Multiple sequence alignment - TraesCS2A01G277600

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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 TraesCS2A01G277600 chr2A 100.000 2336 0 0 1 2336 459798937 459801272 0.000000e+00 4314.0
1 TraesCS2A01G277600 chr2A 81.757 148 17 6 448 586 612845961 612845815 5.280000e-22 115.0
2 TraesCS2A01G277600 chr2A 100.000 28 0 0 444 471 759577686 759577713 4.000000e-03 52.8
3 TraesCS2A01G277600 chr2D 88.585 1717 116 34 3 1666 346088290 346089979 0.000000e+00 2012.0
4 TraesCS2A01G277600 chr2D 86.667 90 11 1 501 590 461083435 461083347 5.310000e-17 99.0
5 TraesCS2A01G277600 chr2B 90.052 965 58 18 729 1658 412057779 412058740 0.000000e+00 1216.0
6 TraesCS2A01G277600 chr2B 87.057 734 36 11 1 708 412050979 412051679 0.000000e+00 774.0
7 TraesCS2A01G277600 chr2B 80.563 710 71 33 1661 2336 412058797 412059473 3.490000e-133 484.0
8 TraesCS2A01G277600 chr2B 74.854 171 35 7 1880 2046 789534152 789534318 1.160000e-08 71.3
9 TraesCS2A01G277600 chr2B 97.222 36 1 0 694 729 412057725 412057760 6.970000e-06 62.1
10 TraesCS2A01G277600 chr7D 74.699 332 68 15 1723 2046 563891601 563891278 1.460000e-27 134.0
11 TraesCS2A01G277600 chr4A 81.818 154 18 6 446 590 598724607 598724455 1.130000e-23 121.0
12 TraesCS2A01G277600 chr4A 73.793 290 62 12 1757 2039 740924794 740924512 4.110000e-18 102.0
13 TraesCS2A01G277600 chr3B 88.000 100 11 1 491 590 814657916 814658014 1.470000e-22 117.0
14 TraesCS2A01G277600 chr4D 88.889 90 9 1 501 590 4772220 4772132 2.450000e-20 110.0
15 TraesCS2A01G277600 chr1D 86.000 100 13 1 491 590 168483952 168483854 3.170000e-19 106.0
16 TraesCS2A01G277600 chr1D 97.143 35 1 0 441 475 447468614 447468580 2.510000e-05 60.2
17 TraesCS2A01G277600 chr3D 74.016 254 62 4 1793 2044 536983839 536984090 1.480000e-17 100.0
18 TraesCS2A01G277600 chr1A 85.000 100 14 1 491 590 217608447 217608349 1.480000e-17 100.0
19 TraesCS2A01G277600 chr4B 72.365 351 74 19 1707 2046 72658383 72658721 3.200000e-14 89.8
20 TraesCS2A01G277600 chr6B 77.305 141 24 7 1910 2046 163957178 163957042 2.490000e-10 76.8
21 TraesCS2A01G277600 chrUn 100.000 28 0 0 444 471 269590356 269590383 4.000000e-03 52.8
22 TraesCS2A01G277600 chr6A 100.000 28 0 0 443 470 307208787 307208814 4.000000e-03 52.8
23 TraesCS2A01G277600 chr5B 100.000 28 0 0 444 471 524358406 524358433 4.000000e-03 52.8


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 TraesCS2A01G277600 chr2A 459798937 459801272 2335 False 4314.000000 4314 100.000 1 2336 1 chr2A.!!$F1 2335
1 TraesCS2A01G277600 chr2D 346088290 346089979 1689 False 2012.000000 2012 88.585 3 1666 1 chr2D.!!$F1 1663
2 TraesCS2A01G277600 chr2B 412050979 412051679 700 False 774.000000 774 87.057 1 708 1 chr2B.!!$F1 707
3 TraesCS2A01G277600 chr2B 412057725 412059473 1748 False 587.366667 1216 89.279 694 2336 3 chr2B.!!$F3 1642

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
295 315 0.885879 CTTTTCCCTAACCGGCCAAC 59.114 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2389 0.110104 GCCCCATCAAGGAGGAGATG 59.89 60.0 0.0 0.0 41.22 2.9 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
79 80 7.033185 ACACCATATTCCGAAATAAAAAGTGC 58.967 34.615 0.00 0.00 31.28 4.40
134 135 4.962362 TGTGTATGACAGATGTGGGTATCT 59.038 41.667 0.00 0.00 37.90 1.98
295 315 0.885879 CTTTTCCCTAACCGGCCAAC 59.114 55.000 0.00 0.00 0.00 3.77
299 319 1.190833 TCCCTAACCGGCCAACGTAA 61.191 55.000 0.00 0.00 42.24 3.18
307 328 1.434555 CGGCCAACGTAACTGAATGA 58.565 50.000 2.24 0.00 37.93 2.57
317 338 4.081420 ACGTAACTGAATGATGCCTTCTCT 60.081 41.667 0.00 0.00 0.00 3.10
330 351 1.909302 CCTTCTCTAAGGCCCACTTCA 59.091 52.381 0.00 0.00 45.78 3.02
336 357 4.534500 TCTCTAAGGCCCACTTCACATTTA 59.466 41.667 0.00 0.00 40.64 1.40
338 359 5.826643 TCTAAGGCCCACTTCACATTTAAT 58.173 37.500 0.00 0.00 40.64 1.40
417 440 9.920133 TCATTCATTCGAAATTTCCAACAAATA 57.080 25.926 12.54 0.00 34.01 1.40
531 554 8.641499 TTGTGTTTGTTCATTCATTTAAGTCC 57.359 30.769 0.00 0.00 0.00 3.85
651 674 1.202486 TCGGGTGCATAAATCGGACTC 60.202 52.381 0.00 0.00 0.00 3.36
777 826 2.301346 CTCTTGTACCCATGATTGGCC 58.699 52.381 0.00 0.00 42.15 5.36
787 836 1.062880 CATGATTGGCCGCAAAAATGC 59.937 47.619 0.00 0.00 0.00 3.56
840 889 7.107542 ACTCTACATTTAAATACGGCCAAAGA 58.892 34.615 2.24 0.00 0.00 2.52
879 937 3.508840 GGCCACGAGAATTGCCCG 61.509 66.667 0.00 0.00 37.94 6.13
893 951 1.153025 GCCCGATACCAAACCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
906 964 4.770010 CCAAACCTCCCTTTATAAGTTGCA 59.230 41.667 0.00 0.00 0.00 4.08
927 996 1.134075 CCGAGTCTACCGTGACACG 59.866 63.158 21.02 21.02 45.62 4.49
928 997 1.511464 CGAGTCTACCGTGACACGC 60.511 63.158 22.46 8.39 42.01 5.34
929 998 1.511464 GAGTCTACCGTGACACGCG 60.511 63.158 22.46 17.02 40.91 6.01
930 999 1.904852 GAGTCTACCGTGACACGCGA 61.905 60.000 22.46 14.34 40.91 5.87
931 1000 1.795177 GTCTACCGTGACACGCGAC 60.795 63.158 22.46 20.86 40.91 5.19
932 1001 2.868331 CTACCGTGACACGCGACG 60.868 66.667 22.46 12.75 40.91 5.12
949 1018 3.456365 GCTCGCTCTCCTCCAGCA 61.456 66.667 0.00 0.00 36.61 4.41
1499 1572 5.403897 TCGATTGTTCTTGTTCACAGAAC 57.596 39.130 5.96 5.96 41.43 3.01
1538 1614 4.365514 TGACTTTAGGCCATCTTCAACA 57.634 40.909 5.01 0.00 0.00 3.33
1540 1616 4.072131 GACTTTAGGCCATCTTCAACACA 58.928 43.478 5.01 0.00 0.00 3.72
1545 1621 0.598065 GCCATCTTCAACACACACCC 59.402 55.000 0.00 0.00 0.00 4.61
1570 1667 3.220110 GTGGATACGGATGTAGGAGTCA 58.780 50.000 0.00 0.00 42.51 3.41
1575 1672 0.103208 CGGATGTAGGAGTCAGCCAC 59.897 60.000 0.00 0.00 40.84 5.01
1581 1678 0.472925 TAGGAGTCAGCCACCCAACA 60.473 55.000 0.00 0.00 0.00 3.33
1586 1683 0.396811 GTCAGCCACCCAACACTACT 59.603 55.000 0.00 0.00 0.00 2.57
1587 1684 1.136828 TCAGCCACCCAACACTACTT 58.863 50.000 0.00 0.00 0.00 2.24
1641 1739 7.547227 TCAGAAGAATTTCATCAGATACGACA 58.453 34.615 4.61 0.00 35.70 4.35
1658 1756 9.877178 AGATACGACAGATTTCATTAAAGTTCT 57.123 29.630 0.00 0.00 0.00 3.01
1739 1906 2.281692 TCGTCGTCGTCCCTCCAA 60.282 61.111 1.33 0.00 38.33 3.53
1749 1916 2.211410 TCCCTCCAACGGCGAAAGA 61.211 57.895 16.62 5.56 0.00 2.52
1783 1950 3.512516 GCAGCCTTGTCCGATGGC 61.513 66.667 0.00 0.00 43.89 4.40
1787 1954 3.403936 GCCTTGTCCGATGGCTATT 57.596 52.632 0.00 0.00 40.96 1.73
1789 1956 1.334869 GCCTTGTCCGATGGCTATTTG 59.665 52.381 0.00 0.00 40.96 2.32
1792 1959 1.667236 TGTCCGATGGCTATTTGCTG 58.333 50.000 0.00 0.00 42.39 4.41
1825 1992 1.519326 TACTCAGCCTCCTCCTGGGT 61.519 60.000 0.00 0.00 45.49 4.51
1830 1997 1.306226 GCCTCCTCCTGGGTAGTGT 60.306 63.158 0.00 0.00 36.25 3.55
1836 2003 0.041238 CTCCTGGGTAGTGTGGAGGA 59.959 60.000 0.00 0.00 41.59 3.71
1838 2005 0.252284 CCTGGGTAGTGTGGAGGACT 60.252 60.000 0.00 0.00 0.00 3.85
1839 2006 0.898320 CTGGGTAGTGTGGAGGACTG 59.102 60.000 0.00 0.00 0.00 3.51
1840 2007 0.485543 TGGGTAGTGTGGAGGACTGA 59.514 55.000 0.00 0.00 0.00 3.41
1842 2009 0.896226 GGTAGTGTGGAGGACTGACC 59.104 60.000 0.00 0.00 39.35 4.02
1845 2012 1.906824 GTGTGGAGGACTGACCCGA 60.907 63.158 0.00 0.00 40.05 5.14
1854 2021 0.605319 GACTGACCCGACCAATGCAA 60.605 55.000 0.00 0.00 0.00 4.08
1860 2027 0.179166 CCCGACCAATGCAAATGACG 60.179 55.000 4.54 9.06 0.00 4.35
1904 2071 2.751436 CCCCTGCCGACATTGGTG 60.751 66.667 0.00 0.00 0.00 4.17
1933 2100 1.224069 CTATGCGCCCATTCCTCGTG 61.224 60.000 4.18 0.00 32.85 4.35
1940 2107 1.717032 CCCATTCCTCGTGGATCCTA 58.283 55.000 14.23 0.00 42.81 2.94
1948 2115 1.957177 CTCGTGGATCCTAGCAAGCTA 59.043 52.381 14.23 1.37 0.00 3.32
1957 2124 2.567169 TCCTAGCAAGCTAGCTGTCAAA 59.433 45.455 20.16 2.43 46.11 2.69
1966 2133 0.400213 TAGCTGTCAAAGGTGGTGGG 59.600 55.000 0.00 0.00 37.17 4.61
1970 2137 1.282653 TGTCAAAGGTGGTGGGGACA 61.283 55.000 0.00 0.00 38.70 4.02
1991 2159 2.505118 GCGGTCGTCTCTGCTGTC 60.505 66.667 0.00 0.00 36.83 3.51
1993 2161 2.505118 GGTCGTCTCTGCTGTCGC 60.505 66.667 0.00 0.00 0.00 5.19
2000 2168 0.457443 TCTCTGCTGTCGCGATGAAT 59.543 50.000 14.06 0.00 39.65 2.57
2040 2208 0.247736 GGCGAGGTCTGAGTCATTGT 59.752 55.000 0.00 0.00 0.00 2.71
2046 2214 1.625818 GGTCTGAGTCATTGTGGACCT 59.374 52.381 17.22 0.00 39.79 3.85
2049 2217 0.320683 TGAGTCATTGTGGACCTGCG 60.321 55.000 0.00 0.00 38.59 5.18
2053 2221 1.374125 CATTGTGGACCTGCGTCGA 60.374 57.895 0.00 0.00 40.17 4.20
2058 2226 1.300620 TGGACCTGCGTCGAACTTG 60.301 57.895 0.00 0.00 40.17 3.16
2059 2227 2.027625 GGACCTGCGTCGAACTTGG 61.028 63.158 0.00 0.00 40.17 3.61
2060 2228 1.300697 GACCTGCGTCGAACTTGGT 60.301 57.895 0.00 0.00 0.00 3.67
2061 2229 1.557443 GACCTGCGTCGAACTTGGTG 61.557 60.000 0.00 0.00 0.00 4.17
2062 2230 1.300620 CCTGCGTCGAACTTGGTGA 60.301 57.895 0.00 0.00 0.00 4.02
2063 2231 0.878523 CCTGCGTCGAACTTGGTGAA 60.879 55.000 0.00 0.00 0.00 3.18
2064 2232 0.232303 CTGCGTCGAACTTGGTGAAC 59.768 55.000 0.00 0.00 0.00 3.18
2065 2233 0.460459 TGCGTCGAACTTGGTGAACA 60.460 50.000 0.00 0.00 0.00 3.18
2066 2234 0.042448 GCGTCGAACTTGGTGAACAC 60.042 55.000 0.00 0.00 0.00 3.32
2099 2267 2.973600 GTTGCGCCGGTTGTACCA 60.974 61.111 4.18 0.00 38.47 3.25
2102 2270 2.435234 GCGCCGGTTGTACCATGA 60.435 61.111 1.90 0.00 38.47 3.07
2103 2271 2.746803 GCGCCGGTTGTACCATGAC 61.747 63.158 1.90 0.00 38.47 3.06
2113 2281 3.076258 TACCATGACTGCCGCCTCG 62.076 63.158 0.00 0.00 0.00 4.63
2129 2297 3.443925 CGCTGTGCTCCTCCTCGA 61.444 66.667 0.00 0.00 0.00 4.04
2137 2305 0.456995 GCTCCTCCTCGAAGACAACG 60.457 60.000 0.00 0.00 0.00 4.10
2138 2306 0.882474 CTCCTCCTCGAAGACAACGT 59.118 55.000 0.00 0.00 0.00 3.99
2148 2332 2.753931 AAGACAACGTACCGCCGACC 62.754 60.000 0.00 0.00 0.00 4.79
2233 2418 4.476752 GATGGGGCGGCGGTTGTA 62.477 66.667 9.78 0.00 0.00 2.41
2234 2419 4.483243 ATGGGGCGGCGGTTGTAG 62.483 66.667 9.78 0.00 0.00 2.74
2263 2448 3.359523 CATGGGCCCATCGATGCG 61.360 66.667 35.42 18.64 33.90 4.73
2264 2449 3.559263 ATGGGCCCATCGATGCGA 61.559 61.111 32.75 2.57 41.13 5.10
2279 2464 4.185413 CGAGCGTACTGGTTGCAT 57.815 55.556 0.00 0.00 0.00 3.96
2288 2473 4.634703 TGGTTGCATGCCGACGGT 62.635 61.111 16.68 0.00 0.00 4.83
2304 2489 1.892819 CGGTGACACTGGCTCATCCT 61.893 60.000 6.51 0.00 35.26 3.24
2310 2495 0.036952 CACTGGCTCATCCTTGACGT 60.037 55.000 0.00 0.00 35.26 4.34
2313 2498 1.478510 CTGGCTCATCCTTGACGTAGT 59.521 52.381 0.00 0.00 39.04 2.73
2329 2514 1.033746 TAGTGTCCGATCCCGACACC 61.034 60.000 25.93 14.71 42.32 4.16
2332 2517 1.227263 GTCCGATCCCGACACCATG 60.227 63.158 3.30 0.00 38.22 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.596836 ATTTCGGAATATGGTGTTGCATT 57.403 34.783 0.00 0.00 0.00 3.56
96 97 8.614469 TGTCATACACACATAGACAAATCAAA 57.386 30.769 0.00 0.00 36.39 2.69
134 135 3.072476 GGTGAGCTAGGCAACCCATATTA 59.928 47.826 0.00 0.00 33.36 0.98
182 183 1.402062 GCACAAGCAAAGCCTCTTAGC 60.402 52.381 0.00 0.00 41.58 3.09
295 315 4.437239 AGAGAAGGCATCATTCAGTTACG 58.563 43.478 0.00 0.00 0.00 3.18
299 319 5.033589 CCTTAGAGAAGGCATCATTCAGT 57.966 43.478 0.00 0.00 45.91 3.41
317 338 6.926630 AAATTAAATGTGAAGTGGGCCTTA 57.073 33.333 4.53 0.00 32.03 2.69
330 351 9.558396 ACAATCATTGTCACCAAAATTAAATGT 57.442 25.926 0.00 0.00 40.56 2.71
336 357 5.927819 ACCACAATCATTGTCACCAAAATT 58.072 33.333 0.00 0.00 43.23 1.82
338 359 6.453943 CATACCACAATCATTGTCACCAAAA 58.546 36.000 0.00 0.00 43.23 2.44
384 407 8.093307 TGGAAATTTCGAATGAATGAAAATCCA 58.907 29.630 11.95 15.60 43.85 3.41
385 408 8.477984 TGGAAATTTCGAATGAATGAAAATCC 57.522 30.769 11.95 12.33 40.69 3.01
386 409 9.745323 GTTGGAAATTTCGAATGAATGAAAATC 57.255 29.630 17.14 0.00 37.60 2.17
387 410 9.270640 TGTTGGAAATTTCGAATGAATGAAAAT 57.729 25.926 17.14 0.00 37.60 1.82
388 411 8.654230 TGTTGGAAATTTCGAATGAATGAAAA 57.346 26.923 17.14 0.00 37.60 2.29
417 440 2.315176 TGCCTTTAACTGGTTGTGCAT 58.685 42.857 0.00 0.00 0.00 3.96
565 588 5.751586 ACACCCTCCGTTCACAAATATAAT 58.248 37.500 0.00 0.00 0.00 1.28
651 674 0.525668 CGCGTGCTTACTCACCTAGG 60.526 60.000 7.41 7.41 33.57 3.02
787 836 3.767230 CGCACAGAACTGACCGCG 61.767 66.667 17.18 17.18 39.33 6.46
840 889 3.496870 CCCACTGTCTTTGCTTTACTCCT 60.497 47.826 0.00 0.00 0.00 3.69
879 937 7.201794 GCAACTTATAAAGGGAGGTTTGGTATC 60.202 40.741 0.00 0.00 0.00 2.24
893 951 3.270877 ACTCGGGCTGCAACTTATAAAG 58.729 45.455 0.50 0.00 0.00 1.85
906 964 2.045131 GTCACGGTAGACTCGGGCT 61.045 63.158 0.00 0.00 35.65 5.19
928 997 4.244802 GGAGGAGAGCGAGCGTCG 62.245 72.222 3.50 3.50 43.89 5.12
929 998 3.119709 CTGGAGGAGAGCGAGCGTC 62.120 68.421 0.00 0.00 0.00 5.19
930 999 3.137459 CTGGAGGAGAGCGAGCGT 61.137 66.667 0.00 0.00 0.00 5.07
931 1000 4.567385 GCTGGAGGAGAGCGAGCG 62.567 72.222 0.00 0.00 0.00 5.03
932 1001 3.429080 CTGCTGGAGGAGAGCGAGC 62.429 68.421 0.00 0.00 39.47 5.03
933 1002 2.806929 CTGCTGGAGGAGAGCGAG 59.193 66.667 0.00 0.00 39.47 5.03
934 1003 3.456365 GCTGCTGGAGGAGAGCGA 61.456 66.667 0.00 0.00 39.47 4.93
936 1005 2.904470 CTTCGCTGCTGGAGGAGAGC 62.904 65.000 0.00 0.00 35.31 4.09
937 1006 1.141449 CTTCGCTGCTGGAGGAGAG 59.859 63.158 0.00 0.00 35.31 3.20
949 1018 2.698803 TGTGTATGACAATGCTTCGCT 58.301 42.857 0.00 0.00 0.00 4.93
952 1021 5.221880 TGCTTTTGTGTATGACAATGCTTC 58.778 37.500 0.00 0.00 44.23 3.86
961 1030 5.804639 ACCTGTAGATGCTTTTGTGTATGA 58.195 37.500 0.00 0.00 0.00 2.15
1082 1155 4.807039 CCCCTGTACCGGCGAACG 62.807 72.222 9.30 0.00 43.80 3.95
1091 1164 3.711541 CTGTACGCCGCCCCTGTAC 62.712 68.421 0.00 0.75 39.08 2.90
1101 1174 2.954868 CCGTCGATGCTGTACGCC 60.955 66.667 0.00 0.00 38.05 5.68
1104 1177 3.617538 GCGCCGTCGATGCTGTAC 61.618 66.667 0.00 0.00 38.10 2.90
1144 1217 0.250234 TCCTCCAGCTTCATCAACGG 59.750 55.000 0.00 0.00 0.00 4.44
1148 1221 1.900351 CCGTCCTCCAGCTTCATCA 59.100 57.895 0.00 0.00 0.00 3.07
1278 1351 1.454479 GGTGTACGATCCTCCGGGA 60.454 63.158 0.00 0.00 46.81 5.14
1499 1572 3.312421 AGTCAAAATTATCGACGCCATGG 59.688 43.478 7.63 7.63 34.80 3.66
1538 1614 1.588082 GTATCCACGACGGGTGTGT 59.412 57.895 0.00 0.00 45.52 3.72
1551 1648 2.229302 GCTGACTCCTACATCCGTATCC 59.771 54.545 0.00 0.00 0.00 2.59
1570 1667 2.051692 TGTAAGTAGTGTTGGGTGGCT 58.948 47.619 0.00 0.00 0.00 4.75
1616 1714 7.547227 TGTCGTATCTGATGAAATTCTTCTGA 58.453 34.615 16.47 16.47 34.68 3.27
1618 1716 7.776107 TCTGTCGTATCTGATGAAATTCTTCT 58.224 34.615 9.74 0.00 32.33 2.85
1621 1719 8.954950 AAATCTGTCGTATCTGATGAAATTCT 57.045 30.769 0.00 0.00 0.00 2.40
1633 1731 9.907576 CAGAACTTTAATGAAATCTGTCGTATC 57.092 33.333 11.61 0.00 31.49 2.24
1669 1821 0.966920 AAGATGGTCGCCCGGTATAG 59.033 55.000 0.00 0.00 0.00 1.31
1685 1837 2.356553 GTGGCCACGCGTACAAGA 60.357 61.111 22.49 0.00 0.00 3.02
1709 1861 3.456039 GACGACACGAACGGCGAC 61.456 66.667 16.62 6.32 44.57 5.19
1739 1906 0.526662 CTCTGGTACTCTTTCGCCGT 59.473 55.000 0.00 0.00 0.00 5.68
1745 1912 1.900545 GCGGCCCTCTGGTACTCTTT 61.901 60.000 0.00 0.00 0.00 2.52
1783 1950 2.606725 CTCCTTCACGAGCAGCAAATAG 59.393 50.000 0.00 0.00 0.00 1.73
1785 1952 1.446907 CTCCTTCACGAGCAGCAAAT 58.553 50.000 0.00 0.00 0.00 2.32
1787 1954 4.681421 CTCCTTCACGAGCAGCAA 57.319 55.556 0.00 0.00 0.00 3.91
1810 1977 1.002274 ACTACCCAGGAGGAGGCTG 59.998 63.158 0.00 0.00 39.89 4.85
1825 1992 0.611062 CGGGTCAGTCCTCCACACTA 60.611 60.000 0.00 0.00 36.25 2.74
1830 1997 2.283676 GGTCGGGTCAGTCCTCCA 60.284 66.667 0.00 0.00 36.25 3.86
1836 2003 0.179004 TTTGCATTGGTCGGGTCAGT 60.179 50.000 0.00 0.00 0.00 3.41
1838 2005 0.887247 CATTTGCATTGGTCGGGTCA 59.113 50.000 0.00 0.00 0.00 4.02
1839 2006 1.135402 GTCATTTGCATTGGTCGGGTC 60.135 52.381 0.00 0.00 0.00 4.46
1840 2007 0.887933 GTCATTTGCATTGGTCGGGT 59.112 50.000 0.00 0.00 0.00 5.28
1842 2009 0.798009 GCGTCATTTGCATTGGTCGG 60.798 55.000 0.00 0.00 0.00 4.79
1845 2012 0.168788 CGAGCGTCATTTGCATTGGT 59.831 50.000 0.00 0.00 33.85 3.67
1894 2061 1.350193 CGACTCCTTCACCAATGTCG 58.650 55.000 0.00 0.00 40.55 4.35
1898 2065 2.743183 GCATAGCGACTCCTTCACCAAT 60.743 50.000 0.00 0.00 0.00 3.16
1933 2100 1.691434 ACAGCTAGCTTGCTAGGATCC 59.309 52.381 22.24 2.48 41.98 3.36
1940 2107 1.072965 ACCTTTGACAGCTAGCTTGCT 59.927 47.619 16.46 17.30 45.18 3.91
1948 2115 1.151450 CCCACCACCTTTGACAGCT 59.849 57.895 0.00 0.00 0.00 4.24
2019 2187 0.247736 AATGACTCAGACCTCGCCAC 59.752 55.000 0.00 0.00 0.00 5.01
2023 2191 1.546029 TCCACAATGACTCAGACCTCG 59.454 52.381 0.00 0.00 0.00 4.63
2040 2208 1.300620 CAAGTTCGACGCAGGTCCA 60.301 57.895 0.00 0.00 40.17 4.02
2046 2214 0.460459 TGTTCACCAAGTTCGACGCA 60.460 50.000 0.00 0.00 0.00 5.24
2049 2217 0.580104 CGGTGTTCACCAAGTTCGAC 59.420 55.000 19.90 0.00 0.00 4.20
2053 2221 0.812412 CGGTCGGTGTTCACCAAGTT 60.812 55.000 19.90 0.00 32.33 2.66
2081 2249 2.973600 GGTACAACCGGCGCAACA 60.974 61.111 10.83 0.00 0.00 3.33
2099 2267 4.827087 CAGCGAGGCGGCAGTCAT 62.827 66.667 13.08 0.00 34.64 3.06
2113 2281 1.153667 CTTCGAGGAGGAGCACAGC 60.154 63.158 0.00 0.00 0.00 4.40
2117 2285 0.603569 GTTGTCTTCGAGGAGGAGCA 59.396 55.000 0.00 0.00 0.00 4.26
2148 2332 2.759973 TAGCTCAGAGGTGGCGGG 60.760 66.667 12.66 0.00 0.00 6.13
2152 2336 4.616180 TCCTCCACTAGCTCAGAGGTGG 62.616 59.091 12.66 14.08 45.20 4.61
2154 2338 1.003646 TCCTCCACTAGCTCAGAGGT 58.996 55.000 16.51 7.43 45.16 3.85
2163 2347 2.150051 GGGCCCCATCCTCCACTAG 61.150 68.421 12.23 0.00 0.00 2.57
2194 2378 1.153549 GAGGAGATGCCACCGTGAC 60.154 63.158 0.00 0.00 40.02 3.67
2204 2389 0.110104 GCCCCATCAAGGAGGAGATG 59.890 60.000 0.00 0.00 41.22 2.90
2206 2391 2.066393 CGCCCCATCAAGGAGGAGA 61.066 63.158 0.00 0.00 41.22 3.71
2242 2427 3.832237 ATCGATGGGCCCATGTCGC 62.832 63.158 42.21 25.27 36.70 5.19
2243 2428 1.962822 CATCGATGGGCCCATGTCG 60.963 63.158 42.21 36.95 36.70 4.35
2244 2429 2.263741 GCATCGATGGGCCCATGTC 61.264 63.158 42.21 27.74 36.70 3.06
2245 2430 2.203394 GCATCGATGGGCCCATGT 60.203 61.111 42.21 21.70 36.70 3.21
2246 2431 3.359523 CGCATCGATGGGCCCATG 61.360 66.667 42.21 30.19 36.70 3.66
2247 2432 3.541950 CTCGCATCGATGGGCCCAT 62.542 63.158 38.12 38.12 40.18 4.00
2248 2433 4.240103 CTCGCATCGATGGGCCCA 62.240 66.667 30.92 30.92 40.18 5.36
2263 2448 1.425428 GCATGCAACCAGTACGCTC 59.575 57.895 14.21 0.00 0.00 5.03
2264 2449 2.040544 GGCATGCAACCAGTACGCT 61.041 57.895 21.36 0.00 0.00 5.07
2278 2463 2.048222 CAGTGTCACCGTCGGCAT 60.048 61.111 12.28 0.00 0.00 4.40
2279 2464 4.293648 CCAGTGTCACCGTCGGCA 62.294 66.667 12.28 0.00 0.00 5.69
2288 2473 1.002430 GTCAAGGATGAGCCAGTGTCA 59.998 52.381 0.00 0.00 40.02 3.58
2310 2495 1.033746 GGTGTCGGGATCGGACACTA 61.034 60.000 30.97 8.52 41.94 2.74
2313 2498 1.684391 ATGGTGTCGGGATCGGACA 60.684 57.895 12.62 12.62 36.95 4.02


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

AutoCloner maintained by Alex Coulton.