Multiple sequence alignment - TraesCS3A01G087600

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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 TraesCS3A01G087600 chr3A 100.000 2368 0 0 669 3036 56408851 56411218 0.000000e+00 4373.0
1 TraesCS3A01G087600 chr3A 100.000 370 0 0 1 370 56408183 56408552 0.000000e+00 684.0
2 TraesCS3A01G087600 chr3B 88.650 1533 108 27 722 2246 69620263 69621737 0.000000e+00 1807.0
3 TraesCS3A01G087600 chr3B 95.019 803 30 5 2238 3036 69623363 69624159 0.000000e+00 1253.0
4 TraesCS3A01G087600 chr3B 84.574 1316 124 36 693 1985 69362256 69360997 0.000000e+00 1232.0
5 TraesCS3A01G087600 chr3B 90.719 334 26 4 3 333 69619541 69619872 9.990000e-120 440.0
6 TraesCS3A01G087600 chr3B 78.537 205 36 7 2832 3031 169400835 169401036 8.830000e-26 128.0
7 TraesCS3A01G087600 chr3B 95.588 68 3 0 2164 2231 69360860 69360793 3.200000e-20 110.0
8 TraesCS3A01G087600 chr3B 94.444 54 2 1 2384 2437 69360436 69360384 6.980000e-12 82.4
9 TraesCS3A01G087600 chr3B 94.737 38 2 0 2068 2105 69360919 69360882 3.270000e-05 60.2
10 TraesCS3A01G087600 chr3D 86.724 821 69 17 2243 3030 44222251 44223064 0.000000e+00 876.0
11 TraesCS3A01G087600 chr3D 90.476 357 18 7 1554 1910 44221612 44221952 9.920000e-125 457.0
12 TraesCS3A01G087600 chr3D 83.058 484 29 20 693 1169 44221184 44221621 1.020000e-104 390.0
13 TraesCS3A01G087600 chr3D 84.615 143 16 3 1969 2105 44221962 44222104 1.470000e-28 137.0
14 TraesCS3A01G087600 chr6A 77.562 771 149 17 1069 1818 15375335 15376102 7.720000e-121 444.0
15 TraesCS3A01G087600 chr5B 76.942 811 143 33 1045 1823 640872627 640873425 3.620000e-114 422.0
16 TraesCS3A01G087600 chr5A 76.215 782 146 28 1069 1816 637589467 637590242 7.950000e-101 377.0
17 TraesCS3A01G087600 chr5A 89.130 46 4 1 2236 2281 619465211 619465167 4.230000e-04 56.5
18 TraesCS3A01G087600 chr6B 74.901 757 151 27 1086 1824 25663441 25664176 2.940000e-80 309.0
19 TraesCS3A01G087600 chr5D 80.220 273 48 4 1036 1303 509942201 509942472 1.850000e-47 200.0
20 TraesCS3A01G087600 chr5D 88.462 52 2 4 2216 2267 415721570 415721617 3.270000e-05 60.2
21 TraesCS3A01G087600 chr6D 88.660 97 11 0 1076 1172 14019732 14019828 5.320000e-23 119.0
22 TraesCS3A01G087600 chr1B 86.735 98 12 1 216 313 31631266 31631170 1.150000e-19 108.0
23 TraesCS3A01G087600 chr7A 85.859 99 13 1 245 343 609350066 609349969 1.490000e-18 104.0
24 TraesCS3A01G087600 chr4A 100.000 29 0 0 2971 2999 694894541 694894513 2.000000e-03 54.7
25 TraesCS3A01G087600 chr1A 100.000 29 0 0 2971 2999 496067309 496067281 2.000000e-03 54.7


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 TraesCS3A01G087600 chr3A 56408183 56411218 3035 False 2528.500000 4373 100.000000 1 3036 2 chr3A.!!$F1 3035
1 TraesCS3A01G087600 chr3B 69619541 69624159 4618 False 1166.666667 1807 91.462667 3 3036 3 chr3B.!!$F2 3033
2 TraesCS3A01G087600 chr3B 69360384 69362256 1872 True 371.150000 1232 92.335750 693 2437 4 chr3B.!!$R1 1744
3 TraesCS3A01G087600 chr3D 44221184 44223064 1880 False 465.000000 876 86.218250 693 3030 4 chr3D.!!$F1 2337
4 TraesCS3A01G087600 chr6A 15375335 15376102 767 False 444.000000 444 77.562000 1069 1818 1 chr6A.!!$F1 749
5 TraesCS3A01G087600 chr5B 640872627 640873425 798 False 422.000000 422 76.942000 1045 1823 1 chr5B.!!$F1 778
6 TraesCS3A01G087600 chr5A 637589467 637590242 775 False 377.000000 377 76.215000 1069 1816 1 chr5A.!!$F1 747
7 TraesCS3A01G087600 chr6B 25663441 25664176 735 False 309.000000 309 74.901000 1086 1824 1 chr6B.!!$F1 738

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
258 261 0.785378 CACACACCGCATGCAAAATG 59.215 50.0 19.57 12.52 0.00 2.32 F
1299 1876 0.109272 TGCACTCGTTGGAGATCGAC 60.109 55.0 0.00 0.00 43.27 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 2074 0.320334 TCAGATGCGGTGAAGCGAAA 60.320 50.0 6.02 0.0 40.67 3.46 R
2107 3168 0.393673 TATGTGATTGCGGGTGGGTG 60.394 55.0 0.00 0.0 0.00 4.61 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
81 82 3.131396 TCTGAAAGAGCAGAAAACGGAC 58.869 45.455 0.00 0.00 41.65 4.79
98 99 3.181463 ACGGACAGTAGTAAACCTGCAAA 60.181 43.478 0.00 0.00 0.00 3.68
104 105 6.068670 ACAGTAGTAAACCTGCAAAGGAAAT 58.931 36.000 0.00 0.00 0.00 2.17
106 107 7.722285 ACAGTAGTAAACCTGCAAAGGAAATTA 59.278 33.333 0.00 0.00 0.00 1.40
107 108 8.021396 CAGTAGTAAACCTGCAAAGGAAATTAC 58.979 37.037 0.00 5.74 32.19 1.89
108 109 6.969993 AGTAAACCTGCAAAGGAAATTACA 57.030 33.333 15.35 0.00 33.25 2.41
109 110 6.745116 AGTAAACCTGCAAAGGAAATTACAC 58.255 36.000 15.35 0.00 33.25 2.90
110 111 5.606348 AAACCTGCAAAGGAAATTACACA 57.394 34.783 0.00 0.00 0.00 3.72
111 112 5.806654 AACCTGCAAAGGAAATTACACAT 57.193 34.783 0.00 0.00 0.00 3.21
117 120 9.218440 CCTGCAAAGGAAATTACACATAAAAAT 57.782 29.630 0.00 0.00 0.00 1.82
134 137 7.920682 ACATAAAAATTCAGAAACAGTCACCAC 59.079 33.333 0.00 0.00 0.00 4.16
189 192 7.269316 TCGTGGACATAACTAAAGATGCAATA 58.731 34.615 0.00 0.00 0.00 1.90
190 193 7.223971 TCGTGGACATAACTAAAGATGCAATAC 59.776 37.037 0.00 0.00 0.00 1.89
205 208 2.862512 CAATACGCGTGGCTCAAATTT 58.137 42.857 24.59 0.00 0.00 1.82
210 213 1.632422 GCGTGGCTCAAATTTGATGG 58.368 50.000 20.76 11.62 36.46 3.51
231 234 6.320494 TGGTAAAATTTGCATACAACGACT 57.680 33.333 0.00 0.00 34.87 4.18
233 236 5.506832 GGTAAAATTTGCATACAACGACTCG 59.493 40.000 0.00 0.00 34.87 4.18
243 246 2.244651 AACGACTCGGCAAGCACAC 61.245 57.895 2.98 0.00 0.00 3.82
258 261 0.785378 CACACACCGCATGCAAAATG 59.215 50.000 19.57 12.52 0.00 2.32
293 296 5.948742 AAGAAAAGATAGGAGAGGAGGTG 57.051 43.478 0.00 0.00 0.00 4.00
294 297 5.213868 AGAAAAGATAGGAGAGGAGGTGA 57.786 43.478 0.00 0.00 0.00 4.02
297 300 4.618378 AAGATAGGAGAGGAGGTGACTT 57.382 45.455 0.00 0.00 44.43 3.01
298 301 3.909732 AGATAGGAGAGGAGGTGACTTG 58.090 50.000 0.00 0.00 44.43 3.16
302 305 1.633774 GAGAGGAGGTGACTTGGTCA 58.366 55.000 0.00 0.00 44.43 4.02
316 319 1.796017 TGGTCACCACTACCTTCACA 58.204 50.000 0.00 0.00 37.91 3.58
317 320 2.334977 TGGTCACCACTACCTTCACAT 58.665 47.619 0.00 0.00 37.91 3.21
324 327 2.567169 CCACTACCTTCACATGACAGGA 59.433 50.000 14.15 0.00 0.00 3.86
333 336 0.972983 ACATGACAGGACGGAGGAGG 60.973 60.000 0.00 0.00 0.00 4.30
334 337 2.060980 ATGACAGGACGGAGGAGGC 61.061 63.158 0.00 0.00 0.00 4.70
335 338 2.680352 GACAGGACGGAGGAGGCA 60.680 66.667 0.00 0.00 0.00 4.75
336 339 2.681778 ACAGGACGGAGGAGGCAG 60.682 66.667 0.00 0.00 0.00 4.85
337 340 4.154347 CAGGACGGAGGAGGCAGC 62.154 72.222 0.00 0.00 0.00 5.25
362 487 2.102357 CGACGACGATGTGGGGAG 59.898 66.667 0.00 0.00 42.66 4.30
366 491 4.176752 GACGATGTGGGGAGGGGC 62.177 72.222 0.00 0.00 0.00 5.80
703 837 6.381420 TGGAAACAATCAGGTTTTAGGAAACA 59.619 34.615 4.64 0.00 41.69 2.83
704 838 7.093289 TGGAAACAATCAGGTTTTAGGAAACAA 60.093 33.333 4.64 0.00 41.69 2.83
753 887 1.021390 GGATCGGTGCACCACAGAAG 61.021 60.000 34.16 17.53 41.26 2.85
767 901 6.128391 GCACCACAGAAGAAATCATAACGTTA 60.128 38.462 11.02 11.02 0.00 3.18
768 902 7.414098 GCACCACAGAAGAAATCATAACGTTAT 60.414 37.037 15.07 15.07 0.00 1.89
769 903 8.116753 CACCACAGAAGAAATCATAACGTTATC 58.883 37.037 17.82 7.72 0.00 1.75
846 984 7.855784 ATTAAGGAAACAGATCCCAGTTTTT 57.144 32.000 9.15 4.87 40.59 1.94
874 1015 4.352893 AGGGGTAACAGATCCCAAAATTG 58.647 43.478 0.00 0.00 45.06 2.32
888 1033 4.035208 CCCAAAATTGTAGGACGTAGATGC 59.965 45.833 0.00 0.00 0.00 3.91
897 1042 4.273148 AGGACGTAGATGCTTTGTTTCT 57.727 40.909 0.00 0.00 0.00 2.52
900 1045 6.407202 AGGACGTAGATGCTTTGTTTCTTAT 58.593 36.000 0.00 0.00 0.00 1.73
901 1046 7.553334 AGGACGTAGATGCTTTGTTTCTTATA 58.447 34.615 0.00 0.00 0.00 0.98
902 1047 8.204836 AGGACGTAGATGCTTTGTTTCTTATAT 58.795 33.333 0.00 0.00 0.00 0.86
903 1048 8.488764 GGACGTAGATGCTTTGTTTCTTATATC 58.511 37.037 0.00 0.00 0.00 1.63
904 1049 9.250624 GACGTAGATGCTTTGTTTCTTATATCT 57.749 33.333 0.00 0.00 0.00 1.98
905 1050 9.601217 ACGTAGATGCTTTGTTTCTTATATCTT 57.399 29.630 0.00 0.00 0.00 2.40
983 1138 7.464273 TCAGGTTCCAGATATATAAGGACGTA 58.536 38.462 5.36 0.00 0.00 3.57
1011 1166 2.355209 GCTCCTTTCAATCGACCTCCTT 60.355 50.000 0.00 0.00 0.00 3.36
1187 1764 1.201429 AGCCACCTCTGGAAATCCGT 61.201 55.000 0.00 0.00 40.55 4.69
1193 1770 2.513897 CTGGAAATCCGTCCCCGC 60.514 66.667 0.00 0.00 39.43 6.13
1246 1823 2.035961 CTCCTCTTCGTCAACAACCTCA 59.964 50.000 0.00 0.00 0.00 3.86
1251 1828 4.307432 TCTTCGTCAACAACCTCATCTTC 58.693 43.478 0.00 0.00 0.00 2.87
1254 1831 3.057019 CGTCAACAACCTCATCTTCGAA 58.943 45.455 0.00 0.00 0.00 3.71
1258 1835 1.270094 ACAACCTCATCTTCGAACGCA 60.270 47.619 0.00 0.00 0.00 5.24
1259 1836 1.798223 CAACCTCATCTTCGAACGCAA 59.202 47.619 0.00 0.00 0.00 4.85
1268 1845 3.479269 CGAACGCAACCTCGGCTC 61.479 66.667 0.00 0.00 0.00 4.70
1269 1846 3.119096 GAACGCAACCTCGGCTCC 61.119 66.667 0.00 0.00 0.00 4.70
1297 1874 1.416813 GCTGCACTCGTTGGAGATCG 61.417 60.000 11.38 0.00 46.53 3.69
1299 1876 0.109272 TGCACTCGTTGGAGATCGAC 60.109 55.000 0.00 0.00 43.27 4.20
1356 1933 2.858868 CTGCTTGACTGCGACTGC 59.141 61.111 0.00 0.00 43.20 4.40
1374 1951 1.671880 GCAACTTCGACGACTACCGC 61.672 60.000 0.00 0.00 43.32 5.68
1375 1952 1.069378 CAACTTCGACGACTACCGCC 61.069 60.000 0.00 0.00 43.32 6.13
1380 1957 3.741476 GACGACTACCGCCACCGT 61.741 66.667 0.00 0.00 43.32 4.83
1393 1970 2.126071 ACCGTCGCGAGGTCAATG 60.126 61.111 25.31 13.21 37.44 2.82
1397 1974 3.700970 TCGCGAGGTCAATGCCCA 61.701 61.111 3.71 0.00 0.00 5.36
1468 2045 3.706373 GGGCCTGCTTCGGTGAGA 61.706 66.667 0.84 0.00 0.00 3.27
1506 2083 2.351276 GCCCTCCCTTTCGCTTCA 59.649 61.111 0.00 0.00 0.00 3.02
1517 2094 1.014044 TTCGCTTCACCGCATCTGAC 61.014 55.000 0.00 0.00 0.00 3.51
1519 2096 1.446099 GCTTCACCGCATCTGACGA 60.446 57.895 0.00 0.00 0.00 4.20
1524 2101 0.802222 CACCGCATCTGACGACGATT 60.802 55.000 0.00 0.00 0.00 3.34
1550 2127 3.121030 CGCCGTTTGCCTCAGAGG 61.121 66.667 12.81 12.81 38.80 3.69
1747 2729 0.041312 CACGCCAAGACTCCGTTTTG 60.041 55.000 0.00 0.00 32.18 2.44
1849 2840 3.547746 TGATGTGTGATGGTGATGATGG 58.452 45.455 0.00 0.00 0.00 3.51
1890 2881 2.565834 ACCGTGAATGCTACTACCAACT 59.434 45.455 0.00 0.00 0.00 3.16
1959 2950 5.409520 CACTACATTAGTCAAGCAGAAGCAA 59.590 40.000 0.00 0.00 39.29 3.91
1964 2955 0.386478 GTCAAGCAGAAGCAAAGCCG 60.386 55.000 0.00 0.00 45.49 5.52
1967 2958 1.135859 CAAGCAGAAGCAAAGCCGTAG 60.136 52.381 0.00 0.00 45.49 3.51
2028 3084 6.587226 ACATAAGACGAACAATACACGCTTTA 59.413 34.615 0.00 0.00 0.00 1.85
2034 3090 8.347771 AGACGAACAATACACGCTTTATCTATA 58.652 33.333 0.00 0.00 0.00 1.31
2099 3160 7.938563 TTTTGGTAGGAAACAATTTGAATCG 57.061 32.000 2.79 0.00 0.00 3.34
2107 3168 3.934457 ACAATTTGAATCGGTTGGACC 57.066 42.857 2.79 0.00 34.05 4.46
2109 3170 3.005367 ACAATTTGAATCGGTTGGACCAC 59.995 43.478 2.79 0.00 38.47 4.16
2111 3172 0.250989 TTGAATCGGTTGGACCACCC 60.251 55.000 0.00 0.00 38.47 4.61
2112 3173 1.377229 GAATCGGTTGGACCACCCA 59.623 57.895 9.02 0.00 44.93 4.51
2113 3174 0.958876 GAATCGGTTGGACCACCCAC 60.959 60.000 9.02 0.00 46.62 4.61
2114 3175 2.420466 AATCGGTTGGACCACCCACC 62.420 60.000 9.02 6.32 46.62 4.61
2115 3176 4.653888 CGGTTGGACCACCCACCC 62.654 72.222 9.02 0.00 45.79 4.61
2116 3177 4.653888 GGTTGGACCACCCACCCG 62.654 72.222 2.53 0.00 46.62 5.28
2120 3181 4.360405 GGACCACCCACCCGCAAT 62.360 66.667 0.00 0.00 34.14 3.56
2121 3182 2.750237 GACCACCCACCCGCAATC 60.750 66.667 0.00 0.00 0.00 2.67
2122 3183 3.561120 GACCACCCACCCGCAATCA 62.561 63.158 0.00 0.00 0.00 2.57
2123 3184 3.061848 CCACCCACCCGCAATCAC 61.062 66.667 0.00 0.00 0.00 3.06
2124 3185 2.282110 CACCCACCCGCAATCACA 60.282 61.111 0.00 0.00 0.00 3.58
2125 3186 1.678635 CACCCACCCGCAATCACAT 60.679 57.895 0.00 0.00 0.00 3.21
2126 3187 0.393673 CACCCACCCGCAATCACATA 60.394 55.000 0.00 0.00 0.00 2.29
2127 3188 0.329931 ACCCACCCGCAATCACATAA 59.670 50.000 0.00 0.00 0.00 1.90
2128 3189 1.272203 ACCCACCCGCAATCACATAAA 60.272 47.619 0.00 0.00 0.00 1.40
2129 3190 2.031120 CCCACCCGCAATCACATAAAT 58.969 47.619 0.00 0.00 0.00 1.40
2156 3217 3.222287 GCATCCATTGCCCCCTAAA 57.778 52.632 0.00 0.00 46.15 1.85
2336 5218 7.087639 CCACTCAAACAAGTTTCAAGTAACAA 58.912 34.615 8.90 0.00 29.58 2.83
2337 5219 7.596995 CCACTCAAACAAGTTTCAAGTAACAAA 59.403 33.333 8.90 0.00 29.58 2.83
2396 5317 0.179000 CACTCGCCCCTTCTAAGCAT 59.821 55.000 0.00 0.00 0.00 3.79
2461 5382 3.257393 ACTTTCAGACGATCAGACATGC 58.743 45.455 0.00 0.00 0.00 4.06
2526 5447 5.932303 CGGTATATGGGTGATGAAACCTAAG 59.068 44.000 0.00 0.00 40.35 2.18
2536 5457 6.823689 GGTGATGAAACCTAAGATCTAGCAAA 59.176 38.462 0.00 0.00 37.24 3.68
2562 5483 7.074653 AGTATTAGTCAAAGGTTCCAGAACA 57.925 36.000 12.32 0.00 42.85 3.18
2647 5568 9.691362 GGAATAAAGTCAGAAGCAAAAACAATA 57.309 29.630 0.00 0.00 0.00 1.90
2676 5597 9.747898 AGTACTCAAATTAACATGGTGGATAAA 57.252 29.630 0.00 0.00 0.00 1.40
2771 5694 1.003545 CCGCTAGATTGATTGCAACCG 60.004 52.381 0.00 0.00 36.72 4.44
2816 5739 5.128499 AGACTTTCATCCTAGACTGACCATG 59.872 44.000 0.00 0.00 0.00 3.66
2865 5788 2.221749 CCGGATGCTAATTCATGTCGTG 59.778 50.000 0.00 0.00 0.00 4.35
2916 5858 1.595794 GTTGGATTGTCGACACGTGTT 59.404 47.619 24.26 5.13 0.00 3.32
2927 5869 2.220133 CGACACGTGTTCGGAGAAAAAT 59.780 45.455 24.26 0.00 45.90 1.82
2996 5944 1.957113 GCAAAATCCCCACCTCCTCTG 60.957 57.143 0.00 0.00 0.00 3.35
3010 5958 2.847234 TCTGCACCCACCCGAACT 60.847 61.111 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.765510 ACACCTCAGGGTTTCCAGAC 59.234 55.000 0.00 0.00 44.73 3.51
1 2 1.975680 GTACACCTCAGGGTTTCCAGA 59.024 52.381 0.00 0.00 44.73 3.86
4 5 1.975680 TCAGTACACCTCAGGGTTTCC 59.024 52.381 0.00 0.00 44.73 3.13
18 19 8.113062 CGATCATCTCTGTTGAAATTTCAGTAC 58.887 37.037 19.64 16.42 38.61 2.73
29 30 4.825422 AGCTTTTCGATCATCTCTGTTGA 58.175 39.130 0.00 0.00 0.00 3.18
78 79 3.751698 CCTTTGCAGGTTTACTACTGTCC 59.248 47.826 0.00 0.00 37.07 4.02
81 82 6.575162 ATTTCCTTTGCAGGTTTACTACTG 57.425 37.500 0.00 0.00 41.69 2.74
106 107 7.920682 GGTGACTGTTTCTGAATTTTTATGTGT 59.079 33.333 0.00 0.00 0.00 3.72
107 108 7.920151 TGGTGACTGTTTCTGAATTTTTATGTG 59.080 33.333 0.00 0.00 0.00 3.21
108 109 7.920682 GTGGTGACTGTTTCTGAATTTTTATGT 59.079 33.333 0.00 0.00 0.00 2.29
109 110 7.382218 GGTGGTGACTGTTTCTGAATTTTTATG 59.618 37.037 0.00 0.00 0.00 1.90
110 111 7.069331 TGGTGGTGACTGTTTCTGAATTTTTAT 59.931 33.333 0.00 0.00 0.00 1.40
111 112 6.378564 TGGTGGTGACTGTTTCTGAATTTTTA 59.621 34.615 0.00 0.00 0.00 1.52
117 120 3.358111 TTGGTGGTGACTGTTTCTGAA 57.642 42.857 0.00 0.00 0.00 3.02
119 122 4.097741 TCAATTTGGTGGTGACTGTTTCTG 59.902 41.667 0.00 0.00 0.00 3.02
120 123 4.277476 TCAATTTGGTGGTGACTGTTTCT 58.723 39.130 0.00 0.00 0.00 2.52
127 130 3.504520 ACCGTATTCAATTTGGTGGTGAC 59.495 43.478 0.00 0.00 0.00 3.67
134 137 3.627577 CCTCAGGACCGTATTCAATTTGG 59.372 47.826 0.00 0.00 0.00 3.28
189 192 0.881118 ATCAAATTTGAGCCACGCGT 59.119 45.000 24.17 5.58 41.08 6.01
190 193 1.261989 CATCAAATTTGAGCCACGCG 58.738 50.000 24.17 3.53 41.08 6.01
205 208 6.804295 GTCGTTGTATGCAAATTTTACCATCA 59.196 34.615 0.00 0.00 36.22 3.07
210 213 5.506832 CCGAGTCGTTGTATGCAAATTTTAC 59.493 40.000 12.31 0.00 36.22 2.01
233 236 3.673484 ATGCGGTGTGTGCTTGCC 61.673 61.111 0.00 0.00 0.00 4.52
243 246 2.456989 GATCTCATTTTGCATGCGGTG 58.543 47.619 14.09 8.97 0.00 4.94
258 261 6.319911 CCTATCTTTTCTTTGGTTGGGATCTC 59.680 42.308 0.00 0.00 0.00 2.75
293 296 2.367567 TGAAGGTAGTGGTGACCAAGTC 59.632 50.000 5.57 0.00 39.65 3.01
294 297 2.104281 GTGAAGGTAGTGGTGACCAAGT 59.896 50.000 5.57 0.00 39.65 3.16
297 300 1.796017 TGTGAAGGTAGTGGTGACCA 58.204 50.000 0.00 0.00 39.65 4.02
298 301 2.301870 TCATGTGAAGGTAGTGGTGACC 59.698 50.000 0.00 0.00 37.22 4.02
302 305 2.303022 CCTGTCATGTGAAGGTAGTGGT 59.697 50.000 0.00 0.00 0.00 4.16
303 306 2.567169 TCCTGTCATGTGAAGGTAGTGG 59.433 50.000 9.78 0.00 32.59 4.00
316 319 2.060980 GCCTCCTCCGTCCTGTCAT 61.061 63.158 0.00 0.00 0.00 3.06
317 320 2.680352 GCCTCCTCCGTCCTGTCA 60.680 66.667 0.00 0.00 0.00 3.58
337 340 3.807538 ATCGTCGTCGTCCACCGG 61.808 66.667 0.00 0.00 38.33 5.28
668 793 2.229690 ATTGTTTCCATGGGCGCTGC 62.230 55.000 13.02 0.00 0.00 5.25
669 794 0.179129 GATTGTTTCCATGGGCGCTG 60.179 55.000 13.02 0.00 0.00 5.18
670 795 0.611618 TGATTGTTTCCATGGGCGCT 60.612 50.000 13.02 0.00 0.00 5.92
671 796 0.179129 CTGATTGTTTCCATGGGCGC 60.179 55.000 13.02 0.00 0.00 6.53
672 797 0.457035 CCTGATTGTTTCCATGGGCG 59.543 55.000 13.02 0.00 0.00 6.13
673 798 1.560505 ACCTGATTGTTTCCATGGGC 58.439 50.000 13.02 3.37 0.00 5.36
674 799 4.622260 AAAACCTGATTGTTTCCATGGG 57.378 40.909 13.02 0.00 37.46 4.00
675 800 5.480073 TCCTAAAACCTGATTGTTTCCATGG 59.520 40.000 4.97 4.97 37.46 3.66
676 801 6.588719 TCCTAAAACCTGATTGTTTCCATG 57.411 37.500 0.00 0.00 37.46 3.66
677 802 7.070571 TGTTTCCTAAAACCTGATTGTTTCCAT 59.929 33.333 0.00 0.00 43.44 3.41
678 803 6.381420 TGTTTCCTAAAACCTGATTGTTTCCA 59.619 34.615 0.00 0.00 43.44 3.53
679 804 6.811954 TGTTTCCTAAAACCTGATTGTTTCC 58.188 36.000 0.00 0.00 43.44 3.13
680 805 8.710835 TTTGTTTCCTAAAACCTGATTGTTTC 57.289 30.769 0.00 0.00 43.44 2.78
681 806 9.508642 TTTTTGTTTCCTAAAACCTGATTGTTT 57.491 25.926 0.00 0.00 43.44 2.83
703 837 8.862085 TCAGTTTCCTTAAAATCCCGTATTTTT 58.138 29.630 10.01 2.46 43.75 1.94
704 838 8.411991 TCAGTTTCCTTAAAATCCCGTATTTT 57.588 30.769 9.74 9.74 46.92 1.82
753 887 7.639039 TGCTTCCATGATAACGTTATGATTTC 58.361 34.615 24.90 11.73 0.00 2.17
846 984 1.920351 GGATCTGTTACCCCTCCCAAA 59.080 52.381 0.00 0.00 0.00 3.28
849 987 0.327191 TGGGATCTGTTACCCCTCCC 60.327 60.000 0.00 6.35 45.01 4.30
874 1015 5.169295 AGAAACAAAGCATCTACGTCCTAC 58.831 41.667 0.00 0.00 0.00 3.18
913 1058 9.582648 AAACCCCAGCTCGTAATAATAATTAAT 57.417 29.630 0.00 0.00 29.41 1.40
914 1059 8.983702 AAACCCCAGCTCGTAATAATAATTAA 57.016 30.769 0.00 0.00 29.41 1.40
915 1060 7.662669 GGAAACCCCAGCTCGTAATAATAATTA 59.337 37.037 0.00 0.00 34.14 1.40
916 1061 6.489022 GGAAACCCCAGCTCGTAATAATAATT 59.511 38.462 0.00 0.00 34.14 1.40
917 1062 6.002082 GGAAACCCCAGCTCGTAATAATAAT 58.998 40.000 0.00 0.00 34.14 1.28
918 1063 5.370679 GGAAACCCCAGCTCGTAATAATAA 58.629 41.667 0.00 0.00 34.14 1.40
919 1064 4.964593 GGAAACCCCAGCTCGTAATAATA 58.035 43.478 0.00 0.00 34.14 0.98
920 1065 3.816994 GGAAACCCCAGCTCGTAATAAT 58.183 45.455 0.00 0.00 34.14 1.28
921 1066 3.271055 GGAAACCCCAGCTCGTAATAA 57.729 47.619 0.00 0.00 34.14 1.40
954 1104 9.482175 GTCCTTATATATCTGGAACCTGATACT 57.518 37.037 18.03 12.78 38.85 2.12
955 1105 8.407064 CGTCCTTATATATCTGGAACCTGATAC 58.593 40.741 18.03 8.42 38.85 2.24
956 1106 8.114102 ACGTCCTTATATATCTGGAACCTGATA 58.886 37.037 17.99 17.99 39.79 2.15
957 1107 6.954684 ACGTCCTTATATATCTGGAACCTGAT 59.045 38.462 15.38 15.38 38.06 2.90
960 1110 7.236529 TGTACGTCCTTATATATCTGGAACCT 58.763 38.462 0.00 0.00 0.00 3.50
983 1138 1.683011 CGATTGAAAGGAGCCCCATGT 60.683 52.381 0.00 0.00 33.88 3.21
1168 1745 1.201429 ACGGATTTCCAGAGGTGGCT 61.201 55.000 0.00 0.00 44.60 4.75
1217 1794 1.618837 TGACGAAGAGGAGGAACTTGG 59.381 52.381 0.00 0.00 41.55 3.61
1246 1823 0.736325 CCGAGGTTGCGTTCGAAGAT 60.736 55.000 0.00 0.00 39.06 2.40
1251 1828 3.479269 GAGCCGAGGTTGCGTTCG 61.479 66.667 0.00 0.00 36.62 3.95
1317 1894 1.520342 GCAGTAAGAGCAGGCGAGG 60.520 63.158 0.00 0.00 0.00 4.63
1320 1897 2.084844 CTTGCAGTAAGAGCAGGCG 58.915 57.895 0.00 0.00 43.75 5.52
1356 1933 1.069378 GGCGGTAGTCGTCGAAGTTG 61.069 60.000 0.00 0.00 41.72 3.16
1357 1934 1.211190 GGCGGTAGTCGTCGAAGTT 59.789 57.895 0.00 0.00 41.72 2.66
1374 1951 3.642778 ATTGACCTCGCGACGGTGG 62.643 63.158 27.44 19.92 34.19 4.61
1375 1952 2.126071 ATTGACCTCGCGACGGTG 60.126 61.111 27.44 10.16 34.19 4.94
1380 1957 3.664025 CTGGGCATTGACCTCGCGA 62.664 63.158 9.26 9.26 0.00 5.87
1384 1961 1.450312 CGACCTGGGCATTGACCTC 60.450 63.158 10.60 0.00 0.00 3.85
1393 1970 4.436998 CCAGTCGTCGACCTGGGC 62.437 72.222 25.17 8.86 31.82 5.36
1397 1974 1.972223 CTGACCCAGTCGTCGACCT 60.972 63.158 21.40 6.64 34.95 3.85
1462 2039 2.663196 CTTCCACCGGGTCTCACC 59.337 66.667 6.32 0.00 37.60 4.02
1463 2040 2.047179 GCTTCCACCGGGTCTCAC 60.047 66.667 6.32 0.00 34.93 3.51
1497 2074 0.320334 TCAGATGCGGTGAAGCGAAA 60.320 50.000 6.02 0.00 40.67 3.46
1502 2079 1.406219 CGTCGTCAGATGCGGTGAAG 61.406 60.000 0.00 0.00 0.00 3.02
1503 2080 1.443702 CGTCGTCAGATGCGGTGAA 60.444 57.895 0.00 0.00 0.00 3.18
1506 2083 0.525668 GAATCGTCGTCAGATGCGGT 60.526 55.000 6.62 0.00 33.49 5.68
1519 2096 2.181021 GGCGTCGAGGTGAATCGT 59.819 61.111 7.01 0.00 43.20 3.73
1524 2101 2.355363 CAAACGGCGTCGAGGTGA 60.355 61.111 20.03 0.00 40.11 4.02
1550 2127 4.400961 AGAAGTCCAGCTGGCCGC 62.401 66.667 28.91 19.21 39.57 6.53
1590 2569 1.882167 GCAGAGCACGAGATCCAGC 60.882 63.158 0.00 0.00 0.00 4.85
1747 2729 7.436430 TGTCGTAGTTATCAGATATCTCCAC 57.564 40.000 1.03 0.00 0.00 4.02
1785 2767 1.750018 CAACCATGGCGCCATCTCA 60.750 57.895 38.60 13.29 33.90 3.27
1849 2840 4.196971 GGTCTATGGGTATGGTGAACAAC 58.803 47.826 0.00 0.00 0.00 3.32
1867 2858 2.453521 TGGTAGTAGCATTCACGGTCT 58.546 47.619 0.00 0.00 0.00 3.85
1934 2925 4.932200 GCTTCTGCTTGACTAATGTAGTGT 59.068 41.667 0.00 0.00 36.20 3.55
2010 3066 9.125906 GATATAGATAAAGCGTGTATTGTTCGT 57.874 33.333 0.00 0.00 0.00 3.85
2018 3074 9.888878 GTACAACAGATATAGATAAAGCGTGTA 57.111 33.333 0.00 0.00 0.00 2.90
2028 3084 9.547753 GGTGTTCATTGTACAACAGATATAGAT 57.452 33.333 11.22 0.00 33.16 1.98
2034 3090 3.751175 CGGGTGTTCATTGTACAACAGAT 59.249 43.478 11.22 0.00 34.89 2.90
2107 3168 0.393673 TATGTGATTGCGGGTGGGTG 60.394 55.000 0.00 0.00 0.00 4.61
2109 3170 1.468985 TTTATGTGATTGCGGGTGGG 58.531 50.000 0.00 0.00 0.00 4.61
2111 3172 3.378112 ACTGATTTATGTGATTGCGGGTG 59.622 43.478 0.00 0.00 0.00 4.61
2112 3173 3.620488 ACTGATTTATGTGATTGCGGGT 58.380 40.909 0.00 0.00 0.00 5.28
2113 3174 5.469760 TCATACTGATTTATGTGATTGCGGG 59.530 40.000 0.00 0.00 32.17 6.13
2114 3175 6.544038 TCATACTGATTTATGTGATTGCGG 57.456 37.500 0.00 0.00 32.17 5.69
2115 3176 6.075918 GCTCATACTGATTTATGTGATTGCG 58.924 40.000 0.00 0.00 32.17 4.85
2116 3177 6.962686 TGCTCATACTGATTTATGTGATTGC 58.037 36.000 0.00 0.00 32.17 3.56
2117 3178 8.235226 GGATGCTCATACTGATTTATGTGATTG 58.765 37.037 0.00 0.00 32.17 2.67
2118 3179 7.940688 TGGATGCTCATACTGATTTATGTGATT 59.059 33.333 0.00 0.00 32.17 2.57
2119 3180 7.455891 TGGATGCTCATACTGATTTATGTGAT 58.544 34.615 0.00 0.00 32.17 3.06
2120 3181 6.829849 TGGATGCTCATACTGATTTATGTGA 58.170 36.000 0.00 0.00 32.17 3.58
2121 3182 7.683437 ATGGATGCTCATACTGATTTATGTG 57.317 36.000 0.00 0.00 32.17 3.21
2122 3183 8.107399 CAATGGATGCTCATACTGATTTATGT 57.893 34.615 0.00 0.00 32.17 2.29
2396 5317 3.006247 TGCACGCAACTGCTATCATTAA 58.994 40.909 0.00 0.00 38.07 1.40
2449 5370 3.192466 TGTCATCAAGCATGTCTGATCG 58.808 45.455 8.26 5.85 33.66 3.69
2536 5457 7.996644 TGTTCTGGAACCTTTGACTAATACTTT 59.003 33.333 10.44 0.00 40.46 2.66
2544 5465 7.004086 TGATAAATGTTCTGGAACCTTTGACT 58.996 34.615 19.38 9.44 38.77 3.41
2562 5483 9.396022 ACTGGACGTTTCTATCATTTGATAAAT 57.604 29.630 0.00 0.00 36.66 1.40
2647 5568 7.001674 TCCACCATGTTAATTTGAGTACTTGT 58.998 34.615 0.00 0.00 0.00 3.16
2696 5617 3.451402 TGGCAGTTCTCTAGTACTCCA 57.549 47.619 0.00 0.00 0.00 3.86
2733 5656 1.946768 CGGGTGCTTCTTTCACTTCAA 59.053 47.619 0.00 0.00 34.97 2.69
2816 5739 3.318017 CCTAGCAGACGCCATATTGTAC 58.682 50.000 0.00 0.00 39.83 2.90
2916 5858 1.632422 GGCGTACGATTTTTCTCCGA 58.368 50.000 21.65 0.00 0.00 4.55
2996 5944 2.267961 CCTAGTTCGGGTGGGTGC 59.732 66.667 0.00 0.00 0.00 5.01
3010 5958 2.276116 GGATCTCGCCATCGCCCTA 61.276 63.158 0.00 0.00 35.26 3.53


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

AutoCloner maintained by Alex Coulton.