Multiple sequence alignment - TraesCS7B01G121100

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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 TraesCS7B01G121100 chr7B 100.000 3093 0 0 1 3093 141578650 141581742 0.000000e+00 5712
1 TraesCS7B01G121100 chr7A 94.750 2876 100 18 238 3088 178000182 178003031 0.000000e+00 4427
2 TraesCS7B01G121100 chr7A 93.084 347 13 4 238 574 177955406 177955751 5.960000e-137 497
3 TraesCS7B01G121100 chr7D 95.471 1987 67 11 234 2215 175887967 175889935 0.000000e+00 3149
4 TraesCS7B01G121100 chr7D 85.816 705 66 7 2387 3088 175916023 175916696 0.000000e+00 717
5 TraesCS7B01G121100 chr7D 93.064 173 11 1 62 233 183788794 183788622 5.120000e-63 252
6 TraesCS7B01G121100 chr7D 92.614 176 11 2 65 239 448031617 448031791 5.120000e-63 252
7 TraesCS7B01G121100 chr7D 89.610 154 11 5 2231 2380 175889917 175890069 1.130000e-44 191
8 TraesCS7B01G121100 chr3B 94.083 169 8 2 65 232 749713693 749713526 3.960000e-64 255
9 TraesCS7B01G121100 chr3B 91.620 179 11 4 69 246 120617077 120616902 8.570000e-61 244
10 TraesCS7B01G121100 chr1B 93.529 170 9 2 64 232 242176187 242176019 5.120000e-63 252
11 TraesCS7B01G121100 chr1B 77.596 183 35 6 2453 2631 580442365 580442185 4.220000e-19 106
12 TraesCS7B01G121100 chr5A 93.491 169 10 1 65 232 456897734 456897902 1.840000e-62 250
13 TraesCS7B01G121100 chr1D 93.023 172 11 1 69 239 81276355 81276526 1.840000e-62 250
14 TraesCS7B01G121100 chr5D 92.486 173 11 2 61 232 420206214 420206043 2.380000e-61 246
15 TraesCS7B01G121100 chr3D 90.811 185 14 3 54 236 458565646 458565463 8.570000e-61 244
16 TraesCS7B01G121100 chr1A 85.567 97 10 4 2534 2629 526743991 526743898 7.060000e-17 99


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 TraesCS7B01G121100 chr7B 141578650 141581742 3092 False 5712 5712 100.0000 1 3093 1 chr7B.!!$F1 3092
1 TraesCS7B01G121100 chr7A 178000182 178003031 2849 False 4427 4427 94.7500 238 3088 1 chr7A.!!$F2 2850
2 TraesCS7B01G121100 chr7D 175887967 175890069 2102 False 1670 3149 92.5405 234 2380 2 chr7D.!!$F3 2146
3 TraesCS7B01G121100 chr7D 175916023 175916696 673 False 717 717 85.8160 2387 3088 1 chr7D.!!$F1 701

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
32 33 0.036294 AAGTAGCAGCGAAGGAACCC 60.036 55.0 0.00 0.0 0.00 4.11 F
861 870 0.037326 CTCCATGTACAGTGGCGTGT 60.037 55.0 15.54 0.0 36.66 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1186 1.153823 CGGTGAGGATGTCCGTGAC 60.154 63.158 0.0 0.0 42.08 3.67 R
2155 2182 0.387239 GGTCCATGCAACGCAGAAAC 60.387 55.000 0.0 0.0 43.65 2.78 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
19 20 2.327200 AATGGGCCGAGTTAAGTAGC 57.673 50.000 0.00 0.00 0.00 3.58
20 21 1.200519 ATGGGCCGAGTTAAGTAGCA 58.799 50.000 0.00 0.00 0.00 3.49
21 22 0.535335 TGGGCCGAGTTAAGTAGCAG 59.465 55.000 0.00 0.00 0.00 4.24
22 23 0.810426 GGGCCGAGTTAAGTAGCAGC 60.810 60.000 0.00 0.00 0.00 5.25
23 24 1.146358 GGCCGAGTTAAGTAGCAGCG 61.146 60.000 7.02 0.00 0.00 5.18
24 25 0.179145 GCCGAGTTAAGTAGCAGCGA 60.179 55.000 0.00 0.00 0.00 4.93
25 26 1.734707 GCCGAGTTAAGTAGCAGCGAA 60.735 52.381 0.00 0.00 0.00 4.70
26 27 2.186076 CCGAGTTAAGTAGCAGCGAAG 58.814 52.381 0.00 0.00 0.00 3.79
27 28 2.186076 CGAGTTAAGTAGCAGCGAAGG 58.814 52.381 0.00 0.00 0.00 3.46
28 29 2.159421 CGAGTTAAGTAGCAGCGAAGGA 60.159 50.000 0.00 0.00 0.00 3.36
29 30 3.672511 CGAGTTAAGTAGCAGCGAAGGAA 60.673 47.826 0.00 0.00 0.00 3.36
30 31 3.586892 AGTTAAGTAGCAGCGAAGGAAC 58.413 45.455 0.00 0.00 0.00 3.62
31 32 2.667473 TAAGTAGCAGCGAAGGAACC 57.333 50.000 0.00 0.00 0.00 3.62
32 33 0.036294 AAGTAGCAGCGAAGGAACCC 60.036 55.000 0.00 0.00 0.00 4.11
33 34 1.449778 GTAGCAGCGAAGGAACCCC 60.450 63.158 0.00 0.00 0.00 4.95
34 35 1.916273 TAGCAGCGAAGGAACCCCA 60.916 57.895 0.00 0.00 33.88 4.96
35 36 1.485294 TAGCAGCGAAGGAACCCCAA 61.485 55.000 0.00 0.00 33.88 4.12
36 37 1.901464 GCAGCGAAGGAACCCCAAA 60.901 57.895 0.00 0.00 33.88 3.28
37 38 1.956802 CAGCGAAGGAACCCCAAAC 59.043 57.895 0.00 0.00 33.88 2.93
38 39 1.228459 AGCGAAGGAACCCCAAACC 60.228 57.895 0.00 0.00 33.88 3.27
39 40 1.529713 GCGAAGGAACCCCAAACCA 60.530 57.895 0.00 0.00 33.88 3.67
40 41 1.524008 GCGAAGGAACCCCAAACCAG 61.524 60.000 0.00 0.00 33.88 4.00
41 42 1.524008 CGAAGGAACCCCAAACCAGC 61.524 60.000 0.00 0.00 33.88 4.85
42 43 0.469144 GAAGGAACCCCAAACCAGCA 60.469 55.000 0.00 0.00 33.88 4.41
43 44 0.190815 AAGGAACCCCAAACCAGCAT 59.809 50.000 0.00 0.00 33.88 3.79
44 45 0.542702 AGGAACCCCAAACCAGCATG 60.543 55.000 0.00 0.00 33.88 4.06
45 46 0.541764 GGAACCCCAAACCAGCATGA 60.542 55.000 0.00 0.00 39.69 3.07
46 47 0.603065 GAACCCCAAACCAGCATGAC 59.397 55.000 0.00 0.00 39.69 3.06
47 48 0.831711 AACCCCAAACCAGCATGACC 60.832 55.000 0.00 0.00 39.69 4.02
48 49 1.228831 CCCCAAACCAGCATGACCA 60.229 57.895 0.00 0.00 39.69 4.02
49 50 0.831288 CCCCAAACCAGCATGACCAA 60.831 55.000 0.00 0.00 39.69 3.67
50 51 0.318120 CCCAAACCAGCATGACCAAC 59.682 55.000 0.00 0.00 39.69 3.77
51 52 0.039256 CCAAACCAGCATGACCAACG 60.039 55.000 0.00 0.00 39.69 4.10
52 53 0.667993 CAAACCAGCATGACCAACGT 59.332 50.000 0.00 0.00 39.69 3.99
53 54 1.876799 CAAACCAGCATGACCAACGTA 59.123 47.619 0.00 0.00 39.69 3.57
54 55 2.264005 AACCAGCATGACCAACGTAA 57.736 45.000 0.00 0.00 39.69 3.18
55 56 1.519408 ACCAGCATGACCAACGTAAC 58.481 50.000 0.00 0.00 39.69 2.50
56 57 1.071699 ACCAGCATGACCAACGTAACT 59.928 47.619 0.00 0.00 39.69 2.24
57 58 1.732259 CCAGCATGACCAACGTAACTC 59.268 52.381 0.00 0.00 39.69 3.01
58 59 1.732259 CAGCATGACCAACGTAACTCC 59.268 52.381 0.00 0.00 39.69 3.85
59 60 1.346395 AGCATGACCAACGTAACTCCA 59.654 47.619 0.00 0.00 0.00 3.86
60 61 2.147958 GCATGACCAACGTAACTCCAA 58.852 47.619 0.00 0.00 0.00 3.53
61 62 2.550606 GCATGACCAACGTAACTCCAAA 59.449 45.455 0.00 0.00 0.00 3.28
62 63 3.003897 GCATGACCAACGTAACTCCAAAA 59.996 43.478 0.00 0.00 0.00 2.44
63 64 4.498345 GCATGACCAACGTAACTCCAAAAA 60.498 41.667 0.00 0.00 0.00 1.94
81 82 3.950087 AAAAACGTACTTCCACCGTTC 57.050 42.857 0.00 0.00 43.32 3.95
82 83 1.869774 AAACGTACTTCCACCGTTCC 58.130 50.000 0.00 0.00 43.32 3.62
83 84 1.043022 AACGTACTTCCACCGTTCCT 58.957 50.000 0.00 0.00 40.46 3.36
84 85 1.909700 ACGTACTTCCACCGTTCCTA 58.090 50.000 0.00 0.00 0.00 2.94
85 86 2.238521 ACGTACTTCCACCGTTCCTAA 58.761 47.619 0.00 0.00 0.00 2.69
86 87 2.627699 ACGTACTTCCACCGTTCCTAAA 59.372 45.455 0.00 0.00 0.00 1.85
87 88 3.259123 ACGTACTTCCACCGTTCCTAAAT 59.741 43.478 0.00 0.00 0.00 1.40
88 89 4.462483 ACGTACTTCCACCGTTCCTAAATA 59.538 41.667 0.00 0.00 0.00 1.40
89 90 5.127682 ACGTACTTCCACCGTTCCTAAATAT 59.872 40.000 0.00 0.00 0.00 1.28
90 91 6.044682 CGTACTTCCACCGTTCCTAAATATT 58.955 40.000 0.00 0.00 0.00 1.28
91 92 6.536224 CGTACTTCCACCGTTCCTAAATATTT 59.464 38.462 5.89 5.89 0.00 1.40
92 93 6.753107 ACTTCCACCGTTCCTAAATATTTG 57.247 37.500 11.05 1.40 0.00 2.32
93 94 6.243148 ACTTCCACCGTTCCTAAATATTTGT 58.757 36.000 11.05 0.00 0.00 2.83
94 95 6.373495 ACTTCCACCGTTCCTAAATATTTGTC 59.627 38.462 11.05 0.00 0.00 3.18
95 96 6.057321 TCCACCGTTCCTAAATATTTGTCT 57.943 37.500 11.05 0.00 0.00 3.41
96 97 6.478129 TCCACCGTTCCTAAATATTTGTCTT 58.522 36.000 11.05 0.00 0.00 3.01
97 98 6.943718 TCCACCGTTCCTAAATATTTGTCTTT 59.056 34.615 11.05 0.00 0.00 2.52
98 99 7.449086 TCCACCGTTCCTAAATATTTGTCTTTT 59.551 33.333 11.05 0.00 0.00 2.27
99 100 8.085909 CCACCGTTCCTAAATATTTGTCTTTTT 58.914 33.333 11.05 0.00 0.00 1.94
126 127 8.830580 AGAATTTCAAATGGACTATCACATACG 58.169 33.333 0.00 0.00 0.00 3.06
127 128 8.731275 AATTTCAAATGGACTATCACATACGA 57.269 30.769 0.00 0.00 0.00 3.43
128 129 8.731275 ATTTCAAATGGACTATCACATACGAA 57.269 30.769 0.00 0.00 0.00 3.85
129 130 8.731275 TTTCAAATGGACTATCACATACGAAT 57.269 30.769 0.00 0.00 0.00 3.34
130 131 7.713764 TCAAATGGACTATCACATACGAATG 57.286 36.000 0.00 0.00 39.17 2.67
132 133 8.417884 TCAAATGGACTATCACATACGAATGTA 58.582 33.333 0.00 0.00 44.70 2.29
133 134 9.208022 CAAATGGACTATCACATACGAATGTAT 57.792 33.333 0.00 0.00 44.70 2.29
170 171 8.721478 TCTAAAGTGTAGATTCACTCATTTTGC 58.279 33.333 0.00 0.00 46.25 3.68
171 172 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
172 173 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
173 174 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
174 175 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
175 176 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
176 177 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
177 178 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
178 179 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
179 180 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
180 181 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
181 182 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
182 183 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
183 184 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
184 185 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
185 186 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
186 187 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
187 188 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
188 189 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
189 190 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
190 191 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
191 192 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
192 193 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
193 194 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
194 195 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
195 196 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
196 197 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
197 198 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
198 199 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
199 200 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
203 204 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
206 207 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
301 302 5.747342 ACCACTTTACCACACTGTCTTAAA 58.253 37.500 0.00 0.00 0.00 1.52
317 318 3.262405 TCTTAAAGGAGGCCGTGTACATT 59.738 43.478 0.00 0.00 0.00 2.71
326 327 1.264826 GCCGTGTACATTTGTTTCCGT 59.735 47.619 0.00 0.00 0.00 4.69
509 514 2.972505 CGGCCACAAGAAGCACGT 60.973 61.111 2.24 0.00 0.00 4.49
574 579 2.890311 CCAAACAAGGCTCATTACCACA 59.110 45.455 0.00 0.00 0.00 4.17
608 613 0.112606 TCCCATTTTTACCACGGCCA 59.887 50.000 2.24 0.00 0.00 5.36
623 628 1.518302 GCCACCATTGATGCATGCA 59.482 52.632 25.04 25.04 0.00 3.96
625 630 0.179094 CCACCATTGATGCATGCACC 60.179 55.000 25.37 15.61 0.00 5.01
629 634 0.452585 CATTGATGCATGCACCGTCA 59.547 50.000 25.37 20.24 0.00 4.35
630 635 1.135344 CATTGATGCATGCACCGTCAA 60.135 47.619 28.18 28.18 41.06 3.18
715 720 1.714899 GCGCACAAATAGCATCCGGT 61.715 55.000 0.30 0.00 0.00 5.28
716 721 0.304705 CGCACAAATAGCATCCGGTC 59.695 55.000 0.00 0.00 0.00 4.79
717 722 1.378531 GCACAAATAGCATCCGGTCA 58.621 50.000 0.00 0.00 0.00 4.02
861 870 0.037326 CTCCATGTACAGTGGCGTGT 60.037 55.000 15.54 0.00 36.66 4.49
1181 1194 3.698463 CGGCACAACGTCACGGAC 61.698 66.667 0.35 0.00 0.00 4.79
1188 1201 0.038618 CAACGTCACGGACATCCTCA 60.039 55.000 0.35 0.00 32.09 3.86
1267 1280 4.965858 CGAGATCGACGGGCGCTC 62.966 72.222 7.64 0.06 43.02 5.03
1576 1589 0.680061 GTGAAGTCGGTCAAGGAGGT 59.320 55.000 0.00 0.00 0.00 3.85
1726 1751 4.803908 GGCCCCTGCACCTGCTAC 62.804 72.222 0.00 0.00 42.66 3.58
2086 2112 1.136147 CGCTGGCAGATTTGAGCAC 59.864 57.895 20.86 0.00 0.00 4.40
2128 2155 3.674997 GTTTAGTCAAGGAGTGCATGGA 58.325 45.455 0.00 0.00 0.00 3.41
2216 2244 5.927819 TGAATCTTGCAAATCCACCTTTTT 58.072 33.333 0.00 0.00 0.00 1.94
2330 2362 2.183478 TGCACGATCACATGGAAACT 57.817 45.000 0.00 0.00 0.00 2.66
2437 2470 1.374343 AAGCCGATCTCTCGTGCGTA 61.374 55.000 0.00 0.00 43.49 4.42
2470 2503 2.612212 ACAAATCTCAACACGGTGACAC 59.388 45.455 16.29 0.00 0.00 3.67
2544 2577 3.500680 GCACACAAAAGTTTCGATCCCTA 59.499 43.478 0.00 0.00 0.00 3.53
2546 2579 5.631026 CACACAAAAGTTTCGATCCCTATG 58.369 41.667 0.00 0.00 0.00 2.23
2564 2597 2.905415 TGGCAATCTGAGGGAACAAT 57.095 45.000 0.00 0.00 0.00 2.71
2658 2691 2.636830 CTCCAAACTAGCATGGACTGG 58.363 52.381 11.97 1.56 40.74 4.00
2778 2811 3.123959 CGACAACCAAAACCTACCATACG 59.876 47.826 0.00 0.00 0.00 3.06
2796 2829 0.591170 CGACCAAAACGGCATCACTT 59.409 50.000 0.00 0.00 39.03 3.16
2827 2860 0.108585 ACCACATCCTCACACACCAC 59.891 55.000 0.00 0.00 0.00 4.16
2840 2873 2.819608 ACACACCACCATGAAGCAATAC 59.180 45.455 0.00 0.00 0.00 1.89
2887 2920 5.284861 TCTAAGCTACAACAAGGTCACAA 57.715 39.130 0.00 0.00 0.00 3.33
2987 3023 4.349365 AGAAGAGGAGGAAGAAGAATCGT 58.651 43.478 0.00 0.00 0.00 3.73
3084 3121 0.393132 GCTCGAAGGGGAAAGGGAAG 60.393 60.000 0.00 0.00 0.00 3.46
3088 3125 1.282157 CGAAGGGGAAAGGGAAGTGAT 59.718 52.381 0.00 0.00 0.00 3.06
3089 3126 2.728007 GAAGGGGAAAGGGAAGTGATG 58.272 52.381 0.00 0.00 0.00 3.07
3090 3127 1.002857 AGGGGAAAGGGAAGTGATGG 58.997 55.000 0.00 0.00 0.00 3.51
3091 3128 0.704664 GGGGAAAGGGAAGTGATGGT 59.295 55.000 0.00 0.00 0.00 3.55
3092 3129 1.616994 GGGGAAAGGGAAGTGATGGTG 60.617 57.143 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.557832 TGCTACTTAACTCGGCCCATT 59.442 47.619 0.00 0.00 0.00 3.16
1 2 1.139058 CTGCTACTTAACTCGGCCCAT 59.861 52.381 0.00 0.00 0.00 4.00
2 3 0.535335 CTGCTACTTAACTCGGCCCA 59.465 55.000 0.00 0.00 0.00 5.36
3 4 0.810426 GCTGCTACTTAACTCGGCCC 60.810 60.000 0.00 0.00 0.00 5.80
4 5 1.146358 CGCTGCTACTTAACTCGGCC 61.146 60.000 0.00 0.00 0.00 6.13
5 6 0.179145 TCGCTGCTACTTAACTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
6 7 2.186076 CTTCGCTGCTACTTAACTCGG 58.814 52.381 0.00 0.00 0.00 4.63
7 8 2.159421 TCCTTCGCTGCTACTTAACTCG 60.159 50.000 0.00 0.00 0.00 4.18
8 9 3.505464 TCCTTCGCTGCTACTTAACTC 57.495 47.619 0.00 0.00 0.00 3.01
9 10 3.586892 GTTCCTTCGCTGCTACTTAACT 58.413 45.455 0.00 0.00 0.00 2.24
10 11 2.671888 GGTTCCTTCGCTGCTACTTAAC 59.328 50.000 0.00 0.00 0.00 2.01
11 12 2.354403 GGGTTCCTTCGCTGCTACTTAA 60.354 50.000 0.00 0.00 0.00 1.85
12 13 1.206371 GGGTTCCTTCGCTGCTACTTA 59.794 52.381 0.00 0.00 0.00 2.24
13 14 0.036294 GGGTTCCTTCGCTGCTACTT 60.036 55.000 0.00 0.00 0.00 2.24
14 15 1.597461 GGGTTCCTTCGCTGCTACT 59.403 57.895 0.00 0.00 0.00 2.57
15 16 1.449778 GGGGTTCCTTCGCTGCTAC 60.450 63.158 0.00 0.00 0.00 3.58
16 17 1.485294 TTGGGGTTCCTTCGCTGCTA 61.485 55.000 0.00 0.00 0.00 3.49
17 18 2.351924 TTTGGGGTTCCTTCGCTGCT 62.352 55.000 0.00 0.00 0.00 4.24
18 19 1.901464 TTTGGGGTTCCTTCGCTGC 60.901 57.895 0.00 0.00 0.00 5.25
19 20 1.524008 GGTTTGGGGTTCCTTCGCTG 61.524 60.000 0.00 0.00 0.00 5.18
20 21 1.228459 GGTTTGGGGTTCCTTCGCT 60.228 57.895 0.00 0.00 0.00 4.93
21 22 1.524008 CTGGTTTGGGGTTCCTTCGC 61.524 60.000 0.00 0.00 0.00 4.70
22 23 1.524008 GCTGGTTTGGGGTTCCTTCG 61.524 60.000 0.00 0.00 0.00 3.79
23 24 0.469144 TGCTGGTTTGGGGTTCCTTC 60.469 55.000 0.00 0.00 0.00 3.46
24 25 0.190815 ATGCTGGTTTGGGGTTCCTT 59.809 50.000 0.00 0.00 0.00 3.36
25 26 0.542702 CATGCTGGTTTGGGGTTCCT 60.543 55.000 0.00 0.00 0.00 3.36
26 27 0.541764 TCATGCTGGTTTGGGGTTCC 60.542 55.000 0.00 0.00 0.00 3.62
27 28 0.603065 GTCATGCTGGTTTGGGGTTC 59.397 55.000 0.00 0.00 0.00 3.62
28 29 0.831711 GGTCATGCTGGTTTGGGGTT 60.832 55.000 0.00 0.00 0.00 4.11
29 30 1.228862 GGTCATGCTGGTTTGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
30 31 0.831288 TTGGTCATGCTGGTTTGGGG 60.831 55.000 0.00 0.00 0.00 4.96
31 32 0.318120 GTTGGTCATGCTGGTTTGGG 59.682 55.000 0.00 0.00 0.00 4.12
32 33 0.039256 CGTTGGTCATGCTGGTTTGG 60.039 55.000 0.00 0.00 0.00 3.28
33 34 0.667993 ACGTTGGTCATGCTGGTTTG 59.332 50.000 0.00 0.00 0.00 2.93
34 35 2.264005 TACGTTGGTCATGCTGGTTT 57.736 45.000 0.00 0.00 0.00 3.27
35 36 1.877443 GTTACGTTGGTCATGCTGGTT 59.123 47.619 0.00 0.00 0.00 3.67
36 37 1.071699 AGTTACGTTGGTCATGCTGGT 59.928 47.619 0.00 0.00 0.00 4.00
37 38 1.732259 GAGTTACGTTGGTCATGCTGG 59.268 52.381 0.00 0.00 0.00 4.85
38 39 1.732259 GGAGTTACGTTGGTCATGCTG 59.268 52.381 0.00 0.00 0.00 4.41
39 40 1.346395 TGGAGTTACGTTGGTCATGCT 59.654 47.619 0.00 0.00 0.00 3.79
40 41 1.803334 TGGAGTTACGTTGGTCATGC 58.197 50.000 0.00 0.00 0.00 4.06
41 42 4.822036 TTTTGGAGTTACGTTGGTCATG 57.178 40.909 0.00 0.00 0.00 3.07
65 66 1.909700 TAGGAACGGTGGAAGTACGT 58.090 50.000 0.00 0.00 43.43 3.57
66 67 3.302365 TTTAGGAACGGTGGAAGTACG 57.698 47.619 0.00 0.00 0.00 3.67
67 68 7.335171 ACAAATATTTAGGAACGGTGGAAGTAC 59.665 37.037 0.00 0.00 0.00 2.73
68 69 7.396418 ACAAATATTTAGGAACGGTGGAAGTA 58.604 34.615 0.00 0.00 0.00 2.24
69 70 6.243148 ACAAATATTTAGGAACGGTGGAAGT 58.757 36.000 0.00 0.00 0.00 3.01
70 71 6.598064 AGACAAATATTTAGGAACGGTGGAAG 59.402 38.462 0.00 0.00 0.00 3.46
71 72 6.478129 AGACAAATATTTAGGAACGGTGGAA 58.522 36.000 0.00 0.00 0.00 3.53
72 73 6.057321 AGACAAATATTTAGGAACGGTGGA 57.943 37.500 0.00 0.00 0.00 4.02
73 74 6.753107 AAGACAAATATTTAGGAACGGTGG 57.247 37.500 0.00 0.00 0.00 4.61
100 101 8.830580 CGTATGTGATAGTCCATTTGAAATTCT 58.169 33.333 0.00 0.00 0.00 2.40
101 102 8.826710 TCGTATGTGATAGTCCATTTGAAATTC 58.173 33.333 0.00 0.00 0.00 2.17
102 103 8.731275 TCGTATGTGATAGTCCATTTGAAATT 57.269 30.769 0.00 0.00 0.00 1.82
103 104 8.731275 TTCGTATGTGATAGTCCATTTGAAAT 57.269 30.769 0.00 0.00 0.00 2.17
104 105 8.611757 CATTCGTATGTGATAGTCCATTTGAAA 58.388 33.333 0.00 0.00 0.00 2.69
105 106 7.768582 ACATTCGTATGTGATAGTCCATTTGAA 59.231 33.333 6.89 0.00 43.29 2.69
106 107 7.272244 ACATTCGTATGTGATAGTCCATTTGA 58.728 34.615 6.89 0.00 43.29 2.69
107 108 7.482654 ACATTCGTATGTGATAGTCCATTTG 57.517 36.000 6.89 0.00 43.29 2.32
150 151 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
151 152 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
152 153 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
153 154 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
154 155 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
155 156 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
156 157 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
157 158 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
158 159 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
159 160 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
160 161 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
161 162 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
162 163 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
163 164 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
164 165 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
165 166 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
166 167 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
167 168 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
168 169 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
169 170 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
170 171 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
171 172 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
172 173 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
173 174 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
177 178 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
180 181 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
210 211 9.327731 CCTAGTACTTCCTCCATTCCTAAATAT 57.672 37.037 0.00 0.00 0.00 1.28
211 212 7.234988 GCCTAGTACTTCCTCCATTCCTAAATA 59.765 40.741 0.00 0.00 0.00 1.40
212 213 6.043358 GCCTAGTACTTCCTCCATTCCTAAAT 59.957 42.308 0.00 0.00 0.00 1.40
213 214 5.365895 GCCTAGTACTTCCTCCATTCCTAAA 59.634 44.000 0.00 0.00 0.00 1.85
214 215 4.900054 GCCTAGTACTTCCTCCATTCCTAA 59.100 45.833 0.00 0.00 0.00 2.69
215 216 4.078805 TGCCTAGTACTTCCTCCATTCCTA 60.079 45.833 0.00 0.00 0.00 2.94
216 217 3.310193 GCCTAGTACTTCCTCCATTCCT 58.690 50.000 0.00 0.00 0.00 3.36
217 218 3.039011 TGCCTAGTACTTCCTCCATTCC 58.961 50.000 0.00 0.00 0.00 3.01
218 219 3.070302 CCTGCCTAGTACTTCCTCCATTC 59.930 52.174 0.00 0.00 0.00 2.67
219 220 3.041946 CCTGCCTAGTACTTCCTCCATT 58.958 50.000 0.00 0.00 0.00 3.16
220 221 2.022918 ACCTGCCTAGTACTTCCTCCAT 60.023 50.000 0.00 0.00 0.00 3.41
221 222 1.361543 ACCTGCCTAGTACTTCCTCCA 59.638 52.381 0.00 0.00 0.00 3.86
222 223 2.162264 ACCTGCCTAGTACTTCCTCC 57.838 55.000 0.00 0.00 0.00 4.30
223 224 4.139038 CTCTACCTGCCTAGTACTTCCTC 58.861 52.174 0.00 0.00 0.00 3.71
224 225 3.688991 GCTCTACCTGCCTAGTACTTCCT 60.689 52.174 0.00 0.00 0.00 3.36
225 226 2.624364 GCTCTACCTGCCTAGTACTTCC 59.376 54.545 0.00 0.00 0.00 3.46
226 227 2.624364 GGCTCTACCTGCCTAGTACTTC 59.376 54.545 0.00 0.00 46.38 3.01
227 228 2.668625 GGCTCTACCTGCCTAGTACTT 58.331 52.381 0.00 0.00 46.38 2.24
228 229 2.368311 GGCTCTACCTGCCTAGTACT 57.632 55.000 0.00 0.00 46.38 2.73
249 250 2.772287 CTCTTTCCTGGAAACTTCGCT 58.228 47.619 17.65 0.00 0.00 4.93
301 302 0.690762 ACAAATGTACACGGCCTCCT 59.309 50.000 0.00 0.00 0.00 3.69
317 318 6.144724 CACAAGAAACAAGAAAACGGAAACAA 59.855 34.615 0.00 0.00 0.00 2.83
326 327 6.817765 AGAGTGTCACAAGAAACAAGAAAA 57.182 33.333 5.62 0.00 34.22 2.29
509 514 1.623811 GGTCTGTCCTCTGCTACCAAA 59.376 52.381 0.00 0.00 0.00 3.28
574 579 5.908562 AAATGGGAGATGATGAGAGATGT 57.091 39.130 0.00 0.00 0.00 3.06
608 613 0.966875 ACGGTGCATGCATCAATGGT 60.967 50.000 29.40 16.59 0.00 3.55
623 628 0.942252 GGACGAAAGCTTTTGACGGT 59.058 50.000 29.30 14.86 0.00 4.83
625 630 0.110823 CCGGACGAAAGCTTTTGACG 60.111 55.000 29.30 27.70 0.00 4.35
629 634 1.332686 GACAACCGGACGAAAGCTTTT 59.667 47.619 14.05 0.00 0.00 2.27
630 635 0.942252 GACAACCGGACGAAAGCTTT 59.058 50.000 12.53 12.53 0.00 3.51
657 662 1.589716 CCCGCTCTTTGCCTCTTTGG 61.590 60.000 0.00 0.00 38.78 3.28
695 700 1.009675 CGGATGCTATTTGTGCGCC 60.010 57.895 4.18 0.00 0.00 6.53
715 720 4.822026 TCAATGCATGCAATTTGTGATGA 58.178 34.783 26.68 14.83 0.00 2.92
716 721 5.733226 ATCAATGCATGCAATTTGTGATG 57.267 34.783 26.68 12.91 0.00 3.07
717 722 5.877564 TGAATCAATGCATGCAATTTGTGAT 59.122 32.000 26.68 22.21 0.00 3.06
1110 1123 2.667418 GAGCAGCAGCAGGAGGAA 59.333 61.111 3.17 0.00 45.49 3.36
1173 1186 1.153823 CGGTGAGGATGTCCGTGAC 60.154 63.158 0.00 0.00 42.08 3.67
1181 1194 2.202797 CTGGCGACGGTGAGGATG 60.203 66.667 0.00 0.00 0.00 3.51
1612 1625 1.511305 GCGGTGAAGGACGAGATGA 59.489 57.895 0.00 0.00 0.00 2.92
1841 1866 4.988716 TGGTCTCCGTCCGCACCT 62.989 66.667 0.00 0.00 0.00 4.00
2155 2182 0.387239 GGTCCATGCAACGCAGAAAC 60.387 55.000 0.00 0.00 43.65 2.78
2216 2244 4.371624 TGCAAGATCCCTCAAAGAAGAA 57.628 40.909 0.00 0.00 0.00 2.52
2218 2246 5.393896 GGATTTGCAAGATCCCTCAAAGAAG 60.394 44.000 20.96 0.00 37.65 2.85
2330 2362 4.406648 ACTAATGCTGTTGGATCGATCA 57.593 40.909 25.93 10.23 0.00 2.92
2385 2417 9.754382 AACGTTTACTATACATCATTTCCGTAT 57.246 29.630 0.00 0.00 0.00 3.06
2405 2438 0.391597 TCGGCTTCCAGAGAACGTTT 59.608 50.000 0.46 0.00 0.00 3.60
2437 2470 2.225091 TGAGATTTGTGCCTGGGATTGT 60.225 45.455 0.00 0.00 0.00 2.71
2470 2503 4.459331 CCCGCCGCAATTGTCACG 62.459 66.667 7.40 8.07 0.00 4.35
2532 2565 3.499918 CAGATTGCCATAGGGATCGAAAC 59.500 47.826 0.00 0.00 35.59 2.78
2544 2577 2.905415 TTGTTCCCTCAGATTGCCAT 57.095 45.000 0.00 0.00 0.00 4.40
2546 2579 1.135721 GCATTGTTCCCTCAGATTGCC 59.864 52.381 0.00 0.00 0.00 4.52
2564 2597 1.223487 GGATAAGACGGGGCTTGCA 59.777 57.895 0.00 0.00 0.00 4.08
2658 2691 4.184629 GGTAGTGTGGTGAGATTGATGAC 58.815 47.826 0.00 0.00 0.00 3.06
2744 2777 6.866248 GGTTTTGGTTGTCGTTAATGATGATT 59.134 34.615 0.00 0.00 0.00 2.57
2778 2811 1.336755 ACAAGTGATGCCGTTTTGGTC 59.663 47.619 0.00 0.00 41.21 4.02
2796 2829 5.536538 GTGAGGATGTGGTAGATCAGATACA 59.463 44.000 0.00 0.00 0.00 2.29
2827 2860 7.386299 GTGGTAGATTAGAGTATTGCTTCATGG 59.614 40.741 0.00 0.00 0.00 3.66
3011 3047 0.733150 GGTAAGTTGCGCCATCTTCC 59.267 55.000 4.18 6.93 0.00 3.46
3061 3098 0.036875 CCTTTCCCCTTCGAGCACTT 59.963 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.