Multiple sequence alignment - TraesCS5D01G141000

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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 TraesCS5D01G141000 chr5D 100.000 4765 0 0 1 4765 224873814 224869050 0.000000e+00 8800.0
1 TraesCS5D01G141000 chr5D 87.416 596 35 14 1 593 485357023 485357581 0.000000e+00 649.0
2 TraesCS5D01G141000 chr5B 93.836 3942 154 40 608 4493 246585570 246589478 0.000000e+00 5851.0
3 TraesCS5D01G141000 chr5B 94.420 2724 119 15 1793 4493 235446018 235443305 0.000000e+00 4157.0
4 TraesCS5D01G141000 chr5B 93.051 921 28 15 908 1801 235447853 235446942 0.000000e+00 1314.0
5 TraesCS5D01G141000 chr5B 90.476 315 23 3 608 916 235449054 235448741 4.440000e-110 409.0
6 TraesCS5D01G141000 chr5B 79.752 242 38 10 4464 4699 122614533 122614769 1.060000e-36 165.0
7 TraesCS5D01G141000 chr5A 94.498 3708 146 26 644 4326 299360706 299357032 0.000000e+00 5664.0
8 TraesCS5D01G141000 chr5A 89.474 456 37 5 4312 4765 299356885 299356439 2.490000e-157 566.0
9 TraesCS5D01G141000 chr5A 85.549 173 24 1 424 596 237453537 237453366 3.790000e-41 180.0
10 TraesCS5D01G141000 chr3A 95.805 596 24 1 1 596 63902743 63902149 0.000000e+00 961.0
11 TraesCS5D01G141000 chr3A 88.275 597 46 5 1 596 451141474 451142047 0.000000e+00 693.0
12 TraesCS5D01G141000 chr4A 95.638 596 25 1 1 596 405575222 405574628 0.000000e+00 955.0
13 TraesCS5D01G141000 chr2D 91.980 586 33 7 1 585 642504257 642503685 0.000000e+00 809.0
14 TraesCS5D01G141000 chr2A 89.430 596 39 8 1 595 617636899 617636327 0.000000e+00 730.0
15 TraesCS5D01G141000 chr6B 83.860 285 44 2 4404 4687 417237365 417237082 2.190000e-68 270.0
16 TraesCS5D01G141000 chr6A 81.887 265 42 6 4441 4701 383476157 383475895 8.030000e-53 219.0
17 TraesCS5D01G141000 chr1A 84.878 205 20 9 4415 4614 380294799 380294997 3.760000e-46 196.0
18 TraesCS5D01G141000 chr1A 87.313 134 13 3 1714 1845 433014549 433014418 2.970000e-32 150.0
19 TraesCS5D01G141000 chr1B 78.930 299 43 19 4475 4764 496075703 496075416 8.140000e-43 185.0
20 TraesCS5D01G141000 chr3B 80.603 232 37 6 4473 4699 800104089 800103861 6.340000e-39 172.0
21 TraesCS5D01G141000 chr3B 81.223 229 27 12 4464 4683 815467196 815466975 2.280000e-38 171.0
22 TraesCS5D01G141000 chr2B 84.483 174 26 1 422 595 342276428 342276256 2.280000e-38 171.0
23 TraesCS5D01G141000 chr7B 76.568 303 58 13 4464 4758 727861346 727861643 2.300000e-33 154.0
24 TraesCS5D01G141000 chr7A 73.554 242 43 17 4535 4765 727294022 727294253 6.610000e-09 73.1


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 TraesCS5D01G141000 chr5D 224869050 224873814 4764 True 8800 8800 100.000 1 4765 1 chr5D.!!$R1 4764
1 TraesCS5D01G141000 chr5D 485357023 485357581 558 False 649 649 87.416 1 593 1 chr5D.!!$F1 592
2 TraesCS5D01G141000 chr5B 246585570 246589478 3908 False 5851 5851 93.836 608 4493 1 chr5B.!!$F2 3885
3 TraesCS5D01G141000 chr5B 235443305 235449054 5749 True 1960 4157 92.649 608 4493 3 chr5B.!!$R1 3885
4 TraesCS5D01G141000 chr5A 299356439 299360706 4267 True 3115 5664 91.986 644 4765 2 chr5A.!!$R2 4121
5 TraesCS5D01G141000 chr3A 63902149 63902743 594 True 961 961 95.805 1 596 1 chr3A.!!$R1 595
6 TraesCS5D01G141000 chr3A 451141474 451142047 573 False 693 693 88.275 1 596 1 chr3A.!!$F1 595
7 TraesCS5D01G141000 chr4A 405574628 405575222 594 True 955 955 95.638 1 596 1 chr4A.!!$R1 595
8 TraesCS5D01G141000 chr2D 642503685 642504257 572 True 809 809 91.980 1 585 1 chr2D.!!$R1 584
9 TraesCS5D01G141000 chr2A 617636327 617636899 572 True 730 730 89.430 1 595 1 chr2A.!!$R1 594

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
951 1862 0.036306 ATCACACCCAAACCCTCGAC 59.964 55.000 0.00 0.0 0.00 4.20 F
1803 3673 0.253160 TGTACAAGGCCTGGAGGGAT 60.253 55.000 16.25 0.0 37.23 3.85 F
1965 3835 0.613777 AGAAAAAGACGCCGGATCCT 59.386 50.000 5.05 0.0 0.00 3.24 F
2220 4103 1.001181 GCCCATGTTTCACAACTGCAT 59.999 47.619 0.00 0.0 33.58 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2522 4405 0.178533 TTGGTTCGTTCGGTCCTGTT 59.821 50.0 0.00 0.0 0.00 3.16 R
2610 4494 0.813184 CGCATTTGGTTCCTGCTCAT 59.187 50.0 0.00 0.0 33.75 2.90 R
3722 5622 1.089920 CATTTTCAGCAGGTCCCTCG 58.910 55.0 0.00 0.0 0.00 4.63 R
3793 5693 2.883386 GACTCCACGGGTATATTCGACT 59.117 50.0 4.98 0.0 0.00 4.18 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
28 29 4.918583 AGAGACGACGATGAAGAGAAAAAC 59.081 41.667 0.00 0.00 0.00 2.43
40 41 2.884639 AGAGAAAAACCGGTGTCCATTG 59.115 45.455 8.52 0.00 0.00 2.82
165 169 3.353836 CGAACCCCCAACGCACTG 61.354 66.667 0.00 0.00 0.00 3.66
252 256 3.024043 GCGTGCTGTTTTGCCACG 61.024 61.111 7.91 7.91 38.99 4.94
525 530 5.189928 TGTCAAAACTGTGGTATCTTGTGT 58.810 37.500 0.00 0.00 0.00 3.72
544 549 8.397906 TCTTGTGTCTACATGCTAAAATATTGC 58.602 33.333 0.00 0.00 36.53 3.56
596 601 4.941873 ACTTTGCTACCAAACATAGCCTAC 59.058 41.667 1.78 0.00 43.75 3.18
597 602 4.561500 TTGCTACCAAACATAGCCTACA 57.438 40.909 1.78 0.00 43.75 2.74
598 603 4.561500 TGCTACCAAACATAGCCTACAA 57.438 40.909 1.78 0.00 43.75 2.41
599 604 5.110814 TGCTACCAAACATAGCCTACAAT 57.889 39.130 1.78 0.00 43.75 2.71
600 605 4.881273 TGCTACCAAACATAGCCTACAATG 59.119 41.667 1.78 0.00 43.75 2.82
601 606 4.261197 GCTACCAAACATAGCCTACAATGC 60.261 45.833 0.00 0.00 39.36 3.56
602 607 3.696045 ACCAAACATAGCCTACAATGCA 58.304 40.909 0.00 0.00 0.00 3.96
603 608 4.085733 ACCAAACATAGCCTACAATGCAA 58.914 39.130 0.00 0.00 0.00 4.08
604 609 4.526262 ACCAAACATAGCCTACAATGCAAA 59.474 37.500 0.00 0.00 0.00 3.68
605 610 5.011533 ACCAAACATAGCCTACAATGCAAAA 59.988 36.000 0.00 0.00 0.00 2.44
606 611 5.931146 CCAAACATAGCCTACAATGCAAAAA 59.069 36.000 0.00 0.00 0.00 1.94
634 639 3.017323 CATCCAATCGCCGCACTC 58.983 61.111 0.00 0.00 0.00 3.51
640 645 1.139989 CAATCGCCGCACTCGATAAT 58.860 50.000 5.38 0.00 44.80 1.28
650 655 4.369182 CGCACTCGATAATAAGTCCCTTT 58.631 43.478 0.00 0.00 38.10 3.11
659 664 6.420008 CGATAATAAGTCCCTTTCCGTGTTAG 59.580 42.308 0.00 0.00 0.00 2.34
694 703 0.400381 TAGGCAGGCAGATGGGATGA 60.400 55.000 0.00 0.00 0.00 2.92
863 873 0.752658 AAAAAGGAAGCTTTGGCGCT 59.247 45.000 7.64 0.00 44.37 5.92
951 1862 0.036306 ATCACACCCAAACCCTCGAC 59.964 55.000 0.00 0.00 0.00 4.20
952 1863 1.599797 CACACCCAAACCCTCGACC 60.600 63.158 0.00 0.00 0.00 4.79
953 1864 1.768888 ACACCCAAACCCTCGACCT 60.769 57.895 0.00 0.00 0.00 3.85
954 1865 1.302511 CACCCAAACCCTCGACCTG 60.303 63.158 0.00 0.00 0.00 4.00
955 1866 2.351276 CCCAAACCCTCGACCTGG 59.649 66.667 0.00 0.00 0.00 4.45
956 1867 2.221299 CCCAAACCCTCGACCTGGA 61.221 63.158 0.00 0.00 0.00 3.86
984 1895 0.988145 CCAATCCCCAGCTCCCTACA 60.988 60.000 0.00 0.00 0.00 2.74
998 1909 1.395826 CCTACAGCTCCTCTTCCCCG 61.396 65.000 0.00 0.00 0.00 5.73
1605 2543 2.606519 AGCACCAAGGGCTACCGA 60.607 61.111 0.00 0.00 40.47 4.69
1803 3673 0.253160 TGTACAAGGCCTGGAGGGAT 60.253 55.000 16.25 0.00 37.23 3.85
1824 3694 6.043411 GGATAAGTATGCCGATGAAGGATAC 58.957 44.000 0.00 0.00 0.00 2.24
1837 3707 2.581216 AGGATACGGCGAAGGAGATA 57.419 50.000 16.62 0.00 46.39 1.98
1839 3709 3.432378 AGGATACGGCGAAGGAGATATT 58.568 45.455 16.62 0.00 46.39 1.28
1965 3835 0.613777 AGAAAAAGACGCCGGATCCT 59.386 50.000 5.05 0.00 0.00 3.24
2012 3882 8.964476 TTAAGGTTCCTCTTCATATGTTCATC 57.036 34.615 1.90 0.00 0.00 2.92
2191 4074 6.158598 GCACCTATGTCATTTGTCATTTGTT 58.841 36.000 0.00 0.00 0.00 2.83
2194 4077 8.084073 CACCTATGTCATTTGTCATTTGTTCTT 58.916 33.333 0.00 0.00 0.00 2.52
2207 4090 2.949177 TGTTCTTGTACTGCCCATGT 57.051 45.000 0.00 0.00 0.00 3.21
2220 4103 1.001181 GCCCATGTTTCACAACTGCAT 59.999 47.619 0.00 0.00 33.58 3.96
2221 4104 2.548493 GCCCATGTTTCACAACTGCATT 60.548 45.455 0.00 0.00 33.58 3.56
2222 4105 3.061322 CCCATGTTTCACAACTGCATTG 58.939 45.455 7.16 7.16 44.60 2.82
2234 4117 4.001248 GCATTGGCAGCTACCACA 57.999 55.556 4.73 0.00 40.19 4.17
2246 4129 2.110011 AGCTACCACACCCCTTTTTGAT 59.890 45.455 0.00 0.00 0.00 2.57
2247 4130 2.897326 GCTACCACACCCCTTTTTGATT 59.103 45.455 0.00 0.00 0.00 2.57
2270 4153 2.029918 GGGTGCATTCTGTCCTTTTCAC 60.030 50.000 0.00 0.00 0.00 3.18
2278 4161 4.301072 TCTGTCCTTTTCACCCTTATGG 57.699 45.455 0.00 0.00 41.37 2.74
2281 4164 3.017442 GTCCTTTTCACCCTTATGGCTC 58.983 50.000 0.00 0.00 37.83 4.70
2303 4186 4.832266 TCATGCAAGTTCCAAATACCTGTT 59.168 37.500 0.00 0.00 0.00 3.16
2305 4188 5.606348 TGCAAGTTCCAAATACCTGTTTT 57.394 34.783 0.00 0.00 0.00 2.43
2313 4196 3.059166 CAAATACCTGTTTTGGCACTGC 58.941 45.455 0.00 0.00 31.82 4.40
2349 4232 4.178540 GTTCCAAATCTCCATTGCACATG 58.821 43.478 0.00 0.00 0.00 3.21
2363 4246 4.123497 TGCACATGCTAGAACTTACGAT 57.877 40.909 5.31 0.00 42.66 3.73
2411 4294 1.253100 TTCCAATTCCCACGCTTTCC 58.747 50.000 0.00 0.00 0.00 3.13
2446 4329 2.096119 GCGTTTGGTTTGCATACTACGT 60.096 45.455 20.70 0.00 0.00 3.57
2451 4334 3.592059 TGGTTTGCATACTACGTCTTCC 58.408 45.455 7.25 0.00 0.00 3.46
2467 4350 4.142534 CGTCTTCCGTAGTAGTGATTTCCA 60.143 45.833 0.00 0.00 0.00 3.53
2479 4362 2.986479 GTGATTTCCAATGTGCGGTTTC 59.014 45.455 0.00 0.00 0.00 2.78
2522 4405 2.093869 CGGAAGGTGATTAGGAAACCGA 60.094 50.000 0.00 0.00 40.16 4.69
2551 4434 3.426426 CCGAACGAACCAAACAAAGTCAA 60.426 43.478 0.00 0.00 0.00 3.18
2610 4494 7.147514 ACCTATACCGAAACCCATTACATTACA 60.148 37.037 0.00 0.00 0.00 2.41
2626 4510 5.018809 ACATTACATGAGCAGGAACCAAAT 58.981 37.500 0.00 0.00 0.00 2.32
2699 4583 8.725256 AGATAGTCACCTAGTCAACCTAATAGA 58.275 37.037 0.00 0.00 0.00 1.98
2821 4709 4.987408 TCAAGTGGCATATGTCAAATGG 57.013 40.909 12.49 1.59 0.00 3.16
2827 4715 4.595762 GGCATATGTCAAATGGCATCTT 57.404 40.909 3.37 0.00 46.21 2.40
3031 4919 4.472108 CCACTACTTACCACCCCTTCATAA 59.528 45.833 0.00 0.00 0.00 1.90
3069 4957 5.749596 TTTTCCGGCACATCATAGTTATG 57.250 39.130 0.00 0.00 35.04 1.90
3078 4966 3.809832 ACATCATAGTTATGCTGGTTCGC 59.190 43.478 7.61 0.00 34.93 4.70
3105 4993 3.870274 TCTGCACATTCCTGATTCTCAG 58.130 45.455 0.00 0.00 43.91 3.35
3137 5025 4.704540 TGTCTTTGTTAGCCCATTGGTATG 59.295 41.667 1.20 0.00 0.00 2.39
3138 5026 4.947388 GTCTTTGTTAGCCCATTGGTATGA 59.053 41.667 1.20 0.00 33.37 2.15
3149 5037 5.594926 CCCATTGGTATGAGAATTCAAAGC 58.405 41.667 8.44 0.40 36.78 3.51
3179 5067 6.031471 ACGTTGTGGTTAATTTCTTGTTCAC 58.969 36.000 0.00 0.00 0.00 3.18
3286 5174 9.275572 ACAAGGATTTAGTTACCCTATTGTAGA 57.724 33.333 0.00 0.00 27.40 2.59
3289 5177 9.670442 AGGATTTAGTTACCCTATTGTAGATCA 57.330 33.333 0.00 0.00 0.00 2.92
3336 5231 5.344743 ACATATACAGTCAACAGACCCTG 57.655 43.478 0.00 0.00 37.52 4.45
3440 5340 6.013725 TGCTTCCAACTTCTCCAAACTCTATA 60.014 38.462 0.00 0.00 0.00 1.31
3602 5502 1.521010 CTCACTGCCTGATGAGCCG 60.521 63.158 0.00 0.00 36.22 5.52
3647 5547 1.886542 GGGCCTGATTTCACGTTCTTT 59.113 47.619 0.84 0.00 0.00 2.52
3695 5595 3.197790 CGGCCAATGAGCGAGGTG 61.198 66.667 2.24 0.00 0.00 4.00
3722 5622 2.877168 CCAGGCATATGAGCTGAAGAAC 59.123 50.000 6.97 0.00 34.17 3.01
3800 5700 7.144722 TGCTGTTTTCATTATTCAGTCGAAT 57.855 32.000 0.00 0.00 44.24 3.34
3930 5830 6.294176 GCTGGTTTCTTGATTATTATGGCGAT 60.294 38.462 0.00 0.00 0.00 4.58
4115 6015 7.974675 AGTTATGAACATACCGATTTGTGAAG 58.025 34.615 0.00 0.00 0.00 3.02
4118 6018 6.480524 TGAACATACCGATTTGTGAAGAAG 57.519 37.500 0.00 0.00 0.00 2.85
4247 6149 1.949525 GCAAGCAGTTTTGTCTCTCCA 59.050 47.619 0.00 0.00 0.00 3.86
4356 6421 6.050432 AGTTGCATTTATCGTATCCCGTTTA 58.950 36.000 0.00 0.00 37.94 2.01
4447 6512 3.866582 GGATGAGCCCGGGAGTGG 61.867 72.222 29.31 0.00 0.00 4.00
4521 6587 1.881973 TGGTGAAAGATGCTTGAGTGC 59.118 47.619 0.00 0.00 0.00 4.40
4525 6591 1.532868 GAAAGATGCTTGAGTGCGTGT 59.467 47.619 0.00 0.00 35.36 4.49
4546 6612 5.176223 GTGTTGTTCATGCCAAATTTCAGAG 59.824 40.000 0.00 0.00 0.00 3.35
4570 6636 7.947282 AGTATTTGGACATCTAAGTAGCTCTC 58.053 38.462 0.00 0.00 0.00 3.20
4571 6637 6.798427 ATTTGGACATCTAAGTAGCTCTCA 57.202 37.500 0.00 0.00 0.00 3.27
4577 6643 6.232581 ACATCTAAGTAGCTCTCAGCAAAT 57.767 37.500 0.00 0.00 45.56 2.32
4585 6651 6.648192 AGTAGCTCTCAGCAAATAAGACAAT 58.352 36.000 0.00 0.00 45.56 2.71
4607 6673 5.503662 TTTCGGGGTCTGAAAAAGTTTAC 57.496 39.130 0.00 0.00 32.70 2.01
4616 6682 7.916977 GGGTCTGAAAAAGTTTACGTTTTGTAT 59.083 33.333 10.47 0.00 37.59 2.29
4637 6703 7.335627 TGTATTATTCGGACCTGAATTTGTCT 58.664 34.615 14.10 0.00 39.27 3.41
4638 6704 7.827236 TGTATTATTCGGACCTGAATTTGTCTT 59.173 33.333 14.10 0.00 39.27 3.01
4639 6705 7.703058 ATTATTCGGACCTGAATTTGTCTTT 57.297 32.000 14.10 0.00 39.27 2.52
4640 6706 7.519032 TTATTCGGACCTGAATTTGTCTTTT 57.481 32.000 14.10 0.00 39.27 2.27
4641 6707 5.845391 TTCGGACCTGAATTTGTCTTTTT 57.155 34.783 0.00 0.00 0.00 1.94
4672 6738 3.559242 GCTACTCAGATGTCCAAATGCTC 59.441 47.826 0.00 0.00 0.00 4.26
4674 6740 5.452496 GCTACTCAGATGTCCAAATGCTCTA 60.452 44.000 0.00 0.00 0.00 2.43
4689 6755 3.896122 TGCTCTAAAATTTGGCACGAAC 58.104 40.909 0.00 0.00 0.00 3.95
4701 6767 1.502231 GCACGAACATCACACACTCT 58.498 50.000 0.00 0.00 0.00 3.24
4709 6775 4.383850 ACATCACACACTCTAGCATCTC 57.616 45.455 0.00 0.00 0.00 2.75
4723 6789 4.090761 AGCATCTCTCACCACAAAAAGA 57.909 40.909 0.00 0.00 0.00 2.52
4728 6794 6.459298 GCATCTCTCACCACAAAAAGATATGG 60.459 42.308 0.00 0.00 38.26 2.74
4729 6795 6.373005 TCTCTCACCACAAAAAGATATGGA 57.627 37.500 0.00 0.00 36.04 3.41
4730 6796 6.778821 TCTCTCACCACAAAAAGATATGGAA 58.221 36.000 0.00 0.00 36.04 3.53
4731 6797 7.230747 TCTCTCACCACAAAAAGATATGGAAA 58.769 34.615 0.00 0.00 36.04 3.13
4732 6798 7.723616 TCTCTCACCACAAAAAGATATGGAAAA 59.276 33.333 0.00 0.00 36.04 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.024579 GCAGTACCAATGGACACCGG 61.025 60.000 6.16 0.00 0.00 5.28
165 169 0.716108 CACATTCGAGCTCGGACAAC 59.284 55.000 33.98 0.00 40.29 3.32
199 203 0.535102 ACCAGCAGTAGCACACAACC 60.535 55.000 0.00 0.00 45.49 3.77
525 530 9.571810 CAAAACTGCAATATTTTAGCATGTAGA 57.428 29.630 0.00 0.00 37.68 2.59
544 549 7.042187 TGCAAAAACCATAGTATTGCAAAACTG 60.042 33.333 1.71 0.00 46.98 3.16
603 608 3.951775 TTGGATGCCACGCTTATTTTT 57.048 38.095 0.00 0.00 30.78 1.94
604 609 3.489059 CGATTGGATGCCACGCTTATTTT 60.489 43.478 0.00 0.00 30.78 1.82
605 610 2.033299 CGATTGGATGCCACGCTTATTT 59.967 45.455 0.00 0.00 30.78 1.40
606 611 1.603802 CGATTGGATGCCACGCTTATT 59.396 47.619 0.00 0.00 30.78 1.40
607 612 1.229428 CGATTGGATGCCACGCTTAT 58.771 50.000 0.00 0.00 30.78 1.73
608 613 1.436195 GCGATTGGATGCCACGCTTA 61.436 55.000 12.41 0.00 42.87 3.09
609 614 2.764314 GCGATTGGATGCCACGCTT 61.764 57.895 12.41 0.00 42.87 4.68
610 615 3.204827 GCGATTGGATGCCACGCT 61.205 61.111 12.41 0.00 42.87 5.07
619 624 1.730451 TATCGAGTGCGGCGATTGGA 61.730 55.000 12.98 1.60 45.29 3.53
621 626 1.139989 ATTATCGAGTGCGGCGATTG 58.860 50.000 12.98 0.00 45.29 2.67
628 633 3.644884 AGGGACTTATTATCGAGTGCG 57.355 47.619 0.00 0.00 35.37 5.34
650 655 6.040616 ACTCTCTCTTTTCTTTCTAACACGGA 59.959 38.462 0.00 0.00 0.00 4.69
659 664 5.175127 CCTGCCTACTCTCTCTTTTCTTTC 58.825 45.833 0.00 0.00 0.00 2.62
711 720 2.571212 CACAGGCACAAACAAGTCCTA 58.429 47.619 0.00 0.00 0.00 2.94
715 724 1.312371 ACGCACAGGCACAAACAAGT 61.312 50.000 0.00 0.00 41.24 3.16
951 1862 3.350031 ATTGGGAAGCGGCTCCAGG 62.350 63.158 1.45 0.00 37.20 4.45
952 1863 1.821332 GATTGGGAAGCGGCTCCAG 60.821 63.158 1.45 0.00 37.20 3.86
953 1864 2.272146 GATTGGGAAGCGGCTCCA 59.728 61.111 1.45 4.36 37.20 3.86
954 1865 2.517166 GGATTGGGAAGCGGCTCC 60.517 66.667 1.45 6.44 34.41 4.70
955 1866 2.517166 GGGATTGGGAAGCGGCTC 60.517 66.667 1.45 0.00 0.00 4.70
956 1867 4.129148 GGGGATTGGGAAGCGGCT 62.129 66.667 0.00 0.00 0.00 5.52
984 1895 1.764054 CATCCGGGGAAGAGGAGCT 60.764 63.158 0.00 0.00 40.26 4.09
1512 2450 1.123861 AGAGGAGCACAGGCAGTTCA 61.124 55.000 0.00 0.00 44.61 3.18
1605 2543 0.742990 CACGGGTGGCACGTATCATT 60.743 55.000 12.17 0.00 43.58 2.57
1803 3673 4.082408 CCGTATCCTTCATCGGCATACTTA 60.082 45.833 0.00 0.00 36.68 2.24
1824 3694 1.337260 CCCAGAATATCTCCTTCGCCG 60.337 57.143 0.00 0.00 0.00 6.46
1827 3697 3.323403 AGAAGCCCAGAATATCTCCTTCG 59.677 47.826 0.00 0.00 32.72 3.79
1837 3707 5.435291 CAGAGAAATGTAGAAGCCCAGAAT 58.565 41.667 0.00 0.00 0.00 2.40
1839 3709 3.369892 GCAGAGAAATGTAGAAGCCCAGA 60.370 47.826 0.00 0.00 0.00 3.86
1914 3784 1.276989 CCTTGTGCATGGAAAGGCATT 59.723 47.619 12.65 0.00 42.75 3.56
1965 3835 5.825593 AGAAAGATTACTCACCAGGAACA 57.174 39.130 0.00 0.00 0.00 3.18
2012 3882 5.450965 CCATTCCTGCAGTTTAGCATAAAGG 60.451 44.000 13.81 0.00 44.68 3.11
2077 3953 8.849168 CAAGTAGCCCATATATTCACATTGAAA 58.151 33.333 0.00 0.00 40.12 2.69
2080 3956 7.984422 TCAAGTAGCCCATATATTCACATTG 57.016 36.000 0.00 0.00 0.00 2.82
2168 4051 7.596494 AGAACAAATGACAAATGACATAGGTG 58.404 34.615 0.00 2.11 30.75 4.00
2175 4058 7.096477 GCAGTACAAGAACAAATGACAAATGAC 60.096 37.037 0.00 0.00 0.00 3.06
2191 4074 3.146066 GTGAAACATGGGCAGTACAAGA 58.854 45.455 0.00 0.00 36.32 3.02
2194 4077 2.647683 TGTGAAACATGGGCAGTACA 57.352 45.000 0.00 0.00 45.67 2.90
2220 4103 2.434331 GGGTGTGGTAGCTGCCAA 59.566 61.111 26.24 12.89 40.68 4.52
2221 4104 3.646715 GGGGTGTGGTAGCTGCCA 61.647 66.667 20.78 20.78 35.93 4.92
2222 4105 2.426305 AAAGGGGTGTGGTAGCTGCC 62.426 60.000 14.87 14.87 0.00 4.85
2231 4114 3.124578 CCCAAATCAAAAAGGGGTGTG 57.875 47.619 0.00 0.00 37.66 3.82
2246 4129 2.380064 AAGGACAGAATGCACCCAAA 57.620 45.000 0.00 0.00 42.53 3.28
2247 4130 2.380064 AAAGGACAGAATGCACCCAA 57.620 45.000 0.00 0.00 42.53 4.12
2270 4153 2.062971 ACTTGCATGAGCCATAAGGG 57.937 50.000 6.60 0.00 41.13 3.95
2278 4161 3.445096 AGGTATTTGGAACTTGCATGAGC 59.555 43.478 6.60 0.00 42.57 4.26
2281 4164 4.789012 ACAGGTATTTGGAACTTGCATG 57.211 40.909 0.00 0.00 0.00 4.06
2303 4186 5.236263 CACATATAAGTATCGCAGTGCCAAA 59.764 40.000 10.11 0.00 0.00 3.28
2305 4188 4.202212 ACACATATAAGTATCGCAGTGCCA 60.202 41.667 10.11 0.00 0.00 4.92
2313 4196 8.926710 GGAGATTTGGAACACATATAAGTATCG 58.073 37.037 0.00 0.00 39.29 2.92
2349 4232 4.689345 ACCAAACACATCGTAAGTTCTAGC 59.311 41.667 0.00 0.00 39.48 3.42
2363 4246 1.025812 AATTCGCCGAACCAAACACA 58.974 45.000 0.00 0.00 0.00 3.72
2411 4294 0.238289 AAACGCATTCTGCACTTCCG 59.762 50.000 0.00 0.00 45.36 4.30
2446 4329 5.988310 TTGGAAATCACTACTACGGAAGA 57.012 39.130 0.00 0.00 0.00 2.87
2451 4334 4.259810 CGCACATTGGAAATCACTACTACG 60.260 45.833 0.00 0.00 0.00 3.51
2459 4342 2.351253 CGAAACCGCACATTGGAAATCA 60.351 45.455 0.00 0.00 0.00 2.57
2479 4362 1.003972 TCAGCTTGTTTCGACTTTGCG 60.004 47.619 0.00 0.00 0.00 4.85
2493 4376 0.326264 AATCACCTTCCGCTCAGCTT 59.674 50.000 0.00 0.00 0.00 3.74
2522 4405 0.178533 TTGGTTCGTTCGGTCCTGTT 59.821 50.000 0.00 0.00 0.00 3.16
2578 4461 3.118665 TGGGTTTCGGTATAGGTAAGTGC 60.119 47.826 0.00 0.00 0.00 4.40
2610 4494 0.813184 CGCATTTGGTTCCTGCTCAT 59.187 50.000 0.00 0.00 33.75 2.90
2626 4510 5.050023 TGAGTGAAATGAAATTAACGACGCA 60.050 36.000 0.00 0.00 33.67 5.24
2811 4695 6.324819 CGTTTTAGAAGATGCCATTTGACAT 58.675 36.000 0.00 0.00 0.00 3.06
2821 4709 2.160417 ACTGCTGCGTTTTAGAAGATGC 59.840 45.455 0.00 0.00 0.00 3.91
2894 4782 8.110271 TGAAACAATATACACCATCCCTAACAA 58.890 33.333 0.00 0.00 0.00 2.83
2898 4786 7.684317 TCTGAAACAATATACACCATCCCTA 57.316 36.000 0.00 0.00 0.00 3.53
2900 4788 9.167311 GATATCTGAAACAATATACACCATCCC 57.833 37.037 0.00 0.00 0.00 3.85
2939 4827 1.167851 CGTGGAACATGGACATTGCT 58.832 50.000 0.00 0.00 44.52 3.91
2940 4828 3.700577 CGTGGAACATGGACATTGC 57.299 52.632 0.00 0.00 44.52 3.56
3016 4904 6.617784 TGATACATTCTTATGAAGGGGTGGTA 59.382 38.462 7.76 0.00 38.19 3.25
3031 4919 4.818546 CCGGAAAAGCAGATGATACATTCT 59.181 41.667 0.00 0.00 0.00 2.40
3069 4957 1.208614 CAGAAGCAAGCGAACCAGC 59.791 57.895 0.00 0.00 37.41 4.85
3078 4966 8.538492 GAGAATCAGGAATGTGCAGAAGCAAG 62.538 46.154 0.00 0.00 44.68 4.01
3105 4993 4.546570 GGCTAACAAAGACATGGTTTGAC 58.453 43.478 22.68 6.57 38.13 3.18
3137 5025 6.521133 CACAACGTCATAAGCTTTGAATTCTC 59.479 38.462 3.20 0.00 0.00 2.87
3138 5026 6.373779 CACAACGTCATAAGCTTTGAATTCT 58.626 36.000 3.20 0.00 0.00 2.40
3149 5037 8.073768 ACAAGAAATTAACCACAACGTCATAAG 58.926 33.333 0.00 0.00 0.00 1.73
3179 5067 8.021955 TGATAGACTAGATATGCAAAAATGCG 57.978 34.615 0.00 0.00 37.69 4.73
3289 5177 9.131791 GTACTGAACACCCCAATATTGAATATT 57.868 33.333 17.23 4.65 35.92 1.28
3292 5187 6.489603 TGTACTGAACACCCCAATATTGAAT 58.510 36.000 17.23 0.00 31.43 2.57
3300 5195 5.486063 ACTGTATATGTACTGAACACCCCAA 59.514 40.000 12.41 0.00 42.09 4.12
3344 5239 3.007398 TGCAAAAACACCAAGGAAACACT 59.993 39.130 0.00 0.00 0.00 3.55
3440 5340 1.705186 ACAAGACAACAGGCCCTATGT 59.295 47.619 0.00 0.88 0.00 2.29
3602 5502 4.137543 AGTTGAACCTGACCTCACAATTC 58.862 43.478 0.00 0.00 0.00 2.17
3722 5622 1.089920 CATTTTCAGCAGGTCCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
3793 5693 2.883386 GACTCCACGGGTATATTCGACT 59.117 50.000 4.98 0.00 0.00 4.18
3930 5830 7.757526 ACGCAATAAAATATGTTCAGTAAGCA 58.242 30.769 0.00 0.00 0.00 3.91
4247 6149 5.479124 ACGTGGAGAACTAAGTGGTAAAT 57.521 39.130 0.00 0.00 0.00 1.40
4356 6421 2.039084 AGGAGCTCCGTTGAACAAGATT 59.961 45.455 26.95 1.42 42.08 2.40
4503 6569 1.532868 ACGCACTCAAGCATCTTTCAC 59.467 47.619 0.00 0.00 0.00 3.18
4505 6571 1.532868 ACACGCACTCAAGCATCTTTC 59.467 47.619 0.00 0.00 0.00 2.62
4510 6576 1.002468 GAACAACACGCACTCAAGCAT 60.002 47.619 0.00 0.00 0.00 3.79
4521 6587 3.801050 TGAAATTTGGCATGAACAACACG 59.199 39.130 0.00 0.00 0.00 4.49
4525 6591 5.534207 ACTCTGAAATTTGGCATGAACAA 57.466 34.783 0.00 0.00 0.00 2.83
4546 6612 7.717568 TGAGAGCTACTTAGATGTCCAAATAC 58.282 38.462 0.00 0.00 31.79 1.89
4558 6624 7.261325 TGTCTTATTTGCTGAGAGCTACTTAG 58.739 38.462 0.00 0.00 42.97 2.18
4570 6636 4.082245 ACCCCGAAATTGTCTTATTTGCTG 60.082 41.667 0.00 0.00 0.00 4.41
4571 6637 4.086457 ACCCCGAAATTGTCTTATTTGCT 58.914 39.130 0.00 0.00 0.00 3.91
4577 6643 4.627284 TTCAGACCCCGAAATTGTCTTA 57.373 40.909 0.00 0.00 37.25 2.10
4585 6651 4.035441 CGTAAACTTTTTCAGACCCCGAAA 59.965 41.667 0.00 0.00 0.00 3.46
4607 6673 6.411630 TTCAGGTCCGAATAATACAAAACG 57.588 37.500 0.00 0.00 0.00 3.60
4616 6682 7.519032 AAAAGACAAATTCAGGTCCGAATAA 57.481 32.000 8.69 0.00 34.49 1.40
4665 6731 5.132897 TCGTGCCAAATTTTAGAGCATTT 57.867 34.783 5.54 0.00 35.62 2.32
4672 6738 5.116983 GTGTGATGTTCGTGCCAAATTTTAG 59.883 40.000 0.00 0.00 0.00 1.85
4674 6740 3.801594 GTGTGATGTTCGTGCCAAATTTT 59.198 39.130 0.00 0.00 0.00 1.82
4689 6755 4.097589 TGAGAGATGCTAGAGTGTGTGATG 59.902 45.833 0.00 0.00 0.00 3.07
4701 6767 5.227569 TCTTTTTGTGGTGAGAGATGCTA 57.772 39.130 0.00 0.00 0.00 3.49
4709 6775 9.492973 AAATTTTCCATATCTTTTTGTGGTGAG 57.507 29.630 0.00 0.00 33.47 3.51


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

AutoCloner maintained by Alex Coulton.