Multiple sequence alignment - TraesCS7D01G075900

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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 TraesCS7D01G075900 chr7D 100.000 3038 0 0 1 3038 45030804 45027767 0.000000e+00 5611.0
1 TraesCS7D01G075900 chr7D 91.932 1760 107 20 716 2452 45220597 45222344 0.000000e+00 2431.0
2 TraesCS7D01G075900 chr7D 92.772 1259 86 4 990 2244 45056242 45057499 0.000000e+00 1816.0
3 TraesCS7D01G075900 chr7D 89.878 573 45 7 2055 2622 45057497 45058061 0.000000e+00 725.0
4 TraesCS7D01G075900 chr7D 90.323 93 4 3 482 571 45216403 45216313 1.910000e-22 117.0
5 TraesCS7D01G075900 chr7D 94.444 54 3 0 716 769 45211822 45211769 1.940000e-12 84.2
6 TraesCS7D01G075900 chrUn 92.603 1798 102 12 485 2256 330011915 330013707 0.000000e+00 2555.0
7 TraesCS7D01G075900 chrUn 93.298 1507 69 10 151 1633 391209995 391211493 0.000000e+00 2194.0
8 TraesCS7D01G075900 chrUn 93.360 1476 66 10 182 1633 397188543 397187076 0.000000e+00 2154.0
9 TraesCS7D01G075900 chrUn 91.468 1465 109 7 1462 2920 396475172 396476626 0.000000e+00 1999.0
10 TraesCS7D01G075900 chrUn 91.195 1465 113 7 1462 2920 358915193 358916647 0.000000e+00 1977.0
11 TraesCS7D01G075900 chrUn 91.097 1449 113 7 1511 2953 252047990 252049428 0.000000e+00 1947.0
12 TraesCS7D01G075900 chr1A 92.436 1798 105 12 485 2256 12638630 12640422 0.000000e+00 2538.0
13 TraesCS7D01G075900 chr1A 91.389 1498 113 7 1462 2953 12642349 12643836 0.000000e+00 2037.0
14 TraesCS7D01G075900 chr7A 90.229 1310 88 26 871 2158 47435808 47437099 0.000000e+00 1674.0
15 TraesCS7D01G075900 chr7A 94.140 529 23 4 51 575 47384299 47383775 0.000000e+00 798.0
16 TraesCS7D01G075900 chr7A 85.047 214 5 3 631 822 47383765 47383557 3.090000e-45 193.0
17 TraesCS7D01G075900 chr3D 82.519 1064 158 16 1001 2051 591624532 591625580 0.000000e+00 909.0
18 TraesCS7D01G075900 chr4A 86.232 414 48 6 2208 2621 656771621 656772025 1.000000e-119 440.0
19 TraesCS7D01G075900 chr5B 82.767 412 65 2 2226 2637 353016270 353015865 2.230000e-96 363.0
20 TraesCS7D01G075900 chr5D 82.524 412 66 2 2226 2637 308220701 308220296 1.040000e-94 357.0


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 TraesCS7D01G075900 chr7D 45027767 45030804 3037 True 5611.0 5611 100.0000 1 3038 1 chr7D.!!$R1 3037
1 TraesCS7D01G075900 chr7D 45220597 45222344 1747 False 2431.0 2431 91.9320 716 2452 1 chr7D.!!$F1 1736
2 TraesCS7D01G075900 chr7D 45056242 45058061 1819 False 1270.5 1816 91.3250 990 2622 2 chr7D.!!$F2 1632
3 TraesCS7D01G075900 chrUn 330011915 330013707 1792 False 2555.0 2555 92.6030 485 2256 1 chrUn.!!$F2 1771
4 TraesCS7D01G075900 chrUn 391209995 391211493 1498 False 2194.0 2194 93.2980 151 1633 1 chrUn.!!$F4 1482
5 TraesCS7D01G075900 chrUn 397187076 397188543 1467 True 2154.0 2154 93.3600 182 1633 1 chrUn.!!$R1 1451
6 TraesCS7D01G075900 chrUn 396475172 396476626 1454 False 1999.0 1999 91.4680 1462 2920 1 chrUn.!!$F5 1458
7 TraesCS7D01G075900 chrUn 358915193 358916647 1454 False 1977.0 1977 91.1950 1462 2920 1 chrUn.!!$F3 1458
8 TraesCS7D01G075900 chrUn 252047990 252049428 1438 False 1947.0 1947 91.0970 1511 2953 1 chrUn.!!$F1 1442
9 TraesCS7D01G075900 chr1A 12638630 12643836 5206 False 2287.5 2538 91.9125 485 2953 2 chr1A.!!$F1 2468
10 TraesCS7D01G075900 chr7A 47435808 47437099 1291 False 1674.0 1674 90.2290 871 2158 1 chr7A.!!$F1 1287
11 TraesCS7D01G075900 chr7A 47383557 47384299 742 True 495.5 798 89.5935 51 822 2 chr7A.!!$R1 771
12 TraesCS7D01G075900 chr3D 591624532 591625580 1048 False 909.0 909 82.5190 1001 2051 1 chr3D.!!$F1 1050

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
40 41 0.032952 TCTACGGACAGTGGTGCAAC 59.967 55.0 0.0 0.0 34.61 4.17 F
781 813 0.109689 CCAACTCGACTCCACTCGAC 60.110 60.0 0.0 0.0 37.76 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2061 0.249911 CCACCGAGCCCAAGTATAGC 60.25 60.0 0.0 0.0 0.0 2.97 R
2687 5506 0.030092 TCCCTTGCTACTAGGCCCAT 60.03 55.0 0.0 0.0 0.0 4.00 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
23 24 2.188994 GGCAGCGAGGCATTCTCT 59.811 61.111 1.18 0.00 43.51 3.10
24 25 1.443407 GGCAGCGAGGCATTCTCTA 59.557 57.895 1.18 0.00 43.51 2.43
25 26 0.878086 GGCAGCGAGGCATTCTCTAC 60.878 60.000 1.18 0.00 43.51 2.59
26 27 1.211818 GCAGCGAGGCATTCTCTACG 61.212 60.000 0.00 0.00 40.30 3.51
27 28 0.596083 CAGCGAGGCATTCTCTACGG 60.596 60.000 0.00 0.00 40.30 4.02
28 29 0.752009 AGCGAGGCATTCTCTACGGA 60.752 55.000 0.00 0.00 40.30 4.69
29 30 0.595310 GCGAGGCATTCTCTACGGAC 60.595 60.000 0.00 0.00 40.30 4.79
30 31 0.738975 CGAGGCATTCTCTACGGACA 59.261 55.000 0.00 0.00 40.30 4.02
31 32 1.268794 CGAGGCATTCTCTACGGACAG 60.269 57.143 0.00 0.00 40.30 3.51
32 33 1.751924 GAGGCATTCTCTACGGACAGT 59.248 52.381 0.00 0.00 39.38 3.55
33 34 1.478510 AGGCATTCTCTACGGACAGTG 59.521 52.381 0.00 0.00 0.00 3.66
34 35 1.471676 GGCATTCTCTACGGACAGTGG 60.472 57.143 0.00 0.00 0.00 4.00
35 36 1.204941 GCATTCTCTACGGACAGTGGT 59.795 52.381 0.00 0.00 32.65 4.16
36 37 2.881074 CATTCTCTACGGACAGTGGTG 58.119 52.381 0.00 0.00 32.65 4.17
37 38 0.601558 TTCTCTACGGACAGTGGTGC 59.398 55.000 0.00 0.00 32.65 5.01
38 39 0.538746 TCTCTACGGACAGTGGTGCA 60.539 55.000 0.00 0.00 34.61 4.57
39 40 0.317160 CTCTACGGACAGTGGTGCAA 59.683 55.000 0.00 0.00 34.61 4.08
40 41 0.032952 TCTACGGACAGTGGTGCAAC 59.967 55.000 0.00 0.00 34.61 4.17
41 42 1.282248 CTACGGACAGTGGTGCAACG 61.282 60.000 0.00 0.00 38.12 4.10
42 43 1.736365 TACGGACAGTGGTGCAACGA 61.736 55.000 0.00 0.00 38.12 3.85
43 44 1.667830 CGGACAGTGGTGCAACGAT 60.668 57.895 0.00 0.00 38.12 3.73
44 45 1.626654 CGGACAGTGGTGCAACGATC 61.627 60.000 0.00 0.00 38.12 3.69
45 46 0.320771 GGACAGTGGTGCAACGATCT 60.321 55.000 0.00 0.00 38.12 2.75
46 47 1.071605 GACAGTGGTGCAACGATCTC 58.928 55.000 0.00 0.00 38.12 2.75
47 48 0.681733 ACAGTGGTGCAACGATCTCT 59.318 50.000 0.00 0.00 38.12 3.10
48 49 1.893137 ACAGTGGTGCAACGATCTCTA 59.107 47.619 0.00 0.00 38.12 2.43
49 50 2.497675 ACAGTGGTGCAACGATCTCTAT 59.502 45.455 0.00 0.00 38.12 1.98
57 58 3.181462 TGCAACGATCTCTATTGGCATCT 60.181 43.478 0.00 0.00 0.00 2.90
63 64 1.609072 TCTCTATTGGCATCTCGGTCG 59.391 52.381 0.00 0.00 0.00 4.79
90 91 2.114616 AGGACACTTAGCTCCTCCATG 58.885 52.381 0.00 0.00 30.37 3.66
91 92 1.834263 GGACACTTAGCTCCTCCATGT 59.166 52.381 0.00 0.00 0.00 3.21
128 129 3.359523 CGGTCGTCGTGGTGGAGA 61.360 66.667 0.00 0.00 0.00 3.71
195 196 2.906389 CTCCTATAGGCTATGGCAACCA 59.094 50.000 17.24 0.00 40.87 3.67
368 372 2.323580 ACGACGGTCGAGTCAGGAC 61.324 63.158 34.40 0.00 43.74 3.85
415 419 8.978539 ACTGTTGAAGACTTTTTCTTTTGAAAC 58.021 29.630 0.00 0.00 45.24 2.78
557 565 3.426695 CGTTGGATGTGAAATGAGGCTTC 60.427 47.826 0.00 0.00 0.00 3.86
710 718 3.113979 CCGGCGGGAAACACGTAC 61.114 66.667 20.56 0.00 34.06 3.67
711 719 3.472298 CGGCGGGAAACACGTACG 61.472 66.667 15.01 15.01 0.00 3.67
712 720 2.356194 GGCGGGAAACACGTACGT 60.356 61.111 16.72 16.72 0.00 3.57
713 721 1.080839 GGCGGGAAACACGTACGTA 60.081 57.895 22.34 0.00 0.00 3.57
714 722 1.344226 GGCGGGAAACACGTACGTAC 61.344 60.000 22.34 15.90 0.00 3.67
764 796 2.775351 GGTTGCCGATTCGAATCCA 58.225 52.632 27.91 19.56 31.68 3.41
774 806 2.649331 TTCGAATCCAACTCGACTCC 57.351 50.000 0.00 0.00 44.52 3.85
781 813 0.109689 CCAACTCGACTCCACTCGAC 60.110 60.000 0.00 0.00 37.76 4.20
903 939 4.040217 CCCTTCAATCCATCAAACCAAACA 59.960 41.667 0.00 0.00 0.00 2.83
932 974 1.068816 CAGATCGACACACACGGTACA 60.069 52.381 0.00 0.00 0.00 2.90
1041 1111 4.680237 CTCAAGGCCACCGTCGCA 62.680 66.667 5.01 0.00 0.00 5.10
1155 1225 4.329545 GGAGAAGTGCACGGGCCA 62.330 66.667 7.46 0.00 40.13 5.36
1941 2019 1.561542 GAGGAGATGAGAGGGCCAAAA 59.438 52.381 6.18 0.00 0.00 2.44
1983 2061 2.099141 TGGAAAGAGATGACGGCAAG 57.901 50.000 0.00 0.00 0.00 4.01
2177 4993 6.842163 AGCAAACCATCTGTTATTTACTTCG 58.158 36.000 0.00 0.00 35.67 3.79
2178 4994 5.511729 GCAAACCATCTGTTATTTACTTCGC 59.488 40.000 0.00 0.00 35.67 4.70
2250 5066 3.126001 TGCAAACTTGAAGAGACGGAT 57.874 42.857 0.00 0.00 0.00 4.18
2369 5185 3.483954 CCGTTCTTGGCATCTCCAT 57.516 52.632 0.00 0.00 46.04 3.41
2372 5188 1.402968 CGTTCTTGGCATCTCCATTGG 59.597 52.381 0.00 0.00 46.04 3.16
2383 5199 1.672854 CTCCATTGGCGACGACCCTA 61.673 60.000 0.00 0.00 0.00 3.53
2482 5298 2.805313 ATCCCTGGTCGCCTCTGTCA 62.805 60.000 0.00 0.00 0.00 3.58
2572 5391 1.963338 GCAGTGACGAAGCAGCCTT 60.963 57.895 0.00 0.00 0.00 4.35
2603 5422 2.341911 TGGCGACAACGAGATGCA 59.658 55.556 0.00 0.00 42.66 3.96
2633 5452 4.539083 TCACAGCCACGCCGTTGT 62.539 61.111 0.00 0.00 0.00 3.32
2647 5466 0.320683 CGTTGTGGAGCACTGATCCA 60.321 55.000 12.17 12.17 46.41 3.41
2675 5494 0.038599 TGCTTGTGCATGGGACTCAT 59.961 50.000 0.00 0.00 45.31 2.90
2687 5506 1.315690 GGACTCATCCGTATCCGTGA 58.684 55.000 0.00 0.00 34.48 4.35
2724 5543 0.246635 GAGGTTGGAGAGCAGCGTAA 59.753 55.000 0.00 0.00 0.00 3.18
2753 5572 1.371183 CAAGACCCACGCTCCAGAA 59.629 57.895 0.00 0.00 0.00 3.02
2777 5598 0.108186 TGACGACTCCATCACCATGC 60.108 55.000 0.00 0.00 0.00 4.06
2815 5636 3.134127 GGGCGTCTGCATTGACCC 61.134 66.667 0.86 0.33 45.35 4.46
2816 5637 3.134127 GGCGTCTGCATTGACCCC 61.134 66.667 0.86 0.00 45.35 4.95
2817 5638 3.134127 GCGTCTGCATTGACCCCC 61.134 66.667 0.86 0.00 42.15 5.40
2872 5693 2.125552 CGCGATCAAGGACAGGCA 60.126 61.111 0.00 0.00 0.00 4.75
2877 5698 0.393537 GATCAAGGACAGGCACCAGG 60.394 60.000 0.00 0.00 0.00 4.45
2881 5702 2.358737 GGACAGGCACCAGGAACG 60.359 66.667 0.00 0.00 0.00 3.95
2884 5705 1.003355 ACAGGCACCAGGAACGATG 60.003 57.895 0.00 0.00 0.00 3.84
2885 5706 1.003355 CAGGCACCAGGAACGATGT 60.003 57.895 0.00 0.00 0.00 3.06
2894 5715 2.175811 GAACGATGTGCAACCGCC 59.824 61.111 0.00 0.00 37.32 6.13
2898 5719 1.285641 CGATGTGCAACCGCCTTTT 59.714 52.632 0.00 0.00 37.32 2.27
2904 5725 1.154035 GCAACCGCCTTTTCATCCG 60.154 57.895 0.00 0.00 0.00 4.18
2905 5726 1.154035 CAACCGCCTTTTCATCCGC 60.154 57.895 0.00 0.00 0.00 5.54
2910 5731 3.089784 CCTTTTCATCCGCGTCCG 58.910 61.111 4.92 0.00 0.00 4.79
2911 5732 1.740296 CCTTTTCATCCGCGTCCGT 60.740 57.895 4.92 0.00 0.00 4.69
2914 5735 3.867700 TTTCATCCGCGTCCGTGCA 62.868 57.895 4.92 0.00 34.15 4.57
2920 5741 4.368808 CGCGTCCGTGCAAAGGTG 62.369 66.667 0.00 5.13 36.59 4.00
2963 5784 2.504519 GGCACGGTAGGGTGGATC 59.495 66.667 0.00 0.00 38.36 3.36
2964 5785 2.106332 GCACGGTAGGGTGGATCG 59.894 66.667 0.00 0.00 38.36 3.69
2965 5786 2.812499 CACGGTAGGGTGGATCGG 59.188 66.667 0.00 0.00 34.27 4.18
2966 5787 2.443390 ACGGTAGGGTGGATCGGG 60.443 66.667 0.00 0.00 0.00 5.14
2967 5788 2.123597 CGGTAGGGTGGATCGGGA 60.124 66.667 0.00 0.00 0.00 5.14
2968 5789 2.201022 CGGTAGGGTGGATCGGGAG 61.201 68.421 0.00 0.00 0.00 4.30
2969 5790 1.075450 GGTAGGGTGGATCGGGAGT 60.075 63.158 0.00 0.00 0.00 3.85
2970 5791 1.114119 GGTAGGGTGGATCGGGAGTC 61.114 65.000 0.00 0.00 0.00 3.36
2971 5792 0.106116 GTAGGGTGGATCGGGAGTCT 60.106 60.000 0.00 0.00 0.00 3.24
2972 5793 0.106167 TAGGGTGGATCGGGAGTCTG 60.106 60.000 0.00 0.00 0.00 3.51
2973 5794 2.435693 GGGTGGATCGGGAGTCTGG 61.436 68.421 0.00 0.00 0.00 3.86
2974 5795 1.381327 GGTGGATCGGGAGTCTGGA 60.381 63.158 0.00 0.00 0.00 3.86
2975 5796 1.677637 GGTGGATCGGGAGTCTGGAC 61.678 65.000 0.00 0.00 0.00 4.02
2976 5797 0.970937 GTGGATCGGGAGTCTGGACA 60.971 60.000 3.51 0.00 0.00 4.02
2977 5798 0.970937 TGGATCGGGAGTCTGGACAC 60.971 60.000 3.51 0.00 0.00 3.67
2978 5799 0.684805 GGATCGGGAGTCTGGACACT 60.685 60.000 3.51 0.00 0.00 3.55
2979 5800 0.457851 GATCGGGAGTCTGGACACTG 59.542 60.000 3.51 1.56 0.00 3.66
2980 5801 0.972983 ATCGGGAGTCTGGACACTGG 60.973 60.000 3.51 0.00 0.00 4.00
2981 5802 1.606601 CGGGAGTCTGGACACTGGA 60.607 63.158 3.51 0.00 0.00 3.86
2982 5803 1.878656 CGGGAGTCTGGACACTGGAC 61.879 65.000 3.51 0.00 0.00 4.02
2983 5804 1.587054 GGAGTCTGGACACTGGACG 59.413 63.158 3.51 0.00 35.42 4.79
2984 5805 1.080434 GAGTCTGGACACTGGACGC 60.080 63.158 3.51 0.00 35.42 5.19
2985 5806 2.430921 GTCTGGACACTGGACGCG 60.431 66.667 3.53 3.53 0.00 6.01
2986 5807 4.357947 TCTGGACACTGGACGCGC 62.358 66.667 5.73 0.00 0.00 6.86
3001 5822 4.183686 CGCCGGCATCCAAAGCTG 62.184 66.667 28.98 0.98 38.10 4.24
3002 5823 4.503314 GCCGGCATCCAAAGCTGC 62.503 66.667 24.80 0.00 37.05 5.25
3003 5824 2.753043 CCGGCATCCAAAGCTGCT 60.753 61.111 0.00 0.00 38.45 4.24
3004 5825 2.345760 CCGGCATCCAAAGCTGCTT 61.346 57.895 9.53 9.53 38.45 3.91
3005 5826 1.138247 CGGCATCCAAAGCTGCTTC 59.862 57.895 16.28 1.52 38.45 3.86
3006 5827 1.138247 GGCATCCAAAGCTGCTTCG 59.862 57.895 16.28 3.99 38.45 3.79
3007 5828 1.589716 GGCATCCAAAGCTGCTTCGT 61.590 55.000 16.28 0.00 38.45 3.85
3008 5829 0.242017 GCATCCAAAGCTGCTTCGTT 59.758 50.000 16.28 0.00 35.49 3.85
3009 5830 1.973138 CATCCAAAGCTGCTTCGTTG 58.027 50.000 16.28 10.31 0.00 4.10
3010 5831 0.883833 ATCCAAAGCTGCTTCGTTGG 59.116 50.000 20.51 20.51 43.77 3.77
3011 5832 1.372128 CCAAAGCTGCTTCGTTGGC 60.372 57.895 16.28 0.00 38.40 4.52
3012 5833 1.727022 CAAAGCTGCTTCGTTGGCG 60.727 57.895 16.28 0.00 39.92 5.69
3013 5834 3.542629 AAAGCTGCTTCGTTGGCGC 62.543 57.895 16.28 0.00 38.14 6.53
3016 5837 3.793144 CTGCTTCGTTGGCGCCTC 61.793 66.667 29.70 19.22 38.14 4.70
3017 5838 4.314440 TGCTTCGTTGGCGCCTCT 62.314 61.111 29.70 0.00 38.14 3.69
3018 5839 3.793144 GCTTCGTTGGCGCCTCTG 61.793 66.667 29.70 16.78 38.14 3.35
3019 5840 3.121030 CTTCGTTGGCGCCTCTGG 61.121 66.667 29.70 14.26 38.14 3.86
3029 5850 2.435059 GCCTCTGGCTTGACGGAC 60.435 66.667 0.73 0.00 46.69 4.79
3030 5851 2.948720 GCCTCTGGCTTGACGGACT 61.949 63.158 0.73 0.00 46.69 3.85
3031 5852 1.216710 CCTCTGGCTTGACGGACTC 59.783 63.158 0.00 0.00 0.00 3.36
3032 5853 1.216710 CTCTGGCTTGACGGACTCC 59.783 63.158 0.00 0.00 0.00 3.85
3033 5854 1.533033 TCTGGCTTGACGGACTCCA 60.533 57.895 0.00 0.00 0.00 3.86
3034 5855 1.374758 CTGGCTTGACGGACTCCAC 60.375 63.158 0.00 0.00 0.00 4.02
3035 5856 2.432628 GGCTTGACGGACTCCACG 60.433 66.667 0.00 0.00 37.36 4.94
3037 5858 2.022129 GCTTGACGGACTCCACGTG 61.022 63.158 9.08 9.08 45.68 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.056481 GAATGCCTCGCTGCCATCAC 62.056 60.000 0.00 0.00 0.00 3.06
2 3 1.820906 GAATGCCTCGCTGCCATCA 60.821 57.895 0.00 0.00 0.00 3.07
3 4 1.505477 GAGAATGCCTCGCTGCCATC 61.505 60.000 0.00 0.00 31.32 3.51
4 5 1.525535 GAGAATGCCTCGCTGCCAT 60.526 57.895 0.00 0.00 31.32 4.40
5 6 1.329913 TAGAGAATGCCTCGCTGCCA 61.330 55.000 0.00 0.00 46.49 4.92
6 7 0.878086 GTAGAGAATGCCTCGCTGCC 60.878 60.000 0.00 0.00 46.49 4.85
7 8 1.211818 CGTAGAGAATGCCTCGCTGC 61.212 60.000 0.00 0.00 46.49 5.25
8 9 0.596083 CCGTAGAGAATGCCTCGCTG 60.596 60.000 0.25 0.00 46.49 5.18
9 10 0.752009 TCCGTAGAGAATGCCTCGCT 60.752 55.000 0.00 0.00 46.49 4.93
10 11 0.595310 GTCCGTAGAGAATGCCTCGC 60.595 60.000 0.00 0.00 46.49 5.03
11 12 0.738975 TGTCCGTAGAGAATGCCTCG 59.261 55.000 0.00 0.00 46.49 4.63
12 13 1.751924 ACTGTCCGTAGAGAATGCCTC 59.248 52.381 0.00 0.00 42.28 4.70
13 14 1.478510 CACTGTCCGTAGAGAATGCCT 59.521 52.381 0.00 0.00 0.00 4.75
14 15 1.471676 CCACTGTCCGTAGAGAATGCC 60.472 57.143 0.00 0.00 0.00 4.40
15 16 1.204941 ACCACTGTCCGTAGAGAATGC 59.795 52.381 0.00 0.00 0.00 3.56
16 17 2.881074 CACCACTGTCCGTAGAGAATG 58.119 52.381 0.00 0.00 0.00 2.67
17 18 1.204941 GCACCACTGTCCGTAGAGAAT 59.795 52.381 0.00 0.00 0.00 2.40
18 19 0.601558 GCACCACTGTCCGTAGAGAA 59.398 55.000 0.00 0.00 0.00 2.87
19 20 0.538746 TGCACCACTGTCCGTAGAGA 60.539 55.000 0.00 0.00 0.00 3.10
20 21 0.317160 TTGCACCACTGTCCGTAGAG 59.683 55.000 0.00 0.00 0.00 2.43
21 22 0.032952 GTTGCACCACTGTCCGTAGA 59.967 55.000 0.00 0.00 0.00 2.59
22 23 1.282248 CGTTGCACCACTGTCCGTAG 61.282 60.000 0.00 0.00 0.00 3.51
23 24 1.300311 CGTTGCACCACTGTCCGTA 60.300 57.895 0.00 0.00 0.00 4.02
24 25 2.377628 ATCGTTGCACCACTGTCCGT 62.378 55.000 0.00 0.00 0.00 4.69
25 26 1.626654 GATCGTTGCACCACTGTCCG 61.627 60.000 0.00 0.00 0.00 4.79
26 27 0.320771 AGATCGTTGCACCACTGTCC 60.321 55.000 0.00 0.00 0.00 4.02
27 28 1.071605 GAGATCGTTGCACCACTGTC 58.928 55.000 0.00 0.00 0.00 3.51
28 29 0.681733 AGAGATCGTTGCACCACTGT 59.318 50.000 0.00 0.00 0.00 3.55
29 30 2.654749 TAGAGATCGTTGCACCACTG 57.345 50.000 0.00 0.00 0.00 3.66
30 31 3.525537 CAATAGAGATCGTTGCACCACT 58.474 45.455 0.00 0.00 0.00 4.00
31 32 2.609459 CCAATAGAGATCGTTGCACCAC 59.391 50.000 0.00 0.00 0.00 4.16
32 33 2.905075 CCAATAGAGATCGTTGCACCA 58.095 47.619 0.00 0.00 0.00 4.17
33 34 1.599542 GCCAATAGAGATCGTTGCACC 59.400 52.381 0.00 0.00 0.00 5.01
34 35 2.279741 TGCCAATAGAGATCGTTGCAC 58.720 47.619 0.00 0.00 0.00 4.57
35 36 2.689553 TGCCAATAGAGATCGTTGCA 57.310 45.000 0.00 0.00 0.00 4.08
36 37 3.397482 AGATGCCAATAGAGATCGTTGC 58.603 45.455 0.00 0.00 0.00 4.17
37 38 3.672397 CGAGATGCCAATAGAGATCGTTG 59.328 47.826 0.00 0.00 0.00 4.10
38 39 3.305676 CCGAGATGCCAATAGAGATCGTT 60.306 47.826 0.00 0.00 0.00 3.85
39 40 2.230025 CCGAGATGCCAATAGAGATCGT 59.770 50.000 0.00 0.00 0.00 3.73
40 41 2.230025 ACCGAGATGCCAATAGAGATCG 59.770 50.000 0.00 0.00 0.00 3.69
41 42 3.671971 CGACCGAGATGCCAATAGAGATC 60.672 52.174 0.00 0.00 0.00 2.75
42 43 2.230025 CGACCGAGATGCCAATAGAGAT 59.770 50.000 0.00 0.00 0.00 2.75
43 44 1.609072 CGACCGAGATGCCAATAGAGA 59.391 52.381 0.00 0.00 0.00 3.10
44 45 1.338337 ACGACCGAGATGCCAATAGAG 59.662 52.381 0.00 0.00 0.00 2.43
45 46 1.337071 GACGACCGAGATGCCAATAGA 59.663 52.381 0.00 0.00 0.00 1.98
46 47 1.338337 AGACGACCGAGATGCCAATAG 59.662 52.381 0.00 0.00 0.00 1.73
47 48 1.067060 CAGACGACCGAGATGCCAATA 59.933 52.381 0.00 0.00 0.00 1.90
48 49 0.179100 CAGACGACCGAGATGCCAAT 60.179 55.000 0.00 0.00 0.00 3.16
49 50 1.215382 CAGACGACCGAGATGCCAA 59.785 57.895 0.00 0.00 0.00 4.52
57 58 2.197605 TGTCCTTGCAGACGACCGA 61.198 57.895 7.25 0.00 39.77 4.69
63 64 2.342179 GAGCTAAGTGTCCTTGCAGAC 58.658 52.381 0.00 0.00 37.28 3.51
90 91 2.678336 GGAGTGGTCCGAATTCATGAAC 59.322 50.000 11.07 4.74 31.37 3.18
91 92 2.985896 GGAGTGGTCCGAATTCATGAA 58.014 47.619 11.26 11.26 31.37 2.57
116 117 1.509703 GGTTCTTTCTCCACCACGAC 58.490 55.000 0.00 0.00 0.00 4.34
195 196 3.148279 GAGGAGGACCGGCGTCAT 61.148 66.667 6.01 3.08 41.13 3.06
227 228 1.030457 TTAGAAGAGATCCGCCGTCC 58.970 55.000 0.00 0.00 0.00 4.79
231 232 2.611722 GCCTCATTAGAAGAGATCCGCC 60.612 54.545 0.00 0.00 35.09 6.13
234 235 4.906747 ATGGCCTCATTAGAAGAGATCC 57.093 45.455 3.32 0.00 35.09 3.36
275 276 2.572095 ATCATCGACGCTTTCCGCCA 62.572 55.000 0.00 0.00 41.76 5.69
286 287 1.600663 CCGCCACTAGACATCATCGAC 60.601 57.143 0.00 0.00 0.00 4.20
368 372 2.728318 TGTATAGCTAGCTACGACGTCG 59.272 50.000 34.58 34.58 46.33 5.12
415 419 6.718454 AAGATCTCATCTTCAACAGTTTCG 57.282 37.500 0.00 0.00 46.17 3.46
710 718 5.287035 GGTACAAGGAAAACAGATACGTACG 59.713 44.000 15.01 15.01 0.00 3.67
711 719 5.578336 GGGTACAAGGAAAACAGATACGTAC 59.422 44.000 0.00 0.00 0.00 3.67
712 720 5.622007 CGGGTACAAGGAAAACAGATACGTA 60.622 44.000 0.00 0.00 0.00 3.57
713 721 4.572909 GGGTACAAGGAAAACAGATACGT 58.427 43.478 0.00 0.00 0.00 3.57
714 722 3.615496 CGGGTACAAGGAAAACAGATACG 59.385 47.826 0.00 0.00 0.00 3.06
774 806 2.179517 GACGGAGGCAGTCGAGTG 59.820 66.667 16.15 16.15 0.00 3.51
781 813 4.180946 CGAGACGGACGGAGGCAG 62.181 72.222 0.00 0.00 0.00 4.85
874 910 2.278245 TGATGGATTGAAGGGAGGTGT 58.722 47.619 0.00 0.00 0.00 4.16
903 939 1.276138 TGTGTCGATCTGCTGGATGTT 59.724 47.619 0.00 0.00 34.33 2.71
932 974 1.882352 GCTGTTCGATGGAGGTTGGTT 60.882 52.381 0.00 0.00 0.00 3.67
1041 1111 3.018149 GAGAAGGACGAGTATGACCAGT 58.982 50.000 0.00 0.00 0.00 4.00
1155 1225 2.746671 TCGAAGGCGACGCTCTCT 60.747 61.111 20.77 5.45 42.51 3.10
1350 1426 1.333619 GTTTTCTGGTTGAAGCGCAGA 59.666 47.619 11.47 0.00 35.89 4.26
1941 2019 0.472471 TCTCGGTTGGCCTGACTTTT 59.528 50.000 3.32 0.00 0.00 2.27
1983 2061 0.249911 CCACCGAGCCCAAGTATAGC 60.250 60.000 0.00 0.00 0.00 2.97
2177 4993 6.668323 TCAGCAACTTGTCTAACATTAAAGC 58.332 36.000 0.00 0.00 0.00 3.51
2178 4994 7.752239 CCATCAGCAACTTGTCTAACATTAAAG 59.248 37.037 0.00 0.00 0.00 1.85
2250 5066 3.740397 CCGTCGACACGCCCTACA 61.740 66.667 17.16 0.00 45.29 2.74
2368 5184 1.153706 CGTTAGGGTCGTCGCCAAT 60.154 57.895 7.78 0.00 0.00 3.16
2369 5185 2.259204 CGTTAGGGTCGTCGCCAA 59.741 61.111 7.78 0.00 0.00 4.52
2383 5199 1.741770 GAACTCCATGAGCGCCGTT 60.742 57.895 2.29 0.00 32.04 4.44
2554 5370 1.905922 GAAGGCTGCTTCGTCACTGC 61.906 60.000 0.00 0.00 0.00 4.40
2572 5391 2.470983 TCGCCAAGACATTGTCATGA 57.529 45.000 20.49 7.69 33.78 3.07
2603 5422 3.362399 CTGTGAGCGCCGACAGGAT 62.362 63.158 22.74 0.00 41.02 3.24
2633 5452 2.885135 ATTGTTGGATCAGTGCTCCA 57.115 45.000 11.72 11.72 41.03 3.86
2687 5506 0.030092 TCCCTTGCTACTAGGCCCAT 60.030 55.000 0.00 0.00 0.00 4.00
2753 5572 0.101399 GTGATGGAGTCGTCATCGCT 59.899 55.000 12.89 0.00 44.29 4.93
2758 5579 0.108186 GCATGGTGATGGAGTCGTCA 60.108 55.000 0.00 0.00 36.64 4.35
2853 5674 2.892425 CCTGTCCTTGATCGCGGC 60.892 66.667 6.13 0.00 0.00 6.53
2862 5683 1.456287 GTTCCTGGTGCCTGTCCTT 59.544 57.895 0.00 0.00 0.00 3.36
2872 5693 0.889186 GGTTGCACATCGTTCCTGGT 60.889 55.000 0.00 0.00 0.00 4.00
2877 5698 1.852067 AAGGCGGTTGCACATCGTTC 61.852 55.000 0.00 0.00 45.35 3.95
2881 5702 0.313672 TGAAAAGGCGGTTGCACATC 59.686 50.000 0.00 0.00 45.35 3.06
2884 5705 0.388520 GGATGAAAAGGCGGTTGCAC 60.389 55.000 0.00 0.00 45.35 4.57
2885 5706 1.861542 CGGATGAAAAGGCGGTTGCA 61.862 55.000 0.00 0.00 45.35 4.08
2894 5715 1.419922 CACGGACGCGGATGAAAAG 59.580 57.895 12.47 0.00 0.00 2.27
2898 5719 3.867700 TTTGCACGGACGCGGATGA 62.868 57.895 12.47 0.00 33.35 2.92
2904 5725 4.025401 CCACCTTTGCACGGACGC 62.025 66.667 8.17 0.00 0.00 5.19
2905 5726 4.025401 GCCACCTTTGCACGGACG 62.025 66.667 8.17 0.00 0.00 4.79
2910 5731 3.977244 CCACGGCCACCTTTGCAC 61.977 66.667 2.24 0.00 0.00 4.57
2914 5735 3.223589 GTTGCCACGGCCACCTTT 61.224 61.111 2.24 0.00 41.09 3.11
2953 5774 0.106167 CAGACTCCCGATCCACCCTA 60.106 60.000 0.00 0.00 0.00 3.53
2954 5775 1.381872 CAGACTCCCGATCCACCCT 60.382 63.158 0.00 0.00 0.00 4.34
2955 5776 2.435693 CCAGACTCCCGATCCACCC 61.436 68.421 0.00 0.00 0.00 4.61
2956 5777 1.381327 TCCAGACTCCCGATCCACC 60.381 63.158 0.00 0.00 0.00 4.61
2957 5778 0.970937 TGTCCAGACTCCCGATCCAC 60.971 60.000 0.00 0.00 0.00 4.02
2958 5779 0.970937 GTGTCCAGACTCCCGATCCA 60.971 60.000 0.00 0.00 0.00 3.41
2959 5780 0.684805 AGTGTCCAGACTCCCGATCC 60.685 60.000 0.00 0.00 0.00 3.36
2960 5781 0.457851 CAGTGTCCAGACTCCCGATC 59.542 60.000 0.00 0.00 0.00 3.69
2961 5782 0.972983 CCAGTGTCCAGACTCCCGAT 60.973 60.000 0.00 0.00 0.00 4.18
2962 5783 1.606601 CCAGTGTCCAGACTCCCGA 60.607 63.158 0.00 0.00 0.00 5.14
2963 5784 1.606601 TCCAGTGTCCAGACTCCCG 60.607 63.158 0.00 0.00 0.00 5.14
2964 5785 1.878656 CGTCCAGTGTCCAGACTCCC 61.879 65.000 0.00 0.00 0.00 4.30
2965 5786 1.587054 CGTCCAGTGTCCAGACTCC 59.413 63.158 0.00 0.00 0.00 3.85
2966 5787 1.080434 GCGTCCAGTGTCCAGACTC 60.080 63.158 0.00 0.00 0.00 3.36
2967 5788 2.920645 CGCGTCCAGTGTCCAGACT 61.921 63.158 0.00 0.00 0.00 3.24
2968 5789 2.430921 CGCGTCCAGTGTCCAGAC 60.431 66.667 0.00 0.00 0.00 3.51
2969 5790 4.357947 GCGCGTCCAGTGTCCAGA 62.358 66.667 8.43 0.00 0.00 3.86
2984 5805 4.183686 CAGCTTTGGATGCCGGCG 62.184 66.667 23.90 6.39 0.00 6.46
2990 5811 1.401931 CCAACGAAGCAGCTTTGGATG 60.402 52.381 23.96 20.43 38.94 3.51
2991 5812 0.883833 CCAACGAAGCAGCTTTGGAT 59.116 50.000 23.96 11.39 38.94 3.41
2992 5813 1.795170 GCCAACGAAGCAGCTTTGGA 61.795 55.000 23.44 0.00 38.94 3.53
2993 5814 1.372128 GCCAACGAAGCAGCTTTGG 60.372 57.895 23.96 20.45 39.44 3.28
2994 5815 1.727022 CGCCAACGAAGCAGCTTTG 60.727 57.895 19.55 19.55 43.93 2.77
2995 5816 2.639286 CGCCAACGAAGCAGCTTT 59.361 55.556 9.62 0.00 43.93 3.51
2996 5817 4.030452 GCGCCAACGAAGCAGCTT 62.030 61.111 7.60 7.60 43.93 3.74
2999 5820 3.793144 GAGGCGCCAACGAAGCAG 61.793 66.667 31.54 0.00 43.93 4.24
3000 5821 4.314440 AGAGGCGCCAACGAAGCA 62.314 61.111 31.54 0.00 43.93 3.91
3001 5822 3.793144 CAGAGGCGCCAACGAAGC 61.793 66.667 31.54 8.32 43.93 3.86
3002 5823 3.121030 CCAGAGGCGCCAACGAAG 61.121 66.667 31.54 16.03 43.93 3.79
3013 5834 1.216710 GAGTCCGTCAAGCCAGAGG 59.783 63.158 0.00 0.00 0.00 3.69
3014 5835 1.216710 GGAGTCCGTCAAGCCAGAG 59.783 63.158 0.00 0.00 0.00 3.35
3015 5836 1.533033 TGGAGTCCGTCAAGCCAGA 60.533 57.895 4.30 0.00 0.00 3.86
3016 5837 1.374758 GTGGAGTCCGTCAAGCCAG 60.375 63.158 4.30 0.00 0.00 4.85
3017 5838 2.741092 GTGGAGTCCGTCAAGCCA 59.259 61.111 4.30 0.00 0.00 4.75
3018 5839 2.432628 CGTGGAGTCCGTCAAGCC 60.433 66.667 4.30 0.00 0.00 4.35
3019 5840 2.022129 CACGTGGAGTCCGTCAAGC 61.022 63.158 7.95 0.00 36.17 4.01
3020 5841 4.245054 CACGTGGAGTCCGTCAAG 57.755 61.111 7.95 0.00 36.17 3.02


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

AutoCloner maintained by Alex Coulton.