Multiple sequence alignment - TraesCS2A01G115100

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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 TraesCS2A01G115100 chr2A 100.000 3115 0 0 1 3115 65675262 65672148 0.000000e+00 5753
1 TraesCS2A01G115100 chr2D 93.672 2639 130 19 506 3115 64192026 64189396 0.000000e+00 3914
2 TraesCS2A01G115100 chr2D 88.800 500 49 7 5 502 64192560 64192066 9.550000e-170 606
3 TraesCS2A01G115100 chr2B 91.784 2349 152 23 506 2820 100343767 100341426 0.000000e+00 3230
4 TraesCS2A01G115100 chr2B 86.133 375 47 3 4 377 100344272 100343902 1.740000e-107 399
5 TraesCS2A01G115100 chr2B 91.441 222 12 4 2855 3071 100341427 100341208 6.530000e-77 298
6 TraesCS2A01G115100 chr2B 91.765 85 7 0 418 502 100343891 100343807 5.460000e-23 119


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 TraesCS2A01G115100 chr2A 65672148 65675262 3114 True 5753.0 5753 100.00000 1 3115 1 chr2A.!!$R1 3114
1 TraesCS2A01G115100 chr2D 64189396 64192560 3164 True 2260.0 3914 91.23600 5 3115 2 chr2D.!!$R1 3110
2 TraesCS2A01G115100 chr2B 100341208 100344272 3064 True 1011.5 3230 90.28075 4 3071 4 chr2B.!!$R1 3067

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
110 111 0.025513 CGCTTGAAAATCTCGCTCCG 59.974 55.0 0.0 0.0 0.00 4.63 F
752 799 0.033228 CATTTTCCTGTTTGGCCGCA 59.967 50.0 0.0 0.0 35.26 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1128 0.243636 GGTTGCAATGCCACAGTACC 59.756 55.0 11.57 2.07 0.0 3.34 R
2429 2488 1.118838 CAAACAGCCCCTTCACCAAA 58.881 50.0 0.00 0.00 0.0 3.28 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
36 37 4.530857 CGCACCCGTCCATCTCCC 62.531 72.222 0.00 0.00 0.00 4.30
61 62 2.052414 CCGAGGTACGTCGCGATC 60.052 66.667 27.80 3.10 38.69 3.69
74 75 2.452064 GCGATCCCATCCTCCCCAA 61.452 63.158 0.00 0.00 0.00 4.12
78 79 2.068977 GATCCCATCCTCCCCAAATCT 58.931 52.381 0.00 0.00 0.00 2.40
95 96 2.472695 TCTATCCACTGTTTGCGCTT 57.527 45.000 9.73 0.00 0.00 4.68
98 99 1.317613 ATCCACTGTTTGCGCTTGAA 58.682 45.000 9.73 0.00 0.00 2.69
107 108 0.874390 TTGCGCTTGAAAATCTCGCT 59.126 45.000 9.73 0.00 45.24 4.93
110 111 0.025513 CGCTTGAAAATCTCGCTCCG 59.974 55.000 0.00 0.00 0.00 4.63
148 149 0.963962 TTATCGCCGGACCTGTATCC 59.036 55.000 5.05 0.00 35.16 2.59
149 150 0.111832 TATCGCCGGACCTGTATCCT 59.888 55.000 5.05 0.00 36.52 3.24
212 213 2.226437 AGAATTTTGTGCGCGTGATCTT 59.774 40.909 8.43 0.00 0.00 2.40
267 268 2.509916 CCCAGAGGATGCCAGAGC 59.490 66.667 0.00 0.00 35.36 4.09
268 269 2.108566 CCAGAGGATGCCAGAGCG 59.891 66.667 0.00 0.00 44.31 5.03
271 272 2.132996 AGAGGATGCCAGAGCGGAG 61.133 63.158 0.00 0.00 44.31 4.63
273 274 3.157252 GGATGCCAGAGCGGAGGA 61.157 66.667 0.00 0.00 44.31 3.71
284 285 1.763545 GAGCGGAGGAGATAGGGTTTT 59.236 52.381 0.00 0.00 0.00 2.43
301 304 6.494059 AGGGTTTTTGGCTGTAATCTTAGAT 58.506 36.000 0.00 0.00 0.00 1.98
327 330 6.371809 TTTTCATAATGAGGTACCAATCGC 57.628 37.500 15.94 0.00 0.00 4.58
330 333 6.413783 TCATAATGAGGTACCAATCGCTTA 57.586 37.500 15.94 6.57 0.00 3.09
331 334 6.455647 TCATAATGAGGTACCAATCGCTTAG 58.544 40.000 15.94 0.00 0.00 2.18
333 336 3.520290 TGAGGTACCAATCGCTTAGTG 57.480 47.619 15.94 0.00 0.00 2.74
334 337 2.202566 GAGGTACCAATCGCTTAGTGC 58.797 52.381 15.94 0.00 38.57 4.40
335 338 1.134491 AGGTACCAATCGCTTAGTGCC 60.134 52.381 15.94 0.00 38.78 5.01
336 339 1.406341 GGTACCAATCGCTTAGTGCCA 60.406 52.381 7.15 0.00 38.78 4.92
338 341 0.324943 ACCAATCGCTTAGTGCCAGT 59.675 50.000 0.00 0.00 38.78 4.00
339 342 0.729116 CCAATCGCTTAGTGCCAGTG 59.271 55.000 0.00 0.00 38.78 3.66
340 343 0.729116 CAATCGCTTAGTGCCAGTGG 59.271 55.000 4.20 4.20 38.78 4.00
341 344 0.613260 AATCGCTTAGTGCCAGTGGA 59.387 50.000 15.20 0.00 38.78 4.02
395 398 1.440353 GAATGCGTGTGGTCGTTGC 60.440 57.895 0.00 0.00 0.00 4.17
414 417 7.641411 GTCGTTGCTCATAACTACTTCGTATAA 59.359 37.037 0.00 0.00 0.00 0.98
422 425 9.956720 TCATAACTACTTCGTATAAAACCTAGC 57.043 33.333 0.00 0.00 0.00 3.42
423 426 9.740239 CATAACTACTTCGTATAAAACCTAGCA 57.260 33.333 0.00 0.00 0.00 3.49
449 452 2.506957 GGCTGGTTGGGTGTTTGGG 61.507 63.158 0.00 0.00 0.00 4.12
460 463 2.224185 GGGTGTTTGGGCGAATTTCTTT 60.224 45.455 0.00 0.00 0.00 2.52
520 559 5.815850 TGCACGTATGTATTTGGCTAAATG 58.184 37.500 17.44 2.90 37.12 2.32
565 604 3.976169 TGTAAAGTTGTTCATGCCTTGC 58.024 40.909 0.00 0.00 0.00 4.01
569 608 1.761784 AGTTGTTCATGCCTTGCCAAA 59.238 42.857 0.00 0.00 0.00 3.28
570 609 2.369532 AGTTGTTCATGCCTTGCCAAAT 59.630 40.909 0.00 0.00 0.00 2.32
571 610 3.140623 GTTGTTCATGCCTTGCCAAATT 58.859 40.909 0.00 0.00 0.00 1.82
613 653 4.963318 TTGGATCAATGGCTCCTACTAG 57.037 45.455 0.00 0.00 32.47 2.57
752 799 0.033228 CATTTTCCTGTTTGGCCGCA 59.967 50.000 0.00 0.00 35.26 5.69
768 815 0.537371 CGCAAGGGGTCTGGTTTCTT 60.537 55.000 0.00 0.00 0.00 2.52
769 816 1.704641 GCAAGGGGTCTGGTTTCTTT 58.295 50.000 0.00 0.00 0.00 2.52
776 823 4.540502 AGGGGTCTGGTTTCTTTAGCTATT 59.459 41.667 0.00 0.00 0.00 1.73
827 874 7.201821 GCAGCTGTACTATTTGGAATAAACCAT 60.202 37.037 16.64 0.00 39.82 3.55
839 886 6.650120 TGGAATAAACCATAGGAGAGTTCAC 58.350 40.000 0.00 0.00 34.77 3.18
865 912 5.529060 GTCATCCTTGTATCTGGGTTTGATC 59.471 44.000 0.00 0.00 0.00 2.92
932 979 3.388024 AGTGTCCTTTGCAACTAGTCTCA 59.612 43.478 0.00 0.00 0.00 3.27
960 1007 8.175069 TGCTAAATATGAATGTGTTTCTTCGAC 58.825 33.333 0.00 0.00 35.23 4.20
1081 1128 4.860352 TGATGTATTGTCGTCTTGGTTACG 59.140 41.667 0.00 0.00 41.64 3.18
1170 1217 3.435601 GGATCATAACTGCCAAGGACCAT 60.436 47.826 0.00 0.00 0.00 3.55
1509 1566 2.483106 CTGCACACATTGAGTCCTTGAG 59.517 50.000 0.00 0.00 0.00 3.02
1517 1574 3.558931 TTGAGTCCTTGAGTTTCAGCA 57.441 42.857 0.00 0.00 0.00 4.41
1532 1589 9.337396 TGAGTTTCAGCAGTAATTTTTCTTCTA 57.663 29.630 0.00 0.00 0.00 2.10
1618 1675 5.798132 TGAGATCAGTAGCATGAAACTGTT 58.202 37.500 20.75 15.43 42.96 3.16
1645 1702 5.244626 CCCACTCAAATTGAAGGTTCATTCT 59.755 40.000 11.56 0.00 37.00 2.40
1655 1712 8.868522 ATTGAAGGTTCATTCTCTAATTCACA 57.131 30.769 0.00 0.00 37.00 3.58
1685 1742 8.834465 AGCTTCTTTTATCTGCAGTTATACATG 58.166 33.333 14.67 1.50 0.00 3.21
1730 1787 5.879763 TGAGATTCTCCAGAACCAAAATGA 58.120 37.500 11.12 0.00 36.80 2.57
1818 1876 7.661536 ACATGTACAGATATACTTGGTCAGT 57.338 36.000 0.00 0.00 39.87 3.41
1821 1879 7.476540 TGTACAGATATACTTGGTCAGTTGT 57.523 36.000 0.00 0.00 36.88 3.32
1866 1924 5.066968 TGGCTGAAACGTTTTCTTTTTCT 57.933 34.783 15.89 0.00 31.68 2.52
1874 1932 6.746745 AACGTTTTCTTTTTCTACTGGTCA 57.253 33.333 0.00 0.00 0.00 4.02
1877 1935 7.858583 ACGTTTTCTTTTTCTACTGGTCATAC 58.141 34.615 0.00 0.00 0.00 2.39
1878 1936 7.496591 ACGTTTTCTTTTTCTACTGGTCATACA 59.503 33.333 0.00 0.00 0.00 2.29
1898 1956 8.141909 TCATACAGTGTATTGCTATCCTTGTAC 58.858 37.037 13.25 0.00 0.00 2.90
1900 1958 6.106673 ACAGTGTATTGCTATCCTTGTACAC 58.893 40.000 0.00 5.57 41.14 2.90
1902 1960 6.818644 CAGTGTATTGCTATCCTTGTACACTT 59.181 38.462 11.90 0.00 45.77 3.16
1928 1986 6.811253 TTTCTGTTTGCATCGGTTATTACT 57.189 33.333 0.00 0.00 0.00 2.24
1932 1990 7.045416 TCTGTTTGCATCGGTTATTACTGTAT 58.955 34.615 0.00 0.00 32.23 2.29
2127 2185 0.179134 GCAGTAGATGAGTTCCGCGT 60.179 55.000 4.92 0.00 0.00 6.01
2130 2188 1.141019 TAGATGAGTTCCGCGTGGC 59.859 57.895 11.05 0.00 34.14 5.01
2261 2319 1.890876 ACGCAGTGCTTATGGAAACA 58.109 45.000 14.33 0.00 44.37 2.83
2354 2412 4.338964 TGTAATATGCTTCCTGGCAATGTG 59.661 41.667 0.00 0.00 45.68 3.21
2396 2455 0.103937 AGTCGCTGCTCTTATGGCTC 59.896 55.000 0.00 0.00 0.00 4.70
2429 2488 5.726980 TTGTGCTTGCTTTCTCCAATAAT 57.273 34.783 0.00 0.00 0.00 1.28
2455 2514 2.171003 GAAGGGGCTGTTTGCTGTTAT 58.829 47.619 0.00 0.00 42.39 1.89
2460 2519 3.447229 GGGGCTGTTTGCTGTTATATGTT 59.553 43.478 0.00 0.00 42.39 2.71
2471 2534 9.787532 TTTGCTGTTATATGTTTCTCTAATTGC 57.212 29.630 0.00 0.00 0.00 3.56
2476 2539 8.773645 TGTTATATGTTTCTCTAATTGCCATCG 58.226 33.333 0.00 0.00 0.00 3.84
2543 2606 2.899900 GGGGAGATCCATAAAAATGGGC 59.100 50.000 4.64 0.00 41.95 5.36
2552 2615 6.371595 TCCATAAAAATGGGCAAGATTGTT 57.628 33.333 4.64 0.00 41.95 2.83
2603 2666 2.094545 GCAACCAGTGGCTTATTCCAAG 60.095 50.000 9.78 0.00 37.96 3.61
2613 2676 6.380846 AGTGGCTTATTCCAAGCATGAATAAA 59.619 34.615 10.82 1.59 44.71 1.40
2695 2758 4.822036 TGTGCAAAAGCAACGTACTATT 57.178 36.364 0.00 0.00 0.00 1.73
2713 2779 8.269424 CGTACTATTGTTGATTCTTGATGTAGC 58.731 37.037 0.00 0.00 0.00 3.58
2745 2828 6.210185 AGCTATTTGAAAAACAGAAGGCTCAT 59.790 34.615 0.00 0.00 0.00 2.90
2752 2835 6.549364 TGAAAAACAGAAGGCTCATAGGAAAA 59.451 34.615 0.00 0.00 0.00 2.29
2763 2846 5.120830 GGCTCATAGGAAAATACATACTGCG 59.879 44.000 0.00 0.00 0.00 5.18
2768 2851 9.256477 TCATAGGAAAATACATACTGCGTTTAG 57.744 33.333 0.00 0.00 0.00 1.85
2771 2854 8.197988 AGGAAAATACATACTGCGTTTAGAAG 57.802 34.615 0.00 0.00 0.00 2.85
2775 2858 7.757097 AATACATACTGCGTTTAGAAGTCAG 57.243 36.000 0.00 0.00 38.30 3.51
2785 2868 5.298347 CGTTTAGAAGTCAGAAGAAACCCT 58.702 41.667 0.00 0.00 0.00 4.34
2818 2901 2.414612 TGAGCCCCCGGTAGATAAAAT 58.585 47.619 0.00 0.00 0.00 1.82
2819 2902 2.781174 TGAGCCCCCGGTAGATAAAATT 59.219 45.455 0.00 0.00 0.00 1.82
2820 2903 3.181448 TGAGCCCCCGGTAGATAAAATTC 60.181 47.826 0.00 0.00 0.00 2.17
2821 2904 2.781174 AGCCCCCGGTAGATAAAATTCA 59.219 45.455 0.00 0.00 0.00 2.57
2822 2905 2.882761 GCCCCCGGTAGATAAAATTCAC 59.117 50.000 0.00 0.00 0.00 3.18
2823 2906 3.686120 GCCCCCGGTAGATAAAATTCACA 60.686 47.826 0.00 0.00 0.00 3.58
2824 2907 4.725490 CCCCCGGTAGATAAAATTCACAT 58.275 43.478 0.00 0.00 0.00 3.21
2825 2908 5.746656 GCCCCCGGTAGATAAAATTCACATA 60.747 44.000 0.00 0.00 0.00 2.29
2826 2909 6.300703 CCCCCGGTAGATAAAATTCACATAA 58.699 40.000 0.00 0.00 0.00 1.90
2827 2910 6.946009 CCCCCGGTAGATAAAATTCACATAAT 59.054 38.462 0.00 0.00 0.00 1.28
2828 2911 7.450323 CCCCCGGTAGATAAAATTCACATAATT 59.550 37.037 0.00 0.00 0.00 1.40
2829 2912 8.856103 CCCCGGTAGATAAAATTCACATAATTT 58.144 33.333 0.00 0.00 0.00 1.82
2847 2930 9.423061 ACATAATTTTGTTTCTAGATGGTTTGC 57.577 29.630 0.00 0.00 0.00 3.68
2848 2931 9.643693 CATAATTTTGTTTCTAGATGGTTTGCT 57.356 29.630 0.00 0.00 0.00 3.91
2849 2932 7.951530 AATTTTGTTTCTAGATGGTTTGCTG 57.048 32.000 0.00 0.00 0.00 4.41
2850 2933 6.463995 TTTTGTTTCTAGATGGTTTGCTGT 57.536 33.333 0.00 0.00 0.00 4.40
2851 2934 5.437289 TTGTTTCTAGATGGTTTGCTGTG 57.563 39.130 0.00 0.00 0.00 3.66
2852 2935 4.460263 TGTTTCTAGATGGTTTGCTGTGT 58.540 39.130 0.00 0.00 0.00 3.72
2853 2936 4.887071 TGTTTCTAGATGGTTTGCTGTGTT 59.113 37.500 0.00 0.00 0.00 3.32
2887 3006 3.106738 AGCAAAGCAAGCTGACTGT 57.893 47.368 0.00 0.00 41.61 3.55
2888 3007 1.396653 AGCAAAGCAAGCTGACTGTT 58.603 45.000 0.00 0.00 41.61 3.16
2889 3008 1.066605 AGCAAAGCAAGCTGACTGTTG 59.933 47.619 0.00 0.00 41.61 3.33
2954 3077 1.902508 CCACCCAAAGCAGAGAGTCTA 59.097 52.381 0.00 0.00 0.00 2.59
2955 3078 2.093764 CCACCCAAAGCAGAGAGTCTAG 60.094 54.545 0.00 0.00 0.00 2.43
3107 3230 0.552367 TCCTTGATGTCCCCCACCAT 60.552 55.000 0.00 0.00 0.00 3.55
3108 3231 0.106519 CCTTGATGTCCCCCACCATC 60.107 60.000 0.00 0.00 38.34 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.457443 GACGTACCTCGGTTAAGGGG 59.543 60.000 0.00 0.00 44.69 4.79
41 42 1.089481 ATCGCGACGTACCTCGGTTA 61.089 55.000 12.93 0.00 44.69 2.85
42 43 2.315038 GATCGCGACGTACCTCGGTT 62.315 60.000 12.93 0.00 44.69 4.44
43 44 2.817423 GATCGCGACGTACCTCGGT 61.817 63.158 12.93 0.00 44.69 4.69
61 62 2.310052 GGATAGATTTGGGGAGGATGGG 59.690 54.545 0.00 0.00 0.00 4.00
74 75 2.991250 AGCGCAAACAGTGGATAGATT 58.009 42.857 11.47 0.00 0.00 2.40
78 79 2.177394 TCAAGCGCAAACAGTGGATA 57.823 45.000 11.47 0.00 0.00 2.59
95 96 2.743636 AAGACGGAGCGAGATTTTCA 57.256 45.000 0.00 0.00 0.00 2.69
98 99 4.201822 GCAAATTAAGACGGAGCGAGATTT 60.202 41.667 0.00 0.00 0.00 2.17
107 108 1.067706 TCGACGGCAAATTAAGACGGA 60.068 47.619 10.38 0.00 43.13 4.69
110 111 5.713822 ATAACTCGACGGCAAATTAAGAC 57.286 39.130 0.00 0.00 0.00 3.01
148 149 4.220693 TGTAGGACACAAATCATCCCAG 57.779 45.455 0.00 0.00 32.95 4.45
149 150 4.860802 ATGTAGGACACAAATCATCCCA 57.139 40.909 0.00 0.00 41.55 4.37
197 198 1.396648 CCATAAAGATCACGCGCACAA 59.603 47.619 5.73 0.00 0.00 3.33
199 200 1.006832 ACCATAAAGATCACGCGCAC 58.993 50.000 5.73 0.00 0.00 5.34
201 202 1.332028 CGAACCATAAAGATCACGCGC 60.332 52.381 5.73 0.00 0.00 6.86
212 213 2.106074 CGCAGCAGCCGAACCATAA 61.106 57.895 0.00 0.00 37.52 1.90
239 240 2.202932 CTCTGGGCATCGAACGGG 60.203 66.667 0.00 0.00 0.00 5.28
267 268 2.919228 CCAAAAACCCTATCTCCTCCG 58.081 52.381 0.00 0.00 0.00 4.63
268 269 2.242452 AGCCAAAAACCCTATCTCCTCC 59.758 50.000 0.00 0.00 0.00 4.30
271 272 3.087370 ACAGCCAAAAACCCTATCTCC 57.913 47.619 0.00 0.00 0.00 3.71
273 274 6.079712 AGATTACAGCCAAAAACCCTATCT 57.920 37.500 0.00 0.00 0.00 1.98
301 304 8.564574 GCGATTGGTACCTCATTATGAAAAATA 58.435 33.333 14.36 0.00 0.00 1.40
308 311 6.146184 CACTAAGCGATTGGTACCTCATTATG 59.854 42.308 14.36 1.67 0.00 1.90
320 323 2.608863 CCACTGGCACTAAGCGATTGG 61.609 57.143 0.00 0.00 43.31 3.16
327 330 1.609061 CCACTGTCCACTGGCACTAAG 60.609 57.143 0.00 0.00 0.00 2.18
330 333 0.762842 TACCACTGTCCACTGGCACT 60.763 55.000 0.00 0.00 0.00 4.40
331 334 0.320771 CTACCACTGTCCACTGGCAC 60.321 60.000 0.00 0.00 0.00 5.01
333 336 0.396811 AACTACCACTGTCCACTGGC 59.603 55.000 0.00 0.00 0.00 4.85
334 337 1.416401 ACAACTACCACTGTCCACTGG 59.584 52.381 0.00 0.00 0.00 4.00
335 338 2.910688 ACAACTACCACTGTCCACTG 57.089 50.000 0.00 0.00 0.00 3.66
336 339 3.054655 ACAAACAACTACCACTGTCCACT 60.055 43.478 0.00 0.00 0.00 4.00
338 341 3.637911 ACAAACAACTACCACTGTCCA 57.362 42.857 0.00 0.00 0.00 4.02
339 342 3.488553 GCAACAAACAACTACCACTGTCC 60.489 47.826 0.00 0.00 0.00 4.02
340 343 3.691498 GCAACAAACAACTACCACTGTC 58.309 45.455 0.00 0.00 0.00 3.51
341 344 2.096819 CGCAACAAACAACTACCACTGT 59.903 45.455 0.00 0.00 0.00 3.55
414 417 4.660771 ACCAGCCTATAATCTGCTAGGTTT 59.339 41.667 0.00 0.00 37.43 3.27
422 425 3.117888 ACACCCAACCAGCCTATAATCTG 60.118 47.826 0.00 0.00 0.00 2.90
423 426 3.123273 ACACCCAACCAGCCTATAATCT 58.877 45.455 0.00 0.00 0.00 2.40
449 452 4.168760 CTGAACCCATCAAAGAAATTCGC 58.831 43.478 0.00 0.00 37.67 4.70
460 463 1.065410 ACACCCACCTGAACCCATCA 61.065 55.000 0.00 0.00 36.38 3.07
504 543 6.610830 TGGATTGGACATTTAGCCAAATACAT 59.389 34.615 0.00 0.00 46.31 2.29
520 559 8.636213 ACATGAATGATAAAAGATGGATTGGAC 58.364 33.333 0.00 0.00 0.00 4.02
550 589 2.237393 TTTGGCAAGGCATGAACAAC 57.763 45.000 0.00 0.00 30.40 3.32
565 604 1.550072 AGGATTTGGGCGTCAATTTGG 59.450 47.619 0.00 0.00 34.98 3.28
569 608 1.923356 AACAGGATTTGGGCGTCAAT 58.077 45.000 0.00 0.00 34.98 2.57
570 609 2.570415 TAACAGGATTTGGGCGTCAA 57.430 45.000 0.00 0.00 0.00 3.18
571 610 2.799126 ATAACAGGATTTGGGCGTCA 57.201 45.000 0.00 0.00 0.00 4.35
613 653 3.676291 TGAATAAAAACCAGGCAAGCC 57.324 42.857 2.02 2.02 0.00 4.35
661 702 2.231478 CAGTCACGTTGATCAGTACCCT 59.769 50.000 0.00 0.00 0.00 4.34
752 799 2.716969 AGCTAAAGAAACCAGACCCCTT 59.283 45.455 0.00 0.00 0.00 3.95
768 815 2.862512 GCAACTGCGCAAAATAGCTAA 58.137 42.857 13.05 0.00 0.00 3.09
769 816 2.542766 GCAACTGCGCAAAATAGCTA 57.457 45.000 13.05 0.00 0.00 3.32
789 836 1.871080 ACAGCTGCTGTCAACAGTAC 58.129 50.000 28.49 3.18 41.21 2.73
827 874 4.323569 AGGATGACTGTGAACTCTCCTA 57.676 45.455 0.00 0.00 30.04 2.94
839 886 4.494091 AACCCAGATACAAGGATGACTG 57.506 45.455 0.00 0.00 0.00 3.51
932 979 8.177663 CGAAGAAACACATTCATATTTAGCAGT 58.822 33.333 0.00 0.00 40.72 4.40
960 1007 2.740055 GGACACTGCTGCAGGTCG 60.740 66.667 31.00 21.13 34.70 4.79
1081 1128 0.243636 GGTTGCAATGCCACAGTACC 59.756 55.000 11.57 2.07 0.00 3.34
1170 1217 1.351076 TGTTGATCTGGACAGAGGCA 58.649 50.000 8.14 5.97 41.33 4.75
1435 1492 7.333528 TGACCAATGCAAAGGATATCTTAAC 57.666 36.000 14.09 0.00 34.78 2.01
1509 1566 8.906693 GCTTAGAAGAAAAATTACTGCTGAAAC 58.093 33.333 0.00 0.00 0.00 2.78
1532 1589 5.012354 ACTGGAATCATGGAATGTTTTGCTT 59.988 36.000 0.00 0.00 46.80 3.91
1596 1653 6.541086 CAAACAGTTTCATGCTACTGATCTC 58.459 40.000 24.74 0.00 43.45 2.75
1618 1675 2.676748 ACCTTCAATTTGAGTGGGCAA 58.323 42.857 18.48 0.00 0.00 4.52
1653 1710 5.709164 ACTGCAGATAAAAGAAGCTTGATGT 59.291 36.000 23.35 0.00 0.00 3.06
1655 1712 6.830873 AACTGCAGATAAAAGAAGCTTGAT 57.169 33.333 23.35 0.00 0.00 2.57
1685 1742 8.556194 TCTCAAACTGTGTCACATATGTAAAAC 58.444 33.333 8.32 0.00 0.00 2.43
1687 1744 8.846943 ATCTCAAACTGTGTCACATATGTAAA 57.153 30.769 8.32 0.00 0.00 2.01
1751 1808 7.645340 GGGTTCATCTAAACATCATGATTTTCG 59.355 37.037 5.16 6.93 0.00 3.46
1798 1856 6.255887 GCACAACTGACCAAGTATATCTGTAC 59.744 42.308 0.00 0.00 38.56 2.90
1818 1876 6.000840 TCAAGTTACCAATACTCATGCACAA 58.999 36.000 0.00 0.00 0.00 3.33
1821 1879 5.643348 CAGTCAAGTTACCAATACTCATGCA 59.357 40.000 0.00 0.00 0.00 3.96
1866 1924 5.932619 AGCAATACACTGTATGACCAGTA 57.067 39.130 2.31 0.00 43.70 2.74
1874 1932 7.926555 GTGTACAAGGATAGCAATACACTGTAT 59.073 37.037 0.00 0.00 39.39 2.29
1877 1935 6.341316 AGTGTACAAGGATAGCAATACACTG 58.659 40.000 12.68 0.00 46.70 3.66
1878 1936 6.546428 AGTGTACAAGGATAGCAATACACT 57.454 37.500 8.64 8.64 44.82 3.55
1886 1944 6.204882 ACAGAAAACAAGTGTACAAGGATAGC 59.795 38.462 0.00 0.00 0.00 2.97
1898 1956 3.486841 CCGATGCAAACAGAAAACAAGTG 59.513 43.478 0.00 0.00 0.00 3.16
1900 1958 3.705604 ACCGATGCAAACAGAAAACAAG 58.294 40.909 0.00 0.00 0.00 3.16
1902 1960 3.791973 AACCGATGCAAACAGAAAACA 57.208 38.095 0.00 0.00 0.00 2.83
1928 1986 2.496070 ACAGAGTAGCCGCAAGAATACA 59.504 45.455 0.00 0.00 43.02 2.29
1932 1990 1.135489 CGTACAGAGTAGCCGCAAGAA 60.135 52.381 0.00 0.00 43.02 2.52
2146 2204 8.410912 AGGTTTAAAGCGGTTTCATAAATATCC 58.589 33.333 17.03 9.26 0.00 2.59
2354 2412 8.707938 ACTAAAATGCATTTAAGAATTCAGGC 57.292 30.769 24.35 0.53 33.20 4.85
2365 2423 4.635765 AGAGCAGCGACTAAAATGCATTTA 59.364 37.500 24.35 11.96 41.14 1.40
2396 2455 4.978083 AGCAAGCACAATAATCCAAGAG 57.022 40.909 0.00 0.00 0.00 2.85
2429 2488 1.118838 CAAACAGCCCCTTCACCAAA 58.881 50.000 0.00 0.00 0.00 3.28
2471 2534 2.582052 AGAGACTTCTAGAGCCGATGG 58.418 52.381 0.00 0.00 0.00 3.51
2476 2539 6.693466 AGTTTGTAAAGAGACTTCTAGAGCC 58.307 40.000 0.00 0.00 31.96 4.70
2520 2583 3.157087 CCATTTTTATGGATCTCCCCCG 58.843 50.000 0.00 0.00 44.39 5.73
2543 2606 4.346734 AGTTAGATGCGCAACAATCTTG 57.653 40.909 17.11 0.00 0.00 3.02
2552 2615 9.305925 CTAATGATGATTATAGTTAGATGCGCA 57.694 33.333 14.96 14.96 0.00 6.09
2688 2751 8.552034 GGCTACATCAAGAATCAACAATAGTAC 58.448 37.037 0.00 0.00 0.00 2.73
2695 2758 5.164620 TCAGGCTACATCAAGAATCAACA 57.835 39.130 0.00 0.00 0.00 3.33
2713 2779 7.149569 TCTGTTTTTCAAATAGCTCATCAGG 57.850 36.000 0.00 0.00 0.00 3.86
2745 2828 9.309516 CTTCTAAACGCAGTATGTATTTTCCTA 57.690 33.333 0.00 0.00 45.00 2.94
2752 2835 7.096884 TCTGACTTCTAAACGCAGTATGTAT 57.903 36.000 0.00 0.00 45.00 2.29
2763 2846 6.056236 ACAGGGTTTCTTCTGACTTCTAAAC 58.944 40.000 0.00 0.00 35.20 2.01
2768 2851 5.855045 TCTAACAGGGTTTCTTCTGACTTC 58.145 41.667 0.00 0.00 35.20 3.01
2771 2854 5.365619 TGTTCTAACAGGGTTTCTTCTGAC 58.634 41.667 0.00 0.00 34.30 3.51
2775 2858 6.655003 TCATGATGTTCTAACAGGGTTTCTTC 59.345 38.462 1.62 0.00 43.04 2.87
2785 2868 2.092429 GGGGGCTCATGATGTTCTAACA 60.092 50.000 0.00 0.00 44.06 2.41
2821 2904 9.423061 GCAAACCATCTAGAAACAAAATTATGT 57.577 29.630 0.00 0.00 34.24 2.29
2822 2905 9.643693 AGCAAACCATCTAGAAACAAAATTATG 57.356 29.630 0.00 0.00 0.00 1.90
2823 2906 9.643693 CAGCAAACCATCTAGAAACAAAATTAT 57.356 29.630 0.00 0.00 0.00 1.28
2824 2907 8.637986 ACAGCAAACCATCTAGAAACAAAATTA 58.362 29.630 0.00 0.00 0.00 1.40
2825 2908 7.439056 CACAGCAAACCATCTAGAAACAAAATT 59.561 33.333 0.00 0.00 0.00 1.82
2826 2909 6.925165 CACAGCAAACCATCTAGAAACAAAAT 59.075 34.615 0.00 0.00 0.00 1.82
2827 2910 6.127479 ACACAGCAAACCATCTAGAAACAAAA 60.127 34.615 0.00 0.00 0.00 2.44
2828 2911 5.359576 ACACAGCAAACCATCTAGAAACAAA 59.640 36.000 0.00 0.00 0.00 2.83
2829 2912 4.887071 ACACAGCAAACCATCTAGAAACAA 59.113 37.500 0.00 0.00 0.00 2.83
2830 2913 4.460263 ACACAGCAAACCATCTAGAAACA 58.540 39.130 0.00 0.00 0.00 2.83
2831 2914 5.438761 AACACAGCAAACCATCTAGAAAC 57.561 39.130 0.00 0.00 0.00 2.78
2832 2915 6.272318 CAAAACACAGCAAACCATCTAGAAA 58.728 36.000 0.00 0.00 0.00 2.52
2833 2916 5.735922 GCAAAACACAGCAAACCATCTAGAA 60.736 40.000 0.00 0.00 0.00 2.10
2834 2917 4.261572 GCAAAACACAGCAAACCATCTAGA 60.262 41.667 0.00 0.00 0.00 2.43
2835 2918 3.983344 GCAAAACACAGCAAACCATCTAG 59.017 43.478 0.00 0.00 0.00 2.43
2836 2919 3.243704 GGCAAAACACAGCAAACCATCTA 60.244 43.478 0.00 0.00 0.00 1.98
2837 2920 2.483538 GGCAAAACACAGCAAACCATCT 60.484 45.455 0.00 0.00 0.00 2.90
2838 2921 1.866601 GGCAAAACACAGCAAACCATC 59.133 47.619 0.00 0.00 0.00 3.51
2839 2922 1.209019 TGGCAAAACACAGCAAACCAT 59.791 42.857 0.00 0.00 0.00 3.55
2840 2923 0.610174 TGGCAAAACACAGCAAACCA 59.390 45.000 0.00 0.00 0.00 3.67
2841 2924 1.665169 CTTGGCAAAACACAGCAAACC 59.335 47.619 0.00 0.00 0.00 3.27
2842 2925 2.345876 ACTTGGCAAAACACAGCAAAC 58.654 42.857 0.00 0.00 0.00 2.93
2843 2926 2.758736 ACTTGGCAAAACACAGCAAA 57.241 40.000 0.00 0.00 0.00 3.68
2844 2927 3.382865 TGATACTTGGCAAAACACAGCAA 59.617 39.130 0.00 0.00 0.00 3.91
2845 2928 2.954989 TGATACTTGGCAAAACACAGCA 59.045 40.909 0.00 0.00 0.00 4.41
2846 2929 3.568538 CTGATACTTGGCAAAACACAGC 58.431 45.455 0.00 0.00 0.00 4.40
2847 2930 3.004629 TGCTGATACTTGGCAAAACACAG 59.995 43.478 0.00 10.02 32.79 3.66
2848 2931 2.954989 TGCTGATACTTGGCAAAACACA 59.045 40.909 0.00 0.00 32.79 3.72
2849 2932 3.568538 CTGCTGATACTTGGCAAAACAC 58.431 45.455 0.00 0.00 35.49 3.32
2850 2933 2.030007 GCTGCTGATACTTGGCAAAACA 60.030 45.455 0.00 0.00 35.49 2.83
2851 2934 2.030007 TGCTGCTGATACTTGGCAAAAC 60.030 45.455 0.00 0.00 35.49 2.43
2852 2935 2.237643 TGCTGCTGATACTTGGCAAAA 58.762 42.857 0.00 0.00 35.49 2.44
2853 2936 1.908344 TGCTGCTGATACTTGGCAAA 58.092 45.000 0.00 0.00 35.49 3.68
2883 3002 3.646162 TGTACTCAATGTCTCCCAACAGT 59.354 43.478 0.00 0.00 31.50 3.55
2884 3003 3.997021 GTGTACTCAATGTCTCCCAACAG 59.003 47.826 0.00 0.00 31.50 3.16
2885 3004 3.646162 AGTGTACTCAATGTCTCCCAACA 59.354 43.478 0.00 0.00 0.00 3.33
2886 3005 3.997021 CAGTGTACTCAATGTCTCCCAAC 59.003 47.826 0.00 0.00 35.32 3.77
2887 3006 4.271696 CAGTGTACTCAATGTCTCCCAA 57.728 45.455 0.00 0.00 35.32 4.12
2888 3007 3.961480 CAGTGTACTCAATGTCTCCCA 57.039 47.619 0.00 0.00 35.32 4.37
2954 3077 6.039382 CACTTTTGTAACAAAAGGTAGGAGCT 59.961 38.462 22.85 0.00 40.54 4.09
2955 3078 6.183360 ACACTTTTGTAACAAAAGGTAGGAGC 60.183 38.462 22.85 0.00 40.54 4.70
3013 3136 3.883830 ACTTGGATTTTTGTGTGTGCA 57.116 38.095 0.00 0.00 0.00 4.57
3031 3154 0.321122 GAGCACCTACAGCTGCAACT 60.321 55.000 15.27 2.60 43.58 3.16
3057 3180 4.904251 ACACATCTTCCTATCCACTGCTAT 59.096 41.667 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.