Multiple sequence alignment - TraesCS1B01G395500

Loading Multiple Alignment...

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 TraesCS1B01G395500 chr1B 100.000 2238 0 0 741 2978 627149254 627151491 0.000000e+00 4133
1 TraesCS1B01G395500 chr1B 100.000 367 0 0 1 367 627148514 627148880 0.000000e+00 678
2 TraesCS1B01G395500 chr1D 89.071 1949 120 48 742 2646 457539859 457541758 0.000000e+00 2333
3 TraesCS1B01G395500 chr1D 86.486 333 35 6 2648 2978 457541791 457542115 1.020000e-94 357
4 TraesCS1B01G395500 chr1A 91.837 980 47 18 1245 2210 550117745 550118705 0.000000e+00 1336
5 TraesCS1B01G395500 chr1A 95.710 303 13 0 2208 2510 550130699 550131001 3.450000e-134 488
6 TraesCS1B01G395500 chr1A 88.822 331 22 7 2650 2978 550131242 550131559 2.780000e-105 392
7 TraesCS1B01G395500 chr1A 84.140 372 47 5 1 361 550116652 550117022 1.700000e-92 350
8 TraesCS1B01G395500 chr1A 96.825 126 4 0 921 1046 550117255 550117380 8.360000e-51 211
9 TraesCS1B01G395500 chr1A 89.516 124 11 2 2524 2646 550131085 550131207 3.970000e-34 156


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 TraesCS1B01G395500 chr1B 627148514 627151491 2977 False 2405.500000 4133 100.000000 1 2978 2 chr1B.!!$F1 2977
1 TraesCS1B01G395500 chr1D 457539859 457542115 2256 False 1345.000000 2333 87.778500 742 2978 2 chr1D.!!$F1 2236
2 TraesCS1B01G395500 chr1A 550116652 550118705 2053 False 632.333333 1336 90.934000 1 2210 3 chr1A.!!$F1 2209
3 TraesCS1B01G395500 chr1A 550130699 550131559 860 False 345.333333 488 91.349333 2208 2978 3 chr1A.!!$F2 770

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
235 236 0.168788 CAATAGCCCAACGCACTGTG 59.831 55.0 2.76 2.76 41.38 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2301 0.106569 CAGTAATGGGCATCAGGGCA 60.107 55.0 0.0 0.0 45.66 5.36 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
67 68 4.876107 AGTAAATATGGAAGCTTCACCGTG 59.124 41.667 27.02 0.00 0.00 4.94
69 70 0.323302 TATGGAAGCTTCACCGTGCA 59.677 50.000 27.02 15.01 0.00 4.57
70 71 0.957395 ATGGAAGCTTCACCGTGCAG 60.957 55.000 27.02 0.00 0.00 4.41
77 78 1.202076 GCTTCACCGTGCAGCTTATTC 60.202 52.381 14.98 0.00 0.00 1.75
79 80 0.739462 TCACCGTGCAGCTTATTCGG 60.739 55.000 8.00 8.00 45.53 4.30
82 83 2.106074 CGTGCAGCTTATTCGGCCA 61.106 57.895 2.24 0.00 0.00 5.36
103 104 2.115427 TGAGACACACAAGGGTTCTGA 58.885 47.619 0.00 0.00 0.00 3.27
137 138 5.192722 TCATCATGGGGTTAGTACCATTGAA 59.807 40.000 0.00 0.00 44.85 2.69
138 139 5.110814 TCATGGGGTTAGTACCATTGAAG 57.889 43.478 0.00 0.00 44.85 3.02
144 145 3.528532 GTTAGTACCATTGAAGGACCGG 58.471 50.000 0.00 0.00 0.00 5.28
180 181 6.461370 CCCACTCAGAATTTGTCACAATTTGA 60.461 38.462 2.79 0.00 0.00 2.69
211 212 5.722021 GTTGACAAACCCACAATCCTAAT 57.278 39.130 0.00 0.00 0.00 1.73
215 216 6.548321 TGACAAACCCACAATCCTAATAACT 58.452 36.000 0.00 0.00 0.00 2.24
216 217 6.657541 TGACAAACCCACAATCCTAATAACTC 59.342 38.462 0.00 0.00 0.00 3.01
232 233 0.324943 ACTCAATAGCCCAACGCACT 59.675 50.000 0.00 0.00 41.38 4.40
235 236 0.168788 CAATAGCCCAACGCACTGTG 59.831 55.000 2.76 2.76 41.38 3.66
245 246 2.094762 ACGCACTGTGTATTTCCTCC 57.905 50.000 9.86 0.00 0.00 4.30
246 247 1.623811 ACGCACTGTGTATTTCCTCCT 59.376 47.619 9.86 0.00 0.00 3.69
247 248 2.829720 ACGCACTGTGTATTTCCTCCTA 59.170 45.455 9.86 0.00 0.00 2.94
266 277 1.183549 AGAGCGTGACCTAAATCGGT 58.816 50.000 0.00 0.00 40.80 4.69
272 283 1.518774 GACCTAAATCGGTCGGCCA 59.481 57.895 6.96 0.00 43.56 5.36
287 298 2.358737 CCACCGCTTGACCAGACC 60.359 66.667 0.00 0.00 0.00 3.85
288 299 2.743718 CACCGCTTGACCAGACCT 59.256 61.111 0.00 0.00 0.00 3.85
296 307 0.840722 TTGACCAGACCTTCCCCTCC 60.841 60.000 0.00 0.00 0.00 4.30
299 310 2.456840 CAGACCTTCCCCTCCCCT 59.543 66.667 0.00 0.00 0.00 4.79
325 336 0.900647 CACTCCCTCCCTCTCGTTGT 60.901 60.000 0.00 0.00 0.00 3.32
330 341 3.685214 CTCCCTCTCGTTGTCGCCG 62.685 68.421 0.00 0.00 36.96 6.46
350 362 4.113815 CCTCCGCTCAATGGCCCA 62.114 66.667 0.00 0.00 0.00 5.36
354 366 2.717485 CGCTCAATGGCCCAATCG 59.283 61.111 0.00 0.00 0.00 3.34
782 794 2.670251 CGGGGCCGCTTTGTTGTA 60.670 61.111 18.79 0.00 0.00 2.41
788 800 1.607148 GGCCGCTTTGTTGTAAGACTT 59.393 47.619 0.00 0.00 0.00 3.01
803 815 8.798153 GTTGTAAGACTTTGATTGAACAACTTG 58.202 33.333 15.72 0.00 41.22 3.16
806 818 6.515272 AGACTTTGATTGAACAACTTGTGT 57.485 33.333 0.00 0.00 44.64 3.72
829 841 9.730420 GTGTTATTCTTTTGCCAAATATCGTAT 57.270 29.630 0.00 0.00 0.00 3.06
857 882 8.936070 TGAGATTTGGATTATGCAGATTTTTG 57.064 30.769 0.00 0.00 0.00 2.44
861 886 9.763465 GATTTGGATTATGCAGATTTTTGTTTG 57.237 29.630 0.00 0.00 0.00 2.93
871 896 5.051816 CAGATTTTTGTTTGGAGTGTGCAT 58.948 37.500 0.00 0.00 0.00 3.96
873 898 6.869913 CAGATTTTTGTTTGGAGTGTGCATAT 59.130 34.615 0.00 0.00 0.00 1.78
878 903 3.758023 TGTTTGGAGTGTGCATATCCTTG 59.242 43.478 13.85 0.00 34.04 3.61
880 905 3.548745 TGGAGTGTGCATATCCTTGAG 57.451 47.619 13.85 0.00 34.04 3.02
881 906 3.106827 TGGAGTGTGCATATCCTTGAGA 58.893 45.455 13.85 0.00 34.04 3.27
882 907 3.713248 TGGAGTGTGCATATCCTTGAGAT 59.287 43.478 13.85 0.00 39.15 2.75
883 908 4.901250 TGGAGTGTGCATATCCTTGAGATA 59.099 41.667 13.85 0.00 41.73 1.98
884 909 5.011431 TGGAGTGTGCATATCCTTGAGATAG 59.989 44.000 13.85 0.00 40.82 2.08
886 911 6.463614 GGAGTGTGCATATCCTTGAGATAGTT 60.464 42.308 7.38 0.00 40.82 2.24
887 912 6.520272 AGTGTGCATATCCTTGAGATAGTTC 58.480 40.000 0.00 0.00 40.82 3.01
888 913 6.098838 AGTGTGCATATCCTTGAGATAGTTCA 59.901 38.462 0.00 0.00 40.82 3.18
889 914 6.933521 GTGTGCATATCCTTGAGATAGTTCAT 59.066 38.462 0.00 0.00 40.82 2.57
890 915 8.090831 GTGTGCATATCCTTGAGATAGTTCATA 58.909 37.037 0.00 0.00 40.82 2.15
891 916 8.090831 TGTGCATATCCTTGAGATAGTTCATAC 58.909 37.037 0.00 0.00 40.82 2.39
892 917 7.547370 GTGCATATCCTTGAGATAGTTCATACC 59.453 40.741 0.00 0.00 40.82 2.73
901 926 5.905331 TGAGATAGTTCATACCATGGGAGTT 59.095 40.000 18.09 0.00 0.00 3.01
902 927 6.042093 TGAGATAGTTCATACCATGGGAGTTC 59.958 42.308 18.09 0.00 0.00 3.01
1006 1051 0.107459 GAGTTCTGGTGGGATGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
1067 1112 3.381045 CTTTTCAAAAACCTCGCCCTTC 58.619 45.455 0.00 0.00 0.00 3.46
1071 1116 0.187606 AAAAACCTCGCCCTTCCCTT 59.812 50.000 0.00 0.00 0.00 3.95
1072 1117 0.251209 AAAACCTCGCCCTTCCCTTC 60.251 55.000 0.00 0.00 0.00 3.46
1073 1118 2.138453 AAACCTCGCCCTTCCCTTCC 62.138 60.000 0.00 0.00 0.00 3.46
1074 1119 3.798511 CCTCGCCCTTCCCTTCCC 61.799 72.222 0.00 0.00 0.00 3.97
1075 1120 3.798511 CTCGCCCTTCCCTTCCCC 61.799 72.222 0.00 0.00 0.00 4.81
1098 1143 0.916358 CCTGGTTCATCTCCCCCTGT 60.916 60.000 0.00 0.00 0.00 4.00
1131 1176 1.514228 GCGCGACTCTCGTCAATCA 60.514 57.895 12.10 0.00 42.81 2.57
1350 1567 3.465403 CCGTCTCCTCCCCAGCAG 61.465 72.222 0.00 0.00 0.00 4.24
1381 1598 1.605451 TCGCCGGACAAGGAGAAGA 60.605 57.895 5.05 0.00 37.16 2.87
1488 1705 1.810030 GTCCAGATCAACGGACGCC 60.810 63.158 11.76 0.00 42.19 5.68
1699 1916 0.663568 CGACGTAAGCATCCGATCCC 60.664 60.000 0.00 0.00 45.62 3.85
1701 1918 1.046472 ACGTAAGCATCCGATCCCCA 61.046 55.000 0.00 0.00 45.62 4.96
1708 1932 0.541392 CATCCGATCCCCAACTCACA 59.459 55.000 0.00 0.00 0.00 3.58
1732 1964 2.420547 CGATTCCTTCCTTCCTCATGCA 60.421 50.000 0.00 0.00 0.00 3.96
1733 1965 2.795231 TTCCTTCCTTCCTCATGCAG 57.205 50.000 0.00 0.00 0.00 4.41
1735 1967 0.750911 CCTTCCTTCCTCATGCAGGC 60.751 60.000 0.00 0.00 43.08 4.85
1736 1968 1.078214 TTCCTTCCTCATGCAGGCG 60.078 57.895 0.00 0.00 43.08 5.52
1737 1969 3.207669 CCTTCCTCATGCAGGCGC 61.208 66.667 0.00 0.00 43.08 6.53
1738 1970 2.124819 CTTCCTCATGCAGGCGCT 60.125 61.111 7.64 0.00 43.08 5.92
1739 1971 2.437180 TTCCTCATGCAGGCGCTG 60.437 61.111 7.64 4.78 43.08 5.18
1740 1972 3.258228 TTCCTCATGCAGGCGCTGT 62.258 57.895 7.64 0.00 43.08 4.40
1741 1973 3.506096 CCTCATGCAGGCGCTGTG 61.506 66.667 7.64 6.65 39.64 3.66
1742 1974 4.175489 CTCATGCAGGCGCTGTGC 62.175 66.667 23.16 23.16 45.38 4.57
1746 1978 4.045771 TGCAGGCGCTGTGCATTG 62.046 61.111 27.04 13.15 45.96 2.82
1753 1985 2.830772 GCGCTGTGCATTGATTAAGA 57.169 45.000 8.57 0.00 45.45 2.10
1754 1986 2.713011 GCGCTGTGCATTGATTAAGAG 58.287 47.619 8.57 0.00 45.45 2.85
1755 1987 2.352651 GCGCTGTGCATTGATTAAGAGA 59.647 45.455 8.57 0.00 45.45 3.10
1756 1988 3.003068 GCGCTGTGCATTGATTAAGAGAT 59.997 43.478 8.57 0.00 45.45 2.75
1757 1989 4.770287 CGCTGTGCATTGATTAAGAGATC 58.230 43.478 0.00 0.00 0.00 2.75
1758 1990 4.510711 CGCTGTGCATTGATTAAGAGATCT 59.489 41.667 0.00 0.00 0.00 2.75
1940 2181 5.859495 TGTTTCCAACAAAGTTGGTTCTTT 58.141 33.333 23.74 0.00 38.72 2.52
1948 2189 7.360017 CCAACAAAGTTGGTTCTTTTTCTTCAC 60.360 37.037 18.37 0.00 35.77 3.18
2031 2272 2.165998 GCAACTTCTCAATTGCTCCCT 58.834 47.619 0.00 0.00 46.21 4.20
2058 2301 4.574674 TTCTTCCTGTGATGGCTAACAT 57.425 40.909 0.00 0.00 44.18 2.71
2118 2361 2.912956 AGGTAGAGGACAGCAAATTGGA 59.087 45.455 0.00 0.00 0.00 3.53
2160 2403 5.646360 AGTGGTTTTGTATACAGATTTCCCG 59.354 40.000 5.56 0.00 0.00 5.14
2203 2446 4.635765 CGATGGGAAAGTTTATGCTTCAGA 59.364 41.667 0.00 0.00 0.00 3.27
2217 2460 3.181482 TGCTTCAGAGTGCTAGCTATGTC 60.181 47.826 17.23 7.14 34.77 3.06
2224 2467 2.496070 AGTGCTAGCTATGTCGGTTTGA 59.504 45.455 17.23 0.00 0.00 2.69
2297 2540 6.389906 GGAAGCAGCTATGTTTTGTACATTT 58.610 36.000 0.00 0.00 45.19 2.32
2298 2541 6.308766 GGAAGCAGCTATGTTTTGTACATTTG 59.691 38.462 0.00 0.00 45.19 2.32
2356 2599 6.303839 TGGAAGTGAAAGTAATAGGTGCTTT 58.696 36.000 0.00 0.00 43.96 3.51
2466 2709 7.509141 TTATCAGACAAAGTTTGCATCTTGA 57.491 32.000 15.59 11.70 0.00 3.02
2479 2722 6.992063 TTGCATCTTGACTTATCTCCTTTC 57.008 37.500 0.00 0.00 0.00 2.62
2522 2835 9.883142 AAAGTTTTCTTTCACATTTATTGACCA 57.117 25.926 0.00 0.00 45.77 4.02
2604 2917 4.156556 GCTGCATGACATTCTTACCTTCAA 59.843 41.667 0.00 0.00 0.00 2.69
2646 2960 6.025749 TGTGGTGTTACATTTGTTGTTTCA 57.974 33.333 0.00 0.00 39.87 2.69
2681 3026 3.681593 GCCATCACCCTGTTTTACAGTA 58.318 45.455 6.13 0.00 44.50 2.74
2760 3107 7.379529 GTGTTCTTGAGGATGTTTACATGTTTG 59.620 37.037 2.30 0.00 36.57 2.93
2768 3115 8.181904 AGGATGTTTACATGTTTGTTGAGATT 57.818 30.769 2.30 0.00 36.57 2.40
2770 3117 7.867403 GGATGTTTACATGTTTGTTGAGATTGT 59.133 33.333 2.30 0.00 36.57 2.71
2879 3226 0.889306 AGCTCGAGACCAGGTTGTAC 59.111 55.000 18.75 0.00 0.00 2.90
2880 3227 0.108756 GCTCGAGACCAGGTTGTACC 60.109 60.000 18.75 0.00 38.99 3.34
2942 3291 7.461749 TCTCCATAGTTATCCATTCATTTCCC 58.538 38.462 0.00 0.00 0.00 3.97
2946 3295 8.579863 CCATAGTTATCCATTCATTTCCCTTTC 58.420 37.037 0.00 0.00 0.00 2.62
2959 3308 8.491045 TCATTTCCCTTTCCTTATTTCACTTT 57.509 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.656542 GGTGAAGCTTCCATATTTACTACCTAC 59.343 40.741 23.42 8.67 0.00 3.18
43 44 6.046593 CACGGTGAAGCTTCCATATTTACTA 58.953 40.000 23.42 0.00 0.00 1.82
67 68 0.590195 CTCATGGCCGAATAAGCTGC 59.410 55.000 0.00 0.00 0.00 5.25
69 70 1.486310 TGTCTCATGGCCGAATAAGCT 59.514 47.619 0.00 0.00 0.00 3.74
70 71 1.599542 GTGTCTCATGGCCGAATAAGC 59.400 52.381 0.00 0.00 0.00 3.09
77 78 1.300971 CCTTGTGTGTCTCATGGCCG 61.301 60.000 0.00 0.00 0.00 6.13
79 80 0.250901 ACCCTTGTGTGTCTCATGGC 60.251 55.000 0.00 0.00 0.00 4.40
82 83 2.705658 TCAGAACCCTTGTGTGTCTCAT 59.294 45.455 0.00 0.00 0.00 2.90
103 104 0.322456 CCCATGATGAACCCACACGT 60.322 55.000 0.00 0.00 0.00 4.49
151 152 3.251004 GTGACAAATTCTGAGTGGGTCAC 59.749 47.826 16.18 16.18 44.35 3.67
154 155 3.576078 TGTGACAAATTCTGAGTGGGT 57.424 42.857 0.00 0.00 0.00 4.51
190 191 7.007723 AGTTATTAGGATTGTGGGTTTGTCAA 58.992 34.615 0.00 0.00 0.00 3.18
191 192 6.548321 AGTTATTAGGATTGTGGGTTTGTCA 58.452 36.000 0.00 0.00 0.00 3.58
192 193 6.657541 TGAGTTATTAGGATTGTGGGTTTGTC 59.342 38.462 0.00 0.00 0.00 3.18
197 198 6.998673 GCTATTGAGTTATTAGGATTGTGGGT 59.001 38.462 0.00 0.00 0.00 4.51
205 206 5.607477 CGTTGGGCTATTGAGTTATTAGGA 58.393 41.667 0.00 0.00 0.00 2.94
211 212 2.027561 AGTGCGTTGGGCTATTGAGTTA 60.028 45.455 0.00 0.00 44.05 2.24
215 216 0.036164 ACAGTGCGTTGGGCTATTGA 59.964 50.000 0.00 0.00 44.05 2.57
216 217 0.168788 CACAGTGCGTTGGGCTATTG 59.831 55.000 0.00 0.00 44.05 1.90
232 233 3.130516 CACGCTCTAGGAGGAAATACACA 59.869 47.826 0.00 0.00 0.00 3.72
235 236 3.243468 GGTCACGCTCTAGGAGGAAATAC 60.243 52.174 0.00 0.00 0.00 1.89
245 246 2.358267 ACCGATTTAGGTCACGCTCTAG 59.642 50.000 0.00 0.00 41.46 2.43
246 247 2.372264 ACCGATTTAGGTCACGCTCTA 58.628 47.619 0.00 0.00 41.46 2.43
247 248 1.183549 ACCGATTTAGGTCACGCTCT 58.816 50.000 0.00 0.00 41.46 4.09
272 283 1.371558 GAAGGTCTGGTCAAGCGGT 59.628 57.895 0.00 0.00 0.00 5.68
279 290 1.996187 GGGAGGGGAAGGTCTGGTC 60.996 68.421 0.00 0.00 0.00 4.02
303 314 3.151022 GAGAGGGAGGGAGTGGCG 61.151 72.222 0.00 0.00 0.00 5.69
309 320 1.677966 CGACAACGAGAGGGAGGGA 60.678 63.158 0.00 0.00 42.66 4.20
767 779 0.240145 GTCTTACAACAAAGCGGCCC 59.760 55.000 0.00 0.00 0.00 5.80
768 780 1.235724 AGTCTTACAACAAAGCGGCC 58.764 50.000 0.00 0.00 0.00 6.13
782 794 6.924111 ACACAAGTTGTTCAATCAAAGTCTT 58.076 32.000 5.57 0.00 33.09 3.01
803 815 9.730420 ATACGATATTTGGCAAAAGAATAACAC 57.270 29.630 17.70 1.31 0.00 3.32
835 859 9.763465 CAAACAAAAATCTGCATAATCCAAATC 57.237 29.630 0.00 0.00 0.00 2.17
857 882 4.009675 TCAAGGATATGCACACTCCAAAC 58.990 43.478 12.22 0.00 0.00 2.93
861 886 3.827008 TCTCAAGGATATGCACACTCC 57.173 47.619 0.00 0.00 0.00 3.85
871 896 7.180946 CCCATGGTATGAACTATCTCAAGGATA 59.819 40.741 11.73 0.00 35.98 2.59
873 898 5.307976 CCCATGGTATGAACTATCTCAAGGA 59.692 44.000 11.73 0.00 0.00 3.36
878 903 6.426646 AACTCCCATGGTATGAACTATCTC 57.573 41.667 11.73 0.00 0.00 2.75
880 905 5.071788 TGGAACTCCCATGGTATGAACTATC 59.928 44.000 11.73 0.00 40.82 2.08
881 906 4.975147 TGGAACTCCCATGGTATGAACTAT 59.025 41.667 11.73 0.00 40.82 2.12
882 907 4.367166 TGGAACTCCCATGGTATGAACTA 58.633 43.478 11.73 0.00 40.82 2.24
883 908 3.189606 TGGAACTCCCATGGTATGAACT 58.810 45.455 11.73 0.00 40.82 3.01
884 909 3.644966 TGGAACTCCCATGGTATGAAC 57.355 47.619 11.73 0.00 40.82 3.18
886 911 3.308832 GGTTTGGAACTCCCATGGTATGA 60.309 47.826 11.73 0.00 46.10 2.15
887 912 3.023832 GGTTTGGAACTCCCATGGTATG 58.976 50.000 11.73 2.61 46.10 2.39
888 913 2.024369 GGGTTTGGAACTCCCATGGTAT 60.024 50.000 11.73 0.00 46.10 2.73
889 914 1.356398 GGGTTTGGAACTCCCATGGTA 59.644 52.381 11.73 0.00 46.10 3.25
890 915 0.114364 GGGTTTGGAACTCCCATGGT 59.886 55.000 11.73 0.00 46.10 3.55
891 916 0.114168 TGGGTTTGGAACTCCCATGG 59.886 55.000 4.14 4.14 46.10 3.66
892 917 3.763931 TGGGTTTGGAACTCCCATG 57.236 52.632 0.00 0.00 46.10 3.66
978 1023 4.821589 CCAGAACTCGGCCGCCTC 62.822 72.222 23.51 16.31 0.00 4.70
1067 1112 3.910646 AACCAGGGGAGGGGAAGGG 62.911 68.421 0.00 0.00 0.00 3.95
1071 1116 1.307866 GATGAACCAGGGGAGGGGA 60.308 63.158 0.00 0.00 0.00 4.81
1072 1117 1.308216 AGATGAACCAGGGGAGGGG 60.308 63.158 0.00 0.00 0.00 4.79
1073 1118 1.348775 GGAGATGAACCAGGGGAGGG 61.349 65.000 0.00 0.00 0.00 4.30
1074 1119 1.348775 GGGAGATGAACCAGGGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
1075 1120 1.348775 GGGGAGATGAACCAGGGGAG 61.349 65.000 0.00 0.00 0.00 4.30
1131 1176 0.250038 CCGCCATGAGAACCATCGAT 60.250 55.000 0.00 0.00 31.94 3.59
1242 1459 1.078143 GAAGCAATCGAGTGGGGCT 60.078 57.895 15.48 2.36 36.13 5.19
1243 1460 1.078143 AGAAGCAATCGAGTGGGGC 60.078 57.895 15.48 0.00 0.00 5.80
1244 1461 0.462759 GGAGAAGCAATCGAGTGGGG 60.463 60.000 15.48 0.00 0.00 4.96
1245 1462 0.539051 AGGAGAAGCAATCGAGTGGG 59.461 55.000 15.48 0.00 0.00 4.61
1246 1463 2.275318 GAAGGAGAAGCAATCGAGTGG 58.725 52.381 15.48 0.00 0.00 4.00
1247 1464 2.670414 GTGAAGGAGAAGCAATCGAGTG 59.330 50.000 8.83 8.83 0.00 3.51
1248 1465 2.354203 GGTGAAGGAGAAGCAATCGAGT 60.354 50.000 0.00 0.00 0.00 4.18
1462 1679 0.462047 GTTGATCTGGACGCGGGATT 60.462 55.000 12.47 0.00 0.00 3.01
1699 1916 1.742761 AGGAATCGCATGTGAGTTGG 58.257 50.000 15.24 0.00 0.00 3.77
1701 1918 2.026822 AGGAAGGAATCGCATGTGAGTT 60.027 45.455 15.24 9.03 0.00 3.01
1708 1932 1.839994 TGAGGAAGGAAGGAATCGCAT 59.160 47.619 0.00 0.00 0.00 4.73
1732 1964 1.402968 CTTAATCAATGCACAGCGCCT 59.597 47.619 2.29 0.00 41.33 5.52
1733 1965 1.401552 TCTTAATCAATGCACAGCGCC 59.598 47.619 2.29 0.00 41.33 6.53
1735 1967 4.510711 AGATCTCTTAATCAATGCACAGCG 59.489 41.667 0.00 0.00 0.00 5.18
1736 1968 7.603404 AGATAGATCTCTTAATCAATGCACAGC 59.397 37.037 0.00 0.00 29.30 4.40
1737 1969 9.491675 AAGATAGATCTCTTAATCAATGCACAG 57.508 33.333 0.00 0.00 35.76 3.66
1738 1970 9.269453 CAAGATAGATCTCTTAATCAATGCACA 57.731 33.333 0.00 0.00 35.76 4.57
1739 1971 8.719648 CCAAGATAGATCTCTTAATCAATGCAC 58.280 37.037 0.00 0.00 35.76 4.57
1740 1972 7.881751 CCCAAGATAGATCTCTTAATCAATGCA 59.118 37.037 0.00 0.00 35.76 3.96
1741 1973 7.882271 ACCCAAGATAGATCTCTTAATCAATGC 59.118 37.037 0.00 0.00 35.76 3.56
1742 1974 9.434420 GACCCAAGATAGATCTCTTAATCAATG 57.566 37.037 0.00 0.81 35.76 2.82
1743 1975 8.601546 GGACCCAAGATAGATCTCTTAATCAAT 58.398 37.037 0.00 0.00 35.76 2.57
1744 1976 7.255977 CGGACCCAAGATAGATCTCTTAATCAA 60.256 40.741 0.00 0.00 35.76 2.57
1745 1977 6.209589 CGGACCCAAGATAGATCTCTTAATCA 59.790 42.308 0.00 0.00 35.76 2.57
1746 1978 6.626302 CGGACCCAAGATAGATCTCTTAATC 58.374 44.000 0.00 0.00 35.76 1.75
1747 1979 5.046950 GCGGACCCAAGATAGATCTCTTAAT 60.047 44.000 0.00 0.00 35.76 1.40
1748 1980 4.281182 GCGGACCCAAGATAGATCTCTTAA 59.719 45.833 0.00 0.00 35.76 1.85
1749 1981 3.827302 GCGGACCCAAGATAGATCTCTTA 59.173 47.826 0.00 0.00 35.76 2.10
1750 1982 2.630580 GCGGACCCAAGATAGATCTCTT 59.369 50.000 0.00 0.00 35.76 2.85
1751 1983 2.243810 GCGGACCCAAGATAGATCTCT 58.756 52.381 0.00 0.00 35.76 3.10
1752 1984 1.273886 GGCGGACCCAAGATAGATCTC 59.726 57.143 0.00 0.00 35.76 2.75
1753 1985 1.133009 AGGCGGACCCAAGATAGATCT 60.133 52.381 0.00 0.00 35.91 2.75
1754 1986 1.273886 GAGGCGGACCCAAGATAGATC 59.726 57.143 0.00 0.00 36.11 2.75
1755 1987 1.343069 GAGGCGGACCCAAGATAGAT 58.657 55.000 0.00 0.00 36.11 1.98
1756 1988 1.107538 CGAGGCGGACCCAAGATAGA 61.108 60.000 0.00 0.00 36.11 1.98
1757 1989 1.364171 CGAGGCGGACCCAAGATAG 59.636 63.158 0.00 0.00 36.11 2.08
1758 1990 3.533720 CGAGGCGGACCCAAGATA 58.466 61.111 0.00 0.00 36.11 1.98
1782 2015 4.987912 CCAAGGAGCGAGAATCTCTTAATC 59.012 45.833 8.77 1.24 24.78 1.75
1894 2135 1.227263 CCTAACTGATGGGTCGGCG 60.227 63.158 0.00 0.00 33.84 6.46
1940 2181 2.904011 AACAAACGCACGTGAAGAAA 57.096 40.000 22.23 0.00 0.00 2.52
1948 2189 2.108700 CAAGAGGAAAACAAACGCACG 58.891 47.619 0.00 0.00 0.00 5.34
2031 2272 5.441718 AGCCATCACAGGAAGAAAGATAA 57.558 39.130 0.00 0.00 0.00 1.75
2058 2301 0.106569 CAGTAATGGGCATCAGGGCA 60.107 55.000 0.00 0.00 45.66 5.36
2118 2361 5.342866 ACCACTCAAGGAACCTAACTAGAT 58.657 41.667 0.00 0.00 0.00 1.98
2160 2403 2.413453 CGTTCTGGCAGCTCTTCTAAAC 59.587 50.000 10.34 5.53 0.00 2.01
2203 2446 2.496070 TCAAACCGACATAGCTAGCACT 59.504 45.455 18.83 0.00 0.00 4.40
2217 2460 4.250464 TGCAGGAACTATACTTCAAACCG 58.750 43.478 0.00 0.00 36.02 4.44
2224 2467 4.559862 ACAAGCTGCAGGAACTATACTT 57.440 40.909 17.12 4.46 36.02 2.24
2297 2540 8.731605 TGTCCAACGCTATTTGATAATTTAACA 58.268 29.630 0.00 0.00 0.00 2.41
2298 2541 9.730420 ATGTCCAACGCTATTTGATAATTTAAC 57.270 29.630 0.00 0.00 0.00 2.01
2315 2558 2.364632 TCCAATTAGCCATGTCCAACG 58.635 47.619 0.00 0.00 0.00 4.10
2466 2709 9.520515 AAACATTACACATGAAAGGAGATAAGT 57.479 29.630 0.00 0.00 0.00 2.24
2479 2722 9.520204 AGAAAACTTTCAGAAACATTACACATG 57.480 29.630 5.07 0.00 39.61 3.21
2604 2917 7.829211 ACACCACATCTACAAGTATAAGCATTT 59.171 33.333 0.00 0.00 0.00 2.32
2621 2935 6.754209 TGAAACAACAAATGTAACACCACATC 59.246 34.615 0.00 0.00 42.99 3.06
2625 2939 6.071896 TGTCTGAAACAACAAATGTAACACCA 60.072 34.615 0.00 0.00 42.99 4.17
2646 2960 2.599645 GATGGCGGGTGAGCATGTCT 62.600 60.000 0.00 0.00 39.27 3.41
2701 3048 4.867047 AGAATGCTTTGTCATACTCACGAG 59.133 41.667 0.00 0.00 0.00 4.18
2704 3051 4.697352 ACCAGAATGCTTTGTCATACTCAC 59.303 41.667 0.00 0.00 31.97 3.51
2768 3115 5.375773 TCCATCAGTGTTTGAATGAGAACA 58.624 37.500 0.00 0.00 39.77 3.18
2770 3117 6.298361 TCTTCCATCAGTGTTTGAATGAGAA 58.702 36.000 0.00 0.00 39.77 2.87
2776 3123 8.762645 AGTATCTATCTTCCATCAGTGTTTGAA 58.237 33.333 0.00 0.00 39.77 2.69
2777 3124 8.311395 AGTATCTATCTTCCATCAGTGTTTGA 57.689 34.615 0.00 0.00 40.85 2.69
2778 3125 7.380870 CGAGTATCTATCTTCCATCAGTGTTTG 59.619 40.741 0.00 0.00 0.00 2.93
2779 3126 7.068839 ACGAGTATCTATCTTCCATCAGTGTTT 59.931 37.037 0.00 0.00 0.00 2.83
2780 3127 6.547880 ACGAGTATCTATCTTCCATCAGTGTT 59.452 38.462 0.00 0.00 0.00 3.32
2781 3128 6.065374 ACGAGTATCTATCTTCCATCAGTGT 58.935 40.000 0.00 0.00 0.00 3.55
2782 3129 6.567687 ACGAGTATCTATCTTCCATCAGTG 57.432 41.667 0.00 0.00 0.00 3.66
2817 3164 1.336125 GCCAAAGAGTCATGCTATGCC 59.664 52.381 0.00 0.00 0.00 4.40
2879 3226 4.148128 ACACAGATAAGCAGGAGATTGG 57.852 45.455 0.00 0.00 0.00 3.16
2880 3227 6.765036 ACATAACACAGATAAGCAGGAGATTG 59.235 38.462 0.00 0.00 0.00 2.67
2942 3291 9.801873 TGAACAAGAAAAGTGAAATAAGGAAAG 57.198 29.630 0.00 0.00 0.00 2.62
2946 3295 7.869429 AGCATGAACAAGAAAAGTGAAATAAGG 59.131 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.