Multiple sequence alignment - TraesCS1A01G197300

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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 TraesCS1A01G197300 chr1A 100.000 4422 0 0 1 4422 355339581 355335160 0.000000e+00 8167.0
1 TraesCS1A01G197300 chr1B 93.721 3042 110 39 735 3739 385216082 385213085 0.000000e+00 4484.0
2 TraesCS1A01G197300 chr1B 91.718 652 32 10 1 650 385219207 385218576 0.000000e+00 885.0
3 TraesCS1A01G197300 chr1B 95.408 196 9 0 4227 4422 619172392 619172197 3.320000e-81 313.0
4 TraesCS1A01G197300 chr1B 94.531 128 6 1 3805 3932 385212918 385212792 3.490000e-46 196.0
5 TraesCS1A01G197300 chr1B 95.699 93 4 0 3733 3825 385213022 385212930 2.760000e-32 150.0
6 TraesCS1A01G197300 chr1B 88.800 125 4 3 3923 4037 385176094 385175970 1.280000e-30 145.0
7 TraesCS1A01G197300 chr1D 94.019 2558 95 28 1570 4102 283576859 283574335 0.000000e+00 3823.0
8 TraesCS1A01G197300 chr1D 91.975 648 26 14 16 659 283580963 283580338 0.000000e+00 885.0
9 TraesCS1A01G197300 chr1D 90.000 610 36 14 734 1326 283577739 283577138 0.000000e+00 765.0
10 TraesCS1A01G197300 chr1D 95.408 196 9 0 4227 4422 283574054 283573859 3.320000e-81 313.0
11 TraesCS1A01G197300 chr1D 95.408 196 9 0 4227 4422 350954812 350954617 3.320000e-81 313.0
12 TraesCS1A01G197300 chr1D 92.093 215 11 3 1342 1555 283577153 283576944 9.300000e-77 298.0
13 TraesCS1A01G197300 chr1D 94.444 126 7 0 4102 4227 283574213 283574088 1.250000e-45 195.0
14 TraesCS1A01G197300 chrUn 95.408 196 9 0 4227 4422 45082595 45082400 3.320000e-81 313.0
15 TraesCS1A01G197300 chrUn 95.408 196 9 0 4227 4422 182433768 182433963 3.320000e-81 313.0
16 TraesCS1A01G197300 chrUn 95.408 196 9 0 4227 4422 182463258 182463453 3.320000e-81 313.0
17 TraesCS1A01G197300 chr7D 95.408 196 9 0 4227 4422 381955148 381954953 3.320000e-81 313.0
18 TraesCS1A01G197300 chr7D 92.308 52 4 0 2947 2998 183326911 183326860 1.710000e-09 75.0
19 TraesCS1A01G197300 chr7D 100.000 28 0 0 2969 2996 42838869 42838896 8.000000e-03 52.8
20 TraesCS1A01G197300 chr7D 100.000 28 0 0 2978 3005 126669715 126669688 8.000000e-03 52.8
21 TraesCS1A01G197300 chr6D 95.408 196 9 0 4227 4422 57909061 57909256 3.320000e-81 313.0
22 TraesCS1A01G197300 chr5B 95.408 196 9 0 4227 4422 130592486 130592291 3.320000e-81 313.0
23 TraesCS1A01G197300 chr6A 84.507 71 5 5 2955 3020 40610917 40610848 1.030000e-06 65.8
24 TraesCS1A01G197300 chr7A 100.000 28 0 0 2969 2996 42523440 42523467 8.000000e-03 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 TraesCS1A01G197300 chr1A 355335160 355339581 4421 True 8167.00 8167 100.000000 1 4422 1 chr1A.!!$R1 4421
1 TraesCS1A01G197300 chr1B 385212792 385219207 6415 True 1428.75 4484 93.917250 1 3932 4 chr1B.!!$R3 3931
2 TraesCS1A01G197300 chr1D 283573859 283580963 7104 True 1046.50 3823 92.989833 16 4422 6 chr1D.!!$R2 4406

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
665 669 0.036875 GCTTGGTAGGGTTGCAGAGT 59.963 55.0 0.00 0.0 0.00 3.24 F
830 5016 0.250424 GGCCCAGTTGCAAAATGCTT 60.250 50.0 0.00 0.0 45.31 3.91 F
960 5159 0.319383 CGGATCGGCCATTGAGAGAG 60.319 60.0 2.24 0.0 35.94 3.20 F
1238 5441 0.597637 CCTCGCGTGTCAGTTCACTT 60.598 55.0 5.77 0.0 36.33 3.16 F
1826 6100 0.672342 CTTTGCTGCTGCTTCCAGTT 59.328 50.0 17.00 0.0 41.26 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 6511 0.762418 ACAACCACACATCCCTTCGA 59.238 50.000 0.0 0.0 0.0 3.71 R
2234 6512 0.874390 CACAACCACACATCCCTTCG 59.126 55.000 0.0 0.0 0.0 3.79 R
2797 7079 4.512484 GAAAGAGACAGCTTGCCTTATCT 58.488 43.478 0.0 0.0 0.0 1.98 R
3159 7448 3.411446 TCTACTTGCACACATCAAAGGG 58.589 45.455 0.0 0.0 0.0 3.95 R
3592 7884 0.320374 ACCGAATCGCCAGTTTCTCA 59.680 50.000 0.0 0.0 0.0 3.27 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
62 64 4.585955 ACATAGTATGTCCATCACGGTC 57.414 45.455 10.10 0.00 39.92 4.79
63 65 3.321111 ACATAGTATGTCCATCACGGTCC 59.679 47.826 10.10 0.00 39.92 4.46
64 66 1.860641 AGTATGTCCATCACGGTCCA 58.139 50.000 0.00 0.00 35.57 4.02
65 67 1.480954 AGTATGTCCATCACGGTCCAC 59.519 52.381 0.00 0.00 35.57 4.02
66 68 1.480954 GTATGTCCATCACGGTCCACT 59.519 52.381 0.00 0.00 35.57 4.00
67 69 0.984230 ATGTCCATCACGGTCCACTT 59.016 50.000 0.00 0.00 35.57 3.16
88 90 5.466058 ACTTCCACTACATCGATCGTAGTAG 59.534 44.000 29.96 29.96 46.03 2.57
90 92 6.089249 TCCACTACATCGATCGTAGTAGTA 57.911 41.667 33.19 24.31 46.03 1.82
91 93 6.515832 TCCACTACATCGATCGTAGTAGTAA 58.484 40.000 33.19 26.28 46.03 2.24
92 94 6.422100 TCCACTACATCGATCGTAGTAGTAAC 59.578 42.308 33.19 0.00 46.03 2.50
100 102 6.218746 TCGATCGTAGTAGTAACATAGCTGA 58.781 40.000 15.94 0.00 0.00 4.26
133 135 2.915869 ACTGGGAGATTAACAGGGTCA 58.084 47.619 0.00 0.00 36.57 4.02
134 136 2.572104 ACTGGGAGATTAACAGGGTCAC 59.428 50.000 0.00 0.00 36.57 3.67
135 137 2.571653 CTGGGAGATTAACAGGGTCACA 59.428 50.000 0.00 0.00 0.00 3.58
136 138 3.189606 TGGGAGATTAACAGGGTCACAT 58.810 45.455 0.00 0.00 0.00 3.21
137 139 3.199946 TGGGAGATTAACAGGGTCACATC 59.800 47.826 0.00 0.00 0.00 3.06
148 150 2.026822 AGGGTCACATCACATTCAGACC 60.027 50.000 0.00 0.00 43.60 3.85
193 195 1.958205 GAAGCGAGGCGGGATGATG 60.958 63.158 0.00 0.00 0.00 3.07
265 267 1.143373 TTGACGACGATGCGTATGCC 61.143 55.000 0.00 0.00 45.72 4.40
358 361 1.584495 GCCCGCCTTTTACCACTTG 59.416 57.895 0.00 0.00 0.00 3.16
372 375 2.111613 ACCACTTGGGAATTGGATGGAA 59.888 45.455 0.00 0.00 41.15 3.53
373 376 3.246094 ACCACTTGGGAATTGGATGGAAT 60.246 43.478 0.00 0.00 41.15 3.01
377 380 3.119009 TGGGAATTGGATGGAATTGCT 57.881 42.857 0.00 0.00 34.87 3.91
422 425 3.885521 CTAGCCCGTCCGTCCGTC 61.886 72.222 0.00 0.00 0.00 4.79
427 430 4.508128 CCGTCCGTCCGTCCATGG 62.508 72.222 4.97 4.97 0.00 3.66
428 431 3.445687 CGTCCGTCCGTCCATGGA 61.446 66.667 11.44 11.44 35.04 3.41
458 461 1.207593 GTGCGCACACTCATTCACC 59.792 57.895 34.52 2.71 43.85 4.02
575 579 4.653888 CTTTTCCGGCCGGGTGGT 62.654 66.667 42.36 0.00 37.67 4.16
597 601 1.071239 CGATGATCGTTTGACGGATGC 60.071 52.381 6.68 0.00 42.81 3.91
641 645 1.293924 GATGGAATGACACCGCTGAG 58.706 55.000 0.00 0.00 0.00 3.35
650 654 1.461127 GACACCGCTGAGTTAAGCTTG 59.539 52.381 9.86 0.00 41.24 4.01
652 656 0.396811 ACCGCTGAGTTAAGCTTGGT 59.603 50.000 9.86 1.70 41.24 3.67
653 657 1.621814 ACCGCTGAGTTAAGCTTGGTA 59.378 47.619 9.86 0.00 41.24 3.25
654 658 2.271800 CCGCTGAGTTAAGCTTGGTAG 58.728 52.381 9.86 1.68 41.24 3.18
655 659 2.271800 CGCTGAGTTAAGCTTGGTAGG 58.728 52.381 9.86 0.00 41.24 3.18
657 661 2.027100 GCTGAGTTAAGCTTGGTAGGGT 60.027 50.000 9.86 0.00 40.20 4.34
659 663 4.003648 CTGAGTTAAGCTTGGTAGGGTTG 58.996 47.826 9.86 0.00 0.00 3.77
660 664 2.747989 GAGTTAAGCTTGGTAGGGTTGC 59.252 50.000 9.86 0.00 0.00 4.17
661 665 2.107552 AGTTAAGCTTGGTAGGGTTGCA 59.892 45.455 9.86 0.00 0.00 4.08
662 666 2.488153 GTTAAGCTTGGTAGGGTTGCAG 59.512 50.000 9.86 0.00 0.00 4.41
663 667 0.771127 AAGCTTGGTAGGGTTGCAGA 59.229 50.000 0.00 0.00 0.00 4.26
664 668 0.326264 AGCTTGGTAGGGTTGCAGAG 59.674 55.000 0.00 0.00 0.00 3.35
665 669 0.036875 GCTTGGTAGGGTTGCAGAGT 59.963 55.000 0.00 0.00 0.00 3.24
666 670 1.278127 GCTTGGTAGGGTTGCAGAGTA 59.722 52.381 0.00 0.00 0.00 2.59
667 671 2.092914 GCTTGGTAGGGTTGCAGAGTAT 60.093 50.000 0.00 0.00 0.00 2.12
668 672 3.535561 CTTGGTAGGGTTGCAGAGTATG 58.464 50.000 0.00 0.00 0.00 2.39
698 702 4.762289 AAAGATAGGGTTGTAGAGCTGG 57.238 45.455 0.00 0.00 0.00 4.85
699 703 3.689872 AGATAGGGTTGTAGAGCTGGA 57.310 47.619 0.00 0.00 0.00 3.86
700 704 3.571590 AGATAGGGTTGTAGAGCTGGAG 58.428 50.000 0.00 0.00 0.00 3.86
701 705 2.921834 TAGGGTTGTAGAGCTGGAGT 57.078 50.000 0.00 0.00 0.00 3.85
702 706 2.031495 AGGGTTGTAGAGCTGGAGTT 57.969 50.000 0.00 0.00 0.00 3.01
703 707 1.903183 AGGGTTGTAGAGCTGGAGTTC 59.097 52.381 0.00 0.00 0.00 3.01
704 708 1.623811 GGGTTGTAGAGCTGGAGTTCA 59.376 52.381 0.00 0.00 0.00 3.18
705 709 2.237392 GGGTTGTAGAGCTGGAGTTCAT 59.763 50.000 0.00 0.00 0.00 2.57
706 710 3.307762 GGGTTGTAGAGCTGGAGTTCATT 60.308 47.826 0.00 0.00 0.00 2.57
707 711 3.935828 GGTTGTAGAGCTGGAGTTCATTC 59.064 47.826 0.00 0.00 0.00 2.67
708 712 4.323104 GGTTGTAGAGCTGGAGTTCATTCT 60.323 45.833 0.00 0.00 0.00 2.40
709 713 5.105310 GGTTGTAGAGCTGGAGTTCATTCTA 60.105 44.000 0.00 0.00 0.00 2.10
710 714 5.843673 TGTAGAGCTGGAGTTCATTCTAG 57.156 43.478 0.00 0.00 0.00 2.43
711 715 5.265191 TGTAGAGCTGGAGTTCATTCTAGT 58.735 41.667 0.00 0.00 0.00 2.57
749 4925 4.775236 AGACATTGGAGTTCATTCTAGGC 58.225 43.478 0.00 0.00 0.00 3.93
765 4941 3.207669 GCGAAGGAGGCTGCCATG 61.208 66.667 22.65 4.54 0.00 3.66
828 5014 2.028733 CGGCCCAGTTGCAAAATGC 61.029 57.895 0.00 1.52 41.24 3.56
830 5016 0.250424 GGCCCAGTTGCAAAATGCTT 60.250 50.000 0.00 0.00 45.31 3.91
907 5106 2.177233 TCGCCTATCTCCTCCTACCTTT 59.823 50.000 0.00 0.00 0.00 3.11
925 5124 7.445402 CCTACCTTTCATTCTAGAGAGAGAGAG 59.555 44.444 12.72 6.20 31.77 3.20
926 5125 6.969043 ACCTTTCATTCTAGAGAGAGAGAGA 58.031 40.000 12.72 0.00 31.77 3.10
941 5140 2.021039 GAGAGAGGCATCGCATCGC 61.021 63.158 4.63 0.00 44.44 4.58
959 5158 1.742146 CGGATCGGCCATTGAGAGA 59.258 57.895 2.24 0.00 35.94 3.10
960 5159 0.319383 CGGATCGGCCATTGAGAGAG 60.319 60.000 2.24 0.00 35.94 3.20
1066 5266 1.376037 CTCACCAACTTCCTCCGCC 60.376 63.158 0.00 0.00 0.00 6.13
1238 5441 0.597637 CCTCGCGTGTCAGTTCACTT 60.598 55.000 5.77 0.00 36.33 3.16
1262 5465 2.288961 TTGGGATCGCTAGTTTCGTC 57.711 50.000 11.46 0.00 0.00 4.20
1306 5509 5.589855 CCAAATGAGTAGGCAACATCACATA 59.410 40.000 0.00 0.00 41.41 2.29
1328 5531 7.880195 ACATATTCACCTACTGCCTCAAATATC 59.120 37.037 0.00 0.00 0.00 1.63
1366 5569 5.822519 CCTGCTGCCTCAAATTACATAGTAA 59.177 40.000 0.00 0.00 0.00 2.24
1494 5698 1.529622 CGGTACACAAATGCATCTGCG 60.530 52.381 0.00 0.00 45.83 5.18
1578 5852 8.685838 AAGGTAATAGTACAACACAACACAAT 57.314 30.769 2.37 0.00 31.21 2.71
1593 5867 1.244019 ACAATGAGAAAGTGCGGGGC 61.244 55.000 0.00 0.00 0.00 5.80
1594 5868 1.074775 AATGAGAAAGTGCGGGGCA 59.925 52.632 0.00 0.00 35.60 5.36
1595 5869 0.962356 AATGAGAAAGTGCGGGGCAG 60.962 55.000 0.00 0.00 40.08 4.85
1598 5872 4.043200 GAAAGTGCGGGGCAGTGC 62.043 66.667 6.55 6.55 41.77 4.40
1617 5891 4.096382 AGTGCAAAATTCATACCATCGGTC 59.904 41.667 0.00 0.00 37.09 4.79
1618 5892 4.013050 TGCAAAATTCATACCATCGGTCA 58.987 39.130 0.00 0.00 37.09 4.02
1698 5972 4.504826 GCTTTTCGATTAGTAGCAGGACTC 59.495 45.833 0.00 0.00 0.00 3.36
1716 5990 6.096705 CAGGACTCTAGCATCCCAGAATATAG 59.903 46.154 8.15 0.00 35.38 1.31
1752 6026 9.435570 ACCTAGGTACACATTACAATTAGATCT 57.564 33.333 14.41 0.00 0.00 2.75
1798 6072 8.635765 TTAAGGTATCTTCTTTGTGAAAGCAT 57.364 30.769 0.00 0.00 38.39 3.79
1826 6100 0.672342 CTTTGCTGCTGCTTCCAGTT 59.328 50.000 17.00 0.00 41.26 3.16
1840 6114 7.195374 TGCTTCCAGTTATTACTTGATAGGT 57.805 36.000 0.00 0.00 30.26 3.08
1863 6137 7.338196 AGGTGTATATATCGTTCCATCAGAGAG 59.662 40.741 0.00 0.00 0.00 3.20
1892 6169 8.849490 CATTTTTATTGTGATGAACTGGTTACG 58.151 33.333 0.00 0.00 0.00 3.18
1920 6197 1.683385 GCTTCAAGCCTTCAAGTTGGT 59.317 47.619 0.00 0.00 34.48 3.67
1960 6237 6.874288 AGGAATCACTTTCACTCTTTTCAG 57.126 37.500 0.00 0.00 35.94 3.02
1999 6277 2.175202 TGTGTTGCTTTTTGGTGGAGT 58.825 42.857 0.00 0.00 0.00 3.85
2028 6306 7.606456 CACCATGTACACTAACCTATTCTTGTT 59.394 37.037 0.00 0.00 0.00 2.83
2233 6511 3.245052 CCTCCCATCTCTCCAGTTTTGTT 60.245 47.826 0.00 0.00 0.00 2.83
2234 6512 4.006319 CTCCCATCTCTCCAGTTTTGTTC 58.994 47.826 0.00 0.00 0.00 3.18
2797 7079 2.289631 CCACATTACAGACAGCACTGGA 60.290 50.000 2.21 0.00 41.59 3.86
2811 7093 2.286872 CACTGGAGATAAGGCAAGCTG 58.713 52.381 0.00 0.00 0.00 4.24
2879 7165 3.118038 TGCTTTATCCGTTTAGGCAGGAT 60.118 43.478 1.68 1.68 45.75 3.24
2922 7208 4.835056 ACCTAAGTTGTACTACCTCCGTTT 59.165 41.667 3.72 0.00 0.00 3.60
3021 7307 1.726853 AATGAGCACTTAGGCGTGTC 58.273 50.000 0.00 0.00 39.27 3.67
3043 7329 5.416952 GTCTATAAGGCCATGGAATCAATGG 59.583 44.000 18.40 12.34 38.45 3.16
3426 7715 0.908198 GAAGAGGCCACCTGATCTGT 59.092 55.000 5.01 0.00 31.76 3.41
3427 7716 2.111384 GAAGAGGCCACCTGATCTGTA 58.889 52.381 5.01 0.00 31.76 2.74
3480 7770 1.274798 GCATTTGGTTTGGTGTCGCG 61.275 55.000 0.00 0.00 0.00 5.87
3500 7790 2.007608 GGATCTAAAACCGCCAGTCAC 58.992 52.381 0.00 0.00 0.00 3.67
3576 7866 6.095377 CCTGCCACTGAACAATTTTAATCTC 58.905 40.000 0.00 0.00 0.00 2.75
3592 7884 2.885135 TCTCTGTGGATGTGGCAATT 57.115 45.000 0.00 0.00 0.00 2.32
3638 7930 4.498009 CGGTGTTTGCATTGAAGAGTTTCT 60.498 41.667 0.00 0.00 34.31 2.52
3849 8244 2.037847 GAAACCTGGGCATGGGCT 59.962 61.111 0.00 0.00 40.87 5.19
4020 8425 5.535753 AACAGGTTTGGAAAAGAAGATGG 57.464 39.130 0.00 0.00 0.00 3.51
4057 8462 1.702401 TGAAGTTGGGCCACTGACATA 59.298 47.619 5.23 0.00 0.00 2.29
4076 8481 0.624500 ATGGGCCCACCTATCAGTGT 60.625 55.000 31.51 3.31 41.11 3.55
4081 8486 1.285280 CCCACCTATCAGTGTCCCAA 58.715 55.000 0.00 0.00 35.93 4.12
4131 8658 6.655078 ATGCATCTTTTCTAGTTTGGTTGT 57.345 33.333 0.00 0.00 0.00 3.32
4179 8706 8.658619 AGAATATTCCTCTTAGATGCAGAACAT 58.341 33.333 11.92 0.00 43.54 2.71
4197 8724 0.527565 ATGCTTGATCCGCAACCAAC 59.472 50.000 10.34 0.00 41.26 3.77
4216 8743 6.827727 ACCAACTTCTTAGTACATCAACACT 58.172 36.000 0.00 0.00 33.17 3.55
4260 8821 1.376037 GGGCCTCTCAACCAAGACG 60.376 63.158 0.84 0.00 0.00 4.18
4264 8825 0.314302 CCTCTCAACCAAGACGTCGT 59.686 55.000 10.46 3.44 0.00 4.34
4293 8854 3.195825 CGAGTGGGGACTCTACTGAATTT 59.804 47.826 0.00 0.00 33.52 1.82
4317 8878 4.295201 AGCATGGGTGTGGTAGATTACTA 58.705 43.478 0.00 0.00 0.00 1.82
4318 8879 4.907875 AGCATGGGTGTGGTAGATTACTAT 59.092 41.667 0.00 0.00 0.00 2.12
4325 8886 6.406177 GGGTGTGGTAGATTACTATCGTGAAA 60.406 42.308 0.00 0.00 35.85 2.69
4345 8906 1.115467 CCGGACCTCTATGAGTGCTT 58.885 55.000 0.00 0.00 0.00 3.91
4358 8919 0.676782 AGTGCTTTACATGGCCGGAC 60.677 55.000 5.05 0.56 0.00 4.79
4408 8969 4.942944 TGGAGTGGGAAGTACTCAAGATA 58.057 43.478 0.00 0.00 44.92 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 2.099263 ACGATCGATGTAGTGGAAGTGG 59.901 50.000 24.34 0.00 0.00 4.00
63 65 3.422417 ACGATCGATGTAGTGGAAGTG 57.578 47.619 24.34 0.00 0.00 3.16
64 66 4.815040 CTACGATCGATGTAGTGGAAGT 57.185 45.455 24.34 0.00 35.63 3.01
88 90 4.045104 CACGACCAGATCAGCTATGTTAC 58.955 47.826 0.00 0.00 0.00 2.50
90 92 2.497675 ACACGACCAGATCAGCTATGTT 59.502 45.455 0.00 0.00 0.00 2.71
91 93 2.103373 ACACGACCAGATCAGCTATGT 58.897 47.619 0.00 0.00 0.00 2.29
92 94 2.879002 ACACGACCAGATCAGCTATG 57.121 50.000 0.00 0.00 0.00 2.23
100 102 1.825474 CTCCCAGTAACACGACCAGAT 59.175 52.381 0.00 0.00 0.00 2.90
133 135 2.932622 GCTGTCGGTCTGAATGTGATGT 60.933 50.000 0.00 0.00 0.00 3.06
134 136 1.662629 GCTGTCGGTCTGAATGTGATG 59.337 52.381 0.00 0.00 0.00 3.07
135 137 1.552337 AGCTGTCGGTCTGAATGTGAT 59.448 47.619 0.00 0.00 0.00 3.06
136 138 0.969149 AGCTGTCGGTCTGAATGTGA 59.031 50.000 0.00 0.00 0.00 3.58
137 139 2.263077 GTAGCTGTCGGTCTGAATGTG 58.737 52.381 0.00 0.00 0.00 3.21
193 195 2.105128 CGATCAGGTCCGCCTCAC 59.895 66.667 0.00 0.00 44.97 3.51
358 361 3.033184 TGAGCAATTCCATCCAATTCCC 58.967 45.455 0.00 0.00 0.00 3.97
372 375 0.685458 GTTGATGGGGCCTGAGCAAT 60.685 55.000 0.84 0.00 42.56 3.56
373 376 1.304381 GTTGATGGGGCCTGAGCAA 60.304 57.895 0.84 2.79 42.56 3.91
377 380 3.727258 CGGGTTGATGGGGCCTGA 61.727 66.667 0.84 0.00 0.00 3.86
412 415 2.183555 GTCCATGGACGGACGGAC 59.816 66.667 28.52 4.57 45.77 4.79
420 423 3.310860 AACCCGAGCGTCCATGGAC 62.311 63.158 31.59 31.59 41.40 4.02
422 425 2.511600 GAACCCGAGCGTCCATGG 60.512 66.667 4.97 4.97 0.00 3.66
423 426 2.885644 CGAACCCGAGCGTCCATG 60.886 66.667 0.00 0.00 38.22 3.66
425 428 4.351938 CACGAACCCGAGCGTCCA 62.352 66.667 0.00 0.00 38.92 4.02
575 579 2.640346 TCCGTCAAACGATCATCGAA 57.360 45.000 15.60 0.00 46.05 3.71
597 601 3.857854 CGCAGCAAGCTAGCCACG 61.858 66.667 12.13 0.66 42.61 4.94
614 618 0.676466 TGTCATTCCATCGGCCACAC 60.676 55.000 2.24 0.00 0.00 3.82
641 645 2.488153 CTGCAACCCTACCAAGCTTAAC 59.512 50.000 0.00 0.00 0.00 2.01
688 692 5.265191 ACTAGAATGAACTCCAGCTCTACA 58.735 41.667 0.00 0.00 0.00 2.74
690 694 6.859112 AAACTAGAATGAACTCCAGCTCTA 57.141 37.500 0.00 0.00 0.00 2.43
723 727 5.246981 AGAATGAACTCCAATGTCTCCAA 57.753 39.130 0.00 0.00 0.00 3.53
724 728 4.916041 AGAATGAACTCCAATGTCTCCA 57.084 40.909 0.00 0.00 0.00 3.86
730 734 3.797039 TCGCCTAGAATGAACTCCAATG 58.203 45.455 0.00 0.00 0.00 2.82
731 735 4.446371 CTTCGCCTAGAATGAACTCCAAT 58.554 43.478 0.00 0.00 38.34 3.16
732 736 3.369471 CCTTCGCCTAGAATGAACTCCAA 60.369 47.826 0.00 0.00 38.34 3.53
749 4925 2.515523 CCATGGCAGCCTCCTTCG 60.516 66.667 14.15 0.00 0.00 3.79
788 4974 6.106003 CCGAGCCATATTGTTATGCATACTA 58.894 40.000 5.74 0.00 34.94 1.82
907 5106 5.221722 GCCTCTCTCTCTCTCTCTAGAATGA 60.222 48.000 0.00 0.00 0.00 2.57
941 5140 0.319383 CTCTCTCAATGGCCGATCCG 60.319 60.000 0.00 0.00 37.80 4.18
942 5141 1.043816 TCTCTCTCAATGGCCGATCC 58.956 55.000 0.00 0.00 0.00 3.36
943 5142 2.478831 GTTCTCTCTCAATGGCCGATC 58.521 52.381 0.00 0.00 0.00 3.69
944 5143 1.202463 CGTTCTCTCTCAATGGCCGAT 60.202 52.381 0.00 0.00 0.00 4.18
945 5144 0.173481 CGTTCTCTCTCAATGGCCGA 59.827 55.000 0.00 0.00 0.00 5.54
946 5145 0.173481 TCGTTCTCTCTCAATGGCCG 59.827 55.000 0.00 0.00 0.00 6.13
947 5146 2.275318 CTTCGTTCTCTCTCAATGGCC 58.725 52.381 0.00 0.00 0.00 5.36
959 5158 3.007973 GCCGCTCTCCCTTCGTTCT 62.008 63.158 0.00 0.00 0.00 3.01
960 5159 2.509561 GCCGCTCTCCCTTCGTTC 60.510 66.667 0.00 0.00 0.00 3.95
1032 5232 0.984961 TGAGGCCCTTCTCCCTGATG 60.985 60.000 0.00 0.00 33.04 3.07
1227 5430 6.292919 GCGATCCCAATAATAAGTGAACTGAC 60.293 42.308 0.00 0.00 0.00 3.51
1234 5437 7.359264 CGAAACTAGCGATCCCAATAATAAGTG 60.359 40.741 0.00 0.00 0.00 3.16
1238 5441 6.092955 ACGAAACTAGCGATCCCAATAATA 57.907 37.500 0.00 0.00 0.00 0.98
1262 5465 3.131933 TGGGTTCATTAATTTGGATGCGG 59.868 43.478 0.00 0.00 0.00 5.69
1306 5509 5.456763 GGGATATTTGAGGCAGTAGGTGAAT 60.457 44.000 0.00 0.00 0.00 2.57
1328 5531 4.222810 AGGCAGCAGGTTTATTTTTAAGGG 59.777 41.667 0.00 0.00 0.00 3.95
1345 5548 5.529060 AGCTTACTATGTAATTTGAGGCAGC 59.471 40.000 0.00 0.00 0.00 5.25
1366 5569 6.543831 AGAATAATTTCGAAGGCATGTAAGCT 59.456 34.615 0.00 0.00 36.93 3.74
1562 5766 6.468956 CACTTTCTCATTGTGTTGTGTTGTAC 59.531 38.462 0.00 0.00 0.00 2.90
1564 5768 5.401550 CACTTTCTCATTGTGTTGTGTTGT 58.598 37.500 0.00 0.00 0.00 3.32
1578 5852 2.032528 CTGCCCCGCACTTTCTCA 59.967 61.111 0.00 0.00 33.79 3.27
1593 5867 4.142403 ACCGATGGTATGAATTTTGCACTG 60.142 41.667 0.00 0.00 32.11 3.66
1594 5868 4.016444 ACCGATGGTATGAATTTTGCACT 58.984 39.130 0.00 0.00 32.11 4.40
1595 5869 4.142491 TGACCGATGGTATGAATTTTGCAC 60.142 41.667 0.00 0.00 35.25 4.57
1598 5872 4.498009 GGCTGACCGATGGTATGAATTTTG 60.498 45.833 0.00 0.00 35.25 2.44
1646 5920 3.896888 TGGAAGGTGAAAGCACATGAAAT 59.103 39.130 0.00 0.00 46.96 2.17
1840 6114 6.659242 TGCTCTCTGATGGAACGATATATACA 59.341 38.462 0.00 0.00 0.00 2.29
1849 6123 2.306341 ATGTGCTCTCTGATGGAACG 57.694 50.000 0.00 0.00 0.00 3.95
1863 6137 6.646240 ACCAGTTCATCACAATAAAAATGTGC 59.354 34.615 1.91 0.00 46.05 4.57
1920 6197 4.799715 TTCCTTTTAAGAAGTGGGGACA 57.200 40.909 0.00 0.00 38.70 4.02
1999 6277 8.777578 AGAATAGGTTAGTGTACATGGTGATA 57.222 34.615 0.00 0.00 0.00 2.15
2028 6306 8.934023 ATTTAAAAACAGTCCAGAGAATACCA 57.066 30.769 0.00 0.00 0.00 3.25
2068 6346 4.917906 ACTATGGAATTCTATGAGGCCC 57.082 45.455 14.10 0.00 0.00 5.80
2070 6348 6.127196 CCTCCTACTATGGAATTCTATGAGGC 60.127 46.154 16.93 0.00 35.43 4.70
2233 6511 0.762418 ACAACCACACATCCCTTCGA 59.238 50.000 0.00 0.00 0.00 3.71
2234 6512 0.874390 CACAACCACACATCCCTTCG 59.126 55.000 0.00 0.00 0.00 3.79
2797 7079 4.512484 GAAAGAGACAGCTTGCCTTATCT 58.488 43.478 0.00 0.00 0.00 1.98
2811 7093 5.707764 AGGAAAATAGCACAAGGAAAGAGAC 59.292 40.000 0.00 0.00 0.00 3.36
2879 7165 9.226606 CTTAGGTAATACATGTTGTTCAGGAAA 57.773 33.333 2.30 0.00 0.00 3.13
3016 7302 3.469008 TTCCATGGCCTTATAGACACG 57.531 47.619 6.96 0.00 0.00 4.49
3021 7307 4.708421 CCCATTGATTCCATGGCCTTATAG 59.292 45.833 6.96 0.00 34.24 1.31
3043 7329 9.856488 GGGAAAATAAGAAAACTTTCATAGTCC 57.144 33.333 5.07 5.82 39.61 3.85
3080 7369 9.562583 GCACCGTTCAAATAATAATCAAACTTA 57.437 29.630 0.00 0.00 0.00 2.24
3159 7448 3.411446 TCTACTTGCACACATCAAAGGG 58.589 45.455 0.00 0.00 0.00 3.95
3426 7715 8.742125 AAGAGGATTATCAGGTACCATTCATA 57.258 34.615 15.94 1.49 0.00 2.15
3427 7716 7.515514 AGAAGAGGATTATCAGGTACCATTCAT 59.484 37.037 15.94 2.48 0.00 2.57
3480 7770 2.007608 GTGACTGGCGGTTTTAGATCC 58.992 52.381 0.00 0.00 0.00 3.36
3500 7790 2.162681 GTCCAGTCCATGAAACCAAGG 58.837 52.381 0.00 0.00 0.00 3.61
3576 7866 2.439409 TCTCAATTGCCACATCCACAG 58.561 47.619 0.00 0.00 0.00 3.66
3592 7884 0.320374 ACCGAATCGCCAGTTTCTCA 59.680 50.000 0.00 0.00 0.00 3.27
3954 8349 5.408079 AATACAGTGGGATGGAATGGATT 57.592 39.130 0.00 0.00 0.00 3.01
3955 8350 5.135020 AGAAATACAGTGGGATGGAATGGAT 59.865 40.000 0.00 0.00 0.00 3.41
4020 8425 2.046285 CACCCGGGTCTTCATTGCC 61.046 63.158 27.51 0.00 0.00 4.52
4057 8462 0.624500 ACACTGATAGGTGGGCCCAT 60.625 55.000 31.45 16.64 41.09 4.00
4097 8502 6.651755 AGAAAAGATGCATTTTTATTGGCG 57.348 33.333 14.92 0.00 32.62 5.69
4138 8665 9.838339 GAGGAATATTCTCTTAAGATGAACCAA 57.162 33.333 14.95 3.14 0.00 3.67
4153 8680 8.027524 TGTTCTGCATCTAAGAGGAATATTCT 57.972 34.615 14.95 1.62 0.00 2.40
4189 8716 6.017440 TGTTGATGTACTAAGAAGTTGGTTGC 60.017 38.462 0.00 0.00 37.15 4.17
4197 8724 9.347934 CACTTCTAGTGTTGATGTACTAAGAAG 57.652 37.037 0.00 0.00 41.19 2.85
4216 8743 0.830648 CCCATCTTCCGCCACTTCTA 59.169 55.000 0.00 0.00 0.00 2.10
4260 8821 3.041940 CCACTCGCCAACCACGAC 61.042 66.667 0.00 0.00 35.35 4.34
4264 8825 3.948719 GTCCCCACTCGCCAACCA 61.949 66.667 0.00 0.00 0.00 3.67
4293 8854 4.719773 AGTAATCTACCACACCCATGCTAA 59.280 41.667 0.00 0.00 0.00 3.09
4317 8878 1.843368 TAGAGGTCCGGTTTCACGAT 58.157 50.000 0.00 0.00 35.47 3.73
4318 8879 1.475280 CATAGAGGTCCGGTTTCACGA 59.525 52.381 0.00 0.00 35.47 4.35
4325 8886 0.033011 AGCACTCATAGAGGTCCGGT 60.033 55.000 0.00 0.00 33.35 5.28
4358 8919 9.396022 TGGATCTAGTTTTTAGAATAGCTTTGG 57.604 33.333 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.