Multiple sequence alignment - TraesCS3D01G179000

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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 TraesCS3D01G179000 chr3D 100.000 4691 0 0 1 4691 160704725 160709415 0.000000e+00 8663
1 TraesCS3D01G179000 chr3A 95.500 3533 95 38 1 3519 187253883 187257365 0.000000e+00 5585
2 TraesCS3D01G179000 chr3A 90.698 817 49 13 3881 4691 12593070 12592275 0.000000e+00 1062
3 TraesCS3D01G179000 chr3A 90.575 817 50 13 3881 4691 12608699 12607904 0.000000e+00 1057
4 TraesCS3D01G179000 chr3A 96.685 362 9 3 3512 3870 187272568 187272929 2.420000e-167 599
5 TraesCS3D01G179000 chr3B 94.232 1907 82 15 1796 3689 237494675 237496566 0.000000e+00 2887
6 TraesCS3D01G179000 chr3B 93.281 1027 41 13 682 1706 237493643 237494643 0.000000e+00 1489
7 TraesCS3D01G179000 chr3B 85.227 176 12 7 3691 3866 237500019 237500180 8.070000e-38 169
8 TraesCS3D01G179000 chr1B 91.299 816 56 9 3881 4691 665452348 665451543 0.000000e+00 1099
9 TraesCS3D01G179000 chr7D 91.141 824 43 15 3880 4690 561542280 561543086 0.000000e+00 1090
10 TraesCS3D01G179000 chr7D 91.187 817 50 12 3880 4689 566252167 566251366 0.000000e+00 1090
11 TraesCS3D01G179000 chr4A 88.739 817 56 11 3880 4691 602242596 602243381 0.000000e+00 966
12 TraesCS3D01G179000 chr7A 88.793 812 54 20 3883 4691 608509094 608508317 0.000000e+00 961
13 TraesCS3D01G179000 chr5A 89.631 434 39 5 3880 4313 306991337 306990910 8.870000e-152 547
14 TraesCS3D01G179000 chr5A 79.792 480 87 8 3175 3652 585020949 585021420 1.620000e-89 340
15 TraesCS3D01G179000 chr5A 91.827 208 15 2 4486 4691 306963508 306963301 5.940000e-74 289
16 TraesCS3D01G179000 chr5A 91.509 212 14 4 4482 4691 306972887 306972678 5.940000e-74 289
17 TraesCS3D01G179000 chr5A 77.249 378 80 6 3278 3652 585398643 585399017 2.840000e-52 217
18 TraesCS3D01G179000 chr6D 89.785 372 28 9 3881 4249 446950071 446950435 7.110000e-128 468
19 TraesCS3D01G179000 chr5D 82.825 361 62 0 3292 3652 464818152 464818512 1.630000e-84 324


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 TraesCS3D01G179000 chr3D 160704725 160709415 4690 False 8663 8663 100.000000 1 4691 1 chr3D.!!$F1 4690
1 TraesCS3D01G179000 chr3A 187253883 187257365 3482 False 5585 5585 95.500000 1 3519 1 chr3A.!!$F1 3518
2 TraesCS3D01G179000 chr3A 12592275 12593070 795 True 1062 1062 90.698000 3881 4691 1 chr3A.!!$R1 810
3 TraesCS3D01G179000 chr3A 12607904 12608699 795 True 1057 1057 90.575000 3881 4691 1 chr3A.!!$R2 810
4 TraesCS3D01G179000 chr3B 237493643 237500180 6537 False 1515 2887 90.913333 682 3866 3 chr3B.!!$F1 3184
5 TraesCS3D01G179000 chr1B 665451543 665452348 805 True 1099 1099 91.299000 3881 4691 1 chr1B.!!$R1 810
6 TraesCS3D01G179000 chr7D 561542280 561543086 806 False 1090 1090 91.141000 3880 4690 1 chr7D.!!$F1 810
7 TraesCS3D01G179000 chr7D 566251366 566252167 801 True 1090 1090 91.187000 3880 4689 1 chr7D.!!$R1 809
8 TraesCS3D01G179000 chr4A 602242596 602243381 785 False 966 966 88.739000 3880 4691 1 chr4A.!!$F1 811
9 TraesCS3D01G179000 chr7A 608508317 608509094 777 True 961 961 88.793000 3883 4691 1 chr7A.!!$R1 808

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
926 930 0.037447 AAAGGCAGAGTGCTCCTTCC 59.963 55.0 0.0 0.0 44.28 3.46 F
1807 1829 0.534203 AACCCACTTGCACCTACGTG 60.534 55.0 0.0 0.0 43.35 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 2423 0.109532 TGATGAGGAAACGGTTGGCA 59.89 50.0 0.0 0.00 0.00 4.92 R
3703 7184 0.390472 GAGTTTCCCTCAGTGAGCGG 60.39 60.0 15.1 16.36 40.17 5.52 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
27 28 4.670199 TCGATCTACGAGGGGCAA 57.330 55.556 0.00 0.00 46.45 4.52
41 42 2.302733 AGGGGCAAACAAATTGGACATC 59.697 45.455 0.00 0.00 39.54 3.06
92 93 5.181748 CCTTCTTTTCCTCTAGTGGATGTG 58.818 45.833 14.15 7.53 35.83 3.21
142 144 0.459078 GTTAGAGGGGTGGTACTCGC 59.541 60.000 0.00 0.00 38.72 5.03
145 147 3.061260 GAGGGGTGGTACTCGCGAC 62.061 68.421 3.71 0.00 35.59 5.19
158 160 4.747529 GCGACGTTAGGGGCGGTT 62.748 66.667 0.00 0.00 0.00 4.44
161 163 1.739196 GACGTTAGGGGCGGTTGAC 60.739 63.158 0.00 0.00 0.00 3.18
168 170 3.961414 GGGCGGTTGACAAGGGGA 61.961 66.667 0.00 0.00 0.00 4.81
181 183 1.279271 CAAGGGGAAGACGAGTTGGAT 59.721 52.381 0.00 0.00 0.00 3.41
194 196 1.918262 AGTTGGATGATGGGAGCTTGA 59.082 47.619 0.00 0.00 0.00 3.02
228 231 4.828925 GCCTCCTGCTCCTGCGAC 62.829 72.222 0.00 0.00 43.34 5.19
322 325 1.278637 GGTTTCAGTCGCGGTGTTG 59.721 57.895 6.13 0.00 0.00 3.33
323 326 1.278637 GTTTCAGTCGCGGTGTTGG 59.721 57.895 6.13 0.00 0.00 3.77
324 327 2.539338 TTTCAGTCGCGGTGTTGGC 61.539 57.895 6.13 0.00 0.00 4.52
325 328 4.980805 TCAGTCGCGGTGTTGGCC 62.981 66.667 6.13 0.00 0.00 5.36
406 409 1.138266 TCGCGGAAGGAGATAAAAGGG 59.862 52.381 6.13 0.00 0.00 3.95
414 417 5.648526 GGAAGGAGATAAAAGGGTTGAGAAC 59.351 44.000 0.00 0.00 0.00 3.01
438 441 5.243730 CCCTCCTCAAACTGCTTAATTTTGA 59.756 40.000 0.00 0.00 35.68 2.69
475 478 3.825908 TTGAGGAGCAACCCCTATTTT 57.174 42.857 0.00 0.00 40.05 1.82
514 517 5.648092 CGGTTTTGAGGGAAGATCTACAAAT 59.352 40.000 0.00 0.00 0.00 2.32
572 575 4.081972 GGAAAGAAGATTTGAGGAAAGGGC 60.082 45.833 0.00 0.00 0.00 5.19
599 602 5.112686 AGATGCTCTTACTGAAAATCGGAC 58.887 41.667 0.00 0.00 0.00 4.79
617 620 3.118555 CGGACAACCCACTTATCATGGTA 60.119 47.826 0.00 0.00 35.23 3.25
694 697 3.411446 TCAGATGGTTCAAATGCGTCTT 58.589 40.909 0.00 0.00 0.00 3.01
695 698 4.574892 TCAGATGGTTCAAATGCGTCTTA 58.425 39.130 0.00 0.00 0.00 2.10
808 812 5.120674 ACAAAAGCTCTTGAACAAAGCAAAC 59.879 36.000 6.82 0.00 38.51 2.93
896 900 3.267900 CGGATAAGTACGCACTGGG 57.732 57.895 0.00 0.00 34.36 4.45
897 901 0.742505 CGGATAAGTACGCACTGGGA 59.257 55.000 0.00 0.00 34.36 4.37
898 902 1.340248 CGGATAAGTACGCACTGGGAT 59.660 52.381 0.00 0.00 34.36 3.85
899 903 2.755650 GGATAAGTACGCACTGGGATG 58.244 52.381 0.00 0.00 34.36 3.51
901 905 0.828022 TAAGTACGCACTGGGATGGG 59.172 55.000 0.00 0.00 34.36 4.00
902 906 2.513897 GTACGCACTGGGATGGGC 60.514 66.667 0.00 0.00 36.02 5.36
906 910 4.101448 GCACTGGGATGGGCGAGT 62.101 66.667 0.00 0.00 0.00 4.18
926 930 0.037447 AAAGGCAGAGTGCTCCTTCC 59.963 55.000 0.00 0.00 44.28 3.46
1241 1261 5.104193 AGGAGTTCTTCATAGGTACTCCGTA 60.104 44.000 12.44 0.00 46.74 4.02
1454 1474 4.891727 GGCATCGACGCCGTCCAT 62.892 66.667 6.81 0.61 43.52 3.41
1544 1564 8.169977 ACCTAGGTCAATAACGTTAATCGATA 57.830 34.615 9.21 1.40 42.86 2.92
1730 1752 8.221965 AGTAAAAGAAAATTCAAACGAGGAGT 57.778 30.769 0.00 0.00 0.00 3.85
1731 1753 8.343366 AGTAAAAGAAAATTCAAACGAGGAGTC 58.657 33.333 0.00 0.00 0.00 3.36
1732 1754 6.944234 AAAGAAAATTCAAACGAGGAGTCT 57.056 33.333 0.00 0.00 0.00 3.24
1735 1757 6.522054 AGAAAATTCAAACGAGGAGTCTACA 58.478 36.000 0.00 0.00 0.00 2.74
1736 1758 7.162082 AGAAAATTCAAACGAGGAGTCTACAT 58.838 34.615 0.00 0.00 0.00 2.29
1742 1764 5.067413 TCAAACGAGGAGTCTACATACATCC 59.933 44.000 0.00 0.00 0.00 3.51
1743 1765 3.139850 ACGAGGAGTCTACATACATCCG 58.860 50.000 0.00 0.00 35.13 4.18
1744 1766 3.181457 ACGAGGAGTCTACATACATCCGA 60.181 47.826 0.00 0.00 35.13 4.55
1745 1767 3.813724 CGAGGAGTCTACATACATCCGAA 59.186 47.826 0.00 0.00 35.13 4.30
1748 1770 5.202004 AGGAGTCTACATACATCCGAAACT 58.798 41.667 0.00 0.00 35.13 2.66
1749 1771 6.363065 AGGAGTCTACATACATCCGAAACTA 58.637 40.000 0.00 0.00 35.13 2.24
1750 1772 6.832384 AGGAGTCTACATACATCCGAAACTAA 59.168 38.462 0.00 0.00 35.13 2.24
1751 1773 7.506261 AGGAGTCTACATACATCCGAAACTAAT 59.494 37.037 0.00 0.00 35.13 1.73
1752 1774 8.790718 GGAGTCTACATACATCCGAAACTAATA 58.209 37.037 0.00 0.00 0.00 0.98
1755 1777 9.355215 GTCTACATACATCCGAAACTAATATGG 57.645 37.037 0.00 0.00 0.00 2.74
1756 1778 9.304335 TCTACATACATCCGAAACTAATATGGA 57.696 33.333 0.00 0.00 0.00 3.41
1757 1779 9.923143 CTACATACATCCGAAACTAATATGGAA 57.077 33.333 0.00 0.00 31.42 3.53
1758 1780 8.603242 ACATACATCCGAAACTAATATGGAAC 57.397 34.615 0.00 0.00 31.42 3.62
1759 1781 7.384115 ACATACATCCGAAACTAATATGGAACG 59.616 37.037 0.00 0.00 31.42 3.95
1760 1782 5.054477 ACATCCGAAACTAATATGGAACGG 58.946 41.667 0.00 0.00 40.36 4.44
1762 1784 4.940463 TCCGAAACTAATATGGAACGGAG 58.060 43.478 0.00 0.00 42.32 4.63
1763 1785 4.056050 CCGAAACTAATATGGAACGGAGG 58.944 47.826 0.00 0.00 41.30 4.30
1764 1786 4.056050 CGAAACTAATATGGAACGGAGGG 58.944 47.826 0.00 0.00 0.00 4.30
1765 1787 4.202182 CGAAACTAATATGGAACGGAGGGA 60.202 45.833 0.00 0.00 0.00 4.20
1766 1788 5.677567 GAAACTAATATGGAACGGAGGGAA 58.322 41.667 0.00 0.00 0.00 3.97
1807 1829 0.534203 AACCCACTTGCACCTACGTG 60.534 55.000 0.00 0.00 43.35 4.49
1940 1970 4.272261 TCGGTCTTATATGCAACGTACGTA 59.728 41.667 23.12 6.57 0.00 3.57
2039 2069 0.593263 GGATACCCTACGTGTTCGCG 60.593 60.000 0.00 0.00 41.18 5.87
2393 2423 2.751436 AACGGCGCCAAGATGCAT 60.751 55.556 28.98 0.00 0.00 3.96
3151 3181 3.864686 CCAAGCGGCAACCGATCG 61.865 66.667 10.78 8.51 44.45 3.69
3153 3183 2.173669 CAAGCGGCAACCGATCGAT 61.174 57.895 18.66 0.00 44.45 3.59
3435 3465 3.626924 GTGGTGCTGGTCTCCGGT 61.627 66.667 0.00 0.00 31.34 5.28
3469 3499 4.508128 AGCCGTACATGGACGCGG 62.508 66.667 25.39 13.89 46.17 6.46
3685 3715 0.978907 TGCTGACATGGAAGCTCTGA 59.021 50.000 19.04 0.78 40.21 3.27
3689 3719 3.001414 CTGACATGGAAGCTCTGAACTG 58.999 50.000 0.00 0.00 0.00 3.16
3697 7178 4.057432 GGAAGCTCTGAACTGATAGATGC 58.943 47.826 0.00 0.00 0.00 3.91
3703 7184 0.864455 GAACTGATAGATGCGCCTGC 59.136 55.000 4.18 0.00 43.20 4.85
3704 7185 0.533755 AACTGATAGATGCGCCTGCC 60.534 55.000 4.18 0.00 41.78 4.85
3716 7197 4.463879 CCTGCCGCTCACTGAGGG 62.464 72.222 14.76 14.76 41.39 4.30
3728 7209 1.153745 CTGAGGGAAACTCCGCTCG 60.154 63.158 0.00 0.00 46.01 5.03
3730 7211 3.296709 GAGGGAAACTCCGCTCGCA 62.297 63.158 0.00 0.00 40.49 5.10
3739 7220 0.669318 CTCCGCTCGCAGTGGTTTAA 60.669 55.000 13.25 0.00 45.85 1.52
3741 7222 0.669318 CCGCTCGCAGTGGTTTAAGA 60.669 55.000 7.38 0.00 40.92 2.10
3742 7223 0.716108 CGCTCGCAGTGGTTTAAGAG 59.284 55.000 0.00 0.00 0.00 2.85
3744 7225 2.413837 GCTCGCAGTGGTTTAAGAGAA 58.586 47.619 0.00 0.00 0.00 2.87
3745 7226 3.003480 GCTCGCAGTGGTTTAAGAGAAT 58.997 45.455 0.00 0.00 0.00 2.40
3747 7228 4.630069 GCTCGCAGTGGTTTAAGAGAATTA 59.370 41.667 0.00 0.00 0.00 1.40
3748 7229 5.220491 GCTCGCAGTGGTTTAAGAGAATTAG 60.220 44.000 0.00 0.00 0.00 1.73
3750 7231 4.631813 CGCAGTGGTTTAAGAGAATTAGCT 59.368 41.667 0.00 0.00 0.00 3.32
3754 7235 7.010645 GCAGTGGTTTAAGAGAATTAGCTACTC 59.989 40.741 0.00 0.00 0.00 2.59
3755 7236 7.492994 CAGTGGTTTAAGAGAATTAGCTACTCC 59.507 40.741 6.30 0.00 0.00 3.85
3757 7238 7.492994 GTGGTTTAAGAGAATTAGCTACTCCTG 59.507 40.741 6.30 0.00 0.00 3.86
3758 7239 6.480651 GGTTTAAGAGAATTAGCTACTCCTGC 59.519 42.308 6.30 0.00 0.00 4.85
3759 7240 4.314740 AAGAGAATTAGCTACTCCTGCG 57.685 45.455 6.30 0.00 35.28 5.18
3760 7241 2.035321 AGAGAATTAGCTACTCCTGCGC 59.965 50.000 0.00 0.00 35.28 6.09
3761 7242 1.757118 AGAATTAGCTACTCCTGCGCA 59.243 47.619 10.98 10.98 35.28 6.09
3762 7243 2.168521 AGAATTAGCTACTCCTGCGCAA 59.831 45.455 13.05 0.00 35.28 4.85
3763 7244 1.941325 ATTAGCTACTCCTGCGCAAC 58.059 50.000 13.05 0.00 35.28 4.17
3764 7245 0.895530 TTAGCTACTCCTGCGCAACT 59.104 50.000 13.05 2.93 35.28 3.16
3765 7246 1.758936 TAGCTACTCCTGCGCAACTA 58.241 50.000 13.05 0.00 35.28 2.24
3766 7247 0.895530 AGCTACTCCTGCGCAACTAA 59.104 50.000 13.05 0.00 35.28 2.24
3767 7248 1.482593 AGCTACTCCTGCGCAACTAAT 59.517 47.619 13.05 0.00 35.28 1.73
3768 7249 2.093447 AGCTACTCCTGCGCAACTAATT 60.093 45.455 13.05 0.00 35.28 1.40
3769 7250 2.678336 GCTACTCCTGCGCAACTAATTT 59.322 45.455 13.05 0.00 0.00 1.82
3770 7251 3.869246 GCTACTCCTGCGCAACTAATTTA 59.131 43.478 13.05 0.00 0.00 1.40
3828 7309 2.113860 ACTGTTTGCTGTGTGTCAGT 57.886 45.000 0.00 0.00 45.23 3.41
3862 7343 3.215151 CATCAGAGCTAGACGTTCCCTA 58.785 50.000 0.00 0.00 0.00 3.53
3866 7347 4.525487 TCAGAGCTAGACGTTCCCTAAAAA 59.475 41.667 0.00 0.00 0.00 1.94
4020 7501 1.295423 CCGGTTCGTCCTGGACAAT 59.705 57.895 25.42 0.00 33.75 2.71
4029 7510 2.290705 CGTCCTGGACAATAAACCCCTT 60.291 50.000 25.42 0.00 32.09 3.95
4035 7516 5.279456 CCTGGACAATAAACCCCTTCAAAAG 60.279 44.000 0.00 0.00 0.00 2.27
4066 7547 2.060383 CACCCGCCTGATCTCCAGA 61.060 63.158 0.00 0.00 45.78 3.86
4088 7569 1.179152 CACACATCACATGCCCACAT 58.821 50.000 0.00 0.00 36.79 3.21
4172 7653 8.169977 AGAAATTGCTTCATCTACAAACAGAA 57.830 30.769 0.00 0.00 36.40 3.02
4364 7851 8.877864 TCCAGTGTAAATTCACCATAAATTCT 57.122 30.769 0.00 0.00 38.91 2.40
4400 7887 8.837788 AAACTGTAACTACTGGTAATTACACC 57.162 34.615 17.16 4.18 34.21 4.16
4437 7924 7.657761 CCTAGAAAATTACAGTGCGAATCCTAT 59.342 37.037 0.00 0.00 0.00 2.57
4539 8027 6.596497 GCAAATTAAACTGTAGGTGCCTAGTA 59.404 38.462 0.00 0.00 0.00 1.82
4627 8124 8.621286 CAAGACAAAAGATTACACTGTAAACCT 58.379 33.333 5.73 4.07 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.003759 CCTCGTAGATCGACCTTGACG 60.004 57.143 0.00 0.00 44.01 4.35
7 8 1.528776 GCCCCTCGTAGATCGACCT 60.529 63.158 0.00 0.00 44.01 3.85
18 19 0.965439 TCCAATTTGTTTGCCCCTCG 59.035 50.000 0.00 0.00 33.73 4.63
27 28 3.679389 AGCTCTCGATGTCCAATTTGTT 58.321 40.909 0.00 0.00 0.00 2.83
92 93 2.750888 GCCCCGATTTCTCGCACAC 61.751 63.158 0.00 0.00 43.66 3.82
142 144 2.812178 CAACCGCCCCTAACGTCG 60.812 66.667 0.00 0.00 0.00 5.12
145 147 1.296056 CTTGTCAACCGCCCCTAACG 61.296 60.000 0.00 0.00 0.00 3.18
158 160 1.070134 CAACTCGTCTTCCCCTTGTCA 59.930 52.381 0.00 0.00 0.00 3.58
161 163 0.685097 TCCAACTCGTCTTCCCCTTG 59.315 55.000 0.00 0.00 0.00 3.61
168 170 2.169352 CTCCCATCATCCAACTCGTCTT 59.831 50.000 0.00 0.00 0.00 3.01
181 183 3.001514 GGGCTCAAGCTCCCATCA 58.998 61.111 3.30 0.00 42.18 3.07
322 325 2.717139 CTTCTCCTTATCCGCCGGCC 62.717 65.000 23.46 2.84 0.00 6.13
323 326 1.301009 CTTCTCCTTATCCGCCGGC 60.301 63.158 19.07 19.07 0.00 6.13
324 327 1.367840 CCTTCTCCTTATCCGCCGG 59.632 63.158 0.00 0.00 0.00 6.13
325 328 1.301009 GCCTTCTCCTTATCCGCCG 60.301 63.158 0.00 0.00 0.00 6.46
358 361 1.491668 ACCTTTGACAAAACCCCACC 58.508 50.000 1.62 0.00 0.00 4.61
406 409 3.142174 CAGTTTGAGGAGGGTTCTCAAC 58.858 50.000 6.08 3.27 46.84 3.18
414 417 5.243730 TCAAAATTAAGCAGTTTGAGGAGGG 59.756 40.000 0.00 0.00 36.58 4.30
438 441 3.181439 CCTCAAAACACCTCCTTCCTTCT 60.181 47.826 0.00 0.00 0.00 2.85
475 478 6.403855 CCTCAAAACCGTTAACTTCTCACAAA 60.404 38.462 3.71 0.00 0.00 2.83
532 535 4.346709 TCTTTCCACCCCCTGAAAATTTTC 59.653 41.667 21.60 21.60 37.69 2.29
599 602 4.096382 GCTTGTACCATGATAAGTGGGTTG 59.904 45.833 0.00 0.00 41.14 3.77
694 697 2.803030 AGCTAACCTCACGGTCTCTA 57.197 50.000 0.00 0.00 44.73 2.43
695 698 1.926108 AAGCTAACCTCACGGTCTCT 58.074 50.000 0.00 0.00 44.73 3.10
822 826 2.428960 AAAATTTCACGCACGCCCCC 62.429 55.000 0.00 0.00 0.00 5.40
879 883 2.548067 CCATCCCAGTGCGTACTTATCC 60.548 54.545 2.37 0.00 34.07 2.59
880 884 2.548067 CCCATCCCAGTGCGTACTTATC 60.548 54.545 2.37 0.00 34.07 1.75
893 897 1.912220 CCTTTACTCGCCCATCCCA 59.088 57.895 0.00 0.00 0.00 4.37
895 899 0.815615 CTGCCTTTACTCGCCCATCC 60.816 60.000 0.00 0.00 0.00 3.51
896 900 0.178068 TCTGCCTTTACTCGCCCATC 59.822 55.000 0.00 0.00 0.00 3.51
897 901 0.179000 CTCTGCCTTTACTCGCCCAT 59.821 55.000 0.00 0.00 0.00 4.00
898 902 1.192146 ACTCTGCCTTTACTCGCCCA 61.192 55.000 0.00 0.00 0.00 5.36
899 903 0.741221 CACTCTGCCTTTACTCGCCC 60.741 60.000 0.00 0.00 0.00 6.13
901 905 0.390472 AGCACTCTGCCTTTACTCGC 60.390 55.000 0.00 0.00 46.52 5.03
902 906 1.634702 GAGCACTCTGCCTTTACTCG 58.365 55.000 0.00 0.00 46.52 4.18
903 907 1.552792 AGGAGCACTCTGCCTTTACTC 59.447 52.381 0.00 0.00 46.52 2.59
904 908 1.650528 AGGAGCACTCTGCCTTTACT 58.349 50.000 0.00 0.00 46.52 2.24
905 909 2.351455 GAAGGAGCACTCTGCCTTTAC 58.649 52.381 0.00 0.00 46.52 2.01
906 910 1.279271 GGAAGGAGCACTCTGCCTTTA 59.721 52.381 0.00 0.00 46.52 1.85
926 930 1.796459 GTTGTACGGTTGTAGCAGTGG 59.204 52.381 0.00 0.00 0.00 4.00
1241 1261 4.389664 GCACGTGAAATGCATATACGAT 57.610 40.909 26.60 14.14 42.88 3.73
1544 1564 7.724506 TGTACTATTAGAGAACCCATCGATCTT 59.275 37.037 0.00 0.00 0.00 2.40
1730 1752 9.304335 TCCATATTAGTTTCGGATGTATGTAGA 57.696 33.333 0.00 0.00 0.00 2.59
1731 1753 9.923143 TTCCATATTAGTTTCGGATGTATGTAG 57.077 33.333 0.00 0.00 0.00 2.74
1732 1754 9.701098 GTTCCATATTAGTTTCGGATGTATGTA 57.299 33.333 0.00 0.00 0.00 2.29
1735 1757 6.872020 CCGTTCCATATTAGTTTCGGATGTAT 59.128 38.462 0.00 0.00 39.17 2.29
1736 1758 6.040729 TCCGTTCCATATTAGTTTCGGATGTA 59.959 38.462 0.00 0.00 40.46 2.29
1742 1764 4.056050 CCCTCCGTTCCATATTAGTTTCG 58.944 47.826 0.00 0.00 0.00 3.46
1743 1765 5.286267 TCCCTCCGTTCCATATTAGTTTC 57.714 43.478 0.00 0.00 0.00 2.78
1744 1766 5.703730 TTCCCTCCGTTCCATATTAGTTT 57.296 39.130 0.00 0.00 0.00 2.66
1745 1767 5.906772 ATTCCCTCCGTTCCATATTAGTT 57.093 39.130 0.00 0.00 0.00 2.24
1748 1770 6.151648 CGTAGTATTCCCTCCGTTCCATATTA 59.848 42.308 0.00 0.00 0.00 0.98
1749 1771 5.047519 CGTAGTATTCCCTCCGTTCCATATT 60.048 44.000 0.00 0.00 0.00 1.28
1750 1772 4.461781 CGTAGTATTCCCTCCGTTCCATAT 59.538 45.833 0.00 0.00 0.00 1.78
1751 1773 3.822735 CGTAGTATTCCCTCCGTTCCATA 59.177 47.826 0.00 0.00 0.00 2.74
1752 1774 2.626743 CGTAGTATTCCCTCCGTTCCAT 59.373 50.000 0.00 0.00 0.00 3.41
1753 1775 2.026641 CGTAGTATTCCCTCCGTTCCA 58.973 52.381 0.00 0.00 0.00 3.53
1754 1776 2.027385 ACGTAGTATTCCCTCCGTTCC 58.973 52.381 0.00 0.00 41.94 3.62
1755 1777 3.442100 CAACGTAGTATTCCCTCCGTTC 58.558 50.000 0.00 0.00 45.00 3.95
1756 1778 2.417787 GCAACGTAGTATTCCCTCCGTT 60.418 50.000 0.00 0.00 45.00 4.44
1757 1779 1.135721 GCAACGTAGTATTCCCTCCGT 59.864 52.381 0.00 0.00 45.00 4.69
1758 1780 1.135527 TGCAACGTAGTATTCCCTCCG 59.864 52.381 0.00 0.00 45.00 4.63
1759 1781 2.167900 AGTGCAACGTAGTATTCCCTCC 59.832 50.000 0.00 0.00 45.00 4.30
1760 1782 3.521947 AGTGCAACGTAGTATTCCCTC 57.478 47.619 0.00 0.00 45.00 4.30
1761 1783 3.596214 CAAGTGCAACGTAGTATTCCCT 58.404 45.455 0.00 0.00 45.00 4.20
1762 1784 2.095372 GCAAGTGCAACGTAGTATTCCC 59.905 50.000 0.00 0.00 45.00 3.97
1763 1785 3.385079 GCAAGTGCAACGTAGTATTCC 57.615 47.619 0.00 0.00 45.00 3.01
1807 1829 7.916977 TGCACTTATGATTTTGAATCTATGTGC 59.083 33.333 22.80 22.80 42.96 4.57
1904 1934 2.223803 AGACCGAGTTCACCTCAGAT 57.776 50.000 0.00 0.00 40.48 2.90
1940 1970 2.732658 GACCAACAGACCGACCGT 59.267 61.111 0.00 0.00 0.00 4.83
1944 1974 2.214216 CCCTGGACCAACAGACCGA 61.214 63.158 0.00 0.00 40.97 4.69
2027 2057 3.823421 CACGGCGCGAACACGTAG 61.823 66.667 12.10 5.81 39.02 3.51
2277 2307 3.047877 GTCGTGGAAAGTGGCCGG 61.048 66.667 0.00 0.00 0.00 6.13
2393 2423 0.109532 TGATGAGGAAACGGTTGGCA 59.890 50.000 0.00 0.00 0.00 4.92
3001 3031 3.842923 CGGCGACCAGGATGCTCT 61.843 66.667 0.00 0.00 31.97 4.09
3151 3181 7.149351 CGTTCACGTTGTTAGTTTCATTCAATC 60.149 37.037 0.00 0.00 34.11 2.67
3153 3183 5.960683 CGTTCACGTTGTTAGTTTCATTCAA 59.039 36.000 0.00 0.00 34.11 2.69
3379 3409 2.880879 CACGTCCTGGATCACGCG 60.881 66.667 3.53 3.53 39.73 6.01
3534 3564 2.505557 GTGAACCCGTAGTCGCCG 60.506 66.667 0.00 0.00 35.54 6.46
3666 3696 0.978907 TCAGAGCTTCCATGTCAGCA 59.021 50.000 14.14 0.00 38.61 4.41
3672 3702 5.273674 TCTATCAGTTCAGAGCTTCCATG 57.726 43.478 0.00 0.00 0.00 3.66
3685 3715 0.533755 GGCAGGCGCATCTATCAGTT 60.534 55.000 10.83 0.00 41.24 3.16
3689 3719 3.418068 GCGGCAGGCGCATCTATC 61.418 66.667 34.33 4.21 41.24 2.08
3703 7184 0.390472 GAGTTTCCCTCAGTGAGCGG 60.390 60.000 15.10 16.36 40.17 5.52
3704 7185 0.390472 GGAGTTTCCCTCAGTGAGCG 60.390 60.000 15.10 6.54 42.40 5.03
3708 7189 0.390472 GAGCGGAGTTTCCCTCAGTG 60.390 60.000 8.04 0.00 42.40 3.66
3716 7197 2.383527 CCACTGCGAGCGGAGTTTC 61.384 63.158 14.32 0.00 44.30 2.78
3728 7209 6.819146 AGTAGCTAATTCTCTTAAACCACTGC 59.181 38.462 0.00 0.00 0.00 4.40
3730 7211 7.400627 AGGAGTAGCTAATTCTCTTAAACCACT 59.599 37.037 0.00 0.00 0.00 4.00
3739 7220 2.035321 GCGCAGGAGTAGCTAATTCTCT 59.965 50.000 0.30 0.00 0.00 3.10
3741 7222 1.757118 TGCGCAGGAGTAGCTAATTCT 59.243 47.619 5.66 0.00 0.00 2.40
3742 7223 2.225068 TGCGCAGGAGTAGCTAATTC 57.775 50.000 5.66 0.00 0.00 2.17
3744 7225 1.482593 AGTTGCGCAGGAGTAGCTAAT 59.517 47.619 11.31 0.00 0.00 1.73
3745 7226 0.895530 AGTTGCGCAGGAGTAGCTAA 59.104 50.000 11.31 0.00 0.00 3.09
3747 7228 0.895530 TTAGTTGCGCAGGAGTAGCT 59.104 50.000 11.31 0.00 0.00 3.32
3748 7229 1.941325 ATTAGTTGCGCAGGAGTAGC 58.059 50.000 11.31 0.00 0.00 3.58
3750 7231 8.671384 AATAATAAATTAGTTGCGCAGGAGTA 57.329 30.769 11.31 0.55 0.00 2.59
3754 7235 8.075574 TGATGAATAATAAATTAGTTGCGCAGG 58.924 33.333 11.31 0.00 0.00 4.85
3755 7236 9.110617 CTGATGAATAATAAATTAGTTGCGCAG 57.889 33.333 11.31 0.00 0.00 5.18
3757 7238 9.831737 ATCTGATGAATAATAAATTAGTTGCGC 57.168 29.630 0.00 0.00 0.00 6.09
3844 7325 4.451629 TTTTAGGGAACGTCTAGCTCTG 57.548 45.455 0.00 0.00 0.00 3.35
3866 7347 5.993748 TGAAAAACAGGACAGTCCTTTTT 57.006 34.783 23.72 23.72 46.91 1.94
3867 7348 5.993748 TTGAAAAACAGGACAGTCCTTTT 57.006 34.783 20.57 17.22 46.91 2.27
3868 7349 6.544928 AATTGAAAAACAGGACAGTCCTTT 57.455 33.333 20.57 11.34 46.91 3.11
3869 7350 5.221048 CGAATTGAAAAACAGGACAGTCCTT 60.221 40.000 20.57 4.73 46.91 3.36
3870 7351 7.356479 TTCGAATTGAAAAACAGGACAGTCCT 61.356 38.462 17.31 17.31 39.85 3.85
3871 7352 4.274950 TCGAATTGAAAAACAGGACAGTCC 59.725 41.667 12.25 12.25 36.58 3.85
3872 7353 5.418310 TCGAATTGAAAAACAGGACAGTC 57.582 39.130 0.00 0.00 0.00 3.51
3873 7354 5.828299 TTCGAATTGAAAAACAGGACAGT 57.172 34.783 0.00 0.00 32.37 3.55
3973 7454 1.360185 TTAGCCCCAACCCGTTTAGA 58.640 50.000 0.00 0.00 0.00 2.10
3985 7466 0.815095 CGGGTCAAATGTTTAGCCCC 59.185 55.000 9.51 0.00 32.76 5.80
4020 7501 4.672899 CCCTGATCTTTTGAAGGGGTTTA 58.327 43.478 5.77 0.00 41.06 2.01
4029 7510 1.146774 TGTTGGCCCCTGATCTTTTGA 59.853 47.619 0.00 0.00 0.00 2.69
4035 7516 2.043953 GGGTGTTGGCCCCTGATC 60.044 66.667 0.00 0.00 42.89 2.92
4066 7547 0.178967 TGGGCATGTGATGTGTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
4088 7569 1.600023 CTTTGCGTGGGTTCCAAGTA 58.400 50.000 2.24 0.00 35.50 2.24
4172 7653 9.842775 TTCAGAATTATAGCTGATGTTGATCTT 57.157 29.630 0.00 0.00 40.51 2.40
4400 7887 9.449719 ACTGTAATTTTCTAGGATTTACTGGTG 57.550 33.333 12.21 3.38 0.00 4.17
4437 7924 7.548097 TCACTGGTTTTTGCACTGTAAATTTA 58.452 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.