Multiple sequence alignment - TraesCS2D01G540900

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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 TraesCS2D01G540900 chr2D 100.000 2523 0 0 1 2523 620322296 620319774 0.000000e+00 4660.0
1 TraesCS2D01G540900 chr4B 92.868 2005 97 22 84 2059 637347225 637345238 0.000000e+00 2868.0
2 TraesCS2D01G540900 chr4B 82.888 374 57 5 2156 2523 637344056 637343684 1.870000e-86 329.0
3 TraesCS2D01G540900 chr4B 81.962 316 46 3 2209 2523 637344305 637344000 8.950000e-65 257.0
4 TraesCS2D01G540900 chr4B 87.838 148 13 3 2375 2518 637344424 637344278 4.320000e-38 169.0
5 TraesCS2D01G540900 chr3B 92.482 1902 109 19 433 2319 299750855 299748973 0.000000e+00 2689.0
6 TraesCS2D01G540900 chr3B 92.767 318 19 2 124 438 299768355 299768039 8.230000e-125 457.0
7 TraesCS2D01G540900 chr3B 89.174 351 28 1 2171 2521 299749150 299748810 1.790000e-116 429.0
8 TraesCS2D01G540900 chr3B 80.278 360 62 8 2156 2512 299748864 299748511 1.920000e-66 263.0
9 TraesCS2D01G540900 chr1B 93.968 1177 58 9 888 2059 12395791 12394623 0.000000e+00 1768.0
10 TraesCS2D01G540900 chr1B 91.653 611 41 4 84 686 12396418 12395810 0.000000e+00 837.0
11 TraesCS2D01G540900 chr1B 88.210 229 23 3 2297 2521 12393096 12392868 1.150000e-68 270.0
12 TraesCS2D01G540900 chr1B 84.252 254 39 1 2209 2461 12393705 12393452 1.940000e-61 246.0
13 TraesCS2D01G540900 chr1B 89.865 148 10 3 2375 2518 12393824 12393678 4.290000e-43 185.0
14 TraesCS2D01G540900 chr1B 80.808 99 9 5 256 345 4857511 4857608 4.500000e-08 69.4
15 TraesCS2D01G540900 chr7A 89.270 671 54 12 1325 1987 707987774 707988434 0.000000e+00 824.0
16 TraesCS2D01G540900 chr7A 88.024 668 65 10 1327 1990 30225669 30225013 0.000000e+00 776.0
17 TraesCS2D01G540900 chr5A 88.473 668 62 10 1327 1990 608038427 608037771 0.000000e+00 793.0
18 TraesCS2D01G540900 chr5A 83.226 155 26 0 2158 2312 608036731 608036577 2.620000e-30 143.0
19 TraesCS2D01G540900 chr6B 86.807 667 62 14 1325 1986 46409626 46408981 0.000000e+00 721.0
20 TraesCS2D01G540900 chr6B 85.672 670 68 13 1328 1990 30418061 30417413 0.000000e+00 680.0
21 TraesCS2D01G540900 chr5B 89.873 553 43 5 1325 1873 38456869 38456326 0.000000e+00 699.0
22 TraesCS2D01G540900 chr3D 77.540 374 76 5 2155 2523 601999535 601999165 4.230000e-53 219.0
23 TraesCS2D01G540900 chr3D 86.429 140 19 0 2175 2314 35686697 35686836 1.210000e-33 154.0
24 TraesCS2D01G540900 chr3A 83.843 229 19 3 750 960 44580854 44581082 4.260000e-48 202.0
25 TraesCS2D01G540900 chr3A 77.959 245 17 12 342 552 61240393 61240152 4.410000e-23 119.0
26 TraesCS2D01G540900 chr3A 92.308 78 6 0 1169 1246 44583486 44583563 7.380000e-21 111.0
27 TraesCS2D01G540900 chr3A 89.706 68 5 2 955 1020 44582838 44582771 4.470000e-13 86.1
28 TraesCS2D01G540900 chr5D 93.636 110 7 0 1154 1263 450172210 450172319 5.580000e-37 165.0


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 TraesCS2D01G540900 chr2D 620319774 620322296 2522 True 4660.00 4660 100.000000 1 2523 1 chr2D.!!$R1 2522
1 TraesCS2D01G540900 chr4B 637343684 637347225 3541 True 905.75 2868 86.389000 84 2523 4 chr4B.!!$R1 2439
2 TraesCS2D01G540900 chr3B 299748511 299750855 2344 True 1127.00 2689 87.311333 433 2521 3 chr3B.!!$R2 2088
3 TraesCS2D01G540900 chr1B 12392868 12396418 3550 True 661.20 1768 89.589600 84 2521 5 chr1B.!!$R1 2437
4 TraesCS2D01G540900 chr7A 707987774 707988434 660 False 824.00 824 89.270000 1325 1987 1 chr7A.!!$F1 662
5 TraesCS2D01G540900 chr7A 30225013 30225669 656 True 776.00 776 88.024000 1327 1990 1 chr7A.!!$R1 663
6 TraesCS2D01G540900 chr5A 608036577 608038427 1850 True 468.00 793 85.849500 1327 2312 2 chr5A.!!$R1 985
7 TraesCS2D01G540900 chr6B 46408981 46409626 645 True 721.00 721 86.807000 1325 1986 1 chr6B.!!$R2 661
8 TraesCS2D01G540900 chr6B 30417413 30418061 648 True 680.00 680 85.672000 1328 1990 1 chr6B.!!$R1 662
9 TraesCS2D01G540900 chr5B 38456326 38456869 543 True 699.00 699 89.873000 1325 1873 1 chr5B.!!$R1 548


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
562 573 0.179032 TAGGCAACGGCATACATGGG 60.179 55.0 0.0 0.0 43.71 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 3939 0.402504 TAGTCGTTTGGGCCCACAAT 59.597 50.0 28.7 10.82 0.0 2.71 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
27 28 9.930158 TGTAAATACTTCTATTTTATTGCCCCT 57.070 29.630 0.00 0.00 34.83 4.79
34 35 9.930158 ACTTCTATTTTATTGCCCCTATGTTAA 57.070 29.630 0.00 0.00 0.00 2.01
40 41 6.627395 TTATTGCCCCTATGTTAATGAACG 57.373 37.500 0.00 0.00 38.51 3.95
41 42 3.916359 TGCCCCTATGTTAATGAACGA 57.084 42.857 0.00 0.00 38.51 3.85
42 43 4.223556 TGCCCCTATGTTAATGAACGAA 57.776 40.909 0.00 0.00 38.51 3.85
43 44 4.787551 TGCCCCTATGTTAATGAACGAAT 58.212 39.130 0.00 0.00 38.51 3.34
44 45 4.819630 TGCCCCTATGTTAATGAACGAATC 59.180 41.667 0.00 0.00 38.51 2.52
45 46 4.819630 GCCCCTATGTTAATGAACGAATCA 59.180 41.667 0.00 0.00 43.67 2.57
46 47 5.298276 GCCCCTATGTTAATGAACGAATCAA 59.702 40.000 0.00 0.00 42.54 2.57
47 48 6.016276 GCCCCTATGTTAATGAACGAATCAAT 60.016 38.462 0.00 0.00 42.54 2.57
48 49 7.174253 GCCCCTATGTTAATGAACGAATCAATA 59.826 37.037 0.00 0.00 42.54 1.90
49 50 9.062524 CCCCTATGTTAATGAACGAATCAATAA 57.937 33.333 0.00 0.00 42.54 1.40
55 56 9.554724 TGTTAATGAACGAATCAATAAAAGCTC 57.445 29.630 0.00 0.00 42.54 4.09
56 57 9.010366 GTTAATGAACGAATCAATAAAAGCTCC 57.990 33.333 0.00 0.00 42.54 4.70
57 58 7.396540 AATGAACGAATCAATAAAAGCTCCT 57.603 32.000 0.00 0.00 42.54 3.69
58 59 8.506168 AATGAACGAATCAATAAAAGCTCCTA 57.494 30.769 0.00 0.00 42.54 2.94
59 60 8.682936 ATGAACGAATCAATAAAAGCTCCTAT 57.317 30.769 0.00 0.00 42.54 2.57
60 61 8.506168 TGAACGAATCAATAAAAGCTCCTATT 57.494 30.769 0.00 0.00 34.30 1.73
61 62 8.956426 TGAACGAATCAATAAAAGCTCCTATTT 58.044 29.630 0.00 0.00 34.30 1.40
62 63 9.439537 GAACGAATCAATAAAAGCTCCTATTTC 57.560 33.333 0.00 0.00 0.00 2.17
63 64 8.506168 ACGAATCAATAAAAGCTCCTATTTCA 57.494 30.769 0.00 0.00 0.00 2.69
64 65 8.616076 ACGAATCAATAAAAGCTCCTATTTCAG 58.384 33.333 0.00 0.00 0.00 3.02
65 66 8.830580 CGAATCAATAAAAGCTCCTATTTCAGA 58.169 33.333 0.00 0.00 0.00 3.27
67 68 8.688747 ATCAATAAAAGCTCCTATTTCAGAGG 57.311 34.615 0.00 0.00 35.17 3.69
68 69 7.861629 TCAATAAAAGCTCCTATTTCAGAGGA 58.138 34.615 0.00 0.00 40.95 3.71
69 70 8.328758 TCAATAAAAGCTCCTATTTCAGAGGAA 58.671 33.333 0.00 0.00 42.63 3.36
70 71 8.960591 CAATAAAAGCTCCTATTTCAGAGGAAA 58.039 33.333 0.00 0.00 46.36 3.13
71 72 9.533831 AATAAAAGCTCCTATTTCAGAGGAAAA 57.466 29.630 0.00 0.00 45.52 2.29
72 73 7.839680 AAAAGCTCCTATTTCAGAGGAAAAA 57.160 32.000 0.00 0.00 45.52 1.94
95 96 6.862944 AAACATGTTTATGGCGAATTTACG 57.137 33.333 22.10 0.00 38.66 3.18
118 119 1.540363 CCGTCCATCCACCTTAATCGG 60.540 57.143 0.00 0.00 0.00 4.18
120 121 2.037251 CGTCCATCCACCTTAATCGGAT 59.963 50.000 0.00 0.00 40.23 4.18
127 128 3.275617 CACCTTAATCGGATGGTGGAA 57.724 47.619 14.94 0.00 44.33 3.53
142 145 6.596497 GGATGGTGGAAAAATAGAAGTTACGA 59.404 38.462 0.00 0.00 0.00 3.43
156 159 7.101993 AGAAGTTACGACGAGTTACAAAATG 57.898 36.000 0.00 0.00 35.03 2.32
166 169 7.057149 ACGAGTTACAAAATGAGAATTACGG 57.943 36.000 0.00 0.00 0.00 4.02
197 200 1.941377 TAACAGTGGGACCGGTACAT 58.059 50.000 21.02 0.00 0.00 2.29
203 206 1.808343 GTGGGACCGGTACATGTTTTC 59.192 52.381 21.02 0.00 0.00 2.29
223 226 5.890424 TTCGATGGGACCAGTTATTTTTC 57.110 39.130 0.00 0.00 0.00 2.29
226 229 3.791953 TGGGACCAGTTATTTTTCCGA 57.208 42.857 0.00 0.00 0.00 4.55
258 261 4.760204 TCCGTCTTGGAAAATTTCTCTTCC 59.240 41.667 5.65 0.00 46.38 3.46
290 293 2.746277 ACAGTTTCCGCGGCCATC 60.746 61.111 23.51 10.76 0.00 3.51
402 405 1.760086 ATCCCTGGTCTCGCTCCTG 60.760 63.158 0.00 0.00 0.00 3.86
405 408 4.504916 CTGGTCTCGCTCCTGCCG 62.505 72.222 0.00 0.00 35.36 5.69
505 516 2.650116 GCCTCCTCCGTTGAGCAGA 61.650 63.158 0.00 0.00 37.29 4.26
549 560 2.589157 CCAGTCCGTGGGTAGGCAA 61.589 63.158 0.00 0.00 43.63 4.52
551 562 2.433664 GTCCGTGGGTAGGCAACG 60.434 66.667 0.00 0.00 46.39 4.10
562 573 0.179032 TAGGCAACGGCATACATGGG 60.179 55.000 0.00 0.00 43.71 4.00
609 620 3.553375 TCCGATCCCATATTACCTCCA 57.447 47.619 0.00 0.00 0.00 3.86
620 631 0.759959 TTACCTCCAGCACGGTTCAA 59.240 50.000 0.00 0.00 34.76 2.69
850 870 5.007234 TGTTCTATTGTGAAGTCGGTGTTTG 59.993 40.000 0.00 0.00 0.00 2.93
868 888 7.574967 CGGTGTTTGCTATTTCTTCCTACAAAT 60.575 37.037 0.00 0.00 0.00 2.32
1029 1059 7.068593 ACAGTTGATCAATTGGAAGAACTGAAA 59.931 33.333 28.17 3.52 44.14 2.69
1040 1070 2.310538 AGAACTGAAAGCCCTTTGGTG 58.689 47.619 0.00 0.00 37.60 4.17
1084 1114 6.830324 TGATCTTTGGGGAATAACATCTGAAG 59.170 38.462 0.00 0.00 0.00 3.02
1098 1128 9.917887 ATAACATCTGAAGAATGGAAAGAGATT 57.082 29.630 0.00 0.00 0.00 2.40
1127 1157 2.472029 AGGAACAGACCCATCTACAGG 58.528 52.381 0.00 0.00 32.25 4.00
1205 1235 5.758296 AGTTACTGTACATATGCATTTCCCG 59.242 40.000 3.54 0.00 0.00 5.14
1283 1313 2.555199 CATTAAGAGGTGGAGGCTTCG 58.445 52.381 0.00 0.00 0.00 3.79
1396 1433 4.445452 AATTGCTTTACTCACCATGCTG 57.555 40.909 0.00 0.00 0.00 4.41
1431 1471 1.839424 AAATTACAGGCAGGCAGGAC 58.161 50.000 0.00 0.00 0.00 3.85
1485 1525 3.505680 TCTGCATTCCGTATTTTTGCTGT 59.494 39.130 0.00 0.00 34.89 4.40
1560 1600 3.536158 TTTGGAGAACGCTTTTGATCG 57.464 42.857 0.00 0.00 0.00 3.69
1685 1726 5.698832 TCCATTTCATGCAGTTTACTTTCG 58.301 37.500 0.00 0.00 0.00 3.46
1831 1877 1.739466 GATGCTCGAATTGAAGTGGCA 59.261 47.619 0.00 0.00 0.00 4.92
1839 1885 3.361644 CGAATTGAAGTGGCATTTGTTCG 59.638 43.478 14.94 14.94 0.00 3.95
1880 1926 4.546570 TCAACATACACGAGAACAGAGTG 58.453 43.478 0.00 0.00 41.28 3.51
1903 1949 3.008375 TCATACTTGAAGTGAGCAAGGCT 59.992 43.478 8.33 0.00 45.31 4.58
1905 1951 2.225467 ACTTGAAGTGAGCAAGGCTTC 58.775 47.619 0.00 0.00 45.31 3.86
1948 1994 3.589988 CCTGAACTAGTGAACGCTGAAT 58.410 45.455 0.00 0.00 0.00 2.57
1992 2038 2.807108 GCGAGGTGTTCTTTTCTCCAGT 60.807 50.000 0.00 0.00 0.00 4.00
2052 2154 2.030805 AGCAAAACCGTCTCTGCATTTC 60.031 45.455 0.00 0.00 37.26 2.17
2078 2183 0.944311 CTCACGTGTGCGCTAAAGGT 60.944 55.000 16.51 2.88 42.83 3.50
2093 2350 8.732531 TGCGCTAAAGGTATAGTAATTTTGTTT 58.267 29.630 9.73 0.00 0.00 2.83
2094 2351 9.218359 GCGCTAAAGGTATAGTAATTTTGTTTC 57.782 33.333 0.00 0.00 0.00 2.78
2143 3004 4.260620 CCAGTCGACTGAAATTTCGTTTGT 60.261 41.667 40.21 9.15 46.59 2.83
2147 3008 2.719046 GACTGAAATTTCGTTTGTGCCG 59.281 45.455 13.34 0.00 0.00 5.69
2201 3207 6.737301 CGAACGACTAAGATCGATACTTATGG 59.263 42.308 13.91 8.74 45.13 2.74
2203 3209 5.415077 ACGACTAAGATCGATACTTATGGGG 59.585 44.000 13.91 8.03 45.13 4.96
2221 3793 0.379669 GGCCGAACGACTAAGATCGA 59.620 55.000 1.63 0.00 45.13 3.59
2241 3844 3.707793 GATACTAGTGAGCCCAAACGAG 58.292 50.000 5.39 0.00 0.00 4.18
2261 3864 3.438183 AGTAAGATCGGTACTTGTGGGT 58.562 45.455 6.36 0.00 0.00 4.51
2262 3865 3.446516 AGTAAGATCGGTACTTGTGGGTC 59.553 47.826 6.36 0.00 0.00 4.46
2264 3867 0.899720 GATCGGTACTTGTGGGTCCA 59.100 55.000 0.00 0.00 0.00 4.02
2266 3869 0.393820 TCGGTACTTGTGGGTCCAAC 59.606 55.000 0.00 0.00 0.00 3.77
2270 3927 2.490168 GGTACTTGTGGGTCCAACCAAT 60.490 50.000 0.00 0.00 43.34 3.16
2281 3938 5.131308 TGGGTCCAACCAATTAAGATCGATA 59.869 40.000 0.00 0.00 41.02 2.92
2282 3939 6.059484 GGGTCCAACCAATTAAGATCGATAA 58.941 40.000 0.00 0.00 41.02 1.75
2296 3953 2.096248 TCGATAATTGTGGGCCCAAAC 58.904 47.619 30.64 16.86 0.00 2.93
2304 3961 0.035739 GTGGGCCCAAACGACTAAGA 59.964 55.000 30.64 0.00 0.00 2.10
2306 3963 1.353022 TGGGCCCAAACGACTAAGATT 59.647 47.619 26.33 0.00 0.00 2.40
2312 4348 4.828829 CCCAAACGACTAAGATTGGTACT 58.171 43.478 0.00 0.00 40.94 2.73
2315 4351 5.390567 CCAAACGACTAAGATTGGTACTTGC 60.391 44.000 0.00 0.00 38.68 4.01
2319 4355 2.835764 ACTAAGATTGGTACTTGCGGGA 59.164 45.455 0.00 0.00 0.00 5.14
2325 4361 0.402504 TGGTACTTGCGGGACCAAAT 59.597 50.000 10.67 0.00 40.29 2.32
2346 4382 5.916661 ATGACTAAGATCCGTACTTGTGT 57.083 39.130 0.00 0.00 0.00 3.72
2395 4431 2.358267 CTGAGCGAATAAGACCGGTACT 59.642 50.000 7.34 3.50 36.60 2.73
2484 4524 4.677673 AAGTAAGAACGGTACTTGTGGT 57.322 40.909 0.00 0.00 39.70 4.16
2518 4558 0.469917 ATCGATACTTGTGGGCCTGG 59.530 55.000 4.53 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.930158 AGGGGCAATAAAATAGAAGTATTTACA 57.070 29.630 0.00 0.00 37.79 2.41
8 9 9.930158 TTAACATAGGGGCAATAAAATAGAAGT 57.070 29.630 0.00 0.00 0.00 3.01
14 15 8.141268 CGTTCATTAACATAGGGGCAATAAAAT 58.859 33.333 0.00 0.00 35.16 1.82
15 16 7.339721 TCGTTCATTAACATAGGGGCAATAAAA 59.660 33.333 0.00 0.00 35.16 1.52
16 17 6.829298 TCGTTCATTAACATAGGGGCAATAAA 59.171 34.615 0.00 0.00 35.16 1.40
17 18 6.358178 TCGTTCATTAACATAGGGGCAATAA 58.642 36.000 0.00 0.00 35.16 1.40
18 19 5.931294 TCGTTCATTAACATAGGGGCAATA 58.069 37.500 0.00 0.00 35.16 1.90
19 20 4.787551 TCGTTCATTAACATAGGGGCAAT 58.212 39.130 0.00 0.00 35.16 3.56
20 21 4.223556 TCGTTCATTAACATAGGGGCAA 57.776 40.909 0.00 0.00 35.16 4.52
21 22 3.916359 TCGTTCATTAACATAGGGGCA 57.084 42.857 0.00 0.00 35.16 5.36
22 23 4.819630 TGATTCGTTCATTAACATAGGGGC 59.180 41.667 0.00 0.00 35.16 5.80
23 24 6.935741 TTGATTCGTTCATTAACATAGGGG 57.064 37.500 0.00 0.00 35.16 4.79
29 30 9.554724 GAGCTTTTATTGATTCGTTCATTAACA 57.445 29.630 0.00 0.00 35.16 2.41
30 31 9.010366 GGAGCTTTTATTGATTCGTTCATTAAC 57.990 33.333 0.00 0.00 32.59 2.01
31 32 8.956426 AGGAGCTTTTATTGATTCGTTCATTAA 58.044 29.630 0.00 0.00 33.34 1.40
32 33 8.506168 AGGAGCTTTTATTGATTCGTTCATTA 57.494 30.769 0.00 0.00 33.34 1.90
33 34 7.396540 AGGAGCTTTTATTGATTCGTTCATT 57.603 32.000 0.00 0.00 33.34 2.57
34 35 8.682936 ATAGGAGCTTTTATTGATTCGTTCAT 57.317 30.769 0.00 0.00 33.34 2.57
35 36 8.506168 AATAGGAGCTTTTATTGATTCGTTCA 57.494 30.769 0.00 0.00 0.00 3.18
36 37 9.439537 GAAATAGGAGCTTTTATTGATTCGTTC 57.560 33.333 0.00 0.00 0.00 3.95
37 38 8.956426 TGAAATAGGAGCTTTTATTGATTCGTT 58.044 29.630 0.00 0.00 0.00 3.85
38 39 8.506168 TGAAATAGGAGCTTTTATTGATTCGT 57.494 30.769 0.00 0.00 0.00 3.85
39 40 8.830580 TCTGAAATAGGAGCTTTTATTGATTCG 58.169 33.333 0.00 0.00 0.00 3.34
41 42 9.129532 CCTCTGAAATAGGAGCTTTTATTGATT 57.870 33.333 0.00 0.00 36.08 2.57
42 43 8.497745 TCCTCTGAAATAGGAGCTTTTATTGAT 58.502 33.333 0.00 0.00 38.24 2.57
43 44 7.861629 TCCTCTGAAATAGGAGCTTTTATTGA 58.138 34.615 0.00 0.00 38.24 2.57
44 45 8.511604 TTCCTCTGAAATAGGAGCTTTTATTG 57.488 34.615 0.00 0.00 43.90 1.90
45 46 9.533831 TTTTCCTCTGAAATAGGAGCTTTTATT 57.466 29.630 0.00 0.00 43.90 1.40
46 47 9.533831 TTTTTCCTCTGAAATAGGAGCTTTTAT 57.466 29.630 0.00 0.00 43.90 1.40
47 48 8.934023 TTTTTCCTCTGAAATAGGAGCTTTTA 57.066 30.769 0.00 0.00 43.90 1.52
48 49 7.839680 TTTTTCCTCTGAAATAGGAGCTTTT 57.160 32.000 0.00 0.00 43.90 2.27
70 71 7.595502 TCGTAAATTCGCCATAAACATGTTTTT 59.404 29.630 27.66 17.84 34.23 1.94
71 72 7.085116 TCGTAAATTCGCCATAAACATGTTTT 58.915 30.769 27.66 13.43 34.23 2.43
72 73 6.613233 TCGTAAATTCGCCATAAACATGTTT 58.387 32.000 25.99 25.99 36.63 2.83
73 74 6.184580 TCGTAAATTCGCCATAAACATGTT 57.815 33.333 4.92 4.92 0.00 2.71
74 75 5.729454 GCTCGTAAATTCGCCATAAACATGT 60.729 40.000 0.00 0.00 0.00 3.21
75 76 4.670621 GCTCGTAAATTCGCCATAAACATG 59.329 41.667 0.00 0.00 0.00 3.21
76 77 4.261031 GGCTCGTAAATTCGCCATAAACAT 60.261 41.667 0.00 0.00 42.06 2.71
77 78 3.064271 GGCTCGTAAATTCGCCATAAACA 59.936 43.478 0.00 0.00 42.06 2.83
78 79 3.614588 GGCTCGTAAATTCGCCATAAAC 58.385 45.455 0.00 0.00 42.06 2.01
79 80 2.285756 CGGCTCGTAAATTCGCCATAAA 59.714 45.455 0.00 0.00 42.59 1.40
80 81 1.862201 CGGCTCGTAAATTCGCCATAA 59.138 47.619 0.00 0.00 42.59 1.90
81 82 1.202440 ACGGCTCGTAAATTCGCCATA 60.202 47.619 0.00 0.00 42.59 2.74
82 83 0.461339 ACGGCTCGTAAATTCGCCAT 60.461 50.000 0.00 0.00 42.59 4.40
95 96 0.539986 TTAAGGTGGATGGACGGCTC 59.460 55.000 0.00 0.00 0.00 4.70
118 119 7.461918 GTCGTAACTTCTATTTTTCCACCATC 58.538 38.462 0.00 0.00 0.00 3.51
120 121 5.406175 CGTCGTAACTTCTATTTTTCCACCA 59.594 40.000 0.00 0.00 0.00 4.17
126 127 8.801715 TGTAACTCGTCGTAACTTCTATTTTT 57.198 30.769 0.00 0.00 0.00 1.94
127 128 8.801715 TTGTAACTCGTCGTAACTTCTATTTT 57.198 30.769 0.00 0.00 0.00 1.82
142 145 6.091713 CCCGTAATTCTCATTTTGTAACTCGT 59.908 38.462 0.00 0.00 0.00 4.18
166 169 6.204108 CGGTCCCACTGTTATATGTAATTTCC 59.796 42.308 0.00 0.00 0.00 3.13
182 185 1.061546 AAACATGTACCGGTCCCACT 58.938 50.000 12.40 0.00 0.00 4.00
197 200 2.649531 AACTGGTCCCATCGAAAACA 57.350 45.000 0.00 0.00 0.00 2.83
203 206 3.064820 CGGAAAAATAACTGGTCCCATCG 59.935 47.826 0.00 0.00 0.00 3.84
223 226 1.067212 CAAGACGGATCTACCCTTCGG 59.933 57.143 0.00 0.00 33.57 4.30
226 229 2.544844 TCCAAGACGGATCTACCCTT 57.455 50.000 0.00 0.00 39.64 3.95
290 293 1.301716 CCGGATTATCTGCGTGGGG 60.302 63.158 0.00 0.00 36.91 4.96
347 350 3.204827 CCTTGATTGAGGCCGCCG 61.205 66.667 3.22 0.00 0.00 6.46
361 364 2.115266 CCGGTGGTTGCTTCCCTT 59.885 61.111 0.00 0.00 0.00 3.95
382 385 2.107953 GAGCGAGACCAGGGATGC 59.892 66.667 0.00 0.00 0.00 3.91
384 387 1.760086 CAGGAGCGAGACCAGGGAT 60.760 63.158 0.00 0.00 0.00 3.85
505 516 4.988598 CTTGCTGGGCGTCACCGT 62.989 66.667 0.00 0.00 40.62 4.83
549 560 0.179056 GCTACACCCATGTATGCCGT 60.179 55.000 0.00 0.00 40.57 5.68
551 562 1.134098 ACTGCTACACCCATGTATGCC 60.134 52.381 0.00 0.00 40.57 4.40
609 620 1.371558 GGAGGAGTTGAACCGTGCT 59.628 57.895 0.00 0.00 0.00 4.40
620 631 1.083141 GGAAGGGAAGGGGAGGAGT 59.917 63.158 0.00 0.00 0.00 3.85
686 699 9.765795 AGAAACAATGAACTACTATAGGCATAC 57.234 33.333 4.43 0.00 0.00 2.39
812 829 9.435688 TCACAATAGAACAAATATGGGATATCG 57.564 33.333 0.00 0.00 0.00 2.92
1029 1059 0.106015 AGAAAGCACACCAAAGGGCT 60.106 50.000 0.00 0.00 37.90 5.19
1040 1070 3.214328 TCAGTTCCAGGAAAGAAAGCAC 58.786 45.455 2.45 0.00 0.00 4.40
1084 1114 3.511146 TGCCAACCAATCTCTTTCCATTC 59.489 43.478 0.00 0.00 0.00 2.67
1098 1128 0.467290 GGTCTGTTCCTTGCCAACCA 60.467 55.000 0.00 0.00 0.00 3.67
1205 1235 9.069082 TCCTAGTTTAGCTACAGAATACTGATC 57.931 37.037 0.00 0.00 46.03 2.92
1283 1313 9.411801 GAAGAATAACAAATTTTCCAAGGAGAC 57.588 33.333 0.00 0.00 0.00 3.36
1396 1433 9.181805 GCCTGTAATTTACTTCTTCAAAAAGAC 57.818 33.333 7.99 0.00 41.23 3.01
1431 1471 1.691196 TGGAAGAAGCAGTTGTTGGG 58.309 50.000 0.00 0.00 0.00 4.12
1485 1525 6.636454 AACTGGGAACTGATGGATAGTTAA 57.364 37.500 0.00 0.00 38.42 2.01
1560 1600 1.008079 GTGCTGCAAGTTGCCACTC 60.008 57.895 24.59 13.28 44.23 3.51
1685 1726 8.503196 TGTACATGACATATGTTCACAAGAAAC 58.497 33.333 10.30 5.90 31.62 2.78
1722 1766 4.515028 TCCTAGATTTCTGTCCGGACTA 57.485 45.455 33.39 19.81 0.00 2.59
1807 1852 2.417586 CACTTCAATTCGAGCATCAGCA 59.582 45.455 0.00 0.00 45.49 4.41
1831 1877 5.122396 GCATTAGTCTGAAGTCCGAACAAAT 59.878 40.000 0.00 0.00 0.00 2.32
1839 1885 6.341316 TGTTGATAGCATTAGTCTGAAGTCC 58.659 40.000 0.00 0.00 0.00 3.85
1880 1926 3.126000 GCCTTGCTCACTTCAAGTATGAC 59.874 47.826 0.00 0.00 39.30 3.06
1903 1949 2.079421 AGGGGATATACCTCGGAGGAA 58.921 52.381 30.13 14.89 45.50 3.36
1905 1951 1.358103 TCAGGGGATATACCTCGGAGG 59.642 57.143 22.40 22.40 45.50 4.30
1948 1994 2.280797 GGCACGTGTCTTCAGGCA 60.281 61.111 18.38 0.00 33.37 4.75
2052 2154 2.639286 GCACACGTGAGCCCAAAG 59.361 61.111 25.07 4.56 0.00 2.77
2093 2350 5.395657 CCTCGCCATTGCCTATATTATGAGA 60.396 44.000 0.00 0.00 0.00 3.27
2094 2351 4.813161 CCTCGCCATTGCCTATATTATGAG 59.187 45.833 0.00 0.00 0.00 2.90
2095 2352 4.469586 TCCTCGCCATTGCCTATATTATGA 59.530 41.667 0.00 0.00 0.00 2.15
2121 2458 4.666176 CACAAACGAAATTTCAGTCGACTG 59.334 41.667 34.76 34.76 45.08 3.51
2147 3008 3.919223 AGTATCGATCTTAGCCGTTCC 57.081 47.619 0.00 0.00 0.00 3.62
2153 3014 4.434520 GGCCCATAAGTATCGATCTTAGC 58.565 47.826 0.00 9.29 32.13 3.09
2201 3207 0.594284 CGATCTTAGTCGTTCGGCCC 60.594 60.000 0.00 0.00 36.88 5.80
2203 3209 2.402640 ATCGATCTTAGTCGTTCGGC 57.597 50.000 0.00 0.00 42.07 5.54
2221 3793 3.097614 ACTCGTTTGGGCTCACTAGTAT 58.902 45.455 0.00 0.00 0.00 2.12
2241 3844 3.429960 GGACCCACAAGTACCGATCTTAC 60.430 52.174 0.00 0.00 0.00 2.34
2249 3852 0.475044 TGGTTGGACCCACAAGTACC 59.525 55.000 0.00 0.95 37.50 3.34
2261 3864 8.620416 CACAATTATCGATCTTAATTGGTTGGA 58.380 33.333 25.13 3.15 45.17 3.53
2262 3865 7.862372 CCACAATTATCGATCTTAATTGGTTGG 59.138 37.037 25.13 21.46 45.17 3.77
2264 3867 7.470009 GCCCACAATTATCGATCTTAATTGGTT 60.470 37.037 25.13 11.01 45.17 3.67
2266 3869 6.381801 GCCCACAATTATCGATCTTAATTGG 58.618 40.000 25.13 17.50 45.17 3.16
2270 3927 4.141367 TGGGCCCACAATTATCGATCTTAA 60.141 41.667 24.45 0.00 0.00 1.85
2281 3938 0.469144 AGTCGTTTGGGCCCACAATT 60.469 50.000 28.70 5.29 0.00 2.32
2282 3939 0.402504 TAGTCGTTTGGGCCCACAAT 59.597 50.000 28.70 10.82 0.00 2.71
2296 3953 2.858344 CCGCAAGTACCAATCTTAGTCG 59.142 50.000 0.00 0.00 0.00 4.18
2304 3961 2.071502 TGGTCCCGCAAGTACCAAT 58.928 52.632 0.00 0.00 45.22 3.16
2306 3963 0.402504 ATTTGGTCCCGCAAGTACCA 59.597 50.000 0.00 0.00 46.13 3.25
2312 4348 2.039216 TCTTAGTCATTTGGTCCCGCAA 59.961 45.455 0.00 0.00 0.00 4.85
2315 4351 3.467803 GGATCTTAGTCATTTGGTCCCG 58.532 50.000 0.00 0.00 0.00 5.14
2319 4355 5.934402 AGTACGGATCTTAGTCATTTGGT 57.066 39.130 0.00 0.00 0.00 3.67
2325 4361 4.617530 GCACACAAGTACGGATCTTAGTCA 60.618 45.833 0.00 0.00 0.00 3.41
2346 4382 4.025061 GCTACTATCTTAGTCGTTCGAGCA 60.025 45.833 0.00 0.00 40.14 4.26
2395 4431 2.435069 TCTTAGTTGTTCGGACCCACAA 59.565 45.455 0.00 0.53 0.00 3.33
2457 4493 7.144000 CACAAGTACCGTTCTTACTTACTCTT 58.856 38.462 0.00 0.00 37.62 2.85
2461 4497 5.532557 ACCACAAGTACCGTTCTTACTTAC 58.467 41.667 0.00 0.00 37.62 2.34
2463 4499 4.677673 ACCACAAGTACCGTTCTTACTT 57.322 40.909 0.00 0.00 39.83 2.24
2484 4524 7.285629 ACAAGTATCGATCTTAGTCATCCAGAA 59.714 37.037 0.00 0.00 0.00 3.02



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

AutoCloner maintained by Alex Coulton.