Multiple sequence alignment - TraesCS2A01G197800

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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 TraesCS2A01G197800 chr2A 100.000 8180 0 0 1 8180 167946895 167955074 0 15106
1 TraesCS2A01G197800 chr2B 94.858 8246 190 83 6 8180 215198206 215206288 0 12663
2 TraesCS2A01G197800 chr2D 96.410 5181 83 31 3033 8180 157887923 157893033 0 8442
3 TraesCS2A01G197800 chr2D 92.860 3025 90 26 6 2989 157884987 157887926 0 4274


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 TraesCS2A01G197800 chr2A 167946895 167955074 8179 False 15106 15106 100.000 1 8180 1 chr2A.!!$F1 8179
1 TraesCS2A01G197800 chr2B 215198206 215206288 8082 False 12663 12663 94.858 6 8180 1 chr2B.!!$F1 8174
2 TraesCS2A01G197800 chr2D 157884987 157893033 8046 False 6358 8442 94.635 6 8180 2 chr2D.!!$F1 8174

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
864 884 0.614979 CGAGGGGAAGGAGAAGGACA 60.615 60.0 0.00 0.0 0.00 4.02 F
2180 2232 0.597568 TGGGCAGCTCGTCAATTTTG 59.402 50.0 0.00 0.0 0.00 2.44 F
3204 3272 0.975887 TTTTGCTGGGATTTCAGGCC 59.024 50.0 0.00 0.0 35.43 5.19 F
3584 3655 0.762418 CCCCTATGCCAATGACCGTA 59.238 55.0 0.00 0.0 0.00 4.02 F
4986 5063 1.166531 GCAACCAGCGTCCTGTTCTT 61.167 55.0 0.00 0.0 37.38 2.52 F
5396 5473 0.397941 TCAGCCCAGTCTGTTCAAGG 59.602 55.0 0.00 0.0 35.63 3.61 F
5822 5899 0.601558 CAATTCCAGCAGCAGCAACT 59.398 50.0 3.17 0.0 45.49 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 2283 0.038801 GGCAAAAGCAGTGAGGAAGC 60.039 55.000 0.00 0.00 0.00 3.86 R
3562 3633 1.145571 GGTCATTGGCATAGGGGGTA 58.854 55.000 0.00 0.00 0.00 3.69 R
4579 4656 0.036732 AAGCTCAAGTTCATGGCCGA 59.963 50.000 0.00 0.00 0.00 5.54 R
5396 5473 0.527565 CTGGGGTTTATGCTGTGCAC 59.472 55.000 10.75 10.75 43.04 4.57 R
5823 5900 1.007734 CTGTTGCTGCTGCTGTTGG 60.008 57.895 17.00 0.18 40.48 3.77 R
7020 7130 0.621609 TGGTAGGCTTTACGGGCATT 59.378 50.000 0.00 0.00 0.00 3.56 R
7539 7649 1.003597 CCAGAGCAGAGCAGCACTT 60.004 57.895 0.00 0.00 33.05 3.16 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
108 109 2.854522 AAAAAGCGGATGAGACGGG 58.145 52.632 0.00 0.00 0.00 5.28
114 115 1.662608 CGGATGAGACGGGGAGATG 59.337 63.158 0.00 0.00 0.00 2.90
322 332 3.187700 CGTAGCGCCACTTCTTTATTCT 58.812 45.455 2.29 0.00 0.00 2.40
323 333 3.617263 CGTAGCGCCACTTCTTTATTCTT 59.383 43.478 2.29 0.00 0.00 2.52
324 334 4.092968 CGTAGCGCCACTTCTTTATTCTTT 59.907 41.667 2.29 0.00 0.00 2.52
325 335 5.390567 CGTAGCGCCACTTCTTTATTCTTTT 60.391 40.000 2.29 0.00 0.00 2.27
326 336 5.048153 AGCGCCACTTCTTTATTCTTTTC 57.952 39.130 2.29 0.00 0.00 2.29
327 337 4.082733 AGCGCCACTTCTTTATTCTTTTCC 60.083 41.667 2.29 0.00 0.00 3.13
328 338 4.082733 GCGCCACTTCTTTATTCTTTTCCT 60.083 41.667 0.00 0.00 0.00 3.36
329 339 5.123344 GCGCCACTTCTTTATTCTTTTCCTA 59.877 40.000 0.00 0.00 0.00 2.94
362 382 6.380095 TTTATTTTGCGTGGAGTGTTAAGT 57.620 33.333 0.00 0.00 0.00 2.24
448 468 0.986019 CCACCCACCCACCTGCTATA 60.986 60.000 0.00 0.00 0.00 1.31
469 489 4.729856 CGTGGACGGTTCGGGGAC 62.730 72.222 0.00 0.00 35.37 4.46
569 589 2.892334 CGTGTTCCGTTGGGTGCTG 61.892 63.158 0.00 0.00 33.83 4.41
809 829 2.706723 TCTAGGAGAGGAGTAGCATCGT 59.293 50.000 0.00 0.00 31.26 3.73
863 883 1.962321 GCGAGGGGAAGGAGAAGGAC 61.962 65.000 0.00 0.00 0.00 3.85
864 884 0.614979 CGAGGGGAAGGAGAAGGACA 60.615 60.000 0.00 0.00 0.00 4.02
865 885 1.657804 GAGGGGAAGGAGAAGGACAA 58.342 55.000 0.00 0.00 0.00 3.18
866 886 1.557371 GAGGGGAAGGAGAAGGACAAG 59.443 57.143 0.00 0.00 0.00 3.16
868 888 1.657804 GGGAAGGAGAAGGACAAGGA 58.342 55.000 0.00 0.00 0.00 3.36
870 890 1.557371 GGAAGGAGAAGGACAAGGAGG 59.443 57.143 0.00 0.00 0.00 4.30
871 891 1.557371 GAAGGAGAAGGACAAGGAGGG 59.443 57.143 0.00 0.00 0.00 4.30
872 892 0.912006 AGGAGAAGGACAAGGAGGGC 60.912 60.000 0.00 0.00 0.00 5.19
873 893 1.219393 GAGAAGGACAAGGAGGGCG 59.781 63.158 0.00 0.00 0.00 6.13
874 894 2.245438 GAGAAGGACAAGGAGGGCGG 62.245 65.000 0.00 0.00 0.00 6.13
875 895 3.330720 AAGGACAAGGAGGGCGGG 61.331 66.667 0.00 0.00 0.00 6.13
878 898 4.475135 GACAAGGAGGGCGGGCTC 62.475 72.222 0.26 0.00 0.00 4.70
880 900 4.168291 CAAGGAGGGCGGGCTCTC 62.168 72.222 12.13 12.13 42.60 3.20
881 901 4.406763 AAGGAGGGCGGGCTCTCT 62.407 66.667 19.19 3.90 42.89 3.10
882 902 4.851214 AGGAGGGCGGGCTCTCTC 62.851 72.222 19.19 10.09 42.89 3.20
893 927 2.542907 GCTCTCTCGCTCTCTCCCG 61.543 68.421 0.00 0.00 0.00 5.14
903 937 2.125350 CTCTCCCGCTGCCTTGTC 60.125 66.667 0.00 0.00 0.00 3.18
1533 1581 3.606422 CACCGCAAAACAAGCAAATTTC 58.394 40.909 0.00 0.00 0.00 2.17
1541 1589 3.473923 ACAAGCAAATTTCCACCCTTG 57.526 42.857 0.00 0.00 36.62 3.61
1553 1601 1.600916 ACCCTTGTTGCCGCTTCTC 60.601 57.895 0.00 0.00 0.00 2.87
1561 1609 0.606401 TTGCCGCTTCTCTTTCCCTG 60.606 55.000 0.00 0.00 0.00 4.45
1567 1615 2.797792 CGCTTCTCTTTCCCTGATCTCG 60.798 54.545 0.00 0.00 0.00 4.04
1568 1616 2.428890 GCTTCTCTTTCCCTGATCTCGA 59.571 50.000 0.00 0.00 0.00 4.04
1765 1813 1.370051 GCGTTTTTCAGGCCGACAC 60.370 57.895 0.00 0.00 0.00 3.67
1790 1838 2.715336 CCATCTCCCCTCATGATTCCTT 59.285 50.000 0.00 0.00 0.00 3.36
1791 1839 3.912528 CCATCTCCCCTCATGATTCCTTA 59.087 47.826 0.00 0.00 0.00 2.69
1797 1845 5.039645 TCCCCTCATGATTCCTTAAACTCT 58.960 41.667 0.00 0.00 0.00 3.24
2065 2117 4.660938 AACCACAAGCCGGAGCCC 62.661 66.667 5.05 0.00 41.25 5.19
2121 2173 2.885861 GGCTCCGTCGTCATCTGT 59.114 61.111 0.00 0.00 0.00 3.41
2180 2232 0.597568 TGGGCAGCTCGTCAATTTTG 59.402 50.000 0.00 0.00 0.00 2.44
2186 2238 4.094887 GGCAGCTCGTCAATTTTGATCTTA 59.905 41.667 0.00 0.00 39.73 2.10
2367 2420 2.281484 GAAGTGCTTCCGGTGGCA 60.281 61.111 17.21 17.21 36.01 4.92
2420 2479 2.551270 CGAAAGTGTCGCCAGCAC 59.449 61.111 0.00 0.00 44.14 4.40
2422 2481 2.954753 GAAAGTGTCGCCAGCACCG 61.955 63.158 0.00 0.00 37.56 4.94
2743 2802 6.251589 GTGCCGATCTGATTAGTATATTCACG 59.748 42.308 0.00 0.00 29.00 4.35
2750 2809 8.449085 TCTGATTAGTATATTCACGATTTCGC 57.551 34.615 0.00 0.00 44.43 4.70
2788 2847 2.627515 TTATCAGTGAGCTGGCATCC 57.372 50.000 0.00 0.00 42.78 3.51
2843 2902 4.973168 TCTCATGGTGGGTATATGCTTTC 58.027 43.478 0.00 0.00 0.00 2.62
2844 2903 4.411869 TCTCATGGTGGGTATATGCTTTCA 59.588 41.667 0.00 0.00 0.00 2.69
3175 3243 5.106197 TGTTTGATTCTGATCGGTCCATTTG 60.106 40.000 0.42 0.00 34.91 2.32
3192 3260 5.754406 TCCATTTGTTGTTCATCTTTTGCTG 59.246 36.000 0.00 0.00 0.00 4.41
3193 3261 5.049954 CCATTTGTTGTTCATCTTTTGCTGG 60.050 40.000 0.00 0.00 0.00 4.85
3204 3272 0.975887 TTTTGCTGGGATTTCAGGCC 59.024 50.000 0.00 0.00 35.43 5.19
3206 3274 2.830370 GCTGGGATTTCAGGCCGG 60.830 66.667 0.00 0.00 35.43 6.13
3523 3594 8.696410 TTTGTAAAAGGTGATTCTTTGTTGAC 57.304 30.769 0.00 0.00 37.09 3.18
3566 3637 1.744114 GCTCTACCTGCTGCTTTACCC 60.744 57.143 0.00 0.00 0.00 3.69
3584 3655 0.762418 CCCCTATGCCAATGACCGTA 59.238 55.000 0.00 0.00 0.00 4.02
3808 3879 3.746045 ACAGGTTCGCTTTCTCACTTA 57.254 42.857 0.00 0.00 0.00 2.24
3869 3940 5.514500 TGCCAAGTCTAAAGGTTTCCTAT 57.486 39.130 0.00 0.00 31.13 2.57
3909 3980 4.778143 CCACTGCCAGTACGCCCC 62.778 72.222 0.00 0.00 0.00 5.80
4733 4810 1.985662 CAGGCCCAGGTGTACCGTA 60.986 63.158 0.00 0.00 42.08 4.02
4816 4893 6.018507 GCAGCAACAAAATCATCAGAAAAACT 60.019 34.615 0.00 0.00 0.00 2.66
4986 5063 1.166531 GCAACCAGCGTCCTGTTCTT 61.167 55.000 0.00 0.00 37.38 2.52
5142 5219 1.721664 CGTTGATGCCATCTGCTGGG 61.722 60.000 6.21 0.00 46.06 4.45
5396 5473 0.397941 TCAGCCCAGTCTGTTCAAGG 59.602 55.000 0.00 0.00 35.63 3.61
5822 5899 0.601558 CAATTCCAGCAGCAGCAACT 59.398 50.000 3.17 0.00 45.49 3.16
5823 5900 0.886563 AATTCCAGCAGCAGCAACTC 59.113 50.000 3.17 0.00 45.49 3.01
5826 5909 1.900016 CCAGCAGCAGCAACTCCAA 60.900 57.895 3.17 0.00 45.49 3.53
5832 5915 1.170919 AGCAGCAACTCCAACAGCAG 61.171 55.000 0.00 0.00 0.00 4.24
5834 5917 1.152902 AGCAACTCCAACAGCAGCA 60.153 52.632 0.00 0.00 0.00 4.41
5835 5918 1.170919 AGCAACTCCAACAGCAGCAG 61.171 55.000 0.00 0.00 0.00 4.24
5838 5921 0.752743 AACTCCAACAGCAGCAGCAA 60.753 50.000 3.17 0.00 45.49 3.91
5849 5932 1.826921 AGCAGCAACAGCAGCAACT 60.827 52.632 7.56 0.00 42.49 3.16
5850 5933 1.371389 GCAGCAACAGCAGCAACTC 60.371 57.895 0.00 0.00 40.13 3.01
5865 5948 2.671963 CTCCAGCAGCAGCAGCAA 60.672 61.111 12.92 0.00 45.49 3.91
5888 5971 2.981909 GCAACTCCAGCAGCAGCA 60.982 61.111 3.17 0.00 45.49 4.41
5889 5972 2.979197 GCAACTCCAGCAGCAGCAG 61.979 63.158 3.17 0.00 45.49 4.24
5890 5973 2.672307 AACTCCAGCAGCAGCAGC 60.672 61.111 3.17 0.46 45.49 5.25
5907 5993 2.725641 CAACAGCAGCAGCAGCAA 59.274 55.556 12.92 0.00 45.49 3.91
5964 6053 1.335810 CTTCAGAAACAGCAGCAGCAA 59.664 47.619 3.17 0.00 45.49 3.91
6060 6149 1.395573 CGTTTGAGTGCGACGAACTTC 60.396 52.381 10.51 4.33 38.99 3.01
6366 6455 2.814269 TCTCGATCTTCAAATGCTCCG 58.186 47.619 0.00 0.00 0.00 4.63
6640 6729 2.029649 CCCTCATTGAAACAACAGCAGG 60.030 50.000 0.00 0.00 0.00 4.85
6775 6864 2.858868 CTGACAAGACGCAGCAGC 59.141 61.111 0.00 0.00 37.42 5.25
6776 6865 1.957695 CTGACAAGACGCAGCAGCA 60.958 57.895 0.82 0.00 42.27 4.41
6777 6866 1.898459 CTGACAAGACGCAGCAGCAG 61.898 60.000 0.82 0.00 42.27 4.24
6778 6867 3.306134 GACAAGACGCAGCAGCAGC 62.306 63.158 0.82 0.00 42.27 5.25
6779 6868 3.351416 CAAGACGCAGCAGCAGCA 61.351 61.111 10.77 0.00 45.49 4.41
6780 6869 3.048475 AAGACGCAGCAGCAGCAG 61.048 61.111 10.77 5.43 45.49 4.24
6864 6968 2.045926 ACATCTGCGGTTCCAGCC 60.046 61.111 0.00 0.00 32.87 4.85
7186 7296 5.131475 TGTTTGTCAGGTAAGTAAAGGACCT 59.869 40.000 0.00 0.00 44.65 3.85
7277 7387 3.177600 GCGGAAGAAGCGATTGCA 58.822 55.556 7.90 0.00 46.23 4.08
7375 7485 4.518970 TCTGGCAAATCTGTGGAGTAAAAC 59.481 41.667 0.00 0.00 0.00 2.43
7461 7571 0.623723 TGGAGGTGCATAGAAACCCC 59.376 55.000 0.00 0.00 37.13 4.95
7533 7643 2.018086 CTCCCCTCCCCTCTCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
7534 7644 2.015726 TCCCCTCCCCTCTCCTCTC 61.016 68.421 0.00 0.00 0.00 3.20
7535 7645 2.612251 CCCTCCCCTCTCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
7536 7646 2.018086 CCCTCCCCTCTCCTCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
7537 7647 1.541672 CCTCCCCTCTCCTCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
7539 7649 1.307953 TCCCCTCTCCTCTCCTCGA 60.308 63.158 0.00 0.00 0.00 4.04
7540 7650 0.919780 TCCCCTCTCCTCTCCTCGAA 60.920 60.000 0.00 0.00 0.00 3.71
7541 7651 0.467290 CCCCTCTCCTCTCCTCGAAG 60.467 65.000 0.00 0.00 0.00 3.79
7580 7690 5.644206 GGTCTGGTCTCTTTAGATTTGTTCC 59.356 44.000 0.00 0.00 33.30 3.62
7671 7782 0.322366 GCTGCTCTTGCCTTCCTCTT 60.322 55.000 0.00 0.00 38.71 2.85
7672 7783 1.885790 GCTGCTCTTGCCTTCCTCTTT 60.886 52.381 0.00 0.00 38.71 2.52
7673 7784 2.512705 CTGCTCTTGCCTTCCTCTTTT 58.487 47.619 0.00 0.00 38.71 2.27
7674 7785 2.487372 CTGCTCTTGCCTTCCTCTTTTC 59.513 50.000 0.00 0.00 38.71 2.29
7842 7956 2.359531 TGTTTTAGAAACAACTGGGGCG 59.640 45.455 3.92 0.00 0.00 6.13
7868 7983 4.022676 GGCAGAGAGGCAGATAAGTAGTAC 60.023 50.000 0.00 0.00 43.51 2.73
7898 8030 4.062991 TGTTGCATAGCATAGCATGAGAG 58.937 43.478 0.00 0.00 40.94 3.20
7939 8087 2.413634 GGGTGTGTGCGTTGTAATTAGC 60.414 50.000 0.00 0.00 0.00 3.09
7940 8088 2.482721 GGTGTGTGCGTTGTAATTAGCT 59.517 45.455 0.00 0.00 0.00 3.32
7941 8089 3.680937 GGTGTGTGCGTTGTAATTAGCTA 59.319 43.478 0.00 0.00 0.00 3.32
7942 8090 4.201685 GGTGTGTGCGTTGTAATTAGCTAG 60.202 45.833 0.00 0.00 0.00 3.42
7943 8091 3.930229 TGTGTGCGTTGTAATTAGCTAGG 59.070 43.478 0.00 0.00 0.00 3.02
7944 8092 3.930848 GTGTGCGTTGTAATTAGCTAGGT 59.069 43.478 0.00 0.00 0.00 3.08
7945 8093 5.104374 GTGTGCGTTGTAATTAGCTAGGTA 58.896 41.667 0.00 0.00 0.00 3.08
7946 8094 5.231568 GTGTGCGTTGTAATTAGCTAGGTAG 59.768 44.000 1.31 0.00 0.00 3.18
8021 8172 6.467677 TCTTGTTAAGATAGCAAAGCAGAGT 58.532 36.000 0.00 0.00 31.20 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 0.676782 CCCCGTCTCATCCGCTTTTT 60.677 55.000 0.00 0.00 0.00 1.94
91 92 1.078426 CCCCGTCTCATCCGCTTTT 60.078 57.895 0.00 0.00 0.00 2.27
92 93 1.961180 CTCCCCGTCTCATCCGCTTT 61.961 60.000 0.00 0.00 0.00 3.51
93 94 2.363795 TCCCCGTCTCATCCGCTT 60.364 61.111 0.00 0.00 0.00 4.68
94 95 2.648613 ATCTCCCCGTCTCATCCGCT 62.649 60.000 0.00 0.00 0.00 5.52
145 146 4.421515 CTCCAGGCAGGCAGTGGG 62.422 72.222 10.86 1.27 37.29 4.61
323 333 9.134734 CGCAAAATAAATAAAGCAAGTAGGAAA 57.865 29.630 0.00 0.00 0.00 3.13
324 334 8.301002 ACGCAAAATAAATAAAGCAAGTAGGAA 58.699 29.630 0.00 0.00 0.00 3.36
325 335 7.753132 CACGCAAAATAAATAAAGCAAGTAGGA 59.247 33.333 0.00 0.00 0.00 2.94
326 336 7.009174 CCACGCAAAATAAATAAAGCAAGTAGG 59.991 37.037 0.00 0.00 0.00 3.18
327 337 7.753132 TCCACGCAAAATAAATAAAGCAAGTAG 59.247 33.333 0.00 0.00 0.00 2.57
328 338 7.594714 TCCACGCAAAATAAATAAAGCAAGTA 58.405 30.769 0.00 0.00 0.00 2.24
329 339 6.451393 TCCACGCAAAATAAATAAAGCAAGT 58.549 32.000 0.00 0.00 0.00 3.16
502 522 2.053865 AACAAGCATGGCCCGATGG 61.054 57.895 0.00 0.00 0.00 3.51
809 829 1.221635 CTCCCTCTCCCTCTCTCTCA 58.778 60.000 0.00 0.00 0.00 3.27
815 835 2.070573 GTATCTCCTCCCTCTCCCTCT 58.929 57.143 0.00 0.00 0.00 3.69
819 839 1.422402 ACGAGTATCTCCTCCCTCTCC 59.578 57.143 0.00 0.00 0.00 3.71
820 840 2.105134 TCACGAGTATCTCCTCCCTCTC 59.895 54.545 0.00 0.00 0.00 3.20
821 841 2.105821 CTCACGAGTATCTCCTCCCTCT 59.894 54.545 0.00 0.00 0.00 3.69
822 842 2.500229 CTCACGAGTATCTCCTCCCTC 58.500 57.143 0.00 0.00 0.00 4.30
863 883 4.168291 GAGAGCCCGCCCTCCTTG 62.168 72.222 0.00 0.00 32.17 3.61
864 884 4.406763 AGAGAGCCCGCCCTCCTT 62.407 66.667 0.00 0.00 32.17 3.36
865 885 4.851214 GAGAGAGCCCGCCCTCCT 62.851 72.222 0.00 0.00 32.17 3.69
872 892 2.515991 AGAGAGCGAGAGAGCCCG 60.516 66.667 0.00 0.00 38.01 6.13
873 893 2.193536 GGAGAGAGCGAGAGAGCCC 61.194 68.421 0.00 0.00 38.01 5.19
874 894 2.193536 GGGAGAGAGCGAGAGAGCC 61.194 68.421 0.00 0.00 38.01 4.70
875 895 2.542907 CGGGAGAGAGCGAGAGAGC 61.543 68.421 0.00 0.00 37.41 4.09
876 896 2.542907 GCGGGAGAGAGCGAGAGAG 61.543 68.421 0.00 0.00 0.00 3.20
877 897 2.515057 GCGGGAGAGAGCGAGAGA 60.515 66.667 0.00 0.00 0.00 3.10
878 898 2.515991 AGCGGGAGAGAGCGAGAG 60.516 66.667 0.00 0.00 38.61 3.20
879 899 2.826287 CAGCGGGAGAGAGCGAGA 60.826 66.667 0.00 0.00 38.61 4.04
880 900 4.567385 GCAGCGGGAGAGAGCGAG 62.567 72.222 0.00 0.00 38.61 5.03
883 903 3.780173 AAGGCAGCGGGAGAGAGC 61.780 66.667 0.00 0.00 0.00 4.09
884 904 2.186384 CAAGGCAGCGGGAGAGAG 59.814 66.667 0.00 0.00 0.00 3.20
885 905 2.604686 ACAAGGCAGCGGGAGAGA 60.605 61.111 0.00 0.00 0.00 3.10
1152 1197 1.503542 GTTGCCGTTGAGCATGAGG 59.496 57.895 0.00 0.00 43.64 3.86
1335 1380 2.668550 CTGCTGCTGCTGCTGTGA 60.669 61.111 27.67 10.41 39.81 3.58
1402 1450 3.781307 CCCCTTCCGGTGCATCGA 61.781 66.667 23.56 3.90 0.00 3.59
1403 1451 4.856801 CCCCCTTCCGGTGCATCG 62.857 72.222 13.72 13.72 0.00 3.84
1533 1581 2.912025 AAGCGGCAACAAGGGTGG 60.912 61.111 1.45 0.00 0.00 4.61
1541 1589 0.606673 AGGGAAAGAGAAGCGGCAAC 60.607 55.000 1.45 0.00 0.00 4.17
1553 1601 0.528684 GCCGTCGAGATCAGGGAAAG 60.529 60.000 0.00 0.00 0.00 2.62
1561 1609 1.298488 GAGGAACGCCGTCGAGATC 60.298 63.158 0.00 0.00 39.96 2.75
1567 1615 1.493134 AAAACACGAGGAACGCCGTC 61.493 55.000 0.00 0.00 46.94 4.79
1568 1616 1.493134 GAAAACACGAGGAACGCCGT 61.493 55.000 0.00 0.00 46.94 5.68
1731 1779 1.207593 CGCACCAGCTTTTTCCGAG 59.792 57.895 0.00 0.00 39.10 4.63
1765 1813 4.333690 GAATCATGAGGGGAGATGGATTG 58.666 47.826 0.09 0.00 0.00 2.67
1790 1838 5.944007 GGAAATCAGTAAGGGCAAGAGTTTA 59.056 40.000 0.00 0.00 0.00 2.01
1791 1839 4.767409 GGAAATCAGTAAGGGCAAGAGTTT 59.233 41.667 0.00 0.00 0.00 2.66
1797 1845 2.919602 AGAGGGAAATCAGTAAGGGCAA 59.080 45.455 0.00 0.00 0.00 4.52
2230 2283 0.038801 GGCAAAAGCAGTGAGGAAGC 60.039 55.000 0.00 0.00 0.00 3.86
2279 2332 2.056577 GGTTCTCGTTGTCGTACTTGG 58.943 52.381 0.00 0.00 38.33 3.61
2341 2394 2.982744 GAAGCACTTCCGGCCTTGC 61.983 63.158 11.76 11.76 33.64 4.01
2357 2410 0.911769 ATCTGATCTTGCCACCGGAA 59.088 50.000 9.46 0.00 0.00 4.30
2367 2420 0.176680 ACGGCTTCGCATCTGATCTT 59.823 50.000 0.00 0.00 37.41 2.40
2520 2579 1.613925 GGATCCCGTCGATCTGATTCA 59.386 52.381 0.00 0.00 45.90 2.57
2743 2802 8.912112 AAAAATAAAACAATTCACGCGAAATC 57.088 26.923 15.93 0.00 34.01 2.17
2843 2902 3.318839 AGACCAATTCAACCACACACATG 59.681 43.478 0.00 0.00 0.00 3.21
2844 2903 3.565307 AGACCAATTCAACCACACACAT 58.435 40.909 0.00 0.00 0.00 3.21
2954 3022 3.265479 AGGGGAGAGAAAAAGGTGAGATG 59.735 47.826 0.00 0.00 0.00 2.90
3175 3243 4.525912 ATCCCAGCAAAAGATGAACAAC 57.474 40.909 0.00 0.00 0.00 3.32
3192 3260 2.193248 CTCCCGGCCTGAAATCCC 59.807 66.667 0.00 0.00 0.00 3.85
3193 3261 1.147153 CTCTCCCGGCCTGAAATCC 59.853 63.158 0.00 0.00 0.00 3.01
3204 3272 4.579869 TCTTTTCAGAATTTCCTCTCCCG 58.420 43.478 0.00 0.00 0.00 5.14
3206 3274 7.751768 TCTTTCTTTTCAGAATTTCCTCTCC 57.248 36.000 0.00 0.00 38.89 3.71
3523 3594 2.232208 GCCAGATGAGGAAAAACCCAAG 59.768 50.000 0.00 0.00 40.05 3.61
3562 3633 1.145571 GGTCATTGGCATAGGGGGTA 58.854 55.000 0.00 0.00 0.00 3.69
3566 3637 1.270839 CCTACGGTCATTGGCATAGGG 60.271 57.143 9.08 0.00 0.00 3.53
3808 3879 3.073062 AGACAGAAACCACACCATAGCTT 59.927 43.478 0.00 0.00 0.00 3.74
4536 4613 2.042831 GTGGGCAGTGGCAGATGAC 61.043 63.158 19.48 0.34 43.71 3.06
4575 4652 1.063006 CAAGTTCATGGCCGATGCG 59.937 57.895 0.00 0.00 38.85 4.73
4579 4656 0.036732 AAGCTCAAGTTCATGGCCGA 59.963 50.000 0.00 0.00 0.00 5.54
4733 4810 3.055094 AGAGTAGACATGCCCGTTGAAAT 60.055 43.478 0.00 0.00 0.00 2.17
4816 4893 1.250328 CCAGACAAGCTTGGCATTGA 58.750 50.000 33.20 0.00 39.18 2.57
4986 5063 1.676678 GGTGAGCGAGGCCATGTAGA 61.677 60.000 5.01 0.00 0.00 2.59
5142 5219 7.490725 TCATTCGATTTCTTCTCACTCTGATTC 59.509 37.037 0.00 0.00 0.00 2.52
5396 5473 0.527565 CTGGGGTTTATGCTGTGCAC 59.472 55.000 10.75 10.75 43.04 4.57
5727 5804 1.748122 CTGCTGCTGGGACATGGTC 60.748 63.158 0.00 0.00 38.20 4.02
5822 5899 1.449726 CTGTTGCTGCTGCTGTTGGA 61.450 55.000 17.00 0.00 40.48 3.53
5823 5900 1.007734 CTGTTGCTGCTGCTGTTGG 60.008 57.895 17.00 0.18 40.48 3.77
5826 5909 2.517638 TGCTGTTGCTGCTGCTGT 60.518 55.556 17.00 0.00 40.48 4.40
5834 5917 1.152902 TGGAGTTGCTGCTGTTGCT 60.153 52.632 0.00 0.00 40.48 3.91
5835 5918 1.285023 CTGGAGTTGCTGCTGTTGC 59.715 57.895 0.00 0.00 40.20 4.17
5838 5921 1.600076 CTGCTGGAGTTGCTGCTGT 60.600 57.895 0.00 0.00 0.00 4.40
5849 5932 2.981909 GTTGCTGCTGCTGCTGGA 60.982 61.111 27.67 16.80 40.48 3.86
5850 5933 3.268965 CTGTTGCTGCTGCTGCTGG 62.269 63.158 27.67 12.95 40.48 4.85
5865 5948 1.600076 CTGCTGGAGTTGCTGCTGT 60.600 57.895 0.00 0.00 0.00 4.40
5888 5971 3.671411 GCTGCTGCTGCTGTTGCT 61.671 61.111 22.10 0.00 39.81 3.91
5889 5972 3.493830 TTGCTGCTGCTGCTGTTGC 62.494 57.895 27.67 16.48 39.81 4.17
5890 5973 1.660575 GTTGCTGCTGCTGCTGTTG 60.661 57.895 27.67 8.62 39.81 3.33
5907 5993 1.434696 GTGCTGCTGCTGTTGTTGT 59.565 52.632 17.00 0.00 40.48 3.32
5964 6053 7.211573 TCAGATGATTTTGAAACAATTGCTGT 58.788 30.769 5.05 0.00 41.27 4.40
6366 6455 1.896660 TGGCGAACCAGAAGCAACC 60.897 57.895 0.00 0.00 42.67 3.77
6640 6729 2.676471 ATGGCCTTGTGGGAACGC 60.676 61.111 3.32 0.00 42.66 4.84
6669 6758 4.322198 GCAAAGGCATTGGAGATGAAGAAA 60.322 41.667 4.48 0.00 39.54 2.52
6778 6867 1.137614 CATTCTGCTGCTGCTGCTG 59.862 57.895 27.67 26.32 40.48 4.41
6779 6868 2.701780 GCATTCTGCTGCTGCTGCT 61.702 57.895 27.67 8.85 40.96 4.24
6780 6869 2.202623 GCATTCTGCTGCTGCTGC 60.203 61.111 22.51 22.51 40.96 5.25
6864 6968 2.099652 TATGAGCCTTCCCCGCATCG 62.100 60.000 0.00 0.00 0.00 3.84
7020 7130 0.621609 TGGTAGGCTTTACGGGCATT 59.378 50.000 0.00 0.00 0.00 3.56
7186 7296 2.434843 CCCCATGCTCTGGCGTCTA 61.435 63.158 0.73 0.00 44.46 2.59
7204 7314 2.402305 CCGACTCAGATTAGCAGCATC 58.598 52.381 0.00 0.00 0.00 3.91
7277 7387 3.416253 CAGCTATGCCTCTTGCCAT 57.584 52.632 0.00 0.00 40.16 4.40
7375 7485 2.809861 ATCAGCCAGCCGTTCCACAG 62.810 60.000 0.00 0.00 0.00 3.66
7533 7643 1.588597 CAGAGCAGCACTTCGAGGA 59.411 57.895 0.00 0.00 0.00 3.71
7534 7644 2.099431 GCAGAGCAGCACTTCGAGG 61.099 63.158 0.00 0.00 0.00 4.63
7535 7645 1.077645 GAGCAGAGCAGCACTTCGAG 61.078 60.000 0.00 0.00 36.85 4.04
7536 7646 1.080230 GAGCAGAGCAGCACTTCGA 60.080 57.895 0.00 0.00 36.85 3.71
7537 7647 1.079956 AGAGCAGAGCAGCACTTCG 60.080 57.895 0.00 0.00 31.19 3.79
7539 7649 1.003597 CCAGAGCAGAGCAGCACTT 60.004 57.895 0.00 0.00 33.05 3.16
7540 7650 2.169937 GACCAGAGCAGAGCAGCACT 62.170 60.000 0.00 0.00 35.80 4.40
7541 7651 1.741032 GACCAGAGCAGAGCAGCAC 60.741 63.158 0.00 0.00 36.85 4.40
7580 7690 7.535139 TCCTTCAGTTAAGACAACAACAAAAG 58.465 34.615 0.00 0.00 37.38 2.27
7671 7782 9.981114 AAAGAAACACAGAAAGAAAGAAAGAAA 57.019 25.926 0.00 0.00 0.00 2.52
7672 7783 9.626045 GAAAGAAACACAGAAAGAAAGAAAGAA 57.374 29.630 0.00 0.00 0.00 2.52
7673 7784 8.244113 GGAAAGAAACACAGAAAGAAAGAAAGA 58.756 33.333 0.00 0.00 0.00 2.52
7674 7785 8.246871 AGGAAAGAAACACAGAAAGAAAGAAAG 58.753 33.333 0.00 0.00 0.00 2.62
7708 7819 6.295249 TGAGTATTGACAAAACACATGGAGA 58.705 36.000 0.00 0.00 0.00 3.71
7842 7956 1.344114 CTTATCTGCCTCTCTGCCTCC 59.656 57.143 0.00 0.00 0.00 4.30
7868 7983 5.985530 TGCTATGCTATGCAACAACTACTAG 59.014 40.000 0.00 0.00 43.62 2.57
7898 8030 1.270550 CAAAAGGCAGGTCATGGTCAC 59.729 52.381 0.00 0.00 0.00 3.67
7939 8087 7.113658 TCATTTCTTCTACAAGGCTACCTAG 57.886 40.000 0.00 0.00 31.13 3.02
7940 8088 7.490657 TTCATTTCTTCTACAAGGCTACCTA 57.509 36.000 0.00 0.00 31.13 3.08
7941 8089 6.374417 TTCATTTCTTCTACAAGGCTACCT 57.626 37.500 0.00 0.00 33.87 3.08
7942 8090 6.823689 TGATTCATTTCTTCTACAAGGCTACC 59.176 38.462 0.00 0.00 0.00 3.18
7943 8091 7.849804 TGATTCATTTCTTCTACAAGGCTAC 57.150 36.000 0.00 0.00 0.00 3.58
7944 8092 9.113838 GATTGATTCATTTCTTCTACAAGGCTA 57.886 33.333 0.00 0.00 0.00 3.93
7945 8093 7.613022 TGATTGATTCATTTCTTCTACAAGGCT 59.387 33.333 0.00 0.00 0.00 4.58
7946 8094 7.765307 TGATTGATTCATTTCTTCTACAAGGC 58.235 34.615 0.00 0.00 0.00 4.35
7947 8095 9.784680 CTTGATTGATTCATTTCTTCTACAAGG 57.215 33.333 0.00 0.00 33.34 3.61
7948 8096 9.784680 CCTTGATTGATTCATTTCTTCTACAAG 57.215 33.333 0.00 0.00 33.34 3.16
7949 8097 8.246180 GCCTTGATTGATTCATTTCTTCTACAA 58.754 33.333 0.00 0.00 33.34 2.41
7950 8098 7.414429 CGCCTTGATTGATTCATTTCTTCTACA 60.414 37.037 0.00 0.00 33.34 2.74
7951 8099 6.909357 CGCCTTGATTGATTCATTTCTTCTAC 59.091 38.462 0.00 0.00 33.34 2.59
7952 8100 6.038603 CCGCCTTGATTGATTCATTTCTTCTA 59.961 38.462 0.00 0.00 33.34 2.10
7953 8101 5.163581 CCGCCTTGATTGATTCATTTCTTCT 60.164 40.000 0.00 0.00 33.34 2.85
7954 8102 5.039333 CCGCCTTGATTGATTCATTTCTTC 58.961 41.667 0.00 0.00 33.34 2.87
8021 8172 3.264193 AGTCATCACACAGGCCAGAATTA 59.736 43.478 5.01 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.