Multiple sequence alignment - TraesCS1B01G338100

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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 TraesCS1B01G338100 chr1B 100.000 2549 0 0 1 2549 566185228 566182680 0.000000e+00 4708.0
1 TraesCS1B01G338100 chr1B 95.385 260 12 0 2290 2549 569883384 569883643 5.070000e-112 414.0
2 TraesCS1B01G338100 chr1B 81.214 527 43 26 1780 2289 593241227 593241714 8.610000e-100 374.0
3 TraesCS1B01G338100 chr1B 81.910 199 22 10 893 1091 566389059 566388875 3.400000e-34 156.0
4 TraesCS1B01G338100 chr1B 85.106 141 17 3 1780 1916 654864319 654864459 9.510000e-30 141.0
5 TraesCS1B01G338100 chr1B 93.750 48 3 0 1361 1408 566388656 566388609 3.520000e-09 73.1
6 TraesCS1B01G338100 chr1B 89.130 46 4 1 1 45 153724769 153724724 3.540000e-04 56.5
7 TraesCS1B01G338100 chr1B 100.000 29 0 0 2017 2045 560981346 560981374 1.000000e-03 54.7
8 TraesCS1B01G338100 chr1A 93.042 1121 55 13 664 1777 516041659 516040555 0.000000e+00 1616.0
9 TraesCS1B01G338100 chr1A 91.264 641 53 3 29 667 516042404 516041765 0.000000e+00 870.0
10 TraesCS1B01G338100 chr1A 87.500 48 4 2 1 48 29719643 29719598 1.000000e-03 54.7
11 TraesCS1B01G338100 chr1D 95.345 666 24 2 1112 1777 418661703 418661045 0.000000e+00 1051.0
12 TraesCS1B01G338100 chr1D 92.781 374 26 1 712 1084 418667663 418667290 8.020000e-150 540.0
13 TraesCS1B01G338100 chr1D 80.066 301 36 19 848 1140 419296742 419296458 4.300000e-48 202.0
14 TraesCS1B01G338100 chr1D 80.972 247 24 14 849 1091 418880329 418880102 9.370000e-40 174.0
15 TraesCS1B01G338100 chr1D 79.747 237 27 16 859 1091 419172743 419172524 4.390000e-33 152.0
16 TraesCS1B01G338100 chr1D 79.255 188 23 13 904 1091 418670465 418670294 1.600000e-22 117.0
17 TraesCS1B01G338100 chr1D 93.548 62 4 0 740 801 419296821 419296760 2.700000e-15 93.5
18 TraesCS1B01G338100 chr1D 98.039 51 1 0 34 84 418667708 418667658 3.490000e-14 89.8
19 TraesCS1B01G338100 chr1D 89.041 73 6 1 729 801 418756256 418756186 3.490000e-14 89.8
20 TraesCS1B01G338100 chr1D 80.531 113 11 4 684 785 419172876 419172764 2.720000e-10 76.8
21 TraesCS1B01G338100 chr3A 89.147 516 46 9 1780 2292 640343398 640343906 3.580000e-178 634.0
22 TraesCS1B01G338100 chr3A 96.923 260 8 0 2290 2549 640345857 640346116 1.080000e-118 436.0
23 TraesCS1B01G338100 chr3A 89.873 79 6 2 1970 2047 750314265 750314342 1.610000e-17 100.0
24 TraesCS1B01G338100 chr4D 88.743 533 33 14 1780 2292 40013245 40013770 5.990000e-176 627.0
25 TraesCS1B01G338100 chr4D 97.692 260 6 0 2290 2549 248925030 248924771 5.000000e-122 448.0
26 TraesCS1B01G338100 chr4D 97.656 256 6 0 2294 2549 40015731 40015986 8.370000e-120 440.0
27 TraesCS1B01G338100 chr4D 86.810 326 8 15 1780 2090 248927569 248927264 5.260000e-87 331.0
28 TraesCS1B01G338100 chr4D 93.333 60 4 0 2236 2295 248927052 248926993 3.490000e-14 89.8
29 TraesCS1B01G338100 chr2B 85.366 533 38 29 1780 2292 406444777 406444265 1.350000e-142 516.0
30 TraesCS1B01G338100 chr2B 83.239 531 46 28 1786 2292 24275093 24275604 5.000000e-122 448.0
31 TraesCS1B01G338100 chr2B 82.472 542 43 28 1780 2292 670847987 670847469 6.520000e-116 427.0
32 TraesCS1B01G338100 chr2B 84.892 139 19 2 1780 1916 214277145 214277283 3.420000e-29 139.0
33 TraesCS1B01G338100 chr2B 96.970 33 1 0 1 33 16808955 16808987 3.540000e-04 56.5
34 TraesCS1B01G338100 chr7B 84.848 495 39 23 1811 2289 740163922 740164396 1.380000e-127 466.0
35 TraesCS1B01G338100 chr7B 96.538 260 9 0 2290 2549 740166354 740166613 5.040000e-117 431.0
36 TraesCS1B01G338100 chr7B 85.612 139 17 3 1781 1916 122951772 122951910 2.640000e-30 143.0
37 TraesCS1B01G338100 chr6A 96.923 260 8 0 2290 2549 594763131 594762872 1.080000e-118 436.0
38 TraesCS1B01G338100 chrUn 96.154 260 10 0 2290 2549 71487038 71486779 2.340000e-115 425.0
39 TraesCS1B01G338100 chrUn 96.154 260 10 0 2290 2549 291953751 291953492 2.340000e-115 425.0
40 TraesCS1B01G338100 chrUn 95.769 260 11 0 2290 2549 71429374 71429115 1.090000e-113 420.0
41 TraesCS1B01G338100 chr2A 75.728 515 67 35 1780 2277 136736577 136736104 3.320000e-49 206.0
42 TraesCS1B01G338100 chr4B 78.755 273 37 15 1777 2038 435169685 435169947 2.030000e-36 163.0
43 TraesCS1B01G338100 chr7D 85.714 84 12 0 1008 1091 25360687 25360604 3.490000e-14 89.8
44 TraesCS1B01G338100 chr7A 100.000 34 0 0 1 34 116687026 116686993 2.120000e-06 63.9
45 TraesCS1B01G338100 chr7A 92.683 41 1 2 1 40 227417329 227417368 9.850000e-05 58.4
46 TraesCS1B01G338100 chr7A 87.500 48 4 2 1 48 60880037 60879992 1.000000e-03 54.7
47 TraesCS1B01G338100 chr5A 100.000 34 0 0 1 34 132015161 132015128 2.120000e-06 63.9
48 TraesCS1B01G338100 chr5A 92.500 40 3 0 1 40 537659303 537659342 9.850000e-05 58.4
49 TraesCS1B01G338100 chr5A 84.375 64 4 6 1 62 548487193 548487252 9.850000e-05 58.4
50 TraesCS1B01G338100 chr6B 100.000 29 0 0 2017 2045 286954465 286954437 1.000000e-03 54.7


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 TraesCS1B01G338100 chr1B 566182680 566185228 2548 True 4708.000000 4708 100.000000 1 2549 1 chr1B.!!$R2 2548
1 TraesCS1B01G338100 chr1A 516040555 516042404 1849 True 1243.000000 1616 92.153000 29 1777 2 chr1A.!!$R2 1748
2 TraesCS1B01G338100 chr1D 418661045 418661703 658 True 1051.000000 1051 95.345000 1112 1777 1 chr1D.!!$R1 665
3 TraesCS1B01G338100 chr1D 418667290 418670465 3175 True 248.933333 540 90.025000 34 1091 3 chr1D.!!$R4 1057
4 TraesCS1B01G338100 chr3A 640343398 640346116 2718 False 535.000000 634 93.035000 1780 2549 2 chr3A.!!$F2 769
5 TraesCS1B01G338100 chr4D 40013245 40015986 2741 False 533.500000 627 93.199500 1780 2549 2 chr4D.!!$F1 769
6 TraesCS1B01G338100 chr4D 248924771 248927569 2798 True 289.600000 448 92.611667 1780 2549 3 chr4D.!!$R1 769
7 TraesCS1B01G338100 chr2B 406444265 406444777 512 True 516.000000 516 85.366000 1780 2292 1 chr2B.!!$R1 512
8 TraesCS1B01G338100 chr2B 24275093 24275604 511 False 448.000000 448 83.239000 1786 2292 1 chr2B.!!$F2 506
9 TraesCS1B01G338100 chr2B 670847469 670847987 518 True 427.000000 427 82.472000 1780 2292 1 chr2B.!!$R2 512
10 TraesCS1B01G338100 chr7B 740163922 740166613 2691 False 448.500000 466 90.693000 1811 2549 2 chr7B.!!$F2 738

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
577 3303 0.321653 GTGCCGGGTCAAGATGAGTT 60.322 55.0 2.18 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 4613 1.121378 TCCGCCCATATTAACGACCA 58.879 50.0 0.0 0.0 0.0 4.02 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
22 23 5.488645 TTCACGTTTGACCCTTTTTCTAC 57.511 39.130 0.00 0.00 0.00 2.59
23 24 4.773013 TCACGTTTGACCCTTTTTCTACT 58.227 39.130 0.00 0.00 0.00 2.57
25 26 5.987347 TCACGTTTGACCCTTTTTCTACTAG 59.013 40.000 0.00 0.00 0.00 2.57
26 27 5.756833 CACGTTTGACCCTTTTTCTACTAGT 59.243 40.000 0.00 0.00 0.00 2.57
27 28 5.756833 ACGTTTGACCCTTTTTCTACTAGTG 59.243 40.000 5.39 0.00 0.00 2.74
28 29 5.178809 CGTTTGACCCTTTTTCTACTAGTGG 59.821 44.000 5.39 1.87 0.00 4.00
30 31 6.503560 TTGACCCTTTTTCTACTAGTGGAA 57.496 37.500 16.90 16.90 0.00 3.53
31 32 6.110411 TGACCCTTTTTCTACTAGTGGAAG 57.890 41.667 19.44 11.50 31.74 3.46
32 33 5.605488 TGACCCTTTTTCTACTAGTGGAAGT 59.395 40.000 19.44 14.26 31.74 3.01
34 35 6.531923 ACCCTTTTTCTACTAGTGGAAGTTC 58.468 40.000 19.44 0.00 31.74 3.01
35 36 6.100714 ACCCTTTTTCTACTAGTGGAAGTTCA 59.899 38.462 19.44 4.61 31.74 3.18
36 37 7.168905 CCCTTTTTCTACTAGTGGAAGTTCAT 58.831 38.462 19.44 0.00 31.74 2.57
37 38 7.119846 CCCTTTTTCTACTAGTGGAAGTTCATG 59.880 40.741 19.44 9.15 31.74 3.07
73 2798 6.031751 AGAAGAATAGAAGAGAACACGCTT 57.968 37.500 0.00 0.00 0.00 4.68
91 2816 3.208594 GCTTGAGATGCCATGTATGTCA 58.791 45.455 3.76 3.76 0.00 3.58
95 2820 3.628942 TGAGATGCCATGTATGTCAAAGC 59.371 43.478 5.04 0.00 26.82 3.51
123 2848 7.796958 AAAAACATCTTTATTAAGCGCACTC 57.203 32.000 11.47 0.00 0.00 3.51
126 2851 4.267928 ACATCTTTATTAAGCGCACTCGTC 59.732 41.667 11.47 0.00 38.14 4.20
127 2852 3.184541 TCTTTATTAAGCGCACTCGTCC 58.815 45.455 11.47 0.00 38.14 4.79
136 2861 1.202031 GCGCACTCGTCCTAATTTTGG 60.202 52.381 0.30 0.00 38.14 3.28
148 2873 7.392113 TCGTCCTAATTTTGGAATAACACATGT 59.608 33.333 0.95 0.00 35.10 3.21
180 2905 4.569966 CACAACCAAAAGCATAAACAAGCA 59.430 37.500 0.00 0.00 0.00 3.91
269 2994 4.771590 TTCTGTCAAAATTGCTAGCAGG 57.228 40.909 18.45 6.78 0.00 4.85
273 2998 2.030007 GTCAAAATTGCTAGCAGGTGCA 60.030 45.455 18.45 2.54 45.16 4.57
314 3039 3.119708 GCCATGACCTGAAGATGTTTGTC 60.120 47.826 0.00 0.00 0.00 3.18
316 3041 3.140325 TGACCTGAAGATGTTTGTCCC 57.860 47.619 0.00 0.00 0.00 4.46
317 3042 2.224769 TGACCTGAAGATGTTTGTCCCC 60.225 50.000 0.00 0.00 0.00 4.81
318 3043 2.040412 GACCTGAAGATGTTTGTCCCCT 59.960 50.000 0.00 0.00 0.00 4.79
326 3051 1.282382 TGTTTGTCCCCTAGTAGCCC 58.718 55.000 0.00 0.00 0.00 5.19
333 3058 1.054978 CCCCTAGTAGCCCCCTTGTC 61.055 65.000 0.00 0.00 0.00 3.18
365 3090 4.912528 GAAGTGCTTCGGAAAGACTTAG 57.087 45.455 11.87 0.00 35.19 2.18
371 3097 3.997681 GCTTCGGAAAGACTTAGCTTCTT 59.002 43.478 0.00 0.00 34.14 2.52
373 3099 5.049336 GCTTCGGAAAGACTTAGCTTCTTTT 60.049 40.000 12.08 0.00 42.21 2.27
375 3101 6.300354 TCGGAAAGACTTAGCTTCTTTTTG 57.700 37.500 12.08 8.61 42.21 2.44
378 3104 6.972901 CGGAAAGACTTAGCTTCTTTTTGTTT 59.027 34.615 12.08 0.00 42.21 2.83
400 3126 6.490566 TTTGAATGTCTCACATGATGTCTG 57.509 37.500 0.00 0.00 37.97 3.51
406 3132 0.393402 TCACATGATGTCTGCAGGGC 60.393 55.000 15.13 8.06 0.00 5.19
407 3133 1.077212 ACATGATGTCTGCAGGGCC 60.077 57.895 15.13 0.00 0.00 5.80
434 3160 9.502091 AGTACATAAAAATCAGCTCTTGTTACA 57.498 29.630 0.00 0.00 0.00 2.41
444 3170 6.863275 TCAGCTCTTGTTACAGATTAATCGA 58.137 36.000 9.78 0.00 0.00 3.59
494 3220 1.039856 TCTTCCAAAACAAGGCAGCC 58.960 50.000 1.84 1.84 0.00 4.85
521 3247 4.825422 AGATTCAAAGACAATCTCGAGCA 58.175 39.130 7.81 0.00 36.04 4.26
527 3253 5.121298 TCAAAGACAATCTCGAGCAATTCAG 59.879 40.000 7.81 0.00 0.00 3.02
535 3261 4.380531 TCTCGAGCAATTCAGTTTTGTCT 58.619 39.130 7.81 0.00 0.00 3.41
543 3269 5.561725 GCAATTCAGTTTTGTCTCTCCACTC 60.562 44.000 0.00 0.00 0.00 3.51
544 3270 5.559148 ATTCAGTTTTGTCTCTCCACTCT 57.441 39.130 0.00 0.00 0.00 3.24
577 3303 0.321653 GTGCCGGGTCAAGATGAGTT 60.322 55.000 2.18 0.00 0.00 3.01
688 3527 6.083925 ACGTACGTACTAGTTTAGTTCTCG 57.916 41.667 21.41 7.44 40.14 4.04
711 3550 5.590259 CGACTGAGATTATCCAACCCAAATT 59.410 40.000 0.00 0.00 0.00 1.82
789 3628 4.940046 AGATCTCAACATGCAACTTGGTAG 59.060 41.667 0.00 0.00 0.00 3.18
790 3629 4.085357 TCTCAACATGCAACTTGGTAGT 57.915 40.909 0.00 0.00 35.68 2.73
898 3737 8.465999 CAATCTTTGGTGCCTGTACATAAATAA 58.534 33.333 0.00 0.00 0.00 1.40
996 3838 2.472695 TTGCTTGCTGTCTCCGTAAT 57.527 45.000 0.00 0.00 0.00 1.89
1011 3853 2.104111 CCGTAATACAATGGCTCCAGGA 59.896 50.000 0.00 0.00 0.00 3.86
1185 4030 2.285069 ATACCACCACCTCCGGCA 60.285 61.111 0.00 0.00 0.00 5.69
1338 4183 2.158475 TGAACCTTCCTGCAATTCCTGT 60.158 45.455 0.00 0.00 0.00 4.00
1604 4449 1.803334 TATGGTCAAACGTGTCTGCC 58.197 50.000 0.00 0.00 0.00 4.85
1657 4502 6.322201 TCATGAGTCATGTGTATGAGAAGCTA 59.678 38.462 28.03 5.32 43.66 3.32
1695 4540 3.423154 GGAAGCTGTCGTTGGGCG 61.423 66.667 0.00 0.00 43.01 6.13
1697 4542 4.927782 AAGCTGTCGTTGGGCGCA 62.928 61.111 10.83 0.00 41.07 6.09
1772 4617 4.157289 ACATCTGTGAAGCAATCAATGGTC 59.843 41.667 7.28 0.00 40.50 4.02
1777 4622 4.517075 TGTGAAGCAATCAATGGTCGTTAA 59.483 37.500 0.00 0.00 40.50 2.01
1778 4623 5.182950 TGTGAAGCAATCAATGGTCGTTAAT 59.817 36.000 0.00 0.00 40.50 1.40
1871 4721 3.644953 AAAAACTTTGGCCTGGGGA 57.355 47.368 3.32 0.00 0.00 4.81
1897 4747 3.971702 GGTCCAAGCCCAGGCAGT 61.972 66.667 12.03 0.00 44.88 4.40
2449 7441 9.535878 GGTAACTTACAACCATCATTTCAAAAA 57.464 29.630 1.40 0.00 35.73 1.94
2528 7520 4.933400 GCGGAAAGGTCTACTCAATTGTTA 59.067 41.667 5.13 0.00 0.00 2.41
2533 7525 9.886132 GGAAAGGTCTACTCAATTGTTAAGATA 57.114 33.333 5.13 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.187687 AGTAGAAAAAGGGTCAAACGTGAA 58.812 37.500 0.00 0.0 34.87 3.18
2 3 5.756833 ACTAGTAGAAAAAGGGTCAAACGTG 59.243 40.000 3.59 0.0 0.00 4.49
3 4 5.756833 CACTAGTAGAAAAAGGGTCAAACGT 59.243 40.000 3.59 0.0 0.00 3.99
4 5 5.178809 CCACTAGTAGAAAAAGGGTCAAACG 59.821 44.000 3.59 0.0 0.00 3.60
5 6 6.293698 TCCACTAGTAGAAAAAGGGTCAAAC 58.706 40.000 3.59 0.0 0.00 2.93
6 7 6.503560 TCCACTAGTAGAAAAAGGGTCAAA 57.496 37.500 3.59 0.0 0.00 2.69
7 8 6.100714 ACTTCCACTAGTAGAAAAAGGGTCAA 59.899 38.462 3.59 0.0 0.00 3.18
8 9 5.605488 ACTTCCACTAGTAGAAAAAGGGTCA 59.395 40.000 3.59 0.0 0.00 4.02
9 10 6.111669 ACTTCCACTAGTAGAAAAAGGGTC 57.888 41.667 3.59 0.0 0.00 4.46
10 11 6.100714 TGAACTTCCACTAGTAGAAAAAGGGT 59.899 38.462 3.59 0.0 0.00 4.34
11 12 6.531021 TGAACTTCCACTAGTAGAAAAAGGG 58.469 40.000 3.59 0.0 0.00 3.95
12 13 7.119846 CCATGAACTTCCACTAGTAGAAAAAGG 59.880 40.741 3.59 0.0 0.00 3.11
14 15 7.660208 GTCCATGAACTTCCACTAGTAGAAAAA 59.340 37.037 3.59 0.0 0.00 1.94
15 16 7.016268 AGTCCATGAACTTCCACTAGTAGAAAA 59.984 37.037 3.59 0.0 0.00 2.29
16 17 6.497259 AGTCCATGAACTTCCACTAGTAGAAA 59.503 38.462 3.59 0.0 0.00 2.52
18 19 5.580998 AGTCCATGAACTTCCACTAGTAGA 58.419 41.667 3.59 0.0 0.00 2.59
19 20 5.923733 AGTCCATGAACTTCCACTAGTAG 57.076 43.478 0.00 0.0 0.00 2.57
21 22 4.263068 CCAAGTCCATGAACTTCCACTAGT 60.263 45.833 0.00 0.0 37.38 2.57
22 23 4.256920 CCAAGTCCATGAACTTCCACTAG 58.743 47.826 0.00 0.0 37.38 2.57
23 24 3.650942 ACCAAGTCCATGAACTTCCACTA 59.349 43.478 0.00 0.0 37.38 2.74
25 26 2.814336 GACCAAGTCCATGAACTTCCAC 59.186 50.000 0.00 0.0 37.38 4.02
26 27 2.441375 TGACCAAGTCCATGAACTTCCA 59.559 45.455 0.00 0.0 37.38 3.53
27 28 3.140325 TGACCAAGTCCATGAACTTCC 57.860 47.619 0.00 0.0 37.38 3.46
28 29 6.173339 TCTATTGACCAAGTCCATGAACTTC 58.827 40.000 0.00 0.0 37.38 3.01
30 31 5.762179 TCTATTGACCAAGTCCATGAACT 57.238 39.130 0.00 0.0 0.00 3.01
31 32 6.173339 TCTTCTATTGACCAAGTCCATGAAC 58.827 40.000 0.00 0.0 0.00 3.18
32 33 6.373005 TCTTCTATTGACCAAGTCCATGAA 57.627 37.500 0.00 0.0 0.00 2.57
34 35 8.206867 TCTATTCTTCTATTGACCAAGTCCATG 58.793 37.037 0.00 0.0 0.00 3.66
35 36 8.324191 TCTATTCTTCTATTGACCAAGTCCAT 57.676 34.615 0.00 0.0 0.00 3.41
36 37 7.733773 TCTATTCTTCTATTGACCAAGTCCA 57.266 36.000 0.00 0.0 0.00 4.02
37 38 8.478877 TCTTCTATTCTTCTATTGACCAAGTCC 58.521 37.037 0.00 0.0 0.00 3.85
73 2798 3.628942 GCTTTGACATACATGGCATCTCA 59.371 43.478 0.00 0.0 46.90 3.27
103 2828 4.181578 ACGAGTGCGCTTAATAAAGATGT 58.818 39.130 9.73 0.0 42.48 3.06
117 2842 2.343101 TCCAAAATTAGGACGAGTGCG 58.657 47.619 0.00 0.0 44.79 5.34
119 2844 7.094975 TGTGTTATTCCAAAATTAGGACGAGTG 60.095 37.037 0.00 0.0 34.19 3.51
123 2848 7.535139 ACATGTGTTATTCCAAAATTAGGACG 58.465 34.615 0.00 0.0 34.19 4.79
136 2861 8.911662 GTTGTGTCCAAATTACATGTGTTATTC 58.088 33.333 9.11 0.0 30.94 1.75
156 2881 4.570369 GCTTGTTTATGCTTTTGGTTGTGT 59.430 37.500 0.00 0.0 0.00 3.72
269 2994 4.438744 CGATTGGTTCCTCCTTATTTGCAC 60.439 45.833 0.00 0.0 37.07 4.57
273 2998 3.288092 GGCGATTGGTTCCTCCTTATTT 58.712 45.455 0.00 0.0 37.07 1.40
314 3039 1.004361 ACAAGGGGGCTACTAGGGG 59.996 63.158 0.00 0.0 0.00 4.79
316 3041 1.400530 CCGACAAGGGGGCTACTAGG 61.401 65.000 0.00 0.0 35.97 3.02
317 3042 2.029307 GCCGACAAGGGGGCTACTAG 62.029 65.000 0.00 0.0 45.93 2.57
318 3043 2.062177 GCCGACAAGGGGGCTACTA 61.062 63.158 0.00 0.0 45.93 1.82
361 3086 9.305925 AGACATTCAAAACAAAAAGAAGCTAAG 57.694 29.630 0.00 0.0 0.00 2.18
365 3090 7.063308 TGTGAGACATTCAAAACAAAAAGAAGC 59.937 33.333 0.00 0.0 37.61 3.86
371 3097 7.980662 ACATCATGTGAGACATTCAAAACAAAA 59.019 29.630 0.00 0.0 36.53 2.44
373 3099 7.013559 AGACATCATGTGAGACATTCAAAACAA 59.986 33.333 0.00 0.0 36.53 2.83
375 3101 6.800408 CAGACATCATGTGAGACATTCAAAAC 59.200 38.462 0.00 0.0 36.53 2.43
378 3104 4.393990 GCAGACATCATGTGAGACATTCAA 59.606 41.667 0.00 0.0 36.53 2.69
400 3126 3.699038 TGATTTTTATGTACTGGCCCTGC 59.301 43.478 0.00 0.0 0.00 4.85
406 3132 7.383102 ACAAGAGCTGATTTTTATGTACTGG 57.617 36.000 0.00 0.0 0.00 4.00
407 3133 9.760660 GTAACAAGAGCTGATTTTTATGTACTG 57.239 33.333 0.00 0.0 0.00 2.74
494 3220 4.656041 GAGATTGTCTTTGAATCTTGGCG 58.344 43.478 0.00 0.0 39.72 5.69
502 3228 5.469760 TGAATTGCTCGAGATTGTCTTTGAA 59.530 36.000 18.75 0.0 0.00 2.69
521 3247 5.762218 CAGAGTGGAGAGACAAAACTGAATT 59.238 40.000 0.00 0.0 0.00 2.17
527 3253 4.249661 GGATCAGAGTGGAGAGACAAAAC 58.750 47.826 0.00 0.0 0.00 2.43
535 3261 1.203300 TGGGTTGGATCAGAGTGGAGA 60.203 52.381 0.00 0.0 0.00 3.71
543 3269 0.890683 GGCACTTTGGGTTGGATCAG 59.109 55.000 0.00 0.0 0.00 2.90
544 3270 0.893270 CGGCACTTTGGGTTGGATCA 60.893 55.000 0.00 0.0 0.00 2.92
614 3341 0.396435 AGTTTGGATCTGCACCGACA 59.604 50.000 0.00 0.0 0.00 4.35
645 3372 8.598924 CGTACGTACTATCTAGGTATACATTGG 58.401 40.741 22.55 0.0 0.00 3.16
688 3527 6.681368 GCAATTTGGGTTGGATAATCTCAGTC 60.681 42.308 0.00 0.0 0.00 3.51
711 3550 2.637382 TGTTACTCATCTTGACCAGGCA 59.363 45.455 0.00 0.0 0.00 4.75
789 3628 6.470557 TTGTATTCGTAGCTTGGTAAACAC 57.529 37.500 0.00 0.0 0.00 3.32
790 3629 7.388224 TGAATTGTATTCGTAGCTTGGTAAACA 59.612 33.333 0.00 0.0 0.00 2.83
890 3729 6.953843 TGGTGCACATACGACATTATTTATG 58.046 36.000 20.43 0.0 40.26 1.90
898 3737 0.036483 TGCTGGTGCACATACGACAT 60.036 50.000 20.43 0.0 45.31 3.06
996 3838 1.141657 GCTGATCCTGGAGCCATTGTA 59.858 52.381 9.83 0.0 0.00 2.41
1113 3955 3.284449 GTTGGTGGTGGCGGTGAC 61.284 66.667 0.00 0.0 0.00 3.67
1114 3956 3.469863 GAGTTGGTGGTGGCGGTGA 62.470 63.158 0.00 0.0 0.00 4.02
1115 3957 2.978010 GAGTTGGTGGTGGCGGTG 60.978 66.667 0.00 0.0 0.00 4.94
1116 3958 4.265056 GGAGTTGGTGGTGGCGGT 62.265 66.667 0.00 0.0 0.00 5.68
1122 3964 0.991355 TGGGAGTTGGAGTTGGTGGT 60.991 55.000 0.00 0.0 0.00 4.16
1185 4030 2.123769 TTTGGTGGCAGCAGCACT 60.124 55.556 19.65 0.0 44.61 4.40
1230 4075 2.520536 GCAGGATATCACCGGCCCT 61.521 63.158 0.00 0.0 43.33 5.19
1231 4076 2.032681 GCAGGATATCACCGGCCC 59.967 66.667 0.00 0.0 43.33 5.80
1657 4502 7.147949 GCTTCCATATTATTGGCTTATGCTCAT 60.148 37.037 0.13 0.0 39.59 2.90
1695 4540 2.460757 AACCATTGTGCCAAGATTGC 57.539 45.000 0.00 0.0 0.00 3.56
1697 4542 4.571919 CATCAAACCATTGTGCCAAGATT 58.428 39.130 0.00 0.0 37.79 2.40
1768 4613 1.121378 TCCGCCCATATTAACGACCA 58.879 50.000 0.00 0.0 0.00 4.02
1772 4617 2.227865 CCCAAATCCGCCCATATTAACG 59.772 50.000 0.00 0.0 0.00 3.18
1777 4622 1.228862 GGCCCAAATCCGCCCATAT 60.229 57.895 0.00 0.0 39.39 1.78
1778 4623 2.197324 GGCCCAAATCCGCCCATA 59.803 61.111 0.00 0.0 39.39 2.74
1871 4721 4.357279 GCTTGGACCTGGGCTGCT 62.357 66.667 0.00 0.0 0.00 4.24
2166 5083 3.426568 GCGAACAGGACAGCAGCC 61.427 66.667 0.00 0.0 0.00 4.85
2449 7441 9.256477 GATCATGCAACACATTGAATATTTCAT 57.744 29.630 0.00 0.0 39.84 2.57
2507 7499 8.794335 ATCTTAACAATTGAGTAGACCTTTCC 57.206 34.615 13.59 0.0 0.00 3.13


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

AutoCloner maintained by Alex Coulton.