Multiple sequence alignment - TraesCS5D01G195900

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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 TraesCS5D01G195900 chr5D 100.000 2868 0 0 2112 4979 299421684 299424551 0.000000e+00 5297.0
1 TraesCS5D01G195900 chr5D 100.000 1875 0 0 1 1875 299419573 299421447 0.000000e+00 3463.0
2 TraesCS5D01G195900 chr5B 94.781 1897 67 9 1 1875 340718069 340719955 0.000000e+00 2926.0
3 TraesCS5D01G195900 chr5B 90.646 1657 97 25 3342 4976 340719954 340721574 0.000000e+00 2148.0
4 TraesCS5D01G195900 chr5B 96.872 1247 29 1 2112 3348 669295810 669297056 0.000000e+00 2078.0
5 TraesCS5D01G195900 chr5A 93.235 1567 77 11 3342 4900 396707938 396709483 0.000000e+00 2279.0
6 TraesCS5D01G195900 chr5A 96.976 992 24 5 886 1875 396706952 396707939 0.000000e+00 1661.0
7 TraesCS5D01G195900 chr5A 92.773 595 26 1 1 595 396706376 396706953 0.000000e+00 845.0
8 TraesCS5D01G195900 chr5A 94.872 39 2 0 4932 4970 396709495 396709533 1.500000e-05 62.1
9 TraesCS5D01G195900 chr3D 98.629 1240 7 1 2112 3341 45492392 45493631 0.000000e+00 2187.0
10 TraesCS5D01G195900 chr7D 98.387 1240 4 2 2112 3341 66827902 66826669 0.000000e+00 2165.0
11 TraesCS5D01G195900 chr7D 97.232 1192 15 3 2112 3292 551744318 551745502 0.000000e+00 2002.0
12 TraesCS5D01G195900 chr7B 98.065 1240 13 2 2112 3341 92905299 92906537 0.000000e+00 2146.0
13 TraesCS5D01G195900 chr7B 97.500 1240 17 5 2112 3341 179914579 179913344 0.000000e+00 2106.0
14 TraesCS5D01G195900 chr3A 97.985 1241 15 1 2112 3342 38331517 38332757 0.000000e+00 2145.0
15 TraesCS5D01G195900 chr6A 97.742 1240 18 1 2112 3341 39500108 39498869 0.000000e+00 2126.0
16 TraesCS5D01G195900 chr1B 97.238 1231 31 2 2112 3342 132064463 132063236 0.000000e+00 2082.0
17 TraesCS5D01G195900 chrUn 97.268 732 10 1 2622 3343 296242516 296241785 0.000000e+00 1232.0
18 TraesCS5D01G195900 chr6B 94.294 333 9 1 3019 3341 368479603 368479271 7.440000e-138 501.0
19 TraesCS5D01G195900 chr2A 86.331 417 52 3 3556 3968 41462840 41462425 2.730000e-122 449.0
20 TraesCS5D01G195900 chr2B 86.494 385 51 1 3556 3940 63783369 63782986 5.960000e-114 422.0


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 TraesCS5D01G195900 chr5D 299419573 299424551 4978 False 4380.000 5297 100.0000 1 4979 2 chr5D.!!$F1 4978
1 TraesCS5D01G195900 chr5B 340718069 340721574 3505 False 2537.000 2926 92.7135 1 4976 2 chr5B.!!$F2 4975
2 TraesCS5D01G195900 chr5B 669295810 669297056 1246 False 2078.000 2078 96.8720 2112 3348 1 chr5B.!!$F1 1236
3 TraesCS5D01G195900 chr5A 396706376 396709533 3157 False 1211.775 2279 94.4640 1 4970 4 chr5A.!!$F1 4969
4 TraesCS5D01G195900 chr3D 45492392 45493631 1239 False 2187.000 2187 98.6290 2112 3341 1 chr3D.!!$F1 1229
5 TraesCS5D01G195900 chr7D 66826669 66827902 1233 True 2165.000 2165 98.3870 2112 3341 1 chr7D.!!$R1 1229
6 TraesCS5D01G195900 chr7D 551744318 551745502 1184 False 2002.000 2002 97.2320 2112 3292 1 chr7D.!!$F1 1180
7 TraesCS5D01G195900 chr7B 92905299 92906537 1238 False 2146.000 2146 98.0650 2112 3341 1 chr7B.!!$F1 1229
8 TraesCS5D01G195900 chr7B 179913344 179914579 1235 True 2106.000 2106 97.5000 2112 3341 1 chr7B.!!$R1 1229
9 TraesCS5D01G195900 chr3A 38331517 38332757 1240 False 2145.000 2145 97.9850 2112 3342 1 chr3A.!!$F1 1230
10 TraesCS5D01G195900 chr6A 39498869 39500108 1239 True 2126.000 2126 97.7420 2112 3341 1 chr6A.!!$R1 1229
11 TraesCS5D01G195900 chr1B 132063236 132064463 1227 True 2082.000 2082 97.2380 2112 3342 1 chr1B.!!$R1 1230
12 TraesCS5D01G195900 chrUn 296241785 296242516 731 True 1232.000 1232 97.2680 2622 3343 1 chrUn.!!$R1 721

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
652 654 0.110823 CGTGCCGTGCTTTCACTTAC 60.111 55.000 0.0 0.0 40.99 2.34 F
1149 1169 0.320421 TTGGTTACCTCTCACTGCGC 60.320 55.000 0.0 0.0 0.00 6.09 F
1874 1899 1.064758 TCTTGTTCACTGCCCTGTTGT 60.065 47.619 0.0 0.0 0.00 3.32 F
3657 3707 0.731514 CTGCAGCCAATGACAAAGCG 60.732 55.000 0.0 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1505 3.991605 CGAAATTTCGTGGACAGGTAG 57.008 47.619 28.21 0.21 45.09 3.18 R
2396 2427 7.563188 GGCATCTATGGAGATTAGGATAGAGAA 59.437 40.741 0.00 0.00 40.68 2.87 R
3685 3735 0.613292 TCGGCTTCTCCTTCTGCTCT 60.613 55.000 0.00 0.00 0.00 4.09 R
4925 5010 0.462375 TGCCTGTTGTACGTCTGTGT 59.538 50.000 0.00 0.00 0.00 3.72 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
21 22 2.555325 GGTAATTAAACCCCTATGCGGC 59.445 50.000 0.00 0.00 33.02 6.53
31 32 4.444838 TATGCGGCCGTCTTGCGT 62.445 61.111 28.70 13.35 39.32 5.24
84 85 6.382859 TGGCTGTATCTCTCCATAGTTTGTAA 59.617 38.462 0.00 0.00 0.00 2.41
119 120 5.236695 GCTACTCCCTTCGATCCAAAATAAC 59.763 44.000 0.00 0.00 0.00 1.89
122 123 5.648092 ACTCCCTTCGATCCAAAATAACTTG 59.352 40.000 0.00 0.00 0.00 3.16
159 160 1.607148 GGTTAGTTCACAACTGCCACC 59.393 52.381 0.00 0.06 42.84 4.61
184 185 1.671979 TGTGGATCGGAGGTAGTACG 58.328 55.000 0.00 0.00 0.00 3.67
185 186 0.310232 GTGGATCGGAGGTAGTACGC 59.690 60.000 0.00 0.00 0.00 4.42
242 243 3.056107 TCACCTCTGATTTAAGTCACCCG 60.056 47.826 0.00 0.00 0.00 5.28
306 307 5.182001 ACTTAGTTATTCTGGCAAAGCTGTG 59.818 40.000 0.00 0.00 0.00 3.66
328 329 7.317390 TGTGCTTCGTAGTTATATTTGTCTGA 58.683 34.615 0.00 0.00 0.00 3.27
402 404 5.981088 TGTGTTGCCTCATGAATTTATGT 57.019 34.783 9.77 0.00 0.00 2.29
446 448 8.349245 TCACTGTTTCAACTTGTAATGGTATTG 58.651 33.333 0.00 0.00 0.00 1.90
652 654 0.110823 CGTGCCGTGCTTTCACTTAC 60.111 55.000 0.00 0.00 40.99 2.34
661 663 4.024893 CGTGCTTTCACTTACTGTGTGATT 60.025 41.667 2.31 0.00 46.27 2.57
785 805 5.216622 TGGTAGCCAGATAATCAGTAGGTT 58.783 41.667 0.00 0.00 0.00 3.50
793 813 6.983307 CCAGATAATCAGTAGGTTGTTCAGAG 59.017 42.308 0.00 0.00 0.00 3.35
805 825 4.127171 GTTGTTCAGAGACTTGGCACTTA 58.873 43.478 0.00 0.00 0.00 2.24
879 899 9.739276 ATATCTGATGTCAGTTTGGAACTTTAA 57.261 29.630 9.65 0.00 44.12 1.52
1149 1169 0.320421 TTGGTTACCTCTCACTGCGC 60.320 55.000 0.00 0.00 0.00 6.09
1259 1279 6.432802 AGCAATCGTAACAAATGAAAAACG 57.567 33.333 0.00 0.00 0.00 3.60
1264 1284 8.635124 CAATCGTAACAAATGAAAAACGCTTAT 58.365 29.630 0.00 0.00 0.00 1.73
1265 1285 7.541743 TCGTAACAAATGAAAAACGCTTATG 57.458 32.000 0.00 0.00 0.00 1.90
1483 1505 3.302699 GTCGTACGTCTTTGATGGTAAGC 59.697 47.826 16.05 0.00 0.00 3.09
1555 1577 6.535540 TGTGTCCAGTTTTAGCCTTATGTTA 58.464 36.000 0.00 0.00 0.00 2.41
1866 1891 4.370364 TGAAAAGGTTCTTGTTCACTGC 57.630 40.909 0.00 0.00 34.60 4.40
1873 1898 1.679139 TCTTGTTCACTGCCCTGTTG 58.321 50.000 0.00 0.00 0.00 3.33
1874 1899 1.064758 TCTTGTTCACTGCCCTGTTGT 60.065 47.619 0.00 0.00 0.00 3.32
2396 2427 4.575885 TCTAGTGTTTAAGGATTTGCGCT 58.424 39.130 9.73 0.00 0.00 5.92
3350 3399 5.768662 GCCTTAAAAACAGAGGTCCTAAAGT 59.231 40.000 0.00 0.00 33.03 2.66
3394 3443 3.119291 TGTTTTGCAAATGTTGTAGGCG 58.881 40.909 13.65 0.00 0.00 5.52
3590 3640 4.455533 TGCGTGCTCAGAATTATCTTTTGT 59.544 37.500 0.00 0.00 32.03 2.83
3617 3667 9.995003 ATATTTAACATCAATGTGGTTTTGTGT 57.005 25.926 0.00 0.00 41.61 3.72
3639 3689 2.264455 ACAGCTTCAAGGATGAGGTCT 58.736 47.619 0.00 0.00 36.78 3.85
3657 3707 0.731514 CTGCAGCCAATGACAAAGCG 60.732 55.000 0.00 0.00 0.00 4.68
3675 3725 2.087646 GCGGAGGCTGAAAAGATTCTT 58.912 47.619 0.00 0.00 36.48 2.52
3693 3743 9.512588 AAGATTCTTCAGATTAAAAGAGCAGAA 57.487 29.630 0.00 0.00 33.32 3.02
4049 4099 6.668541 AGTTCTTCATCATTCACCATTACG 57.331 37.500 0.00 0.00 0.00 3.18
4054 4104 6.479990 TCTTCATCATTCACCATTACGCTAAG 59.520 38.462 0.00 0.00 0.00 2.18
4071 4121 6.646636 ACGCTAAGAACATATTTTATGCGAC 58.353 36.000 0.00 0.00 41.79 5.19
4118 4168 9.784680 AGTAATTTATCTACGTGTGTGAACTAG 57.215 33.333 0.00 0.00 0.00 2.57
4150 4200 7.106439 AGTTGTGAATTTTACATGGTGTGAA 57.894 32.000 0.00 0.00 0.00 3.18
4151 4201 6.978080 AGTTGTGAATTTTACATGGTGTGAAC 59.022 34.615 0.00 0.00 0.00 3.18
4152 4202 6.707440 TGTGAATTTTACATGGTGTGAACT 57.293 33.333 0.00 0.00 0.00 3.01
4236 4286 3.411446 TCCTGAATGGTACTTGTTGCTG 58.589 45.455 0.00 0.00 37.07 4.41
4305 4355 1.676014 GGTGACACTCCACTATGGTGC 60.676 57.143 3.19 0.00 41.75 5.01
4315 4365 3.568007 TCCACTATGGTGCTTGTGTTTTC 59.432 43.478 3.19 0.00 41.75 2.29
4344 4394 1.982660 TATCTCGGTCGGATTGAGCT 58.017 50.000 0.00 0.00 43.02 4.09
4347 4397 2.097036 TCTCGGTCGGATTGAGCTTAA 58.903 47.619 0.00 0.00 43.02 1.85
4356 4409 3.378112 CGGATTGAGCTTAATGGCTTTGA 59.622 43.478 8.68 0.00 43.20 2.69
4390 4454 5.008331 AGAATGATGTGCAGTTGTTCTCAT 58.992 37.500 0.00 0.00 0.00 2.90
4457 4521 1.155889 TGCTACAATTGCAGTCCACG 58.844 50.000 5.05 0.00 35.31 4.94
4476 4540 5.304357 TCCACGCTCTTAATTCCTGATGATA 59.696 40.000 0.00 0.00 0.00 2.15
4519 4583 5.927030 ACTGCACACTGTAAATTCAATACG 58.073 37.500 0.00 0.00 0.00 3.06
4595 4667 5.353400 CACTGACACTGAATATGCTTGTGAT 59.647 40.000 12.35 0.68 33.41 3.06
4688 4765 1.005037 GCATGGCGATCGGGTATCA 60.005 57.895 18.30 0.00 33.87 2.15
4703 4780 3.512680 GGTATCAGACTTGACGTTGAGG 58.487 50.000 0.00 0.00 35.83 3.86
4827 4904 7.571080 GGGTTACCGATCAAAAATAATACCA 57.429 36.000 0.00 0.00 0.00 3.25
4829 4906 7.283807 GGGTTACCGATCAAAAATAATACCACT 59.716 37.037 0.00 0.00 0.00 4.00
4830 4907 8.340443 GGTTACCGATCAAAAATAATACCACTC 58.660 37.037 0.00 0.00 0.00 3.51
4831 4908 6.937436 ACCGATCAAAAATAATACCACTCC 57.063 37.500 0.00 0.00 0.00 3.85
4834 4911 8.437575 ACCGATCAAAAATAATACCACTCCTAT 58.562 33.333 0.00 0.00 0.00 2.57
4838 4915 8.815565 TCAAAAATAATACCACTCCTATTGCA 57.184 30.769 0.00 0.00 0.00 4.08
4839 4916 9.420118 TCAAAAATAATACCACTCCTATTGCAT 57.580 29.630 0.00 0.00 0.00 3.96
4861 4938 7.090173 GCATATACACTGACCAAAACACAAAT 58.910 34.615 0.00 0.00 0.00 2.32
4868 4946 5.009010 ACTGACCAAAACACAAATAGCTCAG 59.991 40.000 0.00 0.00 0.00 3.35
4914 4999 0.602905 AAGTTCGGGGAGCTCAAACG 60.603 55.000 17.19 15.97 0.00 3.60
4915 5000 2.033194 GTTCGGGGAGCTCAAACGG 61.033 63.158 17.19 9.49 0.00 4.44
4916 5001 2.211410 TTCGGGGAGCTCAAACGGA 61.211 57.895 17.19 8.44 0.00 4.69
4917 5002 2.434359 CGGGGAGCTCAAACGGAC 60.434 66.667 17.19 0.00 0.00 4.79
4918 5003 2.943978 CGGGGAGCTCAAACGGACT 61.944 63.158 17.19 0.00 0.00 3.85
4919 5004 1.375326 GGGGAGCTCAAACGGACTT 59.625 57.895 17.19 0.00 0.00 3.01
4920 5005 0.955919 GGGGAGCTCAAACGGACTTG 60.956 60.000 17.19 0.00 0.00 3.16
4921 5006 0.034896 GGGAGCTCAAACGGACTTGA 59.965 55.000 17.19 0.00 34.22 3.02
4922 5007 1.339151 GGGAGCTCAAACGGACTTGAT 60.339 52.381 17.19 0.00 34.86 2.57
4923 5008 2.003301 GGAGCTCAAACGGACTTGATC 58.997 52.381 17.19 0.00 34.86 2.92
4924 5009 1.656095 GAGCTCAAACGGACTTGATCG 59.344 52.381 9.40 0.00 34.86 3.69
4925 5010 1.272490 AGCTCAAACGGACTTGATCGA 59.728 47.619 0.00 0.00 34.86 3.59
4926 5011 1.390463 GCTCAAACGGACTTGATCGAC 59.610 52.381 0.00 0.00 34.86 4.20
4938 5023 3.004002 ACTTGATCGACACAGACGTACAA 59.996 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.625315 ACATGACAACTCAGGCTAGCA 59.375 47.619 18.24 0.00 30.93 3.49
84 85 7.179076 TCGAAGGGAGTAGCTTAAATAAACT 57.821 36.000 0.00 0.00 0.00 2.66
159 160 2.200373 ACCTCCGATCCACAAAAAGG 57.800 50.000 0.00 0.00 0.00 3.11
184 185 2.234143 GGAATTCCTGGGAGCTAATGC 58.766 52.381 17.73 0.00 40.05 3.56
185 186 3.484407 CTGGAATTCCTGGGAGCTAATG 58.516 50.000 24.73 0.00 36.82 1.90
242 243 5.797434 GTGAAAGAAATAAGCTAAGTGCAGC 59.203 40.000 0.00 0.00 45.94 5.25
351 352 7.883391 TTCAAAACCAGTTACCATAAGACAA 57.117 32.000 0.00 0.00 0.00 3.18
402 404 7.482169 ACAGTGAGACCTCTGAAAATACATA 57.518 36.000 0.00 0.00 37.35 2.29
468 470 8.035394 TCCTACTTCAAGCAAAGAGTATTACAG 58.965 37.037 0.00 0.00 0.00 2.74
785 805 3.388024 ACTAAGTGCCAAGTCTCTGAACA 59.612 43.478 0.00 0.00 0.00 3.18
793 813 4.342665 AGATAGCCTACTAAGTGCCAAGTC 59.657 45.833 0.00 0.00 30.45 3.01
805 825 7.246171 CCAAATACATGGTAGATAGCCTACT 57.754 40.000 0.00 0.00 45.50 2.57
879 899 6.884295 TCATCATCGAAGGATAACCAAACTTT 59.116 34.615 3.00 0.00 38.94 2.66
1014 1034 3.073062 ACTGATCAACCTGCACTAAACCT 59.927 43.478 0.00 0.00 0.00 3.50
1149 1169 1.337821 GGACGTCTAGCTGTTTCACG 58.662 55.000 16.46 0.00 36.54 4.35
1243 1263 7.099666 TGCATAAGCGTTTTTCATTTGTTAC 57.900 32.000 0.00 0.00 46.23 2.50
1290 1310 8.749354 AGGAAAGTGTTTTCATTTGTAGAAAGT 58.251 29.630 2.85 0.00 43.62 2.66
1483 1505 3.991605 CGAAATTTCGTGGACAGGTAG 57.008 47.619 28.21 0.21 45.09 3.18
1574 1598 7.224522 AGAAAATCTGCAGCTTCAGTTAAAT 57.775 32.000 13.22 0.00 35.63 1.40
1575 1599 6.639632 AGAAAATCTGCAGCTTCAGTTAAA 57.360 33.333 13.22 0.00 35.63 1.52
2396 2427 7.563188 GGCATCTATGGAGATTAGGATAGAGAA 59.437 40.741 0.00 0.00 40.68 2.87
3350 3399 6.892456 ACAGGTCAGTCAAGATATTCTCTGTA 59.108 38.462 0.00 0.00 33.29 2.74
3394 3443 8.535335 ACAATCTCATACCCATACATAGACATC 58.465 37.037 0.00 0.00 0.00 3.06
3517 3567 6.413892 TGCCACTTTAATCTGATGTATGTGA 58.586 36.000 14.50 0.00 0.00 3.58
3536 3586 6.483307 TCATCTAGTATATGTTTTGCTGCCAC 59.517 38.462 0.00 0.00 0.00 5.01
3595 3645 8.251026 TGTTACACAAAACCACATTGATGTTAA 58.749 29.630 0.00 0.00 39.39 2.01
3602 3652 4.681744 AGCTGTTACACAAAACCACATTG 58.318 39.130 0.00 0.00 0.00 2.82
3617 3667 3.840666 AGACCTCATCCTTGAAGCTGTTA 59.159 43.478 0.00 0.00 0.00 2.41
3627 3677 1.203441 TGGCTGCAGACCTCATCCTT 61.203 55.000 19.23 0.00 0.00 3.36
3639 3689 1.286570 CGCTTTGTCATTGGCTGCA 59.713 52.632 0.50 0.00 0.00 4.41
3657 3707 4.961435 CTGAAGAATCTTTTCAGCCTCC 57.039 45.455 0.00 0.00 43.38 4.30
3675 3725 6.611613 TCTCCTTCTGCTCTTTTAATCTGA 57.388 37.500 0.00 0.00 0.00 3.27
3685 3735 0.613292 TCGGCTTCTCCTTCTGCTCT 60.613 55.000 0.00 0.00 0.00 4.09
3693 3743 1.343069 ACTTTGACTCGGCTTCTCCT 58.657 50.000 0.00 0.00 0.00 3.69
4049 4099 7.851508 TCTGTCGCATAAAATATGTTCTTAGC 58.148 34.615 0.00 0.00 0.00 3.09
4071 4121 3.270027 TCACGACCTTGCCAAATATCTG 58.730 45.455 0.00 0.00 0.00 2.90
4118 4168 9.109533 CCATGTAAAATTCACAACTTAACGTAC 57.890 33.333 0.00 0.00 0.00 3.67
4152 4202 9.504708 GCAAGTCTGATTATCTAGGTAGTAGTA 57.495 37.037 0.00 0.00 0.00 1.82
4236 4286 0.964358 ATCCAGGCTCACTTGCAAGC 60.964 55.000 26.27 13.13 37.80 4.01
4290 4340 2.079158 CACAAGCACCATAGTGGAGTG 58.921 52.381 2.45 0.00 44.69 3.51
4305 4355 6.963796 AGATAAACTCAGCAGAAAACACAAG 58.036 36.000 0.00 0.00 0.00 3.16
4315 4365 2.455032 CGACCGAGATAAACTCAGCAG 58.545 52.381 0.00 0.00 45.14 4.24
4334 4384 3.378112 TCAAAGCCATTAAGCTCAATCCG 59.622 43.478 0.00 0.00 44.11 4.18
4390 4454 6.832520 TCAAAATCTGCTATTGCCACTTTA 57.167 33.333 0.00 0.00 38.71 1.85
4476 4540 8.932791 GTGCAGTTGTACAGTTATACACTTTAT 58.067 33.333 0.00 0.00 34.79 1.40
4519 4583 5.820423 TGTGTACATACATGCCTGATAAACC 59.180 40.000 0.00 0.00 38.63 3.27
4548 4620 2.949447 ACCAGCACAAGACCAATCTTT 58.051 42.857 0.00 0.00 42.91 2.52
4595 4667 1.377987 GGGCACCGGAGTTGCATTA 60.378 57.895 9.46 0.00 40.86 1.90
4646 4723 1.353694 ACTTGCTCCATCAGAAGCCTT 59.646 47.619 0.00 0.00 0.00 4.35
4688 4765 1.122019 AGGGCCTCAACGTCAAGTCT 61.122 55.000 0.00 0.00 0.00 3.24
4823 4900 6.780522 TCAGTGTATATGCAATAGGAGTGGTA 59.219 38.462 0.00 0.00 28.50 3.25
4824 4901 5.602561 TCAGTGTATATGCAATAGGAGTGGT 59.397 40.000 0.00 0.00 28.50 4.16
4825 4902 5.928839 GTCAGTGTATATGCAATAGGAGTGG 59.071 44.000 0.00 0.00 28.50 4.00
4827 4904 5.602561 TGGTCAGTGTATATGCAATAGGAGT 59.397 40.000 0.00 0.00 28.50 3.85
4829 4906 6.493189 TTGGTCAGTGTATATGCAATAGGA 57.507 37.500 0.00 0.00 28.50 2.94
4830 4907 7.066887 TGTTTTGGTCAGTGTATATGCAATAGG 59.933 37.037 0.00 0.00 28.50 2.57
4831 4908 7.910162 GTGTTTTGGTCAGTGTATATGCAATAG 59.090 37.037 0.00 0.00 28.50 1.73
4834 4911 5.532779 TGTGTTTTGGTCAGTGTATATGCAA 59.467 36.000 0.00 0.00 0.00 4.08
4838 4915 8.458843 GCTATTTGTGTTTTGGTCAGTGTATAT 58.541 33.333 0.00 0.00 0.00 0.86
4839 4916 7.663905 AGCTATTTGTGTTTTGGTCAGTGTATA 59.336 33.333 0.00 0.00 0.00 1.47
4861 4938 4.005650 CTGAAGCACAAAATCCTGAGCTA 58.994 43.478 0.00 0.00 41.61 3.32
4868 4946 2.669391 CGCCTTCTGAAGCACAAAATCC 60.669 50.000 11.93 0.00 0.00 3.01
4914 4999 1.068472 ACGTCTGTGTCGATCAAGTCC 60.068 52.381 0.00 0.00 0.00 3.85
4915 5000 2.333389 ACGTCTGTGTCGATCAAGTC 57.667 50.000 0.00 0.00 0.00 3.01
4916 5001 2.551032 TGTACGTCTGTGTCGATCAAGT 59.449 45.455 0.00 0.00 0.00 3.16
4917 5002 3.197434 TGTACGTCTGTGTCGATCAAG 57.803 47.619 0.00 0.00 0.00 3.02
4918 5003 3.243134 TGTTGTACGTCTGTGTCGATCAA 60.243 43.478 0.00 0.00 0.00 2.57
4919 5004 2.291190 TGTTGTACGTCTGTGTCGATCA 59.709 45.455 0.00 0.00 0.00 2.92
4920 5005 2.909244 CTGTTGTACGTCTGTGTCGATC 59.091 50.000 0.00 0.00 0.00 3.69
4921 5006 2.351447 CCTGTTGTACGTCTGTGTCGAT 60.351 50.000 0.00 0.00 0.00 3.59
4922 5007 1.002142 CCTGTTGTACGTCTGTGTCGA 60.002 52.381 0.00 0.00 0.00 4.20
4923 5008 1.405461 CCTGTTGTACGTCTGTGTCG 58.595 55.000 0.00 0.00 0.00 4.35
4924 5009 1.137513 GCCTGTTGTACGTCTGTGTC 58.862 55.000 0.00 0.00 0.00 3.67
4925 5010 0.462375 TGCCTGTTGTACGTCTGTGT 59.538 50.000 0.00 0.00 0.00 3.72
4926 5011 1.577468 TTGCCTGTTGTACGTCTGTG 58.423 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.