Multiple sequence alignment - TraesCS1D01G247400

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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 TraesCS1D01G247400 chr1D 100.000 2318 0 0 1 2318 340299534 340301851 0.000000e+00 4281
1 TraesCS1D01G247400 chr1A 92.396 1394 60 17 1 1372 440028847 440030216 0.000000e+00 1945
2 TraesCS1D01G247400 chr1A 85.935 711 76 17 1597 2290 440030220 440030923 0.000000e+00 737
3 TraesCS1D01G247400 chr1B 91.770 1130 54 15 554 1671 455212106 455213208 0.000000e+00 1535
4 TraesCS1D01G247400 chr1B 96.929 521 15 1 1 521 455211436 455211955 0.000000e+00 872
5 TraesCS1D01G247400 chr1B 81.798 456 67 9 1623 2072 322959157 322958712 3.640000e-98 368
6 TraesCS1D01G247400 chr1B 81.696 448 64 12 1617 2057 449594943 449595379 7.880000e-95 357
7 TraesCS1D01G247400 chr1B 81.726 197 25 9 1615 1804 60200211 60200019 1.110000e-33 154
8 TraesCS1D01G247400 chr4B 81.917 459 65 11 1621 2072 637987666 637988113 2.810000e-99 372
9 TraesCS1D01G247400 chr5D 81.172 478 64 11 1617 2072 443309847 443310320 6.090000e-96 361
10 TraesCS1D01G247400 chr5D 83.754 357 54 4 1717 2072 341615222 341615575 3.690000e-88 335
11 TraesCS1D01G247400 chr3D 84.722 360 45 9 1717 2072 49623316 49622963 3.660000e-93 351
12 TraesCS1D01G247400 chr3D 78.615 491 67 19 1609 2072 85220133 85219654 8.100000e-75 291
13 TraesCS1D01G247400 chr2A 80.837 454 68 12 1620 2072 738022241 738022676 2.850000e-89 339
14 TraesCS1D01G247400 chr6B 83.240 358 54 5 1717 2072 483528290 483528643 7.990000e-85 324
15 TraesCS1D01G247400 chr6B 79.695 197 27 11 1620 1808 568081751 568081560 1.870000e-26 130
16 TraesCS1D01G247400 chr3A 82.825 361 48 11 1717 2072 471316588 471316939 6.220000e-81 311
17 TraesCS1D01G247400 chr7D 77.963 481 66 22 1616 2067 453107024 453107493 4.910000e-67 265
18 TraesCS1D01G247400 chr6D 82.843 204 24 5 1613 1808 303028580 303028780 3.060000e-39 172


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 TraesCS1D01G247400 chr1D 340299534 340301851 2317 False 4281.0 4281 100.0000 1 2318 1 chr1D.!!$F1 2317
1 TraesCS1D01G247400 chr1A 440028847 440030923 2076 False 1341.0 1945 89.1655 1 2290 2 chr1A.!!$F1 2289
2 TraesCS1D01G247400 chr1B 455211436 455213208 1772 False 1203.5 1535 94.3495 1 1671 2 chr1B.!!$F2 1670

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
665 799 0.107654 ACCGACATAGCCTTGCTTCC 60.108 55.0 0.0 0.0 40.44 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2122 0.100861 GTTCTACTCTTCCTCGCCGG 59.899 60.0 0.0 0.0 0.0 6.13 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
55 56 2.955614 CAGCCTGCTGGAATTTTGAAG 58.044 47.619 14.77 0.00 40.17 3.02
215 216 8.123639 TGCTATATCCAGTGAGAGTAAATACC 57.876 38.462 0.00 0.00 0.00 2.73
291 292 2.987149 ACTATGTCAGCGTTGAGTTTCG 59.013 45.455 0.73 0.00 32.98 3.46
380 381 0.798776 GATGTGTCCCGCAGACTTTG 59.201 55.000 5.56 0.00 46.46 2.77
510 511 9.703892 AGCATTTTACAACATTTTGTTAGCATA 57.296 25.926 1.97 0.00 43.89 3.14
573 707 2.258726 GGGGTTGAGACGTTGCACC 61.259 63.158 0.00 0.00 0.00 5.01
622 756 2.158841 GCTTGTTGGAAAATACGAGCGA 59.841 45.455 0.00 0.00 40.76 4.93
632 766 1.516365 ATACGAGCGATCCGAGTGGG 61.516 60.000 0.00 0.00 35.24 4.61
654 788 2.803956 AGTGAAGTCCAGACCGACATA 58.196 47.619 0.00 0.00 35.07 2.29
662 796 0.176680 CAGACCGACATAGCCTTGCT 59.823 55.000 0.00 0.00 43.41 3.91
664 798 1.134670 AGACCGACATAGCCTTGCTTC 60.135 52.381 0.00 0.00 40.44 3.86
665 799 0.107654 ACCGACATAGCCTTGCTTCC 60.108 55.000 0.00 0.00 40.44 3.46
687 833 2.953161 GCCACCCCTTTCCGGATAAAAT 60.953 50.000 4.15 0.00 33.16 1.82
692 838 3.004002 CCCCTTTCCGGATAAAATAACGC 59.996 47.826 4.15 0.00 33.16 4.84
694 840 4.261031 CCCTTTCCGGATAAAATAACGCTG 60.261 45.833 4.15 0.00 33.16 5.18
711 857 0.176680 CTGGTCTTCCTACGCTGCAT 59.823 55.000 0.00 0.00 34.23 3.96
712 858 1.409064 CTGGTCTTCCTACGCTGCATA 59.591 52.381 0.00 0.00 34.23 3.14
713 859 1.136305 TGGTCTTCCTACGCTGCATAC 59.864 52.381 0.00 0.00 34.23 2.39
727 873 3.428452 GCTGCATACTAGGTTACGTGTGA 60.428 47.826 0.00 0.00 0.00 3.58
742 888 7.201803 GGTTACGTGTGATCTACTCTTCCTATT 60.202 40.741 0.00 0.00 0.00 1.73
770 916 1.981495 CCTTCCTTCCACTCTGGTCTT 59.019 52.381 0.00 0.00 39.03 3.01
814 962 1.396653 GCTGCCAAGATACCTGCAAT 58.603 50.000 0.00 0.00 32.58 3.56
815 963 1.336125 GCTGCCAAGATACCTGCAATC 59.664 52.381 0.00 0.00 32.58 2.67
816 964 1.952296 CTGCCAAGATACCTGCAATCC 59.048 52.381 0.00 0.00 32.58 3.01
817 965 1.565759 TGCCAAGATACCTGCAATCCT 59.434 47.619 0.00 0.00 0.00 3.24
818 966 1.952296 GCCAAGATACCTGCAATCCTG 59.048 52.381 0.00 0.00 0.00 3.86
819 967 2.579873 CCAAGATACCTGCAATCCTGG 58.420 52.381 1.06 1.06 38.43 4.45
820 968 1.952296 CAAGATACCTGCAATCCTGGC 59.048 52.381 0.00 0.00 36.07 4.85
821 969 1.216064 AGATACCTGCAATCCTGGCA 58.784 50.000 0.00 0.00 39.32 4.92
822 970 1.565759 AGATACCTGCAATCCTGGCAA 59.434 47.619 0.00 0.00 41.39 4.52
828 976 2.562298 CCTGCAATCCTGGCAACTAAAA 59.438 45.455 0.00 0.00 41.39 1.52
843 991 0.249826 TAAAACGCGTCGGGTTTCCT 60.250 50.000 32.17 22.92 45.43 3.36
890 1038 6.755141 CGCCTTACATATACGCTACCATAATT 59.245 38.462 0.00 0.00 0.00 1.40
898 1046 8.869897 CATATACGCTACCATAATTCACGAAAT 58.130 33.333 0.00 0.00 0.00 2.17
903 1051 5.277828 GCTACCATAATTCACGAAATGGGAC 60.278 44.000 12.81 1.81 42.66 4.46
937 1085 0.391661 ACAAGGATGCGCTGACGAAT 60.392 50.000 9.73 0.00 41.53 3.34
1210 1358 1.465188 TTGGGGGCCAGGAAGAGAA 60.465 57.895 4.39 0.00 33.81 2.87
1255 1403 2.654877 GAGGCTTGGTCGTCGGAA 59.345 61.111 0.00 0.00 0.00 4.30
1260 1408 1.669440 CTTGGTCGTCGGAAGGGAA 59.331 57.895 0.00 0.00 0.00 3.97
1372 1520 2.912956 AGTTTGTGGATTCTGGGCTAGA 59.087 45.455 0.00 0.00 0.00 2.43
1377 1525 1.207089 TGGATTCTGGGCTAGACAACG 59.793 52.381 0.00 0.00 34.43 4.10
1403 1551 7.591795 GTCACTGAACAAGATATCGACGATAAT 59.408 37.037 20.63 10.35 0.00 1.28
1474 1622 0.671781 CTTTGGAGGACAGCCAGACG 60.672 60.000 0.00 0.00 36.64 4.18
1511 1659 1.757682 GTGTGAGTTTTGGTGGGTGA 58.242 50.000 0.00 0.00 0.00 4.02
1525 1673 1.071699 TGGGTGAACTGCTGACCTAAC 59.928 52.381 0.00 0.00 0.00 2.34
1544 1692 6.177610 CCTAACCTTTCACTTGTTATAGGCA 58.822 40.000 0.00 0.00 0.00 4.75
1628 1776 0.758734 TGGTCATTAGGGGCATCTCG 59.241 55.000 0.00 0.00 0.00 4.04
1673 1821 0.038618 CACATCCGTCCGTGAACAGA 60.039 55.000 0.00 0.00 35.02 3.41
1684 1832 1.048601 GTGAACAGAGGGACCAGTCA 58.951 55.000 0.00 0.00 0.00 3.41
1685 1833 1.001406 GTGAACAGAGGGACCAGTCAG 59.999 57.143 0.00 0.00 0.00 3.51
1688 1836 2.118513 AGAGGGACCAGTCAGCGT 59.881 61.111 0.00 0.00 0.00 5.07
1693 1841 1.443872 GGACCAGTCAGCGTACACG 60.444 63.158 0.00 0.00 43.27 4.49
1694 1842 1.443872 GACCAGTCAGCGTACACGG 60.444 63.158 3.67 0.00 40.23 4.94
1706 1854 2.420568 TACACGGATGCGGGAGGAC 61.421 63.158 18.37 0.00 0.00 3.85
1707 1855 3.770040 CACGGATGCGGGAGGACA 61.770 66.667 12.44 0.00 0.00 4.02
1712 1860 0.394352 GGATGCGGGAGGACAACATT 60.394 55.000 0.00 0.00 0.00 2.71
1715 1863 0.109532 TGCGGGAGGACAACATTCAA 59.890 50.000 0.00 0.00 0.00 2.69
1728 1882 6.687105 GGACAACATTCAACGCTATACATTTC 59.313 38.462 0.00 0.00 0.00 2.17
1733 1887 7.816640 ACATTCAACGCTATACATTTCAAACT 58.183 30.769 0.00 0.00 0.00 2.66
1734 1888 8.941977 ACATTCAACGCTATACATTTCAAACTA 58.058 29.630 0.00 0.00 0.00 2.24
1770 1924 3.613737 CCGGATGAAATTCATGCAAACAC 59.386 43.478 23.55 4.52 44.18 3.32
1772 1926 3.613737 GGATGAAATTCATGCAAACACGG 59.386 43.478 20.18 0.00 43.55 4.94
1781 1935 1.006688 GCAAACACGGCCGGATTTT 60.007 52.632 31.76 21.19 0.00 1.82
1815 1989 9.438291 CATGACGGATTTCATTACATTTAGAAC 57.562 33.333 0.00 0.00 33.74 3.01
1817 1991 9.173021 TGACGGATTTCATTACATTTAGAACAT 57.827 29.630 0.00 0.00 0.00 2.71
1858 2032 2.322658 CCCTAAACCTATCCTACGGCA 58.677 52.381 0.00 0.00 0.00 5.69
1888 2062 2.430367 GTCCAAGCCCGTGTCCTT 59.570 61.111 0.00 0.00 0.00 3.36
1896 2070 0.250513 GCCCGTGTCCTTCTTCATCT 59.749 55.000 0.00 0.00 0.00 2.90
1905 2079 2.755655 TCCTTCTTCATCTGTCGTCTCC 59.244 50.000 0.00 0.00 0.00 3.71
1906 2080 2.493675 CCTTCTTCATCTGTCGTCTCCA 59.506 50.000 0.00 0.00 0.00 3.86
1914 2088 0.459237 CTGTCGTCTCCATGAGCACC 60.459 60.000 0.00 0.00 0.00 5.01
1918 2092 1.517257 GTCTCCATGAGCACCGACG 60.517 63.158 0.00 0.00 0.00 5.12
1924 2098 1.491670 CATGAGCACCGACGATAAGG 58.508 55.000 0.00 0.00 0.00 2.69
1926 2100 1.320344 TGAGCACCGACGATAAGGCT 61.320 55.000 0.00 0.00 0.00 4.58
1939 2113 3.806521 CGATAAGGCTGATGAAGTGAAGG 59.193 47.826 0.00 0.00 0.00 3.46
1948 2122 2.533266 TGAAGTGAAGGTGCAGTCTC 57.467 50.000 0.00 0.00 0.00 3.36
1969 2143 1.201647 CGGCGAGGAAGAGTAGAACAA 59.798 52.381 0.00 0.00 0.00 2.83
1982 2156 0.969894 AGAACAAGGGAGACAGACCG 59.030 55.000 0.00 0.00 0.00 4.79
1983 2157 0.037232 GAACAAGGGAGACAGACCGG 60.037 60.000 0.00 0.00 0.00 5.28
1988 2162 4.083862 GGAGACAGACCGGCCCAC 62.084 72.222 0.00 0.00 0.00 4.61
2018 2192 4.803426 GCACCTCCGCCTCTCGTG 62.803 72.222 0.00 0.00 36.19 4.35
2032 2206 2.025155 TCTCGTGGCCTACTCATTCTC 58.975 52.381 3.32 0.00 0.00 2.87
2034 2208 0.738975 CGTGGCCTACTCATTCTCGA 59.261 55.000 3.32 0.00 0.00 4.04
2044 2218 1.746220 CTCATTCTCGAAGGAGTCCGT 59.254 52.381 11.90 0.00 42.38 4.69
2052 2226 1.542492 GAAGGAGTCCGTGACCTGTA 58.458 55.000 0.93 0.00 34.03 2.74
2057 2231 0.535780 AGTCCGTGACCTGTACGTCA 60.536 55.000 0.00 0.02 40.44 4.35
2105 2279 7.275920 AGTGAAGTGGAGTTAGCATTATAAGG 58.724 38.462 0.00 0.00 0.00 2.69
2107 2281 8.202137 GTGAAGTGGAGTTAGCATTATAAGGTA 58.798 37.037 0.00 0.00 0.00 3.08
2114 2288 8.422566 GGAGTTAGCATTATAAGGTAAGACACT 58.577 37.037 0.00 0.00 30.49 3.55
2146 2320 0.454600 CAAGCGATGGAAATGCAGCT 59.545 50.000 0.00 0.00 36.40 4.24
2147 2321 0.454600 AAGCGATGGAAATGCAGCTG 59.545 50.000 10.11 10.11 34.94 4.24
2151 2325 1.760192 GATGGAAATGCAGCTGAGGT 58.240 50.000 20.43 0.00 0.00 3.85
2156 2330 4.088634 TGGAAATGCAGCTGAGGTTTTAT 58.911 39.130 20.43 0.00 0.00 1.40
2266 2440 7.547370 GCTAGAGTTGAGAAGCTGATAAAAGAA 59.453 37.037 0.00 0.00 32.18 2.52
2269 2443 8.782144 AGAGTTGAGAAGCTGATAAAAGAAAAG 58.218 33.333 0.00 0.00 0.00 2.27
2277 2451 8.634475 AAGCTGATAAAAGAAAAGACACAAAC 57.366 30.769 0.00 0.00 0.00 2.93
2290 2464 6.635030 AAGACACAAACCTCCTTCATAAAC 57.365 37.500 0.00 0.00 0.00 2.01
2291 2465 5.690865 AGACACAAACCTCCTTCATAAACA 58.309 37.500 0.00 0.00 0.00 2.83
2292 2466 6.126409 AGACACAAACCTCCTTCATAAACAA 58.874 36.000 0.00 0.00 0.00 2.83
2293 2467 6.263168 AGACACAAACCTCCTTCATAAACAAG 59.737 38.462 0.00 0.00 0.00 3.16
2294 2468 6.126409 ACACAAACCTCCTTCATAAACAAGA 58.874 36.000 0.00 0.00 0.00 3.02
2295 2469 6.039382 ACACAAACCTCCTTCATAAACAAGAC 59.961 38.462 0.00 0.00 0.00 3.01
2296 2470 6.039270 CACAAACCTCCTTCATAAACAAGACA 59.961 38.462 0.00 0.00 0.00 3.41
2297 2471 6.605594 ACAAACCTCCTTCATAAACAAGACAA 59.394 34.615 0.00 0.00 0.00 3.18
2298 2472 7.123547 ACAAACCTCCTTCATAAACAAGACAAA 59.876 33.333 0.00 0.00 0.00 2.83
2299 2473 7.654022 AACCTCCTTCATAAACAAGACAAAA 57.346 32.000 0.00 0.00 0.00 2.44
2300 2474 7.654022 ACCTCCTTCATAAACAAGACAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
2301 2475 7.489160 ACCTCCTTCATAAACAAGACAAAAAC 58.511 34.615 0.00 0.00 0.00 2.43
2302 2476 7.342026 ACCTCCTTCATAAACAAGACAAAAACT 59.658 33.333 0.00 0.00 0.00 2.66
2303 2477 7.649306 CCTCCTTCATAAACAAGACAAAAACTG 59.351 37.037 0.00 0.00 0.00 3.16
2304 2478 7.488322 TCCTTCATAAACAAGACAAAAACTGG 58.512 34.615 0.00 0.00 0.00 4.00
2305 2479 7.123547 TCCTTCATAAACAAGACAAAAACTGGT 59.876 33.333 0.00 0.00 0.00 4.00
2306 2480 7.763985 CCTTCATAAACAAGACAAAAACTGGTT 59.236 33.333 0.00 0.00 33.55 3.67
2307 2481 8.472683 TTCATAAACAAGACAAAAACTGGTTG 57.527 30.769 0.00 0.00 32.65 3.77
2308 2482 7.607250 TCATAAACAAGACAAAAACTGGTTGT 58.393 30.769 0.00 0.00 41.84 3.32
2309 2483 7.543868 TCATAAACAAGACAAAAACTGGTTGTG 59.456 33.333 0.00 0.00 39.29 3.33
2310 2484 4.864704 ACAAGACAAAAACTGGTTGTGT 57.135 36.364 0.00 0.00 39.29 3.72
2311 2485 4.805219 ACAAGACAAAAACTGGTTGTGTC 58.195 39.130 18.92 18.92 39.29 3.67
2312 2486 4.279671 ACAAGACAAAAACTGGTTGTGTCA 59.720 37.500 26.07 0.00 39.29 3.58
2313 2487 5.047377 ACAAGACAAAAACTGGTTGTGTCAT 60.047 36.000 26.07 14.84 39.29 3.06
2314 2488 5.248870 AGACAAAAACTGGTTGTGTCATC 57.751 39.130 26.07 4.89 39.29 2.92
2315 2489 4.097892 AGACAAAAACTGGTTGTGTCATCC 59.902 41.667 26.07 4.56 39.29 3.51
2316 2490 4.023291 ACAAAAACTGGTTGTGTCATCCT 58.977 39.130 0.00 0.00 37.80 3.24
2317 2491 4.466015 ACAAAAACTGGTTGTGTCATCCTT 59.534 37.500 0.00 0.00 37.80 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.276421 TCACCTTCAGTAGCAGGCTTC 59.724 52.381 0.00 0.00 30.45 3.86
147 148 2.287427 CGTCCCGTCGCTCTATTTATGT 60.287 50.000 0.00 0.00 0.00 2.29
173 174 3.738830 AGCAACATCACAACATGCTTT 57.261 38.095 0.00 0.00 44.43 3.51
215 216 4.536065 TGAAATTTACAGCGAGCAAACTG 58.464 39.130 0.00 0.00 39.86 3.16
291 292 1.344763 AGTTGCTACTGTCCCAGTGAC 59.655 52.381 0.00 0.22 45.01 3.67
302 303 4.286032 TCCCAAATGTCAGTAGTTGCTACT 59.714 41.667 6.00 6.00 46.75 2.57
380 381 0.666274 TCCACGTGCTCGACATTCAC 60.666 55.000 16.04 0.00 40.62 3.18
528 529 9.349713 ACTTGAAACAGAAACATATACTCCAAA 57.650 29.630 0.00 0.00 0.00 3.28
529 530 8.783093 CACTTGAAACAGAAACATATACTCCAA 58.217 33.333 0.00 0.00 0.00 3.53
546 547 1.602377 CGTCTCAACCCCACTTGAAAC 59.398 52.381 0.00 0.00 29.66 2.78
573 707 0.504384 CGCACGCAATATTCTCTCCG 59.496 55.000 0.00 0.00 0.00 4.63
622 756 1.550976 GACTTCACTTCCCACTCGGAT 59.449 52.381 0.00 0.00 41.63 4.18
632 766 1.340248 TGTCGGTCTGGACTTCACTTC 59.660 52.381 0.67 0.00 37.81 3.01
662 796 4.338710 CGGAAAGGGGTGGCGGAA 62.339 66.667 0.00 0.00 0.00 4.30
665 799 2.260088 TTATCCGGAAAGGGGTGGCG 62.260 60.000 9.01 0.00 41.52 5.69
687 833 0.171903 GCGTAGGAAGACCAGCGTTA 59.828 55.000 0.00 0.00 37.67 3.18
692 838 0.176680 ATGCAGCGTAGGAAGACCAG 59.823 55.000 0.00 0.00 38.94 4.00
694 840 1.409427 AGTATGCAGCGTAGGAAGACC 59.591 52.381 0.00 0.00 0.00 3.85
711 857 6.882656 AGAGTAGATCACACGTAACCTAGTA 58.117 40.000 0.00 0.00 0.00 1.82
712 858 5.743117 AGAGTAGATCACACGTAACCTAGT 58.257 41.667 0.00 0.00 0.00 2.57
713 859 6.238429 GGAAGAGTAGATCACACGTAACCTAG 60.238 46.154 0.00 0.00 0.00 3.02
727 873 7.466804 AGGATCGAGAAATAGGAAGAGTAGAT 58.533 38.462 0.00 0.00 0.00 1.98
742 888 2.761208 GAGTGGAAGGAAGGATCGAGAA 59.239 50.000 0.00 0.00 0.00 2.87
774 920 7.362920 GGCAGCCAAGTTCATTCTTTTCTTATA 60.363 37.037 6.55 0.00 0.00 0.98
775 921 6.393171 GCAGCCAAGTTCATTCTTTTCTTAT 58.607 36.000 0.00 0.00 0.00 1.73
814 962 0.533308 ACGCGTTTTAGTTGCCAGGA 60.533 50.000 5.58 0.00 0.00 3.86
815 963 0.110373 GACGCGTTTTAGTTGCCAGG 60.110 55.000 15.53 0.00 0.00 4.45
816 964 0.450482 CGACGCGTTTTAGTTGCCAG 60.450 55.000 15.53 0.00 0.00 4.85
817 965 1.565591 CGACGCGTTTTAGTTGCCA 59.434 52.632 15.53 0.00 0.00 4.92
818 966 1.154543 CCGACGCGTTTTAGTTGCC 60.155 57.895 15.53 0.00 0.00 4.52
819 967 1.154543 CCCGACGCGTTTTAGTTGC 60.155 57.895 15.53 0.00 0.00 4.17
820 968 0.582960 AACCCGACGCGTTTTAGTTG 59.417 50.000 15.53 0.52 0.00 3.16
821 969 1.261354 GAAACCCGACGCGTTTTAGTT 59.739 47.619 15.53 12.46 33.65 2.24
822 970 0.861185 GAAACCCGACGCGTTTTAGT 59.139 50.000 15.53 6.24 33.65 2.24
828 976 1.140375 GATAGGAAACCCGACGCGT 59.860 57.895 13.85 13.85 0.00 6.01
890 1038 1.594833 CTCGGGTCCCATTTCGTGA 59.405 57.895 9.12 0.00 0.00 4.35
898 1046 2.682136 TCGATTGCTCGGGTCCCA 60.682 61.111 9.12 0.00 45.10 4.37
995 1143 1.605753 CCCGGACATCGTCATCTCTA 58.394 55.000 0.73 0.00 37.11 2.43
1243 1391 1.669440 CTTCCCTTCCGACGACCAA 59.331 57.895 0.00 0.00 0.00 3.67
1372 1520 4.621460 CGATATCTTGTTCAGTGACGTTGT 59.379 41.667 0.34 0.00 0.00 3.32
1377 1525 4.659088 TCGTCGATATCTTGTTCAGTGAC 58.341 43.478 0.34 0.00 0.00 3.67
1403 1551 3.554752 GCTAAATTGCAACTTTCCCAGCA 60.555 43.478 0.00 0.00 34.79 4.41
1474 1622 1.068741 CACGCTAATCTACTCCCACCC 59.931 57.143 0.00 0.00 0.00 4.61
1511 1659 3.136626 AGTGAAAGGTTAGGTCAGCAGTT 59.863 43.478 0.00 0.00 0.00 3.16
1525 1673 3.947834 CCCTGCCTATAACAAGTGAAAGG 59.052 47.826 0.00 0.00 0.00 3.11
1544 1692 1.710809 AGATGTTTACAACAGGCCCCT 59.289 47.619 0.00 0.00 45.95 4.79
1620 1768 2.750888 GGTTGCCGTTCGAGATGCC 61.751 63.158 0.00 0.00 0.00 4.40
1628 1776 4.359971 AAAATATTACGGGTTGCCGTTC 57.640 40.909 0.00 0.00 44.38 3.95
1650 1798 0.393448 TTCACGGACGGATGTGGAAA 59.607 50.000 0.00 0.00 36.74 3.13
1673 1821 1.228769 TGTACGCTGACTGGTCCCT 60.229 57.895 0.00 0.00 0.00 4.20
1684 1832 4.508128 CCCGCATCCGTGTACGCT 62.508 66.667 4.67 0.00 38.18 5.07
1685 1833 4.501714 TCCCGCATCCGTGTACGC 62.502 66.667 0.00 0.00 38.18 4.42
1688 1836 2.043752 TCCTCCCGCATCCGTGTA 60.044 61.111 0.00 0.00 0.00 2.90
1693 1841 0.394352 AATGTTGTCCTCCCGCATCC 60.394 55.000 0.00 0.00 0.00 3.51
1694 1842 1.017387 GAATGTTGTCCTCCCGCATC 58.983 55.000 0.00 0.00 0.00 3.91
1706 1854 8.365210 GTTTGAAATGTATAGCGTTGAATGTTG 58.635 33.333 0.00 0.00 0.00 3.33
1707 1855 8.296713 AGTTTGAAATGTATAGCGTTGAATGTT 58.703 29.630 0.00 0.00 0.00 2.71
1741 1895 4.091800 GCATGAATTTCATCCGGTTTGTTG 59.908 41.667 8.95 0.00 34.28 3.33
1743 1897 3.257873 TGCATGAATTTCATCCGGTTTGT 59.742 39.130 8.95 0.00 34.28 2.83
1770 1924 4.035792 TCATGTTTGTATAAAATCCGGCCG 59.964 41.667 21.04 21.04 0.00 6.13
1772 1926 4.967575 CGTCATGTTTGTATAAAATCCGGC 59.032 41.667 0.00 0.00 0.00 6.13
1781 1935 9.384764 TGTAATGAAATCCGTCATGTTTGTATA 57.615 29.630 0.00 0.00 38.28 1.47
1827 2001 1.189524 GGTTTAGGGGCGGGCTTTTT 61.190 55.000 0.26 0.00 0.00 1.94
1828 2002 1.608336 GGTTTAGGGGCGGGCTTTT 60.608 57.895 0.26 0.00 0.00 2.27
1829 2003 1.209523 TAGGTTTAGGGGCGGGCTTT 61.210 55.000 0.26 0.00 0.00 3.51
1830 2004 0.991893 ATAGGTTTAGGGGCGGGCTT 60.992 55.000 0.26 0.00 0.00 4.35
1831 2005 1.385489 ATAGGTTTAGGGGCGGGCT 60.385 57.895 0.26 0.00 0.00 5.19
1832 2006 1.072678 GATAGGTTTAGGGGCGGGC 59.927 63.158 0.00 0.00 0.00 6.13
1833 2007 0.767060 AGGATAGGTTTAGGGGCGGG 60.767 60.000 0.00 0.00 0.00 6.13
1869 2043 2.668550 GGACACGGGCTTGGACAC 60.669 66.667 0.00 0.00 0.00 3.67
1878 2052 1.276421 ACAGATGAAGAAGGACACGGG 59.724 52.381 0.00 0.00 0.00 5.28
1888 2062 3.356290 TCATGGAGACGACAGATGAAGA 58.644 45.455 0.00 0.00 0.00 2.87
1896 2070 1.591703 GGTGCTCATGGAGACGACA 59.408 57.895 0.00 0.00 0.00 4.35
1905 2079 1.491670 CCTTATCGTCGGTGCTCATG 58.508 55.000 0.00 0.00 0.00 3.07
1906 2080 0.249489 GCCTTATCGTCGGTGCTCAT 60.249 55.000 0.00 0.00 0.00 2.90
1914 2088 2.791560 CACTTCATCAGCCTTATCGTCG 59.208 50.000 0.00 0.00 0.00 5.12
1918 2092 4.574013 CACCTTCACTTCATCAGCCTTATC 59.426 45.833 0.00 0.00 0.00 1.75
1924 2098 1.467734 CTGCACCTTCACTTCATCAGC 59.532 52.381 0.00 0.00 0.00 4.26
1926 2100 2.369860 AGACTGCACCTTCACTTCATCA 59.630 45.455 0.00 0.00 0.00 3.07
1939 2113 4.803426 CCTCGCCGGAGACTGCAC 62.803 72.222 5.05 0.00 43.27 4.57
1948 2122 0.100861 GTTCTACTCTTCCTCGCCGG 59.899 60.000 0.00 0.00 0.00 6.13
1988 2162 0.962356 GAGGTGCCTTGTGTCCCATG 60.962 60.000 0.00 0.00 0.00 3.66
2014 2188 0.738975 CGAGAATGAGTAGGCCACGA 59.261 55.000 5.01 0.00 0.00 4.35
2018 2192 2.032620 TCCTTCGAGAATGAGTAGGCC 58.967 52.381 0.00 0.00 0.00 5.19
2032 2206 1.213013 CAGGTCACGGACTCCTTCG 59.787 63.158 4.41 0.00 32.47 3.79
2034 2208 1.254954 GTACAGGTCACGGACTCCTT 58.745 55.000 4.41 0.00 32.47 3.36
2057 2231 6.883217 ACTATATATAACTCACGTCCATCGGT 59.117 38.462 0.00 0.00 44.69 4.69
2060 2234 9.776158 CTTCACTATATATAACTCACGTCCATC 57.224 37.037 0.00 0.00 0.00 3.51
2146 2320 7.789273 TTCGTTCAACTACAATAAAACCTCA 57.211 32.000 0.00 0.00 0.00 3.86
2147 2321 7.588854 GGTTTCGTTCAACTACAATAAAACCTC 59.411 37.037 0.00 0.00 39.81 3.85
2151 2325 8.622157 TGATGGTTTCGTTCAACTACAATAAAA 58.378 29.630 0.00 0.00 0.00 1.52
2156 2330 5.107259 CGATGATGGTTTCGTTCAACTACAA 60.107 40.000 0.00 0.00 0.00 2.41
2232 2406 2.272678 TCTCAACTCTAGCTCGACTCG 58.727 52.381 0.00 0.00 0.00 4.18
2241 2415 8.994429 TTCTTTTATCAGCTTCTCAACTCTAG 57.006 34.615 0.00 0.00 0.00 2.43
2266 2440 6.605594 TGTTTATGAAGGAGGTTTGTGTCTTT 59.394 34.615 0.00 0.00 0.00 2.52
2269 2443 6.262273 TCTTGTTTATGAAGGAGGTTTGTGTC 59.738 38.462 0.00 0.00 0.00 3.67
2277 2451 7.649306 CAGTTTTTGTCTTGTTTATGAAGGAGG 59.351 37.037 0.00 0.00 0.00 4.30
2290 2464 4.804108 TGACACAACCAGTTTTTGTCTTG 58.196 39.130 17.05 0.00 34.91 3.02
2291 2465 5.394115 GGATGACACAACCAGTTTTTGTCTT 60.394 40.000 17.05 13.03 34.91 3.01
2292 2466 4.097892 GGATGACACAACCAGTTTTTGTCT 59.902 41.667 17.05 7.86 34.91 3.41
2293 2467 4.097892 AGGATGACACAACCAGTTTTTGTC 59.902 41.667 12.27 12.27 34.91 3.18
2294 2468 4.023291 AGGATGACACAACCAGTTTTTGT 58.977 39.130 0.00 0.00 37.69 2.83
2295 2469 4.654091 AGGATGACACAACCAGTTTTTG 57.346 40.909 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.