Multiple sequence alignment - TraesCS3A01G375700

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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 TraesCS3A01G375700 chr3A 100.000 2384 0 0 1 2384 624857895 624860278 0.000000e+00 4403
1 TraesCS3A01G375700 chr3A 96.591 264 9 0 1625 1888 739760534 739760797 2.810000e-119 438
2 TraesCS3A01G375700 chr3D 91.280 1640 109 16 1 1623 481710079 481711701 0.000000e+00 2206
3 TraesCS3A01G375700 chr3D 91.915 235 10 4 1883 2113 481711698 481711927 1.060000e-83 320
4 TraesCS3A01G375700 chr3B 90.918 1013 64 14 619 1623 643265837 643266829 0.000000e+00 1336
5 TraesCS3A01G375700 chr3B 87.719 399 31 7 1992 2382 643266967 643267355 1.300000e-122 449
6 TraesCS3A01G375700 chr3B 89.333 150 12 3 375 524 643265354 643265499 4.050000e-43 185
7 TraesCS3A01G375700 chr3B 89.683 126 9 1 1883 2008 643266826 643266947 8.820000e-35 158
8 TraesCS3A01G375700 chr3B 88.496 113 12 1 8 119 643265244 643265356 4.130000e-28 135
9 TraesCS3A01G375700 chr3B 94.521 73 4 0 549 621 643265496 643265568 1.940000e-21 113
10 TraesCS3A01G375700 chr4A 97.358 265 7 0 1624 1888 58911535 58911799 3.610000e-123 451
11 TraesCS3A01G375700 chr4A 96.958 263 8 0 1625 1887 47406427 47406165 2.170000e-120 442
12 TraesCS3A01G375700 chr4A 95.038 262 13 0 1625 1886 715443649 715443388 1.710000e-111 412
13 TraesCS3A01G375700 chr1A 96.981 265 8 0 1625 1889 497217413 497217149 1.680000e-121 446
14 TraesCS3A01G375700 chr1A 76.243 362 59 18 997 1349 470300491 470300834 1.470000e-37 167
15 TraesCS3A01G375700 chr2A 96.642 268 7 2 1620 1887 715888840 715888575 6.050000e-121 444
16 TraesCS3A01G375700 chr6A 96.512 258 9 0 1624 1881 18540827 18540570 6.090000e-116 427
17 TraesCS3A01G375700 chrUn 94.872 273 13 1 1615 1886 271930670 271930942 2.190000e-115 425
18 TraesCS3A01G375700 chr6D 95.402 261 12 0 1626 1886 248316078 248316338 1.320000e-112 416
19 TraesCS3A01G375700 chr6D 88.258 264 30 1 116 378 348087598 348087861 4.950000e-82 315
20 TraesCS3A01G375700 chr6D 86.517 267 32 3 118 381 445836834 445836569 8.340000e-75 291
21 TraesCS3A01G375700 chr5A 88.123 261 30 1 118 377 83023085 83022825 2.300000e-80 309
22 TraesCS3A01G375700 chr4D 86.545 275 32 4 109 380 145579498 145579770 4.980000e-77 298
23 TraesCS3A01G375700 chr4D 87.023 262 29 4 118 377 9306374 9306116 8.340000e-75 291
24 TraesCS3A01G375700 chr7D 86.296 270 35 2 117 384 363048924 363048655 2.320000e-75 292
25 TraesCS3A01G375700 chr5B 85.985 264 34 3 116 377 314297470 314297208 1.800000e-71 279
26 TraesCS3A01G375700 chr1B 85.874 269 29 6 117 380 666008802 666009066 6.490000e-71 278
27 TraesCS3A01G375700 chr1D 81.776 214 30 7 1145 1349 371186473 371186686 1.130000e-38 171


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 TraesCS3A01G375700 chr3A 624857895 624860278 2383 False 4403 4403 100.000000 1 2384 1 chr3A.!!$F1 2383
1 TraesCS3A01G375700 chr3D 481710079 481711927 1848 False 1263 2206 91.597500 1 2113 2 chr3D.!!$F1 2112
2 TraesCS3A01G375700 chr3B 643265244 643267355 2111 False 396 1336 90.111667 8 2382 6 chr3B.!!$F1 2374

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
97 99 0.103937 TTTTGCGGGGAAAGTTGCAG 59.896 50.0 0.0 0.0 38.75 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2172 0.397254 CCACCAGATACTCCCTCCGT 60.397 60.0 0.0 0.0 0.0 4.69 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
78 80 3.119495 GCCAAGTTGCATATCGTCCTTTT 60.119 43.478 0.00 0.00 0.00 2.27
97 99 0.103937 TTTTGCGGGGAAAGTTGCAG 59.896 50.000 0.00 0.00 38.75 4.41
119 121 9.098355 TGCAGAACATTAAATCTACTGATGTAC 57.902 33.333 0.00 0.00 32.44 2.90
141 143 8.607713 TGTACTCCTCCATTTTTATTTACTCCA 58.392 33.333 0.00 0.00 0.00 3.86
228 230 1.000385 ACGTGCACCACCAAATCAATG 60.000 47.619 12.15 0.00 0.00 2.82
235 237 2.027007 ACCACCAAATCAATGCCATTGG 60.027 45.455 16.96 5.06 46.14 3.16
238 240 4.101274 CCACCAAATCAATGCCATTGGATA 59.899 41.667 16.96 0.00 44.01 2.59
289 294 9.899661 ATATAAGCTTGTTACTGTAAATGTCCA 57.100 29.630 9.86 0.00 0.00 4.02
290 295 5.941948 AGCTTGTTACTGTAAATGTCCAC 57.058 39.130 1.10 0.00 0.00 4.02
302 307 9.077885 ACTGTAAATGTCCACATTGTTTTCTAT 57.922 29.630 5.70 0.00 45.06 1.98
310 315 8.356657 TGTCCACATTGTTTTCTATAAACTTGG 58.643 33.333 0.00 0.00 0.00 3.61
352 357 5.697848 ACTTTAGTCAAAGCTAATACGCG 57.302 39.130 3.53 3.53 44.27 6.01
356 361 2.426024 AGTCAAAGCTAATACGCGGAGA 59.574 45.455 12.47 0.00 34.40 3.71
360 365 4.092383 TCAAAGCTAATACGCGGAGAAAAC 59.908 41.667 12.47 0.00 34.40 2.43
367 372 2.923605 ACGCGGAGAAAACAAAAACA 57.076 40.000 12.47 0.00 0.00 2.83
368 373 3.430333 ACGCGGAGAAAACAAAAACAT 57.570 38.095 12.47 0.00 0.00 2.71
462 467 6.378582 ACATTGTCAAGCGTTCGATAAAAAT 58.621 32.000 0.00 0.00 0.00 1.82
505 510 8.131731 TCAATCTCACTAATGTAGATGTTCTCG 58.868 37.037 0.00 0.00 30.50 4.04
508 513 7.643579 TCTCACTAATGTAGATGTTCTCGATG 58.356 38.462 0.00 0.00 0.00 3.84
566 574 0.622738 ACTCCATCCAGCCTCCACAT 60.623 55.000 0.00 0.00 0.00 3.21
568 576 1.227764 CCATCCAGCCTCCACATCG 60.228 63.158 0.00 0.00 0.00 3.84
638 917 4.577834 ATTAAAGAAAACCACCACCACG 57.422 40.909 0.00 0.00 0.00 4.94
639 918 0.458260 AAAGAAAACCACCACCACGC 59.542 50.000 0.00 0.00 0.00 5.34
652 931 3.522731 CACGCTCCTCCTCCTCCG 61.523 72.222 0.00 0.00 0.00 4.63
665 944 3.119245 TCCTCCTCCGCATTATATAACGC 60.119 47.826 3.44 3.44 0.00 4.84
671 950 4.171005 TCCGCATTATATAACGCAGCTAC 58.829 43.478 13.44 0.00 0.00 3.58
678 957 1.329256 ATAACGCAGCTACGGGAGAT 58.671 50.000 11.74 0.00 37.37 2.75
753 1032 2.047274 AATCCACCAGCACGTCGG 60.047 61.111 0.00 0.00 0.00 4.79
799 1082 2.499685 GCATACCCTTCGCCGAGT 59.500 61.111 0.00 0.00 0.00 4.18
800 1083 1.153429 GCATACCCTTCGCCGAGTT 60.153 57.895 0.00 0.00 0.00 3.01
823 1106 4.745751 TCCAAGGTAACGCCCGCG 62.746 66.667 7.69 7.69 46.39 6.46
890 1175 2.527624 TGGCAGCTCCACTCCTGT 60.528 61.111 1.25 0.00 40.72 4.00
891 1176 2.046507 GGCAGCTCCACTCCTGTG 60.047 66.667 0.00 0.00 43.45 3.66
925 1210 0.249447 TGTGTGTTGTGAGCTCGAGG 60.249 55.000 15.58 0.00 0.00 4.63
1007 1292 1.596934 GGTGGTCGAGGATGAGCAA 59.403 57.895 0.00 0.00 46.76 3.91
1134 1428 4.521292 GGGGGCGGGAATGATGCA 62.521 66.667 0.00 0.00 0.00 3.96
1414 1712 1.205893 GACCTCAGCTCGTTCCTTCAT 59.794 52.381 0.00 0.00 0.00 2.57
1423 1721 1.201647 TCGTTCCTTCATGTCGTCTCC 59.798 52.381 0.00 0.00 0.00 3.71
1438 1736 0.753262 TCTCCTAGCTTCGCCATTCC 59.247 55.000 0.00 0.00 0.00 3.01
1502 1800 1.517257 AGAGAATCGTTGGCTCGCG 60.517 57.895 0.00 0.00 42.67 5.87
1546 1844 3.118261 TCATAGACCTGTTCTTCCATGCC 60.118 47.826 0.00 0.00 35.55 4.40
1618 1916 1.851658 AGCGCGTCTTTTGCAATTTT 58.148 40.000 8.43 0.00 0.00 1.82
1623 1921 4.380382 GCGCGTCTTTTGCAATTTTAGTAA 59.620 37.500 8.43 0.00 0.00 2.24
1624 1922 5.441485 GCGCGTCTTTTGCAATTTTAGTAAG 60.441 40.000 8.43 0.00 0.00 2.34
1625 1923 5.623673 CGCGTCTTTTGCAATTTTAGTAAGT 59.376 36.000 0.00 0.00 0.00 2.24
1626 1924 6.793203 CGCGTCTTTTGCAATTTTAGTAAGTA 59.207 34.615 0.00 0.00 0.00 2.24
1627 1925 7.480542 CGCGTCTTTTGCAATTTTAGTAAGTAT 59.519 33.333 0.00 0.00 0.00 2.12
1628 1926 9.124807 GCGTCTTTTGCAATTTTAGTAAGTATT 57.875 29.630 0.00 0.00 0.00 1.89
1634 1932 7.875327 TGCAATTTTAGTAAGTATTCCCTCC 57.125 36.000 0.00 0.00 0.00 4.30
1635 1933 6.540914 TGCAATTTTAGTAAGTATTCCCTCCG 59.459 38.462 0.00 0.00 0.00 4.63
1636 1934 6.541278 GCAATTTTAGTAAGTATTCCCTCCGT 59.459 38.462 0.00 0.00 0.00 4.69
1637 1935 7.066645 GCAATTTTAGTAAGTATTCCCTCCGTT 59.933 37.037 0.00 0.00 0.00 4.44
1638 1936 8.953313 CAATTTTAGTAAGTATTCCCTCCGTTT 58.047 33.333 0.00 0.00 0.00 3.60
1639 1937 9.524496 AATTTTAGTAAGTATTCCCTCCGTTTT 57.476 29.630 0.00 0.00 0.00 2.43
1640 1938 8.922931 TTTTAGTAAGTATTCCCTCCGTTTTT 57.077 30.769 0.00 0.00 0.00 1.94
1648 1946 8.728337 AGTATTCCCTCCGTTTTTATTTAGTC 57.272 34.615 0.00 0.00 0.00 2.59
1649 1947 8.546322 AGTATTCCCTCCGTTTTTATTTAGTCT 58.454 33.333 0.00 0.00 0.00 3.24
1650 1948 7.625828 ATTCCCTCCGTTTTTATTTAGTCTG 57.374 36.000 0.00 0.00 0.00 3.51
1651 1949 4.939439 TCCCTCCGTTTTTATTTAGTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
1652 1950 4.698304 CCCTCCGTTTTTATTTAGTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
1653 1951 5.357032 CCCTCCGTTTTTATTTAGTCTGCAT 59.643 40.000 0.00 0.00 0.00 3.96
1654 1952 6.540914 CCCTCCGTTTTTATTTAGTCTGCATA 59.459 38.462 0.00 0.00 0.00 3.14
1655 1953 7.228706 CCCTCCGTTTTTATTTAGTCTGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
1656 1954 8.621286 CCTCCGTTTTTATTTAGTCTGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
1659 1957 9.382244 CCGTTTTTATTTAGTCTGCATATTAGC 57.618 33.333 0.00 0.00 0.00 3.09
1665 1963 9.627123 TTATTTAGTCTGCATATTAGCTTTGGT 57.373 29.630 0.00 0.00 34.99 3.67
1666 1964 7.553881 TTTAGTCTGCATATTAGCTTTGGTC 57.446 36.000 0.00 0.00 34.99 4.02
1667 1965 5.102953 AGTCTGCATATTAGCTTTGGTCA 57.897 39.130 0.00 0.00 34.99 4.02
1668 1966 5.500234 AGTCTGCATATTAGCTTTGGTCAA 58.500 37.500 0.00 0.00 34.99 3.18
1669 1967 5.945784 AGTCTGCATATTAGCTTTGGTCAAA 59.054 36.000 0.00 0.00 34.99 2.69
1691 1989 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
1692 1990 6.759497 AGTCAAGCTTTGTAAACTTTGACT 57.241 33.333 17.37 17.37 32.23 3.41
1693 1991 7.859325 AGTCAAGCTTTGTAAACTTTGACTA 57.141 32.000 19.57 0.00 33.77 2.59
1694 1992 8.276252 AGTCAAGCTTTGTAAACTTTGACTAA 57.724 30.769 19.57 0.00 33.77 2.24
1695 1993 8.398665 AGTCAAGCTTTGTAAACTTTGACTAAG 58.601 33.333 19.57 3.76 39.87 2.18
1861 2159 6.985188 GACTTCAGTCAAACCTAATATGCA 57.015 37.500 1.86 0.00 44.18 3.96
1862 2160 6.992063 ACTTCAGTCAAACCTAATATGCAG 57.008 37.500 0.00 0.00 0.00 4.41
1863 2161 6.711277 ACTTCAGTCAAACCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
1864 2162 6.595716 ACTTCAGTCAAACCTAATATGCAGAC 59.404 38.462 0.00 0.00 0.00 3.51
1865 2163 6.299805 TCAGTCAAACCTAATATGCAGACT 57.700 37.500 0.00 0.00 35.66 3.24
1866 2164 7.418337 TCAGTCAAACCTAATATGCAGACTA 57.582 36.000 0.00 0.00 33.72 2.59
1867 2165 7.847096 TCAGTCAAACCTAATATGCAGACTAA 58.153 34.615 0.00 0.00 33.72 2.24
1868 2166 8.318412 TCAGTCAAACCTAATATGCAGACTAAA 58.682 33.333 0.00 0.00 33.72 1.85
1869 2167 9.113838 CAGTCAAACCTAATATGCAGACTAAAT 57.886 33.333 0.00 0.00 33.72 1.40
1876 2174 9.477484 ACCTAATATGCAGACTAAATAGAAACG 57.523 33.333 0.00 0.00 0.00 3.60
1877 2175 8.926710 CCTAATATGCAGACTAAATAGAAACGG 58.073 37.037 0.00 0.00 0.00 4.44
1878 2176 9.692749 CTAATATGCAGACTAAATAGAAACGGA 57.307 33.333 0.00 0.00 0.00 4.69
1879 2177 8.594881 AATATGCAGACTAAATAGAAACGGAG 57.405 34.615 0.00 0.00 0.00 4.63
1880 2178 4.755411 TGCAGACTAAATAGAAACGGAGG 58.245 43.478 0.00 0.00 0.00 4.30
1881 2179 4.120589 GCAGACTAAATAGAAACGGAGGG 58.879 47.826 0.00 0.00 0.00 4.30
1882 2180 4.142004 GCAGACTAAATAGAAACGGAGGGA 60.142 45.833 0.00 0.00 0.00 4.20
1883 2181 5.593010 CAGACTAAATAGAAACGGAGGGAG 58.407 45.833 0.00 0.00 0.00 4.30
1884 2182 5.127356 CAGACTAAATAGAAACGGAGGGAGT 59.873 44.000 0.00 0.00 0.00 3.85
1885 2183 6.320672 CAGACTAAATAGAAACGGAGGGAGTA 59.679 42.308 0.00 0.00 0.00 2.59
1886 2184 7.014422 CAGACTAAATAGAAACGGAGGGAGTAT 59.986 40.741 0.00 0.00 0.00 2.12
1887 2185 7.231115 AGACTAAATAGAAACGGAGGGAGTATC 59.769 40.741 0.00 0.00 0.00 2.24
1900 2198 1.137872 GGAGTATCTGGTGGTCTGCTG 59.862 57.143 0.00 0.00 33.73 4.41
1912 2210 2.302733 TGGTCTGCTGAGAATTACTGCA 59.697 45.455 13.09 13.09 39.20 4.41
2112 2449 8.741101 TTGAATGAATTGGTTCGTCATTAAAG 57.259 30.769 0.00 0.00 41.03 1.85
2113 2450 6.806249 TGAATGAATTGGTTCGTCATTAAAGC 59.194 34.615 0.00 0.00 41.03 3.51
2126 2467 7.047891 TCGTCATTAAAGCTTCCACAATATCT 58.952 34.615 0.00 0.00 0.00 1.98
2166 2507 1.073199 CGGTGCCTTCCTTGAGGTT 59.927 57.895 0.00 0.00 39.11 3.50
2167 2508 0.537371 CGGTGCCTTCCTTGAGGTTT 60.537 55.000 0.00 0.00 39.11 3.27
2168 2509 1.271163 CGGTGCCTTCCTTGAGGTTTA 60.271 52.381 0.00 0.00 39.11 2.01
2169 2510 2.618045 CGGTGCCTTCCTTGAGGTTTAT 60.618 50.000 0.00 0.00 39.11 1.40
2170 2511 3.370103 CGGTGCCTTCCTTGAGGTTTATA 60.370 47.826 0.00 0.00 39.11 0.98
2171 2512 4.686122 CGGTGCCTTCCTTGAGGTTTATAT 60.686 45.833 0.00 0.00 39.11 0.86
2172 2513 5.201243 GGTGCCTTCCTTGAGGTTTATATT 58.799 41.667 0.00 0.00 39.11 1.28
2200 2541 5.722021 AACCCTACAAAATTTACCTGCAG 57.278 39.130 6.78 6.78 0.00 4.41
2203 2544 3.763897 CCTACAAAATTTACCTGCAGGCT 59.236 43.478 33.06 21.13 39.32 4.58
2205 2546 3.230134 ACAAAATTTACCTGCAGGCTCA 58.770 40.909 33.06 16.61 39.32 4.26
2215 2556 0.675083 TGCAGGCTCACAAACATTGG 59.325 50.000 0.00 0.00 34.12 3.16
2273 2614 4.739046 AACTGTCAAGAAAAGAGCATCG 57.261 40.909 0.00 0.00 42.67 3.84
2292 2633 3.531538 TCGAATTGAGGCCATCTTACAC 58.468 45.455 5.01 0.00 0.00 2.90
2304 2645 4.459337 GCCATCTTACACCCATAATTAGGC 59.541 45.833 0.00 0.00 0.00 3.93
2313 2654 4.214119 CACCCATAATTAGGCTTCATGACG 59.786 45.833 0.00 0.00 0.00 4.35
2317 2658 6.039270 CCCATAATTAGGCTTCATGACGAAAA 59.961 38.462 2.89 0.00 31.71 2.29
2321 2662 1.535462 AGGCTTCATGACGAAAAACCG 59.465 47.619 2.89 0.00 31.71 4.44
2326 2667 0.309302 CATGACGAAAAACCGCCACA 59.691 50.000 0.00 0.00 0.00 4.17
2328 2669 1.368374 GACGAAAAACCGCCACACG 60.368 57.895 0.00 0.00 43.15 4.49
2338 2679 1.340889 ACCGCCACACGTTAAGAGTTA 59.659 47.619 0.00 0.00 41.42 2.24
2368 2710 4.584325 AGAGCAACTCTAGCAGATTCCTAG 59.416 45.833 0.00 0.00 39.28 3.02
2382 2724 0.252558 TCCTAGACCCAACACCCTCC 60.253 60.000 0.00 0.00 0.00 4.30
2383 2725 0.546747 CCTAGACCCAACACCCTCCA 60.547 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.209589 TGCAACTTGGCCAGTAAATAACAATA 59.790 34.615 5.11 0.00 32.94 1.90
78 80 0.103937 CTGCAACTTTCCCCGCAAAA 59.896 50.000 0.00 0.00 33.21 2.44
119 121 7.938140 TGTGGAGTAAATAAAAATGGAGGAG 57.062 36.000 0.00 0.00 0.00 3.69
209 211 1.700523 CATTGATTTGGTGGTGCACG 58.299 50.000 11.45 0.00 34.83 5.34
210 212 1.431496 GCATTGATTTGGTGGTGCAC 58.569 50.000 8.80 8.80 33.09 4.57
228 230 2.300433 TGCAGTGATGTATCCAATGGC 58.700 47.619 0.00 0.00 31.12 4.40
238 240 8.454570 TGATGTGAAAATATATGCAGTGATGT 57.545 30.769 0.00 0.00 0.00 3.06
269 271 5.682943 TGTGGACATTTACAGTAACAAGC 57.317 39.130 0.00 0.00 0.00 4.01
270 272 7.648142 ACAATGTGGACATTTACAGTAACAAG 58.352 34.615 2.14 0.00 43.48 3.16
287 292 8.356657 TGACCAAGTTTATAGAAAACAATGTGG 58.643 33.333 3.70 7.07 32.81 4.17
334 339 3.628942 TCTCCGCGTATTAGCTTTGACTA 59.371 43.478 4.92 0.00 34.40 2.59
336 341 2.805845 TCTCCGCGTATTAGCTTTGAC 58.194 47.619 4.92 0.00 34.40 3.18
343 348 6.137415 TGTTTTTGTTTTCTCCGCGTATTAG 58.863 36.000 4.92 0.00 0.00 1.73
349 354 4.778904 TCTATGTTTTTGTTTTCTCCGCG 58.221 39.130 0.00 0.00 0.00 6.46
350 355 5.997385 TCTCTATGTTTTTGTTTTCTCCGC 58.003 37.500 0.00 0.00 0.00 5.54
398 403 9.646522 AAATAATCATGCCAAACTATAGGTCTT 57.353 29.630 4.43 0.00 0.00 3.01
468 473 9.725019 ACATTAGTGAGATTGATTGTACAAGAA 57.275 29.630 14.65 9.57 33.22 2.52
505 510 2.237393 GGGAGCATCACTCACTCATC 57.763 55.000 0.00 0.00 46.18 2.92
566 574 3.006859 TCAATCTCCTTCAAGCTGAACGA 59.993 43.478 0.00 0.00 32.21 3.85
568 576 3.438434 GGTCAATCTCCTTCAAGCTGAAC 59.562 47.826 0.00 0.00 32.21 3.18
582 590 2.569059 CATTGATGCTCCGGTCAATCT 58.431 47.619 13.52 0.00 41.70 2.40
638 917 1.115930 TAATGCGGAGGAGGAGGAGC 61.116 60.000 0.00 0.00 0.00 4.70
639 918 1.638529 ATAATGCGGAGGAGGAGGAG 58.361 55.000 0.00 0.00 0.00 3.69
652 931 3.306166 CCCGTAGCTGCGTTATATAATGC 59.694 47.826 26.20 26.20 45.85 3.56
665 944 0.678395 ATGAGCATCTCCCGTAGCTG 59.322 55.000 0.00 0.00 37.48 4.24
671 950 2.028420 TTTGTCATGAGCATCTCCCG 57.972 50.000 0.00 0.00 34.92 5.14
678 957 3.930229 GGTACGTGTATTTGTCATGAGCA 59.070 43.478 0.00 0.00 0.00 4.26
681 960 4.500127 CTGGGTACGTGTATTTGTCATGA 58.500 43.478 0.00 0.00 0.00 3.07
794 1077 4.151157 CGTTACCTTGGACTTAAAACTCGG 59.849 45.833 0.00 0.00 0.00 4.63
799 1082 3.148412 GGGCGTTACCTTGGACTTAAAA 58.852 45.455 0.00 0.00 39.10 1.52
800 1083 2.781923 GGGCGTTACCTTGGACTTAAA 58.218 47.619 0.00 0.00 39.10 1.52
891 1176 3.878778 ACACACAGAAATGGATAGCTCC 58.121 45.455 0.00 0.00 42.45 4.70
925 1210 2.860293 CGACGGTGACATTGGTGC 59.140 61.111 0.00 0.00 0.00 5.01
1007 1292 4.250305 ACACCTTGCCGCCGTTCT 62.250 61.111 0.00 0.00 0.00 3.01
1402 1700 2.520979 GAGACGACATGAAGGAACGAG 58.479 52.381 0.00 0.00 0.00 4.18
1474 1772 7.412563 CGAGCCAACGATTCTCTGTTTAATTAA 60.413 37.037 0.00 0.00 35.09 1.40
1475 1773 6.035650 CGAGCCAACGATTCTCTGTTTAATTA 59.964 38.462 0.00 0.00 35.09 1.40
1476 1774 5.163854 CGAGCCAACGATTCTCTGTTTAATT 60.164 40.000 0.00 0.00 35.09 1.40
1478 1776 3.678072 CGAGCCAACGATTCTCTGTTTAA 59.322 43.478 0.00 0.00 35.09 1.52
1483 1781 1.746727 CGCGAGCCAACGATTCTCTG 61.747 60.000 0.00 0.00 35.09 3.35
1502 1800 8.862550 ATGAAATAATTTCTTTTGATCGGCTC 57.137 30.769 0.00 0.00 40.32 4.70
1555 1853 1.516386 CCAACTCCATCGACCGACG 60.516 63.158 0.00 0.00 44.09 5.12
1623 1921 8.546322 AGACTAAATAAAAACGGAGGGAATACT 58.454 33.333 0.00 0.00 0.00 2.12
1624 1922 8.610035 CAGACTAAATAAAAACGGAGGGAATAC 58.390 37.037 0.00 0.00 0.00 1.89
1625 1923 7.281549 GCAGACTAAATAAAAACGGAGGGAATA 59.718 37.037 0.00 0.00 0.00 1.75
1626 1924 6.095021 GCAGACTAAATAAAAACGGAGGGAAT 59.905 38.462 0.00 0.00 0.00 3.01
1627 1925 5.413523 GCAGACTAAATAAAAACGGAGGGAA 59.586 40.000 0.00 0.00 0.00 3.97
1628 1926 4.939439 GCAGACTAAATAAAAACGGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
1629 1927 4.698304 TGCAGACTAAATAAAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
1630 1928 5.873179 TGCAGACTAAATAAAAACGGAGG 57.127 39.130 0.00 0.00 0.00 4.30
1633 1931 9.382244 GCTAATATGCAGACTAAATAAAAACGG 57.618 33.333 0.00 0.00 0.00 4.44
1639 1937 9.627123 ACCAAAGCTAATATGCAGACTAAATAA 57.373 29.630 0.00 0.00 34.99 1.40
1640 1938 9.273016 GACCAAAGCTAATATGCAGACTAAATA 57.727 33.333 0.00 0.00 34.99 1.40
1641 1939 7.775093 TGACCAAAGCTAATATGCAGACTAAAT 59.225 33.333 0.00 0.00 34.99 1.40
1642 1940 7.109501 TGACCAAAGCTAATATGCAGACTAAA 58.890 34.615 0.00 0.00 34.99 1.85
1643 1941 6.649155 TGACCAAAGCTAATATGCAGACTAA 58.351 36.000 0.00 0.00 34.99 2.24
1644 1942 6.233905 TGACCAAAGCTAATATGCAGACTA 57.766 37.500 0.00 0.00 34.99 2.59
1645 1943 5.102953 TGACCAAAGCTAATATGCAGACT 57.897 39.130 0.00 0.00 34.99 3.24
1646 1944 5.818136 TTGACCAAAGCTAATATGCAGAC 57.182 39.130 0.00 0.00 34.99 3.51
1647 1945 6.441093 CTTTGACCAAAGCTAATATGCAGA 57.559 37.500 9.25 0.00 40.94 4.26
1668 1966 7.158099 AGTCAAAGTTTACAAAGCTTGACTT 57.842 32.000 17.55 3.36 42.47 3.01
1669 1967 6.759497 AGTCAAAGTTTACAAAGCTTGACT 57.241 33.333 17.55 17.55 41.47 3.41
1670 1968 8.182227 ACTTAGTCAAAGTTTACAAAGCTTGAC 58.818 33.333 0.00 14.97 46.61 3.18
1671 1969 8.276252 ACTTAGTCAAAGTTTACAAAGCTTGA 57.724 30.769 0.00 0.00 46.61 3.02
1838 2136 6.818644 TCTGCATATTAGGTTTGACTGAAGTC 59.181 38.462 3.41 3.41 44.97 3.01
1839 2137 6.595716 GTCTGCATATTAGGTTTGACTGAAGT 59.404 38.462 0.00 0.00 0.00 3.01
1840 2138 6.820656 AGTCTGCATATTAGGTTTGACTGAAG 59.179 38.462 0.00 0.00 33.09 3.02
1841 2139 6.711277 AGTCTGCATATTAGGTTTGACTGAA 58.289 36.000 0.00 0.00 33.09 3.02
1842 2140 6.299805 AGTCTGCATATTAGGTTTGACTGA 57.700 37.500 0.00 0.00 33.09 3.41
1843 2141 8.492673 TTTAGTCTGCATATTAGGTTTGACTG 57.507 34.615 7.85 0.00 35.52 3.51
1850 2148 9.477484 CGTTTCTATTTAGTCTGCATATTAGGT 57.523 33.333 0.00 0.00 0.00 3.08
1851 2149 8.926710 CCGTTTCTATTTAGTCTGCATATTAGG 58.073 37.037 0.00 0.00 0.00 2.69
1852 2150 9.692749 TCCGTTTCTATTTAGTCTGCATATTAG 57.307 33.333 0.00 0.00 0.00 1.73
1853 2151 9.692749 CTCCGTTTCTATTTAGTCTGCATATTA 57.307 33.333 0.00 0.00 0.00 0.98
1854 2152 7.657761 CCTCCGTTTCTATTTAGTCTGCATATT 59.342 37.037 0.00 0.00 0.00 1.28
1855 2153 7.155328 CCTCCGTTTCTATTTAGTCTGCATAT 58.845 38.462 0.00 0.00 0.00 1.78
1856 2154 6.462487 CCCTCCGTTTCTATTTAGTCTGCATA 60.462 42.308 0.00 0.00 0.00 3.14
1857 2155 5.360591 CCTCCGTTTCTATTTAGTCTGCAT 58.639 41.667 0.00 0.00 0.00 3.96
1858 2156 4.382685 CCCTCCGTTTCTATTTAGTCTGCA 60.383 45.833 0.00 0.00 0.00 4.41
1859 2157 4.120589 CCCTCCGTTTCTATTTAGTCTGC 58.879 47.826 0.00 0.00 0.00 4.26
1860 2158 5.127356 ACTCCCTCCGTTTCTATTTAGTCTG 59.873 44.000 0.00 0.00 0.00 3.51
1861 2159 5.270794 ACTCCCTCCGTTTCTATTTAGTCT 58.729 41.667 0.00 0.00 0.00 3.24
1862 2160 5.595257 ACTCCCTCCGTTTCTATTTAGTC 57.405 43.478 0.00 0.00 0.00 2.59
1863 2161 7.014422 CAGATACTCCCTCCGTTTCTATTTAGT 59.986 40.741 0.00 0.00 0.00 2.24
1864 2162 7.371936 CAGATACTCCCTCCGTTTCTATTTAG 58.628 42.308 0.00 0.00 0.00 1.85
1865 2163 6.267014 CCAGATACTCCCTCCGTTTCTATTTA 59.733 42.308 0.00 0.00 0.00 1.40
1866 2164 5.070580 CCAGATACTCCCTCCGTTTCTATTT 59.929 44.000 0.00 0.00 0.00 1.40
1867 2165 4.589374 CCAGATACTCCCTCCGTTTCTATT 59.411 45.833 0.00 0.00 0.00 1.73
1868 2166 4.153411 CCAGATACTCCCTCCGTTTCTAT 58.847 47.826 0.00 0.00 0.00 1.98
1869 2167 3.053095 ACCAGATACTCCCTCCGTTTCTA 60.053 47.826 0.00 0.00 0.00 2.10
1870 2168 2.292323 ACCAGATACTCCCTCCGTTTCT 60.292 50.000 0.00 0.00 0.00 2.52
1871 2169 2.108970 ACCAGATACTCCCTCCGTTTC 58.891 52.381 0.00 0.00 0.00 2.78
1872 2170 1.831736 CACCAGATACTCCCTCCGTTT 59.168 52.381 0.00 0.00 0.00 3.60
1873 2171 1.486211 CACCAGATACTCCCTCCGTT 58.514 55.000 0.00 0.00 0.00 4.44
1874 2172 0.397254 CCACCAGATACTCCCTCCGT 60.397 60.000 0.00 0.00 0.00 4.69
1875 2173 0.397254 ACCACCAGATACTCCCTCCG 60.397 60.000 0.00 0.00 0.00 4.63
1876 2174 1.062810 AGACCACCAGATACTCCCTCC 60.063 57.143 0.00 0.00 0.00 4.30
1877 2175 2.035632 CAGACCACCAGATACTCCCTC 58.964 57.143 0.00 0.00 0.00 4.30
1878 2176 1.967274 GCAGACCACCAGATACTCCCT 60.967 57.143 0.00 0.00 0.00 4.20
1879 2177 0.466124 GCAGACCACCAGATACTCCC 59.534 60.000 0.00 0.00 0.00 4.30
1880 2178 1.137872 CAGCAGACCACCAGATACTCC 59.862 57.143 0.00 0.00 0.00 3.85
1881 2179 2.100584 CTCAGCAGACCACCAGATACTC 59.899 54.545 0.00 0.00 0.00 2.59
1882 2180 2.106566 CTCAGCAGACCACCAGATACT 58.893 52.381 0.00 0.00 0.00 2.12
1883 2181 2.103373 TCTCAGCAGACCACCAGATAC 58.897 52.381 0.00 0.00 0.00 2.24
1884 2182 2.532250 TCTCAGCAGACCACCAGATA 57.468 50.000 0.00 0.00 0.00 1.98
1885 2183 1.649321 TTCTCAGCAGACCACCAGAT 58.351 50.000 0.00 0.00 0.00 2.90
1886 2184 1.649321 ATTCTCAGCAGACCACCAGA 58.351 50.000 0.00 0.00 0.00 3.86
1887 2185 2.486472 AATTCTCAGCAGACCACCAG 57.514 50.000 0.00 0.00 0.00 4.00
1912 2210 6.854496 TTACTTAAATCTTTGCACTGTCGT 57.146 33.333 0.00 0.00 0.00 4.34
1930 2228 9.512588 AAATGTTCATGACAGAGAAGATTACTT 57.487 29.630 12.96 0.00 42.62 2.24
1931 2229 8.944029 CAAATGTTCATGACAGAGAAGATTACT 58.056 33.333 12.96 1.40 42.62 2.24
1932 2230 8.939929 TCAAATGTTCATGACAGAGAAGATTAC 58.060 33.333 12.96 0.00 42.62 1.89
2011 2345 4.335594 GCCAATCACCCTAGTACATTGTTC 59.664 45.833 0.00 0.00 0.00 3.18
2013 2347 3.371595 GGCCAATCACCCTAGTACATTGT 60.372 47.826 0.00 0.00 0.00 2.71
2019 2353 3.268334 ACATTTGGCCAATCACCCTAGTA 59.732 43.478 21.26 0.00 0.00 1.82
2020 2354 2.042979 ACATTTGGCCAATCACCCTAGT 59.957 45.455 21.26 6.42 0.00 2.57
2022 2356 2.917713 ACATTTGGCCAATCACCCTA 57.082 45.000 21.26 1.89 0.00 3.53
2112 2449 4.808558 TGCAAACAAGATATTGTGGAAGC 58.191 39.130 6.46 9.06 34.99 3.86
2113 2450 5.404946 CCTGCAAACAAGATATTGTGGAAG 58.595 41.667 6.46 6.35 34.99 3.46
2186 2527 3.230134 TGTGAGCCTGCAGGTAAATTTT 58.770 40.909 32.81 10.73 37.57 1.82
2197 2538 0.961019 TCCAATGTTTGTGAGCCTGC 59.039 50.000 0.00 0.00 0.00 4.85
2245 2586 5.677091 GCTCTTTTCTTGACAGTTTGCTTCA 60.677 40.000 0.00 0.00 0.00 3.02
2246 2587 4.737279 GCTCTTTTCTTGACAGTTTGCTTC 59.263 41.667 0.00 0.00 0.00 3.86
2248 2589 3.696051 TGCTCTTTTCTTGACAGTTTGCT 59.304 39.130 0.00 0.00 0.00 3.91
2261 2602 3.488216 GGCCTCAATTCGATGCTCTTTTC 60.488 47.826 0.00 0.00 35.72 2.29
2273 2614 2.952310 GGGTGTAAGATGGCCTCAATTC 59.048 50.000 3.32 0.00 0.00 2.17
2282 2623 5.880901 AGCCTAATTATGGGTGTAAGATGG 58.119 41.667 5.27 0.00 33.62 3.51
2292 2633 4.641396 TCGTCATGAAGCCTAATTATGGG 58.359 43.478 3.49 0.00 0.00 4.00
2304 2645 1.265635 TGGCGGTTTTTCGTCATGAAG 59.734 47.619 0.00 0.00 39.98 3.02
2313 2654 2.031930 TCTTAACGTGTGGCGGTTTTTC 59.968 45.455 0.00 0.00 46.52 2.29
2317 2658 0.105408 ACTCTTAACGTGTGGCGGTT 59.895 50.000 0.00 0.00 46.52 4.44
2321 2662 4.304939 AGTCTTAACTCTTAACGTGTGGC 58.695 43.478 0.00 0.00 0.00 5.01
2326 2667 7.211966 TGCTCTTAGTCTTAACTCTTAACGT 57.788 36.000 0.00 0.00 36.92 3.99
2328 2669 9.131416 GAGTTGCTCTTAGTCTTAACTCTTAAC 57.869 37.037 0.00 0.00 40.29 2.01
2338 2679 5.013547 TCTGCTAGAGTTGCTCTTAGTCTT 58.986 41.667 3.87 0.00 41.50 3.01


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

AutoCloner maintained by Alex Coulton.