Multiple sequence alignment - TraesCS3D01G440900

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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 TraesCS3D01G440900 chr3D 100.000 4142 0 0 1 4142 551270726 551274867 0.000000e+00 7649.0
1 TraesCS3D01G440900 chr3D 86.905 756 83 8 2468 3222 551392286 551391546 0.000000e+00 833.0
2 TraesCS3D01G440900 chr3D 83.784 740 77 16 1211 1928 551393669 551392951 0.000000e+00 662.0
3 TraesCS3D01G440900 chr3D 88.610 439 47 3 1928 2363 551392902 551392464 7.880000e-147 531.0
4 TraesCS3D01G440900 chr3D 74.348 230 38 16 3898 4118 560928054 560928271 1.230000e-10 78.7
5 TraesCS3D01G440900 chr3A 90.317 3088 166 48 554 3598 688578158 688581155 0.000000e+00 3923.0
6 TraesCS3D01G440900 chr3A 83.777 1276 127 36 1206 2420 688616289 688617545 0.000000e+00 1136.0
7 TraesCS3D01G440900 chr3A 89.877 405 26 9 1 397 688576573 688576970 1.330000e-139 507.0
8 TraesCS3D01G440900 chr3A 86.147 462 61 3 2744 3205 688618394 688618852 2.880000e-136 496.0
9 TraesCS3D01G440900 chr3A 93.305 239 16 0 2463 2701 688618140 688618378 1.830000e-93 353.0
10 TraesCS3D01G440900 chr3A 91.057 246 13 1 3669 3914 688581563 688581799 1.440000e-84 324.0
11 TraesCS3D01G440900 chr3A 90.558 233 18 3 3909 4139 688581983 688582213 5.200000e-79 305.0
12 TraesCS3D01G440900 chr3A 92.742 124 9 0 396 519 688578039 688578162 3.290000e-41 180.0
13 TraesCS3D01G440900 chr3B 90.643 1742 113 23 1547 3254 730938454 730940179 0.000000e+00 2268.0
14 TraesCS3D01G440900 chr3B 88.959 1114 79 20 91 1175 730936878 730937976 0.000000e+00 1336.0
15 TraesCS3D01G440900 chr3B 87.046 826 82 19 3285 4100 730940178 730940988 0.000000e+00 909.0
16 TraesCS3D01G440900 chr3B 88.874 746 72 9 2527 3267 731264914 731265653 0.000000e+00 907.0
17 TraesCS3D01G440900 chr3B 83.754 714 83 16 1211 1913 731263506 731264197 0.000000e+00 645.0
18 TraesCS3D01G440900 chr3B 86.275 510 44 13 1930 2421 731264303 731264804 7.880000e-147 531.0
19 TraesCS3D01G440900 chr3B 90.060 332 20 7 1187 1512 730938133 730938457 6.400000e-113 418.0
20 TraesCS3D01G440900 chr3B 93.333 75 5 0 551 625 731262624 731262698 1.220000e-20 111.0
21 TraesCS3D01G440900 chr3B 89.655 58 6 0 1 58 730936810 730936867 1.600000e-09 75.0
22 TraesCS3D01G440900 chr4A 90.746 724 47 6 2131 2836 11173973 11174694 0.000000e+00 948.0
23 TraesCS3D01G440900 chr7D 90.193 724 51 6 2131 2836 165953481 165952760 0.000000e+00 926.0
24 TraesCS3D01G440900 chr6B 83.217 143 16 7 3978 4118 664696520 664696656 1.560000e-24 124.0
25 TraesCS3D01G440900 chr1B 79.054 148 21 7 3987 4129 610039271 610039413 4.410000e-15 93.5


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 TraesCS3D01G440900 chr3D 551270726 551274867 4141 False 7649.000000 7649 100.0000 1 4142 1 chr3D.!!$F1 4141
1 TraesCS3D01G440900 chr3D 551391546 551393669 2123 True 675.333333 833 86.4330 1211 3222 3 chr3D.!!$R1 2011
2 TraesCS3D01G440900 chr3A 688576573 688582213 5640 False 1047.800000 3923 90.9102 1 4139 5 chr3A.!!$F1 4138
3 TraesCS3D01G440900 chr3A 688616289 688618852 2563 False 661.666667 1136 87.7430 1206 3205 3 chr3A.!!$F2 1999
4 TraesCS3D01G440900 chr3B 730936810 730940988 4178 False 1001.200000 2268 89.2726 1 4100 5 chr3B.!!$F1 4099
5 TraesCS3D01G440900 chr3B 731262624 731265653 3029 False 548.500000 907 88.0590 551 3267 4 chr3B.!!$F2 2716
6 TraesCS3D01G440900 chr4A 11173973 11174694 721 False 948.000000 948 90.7460 2131 2836 1 chr4A.!!$F1 705
7 TraesCS3D01G440900 chr7D 165952760 165953481 721 True 926.000000 926 90.1930 2131 2836 1 chr7D.!!$R1 705

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
98 99 0.186386 ACCGGGGACACCATGAAAAA 59.814 50.0 6.32 0.0 40.22 1.94 F
744 1992 0.322997 CTTGGCCACCGAATTACCCA 60.323 55.0 3.88 0.0 0.00 4.51 F
2039 3658 0.179000 CTGATGGCTACCCACTGGAC 59.821 60.0 0.00 0.0 45.77 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 3332 0.451383 TACCGTCCGTATCAACACCG 59.549 55.0 0.00 0.0 0.00 4.94 R
2636 4852 2.094545 GGAAAGCCAACTAGTGCCATTG 60.095 50.0 0.00 0.0 0.00 2.82 R
3146 5369 0.103208 AAAATGTGCCAACCGCGAAA 59.897 45.0 8.23 0.0 42.08 3.46 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
39 40 9.543018 GATTGAGCTAAAATAATAACCATACGC 57.457 33.333 0.00 0.00 0.00 4.42
42 43 8.339714 TGAGCTAAAATAATAACCATACGCAAC 58.660 33.333 0.00 0.00 0.00 4.17
44 45 8.126700 AGCTAAAATAATAACCATACGCAACAC 58.873 33.333 0.00 0.00 0.00 3.32
45 46 8.126700 GCTAAAATAATAACCATACGCAACACT 58.873 33.333 0.00 0.00 0.00 3.55
74 75 3.770263 TTTCTACGAGTGGACCATACG 57.230 47.619 17.48 17.48 0.00 3.06
78 79 4.454678 TCTACGAGTGGACCATACGTAAT 58.545 43.478 24.96 11.31 38.58 1.89
82 83 3.607775 CGAGTGGACCATACGTAATACCG 60.608 52.174 0.00 0.00 0.00 4.02
98 99 0.186386 ACCGGGGACACCATGAAAAA 59.814 50.000 6.32 0.00 40.22 1.94
106 107 3.181520 GGACACCATGAAAAAGTCGATCG 60.182 47.826 9.36 9.36 0.00 3.69
169 170 4.831674 TCATTCACTGTCCTGACATCAT 57.168 40.909 0.00 0.00 41.01 2.45
207 209 4.120589 CTGAGTCTGATCATGATGGTGTG 58.879 47.826 14.30 0.00 0.00 3.82
220 222 1.303806 GGTGTGGCATTAACCGGGT 60.304 57.895 6.32 0.00 0.00 5.28
221 223 0.896479 GGTGTGGCATTAACCGGGTT 60.896 55.000 17.83 17.83 0.00 4.11
222 224 1.613785 GGTGTGGCATTAACCGGGTTA 60.614 52.381 15.52 15.52 0.00 2.85
223 225 2.161030 GTGTGGCATTAACCGGGTTAA 58.839 47.619 29.02 29.02 41.32 2.01
226 228 3.193691 TGTGGCATTAACCGGGTTAATTG 59.806 43.478 32.50 27.26 43.46 2.32
243 245 4.584638 AATTGGGTGGAGTAGCACAATA 57.415 40.909 0.00 0.00 31.76 1.90
256 258 6.167685 AGTAGCACAATATCAAACCGTAACA 58.832 36.000 0.00 0.00 0.00 2.41
291 293 8.453320 GCCAATTTTAATTTCCTTCCAGAAATG 58.547 33.333 0.59 0.00 43.90 2.32
322 330 2.348872 GCACACAAAGTCATCAGTGTCG 60.349 50.000 0.00 0.00 42.79 4.35
336 344 7.587757 GTCATCAGTGTCGATAAAAATATTGGC 59.412 37.037 0.00 0.00 0.00 4.52
357 365 4.857037 GGCCAAGTATTCAATTCGTTTGAC 59.143 41.667 0.00 0.00 43.99 3.18
397 407 1.271543 TGAGGACAGAGCCAATGGTTG 60.272 52.381 0.00 0.02 0.00 3.77
512 1595 6.430616 TGACATTTTCTGATGTTCTATGTGCA 59.569 34.615 0.00 0.00 40.21 4.57
536 1619 2.370647 GACTGCAGCGGGGTAGATCC 62.371 65.000 15.27 0.00 0.00 3.36
636 1723 0.618981 CCCTACCCTCCACAGAAACC 59.381 60.000 0.00 0.00 0.00 3.27
737 1944 1.669760 CGTTAGCTTGGCCACCGAA 60.670 57.895 3.88 0.00 0.00 4.30
738 1945 1.024579 CGTTAGCTTGGCCACCGAAT 61.025 55.000 3.88 0.00 0.00 3.34
739 1946 1.173913 GTTAGCTTGGCCACCGAATT 58.826 50.000 3.88 0.00 0.00 2.17
744 1992 0.322997 CTTGGCCACCGAATTACCCA 60.323 55.000 3.88 0.00 0.00 4.51
799 2061 1.463444 GTGGAGATTCCGTTTGGTTCG 59.537 52.381 0.00 0.00 40.17 3.95
800 2062 1.071071 TGGAGATTCCGTTTGGTTCGT 59.929 47.619 0.00 0.00 40.17 3.85
801 2063 2.299582 TGGAGATTCCGTTTGGTTCGTA 59.700 45.455 0.00 0.00 40.17 3.43
845 2129 1.618343 TCTTCTGTGCCGAGATGAACA 59.382 47.619 0.00 0.00 0.00 3.18
852 2136 1.144969 GCCGAGATGAACAAACGACA 58.855 50.000 0.00 0.00 0.00 4.35
857 2141 3.362014 CGAGATGAACAAACGACACACAG 60.362 47.826 0.00 0.00 0.00 3.66
860 2144 1.396648 TGAACAAACGACACACAGCTG 59.603 47.619 13.48 13.48 0.00 4.24
896 2180 6.402011 GCTCTGCTTTCTGAATTCACTCTTAC 60.402 42.308 3.38 0.00 0.00 2.34
1002 2295 1.344114 CCCTTTGGTTGGTTGGTCATG 59.656 52.381 0.00 0.00 0.00 3.07
1274 2741 4.035208 GCCCAGTTATTCATCGGTGTAAAG 59.965 45.833 0.00 0.00 0.00 1.85
1366 2871 4.820897 ACTAGCGCTTATGCATATGCTAA 58.179 39.130 30.60 19.81 42.66 3.09
1547 3058 9.974980 TTTACTTGAAATAAACTGGGAACAATC 57.025 29.630 0.00 0.00 42.06 2.67
1549 3060 7.661040 ACTTGAAATAAACTGGGAACAATCAG 58.339 34.615 0.00 0.00 42.06 2.90
1553 3064 1.620822 AACTGGGAACAATCAGTGCC 58.379 50.000 0.00 0.00 46.41 5.01
1708 3226 0.591659 GACGTCAAGGGCTTCAAACC 59.408 55.000 11.55 0.00 0.00 3.27
1739 3257 2.224992 TGTGGCTGTTGGGACATACATT 60.225 45.455 0.00 0.00 39.30 2.71
1771 3289 3.247411 CGTGACTGTGACAACTGCAATAA 59.753 43.478 0.00 0.00 0.00 1.40
1796 3314 1.795286 CTCGAGAACCACTGCTCAAAC 59.205 52.381 6.58 0.00 0.00 2.93
1814 3332 7.009440 GCTCAAACTTTGTTTTCACTTTCAAC 58.991 34.615 1.44 0.00 0.00 3.18
1928 3446 6.998074 AGTTCTGAATTTGGTGTAGATTGTCA 59.002 34.615 0.00 0.00 0.00 3.58
1943 3553 8.584157 TGTAGATTGTCAATTATTGTTTGCCTT 58.416 29.630 4.77 0.00 0.00 4.35
1946 3556 8.316214 AGATTGTCAATTATTGTTTGCCTTCAT 58.684 29.630 4.77 0.00 0.00 2.57
1950 3560 7.092716 GTCAATTATTGTTTGCCTTCATGTCT 58.907 34.615 4.77 0.00 0.00 3.41
2039 3658 0.179000 CTGATGGCTACCCACTGGAC 59.821 60.000 0.00 0.00 45.77 4.02
2312 3936 9.308318 GAGGTACTGAACATCTTAATCTCTTTC 57.692 37.037 0.00 0.00 41.55 2.62
2432 4083 1.598132 CAGAGCTCATTCTGCAATCGG 59.402 52.381 17.77 0.00 38.28 4.18
2546 4762 9.691362 ATAACGAAATGATTTACTTTTGCAGTT 57.309 25.926 0.00 0.00 36.88 3.16
2636 4852 1.334149 GCTTCTGAAAGTTCGTGGCAC 60.334 52.381 7.79 7.79 34.79 5.01
2661 4877 1.168714 CACTAGTTGGCTTTCCTGGC 58.831 55.000 0.00 0.00 0.00 4.85
2703 4919 6.744112 TGCAACACTTAATCTGGGTAAAAAG 58.256 36.000 0.00 0.00 0.00 2.27
2709 4925 7.447545 ACACTTAATCTGGGTAAAAAGACCTTC 59.552 37.037 0.00 0.00 39.66 3.46
2742 4958 4.783764 ACAGTTAAAATAGTTGCAGGGC 57.216 40.909 0.00 0.00 0.00 5.19
2802 5023 5.086104 AGACTGTATGCCGTAAAACAGAT 57.914 39.130 8.21 0.00 41.47 2.90
2817 5038 2.631062 AACAGATCACTGGTTGTCGGTA 59.369 45.455 0.00 0.00 41.81 4.02
2837 5058 1.408969 TCCTGGTTCAAAACTTGGCC 58.591 50.000 0.00 0.00 0.00 5.36
2840 5061 1.480137 CTGGTTCAAAACTTGGCCACA 59.520 47.619 3.88 0.00 34.31 4.17
2885 5106 3.994204 ATGTTGTTACCGGTGTTTTCC 57.006 42.857 19.93 0.90 0.00 3.13
3006 5229 7.074237 ACAAAGGATACCCAGGAGATGATAAAT 59.926 37.037 0.00 0.00 33.88 1.40
3023 5246 0.664166 AATTTCTGCGCGGCAAACAG 60.664 50.000 12.58 6.26 38.41 3.16
3306 5531 9.961265 AAGATTGTTGTGAAGATATGCATATTG 57.039 29.630 20.00 0.00 0.00 1.90
3383 5609 7.928908 TCAAATTTTCTGAATTTTCGACTGG 57.071 32.000 0.00 0.00 0.00 4.00
3490 5718 8.926715 ATTGGAAAATTTTACCTCGCTTATTC 57.073 30.769 10.68 0.00 0.00 1.75
3507 5735 0.914644 TTCCTGGGGCTGATCAAGAG 59.085 55.000 0.00 0.00 0.00 2.85
3602 5830 7.656707 ATGTTTAGACAAAAATGAATGTGGC 57.343 32.000 0.00 0.00 39.66 5.01
3603 5831 5.689514 TGTTTAGACAAAAATGAATGTGGCG 59.310 36.000 0.00 0.00 31.49 5.69
3606 5834 3.317711 AGACAAAAATGAATGTGGCGTCA 59.682 39.130 0.00 0.00 0.00 4.35
3608 5836 4.630111 ACAAAAATGAATGTGGCGTCAAT 58.370 34.783 0.00 0.00 0.00 2.57
3609 5837 5.777802 ACAAAAATGAATGTGGCGTCAATA 58.222 33.333 0.00 0.00 0.00 1.90
3610 5838 5.863397 ACAAAAATGAATGTGGCGTCAATAG 59.137 36.000 0.00 0.00 0.00 1.73
3612 5840 6.751514 AAAATGAATGTGGCGTCAATAGTA 57.248 33.333 0.00 0.00 0.00 1.82
3613 5841 5.734855 AATGAATGTGGCGTCAATAGTAC 57.265 39.130 0.00 0.00 0.00 2.73
3614 5842 4.465632 TGAATGTGGCGTCAATAGTACT 57.534 40.909 0.00 0.00 0.00 2.73
3615 5843 4.180817 TGAATGTGGCGTCAATAGTACTG 58.819 43.478 5.39 0.00 0.00 2.74
3616 5844 2.004583 TGTGGCGTCAATAGTACTGC 57.995 50.000 5.39 0.00 0.00 4.40
3617 5845 1.548719 TGTGGCGTCAATAGTACTGCT 59.451 47.619 5.39 0.00 0.00 4.24
3618 5846 1.927174 GTGGCGTCAATAGTACTGCTG 59.073 52.381 5.39 2.58 0.00 4.41
3620 5848 2.159240 TGGCGTCAATAGTACTGCTGAG 60.159 50.000 5.39 4.00 0.00 3.35
3642 5872 3.305177 GAGCCCCGCTTCGGTACAA 62.305 63.158 4.47 0.00 46.80 2.41
3643 5873 2.358984 GCCCCGCTTCGGTACAAA 60.359 61.111 4.47 0.00 46.80 2.83
3644 5874 1.967494 GCCCCGCTTCGGTACAAAA 60.967 57.895 4.47 0.00 46.80 2.44
3645 5875 1.871077 CCCCGCTTCGGTACAAAAC 59.129 57.895 4.47 0.00 46.80 2.43
3646 5876 0.885596 CCCCGCTTCGGTACAAAACA 60.886 55.000 4.47 0.00 46.80 2.83
3647 5877 0.945813 CCCGCTTCGGTACAAAACAA 59.054 50.000 4.47 0.00 46.80 2.83
3648 5878 1.069500 CCCGCTTCGGTACAAAACAAG 60.069 52.381 4.47 0.00 46.80 3.16
3651 5881 2.349155 CGCTTCGGTACAAAACAAGTCC 60.349 50.000 0.00 0.00 0.00 3.85
3653 5883 3.473625 CTTCGGTACAAAACAAGTCCCT 58.526 45.455 0.00 0.00 0.00 4.20
3654 5884 2.841215 TCGGTACAAAACAAGTCCCTG 58.159 47.619 0.00 0.00 0.00 4.45
3655 5885 1.877443 CGGTACAAAACAAGTCCCTGG 59.123 52.381 0.00 0.00 0.00 4.45
3656 5886 2.235891 GGTACAAAACAAGTCCCTGGG 58.764 52.381 6.33 6.33 0.00 4.45
3657 5887 2.423803 GGTACAAAACAAGTCCCTGGGT 60.424 50.000 13.56 0.00 0.00 4.51
3658 5888 3.181441 GGTACAAAACAAGTCCCTGGGTA 60.181 47.826 13.56 0.00 0.00 3.69
3659 5889 3.673543 ACAAAACAAGTCCCTGGGTAA 57.326 42.857 13.56 0.00 0.00 2.85
3660 5890 3.983821 ACAAAACAAGTCCCTGGGTAAA 58.016 40.909 13.56 0.00 0.00 2.01
3661 5891 3.702548 ACAAAACAAGTCCCTGGGTAAAC 59.297 43.478 13.56 3.54 0.00 2.01
3689 6254 3.096092 GGGCAATATGGACCTTTGACAA 58.904 45.455 0.00 0.00 31.16 3.18
3693 6258 5.105392 GGCAATATGGACCTTTGACAAATCA 60.105 40.000 0.05 0.00 0.00 2.57
3779 6344 2.361610 CACCTTGGCGGGCTCATT 60.362 61.111 2.38 0.00 36.97 2.57
3792 6357 4.680440 GCGGGCTCATTCCATTTATGTTTT 60.680 41.667 0.00 0.00 0.00 2.43
3793 6358 5.418676 CGGGCTCATTCCATTTATGTTTTT 58.581 37.500 0.00 0.00 0.00 1.94
3794 6359 5.519927 CGGGCTCATTCCATTTATGTTTTTC 59.480 40.000 0.00 0.00 0.00 2.29
3944 6698 0.110486 AAGCATGTGTTCCCGGACTT 59.890 50.000 0.73 0.00 0.00 3.01
3974 6729 3.502211 CAGTTCAGCCGGTTTTATTCTGT 59.498 43.478 1.90 0.00 0.00 3.41
4036 6793 8.550710 TCGTTTTCCTTTCTTAAATCGGAATA 57.449 30.769 0.00 0.00 34.08 1.75
4139 6897 9.820725 TGAACATTCTGAAATTCATGAACTTTT 57.179 25.926 11.07 8.52 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.288395 CCCGGTATTACGTATGGTCCAC 60.288 54.545 0.00 0.00 0.00 4.02
74 75 1.764134 TCATGGTGTCCCCGGTATTAC 59.236 52.381 0.00 0.00 35.15 1.89
78 79 1.065647 TTTTCATGGTGTCCCCGGTA 58.934 50.000 0.00 0.00 35.15 4.02
82 83 1.539827 CGACTTTTTCATGGTGTCCCC 59.460 52.381 0.00 0.00 0.00 4.81
98 99 1.598132 CTGTGACGGTATCGATCGACT 59.402 52.381 22.06 12.20 40.11 4.18
169 170 1.879380 CTCAGACCACGGCATTTTTCA 59.121 47.619 0.00 0.00 0.00 2.69
207 209 2.101750 CCCAATTAACCCGGTTAATGCC 59.898 50.000 28.56 0.00 44.65 4.40
220 222 4.374689 TTGTGCTACTCCACCCAATTAA 57.625 40.909 0.00 0.00 34.85 1.40
221 223 4.584638 ATTGTGCTACTCCACCCAATTA 57.415 40.909 0.00 0.00 34.85 1.40
222 224 2.969821 TTGTGCTACTCCACCCAATT 57.030 45.000 0.00 0.00 34.85 2.32
223 225 4.165950 TGATATTGTGCTACTCCACCCAAT 59.834 41.667 0.00 0.00 34.85 3.16
226 228 3.838244 TGATATTGTGCTACTCCACCC 57.162 47.619 0.00 0.00 34.85 4.61
243 245 5.065988 GGCAGTTCATATGTTACGGTTTGAT 59.934 40.000 1.90 0.00 0.00 2.57
291 293 1.542915 ACTTTGTGTGCATGCTGATCC 59.457 47.619 20.33 3.00 0.00 3.36
357 365 5.123502 CCTCATTGGATTCAAGTGACTGAAG 59.876 44.000 0.00 0.00 38.66 3.02
383 393 6.017109 GGTTACATATACAACCATTGGCTCTG 60.017 42.308 1.54 0.52 43.13 3.35
397 407 5.756833 CCTTCGGGACAAAGGTTACATATAC 59.243 44.000 0.00 0.00 37.25 1.47
485 1565 7.361542 GCACATAGAACATCAGAAAATGTCACT 60.362 37.037 0.00 0.00 38.92 3.41
486 1566 6.744537 GCACATAGAACATCAGAAAATGTCAC 59.255 38.462 0.00 0.00 38.92 3.67
536 1619 1.928653 CACGTACGTGTTGTGGGTG 59.071 57.895 34.48 10.93 40.91 4.61
543 1626 1.945662 GTGGTCGCACGTACGTGTT 60.946 57.895 39.56 10.66 46.90 3.32
691 1869 1.122019 CGGAAGGGGATCGGGAGAAT 61.122 60.000 0.00 0.00 45.37 2.40
737 1944 3.308401 GGGCAGGAAATGAATGGGTAAT 58.692 45.455 0.00 0.00 0.00 1.89
738 1945 2.043664 TGGGCAGGAAATGAATGGGTAA 59.956 45.455 0.00 0.00 0.00 2.85
739 1946 1.643286 TGGGCAGGAAATGAATGGGTA 59.357 47.619 0.00 0.00 0.00 3.69
744 1992 1.322538 GGCGTGGGCAGGAAATGAAT 61.323 55.000 0.00 0.00 42.47 2.57
799 2061 1.134560 CCAGAGGCTTGGTCGTACTAC 59.865 57.143 7.35 0.00 33.38 2.73
800 2062 1.471119 CCAGAGGCTTGGTCGTACTA 58.529 55.000 7.35 0.00 33.38 1.82
801 2063 2.277858 CCAGAGGCTTGGTCGTACT 58.722 57.895 7.35 0.00 33.38 2.73
845 2129 2.560504 TGATTCAGCTGTGTGTCGTTT 58.439 42.857 14.67 0.00 0.00 3.60
852 2136 1.610522 GCAGGTTTGATTCAGCTGTGT 59.389 47.619 14.67 3.21 41.08 3.72
857 2141 1.135460 GCAGAGCAGGTTTGATTCAGC 60.135 52.381 0.00 0.00 0.00 4.26
860 2144 3.505293 AGAAAGCAGAGCAGGTTTGATTC 59.495 43.478 5.86 0.00 39.12 2.52
1274 2741 3.318275 TCGGCAAGGATGTCTACTCATAC 59.682 47.826 0.00 0.00 0.00 2.39
1366 2871 6.016555 ACAGCCCTGGTAAAATTAATCAGTT 58.983 36.000 0.00 0.00 34.19 3.16
1376 2881 1.693062 TGTCGTACAGCCCTGGTAAAA 59.307 47.619 0.00 0.00 34.19 1.52
1377 2882 1.340088 TGTCGTACAGCCCTGGTAAA 58.660 50.000 0.00 0.00 34.19 2.01
1536 3045 1.915141 AAGGCACTGATTGTTCCCAG 58.085 50.000 0.00 0.00 40.86 4.45
1546 3057 4.269183 TCAACAGAAAGAAAAGGCACTGA 58.731 39.130 0.00 0.00 40.86 3.41
1547 3058 4.637483 TCAACAGAAAGAAAAGGCACTG 57.363 40.909 0.00 0.00 40.86 3.66
1549 3060 5.460091 GTCAATCAACAGAAAGAAAAGGCAC 59.540 40.000 0.00 0.00 0.00 5.01
1553 3064 5.068987 TGGGGTCAATCAACAGAAAGAAAAG 59.931 40.000 0.00 0.00 0.00 2.27
1688 3206 0.591659 GTTTGAAGCCCTTGACGTCC 59.408 55.000 14.12 0.00 0.00 4.79
1739 3257 1.616374 TCACAGTCACGGCATGAGTTA 59.384 47.619 0.00 0.00 39.10 2.24
1771 3289 1.536943 GCAGTGGTTCTCGAGGAGGT 61.537 60.000 13.56 0.00 0.00 3.85
1796 3314 4.920927 ACACCGTTGAAAGTGAAAACAAAG 59.079 37.500 3.89 0.00 37.43 2.77
1814 3332 0.451383 TACCGTCCGTATCAACACCG 59.549 55.000 0.00 0.00 0.00 4.94
1928 3446 9.423061 GTTTAGACATGAAGGCAAACAATAATT 57.577 29.630 0.00 0.00 31.04 1.40
1935 3545 3.572255 TGGGTTTAGACATGAAGGCAAAC 59.428 43.478 0.00 2.52 0.00 2.93
1943 3553 6.001460 ACGAGAAAATTGGGTTTAGACATGA 58.999 36.000 0.00 0.00 0.00 3.07
1946 3556 9.158233 CTTATACGAGAAAATTGGGTTTAGACA 57.842 33.333 0.00 0.00 0.00 3.41
2312 3936 4.361451 AGTTGTTTCACACTCAGCTTTG 57.639 40.909 0.00 0.00 0.00 2.77
2432 4083 5.981315 TCGCACAAAATAGTATAGGCAGTAC 59.019 40.000 0.00 0.00 0.00 2.73
2513 4729 9.755064 AAAGTAAATCATTTCGTTATTCTCACG 57.245 29.630 0.00 0.00 39.08 4.35
2546 4762 8.308931 CAATGAAATCCAGAGAATTTTTCAGGA 58.691 33.333 3.94 3.94 39.04 3.86
2636 4852 2.094545 GGAAAGCCAACTAGTGCCATTG 60.095 50.000 0.00 0.00 0.00 2.82
2703 4919 9.895138 TTTAACTGTATTGGTAATAGGAAGGTC 57.105 33.333 0.00 0.00 0.00 3.85
2775 4995 6.399743 TGTTTTACGGCATACAGTCTCATAA 58.600 36.000 0.00 0.00 0.00 1.90
2802 5023 1.548719 CAGGATACCGACAACCAGTGA 59.451 52.381 0.00 0.00 37.17 3.41
2813 5034 3.190535 CCAAGTTTTGAACCAGGATACCG 59.809 47.826 0.00 0.00 37.17 4.02
2817 5038 1.970640 GGCCAAGTTTTGAACCAGGAT 59.029 47.619 0.00 0.00 0.00 3.24
2837 5058 8.438513 CGAATGCTTATATATCCTCAACTTGTG 58.561 37.037 0.00 0.00 0.00 3.33
2840 5061 9.950496 ATTCGAATGCTTATATATCCTCAACTT 57.050 29.630 10.50 0.00 0.00 2.66
2885 5106 3.670627 GCCGAAAGCCAGTTTCATTACAG 60.671 47.826 0.00 0.00 44.38 2.74
3006 5229 1.719725 TTCTGTTTGCCGCGCAGAAA 61.720 50.000 19.37 7.33 43.56 2.52
3023 5246 7.823745 ATCACCTCAACATTTGGGTATATTC 57.176 36.000 0.00 0.00 34.04 1.75
3146 5369 0.103208 AAAATGTGCCAACCGCGAAA 59.897 45.000 8.23 0.00 42.08 3.46
3383 5609 0.944386 ACCATTGCTCACGTGTTGAC 59.056 50.000 16.51 4.28 0.00 3.18
3445 5673 7.282585 TCCAATATTGTCTATCAAAGGTCCTG 58.717 38.462 14.25 0.00 39.62 3.86
3483 5711 1.143684 TGATCAGCCCCAGGAATAAGC 59.856 52.381 0.00 0.00 0.00 3.09
3490 5718 1.153005 GCTCTTGATCAGCCCCAGG 60.153 63.158 0.00 0.00 0.00 4.45
3507 5735 0.599558 TTTGCTTCTGTGATGCAGGC 59.400 50.000 7.88 0.00 45.08 4.85
3598 5826 1.927174 CAGCAGTACTATTGACGCCAC 59.073 52.381 0.00 0.00 0.00 5.01
3599 5827 1.822371 TCAGCAGTACTATTGACGCCA 59.178 47.619 0.00 0.00 0.00 5.69
3600 5828 2.464865 CTCAGCAGTACTATTGACGCC 58.535 52.381 0.00 0.00 0.00 5.68
3601 5829 1.855360 GCTCAGCAGTACTATTGACGC 59.145 52.381 0.00 5.09 0.00 5.19
3602 5830 3.150848 TGCTCAGCAGTACTATTGACG 57.849 47.619 0.00 0.00 33.32 4.35
3603 5831 4.748892 TCTTGCTCAGCAGTACTATTGAC 58.251 43.478 0.00 0.00 40.61 3.18
3606 5834 3.431486 GGCTCTTGCTCAGCAGTACTATT 60.431 47.826 0.00 0.00 40.61 1.73
3608 5836 1.478510 GGCTCTTGCTCAGCAGTACTA 59.521 52.381 0.00 0.00 40.61 1.82
3609 5837 0.248843 GGCTCTTGCTCAGCAGTACT 59.751 55.000 0.00 0.00 40.61 2.73
3610 5838 0.742635 GGGCTCTTGCTCAGCAGTAC 60.743 60.000 0.00 0.00 40.61 2.73
3612 5840 2.350514 GGGCTCTTGCTCAGCAGT 59.649 61.111 0.00 0.00 40.61 4.40
3613 5841 2.438075 GGGGCTCTTGCTCAGCAG 60.438 66.667 0.00 0.00 42.67 4.24
3614 5842 4.399395 CGGGGCTCTTGCTCAGCA 62.399 66.667 0.00 0.00 42.67 4.41
3616 5844 3.618780 AAGCGGGGCTCTTGCTCAG 62.619 63.158 4.34 0.00 42.67 3.35
3617 5845 3.612247 GAAGCGGGGCTCTTGCTCA 62.612 63.158 4.34 0.00 42.67 4.26
3618 5846 2.821810 GAAGCGGGGCTCTTGCTC 60.822 66.667 4.34 0.00 38.25 4.26
3642 5872 3.965470 AGTTTACCCAGGGACTTGTTT 57.035 42.857 14.54 0.00 34.60 2.83
3643 5873 6.707273 TTATAGTTTACCCAGGGACTTGTT 57.293 37.500 14.54 0.00 34.60 2.83
3644 5874 6.296836 CCTTTATAGTTTACCCAGGGACTTGT 60.297 42.308 14.54 0.81 34.60 3.16
3645 5875 6.120220 CCTTTATAGTTTACCCAGGGACTTG 58.880 44.000 14.54 0.00 34.60 3.16
3646 5876 5.193124 CCCTTTATAGTTTACCCAGGGACTT 59.807 44.000 14.54 0.00 42.03 3.01
3647 5877 4.725304 CCCTTTATAGTTTACCCAGGGACT 59.275 45.833 14.54 8.16 42.03 3.85
3648 5878 4.688045 GCCCTTTATAGTTTACCCAGGGAC 60.688 50.000 14.54 0.00 42.03 4.46
3651 5881 4.513406 TGCCCTTTATAGTTTACCCAGG 57.487 45.455 0.00 0.00 0.00 4.45
3653 5883 7.007723 CCATATTGCCCTTTATAGTTTACCCA 58.992 38.462 0.00 0.00 0.00 4.51
3654 5884 7.176165 GTCCATATTGCCCTTTATAGTTTACCC 59.824 40.741 0.00 0.00 0.00 3.69
3655 5885 7.176165 GGTCCATATTGCCCTTTATAGTTTACC 59.824 40.741 0.00 0.00 0.00 2.85
3656 5886 7.942894 AGGTCCATATTGCCCTTTATAGTTTAC 59.057 37.037 0.00 0.00 0.00 2.01
3657 5887 8.052621 AGGTCCATATTGCCCTTTATAGTTTA 57.947 34.615 0.00 0.00 0.00 2.01
3658 5888 6.922540 AGGTCCATATTGCCCTTTATAGTTT 58.077 36.000 0.00 0.00 0.00 2.66
3659 5889 6.530601 AGGTCCATATTGCCCTTTATAGTT 57.469 37.500 0.00 0.00 0.00 2.24
3660 5890 6.530601 AAGGTCCATATTGCCCTTTATAGT 57.469 37.500 0.00 0.00 33.55 2.12
3661 5891 7.004086 TCAAAGGTCCATATTGCCCTTTATAG 58.996 38.462 1.87 0.00 43.61 1.31
3693 6258 6.374333 GTGACCCATCATACAAAACTGTGTAT 59.626 38.462 0.00 0.00 43.89 2.29
3737 6302 2.248280 AACACTGTATTGACGCCACA 57.752 45.000 0.00 0.00 0.00 4.17
4068 6826 9.642327 CATGAAATTTGTGAAATGAGGTTCATA 57.358 29.630 0.00 0.00 39.61 2.15
4069 6827 8.369424 TCATGAAATTTGTGAAATGAGGTTCAT 58.631 29.630 0.00 0.00 39.61 2.57


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

AutoCloner maintained by Alex Coulton.