 50.000 0.00 0.00 0.00 1.85
140 141 8.300466 CATTTCTTTGACAAGTAATTCGGGACG 61.300 40.741 0.00 0.00 39.36 4.79
145 146 8.853345 CAATCCATTTCTTTGACAAGTAATTCG 58.147 33.333 0.00 0.00 29.89 3.34
158 159 4.853924 ACTTGTCGCAATCCATTTCTTT 57.146 36.364 0.00 0.00 0.00 2.52
343 355 5.276207 CGACGAGCGTTCAACATGTTTATAT 60.276 40.000 8.77 0.00 34.64 0.86
410 439 5.896073 AAGGGGTAGATCCAAGTATTCTG 57.104 43.478 0.00 0.00 38.11 3.02
417 446 4.957684 ATACGAAAGGGGTAGATCCAAG 57.042 45.455 0.00 0.00 38.11 3.61
534 588 2.540228 ATGGCGACGATGCATGCAG 61.540 57.895 26.69 15.79 36.28 4.41
537 591 0.936600 TAACATGGCGACGATGCATG 59.063 50.000 2.46 0.00 36.28 4.06
538 592 1.202521 TCTAACATGGCGACGATGCAT 60.203 47.619 0.00 0.00 36.28 3.96
545 599 2.953466 TACCAGTCTAACATGGCGAC 57.047 50.000 0.00 0.27 40.45 5.19
613 668 4.394729 ACCTCATTTAGTTTGCGAGGAAA 58.605 39.130 10.59 0.00 45.08 3.13
617 672 5.106555 ACATGAACCTCATTTAGTTTGCGAG 60.107 40.000 0.00 0.00 34.28 5.03
618 673 4.759693 ACATGAACCTCATTTAGTTTGCGA 59.240 37.500 0.00 0.00 34.28 5.10
619 674 5.046910 ACATGAACCTCATTTAGTTTGCG 57.953 39.130 0.00 0.00 34.28 4.85
620 675 8.810652 TTTAACATGAACCTCATTTAGTTTGC 57.189 30.769 0.00 0.00 34.28 3.68
691 749 4.494091 GAGAATCCACTCTCCCATTTCA 57.506 45.455 0.00 0.00 36.60 2.69
714 772 2.099098 AGAGGTGCCAAACGTTTCTTTG 59.901 45.455 11.37 0.00 0.00 2.77
969 1027 2.372690 CGCCGGTCAGTTCACTTCG 61.373 63.158 1.90 0.00 0.00 3.79
1126 1184 2.285368 AGCCATCCCACCGGAGAA 60.285 61.111 9.46 0.00 43.12 2.87
1138 1196 0.620556 ACGGGAGTTTGATCAGCCAT 59.379 50.000 0.00 0.00 43.33 4.40
1236 1294 1.899814 TGCGTTGGGTCTGTCTAATCT 59.100 47.619 0.00 0.00 0.00 2.40
1248 1306 2.093306 TGAGATTACACTGCGTTGGG 57.907 50.000 0.00 0.00 0.00 4.12
1263 1321 9.878599 GTCAAATAAAGAATTTTCTCGTTGAGA 57.121 29.630 0.00 0.00 40.09 3.27
1264 1322 9.663904 TGTCAAATAAAGAATTTTCTCGTTGAG 57.336 29.630 0.00 0.00 40.09 3.02
1265 1323 9.445786 GTGTCAAATAAAGAATTTTCTCGTTGA 57.554 29.630 0.00 0.11 40.09 3.18
1266 1324 9.450807 AGTGTCAAATAAAGAATTTTCTCGTTG 57.549 29.630 0.00 0.00 40.09 4.10
1267 1325 9.450807 CAGTGTCAAATAAAGAATTTTCTCGTT 57.549 29.630 0.00 0.00 40.09 3.85
1268 1326 8.621286 ACAGTGTCAAATAAAGAATTTTCTCGT 58.379 29.630 0.00 0.00 40.09 4.18
1269 1327 9.450807 AACAGTGTCAAATAAAGAATTTTCTCG 57.549 29.630 0.00 0.00 40.09 4.04
1387 1445 6.945435 TCAGGTGTTATTTAGGCTCAAAATGA 59.055 34.615 5.67 0.00 0.00 2.57
1404 1462 4.359706 GCAAAATCGTCTTTTCAGGTGTT 58.640 39.130 0.00 0.00 0.00 3.32
1438 1496 1.079474 ACACGGATGCGCACACATA 60.079 52.632 14.90 0.00 0.00 2.29
1446 1504 0.179217 CAACATCACACACGGATGCG 60.179 55.000 4.58 4.58 44.68 4.73
1447 1505 0.454957 GCAACATCACACACGGATGC 60.455 55.000 0.00 0.00 44.68 3.91
1449 1507 0.602638 ACGCAACATCACACACGGAT 60.603 50.000 0.00 0.00 0.00 4.18
1450 1508 1.218875 GACGCAACATCACACACGGA 61.219 55.000 0.00 0.00 0.00 4.69
1451 1509 1.204062 GACGCAACATCACACACGG 59.796 57.895 0.00 0.00 0.00 4.94
1460 1520 2.260869 GCACCCACAGACGCAACAT 61.261 57.895 0.00 0.00 0.00 2.71
1521 1598 4.854924 ACACGCAGGCAGCACACA 62.855 61.111 1.96 0.00 46.13 3.72
1545 1646 4.528740 GCACGCACACACACGCAA 62.529 61.111 0.00 0.00 0.00 4.85
1556 1707 2.025870 GCAACACACATGCACGCA 59.974 55.556 0.00 0.00 43.29 5.24
1666 1891 5.103515 ACTCTTTTGCCCCTCATATGGTATT 60.104 40.000 2.13 0.00 0.00 1.89
1702 1927 4.157656 TCCGTTCATTTTGAGCCTAAATGG 59.842 41.667 15.97 0.00 41.24 3.16
1720 1945 9.635404 TTTTATTCCCTATATGACAATTCCGTT 57.365 29.630 0.00 0.00 0.00 4.44
1756 1981 7.839680 AACAATTTCTTCCCTATTTGACACT 57.160 32.000 0.00 0.00 0.00 3.55
1776 2001 8.868916 GCTTCTTTATTTGACACTGAAAAACAA 58.131 29.630 0.00 0.00 0.00 2.83
1777 2002 8.031864 TGCTTCTTTATTTGACACTGAAAAACA 58.968 29.630 0.00 0.00 0.00 2.83
1778 2003 8.406172 TGCTTCTTTATTTGACACTGAAAAAC 57.594 30.769 0.00 0.00 0.00 2.43
1783 2008 7.750229 AATCTGCTTCTTTATTTGACACTGA 57.250 32.000 0.00 0.00 0.00 3.41
1922 2149 9.914923 CTTTAACAAAAACAACTTAGAAATGGC 57.085 29.630 0.00 0.00 0.00 4.40
1995 2225 5.944049 ATCGTTGTACGTGTATCAATGTC 57.056 39.130 0.00 0.00 43.14 3.06
2000 2230 4.707030 AGGAATCGTTGTACGTGTATCA 57.293 40.909 0.00 0.00 43.14 2.15
2003 2233 5.752472 TCAAAAAGGAATCGTTGTACGTGTA 59.248 36.000 0.00 0.00 43.14 2.90
2043 2273 5.886992 TGCGATCGAACGGTAATATGATAT 58.113 37.500 21.57 0.00 0.00 1.63
2086 2316 2.766263 TGAATCTACCTCGCAACAGGAT 59.234 45.455 0.36 0.00 36.96 3.24
2093 2323 6.582636 ACATCTAAATTGAATCTACCTCGCA 58.417 36.000 0.00 0.00 0.00 5.10
2105 2335 9.613428 AAAGTCCAATATCGACATCTAAATTGA 57.387 29.630 0.00 0.00 32.41 2.57
2112 2342 6.127338 TGAGACAAAGTCCAATATCGACATCT 60.127 38.462 0.00 3.56 32.18 2.90
2115 2345 5.400066 TGAGACAAAGTCCAATATCGACA 57.600 39.130 0.00 0.00 32.18 4.35
2145 2375 3.188048 CGGCCTCTGCATTGAGATTATTC 59.812 47.826 0.00 0.00 40.13 1.75
2154 2384 0.674581 TGTCTTCGGCCTCTGCATTG 60.675 55.000 0.00 0.00 40.13 2.82
2155 2385 0.254178 ATGTCTTCGGCCTCTGCATT 59.746 50.000 0.00 0.00 40.13 3.56
2159 2389 0.462759 GGGAATGTCTTCGGCCTCTG 60.463 60.000 0.00 0.00 31.75 3.35
2160 2390 1.627297 GGGGAATGTCTTCGGCCTCT 61.627 60.000 0.00 0.00 31.75 3.69
2187 2417 0.183971 TCCTGCCGGTTCCTCAAAAA 59.816 50.000 1.90 0.00 0.00 1.94
2188 2418 0.250727 CTCCTGCCGGTTCCTCAAAA 60.251 55.000 1.90 0.00 0.00 2.44
2189 2419 1.374947 CTCCTGCCGGTTCCTCAAA 59.625 57.895 1.90 0.00 0.00 2.69
2190 2420 3.068881 CTCCTGCCGGTTCCTCAA 58.931 61.111 1.90 0.00 0.00 3.02
2191 2421 3.706373 GCTCCTGCCGGTTCCTCA 61.706 66.667 1.90 0.00 0.00 3.86
2192 2422 3.706373 TGCTCCTGCCGGTTCCTC 61.706 66.667 1.90 0.00 38.71 3.71
2193 2423 4.021925 GTGCTCCTGCCGGTTCCT 62.022 66.667 1.90 0.00 38.71 3.36
2194 2424 4.021925 AGTGCTCCTGCCGGTTCC 62.022 66.667 1.90 0.00 38.71 3.62
2195 2425 2.743928 CAGTGCTCCTGCCGGTTC 60.744 66.667 1.90 0.00 38.71 3.62
2202 2432 1.542492 ATGAAAAGGCAGTGCTCCTG 58.458 50.000 16.11 0.20 44.53 3.86
2203 2433 3.659183 ATATGAAAAGGCAGTGCTCCT 57.341 42.857 16.11 0.92 34.90 3.69
2204 2434 5.126067 TCTTATATGAAAAGGCAGTGCTCC 58.874 41.667 16.11 0.00 0.00 4.70
2205 2435 6.238593 CCTTCTTATATGAAAAGGCAGTGCTC 60.239 42.308 16.11 5.03 32.50 4.26
2206 2436 5.591877 CCTTCTTATATGAAAAGGCAGTGCT 59.408 40.000 16.11 0.00 32.50 4.40
2207 2437 5.358160 ACCTTCTTATATGAAAAGGCAGTGC 59.642 40.000 6.55 6.55 41.65 4.40
2208 2438 7.770897 ACTACCTTCTTATATGAAAAGGCAGTG 59.229 37.037 4.98 0.00 41.69 3.66
2209 2439 7.862675 ACTACCTTCTTATATGAAAAGGCAGT 58.137 34.615 0.57 0.57 41.65 4.40
2210 2440 8.738645 AACTACCTTCTTATATGAAAAGGCAG 57.261 34.615 0.00 0.00 41.65 4.85


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

AutoCloner maintained by Alex Coulton.