Multiple sequence alignment - TraesCS2A01G308200

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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 TraesCS2A01G308200 chr2A 100.000 6272 0 0 1 6272 529957960 529951689 0.000000e+00 11583.0
1 TraesCS2A01G308200 chr2A 95.211 522 8 2 5751 6272 740376353 740376857 0.000000e+00 809.0
2 TraesCS2A01G308200 chr2A 93.048 187 7 1 3451 3631 529954332 529954146 1.040000e-67 268.0
3 TraesCS2A01G308200 chr2A 93.048 187 7 1 3629 3815 529954510 529954330 1.040000e-67 268.0
4 TraesCS2A01G308200 chr2A 79.420 345 43 14 5748 6068 161932310 161931970 1.060000e-52 219.0
5 TraesCS2A01G308200 chr2A 95.918 49 2 0 4735 4783 170470500 170470452 5.210000e-11 80.5
6 TraesCS2A01G308200 chr2A 100.000 43 0 0 5639 5681 529952280 529952238 5.210000e-11 80.5
7 TraesCS2A01G308200 chr2A 100.000 43 0 0 5681 5723 529952322 529952280 5.210000e-11 80.5
8 TraesCS2A01G308200 chr2D 97.124 4346 97 14 5 4340 392166101 392161774 0.000000e+00 7308.0
9 TraesCS2A01G308200 chr2D 95.938 1354 39 8 4341 5681 392161674 392160324 0.000000e+00 2182.0
10 TraesCS2A01G308200 chr2D 94.022 184 7 1 3451 3630 392162487 392162304 6.190000e-70 276.0
11 TraesCS2A01G308200 chr2D 93.583 187 6 1 3629 3815 392162665 392162485 2.230000e-69 274.0
12 TraesCS2A01G308200 chr2B 93.168 2020 105 13 5 2014 464292723 464290727 0.000000e+00 2935.0
13 TraesCS2A01G308200 chr2B 95.818 1650 50 7 1998 3631 464290625 464288979 0.000000e+00 2647.0
14 TraesCS2A01G308200 chr2B 93.785 724 26 6 3629 4340 464289159 464288443 0.000000e+00 1070.0
15 TraesCS2A01G308200 chr2B 95.031 644 29 2 5041 5681 464287392 464286749 0.000000e+00 1009.0
16 TraesCS2A01G308200 chr2B 88.865 458 27 7 4340 4779 464288248 464287797 5.530000e-150 542.0
17 TraesCS2A01G308200 chr2B 89.231 260 18 7 4794 5049 464287672 464287419 3.650000e-82 316.0
18 TraesCS2A01G308200 chr2B 100.000 70 0 0 5681 5750 464286791 464286722 5.100000e-26 130.0
19 TraesCS2A01G308200 chr5B 99.042 522 5 0 5751 6272 82237407 82236886 0.000000e+00 937.0
20 TraesCS2A01G308200 chr5B 94.476 525 9 3 5748 6272 516462516 516462012 0.000000e+00 791.0
21 TraesCS2A01G308200 chr4B 96.374 524 18 1 5750 6272 588224397 588224920 0.000000e+00 861.0
22 TraesCS2A01G308200 chr4B 87.611 226 20 6 5754 5972 588225353 588225129 8.070000e-64 255.0
23 TraesCS2A01G308200 chr4B 97.143 35 1 0 6085 6119 588224810 588224844 6.790000e-05 60.2
24 TraesCS2A01G308200 chrUn 100.000 384 0 0 3858 4241 480835893 480836276 0.000000e+00 710.0
25 TraesCS2A01G308200 chr7D 84.180 512 54 14 5750 6255 500234861 500234371 7.360000e-129 472.0
26 TraesCS2A01G308200 chr3B 82.364 516 60 15 5750 6255 736158868 736158374 2.700000e-113 420.0
27 TraesCS2A01G308200 chr6B 81.262 507 74 9 5747 6252 588900358 588899872 2.120000e-104 390.0
28 TraesCS2A01G308200 chr7B 79.264 516 56 24 5751 6255 711049133 711049608 4.720000e-81 313.0
29 TraesCS2A01G308200 chr1D 89.610 154 15 1 3825 3978 364493221 364493373 1.780000e-45 195.0
30 TraesCS2A01G308200 chr1D 87.755 49 4 1 4735 4783 77368431 77368385 8.780000e-04 56.5
31 TraesCS2A01G308200 chr1B 87.097 155 19 1 3821 3975 487776231 487776384 2.320000e-39 174.0
32 TraesCS2A01G308200 chr3D 92.000 50 4 0 4734 4783 568838491 568838442 3.140000e-08 71.3
33 TraesCS2A01G308200 chr3D 93.478 46 3 0 4738 4783 473457382 473457427 1.130000e-07 69.4
34 TraesCS2A01G308200 chr1A 91.892 37 3 0 4735 4771 108696015 108695979 1.100000e-02 52.8


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 TraesCS2A01G308200 chr2A 529951689 529957960 6271 True 11583.000000 11583 100.000000 1 6272 1 chr2A.!!$R3 6271
1 TraesCS2A01G308200 chr2A 740376353 740376857 504 False 809.000000 809 95.211000 5751 6272 1 chr2A.!!$F1 521
2 TraesCS2A01G308200 chr2D 392160324 392166101 5777 True 2510.000000 7308 95.166750 5 5681 4 chr2D.!!$R1 5676
3 TraesCS2A01G308200 chr2B 464286722 464292723 6001 True 1235.571429 2935 93.699714 5 5750 7 chr2B.!!$R1 5745
4 TraesCS2A01G308200 chr5B 82236886 82237407 521 True 937.000000 937 99.042000 5751 6272 1 chr5B.!!$R1 521
5 TraesCS2A01G308200 chr5B 516462012 516462516 504 True 791.000000 791 94.476000 5748 6272 1 chr5B.!!$R2 524
6 TraesCS2A01G308200 chr4B 588224397 588224920 523 False 460.600000 861 96.758500 5750 6272 2 chr4B.!!$F1 522

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
500 513 0.311165 TCTAGCGAGGATTAGCGTGC 59.689 55.000 0.00 0.00 38.61 5.34 F
585 598 0.801251 GCATTGAGCGGATATGAGCC 59.199 55.000 0.00 0.00 0.00 4.70 F
1365 1385 1.004560 TTTGGTCTCAGAGCAGCGG 60.005 57.895 6.67 0.00 41.12 5.52 F
1553 1573 2.545731 TGGCCTTTGAAAAAGAAACGC 58.454 42.857 3.32 0.00 0.00 4.84 F
3378 3532 2.488937 TGAACGCATTGATCAGCAACAT 59.511 40.909 7.61 0.00 39.78 2.71 F
4621 5000 1.214175 TCTGGAAGAACTTGGCACCAA 59.786 47.619 1.46 1.46 42.31 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1385 1.002868 TTGAGCCTTCTCTGCAGCC 60.003 57.895 9.47 0.0 40.03 4.85 R
2106 2246 1.696063 ACCTGAAGCAAATGCAGTGT 58.304 45.000 8.28 0.0 45.16 3.55 R
2836 2982 3.119352 GGGACTTTGAAATCTGTGGATGC 60.119 47.826 0.00 0.0 31.75 3.91 R
3534 3688 0.320421 TGGGAGCGTTTTTCCTCTCG 60.320 55.000 0.00 0.0 35.01 4.04 R
4670 5049 0.178992 CCTGAACCAGCCCTTTCACA 60.179 55.000 0.00 0.0 0.00 3.58 R
5686 6219 0.249238 CTCTGAGCATGGCCGTCTAC 60.249 60.000 0.00 0.0 0.00 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
41 42 1.423395 CGCGAGGATGATTTCTAGGC 58.577 55.000 0.00 0.00 0.00 3.93
287 289 4.037923 TGTTTCTTGGTTCTTGGATTCTGC 59.962 41.667 0.00 0.00 0.00 4.26
303 305 1.493950 CTGCGAATCGGAGTGGCATC 61.494 60.000 16.01 0.00 40.30 3.91
341 349 3.186106 CGGCATGACGCATTTCCA 58.814 55.556 8.66 0.00 45.17 3.53
342 350 1.729276 CGGCATGACGCATTTCCAT 59.271 52.632 8.66 0.00 45.17 3.41
343 351 0.593008 CGGCATGACGCATTTCCATG 60.593 55.000 8.66 0.00 45.17 3.66
373 381 5.518848 TCTGAAGTGCATTTTGTTGATGT 57.481 34.783 0.00 0.00 0.00 3.06
402 413 5.453567 AAATGGTAGAACTTCTTGGTTGC 57.546 39.130 0.00 0.00 0.00 4.17
417 428 3.030291 TGGTTGCTGGATTTCAAGTGTT 58.970 40.909 0.00 0.00 0.00 3.32
486 499 6.106673 TGAGCTGGTTACTGTATTTTCTAGC 58.893 40.000 0.00 0.00 0.00 3.42
495 508 9.182933 GTTACTGTATTTTCTAGCGAGGATTAG 57.817 37.037 0.00 0.00 0.00 1.73
500 513 0.311165 TCTAGCGAGGATTAGCGTGC 59.689 55.000 0.00 0.00 38.61 5.34
585 598 0.801251 GCATTGAGCGGATATGAGCC 59.199 55.000 0.00 0.00 0.00 4.70
665 678 9.764363 TTTACATAGGAGATTAGCTTGTACATG 57.236 33.333 0.00 0.00 0.00 3.21
720 733 3.736213 CACGACATTGTGTGATTAGTGC 58.264 45.455 11.56 0.00 38.36 4.40
722 735 3.433274 ACGACATTGTGTGATTAGTGCAG 59.567 43.478 0.00 0.00 0.00 4.41
729 742 7.391554 ACATTGTGTGATTAGTGCAGAAGTTAT 59.608 33.333 0.00 0.00 0.00 1.89
745 758 4.143986 AGTTATAGGCTGGAGTTGAAGC 57.856 45.455 0.00 0.00 38.76 3.86
746 759 3.519510 AGTTATAGGCTGGAGTTGAAGCA 59.480 43.478 0.00 0.00 41.36 3.91
818 833 5.533528 ACAAAAGTTACTGTACCCATGAACC 59.466 40.000 0.00 0.00 0.00 3.62
819 834 4.986054 AAGTTACTGTACCCATGAACCA 57.014 40.909 0.00 0.00 0.00 3.67
826 841 3.879295 CTGTACCCATGAACCAATGCTAG 59.121 47.826 0.00 0.00 0.00 3.42
956 971 5.580297 ACTGTTGTTAAATTTTGCAGGTGTG 59.420 36.000 0.00 0.00 0.00 3.82
963 978 1.464734 TTTTGCAGGTGTGGAACGAA 58.535 45.000 0.00 0.00 42.39 3.85
969 984 2.223711 GCAGGTGTGGAACGAATTGTTT 60.224 45.455 0.00 0.00 42.09 2.83
970 985 3.371168 CAGGTGTGGAACGAATTGTTTG 58.629 45.455 0.00 0.00 42.09 2.93
1365 1385 1.004560 TTTGGTCTCAGAGCAGCGG 60.005 57.895 6.67 0.00 41.12 5.52
1553 1573 2.545731 TGGCCTTTGAAAAAGAAACGC 58.454 42.857 3.32 0.00 0.00 4.84
1837 1857 8.755028 TCCATTGATTCATCACATTTGATTTCT 58.245 29.630 0.00 0.00 40.79 2.52
1985 2005 3.753272 TCTGCAGTGAGGCTATTTTTCAC 59.247 43.478 14.67 0.00 41.10 3.18
2035 2173 8.749354 TCTATGATATTTCCATACGCTACATGT 58.251 33.333 2.69 2.69 0.00 3.21
2106 2246 8.749026 TTGTGTTATATTTTTAAGGCCGGATA 57.251 30.769 5.05 0.00 0.00 2.59
2387 2530 7.429340 GTGGTCGTAATATGCTCAAGATTTTTG 59.571 37.037 0.00 0.00 0.00 2.44
2670 2813 6.659361 ATTCATGTCATCTCTTTCACTTCG 57.341 37.500 0.00 0.00 0.00 3.79
2836 2982 3.822735 TCTTTTGTCAAAGAGATGCCCAG 59.177 43.478 0.00 0.00 42.99 4.45
3042 3188 8.876275 TCAATTTGCTTATTAATGATGAAGGC 57.124 30.769 0.00 0.00 0.00 4.35
3166 3320 7.835682 TCTGTTCCCTGAAACATGAATCATATT 59.164 33.333 0.00 0.00 38.41 1.28
3378 3532 2.488937 TGAACGCATTGATCAGCAACAT 59.511 40.909 7.61 0.00 39.78 2.71
3472 3626 5.636543 GCAACAGAAAAGGAAATGAATCAGG 59.363 40.000 0.00 0.00 0.00 3.86
3534 3688 2.803133 GCTTGTGGCAAAAGAAGGGAAC 60.803 50.000 21.55 0.00 41.35 3.62
3666 3820 3.769739 TCAGACAAATGCTGTACAGGT 57.230 42.857 23.95 12.74 38.84 4.00
3708 3862 1.269936 CCAGCTTGTGGCAAAAGAAGG 60.270 52.381 21.55 16.34 44.79 3.46
3724 3878 4.374689 AGAAGGGAAGGAGAGGAAAAAC 57.625 45.455 0.00 0.00 0.00 2.43
3778 3932 3.031736 GCATCTGGTGAGAACCTACCTA 58.968 50.000 0.00 0.00 37.84 3.08
3779 3933 3.643792 GCATCTGGTGAGAACCTACCTAT 59.356 47.826 0.00 0.00 37.84 2.57
3780 3934 4.833380 GCATCTGGTGAGAACCTACCTATA 59.167 45.833 0.00 0.00 37.84 1.31
4241 4397 7.016153 ACAACAAGATAAGGTATGGAACTGA 57.984 36.000 0.00 0.00 0.00 3.41
4426 4798 7.041372 TCCTAGTTTCTGTTCTGTGCATTTTAC 60.041 37.037 0.00 0.00 0.00 2.01
4621 5000 1.214175 TCTGGAAGAACTTGGCACCAA 59.786 47.619 1.46 1.46 42.31 3.67
4631 5010 3.530535 ACTTGGCACCAAATTTTGTGAC 58.469 40.909 22.76 20.90 35.33 3.67
4759 5141 1.755380 CTTCCTCCGTCCGGAATTAGT 59.245 52.381 5.23 0.00 44.66 2.24
4786 5168 4.460263 GCCCAAATGGATGTATCTACACA 58.540 43.478 0.00 0.00 34.96 3.72
4787 5169 5.072741 GCCCAAATGGATGTATCTACACAT 58.927 41.667 0.00 0.00 41.83 3.21
4833 5326 3.922171 AAGTTTCCAATGCCAAACCAA 57.078 38.095 3.38 0.00 33.66 3.67
4840 5333 4.163427 TCCAATGCCAAACCAAGGAAATA 58.837 39.130 0.00 0.00 0.00 1.40
4843 5336 5.338219 CCAATGCCAAACCAAGGAAATATCA 60.338 40.000 0.00 0.00 0.00 2.15
4881 5374 2.154462 CCCAGCGTTCTTCACTGAAAT 58.846 47.619 0.00 0.00 33.10 2.17
4882 5375 2.095567 CCCAGCGTTCTTCACTGAAATG 60.096 50.000 0.00 0.00 33.10 2.32
4883 5376 2.807967 CCAGCGTTCTTCACTGAAATGA 59.192 45.455 0.00 0.00 33.10 2.57
4886 5379 5.455392 CAGCGTTCTTCACTGAAATGAAAT 58.545 37.500 0.00 0.00 38.12 2.17
4887 5380 5.341462 CAGCGTTCTTCACTGAAATGAAATG 59.659 40.000 0.00 0.00 38.12 2.32
4888 5381 5.239306 AGCGTTCTTCACTGAAATGAAATGA 59.761 36.000 0.00 0.00 38.12 2.57
4889 5382 6.072286 AGCGTTCTTCACTGAAATGAAATGAT 60.072 34.615 0.00 0.00 38.12 2.45
5054 5584 3.003378 AGGTTCGCAGAAGCAAAACTAAC 59.997 43.478 18.01 0.00 45.90 2.34
5065 5595 7.377131 CAGAAGCAAAACTAACAAGTAGCTTTC 59.623 37.037 0.00 0.00 40.73 2.62
5145 5676 4.024556 CAGTTGTTAGTTGAAGAGGCTGTG 60.025 45.833 0.00 0.00 0.00 3.66
5157 5688 3.947841 GCTGTGTTGCGGCGTTCA 61.948 61.111 9.37 2.55 39.99 3.18
5230 5761 1.608055 TGTCAACACATGGAAGCCTG 58.392 50.000 0.00 0.00 0.00 4.85
5308 5839 6.509523 AGGCTACTTTTTGTATGGCCTATA 57.490 37.500 3.32 0.00 45.37 1.31
5325 5856 5.163405 GGCCTATATGTTGTCTCAACTCTGA 60.163 44.000 12.66 0.00 0.00 3.27
5339 5870 1.357079 ACTCTGAACCGTAGTAGGGGT 59.643 52.381 13.33 6.48 38.44 4.95
5406 5937 2.102578 GCTGCATGTAATTTGACCCCT 58.897 47.619 0.00 0.00 0.00 4.79
5466 5997 1.266718 GAAGTGGCGATGCTGAAAACA 59.733 47.619 0.00 0.00 0.00 2.83
5591 6124 1.174712 ACTGTTGGATGTGTGCTGGC 61.175 55.000 0.00 0.00 0.00 4.85
5605 6138 2.022240 GCTGGCTCCTAGCTACGCTT 62.022 60.000 0.00 0.00 41.99 4.68
5685 6218 4.468689 GGAGGCAGGGCGGTGTAC 62.469 72.222 0.00 0.00 0.00 2.90
5688 6221 3.762247 GGCAGGGCGGTGTACGTA 61.762 66.667 0.00 0.00 46.52 3.57
5689 6222 2.202703 GCAGGGCGGTGTACGTAG 60.203 66.667 0.00 0.00 46.52 3.51
5690 6223 2.703798 GCAGGGCGGTGTACGTAGA 61.704 63.158 0.00 0.00 46.52 2.59
5691 6224 1.138247 CAGGGCGGTGTACGTAGAC 59.862 63.158 14.16 14.16 46.52 2.59
5692 6225 2.100991 GGGCGGTGTACGTAGACG 59.899 66.667 15.78 11.94 46.52 4.18
5693 6226 2.100991 GGCGGTGTACGTAGACGG 59.899 66.667 21.44 21.44 46.52 4.79
5694 6227 2.577911 GCGGTGTACGTAGACGGC 60.578 66.667 30.12 30.12 46.52 5.68
5695 6228 2.100991 CGGTGTACGTAGACGGCC 59.899 66.667 15.78 2.58 44.95 6.13
5696 6229 2.689785 CGGTGTACGTAGACGGCCA 61.690 63.158 15.78 0.00 44.95 5.36
5697 6230 1.811860 GGTGTACGTAGACGGCCAT 59.188 57.895 15.78 0.00 44.95 4.40
5698 6231 0.526954 GGTGTACGTAGACGGCCATG 60.527 60.000 15.78 0.00 44.95 3.66
5699 6232 1.140161 TGTACGTAGACGGCCATGC 59.860 57.895 2.24 0.00 44.95 4.06
5700 6233 1.317431 TGTACGTAGACGGCCATGCT 61.317 55.000 2.24 0.00 44.95 3.79
5701 6234 0.594284 GTACGTAGACGGCCATGCTC 60.594 60.000 2.24 0.00 44.95 4.26
5702 6235 1.033202 TACGTAGACGGCCATGCTCA 61.033 55.000 2.24 0.00 44.95 4.26
5703 6236 1.589993 CGTAGACGGCCATGCTCAG 60.590 63.158 2.24 0.00 35.37 3.35
5704 6237 1.816537 GTAGACGGCCATGCTCAGA 59.183 57.895 2.24 0.00 0.00 3.27
5705 6238 0.249238 GTAGACGGCCATGCTCAGAG 60.249 60.000 2.24 0.00 0.00 3.35
5706 6239 2.021068 TAGACGGCCATGCTCAGAGC 62.021 60.000 16.21 16.21 42.82 4.09
5707 6240 4.827087 ACGGCCATGCTCAGAGCG 62.827 66.667 17.81 4.70 46.26 5.03
5708 6241 4.827087 CGGCCATGCTCAGAGCGT 62.827 66.667 17.81 14.90 46.26 5.07
5713 6246 2.898738 ATGCTCAGAGCGTGGGAG 59.101 61.111 16.82 0.00 46.26 4.30
5714 6247 2.729479 ATGCTCAGAGCGTGGGAGG 61.729 63.158 16.82 0.00 46.26 4.30
5715 6248 4.828925 GCTCAGAGCGTGGGAGGC 62.829 72.222 6.67 0.00 0.00 4.70
5716 6249 3.385384 CTCAGAGCGTGGGAGGCA 61.385 66.667 0.00 0.00 0.00 4.75
5717 6250 3.368190 CTCAGAGCGTGGGAGGCAG 62.368 68.421 0.00 0.00 0.00 4.85
5718 6251 4.463879 CAGAGCGTGGGAGGCAGG 62.464 72.222 0.00 0.00 0.00 4.85
5842 6375 2.324014 AAAGACCACCTGCAGCGTGA 62.324 55.000 27.05 0.00 32.77 4.35
6109 6642 9.057089 CGGTAAATGGATAGAGCTATTTTCTTT 57.943 33.333 0.00 0.00 32.31 2.52
6262 6795 2.386661 ACAATAGCCCAGTTCGTCAG 57.613 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.573201 GCGCATAACAGAACCCACTAATAA 59.427 41.667 0.30 0.00 0.00 1.40
2 3 4.124238 GCGCATAACAGAACCCACTAATA 58.876 43.478 0.30 0.00 0.00 0.98
3 4 2.943033 GCGCATAACAGAACCCACTAAT 59.057 45.455 0.30 0.00 0.00 1.73
19 20 2.611473 CCTAGAAATCATCCTCGCGCAT 60.611 50.000 8.75 0.00 0.00 4.73
181 182 4.115199 GCGACCAAGCCTCCCCAT 62.115 66.667 0.00 0.00 0.00 4.00
199 200 4.244862 CAATTAATGGGGCGATTAATGGC 58.755 43.478 13.54 13.54 38.15 4.40
256 258 5.395103 CCAAGAACCAAGAAACACCATGAAA 60.395 40.000 0.00 0.00 0.00 2.69
257 259 4.099266 CCAAGAACCAAGAAACACCATGAA 59.901 41.667 0.00 0.00 0.00 2.57
287 289 1.212616 GAAGATGCCACTCCGATTCG 58.787 55.000 0.00 0.00 0.00 3.34
303 305 3.122278 CGCTTTCAACAAATGGCATGAAG 59.878 43.478 0.00 0.00 33.71 3.02
338 346 3.270027 CACTTCAGATTTACGGCATGGA 58.730 45.455 0.00 0.00 0.00 3.41
339 347 2.223340 GCACTTCAGATTTACGGCATGG 60.223 50.000 0.00 0.00 0.00 3.66
340 348 2.419673 TGCACTTCAGATTTACGGCATG 59.580 45.455 0.00 0.00 0.00 4.06
341 349 2.710377 TGCACTTCAGATTTACGGCAT 58.290 42.857 0.00 0.00 0.00 4.40
342 350 2.177394 TGCACTTCAGATTTACGGCA 57.823 45.000 0.00 0.00 0.00 5.69
343 351 3.764885 AATGCACTTCAGATTTACGGC 57.235 42.857 0.00 0.00 0.00 5.68
402 413 3.996150 AGTGCAACACTTGAAATCCAG 57.004 42.857 0.00 0.00 42.59 3.86
417 428 4.835284 TCTATAACATGACCCAAGTGCA 57.165 40.909 0.00 0.00 0.00 4.57
428 439 4.809673 TGCAGCCGTAGATCTATAACATG 58.190 43.478 5.57 3.56 0.00 3.21
486 499 0.458543 ACAGTGCACGCTAATCCTCG 60.459 55.000 12.01 0.00 0.00 4.63
495 508 1.148310 ACATTCTGTACAGTGCACGC 58.852 50.000 21.99 4.07 0.00 5.34
533 546 5.358725 ACGATGTCCTTGTGTTAAACCTTTT 59.641 36.000 0.00 0.00 0.00 2.27
575 588 7.907214 AAAATACAGTAATCGGCTCATATCC 57.093 36.000 0.00 0.00 0.00 2.59
720 733 5.344743 TCAACTCCAGCCTATAACTTCTG 57.655 43.478 0.00 0.00 0.00 3.02
722 735 4.572795 GCTTCAACTCCAGCCTATAACTTC 59.427 45.833 0.00 0.00 0.00 3.01
729 742 2.040278 ACATTGCTTCAACTCCAGCCTA 59.960 45.455 0.00 0.00 34.91 3.93
745 758 8.711457 GGAACAACAAATGGAAGAATAACATTG 58.289 33.333 0.00 0.00 35.22 2.82
746 759 8.428063 TGGAACAACAAATGGAAGAATAACATT 58.572 29.630 0.00 0.00 33.47 2.71
846 861 3.073062 ACAAGACAAGGAGCAGGTAATGT 59.927 43.478 0.00 0.00 0.00 2.71
956 971 6.416750 CCTCTACAAAACAAACAATTCGTTCC 59.583 38.462 0.00 0.00 36.59 3.62
969 984 8.212312 TCCTTGTAATACAACCTCTACAAAACA 58.788 33.333 1.08 0.00 34.71 2.83
970 985 8.501580 GTCCTTGTAATACAACCTCTACAAAAC 58.498 37.037 1.08 0.00 34.71 2.43
1296 1316 3.502211 CAGACACCTTACATGTCCAAACC 59.498 47.826 0.00 0.00 46.38 3.27
1365 1385 1.002868 TTGAGCCTTCTCTGCAGCC 60.003 57.895 9.47 0.00 40.03 4.85
2035 2173 7.259882 TCCGCGTTCTTCACTAAATAGAATAA 58.740 34.615 4.92 0.00 31.25 1.40
2106 2246 1.696063 ACCTGAAGCAAATGCAGTGT 58.304 45.000 8.28 0.00 45.16 3.55
2387 2530 5.010012 AGTTTTGTGATGTTGATTCCCTGAC 59.990 40.000 0.00 0.00 0.00 3.51
2836 2982 3.119352 GGGACTTTGAAATCTGTGGATGC 60.119 47.826 0.00 0.00 31.75 3.91
3166 3320 7.225011 CAGGTGACTAGAGATACCTACATACA 58.775 42.308 0.00 0.00 41.42 2.29
3472 3626 1.202336 GCCATCCTGTACAGCATTTGC 60.202 52.381 17.86 9.59 42.49 3.68
3534 3688 0.320421 TGGGAGCGTTTTTCCTCTCG 60.320 55.000 0.00 0.00 35.01 4.04
3666 3820 2.116827 ATTAACATTCCCGTTGCCGA 57.883 45.000 0.00 0.00 35.63 5.54
3675 3829 4.202050 CCACAAGCTGGCTATTAACATTCC 60.202 45.833 0.00 0.00 31.36 3.01
3708 3862 2.077627 GAGCGTTTTTCCTCTCCTTCC 58.922 52.381 0.00 0.00 0.00 3.46
4426 4798 2.232452 AGGTTGACAGAGGACAAGATCG 59.768 50.000 0.00 0.00 29.60 3.69
4621 5000 5.459762 CAGTTTTCAGCGATGTCACAAAATT 59.540 36.000 0.00 0.00 0.00 1.82
4631 5010 1.466167 CCTGACCAGTTTTCAGCGATG 59.534 52.381 0.00 0.00 39.43 3.84
4670 5049 0.178992 CCTGAACCAGCCCTTTCACA 60.179 55.000 0.00 0.00 0.00 3.58
4759 5141 2.498644 TACATCCATTTGGGCGACAA 57.501 45.000 0.00 0.00 37.28 3.18
4786 5168 6.156429 GGATAATTTCTACTCCACCCGGATAT 59.844 42.308 0.73 0.00 41.79 1.63
4787 5169 5.482878 GGATAATTTCTACTCCACCCGGATA 59.517 44.000 0.73 0.00 41.79 2.59
4858 5351 1.598130 AGTGAAGAACGCTGGGCAC 60.598 57.895 0.00 0.00 37.99 5.01
5054 5584 5.043248 CACAAACAAAGGGAAAGCTACTTG 58.957 41.667 0.00 0.00 0.00 3.16
5065 5595 8.686334 AGCATTACTATATTCACAAACAAAGGG 58.314 33.333 0.00 0.00 0.00 3.95
5145 5676 2.380410 ACGAGATGAACGCCGCAAC 61.380 57.895 0.00 0.00 0.00 4.17
5157 5688 2.695147 TGGATGAGCATGTACACGAGAT 59.305 45.455 0.00 0.00 0.00 2.75
5230 5761 7.630924 TCTTTCGATCTGTTTCTCTTTTGAAC 58.369 34.615 0.00 0.00 0.00 3.18
5256 5787 5.434408 TCTATCAACTAAGTAGCTCGGTCA 58.566 41.667 0.00 0.00 0.00 4.02
5259 5790 5.473846 TCCATCTATCAACTAAGTAGCTCGG 59.526 44.000 0.00 0.00 0.00 4.63
5308 5839 3.181465 ACGGTTCAGAGTTGAGACAACAT 60.181 43.478 15.29 2.81 34.15 2.71
5325 5856 3.842436 AGAAATGAACCCCTACTACGGTT 59.158 43.478 0.00 0.00 45.12 4.44
5339 5870 4.084641 CGAAAATTTGGCGCAAGAAATGAA 60.085 37.500 10.83 0.00 43.02 2.57
5406 5937 5.607477 ACAAAGAAAACATCGACTCTACCA 58.393 37.500 0.00 0.00 0.00 3.25
5466 5997 6.879400 AGAACAGATTCCTAGCTAACGATTT 58.121 36.000 0.00 0.00 35.18 2.17
5509 6040 0.593128 CTTGTGAAAGGGCGTGGAAG 59.407 55.000 0.00 0.00 0.00 3.46
5556 6087 2.233271 ACAGTCAGCCATGGAAAACTG 58.767 47.619 26.53 26.53 39.90 3.16
5557 6088 2.624838 CAACAGTCAGCCATGGAAAACT 59.375 45.455 18.40 11.65 0.00 2.66
5681 6214 1.140161 GCATGGCCGTCTACGTACA 59.860 57.895 0.00 0.65 37.74 2.90
5683 6216 1.033202 TGAGCATGGCCGTCTACGTA 61.033 55.000 0.00 0.00 37.74 3.57
5685 6218 1.589993 CTGAGCATGGCCGTCTACG 60.590 63.158 0.00 0.00 39.44 3.51
5686 6219 0.249238 CTCTGAGCATGGCCGTCTAC 60.249 60.000 0.00 0.00 0.00 2.59
5687 6220 2.021068 GCTCTGAGCATGGCCGTCTA 62.021 60.000 24.02 0.00 41.89 2.59
5688 6221 2.898738 CTCTGAGCATGGCCGTCT 59.101 61.111 0.00 0.00 0.00 4.18
5689 6222 2.894387 GCTCTGAGCATGGCCGTC 60.894 66.667 24.02 0.00 41.89 4.79
5690 6223 4.827087 CGCTCTGAGCATGGCCGT 62.827 66.667 27.46 0.00 42.58 5.68
5691 6224 4.827087 ACGCTCTGAGCATGGCCG 62.827 66.667 27.46 13.44 42.58 6.13
5692 6225 3.200593 CACGCTCTGAGCATGGCC 61.201 66.667 27.46 0.00 42.58 5.36
5695 6228 1.521010 CTCCCACGCTCTGAGCATG 60.521 63.158 27.46 22.94 42.58 4.06
5696 6229 2.729479 CCTCCCACGCTCTGAGCAT 61.729 63.158 27.46 11.86 42.58 3.79
5697 6230 3.385384 CCTCCCACGCTCTGAGCA 61.385 66.667 27.46 8.34 42.58 4.26
5698 6231 4.828925 GCCTCCCACGCTCTGAGC 62.829 72.222 19.53 19.53 38.02 4.26
5699 6232 3.368190 CTGCCTCCCACGCTCTGAG 62.368 68.421 0.00 0.00 0.00 3.35
5700 6233 3.385384 CTGCCTCCCACGCTCTGA 61.385 66.667 0.00 0.00 0.00 3.27
5701 6234 4.463879 CCTGCCTCCCACGCTCTG 62.464 72.222 0.00 0.00 0.00 3.35
5715 6248 3.740128 ATAGACTTGCGCCGCCCTG 62.740 63.158 6.63 0.00 0.00 4.45
5716 6249 3.470888 ATAGACTTGCGCCGCCCT 61.471 61.111 6.63 0.85 0.00 5.19
5717 6250 3.272334 CATAGACTTGCGCCGCCC 61.272 66.667 6.63 0.00 0.00 6.13
5718 6251 3.941836 GCATAGACTTGCGCCGCC 61.942 66.667 6.63 0.00 32.06 6.13
5719 6252 3.941836 GGCATAGACTTGCGCCGC 61.942 66.667 4.18 0.00 43.71 6.53
5721 6254 2.813179 CGTGGCATAGACTTGCGCC 61.813 63.158 4.18 0.00 43.71 6.53
5722 6255 2.703409 CGTGGCATAGACTTGCGC 59.297 61.111 0.00 0.00 43.71 6.09
5723 6256 1.421410 GACCGTGGCATAGACTTGCG 61.421 60.000 0.00 0.00 43.71 4.85
5724 6257 0.391130 TGACCGTGGCATAGACTTGC 60.391 55.000 0.00 2.19 42.01 4.01
5725 6258 1.935873 CATGACCGTGGCATAGACTTG 59.064 52.381 0.00 0.00 0.00 3.16
5726 6259 1.555075 ACATGACCGTGGCATAGACTT 59.445 47.619 0.00 0.00 0.00 3.01
5727 6260 1.195115 ACATGACCGTGGCATAGACT 58.805 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.