Multiple sequence alignment - TraesCS2A01G205700

Loading Multiple Alignment...

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 TraesCS2A01G205700 chr2A 100.000 2872 0 0 1 2872 184498810 184501681 0.000000e+00 5304
1 TraesCS2A01G205700 chr2A 94.469 669 37 0 2193 2861 751400169 751400837 0.000000e+00 1031
2 TraesCS2A01G205700 chr2A 93.382 680 41 1 2193 2872 54439462 54438787 0.000000e+00 1003
3 TraesCS2A01G205700 chr2D 95.731 1429 39 9 697 2123 166204568 166203160 0.000000e+00 2281
4 TraesCS2A01G205700 chr2D 91.860 688 48 6 2186 2872 206998094 206998774 0.000000e+00 953
5 TraesCS2A01G205700 chr2D 93.006 529 29 6 1 525 166205273 166204749 0.000000e+00 765
6 TraesCS2A01G205700 chr2D 93.289 149 9 1 547 695 109696120 109695973 4.820000e-53 219
7 TraesCS2A01G205700 chr2D 93.243 148 7 2 547 694 469137647 469137791 6.230000e-52 215
8 TraesCS2A01G205700 chr2B 94.925 1458 28 11 694 2120 231603590 231605032 0.000000e+00 2241
9 TraesCS2A01G205700 chr2B 93.277 357 13 4 150 496 231603241 231603596 1.530000e-142 516
10 TraesCS2A01G205700 chr2B 92.568 148 10 1 547 694 411854060 411854206 8.060000e-51 211
11 TraesCS2A01G205700 chr2B 89.873 158 13 2 1 155 231601700 231601857 1.750000e-47 200
12 TraesCS2A01G205700 chrUn 93.913 690 31 2 2193 2872 112547885 112548573 0.000000e+00 1031
13 TraesCS2A01G205700 chr3D 93.979 681 36 2 2193 2872 447593284 447593960 0.000000e+00 1026
14 TraesCS2A01G205700 chr3D 93.333 675 39 4 2199 2872 155683886 155683217 0.000000e+00 992
15 TraesCS2A01G205700 chr3D 92.952 681 43 2 2193 2872 580644015 580644691 0.000000e+00 987
16 TraesCS2A01G205700 chr3D 92.364 681 47 2 2193 2872 609767759 609768435 0.000000e+00 965
17 TraesCS2A01G205700 chr1D 93.539 681 39 2 2193 2872 422842688 422843364 0.000000e+00 1009
18 TraesCS2A01G205700 chr1D 94.558 147 6 2 547 693 470861786 470861930 2.880000e-55 226
19 TraesCS2A01G205700 chr6D 93.506 154 8 2 547 699 10733225 10733377 8.010000e-56 228
20 TraesCS2A01G205700 chr5D 91.071 168 8 5 529 694 246302773 246302935 1.340000e-53 220
21 TraesCS2A01G205700 chr4D 93.243 148 8 2 547 693 456251202 456251056 1.730000e-52 217
22 TraesCS2A01G205700 chr4D 93.151 146 8 2 548 693 67287325 67287468 2.240000e-51 213
23 TraesCS2A01G205700 chr7D 88.000 175 13 4 520 694 65605375 65605209 1.750000e-47 200


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 TraesCS2A01G205700 chr2A 184498810 184501681 2871 False 5304.000000 5304 100.000000 1 2872 1 chr2A.!!$F1 2871
1 TraesCS2A01G205700 chr2A 751400169 751400837 668 False 1031.000000 1031 94.469000 2193 2861 1 chr2A.!!$F2 668
2 TraesCS2A01G205700 chr2A 54438787 54439462 675 True 1003.000000 1003 93.382000 2193 2872 1 chr2A.!!$R1 679
3 TraesCS2A01G205700 chr2D 166203160 166205273 2113 True 1523.000000 2281 94.368500 1 2123 2 chr2D.!!$R2 2122
4 TraesCS2A01G205700 chr2D 206998094 206998774 680 False 953.000000 953 91.860000 2186 2872 1 chr2D.!!$F1 686
5 TraesCS2A01G205700 chr2B 231601700 231605032 3332 False 985.666667 2241 92.691667 1 2120 3 chr2B.!!$F2 2119
6 TraesCS2A01G205700 chrUn 112547885 112548573 688 False 1031.000000 1031 93.913000 2193 2872 1 chrUn.!!$F1 679
7 TraesCS2A01G205700 chr3D 447593284 447593960 676 False 1026.000000 1026 93.979000 2193 2872 1 chr3D.!!$F1 679
8 TraesCS2A01G205700 chr3D 155683217 155683886 669 True 992.000000 992 93.333000 2199 2872 1 chr3D.!!$R1 673
9 TraesCS2A01G205700 chr3D 580644015 580644691 676 False 987.000000 987 92.952000 2193 2872 1 chr3D.!!$F2 679
10 TraesCS2A01G205700 chr3D 609767759 609768435 676 False 965.000000 965 92.364000 2193 2872 1 chr3D.!!$F3 679
11 TraesCS2A01G205700 chr1D 422842688 422843364 676 False 1009.000000 1009 93.539000 2193 2872 1 chr1D.!!$F1 679

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
353 1749 0.39113 CCGGACGAAGCAAAGGATCA 60.391 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 3739 0.248054 GCAAATATGACACCCGCGTG 60.248 55.0 4.92 0.0 46.11 5.34 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
87 88 1.741770 GCCGGCACACAGGAACTAG 60.742 63.158 24.80 0.00 36.02 2.57
96 97 3.192422 CACACAGGAACTAGAGAGACTGG 59.808 52.174 0.00 0.00 36.02 4.00
97 98 3.074687 ACACAGGAACTAGAGAGACTGGA 59.925 47.826 0.00 0.00 36.02 3.86
98 99 4.264172 ACACAGGAACTAGAGAGACTGGAT 60.264 45.833 0.00 0.00 36.02 3.41
99 100 4.709397 CACAGGAACTAGAGAGACTGGATT 59.291 45.833 0.00 0.00 36.02 3.01
100 101 5.888724 CACAGGAACTAGAGAGACTGGATTA 59.111 44.000 0.00 0.00 36.02 1.75
101 102 6.039270 CACAGGAACTAGAGAGACTGGATTAG 59.961 46.154 0.00 0.00 36.02 1.73
165 1558 2.382746 CGACACACCATGGACAGCG 61.383 63.158 21.47 11.28 0.00 5.18
267 1663 3.642778 AACCACTCGCCGATGGACG 62.643 63.158 18.24 0.00 39.46 4.79
268 1664 3.822192 CCACTCGCCGATGGACGA 61.822 66.667 9.15 3.20 45.77 4.20
269 1665 2.579787 CACTCGCCGATGGACGAC 60.580 66.667 0.00 0.00 45.77 4.34
270 1666 3.060000 ACTCGCCGATGGACGACA 61.060 61.111 0.00 0.00 45.77 4.35
271 1667 2.579787 CTCGCCGATGGACGACAC 60.580 66.667 0.00 0.00 45.77 3.67
303 1699 0.667487 TTCAGCGAACCAGAAGCTCG 60.667 55.000 0.00 0.00 39.48 5.03
305 1701 1.373497 AGCGAACCAGAAGCTCGTG 60.373 57.895 0.00 0.00 36.33 4.35
307 1703 1.618640 GCGAACCAGAAGCTCGTGAC 61.619 60.000 0.00 0.00 35.06 3.67
353 1749 0.391130 CCGGACGAAGCAAAGGATCA 60.391 55.000 0.00 0.00 0.00 2.92
545 1947 7.569599 AGAAGAAATAAGGGTCTGTTTAGGA 57.430 36.000 0.00 0.00 0.00 2.94
546 1948 8.164057 AGAAGAAATAAGGGTCTGTTTAGGAT 57.836 34.615 0.00 0.00 0.00 3.24
547 1949 9.280456 AGAAGAAATAAGGGTCTGTTTAGGATA 57.720 33.333 0.00 0.00 0.00 2.59
549 1951 9.853177 AAGAAATAAGGGTCTGTTTAGGATATG 57.147 33.333 0.00 0.00 0.00 1.78
550 1952 9.004231 AGAAATAAGGGTCTGTTTAGGATATGT 57.996 33.333 0.00 0.00 0.00 2.29
551 1953 9.274206 GAAATAAGGGTCTGTTTAGGATATGTC 57.726 37.037 0.00 0.00 0.00 3.06
552 1954 7.931015 ATAAGGGTCTGTTTAGGATATGTCA 57.069 36.000 0.00 0.00 0.00 3.58
553 1955 5.615925 AGGGTCTGTTTAGGATATGTCAC 57.384 43.478 0.00 0.00 0.00 3.67
554 1956 5.030147 AGGGTCTGTTTAGGATATGTCACA 58.970 41.667 0.00 0.00 0.00 3.58
555 1957 5.667626 AGGGTCTGTTTAGGATATGTCACAT 59.332 40.000 0.00 0.00 0.00 3.21
556 1958 5.992217 GGGTCTGTTTAGGATATGTCACATC 59.008 44.000 0.00 0.00 0.00 3.06
557 1959 6.183361 GGGTCTGTTTAGGATATGTCACATCT 60.183 42.308 0.00 0.00 0.00 2.90
558 1960 7.015292 GGGTCTGTTTAGGATATGTCACATCTA 59.985 40.741 0.00 0.00 0.00 1.98
559 1961 8.421784 GGTCTGTTTAGGATATGTCACATCTAA 58.578 37.037 0.00 0.00 0.00 2.10
560 1962 9.469807 GTCTGTTTAGGATATGTCACATCTAAG 57.530 37.037 0.00 0.00 0.00 2.18
561 1963 9.421399 TCTGTTTAGGATATGTCACATCTAAGA 57.579 33.333 0.00 0.00 0.00 2.10
577 1979 6.580788 CATCTAAGATTGATGTCCACTCTGT 58.419 40.000 0.00 0.00 35.32 3.41
578 1980 6.611613 TCTAAGATTGATGTCCACTCTGTT 57.388 37.500 0.00 0.00 35.32 3.16
579 1981 7.009179 TCTAAGATTGATGTCCACTCTGTTT 57.991 36.000 0.00 0.00 35.32 2.83
580 1982 8.134202 TCTAAGATTGATGTCCACTCTGTTTA 57.866 34.615 0.00 0.00 35.32 2.01
581 1983 8.762645 TCTAAGATTGATGTCCACTCTGTTTAT 58.237 33.333 0.00 0.00 35.32 1.40
582 1984 7.621428 AAGATTGATGTCCACTCTGTTTATG 57.379 36.000 0.00 0.00 35.32 1.90
583 1985 6.118170 AGATTGATGTCCACTCTGTTTATGG 58.882 40.000 0.00 0.00 34.05 2.74
584 1986 4.908601 TGATGTCCACTCTGTTTATGGT 57.091 40.909 0.00 0.00 34.89 3.55
585 1987 4.832248 TGATGTCCACTCTGTTTATGGTC 58.168 43.478 0.00 0.00 34.89 4.02
586 1988 4.532126 TGATGTCCACTCTGTTTATGGTCT 59.468 41.667 0.00 0.00 34.89 3.85
587 1989 5.719563 TGATGTCCACTCTGTTTATGGTCTA 59.280 40.000 0.00 0.00 34.89 2.59
588 1990 6.384015 TGATGTCCACTCTGTTTATGGTCTAT 59.616 38.462 0.00 0.00 34.89 1.98
589 1991 6.620877 TGTCCACTCTGTTTATGGTCTATT 57.379 37.500 0.00 0.00 34.89 1.73
590 1992 7.016153 TGTCCACTCTGTTTATGGTCTATTT 57.984 36.000 0.00 0.00 34.89 1.40
591 1993 7.458397 TGTCCACTCTGTTTATGGTCTATTTT 58.542 34.615 0.00 0.00 34.89 1.82
592 1994 7.942341 TGTCCACTCTGTTTATGGTCTATTTTT 59.058 33.333 0.00 0.00 34.89 1.94
658 2060 4.963318 TGGGAGATTAGATGTGACATCC 57.037 45.455 21.05 6.28 0.00 3.51
659 2061 4.560739 TGGGAGATTAGATGTGACATCCT 58.439 43.478 21.05 11.37 0.00 3.24
665 2067 9.396022 GGAGATTAGATGTGACATCCTTAAAAA 57.604 33.333 21.05 7.53 0.00 1.94
720 2253 4.106925 GGAGAGGCTGTGGGCAGG 62.107 72.222 0.00 0.00 42.78 4.85
756 2293 4.408821 GCACACATGGGCGGAGGA 62.409 66.667 0.00 0.00 33.30 3.71
757 2294 2.124983 CACACATGGGCGGAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
758 2295 3.402681 ACACATGGGCGGAGGAGG 61.403 66.667 0.00 0.00 0.00 4.30
822 2371 2.375345 CCCAGGCTGGTATCCCGTT 61.375 63.158 30.68 0.00 35.17 4.44
826 2375 2.895372 GCTGGTATCCCGTTGCCG 60.895 66.667 0.00 0.00 0.00 5.69
827 2376 2.582436 CTGGTATCCCGTTGCCGT 59.418 61.111 0.00 0.00 0.00 5.68
958 2507 0.661020 CTTTCCCACCACGTTGACAC 59.339 55.000 0.00 0.00 0.00 3.67
1434 2983 3.078196 TCGCCCGCCATGAAGGTA 61.078 61.111 0.00 0.00 40.61 3.08
1435 2984 2.895372 CGCCCGCCATGAAGGTAC 60.895 66.667 0.00 0.00 40.61 3.34
1436 2985 2.895372 GCCCGCCATGAAGGTACG 60.895 66.667 0.00 0.00 40.61 3.67
1437 2986 2.895372 CCCGCCATGAAGGTACGC 60.895 66.667 0.00 0.00 40.61 4.42
1470 3027 0.897863 GCATGCACCCACCACCTTAA 60.898 55.000 14.21 0.00 0.00 1.85
1471 3028 1.176527 CATGCACCCACCACCTTAAG 58.823 55.000 0.00 0.00 0.00 1.85
1472 3029 1.072266 ATGCACCCACCACCTTAAGA 58.928 50.000 3.36 0.00 0.00 2.10
1929 3501 3.692406 GACGACCAGGGGAGCGTT 61.692 66.667 8.68 0.00 37.37 4.84
1936 3508 2.281761 AGGGGAGCGTTGCACAAG 60.282 61.111 0.00 0.00 0.00 3.16
1956 3528 8.507249 GCACAAGTATTCTTTGTAGAGTTTGAT 58.493 33.333 0.00 0.00 0.00 2.57
1969 3541 2.663119 GAGTTTGATTTGATTGGCGTGC 59.337 45.455 0.00 0.00 0.00 5.34
2046 3618 9.994432 GAACAATGGTTGTATCTTCTTGAATAG 57.006 33.333 0.00 0.00 44.59 1.73
2071 3645 7.940137 AGACCAAGATAGTACAGTAGTCTATGG 59.060 40.741 0.00 0.44 30.65 2.74
2120 3694 5.638234 AGAAATCGAAGTTACACTAAGGTGC 59.362 40.000 0.00 0.00 46.57 5.01
2123 3697 3.057033 TCGAAGTTACACTAAGGTGCCTC 60.057 47.826 0.00 0.00 46.57 4.70
2124 3698 3.056749 CGAAGTTACACTAAGGTGCCTCT 60.057 47.826 0.00 0.00 46.57 3.69
2125 3699 3.963428 AGTTACACTAAGGTGCCTCTG 57.037 47.619 0.00 0.00 46.57 3.35
2126 3700 3.507411 AGTTACACTAAGGTGCCTCTGA 58.493 45.455 0.00 0.00 46.57 3.27
2127 3701 3.511934 AGTTACACTAAGGTGCCTCTGAG 59.488 47.826 0.00 0.00 46.57 3.35
2128 3702 2.310779 ACACTAAGGTGCCTCTGAGA 57.689 50.000 6.17 0.00 46.57 3.27
2129 3703 2.609747 ACACTAAGGTGCCTCTGAGAA 58.390 47.619 6.17 0.00 46.57 2.87
2130 3704 2.300437 ACACTAAGGTGCCTCTGAGAAC 59.700 50.000 6.17 4.18 46.57 3.01
2131 3705 1.903183 ACTAAGGTGCCTCTGAGAACC 59.097 52.381 17.07 17.07 0.00 3.62
2132 3706 2.183679 CTAAGGTGCCTCTGAGAACCT 58.816 52.381 20.08 20.08 45.01 3.50
2133 3707 2.327325 AAGGTGCCTCTGAGAACCTA 57.673 50.000 23.75 0.00 42.25 3.08
2134 3708 2.327325 AGGTGCCTCTGAGAACCTAA 57.673 50.000 22.79 0.00 41.28 2.69
2135 3709 2.621070 AGGTGCCTCTGAGAACCTAAA 58.379 47.619 22.79 0.00 41.28 1.85
2136 3710 2.979678 AGGTGCCTCTGAGAACCTAAAA 59.020 45.455 22.79 0.00 41.28 1.52
2137 3711 3.589288 AGGTGCCTCTGAGAACCTAAAAT 59.411 43.478 22.79 6.39 41.28 1.82
2138 3712 3.942115 GGTGCCTCTGAGAACCTAAAATC 59.058 47.826 17.36 0.00 0.00 2.17
2139 3713 4.565652 GGTGCCTCTGAGAACCTAAAATCA 60.566 45.833 17.36 0.00 0.00 2.57
2140 3714 5.189180 GTGCCTCTGAGAACCTAAAATCAT 58.811 41.667 6.17 0.00 0.00 2.45
2141 3715 5.649831 GTGCCTCTGAGAACCTAAAATCATT 59.350 40.000 6.17 0.00 0.00 2.57
2142 3716 6.823689 GTGCCTCTGAGAACCTAAAATCATTA 59.176 38.462 6.17 0.00 0.00 1.90
2143 3717 7.336931 GTGCCTCTGAGAACCTAAAATCATTAA 59.663 37.037 6.17 0.00 0.00 1.40
2144 3718 7.888021 TGCCTCTGAGAACCTAAAATCATTAAA 59.112 33.333 6.17 0.00 0.00 1.52
2145 3719 8.907885 GCCTCTGAGAACCTAAAATCATTAAAT 58.092 33.333 6.17 0.00 0.00 1.40
2151 3725 9.803315 GAGAACCTAAAATCATTAAATGAACCC 57.197 33.333 0.00 0.00 43.50 4.11
2152 3726 9.320295 AGAACCTAAAATCATTAAATGAACCCA 57.680 29.630 0.00 0.00 43.50 4.51
2153 3727 9.936759 GAACCTAAAATCATTAAATGAACCCAA 57.063 29.630 0.00 0.00 43.50 4.12
2162 3736 9.748708 ATCATTAAATGAACCCAAATGATAACG 57.251 29.630 6.98 0.00 42.51 3.18
2163 3737 7.704472 TCATTAAATGAACCCAAATGATAACGC 59.296 33.333 0.00 0.00 36.11 4.84
2164 3738 4.385358 AATGAACCCAAATGATAACGCC 57.615 40.909 0.00 0.00 0.00 5.68
2165 3739 2.096248 TGAACCCAAATGATAACGCCC 58.904 47.619 0.00 0.00 0.00 6.13
2166 3740 2.096248 GAACCCAAATGATAACGCCCA 58.904 47.619 0.00 0.00 0.00 5.36
2167 3741 1.470051 ACCCAAATGATAACGCCCAC 58.530 50.000 0.00 0.00 0.00 4.61
2169 3743 0.248458 CCAAATGATAACGCCCACGC 60.248 55.000 0.00 0.00 45.53 5.34
2181 3755 4.532490 CCACGCGGGTGTCATATT 57.468 55.556 28.09 0.00 42.80 1.28
2182 3756 2.775351 CCACGCGGGTGTCATATTT 58.225 52.632 28.09 0.00 42.80 1.40
2183 3757 0.376852 CCACGCGGGTGTCATATTTG 59.623 55.000 28.09 9.05 42.80 2.32
2184 3758 0.248054 CACGCGGGTGTCATATTTGC 60.248 55.000 23.30 0.00 39.38 3.68
2185 3759 0.675208 ACGCGGGTGTCATATTTGCA 60.675 50.000 12.47 0.00 0.00 4.08
2186 3760 0.248054 CGCGGGTGTCATATTTGCAC 60.248 55.000 0.00 0.00 32.52 4.57
2187 3761 0.808125 GCGGGTGTCATATTTGCACA 59.192 50.000 10.84 0.00 33.96 4.57
2188 3762 1.405105 GCGGGTGTCATATTTGCACAT 59.595 47.619 10.84 0.00 33.96 3.21
2189 3763 2.541588 GCGGGTGTCATATTTGCACATC 60.542 50.000 10.84 3.23 33.96 3.06
2190 3764 2.286359 CGGGTGTCATATTTGCACATCG 60.286 50.000 10.84 9.92 33.96 3.84
2191 3765 2.541588 GGGTGTCATATTTGCACATCGC 60.542 50.000 10.84 0.00 42.89 4.58
2210 3784 3.320541 TCGCAATTGAAAGAAACCACCAT 59.679 39.130 10.34 0.00 0.00 3.55
2224 3798 2.034124 CCACCATATTTGGGGCTTCTG 58.966 52.381 7.15 0.00 45.95 3.02
2230 3804 4.709397 CCATATTTGGGGCTTCTGTTACAA 59.291 41.667 0.00 0.00 39.56 2.41
2266 3840 3.928375 CGCTAATCTTTTGCAAAAGCCAT 59.072 39.130 36.33 26.27 43.85 4.40
2332 3906 2.739287 CGCGGTTGAGGGCGTTTA 60.739 61.111 0.00 0.00 46.79 2.01
2334 3908 1.962306 GCGGTTGAGGGCGTTTACA 60.962 57.895 0.00 0.00 0.00 2.41
2338 3912 1.002142 GGTTGAGGGCGTTTACAACAC 60.002 52.381 0.00 0.00 42.61 3.32
2455 4029 4.394712 GCACCCGACCAGACCAGG 62.395 72.222 0.00 0.00 0.00 4.45
2567 4142 3.403624 GGTGCTGGAGATCCACCA 58.596 61.111 11.83 10.25 46.38 4.17
2670 4245 2.571757 CTACTGCGTTCGCCCAGA 59.428 61.111 14.44 0.00 33.40 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 4.238514 GTGTGTCACAGTGGAGTCTAATC 58.761 47.826 5.74 0.00 34.08 1.75
97 98 3.006967 GGTGTGTCACAGTGGAGTCTAAT 59.993 47.826 5.74 0.00 35.86 1.73
98 99 2.364324 GGTGTGTCACAGTGGAGTCTAA 59.636 50.000 5.74 0.00 35.86 2.10
99 100 1.961394 GGTGTGTCACAGTGGAGTCTA 59.039 52.381 5.74 0.00 35.86 2.59
100 101 0.753262 GGTGTGTCACAGTGGAGTCT 59.247 55.000 5.74 0.00 35.86 3.24
101 102 0.464036 TGGTGTGTCACAGTGGAGTC 59.536 55.000 5.74 0.00 35.86 3.36
139 142 1.334960 CCATGGTGTGTCGCAGTTTTC 60.335 52.381 2.57 0.00 0.00 2.29
147 151 2.382746 CGCTGTCCATGGTGTGTCG 61.383 63.158 12.58 6.70 0.00 4.35
165 1558 1.805945 CACGCCGACCTAGCTGTTC 60.806 63.158 0.00 0.00 0.00 3.18
267 1663 2.544267 CTGAAAAGTGAGAACGGGTGTC 59.456 50.000 0.00 0.00 0.00 3.67
268 1664 2.561569 CTGAAAAGTGAGAACGGGTGT 58.438 47.619 0.00 0.00 0.00 4.16
269 1665 1.264288 GCTGAAAAGTGAGAACGGGTG 59.736 52.381 0.00 0.00 0.00 4.61
270 1666 1.594331 GCTGAAAAGTGAGAACGGGT 58.406 50.000 0.00 0.00 0.00 5.28
271 1667 0.512952 CGCTGAAAAGTGAGAACGGG 59.487 55.000 0.00 0.00 0.00 5.28
279 1675 2.603173 GCTTCTGGTTCGCTGAAAAGTG 60.603 50.000 0.00 0.00 0.00 3.16
303 1699 0.952984 GCAGCCAAGTGGAGAGTCAC 60.953 60.000 0.18 0.00 37.39 3.67
305 1701 1.739562 CGCAGCCAAGTGGAGAGTC 60.740 63.158 0.18 0.00 37.39 3.36
307 1703 2.435586 CCGCAGCCAAGTGGAGAG 60.436 66.667 0.18 0.00 41.75 3.20
353 1749 2.441750 TGCTCCCCTGTTCTAAACTGTT 59.558 45.455 0.00 0.00 0.00 3.16
525 1927 9.274206 GACATATCCTAAACAGACCCTTATTTC 57.726 37.037 0.00 0.00 0.00 2.17
526 1928 8.778059 TGACATATCCTAAACAGACCCTTATTT 58.222 33.333 0.00 0.00 0.00 1.40
529 1931 6.670464 TGTGACATATCCTAAACAGACCCTTA 59.330 38.462 0.00 0.00 0.00 2.69
531 1933 5.030147 TGTGACATATCCTAAACAGACCCT 58.970 41.667 0.00 0.00 0.00 4.34
532 1934 5.353394 TGTGACATATCCTAAACAGACCC 57.647 43.478 0.00 0.00 0.00 4.46
533 1935 6.821388 AGATGTGACATATCCTAAACAGACC 58.179 40.000 8.44 0.00 0.00 3.85
534 1936 9.469807 CTTAGATGTGACATATCCTAAACAGAC 57.530 37.037 8.44 0.00 0.00 3.51
560 1962 5.882557 ACCATAAACAGAGTGGACATCAATC 59.117 40.000 0.00 0.00 40.45 2.67
561 1963 5.819991 ACCATAAACAGAGTGGACATCAAT 58.180 37.500 0.00 0.00 36.82 2.57
562 1964 5.013079 AGACCATAAACAGAGTGGACATCAA 59.987 40.000 0.00 0.00 36.82 2.57
563 1965 4.532126 AGACCATAAACAGAGTGGACATCA 59.468 41.667 0.00 0.00 36.82 3.07
564 1966 5.091261 AGACCATAAACAGAGTGGACATC 57.909 43.478 0.00 0.00 36.82 3.06
565 1967 6.814954 ATAGACCATAAACAGAGTGGACAT 57.185 37.500 0.00 0.00 36.82 3.06
566 1968 6.620877 AATAGACCATAAACAGAGTGGACA 57.379 37.500 0.00 0.00 36.82 4.02
567 1969 7.923414 AAAATAGACCATAAACAGAGTGGAC 57.077 36.000 0.00 0.00 36.82 4.02
632 2034 8.105829 GGATGTCACATCTAATCTCCCATAAAT 58.894 37.037 17.46 0.00 0.00 1.40
633 2035 7.293299 AGGATGTCACATCTAATCTCCCATAAA 59.707 37.037 17.46 0.00 0.00 1.40
634 2036 6.789457 AGGATGTCACATCTAATCTCCCATAA 59.211 38.462 17.46 0.00 0.00 1.90
635 2037 6.326161 AGGATGTCACATCTAATCTCCCATA 58.674 40.000 17.46 0.00 0.00 2.74
636 2038 5.161135 AGGATGTCACATCTAATCTCCCAT 58.839 41.667 17.46 0.00 0.00 4.00
637 2039 4.560739 AGGATGTCACATCTAATCTCCCA 58.439 43.478 17.46 0.00 0.00 4.37
638 2040 5.559148 AAGGATGTCACATCTAATCTCCC 57.441 43.478 17.46 0.00 0.00 4.30
639 2041 8.964476 TTTTAAGGATGTCACATCTAATCTCC 57.036 34.615 17.46 0.18 0.00 3.71
670 2072 9.996554 TCTTCAGTTTGTCTAATTCACATCTAA 57.003 29.630 0.00 0.00 0.00 2.10
685 2087 6.151817 GCCTCTCCATTATTTCTTCAGTTTGT 59.848 38.462 0.00 0.00 0.00 2.83
686 2088 6.376581 AGCCTCTCCATTATTTCTTCAGTTTG 59.623 38.462 0.00 0.00 0.00 2.93
687 2089 6.376581 CAGCCTCTCCATTATTTCTTCAGTTT 59.623 38.462 0.00 0.00 0.00 2.66
688 2090 5.884792 CAGCCTCTCCATTATTTCTTCAGTT 59.115 40.000 0.00 0.00 0.00 3.16
689 2091 5.045286 ACAGCCTCTCCATTATTTCTTCAGT 60.045 40.000 0.00 0.00 0.00 3.41
690 2092 5.296283 CACAGCCTCTCCATTATTTCTTCAG 59.704 44.000 0.00 0.00 0.00 3.02
691 2093 5.188434 CACAGCCTCTCCATTATTTCTTCA 58.812 41.667 0.00 0.00 0.00 3.02
692 2094 4.578105 CCACAGCCTCTCCATTATTTCTTC 59.422 45.833 0.00 0.00 0.00 2.87
693 2095 4.530875 CCACAGCCTCTCCATTATTTCTT 58.469 43.478 0.00 0.00 0.00 2.52
695 2097 3.217626 CCCACAGCCTCTCCATTATTTC 58.782 50.000 0.00 0.00 0.00 2.17
1470 3027 2.146342 CAGAGCACCGTCAACAATTCT 58.854 47.619 0.00 0.00 0.00 2.40
1471 3028 2.143122 TCAGAGCACCGTCAACAATTC 58.857 47.619 0.00 0.00 0.00 2.17
1472 3029 2.254546 TCAGAGCACCGTCAACAATT 57.745 45.000 0.00 0.00 0.00 2.32
1909 3481 3.775654 GCTCCCCTGGTCGTCTGG 61.776 72.222 0.00 0.00 0.00 3.86
1916 3488 4.643387 GTGCAACGCTCCCCTGGT 62.643 66.667 0.00 0.00 0.00 4.00
1924 3496 3.315191 ACAAAGAATACTTGTGCAACGCT 59.685 39.130 0.00 0.00 42.39 5.07
1929 3501 7.497579 TCAAACTCTACAAAGAATACTTGTGCA 59.502 33.333 0.00 0.00 36.39 4.57
1956 3528 2.254951 CGCAGCACGCCAATCAAA 59.745 55.556 0.00 0.00 37.30 2.69
1969 3541 4.404507 AAGTGCTATTACAACAACGCAG 57.595 40.909 0.00 0.00 0.00 5.18
2046 3618 7.937942 TCCATAGACTACTGTACTATCTTGGTC 59.062 40.741 0.00 0.00 0.00 4.02
2069 3643 0.957362 TCGCATTTGTGCATGTTCCA 59.043 45.000 0.00 0.00 34.41 3.53
2071 3645 4.620609 TGTTATTCGCATTTGTGCATGTTC 59.379 37.500 0.00 0.00 34.41 3.18
2125 3699 9.803315 GGGTTCATTTAATGATTTTAGGTTCTC 57.197 33.333 8.56 0.00 39.39 2.87
2126 3700 9.320295 TGGGTTCATTTAATGATTTTAGGTTCT 57.680 29.630 8.56 0.00 39.39 3.01
2127 3701 9.936759 TTGGGTTCATTTAATGATTTTAGGTTC 57.063 29.630 8.56 0.00 39.39 3.62
2136 3710 9.748708 CGTTATCATTTGGGTTCATTTAATGAT 57.251 29.630 8.56 11.81 44.06 2.45
2137 3711 7.704472 GCGTTATCATTTGGGTTCATTTAATGA 59.296 33.333 3.20 3.20 38.95 2.57
2138 3712 7.042791 GGCGTTATCATTTGGGTTCATTTAATG 60.043 37.037 0.00 0.00 0.00 1.90
2139 3713 6.983890 GGCGTTATCATTTGGGTTCATTTAAT 59.016 34.615 0.00 0.00 0.00 1.40
2140 3714 6.334202 GGCGTTATCATTTGGGTTCATTTAA 58.666 36.000 0.00 0.00 0.00 1.52
2141 3715 5.163499 GGGCGTTATCATTTGGGTTCATTTA 60.163 40.000 0.00 0.00 0.00 1.40
2142 3716 4.382577 GGGCGTTATCATTTGGGTTCATTT 60.383 41.667 0.00 0.00 0.00 2.32
2143 3717 3.132111 GGGCGTTATCATTTGGGTTCATT 59.868 43.478 0.00 0.00 0.00 2.57
2144 3718 2.693074 GGGCGTTATCATTTGGGTTCAT 59.307 45.455 0.00 0.00 0.00 2.57
2145 3719 2.096248 GGGCGTTATCATTTGGGTTCA 58.904 47.619 0.00 0.00 0.00 3.18
2146 3720 2.096248 TGGGCGTTATCATTTGGGTTC 58.904 47.619 0.00 0.00 0.00 3.62
2147 3721 1.822371 GTGGGCGTTATCATTTGGGTT 59.178 47.619 0.00 0.00 0.00 4.11
2148 3722 1.470051 GTGGGCGTTATCATTTGGGT 58.530 50.000 0.00 0.00 0.00 4.51
2149 3723 0.380378 CGTGGGCGTTATCATTTGGG 59.620 55.000 0.00 0.00 0.00 4.12
2150 3724 0.248458 GCGTGGGCGTTATCATTTGG 60.248 55.000 0.00 0.00 40.81 3.28
2151 3725 3.234368 GCGTGGGCGTTATCATTTG 57.766 52.632 0.00 0.00 40.81 2.32
2164 3738 0.376852 CAAATATGACACCCGCGTGG 59.623 55.000 8.42 8.42 44.86 4.94
2165 3739 0.248054 GCAAATATGACACCCGCGTG 60.248 55.000 4.92 0.00 46.11 5.34
2166 3740 0.675208 TGCAAATATGACACCCGCGT 60.675 50.000 4.92 0.00 0.00 6.01
2167 3741 0.248054 GTGCAAATATGACACCCGCG 60.248 55.000 0.00 0.00 31.54 6.46
2168 3742 0.808125 TGTGCAAATATGACACCCGC 59.192 50.000 0.00 0.00 34.64 6.13
2169 3743 2.286359 CGATGTGCAAATATGACACCCG 60.286 50.000 0.00 0.00 34.64 5.28
2170 3744 2.541588 GCGATGTGCAAATATGACACCC 60.542 50.000 0.00 0.00 45.45 4.61
2171 3745 2.719798 GCGATGTGCAAATATGACACC 58.280 47.619 0.00 0.00 45.45 4.16
2183 3757 3.121778 GGTTTCTTTCAATTGCGATGTGC 59.878 43.478 0.00 0.00 46.70 4.57
2184 3758 4.148696 GTGGTTTCTTTCAATTGCGATGTG 59.851 41.667 0.00 0.00 0.00 3.21
2185 3759 4.298332 GTGGTTTCTTTCAATTGCGATGT 58.702 39.130 0.00 0.00 0.00 3.06
2186 3760 3.674753 GGTGGTTTCTTTCAATTGCGATG 59.325 43.478 0.00 0.00 0.00 3.84
2187 3761 3.320541 TGGTGGTTTCTTTCAATTGCGAT 59.679 39.130 0.00 0.00 0.00 4.58
2188 3762 2.690497 TGGTGGTTTCTTTCAATTGCGA 59.310 40.909 0.00 0.00 0.00 5.10
2189 3763 3.090952 TGGTGGTTTCTTTCAATTGCG 57.909 42.857 0.00 0.00 0.00 4.85
2190 3764 7.361116 CCAAATATGGTGGTTTCTTTCAATTGC 60.361 37.037 0.00 0.00 42.18 3.56
2191 3765 7.119553 CCCAAATATGGTGGTTTCTTTCAATTG 59.880 37.037 0.00 0.00 46.01 2.32
2197 3771 3.263170 GCCCCAAATATGGTGGTTTCTTT 59.737 43.478 5.25 0.00 46.01 2.52
2210 3784 6.732896 TTTTTGTAACAGAAGCCCCAAATA 57.267 33.333 0.00 0.00 0.00 1.40
2230 3804 9.573133 CAAAAGATTAGCGATCAGGTTATTTTT 57.427 29.630 6.01 0.00 37.22 1.94
2235 3809 5.182487 TGCAAAAGATTAGCGATCAGGTTA 58.818 37.500 6.01 0.00 37.22 2.85
2266 3840 3.889196 AAACTTTTACTGAATGCGCGA 57.111 38.095 12.10 0.00 0.00 5.87
2332 3906 2.937959 AATTGGGCCCCACGTGTTGT 62.938 55.000 22.27 0.00 30.78 3.32
2334 3908 1.458588 AAATTGGGCCCCACGTGTT 60.459 52.632 22.27 1.48 30.78 3.32
2455 4029 3.160748 GGAGCTGGAGGGAGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
2567 4142 2.355193 GGAGCTCCCGCAGAACTCT 61.355 63.158 23.19 0.00 37.76 3.24
2670 4245 2.046314 CGGATTGGCCTTCACCGT 60.046 61.111 17.94 0.00 38.97 4.83


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

AutoCloner maintained by Alex Coulton.