Multiple sequence alignment - TraesCS5B01G047800

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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 TraesCS5B01G047800 chr5B 100.000 2167 0 0 1 2167 53738215 53736049 0.000000e+00 4002.0
1 TraesCS5B01G047800 chr5B 100.000 481 0 0 2369 2849 53735847 53735367 0.000000e+00 889.0
2 TraesCS5B01G047800 chr5D 96.097 1076 28 7 677 1745 50819717 50818649 0.000000e+00 1742.0
3 TraesCS5B01G047800 chr5D 93.489 599 37 1 76 674 50827033 50826437 0.000000e+00 889.0
4 TraesCS5B01G047800 chr5D 89.241 474 41 4 2376 2849 50816601 50816138 4.090000e-163 584.0
5 TraesCS5B01G047800 chr5D 91.003 289 25 1 1365 1652 50733744 50734032 3.440000e-104 388.0
6 TraesCS5B01G047800 chr5D 87.576 330 26 3 1763 2077 50816937 50816608 4.480000e-98 368.0
7 TraesCS5B01G047800 chr5D 81.373 204 23 9 1647 1839 50771427 50771626 4.920000e-33 152.0
8 TraesCS5B01G047800 chr5D 100.000 29 0 0 925 953 50819505 50819477 1.000000e-03 54.7
9 TraesCS5B01G047800 chr5A 87.234 846 44 20 33 858 40155572 40154771 0.000000e+00 905.0
10 TraesCS5B01G047800 chr5A 94.659 543 27 1 1214 1754 40153764 40153222 0.000000e+00 841.0
11 TraesCS5B01G047800 chr5A 88.186 474 46 5 2376 2849 40152804 40152341 8.920000e-155 556.0
12 TraesCS5B01G047800 chr5A 85.828 501 53 10 1350 1839 40086826 40087319 1.510000e-142 516.0
13 TraesCS5B01G047800 chr5A 88.218 331 24 1 1760 2075 40153143 40152813 5.760000e-102 381.0
14 TraesCS5B01G047800 chr5A 86.726 226 19 7 1004 1225 40154694 40154476 1.020000e-59 241.0
15 TraesCS5B01G047800 chr5A 95.699 93 3 1 2075 2167 680858728 680858819 6.360000e-32 148.0
16 TraesCS5B01G047800 chr5A 94.681 94 4 1 912 1004 40154822 40154729 8.230000e-31 145.0
17 TraesCS5B01G047800 chr5A 95.000 40 2 0 30 69 40157720 40157681 2.370000e-06 63.9
18 TraesCS5B01G047800 chr1A 97.778 90 2 0 2078 2167 574840975 574841064 3.800000e-34 156.0
19 TraesCS5B01G047800 chr7A 97.778 90 1 1 2078 2167 556133632 556133544 1.370000e-33 154.0
20 TraesCS5B01G047800 chr7A 95.604 91 4 0 2077 2167 700681277 700681187 2.290000e-31 147.0
21 TraesCS5B01G047800 chr3A 96.667 90 3 0 2078 2167 698732367 698732456 1.770000e-32 150.0
22 TraesCS5B01G047800 chr7B 95.652 92 3 1 2076 2167 713467145 713467055 2.290000e-31 147.0
23 TraesCS5B01G047800 chr4A 96.629 89 2 1 2079 2167 686991630 686991543 2.290000e-31 147.0
24 TraesCS5B01G047800 chr6B 95.604 91 3 1 2077 2167 694439622 694439533 8.230000e-31 145.0
25 TraesCS5B01G047800 chr6A 94.681 94 4 1 2074 2167 105612242 105612334 8.230000e-31 145.0


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 TraesCS5B01G047800 chr5B 53735367 53738215 2848 True 2445.500000 4002 100.0000 1 2849 2 chr5B.!!$R1 2848
1 TraesCS5B01G047800 chr5D 50826437 50827033 596 True 889.000000 889 93.4890 76 674 1 chr5D.!!$R1 598
2 TraesCS5B01G047800 chr5D 50816138 50819717 3579 True 687.175000 1742 93.2285 677 2849 4 chr5D.!!$R2 2172
3 TraesCS5B01G047800 chr5A 40152341 40157720 5379 True 447.557143 905 90.6720 30 2849 7 chr5A.!!$R1 2819

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
79 2238 0.391661 TTGGAGGAGCGTCAATCTGC 60.392 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 6601 0.178998 GGATCCACTGGCTGATGCAT 60.179 55.0 6.95 0.0 41.91 3.96 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
25 26 8.261492 AGATGTGAGAAAAGTAGCATAAACTG 57.739 34.615 0.00 0.00 0.00 3.16
26 27 7.880195 AGATGTGAGAAAAGTAGCATAAACTGT 59.120 33.333 0.00 0.00 0.00 3.55
27 28 7.801716 TGTGAGAAAAGTAGCATAAACTGTT 57.198 32.000 0.00 0.00 0.00 3.16
28 29 8.896320 TGTGAGAAAAGTAGCATAAACTGTTA 57.104 30.769 0.00 0.00 0.00 2.41
60 61 4.437121 GCAATACGTACGACAGAGAAGAGT 60.437 45.833 24.41 0.00 0.00 3.24
61 62 5.629097 CAATACGTACGACAGAGAAGAGTT 58.371 41.667 24.41 0.00 0.00 3.01
69 70 1.899142 ACAGAGAAGAGTTGGAGGAGC 59.101 52.381 0.00 0.00 0.00 4.70
70 71 1.135141 CAGAGAAGAGTTGGAGGAGCG 60.135 57.143 0.00 0.00 0.00 5.03
71 72 0.892063 GAGAAGAGTTGGAGGAGCGT 59.108 55.000 0.00 0.00 0.00 5.07
73 74 0.603569 GAAGAGTTGGAGGAGCGTCA 59.396 55.000 0.00 0.00 0.00 4.35
79 2238 0.391661 TTGGAGGAGCGTCAATCTGC 60.392 55.000 0.00 0.00 0.00 4.26
107 2266 4.502282 TGCGTTTCATCATGTTTCACAAAC 59.498 37.500 0.00 0.00 41.73 2.93
124 2283 4.522405 CACAAACAAATGTATCCCAGACCA 59.478 41.667 0.00 0.00 30.84 4.02
146 2305 3.880047 AAGATTTGCATGGTGATGTGG 57.120 42.857 0.00 0.00 31.50 4.17
411 2570 4.742201 CACGTCCCCGCCTCTGTG 62.742 72.222 0.00 0.00 37.70 3.66
475 2634 3.291167 GACGTTGAAAGCCGGCGAC 62.291 63.158 23.20 16.70 0.00 5.19
582 2741 3.296584 GCGAACGGCGACATAGAC 58.703 61.111 16.62 0.00 44.57 2.59
590 2749 1.061131 CGGCGACATAGACAAAAGCTG 59.939 52.381 0.00 0.00 0.00 4.24
601 2760 1.321474 CAAAAGCTGCCAAGGTCAGA 58.679 50.000 12.62 0.00 33.54 3.27
604 2763 0.403271 AAGCTGCCAAGGTCAGACAT 59.597 50.000 2.17 0.00 33.54 3.06
629 2788 7.984391 TGCGACAATTATTAGAATGACACATT 58.016 30.769 0.00 0.00 0.00 2.71
674 2833 3.248446 TTGGACGGGGGCTTCGAAG 62.248 63.158 21.02 21.02 0.00 3.79
675 2834 4.468689 GGACGGGGGCTTCGAAGG 62.469 72.222 25.77 11.59 0.00 3.46
745 2908 5.053811 CCCTGGTTTGTTTTGTGGTTTATC 58.946 41.667 0.00 0.00 0.00 1.75
770 2933 2.812178 CGGTTGGACTAACGGCGG 60.812 66.667 13.24 0.00 40.28 6.13
771 2934 2.435410 GGTTGGACTAACGGCGGG 60.435 66.667 13.24 3.31 40.28 6.13
772 2935 2.435410 GTTGGACTAACGGCGGGG 60.435 66.667 13.24 2.91 0.00 5.73
773 2936 2.924101 TTGGACTAACGGCGGGGT 60.924 61.111 13.24 6.61 0.00 4.95
774 2937 1.608918 TTGGACTAACGGCGGGGTA 60.609 57.895 13.24 0.00 0.00 3.69
835 3002 0.596577 TGTGAACCGACTTCCTCTCG 59.403 55.000 0.00 0.00 0.00 4.04
870 3037 9.429600 GTAAAAACCGACTTATATTTGGATTCG 57.570 33.333 0.00 0.00 0.00 3.34
872 3039 6.598753 AACCGACTTATATTTGGATTCGTG 57.401 37.500 0.00 0.00 0.00 4.35
898 3065 2.872858 GTTTCTGAGCTGAACCGACTTT 59.127 45.455 0.00 0.00 0.00 2.66
990 3158 4.397103 TCTTACGTTCTGAGCCGAATTCTA 59.603 41.667 3.52 0.00 0.00 2.10
1014 3218 7.463961 AGTCTAACTCAAAGGATTCTTACGA 57.536 36.000 0.00 0.00 32.01 3.43
1099 3306 1.535462 ACGGCACATCTTGTAAGTTGC 59.465 47.619 3.29 5.31 30.64 4.17
1162 3369 1.612442 AGCCGGAGTCCAAGCCTAA 60.612 57.895 5.05 0.00 0.00 2.69
1163 3370 1.153349 GCCGGAGTCCAAGCCTAAG 60.153 63.158 5.05 0.00 0.00 2.18
1164 3371 1.153349 CCGGAGTCCAAGCCTAAGC 60.153 63.158 10.49 0.00 40.32 3.09
1187 3394 2.936829 TACGAGCTGCGATCCTTGCG 62.937 60.000 11.64 0.00 44.57 4.85
1194 3401 0.104671 TGCGATCCTTGCGATCATCA 59.895 50.000 0.00 0.00 46.85 3.07
1268 4198 3.378427 GCATTCACCTTGATCCCAGTTAC 59.622 47.826 0.00 0.00 0.00 2.50
1559 4489 2.202892 GAACTGCGATCGGGGGAC 60.203 66.667 18.30 0.00 0.00 4.46
1658 4588 2.829120 GAGGCAGTCTTTCCTACTCTGT 59.171 50.000 0.00 0.00 31.71 3.41
1692 4622 2.537401 GCCAAGACTATGTACACCGTC 58.463 52.381 15.15 15.15 0.00 4.79
1734 4666 0.763652 AGTCTAGGATGGCATGGCTG 59.236 55.000 21.08 4.07 0.00 4.85
1754 4686 4.499696 GCTGGCTTGCTTCTTCTTTGTTTA 60.500 41.667 0.00 0.00 0.00 2.01
1755 4687 4.932146 TGGCTTGCTTCTTCTTTGTTTAC 58.068 39.130 0.00 0.00 0.00 2.01
1804 6457 9.469807 CCTTGAAGCTACTATTACATCTTGTAG 57.530 37.037 0.00 0.00 33.92 2.74
1826 6479 4.762251 AGGAGTACTTTTCTTGATTGCCAC 59.238 41.667 0.00 0.00 0.00 5.01
1836 6489 6.647334 TTCTTGATTGCCACAATTGTAAGA 57.353 33.333 11.53 11.68 0.00 2.10
1847 6500 6.481134 CCACAATTGTAAGATGTTCATCTCG 58.519 40.000 11.53 0.00 0.00 4.04
1863 6516 2.168496 TCTCGTCTTTCAATCTCCGGT 58.832 47.619 0.00 0.00 0.00 5.28
2000 6668 3.764160 CTGCGGGGGCTCATCTTCC 62.764 68.421 0.00 0.00 0.00 3.46
2014 6682 3.316573 CTTCCTGGGAGGTCGTGGC 62.317 68.421 0.00 0.00 36.53 5.01
2060 6728 1.587054 CTCTCCTCGTGTGGTGGTC 59.413 63.158 0.00 0.00 0.00 4.02
2078 6746 4.467084 GGAATGCCGCCGAGGTCA 62.467 66.667 0.00 0.00 43.70 4.02
2079 6747 2.892425 GAATGCCGCCGAGGTCAG 60.892 66.667 0.00 0.00 43.70 3.51
2080 6748 3.665675 GAATGCCGCCGAGGTCAGT 62.666 63.158 0.00 0.00 43.70 3.41
2081 6749 3.958147 AATGCCGCCGAGGTCAGTG 62.958 63.158 0.00 0.00 43.70 3.66
2087 6755 4.135153 CCGAGGTCAGTGGCGGAG 62.135 72.222 0.00 0.00 46.29 4.63
2100 6768 3.211288 CGGAGCCAGGATTCGAGT 58.789 61.111 0.00 0.00 0.00 4.18
2101 6769 2.415825 CGGAGCCAGGATTCGAGTA 58.584 57.895 0.00 0.00 0.00 2.59
2102 6770 0.962489 CGGAGCCAGGATTCGAGTAT 59.038 55.000 0.00 0.00 0.00 2.12
2103 6771 2.160205 CGGAGCCAGGATTCGAGTATA 58.840 52.381 0.00 0.00 0.00 1.47
2104 6772 2.162608 CGGAGCCAGGATTCGAGTATAG 59.837 54.545 0.00 0.00 0.00 1.31
2105 6773 2.494073 GGAGCCAGGATTCGAGTATAGG 59.506 54.545 0.00 0.00 0.00 2.57
2106 6774 2.494073 GAGCCAGGATTCGAGTATAGGG 59.506 54.545 0.00 0.00 0.00 3.53
2107 6775 1.550976 GCCAGGATTCGAGTATAGGGG 59.449 57.143 0.00 0.00 0.00 4.79
2108 6776 2.180276 CCAGGATTCGAGTATAGGGGG 58.820 57.143 0.00 0.00 0.00 5.40
2123 6791 4.500265 GGGGGCCGAGTACGTATA 57.500 61.111 0.00 0.00 37.88 1.47
2124 6792 2.967270 GGGGGCCGAGTACGTATAT 58.033 57.895 0.00 0.00 37.88 0.86
2125 6793 1.260544 GGGGGCCGAGTACGTATATT 58.739 55.000 0.00 0.00 37.88 1.28
2126 6794 1.067354 GGGGGCCGAGTACGTATATTG 60.067 57.143 0.00 0.00 37.88 1.90
2127 6795 1.888512 GGGGCCGAGTACGTATATTGA 59.111 52.381 0.00 0.00 37.88 2.57
2128 6796 2.494870 GGGGCCGAGTACGTATATTGAT 59.505 50.000 0.00 0.00 37.88 2.57
2129 6797 3.428589 GGGGCCGAGTACGTATATTGATC 60.429 52.174 0.00 0.00 37.88 2.92
2130 6798 3.442977 GGGCCGAGTACGTATATTGATCT 59.557 47.826 0.00 0.00 37.88 2.75
2131 6799 4.637534 GGGCCGAGTACGTATATTGATCTA 59.362 45.833 0.00 0.00 37.88 1.98
2132 6800 5.124457 GGGCCGAGTACGTATATTGATCTAA 59.876 44.000 0.00 0.00 37.88 2.10
2133 6801 6.183360 GGGCCGAGTACGTATATTGATCTAAT 60.183 42.308 0.00 0.00 37.88 1.73
2134 6802 6.911511 GGCCGAGTACGTATATTGATCTAATC 59.088 42.308 0.00 0.00 37.88 1.75
2135 6803 7.201714 GGCCGAGTACGTATATTGATCTAATCT 60.202 40.741 0.00 0.00 37.88 2.40
2136 6804 8.182881 GCCGAGTACGTATATTGATCTAATCTT 58.817 37.037 0.00 0.00 37.88 2.40
2137 6805 9.491934 CCGAGTACGTATATTGATCTAATCTTG 57.508 37.037 0.00 0.00 37.88 3.02
2151 6819 9.529325 TGATCTAATCTTGTTGGTAATTACTCG 57.471 33.333 15.05 0.00 0.00 4.18
2152 6820 9.530633 GATCTAATCTTGTTGGTAATTACTCGT 57.469 33.333 15.05 0.00 0.00 4.18
2153 6821 8.922058 TCTAATCTTGTTGGTAATTACTCGTC 57.078 34.615 15.05 0.00 0.00 4.20
2154 6822 6.642683 AATCTTGTTGGTAATTACTCGTCG 57.357 37.500 15.05 0.00 0.00 5.12
2155 6823 3.922240 TCTTGTTGGTAATTACTCGTCGC 59.078 43.478 15.05 0.00 0.00 5.19
2156 6824 3.581024 TGTTGGTAATTACTCGTCGCT 57.419 42.857 15.05 0.00 0.00 4.93
2157 6825 3.504863 TGTTGGTAATTACTCGTCGCTC 58.495 45.455 15.05 0.00 0.00 5.03
2158 6826 2.856557 GTTGGTAATTACTCGTCGCTCC 59.143 50.000 15.05 0.00 0.00 4.70
2159 6827 2.372264 TGGTAATTACTCGTCGCTCCT 58.628 47.619 15.05 0.00 0.00 3.69
2160 6828 3.544684 TGGTAATTACTCGTCGCTCCTA 58.455 45.455 15.05 0.00 0.00 2.94
2161 6829 3.313526 TGGTAATTACTCGTCGCTCCTAC 59.686 47.826 15.05 0.00 0.00 3.18
2162 6830 3.563390 GGTAATTACTCGTCGCTCCTACT 59.437 47.826 15.05 0.00 0.00 2.57
2163 6831 4.752101 GGTAATTACTCGTCGCTCCTACTA 59.248 45.833 15.05 0.00 0.00 1.82
2164 6832 5.237344 GGTAATTACTCGTCGCTCCTACTAA 59.763 44.000 15.05 0.00 0.00 2.24
2165 6833 5.824904 AATTACTCGTCGCTCCTACTAAA 57.175 39.130 0.00 0.00 0.00 1.85
2166 6834 5.824904 ATTACTCGTCGCTCCTACTAAAA 57.175 39.130 0.00 0.00 0.00 1.52
2385 7053 2.028484 GGTCAACCGTGCTCGTCA 59.972 61.111 7.47 0.00 35.01 4.35
2396 7064 0.321475 TGCTCGTCATTGCATGGTGA 60.321 50.000 0.00 0.00 33.94 4.02
2407 7075 1.469703 TGCATGGTGAAAGAAGATGCG 59.530 47.619 0.00 0.00 41.92 4.73
2437 7105 1.562008 TCTCGGTCAGATCTGGTCTCT 59.438 52.381 22.42 0.00 34.00 3.10
2519 7187 2.936498 CACTTTCGTCCATGGTATGTCC 59.064 50.000 12.58 0.00 0.00 4.02
2520 7188 2.093128 ACTTTCGTCCATGGTATGTCCC 60.093 50.000 12.58 0.00 34.77 4.46
2521 7189 1.574263 TTCGTCCATGGTATGTCCCA 58.426 50.000 12.58 0.00 39.27 4.37
2565 7233 0.178767 TGTCTTGCTGCTGTGAGTGT 59.821 50.000 0.00 0.00 0.00 3.55
2586 7254 0.179040 GTGTTCGGGGTTTGGAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
2599 7267 5.891980 TTTGGAGTCAATGTGCAGGAGCA 62.892 47.826 0.00 0.00 39.62 4.26
2617 7285 0.542702 CAAGGTTTGGATGCCTGGGT 60.543 55.000 0.00 0.00 34.90 4.51
2662 7330 3.258622 TCACATTGGATTTTCAGCATGCA 59.741 39.130 21.98 0.00 34.76 3.96
2697 7365 3.005684 GTGATGGTTGCATCTTTTGGTCA 59.994 43.478 0.00 0.00 33.01 4.02
2706 7374 0.893270 TCTTTTGGTCATGTGGGCGG 60.893 55.000 0.00 0.00 0.00 6.13
2709 7377 4.720902 TGGTCATGTGGGCGGCTG 62.721 66.667 9.56 0.00 0.00 4.85
2710 7378 4.722700 GGTCATGTGGGCGGCTGT 62.723 66.667 9.56 0.00 0.00 4.40
2711 7379 3.434319 GTCATGTGGGCGGCTGTG 61.434 66.667 9.56 3.07 0.00 3.66
2730 7398 0.317938 GTAGGATGTAGCGCTCGGTG 60.318 60.000 16.34 0.00 0.00 4.94
2742 7410 1.139734 CTCGGTGATCCTGGTGTCG 59.860 63.158 0.00 0.00 0.00 4.35
2743 7411 2.184322 CGGTGATCCTGGTGTCGG 59.816 66.667 0.00 0.00 0.00 4.79
2764 7432 1.903404 GTGCCTTGGAAGTGGTGGG 60.903 63.158 0.00 0.00 0.00 4.61
2770 7438 1.071314 TTGGAAGTGGTGGGTCCCAT 61.071 55.000 15.49 0.00 36.74 4.00
2776 7444 0.106149 GTGGTGGGTCCCATATCGTC 59.894 60.000 15.49 0.00 36.74 4.20
2777 7445 0.325765 TGGTGGGTCCCATATCGTCA 60.326 55.000 15.49 3.62 35.28 4.35
2786 7454 3.129638 GTCCCATATCGTCATCTAGAGGC 59.870 52.174 0.00 0.00 32.24 4.70
2790 7458 4.381398 CCATATCGTCATCTAGAGGCCTTG 60.381 50.000 6.77 0.00 32.24 3.61
2791 7459 2.145397 TCGTCATCTAGAGGCCTTGT 57.855 50.000 6.77 0.00 32.24 3.16
2792 7460 2.457598 TCGTCATCTAGAGGCCTTGTT 58.542 47.619 6.77 0.00 32.24 2.83
2793 7461 2.832129 TCGTCATCTAGAGGCCTTGTTT 59.168 45.455 6.77 0.00 32.24 2.83
2794 7462 2.932614 CGTCATCTAGAGGCCTTGTTTG 59.067 50.000 6.77 1.73 0.00 2.93
2795 7463 3.274288 GTCATCTAGAGGCCTTGTTTGG 58.726 50.000 6.77 0.00 0.00 3.28
2796 7464 2.912956 TCATCTAGAGGCCTTGTTTGGT 59.087 45.455 6.77 0.00 0.00 3.67
2811 7479 2.032681 GGTGGCGGCTTGTCTTCT 59.967 61.111 11.43 0.00 0.00 2.85
2832 7500 1.075374 CTTGGGGTGGATTGGTTCTCA 59.925 52.381 0.00 0.00 0.00 3.27
2841 7509 2.041755 GGATTGGTTCTCAGGGTTCCTT 59.958 50.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.880195 ACAGTTTATGCTACTTTTCTCACATCT 59.120 33.333 0.00 0.00 0.00 2.90
1 2 8.034058 ACAGTTTATGCTACTTTTCTCACATC 57.966 34.615 0.00 0.00 0.00 3.06
2 3 7.986085 ACAGTTTATGCTACTTTTCTCACAT 57.014 32.000 0.00 0.00 0.00 3.21
3 4 7.801716 AACAGTTTATGCTACTTTTCTCACA 57.198 32.000 0.00 0.00 0.00 3.58
22 23 8.961092 CGTACGTATTGCTGTAATAATAACAGT 58.039 33.333 7.22 0.00 45.01 3.55
23 24 9.172820 TCGTACGTATTGCTGTAATAATAACAG 57.827 33.333 16.05 0.00 45.80 3.16
24 25 8.957028 GTCGTACGTATTGCTGTAATAATAACA 58.043 33.333 16.05 0.00 33.22 2.41
25 26 8.957028 TGTCGTACGTATTGCTGTAATAATAAC 58.043 33.333 16.05 0.00 33.22 1.89
26 27 9.172820 CTGTCGTACGTATTGCTGTAATAATAA 57.827 33.333 16.05 0.00 33.22 1.40
27 28 8.558700 TCTGTCGTACGTATTGCTGTAATAATA 58.441 33.333 16.05 0.00 33.22 0.98
28 29 7.420002 TCTGTCGTACGTATTGCTGTAATAAT 58.580 34.615 16.05 0.00 33.22 1.28
60 61 0.391661 GCAGATTGACGCTCCTCCAA 60.392 55.000 0.00 0.00 0.00 3.53
61 62 1.219124 GCAGATTGACGCTCCTCCA 59.781 57.895 0.00 0.00 0.00 3.86
69 70 1.350193 ACGCAACTAGCAGATTGACG 58.650 50.000 0.00 0.00 46.13 4.35
70 71 3.186409 TGAAACGCAACTAGCAGATTGAC 59.814 43.478 0.00 0.00 46.13 3.18
71 72 3.398406 TGAAACGCAACTAGCAGATTGA 58.602 40.909 0.00 0.00 46.13 2.57
73 74 4.002982 TGATGAAACGCAACTAGCAGATT 58.997 39.130 0.00 0.00 46.13 2.40
79 2238 5.565259 GTGAAACATGATGAAACGCAACTAG 59.435 40.000 0.00 0.00 36.32 2.57
107 2266 6.780457 ATCTTTTGGTCTGGGATACATTTG 57.220 37.500 0.00 0.00 39.74 2.32
108 2267 7.614494 CAAATCTTTTGGTCTGGGATACATTT 58.386 34.615 0.00 0.00 39.74 2.32
124 2283 4.040706 ACCACATCACCATGCAAATCTTTT 59.959 37.500 0.00 0.00 32.57 2.27
146 2305 1.875963 CCAAGTTGGATGCCACGAC 59.124 57.895 17.60 0.00 40.96 4.34
310 2469 0.806102 AAGGTTCGATCGCCATGACG 60.806 55.000 11.09 0.00 0.00 4.35
475 2634 2.516923 GGGATATATCGCAACGACTCG 58.483 52.381 21.44 0.00 39.18 4.18
578 2737 2.158682 TGACCTTGGCAGCTTTTGTCTA 60.159 45.455 0.00 0.00 30.85 2.59
580 2739 1.000938 CTGACCTTGGCAGCTTTTGTC 60.001 52.381 0.00 0.00 29.34 3.18
582 2741 1.000938 GTCTGACCTTGGCAGCTTTTG 60.001 52.381 0.00 0.00 38.81 2.44
590 2749 1.375908 TCGCATGTCTGACCTTGGC 60.376 57.895 5.17 3.02 0.00 4.52
601 2760 7.065683 TGTGTCATTCTAATAATTGTCGCATGT 59.934 33.333 0.00 0.00 0.00 3.21
604 2763 6.976636 TGTGTCATTCTAATAATTGTCGCA 57.023 33.333 0.00 0.00 0.00 5.10
639 2798 1.013005 CAAGCACAGAGACAGAGGCG 61.013 60.000 0.00 0.00 0.00 5.52
671 2830 0.531753 GATCCCGAAGCTGCTCCTTC 60.532 60.000 1.00 0.00 38.24 3.46
674 2833 2.049627 ATGGATCCCGAAGCTGCTCC 62.050 60.000 9.90 0.00 0.00 4.70
675 2834 0.883814 CATGGATCCCGAAGCTGCTC 60.884 60.000 9.90 0.00 0.00 4.26
745 2908 0.320374 TTAGTCCAACCGTCTGCCTG 59.680 55.000 0.00 0.00 0.00 4.85
770 2933 7.601508 CGTGAGGTCCTACAAATAAATATACCC 59.398 40.741 0.00 0.00 0.00 3.69
771 2934 8.362639 TCGTGAGGTCCTACAAATAAATATACC 58.637 37.037 0.00 0.00 0.00 2.73
772 2935 9.408069 CTCGTGAGGTCCTACAAATAAATATAC 57.592 37.037 0.00 0.00 0.00 1.47
773 2936 9.358406 TCTCGTGAGGTCCTACAAATAAATATA 57.642 33.333 0.00 0.00 0.00 0.86
774 2937 8.246430 TCTCGTGAGGTCCTACAAATAAATAT 57.754 34.615 0.00 0.00 0.00 1.28
835 3002 3.671716 AGTCGGTTTTTACATGGAGTCC 58.328 45.455 0.73 0.73 0.00 3.85
870 3037 3.059800 GGTTCAGCTCAGAAACGTAACAC 60.060 47.826 0.00 0.00 0.00 3.32
872 3039 3.790212 GGTTCAGCTCAGAAACGTAAC 57.210 47.619 0.00 0.00 0.00 2.50
898 3065 4.038763 ACACGTTACATGGAGTTTGAGAGA 59.961 41.667 0.00 0.00 0.00 3.10
1164 3371 1.659954 GGATCGCAGCTCGTAGCAG 60.660 63.158 9.09 3.00 45.56 4.24
1165 3372 1.667154 AAGGATCGCAGCTCGTAGCA 61.667 55.000 9.09 0.00 45.56 3.49
1187 3394 3.363128 CGACGCATAGTGTGATGATGATC 59.637 47.826 0.00 0.00 0.00 2.92
1194 3401 1.515487 TGCCGACGCATAGTGTGAT 59.485 52.632 0.00 0.00 41.12 3.06
1212 3419 6.825721 CACTTTTGAAGCCCTAGTATCAGAAT 59.174 38.462 0.00 0.00 0.00 2.40
1544 4474 2.683933 AAGTCCCCCGATCGCAGT 60.684 61.111 10.32 0.00 0.00 4.40
1559 4489 0.679505 TCTCCACCACGAACTCCAAG 59.320 55.000 0.00 0.00 0.00 3.61
1658 4588 4.577677 TGGCCAGGCTTTGCACGA 62.578 61.111 12.43 0.00 0.00 4.35
1692 4622 1.134367 TCTTCGCGTTGGGAGTAGATG 59.866 52.381 5.77 0.00 0.00 2.90
1734 4666 5.188327 AGTAAACAAAGAAGAAGCAAGCC 57.812 39.130 0.00 0.00 0.00 4.35
1804 6457 4.518970 TGTGGCAATCAAGAAAAGTACTCC 59.481 41.667 0.00 0.00 0.00 3.85
1836 6489 5.814705 GGAGATTGAAAGACGAGATGAACAT 59.185 40.000 0.00 0.00 0.00 2.71
1847 6500 4.998033 AGAAAGAACCGGAGATTGAAAGAC 59.002 41.667 9.46 0.00 0.00 3.01
1863 6516 3.664107 CAACACATCGAGGGAGAAAGAA 58.336 45.455 0.69 0.00 0.00 2.52
1933 6601 0.178998 GGATCCACTGGCTGATGCAT 60.179 55.000 6.95 0.00 41.91 3.96
1987 6655 1.694169 TCCCAGGAAGATGAGCCCC 60.694 63.158 0.00 0.00 0.00 5.80
2028 6696 2.835431 AGAGGGAGATGACCGCCG 60.835 66.667 0.00 0.00 35.33 6.46
2034 6702 0.626382 ACACGAGGAGAGGGAGATGA 59.374 55.000 0.00 0.00 0.00 2.92
2036 6704 0.396417 CCACACGAGGAGAGGGAGAT 60.396 60.000 0.00 0.00 0.00 2.75
2042 6710 1.587054 GACCACCACACGAGGAGAG 59.413 63.158 0.00 0.00 0.00 3.20
2082 6750 1.735376 TACTCGAATCCTGGCTCCGC 61.735 60.000 0.00 0.00 0.00 5.54
2083 6751 0.962489 ATACTCGAATCCTGGCTCCG 59.038 55.000 0.00 0.00 0.00 4.63
2084 6752 2.494073 CCTATACTCGAATCCTGGCTCC 59.506 54.545 0.00 0.00 0.00 4.70
2085 6753 2.494073 CCCTATACTCGAATCCTGGCTC 59.506 54.545 0.00 0.00 0.00 4.70
2086 6754 2.530701 CCCTATACTCGAATCCTGGCT 58.469 52.381 0.00 0.00 0.00 4.75
2087 6755 1.550976 CCCCTATACTCGAATCCTGGC 59.449 57.143 0.00 0.00 0.00 4.85
2088 6756 2.180276 CCCCCTATACTCGAATCCTGG 58.820 57.143 0.00 0.00 0.00 4.45
2106 6774 1.067354 CAATATACGTACTCGGCCCCC 60.067 57.143 0.00 0.00 41.85 5.40
2107 6775 1.888512 TCAATATACGTACTCGGCCCC 59.111 52.381 0.00 0.00 41.85 5.80
2108 6776 3.442977 AGATCAATATACGTACTCGGCCC 59.557 47.826 0.00 0.00 41.85 5.80
2109 6777 4.698583 AGATCAATATACGTACTCGGCC 57.301 45.455 0.00 0.00 41.85 6.13
2110 6778 7.695820 AGATTAGATCAATATACGTACTCGGC 58.304 38.462 0.00 0.00 41.85 5.54
2111 6779 9.491934 CAAGATTAGATCAATATACGTACTCGG 57.508 37.037 0.00 0.00 41.85 4.63
2125 6793 9.529325 CGAGTAATTACCAACAAGATTAGATCA 57.471 33.333 12.05 0.00 0.00 2.92
2126 6794 9.530633 ACGAGTAATTACCAACAAGATTAGATC 57.469 33.333 12.05 0.00 0.00 2.75
2127 6795 9.530633 GACGAGTAATTACCAACAAGATTAGAT 57.469 33.333 12.05 0.00 0.00 1.98
2128 6796 7.699391 CGACGAGTAATTACCAACAAGATTAGA 59.301 37.037 12.05 0.00 0.00 2.10
2129 6797 7.514747 GCGACGAGTAATTACCAACAAGATTAG 60.515 40.741 12.05 0.00 0.00 1.73
2130 6798 6.254157 GCGACGAGTAATTACCAACAAGATTA 59.746 38.462 12.05 0.00 0.00 1.75
2131 6799 5.063060 GCGACGAGTAATTACCAACAAGATT 59.937 40.000 12.05 0.00 0.00 2.40
2132 6800 4.565564 GCGACGAGTAATTACCAACAAGAT 59.434 41.667 12.05 0.00 0.00 2.40
2133 6801 3.922240 GCGACGAGTAATTACCAACAAGA 59.078 43.478 12.05 0.00 0.00 3.02
2134 6802 3.924686 AGCGACGAGTAATTACCAACAAG 59.075 43.478 12.05 1.79 0.00 3.16
2135 6803 3.916761 AGCGACGAGTAATTACCAACAA 58.083 40.909 12.05 0.00 0.00 2.83
2136 6804 3.504863 GAGCGACGAGTAATTACCAACA 58.495 45.455 12.05 0.00 0.00 3.33
2137 6805 2.856557 GGAGCGACGAGTAATTACCAAC 59.143 50.000 12.05 3.89 0.00 3.77
2138 6806 2.756760 AGGAGCGACGAGTAATTACCAA 59.243 45.455 12.05 0.00 0.00 3.67
2139 6807 2.372264 AGGAGCGACGAGTAATTACCA 58.628 47.619 12.05 0.00 0.00 3.25
2140 6808 3.563390 AGTAGGAGCGACGAGTAATTACC 59.437 47.826 12.05 3.36 0.00 2.85
2141 6809 4.809815 AGTAGGAGCGACGAGTAATTAC 57.190 45.455 7.57 7.57 0.00 1.89
2142 6810 6.925610 TTTAGTAGGAGCGACGAGTAATTA 57.074 37.500 0.00 0.00 0.00 1.40
2143 6811 5.824904 TTTAGTAGGAGCGACGAGTAATT 57.175 39.130 0.00 0.00 0.00 1.40
2144 6812 5.824904 TTTTAGTAGGAGCGACGAGTAAT 57.175 39.130 0.00 0.00 0.00 1.89
2368 7036 0.949105 AATGACGAGCACGGTTGACC 60.949 55.000 8.74 0.00 44.46 4.02
2373 7041 1.375908 ATGCAATGACGAGCACGGT 60.376 52.632 8.74 0.00 44.49 4.83
2374 7042 3.489731 ATGCAATGACGAGCACGG 58.510 55.556 8.74 0.00 44.49 4.94
2385 7053 3.428452 CGCATCTTCTTTCACCATGCAAT 60.428 43.478 0.00 0.00 39.94 3.56
2396 7064 1.826385 CAACCCTCCGCATCTTCTTT 58.174 50.000 0.00 0.00 0.00 2.52
2407 7075 2.232298 CTGACCGAGAGCAACCCTCC 62.232 65.000 0.00 0.00 41.74 4.30
2437 7105 1.950909 GTGAACCCAAATCGGTCAACA 59.049 47.619 0.00 0.00 33.98 3.33
2499 7167 2.093128 GGGACATACCATGGACGAAAGT 60.093 50.000 21.47 7.71 44.88 2.66
2520 7188 0.326264 CACCTCCTTTCCAGTCCCTG 59.674 60.000 0.00 0.00 0.00 4.45
2521 7189 0.104409 ACACCTCCTTTCCAGTCCCT 60.104 55.000 0.00 0.00 0.00 4.20
2565 7233 1.149627 CTCCAAACCCCGAACACCA 59.850 57.895 0.00 0.00 0.00 4.17
2599 7267 1.005924 CTACCCAGGCATCCAAACCTT 59.994 52.381 0.00 0.00 32.56 3.50
2626 7294 2.357517 GTGACAGACCGCCACCTG 60.358 66.667 0.00 0.00 36.53 4.00
2643 7311 4.693283 AGATGCATGCTGAAAATCCAATG 58.307 39.130 20.33 0.00 0.00 2.82
2662 7330 1.176527 CCATCACCACCGCAAAAGAT 58.823 50.000 0.00 0.00 0.00 2.40
2697 7365 2.268920 CTACACAGCCGCCCACAT 59.731 61.111 0.00 0.00 0.00 3.21
2706 7374 0.103208 AGCGCTACATCCTACACAGC 59.897 55.000 8.99 0.00 0.00 4.40
2709 7377 0.317938 CCGAGCGCTACATCCTACAC 60.318 60.000 11.50 0.00 0.00 2.90
2710 7378 0.750546 ACCGAGCGCTACATCCTACA 60.751 55.000 11.50 0.00 0.00 2.74
2711 7379 0.317938 CACCGAGCGCTACATCCTAC 60.318 60.000 11.50 0.00 0.00 3.18
2730 7398 3.771160 ACCGCCGACACCAGGATC 61.771 66.667 0.00 0.00 0.00 3.36
2743 7411 3.365265 CCACTTCCAAGGCACCGC 61.365 66.667 0.00 0.00 0.00 5.68
2749 7417 1.074951 GGACCCACCACTTCCAAGG 59.925 63.158 0.00 0.00 38.79 3.61
2764 7432 3.129638 GCCTCTAGATGACGATATGGGAC 59.870 52.174 0.00 0.00 0.00 4.46
2770 7438 3.833732 ACAAGGCCTCTAGATGACGATA 58.166 45.455 5.23 0.00 0.00 2.92
2776 7444 3.012518 CACCAAACAAGGCCTCTAGATG 58.987 50.000 5.23 1.84 0.00 2.90
2777 7445 2.025887 CCACCAAACAAGGCCTCTAGAT 60.026 50.000 5.23 0.00 0.00 1.98
2786 7454 2.498056 AAGCCGCCACCAAACAAGG 61.498 57.895 0.00 0.00 0.00 3.61
2790 7458 1.734388 AAGACAAGCCGCCACCAAAC 61.734 55.000 0.00 0.00 0.00 2.93
2791 7459 1.452145 GAAGACAAGCCGCCACCAAA 61.452 55.000 0.00 0.00 0.00 3.28
2792 7460 1.896660 GAAGACAAGCCGCCACCAA 60.897 57.895 0.00 0.00 0.00 3.67
2793 7461 2.281484 GAAGACAAGCCGCCACCA 60.281 61.111 0.00 0.00 0.00 4.17
2794 7462 2.032681 AGAAGACAAGCCGCCACC 59.967 61.111 0.00 0.00 0.00 4.61
2795 7463 0.603975 AAGAGAAGACAAGCCGCCAC 60.604 55.000 0.00 0.00 0.00 5.01
2796 7464 0.603707 CAAGAGAAGACAAGCCGCCA 60.604 55.000 0.00 0.00 0.00 5.69
2811 7479 1.354368 GAGAACCAATCCACCCCAAGA 59.646 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.