Multiple sequence alignment - TraesCS1B01G351100

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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 TraesCS1B01G351100 chr1B 100.000 3395 0 0 1 3395 581415952 581412558 0.000000e+00 6270
1 TraesCS1B01G351100 chr1A 90.716 2025 128 27 4 1994 528067481 528065483 0.000000e+00 2643
2 TraesCS1B01G351100 chr1A 91.240 742 58 4 2008 2745 528065436 528064698 0.000000e+00 1003
3 TraesCS1B01G351100 chr1A 94.023 619 24 2 2777 3395 528064698 528064093 0.000000e+00 926
4 TraesCS1B01G351100 chr1A 77.433 935 130 44 1 891 528070692 528069795 1.830000e-132 483
5 TraesCS1B01G351100 chr1D 90.675 1866 122 24 1 1831 430470355 430468507 0.000000e+00 2435
6 TraesCS1B01G351100 chr1D 90.337 1604 95 26 1829 3395 430468469 430466889 0.000000e+00 2049
7 TraesCS1B01G351100 chr1D 78.070 912 121 42 21 891 430473499 430472626 1.410000e-138 503
8 TraesCS1B01G351100 chrUn 78.114 1453 212 57 312 1727 110702080 110700697 0.000000e+00 824
9 TraesCS1B01G351100 chrUn 78.947 741 122 20 1001 1725 110688709 110687987 1.100000e-129 473
10 TraesCS1B01G351100 chrUn 85.194 412 49 9 2086 2488 110690941 110690533 2.440000e-111 412
11 TraesCS1B01G351100 chrUn 82.529 435 62 12 2140 2560 110700126 110699692 1.490000e-98 370
12 TraesCS1B01G351100 chrUn 84.751 341 45 4 2123 2456 110687891 110687551 5.430000e-88 335
13 TraesCS1B01G351100 chrUn 83.529 255 36 6 1263 1514 110692093 110691842 2.040000e-57 233
14 TraesCS1B01G351100 chrUn 90.909 99 5 1 3080 3178 104133769 104133863 2.750000e-26 130
15 TraesCS1B01G351100 chr4B 76.669 1453 217 66 309 1725 660517908 660519274 0.000000e+00 693
16 TraesCS1B01G351100 chr4B 76.371 1422 213 59 312 1684 660685614 660684267 0.000000e+00 651
17 TraesCS1B01G351100 chr4B 87.500 336 40 2 2123 2456 660683707 660683372 1.480000e-103 387
18 TraesCS1B01G351100 chr4B 88.179 313 36 1 2123 2434 660519530 660519842 4.140000e-99 372
19 TraesCS1B01G351100 chr5A 86.111 360 36 3 2072 2420 700785563 700785207 3.200000e-100 375
20 TraesCS1B01G351100 chr5A 86.228 334 42 4 2123 2453 700695183 700694851 3.220000e-95 359
21 TraesCS1B01G351100 chr5A 74.795 611 108 24 309 896 700787334 700786747 2.040000e-57 233
22 TraesCS1B01G351100 chr3B 90.909 99 5 1 3080 3178 40135016 40134922 2.750000e-26 130
23 TraesCS1B01G351100 chr3B 86.916 107 9 2 3082 3188 828800902 828800801 7.700000e-22 115
24 TraesCS1B01G351100 chr2D 88.991 109 7 2 3080 3188 133780530 133780427 2.750000e-26 130
25 TraesCS1B01G351100 chr3A 88.073 109 8 2 3080 3188 52048832 52048729 1.280000e-24 124
26 TraesCS1B01G351100 chr7B 85.321 109 9 4 3082 3188 498879198 498879301 4.630000e-19 106


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 TraesCS1B01G351100 chr1B 581412558 581415952 3394 True 6270.000000 6270 100.000000 1 3395 1 chr1B.!!$R1 3394
1 TraesCS1B01G351100 chr1A 528064093 528070692 6599 True 1263.750000 2643 88.353000 1 3395 4 chr1A.!!$R1 3394
2 TraesCS1B01G351100 chr1D 430466889 430473499 6610 True 1662.333333 2435 86.360667 1 3395 3 chr1D.!!$R1 3394
3 TraesCS1B01G351100 chrUn 110699692 110702080 2388 True 597.000000 824 80.321500 312 2560 2 chrUn.!!$R2 2248
4 TraesCS1B01G351100 chrUn 110687551 110692093 4542 True 363.250000 473 83.105250 1001 2488 4 chrUn.!!$R1 1487
5 TraesCS1B01G351100 chr4B 660517908 660519842 1934 False 532.500000 693 82.424000 309 2434 2 chr4B.!!$F1 2125
6 TraesCS1B01G351100 chr4B 660683372 660685614 2242 True 519.000000 651 81.935500 312 2456 2 chr4B.!!$R1 2144
7 TraesCS1B01G351100 chr5A 700785207 700787334 2127 True 304.000000 375 80.453000 309 2420 2 chr5A.!!$R2 2111

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
209 3437 0.239082 TGCATGCAGCTCACTTTTCG 59.761 50.0 18.46 0.0 45.94 3.46 F
210 3438 1.069378 GCATGCAGCTCACTTTTCGC 61.069 55.0 14.21 0.0 41.15 4.70 F
211 3439 0.239082 CATGCAGCTCACTTTTCGCA 59.761 50.0 0.00 0.0 0.00 5.10 F
1492 4816 1.116308 TTCTCGCCAATACGATCCCA 58.884 50.0 0.00 0.0 42.02 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 4813 0.323725 CAGATGGGTGGAGGTTTGGG 60.324 60.0 0.00 0.0 0.0 4.12 R
1490 4814 0.405585 ACAGATGGGTGGAGGTTTGG 59.594 55.0 0.00 0.0 0.0 3.28 R
1615 4948 0.833287 ATCATACCGAAGCTGCCACT 59.167 50.0 0.00 0.0 0.0 4.00 R
3275 7147 0.179045 ACCACTTCTGCGCTCACTTT 60.179 50.0 9.73 0.0 0.0 2.66 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
23 3248 3.134081 TGCTGGGCTGGATAACTACTAAC 59.866 47.826 0.00 0.00 0.00 2.34
56 3282 4.045636 ACTAAAGCCAACACAAAAGCAG 57.954 40.909 0.00 0.00 0.00 4.24
58 3284 3.825143 AAAGCCAACACAAAAGCAGAT 57.175 38.095 0.00 0.00 0.00 2.90
60 3286 3.102052 AGCCAACACAAAAGCAGATTG 57.898 42.857 0.00 0.00 0.00 2.67
95 3321 6.096423 AGCAATATCAGCAACACAATGAAGAT 59.904 34.615 3.33 0.00 0.00 2.40
108 3334 9.961265 AACACAATGAAGATATGCAATGATTAG 57.039 29.630 0.00 0.00 0.00 1.73
124 3350 7.578571 GCAATGATTAGGCTAGTGCTAGTCTAT 60.579 40.741 17.92 10.35 46.18 1.98
163 3391 4.981806 AGCTAAAAGTTGCACAGAACAA 57.018 36.364 0.00 0.00 0.00 2.83
164 3392 5.323371 AGCTAAAAGTTGCACAGAACAAA 57.677 34.783 0.00 0.00 0.00 2.83
165 3393 5.343249 AGCTAAAAGTTGCACAGAACAAAG 58.657 37.500 0.00 0.00 0.00 2.77
166 3394 5.125417 AGCTAAAAGTTGCACAGAACAAAGA 59.875 36.000 0.00 0.00 0.00 2.52
167 3395 5.804979 GCTAAAAGTTGCACAGAACAAAGAA 59.195 36.000 0.00 0.00 0.00 2.52
168 3396 6.237569 GCTAAAAGTTGCACAGAACAAAGAAC 60.238 38.462 0.00 0.00 0.00 3.01
169 3397 4.782019 AAGTTGCACAGAACAAAGAACA 57.218 36.364 0.00 0.00 0.00 3.18
208 3436 2.163815 AGATGCATGCAGCTCACTTTTC 59.836 45.455 31.79 17.33 38.39 2.29
209 3437 0.239082 TGCATGCAGCTCACTTTTCG 59.761 50.000 18.46 0.00 45.94 3.46
210 3438 1.069378 GCATGCAGCTCACTTTTCGC 61.069 55.000 14.21 0.00 41.15 4.70
211 3439 0.239082 CATGCAGCTCACTTTTCGCA 59.761 50.000 0.00 0.00 0.00 5.10
215 3443 2.551887 TGCAGCTCACTTTTCGCATAAA 59.448 40.909 0.00 0.00 0.00 1.40
216 3444 2.911102 GCAGCTCACTTTTCGCATAAAC 59.089 45.455 0.00 0.00 0.00 2.01
219 3447 4.065088 AGCTCACTTTTCGCATAAACAGA 58.935 39.130 0.00 0.00 0.00 3.41
227 3460 6.204688 ACTTTTCGCATAAACAGAAGTGATGA 59.795 34.615 0.00 0.00 0.00 2.92
248 3481 4.466370 TGACCCTGTTCCAACATAGAGTAG 59.534 45.833 0.00 0.00 38.41 2.57
251 3484 3.119101 CCTGTTCCAACATAGAGTAGCGT 60.119 47.826 0.00 0.00 38.41 5.07
305 3538 6.500041 TCCACTTTGTAAACAACAGTAATGC 58.500 36.000 0.00 0.00 39.87 3.56
306 3539 6.320164 TCCACTTTGTAAACAACAGTAATGCT 59.680 34.615 0.00 0.00 39.87 3.79
307 3540 6.978080 CCACTTTGTAAACAACAGTAATGCTT 59.022 34.615 0.00 0.00 39.87 3.91
338 3590 3.056607 GTGGGTTGCAAGCATATGTTTCT 60.057 43.478 28.22 0.00 0.00 2.52
343 3595 5.870978 GGTTGCAAGCATATGTTTCTCATTT 59.129 36.000 23.18 0.00 37.91 2.32
441 3694 7.461749 TCAGAAGGGAAAACATCTTCTAATGT 58.538 34.615 4.76 0.00 43.52 2.71
452 3705 6.985117 ACATCTTCTAATGTTGTGCAAATGT 58.015 32.000 0.00 0.00 36.47 2.71
453 3706 6.864685 ACATCTTCTAATGTTGTGCAAATGTG 59.135 34.615 0.00 0.00 36.47 3.21
476 3729 5.578727 TGTTACATGCCAACAAGAAAACAAC 59.421 36.000 10.23 0.00 33.11 3.32
554 3818 5.827797 TGCAGTTGAAATGAAGAACCTAAGT 59.172 36.000 0.00 0.00 0.00 2.24
559 3823 8.362639 AGTTGAAATGAAGAACCTAAGTACGTA 58.637 33.333 0.00 0.00 0.00 3.57
581 3847 7.869429 ACGTAAAGTACAACTACATGTTTAGCT 59.131 33.333 2.30 0.00 36.63 3.32
592 3858 8.256611 ACTACATGTTTAGCTTCACTACATTG 57.743 34.615 2.30 0.00 27.11 2.82
593 3859 7.878127 ACTACATGTTTAGCTTCACTACATTGT 59.122 33.333 2.30 0.00 27.11 2.71
594 3860 7.510549 ACATGTTTAGCTTCACTACATTGTT 57.489 32.000 0.00 0.00 27.11 2.83
595 3861 8.615878 ACATGTTTAGCTTCACTACATTGTTA 57.384 30.769 0.00 0.00 27.11 2.41
630 3897 9.312904 CAGAAATATGGTACCCATTATTTCCAT 57.687 33.333 27.78 18.07 42.23 3.41
642 3909 7.006509 CCCATTATTTCCATAGAGGTTGTGAT 58.993 38.462 0.00 0.00 39.02 3.06
644 3911 7.941238 CCATTATTTCCATAGAGGTTGTGATCT 59.059 37.037 0.00 0.00 39.02 2.75
654 3929 4.225942 AGAGGTTGTGATCTAAGGAATGCA 59.774 41.667 0.00 0.00 0.00 3.96
710 3989 4.453478 CAGTATACCACAGCCATGCTAATG 59.547 45.833 0.00 0.00 36.40 1.90
784 4071 6.363626 CCATAAAGTTCAGGATCTAATCGACG 59.636 42.308 0.00 0.00 0.00 5.12
793 4080 7.882179 TCAGGATCTAATCGACGAATATCAAA 58.118 34.615 0.00 0.00 0.00 2.69
804 4095 5.549548 CGACGAATATCAAAGACGTTACGTG 60.550 44.000 17.19 0.15 41.37 4.49
805 4096 5.156355 ACGAATATCAAAGACGTTACGTGT 58.844 37.500 17.19 8.85 41.37 4.49
806 4097 6.314018 ACGAATATCAAAGACGTTACGTGTA 58.686 36.000 17.19 0.00 41.37 2.90
807 4098 6.968904 ACGAATATCAAAGACGTTACGTGTAT 59.031 34.615 17.19 4.52 41.37 2.29
817 4108 3.501828 ACGTTACGTGTATACAGGTGACA 59.498 43.478 33.80 19.16 45.45 3.58
820 4111 3.570926 ACGTGTATACAGGTGACACAG 57.429 47.619 25.97 6.67 42.93 3.66
917 4208 7.009631 GTGCAAGTAGTTCATACATAGACACAG 59.990 40.741 0.00 0.00 36.79 3.66
932 4223 4.192317 AGACACAGTTTGTTTCAGGTCTC 58.808 43.478 0.00 0.00 39.17 3.36
956 4247 8.453238 TCTAGAGAGCTAGGTTAACACAATAG 57.547 38.462 8.10 5.20 43.52 1.73
966 4258 5.001232 GGTTAACACAATAGCAGACAAGGA 58.999 41.667 8.10 0.00 0.00 3.36
967 4259 5.106673 GGTTAACACAATAGCAGACAAGGAC 60.107 44.000 8.10 0.00 0.00 3.85
974 4266 1.352083 AGCAGACAAGGACAAGGCTA 58.648 50.000 0.00 0.00 0.00 3.93
994 4286 5.280062 GGCTATTAATTGGTAGTCCTCCTCC 60.280 48.000 0.00 0.00 34.23 4.30
1036 4328 2.037511 CCATTGGTTGTGGCTCATGTTT 59.962 45.455 0.00 0.00 0.00 2.83
1074 4366 5.353956 TGATCCATTTACATCAACTGTTCCG 59.646 40.000 0.00 0.00 39.39 4.30
1182 4474 1.674221 GGTGGCAGTGACATGAGAGTC 60.674 57.143 0.00 0.00 38.99 3.36
1188 4480 3.636300 GCAGTGACATGAGAGTCCTCTAT 59.364 47.826 0.00 0.00 40.61 1.98
1341 4644 8.807948 TTAATTTACTCCTAGCAAGCTCAAAT 57.192 30.769 0.00 0.00 0.00 2.32
1343 4650 2.996631 ACTCCTAGCAAGCTCAAATGG 58.003 47.619 0.00 0.00 0.00 3.16
1488 4812 5.597806 TGTTCTTATTCTCGCCAATACGAT 58.402 37.500 0.00 0.00 42.02 3.73
1489 4813 5.690409 TGTTCTTATTCTCGCCAATACGATC 59.310 40.000 0.00 0.00 42.02 3.69
1490 4814 4.806330 TCTTATTCTCGCCAATACGATCC 58.194 43.478 0.00 0.00 42.02 3.36
1491 4815 2.457366 ATTCTCGCCAATACGATCCC 57.543 50.000 0.00 0.00 42.02 3.85
1492 4816 1.116308 TTCTCGCCAATACGATCCCA 58.884 50.000 0.00 0.00 42.02 4.37
1493 4817 1.116308 TCTCGCCAATACGATCCCAA 58.884 50.000 0.00 0.00 42.02 4.12
1494 4818 1.483004 TCTCGCCAATACGATCCCAAA 59.517 47.619 0.00 0.00 42.02 3.28
1516 4840 1.815003 CTCCACCCATCTGTTTTCTGC 59.185 52.381 0.00 0.00 0.00 4.26
1615 4948 1.553248 CCGACATCCCTGGAACAACTA 59.447 52.381 0.00 0.00 38.70 2.24
1619 4952 2.305927 ACATCCCTGGAACAACTAGTGG 59.694 50.000 0.00 0.00 38.70 4.00
1661 4994 8.497554 GTCATGCATAACAATTTGTTCAATGTT 58.502 29.630 17.64 7.22 40.22 2.71
1686 5020 9.943163 TTATTTTTGGTTTTAGCTGAATTTTGC 57.057 25.926 0.00 0.00 0.00 3.68
1687 5021 6.992063 TTTTGGTTTTAGCTGAATTTTGCA 57.008 29.167 0.00 0.00 0.00 4.08
1741 5188 2.599082 CCTCAAACGACTCGATACAAGC 59.401 50.000 5.20 0.00 0.00 4.01
1859 5353 9.278978 AGCCTAAAGAAGAAAGAACTCTTAAAG 57.721 33.333 0.00 0.00 35.76 1.85
1865 5359 7.051000 AGAAGAAAGAACTCTTAAAGCAGTGT 58.949 34.615 0.00 0.00 35.76 3.55
1866 5360 6.610741 AGAAAGAACTCTTAAAGCAGTGTG 57.389 37.500 0.00 0.00 34.61 3.82
1994 5538 7.937649 ACTGGTTTTGAAGAGTTTTATGGTAC 58.062 34.615 0.00 0.00 0.00 3.34
2036 5614 9.153479 ACAGCAGATTATATTAGAAGACTCCTT 57.847 33.333 0.00 0.00 34.81 3.36
2063 5641 4.930405 GCCTAGAACTGAACAAAGTAGACC 59.070 45.833 0.00 0.00 0.00 3.85
2066 5644 5.353394 AGAACTGAACAAAGTAGACCACA 57.647 39.130 0.00 0.00 0.00 4.17
2068 5646 5.992217 AGAACTGAACAAAGTAGACCACATC 59.008 40.000 0.00 0.00 0.00 3.06
2084 5662 5.670485 ACCACATCGCAGATAAATGACTAA 58.330 37.500 0.00 0.00 45.12 2.24
2238 6068 2.300967 CCAGCAACTAGGCAGGGGA 61.301 63.158 0.00 0.00 36.85 4.81
2280 6110 1.532437 CGACACAATTTCAGCTGCAGA 59.468 47.619 20.43 0.00 0.00 4.26
2352 6182 2.307098 CTGTCAAAGGGAAGGTGGATCT 59.693 50.000 0.00 0.00 0.00 2.75
2445 6284 7.710907 CCATTATATGCTGTACTGTAGTGTTGT 59.289 37.037 1.46 0.00 0.00 3.32
2447 6286 9.745880 ATTATATGCTGTACTGTAGTGTTGTAC 57.254 33.333 1.46 0.00 37.60 2.90
2588 6455 5.994250 TCATGGAAAGTATTCTTGAGGGAG 58.006 41.667 0.00 0.00 35.79 4.30
2605 6472 6.395629 TGAGGGAGTACAAAAGATAAACTCG 58.604 40.000 0.00 0.00 37.93 4.18
2607 6474 5.482878 AGGGAGTACAAAAGATAAACTCGGA 59.517 40.000 0.00 0.00 37.93 4.55
2617 6484 9.893305 CAAAAGATAAACTCGGACTTTTACAAT 57.107 29.630 0.00 0.00 38.26 2.71
2661 6531 5.454755 TAGTTTCTACTCAGCACCTGCTTTT 60.455 40.000 0.00 0.00 41.74 2.27
2679 6549 9.788960 CCTGCTTTTCATTTTAATAGGTTCTAC 57.211 33.333 0.00 0.00 0.00 2.59
2734 6604 7.368198 AGTTATTTTGGAAAGTAAGCCCAAA 57.632 32.000 0.00 0.00 45.16 3.28
2772 6644 6.909550 AGGCAATATTGGTCAACTTTGTAA 57.090 33.333 17.02 0.00 0.00 2.41
2852 6724 1.398958 TTCAAAGCAACAGGGGTGCC 61.399 55.000 2.08 0.00 0.00 5.01
2956 6828 3.843027 AGAAGCATATCATCGGGAGGAAT 59.157 43.478 0.00 0.00 0.00 3.01
3047 6919 2.259618 GTTCGATAAAGTGCGAGCTCA 58.740 47.619 15.40 0.00 37.85 4.26
3071 6943 3.518705 AGATCTCAAACTGCAGTCCAGAT 59.481 43.478 24.66 24.66 44.64 2.90
3073 6945 4.462508 TCTCAAACTGCAGTCCAGATAG 57.537 45.455 21.95 11.82 44.64 2.08
3095 6967 4.020128 AGTTCACTGTCCATTTCCTCTACC 60.020 45.833 0.00 0.00 0.00 3.18
3119 6991 0.326264 TCCTTGCTGCTTCCTTCTCC 59.674 55.000 0.00 0.00 0.00 3.71
3149 7021 0.689623 GATCCCCATACAGGAGGCTG 59.310 60.000 0.00 0.00 41.22 4.85
3161 7033 1.381928 GGAGGCTGACATGTGGCATG 61.382 60.000 18.23 7.48 29.25 4.06
3180 7052 5.099484 CATGTATGCTGCAATCGTGTAAT 57.901 39.130 6.36 0.00 0.00 1.89
3181 7053 5.513376 CATGTATGCTGCAATCGTGTAATT 58.487 37.500 6.36 0.00 0.00 1.40
3281 7153 4.705110 TGATCTCTGAAACCCAAAGTGA 57.295 40.909 0.00 0.00 0.00 3.41
3332 7204 5.181811 CACCTGCAACATTCAGATAACTTGA 59.818 40.000 0.00 0.00 33.54 3.02
3346 7218 8.749354 TCAGATAACTTGACATAAGCAGAAGTA 58.251 33.333 0.00 0.00 0.00 2.24
3368 7240 5.204673 ACAGAGCAAATAATCGAAACGTC 57.795 39.130 0.00 0.00 0.00 4.34
3377 7249 4.957363 CGAAACGTCGTGCAAACA 57.043 50.000 0.00 0.00 42.53 2.83
3385 7257 0.315869 GTCGTGCAAACAACACCTCG 60.316 55.000 0.00 0.00 34.45 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.101917 GCGTTAGTAGTTATCCAGCCCA 59.898 50.000 0.00 0.00 0.00 5.36
6 7 3.121544 GTGCGTTAGTAGTTATCCAGCC 58.878 50.000 0.00 0.00 0.00 4.85
23 3248 2.031857 TGGCTTTAGTTTTAACCGTGCG 60.032 45.455 0.00 0.00 0.00 5.34
56 3282 8.084073 TGCTGATATTGCTTATTTAAGGCAATC 58.916 33.333 14.25 5.00 39.01 2.67
58 3284 7.345422 TGCTGATATTGCTTATTTAAGGCAA 57.655 32.000 0.00 0.00 35.47 4.52
60 3286 7.168135 GTGTTGCTGATATTGCTTATTTAAGGC 59.832 37.037 0.00 0.00 33.95 4.35
95 3321 5.233083 AGCACTAGCCTAATCATTGCATA 57.767 39.130 0.00 0.00 43.56 3.14
108 3334 6.912082 GGTAGTTTATAGACTAGCACTAGCC 58.088 44.000 21.50 7.64 45.39 3.93
163 3391 6.899393 TCTTGAAGCCATTGTTATGTTCTT 57.101 33.333 0.00 0.00 0.00 2.52
164 3392 6.716628 TCTTCTTGAAGCCATTGTTATGTTCT 59.283 34.615 5.56 0.00 0.00 3.01
165 3393 6.913170 TCTTCTTGAAGCCATTGTTATGTTC 58.087 36.000 5.56 0.00 0.00 3.18
166 3394 6.899393 TCTTCTTGAAGCCATTGTTATGTT 57.101 33.333 5.56 0.00 0.00 2.71
167 3395 6.626623 GCATCTTCTTGAAGCCATTGTTATGT 60.627 38.462 5.56 0.00 33.69 2.29
168 3396 5.747197 GCATCTTCTTGAAGCCATTGTTATG 59.253 40.000 5.56 3.60 33.69 1.90
169 3397 5.419788 TGCATCTTCTTGAAGCCATTGTTAT 59.580 36.000 5.56 0.00 38.50 1.89
208 3436 3.063997 GGGTCATCACTTCTGTTTATGCG 59.936 47.826 0.00 0.00 0.00 4.73
209 3437 4.095483 CAGGGTCATCACTTCTGTTTATGC 59.905 45.833 0.00 0.00 0.00 3.14
210 3438 5.248640 ACAGGGTCATCACTTCTGTTTATG 58.751 41.667 0.00 0.00 35.15 1.90
211 3439 5.505181 ACAGGGTCATCACTTCTGTTTAT 57.495 39.130 0.00 0.00 35.15 1.40
215 3443 2.039084 GGAACAGGGTCATCACTTCTGT 59.961 50.000 0.00 0.00 38.06 3.41
216 3444 2.038952 TGGAACAGGGTCATCACTTCTG 59.961 50.000 0.00 0.00 33.14 3.02
219 3447 2.174639 TGTTGGAACAGGGTCATCACTT 59.825 45.455 0.00 0.00 42.39 3.16
227 3460 3.197983 GCTACTCTATGTTGGAACAGGGT 59.802 47.826 0.00 0.00 43.04 4.34
248 3481 2.355009 CCTGCCAAGTTGCAACGC 60.355 61.111 23.21 20.20 41.51 4.84
251 3484 0.682532 TGTGACCTGCCAAGTTGCAA 60.683 50.000 0.00 0.00 41.51 4.08
282 3515 6.503524 AGCATTACTGTTGTTTACAAAGTGG 58.496 36.000 14.83 9.10 37.63 4.00
305 3538 1.539388 TGCAACCCACTTAATCGCAAG 59.461 47.619 0.00 0.00 0.00 4.01
306 3539 1.610363 TGCAACCCACTTAATCGCAA 58.390 45.000 0.00 0.00 0.00 4.85
307 3540 1.539388 CTTGCAACCCACTTAATCGCA 59.461 47.619 0.00 0.00 0.00 5.10
338 3590 9.679661 TTGCATAAAATGGACTAGTAGAAATGA 57.320 29.630 3.59 0.00 0.00 2.57
343 3595 7.072454 AGGGATTGCATAAAATGGACTAGTAGA 59.928 37.037 3.59 0.00 0.00 2.59
389 3641 7.189079 ACTCATATTCCTTATAGCTTAGGGC 57.811 40.000 0.00 0.00 42.19 5.19
429 3682 6.864685 ACACATTTGCACAACATTAGAAGATG 59.135 34.615 0.00 0.00 0.00 2.90
435 3688 7.619776 GCATGTAACACATTTGCACAACATTAG 60.620 37.037 0.00 0.00 36.53 1.73
441 3694 3.181472 TGGCATGTAACACATTTGCACAA 60.181 39.130 7.08 0.00 36.53 3.33
452 3705 5.330455 TGTTTTCTTGTTGGCATGTAACA 57.670 34.783 11.89 11.89 36.34 2.41
453 3706 5.578727 TGTTGTTTTCTTGTTGGCATGTAAC 59.421 36.000 7.71 7.71 0.00 2.50
554 3818 9.128107 GCTAAACATGTAGTTGTACTTTACGTA 57.872 33.333 0.00 0.00 41.19 3.57
559 3823 8.557029 GTGAAGCTAAACATGTAGTTGTACTTT 58.443 33.333 0.00 0.00 41.19 2.66
567 3831 7.878127 ACAATGTAGTGAAGCTAAACATGTAGT 59.122 33.333 0.00 0.00 29.50 2.73
577 3843 9.953565 AACCTAATTAACAATGTAGTGAAGCTA 57.046 29.630 0.00 0.00 0.00 3.32
630 3897 5.425217 TGCATTCCTTAGATCACAACCTCTA 59.575 40.000 0.00 0.00 0.00 2.43
642 3909 5.509163 GGCGATAGTTAGTGCATTCCTTAGA 60.509 44.000 0.00 0.00 39.35 2.10
644 3911 4.502604 GGGCGATAGTTAGTGCATTCCTTA 60.503 45.833 0.00 0.00 39.35 2.69
654 3929 4.189231 GTGAATTGTGGGCGATAGTTAGT 58.811 43.478 0.00 0.00 39.35 2.24
710 3989 1.198637 GCATGCTTAAGCCATCCGATC 59.801 52.381 24.30 2.01 41.18 3.69
784 4071 9.225201 TGTATACACGTAACGTCTTTGATATTC 57.775 33.333 0.08 0.00 38.32 1.75
793 4080 4.002982 TCACCTGTATACACGTAACGTCT 58.997 43.478 0.08 0.00 38.32 4.18
804 4095 5.577164 GTCATGTTCTGTGTCACCTGTATAC 59.423 44.000 0.00 0.00 0.00 1.47
805 4096 5.621329 CGTCATGTTCTGTGTCACCTGTATA 60.621 44.000 0.00 0.00 0.00 1.47
806 4097 4.569943 GTCATGTTCTGTGTCACCTGTAT 58.430 43.478 0.00 0.00 0.00 2.29
807 4098 3.552068 CGTCATGTTCTGTGTCACCTGTA 60.552 47.826 0.00 0.00 0.00 2.74
817 4108 4.983671 TGATACTAGCGTCATGTTCTGT 57.016 40.909 0.00 0.00 0.00 3.41
820 4111 6.648725 AGTTTTGATACTAGCGTCATGTTC 57.351 37.500 0.00 0.00 0.00 3.18
917 4208 4.926832 GCTCTCTAGAGACCTGAAACAAAC 59.073 45.833 18.76 0.00 44.74 2.93
932 4223 7.142680 GCTATTGTGTTAACCTAGCTCTCTAG 58.857 42.308 2.48 0.00 41.52 2.43
956 4247 2.409948 ATAGCCTTGTCCTTGTCTGC 57.590 50.000 0.00 0.00 0.00 4.26
966 4258 6.409349 GGAGGACTACCAATTAATAGCCTTGT 60.409 42.308 10.08 0.00 38.94 3.16
967 4259 5.998363 GGAGGACTACCAATTAATAGCCTTG 59.002 44.000 10.08 0.00 38.94 3.61
974 4266 5.289510 ACTGGAGGAGGACTACCAATTAAT 58.710 41.667 0.00 0.00 38.94 1.40
994 4286 0.313987 TCCGCTGCCGACATATACTG 59.686 55.000 0.00 0.00 36.29 2.74
1074 4366 3.543680 TTGTTGTAGGCTATCCTGAGC 57.456 47.619 0.00 0.00 44.08 4.26
1182 4474 4.484912 AGAAGCTTACCAGGGTATAGAGG 58.515 47.826 0.00 0.00 0.00 3.69
1188 4480 4.944177 AGAGTTAGAAGCTTACCAGGGTA 58.056 43.478 0.00 0.00 0.00 3.69
1334 4637 8.408601 ACAAGTTAACATATGATCCATTTGAGC 58.591 33.333 10.38 0.00 29.79 4.26
1341 4644 8.862325 ACTCAAACAAGTTAACATATGATCCA 57.138 30.769 10.38 0.00 0.00 3.41
1488 4812 0.477597 AGATGGGTGGAGGTTTGGGA 60.478 55.000 0.00 0.00 0.00 4.37
1489 4813 0.323725 CAGATGGGTGGAGGTTTGGG 60.324 60.000 0.00 0.00 0.00 4.12
1490 4814 0.405585 ACAGATGGGTGGAGGTTTGG 59.594 55.000 0.00 0.00 0.00 3.28
1491 4815 2.292828 AACAGATGGGTGGAGGTTTG 57.707 50.000 0.00 0.00 0.00 2.93
1492 4816 3.117131 AGAAAACAGATGGGTGGAGGTTT 60.117 43.478 0.00 0.00 0.00 3.27
1493 4817 2.447047 AGAAAACAGATGGGTGGAGGTT 59.553 45.455 0.00 0.00 0.00 3.50
1494 4818 2.065799 AGAAAACAGATGGGTGGAGGT 58.934 47.619 0.00 0.00 0.00 3.85
1516 4840 4.827284 AGCATATATCAAAAGTTTCGGGGG 59.173 41.667 0.00 0.00 0.00 5.40
1596 4929 2.233922 ACTAGTTGTTCCAGGGATGTCG 59.766 50.000 0.00 0.00 0.00 4.35
1615 4948 0.833287 ATCATACCGAAGCTGCCACT 59.167 50.000 0.00 0.00 0.00 4.00
1619 4952 1.939974 TGACATCATACCGAAGCTGC 58.060 50.000 0.00 0.00 0.00 5.25
1661 4994 9.113838 TGCAAAATTCAGCTAAAACCAAAAATA 57.886 25.926 0.00 0.00 0.00 1.40
1686 5020 6.387041 AACATGACCTGATTTATGCATCTG 57.613 37.500 0.19 0.00 0.00 2.90
1687 5021 7.776969 ACTTAACATGACCTGATTTATGCATCT 59.223 33.333 0.19 0.00 0.00 2.90
1694 5028 9.010029 GGAAAGAACTTAACATGACCTGATTTA 57.990 33.333 0.00 0.00 0.00 1.40
1703 5066 6.017440 CGTTTGAGGGAAAGAACTTAACATGA 60.017 38.462 0.00 0.00 0.00 3.07
1800 5253 9.088987 ACAAATGTCATTTTACCCTGTTTAGAT 57.911 29.630 8.12 0.00 0.00 1.98
1859 5353 6.803154 AGGAAATTCTTAAGTACACACTGC 57.197 37.500 1.63 0.00 34.36 4.40
1916 5451 7.899330 GCATGAATTTTGTGTTTGTACATATGC 59.101 33.333 1.58 0.00 36.50 3.14
1919 5454 8.877808 TTGCATGAATTTTGTGTTTGTACATA 57.122 26.923 0.00 0.00 36.50 2.29
1991 5535 7.610692 TCTGCTGTATATGTATAGGGAGTGTAC 59.389 40.741 0.00 0.00 0.00 2.90
1994 5538 7.652524 ATCTGCTGTATATGTATAGGGAGTG 57.347 40.000 0.00 0.00 0.00 3.51
2032 5610 4.787551 TGTTCAGTTCTAGGCAAAAAGGA 58.212 39.130 0.00 0.00 0.00 3.36
2036 5614 7.012044 GTCTACTTTGTTCAGTTCTAGGCAAAA 59.988 37.037 0.00 0.00 0.00 2.44
2063 5641 7.633621 ACATTTAGTCATTTATCTGCGATGTG 58.366 34.615 0.00 0.06 0.00 3.21
2066 5644 8.345565 GGAAACATTTAGTCATTTATCTGCGAT 58.654 33.333 0.00 0.00 0.00 4.58
2068 5646 7.429340 GTGGAAACATTTAGTCATTTATCTGCG 59.571 37.037 0.00 0.00 46.14 5.18
2084 5662 7.287696 AGAGTAATTCAACTTGGTGGAAACATT 59.712 33.333 0.00 0.00 46.14 2.71
2145 5975 1.364626 CTACAAGCTCTTGGCCTGCG 61.365 60.000 3.32 0.00 44.45 5.18
2238 6068 3.784338 CACATCTGGTGCAAAAACTGTT 58.216 40.909 0.00 0.00 41.36 3.16
2280 6110 0.666374 GGTACTGCCGTGCAAAGTTT 59.334 50.000 0.00 0.00 38.41 2.66
2352 6182 0.322187 GCCTAAACCTTCTTCCGCCA 60.322 55.000 0.00 0.00 0.00 5.69
2523 6390 9.976776 ATGATTGAGATATATTCCATCAAGCTT 57.023 29.630 14.60 0.00 37.23 3.74
2545 6412 8.663167 TCCATGATCAGGTGATTAACTAATGAT 58.337 33.333 6.62 0.00 34.37 2.45
2560 6427 6.485984 CCTCAAGAATACTTTCCATGATCAGG 59.514 42.308 0.09 0.00 33.70 3.86
2588 6455 9.803130 GTAAAAGTCCGAGTTTATCTTTTGTAC 57.197 33.333 1.55 0.00 38.31 2.90
2670 6540 9.431887 GTGTGTTGATTTATTCAGTAGAACCTA 57.568 33.333 0.00 0.00 36.39 3.08
2672 6542 8.230486 CAGTGTGTTGATTTATTCAGTAGAACC 58.770 37.037 0.00 0.00 36.39 3.62
2719 6589 9.582431 GTCTAAAATATTTTGGGCTTACTTTCC 57.418 33.333 21.19 0.00 31.60 3.13
2725 6595 8.463607 CCTTTCGTCTAAAATATTTTGGGCTTA 58.536 33.333 21.76 10.62 32.03 3.09
2734 6604 9.965824 CCAATATTGCCTTTCGTCTAAAATATT 57.034 29.630 10.11 0.00 0.00 1.28
2798 6670 0.331616 ACATTGGACCTACCTTGGGC 59.668 55.000 0.00 0.00 39.86 5.36
2852 6724 5.989551 TGATGTAATGATGTGAATGTCCG 57.010 39.130 0.00 0.00 0.00 4.79
2956 6828 2.028112 CACCTTGGGAAGAAGTGATCGA 60.028 50.000 0.00 0.00 0.00 3.59
3047 6919 2.902486 TGGACTGCAGTTTGAGATCTCT 59.098 45.455 22.65 0.00 0.00 3.10
3071 6943 5.187186 GGTAGAGGAAATGGACAGTGAACTA 59.813 44.000 0.00 0.00 0.00 2.24
3073 6945 4.020128 AGGTAGAGGAAATGGACAGTGAAC 60.020 45.833 0.00 0.00 0.00 3.18
3095 6967 2.197283 AGGAAGCAGCAAGGAAGAAG 57.803 50.000 0.00 0.00 0.00 2.85
3119 6991 3.889538 TGTATGGGGATCTAACAGACGAG 59.110 47.826 0.00 0.00 0.00 4.18
3161 7033 7.483375 TGTTTTAATTACACGATTGCAGCATAC 59.517 33.333 0.00 0.00 0.00 2.39
3180 7052 9.340695 GTTGATGACAATCGATTCATGTTTTAA 57.659 29.630 15.60 2.79 38.32 1.52
3181 7053 8.729756 AGTTGATGACAATCGATTCATGTTTTA 58.270 29.630 15.60 1.78 38.32 1.52
3244 7116 0.973632 ATCAACCCGTGAGTGCAGTA 59.026 50.000 0.00 0.00 40.43 2.74
3275 7147 0.179045 ACCACTTCTGCGCTCACTTT 60.179 50.000 9.73 0.00 0.00 2.66
3332 7204 4.808414 TGCTCTGTACTTCTGCTTATGT 57.192 40.909 0.00 0.00 0.00 2.29
3346 7218 5.204673 GACGTTTCGATTATTTGCTCTGT 57.795 39.130 0.00 0.00 0.00 3.41
3368 7240 1.654137 GCGAGGTGTTGTTTGCACG 60.654 57.895 0.00 0.00 37.70 5.34


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

AutoCloner maintained by Alex Coulton.