Multiple sequence alignment - TraesCS7A01G478700

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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 TraesCS7A01G478700 chr7A 100.000 2645 0 0 1 2645 671484848 671482204 0.000000e+00 4885.0
1 TraesCS7A01G478700 chr7D 91.362 1945 93 24 141 2075 579962700 579960821 0.000000e+00 2591.0
2 TraesCS7A01G478700 chr7D 87.013 231 25 5 2275 2504 579958799 579958573 3.380000e-64 255.0
3 TraesCS7A01G478700 chr7D 87.261 157 9 2 2067 2212 579958968 579958812 4.530000e-38 169.0
4 TraesCS7A01G478700 chr7B 91.202 1489 78 29 194 1675 646211190 646209748 0.000000e+00 1975.0
5 TraesCS7A01G478700 chr7B 86.131 959 58 31 1722 2645 646209738 646208820 0.000000e+00 965.0
6 TraesCS7A01G478700 chr6B 81.517 211 25 10 1127 1333 207155633 207155433 7.580000e-36 161.0
7 TraesCS7A01G478700 chr6A 81.221 213 26 10 1125 1333 145134357 145134155 2.730000e-35 159.0
8 TraesCS7A01G478700 chr6D 80.569 211 31 7 1125 1333 116953093 116952891 1.270000e-33 154.0
9 TraesCS7A01G478700 chr5A 95.122 41 2 0 76 116 674636090 674636050 6.110000e-07 65.8
10 TraesCS7A01G478700 chr2A 89.583 48 5 0 76 123 25105778 25105731 7.910000e-06 62.1
11 TraesCS7A01G478700 chr2A 87.755 49 4 2 76 123 385536366 385536413 3.680000e-04 56.5
12 TraesCS7A01G478700 chr2D 86.000 50 5 2 76 124 194714205 194714157 5.000000e-03 52.8


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 TraesCS7A01G478700 chr7A 671482204 671484848 2644 True 4885 4885 100.000000 1 2645 1 chr7A.!!$R1 2644
1 TraesCS7A01G478700 chr7D 579958573 579962700 4127 True 1005 2591 88.545333 141 2504 3 chr7D.!!$R1 2363
2 TraesCS7A01G478700 chr7B 646208820 646211190 2370 True 1470 1975 88.666500 194 2645 2 chr7B.!!$R1 2451

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
54 55 0.106918 TAGGTTGCCCGCCATTTAGG 60.107 55.0 0.0 0.0 41.84 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1721 0.249073 CTCGATCGGACGCCAATTCT 60.249 55.0 16.41 0.0 0.0 2.4 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
28 29 1.463674 CCCTAGTTTGGGTGATGTGC 58.536 55.000 0.00 0.00 42.25 4.57
29 30 1.271871 CCCTAGTTTGGGTGATGTGCA 60.272 52.381 0.00 0.00 42.25 4.57
30 31 2.621407 CCCTAGTTTGGGTGATGTGCAT 60.621 50.000 0.00 0.00 42.25 3.96
31 32 2.424601 CCTAGTTTGGGTGATGTGCATG 59.575 50.000 0.00 0.00 0.00 4.06
32 33 1.999648 AGTTTGGGTGATGTGCATGT 58.000 45.000 0.00 0.00 0.00 3.21
33 34 3.153369 AGTTTGGGTGATGTGCATGTA 57.847 42.857 0.00 0.00 0.00 2.29
34 35 3.495331 AGTTTGGGTGATGTGCATGTAA 58.505 40.909 0.00 0.00 0.00 2.41
35 36 4.088634 AGTTTGGGTGATGTGCATGTAAT 58.911 39.130 0.00 0.00 0.00 1.89
36 37 5.260424 AGTTTGGGTGATGTGCATGTAATA 58.740 37.500 0.00 0.00 0.00 0.98
37 38 5.357878 AGTTTGGGTGATGTGCATGTAATAG 59.642 40.000 0.00 0.00 0.00 1.73
38 39 3.819368 TGGGTGATGTGCATGTAATAGG 58.181 45.455 0.00 0.00 0.00 2.57
39 40 3.201930 TGGGTGATGTGCATGTAATAGGT 59.798 43.478 0.00 0.00 0.00 3.08
40 41 4.207165 GGGTGATGTGCATGTAATAGGTT 58.793 43.478 0.00 0.00 0.00 3.50
41 42 4.036734 GGGTGATGTGCATGTAATAGGTTG 59.963 45.833 0.00 0.00 0.00 3.77
42 43 4.498009 GGTGATGTGCATGTAATAGGTTGC 60.498 45.833 0.00 0.00 35.67 4.17
43 44 3.631686 TGATGTGCATGTAATAGGTTGCC 59.368 43.478 0.00 0.00 34.20 4.52
44 45 2.374184 TGTGCATGTAATAGGTTGCCC 58.626 47.619 0.00 0.00 34.20 5.36
45 46 1.333619 GTGCATGTAATAGGTTGCCCG 59.666 52.381 0.00 0.00 34.20 6.13
46 47 0.310854 GCATGTAATAGGTTGCCCGC 59.689 55.000 0.00 0.00 35.12 6.13
47 48 0.951558 CATGTAATAGGTTGCCCGCC 59.048 55.000 0.00 0.00 35.12 6.13
48 49 0.548989 ATGTAATAGGTTGCCCGCCA 59.451 50.000 0.00 0.00 35.12 5.69
49 50 0.548989 TGTAATAGGTTGCCCGCCAT 59.451 50.000 0.00 0.00 35.12 4.40
50 51 1.064314 TGTAATAGGTTGCCCGCCATT 60.064 47.619 0.00 0.00 35.12 3.16
51 52 2.028876 GTAATAGGTTGCCCGCCATTT 58.971 47.619 0.00 0.00 35.12 2.32
52 53 2.445682 AATAGGTTGCCCGCCATTTA 57.554 45.000 0.00 0.00 35.12 1.40
53 54 1.981256 ATAGGTTGCCCGCCATTTAG 58.019 50.000 0.00 0.00 35.12 1.85
54 55 0.106918 TAGGTTGCCCGCCATTTAGG 60.107 55.000 0.00 0.00 41.84 2.69
55 56 1.680989 GGTTGCCCGCCATTTAGGT 60.681 57.895 0.00 0.00 40.61 3.08
56 57 0.394625 GGTTGCCCGCCATTTAGGTA 60.395 55.000 0.00 0.00 40.61 3.08
57 58 1.687563 GTTGCCCGCCATTTAGGTAT 58.312 50.000 0.00 0.00 40.61 2.73
58 59 1.336755 GTTGCCCGCCATTTAGGTATG 59.663 52.381 0.00 0.00 40.61 2.39
59 60 0.548989 TGCCCGCCATTTAGGTATGT 59.451 50.000 0.00 0.00 40.61 2.29
60 61 0.951558 GCCCGCCATTTAGGTATGTG 59.048 55.000 0.00 0.00 40.61 3.21
61 62 1.749286 GCCCGCCATTTAGGTATGTGT 60.749 52.381 0.00 0.00 40.61 3.72
62 63 2.650322 CCCGCCATTTAGGTATGTGTT 58.350 47.619 0.00 0.00 40.61 3.32
63 64 3.020984 CCCGCCATTTAGGTATGTGTTT 58.979 45.455 0.00 0.00 40.61 2.83
64 65 3.066203 CCCGCCATTTAGGTATGTGTTTC 59.934 47.826 0.00 0.00 40.61 2.78
65 66 3.692101 CCGCCATTTAGGTATGTGTTTCA 59.308 43.478 0.00 0.00 40.61 2.69
66 67 4.338118 CCGCCATTTAGGTATGTGTTTCAT 59.662 41.667 0.00 0.00 40.61 2.57
67 68 5.505654 CCGCCATTTAGGTATGTGTTTCATC 60.506 44.000 0.00 0.00 40.61 2.92
68 69 5.065859 CGCCATTTAGGTATGTGTTTCATCA 59.934 40.000 0.00 0.00 40.61 3.07
69 70 6.265577 GCCATTTAGGTATGTGTTTCATCAC 58.734 40.000 0.00 0.00 40.61 3.06
70 71 6.095440 GCCATTTAGGTATGTGTTTCATCACT 59.905 38.462 0.00 0.00 40.61 3.41
71 72 7.362920 GCCATTTAGGTATGTGTTTCATCACTT 60.363 37.037 0.00 0.00 40.61 3.16
72 73 8.522830 CCATTTAGGTATGTGTTTCATCACTTT 58.477 33.333 0.00 0.00 38.90 2.66
73 74 9.912634 CATTTAGGTATGTGTTTCATCACTTTT 57.087 29.630 0.00 0.00 38.90 2.27
133 134 4.354893 ACTATACTAGTGACGGAGGGAG 57.645 50.000 5.39 0.00 37.69 4.30
134 135 3.715834 ACTATACTAGTGACGGAGGGAGT 59.284 47.826 5.39 0.00 37.69 3.85
135 136 4.904251 ACTATACTAGTGACGGAGGGAGTA 59.096 45.833 5.39 0.00 37.69 2.59
136 137 2.416680 ACTAGTGACGGAGGGAGTAC 57.583 55.000 0.00 0.00 0.00 2.73
137 138 1.632409 ACTAGTGACGGAGGGAGTACA 59.368 52.381 0.00 0.00 0.00 2.90
138 139 2.040813 ACTAGTGACGGAGGGAGTACAA 59.959 50.000 0.00 0.00 0.00 2.41
139 140 1.546961 AGTGACGGAGGGAGTACAAG 58.453 55.000 0.00 0.00 0.00 3.16
152 153 5.059833 GGGAGTACAAGAGGCTAAATCATG 58.940 45.833 0.00 0.00 0.00 3.07
154 155 5.755861 GGAGTACAAGAGGCTAAATCATGTC 59.244 44.000 0.00 0.00 31.60 3.06
158 159 4.946157 ACAAGAGGCTAAATCATGTCTTGG 59.054 41.667 17.59 6.13 43.34 3.61
168 170 4.640771 ATCATGTCTTGGGTGTAACTGT 57.359 40.909 0.00 0.00 36.74 3.55
185 187 8.440833 GTGTAACTGTAATGAGTGGTTGTAATC 58.559 37.037 0.00 0.00 0.00 1.75
186 188 6.721571 AACTGTAATGAGTGGTTGTAATCG 57.278 37.500 0.00 0.00 0.00 3.34
222 224 3.736094 TCAGATCAGAGTGGGGGTAATT 58.264 45.455 0.00 0.00 0.00 1.40
224 226 4.540099 TCAGATCAGAGTGGGGGTAATTTT 59.460 41.667 0.00 0.00 0.00 1.82
238 241 5.278808 GGGGTAATTTTGTCTCCACTGAAAC 60.279 44.000 0.00 0.00 0.00 2.78
283 286 6.261381 TGAGTGATTTTGTAGTGGGTTGTTAC 59.739 38.462 0.00 0.00 0.00 2.50
429 435 2.028130 GACAGTGATCCATCCGTCTCT 58.972 52.381 0.00 0.00 0.00 3.10
439 445 2.108168 CATCCGTCTCTTCCCAAGGTA 58.892 52.381 0.00 0.00 0.00 3.08
470 476 3.810896 GCCGGAATTCACGTGGGC 61.811 66.667 17.00 15.37 0.00 5.36
530 541 1.743995 CCATCCGTTGTCCGTTCCC 60.744 63.158 0.00 0.00 33.66 3.97
544 555 0.608308 GTTCCCCTTCCCAGTTTCCG 60.608 60.000 0.00 0.00 0.00 4.30
568 579 1.226888 GGTTCCTCCGATCGTTCCG 60.227 63.158 15.09 0.00 0.00 4.30
935 946 0.973632 TAGCTCCCAAAGACGCAAGA 59.026 50.000 0.00 0.00 43.62 3.02
946 957 0.389687 GACGCAAGAAGAGCTGAGCT 60.390 55.000 6.69 6.69 41.58 4.09
952 963 0.975135 AGAAGAGCTGAGCTGAGCAA 59.025 50.000 27.28 0.00 39.88 3.91
1042 1053 2.281484 GCTTCGCCAACTGGACCA 60.281 61.111 0.00 0.00 37.39 4.02
1065 1076 1.351012 CCTCTACCGCTACGACACG 59.649 63.158 0.00 0.00 0.00 4.49
1068 1079 3.746409 CTACCGCTACGACACGCCC 62.746 68.421 0.00 0.00 0.00 6.13
1651 1665 3.198068 GGCTACTTTGCTTGATCGATCA 58.802 45.455 23.99 23.99 34.44 2.92
1700 1714 6.224420 ACGGAGTGAAAGATTTTAGAAACG 57.776 37.500 0.00 0.00 42.51 3.60
1707 1721 5.467399 TGAAAGATTTTAGAAACGCGGAGAA 59.533 36.000 12.47 0.00 0.00 2.87
1718 1732 1.716172 GCGGAGAAGAATTGGCGTC 59.284 57.895 0.00 0.00 0.00 5.19
1730 1744 2.655685 GGCGTCCGATCGAGCTTC 60.656 66.667 18.66 3.95 0.00 3.86
1759 1773 5.580297 TGAATTTCTTGGCTTGTTTGTTCAC 59.420 36.000 0.00 0.00 0.00 3.18
1760 1774 4.799564 TTTCTTGGCTTGTTTGTTCACT 57.200 36.364 0.00 0.00 0.00 3.41
1761 1775 3.781079 TCTTGGCTTGTTTGTTCACTG 57.219 42.857 0.00 0.00 0.00 3.66
1762 1776 3.088532 TCTTGGCTTGTTTGTTCACTGT 58.911 40.909 0.00 0.00 0.00 3.55
1763 1777 3.509575 TCTTGGCTTGTTTGTTCACTGTT 59.490 39.130 0.00 0.00 0.00 3.16
1764 1778 3.502191 TGGCTTGTTTGTTCACTGTTC 57.498 42.857 0.00 0.00 0.00 3.18
1765 1779 2.822561 TGGCTTGTTTGTTCACTGTTCA 59.177 40.909 0.00 0.00 0.00 3.18
1784 1798 3.449918 TCAGGGTAGTTCATCCATCACA 58.550 45.455 0.00 0.00 0.00 3.58
1853 1867 0.944311 ATTTTGTCACTCTCGCGCGT 60.944 50.000 30.98 7.39 0.00 6.01
1854 1868 1.545614 TTTTGTCACTCTCGCGCGTC 61.546 55.000 30.98 12.38 0.00 5.19
1943 1963 0.541863 GAAGTGATCGGTGGGTGGAT 59.458 55.000 0.00 0.00 0.00 3.41
2102 3983 2.494918 GTGACGATCGGGGGTCAG 59.505 66.667 20.98 0.00 43.27 3.51
2182 4078 6.346040 GCTCCAACGATCAAAAACTCAAATTG 60.346 38.462 0.00 0.00 0.00 2.32
2190 4086 9.919348 CGATCAAAAACTCAAATTGAAATGTTT 57.081 25.926 6.15 6.15 36.72 2.83
2228 4125 0.106149 ACAGTGGACGTTCCCAAGAC 59.894 55.000 0.00 0.00 38.06 3.01
2234 4131 0.517316 GACGTTCCCAAGACATGTGC 59.483 55.000 1.15 0.00 0.00 4.57
2247 4144 0.460284 CATGTGCCCACGTCCTCTAC 60.460 60.000 0.00 0.00 0.00 2.59
2258 4155 4.025145 CCACGTCCTCTACAAAGTTCAAAC 60.025 45.833 0.00 0.00 0.00 2.93
2259 4156 4.569162 CACGTCCTCTACAAAGTTCAAACA 59.431 41.667 0.00 0.00 0.00 2.83
2269 4166 8.237949 TCTACAAAGTTCAAACACAAATTCGAA 58.762 29.630 0.00 0.00 0.00 3.71
2272 4169 9.360093 ACAAAGTTCAAACACAAATTCGAAATA 57.640 25.926 0.00 0.00 0.00 1.40
2273 4170 9.618410 CAAAGTTCAAACACAAATTCGAAATAC 57.382 29.630 0.00 0.00 0.00 1.89
2277 4174 7.672351 TCAAACACAAATTCGAAATACACAC 57.328 32.000 0.00 0.00 0.00 3.82
2291 4197 7.694784 TCGAAATACACACAGAGAAACAAAAAC 59.305 33.333 0.00 0.00 0.00 2.43
2299 4205 6.866248 ACACAGAGAAACAAAAACGACAAATT 59.134 30.769 0.00 0.00 0.00 1.82
2306 4212 6.826893 AACAAAAACGACAAATTCAGGATG 57.173 33.333 0.00 0.00 37.54 3.51
2342 4248 2.314323 AGGCAAAAGCAAAACACCAG 57.686 45.000 0.00 0.00 0.00 4.00
2350 4256 1.480545 AGCAAAACACCAGGGTTTCAC 59.519 47.619 0.00 0.00 39.93 3.18
2362 4268 2.131972 GGGTTTCACGTTTGGATTTGC 58.868 47.619 0.00 0.00 0.00 3.68
2368 4274 3.452474 TCACGTTTGGATTTGCCTTTTG 58.548 40.909 0.00 0.00 37.63 2.44
2369 4275 3.131223 TCACGTTTGGATTTGCCTTTTGA 59.869 39.130 0.00 0.00 37.63 2.69
2378 4284 6.590068 TGGATTTGCCTTTTGATTTCTCAAA 58.410 32.000 0.00 0.00 41.96 2.69
2402 4308 7.924103 AGTGTATTTTGGTTTTCGATTTGAC 57.076 32.000 0.00 0.00 0.00 3.18
2445 4351 3.755378 GGCACATGTCTTGAGAACATTCT 59.245 43.478 0.00 0.00 41.00 2.40
2633 4544 2.241176 TGGCTTTAATTCGGGATGAGGT 59.759 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.198827 TGCACATCACCCAAACTAGG 57.801 50.000 0.00 0.00 0.00 3.02
11 12 3.084039 ACATGCACATCACCCAAACTAG 58.916 45.455 0.00 0.00 0.00 2.57
12 13 3.153369 ACATGCACATCACCCAAACTA 57.847 42.857 0.00 0.00 0.00 2.24
13 14 1.999648 ACATGCACATCACCCAAACT 58.000 45.000 0.00 0.00 0.00 2.66
14 15 3.932545 TTACATGCACATCACCCAAAC 57.067 42.857 0.00 0.00 0.00 2.93
15 16 4.644234 CCTATTACATGCACATCACCCAAA 59.356 41.667 0.00 0.00 0.00 3.28
16 17 4.206375 CCTATTACATGCACATCACCCAA 58.794 43.478 0.00 0.00 0.00 4.12
17 18 3.201930 ACCTATTACATGCACATCACCCA 59.798 43.478 0.00 0.00 0.00 4.51
18 19 3.820557 ACCTATTACATGCACATCACCC 58.179 45.455 0.00 0.00 0.00 4.61
19 20 4.498009 GCAACCTATTACATGCACATCACC 60.498 45.833 0.00 0.00 38.63 4.02
20 21 4.498009 GGCAACCTATTACATGCACATCAC 60.498 45.833 0.00 0.00 40.51 3.06
21 22 3.631686 GGCAACCTATTACATGCACATCA 59.368 43.478 0.00 0.00 40.51 3.07
22 23 4.228912 GGCAACCTATTACATGCACATC 57.771 45.455 0.00 0.00 40.51 3.06
37 38 0.394625 TACCTAAATGGCGGGCAACC 60.395 55.000 8.78 0.00 46.81 3.77
38 39 1.336755 CATACCTAAATGGCGGGCAAC 59.663 52.381 8.78 0.00 40.22 4.17
39 40 1.064314 ACATACCTAAATGGCGGGCAA 60.064 47.619 8.78 0.00 40.22 4.52
40 41 0.548989 ACATACCTAAATGGCGGGCA 59.451 50.000 6.74 6.74 40.22 5.36
41 42 0.951558 CACATACCTAAATGGCGGGC 59.048 55.000 0.00 0.00 40.22 6.13
42 43 2.341846 ACACATACCTAAATGGCGGG 57.658 50.000 0.00 0.00 40.22 6.13
43 44 3.692101 TGAAACACATACCTAAATGGCGG 59.308 43.478 0.00 0.00 40.22 6.13
44 45 4.955925 TGAAACACATACCTAAATGGCG 57.044 40.909 0.00 0.00 40.22 5.69
45 46 6.095440 AGTGATGAAACACATACCTAAATGGC 59.905 38.462 0.00 0.00 42.45 4.40
46 47 7.630242 AGTGATGAAACACATACCTAAATGG 57.370 36.000 0.00 0.00 42.45 3.16
47 48 9.912634 AAAAGTGATGAAACACATACCTAAATG 57.087 29.630 0.00 0.00 42.45 2.32
113 114 4.354893 ACTCCCTCCGTCACTAGTATAG 57.645 50.000 0.00 0.00 46.50 1.31
114 115 4.655649 TGTACTCCCTCCGTCACTAGTATA 59.344 45.833 0.00 0.00 0.00 1.47
115 116 3.457380 TGTACTCCCTCCGTCACTAGTAT 59.543 47.826 0.00 0.00 0.00 2.12
116 117 2.840038 TGTACTCCCTCCGTCACTAGTA 59.160 50.000 0.00 0.00 0.00 1.82
117 118 1.632409 TGTACTCCCTCCGTCACTAGT 59.368 52.381 0.00 0.00 0.00 2.57
118 119 2.414994 TGTACTCCCTCCGTCACTAG 57.585 55.000 0.00 0.00 0.00 2.57
119 120 2.306805 TCTTGTACTCCCTCCGTCACTA 59.693 50.000 0.00 0.00 0.00 2.74
120 121 1.075050 TCTTGTACTCCCTCCGTCACT 59.925 52.381 0.00 0.00 0.00 3.41
121 122 1.473278 CTCTTGTACTCCCTCCGTCAC 59.527 57.143 0.00 0.00 0.00 3.67
122 123 1.616187 CCTCTTGTACTCCCTCCGTCA 60.616 57.143 0.00 0.00 0.00 4.35
123 124 1.104630 CCTCTTGTACTCCCTCCGTC 58.895 60.000 0.00 0.00 0.00 4.79
124 125 0.971447 GCCTCTTGTACTCCCTCCGT 60.971 60.000 0.00 0.00 0.00 4.69
125 126 0.684805 AGCCTCTTGTACTCCCTCCG 60.685 60.000 0.00 0.00 0.00 4.63
126 127 2.456073 TAGCCTCTTGTACTCCCTCC 57.544 55.000 0.00 0.00 0.00 4.30
127 128 4.406003 TGATTTAGCCTCTTGTACTCCCTC 59.594 45.833 0.00 0.00 0.00 4.30
128 129 4.362677 TGATTTAGCCTCTTGTACTCCCT 58.637 43.478 0.00 0.00 0.00 4.20
129 130 4.755266 TGATTTAGCCTCTTGTACTCCC 57.245 45.455 0.00 0.00 0.00 4.30
130 131 5.675538 ACATGATTTAGCCTCTTGTACTCC 58.324 41.667 0.00 0.00 31.47 3.85
131 132 6.578023 AGACATGATTTAGCCTCTTGTACTC 58.422 40.000 0.00 0.00 32.87 2.59
132 133 6.552445 AGACATGATTTAGCCTCTTGTACT 57.448 37.500 0.00 0.00 32.87 2.73
133 134 6.037610 CCAAGACATGATTTAGCCTCTTGTAC 59.962 42.308 13.97 0.00 35.06 2.90
134 135 6.115446 CCAAGACATGATTTAGCCTCTTGTA 58.885 40.000 13.97 0.00 35.06 2.41
135 136 4.946157 CCAAGACATGATTTAGCCTCTTGT 59.054 41.667 13.97 0.00 35.06 3.16
136 137 4.337555 CCCAAGACATGATTTAGCCTCTTG 59.662 45.833 0.00 5.60 36.11 3.02
137 138 4.018050 ACCCAAGACATGATTTAGCCTCTT 60.018 41.667 0.00 0.00 0.00 2.85
138 139 3.525199 ACCCAAGACATGATTTAGCCTCT 59.475 43.478 0.00 0.00 0.00 3.69
139 140 3.629398 CACCCAAGACATGATTTAGCCTC 59.371 47.826 0.00 0.00 0.00 4.70
152 153 5.408604 CACTCATTACAGTTACACCCAAGAC 59.591 44.000 0.00 0.00 0.00 3.01
154 155 4.695455 CCACTCATTACAGTTACACCCAAG 59.305 45.833 0.00 0.00 0.00 3.61
158 159 5.061179 ACAACCACTCATTACAGTTACACC 58.939 41.667 0.00 0.00 0.00 4.16
168 170 5.106475 GCCAAACGATTACAACCACTCATTA 60.106 40.000 0.00 0.00 0.00 1.90
185 187 4.692155 TGATCTGATGCATATAGCCAAACG 59.308 41.667 0.00 0.00 44.83 3.60
186 188 5.936372 TCTGATCTGATGCATATAGCCAAAC 59.064 40.000 0.00 0.00 44.83 2.93
222 224 4.439974 GCATGTTGTTTCAGTGGAGACAAA 60.440 41.667 2.86 0.00 46.03 2.83
224 226 2.618241 GCATGTTGTTTCAGTGGAGACA 59.382 45.455 0.00 0.00 36.45 3.41
238 241 4.664188 TCATCGTTTCATCATGCATGTTG 58.336 39.130 25.45 25.45 33.66 3.33
291 294 7.125053 ACCATCTGTCTGTTTTTCCCTTTAAAA 59.875 33.333 0.00 0.00 0.00 1.52
294 297 5.701224 ACCATCTGTCTGTTTTTCCCTTTA 58.299 37.500 0.00 0.00 0.00 1.85
338 344 4.802307 TCAGCTATCTCAGAGAATGACCT 58.198 43.478 3.63 0.00 33.22 3.85
397 403 3.068873 GGATCACTGTCAGTATCCACCTC 59.931 52.174 23.18 8.92 38.23 3.85
429 435 0.892063 GCGCCATTTTACCTTGGGAA 59.108 50.000 0.00 0.00 33.40 3.97
457 463 1.087501 GGAAGAGCCCACGTGAATTC 58.912 55.000 19.30 12.44 0.00 2.17
470 476 1.882352 CGTTTTGGGTGGAGGGAAGAG 60.882 57.143 0.00 0.00 0.00 2.85
530 541 2.741486 TTCGGCGGAAACTGGGAAGG 62.741 60.000 7.21 0.00 0.00 3.46
544 555 1.227292 GATCGGAGGAACCTTCGGC 60.227 63.158 19.58 9.87 44.62 5.54
677 688 4.619227 CAACCTGTGGACCCGCGT 62.619 66.667 4.92 0.00 0.00 6.01
870 881 1.779683 GGCGTCCGATTTATAGCGC 59.220 57.895 0.00 0.00 43.46 5.92
909 920 2.359531 CGTCTTTGGGAGCTACTAGGAG 59.640 54.545 0.00 0.00 0.00 3.69
935 946 1.810959 CTTTGCTCAGCTCAGCTCTT 58.189 50.000 12.05 0.00 40.39 2.85
946 957 0.313043 GCTCTGCTTTGCTTTGCTCA 59.687 50.000 0.00 0.00 0.00 4.26
952 963 1.575576 CGCTCTGCTCTGCTTTGCTT 61.576 55.000 0.00 0.00 0.00 3.91
1042 1053 0.391661 TCGTAGCGGTAGAGGTCGTT 60.392 55.000 0.00 0.00 0.00 3.85
1347 1358 2.892425 CCGCCGAAGCTGATGACC 60.892 66.667 0.00 0.00 36.60 4.02
1494 1505 3.054503 GAGTGCTGCAGGTGGCTG 61.055 66.667 17.12 0.00 45.15 4.85
1495 1506 4.341783 GGAGTGCTGCAGGTGGCT 62.342 66.667 17.12 0.00 45.15 4.75
1651 1665 8.739039 TGCATGCAACTTAGTTAATAATCACTT 58.261 29.630 20.30 0.00 0.00 3.16
1671 1685 1.089920 ATCTTTCACTCCGTGCATGC 58.910 50.000 11.82 11.82 32.98 4.06
1700 1714 1.706287 GGACGCCAATTCTTCTCCGC 61.706 60.000 0.00 0.00 0.00 5.54
1707 1721 0.249073 CTCGATCGGACGCCAATTCT 60.249 55.000 16.41 0.00 0.00 2.40
1718 1732 1.996292 TCAAACAGAAGCTCGATCGG 58.004 50.000 16.41 7.26 0.00 4.18
1730 1744 6.092533 ACAAACAAGCCAAGAAATTCAAACAG 59.907 34.615 0.00 0.00 0.00 3.16
1759 1773 3.981071 TGGATGAACTACCCTGAACAG 57.019 47.619 0.00 0.00 0.00 3.16
1760 1774 3.843619 TGATGGATGAACTACCCTGAACA 59.156 43.478 0.00 0.00 0.00 3.18
1761 1775 4.192317 GTGATGGATGAACTACCCTGAAC 58.808 47.826 0.00 0.00 0.00 3.18
1762 1776 3.843619 TGTGATGGATGAACTACCCTGAA 59.156 43.478 0.00 0.00 0.00 3.02
1763 1777 3.449918 TGTGATGGATGAACTACCCTGA 58.550 45.455 0.00 0.00 0.00 3.86
1764 1778 3.912496 TGTGATGGATGAACTACCCTG 57.088 47.619 0.00 0.00 0.00 4.45
1765 1779 4.428294 CATGTGATGGATGAACTACCCT 57.572 45.455 0.00 0.00 0.00 4.34
1784 1798 9.448438 TTCAAATATTTACATATAGCGCTCCAT 57.552 29.630 16.34 5.31 0.00 3.41
1787 1801 7.898309 CCGTTCAAATATTTACATATAGCGCTC 59.102 37.037 16.34 0.00 0.00 5.03
1856 1870 0.436150 CGCATCATAATCCGCACGAG 59.564 55.000 0.00 0.00 0.00 4.18
1875 1889 3.004734 CCATCGGTTTCTCCCATTAATGC 59.995 47.826 10.11 0.00 0.00 3.56
1943 1963 5.279406 CCTTGCTTGTAAAACAATCCATCCA 60.279 40.000 0.00 0.00 37.48 3.41
2047 2067 1.153784 GCATGCAATTGTGTCCCCG 60.154 57.895 14.21 0.00 0.00 5.73
2102 3983 1.731160 GCAGCATGACAAGTCTGACTC 59.269 52.381 11.31 0.00 39.69 3.36
2134 4015 1.990799 CGAGCATACGAGTGTTTGGA 58.009 50.000 0.00 0.00 35.09 3.53
2217 4114 1.586154 GGGCACATGTCTTGGGAACG 61.586 60.000 0.00 0.00 0.00 3.95
2228 4125 0.460284 GTAGAGGACGTGGGCACATG 60.460 60.000 6.63 6.63 39.55 3.21
2234 4131 2.036733 TGAACTTTGTAGAGGACGTGGG 59.963 50.000 0.00 0.00 0.00 4.61
2247 4144 9.618410 GTATTTCGAATTTGTGTTTGAACTTTG 57.382 29.630 0.00 0.00 32.60 2.77
2258 4155 6.887368 TCTCTGTGTGTATTTCGAATTTGTG 58.113 36.000 0.00 0.00 0.00 3.33
2259 4156 7.490962 TTCTCTGTGTGTATTTCGAATTTGT 57.509 32.000 0.00 0.00 0.00 2.83
2269 4166 6.964934 GTCGTTTTTGTTTCTCTGTGTGTATT 59.035 34.615 0.00 0.00 0.00 1.89
2272 4169 4.214545 TGTCGTTTTTGTTTCTCTGTGTGT 59.785 37.500 0.00 0.00 0.00 3.72
2273 4170 4.717991 TGTCGTTTTTGTTTCTCTGTGTG 58.282 39.130 0.00 0.00 0.00 3.82
2277 4174 7.253750 CCTGAATTTGTCGTTTTTGTTTCTCTG 60.254 37.037 0.00 0.00 0.00 3.35
2291 4197 6.481134 CACACTATTCATCCTGAATTTGTCG 58.519 40.000 7.60 5.98 44.03 4.35
2299 4205 3.998913 TTGGCACACTATTCATCCTGA 57.001 42.857 0.00 0.00 39.29 3.86
2323 4229 1.134431 CCTGGTGTTTTGCTTTTGCCT 60.134 47.619 0.00 0.00 46.87 4.75
2324 4230 1.298602 CCTGGTGTTTTGCTTTTGCC 58.701 50.000 0.00 0.00 46.87 4.52
2325 4231 4.426183 AAACCCTGGTGTTTTGCTTTTGC 61.426 43.478 7.27 0.00 34.92 3.68
2326 4232 2.689553 ACCCTGGTGTTTTGCTTTTG 57.310 45.000 0.00 0.00 0.00 2.44
2330 4236 1.480545 GTGAAACCCTGGTGTTTTGCT 59.519 47.619 12.51 0.00 38.51 3.91
2331 4237 1.801025 CGTGAAACCCTGGTGTTTTGC 60.801 52.381 12.51 8.82 38.51 3.68
2332 4238 1.474879 ACGTGAAACCCTGGTGTTTTG 59.525 47.619 12.51 9.33 38.51 2.44
2342 4248 2.131972 GCAAATCCAAACGTGAAACCC 58.868 47.619 0.00 0.00 0.00 4.11
2350 4256 5.466393 AGAAATCAAAAGGCAAATCCAAACG 59.534 36.000 0.00 0.00 37.29 3.60
2369 4275 9.030301 CGAAAACCAAAATACACTTTGAGAAAT 57.970 29.630 0.00 0.00 38.35 2.17
2378 4284 6.921307 GGTCAAATCGAAAACCAAAATACACT 59.079 34.615 0.00 0.00 0.00 3.55
2389 4295 6.741109 TCCCTAAAAAGGTCAAATCGAAAAC 58.259 36.000 0.00 0.00 0.00 2.43
2402 4308 7.996644 TGTGCCTACTTATTATCCCTAAAAAGG 59.003 37.037 0.00 0.00 0.00 3.11
2420 4326 3.664107 TGTTCTCAAGACATGTGCCTAC 58.336 45.455 1.15 0.00 0.00 3.18
2486 4395 5.448632 CCTTCACATGCTCCCGTTTTTATAC 60.449 44.000 0.00 0.00 0.00 1.47
2564 4473 4.056050 GGTAGCAGTTTCTTCTTTCGTCA 58.944 43.478 0.00 0.00 0.00 4.35
2565 4474 4.056050 TGGTAGCAGTTTCTTCTTTCGTC 58.944 43.478 0.00 0.00 0.00 4.20
2577 4486 3.735591 ACACGTACAATTGGTAGCAGTT 58.264 40.909 10.83 0.00 31.13 3.16


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

AutoCloner maintained by Alex Coulton.