Multiple sequence alignment - TraesCS1B01G437000

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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 TraesCS1B01G437000 chr1B 100.000 2531 0 0 1 2531 659947964 659950494 0.000000e+00 4674.0
1 TraesCS1B01G437000 chr1B 84.314 204 11 8 303 486 659913152 659913354 2.000000e-41 180.0
2 TraesCS1B01G437000 chr1D 85.399 2041 126 80 44 2002 474719192 474721142 0.000000e+00 1960.0
3 TraesCS1B01G437000 chr1D 84.615 429 49 9 2061 2479 474721421 474721842 6.520000e-111 411.0
4 TraesCS1B01G437000 chr1A 82.918 2008 156 88 43 2007 570247438 570249301 0.000000e+00 1635.0
5 TraesCS1B01G437000 chr1A 80.625 480 68 15 2061 2528 570249686 570250152 5.180000e-92 348.0
6 TraesCS1B01G437000 chr1A 81.731 104 17 2 2425 2526 545030037 545029934 4.490000e-13 86.1
7 TraesCS1B01G437000 chr2A 82.500 80 12 2 2434 2512 205926340 205926418 4.520000e-08 69.4


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 TraesCS1B01G437000 chr1B 659947964 659950494 2530 False 4674.0 4674 100.0000 1 2531 1 chr1B.!!$F2 2530
1 TraesCS1B01G437000 chr1D 474719192 474721842 2650 False 1185.5 1960 85.0070 44 2479 2 chr1D.!!$F1 2435
2 TraesCS1B01G437000 chr1A 570247438 570250152 2714 False 991.5 1635 81.7715 43 2528 2 chr1A.!!$F1 2485

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
551 570 0.106149 AAATCGGACGCTATCACCCC 59.894 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2156 0.036732 ATCAGCGGCCAGTCAAGAAA 59.963 50.0 2.24 0.0 0.0 2.52 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
53 54 4.890988 TCTATCCTAACATCCCCACTTGA 58.109 43.478 0.00 0.00 0.00 3.02
57 58 6.590656 ATCCTAACATCCCCACTTGATTAA 57.409 37.500 0.00 0.00 0.00 1.40
59 60 6.364701 TCCTAACATCCCCACTTGATTAATG 58.635 40.000 0.00 0.00 0.00 1.90
67 68 6.945218 TCCCCACTTGATTAATGAATTTTGG 58.055 36.000 0.00 0.00 0.00 3.28
82 83 8.880878 ATGAATTTTGGTTGTTGGTAAACTAC 57.119 30.769 0.00 0.00 40.12 2.73
107 108 6.396829 ACAAAAGGGAGTTCAGAAATCAAG 57.603 37.500 12.50 0.00 0.00 3.02
111 122 5.768980 AGGGAGTTCAGAAATCAAGATGA 57.231 39.130 12.50 0.00 0.00 2.92
164 175 9.634021 TCATCTTCTGATCAATGTACTACTACT 57.366 33.333 0.00 0.00 0.00 2.57
165 176 9.676195 CATCTTCTGATCAATGTACTACTACTG 57.324 37.037 0.00 0.00 0.00 2.74
166 177 8.809468 TCTTCTGATCAATGTACTACTACTGT 57.191 34.615 0.00 0.00 0.00 3.55
167 178 8.678199 TCTTCTGATCAATGTACTACTACTGTG 58.322 37.037 0.00 0.00 0.00 3.66
168 179 8.575649 TTCTGATCAATGTACTACTACTGTGA 57.424 34.615 0.00 0.00 0.00 3.58
169 180 8.575649 TCTGATCAATGTACTACTACTGTGAA 57.424 34.615 0.00 0.00 0.00 3.18
170 181 8.678199 TCTGATCAATGTACTACTACTGTGAAG 58.322 37.037 0.00 0.00 0.00 3.02
191 202 3.964031 AGTCTGAACCTGTTCTTCACTCT 59.036 43.478 11.03 0.21 40.14 3.24
192 203 4.054671 GTCTGAACCTGTTCTTCACTCTG 58.945 47.826 11.03 0.00 40.14 3.35
193 204 3.070159 TCTGAACCTGTTCTTCACTCTGG 59.930 47.826 11.03 0.00 40.14 3.86
194 205 3.038280 TGAACCTGTTCTTCACTCTGGA 58.962 45.455 11.03 0.00 40.14 3.86
195 206 3.070159 TGAACCTGTTCTTCACTCTGGAG 59.930 47.826 11.03 0.00 40.14 3.86
299 317 2.937149 GGACTGGAAGCGAAGGAAATAC 59.063 50.000 0.00 0.00 37.60 1.89
367 385 1.448540 AGTTGGCGCTCTGAATCCG 60.449 57.895 7.64 0.00 0.00 4.18
549 568 1.129326 CGAAATCGGACGCTATCACC 58.871 55.000 0.00 0.00 35.37 4.02
550 569 1.499049 GAAATCGGACGCTATCACCC 58.501 55.000 0.00 0.00 0.00 4.61
551 570 0.106149 AAATCGGACGCTATCACCCC 59.894 55.000 0.00 0.00 0.00 4.95
552 571 0.759436 AATCGGACGCTATCACCCCT 60.759 55.000 0.00 0.00 0.00 4.79
553 572 0.759436 ATCGGACGCTATCACCCCTT 60.759 55.000 0.00 0.00 0.00 3.95
554 573 1.067582 CGGACGCTATCACCCCTTC 59.932 63.158 0.00 0.00 0.00 3.46
555 574 1.067582 GGACGCTATCACCCCTTCG 59.932 63.158 0.00 0.00 0.00 3.79
556 575 1.673808 GGACGCTATCACCCCTTCGT 61.674 60.000 0.00 0.00 0.00 3.85
557 576 0.175073 GACGCTATCACCCCTTCGTT 59.825 55.000 0.00 0.00 0.00 3.85
667 706 3.265791 GAGTGAATCTCTTGGATGCGTT 58.734 45.455 0.00 0.00 39.86 4.84
694 733 2.402388 CTGCGCGCTTTGATCTGG 59.598 61.111 33.29 6.90 0.00 3.86
699 754 3.880846 CGCTTTGATCTGGGCGGC 61.881 66.667 15.18 0.00 43.25 6.53
729 784 1.072331 AGACGTGGGAGTGAATTGCTT 59.928 47.619 0.00 0.00 0.00 3.91
747 802 2.281498 GCTTGCCGTTTTTCACAGTTTC 59.719 45.455 0.00 0.00 0.00 2.78
750 805 1.862411 GCCGTTTTTCACAGTTTCGGG 60.862 52.381 0.00 0.00 37.44 5.14
754 809 1.757682 TTTTCACAGTTTCGGGTGCT 58.242 45.000 0.00 0.00 35.04 4.40
755 810 1.757682 TTTCACAGTTTCGGGTGCTT 58.242 45.000 0.00 0.00 35.04 3.91
756 811 1.021202 TTCACAGTTTCGGGTGCTTG 58.979 50.000 0.00 0.00 35.04 4.01
757 812 0.817634 TCACAGTTTCGGGTGCTTGG 60.818 55.000 0.00 0.00 35.04 3.61
758 813 1.101049 CACAGTTTCGGGTGCTTGGT 61.101 55.000 0.00 0.00 0.00 3.67
759 814 1.101049 ACAGTTTCGGGTGCTTGGTG 61.101 55.000 0.00 0.00 0.00 4.17
760 815 1.528309 AGTTTCGGGTGCTTGGTGG 60.528 57.895 0.00 0.00 0.00 4.61
761 816 1.826487 GTTTCGGGTGCTTGGTGGT 60.826 57.895 0.00 0.00 0.00 4.16
762 817 0.535553 GTTTCGGGTGCTTGGTGGTA 60.536 55.000 0.00 0.00 0.00 3.25
766 821 1.541310 CGGGTGCTTGGTGGTAGAGA 61.541 60.000 0.00 0.00 0.00 3.10
768 823 1.073284 GGGTGCTTGGTGGTAGAGAAA 59.927 52.381 0.00 0.00 0.00 2.52
772 827 3.748568 GTGCTTGGTGGTAGAGAAAAGAG 59.251 47.826 0.00 0.00 0.00 2.85
877 938 3.166630 GCGCTCTCGTGTCACGAC 61.167 66.667 23.70 13.43 46.73 4.34
878 939 2.502080 CGCTCTCGTGTCACGACC 60.502 66.667 23.70 13.52 46.73 4.79
879 940 2.126424 GCTCTCGTGTCACGACCC 60.126 66.667 23.70 11.02 46.73 4.46
880 941 2.176055 CTCTCGTGTCACGACCCG 59.824 66.667 23.70 14.52 46.73 5.28
898 971 2.710902 GGCCATTTCCTCCGTTGCC 61.711 63.158 0.00 0.00 0.00 4.52
925 998 2.375845 TCCCCAGGCTAGCTACTACTAG 59.624 54.545 15.72 0.00 42.20 2.57
933 1006 3.992643 CTAGCTACTACTAGCCGACTGA 58.007 50.000 0.00 0.00 46.01 3.41
934 1007 2.563702 AGCTACTACTAGCCGACTGAC 58.436 52.381 0.00 0.00 46.01 3.51
935 1008 1.603326 GCTACTACTAGCCGACTGACC 59.397 57.143 0.00 0.00 39.79 4.02
936 1009 2.915349 CTACTACTAGCCGACTGACCA 58.085 52.381 0.00 0.00 0.00 4.02
937 1010 1.461559 ACTACTAGCCGACTGACCAC 58.538 55.000 0.00 0.00 0.00 4.16
938 1011 1.271762 ACTACTAGCCGACTGACCACA 60.272 52.381 0.00 0.00 0.00 4.17
990 1067 2.627737 GCTCCGTCTGACCGTCTGT 61.628 63.158 1.55 0.00 0.00 3.41
996 1073 1.599797 TCTGACCGTCTGTCTGCGA 60.600 57.895 0.00 0.00 44.75 5.10
1605 1710 1.079127 CGGCGGGTCAACTTCAGAT 60.079 57.895 0.00 0.00 0.00 2.90
1606 1711 0.174845 CGGCGGGTCAACTTCAGATA 59.825 55.000 0.00 0.00 0.00 1.98
1611 1716 3.804873 GCGGGTCAACTTCAGATATCTTC 59.195 47.826 1.33 0.00 0.00 2.87
1613 1718 5.221263 GCGGGTCAACTTCAGATATCTTCTA 60.221 44.000 1.33 0.00 31.77 2.10
1615 1720 6.220201 GGGTCAACTTCAGATATCTTCTAGC 58.780 44.000 1.33 0.00 31.77 3.42
1619 1724 5.467035 ACTTCAGATATCTTCTAGCAGCC 57.533 43.478 1.33 0.00 31.77 4.85
1620 1725 5.147032 ACTTCAGATATCTTCTAGCAGCCT 58.853 41.667 1.33 0.00 31.77 4.58
1621 1726 5.010922 ACTTCAGATATCTTCTAGCAGCCTG 59.989 44.000 1.33 0.00 31.77 4.85
1632 1737 1.449246 GCAGCCTGGCAGTAGTGAG 60.449 63.158 22.65 0.00 0.00 3.51
1662 1767 2.431454 TACGATCAGCCGGGTGCAT 61.431 57.895 28.72 21.16 44.83 3.96
1741 1847 5.118357 CGAATCTCGATTTATTCAGAGCTGG 59.882 44.000 0.00 0.00 43.74 4.85
1764 1870 8.196802 TGGTTAGAATTGACATGTTATCTTCG 57.803 34.615 0.00 0.00 0.00 3.79
1774 1880 6.992123 TGACATGTTATCTTCGATTTGCCTAT 59.008 34.615 0.00 0.00 0.00 2.57
1775 1881 7.041848 TGACATGTTATCTTCGATTTGCCTATG 60.042 37.037 0.00 0.00 0.00 2.23
1780 1886 3.995199 TCTTCGATTTGCCTATGCCTAG 58.005 45.455 0.00 0.00 36.33 3.02
1781 1887 3.388024 TCTTCGATTTGCCTATGCCTAGT 59.612 43.478 0.00 0.00 36.33 2.57
1782 1888 3.111853 TCGATTTGCCTATGCCTAGTG 57.888 47.619 0.00 0.00 36.33 2.74
1785 1891 3.554960 CGATTTGCCTATGCCTAGTGCTA 60.555 47.826 9.59 2.14 42.00 3.49
1805 1911 4.375506 GCTAATTAGAAGCGTGCGAATCTC 60.376 45.833 16.85 0.00 0.00 2.75
1811 1917 1.016130 AGCGTGCGAATCTCAACTGG 61.016 55.000 0.00 0.00 0.00 4.00
1858 1964 2.310538 GGAATCCACATCATGTTCCCC 58.689 52.381 0.00 0.00 33.80 4.81
1859 1965 2.310538 GAATCCACATCATGTTCCCCC 58.689 52.381 0.00 0.00 0.00 5.40
1861 1967 1.381867 TCCACATCATGTTCCCCCTT 58.618 50.000 0.00 0.00 0.00 3.95
1862 1968 1.005805 TCCACATCATGTTCCCCCTTG 59.994 52.381 0.00 0.00 0.00 3.61
1863 1969 0.819582 CACATCATGTTCCCCCTTGC 59.180 55.000 0.00 0.00 0.00 4.01
1864 1970 0.409092 ACATCATGTTCCCCCTTGCA 59.591 50.000 0.00 0.00 0.00 4.08
1885 2025 7.308450 TGCATTTGCCTATCTATACTTCTCT 57.692 36.000 0.00 0.00 41.18 3.10
1886 2026 7.739825 TGCATTTGCCTATCTATACTTCTCTT 58.260 34.615 0.00 0.00 41.18 2.85
1887 2027 8.870116 TGCATTTGCCTATCTATACTTCTCTTA 58.130 33.333 0.00 0.00 41.18 2.10
1888 2028 9.364989 GCATTTGCCTATCTATACTTCTCTTAG 57.635 37.037 0.00 0.00 34.31 2.18
1952 2092 1.747206 GCTGCCCGTTATGGTTCTCAT 60.747 52.381 0.00 0.00 39.78 2.90
1953 2093 2.484770 GCTGCCCGTTATGGTTCTCATA 60.485 50.000 0.00 0.00 37.30 2.15
1954 2094 3.393800 CTGCCCGTTATGGTTCTCATAG 58.606 50.000 0.00 0.00 39.29 2.23
1993 2134 9.190317 GTAGAAAAAGAAATGATATGGTCCCTT 57.810 33.333 0.00 0.00 0.00 3.95
2002 2143 3.694072 TGATATGGTCCCTTGCGAAAAAG 59.306 43.478 0.00 0.00 0.00 2.27
2011 2152 2.753296 CTTGCGAAAAAGGAAATGGCA 58.247 42.857 0.00 0.00 0.00 4.92
2012 2153 3.328505 CTTGCGAAAAAGGAAATGGCAT 58.671 40.909 0.00 0.00 0.00 4.40
2013 2154 3.399440 TGCGAAAAAGGAAATGGCATT 57.601 38.095 6.96 6.96 0.00 3.56
2014 2155 3.324993 TGCGAAAAAGGAAATGGCATTC 58.675 40.909 14.04 7.11 0.00 2.67
2015 2156 3.006752 TGCGAAAAAGGAAATGGCATTCT 59.993 39.130 14.04 4.31 0.00 2.40
2017 2158 4.452114 GCGAAAAAGGAAATGGCATTCTTT 59.548 37.500 14.04 15.73 30.79 2.52
2020 2161 6.424812 CGAAAAAGGAAATGGCATTCTTTCTT 59.575 34.615 20.61 17.05 33.02 2.52
2021 2162 7.500720 AAAAAGGAAATGGCATTCTTTCTTG 57.499 32.000 20.61 0.00 33.02 3.02
2022 2163 6.423776 AAAGGAAATGGCATTCTTTCTTGA 57.576 33.333 14.04 0.00 33.02 3.02
2023 2164 5.397142 AGGAAATGGCATTCTTTCTTGAC 57.603 39.130 14.04 0.00 33.02 3.18
2024 2165 5.082425 AGGAAATGGCATTCTTTCTTGACT 58.918 37.500 14.04 0.00 33.02 3.41
2025 2166 5.047519 AGGAAATGGCATTCTTTCTTGACTG 60.048 40.000 14.04 0.00 33.02 3.51
2026 2167 4.796038 AATGGCATTCTTTCTTGACTGG 57.204 40.909 6.96 0.00 0.00 4.00
2027 2168 1.888512 TGGCATTCTTTCTTGACTGGC 59.111 47.619 0.00 0.00 40.70 4.85
2045 2487 0.955428 GCCGCTGATTCACTCAACCA 60.955 55.000 0.00 0.00 32.14 3.67
2054 2496 0.828022 TCACTCAACCAACCGTCACT 59.172 50.000 0.00 0.00 0.00 3.41
2072 2553 0.393537 CTTGACTGGCCTCCACCATC 60.394 60.000 3.32 0.00 39.54 3.51
2107 2588 1.419387 CCCTTCTCCTAGGCAGATTGG 59.581 57.143 2.96 12.12 33.73 3.16
2114 2595 3.114606 TCCTAGGCAGATTGGTCAATGA 58.885 45.455 2.96 0.00 0.00 2.57
2162 2643 8.579850 TCTCTATAACATGGCAAGTTTGAAAT 57.420 30.769 13.77 3.82 0.00 2.17
2200 2682 5.041951 TCACGTGGCAAATTAAGAACATC 57.958 39.130 17.00 0.00 0.00 3.06
2201 2683 4.083003 TCACGTGGCAAATTAAGAACATCC 60.083 41.667 17.00 0.00 0.00 3.51
2202 2684 3.192633 ACGTGGCAAATTAAGAACATCCC 59.807 43.478 0.00 0.00 0.00 3.85
2204 2686 3.442273 GTGGCAAATTAAGAACATCCCGA 59.558 43.478 0.00 0.00 0.00 5.14
2212 2701 7.461182 AATTAAGAACATCCCGAAAACATGA 57.539 32.000 0.00 0.00 0.00 3.07
2263 2752 6.735063 CGACATTTTTACGATTACACTTGTCC 59.265 38.462 0.00 0.00 0.00 4.02
2374 2863 3.857157 TTTGTAAGTCTGCCTTGTCCT 57.143 42.857 0.00 0.00 34.46 3.85
2375 2864 3.402628 TTGTAAGTCTGCCTTGTCCTC 57.597 47.619 0.00 0.00 34.46 3.71
2471 2964 7.971368 AGGTACCATGGCAATTTTACTAATT 57.029 32.000 15.94 0.00 0.00 1.40
2473 2966 9.131791 AGGTACCATGGCAATTTTACTAATTAG 57.868 33.333 15.94 11.05 0.00 1.73
2474 2967 9.127277 GGTACCATGGCAATTTTACTAATTAGA 57.873 33.333 19.38 0.27 0.00 2.10
2475 2968 9.946165 GTACCATGGCAATTTTACTAATTAGAC 57.054 33.333 19.38 0.00 0.00 2.59
2476 2969 8.007405 ACCATGGCAATTTTACTAATTAGACC 57.993 34.615 19.38 7.34 0.00 3.85
2477 2970 7.617723 ACCATGGCAATTTTACTAATTAGACCA 59.382 33.333 19.38 11.86 0.00 4.02
2478 2971 8.641541 CCATGGCAATTTTACTAATTAGACCAT 58.358 33.333 19.38 13.27 33.42 3.55
2479 2972 9.467258 CATGGCAATTTTACTAATTAGACCATG 57.533 33.333 19.38 18.94 42.42 3.66
2480 2973 8.006298 TGGCAATTTTACTAATTAGACCATGG 57.994 34.615 19.38 11.19 0.00 3.66
2481 2974 6.923508 GGCAATTTTACTAATTAGACCATGGC 59.076 38.462 19.38 15.73 0.00 4.40
2482 2975 6.636850 GCAATTTTACTAATTAGACCATGGCG 59.363 38.462 19.38 2.78 0.00 5.69
2483 2976 6.877611 ATTTTACTAATTAGACCATGGCGG 57.122 37.500 19.38 0.00 42.50 6.13
2503 3019 4.321675 GCGGTTTTTCAATTAGACCATGGT 60.322 41.667 19.89 19.89 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.960064 AGTGGGGATGTTAGGATAGAATAAAAT 58.040 33.333 0.00 0.00 0.00 1.82
25 26 8.344939 AGTGGGGATGTTAGGATAGAATAAAA 57.655 34.615 0.00 0.00 0.00 1.52
26 27 7.947782 AGTGGGGATGTTAGGATAGAATAAA 57.052 36.000 0.00 0.00 0.00 1.40
27 28 7.570982 TCAAGTGGGGATGTTAGGATAGAATAA 59.429 37.037 0.00 0.00 0.00 1.40
28 29 7.079700 TCAAGTGGGGATGTTAGGATAGAATA 58.920 38.462 0.00 0.00 0.00 1.75
29 30 5.911178 TCAAGTGGGGATGTTAGGATAGAAT 59.089 40.000 0.00 0.00 0.00 2.40
30 31 5.285401 TCAAGTGGGGATGTTAGGATAGAA 58.715 41.667 0.00 0.00 0.00 2.10
31 32 4.890988 TCAAGTGGGGATGTTAGGATAGA 58.109 43.478 0.00 0.00 0.00 1.98
32 33 5.832539 ATCAAGTGGGGATGTTAGGATAG 57.167 43.478 0.00 0.00 0.00 2.08
33 34 7.699709 TTAATCAAGTGGGGATGTTAGGATA 57.300 36.000 0.00 0.00 0.00 2.59
34 35 6.590656 TTAATCAAGTGGGGATGTTAGGAT 57.409 37.500 0.00 0.00 0.00 3.24
35 36 6.159575 TCATTAATCAAGTGGGGATGTTAGGA 59.840 38.462 0.00 0.00 0.00 2.94
36 37 6.364701 TCATTAATCAAGTGGGGATGTTAGG 58.635 40.000 0.00 0.00 0.00 2.69
37 38 7.880160 TTCATTAATCAAGTGGGGATGTTAG 57.120 36.000 0.00 0.00 0.00 2.34
38 39 8.837099 AATTCATTAATCAAGTGGGGATGTTA 57.163 30.769 0.00 0.00 0.00 2.41
39 40 7.738437 AATTCATTAATCAAGTGGGGATGTT 57.262 32.000 0.00 0.00 0.00 2.71
40 41 7.738437 AAATTCATTAATCAAGTGGGGATGT 57.262 32.000 0.00 0.00 0.00 3.06
41 42 7.496591 CCAAAATTCATTAATCAAGTGGGGATG 59.503 37.037 0.00 0.00 0.00 3.51
57 58 8.478877 TGTAGTTTACCAACAACCAAAATTCAT 58.521 29.630 0.00 0.00 35.05 2.57
59 60 8.597227 GTTGTAGTTTACCAACAACCAAAATTC 58.403 33.333 13.68 0.00 44.53 2.17
82 83 6.147864 TGATTTCTGAACTCCCTTTTGTTG 57.852 37.500 5.45 0.00 0.00 3.33
90 91 4.637977 GGTCATCTTGATTTCTGAACTCCC 59.362 45.833 5.45 0.00 0.00 4.30
107 108 3.784511 ATGATGGACAGGATGGTCATC 57.215 47.619 2.52 2.52 44.29 2.92
111 122 1.285667 TGCAATGATGGACAGGATGGT 59.714 47.619 0.00 0.00 43.62 3.55
164 175 4.081142 TGAAGAACAGGTTCAGACTTCACA 60.081 41.667 14.06 0.98 41.84 3.58
165 176 4.442706 TGAAGAACAGGTTCAGACTTCAC 58.557 43.478 14.06 0.00 41.84 3.18
166 177 4.162320 AGTGAAGAACAGGTTCAGACTTCA 59.838 41.667 14.06 11.35 41.84 3.02
167 178 4.698575 AGTGAAGAACAGGTTCAGACTTC 58.301 43.478 14.06 9.22 41.84 3.01
168 179 4.407296 AGAGTGAAGAACAGGTTCAGACTT 59.593 41.667 14.06 0.14 41.84 3.01
169 180 3.964031 AGAGTGAAGAACAGGTTCAGACT 59.036 43.478 14.06 11.32 41.84 3.24
170 181 4.054671 CAGAGTGAAGAACAGGTTCAGAC 58.945 47.826 14.06 7.34 41.84 3.51
232 243 2.443255 AGAGATTTGTTCTGTGTGGGGT 59.557 45.455 0.00 0.00 33.74 4.95
233 244 3.077359 GAGAGATTTGTTCTGTGTGGGG 58.923 50.000 0.00 0.00 33.74 4.96
235 246 3.188048 GCAGAGAGATTTGTTCTGTGTGG 59.812 47.826 3.07 0.00 38.88 4.17
239 250 4.070716 CAAGGCAGAGAGATTTGTTCTGT 58.929 43.478 3.07 0.00 40.29 3.41
240 251 3.439476 CCAAGGCAGAGAGATTTGTTCTG 59.561 47.826 0.00 0.00 40.93 3.02
241 252 3.683802 CCAAGGCAGAGAGATTTGTTCT 58.316 45.455 0.00 0.00 37.41 3.01
279 297 2.603560 CGTATTTCCTTCGCTTCCAGTC 59.396 50.000 0.00 0.00 0.00 3.51
299 317 3.373130 TGTCTGATCCTCTTGTACGTACG 59.627 47.826 20.18 15.01 0.00 3.67
455 473 0.177141 TTTATCCTCCCACGCTTCCG 59.823 55.000 0.00 0.00 41.14 4.30
543 562 5.687166 ACAAGATAAACGAAGGGGTGATA 57.313 39.130 0.00 0.00 0.00 2.15
544 563 4.569719 ACAAGATAAACGAAGGGGTGAT 57.430 40.909 0.00 0.00 0.00 3.06
545 564 4.322953 GGTACAAGATAAACGAAGGGGTGA 60.323 45.833 0.00 0.00 0.00 4.02
546 565 3.937079 GGTACAAGATAAACGAAGGGGTG 59.063 47.826 0.00 0.00 0.00 4.61
547 566 3.054875 GGGTACAAGATAAACGAAGGGGT 60.055 47.826 0.00 0.00 0.00 4.95
548 567 3.538591 GGGTACAAGATAAACGAAGGGG 58.461 50.000 0.00 0.00 0.00 4.79
549 568 3.192466 CGGGTACAAGATAAACGAAGGG 58.808 50.000 0.00 0.00 0.00 3.95
550 569 2.606272 GCGGGTACAAGATAAACGAAGG 59.394 50.000 0.00 0.00 0.00 3.46
551 570 2.280708 CGCGGGTACAAGATAAACGAAG 59.719 50.000 0.00 0.00 0.00 3.79
552 571 2.261345 CGCGGGTACAAGATAAACGAA 58.739 47.619 0.00 0.00 0.00 3.85
553 572 1.912001 CGCGGGTACAAGATAAACGA 58.088 50.000 0.00 0.00 0.00 3.85
554 573 0.299597 GCGCGGGTACAAGATAAACG 59.700 55.000 8.83 0.00 0.00 3.60
555 574 0.654160 GGCGCGGGTACAAGATAAAC 59.346 55.000 8.83 0.00 0.00 2.01
556 575 0.462403 GGGCGCGGGTACAAGATAAA 60.462 55.000 8.83 0.00 0.00 1.40
557 576 1.144496 GGGCGCGGGTACAAGATAA 59.856 57.895 8.83 0.00 0.00 1.75
606 640 6.974622 GCGGTAAAAACTTTGATGATGATGAT 59.025 34.615 0.00 0.00 0.00 2.45
607 641 6.072230 TGCGGTAAAAACTTTGATGATGATGA 60.072 34.615 0.00 0.00 0.00 2.92
608 642 6.033831 GTGCGGTAAAAACTTTGATGATGATG 59.966 38.462 0.00 0.00 0.00 3.07
699 754 2.126307 CCACGTCTGTCAGGCTCG 60.126 66.667 2.39 7.09 0.00 5.03
729 784 1.202200 CCGAAACTGTGAAAAACGGCA 60.202 47.619 0.00 0.00 38.92 5.69
747 802 1.079127 CTCTACCACCAAGCACCCG 60.079 63.158 0.00 0.00 0.00 5.28
750 805 3.740115 TCTTTTCTCTACCACCAAGCAC 58.260 45.455 0.00 0.00 0.00 4.40
754 809 3.904339 AGCTCTCTTTTCTCTACCACCAA 59.096 43.478 0.00 0.00 0.00 3.67
755 810 3.511477 AGCTCTCTTTTCTCTACCACCA 58.489 45.455 0.00 0.00 0.00 4.17
756 811 3.767131 AGAGCTCTCTTTTCTCTACCACC 59.233 47.826 11.45 0.00 36.31 4.61
757 812 4.142249 GGAGAGCTCTCTTTTCTCTACCAC 60.142 50.000 36.09 15.89 42.48 4.16
758 813 4.020543 GGAGAGCTCTCTTTTCTCTACCA 58.979 47.826 36.09 0.00 42.48 3.25
759 814 4.278310 AGGAGAGCTCTCTTTTCTCTACC 58.722 47.826 36.09 20.27 42.48 3.18
760 815 5.914898 AAGGAGAGCTCTCTTTTCTCTAC 57.085 43.478 36.09 19.90 38.90 2.59
761 816 6.926630 AAAAGGAGAGCTCTCTTTTCTCTA 57.073 37.500 38.56 0.00 46.96 2.43
762 817 5.823861 AAAAGGAGAGCTCTCTTTTCTCT 57.176 39.130 38.56 27.05 46.96 3.10
768 823 3.517500 CCCAGTAAAAGGAGAGCTCTCTT 59.482 47.826 36.09 29.63 42.48 2.85
772 827 1.740718 CGCCCAGTAAAAGGAGAGCTC 60.741 57.143 5.27 5.27 0.00 4.09
813 871 0.607217 GGGTAAACAGTTGGGACGGG 60.607 60.000 0.00 0.00 0.00 5.28
814 872 0.952010 CGGGTAAACAGTTGGGACGG 60.952 60.000 0.00 0.00 0.00 4.79
815 873 0.033781 TCGGGTAAACAGTTGGGACG 59.966 55.000 0.00 0.00 0.00 4.79
816 874 1.875514 GTTCGGGTAAACAGTTGGGAC 59.124 52.381 0.00 0.00 0.00 4.46
817 875 1.202794 GGTTCGGGTAAACAGTTGGGA 60.203 52.381 0.00 0.00 0.00 4.37
818 876 1.241165 GGTTCGGGTAAACAGTTGGG 58.759 55.000 0.00 0.00 0.00 4.12
872 933 3.131478 GGAAATGGCCGGGTCGTG 61.131 66.667 2.18 0.00 0.00 4.35
873 934 3.325201 GAGGAAATGGCCGGGTCGT 62.325 63.158 2.18 0.00 0.00 4.34
874 935 2.513897 GAGGAAATGGCCGGGTCG 60.514 66.667 2.18 0.00 0.00 4.79
875 936 2.124278 GGAGGAAATGGCCGGGTC 60.124 66.667 2.18 0.00 0.00 4.46
876 937 4.109675 CGGAGGAAATGGCCGGGT 62.110 66.667 2.18 0.00 41.29 5.28
880 941 2.710902 GGCAACGGAGGAAATGGCC 61.711 63.158 0.00 0.00 32.71 5.36
932 1005 4.275689 TGAATTGTGATTGTGACTGTGGTC 59.724 41.667 0.00 0.00 42.42 4.02
933 1006 4.036734 GTGAATTGTGATTGTGACTGTGGT 59.963 41.667 0.00 0.00 0.00 4.16
934 1007 4.036616 TGTGAATTGTGATTGTGACTGTGG 59.963 41.667 0.00 0.00 0.00 4.17
935 1008 5.172460 TGTGAATTGTGATTGTGACTGTG 57.828 39.130 0.00 0.00 0.00 3.66
936 1009 5.833406 TTGTGAATTGTGATTGTGACTGT 57.167 34.783 0.00 0.00 0.00 3.55
937 1010 6.020440 GTGTTTGTGAATTGTGATTGTGACTG 60.020 38.462 0.00 0.00 0.00 3.51
938 1011 6.035843 GTGTTTGTGAATTGTGATTGTGACT 58.964 36.000 0.00 0.00 0.00 3.41
940 1013 5.126869 AGGTGTTTGTGAATTGTGATTGTGA 59.873 36.000 0.00 0.00 0.00 3.58
941 1014 5.350633 AGGTGTTTGTGAATTGTGATTGTG 58.649 37.500 0.00 0.00 0.00 3.33
942 1015 5.596836 AGGTGTTTGTGAATTGTGATTGT 57.403 34.783 0.00 0.00 0.00 2.71
943 1016 6.707711 CAAAGGTGTTTGTGAATTGTGATTG 58.292 36.000 0.00 0.00 38.64 2.67
944 1017 5.294060 GCAAAGGTGTTTGTGAATTGTGATT 59.706 36.000 0.23 0.00 44.37 2.57
945 1018 4.810491 GCAAAGGTGTTTGTGAATTGTGAT 59.190 37.500 0.23 0.00 44.37 3.06
946 1019 4.081752 AGCAAAGGTGTTTGTGAATTGTGA 60.082 37.500 0.23 0.00 44.37 3.58
947 1020 4.183101 AGCAAAGGTGTTTGTGAATTGTG 58.817 39.130 0.23 0.00 44.37 3.33
948 1021 4.470334 AGCAAAGGTGTTTGTGAATTGT 57.530 36.364 0.23 0.00 44.37 2.71
949 1022 4.034279 CCAAGCAAAGGTGTTTGTGAATTG 59.966 41.667 3.20 0.00 44.37 2.32
950 1023 4.190772 CCAAGCAAAGGTGTTTGTGAATT 58.809 39.130 3.20 0.00 44.37 2.17
951 1024 3.795877 CCAAGCAAAGGTGTTTGTGAAT 58.204 40.909 3.20 0.00 44.37 2.57
952 1025 2.676463 GCCAAGCAAAGGTGTTTGTGAA 60.676 45.455 3.20 0.00 44.37 3.18
990 1067 0.940991 CGCCAATCATCGATCGCAGA 60.941 55.000 11.09 10.98 45.75 4.26
996 1073 2.281761 GCCCCGCCAATCATCGAT 60.282 61.111 0.00 0.00 0.00 3.59
1422 1523 3.808771 ATCATCGACGTCTCGCGCC 62.809 63.158 14.70 0.00 46.11 6.53
1423 1524 2.350852 GATCATCGACGTCTCGCGC 61.351 63.158 14.70 0.00 46.11 6.86
1425 1526 1.256284 CGTGATCATCGACGTCTCGC 61.256 60.000 14.70 9.42 39.96 5.03
1426 1527 0.300789 TCGTGATCATCGACGTCTCG 59.699 55.000 14.70 1.54 41.65 4.04
1430 1531 1.064296 GCCTCGTGATCATCGACGT 59.936 57.895 13.87 0.00 36.91 4.34
1605 1710 1.690893 CTGCCAGGCTGCTAGAAGATA 59.309 52.381 14.15 0.00 0.00 1.98
1606 1711 0.469070 CTGCCAGGCTGCTAGAAGAT 59.531 55.000 14.15 0.00 0.00 2.40
1611 1716 0.179089 CACTACTGCCAGGCTGCTAG 60.179 60.000 17.99 18.17 0.00 3.42
1613 1718 1.897225 CTCACTACTGCCAGGCTGCT 61.897 60.000 17.99 8.19 0.00 4.24
1615 1720 1.135915 CTACTCACTACTGCCAGGCTG 59.864 57.143 16.57 16.57 0.00 4.85
1619 1724 3.085533 ACTCACTACTCACTACTGCCAG 58.914 50.000 0.00 0.00 0.00 4.85
1620 1725 3.156288 ACTCACTACTCACTACTGCCA 57.844 47.619 0.00 0.00 0.00 4.92
1621 1726 3.063725 CGTACTCACTACTCACTACTGCC 59.936 52.174 0.00 0.00 0.00 4.85
1632 1737 3.303001 GGCTGATCGTACGTACTCACTAC 60.303 52.174 22.55 10.46 0.00 2.73
1775 1881 3.491267 CACGCTTCTAATTAGCACTAGGC 59.509 47.826 7.67 2.19 45.30 3.93
1780 1886 1.924524 TCGCACGCTTCTAATTAGCAC 59.075 47.619 7.67 0.00 38.55 4.40
1781 1887 2.287393 TCGCACGCTTCTAATTAGCA 57.713 45.000 7.67 0.00 38.55 3.49
1782 1888 3.491267 AGATTCGCACGCTTCTAATTAGC 59.509 43.478 7.67 0.00 35.29 3.09
1785 1891 3.521560 TGAGATTCGCACGCTTCTAATT 58.478 40.909 0.00 0.00 0.00 1.40
1805 1911 1.648720 CAACACGTGCTCCCAGTTG 59.351 57.895 17.22 6.94 34.39 3.16
1811 1917 2.946762 GAAGCCAACACGTGCTCC 59.053 61.111 17.22 1.46 36.66 4.70
1858 1964 6.939163 AGAAGTATAGATAGGCAAATGCAAGG 59.061 38.462 7.80 0.00 44.36 3.61
1859 1965 7.877097 AGAGAAGTATAGATAGGCAAATGCAAG 59.123 37.037 7.80 0.00 44.36 4.01
1861 1967 7.308450 AGAGAAGTATAGATAGGCAAATGCA 57.692 36.000 7.80 0.00 44.36 3.96
1862 1968 9.364989 CTAAGAGAAGTATAGATAGGCAAATGC 57.635 37.037 0.00 0.00 41.14 3.56
1885 2025 9.436957 GTGGAAATGAAAGAGAAGATGTACTAA 57.563 33.333 0.00 0.00 0.00 2.24
1886 2026 8.816894 AGTGGAAATGAAAGAGAAGATGTACTA 58.183 33.333 0.00 0.00 0.00 1.82
1887 2027 7.684529 AGTGGAAATGAAAGAGAAGATGTACT 58.315 34.615 0.00 0.00 0.00 2.73
1888 2028 7.913674 AGTGGAAATGAAAGAGAAGATGTAC 57.086 36.000 0.00 0.00 0.00 2.90
1889 2029 7.939039 ACAAGTGGAAATGAAAGAGAAGATGTA 59.061 33.333 0.00 0.00 0.00 2.29
1890 2030 6.774656 ACAAGTGGAAATGAAAGAGAAGATGT 59.225 34.615 0.00 0.00 0.00 3.06
1891 2031 7.211966 ACAAGTGGAAATGAAAGAGAAGATG 57.788 36.000 0.00 0.00 0.00 2.90
1892 2032 7.830099 AACAAGTGGAAATGAAAGAGAAGAT 57.170 32.000 0.00 0.00 0.00 2.40
1893 2033 7.645058 AAACAAGTGGAAATGAAAGAGAAGA 57.355 32.000 0.00 0.00 0.00 2.87
1894 2034 8.707938 AAAAACAAGTGGAAATGAAAGAGAAG 57.292 30.769 0.00 0.00 0.00 2.85
1921 2061 0.958822 ACGGGCAGCGAAAAAGAAAT 59.041 45.000 0.00 0.00 0.00 2.17
1931 2071 1.429148 GAGAACCATAACGGGCAGCG 61.429 60.000 0.00 0.00 40.22 5.18
1977 2118 3.576078 TCGCAAGGGACCATATCATTT 57.424 42.857 0.00 0.00 38.47 2.32
1993 2134 3.006752 AGAATGCCATTTCCTTTTTCGCA 59.993 39.130 0.00 0.00 0.00 5.10
2002 2143 5.166398 CAGTCAAGAAAGAATGCCATTTCC 58.834 41.667 0.00 0.00 36.31 3.13
2004 2145 4.562143 GCCAGTCAAGAAAGAATGCCATTT 60.562 41.667 0.00 0.00 32.61 2.32
2005 2146 3.056322 GCCAGTCAAGAAAGAATGCCATT 60.056 43.478 0.00 0.00 32.61 3.16
2007 2148 1.888512 GCCAGTCAAGAAAGAATGCCA 59.111 47.619 0.00 0.00 32.61 4.92
2008 2149 1.203287 GGCCAGTCAAGAAAGAATGCC 59.797 52.381 0.00 0.00 32.61 4.40
2009 2150 1.135575 CGGCCAGTCAAGAAAGAATGC 60.136 52.381 2.24 0.00 32.61 3.56
2010 2151 1.135575 GCGGCCAGTCAAGAAAGAATG 60.136 52.381 2.24 0.00 33.67 2.67
2011 2152 1.168714 GCGGCCAGTCAAGAAAGAAT 58.831 50.000 2.24 0.00 0.00 2.40
2012 2153 0.108585 AGCGGCCAGTCAAGAAAGAA 59.891 50.000 2.24 0.00 0.00 2.52
2013 2154 0.603707 CAGCGGCCAGTCAAGAAAGA 60.604 55.000 2.24 0.00 0.00 2.52
2014 2155 0.603707 TCAGCGGCCAGTCAAGAAAG 60.604 55.000 2.24 0.00 0.00 2.62
2015 2156 0.036732 ATCAGCGGCCAGTCAAGAAA 59.963 50.000 2.24 0.00 0.00 2.52
2017 2158 0.391661 GAATCAGCGGCCAGTCAAGA 60.392 55.000 2.24 0.00 0.00 3.02
2020 2161 1.375908 GTGAATCAGCGGCCAGTCA 60.376 57.895 2.24 0.00 0.00 3.41
2021 2162 1.078848 AGTGAATCAGCGGCCAGTC 60.079 57.895 2.24 0.00 0.00 3.51
2022 2163 1.078848 GAGTGAATCAGCGGCCAGT 60.079 57.895 2.24 0.00 0.00 4.00
2023 2164 0.674581 TTGAGTGAATCAGCGGCCAG 60.675 55.000 2.24 0.00 39.68 4.85
2024 2165 0.955428 GTTGAGTGAATCAGCGGCCA 60.955 55.000 2.24 0.00 39.68 5.36
2025 2166 1.648467 GGTTGAGTGAATCAGCGGCC 61.648 60.000 0.00 0.00 39.88 6.13
2026 2167 0.955428 TGGTTGAGTGAATCAGCGGC 60.955 55.000 0.00 0.00 39.88 6.53
2027 2168 1.197721 GTTGGTTGAGTGAATCAGCGG 59.802 52.381 0.00 0.00 39.88 5.52
2054 2496 1.685224 GATGGTGGAGGCCAGTCAA 59.315 57.895 5.01 0.00 42.47 3.18
2085 2566 0.104725 ATCTGCCTAGGAGAAGGGGG 60.105 60.000 14.75 0.00 37.11 5.40
2167 2648 7.489574 AATTTGCCACGTGATTGTTAAAAAT 57.510 28.000 19.30 7.79 0.00 1.82
2176 2657 5.446143 TGTTCTTAATTTGCCACGTGATT 57.554 34.783 19.30 11.20 0.00 2.57
2182 2663 3.442273 TCGGGATGTTCTTAATTTGCCAC 59.558 43.478 0.00 0.00 0.00 5.01
2200 2682 6.783892 ATTTCAATTTGTCATGTTTTCGGG 57.216 33.333 0.00 0.00 0.00 5.14
2201 2683 8.924691 ACATATTTCAATTTGTCATGTTTTCGG 58.075 29.630 0.00 0.00 0.00 4.30
2212 2701 9.638239 GTGTGACCATTACATATTTCAATTTGT 57.362 29.630 0.00 1.92 35.32 2.83
2351 2840 4.042187 AGGACAAGGCAGACTTACAAATCT 59.958 41.667 0.00 0.00 37.29 2.40
2432 2925 8.531146 GCCATGGTACCTATAATAAAATTGCAT 58.469 33.333 14.67 0.00 0.00 3.96
2475 2968 4.173256 GTCTAATTGAAAAACCGCCATGG 58.827 43.478 7.63 7.63 46.41 3.66
2476 2969 4.173256 GGTCTAATTGAAAAACCGCCATG 58.827 43.478 0.00 0.00 0.00 3.66
2477 2970 3.829601 TGGTCTAATTGAAAAACCGCCAT 59.170 39.130 0.00 0.00 32.50 4.40
2478 2971 3.223435 TGGTCTAATTGAAAAACCGCCA 58.777 40.909 0.00 0.00 32.50 5.69
2479 2972 3.926821 TGGTCTAATTGAAAAACCGCC 57.073 42.857 0.00 0.00 32.50 6.13
2480 2973 4.173256 CCATGGTCTAATTGAAAAACCGC 58.827 43.478 2.57 0.00 32.50 5.68
2481 2974 5.385509 ACCATGGTCTAATTGAAAAACCG 57.614 39.130 13.00 0.00 32.50 4.44
2482 2975 7.462571 ACTACCATGGTCTAATTGAAAAACC 57.537 36.000 23.76 0.00 0.00 3.27
2483 2976 9.758651 AAAACTACCATGGTCTAATTGAAAAAC 57.241 29.630 23.76 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.