Multiple sequence alignment - TraesCS6D01G378000

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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 TraesCS6D01G378000 chr6D 100.000 3410 0 0 1 3410 460575626 460572217 0.000000e+00 6298
1 TraesCS6D01G378000 chr6B 91.258 3283 134 58 167 3410 701663289 701660121 0.000000e+00 4331
2 TraesCS6D01G378000 chr6A 93.497 1138 60 13 2280 3410 606767063 606765933 0.000000e+00 1679
3 TraesCS6D01G378000 chr6A 87.620 1349 81 26 160 1484 606769088 606767802 0.000000e+00 1487
4 TraesCS6D01G378000 chr6A 92.875 786 34 15 1373 2146 606767863 606767088 0.000000e+00 1122
5 TraesCS6D01G378000 chr5D 91.509 106 6 2 2170 2274 477322305 477322202 3.550000e-30 143
6 TraesCS6D01G378000 chr1B 95.506 89 2 2 2186 2273 456268172 456268085 1.280000e-29 141
7 TraesCS6D01G378000 chr7D 93.617 94 4 2 2182 2274 22964250 22964342 4.590000e-29 139
8 TraesCS6D01G378000 chr4D 94.505 91 4 1 2187 2276 434161611 434161701 4.590000e-29 139
9 TraesCS6D01G378000 chr1D 92.784 97 5 2 2179 2273 440050454 440050358 4.590000e-29 139
10 TraesCS6D01G378000 chr1D 91.089 101 5 4 2192 2291 301353507 301353604 2.130000e-27 134
11 TraesCS6D01G378000 chr3D 92.708 96 6 1 2180 2275 312907600 312907506 1.650000e-28 137
12 TraesCS6D01G378000 chr7A 89.815 108 8 3 2187 2292 485195292 485195186 5.940000e-28 135


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 TraesCS6D01G378000 chr6D 460572217 460575626 3409 True 6298.000000 6298 100.000000 1 3410 1 chr6D.!!$R1 3409
1 TraesCS6D01G378000 chr6B 701660121 701663289 3168 True 4331.000000 4331 91.258000 167 3410 1 chr6B.!!$R1 3243
2 TraesCS6D01G378000 chr6A 606765933 606769088 3155 True 1429.333333 1679 91.330667 160 3410 3 chr6A.!!$R1 3250

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
883 917 0.034476 CTTCTCAGCAGCACCAGTCA 59.966 55.0 0.00 0.0 0.0 3.41 F
1098 1145 0.466922 AACAGCTAGCATCCATGGCC 60.467 55.0 18.83 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2140 0.179181 GCATCTGTTGGCATCACACG 60.179 55.000 0.00 0.0 0.00 4.49 R
2410 2526 1.225426 GGCATGGACTCCTGCATCA 59.775 57.895 16.63 0.0 40.18 3.07 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
24 25 7.490962 TTGCGGTTGGATATTTATAACTCTG 57.509 36.000 0.00 0.00 0.00 3.35
25 26 5.468746 TGCGGTTGGATATTTATAACTCTGC 59.531 40.000 0.00 0.00 0.00 4.26
26 27 5.701290 GCGGTTGGATATTTATAACTCTGCT 59.299 40.000 0.00 0.00 0.00 4.24
27 28 6.347725 GCGGTTGGATATTTATAACTCTGCTG 60.348 42.308 0.00 0.00 0.00 4.41
28 29 6.706270 CGGTTGGATATTTATAACTCTGCTGT 59.294 38.462 0.00 0.00 0.00 4.40
29 30 7.307396 CGGTTGGATATTTATAACTCTGCTGTG 60.307 40.741 0.00 0.00 0.00 3.66
30 31 7.355778 GTTGGATATTTATAACTCTGCTGTGC 58.644 38.462 0.00 0.00 0.00 4.57
31 32 6.591001 TGGATATTTATAACTCTGCTGTGCA 58.409 36.000 0.00 0.00 36.92 4.57
32 33 7.226441 TGGATATTTATAACTCTGCTGTGCAT 58.774 34.615 0.00 0.00 38.13 3.96
33 34 7.173735 TGGATATTTATAACTCTGCTGTGCATG 59.826 37.037 0.00 0.00 38.13 4.06
34 35 7.173907 GGATATTTATAACTCTGCTGTGCATGT 59.826 37.037 0.00 0.00 38.13 3.21
35 36 5.550232 TTTATAACTCTGCTGTGCATGTG 57.450 39.130 0.00 0.00 38.13 3.21
36 37 2.549064 TAACTCTGCTGTGCATGTGT 57.451 45.000 0.00 0.00 38.13 3.72
37 38 1.683943 AACTCTGCTGTGCATGTGTT 58.316 45.000 0.00 0.00 38.13 3.32
38 39 0.949397 ACTCTGCTGTGCATGTGTTG 59.051 50.000 0.00 0.00 38.13 3.33
69 70 1.618487 TGCCAGTGCAACATGATTGA 58.382 45.000 0.00 0.00 46.66 2.57
70 71 1.962100 TGCCAGTGCAACATGATTGAA 59.038 42.857 0.00 0.00 46.66 2.69
71 72 2.029739 TGCCAGTGCAACATGATTGAAG 60.030 45.455 0.00 0.00 46.66 3.02
72 73 2.229543 GCCAGTGCAACATGATTGAAGA 59.770 45.455 0.00 0.00 41.43 2.87
73 74 3.119245 GCCAGTGCAACATGATTGAAGAT 60.119 43.478 0.00 0.00 41.43 2.40
74 75 4.619863 GCCAGTGCAACATGATTGAAGATT 60.620 41.667 0.00 0.00 41.43 2.40
75 76 5.100259 CCAGTGCAACATGATTGAAGATTC 58.900 41.667 0.00 0.00 41.43 2.52
76 77 4.791676 CAGTGCAACATGATTGAAGATTCG 59.208 41.667 0.00 0.00 41.43 3.34
77 78 4.456911 AGTGCAACATGATTGAAGATTCGT 59.543 37.500 0.00 0.00 41.43 3.85
78 79 4.556135 GTGCAACATGATTGAAGATTCGTG 59.444 41.667 0.00 0.00 36.32 4.35
79 80 3.545078 GCAACATGATTGAAGATTCGTGC 59.455 43.478 0.00 0.00 33.13 5.34
80 81 4.673580 GCAACATGATTGAAGATTCGTGCT 60.674 41.667 0.00 0.00 33.13 4.40
81 82 4.611310 ACATGATTGAAGATTCGTGCTG 57.389 40.909 0.00 0.00 33.13 4.41
82 83 4.256110 ACATGATTGAAGATTCGTGCTGA 58.744 39.130 0.00 0.00 33.13 4.26
83 84 4.880120 ACATGATTGAAGATTCGTGCTGAT 59.120 37.500 0.00 0.00 33.13 2.90
84 85 5.356190 ACATGATTGAAGATTCGTGCTGATT 59.644 36.000 0.00 0.00 33.13 2.57
85 86 5.475273 TGATTGAAGATTCGTGCTGATTC 57.525 39.130 0.00 0.00 0.00 2.52
86 87 5.181009 TGATTGAAGATTCGTGCTGATTCT 58.819 37.500 0.00 0.00 38.61 2.40
87 88 5.645067 TGATTGAAGATTCGTGCTGATTCTT 59.355 36.000 13.07 13.07 45.39 2.52
88 89 5.947228 TTGAAGATTCGTGCTGATTCTTT 57.053 34.783 13.89 3.72 43.71 2.52
89 90 5.947228 TGAAGATTCGTGCTGATTCTTTT 57.053 34.783 13.89 0.00 43.71 2.27
90 91 6.317789 TGAAGATTCGTGCTGATTCTTTTT 57.682 33.333 13.89 0.00 43.71 1.94
118 119 4.511457 CACAGTATTCGTGCTGATTCTG 57.489 45.455 0.58 0.00 36.62 3.02
119 120 2.932614 ACAGTATTCGTGCTGATTCTGC 59.067 45.455 8.46 8.46 36.62 4.26
120 121 2.931969 CAGTATTCGTGCTGATTCTGCA 59.068 45.455 13.50 13.50 36.05 4.41
121 122 3.001026 CAGTATTCGTGCTGATTCTGCAG 59.999 47.826 17.31 7.63 38.86 4.41
128 129 2.093216 CTGATTCTGCAGCGTTCCC 58.907 57.895 9.47 0.00 0.00 3.97
129 130 0.392193 CTGATTCTGCAGCGTTCCCT 60.392 55.000 9.47 0.00 0.00 4.20
130 131 0.674581 TGATTCTGCAGCGTTCCCTG 60.675 55.000 9.47 0.00 35.93 4.45
131 132 1.372087 GATTCTGCAGCGTTCCCTGG 61.372 60.000 9.47 0.00 33.44 4.45
132 133 2.826777 ATTCTGCAGCGTTCCCTGGG 62.827 60.000 9.47 6.33 33.44 4.45
133 134 4.020617 CTGCAGCGTTCCCTGGGA 62.021 66.667 12.53 12.53 33.44 4.37
134 135 4.329545 TGCAGCGTTCCCTGGGAC 62.330 66.667 16.85 9.96 33.44 4.46
135 136 4.021925 GCAGCGTTCCCTGGGACT 62.022 66.667 16.85 6.74 33.44 3.85
136 137 2.046892 CAGCGTTCCCTGGGACTG 60.047 66.667 16.85 15.81 0.00 3.51
144 145 2.042762 CCTGGGACTGGGATGGGA 59.957 66.667 0.00 0.00 44.20 4.37
145 146 2.074948 CCTGGGACTGGGATGGGAG 61.075 68.421 0.00 0.00 44.20 4.30
146 147 1.003442 CTGGGACTGGGATGGGAGA 59.997 63.158 0.00 0.00 0.00 3.71
147 148 0.401105 CTGGGACTGGGATGGGAGAT 60.401 60.000 0.00 0.00 0.00 2.75
148 149 0.046242 TGGGACTGGGATGGGAGATT 59.954 55.000 0.00 0.00 0.00 2.40
149 150 0.767998 GGGACTGGGATGGGAGATTC 59.232 60.000 0.00 0.00 0.00 2.52
150 151 1.697291 GGGACTGGGATGGGAGATTCT 60.697 57.143 0.00 0.00 0.00 2.40
151 152 1.419387 GGACTGGGATGGGAGATTCTG 59.581 57.143 0.00 0.00 0.00 3.02
152 153 0.842635 ACTGGGATGGGAGATTCTGC 59.157 55.000 0.00 0.00 0.00 4.26
153 154 0.250209 CTGGGATGGGAGATTCTGCG 60.250 60.000 0.00 0.00 0.00 5.18
154 155 1.599240 GGGATGGGAGATTCTGCGC 60.599 63.158 0.00 0.00 0.00 6.09
155 156 1.449353 GGATGGGAGATTCTGCGCT 59.551 57.895 9.73 0.00 0.00 5.92
156 157 0.883814 GGATGGGAGATTCTGCGCTG 60.884 60.000 9.73 8.88 0.00 5.18
157 158 1.505477 GATGGGAGATTCTGCGCTGC 61.505 60.000 9.73 0.00 0.00 5.25
158 159 3.267860 GGGAGATTCTGCGCTGCG 61.268 66.667 19.17 19.17 0.00 5.18
216 223 1.805428 GCTGGATCCTCTCTCTCGCC 61.805 65.000 14.23 0.00 0.00 5.54
221 228 1.754226 GATCCTCTCTCTCGCCTGTTT 59.246 52.381 0.00 0.00 0.00 2.83
232 239 2.434331 CCTGTTTTCCGCCCCAGA 59.566 61.111 0.00 0.00 0.00 3.86
233 240 1.000896 CCTGTTTTCCGCCCCAGAT 60.001 57.895 0.00 0.00 0.00 2.90
234 241 0.611896 CCTGTTTTCCGCCCCAGATT 60.612 55.000 0.00 0.00 0.00 2.40
235 242 0.811281 CTGTTTTCCGCCCCAGATTC 59.189 55.000 0.00 0.00 0.00 2.52
246 253 3.025978 GCCCCAGATTCATTCATTCACA 58.974 45.455 0.00 0.00 0.00 3.58
299 306 3.699894 CCGACAGGTCAGCAGGCT 61.700 66.667 0.00 0.00 0.00 4.58
301 308 2.935740 CGACAGGTCAGCAGGCTCA 61.936 63.158 0.00 0.00 0.00 4.26
521 537 4.760047 CGGGCCACTGTTCCGAGG 62.760 72.222 4.39 0.00 45.96 4.63
649 671 1.878211 TAGGTGCACATCCAGATCCA 58.122 50.000 20.43 0.00 0.00 3.41
768 796 3.998913 TTCACTGCCATGATTCTACCA 57.001 42.857 0.00 0.00 0.00 3.25
799 833 3.252400 GAAGCTCACTGATCACACAGAG 58.748 50.000 0.00 0.00 40.63 3.35
801 835 3.098377 AGCTCACTGATCACACAGAGAT 58.902 45.455 11.19 4.29 40.63 2.75
802 836 4.276642 AGCTCACTGATCACACAGAGATA 58.723 43.478 11.19 0.00 40.63 1.98
803 837 4.894705 AGCTCACTGATCACACAGAGATAT 59.105 41.667 11.19 0.00 40.63 1.63
804 838 6.067350 AGCTCACTGATCACACAGAGATATA 58.933 40.000 11.19 0.00 40.63 0.86
805 839 6.016360 AGCTCACTGATCACACAGAGATATAC 60.016 42.308 11.19 0.00 40.63 1.47
806 840 6.016360 GCTCACTGATCACACAGAGATATACT 60.016 42.308 11.19 0.00 40.63 2.12
807 841 7.503521 TCACTGATCACACAGAGATATACTC 57.496 40.000 0.00 0.00 45.22 2.59
808 842 6.488344 TCACTGATCACACAGAGATATACTCC 59.512 42.308 0.00 0.00 45.96 3.85
809 843 6.489700 CACTGATCACACAGAGATATACTCCT 59.510 42.308 0.00 0.00 45.96 3.69
810 844 7.663493 CACTGATCACACAGAGATATACTCCTA 59.337 40.741 0.00 0.00 45.96 2.94
811 845 7.882791 ACTGATCACACAGAGATATACTCCTAG 59.117 40.741 0.00 0.00 45.96 3.02
812 846 7.978925 TGATCACACAGAGATATACTCCTAGA 58.021 38.462 0.00 0.00 45.96 2.43
813 847 8.610369 TGATCACACAGAGATATACTCCTAGAT 58.390 37.037 0.00 0.00 45.96 1.98
838 872 2.290531 ATCTGTCAGCACACTCATCG 57.709 50.000 0.00 0.00 0.00 3.84
859 893 2.550208 GGTCGTCAAGTCAAAGTGGGAT 60.550 50.000 0.00 0.00 0.00 3.85
860 894 2.737252 GTCGTCAAGTCAAAGTGGGATC 59.263 50.000 0.00 0.00 0.00 3.36
861 895 2.632996 TCGTCAAGTCAAAGTGGGATCT 59.367 45.455 0.00 0.00 0.00 2.75
862 896 2.996621 CGTCAAGTCAAAGTGGGATCTC 59.003 50.000 0.00 0.00 0.00 2.75
863 897 3.554960 CGTCAAGTCAAAGTGGGATCTCA 60.555 47.826 0.00 0.00 0.00 3.27
864 898 3.748568 GTCAAGTCAAAGTGGGATCTCAC 59.251 47.826 18.52 18.52 37.89 3.51
883 917 0.034476 CTTCTCAGCAGCACCAGTCA 59.966 55.000 0.00 0.00 0.00 3.41
889 923 1.963338 GCAGCACCAGTCACTCACC 60.963 63.158 0.00 0.00 0.00 4.02
913 947 4.399395 TGGGCCAGCGAGCTCTTG 62.399 66.667 12.85 9.94 33.00 3.02
916 950 4.774503 GCCAGCGAGCTCTTGCCT 62.775 66.667 12.85 0.00 40.86 4.75
945 982 1.528542 CATGCCCATCCAGCTCAGG 60.529 63.158 0.00 0.00 0.00 3.86
1068 1115 3.466836 CACACAAGACAAGGAAGCAGTA 58.533 45.455 0.00 0.00 0.00 2.74
1069 1116 3.876914 CACACAAGACAAGGAAGCAGTAA 59.123 43.478 0.00 0.00 0.00 2.24
1070 1117 4.024556 CACACAAGACAAGGAAGCAGTAAG 60.025 45.833 0.00 0.00 0.00 2.34
1071 1118 3.058639 CACAAGACAAGGAAGCAGTAAGC 60.059 47.826 0.00 0.00 46.19 3.09
1098 1145 0.466922 AACAGCTAGCATCCATGGCC 60.467 55.000 18.83 0.00 0.00 5.36
1149 1196 0.850100 TCAAAGGGGCCAAGACTGAA 59.150 50.000 4.39 0.00 0.00 3.02
1212 1262 2.047655 TCCACGTTCATGGACGGC 60.048 61.111 29.26 0.00 44.14 5.68
1391 1442 2.486982 TGCTTCTTCTTGCTGATCTTGC 59.513 45.455 0.00 0.00 0.00 4.01
1400 1451 1.622312 TGCTGATCTTGCAGTCTCTGT 59.378 47.619 9.33 0.00 38.17 3.41
1443 1494 5.078411 TCTTCTTCCTGCTGATCTTGTAC 57.922 43.478 0.00 0.00 0.00 2.90
1658 1765 4.747529 ACAGCGCTCGCAGATGCA 62.748 61.111 7.13 0.00 44.88 3.96
1684 1791 1.226046 CGTCGTCAAGAGCGATCGT 60.226 57.895 17.81 3.24 40.59 3.73
1757 1869 4.941263 TCTGTTTTACACACAACTCTTGCT 59.059 37.500 0.00 0.00 0.00 3.91
1777 1889 2.434359 CTTTCGGGTCCGGCAGAC 60.434 66.667 9.68 0.00 45.51 3.51
1860 1973 5.483937 ACCTCAGTATCACCATCTTGTGTTA 59.516 40.000 0.00 0.00 37.51 2.41
1884 1997 7.020914 AGCTAATCTAGTTGCTATTTGTTGC 57.979 36.000 0.00 0.00 33.64 4.17
1892 2005 3.266541 TGCTATTTGTTGCAACAGTCG 57.733 42.857 29.50 20.00 40.50 4.18
1986 2100 9.906660 GTAATTGTTGTTTCCACTCATCATTTA 57.093 29.630 0.00 0.00 0.00 1.40
1990 2104 9.829507 TTGTTGTTTCCACTCATCATTTATTTT 57.170 25.926 0.00 0.00 0.00 1.82
2021 2135 9.719279 TTTGTTTCCAGTTAATTTAACAGTACG 57.281 29.630 18.83 2.30 41.07 3.67
2022 2136 7.354257 TGTTTCCAGTTAATTTAACAGTACGC 58.646 34.615 18.83 7.61 41.07 4.42
2023 2137 7.012138 TGTTTCCAGTTAATTTAACAGTACGCA 59.988 33.333 18.83 9.56 41.07 5.24
2025 2139 7.675962 TCCAGTTAATTTAACAGTACGCAAT 57.324 32.000 18.83 0.00 41.07 3.56
2026 2140 7.745015 TCCAGTTAATTTAACAGTACGCAATC 58.255 34.615 18.83 0.00 41.07 2.67
2027 2141 6.681178 CCAGTTAATTTAACAGTACGCAATCG 59.319 38.462 18.83 0.00 41.07 3.34
2141 2255 3.125698 ACAGAAAACACGACAAAACCG 57.874 42.857 0.00 0.00 0.00 4.44
2149 2263 1.533731 CACGACAAAACCGGCAGTAAT 59.466 47.619 0.00 0.00 0.00 1.89
2151 2265 1.533731 CGACAAAACCGGCAGTAATGT 59.466 47.619 0.00 0.00 31.91 2.71
2153 2267 3.181524 CGACAAAACCGGCAGTAATGTAG 60.182 47.826 0.00 0.00 30.01 2.74
2154 2268 3.746940 ACAAAACCGGCAGTAATGTAGT 58.253 40.909 0.00 0.00 0.00 2.73
2155 2269 3.500680 ACAAAACCGGCAGTAATGTAGTG 59.499 43.478 0.00 0.00 0.00 2.74
2156 2270 3.412237 AAACCGGCAGTAATGTAGTGT 57.588 42.857 0.00 0.00 0.00 3.55
2157 2271 3.412237 AACCGGCAGTAATGTAGTGTT 57.588 42.857 0.00 0.00 0.00 3.32
2158 2272 3.412237 ACCGGCAGTAATGTAGTGTTT 57.588 42.857 0.00 0.00 0.00 2.83
2159 2273 3.746940 ACCGGCAGTAATGTAGTGTTTT 58.253 40.909 0.00 0.00 0.00 2.43
2160 2274 4.139038 ACCGGCAGTAATGTAGTGTTTTT 58.861 39.130 0.00 0.00 0.00 1.94
2181 2295 7.733402 TTTTTACACTAATGTAGGAGCGTTT 57.267 32.000 0.00 0.00 42.29 3.60
2183 2297 7.733402 TTTACACTAATGTAGGAGCGTTTTT 57.267 32.000 0.00 0.00 42.29 1.94
2251 2366 4.732285 ATGTAGTGTCAAAACGCTCTTG 57.268 40.909 0.00 0.00 42.59 3.02
2410 2526 3.084786 GAGGCCATGCTGAAGTTTTAGT 58.915 45.455 5.01 0.00 0.00 2.24
2443 2559 0.623723 ATGCCCGGTACTTGTGGATT 59.376 50.000 0.00 0.00 0.00 3.01
2444 2560 0.402504 TGCCCGGTACTTGTGGATTT 59.597 50.000 0.00 0.00 0.00 2.17
2507 2624 8.630917 GGCAGATCTATAGTCTGTAAAAGTGTA 58.369 37.037 22.41 0.00 43.86 2.90
2844 2964 9.632638 AGTTTTATCACCAAAGATGTATAGCAT 57.367 29.630 0.00 0.00 41.24 3.79
2920 3040 2.152016 ACGAAGTTCCTTTGCCTTAGC 58.848 47.619 0.00 0.00 37.78 3.09
2933 3053 1.270839 GCCTTAGCCACTCAACAGACA 60.271 52.381 0.00 0.00 0.00 3.41
2948 3068 5.897250 TCAACAGACAAGGACTATATGCCTA 59.103 40.000 0.00 0.00 33.20 3.93
2964 3085 3.801698 TGCCTATGAGCACTTCATCTTC 58.198 45.455 0.00 0.00 43.03 2.87
2986 3107 4.887071 TCTGAAGAAAAAGCAGTGCCTTTA 59.113 37.500 12.58 3.55 34.12 1.85
3027 3148 5.239525 ACATCTTTGAGCACTTCAGGTAAAC 59.760 40.000 0.00 0.00 37.07 2.01
3125 3247 8.416329 ACCAGAGAATATAACCAATTCAAATGC 58.584 33.333 0.00 0.00 36.09 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.017440 GCAGAGTTATAAATATCCAACCGCAA 60.017 38.462 0.00 0.00 0.00 4.85
1 2 5.468746 GCAGAGTTATAAATATCCAACCGCA 59.531 40.000 0.00 0.00 0.00 5.69
2 3 5.701290 AGCAGAGTTATAAATATCCAACCGC 59.299 40.000 0.00 0.00 0.00 5.68
3 4 6.706270 ACAGCAGAGTTATAAATATCCAACCG 59.294 38.462 0.00 0.00 0.00 4.44
4 5 7.520614 GCACAGCAGAGTTATAAATATCCAACC 60.521 40.741 0.00 0.00 0.00 3.77
5 6 7.012327 TGCACAGCAGAGTTATAAATATCCAAC 59.988 37.037 0.00 0.00 33.32 3.77
6 7 7.053498 TGCACAGCAGAGTTATAAATATCCAA 58.947 34.615 0.00 0.00 33.32 3.53
7 8 6.591001 TGCACAGCAGAGTTATAAATATCCA 58.409 36.000 0.00 0.00 33.32 3.41
8 9 7.173907 ACATGCACAGCAGAGTTATAAATATCC 59.826 37.037 0.00 0.00 43.65 2.59
9 10 8.013947 CACATGCACAGCAGAGTTATAAATATC 58.986 37.037 0.00 0.00 43.65 1.63
10 11 7.500227 ACACATGCACAGCAGAGTTATAAATAT 59.500 33.333 0.00 0.00 43.65 1.28
11 12 6.823182 ACACATGCACAGCAGAGTTATAAATA 59.177 34.615 0.00 0.00 43.65 1.40
12 13 5.649395 ACACATGCACAGCAGAGTTATAAAT 59.351 36.000 0.00 0.00 43.65 1.40
13 14 5.003160 ACACATGCACAGCAGAGTTATAAA 58.997 37.500 0.00 0.00 43.65 1.40
14 15 4.578871 ACACATGCACAGCAGAGTTATAA 58.421 39.130 0.00 0.00 43.65 0.98
15 16 4.206477 ACACATGCACAGCAGAGTTATA 57.794 40.909 0.00 0.00 43.65 0.98
16 17 3.063510 ACACATGCACAGCAGAGTTAT 57.936 42.857 0.00 0.00 43.65 1.89
17 18 2.549064 ACACATGCACAGCAGAGTTA 57.451 45.000 0.00 0.00 43.65 2.24
18 19 1.335810 CAACACATGCACAGCAGAGTT 59.664 47.619 0.00 0.00 43.65 3.01
19 20 0.949397 CAACACATGCACAGCAGAGT 59.051 50.000 0.00 0.00 43.65 3.24
20 21 3.767287 CAACACATGCACAGCAGAG 57.233 52.632 0.00 0.00 43.65 3.35
51 52 2.229543 TCTTCAATCATGTTGCACTGGC 59.770 45.455 0.00 0.00 41.68 4.85
52 53 4.713824 ATCTTCAATCATGTTGCACTGG 57.286 40.909 0.00 0.00 0.00 4.00
53 54 4.791676 CGAATCTTCAATCATGTTGCACTG 59.208 41.667 0.00 0.00 0.00 3.66
54 55 4.456911 ACGAATCTTCAATCATGTTGCACT 59.543 37.500 0.00 0.00 0.00 4.40
55 56 4.556135 CACGAATCTTCAATCATGTTGCAC 59.444 41.667 0.00 0.00 0.00 4.57
56 57 4.725359 CACGAATCTTCAATCATGTTGCA 58.275 39.130 0.00 0.00 0.00 4.08
57 58 3.545078 GCACGAATCTTCAATCATGTTGC 59.455 43.478 0.00 0.00 0.00 4.17
58 59 4.791676 CAGCACGAATCTTCAATCATGTTG 59.208 41.667 0.00 0.00 0.00 3.33
59 60 4.696877 TCAGCACGAATCTTCAATCATGTT 59.303 37.500 0.00 0.00 0.00 2.71
60 61 4.256110 TCAGCACGAATCTTCAATCATGT 58.744 39.130 0.00 0.00 0.00 3.21
61 62 4.870221 TCAGCACGAATCTTCAATCATG 57.130 40.909 0.00 0.00 0.00 3.07
62 63 5.821470 AGAATCAGCACGAATCTTCAATCAT 59.179 36.000 0.00 0.00 28.87 2.45
63 64 5.181009 AGAATCAGCACGAATCTTCAATCA 58.819 37.500 0.00 0.00 28.87 2.57
64 65 5.731599 AGAATCAGCACGAATCTTCAATC 57.268 39.130 0.00 0.00 28.87 2.67
65 66 6.506500 AAAGAATCAGCACGAATCTTCAAT 57.493 33.333 6.86 0.00 42.02 2.57
66 67 5.947228 AAAGAATCAGCACGAATCTTCAA 57.053 34.783 6.86 0.00 42.02 2.69
67 68 5.947228 AAAAGAATCAGCACGAATCTTCA 57.053 34.783 6.86 0.00 42.02 3.02
97 98 3.242220 GCAGAATCAGCACGAATACTGTG 60.242 47.826 0.00 0.00 40.32 3.66
98 99 2.932614 GCAGAATCAGCACGAATACTGT 59.067 45.455 0.00 0.00 35.37 3.55
99 100 2.931969 TGCAGAATCAGCACGAATACTG 59.068 45.455 0.00 0.00 37.02 2.74
100 101 3.193263 CTGCAGAATCAGCACGAATACT 58.807 45.455 8.42 0.00 37.02 2.12
101 102 3.582444 CTGCAGAATCAGCACGAATAC 57.418 47.619 8.42 0.00 37.02 1.89
110 111 0.392193 AGGGAACGCTGCAGAATCAG 60.392 55.000 20.43 4.97 37.15 2.90
111 112 0.674581 CAGGGAACGCTGCAGAATCA 60.675 55.000 20.43 0.00 0.00 2.57
112 113 1.372087 CCAGGGAACGCTGCAGAATC 61.372 60.000 20.43 11.47 0.00 2.52
113 114 1.377725 CCAGGGAACGCTGCAGAAT 60.378 57.895 20.43 0.00 0.00 2.40
114 115 2.032528 CCAGGGAACGCTGCAGAA 59.967 61.111 20.43 0.00 0.00 3.02
115 116 4.020617 CCCAGGGAACGCTGCAGA 62.021 66.667 20.43 0.00 0.00 4.26
116 117 4.020617 TCCCAGGGAACGCTGCAG 62.021 66.667 5.36 10.11 0.00 4.41
117 118 4.329545 GTCCCAGGGAACGCTGCA 62.330 66.667 10.89 0.00 31.38 4.41
118 119 4.021925 AGTCCCAGGGAACGCTGC 62.022 66.667 10.89 0.00 31.38 5.25
119 120 2.046892 CAGTCCCAGGGAACGCTG 60.047 66.667 10.89 10.14 31.38 5.18
120 121 3.322466 CCAGTCCCAGGGAACGCT 61.322 66.667 10.89 0.00 31.38 5.07
127 128 2.042762 TCCCATCCCAGTCCCAGG 59.957 66.667 0.00 0.00 0.00 4.45
128 129 0.401105 ATCTCCCATCCCAGTCCCAG 60.401 60.000 0.00 0.00 0.00 4.45
129 130 0.046242 AATCTCCCATCCCAGTCCCA 59.954 55.000 0.00 0.00 0.00 4.37
130 131 0.767998 GAATCTCCCATCCCAGTCCC 59.232 60.000 0.00 0.00 0.00 4.46
131 132 1.419387 CAGAATCTCCCATCCCAGTCC 59.581 57.143 0.00 0.00 0.00 3.85
132 133 1.202746 GCAGAATCTCCCATCCCAGTC 60.203 57.143 0.00 0.00 0.00 3.51
133 134 0.842635 GCAGAATCTCCCATCCCAGT 59.157 55.000 0.00 0.00 0.00 4.00
134 135 0.250209 CGCAGAATCTCCCATCCCAG 60.250 60.000 0.00 0.00 0.00 4.45
135 136 1.832219 CGCAGAATCTCCCATCCCA 59.168 57.895 0.00 0.00 0.00 4.37
136 137 1.599240 GCGCAGAATCTCCCATCCC 60.599 63.158 0.30 0.00 0.00 3.85
137 138 0.883814 CAGCGCAGAATCTCCCATCC 60.884 60.000 11.47 0.00 0.00 3.51
138 139 1.505477 GCAGCGCAGAATCTCCCATC 61.505 60.000 11.47 0.00 0.00 3.51
139 140 1.525535 GCAGCGCAGAATCTCCCAT 60.526 57.895 11.47 0.00 0.00 4.00
140 141 2.124983 GCAGCGCAGAATCTCCCA 60.125 61.111 11.47 0.00 0.00 4.37
141 142 3.267860 CGCAGCGCAGAATCTCCC 61.268 66.667 11.47 0.00 0.00 4.30
165 166 1.478105 GGGCTGGAAGATCATGATGCA 60.478 52.381 14.30 0.29 34.07 3.96
216 223 0.811281 GAATCTGGGGCGGAAAACAG 59.189 55.000 0.00 0.00 0.00 3.16
221 228 0.623194 TGAATGAATCTGGGGCGGAA 59.377 50.000 0.00 0.00 0.00 4.30
232 239 4.722194 CGGTTTCGTGTGAATGAATGAAT 58.278 39.130 0.00 0.00 33.20 2.57
233 240 4.140518 CGGTTTCGTGTGAATGAATGAA 57.859 40.909 0.00 0.00 33.20 2.57
234 241 3.804518 CGGTTTCGTGTGAATGAATGA 57.195 42.857 0.00 0.00 33.20 2.57
510 526 1.841556 TGCTTCCCCTCGGAACAGT 60.842 57.895 0.00 0.00 43.57 3.55
512 528 2.747686 GTGCTTCCCCTCGGAACA 59.252 61.111 0.00 0.00 43.57 3.18
536 552 2.741211 GACGTGGAGTTTCCCGGC 60.741 66.667 0.00 4.25 35.03 6.13
649 671 0.920763 TTCATGGAGGCTGGGGTGAT 60.921 55.000 0.00 0.00 0.00 3.06
768 796 0.475906 AGTGAGCTTCAGCCAAGGTT 59.524 50.000 0.00 0.00 43.17 3.50
803 837 9.588096 TGCTGACAGATAAAATATCTAGGAGTA 57.412 33.333 6.65 0.00 0.00 2.59
804 838 8.364142 GTGCTGACAGATAAAATATCTAGGAGT 58.636 37.037 6.65 0.00 0.00 3.85
805 839 8.363390 TGTGCTGACAGATAAAATATCTAGGAG 58.637 37.037 6.65 0.00 0.00 3.69
806 840 8.144478 GTGTGCTGACAGATAAAATATCTAGGA 58.856 37.037 6.65 0.00 30.74 2.94
807 841 8.147058 AGTGTGCTGACAGATAAAATATCTAGG 58.853 37.037 6.65 0.00 30.74 3.02
808 842 9.190858 GAGTGTGCTGACAGATAAAATATCTAG 57.809 37.037 6.65 0.00 30.74 2.43
809 843 8.695456 TGAGTGTGCTGACAGATAAAATATCTA 58.305 33.333 6.65 0.00 30.74 1.98
810 844 7.559486 TGAGTGTGCTGACAGATAAAATATCT 58.441 34.615 6.65 0.00 30.74 1.98
811 845 7.776933 TGAGTGTGCTGACAGATAAAATATC 57.223 36.000 6.65 0.00 30.74 1.63
812 846 7.170489 CGATGAGTGTGCTGACAGATAAAATAT 59.830 37.037 6.65 0.00 30.74 1.28
813 847 6.476706 CGATGAGTGTGCTGACAGATAAAATA 59.523 38.462 6.65 0.00 30.74 1.40
814 848 5.292834 CGATGAGTGTGCTGACAGATAAAAT 59.707 40.000 6.65 0.00 30.74 1.82
815 849 4.627035 CGATGAGTGTGCTGACAGATAAAA 59.373 41.667 6.65 0.00 30.74 1.52
838 872 1.202604 TCCCACTTTGACTTGACGACC 60.203 52.381 0.00 0.00 0.00 4.79
859 893 0.319728 GGTGCTGCTGAGAAGTGAGA 59.680 55.000 0.00 0.00 0.00 3.27
860 894 0.034476 TGGTGCTGCTGAGAAGTGAG 59.966 55.000 0.00 0.00 0.00 3.51
861 895 0.034476 CTGGTGCTGCTGAGAAGTGA 59.966 55.000 0.00 0.00 0.00 3.41
862 896 0.250209 ACTGGTGCTGCTGAGAAGTG 60.250 55.000 0.00 0.00 0.00 3.16
863 897 0.034616 GACTGGTGCTGCTGAGAAGT 59.965 55.000 0.00 0.00 0.00 3.01
864 898 0.034476 TGACTGGTGCTGCTGAGAAG 59.966 55.000 0.00 0.00 0.00 2.85
865 899 0.250038 GTGACTGGTGCTGCTGAGAA 60.250 55.000 0.00 0.00 0.00 2.87
905 939 1.823041 GCATGGGAGGCAAGAGCTC 60.823 63.158 5.27 5.27 41.70 4.09
906 940 2.146146 TTGCATGGGAGGCAAGAGCT 62.146 55.000 0.00 0.00 45.57 4.09
907 941 1.679977 TTGCATGGGAGGCAAGAGC 60.680 57.895 0.00 0.00 45.57 4.09
908 942 4.749323 TTGCATGGGAGGCAAGAG 57.251 55.556 0.00 0.00 45.57 2.85
913 947 2.812499 CATGCTTGCATGGGAGGC 59.188 61.111 23.42 0.00 0.00 4.70
945 982 3.868077 GCTCCATGTCTATTGTCAGTGAC 59.132 47.826 16.68 16.68 0.00 3.67
959 1000 2.369633 TGCTGGGATCGCTCCATGT 61.370 57.895 7.74 0.00 44.08 3.21
1036 1080 4.143986 TGTCTTGTGTGGATGTTGTGTA 57.856 40.909 0.00 0.00 0.00 2.90
1038 1082 3.243168 CCTTGTCTTGTGTGGATGTTGTG 60.243 47.826 0.00 0.00 0.00 3.33
1068 1115 1.941668 GCTAGCTGTTCTTCACCGCTT 60.942 52.381 7.70 0.00 42.98 4.68
1069 1116 0.390472 GCTAGCTGTTCTTCACCGCT 60.390 55.000 7.70 0.00 46.78 5.52
1070 1117 0.670546 TGCTAGCTGTTCTTCACCGC 60.671 55.000 17.23 0.00 35.89 5.68
1071 1118 1.929836 GATGCTAGCTGTTCTTCACCG 59.070 52.381 17.23 0.00 0.00 4.94
1072 1119 2.284190 GGATGCTAGCTGTTCTTCACC 58.716 52.381 17.23 2.66 0.00 4.02
1073 1120 2.977914 TGGATGCTAGCTGTTCTTCAC 58.022 47.619 17.23 0.00 0.00 3.18
1074 1121 3.538591 CATGGATGCTAGCTGTTCTTCA 58.461 45.455 17.23 5.26 0.00 3.02
1080 1127 1.150081 GGCCATGGATGCTAGCTGT 59.850 57.895 18.40 4.43 0.00 4.40
1081 1128 0.889638 CAGGCCATGGATGCTAGCTG 60.890 60.000 18.40 5.04 0.00 4.24
1149 1196 0.041833 TGGCTCTACCTCTTCTGGCT 59.958 55.000 0.00 0.00 40.22 4.75
1311 1361 1.901085 CTGCTGGGACTGGAGGTAC 59.099 63.158 0.00 0.00 41.60 3.34
1391 1442 2.951642 GAGAGGAGATGGACAGAGACTG 59.048 54.545 0.00 0.00 37.52 3.51
1400 1451 3.043465 AGCATCAAGAGAGGAGATGGA 57.957 47.619 0.00 0.00 39.53 3.41
1443 1494 4.525996 TCAAGAGAGGAGATGACAGAGAG 58.474 47.826 0.00 0.00 0.00 3.20
1658 1765 1.654954 CTCTTGACGACGACCCCGAT 61.655 60.000 0.00 0.00 39.50 4.18
1772 1884 3.489785 TCTTTTTCTTCTTCGTCGTCTGC 59.510 43.478 0.00 0.00 0.00 4.26
1777 1889 5.637104 TTCTGTCTTTTTCTTCTTCGTCG 57.363 39.130 0.00 0.00 0.00 5.12
1778 1890 8.175716 TCTTTTTCTGTCTTTTTCTTCTTCGTC 58.824 33.333 0.00 0.00 0.00 4.20
1779 1891 8.040716 TCTTTTTCTGTCTTTTTCTTCTTCGT 57.959 30.769 0.00 0.00 0.00 3.85
1780 1892 8.895932 TTCTTTTTCTGTCTTTTTCTTCTTCG 57.104 30.769 0.00 0.00 0.00 3.79
1860 1973 6.599244 TGCAACAAATAGCAACTAGATTAGCT 59.401 34.615 0.00 2.51 37.90 3.32
1884 1997 3.422343 GCAATCTTCGTCTTCGACTGTTG 60.422 47.826 0.00 0.00 46.03 3.33
1890 2003 3.182182 CATCTGCAATCTTCGTCTTCGA 58.818 45.455 0.00 0.00 44.66 3.71
1892 2005 3.928992 TCACATCTGCAATCTTCGTCTTC 59.071 43.478 0.00 0.00 0.00 2.87
2020 2134 0.794229 GTTGGCATCACACGATTGCG 60.794 55.000 0.00 0.00 44.79 4.85
2021 2135 0.240678 TGTTGGCATCACACGATTGC 59.759 50.000 0.00 0.00 0.00 3.56
2022 2136 1.805943 TCTGTTGGCATCACACGATTG 59.194 47.619 0.00 0.00 0.00 2.67
2023 2137 2.183478 TCTGTTGGCATCACACGATT 57.817 45.000 0.00 0.00 0.00 3.34
2025 2139 1.441738 CATCTGTTGGCATCACACGA 58.558 50.000 0.00 0.00 0.00 4.35
2026 2140 0.179181 GCATCTGTTGGCATCACACG 60.179 55.000 0.00 0.00 0.00 4.49
2027 2141 3.708195 GCATCTGTTGGCATCACAC 57.292 52.632 0.00 0.00 0.00 3.82
2157 2271 7.733402 AAACGCTCCTACATTAGTGTAAAAA 57.267 32.000 0.00 0.00 40.16 1.94
2158 2272 7.733402 AAAACGCTCCTACATTAGTGTAAAA 57.267 32.000 0.00 0.00 40.16 1.52
2159 2273 7.733402 AAAAACGCTCCTACATTAGTGTAAA 57.267 32.000 0.00 0.00 40.16 2.01
2235 2349 6.021596 CCATAATACAAGAGCGTTTTGACAC 58.978 40.000 5.15 0.00 0.00 3.67
2251 2366 2.606378 ACTCCCTCCGTCCCATAATAC 58.394 52.381 0.00 0.00 0.00 1.89
2410 2526 1.225426 GGCATGGACTCCTGCATCA 59.775 57.895 16.63 0.00 40.18 3.07
2443 2559 3.125487 CCGCGGACACACATATTTACAAA 59.875 43.478 24.07 0.00 0.00 2.83
2444 2560 2.673862 CCGCGGACACACATATTTACAA 59.326 45.455 24.07 0.00 0.00 2.41
2507 2624 5.007724 GCTTATTTTTGCGATACAGGCTACT 59.992 40.000 0.00 0.00 0.00 2.57
2916 3036 2.703536 TCCTTGTCTGTTGAGTGGCTAA 59.296 45.455 0.00 0.00 0.00 3.09
2920 3040 2.918712 AGTCCTTGTCTGTTGAGTGG 57.081 50.000 0.00 0.00 0.00 4.00
2933 3053 5.090139 AGTGCTCATAGGCATATAGTCCTT 58.910 41.667 0.00 0.00 44.34 3.36
2961 3081 3.317430 AGGCACTGCTTTTTCTTCAGAAG 59.683 43.478 3.45 3.45 37.18 2.85
2964 3085 3.722728 AAGGCACTGCTTTTTCTTCAG 57.277 42.857 0.00 0.00 40.86 3.02


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

AutoCloner maintained by Alex Coulton.