Multiple sequence alignment - TraesCS2A01G182900

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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 TraesCS2A01G182900 chr2A 100.000 3802 0 0 1 3802 142706925 142710726 0.000000e+00 7022
1 TraesCS2A01G182900 chr2D 96.042 3638 67 24 222 3802 134790074 134793691 0.000000e+00 5849
2 TraesCS2A01G182900 chr2B 95.276 3662 79 36 222 3802 191741400 191745048 0.000000e+00 5718
3 TraesCS2A01G182900 chr5D 92.857 224 15 1 1 223 58674131 58674354 1.320000e-84 324
4 TraesCS2A01G182900 chr5A 92.857 224 15 1 3 225 604748433 604748210 1.320000e-84 324
5 TraesCS2A01G182900 chr5A 92.444 225 14 3 4 225 94080598 94080822 6.130000e-83 318
6 TraesCS2A01G182900 chr7A 91.775 231 17 2 3 231 477310047 477309817 1.700000e-83 320
7 TraesCS2A01G182900 chr7A 92.105 228 17 1 1 227 645255722 645255949 1.700000e-83 320
8 TraesCS2A01G182900 chr3A 92.105 228 16 2 1 226 475394498 475394725 1.700000e-83 320
9 TraesCS2A01G182900 chr3A 91.667 228 17 2 1 226 454772135 454771908 7.930000e-82 315
10 TraesCS2A01G182900 chr1A 92.411 224 16 1 1 223 475200460 475200683 6.130000e-83 318
11 TraesCS2A01G182900 chr1A 92.035 226 16 2 3 226 557965986 557966211 2.200000e-82 316


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 TraesCS2A01G182900 chr2A 142706925 142710726 3801 False 7022 7022 100.000 1 3802 1 chr2A.!!$F1 3801
1 TraesCS2A01G182900 chr2D 134790074 134793691 3617 False 5849 5849 96.042 222 3802 1 chr2D.!!$F1 3580
2 TraesCS2A01G182900 chr2B 191741400 191745048 3648 False 5718 5718 95.276 222 3802 1 chr2B.!!$F1 3580

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
535 584 0.452784 CGCAGCAGTAAAAACTCGGC 60.453 55.0 0.00 0.0 0.00 5.54 F
1238 1341 0.179215 GCTGGAATTCAGTGCGTTCG 60.179 55.0 7.93 0.0 45.08 3.95 F
1941 2052 0.690762 ACCCACAGCAATACGAAGGT 59.309 50.0 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1503 0.332972 AAAGCTTCCCTAAGGGCCAG 59.667 55.000 6.18 0.00 43.94 4.85 R
2597 2708 0.179225 CGCGGAACATTGTTTCCTCG 60.179 55.000 3.08 9.16 44.80 4.63 R
2884 2995 1.067565 GCAACGTCAGTCTCATCTCCA 60.068 52.381 0.00 0.00 0.00 3.86 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
22 23 5.665916 AAGCCCTTTGATTTGTAGGAATG 57.334 39.130 0.00 0.00 0.00 2.67
23 24 4.026052 AGCCCTTTGATTTGTAGGAATGG 58.974 43.478 0.00 0.00 0.00 3.16
24 25 4.023291 GCCCTTTGATTTGTAGGAATGGA 58.977 43.478 0.00 0.00 0.00 3.41
25 26 4.651045 GCCCTTTGATTTGTAGGAATGGAT 59.349 41.667 0.00 0.00 0.00 3.41
26 27 5.129320 GCCCTTTGATTTGTAGGAATGGATT 59.871 40.000 0.00 0.00 0.00 3.01
27 28 6.683861 GCCCTTTGATTTGTAGGAATGGATTC 60.684 42.308 0.00 0.00 36.08 2.52
28 29 6.380846 CCCTTTGATTTGTAGGAATGGATTCA 59.619 38.462 1.94 0.00 38.53 2.57
29 30 7.070322 CCCTTTGATTTGTAGGAATGGATTCAT 59.930 37.037 1.94 0.00 38.53 2.57
30 31 9.135189 CCTTTGATTTGTAGGAATGGATTCATA 57.865 33.333 1.94 0.00 38.53 2.15
42 43 8.059798 GGAATGGATTCATATTCCCATGTAAG 57.940 38.462 15.73 0.00 44.17 2.34
43 44 7.890127 GGAATGGATTCATATTCCCATGTAAGA 59.110 37.037 15.73 0.00 44.17 2.10
44 45 9.471702 GAATGGATTCATATTCCCATGTAAGAT 57.528 33.333 0.00 0.00 39.19 2.40
47 48 8.551440 TGGATTCATATTCCCATGTAAGATAGG 58.449 37.037 0.00 0.00 31.87 2.57
48 49 8.772250 GGATTCATATTCCCATGTAAGATAGGA 58.228 37.037 0.00 0.00 0.00 2.94
52 53 9.337714 TCATATTCCCATGTAAGATAGGAATCA 57.662 33.333 11.86 2.98 44.29 2.57
53 54 9.964354 CATATTCCCATGTAAGATAGGAATCAA 57.036 33.333 11.86 0.00 44.29 2.57
56 57 6.701340 TCCCATGTAAGATAGGAATCAATCG 58.299 40.000 0.00 0.00 34.28 3.34
57 58 6.270000 TCCCATGTAAGATAGGAATCAATCGT 59.730 38.462 0.00 0.00 34.28 3.73
58 59 6.936900 CCCATGTAAGATAGGAATCAATCGTT 59.063 38.462 0.00 0.00 34.28 3.85
59 60 7.118390 CCCATGTAAGATAGGAATCAATCGTTC 59.882 40.741 0.00 0.00 34.28 3.95
60 61 7.657354 CCATGTAAGATAGGAATCAATCGTTCA 59.343 37.037 0.00 0.00 34.28 3.18
61 62 8.491152 CATGTAAGATAGGAATCAATCGTTCAC 58.509 37.037 0.00 0.00 34.28 3.18
62 63 7.552459 TGTAAGATAGGAATCAATCGTTCACA 58.448 34.615 0.00 0.00 34.28 3.58
63 64 8.204160 TGTAAGATAGGAATCAATCGTTCACAT 58.796 33.333 0.00 0.00 34.28 3.21
64 65 9.046296 GTAAGATAGGAATCAATCGTTCACATT 57.954 33.333 0.00 0.00 34.28 2.71
65 66 8.511604 AAGATAGGAATCAATCGTTCACATTT 57.488 30.769 0.00 0.00 34.28 2.32
66 67 8.511604 AGATAGGAATCAATCGTTCACATTTT 57.488 30.769 0.00 0.00 34.28 1.82
67 68 8.400947 AGATAGGAATCAATCGTTCACATTTTG 58.599 33.333 0.00 0.00 34.28 2.44
68 69 6.573664 AGGAATCAATCGTTCACATTTTGA 57.426 33.333 0.00 0.00 0.00 2.69
69 70 6.980593 AGGAATCAATCGTTCACATTTTGAA 58.019 32.000 0.00 0.00 42.26 2.69
70 71 7.086376 AGGAATCAATCGTTCACATTTTGAAG 58.914 34.615 0.00 0.00 45.23 3.02
71 72 6.308766 GGAATCAATCGTTCACATTTTGAAGG 59.691 38.462 0.00 0.00 45.23 3.46
99 100 8.635765 AAAAACATTAGCTAAGACTCAATGGA 57.364 30.769 12.54 0.00 32.20 3.41
100 101 8.635765 AAAACATTAGCTAAGACTCAATGGAA 57.364 30.769 12.54 0.00 32.20 3.53
101 102 8.635765 AAACATTAGCTAAGACTCAATGGAAA 57.364 30.769 12.54 0.00 32.20 3.13
102 103 8.635765 AACATTAGCTAAGACTCAATGGAAAA 57.364 30.769 12.54 0.00 32.20 2.29
103 104 8.635765 ACATTAGCTAAGACTCAATGGAAAAA 57.364 30.769 12.54 0.00 32.20 1.94
104 105 9.247861 ACATTAGCTAAGACTCAATGGAAAAAT 57.752 29.630 12.54 0.00 32.20 1.82
107 108 6.846350 AGCTAAGACTCAATGGAAAAATTCG 58.154 36.000 0.00 0.00 0.00 3.34
108 109 6.431234 AGCTAAGACTCAATGGAAAAATTCGT 59.569 34.615 0.00 0.00 0.00 3.85
109 110 7.606456 AGCTAAGACTCAATGGAAAAATTCGTA 59.394 33.333 0.00 0.00 0.00 3.43
110 111 8.398665 GCTAAGACTCAATGGAAAAATTCGTAT 58.601 33.333 0.00 0.00 0.00 3.06
111 112 9.922305 CTAAGACTCAATGGAAAAATTCGTATC 57.078 33.333 0.00 0.00 0.00 2.24
112 113 7.321745 AGACTCAATGGAAAAATTCGTATCC 57.678 36.000 0.00 0.00 0.00 2.59
113 114 7.112779 AGACTCAATGGAAAAATTCGTATCCT 58.887 34.615 0.00 0.00 33.02 3.24
114 115 8.265055 AGACTCAATGGAAAAATTCGTATCCTA 58.735 33.333 0.00 0.00 33.02 2.94
115 116 8.980481 ACTCAATGGAAAAATTCGTATCCTAT 57.020 30.769 0.00 0.00 33.02 2.57
116 117 8.840321 ACTCAATGGAAAAATTCGTATCCTATG 58.160 33.333 0.00 0.00 33.02 2.23
117 118 7.648142 TCAATGGAAAAATTCGTATCCTATGC 58.352 34.615 0.00 0.00 33.02 3.14
118 119 7.284261 TCAATGGAAAAATTCGTATCCTATGCA 59.716 33.333 0.00 0.00 33.02 3.96
119 120 7.765695 ATGGAAAAATTCGTATCCTATGCAT 57.234 32.000 3.79 3.79 33.02 3.96
120 121 7.202016 TGGAAAAATTCGTATCCTATGCATC 57.798 36.000 0.19 0.00 33.02 3.91
121 122 6.770303 TGGAAAAATTCGTATCCTATGCATCA 59.230 34.615 0.19 0.00 33.02 3.07
122 123 7.284261 TGGAAAAATTCGTATCCTATGCATCAA 59.716 33.333 0.19 0.00 33.02 2.57
123 124 8.134895 GGAAAAATTCGTATCCTATGCATCAAA 58.865 33.333 0.19 0.00 0.00 2.69
124 125 9.683069 GAAAAATTCGTATCCTATGCATCAAAT 57.317 29.630 0.19 0.00 0.00 2.32
125 126 9.467258 AAAAATTCGTATCCTATGCATCAAATG 57.533 29.630 0.19 0.00 0.00 2.32
126 127 7.984422 AATTCGTATCCTATGCATCAAATGA 57.016 32.000 0.19 0.00 0.00 2.57
127 128 6.785488 TTCGTATCCTATGCATCAAATGAC 57.215 37.500 0.19 0.00 0.00 3.06
128 129 5.852827 TCGTATCCTATGCATCAAATGACA 58.147 37.500 0.19 0.00 0.00 3.58
129 130 6.466812 TCGTATCCTATGCATCAAATGACAT 58.533 36.000 0.19 0.00 33.67 3.06
130 131 6.591448 TCGTATCCTATGCATCAAATGACATC 59.409 38.462 0.19 0.00 32.25 3.06
131 132 6.592994 CGTATCCTATGCATCAAATGACATCT 59.407 38.462 0.19 0.00 32.25 2.90
132 133 7.201504 CGTATCCTATGCATCAAATGACATCTC 60.202 40.741 0.19 0.00 32.25 2.75
133 134 5.311265 TCCTATGCATCAAATGACATCTCC 58.689 41.667 0.19 0.00 32.25 3.71
134 135 5.072736 TCCTATGCATCAAATGACATCTCCT 59.927 40.000 0.19 0.00 32.25 3.69
135 136 5.768662 CCTATGCATCAAATGACATCTCCTT 59.231 40.000 0.19 0.00 32.25 3.36
136 137 6.264744 CCTATGCATCAAATGACATCTCCTTT 59.735 38.462 0.19 0.00 32.25 3.11
137 138 5.988310 TGCATCAAATGACATCTCCTTTT 57.012 34.783 0.00 0.00 0.00 2.27
138 139 5.957798 TGCATCAAATGACATCTCCTTTTC 58.042 37.500 0.00 0.00 0.00 2.29
139 140 5.713389 TGCATCAAATGACATCTCCTTTTCT 59.287 36.000 0.00 0.00 0.00 2.52
140 141 6.885918 TGCATCAAATGACATCTCCTTTTCTA 59.114 34.615 0.00 0.00 0.00 2.10
141 142 7.558807 TGCATCAAATGACATCTCCTTTTCTAT 59.441 33.333 0.00 0.00 0.00 1.98
142 143 9.060347 GCATCAAATGACATCTCCTTTTCTATA 57.940 33.333 0.00 0.00 0.00 1.31
155 156 9.553064 TCTCCTTTTCTATAAGAATTGAGATGC 57.447 33.333 8.21 0.00 33.67 3.91
156 157 9.334947 CTCCTTTTCTATAAGAATTGAGATGCA 57.665 33.333 0.00 0.00 33.67 3.96
157 158 9.857656 TCCTTTTCTATAAGAATTGAGATGCAT 57.142 29.630 0.00 0.00 33.67 3.96
158 159 9.894783 CCTTTTCTATAAGAATTGAGATGCATG 57.105 33.333 2.46 0.00 33.67 4.06
161 162 9.617523 TTTCTATAAGAATTGAGATGCATGTCA 57.382 29.630 21.70 21.70 33.67 3.58
162 163 9.788889 TTCTATAAGAATTGAGATGCATGTCAT 57.211 29.630 25.41 13.07 38.32 3.06
172 173 3.806380 GATGCATGTCATCTCACTTCCT 58.194 45.455 2.46 0.00 46.29 3.36
173 174 4.953667 GATGCATGTCATCTCACTTCCTA 58.046 43.478 2.46 0.00 46.29 2.94
174 175 5.549347 GATGCATGTCATCTCACTTCCTAT 58.451 41.667 2.46 0.00 46.29 2.57
175 176 4.700700 TGCATGTCATCTCACTTCCTATG 58.299 43.478 0.00 0.00 0.00 2.23
176 177 4.406649 TGCATGTCATCTCACTTCCTATGA 59.593 41.667 0.00 0.00 0.00 2.15
177 178 5.071384 TGCATGTCATCTCACTTCCTATGAT 59.929 40.000 0.00 0.00 31.49 2.45
178 179 5.996513 GCATGTCATCTCACTTCCTATGATT 59.003 40.000 0.00 0.00 31.49 2.57
179 180 6.485984 GCATGTCATCTCACTTCCTATGATTT 59.514 38.462 0.00 0.00 31.49 2.17
180 181 7.013083 GCATGTCATCTCACTTCCTATGATTTT 59.987 37.037 0.00 0.00 31.49 1.82
181 182 8.557864 CATGTCATCTCACTTCCTATGATTTTC 58.442 37.037 0.00 0.00 31.49 2.29
182 183 7.050377 TGTCATCTCACTTCCTATGATTTTCC 58.950 38.462 0.00 0.00 31.49 3.13
183 184 7.092712 TGTCATCTCACTTCCTATGATTTTCCT 60.093 37.037 0.00 0.00 31.49 3.36
184 185 8.424918 GTCATCTCACTTCCTATGATTTTCCTA 58.575 37.037 0.00 0.00 31.49 2.94
185 186 9.163894 TCATCTCACTTCCTATGATTTTCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
186 187 9.790344 CATCTCACTTCCTATGATTTTCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
188 189 8.432805 TCTCACTTCCTATGATTTTCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
189 190 8.337118 TCACTTCCTATGATTTTCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
190 191 9.447279 TCACTTCCTATGATTTTCCTATTCCTA 57.553 33.333 0.00 0.00 0.00 2.94
191 192 9.495572 CACTTCCTATGATTTTCCTATTCCTAC 57.504 37.037 0.00 0.00 0.00 3.18
192 193 9.225682 ACTTCCTATGATTTTCCTATTCCTACA 57.774 33.333 0.00 0.00 0.00 2.74
219 220 9.732130 ATATTCCTATCTTATGAACAAAGGAGC 57.268 33.333 0.00 0.00 0.00 4.70
220 221 5.930135 TCCTATCTTATGAACAAAGGAGCC 58.070 41.667 0.00 0.00 0.00 4.70
284 285 3.424703 TGCAATGGAAGGAAAGAGAAGG 58.575 45.455 0.00 0.00 0.00 3.46
288 289 5.011023 GCAATGGAAGGAAAGAGAAGGAAAA 59.989 40.000 0.00 0.00 0.00 2.29
371 372 1.079127 CAGGCCTAACCAGTCCACG 60.079 63.158 3.98 0.00 43.14 4.94
535 584 0.452784 CGCAGCAGTAAAAACTCGGC 60.453 55.000 0.00 0.00 0.00 5.54
543 595 3.058224 CAGTAAAAACTCGGCAAGGAAGG 60.058 47.826 0.00 0.00 0.00 3.46
545 597 2.358322 AAAACTCGGCAAGGAAGGAA 57.642 45.000 0.00 0.00 0.00 3.36
546 598 1.897560 AAACTCGGCAAGGAAGGAAG 58.102 50.000 0.00 0.00 0.00 3.46
547 599 0.606673 AACTCGGCAAGGAAGGAAGC 60.607 55.000 0.00 0.00 0.00 3.86
548 600 1.003355 CTCGGCAAGGAAGGAAGCA 60.003 57.895 0.00 0.00 0.00 3.91
549 601 1.003355 TCGGCAAGGAAGGAAGCAG 60.003 57.895 0.00 0.00 0.00 4.24
550 602 2.694760 CGGCAAGGAAGGAAGCAGC 61.695 63.158 0.00 0.00 0.00 5.25
551 603 1.303970 GGCAAGGAAGGAAGCAGCT 60.304 57.895 0.00 0.00 0.00 4.24
552 604 1.593296 GGCAAGGAAGGAAGCAGCTG 61.593 60.000 10.11 10.11 0.00 4.24
553 605 1.881602 CAAGGAAGGAAGCAGCTGC 59.118 57.895 31.53 31.53 42.49 5.25
739 809 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
741 811 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
742 812 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
745 815 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
746 816 4.596585 CACCACCACCACCACCCC 62.597 72.222 0.00 0.00 0.00 4.95
747 817 4.855230 ACCACCACCACCACCCCT 62.855 66.667 0.00 0.00 0.00 4.79
748 818 2.530661 CCACCACCACCACCCCTA 60.531 66.667 0.00 0.00 0.00 3.53
749 819 2.754375 CACCACCACCACCCCTAC 59.246 66.667 0.00 0.00 0.00 3.18
750 820 2.530916 ACCACCACCACCCCTACC 60.531 66.667 0.00 0.00 0.00 3.18
751 821 3.712907 CCACCACCACCCCTACCG 61.713 72.222 0.00 0.00 0.00 4.02
752 822 4.404098 CACCACCACCCCTACCGC 62.404 72.222 0.00 0.00 0.00 5.68
1153 1253 1.195115 GAGGGGGATTTTGGGCTTTC 58.805 55.000 0.00 0.00 0.00 2.62
1206 1306 4.706962 ACTGTTGCTTTCAGGGGATTTATC 59.293 41.667 7.87 0.00 37.25 1.75
1232 1335 7.137426 GCTATTATTTGAGCTGGAATTCAGTG 58.863 38.462 7.93 0.00 45.08 3.66
1238 1341 0.179215 GCTGGAATTCAGTGCGTTCG 60.179 55.000 7.93 0.00 45.08 3.95
1392 1503 1.377202 TCTTGCCCTTGTCGGATGC 60.377 57.895 0.00 0.00 33.16 3.91
1500 1611 2.361757 CCACATTTTCAGTTGGTGCTCA 59.638 45.455 0.00 0.00 0.00 4.26
1543 1654 7.884816 TTAGTTATAATGGCGTGCTTATCTC 57.115 36.000 0.00 0.00 0.00 2.75
1754 1865 2.964438 TTCGACTGTTGCTTCGCCGT 62.964 55.000 0.00 0.00 35.15 5.68
1800 1911 3.010584 ACAGGGATTACTTGAGTGGCATT 59.989 43.478 0.00 0.00 0.00 3.56
1888 1999 4.118410 CAAGAGGAGTCGGATTTCAGATG 58.882 47.826 0.00 0.00 0.00 2.90
1941 2052 0.690762 ACCCACAGCAATACGAAGGT 59.309 50.000 0.00 0.00 0.00 3.50
2296 2407 4.246458 GGATTCTGTAGTTCTCCACACAC 58.754 47.826 0.00 0.00 0.00 3.82
2358 2469 1.278238 GTATTCACGGGCAAGACTCG 58.722 55.000 0.00 0.00 0.00 4.18
2767 2878 7.092716 GCTTCTATGCCTTTCTTCAATTTTCA 58.907 34.615 0.00 0.00 0.00 2.69
2843 2954 4.468153 AGGTACTCTTTTCAGACCCTCATC 59.532 45.833 0.00 0.00 0.00 2.92
2884 2995 2.634815 TAGAAGAGGTAGGCGACGAT 57.365 50.000 0.00 0.00 0.00 3.73
2899 3010 2.286713 CGACGATGGAGATGAGACTGAC 60.287 54.545 0.00 0.00 0.00 3.51
3004 3115 9.048446 CAGTCAACTGATGGAAAAATTTCATTT 57.952 29.630 4.05 0.00 46.59 2.32
3072 3183 2.192187 GCAGCCTAGGGAAGCATGC 61.192 63.158 10.51 10.51 0.00 4.06
3605 3716 7.885399 AGAAAGCAGTAGTTGATAATGGAAACT 59.115 33.333 0.00 0.00 37.82 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.467438 CCATTCCTACAAATCAAAGGGCTT 59.533 41.667 0.00 0.00 0.00 4.35
1 2 4.026052 CCATTCCTACAAATCAAAGGGCT 58.974 43.478 0.00 0.00 0.00 5.19
2 3 4.023291 TCCATTCCTACAAATCAAAGGGC 58.977 43.478 0.00 0.00 0.00 5.19
3 4 6.380846 TGAATCCATTCCTACAAATCAAAGGG 59.619 38.462 0.00 0.00 35.97 3.95
4 5 7.408756 TGAATCCATTCCTACAAATCAAAGG 57.591 36.000 0.00 0.00 35.97 3.11
8 9 9.300681 GGAATATGAATCCATTCCTACAAATCA 57.699 33.333 13.43 0.00 44.56 2.57
9 10 8.743714 GGGAATATGAATCCATTCCTACAAATC 58.256 37.037 17.70 2.76 46.35 2.17
10 11 8.233820 TGGGAATATGAATCCATTCCTACAAAT 58.766 33.333 17.70 0.00 46.35 2.32
11 12 7.590907 TGGGAATATGAATCCATTCCTACAAA 58.409 34.615 17.70 3.43 46.35 2.83
12 13 7.160457 TGGGAATATGAATCCATTCCTACAA 57.840 36.000 17.70 5.12 46.35 2.41
13 14 6.778542 TGGGAATATGAATCCATTCCTACA 57.221 37.500 17.70 9.54 46.35 2.74
14 15 7.177878 ACATGGGAATATGAATCCATTCCTAC 58.822 38.462 17.70 7.75 46.35 3.18
15 16 7.347319 ACATGGGAATATGAATCCATTCCTA 57.653 36.000 17.70 14.30 46.35 2.94
16 17 6.223574 ACATGGGAATATGAATCCATTCCT 57.776 37.500 17.70 3.11 46.35 3.36
17 18 7.890127 TCTTACATGGGAATATGAATCCATTCC 59.110 37.037 12.68 12.68 46.39 3.01
18 19 8.868522 TCTTACATGGGAATATGAATCCATTC 57.131 34.615 0.00 0.00 37.86 2.67
21 22 8.551440 CCTATCTTACATGGGAATATGAATCCA 58.449 37.037 0.00 0.00 38.80 3.41
22 23 8.772250 TCCTATCTTACATGGGAATATGAATCC 58.228 37.037 0.00 0.00 36.16 3.01
26 27 9.337714 TGATTCCTATCTTACATGGGAATATGA 57.662 33.333 11.10 0.00 45.50 2.15
27 28 9.964354 TTGATTCCTATCTTACATGGGAATATG 57.036 33.333 11.10 0.00 45.50 1.78
31 32 7.161404 CGATTGATTCCTATCTTACATGGGAA 58.839 38.462 0.00 2.28 41.77 3.97
32 33 6.270000 ACGATTGATTCCTATCTTACATGGGA 59.730 38.462 0.00 0.00 0.00 4.37
33 34 6.467677 ACGATTGATTCCTATCTTACATGGG 58.532 40.000 0.00 0.00 0.00 4.00
34 35 7.657354 TGAACGATTGATTCCTATCTTACATGG 59.343 37.037 0.00 0.00 0.00 3.66
35 36 8.491152 GTGAACGATTGATTCCTATCTTACATG 58.509 37.037 0.00 0.00 0.00 3.21
36 37 8.204160 TGTGAACGATTGATTCCTATCTTACAT 58.796 33.333 0.00 0.00 0.00 2.29
37 38 7.552459 TGTGAACGATTGATTCCTATCTTACA 58.448 34.615 0.00 0.00 0.00 2.41
38 39 8.594881 ATGTGAACGATTGATTCCTATCTTAC 57.405 34.615 0.00 0.00 0.00 2.34
39 40 9.613428 AAATGTGAACGATTGATTCCTATCTTA 57.387 29.630 0.00 0.00 0.00 2.10
40 41 8.511604 AAATGTGAACGATTGATTCCTATCTT 57.488 30.769 0.00 0.00 0.00 2.40
41 42 8.400947 CAAAATGTGAACGATTGATTCCTATCT 58.599 33.333 0.00 0.00 0.00 1.98
42 43 8.397906 TCAAAATGTGAACGATTGATTCCTATC 58.602 33.333 0.00 0.00 31.51 2.08
43 44 8.279970 TCAAAATGTGAACGATTGATTCCTAT 57.720 30.769 0.00 0.00 31.51 2.57
44 45 7.680442 TCAAAATGTGAACGATTGATTCCTA 57.320 32.000 0.00 0.00 31.51 2.94
45 46 6.573664 TCAAAATGTGAACGATTGATTCCT 57.426 33.333 0.00 0.00 31.51 3.36
46 47 6.308766 CCTTCAAAATGTGAACGATTGATTCC 59.691 38.462 0.00 0.00 41.47 3.01
47 48 7.083858 TCCTTCAAAATGTGAACGATTGATTC 58.916 34.615 0.00 0.00 41.47 2.52
48 49 6.980593 TCCTTCAAAATGTGAACGATTGATT 58.019 32.000 0.00 0.00 41.47 2.57
49 50 6.573664 TCCTTCAAAATGTGAACGATTGAT 57.426 33.333 0.00 0.00 41.47 2.57
50 51 6.384258 TTCCTTCAAAATGTGAACGATTGA 57.616 33.333 0.00 0.00 41.47 2.57
51 52 7.462109 TTTTCCTTCAAAATGTGAACGATTG 57.538 32.000 0.00 0.00 41.47 2.67
74 75 8.635765 TCCATTGAGTCTTAGCTAATGTTTTT 57.364 30.769 6.64 0.00 0.00 1.94
75 76 8.635765 TTCCATTGAGTCTTAGCTAATGTTTT 57.364 30.769 6.64 0.00 0.00 2.43
76 77 8.635765 TTTCCATTGAGTCTTAGCTAATGTTT 57.364 30.769 6.64 0.00 0.00 2.83
77 78 8.635765 TTTTCCATTGAGTCTTAGCTAATGTT 57.364 30.769 6.64 0.00 0.00 2.71
78 79 8.635765 TTTTTCCATTGAGTCTTAGCTAATGT 57.364 30.769 6.64 0.00 0.00 2.71
81 82 8.450964 CGAATTTTTCCATTGAGTCTTAGCTAA 58.549 33.333 5.94 5.94 0.00 3.09
82 83 7.606456 ACGAATTTTTCCATTGAGTCTTAGCTA 59.394 33.333 0.00 0.00 0.00 3.32
83 84 6.431234 ACGAATTTTTCCATTGAGTCTTAGCT 59.569 34.615 0.00 0.00 0.00 3.32
84 85 6.612306 ACGAATTTTTCCATTGAGTCTTAGC 58.388 36.000 0.00 0.00 0.00 3.09
85 86 9.922305 GATACGAATTTTTCCATTGAGTCTTAG 57.078 33.333 0.00 0.00 0.00 2.18
86 87 8.889717 GGATACGAATTTTTCCATTGAGTCTTA 58.110 33.333 0.00 0.00 0.00 2.10
87 88 7.611855 AGGATACGAATTTTTCCATTGAGTCTT 59.388 33.333 0.00 0.00 46.39 3.01
88 89 7.112779 AGGATACGAATTTTTCCATTGAGTCT 58.887 34.615 0.00 0.00 46.39 3.24
89 90 7.321745 AGGATACGAATTTTTCCATTGAGTC 57.678 36.000 0.00 0.00 46.39 3.36
90 91 8.840321 CATAGGATACGAATTTTTCCATTGAGT 58.160 33.333 0.00 0.00 46.39 3.41
91 92 7.805071 GCATAGGATACGAATTTTTCCATTGAG 59.195 37.037 0.00 0.00 46.39 3.02
92 93 7.284261 TGCATAGGATACGAATTTTTCCATTGA 59.716 33.333 0.00 0.00 46.39 2.57
93 94 7.424803 TGCATAGGATACGAATTTTTCCATTG 58.575 34.615 0.00 0.00 46.39 2.82
94 95 7.581213 TGCATAGGATACGAATTTTTCCATT 57.419 32.000 0.00 0.00 46.39 3.16
95 96 7.448161 TGATGCATAGGATACGAATTTTTCCAT 59.552 33.333 0.00 0.00 46.39 3.41
96 97 6.770303 TGATGCATAGGATACGAATTTTTCCA 59.230 34.615 0.00 0.00 46.39 3.53
97 98 7.202016 TGATGCATAGGATACGAATTTTTCC 57.798 36.000 0.00 0.00 46.39 3.13
98 99 9.683069 ATTTGATGCATAGGATACGAATTTTTC 57.317 29.630 0.00 0.00 46.39 2.29
99 100 9.467258 CATTTGATGCATAGGATACGAATTTTT 57.533 29.630 0.00 0.00 46.39 1.94
100 101 8.849168 TCATTTGATGCATAGGATACGAATTTT 58.151 29.630 0.00 0.00 46.39 1.82
101 102 8.292448 GTCATTTGATGCATAGGATACGAATTT 58.708 33.333 0.00 0.00 46.39 1.82
102 103 7.445096 TGTCATTTGATGCATAGGATACGAATT 59.555 33.333 0.00 0.00 46.39 2.17
103 104 6.936335 TGTCATTTGATGCATAGGATACGAAT 59.064 34.615 0.00 0.00 46.39 3.34
104 105 6.287525 TGTCATTTGATGCATAGGATACGAA 58.712 36.000 0.00 0.00 46.39 3.85
105 106 5.852827 TGTCATTTGATGCATAGGATACGA 58.147 37.500 0.00 0.00 46.39 3.43
106 107 6.592994 AGATGTCATTTGATGCATAGGATACG 59.407 38.462 0.00 0.00 33.20 3.06
107 108 7.065563 GGAGATGTCATTTGATGCATAGGATAC 59.934 40.741 0.00 0.00 30.80 2.24
108 109 7.037802 AGGAGATGTCATTTGATGCATAGGATA 60.038 37.037 0.00 0.00 30.80 2.59
109 110 5.944599 GGAGATGTCATTTGATGCATAGGAT 59.055 40.000 0.00 0.00 30.80 3.24
110 111 5.072736 AGGAGATGTCATTTGATGCATAGGA 59.927 40.000 0.00 0.00 30.80 2.94
111 112 5.314529 AGGAGATGTCATTTGATGCATAGG 58.685 41.667 0.00 0.00 30.80 2.57
112 113 6.879276 AAGGAGATGTCATTTGATGCATAG 57.121 37.500 0.00 0.00 30.80 2.23
113 114 7.558807 AGAAAAGGAGATGTCATTTGATGCATA 59.441 33.333 3.04 0.00 36.80 3.14
114 115 6.380274 AGAAAAGGAGATGTCATTTGATGCAT 59.620 34.615 0.00 0.00 36.80 3.96
115 116 5.713389 AGAAAAGGAGATGTCATTTGATGCA 59.287 36.000 3.04 0.00 36.80 3.96
116 117 6.205101 AGAAAAGGAGATGTCATTTGATGC 57.795 37.500 3.04 0.00 36.80 3.91
129 130 9.553064 GCATCTCAATTCTTATAGAAAAGGAGA 57.447 33.333 14.63 14.63 40.06 3.71
130 131 9.334947 TGCATCTCAATTCTTATAGAAAAGGAG 57.665 33.333 0.00 0.00 37.82 3.69
131 132 9.857656 ATGCATCTCAATTCTTATAGAAAAGGA 57.142 29.630 0.00 0.00 37.82 3.36
132 133 9.894783 CATGCATCTCAATTCTTATAGAAAAGG 57.105 33.333 0.00 0.00 37.82 3.11
135 136 9.617523 TGACATGCATCTCAATTCTTATAGAAA 57.382 29.630 1.73 0.00 37.82 2.52
136 137 9.788889 ATGACATGCATCTCAATTCTTATAGAA 57.211 29.630 8.81 0.00 33.23 2.10
152 153 3.928005 AGGAAGTGAGATGACATGCAT 57.072 42.857 0.00 0.00 40.77 3.96
153 154 4.406649 TCATAGGAAGTGAGATGACATGCA 59.593 41.667 0.00 0.00 0.00 3.96
154 155 4.953667 TCATAGGAAGTGAGATGACATGC 58.046 43.478 0.00 0.00 0.00 4.06
155 156 8.447924 AAAATCATAGGAAGTGAGATGACATG 57.552 34.615 0.00 0.00 31.41 3.21
156 157 7.718753 GGAAAATCATAGGAAGTGAGATGACAT 59.281 37.037 0.00 0.00 31.41 3.06
157 158 7.050377 GGAAAATCATAGGAAGTGAGATGACA 58.950 38.462 0.00 0.00 31.41 3.58
158 159 7.278875 AGGAAAATCATAGGAAGTGAGATGAC 58.721 38.462 0.00 0.00 31.41 3.06
159 160 7.443302 AGGAAAATCATAGGAAGTGAGATGA 57.557 36.000 0.00 0.00 33.09 2.92
160 161 9.790344 AATAGGAAAATCATAGGAAGTGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
162 163 8.432805 GGAATAGGAAAATCATAGGAAGTGAGA 58.567 37.037 0.00 0.00 0.00 3.27
163 164 8.435982 AGGAATAGGAAAATCATAGGAAGTGAG 58.564 37.037 0.00 0.00 0.00 3.51
164 165 8.337118 AGGAATAGGAAAATCATAGGAAGTGA 57.663 34.615 0.00 0.00 0.00 3.41
165 166 9.495572 GTAGGAATAGGAAAATCATAGGAAGTG 57.504 37.037 0.00 0.00 0.00 3.16
166 167 9.225682 TGTAGGAATAGGAAAATCATAGGAAGT 57.774 33.333 0.00 0.00 0.00 3.01
193 194 9.732130 GCTCCTTTGTTCATAAGATAGGAATAT 57.268 33.333 0.00 0.00 30.67 1.28
194 195 8.157476 GGCTCCTTTGTTCATAAGATAGGAATA 58.843 37.037 0.00 0.00 30.67 1.75
195 196 7.001073 GGCTCCTTTGTTCATAAGATAGGAAT 58.999 38.462 0.00 0.00 30.67 3.01
196 197 6.357367 GGCTCCTTTGTTCATAAGATAGGAA 58.643 40.000 0.00 0.00 30.51 3.36
197 198 5.163195 GGGCTCCTTTGTTCATAAGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
198 199 5.066593 GGGCTCCTTTGTTCATAAGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
199 200 5.934781 AGGGCTCCTTTGTTCATAAGATAG 58.065 41.667 0.00 0.00 0.00 2.08
200 201 5.975988 AGGGCTCCTTTGTTCATAAGATA 57.024 39.130 0.00 0.00 0.00 1.98
201 202 4.870021 AGGGCTCCTTTGTTCATAAGAT 57.130 40.909 0.00 0.00 0.00 2.40
202 203 5.772393 TTAGGGCTCCTTTGTTCATAAGA 57.228 39.130 0.00 0.00 34.61 2.10
203 204 5.946377 AGTTTAGGGCTCCTTTGTTCATAAG 59.054 40.000 0.00 0.00 34.61 1.73
204 205 5.887754 AGTTTAGGGCTCCTTTGTTCATAA 58.112 37.500 0.00 0.00 34.61 1.90
205 206 5.497474 GAGTTTAGGGCTCCTTTGTTCATA 58.503 41.667 0.00 0.00 34.61 2.15
206 207 4.336280 GAGTTTAGGGCTCCTTTGTTCAT 58.664 43.478 0.00 0.00 34.61 2.57
207 208 3.751518 GAGTTTAGGGCTCCTTTGTTCA 58.248 45.455 0.00 0.00 34.61 3.18
208 209 2.742589 CGAGTTTAGGGCTCCTTTGTTC 59.257 50.000 0.00 0.00 34.61 3.18
209 210 2.552373 CCGAGTTTAGGGCTCCTTTGTT 60.552 50.000 0.00 0.00 34.61 2.83
210 211 1.003233 CCGAGTTTAGGGCTCCTTTGT 59.997 52.381 0.00 0.00 34.61 2.83
211 212 1.739067 CCGAGTTTAGGGCTCCTTTG 58.261 55.000 0.00 0.00 34.61 2.77
212 213 0.035343 GCCGAGTTTAGGGCTCCTTT 60.035 55.000 0.00 0.00 45.93 3.11
213 214 1.602771 GCCGAGTTTAGGGCTCCTT 59.397 57.895 0.00 0.00 45.93 3.36
214 215 3.310652 GCCGAGTTTAGGGCTCCT 58.689 61.111 0.00 0.00 45.93 3.69
219 220 0.106894 GGATCTGGCCGAGTTTAGGG 59.893 60.000 0.00 0.00 0.00 3.53
220 221 3.688553 GGATCTGGCCGAGTTTAGG 57.311 57.895 0.00 0.00 0.00 2.69
489 537 2.737252 TGCGCTTTTTCCGTTTTGTTTT 59.263 36.364 9.73 0.00 0.00 2.43
535 584 1.881602 GCAGCTGCTTCCTTCCTTG 59.118 57.895 31.33 0.00 38.21 3.61
751 821 4.832608 CTAGGGTTCCGCGGTGGC 62.833 72.222 27.15 15.86 37.80 5.01
752 822 4.157120 CCTAGGGTTCCGCGGTGG 62.157 72.222 27.15 7.10 40.09 4.61
753 823 4.157120 CCCTAGGGTTCCGCGGTG 62.157 72.222 27.15 0.00 0.00 4.94
973 1047 2.040359 CCTCTTCCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
1116 1199 0.958382 TCGGAACAAGCAAATCCCCG 60.958 55.000 0.00 0.00 37.08 5.73
1206 1306 6.017605 ACTGAATTCCAGCTCAAATAATAGCG 60.018 38.462 2.27 0.00 46.81 4.26
1232 1335 4.430423 CGCAGTGCTTCCGAACGC 62.430 66.667 14.33 0.00 0.00 4.84
1246 1349 8.487313 TCAAAATTTACTAAATCTAGCTCGCA 57.513 30.769 0.00 0.00 0.00 5.10
1392 1503 0.332972 AAAGCTTCCCTAAGGGCCAG 59.667 55.000 6.18 0.00 43.94 4.85
1543 1654 4.898829 TTATCCGCATGGTTTCATCAAG 57.101 40.909 0.00 0.00 36.30 3.02
1754 1865 2.863383 ATCCTCACCCATGGCCTCCA 62.863 60.000 6.09 0.00 38.19 3.86
1800 1911 2.515757 TCCTGCAACTGCGCAACA 60.516 55.556 13.05 6.73 45.83 3.33
1941 2052 1.376466 GAGCTGAAGGAGTGGGCAA 59.624 57.895 0.00 0.00 0.00 4.52
2296 2407 5.059833 CCCTTCGGAATCAAATCTAGGAAG 58.940 45.833 0.00 0.00 0.00 3.46
2358 2469 2.037251 TGCACTCTTGTTACCAGGACTC 59.963 50.000 0.00 0.00 0.00 3.36
2597 2708 0.179225 CGCGGAACATTGTTTCCTCG 60.179 55.000 3.08 9.16 44.80 4.63
2767 2878 3.554934 TGCACAGGAGACAAACAGAAAT 58.445 40.909 0.00 0.00 0.00 2.17
2884 2995 1.067565 GCAACGTCAGTCTCATCTCCA 60.068 52.381 0.00 0.00 0.00 3.86
2899 3010 2.098607 TCCTGTATCTACGGAAGCAACG 59.901 50.000 0.00 0.00 34.49 4.10
2989 3100 6.600822 TGCCAACTTCAAATGAAATTTTTCCA 59.399 30.769 0.00 0.00 46.10 3.53
3004 3115 2.290367 CGATTCTGTGTTGCCAACTTCA 59.710 45.455 9.30 7.38 0.00 3.02
3072 3183 7.902387 ATAATCTTCACATCCTCATCAATCG 57.098 36.000 0.00 0.00 0.00 3.34
3399 3510 7.653311 CCAGATCAGTGTATGTCGATATTTTCA 59.347 37.037 0.00 0.00 0.00 2.69
3605 3716 4.020543 ACAGTTTTTACCTCCTGCACAAA 58.979 39.130 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.