Multiple sequence alignment - TraesCS2B01G609400

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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 TraesCS2B01G609400 chr2B 100.000 2780 0 0 1 2780 789603113 789600334 0.000000e+00 5134.0
1 TraesCS2B01G609400 chr2B 98.196 776 13 1 2006 2780 789584230 789583455 0.000000e+00 1354.0
2 TraesCS2B01G609400 chr2B 98.067 776 14 1 2006 2780 789592652 789591877 0.000000e+00 1349.0
3 TraesCS2B01G609400 chr2B 81.575 749 113 12 1037 1778 789670346 789669616 1.840000e-166 595.0
4 TraesCS2B01G609400 chr2B 98.667 225 3 0 2556 2780 789580680 789580456 1.550000e-107 399.0
5 TraesCS2B01G609400 chr2B 87.137 241 31 0 1029 1269 789609676 789609436 9.810000e-70 274.0
6 TraesCS2B01G609400 chr2B 85.535 159 17 3 795 953 789620546 789620394 7.970000e-36 161.0
7 TraesCS2B01G609400 chr2A 89.879 1907 148 21 1 1869 771711868 771713767 0.000000e+00 2410.0
8 TraesCS2B01G609400 chr2A 83.460 792 89 18 998 1778 771609509 771610269 0.000000e+00 699.0
9 TraesCS2B01G609400 chr2A 80.552 797 113 28 1006 1778 771547102 771547880 2.400000e-160 575.0
10 TraesCS2B01G609400 chr2A 85.358 321 43 2 1 317 771598045 771598365 2.060000e-86 329.0
11 TraesCS2B01G609400 chr2A 84.831 178 12 9 835 998 771609290 771609466 6.160000e-37 165.0
12 TraesCS2B01G609400 chr2D 90.167 1017 77 10 1 1000 645946802 645947812 0.000000e+00 1303.0
13 TraesCS2B01G609400 chr2D 92.898 873 61 1 998 1869 645947844 645948716 0.000000e+00 1267.0
14 TraesCS2B01G609400 chr2D 82.419 802 99 18 997 1778 645893375 645894154 0.000000e+00 662.0
15 TraesCS2B01G609400 chr2D 84.615 390 55 4 1 385 645880457 645880846 1.560000e-102 383.0
16 TraesCS2B01G609400 chr2D 87.395 238 30 0 1029 1266 645933389 645933626 9.810000e-70 274.0
17 TraesCS2B01G609400 chrUn 98.347 484 8 0 2006 2489 342989533 342989050 0.000000e+00 850.0
18 TraesCS2B01G609400 chr3D 78.982 609 101 21 1909 2502 64196708 64197304 9.340000e-105 390.0
19 TraesCS2B01G609400 chr3A 79.259 405 75 7 1945 2342 74367749 74368151 9.810000e-70 274.0
20 TraesCS2B01G609400 chr7A 93.617 47 2 1 2452 2497 218252147 218252101 4.970000e-08 69.4
21 TraesCS2B01G609400 chr1D 94.737 38 2 0 2555 2592 196825789 196825826 2.990000e-05 60.2
22 TraesCS2B01G609400 chr1B 94.737 38 2 0 2555 2592 277459372 277459409 2.990000e-05 60.2


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 TraesCS2B01G609400 chr2B 789600334 789603113 2779 True 5134.0 5134 100.0000 1 2780 1 chr2B.!!$R2 2779
1 TraesCS2B01G609400 chr2B 789591877 789592652 775 True 1349.0 1349 98.0670 2006 2780 1 chr2B.!!$R1 774
2 TraesCS2B01G609400 chr2B 789580456 789584230 3774 True 876.5 1354 98.4315 2006 2780 2 chr2B.!!$R6 774
3 TraesCS2B01G609400 chr2B 789669616 789670346 730 True 595.0 595 81.5750 1037 1778 1 chr2B.!!$R5 741
4 TraesCS2B01G609400 chr2A 771711868 771713767 1899 False 2410.0 2410 89.8790 1 1869 1 chr2A.!!$F3 1868
5 TraesCS2B01G609400 chr2A 771547102 771547880 778 False 575.0 575 80.5520 1006 1778 1 chr2A.!!$F1 772
6 TraesCS2B01G609400 chr2A 771609290 771610269 979 False 432.0 699 84.1455 835 1778 2 chr2A.!!$F4 943
7 TraesCS2B01G609400 chr2D 645946802 645948716 1914 False 1285.0 1303 91.5325 1 1869 2 chr2D.!!$F4 1868
8 TraesCS2B01G609400 chr2D 645893375 645894154 779 False 662.0 662 82.4190 997 1778 1 chr2D.!!$F2 781
9 TraesCS2B01G609400 chr3D 64196708 64197304 596 False 390.0 390 78.9820 1909 2502 1 chr3D.!!$F1 593

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
210 218 0.179084 CCTTCTATTTGCCGAGCGGA 60.179 55.0 13.94 0.0 37.50 5.54 F
621 645 0.320771 CAGGGACCGACTTTCCACTG 60.321 60.0 0.00 0.0 34.45 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1592 0.234884 CGTGAAAAACCTCGTCTGGC 59.765 55.0 0.0 0.0 0.00 4.85 R
1905 2043 0.392461 GGTCCTGCATCGTAAGCCAA 60.392 55.0 0.0 0.0 37.18 4.52 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
93 95 7.921786 TTGATGTTATAGCTACAAACTTGCT 57.078 32.000 17.30 0.00 40.43 3.91
95 97 7.751732 TGATGTTATAGCTACAAACTTGCTTG 58.248 34.615 17.30 0.00 38.15 4.01
170 178 5.714806 ACGAACATTTCCCCATGTATTCTTT 59.285 36.000 0.00 0.00 36.30 2.52
183 191 2.254546 ATTCTTTCAGCACGACACCA 57.745 45.000 0.00 0.00 0.00 4.17
210 218 0.179084 CCTTCTATTTGCCGAGCGGA 60.179 55.000 13.94 0.00 37.50 5.54
228 243 2.810650 GGACACACATCCGTGACTATC 58.189 52.381 0.00 0.00 46.80 2.08
230 245 3.179830 GACACACATCCGTGACTATCAC 58.820 50.000 0.00 0.00 46.80 3.06
256 271 3.811497 ACAATGATATCACCAGCACATCG 59.189 43.478 7.78 0.00 0.00 3.84
262 277 0.324614 TCACCAGCACATCGGTTGAT 59.675 50.000 0.00 0.00 31.41 2.57
266 281 4.126437 CACCAGCACATCGGTTGATATAA 58.874 43.478 0.00 0.00 31.41 0.98
273 288 6.425114 AGCACATCGGTTGATATAAAGATGTC 59.575 38.462 5.99 3.01 44.43 3.06
274 289 6.202762 GCACATCGGTTGATATAAAGATGTCA 59.797 38.462 5.99 0.00 44.43 3.58
294 309 1.067425 AGGTTGCGCGTTACTATGTCA 60.067 47.619 8.43 0.00 0.00 3.58
309 324 6.589830 ACTATGTCACGCTGTAATGAAATC 57.410 37.500 0.00 0.00 0.00 2.17
317 332 7.915397 GTCACGCTGTAATGAAATCCATAAAAT 59.085 33.333 0.00 0.00 34.45 1.82
319 334 9.729023 CACGCTGTAATGAAATCCATAAAATTA 57.271 29.630 0.00 0.00 34.45 1.40
345 360 6.670233 ACACGCAATATTTTTAAACGAAGGA 58.330 32.000 0.00 0.00 0.00 3.36
346 361 7.140048 ACACGCAATATTTTTAAACGAAGGAA 58.860 30.769 0.00 0.00 0.00 3.36
392 408 7.820044 TTAAACAAGTTGTCATTGTCCAAAC 57.180 32.000 9.40 0.00 39.91 2.93
432 448 4.298332 GTTCCAATCGAATTGCAACAGTT 58.702 39.130 0.00 0.00 39.96 3.16
436 452 6.507900 TCCAATCGAATTGCAACAGTTAAAA 58.492 32.000 0.00 0.00 38.92 1.52
463 479 3.901797 GAGTGGGCTGTTGGGACCG 62.902 68.421 0.00 0.00 37.14 4.79
481 497 5.221581 GGGACCGCCTAACATCTATCTTTAA 60.222 44.000 0.00 0.00 0.00 1.52
482 498 6.465084 GGACCGCCTAACATCTATCTTTAAT 58.535 40.000 0.00 0.00 0.00 1.40
483 499 6.935208 GGACCGCCTAACATCTATCTTTAATT 59.065 38.462 0.00 0.00 0.00 1.40
484 500 8.092687 GGACCGCCTAACATCTATCTTTAATTA 58.907 37.037 0.00 0.00 0.00 1.40
485 501 8.828688 ACCGCCTAACATCTATCTTTAATTAC 57.171 34.615 0.00 0.00 0.00 1.89
486 502 7.597743 ACCGCCTAACATCTATCTTTAATTACG 59.402 37.037 0.00 0.00 0.00 3.18
487 503 7.063074 CCGCCTAACATCTATCTTTAATTACGG 59.937 40.741 0.00 0.00 0.00 4.02
488 504 7.063074 CGCCTAACATCTATCTTTAATTACGGG 59.937 40.741 0.00 0.00 0.00 5.28
495 511 9.116067 CATCTATCTTTAATTACGGGTTTTCCA 57.884 33.333 0.00 0.00 42.91 3.53
525 541 3.702330 TCGGACATATTCAACTACGCAG 58.298 45.455 0.00 0.00 0.00 5.18
569 585 1.619332 AGGTTCCCTCGTCTCTTTCAC 59.381 52.381 0.00 0.00 0.00 3.18
610 634 2.662866 TCTATCACCTTACAGGGACCG 58.337 52.381 0.00 0.00 40.58 4.79
621 645 0.320771 CAGGGACCGACTTTCCACTG 60.321 60.000 0.00 0.00 34.45 3.66
644 668 2.634600 GGGCATATACAACAACACCGA 58.365 47.619 0.00 0.00 0.00 4.69
651 675 7.360101 GGCATATACAACAACACCGATCTAATC 60.360 40.741 0.00 0.00 0.00 1.75
661 685 6.963049 ACACCGATCTAATCAAGTGTTTAC 57.037 37.500 6.83 0.00 41.11 2.01
702 726 0.742505 ATGATGCATGCAACGGAAGG 59.257 50.000 26.68 0.00 0.00 3.46
704 728 2.008268 GATGCATGCAACGGAAGGGG 62.008 60.000 26.68 0.00 0.00 4.79
752 776 2.229543 TGCTGCCTTCTTGCATAAACAG 59.770 45.455 0.00 0.00 41.16 3.16
986 1023 0.671781 CTGCCTTGACCAGAGTTCGG 60.672 60.000 0.00 0.00 32.03 4.30
1077 1164 2.357034 AACGAGTTCGGCATGCGT 60.357 55.556 12.44 0.00 44.95 5.24
1267 1354 2.207924 ATCGACGAGGTATGGGGCC 61.208 63.158 3.01 0.00 0.00 5.80
1285 1381 1.600636 CAGGAAGCCCGTTTGCTCA 60.601 57.895 0.00 0.00 41.80 4.26
1378 1474 5.581126 AACTGCTGTCACTTCAATTTTCA 57.419 34.783 0.00 0.00 0.00 2.69
1380 1476 3.968649 TGCTGTCACTTCAATTTTCAGC 58.031 40.909 0.00 0.00 44.39 4.26
1420 1550 3.665848 CGTTGCCGACGTGTTCATTTATT 60.666 43.478 0.00 0.00 46.49 1.40
1428 1566 5.507876 CGACGTGTTCATTTATTTGTGATGG 59.492 40.000 0.00 0.00 0.00 3.51
1433 1571 6.808212 GTGTTCATTTATTTGTGATGGTCTGG 59.192 38.462 0.00 0.00 0.00 3.86
1454 1592 4.701651 TGGATGAAATTAGGTGTTCAGCAG 59.298 41.667 4.86 0.00 40.95 4.24
1573 1711 0.944386 GTGCTTCTTTTCTGGCGACA 59.056 50.000 0.00 0.00 39.59 4.35
1575 1713 2.030805 GTGCTTCTTTTCTGGCGACAAT 60.031 45.455 0.00 0.00 42.06 2.71
1593 1731 3.188460 ACAATTTCGGATTCTTGGACGTG 59.812 43.478 0.00 0.00 0.00 4.49
1608 1746 2.280628 GACGTGGTCTTCATCCCATTC 58.719 52.381 0.00 0.00 32.32 2.67
1635 1773 2.522836 TGTTTTACGGGTACGAGCAA 57.477 45.000 0.00 0.00 44.60 3.91
1648 1786 1.837439 ACGAGCAACATGGAGGGATTA 59.163 47.619 0.00 0.00 0.00 1.75
1668 1806 2.669133 CCTCGAGGTGGAATGCCCA 61.669 63.158 24.04 0.00 44.25 5.36
1676 1814 3.453916 TGGAATGCCCAAAGCTCAA 57.546 47.368 0.00 0.00 43.29 3.02
1784 1922 3.177600 CGGCATTGAGTGAACCGG 58.822 61.111 0.00 0.00 40.18 5.28
1811 1949 1.872653 GCCGAATCGAATGTACTCCCC 60.873 57.143 3.36 0.00 0.00 4.81
1812 1950 1.687123 CCGAATCGAATGTACTCCCCT 59.313 52.381 3.36 0.00 0.00 4.79
1819 1957 2.629051 GAATGTACTCCCCTTGTTCCG 58.371 52.381 0.00 0.00 0.00 4.30
1828 1966 4.705023 ACTCCCCTTGTTCCGAAATAATTG 59.295 41.667 0.00 0.00 0.00 2.32
1856 1994 7.996644 AGTTGTAGGATTTTCCTTAGTCAAACA 59.003 33.333 0.59 0.00 46.91 2.83
1878 2016 9.500785 AAACATAATAAAGTTTGGAAACCATGG 57.499 29.630 11.19 11.19 39.71 3.66
1879 2017 8.429237 ACATAATAAAGTTTGGAAACCATGGA 57.571 30.769 21.47 0.00 39.71 3.41
1880 2018 8.311109 ACATAATAAAGTTTGGAAACCATGGAC 58.689 33.333 21.47 9.21 39.71 4.02
1881 2019 6.739331 AATAAAGTTTGGAAACCATGGACA 57.261 33.333 21.47 8.90 39.71 4.02
1882 2020 4.400529 AAAGTTTGGAAACCATGGACAC 57.599 40.909 21.47 8.46 39.71 3.67
1883 2021 2.316108 AGTTTGGAAACCATGGACACC 58.684 47.619 21.47 17.45 39.71 4.16
1884 2022 1.000717 GTTTGGAAACCATGGACACCG 60.001 52.381 21.47 0.00 31.53 4.94
1885 2023 0.183971 TTGGAAACCATGGACACCGT 59.816 50.000 21.47 0.00 31.53 4.83
1886 2024 0.183971 TGGAAACCATGGACACCGTT 59.816 50.000 21.47 0.00 0.00 4.44
1887 2025 0.879090 GGAAACCATGGACACCGTTC 59.121 55.000 21.47 10.90 0.00 3.95
1888 2026 0.879090 GAAACCATGGACACCGTTCC 59.121 55.000 21.47 0.00 36.03 3.62
1889 2027 0.887387 AAACCATGGACACCGTTCCG 60.887 55.000 21.47 0.00 38.69 4.30
1890 2028 3.124921 CCATGGACACCGTTCCGC 61.125 66.667 5.56 0.00 38.69 5.54
1891 2029 2.358125 CATGGACACCGTTCCGCA 60.358 61.111 0.00 0.00 38.69 5.69
1892 2030 1.745115 CATGGACACCGTTCCGCAT 60.745 57.895 0.00 0.00 38.69 4.73
1893 2031 1.449601 ATGGACACCGTTCCGCATC 60.450 57.895 0.00 0.00 38.69 3.91
1894 2032 3.186047 GGACACCGTTCCGCATCG 61.186 66.667 0.00 0.00 0.00 3.84
1895 2033 2.126228 GACACCGTTCCGCATCGA 60.126 61.111 0.00 0.00 0.00 3.59
1896 2034 2.126071 ACACCGTTCCGCATCGAG 60.126 61.111 0.00 0.00 0.00 4.04
1897 2035 2.126071 CACCGTTCCGCATCGAGT 60.126 61.111 0.00 0.00 0.00 4.18
1898 2036 1.736645 CACCGTTCCGCATCGAGTT 60.737 57.895 0.00 0.00 0.00 3.01
1899 2037 1.445582 ACCGTTCCGCATCGAGTTC 60.446 57.895 0.00 0.00 0.00 3.01
1900 2038 1.153823 CCGTTCCGCATCGAGTTCT 60.154 57.895 0.00 0.00 0.00 3.01
1901 2039 0.736325 CCGTTCCGCATCGAGTTCTT 60.736 55.000 0.00 0.00 0.00 2.52
1902 2040 0.640768 CGTTCCGCATCGAGTTCTTC 59.359 55.000 0.00 0.00 0.00 2.87
1903 2041 1.710013 GTTCCGCATCGAGTTCTTCA 58.290 50.000 0.00 0.00 0.00 3.02
1904 2042 2.271800 GTTCCGCATCGAGTTCTTCAT 58.728 47.619 0.00 0.00 0.00 2.57
1905 2043 2.672961 TCCGCATCGAGTTCTTCATT 57.327 45.000 0.00 0.00 0.00 2.57
1906 2044 2.972625 TCCGCATCGAGTTCTTCATTT 58.027 42.857 0.00 0.00 0.00 2.32
1907 2045 2.672874 TCCGCATCGAGTTCTTCATTTG 59.327 45.455 0.00 0.00 0.00 2.32
1912 2050 4.094887 GCATCGAGTTCTTCATTTGGCTTA 59.905 41.667 0.00 0.00 0.00 3.09
1913 2051 5.563842 CATCGAGTTCTTCATTTGGCTTAC 58.436 41.667 0.00 0.00 0.00 2.34
1928 2066 0.384309 CTTACGATGCAGGACCGCTA 59.616 55.000 9.24 0.00 0.00 4.26
1929 2067 1.000163 CTTACGATGCAGGACCGCTAT 60.000 52.381 9.24 2.72 0.00 2.97
1933 2071 0.886490 GATGCAGGACCGCTATTGGG 60.886 60.000 9.24 0.00 0.00 4.12
1935 2073 2.589540 CAGGACCGCTATTGGGCA 59.410 61.111 0.00 0.00 39.59 5.36
1939 2077 3.697439 GACCGCTATTGGGCAGCCA 62.697 63.158 15.19 0.00 36.84 4.75
1942 2080 1.394266 CCGCTATTGGGCAGCCAATT 61.394 55.000 15.19 0.14 40.39 2.32
1943 2081 0.249155 CGCTATTGGGCAGCCAATTG 60.249 55.000 15.19 12.57 40.39 2.32
1959 2097 2.391724 ATTGTCTTGCCCGTCACGGT 62.392 55.000 16.87 0.00 46.80 4.83
1962 2100 2.030562 CTTGCCCGTCACGGTCTT 59.969 61.111 16.87 0.00 46.80 3.01
1966 2104 2.995574 CCCGTCACGGTCTTCCCT 60.996 66.667 16.87 0.00 46.80 4.20
1969 2107 1.509923 CGTCACGGTCTTCCCTACC 59.490 63.158 0.00 0.00 0.00 3.18
1975 2113 1.328430 CGGTCTTCCCTACCAGTCCC 61.328 65.000 0.00 0.00 36.78 4.46
1976 2114 1.328430 GGTCTTCCCTACCAGTCCCG 61.328 65.000 0.00 0.00 36.96 5.14
1977 2115 0.324091 GTCTTCCCTACCAGTCCCGA 60.324 60.000 0.00 0.00 0.00 5.14
2020 2160 8.540507 AGAAGAGGAAACTATGTAGCATCTTA 57.459 34.615 0.00 0.00 44.43 2.10
2419 2565 1.061131 CTCTTTGCGTACATGGCTTCG 59.939 52.381 0.00 0.00 0.00 3.79
2435 2582 0.950555 TTCGTGAGCGCTTGCAATCT 60.951 50.000 13.26 0.00 42.66 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 82 3.708563 TCAACCAAGCAAGTTTGTAGC 57.291 42.857 0.00 0.00 0.00 3.58
85 87 3.684305 GCAAAGTTCAACCAAGCAAGTTT 59.316 39.130 0.00 0.00 0.00 2.66
170 178 0.676736 TACACATGGTGTCGTGCTGA 59.323 50.000 5.13 0.00 43.92 4.26
183 191 5.290493 TCGGCAAATAGAAGGATACACAT 57.710 39.130 0.00 0.00 41.41 3.21
210 218 3.232213 GTGATAGTCACGGATGTGTGT 57.768 47.619 0.00 0.00 46.49 3.72
223 238 8.250143 TGGTGATATCATTGTAGTGTGATAGT 57.750 34.615 9.02 0.00 39.79 2.12
228 243 5.007039 GTGCTGGTGATATCATTGTAGTGTG 59.993 44.000 9.02 0.00 0.00 3.82
230 245 5.118286 TGTGCTGGTGATATCATTGTAGTG 58.882 41.667 9.02 0.00 0.00 2.74
244 259 2.022764 TATCAACCGATGTGCTGGTG 57.977 50.000 0.00 0.00 38.82 4.17
256 271 6.511767 CGCAACCTGACATCTTTATATCAACC 60.512 42.308 0.00 0.00 0.00 3.77
262 277 2.863740 CGCGCAACCTGACATCTTTATA 59.136 45.455 8.75 0.00 0.00 0.98
266 281 0.884704 AACGCGCAACCTGACATCTT 60.885 50.000 5.73 0.00 0.00 2.40
273 288 1.323534 GACATAGTAACGCGCAACCTG 59.676 52.381 5.73 7.94 0.00 4.00
274 289 1.067425 TGACATAGTAACGCGCAACCT 60.067 47.619 5.73 0.00 0.00 3.50
319 334 8.452534 TCCTTCGTTTAAAAATATTGCGTGTAT 58.547 29.630 0.00 0.00 0.00 2.29
323 338 9.281075 GTATTCCTTCGTTTAAAAATATTGCGT 57.719 29.630 0.00 0.00 0.00 5.24
337 352 9.319143 CTCATTTCTATCTTGTATTCCTTCGTT 57.681 33.333 0.00 0.00 0.00 3.85
392 408 7.548196 TTGGAACGATTAGTTAATTAGCTGG 57.452 36.000 11.72 2.07 44.35 4.85
436 452 1.142688 ACAGCCCACTCCCTGGATTT 61.143 55.000 0.00 0.00 43.95 2.17
439 455 2.121963 AACAGCCCACTCCCTGGA 60.122 61.111 0.00 0.00 43.95 3.86
442 458 3.260100 CCCAACAGCCCACTCCCT 61.260 66.667 0.00 0.00 0.00 4.20
463 479 7.876582 ACCCGTAATTAAAGATAGATGTTAGGC 59.123 37.037 0.00 0.00 0.00 3.93
481 497 1.310216 GCGGCTGGAAAACCCGTAAT 61.310 55.000 0.00 0.00 43.70 1.89
482 498 1.967494 GCGGCTGGAAAACCCGTAA 60.967 57.895 0.00 0.00 43.70 3.18
483 499 2.358984 GCGGCTGGAAAACCCGTA 60.359 61.111 0.00 0.00 43.70 4.02
484 500 2.472414 TATGCGGCTGGAAAACCCGT 62.472 55.000 0.00 0.00 43.70 5.28
485 501 1.101049 ATATGCGGCTGGAAAACCCG 61.101 55.000 0.00 0.00 44.58 5.28
486 502 0.668535 GATATGCGGCTGGAAAACCC 59.331 55.000 0.00 0.00 0.00 4.11
487 503 0.307760 CGATATGCGGCTGGAAAACC 59.692 55.000 0.00 0.00 36.03 3.27
488 504 3.825812 CGATATGCGGCTGGAAAAC 57.174 52.632 0.00 0.00 36.03 2.43
525 541 1.235724 AGTTCCAAGTAGCAAACGCC 58.764 50.000 0.00 0.00 0.00 5.68
600 616 0.971386 GTGGAAAGTCGGTCCCTGTA 59.029 55.000 0.00 0.00 33.89 2.74
602 618 0.320771 CAGTGGAAAGTCGGTCCCTG 60.321 60.000 0.00 0.00 33.89 4.45
610 634 0.321653 ATGCCCGACAGTGGAAAGTC 60.322 55.000 0.00 0.00 0.00 3.01
621 645 2.353579 GGTGTTGTTGTATATGCCCGAC 59.646 50.000 0.00 0.00 0.00 4.79
651 675 7.227910 ACACCCACACTAATAAGTAAACACTTG 59.772 37.037 0.35 0.00 33.48 3.16
661 685 3.270877 GGCTGACACCCACACTAATAAG 58.729 50.000 0.00 0.00 0.00 1.73
752 776 3.128589 TCAGTGTTTGTTCACTTGGAAGC 59.871 43.478 0.00 0.00 44.92 3.86
772 796 3.578272 GTGCCGTGCAACCGTTCA 61.578 61.111 0.00 0.00 41.47 3.18
847 871 8.398665 ACAATTAGAGAAAAGTAAATCATCGCC 58.601 33.333 0.00 0.00 0.00 5.54
1179 1266 2.124151 ATGGGGATTGAGCGGTGC 60.124 61.111 0.00 0.00 0.00 5.01
1188 1275 1.152649 GGTGGATGAGGATGGGGATT 58.847 55.000 0.00 0.00 0.00 3.01
1267 1354 1.600636 TGAGCAAACGGGCTTCCTG 60.601 57.895 0.04 0.00 45.99 3.86
1329 1425 6.127758 GCATACATACCTTGTGGTCAATGAAA 60.128 38.462 5.33 0.00 44.78 2.69
1420 1550 5.887598 CCTAATTTCATCCAGACCATCACAA 59.112 40.000 0.00 0.00 0.00 3.33
1428 1566 5.163713 GCTGAACACCTAATTTCATCCAGAC 60.164 44.000 0.00 0.00 31.41 3.51
1433 1571 4.439289 GGCTGCTGAACACCTAATTTCATC 60.439 45.833 0.00 0.00 31.41 2.92
1454 1592 0.234884 CGTGAAAAACCTCGTCTGGC 59.765 55.000 0.00 0.00 0.00 4.85
1514 1652 4.283678 CTCTAGACGTTTAAGATGCTCGG 58.716 47.826 0.00 0.00 0.00 4.63
1573 1711 2.747446 CCACGTCCAAGAATCCGAAATT 59.253 45.455 0.00 0.00 0.00 1.82
1575 1713 1.071071 ACCACGTCCAAGAATCCGAAA 59.929 47.619 0.00 0.00 0.00 3.46
1593 1731 2.948315 GCTTGAGAATGGGATGAAGACC 59.052 50.000 0.00 0.00 0.00 3.85
1608 1746 3.181524 CGTACCCGTAAAACATGCTTGAG 60.182 47.826 6.60 0.00 0.00 3.02
1668 1806 0.615331 TCTCCCATCGCTTGAGCTTT 59.385 50.000 1.07 0.00 39.32 3.51
1676 1814 1.965754 GCACCTCTTCTCCCATCGCT 61.966 60.000 0.00 0.00 0.00 4.93
1784 1922 1.597663 ACATTCGATTCGGCCGAAATC 59.402 47.619 41.31 32.58 46.97 2.17
1792 1930 1.687123 AGGGGAGTACATTCGATTCGG 59.313 52.381 6.18 0.00 0.00 4.30
1811 1949 9.329913 CTACAACTTCAATTATTTCGGAACAAG 57.670 33.333 0.00 0.00 0.00 3.16
1812 1950 8.293867 CCTACAACTTCAATTATTTCGGAACAA 58.706 33.333 0.00 0.00 0.00 2.83
1856 1994 8.311109 GTGTCCATGGTTTCCAAACTTTATTAT 58.689 33.333 12.58 0.00 36.95 1.28
1858 1996 6.463755 GGTGTCCATGGTTTCCAAACTTTATT 60.464 38.462 12.58 0.00 36.95 1.40
1859 1997 5.011635 GGTGTCCATGGTTTCCAAACTTTAT 59.988 40.000 12.58 0.00 36.95 1.40
1869 2007 0.879090 GGAACGGTGTCCATGGTTTC 59.121 55.000 12.58 4.59 37.65 2.78
1870 2008 3.030415 GGAACGGTGTCCATGGTTT 57.970 52.632 12.58 0.00 37.65 3.27
1871 2009 4.813346 GGAACGGTGTCCATGGTT 57.187 55.556 12.58 0.00 37.65 3.67
1884 2022 1.710013 TGAAGAACTCGATGCGGAAC 58.290 50.000 0.00 0.00 0.00 3.62
1885 2023 2.672961 ATGAAGAACTCGATGCGGAA 57.327 45.000 0.00 0.00 0.00 4.30
1886 2024 2.672874 CAAATGAAGAACTCGATGCGGA 59.327 45.455 0.00 0.00 0.00 5.54
1887 2025 2.223112 CCAAATGAAGAACTCGATGCGG 60.223 50.000 0.00 0.00 0.00 5.69
1888 2026 2.789092 GCCAAATGAAGAACTCGATGCG 60.789 50.000 0.00 0.00 0.00 4.73
1889 2027 2.421424 AGCCAAATGAAGAACTCGATGC 59.579 45.455 0.00 0.00 0.00 3.91
1890 2028 4.691860 AAGCCAAATGAAGAACTCGATG 57.308 40.909 0.00 0.00 0.00 3.84
1891 2029 4.330074 CGTAAGCCAAATGAAGAACTCGAT 59.670 41.667 0.00 0.00 0.00 3.59
1892 2030 3.678072 CGTAAGCCAAATGAAGAACTCGA 59.322 43.478 0.00 0.00 0.00 4.04
1893 2031 3.678072 TCGTAAGCCAAATGAAGAACTCG 59.322 43.478 0.00 0.00 37.18 4.18
1894 2032 5.563842 CATCGTAAGCCAAATGAAGAACTC 58.436 41.667 0.00 0.00 37.18 3.01
1895 2033 4.142600 GCATCGTAAGCCAAATGAAGAACT 60.143 41.667 0.00 0.00 37.18 3.01
1896 2034 4.098416 GCATCGTAAGCCAAATGAAGAAC 58.902 43.478 0.00 0.00 37.18 3.01
1897 2035 3.755905 TGCATCGTAAGCCAAATGAAGAA 59.244 39.130 0.00 0.00 37.18 2.52
1898 2036 3.342719 TGCATCGTAAGCCAAATGAAGA 58.657 40.909 0.00 0.00 37.18 2.87
1899 2037 3.488047 CCTGCATCGTAAGCCAAATGAAG 60.488 47.826 0.00 0.00 37.18 3.02
1900 2038 2.423185 CCTGCATCGTAAGCCAAATGAA 59.577 45.455 0.00 0.00 37.18 2.57
1901 2039 2.016318 CCTGCATCGTAAGCCAAATGA 58.984 47.619 0.00 0.00 37.18 2.57
1902 2040 2.016318 TCCTGCATCGTAAGCCAAATG 58.984 47.619 0.00 0.00 37.18 2.32
1903 2041 2.017049 GTCCTGCATCGTAAGCCAAAT 58.983 47.619 0.00 0.00 37.18 2.32
1904 2042 1.448985 GTCCTGCATCGTAAGCCAAA 58.551 50.000 0.00 0.00 37.18 3.28
1905 2043 0.392461 GGTCCTGCATCGTAAGCCAA 60.392 55.000 0.00 0.00 37.18 4.52
1906 2044 1.220749 GGTCCTGCATCGTAAGCCA 59.779 57.895 0.00 0.00 37.18 4.75
1907 2045 1.883084 CGGTCCTGCATCGTAAGCC 60.883 63.158 0.00 0.00 37.18 4.35
1912 2050 0.530650 CAATAGCGGTCCTGCATCGT 60.531 55.000 8.15 0.00 37.31 3.73
1913 2051 1.224069 CCAATAGCGGTCCTGCATCG 61.224 60.000 8.15 0.00 37.31 3.84
1933 2071 1.079612 GGGCAAGACAATTGGCTGC 60.080 57.895 16.33 19.23 43.51 5.25
1935 2073 1.228552 ACGGGCAAGACAATTGGCT 60.229 52.632 8.40 8.40 43.51 4.75
1939 2077 1.234615 CCGTGACGGGCAAGACAATT 61.235 55.000 17.80 0.00 44.15 2.32
1959 2097 0.635009 ATCGGGACTGGTAGGGAAGA 59.365 55.000 0.00 0.00 0.00 2.87
1962 2100 0.686441 CACATCGGGACTGGTAGGGA 60.686 60.000 0.00 0.00 0.00 4.20
1966 2104 0.907704 AAGGCACATCGGGACTGGTA 60.908 55.000 0.00 0.00 0.00 3.25
1969 2107 0.742281 CAGAAGGCACATCGGGACTG 60.742 60.000 0.00 0.00 0.00 3.51
1975 2113 2.456119 GGTCGCAGAAGGCACATCG 61.456 63.158 0.00 0.00 45.17 3.84
1976 2114 0.955428 TTGGTCGCAGAAGGCACATC 60.955 55.000 0.00 0.00 45.17 3.06
1977 2115 0.957395 CTTGGTCGCAGAAGGCACAT 60.957 55.000 0.00 0.00 45.17 3.21
2020 2160 2.032681 GAAAGACCAGCCTGCCGT 59.967 61.111 0.00 0.00 0.00 5.68
2419 2565 0.731417 ATGAGATTGCAAGCGCTCAC 59.269 50.000 23.39 6.52 39.88 3.51
2665 5814 9.634021 AAATAATTGAAGTTCTAGGATTCTCCC 57.366 33.333 4.17 0.00 37.19 4.30


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

AutoCloner maintained by Alex Coulton.