Multiple sequence alignment - TraesCS1D01G144500

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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 TraesCS1D01G144500 chr1D 100.000 1385 0 0 985 2369 199841068 199842452 0.000000e+00 2558.0
1 TraesCS1D01G144500 chr1D 100.000 695 0 0 1 695 199840084 199840778 0.000000e+00 1284.0
2 TraesCS1D01G144500 chr1D 95.497 644 27 2 1 643 435970969 435971611 0.000000e+00 1027.0
3 TraesCS1D01G144500 chr1D 91.111 90 4 2 1390 1475 295954213 295954302 4.140000e-23 119.0
4 TraesCS1D01G144500 chr1A 88.293 1418 78 28 985 2369 252321610 252322972 0.000000e+00 1618.0
5 TraesCS1D01G144500 chr3D 95.963 644 24 2 1 643 597285668 597285026 0.000000e+00 1044.0
6 TraesCS1D01G144500 chr3D 94.384 641 26 3 1 640 44063186 44062555 0.000000e+00 976.0
7 TraesCS1D01G144500 chr3D 92.941 85 5 1 1392 1476 61804611 61804528 3.200000e-24 122.0
8 TraesCS1D01G144500 chr3D 87.931 58 6 1 545 602 245584831 245584887 1.520000e-07 67.6
9 TraesCS1D01G144500 chr6D 95.223 649 25 3 1 644 426338557 426337910 0.000000e+00 1022.0
10 TraesCS1D01G144500 chr1B 92.494 413 16 7 985 1391 286610074 286610477 5.680000e-161 577.0
11 TraesCS1D01G144500 chr1B 83.613 537 39 24 1750 2260 286610817 286611330 2.150000e-125 459.0
12 TraesCS1D01G144500 chr1B 90.301 299 21 5 1471 1764 286610475 286610770 3.690000e-103 385.0
13 TraesCS1D01G144500 chr1B 99.200 125 1 0 2245 2369 286611344 286611468 2.370000e-55 226.0
14 TraesCS1D01G144500 chr1B 92.857 42 3 0 460 501 662174048 662174089 7.070000e-06 62.1
15 TraesCS1D01G144500 chr2D 89.796 98 6 2 1390 1483 14895273 14895370 3.200000e-24 122.0
16 TraesCS1D01G144500 chr2D 90.323 93 5 2 1391 1479 378043180 378043088 4.140000e-23 119.0
17 TraesCS1D01G144500 chr7B 91.209 91 5 1 1386 1473 517395874 517395784 1.150000e-23 121.0
18 TraesCS1D01G144500 chr4D 87.037 108 10 4 1390 1495 384974368 384974263 4.140000e-23 119.0
19 TraesCS1D01G144500 chr4D 88.542 96 7 2 1390 1481 124628767 124628862 1.920000e-21 113.0
20 TraesCS1D01G144500 chr6B 86.364 110 8 5 1391 1494 717901623 717901515 1.920000e-21 113.0
21 TraesCS1D01G144500 chr6B 87.879 99 6 5 1391 1485 471227665 471227569 6.920000e-21 111.0
22 TraesCS1D01G144500 chr3B 95.122 41 1 1 545 585 331951698 331951737 1.970000e-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 TraesCS1D01G144500 chr1D 199840084 199842452 2368 False 1921.00 2558 100.000 1 2369 2 chr1D.!!$F3 2368
1 TraesCS1D01G144500 chr1D 435970969 435971611 642 False 1027.00 1027 95.497 1 643 1 chr1D.!!$F2 642
2 TraesCS1D01G144500 chr1A 252321610 252322972 1362 False 1618.00 1618 88.293 985 2369 1 chr1A.!!$F1 1384
3 TraesCS1D01G144500 chr3D 597285026 597285668 642 True 1044.00 1044 95.963 1 643 1 chr3D.!!$R3 642
4 TraesCS1D01G144500 chr3D 44062555 44063186 631 True 976.00 976 94.384 1 640 1 chr3D.!!$R1 639
5 TraesCS1D01G144500 chr6D 426337910 426338557 647 True 1022.00 1022 95.223 1 644 1 chr6D.!!$R1 643
6 TraesCS1D01G144500 chr1B 286610074 286611468 1394 False 411.75 577 91.402 985 2369 4 chr1B.!!$F2 1384

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
666 673 0.038744 CCAATGGCCAACCTCTCACT 59.961 55.0 10.96 0.0 36.63 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1525 0.544697 GGACCGATTAGGGGCAAAGA 59.455 55.0 0.0 0.0 46.96 2.52 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
40 41 0.750249 TGCCGTCGATGGTGTCATAT 59.250 50.000 24.33 0.00 32.98 1.78
41 42 1.957877 TGCCGTCGATGGTGTCATATA 59.042 47.619 24.33 0.00 32.98 0.86
97 98 2.174969 TCGAAAACAACACGCGCCT 61.175 52.632 5.73 0.00 0.00 5.52
170 171 2.165167 CTCCCATCAAGCACAACACAT 58.835 47.619 0.00 0.00 0.00 3.21
174 175 2.293955 CCATCAAGCACAACACATCACA 59.706 45.455 0.00 0.00 0.00 3.58
190 191 1.616374 TCACAGTCGATGGTGTAGCAA 59.384 47.619 16.01 0.00 36.43 3.91
206 207 1.885157 CAATTGTCGCCATGGCTGT 59.115 52.632 33.07 12.21 39.32 4.40
220 221 0.179018 GGCTGTTGAGGAGGTTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
267 268 3.994392 GTCAATGGTGTCATAGTCGTTGT 59.006 43.478 0.00 0.00 32.44 3.32
268 269 4.451096 GTCAATGGTGTCATAGTCGTTGTT 59.549 41.667 0.00 0.00 32.44 2.83
271 272 4.587584 TGGTGTCATAGTCGTTGTTGTA 57.412 40.909 0.00 0.00 0.00 2.41
547 553 4.995487 ACTCAGTTTGACTTATCCCGTTTC 59.005 41.667 0.00 0.00 0.00 2.78
616 623 4.521010 CGTTTAAACAAAGTCGGTTCTCC 58.479 43.478 18.07 0.00 0.00 3.71
644 651 2.650322 TGGCTATCCAAACAACCCCTAA 59.350 45.455 0.00 0.00 39.99 2.69
645 652 3.076182 TGGCTATCCAAACAACCCCTAAA 59.924 43.478 0.00 0.00 39.99 1.85
646 653 4.090819 GGCTATCCAAACAACCCCTAAAA 58.909 43.478 0.00 0.00 0.00 1.52
647 654 4.081862 GGCTATCCAAACAACCCCTAAAAC 60.082 45.833 0.00 0.00 0.00 2.43
648 655 4.081862 GCTATCCAAACAACCCCTAAAACC 60.082 45.833 0.00 0.00 0.00 3.27
649 656 3.399952 TCCAAACAACCCCTAAAACCA 57.600 42.857 0.00 0.00 0.00 3.67
650 657 3.721021 TCCAAACAACCCCTAAAACCAA 58.279 40.909 0.00 0.00 0.00 3.67
651 658 4.299485 TCCAAACAACCCCTAAAACCAAT 58.701 39.130 0.00 0.00 0.00 3.16
652 659 4.101741 TCCAAACAACCCCTAAAACCAATG 59.898 41.667 0.00 0.00 0.00 2.82
653 660 4.384940 CAAACAACCCCTAAAACCAATGG 58.615 43.478 0.00 0.00 0.00 3.16
654 661 1.974957 ACAACCCCTAAAACCAATGGC 59.025 47.619 0.00 0.00 0.00 4.40
655 662 1.277842 CAACCCCTAAAACCAATGGCC 59.722 52.381 0.00 0.00 0.00 5.36
656 663 0.489567 ACCCCTAAAACCAATGGCCA 59.510 50.000 8.56 8.56 0.00 5.36
657 664 1.132689 ACCCCTAAAACCAATGGCCAA 60.133 47.619 10.96 0.00 0.00 4.52
658 665 1.277842 CCCCTAAAACCAATGGCCAAC 59.722 52.381 10.96 0.00 0.00 3.77
659 666 1.277842 CCCTAAAACCAATGGCCAACC 59.722 52.381 10.96 0.00 0.00 3.77
660 667 2.256306 CCTAAAACCAATGGCCAACCT 58.744 47.619 10.96 0.00 36.63 3.50
661 668 2.233676 CCTAAAACCAATGGCCAACCTC 59.766 50.000 10.96 0.00 36.63 3.85
662 669 2.101640 AAAACCAATGGCCAACCTCT 57.898 45.000 10.96 0.00 36.63 3.69
663 670 1.632589 AAACCAATGGCCAACCTCTC 58.367 50.000 10.96 0.00 36.63 3.20
664 671 0.482446 AACCAATGGCCAACCTCTCA 59.518 50.000 10.96 0.00 36.63 3.27
665 672 0.251341 ACCAATGGCCAACCTCTCAC 60.251 55.000 10.96 0.00 36.63 3.51
666 673 0.038744 CCAATGGCCAACCTCTCACT 59.961 55.000 10.96 0.00 36.63 3.41
667 674 1.457346 CAATGGCCAACCTCTCACTC 58.543 55.000 10.96 0.00 36.63 3.51
668 675 1.004044 CAATGGCCAACCTCTCACTCT 59.996 52.381 10.96 0.00 36.63 3.24
669 676 0.908198 ATGGCCAACCTCTCACTCTC 59.092 55.000 10.96 0.00 36.63 3.20
670 677 1.194781 TGGCCAACCTCTCACTCTCC 61.195 60.000 0.61 0.00 36.63 3.71
671 678 0.907230 GGCCAACCTCTCACTCTCCT 60.907 60.000 0.00 0.00 0.00 3.69
672 679 0.248843 GCCAACCTCTCACTCTCCTG 59.751 60.000 0.00 0.00 0.00 3.86
673 680 1.930251 CCAACCTCTCACTCTCCTGA 58.070 55.000 0.00 0.00 0.00 3.86
674 681 2.465813 CCAACCTCTCACTCTCCTGAT 58.534 52.381 0.00 0.00 0.00 2.90
675 682 2.430332 CCAACCTCTCACTCTCCTGATC 59.570 54.545 0.00 0.00 0.00 2.92
676 683 2.430332 CAACCTCTCACTCTCCTGATCC 59.570 54.545 0.00 0.00 0.00 3.36
677 684 1.929494 ACCTCTCACTCTCCTGATCCT 59.071 52.381 0.00 0.00 0.00 3.24
678 685 2.091885 ACCTCTCACTCTCCTGATCCTC 60.092 54.545 0.00 0.00 0.00 3.71
679 686 2.091939 CCTCTCACTCTCCTGATCCTCA 60.092 54.545 0.00 0.00 0.00 3.86
680 687 3.626983 CCTCTCACTCTCCTGATCCTCAA 60.627 52.174 0.00 0.00 0.00 3.02
681 688 4.022603 CTCTCACTCTCCTGATCCTCAAA 58.977 47.826 0.00 0.00 0.00 2.69
682 689 4.420206 TCTCACTCTCCTGATCCTCAAAA 58.580 43.478 0.00 0.00 0.00 2.44
683 690 4.840680 TCTCACTCTCCTGATCCTCAAAAA 59.159 41.667 0.00 0.00 0.00 1.94
1104 1117 2.131067 GCTCCTCCTCCCTCCTTCG 61.131 68.421 0.00 0.00 0.00 3.79
1220 1233 4.514577 CCAGCACGACCCGCTAGG 62.515 72.222 0.00 0.00 37.72 3.02
1377 1390 1.473434 CGACCTTACTGAAGCCCATCC 60.473 57.143 0.00 0.00 0.00 3.51
1391 1404 0.106149 CCATCCCGGCTGTTAGGTAC 59.894 60.000 0.00 0.00 0.00 3.34
1419 1433 4.406003 CCCTCCGTCCCATAATATAAGAGG 59.594 50.000 0.00 0.00 38.47 3.69
1423 1437 5.847817 TCCGTCCCATAATATAAGAGGGTTT 59.152 40.000 0.00 0.00 40.48 3.27
1424 1438 6.330778 TCCGTCCCATAATATAAGAGGGTTTT 59.669 38.462 0.00 0.00 40.48 2.43
1425 1439 7.002276 CCGTCCCATAATATAAGAGGGTTTTT 58.998 38.462 0.00 0.00 40.48 1.94
1473 1487 2.787473 TTACGAGACGGAGGGAGTAA 57.213 50.000 0.00 0.00 0.00 2.24
1474 1488 3.287867 TTACGAGACGGAGGGAGTAAT 57.712 47.619 0.00 0.00 0.00 1.89
1475 1489 4.422073 TTACGAGACGGAGGGAGTAATA 57.578 45.455 0.00 0.00 0.00 0.98
1516 1530 1.888512 CATCAGTGTTGGGGGTCTTTG 59.111 52.381 0.00 0.00 0.00 2.77
1527 1541 0.465642 GGGTCTTTGCCCCTAATCGG 60.466 60.000 0.00 0.00 42.89 4.18
1535 1549 1.049289 GCCCCTAATCGGTCCAGTCT 61.049 60.000 0.00 0.00 0.00 3.24
1573 1587 4.000988 CCCGTGCCACTAATTATCATACC 58.999 47.826 0.00 0.00 0.00 2.73
1635 1649 5.941733 TGCTTAAGATTACTGCACACAATG 58.058 37.500 6.67 0.00 0.00 2.82
1656 1670 3.949754 TGTGATCCAATGATTCCTTCAGC 59.050 43.478 0.00 0.00 37.89 4.26
1669 1683 4.111375 TCCTTCAGCGTGAGTTTATCTC 57.889 45.455 0.00 0.00 43.03 2.75
1695 1709 5.105351 ACTCGGTGTCTGAAATGATATGTGA 60.105 40.000 0.00 0.00 0.00 3.58
1716 1733 5.929697 GATGCGAAATGGATCATGTCTTA 57.070 39.130 0.00 0.00 44.27 2.10
1769 1847 6.061441 TGCTAACTCTTTTTGGTTGATGAGA 58.939 36.000 0.00 0.00 0.00 3.27
1780 1858 9.859427 TTTTTGGTTGATGAGATTAAGCTAATG 57.141 29.630 0.00 0.00 0.00 1.90
1833 1911 2.036604 CCACCCAAAATAGTGCCGTTTT 59.963 45.455 0.00 0.00 32.48 2.43
1848 1927 4.173256 GCCGTTTTATTTAAGCTGTGCAT 58.827 39.130 0.00 0.00 0.00 3.96
1854 1933 8.172484 CGTTTTATTTAAGCTGTGCATGTACTA 58.828 33.333 15.25 1.16 0.00 1.82
1855 1934 9.274065 GTTTTATTTAAGCTGTGCATGTACTAC 57.726 33.333 15.25 7.03 0.00 2.73
1856 1935 8.786826 TTTATTTAAGCTGTGCATGTACTACT 57.213 30.769 15.25 9.16 0.00 2.57
1857 1936 6.910536 ATTTAAGCTGTGCATGTACTACTC 57.089 37.500 15.25 2.02 0.00 2.59
1858 1937 3.961480 AAGCTGTGCATGTACTACTCA 57.039 42.857 15.25 0.00 0.00 3.41
1859 1938 4.478206 AAGCTGTGCATGTACTACTCAT 57.522 40.909 15.25 0.00 0.00 2.90
1860 1939 3.790091 AGCTGTGCATGTACTACTCATG 58.210 45.455 15.25 0.00 43.58 3.07
1861 1940 3.196469 AGCTGTGCATGTACTACTCATGT 59.804 43.478 15.25 0.00 42.94 3.21
1862 1941 3.935203 GCTGTGCATGTACTACTCATGTT 59.065 43.478 15.25 0.00 42.94 2.71
1863 1942 5.105351 AGCTGTGCATGTACTACTCATGTTA 60.105 40.000 15.25 0.00 42.94 2.41
1864 1943 5.005779 GCTGTGCATGTACTACTCATGTTAC 59.994 44.000 15.25 7.66 42.94 2.50
1865 1944 6.031751 TGTGCATGTACTACTCATGTTACA 57.968 37.500 15.25 9.56 42.94 2.41
1866 1945 6.639563 TGTGCATGTACTACTCATGTTACAT 58.360 36.000 15.25 0.00 42.94 2.29
1867 1946 6.756542 TGTGCATGTACTACTCATGTTACATC 59.243 38.462 15.25 0.00 42.94 3.06
1868 1947 6.756542 GTGCATGTACTACTCATGTTACATCA 59.243 38.462 6.69 0.00 42.94 3.07
1869 1948 7.439356 GTGCATGTACTACTCATGTTACATCAT 59.561 37.037 6.69 0.00 42.94 2.45
1870 1949 7.986889 TGCATGTACTACTCATGTTACATCATT 59.013 33.333 0.00 0.00 42.94 2.57
1871 1950 8.830580 GCATGTACTACTCATGTTACATCATTT 58.169 33.333 0.00 0.00 42.94 2.32
1874 1953 9.529325 TGTACTACTCATGTTACATCATTTAGC 57.471 33.333 0.00 0.00 0.00 3.09
1875 1954 9.529325 GTACTACTCATGTTACATCATTTAGCA 57.471 33.333 0.00 0.00 0.00 3.49
1902 1981 5.277058 GCTAAGTCAATGATCCACGAACATC 60.277 44.000 0.00 0.00 0.00 3.06
1987 2066 6.389830 AACTGCATGTTTTGATTGTGAGTA 57.610 33.333 0.00 0.00 34.84 2.59
1999 2078 5.470368 TGATTGTGAGTAGTGCTAGTTGAC 58.530 41.667 0.00 0.00 0.00 3.18
2009 2088 3.433615 AGTGCTAGTTGACGAAATTCAGC 59.566 43.478 0.00 0.00 0.00 4.26
2064 2143 6.074088 CGCTGAAATATATGAAACGAGAGCTT 60.074 38.462 0.00 0.00 0.00 3.74
2112 2191 9.914131 GTAAAAACATTATTTTCTCAGAAGCCT 57.086 29.630 0.00 0.00 34.51 4.58
2126 2205 4.901849 TCAGAAGCCTAAGTATAGCCACAT 59.098 41.667 0.00 0.00 0.00 3.21
2127 2206 4.993584 CAGAAGCCTAAGTATAGCCACATG 59.006 45.833 0.00 0.00 0.00 3.21
2129 2208 5.545723 AGAAGCCTAAGTATAGCCACATGAT 59.454 40.000 0.00 0.00 0.00 2.45
2176 2284 4.042187 AGTCCCCATGCTCCATTTATCTAC 59.958 45.833 0.00 0.00 0.00 2.59
2190 2298 7.337184 TCCATTTATCTACGGACTAGCTGATAG 59.663 40.741 0.00 0.00 37.53 2.08
2192 2300 9.163899 CATTTATCTACGGACTAGCTGATAGTA 57.836 37.037 5.45 0.00 45.06 1.82
2193 2301 8.545229 TTTATCTACGGACTAGCTGATAGTAC 57.455 38.462 5.45 5.33 45.06 2.73
2194 2302 5.541953 TCTACGGACTAGCTGATAGTACA 57.458 43.478 15.05 0.00 44.65 2.90
2195 2303 5.295950 TCTACGGACTAGCTGATAGTACAC 58.704 45.833 15.05 4.41 44.65 2.90
2196 2304 3.882444 ACGGACTAGCTGATAGTACACA 58.118 45.455 15.05 0.00 44.65 3.72
2226 2334 9.583765 AAATACAAACCGTTTTACAAGCTTTTA 57.416 25.926 0.00 0.00 0.00 1.52
2242 2350 7.281100 ACAAGCTTTTATAGATACCTCACAAGC 59.719 37.037 0.00 0.00 35.41 4.01
2362 2499 1.475280 CATGGGTTCAGTTCAGGCATG 59.525 52.381 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 1.253100 TGCTACACCATCGACTGTGA 58.747 50.000 19.69 5.89 36.35 3.58
174 175 3.262420 GACAATTGCTACACCATCGACT 58.738 45.455 5.05 0.00 0.00 4.18
206 207 1.810031 CGAGCAACACAACCTCCTCAA 60.810 52.381 0.00 0.00 0.00 3.02
267 268 0.108329 GACCTGCTTAGCGGCTACAA 60.108 55.000 9.68 0.00 32.89 2.41
268 269 1.515954 GACCTGCTTAGCGGCTACA 59.484 57.895 9.68 4.69 32.89 2.74
271 272 3.382832 ACGACCTGCTTAGCGGCT 61.383 61.111 7.98 7.98 32.89 5.52
302 303 1.080298 TTGCTGACGACGTGTTGTTT 58.920 45.000 4.58 0.00 0.00 2.83
370 371 2.663196 GTACCTCACGGCAAGCCT 59.337 61.111 9.73 0.00 0.00 4.58
585 592 6.633634 CCGACTTTGTTTAAACGCAATTTCTA 59.366 34.615 13.45 0.00 0.00 2.10
616 623 4.379082 GGTTGTTTGGATAGCCAGTTTACG 60.379 45.833 0.00 0.00 46.91 3.18
617 624 4.082408 GGGTTGTTTGGATAGCCAGTTTAC 60.082 45.833 0.00 0.00 46.91 2.01
644 651 1.133199 TGAGAGGTTGGCCATTGGTTT 60.133 47.619 6.09 0.00 37.19 3.27
645 652 0.482446 TGAGAGGTTGGCCATTGGTT 59.518 50.000 6.09 0.00 37.19 3.67
646 653 0.251341 GTGAGAGGTTGGCCATTGGT 60.251 55.000 6.09 0.00 37.19 3.67
647 654 0.038744 AGTGAGAGGTTGGCCATTGG 59.961 55.000 6.09 0.00 37.19 3.16
648 655 1.004044 AGAGTGAGAGGTTGGCCATTG 59.996 52.381 6.09 0.00 37.19 2.82
649 656 1.280421 GAGAGTGAGAGGTTGGCCATT 59.720 52.381 6.09 0.00 37.19 3.16
650 657 0.908198 GAGAGTGAGAGGTTGGCCAT 59.092 55.000 6.09 0.00 37.19 4.40
651 658 1.194781 GGAGAGTGAGAGGTTGGCCA 61.195 60.000 0.00 0.00 37.19 5.36
652 659 0.907230 AGGAGAGTGAGAGGTTGGCC 60.907 60.000 0.00 0.00 0.00 5.36
653 660 0.248843 CAGGAGAGTGAGAGGTTGGC 59.751 60.000 0.00 0.00 0.00 4.52
654 661 1.930251 TCAGGAGAGTGAGAGGTTGG 58.070 55.000 0.00 0.00 0.00 3.77
655 662 2.430332 GGATCAGGAGAGTGAGAGGTTG 59.570 54.545 0.00 0.00 0.00 3.77
656 663 2.314549 AGGATCAGGAGAGTGAGAGGTT 59.685 50.000 0.00 0.00 0.00 3.50
657 664 1.929494 AGGATCAGGAGAGTGAGAGGT 59.071 52.381 0.00 0.00 0.00 3.85
658 665 2.091939 TGAGGATCAGGAGAGTGAGAGG 60.092 54.545 0.00 0.00 42.56 3.69
659 666 3.295585 TGAGGATCAGGAGAGTGAGAG 57.704 52.381 0.00 0.00 42.56 3.20
1061 1074 2.348888 GGAAGGGAACGAGGAGCGA 61.349 63.158 0.00 0.00 44.57 4.93
1071 1084 1.677552 GAGCGTTGGAGGAAGGGAA 59.322 57.895 0.00 0.00 0.00 3.97
1220 1233 4.410400 CCAACCTCACCGCCTCCC 62.410 72.222 0.00 0.00 0.00 4.30
1356 1369 1.480954 GATGGGCTTCAGTAAGGTCGA 59.519 52.381 0.00 0.00 32.98 4.20
1377 1390 1.680207 GGAGTAGTACCTAACAGCCGG 59.320 57.143 0.00 0.00 0.00 6.13
1391 1404 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
1440 1454 7.486647 TCCGTCTCGTAATATAAGAGCTTTTT 58.513 34.615 0.00 0.00 34.82 1.94
1441 1455 7.035840 TCCGTCTCGTAATATAAGAGCTTTT 57.964 36.000 0.00 0.00 34.82 2.27
1442 1456 6.294065 CCTCCGTCTCGTAATATAAGAGCTTT 60.294 42.308 0.00 0.00 34.82 3.51
1443 1457 5.181622 CCTCCGTCTCGTAATATAAGAGCTT 59.818 44.000 0.00 0.00 34.82 3.74
1444 1458 4.696402 CCTCCGTCTCGTAATATAAGAGCT 59.304 45.833 0.00 0.00 34.82 4.09
1457 1471 7.640852 CAATATATATTACTCCCTCCGTCTCG 58.359 42.308 7.65 0.00 0.00 4.04
1459 1473 6.895756 TGCAATATATATTACTCCCTCCGTCT 59.104 38.462 7.65 0.00 0.00 4.18
1495 1509 1.149101 AAGACCCCCAACACTGATGT 58.851 50.000 0.00 0.00 42.46 3.06
1497 1511 1.823250 GCAAAGACCCCCAACACTGAT 60.823 52.381 0.00 0.00 0.00 2.90
1510 1524 1.664873 GACCGATTAGGGGCAAAGAC 58.335 55.000 0.00 0.00 46.96 3.01
1511 1525 0.544697 GGACCGATTAGGGGCAAAGA 59.455 55.000 0.00 0.00 46.96 2.52
1516 1530 1.049289 AGACTGGACCGATTAGGGGC 61.049 60.000 0.00 0.00 46.96 5.80
1522 1536 2.761208 CAACTCCTAGACTGGACCGATT 59.239 50.000 0.00 0.00 31.94 3.34
1527 1541 4.892934 AGATGATCAACTCCTAGACTGGAC 59.107 45.833 0.00 0.00 31.94 4.02
1573 1587 0.940126 GCACAGGATAGTCATTGGCG 59.060 55.000 0.00 0.00 0.00 5.69
1629 1643 5.847111 AGGAATCATTGGATCACATTGTG 57.153 39.130 10.64 10.64 33.34 3.33
1634 1648 3.949754 GCTGAAGGAATCATTGGATCACA 59.050 43.478 0.00 0.00 37.44 3.58
1635 1649 3.003068 CGCTGAAGGAATCATTGGATCAC 59.997 47.826 0.00 0.00 37.44 3.06
1648 1662 3.119101 GGAGATAAACTCACGCTGAAGGA 60.119 47.826 0.00 0.00 46.54 3.36
1656 1670 2.163815 ACCGAGTGGAGATAAACTCACG 59.836 50.000 3.94 0.00 46.54 4.35
1669 1683 2.455674 TCATTTCAGACACCGAGTGG 57.544 50.000 8.57 0.00 37.94 4.00
1695 1709 4.516698 GGTAAGACATGATCCATTTCGCAT 59.483 41.667 0.00 0.00 0.00 4.73
1735 1752 7.615757 ACCAAAAAGAGTTAGCAAGGCTATAAT 59.384 33.333 0.00 0.00 41.01 1.28
1780 1858 9.431887 TGAACAGTTACCAGTTAAGATATGAAC 57.568 33.333 0.00 0.00 0.00 3.18
1796 1874 2.882761 GGGTGGGAAAGTGAACAGTTAC 59.117 50.000 0.00 0.00 0.00 2.50
1833 1911 7.552459 TGAGTAGTACATGCACAGCTTAAATA 58.448 34.615 2.52 0.00 0.00 1.40
1848 1927 9.529325 GCTAAATGATGTAACATGAGTAGTACA 57.471 33.333 0.00 0.31 0.00 2.90
1854 1933 6.259608 GCTCTGCTAAATGATGTAACATGAGT 59.740 38.462 0.00 0.00 0.00 3.41
1855 1934 6.482641 AGCTCTGCTAAATGATGTAACATGAG 59.517 38.462 0.00 0.00 36.99 2.90
1856 1935 6.351711 AGCTCTGCTAAATGATGTAACATGA 58.648 36.000 0.00 0.00 36.99 3.07
1857 1936 6.615264 AGCTCTGCTAAATGATGTAACATG 57.385 37.500 0.00 0.00 36.99 3.21
1870 1949 5.129320 TGGATCATTGACTTAGCTCTGCTAA 59.871 40.000 10.93 10.93 46.97 3.09
1871 1950 4.651045 TGGATCATTGACTTAGCTCTGCTA 59.349 41.667 0.00 0.00 40.44 3.49
1872 1951 3.453717 TGGATCATTGACTTAGCTCTGCT 59.546 43.478 0.00 0.00 43.41 4.24
1873 1952 3.559242 GTGGATCATTGACTTAGCTCTGC 59.441 47.826 0.00 0.00 0.00 4.26
1874 1953 3.801050 CGTGGATCATTGACTTAGCTCTG 59.199 47.826 0.00 0.00 0.00 3.35
1875 1954 3.701542 TCGTGGATCATTGACTTAGCTCT 59.298 43.478 0.00 0.00 0.00 4.09
1885 1964 3.605461 GCATCGATGTTCGTGGATCATTG 60.605 47.826 25.47 0.00 41.35 2.82
1902 1981 8.894409 TTTAAAACATGTAATCAGAAGCATCG 57.106 30.769 0.00 0.00 0.00 3.84
1938 2017 9.784531 TTGAATCAAACTAAGAAACTGAGATCT 57.215 29.630 0.00 0.00 0.00 2.75
1987 2066 3.433615 GCTGAATTTCGTCAACTAGCACT 59.566 43.478 0.00 0.00 0.00 4.40
1999 2078 5.037385 TCATCTTAGTCTCGCTGAATTTCG 58.963 41.667 0.00 0.00 0.00 3.46
2176 2284 4.895224 TTGTGTACTATCAGCTAGTCCG 57.105 45.455 0.00 0.00 41.10 4.79
2192 2300 9.798994 TGTAAAACGGTTTGTATTTTATTGTGT 57.201 25.926 9.15 0.00 32.16 3.72
2195 2303 9.786224 GCTTGTAAAACGGTTTGTATTTTATTG 57.214 29.630 9.15 0.00 32.16 1.90
2196 2304 9.752961 AGCTTGTAAAACGGTTTGTATTTTATT 57.247 25.926 9.15 0.00 32.16 1.40
2226 2334 5.045578 AGTTTGTGGCTTGTGAGGTATCTAT 60.046 40.000 0.00 0.00 0.00 1.98
2233 2341 1.334869 GTGAGTTTGTGGCTTGTGAGG 59.665 52.381 0.00 0.00 0.00 3.86
2242 2350 6.960992 CGTGATAATATTGTGTGAGTTTGTGG 59.039 38.462 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.