Multiple sequence alignment - TraesCS5D01G372600

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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 TraesCS5D01G372600 chr5D 100.000 6633 0 0 1 6633 446400082 446406714 0.000000e+00 12249.0
1 TraesCS5D01G372600 chr5A 94.707 6084 201 60 609 6633 564074997 564081018 0.000000e+00 9339.0
2 TraesCS5D01G372600 chr5A 93.878 441 27 0 1 441 564073803 564074243 0.000000e+00 665.0
3 TraesCS5D01G372600 chr5A 94.949 99 2 2 636 731 650246612 650246710 1.150000e-32 152.0
4 TraesCS5D01G372600 chr5A 96.667 90 2 1 636 725 644821114 644821026 1.490000e-31 148.0
5 TraesCS5D01G372600 chr5B 95.512 4479 154 18 2176 6633 544331268 544335720 0.000000e+00 7114.0
6 TraesCS5D01G372600 chr5B 90.588 595 31 11 1181 1751 544330140 544330733 0.000000e+00 765.0
7 TraesCS5D01G372600 chr5B 85.040 742 50 39 441 1152 544329437 544330147 0.000000e+00 699.0
8 TraesCS5D01G372600 chr5B 90.456 461 24 10 1 441 544328619 544329079 2.060000e-164 590.0
9 TraesCS5D01G372600 chr5B 86.099 446 45 10 1752 2183 544330802 544331244 1.300000e-126 464.0
10 TraesCS5D01G372600 chr5B 91.228 114 2 7 632 741 658381025 658381134 1.490000e-31 148.0
11 TraesCS5D01G372600 chr3D 96.809 94 1 2 636 729 3302152 3302243 8.910000e-34 156.0
12 TraesCS5D01G372600 chr3D 91.667 108 3 4 618 723 3309456 3309559 1.930000e-30 145.0
13 TraesCS5D01G372600 chr7B 96.739 92 1 2 643 732 677968307 677968216 1.150000e-32 152.0
14 TraesCS5D01G372600 chr7B 96.739 92 1 2 643 732 678012064 678011973 1.150000e-32 152.0
15 TraesCS5D01G372600 chr4D 86.667 60 8 0 4372 4431 283882119 283882060 4.290000e-07 67.6
16 TraesCS5D01G372600 chr1D 92.308 39 3 0 4379 4417 111092275 111092313 1.000000e-03 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 TraesCS5D01G372600 chr5D 446400082 446406714 6632 False 12249.0 12249 100.0000 1 6633 1 chr5D.!!$F1 6632
1 TraesCS5D01G372600 chr5A 564073803 564081018 7215 False 5002.0 9339 94.2925 1 6633 2 chr5A.!!$F2 6632
2 TraesCS5D01G372600 chr5B 544328619 544335720 7101 False 1926.4 7114 89.5390 1 6633 5 chr5B.!!$F2 6632

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
167 172 0.537653 TGGTCAAACGTCTCACACCA 59.462 50.0 0.00 0.0 0.00 4.17 F
1173 1833 0.108585 ATTGCCAGCCCATACGTAGG 59.891 55.0 0.08 0.0 0.00 3.18 F
1488 2187 0.322648 CATGGAGCAGTGACCTGTCA 59.677 55.0 0.00 0.0 41.02 3.58 F
2970 3785 0.388649 CAAAGAGAGTGACGTCGGGG 60.389 60.0 11.62 0.0 0.00 5.73 F
4131 4955 0.580578 CATGAAATCTGCTCGCCTCG 59.419 55.0 0.00 0.0 0.00 4.63 F
5100 5927 0.036294 GAGTCCTTCTTTCCCCGTGG 60.036 60.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2758 1.005294 GCTTCCGACGTTTCTGCGTA 61.005 55.000 0.00 0.0 45.79 4.42 R
2952 3767 0.826672 ACCCCGACGTCACTCTCTTT 60.827 55.000 17.16 0.0 0.00 2.52 R
3041 3856 1.686052 GGAGAGGATCGCTTCATCTGT 59.314 52.381 7.03 0.0 45.18 3.41 R
4509 5335 1.133853 GCTTTGAGCTGGGGATCAGAT 60.134 52.381 0.00 0.0 45.95 2.90 R
5163 5990 0.250901 ACCTACTTGTGCTTGCCCAG 60.251 55.000 0.00 0.0 0.00 4.45 R
5927 6763 0.944386 GCTGATTTGTGTGTGTCCGT 59.056 50.000 0.00 0.0 0.00 4.69 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
167 172 0.537653 TGGTCAAACGTCTCACACCA 59.462 50.000 0.00 0.00 0.00 4.17
342 362 4.796231 ATGCTCGTGTCGGCCGTC 62.796 66.667 27.15 21.30 0.00 4.79
396 416 0.674895 GGAAGCTGAGCGACCACATT 60.675 55.000 15.53 0.00 0.00 2.71
451 840 1.001268 CTGCAGCTGCCATCAATCATC 60.001 52.381 34.64 4.39 41.18 2.92
453 842 1.589803 CAGCTGCCATCAATCATCGA 58.410 50.000 0.00 0.00 0.00 3.59
525 914 2.604912 TGCTCTCTGACTCCTACCAA 57.395 50.000 0.00 0.00 0.00 3.67
527 916 3.027412 TGCTCTCTGACTCCTACCAATC 58.973 50.000 0.00 0.00 0.00 2.67
541 930 5.013547 CCTACCAATCGATGTATCTCTCCT 58.986 45.833 0.00 0.00 0.00 3.69
723 1360 1.211457 ACCACCTAGACTACGACGGAT 59.789 52.381 0.00 0.00 0.00 4.18
743 1380 4.035324 GGATCTTGTTGATACGACTCTCGA 59.965 45.833 0.00 0.00 37.54 4.04
748 1385 6.315642 TCTTGTTGATACGACTCTCGATTAGT 59.684 38.462 0.00 0.47 43.74 2.24
749 1386 6.045698 TGTTGATACGACTCTCGATTAGTC 57.954 41.667 14.91 14.91 43.74 2.59
752 1389 6.288426 TGATACGACTCTCGATTAGTCTTG 57.712 41.667 19.89 11.51 43.74 3.02
753 1390 5.816258 TGATACGACTCTCGATTAGTCTTGT 59.184 40.000 19.89 15.19 43.74 3.16
756 1393 5.867166 ACGACTCTCGATTAGTCTTGTTAC 58.133 41.667 19.89 0.69 43.74 2.50
759 1396 4.025015 TCTCGATTAGTCTTGTTACCGC 57.975 45.455 0.00 0.00 0.00 5.68
760 1397 3.114065 CTCGATTAGTCTTGTTACCGCC 58.886 50.000 0.00 0.00 0.00 6.13
761 1398 2.492881 TCGATTAGTCTTGTTACCGCCA 59.507 45.455 0.00 0.00 0.00 5.69
762 1399 3.131577 TCGATTAGTCTTGTTACCGCCAT 59.868 43.478 0.00 0.00 0.00 4.40
763 1400 3.489785 CGATTAGTCTTGTTACCGCCATC 59.510 47.826 0.00 0.00 0.00 3.51
764 1401 2.572191 TAGTCTTGTTACCGCCATCG 57.428 50.000 0.00 0.00 0.00 3.84
767 1404 1.449601 CTTGTTACCGCCATCGCCT 60.450 57.895 0.00 0.00 0.00 5.52
768 1405 1.429148 CTTGTTACCGCCATCGCCTC 61.429 60.000 0.00 0.00 0.00 4.70
789 1442 3.083349 CCGGGCAGGTGAGATGGA 61.083 66.667 0.00 0.00 34.51 3.41
848 1501 4.918201 CCGGCGCCATCTTCCTCC 62.918 72.222 28.98 0.00 0.00 4.30
850 1503 4.918201 GGCGCCATCTTCCTCCCG 62.918 72.222 24.80 0.00 0.00 5.14
852 1505 4.918201 CGCCATCTTCCTCCCGCC 62.918 72.222 0.00 0.00 0.00 6.13
854 1507 2.770048 CCATCTTCCTCCCGCCCT 60.770 66.667 0.00 0.00 0.00 5.19
855 1508 2.812619 CCATCTTCCTCCCGCCCTC 61.813 68.421 0.00 0.00 0.00 4.30
856 1509 2.840102 ATCTTCCTCCCGCCCTCG 60.840 66.667 0.00 0.00 0.00 4.63
902 1555 1.755395 CCCACATCCACATGCCCAG 60.755 63.158 0.00 0.00 32.57 4.45
903 1556 1.755395 CCACATCCACATGCCCAGG 60.755 63.158 0.00 0.00 32.57 4.45
911 1564 4.889112 CATGCCCAGGCGCCATCT 62.889 66.667 31.54 4.59 45.51 2.90
912 1565 4.575973 ATGCCCAGGCGCCATCTC 62.576 66.667 31.54 15.31 45.51 2.75
1155 1815 4.574674 TCCTGCCTTCAGAACATTACAT 57.425 40.909 0.00 0.00 42.95 2.29
1158 1818 4.418392 CTGCCTTCAGAACATTACATTGC 58.582 43.478 0.00 0.00 42.95 3.56
1159 1819 3.193267 TGCCTTCAGAACATTACATTGCC 59.807 43.478 0.00 0.00 0.00 4.52
1160 1820 3.193267 GCCTTCAGAACATTACATTGCCA 59.807 43.478 0.00 0.00 0.00 4.92
1161 1821 4.676196 GCCTTCAGAACATTACATTGCCAG 60.676 45.833 0.00 0.00 0.00 4.85
1162 1822 4.418392 CTTCAGAACATTACATTGCCAGC 58.582 43.478 0.00 0.00 0.00 4.85
1163 1823 2.754552 TCAGAACATTACATTGCCAGCC 59.245 45.455 0.00 0.00 0.00 4.85
1164 1824 2.102578 AGAACATTACATTGCCAGCCC 58.897 47.619 0.00 0.00 0.00 5.19
1165 1825 1.824230 GAACATTACATTGCCAGCCCA 59.176 47.619 0.00 0.00 0.00 5.36
1166 1826 2.163810 ACATTACATTGCCAGCCCAT 57.836 45.000 0.00 0.00 0.00 4.00
1167 1827 3.311167 ACATTACATTGCCAGCCCATA 57.689 42.857 0.00 0.00 0.00 2.74
1168 1828 2.958355 ACATTACATTGCCAGCCCATAC 59.042 45.455 0.00 0.00 0.00 2.39
1169 1829 1.674359 TTACATTGCCAGCCCATACG 58.326 50.000 0.00 0.00 0.00 3.06
1170 1830 0.544223 TACATTGCCAGCCCATACGT 59.456 50.000 0.00 0.00 0.00 3.57
1171 1831 0.544223 ACATTGCCAGCCCATACGTA 59.456 50.000 0.00 0.00 0.00 3.57
1172 1832 1.229428 CATTGCCAGCCCATACGTAG 58.771 55.000 0.08 0.00 0.00 3.51
1173 1833 0.108585 ATTGCCAGCCCATACGTAGG 59.891 55.000 0.08 0.00 0.00 3.18
1174 1834 1.268992 TTGCCAGCCCATACGTAGGT 61.269 55.000 6.48 0.00 0.00 3.08
1175 1835 1.268992 TGCCAGCCCATACGTAGGTT 61.269 55.000 6.48 0.00 0.00 3.50
1281 1942 2.328099 GCTGGACAACTGGAAGGCG 61.328 63.158 0.00 0.00 39.30 5.52
1362 2023 8.062065 ACAATTCCGTCACCAAAATGTAATAT 57.938 30.769 0.00 0.00 0.00 1.28
1363 2024 8.527810 ACAATTCCGTCACCAAAATGTAATATT 58.472 29.630 0.00 0.00 0.00 1.28
1364 2025 9.364989 CAATTCCGTCACCAAAATGTAATATTT 57.635 29.630 0.00 0.00 0.00 1.40
1365 2026 9.936759 AATTCCGTCACCAAAATGTAATATTTT 57.063 25.926 0.00 0.00 0.00 1.82
1366 2027 9.936759 ATTCCGTCACCAAAATGTAATATTTTT 57.063 25.926 0.00 0.00 0.00 1.94
1417 2097 0.684479 GTGAAATCCCAAGCCCCCTC 60.684 60.000 0.00 0.00 0.00 4.30
1488 2187 0.322648 CATGGAGCAGTGACCTGTCA 59.677 55.000 0.00 0.00 41.02 3.58
1580 2279 2.243810 GCCCAACTGTGAACCCAAATA 58.756 47.619 0.00 0.00 0.00 1.40
1741 2440 6.430000 GGTTCAGCTGTAAGTTCATTTTCCTA 59.570 38.462 14.67 0.00 35.30 2.94
1915 2682 9.593134 GAGACACTGTAAGAATCTATTTCATGT 57.407 33.333 0.00 0.00 36.75 3.21
1984 2758 1.136110 CCAAACTGCCTTTTCAACGGT 59.864 47.619 0.00 0.00 0.00 4.83
1985 2759 2.359531 CCAAACTGCCTTTTCAACGGTA 59.640 45.455 0.00 0.00 0.00 4.02
2024 2798 3.189702 GCAATCACTTAAACGGGCAGTTA 59.810 43.478 2.82 0.00 43.37 2.24
2036 2810 1.883926 GGGCAGTTAACGGACATGTTT 59.116 47.619 13.81 0.00 33.32 2.83
2077 2851 7.116948 GCTCTCGACAATGTAAGTTATGCATAT 59.883 37.037 7.36 0.00 32.69 1.78
2162 2941 3.795623 AGTAATGTCGCGGTAACAGAT 57.204 42.857 6.13 0.00 0.00 2.90
2177 2986 7.375834 CGGTAACAGATATTTAGCCTGTGATA 58.624 38.462 0.00 0.00 40.61 2.15
2197 3006 2.693069 ACTTGATTTGACCAGAGCTCG 58.307 47.619 8.37 3.24 0.00 5.03
2217 3026 8.019769 AGCTCGTTAATTTTCTTCTTACAGTC 57.980 34.615 0.00 0.00 0.00 3.51
2321 3130 2.417719 CCTCAAGACACTGTAAGGCAC 58.582 52.381 0.00 0.00 39.30 5.01
2325 3134 1.424638 AGACACTGTAAGGCACCTGT 58.575 50.000 0.00 0.00 39.30 4.00
2390 3199 9.434420 AACAAATGACTGTCAATCTTTTCAAAA 57.566 25.926 15.31 0.00 0.00 2.44
2391 3200 9.434420 ACAAATGACTGTCAATCTTTTCAAAAA 57.566 25.926 15.31 0.00 0.00 1.94
2523 3338 6.438425 ACTGCCATCTCAAACCAATTTTATCT 59.562 34.615 0.00 0.00 0.00 1.98
2549 3364 6.150976 CCATGGTTAAAAGTGTATGCTTCTGA 59.849 38.462 2.57 0.00 0.00 3.27
2952 3767 3.531207 CGGGAGCCTCATCGAGCA 61.531 66.667 0.00 0.00 0.00 4.26
2970 3785 0.388649 CAAAGAGAGTGACGTCGGGG 60.389 60.000 11.62 0.00 0.00 5.73
3033 3848 4.005650 CCTTGCAGCTGTTATTCTCTTGA 58.994 43.478 16.64 0.00 0.00 3.02
3041 3856 6.646653 CAGCTGTTATTCTCTTGACAGTGTTA 59.353 38.462 5.25 0.00 41.11 2.41
3234 4052 5.480642 TTTTGCAGGCCATTCTTCAATAA 57.519 34.783 5.01 0.00 0.00 1.40
3324 4142 5.045215 AGACGATGAACGACAACAAGTTTA 58.955 37.500 0.00 0.00 45.77 2.01
3565 4387 2.338500 GAGAAGTCAACGTTGCCTAGG 58.662 52.381 23.47 3.67 0.00 3.02
3578 4400 5.048507 CGTTGCCTAGGACTTATAGTTTCC 58.951 45.833 14.75 0.00 0.00 3.13
3739 4563 4.452455 CCATGTCCCATAATCGAAGCTTAC 59.548 45.833 0.00 0.00 0.00 2.34
4117 4941 4.901197 TCTGTTTAGGTACCTGCATGAA 57.099 40.909 25.33 7.36 0.00 2.57
4131 4955 0.580578 CATGAAATCTGCTCGCCTCG 59.419 55.000 0.00 0.00 0.00 4.63
4497 5323 7.781324 ATTCCTGTGAACTGAAATGGTAATT 57.219 32.000 0.00 0.00 32.13 1.40
4509 5335 7.230510 ACTGAAATGGTAATTTGTGAGCTGTTA 59.769 33.333 0.00 0.00 36.10 2.41
4582 5408 4.363990 CCGCAGCTCCACGACAGT 62.364 66.667 2.04 0.00 0.00 3.55
4833 5660 2.917227 TGTCGCAGGAGCTCACCA 60.917 61.111 17.19 0.00 39.10 4.17
5019 5846 1.270785 TGTATGTGAGTGTGGGTGCTG 60.271 52.381 0.00 0.00 0.00 4.41
5100 5927 0.036294 GAGTCCTTCTTTCCCCGTGG 60.036 60.000 0.00 0.00 0.00 4.94
5163 5990 7.865707 TGATACTTCACTGAAAAGAAAGCTTC 58.134 34.615 0.00 0.00 31.82 3.86
5284 6112 2.360801 GCAAACTCCACACAAGGCTAAA 59.639 45.455 0.00 0.00 0.00 1.85
5302 6130 3.807631 AACAGCAAGCGCCGTCTCA 62.808 57.895 2.29 0.00 39.83 3.27
5325 6153 8.256611 TCAGCATTCTTCTTCTAATACACAAC 57.743 34.615 0.00 0.00 0.00 3.32
5326 6154 7.334421 TCAGCATTCTTCTTCTAATACACAACC 59.666 37.037 0.00 0.00 0.00 3.77
5365 6193 5.796813 AGTGTTCGAGAAAAGAAAACGAAG 58.203 37.500 0.00 0.00 42.09 3.79
5447 6275 4.770531 ACCACTACTACTGACTTGCATACA 59.229 41.667 0.00 0.00 0.00 2.29
5746 6582 0.319083 ACGACGTGGATTACCTGCAA 59.681 50.000 3.97 0.00 37.04 4.08
5818 6654 1.334160 TTCTGACGGCTGGTTCTGTA 58.666 50.000 0.00 0.00 0.00 2.74
5848 6684 2.060567 TTGCTGCTTCCTCCAGTGCT 62.061 55.000 0.00 0.00 32.93 4.40
5980 6816 5.047660 ACTGTAGTTCTTCAGACATGGAGAC 60.048 44.000 12.12 0.00 41.00 3.36
6084 6920 2.134789 AGGAACTGGCCAGCAATAAG 57.865 50.000 33.06 8.68 37.18 1.73
6239 7075 2.383527 CGAAACTCGCCAGCCTGAC 61.384 63.158 0.00 0.00 31.14 3.51
6378 7214 4.337304 TGAGCTCCCAGCCCCAGA 62.337 66.667 12.15 0.00 43.77 3.86
6390 7226 1.482593 AGCCCCAGACTTCATAACTCG 59.517 52.381 0.00 0.00 0.00 4.18
6603 7439 0.178961 AAACCCTTGGAGCCAGGAAC 60.179 55.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.475403 GTCAGGGATTCCGTCTGAGA 58.525 55.000 10.82 0.00 38.09 3.27
126 127 7.398024 ACCAAAGAGATTTAGCAGAATACAGT 58.602 34.615 0.00 0.00 0.00 3.55
321 341 2.125912 GCCGACACGAGCATCACT 60.126 61.111 0.00 0.00 33.17 3.41
342 362 2.183555 GGGAAGTAGGACACGGCG 59.816 66.667 4.80 4.80 0.00 6.46
412 433 1.542915 AGCAATGTCATTGTCAGGTGC 59.457 47.619 23.27 10.63 42.20 5.01
525 914 5.536538 TGCAAGTAAGGAGAGATACATCGAT 59.463 40.000 0.00 0.00 0.00 3.59
527 916 5.188327 TGCAAGTAAGGAGAGATACATCG 57.812 43.478 0.00 0.00 0.00 3.84
600 1223 9.656040 TGCAGAAATGCAACATTTTCTAATTAT 57.344 25.926 11.63 0.00 42.40 1.28
634 1257 6.857451 GGCGACGGAATTCTTTTTAGTTTTTA 59.143 34.615 5.23 0.00 0.00 1.52
637 1260 4.790878 GGCGACGGAATTCTTTTTAGTTT 58.209 39.130 5.23 0.00 0.00 2.66
638 1261 4.414999 GGCGACGGAATTCTTTTTAGTT 57.585 40.909 5.23 0.00 0.00 2.24
723 1360 5.562506 AATCGAGAGTCGTATCAACAAGA 57.437 39.130 0.00 0.00 41.35 3.02
735 1372 5.264712 CGGTAACAAGACTAATCGAGAGTC 58.735 45.833 18.23 18.23 43.12 3.36
737 1374 4.036352 GCGGTAACAAGACTAATCGAGAG 58.964 47.826 0.00 0.00 0.00 3.20
741 1378 2.883574 TGGCGGTAACAAGACTAATCG 58.116 47.619 0.00 0.00 0.00 3.34
743 1380 3.454375 CGATGGCGGTAACAAGACTAAT 58.546 45.455 0.00 0.00 0.00 1.73
748 1385 1.448893 GGCGATGGCGGTAACAAGA 60.449 57.895 0.00 0.00 41.24 3.02
749 1386 1.429148 GAGGCGATGGCGGTAACAAG 61.429 60.000 0.00 0.00 41.24 3.16
752 1389 2.960129 CGAGGCGATGGCGGTAAC 60.960 66.667 0.00 0.00 41.24 2.50
753 1390 4.215742 CCGAGGCGATGGCGGTAA 62.216 66.667 0.00 0.00 41.24 2.85
771 1408 4.181010 CCATCTCACCTGCCCGGG 62.181 72.222 19.09 19.09 36.97 5.73
772 1409 2.669133 TTCCATCTCACCTGCCCGG 61.669 63.158 0.00 0.00 39.35 5.73
773 1410 1.450312 GTTCCATCTCACCTGCCCG 60.450 63.158 0.00 0.00 0.00 6.13
774 1411 1.077429 GGTTCCATCTCACCTGCCC 60.077 63.158 0.00 0.00 0.00 5.36
775 1412 0.329596 AAGGTTCCATCTCACCTGCC 59.670 55.000 0.00 0.00 43.05 4.85
776 1413 1.003580 TGAAGGTTCCATCTCACCTGC 59.996 52.381 0.00 0.00 43.05 4.85
777 1414 3.423539 TTGAAGGTTCCATCTCACCTG 57.576 47.619 0.00 0.00 43.05 4.00
778 1415 4.145052 GTTTTGAAGGTTCCATCTCACCT 58.855 43.478 0.00 0.00 46.04 4.00
779 1416 3.058224 CGTTTTGAAGGTTCCATCTCACC 60.058 47.826 0.00 0.00 0.00 4.02
781 1418 4.065088 CTCGTTTTGAAGGTTCCATCTCA 58.935 43.478 0.00 0.00 0.00 3.27
789 1442 0.185175 AGCCCCTCGTTTTGAAGGTT 59.815 50.000 0.00 0.00 0.00 3.50
859 1512 3.995506 AAATTGGGAGGGAGGCGCG 62.996 63.158 0.00 0.00 0.00 6.86
860 1513 0.395173 TAAAATTGGGAGGGAGGCGC 60.395 55.000 0.00 0.00 0.00 6.53
903 1556 4.916293 TCATGGCGGAGATGGCGC 62.916 66.667 0.00 0.00 37.19 6.53
914 1567 2.086251 CTCCTCCTCTCGCTCATGGC 62.086 65.000 0.00 0.00 37.64 4.40
915 1568 0.467106 TCTCCTCCTCTCGCTCATGG 60.467 60.000 0.00 0.00 0.00 3.66
916 1569 0.953727 CTCTCCTCCTCTCGCTCATG 59.046 60.000 0.00 0.00 0.00 3.07
959 1612 3.966930 GAGGGAGGGAGGCGTGTCT 62.967 68.421 0.00 0.00 0.00 3.41
1155 1815 1.268992 ACCTACGTATGGGCTGGCAA 61.269 55.000 13.41 0.00 0.00 4.52
1158 1818 1.120530 AGAACCTACGTATGGGCTGG 58.879 55.000 13.41 5.60 0.00 4.85
1159 1819 1.754803 TCAGAACCTACGTATGGGCTG 59.245 52.381 18.79 18.79 34.57 4.85
1160 1820 2.154567 TCAGAACCTACGTATGGGCT 57.845 50.000 13.41 8.54 0.00 5.19
1161 1821 2.429610 TCTTCAGAACCTACGTATGGGC 59.570 50.000 13.41 6.92 0.00 5.36
1162 1822 4.430908 GTTCTTCAGAACCTACGTATGGG 58.569 47.826 8.31 7.49 46.42 4.00
1174 1834 5.811399 ACGTCACAAAATGTTCTTCAGAA 57.189 34.783 0.00 0.00 0.00 3.02
1175 1835 5.811399 AACGTCACAAAATGTTCTTCAGA 57.189 34.783 0.00 0.00 0.00 3.27
1363 2024 5.925907 GCAAGAAGCTTTGTTTGACAAAAA 58.074 33.333 18.00 0.00 46.15 1.94
1364 2025 5.529014 GCAAGAAGCTTTGTTTGACAAAA 57.471 34.783 18.00 0.00 46.15 2.44
1375 2036 7.133334 ACAATGGTGTTGAGCAAGAAGCTTT 62.133 40.000 0.00 0.00 45.56 3.51
1378 2058 2.035066 ACAATGGTGTTGAGCAAGAAGC 59.965 45.455 0.00 0.00 38.06 3.86
1391 2071 2.354003 GGCTTGGGATTTCACAATGGTG 60.354 50.000 0.00 0.00 46.66 4.17
1417 2097 7.026631 TGTTAAACATTCTGTGTGAGGAAAG 57.973 36.000 0.00 0.00 41.14 2.62
1580 2279 1.409427 GGTCGATGAACCGGAGAGAAT 59.591 52.381 9.46 0.00 0.00 2.40
1984 2758 1.005294 GCTTCCGACGTTTCTGCGTA 61.005 55.000 0.00 0.00 45.79 4.42
2024 2798 2.215196 AGTTGCGTAAACATGTCCGTT 58.785 42.857 0.00 0.00 41.61 4.44
2036 2810 2.413837 GAGAGCTTTGGAAGTTGCGTA 58.586 47.619 0.00 0.00 0.00 4.42
2134 2913 2.738314 ACCGCGACATTACTAACAAACC 59.262 45.455 8.23 0.00 0.00 3.27
2142 2921 3.795623 ATCTGTTACCGCGACATTACT 57.204 42.857 8.23 0.00 0.00 2.24
2162 2941 9.109393 GTCAAATCAAGTATCACAGGCTAAATA 57.891 33.333 0.00 0.00 0.00 1.40
2177 2986 2.037772 ACGAGCTCTGGTCAAATCAAGT 59.962 45.455 12.85 0.00 0.00 3.16
2197 3006 9.899226 ATTGCTGACTGTAAGAAGAAAATTAAC 57.101 29.630 0.00 0.00 37.43 2.01
2217 3026 6.263344 CCTGATGACACAAATAGAATTGCTG 58.737 40.000 0.00 0.00 33.52 4.41
2321 3130 6.109359 CCAGTGAAGTTCCTAAGAATACAGG 58.891 44.000 0.00 0.00 33.67 4.00
2325 3134 7.676683 ATAGCCAGTGAAGTTCCTAAGAATA 57.323 36.000 0.00 0.00 33.67 1.75
2394 3203 9.153479 GCTCTCCAAGTTCCTGGATATATATAT 57.847 37.037 4.86 4.86 44.59 0.86
2395 3204 8.122481 TGCTCTCCAAGTTCCTGGATATATATA 58.878 37.037 0.00 0.00 44.59 0.86
2523 3338 6.150976 CAGAAGCATACACTTTTAACCATGGA 59.849 38.462 21.47 0.00 0.00 3.41
2549 3364 9.941325 TTGCATTTCCATGTTGAAGTAATTAAT 57.059 25.926 0.00 0.00 32.28 1.40
2651 3466 9.752961 CACTCATGCAAATATATGGATTTGAAA 57.247 29.630 13.00 3.40 45.70 2.69
2952 3767 0.826672 ACCCCGACGTCACTCTCTTT 60.827 55.000 17.16 0.00 0.00 2.52
2970 3785 3.181523 GCTCCGATAAAGAAACCGTTGAC 60.182 47.826 0.00 0.00 0.00 3.18
3033 3848 3.660501 TCGCTTCATCTGTAACACTGT 57.339 42.857 0.00 0.00 0.00 3.55
3041 3856 1.686052 GGAGAGGATCGCTTCATCTGT 59.314 52.381 7.03 0.00 45.18 3.41
3324 4142 4.096382 CCGCCTAGAATTGTTTAGCATGTT 59.904 41.667 0.00 0.00 0.00 2.71
3496 4317 6.405278 TTTTCTCTGAATTTGGAGGGAAAC 57.595 37.500 7.34 0.00 38.20 2.78
3565 4387 9.668497 ACCATTTTGTAGAGGAAACTATAAGTC 57.332 33.333 0.00 0.00 44.43 3.01
3578 4400 6.539826 TGCATATCTGACACCATTTTGTAGAG 59.460 38.462 0.00 0.00 0.00 2.43
3739 4563 7.543172 CACCTGAAAAATCATCATGGTAAACAG 59.457 37.037 0.00 0.00 31.50 3.16
4117 4941 1.365633 GATCCGAGGCGAGCAGATT 59.634 57.895 0.00 0.00 0.00 2.40
4131 4955 6.599244 TGACTTTATGTTCTTGTGGATGATCC 59.401 38.462 4.05 4.05 36.96 3.36
4497 5323 3.118261 GGGGATCAGATAACAGCTCACAA 60.118 47.826 0.00 0.00 0.00 3.33
4509 5335 1.133853 GCTTTGAGCTGGGGATCAGAT 60.134 52.381 0.00 0.00 45.95 2.90
4673 5499 1.920835 GAGAGGGCTGAACCTGGGT 60.921 63.158 0.00 0.00 42.10 4.51
4674 5500 1.920325 TGAGAGGGCTGAACCTGGG 60.920 63.158 0.00 0.00 42.10 4.45
4710 5536 2.687700 ACATGTGAGACCTGATCAGC 57.312 50.000 17.76 4.68 0.00 4.26
4868 5695 2.579201 GCGCTGTAGAGGAAGCCA 59.421 61.111 0.00 0.00 35.98 4.75
5019 5846 8.076178 ACACATTTCACTACAGTAGAAAAATGC 58.924 33.333 28.98 0.00 40.54 3.56
5100 5927 5.001232 TGCTCTCTTTACATGGGTAAACAC 58.999 41.667 0.00 0.00 42.86 3.32
5163 5990 0.250901 ACCTACTTGTGCTTGCCCAG 60.251 55.000 0.00 0.00 0.00 4.45
5174 6001 9.823647 ATGATCTTTGATGTTACTACCTACTTG 57.176 33.333 0.00 0.00 0.00 3.16
5302 6130 7.119846 GTGGTTGTGTATTAGAAGAAGAATGCT 59.880 37.037 0.00 0.00 0.00 3.79
5325 6153 4.934942 TCGTCGTGGTGCGTGTGG 62.935 66.667 0.00 0.00 42.13 4.17
5326 6154 3.394874 CTCGTCGTGGTGCGTGTG 61.395 66.667 0.00 0.00 42.13 3.82
5365 6193 2.035449 GGTGGTGGTTGTTTTAGCCTTC 59.965 50.000 0.00 0.00 0.00 3.46
5447 6275 7.385267 ACGATGTATACTAGGTCTCGATTACT 58.615 38.462 4.17 0.00 0.00 2.24
5731 6567 0.748005 CCCCTTGCAGGTAATCCACG 60.748 60.000 0.00 0.00 31.93 4.94
5927 6763 0.944386 GCTGATTTGTGTGTGTCCGT 59.056 50.000 0.00 0.00 0.00 4.69
5980 6816 5.008019 AGCAATCTGTTTATACCTGCAATCG 59.992 40.000 0.00 0.00 0.00 3.34
6084 6920 3.649073 ACGGCAAATGAACTTTTAAGGC 58.351 40.909 0.00 0.00 0.00 4.35
6390 7226 1.077716 AAGGCCCATGCTCGTAACC 60.078 57.895 0.00 0.00 37.74 2.85
6603 7439 2.606725 CAGAGTGAAAGCCGCTATCAAG 59.393 50.000 0.00 0.00 35.38 3.02


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

AutoCloner maintained by Alex Coulton.