Multiple sequence alignment - TraesCS2D01G299000

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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 TraesCS2D01G299000 chr2D 100.000 2961 0 0 1 2961 381061963 381064923 0.000000e+00 5469.0
1 TraesCS2D01G299000 chr2D 95.679 1319 47 6 1 1316 637754610 637755921 0.000000e+00 2111.0
2 TraesCS2D01G299000 chr2D 96.308 975 33 2 1989 2961 651075446 651076419 0.000000e+00 1598.0
3 TraesCS2D01G299000 chr2D 84.336 1047 101 35 588 1618 637432551 637431552 0.000000e+00 966.0
4 TraesCS2D01G299000 chr7D 96.721 976 29 2 1989 2961 618740064 618741039 0.000000e+00 1622.0
5 TraesCS2D01G299000 chr7D 96.418 977 31 3 1989 2961 1754457 1755433 0.000000e+00 1607.0
6 TraesCS2D01G299000 chr7D 96.205 975 33 3 1989 2961 596584230 596585202 0.000000e+00 1592.0
7 TraesCS2D01G299000 chr7D 93.423 593 33 5 1 591 39590136 39590724 0.000000e+00 874.0
8 TraesCS2D01G299000 chr7D 92.320 612 39 6 1 606 265080119 265079510 0.000000e+00 863.0
9 TraesCS2D01G299000 chr3D 96.410 975 32 2 1990 2961 608061733 608060759 0.000000e+00 1604.0
10 TraesCS2D01G299000 chr3D 93.878 98 6 0 1609 1706 509255103 509255200 6.610000e-32 148.0
11 TraesCS2D01G299000 chr5D 96.315 977 32 2 1989 2961 451155493 451154517 0.000000e+00 1602.0
12 TraesCS2D01G299000 chr5D 96.209 976 34 2 1989 2961 556380825 556381800 0.000000e+00 1594.0
13 TraesCS2D01G299000 chr5D 96.205 975 33 3 1989 2961 517353703 517352731 0.000000e+00 1592.0
14 TraesCS2D01G299000 chr5D 95.000 100 4 1 1611 1709 367998078 367998177 3.950000e-34 156.0
15 TraesCS2D01G299000 chr4D 95.854 989 33 5 1979 2961 450163885 450164871 0.000000e+00 1592.0
16 TraesCS2D01G299000 chr4D 93.548 589 36 2 1 587 120067162 120066574 0.000000e+00 876.0
17 TraesCS2D01G299000 chr2A 84.359 991 121 19 588 1565 762621831 762622800 0.000000e+00 941.0
18 TraesCS2D01G299000 chr2A 84.516 620 22 20 1028 1620 762152159 762151587 2.010000e-151 545.0
19 TraesCS2D01G299000 chr2A 88.983 236 17 3 1767 1993 762151513 762151278 1.740000e-72 283.0
20 TraesCS2D01G299000 chr2A 82.237 304 39 6 1702 1990 762622845 762623148 6.340000e-62 248.0
21 TraesCS2D01G299000 chr2A 88.182 110 5 1 673 782 762152406 762152305 1.110000e-24 124.0
22 TraesCS2D01G299000 chr1A 94.088 592 31 4 2 589 543940244 543940835 0.000000e+00 896.0
23 TraesCS2D01G299000 chr1A 93.559 590 34 3 2 587 543948059 543948648 0.000000e+00 876.0
24 TraesCS2D01G299000 chr4B 93.718 589 35 2 1 587 27330779 27331367 0.000000e+00 881.0
25 TraesCS2D01G299000 chr7B 93.707 588 36 1 1 587 36960834 36961421 0.000000e+00 880.0
26 TraesCS2D01G299000 chr7A 93.846 585 33 3 6 587 717947467 717946883 0.000000e+00 878.0
27 TraesCS2D01G299000 chrUn 88.069 637 50 16 991 1618 24000454 23999835 0.000000e+00 732.0
28 TraesCS2D01G299000 chrUn 83.987 306 34 5 1703 1993 23999833 23999528 2.250000e-71 279.0
29 TraesCS2D01G299000 chrUn 92.523 107 7 1 1600 1706 23900955 23900850 5.110000e-33 152.0
30 TraesCS2D01G299000 chrUn 93.204 103 3 4 1613 1712 135090713 135090814 6.610000e-32 148.0
31 TraesCS2D01G299000 chrUn 86.066 122 17 0 588 709 24000646 24000525 6.660000e-27 132.0
32 TraesCS2D01G299000 chrUn 93.617 47 3 0 772 818 24000507 24000461 1.470000e-08 71.3
33 TraesCS2D01G299000 chr2B 95.192 416 19 1 598 1012 795265773 795266188 0.000000e+00 656.0
34 TraesCS2D01G299000 chr2B 83.902 615 24 20 1028 1620 795275618 795276179 4.370000e-143 518.0
35 TraesCS2D01G299000 chr2B 88.841 233 17 4 1767 1990 795276253 795276485 8.080000e-71 278.0
36 TraesCS2D01G299000 chr2B 96.739 92 3 0 1612 1703 240186230 240186321 1.420000e-33 154.0
37 TraesCS2D01G299000 chr2B 92.523 107 7 1 1600 1706 799161157 799161052 5.110000e-33 152.0
38 TraesCS2D01G299000 chr2B 92.523 107 7 1 1600 1706 799214313 799214208 5.110000e-33 152.0
39 TraesCS2D01G299000 chr2B 91.667 108 8 1 1618 1724 41129578 41129471 6.610000e-32 148.0
40 TraesCS2D01G299000 chr2B 88.182 110 5 1 673 782 795275373 795275474 1.110000e-24 124.0
41 TraesCS2D01G299000 chr2B 91.667 48 4 0 841 888 118318675 118318722 1.900000e-07 67.6
42 TraesCS2D01G299000 chr6A 74.948 479 80 20 588 1061 47269540 47269097 1.810000e-42 183.0
43 TraesCS2D01G299000 chr6D 74.792 480 82 20 588 1062 21514753 21515198 2.340000e-41 180.0
44 TraesCS2D01G299000 chr4A 95.050 101 3 2 1604 1703 712733809 712733710 1.100000e-34 158.0
45 TraesCS2D01G299000 chr3B 90.909 99 9 0 588 686 433936520 433936422 1.850000e-27 134.0
46 TraesCS2D01G299000 chr3B 95.000 40 2 0 849 888 586866104 586866065 2.460000e-06 63.9
47 TraesCS2D01G299000 chr3A 94.872 39 2 0 850 888 26869209 26869171 8.860000e-06 62.1


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 TraesCS2D01G299000 chr2D 381061963 381064923 2960 False 5469.000000 5469 100.00000 1 2961 1 chr2D.!!$F1 2960
1 TraesCS2D01G299000 chr2D 637754610 637755921 1311 False 2111.000000 2111 95.67900 1 1316 1 chr2D.!!$F2 1315
2 TraesCS2D01G299000 chr2D 651075446 651076419 973 False 1598.000000 1598 96.30800 1989 2961 1 chr2D.!!$F3 972
3 TraesCS2D01G299000 chr2D 637431552 637432551 999 True 966.000000 966 84.33600 588 1618 1 chr2D.!!$R1 1030
4 TraesCS2D01G299000 chr7D 618740064 618741039 975 False 1622.000000 1622 96.72100 1989 2961 1 chr7D.!!$F4 972
5 TraesCS2D01G299000 chr7D 1754457 1755433 976 False 1607.000000 1607 96.41800 1989 2961 1 chr7D.!!$F1 972
6 TraesCS2D01G299000 chr7D 596584230 596585202 972 False 1592.000000 1592 96.20500 1989 2961 1 chr7D.!!$F3 972
7 TraesCS2D01G299000 chr7D 39590136 39590724 588 False 874.000000 874 93.42300 1 591 1 chr7D.!!$F2 590
8 TraesCS2D01G299000 chr7D 265079510 265080119 609 True 863.000000 863 92.32000 1 606 1 chr7D.!!$R1 605
9 TraesCS2D01G299000 chr3D 608060759 608061733 974 True 1604.000000 1604 96.41000 1990 2961 1 chr3D.!!$R1 971
10 TraesCS2D01G299000 chr5D 451154517 451155493 976 True 1602.000000 1602 96.31500 1989 2961 1 chr5D.!!$R1 972
11 TraesCS2D01G299000 chr5D 556380825 556381800 975 False 1594.000000 1594 96.20900 1989 2961 1 chr5D.!!$F2 972
12 TraesCS2D01G299000 chr5D 517352731 517353703 972 True 1592.000000 1592 96.20500 1989 2961 1 chr5D.!!$R2 972
13 TraesCS2D01G299000 chr4D 450163885 450164871 986 False 1592.000000 1592 95.85400 1979 2961 1 chr4D.!!$F1 982
14 TraesCS2D01G299000 chr4D 120066574 120067162 588 True 876.000000 876 93.54800 1 587 1 chr4D.!!$R1 586
15 TraesCS2D01G299000 chr2A 762621831 762623148 1317 False 594.500000 941 83.29800 588 1990 2 chr2A.!!$F1 1402
16 TraesCS2D01G299000 chr2A 762151278 762152406 1128 True 317.333333 545 87.22700 673 1993 3 chr2A.!!$R1 1320
17 TraesCS2D01G299000 chr1A 543940244 543940835 591 False 896.000000 896 94.08800 2 589 1 chr1A.!!$F1 587
18 TraesCS2D01G299000 chr1A 543948059 543948648 589 False 876.000000 876 93.55900 2 587 1 chr1A.!!$F2 585
19 TraesCS2D01G299000 chr4B 27330779 27331367 588 False 881.000000 881 93.71800 1 587 1 chr4B.!!$F1 586
20 TraesCS2D01G299000 chr7B 36960834 36961421 587 False 880.000000 880 93.70700 1 587 1 chr7B.!!$F1 586
21 TraesCS2D01G299000 chr7A 717946883 717947467 584 True 878.000000 878 93.84600 6 587 1 chr7A.!!$R1 581
22 TraesCS2D01G299000 chrUn 23999528 24000646 1118 True 303.575000 732 87.93475 588 1993 4 chrUn.!!$R2 1405
23 TraesCS2D01G299000 chr2B 795275373 795276485 1112 False 306.666667 518 86.97500 673 1990 3 chr2B.!!$F4 1317

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
540 553 2.139917 GGTGTCGTGCTTGTGTGATTA 58.860 47.619 0.0 0.0 0.0 1.75 F
1634 1769 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1972 0.242825 TTGCAGTAGACCTTCCGTCG 59.757 55.0 0.0 0.0 46.92 5.12 R
2732 2900 0.248012 TGTCACGTTGGTCGGCATAT 59.752 50.0 0.0 0.0 44.69 1.78 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
124 127 2.759973 TCTGGGAGTAGCAGCGGG 60.760 66.667 0.00 0.00 0.00 6.13
201 204 5.160607 TCAAGGTGGTGAAGAATATTCGT 57.839 39.130 9.78 6.71 0.00 3.85
278 285 5.530915 CAGTTGGACTTGATTTTGGACTGTA 59.469 40.000 0.00 0.00 0.00 2.74
345 354 3.850752 AGGCCTCTCATATATATCGGGG 58.149 50.000 0.00 3.89 0.00 5.73
346 355 3.467483 AGGCCTCTCATATATATCGGGGA 59.533 47.826 0.00 0.00 0.00 4.81
454 465 2.736081 GCGGTATTGTGACGGTGTCATA 60.736 50.000 2.62 0.00 44.63 2.15
540 553 2.139917 GGTGTCGTGCTTGTGTGATTA 58.860 47.619 0.00 0.00 0.00 1.75
541 554 2.742053 GGTGTCGTGCTTGTGTGATTAT 59.258 45.455 0.00 0.00 0.00 1.28
595 608 6.480763 TGGATTTATTCTAACAAGCACCTCA 58.519 36.000 0.00 0.00 0.00 3.86
749 763 6.331845 TGCACTGTGAAATAATTATTGCAGG 58.668 36.000 25.12 19.88 32.04 4.85
818 832 7.609760 ATGCAAATGATTCGTTGAGTAAGTA 57.390 32.000 0.00 0.00 0.00 2.24
887 901 7.855904 CCCATAATATTAGAGCGTTTTTGACAC 59.144 37.037 1.02 0.00 0.00 3.67
889 903 9.767684 CATAATATTAGAGCGTTTTTGACACAA 57.232 29.630 1.02 0.00 0.00 3.33
900 914 6.450667 GCGTTTTTGACACAATATTAAGCGAC 60.451 38.462 5.62 0.00 0.00 5.19
901 915 6.795114 CGTTTTTGACACAATATTAAGCGACT 59.205 34.615 0.00 0.00 0.00 4.18
902 916 7.006210 CGTTTTTGACACAATATTAAGCGACTC 59.994 37.037 0.00 0.00 0.00 3.36
903 917 7.428282 TTTTGACACAATATTAAGCGACTCA 57.572 32.000 0.00 0.00 0.00 3.41
904 918 6.647212 TTGACACAATATTAAGCGACTCAG 57.353 37.500 0.00 0.00 0.00 3.35
905 919 5.109210 TGACACAATATTAAGCGACTCAGG 58.891 41.667 0.00 0.00 0.00 3.86
906 920 4.442706 ACACAATATTAAGCGACTCAGGG 58.557 43.478 0.00 0.00 0.00 4.45
1026 1048 1.824852 ACATGTCTGATGCTACCACGA 59.175 47.619 0.00 0.00 0.00 4.35
1207 1316 5.022227 AGAGGAATCCCTGCTATATCAGT 57.978 43.478 0.00 0.00 44.53 3.41
1264 1378 3.403038 GGTCTTTGATGCTGTACACTGT 58.597 45.455 0.00 0.00 0.00 3.55
1322 1440 4.706842 TTCTTCTACAACAAGCCTCCTT 57.293 40.909 0.00 0.00 0.00 3.36
1418 1539 9.371136 CTTGCTAGAATTGAACAGACTATTACA 57.629 33.333 0.00 0.00 0.00 2.41
1460 1581 2.892215 GGTCTGCTACTCCTGTATACCC 59.108 54.545 0.00 0.00 0.00 3.69
1462 1583 1.887198 CTGCTACTCCTGTATACCCGG 59.113 57.143 0.00 0.00 0.00 5.73
1488 1609 4.132336 TGCCAGAAGATGTCAAGATATGC 58.868 43.478 0.00 0.00 0.00 3.14
1502 1623 7.120579 TGTCAAGATATGCGAAGGTAAATTGTT 59.879 33.333 0.00 0.00 0.00 2.83
1513 1634 7.753132 GCGAAGGTAAATTGTTTGATGATTACA 59.247 33.333 0.00 0.00 0.00 2.41
1514 1635 9.787532 CGAAGGTAAATTGTTTGATGATTACAT 57.212 29.630 0.00 0.00 39.67 2.29
1605 1740 7.370383 ACTGTTGTGATGAAATGGTGAATTAC 58.630 34.615 0.00 0.00 0.00 1.89
1628 1763 9.902684 TTACTTATCTAATATCTACTCCCTCCG 57.097 37.037 0.00 0.00 0.00 4.63
1629 1764 7.931046 ACTTATCTAATATCTACTCCCTCCGT 58.069 38.462 0.00 0.00 0.00 4.69
1630 1765 8.048514 ACTTATCTAATATCTACTCCCTCCGTC 58.951 40.741 0.00 0.00 0.00 4.79
1631 1766 5.176741 TCTAATATCTACTCCCTCCGTCC 57.823 47.826 0.00 0.00 0.00 4.79
1632 1767 2.903375 ATATCTACTCCCTCCGTCCC 57.097 55.000 0.00 0.00 0.00 4.46
1633 1768 1.526315 TATCTACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
1634 1769 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
1635 1770 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
1636 1771 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
1637 1772 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
1638 1773 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1639 1774 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1640 1775 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1641 1776 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1642 1777 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
1643 1778 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1644 1779 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
1646 1781 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1647 1782 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1648 1783 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1649 1784 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1650 1785 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1697 1832 3.126831 GTCTTGCATTATGAGACGGAGG 58.873 50.000 0.00 0.00 31.54 4.30
1698 1833 2.103094 TCTTGCATTATGAGACGGAGGG 59.897 50.000 0.00 0.00 0.00 4.30
1699 1834 1.788229 TGCATTATGAGACGGAGGGA 58.212 50.000 0.00 0.00 0.00 4.20
1700 1835 1.688735 TGCATTATGAGACGGAGGGAG 59.311 52.381 0.00 0.00 0.00 4.30
1723 1858 5.645497 AGTATTTTGTTTTGCACTTTGCCAA 59.355 32.000 0.00 0.00 44.23 4.52
1755 1890 2.813754 TCTAACAAGGTCAATGTGCTGC 59.186 45.455 0.00 0.00 0.00 5.25
1759 1894 2.366266 ACAAGGTCAATGTGCTGCAAAT 59.634 40.909 2.77 0.11 0.00 2.32
1760 1895 3.573538 ACAAGGTCAATGTGCTGCAAATA 59.426 39.130 5.59 0.00 0.00 1.40
1761 1896 4.221262 ACAAGGTCAATGTGCTGCAAATAT 59.779 37.500 5.59 0.00 0.00 1.28
1762 1897 5.172934 CAAGGTCAATGTGCTGCAAATATT 58.827 37.500 5.59 4.15 0.00 1.28
1796 1947 3.239941 CGAGTAGGTGTAGCGATTTTTCG 59.760 47.826 0.00 0.00 0.00 3.46
1802 1953 3.187842 GGTGTAGCGATTTTTCGGAAACT 59.812 43.478 1.96 0.00 0.00 2.66
1821 1972 1.933853 CTAATGGACAACCGCTGCTAC 59.066 52.381 0.00 0.00 39.42 3.58
1834 1986 1.376543 CTGCTACGACGGAAGGTCTA 58.623 55.000 0.00 0.00 43.79 2.59
1996 2156 5.070001 CCTTCAGGAATGTTTCACTGGTAA 58.930 41.667 0.00 0.00 37.39 2.85
2046 2206 2.017113 GCCCATTAGTCCCGGTTCTTG 61.017 57.143 0.00 0.00 0.00 3.02
2125 2285 2.983592 CCTCGCGGGCTTTGGTTT 60.984 61.111 6.13 0.00 0.00 3.27
2129 2289 2.258013 CGCGGGCTTTGGTTTCAGA 61.258 57.895 0.00 0.00 0.00 3.27
2191 2351 2.688666 AATGGGCCTCGCTCCTGA 60.689 61.111 4.53 0.00 0.00 3.86
2209 2369 2.242196 CTGACCCATAACCATTGGTCCT 59.758 50.000 9.22 0.00 43.38 3.85
2319 2481 2.752807 GGCGAGGGGAGGGCATTTA 61.753 63.158 0.00 0.00 0.00 1.40
2326 2488 0.033109 GGGAGGGCATTTAGGTGCTT 60.033 55.000 0.00 0.00 44.45 3.91
2440 2602 6.249951 TCCATTTTCCCCGAGATTTTTCTAA 58.750 36.000 0.00 0.00 0.00 2.10
2651 2817 3.476419 CTGGTATCCGCCCCCGTT 61.476 66.667 0.00 0.00 0.00 4.44
2948 3120 0.820891 AGGATGGATGCAATGCGGTC 60.821 55.000 0.00 1.04 37.56 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 127 0.872021 CTTGAGATACGCCGTGAGCC 60.872 60.000 0.00 0.00 38.78 4.70
201 204 5.123227 CAACTCTAACAAACTCCACCTTGA 58.877 41.667 0.00 0.00 0.00 3.02
278 285 3.769844 CACAACTCCTACCCTGTCTACAT 59.230 47.826 0.00 0.00 0.00 2.29
345 354 5.629849 GCATAGGTTACATCGTGTGTCTATC 59.370 44.000 0.00 0.00 42.29 2.08
346 355 5.509163 GGCATAGGTTACATCGTGTGTCTAT 60.509 44.000 0.00 0.41 42.29 1.98
454 465 3.148279 CTACGGGCGCTCTTCCCT 61.148 66.667 5.36 0.00 41.69 4.20
540 553 2.361438 GTCGATCTACCGAGGACCAAAT 59.639 50.000 0.00 0.00 39.43 2.32
541 554 1.747355 GTCGATCTACCGAGGACCAAA 59.253 52.381 0.00 0.00 39.43 3.28
818 832 0.733729 TACAAAAACTTGTGCGCGGT 59.266 45.000 8.83 0.00 36.44 5.68
853 867 5.363868 CGCTCTAATATTATGGGATGGAGGA 59.636 44.000 0.00 0.00 0.00 3.71
887 901 4.950050 ACTCCCTGAGTCGCTTAATATTG 58.050 43.478 0.00 0.00 38.71 1.90
889 903 5.138276 TGTACTCCCTGAGTCGCTTAATAT 58.862 41.667 0.00 0.00 42.40 1.28
890 904 4.529897 TGTACTCCCTGAGTCGCTTAATA 58.470 43.478 0.00 0.00 42.40 0.98
891 905 3.362706 TGTACTCCCTGAGTCGCTTAAT 58.637 45.455 0.00 0.00 42.40 1.40
893 907 2.502142 TGTACTCCCTGAGTCGCTTA 57.498 50.000 0.00 0.00 42.40 3.09
894 908 1.853963 ATGTACTCCCTGAGTCGCTT 58.146 50.000 0.00 0.00 42.40 4.68
895 909 2.730934 TATGTACTCCCTGAGTCGCT 57.269 50.000 0.00 0.00 42.40 4.93
1026 1048 1.251251 GCCACATCTTTCTGTGCCTT 58.749 50.000 0.00 0.00 44.16 4.35
1207 1316 1.910671 AGCCTTTCGTACCCATAACCA 59.089 47.619 0.00 0.00 0.00 3.67
1264 1378 1.135112 CATGGTACTCTACAGCGTGCA 60.135 52.381 0.00 0.00 0.00 4.57
1306 1420 4.819630 TGTACAAAAGGAGGCTTGTTGTAG 59.180 41.667 2.82 0.00 35.84 2.74
1418 1539 1.214424 ACACAAAGTAACCACCAGGCT 59.786 47.619 0.00 0.00 39.06 4.58
1460 1581 0.809241 GACATCTTCTGGCAGCTCCG 60.809 60.000 10.34 0.00 37.80 4.63
1462 1583 2.008329 CTTGACATCTTCTGGCAGCTC 58.992 52.381 10.34 0.00 45.91 4.09
1464 1585 2.105006 TCTTGACATCTTCTGGCAGC 57.895 50.000 10.34 0.00 45.91 5.25
1488 1609 9.787532 ATGTAATCATCAAACAATTTACCTTCG 57.212 29.630 0.00 0.00 0.00 3.79
1605 1740 7.499895 GGACGGAGGGAGTAGATATTAGATAAG 59.500 44.444 0.00 0.00 0.00 1.73
1620 1755 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1621 1756 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1622 1757 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1623 1758 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
1624 1759 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1625 1760 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1676 1811 3.126831 CCTCCGTCTCATAATGCAAGAC 58.873 50.000 5.56 5.56 36.82 3.01
1677 1812 2.103094 CCCTCCGTCTCATAATGCAAGA 59.897 50.000 0.00 0.00 0.00 3.02
1678 1813 2.103094 TCCCTCCGTCTCATAATGCAAG 59.897 50.000 0.00 0.00 0.00 4.01
1679 1814 2.103094 CTCCCTCCGTCTCATAATGCAA 59.897 50.000 0.00 0.00 0.00 4.08
1680 1815 1.688735 CTCCCTCCGTCTCATAATGCA 59.311 52.381 0.00 0.00 0.00 3.96
1681 1816 1.689273 ACTCCCTCCGTCTCATAATGC 59.311 52.381 0.00 0.00 0.00 3.56
1682 1817 5.730296 AATACTCCCTCCGTCTCATAATG 57.270 43.478 0.00 0.00 0.00 1.90
1683 1818 6.099845 ACAAAATACTCCCTCCGTCTCATAAT 59.900 38.462 0.00 0.00 0.00 1.28
1684 1819 5.424252 ACAAAATACTCCCTCCGTCTCATAA 59.576 40.000 0.00 0.00 0.00 1.90
1685 1820 4.960469 ACAAAATACTCCCTCCGTCTCATA 59.040 41.667 0.00 0.00 0.00 2.15
1686 1821 3.775316 ACAAAATACTCCCTCCGTCTCAT 59.225 43.478 0.00 0.00 0.00 2.90
1687 1822 3.170717 ACAAAATACTCCCTCCGTCTCA 58.829 45.455 0.00 0.00 0.00 3.27
1688 1823 3.889520 ACAAAATACTCCCTCCGTCTC 57.110 47.619 0.00 0.00 0.00 3.36
1689 1824 4.635699 AAACAAAATACTCCCTCCGTCT 57.364 40.909 0.00 0.00 0.00 4.18
1690 1825 4.615223 GCAAAACAAAATACTCCCTCCGTC 60.615 45.833 0.00 0.00 0.00 4.79
1691 1826 3.254903 GCAAAACAAAATACTCCCTCCGT 59.745 43.478 0.00 0.00 0.00 4.69
1692 1827 3.254657 TGCAAAACAAAATACTCCCTCCG 59.745 43.478 0.00 0.00 0.00 4.63
1693 1828 4.280929 AGTGCAAAACAAAATACTCCCTCC 59.719 41.667 0.00 0.00 0.00 4.30
1694 1829 5.453567 AGTGCAAAACAAAATACTCCCTC 57.546 39.130 0.00 0.00 0.00 4.30
1695 1830 5.869649 AAGTGCAAAACAAAATACTCCCT 57.130 34.783 0.00 0.00 0.00 4.20
1696 1831 5.277297 GCAAAGTGCAAAACAAAATACTCCC 60.277 40.000 0.00 0.00 44.26 4.30
1697 1832 5.737353 GCAAAGTGCAAAACAAAATACTCC 58.263 37.500 0.00 0.00 44.26 3.85
1723 1858 2.563179 ACCTTGTTAGAGCAGACATCGT 59.437 45.455 0.00 0.00 0.00 3.73
1759 1894 8.246430 ACACCTACTCGATTTATCCTGAAATA 57.754 34.615 0.00 0.00 0.00 1.40
1760 1895 7.125792 ACACCTACTCGATTTATCCTGAAAT 57.874 36.000 0.00 0.00 0.00 2.17
1761 1896 6.540438 ACACCTACTCGATTTATCCTGAAA 57.460 37.500 0.00 0.00 0.00 2.69
1762 1897 6.238953 GCTACACCTACTCGATTTATCCTGAA 60.239 42.308 0.00 0.00 0.00 3.02
1796 1947 2.161609 CAGCGGTTGTCCATTAGTTTCC 59.838 50.000 0.00 0.00 0.00 3.13
1802 1953 1.737696 CGTAGCAGCGGTTGTCCATTA 60.738 52.381 0.00 0.00 0.00 1.90
1821 1972 0.242825 TTGCAGTAGACCTTCCGTCG 59.757 55.000 0.00 0.00 46.92 5.12
1834 1986 0.466189 CACAGTGGAGGGTTTGCAGT 60.466 55.000 0.00 0.00 0.00 4.40
1955 2115 8.894592 TCCTGAAGGGCAATAAGAGAATATATT 58.105 33.333 0.00 0.00 35.41 1.28
2046 2206 1.734117 CGTTGGTCCCGGTTCGTAC 60.734 63.158 0.00 0.00 0.00 3.67
2129 2289 2.403252 GACAAATGGGTCCAGACGAT 57.597 50.000 0.00 0.00 0.00 3.73
2191 2351 1.287739 CCAGGACCAATGGTTATGGGT 59.712 52.381 22.15 0.00 43.63 4.51
2326 2488 2.466846 TGTGCATAGGAGGTGAGCTAA 58.533 47.619 0.00 0.00 0.00 3.09
2440 2602 1.080974 CGTGACGGACCGCTAAACT 60.081 57.895 15.39 0.00 0.00 2.66
2612 2778 8.540388 ACCAGAACCATCGCACTATATAATAAT 58.460 33.333 0.00 0.00 0.00 1.28
2651 2817 1.043116 CATAGACAGGACGAGGGCCA 61.043 60.000 6.18 0.00 0.00 5.36
2732 2900 0.248012 TGTCACGTTGGTCGGCATAT 59.752 50.000 0.00 0.00 44.69 1.78
2930 3102 1.656441 GACCGCATTGCATCCATCC 59.344 57.895 9.69 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.