Multiple sequence alignment - TraesCS7B01G460200

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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 TraesCS7B01G460200 chr7B 100.000 2980 0 0 1 2980 717871581 717874560 0.000000e+00 5504.0
1 TraesCS7B01G460200 chr7B 91.279 1720 135 2 709 2413 717982293 717984012 0.000000e+00 2331.0
2 TraesCS7B01G460200 chr7B 89.254 335 36 0 2579 2913 717984335 717984669 1.280000e-113 420.0
3 TraesCS7B01G460200 chr7B 83.636 275 37 6 1 275 717908127 717908393 4.930000e-63 252.0
4 TraesCS7B01G460200 chr7B 85.171 263 20 6 423 667 717981741 717982002 4.930000e-63 252.0
5 TraesCS7B01G460200 chr7B 86.713 143 19 0 823 965 717982157 717982299 3.070000e-35 159.0
6 TraesCS7B01G460200 chr7B 93.204 103 7 0 821 923 717872291 717872393 5.140000e-33 152.0
7 TraesCS7B01G460200 chr7B 93.204 103 7 0 711 813 717872401 717872503 5.140000e-33 152.0
8 TraesCS7B01G460200 chr7B 89.320 103 11 0 711 813 717982407 717982509 2.410000e-26 130.0
9 TraesCS7B01G460200 chr7B 87.736 106 13 0 708 813 717982152 717982257 1.120000e-24 124.0
10 TraesCS7B01G460200 chr7A 88.875 1564 145 12 885 2426 717408924 717407368 0.000000e+00 1897.0
11 TraesCS7B01G460200 chr7A 88.296 675 76 2 983 1654 717173348 717172674 0.000000e+00 806.0
12 TraesCS7B01G460200 chr7A 88.985 581 60 4 1611 2189 717366473 717365895 0.000000e+00 715.0
13 TraesCS7B01G460200 chr7A 84.779 565 77 6 2425 2980 717407325 717406761 2.590000e-155 558.0
14 TraesCS7B01G460200 chr7A 84.926 544 65 8 2425 2959 717365664 717365129 4.370000e-148 534.0
15 TraesCS7B01G460200 chr7A 91.154 260 20 2 708 967 717173674 717173418 1.700000e-92 350.0
16 TraesCS7B01G460200 chr7A 86.432 199 20 5 2238 2432 717365896 717365701 8.370000e-51 211.0
17 TraesCS7B01G460200 chr7A 89.655 145 15 0 821 965 717409110 717408966 5.070000e-43 185.0
18 TraesCS7B01G460200 chr7A 93.333 105 7 0 708 812 717173814 717173710 3.980000e-34 156.0
19 TraesCS7B01G460200 chr7D 90.165 1088 101 5 1349 2432 621970751 621969666 0.000000e+00 1411.0
20 TraesCS7B01G460200 chr7D 88.392 827 87 6 1611 2432 621863663 621862841 0.000000e+00 987.0
21 TraesCS7B01G460200 chr7D 90.000 650 43 5 708 1344 621973802 621973162 0.000000e+00 821.0
22 TraesCS7B01G460200 chr7D 85.841 565 68 7 2425 2980 621862804 621862243 9.200000e-165 590.0
23 TraesCS7B01G460200 chr7D 84.956 565 76 5 2425 2980 621969629 621969065 5.580000e-157 564.0
24 TraesCS7B01G460200 chr7D 90.625 288 11 4 391 662 621974378 621974091 4.690000e-98 368.0
25 TraesCS7B01G460200 chr7D 84.444 405 30 14 1 404 621974990 621974618 4.690000e-98 368.0
26 TraesCS7B01G460200 chr7D 93.204 103 7 0 711 813 621973689 621973587 5.140000e-33 152.0
27 TraesCS7B01G460200 chr7D 96.154 52 2 0 884 935 621654217 621654166 5.290000e-13 86.1
28 TraesCS7B01G460200 chr7D 97.561 41 1 0 773 813 621654218 621654178 1.480000e-08 71.3
29 TraesCS7B01G460200 chr2A 85.458 502 69 4 1933 2432 50690644 50690145 1.220000e-143 520.0


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 TraesCS7B01G460200 chr7B 717871581 717874560 2979 False 1936.000000 5504 95.469333 1 2980 3 chr7B.!!$F2 2979
1 TraesCS7B01G460200 chr7B 717981741 717984669 2928 False 569.333333 2331 88.245500 423 2913 6 chr7B.!!$F3 2490
2 TraesCS7B01G460200 chr7A 717406761 717409110 2349 True 880.000000 1897 87.769667 821 2980 3 chr7A.!!$R3 2159
3 TraesCS7B01G460200 chr7A 717365129 717366473 1344 True 486.666667 715 86.781000 1611 2959 3 chr7A.!!$R2 1348
4 TraesCS7B01G460200 chr7A 717172674 717173814 1140 True 437.333333 806 90.927667 708 1654 3 chr7A.!!$R1 946
5 TraesCS7B01G460200 chr7D 621862243 621863663 1420 True 788.500000 987 87.116500 1611 2980 2 chr7D.!!$R2 1369
6 TraesCS7B01G460200 chr7D 621969065 621974990 5925 True 614.000000 1411 88.899000 1 2980 6 chr7D.!!$R3 2979

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
667 937 0.250814 TAAATCGTTGGCCCGTTGGT 60.251 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 6064 0.040336 GCAATGCTGAGATCATGCCG 60.04 55.0 0.0 0.0 0.0 5.69 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
24 25 3.900941 AGTGAATTTGTTGCGTGATTCC 58.099 40.909 0.00 0.00 0.00 3.01
37 38 1.145377 GATTCCGCCGGCTAAGGAA 59.855 57.895 29.10 29.10 46.58 3.36
39 40 2.325393 ATTCCGCCGGCTAAGGAAGG 62.325 60.000 29.92 20.64 45.85 3.46
40 41 3.467226 CCGCCGGCTAAGGAAGGA 61.467 66.667 26.68 0.00 34.09 3.36
41 42 2.107141 CGCCGGCTAAGGAAGGAG 59.893 66.667 26.68 0.00 0.00 3.69
42 43 2.423898 CGCCGGCTAAGGAAGGAGA 61.424 63.158 26.68 0.00 0.00 3.71
43 44 1.749334 CGCCGGCTAAGGAAGGAGAT 61.749 60.000 26.68 0.00 0.00 2.75
64 65 8.663911 GGAGATCTGACTTAATCAAAAACTCTG 58.336 37.037 0.00 0.00 36.69 3.35
108 109 5.587443 TCCAGTTCATGCTGATCTGTTATTG 59.413 40.000 16.33 7.01 40.70 1.90
115 116 3.134623 TGCTGATCTGTTATTGGTCCGAT 59.865 43.478 0.00 0.00 0.00 4.18
135 136 3.677002 GAGCATCTACAGAGGTGGC 57.323 57.895 0.00 0.00 34.01 5.01
136 137 0.826715 GAGCATCTACAGAGGTGGCA 59.173 55.000 0.00 0.00 34.01 4.92
137 138 1.415659 GAGCATCTACAGAGGTGGCAT 59.584 52.381 0.00 0.00 34.01 4.40
159 160 2.029838 ATCTGTTCGGGCAGTGATTC 57.970 50.000 0.00 0.00 37.70 2.52
168 169 0.824759 GGCAGTGATTCGGTAGGTCT 59.175 55.000 0.00 0.00 0.00 3.85
171 172 1.409427 CAGTGATTCGGTAGGTCTCCC 59.591 57.143 0.00 0.00 0.00 4.30
178 179 1.375098 CGGTAGGTCTCCCAGACGTC 61.375 65.000 7.70 7.70 45.96 4.34
180 181 1.096416 GTAGGTCTCCCAGACGTCTG 58.904 60.000 33.87 33.87 45.96 3.51
183 184 1.316706 GGTCTCCCAGACGTCTGAGG 61.317 65.000 40.21 35.19 45.96 3.86
186 187 1.533033 TCCCAGACGTCTGAGGCAA 60.533 57.895 40.21 23.03 46.59 4.52
196 197 2.224621 CGTCTGAGGCAAATATGGGGAT 60.225 50.000 0.00 0.00 0.00 3.85
198 199 2.785269 TCTGAGGCAAATATGGGGATGT 59.215 45.455 0.00 0.00 0.00 3.06
199 200 3.152341 CTGAGGCAAATATGGGGATGTC 58.848 50.000 0.00 0.00 0.00 3.06
200 201 2.158475 TGAGGCAAATATGGGGATGTCC 60.158 50.000 0.00 0.00 0.00 4.02
201 202 1.202927 AGGCAAATATGGGGATGTCCG 60.203 52.381 0.00 0.00 36.71 4.79
202 203 1.247567 GCAAATATGGGGATGTCCGG 58.752 55.000 0.00 0.00 36.71 5.14
203 204 1.202879 GCAAATATGGGGATGTCCGGA 60.203 52.381 0.00 0.00 36.71 5.14
204 205 2.555227 GCAAATATGGGGATGTCCGGAT 60.555 50.000 7.81 0.00 36.71 4.18
205 206 3.084039 CAAATATGGGGATGTCCGGATG 58.916 50.000 7.81 0.00 36.71 3.51
206 207 0.620556 ATATGGGGATGTCCGGATGC 59.379 55.000 7.81 0.00 36.71 3.91
207 208 0.766288 TATGGGGATGTCCGGATGCA 60.766 55.000 7.81 1.18 36.71 3.96
208 209 1.429543 ATGGGGATGTCCGGATGCAT 61.430 55.000 7.81 7.47 36.71 3.96
209 210 1.302832 GGGGATGTCCGGATGCATC 60.303 63.158 21.32 21.32 40.36 3.91
234 235 0.580104 CGCCGGATCCGTTTAACATC 59.420 55.000 31.22 9.49 37.81 3.06
264 266 4.594970 TGTCAAACAAAAGAAGGACAGGA 58.405 39.130 0.00 0.00 32.13 3.86
269 271 3.490348 ACAAAAGAAGGACAGGACATGG 58.510 45.455 0.00 0.00 0.00 3.66
272 274 0.898320 AGAAGGACAGGACATGGTCG 59.102 55.000 0.00 0.00 34.87 4.79
276 278 1.221840 GACAGGACATGGTCGCCAT 59.778 57.895 5.65 5.65 46.37 4.40
278 280 1.221566 CAGGACATGGTCGCCATCA 59.778 57.895 8.21 0.00 43.15 3.07
320 322 2.749076 GCAGTATGTGAAGCCAACATCA 59.251 45.455 0.19 0.00 39.31 3.07
329 331 0.892755 AGCCAACATCAATGCTGGTG 59.107 50.000 12.67 0.00 44.02 4.17
331 333 1.403249 GCCAACATCAATGCTGGTGTC 60.403 52.381 12.67 0.00 46.56 3.67
377 379 3.644335 ACTACCCTAGGTCTTGGATGTC 58.356 50.000 8.29 0.00 37.09 3.06
380 382 2.225908 ACCCTAGGTCTTGGATGTCCTT 60.226 50.000 8.29 0.00 36.82 3.36
381 383 2.846827 CCCTAGGTCTTGGATGTCCTTT 59.153 50.000 8.29 0.00 36.82 3.11
383 385 4.473559 CCCTAGGTCTTGGATGTCCTTTTA 59.526 45.833 8.29 0.00 36.82 1.52
384 386 5.429130 CCTAGGTCTTGGATGTCCTTTTAC 58.571 45.833 0.00 0.00 36.82 2.01
385 387 5.189934 CCTAGGTCTTGGATGTCCTTTTACT 59.810 44.000 0.00 0.00 36.82 2.24
387 389 6.697641 AGGTCTTGGATGTCCTTTTACTTA 57.302 37.500 0.09 0.00 36.82 2.24
388 390 7.086685 AGGTCTTGGATGTCCTTTTACTTAA 57.913 36.000 0.09 0.00 36.82 1.85
389 391 7.699878 AGGTCTTGGATGTCCTTTTACTTAAT 58.300 34.615 0.09 0.00 36.82 1.40
481 734 7.909777 TTCGCTCTAATTTCGTGATAACTAG 57.090 36.000 0.00 0.00 0.00 2.57
492 760 6.525578 TCGTGATAACTAGGACAGAACATT 57.474 37.500 0.00 0.00 0.00 2.71
520 788 8.641498 AATGGACAGAAGACAAAATGTTAGAT 57.359 30.769 0.00 0.00 0.00 1.98
559 827 9.868277 AGACAAAATGACAGAAATAAACAACAA 57.132 25.926 0.00 0.00 0.00 2.83
617 885 2.430465 AGATGGCTTGCACTTGTACTG 58.570 47.619 0.00 0.00 0.00 2.74
634 902 2.825205 ACTGCCAAAAATGCAACAGAC 58.175 42.857 0.00 0.00 38.46 3.51
663 933 5.105675 ACAAAATAATAAATCGTTGGCCCGT 60.106 36.000 0.00 0.00 0.00 5.28
667 937 0.250814 TAAATCGTTGGCCCGTTGGT 60.251 50.000 0.00 0.00 0.00 3.67
668 938 1.801309 AAATCGTTGGCCCGTTGGTG 61.801 55.000 0.00 0.00 0.00 4.17
699 982 6.380274 AGTGTCTATTCCTTCCGATTAAGTGA 59.620 38.462 0.00 0.00 0.00 3.41
703 986 3.247006 TCCTTCCGATTAAGTGACTGC 57.753 47.619 0.00 0.00 0.00 4.40
704 987 2.565391 TCCTTCCGATTAAGTGACTGCA 59.435 45.455 0.00 0.00 0.00 4.41
825 1484 1.682684 GGGCACGAGGAGGAGAGAA 60.683 63.158 0.00 0.00 0.00 2.87
951 1732 5.374921 AGCTCTGCATCTTGCTATGTTAAT 58.625 37.500 0.75 0.00 45.31 1.40
1024 1859 4.383861 CTGAGGCGCTGGTGAGCA 62.384 66.667 7.64 0.00 46.62 4.26
1029 1864 2.186384 GCGCTGGTGAGCATCTCT 59.814 61.111 0.00 0.00 46.62 3.10
1041 1876 2.298729 GAGCATCTCTACAGGGGTGATC 59.701 54.545 0.00 0.00 0.00 2.92
1081 1916 0.033109 AGCCACTTTAATGGGGGAGC 60.033 55.000 11.39 0.00 40.43 4.70
1182 2017 3.450457 AGAAGCTCGAGAACATGGAAGAT 59.550 43.478 18.75 0.00 0.00 2.40
1388 4629 4.586001 ACAAATCCAACAGCTGAAGACATT 59.414 37.500 23.35 8.61 0.00 2.71
1401 4642 3.807622 TGAAGACATTGGTCAAAGACGTC 59.192 43.478 7.70 7.70 46.80 4.34
1410 4651 0.939577 TCAAAGACGTCAGTGAGCGC 60.940 55.000 19.50 0.00 0.00 5.92
1556 4797 0.525761 ATCAAATTGTTGACGGCCGG 59.474 50.000 31.76 11.88 46.40 6.13
1559 4800 4.733542 ATTGTTGACGGCCGGGGG 62.734 66.667 31.76 0.90 0.00 5.40
1658 4906 4.962362 TCAAGTATACCATGAGCTTGGAGA 59.038 41.667 11.52 0.00 39.25 3.71
1764 5013 0.186143 TGCCACAACCAACCCATACA 59.814 50.000 0.00 0.00 0.00 2.29
1768 5017 2.488167 CCACAACCAACCCATACAGACA 60.488 50.000 0.00 0.00 0.00 3.41
1790 5039 1.063174 GGCGCAAGATCTCATTGACAC 59.937 52.381 10.83 0.00 43.02 3.67
1801 5050 4.825422 TCTCATTGACACCATCAGAGAAC 58.175 43.478 0.00 0.00 36.30 3.01
1854 5103 6.058183 ACTTCTCAATCCCTATTGTATGCAC 58.942 40.000 0.00 0.00 42.66 4.57
1893 5142 1.089123 AGTCCCCAATTTGCCCCTTA 58.911 50.000 0.00 0.00 0.00 2.69
1898 5147 4.055820 TCCCCAATTTGCCCCTTATACTA 58.944 43.478 0.00 0.00 0.00 1.82
1980 5237 5.048083 TGGCAGGTACTTTTTCATCATTGAC 60.048 40.000 0.00 0.00 34.60 3.18
2005 5262 6.039382 CGATATATGGGACGAATCAGTATGGA 59.961 42.308 0.00 0.00 36.16 3.41
2029 5286 3.965292 TTATTCGTTGTGCGTTTCCAA 57.035 38.095 0.00 0.00 42.13 3.53
2063 5320 5.570320 AGGTAGCAAAGTAATCACAACCAT 58.430 37.500 0.00 0.00 0.00 3.55
2067 5324 4.460382 AGCAAAGTAATCACAACCATGAGG 59.540 41.667 0.00 0.00 42.21 3.86
2070 5327 6.678900 GCAAAGTAATCACAACCATGAGGATC 60.679 42.308 0.00 0.00 38.69 3.36
2076 5333 1.482593 ACAACCATGAGGATCGAGACC 59.517 52.381 0.00 3.60 38.61 3.85
2103 5360 4.847255 GCAACCTGCAACGATCAC 57.153 55.556 0.00 0.00 44.26 3.06
2134 5391 8.816894 AGTTCATTTACAAGATGAGTCCTCTTA 58.183 33.333 9.97 0.00 35.17 2.10
2149 5406 8.324306 TGAGTCCTCTTAATGATCAAAACTCAT 58.676 33.333 0.00 0.00 35.70 2.90
2189 5446 7.711339 CAGTATAGTTGGACAGGTTAATCTTCC 59.289 40.741 9.00 9.00 0.00 3.46
2191 5448 3.326880 AGTTGGACAGGTTAATCTTCCGT 59.673 43.478 10.49 0.00 0.00 4.69
2239 5496 8.877864 AATTCTATAAAAATGTGGTGGTCTCA 57.122 30.769 0.00 0.00 0.00 3.27
2251 5508 2.418197 GGTGGTCTCACGCTTGCTATTA 60.418 50.000 0.00 0.00 44.50 0.98
2293 5553 3.055819 GGTCAGTCAGCCAACTAGATCAA 60.056 47.826 0.00 0.00 0.00 2.57
2295 5555 5.163405 GGTCAGTCAGCCAACTAGATCAATA 60.163 44.000 0.00 0.00 0.00 1.90
2296 5556 5.982516 GTCAGTCAGCCAACTAGATCAATAG 59.017 44.000 0.00 0.00 0.00 1.73
2297 5557 5.893824 TCAGTCAGCCAACTAGATCAATAGA 59.106 40.000 0.00 0.00 0.00 1.98
2298 5558 6.040278 TCAGTCAGCCAACTAGATCAATAGAG 59.960 42.308 0.00 0.00 0.00 2.43
2308 5568 7.609097 ACTAGATCAATAGAGCAATGGAAGA 57.391 36.000 0.00 0.00 30.99 2.87
2370 5630 2.305927 GACTTTGGAGGGGATGAGACAA 59.694 50.000 0.00 0.00 0.00 3.18
2374 5634 3.421394 TGGAGGGGATGAGACAAGTAT 57.579 47.619 0.00 0.00 0.00 2.12
2402 5662 4.806247 CCTTAGCTACAACAATCTTCCTCG 59.194 45.833 0.00 0.00 0.00 4.63
2405 5665 3.258372 AGCTACAACAATCTTCCTCGTCA 59.742 43.478 0.00 0.00 0.00 4.35
2413 5673 5.738909 ACAATCTTCCTCGTCATCTCAAAT 58.261 37.500 0.00 0.00 0.00 2.32
2418 5678 3.461061 TCCTCGTCATCTCAAATCATGC 58.539 45.455 0.00 0.00 0.00 4.06
2461 5765 1.743394 GTGGCTTAAGGTTTCATCCCG 59.257 52.381 4.29 0.00 0.00 5.14
2514 5819 5.523916 TCGCTGGAATTACTTTAATGAGCTC 59.476 40.000 6.82 6.82 0.00 4.09
2533 5838 4.248691 CTCGTCAATAGGAGCATGATCA 57.751 45.455 13.85 0.00 31.38 2.92
2544 5953 5.324409 AGGAGCATGATCAAACCTACAAAA 58.676 37.500 13.85 0.00 0.00 2.44
2548 5957 7.603784 GGAGCATGATCAAACCTACAAAAATTT 59.396 33.333 13.85 0.00 0.00 1.82
2559 5968 9.990360 AAACCTACAAAAATTTGGTATAACAGG 57.010 29.630 10.38 4.97 42.34 4.00
2566 5975 4.862641 ATTTGGTATAACAGGCAGGTCT 57.137 40.909 0.00 0.00 0.00 3.85
2577 5986 3.010584 ACAGGCAGGTCTTGGAATGTAAT 59.989 43.478 0.00 0.00 0.00 1.89
2631 6048 6.926272 TCAGAAGAAGAGAAGTTTCTTAGTGC 59.074 38.462 0.66 0.00 43.07 4.40
2690 6107 4.083581 AGCAAAGTTCATCGAATTTCCG 57.916 40.909 0.00 0.00 0.00 4.30
2701 6118 3.468770 TCGAATTTCCGTTCAGTTGGAA 58.531 40.909 0.00 0.00 42.35 3.53
2710 6127 3.270027 CGTTCAGTTGGAATATGGAGCA 58.730 45.455 0.00 0.00 37.93 4.26
2787 6209 1.698506 TTTGGCAAGTCCCGTTTCAT 58.301 45.000 0.00 0.00 0.00 2.57
2788 6210 2.570415 TTGGCAAGTCCCGTTTCATA 57.430 45.000 0.00 0.00 0.00 2.15
2848 6270 1.296715 GGATTGTCAGGGTGCTCGT 59.703 57.895 0.00 0.00 0.00 4.18
2883 6305 5.527582 GGATTGACCTCACACCAATATGTAC 59.472 44.000 0.00 0.00 35.41 2.90
2921 6343 2.507452 TGAGCATCAGCATCCCCG 59.493 61.111 0.00 0.00 42.56 5.73
2959 6381 4.145052 CCCTTATTCTGCCAACCCTAATC 58.855 47.826 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.749334 ATCTCCTTCCTTAGCCGGCG 61.749 60.000 23.20 6.78 0.00 6.46
26 27 1.342819 CAGATCTCCTTCCTTAGCCGG 59.657 57.143 0.00 0.00 0.00 6.13
37 38 8.601546 AGAGTTTTTGATTAAGTCAGATCTCCT 58.398 33.333 0.00 0.00 38.29 3.69
39 40 8.663911 CCAGAGTTTTTGATTAAGTCAGATCTC 58.336 37.037 0.00 0.00 38.29 2.75
40 41 8.160106 ACCAGAGTTTTTGATTAAGTCAGATCT 58.840 33.333 0.00 0.00 38.29 2.75
41 42 8.329203 ACCAGAGTTTTTGATTAAGTCAGATC 57.671 34.615 0.00 0.00 38.29 2.75
42 43 9.442047 CTACCAGAGTTTTTGATTAAGTCAGAT 57.558 33.333 0.00 0.00 38.29 2.90
43 44 7.387948 GCTACCAGAGTTTTTGATTAAGTCAGA 59.612 37.037 0.00 0.00 38.29 3.27
64 65 0.178301 GTTGACCTAGGGCTGCTACC 59.822 60.000 17.75 0.00 0.00 3.18
108 109 3.413327 TCTGTAGATGCTCTATCGGACC 58.587 50.000 0.00 0.00 40.86 4.46
115 116 2.311463 GCCACCTCTGTAGATGCTCTA 58.689 52.381 0.00 0.00 0.00 2.43
129 130 2.643551 CCGAACAGATAAATGCCACCT 58.356 47.619 0.00 0.00 0.00 4.00
130 131 1.676006 CCCGAACAGATAAATGCCACC 59.324 52.381 0.00 0.00 0.00 4.61
131 132 1.065551 GCCCGAACAGATAAATGCCAC 59.934 52.381 0.00 0.00 0.00 5.01
132 133 1.340502 TGCCCGAACAGATAAATGCCA 60.341 47.619 0.00 0.00 0.00 4.92
133 134 1.334869 CTGCCCGAACAGATAAATGCC 59.665 52.381 0.00 0.00 40.25 4.40
134 135 2.017049 ACTGCCCGAACAGATAAATGC 58.983 47.619 11.05 0.00 40.25 3.56
135 136 3.270027 TCACTGCCCGAACAGATAAATG 58.730 45.455 11.05 0.12 40.25 2.32
136 137 3.627395 TCACTGCCCGAACAGATAAAT 57.373 42.857 11.05 0.00 40.25 1.40
137 138 3.627395 ATCACTGCCCGAACAGATAAA 57.373 42.857 11.05 0.00 40.25 1.40
171 172 2.868583 CCATATTTGCCTCAGACGTCTG 59.131 50.000 34.76 34.76 45.08 3.51
178 179 3.152341 GACATCCCCATATTTGCCTCAG 58.848 50.000 0.00 0.00 0.00 3.35
180 181 2.519013 GGACATCCCCATATTTGCCTC 58.481 52.381 0.00 0.00 0.00 4.70
183 184 1.202879 TCCGGACATCCCCATATTTGC 60.203 52.381 0.00 0.00 0.00 3.68
186 187 1.004745 GCATCCGGACATCCCCATATT 59.995 52.381 6.12 0.00 0.00 1.28
212 213 1.448189 TTAAACGGATCCGGCGTGG 60.448 57.895 35.87 9.83 44.69 4.94
213 214 1.015085 TGTTAAACGGATCCGGCGTG 61.015 55.000 35.87 10.60 44.69 5.34
214 215 0.108041 ATGTTAAACGGATCCGGCGT 60.108 50.000 35.87 22.62 44.69 5.68
215 216 0.580104 GATGTTAAACGGATCCGGCG 59.420 55.000 35.87 13.56 44.69 6.46
216 217 0.580104 CGATGTTAAACGGATCCGGC 59.420 55.000 35.87 20.21 44.69 6.13
234 235 4.829064 TCTTTTGTTTGACATCTTCCCG 57.171 40.909 0.00 0.00 0.00 5.14
251 253 2.289694 CGACCATGTCCTGTCCTTCTTT 60.290 50.000 0.00 0.00 0.00 2.52
264 266 0.752743 CCCAATGATGGCGACCATGT 60.753 55.000 14.84 2.72 45.26 3.21
269 271 0.107214 TCTTCCCCAATGATGGCGAC 60.107 55.000 0.00 0.00 46.09 5.19
272 274 3.033184 TGATTTCTTCCCCAATGATGGC 58.967 45.455 0.00 0.00 46.09 4.40
276 278 4.823442 CGATCATGATTTCTTCCCCAATGA 59.177 41.667 10.14 0.00 0.00 2.57
278 280 3.571401 GCGATCATGATTTCTTCCCCAAT 59.429 43.478 10.14 0.00 0.00 3.16
289 291 4.212847 GCTTCACATACTGCGATCATGATT 59.787 41.667 10.14 0.00 0.00 2.57
290 292 3.744942 GCTTCACATACTGCGATCATGAT 59.255 43.478 8.25 8.25 0.00 2.45
314 316 1.167851 CGGACACCAGCATTGATGTT 58.832 50.000 0.68 0.00 0.00 2.71
320 322 0.247736 GAGTCTCGGACACCAGCATT 59.752 55.000 6.78 0.00 34.60 3.56
361 363 4.576330 AAAAGGACATCCAAGACCTAGG 57.424 45.455 7.41 7.41 38.89 3.02
424 676 5.811399 TCGAATTTCGTATGAAAAGCCAT 57.189 34.783 17.61 0.00 46.53 4.40
444 697 1.596260 AGAGCGAATGCAATGTCATCG 59.404 47.619 0.00 0.00 46.23 3.84
481 734 6.817765 TCTGTCCATTTTAATGTTCTGTCC 57.182 37.500 2.13 0.00 34.60 4.02
520 788 6.486320 TGTCATTTTGTCTATTGTCAGCTTCA 59.514 34.615 0.00 0.00 0.00 3.02
559 827 2.592512 TCCTCCTACCTTCCCTTCTCAT 59.407 50.000 0.00 0.00 0.00 2.90
617 885 2.548875 TGTGTCTGTTGCATTTTTGGC 58.451 42.857 0.00 0.00 0.00 4.52
634 902 7.954786 GGCCAACGATTTATTATTTTGTTTGTG 59.045 33.333 0.00 0.00 0.00 3.33
663 933 4.777896 AGGAATAGACACTTAGCTCACCAA 59.222 41.667 0.00 0.00 0.00 3.67
667 937 4.098044 CGGAAGGAATAGACACTTAGCTCA 59.902 45.833 0.00 0.00 0.00 4.26
668 938 4.338682 TCGGAAGGAATAGACACTTAGCTC 59.661 45.833 0.00 0.00 0.00 4.09
699 982 4.752101 GTGTGTGATCTCTTTTAGTGCAGT 59.248 41.667 0.00 0.00 0.00 4.40
703 986 5.760253 AGGTTGTGTGTGATCTCTTTTAGTG 59.240 40.000 0.00 0.00 0.00 2.74
704 987 5.930135 AGGTTGTGTGTGATCTCTTTTAGT 58.070 37.500 0.00 0.00 0.00 2.24
706 989 5.924356 TGAGGTTGTGTGTGATCTCTTTTA 58.076 37.500 0.00 0.00 0.00 1.52
787 1446 4.591072 GCCCATGGTCTTATCTCTTCTAGT 59.409 45.833 11.73 0.00 0.00 2.57
825 1484 0.748005 GTGGCAGAGGTTGTGTGTGT 60.748 55.000 0.00 0.00 0.00 3.72
951 1732 2.304180 CCCTCAGCTCTCTTTTTCTGGA 59.696 50.000 0.00 0.00 0.00 3.86
1024 1859 3.964031 GAGTTGATCACCCCTGTAGAGAT 59.036 47.826 0.00 0.00 0.00 2.75
1029 1864 2.832129 GACAGAGTTGATCACCCCTGTA 59.168 50.000 7.41 0.00 38.95 2.74
1081 1916 2.613595 TGCTCTTGTGCTTTGTGTACTG 59.386 45.455 0.00 0.00 32.31 2.74
1182 2017 1.625315 CTGGTCTGTGGATCCAGTTCA 59.375 52.381 16.81 9.14 42.42 3.18
1388 4629 1.538204 GCTCACTGACGTCTTTGACCA 60.538 52.381 17.92 0.00 0.00 4.02
1401 4642 2.680913 CCTTTTCCGGCGCTCACTG 61.681 63.158 7.64 0.00 0.00 3.66
1410 4651 5.123227 TCATCAAGCTTATACCTTTTCCGG 58.877 41.667 0.00 0.00 0.00 5.14
1499 4740 1.331214 CTCCATGCCAACAAGGTTGT 58.669 50.000 8.16 0.00 44.72 3.32
1658 4906 5.221501 ACAAAAACCTTGCAGTCATATTGCT 60.222 36.000 0.00 0.00 42.02 3.91
1697 4945 5.636965 CCGAGAAGCTTCATCATATTAGGTG 59.363 44.000 27.57 6.87 0.00 4.00
1764 5013 0.610174 TGAGATCTTGCGCCTTGTCT 59.390 50.000 4.18 3.24 0.00 3.41
1768 5017 2.012673 GTCAATGAGATCTTGCGCCTT 58.987 47.619 4.18 0.00 0.00 4.35
1790 5039 8.783833 TTTTTCTCTTAGATGTTCTCTGATGG 57.216 34.615 0.00 0.00 35.28 3.51
1854 5103 5.248870 ACTGTAAAACCTCAAAGCAACTG 57.751 39.130 0.00 0.00 0.00 3.16
1947 5204 5.462530 AAAAGTACCTGCCAATGGTTTAC 57.537 39.130 0.00 0.00 38.88 2.01
1952 5209 4.220382 TGATGAAAAAGTACCTGCCAATGG 59.780 41.667 0.00 0.00 0.00 3.16
1980 5237 6.039382 TCCATACTGATTCGTCCCATATATCG 59.961 42.308 0.00 0.00 0.00 2.92
2063 5320 0.180642 AGCTACGGTCTCGATCCTCA 59.819 55.000 0.00 0.00 40.11 3.86
2067 5324 2.031069 TGCATTAGCTACGGTCTCGATC 60.031 50.000 0.00 0.00 42.74 3.69
2070 5327 1.852895 GTTGCATTAGCTACGGTCTCG 59.147 52.381 0.00 0.00 42.74 4.04
2098 5355 7.615582 TCTTGTAAATGAACTCATGGTGATC 57.384 36.000 0.00 0.00 36.56 2.92
2103 5360 7.201679 GGACTCATCTTGTAAATGAACTCATGG 60.202 40.741 0.00 0.00 36.56 3.66
2168 5425 4.529377 ACGGAAGATTAACCTGTCCAACTA 59.471 41.667 0.00 0.00 0.00 2.24
2182 5439 7.436673 CGAAATCTCTTCTAATGACGGAAGATT 59.563 37.037 5.97 0.00 44.30 2.40
2189 5446 7.685532 TCATTCGAAATCTCTTCTAATGACG 57.314 36.000 0.00 0.00 36.40 4.35
2221 5478 2.550606 GCGTGAGACCACCACATTTTTA 59.449 45.455 0.00 0.00 40.12 1.52
2239 5496 5.300752 AGCAATACTGATAATAGCAAGCGT 58.699 37.500 0.00 0.00 0.00 5.07
2251 5508 6.711277 TGACCAAAAGACTAGCAATACTGAT 58.289 36.000 0.00 0.00 0.00 2.90
2273 5530 5.893824 TCTATTGATCTAGTTGGCTGACTGA 59.106 40.000 0.00 1.90 0.00 3.41
2293 5553 4.337555 GCACACATTCTTCCATTGCTCTAT 59.662 41.667 0.00 0.00 0.00 1.98
2295 5555 2.490903 GCACACATTCTTCCATTGCTCT 59.509 45.455 0.00 0.00 0.00 4.09
2296 5556 2.229543 TGCACACATTCTTCCATTGCTC 59.770 45.455 0.00 0.00 0.00 4.26
2297 5557 2.241160 TGCACACATTCTTCCATTGCT 58.759 42.857 0.00 0.00 0.00 3.91
2298 5558 2.728690 TGCACACATTCTTCCATTGC 57.271 45.000 0.00 0.00 0.00 3.56
2308 5568 6.088016 TGAGCTTAAAGAATTGCACACATT 57.912 33.333 0.00 0.00 0.00 2.71
2348 5608 2.192263 GTCTCATCCCCTCCAAAGTCT 58.808 52.381 0.00 0.00 0.00 3.24
2370 5630 8.322091 AGATTGTTGTAGCTAAGGTTCAATACT 58.678 33.333 0.00 1.45 0.00 2.12
2374 5634 6.430000 GGAAGATTGTTGTAGCTAAGGTTCAA 59.570 38.462 0.00 0.00 0.00 2.69
2402 5662 4.634184 AGCAAGCATGATTTGAGATGAC 57.366 40.909 12.84 0.00 0.00 3.06
2405 5665 7.584122 AAAGATAGCAAGCATGATTTGAGAT 57.416 32.000 12.84 6.07 0.00 2.75
2413 5673 3.379372 GCCTCAAAAGATAGCAAGCATGA 59.621 43.478 0.00 0.00 0.00 3.07
2418 5678 4.441079 CCCATTGCCTCAAAAGATAGCAAG 60.441 45.833 0.00 0.00 45.67 4.01
2447 5751 5.486735 TGTACTTTCGGGATGAAACCTTA 57.513 39.130 0.00 0.00 41.59 2.69
2461 5765 1.678101 GCATCCTGGCCATGTACTTTC 59.322 52.381 5.51 0.00 0.00 2.62
2514 5819 4.024556 GGTTTGATCATGCTCCTATTGACG 60.025 45.833 0.00 0.00 0.00 4.35
2533 5838 9.990360 CCTGTTATACCAAATTTTTGTAGGTTT 57.010 29.630 2.78 0.00 36.45 3.27
2544 5953 5.193099 AGACCTGCCTGTTATACCAAATT 57.807 39.130 0.00 0.00 0.00 1.82
2548 5957 2.238646 CCAAGACCTGCCTGTTATACCA 59.761 50.000 0.00 0.00 0.00 3.25
2553 5962 2.375174 ACATTCCAAGACCTGCCTGTTA 59.625 45.455 0.00 0.00 0.00 2.41
2556 5965 2.787473 TACATTCCAAGACCTGCCTG 57.213 50.000 0.00 0.00 0.00 4.85
2557 5966 4.322057 AATTACATTCCAAGACCTGCCT 57.678 40.909 0.00 0.00 0.00 4.75
2559 5968 6.942532 TCATAATTACATTCCAAGACCTGC 57.057 37.500 0.00 0.00 0.00 4.85
2596 6013 6.547880 ACTTCTCTTCTTCTGAGTTGTGTCTA 59.452 38.462 0.00 0.00 33.59 2.59
2601 6018 6.883744 AGAAACTTCTCTTCTTCTGAGTTGT 58.116 36.000 0.00 0.00 29.94 3.32
2605 6022 7.116233 GCACTAAGAAACTTCTCTTCTTCTGAG 59.884 40.741 1.29 0.00 41.21 3.35
2608 6025 5.923684 CGCACTAAGAAACTTCTCTTCTTCT 59.076 40.000 1.29 0.00 41.21 2.85
2631 6048 1.607148 TGCCGTGTAGATCATCTACCG 59.393 52.381 20.21 20.31 46.64 4.02
2647 6064 0.040336 GCAATGCTGAGATCATGCCG 60.040 55.000 0.00 0.00 0.00 5.69
2674 6091 4.315803 ACTGAACGGAAATTCGATGAACT 58.684 39.130 0.00 0.00 0.00 3.01
2690 6107 5.643379 TTTGCTCCATATTCCAACTGAAC 57.357 39.130 0.00 0.00 35.31 3.18
2701 6118 3.634504 TGTGCCTTCATTTGCTCCATAT 58.365 40.909 0.00 0.00 0.00 1.78
2710 6127 3.754965 TGCTTCTACTGTGCCTTCATTT 58.245 40.909 0.00 0.00 0.00 2.32
2788 6210 9.911788 ATGGACTTGAGTTCATACATAGAAAAT 57.088 29.630 3.06 0.00 42.23 1.82
2893 6315 5.286267 TGCTGATGCTCAAATATCTGAGA 57.714 39.130 10.34 0.00 44.82 3.27
2921 6343 1.671379 GGGTTGCCGTCTGTTCCTC 60.671 63.158 0.00 0.00 0.00 3.71
2931 6353 2.106844 GGCAGAATAAGGGTTGCCG 58.893 57.895 0.00 0.00 45.68 5.69
2959 6381 0.887933 CCAAATGTTTCAGGTCCCCG 59.112 55.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.