Multiple sequence alignment - TraesCS6A01G030000

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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 TraesCS6A01G030000 chr6A 100.000 3167 0 0 1 3167 15646287 15649453 0.000000e+00 5849.0
1 TraesCS6A01G030000 chr6A 82.218 1434 228 16 973 2398 15873215 15871801 0.000000e+00 1210.0
2 TraesCS6A01G030000 chr6A 80.038 1593 258 39 829 2405 15684716 15686264 0.000000e+00 1125.0
3 TraesCS6A01G030000 chr6A 81.009 1169 183 26 969 2120 16628964 16630110 0.000000e+00 893.0
4 TraesCS6A01G030000 chr6A 81.992 261 35 9 2583 2832 16616241 16616500 8.900000e-51 211.0
5 TraesCS6A01G030000 chr6A 87.879 132 11 5 215 344 15915783 15915655 1.970000e-32 150.0
6 TraesCS6A01G030000 chr6B 84.930 2860 306 54 1 2783 26290319 26293130 0.000000e+00 2778.0
7 TraesCS6A01G030000 chr6B 81.205 1527 231 29 989 2467 26248035 26249553 0.000000e+00 1179.0
8 TraesCS6A01G030000 chr6B 80.064 1560 261 22 989 2506 26856874 26855323 0.000000e+00 1112.0
9 TraesCS6A01G030000 chr6B 80.064 1570 249 36 989 2506 26841982 26840425 0.000000e+00 1107.0
10 TraesCS6A01G030000 chr6B 80.062 1600 226 47 829 2401 26389064 26390597 0.000000e+00 1101.0
11 TraesCS6A01G030000 chr6B 80.218 1466 253 24 956 2405 26488567 26490011 0.000000e+00 1066.0
12 TraesCS6A01G030000 chr6B 80.382 1203 198 25 951 2145 59305359 59304187 0.000000e+00 880.0
13 TraesCS6A01G030000 chr6B 80.167 1200 197 29 951 2142 28471426 28472592 0.000000e+00 859.0
14 TraesCS6A01G030000 chr6B 75.777 1222 236 52 979 2171 13818937 13817747 2.130000e-156 562.0
15 TraesCS6A01G030000 chr6B 79.847 655 115 13 1755 2404 28495978 28496620 2.230000e-126 462.0
16 TraesCS6A01G030000 chr6B 88.384 198 18 3 2973 3167 26839976 26839781 1.900000e-57 233.0
17 TraesCS6A01G030000 chr6B 88.384 198 18 3 2973 3167 26854874 26854679 1.900000e-57 233.0
18 TraesCS6A01G030000 chr6B 87.562 201 22 3 2970 3167 26250217 26250417 2.460000e-56 230.0
19 TraesCS6A01G030000 chr6B 86.905 168 21 1 2669 2835 27061255 27061088 1.500000e-43 187.0
20 TraesCS6A01G030000 chr6B 87.786 131 14 2 215 344 26722863 26722734 5.470000e-33 152.0
21 TraesCS6A01G030000 chr6B 88.679 106 11 1 829 934 26721655 26721551 9.220000e-26 128.0
22 TraesCS6A01G030000 chr6B 91.525 59 4 1 10 68 26486960 26487017 2.620000e-11 80.5
23 TraesCS6A01G030000 chr6D 81.678 1883 258 34 965 2783 14422042 14423901 0.000000e+00 1485.0
24 TraesCS6A01G030000 chr6D 80.830 1591 256 31 833 2405 14483540 14485099 0.000000e+00 1203.0
25 TraesCS6A01G030000 chr6D 80.541 1182 182 27 950 2118 16368933 16370079 0.000000e+00 865.0
26 TraesCS6A01G030000 chr6D 81.988 1016 167 11 1401 2409 14518038 14519044 0.000000e+00 848.0
27 TraesCS6A01G030000 chr6D 79.811 951 158 29 1475 2409 14435570 14436502 0.000000e+00 662.0
28 TraesCS6A01G030000 chr6D 88.963 299 26 5 2546 2841 14424010 14424304 2.320000e-96 363.0
29 TraesCS6A01G030000 chr6D 82.394 142 11 4 2839 2968 14463811 14463950 9.290000e-21 111.0
30 TraesCS6A01G030000 chr1B 81.070 1458 225 39 974 2409 48062374 48060946 0.000000e+00 1116.0
31 TraesCS6A01G030000 chr2A 83.624 458 47 12 354 788 681468293 681467841 3.800000e-109 405.0
32 TraesCS6A01G030000 chr1D 96.471 170 6 0 2998 3167 82251079 82251248 6.690000e-72 281.0
33 TraesCS6A01G030000 chr4A 94.152 171 9 1 2998 3167 479132320 479132490 3.130000e-65 259.0
34 TraesCS6A01G030000 chrUn 88.384 198 18 3 2973 3167 261310675 261310870 1.900000e-57 233.0
35 TraesCS6A01G030000 chr7A 84.615 169 24 2 2669 2836 692544788 692544955 1.950000e-37 167.0
36 TraesCS6A01G030000 chr7B 82.317 164 21 6 1986 2145 513480021 513479862 5.510000e-28 135.0


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 TraesCS6A01G030000 chr6A 15646287 15649453 3166 False 5849.00 5849 100.0000 1 3167 1 chr6A.!!$F1 3166
1 TraesCS6A01G030000 chr6A 15871801 15873215 1414 True 1210.00 1210 82.2180 973 2398 1 chr6A.!!$R1 1425
2 TraesCS6A01G030000 chr6A 15684716 15686264 1548 False 1125.00 1125 80.0380 829 2405 1 chr6A.!!$F2 1576
3 TraesCS6A01G030000 chr6A 16628964 16630110 1146 False 893.00 893 81.0090 969 2120 1 chr6A.!!$F4 1151
4 TraesCS6A01G030000 chr6B 26290319 26293130 2811 False 2778.00 2778 84.9300 1 2783 1 chr6B.!!$F1 2782
5 TraesCS6A01G030000 chr6B 26389064 26390597 1533 False 1101.00 1101 80.0620 829 2401 1 chr6B.!!$F2 1572
6 TraesCS6A01G030000 chr6B 59304187 59305359 1172 True 880.00 880 80.3820 951 2145 1 chr6B.!!$R3 1194
7 TraesCS6A01G030000 chr6B 28471426 28472592 1166 False 859.00 859 80.1670 951 2142 1 chr6B.!!$F3 1191
8 TraesCS6A01G030000 chr6B 26248035 26250417 2382 False 704.50 1179 84.3835 989 3167 2 chr6B.!!$F5 2178
9 TraesCS6A01G030000 chr6B 26854679 26856874 2195 True 672.50 1112 84.2240 989 3167 2 chr6B.!!$R6 2178
10 TraesCS6A01G030000 chr6B 26839781 26841982 2201 True 670.00 1107 84.2240 989 3167 2 chr6B.!!$R5 2178
11 TraesCS6A01G030000 chr6B 26486960 26490011 3051 False 573.25 1066 85.8715 10 2405 2 chr6B.!!$F6 2395
12 TraesCS6A01G030000 chr6B 13817747 13818937 1190 True 562.00 562 75.7770 979 2171 1 chr6B.!!$R1 1192
13 TraesCS6A01G030000 chr6B 28495978 28496620 642 False 462.00 462 79.8470 1755 2404 1 chr6B.!!$F4 649
14 TraesCS6A01G030000 chr6D 14483540 14485099 1559 False 1203.00 1203 80.8300 833 2405 1 chr6D.!!$F3 1572
15 TraesCS6A01G030000 chr6D 14422042 14424304 2262 False 924.00 1485 85.3205 965 2841 2 chr6D.!!$F6 1876
16 TraesCS6A01G030000 chr6D 16368933 16370079 1146 False 865.00 865 80.5410 950 2118 1 chr6D.!!$F5 1168
17 TraesCS6A01G030000 chr6D 14518038 14519044 1006 False 848.00 848 81.9880 1401 2409 1 chr6D.!!$F4 1008
18 TraesCS6A01G030000 chr6D 14435570 14436502 932 False 662.00 662 79.8110 1475 2409 1 chr6D.!!$F1 934
19 TraesCS6A01G030000 chr1B 48060946 48062374 1428 True 1116.00 1116 81.0700 974 2409 1 chr1B.!!$R1 1435

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
942 1966 1.071471 CCCACAGACAGACCACACC 59.929 63.158 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 3688 0.108186 TCTTGGCAGGCTGTGTATCG 60.108 55.0 17.16 0.63 0.0 2.92 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
43 44 8.788325 AAGTCATCAACTACAATAAAGTACCC 57.212 34.615 0.00 0.00 37.17 3.69
48 49 7.069877 TCAACTACAATAAAGTACCCACTGT 57.930 36.000 0.00 0.00 34.36 3.55
157 308 1.745087 GGATGATGACACACGCCAATT 59.255 47.619 0.00 0.00 0.00 2.32
162 313 2.093306 TGACACACGCCAATTCTAGG 57.907 50.000 0.00 0.00 0.00 3.02
163 314 1.621317 TGACACACGCCAATTCTAGGA 59.379 47.619 0.00 0.00 0.00 2.94
164 315 2.037902 TGACACACGCCAATTCTAGGAA 59.962 45.455 0.00 0.00 0.00 3.36
252 903 3.536956 TTCATCTTACATCCACCGACC 57.463 47.619 0.00 0.00 0.00 4.79
258 909 4.157120 CATCCACCGACCCCGTCC 62.157 72.222 0.00 0.00 0.00 4.79
275 926 2.677875 CCTGGGCCTGAAGCAACC 60.678 66.667 12.58 0.00 46.50 3.77
413 1229 5.242069 TCTGAACTTTGTTCGCAAATTCA 57.758 34.783 6.05 12.50 44.97 2.57
414 1230 5.273170 TCTGAACTTTGTTCGCAAATTCAG 58.727 37.500 21.87 21.87 46.60 3.02
423 1239 6.900568 TGTTCGCAAATTCAGAAAATGTTT 57.099 29.167 0.00 0.00 0.00 2.83
429 1245 5.530543 GCAAATTCAGAAAATGTTTGGGGAA 59.469 36.000 8.41 0.00 29.74 3.97
505 1323 9.058174 TGTTCTCGATTAATAAAAACTGTTCCA 57.942 29.630 0.00 0.00 0.00 3.53
523 1341 6.215121 TGTTCCAGTTTGCATATTTGTTCAG 58.785 36.000 0.00 0.00 0.00 3.02
546 1364 9.299963 TCAGTAATTCAAAAGTTGTTCATGTTG 57.700 29.630 0.00 0.00 0.00 3.33
621 1640 7.863666 ACAATGATTTCAAACAAAATCGCAAT 58.136 26.923 5.24 0.00 44.85 3.56
769 1788 7.277981 TCAAATTTTGTTCGGGAATTTCGAAAA 59.722 29.630 15.66 10.17 46.14 2.29
790 1809 8.821894 CGAAAAATGTTTCCACTTTTAAATGGA 58.178 29.630 6.46 6.46 43.42 3.41
815 1834 1.490910 GGACCATTAACAGAGGGGGAG 59.509 57.143 0.00 0.00 0.00 4.30
816 1835 2.197465 GACCATTAACAGAGGGGGAGT 58.803 52.381 0.00 0.00 0.00 3.85
817 1836 2.170817 GACCATTAACAGAGGGGGAGTC 59.829 54.545 0.00 0.00 0.00 3.36
818 1837 2.225908 ACCATTAACAGAGGGGGAGTCT 60.226 50.000 0.00 0.00 0.00 3.24
819 1838 3.013648 ACCATTAACAGAGGGGGAGTCTA 59.986 47.826 0.00 0.00 0.00 2.59
820 1839 3.643792 CCATTAACAGAGGGGGAGTCTAG 59.356 52.174 0.00 0.00 0.00 2.43
821 1840 4.290942 CATTAACAGAGGGGGAGTCTAGT 58.709 47.826 0.00 0.00 0.00 2.57
839 1858 8.170999 AGTCTAGTGTCGACGATTAAAAATTC 57.829 34.615 11.62 0.00 36.53 2.17
846 1865 3.691498 GACGATTAAAAATTCGGCCCAG 58.309 45.455 0.00 0.00 37.41 4.45
880 1899 2.808543 GCTGAACCGAATGACAAGAACT 59.191 45.455 0.00 0.00 0.00 3.01
930 1954 2.827921 CCATTTCTTTCCTTCCCCACAG 59.172 50.000 0.00 0.00 0.00 3.66
934 1958 1.699634 TCTTTCCTTCCCCACAGACAG 59.300 52.381 0.00 0.00 0.00 3.51
942 1966 1.071471 CCCACAGACAGACCACACC 59.929 63.158 0.00 0.00 0.00 4.16
1343 2431 2.982130 CGTGGAGAGAACCCTGGG 59.018 66.667 12.28 12.28 0.00 4.45
1525 2622 3.107402 AGTGCTCACCCTATCTTCTCA 57.893 47.619 0.00 0.00 0.00 3.27
1605 2702 2.165030 AGCTGCTTGTGATATTGCCAAC 59.835 45.455 0.00 0.00 0.00 3.77
1609 2706 2.754552 GCTTGTGATATTGCCAACCTGA 59.245 45.455 0.00 0.00 0.00 3.86
1616 2713 0.114954 ATTGCCAACCTGACCATGGT 59.885 50.000 19.89 19.89 39.91 3.55
1620 2717 2.225242 TGCCAACCTGACCATGGTTATT 60.225 45.455 20.85 4.09 45.05 1.40
1621 2718 2.831526 GCCAACCTGACCATGGTTATTT 59.168 45.455 20.85 8.28 45.05 1.40
1636 2733 1.607225 TATTTGGGGGATGCTGACCT 58.393 50.000 0.00 0.00 0.00 3.85
1639 2736 3.866582 GGGGGATGCTGACCTCCG 61.867 72.222 0.00 0.00 38.37 4.63
1715 2812 1.003580 TGGCTCTGGGATGTTCAGAAC 59.996 52.381 6.32 6.32 40.29 3.01
1812 2909 2.990066 GGTCTGATACCCAAGTGAGG 57.010 55.000 0.00 0.00 43.16 3.86
1814 2911 2.838202 GGTCTGATACCCAAGTGAGGAA 59.162 50.000 0.00 0.00 43.16 3.36
1821 2918 1.985159 ACCCAAGTGAGGAATGCTGTA 59.015 47.619 0.00 0.00 0.00 2.74
1858 2955 1.672356 CTGGGCAGGTCAAAGGACG 60.672 63.158 0.00 0.00 45.28 4.79
1860 2957 2.281484 GGCAGGTCAAAGGACGCA 60.281 61.111 0.00 0.00 45.28 5.24
1888 2985 2.656560 CAGGTCCGAGTTCCTGTTAG 57.343 55.000 3.38 0.00 44.19 2.34
1921 3018 1.659794 GAACCCGTGTGCATTGCTT 59.340 52.632 10.49 0.00 0.00 3.91
1995 3092 6.856426 GGTGCTATGTTGTAAAGTTTCTCAAC 59.144 38.462 20.27 20.27 40.03 3.18
2064 3161 2.943449 AGACCGAGAAGGATTTCGTC 57.057 50.000 0.00 0.00 45.00 4.20
2067 3164 1.542915 ACCGAGAAGGATTTCGTCGAA 59.457 47.619 2.90 2.90 45.00 3.71
2147 3244 1.228552 GCAAAGGGGAAGTGCCAGA 60.229 57.895 0.00 0.00 38.95 3.86
2148 3245 1.246737 GCAAAGGGGAAGTGCCAGAG 61.247 60.000 0.00 0.00 38.95 3.35
2154 3251 2.110721 AGGGGAAGTGCCAGAGAATTTT 59.889 45.455 0.00 0.00 38.95 1.82
2234 3336 8.396272 ACAAAGTTTTCACTCTGCATAGTAAT 57.604 30.769 4.19 0.00 30.45 1.89
2251 3355 9.555727 GCATAGTAATCTGGTAATTCCTGTTTA 57.444 33.333 0.00 0.00 36.66 2.01
2274 3378 5.140454 AGGTGTTCTTTGCCAAACTAGATT 58.860 37.500 0.00 0.00 0.00 2.40
2336 3445 5.565592 TGGTCATTGCTAAATGCTAACTG 57.434 39.130 0.00 0.00 42.55 3.16
2491 3630 4.763793 CCAGTTCCATTCTCTCATGTGTTT 59.236 41.667 0.00 0.00 0.00 2.83
2493 3632 6.128172 CCAGTTCCATTCTCTCATGTGTTTAC 60.128 42.308 0.00 0.00 0.00 2.01
2512 3651 8.617809 GTGTTTACATTTTAAGAGTGAACTGGA 58.382 33.333 0.00 0.00 34.19 3.86
2519 3658 5.623956 TTAAGAGTGAACTGGAAAGTGGA 57.376 39.130 0.00 0.00 0.00 4.02
2526 3665 3.960102 TGAACTGGAAAGTGGAATTTGCT 59.040 39.130 0.00 0.00 32.30 3.91
2547 3710 1.906105 GCACCCCACCTTCCGATACA 61.906 60.000 0.00 0.00 0.00 2.29
2566 3729 1.303888 CAGCCTGCCAAGATGGTGT 60.304 57.895 0.00 0.00 40.46 4.16
2577 3740 4.623886 GCCAAGATGGTGTTCAGTGAGATA 60.624 45.833 0.00 0.00 40.46 1.98
2583 3746 6.876257 AGATGGTGTTCAGTGAGATAAAACTC 59.124 38.462 0.00 0.00 37.42 3.01
2598 3761 4.519906 AAAACTCCTTCCACCAAGAAGA 57.480 40.909 2.91 0.00 45.08 2.87
2599 3762 4.519906 AAACTCCTTCCACCAAGAAGAA 57.480 40.909 2.91 0.00 45.08 2.52
2603 3766 3.754965 TCCTTCCACCAAGAAGAACATG 58.245 45.455 2.91 0.00 45.08 3.21
2610 3773 2.375174 ACCAAGAAGAACATGTGGCCTA 59.625 45.455 3.32 0.00 32.27 3.93
2622 3785 1.419762 TGTGGCCTAAAACTCTGCTCA 59.580 47.619 3.32 0.00 0.00 4.26
2625 4135 2.289694 TGGCCTAAAACTCTGCTCACTC 60.290 50.000 3.32 0.00 0.00 3.51
2654 4259 7.496529 TTTTTGAGAAGTACACCTCAATCTG 57.503 36.000 22.28 0.00 45.43 2.90
2682 4288 9.262358 CTGGTAGATATCCTTTTGTTAGTAAGC 57.738 37.037 0.00 0.00 0.00 3.09
2739 4346 5.384336 TCTTCTGGTCATTGGTTGATTTCA 58.616 37.500 0.00 0.00 36.54 2.69
2765 4372 2.481568 TGAAATCTGCACTTGCTTCTCG 59.518 45.455 2.33 0.00 42.66 4.04
2793 4400 8.400186 TGTATCATTGCTTCATGTCATTAGTTG 58.600 33.333 0.00 0.00 0.00 3.16
2841 4448 1.352083 AGCTGCAGAACTGTAGGGAA 58.648 50.000 20.43 0.00 42.45 3.97
2853 4493 7.012704 CAGAACTGTAGGGAAAATATCATGTGG 59.987 40.741 0.00 0.00 0.00 4.17
2885 4527 6.579865 AGTGTCCTGGTTATATTTTACCTCG 58.420 40.000 0.00 0.00 35.41 4.63
2911 4563 7.411486 TTTAATGTGGTCCTGTTTTTCTTGA 57.589 32.000 0.00 0.00 0.00 3.02
2917 4569 4.517453 TGGTCCTGTTTTTCTTGATTACGG 59.483 41.667 0.00 0.00 0.00 4.02
2918 4570 4.082949 GGTCCTGTTTTTCTTGATTACGGG 60.083 45.833 0.00 0.00 36.74 5.28
2968 4621 0.029300 CTTGTGCGTTGGTTGTCAGG 59.971 55.000 0.00 0.00 0.00 3.86
2975 4677 0.668535 GTTGGTTGTCAGGTTGCCTC 59.331 55.000 0.00 0.00 0.00 4.70
3004 4707 6.870971 TTCTGTTGTTTCCATACAGGTTAC 57.129 37.500 0.00 0.00 39.71 2.50
3011 4714 3.323774 TCCATACAGGTTACTCGGGAT 57.676 47.619 0.00 0.00 39.02 3.85
3023 4726 7.813148 CAGGTTACTCGGGATTACATACTTATG 59.187 40.741 0.00 0.00 39.55 1.90
3028 4731 7.051623 ACTCGGGATTACATACTTATGCAAAA 58.948 34.615 0.00 0.00 37.19 2.44
3057 4762 1.000283 TGTTTTAATTGCTGCCACGGG 60.000 47.619 0.00 0.00 0.00 5.28
3060 4765 1.621992 TTAATTGCTGCCACGGGAAA 58.378 45.000 0.00 0.00 0.00 3.13
3067 4772 1.228003 TGCCACGGGAAATCGTTGT 60.228 52.632 0.00 0.00 41.86 3.32
3100 4805 4.512944 TGTCACAAGAGATTTGAAGAGCAC 59.487 41.667 0.00 0.00 0.00 4.40
3112 4817 8.295288 AGATTTGAAGAGCACAGTTTTTCTATG 58.705 33.333 0.00 0.00 0.00 2.23
3155 4860 3.245443 TGGACCTGGAGATAGATAGCCTC 60.245 52.174 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.097047 CGACTAACTTGTGCAAAATTTACAGTG 60.097 37.037 1.08 0.00 0.00 3.66
48 49 7.917597 TGTACGACTAACTTGTGCAAAATTTA 58.082 30.769 0.00 0.00 0.00 1.40
228 879 5.357032 GGTCGGTGGATGTAAGATGAATTTT 59.643 40.000 0.00 0.00 0.00 1.82
258 909 2.677875 GGTTGCTTCAGGCCCAGG 60.678 66.667 0.00 0.00 40.92 4.45
275 926 3.217626 AGAAGCTCTTGGGTTTCAACAG 58.782 45.455 0.31 0.00 35.61 3.16
304 955 1.975660 TTTTGGTTTGCTCTAGCCGT 58.024 45.000 0.00 0.00 41.18 5.68
413 1229 9.859152 TTTTATCAAATTCCCCAAACATTTTCT 57.141 25.926 0.00 0.00 0.00 2.52
505 1323 9.979578 TTGAATTACTGAACAAATATGCAAACT 57.020 25.926 0.00 0.00 0.00 2.66
523 1341 9.081997 TGACAACATGAACAACTTTTGAATTAC 57.918 29.630 0.00 0.00 0.00 1.89
733 1752 6.426327 CCGAACAAAATTTGAAAATGGGAAC 58.574 36.000 13.19 0.00 0.00 3.62
734 1753 5.529060 CCCGAACAAAATTTGAAAATGGGAA 59.471 36.000 13.19 0.00 33.52 3.97
740 1759 7.277981 TCGAAATTCCCGAACAAAATTTGAAAA 59.722 29.630 13.19 0.00 33.85 2.29
753 1772 5.692654 GGAAACATTTTTCGAAATTCCCGAA 59.307 36.000 21.70 10.01 41.97 4.30
790 1809 4.106341 CCCCCTCTGTTAATGGTCCAATAT 59.894 45.833 0.00 0.00 0.00 1.28
792 1811 2.244769 CCCCCTCTGTTAATGGTCCAAT 59.755 50.000 0.00 0.00 0.00 3.16
815 1834 7.103021 CGAATTTTTAATCGTCGACACTAGAC 58.897 38.462 17.16 0.00 34.48 2.59
816 1835 6.252015 CCGAATTTTTAATCGTCGACACTAGA 59.748 38.462 17.16 4.76 37.36 2.43
817 1836 6.400422 CCGAATTTTTAATCGTCGACACTAG 58.600 40.000 17.16 0.00 37.36 2.57
818 1837 5.220265 GCCGAATTTTTAATCGTCGACACTA 60.220 40.000 17.16 0.01 37.36 2.74
819 1838 4.435121 GCCGAATTTTTAATCGTCGACACT 60.435 41.667 17.16 1.12 37.36 3.55
820 1839 3.777161 GCCGAATTTTTAATCGTCGACAC 59.223 43.478 17.16 0.00 37.36 3.67
821 1840 3.181518 GGCCGAATTTTTAATCGTCGACA 60.182 43.478 17.16 3.13 37.36 4.35
880 1899 1.826720 GAGAATGGGCTGCCATTTTCA 59.173 47.619 22.05 9.11 39.53 2.69
930 1954 3.751518 AGGTATTTTGGTGTGGTCTGTC 58.248 45.455 0.00 0.00 0.00 3.51
934 1958 2.081462 CGGAGGTATTTTGGTGTGGTC 58.919 52.381 0.00 0.00 0.00 4.02
942 1966 2.819552 CGGCGGCGGAGGTATTTTG 61.820 63.158 25.36 0.00 0.00 2.44
1428 2519 1.663074 GGAGACGATGGATCTGCGC 60.663 63.158 0.00 0.00 0.00 6.09
1525 2622 2.048023 TCGTATCAAGGTCCCGCGT 61.048 57.895 4.92 0.00 0.00 6.01
1605 2702 2.387757 CCCCAAATAACCATGGTCAGG 58.612 52.381 20.07 14.89 34.79 3.86
1609 2706 2.959171 GCATCCCCCAAATAACCATGGT 60.959 50.000 13.00 13.00 34.79 3.55
1616 2713 1.929494 AGGTCAGCATCCCCCAAATAA 59.071 47.619 0.00 0.00 0.00 1.40
1620 2717 2.308722 GGAGGTCAGCATCCCCCAA 61.309 63.158 0.00 0.00 39.51 4.12
1621 2718 2.692368 GGAGGTCAGCATCCCCCA 60.692 66.667 0.00 0.00 39.51 4.96
1657 2754 2.819595 GGCGCATGTCACCATCGT 60.820 61.111 10.83 0.00 0.00 3.73
1812 2909 2.634940 TGGAGCCCTAGATACAGCATTC 59.365 50.000 0.00 0.00 0.00 2.67
1814 2911 2.405618 TGGAGCCCTAGATACAGCAT 57.594 50.000 0.00 0.00 0.00 3.79
1821 2918 0.110104 GCAGCATTGGAGCCCTAGAT 59.890 55.000 0.00 0.00 34.23 1.98
1888 2985 3.650950 TTCCAGCCCCACCTCAGC 61.651 66.667 0.00 0.00 0.00 4.26
1913 3010 4.928661 ATTATCGGTCGATAAGCAATGC 57.071 40.909 23.86 0.00 46.26 3.56
1921 3018 6.879276 AAGACAGAGAATTATCGGTCGATA 57.121 37.500 21.99 8.76 45.50 2.92
1995 3092 3.970610 CGCGATCTAGCAATCCATTTTTG 59.029 43.478 0.00 0.00 36.85 2.44
1996 3093 3.876914 TCGCGATCTAGCAATCCATTTTT 59.123 39.130 3.71 0.00 36.85 1.94
2064 3161 6.147821 CCTTGTGAGGGCATATATACTTTTCG 59.852 42.308 0.00 0.00 39.55 3.46
2067 3164 6.763715 TCCTTGTGAGGGCATATATACTTT 57.236 37.500 0.00 0.00 43.72 2.66
2147 3244 9.753674 TCCTGGTTCATGTAAATCTAAAATTCT 57.246 29.630 0.00 0.00 0.00 2.40
2154 3251 5.104527 CCCACTCCTGGTTCATGTAAATCTA 60.105 44.000 0.00 0.00 35.46 1.98
2234 3336 5.836024 ACACCTAAACAGGAATTACCAGA 57.164 39.130 0.00 0.00 42.04 3.86
2251 3355 4.164843 TCTAGTTTGGCAAAGAACACCT 57.835 40.909 13.94 8.25 0.00 4.00
2274 3378 7.120579 CAGGCATACTACAGAAAATAACCAACA 59.879 37.037 0.00 0.00 0.00 3.33
2356 3469 5.191522 TCAACATATCAGGGTTCAGGAATGA 59.808 40.000 0.00 0.00 0.00 2.57
2357 3470 5.439721 TCAACATATCAGGGTTCAGGAATG 58.560 41.667 0.00 0.00 0.00 2.67
2491 3630 8.836413 CACTTTCCAGTTCACTCTTAAAATGTA 58.164 33.333 0.00 0.00 0.00 2.29
2493 3632 7.013274 TCCACTTTCCAGTTCACTCTTAAAATG 59.987 37.037 0.00 0.00 0.00 2.32
2507 3646 2.629617 CCAGCAAATTCCACTTTCCAGT 59.370 45.455 0.00 0.00 0.00 4.00
2512 3651 1.070601 GGTGCCAGCAAATTCCACTTT 59.929 47.619 0.00 0.00 0.00 2.66
2519 3658 2.216331 GGTGGGGTGCCAGCAAATT 61.216 57.895 0.00 0.00 38.01 1.82
2541 3688 0.108186 TCTTGGCAGGCTGTGTATCG 60.108 55.000 17.16 0.63 0.00 2.92
2547 3710 1.303888 CACCATCTTGGCAGGCTGT 60.304 57.895 17.16 0.00 42.67 4.40
2566 3729 6.231211 GTGGAAGGAGTTTTATCTCACTGAA 58.769 40.000 0.00 0.00 36.30 3.02
2577 3740 4.519906 TCTTCTTGGTGGAAGGAGTTTT 57.480 40.909 0.00 0.00 41.94 2.43
2583 3746 3.254166 CACATGTTCTTCTTGGTGGAAGG 59.746 47.826 0.00 0.00 41.94 3.46
2598 3761 2.558359 GCAGAGTTTTAGGCCACATGTT 59.442 45.455 5.01 0.00 0.00 2.71
2599 3762 2.162681 GCAGAGTTTTAGGCCACATGT 58.837 47.619 5.01 0.00 0.00 3.21
2603 3766 1.807142 GTGAGCAGAGTTTTAGGCCAC 59.193 52.381 5.01 0.00 0.00 5.01
2644 4249 5.777732 GGATATCTACCAGACAGATTGAGGT 59.222 44.000 2.05 0.00 34.58 3.85
2652 4257 8.478877 ACTAACAAAAGGATATCTACCAGACAG 58.521 37.037 2.05 0.00 0.00 3.51
2700 4307 6.226787 ACCAGAAGAAGCATATCTTAATCGG 58.773 40.000 0.14 2.33 39.70 4.18
2739 4346 5.709164 AGAAGCAAGTGCAGATTTCAGTAAT 59.291 36.000 6.00 0.00 45.16 1.89
2765 4372 8.400947 ACTAATGACATGAAGCAATGATACAAC 58.599 33.333 0.00 0.00 0.00 3.32
2793 4400 5.178809 ACAACTAACTGTAAGGCGTGAATTC 59.821 40.000 0.00 0.00 39.30 2.17
2880 4522 1.628846 AGGACCACATTAAAGCGAGGT 59.371 47.619 0.00 0.00 0.00 3.85
2885 4527 5.842907 AGAAAAACAGGACCACATTAAAGC 58.157 37.500 0.00 0.00 0.00 3.51
2911 4563 4.648651 AGCACTAACAAAGAACCCGTAAT 58.351 39.130 0.00 0.00 0.00 1.89
2917 4569 4.793028 GCAAAGGAGCACTAACAAAGAACC 60.793 45.833 0.00 0.00 0.00 3.62
2918 4570 4.202010 TGCAAAGGAGCACTAACAAAGAAC 60.202 41.667 0.00 0.00 40.11 3.01
2955 4608 1.101049 AGGCAACCTGACAACCAACG 61.101 55.000 0.00 0.00 29.57 4.10
2956 4609 0.668535 GAGGCAACCTGACAACCAAC 59.331 55.000 0.00 0.00 31.76 3.77
2968 4621 4.483476 ACAACAGAAAATACGAGGCAAC 57.517 40.909 0.00 0.00 0.00 4.17
3004 4707 7.441157 TCTTTTGCATAAGTATGTAATCCCGAG 59.559 37.037 15.30 0.00 37.94 4.63
3028 4731 7.384932 GTGGCAGCAATTAAAACAGTATTTTCT 59.615 33.333 0.00 0.00 0.00 2.52
3057 4762 5.912396 TGACAATTACTTGCACAACGATTTC 59.088 36.000 0.00 0.00 35.69 2.17
3060 4765 4.274705 TGTGACAATTACTTGCACAACGAT 59.725 37.500 15.45 0.00 41.76 3.73
3067 4772 6.882610 AATCTCTTGTGACAATTACTTGCA 57.117 33.333 0.00 0.00 35.69 4.08
3100 4805 8.671921 AGTAAGATCATGCACATAGAAAAACTG 58.328 33.333 0.00 0.00 0.00 3.16
3112 4817 6.201806 GTCCACATCTAAGTAAGATCATGCAC 59.798 42.308 0.00 0.00 43.42 4.57
3117 4822 5.363868 CCAGGTCCACATCTAAGTAAGATCA 59.636 44.000 0.00 0.00 43.42 2.92


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

AutoCloner maintained by Alex Coulton.