Multiple sequence alignment - TraesCS2A01G404900

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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 TraesCS2A01G404900 chr2A 100.000 5862 0 0 1 5862 660509298 660515159 0.000000e+00 10826.0
1 TraesCS2A01G404900 chr2D 94.047 4485 145 28 4 4402 516703865 516708313 0.000000e+00 6691.0
2 TraesCS2A01G404900 chr2D 92.084 1478 63 24 4401 5858 516708475 516709918 0.000000e+00 2032.0
3 TraesCS2A01G404900 chr2D 91.129 124 9 1 5688 5811 516811858 516811979 3.630000e-37 167.0
4 TraesCS2A01G404900 chr2B 94.393 2907 103 24 2853 5724 608447044 608449925 0.000000e+00 4410.0
5 TraesCS2A01G404900 chr2B 92.284 2307 106 26 382 2649 608444777 608447050 0.000000e+00 3208.0
6 TraesCS2A01G404900 chr2B 90.380 395 12 5 1 378 608444350 608444735 4.080000e-136 496.0
7 TraesCS2A01G404900 chr2B 94.595 185 7 2 5676 5858 608449925 608450108 3.460000e-72 283.0
8 TraesCS2A01G404900 chr3B 86.777 242 24 5 3737 3976 778446689 778446454 4.500000e-66 263.0
9 TraesCS2A01G404900 chr6B 90.385 52 4 1 2871 2921 451927500 451927449 3.790000e-07 67.6


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 TraesCS2A01G404900 chr2A 660509298 660515159 5861 False 10826.00 10826 100.0000 1 5862 1 chr2A.!!$F1 5861
1 TraesCS2A01G404900 chr2D 516703865 516709918 6053 False 4361.50 6691 93.0655 4 5858 2 chr2D.!!$F2 5854
2 TraesCS2A01G404900 chr2B 608444350 608450108 5758 False 2099.25 4410 92.9130 1 5858 4 chr2B.!!$F1 5857

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
943 1009 0.251297 TGCAGGGAAGGTGATGTTGG 60.251 55.000 0.00 0.0 0.00 3.77 F
2178 2270 0.176680 AGTAGCAACAGCAGATCCCG 59.823 55.000 0.00 0.0 0.00 5.14 F
3137 3248 0.753262 GGAAGGCGGCTCAGATTCTA 59.247 55.000 13.70 0.0 0.00 2.10 F
3160 3271 1.276989 CAACCCCTTTTGCATCATGCT 59.723 47.619 11.84 0.0 45.31 3.79 F
4131 4253 0.247460 CATCGTGTCTTCCTCCAGCA 59.753 55.000 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2748 0.175760 GCAGCTACTGGTCGGATCAA 59.824 55.000 0.00 0.0 31.21 2.57 R
4110 4232 0.534412 CTGGAGGAAGACACGATGCT 59.466 55.000 0.00 0.0 0.00 3.79 R
4131 4253 1.002257 TGACGCAATGCCCATCTGT 60.002 52.632 0.00 0.0 0.00 3.41 R
4344 4466 1.067212 ACAAAGTCGCGAACACTCTCT 59.933 47.619 12.06 0.0 0.00 3.10 R
5555 5883 1.014564 GCTTCTCGCCTTTGCTACGT 61.015 55.000 0.00 0.0 34.43 3.57 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
199 218 4.184079 TCTCTAAGACAGCCGGTTAAAC 57.816 45.455 1.90 0.00 0.00 2.01
200 219 3.056322 TCTCTAAGACAGCCGGTTAAACC 60.056 47.826 1.90 0.00 34.05 3.27
201 220 2.901839 TCTAAGACAGCCGGTTAAACCT 59.098 45.455 1.90 0.00 35.66 3.50
425 483 0.886563 AATCCTCTGTGCAAGCAAGC 59.113 50.000 0.00 0.00 0.00 4.01
428 486 1.081376 CTCTGTGCAAGCAAGCTGC 60.081 57.895 0.00 2.56 45.46 5.25
548 606 2.415512 GCCTGAATCGCGTACTCTTTTT 59.584 45.455 5.77 0.00 0.00 1.94
585 643 2.156917 GTTGGTACTTGGGTAGGTTGC 58.843 52.381 0.00 0.00 0.00 4.17
613 671 1.821136 CTCTTTCATTGCCCCAGGTTC 59.179 52.381 0.00 0.00 0.00 3.62
617 675 2.037847 ATTGCCCCAGGTTCTGCC 59.962 61.111 0.00 0.00 37.58 4.85
641 699 1.228245 TGGCCTTGTTGCTCTCACC 60.228 57.895 3.32 0.00 0.00 4.02
646 704 2.693069 CCTTGTTGCTCTCACCTGTAG 58.307 52.381 0.00 0.00 0.00 2.74
647 705 2.072298 CTTGTTGCTCTCACCTGTAGC 58.928 52.381 0.00 0.00 36.77 3.58
648 706 1.342074 TGTTGCTCTCACCTGTAGCT 58.658 50.000 0.00 0.00 37.16 3.32
650 708 1.001406 GTTGCTCTCACCTGTAGCTGT 59.999 52.381 0.00 0.00 37.16 4.40
652 710 1.694150 TGCTCTCACCTGTAGCTGTTT 59.306 47.619 0.00 0.00 37.16 2.83
653 711 2.072298 GCTCTCACCTGTAGCTGTTTG 58.928 52.381 0.00 0.00 33.40 2.93
654 712 2.072298 CTCTCACCTGTAGCTGTTTGC 58.928 52.381 0.00 0.00 43.29 3.68
682 747 6.147821 CCATGTTCTATTGAAACGAACTCAGT 59.852 38.462 10.04 0.00 38.23 3.41
683 748 7.330946 CCATGTTCTATTGAAACGAACTCAGTA 59.669 37.037 10.04 0.00 38.23 2.74
684 749 7.869016 TGTTCTATTGAAACGAACTCAGTAG 57.131 36.000 10.04 0.00 38.23 2.57
685 750 7.431249 TGTTCTATTGAAACGAACTCAGTAGT 58.569 34.615 10.04 0.00 38.23 2.73
693 758 6.892310 AAACGAACTCAGTAGTACGTTTTT 57.108 33.333 14.48 0.95 46.39 1.94
822 888 5.983540 AGTAACCATCAAGTGAGGATTCTC 58.016 41.667 0.00 0.00 40.36 2.87
823 889 4.916041 AACCATCAAGTGAGGATTCTCA 57.084 40.909 0.00 0.00 46.81 3.27
853 919 5.817296 TGATCTGATTCGTACTGGAATTTGG 59.183 40.000 0.00 0.00 36.79 3.28
868 934 2.131776 TTTGGTTTGTCAGTCGGGTT 57.868 45.000 0.00 0.00 0.00 4.11
869 935 1.670791 TTGGTTTGTCAGTCGGGTTC 58.329 50.000 0.00 0.00 0.00 3.62
875 941 1.254026 TGTCAGTCGGGTTCTGTAGG 58.746 55.000 0.00 0.00 34.86 3.18
943 1009 0.251297 TGCAGGGAAGGTGATGTTGG 60.251 55.000 0.00 0.00 0.00 3.77
958 1024 1.160137 GTTGGTTGATCTTGAGCGCT 58.840 50.000 11.27 11.27 0.00 5.92
985 1051 2.297701 AGTGCACAGGTTTCGAACAAT 58.702 42.857 21.04 0.00 0.00 2.71
1030 1096 1.153005 CTTGAGCTCCTCATGCCCC 60.153 63.158 12.15 0.00 40.39 5.80
1188 1254 1.689984 TGCTGCACCTTGTCATGAAA 58.310 45.000 0.00 0.00 0.00 2.69
1302 1393 2.094338 AGTCGGTAAAACCTCTAAGCGG 60.094 50.000 0.00 0.00 35.66 5.52
1325 1416 8.531530 GCGGTTTCTTTATGTGCTAAATAATTG 58.468 33.333 0.00 0.00 0.00 2.32
1349 1440 7.420002 TGCAGTGATATGTTTAATGATCTTGC 58.580 34.615 0.00 0.00 33.79 4.01
1520 1611 4.324797 GGCATAACCCCTACTTTGTTACCT 60.325 45.833 0.00 0.00 0.00 3.08
1530 1621 1.801309 TTTGTTACCTTGCCGCAGCC 61.801 55.000 0.00 0.00 38.69 4.85
1606 1697 8.853126 GGTTTACCCTTTTCTACATTTAAGTGT 58.147 33.333 8.77 8.77 36.13 3.55
1631 1722 7.510549 TGATGCTAAGCTGTTTCTTTACTTT 57.489 32.000 0.00 0.00 0.00 2.66
1665 1756 2.665649 ACTGTCGGATAAACGATGCA 57.334 45.000 0.00 0.00 45.47 3.96
1700 1791 0.395311 CCTGTGGAATGGATGCTGCT 60.395 55.000 0.00 0.00 0.00 4.24
1703 1794 0.179119 GTGGAATGGATGCTGCTTGC 60.179 55.000 0.00 0.00 43.25 4.01
2106 2198 1.704628 TGGTCAGCTTTCTGGGATTGA 59.295 47.619 0.00 0.00 40.69 2.57
2176 2268 1.399791 GCAAGTAGCAACAGCAGATCC 59.600 52.381 0.00 0.00 44.79 3.36
2178 2270 0.176680 AGTAGCAACAGCAGATCCCG 59.823 55.000 0.00 0.00 0.00 5.14
2235 2328 2.427506 GGATCTTGAAGAAACGGTGCT 58.572 47.619 0.00 0.00 0.00 4.40
2380 2475 6.263344 CAGCAATTCACTTGATCCTACAATG 58.737 40.000 0.00 0.00 36.97 2.82
2527 2623 6.790232 TCCTCTTTTCCTGAAACAAATGTT 57.210 33.333 0.00 0.00 40.50 2.71
2528 2624 7.889873 TCCTCTTTTCCTGAAACAAATGTTA 57.110 32.000 0.00 0.00 37.25 2.41
2529 2625 7.712797 TCCTCTTTTCCTGAAACAAATGTTAC 58.287 34.615 0.00 0.00 37.25 2.50
2686 2782 1.482182 AGCTGCCACATCGATTCACTA 59.518 47.619 0.00 0.00 0.00 2.74
2753 2849 5.721000 AGCAATTCCCTGGAAATGATGTAAA 59.279 36.000 16.36 0.00 37.23 2.01
2754 2850 5.812127 GCAATTCCCTGGAAATGATGTAAAC 59.188 40.000 16.36 0.00 37.23 2.01
2756 2852 7.558604 CAATTCCCTGGAAATGATGTAAACAT 58.441 34.615 8.04 0.00 37.23 2.71
2757 2853 6.528537 TTCCCTGGAAATGATGTAAACATG 57.471 37.500 0.00 0.00 36.57 3.21
2778 2888 7.836842 ACATGTATCGATTACACCATATGCTA 58.163 34.615 1.71 0.00 43.46 3.49
2823 2933 8.297426 GCCTTACAAGACTTAAAAGTAGCATTT 58.703 33.333 0.00 0.00 39.88 2.32
2864 2974 1.834188 ACTTTGGATGTTAAGGCCCG 58.166 50.000 0.00 0.00 0.00 6.13
2943 3054 2.610433 GGCTTATTGGCTTTTGAGTGC 58.390 47.619 0.00 0.00 38.32 4.40
3027 3138 1.601663 GCAATGTAGCGTTTGGTGCAA 60.602 47.619 0.00 0.00 41.49 4.08
3028 3139 2.318578 CAATGTAGCGTTTGGTGCAAG 58.681 47.619 0.00 0.00 41.49 4.01
3075 3186 6.903883 TCTCTTTCTTTACTGTGTGTGTTC 57.096 37.500 0.00 0.00 0.00 3.18
3137 3248 0.753262 GGAAGGCGGCTCAGATTCTA 59.247 55.000 13.70 0.00 0.00 2.10
3160 3271 1.276989 CAACCCCTTTTGCATCATGCT 59.723 47.619 11.84 0.00 45.31 3.79
3285 3396 1.886422 TATGTATGTCCACTGCCCCA 58.114 50.000 0.00 0.00 0.00 4.96
3487 3598 3.391296 TGTAATCTCACAGGGGAATAGGC 59.609 47.826 0.00 0.00 0.00 3.93
3511 3622 4.082787 ACTGTCCACACTTTGAGTTGTTTG 60.083 41.667 0.00 0.00 0.00 2.93
3699 3811 9.296400 GCTGAATTAATTAATTGCTTTTCGGTA 57.704 29.630 24.60 0.00 36.13 4.02
4042 4155 6.154534 GGTATTTATCTTTCCAAGTTGGCCTT 59.845 38.462 17.68 2.84 37.47 4.35
4131 4253 0.247460 CATCGTGTCTTCCTCCAGCA 59.753 55.000 0.00 0.00 0.00 4.41
4196 4318 4.962995 TGCTAAACCCTATGAGCTCTTAGT 59.037 41.667 26.41 15.41 35.89 2.24
4344 4466 7.094508 TGAGAGAAGTGCAACAAACATAAAA 57.905 32.000 0.00 0.00 41.43 1.52
4564 4849 6.552008 TCAGGTGATCCAGGATTTTAAGTTT 58.448 36.000 2.53 0.00 35.89 2.66
4585 4870 0.238289 CTGTTAACCAAGCAGTGCGG 59.762 55.000 10.00 8.56 0.00 5.69
4672 4957 2.046988 TGGGTGAGTGCAGCATCG 60.047 61.111 0.00 0.00 44.15 3.84
4753 5038 1.344438 GGGGTCTTGAAGGGCAAAAAG 59.656 52.381 0.00 0.00 35.74 2.27
4813 5101 0.464452 GGGGAGGTGGTGATAAGACG 59.536 60.000 0.00 0.00 0.00 4.18
4877 5165 7.174080 TGAAGAATTGACGATTTAACCATGTGA 59.826 33.333 0.00 0.00 0.00 3.58
4924 5212 1.507141 CGTGAAACAAGGAAGCGGCT 61.507 55.000 0.00 0.00 35.74 5.52
4957 5245 5.705441 CAGAAATTACTGGTAACCTTCTGCA 59.295 40.000 21.14 0.00 39.18 4.41
4993 5283 2.170738 TGCCTATGCAAGTTCACGC 58.829 52.632 0.00 0.00 46.66 5.34
5086 5376 5.621193 TCTTCTTTCCAAAAGGACTGGTAG 58.379 41.667 0.00 0.00 35.30 3.18
5120 5410 4.930963 TGTTACAACTTCAATTGGTGCTG 58.069 39.130 5.42 3.39 33.63 4.41
5251 5542 4.595762 TCGTTACTGTAAAGAGCTGGTT 57.404 40.909 11.33 0.00 0.00 3.67
5328 5620 6.449635 TGCATGAACTGTTTATTCCATACC 57.550 37.500 0.00 0.00 0.00 2.73
5499 5805 5.941948 GTGTATGCAAGTAACACTTTCCT 57.058 39.130 14.25 0.00 36.03 3.36
5500 5806 6.313744 GTGTATGCAAGTAACACTTTCCTT 57.686 37.500 14.25 0.00 36.03 3.36
5501 5807 6.735130 GTGTATGCAAGTAACACTTTCCTTT 58.265 36.000 14.25 0.00 36.03 3.11
5502 5808 6.856426 GTGTATGCAAGTAACACTTTCCTTTC 59.144 38.462 14.25 0.00 36.03 2.62
5534 5840 9.093970 GTTCTTTTGTGGGGTATTTTATTATGC 57.906 33.333 0.00 0.00 0.00 3.14
5587 5915 2.048127 GAAGCCTCGTCTTGCCGT 60.048 61.111 0.00 0.00 0.00 5.68
5652 5983 3.537206 GAAGCTGGCTGTGGTCGGT 62.537 63.158 0.00 0.00 0.00 4.69
5692 6023 5.045872 GTGATTTGCATGGGCTTATTTCTC 58.954 41.667 0.00 0.00 41.91 2.87
5693 6024 4.710865 TGATTTGCATGGGCTTATTTCTCA 59.289 37.500 0.00 0.00 41.91 3.27
5694 6025 4.454728 TTTGCATGGGCTTATTTCTCAC 57.545 40.909 0.00 0.00 41.91 3.51
5695 6026 3.370840 TGCATGGGCTTATTTCTCACT 57.629 42.857 0.00 0.00 41.91 3.41
5696 6027 4.502105 TGCATGGGCTTATTTCTCACTA 57.498 40.909 0.00 0.00 41.91 2.74
5697 6028 5.052693 TGCATGGGCTTATTTCTCACTAT 57.947 39.130 0.00 0.00 41.91 2.12
5698 6029 4.823442 TGCATGGGCTTATTTCTCACTATG 59.177 41.667 0.00 0.00 41.91 2.23
5699 6030 4.823989 GCATGGGCTTATTTCTCACTATGT 59.176 41.667 0.00 0.00 36.96 2.29
5700 6031 5.278169 GCATGGGCTTATTTCTCACTATGTG 60.278 44.000 0.00 0.00 36.96 3.21
5701 6032 4.780815 TGGGCTTATTTCTCACTATGTGG 58.219 43.478 0.00 0.00 33.87 4.17
5702 6033 3.565902 GGGCTTATTTCTCACTATGTGGC 59.434 47.826 0.00 0.00 33.87 5.01
5703 6034 3.565902 GGCTTATTTCTCACTATGTGGCC 59.434 47.826 0.00 0.00 33.87 5.36
5704 6035 4.455606 GCTTATTTCTCACTATGTGGCCT 58.544 43.478 3.32 0.00 33.87 5.19
5705 6036 4.513318 GCTTATTTCTCACTATGTGGCCTC 59.487 45.833 3.32 0.00 33.87 4.70
5706 6037 5.686124 GCTTATTTCTCACTATGTGGCCTCT 60.686 44.000 3.32 0.00 33.87 3.69
5707 6038 3.616956 TTTCTCACTATGTGGCCTCTG 57.383 47.619 3.32 0.00 33.87 3.35
5708 6039 2.532250 TCTCACTATGTGGCCTCTGA 57.468 50.000 3.32 0.00 33.87 3.27
5767 6165 7.010552 CGAATCCATTTTTACAGTGGAGTAGAG 59.989 40.741 0.00 0.00 44.59 2.43
5769 6167 6.698380 TCCATTTTTACAGTGGAGTAGAGAC 58.302 40.000 0.00 0.00 37.12 3.36
5772 6170 8.258007 CCATTTTTACAGTGGAGTAGAGACATA 58.742 37.037 0.00 0.00 34.94 2.29
5773 6171 9.653287 CATTTTTACAGTGGAGTAGAGACATAA 57.347 33.333 0.00 0.00 0.00 1.90
5813 6211 1.798223 CCACACATCCAACTGTACGTG 59.202 52.381 0.00 0.00 0.00 4.49
5858 6256 4.588899 TCTTGGTCCAATTCATAGGTGTG 58.411 43.478 4.34 0.00 0.00 3.82
5859 6257 3.364460 TGGTCCAATTCATAGGTGTGG 57.636 47.619 0.00 0.00 0.00 4.17
5860 6258 2.024414 GGTCCAATTCATAGGTGTGGC 58.976 52.381 0.00 0.00 0.00 5.01
5861 6259 2.357154 GGTCCAATTCATAGGTGTGGCT 60.357 50.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 218 1.446272 GACGTGGCGGAGAAGAAGG 60.446 63.158 0.00 0.00 0.00 3.46
200 219 0.734253 CTGACGTGGCGGAGAAGAAG 60.734 60.000 0.00 0.00 0.00 2.85
201 220 1.289066 CTGACGTGGCGGAGAAGAA 59.711 57.895 0.00 0.00 0.00 2.52
425 483 0.108615 AATTCGACTCCACGGAGCAG 60.109 55.000 13.16 7.45 45.54 4.24
428 486 0.170561 ACGAATTCGACTCCACGGAG 59.829 55.000 33.05 11.67 44.07 4.63
548 606 2.814919 CCAACAATAACTAACGGCACCA 59.185 45.455 0.00 0.00 0.00 4.17
585 643 0.453390 GCAATGAAAGAGGGCGAAGG 59.547 55.000 0.00 0.00 0.00 3.46
617 675 0.032540 GAGCAACAAGGCCACCAAAG 59.967 55.000 5.01 0.00 0.00 2.77
619 677 0.823356 GAGAGCAACAAGGCCACCAA 60.823 55.000 5.01 0.00 0.00 3.67
622 680 1.518903 GGTGAGAGCAACAAGGCCAC 61.519 60.000 5.01 0.00 0.00 5.01
629 687 1.001293 CAGCTACAGGTGAGAGCAACA 59.999 52.381 2.20 0.00 45.66 3.33
641 699 1.129251 CATGGACGCAAACAGCTACAG 59.871 52.381 0.00 0.00 42.61 2.74
646 704 0.593128 AGAACATGGACGCAAACAGC 59.407 50.000 0.00 0.00 40.87 4.40
647 705 4.154015 TCAATAGAACATGGACGCAAACAG 59.846 41.667 0.00 0.00 0.00 3.16
648 706 4.068599 TCAATAGAACATGGACGCAAACA 58.931 39.130 0.00 0.00 0.00 2.83
650 708 5.457140 GTTTCAATAGAACATGGACGCAAA 58.543 37.500 0.00 0.00 32.39 3.68
652 710 3.124466 CGTTTCAATAGAACATGGACGCA 59.876 43.478 0.00 0.00 32.39 5.24
653 711 3.369756 TCGTTTCAATAGAACATGGACGC 59.630 43.478 0.00 0.00 32.39 5.19
654 712 5.120208 AGTTCGTTTCAATAGAACATGGACG 59.880 40.000 9.71 0.00 44.67 4.79
656 714 6.227522 TGAGTTCGTTTCAATAGAACATGGA 58.772 36.000 9.71 0.00 44.67 3.41
658 716 7.121974 ACTGAGTTCGTTTCAATAGAACATG 57.878 36.000 9.71 0.00 44.67 3.21
659 717 8.088981 ACTACTGAGTTCGTTTCAATAGAACAT 58.911 33.333 9.71 0.00 44.67 2.71
693 758 1.299648 CGACAGCCCCAATCTGGAA 59.700 57.895 0.00 0.00 40.96 3.53
746 812 4.532126 TCTGAACCTGTCACTGATACCAAT 59.468 41.667 0.00 0.00 31.13 3.16
751 817 6.266786 TGTTAGTTCTGAACCTGTCACTGATA 59.733 38.462 16.48 0.00 31.13 2.15
787 853 3.070159 TGATGGTTACTATCTGCAGAGCC 59.930 47.826 22.96 15.71 0.00 4.70
822 888 6.758416 TCCAGTACGAATCAGATCAAATTCTG 59.242 38.462 14.50 11.39 43.70 3.02
823 889 6.878317 TCCAGTACGAATCAGATCAAATTCT 58.122 36.000 14.50 7.41 31.15 2.40
835 901 6.009115 ACAAACCAAATTCCAGTACGAATC 57.991 37.500 0.00 0.00 31.14 2.52
840 906 5.560183 CGACTGACAAACCAAATTCCAGTAC 60.560 44.000 0.00 0.00 34.06 2.73
853 919 1.949465 ACAGAACCCGACTGACAAAC 58.051 50.000 0.00 0.00 38.55 2.93
875 941 1.444212 ACGTCGCAATGGCAAATGC 60.444 52.632 16.12 16.12 41.24 3.56
943 1009 1.800586 TCACAAGCGCTCAAGATCAAC 59.199 47.619 12.06 0.00 0.00 3.18
958 1024 2.805671 CGAAACCTGTGCACTATCACAA 59.194 45.455 19.41 0.00 45.22 3.33
1030 1096 2.916716 GTGTTTTGTATTGCGCCATCAG 59.083 45.455 4.18 0.00 0.00 2.90
1325 1416 7.646314 AGCAAGATCATTAAACATATCACTGC 58.354 34.615 0.00 0.00 33.27 4.40
1349 1440 6.712547 AGAAACATACTGTTCCAAAAGGAGAG 59.287 38.462 0.00 0.00 40.14 3.20
1498 1589 4.851843 AGGTAACAAAGTAGGGGTTATGC 58.148 43.478 0.00 0.00 41.41 3.14
1530 1621 2.036217 TGCAATTCCAGAACCAAAGCTG 59.964 45.455 0.00 0.00 0.00 4.24
1597 1688 6.824305 ACAGCTTAGCATCAACACTTAAAT 57.176 33.333 7.07 0.00 0.00 1.40
1606 1697 7.510549 AAGTAAAGAAACAGCTTAGCATCAA 57.489 32.000 7.07 0.00 0.00 2.57
1665 1756 3.494749 CCACAGGGTTGCATTGTTCAAAT 60.495 43.478 0.00 0.00 0.00 2.32
1682 1773 1.134367 CAAGCAGCATCCATTCCACAG 59.866 52.381 0.00 0.00 0.00 3.66
1700 1791 2.315176 ACAAGGCACTGGTAAATGCAA 58.685 42.857 0.00 0.00 43.49 4.08
1802 1893 2.496899 TCACTCCAGGAAATTCCAGC 57.503 50.000 15.21 0.00 39.61 4.85
2106 2198 1.893808 CTCGCTGTTGCTGGGTGTT 60.894 57.895 0.00 0.00 36.97 3.32
2171 2263 4.547859 GCAGATGTTGCGGGATCT 57.452 55.556 0.00 0.00 44.09 2.75
2205 2298 0.400213 TTCAAGATCCCAGCAACCGT 59.600 50.000 0.00 0.00 0.00 4.83
2235 2328 6.005823 TGAATCAGAAGCAGATCCAAGAAAA 58.994 36.000 0.00 0.00 0.00 2.29
2302 2395 0.337773 TTTTATGGCATCAGGGGGCA 59.662 50.000 1.65 0.00 45.36 5.36
2527 2623 7.561021 TGCATGTGAAAACAAGAAAGTAGTA 57.439 32.000 0.00 0.00 0.00 1.82
2528 2624 6.449635 TGCATGTGAAAACAAGAAAGTAGT 57.550 33.333 0.00 0.00 0.00 2.73
2529 2625 9.462174 TTTATGCATGTGAAAACAAGAAAGTAG 57.538 29.630 10.16 0.00 0.00 2.57
2635 2731 7.593273 GTCGGATCAACAATTAACATTTGACAA 59.407 33.333 0.00 0.00 30.99 3.18
2652 2748 0.175760 GCAGCTACTGGTCGGATCAA 59.824 55.000 0.00 0.00 31.21 2.57
2653 2749 1.676678 GGCAGCTACTGGTCGGATCA 61.677 60.000 0.00 0.00 31.21 2.92
2654 2750 1.068250 GGCAGCTACTGGTCGGATC 59.932 63.158 0.00 0.00 31.21 3.36
2658 2754 0.807667 GATGTGGCAGCTACTGGTCG 60.808 60.000 10.64 0.00 31.21 4.79
2686 2782 4.162690 GCCGAAGCCAGACCCGAT 62.163 66.667 0.00 0.00 0.00 4.18
2694 2790 4.087892 GAGCCAGAGCCGAAGCCA 62.088 66.667 0.00 0.00 41.25 4.75
2733 2829 6.669154 ACATGTTTACATCATTTCCAGGGAAT 59.331 34.615 0.83 0.00 33.61 3.01
2753 2849 6.701340 AGCATATGGTGTAATCGATACATGT 58.299 36.000 6.62 2.69 45.87 3.21
2754 2850 8.702163 TTAGCATATGGTGTAATCGATACATG 57.298 34.615 17.58 0.00 45.87 3.21
2756 2852 8.364894 AGTTTAGCATATGGTGTAATCGATACA 58.635 33.333 17.58 0.86 42.22 2.29
2757 2853 8.758633 AGTTTAGCATATGGTGTAATCGATAC 57.241 34.615 17.58 1.52 34.92 2.24
2778 2888 8.090214 TGTAAGGCATTAACTCGTAAGTAGTTT 58.910 33.333 0.00 0.00 38.23 2.66
2864 2974 3.118665 TGTGCTCCCGGTATTTAGTTACC 60.119 47.826 0.00 0.00 38.63 2.85
2937 3048 4.584638 AACAATAATGGTAGGGCACTCA 57.415 40.909 0.00 0.00 0.00 3.41
2938 3049 4.947388 TCAAACAATAATGGTAGGGCACTC 59.053 41.667 0.00 0.00 0.00 3.51
2939 3050 4.929479 TCAAACAATAATGGTAGGGCACT 58.071 39.130 0.00 0.00 0.00 4.40
2940 3051 5.852282 ATCAAACAATAATGGTAGGGCAC 57.148 39.130 0.00 0.00 0.00 5.01
2941 3052 6.438741 TGAAATCAAACAATAATGGTAGGGCA 59.561 34.615 0.00 0.00 0.00 5.36
2942 3053 6.756542 GTGAAATCAAACAATAATGGTAGGGC 59.243 38.462 0.00 0.00 0.00 5.19
2943 3054 8.066612 AGTGAAATCAAACAATAATGGTAGGG 57.933 34.615 0.00 0.00 0.00 3.53
3027 3138 8.706322 AAATACAGAAAAGGGAATACACAACT 57.294 30.769 0.00 0.00 0.00 3.16
3028 3139 8.793592 AGAAATACAGAAAAGGGAATACACAAC 58.206 33.333 0.00 0.00 0.00 3.32
3160 3271 6.302535 TGGTGTATAATTCCTTTCTCGGAA 57.697 37.500 0.00 0.00 46.37 4.30
3175 3286 5.360649 TCACGGGAAAATGATGGTGTATA 57.639 39.130 0.00 0.00 0.00 1.47
3363 3474 5.930837 AAAGAGATAAGCTAGCTGTGAGT 57.069 39.130 20.16 4.30 0.00 3.41
3466 3577 3.391296 TGCCTATTCCCCTGTGAGATTAC 59.609 47.826 0.00 0.00 0.00 1.89
3487 3598 3.009723 ACAACTCAAAGTGTGGACAGTG 58.990 45.455 0.00 0.00 0.00 3.66
3511 3622 4.991056 TCTACACATTGAACTCTTCTGCAC 59.009 41.667 0.00 0.00 0.00 4.57
3604 3716 6.653526 TTTCTGATGATTGGAGAGCAAAAA 57.346 33.333 0.00 0.00 0.00 1.94
3642 3754 0.773644 AGGCTTCAAGGGAAAGAGCA 59.226 50.000 0.00 0.00 31.35 4.26
3729 3842 8.962884 TGCATCAAAAAGATATGTAAGAGCTA 57.037 30.769 0.00 0.00 34.43 3.32
3730 3843 7.772292 TCTGCATCAAAAAGATATGTAAGAGCT 59.228 33.333 0.00 0.00 34.43 4.09
4008 4121 8.908786 TTGGAAAGATAAATACCTCTATGCAG 57.091 34.615 0.00 0.00 0.00 4.41
4042 4155 7.558444 TCTTAAAACCAAAGCTAAGGAAACTCA 59.442 33.333 11.07 0.00 42.68 3.41
4043 4156 7.937649 TCTTAAAACCAAAGCTAAGGAAACTC 58.062 34.615 11.07 0.00 42.68 3.01
4110 4232 0.534412 CTGGAGGAAGACACGATGCT 59.466 55.000 0.00 0.00 0.00 3.79
4131 4253 1.002257 TGACGCAATGCCCATCTGT 60.002 52.632 0.00 0.00 0.00 3.41
4344 4466 1.067212 ACAAAGTCGCGAACACTCTCT 59.933 47.619 12.06 0.00 0.00 3.10
4404 4689 9.813080 GAAGTGTATTGTCTGTAAAGATTTGTC 57.187 33.333 0.00 0.00 0.00 3.18
4564 4849 2.139917 CGCACTGCTTGGTTAACAGTA 58.860 47.619 8.10 0.00 42.59 2.74
4585 4870 4.699522 AACCGCTTCTCCACCGGC 62.700 66.667 0.00 0.00 45.58 6.13
4672 4957 2.182030 CGAACCGGTCTCTCTGGC 59.818 66.667 8.04 0.00 46.11 4.85
4756 5041 1.681793 ACTGTGCTGACAACTCTACGT 59.318 47.619 0.00 0.00 0.00 3.57
4924 5212 3.181445 ACCAGTAATTTCTGTGACAGCCA 60.181 43.478 7.93 0.00 34.02 4.75
4931 5219 6.348540 GCAGAAGGTTACCAGTAATTTCTGTG 60.349 42.308 27.01 16.50 42.94 3.66
4957 5245 1.580815 CAACAAAATTGGCCAGCGTT 58.419 45.000 5.11 3.49 0.00 4.84
4993 5283 2.069273 GCTACCTACAACACAGCACAG 58.931 52.381 0.00 0.00 32.46 3.66
5086 5376 7.214467 TGAAGTTGTAACAATCAATTCCCTC 57.786 36.000 0.00 0.00 0.00 4.30
5326 5618 5.705609 AATTTATTTCACACGCAAGAGGT 57.294 34.783 0.00 0.00 43.62 3.85
5328 5620 7.298122 ACACTAATTTATTTCACACGCAAGAG 58.702 34.615 0.00 0.00 43.62 2.85
5369 5661 4.070716 GCAAGAGAGCACATAGGCATAAT 58.929 43.478 0.00 0.00 35.83 1.28
5370 5662 3.118298 TGCAAGAGAGCACATAGGCATAA 60.118 43.478 0.00 0.00 40.11 1.90
5371 5663 2.435437 TGCAAGAGAGCACATAGGCATA 59.565 45.455 0.00 0.00 40.11 3.14
5466 5767 7.062956 TGTTACTTGCATACACTATGAGAAACG 59.937 37.037 0.00 0.00 38.45 3.60
5498 5804 4.815846 CCCCACAAAAGAACCAATTGAAAG 59.184 41.667 7.12 0.00 0.00 2.62
5499 5805 4.226168 ACCCCACAAAAGAACCAATTGAAA 59.774 37.500 7.12 0.00 0.00 2.69
5500 5806 3.777522 ACCCCACAAAAGAACCAATTGAA 59.222 39.130 7.12 0.00 0.00 2.69
5501 5807 3.379452 ACCCCACAAAAGAACCAATTGA 58.621 40.909 7.12 0.00 0.00 2.57
5502 5808 3.836365 ACCCCACAAAAGAACCAATTG 57.164 42.857 0.00 0.00 0.00 2.32
5555 5883 1.014564 GCTTCTCGCCTTTGCTACGT 61.015 55.000 0.00 0.00 34.43 3.57
5692 6023 1.945394 GCAATCAGAGGCCACATAGTG 59.055 52.381 5.01 1.36 0.00 2.74
5693 6024 2.338577 GCAATCAGAGGCCACATAGT 57.661 50.000 5.01 0.00 0.00 2.12
5701 6032 5.588958 ATTTTTCTTAGGCAATCAGAGGC 57.411 39.130 0.00 0.00 0.00 4.70
5702 6033 6.238484 CGGTATTTTTCTTAGGCAATCAGAGG 60.238 42.308 0.00 0.00 0.00 3.69
5703 6034 6.316390 ACGGTATTTTTCTTAGGCAATCAGAG 59.684 38.462 0.00 0.00 0.00 3.35
5704 6035 6.093495 CACGGTATTTTTCTTAGGCAATCAGA 59.907 38.462 0.00 0.00 0.00 3.27
5705 6036 6.128007 ACACGGTATTTTTCTTAGGCAATCAG 60.128 38.462 0.00 0.00 0.00 2.90
5706 6037 5.708230 ACACGGTATTTTTCTTAGGCAATCA 59.292 36.000 0.00 0.00 0.00 2.57
5707 6038 6.027749 CACACGGTATTTTTCTTAGGCAATC 58.972 40.000 0.00 0.00 0.00 2.67
5708 6039 5.621329 GCACACGGTATTTTTCTTAGGCAAT 60.621 40.000 0.00 0.00 0.00 3.56
5717 6065 5.600908 TGTAAGAGCACACGGTATTTTTC 57.399 39.130 0.00 0.00 0.00 2.29
5767 6165 7.132863 GGAATATTTTCTTGTCGGCTTATGTC 58.867 38.462 0.00 0.00 32.16 3.06
5769 6167 6.438763 GGGAATATTTTCTTGTCGGCTTATG 58.561 40.000 0.00 0.00 32.16 1.90
5772 6170 3.699538 GGGGAATATTTTCTTGTCGGCTT 59.300 43.478 0.00 0.00 32.16 4.35
5773 6171 3.288092 GGGGAATATTTTCTTGTCGGCT 58.712 45.455 0.00 0.00 32.16 5.52
5813 6211 9.764363 AAGAAGATGGTTTAACTTTGGAATTTC 57.236 29.630 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.