Multiple sequence alignment - TraesCS7D01G272400

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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 TraesCS7D01G272400 chr7D 100.000 2705 0 0 1 2705 262699956 262697252 0.000000e+00 4996
1 TraesCS7D01G272400 chr7D 89.815 108 11 0 1286 1393 13029143 13029036 3.630000e-29 139
2 TraesCS7D01G272400 chr7B 91.398 2639 127 47 2 2593 241106686 241109271 0.000000e+00 3524
3 TraesCS7D01G272400 chr7B 91.150 113 10 0 2591 2703 241109379 241109491 1.300000e-33 154
4 TraesCS7D01G272400 chr7A 87.500 2408 111 68 403 2705 285577215 285574893 0.000000e+00 2604
5 TraesCS7D01G272400 chr7A 89.815 108 11 0 1286 1393 12429278 12429171 3.630000e-29 139
6 TraesCS7D01G272400 chr7A 89.815 108 11 0 1286 1393 12454967 12454860 3.630000e-29 139
7 TraesCS7D01G272400 chr7A 89.815 108 11 0 1286 1393 12652362 12652255 3.630000e-29 139
8 TraesCS7D01G272400 chr3A 90.037 271 24 3 996 1265 633922097 633922365 5.540000e-92 348
9 TraesCS7D01G272400 chr3B 89.299 271 26 3 996 1265 653152047 653152315 1.200000e-88 337
10 TraesCS7D01G272400 chr5D 89.434 265 28 0 1001 1265 425077485 425077221 4.320000e-88 335
11 TraesCS7D01G272400 chr3D 88.971 272 27 3 995 1265 492131419 492131688 1.550000e-87 333
12 TraesCS7D01G272400 chr5B 89.057 265 29 0 1001 1265 514279627 514279363 2.010000e-86 329
13 TraesCS7D01G272400 chr5A 88.679 265 30 0 1001 1265 539093485 539093221 9.340000e-85 324
14 TraesCS7D01G272400 chr1A 88.192 271 29 3 996 1265 463461701 463461433 1.210000e-83 320
15 TraesCS7D01G272400 chr4A 89.815 108 11 0 1286 1393 724782995 724783102 3.630000e-29 139
16 TraesCS7D01G272400 chr4A 84.783 138 18 3 1258 1393 724579773 724579637 4.700000e-28 135
17 TraesCS7D01G272400 chr4A 85.366 123 18 0 1261 1383 517884847 517884969 7.860000e-26 128


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 TraesCS7D01G272400 chr7D 262697252 262699956 2704 True 4996 4996 100.000 1 2705 1 chr7D.!!$R2 2704
1 TraesCS7D01G272400 chr7B 241106686 241109491 2805 False 1839 3524 91.274 2 2703 2 chr7B.!!$F1 2701
2 TraesCS7D01G272400 chr7A 285574893 285577215 2322 True 2604 2604 87.500 403 2705 1 chr7A.!!$R4 2302

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
111 112 0.036388 TCACCCGACATTTGAGGAGC 60.036 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 1955 0.118144 AGGAGGGCAGGGAGGATATC 59.882 60.0 0.0 0.0 0.0 1.63 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
45 46 3.660501 TCCGTTGGATCATCTATTCGG 57.339 47.619 8.25 8.25 38.36 4.30
46 47 3.227614 TCCGTTGGATCATCTATTCGGA 58.772 45.455 11.78 11.78 42.52 4.55
47 48 3.832490 TCCGTTGGATCATCTATTCGGAT 59.168 43.478 11.78 0.00 40.46 4.18
48 49 4.082190 TCCGTTGGATCATCTATTCGGATC 60.082 45.833 11.78 0.00 40.46 3.36
49 50 4.321974 CCGTTGGATCATCTATTCGGATCA 60.322 45.833 8.72 0.00 39.30 2.92
50 51 5.230182 CGTTGGATCATCTATTCGGATCAA 58.770 41.667 0.00 0.00 39.30 2.57
53 54 4.187694 GGATCATCTATTCGGATCAAGGC 58.812 47.826 0.00 0.00 39.30 4.35
54 55 3.303881 TCATCTATTCGGATCAAGGCG 57.696 47.619 0.00 0.00 0.00 5.52
55 56 1.728971 CATCTATTCGGATCAAGGCGC 59.271 52.381 0.00 0.00 0.00 6.53
56 57 0.750249 TCTATTCGGATCAAGGCGCA 59.250 50.000 10.83 0.00 0.00 6.09
57 58 1.143305 CTATTCGGATCAAGGCGCAG 58.857 55.000 10.83 0.00 0.00 5.18
58 59 0.750249 TATTCGGATCAAGGCGCAGA 59.250 50.000 10.83 3.97 0.00 4.26
59 60 0.107456 ATTCGGATCAAGGCGCAGAT 59.893 50.000 10.83 9.53 0.00 2.90
60 61 0.811219 TTCGGATCAAGGCGCAGATG 60.811 55.000 10.83 4.67 0.00 2.90
62 63 1.146930 GGATCAAGGCGCAGATGGA 59.853 57.895 10.83 0.00 0.00 3.41
63 64 0.250640 GGATCAAGGCGCAGATGGAT 60.251 55.000 10.83 2.48 0.00 3.41
64 65 0.873054 GATCAAGGCGCAGATGGATG 59.127 55.000 10.83 0.00 0.00 3.51
65 66 0.536687 ATCAAGGCGCAGATGGATGG 60.537 55.000 10.83 0.00 0.00 3.51
66 67 1.452651 CAAGGCGCAGATGGATGGT 60.453 57.895 10.83 0.00 0.00 3.55
67 68 1.033746 CAAGGCGCAGATGGATGGTT 61.034 55.000 10.83 0.00 0.00 3.67
68 69 1.033746 AAGGCGCAGATGGATGGTTG 61.034 55.000 10.83 0.00 0.00 3.77
69 70 2.410469 GCGCAGATGGATGGTTGC 59.590 61.111 0.30 0.00 0.00 4.17
70 71 2.409055 GCGCAGATGGATGGTTGCA 61.409 57.895 0.30 0.00 36.37 4.08
71 72 1.725665 CGCAGATGGATGGTTGCAG 59.274 57.895 0.00 0.00 36.37 4.41
72 73 0.745486 CGCAGATGGATGGTTGCAGA 60.745 55.000 0.00 0.00 36.37 4.26
73 74 0.737219 GCAGATGGATGGTTGCAGAC 59.263 55.000 0.00 0.00 36.59 3.51
74 75 1.951895 GCAGATGGATGGTTGCAGACA 60.952 52.381 0.00 0.00 36.59 3.41
75 76 1.741706 CAGATGGATGGTTGCAGACAC 59.258 52.381 0.00 0.00 0.00 3.67
76 77 0.729116 GATGGATGGTTGCAGACACG 59.271 55.000 0.00 0.00 0.00 4.49
77 78 0.036732 ATGGATGGTTGCAGACACGT 59.963 50.000 0.00 0.00 0.00 4.49
78 79 0.884259 TGGATGGTTGCAGACACGTG 60.884 55.000 15.48 15.48 0.00 4.49
84 85 4.624364 TGCAGACACGTGCCCCTG 62.624 66.667 17.22 20.00 43.28 4.45
94 95 1.861542 CGTGCCCCTGCGAATTTTCA 61.862 55.000 0.00 0.00 41.78 2.69
103 104 1.883275 TGCGAATTTTCACCCGACATT 59.117 42.857 0.00 0.00 0.00 2.71
111 112 0.036388 TCACCCGACATTTGAGGAGC 60.036 55.000 0.00 0.00 0.00 4.70
119 120 4.202264 CCGACATTTGAGGAGCTAAGGTAT 60.202 45.833 0.00 0.00 0.00 2.73
121 122 5.921408 CGACATTTGAGGAGCTAAGGTATAC 59.079 44.000 0.00 0.00 0.00 1.47
134 135 3.802948 AGGTATACGAGGCAGTTTGAG 57.197 47.619 0.00 0.00 0.00 3.02
174 176 7.790798 TGAGTTAAGGTATATAGGGGCACTTTA 59.209 37.037 0.00 0.00 0.00 1.85
179 181 6.631107 AGGTATATAGGGGCACTTTAAGAGA 58.369 40.000 0.00 0.00 0.00 3.10
180 182 7.257146 AGGTATATAGGGGCACTTTAAGAGAT 58.743 38.462 0.00 0.00 0.00 2.75
181 183 7.739904 AGGTATATAGGGGCACTTTAAGAGATT 59.260 37.037 0.00 0.00 0.00 2.40
205 207 9.898152 ATTAAATTATAAGGGATCAGCTAGAGC 57.102 33.333 0.00 0.00 42.49 4.09
225 228 3.016736 GCTGCACTAAAAGGCCAATCTA 58.983 45.455 5.01 0.00 0.00 1.98
226 229 3.633986 GCTGCACTAAAAGGCCAATCTAT 59.366 43.478 5.01 0.00 0.00 1.98
240 243 4.333926 GCCAATCTATGTTGAAGGACACTC 59.666 45.833 0.00 0.00 31.30 3.51
251 254 5.034852 TGAAGGACACTCAAGTTCAATGA 57.965 39.130 0.00 0.00 0.00 2.57
258 261 7.768120 AGGACACTCAAGTTCAATGATAAGATC 59.232 37.037 0.00 0.00 0.00 2.75
311 315 8.496916 TCCAAGTTATAAAAATCTACCCTACCC 58.503 37.037 0.00 0.00 0.00 3.69
312 316 8.500238 CCAAGTTATAAAAATCTACCCTACCCT 58.500 37.037 0.00 0.00 0.00 4.34
315 319 8.864087 AGTTATAAAAATCTACCCTACCCTACG 58.136 37.037 0.00 0.00 0.00 3.51
329 333 6.211515 CCTACCCTACGTTACATTGTGATAC 58.788 44.000 0.00 0.00 0.00 2.24
351 355 3.610911 GAAGGGAGTAGGAACCATGTTG 58.389 50.000 0.00 0.00 0.00 3.33
393 397 7.777440 AGGAAGAAATATCATTTGAGTTCCTCC 59.223 37.037 10.77 9.18 37.32 4.30
394 398 7.013750 GGAAGAAATATCATTTGAGTTCCTCCC 59.986 40.741 0.00 0.00 0.00 4.30
395 399 7.218314 AGAAATATCATTTGAGTTCCTCCCT 57.782 36.000 0.00 0.00 0.00 4.20
396 400 8.337118 AGAAATATCATTTGAGTTCCTCCCTA 57.663 34.615 0.00 0.00 0.00 3.53
397 401 8.953665 AGAAATATCATTTGAGTTCCTCCCTAT 58.046 33.333 0.00 0.00 0.00 2.57
398 402 9.225436 GAAATATCATTTGAGTTCCTCCCTATC 57.775 37.037 0.00 0.00 0.00 2.08
399 403 8.517323 AATATCATTTGAGTTCCTCCCTATCT 57.483 34.615 0.00 0.00 0.00 1.98
400 404 5.620738 TCATTTGAGTTCCTCCCTATCTG 57.379 43.478 0.00 0.00 0.00 2.90
416 423 6.613271 TCCCTATCTGCCTATCTGGATATTTC 59.387 42.308 0.00 0.00 38.35 2.17
437 444 2.900167 GACACGGTGGCGGGAAAAC 61.900 63.158 13.48 0.00 0.00 2.43
439 449 3.881104 ACGGTGGCGGGAAAACCT 61.881 61.111 0.00 0.00 36.97 3.50
638 679 3.064931 GTGCTTTCGCTTTGTACCTACT 58.935 45.455 0.00 0.00 36.97 2.57
795 841 4.305539 ACCAACCAACTCATCATCATCA 57.694 40.909 0.00 0.00 0.00 3.07
796 842 4.863548 ACCAACCAACTCATCATCATCAT 58.136 39.130 0.00 0.00 0.00 2.45
818 864 6.491062 TCATCATCATCCTCTCTTTCTCTCTC 59.509 42.308 0.00 0.00 0.00 3.20
861 914 0.612229 TCCCAAGAGAGCAAGCAGAG 59.388 55.000 0.00 0.00 0.00 3.35
946 1004 2.972505 CACACCCACACGTGAGCC 60.973 66.667 25.01 0.00 37.20 4.70
967 1028 1.372128 GCAAAAGCAAGGCGGACAG 60.372 57.895 0.00 0.00 0.00 3.51
973 1034 2.668280 GCAAGGCGGACAGACGTTC 61.668 63.158 0.00 0.00 35.98 3.95
1005 1067 0.106519 AAGAAAGATCGGCCATGGGG 60.107 55.000 15.13 0.00 37.18 4.96
1006 1068 0.988145 AGAAAGATCGGCCATGGGGA 60.988 55.000 15.13 0.00 35.59 4.81
1008 1070 0.988145 AAAGATCGGCCATGGGGAGA 60.988 55.000 15.13 0.00 35.59 3.71
1245 1307 0.829333 AGCTCATCGTCAAGCTCCAT 59.171 50.000 0.00 0.00 45.57 3.41
1429 1500 2.364186 TCCATCCTGCAGAGGCGA 60.364 61.111 17.39 3.73 45.35 5.54
1437 1514 2.669569 GCAGAGGCGACCAAGCAA 60.670 61.111 0.00 0.00 39.27 3.91
1439 1516 1.597854 CAGAGGCGACCAAGCAACA 60.598 57.895 0.00 0.00 39.27 3.33
1467 1544 3.077556 GAGAGGAAGCCGCCCAGA 61.078 66.667 0.00 0.00 0.00 3.86
1608 1691 2.124983 TTCCGCTGCAGCATCCTC 60.125 61.111 36.03 8.11 42.21 3.71
1799 1892 9.668497 TTTAGCTCTTAGGAAAAGAAATACTCC 57.332 33.333 0.00 0.00 0.00 3.85
1800 1893 7.503492 AGCTCTTAGGAAAAGAAATACTCCT 57.497 36.000 0.00 0.00 41.29 3.69
1831 1924 2.157640 AGATGGTGAGGAGGAGACTG 57.842 55.000 0.00 0.00 44.43 3.51
1832 1925 1.118838 GATGGTGAGGAGGAGACTGG 58.881 60.000 0.00 0.00 44.43 4.00
1833 1926 0.415429 ATGGTGAGGAGGAGACTGGT 59.585 55.000 0.00 0.00 44.43 4.00
1834 1927 1.081481 TGGTGAGGAGGAGACTGGTA 58.919 55.000 0.00 0.00 44.43 3.25
1835 1928 1.646447 TGGTGAGGAGGAGACTGGTAT 59.354 52.381 0.00 0.00 44.43 2.73
1836 1929 2.035632 GGTGAGGAGGAGACTGGTATG 58.964 57.143 0.00 0.00 44.43 2.39
1862 1955 7.331193 GGTATTATTAGGTGAGGATTTGTAGCG 59.669 40.741 0.00 0.00 0.00 4.26
1864 1957 5.552870 ATTAGGTGAGGATTTGTAGCGAT 57.447 39.130 0.00 0.00 0.00 4.58
1898 1991 2.426738 CTCCTCGATCTGCTCAGTTTCT 59.573 50.000 0.00 0.00 0.00 2.52
1950 2051 9.450807 GAAATGGAACGGAATGAAATAATACAG 57.549 33.333 0.00 0.00 0.00 2.74
1953 2054 8.428186 TGGAACGGAATGAAATAATACAGTAC 57.572 34.615 0.00 0.00 0.00 2.73
2015 2118 3.394274 TGAACATCTCCTCAAACTTCCCA 59.606 43.478 0.00 0.00 0.00 4.37
2073 2177 6.926272 GCAAGAGTATGAAATGAGTACTAGGG 59.074 42.308 0.00 0.00 0.00 3.53
2102 2206 5.583854 TCATTAGTTCGTTACTACTCGCTCT 59.416 40.000 0.69 0.00 39.05 4.09
2111 2215 5.733572 CGTTACTACTCGCTCTGTTCTAAAG 59.266 44.000 0.00 0.00 0.00 1.85
2136 2240 4.781071 AGTGTCGTAGTTTCAGTTAGACG 58.219 43.478 0.00 0.00 0.00 4.18
2142 2246 3.027974 AGTTTCAGTTAGACGGTGCTC 57.972 47.619 0.00 0.00 0.00 4.26
2216 2325 0.610232 GGTGCAGATTGGTTGGAGCT 60.610 55.000 0.00 0.00 32.57 4.09
2378 2497 3.364460 TGTTGGATTGGATCGGATTGT 57.636 42.857 0.00 0.00 0.00 2.71
2418 2547 2.891112 CTTTGTGTTGTGTTGGTGCAT 58.109 42.857 0.00 0.00 0.00 3.96
2467 2596 0.472471 TTTGGGTTGCTTCGGAGTCT 59.528 50.000 0.00 0.00 0.00 3.24
2511 2642 4.281941 ACCAAAAGGCTGAATTTCCTCTTC 59.718 41.667 0.00 0.00 0.00 2.87
2516 2647 6.737720 AAGGCTGAATTTCCTCTTCTTTTT 57.262 33.333 0.00 0.00 0.00 1.94
2539 2670 6.956202 TTTTTACCAACGAAAATGGACCTA 57.044 33.333 0.00 0.00 40.56 3.08
2579 2712 0.183731 AGGGAGAAATGGGCCGATTC 59.816 55.000 13.92 9.38 0.00 2.52
2622 2865 8.510358 TTAAAATATCATCTCCTCCTCCATCA 57.490 34.615 0.00 0.00 0.00 3.07
2659 2902 1.902508 ACTCTGAAATTCCCGCTCTCA 59.097 47.619 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.660501 TCCGAATAGATGATCCAACGG 57.339 47.619 10.17 10.17 40.36 4.44
37 38 0.750249 TGCGCCTTGATCCGAATAGA 59.250 50.000 4.18 0.00 0.00 1.98
38 39 1.143305 CTGCGCCTTGATCCGAATAG 58.857 55.000 4.18 0.00 0.00 1.73
39 40 0.750249 TCTGCGCCTTGATCCGAATA 59.250 50.000 4.18 0.00 0.00 1.75
40 41 0.107456 ATCTGCGCCTTGATCCGAAT 59.893 50.000 4.18 0.00 0.00 3.34
41 42 0.811219 CATCTGCGCCTTGATCCGAA 60.811 55.000 4.18 0.00 0.00 4.30
42 43 1.227350 CATCTGCGCCTTGATCCGA 60.227 57.895 4.18 0.00 0.00 4.55
45 46 0.873054 CATCCATCTGCGCCTTGATC 59.127 55.000 4.18 0.00 0.00 2.92
46 47 0.536687 CCATCCATCTGCGCCTTGAT 60.537 55.000 4.18 3.10 0.00 2.57
47 48 1.153107 CCATCCATCTGCGCCTTGA 60.153 57.895 4.18 0.26 0.00 3.02
48 49 1.033746 AACCATCCATCTGCGCCTTG 61.034 55.000 4.18 0.00 0.00 3.61
49 50 1.033746 CAACCATCCATCTGCGCCTT 61.034 55.000 4.18 0.00 0.00 4.35
50 51 1.452651 CAACCATCCATCTGCGCCT 60.453 57.895 4.18 0.00 0.00 5.52
53 54 0.745486 TCTGCAACCATCCATCTGCG 60.745 55.000 0.00 0.00 37.62 5.18
54 55 0.737219 GTCTGCAACCATCCATCTGC 59.263 55.000 0.00 0.00 35.32 4.26
55 56 1.741706 GTGTCTGCAACCATCCATCTG 59.258 52.381 0.00 0.00 0.00 2.90
56 57 1.676916 CGTGTCTGCAACCATCCATCT 60.677 52.381 0.00 0.00 0.00 2.90
57 58 0.729116 CGTGTCTGCAACCATCCATC 59.271 55.000 0.00 0.00 0.00 3.51
58 59 0.036732 ACGTGTCTGCAACCATCCAT 59.963 50.000 0.00 0.00 0.00 3.41
59 60 0.884259 CACGTGTCTGCAACCATCCA 60.884 55.000 7.58 0.00 0.00 3.41
60 61 1.868997 CACGTGTCTGCAACCATCC 59.131 57.895 7.58 0.00 0.00 3.51
62 63 2.260869 GGCACGTGTCTGCAACCAT 61.261 57.895 18.38 0.00 39.08 3.55
63 64 2.899838 GGCACGTGTCTGCAACCA 60.900 61.111 18.38 0.00 39.08 3.67
64 65 3.660111 GGGCACGTGTCTGCAACC 61.660 66.667 21.13 8.85 39.08 3.77
65 66 3.660111 GGGGCACGTGTCTGCAAC 61.660 66.667 21.13 2.07 39.08 4.17
66 67 3.872603 AGGGGCACGTGTCTGCAA 61.873 61.111 21.13 0.00 39.08 4.08
67 68 4.624364 CAGGGGCACGTGTCTGCA 62.624 66.667 21.13 0.00 39.08 4.41
71 72 4.980805 TTCGCAGGGGCACGTGTC 62.981 66.667 18.38 15.79 41.24 3.67
72 73 3.842925 AATTCGCAGGGGCACGTGT 62.843 57.895 18.38 0.00 41.24 4.49
73 74 2.141122 AAAATTCGCAGGGGCACGTG 62.141 55.000 12.28 12.28 41.24 4.49
74 75 1.862602 GAAAATTCGCAGGGGCACGT 61.863 55.000 0.00 0.00 41.24 4.49
75 76 1.154035 GAAAATTCGCAGGGGCACG 60.154 57.895 0.00 0.00 41.24 5.34
76 77 0.388520 GTGAAAATTCGCAGGGGCAC 60.389 55.000 1.98 0.00 41.24 5.01
77 78 1.531739 GGTGAAAATTCGCAGGGGCA 61.532 55.000 8.77 0.00 41.24 5.36
78 79 1.215382 GGTGAAAATTCGCAGGGGC 59.785 57.895 8.77 0.00 39.38 5.80
84 85 2.629639 AATGTCGGGTGAAAATTCGC 57.370 45.000 0.00 0.00 36.98 4.70
85 86 4.153958 TCAAATGTCGGGTGAAAATTCG 57.846 40.909 0.00 0.00 0.00 3.34
94 95 1.568504 TAGCTCCTCAAATGTCGGGT 58.431 50.000 0.00 0.00 0.00 5.28
103 104 4.142790 CCTCGTATACCTTAGCTCCTCAA 58.857 47.826 0.00 0.00 0.00 3.02
111 112 5.067413 TCTCAAACTGCCTCGTATACCTTAG 59.933 44.000 0.00 0.00 0.00 2.18
119 120 1.629043 ACCTCTCAAACTGCCTCGTA 58.371 50.000 0.00 0.00 0.00 3.43
121 122 2.743636 TAACCTCTCAAACTGCCTCG 57.256 50.000 0.00 0.00 0.00 4.63
179 181 9.898152 GCTCTAGCTGATCCCTTATAATTTAAT 57.102 33.333 0.00 0.00 38.21 1.40
205 207 4.641989 ACATAGATTGGCCTTTTAGTGCAG 59.358 41.667 3.32 0.00 0.00 4.41
208 210 6.757897 TCAACATAGATTGGCCTTTTAGTG 57.242 37.500 3.32 0.00 0.00 2.74
209 211 6.378280 CCTTCAACATAGATTGGCCTTTTAGT 59.622 38.462 3.32 0.00 0.00 2.24
225 228 4.780815 TGAACTTGAGTGTCCTTCAACAT 58.219 39.130 0.00 0.00 31.66 2.71
226 229 4.214986 TGAACTTGAGTGTCCTTCAACA 57.785 40.909 0.00 0.00 31.66 3.33
240 243 9.731819 CTCATTTGGATCTTATCATTGAACTTG 57.268 33.333 0.00 0.00 0.00 3.16
251 254 9.183368 GTTTCTTCTTCCTCATTTGGATCTTAT 57.817 33.333 0.00 0.00 35.83 1.73
294 298 7.617723 TGTAACGTAGGGTAGGGTAGATTTTTA 59.382 37.037 0.00 0.00 0.00 1.52
310 314 5.457799 CCTTCGTATCACAATGTAACGTAGG 59.542 44.000 18.50 18.50 42.13 3.18
311 315 5.457799 CCCTTCGTATCACAATGTAACGTAG 59.542 44.000 12.52 12.09 35.21 3.51
312 316 5.125257 TCCCTTCGTATCACAATGTAACGTA 59.875 40.000 12.52 5.17 35.21 3.57
313 317 4.082081 TCCCTTCGTATCACAATGTAACGT 60.082 41.667 12.52 0.00 35.21 3.99
314 318 4.426416 TCCCTTCGTATCACAATGTAACG 58.574 43.478 8.25 8.25 34.99 3.18
315 319 5.416947 ACTCCCTTCGTATCACAATGTAAC 58.583 41.667 0.00 0.00 0.00 2.50
329 333 1.831736 ACATGGTTCCTACTCCCTTCG 59.168 52.381 0.00 0.00 0.00 3.79
351 355 7.964604 TTTCTTCCTTTCTCTAGTTTGCTAC 57.035 36.000 0.00 0.00 0.00 3.58
393 397 7.418827 CCTGAAATATCCAGATAGGCAGATAGG 60.419 44.444 12.24 0.00 37.29 2.57
394 398 7.344093 TCCTGAAATATCCAGATAGGCAGATAG 59.656 40.741 12.24 0.00 37.29 2.08
395 399 7.124901 GTCCTGAAATATCCAGATAGGCAGATA 59.875 40.741 12.24 0.00 37.29 1.98
396 400 6.028131 TCCTGAAATATCCAGATAGGCAGAT 58.972 40.000 12.24 0.00 37.29 2.90
397 401 5.247110 GTCCTGAAATATCCAGATAGGCAGA 59.753 44.000 12.24 0.00 37.29 4.26
398 402 5.012458 TGTCCTGAAATATCCAGATAGGCAG 59.988 44.000 6.64 0.00 37.29 4.85
399 403 4.907269 TGTCCTGAAATATCCAGATAGGCA 59.093 41.667 6.64 0.00 37.29 4.75
400 404 5.241662 GTGTCCTGAAATATCCAGATAGGC 58.758 45.833 6.64 0.00 37.29 3.93
434 441 3.408853 GCCCCTCGCCCTAGGTTT 61.409 66.667 8.29 0.00 34.56 3.27
534 564 2.641439 TAACGGTGAACGGTGGCGTT 62.641 55.000 0.00 0.00 45.97 4.84
638 679 3.952508 TGCAAGGCGGCAGAGGAA 61.953 61.111 13.08 0.00 39.25 3.36
795 841 5.776716 GGAGAGAGAAAGAGAGGATGATGAT 59.223 44.000 0.00 0.00 0.00 2.45
796 842 5.139727 GGAGAGAGAAAGAGAGGATGATGA 58.860 45.833 0.00 0.00 0.00 2.92
861 914 2.438800 TATATAGGCGGCTCCTCTCC 57.561 55.000 17.67 0.00 43.20 3.71
902 955 2.902343 GTGCGGGCTAGATTGGGC 60.902 66.667 0.00 0.00 0.00 5.36
924 977 4.903010 ACGTGTGGGTGTGGCGTC 62.903 66.667 0.00 0.00 0.00 5.19
967 1028 1.588674 TTGATGGTGGTGTGAACGTC 58.411 50.000 0.00 0.00 0.00 4.34
973 1034 4.378770 CGATCTTTCTTTGATGGTGGTGTG 60.379 45.833 0.00 0.00 0.00 3.82
1396 1467 2.126031 GACGAAGGAGACGGTGGC 60.126 66.667 0.00 0.00 34.93 5.01
1429 1500 2.972505 CGTCGCCTGTTGCTTGGT 60.973 61.111 0.00 0.00 38.05 3.67
1437 1514 2.752238 CTCTCCTCCGTCGCCTGT 60.752 66.667 0.00 0.00 0.00 4.00
1439 1516 3.283812 TTCCTCTCCTCCGTCGCCT 62.284 63.158 0.00 0.00 0.00 5.52
1467 1544 2.610859 AGGTTGAGGTCCGGGCAT 60.611 61.111 9.07 0.00 0.00 4.40
1608 1691 2.493973 GCCGCTCCTCTCACTCTG 59.506 66.667 0.00 0.00 0.00 3.35
1798 1891 5.998981 CCTCACCATCTACTAGTACTGTAGG 59.001 48.000 21.85 14.59 38.25 3.18
1799 1892 6.828788 TCCTCACCATCTACTAGTACTGTAG 58.171 44.000 18.72 18.72 38.85 2.74
1800 1893 6.183361 CCTCCTCACCATCTACTAGTACTGTA 60.183 46.154 5.39 5.43 0.00 2.74
1831 1924 9.449719 CAAATCCTCACCTAATAATACCATACC 57.550 37.037 0.00 0.00 0.00 2.73
1835 1928 8.154856 GCTACAAATCCTCACCTAATAATACCA 58.845 37.037 0.00 0.00 0.00 3.25
1836 1929 7.331193 CGCTACAAATCCTCACCTAATAATACC 59.669 40.741 0.00 0.00 0.00 2.73
1862 1955 0.118144 AGGAGGGCAGGGAGGATATC 59.882 60.000 0.00 0.00 0.00 1.63
1864 1957 1.549297 GAGGAGGGCAGGGAGGATA 59.451 63.158 0.00 0.00 0.00 2.59
1898 1991 8.892723 CATCAGTGGAGCAGTAATAATTTACAA 58.107 33.333 0.00 0.00 40.20 2.41
1950 2051 6.564854 AACGCACTGAATTAAGTATCGTAC 57.435 37.500 17.67 0.00 37.48 3.67
1953 2054 5.490213 GGAAACGCACTGAATTAAGTATCG 58.510 41.667 12.67 12.67 33.90 2.92
1960 2061 2.752354 CCATGGGAAACGCACTGAATTA 59.248 45.455 2.85 0.00 0.00 1.40
2015 2118 3.845781 TCAGTTGCCACTTCTCTTCTT 57.154 42.857 0.00 0.00 0.00 2.52
2073 2177 6.021626 CGAGTAGTAACGAACTAATGACAAGC 60.022 42.308 7.24 0.00 42.37 4.01
2102 2206 8.190122 TGAAACTACGACACTTACTTTAGAACA 58.810 33.333 0.00 0.00 0.00 3.18
2111 2215 6.301842 CGTCTAACTGAAACTACGACACTTAC 59.698 42.308 0.00 0.00 32.35 2.34
2136 2240 0.036388 TGAAGAATCCCACGAGCACC 60.036 55.000 0.00 0.00 0.00 5.01
2142 2246 5.627499 TCTTGAAATTGAAGAATCCCACG 57.373 39.130 0.00 0.00 0.00 4.94
2216 2325 2.257207 ACAGCTCTACCTAACTTGCCA 58.743 47.619 0.00 0.00 0.00 4.92
2302 2421 2.892425 CGGGCGGCATCTCAACTC 60.892 66.667 12.47 0.00 0.00 3.01
2378 2497 2.274104 GCGCCTCCAACCCCAATA 59.726 61.111 0.00 0.00 0.00 1.90
2418 2547 5.010112 CGATAGAATCTAGCAAGGACAGGAA 59.990 44.000 6.35 0.00 39.76 3.36
2473 2602 5.507482 GCCTTTTGGTTAGTCTTTTCAGACC 60.507 44.000 0.00 0.00 45.48 3.85
2516 2647 5.855740 AGGTCCATTTTCGTTGGTAAAAA 57.144 34.783 0.00 0.00 35.64 1.94
2606 2849 1.350071 CCCTGATGGAGGAGGAGATG 58.650 60.000 0.00 0.00 46.33 2.90
2622 2865 3.978193 TCCATTTGTGGCGCCCCT 61.978 61.111 26.77 0.00 0.00 4.79
2659 2902 2.693591 TCCACTGACGACTGACTTTTCT 59.306 45.455 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.