Multiple sequence alignment - TraesCS1A01G220000

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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 TraesCS1A01G220000 chr1A 100.000 2849 0 0 1 2849 388848129 388850977 0.000000e+00 5262
1 TraesCS1A01G220000 chr1A 94.824 850 29 13 1 842 460601387 460602229 0.000000e+00 1312
2 TraesCS1A01G220000 chr1B 92.098 2050 64 33 838 2849 418821031 418823020 0.000000e+00 2798
3 TraesCS1A01G220000 chr1D 91.675 2066 78 35 838 2849 309087650 309089675 0.000000e+00 2776
4 TraesCS1A01G220000 chr5A 93.936 841 37 12 1 834 7707671 7708504 0.000000e+00 1258
5 TraesCS1A01G220000 chr3A 92.399 842 48 14 1 834 721562858 721562025 0.000000e+00 1186
6 TraesCS1A01G220000 chr6A 93.366 618 33 7 226 837 10984874 10985489 0.000000e+00 907
7 TraesCS1A01G220000 chr6A 91.973 299 14 9 1 297 10984725 10985015 7.350000e-111 411
8 TraesCS1A01G220000 chr6A 87.226 274 28 6 1263 1534 465389774 465390042 3.570000e-79 305
9 TraesCS1A01G220000 chrUn 93.065 620 33 7 226 838 275311597 275312213 0.000000e+00 898
10 TraesCS1A01G220000 chrUn 90.635 299 18 9 1 297 275311448 275311738 3.440000e-104 388
11 TraesCS1A01G220000 chr3B 92.382 617 37 7 226 834 8497396 8498010 0.000000e+00 870
12 TraesCS1A01G220000 chr3B 93.153 555 31 4 298 846 34157469 34156916 0.000000e+00 808
13 TraesCS1A01G220000 chr3B 93.153 555 31 4 298 846 34213325 34212772 0.000000e+00 808
14 TraesCS1A01G220000 chr3B 93.002 543 31 5 298 834 441279285 441279826 0.000000e+00 785
15 TraesCS1A01G220000 chr3B 90.604 298 20 7 1 297 8497247 8497537 3.440000e-104 388
16 TraesCS1A01G220000 chr3B 90.708 226 13 7 1 225 441279137 441279355 7.720000e-76 294
17 TraesCS1A01G220000 chr2A 87.273 275 30 4 1263 1536 672265685 672265415 2.760000e-80 309
18 TraesCS1A01G220000 chr6B 86.496 274 30 6 1263 1534 495543786 495543518 7.720000e-76 294
19 TraesCS1A01G220000 chr2D 86.131 274 35 2 1263 1536 527272567 527272297 2.780000e-75 292
20 TraesCS1A01G220000 chr2D 86.364 264 31 4 1274 1536 527293785 527293526 1.670000e-72 283
21 TraesCS1A01G220000 chr6D 86.131 274 31 6 1263 1534 326760698 326760966 3.590000e-74 289
22 TraesCS1A01G220000 chr4B 89.823 226 15 7 1 225 506904982 506904764 1.670000e-72 283
23 TraesCS1A01G220000 chr2B 89.868 227 14 6 1 225 790812649 790812868 1.670000e-72 283
24 TraesCS1A01G220000 chr2B 85.455 275 35 4 1263 1536 624287309 624287039 6.010000e-72 281


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 TraesCS1A01G220000 chr1A 388848129 388850977 2848 False 5262.0 5262 100.0000 1 2849 1 chr1A.!!$F1 2848
1 TraesCS1A01G220000 chr1A 460601387 460602229 842 False 1312.0 1312 94.8240 1 842 1 chr1A.!!$F2 841
2 TraesCS1A01G220000 chr1B 418821031 418823020 1989 False 2798.0 2798 92.0980 838 2849 1 chr1B.!!$F1 2011
3 TraesCS1A01G220000 chr1D 309087650 309089675 2025 False 2776.0 2776 91.6750 838 2849 1 chr1D.!!$F1 2011
4 TraesCS1A01G220000 chr5A 7707671 7708504 833 False 1258.0 1258 93.9360 1 834 1 chr5A.!!$F1 833
5 TraesCS1A01G220000 chr3A 721562025 721562858 833 True 1186.0 1186 92.3990 1 834 1 chr3A.!!$R1 833
6 TraesCS1A01G220000 chr6A 10984725 10985489 764 False 659.0 907 92.6695 1 837 2 chr6A.!!$F2 836
7 TraesCS1A01G220000 chrUn 275311448 275312213 765 False 643.0 898 91.8500 1 838 2 chrUn.!!$F1 837
8 TraesCS1A01G220000 chr3B 34156916 34157469 553 True 808.0 808 93.1530 298 846 1 chr3B.!!$R1 548
9 TraesCS1A01G220000 chr3B 34212772 34213325 553 True 808.0 808 93.1530 298 846 1 chr3B.!!$R2 548
10 TraesCS1A01G220000 chr3B 8497247 8498010 763 False 629.0 870 91.4930 1 834 2 chr3B.!!$F1 833
11 TraesCS1A01G220000 chr3B 441279137 441279826 689 False 539.5 785 91.8550 1 834 2 chr3B.!!$F2 833

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
99 101 0.098025 ACGTTGCAAAACAGACGTGG 59.902 50.000 10.92 0.0 41.30 4.94 F
101 103 0.179150 GTTGCAAAACAGACGTGGCA 60.179 50.000 0.00 0.0 0.00 4.92 F
433 510 0.399833 TGGACAGTTGCCATGTAGCA 59.600 50.000 0.00 0.0 42.17 3.49 F
1579 1688 1.001269 TCCACGGATCAGTCGGAGT 60.001 57.895 11.19 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1342 0.110328 TGCTCTTCTTCGTCGTCGTC 60.110 55.000 1.33 0.00 38.33 4.20 R
1237 1343 0.309922 TTGCTCTTCTTCGTCGTCGT 59.690 50.000 1.33 0.00 38.33 4.34 R
1743 1852 0.657659 CGAATCCGTCCTCGATGTCG 60.658 60.000 0.81 0.81 37.23 4.35 R
2589 2727 1.363807 GCCACCTTTTGTCTGCACC 59.636 57.895 0.00 0.00 0.00 5.01 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
64 66 4.413760 AGAGTTGCCACCTACTAACACTA 58.586 43.478 0.00 0.00 0.00 2.74
73 75 5.243283 CCACCTACTAACACTAGACAGTTGT 59.757 44.000 0.00 3.12 30.46 3.32
86 88 3.541711 GACAGTTGTCATGTAACGTTGC 58.458 45.455 11.99 10.76 44.18 4.17
93 95 4.346970 TGTCATGTAACGTTGCAAAACAG 58.653 39.130 22.80 10.61 0.00 3.16
94 96 4.095036 TGTCATGTAACGTTGCAAAACAGA 59.905 37.500 22.80 12.53 0.00 3.41
95 97 4.436523 GTCATGTAACGTTGCAAAACAGAC 59.563 41.667 22.80 18.85 0.00 3.51
96 98 3.040990 TGTAACGTTGCAAAACAGACG 57.959 42.857 17.05 2.07 38.16 4.18
97 99 2.415857 TGTAACGTTGCAAAACAGACGT 59.584 40.909 17.05 2.86 43.18 4.34
98 100 1.889891 AACGTTGCAAAACAGACGTG 58.110 45.000 12.29 0.00 41.69 4.49
99 101 0.098025 ACGTTGCAAAACAGACGTGG 59.902 50.000 10.92 0.00 41.30 4.94
100 102 1.199852 CGTTGCAAAACAGACGTGGC 61.200 55.000 0.00 0.00 32.05 5.01
101 103 0.179150 GTTGCAAAACAGACGTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
102 104 0.528017 TTGCAAAACAGACGTGGCAA 59.472 45.000 0.00 0.00 36.03 4.52
103 105 0.179150 TGCAAAACAGACGTGGCAAC 60.179 50.000 0.00 0.00 0.00 4.17
137 141 6.534475 TCGGGTAAAAAGAGAGTTGCTATA 57.466 37.500 0.00 0.00 0.00 1.31
257 262 4.097741 GCCATGTATCCTGCAAAACACATA 59.902 41.667 4.03 0.00 0.00 2.29
284 289 1.327303 GATGGCTTTTGGTGTGTGGA 58.673 50.000 0.00 0.00 0.00 4.02
341 417 1.999648 AACACATGGCAACTGATGGT 58.000 45.000 0.00 0.00 37.61 3.55
415 492 3.326747 GAGTTGCCACCTACTAACACTG 58.673 50.000 0.00 0.00 0.00 3.66
431 508 2.079158 CACTGGACAGTTGCCATGTAG 58.921 52.381 1.49 0.00 40.20 2.74
433 510 0.399833 TGGACAGTTGCCATGTAGCA 59.600 50.000 0.00 0.00 42.17 3.49
437 514 3.334691 GACAGTTGCCATGTAGCACTAA 58.665 45.455 0.00 0.00 43.97 2.24
483 567 3.127030 CGGGTAAAAAGAGAGTTGCCATC 59.873 47.826 0.00 0.00 31.65 3.51
579 665 1.003839 GGGTGAATGGCAGTCGTGA 60.004 57.895 10.64 0.00 0.00 4.35
591 677 3.257393 GCAGTCGTGAGAGATGTGAAAT 58.743 45.455 0.00 0.00 43.49 2.17
631 717 4.077188 GCGCGACAGCAGTTCCAC 62.077 66.667 12.10 0.00 45.49 4.02
808 895 1.302192 GTGGGCGAGTTGGCTAACA 60.302 57.895 15.86 0.00 44.11 2.41
879 966 4.072839 CAGTAAACTTTTCTCCCACCTCC 58.927 47.826 0.00 0.00 0.00 4.30
1199 1305 4.465446 CGAGGGAGAGGGAGGGCA 62.465 72.222 0.00 0.00 0.00 5.36
1226 1332 2.416432 CGGAGGAGGGGAAGACGAC 61.416 68.421 0.00 0.00 0.00 4.34
1227 1333 2.416432 GGAGGAGGGGAAGACGACG 61.416 68.421 0.00 0.00 0.00 5.12
1228 1334 1.378250 GAGGAGGGGAAGACGACGA 60.378 63.158 0.00 0.00 0.00 4.20
1229 1335 1.655885 GAGGAGGGGAAGACGACGAC 61.656 65.000 0.00 0.00 0.00 4.34
1230 1336 2.484203 GAGGGGAAGACGACGACG 59.516 66.667 5.58 5.58 45.75 5.12
1231 1337 2.033141 AGGGGAAGACGACGACGA 59.967 61.111 15.32 0.00 42.66 4.20
1232 1338 2.177778 GGGGAAGACGACGACGAC 59.822 66.667 15.32 8.08 42.66 4.34
1233 1339 2.202272 GGGAAGACGACGACGACG 60.202 66.667 17.60 17.60 42.66 5.12
1234 1340 2.202272 GGAAGACGACGACGACGG 60.202 66.667 22.36 6.21 44.46 4.79
1235 1341 2.868787 GAAGACGACGACGACGGC 60.869 66.667 22.36 20.21 45.02 5.68
1260 1369 1.004277 CGACGAAGAAGAGCAAGCGT 61.004 55.000 0.00 0.00 34.39 5.07
1579 1688 1.001269 TCCACGGATCAGTCGGAGT 60.001 57.895 11.19 0.00 0.00 3.85
1580 1689 1.030488 TCCACGGATCAGTCGGAGTC 61.030 60.000 11.19 0.00 0.00 3.36
1584 1693 1.374343 CGGATCAGTCGGAGTCGGAA 61.374 60.000 1.41 0.00 36.95 4.30
1710 1819 3.535962 GCGGAGGAGGAGGAGCTG 61.536 72.222 0.00 0.00 0.00 4.24
1711 1820 3.535962 CGGAGGAGGAGGAGCTGC 61.536 72.222 0.00 0.00 0.00 5.25
1712 1821 3.535962 GGAGGAGGAGGAGCTGCG 61.536 72.222 0.00 0.00 0.00 5.18
1743 1852 2.202987 CTGCCGGACCTGCTCATC 60.203 66.667 5.05 0.00 0.00 2.92
1764 1873 0.750546 ACATCGAGGACGGATTCGGA 60.751 55.000 3.06 0.00 41.39 4.55
1924 2033 6.809630 AGTGTAATCTCTTCTTTGCCTTTC 57.190 37.500 0.00 0.00 0.00 2.62
1928 2037 8.138074 GTGTAATCTCTTCTTTGCCTTTCTTTT 58.862 33.333 0.00 0.00 0.00 2.27
2121 2242 2.561478 TCCTAGTGGTTTGACCTTGC 57.439 50.000 0.00 0.00 39.58 4.01
2122 2243 1.073284 TCCTAGTGGTTTGACCTTGCC 59.927 52.381 0.00 0.00 39.58 4.52
2124 2245 2.555227 CCTAGTGGTTTGACCTTGCCAT 60.555 50.000 0.00 0.00 39.58 4.40
2125 2246 1.620822 AGTGGTTTGACCTTGCCATC 58.379 50.000 0.00 0.00 39.58 3.51
2126 2247 1.133513 AGTGGTTTGACCTTGCCATCA 60.134 47.619 0.00 0.00 39.58 3.07
2127 2248 1.270550 GTGGTTTGACCTTGCCATCAG 59.729 52.381 0.00 0.00 39.58 2.90
2128 2249 1.144708 TGGTTTGACCTTGCCATCAGA 59.855 47.619 0.00 0.00 39.58 3.27
2130 2251 2.827921 GGTTTGACCTTGCCATCAGATT 59.172 45.455 0.00 0.00 34.73 2.40
2131 2252 4.016444 GGTTTGACCTTGCCATCAGATTA 58.984 43.478 0.00 0.00 34.73 1.75
2132 2253 4.646492 GGTTTGACCTTGCCATCAGATTAT 59.354 41.667 0.00 0.00 34.73 1.28
2133 2254 5.127682 GGTTTGACCTTGCCATCAGATTATT 59.872 40.000 0.00 0.00 34.73 1.40
2135 2256 4.209538 TGACCTTGCCATCAGATTATTGG 58.790 43.478 0.00 0.00 0.00 3.16
2136 2257 3.569491 ACCTTGCCATCAGATTATTGGG 58.431 45.455 0.00 0.00 0.00 4.12
2137 2258 3.052642 ACCTTGCCATCAGATTATTGGGT 60.053 43.478 0.00 0.00 0.00 4.51
2138 2259 3.319972 CCTTGCCATCAGATTATTGGGTG 59.680 47.826 0.00 0.00 0.00 4.61
2139 2260 3.949586 TGCCATCAGATTATTGGGTGA 57.050 42.857 0.00 0.00 0.00 4.02
2140 2261 4.458256 TGCCATCAGATTATTGGGTGAT 57.542 40.909 0.00 0.00 0.00 3.06
2171 2304 5.907197 ATTCGTTATGCTTGGAATACTCG 57.093 39.130 0.00 0.00 0.00 4.18
2188 2321 3.318017 ACTCGTTGTACTGCATTGAGTC 58.682 45.455 0.00 0.00 37.36 3.36
2265 2398 5.678583 TGAGAAGAAGGAATAGAATGCCAG 58.321 41.667 0.00 0.00 0.00 4.85
2326 2459 9.581289 TTGAAAACTTAATCTATTCCACTTCCA 57.419 29.630 0.00 0.00 0.00 3.53
2327 2460 9.010029 TGAAAACTTAATCTATTCCACTTCCAC 57.990 33.333 0.00 0.00 0.00 4.02
2345 2478 3.009033 TCCACCCCTCACTTGTTTATCAG 59.991 47.826 0.00 0.00 0.00 2.90
2378 2511 1.000938 CTCAACAAGAGGTGCTTTGCC 60.001 52.381 0.00 0.00 40.84 4.52
2436 2569 1.803334 TCCTGTCGTAAACACCATGC 58.197 50.000 0.00 0.00 33.24 4.06
2477 2614 3.071602 TCAGTGAAGTTGGGAGAAGAAGG 59.928 47.826 0.00 0.00 0.00 3.46
2478 2615 3.071602 CAGTGAAGTTGGGAGAAGAAGGA 59.928 47.826 0.00 0.00 0.00 3.36
2479 2616 3.716872 AGTGAAGTTGGGAGAAGAAGGAA 59.283 43.478 0.00 0.00 0.00 3.36
2480 2617 4.068599 GTGAAGTTGGGAGAAGAAGGAAG 58.931 47.826 0.00 0.00 0.00 3.46
2491 2628 6.070710 GGGAGAAGAAGGAAGCTCTTTTACTA 60.071 42.308 0.00 0.00 33.24 1.82
2497 2634 9.574516 AAGAAGGAAGCTCTTTTACTATTCAAA 57.425 29.630 0.00 0.00 28.46 2.69
2503 2640 8.803201 AAGCTCTTTTACTATTCAAAAACAGC 57.197 30.769 0.00 0.00 34.26 4.40
2504 2641 7.940850 AGCTCTTTTACTATTCAAAAACAGCA 58.059 30.769 9.40 0.00 35.37 4.41
2505 2642 8.078596 AGCTCTTTTACTATTCAAAAACAGCAG 58.921 33.333 9.40 0.00 35.37 4.24
2547 2685 6.150976 TGTTGATTTGTGGATATGAGGTTGTC 59.849 38.462 0.00 0.00 0.00 3.18
2566 2704 0.250513 CTGGCTAGTGTTGGTCTCCC 59.749 60.000 0.00 0.00 0.00 4.30
2644 2787 2.561569 CAGTGCAGCATCTCATCATCA 58.438 47.619 0.00 0.00 0.00 3.07
2645 2788 3.142174 CAGTGCAGCATCTCATCATCAT 58.858 45.455 0.00 0.00 0.00 2.45
2646 2789 3.187432 CAGTGCAGCATCTCATCATCATC 59.813 47.826 0.00 0.00 0.00 2.92
2647 2790 3.139077 GTGCAGCATCTCATCATCATCA 58.861 45.455 0.00 0.00 0.00 3.07
2648 2791 3.564225 GTGCAGCATCTCATCATCATCAA 59.436 43.478 0.00 0.00 0.00 2.57
2649 2792 3.564225 TGCAGCATCTCATCATCATCAAC 59.436 43.478 0.00 0.00 0.00 3.18
2650 2793 3.815962 GCAGCATCTCATCATCATCAACT 59.184 43.478 0.00 0.00 0.00 3.16
2651 2794 4.276183 GCAGCATCTCATCATCATCAACTT 59.724 41.667 0.00 0.00 0.00 2.66
2652 2795 5.561145 GCAGCATCTCATCATCATCAACTTC 60.561 44.000 0.00 0.00 0.00 3.01
2737 2884 0.890683 TGCTGCTGATCAAGACGAGA 59.109 50.000 0.00 0.00 0.00 4.04
2770 2926 5.133221 TCTTCTTCTTCTTTTCCTTGTGGG 58.867 41.667 0.00 0.00 0.00 4.61
2780 2936 2.523325 TCCTTGTGGGAGAGAGAGAG 57.477 55.000 0.00 0.00 39.58 3.20
2784 2940 1.377690 TGTGGGAGAGAGAGAGGAGT 58.622 55.000 0.00 0.00 0.00 3.85
2819 2975 1.411246 CATGGCCATCATTTCCAGTGG 59.589 52.381 17.61 1.40 32.92 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 3.247648 GCAACGTTACATGACAACTGTCT 59.752 43.478 0.00 0.00 44.99 3.41
73 75 4.593157 GTCTGTTTTGCAACGTTACATGA 58.407 39.130 0.00 0.00 35.40 3.07
82 84 0.179150 TGCCACGTCTGTTTTGCAAC 60.179 50.000 0.00 0.00 0.00 4.17
83 85 0.528017 TTGCCACGTCTGTTTTGCAA 59.472 45.000 0.00 0.00 34.18 4.08
85 87 0.179150 TGTTGCCACGTCTGTTTTGC 60.179 50.000 0.00 0.00 0.00 3.68
86 88 2.270275 TTGTTGCCACGTCTGTTTTG 57.730 45.000 0.00 0.00 0.00 2.44
93 95 3.552604 ACATGTTATTGTTGCCACGTC 57.447 42.857 0.00 0.00 0.00 4.34
94 96 3.608241 CGAACATGTTATTGTTGCCACGT 60.608 43.478 11.95 0.00 39.85 4.49
95 97 2.908009 CGAACATGTTATTGTTGCCACG 59.092 45.455 11.95 2.81 39.85 4.94
96 98 3.241701 CCGAACATGTTATTGTTGCCAC 58.758 45.455 11.95 0.00 39.85 5.01
97 99 2.230025 CCCGAACATGTTATTGTTGCCA 59.770 45.455 11.95 0.00 39.85 4.92
98 100 2.230266 ACCCGAACATGTTATTGTTGCC 59.770 45.455 11.95 0.00 39.85 4.52
99 101 3.569250 ACCCGAACATGTTATTGTTGC 57.431 42.857 11.95 0.00 39.85 4.17
100 102 7.863375 TCTTTTTACCCGAACATGTTATTGTTG 59.137 33.333 11.95 0.11 39.85 3.33
101 103 7.942990 TCTTTTTACCCGAACATGTTATTGTT 58.057 30.769 11.95 0.00 42.37 2.83
102 104 7.446013 TCTCTTTTTACCCGAACATGTTATTGT 59.554 33.333 11.95 10.84 0.00 2.71
103 105 7.812648 TCTCTTTTTACCCGAACATGTTATTG 58.187 34.615 11.95 5.17 0.00 1.90
106 108 6.527423 ACTCTCTTTTTACCCGAACATGTTA 58.473 36.000 11.95 0.00 0.00 2.41
257 262 2.041701 ACCAAAAGCCATCAGTTTGCT 58.958 42.857 0.00 0.00 36.79 3.91
284 289 2.364448 GCCCTCCCGTCTCCTCTT 60.364 66.667 0.00 0.00 0.00 2.85
341 417 1.566703 TCCTCTCCCACACACCAAAAA 59.433 47.619 0.00 0.00 0.00 1.94
415 492 0.804989 GTGCTACATGGCAACTGTCC 59.195 55.000 0.00 0.00 44.18 4.02
451 535 6.769341 ACTCTCTTTTTACCCGTAACATGTTT 59.231 34.615 17.78 0.09 0.00 2.83
460 544 2.158726 TGGCAACTCTCTTTTTACCCGT 60.159 45.455 0.00 0.00 37.61 5.28
483 567 4.398988 TGCCCTATTTGTGATTGTAAGCAG 59.601 41.667 0.00 0.00 0.00 4.24
579 665 4.383552 GCACCACTCCTATTTCACATCTCT 60.384 45.833 0.00 0.00 0.00 3.10
591 677 4.063967 CGCCACGCACCACTCCTA 62.064 66.667 0.00 0.00 0.00 2.94
879 966 4.284746 GTGGGGGTTTATATGAGAGAGAGG 59.715 50.000 0.00 0.00 0.00 3.69
954 1042 3.282885 GAGGGAAGGAGTATTGGCTTTG 58.717 50.000 0.00 0.00 0.00 2.77
955 1043 2.092914 CGAGGGAAGGAGTATTGGCTTT 60.093 50.000 0.00 0.00 0.00 3.51
956 1044 1.486726 CGAGGGAAGGAGTATTGGCTT 59.513 52.381 0.00 0.00 0.00 4.35
957 1045 1.123928 CGAGGGAAGGAGTATTGGCT 58.876 55.000 0.00 0.00 0.00 4.75
958 1046 0.831307 ACGAGGGAAGGAGTATTGGC 59.169 55.000 0.00 0.00 0.00 4.52
959 1047 1.067212 CGACGAGGGAAGGAGTATTGG 59.933 57.143 0.00 0.00 0.00 3.16
961 1049 1.749634 CACGACGAGGGAAGGAGTATT 59.250 52.381 0.00 0.00 0.00 1.89
1110 1216 2.751913 CGAGGAGGGACACGACGAG 61.752 68.421 0.00 0.00 0.00 4.18
1199 1305 2.695970 CCCTCCTCCGTCTCCTCCT 61.696 68.421 0.00 0.00 0.00 3.69
1230 1336 4.724697 TTCGTCGTCGTCGCCGTC 62.725 66.667 5.34 0.00 39.43 4.79
1231 1337 4.731503 CTTCGTCGTCGTCGCCGT 62.732 66.667 5.34 0.00 39.43 5.68
1232 1338 3.916371 TTCTTCGTCGTCGTCGCCG 62.916 63.158 7.01 0.00 39.77 6.46
1233 1339 2.127118 TTCTTCGTCGTCGTCGCC 60.127 61.111 7.01 0.00 38.33 5.54
1234 1340 1.121281 CTCTTCTTCGTCGTCGTCGC 61.121 60.000 7.01 0.00 38.33 5.19
1235 1341 1.121281 GCTCTTCTTCGTCGTCGTCG 61.121 60.000 5.50 5.50 38.33 5.12
1236 1342 0.110328 TGCTCTTCTTCGTCGTCGTC 60.110 55.000 1.33 0.00 38.33 4.20
1237 1343 0.309922 TTGCTCTTCTTCGTCGTCGT 59.690 50.000 1.33 0.00 38.33 4.34
1260 1369 3.378602 TGCTTCCCGTCGCTGCTA 61.379 61.111 0.00 0.00 0.00 3.49
1579 1688 1.762460 GGATGAGGCCCTCTTCCGA 60.762 63.158 25.18 0.00 42.24 4.55
1580 1689 2.825264 GGATGAGGCCCTCTTCCG 59.175 66.667 25.18 0.00 42.24 4.30
1584 1693 0.693767 CCTCTTGGATGAGGCCCTCT 60.694 60.000 12.94 0.00 45.84 3.69
1711 1820 3.114616 CAGGTCGAACAGCTGCCG 61.115 66.667 15.27 17.74 43.58 5.69
1743 1852 0.657659 CGAATCCGTCCTCGATGTCG 60.658 60.000 0.81 0.81 37.23 4.35
1965 2083 8.699749 GTGCTTATTAAACCAGCAAAGTAAAAG 58.300 33.333 7.87 0.00 44.99 2.27
1976 2094 5.010282 ACTCCCTTGTGCTTATTAAACCAG 58.990 41.667 0.00 0.00 0.00 4.00
2040 2161 6.723339 ACTCTCTCAGGTAACATGTAGTAGT 58.277 40.000 0.00 0.00 41.41 2.73
2041 2162 7.633193 AACTCTCTCAGGTAACATGTAGTAG 57.367 40.000 0.00 0.00 41.41 2.57
2042 2163 9.696572 ATTAACTCTCTCAGGTAACATGTAGTA 57.303 33.333 0.00 0.00 37.09 1.82
2121 2242 7.000472 AGTACAATCACCCAATAATCTGATGG 59.000 38.462 0.00 0.00 0.00 3.51
2122 2243 7.500227 ACAGTACAATCACCCAATAATCTGATG 59.500 37.037 0.00 0.00 0.00 3.07
2124 2245 6.957631 ACAGTACAATCACCCAATAATCTGA 58.042 36.000 0.00 0.00 0.00 3.27
2125 2246 8.908786 ATACAGTACAATCACCCAATAATCTG 57.091 34.615 0.00 0.00 0.00 2.90
2126 2247 9.561069 GAATACAGTACAATCACCCAATAATCT 57.439 33.333 0.00 0.00 0.00 2.40
2127 2248 8.495949 CGAATACAGTACAATCACCCAATAATC 58.504 37.037 0.00 0.00 0.00 1.75
2128 2249 7.990886 ACGAATACAGTACAATCACCCAATAAT 59.009 33.333 0.00 0.00 0.00 1.28
2130 2251 6.880484 ACGAATACAGTACAATCACCCAATA 58.120 36.000 0.00 0.00 0.00 1.90
2131 2252 5.741011 ACGAATACAGTACAATCACCCAAT 58.259 37.500 0.00 0.00 0.00 3.16
2132 2253 5.155278 ACGAATACAGTACAATCACCCAA 57.845 39.130 0.00 0.00 0.00 4.12
2133 2254 4.811969 ACGAATACAGTACAATCACCCA 57.188 40.909 0.00 0.00 0.00 4.51
2135 2256 6.479001 AGCATAACGAATACAGTACAATCACC 59.521 38.462 0.00 0.00 0.00 4.02
2136 2257 7.464830 AGCATAACGAATACAGTACAATCAC 57.535 36.000 0.00 0.00 0.00 3.06
2137 2258 7.011016 CCAAGCATAACGAATACAGTACAATCA 59.989 37.037 0.00 0.00 0.00 2.57
2138 2259 7.223971 TCCAAGCATAACGAATACAGTACAATC 59.776 37.037 0.00 0.00 0.00 2.67
2139 2260 7.045416 TCCAAGCATAACGAATACAGTACAAT 58.955 34.615 0.00 0.00 0.00 2.71
2140 2261 6.399743 TCCAAGCATAACGAATACAGTACAA 58.600 36.000 0.00 0.00 0.00 2.41
2171 2304 3.003480 GGGAGACTCAATGCAGTACAAC 58.997 50.000 4.53 0.00 0.00 3.32
2203 2336 7.280876 TGGCATGACACTCAAATTTATACTCTC 59.719 37.037 0.00 0.00 0.00 3.20
2205 2338 7.320443 TGGCATGACACTCAAATTTATACTC 57.680 36.000 0.00 0.00 0.00 2.59
2207 2340 6.919662 CCATGGCATGACACTCAAATTTATAC 59.080 38.462 28.43 0.00 0.00 1.47
2212 2345 3.433343 TCCATGGCATGACACTCAAATT 58.567 40.909 28.43 0.00 0.00 1.82
2265 2398 2.272678 GCCTCTTAACTTCGAGCTTCC 58.727 52.381 0.00 0.00 0.00 3.46
2322 2455 3.396276 TGATAAACAAGTGAGGGGTGGAA 59.604 43.478 0.00 0.00 0.00 3.53
2323 2456 2.983192 TGATAAACAAGTGAGGGGTGGA 59.017 45.455 0.00 0.00 0.00 4.02
2324 2457 3.347216 CTGATAAACAAGTGAGGGGTGG 58.653 50.000 0.00 0.00 0.00 4.61
2325 2458 2.749621 GCTGATAAACAAGTGAGGGGTG 59.250 50.000 0.00 0.00 0.00 4.61
2326 2459 2.375174 TGCTGATAAACAAGTGAGGGGT 59.625 45.455 0.00 0.00 0.00 4.95
2327 2460 3.071874 TGCTGATAAACAAGTGAGGGG 57.928 47.619 0.00 0.00 0.00 4.79
2345 2478 2.780065 TGTTGAGCAACATCACTTGC 57.220 45.000 11.70 0.00 45.42 4.01
2378 2511 2.736144 ACATGAAATTGCTGGCAGTG 57.264 45.000 17.16 6.15 0.00 3.66
2525 2663 5.882000 CAGACAACCTCATATCCACAAATCA 59.118 40.000 0.00 0.00 0.00 2.57
2526 2664 5.297776 CCAGACAACCTCATATCCACAAATC 59.702 44.000 0.00 0.00 0.00 2.17
2547 2685 3.842869 GGAGACCAACACTAGCCAG 57.157 57.895 0.00 0.00 0.00 4.85
2566 2704 1.676529 CTCTGCTTGCTTGATCATGGG 59.323 52.381 10.35 0.00 0.00 4.00
2589 2727 1.363807 GCCACCTTTTGTCTGCACC 59.636 57.895 0.00 0.00 0.00 5.01
2644 2787 7.744733 AGGAAGAAGAAGAAGAAGAAGTTGAT 58.255 34.615 0.00 0.00 0.00 2.57
2645 2788 7.070571 AGAGGAAGAAGAAGAAGAAGAAGTTGA 59.929 37.037 0.00 0.00 0.00 3.18
2646 2789 7.171337 CAGAGGAAGAAGAAGAAGAAGAAGTTG 59.829 40.741 0.00 0.00 0.00 3.16
2647 2790 7.216494 CAGAGGAAGAAGAAGAAGAAGAAGTT 58.784 38.462 0.00 0.00 0.00 2.66
2648 2791 6.239572 CCAGAGGAAGAAGAAGAAGAAGAAGT 60.240 42.308 0.00 0.00 0.00 3.01
2649 2792 6.165577 CCAGAGGAAGAAGAAGAAGAAGAAG 58.834 44.000 0.00 0.00 0.00 2.85
2650 2793 5.512232 GCCAGAGGAAGAAGAAGAAGAAGAA 60.512 44.000 0.00 0.00 0.00 2.52
2651 2794 4.020662 GCCAGAGGAAGAAGAAGAAGAAGA 60.021 45.833 0.00 0.00 0.00 2.87
2652 2795 4.020307 AGCCAGAGGAAGAAGAAGAAGAAG 60.020 45.833 0.00 0.00 0.00 2.85
2770 2926 3.366052 AACCTCACTCCTCTCTCTCTC 57.634 52.381 0.00 0.00 0.00 3.20
2780 2936 5.450550 GCCATGCTTAAAATAACCTCACTCC 60.451 44.000 0.00 0.00 0.00 3.85
2784 2940 4.348486 TGGCCATGCTTAAAATAACCTCA 58.652 39.130 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.