Multiple sequence alignment - TraesCS4B01G205400

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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 TraesCS4B01G205400 chr4B 100.000 2967 0 0 1 2967 437746707 437749673 0.000000e+00 5480.0
1 TraesCS4B01G205400 chr4B 81.893 243 32 10 1977 2212 57527220 57527457 8.390000e-46 195.0
2 TraesCS4B01G205400 chr4D 89.323 2763 152 61 301 2965 354035877 354038594 0.000000e+00 3336.0
3 TraesCS4B01G205400 chr4D 91.318 311 23 3 2 309 354029122 354029431 3.540000e-114 422.0
4 TraesCS4B01G205400 chr4A 89.223 2060 124 42 965 2965 110910417 110908397 0.000000e+00 2484.0
5 TraesCS4B01G205400 chr4A 85.137 989 76 23 1 931 110911388 110910413 0.000000e+00 946.0
6 TraesCS4B01G205400 chr2D 91.489 611 52 0 1191 1801 323561486 323562096 0.000000e+00 841.0
7 TraesCS4B01G205400 chr2D 91.806 598 49 0 1191 1788 323516937 323516340 0.000000e+00 833.0
8 TraesCS4B01G205400 chr2D 82.143 112 11 7 2857 2965 245481460 245481355 1.470000e-13 87.9
9 TraesCS4B01G205400 chr2D 83.544 79 12 1 371 448 23746441 23746519 4.100000e-09 73.1
10 TraesCS4B01G205400 chr2A 84.767 860 104 19 963 1801 407092596 407091743 0.000000e+00 837.0
11 TraesCS4B01G205400 chr2A 90.835 611 56 0 1191 1801 406964177 406963567 0.000000e+00 819.0
12 TraesCS4B01G205400 chr2A 91.429 595 51 0 1191 1785 406997065 406997659 0.000000e+00 817.0
13 TraesCS4B01G205400 chr2A 82.833 233 34 5 1980 2207 692710592 692710361 1.390000e-48 204.0
14 TraesCS4B01G205400 chr2A 82.143 112 11 7 2857 2965 334943410 334943515 1.470000e-13 87.9
15 TraesCS4B01G205400 chr2A 83.784 74 11 1 376 448 41269550 41269623 5.310000e-08 69.4
16 TraesCS4B01G205400 chr2B 87.535 714 75 10 1079 1782 111669410 111668701 0.000000e+00 813.0
17 TraesCS4B01G205400 chr2B 90.671 611 57 0 1191 1801 391523438 391524048 0.000000e+00 813.0
18 TraesCS4B01G205400 chr2B 83.482 224 28 9 1980 2200 708245542 708245759 1.800000e-47 200.0
19 TraesCS4B01G205400 chr2B 82.812 128 19 3 2688 2812 699748680 699748807 8.690000e-21 111.0
20 TraesCS4B01G205400 chr3A 89.627 241 17 3 396 630 744052800 744052562 1.730000e-77 300.0
21 TraesCS4B01G205400 chr3A 87.500 48 6 0 401 448 547982313 547982360 4.130000e-04 56.5
22 TraesCS4B01G205400 chr6B 83.886 211 30 4 1997 2205 516084159 516083951 6.490000e-47 198.0
23 TraesCS4B01G205400 chr6B 81.197 234 36 7 1980 2207 670039271 670039502 6.530000e-42 182.0
24 TraesCS4B01G205400 chr7B 81.466 232 38 4 1977 2204 602638913 602639143 5.050000e-43 185.0
25 TraesCS4B01G205400 chr7B 83.486 109 15 2 2857 2965 88336764 88336659 6.770000e-17 99.0
26 TraesCS4B01G205400 chr5D 81.900 221 35 4 1986 2202 214614529 214614310 6.530000e-42 182.0
27 TraesCS4B01G205400 chr5D 96.875 32 1 0 408 439 348487304 348487273 1.000000e-03 54.7
28 TraesCS4B01G205400 chr3D 76.080 301 46 19 2688 2965 528344969 528344672 1.860000e-27 134.0
29 TraesCS4B01G205400 chr3D 74.503 302 50 17 2688 2965 436959532 436959234 4.040000e-19 106.0
30 TraesCS4B01G205400 chr7D 82.301 113 14 5 2855 2965 30951744 30951636 3.150000e-15 93.5
31 TraesCS4B01G205400 chr3B 78.767 146 19 12 2817 2960 341300279 341300414 1.470000e-13 87.9
32 TraesCS4B01G205400 chrUn 81.250 112 12 7 2857 2965 24546183 24546288 6.820000e-12 82.4
33 TraesCS4B01G205400 chr1A 82.022 89 14 2 366 452 492234440 492234352 1.140000e-09 75.0


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 TraesCS4B01G205400 chr4B 437746707 437749673 2966 False 5480 5480 100.000 1 2967 1 chr4B.!!$F2 2966
1 TraesCS4B01G205400 chr4D 354035877 354038594 2717 False 3336 3336 89.323 301 2965 1 chr4D.!!$F2 2664
2 TraesCS4B01G205400 chr4A 110908397 110911388 2991 True 1715 2484 87.180 1 2965 2 chr4A.!!$R1 2964
3 TraesCS4B01G205400 chr2D 323561486 323562096 610 False 841 841 91.489 1191 1801 1 chr2D.!!$F2 610
4 TraesCS4B01G205400 chr2D 323516340 323516937 597 True 833 833 91.806 1191 1788 1 chr2D.!!$R2 597
5 TraesCS4B01G205400 chr2A 407091743 407092596 853 True 837 837 84.767 963 1801 1 chr2A.!!$R2 838
6 TraesCS4B01G205400 chr2A 406963567 406964177 610 True 819 819 90.835 1191 1801 1 chr2A.!!$R1 610
7 TraesCS4B01G205400 chr2A 406997065 406997659 594 False 817 817 91.429 1191 1785 1 chr2A.!!$F3 594
8 TraesCS4B01G205400 chr2B 111668701 111669410 709 True 813 813 87.535 1079 1782 1 chr2B.!!$R1 703
9 TraesCS4B01G205400 chr2B 391523438 391524048 610 False 813 813 90.671 1191 1801 1 chr2B.!!$F1 610

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
575 594 0.172803 GCCTCCGACAGTCACGTATT 59.827 55.0 0.41 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2593 0.031111 TGATAGGTGGTGCTAGGGCT 60.031 55.0 0.0 0.0 39.59 5.19 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
17 18 3.121019 CGGCTAGGGAGAAGGTCG 58.879 66.667 0.00 0.00 0.00 4.79
19 20 2.134933 GGCTAGGGAGAAGGTCGGG 61.135 68.421 0.00 0.00 0.00 5.14
21 22 2.042230 TAGGGAGAAGGTCGGGGC 60.042 66.667 0.00 0.00 0.00 5.80
39 41 1.152963 CGGTGGCCTTTAGGGATGG 60.153 63.158 3.32 0.00 37.23 3.51
40 42 1.455773 GGTGGCCTTTAGGGATGGC 60.456 63.158 3.32 0.00 45.47 4.40
43 45 3.847621 GCCTTTAGGGATGGCAGC 58.152 61.111 0.00 0.00 45.50 5.25
66 68 1.874345 GAAGGCCTTCGGAGTCGTCA 61.874 60.000 29.09 0.00 37.69 4.35
74 76 0.253894 TCGGAGTCGTCATAGGACCA 59.746 55.000 1.23 0.00 41.13 4.02
75 77 1.100510 CGGAGTCGTCATAGGACCAA 58.899 55.000 1.23 0.00 41.13 3.67
78 80 1.136500 GAGTCGTCATAGGACCAACCC 59.864 57.143 1.23 0.00 41.13 4.11
79 81 0.899720 GTCGTCATAGGACCAACCCA 59.100 55.000 1.23 0.00 41.13 4.51
87 89 2.840753 GGACCAACCCAGGAGGCAA 61.841 63.158 0.00 0.00 40.58 4.52
89 91 2.069165 GACCAACCCAGGAGGCAAGT 62.069 60.000 0.00 0.00 40.58 3.16
106 108 1.154599 GTGTGCATGTGTTCGCTCG 60.155 57.895 0.00 0.00 0.00 5.03
107 109 1.594021 TGTGCATGTGTTCGCTCGT 60.594 52.632 0.00 0.00 0.00 4.18
120 122 2.383527 GCTCGTGCGGTCCTCAAAG 61.384 63.158 0.00 0.00 0.00 2.77
131 133 3.055385 CGGTCCTCAAAGTTGGGAGATAA 60.055 47.826 6.42 0.00 32.87 1.75
132 134 4.262617 GGTCCTCAAAGTTGGGAGATAAC 58.737 47.826 6.42 0.00 32.87 1.89
143 145 5.782845 AGTTGGGAGATAACTTCACTTCTCT 59.217 40.000 0.00 0.00 34.91 3.10
144 146 6.271159 AGTTGGGAGATAACTTCACTTCTCTT 59.729 38.462 0.00 0.00 34.91 2.85
168 170 3.776969 ACTATCAAGCTTGTCCCTCATGA 59.223 43.478 25.19 3.78 0.00 3.07
214 216 9.736023 GAAAATTATCTTAATGTGTGATCCCAC 57.264 33.333 0.79 0.79 43.46 4.61
217 219 4.860802 TCTTAATGTGTGATCCCACCAT 57.139 40.909 5.83 0.00 42.53 3.55
219 221 5.680619 TCTTAATGTGTGATCCCACCATAC 58.319 41.667 5.83 0.00 42.53 2.39
222 224 1.280710 TGTGTGATCCCACCATACACC 59.719 52.381 5.83 0.00 42.53 4.16
226 228 1.064758 TGATCCCACCATACACCAAGC 60.065 52.381 0.00 0.00 0.00 4.01
241 243 3.097877 CCAAGCTTGGTCCTCAAAAAC 57.902 47.619 33.46 0.00 43.43 2.43
248 250 5.103687 GCTTGGTCCTCAAAAACGTAAAAA 58.896 37.500 0.00 0.00 34.56 1.94
291 293 7.774625 TCATATGTCAATCCTAGAAATTGCACA 59.225 33.333 1.90 14.00 34.73 4.57
292 294 8.573885 CATATGTCAATCCTAGAAATTGCACAT 58.426 33.333 21.70 21.70 37.87 3.21
294 296 7.936496 TGTCAATCCTAGAAATTGCACATAA 57.064 32.000 11.08 0.00 34.73 1.90
327 329 4.894784 TGCATAATAGCAAGCCTACTACC 58.105 43.478 0.00 0.00 42.46 3.18
328 330 4.346709 TGCATAATAGCAAGCCTACTACCA 59.653 41.667 0.00 0.00 42.46 3.25
335 337 2.790433 CAAGCCTACTACCAAGCCAAA 58.210 47.619 0.00 0.00 0.00 3.28
357 359 6.757897 AATCGACTTAATTTGCAATCTCCA 57.242 33.333 0.00 0.00 0.00 3.86
368 371 2.289631 TGCAATCTCCATGTCACGACTT 60.290 45.455 0.00 0.00 0.00 3.01
394 397 8.814038 ACTCCATCCCATAATATAAAAGCATC 57.186 34.615 0.00 0.00 0.00 3.91
511 530 4.629065 CGTCGCTCAACTTAGAAATCAAC 58.371 43.478 0.00 0.00 0.00 3.18
575 594 0.172803 GCCTCCGACAGTCACGTATT 59.827 55.000 0.41 0.00 0.00 1.89
879 941 2.166270 GCTCTTTCAAGGACAGCGG 58.834 57.895 0.00 0.00 0.00 5.52
895 957 4.223953 ACAGCGGAAGGAGGATTATCTTA 58.776 43.478 0.00 0.00 0.00 2.10
896 958 4.282195 ACAGCGGAAGGAGGATTATCTTAG 59.718 45.833 0.00 0.00 0.00 2.18
897 959 3.835395 AGCGGAAGGAGGATTATCTTAGG 59.165 47.826 0.00 0.00 0.00 2.69
898 960 3.055747 GCGGAAGGAGGATTATCTTAGGG 60.056 52.174 0.00 0.00 0.00 3.53
899 961 4.417437 CGGAAGGAGGATTATCTTAGGGA 58.583 47.826 0.00 0.00 0.00 4.20
926 988 9.507329 AACAGTATTGAATCAGTTTGATGTACT 57.493 29.630 0.00 0.00 37.15 2.73
938 1000 8.675504 TCAGTTTGATGTACTACTACTAGCTTC 58.324 37.037 0.00 0.00 0.00 3.86
947 1009 6.579850 ACTACTACTAGCTTCCTTAGGACT 57.420 41.667 0.00 0.00 0.00 3.85
950 1012 3.897141 ACTAGCTTCCTTAGGACTTGC 57.103 47.619 0.00 6.23 0.00 4.01
951 1013 3.173965 ACTAGCTTCCTTAGGACTTGCA 58.826 45.455 17.75 0.00 0.00 4.08
952 1014 2.777832 AGCTTCCTTAGGACTTGCAG 57.222 50.000 17.75 7.49 0.00 4.41
953 1015 1.090728 GCTTCCTTAGGACTTGCAGC 58.909 55.000 0.00 2.97 0.00 5.25
955 1017 1.280421 CTTCCTTAGGACTTGCAGCCT 59.720 52.381 0.00 9.41 38.31 4.58
957 1019 1.705186 TCCTTAGGACTTGCAGCCTTT 59.295 47.619 9.70 0.00 35.73 3.11
1035 1112 1.040646 ACAGCGACAACAAGGAGAGA 58.959 50.000 0.00 0.00 0.00 3.10
1058 1135 8.924511 AGAAAATTAGAAACACAGATCAAGGA 57.075 30.769 0.00 0.00 0.00 3.36
1138 1223 8.274322 TGATCCTCTTCTTAATTCTTATTGCCA 58.726 33.333 0.00 0.00 0.00 4.92
1142 1227 5.588648 TCTTCTTAATTCTTATTGCCACGGG 59.411 40.000 0.00 0.00 0.00 5.28
1174 1259 7.830940 AGATTGATCTGATTTCTGCGATATC 57.169 36.000 0.00 0.00 35.42 1.63
1176 1261 7.546316 AGATTGATCTGATTTCTGCGATATCTG 59.454 37.037 0.34 8.74 35.42 2.90
1177 1262 4.928020 TGATCTGATTTCTGCGATATCTGC 59.072 41.667 11.16 11.16 0.00 4.26
1178 1263 4.597404 TCTGATTTCTGCGATATCTGCT 57.403 40.909 16.64 1.24 0.00 4.24
1180 1265 3.311966 TGATTTCTGCGATATCTGCTCG 58.688 45.455 16.64 10.18 39.11 5.03
1187 1286 3.826466 TGCGATATCTGCTCGTTATCTG 58.174 45.455 16.64 0.00 38.37 2.90
1559 1658 4.083862 GAGACCACGGCCCTCACC 62.084 72.222 0.00 0.00 0.00 4.02
1785 1884 1.074752 GAAGCTCAAAGCCGTCTGAG 58.925 55.000 0.00 0.00 43.77 3.35
1813 1912 1.524621 CCAGCCGTGTCCCATGATC 60.525 63.158 0.00 0.00 0.00 2.92
1819 1918 2.236146 GCCGTGTCCCATGATCCATATA 59.764 50.000 0.00 0.00 0.00 0.86
1825 1924 6.813649 CGTGTCCCATGATCCATATAAACTAG 59.186 42.308 0.00 0.00 0.00 2.57
1826 1925 7.309805 CGTGTCCCATGATCCATATAAACTAGA 60.310 40.741 0.00 0.00 0.00 2.43
1829 1928 8.375506 GTCCCATGATCCATATAAACTAGACAA 58.624 37.037 0.00 0.00 0.00 3.18
1830 1929 9.116080 TCCCATGATCCATATAAACTAGACAAT 57.884 33.333 0.00 0.00 0.00 2.71
1831 1930 9.170734 CCCATGATCCATATAAACTAGACAATG 57.829 37.037 0.00 0.00 0.00 2.82
1832 1931 9.170734 CCATGATCCATATAAACTAGACAATGG 57.829 37.037 0.00 2.63 36.11 3.16
1833 1932 9.948964 CATGATCCATATAAACTAGACAATGGA 57.051 33.333 14.66 14.66 45.02 3.41
1834 1933 9.950496 ATGATCCATATAAACTAGACAATGGAC 57.050 33.333 14.63 11.06 44.07 4.02
1835 1934 8.088365 TGATCCATATAAACTAGACAATGGACG 58.912 37.037 14.63 0.00 44.07 4.79
1836 1935 6.220930 TCCATATAAACTAGACAATGGACGC 58.779 40.000 0.00 0.00 38.31 5.19
1837 1936 5.118664 CCATATAAACTAGACAATGGACGCG 59.881 44.000 3.53 3.53 36.76 6.01
1838 1937 2.736144 AAACTAGACAATGGACGCGA 57.264 45.000 15.93 0.00 0.00 5.87
1839 1938 2.961526 AACTAGACAATGGACGCGAT 57.038 45.000 15.93 0.00 0.00 4.58
1840 1939 2.493713 ACTAGACAATGGACGCGATC 57.506 50.000 15.93 6.63 0.00 3.69
1841 1940 1.268589 ACTAGACAATGGACGCGATCG 60.269 52.381 15.93 11.69 42.43 3.69
1842 1941 1.002792 CTAGACAATGGACGCGATCGA 60.003 52.381 21.57 4.28 39.41 3.59
1843 1942 0.248661 AGACAATGGACGCGATCGAG 60.249 55.000 21.57 19.49 39.41 4.04
1844 1943 0.525668 GACAATGGACGCGATCGAGT 60.526 55.000 24.69 24.69 39.41 4.18
1845 1944 0.802222 ACAATGGACGCGATCGAGTG 60.802 55.000 29.15 16.07 37.18 3.51
1846 1945 1.878522 AATGGACGCGATCGAGTGC 60.879 57.895 30.68 30.68 39.41 4.40
1853 1952 1.805261 CGCGATCGAGTGCATCAGTG 61.805 60.000 21.57 0.00 38.10 3.66
1911 2010 9.495754 GCAGATTTACACAATTCTAGACAATTC 57.504 33.333 0.00 0.00 0.00 2.17
1995 2094 4.095782 GCATTCGGTCTTGGTTTATTAGCA 59.904 41.667 0.00 0.00 0.00 3.49
2009 2108 7.147689 TGGTTTATTAGCACCTCGTATTTAGGA 60.148 37.037 0.00 0.00 37.57 2.94
2012 2111 6.665992 ATTAGCACCTCGTATTTAGGATCA 57.334 37.500 0.00 0.00 37.57 2.92
2211 2310 7.321717 ACAGGACGGAGGTAGTATATACTAA 57.678 40.000 21.51 6.16 40.20 2.24
2296 2395 2.896854 GATTGGCCGCATCGCTGA 60.897 61.111 0.00 0.00 0.00 4.26
2321 2420 1.922570 CGATTTCCTCATCGTCGGTT 58.077 50.000 0.00 0.00 41.03 4.44
2323 2422 1.327764 GATTTCCTCATCGTCGGTTGC 59.672 52.381 0.00 0.00 0.00 4.17
2366 2465 3.787001 CCTTCCCTCCCCTCGCAC 61.787 72.222 0.00 0.00 0.00 5.34
2367 2466 4.148825 CTTCCCTCCCCTCGCACG 62.149 72.222 0.00 0.00 0.00 5.34
2372 2471 3.449227 CTCCCCTCGCACGCACTA 61.449 66.667 0.00 0.00 0.00 2.74
2406 2512 2.120718 ACCCTTCTCACTCCCGCT 59.879 61.111 0.00 0.00 0.00 5.52
2479 2586 0.958091 CACACCCCTCGCATTTTTCA 59.042 50.000 0.00 0.00 0.00 2.69
2486 2593 2.428236 CGCATTTTTCACGCGGCA 60.428 55.556 12.47 0.00 45.08 5.69
2518 2625 0.241213 CCTATCATCGCGACCATCGT 59.759 55.000 12.93 0.00 42.81 3.73
2606 2713 2.097110 TGTAATACCTCTCGCCCCAT 57.903 50.000 0.00 0.00 0.00 4.00
2643 2769 3.777910 GGCGTCGAAGGGGCCTTA 61.778 66.667 0.84 0.00 41.70 2.69
2658 2784 2.234908 GGCCTTATCAGGAGCGTGATAT 59.765 50.000 12.11 0.00 44.19 1.63
2686 2816 3.228188 TGGTGAGGACTTTTGAGCATT 57.772 42.857 0.00 0.00 0.00 3.56
2699 2829 0.165944 GAGCATTCGAAACCCACACG 59.834 55.000 0.00 0.00 0.00 4.49
2713 2843 1.613630 ACACGCTTGGGAGGGATCT 60.614 57.895 0.00 0.00 39.04 2.75
2782 2913 3.003763 AGGGCCTCGAGGTTCACC 61.004 66.667 31.43 25.64 37.57 4.02
2811 2942 4.030195 GCAACACAAAGAACAACGAAGAAC 59.970 41.667 0.00 0.00 0.00 3.01
2867 3019 6.861065 AGATAAAAAGTGTCGATTGTGTGT 57.139 33.333 0.00 0.00 0.00 3.72
2868 3020 7.259290 AGATAAAAAGTGTCGATTGTGTGTT 57.741 32.000 0.00 0.00 0.00 3.32
2881 3033 2.857483 TGTGTGTTGTTCCAATCCGAT 58.143 42.857 0.00 0.00 0.00 4.18
2884 3036 1.135402 GTGTTGTTCCAATCCGATGCC 60.135 52.381 0.00 0.00 0.00 4.40
2888 3040 1.077068 TTCCAATCCGATGCCACCC 60.077 57.895 0.00 0.00 0.00 4.61
2892 3044 1.694169 AATCCGATGCCACCCCTCT 60.694 57.895 0.00 0.00 0.00 3.69
2914 3066 3.392882 TCTACATATACGAGGCGACGAA 58.607 45.455 13.15 0.59 37.03 3.85
2946 3098 3.056536 GCAAGAAAAGGACTCCAAATCCC 60.057 47.826 0.00 0.00 36.86 3.85
2947 3099 3.073274 AGAAAAGGACTCCAAATCCCG 57.927 47.619 0.00 0.00 36.86 5.14
2960 3112 3.427503 CCAAATCCCGTCCAAATCTTTCG 60.428 47.826 0.00 0.00 0.00 3.46
2965 3117 3.251487 TCCCGTCCAAATCTTTCGAAAAC 59.749 43.478 12.41 4.41 0.00 2.43
2966 3118 3.252458 CCCGTCCAAATCTTTCGAAAACT 59.748 43.478 12.41 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.152963 CCATCCCTAAAGGCCACCG 60.153 63.158 5.01 0.00 34.51 4.94
56 58 1.100510 TTGGTCCTATGACGACTCCG 58.899 55.000 0.00 0.00 42.73 4.63
66 68 0.988678 GCCTCCTGGGTTGGTCCTAT 60.989 60.000 0.00 0.00 37.43 2.57
74 76 1.151450 CACACTTGCCTCCTGGGTT 59.849 57.895 0.00 0.00 37.43 4.11
75 77 2.839098 CACACTTGCCTCCTGGGT 59.161 61.111 0.00 0.00 37.43 4.51
87 89 1.560004 CGAGCGAACACATGCACACT 61.560 55.000 0.00 0.00 0.00 3.55
89 91 1.594021 ACGAGCGAACACATGCACA 60.594 52.632 0.00 0.00 0.00 4.57
102 104 2.357034 TTTGAGGACCGCACGAGC 60.357 61.111 0.00 0.00 37.42 5.03
106 108 1.515521 CCCAACTTTGAGGACCGCAC 61.516 60.000 0.00 0.00 0.00 5.34
107 109 1.228124 CCCAACTTTGAGGACCGCA 60.228 57.895 0.00 0.00 0.00 5.69
120 122 6.043854 AGAGAAGTGAAGTTATCTCCCAAC 57.956 41.667 0.00 0.00 39.26 3.77
143 145 3.582647 TGAGGGACAAGCTTGATAGTCAA 59.417 43.478 32.50 9.53 34.79 3.18
144 146 3.173151 TGAGGGACAAGCTTGATAGTCA 58.827 45.455 32.50 23.11 32.79 3.41
184 186 9.956720 GATCACACATTAAGATAATTTTCTGGG 57.043 33.333 0.00 0.00 0.00 4.45
188 190 9.736023 GTGGGATCACACATTAAGATAATTTTC 57.264 33.333 23.36 0.00 43.13 2.29
193 195 6.320434 TGGTGGGATCACACATTAAGATAA 57.680 37.500 28.59 0.64 45.32 1.75
194 196 5.966853 TGGTGGGATCACACATTAAGATA 57.033 39.130 28.59 2.45 45.32 1.98
222 224 2.099098 ACGTTTTTGAGGACCAAGCTTG 59.901 45.455 19.93 19.93 35.94 4.01
257 259 5.045012 AGGATTGACATATGATGCACAGT 57.955 39.130 10.38 0.00 0.00 3.55
258 260 6.461640 TCTAGGATTGACATATGATGCACAG 58.538 40.000 10.38 0.63 0.00 3.66
259 261 6.423776 TCTAGGATTGACATATGATGCACA 57.576 37.500 10.38 0.00 0.00 4.57
260 262 7.734924 TTTCTAGGATTGACATATGATGCAC 57.265 36.000 10.38 0.00 0.00 4.57
268 270 9.625747 TTATGTGCAATTTCTAGGATTGACATA 57.374 29.630 18.20 20.06 37.01 2.29
277 279 8.562892 CCTAATCACTTATGTGCAATTTCTAGG 58.437 37.037 3.90 1.58 43.49 3.02
291 293 9.964354 TTGCTATTATGCATCCTAATCACTTAT 57.036 29.630 0.19 0.00 42.96 1.73
292 294 9.440773 CTTGCTATTATGCATCCTAATCACTTA 57.559 33.333 0.19 0.00 42.96 2.24
294 296 6.373774 GCTTGCTATTATGCATCCTAATCACT 59.626 38.462 0.19 0.00 42.96 3.41
309 311 4.202326 GGCTTGGTAGTAGGCTTGCTATTA 60.202 45.833 0.00 0.00 35.48 0.98
327 329 4.922692 TGCAAATTAAGTCGATTTGGCTTG 59.077 37.500 3.04 5.06 42.14 4.01
328 330 5.132897 TGCAAATTAAGTCGATTTGGCTT 57.867 34.783 3.04 0.00 42.14 4.35
335 337 6.319658 ACATGGAGATTGCAAATTAAGTCGAT 59.680 34.615 1.71 0.00 0.00 3.59
357 359 2.431057 GGGATGGAGTAAGTCGTGACAT 59.569 50.000 2.44 0.00 0.00 3.06
368 371 9.905713 GATGCTTTTATATTATGGGATGGAGTA 57.094 33.333 0.00 0.00 0.00 2.59
419 423 9.677567 CTCCCACCGTTTCATAATATAAAAATG 57.322 33.333 0.00 0.00 0.00 2.32
434 438 2.170166 TCGTATGTACTCCCACCGTTT 58.830 47.619 0.00 0.00 0.00 3.60
511 530 1.339610 TCACCAACCTTGATTTTGCGG 59.660 47.619 0.00 0.00 0.00 5.69
575 594 5.105106 ACCACGTATATGAATCACCAACTCA 60.105 40.000 0.00 0.00 0.00 3.41
869 931 0.618968 ATCCTCCTTCCGCTGTCCTT 60.619 55.000 0.00 0.00 0.00 3.36
879 941 7.138054 TGTTTCCCTAAGATAATCCTCCTTC 57.862 40.000 0.00 0.00 0.00 3.46
895 957 7.004086 TCAAACTGATTCAATACTGTTTCCCT 58.996 34.615 0.00 0.00 36.54 4.20
896 958 7.214467 TCAAACTGATTCAATACTGTTTCCC 57.786 36.000 0.00 0.00 36.54 3.97
897 959 8.299570 ACATCAAACTGATTCAATACTGTTTCC 58.700 33.333 0.00 0.00 34.28 3.13
925 987 6.238814 GCAAGTCCTAAGGAAGCTAGTAGTAG 60.239 46.154 0.00 0.00 31.38 2.57
926 988 5.593502 GCAAGTCCTAAGGAAGCTAGTAGTA 59.406 44.000 0.00 0.00 31.38 1.82
927 989 4.403113 GCAAGTCCTAAGGAAGCTAGTAGT 59.597 45.833 0.00 0.00 31.38 2.73
938 1000 2.206576 AAAGGCTGCAAGTCCTAAGG 57.793 50.000 0.50 0.00 41.78 2.69
1013 1085 4.014406 TCTCTCCTTGTTGTCGCTGTATA 58.986 43.478 0.00 0.00 0.00 1.47
1035 1112 8.924511 TCTCCTTGATCTGTGTTTCTAATTTT 57.075 30.769 0.00 0.00 0.00 1.82
1058 1135 1.840737 TAGCTGCGGAGTTCTCTTCT 58.159 50.000 5.62 0.00 0.00 2.85
1169 1254 4.550422 TGCACAGATAACGAGCAGATATC 58.450 43.478 0.00 0.00 35.56 1.63
1176 1261 2.159226 AGTACCTGCACAGATAACGAGC 60.159 50.000 0.00 0.00 0.00 5.03
1177 1262 3.784701 AGTACCTGCACAGATAACGAG 57.215 47.619 0.00 0.00 0.00 4.18
1178 1263 4.267536 AGTAGTACCTGCACAGATAACGA 58.732 43.478 0.00 0.00 0.00 3.85
1180 1265 4.334759 TCGAGTAGTACCTGCACAGATAAC 59.665 45.833 0.00 0.00 0.00 1.89
1187 1286 1.461559 AGGTCGAGTAGTACCTGCAC 58.538 55.000 0.00 0.00 44.53 4.57
1673 1772 1.756950 ATCGGCTCCAGCGAAGGTA 60.757 57.895 0.00 0.00 43.26 3.08
1757 1856 2.009774 GCTTTGAGCTTCTTGGCGATA 58.990 47.619 0.00 0.00 38.45 2.92
1785 1884 4.148825 ACGGCTGGTGATCGGAGC 62.149 66.667 0.00 2.57 0.00 4.70
1813 1912 5.118664 CGCGTCCATTGTCTAGTTTATATGG 59.881 44.000 0.00 0.00 35.08 2.74
1819 1918 2.736144 TCGCGTCCATTGTCTAGTTT 57.264 45.000 5.77 0.00 0.00 2.66
1825 1924 0.525668 ACTCGATCGCGTCCATTGTC 60.526 55.000 11.09 0.00 38.98 3.18
1826 1925 0.802222 CACTCGATCGCGTCCATTGT 60.802 55.000 11.09 0.00 38.98 2.71
1829 1928 2.278857 GCACTCGATCGCGTCCAT 60.279 61.111 11.09 0.00 38.98 3.41
1830 1929 2.936829 GATGCACTCGATCGCGTCCA 62.937 60.000 11.09 7.39 38.05 4.02
1831 1930 2.278857 ATGCACTCGATCGCGTCC 60.279 61.111 11.09 0.00 38.98 4.79
1832 1931 1.535636 CTGATGCACTCGATCGCGTC 61.536 60.000 11.09 17.26 43.13 5.19
1833 1932 1.587350 CTGATGCACTCGATCGCGT 60.587 57.895 11.09 7.78 38.98 6.01
1834 1933 1.587350 ACTGATGCACTCGATCGCG 60.587 57.895 11.09 6.95 39.35 5.87
1835 1934 1.922903 CACTGATGCACTCGATCGC 59.077 57.895 11.09 0.00 0.00 4.58
1846 1945 5.093457 GTGTCAAATCATCTTGCACTGATG 58.907 41.667 17.97 17.97 41.75 3.07
1853 1952 7.329962 TGAAAATGATGTGTCAAATCATCTTGC 59.670 33.333 17.24 12.73 42.58 4.01
1911 2010 8.801715 ACAAGAAATTAAATGCAGTACAGTTG 57.198 30.769 0.00 0.00 37.13 3.16
2164 2263 9.410556 CTGTTTTATTGGTCCTCTTTGTATTTG 57.589 33.333 0.00 0.00 0.00 2.32
2174 2273 3.007635 CCGTCCTGTTTTATTGGTCCTC 58.992 50.000 0.00 0.00 0.00 3.71
2296 2395 2.010145 CGATGAGGAAATCGTGTGGT 57.990 50.000 0.00 0.00 43.49 4.16
2321 2420 1.288188 TGGTGAGATCCAATCCAGCA 58.712 50.000 0.00 0.00 36.41 4.41
2323 2422 3.211865 CACATGGTGAGATCCAATCCAG 58.788 50.000 0.00 0.00 41.09 3.86
2366 2465 3.660865 ACTTTCCTTTGTAGGTAGTGCG 58.339 45.455 0.00 0.00 42.60 5.34
2367 2466 4.451435 GTGACTTTCCTTTGTAGGTAGTGC 59.549 45.833 0.00 0.00 42.60 4.40
2368 2467 4.995487 GGTGACTTTCCTTTGTAGGTAGTG 59.005 45.833 0.00 0.00 42.60 2.74
2369 2468 4.041321 GGGTGACTTTCCTTTGTAGGTAGT 59.959 45.833 0.00 0.00 42.60 2.73
2370 2469 4.286291 AGGGTGACTTTCCTTTGTAGGTAG 59.714 45.833 0.00 0.00 42.60 3.18
2371 2470 4.237018 AGGGTGACTTTCCTTTGTAGGTA 58.763 43.478 0.00 0.00 42.60 3.08
2372 2471 3.053826 AGGGTGACTTTCCTTTGTAGGT 58.946 45.455 0.00 0.00 42.60 3.08
2386 2485 1.592223 CGGGAGTGAGAAGGGTGAC 59.408 63.158 0.00 0.00 0.00 3.67
2388 2487 2.232298 GAGCGGGAGTGAGAAGGGTG 62.232 65.000 0.00 0.00 0.00 4.61
2406 2512 1.144969 CAACTAAGGCAACGCTTCGA 58.855 50.000 0.00 0.00 46.39 3.71
2416 2522 2.159653 CGACAATGTGAGCAACTAAGGC 60.160 50.000 0.00 0.00 0.00 4.35
2463 2570 1.862602 GCGTGAAAAATGCGAGGGGT 61.863 55.000 0.00 0.00 0.00 4.95
2483 2590 4.803908 GGTGGTGCTAGGGCTGCC 62.804 72.222 11.05 11.05 39.59 4.85
2486 2593 0.031111 TGATAGGTGGTGCTAGGGCT 60.031 55.000 0.00 0.00 39.59 5.19
2518 2625 1.686052 CTGCAAAACCAACCTAGGCAA 59.314 47.619 9.30 0.00 0.00 4.52
2547 2654 0.248866 CAAGGCCAACGACAAACACC 60.249 55.000 5.01 0.00 0.00 4.16
2551 2658 1.732917 CTGCAAGGCCAACGACAAA 59.267 52.632 5.01 0.00 0.00 2.83
2552 2659 2.844451 GCTGCAAGGCCAACGACAA 61.844 57.895 5.01 0.00 0.00 3.18
2553 2660 3.286751 GCTGCAAGGCCAACGACA 61.287 61.111 5.01 0.00 0.00 4.35
2554 2661 3.259425 CTGCTGCAAGGCCAACGAC 62.259 63.158 5.01 0.00 0.00 4.34
2555 2662 2.979676 CTGCTGCAAGGCCAACGA 60.980 61.111 5.01 0.00 0.00 3.85
2579 2686 4.251268 GCGAGAGGTATTACAAGTTTGGT 58.749 43.478 0.00 0.00 0.00 3.67
2584 2691 1.761198 GGGGCGAGAGGTATTACAAGT 59.239 52.381 0.00 0.00 0.00 3.16
2606 2713 4.167268 GCCGAAAGTACACAAACACAAAA 58.833 39.130 0.00 0.00 0.00 2.44
2642 2768 4.505313 GTGTCATATCACGCTCCTGATA 57.495 45.455 0.00 0.00 37.50 2.15
2643 2769 3.377346 GTGTCATATCACGCTCCTGAT 57.623 47.619 0.00 0.00 35.05 2.90
2658 2784 0.828022 AAGTCCTCACCAACGTGTCA 59.172 50.000 0.00 0.00 41.09 3.58
2670 2800 4.467735 GTTTCGAATGCTCAAAAGTCCTC 58.532 43.478 0.00 0.00 0.00 3.71
2671 2801 3.253432 GGTTTCGAATGCTCAAAAGTCCT 59.747 43.478 0.00 0.00 0.00 3.85
2686 2816 1.890041 CCAAGCGTGTGGGTTTCGA 60.890 57.895 0.00 0.00 34.77 3.71
2699 2829 1.069358 CTTACGAGATCCCTCCCAAGC 59.931 57.143 0.00 0.00 36.04 4.01
2713 2843 2.056223 CCTTCGCCCTCCCTTACGA 61.056 63.158 0.00 0.00 0.00 3.43
2724 2854 3.039134 CAACCCACAACCTTCGCC 58.961 61.111 0.00 0.00 0.00 5.54
2782 2913 1.063912 TGTTCTTTGTGTTGCAGAGCG 59.936 47.619 0.00 0.00 30.16 5.03
2868 3020 0.679640 GGTGGCATCGGATTGGAACA 60.680 55.000 0.00 0.00 0.00 3.18
2881 3033 2.561209 TATGTAGAAGAGGGGTGGCA 57.439 50.000 0.00 0.00 0.00 4.92
2884 3036 4.459685 CCTCGTATATGTAGAAGAGGGGTG 59.540 50.000 8.26 0.00 40.98 4.61
2888 3040 4.001652 TCGCCTCGTATATGTAGAAGAGG 58.998 47.826 10.90 10.90 45.79 3.69
2892 3044 3.392882 TCGTCGCCTCGTATATGTAGAA 58.607 45.455 0.00 0.00 0.00 2.10
2914 3066 3.321968 GTCCTTTTCTTGCATGGGAAGTT 59.678 43.478 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.