Multiple sequence alignment - TraesCS5A01G059000

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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 TraesCS5A01G059000 chr5A 100.000 2495 0 0 1 2495 59564139 59566633 0.000000 4608.0
1 TraesCS5A01G059000 chr5D 89.986 2177 171 24 324 2484 68447814 68449959 0.000000 2769.0
2 TraesCS5A01G059000 chr5D 97.059 34 1 0 293 326 68435894 68435927 0.000096 58.4
3 TraesCS5A01G059000 chr5B 90.984 1819 153 10 3 1815 74507632 74509445 0.000000 2440.0
4 TraesCS5A01G059000 chr7D 96.970 33 1 0 1682 1714 628408928 628408896 0.000347 56.5


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 TraesCS5A01G059000 chr5A 59564139 59566633 2494 False 4608 4608 100.000 1 2495 1 chr5A.!!$F1 2494
1 TraesCS5A01G059000 chr5D 68447814 68449959 2145 False 2769 2769 89.986 324 2484 1 chr5D.!!$F2 2160
2 TraesCS5A01G059000 chr5B 74507632 74509445 1813 False 2440 2440 90.984 3 1815 1 chr5B.!!$F1 1812

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
205 206 0.178975 TGCAAAACCGATCCCCAACT 60.179 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1966 0.16923 CAACGACGGTGAGGAGAGAG 59.831 60.0 7.21 0.0 0.0 3.2 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
21 22 4.848562 TCAATACTATAGGCACCTCACG 57.151 45.455 4.43 0.00 0.00 4.35
45 46 2.437180 CTTGCAGCATCTCCGGCA 60.437 61.111 0.00 0.00 0.00 5.69
68 69 0.458543 GTCGCCGATGACATCACAGT 60.459 55.000 15.58 0.00 38.75 3.55
71 72 1.212616 GCCGATGACATCACAGTAGC 58.787 55.000 15.58 4.45 0.00 3.58
76 77 3.867493 CGATGACATCACAGTAGCAACAT 59.133 43.478 15.58 0.00 0.00 2.71
92 93 1.925229 ACATGCAACAACAACAGCAC 58.075 45.000 0.00 0.00 40.14 4.40
95 96 1.138671 GCAACAACAACAGCACGGT 59.861 52.632 0.00 0.00 0.00 4.83
118 119 0.593128 GCCTTGCACATCGTTGTCTT 59.407 50.000 0.00 0.00 32.34 3.01
127 128 2.421073 ACATCGTTGTCTTGCATCATGG 59.579 45.455 0.00 0.00 0.00 3.66
148 149 1.886422 TACAGCACCCCCATGTCATA 58.114 50.000 0.00 0.00 0.00 2.15
156 157 2.765699 ACCCCCATGTCATATTGTTTGC 59.234 45.455 0.00 0.00 0.00 3.68
161 162 4.626604 CCCATGTCATATTGTTTGCAACAC 59.373 41.667 0.00 1.53 41.97 3.32
167 168 1.782044 ATTGTTTGCAACACGGATGC 58.218 45.000 0.00 2.81 41.97 3.91
174 175 0.799534 GCAACACGGATGCAATGAGC 60.800 55.000 0.00 0.00 43.29 4.26
191 192 2.257980 CGGCGCTGGATTTGCAAA 59.742 55.556 15.44 15.44 0.00 3.68
193 194 1.616872 CGGCGCTGGATTTGCAAAAC 61.617 55.000 17.19 13.72 0.00 2.43
197 198 1.402720 CGCTGGATTTGCAAAACCGAT 60.403 47.619 27.31 7.88 33.91 4.18
205 206 0.178975 TGCAAAACCGATCCCCAACT 60.179 50.000 0.00 0.00 0.00 3.16
221 222 0.739813 AACTTGTAGCATCGCCGGTC 60.740 55.000 1.90 0.00 0.00 4.79
233 234 2.897207 CCGGTCGCAGTGGGATTA 59.103 61.111 13.56 0.00 0.00 1.75
258 259 2.345760 CCAAGCATGGGTGAGGTGC 61.346 63.158 0.00 0.00 43.51 5.01
260 261 0.968901 CAAGCATGGGTGAGGTGCAT 60.969 55.000 0.00 0.00 41.19 3.96
265 266 1.267574 ATGGGTGAGGTGCATCTCGT 61.268 55.000 21.71 2.94 36.61 4.18
359 360 0.892755 AGTTCACTTGGACGGCGATA 59.107 50.000 16.62 0.00 0.00 2.92
371 372 1.270412 ACGGCGATACCACAACTCAAA 60.270 47.619 16.62 0.00 39.03 2.69
372 373 1.127951 CGGCGATACCACAACTCAAAC 59.872 52.381 0.00 0.00 39.03 2.93
407 410 2.825836 GCATTCCACTGGCGAGGG 60.826 66.667 0.00 0.00 0.00 4.30
435 438 1.613630 GGAAGAGGGAGAGGGCACA 60.614 63.158 0.00 0.00 0.00 4.57
437 440 1.692762 GGAAGAGGGAGAGGGCACATA 60.693 57.143 0.00 0.00 0.00 2.29
446 449 1.132500 GAGGGCACATAAGTAGGGCT 58.868 55.000 0.00 0.00 0.00 5.19
454 457 4.684485 GCACATAAGTAGGGCTCACTGAAT 60.684 45.833 0.00 0.00 0.00 2.57
509 513 0.320160 AGTCTACCGCCGGTTGAAAC 60.320 55.000 21.47 11.25 38.94 2.78
528 534 7.692908 TGAAACGAATCAATTTCCTTGTTTC 57.307 32.000 12.18 12.18 39.76 2.78
593 599 7.969508 TCATAATCTTGTGTGTGCAAACATATG 59.030 33.333 14.04 14.95 31.49 1.78
612 618 9.448438 AACATATGCTTCAAACATACTAAGACA 57.552 29.630 1.58 0.00 33.03 3.41
647 654 7.678194 TGTTGTTCTTTTATCTTGCTTTTCG 57.322 32.000 0.00 0.00 0.00 3.46
831 839 2.081462 GACACTAATTCCCGGTGGTTG 58.919 52.381 0.00 0.00 35.53 3.77
833 841 2.158579 ACACTAATTCCCGGTGGTTGTT 60.159 45.455 0.00 0.00 35.53 2.83
903 911 6.018262 CGATAATTTCGGCTTATCCTTCAACA 60.018 38.462 0.00 0.00 44.28 3.33
909 917 6.339587 TCGGCTTATCCTTCAACAAAATTT 57.660 33.333 0.00 0.00 0.00 1.82
943 951 4.979204 CGAAAGTGGACGCTACCA 57.021 55.556 0.00 0.00 37.63 3.25
959 967 3.427863 GCTACCACACAAGAGTACGAAAC 59.572 47.826 0.00 0.00 0.00 2.78
1014 1022 3.792401 CGTACACATGGAGGCATCTAAA 58.208 45.455 0.00 0.00 0.00 1.85
1030 1038 2.105134 TCTAAACTCGCCCTTTTGGTCA 59.895 45.455 0.00 0.00 38.10 4.02
1035 1043 0.960364 TCGCCCTTTTGGTCATGCTC 60.960 55.000 0.00 0.00 38.10 4.26
1054 1062 2.703798 GCAATGGCAGCCGTGATGT 61.704 57.895 17.33 0.00 40.72 3.06
1057 1065 1.028330 AATGGCAGCCGTGATGTCTG 61.028 55.000 7.01 0.00 0.00 3.51
1063 1071 2.660064 GCCGTGATGTCTGACCCCT 61.660 63.158 5.17 0.00 0.00 4.79
1245 1253 0.531200 CACAGTACGGGGAGAACCTC 59.469 60.000 0.00 0.00 40.03 3.85
1498 1506 1.889545 GCAGAGGCCATATTGACTCC 58.110 55.000 5.01 0.00 0.00 3.85
1501 1509 2.038295 CAGAGGCCATATTGACTCCCTC 59.962 54.545 5.01 0.00 39.25 4.30
1608 1617 5.331902 GCTGTCGTGCATGTATTTTGTATT 58.668 37.500 5.68 0.00 0.00 1.89
1609 1618 5.227805 GCTGTCGTGCATGTATTTTGTATTG 59.772 40.000 5.68 0.00 0.00 1.90
1611 1620 6.082984 TGTCGTGCATGTATTTTGTATTGTG 58.917 36.000 5.68 0.00 0.00 3.33
1637 1646 8.196378 AGAACCATAAATATGTACTCCCTCTC 57.804 38.462 0.00 0.00 31.82 3.20
1815 1836 1.472480 GTGCATGCAATAAACGGTCCT 59.528 47.619 24.58 0.00 0.00 3.85
1836 1857 7.254017 GGTCCTAGAAAGACAATTCGATTTACG 60.254 40.741 0.00 0.00 38.46 3.18
1843 1864 5.120399 AGACAATTCGATTTACGGGCATTA 58.880 37.500 0.00 0.00 42.82 1.90
1874 1895 4.667262 CTCTATCAACCACTTCACTCTCG 58.333 47.826 0.00 0.00 0.00 4.04
1876 1897 0.750249 TCAACCACTTCACTCTCGCA 59.250 50.000 0.00 0.00 0.00 5.10
1878 1899 0.249911 AACCACTTCACTCTCGCACC 60.250 55.000 0.00 0.00 0.00 5.01
1920 1941 1.002990 GGGACGTCCAAATTCCGGT 60.003 57.895 34.40 0.00 37.91 5.28
1945 1966 1.229368 GGGCCCTCTATCCTCCTCC 60.229 68.421 17.04 0.00 0.00 4.30
1946 1967 1.745879 GGGCCCTCTATCCTCCTCCT 61.746 65.000 17.04 0.00 0.00 3.69
1947 1968 0.252057 GGCCCTCTATCCTCCTCCTC 60.252 65.000 0.00 0.00 0.00 3.71
1962 1983 1.377463 CCTCTCTCCTCACCGTCGT 60.377 63.158 0.00 0.00 0.00 4.34
1970 1991 0.321298 CCTCACCGTCGTTGGGAAAT 60.321 55.000 0.00 0.00 0.00 2.17
1976 1997 1.883021 GTCGTTGGGAAATGCCTGG 59.117 57.895 0.00 0.00 36.66 4.45
1980 2001 1.912763 TTGGGAAATGCCTGGGTGC 60.913 57.895 0.00 0.00 36.66 5.01
1981 2002 2.037847 GGGAAATGCCTGGGTGCT 59.962 61.111 0.00 0.00 36.66 4.40
1982 2003 1.306296 GGGAAATGCCTGGGTGCTA 59.694 57.895 0.00 0.00 36.66 3.49
1997 2018 1.819632 GCTATTGGCGGTGGTGGAG 60.820 63.158 0.00 0.00 0.00 3.86
2036 2057 2.760385 GGGGGTCTGGAGGTCTCG 60.760 72.222 0.00 0.00 0.00 4.04
2047 2068 3.760035 GGTCTCGAGGCTTGGCGA 61.760 66.667 17.97 0.00 35.01 5.54
2072 2093 1.905354 GTGCTCCAAGGGCTGCTTT 60.905 57.895 0.00 0.00 0.00 3.51
2085 2106 2.358247 GCTTTCGCCAACGGGAGA 60.358 61.111 0.00 0.00 41.64 3.71
2163 2184 2.874648 GATGGTGCGGAGATGCCACA 62.875 60.000 0.00 0.00 35.94 4.17
2219 2240 1.305930 GGTGGATGTCTTTGGCGGAC 61.306 60.000 0.00 0.00 0.00 4.79
2236 2257 4.003788 CGGTGGTGAGGCTTCGGT 62.004 66.667 0.00 0.00 0.00 4.69
2251 2272 2.034687 GGTGCTGCAGTGGTGGAT 59.965 61.111 16.64 0.00 0.00 3.41
2258 2279 0.388659 TGCAGTGGTGGATTTGTTGC 59.611 50.000 0.00 0.00 0.00 4.17
2305 2326 2.649034 GCGGTGGAGTCGTCAGAA 59.351 61.111 0.00 0.00 0.00 3.02
2336 2357 1.899534 TGTTGCGGGTGCCTAAACC 60.900 57.895 0.00 0.00 41.78 3.27
2356 2377 1.755395 GCCTGATCTGGCCATGCAA 60.755 57.895 28.37 0.00 46.82 4.08
2366 2387 2.515523 CCATGCAAGGCTCCCGAG 60.516 66.667 0.00 0.00 0.00 4.63
2392 2413 4.460683 GGTGCGGGTGTATCGGCA 62.461 66.667 0.00 0.00 39.97 5.69
2393 2414 2.435234 GTGCGGGTGTATCGGCAA 60.435 61.111 0.00 0.00 42.93 4.52
2395 2416 2.435234 GCGGGTGTATCGGCAACA 60.435 61.111 0.00 0.00 33.87 3.33
2402 2423 1.062587 GTGTATCGGCAACAGTGATGC 59.937 52.381 16.48 16.48 43.08 3.91
2412 2433 2.036571 CAGTGATGCTTGGCTCGCA 61.037 57.895 3.92 3.92 42.25 5.10
2438 2459 0.609957 TGCTTTGGAGGGAGCATGTG 60.610 55.000 0.00 0.00 43.46 3.21
2439 2460 0.322816 GCTTTGGAGGGAGCATGTGA 60.323 55.000 0.00 0.00 38.73 3.58
2444 2465 0.396060 GGAGGGAGCATGTGAGGATC 59.604 60.000 0.00 0.00 0.00 3.36
2466 2487 2.134933 TCCGTGCAGTGGTGGTGTA 61.135 57.895 4.90 0.00 0.00 2.90
2484 2505 1.672881 GTATGTGAAGGGATGCAGTGC 59.327 52.381 8.58 8.58 0.00 4.40
2485 2506 0.038599 ATGTGAAGGGATGCAGTGCA 59.961 50.000 22.22 22.22 44.86 4.57
2494 2515 2.112928 TGCAGTGCATCGGGTTGT 59.887 55.556 15.37 0.00 31.71 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.005472 GCGTGAGGTGCCTATAGTATTGA 59.995 47.826 0.00 0.00 0.00 2.57
1 2 3.005897 AGCGTGAGGTGCCTATAGTATTG 59.994 47.826 0.00 0.00 42.35 1.90
2 3 3.231818 AGCGTGAGGTGCCTATAGTATT 58.768 45.455 0.00 0.00 42.35 1.89
4 5 2.359981 AGCGTGAGGTGCCTATAGTA 57.640 50.000 0.00 0.00 42.35 1.82
5 6 1.955080 GTAGCGTGAGGTGCCTATAGT 59.045 52.381 0.00 0.00 44.53 2.12
6 7 2.030717 CAGTAGCGTGAGGTGCCTATAG 60.031 54.545 0.00 0.00 45.60 1.31
7 8 1.954382 CAGTAGCGTGAGGTGCCTATA 59.046 52.381 0.00 0.00 45.60 1.31
8 9 0.747255 CAGTAGCGTGAGGTGCCTAT 59.253 55.000 0.00 0.00 45.60 2.57
68 69 3.704512 CTGTTGTTGTTGCATGTTGCTA 58.295 40.909 0.75 0.00 45.31 3.49
71 72 2.029486 GTGCTGTTGTTGTTGCATGTTG 59.971 45.455 0.00 0.00 37.76 3.33
76 77 1.138459 CCGTGCTGTTGTTGTTGCA 59.862 52.632 0.00 0.00 0.00 4.08
103 104 1.197492 GATGCAAGACAACGATGTGCA 59.803 47.619 1.86 7.50 40.74 4.57
111 112 4.497006 GCTGTATCCATGATGCAAGACAAC 60.497 45.833 0.00 0.00 34.57 3.32
112 113 3.628942 GCTGTATCCATGATGCAAGACAA 59.371 43.478 0.00 0.00 34.57 3.18
113 114 3.208594 GCTGTATCCATGATGCAAGACA 58.791 45.455 0.00 0.00 34.57 3.41
118 119 1.477377 GGGTGCTGTATCCATGATGCA 60.477 52.381 0.00 0.00 33.91 3.96
127 128 0.546122 TGACATGGGGGTGCTGTATC 59.454 55.000 0.00 0.00 0.00 2.24
133 134 2.071778 ACAATATGACATGGGGGTGC 57.928 50.000 0.00 0.00 0.00 5.01
136 137 2.765135 TGCAAACAATATGACATGGGGG 59.235 45.455 0.00 0.00 0.00 5.40
156 157 0.521867 CGCTCATTGCATCCGTGTTG 60.522 55.000 0.00 0.00 43.06 3.33
161 162 4.303603 CGCCGCTCATTGCATCCG 62.304 66.667 0.00 0.00 43.06 4.18
167 168 1.996786 AAATCCAGCGCCGCTCATTG 61.997 55.000 9.54 0.00 36.40 2.82
168 169 1.750399 AAATCCAGCGCCGCTCATT 60.750 52.632 9.54 7.89 36.40 2.57
174 175 1.372748 TTTTGCAAATCCAGCGCCG 60.373 52.632 13.65 0.00 33.85 6.46
191 192 1.339727 GCTACAAGTTGGGGATCGGTT 60.340 52.381 7.96 0.00 0.00 4.44
193 194 0.251916 TGCTACAAGTTGGGGATCGG 59.748 55.000 7.96 0.00 0.00 4.18
197 198 0.392461 GCGATGCTACAAGTTGGGGA 60.392 55.000 7.96 1.34 0.00 4.81
205 206 2.202690 CGACCGGCGATGCTACAA 60.203 61.111 9.30 0.00 44.57 2.41
241 242 0.968901 ATGCACCTCACCCATGCTTG 60.969 55.000 0.00 0.00 40.13 4.01
256 257 0.536724 ACATGGTGCTACGAGATGCA 59.463 50.000 0.00 0.00 36.79 3.96
278 279 0.110056 GTCACAACATCAGCAAGGCG 60.110 55.000 0.00 0.00 0.00 5.52
359 360 0.834612 TCTCCCGTTTGAGTTGTGGT 59.165 50.000 0.00 0.00 33.93 4.16
371 372 1.187087 CTTTCAGCTACCTCTCCCGT 58.813 55.000 0.00 0.00 0.00 5.28
372 373 0.179097 GCTTTCAGCTACCTCTCCCG 60.179 60.000 0.00 0.00 38.45 5.14
407 410 5.432645 CCTCTCCCTCTTCCTTACATTTTC 58.567 45.833 0.00 0.00 0.00 2.29
528 534 9.769093 GTAAAACTAACCAATAAGCACTGTATG 57.231 33.333 0.00 0.00 0.00 2.39
559 565 7.710044 TGCACACACAAGATTATGACAAAATTT 59.290 29.630 0.00 0.00 0.00 1.82
560 566 7.208777 TGCACACACAAGATTATGACAAAATT 58.791 30.769 0.00 0.00 0.00 1.82
561 567 6.747125 TGCACACACAAGATTATGACAAAAT 58.253 32.000 0.00 0.00 0.00 1.82
565 571 5.067023 TGTTTGCACACACAAGATTATGACA 59.933 36.000 0.45 0.00 0.00 3.58
568 574 7.253850 GCATATGTTTGCACACACAAGATTATG 60.254 37.037 8.06 11.76 42.31 1.90
569 575 6.753279 GCATATGTTTGCACACACAAGATTAT 59.247 34.615 8.06 0.00 42.31 1.28
593 599 7.602517 ATGTCTGTCTTAGTATGTTTGAAGC 57.397 36.000 0.00 0.00 0.00 3.86
831 839 8.078596 GCAGGATGTAATGAAAGGATATTGAAC 58.921 37.037 0.00 0.00 39.31 3.18
833 841 6.716628 GGCAGGATGTAATGAAAGGATATTGA 59.283 38.462 0.00 0.00 39.31 2.57
933 941 0.317479 ACTCTTGTGTGGTAGCGTCC 59.683 55.000 0.00 0.00 0.00 4.79
943 951 6.243811 TGTTTTTGTTTCGTACTCTTGTGT 57.756 33.333 0.00 0.00 0.00 3.72
989 997 1.078426 GCCTCCATGTGTACGCCTT 60.078 57.895 3.51 0.00 0.00 4.35
1014 1022 1.244019 GCATGACCAAAAGGGCGAGT 61.244 55.000 0.00 0.00 42.05 4.18
1030 1038 3.524606 GGCTGCCATTGCGAGCAT 61.525 61.111 15.17 0.00 40.87 3.79
1035 1043 3.511595 ATCACGGCTGCCATTGCG 61.512 61.111 20.29 6.59 41.78 4.85
1049 1057 0.994247 ATTGCAGGGGTCAGACATCA 59.006 50.000 2.17 0.00 0.00 3.07
1054 1062 2.356278 GGCATTGCAGGGGTCAGA 59.644 61.111 11.39 0.00 0.00 3.27
1057 1065 2.757099 CTGGGCATTGCAGGGGTC 60.757 66.667 11.39 0.00 0.00 4.46
1063 1071 2.334946 GCGAGTTCTGGGCATTGCA 61.335 57.895 11.39 0.00 0.00 4.08
1136 1144 3.509137 GACGCGTCCCAGGTCACAA 62.509 63.158 28.61 0.00 0.00 3.33
1261 1269 4.803426 CGCAGCCGTCCAGTCCTC 62.803 72.222 0.00 0.00 0.00 3.71
1275 1283 2.310327 ATATCTTCACGGCCTGCGCA 62.310 55.000 10.98 10.98 36.38 6.09
1498 1506 1.168714 CTCTTCCCCGCAAAAAGAGG 58.831 55.000 3.91 0.00 41.40 3.69
1501 1509 1.586541 GCCTCTTCCCCGCAAAAAG 59.413 57.895 0.00 0.00 0.00 2.27
1608 1617 7.347222 AGGGAGTACATATTTATGGTTCTCACA 59.653 37.037 16.00 0.00 36.10 3.58
1609 1618 7.736893 AGGGAGTACATATTTATGGTTCTCAC 58.263 38.462 0.00 12.53 38.00 3.51
1611 1620 8.196378 AGAGGGAGTACATATTTATGGTTCTC 57.804 38.462 0.00 6.50 38.00 2.87
1738 1758 9.971922 ATGATTCCAACTAAGAAAAGTTTTGAG 57.028 29.630 5.36 3.09 37.61 3.02
1745 1765 9.334693 CTTTCGAATGATTCCAACTAAGAAAAG 57.665 33.333 5.12 0.00 0.00 2.27
1800 1821 4.933400 GTCTTTCTAGGACCGTTTATTGCA 59.067 41.667 0.00 0.00 0.00 4.08
1815 1836 5.292589 GCCCGTAAATCGAATTGTCTTTCTA 59.707 40.000 0.00 0.00 42.86 2.10
1857 1878 0.750249 TGCGAGAGTGAAGTGGTTGA 59.250 50.000 0.00 0.00 0.00 3.18
1920 1941 0.542232 GGATAGAGGGCCCTAAGCGA 60.542 60.000 28.78 9.62 45.17 4.93
1945 1966 0.169230 CAACGACGGTGAGGAGAGAG 59.831 60.000 7.21 0.00 0.00 3.20
1946 1967 1.241990 CCAACGACGGTGAGGAGAGA 61.242 60.000 16.01 0.00 0.00 3.10
1947 1968 1.213013 CCAACGACGGTGAGGAGAG 59.787 63.158 16.01 0.00 0.00 3.20
1962 1983 1.912763 GCACCCAGGCATTTCCCAA 60.913 57.895 0.00 0.00 34.51 4.12
1970 1991 2.044053 GCCAATAGCACCCAGGCA 60.044 61.111 0.00 0.00 44.59 4.75
1976 1997 2.045340 ACCACCGCCAATAGCACC 60.045 61.111 0.00 0.00 44.04 5.01
1980 2001 1.819632 GCTCCACCACCGCCAATAG 60.820 63.158 0.00 0.00 0.00 1.73
1981 2002 2.270850 GCTCCACCACCGCCAATA 59.729 61.111 0.00 0.00 0.00 1.90
1982 2003 4.740822 GGCTCCACCACCGCCAAT 62.741 66.667 0.00 0.00 43.25 3.16
2020 2041 1.755008 CTCGAGACCTCCAGACCCC 60.755 68.421 6.58 0.00 0.00 4.95
2023 2044 0.968393 AAGCCTCGAGACCTCCAGAC 60.968 60.000 15.71 0.00 0.00 3.51
2036 2057 2.892425 CATCGGTCGCCAAGCCTC 60.892 66.667 0.00 0.00 0.00 4.70
2047 2068 2.671070 CCTTGGAGCACCATCGGT 59.329 61.111 2.87 0.00 46.34 4.69
2080 2101 1.689582 ATCGTTGACCCCCTCTCCC 60.690 63.158 0.00 0.00 0.00 4.30
2085 2106 4.096003 CGCCATCGTTGACCCCCT 62.096 66.667 0.00 0.00 0.00 4.79
2133 2154 1.568612 CGCACCATCTCGTTGTTGCT 61.569 55.000 4.51 0.00 0.00 3.91
2140 2161 1.439228 CATCTCCGCACCATCTCGT 59.561 57.895 0.00 0.00 0.00 4.18
2163 2184 2.996734 CCACGCCCCAAAGCCAAT 60.997 61.111 0.00 0.00 0.00 3.16
2203 2224 2.106683 CCGTCCGCCAAAGACATCC 61.107 63.158 0.00 0.00 33.70 3.51
2219 2240 4.003788 ACCGAAGCCTCACCACCG 62.004 66.667 0.00 0.00 0.00 4.94
2236 2257 0.467844 ACAAATCCACCACTGCAGCA 60.468 50.000 15.27 0.00 0.00 4.41
2251 2272 1.357907 GCAGCACACAAAGCAACAAA 58.642 45.000 0.00 0.00 0.00 2.83
2258 2279 2.121564 CTCCACCGCAGCACACAAAG 62.122 60.000 0.00 0.00 0.00 2.77
2291 2312 3.238108 ACATCATTCTGACGACTCCAC 57.762 47.619 0.00 0.00 0.00 4.02
2305 2326 1.001487 CCGCAACACACACAACATCAT 60.001 47.619 0.00 0.00 0.00 2.45
2320 2341 2.670251 CGGTTTAGGCACCCGCAA 60.670 61.111 0.00 0.00 41.24 4.85
2370 2391 4.770874 ATACACCCGCACCCGCAC 62.771 66.667 0.00 0.00 38.40 5.34
2379 2400 1.079405 ACTGTTGCCGATACACCCG 60.079 57.895 0.00 0.00 0.00 5.28
2382 2403 1.062587 GCATCACTGTTGCCGATACAC 59.937 52.381 1.13 0.00 33.95 2.90
2387 2408 1.236616 CCAAGCATCACTGTTGCCGA 61.237 55.000 8.23 0.00 41.06 5.54
2392 2413 1.580845 GCGAGCCAAGCATCACTGTT 61.581 55.000 0.00 0.00 34.19 3.16
2393 2414 2.037136 GCGAGCCAAGCATCACTGT 61.037 57.895 0.00 0.00 34.19 3.55
2395 2416 2.348620 TGCGAGCCAAGCATCACT 59.651 55.556 0.00 0.00 40.01 3.41
2412 2433 1.767681 CTCCCTCCAAAGCAGCTCTAT 59.232 52.381 0.00 0.00 0.00 1.98
2438 2459 1.064946 CTGCACGGACGAGATCCTC 59.935 63.158 0.00 0.00 46.69 3.71
2439 2460 1.679305 ACTGCACGGACGAGATCCT 60.679 57.895 0.00 0.00 46.69 3.24
2444 2465 2.734723 CACCACTGCACGGACGAG 60.735 66.667 4.39 0.00 0.00 4.18
2451 2472 0.874390 CACATACACCACCACTGCAC 59.126 55.000 0.00 0.00 0.00 4.57
2466 2487 0.038599 TGCACTGCATCCCTTCACAT 59.961 50.000 0.00 0.00 31.71 3.21


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

AutoCloner maintained by Alex Coulton.