Multiple sequence alignment - TraesCS5B01G301100

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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 TraesCS5B01G301100 chr5B 100.000 4602 0 0 1 4602 485994482 485999083 0.000000e+00 8499.0
1 TraesCS5B01G301100 chr5B 92.848 769 41 4 1 762 2797762 2797001 0.000000e+00 1103.0
2 TraesCS5B01G301100 chr5D 97.513 2091 34 5 1604 3678 404760472 404762560 0.000000e+00 3557.0
3 TraesCS5B01G301100 chr5D 96.302 649 14 2 968 1606 404759658 404760306 0.000000e+00 1057.0
4 TraesCS5B01G301100 chr5D 87.154 794 56 19 3806 4595 404762627 404763378 0.000000e+00 859.0
5 TraesCS5B01G301100 chr5D 90.476 420 32 3 836 1254 404758190 404758602 8.710000e-152 547.0
6 TraesCS5B01G301100 chr5D 75.843 356 66 18 4225 4571 480742065 480741721 3.680000e-36 163.0
7 TraesCS5B01G301100 chr5A 90.186 2038 137 15 2162 4161 509337444 509335432 0.000000e+00 2597.0
8 TraesCS5B01G301100 chr5A 90.133 1956 139 26 2115 4032 509337442 509339381 0.000000e+00 2494.0
9 TraesCS5B01G301100 chr5A 92.668 832 48 3 1 819 17704789 17705620 0.000000e+00 1186.0
10 TraesCS5B01G301100 chr5A 95.513 156 6 1 4080 4234 509339373 509339528 9.890000e-62 248.0
11 TraesCS5B01G301100 chr7B 91.587 832 57 5 1 819 336807852 336807021 0.000000e+00 1136.0
12 TraesCS5B01G301100 chr3B 90.144 832 69 6 1 819 775078380 775079211 0.000000e+00 1070.0
13 TraesCS5B01G301100 chr3B 89.354 836 75 5 1 823 466646055 466645221 0.000000e+00 1038.0
14 TraesCS5B01G301100 chr3B 89.209 834 74 9 1 820 687742239 687743070 0.000000e+00 1027.0
15 TraesCS5B01G301100 chr3B 87.846 831 88 5 2 819 186645303 186646133 0.000000e+00 963.0
16 TraesCS5B01G301100 chr3B 75.499 351 55 23 4225 4567 519393086 519393413 4.800000e-30 143.0
17 TraesCS5B01G301100 chr2A 89.904 832 71 3 1 819 511127335 511126504 0.000000e+00 1059.0
18 TraesCS5B01G301100 chr2A 78.808 453 93 3 2346 2796 670233791 670233340 7.480000e-78 302.0
19 TraesCS5B01G301100 chr2A 88.350 103 12 0 1012 1114 670235250 670235148 1.740000e-24 124.0
20 TraesCS5B01G301100 chr7A 89.784 832 72 3 1 819 395546717 395547548 0.000000e+00 1053.0
21 TraesCS5B01G301100 chr7A 92.683 41 1 2 3771 3811 48283808 48283770 1.790000e-04 58.4
22 TraesCS5B01G301100 chr1A 90.444 743 51 4 2947 3678 84291466 84292199 0.000000e+00 961.0
23 TraesCS5B01G301100 chr1A 93.500 600 36 3 2352 2949 84275920 84276518 0.000000e+00 889.0
24 TraesCS5B01G301100 chr1A 86.570 618 46 12 996 1601 84275006 84275598 0.000000e+00 647.0
25 TraesCS5B01G301100 chr1A 91.142 429 30 5 3806 4234 84292267 84292687 3.990000e-160 575.0
26 TraesCS5B01G301100 chr1A 97.241 145 4 0 2207 2351 84275600 84275744 3.560000e-61 246.0
27 TraesCS5B01G301100 chr3D 93.002 643 31 2 2207 2835 353141511 353142153 0.000000e+00 926.0
28 TraesCS5B01G301100 chr3D 91.064 470 26 4 2947 3405 353156771 353157235 5.060000e-174 621.0
29 TraesCS5B01G301100 chr3D 84.969 652 53 19 966 1601 353140887 353141509 1.820000e-173 619.0
30 TraesCS5B01G301100 chr3D 92.308 429 25 4 3806 4234 353157527 353157947 1.830000e-168 603.0
31 TraesCS5B01G301100 chr3D 92.544 228 17 0 3451 3678 353157233 353157460 1.230000e-85 327.0
32 TraesCS5B01G301100 chr3D 78.134 343 47 14 4262 4599 590662960 590662641 4.700000e-45 193.0
33 TraesCS5B01G301100 chr3D 91.597 119 10 0 2831 2949 353152572 353152690 1.020000e-36 165.0
34 TraesCS5B01G301100 chr2D 78.781 443 93 1 2346 2787 524578602 524578160 3.480000e-76 296.0
35 TraesCS5B01G301100 chr2D 90.291 103 10 0 1012 1114 524580071 524579969 8.030000e-28 135.0
36 TraesCS5B01G301100 chr2B 78.604 444 92 3 2346 2787 620621380 620621822 1.620000e-74 291.0
37 TraesCS5B01G301100 chr2B 88.350 103 12 0 1012 1114 620619903 620620005 1.740000e-24 124.0
38 TraesCS5B01G301100 chr7D 81.707 328 43 14 4276 4595 490439315 490439633 1.640000e-64 257.0
39 TraesCS5B01G301100 chr1B 78.191 376 62 18 4234 4598 61453295 61452929 5.990000e-54 222.0
40 TraesCS5B01G301100 chr1B 76.508 315 41 12 4280 4592 610898986 610899269 1.730000e-29 141.0
41 TraesCS5B01G301100 chr4D 80.386 311 43 15 4293 4595 215168001 215168301 2.160000e-53 220.0
42 TraesCS5B01G301100 chr4D 76.094 297 31 18 4330 4598 389188168 389187884 8.090000e-23 119.0
43 TraesCS5B01G301100 chr6B 80.657 274 42 11 4247 4515 130297560 130297827 7.810000e-48 202.0
44 TraesCS5B01G301100 chr4A 75.603 373 67 19 4233 4595 540918948 540918590 3.680000e-36 163.0
45 TraesCS5B01G301100 chr4A 75.603 373 66 19 4233 4595 540928656 540928299 1.330000e-35 161.0
46 TraesCS5B01G301100 chr4A 75.335 373 68 19 4233 4595 540914745 540914387 1.710000e-34 158.0
47 TraesCS5B01G301100 chrUn 75.287 348 66 18 4234 4571 247800072 247800409 1.030000e-31 148.0
48 TraesCS5B01G301100 chrUn 78.173 197 32 9 4234 4427 399554342 399554530 1.050000e-21 115.0
49 TraesCS5B01G301100 chr1D 76.157 281 42 11 4230 4509 26285324 26285580 1.740000e-24 124.0
50 TraesCS5B01G301100 chr1D 90.476 84 7 1 4516 4598 74336324 74336241 4.870000e-20 110.0


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 TraesCS5B01G301100 chr5B 485994482 485999083 4601 False 8499.0 8499 100.00000 1 4602 1 chr5B.!!$F1 4601
1 TraesCS5B01G301100 chr5B 2797001 2797762 761 True 1103.0 1103 92.84800 1 762 1 chr5B.!!$R1 761
2 TraesCS5B01G301100 chr5D 404758190 404763378 5188 False 1505.0 3557 92.86125 836 4595 4 chr5D.!!$F1 3759
3 TraesCS5B01G301100 chr5A 509335432 509337444 2012 True 2597.0 2597 90.18600 2162 4161 1 chr5A.!!$R1 1999
4 TraesCS5B01G301100 chr5A 509337442 509339528 2086 False 1371.0 2494 92.82300 2115 4234 2 chr5A.!!$F2 2119
5 TraesCS5B01G301100 chr5A 17704789 17705620 831 False 1186.0 1186 92.66800 1 819 1 chr5A.!!$F1 818
6 TraesCS5B01G301100 chr7B 336807021 336807852 831 True 1136.0 1136 91.58700 1 819 1 chr7B.!!$R1 818
7 TraesCS5B01G301100 chr3B 775078380 775079211 831 False 1070.0 1070 90.14400 1 819 1 chr3B.!!$F4 818
8 TraesCS5B01G301100 chr3B 466645221 466646055 834 True 1038.0 1038 89.35400 1 823 1 chr3B.!!$R1 822
9 TraesCS5B01G301100 chr3B 687742239 687743070 831 False 1027.0 1027 89.20900 1 820 1 chr3B.!!$F3 819
10 TraesCS5B01G301100 chr3B 186645303 186646133 830 False 963.0 963 87.84600 2 819 1 chr3B.!!$F1 817
11 TraesCS5B01G301100 chr2A 511126504 511127335 831 True 1059.0 1059 89.90400 1 819 1 chr2A.!!$R1 818
12 TraesCS5B01G301100 chr2A 670233340 670235250 1910 True 213.0 302 83.57900 1012 2796 2 chr2A.!!$R2 1784
13 TraesCS5B01G301100 chr7A 395546717 395547548 831 False 1053.0 1053 89.78400 1 819 1 chr7A.!!$F1 818
14 TraesCS5B01G301100 chr1A 84291466 84292687 1221 False 768.0 961 90.79300 2947 4234 2 chr1A.!!$F2 1287
15 TraesCS5B01G301100 chr1A 84275006 84276518 1512 False 594.0 889 92.43700 996 2949 3 chr1A.!!$F1 1953
16 TraesCS5B01G301100 chr3D 353140887 353142153 1266 False 772.5 926 88.98550 966 2835 2 chr3D.!!$F2 1869
17 TraesCS5B01G301100 chr3D 353156771 353157947 1176 False 517.0 621 91.97200 2947 4234 3 chr3D.!!$F3 1287
18 TraesCS5B01G301100 chr2D 524578160 524580071 1911 True 215.5 296 84.53600 1012 2787 2 chr2D.!!$R1 1775
19 TraesCS5B01G301100 chr2B 620619903 620621822 1919 False 207.5 291 83.47700 1012 2787 2 chr2B.!!$F1 1775

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
596 602 0.474184 ATTGAAGGATGGCTACCCCG 59.526 55.000 0.00 0.00 35.87 5.73 F
870 1149 0.664166 CAAAATTGTGCGGCGCTCTT 60.664 50.000 33.26 17.27 0.00 2.85 F
968 1247 1.228337 AAACCCTTTCGTTCCCCCG 60.228 57.895 0.00 0.00 0.00 5.73 F
1280 1840 2.283809 CTCCTCCATCCTCGGGGT 59.716 66.667 0.00 0.00 0.00 4.95 F
2589 3855 1.315690 CATGGGATGTGCATGAGGAC 58.684 55.000 0.00 0.00 36.51 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 3038 2.158871 AGTCTAGAAACCGGCAACAACA 60.159 45.455 0.00 0.0 0.00 3.33 R
2191 3206 5.646793 GGAGTCCCAAAATTAAGTACTCCAC 59.353 44.000 14.13 0.0 46.94 4.02 R
2194 3209 5.811100 CGAGGAGTCCCAAAATTAAGTACTC 59.189 44.000 5.25 0.0 33.88 2.59 R
3250 4536 1.959848 GCCAACAGCCTTTCTGGTC 59.040 57.895 0.00 0.0 41.81 4.02 R
4248 5623 0.950836 TTCTCCCATTGCAACACACG 59.049 50.000 0.00 0.0 0.00 4.49 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
184 185 4.261405 CGGTGCTTGTCCAGTTTTTCAATA 60.261 41.667 0.00 0.00 0.00 1.90
273 274 2.551938 GGATAAGCCTTCCTCCTGATGC 60.552 54.545 0.00 0.00 0.00 3.91
323 324 4.521639 AGCAGTGCAAGAATCTTTCATGAA 59.478 37.500 19.20 3.38 30.32 2.57
351 352 2.125106 GTGCAGGCTACGAAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
596 602 0.474184 ATTGAAGGATGGCTACCCCG 59.526 55.000 0.00 0.00 35.87 5.73
618 624 3.810386 GTCTTTGATAAGATCCGAAGCCC 59.190 47.826 0.00 0.00 42.14 5.19
785 801 7.697691 AGTTTGACACTGTCATTGTAAAGAAG 58.302 34.615 12.71 0.00 42.40 2.85
820 836 4.027437 ACCACACCAAGTTGTACCAAAAT 58.973 39.130 1.45 0.00 0.00 1.82
825 841 6.475402 CACACCAAGTTGTACCAAAATCTTTC 59.525 38.462 1.45 0.00 0.00 2.62
826 842 5.685511 CACCAAGTTGTACCAAAATCTTTCG 59.314 40.000 1.45 0.00 0.00 3.46
827 843 5.219633 CCAAGTTGTACCAAAATCTTTCGG 58.780 41.667 1.45 0.00 0.00 4.30
828 844 5.009210 CCAAGTTGTACCAAAATCTTTCGGA 59.991 40.000 1.45 0.00 0.00 4.55
830 846 4.760204 AGTTGTACCAAAATCTTTCGGAGG 59.240 41.667 0.00 0.00 0.00 4.30
831 847 4.360951 TGTACCAAAATCTTTCGGAGGT 57.639 40.909 0.00 0.00 0.00 3.85
832 848 4.320870 TGTACCAAAATCTTTCGGAGGTC 58.679 43.478 0.00 0.00 0.00 3.85
833 849 3.790089 ACCAAAATCTTTCGGAGGTCT 57.210 42.857 0.00 0.00 0.00 3.85
834 850 3.412386 ACCAAAATCTTTCGGAGGTCTG 58.588 45.455 0.00 0.00 0.00 3.51
835 851 3.072476 ACCAAAATCTTTCGGAGGTCTGA 59.928 43.478 0.00 0.00 0.00 3.27
836 852 4.263506 ACCAAAATCTTTCGGAGGTCTGAT 60.264 41.667 0.00 0.00 0.00 2.90
837 853 4.333926 CCAAAATCTTTCGGAGGTCTGATC 59.666 45.833 0.00 0.00 0.00 2.92
838 854 4.826274 AAATCTTTCGGAGGTCTGATCA 57.174 40.909 0.00 0.00 0.00 2.92
839 855 4.826274 AATCTTTCGGAGGTCTGATCAA 57.174 40.909 0.00 0.00 0.00 2.57
840 856 4.826274 ATCTTTCGGAGGTCTGATCAAA 57.174 40.909 0.00 0.00 0.00 2.69
870 1149 0.664166 CAAAATTGTGCGGCGCTCTT 60.664 50.000 33.26 17.27 0.00 2.85
881 1160 4.152625 CGCTCTTCTTTGCCGCCG 62.153 66.667 0.00 0.00 0.00 6.46
888 1167 4.767255 CTTTGCCGCCGCTCCTCT 62.767 66.667 0.00 0.00 35.36 3.69
957 1236 2.753168 GCTCTCCAAAGTCCAAACCCTT 60.753 50.000 0.00 0.00 0.00 3.95
958 1237 3.566351 CTCTCCAAAGTCCAAACCCTTT 58.434 45.455 0.00 0.00 0.00 3.11
960 1239 2.293399 CTCCAAAGTCCAAACCCTTTCG 59.707 50.000 0.00 0.00 0.00 3.46
961 1240 2.028876 CCAAAGTCCAAACCCTTTCGT 58.971 47.619 0.00 0.00 0.00 3.85
963 1242 3.490249 CCAAAGTCCAAACCCTTTCGTTC 60.490 47.826 0.00 0.00 0.00 3.95
968 1247 1.228337 AAACCCTTTCGTTCCCCCG 60.228 57.895 0.00 0.00 0.00 5.73
970 1249 4.029809 CCCTTTCGTTCCCCCGCT 62.030 66.667 0.00 0.00 0.00 5.52
985 1488 4.351054 GCTCCCACACCCACCAGG 62.351 72.222 0.00 0.00 43.78 4.45
1249 1809 3.997064 CTCAGAAGCACCCGCCTCG 62.997 68.421 0.00 0.00 39.83 4.63
1280 1840 2.283809 CTCCTCCATCCTCGGGGT 59.716 66.667 0.00 0.00 0.00 4.95
1597 2185 2.436417 TCCTTCCGCTCTTTTTCCATG 58.564 47.619 0.00 0.00 0.00 3.66
1600 2188 3.005791 CCTTCCGCTCTTTTTCCATGTTT 59.994 43.478 0.00 0.00 0.00 2.83
1654 2639 7.397221 TCATTTGAGTTGTCAGGATAGTGATT 58.603 34.615 0.00 0.00 32.98 2.57
2189 3204 6.376581 AGCTTCCATCATCTAAAAGAAGTTGG 59.623 38.462 0.00 3.84 35.32 3.77
2191 3206 7.452880 TTCCATCATCTAAAAGAAGTTGGTG 57.547 36.000 8.37 0.00 35.44 4.17
2193 3208 6.430925 TCCATCATCTAAAAGAAGTTGGTGTG 59.569 38.462 8.37 0.00 35.44 3.82
2194 3209 6.349611 CCATCATCTAAAAGAAGTTGGTGTGG 60.350 42.308 2.52 0.00 31.56 4.17
2589 3855 1.315690 CATGGGATGTGCATGAGGAC 58.684 55.000 0.00 0.00 36.51 3.85
2730 3996 6.761242 GCCTGAAGGTTTTCAAACTTAACAAT 59.239 34.615 2.55 0.00 42.48 2.71
3250 4536 5.773575 AGTCGCATACTGTGGAGTATAATG 58.226 41.667 0.00 0.00 42.55 1.90
3262 4548 4.721776 TGGAGTATAATGACCAGAAAGGCT 59.278 41.667 0.00 0.00 43.14 4.58
3741 5057 3.383698 TTAGTACTCCCTCTGTCCCAG 57.616 52.381 0.00 0.00 0.00 4.45
3746 5062 0.179936 CTCCCTCTGTCCCAGAATGC 59.820 60.000 0.00 0.00 40.18 3.56
3749 5065 1.064166 CCCTCTGTCCCAGAATGCAAT 60.064 52.381 0.00 0.00 40.18 3.56
3825 5143 5.184671 GGGGGTAGTAAGTATCATTCTACCG 59.815 48.000 11.74 0.00 46.54 4.02
3847 5165 7.060421 ACCGTTTGATATTTAAGATGGTGGAT 58.940 34.615 0.00 0.00 0.00 3.41
3889 5207 2.044860 GGAATAGAATCTCGTGACGCG 58.955 52.381 3.53 3.53 43.01 6.01
3935 5253 8.148351 AGTGTTGTCACAGTACATGTTAGTATT 58.852 33.333 2.30 0.00 46.01 1.89
4014 5332 5.130809 TGATCTGGTGTGGTATCATGATCAA 59.869 40.000 12.53 0.00 36.95 2.57
4062 5436 2.158755 AGTGCAAGTGAACCTGCTAACT 60.159 45.455 5.68 0.00 0.00 2.24
4066 5440 2.726832 AGTGAACCTGCTAACTCGTC 57.273 50.000 0.00 0.00 0.00 4.20
4073 5447 1.528603 CCTGCTAACTCGTCGTACGTC 60.529 57.143 16.05 8.97 43.14 4.34
4079 5453 0.162507 ACTCGTCGTACGTCGTGAAG 59.837 55.000 31.95 24.18 43.14 3.02
4081 5455 2.142239 CGTCGTACGTCGTGAAGCC 61.142 63.158 23.43 0.00 40.80 4.35
4085 5459 1.192436 CGTACGTCGTGAAGCCGATC 61.192 60.000 8.47 0.00 39.34 3.69
4245 5620 8.174733 ACACTTAGTTAGTACTAGCAAGACAA 57.825 34.615 22.90 9.75 38.09 3.18
4248 5623 5.402997 AGTTAGTACTAGCAAGACAACCC 57.597 43.478 17.72 0.00 31.21 4.11
4250 5625 2.245582 AGTACTAGCAAGACAACCCGT 58.754 47.619 0.00 0.00 0.00 5.28
4251 5626 2.029290 AGTACTAGCAAGACAACCCGTG 60.029 50.000 0.00 0.00 0.00 4.94
4252 5627 0.756903 ACTAGCAAGACAACCCGTGT 59.243 50.000 0.00 0.00 45.74 4.49
4253 5628 1.148310 CTAGCAAGACAACCCGTGTG 58.852 55.000 0.00 0.00 41.96 3.82
4254 5629 0.466543 TAGCAAGACAACCCGTGTGT 59.533 50.000 0.00 0.00 41.96 3.72
4255 5630 0.393808 AGCAAGACAACCCGTGTGTT 60.394 50.000 0.00 0.00 44.20 3.32
4261 5636 2.884146 CAACCCGTGTGTTGCAATG 58.116 52.632 0.59 0.00 39.19 2.82
4262 5637 0.597118 CAACCCGTGTGTTGCAATGG 60.597 55.000 0.59 0.00 39.19 3.16
4263 5638 1.743321 AACCCGTGTGTTGCAATGGG 61.743 55.000 11.27 11.27 45.61 4.00
4264 5639 1.900981 CCCGTGTGTTGCAATGGGA 60.901 57.895 7.55 0.00 43.92 4.37
4265 5640 1.580942 CCGTGTGTTGCAATGGGAG 59.419 57.895 0.59 0.00 0.00 4.30
4266 5641 0.888736 CCGTGTGTTGCAATGGGAGA 60.889 55.000 0.59 0.00 0.00 3.71
4314 5689 4.386652 GTCATGACCACATTTTGTTGCATC 59.613 41.667 15.31 0.00 34.15 3.91
4325 5700 4.926860 TTTGTTGCATCACTGAGATACG 57.073 40.909 0.00 0.00 34.43 3.06
4414 5789 8.554835 TCACGAACATATCTTAAATTGTGGAA 57.445 30.769 0.00 0.00 0.00 3.53
4416 5791 9.619316 CACGAACATATCTTAAATTGTGGAAAA 57.381 29.630 0.00 0.00 0.00 2.29
4557 5935 3.061139 GCGAACATTTCTAGAATCGACGG 60.061 47.826 23.61 8.07 32.38 4.79
4561 5939 5.263968 ACATTTCTAGAATCGACGGACAT 57.736 39.130 5.89 0.00 0.00 3.06
4562 5940 5.661458 ACATTTCTAGAATCGACGGACATT 58.339 37.500 5.89 0.00 0.00 2.71
4563 5941 6.106673 ACATTTCTAGAATCGACGGACATTT 58.893 36.000 5.89 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 185 3.084786 GTTTCTGCTGCCTAAGATGGTT 58.915 45.455 0.00 0.00 0.00 3.67
273 274 1.224069 CTGGATAGGCAATGCGTCCG 61.224 60.000 2.87 2.72 31.25 4.79
323 324 0.106519 AGCCTGCACTGGAACTTTGT 60.107 50.000 0.00 0.00 0.00 2.83
351 352 1.756375 CGTGCCAGTCAGCTATTCGC 61.756 60.000 0.00 0.00 39.57 4.70
573 579 3.074538 GGGGTAGCCATCCTTCAATATGT 59.925 47.826 14.06 0.00 0.00 2.29
596 602 3.810386 GGGCTTCGGATCTTATCAAAGAC 59.190 47.826 0.00 0.00 44.40 3.01
618 624 5.278512 GCAGAAAGAAAAACTCCTTACTGGG 60.279 44.000 0.00 0.00 36.20 4.45
820 836 4.040461 ACTTTTGATCAGACCTCCGAAAGA 59.960 41.667 15.62 0.00 0.00 2.52
825 841 3.257393 CAGACTTTTGATCAGACCTCCG 58.743 50.000 0.00 0.00 0.00 4.63
826 842 4.249661 GACAGACTTTTGATCAGACCTCC 58.750 47.826 0.00 0.00 0.00 4.30
827 843 4.249661 GGACAGACTTTTGATCAGACCTC 58.750 47.826 0.00 0.00 0.00 3.85
828 844 3.008485 GGGACAGACTTTTGATCAGACCT 59.992 47.826 0.00 0.00 0.00 3.85
830 846 3.244561 TGGGGACAGACTTTTGATCAGAC 60.245 47.826 0.00 0.00 35.01 3.51
831 847 2.978978 TGGGGACAGACTTTTGATCAGA 59.021 45.455 0.00 0.00 35.01 3.27
832 848 3.423539 TGGGGACAGACTTTTGATCAG 57.576 47.619 0.00 0.00 35.01 2.90
833 849 3.874383 TTGGGGACAGACTTTTGATCA 57.126 42.857 0.00 0.00 44.54 2.92
834 850 5.728637 ATTTTGGGGACAGACTTTTGATC 57.271 39.130 0.00 0.00 44.54 2.92
835 851 5.366477 ACAATTTTGGGGACAGACTTTTGAT 59.634 36.000 0.00 0.00 44.54 2.57
836 852 4.714308 ACAATTTTGGGGACAGACTTTTGA 59.286 37.500 0.00 0.00 44.54 2.69
837 853 4.810491 CACAATTTTGGGGACAGACTTTTG 59.190 41.667 0.00 0.00 44.54 2.44
838 854 4.683129 GCACAATTTTGGGGACAGACTTTT 60.683 41.667 0.00 0.00 44.54 2.27
839 855 3.181466 GCACAATTTTGGGGACAGACTTT 60.181 43.478 0.00 0.00 44.54 2.66
840 856 2.365293 GCACAATTTTGGGGACAGACTT 59.635 45.455 0.00 0.00 44.54 3.01
870 1149 4.760047 GAGGAGCGGCGGCAAAGA 62.760 66.667 19.21 0.00 43.41 2.52
960 1239 4.717313 GTGTGGGAGCGGGGGAAC 62.717 72.222 0.00 0.00 0.00 3.62
968 1247 4.351054 CCTGGTGGGTGTGGGAGC 62.351 72.222 0.00 0.00 0.00 4.70
970 1249 2.415962 ATCTCCTGGTGGGTGTGGGA 62.416 60.000 0.00 0.00 36.25 4.37
985 1488 1.114627 GCCATTGTTGGGGGAATCTC 58.885 55.000 0.00 0.00 43.84 2.75
1122 1628 0.935196 GATACGGCCGCTTAGGTTTG 59.065 55.000 28.58 0.00 43.70 2.93
1442 2005 4.407365 CCAGTACCCAATATTCCCCATTC 58.593 47.826 0.00 0.00 0.00 2.67
1636 2621 7.962995 TCTAAGAATCACTATCCTGACAACT 57.037 36.000 0.00 0.00 0.00 3.16
2023 3038 2.158871 AGTCTAGAAACCGGCAACAACA 60.159 45.455 0.00 0.00 0.00 3.33
2185 3200 6.443792 CCAAAATTAAGTACTCCACACCAAC 58.556 40.000 0.00 0.00 0.00 3.77
2189 3204 6.002082 AGTCCCAAAATTAAGTACTCCACAC 58.998 40.000 0.00 0.00 0.00 3.82
2191 3206 5.646793 GGAGTCCCAAAATTAAGTACTCCAC 59.353 44.000 14.13 0.00 46.94 4.02
2194 3209 5.811100 CGAGGAGTCCCAAAATTAAGTACTC 59.189 44.000 5.25 0.00 33.88 2.59
2589 3855 9.947669 GGATGAAAATCTATTGAGTTGATTCTG 57.052 33.333 0.00 0.00 32.28 3.02
2925 4192 9.547753 AAATCTAGCGATATATTCACACAACTT 57.452 29.630 0.00 0.00 0.00 2.66
2954 4221 9.276590 CTATCAAGTTATGTTGATCTGCCAATA 57.723 33.333 2.44 0.00 42.38 1.90
3250 4536 1.959848 GCCAACAGCCTTTCTGGTC 59.040 57.895 0.00 0.00 41.81 4.02
3262 4548 4.112634 ACTTGGATTTAGAAGGCCAACA 57.887 40.909 5.01 0.00 35.61 3.33
3415 4707 7.141758 TGAGATAATGTCTATTCCCTTGCTT 57.858 36.000 0.00 0.00 37.29 3.91
3577 4869 2.777692 AGTTCTGGTCCAAAGGAAGACA 59.222 45.455 0.00 0.00 34.58 3.41
3580 4872 6.490040 TGATTTAAGTTCTGGTCCAAAGGAAG 59.510 38.462 0.00 0.00 31.38 3.46
3696 5012 8.409358 AATATTATACATTTCTTGGGCAGGAC 57.591 34.615 0.00 0.00 0.00 3.85
3802 5118 5.772169 ACGGTAGAATGATACTTACTACCCC 59.228 44.000 0.00 0.00 45.71 4.95
3825 5143 8.078596 GCAGATCCACCATCTTAAATATCAAAC 58.921 37.037 0.00 0.00 40.20 2.93
3847 5165 2.068519 CGTAGCACAACATTCAGCAGA 58.931 47.619 0.00 0.00 0.00 4.26
3889 5207 7.781548 ACACTGTGAATACGGTTTTATATCC 57.218 36.000 15.86 0.00 43.85 2.59
3971 5289 3.995199 TCAGTTATAGCACTGCCATAGC 58.005 45.455 0.00 0.00 43.51 2.97
3980 5298 4.122776 CCACACCAGATCAGTTATAGCAC 58.877 47.826 0.00 0.00 0.00 4.40
4062 5436 1.154599 GCTTCACGACGTACGACGA 60.155 57.895 38.08 19.86 46.05 4.20
4066 5440 1.192436 GATCGGCTTCACGACGTACG 61.192 60.000 15.01 15.01 46.75 3.67
4079 5453 2.897350 CTTCTTGGGGCGATCGGC 60.897 66.667 31.57 31.57 42.51 5.54
4081 5455 2.897350 GGCTTCTTGGGGCGATCG 60.897 66.667 11.69 11.69 0.00 3.69
4085 5459 2.713967 CCAATGGCTTCTTGGGGCG 61.714 63.158 6.27 0.00 39.62 6.13
4112 5486 4.564782 ATCTTGATCAAAGGAGCAGTCA 57.435 40.909 9.88 0.00 41.08 3.41
4221 5596 7.541437 GGTTGTCTTGCTAGTACTAACTAAGTG 59.459 40.741 3.76 0.00 39.39 3.16
4245 5620 2.199652 CCCATTGCAACACACGGGT 61.200 57.895 0.00 0.00 0.00 5.28
4248 5623 0.950836 TTCTCCCATTGCAACACACG 59.049 50.000 0.00 0.00 0.00 4.49
4274 5649 1.628340 TGACCGTTGGGAGATTGTGAT 59.372 47.619 0.00 0.00 36.97 3.06
4278 5653 2.009774 GTCATGACCGTTGGGAGATTG 58.990 52.381 15.31 0.00 36.97 2.67
4314 5689 4.513318 TGAGAGTGATAGCGTATCTCAGTG 59.487 45.833 5.74 0.00 40.98 3.66
4350 5725 9.984190 TTCATGATTTTCAAAGATTGTTCATGA 57.016 25.926 16.77 16.77 43.69 3.07
4352 5727 9.767228 TGTTCATGATTTTCAAAGATTGTTCAT 57.233 25.926 0.00 0.00 0.00 2.57
4353 5728 9.767228 ATGTTCATGATTTTCAAAGATTGTTCA 57.233 25.926 0.00 0.00 0.00 3.18
4408 5783 7.331934 TGTTCACGAATTTGAAAATTTTCCACA 59.668 29.630 24.51 11.26 38.64 4.17
4409 5784 7.680062 TGTTCACGAATTTGAAAATTTTCCAC 58.320 30.769 24.51 12.04 38.64 4.02
4449 5824 7.465353 TGCTCATGATTTTAGAAAATGTCCA 57.535 32.000 4.98 0.00 38.64 4.02
4522 5900 7.214467 AGAAATGTTCGCCTATTCAAGAAAA 57.786 32.000 0.00 0.00 34.02 2.29
4536 5914 4.204573 GTCCGTCGATTCTAGAAATGTTCG 59.795 45.833 16.51 16.51 34.02 3.95
4540 5918 6.589830 AAATGTCCGTCGATTCTAGAAATG 57.410 37.500 9.71 5.15 0.00 2.32


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

AutoCloner maintained by Alex Coulton.