Multiple sequence alignment - TraesCS4A01G276500

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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 TraesCS4A01G276500 chr4A 100.000 5049 0 0 1 5049 584881453 584886501 0.000000e+00 9324
1 TraesCS4A01G276500 chr4D 91.856 4310 199 65 670 4903 15772389 15768156 0.000000e+00 5875
2 TraesCS4A01G276500 chr4D 86.842 152 14 2 4900 5049 15768044 15767897 1.120000e-36 165
3 TraesCS4A01G276500 chr4B 92.557 4111 213 47 975 5025 26827516 26823439 0.000000e+00 5810
4 TraesCS4A01G276500 chr4B 94.192 637 35 2 1 635 665131153 665131789 0.000000e+00 970
5 TraesCS4A01G276500 chr4B 93.878 637 37 2 1 635 664953550 664954186 0.000000e+00 959
6 TraesCS4A01G276500 chr4B 93.564 637 39 2 1 635 665067482 665068118 0.000000e+00 948
7 TraesCS4A01G276500 chr4B 93.239 636 41 2 2 635 665012976 665013611 0.000000e+00 935
8 TraesCS4A01G276500 chr4B 91.949 236 12 4 636 866 26828214 26827981 1.750000e-84 324
9 TraesCS4A01G276500 chr6D 89.328 1190 88 18 2600 3771 450653647 450654815 0.000000e+00 1458
10 TraesCS4A01G276500 chr6D 89.676 339 14 11 4247 4574 450654815 450655143 3.640000e-111 412
11 TraesCS4A01G276500 chr7B 86.207 1218 129 17 1982 3168 239091063 239092272 0.000000e+00 1282
12 TraesCS4A01G276500 chr7B 85.617 883 76 33 1552 2413 115811353 115812205 0.000000e+00 880
13 TraesCS4A01G276500 chr3B 96.069 636 23 2 2 635 169357599 169356964 0.000000e+00 1035
14 TraesCS4A01G276500 chr2A 95.133 637 29 2 1 635 694788997 694788361 0.000000e+00 1003
15 TraesCS4A01G276500 chr5A 94.992 639 28 4 1 635 30114836 30114198 0.000000e+00 1000
16 TraesCS4A01G276500 chr3A 94.976 637 30 2 1 635 23184925 23184289 0.000000e+00 998
17 TraesCS4A01G276500 chr3A 94.523 639 32 3 1 637 720869112 720868475 0.000000e+00 983
18 TraesCS4A01G276500 chr2B 85.893 879 77 30 1555 2413 334878470 334877619 0.000000e+00 893
19 TraesCS4A01G276500 chr2B 85.552 879 78 34 1555 2413 267912405 267911556 0.000000e+00 874


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 TraesCS4A01G276500 chr4A 584881453 584886501 5048 False 9324 9324 100.000 1 5049 1 chr4A.!!$F1 5048
1 TraesCS4A01G276500 chr4D 15767897 15772389 4492 True 3020 5875 89.349 670 5049 2 chr4D.!!$R1 4379
2 TraesCS4A01G276500 chr4B 26823439 26828214 4775 True 3067 5810 92.253 636 5025 2 chr4B.!!$R1 4389
3 TraesCS4A01G276500 chr4B 665131153 665131789 636 False 970 970 94.192 1 635 1 chr4B.!!$F4 634
4 TraesCS4A01G276500 chr4B 664953550 664954186 636 False 959 959 93.878 1 635 1 chr4B.!!$F1 634
5 TraesCS4A01G276500 chr4B 665067482 665068118 636 False 948 948 93.564 1 635 1 chr4B.!!$F3 634
6 TraesCS4A01G276500 chr4B 665012976 665013611 635 False 935 935 93.239 2 635 1 chr4B.!!$F2 633
7 TraesCS4A01G276500 chr6D 450653647 450655143 1496 False 935 1458 89.502 2600 4574 2 chr6D.!!$F1 1974
8 TraesCS4A01G276500 chr7B 239091063 239092272 1209 False 1282 1282 86.207 1982 3168 1 chr7B.!!$F2 1186
9 TraesCS4A01G276500 chr7B 115811353 115812205 852 False 880 880 85.617 1552 2413 1 chr7B.!!$F1 861
10 TraesCS4A01G276500 chr3B 169356964 169357599 635 True 1035 1035 96.069 2 635 1 chr3B.!!$R1 633
11 TraesCS4A01G276500 chr2A 694788361 694788997 636 True 1003 1003 95.133 1 635 1 chr2A.!!$R1 634
12 TraesCS4A01G276500 chr5A 30114198 30114836 638 True 1000 1000 94.992 1 635 1 chr5A.!!$R1 634
13 TraesCS4A01G276500 chr3A 23184289 23184925 636 True 998 998 94.976 1 635 1 chr3A.!!$R1 634
14 TraesCS4A01G276500 chr3A 720868475 720869112 637 True 983 983 94.523 1 637 1 chr3A.!!$R2 636
15 TraesCS4A01G276500 chr2B 334877619 334878470 851 True 893 893 85.893 1555 2413 1 chr2B.!!$R2 858
16 TraesCS4A01G276500 chr2B 267911556 267912405 849 True 874 874 85.552 1555 2413 1 chr2B.!!$R1 858

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
834 847 1.154543 CGGCGCCACTACGAAAAAC 60.155 57.895 28.98 0.0 34.06 2.43 F
836 849 1.154543 GCGCCACTACGAAAAACCG 60.155 57.895 0.00 0.0 34.06 4.44 F
1415 1809 1.213296 GGTGCCCCCTTCTGATCTAA 58.787 55.000 0.00 0.0 0.00 2.10 F
1702 2132 1.943968 GCATCAGGCGACCAAACTGTA 60.944 52.381 0.00 0.0 34.02 2.74 F
2432 2882 0.950555 TGCTGCAGACAAGTAAGGCG 60.951 55.000 20.43 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 2108 0.537143 TTTGGTCGCCTGATGCAGTT 60.537 50.000 0.00 0.00 41.33 3.16 R
2052 2492 1.130678 GGCCATTTGGGGTTTTGGGA 61.131 55.000 0.00 0.00 37.04 4.37 R
2289 2739 1.215673 TGTACAGTCCCCAGCCAAAAA 59.784 47.619 0.00 0.00 0.00 1.94 R
3632 4143 1.210478 ACAAAGTGTCAGGCTGTCAGT 59.790 47.619 14.68 14.85 0.00 3.41 R
4206 4717 1.375908 CAAGCTTGGCCTGCGTAGA 60.376 57.895 19.14 0.00 35.28 2.59 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
104 105 3.408853 GGGGCCTAACTCCGCCTT 61.409 66.667 0.84 0.00 45.01 4.35
133 134 5.281314 AGGTCATCAATGGGTAGTAGACTT 58.719 41.667 0.00 0.00 0.00 3.01
217 218 2.301870 AGTAGGGCAACGTTGAAGATCA 59.698 45.455 31.62 7.95 35.44 2.92
218 219 2.496899 AGGGCAACGTTGAAGATCAT 57.503 45.000 31.62 9.50 37.60 2.45
236 237 4.577988 TCATAAGATCCCGAAAACCCAA 57.422 40.909 0.00 0.00 0.00 4.12
265 269 2.450476 GTCCTTTGGCCTTGTCATGAT 58.550 47.619 3.32 0.00 0.00 2.45
270 274 4.467769 CTTTGGCCTTGTCATGATATCCT 58.532 43.478 3.32 0.00 0.00 3.24
658 663 4.148825 CCCGAGACTCCAAGCCCG 62.149 72.222 0.00 0.00 0.00 6.13
659 664 3.382832 CCGAGACTCCAAGCCCGT 61.383 66.667 0.00 0.00 0.00 5.28
663 668 3.319198 GACTCCAAGCCCGTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
721 726 1.536766 CACATGTTCACACATTCGCCT 59.463 47.619 0.00 0.00 41.16 5.52
724 729 1.210155 GTTCACACATTCGCCTGGC 59.790 57.895 9.11 9.11 0.00 4.85
736 741 3.579302 CCTGGCCCCACCTGTCAA 61.579 66.667 0.00 0.00 40.22 3.18
834 847 1.154543 CGGCGCCACTACGAAAAAC 60.155 57.895 28.98 0.00 34.06 2.43
836 849 1.154543 GCGCCACTACGAAAAACCG 60.155 57.895 0.00 0.00 34.06 4.44
978 1363 1.450491 GAAGCCTCCTTTCCTCGCC 60.450 63.158 0.00 0.00 0.00 5.54
1007 1393 3.917760 CCTCTCCCCGATGGCGAC 61.918 72.222 0.00 0.00 40.82 5.19
1209 1595 2.688364 CCTTCTGCAAGGTTCGTTTC 57.312 50.000 0.00 0.00 44.11 2.78
1217 1606 2.059541 CAAGGTTCGTTTCCTCTCGTC 58.940 52.381 0.00 0.00 33.76 4.20
1274 1668 2.706552 ATCCGTCCCCTCCCCCTA 60.707 66.667 0.00 0.00 0.00 3.53
1376 1770 1.415716 CCCTCCAGATCCTCCTCCATT 60.416 57.143 0.00 0.00 0.00 3.16
1407 1801 2.193087 TTAGCTTCGGTGCCCCCTTC 62.193 60.000 0.00 0.00 0.00 3.46
1415 1809 1.213296 GGTGCCCCCTTCTGATCTAA 58.787 55.000 0.00 0.00 0.00 2.10
1419 1813 3.454812 GTGCCCCCTTCTGATCTAACTAA 59.545 47.826 0.00 0.00 0.00 2.24
1429 1845 7.987458 CCTTCTGATCTAACTAACTGGCATTTA 59.013 37.037 0.00 0.00 0.00 1.40
1432 1848 6.055588 TGATCTAACTAACTGGCATTTAGGC 58.944 40.000 23.34 9.71 44.50 3.93
1452 1868 5.733676 AGGCTATTTTGTGCTAAAATTGGG 58.266 37.500 14.43 8.77 32.64 4.12
1454 1870 6.439058 AGGCTATTTTGTGCTAAAATTGGGTA 59.561 34.615 14.43 0.67 32.64 3.69
1456 1872 7.320399 GCTATTTTGTGCTAAAATTGGGTAGT 58.680 34.615 14.43 0.00 32.64 2.73
1477 1906 5.568392 AGTTCCAATCTGAAATCTTGCTCT 58.432 37.500 0.00 0.00 0.00 4.09
1575 2004 2.159014 CCACATTTGCCTGCAATATGCT 60.159 45.455 18.39 9.43 45.31 3.79
1578 2007 3.956199 ACATTTGCCTGCAATATGCTACT 59.044 39.130 18.39 5.32 45.31 2.57
1579 2008 5.008911 CACATTTGCCTGCAATATGCTACTA 59.991 40.000 18.39 0.26 45.31 1.82
1580 2009 5.009010 ACATTTGCCTGCAATATGCTACTAC 59.991 40.000 18.39 0.00 45.31 2.73
1702 2132 1.943968 GCATCAGGCGACCAAACTGTA 60.944 52.381 0.00 0.00 34.02 2.74
1752 2182 9.912634 ATTTAATTTCTCACAACACCAACTATG 57.087 29.630 0.00 0.00 0.00 2.23
1753 2183 6.959639 AATTTCTCACAACACCAACTATGT 57.040 33.333 0.00 0.00 0.00 2.29
1754 2184 9.562408 TTAATTTCTCACAACACCAACTATGTA 57.438 29.630 0.00 0.00 0.00 2.29
1755 2185 8.635765 AATTTCTCACAACACCAACTATGTAT 57.364 30.769 0.00 0.00 0.00 2.29
1760 2190 7.334171 TCTCACAACACCAACTATGTATCATTG 59.666 37.037 0.00 0.00 0.00 2.82
1798 2228 5.066375 TGTGCATAATCTCACTGTAATTGCC 59.934 40.000 0.00 0.00 34.49 4.52
1946 2376 8.570068 TCTTGAACTTGGTTAACTTAGTTTGT 57.430 30.769 19.61 5.63 31.41 2.83
1948 2378 7.090953 TGAACTTGGTTAACTTAGTTTGTGG 57.909 36.000 19.61 0.00 31.41 4.17
1974 2404 3.873952 GTCTGCATAGGTTCATGAACTCC 59.126 47.826 31.81 20.05 40.94 3.85
1976 2406 4.164796 TCTGCATAGGTTCATGAACTCCAT 59.835 41.667 31.81 20.93 40.94 3.41
2052 2492 5.128919 GCACTTTGGGATCTAAGATGTGAT 58.871 41.667 8.92 0.00 31.73 3.06
2097 2537 3.003068 GTGAAGCATGCCTCATGTATGTC 59.997 47.826 21.36 3.87 43.10 3.06
2113 2553 6.731292 TGTATGTCATCTAATGGCTACTGT 57.269 37.500 0.00 0.00 35.48 3.55
2132 2572 8.678199 GCTACTGTAATCTAAATGCTCCTTTTT 58.322 33.333 0.00 0.00 0.00 1.94
2141 2581 7.145323 TCTAAATGCTCCTTTTTAACTGCAAC 58.855 34.615 0.00 0.00 34.07 4.17
2149 2590 6.825610 TCCTTTTTAACTGCAACCATCAATT 58.174 32.000 0.00 0.00 0.00 2.32
2152 2593 7.442062 CCTTTTTAACTGCAACCATCAATTTCT 59.558 33.333 0.00 0.00 0.00 2.52
2161 2602 5.290158 GCAACCATCAATTTCTGTAGCAATG 59.710 40.000 0.00 0.00 0.00 2.82
2173 2614 4.805719 TCTGTAGCAATGTAGCATCTTTCG 59.194 41.667 0.00 0.00 36.85 3.46
2277 2727 3.378427 GGCTCGAGCAAAGGTATTGAATT 59.622 43.478 36.27 0.00 44.36 2.17
2279 2729 4.795278 GCTCGAGCAAAGGTATTGAATTTG 59.205 41.667 31.91 0.00 41.59 2.32
2300 2750 3.448301 TGCATAGAATCTTTTTGGCTGGG 59.552 43.478 0.00 0.00 0.00 4.45
2310 2760 1.072266 TTTGGCTGGGGACTGTACAT 58.928 50.000 0.00 0.00 0.00 2.29
2312 2762 1.072266 TGGCTGGGGACTGTACATTT 58.928 50.000 0.00 0.00 0.00 2.32
2315 2765 2.012051 GCTGGGGACTGTACATTTCCG 61.012 57.143 14.55 5.54 0.00 4.30
2317 2767 2.498481 CTGGGGACTGTACATTTCCGTA 59.502 50.000 14.55 7.52 0.00 4.02
2356 2806 3.181329 TGGTCATCTTTAGGGAGCTTCA 58.819 45.455 0.00 0.00 0.00 3.02
2359 2809 4.565652 GGTCATCTTTAGGGAGCTTCAACA 60.566 45.833 0.00 0.00 0.00 3.33
2432 2882 0.950555 TGCTGCAGACAAGTAAGGCG 60.951 55.000 20.43 0.00 0.00 5.52
2539 2990 7.598278 TCAATTATGAACGCACCACTTTTAAT 58.402 30.769 0.00 0.00 30.99 1.40
2554 3005 5.801947 CACTTTTAATACAATGCACCTCTGC 59.198 40.000 0.00 0.00 44.52 4.26
2796 3280 2.985809 CTCTTGCTTGTCTCAAGACTCG 59.014 50.000 12.77 3.88 43.34 4.18
2920 3404 5.182001 GCTTCTGACTTCATAAGCTTTCCAA 59.818 40.000 17.64 0.00 46.27 3.53
3018 3506 6.127168 TGAGTCTTTCTTTGTCAAGGTGAGTA 60.127 38.462 0.00 0.00 0.00 2.59
3021 3509 4.689612 TTCTTTGTCAAGGTGAGTAGCT 57.310 40.909 0.00 0.00 35.86 3.32
3104 3594 2.875296 ACCTGCTTTGGTGCTTGAATA 58.125 42.857 0.00 0.00 39.17 1.75
3404 3900 3.189702 GCTCATGTTGCAATGCCAATTTT 59.810 39.130 0.59 0.00 0.00 1.82
3622 4133 6.318900 AGAACAAGAGTTTGGTTAGGAACTTG 59.681 38.462 0.00 0.00 37.86 3.16
3623 4134 5.751586 ACAAGAGTTTGGTTAGGAACTTGA 58.248 37.500 0.00 0.00 38.14 3.02
3632 4143 5.686753 TGGTTAGGAACTTGAAAACTGCTA 58.313 37.500 0.00 0.00 41.75 3.49
3751 4262 3.010420 GAGGGTAACTGCTCCAAACATC 58.990 50.000 0.00 0.00 0.00 3.06
3839 4350 1.955778 CTGACAGTGAATTGCCAACCA 59.044 47.619 0.00 0.00 0.00 3.67
4074 4585 9.788960 AAGTCAAAACTTTCTGACAAATAAGAC 57.211 29.630 14.17 0.00 43.28 3.01
4145 4656 4.644234 TGGTGAGAATCTTGTTTTTCTGCA 59.356 37.500 0.00 0.00 32.46 4.41
4162 4673 2.146342 TGCAAGAACTTACTCTGCTGC 58.854 47.619 0.00 0.00 32.21 5.25
4192 4703 3.871006 CAGTTCGGCATGCTAACTCATTA 59.129 43.478 26.01 0.76 31.21 1.90
4206 4717 9.507329 TGCTAACTCATTACTCTCATTTTTCTT 57.493 29.630 0.00 0.00 0.00 2.52
4361 4874 6.494835 ACCATCTGCCTTTTCTCTTTGTATTT 59.505 34.615 0.00 0.00 0.00 1.40
4362 4875 7.015584 ACCATCTGCCTTTTCTCTTTGTATTTT 59.984 33.333 0.00 0.00 0.00 1.82
4600 5124 5.868043 GCTGTGCATAGCAATGTCATATA 57.132 39.130 28.24 0.00 41.47 0.86
4705 5229 7.508636 TGGCATGGCTGGAATTATTAAGAAATA 59.491 33.333 21.08 0.00 0.00 1.40
4739 5263 8.558700 ACTTGTTTGAATTAAATGCATGAAACC 58.441 29.630 0.00 0.00 0.00 3.27
4750 5274 4.339872 TGCATGAAACCTGCAATCTTTT 57.660 36.364 0.00 0.00 46.06 2.27
4782 5306 4.766373 TGGAGCTTGCAAAAGAACATATCA 59.234 37.500 0.00 0.00 0.00 2.15
4783 5307 5.243507 TGGAGCTTGCAAAAGAACATATCAA 59.756 36.000 0.00 0.00 0.00 2.57
4812 5336 8.598916 TGGACTTATGGTCAATAGTTGAAACTA 58.401 33.333 5.43 5.43 46.16 2.24
4813 5337 9.614792 GGACTTATGGTCAATAGTTGAAACTAT 57.385 33.333 9.44 9.44 45.03 2.12
4853 5379 3.578688 CCTTACCATCAACAAGCTTTGC 58.421 45.455 0.00 0.00 0.00 3.68
4854 5380 3.256631 CCTTACCATCAACAAGCTTTGCT 59.743 43.478 0.00 0.00 42.56 3.91
4927 5569 9.661187 CTAGCTTAATGCACATATTTTTCTCAG 57.339 33.333 0.00 0.00 45.94 3.35
4996 5638 0.112995 TTCCATGCCTGACCAAGCTT 59.887 50.000 0.00 0.00 0.00 3.74
5015 5657 3.866582 GACCTAGCCCATGCCGCT 61.867 66.667 10.05 10.05 40.45 5.52
5039 5681 7.260387 TCCTATGGTCACTACATTTTTGGTA 57.740 36.000 0.00 0.00 0.00 3.25
5040 5682 7.107542 TCCTATGGTCACTACATTTTTGGTAC 58.892 38.462 0.00 0.00 0.00 3.34
5044 5686 5.529430 TGGTCACTACATTTTTGGTACACAG 59.471 40.000 0.00 0.00 39.29 3.66
5046 5688 6.073222 GGTCACTACATTTTTGGTACACAGAG 60.073 42.308 0.00 0.00 39.29 3.35
5047 5689 6.482308 GTCACTACATTTTTGGTACACAGAGT 59.518 38.462 0.00 0.00 39.29 3.24
5048 5690 7.012044 GTCACTACATTTTTGGTACACAGAGTT 59.988 37.037 0.00 0.00 39.29 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 6.575244 ACTACCCATTGATGACCTTATTGA 57.425 37.500 0.00 0.00 0.00 2.57
115 116 5.964477 TCAAGGAAGTCTACTACCCATTGAT 59.036 40.000 0.00 0.00 0.00 2.57
133 134 0.610174 AGTGCTCGCATTCTCAAGGA 59.390 50.000 0.00 0.00 0.00 3.36
217 218 3.626475 GGGTTGGGTTTTCGGGATCTTAT 60.626 47.826 0.00 0.00 0.00 1.73
218 219 2.291089 GGGTTGGGTTTTCGGGATCTTA 60.291 50.000 0.00 0.00 0.00 2.10
265 269 2.239400 CATGCTGGGTCTCGTAGGATA 58.761 52.381 0.00 0.00 0.00 2.59
270 274 1.685765 AGCCATGCTGGGTCTCGTA 60.686 57.895 1.62 0.00 46.99 3.43
721 726 2.067932 CTCTTTGACAGGTGGGGCCA 62.068 60.000 4.39 0.00 40.61 5.36
724 729 0.320771 CGTCTCTTTGACAGGTGGGG 60.321 60.000 0.00 0.00 45.60 4.96
735 740 1.759236 GTGGGGGTTCCGTCTCTTT 59.241 57.895 0.00 0.00 38.76 2.52
736 741 2.580601 CGTGGGGGTTCCGTCTCTT 61.581 63.158 0.00 0.00 38.76 2.85
964 980 3.798511 GGGGGCGAGGAAAGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
1095 1481 1.422402 GAGGAGAGGTCGGAGAGGTAT 59.578 57.143 0.00 0.00 36.95 2.73
1140 1526 1.226717 GTGCTCGACGGAGATGACC 60.227 63.158 0.00 0.00 43.27 4.02
1207 1593 6.627508 GCCAAATCTAACTAAGACGAGAGGAA 60.628 42.308 0.00 0.00 36.93 3.36
1209 1595 5.044558 GCCAAATCTAACTAAGACGAGAGG 58.955 45.833 0.00 0.00 36.93 3.69
1274 1668 1.000993 AGAGATCTGCGGGACCTGT 59.999 57.895 0.00 0.00 0.00 4.00
1376 1770 2.231478 CCGAAGCTAACCTGACTTCTCA 59.769 50.000 0.00 0.00 38.10 3.27
1407 1801 6.203723 GCCTAAATGCCAGTTAGTTAGATCAG 59.796 42.308 10.65 0.00 29.75 2.90
1415 1809 6.663523 ACAAAATAGCCTAAATGCCAGTTAGT 59.336 34.615 10.65 0.00 0.00 2.24
1419 1813 4.381932 GCACAAAATAGCCTAAATGCCAGT 60.382 41.667 0.00 0.00 0.00 4.00
1429 1845 5.248248 ACCCAATTTTAGCACAAAATAGCCT 59.752 36.000 8.84 0.00 30.38 4.58
1432 1848 9.353999 GAACTACCCAATTTTAGCACAAAATAG 57.646 33.333 8.84 5.90 30.38 1.73
1452 1868 6.597280 AGAGCAAGATTTCAGATTGGAACTAC 59.403 38.462 0.00 0.00 0.00 2.73
1454 1870 5.568392 AGAGCAAGATTTCAGATTGGAACT 58.432 37.500 0.00 0.00 0.00 3.01
1456 1872 6.906157 AAAGAGCAAGATTTCAGATTGGAA 57.094 33.333 0.00 0.00 0.00 3.53
1477 1906 2.548057 CAGCCTCGTTTCAGCTACAAAA 59.452 45.455 0.00 0.00 34.38 2.44
1575 2004 7.665974 TGAGAGACAGAGAAAACAGATGTAGTA 59.334 37.037 0.00 0.00 0.00 1.82
1578 2007 6.901081 TGAGAGACAGAGAAAACAGATGTA 57.099 37.500 0.00 0.00 0.00 2.29
1579 2008 5.798125 TGAGAGACAGAGAAAACAGATGT 57.202 39.130 0.00 0.00 0.00 3.06
1678 2108 0.537143 TTTGGTCGCCTGATGCAGTT 60.537 50.000 0.00 0.00 41.33 3.16
1702 2132 7.984422 TGAACTGATTGATCATGTTGTACTT 57.016 32.000 0.00 0.00 36.02 2.24
1722 2152 8.539674 GTTGGTGTTGTGAGAAATTAAATGAAC 58.460 33.333 0.00 0.00 0.00 3.18
1798 2228 9.078990 TCCATATCTTTACCTGATACAGTACAG 57.921 37.037 0.00 0.00 30.38 2.74
1884 2314 4.773674 AGGATTTGAAGAATGGCATGACAA 59.226 37.500 4.70 2.93 0.00 3.18
1948 2378 4.497006 GTTCATGAACCTATGCAGACATGC 60.497 45.833 25.26 0.00 42.86 4.06
1966 2396 7.557358 TGCATAGACAATAACAATGGAGTTCAT 59.443 33.333 0.00 0.00 37.79 2.57
2052 2492 1.130678 GGCCATTTGGGGTTTTGGGA 61.131 55.000 0.00 0.00 37.04 4.37
2113 2553 9.019656 TGCAGTTAAAAAGGAGCATTTAGATTA 57.980 29.630 0.00 0.00 0.00 1.75
2132 2572 6.349280 GCTACAGAAATTGATGGTTGCAGTTA 60.349 38.462 0.00 0.00 32.00 2.24
2141 2581 6.183360 TGCTACATTGCTACAGAAATTGATGG 60.183 38.462 0.00 0.00 0.00 3.51
2149 2590 5.291858 CGAAAGATGCTACATTGCTACAGAA 59.708 40.000 0.00 0.00 0.00 3.02
2152 2593 3.309682 GCGAAAGATGCTACATTGCTACA 59.690 43.478 0.00 0.00 0.00 2.74
2256 2706 4.622701 AATTCAATACCTTTGCTCGAGC 57.377 40.909 30.42 30.42 42.50 5.03
2277 2727 4.081531 CCCAGCCAAAAAGATTCTATGCAA 60.082 41.667 0.00 0.00 0.00 4.08
2279 2729 3.181472 CCCCAGCCAAAAAGATTCTATGC 60.181 47.826 0.00 0.00 0.00 3.14
2289 2739 1.215673 TGTACAGTCCCCAGCCAAAAA 59.784 47.619 0.00 0.00 0.00 1.94
2295 2745 1.751437 GGAAATGTACAGTCCCCAGC 58.249 55.000 14.79 0.00 0.00 4.85
2300 2750 3.881937 ACCTACGGAAATGTACAGTCC 57.118 47.619 15.46 15.46 0.00 3.85
2310 2760 2.103432 TCAGCAACTGAACCTACGGAAA 59.897 45.455 0.00 0.00 37.57 3.13
2312 2762 1.334160 TCAGCAACTGAACCTACGGA 58.666 50.000 0.00 0.00 37.57 4.69
2315 2765 5.186198 ACCAATATCAGCAACTGAACCTAC 58.814 41.667 0.74 0.00 44.04 3.18
2317 2767 4.263462 TGACCAATATCAGCAACTGAACCT 60.263 41.667 0.74 0.00 44.04 3.50
2324 2774 6.016777 CCCTAAAGATGACCAATATCAGCAAC 60.017 42.308 0.00 0.00 37.47 4.17
2356 2806 4.139786 ACAGAACTGATGTGATGCTTGTT 58.860 39.130 8.87 0.00 0.00 2.83
2359 2809 5.816258 CAGATACAGAACTGATGTGATGCTT 59.184 40.000 8.87 0.00 36.38 3.91
2432 2882 4.021981 GCAGAATAAATAGGATGGGCCAAC 60.022 45.833 11.89 8.12 40.02 3.77
2796 3280 2.159841 CGCAGCAATATACGCACCATAC 60.160 50.000 0.00 0.00 0.00 2.39
3021 3509 4.595781 TGGAAGAGAAGGCTAAACCAGTTA 59.404 41.667 0.00 0.00 43.14 2.24
3104 3594 4.343526 CCATCAGGACTAATAGCAGACTGT 59.656 45.833 3.99 0.00 36.89 3.55
3250 3741 4.502259 GGCTGATCCACCTACATAAGTGAG 60.502 50.000 0.00 0.00 36.01 3.51
3404 3900 2.036217 CCAAAGAGCACCTGAAATTGCA 59.964 45.455 0.00 0.00 41.48 4.08
3622 4133 2.481952 CAGGCTGTCAGTAGCAGTTTTC 59.518 50.000 6.28 0.00 45.46 2.29
3623 4134 2.104792 TCAGGCTGTCAGTAGCAGTTTT 59.895 45.455 15.27 0.00 45.46 2.43
3632 4143 1.210478 ACAAAGTGTCAGGCTGTCAGT 59.790 47.619 14.68 14.85 0.00 3.41
3822 4333 2.071778 ACTGGTTGGCAATTCACTGT 57.928 45.000 1.92 2.38 0.00 3.55
3839 4350 1.472662 CGGAGGGGTGAGTGTGAACT 61.473 60.000 0.00 0.00 0.00 3.01
3862 4373 2.548067 CGTGCCAAACTCCAGTACTCTT 60.548 50.000 0.00 0.00 0.00 2.85
4074 4585 5.697178 CAGCTCAGAAGAATCCATGATACTG 59.303 44.000 0.00 0.00 0.00 2.74
4145 4656 6.370166 GTCAATTAGCAGCAGAGTAAGTTCTT 59.630 38.462 0.00 0.00 0.00 2.52
4162 4673 2.679837 AGCATGCCGAACTGTCAATTAG 59.320 45.455 15.66 0.00 0.00 1.73
4192 4703 4.932200 CCTGCGTAGAAGAAAAATGAGAGT 59.068 41.667 0.53 0.00 0.00 3.24
4206 4717 1.375908 CAAGCTTGGCCTGCGTAGA 60.376 57.895 19.14 0.00 35.28 2.59
4230 4741 2.030958 GTTGCAGGTCCCGTAACCG 61.031 63.158 0.00 0.00 44.49 4.44
4234 4745 1.600023 CAAAAGTTGCAGGTCCCGTA 58.400 50.000 0.00 0.00 0.00 4.02
4361 4874 7.175104 ACCTAACAAGCTCAATGAGGAAATAA 58.825 34.615 12.66 0.00 0.00 1.40
4362 4875 6.721318 ACCTAACAAGCTCAATGAGGAAATA 58.279 36.000 12.66 0.00 0.00 1.40
4488 5006 9.681692 TGTTCAAAGAGATAATTGTCAACATTG 57.318 29.630 4.92 7.68 0.00 2.82
4509 5030 7.174946 GTCCAAATTCCTTTACTCTCATGTTCA 59.825 37.037 0.00 0.00 0.00 3.18
4739 5263 4.400251 TCCAGAGGCATTAAAAGATTGCAG 59.600 41.667 0.82 0.00 36.35 4.41
4750 5274 0.620030 TGCAAGCTCCAGAGGCATTA 59.380 50.000 0.00 0.00 0.00 1.90
4782 5306 7.861629 TCAACTATTGACCATAAGTCCAGATT 58.138 34.615 0.00 0.00 45.68 2.40
4783 5307 7.437713 TCAACTATTGACCATAAGTCCAGAT 57.562 36.000 0.00 0.00 45.68 2.90
4812 5336 1.271597 GGCAGGTCAAAGTGTCCAGAT 60.272 52.381 0.00 0.00 0.00 2.90
4813 5337 0.108585 GGCAGGTCAAAGTGTCCAGA 59.891 55.000 0.00 0.00 0.00 3.86
4878 5404 7.648039 AGTAGCTATTAGCAGTGAAGTACTT 57.352 36.000 17.59 8.13 45.56 2.24
4907 5549 7.779326 TGATCCCTGAGAAAAATATGTGCATTA 59.221 33.333 0.00 0.00 0.00 1.90
4913 5555 7.835682 TGATTGTGATCCCTGAGAAAAATATGT 59.164 33.333 0.00 0.00 0.00 2.29
4925 5567 7.337480 TCAAACAATATGATTGTGATCCCTG 57.663 36.000 5.63 0.00 32.79 4.45
4927 5569 7.546358 TGTTCAAACAATATGATTGTGATCCC 58.454 34.615 5.63 0.00 35.67 3.85
4989 5631 0.038166 TGGGCTAGGTCAAAGCTTGG 59.962 55.000 0.00 0.00 39.97 3.61
4996 5638 2.589540 CGGCATGGGCTAGGTCAA 59.410 61.111 0.00 0.00 40.87 3.18
5015 5657 6.134535 ACCAAAAATGTAGTGACCATAGGA 57.865 37.500 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.