Multiple sequence alignment - TraesCS7A01G300000

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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 TraesCS7A01G300000 chr7A 100.000 2114 0 0 406 2519 414185848 414183735 0.000000e+00 3904
1 TraesCS7A01G300000 chr7A 100.000 258 0 0 1 258 414186253 414185996 6.300000e-131 477
2 TraesCS7A01G300000 chr7B 93.031 2138 98 18 408 2519 318840218 318842330 0.000000e+00 3075
3 TraesCS7A01G300000 chr7B 94.203 138 4 4 1 135 193317167 193317031 9.130000e-50 207
4 TraesCS7A01G300000 chr7D 93.545 1890 62 21 584 2439 371267661 371269524 0.000000e+00 2760
5 TraesCS7A01G300000 chr7D 95.181 83 4 0 2437 2519 371269682 371269764 5.650000e-27 132
6 TraesCS7A01G300000 chr1B 97.674 129 2 1 1 129 51090964 51090837 1.170000e-53 220
7 TraesCS7A01G300000 chr1B 97.581 124 3 0 1 124 35677214 35677337 1.960000e-51 213
8 TraesCS7A01G300000 chr5B 98.387 124 2 0 1 124 55273555 55273678 4.220000e-53 219
9 TraesCS7A01G300000 chr4B 98.361 122 2 0 1 122 67090047 67089926 5.460000e-52 215
10 TraesCS7A01G300000 chr3B 97.600 125 2 1 1 125 685977025 685977148 1.960000e-51 213
11 TraesCS7A01G300000 chr1A 96.875 128 2 2 1 126 249970131 249970004 1.960000e-51 213
12 TraesCS7A01G300000 chr5A 96.094 128 5 0 1 128 118396307 118396434 2.540000e-50 209
13 TraesCS7A01G300000 chr5A 93.525 139 5 4 1 136 119054931 119055068 1.180000e-48 204


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 TraesCS7A01G300000 chr7A 414183735 414186253 2518 True 2190.5 3904 100.000 1 2519 2 chr7A.!!$R1 2518
1 TraesCS7A01G300000 chr7B 318840218 318842330 2112 False 3075.0 3075 93.031 408 2519 1 chr7B.!!$F1 2111
2 TraesCS7A01G300000 chr7D 371267661 371269764 2103 False 1446.0 2760 94.363 584 2519 2 chr7D.!!$F1 1935

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
151 152 0.031857 CGACAGAGGCTGCTATGAGG 59.968 60.0 0.0 0.0 34.37 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1681 1.286553 TCTCTCTCTCTCACCCCCTTC 59.713 57.143 0.0 0.0 0.0 3.46 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
30 31 4.081050 GGAACCAGCACAACCCTC 57.919 61.111 0.00 0.00 0.00 4.30
31 32 1.456287 GGAACCAGCACAACCCTCT 59.544 57.895 0.00 0.00 0.00 3.69
32 33 0.690762 GGAACCAGCACAACCCTCTA 59.309 55.000 0.00 0.00 0.00 2.43
33 34 1.339151 GGAACCAGCACAACCCTCTAG 60.339 57.143 0.00 0.00 0.00 2.43
34 35 0.693049 AACCAGCACAACCCTCTAGG 59.307 55.000 0.00 0.00 43.78 3.02
46 47 2.407340 CCTCTAGGGGTGGCTTATCT 57.593 55.000 0.00 0.00 0.00 1.98
47 48 2.252714 CCTCTAGGGGTGGCTTATCTC 58.747 57.143 0.00 0.00 0.00 2.75
48 49 2.426414 CCTCTAGGGGTGGCTTATCTCA 60.426 54.545 0.00 0.00 0.00 3.27
49 50 3.515562 CTCTAGGGGTGGCTTATCTCAT 58.484 50.000 0.00 0.00 0.00 2.90
50 51 3.906846 CTCTAGGGGTGGCTTATCTCATT 59.093 47.826 0.00 0.00 0.00 2.57
51 52 5.087323 CTCTAGGGGTGGCTTATCTCATTA 58.913 45.833 0.00 0.00 0.00 1.90
52 53 5.665701 TCTAGGGGTGGCTTATCTCATTAT 58.334 41.667 0.00 0.00 0.00 1.28
53 54 6.811574 TCTAGGGGTGGCTTATCTCATTATA 58.188 40.000 0.00 0.00 0.00 0.98
54 55 7.430844 TCTAGGGGTGGCTTATCTCATTATAT 58.569 38.462 0.00 0.00 0.00 0.86
55 56 8.574853 TCTAGGGGTGGCTTATCTCATTATATA 58.425 37.037 0.00 0.00 0.00 0.86
56 57 9.386122 CTAGGGGTGGCTTATCTCATTATATAT 57.614 37.037 0.00 0.00 0.00 0.86
58 59 9.744125 AGGGGTGGCTTATCTCATTATATATAA 57.256 33.333 7.62 7.62 0.00 0.98
110 111 8.843885 ACGTACATAGATACAGAAGCTATACA 57.156 34.615 0.00 0.00 0.00 2.29
111 112 9.451002 ACGTACATAGATACAGAAGCTATACAT 57.549 33.333 0.00 0.00 0.00 2.29
122 123 7.653647 ACAGAAGCTATACATAGTCTAACAGC 58.346 38.462 0.00 0.00 32.96 4.40
123 124 7.285629 ACAGAAGCTATACATAGTCTAACAGCA 59.714 37.037 0.00 0.00 32.96 4.41
124 125 8.138074 CAGAAGCTATACATAGTCTAACAGCAA 58.862 37.037 0.00 0.00 32.96 3.91
125 126 8.138712 AGAAGCTATACATAGTCTAACAGCAAC 58.861 37.037 0.00 0.00 32.96 4.17
126 127 6.750148 AGCTATACATAGTCTAACAGCAACC 58.250 40.000 0.00 0.00 32.96 3.77
127 128 6.323996 AGCTATACATAGTCTAACAGCAACCA 59.676 38.462 0.00 0.00 32.96 3.67
128 129 7.015682 AGCTATACATAGTCTAACAGCAACCAT 59.984 37.037 0.00 0.00 32.96 3.55
129 130 7.329717 GCTATACATAGTCTAACAGCAACCATC 59.670 40.741 0.00 0.00 32.96 3.51
130 131 4.433615 ACATAGTCTAACAGCAACCATCG 58.566 43.478 0.00 0.00 0.00 3.84
131 132 2.386661 AGTCTAACAGCAACCATCGG 57.613 50.000 0.00 0.00 0.00 4.18
132 133 0.727398 GTCTAACAGCAACCATCGGC 59.273 55.000 0.00 0.00 0.00 5.54
133 134 0.739462 TCTAACAGCAACCATCGGCG 60.739 55.000 0.00 0.00 34.54 6.46
134 135 0.739462 CTAACAGCAACCATCGGCGA 60.739 55.000 13.87 13.87 34.54 5.54
135 136 1.017177 TAACAGCAACCATCGGCGAC 61.017 55.000 13.76 0.00 34.54 5.19
136 137 2.741985 CAGCAACCATCGGCGACA 60.742 61.111 13.76 0.00 34.54 4.35
137 138 2.434884 AGCAACCATCGGCGACAG 60.435 61.111 13.76 9.38 34.54 3.51
138 139 2.434185 GCAACCATCGGCGACAGA 60.434 61.111 13.76 0.00 0.00 3.41
139 140 2.456119 GCAACCATCGGCGACAGAG 61.456 63.158 13.76 3.48 0.00 3.35
140 141 1.811266 CAACCATCGGCGACAGAGG 60.811 63.158 13.76 14.68 0.00 3.69
141 142 3.665675 AACCATCGGCGACAGAGGC 62.666 63.158 13.76 0.00 0.00 4.70
142 143 3.842923 CCATCGGCGACAGAGGCT 61.843 66.667 13.76 0.00 34.19 4.58
143 144 2.584418 CATCGGCGACAGAGGCTG 60.584 66.667 13.76 0.00 38.14 4.85
144 145 4.521062 ATCGGCGACAGAGGCTGC 62.521 66.667 13.76 0.00 36.71 5.25
146 147 3.826754 CGGCGACAGAGGCTGCTA 61.827 66.667 0.00 0.00 34.37 3.49
147 148 2.818132 GGCGACAGAGGCTGCTAT 59.182 61.111 0.00 0.00 34.37 2.97
148 149 1.593750 GGCGACAGAGGCTGCTATG 60.594 63.158 0.00 0.00 34.37 2.23
149 150 1.439228 GCGACAGAGGCTGCTATGA 59.561 57.895 0.00 0.00 34.37 2.15
150 151 0.597118 GCGACAGAGGCTGCTATGAG 60.597 60.000 0.00 0.00 34.37 2.90
151 152 0.031857 CGACAGAGGCTGCTATGAGG 59.968 60.000 0.00 0.00 34.37 3.86
152 153 1.407936 GACAGAGGCTGCTATGAGGA 58.592 55.000 0.00 0.00 34.37 3.71
153 154 1.340889 GACAGAGGCTGCTATGAGGAG 59.659 57.143 0.00 0.00 36.68 3.69
154 155 1.063341 ACAGAGGCTGCTATGAGGAGA 60.063 52.381 0.00 0.00 35.49 3.71
155 156 2.250031 CAGAGGCTGCTATGAGGAGAT 58.750 52.381 0.00 0.00 35.49 2.75
156 157 2.028839 CAGAGGCTGCTATGAGGAGATG 60.029 54.545 0.00 0.00 35.49 2.90
157 158 2.158340 AGAGGCTGCTATGAGGAGATGA 60.158 50.000 0.00 0.00 35.49 2.92
158 159 1.969923 AGGCTGCTATGAGGAGATGAC 59.030 52.381 0.00 0.00 35.49 3.06
159 160 1.336702 GGCTGCTATGAGGAGATGACG 60.337 57.143 0.00 0.00 35.49 4.35
160 161 1.611006 GCTGCTATGAGGAGATGACGA 59.389 52.381 0.00 0.00 35.49 4.20
161 162 2.035193 GCTGCTATGAGGAGATGACGAA 59.965 50.000 0.00 0.00 35.49 3.85
162 163 3.491619 GCTGCTATGAGGAGATGACGAAA 60.492 47.826 0.00 0.00 35.49 3.46
163 164 4.686972 CTGCTATGAGGAGATGACGAAAA 58.313 43.478 0.00 0.00 35.49 2.29
164 165 4.686972 TGCTATGAGGAGATGACGAAAAG 58.313 43.478 0.00 0.00 0.00 2.27
165 166 4.054671 GCTATGAGGAGATGACGAAAAGG 58.945 47.826 0.00 0.00 0.00 3.11
166 167 3.550437 ATGAGGAGATGACGAAAAGGG 57.450 47.619 0.00 0.00 0.00 3.95
167 168 1.555075 TGAGGAGATGACGAAAAGGGG 59.445 52.381 0.00 0.00 0.00 4.79
168 169 0.253327 AGGAGATGACGAAAAGGGGC 59.747 55.000 0.00 0.00 0.00 5.80
169 170 0.035439 GGAGATGACGAAAAGGGGCA 60.035 55.000 0.00 0.00 0.00 5.36
170 171 1.373570 GAGATGACGAAAAGGGGCAG 58.626 55.000 0.00 0.00 0.00 4.85
171 172 0.693049 AGATGACGAAAAGGGGCAGT 59.307 50.000 0.00 0.00 0.00 4.40
172 173 0.804989 GATGACGAAAAGGGGCAGTG 59.195 55.000 0.00 0.00 0.00 3.66
173 174 0.400213 ATGACGAAAAGGGGCAGTGA 59.600 50.000 0.00 0.00 0.00 3.41
174 175 0.534203 TGACGAAAAGGGGCAGTGAC 60.534 55.000 0.00 0.00 0.00 3.67
175 176 1.566018 GACGAAAAGGGGCAGTGACG 61.566 60.000 0.00 0.00 0.00 4.35
176 177 2.325082 CGAAAAGGGGCAGTGACGG 61.325 63.158 0.00 0.00 0.00 4.79
177 178 1.228154 GAAAAGGGGCAGTGACGGT 60.228 57.895 0.00 0.00 0.00 4.83
178 179 0.822121 GAAAAGGGGCAGTGACGGTT 60.822 55.000 0.00 0.00 0.00 4.44
179 180 1.106944 AAAAGGGGCAGTGACGGTTG 61.107 55.000 0.00 0.00 0.00 3.77
180 181 4.643387 AGGGGCAGTGACGGTTGC 62.643 66.667 0.00 0.00 39.56 4.17
181 182 4.643387 GGGGCAGTGACGGTTGCT 62.643 66.667 0.00 0.00 40.15 3.91
182 183 3.357079 GGGCAGTGACGGTTGCTG 61.357 66.667 0.00 6.02 40.15 4.41
184 185 4.374702 GCAGTGACGGTTGCTGCG 62.375 66.667 17.51 0.00 44.64 5.18
185 186 4.374702 CAGTGACGGTTGCTGCGC 62.375 66.667 0.00 0.00 0.00 6.09
202 203 4.435436 CGCTGCGGAGTGGTGCTA 62.435 66.667 15.40 0.00 0.00 3.49
203 204 2.815647 GCTGCGGAGTGGTGCTAC 60.816 66.667 5.62 0.00 0.00 3.58
204 205 2.125512 CTGCGGAGTGGTGCTACC 60.126 66.667 0.00 0.00 39.22 3.18
205 206 3.989698 CTGCGGAGTGGTGCTACCG 62.990 68.421 0.00 0.00 42.58 4.02
246 247 2.500369 GCATTGAGCGTGTGTGCG 60.500 61.111 0.00 0.00 40.67 5.34
247 248 2.938253 CATTGAGCGTGTGTGCGT 59.062 55.556 0.00 0.00 40.67 5.24
248 249 1.439201 CATTGAGCGTGTGTGCGTG 60.439 57.895 0.00 0.00 40.67 5.34
249 250 2.606961 ATTGAGCGTGTGTGCGTGG 61.607 57.895 0.00 0.00 40.67 4.94
251 252 4.961511 GAGCGTGTGTGCGTGGGA 62.962 66.667 0.00 0.00 40.67 4.37
252 253 4.969196 AGCGTGTGTGCGTGGGAG 62.969 66.667 0.00 0.00 40.67 4.30
253 254 4.961511 GCGTGTGTGCGTGGGAGA 62.962 66.667 0.00 0.00 0.00 3.71
254 255 2.734723 CGTGTGTGCGTGGGAGAG 60.735 66.667 0.00 0.00 0.00 3.20
255 256 2.734591 GTGTGTGCGTGGGAGAGA 59.265 61.111 0.00 0.00 0.00 3.10
256 257 1.373497 GTGTGTGCGTGGGAGAGAG 60.373 63.158 0.00 0.00 0.00 3.20
257 258 1.832608 TGTGTGCGTGGGAGAGAGT 60.833 57.895 0.00 0.00 0.00 3.24
436 437 2.882137 GTTGTGTTTCCTCCAATCGGAA 59.118 45.455 0.00 0.00 42.21 4.30
437 438 2.500229 TGTGTTTCCTCCAATCGGAAC 58.500 47.619 0.00 0.00 42.21 3.62
492 504 3.659183 AAAAGGCCTAGCTCACATGAT 57.341 42.857 5.16 0.00 0.00 2.45
497 509 3.455910 AGGCCTAGCTCACATGATTTGTA 59.544 43.478 1.29 0.00 36.57 2.41
500 512 4.272018 GCCTAGCTCACATGATTTGTACAG 59.728 45.833 0.00 0.00 36.57 2.74
554 566 5.769484 AGAAGATTTGTGCATGATCATCC 57.231 39.130 4.86 0.00 0.00 3.51
572 584 0.321564 CCTTTGGCAGGTGTCATCGA 60.322 55.000 0.00 0.00 37.99 3.59
595 607 6.013554 ACCCATATATGTAACAAAGCCACT 57.986 37.500 11.73 0.00 0.00 4.00
707 719 0.670546 CTGATATTTCCGGCGGCGAT 60.671 55.000 34.49 20.62 0.00 4.58
708 720 0.250124 TGATATTTCCGGCGGCGATT 60.250 50.000 34.49 15.94 0.00 3.34
783 795 1.852067 AATCTTCCAACCGTGCACGC 61.852 55.000 33.17 0.00 38.18 5.34
809 821 3.489229 CCGTCTATTCTCGCTTGACATGA 60.489 47.826 0.00 0.00 0.00 3.07
810 822 4.105486 CGTCTATTCTCGCTTGACATGAA 58.895 43.478 0.00 0.00 0.00 2.57
811 823 4.562789 CGTCTATTCTCGCTTGACATGAAA 59.437 41.667 0.00 0.00 0.00 2.69
812 824 5.233050 CGTCTATTCTCGCTTGACATGAAAT 59.767 40.000 0.00 0.00 0.00 2.17
849 861 3.192799 CGTAGCCTCCCTCTTCTCA 57.807 57.895 0.00 0.00 0.00 3.27
1543 1565 4.730487 CTCCAAGGAGCAACCCTG 57.270 61.111 2.68 0.00 40.05 4.45
1626 1648 1.303074 CCATCCATCCGCCCATCTG 60.303 63.158 0.00 0.00 0.00 2.90
1632 1654 1.995066 ATCCGCCCATCTGTCCACA 60.995 57.895 0.00 0.00 0.00 4.17
1647 1669 3.285484 GTCCACAGATCCATGCTTTCAT 58.715 45.455 0.00 0.00 0.00 2.57
1666 1688 3.457380 TCATGAGAGAAATCAGAAGGGGG 59.543 47.826 0.00 0.00 31.44 5.40
1758 1802 3.627395 TGGTAGGTGAGGCACTAATTG 57.373 47.619 0.00 0.00 41.55 2.32
1839 1883 4.213694 CACTTGCAGATCCATATGCTCTTC 59.786 45.833 7.63 0.00 44.77 2.87
1840 1884 4.102838 ACTTGCAGATCCATATGCTCTTCT 59.897 41.667 7.63 0.00 44.77 2.85
1870 1914 3.864789 TTTCAGCTCCTCTTCAACCTT 57.135 42.857 0.00 0.00 0.00 3.50
1976 2020 6.287589 TGTGAGGGAAATTAAGAGAGAGAC 57.712 41.667 0.00 0.00 0.00 3.36
2128 2173 5.554822 ACGCGGATTGTATTGTAAAACAT 57.445 34.783 12.47 0.00 0.00 2.71
2130 2175 4.204168 CGCGGATTGTATTGTAAAACATGC 59.796 41.667 0.00 0.00 0.00 4.06
2200 2245 9.057089 GGACTTTTCCCAATAGTAGATATGTTG 57.943 37.037 0.00 0.00 35.57 3.33
2225 2270 3.153919 TCATGTTTGGTGTTTAGAGGGC 58.846 45.455 0.00 0.00 0.00 5.19
2261 2306 7.451877 GTCAGTGTAGATGGGATTAGGATAAGA 59.548 40.741 0.00 0.00 0.00 2.10
2297 2342 6.472163 GCAACGTGCATAGTGCTTAATTAATT 59.528 34.615 5.89 5.89 45.31 1.40
2312 2357 1.368641 TAATTGCCACTGCGTGCTAG 58.631 50.000 3.56 0.00 41.78 3.42
2315 2360 0.669318 TTGCCACTGCGTGCTAGTAC 60.669 55.000 0.08 0.08 41.78 2.73
2316 2361 1.215647 GCCACTGCGTGCTAGTACT 59.784 57.895 9.40 0.00 31.34 2.73
2317 2362 0.454600 GCCACTGCGTGCTAGTACTA 59.545 55.000 9.40 1.89 31.34 1.82
2361 2406 3.306710 CCTGACACTAGTAATGGTGCACA 60.307 47.826 20.43 5.24 36.99 4.57
2475 2688 5.493133 TCTTTCGCCGCAAATACATATTT 57.507 34.783 0.00 0.00 36.39 1.40
2480 2693 5.981174 TCGCCGCAAATACATATTTAAGAC 58.019 37.500 0.00 0.00 34.36 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.323403 TGCTGGTTCCCCAAAACTTATTG 59.677 43.478 0.00 0.00 41.27 1.90
1 2 3.323691 GTGCTGGTTCCCCAAAACTTATT 59.676 43.478 0.00 0.00 41.27 1.40
2 3 2.897326 GTGCTGGTTCCCCAAAACTTAT 59.103 45.455 0.00 0.00 41.27 1.73
3 4 2.312390 GTGCTGGTTCCCCAAAACTTA 58.688 47.619 0.00 0.00 41.27 2.24
4 5 1.119684 GTGCTGGTTCCCCAAAACTT 58.880 50.000 0.00 0.00 41.27 2.66
5 6 0.032615 TGTGCTGGTTCCCCAAAACT 60.033 50.000 0.00 0.00 41.27 2.66
6 7 0.827368 TTGTGCTGGTTCCCCAAAAC 59.173 50.000 0.00 0.00 41.27 2.43
7 8 0.827368 GTTGTGCTGGTTCCCCAAAA 59.173 50.000 0.00 0.00 41.27 2.44
8 9 1.045911 GGTTGTGCTGGTTCCCCAAA 61.046 55.000 0.00 0.00 41.27 3.28
9 10 1.456705 GGTTGTGCTGGTTCCCCAA 60.457 57.895 0.00 0.00 41.27 4.12
10 11 2.197324 GGTTGTGCTGGTTCCCCA 59.803 61.111 0.00 0.00 38.87 4.96
11 12 2.600470 GGGTTGTGCTGGTTCCCC 60.600 66.667 0.00 0.00 32.66 4.81
12 13 1.603739 GAGGGTTGTGCTGGTTCCC 60.604 63.158 0.00 0.00 38.50 3.97
13 14 0.690762 TAGAGGGTTGTGCTGGTTCC 59.309 55.000 0.00 0.00 0.00 3.62
14 15 1.339151 CCTAGAGGGTTGTGCTGGTTC 60.339 57.143 0.00 0.00 0.00 3.62
15 16 0.693049 CCTAGAGGGTTGTGCTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
16 17 2.377136 CCTAGAGGGTTGTGCTGGT 58.623 57.895 0.00 0.00 0.00 4.00
27 28 2.252714 GAGATAAGCCACCCCTAGAGG 58.747 57.143 0.00 0.00 0.00 3.69
28 29 2.964209 TGAGATAAGCCACCCCTAGAG 58.036 52.381 0.00 0.00 0.00 2.43
29 30 3.637821 ATGAGATAAGCCACCCCTAGA 57.362 47.619 0.00 0.00 0.00 2.43
30 31 7.682787 ATATAATGAGATAAGCCACCCCTAG 57.317 40.000 0.00 0.00 0.00 3.02
32 33 9.744125 TTATATATAATGAGATAAGCCACCCCT 57.256 33.333 0.81 0.00 0.00 4.79
84 85 9.933723 TGTATAGCTTCTGTATCTATGTACGTA 57.066 33.333 0.00 0.00 0.00 3.57
85 86 8.843885 TGTATAGCTTCTGTATCTATGTACGT 57.156 34.615 0.00 0.00 0.00 3.57
96 97 8.784994 GCTGTTAGACTATGTATAGCTTCTGTA 58.215 37.037 0.00 0.00 33.68 2.74
97 98 7.285629 TGCTGTTAGACTATGTATAGCTTCTGT 59.714 37.037 0.00 0.00 33.68 3.41
98 99 7.652727 TGCTGTTAGACTATGTATAGCTTCTG 58.347 38.462 0.00 2.24 33.68 3.02
99 100 7.825331 TGCTGTTAGACTATGTATAGCTTCT 57.175 36.000 0.00 0.00 33.68 2.85
100 101 7.382759 GGTTGCTGTTAGACTATGTATAGCTTC 59.617 40.741 0.00 0.00 33.68 3.86
101 102 7.147724 TGGTTGCTGTTAGACTATGTATAGCTT 60.148 37.037 0.00 0.00 33.68 3.74
102 103 6.323996 TGGTTGCTGTTAGACTATGTATAGCT 59.676 38.462 0.00 0.00 33.68 3.32
103 104 6.513180 TGGTTGCTGTTAGACTATGTATAGC 58.487 40.000 0.00 0.00 33.68 2.97
104 105 7.539022 CGATGGTTGCTGTTAGACTATGTATAG 59.461 40.741 0.00 0.00 36.46 1.31
105 106 7.368059 CGATGGTTGCTGTTAGACTATGTATA 58.632 38.462 0.00 0.00 0.00 1.47
106 107 6.216569 CGATGGTTGCTGTTAGACTATGTAT 58.783 40.000 0.00 0.00 0.00 2.29
107 108 5.451381 CCGATGGTTGCTGTTAGACTATGTA 60.451 44.000 0.00 0.00 0.00 2.29
108 109 4.433615 CGATGGTTGCTGTTAGACTATGT 58.566 43.478 0.00 0.00 0.00 2.29
109 110 3.804325 CCGATGGTTGCTGTTAGACTATG 59.196 47.826 0.00 0.00 0.00 2.23
110 111 3.741388 GCCGATGGTTGCTGTTAGACTAT 60.741 47.826 0.00 0.00 0.00 2.12
111 112 2.418197 GCCGATGGTTGCTGTTAGACTA 60.418 50.000 0.00 0.00 0.00 2.59
112 113 1.676014 GCCGATGGTTGCTGTTAGACT 60.676 52.381 0.00 0.00 0.00 3.24
113 114 0.727398 GCCGATGGTTGCTGTTAGAC 59.273 55.000 0.00 0.00 0.00 2.59
114 115 0.739462 CGCCGATGGTTGCTGTTAGA 60.739 55.000 0.00 0.00 0.00 2.10
115 116 0.739462 TCGCCGATGGTTGCTGTTAG 60.739 55.000 0.00 0.00 0.00 2.34
116 117 1.017177 GTCGCCGATGGTTGCTGTTA 61.017 55.000 0.00 0.00 0.00 2.41
117 118 2.031919 TCGCCGATGGTTGCTGTT 59.968 55.556 0.00 0.00 0.00 3.16
118 119 2.742372 GTCGCCGATGGTTGCTGT 60.742 61.111 0.00 0.00 0.00 4.40
119 120 2.741985 TGTCGCCGATGGTTGCTG 60.742 61.111 0.00 0.00 0.00 4.41
120 121 2.434884 CTGTCGCCGATGGTTGCT 60.435 61.111 0.00 0.00 0.00 3.91
121 122 2.434185 TCTGTCGCCGATGGTTGC 60.434 61.111 0.00 0.00 0.00 4.17
122 123 1.811266 CCTCTGTCGCCGATGGTTG 60.811 63.158 0.00 0.00 0.00 3.77
123 124 2.579201 CCTCTGTCGCCGATGGTT 59.421 61.111 0.00 0.00 0.00 3.67
124 125 4.148825 GCCTCTGTCGCCGATGGT 62.149 66.667 0.00 0.00 0.00 3.55
125 126 3.842923 AGCCTCTGTCGCCGATGG 61.843 66.667 0.00 0.00 0.00 3.51
126 127 2.584418 CAGCCTCTGTCGCCGATG 60.584 66.667 0.00 0.00 0.00 3.84
127 128 4.521062 GCAGCCTCTGTCGCCGAT 62.521 66.667 0.00 0.00 33.43 4.18
129 130 3.144120 ATAGCAGCCTCTGTCGCCG 62.144 63.158 0.00 0.00 33.43 6.46
130 131 1.593750 CATAGCAGCCTCTGTCGCC 60.594 63.158 0.00 0.00 33.43 5.54
131 132 0.597118 CTCATAGCAGCCTCTGTCGC 60.597 60.000 0.00 0.00 33.43 5.19
132 133 0.031857 CCTCATAGCAGCCTCTGTCG 59.968 60.000 0.00 0.00 33.43 4.35
133 134 1.340889 CTCCTCATAGCAGCCTCTGTC 59.659 57.143 0.00 0.00 33.43 3.51
134 135 1.063341 TCTCCTCATAGCAGCCTCTGT 60.063 52.381 0.00 0.00 33.43 3.41
135 136 1.702182 TCTCCTCATAGCAGCCTCTG 58.298 55.000 0.00 0.00 34.12 3.35
136 137 2.158340 TCATCTCCTCATAGCAGCCTCT 60.158 50.000 0.00 0.00 0.00 3.69
137 138 2.029110 GTCATCTCCTCATAGCAGCCTC 60.029 54.545 0.00 0.00 0.00 4.70
138 139 1.969923 GTCATCTCCTCATAGCAGCCT 59.030 52.381 0.00 0.00 0.00 4.58
139 140 1.336702 CGTCATCTCCTCATAGCAGCC 60.337 57.143 0.00 0.00 0.00 4.85
140 141 1.611006 TCGTCATCTCCTCATAGCAGC 59.389 52.381 0.00 0.00 0.00 5.25
141 142 3.998099 TTCGTCATCTCCTCATAGCAG 57.002 47.619 0.00 0.00 0.00 4.24
142 143 4.442052 CCTTTTCGTCATCTCCTCATAGCA 60.442 45.833 0.00 0.00 0.00 3.49
143 144 4.054671 CCTTTTCGTCATCTCCTCATAGC 58.945 47.826 0.00 0.00 0.00 2.97
144 145 4.502259 CCCCTTTTCGTCATCTCCTCATAG 60.502 50.000 0.00 0.00 0.00 2.23
145 146 3.388024 CCCCTTTTCGTCATCTCCTCATA 59.612 47.826 0.00 0.00 0.00 2.15
146 147 2.171448 CCCCTTTTCGTCATCTCCTCAT 59.829 50.000 0.00 0.00 0.00 2.90
147 148 1.555075 CCCCTTTTCGTCATCTCCTCA 59.445 52.381 0.00 0.00 0.00 3.86
148 149 1.744114 GCCCCTTTTCGTCATCTCCTC 60.744 57.143 0.00 0.00 0.00 3.71
149 150 0.253327 GCCCCTTTTCGTCATCTCCT 59.747 55.000 0.00 0.00 0.00 3.69
150 151 0.035439 TGCCCCTTTTCGTCATCTCC 60.035 55.000 0.00 0.00 0.00 3.71
151 152 1.339151 ACTGCCCCTTTTCGTCATCTC 60.339 52.381 0.00 0.00 0.00 2.75
152 153 0.693049 ACTGCCCCTTTTCGTCATCT 59.307 50.000 0.00 0.00 0.00 2.90
153 154 0.804989 CACTGCCCCTTTTCGTCATC 59.195 55.000 0.00 0.00 0.00 2.92
154 155 0.400213 TCACTGCCCCTTTTCGTCAT 59.600 50.000 0.00 0.00 0.00 3.06
155 156 0.534203 GTCACTGCCCCTTTTCGTCA 60.534 55.000 0.00 0.00 0.00 4.35
156 157 1.566018 CGTCACTGCCCCTTTTCGTC 61.566 60.000 0.00 0.00 0.00 4.20
157 158 1.597027 CGTCACTGCCCCTTTTCGT 60.597 57.895 0.00 0.00 0.00 3.85
158 159 2.325082 CCGTCACTGCCCCTTTTCG 61.325 63.158 0.00 0.00 0.00 3.46
159 160 0.822121 AACCGTCACTGCCCCTTTTC 60.822 55.000 0.00 0.00 0.00 2.29
160 161 1.106944 CAACCGTCACTGCCCCTTTT 61.107 55.000 0.00 0.00 0.00 2.27
161 162 1.528309 CAACCGTCACTGCCCCTTT 60.528 57.895 0.00 0.00 0.00 3.11
162 163 2.113139 CAACCGTCACTGCCCCTT 59.887 61.111 0.00 0.00 0.00 3.95
163 164 4.643387 GCAACCGTCACTGCCCCT 62.643 66.667 0.00 0.00 32.18 4.79
164 165 4.643387 AGCAACCGTCACTGCCCC 62.643 66.667 0.00 0.00 39.47 5.80
165 166 3.357079 CAGCAACCGTCACTGCCC 61.357 66.667 0.00 0.00 39.47 5.36
185 186 4.435436 TAGCACCACTCCGCAGCG 62.435 66.667 8.18 8.18 0.00 5.18
186 187 2.815647 GTAGCACCACTCCGCAGC 60.816 66.667 0.00 0.00 0.00 5.25
187 188 2.125512 GGTAGCACCACTCCGCAG 60.126 66.667 1.01 0.00 38.42 5.18
188 189 4.063967 CGGTAGCACCACTCCGCA 62.064 66.667 6.21 0.00 38.47 5.69
212 213 4.554363 CTAGCCGCACGTCTCCGG 62.554 72.222 12.93 12.93 46.94 5.14
214 215 4.129737 TGCTAGCCGCACGTCTCC 62.130 66.667 13.29 0.00 45.47 3.71
222 223 2.892425 ACGCTCAATGCTAGCCGC 60.892 61.111 13.29 6.15 40.11 6.53
223 224 1.811266 ACACGCTCAATGCTAGCCG 60.811 57.895 13.29 9.77 40.11 5.52
224 225 1.021390 ACACACGCTCAATGCTAGCC 61.021 55.000 13.29 0.00 40.11 3.93
225 226 0.095935 CACACACGCTCAATGCTAGC 59.904 55.000 8.10 8.10 40.11 3.42
226 227 0.095935 GCACACACGCTCAATGCTAG 59.904 55.000 0.00 0.00 40.11 3.42
227 228 1.625759 CGCACACACGCTCAATGCTA 61.626 55.000 0.00 0.00 40.11 3.49
228 229 2.949106 GCACACACGCTCAATGCT 59.051 55.556 0.00 0.00 40.11 3.79
229 230 2.500369 CGCACACACGCTCAATGC 60.500 61.111 0.00 0.00 38.57 3.56
230 231 1.439201 CACGCACACACGCTCAATG 60.439 57.895 0.00 0.00 36.19 2.82
231 232 2.606961 CCACGCACACACGCTCAAT 61.607 57.895 0.00 0.00 36.19 2.57
232 233 3.268603 CCACGCACACACGCTCAA 61.269 61.111 0.00 0.00 36.19 3.02
234 235 4.961511 TCCCACGCACACACGCTC 62.962 66.667 0.00 0.00 36.19 5.03
235 236 4.969196 CTCCCACGCACACACGCT 62.969 66.667 0.00 0.00 36.19 5.07
236 237 4.961511 TCTCCCACGCACACACGC 62.962 66.667 0.00 0.00 36.19 5.34
237 238 2.734723 CTCTCCCACGCACACACG 60.735 66.667 0.00 0.00 39.50 4.49
238 239 1.373497 CTCTCTCCCACGCACACAC 60.373 63.158 0.00 0.00 0.00 3.82
239 240 1.832608 ACTCTCTCCCACGCACACA 60.833 57.895 0.00 0.00 0.00 3.72
240 241 3.052081 ACTCTCTCCCACGCACAC 58.948 61.111 0.00 0.00 0.00 3.82
405 406 5.222027 TGGAGGAAACACAACCATCAGATAA 60.222 40.000 0.00 0.00 0.00 1.75
406 407 4.288366 TGGAGGAAACACAACCATCAGATA 59.712 41.667 0.00 0.00 0.00 1.98
480 492 5.420725 ACCTGTACAAATCATGTGAGCTA 57.579 39.130 0.00 0.00 43.77 3.32
525 537 9.761504 TGATCATGCACAAATCTTCTTTTAAAA 57.238 25.926 0.00 0.00 0.00 1.52
526 538 9.932207 ATGATCATGCACAAATCTTCTTTTAAA 57.068 25.926 7.59 0.00 0.00 1.52
527 539 9.577110 GATGATCATGCACAAATCTTCTTTTAA 57.423 29.630 14.30 0.00 0.00 1.52
528 540 8.192774 GGATGATCATGCACAAATCTTCTTTTA 58.807 33.333 21.09 0.00 0.00 1.52
535 547 5.163447 CCAAAGGATGATCATGCACAAATCT 60.163 40.000 26.58 3.67 0.00 2.40
554 566 0.798776 GTCGATGACACCTGCCAAAG 59.201 55.000 0.00 0.00 32.09 2.77
572 584 6.013554 AGTGGCTTTGTTACATATATGGGT 57.986 37.500 16.96 0.00 0.00 4.51
609 621 1.742268 ACCCGTAGTTAGCTCGAGAAC 59.258 52.381 18.75 12.76 0.00 3.01
708 720 4.959596 TACTGCTGCGTGCGTGCA 62.960 61.111 10.88 10.88 46.63 4.57
783 795 0.103208 AAGCGAGAATAGACGGGCTG 59.897 55.000 0.00 0.00 0.00 4.85
809 821 6.488817 ACGCGTACTACAAAAGAAAACATTT 58.511 32.000 11.67 0.00 0.00 2.32
810 822 6.051646 ACGCGTACTACAAAAGAAAACATT 57.948 33.333 11.67 0.00 0.00 2.71
811 823 5.662211 ACGCGTACTACAAAAGAAAACAT 57.338 34.783 11.67 0.00 0.00 2.71
812 824 5.332506 GCTACGCGTACTACAAAAGAAAACA 60.333 40.000 16.41 0.00 0.00 2.83
813 825 5.068906 GCTACGCGTACTACAAAAGAAAAC 58.931 41.667 16.41 0.00 0.00 2.43
844 856 2.912956 AGGCTATGTTTGGAGGTGAGAA 59.087 45.455 0.00 0.00 0.00 2.87
845 857 2.237143 CAGGCTATGTTTGGAGGTGAGA 59.763 50.000 0.00 0.00 0.00 3.27
847 859 1.340017 GCAGGCTATGTTTGGAGGTGA 60.340 52.381 0.00 0.00 0.00 4.02
849 861 0.034089 GGCAGGCTATGTTTGGAGGT 60.034 55.000 0.00 0.00 0.00 3.85
1093 1115 2.410687 CGAGCGAGGAGAGGCAGAA 61.411 63.158 0.00 0.00 0.00 3.02
1626 1648 2.715046 TGAAAGCATGGATCTGTGGAC 58.285 47.619 0.00 0.00 0.00 4.02
1647 1669 2.573462 CACCCCCTTCTGATTTCTCTCA 59.427 50.000 0.00 0.00 0.00 3.27
1659 1681 1.286553 TCTCTCTCTCTCACCCCCTTC 59.713 57.143 0.00 0.00 0.00 3.46
1666 1688 1.665679 CGCTCTGTCTCTCTCTCTCAC 59.334 57.143 0.00 0.00 0.00 3.51
1758 1802 1.977293 GCCATCCCTGTCCTCCTCAC 61.977 65.000 0.00 0.00 0.00 3.51
1839 1883 4.463891 AGAGGAGCTGAAAAAGAGAGAGAG 59.536 45.833 0.00 0.00 0.00 3.20
1840 1884 4.415596 AGAGGAGCTGAAAAAGAGAGAGA 58.584 43.478 0.00 0.00 0.00 3.10
1914 1958 8.055790 AGAAAAGGAGAAAAGAAAAGGAGAAGA 58.944 33.333 0.00 0.00 0.00 2.87
1976 2020 8.143193 AGCTATGTACATCTCTCTTTCTTGATG 58.857 37.037 12.68 0.00 41.24 3.07
2087 2132 6.801377 TCCGCGTATATAACTTTGTTATACGG 59.199 38.462 19.67 19.67 45.54 4.02
2109 2154 8.128582 ACATAGCATGTTTTACAATACAATCCG 58.871 33.333 0.00 0.00 41.63 4.18
2128 2173 8.793592 CCTACACTACATACAATCTACATAGCA 58.206 37.037 0.00 0.00 0.00 3.49
2176 2221 7.502561 GGCAACATATCTACTATTGGGAAAAGT 59.497 37.037 0.00 0.00 0.00 2.66
2200 2245 4.380867 CCTCTAAACACCAAACATGATGGC 60.381 45.833 18.25 0.00 41.89 4.40
2225 2270 1.269723 TCTACACTGACGTGAGGCTTG 59.730 52.381 7.04 0.00 43.97 4.01
2246 2291 9.354673 CTTTAAGCAATTCTTATCCTAATCCCA 57.645 33.333 0.00 0.00 37.14 4.37
2282 2327 5.448496 CGCAGTGGCAATTAATTAAGCACTA 60.448 40.000 11.38 0.00 41.24 2.74
2312 2357 3.975168 TTTGAGGGAAGTGGCTAGTAC 57.025 47.619 0.00 0.00 0.00 2.73
2315 2360 4.762289 AGTATTTGAGGGAAGTGGCTAG 57.238 45.455 0.00 0.00 0.00 3.42
2316 2361 4.843728 CAAGTATTTGAGGGAAGTGGCTA 58.156 43.478 0.00 0.00 36.36 3.93
2317 2362 3.690460 CAAGTATTTGAGGGAAGTGGCT 58.310 45.455 0.00 0.00 36.36 4.75
2435 2487 7.095607 GGCGAAAGATGTTATTGACCTATGTAG 60.096 40.741 0.00 0.00 0.00 2.74
2442 2655 2.538939 GCGGCGAAAGATGTTATTGACC 60.539 50.000 12.98 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.