Multiple sequence alignment - TraesCS5A01G390900

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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 TraesCS5A01G390900 chr5A 100.000 6700 0 0 1 6700 586144097 586150796 0.000000e+00 12373
1 TraesCS5A01G390900 chr5D 96.290 6712 202 18 1 6700 465713712 465720388 0.000000e+00 10972
2 TraesCS5A01G390900 chr5D 89.130 184 19 1 5618 5800 399222956 399222773 1.880000e-55 228
3 TraesCS5A01G390900 chr5B 95.115 6735 260 30 1 6700 572946064 572952764 0.000000e+00 10551


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 TraesCS5A01G390900 chr5A 586144097 586150796 6699 False 12373 12373 100.000 1 6700 1 chr5A.!!$F1 6699
1 TraesCS5A01G390900 chr5D 465713712 465720388 6676 False 10972 10972 96.290 1 6700 1 chr5D.!!$F1 6699
2 TraesCS5A01G390900 chr5B 572946064 572952764 6700 False 10551 10551 95.115 1 6700 1 chr5B.!!$F1 6699

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
523 524 0.179089 TTTGTGCTGGCGTTGCAATT 60.179 45.000 0.59 0.00 42.41 2.32 F
1128 1137 1.283793 CCAGGTTGCAGCAAACTCG 59.716 57.895 23.50 13.46 39.61 4.18 F
2346 2355 0.402121 GAGTTGAGGGGGAAGCAGTT 59.598 55.000 0.00 0.00 0.00 3.16 F
2581 2590 0.105760 AATTTCACCCACCAGCACCA 60.106 50.000 0.00 0.00 0.00 4.17 F
3235 3246 0.182061 TAGGCGGAGAGTATCACGGT 59.818 55.000 0.00 0.00 38.03 4.83 F
3439 3450 0.244994 ACTCACTCATCACCTGCGAC 59.755 55.000 0.00 0.00 0.00 5.19 F
4889 4900 0.037877 ATCTGCAGCAGCCTGAAACT 59.962 50.000 18.43 0.00 41.77 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1813 0.382515 GCACAAGCAACCCGTTGTAA 59.617 50.000 9.21 0.0 42.31 2.41 R
2563 2572 0.114954 ATGGTGCTGGTGGGTGAAAT 59.885 50.000 0.00 0.0 0.00 2.17 R
3820 3831 0.165511 CGCAGCTTCTCTTGCAGAAC 59.834 55.000 0.00 0.0 36.08 3.01 R
3856 3867 1.064758 TGCACCAGTTCTCCAGTTTGT 60.065 47.619 0.00 0.0 0.00 2.83 R
4856 4867 0.036732 GCAGATTGTCAGGGGTGACA 59.963 55.000 4.10 4.1 45.85 3.58 R
5342 5353 0.676466 TCCCAACGATGAAATGCGCT 60.676 50.000 9.73 0.0 0.00 5.92 R
6085 6129 1.953138 GCAGCGATCATCGTCTGGG 60.953 63.158 23.85 8.3 42.81 4.45 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
52 53 2.611225 AGTAGCAGTATCAGCCTTGC 57.389 50.000 0.00 0.00 36.83 4.01
205 206 5.530915 TGGAAATCTACAAGTTGTGTGAAGG 59.469 40.000 18.90 2.41 41.89 3.46
334 335 7.307692 GGACACTTCTGAGAATCTTTTTCTGAC 60.308 40.741 0.00 0.00 34.92 3.51
343 344 3.788434 TCTTTTTCTGACTAAAGCGCG 57.212 42.857 0.00 0.00 32.67 6.86
458 459 4.923893 TCTGCAATGAAACAAGTGAACAG 58.076 39.130 0.00 0.00 0.00 3.16
523 524 0.179089 TTTGTGCTGGCGTTGCAATT 60.179 45.000 0.59 0.00 42.41 2.32
539 540 8.070171 GCGTTGCAATTTCTATGTGTTATATCT 58.930 33.333 0.59 0.00 0.00 1.98
540 541 9.373750 CGTTGCAATTTCTATGTGTTATATCTG 57.626 33.333 0.59 0.00 0.00 2.90
659 668 4.725790 ATTTTCAGGCTTTCAGCATACC 57.274 40.909 0.00 0.00 44.75 2.73
664 673 2.421424 CAGGCTTTCAGCATACCAACTC 59.579 50.000 0.00 0.00 44.75 3.01
686 695 2.234414 TGATACCTTGGTACGTGGAACC 59.766 50.000 0.00 0.00 37.53 3.62
881 890 4.212143 TGCCATATATGACATCTGCCTC 57.788 45.455 14.54 0.00 0.00 4.70
961 970 1.439543 AACCTTCACCTCTGCTTCCT 58.560 50.000 0.00 0.00 0.00 3.36
1128 1137 1.283793 CCAGGTTGCAGCAAACTCG 59.716 57.895 23.50 13.46 39.61 4.18
1189 1198 5.072329 AGGATCCATATTTGTACAGACCAGG 59.928 44.000 15.82 0.00 0.00 4.45
1329 1338 3.995636 TCTCTGTTCATACTTAGGCCCT 58.004 45.455 0.00 0.00 0.00 5.19
1804 1813 5.688807 ACAGCAATATCAATTCTACAGGCT 58.311 37.500 0.00 0.00 0.00 4.58
1863 1872 2.095768 GGTGACAACATTGGACATGACG 60.096 50.000 0.00 0.00 0.00 4.35
2091 2100 1.134699 TGCCCTCTTAGCACATTCTCG 60.135 52.381 0.00 0.00 34.69 4.04
2307 2316 5.253330 AGGAATGCCACTCTTCGAATTTTA 58.747 37.500 0.00 0.00 36.29 1.52
2346 2355 0.402121 GAGTTGAGGGGGAAGCAGTT 59.598 55.000 0.00 0.00 0.00 3.16
2460 2469 6.322201 CAGGCCAAATATATGAGAAACTTGGT 59.678 38.462 5.01 0.00 35.37 3.67
2563 2572 1.545582 GCCAAGAATTAGCAGGTGCAA 59.454 47.619 4.48 0.00 45.16 4.08
2577 2586 0.319813 GTGCAATTTCACCCACCAGC 60.320 55.000 0.00 0.00 0.00 4.85
2581 2590 0.105760 AATTTCACCCACCAGCACCA 60.106 50.000 0.00 0.00 0.00 4.17
2603 2613 7.391833 CACCATCCTTTTTCTAATCTATAGGCC 59.608 40.741 0.00 0.00 0.00 5.19
2604 2614 7.295911 ACCATCCTTTTTCTAATCTATAGGCCT 59.704 37.037 11.78 11.78 0.00 5.19
2605 2615 7.826744 CCATCCTTTTTCTAATCTATAGGCCTC 59.173 40.741 9.68 0.00 0.00 4.70
2669 2679 7.411486 TTTGGTAACCTGTGAATTTTCTGAA 57.589 32.000 0.00 0.00 0.00 3.02
2670 2680 7.595819 TTGGTAACCTGTGAATTTTCTGAAT 57.404 32.000 0.00 0.00 0.00 2.57
2671 2681 8.698973 TTGGTAACCTGTGAATTTTCTGAATA 57.301 30.769 0.00 0.00 0.00 1.75
2672 2682 8.335532 TGGTAACCTGTGAATTTTCTGAATAG 57.664 34.615 0.00 0.00 0.00 1.73
2673 2683 8.160765 TGGTAACCTGTGAATTTTCTGAATAGA 58.839 33.333 0.00 0.00 0.00 1.98
2674 2684 9.178758 GGTAACCTGTGAATTTTCTGAATAGAT 57.821 33.333 0.00 0.00 31.81 1.98
2703 2713 9.589111 TGTCAAATATCATTTTGATGGAATGTG 57.411 29.630 3.25 0.00 44.80 3.21
2720 2730 3.902261 TGTGCTTCACATTCACATGAC 57.098 42.857 0.00 0.00 39.62 3.06
2742 2752 3.449746 TGTGGGCCTGCTAAATTAGTT 57.550 42.857 4.53 0.00 0.00 2.24
2745 2755 2.310349 TGGGCCTGCTAAATTAGTTCCA 59.690 45.455 4.53 1.05 0.00 3.53
2795 2805 8.438676 AATATTTGTACCTTACATGACAGCTC 57.561 34.615 0.00 0.00 38.68 4.09
2810 2820 6.072112 TGACAGCTCTACAAAAACAAATCC 57.928 37.500 0.00 0.00 0.00 3.01
2820 2830 9.703892 TCTACAAAAACAAATCCCATTATGTTG 57.296 29.630 0.00 0.00 36.23 3.33
2821 2831 9.487790 CTACAAAAACAAATCCCATTATGTTGT 57.512 29.630 0.00 0.00 36.23 3.32
2822 2832 8.376889 ACAAAAACAAATCCCATTATGTTGTC 57.623 30.769 0.54 0.00 36.23 3.18
2823 2833 8.210265 ACAAAAACAAATCCCATTATGTTGTCT 58.790 29.630 0.54 0.00 36.23 3.41
2824 2834 9.703892 CAAAAACAAATCCCATTATGTTGTCTA 57.296 29.630 0.54 0.00 36.23 2.59
2910 2921 3.488721 GCTCCATGAATCAGTGCATGAAC 60.489 47.826 9.92 0.00 43.43 3.18
2927 2938 5.716094 CATGAACTCAATGAATTTGCCTCA 58.284 37.500 0.00 0.00 35.16 3.86
2936 2947 3.433343 TGAATTTGCCTCACATGGATGT 58.567 40.909 0.00 0.00 42.84 3.06
2948 2959 6.430925 CCTCACATGGATGTAAGAAAAACTCA 59.569 38.462 0.00 0.00 39.39 3.41
2967 2978 2.700371 TCAGAAGACTCCAGTTGAGCAA 59.300 45.455 0.00 0.00 45.61 3.91
2976 2987 2.633967 TCCAGTTGAGCAAATGCCATTT 59.366 40.909 5.23 0.00 43.38 2.32
3157 3168 7.954666 AAGCCTGCTACTAAATATCCAAAAA 57.045 32.000 0.00 0.00 0.00 1.94
3189 3200 9.160496 GATGAGATTGAATGGGAACTCATATAC 57.840 37.037 0.00 0.00 42.51 1.47
3230 3241 8.779354 ATTTCAAATTATAGGCGGAGAGTATC 57.221 34.615 0.00 0.00 0.00 2.24
3231 3242 6.911250 TCAAATTATAGGCGGAGAGTATCA 57.089 37.500 0.00 0.00 37.82 2.15
3232 3243 6.688578 TCAAATTATAGGCGGAGAGTATCAC 58.311 40.000 0.00 0.00 37.82 3.06
3233 3244 4.966965 ATTATAGGCGGAGAGTATCACG 57.033 45.455 0.00 0.00 40.06 4.35
3234 3245 1.535833 ATAGGCGGAGAGTATCACGG 58.464 55.000 0.00 0.00 38.03 4.94
3235 3246 0.182061 TAGGCGGAGAGTATCACGGT 59.818 55.000 0.00 0.00 38.03 4.83
3246 3257 2.095364 AGTATCACGGTCACACTCGTTC 60.095 50.000 0.00 0.00 37.53 3.95
3295 3306 6.652481 CACCCATTATGACAAGGTATCTCATC 59.348 42.308 0.00 0.00 0.00 2.92
3333 3344 2.422127 GCCAATTGCTACCGTTGTACAT 59.578 45.455 0.00 0.00 36.87 2.29
3348 3359 5.221145 CGTTGTACATAGGCTCAGAGAAGAT 60.221 44.000 0.00 0.00 0.00 2.40
3354 3365 5.369110 ACATAGGCTCAGAGAAGATTTCCAT 59.631 40.000 0.00 0.00 0.00 3.41
3384 3395 5.104735 TGCAGAAATTTACCCCACTGTTTTT 60.105 36.000 0.00 0.00 0.00 1.94
3390 3401 0.823460 ACCCCACTGTTTTTGCTGTG 59.177 50.000 0.00 0.00 37.83 3.66
3396 3407 1.670811 ACTGTTTTTGCTGTGGACTCG 59.329 47.619 0.00 0.00 0.00 4.18
3402 3413 1.256812 TTGCTGTGGACTCGAGATCA 58.743 50.000 21.68 13.58 0.00 2.92
3429 3440 5.239525 GGTTTCAGTAAGCAAACTCACTCAT 59.760 40.000 0.00 0.00 33.70 2.90
3433 3444 4.153117 CAGTAAGCAAACTCACTCATCACC 59.847 45.833 0.00 0.00 0.00 4.02
3439 3450 0.244994 ACTCACTCATCACCTGCGAC 59.755 55.000 0.00 0.00 0.00 5.19
3458 3469 5.238432 TGCGACAGACAACAAAGACAATAAT 59.762 36.000 0.00 0.00 0.00 1.28
3533 3544 4.574013 GCATGACTGGAGGTTGAAGAATAG 59.426 45.833 0.00 0.00 0.00 1.73
3540 3551 3.369892 GGAGGTTGAAGAATAGCAGAGCA 60.370 47.826 0.00 0.00 0.00 4.26
3589 3600 2.154567 ATGCCAGCTCAACATTCCAT 57.845 45.000 0.00 0.00 0.00 3.41
3590 3601 1.466856 TGCCAGCTCAACATTCCATC 58.533 50.000 0.00 0.00 0.00 3.51
3656 3667 1.954146 GGAGACGTGCTGTTGCGAA 60.954 57.895 0.00 0.00 43.34 4.70
3783 3794 7.495279 ACATTGAAGTCAATCAAGATAGAGAGC 59.505 37.037 3.51 0.00 44.10 4.09
3801 3812 1.039856 GCAGTGGTGGTTTTGTCCAT 58.960 50.000 0.00 0.00 39.81 3.41
3811 3822 5.070685 GTGGTTTTGTCCATAAAGAGGAGT 58.929 41.667 0.00 0.00 39.81 3.85
3820 3831 4.471386 TCCATAAAGAGGAGTTGGAGAAGG 59.529 45.833 0.00 0.00 32.80 3.46
3822 3833 5.280727 CCATAAAGAGGAGTTGGAGAAGGTT 60.281 44.000 0.00 0.00 0.00 3.50
3855 3866 1.000385 CTGCGCAACCAAATTCCAAGA 60.000 47.619 13.05 0.00 0.00 3.02
3856 3867 1.410517 TGCGCAACCAAATTCCAAGAA 59.589 42.857 8.16 0.00 0.00 2.52
4001 4012 2.140224 TGAGGAAAACAAAGGAGGGGA 58.860 47.619 0.00 0.00 0.00 4.81
4066 4077 1.590238 GGCGTCTCGAATGTGAAGATG 59.410 52.381 0.00 0.00 0.00 2.90
4080 4091 4.466015 TGTGAAGATGTACACATGCTCCTA 59.534 41.667 0.00 0.00 41.19 2.94
4169 4180 4.520111 TGTAGCTGCCAATATATTGCAAGG 59.480 41.667 18.40 7.44 36.48 3.61
4221 4232 4.727448 GCAAAAACAATGCCACAGTTGTTC 60.727 41.667 4.22 0.00 45.05 3.18
4264 4275 7.437748 ACTCTTGAACATATATACTGACTGGC 58.562 38.462 0.00 0.00 0.00 4.85
4440 4451 7.336679 CAGTGATTAATGGTGTCCATGTAAAGA 59.663 37.037 1.86 0.00 44.40 2.52
4469 4480 3.245371 TGGGAATGAAGTTTGGCTCATCT 60.245 43.478 0.00 0.00 0.00 2.90
4491 4502 0.323087 AGATGTGCTTGCATGCTCCA 60.323 50.000 23.31 19.22 0.00 3.86
4620 4631 7.619965 TGACTGTGTGAAATATCTCATACCAA 58.380 34.615 3.76 0.00 36.81 3.67
4640 4651 1.134220 AGAAGGTTCCGTGCAACTCAA 60.134 47.619 0.00 0.00 31.75 3.02
4809 4820 7.930325 TATCAGATGATGACTTCCATGAAGTTC 59.070 37.037 10.55 6.38 42.52 3.01
4865 4876 1.821061 CTGAACTCGCTGTCACCCCT 61.821 60.000 0.00 0.00 0.00 4.79
4889 4900 0.037877 ATCTGCAGCAGCCTGAAACT 59.962 50.000 18.43 0.00 41.77 2.66
4895 4906 1.211457 CAGCAGCCTGAAACTATCCCT 59.789 52.381 0.00 0.00 41.77 4.20
4940 4951 3.531207 CTGGGCATCGCGAGAGGA 61.531 66.667 16.66 0.00 46.52 3.71
5042 5053 4.077108 ACTACGAGTATCACCTTGTGACA 58.923 43.478 0.00 0.00 45.65 3.58
5057 5068 1.070758 GTGACAGAGCTCCACAGGAAA 59.929 52.381 10.93 0.00 0.00 3.13
5120 5131 5.879223 CAGAAAAGTGCCTCAGATGTTCTAT 59.121 40.000 0.00 0.00 0.00 1.98
5171 5182 1.077429 GGTCACAAGGATCCTGCCC 60.077 63.158 17.02 7.33 0.00 5.36
5179 5190 4.881440 GATCCTGCCCGGCATGCA 62.881 66.667 21.36 0.00 38.13 3.96
5186 5197 2.515398 CCCGGCATGCAATCCCTA 59.485 61.111 21.36 0.00 0.00 3.53
5246 5257 0.261696 TGGTGGAGGATCAGATCGGA 59.738 55.000 4.23 0.00 36.25 4.55
5249 5260 1.967066 GTGGAGGATCAGATCGGATGT 59.033 52.381 13.38 0.12 36.25 3.06
5331 5342 3.334583 TGAAGCTCTTAACATTCGCCT 57.665 42.857 0.00 0.00 0.00 5.52
5342 5353 1.207089 ACATTCGCCTTGAAGATCGGA 59.793 47.619 0.00 0.00 40.65 4.55
5345 5356 2.233654 CGCCTTGAAGATCGGAGCG 61.234 63.158 0.00 0.00 35.82 5.03
5420 5431 2.659016 CTGCTTGACTCCTCGGCA 59.341 61.111 0.00 0.00 0.00 5.69
5477 5488 2.183300 GCGGCAGTGATGTACGGA 59.817 61.111 0.00 0.00 0.00 4.69
5480 5491 0.172578 CGGCAGTGATGTACGGAAGA 59.827 55.000 0.00 0.00 0.00 2.87
5492 5503 1.179814 ACGGAAGAGCGAGGAACAGT 61.180 55.000 0.00 0.00 0.00 3.55
5496 5507 1.758440 AAGAGCGAGGAACAGTGGCA 61.758 55.000 0.00 0.00 0.00 4.92
5585 5596 3.706594 GAGTTCTGACAGGGATGGACATA 59.293 47.826 1.81 0.00 0.00 2.29
5753 5768 1.915769 ACAGGTGCCTCCCTCTCAC 60.916 63.158 0.00 0.00 36.75 3.51
5764 5779 1.214062 CCTCTCACGTCACTCTGCC 59.786 63.158 0.00 0.00 0.00 4.85
5785 5800 3.553096 CCGATAGCCTGATAGGTGACAAC 60.553 52.174 0.00 0.00 37.80 3.32
5850 5882 8.039603 TGTCAAAATGTGTGTATTCCTGTATC 57.960 34.615 0.00 0.00 0.00 2.24
5854 5886 7.630242 AAATGTGTGTATTCCTGTATCCTTG 57.370 36.000 0.00 0.00 0.00 3.61
5855 5887 4.513442 TGTGTGTATTCCTGTATCCTTGC 58.487 43.478 0.00 0.00 0.00 4.01
5856 5888 4.019771 TGTGTGTATTCCTGTATCCTTGCA 60.020 41.667 0.00 0.00 0.00 4.08
5857 5889 4.941263 GTGTGTATTCCTGTATCCTTGCAA 59.059 41.667 0.00 0.00 0.00 4.08
5862 5894 4.454728 TTCCTGTATCCTTGCAAATTGC 57.545 40.909 11.58 11.58 45.29 3.56
5867 5899 5.212532 TGTATCCTTGCAAATTGCTTTGT 57.787 34.783 19.34 4.39 45.31 2.83
5893 5925 4.618927 GCTGCTTTGCATTGACCATTTCTA 60.619 41.667 0.00 0.00 38.13 2.10
5898 5930 6.587206 TTTGCATTGACCATTTCTATGTGA 57.413 33.333 0.00 0.00 39.07 3.58
5902 5935 6.183360 TGCATTGACCATTTCTATGTGAATCC 60.183 38.462 0.00 0.00 39.07 3.01
5921 5954 6.667848 TGAATCCTCACACTAATACTGAAGGA 59.332 38.462 0.00 0.00 0.00 3.36
5928 5961 7.492524 TCACACTAATACTGAAGGATGTGATC 58.507 38.462 0.00 0.00 40.05 2.92
5935 5968 3.133721 ACTGAAGGATGTGATCTGCCTAC 59.866 47.826 0.00 0.00 0.00 3.18
5943 5980 5.163703 GGATGTGATCTGCCTACGAGTATAG 60.164 48.000 0.00 0.00 0.00 1.31
6050 6092 0.882927 GCGGCTGCATCGGGTAATTA 60.883 55.000 14.08 0.00 42.15 1.40
6575 6623 0.107081 CACACCAGGTTCCGGTACAA 59.893 55.000 13.64 0.00 34.02 2.41
6651 6699 0.389426 CGAAGGTGACCCGGTACTTG 60.389 60.000 0.00 0.00 35.12 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.963129 TCCTTCACTTCACCACAGTTTT 58.037 40.909 0.00 0.00 0.00 2.43
13 14 9.733556 TGCTACTTTATTTTATCCTTCACTTCA 57.266 29.630 0.00 0.00 0.00 3.02
205 206 5.782893 ACAGAGACTGAGCCTTATATGAC 57.217 43.478 5.76 0.00 35.18 3.06
239 240 2.000048 AGTTAGCCCATCCTTTTCCCA 59.000 47.619 0.00 0.00 0.00 4.37
294 295 5.467063 CAGAAGTGTCCAGGAAGTAAAGAAC 59.533 44.000 0.00 0.00 0.00 3.01
334 335 0.373370 TATTGCAGTGCGCGCTTTAG 59.627 50.000 33.29 19.55 46.97 1.85
377 378 9.295825 TGTCTTACATCACTGGTAATCAATTTT 57.704 29.630 0.00 0.00 30.93 1.82
482 483 7.920682 ACAAATTTTGACAGGAAACATCTACAC 59.079 33.333 15.81 0.00 0.00 2.90
539 540 2.687425 CGTGCACCCATCCAAAATATCA 59.313 45.455 12.15 0.00 0.00 2.15
540 541 2.687935 ACGTGCACCCATCCAAAATATC 59.312 45.455 12.15 0.00 0.00 1.63
541 542 2.733956 ACGTGCACCCATCCAAAATAT 58.266 42.857 12.15 0.00 0.00 1.28
542 543 2.208132 ACGTGCACCCATCCAAAATA 57.792 45.000 12.15 0.00 0.00 1.40
543 544 2.091541 CTACGTGCACCCATCCAAAAT 58.908 47.619 12.15 0.00 0.00 1.82
544 545 1.202830 ACTACGTGCACCCATCCAAAA 60.203 47.619 12.15 0.00 0.00 2.44
545 546 0.398696 ACTACGTGCACCCATCCAAA 59.601 50.000 12.15 0.00 0.00 3.28
546 547 0.398696 AACTACGTGCACCCATCCAA 59.601 50.000 12.15 0.00 0.00 3.53
659 668 4.174009 CACGTACCAAGGTATCAGAGTTG 58.826 47.826 1.74 0.00 32.82 3.16
664 673 3.518590 GTTCCACGTACCAAGGTATCAG 58.481 50.000 1.74 0.75 32.82 2.90
686 695 5.248087 CAAGTATACGAAATCACTTGCGTG 58.752 41.667 1.71 0.00 40.82 5.34
699 708 9.309516 CAAAGCTAATAAGTTCCAAGTATACGA 57.690 33.333 0.00 0.00 0.00 3.43
881 890 5.973565 GGTGTCTGAACAAAACAGATTTCAG 59.026 40.000 0.00 4.18 44.41 3.02
961 970 1.980765 AGAGCAGTTGAATCAGGGACA 59.019 47.619 0.00 0.00 0.00 4.02
1022 1031 3.967326 CTCCTGGTTAGATGGTGATGGTA 59.033 47.826 0.00 0.00 0.00 3.25
1128 1137 0.035458 CCATAGACAAGCCCGATCCC 59.965 60.000 0.00 0.00 0.00 3.85
1189 1198 3.565482 TCAAGCAGAAAGTTGACACCATC 59.435 43.478 0.00 0.00 0.00 3.51
1329 1338 0.674581 CCTGCTTCACATTCGAGCCA 60.675 55.000 0.00 0.00 35.59 4.75
1804 1813 0.382515 GCACAAGCAACCCGTTGTAA 59.617 50.000 9.21 0.00 42.31 2.41
1863 1872 0.836400 TGGACTTCAGAGGGACACCC 60.836 60.000 0.00 0.00 45.90 4.61
2091 2100 0.819259 TGGCTTGTGTCTGAAGTGGC 60.819 55.000 0.00 0.00 0.00 5.01
2307 2316 1.064166 CCCTTGCACCCTCTGAATGAT 60.064 52.381 0.00 0.00 0.00 2.45
2346 2355 9.237187 TGCAAAGTATTCATAATGGTCTGTAAA 57.763 29.630 0.00 0.00 0.00 2.01
2445 2454 5.178797 CCGTTCTGACCAAGTTTCTCATAT 58.821 41.667 0.00 0.00 0.00 1.78
2460 2469 1.766496 AGAACCAAACTCCCGTTCTGA 59.234 47.619 1.11 0.00 43.44 3.27
2563 2572 0.114954 ATGGTGCTGGTGGGTGAAAT 59.885 50.000 0.00 0.00 0.00 2.17
2573 2582 4.952335 AGATTAGAAAAAGGATGGTGCTGG 59.048 41.667 0.00 0.00 0.00 4.85
2577 2586 7.391833 GGCCTATAGATTAGAAAAAGGATGGTG 59.608 40.741 0.00 0.00 0.00 4.17
2581 2590 8.511748 TGAGGCCTATAGATTAGAAAAAGGAT 57.488 34.615 4.42 0.00 0.00 3.24
2633 2643 5.772672 ACAGGTTACCAAAATTGTATGCTGA 59.227 36.000 3.51 0.00 0.00 4.26
2648 2658 8.561738 TCTATTCAGAAAATTCACAGGTTACC 57.438 34.615 0.00 0.00 0.00 2.85
2701 2711 3.902261 TGTCATGTGAATGTGAAGCAC 57.098 42.857 0.00 0.00 34.56 4.40
2703 2713 4.430137 ACATGTCATGTGAATGTGAAGC 57.570 40.909 17.74 0.00 43.01 3.86
2720 2730 3.290710 ACTAATTTAGCAGGCCCACATG 58.709 45.455 0.00 0.00 0.00 3.21
2745 2755 7.197071 TGTATAGCGAAGTCAACAAAATGTT 57.803 32.000 0.00 0.00 42.08 2.71
2768 2778 8.677300 AGCTGTCATGTAAGGTACAAATATTTG 58.323 33.333 23.60 23.60 42.76 2.32
2775 2785 5.479027 TGTAGAGCTGTCATGTAAGGTACAA 59.521 40.000 0.00 0.00 42.76 2.41
2795 2805 9.487790 ACAACATAATGGGATTTGTTTTTGTAG 57.512 29.630 0.00 0.00 30.23 2.74
2824 2834 9.807649 GAAGCATCACATTTATAACCAATTCTT 57.192 29.630 0.00 0.00 0.00 2.52
2910 2921 4.158949 TCCATGTGAGGCAAATTCATTGAG 59.841 41.667 0.00 0.00 41.85 3.02
2927 2938 7.939039 TCTTCTGAGTTTTTCTTACATCCATGT 59.061 33.333 0.00 0.00 44.48 3.21
2936 2947 7.125792 ACTGGAGTCTTCTGAGTTTTTCTTA 57.874 36.000 0.00 0.00 0.00 2.10
2948 2959 3.845781 TTTGCTCAACTGGAGTCTTCT 57.154 42.857 0.00 0.00 45.88 2.85
2967 2978 6.998074 TCTTATTCTCATCGGTAAATGGCATT 59.002 34.615 6.96 6.96 0.00 3.56
2976 2987 7.582667 TGAGTTCATCTTATTCTCATCGGTA 57.417 36.000 0.00 0.00 31.51 4.02
3157 3168 5.837770 TCCCATTCAATCTCATCTATGCT 57.162 39.130 0.00 0.00 0.00 3.79
3165 3176 8.152898 CAGTATATGAGTTCCCATTCAATCTCA 58.847 37.037 0.00 0.00 36.58 3.27
3189 3200 3.415212 TGAAATCAAGAACCTCAGCCAG 58.585 45.455 0.00 0.00 0.00 4.85
3230 3241 3.932289 GGAACGAGTGTGACCGTG 58.068 61.111 0.00 0.00 39.14 4.94
3246 3257 4.643784 AGAACTATAGTTACACAGGGTCGG 59.356 45.833 18.03 0.00 38.56 4.79
3322 3333 2.427453 CTCTGAGCCTATGTACAACGGT 59.573 50.000 0.00 0.00 0.00 4.83
3333 3344 5.426509 TGAATGGAAATCTTCTCTGAGCCTA 59.573 40.000 0.00 0.00 0.00 3.93
3348 3359 6.873076 GGTAAATTTCTGCATGTGAATGGAAA 59.127 34.615 0.00 0.00 0.00 3.13
3354 3365 4.021544 GTGGGGTAAATTTCTGCATGTGAA 60.022 41.667 0.00 0.00 0.00 3.18
3384 3395 1.478631 ATGATCTCGAGTCCACAGCA 58.521 50.000 13.13 1.44 0.00 4.41
3390 3401 3.861840 TGAAACCAATGATCTCGAGTCC 58.138 45.455 13.13 6.11 0.00 3.85
3396 3407 6.500684 TTGCTTACTGAAACCAATGATCTC 57.499 37.500 0.00 0.00 0.00 2.75
3402 3413 5.594317 AGTGAGTTTGCTTACTGAAACCAAT 59.406 36.000 0.00 0.00 39.66 3.16
3429 3440 0.176910 TTGTTGTCTGTCGCAGGTGA 59.823 50.000 6.95 0.00 31.51 4.02
3433 3444 1.933181 TGTCTTTGTTGTCTGTCGCAG 59.067 47.619 1.02 1.02 0.00 5.18
3439 3450 7.424803 TGTTGGATTATTGTCTTTGTTGTCTG 58.575 34.615 0.00 0.00 0.00 3.51
3458 3469 6.361433 TCATAAACTTGAGGAACTTGTTGGA 58.639 36.000 0.00 0.00 41.55 3.53
3533 3544 0.743701 CCACCTGATCACTGCTCTGC 60.744 60.000 0.00 0.00 0.00 4.26
3540 3551 4.567195 TCAGCCCACCTGATCACT 57.433 55.556 0.00 0.00 45.44 3.41
3589 3600 2.030717 GCCTCGATCTCAATCTTAGCGA 60.031 50.000 0.00 0.00 0.00 4.93
3590 3601 2.323959 GCCTCGATCTCAATCTTAGCG 58.676 52.381 0.00 0.00 0.00 4.26
3654 3665 3.129287 CACCCAAGGTATGCAGTGATTTC 59.871 47.826 0.00 0.00 35.10 2.17
3656 3667 2.308570 TCACCCAAGGTATGCAGTGATT 59.691 45.455 0.00 0.00 36.46 2.57
3783 3794 4.582656 TCTTTATGGACAAAACCACCACTG 59.417 41.667 0.00 0.00 43.03 3.66
3801 3812 5.012148 CAGAACCTTCTCCAACTCCTCTTTA 59.988 44.000 0.00 0.00 34.74 1.85
3811 3822 2.705658 TCTCTTGCAGAACCTTCTCCAA 59.294 45.455 0.00 0.00 32.82 3.53
3820 3831 0.165511 CGCAGCTTCTCTTGCAGAAC 59.834 55.000 0.00 0.00 36.08 3.01
3822 3833 4.273811 CGCAGCTTCTCTTGCAGA 57.726 55.556 0.00 0.00 0.00 4.26
3855 3866 2.024414 GCACCAGTTCTCCAGTTTGTT 58.976 47.619 0.00 0.00 0.00 2.83
3856 3867 1.064758 TGCACCAGTTCTCCAGTTTGT 60.065 47.619 0.00 0.00 0.00 2.83
4001 4012 6.382869 GCATAGTTAACTGCCATTTCTCAT 57.617 37.500 18.56 0.00 32.15 2.90
4066 4077 4.389077 GTCACTTGTTAGGAGCATGTGTAC 59.611 45.833 0.00 0.00 40.57 2.90
4440 4451 3.094572 CAAACTTCATTCCCAGCTCCAT 58.905 45.455 0.00 0.00 0.00 3.41
4469 4480 3.181452 TGGAGCATGCAAGCACATCTATA 60.181 43.478 21.98 0.00 28.48 1.31
4491 4502 7.878127 CCTCACCATGTCCGTAATATTTCTATT 59.122 37.037 0.00 0.00 0.00 1.73
4620 4631 0.468226 TGAGTTGCACGGAACCTTCT 59.532 50.000 0.00 0.00 0.00 2.85
4659 4670 6.293955 GGCAGTGACAGTAGAATTTGCTTTAA 60.294 38.462 0.00 0.00 0.00 1.52
4763 4774 0.179702 GCAGATCTCTGGCATGGTCA 59.820 55.000 9.15 0.00 43.94 4.02
4809 4820 6.926826 TGTAAATCATAATACCTACGGTGCAG 59.073 38.462 0.00 0.00 36.19 4.41
4856 4867 0.036732 GCAGATTGTCAGGGGTGACA 59.963 55.000 4.10 4.10 45.85 3.58
4865 4876 0.958876 CAGGCTGCTGCAGATTGTCA 60.959 55.000 32.30 4.14 41.91 3.58
4889 4900 0.824109 CCACGTCTGCTTCAGGGATA 59.176 55.000 0.00 0.00 31.51 2.59
4895 4906 1.608025 GGATCAACCACGTCTGCTTCA 60.608 52.381 0.00 0.00 38.79 3.02
5042 5053 1.988107 TCCATTTTCCTGTGGAGCTCT 59.012 47.619 14.64 0.00 39.51 4.09
5057 5068 5.651530 CTGTAGTTCATCACGTAGTCCATT 58.348 41.667 0.00 0.00 41.61 3.16
5171 5182 3.333414 CGTAGGGATTGCATGCCG 58.667 61.111 16.68 4.66 46.65 5.69
5246 5257 2.767972 TCCACCTGGATCAGATCACAT 58.232 47.619 12.66 0.00 39.78 3.21
5331 5342 1.665679 GAAATGCGCTCCGATCTTCAA 59.334 47.619 9.73 0.00 0.00 2.69
5342 5353 0.676466 TCCCAACGATGAAATGCGCT 60.676 50.000 9.73 0.00 0.00 5.92
5384 5395 3.957586 TGCACCACCTCCCTGCTG 61.958 66.667 0.00 0.00 0.00 4.41
5439 5450 4.051167 TAGAGCCCCCACCGACGA 62.051 66.667 0.00 0.00 0.00 4.20
5477 5488 1.004440 GCCACTGTTCCTCGCTCTT 60.004 57.895 0.00 0.00 0.00 2.85
5480 5491 2.031163 GTGCCACTGTTCCTCGCT 59.969 61.111 0.00 0.00 0.00 4.93
5492 5503 2.282110 CCCATGTCGTTGGTGCCA 60.282 61.111 0.00 0.00 34.77 4.92
5496 5507 2.602676 CCTCCCCCATGTCGTTGGT 61.603 63.158 0.00 0.00 34.77 3.67
5540 5551 0.620556 GCCCTCTCAGGAAATCCACA 59.379 55.000 1.67 0.00 37.67 4.17
5764 5779 3.319405 AGTTGTCACCTATCAGGCTATCG 59.681 47.826 0.00 0.00 39.63 2.92
5785 5800 8.143193 AGAACAGAGCATATTCACTATTCTCAG 58.857 37.037 0.00 0.00 33.86 3.35
5819 5851 7.231317 AGGAATACACACATTTTGACAGAACAT 59.769 33.333 0.00 0.00 0.00 2.71
5821 5853 6.857964 CAGGAATACACACATTTTGACAGAAC 59.142 38.462 0.00 0.00 0.00 3.01
5832 5864 5.126067 GCAAGGATACAGGAATACACACAT 58.874 41.667 0.00 0.00 41.41 3.21
5855 5887 3.955771 AGCAGCAAACAAAGCAATTTG 57.044 38.095 0.00 0.00 38.57 2.32
5856 5888 4.664188 CAAAGCAGCAAACAAAGCAATTT 58.336 34.783 0.00 0.00 0.00 1.82
5857 5889 3.487879 GCAAAGCAGCAAACAAAGCAATT 60.488 39.130 0.00 0.00 0.00 2.32
5873 5905 5.290158 CACATAGAAATGGTCAATGCAAAGC 59.710 40.000 0.00 0.00 37.43 3.51
5898 5930 7.126421 ACATCCTTCAGTATTAGTGTGAGGATT 59.874 37.037 22.59 16.24 38.90 3.01
5902 5935 6.867550 TCACATCCTTCAGTATTAGTGTGAG 58.132 40.000 0.00 0.00 39.57 3.51
5914 5947 3.726607 GTAGGCAGATCACATCCTTCAG 58.273 50.000 0.00 0.00 0.00 3.02
5921 5954 5.317808 ACTATACTCGTAGGCAGATCACAT 58.682 41.667 0.00 0.00 0.00 3.21
5935 5968 4.937696 ATCATCGCTCTGACTATACTCG 57.062 45.455 0.00 0.00 0.00 4.18
5943 5980 8.472683 AGCTTATATAAAATCATCGCTCTGAC 57.527 34.615 0.00 0.00 0.00 3.51
6050 6092 3.118884 GCCATGAATTCAACCTCTGCATT 60.119 43.478 13.09 0.00 0.00 3.56
6085 6129 1.953138 GCAGCGATCATCGTCTGGG 60.953 63.158 23.85 8.30 42.81 4.45
6324 6372 3.366679 GGCAGAAGTACAACTACGTGCTA 60.367 47.826 0.00 0.00 33.12 3.49
6543 6591 2.251642 GGTGTGGCTGTTCGTGGTC 61.252 63.158 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.