Multiple sequence alignment - TraesCS7B01G232900

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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 TraesCS7B01G232900 chr7B 100.000 2399 0 0 1 2399 436602299 436604697 0 4431
1 TraesCS7B01G232900 chr7D 87.959 1852 65 63 1 1735 420414179 420415989 0 2039
2 TraesCS7B01G232900 chr7D 91.667 576 19 15 1833 2399 420416018 420416573 0 771
3 TraesCS7B01G232900 chr7A 83.909 1591 95 52 405 1882 512584978 512583436 0 1371


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 TraesCS7B01G232900 chr7B 436602299 436604697 2398 False 4431 4431 100.000 1 2399 1 chr7B.!!$F1 2398
1 TraesCS7B01G232900 chr7D 420414179 420416573 2394 False 1405 2039 89.813 1 2399 2 chr7D.!!$F1 2398
2 TraesCS7B01G232900 chr7A 512583436 512584978 1542 True 1371 1371 83.909 405 1882 1 chr7A.!!$R1 1477

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
203 235 0.102844 CAAATAATGTGGCTGCGGGG 59.897 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1546 0.179004 GGGAGGAGAGATCGAGAGCA 60.179 60.0 0.0 0.0 0.0 4.26 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
27 28 2.045340 GTGCACGGGCCCTTGTAT 60.045 61.111 27.70 1.76 40.13 2.29
29 30 2.895372 GCACGGGCCCTTGTATCG 60.895 66.667 27.70 11.79 0.00 2.92
48 49 2.510464 TGCGTGTTCACGTGCAGT 60.510 55.556 22.85 0.00 35.26 4.40
52 53 0.939577 CGTGTTCACGTGCAGTAGCT 60.940 55.000 11.67 0.00 42.74 3.32
53 54 1.664874 CGTGTTCACGTGCAGTAGCTA 60.665 52.381 11.67 0.00 42.74 3.32
54 55 1.986378 GTGTTCACGTGCAGTAGCTAG 59.014 52.381 11.67 0.00 42.74 3.42
55 56 0.992802 GTTCACGTGCAGTAGCTAGC 59.007 55.000 11.67 6.62 42.74 3.42
56 57 0.108804 TTCACGTGCAGTAGCTAGCC 60.109 55.000 12.13 0.00 42.74 3.93
57 58 1.519455 CACGTGCAGTAGCTAGCCC 60.519 63.158 12.13 2.00 42.74 5.19
58 59 2.107141 CGTGCAGTAGCTAGCCCC 59.893 66.667 12.13 1.58 42.74 5.80
59 60 2.107141 GTGCAGTAGCTAGCCCCG 59.893 66.667 12.13 0.00 42.74 5.73
60 61 3.849951 TGCAGTAGCTAGCCCCGC 61.850 66.667 12.13 10.00 42.74 6.13
61 62 4.951963 GCAGTAGCTAGCCCCGCG 62.952 72.222 12.13 0.00 37.91 6.46
158 181 1.512996 TATCGACGGAGGCGTCATCC 61.513 60.000 8.91 0.00 38.68 3.51
167 190 2.621763 GGCGTCATCCTTGCCTATG 58.378 57.895 0.00 0.00 45.40 2.23
168 191 0.106708 GGCGTCATCCTTGCCTATGA 59.893 55.000 0.00 0.00 45.40 2.15
169 192 1.271054 GGCGTCATCCTTGCCTATGAT 60.271 52.381 0.00 0.00 45.40 2.45
172 195 3.620374 GCGTCATCCTTGCCTATGATATG 59.380 47.826 0.00 0.00 34.77 1.78
173 196 4.621510 GCGTCATCCTTGCCTATGATATGA 60.622 45.833 0.00 0.00 34.77 2.15
174 197 5.668471 CGTCATCCTTGCCTATGATATGAT 58.332 41.667 0.00 0.00 34.77 2.45
180 212 7.984859 TCCTTGCCTATGATATGATATCAGT 57.015 36.000 18.83 10.59 0.00 3.41
203 235 0.102844 CAAATAATGTGGCTGCGGGG 59.897 55.000 0.00 0.00 0.00 5.73
254 286 1.478510 ACAAACCGTTGGCATCAAACA 59.521 42.857 0.00 0.00 39.22 2.83
259 291 1.130955 CGTTGGCATCAAACAACAGC 58.869 50.000 8.08 0.00 45.39 4.40
287 319 2.237143 TCCAGATTTGATCGAACCTGCT 59.763 45.455 11.28 0.00 0.00 4.24
290 322 2.012673 GATTTGATCGAACCTGCTGCT 58.987 47.619 0.00 0.00 0.00 4.24
363 395 2.531522 TTGGTGCATGATCGATCGAT 57.468 45.000 29.76 29.76 37.59 3.59
390 423 2.810486 GCAGATACGGTGCCGATAC 58.190 57.895 18.16 7.47 42.83 2.24
391 424 1.002250 GCAGATACGGTGCCGATACG 61.002 60.000 18.16 2.97 42.83 3.06
483 531 3.147132 CATGCCATGCCATGCCAT 58.853 55.556 3.39 0.00 36.52 4.40
484 532 1.301637 CATGCCATGCCATGCCATG 60.302 57.895 13.50 13.50 41.71 3.66
485 533 3.177194 ATGCCATGCCATGCCATGC 62.177 57.895 11.13 7.49 40.92 4.06
723 802 4.973055 CCACGCACCGAACCCGAA 62.973 66.667 0.00 0.00 38.22 4.30
724 803 3.708734 CACGCACCGAACCCGAAC 61.709 66.667 0.00 0.00 38.22 3.95
725 804 4.974989 ACGCACCGAACCCGAACC 62.975 66.667 0.00 0.00 38.22 3.62
726 805 4.973055 CGCACCGAACCCGAACCA 62.973 66.667 0.00 0.00 38.22 3.67
769 853 1.550130 CCACACCACACCTATCCCGT 61.550 60.000 0.00 0.00 0.00 5.28
772 856 0.108329 CACCACACCTATCCCGTGAC 60.108 60.000 0.00 0.00 35.17 3.67
776 860 2.443390 ACCTATCCCGTGACCCCG 60.443 66.667 0.00 0.00 0.00 5.73
778 862 3.925090 CTATCCCGTGACCCCGGC 61.925 72.222 0.00 0.00 46.71 6.13
804 888 2.348104 CCACCATGTGCATGCAGCT 61.348 57.895 23.41 8.54 45.94 4.24
816 900 1.181098 ATGCAGCTTTCGTTGCCCTT 61.181 50.000 0.00 0.00 45.52 3.95
819 903 1.227853 AGCTTTCGTTGCCCTTCGT 60.228 52.632 0.00 0.00 0.00 3.85
857 941 2.197324 ACCACGCACCAACCCAAT 59.803 55.556 0.00 0.00 0.00 3.16
957 1056 1.129437 CACCTCTTAGCAAAAGCGAGC 59.871 52.381 0.00 0.00 0.00 5.03
978 1082 3.557264 GCCACTTACCAAAGCTACTCTGT 60.557 47.826 0.00 0.00 36.05 3.41
1099 1219 2.520741 CGGAGGAGAGGGAGGAGC 60.521 72.222 0.00 0.00 0.00 4.70
1146 1269 1.744741 GCTGCTGCAGGAGGAAGAC 60.745 63.158 32.87 14.79 39.41 3.01
1160 1286 0.256464 GAAGACGAGGAGGAGGAGGA 59.744 60.000 0.00 0.00 0.00 3.71
1162 1288 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1163 1289 1.619975 ACGAGGAGGAGGAGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
1164 1290 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1165 1291 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1166 1292 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1167 1293 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1168 1294 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1169 1295 1.230819 AGGAGGAGGAGGAGGAGGT 60.231 63.158 0.00 0.00 0.00 3.85
1170 1296 1.231928 GGAGGAGGAGGAGGAGGTC 59.768 68.421 0.00 0.00 0.00 3.85
1209 1335 1.001393 GGCCGGGATGAAGGTGAAA 60.001 57.895 2.18 0.00 0.00 2.69
1402 1528 3.449227 CCGACGCCACCTAGCTGA 61.449 66.667 0.00 0.00 0.00 4.26
1413 1540 1.544691 ACCTAGCTGACAACCTACACG 59.455 52.381 0.00 0.00 0.00 4.49
1415 1542 0.245539 TAGCTGACAACCTACACGCC 59.754 55.000 0.00 0.00 0.00 5.68
1417 1544 1.006571 CTGACAACCTACACGCCGT 60.007 57.895 0.00 0.00 0.00 5.68
1418 1545 1.007038 TGACAACCTACACGCCGTC 60.007 57.895 0.00 0.00 0.00 4.79
1419 1546 1.288127 GACAACCTACACGCCGTCT 59.712 57.895 0.00 0.00 0.00 4.18
1420 1547 1.006571 ACAACCTACACGCCGTCTG 60.007 57.895 0.00 0.00 0.00 3.51
1422 1549 2.571216 AACCTACACGCCGTCTGCT 61.571 57.895 0.00 0.00 38.05 4.24
1423 1550 2.202623 CCTACACGCCGTCTGCTC 60.203 66.667 0.00 0.00 38.05 4.26
1432 1573 1.444119 GCCGTCTGCTCTCGATCTCT 61.444 60.000 0.00 0.00 36.87 3.10
1442 1583 3.299190 CGATCTCTCCTCCCCGGC 61.299 72.222 0.00 0.00 0.00 6.13
1461 1606 0.742281 CCACCGTGATCAGAGCTTGG 60.742 60.000 0.00 0.00 0.00 3.61
1473 1618 4.232310 GCTTGGTCTCCTCCATGC 57.768 61.111 7.60 7.60 46.08 4.06
1476 1621 1.676746 CTTGGTCTCCTCCATGCATG 58.323 55.000 20.19 20.19 37.33 4.06
1515 1671 1.141881 AGATCCGTCCGTGTGCATC 59.858 57.895 0.00 0.00 0.00 3.91
1617 1776 6.659745 TGAACACCAACTGTACTATGTAGT 57.340 37.500 0.00 0.00 40.24 2.73
1618 1777 7.764141 TGAACACCAACTGTACTATGTAGTA 57.236 36.000 0.00 0.00 37.73 1.82
1619 1778 7.823665 TGAACACCAACTGTACTATGTAGTAG 58.176 38.462 0.27 0.00 39.29 2.57
1620 1779 6.205101 ACACCAACTGTACTATGTAGTAGC 57.795 41.667 0.27 0.00 39.29 3.58
1621 1780 5.126707 ACACCAACTGTACTATGTAGTAGCC 59.873 44.000 0.27 0.00 39.29 3.93
1623 1782 5.360144 ACCAACTGTACTATGTAGTAGCCTG 59.640 44.000 0.27 0.00 39.29 4.85
1624 1783 5.360144 CCAACTGTACTATGTAGTAGCCTGT 59.640 44.000 0.27 0.00 39.29 4.00
1625 1784 6.127423 CCAACTGTACTATGTAGTAGCCTGTT 60.127 42.308 0.27 4.47 39.29 3.16
1626 1785 7.067859 CCAACTGTACTATGTAGTAGCCTGTTA 59.932 40.741 0.27 0.00 39.29 2.41
1627 1786 7.804843 ACTGTACTATGTAGTAGCCTGTTAG 57.195 40.000 0.27 0.00 39.29 2.34
1630 1789 6.485984 TGTACTATGTAGTAGCCTGTTAGAGC 59.514 42.308 0.27 0.00 39.29 4.09
1738 1930 4.759693 TGTTTGTAAATAGTGTGGCCTCAG 59.240 41.667 7.99 0.00 0.00 3.35
1740 1932 5.435686 TTGTAAATAGTGTGGCCTCAGAT 57.564 39.130 7.99 1.96 0.00 2.90
1760 1952 1.153353 CAAATGGCAACGTACCGTCT 58.847 50.000 2.93 0.00 39.99 4.18
1773 1965 0.463654 ACCGTCTGCTGCAGTTTTGA 60.464 50.000 27.24 6.99 32.61 2.69
1775 1967 1.597937 CCGTCTGCTGCAGTTTTGAAC 60.598 52.381 27.24 16.43 32.61 3.18
1794 1988 1.153939 CGGATCGGATCGGATCAGC 60.154 63.158 32.20 20.55 43.69 4.26
1795 1989 1.216710 GGATCGGATCGGATCAGCC 59.783 63.158 32.20 19.38 43.69 4.85
1812 2006 0.525761 GCCGTGGCAATTTTAGCTCA 59.474 50.000 5.89 0.00 41.49 4.26
1813 2007 1.732405 GCCGTGGCAATTTTAGCTCAC 60.732 52.381 5.89 0.00 41.49 3.51
1817 2011 4.298332 CGTGGCAATTTTAGCTCACTTTT 58.702 39.130 0.00 0.00 33.73 2.27
1818 2012 4.744631 CGTGGCAATTTTAGCTCACTTTTT 59.255 37.500 0.00 0.00 33.73 1.94
1874 2080 2.671396 CGCTACCATATTTCCCGCATAC 59.329 50.000 0.00 0.00 0.00 2.39
1882 2088 6.882678 ACCATATTTCCCGCATACTAAATACC 59.117 38.462 0.00 0.00 29.31 2.73
1885 2091 2.318908 TCCCGCATACTAAATACCGGT 58.681 47.619 13.98 13.98 31.94 5.28
1918 2124 3.386768 TTGTGAGTGGTGAAGCTCTAC 57.613 47.619 0.00 0.00 33.22 2.59
1919 2125 2.598565 TGTGAGTGGTGAAGCTCTACT 58.401 47.619 0.00 0.00 33.22 2.57
1920 2126 3.763057 TGTGAGTGGTGAAGCTCTACTA 58.237 45.455 0.00 0.00 33.22 1.82
1921 2127 3.759086 TGTGAGTGGTGAAGCTCTACTAG 59.241 47.826 0.00 0.00 33.22 2.57
1922 2128 3.759618 GTGAGTGGTGAAGCTCTACTAGT 59.240 47.826 0.00 0.00 33.22 2.57
1992 2198 1.066430 CGGAGCAGGGTTAAAGTAGCA 60.066 52.381 0.00 0.00 0.00 3.49
1993 2199 2.614481 CGGAGCAGGGTTAAAGTAGCAA 60.614 50.000 0.00 0.00 0.00 3.91
1994 2200 2.747989 GGAGCAGGGTTAAAGTAGCAAC 59.252 50.000 0.00 0.00 0.00 4.17
2004 2210 0.310854 AAGTAGCAACGCCAAAGTGC 59.689 50.000 0.00 0.00 0.00 4.40
2005 2211 0.535102 AGTAGCAACGCCAAAGTGCT 60.535 50.000 2.63 2.63 39.36 4.40
2006 2212 1.153353 GTAGCAACGCCAAAGTGCTA 58.847 50.000 0.61 0.61 37.08 3.49
2007 2213 1.128692 GTAGCAACGCCAAAGTGCTAG 59.871 52.381 4.91 0.00 38.54 3.42
2015 2221 2.030457 CGCCAAAGTGCTAGTATTTCCG 59.970 50.000 0.00 0.00 0.00 4.30
2077 2283 8.854979 CTACATAGCTGTAGCATATTCTCATC 57.145 38.462 6.65 0.00 46.13 2.92
2078 2284 6.638610 ACATAGCTGTAGCATATTCTCATCC 58.361 40.000 6.65 0.00 45.16 3.51
2079 2285 4.550076 AGCTGTAGCATATTCTCATCCC 57.450 45.455 6.65 0.00 45.16 3.85
2080 2286 3.906218 AGCTGTAGCATATTCTCATCCCA 59.094 43.478 6.65 0.00 45.16 4.37
2081 2287 4.535294 AGCTGTAGCATATTCTCATCCCAT 59.465 41.667 6.65 0.00 45.16 4.00
2103 2309 2.130395 GAAGCAAAAGCAGCAACCTTC 58.870 47.619 0.00 0.00 0.00 3.46
2126 2333 4.174411 GTCAATTCTTGGCCAGGTTAAC 57.826 45.455 15.41 0.00 0.00 2.01
2129 2336 4.280677 TCAATTCTTGGCCAGGTTAACTTG 59.719 41.667 15.41 10.62 0.00 3.16
2153 2360 1.522806 GCCGGTCGATGCATGGTTA 60.523 57.895 2.46 0.00 0.00 2.85
2155 2362 0.655733 CCGGTCGATGCATGGTTAAC 59.344 55.000 2.46 0.00 0.00 2.01
2156 2363 1.364721 CGGTCGATGCATGGTTAACA 58.635 50.000 2.46 0.00 0.00 2.41
2157 2364 1.939934 CGGTCGATGCATGGTTAACAT 59.060 47.619 2.46 0.00 41.57 2.71
2158 2365 3.127589 CGGTCGATGCATGGTTAACATA 58.872 45.455 2.46 0.00 37.84 2.29
2159 2366 3.059868 CGGTCGATGCATGGTTAACATAC 60.060 47.826 2.46 0.00 37.84 2.39
2160 2367 4.127171 GGTCGATGCATGGTTAACATACT 58.873 43.478 2.46 0.00 37.84 2.12
2161 2368 5.294356 GGTCGATGCATGGTTAACATACTA 58.706 41.667 2.46 0.00 37.84 1.82
2162 2369 5.405571 GGTCGATGCATGGTTAACATACTAG 59.594 44.000 2.46 0.00 37.84 2.57
2322 2529 0.458716 GGGTCGCTGCTCTGACTAAC 60.459 60.000 0.00 0.00 35.45 2.34
2336 2543 3.281158 TGACTAACCGATCCACGTATGA 58.719 45.455 0.00 0.00 40.78 2.15
2339 2546 0.462789 AACCGATCCACGTATGACCC 59.537 55.000 0.00 0.00 40.78 4.46
2340 2547 1.007734 CCGATCCACGTATGACCCG 60.008 63.158 0.00 0.00 40.78 5.28
2342 2549 0.382873 CGATCCACGTATGACCCGAA 59.617 55.000 0.00 0.00 37.22 4.30
2343 2550 1.849097 GATCCACGTATGACCCGAAC 58.151 55.000 0.00 0.00 0.00 3.95
2358 2565 2.197577 CCGAACAAAACCACGCATTTT 58.802 42.857 0.00 0.00 0.00 1.82
2362 2572 4.374906 CGAACAAAACCACGCATTTTCATC 60.375 41.667 0.00 0.00 0.00 2.92
2372 2582 3.627577 ACGCATTTTCATCCATCACCTAC 59.372 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 181 7.710044 GGACACTGATATCATATCATAGGCAAG 59.290 40.741 7.85 0.00 0.00 4.01
169 192 9.506018 CCACATTATTTGGACACTGATATCATA 57.494 33.333 5.72 0.00 36.02 2.15
172 195 6.488006 AGCCACATTATTTGGACACTGATATC 59.512 38.462 0.97 0.00 36.02 1.63
173 196 6.263842 CAGCCACATTATTTGGACACTGATAT 59.736 38.462 0.97 0.00 36.02 1.63
174 197 5.589855 CAGCCACATTATTTGGACACTGATA 59.410 40.000 0.97 0.00 36.02 2.15
180 212 1.472082 CGCAGCCACATTATTTGGACA 59.528 47.619 0.97 0.00 36.02 4.02
215 247 6.702723 GGTTTGTGGTAAAGGTTTATGTTTCC 59.297 38.462 0.00 0.00 0.00 3.13
254 286 3.266772 TCAAATCTGGATACTGGGCTGTT 59.733 43.478 0.00 0.00 35.97 3.16
259 291 4.607293 TCGATCAAATCTGGATACTGGG 57.393 45.455 0.00 0.00 35.97 4.45
358 390 1.752358 ATCTGCCGGCTGTCATCGAT 61.752 55.000 29.70 12.43 0.00 3.59
360 392 0.941463 GTATCTGCCGGCTGTCATCG 60.941 60.000 29.70 7.10 0.00 3.84
363 395 2.494445 CGTATCTGCCGGCTGTCA 59.506 61.111 29.70 16.02 0.00 3.58
720 799 0.880278 CCTCTGTGTGGTGTGGTTCG 60.880 60.000 0.00 0.00 0.00 3.95
721 800 1.166531 GCCTCTGTGTGGTGTGGTTC 61.167 60.000 0.00 0.00 0.00 3.62
723 802 2.510906 GCCTCTGTGTGGTGTGGT 59.489 61.111 0.00 0.00 0.00 4.16
724 803 2.281761 GGCCTCTGTGTGGTGTGG 60.282 66.667 0.00 0.00 0.00 4.17
725 804 2.666190 CGGCCTCTGTGTGGTGTG 60.666 66.667 0.00 0.00 0.00 3.82
726 805 4.626081 GCGGCCTCTGTGTGGTGT 62.626 66.667 0.00 0.00 0.00 4.16
753 837 0.108329 GTCACGGGATAGGTGTGGTG 60.108 60.000 0.00 0.00 36.76 4.17
754 838 1.262640 GGTCACGGGATAGGTGTGGT 61.263 60.000 0.00 0.00 36.76 4.16
778 862 4.424711 CACATGGTGGGGTCCGGG 62.425 72.222 0.00 0.00 0.00 5.73
804 888 3.739167 CCACGAAGGGCAACGAAA 58.261 55.556 0.00 0.00 37.60 3.46
857 941 0.532573 CACTAGCTCGGAAGGAAGCA 59.467 55.000 0.00 0.00 0.00 3.91
957 1056 4.021016 AGACAGAGTAGCTTTGGTAAGTGG 60.021 45.833 0.00 0.00 33.74 4.00
978 1082 2.776526 ACAAGGTGGTGGGGCAGA 60.777 61.111 0.00 0.00 0.00 4.26
1146 1269 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1209 1335 2.997897 GCCCTCGTCAGGACCACT 60.998 66.667 0.00 0.00 43.65 4.00
1401 1527 1.007336 CAGACGGCGTGTAGGTTGTC 61.007 60.000 21.19 0.00 0.00 3.18
1402 1528 1.006571 CAGACGGCGTGTAGGTTGT 60.007 57.895 21.19 0.00 0.00 3.32
1413 1540 1.008995 GAGATCGAGAGCAGACGGC 60.009 63.158 0.00 0.00 45.30 5.68
1415 1542 0.586319 GGAGAGATCGAGAGCAGACG 59.414 60.000 0.00 0.00 0.00 4.18
1417 1544 1.202758 GGAGGAGAGATCGAGAGCAGA 60.203 57.143 0.00 0.00 0.00 4.26
1418 1545 1.238439 GGAGGAGAGATCGAGAGCAG 58.762 60.000 0.00 0.00 0.00 4.24
1419 1546 0.179004 GGGAGGAGAGATCGAGAGCA 60.179 60.000 0.00 0.00 0.00 4.26
1420 1547 0.893727 GGGGAGGAGAGATCGAGAGC 60.894 65.000 0.00 0.00 0.00 4.09
1422 1549 1.452368 CGGGGAGGAGAGATCGAGA 59.548 63.158 0.00 0.00 0.00 4.04
1423 1550 1.602323 CCGGGGAGGAGAGATCGAG 60.602 68.421 0.00 0.00 45.00 4.04
1442 1583 0.742281 CCAAGCTCTGATCACGGTGG 60.742 60.000 8.50 0.00 0.00 4.61
1448 1589 2.106566 GAGGAGACCAAGCTCTGATCA 58.893 52.381 0.00 0.00 35.26 2.92
1473 1618 2.615912 GCAAGAAAGCTAGTAGCCCATG 59.384 50.000 18.65 11.87 43.77 3.66
1474 1619 2.507471 AGCAAGAAAGCTAGTAGCCCAT 59.493 45.455 18.65 5.11 43.77 4.00
1475 1620 1.909302 AGCAAGAAAGCTAGTAGCCCA 59.091 47.619 18.65 0.00 43.77 5.36
1476 1621 2.093447 TGAGCAAGAAAGCTAGTAGCCC 60.093 50.000 18.65 8.42 46.75 5.19
1477 1622 3.118956 TCTGAGCAAGAAAGCTAGTAGCC 60.119 47.826 18.65 3.67 46.75 3.93
1515 1671 0.531532 GCCTCTCCATGGATCACACG 60.532 60.000 16.63 2.02 0.00 4.49
1617 1776 3.884091 GCTACTACTGCTCTAACAGGCTA 59.116 47.826 0.00 0.00 42.21 3.93
1618 1777 2.691011 GCTACTACTGCTCTAACAGGCT 59.309 50.000 0.00 0.00 42.21 4.58
1619 1778 2.691011 AGCTACTACTGCTCTAACAGGC 59.309 50.000 0.00 0.00 42.21 4.85
1620 1779 4.399618 TCAAGCTACTACTGCTCTAACAGG 59.600 45.833 0.00 0.00 42.21 4.00
1621 1780 5.568685 TCAAGCTACTACTGCTCTAACAG 57.431 43.478 0.00 0.00 40.22 3.16
1623 1782 7.262048 AGAAATCAAGCTACTACTGCTCTAAC 58.738 38.462 0.00 0.00 40.22 2.34
1624 1783 7.122799 TGAGAAATCAAGCTACTACTGCTCTAA 59.877 37.037 0.00 0.00 40.22 2.10
1625 1784 6.603599 TGAGAAATCAAGCTACTACTGCTCTA 59.396 38.462 0.00 0.00 40.22 2.43
1626 1785 5.420421 TGAGAAATCAAGCTACTACTGCTCT 59.580 40.000 0.00 0.00 40.22 4.09
1627 1786 5.518487 GTGAGAAATCAAGCTACTACTGCTC 59.482 44.000 0.00 0.00 40.22 4.26
1630 1789 5.809562 CCAGTGAGAAATCAAGCTACTACTG 59.190 44.000 0.00 0.00 33.51 2.74
1760 1952 0.749818 TCCGGTTCAAAACTGCAGCA 60.750 50.000 15.27 0.00 36.43 4.41
1787 1981 0.532115 AAAATTGCCACGGCTGATCC 59.468 50.000 9.92 0.00 42.51 3.36
1794 1988 1.812571 AGTGAGCTAAAATTGCCACGG 59.187 47.619 0.00 0.00 37.00 4.94
1795 1989 3.559238 AAGTGAGCTAAAATTGCCACG 57.441 42.857 0.00 0.00 37.00 4.94
1818 2012 9.575868 TGTATACAAGGTTAATCAGGTTCAAAA 57.424 29.630 2.20 0.00 0.00 2.44
1820 2014 9.391006 GATGTATACAAGGTTAATCAGGTTCAA 57.609 33.333 10.14 0.00 0.00 2.69
1821 2015 7.990886 GGATGTATACAAGGTTAATCAGGTTCA 59.009 37.037 10.14 0.00 0.00 3.18
1822 2016 7.990886 TGGATGTATACAAGGTTAATCAGGTTC 59.009 37.037 10.14 0.00 0.00 3.62
1823 2017 7.773690 GTGGATGTATACAAGGTTAATCAGGTT 59.226 37.037 10.14 0.00 0.00 3.50
1824 2018 7.092623 TGTGGATGTATACAAGGTTAATCAGGT 60.093 37.037 10.14 0.00 0.00 4.00
1825 2019 7.279615 TGTGGATGTATACAAGGTTAATCAGG 58.720 38.462 10.14 0.00 0.00 3.86
1826 2020 8.908786 ATGTGGATGTATACAAGGTTAATCAG 57.091 34.615 10.14 0.00 0.00 2.90
1828 2022 8.495949 CGAATGTGGATGTATACAAGGTTAATC 58.504 37.037 10.14 0.70 0.00 1.75
1829 2023 7.041372 GCGAATGTGGATGTATACAAGGTTAAT 60.041 37.037 10.14 0.00 0.00 1.40
1830 2024 6.259167 GCGAATGTGGATGTATACAAGGTTAA 59.741 38.462 10.14 0.00 0.00 2.01
1831 2025 5.756347 GCGAATGTGGATGTATACAAGGTTA 59.244 40.000 10.14 0.00 0.00 2.85
1874 2080 6.861065 ACTTAATCATGCACCGGTATTTAG 57.139 37.500 6.87 9.10 0.00 1.85
1882 2088 4.083324 ACTCACAAACTTAATCATGCACCG 60.083 41.667 0.00 0.00 0.00 4.94
1885 2091 4.826733 ACCACTCACAAACTTAATCATGCA 59.173 37.500 0.00 0.00 0.00 3.96
1918 2124 4.966965 ACACTGTCGGAATGTAGACTAG 57.033 45.455 0.00 0.00 38.16 2.57
1919 2125 5.220989 GCATACACTGTCGGAATGTAGACTA 60.221 44.000 4.85 0.00 38.16 2.59
1920 2126 4.440250 GCATACACTGTCGGAATGTAGACT 60.440 45.833 4.85 0.00 38.16 3.24
1921 2127 3.797256 GCATACACTGTCGGAATGTAGAC 59.203 47.826 4.85 0.00 37.85 2.59
1922 2128 3.445805 TGCATACACTGTCGGAATGTAGA 59.554 43.478 0.00 0.00 32.58 2.59
1992 2198 3.439129 GGAAATACTAGCACTTTGGCGTT 59.561 43.478 0.00 0.00 39.27 4.84
1993 2199 3.007635 GGAAATACTAGCACTTTGGCGT 58.992 45.455 0.00 0.00 39.27 5.68
1994 2200 2.030457 CGGAAATACTAGCACTTTGGCG 59.970 50.000 0.00 0.00 39.27 5.69
2036 2242 7.339598 GCTATGTAGCGGCTCTATAGCACTT 62.340 48.000 31.94 16.58 44.31 3.16
2055 2261 6.047870 GGGATGAGAATATGCTACAGCTATG 58.952 44.000 2.44 0.00 42.66 2.23
2153 2360 7.705325 CGCCTTCATTGTTAGTACTAGTATGTT 59.295 37.037 5.75 0.00 0.00 2.71
2155 2362 6.641314 CCGCCTTCATTGTTAGTACTAGTATG 59.359 42.308 5.75 8.27 0.00 2.39
2156 2363 6.323225 ACCGCCTTCATTGTTAGTACTAGTAT 59.677 38.462 5.75 0.00 0.00 2.12
2157 2364 5.653769 ACCGCCTTCATTGTTAGTACTAGTA 59.346 40.000 2.23 0.00 0.00 1.82
2158 2365 4.465305 ACCGCCTTCATTGTTAGTACTAGT 59.535 41.667 0.00 0.00 0.00 2.57
2159 2366 5.007385 ACCGCCTTCATTGTTAGTACTAG 57.993 43.478 2.23 0.00 0.00 2.57
2160 2367 4.463539 TGACCGCCTTCATTGTTAGTACTA 59.536 41.667 0.00 0.00 0.00 1.82
2161 2368 3.259876 TGACCGCCTTCATTGTTAGTACT 59.740 43.478 0.00 0.00 0.00 2.73
2162 2369 3.592059 TGACCGCCTTCATTGTTAGTAC 58.408 45.455 0.00 0.00 0.00 2.73
2173 2380 0.317854 GCACAAGTTTGACCGCCTTC 60.318 55.000 0.00 0.00 0.00 3.46
2174 2381 1.034838 TGCACAAGTTTGACCGCCTT 61.035 50.000 0.00 0.00 0.00 4.35
2265 2472 0.383949 TCGTGGTTGAAAAAGCTGGC 59.616 50.000 0.00 0.00 0.00 4.85
2310 2517 1.476891 GTGGATCGGTTAGTCAGAGCA 59.523 52.381 0.00 0.00 0.00 4.26
2322 2529 1.007734 CGGGTCATACGTGGATCGG 60.008 63.158 0.00 0.00 44.69 4.18
2336 2543 1.104577 ATGCGTGGTTTTGTTCGGGT 61.105 50.000 0.00 0.00 0.00 5.28
2339 2546 2.854777 TGAAAATGCGTGGTTTTGTTCG 59.145 40.909 0.51 0.00 0.00 3.95
2340 2547 4.084589 GGATGAAAATGCGTGGTTTTGTTC 60.085 41.667 0.51 0.00 0.00 3.18
2342 2549 3.181471 TGGATGAAAATGCGTGGTTTTGT 60.181 39.130 0.51 0.00 0.00 2.83
2343 2550 3.388308 TGGATGAAAATGCGTGGTTTTG 58.612 40.909 0.51 0.00 0.00 2.44
2358 2565 2.835156 TGGAAACGTAGGTGATGGATGA 59.165 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.