Multiple sequence alignment - TraesCS1B01G280300

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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 TraesCS1B01G280300 chr1B 100.000 2516 0 0 1 2516 488473761 488476276 0.000000e+00 4647.0
1 TraesCS1B01G280300 chr1B 78.057 597 110 18 1860 2447 678204987 678205571 8.560000e-95 357.0
2 TraesCS1B01G280300 chr1D 93.088 1823 82 32 1 1795 365082060 365083866 0.000000e+00 2628.0
3 TraesCS1B01G280300 chr1A 94.796 1595 74 3 66 1660 463958524 463960109 0.000000e+00 2477.0
4 TraesCS1B01G280300 chr1A 97.436 39 1 0 1 39 463948962 463949000 1.620000e-07 67.6
5 TraesCS1B01G280300 chr2D 81.791 670 109 11 1830 2491 304335030 304335694 1.320000e-152 549.0
6 TraesCS1B01G280300 chr3A 82.371 641 100 7 1859 2492 749182172 749182806 1.700000e-151 545.0
7 TraesCS1B01G280300 chr3A 79.857 700 123 17 155 845 632041222 632040532 1.740000e-136 496.0
8 TraesCS1B01G280300 chr3A 85.366 328 37 9 1118 1441 632040292 632039972 1.870000e-86 329.0
9 TraesCS1B01G280300 chr3A 77.226 584 105 23 176 742 632295260 632294688 1.450000e-82 316.0
10 TraesCS1B01G280300 chr2A 82.154 650 100 14 1850 2491 382344316 382344957 6.120000e-151 544.0
11 TraesCS1B01G280300 chr2A 81.447 636 111 6 1860 2492 617430062 617429431 4.800000e-142 514.0
12 TraesCS1B01G280300 chr4D 84.007 569 75 9 1929 2493 51456893 51456337 1.320000e-147 532.0
13 TraesCS1B01G280300 chr3B 80.258 699 122 15 155 845 651427238 651426548 1.730000e-141 512.0
14 TraesCS1B01G280300 chr3B 79.450 691 120 18 166 845 489351530 489350851 1.050000e-128 470.0
15 TraesCS1B01G280300 chr3B 85.366 328 37 9 1118 1441 651426299 651425979 1.870000e-86 329.0
16 TraesCS1B01G280300 chr3B 84.756 328 39 9 1118 1441 489350602 489350282 4.040000e-83 318.0
17 TraesCS1B01G280300 chr4B 79.913 687 122 15 167 845 46934226 46933548 8.090000e-135 490.0
18 TraesCS1B01G280300 chr4B 83.841 328 42 9 1118 1441 46933299 46932979 4.070000e-78 302.0
19 TraesCS1B01G280300 chr4B 89.655 58 6 0 156 213 672128282 672128339 9.650000e-10 75.0
20 TraesCS1B01G280300 chr3D 79.881 671 121 12 155 818 488950102 488950765 1.750000e-131 479.0
21 TraesCS1B01G280300 chr3D 78.700 554 96 18 149 691 488893876 488894418 1.430000e-92 350.0
22 TraesCS1B01G280300 chr3D 85.075 335 37 11 1112 1441 488951035 488951361 1.870000e-86 329.0
23 TraesCS1B01G280300 chr2B 79.506 688 125 14 166 845 254626190 254626869 2.260000e-130 475.0
24 TraesCS1B01G280300 chr2B 79.153 614 114 10 1860 2468 164627435 164626831 1.800000e-111 412.0
25 TraesCS1B01G280300 chr2B 85.030 334 39 9 1112 1441 254627112 254627438 1.870000e-86 329.0
26 TraesCS1B01G280300 chr5D 80.404 643 109 15 1859 2491 56806657 56807292 8.150000e-130 473.0
27 TraesCS1B01G280300 chr5D 77.686 605 114 18 1858 2453 260681293 260680701 1.430000e-92 350.0
28 TraesCS1B01G280300 chr5A 79.647 624 119 8 1860 2480 547713899 547713281 2.300000e-120 442.0
29 TraesCS1B01G280300 chr7D 78.223 698 138 12 144 834 89310951 89311641 3.840000e-118 435.0
30 TraesCS1B01G280300 chr7D 85.666 293 38 3 1118 1408 89311908 89312198 3.140000e-79 305.0
31 TraesCS1B01G280300 chr7B 77.983 704 138 14 147 845 40275610 40276301 2.310000e-115 425.0
32 TraesCS1B01G280300 chr6D 77.707 628 119 14 1858 2471 334239106 334238486 5.110000e-97 364.0


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 TraesCS1B01G280300 chr1B 488473761 488476276 2515 False 4647.0 4647 100.0000 1 2516 1 chr1B.!!$F1 2515
1 TraesCS1B01G280300 chr1B 678204987 678205571 584 False 357.0 357 78.0570 1860 2447 1 chr1B.!!$F2 587
2 TraesCS1B01G280300 chr1D 365082060 365083866 1806 False 2628.0 2628 93.0880 1 1795 1 chr1D.!!$F1 1794
3 TraesCS1B01G280300 chr1A 463958524 463960109 1585 False 2477.0 2477 94.7960 66 1660 1 chr1A.!!$F2 1594
4 TraesCS1B01G280300 chr2D 304335030 304335694 664 False 549.0 549 81.7910 1830 2491 1 chr2D.!!$F1 661
5 TraesCS1B01G280300 chr3A 749182172 749182806 634 False 545.0 545 82.3710 1859 2492 1 chr3A.!!$F1 633
6 TraesCS1B01G280300 chr3A 632039972 632041222 1250 True 412.5 496 82.6115 155 1441 2 chr3A.!!$R2 1286
7 TraesCS1B01G280300 chr3A 632294688 632295260 572 True 316.0 316 77.2260 176 742 1 chr3A.!!$R1 566
8 TraesCS1B01G280300 chr2A 382344316 382344957 641 False 544.0 544 82.1540 1850 2491 1 chr2A.!!$F1 641
9 TraesCS1B01G280300 chr2A 617429431 617430062 631 True 514.0 514 81.4470 1860 2492 1 chr2A.!!$R1 632
10 TraesCS1B01G280300 chr4D 51456337 51456893 556 True 532.0 532 84.0070 1929 2493 1 chr4D.!!$R1 564
11 TraesCS1B01G280300 chr3B 651425979 651427238 1259 True 420.5 512 82.8120 155 1441 2 chr3B.!!$R2 1286
12 TraesCS1B01G280300 chr3B 489350282 489351530 1248 True 394.0 470 82.1030 166 1441 2 chr3B.!!$R1 1275
13 TraesCS1B01G280300 chr4B 46932979 46934226 1247 True 396.0 490 81.8770 167 1441 2 chr4B.!!$R1 1274
14 TraesCS1B01G280300 chr3D 488950102 488951361 1259 False 404.0 479 82.4780 155 1441 2 chr3D.!!$F2 1286
15 TraesCS1B01G280300 chr3D 488893876 488894418 542 False 350.0 350 78.7000 149 691 1 chr3D.!!$F1 542
16 TraesCS1B01G280300 chr2B 164626831 164627435 604 True 412.0 412 79.1530 1860 2468 1 chr2B.!!$R1 608
17 TraesCS1B01G280300 chr2B 254626190 254627438 1248 False 402.0 475 82.2680 166 1441 2 chr2B.!!$F1 1275
18 TraesCS1B01G280300 chr5D 56806657 56807292 635 False 473.0 473 80.4040 1859 2491 1 chr5D.!!$F1 632
19 TraesCS1B01G280300 chr5D 260680701 260681293 592 True 350.0 350 77.6860 1858 2453 1 chr5D.!!$R1 595
20 TraesCS1B01G280300 chr5A 547713281 547713899 618 True 442.0 442 79.6470 1860 2480 1 chr5A.!!$R1 620
21 TraesCS1B01G280300 chr7D 89310951 89312198 1247 False 370.0 435 81.9445 144 1408 2 chr7D.!!$F1 1264
22 TraesCS1B01G280300 chr7B 40275610 40276301 691 False 425.0 425 77.9830 147 845 1 chr7B.!!$F1 698
23 TraesCS1B01G280300 chr6D 334238486 334239106 620 True 364.0 364 77.7070 1858 2471 1 chr6D.!!$R1 613


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
922 931 0.301687 CACATCAATGGCTACGTCGC 59.698 55.0 2.96 2.96 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2472 0.179179 GTAGACGAACGAAGACCGGG 60.179 60.0 6.32 0.0 43.93 5.73 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
31 32 7.886629 AGCATGTACACCTTGAATTCATATT 57.113 32.000 9.40 0.00 0.00 1.28
54 55 2.505405 TCCTATGCCTAGCACGAGTAG 58.495 52.381 0.00 0.00 43.04 2.57
56 57 2.486203 CCTATGCCTAGCACGAGTAGAG 59.514 54.545 0.00 0.00 43.04 2.43
57 58 2.060050 ATGCCTAGCACGAGTAGAGT 57.940 50.000 0.00 0.00 43.04 3.24
58 59 2.704464 TGCCTAGCACGAGTAGAGTA 57.296 50.000 0.00 0.00 31.71 2.59
59 60 3.210232 TGCCTAGCACGAGTAGAGTAT 57.790 47.619 0.00 0.00 31.71 2.12
60 61 4.347360 TGCCTAGCACGAGTAGAGTATA 57.653 45.455 0.00 0.00 31.71 1.47
61 62 4.907809 TGCCTAGCACGAGTAGAGTATAT 58.092 43.478 0.00 0.00 31.71 0.86
62 63 6.046290 TGCCTAGCACGAGTAGAGTATATA 57.954 41.667 0.00 0.00 31.71 0.86
63 64 5.873712 TGCCTAGCACGAGTAGAGTATATAC 59.126 44.000 4.60 4.60 31.71 1.47
64 65 6.108015 GCCTAGCACGAGTAGAGTATATACT 58.892 44.000 15.37 15.37 39.71 2.12
118 119 4.275936 GCTGCCTTCTTCTTGTACTTGAAA 59.724 41.667 0.00 0.00 0.00 2.69
235 236 2.860971 AACCAGCTCTGCCCCCTT 60.861 61.111 0.00 0.00 0.00 3.95
364 365 2.820787 CACCTGGTCGTAGAAGAACTCT 59.179 50.000 0.00 0.00 39.69 3.24
385 386 1.746615 CAGGCCGACCATGGTGAAG 60.747 63.158 25.52 13.25 39.06 3.02
897 906 1.796459 CTGAGCACTGCAAATTTTGGC 59.204 47.619 10.96 5.76 0.00 4.52
922 931 0.301687 CACATCAATGGCTACGTCGC 59.698 55.000 2.96 2.96 0.00 5.19
927 936 1.808390 AATGGCTACGTCGCGTTCC 60.808 57.895 5.77 11.57 41.54 3.62
933 953 1.472276 CTACGTCGCGTTCCTGCATC 61.472 60.000 5.77 0.00 41.54 3.91
934 954 1.929806 TACGTCGCGTTCCTGCATCT 61.930 55.000 5.77 0.00 41.54 2.90
942 962 1.202348 CGTTCCTGCATCTCATCGACT 60.202 52.381 0.00 0.00 0.00 4.18
983 1007 3.452990 TCTGAATTACCTGTATTCCGGCA 59.547 43.478 0.00 0.00 0.00 5.69
1037 1061 2.530151 AGGCTGCAAGGGGACTCA 60.530 61.111 0.50 0.00 42.68 3.41
1052 1076 2.668212 TCAACTTCCGCCGCTTGG 60.668 61.111 0.00 0.00 0.00 3.61
1115 1391 4.742201 GCTGCTTGCCGTCGGAGA 62.742 66.667 17.49 0.57 35.15 3.71
1535 1811 1.893808 CCCTGCACGCAGTTTCAGT 60.894 57.895 17.31 0.00 41.61 3.41
1536 1812 1.571460 CCTGCACGCAGTTTCAGTC 59.429 57.895 17.31 0.00 41.61 3.51
1538 1814 2.127609 GCACGCAGTTTCAGTCGC 60.128 61.111 0.00 0.00 41.61 5.19
1543 1819 2.892334 GCAGTTTCAGTCGCGCCAA 61.892 57.895 0.00 0.00 0.00 4.52
1544 1820 1.868997 CAGTTTCAGTCGCGCCAAT 59.131 52.632 0.00 0.00 0.00 3.16
1563 1839 7.487829 GCGCCAATTGAGAAATTTAGAAATGTA 59.512 33.333 7.12 0.00 0.00 2.29
1580 1856 7.441836 AGAAATGTAATGCATACGATCCTGTA 58.558 34.615 0.00 0.00 36.67 2.74
1631 1907 2.493675 CAGAGTGAAATCTCGTCCTCCA 59.506 50.000 0.00 0.00 39.21 3.86
1651 1927 6.771267 CCTCCAAAAATTATACAGTACTCCCC 59.229 42.308 0.00 0.00 0.00 4.81
1652 1928 7.366551 CCTCCAAAAATTATACAGTACTCCCCT 60.367 40.741 0.00 0.00 0.00 4.79
1654 1930 6.771267 CCAAAAATTATACAGTACTCCCCTCC 59.229 42.308 0.00 0.00 0.00 4.30
1655 1931 5.803237 AAATTATACAGTACTCCCCTCCG 57.197 43.478 0.00 0.00 0.00 4.63
1657 1933 2.842645 ATACAGTACTCCCCTCCGTT 57.157 50.000 0.00 0.00 0.00 4.44
1658 1934 2.134789 TACAGTACTCCCCTCCGTTC 57.865 55.000 0.00 0.00 0.00 3.95
1662 1945 1.203149 AGTACTCCCCTCCGTTCAAGT 60.203 52.381 0.00 0.00 0.00 3.16
1677 1960 8.568732 TCCGTTCAAGTTGTTTTGAATATTTC 57.431 30.769 2.11 0.00 45.67 2.17
1817 2104 9.990868 ACTAATTATTGTAAAAAGGATGGGAGT 57.009 29.630 0.00 0.00 0.00 3.85
1820 2107 8.762481 ATTATTGTAAAAAGGATGGGAGTACC 57.238 34.615 0.00 0.00 40.81 3.34
1835 2122 3.391049 GAGTACCAAACAACTCTTCGCT 58.609 45.455 0.00 0.00 39.24 4.93
1842 2129 1.551452 ACAACTCTTCGCTCTAGCCT 58.449 50.000 0.00 0.00 37.91 4.58
1843 2130 1.474879 ACAACTCTTCGCTCTAGCCTC 59.525 52.381 0.00 0.00 37.91 4.70
1846 2133 0.667993 CTCTTCGCTCTAGCCTCCTG 59.332 60.000 0.00 0.00 37.91 3.86
1847 2134 0.256177 TCTTCGCTCTAGCCTCCTGA 59.744 55.000 0.00 0.00 37.91 3.86
1848 2135 1.107114 CTTCGCTCTAGCCTCCTGAA 58.893 55.000 0.00 0.00 37.91 3.02
1856 2143 1.630878 CTAGCCTCCTGAAACCAAGGT 59.369 52.381 0.00 0.00 36.14 3.50
1921 2208 2.482721 CGCGTCTTTTATGGTTCTTGGT 59.517 45.455 0.00 0.00 0.00 3.67
1927 2214 5.710099 GTCTTTTATGGTTCTTGGTCCATGA 59.290 40.000 3.33 3.33 43.28 3.07
2020 2309 1.202348 GGTTTGTGCCATGCTTAGGAC 59.798 52.381 0.00 0.00 0.00 3.85
2032 2323 1.667467 GCTTAGGACGATGAGGCGATC 60.667 57.143 0.00 0.00 34.83 3.69
2074 2365 0.920271 AGGTCCTCCCCGTCTAGTCT 60.920 60.000 0.00 0.00 0.00 3.24
2164 2456 2.499685 GGTCGGCGCCTGTCTTAT 59.500 61.111 26.68 0.00 0.00 1.73
2180 2472 3.873952 GTCTTATGTGGATCTGCTTGGAC 59.126 47.826 0.00 0.00 0.00 4.02
2206 2502 4.398247 GTCTTCGTTCGTCTACGTACATT 58.602 43.478 11.83 0.00 42.01 2.71
2246 2548 2.230508 TCTACGCTTCACTTCATCGGTT 59.769 45.455 0.00 0.00 0.00 4.44
2298 2602 2.488153 GGCCTTAGCATGACGACTTTTT 59.512 45.455 0.00 0.00 42.56 1.94
2312 2616 5.210715 ACGACTTTTTGACTGTCTACTACG 58.789 41.667 9.51 8.58 0.00 3.51
2325 2629 7.849496 ACTGTCTACTACGATAATGTTAGTCG 58.151 38.462 0.00 0.00 40.91 4.18
2384 2688 2.257676 GCTTGCTCCAGTGCTTGC 59.742 61.111 0.00 0.00 0.00 4.01
2458 2766 8.488764 GTGTTCTTTGTACTATCTTGACAGTTC 58.511 37.037 0.00 0.00 0.00 3.01
2476 2784 7.068226 TGACAGTTCATGAATAGATCGGAAGTA 59.932 37.037 12.12 0.00 30.71 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.497332 ACTCGTGCTAGGCATAGGATAA 58.503 45.455 7.62 0.00 41.91 1.75
38 39 2.060050 ACTCTACTCGTGCTAGGCAT 57.940 50.000 0.00 0.00 41.91 4.40
59 60 9.740239 CGTTGGTTAGAATTAGCAGTAAGTATA 57.260 33.333 0.00 0.00 0.00 1.47
60 61 7.709613 CCGTTGGTTAGAATTAGCAGTAAGTAT 59.290 37.037 0.00 0.00 0.00 2.12
61 62 7.037438 CCGTTGGTTAGAATTAGCAGTAAGTA 58.963 38.462 0.00 0.00 0.00 2.24
62 63 5.873164 CCGTTGGTTAGAATTAGCAGTAAGT 59.127 40.000 0.00 0.00 0.00 2.24
63 64 5.873164 ACCGTTGGTTAGAATTAGCAGTAAG 59.127 40.000 0.00 0.00 27.29 2.34
64 65 5.797051 ACCGTTGGTTAGAATTAGCAGTAA 58.203 37.500 0.00 0.00 27.29 2.24
118 119 0.595095 ACGTCTTCTTCGCCGTAACT 59.405 50.000 0.00 0.00 0.00 2.24
364 365 3.965258 ACCATGGTCGGCCTGCAA 61.965 61.111 13.00 0.00 35.27 4.08
897 906 2.537529 CGTAGCCATTGATGTGCTTTCG 60.538 50.000 10.68 11.50 36.32 3.46
905 914 1.145759 ACGCGACGTAGCCATTGATG 61.146 55.000 15.93 1.60 38.73 3.07
913 922 3.542742 GCAGGAACGCGACGTAGC 61.543 66.667 15.93 10.95 39.99 3.58
915 924 1.515519 GATGCAGGAACGCGACGTA 60.516 57.895 15.93 0.00 39.99 3.57
922 931 1.202348 AGTCGATGAGATGCAGGAACG 60.202 52.381 0.00 0.00 0.00 3.95
927 936 2.602211 GTGTTCAGTCGATGAGATGCAG 59.398 50.000 0.00 0.00 39.68 4.41
933 953 0.987715 CAGCGTGTTCAGTCGATGAG 59.012 55.000 0.00 0.00 44.40 2.90
934 954 1.008875 GCAGCGTGTTCAGTCGATGA 61.009 55.000 6.98 0.00 44.40 2.92
942 962 1.029408 AGTGTTTGGCAGCGTGTTCA 61.029 50.000 0.00 0.00 0.00 3.18
983 1007 3.950794 ATCGTGCGGCAACATCGGT 62.951 57.895 3.23 0.00 0.00 4.69
996 1020 1.001624 TTCGCATGAAGCTCATCGTG 58.998 50.000 0.00 3.61 42.61 4.35
997 1021 1.863454 GATTCGCATGAAGCTCATCGT 59.137 47.619 0.00 0.00 42.61 3.73
1037 1061 2.668550 GACCAAGCGGCGGAAGTT 60.669 61.111 9.78 0.00 34.57 2.66
1378 1654 2.066999 CCTCTACCTGGTGGCCCTC 61.067 68.421 10.23 0.00 36.63 4.30
1462 1738 1.079875 CCGGCAATCACAAATGCAGC 61.080 55.000 0.00 0.00 44.32 5.25
1535 1811 3.687212 TCTAAATTTCTCAATTGGCGCGA 59.313 39.130 12.10 0.00 32.57 5.87
1536 1812 4.014847 TCTAAATTTCTCAATTGGCGCG 57.985 40.909 0.00 0.00 32.57 6.86
1538 1814 7.816945 ACATTTCTAAATTTCTCAATTGGCG 57.183 32.000 5.42 0.00 32.57 5.69
1580 1856 4.123497 TCTCCGATGTTTGATTCACGAT 57.877 40.909 0.00 0.00 0.00 3.73
1631 1907 6.157471 ACGGAGGGGAGTACTGTATAATTTTT 59.843 38.462 0.00 0.00 0.00 1.94
1651 1927 8.574196 AAATATTCAAAACAACTTGAACGGAG 57.426 30.769 1.12 0.00 45.52 4.63
1652 1928 8.191446 TGAAATATTCAAAACAACTTGAACGGA 58.809 29.630 1.12 0.00 45.52 4.69
1704 1991 8.024146 ACGCTTTAATGTGTTTTTCACTTTTT 57.976 26.923 1.92 0.00 46.27 1.94
1705 1992 7.544217 AGACGCTTTAATGTGTTTTTCACTTTT 59.456 29.630 8.74 0.36 46.27 2.27
1708 1995 6.038271 AGAGACGCTTTAATGTGTTTTTCACT 59.962 34.615 8.74 1.28 46.27 3.41
1709 1996 6.199393 AGAGACGCTTTAATGTGTTTTTCAC 58.801 36.000 8.74 0.00 46.31 3.18
1710 1997 6.371809 AGAGACGCTTTAATGTGTTTTTCA 57.628 33.333 8.74 0.00 0.00 2.69
1714 2001 9.811995 TGTATATAGAGACGCTTTAATGTGTTT 57.188 29.630 8.74 3.72 0.00 2.83
1715 2002 9.982651 ATGTATATAGAGACGCTTTAATGTGTT 57.017 29.630 8.74 0.66 0.00 3.32
1716 2003 9.627395 GATGTATATAGAGACGCTTTAATGTGT 57.373 33.333 7.22 7.22 0.00 3.72
1717 2004 9.626045 TGATGTATATAGAGACGCTTTAATGTG 57.374 33.333 0.65 0.65 0.00 3.21
1726 2013 8.520835 TGTGAATTTGATGTATATAGAGACGC 57.479 34.615 0.00 0.00 0.00 5.19
1795 2082 8.340757 TGGTACTCCCATCCTTTTTACAATAAT 58.659 33.333 0.00 0.00 38.72 1.28
1796 2083 7.700846 TGGTACTCCCATCCTTTTTACAATAA 58.299 34.615 0.00 0.00 38.72 1.40
1797 2084 7.273457 TGGTACTCCCATCCTTTTTACAATA 57.727 36.000 0.00 0.00 38.72 1.90
1798 2085 6.147437 TGGTACTCCCATCCTTTTTACAAT 57.853 37.500 0.00 0.00 38.72 2.71
1799 2086 5.586155 TGGTACTCCCATCCTTTTTACAA 57.414 39.130 0.00 0.00 38.72 2.41
1800 2087 5.586155 TTGGTACTCCCATCCTTTTTACA 57.414 39.130 0.00 0.00 44.74 2.41
1801 2088 5.771165 TGTTTGGTACTCCCATCCTTTTTAC 59.229 40.000 0.00 0.00 44.74 2.01
1802 2089 5.954757 TGTTTGGTACTCCCATCCTTTTTA 58.045 37.500 0.00 0.00 44.74 1.52
1803 2090 4.810345 TGTTTGGTACTCCCATCCTTTTT 58.190 39.130 0.00 0.00 44.74 1.94
1804 2091 4.463050 TGTTTGGTACTCCCATCCTTTT 57.537 40.909 0.00 0.00 44.74 2.27
1805 2092 4.141018 AGTTGTTTGGTACTCCCATCCTTT 60.141 41.667 0.00 0.00 44.74 3.11
1806 2093 3.397955 AGTTGTTTGGTACTCCCATCCTT 59.602 43.478 0.00 0.00 44.74 3.36
1807 2094 2.986728 AGTTGTTTGGTACTCCCATCCT 59.013 45.455 0.00 0.00 44.74 3.24
1808 2095 3.009143 AGAGTTGTTTGGTACTCCCATCC 59.991 47.826 0.00 0.00 44.74 3.51
1809 2096 4.287766 AGAGTTGTTTGGTACTCCCATC 57.712 45.455 0.00 0.00 44.74 3.51
1810 2097 4.652822 GAAGAGTTGTTTGGTACTCCCAT 58.347 43.478 0.00 0.00 44.74 4.00
1811 2098 3.493699 CGAAGAGTTGTTTGGTACTCCCA 60.494 47.826 0.00 0.00 41.31 4.37
1812 2099 3.064931 CGAAGAGTTGTTTGGTACTCCC 58.935 50.000 0.00 0.00 41.31 4.30
1813 2100 2.479275 GCGAAGAGTTGTTTGGTACTCC 59.521 50.000 0.00 0.00 41.31 3.85
1814 2101 3.391049 AGCGAAGAGTTGTTTGGTACTC 58.609 45.455 0.00 0.00 40.82 2.59
1815 2102 3.069729 AGAGCGAAGAGTTGTTTGGTACT 59.930 43.478 0.00 0.00 0.00 2.73
1816 2103 3.391049 AGAGCGAAGAGTTGTTTGGTAC 58.609 45.455 0.00 0.00 0.00 3.34
1817 2104 3.746045 AGAGCGAAGAGTTGTTTGGTA 57.254 42.857 0.00 0.00 0.00 3.25
1818 2105 2.622064 AGAGCGAAGAGTTGTTTGGT 57.378 45.000 0.00 0.00 0.00 3.67
1819 2106 2.413453 GCTAGAGCGAAGAGTTGTTTGG 59.587 50.000 0.00 0.00 0.00 3.28
1820 2107 2.413453 GGCTAGAGCGAAGAGTTGTTTG 59.587 50.000 0.00 0.00 43.26 2.93
1821 2108 2.300437 AGGCTAGAGCGAAGAGTTGTTT 59.700 45.455 0.00 0.00 43.26 2.83
1822 2109 1.896465 AGGCTAGAGCGAAGAGTTGTT 59.104 47.619 0.00 0.00 43.26 2.83
1823 2110 1.474879 GAGGCTAGAGCGAAGAGTTGT 59.525 52.381 0.00 0.00 43.26 3.32
1824 2111 1.202359 GGAGGCTAGAGCGAAGAGTTG 60.202 57.143 0.00 0.00 43.26 3.16
1825 2112 1.107945 GGAGGCTAGAGCGAAGAGTT 58.892 55.000 0.00 0.00 43.26 3.01
1826 2113 0.257616 AGGAGGCTAGAGCGAAGAGT 59.742 55.000 0.00 0.00 43.26 3.24
1827 2114 0.667993 CAGGAGGCTAGAGCGAAGAG 59.332 60.000 0.00 0.00 43.26 2.85
1828 2115 0.256177 TCAGGAGGCTAGAGCGAAGA 59.744 55.000 0.00 0.00 43.26 2.87
1835 2122 1.909302 CCTTGGTTTCAGGAGGCTAGA 59.091 52.381 0.00 0.00 0.00 2.43
1842 2129 1.351017 CCTAGCACCTTGGTTTCAGGA 59.649 52.381 5.00 0.00 0.00 3.86
1843 2130 1.614317 CCCTAGCACCTTGGTTTCAGG 60.614 57.143 0.00 0.00 0.00 3.86
1846 2133 2.287977 AACCCTAGCACCTTGGTTTC 57.712 50.000 0.00 0.00 37.84 2.78
1847 2134 2.767644 AAACCCTAGCACCTTGGTTT 57.232 45.000 5.93 5.93 44.17 3.27
1848 2135 1.203013 GGAAACCCTAGCACCTTGGTT 60.203 52.381 0.00 0.00 42.73 3.67
1856 2143 0.328258 GAGGCAAGGAAACCCTAGCA 59.672 55.000 0.00 0.00 32.65 3.49
1898 2185 2.467566 AGAACCATAAAAGACGCGGT 57.532 45.000 12.47 0.00 0.00 5.68
1901 2188 3.119955 GGACCAAGAACCATAAAAGACGC 60.120 47.826 0.00 0.00 0.00 5.19
1908 2195 4.044065 ACCTTCATGGACCAAGAACCATAA 59.956 41.667 8.07 0.00 43.89 1.90
1921 2208 1.561769 ATCCACCGCACCTTCATGGA 61.562 55.000 0.00 0.00 43.42 3.41
1986 2274 3.467803 CACAAACCCCGGCAAAATTTTA 58.532 40.909 2.44 0.00 0.00 1.52
1987 2275 2.293170 CACAAACCCCGGCAAAATTTT 58.707 42.857 0.00 0.00 0.00 1.82
1990 2279 1.070615 GCACAAACCCCGGCAAAAT 59.929 52.632 0.00 0.00 0.00 1.82
2032 2323 2.680913 CCACCTTCAAGAAGCCGCG 61.681 63.158 0.00 0.00 37.11 6.46
2155 2447 3.834489 AGCAGATCCACATAAGACAGG 57.166 47.619 0.00 0.00 0.00 4.00
2164 2456 1.685224 GGGTCCAAGCAGATCCACA 59.315 57.895 0.00 0.00 36.98 4.17
2180 2472 0.179179 GTAGACGAACGAAGACCGGG 60.179 60.000 6.32 0.00 43.93 5.73
2246 2548 1.063327 CGCACCAGAACAAAACGCA 59.937 52.632 0.00 0.00 0.00 5.24
2298 2602 8.728337 ACTAACATTATCGTAGTAGACAGTCA 57.272 34.615 2.66 0.00 0.00 3.41
2335 2639 2.520982 CGTCATCGCCCCTCCCTA 60.521 66.667 0.00 0.00 0.00 3.53
2384 2688 0.603569 AGACCACCTAGCAACGACTG 59.396 55.000 0.00 0.00 0.00 3.51



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

AutoCloner maintained by Alex Coulton.