Multiple sequence alignment - TraesCS5D01G357600

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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 TraesCS5D01G357600 chr5D 100.000 2798 0 0 1 2798 438358980 438361777 0.000000e+00 5168.0
1 TraesCS5D01G357600 chr5D 80.997 642 90 21 2011 2644 438387017 438387634 5.420000e-132 481.0
2 TraesCS5D01G357600 chr5B 91.894 2455 135 31 229 2656 532875892 532878309 0.000000e+00 3373.0
3 TraesCS5D01G357600 chr5B 87.407 405 42 7 2257 2661 532891238 532891633 9.130000e-125 457.0
4 TraesCS5D01G357600 chr5B 83.333 486 60 11 2162 2644 532931858 532932325 1.990000e-116 429.0
5 TraesCS5D01G357600 chr5A 92.315 2199 98 31 311 2479 553420213 553422370 0.000000e+00 3059.0
6 TraesCS5D01G357600 chr5A 83.694 509 60 13 2156 2661 553423199 553423687 2.540000e-125 459.0
7 TraesCS5D01G357600 chr5A 80.288 624 80 23 2023 2644 553457915 553458497 5.540000e-117 431.0
8 TraesCS5D01G357600 chr5A 93.478 138 6 2 83 217 553419009 553419146 4.730000e-48 202.0
9 TraesCS5D01G357600 chr1A 92.365 812 59 2 992 1800 566564169 566564980 0.000000e+00 1153.0
10 TraesCS5D01G357600 chr1D 94.816 733 38 0 1068 1800 472560991 472561723 0.000000e+00 1144.0
11 TraesCS5D01G357600 chr1D 78.932 337 53 10 2314 2648 420855880 420856200 2.180000e-51 213.0
12 TraesCS5D01G357600 chr1B 94.816 733 38 0 1068 1800 657272140 657272872 0.000000e+00 1144.0
13 TraesCS5D01G357600 chr1B 89.121 717 78 0 1082 1798 542432434 542431718 0.000000e+00 893.0
14 TraesCS5D01G357600 chr1B 88.935 723 80 0 1076 1798 542579897 542579175 0.000000e+00 893.0
15 TraesCS5D01G357600 chr7A 89.607 712 68 3 1085 1796 288928697 288929402 0.000000e+00 900.0
16 TraesCS5D01G357600 chr7A 87.387 222 17 5 1 221 10416023 10415812 7.740000e-61 244.0
17 TraesCS5D01G357600 chr7D 89.026 729 70 7 1071 1796 264752864 264753585 0.000000e+00 894.0
18 TraesCS5D01G357600 chr7D 86.047 86 11 1 136 221 528577850 528577766 1.070000e-14 91.6
19 TraesCS5D01G357600 chr2D 90.090 222 19 3 1 221 25878409 25878190 4.560000e-73 285.0
20 TraesCS5D01G357600 chr2A 86.036 222 19 6 1 221 767486432 767486222 7.800000e-56 228.0
21 TraesCS5D01G357600 chr7B 91.463 82 6 1 1 82 38973290 38973210 8.190000e-21 111.0


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 TraesCS5D01G357600 chr5D 438358980 438361777 2797 False 5168 5168 100.000 1 2798 1 chr5D.!!$F1 2797
1 TraesCS5D01G357600 chr5D 438387017 438387634 617 False 481 481 80.997 2011 2644 1 chr5D.!!$F2 633
2 TraesCS5D01G357600 chr5B 532875892 532878309 2417 False 3373 3373 91.894 229 2656 1 chr5B.!!$F1 2427
3 TraesCS5D01G357600 chr5A 553419009 553423687 4678 False 1240 3059 89.829 83 2661 3 chr5A.!!$F2 2578
4 TraesCS5D01G357600 chr5A 553457915 553458497 582 False 431 431 80.288 2023 2644 1 chr5A.!!$F1 621
5 TraesCS5D01G357600 chr1A 566564169 566564980 811 False 1153 1153 92.365 992 1800 1 chr1A.!!$F1 808
6 TraesCS5D01G357600 chr1D 472560991 472561723 732 False 1144 1144 94.816 1068 1800 1 chr1D.!!$F2 732
7 TraesCS5D01G357600 chr1B 657272140 657272872 732 False 1144 1144 94.816 1068 1800 1 chr1B.!!$F1 732
8 TraesCS5D01G357600 chr1B 542431718 542432434 716 True 893 893 89.121 1082 1798 1 chr1B.!!$R1 716
9 TraesCS5D01G357600 chr1B 542579175 542579897 722 True 893 893 88.935 1076 1798 1 chr1B.!!$R2 722
10 TraesCS5D01G357600 chr7A 288928697 288929402 705 False 900 900 89.607 1085 1796 1 chr7A.!!$F1 711
11 TraesCS5D01G357600 chr7D 264752864 264753585 721 False 894 894 89.026 1071 1796 1 chr7D.!!$F1 725

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
73 74 0.247934 GCGGCGTAAACAACTATGGC 60.248 55.0 9.37 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2823 1.190643 GCCTAGAGGTTGAGCTGACT 58.809 55.0 0.0 0.0 37.57 3.41 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
56 57 5.469373 TTGTTGCTATCAATAGAGTTGCG 57.531 39.130 1.15 0.00 34.29 4.85
57 58 3.871006 TGTTGCTATCAATAGAGTTGCGG 59.129 43.478 1.15 0.00 34.29 5.69
58 59 2.483876 TGCTATCAATAGAGTTGCGGC 58.516 47.619 1.15 0.00 32.05 6.53
59 60 1.457303 GCTATCAATAGAGTTGCGGCG 59.543 52.381 0.51 0.51 32.05 6.46
60 61 2.743938 CTATCAATAGAGTTGCGGCGT 58.256 47.619 9.37 0.00 32.05 5.68
61 62 2.882927 ATCAATAGAGTTGCGGCGTA 57.117 45.000 9.37 0.00 0.00 4.42
62 63 2.658373 TCAATAGAGTTGCGGCGTAA 57.342 45.000 6.25 6.25 0.00 3.18
63 64 2.962125 TCAATAGAGTTGCGGCGTAAA 58.038 42.857 12.96 2.12 0.00 2.01
64 65 2.669434 TCAATAGAGTTGCGGCGTAAAC 59.331 45.455 12.96 15.07 0.00 2.01
65 66 2.373540 ATAGAGTTGCGGCGTAAACA 57.626 45.000 22.99 5.71 0.00 2.83
66 67 2.151881 TAGAGTTGCGGCGTAAACAA 57.848 45.000 22.99 11.03 0.00 2.83
67 68 0.584876 AGAGTTGCGGCGTAAACAAC 59.415 50.000 22.99 20.04 43.12 3.32
68 69 2.697819 AGTTGCGGCGTAAACAACT 58.302 47.368 20.03 20.03 46.86 3.16
70 71 2.886587 GTTGCGGCGTAAACAACTAT 57.113 45.000 12.96 0.00 40.36 2.12
71 72 2.501881 GTTGCGGCGTAAACAACTATG 58.498 47.619 12.96 0.00 40.36 2.23
72 73 1.080298 TGCGGCGTAAACAACTATGG 58.920 50.000 9.37 0.00 0.00 2.74
73 74 0.247934 GCGGCGTAAACAACTATGGC 60.248 55.000 9.37 0.00 0.00 4.40
74 75 1.080298 CGGCGTAAACAACTATGGCA 58.920 50.000 0.00 0.00 33.95 4.92
75 76 1.465387 CGGCGTAAACAACTATGGCAA 59.535 47.619 0.00 0.00 33.95 4.52
76 77 2.726681 CGGCGTAAACAACTATGGCAAC 60.727 50.000 0.00 0.00 33.95 4.17
140 141 7.714377 CCCTCATCATGTCCAATAGCTATATTC 59.286 40.741 6.68 0.00 28.73 1.75
151 155 9.088987 TCCAATAGCTATATTCACATGTAGTCA 57.911 33.333 6.68 0.00 28.73 3.41
163 167 6.437928 TCACATGTAGTCAAATCACTTTTGC 58.562 36.000 0.00 0.00 43.68 3.68
205 209 4.592351 AGGATCAATCTAGACCCACAGATG 59.408 45.833 0.00 0.00 31.87 2.90
208 212 3.118629 TCAATCTAGACCCACAGATGTGC 60.119 47.826 7.46 0.00 44.34 4.57
256 390 4.102524 ACTTCAGACTTGTCCACAATACCA 59.897 41.667 0.00 0.00 35.02 3.25
271 405 9.467796 TCCACAATACCAACATGTCATATTTAA 57.532 29.630 0.00 0.00 0.00 1.52
284 418 7.566760 TGTCATATTTAATCATCTTGCGGTT 57.433 32.000 0.00 0.00 0.00 4.44
313 447 4.166337 AGTGTATCCTACTACTCTGGAGCA 59.834 45.833 0.00 0.00 32.95 4.26
314 448 4.276431 GTGTATCCTACTACTCTGGAGCAC 59.724 50.000 0.00 0.00 34.86 4.40
315 449 3.963476 ATCCTACTACTCTGGAGCACT 57.037 47.619 0.00 0.00 32.95 4.40
392 1369 6.317789 ACCATGTATTTGTGTGAACAAGAG 57.682 37.500 0.00 0.00 0.00 2.85
397 1374 9.712359 CATGTATTTGTGTGAACAAGAGATATG 57.288 33.333 0.00 0.00 0.00 1.78
506 1524 2.457366 ACGGCAAATATCGATCTCCC 57.543 50.000 0.00 0.00 0.00 4.30
507 1525 1.336887 ACGGCAAATATCGATCTCCCG 60.337 52.381 0.00 10.90 40.21 5.14
508 1526 1.726853 GGCAAATATCGATCTCCCGG 58.273 55.000 0.00 0.00 0.00 5.73
551 1569 2.096596 GCATCAGCAGCCTCAGAAC 58.903 57.895 0.00 0.00 41.58 3.01
577 1595 2.371923 GCGCAACGGCCAAAATCAC 61.372 57.895 0.30 0.00 36.38 3.06
581 1599 0.673437 CAACGGCCAAAATCACCACT 59.327 50.000 2.24 0.00 0.00 4.00
737 1755 2.469516 GCGCGAAATCCACCGGAAT 61.470 57.895 12.10 0.00 34.34 3.01
738 1756 1.641677 CGCGAAATCCACCGGAATC 59.358 57.895 9.46 0.00 34.34 2.52
752 1770 1.202290 CGGAATCCTGCAAAAATCCCG 60.202 52.381 0.00 0.00 0.00 5.14
759 1777 0.521291 TGCAAAAATCCCGAGCTTCG 59.479 50.000 0.00 0.00 40.07 3.79
918 1936 2.345244 CGGCTTCACTCCACAGCT 59.655 61.111 0.00 0.00 33.76 4.24
937 1955 4.988598 CAACGACCACCAGCGCCT 62.989 66.667 2.29 0.00 0.00 5.52
938 1956 4.681978 AACGACCACCAGCGCCTC 62.682 66.667 2.29 0.00 0.00 4.70
941 1959 3.075005 GACCACCAGCGCCTCCTA 61.075 66.667 2.29 0.00 0.00 2.94
942 1960 3.372554 GACCACCAGCGCCTCCTAC 62.373 68.421 2.29 0.00 0.00 3.18
943 1961 3.390521 CCACCAGCGCCTCCTACA 61.391 66.667 2.29 0.00 0.00 2.74
944 1962 2.185350 CACCAGCGCCTCCTACAG 59.815 66.667 2.29 0.00 0.00 2.74
948 1966 2.055042 CAGCGCCTCCTACAGTCCT 61.055 63.158 2.29 0.00 0.00 3.85
1308 2329 2.982130 GAGGTGATCCACTGCCGT 59.018 61.111 0.00 0.00 34.40 5.68
1527 2548 4.814294 GTGGAGGGCTACCGCGTG 62.814 72.222 4.92 0.00 43.47 5.34
1934 2955 0.394762 ATGTTGCATGTGAGGGCGAT 60.395 50.000 0.00 0.00 0.00 4.58
2037 3058 5.063312 GCATCTCTGTTCTTCTGCTTAACTC 59.937 44.000 0.00 0.00 0.00 3.01
2080 3101 6.936335 TCTGAATGTCAAATGCAGAAGTTCTA 59.064 34.615 4.74 0.00 33.11 2.10
2086 3107 7.532571 TGTCAAATGCAGAAGTTCTATGAATG 58.467 34.615 4.74 3.28 0.00 2.67
2090 3111 8.857216 CAAATGCAGAAGTTCTATGAATGTTTC 58.143 33.333 4.74 0.00 0.00 2.78
2107 3128 4.269183 TGTTTCTCTGAAAGTCCAAGCAA 58.731 39.130 0.00 0.00 33.76 3.91
2114 3135 4.275936 TCTGAAAGTCCAAGCAACTAAAGC 59.724 41.667 0.00 0.00 33.76 3.51
2148 3170 6.837048 TCATCAAGACATTCATTCCATCCATT 59.163 34.615 0.00 0.00 0.00 3.16
2149 3171 7.343574 TCATCAAGACATTCATTCCATCCATTT 59.656 33.333 0.00 0.00 0.00 2.32
2150 3172 7.104043 TCAAGACATTCATTCCATCCATTTC 57.896 36.000 0.00 0.00 0.00 2.17
2151 3173 6.664384 TCAAGACATTCATTCCATCCATTTCA 59.336 34.615 0.00 0.00 0.00 2.69
2152 3174 7.178805 TCAAGACATTCATTCCATCCATTTCAA 59.821 33.333 0.00 0.00 0.00 2.69
2153 3175 7.108841 AGACATTCATTCCATCCATTTCAAG 57.891 36.000 0.00 0.00 0.00 3.02
2154 3176 6.666546 AGACATTCATTCCATCCATTTCAAGT 59.333 34.615 0.00 0.00 0.00 3.16
2161 3183 7.656948 TCATTCCATCCATTTCAAGTTTTCAAC 59.343 33.333 0.00 0.00 0.00 3.18
2405 4590 4.392921 TCTTCTCTTCCATCATTCCGAC 57.607 45.455 0.00 0.00 0.00 4.79
2481 4666 1.001974 CCGTTCTCCAAGATGGACACA 59.998 52.381 0.00 0.00 42.67 3.72
2496 4681 0.319555 ACACAACGGACGACATGAGG 60.320 55.000 0.00 0.00 0.00 3.86
2520 4705 3.827898 CTGCTCGGGTCGTCCTCC 61.828 72.222 0.00 0.00 0.00 4.30
2565 4750 0.465824 AGAGCAATGCCTCATCCTGC 60.466 55.000 0.00 0.00 34.26 4.85
2652 4837 4.314740 TGCCTACATGAAACAACCAAAC 57.685 40.909 0.00 0.00 0.00 2.93
2661 4846 3.515502 TGAAACAACCAAACCAACCATCA 59.484 39.130 0.00 0.00 0.00 3.07
2662 4847 3.817709 AACAACCAAACCAACCATCAG 57.182 42.857 0.00 0.00 0.00 2.90
2663 4848 2.038659 ACAACCAAACCAACCATCAGG 58.961 47.619 0.00 0.00 42.21 3.86
2664 4849 2.315176 CAACCAAACCAACCATCAGGA 58.685 47.619 0.00 0.00 38.69 3.86
2665 4850 2.697751 CAACCAAACCAACCATCAGGAA 59.302 45.455 0.00 0.00 38.69 3.36
2666 4851 3.258722 ACCAAACCAACCATCAGGAAT 57.741 42.857 0.00 0.00 38.69 3.01
2667 4852 3.586429 ACCAAACCAACCATCAGGAATT 58.414 40.909 0.00 0.00 38.69 2.17
2668 4853 3.324556 ACCAAACCAACCATCAGGAATTG 59.675 43.478 0.00 0.00 38.69 2.32
2669 4854 3.324556 CCAAACCAACCATCAGGAATTGT 59.675 43.478 0.00 0.00 38.69 2.71
2670 4855 4.202346 CCAAACCAACCATCAGGAATTGTT 60.202 41.667 0.00 0.00 38.69 2.83
2671 4856 5.367302 CAAACCAACCATCAGGAATTGTTT 58.633 37.500 0.00 0.00 38.69 2.83
2672 4857 5.628797 AACCAACCATCAGGAATTGTTTT 57.371 34.783 0.00 0.00 38.69 2.43
2673 4858 5.628797 ACCAACCATCAGGAATTGTTTTT 57.371 34.783 0.00 0.00 38.69 1.94
2704 4889 9.788960 TGCTATTATGAATACAGATACGATCAC 57.211 33.333 0.00 0.00 0.00 3.06
2705 4890 9.788960 GCTATTATGAATACAGATACGATCACA 57.211 33.333 0.00 0.00 0.00 3.58
2708 4893 9.981114 ATTATGAATACAGATACGATCACAACA 57.019 29.630 0.00 0.00 0.00 3.33
2709 4894 9.981114 TTATGAATACAGATACGATCACAACAT 57.019 29.630 0.00 0.00 0.00 2.71
2710 4895 7.698836 TGAATACAGATACGATCACAACATG 57.301 36.000 0.00 0.00 0.00 3.21
2711 4896 6.701400 TGAATACAGATACGATCACAACATGG 59.299 38.462 0.00 0.00 0.00 3.66
2712 4897 4.736126 ACAGATACGATCACAACATGGA 57.264 40.909 0.00 0.00 0.00 3.41
2713 4898 4.686972 ACAGATACGATCACAACATGGAG 58.313 43.478 0.00 0.00 0.00 3.86
2714 4899 4.160439 ACAGATACGATCACAACATGGAGT 59.840 41.667 0.00 0.00 0.00 3.85
2715 4900 5.359860 ACAGATACGATCACAACATGGAGTA 59.640 40.000 0.00 0.00 0.00 2.59
2716 4901 5.687730 CAGATACGATCACAACATGGAGTAC 59.312 44.000 0.00 0.00 0.00 2.73
2717 4902 5.594725 AGATACGATCACAACATGGAGTACT 59.405 40.000 0.00 0.00 0.00 2.73
2718 4903 4.111375 ACGATCACAACATGGAGTACTC 57.889 45.455 14.87 14.87 0.00 2.59
2760 4945 9.969001 AGAAGAGTGTCTAGATACTTAGAAACT 57.031 33.333 21.49 11.07 46.25 2.66
2763 4948 9.742144 AGAGTGTCTAGATACTTAGAAACTTCA 57.258 33.333 21.49 0.00 44.52 3.02
2766 4951 9.063739 GTGTCTAGATACTTAGAAACTTCAACG 57.936 37.037 12.05 0.00 35.76 4.10
2767 4952 8.242053 TGTCTAGATACTTAGAAACTTCAACGG 58.758 37.037 0.00 0.00 31.80 4.44
2768 4953 8.242739 GTCTAGATACTTAGAAACTTCAACGGT 58.757 37.037 0.00 0.00 31.80 4.83
2769 4954 8.800332 TCTAGATACTTAGAAACTTCAACGGTT 58.200 33.333 0.00 0.00 0.00 4.44
2770 4955 9.420551 CTAGATACTTAGAAACTTCAACGGTTT 57.579 33.333 0.00 0.00 39.25 3.27
2771 4956 8.084590 AGATACTTAGAAACTTCAACGGTTTG 57.915 34.615 0.00 0.00 37.07 2.93
2772 4957 5.494632 ACTTAGAAACTTCAACGGTTTGG 57.505 39.130 0.00 0.00 37.07 3.28
2773 4958 4.945543 ACTTAGAAACTTCAACGGTTTGGT 59.054 37.500 0.00 0.00 37.07 3.67
2774 4959 5.416639 ACTTAGAAACTTCAACGGTTTGGTT 59.583 36.000 0.00 0.00 37.07 3.67
2775 4960 4.794278 AGAAACTTCAACGGTTTGGTTT 57.206 36.364 12.30 12.30 37.07 3.27
2776 4961 4.490743 AGAAACTTCAACGGTTTGGTTTG 58.509 39.130 15.41 0.00 37.07 2.93
2777 4962 2.951457 ACTTCAACGGTTTGGTTTGG 57.049 45.000 0.00 0.00 33.06 3.28
2778 4963 1.134936 ACTTCAACGGTTTGGTTTGGC 60.135 47.619 0.00 0.00 33.06 4.52
2779 4964 0.895530 TTCAACGGTTTGGTTTGGCA 59.104 45.000 0.00 0.00 33.06 4.92
2780 4965 0.457851 TCAACGGTTTGGTTTGGCAG 59.542 50.000 0.00 0.00 33.06 4.85
2781 4966 0.174617 CAACGGTTTGGTTTGGCAGT 59.825 50.000 0.00 0.00 0.00 4.40
2782 4967 1.405821 CAACGGTTTGGTTTGGCAGTA 59.594 47.619 0.00 0.00 0.00 2.74
2783 4968 1.026584 ACGGTTTGGTTTGGCAGTAC 58.973 50.000 0.00 0.00 0.00 2.73
2784 4969 0.312729 CGGTTTGGTTTGGCAGTACC 59.687 55.000 12.46 12.46 39.84 3.34
2795 4980 1.885887 TGGCAGTACCAGTGAAAATGC 59.114 47.619 8.14 8.14 46.36 3.56
2796 4981 1.885887 GGCAGTACCAGTGAAAATGCA 59.114 47.619 15.65 0.00 38.86 3.96
2797 4982 2.095059 GGCAGTACCAGTGAAAATGCAG 60.095 50.000 15.65 0.00 38.86 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.801377 CGCAACTCTATTGATAGCAACAAAAA 59.199 34.615 0.00 0.00 36.72 1.94
32 33 6.314018 CGCAACTCTATTGATAGCAACAAAA 58.686 36.000 0.00 0.00 36.72 2.44
33 34 5.163764 CCGCAACTCTATTGATAGCAACAAA 60.164 40.000 0.00 0.00 36.72 2.83
34 35 4.332543 CCGCAACTCTATTGATAGCAACAA 59.667 41.667 0.00 0.00 36.72 2.83
35 36 3.871006 CCGCAACTCTATTGATAGCAACA 59.129 43.478 0.00 0.00 36.72 3.33
36 37 3.303395 GCCGCAACTCTATTGATAGCAAC 60.303 47.826 0.00 0.00 36.72 4.17
37 38 2.872245 GCCGCAACTCTATTGATAGCAA 59.128 45.455 0.00 0.00 38.60 3.91
38 39 2.483876 GCCGCAACTCTATTGATAGCA 58.516 47.619 0.00 0.00 0.00 3.49
39 40 1.457303 CGCCGCAACTCTATTGATAGC 59.543 52.381 0.00 0.00 0.00 2.97
40 41 2.743938 ACGCCGCAACTCTATTGATAG 58.256 47.619 0.00 0.00 0.00 2.08
41 42 2.882927 ACGCCGCAACTCTATTGATA 57.117 45.000 0.00 0.00 0.00 2.15
42 43 2.882927 TACGCCGCAACTCTATTGAT 57.117 45.000 0.00 0.00 0.00 2.57
43 44 2.658373 TTACGCCGCAACTCTATTGA 57.342 45.000 0.00 0.00 0.00 2.57
44 45 2.413796 TGTTTACGCCGCAACTCTATTG 59.586 45.455 1.99 0.00 0.00 1.90
45 46 2.690786 TGTTTACGCCGCAACTCTATT 58.309 42.857 1.99 0.00 0.00 1.73
46 47 2.373540 TGTTTACGCCGCAACTCTAT 57.626 45.000 1.99 0.00 0.00 1.98
47 48 1.794116 GTTGTTTACGCCGCAACTCTA 59.206 47.619 1.99 0.00 39.30 2.43
48 49 0.584876 GTTGTTTACGCCGCAACTCT 59.415 50.000 1.99 0.00 39.30 3.24
49 50 0.584876 AGTTGTTTACGCCGCAACTC 59.415 50.000 2.60 0.00 46.61 3.01
50 51 2.697819 AGTTGTTTACGCCGCAACT 58.302 47.368 2.60 2.60 45.28 3.16
51 52 2.501881 CATAGTTGTTTACGCCGCAAC 58.498 47.619 0.00 0.00 41.78 4.17
52 53 1.465387 CCATAGTTGTTTACGCCGCAA 59.535 47.619 0.00 0.00 0.00 4.85
53 54 1.080298 CCATAGTTGTTTACGCCGCA 58.920 50.000 0.00 0.00 0.00 5.69
54 55 0.247934 GCCATAGTTGTTTACGCCGC 60.248 55.000 0.00 0.00 0.00 6.53
55 56 1.080298 TGCCATAGTTGTTTACGCCG 58.920 50.000 0.00 0.00 0.00 6.46
56 57 2.226912 TGTTGCCATAGTTGTTTACGCC 59.773 45.455 0.00 0.00 0.00 5.68
57 58 3.546002 TGTTGCCATAGTTGTTTACGC 57.454 42.857 0.00 0.00 0.00 4.42
58 59 5.289917 TCATGTTGCCATAGTTGTTTACG 57.710 39.130 0.00 0.00 0.00 3.18
59 60 8.458843 ACTAATCATGTTGCCATAGTTGTTTAC 58.541 33.333 0.00 0.00 0.00 2.01
60 61 8.458052 CACTAATCATGTTGCCATAGTTGTTTA 58.542 33.333 0.00 0.00 0.00 2.01
61 62 7.315142 CACTAATCATGTTGCCATAGTTGTTT 58.685 34.615 0.00 0.00 0.00 2.83
62 63 6.625740 GCACTAATCATGTTGCCATAGTTGTT 60.626 38.462 0.00 0.00 0.00 2.83
63 64 5.163622 GCACTAATCATGTTGCCATAGTTGT 60.164 40.000 0.00 0.00 0.00 3.32
64 65 5.276270 GCACTAATCATGTTGCCATAGTTG 58.724 41.667 0.00 0.00 0.00 3.16
65 66 4.035558 CGCACTAATCATGTTGCCATAGTT 59.964 41.667 0.00 0.00 0.00 2.24
66 67 3.561310 CGCACTAATCATGTTGCCATAGT 59.439 43.478 0.00 0.00 0.00 2.12
67 68 3.607775 GCGCACTAATCATGTTGCCATAG 60.608 47.826 0.30 0.00 0.00 2.23
68 69 2.290367 GCGCACTAATCATGTTGCCATA 59.710 45.455 0.30 0.00 0.00 2.74
69 70 1.066002 GCGCACTAATCATGTTGCCAT 59.934 47.619 0.30 0.00 0.00 4.40
70 71 0.451383 GCGCACTAATCATGTTGCCA 59.549 50.000 0.30 0.00 0.00 4.92
71 72 0.451383 TGCGCACTAATCATGTTGCC 59.549 50.000 5.66 0.00 0.00 4.52
72 73 1.135717 TGTGCGCACTAATCATGTTGC 60.136 47.619 37.59 10.40 0.00 4.17
73 74 2.898181 TGTGCGCACTAATCATGTTG 57.102 45.000 37.59 0.00 0.00 3.33
74 75 4.496341 GCTATTGTGCGCACTAATCATGTT 60.496 41.667 37.59 17.96 0.00 2.71
75 76 3.002656 GCTATTGTGCGCACTAATCATGT 59.997 43.478 37.59 18.65 0.00 3.21
76 77 3.548587 GCTATTGTGCGCACTAATCATG 58.451 45.455 37.59 24.89 0.00 3.07
77 78 3.885484 GCTATTGTGCGCACTAATCAT 57.115 42.857 37.59 23.17 0.00 2.45
151 155 6.863126 GCACTTATACACAGCAAAAGTGATTT 59.137 34.615 15.56 0.00 46.29 2.17
155 159 4.023279 TGGCACTTATACACAGCAAAAGTG 60.023 41.667 8.72 8.72 46.18 3.16
163 167 4.769688 TCCTTGATGGCACTTATACACAG 58.230 43.478 0.00 0.00 35.26 3.66
205 209 2.821546 TCACCATCATAGCTTACGCAC 58.178 47.619 0.00 0.00 39.10 5.34
208 212 5.109210 TCACTTTCACCATCATAGCTTACG 58.891 41.667 0.00 0.00 0.00 3.18
217 221 5.296780 GTCTGAAGTTTCACTTTCACCATCA 59.703 40.000 0.00 0.00 38.80 3.07
218 222 5.529060 AGTCTGAAGTTTCACTTTCACCATC 59.471 40.000 0.00 0.00 38.80 3.51
219 223 5.440610 AGTCTGAAGTTTCACTTTCACCAT 58.559 37.500 0.00 0.00 38.80 3.55
220 224 4.843728 AGTCTGAAGTTTCACTTTCACCA 58.156 39.130 0.00 0.00 38.80 4.17
221 225 5.123979 ACAAGTCTGAAGTTTCACTTTCACC 59.876 40.000 0.00 0.00 38.80 4.02
225 229 5.123979 GTGGACAAGTCTGAAGTTTCACTTT 59.876 40.000 0.00 0.00 38.80 2.66
226 230 4.636206 GTGGACAAGTCTGAAGTTTCACTT 59.364 41.667 0.00 0.00 41.95 3.16
227 231 4.192317 GTGGACAAGTCTGAAGTTTCACT 58.808 43.478 0.00 0.00 32.90 3.41
235 369 4.698201 TGGTATTGTGGACAAGTCTGAA 57.302 40.909 0.00 0.00 39.47 3.02
256 390 8.077991 CCGCAAGATGATTAAATATGACATGTT 58.922 33.333 0.00 0.00 43.02 2.71
271 405 3.879295 CACTGGAATAACCGCAAGATGAT 59.121 43.478 0.00 0.00 42.61 2.45
279 413 3.470645 AGGATACACTGGAATAACCGC 57.529 47.619 0.00 0.00 40.02 5.68
313 447 5.163301 CCAATTGCTACTGGTGGTATCTAGT 60.163 44.000 0.00 0.00 33.87 2.57
314 448 5.300752 CCAATTGCTACTGGTGGTATCTAG 58.699 45.833 0.00 0.00 0.00 2.43
315 449 4.444306 GCCAATTGCTACTGGTGGTATCTA 60.444 45.833 0.00 0.00 36.87 1.98
453 1471 3.179265 CGACGTGGCCGACATCAC 61.179 66.667 0.00 0.00 37.88 3.06
733 1751 2.099405 TCGGGATTTTTGCAGGATTCC 58.901 47.619 0.00 0.00 0.00 3.01
737 1755 0.038166 AGCTCGGGATTTTTGCAGGA 59.962 50.000 0.00 0.00 0.00 3.86
738 1756 0.890683 AAGCTCGGGATTTTTGCAGG 59.109 50.000 0.00 0.00 0.00 4.85
902 1920 1.376553 GGAGCTGTGGAGTGAAGCC 60.377 63.158 0.00 0.00 37.68 4.35
918 1936 4.980805 GCGCTGGTGGTCGTTGGA 62.981 66.667 0.00 0.00 0.00 3.53
942 1960 4.354608 GCTGAGGCTGACAGTAGGACTG 62.355 59.091 3.99 5.07 42.59 3.51
943 1961 1.846007 CTGAGGCTGACAGTAGGACT 58.154 55.000 3.99 0.00 0.00 3.85
944 1962 0.174617 GCTGAGGCTGACAGTAGGAC 59.825 60.000 3.99 0.00 37.64 3.85
966 1984 2.794621 GCTAGCTTTGCTTCGGGC 59.205 61.111 7.70 0.00 40.44 6.13
1047 2065 2.227036 CCTGGAGGCCTTCACAGGT 61.227 63.158 29.81 0.48 44.21 4.00
1802 2823 1.190643 GCCTAGAGGTTGAGCTGACT 58.809 55.000 0.00 0.00 37.57 3.41
1934 2955 2.029020 CACACCAACTCCTCATCTCGAA 60.029 50.000 0.00 0.00 0.00 3.71
2080 3101 6.294397 GCTTGGACTTTCAGAGAAACATTCAT 60.294 38.462 0.00 0.00 0.00 2.57
2086 3107 4.336713 AGTTGCTTGGACTTTCAGAGAAAC 59.663 41.667 0.00 0.00 0.00 2.78
2090 3111 5.561725 GCTTTAGTTGCTTGGACTTTCAGAG 60.562 44.000 0.00 0.00 0.00 3.35
2107 3128 8.579006 TGTCTTGATGAATTTGAATGCTTTAGT 58.421 29.630 0.00 0.00 0.00 2.24
2148 3170 7.094420 TGAGTTGATCAGTGTTGAAAACTTGAA 60.094 33.333 0.00 0.00 41.70 2.69
2149 3171 6.374053 TGAGTTGATCAGTGTTGAAAACTTGA 59.626 34.615 0.00 0.00 41.03 3.02
2150 3172 6.554419 TGAGTTGATCAGTGTTGAAAACTTG 58.446 36.000 0.00 0.00 41.03 3.16
2151 3173 6.757897 TGAGTTGATCAGTGTTGAAAACTT 57.242 33.333 0.00 0.00 41.03 2.66
2152 3174 6.150976 TGTTGAGTTGATCAGTGTTGAAAACT 59.849 34.615 0.00 8.04 43.20 2.66
2153 3175 6.321717 TGTTGAGTTGATCAGTGTTGAAAAC 58.678 36.000 0.00 0.00 43.13 2.43
2154 3176 6.507958 TGTTGAGTTGATCAGTGTTGAAAA 57.492 33.333 0.00 0.00 39.68 2.29
2161 3183 4.758674 ACAGGATTGTTGAGTTGATCAGTG 59.241 41.667 0.00 0.00 39.68 3.66
2252 3277 5.579511 GCACTAGTCCTAGCGTTTCATTTTA 59.420 40.000 0.00 0.00 36.66 1.52
2258 3283 2.649331 TGCACTAGTCCTAGCGTTTC 57.351 50.000 0.00 0.00 36.66 2.78
2262 3287 2.531206 GAAGTTGCACTAGTCCTAGCG 58.469 52.381 0.00 0.00 36.66 4.26
2289 3334 7.934120 AGTAGTAACTGCAACTTTCTTCTTCAT 59.066 33.333 0.00 0.00 33.57 2.57
2290 3335 7.224753 CAGTAGTAACTGCAACTTTCTTCTTCA 59.775 37.037 0.00 0.00 46.28 3.02
2291 3336 7.568433 CAGTAGTAACTGCAACTTTCTTCTTC 58.432 38.462 0.00 0.00 46.28 2.87
2405 4590 2.125673 CGAACCAGCCAGGGTACG 60.126 66.667 0.00 0.00 37.53 3.67
2481 4666 2.978824 CCCCTCATGTCGTCCGTT 59.021 61.111 0.00 0.00 0.00 4.44
2532 4717 2.887568 CTCTGCATCCACGTCGGC 60.888 66.667 0.00 0.00 33.14 5.54
2565 4750 1.088340 CCATGGCAGAGAGCTGTTCG 61.088 60.000 0.00 0.00 44.17 3.95
2602 4787 1.925972 GGAGGGAAGGGAAGGCAGT 60.926 63.158 0.00 0.00 0.00 4.40
2647 4832 3.324556 ACAATTCCTGATGGTTGGTTTGG 59.675 43.478 0.00 0.00 34.23 3.28
2678 4863 9.788960 GTGATCGTATCTGTATTCATAATAGCA 57.211 33.333 0.00 0.00 0.00 3.49
2679 4864 9.788960 TGTGATCGTATCTGTATTCATAATAGC 57.211 33.333 0.00 0.00 0.00 2.97
2682 4867 9.981114 TGTTGTGATCGTATCTGTATTCATAAT 57.019 29.630 0.00 0.00 0.00 1.28
2683 4868 9.981114 ATGTTGTGATCGTATCTGTATTCATAA 57.019 29.630 0.00 0.00 0.00 1.90
2684 4869 9.410556 CATGTTGTGATCGTATCTGTATTCATA 57.589 33.333 0.00 0.00 0.00 2.15
2685 4870 7.386025 CCATGTTGTGATCGTATCTGTATTCAT 59.614 37.037 0.00 0.00 0.00 2.57
2686 4871 6.701400 CCATGTTGTGATCGTATCTGTATTCA 59.299 38.462 0.00 0.00 0.00 2.57
2687 4872 6.923508 TCCATGTTGTGATCGTATCTGTATTC 59.076 38.462 0.00 0.00 0.00 1.75
2688 4873 6.816136 TCCATGTTGTGATCGTATCTGTATT 58.184 36.000 0.00 0.00 0.00 1.89
2689 4874 6.040955 ACTCCATGTTGTGATCGTATCTGTAT 59.959 38.462 0.00 0.00 0.00 2.29
2690 4875 5.359860 ACTCCATGTTGTGATCGTATCTGTA 59.640 40.000 0.00 0.00 0.00 2.74
2691 4876 4.160439 ACTCCATGTTGTGATCGTATCTGT 59.840 41.667 0.00 0.00 0.00 3.41
2692 4877 4.686972 ACTCCATGTTGTGATCGTATCTG 58.313 43.478 0.00 0.00 0.00 2.90
2693 4878 5.594725 AGTACTCCATGTTGTGATCGTATCT 59.405 40.000 0.00 0.00 0.00 1.98
2694 4879 5.833082 AGTACTCCATGTTGTGATCGTATC 58.167 41.667 0.00 0.00 0.00 2.24
2695 4880 5.833082 GAGTACTCCATGTTGTGATCGTAT 58.167 41.667 12.13 0.00 0.00 3.06
2696 4881 5.244785 GAGTACTCCATGTTGTGATCGTA 57.755 43.478 12.13 0.00 0.00 3.43
2697 4882 4.111375 GAGTACTCCATGTTGTGATCGT 57.889 45.455 12.13 0.00 0.00 3.73
2734 4919 9.969001 AGTTTCTAAGTATCTAGACACTCTTCT 57.031 33.333 3.67 0.00 35.10 2.85
2737 4922 9.742144 TGAAGTTTCTAAGTATCTAGACACTCT 57.258 33.333 3.67 0.00 37.76 3.24
2740 4925 9.063739 CGTTGAAGTTTCTAAGTATCTAGACAC 57.936 37.037 0.00 0.00 31.47 3.67
2741 4926 8.242053 CCGTTGAAGTTTCTAAGTATCTAGACA 58.758 37.037 0.00 0.00 0.00 3.41
2742 4927 8.242739 ACCGTTGAAGTTTCTAAGTATCTAGAC 58.757 37.037 0.00 0.00 0.00 2.59
2743 4928 8.345724 ACCGTTGAAGTTTCTAAGTATCTAGA 57.654 34.615 0.00 0.00 0.00 2.43
2744 4929 8.983307 AACCGTTGAAGTTTCTAAGTATCTAG 57.017 34.615 0.00 0.00 0.00 2.43
2745 4930 9.199982 CAAACCGTTGAAGTTTCTAAGTATCTA 57.800 33.333 0.00 0.00 35.28 1.98
2746 4931 7.172703 CCAAACCGTTGAAGTTTCTAAGTATCT 59.827 37.037 0.00 0.00 35.28 1.98
2747 4932 7.041576 ACCAAACCGTTGAAGTTTCTAAGTATC 60.042 37.037 0.00 0.00 35.28 2.24
2748 4933 6.769341 ACCAAACCGTTGAAGTTTCTAAGTAT 59.231 34.615 0.00 0.00 35.28 2.12
2749 4934 6.114767 ACCAAACCGTTGAAGTTTCTAAGTA 58.885 36.000 0.00 0.00 35.28 2.24
2750 4935 4.945543 ACCAAACCGTTGAAGTTTCTAAGT 59.054 37.500 0.00 0.00 35.28 2.24
2751 4936 5.494632 ACCAAACCGTTGAAGTTTCTAAG 57.505 39.130 0.00 0.00 35.28 2.18
2752 4937 5.900865 AACCAAACCGTTGAAGTTTCTAA 57.099 34.783 0.00 0.00 35.28 2.10
2753 4938 5.393243 CCAAACCAAACCGTTGAAGTTTCTA 60.393 40.000 4.43 0.00 35.28 2.10
2754 4939 4.490743 CAAACCAAACCGTTGAAGTTTCT 58.509 39.130 4.43 0.00 35.28 2.52
2755 4940 3.615056 CCAAACCAAACCGTTGAAGTTTC 59.385 43.478 4.43 0.00 35.28 2.78
2756 4941 3.591023 CCAAACCAAACCGTTGAAGTTT 58.409 40.909 2.35 2.35 37.93 2.66
2757 4942 2.675603 GCCAAACCAAACCGTTGAAGTT 60.676 45.455 0.00 0.00 36.83 2.66
2758 4943 1.134936 GCCAAACCAAACCGTTGAAGT 60.135 47.619 0.00 0.00 36.83 3.01
2759 4944 1.134965 TGCCAAACCAAACCGTTGAAG 60.135 47.619 0.00 0.00 36.83 3.02
2760 4945 0.895530 TGCCAAACCAAACCGTTGAA 59.104 45.000 0.00 0.00 36.83 2.69
2761 4946 0.457851 CTGCCAAACCAAACCGTTGA 59.542 50.000 0.00 0.00 36.83 3.18
2762 4947 0.174617 ACTGCCAAACCAAACCGTTG 59.825 50.000 0.00 0.00 34.25 4.10
2763 4948 1.406180 GTACTGCCAAACCAAACCGTT 59.594 47.619 0.00 0.00 0.00 4.44
2764 4949 1.026584 GTACTGCCAAACCAAACCGT 58.973 50.000 0.00 0.00 0.00 4.83
2765 4950 0.312729 GGTACTGCCAAACCAAACCG 59.687 55.000 0.00 0.00 35.73 4.44
2766 4951 1.404843 TGGTACTGCCAAACCAAACC 58.595 50.000 0.00 0.00 45.94 3.27
2775 4960 1.885887 GCATTTTCACTGGTACTGCCA 59.114 47.619 0.00 0.00 46.95 4.92
2776 4961 1.885887 TGCATTTTCACTGGTACTGCC 59.114 47.619 0.00 0.00 37.90 4.85
2777 4962 3.207474 CTGCATTTTCACTGGTACTGC 57.793 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.