Multiple sequence alignment - TraesCS7A01G400500

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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 TraesCS7A01G400500 chr7A 100.000 2572 0 0 1 2572 580506611 580504040 0.000000e+00 4750.0
1 TraesCS7A01G400500 chr7A 92.477 997 68 6 583 1574 627047057 627046063 0.000000e+00 1419.0
2 TraesCS7A01G400500 chr7A 89.091 385 27 7 110 487 580470855 580470479 5.010000e-127 464.0
3 TraesCS7A01G400500 chr7A 87.171 304 31 5 2201 2501 169958315 169958017 3.170000e-89 339.0
4 TraesCS7A01G400500 chr7A 100.000 28 0 0 2091 2118 627234063 627234036 5.000000e-03 52.8
5 TraesCS7A01G400500 chr1B 92.385 998 68 5 583 1574 426498808 426497813 0.000000e+00 1415.0
6 TraesCS7A01G400500 chr1B 91.073 997 77 9 588 1574 133113201 133112207 0.000000e+00 1338.0
7 TraesCS7A01G400500 chr1B 84.688 320 40 4 2185 2501 398840341 398840028 6.910000e-81 311.0
8 TraesCS7A01G400500 chr1B 82.550 149 16 6 1797 1945 133124845 133124707 3.480000e-24 122.0
9 TraesCS7A01G400500 chr1B 97.297 37 1 0 1910 1946 133124671 133124635 2.140000e-06 63.9
10 TraesCS7A01G400500 chr5D 91.900 1000 65 8 582 1574 289422685 289421695 0.000000e+00 1384.0
11 TraesCS7A01G400500 chr5D 91.968 884 62 6 698 1574 289728673 289727792 0.000000e+00 1230.0
12 TraesCS7A01G400500 chr5D 89.793 676 53 10 856 1520 29904637 29905307 0.000000e+00 852.0
13 TraesCS7A01G400500 chr5D 87.043 301 23 10 2201 2491 42081589 42081295 2.470000e-85 326.0
14 TraesCS7A01G400500 chr5D 86.207 87 5 4 2086 2165 29876500 29876414 1.270000e-13 87.9
15 TraesCS7A01G400500 chr7B 90.363 965 85 6 612 1574 588880178 588879220 0.000000e+00 1260.0
16 TraesCS7A01G400500 chr7B 90.593 489 25 7 11 487 537827530 537827051 1.680000e-176 628.0
17 TraesCS7A01G400500 chr7B 89.870 385 24 6 110 487 537673207 537672831 4.980000e-132 481.0
18 TraesCS7A01G400500 chr7B 91.168 351 25 4 1 348 537792200 537791853 3.000000e-129 472.0
19 TraesCS7A01G400500 chr7B 91.419 303 26 0 2228 2530 537825512 537825210 1.420000e-112 416.0
20 TraesCS7A01G400500 chr7B 83.387 313 37 5 2201 2501 589700611 589700302 2.520000e-70 276.0
21 TraesCS7A01G400500 chr7B 91.176 136 9 1 1797 1932 537825887 537825755 5.650000e-42 182.0
22 TraesCS7A01G400500 chr7B 86.207 87 5 4 2086 2165 498300120 498300034 1.270000e-13 87.9
23 TraesCS7A01G400500 chr7B 83.333 96 5 3 2084 2168 537825699 537825604 7.630000e-11 78.7
24 TraesCS7A01G400500 chr7B 100.000 40 0 0 375 414 537791847 537791808 9.870000e-10 75.0
25 TraesCS7A01G400500 chr7B 80.000 100 11 6 1910 2005 588878692 588878598 5.940000e-07 65.8
26 TraesCS7A01G400500 chr6A 91.924 842 64 3 723 1562 107262745 107263584 0.000000e+00 1175.0
27 TraesCS7A01G400500 chr6A 79.263 434 58 17 2091 2495 107264368 107264798 9.070000e-70 274.0
28 TraesCS7A01G400500 chr2B 91.597 714 51 7 863 1574 182135176 182134470 0.000000e+00 977.0
29 TraesCS7A01G400500 chr2B 93.200 250 17 0 583 832 182135423 182135174 4.040000e-98 368.0
30 TraesCS7A01G400500 chr2B 83.607 122 4 7 2054 2165 127790223 127790108 1.630000e-17 100.0
31 TraesCS7A01G400500 chr7D 91.742 666 34 11 1 655 509611439 509610784 0.000000e+00 905.0
32 TraesCS7A01G400500 chr7D 93.391 348 23 0 2225 2572 509598609 509598262 1.360000e-142 516.0
33 TraesCS7A01G400500 chr7D 89.239 381 35 3 2195 2572 509573694 509573317 3.000000e-129 472.0
34 TraesCS7A01G400500 chr7D 88.571 385 29 10 110 487 509556100 509555724 1.090000e-123 453.0
35 TraesCS7A01G400500 chr7D 85.959 292 35 4 2207 2495 545619797 545619509 8.940000e-80 307.0
36 TraesCS7A01G400500 chr7D 84.868 304 34 4 2201 2495 545650604 545650904 1.940000e-76 296.0
37 TraesCS7A01G400500 chr7D 86.996 223 16 5 1573 1794 509602164 509601954 3.310000e-59 239.0
38 TraesCS7A01G400500 chr7D 92.222 90 6 1 1703 1791 509580171 509580082 2.690000e-25 126.0
39 TraesCS7A01G400500 chr5B 89.247 186 12 5 298 483 667412452 667412629 2.570000e-55 226.0
40 TraesCS7A01G400500 chr1A 87.755 196 15 4 289 484 531824252 531824438 1.200000e-53 220.0
41 TraesCS7A01G400500 chrUn 94.737 38 2 0 2084 2121 65755214 65755251 2.760000e-05 60.2
42 TraesCS7A01G400500 chr5A 79.592 98 7 9 2070 2167 30651892 30651808 9.940000e-05 58.4


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 TraesCS7A01G400500 chr7A 580504040 580506611 2571 True 4750.000 4750 100.00000 1 2572 1 chr7A.!!$R3 2571
1 TraesCS7A01G400500 chr7A 627046063 627047057 994 True 1419.000 1419 92.47700 583 1574 1 chr7A.!!$R4 991
2 TraesCS7A01G400500 chr1B 426497813 426498808 995 True 1415.000 1415 92.38500 583 1574 1 chr1B.!!$R3 991
3 TraesCS7A01G400500 chr1B 133112207 133113201 994 True 1338.000 1338 91.07300 588 1574 1 chr1B.!!$R1 986
4 TraesCS7A01G400500 chr5D 289421695 289422685 990 True 1384.000 1384 91.90000 582 1574 1 chr5D.!!$R3 992
5 TraesCS7A01G400500 chr5D 289727792 289728673 881 True 1230.000 1230 91.96800 698 1574 1 chr5D.!!$R4 876
6 TraesCS7A01G400500 chr5D 29904637 29905307 670 False 852.000 852 89.79300 856 1520 1 chr5D.!!$F1 664
7 TraesCS7A01G400500 chr7B 588878598 588880178 1580 True 662.900 1260 85.18150 612 2005 2 chr7B.!!$R6 1393
8 TraesCS7A01G400500 chr7B 537825210 537827530 2320 True 326.175 628 89.13025 11 2530 4 chr7B.!!$R5 2519
9 TraesCS7A01G400500 chr6A 107262745 107264798 2053 False 724.500 1175 85.59350 723 2495 2 chr6A.!!$F1 1772
10 TraesCS7A01G400500 chr2B 182134470 182135423 953 True 672.500 977 92.39850 583 1574 2 chr2B.!!$R2 991
11 TraesCS7A01G400500 chr7D 509610784 509611439 655 True 905.000 905 91.74200 1 655 1 chr7D.!!$R4 654
12 TraesCS7A01G400500 chr7D 509598262 509602164 3902 True 377.500 516 90.19350 1573 2572 2 chr7D.!!$R6 999

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
561 576 0.523072 CCAATGTTCTGGCTTGTCCG 59.477 55.0 0.0 0.0 37.8 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 2172 0.102844 TGCTGCTTGCCAAGTTGAAC 59.897 50.0 6.28 0.0 42.0 3.18 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
30 31 6.814146 ACCTCAAACTTTATTCAGATCGAGTC 59.186 38.462 0.00 0.00 0.00 3.36
168 173 1.519898 GCATGGGGAATTGCGCAAG 60.520 57.895 28.62 16.66 43.44 4.01
169 174 1.142314 CATGGGGAATTGCGCAAGG 59.858 57.895 28.62 11.84 38.28 3.61
181 193 2.009774 TGCGCAAGGATAGAAGAAAGC 58.990 47.619 8.16 0.00 38.28 3.51
216 228 5.048083 GCTAGGATGTCTCTCATAAGTCCTG 60.048 48.000 0.00 0.00 34.09 3.86
218 230 3.323403 GGATGTCTCTCATAAGTCCTGGG 59.677 52.174 0.00 0.00 36.83 4.45
261 275 3.132289 TCATCGTCTTCACCAGGAATACC 59.868 47.826 0.00 0.00 34.32 2.73
264 278 1.134491 GTCTTCACCAGGAATACCCCG 60.134 57.143 0.00 0.00 34.32 5.73
292 306 1.901591 ACAGAACCATGGCAGAACAG 58.098 50.000 13.04 0.00 0.00 3.16
319 333 5.454062 AGTATGAGTAGCTCCAGAAGATGT 58.546 41.667 0.00 0.00 0.00 3.06
356 370 1.271871 TGAGGTACCAGCAAACCCATG 60.272 52.381 15.94 0.00 36.34 3.66
372 386 2.123769 TGCCCAGCATATGCCACC 60.124 61.111 23.96 10.66 43.38 4.61
416 430 1.887198 ACTTCCCAGTGAGTACAGACG 59.113 52.381 0.00 0.00 0.00 4.18
417 431 1.887198 CTTCCCAGTGAGTACAGACGT 59.113 52.381 0.00 0.00 0.00 4.34
418 432 2.865119 TCCCAGTGAGTACAGACGTA 57.135 50.000 0.00 0.00 0.00 3.57
496 510 6.037172 GTGAACTGTATAGCCAACGATTTCAT 59.963 38.462 0.00 0.00 0.00 2.57
509 523 2.353889 CGATTTCATGTCTGGAGCTTGG 59.646 50.000 0.00 0.00 0.00 3.61
512 526 3.726557 TTCATGTCTGGAGCTTGGAAT 57.273 42.857 0.00 0.00 0.00 3.01
515 529 2.479566 TGTCTGGAGCTTGGAATGAC 57.520 50.000 0.00 0.00 0.00 3.06
519 533 1.452108 GGAGCTTGGAATGACGGGG 60.452 63.158 0.00 0.00 0.00 5.73
521 535 2.198304 GAGCTTGGAATGACGGGGGT 62.198 60.000 0.00 0.00 0.00 4.95
522 536 2.046285 GCTTGGAATGACGGGGGTG 61.046 63.158 0.00 0.00 0.00 4.61
523 537 2.034999 TTGGAATGACGGGGGTGC 59.965 61.111 0.00 0.00 0.00 5.01
561 576 0.523072 CCAATGTTCTGGCTTGTCCG 59.477 55.000 0.00 0.00 37.80 4.79
655 670 4.265073 CCATTGCTAAACTGGTCTAAGCT 58.735 43.478 0.00 0.00 34.28 3.74
671 686 9.692749 TGGTCTAAGCTATTCAAGATAATTACG 57.307 33.333 0.00 0.00 0.00 3.18
680 695 6.907206 TTCAAGATAATTACGGGGTTAACG 57.093 37.500 0.00 0.00 37.36 3.18
681 696 6.219417 TCAAGATAATTACGGGGTTAACGA 57.781 37.500 0.00 0.00 34.93 3.85
746 761 2.614057 CCACAGAGACTTGAAACCACAC 59.386 50.000 0.00 0.00 0.00 3.82
825 840 5.814705 AGAGCATTGAGTTTAGATGTAGCAC 59.185 40.000 0.00 0.00 0.00 4.40
977 1127 4.025360 TGGTTACAAAGCTCCGGAGTATA 58.975 43.478 31.43 14.31 0.00 1.47
978 1128 4.652421 TGGTTACAAAGCTCCGGAGTATAT 59.348 41.667 31.43 16.28 0.00 0.86
985 1135 3.169099 AGCTCCGGAGTATATGCATCTT 58.831 45.455 31.43 0.00 0.00 2.40
1304 1469 2.874457 GCTTGTGGATCCGTTGTTAGGT 60.874 50.000 7.39 0.00 0.00 3.08
1353 1518 3.730761 GCGCTCAAGTGGCACTGG 61.731 66.667 22.83 19.40 0.00 4.00
1372 1537 2.373169 TGGTTTGTGCTCAGGAAGATCT 59.627 45.455 0.00 0.00 0.00 2.75
1377 1542 3.036819 TGTGCTCAGGAAGATCTAGCAT 58.963 45.455 17.75 0.00 44.30 3.79
1395 1562 2.050836 ATATCGGCCCGCCATGACAA 62.051 55.000 6.52 0.00 35.37 3.18
1456 1623 2.124695 GGAGCCTAAGCAACCCGG 60.125 66.667 0.00 0.00 43.56 5.73
1523 1693 2.409870 GGGCCAATCAAGCAGGACG 61.410 63.158 4.39 0.00 0.00 4.79
1535 1705 4.645136 TCAAGCAGGACGATAGACATAACT 59.355 41.667 0.00 0.00 41.38 2.24
1544 1714 6.960431 GGACGATAGACATAACTATAACGAGC 59.040 42.308 0.00 0.00 41.38 5.03
1547 1717 7.603404 ACGATAGACATAACTATAACGAGCTCT 59.397 37.037 12.85 0.00 41.38 4.09
1569 1739 2.351544 GCTCCAACGTCGACTAGAGTTT 60.352 50.000 14.70 0.00 0.00 2.66
1574 1744 4.684703 CCAACGTCGACTAGAGTTTGAATT 59.315 41.667 14.70 0.00 0.00 2.17
1575 1745 5.176958 CCAACGTCGACTAGAGTTTGAATTT 59.823 40.000 14.70 0.00 0.00 1.82
1577 1747 6.211664 ACGTCGACTAGAGTTTGAATTTTG 57.788 37.500 14.70 0.00 0.00 2.44
1578 1748 5.176958 ACGTCGACTAGAGTTTGAATTTTGG 59.823 40.000 14.70 0.00 0.00 3.28
1579 1749 5.389516 CGTCGACTAGAGTTTGAATTTTGGG 60.390 44.000 14.70 0.00 0.00 4.12
1580 1750 4.454504 TCGACTAGAGTTTGAATTTTGGGC 59.545 41.667 0.00 0.00 0.00 5.36
1581 1751 4.455877 CGACTAGAGTTTGAATTTTGGGCT 59.544 41.667 0.00 0.00 0.00 5.19
1630 1878 8.920665 CATATTCGAGATACTGAGACCAATTTC 58.079 37.037 0.00 0.00 0.00 2.17
1699 1951 4.707030 TTTTCCATGAGCTGCATTGTAG 57.293 40.909 1.02 0.00 34.15 2.74
1764 2043 2.367567 TCCAGTTCAGCGAAGTTTACCT 59.632 45.455 0.00 0.00 0.00 3.08
1788 2067 4.590222 GGGATTGCTCATATTTGGGAACAT 59.410 41.667 0.00 0.00 42.32 2.71
1794 2073 7.894753 TGCTCATATTTGGGAACATTTATGA 57.105 32.000 0.00 0.00 42.32 2.15
1832 2172 9.687210 TTGAGAAATGAGAAATCATCAAACTTG 57.313 29.630 0.00 0.00 0.00 3.16
1833 2173 8.853126 TGAGAAATGAGAAATCATCAAACTTGT 58.147 29.630 0.00 0.00 0.00 3.16
1834 2174 9.688592 GAGAAATGAGAAATCATCAAACTTGTT 57.311 29.630 0.00 0.00 0.00 2.83
1842 2182 7.707893 AGAAATCATCAAACTTGTTCAACTTGG 59.292 33.333 0.00 0.00 0.00 3.61
1860 4957 1.962144 GCAAGCAGCAACCACAGAT 59.038 52.632 0.00 0.00 44.79 2.90
1865 4962 0.801251 GCAGCAACCACAGATCTCAC 59.199 55.000 0.00 0.00 0.00 3.51
1875 4972 4.169508 CCACAGATCTCACAGTTAAGACG 58.830 47.826 0.00 0.00 0.00 4.18
1916 5077 2.475111 AGAACACGCTACAAACACATCG 59.525 45.455 0.00 0.00 0.00 3.84
1973 5138 7.597288 AAAAAGTTCCTAATGCACCTAAGTT 57.403 32.000 0.00 0.00 0.00 2.66
1974 5139 6.819397 AAAGTTCCTAATGCACCTAAGTTC 57.181 37.500 0.00 0.00 0.00 3.01
1975 5140 5.499004 AGTTCCTAATGCACCTAAGTTCA 57.501 39.130 0.00 0.00 0.00 3.18
1976 5141 6.067217 AGTTCCTAATGCACCTAAGTTCAT 57.933 37.500 0.00 0.00 30.55 2.57
1977 5142 7.195374 AGTTCCTAATGCACCTAAGTTCATA 57.805 36.000 0.00 0.00 29.10 2.15
1978 5143 7.275920 AGTTCCTAATGCACCTAAGTTCATAG 58.724 38.462 0.00 0.00 29.10 2.23
1979 5144 6.808321 TCCTAATGCACCTAAGTTCATAGT 57.192 37.500 0.00 0.00 29.10 2.12
1980 5145 7.195374 TCCTAATGCACCTAAGTTCATAGTT 57.805 36.000 0.00 0.00 29.10 2.24
1981 5146 8.313944 TCCTAATGCACCTAAGTTCATAGTTA 57.686 34.615 0.00 0.00 29.10 2.24
1982 5147 8.764558 TCCTAATGCACCTAAGTTCATAGTTAA 58.235 33.333 0.00 0.00 29.10 2.01
1983 5148 9.391006 CCTAATGCACCTAAGTTCATAGTTAAA 57.609 33.333 0.00 0.00 29.10 1.52
1985 5150 8.630054 AATGCACCTAAGTTCATAGTTAAACA 57.370 30.769 0.00 0.00 29.10 2.83
1986 5151 8.807948 ATGCACCTAAGTTCATAGTTAAACAT 57.192 30.769 0.00 0.00 27.22 2.71
1987 5152 8.263940 TGCACCTAAGTTCATAGTTAAACATC 57.736 34.615 0.00 0.00 0.00 3.06
1988 5153 8.100791 TGCACCTAAGTTCATAGTTAAACATCT 58.899 33.333 0.00 0.00 0.00 2.90
1989 5154 8.947115 GCACCTAAGTTCATAGTTAAACATCTT 58.053 33.333 0.00 0.00 0.00 2.40
2007 5172 8.522178 AACATCTTAACTCTGAACTTAAGTCG 57.478 34.615 8.95 1.02 33.44 4.18
2008 5173 6.586844 ACATCTTAACTCTGAACTTAAGTCGC 59.413 38.462 8.95 5.08 33.44 5.19
2009 5174 6.328641 TCTTAACTCTGAACTTAAGTCGCT 57.671 37.500 8.95 0.00 33.44 4.93
2010 5175 6.150318 TCTTAACTCTGAACTTAAGTCGCTG 58.850 40.000 8.95 8.49 33.44 5.18
2011 5176 3.305398 ACTCTGAACTTAAGTCGCTGG 57.695 47.619 8.95 2.80 0.00 4.85
2012 5177 1.996191 CTCTGAACTTAAGTCGCTGGC 59.004 52.381 8.95 0.00 0.00 4.85
2013 5178 1.079503 CTGAACTTAAGTCGCTGGCC 58.920 55.000 8.95 0.00 0.00 5.36
2014 5179 0.321298 TGAACTTAAGTCGCTGGCCC 60.321 55.000 8.95 0.00 0.00 5.80
2015 5180 0.321298 GAACTTAAGTCGCTGGCCCA 60.321 55.000 8.95 0.00 0.00 5.36
2016 5181 0.321653 AACTTAAGTCGCTGGCCCAG 60.322 55.000 8.95 6.32 34.12 4.45
2017 5182 1.192146 ACTTAAGTCGCTGGCCCAGA 61.192 55.000 16.85 0.00 32.44 3.86
2018 5183 0.741221 CTTAAGTCGCTGGCCCAGAC 60.741 60.000 16.85 4.78 32.44 3.51
2039 5204 9.442047 CCAGACTTAAGATGTTTAACTCTGAAT 57.558 33.333 10.09 0.00 31.94 2.57
2054 5471 0.478072 TGAATTATGCCTGGGCCGAT 59.522 50.000 9.28 0.00 41.09 4.18
2078 5507 2.845967 GGATTCATTAGTGCGCGTTTTG 59.154 45.455 8.43 0.00 0.00 2.44
2124 5564 3.119743 TCGGATTCAAATTGCTTGCTCTG 60.120 43.478 0.00 0.00 34.76 3.35
2141 5581 3.519930 GTCTCTCCCGCGTCCCTC 61.520 72.222 4.92 0.00 0.00 4.30
2168 5608 4.151582 TCGCCCCGTTTCCCGATC 62.152 66.667 0.00 0.00 39.56 3.69
2169 5609 4.460683 CGCCCCGTTTCCCGATCA 62.461 66.667 0.00 0.00 39.56 2.92
2170 5610 2.045731 GCCCCGTTTCCCGATCAA 60.046 61.111 0.00 0.00 39.56 2.57
2176 5667 2.205074 CCGTTTCCCGATCAATCTCTG 58.795 52.381 0.00 0.00 39.56 3.35
2190 5681 4.812476 TCTGCCAACGCCGGATCG 62.812 66.667 5.05 1.69 0.00 3.69
2218 5710 4.310672 ATCGTTGCTCTCGCGATC 57.689 55.556 10.36 2.37 40.76 3.69
2223 5715 2.645192 TTGCTCTCGCGATCCCACA 61.645 57.895 10.36 0.81 39.65 4.17
2318 5810 4.821589 CTGCTCTTCCCGCGTCCC 62.822 72.222 4.92 0.00 0.00 4.46
2445 5943 4.475135 GGGGGCGAGCTCCTCAAC 62.475 72.222 14.32 0.00 36.64 3.18
2451 5949 4.443266 GAGCTCCTCAACGCCGCT 62.443 66.667 0.87 0.00 0.00 5.52
2454 5952 2.357517 CTCCTCAACGCCGCTGTT 60.358 61.111 0.00 0.00 0.00 3.16
2517 6018 2.123854 AGTAGCGGCGAGGATCCA 60.124 61.111 15.82 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 173 3.942115 GGAACCACTGCTTTCTTCTATCC 59.058 47.826 0.00 0.00 0.00 2.59
169 174 4.633565 CAGGAACCACTGCTTTCTTCTATC 59.366 45.833 0.00 0.00 0.00 2.08
233 245 1.550524 TGGTGAAGACGATGAAGAGGG 59.449 52.381 0.00 0.00 0.00 4.30
261 275 0.462047 GGTTCTGTATCTGCACCGGG 60.462 60.000 6.32 0.00 0.00 5.73
264 278 2.292267 CCATGGTTCTGTATCTGCACC 58.708 52.381 2.57 0.00 0.00 5.01
292 306 7.753309 TCTTCTGGAGCTACTCATACTATTC 57.247 40.000 0.00 0.00 31.08 1.75
319 333 0.250252 TCACTTGCGATGCTTGTCCA 60.250 50.000 0.00 0.00 0.00 4.02
356 370 1.532316 ATGGTGGCATATGCTGGGC 60.532 57.895 26.12 10.88 41.70 5.36
372 386 0.742505 AATCGCCATTGCTGGACATG 59.257 50.000 0.00 0.00 46.37 3.21
414 428 7.108841 TCCTCATTAAAGCTCTATTGTACGT 57.891 36.000 0.00 0.00 0.00 3.57
415 429 7.867909 TCATCCTCATTAAAGCTCTATTGTACG 59.132 37.037 0.00 0.00 0.00 3.67
416 430 8.983724 GTCATCCTCATTAAAGCTCTATTGTAC 58.016 37.037 0.00 0.00 0.00 2.90
417 431 8.928448 AGTCATCCTCATTAAAGCTCTATTGTA 58.072 33.333 0.00 0.00 0.00 2.41
418 432 7.800092 AGTCATCCTCATTAAAGCTCTATTGT 58.200 34.615 0.00 0.00 0.00 2.71
419 433 8.557864 CAAGTCATCCTCATTAAAGCTCTATTG 58.442 37.037 0.00 0.00 0.00 1.90
420 434 7.228308 GCAAGTCATCCTCATTAAAGCTCTATT 59.772 37.037 0.00 0.00 0.00 1.73
421 435 6.709846 GCAAGTCATCCTCATTAAAGCTCTAT 59.290 38.462 0.00 0.00 0.00 1.98
496 510 1.338105 CGTCATTCCAAGCTCCAGACA 60.338 52.381 0.00 0.00 0.00 3.41
519 533 0.960364 TGAAGAAAGATGGGCGCACC 60.960 55.000 7.46 7.71 40.81 5.01
521 535 1.167851 CTTGAAGAAAGATGGGCGCA 58.832 50.000 10.83 5.70 38.24 6.09
522 536 1.131315 GTCTTGAAGAAAGATGGGCGC 59.869 52.381 0.00 0.00 46.53 6.53
523 537 1.740025 GGTCTTGAAGAAAGATGGGCG 59.260 52.381 0.00 0.00 46.53 6.13
561 576 1.261619 CGTGTGGTTTCAAGTCTCTGC 59.738 52.381 0.00 0.00 0.00 4.26
606 621 6.147656 CCTTTTGTTCTGTCTGCAAAAAGTTT 59.852 34.615 12.52 0.00 40.23 2.66
655 670 8.420222 TCGTTAACCCCGTAATTATCTTGAATA 58.580 33.333 0.00 0.00 0.00 1.75
671 686 2.799017 ACAATTCCCTTCGTTAACCCC 58.201 47.619 0.00 0.00 0.00 4.95
680 695 6.524101 TTATGCAGGTAAACAATTCCCTTC 57.476 37.500 0.00 0.00 0.00 3.46
681 696 5.105351 GCTTATGCAGGTAAACAATTCCCTT 60.105 40.000 0.00 0.00 39.41 3.95
807 822 5.639506 GCTCTTGTGCTACATCTAAACTCAA 59.360 40.000 0.00 0.00 0.00 3.02
825 840 0.603569 ACCCTACTCGTGTGCTCTTG 59.396 55.000 0.00 0.00 0.00 3.02
977 1127 4.160439 TCGAGTAAACTCCTCAAGATGCAT 59.840 41.667 0.00 0.00 39.79 3.96
978 1128 3.509967 TCGAGTAAACTCCTCAAGATGCA 59.490 43.478 4.58 0.00 39.79 3.96
985 1135 4.765339 TGTCTTCATCGAGTAAACTCCTCA 59.235 41.667 4.58 0.00 39.79 3.86
1304 1469 0.030235 CGGCGACTTCATATCCGTCA 59.970 55.000 0.00 0.00 35.75 4.35
1353 1518 3.620821 GCTAGATCTTCCTGAGCACAAAC 59.379 47.826 0.00 0.00 32.67 2.93
1372 1537 2.290287 ATGGCGGGCCGATATGCTA 61.290 57.895 33.44 9.88 39.42 3.49
1377 1542 2.258748 TTTGTCATGGCGGGCCGATA 62.259 55.000 33.44 18.18 39.42 2.92
1395 1562 2.036733 AGTTCAGCATTGCAGCAACATT 59.963 40.909 10.85 0.00 36.85 2.71
1456 1623 0.178068 ACACCCATGGATCAGCGTAC 59.822 55.000 15.22 0.00 0.00 3.67
1523 1693 7.694784 GCAGAGCTCGTTATAGTTATGTCTATC 59.305 40.741 8.37 0.00 33.41 2.08
1544 1714 0.803117 TAGTCGACGTTGGAGCAGAG 59.197 55.000 10.46 0.00 0.00 3.35
1547 1717 0.803117 CTCTAGTCGACGTTGGAGCA 59.197 55.000 10.46 0.00 0.00 4.26
1617 1864 2.414481 CACTCTGCGAAATTGGTCTCAG 59.586 50.000 0.00 0.00 32.68 3.35
1630 1878 6.857964 AGAAACATGTTTATTTTCACTCTGCG 59.142 34.615 23.33 0.00 32.62 5.18
1676 1928 4.546829 ACAATGCAGCTCATGGAAAATT 57.453 36.364 7.33 0.00 35.13 1.82
1764 2043 3.960102 GTTCCCAAATATGAGCAATCCCA 59.040 43.478 0.00 0.00 0.00 4.37
1794 2073 7.572523 TCTCATTTCTCAAGTTGAATGTGTT 57.427 32.000 7.06 0.00 0.00 3.32
1832 2172 0.102844 TGCTGCTTGCCAAGTTGAAC 59.897 50.000 6.28 0.00 42.00 3.18
1833 2173 0.822811 TTGCTGCTTGCCAAGTTGAA 59.177 45.000 6.28 0.00 42.00 2.69
1834 2174 0.102844 GTTGCTGCTTGCCAAGTTGA 59.897 50.000 6.28 0.00 42.00 3.18
1842 2182 0.109412 GATCTGTGGTTGCTGCTTGC 60.109 55.000 0.00 0.00 43.25 4.01
1860 4957 5.938710 AGATCTACACGTCTTAACTGTGAGA 59.061 40.000 0.00 0.00 35.39 3.27
1865 4962 5.096169 CCACAGATCTACACGTCTTAACTG 58.904 45.833 0.00 0.00 0.00 3.16
1875 4972 3.701542 TCTCCATGTCCACAGATCTACAC 59.298 47.826 0.00 0.00 0.00 2.90
1916 5077 2.945668 ACAGCGCTTATTTTGAGATCCC 59.054 45.455 7.50 0.00 0.00 3.85
1955 5120 7.195374 ACTATGAACTTAGGTGCATTAGGAA 57.805 36.000 3.39 0.00 38.50 3.36
1981 5146 8.979574 CGACTTAAGTTCAGAGTTAAGATGTTT 58.020 33.333 10.02 0.00 45.49 2.83
1982 5147 7.116519 GCGACTTAAGTTCAGAGTTAAGATGTT 59.883 37.037 10.02 0.00 45.49 2.71
1983 5148 6.586844 GCGACTTAAGTTCAGAGTTAAGATGT 59.413 38.462 10.02 0.77 45.49 3.06
1984 5149 6.809196 AGCGACTTAAGTTCAGAGTTAAGATG 59.191 38.462 10.02 10.76 45.49 2.90
1985 5150 6.809196 CAGCGACTTAAGTTCAGAGTTAAGAT 59.191 38.462 10.02 5.28 45.49 2.40
1986 5151 6.150318 CAGCGACTTAAGTTCAGAGTTAAGA 58.850 40.000 10.02 0.00 45.49 2.10
1987 5152 5.346281 CCAGCGACTTAAGTTCAGAGTTAAG 59.654 44.000 10.02 10.61 46.89 1.85
1988 5153 5.227908 CCAGCGACTTAAGTTCAGAGTTAA 58.772 41.667 10.02 0.00 31.56 2.01
1989 5154 4.806330 CCAGCGACTTAAGTTCAGAGTTA 58.194 43.478 10.02 0.00 0.00 2.24
1990 5155 3.654414 CCAGCGACTTAAGTTCAGAGTT 58.346 45.455 10.02 0.00 0.00 3.01
1991 5156 2.610727 GCCAGCGACTTAAGTTCAGAGT 60.611 50.000 10.02 0.00 0.00 3.24
1992 5157 1.996191 GCCAGCGACTTAAGTTCAGAG 59.004 52.381 10.02 0.85 0.00 3.35
1993 5158 1.337823 GGCCAGCGACTTAAGTTCAGA 60.338 52.381 10.02 0.00 0.00 3.27
1994 5159 1.079503 GGCCAGCGACTTAAGTTCAG 58.920 55.000 10.02 6.00 0.00 3.02
1995 5160 0.321298 GGGCCAGCGACTTAAGTTCA 60.321 55.000 10.02 0.00 0.00 3.18
1996 5161 0.321298 TGGGCCAGCGACTTAAGTTC 60.321 55.000 10.02 5.21 0.00 3.01
1997 5162 0.321653 CTGGGCCAGCGACTTAAGTT 60.322 55.000 22.68 0.00 0.00 2.66
1998 5163 1.192146 TCTGGGCCAGCGACTTAAGT 61.192 55.000 29.02 8.13 0.00 2.24
1999 5164 0.741221 GTCTGGGCCAGCGACTTAAG 60.741 60.000 29.02 2.62 0.00 1.85
2000 5165 1.192146 AGTCTGGGCCAGCGACTTAA 61.192 55.000 29.02 6.71 34.55 1.85
2001 5166 1.192146 AAGTCTGGGCCAGCGACTTA 61.192 55.000 29.57 12.05 43.85 2.24
2002 5167 1.192146 TAAGTCTGGGCCAGCGACTT 61.192 55.000 31.63 31.63 46.39 3.01
2003 5168 1.192146 TTAAGTCTGGGCCAGCGACT 61.192 55.000 29.02 23.82 39.53 4.18
2004 5169 0.741221 CTTAAGTCTGGGCCAGCGAC 60.741 60.000 29.02 21.93 0.00 5.19
2005 5170 0.902984 TCTTAAGTCTGGGCCAGCGA 60.903 55.000 29.02 10.33 0.00 4.93
2006 5171 0.179000 ATCTTAAGTCTGGGCCAGCG 59.821 55.000 29.02 7.66 0.00 5.18
2007 5172 1.065126 ACATCTTAAGTCTGGGCCAGC 60.065 52.381 29.02 22.23 0.00 4.85
2008 5173 3.356529 AACATCTTAAGTCTGGGCCAG 57.643 47.619 28.01 28.01 0.00 4.85
2009 5174 3.806949 AAACATCTTAAGTCTGGGCCA 57.193 42.857 5.85 5.85 0.00 5.36
2010 5175 5.254115 AGTTAAACATCTTAAGTCTGGGCC 58.746 41.667 1.63 0.00 0.00 5.80
2011 5176 6.174049 AGAGTTAAACATCTTAAGTCTGGGC 58.826 40.000 11.85 0.00 40.93 5.36
2039 5204 1.227823 CGAATCGGCCCAGGCATAA 60.228 57.895 11.50 0.00 44.11 1.90
2054 5471 0.927537 CGCGCACTAATGAATCCGAA 59.072 50.000 8.75 0.00 0.00 4.30
2124 5564 3.519930 GAGGGACGCGGGAGAGAC 61.520 72.222 12.47 0.00 0.00 3.36
2141 5581 1.515521 AACGGGGCGAGCAAGAAAAG 61.516 55.000 0.00 0.00 0.00 2.27
2165 5605 0.659957 GGCGTTGGCAGAGATTGATC 59.340 55.000 0.00 0.00 42.47 2.92
2168 5608 2.753966 CCGGCGTTGGCAGAGATTG 61.754 63.158 6.01 0.00 42.47 2.67
2169 5609 2.257409 ATCCGGCGTTGGCAGAGATT 62.257 55.000 6.01 0.00 42.47 2.40
2170 5610 2.650813 GATCCGGCGTTGGCAGAGAT 62.651 60.000 6.01 0.00 42.47 2.75
2190 5681 1.859135 GCAACGATCAAGCGAACGC 60.859 57.895 11.31 11.31 40.78 4.84
2193 5685 1.350193 GAGAGCAACGATCAAGCGAA 58.650 50.000 0.00 0.00 34.83 4.70
2318 5810 1.094785 CATCAAGGCAGGGTTTACGG 58.905 55.000 0.00 0.00 0.00 4.02
2451 5949 0.821301 TGTTGATCTTGGCGGCAACA 60.821 50.000 21.79 14.72 45.69 3.33
2454 5952 2.334946 GCTGTTGATCTTGGCGGCA 61.335 57.895 7.97 7.97 33.76 5.69
2502 6003 1.040893 TTCTTGGATCCTCGCCGCTA 61.041 55.000 14.23 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.