Multiple sequence alignment - TraesCS1D01G336100

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 TraesCS1D01G336100 chr1D 100.000 3956 0 0 1 3956 426184689 426180734 0.000000e+00 7306
1 TraesCS1D01G336100 chr1B 90.568 3997 269 62 29 3956 575871349 575867392 0.000000e+00 5193
2 TraesCS1D01G336100 chr1A 90.172 3439 241 44 73 3445 521326810 521323403 0.000000e+00 4388
3 TraesCS1D01G336100 chr1A 88.030 401 38 5 3477 3871 521323337 521322941 2.150000e-127 466
4 TraesCS1D01G336100 chr1A 93.243 74 2 1 1 74 521326920 521326850 5.410000e-19 106


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 TraesCS1D01G336100 chr1D 426180734 426184689 3955 True 7306.000000 7306 100.000000 1 3956 1 chr1D.!!$R1 3955
1 TraesCS1D01G336100 chr1B 575867392 575871349 3957 True 5193.000000 5193 90.568000 29 3956 1 chr1B.!!$R1 3927
2 TraesCS1D01G336100 chr1A 521322941 521326920 3979 True 1653.333333 4388 90.481667 1 3871 3 chr1A.!!$R1 3870

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
747 874 0.030369 ACCATCGATTCCTCGTACGC 59.970 55.000 11.24 0.0 45.25 4.42 F
866 1006 0.321653 ACGCCATTCTTCCACTCCAC 60.322 55.000 0.00 0.0 0.00 4.02 F
1827 1976 0.398696 TTATGAGTTGGGTGTGCCGT 59.601 50.000 0.00 0.0 34.97 5.68 F
2097 2248 1.268625 GGAACCCAGTGTTTTAAGCGG 59.731 52.381 0.00 0.0 37.29 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 2859 0.323629 TAAGCTCCGTTGGGGAACAG 59.676 55.000 0.0 0.00 46.61 3.16 R
2880 3035 1.708993 TTGCTTCACCCCAGCTCTGT 61.709 55.000 0.0 0.00 38.19 3.41 R
2922 3077 1.618343 TCCTCAGACGCATGAAACTGA 59.382 47.619 0.0 6.45 37.71 3.41 R
3888 4101 2.660189 AACATTGTATGGCTTGCTGC 57.340 45.000 0.0 0.00 41.94 5.25 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
107 149 9.758651 GTTTATTTTCTGGTTGTAATTTGGTCT 57.241 29.630 0.00 0.00 0.00 3.85
153 206 8.950208 AATAATAGGAGAAACACTAAGCTCAC 57.050 34.615 0.00 0.00 0.00 3.51
154 207 6.613153 AATAGGAGAAACACTAAGCTCACT 57.387 37.500 0.00 0.00 0.00 3.41
155 208 4.264460 AGGAGAAACACTAAGCTCACTG 57.736 45.455 0.00 0.00 0.00 3.66
156 209 3.898123 AGGAGAAACACTAAGCTCACTGA 59.102 43.478 0.00 0.00 0.00 3.41
157 210 4.530161 AGGAGAAACACTAAGCTCACTGAT 59.470 41.667 0.00 0.00 0.00 2.90
161 214 3.810310 ACACTAAGCTCACTGATAGGC 57.190 47.619 0.00 0.00 0.00 3.93
171 224 1.227263 CTGATAGGCGAACCCACCG 60.227 63.158 0.00 0.00 36.11 4.94
283 370 4.016706 CTGGTCGACCCCACCCAC 62.017 72.222 31.19 4.64 32.24 4.61
299 396 2.749044 ACGCTGCCAATGCCTGAG 60.749 61.111 0.00 0.00 36.33 3.35
306 403 1.372087 GCCAATGCCTGAGTTCTCCG 61.372 60.000 0.00 0.00 0.00 4.63
401 519 2.508663 GCGTCCACGGCCTTACTC 60.509 66.667 0.00 0.00 40.23 2.59
406 527 2.732619 CCACGGCCTTACTCCCTCC 61.733 68.421 0.00 0.00 0.00 4.30
433 554 4.814294 GCGGGATGCCTCGTCGTT 62.814 66.667 0.28 0.00 37.76 3.85
500 627 2.747460 GCGCCTCCATCACAGCAA 60.747 61.111 0.00 0.00 0.00 3.91
700 827 4.657824 CACGCCCTGTCCGAACGT 62.658 66.667 0.00 0.00 37.47 3.99
747 874 0.030369 ACCATCGATTCCTCGTACGC 59.970 55.000 11.24 0.00 45.25 4.42
771 898 1.466950 CCCTCGCAAATTTAACTCGCA 59.533 47.619 0.00 0.00 0.00 5.10
772 899 2.505866 CCTCGCAAATTTAACTCGCAC 58.494 47.619 0.00 0.00 0.00 5.34
773 900 2.095969 CCTCGCAAATTTAACTCGCACA 60.096 45.455 0.00 0.00 0.00 4.57
779 906 4.146443 GCAAATTTAACTCGCACACAGTTC 59.854 41.667 0.00 0.00 35.63 3.01
795 922 2.032634 TTCGTTCAGTCCGCCATGC 61.033 57.895 0.00 0.00 0.00 4.06
798 930 1.210155 GTTCAGTCCGCCATGCAAC 59.790 57.895 0.00 0.00 0.00 4.17
830 970 2.105930 CTGCGCCTACTCTCCTGC 59.894 66.667 4.18 0.00 0.00 4.85
832 972 2.348605 CTGCGCCTACTCTCCTGCTC 62.349 65.000 4.18 0.00 0.00 4.26
866 1006 0.321653 ACGCCATTCTTCCACTCCAC 60.322 55.000 0.00 0.00 0.00 4.02
942 1082 1.878656 AAGTCGTTCTGCTCCCCGAG 61.879 60.000 0.00 0.00 0.00 4.63
943 1083 2.035155 TCGTTCTGCTCCCCGAGA 59.965 61.111 0.00 0.00 0.00 4.04
967 1107 3.039405 GTCGCATTACTGACAGATCTCG 58.961 50.000 10.08 6.07 35.20 4.04
997 1137 1.361668 CCGTGATTGGCTCCTCGTTG 61.362 60.000 0.00 0.00 0.00 4.10
1040 1180 1.682451 TTCCCCTACAATCTCGCCCG 61.682 60.000 0.00 0.00 0.00 6.13
1042 1182 2.658593 CCTACAATCTCGCCCGCG 60.659 66.667 0.00 0.00 41.35 6.46
1061 1201 2.073816 CGGTGCGATGGTACTTTTTCT 58.926 47.619 0.00 0.00 0.00 2.52
1076 1216 7.224949 GGTACTTTTTCTTCCATCCTTCTATCG 59.775 40.741 0.00 0.00 0.00 2.92
1084 1224 2.128035 CATCCTTCTATCGACGGCAAC 58.872 52.381 0.00 0.00 0.00 4.17
1117 1257 7.439381 TCGTAGAAAACTCCAAGTTGTTCTAT 58.561 34.615 13.12 0.00 38.66 1.98
1118 1258 7.929785 TCGTAGAAAACTCCAAGTTGTTCTATT 59.070 33.333 13.12 0.00 38.66 1.73
1119 1259 9.199982 CGTAGAAAACTCCAAGTTGTTCTATTA 57.800 33.333 13.12 0.00 38.66 0.98
1168 1308 7.969536 TGATCAATTTACCATTAGCTAGAGC 57.030 36.000 0.00 0.00 42.49 4.09
1185 1325 3.336468 AGAGCAGATTCAAGCTGACAAG 58.664 45.455 6.90 0.00 42.04 3.16
1331 1471 4.275810 CATGGGGTTCTGTCATCTGAAAT 58.724 43.478 0.00 0.00 34.32 2.17
1341 1481 5.648092 TCTGTCATCTGAAATGAGACTCGTA 59.352 40.000 0.00 0.00 0.00 3.43
1347 1487 5.570344 TCTGAAATGAGACTCGTATTCGAC 58.430 41.667 0.00 0.00 41.35 4.20
1429 1569 2.806818 TCGAGTAGCAGCGGTAGATTAG 59.193 50.000 0.00 0.00 0.00 1.73
1519 1659 3.341263 CCAGGAGGGCATCATCATG 57.659 57.895 0.08 0.00 35.58 3.07
1553 1693 6.176896 TGCTGTATGAAGTGGTAAAGCATTA 58.823 36.000 0.00 0.00 36.50 1.90
1764 1913 4.945246 GGTTTGTAGCCGATGAGAATAGA 58.055 43.478 0.00 0.00 0.00 1.98
1815 1964 4.471386 AGTTACAGGGACATGCTTATGAGT 59.529 41.667 0.00 0.00 0.00 3.41
1827 1976 0.398696 TTATGAGTTGGGTGTGCCGT 59.601 50.000 0.00 0.00 34.97 5.68
1856 2005 2.555757 AGCTCAGAGTCACCAATTTTGC 59.444 45.455 0.00 0.00 0.00 3.68
1910 2059 2.094182 TCTCCGTCTTGCAGGTAATGAC 60.094 50.000 0.00 0.00 0.00 3.06
1964 2115 8.442605 TTTCTTGTTTTCTGTAGTTGTTTTCG 57.557 30.769 0.00 0.00 0.00 3.46
1965 2116 7.136289 TCTTGTTTTCTGTAGTTGTTTTCGT 57.864 32.000 0.00 0.00 0.00 3.85
1969 2120 7.998141 TGTTTTCTGTAGTTGTTTTCGTTTTG 58.002 30.769 0.00 0.00 0.00 2.44
1978 2129 5.235401 AGTTGTTTTCGTTTTGCAAAACTGT 59.765 32.000 38.15 18.55 44.58 3.55
1984 2135 6.473397 TTCGTTTTGCAAAACTGTCAATTT 57.527 29.167 38.15 0.00 44.58 1.82
1985 2136 7.582435 TTCGTTTTGCAAAACTGTCAATTTA 57.418 28.000 38.15 19.07 44.58 1.40
1986 2137 7.763172 TCGTTTTGCAAAACTGTCAATTTAT 57.237 28.000 38.15 0.00 44.58 1.40
1987 2138 7.616673 TCGTTTTGCAAAACTGTCAATTTATG 58.383 30.769 38.15 24.19 44.58 1.90
1988 2139 6.354102 CGTTTTGCAAAACTGTCAATTTATGC 59.646 34.615 38.15 17.48 44.58 3.14
1989 2140 6.915544 TTTGCAAAACTGTCAATTTATGCA 57.084 29.167 10.02 10.46 40.43 3.96
1990 2141 5.903764 TGCAAAACTGTCAATTTATGCAC 57.096 34.783 10.46 0.00 37.61 4.57
1993 2144 6.018913 TGCAAAACTGTCAATTTATGCACAAG 60.019 34.615 10.46 0.00 37.61 3.16
2006 2157 3.731652 TGCACAAGTTTTCAATCCCTG 57.268 42.857 0.00 0.00 0.00 4.45
2022 2173 1.668419 CCTGATTCTAGGGTTTGCCG 58.332 55.000 0.00 0.00 34.06 5.69
2075 2226 4.065088 GTCAGTTTTGATGACTGCCACTA 58.935 43.478 0.00 0.00 43.23 2.74
2097 2248 1.268625 GGAACCCAGTGTTTTAAGCGG 59.731 52.381 0.00 0.00 37.29 5.52
2287 2439 6.272792 TGACTTTTACCCCTTAGTGGTTATGA 59.727 38.462 0.00 0.00 37.31 2.15
2314 2466 6.958255 ACAAATTTGGTTTTGCTAATGCTTC 58.042 32.000 21.74 0.00 39.65 3.86
2315 2467 6.767423 ACAAATTTGGTTTTGCTAATGCTTCT 59.233 30.769 21.74 0.00 39.65 2.85
2316 2468 7.282901 ACAAATTTGGTTTTGCTAATGCTTCTT 59.717 29.630 21.74 0.00 39.65 2.52
2319 2471 5.125100 TGGTTTTGCTAATGCTTCTTCTG 57.875 39.130 0.00 0.00 40.48 3.02
2330 2485 2.093288 TGCTTCTTCTGCTGGTGGATAG 60.093 50.000 0.00 0.00 0.00 2.08
2386 2541 3.713858 TCTTGCACATTTCACACCTTG 57.286 42.857 0.00 0.00 0.00 3.61
2393 2548 4.478699 CACATTTCACACCTTGTAGCATG 58.521 43.478 0.00 0.00 0.00 4.06
2505 2660 3.897936 CCACGCCGGCTAAATTCA 58.102 55.556 26.68 0.00 0.00 2.57
2699 2854 2.732016 CGTCGTGTTCCTGGACCA 59.268 61.111 0.00 0.00 0.00 4.02
2880 3035 2.042464 CCTAGCTCCAGGATGTGCTTA 58.958 52.381 6.99 0.00 40.22 3.09
2981 3136 6.174049 ACCTGACCTTTTAGAATTAGACAGC 58.826 40.000 0.00 0.00 0.00 4.40
3031 3186 1.112113 GGTCAAGGATCGACAGCCTA 58.888 55.000 3.98 0.00 34.97 3.93
3105 3269 5.437289 TGTCATCCACACAAAAGAACATC 57.563 39.130 0.00 0.00 0.00 3.06
3290 3455 3.491766 TCAGACCCTCTACCCTTCATT 57.508 47.619 0.00 0.00 0.00 2.57
3355 3522 3.200605 TCATCACAACACTAGATGGGCAT 59.799 43.478 0.00 0.00 39.59 4.40
3363 3530 6.151144 ACAACACTAGATGGGCATTACTTTTC 59.849 38.462 0.00 0.00 0.00 2.29
3386 3553 1.402456 GGCTTGCAGCTCATTTCAGTG 60.402 52.381 7.85 0.00 41.99 3.66
3388 3555 2.163815 GCTTGCAGCTCATTTCAGTGAT 59.836 45.455 0.00 0.00 38.45 3.06
3396 3563 6.963805 GCAGCTCATTTCAGTGATAAACTTAC 59.036 38.462 0.00 0.00 36.83 2.34
3489 3696 4.816925 GGAACAGGCTAATAAAGGTAGCAG 59.183 45.833 5.85 0.82 44.82 4.24
3702 3912 5.466728 TGCTGAAACGAGCCTGATAAATATC 59.533 40.000 0.00 0.00 38.28 1.63
3745 3955 4.501571 CCATCTAGTGGGTATGAACTTCCG 60.502 50.000 4.04 0.00 44.79 4.30
3769 3979 4.812626 CAGCAAAAGGAAACTGAAAATGCT 59.187 37.500 0.00 0.00 42.68 3.79
3852 4065 3.956848 GGAGCAAAAGGAGGATAGCAAAT 59.043 43.478 0.00 0.00 0.00 2.32
3888 4101 9.755804 TCTCATACATCTAGCAAAAGAATACTG 57.244 33.333 0.00 0.00 0.00 2.74
3889 4102 8.370493 TCATACATCTAGCAAAAGAATACTGC 57.630 34.615 0.00 0.00 36.29 4.40
3918 4138 8.461222 CAAGCCATACAATGTTAAGATTGAGAA 58.539 33.333 26.90 14.44 36.89 2.87
3919 4139 8.757982 AGCCATACAATGTTAAGATTGAGAAT 57.242 30.769 26.90 15.72 36.89 2.40
3920 4140 9.193806 AGCCATACAATGTTAAGATTGAGAATT 57.806 29.630 26.90 10.50 36.89 2.17
3921 4141 9.807649 GCCATACAATGTTAAGATTGAGAATTT 57.192 29.630 26.90 9.88 36.89 1.82
3929 4149 8.675705 TGTTAAGATTGAGAATTTGAGACACA 57.324 30.769 0.00 0.00 0.00 3.72
3941 4161 5.614324 TTTGAGACACATCCGGAGAATAT 57.386 39.130 11.34 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.586319 TTCTGCTCGAACTTTTGCCG 59.414 50.000 0.00 0.00 0.00 5.69
7 8 6.823689 ACATATACCATTCTGCTCGAACTTTT 59.176 34.615 0.00 0.00 33.72 2.27
44 45 5.651387 AGAGTCTTCATTCTCATTGACGA 57.349 39.130 0.00 0.00 33.63 4.20
45 46 6.718454 AAAGAGTCTTCATTCTCATTGACG 57.282 37.500 5.70 0.00 33.63 4.35
46 47 9.213799 AGTAAAAGAGTCTTCATTCTCATTGAC 57.786 33.333 5.70 0.00 33.63 3.18
85 127 9.308000 TGATAGACCAAATTACAACCAGAAAAT 57.692 29.630 0.00 0.00 0.00 1.82
148 201 0.530870 GGGTTCGCCTATCAGTGAGC 60.531 60.000 0.00 0.00 37.45 4.26
149 202 0.824109 TGGGTTCGCCTATCAGTGAG 59.176 55.000 0.00 0.00 37.45 3.51
150 203 0.535335 GTGGGTTCGCCTATCAGTGA 59.465 55.000 0.00 0.00 37.45 3.41
151 204 0.462047 GGTGGGTTCGCCTATCAGTG 60.462 60.000 0.00 0.00 40.31 3.66
152 205 1.905512 GGTGGGTTCGCCTATCAGT 59.094 57.895 0.00 0.00 40.31 3.41
153 206 1.227263 CGGTGGGTTCGCCTATCAG 60.227 63.158 0.00 0.00 41.26 2.90
154 207 1.672854 CTCGGTGGGTTCGCCTATCA 61.673 60.000 0.00 0.00 41.26 2.15
155 208 1.067582 CTCGGTGGGTTCGCCTATC 59.932 63.158 0.00 0.00 41.26 2.08
156 209 1.380785 TCTCGGTGGGTTCGCCTAT 60.381 57.895 0.00 0.00 41.26 2.57
157 210 2.036098 TCTCGGTGGGTTCGCCTA 59.964 61.111 0.00 0.00 41.26 3.93
161 214 1.213013 CAGTCTCTCGGTGGGTTCG 59.787 63.158 0.00 0.00 0.00 3.95
262 349 2.513259 GGTGGGGTCGACCAGTCAA 61.513 63.158 34.40 9.71 42.20 3.18
283 370 2.262471 GAACTCAGGCATTGGCAGCG 62.262 60.000 13.20 1.89 43.71 5.18
418 539 1.227002 GAGAACGACGAGGCATCCC 60.227 63.158 0.00 0.00 0.00 3.85
547 674 1.227002 GAAGATCGTGACCCTCGGC 60.227 63.158 0.00 0.00 0.00 5.54
648 775 4.778415 CGAGGAGCACGACGGTGG 62.778 72.222 0.00 0.00 44.54 4.61
684 811 4.353437 GACGTTCGGACAGGGCGT 62.353 66.667 0.00 0.00 38.55 5.68
728 855 0.030369 GCGTACGAGGAATCGATGGT 59.970 55.000 21.65 0.00 36.85 3.55
731 858 1.370172 GCGCGTACGAGGAATCGAT 60.370 57.895 21.65 0.00 43.93 3.59
747 874 1.199097 AGTTAAATTTGCGAGGGTGCG 59.801 47.619 0.00 0.00 37.81 5.34
771 898 0.874607 GCGGACTGAACGAACTGTGT 60.875 55.000 0.00 0.00 0.00 3.72
772 899 1.557443 GGCGGACTGAACGAACTGTG 61.557 60.000 0.00 0.00 0.00 3.66
773 900 1.300697 GGCGGACTGAACGAACTGT 60.301 57.895 0.00 0.00 0.00 3.55
779 906 2.324330 TTGCATGGCGGACTGAACG 61.324 57.895 0.00 0.00 0.00 3.95
817 957 1.032014 CTGAGAGCAGGAGAGTAGGC 58.968 60.000 0.00 0.00 38.51 3.93
830 970 1.592223 GTCCCCGTGAACCTGAGAG 59.408 63.158 0.00 0.00 0.00 3.20
832 972 2.261671 CGTCCCCGTGAACCTGAG 59.738 66.667 0.00 0.00 0.00 3.35
942 1082 1.135489 TCTGTCAGTAATGCGACGGTC 60.135 52.381 0.00 0.00 39.18 4.79
943 1083 0.885879 TCTGTCAGTAATGCGACGGT 59.114 50.000 0.00 0.00 39.18 4.83
949 1089 2.131183 GCCGAGATCTGTCAGTAATGC 58.869 52.381 0.00 0.00 0.00 3.56
967 1107 2.336667 CCAATCACGGTCAATTTTGCC 58.663 47.619 0.00 0.00 0.00 4.52
997 1137 0.770008 GAAACGTTGCGTGACATTGC 59.230 50.000 0.00 0.00 39.99 3.56
1040 1180 0.519961 AAAAAGTACCATCGCACCGC 59.480 50.000 0.00 0.00 0.00 5.68
1042 1182 3.119955 GGAAGAAAAAGTACCATCGCACC 60.120 47.826 0.00 0.00 0.00 5.01
1076 1216 2.005971 ACGAATCTAAGGTTGCCGTC 57.994 50.000 0.00 0.00 0.00 4.79
1084 1224 7.097834 ACTTGGAGTTTTCTACGAATCTAAGG 58.902 38.462 0.00 0.00 32.30 2.69
1153 1293 6.731292 TTGAATCTGCTCTAGCTAATGGTA 57.269 37.500 3.26 0.00 42.66 3.25
1154 1294 5.609423 CTTGAATCTGCTCTAGCTAATGGT 58.391 41.667 3.26 0.00 42.66 3.55
1168 1308 2.486982 CCCACTTGTCAGCTTGAATCTG 59.513 50.000 0.00 0.00 0.00 2.90
1185 1325 3.138798 CTGCCATCTGCTGCCCAC 61.139 66.667 0.00 0.00 42.00 4.61
1313 1453 4.633565 GTCTCATTTCAGATGACAGAACCC 59.366 45.833 0.00 0.00 0.00 4.11
1341 1481 1.202582 ACTAGACTGCTTGCGTCGAAT 59.797 47.619 0.00 0.00 36.53 3.34
1347 1487 1.728971 CCAAGAACTAGACTGCTTGCG 59.271 52.381 0.00 0.00 37.11 4.85
1400 1540 1.211818 GCTGCTACTCGAATCAGCGG 61.212 60.000 14.14 14.14 41.80 5.52
1406 1546 1.676746 TCTACCGCTGCTACTCGAAT 58.323 50.000 0.00 0.00 0.00 3.34
1429 1569 0.109913 TGCTCCCATGATCCATCAGC 59.890 55.000 0.00 0.00 40.64 4.26
1519 1659 3.445096 ACTTCATACAGCATGGGAAAAGC 59.555 43.478 0.00 0.00 43.62 3.51
1525 1665 2.425143 ACCACTTCATACAGCATGGG 57.575 50.000 0.00 0.00 43.62 4.00
1553 1693 7.458409 ACTTTGCTCAACATGTAATCTTCAT 57.542 32.000 0.00 0.00 0.00 2.57
1764 1913 1.956477 GCCACACCAAGAACAACAGAT 59.044 47.619 0.00 0.00 0.00 2.90
1815 1964 3.893763 CGCAAACGGCACACCCAA 61.894 61.111 0.00 0.00 45.17 4.12
1827 1976 1.669115 GACTCTGAGCTGGCGCAAA 60.669 57.895 10.83 0.00 39.10 3.68
1836 1985 2.294233 TGCAAAATTGGTGACTCTGAGC 59.706 45.455 4.19 0.00 0.00 4.26
1856 2005 4.639755 TCTCTTGATCTAGAGCACAGACTG 59.360 45.833 24.23 0.00 41.18 3.51
1964 2115 7.164008 GTGCATAAATTGACAGTTTTGCAAAAC 59.836 33.333 36.64 36.64 46.54 2.43
1965 2116 7.148356 TGTGCATAAATTGACAGTTTTGCAAAA 60.148 29.630 20.46 20.46 35.96 2.44
1969 2120 5.903764 TGTGCATAAATTGACAGTTTTGC 57.096 34.783 16.36 16.36 0.00 3.68
1978 2129 7.387397 GGGATTGAAAACTTGTGCATAAATTGA 59.613 33.333 0.00 0.00 0.00 2.57
1984 2135 5.076182 TCAGGGATTGAAAACTTGTGCATA 58.924 37.500 0.00 0.00 31.34 3.14
1985 2136 3.896888 TCAGGGATTGAAAACTTGTGCAT 59.103 39.130 0.00 0.00 31.34 3.96
1986 2137 3.295093 TCAGGGATTGAAAACTTGTGCA 58.705 40.909 0.00 0.00 31.34 4.57
1987 2138 4.525912 ATCAGGGATTGAAAACTTGTGC 57.474 40.909 0.00 0.00 39.77 4.57
1988 2139 6.336842 AGAATCAGGGATTGAAAACTTGTG 57.663 37.500 0.00 0.00 39.77 3.33
1989 2140 6.660949 CCTAGAATCAGGGATTGAAAACTTGT 59.339 38.462 0.00 0.00 39.77 3.16
1990 2141 7.093322 CCTAGAATCAGGGATTGAAAACTTG 57.907 40.000 0.00 0.00 39.77 3.16
2006 2157 2.124277 AACCGGCAAACCCTAGAATC 57.876 50.000 0.00 0.00 0.00 2.52
2022 2173 2.412089 CGACGTTGGATCTCTGAAAACC 59.588 50.000 0.00 0.00 0.00 3.27
2075 2226 2.556622 CGCTTAAAACACTGGGTTCCAT 59.443 45.455 0.00 0.00 39.29 3.41
2097 2248 1.060122 CGCGATTTAACCTTCGTCACC 59.940 52.381 0.00 0.00 37.66 4.02
2287 2439 8.620116 AGCATTAGCAAAACCAAATTTGTAAT 57.380 26.923 16.73 9.18 45.49 1.89
2319 2471 1.065854 AGAACACTGCTATCCACCAGC 60.066 52.381 0.00 0.00 39.56 4.85
2386 2541 1.372087 GCAGACTGGCACCATGCTAC 61.372 60.000 4.26 0.00 44.28 3.58
2505 2660 1.680207 GATCGGGCGTAGTAGAAACCT 59.320 52.381 0.00 0.00 0.00 3.50
2699 2854 2.526046 CCGTTGGGGAACAGGTCCT 61.526 63.158 3.92 0.00 46.92 3.85
2704 2859 0.323629 TAAGCTCCGTTGGGGAACAG 59.676 55.000 0.00 0.00 46.61 3.16
2880 3035 1.708993 TTGCTTCACCCCAGCTCTGT 61.709 55.000 0.00 0.00 38.19 3.41
2921 3076 1.728971 CCTCAGACGCATGAAACTGAC 59.271 52.381 0.00 0.00 35.85 3.51
2922 3077 1.618343 TCCTCAGACGCATGAAACTGA 59.382 47.619 0.00 6.45 37.71 3.41
2981 3136 5.762218 AGAATTAGCATTGGCAAGTAGCTAG 59.238 40.000 22.38 0.00 44.61 3.42
3070 3225 7.507829 TGTGTGGATGACATCATATATCAACA 58.492 34.615 17.08 6.76 36.78 3.33
3183 3347 5.699458 CCTAAAATATTTATGCCGTCTCCGT 59.301 40.000 0.01 0.00 0.00 4.69
3290 3455 3.951037 TCTGAAACTTAAAGCAGCCACAA 59.049 39.130 0.00 0.00 0.00 3.33
3396 3563 5.070770 TGCCTGCCTGTTTATTTGTATTG 57.929 39.130 0.00 0.00 0.00 1.90
3472 3677 5.024785 AGACACTGCTACCTTTATTAGCC 57.975 43.478 0.00 0.00 41.20 3.93
3489 3696 5.569413 ACTGTTCATTTTCGTTGAAGACAC 58.431 37.500 0.00 0.00 33.95 3.67
3603 3813 4.888917 AGAAGCTTGAGTTCAGGAAGTAC 58.111 43.478 2.10 0.00 0.00 2.73
3745 3955 4.553351 GCATTTTCAGTTTCCTTTTGCTGC 60.553 41.667 0.00 0.00 0.00 5.25
3769 3979 3.485394 TCTAATGTTCTGTTTGCCTGCA 58.515 40.909 0.00 0.00 0.00 4.41
3852 4065 8.242729 TGCTAGATGTATGAGATTTCTCTTGA 57.757 34.615 8.91 0.00 43.25 3.02
3888 4101 2.660189 AACATTGTATGGCTTGCTGC 57.340 45.000 0.00 0.00 41.94 5.25
3889 4102 5.565592 TCTTAACATTGTATGGCTTGCTG 57.434 39.130 0.00 0.00 33.60 4.41
3918 4138 3.981071 TTCTCCGGATGTGTCTCAAAT 57.019 42.857 3.57 0.00 0.00 2.32
3919 4139 3.981071 ATTCTCCGGATGTGTCTCAAA 57.019 42.857 3.57 0.00 0.00 2.69
3920 4140 6.323996 ACTTATATTCTCCGGATGTGTCTCAA 59.676 38.462 3.57 0.00 0.00 3.02
3921 4141 5.833667 ACTTATATTCTCCGGATGTGTCTCA 59.166 40.000 3.57 0.00 0.00 3.27
3922 4142 6.334102 ACTTATATTCTCCGGATGTGTCTC 57.666 41.667 3.57 0.00 0.00 3.36
3923 4143 6.732896 AACTTATATTCTCCGGATGTGTCT 57.267 37.500 3.57 0.00 0.00 3.41
3924 4144 8.882415 TTTAACTTATATTCTCCGGATGTGTC 57.118 34.615 3.57 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.