Multiple sequence alignment - TraesCS6B01G053400

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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 TraesCS6B01G053400 chr6B 100.000 2416 0 0 1 2416 33037097 33039512 0.000000e+00 4462.0
1 TraesCS6B01G053400 chr6D 89.842 2156 150 33 297 2416 18983996 18986118 0.000000e+00 2704.0
2 TraesCS6B01G053400 chr6D 92.308 312 11 7 1 302 18983633 18983941 4.770000e-117 431.0
3 TraesCS6B01G053400 chr6D 88.328 317 23 6 300 608 450573027 450572717 3.790000e-98 368.0
4 TraesCS6B01G053400 chr6D 87.900 281 24 3 1 271 18958860 18959140 3.000000e-84 322.0
5 TraesCS6B01G053400 chr2D 85.346 1085 67 33 682 1685 534129146 534130219 0.000000e+00 1038.0
6 TraesCS6B01G053400 chr2D 85.732 813 67 25 845 1624 534122862 534123658 0.000000e+00 813.0
7 TraesCS6B01G053400 chr2D 82.686 566 51 23 892 1420 613002466 613001911 2.190000e-125 459.0
8 TraesCS6B01G053400 chr5B 84.823 1074 66 44 682 1685 647879695 647878649 0.000000e+00 990.0
9 TraesCS6B01G053400 chr5D 84.579 1070 76 28 682 1685 515039901 515038855 0.000000e+00 979.0
10 TraesCS6B01G053400 chr5D 88.636 704 34 11 759 1423 515094462 515093766 0.000000e+00 815.0
11 TraesCS6B01G053400 chr5A 85.529 1002 70 20 682 1631 643312296 643311318 0.000000e+00 977.0
12 TraesCS6B01G053400 chr2B 82.218 956 83 34 739 1631 776645958 776645027 0.000000e+00 743.0
13 TraesCS6B01G053400 chr2B 91.724 435 20 4 995 1419 634644125 634644553 7.440000e-165 590.0
14 TraesCS6B01G053400 chr2B 84.615 312 16 13 672 954 634631882 634632190 5.090000e-72 281.0
15 TraesCS6B01G053400 chr2A 87.167 639 51 14 998 1619 677827917 677828541 0.000000e+00 697.0
16 TraesCS6B01G053400 chr2A 91.346 104 8 1 505 608 779324122 779324224 9.010000e-30 141.0
17 TraesCS6B01G053400 chr2A 89.552 67 6 1 8 73 779310884 779310950 1.540000e-12 84.2
18 TraesCS6B01G053400 chr7B 85.217 690 57 24 773 1425 113445686 113445005 0.000000e+00 667.0
19 TraesCS6B01G053400 chr7D 83.247 776 69 37 759 1491 151542749 151541992 0.000000e+00 656.0
20 TraesCS6B01G053400 chr3D 86.349 608 36 25 855 1428 594958432 594957838 9.490000e-174 619.0
21 TraesCS6B01G053400 chr3D 89.516 248 20 3 355 602 548628350 548628591 2.330000e-80 309.0
22 TraesCS6B01G053400 chr3B 86.980 553 28 20 905 1428 798408877 798408340 1.240000e-162 582.0
23 TraesCS6B01G053400 chr3B 79.098 244 32 15 2001 2236 815455931 815455699 1.500000e-32 150.0
24 TraesCS6B01G053400 chr1A 88.644 317 23 6 300 608 96432608 96432919 8.160000e-100 374.0
25 TraesCS6B01G053400 chr1A 92.537 67 4 1 8 73 96432192 96432258 7.110000e-16 95.3
26 TraesCS6B01G053400 chr7A 84.591 318 20 9 301 608 734641454 734641156 3.040000e-74 289.0
27 TraesCS6B01G053400 chr7A 92.537 67 4 1 8 73 734641873 734641807 7.110000e-16 95.3
28 TraesCS6B01G053400 chrUn 90.909 165 11 3 839 999 31317443 31317607 4.040000e-53 219.0
29 TraesCS6B01G053400 chr4A 90.741 108 9 1 1512 1619 639978205 639978311 2.500000e-30 143.0
30 TraesCS6B01G053400 chr1B 88.333 120 12 1 1939 2058 563762433 563762550 2.500000e-30 143.0


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 TraesCS6B01G053400 chr6B 33037097 33039512 2415 False 4462.00 4462 100.0000 1 2416 1 chr6B.!!$F1 2415
1 TraesCS6B01G053400 chr6D 18983633 18986118 2485 False 1567.50 2704 91.0750 1 2416 2 chr6D.!!$F2 2415
2 TraesCS6B01G053400 chr2D 534129146 534130219 1073 False 1038.00 1038 85.3460 682 1685 1 chr2D.!!$F2 1003
3 TraesCS6B01G053400 chr2D 534122862 534123658 796 False 813.00 813 85.7320 845 1624 1 chr2D.!!$F1 779
4 TraesCS6B01G053400 chr2D 613001911 613002466 555 True 459.00 459 82.6860 892 1420 1 chr2D.!!$R1 528
5 TraesCS6B01G053400 chr5B 647878649 647879695 1046 True 990.00 990 84.8230 682 1685 1 chr5B.!!$R1 1003
6 TraesCS6B01G053400 chr5D 515038855 515039901 1046 True 979.00 979 84.5790 682 1685 1 chr5D.!!$R1 1003
7 TraesCS6B01G053400 chr5D 515093766 515094462 696 True 815.00 815 88.6360 759 1423 1 chr5D.!!$R2 664
8 TraesCS6B01G053400 chr5A 643311318 643312296 978 True 977.00 977 85.5290 682 1631 1 chr5A.!!$R1 949
9 TraesCS6B01G053400 chr2B 776645027 776645958 931 True 743.00 743 82.2180 739 1631 1 chr2B.!!$R1 892
10 TraesCS6B01G053400 chr2A 677827917 677828541 624 False 697.00 697 87.1670 998 1619 1 chr2A.!!$F1 621
11 TraesCS6B01G053400 chr7B 113445005 113445686 681 True 667.00 667 85.2170 773 1425 1 chr7B.!!$R1 652
12 TraesCS6B01G053400 chr7D 151541992 151542749 757 True 656.00 656 83.2470 759 1491 1 chr7D.!!$R1 732
13 TraesCS6B01G053400 chr3D 594957838 594958432 594 True 619.00 619 86.3490 855 1428 1 chr3D.!!$R1 573
14 TraesCS6B01G053400 chr3B 798408340 798408877 537 True 582.00 582 86.9800 905 1428 1 chr3B.!!$R1 523
15 TraesCS6B01G053400 chr1A 96432192 96432919 727 False 234.65 374 90.5905 8 608 2 chr1A.!!$F1 600

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
370 524 0.833287 GCTGCCAGGATCCAGTCTTA 59.167 55.0 15.82 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 2039 0.247814 CTAAAACATGCGCCGCTCTG 60.248 55.0 11.67 10.68 0.0 3.35 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
27 29 8.194104 ACTTGTAATGCAATCAGTGTACAAAAA 58.806 29.630 0.00 0.00 36.36 1.94
73 75 8.147058 AGATGTATGTGCAGGTAAAATCTAGAG 58.853 37.037 0.00 0.00 0.00 2.43
115 187 6.258068 ACTCTGTTTCACTACAAAACTAGCAC 59.742 38.462 0.00 0.00 37.48 4.40
122 194 6.521162 TCACTACAAAACTAGCACAATCTCA 58.479 36.000 0.00 0.00 0.00 3.27
167 239 4.503007 CGACGTACATCCCATTAAGTTCAG 59.497 45.833 0.00 0.00 0.00 3.02
212 284 7.816031 AGAAATCCATGTTTGCATCAAGTTAAG 59.184 33.333 0.00 0.00 31.99 1.85
219 291 6.913170 TGTTTGCATCAAGTTAAGGAGAATC 58.087 36.000 0.00 0.00 0.00 2.52
228 308 5.864628 AGTTAAGGAGAATCAAAAGCGAC 57.135 39.130 0.00 0.00 36.25 5.19
230 310 2.115343 AGGAGAATCAAAAGCGACCC 57.885 50.000 0.00 0.00 36.25 4.46
353 507 3.424829 CGTTGTATTGATCTTTGCGTGCT 60.425 43.478 0.00 0.00 0.00 4.40
370 524 0.833287 GCTGCCAGGATCCAGTCTTA 59.167 55.000 15.82 0.00 0.00 2.10
374 528 1.474143 GCCAGGATCCAGTCTTAGTGC 60.474 57.143 15.82 0.00 0.00 4.40
379 533 4.160439 CAGGATCCAGTCTTAGTGCAAGTA 59.840 45.833 15.82 0.00 35.58 2.24
408 562 4.503734 CGTACGAGAGTTCTTCGTCTCTAT 59.496 45.833 10.44 0.00 46.40 1.98
571 726 2.863740 CGACTAAGCACACACACAGAAA 59.136 45.455 0.00 0.00 0.00 2.52
579 734 5.451908 AGCACACACACAGAAATTAAATCG 58.548 37.500 0.00 0.00 0.00 3.34
585 740 7.121168 ACACACACAGAAATTAAATCGGATGAT 59.879 33.333 0.00 0.00 35.98 2.45
598 753 5.958083 AATCGGATGATTGGGAACGAGAGT 61.958 45.833 0.00 0.00 45.12 3.24
637 792 4.673968 AGATACACGAGGCCTATATCCAA 58.326 43.478 4.42 0.00 0.00 3.53
638 793 5.273208 AGATACACGAGGCCTATATCCAAT 58.727 41.667 4.42 0.00 0.00 3.16
643 798 2.165641 CGAGGCCTATATCCAATGCGTA 59.834 50.000 4.42 0.00 0.00 4.42
665 820 4.983671 ATTTTTGGCCTCGGTTATCTTC 57.016 40.909 3.32 0.00 0.00 2.87
671 826 1.407979 GCCTCGGTTATCTTCGGAAGA 59.592 52.381 21.69 21.69 42.69 2.87
805 990 3.264706 TCACCGTCCCAATAAATTCTCCA 59.735 43.478 0.00 0.00 0.00 3.86
816 1005 6.183347 CAATAAATTCTCCAGGTTCCTCACT 58.817 40.000 0.00 0.00 0.00 3.41
843 1043 1.334869 CAACACGCAAAGAAGCTCCTT 59.665 47.619 0.00 0.00 0.00 3.36
868 1068 3.075005 TTAGCTCTTCCGCCGCCT 61.075 61.111 0.00 0.00 0.00 5.52
1248 1504 2.286872 CTCATCCTGGCTGCAAACTAG 58.713 52.381 0.50 0.00 0.00 2.57
1287 1544 1.272490 TCGACCTTACTTGCCAGACAG 59.728 52.381 0.00 0.00 0.00 3.51
1288 1545 1.000955 CGACCTTACTTGCCAGACAGT 59.999 52.381 0.00 0.00 0.00 3.55
1289 1546 2.548067 CGACCTTACTTGCCAGACAGTT 60.548 50.000 0.00 0.00 0.00 3.16
1290 1547 2.808543 GACCTTACTTGCCAGACAGTTG 59.191 50.000 0.00 0.00 0.00 3.16
1291 1548 1.537202 CCTTACTTGCCAGACAGTTGC 59.463 52.381 0.00 0.00 0.00 4.17
1292 1549 2.221169 CTTACTTGCCAGACAGTTGCA 58.779 47.619 0.00 0.00 0.00 4.08
1355 1612 5.625311 CCGCAAGACTTTTAACATCAAGAAC 59.375 40.000 0.00 0.00 43.02 3.01
1446 1714 2.795165 CCTAGCTAGGCACTGTCGA 58.205 57.895 26.62 0.00 41.52 4.20
1448 1716 1.066303 CCTAGCTAGGCACTGTCGAAG 59.934 57.143 26.62 0.00 41.52 3.79
1449 1717 2.017782 CTAGCTAGGCACTGTCGAAGA 58.982 52.381 13.32 0.00 41.52 2.87
1450 1718 1.479709 AGCTAGGCACTGTCGAAGAT 58.520 50.000 0.00 0.00 41.52 2.40
1452 1720 3.226777 AGCTAGGCACTGTCGAAGATAT 58.773 45.455 0.00 0.00 41.52 1.63
1453 1721 4.399219 AGCTAGGCACTGTCGAAGATATA 58.601 43.478 0.00 0.00 41.52 0.86
1455 1723 5.478679 AGCTAGGCACTGTCGAAGATATATT 59.521 40.000 0.00 0.00 41.52 1.28
1457 1725 7.176865 AGCTAGGCACTGTCGAAGATATATTAA 59.823 37.037 0.00 0.00 41.52 1.40
1458 1726 7.976734 GCTAGGCACTGTCGAAGATATATTAAT 59.023 37.037 0.00 0.00 41.52 1.40
1459 1727 9.295214 CTAGGCACTGTCGAAGATATATTAATG 57.705 37.037 0.00 0.00 41.52 1.90
1460 1728 6.591834 AGGCACTGTCGAAGATATATTAATGC 59.408 38.462 0.00 0.00 40.67 3.56
1521 1791 5.421056 AGAATAAACCTATCGTGGTCAGTGA 59.579 40.000 0.00 0.00 39.83 3.41
1612 1902 1.178276 TTTTGCCGTGTGGTTTGAGT 58.822 45.000 0.00 0.00 37.67 3.41
1613 1903 2.039818 TTTGCCGTGTGGTTTGAGTA 57.960 45.000 0.00 0.00 37.67 2.59
1692 2010 1.626686 TTTTCATGTGGCCGTTGGAT 58.373 45.000 0.00 0.00 0.00 3.41
1710 2028 4.436332 TGGATCGTTGTCATGAATCTCTG 58.564 43.478 0.00 0.00 0.00 3.35
1711 2029 3.247173 GGATCGTTGTCATGAATCTCTGC 59.753 47.826 0.00 0.00 0.00 4.26
1721 2039 1.142778 GAATCTCTGCTCCGTCGCAC 61.143 60.000 0.00 0.00 35.74 5.34
1722 2040 1.877576 AATCTCTGCTCCGTCGCACA 61.878 55.000 0.00 0.00 35.74 4.57
1744 2062 2.014128 AGCGGCGCATGTTTTAGTTAT 58.986 42.857 35.02 4.93 0.00 1.89
1745 2063 2.422127 AGCGGCGCATGTTTTAGTTATT 59.578 40.909 35.02 4.41 0.00 1.40
1747 2065 4.274950 AGCGGCGCATGTTTTAGTTATTAT 59.725 37.500 35.02 3.19 0.00 1.28
1748 2066 4.973663 GCGGCGCATGTTTTAGTTATTATT 59.026 37.500 29.21 0.00 0.00 1.40
1750 2068 6.799925 GCGGCGCATGTTTTAGTTATTATTAT 59.200 34.615 29.21 0.00 0.00 1.28
1751 2069 7.325097 GCGGCGCATGTTTTAGTTATTATTATT 59.675 33.333 29.21 0.00 0.00 1.40
1771 2089 3.764237 TTTCAGGTTACAGGTCTCCAC 57.236 47.619 0.00 0.00 0.00 4.02
1786 2104 0.476771 TCCACTTTTCACCCACCCTC 59.523 55.000 0.00 0.00 0.00 4.30
1797 2115 2.432628 CACCCTCGTCTTGACGCC 60.433 66.667 17.11 0.00 0.00 5.68
1801 2119 2.254350 CTCGTCTTGACGCCGACA 59.746 61.111 17.11 0.00 0.00 4.35
1819 2137 0.394899 CAAGGTCCCCAAGATCCTGC 60.395 60.000 0.00 0.00 0.00 4.85
1829 2147 0.888619 AAGATCCTGCGTCACTTCGA 59.111 50.000 0.00 0.00 0.00 3.71
1839 2157 2.732001 GTCACTTCGACGTTTTTGCT 57.268 45.000 0.00 0.00 34.19 3.91
1841 2159 4.186241 GTCACTTCGACGTTTTTGCTAA 57.814 40.909 0.00 0.00 34.19 3.09
1859 2177 3.608759 AAGCCCAGCGAGAGGAGGA 62.609 63.158 0.00 0.00 0.00 3.71
1862 2180 3.535962 CCAGCGAGAGGAGGAGGC 61.536 72.222 0.00 0.00 0.00 4.70
1867 2185 2.352032 CGAGAGGAGGAGGCGGTTT 61.352 63.158 0.00 0.00 0.00 3.27
1868 2186 1.518302 GAGAGGAGGAGGCGGTTTC 59.482 63.158 0.00 0.00 0.00 2.78
1871 2189 2.436824 GGAGGAGGCGGTTTCTGC 60.437 66.667 0.00 0.00 0.00 4.26
1894 2212 1.203063 AGCCGAGAGATAGGTATGGCA 60.203 52.381 2.94 0.00 43.35 4.92
1907 2225 1.844497 GTATGGCAACCTTCTACCCCT 59.156 52.381 0.00 0.00 0.00 4.79
1918 2236 0.333652 TCTACCCCTGACGTCCATGA 59.666 55.000 14.12 0.00 0.00 3.07
1919 2237 1.063190 TCTACCCCTGACGTCCATGAT 60.063 52.381 14.12 0.00 0.00 2.45
1945 2263 2.689983 GGGAACATTGTCCATGGATGTC 59.310 50.000 19.62 11.66 39.70 3.06
1966 2284 6.869695 TGTCTTCTGTTACTCAAAGTGTACA 58.130 36.000 0.00 0.00 0.00 2.90
1968 2286 7.438160 TGTCTTCTGTTACTCAAAGTGTACATG 59.562 37.037 0.00 0.00 0.00 3.21
2019 2337 6.432472 CCATTCCTGGGATATTTTCTTAGCTC 59.568 42.308 0.00 0.00 39.04 4.09
2022 2340 6.595682 TCCTGGGATATTTTCTTAGCTCAAG 58.404 40.000 0.00 0.00 35.38 3.02
2029 2347 7.492994 GGATATTTTCTTAGCTCAAGAGTTCGT 59.507 37.037 0.00 0.00 44.10 3.85
2030 2348 8.779354 ATATTTTCTTAGCTCAAGAGTTCGTT 57.221 30.769 0.00 0.00 44.10 3.85
2031 2349 5.907197 TTTCTTAGCTCAAGAGTTCGTTG 57.093 39.130 0.00 0.00 44.10 4.10
2032 2350 4.848562 TCTTAGCTCAAGAGTTCGTTGA 57.151 40.909 0.00 0.00 38.39 3.18
2033 2351 5.392767 TCTTAGCTCAAGAGTTCGTTGAT 57.607 39.130 0.00 0.00 38.39 2.57
2034 2352 5.784177 TCTTAGCTCAAGAGTTCGTTGATT 58.216 37.500 0.00 0.00 38.39 2.57
2035 2353 6.920817 TCTTAGCTCAAGAGTTCGTTGATTA 58.079 36.000 0.00 0.00 38.39 1.75
2036 2354 7.375834 TCTTAGCTCAAGAGTTCGTTGATTAA 58.624 34.615 0.00 0.00 38.39 1.40
2037 2355 7.870954 TCTTAGCTCAAGAGTTCGTTGATTAAA 59.129 33.333 0.00 0.00 38.39 1.52
2038 2356 6.861065 AGCTCAAGAGTTCGTTGATTAAAA 57.139 33.333 0.00 0.00 33.49 1.52
2039 2357 7.259290 AGCTCAAGAGTTCGTTGATTAAAAA 57.741 32.000 0.00 0.00 33.49 1.94
2063 2381 5.004448 AGAAGAATATGCAGATGGCTGATG 58.996 41.667 0.00 0.00 45.17 3.07
2065 2383 3.329814 AGAATATGCAGATGGCTGATGGA 59.670 43.478 0.00 0.00 45.17 3.41
2074 2392 5.477510 CAGATGGCTGATGGAAGATAGTAC 58.522 45.833 0.00 0.00 45.17 2.73
2077 2395 6.956435 AGATGGCTGATGGAAGATAGTACATA 59.044 38.462 0.00 0.00 0.00 2.29
2082 2400 8.317679 GGCTGATGGAAGATAGTACATATTCTT 58.682 37.037 0.00 0.00 0.00 2.52
2083 2401 9.149225 GCTGATGGAAGATAGTACATATTCTTG 57.851 37.037 0.00 0.00 0.00 3.02
2084 2402 9.650539 CTGATGGAAGATAGTACATATTCTTGG 57.349 37.037 0.00 0.00 0.00 3.61
2113 2434 6.769512 AGTTATCTGTGCTCCTTTGACTTAA 58.230 36.000 0.00 0.00 0.00 1.85
2119 2440 4.134563 GTGCTCCTTTGACTTAAGTTCCA 58.865 43.478 10.02 0.89 0.00 3.53
2132 2453 1.218316 GTTCCAGGCCTGTCTACGG 59.782 63.158 30.63 15.08 0.00 4.02
2134 2455 2.363795 CCAGGCCTGTCTACGGGA 60.364 66.667 30.63 0.00 45.36 5.14
2145 2466 4.997395 CCTGTCTACGGGATAAAATCATGG 59.003 45.833 1.39 0.00 45.36 3.66
2167 2488 5.012664 TGGAGAATAAAAGTAGTGTGGAGCA 59.987 40.000 0.00 0.00 0.00 4.26
2175 2496 2.158986 AGTAGTGTGGAGCATCATCAGC 60.159 50.000 0.00 0.00 36.25 4.26
2179 2500 0.654683 GTGGAGCATCATCAGCGAAC 59.345 55.000 0.00 0.00 36.25 3.95
2191 2512 4.157840 TCATCAGCGAACTTGACTAGCTTA 59.842 41.667 0.00 0.00 35.82 3.09
2194 2515 2.231478 AGCGAACTTGACTAGCTTAGCA 59.769 45.455 7.07 0.00 34.05 3.49
2237 2558 4.065088 GAGCGCCAATTGACCTGAATATA 58.935 43.478 7.12 0.00 0.00 0.86
2238 2559 4.655963 AGCGCCAATTGACCTGAATATAT 58.344 39.130 7.12 0.00 0.00 0.86
2328 2650 7.498070 GCAATTAGCAGTTACAATTTGTCTC 57.502 36.000 5.07 0.90 44.79 3.36
2380 2702 5.086058 CCATTTGTATCACGTTGTAGCAAC 58.914 41.667 2.22 2.22 0.00 4.17
2381 2703 4.735662 TTTGTATCACGTTGTAGCAACC 57.264 40.909 6.44 0.00 0.00 3.77
2407 2729 6.019237 GCTATTTGCGTTTAGGTTCTACTACC 60.019 42.308 0.00 0.00 38.53 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.174946 AGGGACTGTATTTTTGTACACTGATTG 59.825 37.037 0.00 0.00 37.18 2.67
27 29 1.542492 ACGTTGTCGAGGGACTGTAT 58.458 50.000 0.00 0.00 41.55 2.29
73 75 6.178239 ACAGAGTTGTACAAATTTATCCGC 57.822 37.500 10.51 0.00 35.25 5.54
122 194 8.540492 CGTCGATTTAGCTCATATTTACTGTTT 58.460 33.333 0.00 0.00 0.00 2.83
167 239 3.937814 TCTGTGGTGGATATGTTGTGAC 58.062 45.455 0.00 0.00 0.00 3.67
212 284 0.727398 CGGGTCGCTTTTGATTCTCC 59.273 55.000 0.00 0.00 0.00 3.71
219 291 0.596082 AATGAACCGGGTCGCTTTTG 59.404 50.000 16.31 0.00 0.00 2.44
228 308 1.689273 TGGGAAAAACAATGAACCGGG 59.311 47.619 6.32 0.00 0.00 5.73
230 310 8.764524 TTATTATTGGGAAAAACAATGAACCG 57.235 30.769 0.00 0.00 38.84 4.44
310 456 3.133721 CGTCCCAAATCCATCTCTTCTCT 59.866 47.826 0.00 0.00 0.00 3.10
311 457 3.118592 ACGTCCCAAATCCATCTCTTCTC 60.119 47.826 0.00 0.00 0.00 2.87
353 507 1.833630 CACTAAGACTGGATCCTGGCA 59.166 52.381 25.05 5.83 0.00 4.92
370 524 1.066605 CGTACGCCCTATACTTGCACT 59.933 52.381 0.52 0.00 0.00 4.40
374 528 2.877168 ACTCTCGTACGCCCTATACTTG 59.123 50.000 11.24 0.00 0.00 3.16
379 533 2.345124 AGAACTCTCGTACGCCCTAT 57.655 50.000 11.24 0.00 0.00 2.57
559 714 6.429692 TCATCCGATTTAATTTCTGTGTGTGT 59.570 34.615 0.00 0.00 0.00 3.72
571 726 5.373222 TCGTTCCCAATCATCCGATTTAAT 58.627 37.500 0.00 0.00 39.96 1.40
579 734 2.990066 ACTCTCGTTCCCAATCATCC 57.010 50.000 0.00 0.00 0.00 3.51
585 740 4.106825 TCCCCTATATACTCTCGTTCCCAA 59.893 45.833 0.00 0.00 0.00 4.12
620 775 2.350522 GCATTGGATATAGGCCTCGTG 58.649 52.381 9.68 0.00 0.00 4.35
637 792 1.134175 CCGAGGCCAAAAATTACGCAT 59.866 47.619 5.01 0.00 0.00 4.73
638 793 0.523966 CCGAGGCCAAAAATTACGCA 59.476 50.000 5.01 0.00 0.00 5.24
643 798 4.142469 CGAAGATAACCGAGGCCAAAAATT 60.142 41.667 5.01 0.00 0.00 1.82
665 820 5.410439 TCCGTTTCCTTATTTTCTTCTTCCG 59.590 40.000 0.00 0.00 0.00 4.30
671 826 9.433153 CTAGTAGTTCCGTTTCCTTATTTTCTT 57.567 33.333 0.00 0.00 0.00 2.52
746 904 4.351938 TCGGGGTCGTGCTCGTTG 62.352 66.667 8.17 0.00 38.33 4.10
805 990 0.413832 TGGGCTAGAGTGAGGAACCT 59.586 55.000 0.00 0.00 0.00 3.50
816 1005 0.394938 TCTTTGCGTGTTGGGCTAGA 59.605 50.000 0.00 0.00 0.00 2.43
843 1043 1.132643 GCGGAAGAGCTAACGAGAGAA 59.867 52.381 0.00 0.00 0.00 2.87
868 1068 2.706890 GAAACCCTAGCAAATGGACGA 58.293 47.619 0.00 0.00 0.00 4.20
874 1078 2.095415 GCGAAACGAAACCCTAGCAAAT 60.095 45.455 0.00 0.00 0.00 2.32
972 1190 0.744874 CGCCTCCTCGACCTGAAATA 59.255 55.000 0.00 0.00 0.00 1.40
1248 1504 2.096496 CGAGCAATCCCTTGATGTTGAC 59.904 50.000 0.00 0.00 34.04 3.18
1290 1547 2.159421 CCTTGATCATGTCTGCAACTGC 60.159 50.000 0.00 0.00 42.50 4.40
1291 1548 2.422479 CCCTTGATCATGTCTGCAACTG 59.578 50.000 0.00 0.00 0.00 3.16
1292 1549 2.306805 TCCCTTGATCATGTCTGCAACT 59.693 45.455 0.00 0.00 0.00 3.16
1355 1612 1.213013 CTCCTCGGGTGTGAAGTCG 59.787 63.158 0.00 0.00 0.00 4.18
1501 1771 4.707934 TGATCACTGACCACGATAGGTTTA 59.292 41.667 0.00 0.00 43.38 2.01
1692 2010 3.515630 GAGCAGAGATTCATGACAACGA 58.484 45.455 0.00 0.00 0.00 3.85
1721 2039 0.247814 CTAAAACATGCGCCGCTCTG 60.248 55.000 11.67 10.68 0.00 3.35
1722 2040 0.673644 ACTAAAACATGCGCCGCTCT 60.674 50.000 11.67 0.00 0.00 4.09
1744 2062 8.607713 TGGAGACCTGTAACCTGAAAATAATAA 58.392 33.333 0.00 0.00 0.00 1.40
1745 2063 8.044908 GTGGAGACCTGTAACCTGAAAATAATA 58.955 37.037 0.00 0.00 0.00 0.98
1747 2065 6.043938 AGTGGAGACCTGTAACCTGAAAATAA 59.956 38.462 0.00 0.00 0.00 1.40
1748 2066 5.546499 AGTGGAGACCTGTAACCTGAAAATA 59.454 40.000 0.00 0.00 0.00 1.40
1750 2068 3.714798 AGTGGAGACCTGTAACCTGAAAA 59.285 43.478 0.00 0.00 0.00 2.29
1751 2069 3.314693 AGTGGAGACCTGTAACCTGAAA 58.685 45.455 0.00 0.00 0.00 2.69
1754 2072 3.771577 AAAGTGGAGACCTGTAACCTG 57.228 47.619 0.00 0.00 0.00 4.00
1755 2073 3.714798 TGAAAAGTGGAGACCTGTAACCT 59.285 43.478 0.00 0.00 0.00 3.50
1771 2089 0.396811 AGACGAGGGTGGGTGAAAAG 59.603 55.000 0.00 0.00 0.00 2.27
1829 2147 1.269569 GCTGGGCTTTAGCAAAAACGT 60.270 47.619 3.88 0.00 44.36 3.99
1839 2157 1.330655 CCTCCTCTCGCTGGGCTTTA 61.331 60.000 0.00 0.00 0.00 1.85
1841 2159 3.080121 CCTCCTCTCGCTGGGCTT 61.080 66.667 0.00 0.00 0.00 4.35
1867 2185 1.790090 CTATCTCTCGGCTGCGCAGA 61.790 60.000 40.21 19.47 0.00 4.26
1868 2186 1.371512 CTATCTCTCGGCTGCGCAG 60.372 63.158 32.83 32.83 0.00 5.18
1871 2189 1.135546 CATACCTATCTCTCGGCTGCG 60.136 57.143 0.00 0.00 0.00 5.18
1874 2192 1.203063 TGCCATACCTATCTCTCGGCT 60.203 52.381 0.00 0.00 38.87 5.52
1894 2212 1.264295 GACGTCAGGGGTAGAAGGTT 58.736 55.000 11.55 0.00 0.00 3.50
1898 2216 1.191535 CATGGACGTCAGGGGTAGAA 58.808 55.000 18.91 0.00 0.00 2.10
1907 2225 1.141665 CCGCTGATCATGGACGTCA 59.858 57.895 18.91 3.91 0.00 4.35
1918 2236 0.327924 TGGACAATGTTCCCGCTGAT 59.672 50.000 0.00 0.00 34.33 2.90
1919 2237 0.327924 ATGGACAATGTTCCCGCTGA 59.672 50.000 0.00 0.00 34.33 4.26
1945 2263 7.946655 TCATGTACACTTTGAGTAACAGAAG 57.053 36.000 0.00 0.00 30.17 2.85
1994 2312 6.310149 AGCTAAGAAAATATCCCAGGAATGG 58.690 40.000 0.00 0.00 0.00 3.16
2003 2321 7.492994 ACGAACTCTTGAGCTAAGAAAATATCC 59.507 37.037 0.00 0.00 44.47 2.59
2007 2325 6.706270 TCAACGAACTCTTGAGCTAAGAAAAT 59.294 34.615 0.00 0.00 44.47 1.82
2036 2354 6.379133 TCAGCCATCTGCATATTCTTCTTTTT 59.621 34.615 0.00 0.00 44.83 1.94
2037 2355 5.889853 TCAGCCATCTGCATATTCTTCTTTT 59.110 36.000 0.00 0.00 44.83 2.27
2038 2356 5.443283 TCAGCCATCTGCATATTCTTCTTT 58.557 37.500 0.00 0.00 44.83 2.52
2039 2357 5.045012 TCAGCCATCTGCATATTCTTCTT 57.955 39.130 0.00 0.00 44.83 2.52
2040 2358 4.701651 TCAGCCATCTGCATATTCTTCT 57.298 40.909 0.00 0.00 44.83 2.85
2041 2359 4.156190 CCATCAGCCATCTGCATATTCTTC 59.844 45.833 0.00 0.00 44.83 2.87
2063 2381 8.861086 TCTGACCAAGAATATGTACTATCTTCC 58.139 37.037 0.00 0.00 29.54 3.46
2065 2383 9.427821 ACTCTGACCAAGAATATGTACTATCTT 57.572 33.333 0.00 0.00 33.37 2.40
2113 2434 1.258445 CCGTAGACAGGCCTGGAACT 61.258 60.000 35.42 29.16 34.19 3.01
2119 2440 2.170012 TTTATCCCGTAGACAGGCCT 57.830 50.000 0.00 0.00 0.00 5.19
2145 2466 6.818644 TGATGCTCCACACTACTTTTATTCTC 59.181 38.462 0.00 0.00 0.00 2.87
2167 2488 3.131933 AGCTAGTCAAGTTCGCTGATGAT 59.868 43.478 0.00 0.00 0.00 2.45
2175 2496 3.839293 ACTGCTAAGCTAGTCAAGTTCG 58.161 45.455 0.00 0.00 0.00 3.95
2212 2533 1.277842 TCAGGTCAATTGGCGCTCTAA 59.722 47.619 7.64 0.44 0.00 2.10
2309 2631 6.052360 TGTGTGAGACAAATTGTAACTGCTA 58.948 36.000 0.00 0.00 0.00 3.49
2320 2642 5.865552 GCATTTGCTAATGTGTGAGACAAAT 59.134 36.000 19.66 0.00 42.56 2.32
2353 2675 6.150307 TGCTACAACGTGATACAAATGGAAAT 59.850 34.615 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.