Multiple sequence alignment - TraesCS2D01G404500

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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 TraesCS2D01G404500 chr2D 100.000 3316 0 0 1 3316 518813330 518810015 0.000000e+00 6124.0
1 TraesCS2D01G404500 chr2D 91.453 117 10 0 2873 2989 95519664 95519548 9.520000e-36 161.0
2 TraesCS2D01G404500 chr2D 84.722 72 8 3 1838 1907 366089232 366089302 5.940000e-08 69.4
3 TraesCS2D01G404500 chr2B 94.624 1916 54 6 1 1908 611069155 611067281 0.000000e+00 2922.0
4 TraesCS2D01G404500 chr2B 88.143 953 65 34 1907 2851 611067219 611066307 0.000000e+00 1090.0
5 TraesCS2D01G404500 chr2B 93.210 324 17 3 2995 3316 611066254 611065934 3.870000e-129 472.0
6 TraesCS2D01G404500 chr2B 94.318 88 5 0 3218 3305 612071499 612071586 5.770000e-28 135.0
7 TraesCS2D01G404500 chr2B 94.318 88 5 0 3218 3305 612077815 612077902 5.770000e-28 135.0
8 TraesCS2D01G404500 chr2A 92.449 1417 91 12 497 1909 662972023 662970619 0.000000e+00 2010.0
9 TraesCS2D01G404500 chr2A 88.447 1030 52 27 1907 2905 662970558 662969565 0.000000e+00 1181.0
10 TraesCS2D01G404500 chr2A 87.671 511 40 15 1 499 662972554 662972055 1.030000e-159 573.0
11 TraesCS2D01G404500 chr2A 87.476 511 41 15 1 499 663304326 663303827 4.800000e-158 568.0
12 TraesCS2D01G404500 chr2A 87.462 327 11 7 2993 3316 662969444 662969145 1.890000e-92 350.0
13 TraesCS2D01G404500 chr6A 82.105 285 40 8 1 276 564199901 564200183 1.990000e-57 233.0
14 TraesCS2D01G404500 chr6A 80.282 71 13 1 1838 1907 456611684 456611754 6.000000e-03 52.8
15 TraesCS2D01G404500 chr5D 84.685 222 26 3 52 266 530067134 530067354 7.200000e-52 215.0
16 TraesCS2D01G404500 chr5B 88.623 167 16 3 52 217 669294388 669294552 2.020000e-47 200.0
17 TraesCS2D01G404500 chr5B 92.593 108 8 0 2881 2988 124772505 124772398 4.430000e-34 156.0
18 TraesCS2D01G404500 chr3A 81.423 253 37 7 23 266 701237829 701238080 7.260000e-47 198.0
19 TraesCS2D01G404500 chr7B 95.413 109 5 0 2881 2989 513813928 513813820 1.220000e-39 174.0
20 TraesCS2D01G404500 chr4A 95.370 108 5 0 2882 2989 618561442 618561549 4.400000e-39 172.0
21 TraesCS2D01G404500 chr4A 92.105 114 9 0 2876 2989 714067236 714067123 9.520000e-36 161.0
22 TraesCS2D01G404500 chr4A 92.035 113 9 0 2877 2989 544199439 544199327 3.420000e-35 159.0
23 TraesCS2D01G404500 chr1D 79.323 266 39 8 10 266 228800672 228800930 4.400000e-39 172.0
24 TraesCS2D01G404500 chr6B 78.731 268 48 7 9 269 534012550 534012285 1.580000e-38 171.0
25 TraesCS2D01G404500 chr7D 92.241 116 9 0 2874 2989 430095725 430095840 7.360000e-37 165.0
26 TraesCS2D01G404500 chr3D 92.105 114 9 0 2876 2989 378244516 378244629 9.520000e-36 161.0
27 TraesCS2D01G404500 chr3B 92.105 114 7 2 2877 2989 543766777 543766665 3.420000e-35 159.0


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 TraesCS2D01G404500 chr2D 518810015 518813330 3315 True 6124.000000 6124 100.000000 1 3316 1 chr2D.!!$R2 3315
1 TraesCS2D01G404500 chr2B 611065934 611069155 3221 True 1494.666667 2922 91.992333 1 3316 3 chr2B.!!$R1 3315
2 TraesCS2D01G404500 chr2A 662969145 662972554 3409 True 1028.500000 2010 89.007250 1 3316 4 chr2A.!!$R2 3315

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
655 726 0.040499 TAGGTTTTGGGATGGGTGGC 59.96 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2592 2747 0.033405 ATCCAGATTTGCAGGCAGCT 60.033 50.0 2.86 0.0 45.94 4.24 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
159 160 7.230510 ACAGCCAAATCTACAATTTCACAGTTA 59.769 33.333 0.00 0.00 0.00 2.24
231 239 2.031616 TCACAGCTCACAGCAGCC 59.968 61.111 0.00 0.00 45.56 4.85
303 311 2.123854 CCCCTCCCGTCGATCTCA 60.124 66.667 0.00 0.00 0.00 3.27
307 315 1.064946 CTCCCGTCGATCTCACAGC 59.935 63.158 0.00 0.00 0.00 4.40
308 316 2.105128 CCCGTCGATCTCACAGCC 59.895 66.667 0.00 0.00 0.00 4.85
309 317 2.278206 CCGTCGATCTCACAGCCG 60.278 66.667 0.00 0.00 0.00 5.52
310 318 2.951745 CGTCGATCTCACAGCCGC 60.952 66.667 0.00 0.00 0.00 6.53
311 319 2.951745 GTCGATCTCACAGCCGCG 60.952 66.667 0.00 0.00 0.00 6.46
312 320 4.854784 TCGATCTCACAGCCGCGC 62.855 66.667 0.00 0.00 0.00 6.86
314 322 4.854784 GATCTCACAGCCGCGCGA 62.855 66.667 34.63 9.08 0.00 5.87
315 323 4.435436 ATCTCACAGCCGCGCGAA 62.435 61.111 34.63 8.06 0.00 4.70
432 469 1.480137 CTTTCTCCGTGGAGCTCTGAT 59.520 52.381 14.64 0.00 41.71 2.90
655 726 0.040499 TAGGTTTTGGGATGGGTGGC 59.960 55.000 0.00 0.00 0.00 5.01
725 797 8.106462 TGTCATAATTTTCCATACCTGAGAACA 58.894 33.333 0.00 0.00 0.00 3.18
837 909 1.267574 GCCCCTGACTGGTGAGATCA 61.268 60.000 0.00 0.00 0.00 2.92
873 945 1.410517 GCATCCGTGATCTCTTCCTCA 59.589 52.381 0.00 0.00 0.00 3.86
940 1012 9.185680 GGGTTTTGTATACTGTGATCCTAAATT 57.814 33.333 4.17 0.00 0.00 1.82
1007 1079 0.250038 CTGGTGGGTGATATGAGCGG 60.250 60.000 0.00 0.00 0.00 5.52
1199 1271 2.140717 CTCTACGTGCCTTCGGTTTTT 58.859 47.619 0.00 0.00 34.94 1.94
1252 1324 3.110705 ACATTCATGCTGGACTACCTCT 58.889 45.455 0.00 0.00 37.04 3.69
1340 1412 6.322969 TGATAGCCAGAAAATGAGCATGAAAT 59.677 34.615 0.00 0.00 0.00 2.17
1423 1495 0.871722 CGTGGAAATTTGTCGCCTGA 59.128 50.000 0.00 0.00 0.00 3.86
1483 1555 2.569059 CAGGCTGTGATCAACTATGGG 58.431 52.381 6.28 0.00 0.00 4.00
1744 1816 9.393512 AGCTAATTATTGAGATTGATATGAGCC 57.606 33.333 0.00 0.00 0.00 4.70
1745 1817 8.619546 GCTAATTATTGAGATTGATATGAGCCC 58.380 37.037 0.00 0.00 0.00 5.19
1766 1838 3.495753 CCAGTTTTTCCAATGCAAGCTTC 59.504 43.478 0.00 0.00 0.00 3.86
1776 1849 5.419788 TCCAATGCAAGCTTCATGTCTAAAT 59.580 36.000 0.00 0.00 0.00 1.40
1992 2137 2.432444 TGCATAGCTTAACGGTTTGCT 58.568 42.857 19.51 19.51 44.77 3.91
2003 2155 6.672357 GCTTAACGGTTTGCTTATCACTACTG 60.672 42.308 0.00 0.00 0.00 2.74
2004 2156 4.267349 ACGGTTTGCTTATCACTACTGT 57.733 40.909 0.00 0.00 0.00 3.55
2005 2157 4.638304 ACGGTTTGCTTATCACTACTGTT 58.362 39.130 0.00 0.00 29.59 3.16
2006 2158 4.689345 ACGGTTTGCTTATCACTACTGTTC 59.311 41.667 0.00 0.00 29.59 3.18
2007 2159 4.201589 CGGTTTGCTTATCACTACTGTTCG 60.202 45.833 0.00 0.00 0.00 3.95
2008 2160 4.689345 GGTTTGCTTATCACTACTGTTCGT 59.311 41.667 0.00 0.00 0.00 3.85
2009 2161 5.178809 GGTTTGCTTATCACTACTGTTCGTT 59.821 40.000 0.00 0.00 0.00 3.85
2022 2174 7.968956 CACTACTGTTCGTTAGTGAGAATACAT 59.031 37.037 3.15 0.00 41.62 2.29
2023 2175 9.170734 ACTACTGTTCGTTAGTGAGAATACATA 57.829 33.333 0.00 0.00 0.00 2.29
2024 2176 9.653067 CTACTGTTCGTTAGTGAGAATACATAG 57.347 37.037 0.00 0.00 0.00 2.23
2025 2177 7.481642 ACTGTTCGTTAGTGAGAATACATAGG 58.518 38.462 0.00 0.00 0.00 2.57
2026 2178 7.338703 ACTGTTCGTTAGTGAGAATACATAGGA 59.661 37.037 0.00 0.00 0.00 2.94
2027 2179 7.704271 TGTTCGTTAGTGAGAATACATAGGAG 58.296 38.462 0.00 0.00 0.00 3.69
2028 2180 7.555195 TGTTCGTTAGTGAGAATACATAGGAGA 59.445 37.037 0.00 0.00 0.00 3.71
2029 2181 8.569641 GTTCGTTAGTGAGAATACATAGGAGAT 58.430 37.037 0.00 0.00 0.00 2.75
2030 2182 8.100508 TCGTTAGTGAGAATACATAGGAGATG 57.899 38.462 0.00 0.00 0.00 2.90
2031 2183 7.720074 TCGTTAGTGAGAATACATAGGAGATGT 59.280 37.037 0.00 0.00 36.13 3.06
2032 2184 8.353684 CGTTAGTGAGAATACATAGGAGATGTT 58.646 37.037 0.00 0.00 33.76 2.71
2033 2185 9.469807 GTTAGTGAGAATACATAGGAGATGTTG 57.530 37.037 0.00 0.00 33.76 3.33
2034 2186 7.667575 AGTGAGAATACATAGGAGATGTTGT 57.332 36.000 0.00 0.00 33.76 3.32
2035 2187 7.721402 AGTGAGAATACATAGGAGATGTTGTC 58.279 38.462 0.00 0.00 33.76 3.18
2036 2188 7.563188 AGTGAGAATACATAGGAGATGTTGTCT 59.437 37.037 0.00 0.00 40.81 3.41
2067 2219 9.739276 TTTCCTCATAATGTGATTAACTCAAGT 57.261 29.630 0.00 0.00 35.97 3.16
2069 2221 9.817809 TCCTCATAATGTGATTAACTCAAGTAC 57.182 33.333 0.00 0.00 35.97 2.73
2070 2222 9.823647 CCTCATAATGTGATTAACTCAAGTACT 57.176 33.333 0.00 0.00 35.97 2.73
2078 2230 7.652105 TGTGATTAACTCAAGTACTCAACTCAC 59.348 37.037 0.00 3.15 37.50 3.51
2192 2344 0.033796 CCCATGTTGATGAGTGCCCT 60.034 55.000 0.00 0.00 0.00 5.19
2234 2386 2.474410 ACACTCCGACCTTCCATTTC 57.526 50.000 0.00 0.00 0.00 2.17
2255 2407 0.043637 ACCGGGATGGAGAAAGGGTA 59.956 55.000 6.32 0.00 42.00 3.69
2408 2563 7.312899 TCCTTTTCTGAAAAGTCTTGTTTGAC 58.687 34.615 30.45 0.00 44.96 3.18
2468 2623 1.484240 CTAGTTTCTCTCCCAGGCAGG 59.516 57.143 0.00 0.00 37.03 4.85
2469 2624 1.377856 GTTTCTCTCCCAGGCAGGC 60.378 63.158 0.00 0.00 35.39 4.85
2511 2666 4.147219 ACTCGCAAAGCATTTTACACTC 57.853 40.909 0.00 0.00 35.03 3.51
2569 2724 0.253044 TGCTACTGATGGAAGTGGGC 59.747 55.000 0.00 0.00 33.65 5.36
2585 2740 1.833630 TGGGCTGTTCTGGTATCTCTG 59.166 52.381 0.00 0.00 0.00 3.35
2587 2742 2.102252 GGGCTGTTCTGGTATCTCTGAG 59.898 54.545 0.00 0.00 0.00 3.35
2592 2747 5.163468 GCTGTTCTGGTATCTCTGAGAATGA 60.163 44.000 12.00 3.37 0.00 2.57
2613 2768 0.102481 CTGCCTGCAAATCTGGATGC 59.898 55.000 0.00 0.00 42.86 3.91
2614 2769 0.323999 TGCCTGCAAATCTGGATGCT 60.324 50.000 0.00 0.00 42.97 3.79
2714 2879 6.254804 CACGATTGGATATTGTTGTCGTTAGA 59.745 38.462 0.00 0.00 38.59 2.10
2715 2880 6.984474 ACGATTGGATATTGTTGTCGTTAGAT 59.016 34.615 0.00 0.00 37.54 1.98
2733 2898 4.178545 AGATGTACAATTGCTGCCAAAC 57.821 40.909 5.05 0.00 34.05 2.93
2764 2929 5.006552 CCAATGAACAACAACGCAAAGAAAT 59.993 36.000 0.00 0.00 0.00 2.17
2772 2937 1.446618 CGCAAAGAAATGGCTGGCC 60.447 57.895 4.43 4.43 0.00 5.36
2797 2962 6.980978 CGATCCTTGAAGCTTTGTCTAGATAA 59.019 38.462 0.00 0.00 0.00 1.75
2800 2965 7.050377 TCCTTGAAGCTTTGTCTAGATAATGG 58.950 38.462 14.34 7.48 0.00 3.16
2836 3001 1.440708 CAATTACCGGCCGTTACACA 58.559 50.000 26.12 0.00 0.00 3.72
2848 3013 2.230025 CCGTTACACAATTCATGGCCAA 59.770 45.455 10.96 0.00 0.00 4.52
2853 3032 4.829872 ACACAATTCATGGCCAATCAAT 57.170 36.364 10.96 5.34 0.00 2.57
2855 3034 6.297080 ACACAATTCATGGCCAATCAATTA 57.703 33.333 10.96 0.00 0.00 1.40
2861 3040 8.339714 CAATTCATGGCCAATCAATTATCAAAC 58.660 33.333 10.96 0.00 0.00 2.93
2865 3044 5.672503 TGGCCAATCAATTATCAAACATGG 58.327 37.500 0.61 0.00 0.00 3.66
2879 3058 6.841443 TCAAACATGGCAAATAAACTTGTG 57.159 33.333 0.00 0.00 0.00 3.33
2890 3069 0.250338 AAACTTGTGCTCCCTCCGTC 60.250 55.000 0.00 0.00 0.00 4.79
2892 3071 3.649277 CTTGTGCTCCCTCCGTCCG 62.649 68.421 0.00 0.00 0.00 4.79
2893 3072 4.671590 TGTGCTCCCTCCGTCCGA 62.672 66.667 0.00 0.00 0.00 4.55
2899 3078 1.805495 GCTCCCTCCGTCCGAAAATAC 60.805 57.143 0.00 0.00 0.00 1.89
2905 3084 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
2906 3085 2.228582 TCCGTCCGAAAATACTTGTCGA 59.771 45.455 1.13 0.00 36.92 4.20
2907 3086 2.988493 CCGTCCGAAAATACTTGTCGAA 59.012 45.455 1.13 0.00 36.92 3.71
2908 3087 3.060363 CCGTCCGAAAATACTTGTCGAAG 59.940 47.826 1.13 0.00 36.92 3.79
2909 3088 3.916172 CGTCCGAAAATACTTGTCGAAGA 59.084 43.478 1.13 0.00 36.92 2.87
2911 3090 5.107760 CGTCCGAAAATACTTGTCGAAGAAA 60.108 40.000 1.13 0.00 39.69 2.52
2912 3091 6.400727 CGTCCGAAAATACTTGTCGAAGAAAT 60.401 38.462 1.13 0.00 39.69 2.17
2921 3124 6.910536 ACTTGTCGAAGAAATGGATGTATC 57.089 37.500 0.00 0.00 39.69 2.24
2973 3176 9.806203 TCCATTTTTATTCATTGCTATGACAAG 57.194 29.630 10.48 0.00 40.42 3.16
2981 3184 6.603237 TCATTGCTATGACAAGTATTTCCG 57.397 37.500 6.75 0.00 35.87 4.30
2982 3185 5.527214 TCATTGCTATGACAAGTATTTCCGG 59.473 40.000 6.75 0.00 35.87 5.14
3062 3279 3.820557 ACTAAAGTTCATGCACACCAGT 58.179 40.909 0.00 0.00 0.00 4.00
3097 3314 7.153985 TCTCCCATTTGAACATTTGAATGAAC 58.846 34.615 10.48 4.82 39.67 3.18
3269 3486 4.978099 GAGAGGCTCCATCCAAATGAATA 58.022 43.478 11.71 0.00 34.61 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 239 4.446719 GGTTGAGCTGCAAATTCTGAAAAG 59.553 41.667 1.02 0.00 38.44 2.27
408 445 2.125512 CTCCACGGAGAAAGCGGG 60.126 66.667 7.35 0.00 44.53 6.13
432 469 4.649267 TGTGAATTATGGACTTGGTGGA 57.351 40.909 0.00 0.00 0.00 4.02
547 618 1.620822 TCTAGCAGCTGTGTCACTGA 58.379 50.000 16.64 1.93 35.90 3.41
655 726 2.508867 CATCAATTCTTTGCACGGTCG 58.491 47.619 0.00 0.00 32.61 4.79
661 732 5.816258 TCAAAGTTTGCATCAATTCTTTGCA 59.184 32.000 10.90 5.17 44.12 4.08
763 835 9.979897 ATATAGCTCATAGGCATAAAATTGGAA 57.020 29.630 0.00 0.00 34.17 3.53
837 909 3.595758 GCCACACCGCTTGCAACT 61.596 61.111 0.00 0.00 0.00 3.16
873 945 0.613777 GGTCGTTCCTCCACTGGAAT 59.386 55.000 0.00 0.00 46.36 3.01
890 962 6.353082 CCTTATAAATCCTGACACTGAAGGGT 60.353 42.308 0.00 0.00 34.08 4.34
940 1012 2.752358 CCTGCAGTTGGAGCCAGA 59.248 61.111 13.81 0.00 31.63 3.86
1007 1079 1.153168 TTCCTATTGCCTGCCTCGC 60.153 57.895 0.00 0.00 0.00 5.03
1021 1093 0.178861 TTCCTGGCTTCCTCCTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
1252 1324 1.133945 TCTGCCAGTGCCAGTTAAACA 60.134 47.619 0.37 0.00 36.33 2.83
1401 1473 0.109919 GGCGACAAATTTCCACGGAC 60.110 55.000 9.20 0.00 0.00 4.79
1423 1495 8.720562 CCAAAGAGTTCAATCAAAACAAACTTT 58.279 29.630 0.00 0.00 32.60 2.66
1744 1816 3.116079 AGCTTGCATTGGAAAAACTGG 57.884 42.857 0.00 0.00 0.00 4.00
1745 1817 4.121317 TGAAGCTTGCATTGGAAAAACTG 58.879 39.130 2.10 0.00 0.00 3.16
1766 1838 5.163513 GCAGGTTTCACCAATTTAGACATG 58.836 41.667 0.00 0.00 41.95 3.21
1776 1849 4.657013 TGTACATATGCAGGTTTCACCAA 58.343 39.130 1.58 0.00 41.95 3.67
1869 1944 3.004002 GGTGCCTAAGTAAGCGTTTGTTT 59.996 43.478 0.00 0.00 0.00 2.83
1966 2104 6.494842 CAAACCGTTAAGCTATGCAACATAT 58.505 36.000 0.00 0.00 0.00 1.78
1983 2128 4.267349 ACAGTAGTGATAAGCAAACCGT 57.733 40.909 4.09 0.00 0.00 4.83
1992 2137 7.677454 TCTCACTAACGAACAGTAGTGATAA 57.323 36.000 12.53 3.87 45.13 1.75
2003 2155 7.928103 TCTCCTATGTATTCTCACTAACGAAC 58.072 38.462 0.00 0.00 0.00 3.95
2004 2156 8.568794 CATCTCCTATGTATTCTCACTAACGAA 58.431 37.037 0.00 0.00 0.00 3.85
2005 2157 7.720074 ACATCTCCTATGTATTCTCACTAACGA 59.280 37.037 0.00 0.00 0.00 3.85
2006 2158 7.877003 ACATCTCCTATGTATTCTCACTAACG 58.123 38.462 0.00 0.00 0.00 3.18
2007 2159 9.469807 CAACATCTCCTATGTATTCTCACTAAC 57.530 37.037 0.00 0.00 0.00 2.34
2008 2160 9.201989 ACAACATCTCCTATGTATTCTCACTAA 57.798 33.333 0.00 0.00 0.00 2.24
2009 2161 8.768501 ACAACATCTCCTATGTATTCTCACTA 57.231 34.615 0.00 0.00 0.00 2.74
2030 2182 7.121168 TCACATTATGAGGAAATTGGAGACAAC 59.879 37.037 0.00 0.00 42.56 3.32
2031 2183 7.174413 TCACATTATGAGGAAATTGGAGACAA 58.826 34.615 0.00 0.00 43.37 3.18
2032 2184 6.720309 TCACATTATGAGGAAATTGGAGACA 58.280 36.000 0.00 0.00 32.90 3.41
2033 2185 7.814264 ATCACATTATGAGGAAATTGGAGAC 57.186 36.000 0.00 0.00 41.91 3.36
2034 2186 9.919416 TTAATCACATTATGAGGAAATTGGAGA 57.081 29.630 0.00 0.00 41.91 3.71
2035 2187 9.956720 GTTAATCACATTATGAGGAAATTGGAG 57.043 33.333 0.00 0.00 41.91 3.86
2036 2188 9.699410 AGTTAATCACATTATGAGGAAATTGGA 57.301 29.630 0.00 0.00 41.91 3.53
2037 2189 9.956720 GAGTTAATCACATTATGAGGAAATTGG 57.043 33.333 0.00 0.00 41.91 3.16
2041 2193 9.739276 ACTTGAGTTAATCACATTATGAGGAAA 57.261 29.630 0.00 0.00 41.91 3.13
2065 2217 2.249139 GACAGGGGTGAGTTGAGTACT 58.751 52.381 0.00 0.00 40.71 2.73
2066 2218 1.067776 CGACAGGGGTGAGTTGAGTAC 60.068 57.143 0.00 0.00 0.00 2.73
2067 2219 1.202964 TCGACAGGGGTGAGTTGAGTA 60.203 52.381 0.00 0.00 0.00 2.59
2068 2220 0.469331 TCGACAGGGGTGAGTTGAGT 60.469 55.000 0.00 0.00 0.00 3.41
2069 2221 0.898320 ATCGACAGGGGTGAGTTGAG 59.102 55.000 0.00 0.00 0.00 3.02
2070 2222 1.348064 AATCGACAGGGGTGAGTTGA 58.652 50.000 0.00 0.00 0.00 3.18
2071 2223 2.618053 GTAATCGACAGGGGTGAGTTG 58.382 52.381 0.00 0.00 0.00 3.16
2072 2224 1.553704 GGTAATCGACAGGGGTGAGTT 59.446 52.381 0.00 0.00 0.00 3.01
2078 2230 1.830145 CCTGGGTAATCGACAGGGG 59.170 63.158 10.44 0.00 46.24 4.79
2192 2344 7.115805 GTGTATCGTATGTTCTGAGTTGTTTCA 59.884 37.037 0.00 0.00 0.00 2.69
2234 2386 0.759346 CCCTTTCTCCATCCCGGTAG 59.241 60.000 0.00 0.00 35.57 3.18
2255 2407 2.619849 CCCTGCACCAAACATCTCATCT 60.620 50.000 0.00 0.00 0.00 2.90
2408 2563 0.527565 CATTGCCCTTCCTTTCCACG 59.472 55.000 0.00 0.00 0.00 4.94
2468 2623 7.357532 CGAGTAAATCATGAAAAATAATGGCGC 60.358 37.037 0.00 0.00 0.00 6.53
2469 2624 7.357532 GCGAGTAAATCATGAAAAATAATGGCG 60.358 37.037 0.00 0.00 0.00 5.69
2555 2710 1.004044 AGAACAGCCCACTTCCATCAG 59.996 52.381 0.00 0.00 0.00 2.90
2569 2724 6.462552 TCATTCTCAGAGATACCAGAACAG 57.537 41.667 0.00 0.00 0.00 3.16
2585 2740 1.171308 TTTGCAGGCAGCTCATTCTC 58.829 50.000 2.86 0.00 45.94 2.87
2587 2742 1.749634 AGATTTGCAGGCAGCTCATTC 59.250 47.619 2.86 0.00 45.94 2.67
2592 2747 0.033405 ATCCAGATTTGCAGGCAGCT 60.033 50.000 2.86 0.00 45.94 4.24
2614 2769 7.331934 CGAGTGAAAATGTTCCTCTTCAATAGA 59.668 37.037 10.56 0.00 32.85 1.98
2699 2864 8.172484 GCAATTGTACATCTAACGACAACAATA 58.828 33.333 7.40 0.00 35.61 1.90
2714 2879 2.556189 TCGTTTGGCAGCAATTGTACAT 59.444 40.909 7.40 0.00 0.00 2.29
2715 2880 1.950216 TCGTTTGGCAGCAATTGTACA 59.050 42.857 7.40 0.00 0.00 2.90
2733 2898 4.087930 GCGTTGTTGTTCATTGGTTTATCG 59.912 41.667 0.00 0.00 0.00 2.92
2764 2929 2.541547 CTTCAAGGATCGGCCAGCCA 62.542 60.000 9.78 0.00 40.02 4.75
2772 2937 4.748892 TCTAGACAAAGCTTCAAGGATCG 58.251 43.478 0.00 0.00 0.00 3.69
2797 2962 1.136305 GCTGCAATGTGAGCAATCCAT 59.864 47.619 0.00 0.00 42.17 3.41
2836 3001 8.047911 TGTTTGATAATTGATTGGCCATGAATT 58.952 29.630 6.09 13.66 0.00 2.17
2853 3032 8.986847 CACAAGTTTATTTGCCATGTTTGATAA 58.013 29.630 0.00 0.00 0.00 1.75
2855 3034 6.073112 GCACAAGTTTATTTGCCATGTTTGAT 60.073 34.615 0.00 0.00 0.00 2.57
2861 3040 3.928375 GGAGCACAAGTTTATTTGCCATG 59.072 43.478 0.00 0.00 35.47 3.66
2865 3044 3.367395 GGAGGGAGCACAAGTTTATTTGC 60.367 47.826 0.00 0.00 35.08 3.68
2879 3058 0.462789 TATTTTCGGACGGAGGGAGC 59.537 55.000 0.00 0.00 0.00 4.70
2890 3069 6.021596 CCATTTCTTCGACAAGTATTTTCGG 58.978 40.000 0.00 0.00 33.50 4.30
2892 3071 8.237267 ACATCCATTTCTTCGACAAGTATTTTC 58.763 33.333 0.00 0.00 0.00 2.29
2893 3072 8.110860 ACATCCATTTCTTCGACAAGTATTTT 57.889 30.769 0.00 0.00 0.00 1.82
2899 3078 8.138074 TCTAGATACATCCATTTCTTCGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
2944 3147 9.754382 GTCATAGCAATGAATAAAAATGGATGT 57.246 29.630 0.00 0.00 43.69 3.06
2945 3148 9.752961 TGTCATAGCAATGAATAAAAATGGATG 57.247 29.630 0.00 0.00 43.69 3.51
2947 3150 9.806203 CTTGTCATAGCAATGAATAAAAATGGA 57.194 29.630 0.00 0.00 43.69 3.41
2948 3151 9.590451 ACTTGTCATAGCAATGAATAAAAATGG 57.410 29.630 0.00 0.00 43.69 3.16
2955 3158 8.773645 CGGAAATACTTGTCATAGCAATGAATA 58.226 33.333 0.00 0.00 43.69 1.75
2957 3160 6.038161 CCGGAAATACTTGTCATAGCAATGAA 59.962 38.462 0.00 0.00 43.69 2.57
2960 3163 5.527582 GTCCGGAAATACTTGTCATAGCAAT 59.472 40.000 5.23 0.00 0.00 3.56
2963 3166 3.489785 CGTCCGGAAATACTTGTCATAGC 59.510 47.826 5.23 0.00 0.00 2.97
2964 3167 4.049186 CCGTCCGGAAATACTTGTCATAG 58.951 47.826 5.23 0.00 37.50 2.23
2965 3168 3.700539 TCCGTCCGGAAATACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
2967 3170 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2973 3176 7.383102 TCTTATATACTCCGTCCGGAAATAC 57.617 40.000 5.23 0.00 44.66 1.89
2979 3182 5.954296 TTCTTCTTATATACTCCGTCCGG 57.046 43.478 0.00 0.00 0.00 5.14
2980 3183 9.339492 GTAATTTCTTCTTATATACTCCGTCCG 57.661 37.037 0.00 0.00 0.00 4.79
3040 3256 4.968259 ACTGGTGTGCATGAACTTTAGTA 58.032 39.130 5.18 0.00 0.00 1.82
3062 3279 5.894393 TGTTCAAATGGGAGAAGTTGGTTAA 59.106 36.000 0.00 0.00 0.00 2.01
3097 3314 5.756195 TGAAGAAGGTTGTGTTTGAGATG 57.244 39.130 0.00 0.00 0.00 2.90
3152 3369 1.917303 GGCATCCAAATTTGCGTAACG 59.083 47.619 12.92 0.00 39.78 3.18
3269 3486 6.182627 TGTTCAATCATACTTCTGCTTGGAT 58.817 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.