Multiple sequence alignment - TraesCS1A01G271700

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 TraesCS1A01G271700 chr1A 100.000 2951 0 0 1 2951 465281112 465284062 0.000000e+00 5450
1 TraesCS1A01G271700 chr1A 90.455 681 40 9 2278 2951 465301554 465302216 0.000000e+00 874
2 TraesCS1A01G271700 chr1A 76.685 356 58 17 1422 1765 465139905 465140247 1.090000e-39 174
3 TraesCS1A01G271700 chr1B 90.400 2448 118 42 459 2863 489992702 489995075 0.000000e+00 3110
4 TraesCS1A01G271700 chr1B 81.667 300 21 16 1 294 489992236 489992507 4.950000e-53 219
5 TraesCS1A01G271700 chr1B 94.690 113 5 1 311 422 489992492 489992604 1.090000e-39 174
6 TraesCS1A01G271700 chr1D 88.626 2576 164 58 419 2951 366018142 366020631 0.000000e+00 3014
7 TraesCS1A01G271700 chr1D 83.525 261 16 13 39 294 366017725 366017963 4.950000e-53 219
8 TraesCS1A01G271700 chr1D 93.043 115 6 2 313 425 366017950 366018064 1.820000e-37 167


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 TraesCS1A01G271700 chr1A 465281112 465284062 2950 False 5450.000000 5450 100.000 1 2951 1 chr1A.!!$F2 2950
1 TraesCS1A01G271700 chr1A 465301554 465302216 662 False 874.000000 874 90.455 2278 2951 1 chr1A.!!$F3 673
2 TraesCS1A01G271700 chr1B 489992236 489995075 2839 False 1167.666667 3110 88.919 1 2863 3 chr1B.!!$F1 2862
3 TraesCS1A01G271700 chr1D 366017725 366020631 2906 False 1133.333333 3014 88.398 39 2951 3 chr1D.!!$F1 2912

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
926 1039 0.033504 GGTCACGCCTCTCAACTTGA 59.966 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 2960 0.103026 CATCAGATCGAACCGAGCCA 59.897 55.0 0.81 0.0 43.62 4.75 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
26 27 7.373493 CCTCTAATTTTCTGTTTGAATGCACT 58.627 34.615 0.00 0.00 34.24 4.40
28 29 7.077605 TCTAATTTTCTGTTTGAATGCACTCG 58.922 34.615 0.00 0.00 34.24 4.18
31 32 4.472691 TTCTGTTTGAATGCACTCGAAG 57.527 40.909 0.00 0.00 0.00 3.79
37 38 4.864916 TTGAATGCACTCGAAGCTATTC 57.135 40.909 17.63 17.63 33.81 1.75
40 41 1.645034 TGCACTCGAAGCTATTCTGC 58.355 50.000 10.42 0.00 35.66 4.26
52 53 6.183360 CGAAGCTATTCTGCAAATCCAAGTTA 60.183 38.462 0.00 0.00 32.93 2.24
54 55 7.269477 AGCTATTCTGCAAATCCAAGTTATC 57.731 36.000 0.00 0.00 34.99 1.75
81 82 5.277731 GGATTTGCTAGAGTTGCTCTTATGC 60.278 44.000 3.87 7.50 41.50 3.14
134 135 2.999355 GGCAAGAGCACTAGAGAACTTG 59.001 50.000 16.12 16.12 44.61 3.16
140 141 1.276421 GCACTAGAGAACTTGGCCAGA 59.724 52.381 5.11 0.00 0.00 3.86
141 142 2.093235 GCACTAGAGAACTTGGCCAGAT 60.093 50.000 5.11 0.00 0.00 2.90
142 143 3.529533 CACTAGAGAACTTGGCCAGATG 58.470 50.000 5.11 2.96 0.00 2.90
143 144 2.503356 ACTAGAGAACTTGGCCAGATGG 59.497 50.000 5.11 0.17 38.53 3.51
144 145 1.366319 AGAGAACTTGGCCAGATGGT 58.634 50.000 5.11 0.00 37.57 3.55
145 146 1.004044 AGAGAACTTGGCCAGATGGTG 59.996 52.381 5.11 0.00 37.57 4.17
146 147 0.610232 AGAACTTGGCCAGATGGTGC 60.610 55.000 5.11 2.77 37.57 5.01
152 153 4.421365 GCCAGATGGTGCCAAGAA 57.579 55.556 0.00 0.00 37.57 2.52
153 154 2.892025 GCCAGATGGTGCCAAGAAT 58.108 52.632 0.00 0.00 37.57 2.40
238 241 6.737044 AGTGCATACTGTTCGACTCCATCG 62.737 50.000 0.00 0.00 43.47 3.84
290 303 5.236282 CCAGCTGATCATGGTCTATACAAG 58.764 45.833 17.39 0.00 0.00 3.16
291 304 5.221601 CCAGCTGATCATGGTCTATACAAGT 60.222 44.000 17.39 0.00 0.00 3.16
292 305 5.695363 CAGCTGATCATGGTCTATACAAGTG 59.305 44.000 8.42 0.00 0.00 3.16
293 306 4.450419 GCTGATCATGGTCTATACAAGTGC 59.550 45.833 7.64 0.00 0.00 4.40
294 307 5.741383 GCTGATCATGGTCTATACAAGTGCT 60.741 44.000 7.64 0.00 0.00 4.40
295 308 5.847304 TGATCATGGTCTATACAAGTGCTC 58.153 41.667 7.64 0.00 0.00 4.26
296 309 5.363580 TGATCATGGTCTATACAAGTGCTCA 59.636 40.000 7.64 0.00 0.00 4.26
297 310 5.876651 TCATGGTCTATACAAGTGCTCAT 57.123 39.130 0.00 0.00 0.00 2.90
298 311 5.847304 TCATGGTCTATACAAGTGCTCATC 58.153 41.667 0.00 0.00 0.00 2.92
299 312 5.600069 TCATGGTCTATACAAGTGCTCATCT 59.400 40.000 0.00 0.00 0.00 2.90
300 313 6.777580 TCATGGTCTATACAAGTGCTCATCTA 59.222 38.462 0.00 0.00 0.00 1.98
301 314 7.287696 TCATGGTCTATACAAGTGCTCATCTAA 59.712 37.037 0.00 0.00 0.00 2.10
302 315 7.418337 TGGTCTATACAAGTGCTCATCTAAA 57.582 36.000 0.00 0.00 0.00 1.85
303 316 7.847096 TGGTCTATACAAGTGCTCATCTAAAA 58.153 34.615 0.00 0.00 0.00 1.52
304 317 8.318412 TGGTCTATACAAGTGCTCATCTAAAAA 58.682 33.333 0.00 0.00 0.00 1.94
413 426 3.916061 TTGCGTTGCAAGTTGACTC 57.084 47.368 7.16 0.00 43.99 3.36
425 523 4.511527 CAAGTTGACTCTGCCATCACTAT 58.488 43.478 0.00 0.00 0.00 2.12
456 554 8.442374 TCAGGTAAAGTTAGGTGTCCTTTTATT 58.558 33.333 0.00 0.00 34.61 1.40
458 556 9.074576 AGGTAAAGTTAGGTGTCCTTTTATTTG 57.925 33.333 0.00 0.00 34.61 2.32
459 557 8.301720 GGTAAAGTTAGGTGTCCTTTTATTTGG 58.698 37.037 0.00 0.00 34.61 3.28
564 664 1.228552 AAGCATTGGCCTTCACCGT 60.229 52.632 3.32 0.00 42.56 4.83
575 675 0.508641 CTTCACCGTGAAGTGCTTCG 59.491 55.000 26.74 6.58 46.50 3.79
576 676 1.495584 TTCACCGTGAAGTGCTTCGC 61.496 55.000 9.99 13.68 44.25 4.70
590 690 4.982916 AGTGCTTCGCTAAAATATCTACCG 59.017 41.667 0.00 0.00 0.00 4.02
599 699 0.105964 AATATCTACCGGCGCTGCAA 59.894 50.000 11.81 0.00 0.00 4.08
654 754 0.244721 GCTTACGTACGTGTCCCCTT 59.755 55.000 30.25 3.43 0.00 3.95
687 787 3.252215 TCAAGTTGGCATCAAAGTAACCG 59.748 43.478 2.34 0.00 34.28 4.44
703 803 0.802494 ACCGCGTCATTTTCATCACC 59.198 50.000 4.92 0.00 0.00 4.02
711 811 2.945008 TCATTTTCATCACCGATCAGCC 59.055 45.455 0.00 0.00 0.00 4.85
888 999 2.500509 GACCTCATCGGCTTACTCTG 57.499 55.000 0.00 0.00 35.61 3.35
890 1001 0.749649 CCTCATCGGCTTACTCTGCT 59.250 55.000 0.00 0.00 0.00 4.24
911 1024 2.582272 GCATCAGCCCATTTGGTCA 58.418 52.632 0.00 0.00 36.04 4.02
912 1025 0.174162 GCATCAGCCCATTTGGTCAC 59.826 55.000 0.00 0.00 36.04 3.67
914 1027 1.315257 ATCAGCCCATTTGGTCACGC 61.315 55.000 0.00 0.00 36.04 5.34
915 1028 2.676471 AGCCCATTTGGTCACGCC 60.676 61.111 0.00 0.00 36.04 5.68
916 1029 2.676471 GCCCATTTGGTCACGCCT 60.676 61.111 0.00 0.00 38.35 5.52
917 1030 2.700773 GCCCATTTGGTCACGCCTC 61.701 63.158 0.00 0.00 38.35 4.70
918 1031 1.002134 CCCATTTGGTCACGCCTCT 60.002 57.895 0.00 0.00 38.35 3.69
919 1032 1.026718 CCCATTTGGTCACGCCTCTC 61.027 60.000 0.00 0.00 38.35 3.20
920 1033 0.321564 CCATTTGGTCACGCCTCTCA 60.322 55.000 0.00 0.00 38.35 3.27
921 1034 1.522668 CATTTGGTCACGCCTCTCAA 58.477 50.000 0.00 0.00 38.35 3.02
922 1035 1.197721 CATTTGGTCACGCCTCTCAAC 59.802 52.381 0.00 0.00 38.35 3.18
923 1036 0.468226 TTTGGTCACGCCTCTCAACT 59.532 50.000 0.00 0.00 38.35 3.16
924 1037 0.468226 TTGGTCACGCCTCTCAACTT 59.532 50.000 0.00 0.00 38.35 2.66
925 1038 0.249868 TGGTCACGCCTCTCAACTTG 60.250 55.000 0.00 0.00 38.35 3.16
926 1039 0.033504 GGTCACGCCTCTCAACTTGA 59.966 55.000 0.00 0.00 0.00 3.02
927 1040 1.423395 GTCACGCCTCTCAACTTGAG 58.577 55.000 12.02 12.02 45.59 3.02
949 1062 0.250234 CTCAAGTCTTCGCCCATCCA 59.750 55.000 0.00 0.00 0.00 3.41
954 1067 0.598680 GTCTTCGCCCATCCATCTCG 60.599 60.000 0.00 0.00 0.00 4.04
983 1096 1.142748 GTCTGGGAGACATCGGCTG 59.857 63.158 0.00 0.00 44.45 4.85
1035 1148 2.728383 GTCGTGTCCGTCGTGGTG 60.728 66.667 0.00 0.00 39.52 4.17
1041 1154 1.447314 GTCCGTCGTGGTGGGATTC 60.447 63.158 0.00 0.00 39.52 2.52
1103 1216 2.159085 GCACCAAGCTCGAGGTAAGTAT 60.159 50.000 18.94 0.00 41.15 2.12
1120 1233 3.444916 AGTATACGCTTGTGTTCATCCG 58.555 45.455 0.00 0.00 0.00 4.18
1165 1281 0.745845 ACATCGGGATGCTTGTGCTC 60.746 55.000 8.53 0.00 42.39 4.26
1389 1505 1.142748 CGTCCTCTCATGGTGAGCC 59.857 63.158 10.01 3.99 43.95 4.70
1427 1543 0.248907 GATTCGATCCAGGCGACGAA 60.249 55.000 14.24 14.24 45.88 3.85
1455 1580 2.334977 ACGGGGGATGAATATGCTGTA 58.665 47.619 0.00 0.00 0.00 2.74
1863 1996 2.961893 AAACGCGCAGGGGTATGGA 61.962 57.895 5.73 0.00 42.22 3.41
1864 1997 2.869503 AAACGCGCAGGGGTATGGAG 62.870 60.000 5.73 0.00 42.22 3.86
1865 1998 4.609018 CGCGCAGGGGTATGGAGG 62.609 72.222 8.75 0.00 36.55 4.30
1896 2029 2.363795 CCTGCTCAGGGGTACGGA 60.364 66.667 8.03 0.00 44.87 4.69
1899 2032 1.949847 CTGCTCAGGGGTACGGACAG 61.950 65.000 0.00 0.00 0.00 3.51
1910 2052 2.711883 TACGGACAGTTCCACCCCGA 62.712 60.000 0.00 0.00 43.00 5.14
1964 2106 2.159043 CCGTGTAGATTGATCACTGGCT 60.159 50.000 0.00 0.00 0.00 4.75
1970 2112 7.210174 GTGTAGATTGATCACTGGCTTATGTA 58.790 38.462 0.00 0.00 0.00 2.29
1971 2113 7.383572 GTGTAGATTGATCACTGGCTTATGTAG 59.616 40.741 0.00 0.00 0.00 2.74
1972 2114 6.491714 AGATTGATCACTGGCTTATGTAGT 57.508 37.500 0.00 0.00 0.00 2.73
1973 2115 6.893583 AGATTGATCACTGGCTTATGTAGTT 58.106 36.000 0.00 0.00 0.00 2.24
1974 2116 8.023021 AGATTGATCACTGGCTTATGTAGTTA 57.977 34.615 0.00 0.00 0.00 2.24
1975 2117 8.654997 AGATTGATCACTGGCTTATGTAGTTAT 58.345 33.333 0.00 0.00 0.00 1.89
1977 2119 7.124573 TGATCACTGGCTTATGTAGTTATGT 57.875 36.000 0.00 0.00 0.00 2.29
1978 2120 6.986231 TGATCACTGGCTTATGTAGTTATGTG 59.014 38.462 0.00 0.00 0.00 3.21
1979 2121 5.116180 TCACTGGCTTATGTAGTTATGTGC 58.884 41.667 0.00 0.00 0.00 4.57
1980 2122 4.875536 CACTGGCTTATGTAGTTATGTGCA 59.124 41.667 0.00 0.00 0.00 4.57
1981 2123 5.353956 CACTGGCTTATGTAGTTATGTGCAA 59.646 40.000 0.00 0.00 0.00 4.08
1982 2124 5.586243 ACTGGCTTATGTAGTTATGTGCAAG 59.414 40.000 0.00 0.00 0.00 4.01
1983 2125 4.335315 TGGCTTATGTAGTTATGTGCAAGC 59.665 41.667 0.00 0.00 37.11 4.01
1984 2126 4.335315 GGCTTATGTAGTTATGTGCAAGCA 59.665 41.667 0.00 0.00 39.05 3.91
1985 2127 5.009010 GGCTTATGTAGTTATGTGCAAGCAT 59.991 40.000 0.00 0.00 39.05 3.79
1986 2128 5.911280 GCTTATGTAGTTATGTGCAAGCATG 59.089 40.000 0.00 0.00 37.63 4.06
1987 2129 6.458751 GCTTATGTAGTTATGTGCAAGCATGT 60.459 38.462 0.00 0.00 37.63 3.21
1988 2130 4.944962 TGTAGTTATGTGCAAGCATGTC 57.055 40.909 0.00 0.00 0.00 3.06
1989 2131 4.578871 TGTAGTTATGTGCAAGCATGTCT 58.421 39.130 0.00 2.01 0.00 3.41
1990 2132 5.003160 TGTAGTTATGTGCAAGCATGTCTT 58.997 37.500 0.00 0.00 34.78 3.01
2000 2142 4.778534 CAAGCATGTCTTGGTTCTTCAT 57.221 40.909 17.17 0.00 46.50 2.57
2001 2143 4.730657 CAAGCATGTCTTGGTTCTTCATC 58.269 43.478 17.17 0.00 46.50 2.92
2002 2144 4.298103 AGCATGTCTTGGTTCTTCATCT 57.702 40.909 0.00 0.00 29.87 2.90
2003 2145 5.426689 AGCATGTCTTGGTTCTTCATCTA 57.573 39.130 0.00 0.00 29.87 1.98
2007 2149 4.517285 TGTCTTGGTTCTTCATCTATGCC 58.483 43.478 0.00 0.00 0.00 4.40
2017 2159 5.371526 TCTTCATCTATGCCATGTTCTTCC 58.628 41.667 0.00 0.00 0.00 3.46
2022 2164 2.496899 ATGCCATGTTCTTCCGTCTT 57.503 45.000 0.00 0.00 0.00 3.01
2023 2165 1.808411 TGCCATGTTCTTCCGTCTTC 58.192 50.000 0.00 0.00 0.00 2.87
2024 2166 1.087501 GCCATGTTCTTCCGTCTTCC 58.912 55.000 0.00 0.00 0.00 3.46
2025 2167 1.610624 GCCATGTTCTTCCGTCTTCCA 60.611 52.381 0.00 0.00 0.00 3.53
2032 2176 5.800296 TGTTCTTCCGTCTTCCATAATTCA 58.200 37.500 0.00 0.00 0.00 2.57
2122 2267 2.754552 TGCTTGAAAGTGCAAACTGAGT 59.245 40.909 0.00 0.00 36.15 3.41
2173 2318 3.852471 TGATGCGACGAATTTTATCGG 57.148 42.857 0.00 0.00 46.82 4.18
2175 2320 3.244345 TGATGCGACGAATTTTATCGGTC 59.756 43.478 0.00 0.00 46.82 4.79
2200 2345 8.622157 TCTCGTTTATTACAAACATTTCACCAA 58.378 29.630 1.32 0.00 0.00 3.67
2213 2358 7.060383 ACATTTCACCAAATTTACATCCACA 57.940 32.000 0.00 0.00 28.97 4.17
2216 2361 5.703978 TCACCAAATTTACATCCACACAG 57.296 39.130 0.00 0.00 0.00 3.66
2218 2363 4.280677 CACCAAATTTACATCCACACAGGT 59.719 41.667 0.00 0.00 39.02 4.00
2219 2364 4.898861 ACCAAATTTACATCCACACAGGTT 59.101 37.500 0.00 0.00 39.02 3.50
2230 2375 2.290641 CCACACAGGTTAGCACAACTTC 59.709 50.000 1.81 0.00 0.00 3.01
2241 2389 0.588252 CACAACTTCCGCAGAACCAG 59.412 55.000 0.00 0.00 0.00 4.00
2253 2401 2.739379 GCAGAACCAGAAGCTAACTGAC 59.261 50.000 18.46 11.12 37.54 3.51
2269 2417 1.003116 CTGACAACTCTGCTGCACAAC 60.003 52.381 0.00 0.00 0.00 3.32
2310 2459 5.248248 TCTTGAGAGTTCAGAGAGAGAGAGA 59.752 44.000 0.00 0.00 34.15 3.10
2311 2460 5.089970 TGAGAGTTCAGAGAGAGAGAGAG 57.910 47.826 0.00 0.00 0.00 3.20
2777 2953 4.194720 CTCGGTTCTCGGCTCCGG 62.195 72.222 8.59 0.00 43.75 5.14
2779 2955 4.493747 CGGTTCTCGGCTCCGGTC 62.494 72.222 8.59 0.00 40.49 4.79
2780 2956 4.493747 GGTTCTCGGCTCCGGTCG 62.494 72.222 8.59 4.72 42.51 4.79
2785 2961 3.209812 TCGGCTCCGGTCGATCTG 61.210 66.667 8.59 0.00 45.01 2.90
2786 2962 4.271816 CGGCTCCGGTCGATCTGG 62.272 72.222 0.00 0.12 44.06 3.86
2787 2963 4.593864 GGCTCCGGTCGATCTGGC 62.594 72.222 0.00 2.71 42.13 4.85
2788 2964 3.532155 GCTCCGGTCGATCTGGCT 61.532 66.667 0.00 0.00 42.13 4.75
2789 2965 2.725008 CTCCGGTCGATCTGGCTC 59.275 66.667 0.00 0.00 42.13 4.70
2790 2966 3.187699 CTCCGGTCGATCTGGCTCG 62.188 68.421 0.00 0.00 42.13 5.03
2791 2967 4.271816 CCGGTCGATCTGGCTCGG 62.272 72.222 0.00 0.00 39.13 4.63
2900 3082 2.167487 AGAATTCTGGAGAGCTCGGAAC 59.833 50.000 7.30 0.51 0.00 3.62
2914 3096 2.741211 GAACGTCGGACTTGGGCC 60.741 66.667 6.57 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.077605 TCGAGTGCATTCAAACAGAAAATTAG 58.922 34.615 10.08 0.00 40.22 1.73
14 15 2.977405 AGCTTCGAGTGCATTCAAAC 57.023 45.000 10.08 0.00 0.00 2.93
26 27 3.872696 TGGATTTGCAGAATAGCTTCGA 58.127 40.909 0.00 0.00 36.45 3.71
28 29 5.573337 ACTTGGATTTGCAGAATAGCTTC 57.427 39.130 0.00 0.00 34.99 3.86
31 32 6.017934 TCGATAACTTGGATTTGCAGAATAGC 60.018 38.462 0.00 0.00 0.00 2.97
37 38 4.191544 TCCTCGATAACTTGGATTTGCAG 58.808 43.478 0.00 0.00 0.00 4.41
52 53 3.133721 AGCAACTCTAGCAAATCCTCGAT 59.866 43.478 0.00 0.00 0.00 3.59
54 55 2.863137 GAGCAACTCTAGCAAATCCTCG 59.137 50.000 0.00 0.00 0.00 4.63
81 82 1.333791 GCGTTTCCTGAACTTGAACGG 60.334 52.381 8.68 0.00 36.06 4.44
140 141 4.307032 AGTCAACTATTCTTGGCACCAT 57.693 40.909 0.00 0.00 0.00 3.55
141 142 3.788227 AGTCAACTATTCTTGGCACCA 57.212 42.857 0.00 0.00 0.00 4.17
142 143 3.623510 GCTAGTCAACTATTCTTGGCACC 59.376 47.826 0.00 0.00 0.00 5.01
143 144 3.623510 GGCTAGTCAACTATTCTTGGCAC 59.376 47.826 0.00 0.00 32.26 5.01
144 145 3.519510 AGGCTAGTCAACTATTCTTGGCA 59.480 43.478 0.00 0.00 33.70 4.92
145 146 3.873952 CAGGCTAGTCAACTATTCTTGGC 59.126 47.826 0.00 0.00 0.00 4.52
146 147 5.344743 TCAGGCTAGTCAACTATTCTTGG 57.655 43.478 0.00 0.00 0.00 3.61
147 148 6.259608 CCAATCAGGCTAGTCAACTATTCTTG 59.740 42.308 0.00 0.00 0.00 3.02
148 149 6.069963 ACCAATCAGGCTAGTCAACTATTCTT 60.070 38.462 0.00 0.00 43.14 2.52
149 150 5.426833 ACCAATCAGGCTAGTCAACTATTCT 59.573 40.000 0.00 0.00 43.14 2.40
150 151 5.675538 ACCAATCAGGCTAGTCAACTATTC 58.324 41.667 0.00 0.00 43.14 1.75
151 152 5.700402 ACCAATCAGGCTAGTCAACTATT 57.300 39.130 0.00 0.00 43.14 1.73
152 153 6.239714 CCATACCAATCAGGCTAGTCAACTAT 60.240 42.308 0.00 0.00 43.14 2.12
153 154 5.070446 CCATACCAATCAGGCTAGTCAACTA 59.930 44.000 0.00 0.00 43.14 2.24
238 241 2.744202 CCGATGCCTACCAATAATGCTC 59.256 50.000 0.00 0.00 0.00 4.26
269 282 5.741383 GCACTTGTATAGACCATGATCAGCT 60.741 44.000 0.09 0.00 0.00 4.24
305 318 6.296026 TGTGAGCACTTGTATAGACCTTTTT 58.704 36.000 1.99 0.00 0.00 1.94
306 319 5.865085 TGTGAGCACTTGTATAGACCTTTT 58.135 37.500 1.99 0.00 0.00 2.27
307 320 5.482908 CTGTGAGCACTTGTATAGACCTTT 58.517 41.667 1.99 0.00 0.00 3.11
308 321 4.621747 GCTGTGAGCACTTGTATAGACCTT 60.622 45.833 1.99 0.00 41.89 3.50
309 322 3.118956 GCTGTGAGCACTTGTATAGACCT 60.119 47.826 1.99 0.00 41.89 3.85
310 323 3.190874 GCTGTGAGCACTTGTATAGACC 58.809 50.000 1.99 0.00 41.89 3.85
325 338 3.686622 GGAAGCCGATATGCTGTGA 57.313 52.632 0.00 0.00 41.80 3.58
404 417 4.469227 AGATAGTGATGGCAGAGTCAACTT 59.531 41.667 0.00 0.00 0.00 2.66
425 523 5.221581 GGACACCTAACTTTACCTGACAAGA 60.222 44.000 0.00 0.00 0.00 3.02
456 554 7.147966 GGACACCTTACTCTTTTCTTTTTCCAA 60.148 37.037 0.00 0.00 0.00 3.53
458 556 6.546403 AGGACACCTTACTCTTTTCTTTTTCC 59.454 38.462 0.00 0.00 0.00 3.13
459 557 7.569639 AGGACACCTTACTCTTTTCTTTTTC 57.430 36.000 0.00 0.00 0.00 2.29
476 576 4.438744 CGGATTGCTTAATCAAAGGACACC 60.439 45.833 0.00 0.00 34.93 4.16
575 675 2.412089 CAGCGCCGGTAGATATTTTAGC 59.588 50.000 2.29 0.00 0.00 3.09
576 676 2.412089 GCAGCGCCGGTAGATATTTTAG 59.588 50.000 2.29 0.00 0.00 1.85
590 690 2.100991 CTCCGATTTTGCAGCGCC 59.899 61.111 2.29 0.00 0.00 6.53
599 699 1.393539 CGTGAATTCGTGCTCCGATTT 59.606 47.619 0.04 3.61 46.75 2.17
620 720 2.341760 CGTAAGCTCACGACTTGTTAGC 59.658 50.000 2.25 0.00 46.12 3.09
654 754 1.737838 CCAACTTGATCGGCTAGCAA 58.262 50.000 18.24 4.04 31.38 3.91
687 787 2.351418 TGATCGGTGATGAAAATGACGC 59.649 45.455 0.00 0.00 0.00 5.19
703 803 4.453177 AGTCTGATATCATGGCTGATCG 57.547 45.455 5.72 0.00 41.29 3.69
711 811 2.154580 GCGCGACAAGTCTGATATCATG 59.845 50.000 12.10 4.18 0.00 3.07
881 992 2.898729 GCTGATGCCTAGCAGAGTAA 57.101 50.000 0.00 0.00 42.88 2.24
908 1021 3.588277 TCAAGTTGAGAGGCGTGAC 57.412 52.632 0.08 0.00 0.00 3.67
923 1036 1.000955 GGCGAAGACTTGAGACCTCAA 59.999 52.381 11.47 11.47 46.27 3.02
924 1037 0.603569 GGCGAAGACTTGAGACCTCA 59.396 55.000 0.00 0.00 37.91 3.86
925 1038 0.108567 GGGCGAAGACTTGAGACCTC 60.109 60.000 5.17 0.00 32.70 3.85
926 1039 0.832135 TGGGCGAAGACTTGAGACCT 60.832 55.000 12.06 0.00 32.70 3.85
927 1040 0.250513 ATGGGCGAAGACTTGAGACC 59.749 55.000 5.41 5.41 32.70 3.85
928 1041 1.646189 GATGGGCGAAGACTTGAGAC 58.354 55.000 0.00 0.00 32.70 3.36
983 1096 6.256757 CGTCTCCATTTCTCCAGTAATCTTTC 59.743 42.308 0.00 0.00 0.00 2.62
1035 1148 0.330267 TTCCGACCCCAAAGAATCCC 59.670 55.000 0.00 0.00 0.00 3.85
1041 1154 3.431725 GCGCTTCCGACCCCAAAG 61.432 66.667 0.00 0.00 36.29 2.77
1103 1216 1.271379 AGACGGATGAACACAAGCGTA 59.729 47.619 0.00 0.00 0.00 4.42
1120 1233 7.386299 TCAGCTCAGTTTCTTTGAGATTTAGAC 59.614 37.037 6.44 0.00 43.75 2.59
1350 1466 1.702299 GAAGACGACGCCGATGTTG 59.298 57.895 0.00 0.00 39.50 3.33
1402 1518 2.356313 CTGGATCGAATCGGGGCG 60.356 66.667 1.76 0.00 0.00 6.13
1405 1521 2.356313 CGCCTGGATCGAATCGGG 60.356 66.667 1.76 10.78 0.00 5.14
1427 1543 2.595750 TTCATCCCCCGTTGAATTGT 57.404 45.000 0.00 0.00 0.00 2.71
1863 1996 0.336737 CAGGAGGAGGGTACTGTCCT 59.663 60.000 14.32 14.32 42.88 3.85
1864 1997 1.331399 GCAGGAGGAGGGTACTGTCC 61.331 65.000 6.05 6.05 33.62 4.02
1865 1998 0.324830 AGCAGGAGGAGGGTACTGTC 60.325 60.000 0.00 0.00 33.62 3.51
1896 2029 2.185310 GAGCATCGGGGTGGAACTGT 62.185 60.000 0.00 0.00 36.74 3.55
1899 2032 2.124695 GGAGCATCGGGGTGGAAC 60.125 66.667 0.00 0.00 34.37 3.62
1964 2106 6.823182 AGACATGCTTGCACATAACTACATAA 59.177 34.615 0.00 0.00 0.00 1.90
1970 2112 4.430137 CAAGACATGCTTGCACATAACT 57.570 40.909 14.20 0.00 46.67 2.24
1980 2122 4.660168 AGATGAAGAACCAAGACATGCTT 58.340 39.130 0.00 0.00 37.29 3.91
1981 2123 4.298103 AGATGAAGAACCAAGACATGCT 57.702 40.909 0.00 0.00 0.00 3.79
1982 2124 5.505324 GCATAGATGAAGAACCAAGACATGC 60.505 44.000 0.00 0.00 0.00 4.06
1983 2125 5.008415 GGCATAGATGAAGAACCAAGACATG 59.992 44.000 0.00 0.00 0.00 3.21
1984 2126 5.128919 GGCATAGATGAAGAACCAAGACAT 58.871 41.667 0.00 0.00 0.00 3.06
1985 2127 4.019411 TGGCATAGATGAAGAACCAAGACA 60.019 41.667 0.00 0.00 0.00 3.41
1986 2128 4.517285 TGGCATAGATGAAGAACCAAGAC 58.483 43.478 0.00 0.00 0.00 3.01
1987 2129 4.842531 TGGCATAGATGAAGAACCAAGA 57.157 40.909 0.00 0.00 0.00 3.02
1988 2130 4.885907 ACATGGCATAGATGAAGAACCAAG 59.114 41.667 0.00 0.00 0.00 3.61
1989 2131 4.858850 ACATGGCATAGATGAAGAACCAA 58.141 39.130 0.00 0.00 0.00 3.67
1990 2132 4.508551 ACATGGCATAGATGAAGAACCA 57.491 40.909 0.00 0.00 0.00 3.67
1991 2133 5.128919 AGAACATGGCATAGATGAAGAACC 58.871 41.667 0.00 0.00 0.00 3.62
1992 2134 6.238593 GGAAGAACATGGCATAGATGAAGAAC 60.239 42.308 0.00 0.00 0.00 3.01
1993 2135 5.824624 GGAAGAACATGGCATAGATGAAGAA 59.175 40.000 0.00 0.00 0.00 2.52
1994 2136 5.371526 GGAAGAACATGGCATAGATGAAGA 58.628 41.667 0.00 0.00 0.00 2.87
1995 2137 4.212847 CGGAAGAACATGGCATAGATGAAG 59.787 45.833 0.00 0.00 0.00 3.02
1996 2138 4.129380 CGGAAGAACATGGCATAGATGAA 58.871 43.478 0.00 0.00 0.00 2.57
1997 2139 3.134623 ACGGAAGAACATGGCATAGATGA 59.865 43.478 0.00 0.00 0.00 2.92
1998 2140 3.470709 ACGGAAGAACATGGCATAGATG 58.529 45.455 0.00 0.00 0.00 2.90
1999 2141 3.389329 AGACGGAAGAACATGGCATAGAT 59.611 43.478 0.00 0.00 0.00 1.98
2000 2142 2.766263 AGACGGAAGAACATGGCATAGA 59.234 45.455 0.00 0.00 0.00 1.98
2001 2143 3.185246 AGACGGAAGAACATGGCATAG 57.815 47.619 0.00 0.00 0.00 2.23
2002 2144 3.531538 GAAGACGGAAGAACATGGCATA 58.468 45.455 0.00 0.00 0.00 3.14
2003 2145 2.359900 GAAGACGGAAGAACATGGCAT 58.640 47.619 0.00 0.00 0.00 4.40
2007 2149 6.316140 TGAATTATGGAAGACGGAAGAACATG 59.684 38.462 0.00 0.00 0.00 3.21
2017 2159 3.935203 ACACAGCTGAATTATGGAAGACG 59.065 43.478 23.35 0.00 0.00 4.18
2122 2267 5.270083 CGCACACTACACAAAATCTCAAAA 58.730 37.500 0.00 0.00 0.00 2.44
2173 2318 8.071368 TGGTGAAATGTTTGTAATAAACGAGAC 58.929 33.333 0.00 0.00 33.05 3.36
2175 2320 8.789881 TTGGTGAAATGTTTGTAATAAACGAG 57.210 30.769 0.00 0.00 33.05 4.18
2200 2345 5.183140 GTGCTAACCTGTGTGGATGTAAATT 59.817 40.000 0.00 0.00 39.71 1.82
2213 2358 1.878953 CGGAAGTTGTGCTAACCTGT 58.121 50.000 1.57 0.00 0.00 4.00
2216 2361 0.517316 CTGCGGAAGTTGTGCTAACC 59.483 55.000 0.00 0.00 0.00 2.85
2218 2363 1.871039 GTTCTGCGGAAGTTGTGCTAA 59.129 47.619 8.61 0.00 31.46 3.09
2219 2364 1.508632 GTTCTGCGGAAGTTGTGCTA 58.491 50.000 8.61 0.00 31.46 3.49
2230 2375 1.079503 GTTAGCTTCTGGTTCTGCGG 58.920 55.000 0.00 0.00 0.00 5.69
2241 2389 3.431572 CAGCAGAGTTGTCAGTTAGCTTC 59.568 47.826 0.00 0.00 0.00 3.86
2253 2401 0.820891 AGGGTTGTGCAGCAGAGTTG 60.821 55.000 0.00 0.00 0.00 3.16
2269 2417 6.887013 TCTCAAGACAGTAGTAGTACTAGGG 58.113 44.000 10.38 8.18 37.40 3.53
2561 2727 0.608640 TCAAGCTCTTCTTCGTCCCC 59.391 55.000 0.00 0.00 31.27 4.81
2681 2847 3.508762 GGCGATGTTCTTCTTCTTCGTA 58.491 45.455 0.00 0.00 35.00 3.43
2777 2953 1.586564 CGAACCGAGCCAGATCGAC 60.587 63.158 6.92 0.00 45.56 4.20
2778 2954 1.101635 ATCGAACCGAGCCAGATCGA 61.102 55.000 6.92 3.68 45.56 3.59
2779 2955 0.661780 GATCGAACCGAGCCAGATCG 60.662 60.000 0.00 0.00 39.91 3.69
2780 2956 0.671251 AGATCGAACCGAGCCAGATC 59.329 55.000 0.81 0.00 43.62 2.75
2781 2957 0.387202 CAGATCGAACCGAGCCAGAT 59.613 55.000 0.81 0.00 43.62 2.90
2782 2958 0.679960 TCAGATCGAACCGAGCCAGA 60.680 55.000 0.81 0.00 43.62 3.86
2783 2959 0.387202 ATCAGATCGAACCGAGCCAG 59.613 55.000 0.81 0.00 43.62 4.85
2784 2960 0.103026 CATCAGATCGAACCGAGCCA 59.897 55.000 0.81 0.00 43.62 4.75
2785 2961 0.385751 TCATCAGATCGAACCGAGCC 59.614 55.000 0.81 0.00 43.62 4.70
2786 2962 2.123342 CTTCATCAGATCGAACCGAGC 58.877 52.381 0.00 0.00 42.87 5.03
2787 2963 3.111838 CACTTCATCAGATCGAACCGAG 58.888 50.000 0.00 0.00 39.91 4.63
2788 2964 2.492088 ACACTTCATCAGATCGAACCGA 59.508 45.455 0.00 0.00 41.13 4.69
2789 2965 2.881074 ACACTTCATCAGATCGAACCG 58.119 47.619 0.00 0.00 0.00 4.44
2790 2966 3.372206 CCAACACTTCATCAGATCGAACC 59.628 47.826 0.00 0.00 0.00 3.62
2791 2967 3.997021 ACCAACACTTCATCAGATCGAAC 59.003 43.478 0.00 0.00 0.00 3.95
2907 3089 1.153086 CTCAGGATTCCGGCCCAAG 60.153 63.158 0.00 0.00 0.00 3.61
2912 3094 1.599240 GGCATCTCAGGATTCCGGC 60.599 63.158 0.00 0.00 0.00 6.13
2914 3096 0.250209 CAGGGCATCTCAGGATTCCG 60.250 60.000 0.00 0.00 36.36 4.30


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

AutoCloner maintained by Alex Coulton.