Multiple sequence alignment - TraesCS7D01G146100

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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 TraesCS7D01G146100 chr7D 100.000 7236 0 0 1 7236 93500665 93507900 0.000000e+00 13363.0
1 TraesCS7D01G146100 chr7D 89.370 2747 131 59 3973 6666 25408790 25406152 0.000000e+00 3306.0
2 TraesCS7D01G146100 chr7D 94.091 1980 75 14 1 1973 25412745 25410801 0.000000e+00 2970.0
3 TraesCS7D01G146100 chr7D 91.139 1975 127 24 1970 3920 25410721 25408771 0.000000e+00 2634.0
4 TraesCS7D01G146100 chr7D 86.692 1067 128 12 857 1912 613453640 613452577 0.000000e+00 1171.0
5 TraesCS7D01G146100 chr7D 75.763 524 81 25 5916 6398 613447694 613447176 9.450000e-54 222.0
6 TraesCS7D01G146100 chr7D 93.421 76 1 1 2562 2633 93503154 93503229 7.670000e-20 110.0
7 TraesCS7D01G146100 chr7D 93.421 76 1 1 2490 2565 93503226 93503297 7.670000e-20 110.0
8 TraesCS7D01G146100 chr7D 97.826 46 1 0 2520 2565 25410116 25410071 6.020000e-11 80.5
9 TraesCS7D01G146100 chr7B 95.322 3955 142 17 1 3920 46345328 46349274 0.000000e+00 6239.0
10 TraesCS7D01G146100 chr7B 94.945 1899 46 6 3973 5843 46349255 46351131 0.000000e+00 2929.0
11 TraesCS7D01G146100 chr7B 91.482 1444 69 19 5805 7236 46351060 46352461 0.000000e+00 1936.0
12 TraesCS7D01G146100 chr7B 84.714 1171 151 24 796 1948 703305186 703304026 0.000000e+00 1146.0
13 TraesCS7D01G146100 chr7B 81.674 442 59 16 2942 3362 703302815 703302375 1.490000e-91 348.0
14 TraesCS7D01G146100 chr7B 74.798 619 93 31 5916 6479 703299772 703299162 3.400000e-53 220.0
15 TraesCS7D01G146100 chr7B 98.684 76 1 0 2490 2565 46347893 46347968 1.270000e-27 135.0
16 TraesCS7D01G146100 chr7B 90.789 76 3 1 2562 2633 46347821 46347896 1.660000e-16 99.0
17 TraesCS7D01G146100 chr7A 95.851 3784 111 19 172 3920 95800693 95804465 0.000000e+00 6076.0
18 TraesCS7D01G146100 chr7A 95.101 2858 68 8 3973 6764 95804446 95807297 0.000000e+00 4436.0
19 TraesCS7D01G146100 chr7A 93.983 2659 115 23 3 2633 26430153 26427512 0.000000e+00 3982.0
20 TraesCS7D01G146100 chr7A 92.527 1927 94 19 3973 5875 26426170 26424270 0.000000e+00 2715.0
21 TraesCS7D01G146100 chr7A 90.225 1422 81 18 2531 3920 26427546 26426151 0.000000e+00 1803.0
22 TraesCS7D01G146100 chr7A 85.613 1133 143 18 796 1912 704897535 704896407 0.000000e+00 1171.0
23 TraesCS7D01G146100 chr7A 92.748 717 40 6 5784 6494 26424262 26423552 0.000000e+00 1026.0
24 TraesCS7D01G146100 chr7A 95.377 411 17 1 6828 7236 95807305 95807715 0.000000e+00 652.0
25 TraesCS7D01G146100 chr7A 85.985 264 28 7 47 302 26430746 26430484 2.570000e-69 274.0
26 TraesCS7D01G146100 chr7A 97.368 76 2 0 2490 2565 95803087 95803162 5.890000e-26 130.0
27 TraesCS7D01G146100 chr7A 89.691 97 10 0 512 608 672373053 672372957 2.740000e-24 124.0
28 TraesCS7D01G146100 chr7A 96.923 65 2 0 5114 5178 26419055 26418991 7.670000e-20 110.0
29 TraesCS7D01G146100 chr7A 87.234 94 4 6 4723 4814 667224805 667224718 4.620000e-17 100.0
30 TraesCS7D01G146100 chr7A 90.789 76 3 1 2562 2633 95803015 95803090 1.660000e-16 99.0
31 TraesCS7D01G146100 chr7A 82.000 100 12 4 4713 4811 251744848 251744942 6.020000e-11 80.5
32 TraesCS7D01G146100 chr4A 92.428 3962 183 42 1 3920 709907664 709903778 0.000000e+00 5546.0
33 TraesCS7D01G146100 chr4A 93.132 1922 89 20 3973 5875 709903797 709901900 0.000000e+00 2778.0
34 TraesCS7D01G146100 chr4A 92.022 727 50 5 5775 6494 709901940 709901215 0.000000e+00 1014.0
35 TraesCS7D01G146100 chr4A 96.610 59 2 0 6436 6494 709901214 709901156 1.660000e-16 99.0
36 TraesCS7D01G146100 chr2B 90.231 563 47 6 675 1232 158854323 158853764 0.000000e+00 728.0
37 TraesCS7D01G146100 chr3D 94.444 54 3 0 3921 3974 237831496 237831443 4.650000e-12 84.2
38 TraesCS7D01G146100 chr3D 83.146 89 7 6 4723 4811 514263327 514263407 2.800000e-09 75.0
39 TraesCS7D01G146100 chr3A 83.529 85 9 4 4732 4814 725708892 725708811 2.800000e-09 75.0
40 TraesCS7D01G146100 chr4D 79.808 104 13 6 4726 4827 116276906 116276809 1.300000e-07 69.4


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 TraesCS7D01G146100 chr7D 93500665 93507900 7235 False 13363.000000 13363 100.000000 1 7236 1 chr7D.!!$F1 7235
1 TraesCS7D01G146100 chr7D 25406152 25412745 6593 True 2247.625000 3306 93.106500 1 6666 4 chr7D.!!$R3 6665
2 TraesCS7D01G146100 chr7D 613452577 613453640 1063 True 1171.000000 1171 86.692000 857 1912 1 chr7D.!!$R2 1055
3 TraesCS7D01G146100 chr7D 613447176 613447694 518 True 222.000000 222 75.763000 5916 6398 1 chr7D.!!$R1 482
4 TraesCS7D01G146100 chr7B 46345328 46352461 7133 False 2267.600000 6239 94.244400 1 7236 5 chr7B.!!$F1 7235
5 TraesCS7D01G146100 chr7B 703299162 703305186 6024 True 571.333333 1146 80.395333 796 6479 3 chr7B.!!$R1 5683
6 TraesCS7D01G146100 chr7A 95800693 95807715 7022 False 2278.600000 6076 94.897200 172 7236 5 chr7A.!!$F2 7064
7 TraesCS7D01G146100 chr7A 26423552 26430746 7194 True 1960.000000 3982 91.093600 3 6494 5 chr7A.!!$R5 6491
8 TraesCS7D01G146100 chr7A 704896407 704897535 1128 True 1171.000000 1171 85.613000 796 1912 1 chr7A.!!$R4 1116
9 TraesCS7D01G146100 chr4A 709901156 709907664 6508 True 2359.250000 5546 93.548000 1 6494 4 chr4A.!!$R1 6493
10 TraesCS7D01G146100 chr2B 158853764 158854323 559 True 728.000000 728 90.231000 675 1232 1 chr2B.!!$R1 557

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
938 1577 2.703536 TCCTTGCTAGTTTCCAGTGACA 59.296 45.455 0.00 0.0 0.00 3.58 F
1584 2223 0.037590 AAGTTGGCATACCTCGGCAA 59.962 50.000 0.00 0.0 45.54 4.52 F
2782 3646 0.040058 ATCATGCACTTTGCCCCTCA 59.960 50.000 0.00 0.0 44.23 3.86 F
3970 5197 0.107081 TCCCCTGCGTTTTCTCGAAA 59.893 50.000 0.00 0.0 0.00 3.46 F
4864 7070 0.603975 GTTCAAACTCCAGCCGAGCT 60.604 55.000 0.00 0.0 43.01 4.09 F
5800 8014 0.824595 AACAGCAGCAGCACCATCAA 60.825 50.000 3.17 0.0 45.49 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2959 3.057033 GCATGGACAGCAGACAAAGAATT 60.057 43.478 0.00 0.00 0.00 2.17 R
3456 4653 2.815503 CAGGCATCAAATCACACTGTGA 59.184 45.455 15.86 14.26 46.90 3.58 R
3981 5208 0.455410 GCAACACACAAAGCCACAGA 59.545 50.000 0.00 0.00 0.00 3.41 R
5794 8008 1.506718 CTGCTGCTGCTGTTGATGG 59.493 57.895 17.00 0.00 40.48 3.51 R
5991 8346 1.128200 CCCCGTCATACCCATCAGAA 58.872 55.000 0.00 0.00 0.00 3.02 R
7180 9617 0.575390 CGTCGCGTGAACTTTTGTCT 59.425 50.000 5.77 0.00 0.00 3.41 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
45 639 3.002656 CACACTCGTTTCTGCATTGAAGT 59.997 43.478 0.00 0.00 0.00 3.01
142 741 8.148999 TGACCTTTTCTTCTAGTTTCTTAGGTC 58.851 37.037 18.38 18.38 45.05 3.85
331 935 4.502645 GGGTTTGTGTTCTTGTGATTTTCG 59.497 41.667 0.00 0.00 0.00 3.46
343 951 3.123050 GTGATTTTCGCCTTTGCTTGTT 58.877 40.909 0.00 0.00 34.43 2.83
344 952 3.555547 GTGATTTTCGCCTTTGCTTGTTT 59.444 39.130 0.00 0.00 34.43 2.83
345 953 4.742659 GTGATTTTCGCCTTTGCTTGTTTA 59.257 37.500 0.00 0.00 34.43 2.01
378 992 5.534278 TGGTTTGTGATATCTTGCAAGTTCA 59.466 36.000 25.19 21.38 0.00 3.18
413 1028 5.297547 ACATCGCTGAACTTTTCTCACTAA 58.702 37.500 0.00 0.00 0.00 2.24
673 1295 5.698832 TGGAAGTTAAGTCAATGCATTTCG 58.301 37.500 9.83 0.00 0.00 3.46
679 1301 4.675190 AAGTCAATGCATTTCGTCTCTG 57.325 40.909 9.83 0.00 0.00 3.35
697 1319 6.334202 GTCTCTGAGATCGGATTAACACTTT 58.666 40.000 11.07 0.00 0.00 2.66
938 1577 2.703536 TCCTTGCTAGTTTCCAGTGACA 59.296 45.455 0.00 0.00 0.00 3.58
1425 2064 3.637998 CAGTTGATTCAACAGCTGCTT 57.362 42.857 26.73 4.59 45.66 3.91
1539 2178 3.268330 ACAGCAGCATCAGTTATCACAG 58.732 45.455 0.00 0.00 0.00 3.66
1584 2223 0.037590 AAGTTGGCATACCTCGGCAA 59.962 50.000 0.00 0.00 45.54 4.52
1687 2326 5.810587 TGTTCTCGAAGGTTAATGCAGTATC 59.189 40.000 0.00 0.00 0.00 2.24
2034 2767 8.122306 TCAACACTGTTTATTATCGATTACCG 57.878 34.615 1.71 0.00 40.25 4.02
2072 2805 8.574251 AGAAACATAATTTGTATGTGTAGCCA 57.426 30.769 0.00 0.00 37.68 4.75
2218 2975 3.655276 AAGCCAATTCTTTGTCTGCTG 57.345 42.857 0.00 0.00 31.09 4.41
2220 2977 2.555757 AGCCAATTCTTTGTCTGCTGTC 59.444 45.455 0.00 0.00 29.99 3.51
2260 3018 6.206787 TCCAGGGTACTTATTCCTTGATGTA 58.793 40.000 0.00 0.00 33.50 2.29
2410 3174 3.726557 TCCCTTCATGATTGCTCACTT 57.273 42.857 0.00 0.00 33.22 3.16
2782 3646 0.040058 ATCATGCACTTTGCCCCTCA 59.960 50.000 0.00 0.00 44.23 3.86
2785 3650 0.974010 ATGCACTTTGCCCCTCATGG 60.974 55.000 0.00 0.00 44.23 3.66
2846 3711 6.478016 GCTCTTTCTGTTTTGCTTCTTCATTT 59.522 34.615 0.00 0.00 0.00 2.32
3043 4218 1.403647 CCTTGACATGCCGAACGAGTA 60.404 52.381 0.00 0.00 0.00 2.59
3189 4364 8.226112 AGGTATGTTCCTAGTTGTAGTAGCTAT 58.774 37.037 0.00 0.00 35.87 2.97
3225 4408 4.058721 CCTTTTGGGTGTCTTTTCTTGG 57.941 45.455 0.00 0.00 35.46 3.61
3445 4642 2.486982 GGCTGCATATGGTTGAGCTATG 59.513 50.000 4.56 0.00 0.00 2.23
3456 4653 4.350816 TGGTTGAGCTATGGCCTACATATT 59.649 41.667 3.32 0.00 41.07 1.28
3504 4702 7.860373 GCATCTTGTAGTTTTGTGTTTATGACA 59.140 33.333 0.00 0.00 35.42 3.58
3564 4762 3.008485 GTGTGAAAAGACCAGATCCCTCT 59.992 47.826 0.00 0.00 0.00 3.69
3619 4823 9.862371 ACTGTCTACTCAATTAAGTTACAGATG 57.138 33.333 21.90 6.33 40.72 2.90
3658 4882 1.927174 CAAAGACGATTGAGTAGGCCG 59.073 52.381 0.00 0.00 31.84 6.13
3668 4892 5.236478 CGATTGAGTAGGCCGTAATTCATTT 59.764 40.000 0.00 0.00 0.00 2.32
3721 4945 0.250727 TCACTTGCTACAAGTGGGGC 60.251 55.000 29.96 0.11 45.66 5.80
3812 5036 2.982470 GCAATTTGAAAGCTTCCTGTCG 59.018 45.455 0.00 0.00 0.00 4.35
3880 5107 2.428544 ATGGTAAAGCACGGGCATTA 57.571 45.000 14.57 8.15 44.61 1.90
3925 5152 4.589908 TCTTAATCTGTGGCTTTTCTCCC 58.410 43.478 0.00 0.00 0.00 4.30
3926 5153 4.289672 TCTTAATCTGTGGCTTTTCTCCCT 59.710 41.667 0.00 0.00 0.00 4.20
3927 5154 3.532641 AATCTGTGGCTTTTCTCCCTT 57.467 42.857 0.00 0.00 0.00 3.95
3928 5155 3.532641 ATCTGTGGCTTTTCTCCCTTT 57.467 42.857 0.00 0.00 0.00 3.11
3932 5159 3.370104 TGTGGCTTTTCTCCCTTTTCAA 58.630 40.909 0.00 0.00 0.00 2.69
3933 5160 3.966665 TGTGGCTTTTCTCCCTTTTCAAT 59.033 39.130 0.00 0.00 0.00 2.57
3934 5161 4.202243 TGTGGCTTTTCTCCCTTTTCAATG 60.202 41.667 0.00 0.00 0.00 2.82
3935 5162 3.324556 TGGCTTTTCTCCCTTTTCAATGG 59.675 43.478 0.00 0.00 0.00 3.16
3936 5163 3.578282 GGCTTTTCTCCCTTTTCAATGGA 59.422 43.478 0.00 0.00 0.00 3.41
3937 5164 4.040339 GGCTTTTCTCCCTTTTCAATGGAA 59.960 41.667 0.00 0.00 0.00 3.53
3938 5165 5.280164 GGCTTTTCTCCCTTTTCAATGGAAT 60.280 40.000 0.00 0.00 31.93 3.01
3939 5166 5.640783 GCTTTTCTCCCTTTTCAATGGAATG 59.359 40.000 0.00 0.00 31.93 2.67
3940 5167 6.518875 GCTTTTCTCCCTTTTCAATGGAATGA 60.519 38.462 0.00 0.00 31.93 2.57
3941 5168 6.992664 TTTCTCCCTTTTCAATGGAATGAA 57.007 33.333 0.00 0.00 37.53 2.57
3942 5169 6.992664 TTCTCCCTTTTCAATGGAATGAAA 57.007 33.333 0.00 0.00 45.07 2.69
3943 5170 6.345096 TCTCCCTTTTCAATGGAATGAAAC 57.655 37.500 2.20 0.00 46.06 2.78
3945 5172 3.679502 CCCTTTTCAATGGAATGAAACGC 59.320 43.478 2.20 0.00 46.06 4.84
3947 5174 4.749099 CCTTTTCAATGGAATGAAACGCAA 59.251 37.500 2.20 0.00 46.06 4.85
3948 5175 5.107375 CCTTTTCAATGGAATGAAACGCAAG 60.107 40.000 2.20 0.00 46.06 4.01
3949 5176 3.574284 TCAATGGAATGAAACGCAAGG 57.426 42.857 0.00 0.00 46.39 3.61
3953 5180 0.526211 GGAATGAAACGCAAGGGTCC 59.474 55.000 0.00 0.00 46.39 4.46
3954 5181 0.526211 GAATGAAACGCAAGGGTCCC 59.474 55.000 0.00 0.00 46.39 4.46
3964 5191 2.434774 AGGGTCCCCTGCGTTTTC 59.565 61.111 3.51 0.00 46.22 2.29
3965 5192 2.154074 AGGGTCCCCTGCGTTTTCT 61.154 57.895 3.51 0.00 46.22 2.52
3966 5193 1.674651 GGGTCCCCTGCGTTTTCTC 60.675 63.158 0.00 0.00 0.00 2.87
3967 5194 2.033194 GGTCCCCTGCGTTTTCTCG 61.033 63.158 0.00 0.00 0.00 4.04
3968 5195 1.005394 GTCCCCTGCGTTTTCTCGA 60.005 57.895 0.00 0.00 0.00 4.04
3970 5197 0.107081 TCCCCTGCGTTTTCTCGAAA 59.893 50.000 0.00 0.00 0.00 3.46
3971 5198 0.948678 CCCCTGCGTTTTCTCGAAAA 59.051 50.000 0.93 0.93 37.90 2.29
3972 5199 1.335496 CCCCTGCGTTTTCTCGAAAAA 59.665 47.619 6.41 0.00 41.37 1.94
3997 6068 3.118408 TCTTAGTCTGTGGCTTTGTGTGT 60.118 43.478 0.00 0.00 0.00 3.72
4117 6189 4.395231 GCTACTGTCACTAAAAATGGACCC 59.605 45.833 0.00 0.00 0.00 4.46
4384 6522 8.906238 TGGAGTTTCCCTAAGTAGTATTTACT 57.094 34.615 0.00 0.00 36.65 2.24
4483 6661 1.135431 TGGCGTGTTGATTGCTTATGC 60.135 47.619 0.00 0.00 40.20 3.14
4864 7070 0.603975 GTTCAAACTCCAGCCGAGCT 60.604 55.000 0.00 0.00 43.01 4.09
5073 7280 6.808008 AGAGAAACATTTGTGACATAGTGG 57.192 37.500 0.00 0.00 0.00 4.00
5544 7755 2.102553 GCAGGAGGCGTCGAGTAC 59.897 66.667 0.00 0.00 0.00 2.73
5563 7774 1.726853 CCTTCAAAGGTCCTACAGCG 58.273 55.000 0.32 0.00 41.41 5.18
5794 8008 1.947642 GCAACAACAGCAGCAGCAC 60.948 57.895 3.17 0.00 45.49 4.40
5797 8011 1.111116 AACAACAGCAGCAGCACCAT 61.111 50.000 3.17 0.00 45.49 3.55
5800 8014 0.824595 AACAGCAGCAGCACCATCAA 60.825 50.000 3.17 0.00 45.49 2.57
6038 8393 3.540314 ATCTGATCAACAGTGGAGCTC 57.460 47.619 4.71 4.71 45.86 4.09
6269 8658 2.931512 AAAGTCTCGCTACTCTGAGC 57.068 50.000 4.19 0.00 39.20 4.26
6692 9119 1.777272 AGTGGGGATAGATCCTTTGGC 59.223 52.381 8.45 0.00 46.35 4.52
6694 9121 2.175715 GTGGGGATAGATCCTTTGGCTT 59.824 50.000 8.45 0.00 46.35 4.35
6803 9230 8.425703 TCAATAACGTGTTGATATTCCCTGATA 58.574 33.333 11.36 0.00 31.07 2.15
6812 9239 8.141909 TGTTGATATTCCCTGATAGAACTAACG 58.858 37.037 0.00 0.00 0.00 3.18
6821 9248 6.127535 CCCTGATAGAACTAACGTTTCCTACA 60.128 42.308 5.91 0.00 32.39 2.74
6826 9253 5.721232 AGAACTAACGTTTCCTACATGAGG 58.279 41.667 5.91 1.96 39.11 3.86
6917 9345 5.465532 TTGCAGAAAGATTTGCCATGTTA 57.534 34.783 0.00 0.00 39.54 2.41
6919 9347 5.472148 TGCAGAAAGATTTGCCATGTTAAG 58.528 37.500 0.00 0.00 39.54 1.85
7046 9476 2.575532 TCAGAAGAAAGTTGCCACAGG 58.424 47.619 0.00 0.00 0.00 4.00
7144 9581 2.030363 TGTTGCATTAGGAAAACTGCCG 60.030 45.455 0.00 0.00 33.70 5.69
7156 9593 0.036164 AACTGCCGTGCTCCACATAA 59.964 50.000 0.00 0.00 33.40 1.90
7175 9612 6.305399 CACATAAAAATTGCCACGACACTAAG 59.695 38.462 0.00 0.00 0.00 2.18
7180 9617 5.339008 AATTGCCACGACACTAAGATAGA 57.661 39.130 0.00 0.00 0.00 1.98
7192 9629 7.808381 CGACACTAAGATAGAGACAAAAGTTCA 59.192 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 722 5.336531 CGCCTGACCTAAGAAACTAGAAGAA 60.337 44.000 0.00 0.00 0.00 2.52
142 741 0.529337 CACAGCAGATAGACCGCCTG 60.529 60.000 0.00 0.00 0.00 4.85
331 935 6.073819 CCAAACAGTAATAAACAAGCAAAGGC 60.074 38.462 0.00 0.00 41.61 4.35
345 953 8.028938 GCAAGATATCACAAACCAAACAGTAAT 58.971 33.333 5.32 0.00 0.00 1.89
378 992 1.134699 CAGCGATGTACAGTCCCATGT 60.135 52.381 0.33 0.00 37.19 3.21
413 1028 2.301346 CACAAGACAAAGGAAGCTGGT 58.699 47.619 0.00 0.00 0.00 4.00
673 1295 5.508200 AGTGTTAATCCGATCTCAGAGAC 57.492 43.478 0.91 0.00 0.00 3.36
679 1301 6.986904 AAAGGAAAGTGTTAATCCGATCTC 57.013 37.500 0.00 0.00 38.31 2.75
697 1319 9.199645 TGATAAAAATAGCCATCATCAAAAGGA 57.800 29.630 0.00 0.00 0.00 3.36
1425 2064 5.083122 AGATGAAGAGAACTCTGACCTTGA 58.917 41.667 5.06 0.00 40.36 3.02
1539 2178 3.581024 TGTTGATGCTGAGGAAATTGC 57.419 42.857 0.00 0.00 0.00 3.56
1584 2223 2.515901 GGTGGCCTCAACTGTGGT 59.484 61.111 3.32 0.00 0.00 4.16
2034 2767 5.627499 TTATGTTTCTCACTGCCATCAAC 57.373 39.130 0.00 0.00 0.00 3.18
2202 2958 4.482386 CATGGACAGCAGACAAAGAATTG 58.518 43.478 0.00 0.00 42.46 2.32
2203 2959 3.057033 GCATGGACAGCAGACAAAGAATT 60.057 43.478 0.00 0.00 0.00 2.17
2230 2987 4.102681 AGGAATAAGTACCCTGGATTTCGG 59.897 45.833 0.00 0.00 0.00 4.30
2410 3174 8.635328 AGCATAAACAAATCAGCATTCATATGA 58.365 29.630 0.00 0.00 33.37 2.15
2649 3486 6.607600 TGATAAGGTATTCTGTACTGCTCAGT 59.392 38.462 7.73 7.73 45.02 3.41
2782 3646 5.476945 GTCAAGGTGTTCATCTAAAACCCAT 59.523 40.000 0.00 0.00 0.00 4.00
2785 3650 5.531287 ACAGTCAAGGTGTTCATCTAAAACC 59.469 40.000 0.00 0.00 0.00 3.27
2786 3651 6.483640 AGACAGTCAAGGTGTTCATCTAAAAC 59.516 38.462 2.66 0.00 0.00 2.43
2898 4070 4.218312 ACTGGGTGAGCTCAAAAAGAAAT 58.782 39.130 20.19 0.00 0.00 2.17
2902 4077 3.243535 GGAAACTGGGTGAGCTCAAAAAG 60.244 47.826 20.19 17.34 0.00 2.27
3189 4364 3.372566 CCAAAAGGTGCTATGGTATGGGA 60.373 47.826 0.00 0.00 0.00 4.37
3225 4408 3.615224 ATCCACAAATCCACAAATGCC 57.385 42.857 0.00 0.00 0.00 4.40
3445 4642 4.137116 TCACACTGTGAATATGTAGGCC 57.863 45.455 15.86 0.00 39.78 5.19
3456 4653 2.815503 CAGGCATCAAATCACACTGTGA 59.184 45.455 15.86 14.26 46.90 3.58
3504 4702 4.836736 AGCAGCAATGCCCATTAGATTTAT 59.163 37.500 0.00 0.00 34.90 1.40
3564 4762 3.965379 TGGGTGATAAAACTAGCGTGA 57.035 42.857 0.00 0.00 0.00 4.35
3619 4823 3.294493 TGTTTTCCGCCTGCAGCC 61.294 61.111 8.66 0.00 38.78 4.85
3658 4882 8.598075 GCAAACATGAGGATTGAAATGAATTAC 58.402 33.333 0.00 0.00 0.00 1.89
3668 4892 3.633525 GCTATGGCAAACATGAGGATTGA 59.366 43.478 0.00 0.00 40.82 2.57
3721 4945 1.000283 GCAGATACGGTGGAGAGATGG 60.000 57.143 0.00 0.00 0.00 3.51
3812 5036 9.500785 TCCATTTGGAAGGAAAATTTATGAAAC 57.499 29.630 0.00 0.00 42.18 2.78
3846 5071 8.663025 GTGCTTTACCATTTCCTACTAAGTAAC 58.337 37.037 0.00 0.00 0.00 2.50
3925 5152 5.107375 CCTTGCGTTTCATTCCATTGAAAAG 60.107 40.000 8.01 8.01 44.71 2.27
3926 5153 4.749099 CCTTGCGTTTCATTCCATTGAAAA 59.251 37.500 1.52 0.00 44.71 2.29
3927 5154 4.305769 CCTTGCGTTTCATTCCATTGAAA 58.694 39.130 0.00 0.00 41.92 2.69
3928 5155 3.305950 CCCTTGCGTTTCATTCCATTGAA 60.306 43.478 0.00 0.00 33.89 2.69
3932 5159 1.818674 GACCCTTGCGTTTCATTCCAT 59.181 47.619 0.00 0.00 0.00 3.41
3933 5160 1.243902 GACCCTTGCGTTTCATTCCA 58.756 50.000 0.00 0.00 0.00 3.53
3934 5161 0.526211 GGACCCTTGCGTTTCATTCC 59.474 55.000 0.00 0.00 0.00 3.01
3935 5162 0.526211 GGGACCCTTGCGTTTCATTC 59.474 55.000 2.09 0.00 0.00 2.67
3936 5163 2.653557 GGGACCCTTGCGTTTCATT 58.346 52.632 2.09 0.00 0.00 2.57
3937 5164 4.415783 GGGACCCTTGCGTTTCAT 57.584 55.556 2.09 0.00 0.00 2.57
3953 5180 2.766970 TTTTTCGAGAAAACGCAGGG 57.233 45.000 10.18 0.00 39.70 4.45
3970 5197 6.096846 ACACAAAGCCACAGACTAAGATTTTT 59.903 34.615 0.00 0.00 0.00 1.94
3971 5198 5.594317 ACACAAAGCCACAGACTAAGATTTT 59.406 36.000 0.00 0.00 0.00 1.82
3972 5199 5.009010 CACACAAAGCCACAGACTAAGATTT 59.991 40.000 0.00 0.00 0.00 2.17
3975 5202 3.118408 ACACACAAAGCCACAGACTAAGA 60.118 43.478 0.00 0.00 0.00 2.10
3976 5203 3.206150 ACACACAAAGCCACAGACTAAG 58.794 45.455 0.00 0.00 0.00 2.18
3978 5205 2.942376 CAACACACAAAGCCACAGACTA 59.058 45.455 0.00 0.00 0.00 2.59
3979 5206 1.745087 CAACACACAAAGCCACAGACT 59.255 47.619 0.00 0.00 0.00 3.24
3980 5207 1.798813 GCAACACACAAAGCCACAGAC 60.799 52.381 0.00 0.00 0.00 3.51
3981 5208 0.455410 GCAACACACAAAGCCACAGA 59.545 50.000 0.00 0.00 0.00 3.41
3982 5209 0.866906 CGCAACACACAAAGCCACAG 60.867 55.000 0.00 0.00 0.00 3.66
3985 5212 1.943116 AAGCGCAACACACAAAGCCA 61.943 50.000 11.47 0.00 0.00 4.75
3986 5213 0.805711 AAAGCGCAACACACAAAGCC 60.806 50.000 11.47 0.00 0.00 4.35
3987 5214 1.833860 TAAAGCGCAACACACAAAGC 58.166 45.000 11.47 0.00 0.00 3.51
3988 5215 3.434637 AGTTAAAGCGCAACACACAAAG 58.565 40.909 11.47 0.00 0.00 2.77
3989 5216 3.495670 AGTTAAAGCGCAACACACAAA 57.504 38.095 11.47 0.00 0.00 2.83
3990 5217 3.495670 AAGTTAAAGCGCAACACACAA 57.504 38.095 11.47 0.00 0.00 3.33
3997 6068 3.629438 GGTACCAAAGTTAAAGCGCAA 57.371 42.857 11.47 0.00 0.00 4.85
4117 6189 1.007271 ATCGTTCGATAGGCCAGCG 60.007 57.895 5.01 5.95 37.40 5.18
4483 6661 2.302445 CCTCTGATATCTGCCAAGAGGG 59.698 54.545 20.88 8.60 38.15 4.30
4864 7070 7.652524 TTGCATGATATTAGCTGGGTTTTTA 57.347 32.000 0.00 0.00 0.00 1.52
5073 7280 1.619807 ATCAATGGGCAAAGCAGGGC 61.620 55.000 0.00 0.00 0.00 5.19
5544 7755 4.254760 ACCGCTGTAGGACCTTTGAAGG 62.255 54.545 0.00 8.22 42.50 3.46
5563 7774 1.582968 CTGAATGCCACTGTGCACC 59.417 57.895 15.69 0.00 45.48 5.01
5662 7876 4.021192 CCTTGGAAATTGTTATGCTGGTGT 60.021 41.667 0.00 0.00 0.00 4.16
5794 8008 1.506718 CTGCTGCTGCTGTTGATGG 59.493 57.895 17.00 0.00 40.48 3.51
5797 8011 1.824760 TTGCTGCTGCTGCTGTTGA 60.825 52.632 27.67 8.50 39.81 3.18
5800 8014 2.517638 TGTTGCTGCTGCTGCTGT 60.518 55.556 27.67 0.00 39.81 4.40
5991 8346 1.128200 CCCCGTCATACCCATCAGAA 58.872 55.000 0.00 0.00 0.00 3.02
6269 8658 4.274069 CGATATCACCATCAAACAAAGCG 58.726 43.478 3.12 0.00 0.00 4.68
6783 9210 6.098409 AGTTCTATCAGGGAATATCAACACGT 59.902 38.462 0.00 0.00 0.00 4.49
6821 9248 5.043248 CGTTTTTCACTCAAAAAGCCTCAT 58.957 37.500 0.00 0.00 43.27 2.90
6826 9253 2.926838 TGGCGTTTTTCACTCAAAAAGC 59.073 40.909 7.90 7.90 43.27 3.51
6960 9390 3.138304 ACAAATTACTCTGCTGCAACGA 58.862 40.909 3.02 0.00 0.00 3.85
6963 9393 4.616604 GCATGACAAATTACTCTGCTGCAA 60.617 41.667 3.02 0.00 0.00 4.08
7046 9476 4.881273 TGTACCATAGCAAATCATGGACAC 59.119 41.667 7.57 5.64 43.80 3.67
7070 9500 5.368256 TTCTTTTCTGCAGCATTCTTCTC 57.632 39.130 9.47 0.00 0.00 2.87
7144 9581 3.679502 GTGGCAATTTTTATGTGGAGCAC 59.320 43.478 0.00 0.00 34.56 4.40
7156 9593 6.170506 TCTATCTTAGTGTCGTGGCAATTTT 58.829 36.000 0.00 0.00 0.00 1.82
7175 9612 3.918591 TCGCGTGAACTTTTGTCTCTATC 59.081 43.478 5.77 0.00 0.00 2.08
7180 9617 0.575390 CGTCGCGTGAACTTTTGTCT 59.425 50.000 5.77 0.00 0.00 3.41
7192 9629 1.527034 TCCCTATATTAGCGTCGCGT 58.473 50.000 12.30 4.83 0.00 6.01


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

AutoCloner maintained by Alex Coulton.