Multiple sequence alignment - TraesCS1D01G046700

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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 TraesCS1D01G046700 chr1D 100.000 4383 0 0 696 5078 26293509 26297891 0.000000e+00 8094
1 TraesCS1D01G046700 chr1D 86.651 854 75 17 3712 4554 26404188 26405013 0.000000e+00 909
2 TraesCS1D01G046700 chr1D 97.384 497 13 0 4579 5075 26364126 26364622 0.000000e+00 846
3 TraesCS1D01G046700 chr1D 96.988 498 14 1 4579 5076 123597404 123597900 0.000000e+00 835
4 TraesCS1D01G046700 chr1D 96.614 502 17 0 4575 5076 211531588 211532089 0.000000e+00 833
5 TraesCS1D01G046700 chr1D 96.787 498 16 0 4579 5076 26358516 26359013 0.000000e+00 832
6 TraesCS1D01G046700 chr1D 96.787 498 16 0 4579 5076 123603015 123603512 0.000000e+00 832
7 TraesCS1D01G046700 chr1D 100.000 261 0 0 1 261 26292814 26293074 2.750000e-132 483
8 TraesCS1D01G046700 chr1B 92.581 3909 228 33 698 4577 42012731 42016606 0.000000e+00 5555
9 TraesCS1D01G046700 chr1B 86.250 880 79 10 3712 4578 42051900 42052750 0.000000e+00 917
10 TraesCS1D01G046700 chr1B 88.703 239 16 8 1 231 42012358 42012593 1.080000e-71 281
11 TraesCS1D01G046700 chr1A 94.100 2373 112 11 699 3068 27359597 27361944 0.000000e+00 3581
12 TraesCS1D01G046700 chr1A 94.269 1518 73 10 3067 4577 27362026 27363536 0.000000e+00 2309
13 TraesCS1D01G046700 chr1A 90.351 342 31 2 3815 4155 27370033 27370373 1.000000e-121 448
14 TraesCS1D01G046700 chr1A 88.298 376 39 3 3079 3449 27368429 27368804 3.610000e-121 446
15 TraesCS1D01G046700 chr1A 84.816 461 38 13 4112 4554 27370414 27370860 7.810000e-118 435
16 TraesCS1D01G046700 chr1A 90.171 234 11 8 1 225 27359219 27359449 1.380000e-75 294
17 TraesCS1D01G046700 chr7D 97.189 498 14 0 4577 5074 105935407 105934910 0.000000e+00 843
18 TraesCS1D01G046700 chr7D 96.593 499 16 1 4579 5076 615689377 615689875 0.000000e+00 826
19 TraesCS1D01G046700 chr6D 97.189 498 14 0 4579 5076 35464911 35465408 0.000000e+00 843
20 TraesCS1D01G046700 chr3D 96.586 498 17 0 4579 5076 81194442 81194939 0.000000e+00 826


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 TraesCS1D01G046700 chr1D 26292814 26297891 5077 False 4288.500000 8094 100.000000 1 5078 2 chr1D.!!$F7 5077
1 TraesCS1D01G046700 chr1D 26404188 26405013 825 False 909.000000 909 86.651000 3712 4554 1 chr1D.!!$F3 842
2 TraesCS1D01G046700 chr1D 211531588 211532089 501 False 833.000000 833 96.614000 4575 5076 1 chr1D.!!$F6 501
3 TraesCS1D01G046700 chr1B 42012358 42016606 4248 False 2918.000000 5555 90.642000 1 4577 2 chr1B.!!$F2 4576
4 TraesCS1D01G046700 chr1B 42051900 42052750 850 False 917.000000 917 86.250000 3712 4578 1 chr1B.!!$F1 866
5 TraesCS1D01G046700 chr1A 27359219 27363536 4317 False 2061.333333 3581 92.846667 1 4577 3 chr1A.!!$F1 4576
6 TraesCS1D01G046700 chr1A 27368429 27370860 2431 False 443.000000 448 87.821667 3079 4554 3 chr1A.!!$F2 1475

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
904 945 0.716108 GACGCTCCATGTTTGACTCG 59.284 55.000 0.00 0.00 0.00 4.18 F
1195 1246 1.005394 AACATGGCTGCTGCAAAGC 60.005 52.632 17.89 11.72 41.91 3.51 F
1338 1389 1.134580 AGTGACATCCAGAGCAATCCG 60.135 52.381 0.00 0.00 0.00 4.18 F
2946 3006 1.075601 ATTTGGAAGGTCAGGCAGGA 58.924 50.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1911 0.320683 CCGAATGCTCCAGTGACACA 60.321 55.0 8.59 0.00 0.00 3.72 R
2932 2992 0.107459 GTCCATCCTGCCTGACCTTC 60.107 60.0 0.00 0.00 0.00 3.46 R
2955 3015 1.675552 ACGGTGTTGCTAGCTTTTGT 58.324 45.0 17.23 4.28 0.00 2.83 R
4864 5986 0.108138 GATGTCGACCCCAAGTCCAG 60.108 60.0 14.12 0.00 43.08 3.86 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
63 74 2.904866 CGCGAGGAGGAGGAGGAG 60.905 72.222 0.00 0.00 0.00 3.69
64 75 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
65 76 2.520741 CGAGGAGGAGGAGGAGGC 60.521 72.222 0.00 0.00 0.00 4.70
176 190 0.813610 GTTTGTTTGTTGGCCAGGGC 60.814 55.000 5.11 5.91 41.06 5.19
192 206 3.706373 GCCTCTGTTCCGCTCCCA 61.706 66.667 0.00 0.00 0.00 4.37
196 213 1.373570 CTCTGTTCCGCTCCCATTTC 58.626 55.000 0.00 0.00 0.00 2.17
227 246 4.351192 CCTCCGATTTAAATCCGCTTTTG 58.649 43.478 20.01 6.37 31.68 2.44
228 247 4.142469 CCTCCGATTTAAATCCGCTTTTGT 60.142 41.667 20.01 0.00 31.68 2.83
730 764 1.127582 GCTGCTCTTGTTTCGTAGCTG 59.872 52.381 0.00 0.00 35.95 4.24
740 774 4.883083 TGTTTCGTAGCTGAGATTCTGTT 58.117 39.130 0.00 0.00 0.00 3.16
741 775 6.020971 TGTTTCGTAGCTGAGATTCTGTTA 57.979 37.500 0.00 0.00 0.00 2.41
742 776 5.862323 TGTTTCGTAGCTGAGATTCTGTTAC 59.138 40.000 0.00 0.00 31.91 2.50
745 779 7.569639 TTCGTAGCTGAGATTCTGTTACTAT 57.430 36.000 0.00 0.00 32.65 2.12
747 781 8.672823 TCGTAGCTGAGATTCTGTTACTATTA 57.327 34.615 0.00 0.00 32.65 0.98
751 785 8.312669 AGCTGAGATTCTGTTACTATTAGGTT 57.687 34.615 0.00 0.00 0.00 3.50
816 850 7.068593 TCCCGAAATGCAGATTCAAATTTCTAT 59.931 33.333 13.56 0.00 37.04 1.98
903 944 1.795768 TGACGCTCCATGTTTGACTC 58.204 50.000 0.00 0.00 0.00 3.36
904 945 0.716108 GACGCTCCATGTTTGACTCG 59.284 55.000 0.00 0.00 0.00 4.18
910 951 2.143122 TCCATGTTTGACTCGTTCTGC 58.857 47.619 0.00 0.00 0.00 4.26
916 957 1.629013 TTGACTCGTTCTGCTATGCG 58.371 50.000 0.00 0.00 0.00 4.73
925 966 3.194861 GTTCTGCTATGCGTTGACCATA 58.805 45.455 0.00 0.00 0.00 2.74
926 967 3.535280 TCTGCTATGCGTTGACCATAA 57.465 42.857 0.00 0.00 0.00 1.90
927 968 3.867857 TCTGCTATGCGTTGACCATAAA 58.132 40.909 0.00 0.00 0.00 1.40
998 1039 2.124942 CAAGAGGGCGAGGAAGGC 60.125 66.667 0.00 0.00 0.00 4.35
1026 1067 2.030262 GCAGAGGCGCATAGAGGG 59.970 66.667 10.83 0.00 0.00 4.30
1084 1125 4.183101 AGTTTCCACAAGTGTGCATTTTG 58.817 39.130 5.89 0.00 44.34 2.44
1145 1196 1.488812 ACCTGTGGTGCTGTGTCTTTA 59.511 47.619 0.00 0.00 32.98 1.85
1169 1220 1.272490 TGTTTCGCAGGGAGTCACTAG 59.728 52.381 0.00 0.00 0.00 2.57
1195 1246 1.005394 AACATGGCTGCTGCAAAGC 60.005 52.632 17.89 11.72 41.91 3.51
1278 1329 1.439644 GAGGCTGATGGGTCTCGAC 59.560 63.158 0.00 0.00 0.00 4.20
1338 1389 1.134580 AGTGACATCCAGAGCAATCCG 60.135 52.381 0.00 0.00 0.00 4.18
1376 1427 2.853542 TGCTGAGGAAGTGGCCCA 60.854 61.111 0.00 0.00 0.00 5.36
1578 1629 1.462731 ATGCAAAGCGCCTTTCCACA 61.463 50.000 2.29 3.14 41.33 4.17
1591 1642 2.358737 CCACAGACGAAGGCCACC 60.359 66.667 5.01 0.00 0.00 4.61
1680 1731 2.093288 CCTTCAGGAGAGCAGTATTGCA 60.093 50.000 13.16 0.00 45.18 4.08
1702 1753 2.124570 CAGGATTCCCAGGGCACG 60.125 66.667 0.00 0.00 33.88 5.34
1780 1831 2.629617 CAATCCTTTGGGCAAGACAACT 59.370 45.455 0.00 0.00 33.80 3.16
1814 1865 5.163509 CGGAAGTTGATAGTGAATCTGAGGA 60.164 44.000 0.00 0.00 35.45 3.71
1820 1871 4.764308 TGATAGTGAATCTGAGGATCCTCG 59.236 45.833 31.81 25.86 37.92 4.63
1822 1873 2.955660 AGTGAATCTGAGGATCCTCGTC 59.044 50.000 31.81 25.11 45.48 4.20
1842 1902 4.023963 CGTCCTAGTATGCATCTCGAAGAA 60.024 45.833 0.19 0.00 34.09 2.52
1843 1903 5.505819 CGTCCTAGTATGCATCTCGAAGAAA 60.506 44.000 0.19 0.00 34.09 2.52
1844 1904 5.688176 GTCCTAGTATGCATCTCGAAGAAAC 59.312 44.000 0.19 0.00 34.09 2.78
1845 1905 5.594725 TCCTAGTATGCATCTCGAAGAAACT 59.405 40.000 0.19 0.00 34.09 2.66
1847 1907 6.419413 CCTAGTATGCATCTCGAAGAAACTTC 59.581 42.308 0.19 0.00 34.09 3.01
1848 1908 5.724328 AGTATGCATCTCGAAGAAACTTCA 58.276 37.500 0.19 0.00 34.09 3.02
1849 1909 5.809562 AGTATGCATCTCGAAGAAACTTCAG 59.190 40.000 0.19 7.92 34.09 3.02
1850 1910 4.257267 TGCATCTCGAAGAAACTTCAGA 57.743 40.909 11.20 11.79 34.09 3.27
1851 1911 4.825422 TGCATCTCGAAGAAACTTCAGAT 58.175 39.130 11.20 13.08 34.09 2.90
1852 1912 4.628766 TGCATCTCGAAGAAACTTCAGATG 59.371 41.667 26.30 26.30 37.26 2.90
1853 1913 4.629200 GCATCTCGAAGAAACTTCAGATGT 59.371 41.667 28.07 12.74 36.96 3.06
1854 1914 5.445673 GCATCTCGAAGAAACTTCAGATGTG 60.446 44.000 28.07 18.99 36.96 3.21
1855 1915 5.201713 TCTCGAAGAAACTTCAGATGTGT 57.798 39.130 11.20 0.00 34.09 3.72
1896 1956 4.681978 GGGAGCAGGCGTTCACGT 62.682 66.667 0.62 0.00 42.22 4.49
2127 2187 7.173218 CCTGAACAGAAGCTTAGAATACAAACA 59.827 37.037 0.00 0.00 0.00 2.83
2143 2203 7.873699 ATACAAACATCTATAAGGGGTAGCT 57.126 36.000 0.00 0.00 0.00 3.32
2166 2226 5.879763 TGGAAGAAACCATCTGAGAATGAA 58.120 37.500 0.00 0.00 38.79 2.57
2537 2597 5.178797 CCGTGGAGATAATTCAAGAAGTGT 58.821 41.667 0.00 0.00 0.00 3.55
2607 2667 1.616374 ACTGTTGCAAAATTACCGGGG 59.384 47.619 6.32 0.00 0.00 5.73
2647 2707 3.010200 ACTTGCCCATTCTGAAGGATC 57.990 47.619 3.24 0.00 0.00 3.36
2736 2796 2.684881 CAAGCAGAATGGGCGAGTTATT 59.315 45.455 0.00 0.00 35.86 1.40
2865 2925 7.334090 ACATATATAATGAGCATCCAGGTGAC 58.666 38.462 0.00 0.00 0.00 3.67
2876 2936 4.360563 CATCCAGGTGACGTTATCAGTAC 58.639 47.826 0.00 0.00 38.28 2.73
2892 2952 2.495270 CAGTACTGAGGATCACACAGCT 59.505 50.000 18.45 0.00 42.56 4.24
2932 2992 4.426416 ACATGATGATGTGCGAAATTTGG 58.574 39.130 0.00 0.00 41.52 3.28
2946 3006 1.075601 ATTTGGAAGGTCAGGCAGGA 58.924 50.000 0.00 0.00 0.00 3.86
2955 3015 0.615331 GTCAGGCAGGATGGACAGAA 59.385 55.000 0.00 0.00 35.86 3.02
3098 3242 6.839124 ATCTGCCATTATTCTGTTGTCAAA 57.161 33.333 0.00 0.00 0.00 2.69
3109 3254 4.854399 TCTGTTGTCAAATTAGTTTGCCG 58.146 39.130 5.86 0.00 43.47 5.69
3157 3303 5.983720 TGTTCAGTTTTGAGACTACTGCTAC 59.016 40.000 0.00 0.00 39.24 3.58
3158 3304 6.183360 TGTTCAGTTTTGAGACTACTGCTACT 60.183 38.462 0.00 0.00 39.24 2.57
3159 3305 6.406692 TCAGTTTTGAGACTACTGCTACTT 57.593 37.500 0.00 0.00 39.24 2.24
3175 3324 7.743104 ACTGCTACTTTCTCATTATCAAAACG 58.257 34.615 0.00 0.00 0.00 3.60
3424 3573 8.654230 TGACTCTTCTGCACTTAATATGATTC 57.346 34.615 0.00 0.00 0.00 2.52
3510 3662 0.763652 AGATGCTGAAGATGGGCGAT 59.236 50.000 0.00 0.00 0.00 4.58
3591 3839 6.620877 ACAGACATTTCAGATTACCAGGTA 57.379 37.500 0.00 0.00 0.00 3.08
3597 3845 7.112779 ACATTTCAGATTACCAGGTAAAGGAG 58.887 38.462 16.33 7.05 31.56 3.69
3612 3860 0.762461 AGGAGGAGCAGCTACCCATC 60.762 60.000 13.17 0.00 0.00 3.51
3627 3875 5.163195 GCTACCCATCTTTAAGGATGAGGAA 60.163 44.000 27.05 11.59 44.01 3.36
3789 4768 3.185391 CAGACAGGAAGCTTCTTTTCGAC 59.815 47.826 25.05 7.42 0.00 4.20
3807 4786 4.482386 TCGACCTCGTTAACTCAATCTTG 58.518 43.478 3.71 0.00 40.80 3.02
3909 4923 2.694628 AGCTGAAAATGTCTGGCAAACA 59.305 40.909 0.00 0.00 0.00 2.83
4290 5381 6.855763 TCATGCCTCCATTACAAAATTTCT 57.144 33.333 0.00 0.00 0.00 2.52
4341 5438 3.278668 CTGAGATCAGATGCCACCTTT 57.721 47.619 3.67 0.00 46.59 3.11
4369 5473 4.486125 TCACAGCCTTGCAGTAATGATA 57.514 40.909 0.00 0.00 0.00 2.15
4382 5486 5.295292 GCAGTAATGATACAGTTGAGCACAT 59.705 40.000 0.00 0.00 34.29 3.21
4388 5492 6.239217 TGATACAGTTGAGCACATTATCCT 57.761 37.500 0.00 0.00 0.00 3.24
4443 5550 7.602265 GGTCTTTGTTTGGTGCATTATTTGTAT 59.398 33.333 0.00 0.00 0.00 2.29
4447 5554 8.668510 TTGTTTGGTGCATTATTTGTATTGTT 57.331 26.923 0.00 0.00 0.00 2.83
4451 5558 8.749841 TTGGTGCATTATTTGTATTGTTACAC 57.250 30.769 0.00 0.00 38.05 2.90
4452 5559 7.886338 TGGTGCATTATTTGTATTGTTACACA 58.114 30.769 0.00 0.00 38.05 3.72
4472 5579 5.598005 ACACATGATCCAGTTTTCCTTTGAA 59.402 36.000 0.00 0.00 0.00 2.69
4477 5585 8.500773 CATGATCCAGTTTTCCTTTGAATTTTG 58.499 33.333 0.00 0.00 0.00 2.44
4480 5588 5.584251 TCCAGTTTTCCTTTGAATTTTGTGC 59.416 36.000 0.00 0.00 0.00 4.57
4497 5605 7.467557 TTTTGTGCTTCATTTCATTCTTGTC 57.532 32.000 0.00 0.00 0.00 3.18
4499 5607 6.005583 TGTGCTTCATTTCATTCTTGTCTC 57.994 37.500 0.00 0.00 0.00 3.36
4500 5608 5.532032 TGTGCTTCATTTCATTCTTGTCTCA 59.468 36.000 0.00 0.00 0.00 3.27
4502 5610 7.088905 GTGCTTCATTTCATTCTTGTCTCATT 58.911 34.615 0.00 0.00 0.00 2.57
4503 5611 7.272948 GTGCTTCATTTCATTCTTGTCTCATTC 59.727 37.037 0.00 0.00 0.00 2.67
4504 5612 7.040271 TGCTTCATTTCATTCTTGTCTCATTCA 60.040 33.333 0.00 0.00 0.00 2.57
4533 5653 3.186409 ACAATGTTCAATGACTCGGTTCG 59.814 43.478 0.00 0.00 0.00 3.95
4679 5801 2.819422 CAAGTCATGCAATCTGACGG 57.181 50.000 12.10 6.34 46.05 4.79
4803 5925 5.301555 AGGACAGAAACTAGAGCAAAGAAC 58.698 41.667 0.00 0.00 0.00 3.01
4821 5943 7.361542 GCAAAGAACTGTGTCATGACATCTAAT 60.362 37.037 30.10 17.28 43.97 1.73
4838 5960 8.485976 ACATCTAATAGAAAGAGCAAGAACAC 57.514 34.615 0.00 0.00 0.00 3.32
4852 5974 1.006571 AACACGTACGGGACAGCAG 60.007 57.895 27.01 3.29 0.00 4.24
4864 5986 2.185103 GACAGCAGCAGCAGAAGCAC 62.185 60.000 3.17 0.00 45.49 4.40
4877 5999 0.606673 GAAGCACTGGACTTGGGGTC 60.607 60.000 0.00 0.00 43.79 4.46
4916 6038 1.132643 GTCGTTGCTGAGGTAGTCGAT 59.867 52.381 0.00 0.00 32.54 3.59
4952 6074 0.606401 TCGTCGGGGAAGTAGTCGTT 60.606 55.000 0.00 0.00 0.00 3.85
5025 6147 4.040952 CCTTATCACCCTTCTCCCATACAG 59.959 50.000 0.00 0.00 0.00 2.74
5037 6159 2.026262 TCCCATACAGGACTCAAAAGGC 60.026 50.000 0.00 0.00 41.22 4.35
5061 6183 2.042843 CCGGAGGCCTACTGTCCT 60.043 66.667 14.69 0.00 46.14 3.85
5076 6198 4.624364 CCTGACCTGCGGTGCACA 62.624 66.667 20.43 0.00 35.25 4.57
5077 6199 3.349006 CTGACCTGCGGTGCACAC 61.349 66.667 20.43 10.78 35.25 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 190 0.035056 AAATGGGAGCGGAACAGAGG 60.035 55.000 0.00 0.00 0.00 3.69
204 221 2.256117 AGCGGATTTAAATCGGAGGG 57.744 50.000 29.65 14.90 37.79 4.30
719 753 6.094061 AGTAACAGAATCTCAGCTACGAAAC 58.906 40.000 0.00 0.00 0.00 2.78
740 774 8.282982 AGACCAAGAGAGATCAACCTAATAGTA 58.717 37.037 0.00 0.00 0.00 1.82
741 775 7.129425 AGACCAAGAGAGATCAACCTAATAGT 58.871 38.462 0.00 0.00 0.00 2.12
742 776 7.595819 AGACCAAGAGAGATCAACCTAATAG 57.404 40.000 0.00 0.00 0.00 1.73
745 779 6.467677 CAAAGACCAAGAGAGATCAACCTAA 58.532 40.000 0.00 0.00 0.00 2.69
747 781 4.805609 GCAAAGACCAAGAGAGATCAACCT 60.806 45.833 0.00 0.00 0.00 3.50
751 785 5.019470 TCTAGCAAAGACCAAGAGAGATCA 58.981 41.667 0.00 0.00 0.00 2.92
791 825 5.413499 AGAAATTTGAATCTGCATTTCGGG 58.587 37.500 0.00 0.00 39.58 5.14
840 874 6.866010 ATGAACGAAGCATGCTCATTATTA 57.134 33.333 22.93 5.78 0.00 0.98
870 907 8.465999 ACATGGAGCGTCATTCAAATTTATTAA 58.534 29.630 0.00 0.00 0.00 1.40
876 913 4.789012 AACATGGAGCGTCATTCAAATT 57.211 36.364 0.00 0.00 0.00 1.82
887 924 1.126846 GAACGAGTCAAACATGGAGCG 59.873 52.381 0.00 0.00 0.00 5.03
903 944 0.370273 GGTCAACGCATAGCAGAACG 59.630 55.000 0.00 0.00 0.00 3.95
904 945 1.438651 TGGTCAACGCATAGCAGAAC 58.561 50.000 0.00 0.00 0.00 3.01
910 951 5.056480 TCAGGATTTATGGTCAACGCATAG 58.944 41.667 0.00 0.00 0.00 2.23
916 957 5.221126 GGAAGCATCAGGATTTATGGTCAAC 60.221 44.000 0.00 0.00 32.91 3.18
925 966 3.287867 ACATCGGAAGCATCAGGATTT 57.712 42.857 0.00 0.00 0.00 2.17
926 967 3.287867 AACATCGGAAGCATCAGGATT 57.712 42.857 0.00 0.00 0.00 3.01
927 968 3.209410 GAAACATCGGAAGCATCAGGAT 58.791 45.455 0.00 0.00 0.00 3.24
1014 1055 0.753262 TCTCTTTCCCTCTATGCGCC 59.247 55.000 4.18 0.00 0.00 6.53
1016 1057 3.452474 CAGTTCTCTTTCCCTCTATGCG 58.548 50.000 0.00 0.00 0.00 4.73
1026 1067 3.269178 CTCTCCATGCCAGTTCTCTTTC 58.731 50.000 0.00 0.00 0.00 2.62
1084 1125 9.370126 GATCATACAGCAACGAATTTTGTATAC 57.630 33.333 0.00 0.00 34.25 1.47
1169 1220 0.316204 AGCAGCCATGTTCTGTTTGC 59.684 50.000 12.11 3.33 34.33 3.68
1195 1246 1.512926 CCCTCTTTCGTCAAGTGTGG 58.487 55.000 0.00 0.00 33.66 4.17
1338 1389 1.143183 TCCGGATAACTTCAGCCGC 59.857 57.895 0.00 0.00 45.97 6.53
1376 1427 0.179073 CCGATCCTCGCATGAAACCT 60.179 55.000 0.00 0.00 38.82 3.50
1527 1578 0.526524 GCCTCACGAACTCCAGATCG 60.527 60.000 4.83 4.83 44.34 3.69
1533 1584 0.318762 ACTTCTGCCTCACGAACTCC 59.681 55.000 0.00 0.00 0.00 3.85
1578 1629 1.838073 AATTCCGGTGGCCTTCGTCT 61.838 55.000 3.32 0.00 0.00 4.18
1614 1665 4.344978 TGGAGTACAGTATCTCAAGTGCT 58.655 43.478 0.00 0.00 32.93 4.40
1680 1731 0.259938 GCCCTGGGAATCCTGACAAT 59.740 55.000 19.27 0.00 34.32 2.71
1702 1753 2.034179 GCAAACCACTGTAACCAAGGAC 59.966 50.000 0.00 0.00 0.00 3.85
1764 1815 2.609002 GCAAAAGTTGTCTTGCCCAAAG 59.391 45.455 0.11 0.00 41.69 2.77
1773 1824 2.639065 TCCGTTCTGCAAAAGTTGTCT 58.361 42.857 0.00 0.00 0.00 3.41
1780 1831 4.819630 ACTATCAACTTCCGTTCTGCAAAA 59.180 37.500 0.00 0.00 0.00 2.44
1790 1841 5.046529 CCTCAGATTCACTATCAACTTCCG 58.953 45.833 0.00 0.00 35.59 4.30
1800 1851 4.138290 GACGAGGATCCTCAGATTCACTA 58.862 47.826 35.32 0.00 42.86 2.74
1806 1857 2.714250 ACTAGGACGAGGATCCTCAGAT 59.286 50.000 35.32 22.81 46.92 2.90
1809 1860 3.811098 GCATACTAGGACGAGGATCCTCA 60.811 52.174 35.32 18.47 46.92 3.86
1814 1865 4.013728 GAGATGCATACTAGGACGAGGAT 58.986 47.826 0.00 0.00 0.00 3.24
1820 1871 5.440234 TTCTTCGAGATGCATACTAGGAC 57.560 43.478 0.00 0.00 0.00 3.85
1822 1873 5.837437 AGTTTCTTCGAGATGCATACTAGG 58.163 41.667 0.00 0.00 0.00 3.02
1828 1879 4.825422 TCTGAAGTTTCTTCGAGATGCAT 58.175 39.130 0.00 0.00 0.00 3.96
1842 1902 3.805108 GCTCCAGTGACACATCTGAAGTT 60.805 47.826 8.59 0.00 34.02 2.66
1843 1903 2.289320 GCTCCAGTGACACATCTGAAGT 60.289 50.000 8.59 0.00 34.02 3.01
1844 1904 2.289257 TGCTCCAGTGACACATCTGAAG 60.289 50.000 8.59 0.00 34.02 3.02
1845 1905 1.693606 TGCTCCAGTGACACATCTGAA 59.306 47.619 8.59 0.00 34.02 3.02
1847 1907 2.398252 ATGCTCCAGTGACACATCTG 57.602 50.000 8.59 0.00 0.00 2.90
1848 1908 2.676176 CGAATGCTCCAGTGACACATCT 60.676 50.000 8.59 0.00 0.00 2.90
1849 1909 1.662629 CGAATGCTCCAGTGACACATC 59.337 52.381 8.59 0.00 0.00 3.06
1850 1910 1.676916 CCGAATGCTCCAGTGACACAT 60.677 52.381 8.59 0.00 0.00 3.21
1851 1911 0.320683 CCGAATGCTCCAGTGACACA 60.321 55.000 8.59 0.00 0.00 3.72
1852 1912 1.639298 GCCGAATGCTCCAGTGACAC 61.639 60.000 0.00 0.00 36.87 3.67
1853 1913 1.375908 GCCGAATGCTCCAGTGACA 60.376 57.895 0.00 0.00 36.87 3.58
1854 1914 1.375908 TGCCGAATGCTCCAGTGAC 60.376 57.895 0.00 0.00 42.00 3.67
1855 1915 1.375908 GTGCCGAATGCTCCAGTGA 60.376 57.895 0.00 0.00 42.00 3.41
1896 1956 1.173043 CAACAATTTGCGAGGGCCTA 58.827 50.000 5.73 0.00 38.85 3.93
2073 2133 3.740115 TCCTTCTGGTTCTGTAACTTGC 58.260 45.455 0.00 0.00 35.81 4.01
2085 2145 3.474798 TCAGGTGTATCTCCTTCTGGT 57.525 47.619 0.00 0.00 32.37 4.00
2127 2187 5.355670 TCTTCCAGCTACCCCTTATAGAT 57.644 43.478 0.00 0.00 0.00 1.98
2132 2192 2.574824 GGTTTCTTCCAGCTACCCCTTA 59.425 50.000 0.00 0.00 0.00 2.69
2136 2196 2.644676 GATGGTTTCTTCCAGCTACCC 58.355 52.381 0.00 0.00 40.29 3.69
2143 2203 5.503634 TCATTCTCAGATGGTTTCTTCCA 57.496 39.130 0.00 0.00 42.01 3.53
2166 2226 1.003718 GCCAACTCCAAGGTAGCGT 60.004 57.895 0.00 0.00 0.00 5.07
2324 2384 4.837972 AGTAGGAACTGGATTTTCAGCTC 58.162 43.478 0.00 0.00 41.52 4.09
2383 2443 4.381718 GGTTACCTTCGTTGCATCTCTAGT 60.382 45.833 0.00 0.00 0.00 2.57
2412 2472 4.936396 GTTTGAATCTGACAAACGCTTG 57.064 40.909 0.00 0.00 44.32 4.01
2537 2597 6.091076 ACCTGGGAAAATTCCTTGATATGA 57.909 37.500 11.75 0.00 46.72 2.15
2647 2707 8.370940 AGTATCATCAGTGGGTGTATTCAATAG 58.629 37.037 0.00 0.00 0.00 1.73
2697 2757 4.237724 GCTTGGCTTTTCTGATTGGTAAC 58.762 43.478 0.00 0.00 0.00 2.50
2736 2796 7.615365 AGCATATTTTCCTTTCCTACATGAACA 59.385 33.333 0.00 0.00 0.00 3.18
2865 2925 5.163652 TGTGTGATCCTCAGTACTGATAACG 60.164 44.000 25.35 13.68 39.13 3.18
2876 2936 4.397481 TCAATAGCTGTGTGATCCTCAG 57.603 45.455 0.00 8.18 0.00 3.35
2932 2992 0.107459 GTCCATCCTGCCTGACCTTC 60.107 60.000 0.00 0.00 0.00 3.46
2946 3006 3.754965 TGCTAGCTTTTGTTCTGTCCAT 58.245 40.909 17.23 0.00 0.00 3.41
2955 3015 1.675552 ACGGTGTTGCTAGCTTTTGT 58.324 45.000 17.23 4.28 0.00 2.83
3012 3072 7.903145 TGTGTACCTTCAGTGTTATGTTATCT 58.097 34.615 0.00 0.00 0.00 1.98
3098 3242 7.386299 CAGAGCTTATATTCTCGGCAAACTAAT 59.614 37.037 0.00 0.00 34.66 1.73
3107 3252 8.818141 TTTCATAACAGAGCTTATATTCTCGG 57.182 34.615 0.00 0.00 34.66 4.63
3157 3303 9.840427 AATGTTACCGTTTTGATAATGAGAAAG 57.160 29.630 0.00 0.00 0.00 2.62
3159 3305 9.619316 CAAATGTTACCGTTTTGATAATGAGAA 57.381 29.630 0.00 0.00 33.24 2.87
3175 3324 4.022329 CACCTCCTGAAACCAAATGTTACC 60.022 45.833 0.00 0.00 35.67 2.85
3510 3662 3.934457 TCTCTGCGTGTATCAACTTGA 57.066 42.857 0.00 0.00 0.00 3.02
3591 3839 0.547712 TGGGTAGCTGCTCCTCCTTT 60.548 55.000 4.91 0.00 0.00 3.11
3597 3845 3.471680 CTTAAAGATGGGTAGCTGCTCC 58.528 50.000 4.91 7.52 0.00 4.70
3612 3860 4.471386 TCCCTGTCTTCCTCATCCTTAAAG 59.529 45.833 0.00 0.00 0.00 1.85
3627 3875 2.234908 GACATAAGTGCAGTCCCTGTCT 59.765 50.000 17.39 0.00 33.43 3.41
3693 3941 0.954449 CTGAGCTGAACTGCCACTGG 60.954 60.000 0.00 0.00 0.00 4.00
3789 4768 3.372206 CAGCCAAGATTGAGTTAACGAGG 59.628 47.826 0.00 0.00 0.00 4.63
3807 4786 2.512515 GGAGCCGTCATGTCAGCC 60.513 66.667 0.00 0.00 0.00 4.85
3909 4923 3.243907 GGCTCCTTCGCATGAATACTACT 60.244 47.826 0.00 0.00 32.61 2.57
3911 4925 2.698274 TGGCTCCTTCGCATGAATACTA 59.302 45.455 0.00 0.00 32.61 1.82
4290 5381 9.753674 AAATCCAAACTGAAGGAATAACTATGA 57.246 29.630 0.00 0.00 37.48 2.15
4298 5389 9.312904 TCAGATTTAAATCCAAACTGAAGGAAT 57.687 29.630 21.86 0.00 37.48 3.01
4335 5432 0.890683 GCTGTGAATGGGGAAAGGTG 59.109 55.000 0.00 0.00 0.00 4.00
4336 5433 0.251787 GGCTGTGAATGGGGAAAGGT 60.252 55.000 0.00 0.00 0.00 3.50
4341 5438 1.304381 GCAAGGCTGTGAATGGGGA 60.304 57.895 0.00 0.00 0.00 4.81
4369 5473 5.163364 CCTCTAGGATAATGTGCTCAACTGT 60.163 44.000 0.00 0.00 37.39 3.55
4382 5486 8.934023 AATGTTTGTGTTTTCCTCTAGGATAA 57.066 30.769 0.00 0.00 44.98 1.75
4388 5492 8.463930 AATCAGAATGTTTGTGTTTTCCTCTA 57.536 30.769 0.00 0.00 37.40 2.43
4447 5554 6.303054 TCAAAGGAAAACTGGATCATGTGTA 58.697 36.000 0.00 0.00 0.00 2.90
4451 5558 8.500773 CAAAATTCAAAGGAAAACTGGATCATG 58.499 33.333 0.00 0.00 36.43 3.07
4452 5559 8.212995 ACAAAATTCAAAGGAAAACTGGATCAT 58.787 29.630 0.00 0.00 36.43 2.45
4472 5579 7.929785 AGACAAGAATGAAATGAAGCACAAAAT 59.070 29.630 0.00 0.00 0.00 1.82
4477 5585 6.005583 TGAGACAAGAATGAAATGAAGCAC 57.994 37.500 0.00 0.00 0.00 4.40
4480 5588 9.856488 AATGAATGAGACAAGAATGAAATGAAG 57.144 29.630 0.00 0.00 0.00 3.02
4504 5612 6.260377 CGAGTCATTGAACATTGTATGCAAT 58.740 36.000 2.84 2.84 45.42 3.56
4533 5653 5.123979 CACTTCTTATCTTGGCCTTGTAACC 59.876 44.000 3.32 0.00 0.00 2.85
4708 5830 9.042008 TGTTCTAGATGTGTTTAGTTCAAGTTC 57.958 33.333 0.00 0.00 0.00 3.01
4765 5887 8.993424 AGTTTCTGTCCTACATATGATAGGTTT 58.007 33.333 21.12 0.00 40.27 3.27
4783 5905 5.525378 CACAGTTCTTTGCTCTAGTTTCTGT 59.475 40.000 0.00 0.00 33.62 3.41
4803 5925 9.247126 CTCTTTCTATTAGATGTCATGACACAG 57.753 37.037 30.09 18.32 45.05 3.66
4821 5943 4.224433 CGTACGTGTTCTTGCTCTTTCTA 58.776 43.478 7.22 0.00 0.00 2.10
4838 5960 2.507102 CTGCTGCTGTCCCGTACG 60.507 66.667 8.69 8.69 0.00 3.67
4852 5974 0.888285 AAGTCCAGTGCTTCTGCTGC 60.888 55.000 0.00 0.00 42.38 5.25
4864 5986 0.108138 GATGTCGACCCCAAGTCCAG 60.108 60.000 14.12 0.00 43.08 3.86
4877 5999 0.249784 CATGGCTGGAGAGGATGTCG 60.250 60.000 0.00 0.00 0.00 4.35
4916 6038 1.859427 CGACGACTTCTTCCCCGACA 61.859 60.000 0.00 0.00 0.00 4.35
4952 6074 1.066858 GCTTCTTCATCACGGACTCCA 60.067 52.381 0.00 0.00 0.00 3.86
5025 6147 2.183858 GAACCGCGCCTTTTGAGTCC 62.184 60.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.