Multiple sequence alignment - TraesCS6A01G023900

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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 TraesCS6A01G023900 chr6A 100.000 4237 0 0 1 4237 11887195 11882959 0.000000e+00 7825.0
1 TraesCS6A01G023900 chr6A 93.594 2888 173 6 696 3573 11841888 11839003 0.000000e+00 4298.0
2 TraesCS6A01G023900 chr6A 92.910 2285 133 17 61 2332 11855172 11852904 0.000000e+00 3295.0
3 TraesCS6A01G023900 chr6A 92.097 1240 69 10 2343 3573 11852819 11851600 0.000000e+00 1720.0
4 TraesCS6A01G023900 chr6A 86.861 137 13 4 3704 3839 585418722 585418854 9.490000e-32 148.0
5 TraesCS6A01G023900 chr6A 90.909 55 4 1 2376 2429 11852880 11852826 5.880000e-09 73.1
6 TraesCS6A01G023900 chr6D 95.951 3606 110 11 1 3595 10374102 10370522 0.000000e+00 5818.0
7 TraesCS6A01G023900 chr6D 93.634 3566 164 32 61 3595 10346596 10343063 0.000000e+00 5269.0
8 TraesCS6A01G023900 chr6D 92.916 3049 170 12 696 3704 10337941 10334899 0.000000e+00 4392.0
9 TraesCS6A01G023900 chr6D 93.684 285 18 0 3953 4237 10369785 10369501 1.090000e-115 427.0
10 TraesCS6A01G023900 chr6D 86.111 144 11 4 3704 3838 44255015 44254872 3.410000e-31 147.0
11 TraesCS6A01G023900 chr6D 88.462 104 12 0 3838 3941 10342915 10342812 4.450000e-25 126.0
12 TraesCS6A01G023900 chr6D 98.485 66 1 0 3624 3689 10370466 10370401 2.680000e-22 117.0
13 TraesCS6A01G023900 chr6B 92.091 3401 233 20 198 3573 18945105 18941716 0.000000e+00 4758.0
14 TraesCS6A01G023900 chr6B 92.711 3128 205 12 460 3573 19118849 19121967 0.000000e+00 4492.0
15 TraesCS6A01G023900 chr2D 87.671 146 9 4 3703 3839 482800729 482800584 1.220000e-35 161.0
16 TraesCS6A01G023900 chr1D 86.429 140 10 4 3706 3836 436615974 436615835 1.230000e-30 145.0


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 TraesCS6A01G023900 chr6A 11882959 11887195 4236 True 7825.000000 7825 100.000 1 4237 1 chr6A.!!$R2 4236
1 TraesCS6A01G023900 chr6A 11839003 11841888 2885 True 4298.000000 4298 93.594 696 3573 1 chr6A.!!$R1 2877
2 TraesCS6A01G023900 chr6A 11851600 11855172 3572 True 1696.033333 3295 91.972 61 3573 3 chr6A.!!$R3 3512
3 TraesCS6A01G023900 chr6D 10334899 10337941 3042 True 4392.000000 4392 92.916 696 3704 1 chr6D.!!$R1 3008
4 TraesCS6A01G023900 chr6D 10342812 10346596 3784 True 2697.500000 5269 91.048 61 3941 2 chr6D.!!$R3 3880
5 TraesCS6A01G023900 chr6D 10369501 10374102 4601 True 2120.666667 5818 96.040 1 4237 3 chr6D.!!$R4 4236
6 TraesCS6A01G023900 chr6B 18941716 18945105 3389 True 4758.000000 4758 92.091 198 3573 1 chr6B.!!$R1 3375
7 TraesCS6A01G023900 chr6B 19118849 19121967 3118 False 4492.000000 4492 92.711 460 3573 1 chr6B.!!$F1 3113

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
685 703 0.392998 GGAATGGGTCAGCACGTGAT 60.393 55.0 22.23 11.27 37.56 3.06 F
1284 1305 0.326264 CAACCTCTAGCTTGGGCACT 59.674 55.0 0.00 0.00 41.70 4.40 F
2120 2141 1.656652 CCTCCTGTATTTCCTGCACG 58.343 55.0 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 2754 0.588252 CACCGTTCAAGGTCAGCTTG 59.412 55.000 10.54 10.54 43.89 4.01 R
2680 2779 1.915489 ACATCCAGAGTAACATGGCCA 59.085 47.619 8.56 8.56 36.47 5.36 R
3767 3939 0.106708 AGTTCGAAAGTGCAGAGCCA 59.893 50.000 0.00 0.00 0.00 4.75 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
43 44 3.434940 AATGTACTTCACCCAAGGGAC 57.565 47.619 13.15 0.00 36.26 4.46
65 66 5.783111 ACATCTTGCTTGTTAAAATGGACC 58.217 37.500 0.00 0.00 0.00 4.46
262 269 9.444600 TTTGACTAAGATGATACCTTTTACCAC 57.555 33.333 0.00 0.00 0.00 4.16
273 280 5.007385 ACCTTTTACCACGCACTATAGAG 57.993 43.478 6.78 0.00 0.00 2.43
282 289 5.717178 ACCACGCACTATAGAGATTCCATAT 59.283 40.000 6.78 0.00 0.00 1.78
359 367 8.617809 CAAACGGTTGGCTTACATAGTATATTT 58.382 33.333 4.93 0.00 0.00 1.40
429 443 5.752955 CCAAACCCACACATTTTTACTCAAG 59.247 40.000 0.00 0.00 0.00 3.02
476 490 4.537135 TCGCACTTCCTACTCAGAAAAT 57.463 40.909 0.00 0.00 0.00 1.82
663 681 2.071540 CACGTTCATGTCATGAGCAGT 58.928 47.619 24.13 19.62 40.07 4.40
685 703 0.392998 GGAATGGGTCAGCACGTGAT 60.393 55.000 22.23 11.27 37.56 3.06
694 712 1.071299 AGCACGTGATTGGTGAGCA 59.929 52.632 22.23 0.00 37.60 4.26
699 717 3.780902 CACGTGATTGGTGAGCATAGTA 58.219 45.455 10.90 0.00 37.60 1.82
762 780 4.989044 CGCCATAAAACGGAAGGTAAAAT 58.011 39.130 0.00 0.00 0.00 1.82
865 885 3.140623 GGTAGGTGCCAAAAGTCGTTTA 58.859 45.455 0.00 0.00 0.00 2.01
1042 1063 2.026522 GAGGACGATGACCTCCTCG 58.973 63.158 0.00 0.00 45.64 4.63
1250 1271 2.140792 AGCCCCGTGAACTCACTGT 61.141 57.895 8.16 0.00 44.34 3.55
1258 1279 3.384668 CGTGAACTCACTGTTGTCATCT 58.615 45.455 8.16 0.00 44.34 2.90
1284 1305 0.326264 CAACCTCTAGCTTGGGCACT 59.674 55.000 0.00 0.00 41.70 4.40
1297 1318 4.884164 GCTTGGGCACTTATCAAAGAGTAT 59.116 41.667 0.00 0.00 38.54 2.12
1403 1424 1.817941 ACAACGTGGTGTGTCCTGC 60.818 57.895 0.00 0.00 37.07 4.85
1449 1470 3.727258 CCACGCCCCCAATCTCCA 61.727 66.667 0.00 0.00 0.00 3.86
1499 1520 5.768980 AGAATCATGTCCAAAGAAGAGGA 57.231 39.130 0.00 0.00 0.00 3.71
1680 1701 5.971202 GTCCAACAATAAAATCTATGTGCCG 59.029 40.000 0.00 0.00 0.00 5.69
2056 2077 6.630413 GCATAAGGTGTATGAGAAGGAAGACA 60.630 42.308 0.00 0.00 0.00 3.41
2120 2141 1.656652 CCTCCTGTATTTCCTGCACG 58.343 55.000 0.00 0.00 0.00 5.34
2292 2316 8.979574 GTAGCTTAGATCAATACACCAACATAC 58.020 37.037 0.00 0.00 0.00 2.39
2370 2468 1.990799 TAACGGCTCATCAACAGTCG 58.009 50.000 0.00 0.00 44.71 4.18
2418 2517 7.569485 TGGTGGTAGGTACATAATTATTCCTCA 59.431 37.037 13.56 7.26 0.00 3.86
2504 2603 4.547406 AAACGCTACAGTTGGTTTTCTC 57.453 40.909 0.00 0.00 34.14 2.87
2680 2779 1.210967 TGACCTTGAACGGTGAACCTT 59.789 47.619 0.00 0.00 37.42 3.50
3062 3170 7.514784 TGCTTGGTCAATTATATCATTCTGG 57.485 36.000 0.00 0.00 0.00 3.86
3091 3199 7.815398 TGAATGACACATAACATTTGAATGC 57.185 32.000 3.71 0.00 40.04 3.56
3132 3240 6.183361 TGCCTTGTAAATTTTTCTGGTTCCAT 60.183 34.615 0.00 0.00 0.00 3.41
3135 3243 8.773645 CCTTGTAAATTTTTCTGGTTCCATTTC 58.226 33.333 0.00 0.00 0.00 2.17
3346 3455 3.214328 ACATGTGACAACCTGGAAAGTC 58.786 45.455 0.00 5.87 0.00 3.01
3501 3613 3.220110 TGATAGCCCTAGTCTTGTACCG 58.780 50.000 0.00 0.00 0.00 4.02
3520 3632 3.815401 ACCGTGATTTATGCTTGCTATCC 59.185 43.478 0.00 0.00 0.00 2.59
3533 3645 4.878397 GCTTGCTATCCACTCTGTTGTATT 59.122 41.667 0.00 0.00 0.00 1.89
3540 3652 6.824305 ATCCACTCTGTTGTATTTGGAAAG 57.176 37.500 0.00 0.00 36.73 2.62
3615 3776 2.292267 CATGCTGCCACTTTAGGTAGG 58.708 52.381 0.00 0.00 41.18 3.18
3616 3777 1.358152 TGCTGCCACTTTAGGTAGGT 58.642 50.000 0.00 0.00 41.18 3.08
3617 3778 1.003118 TGCTGCCACTTTAGGTAGGTG 59.997 52.381 0.00 0.00 41.18 4.00
3618 3779 1.003233 GCTGCCACTTTAGGTAGGTGT 59.997 52.381 0.00 0.00 41.18 4.16
3619 3780 2.552373 GCTGCCACTTTAGGTAGGTGTT 60.552 50.000 0.00 0.00 41.18 3.32
3620 3781 3.074412 CTGCCACTTTAGGTAGGTGTTG 58.926 50.000 0.00 0.00 37.69 3.33
3621 3782 2.440253 TGCCACTTTAGGTAGGTGTTGT 59.560 45.455 0.00 0.00 0.00 3.32
3622 3783 3.647113 TGCCACTTTAGGTAGGTGTTGTA 59.353 43.478 0.00 0.00 0.00 2.41
3623 3784 4.287585 TGCCACTTTAGGTAGGTGTTGTAT 59.712 41.667 0.00 0.00 0.00 2.29
3624 3785 5.484644 TGCCACTTTAGGTAGGTGTTGTATA 59.515 40.000 0.00 0.00 0.00 1.47
3625 3786 6.047231 GCCACTTTAGGTAGGTGTTGTATAG 58.953 44.000 0.00 0.00 0.00 1.31
3704 3876 6.039717 ACTGCAATTTGTTGTACATCACTCTT 59.960 34.615 6.12 0.00 0.00 2.85
3706 3878 7.584108 TGCAATTTGTTGTACATCACTCTTAG 58.416 34.615 6.12 0.00 0.00 2.18
3708 3880 6.743575 ATTTGTTGTACATCACTCTTAGGC 57.256 37.500 6.12 0.00 0.00 3.93
3709 3881 3.845178 TGTTGTACATCACTCTTAGGCG 58.155 45.455 2.41 0.00 0.00 5.52
3710 3882 2.579207 TGTACATCACTCTTAGGCGC 57.421 50.000 0.00 0.00 0.00 6.53
3711 3883 2.100197 TGTACATCACTCTTAGGCGCT 58.900 47.619 7.64 0.00 0.00 5.92
3712 3884 2.159240 TGTACATCACTCTTAGGCGCTG 60.159 50.000 7.64 0.00 0.00 5.18
3713 3885 0.898320 ACATCACTCTTAGGCGCTGT 59.102 50.000 7.64 0.00 0.00 4.40
3714 3886 1.276421 ACATCACTCTTAGGCGCTGTT 59.724 47.619 7.64 0.00 0.00 3.16
3715 3887 1.929836 CATCACTCTTAGGCGCTGTTC 59.070 52.381 7.64 0.00 0.00 3.18
3716 3888 0.109272 TCACTCTTAGGCGCTGTTCG 60.109 55.000 7.64 0.00 42.12 3.95
3747 3919 3.976339 CTCCGCGGAGATTGAGAAT 57.024 52.632 45.28 0.00 44.53 2.40
3748 3920 1.777101 CTCCGCGGAGATTGAGAATC 58.223 55.000 45.28 0.00 44.53 2.52
3759 3931 3.892588 AGATTGAGAATCTCGGGAGTACC 59.107 47.826 5.73 0.00 44.79 3.34
3769 3941 2.551644 GGGAGTACCGTTTTGCTGG 58.448 57.895 0.00 0.00 36.97 4.85
3770 3942 1.583495 GGGAGTACCGTTTTGCTGGC 61.583 60.000 0.00 0.00 36.97 4.85
3771 3943 0.605589 GGAGTACCGTTTTGCTGGCT 60.606 55.000 0.00 0.00 0.00 4.75
3772 3944 0.796927 GAGTACCGTTTTGCTGGCTC 59.203 55.000 0.00 0.00 0.00 4.70
3773 3945 0.396811 AGTACCGTTTTGCTGGCTCT 59.603 50.000 0.00 0.00 0.00 4.09
3774 3946 0.517316 GTACCGTTTTGCTGGCTCTG 59.483 55.000 0.00 0.00 0.00 3.35
3775 3947 1.234615 TACCGTTTTGCTGGCTCTGC 61.235 55.000 0.00 0.00 0.00 4.26
3776 3948 2.554636 CCGTTTTGCTGGCTCTGCA 61.555 57.895 3.29 3.29 36.58 4.41
3777 3949 1.370900 CGTTTTGCTGGCTCTGCAC 60.371 57.895 6.31 0.00 37.99 4.57
3778 3950 1.789078 CGTTTTGCTGGCTCTGCACT 61.789 55.000 6.31 0.00 37.99 4.40
3779 3951 0.386838 GTTTTGCTGGCTCTGCACTT 59.613 50.000 6.31 0.00 37.99 3.16
3780 3952 1.113788 TTTTGCTGGCTCTGCACTTT 58.886 45.000 6.31 0.00 37.99 2.66
3781 3953 0.670162 TTTGCTGGCTCTGCACTTTC 59.330 50.000 6.31 0.00 37.99 2.62
3782 3954 1.509644 TTGCTGGCTCTGCACTTTCG 61.510 55.000 6.31 0.00 37.99 3.46
3783 3955 1.669115 GCTGGCTCTGCACTTTCGA 60.669 57.895 0.00 0.00 0.00 3.71
3784 3956 1.230635 GCTGGCTCTGCACTTTCGAA 61.231 55.000 0.00 0.00 0.00 3.71
3785 3957 0.514691 CTGGCTCTGCACTTTCGAAC 59.485 55.000 0.00 0.00 0.00 3.95
3786 3958 0.106708 TGGCTCTGCACTTTCGAACT 59.893 50.000 0.00 0.00 0.00 3.01
3787 3959 1.343142 TGGCTCTGCACTTTCGAACTA 59.657 47.619 0.00 0.00 0.00 2.24
3788 3960 2.224185 TGGCTCTGCACTTTCGAACTAA 60.224 45.455 0.00 0.00 0.00 2.24
3789 3961 2.806244 GGCTCTGCACTTTCGAACTAAA 59.194 45.455 0.00 0.00 0.00 1.85
3790 3962 3.250040 GGCTCTGCACTTTCGAACTAAAA 59.750 43.478 0.00 0.00 0.00 1.52
3791 3963 4.212150 GCTCTGCACTTTCGAACTAAAAC 58.788 43.478 0.00 0.00 0.00 2.43
3792 3964 4.024809 GCTCTGCACTTTCGAACTAAAACT 60.025 41.667 0.00 0.00 0.00 2.66
3793 3965 5.652744 TCTGCACTTTCGAACTAAAACTC 57.347 39.130 0.00 0.00 0.00 3.01
3794 3966 4.208460 TCTGCACTTTCGAACTAAAACTCG 59.792 41.667 0.00 0.00 36.39 4.18
3795 3967 3.246699 TGCACTTTCGAACTAAAACTCGG 59.753 43.478 0.00 0.00 35.76 4.63
3796 3968 3.246936 GCACTTTCGAACTAAAACTCGGT 59.753 43.478 0.00 0.00 35.76 4.69
3797 3969 4.607778 GCACTTTCGAACTAAAACTCGGTC 60.608 45.833 0.00 0.00 35.76 4.79
3798 3970 4.505191 CACTTTCGAACTAAAACTCGGTCA 59.495 41.667 0.00 0.00 35.76 4.02
3799 3971 4.743644 ACTTTCGAACTAAAACTCGGTCAG 59.256 41.667 0.00 0.00 35.76 3.51
3800 3972 2.669364 TCGAACTAAAACTCGGTCAGC 58.331 47.619 0.00 0.00 35.76 4.26
3801 3973 1.385743 CGAACTAAAACTCGGTCAGCG 59.614 52.381 0.00 0.00 0.00 5.18
3802 3974 1.725164 GAACTAAAACTCGGTCAGCGG 59.275 52.381 0.00 0.00 0.00 5.52
3803 3975 0.669625 ACTAAAACTCGGTCAGCGGC 60.670 55.000 0.00 0.00 0.00 6.53
3804 3976 1.359459 CTAAAACTCGGTCAGCGGCC 61.359 60.000 0.00 0.00 0.00 6.13
3805 3977 1.823169 TAAAACTCGGTCAGCGGCCT 61.823 55.000 0.00 0.00 0.00 5.19
3806 3978 3.591254 AAACTCGGTCAGCGGCCTC 62.591 63.158 0.00 0.00 0.00 4.70
3828 4000 3.394836 AGCAGAGGGGCTCCGAAC 61.395 66.667 0.00 0.00 41.05 3.95
3829 4001 3.706373 GCAGAGGGGCTCCGAACA 61.706 66.667 0.00 0.00 38.33 3.18
3830 4002 2.581354 CAGAGGGGCTCCGAACAG 59.419 66.667 0.00 0.00 38.33 3.16
3831 4003 2.685380 AGAGGGGCTCCGAACAGG 60.685 66.667 0.00 0.00 42.97 4.00
3832 4004 4.475135 GAGGGGCTCCGAACAGGC 62.475 72.222 0.00 0.00 40.77 4.85
3836 4008 4.035102 GGCTCCGAACAGGCCCTT 62.035 66.667 0.00 0.00 39.96 3.95
3842 4014 0.392595 CCGAACAGGCCCTTAACCTC 60.393 60.000 0.00 0.00 34.42 3.85
3843 4015 0.613777 CGAACAGGCCCTTAACCTCT 59.386 55.000 0.00 0.00 34.42 3.69
3849 4021 1.219724 AGGCCCTTAACCTCTATCGGA 59.780 52.381 0.00 0.00 28.76 4.55
3911 4083 3.305403 GCCGCAACTGCTATATACTCTCA 60.305 47.826 0.00 0.00 39.32 3.27
3915 4087 5.226396 GCAACTGCTATATACTCTCAGTGG 58.774 45.833 0.00 0.00 37.96 4.00
3932 4104 3.560481 CAGTGGCTAATCTGAAGCTCATG 59.440 47.826 1.74 0.00 39.97 3.07
3935 4107 1.878734 GCTAATCTGAAGCTCATGGCC 59.121 52.381 0.00 0.00 43.05 5.36
3941 4113 1.743958 CTGAAGCTCATGGCCTTCTTG 59.256 52.381 19.80 12.58 43.05 3.02
3942 4114 1.101331 GAAGCTCATGGCCTTCTTGG 58.899 55.000 3.32 0.00 43.05 3.61
3960 4619 0.908198 GGCAGATTCCACTCCACTCT 59.092 55.000 0.00 0.00 0.00 3.24
3961 4620 1.406614 GGCAGATTCCACTCCACTCTG 60.407 57.143 0.00 0.00 37.10 3.35
3973 4632 1.218585 CACTCTGCTCTGCTCCTGG 59.781 63.158 0.00 0.00 0.00 4.45
3989 4648 2.590007 GGCCGCAGCATCAGTAGG 60.590 66.667 0.00 0.00 42.56 3.18
3990 4649 3.275338 GCCGCAGCATCAGTAGGC 61.275 66.667 0.00 0.00 39.53 3.93
4009 4668 3.849951 ATCGCGCCGGGATTCAGT 61.850 61.111 11.18 0.00 31.11 3.41
4027 4686 1.871039 AGTTAAACACTCGCGCAACAT 59.129 42.857 8.75 0.00 0.00 2.71
4052 4711 1.682323 TCTGAACTTTGCTGCATTGCA 59.318 42.857 11.50 11.50 41.65 4.08
4075 4734 4.023193 ACGCTTGCTTATTAGTTGCTTGTT 60.023 37.500 0.00 0.00 0.00 2.83
4083 4742 2.605837 TAGTTGCTTGTTGTCACGGA 57.394 45.000 0.00 0.00 0.00 4.69
4084 4743 1.299541 AGTTGCTTGTTGTCACGGAG 58.700 50.000 0.00 0.00 0.00 4.63
4095 4754 0.529773 GTCACGGAGCAGAACACACA 60.530 55.000 0.00 0.00 0.00 3.72
4113 4772 3.513912 ACACACTCCTGATTTGGTCGATA 59.486 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.029346 AGGTCCATTTTAACAAGCAAGATG 57.971 37.500 0.00 0.00 0.00 2.90
455 469 4.537135 ATTTTCTGAGTAGGAAGTGCGA 57.463 40.909 0.00 0.00 0.00 5.10
634 652 0.110486 ACATGAACGTGCTCCCCTTT 59.890 50.000 0.00 0.00 0.00 3.11
663 681 0.179004 ACGTGCTGACCCATTCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
685 703 2.730382 TCGGTCTACTATGCTCACCAA 58.270 47.619 0.00 0.00 0.00 3.67
694 712 3.181422 TGATCCCCACATCGGTCTACTAT 60.181 47.826 0.00 0.00 0.00 2.12
699 717 2.212327 GTGATCCCCACATCGGTCT 58.788 57.895 0.00 0.00 45.03 3.85
762 780 3.957586 CAGCTGTGGGCCACCTGA 61.958 66.667 32.61 14.50 43.05 3.86
865 885 4.022416 TGCTTACGTTTCAGGCAATTGAAT 60.022 37.500 10.34 0.00 36.97 2.57
1042 1063 1.758514 TGCGGAGGAGGATCTCACC 60.759 63.158 0.00 0.00 35.58 4.02
1250 1271 1.565156 GGTTGCGCGACAGATGACAA 61.565 55.000 28.27 0.00 0.00 3.18
1258 1279 2.126071 GCTAGAGGTTGCGCGACA 60.126 61.111 28.27 4.31 0.00 4.35
1284 1305 5.589855 TGGTACCGACGATACTCTTTGATAA 59.410 40.000 7.57 0.00 0.00 1.75
1403 1424 0.033228 GAGGATGTCCATGCCTCTCG 59.967 60.000 8.59 0.00 43.79 4.04
1449 1470 7.779073 AGTAAGCAGTACCGTCAAATAAGTAT 58.221 34.615 0.00 0.00 32.58 2.12
1499 1520 6.317140 CACATACAAGTAAGACAAGGCATCAT 59.683 38.462 0.00 0.00 0.00 2.45
1680 1701 2.057137 TAATGTTGCTCCATCCAGCC 57.943 50.000 0.00 0.00 38.80 4.85
1782 1803 1.671979 CAACATCATCGGCCTGTGAT 58.328 50.000 12.48 12.48 35.54 3.06
1845 1866 0.998928 TGTACCCATTGTGGAGCCAT 59.001 50.000 0.00 0.00 40.96 4.40
2120 2141 1.282157 ACCTTGTAGGATCACCCTTGC 59.718 52.381 0.00 0.00 44.85 4.01
2292 2316 1.078708 ATTCCGCAACTACACCGGG 60.079 57.895 6.32 0.00 42.18 5.73
2347 2445 3.067106 ACTGTTGATGAGCCGTTAACTG 58.933 45.455 3.71 0.00 0.00 3.16
2354 2452 1.354337 CCACGACTGTTGATGAGCCG 61.354 60.000 1.15 0.00 0.00 5.52
2370 2468 5.296780 CCATTCCATGAATGTACTACACCAC 59.703 44.000 13.94 0.00 45.41 4.16
2418 2517 6.632900 GCTTACTAGTCTTCCTAAAATGGCCT 60.633 42.308 3.32 0.00 0.00 5.19
2504 2603 4.825422 ACAACAGTCATGACCACATAGAG 58.175 43.478 22.21 7.13 35.09 2.43
2655 2754 0.588252 CACCGTTCAAGGTCAGCTTG 59.412 55.000 10.54 10.54 43.89 4.01
2680 2779 1.915489 ACATCCAGAGTAACATGGCCA 59.085 47.619 8.56 8.56 36.47 5.36
2893 3000 2.783135 ACACTTGACATGTAGGGCAAG 58.217 47.619 18.52 18.52 42.46 4.01
3070 3178 6.927416 ACAGCATTCAAATGTTATGTGTCAT 58.073 32.000 4.76 0.00 38.65 3.06
3132 3240 6.544931 CAGGGATGAAGATGATTAAGCAGAAA 59.455 38.462 0.00 0.00 0.00 2.52
3135 3243 5.618236 TCAGGGATGAAGATGATTAAGCAG 58.382 41.667 0.00 0.00 0.00 4.24
3346 3455 9.330063 TCTAGATATTAAAAACAGGTGCTCATG 57.670 33.333 0.00 0.00 0.00 3.07
3501 3613 5.762218 AGAGTGGATAGCAAGCATAAATCAC 59.238 40.000 0.00 0.00 0.00 3.06
3520 3632 6.486657 TCTTCCTTTCCAAATACAACAGAGTG 59.513 38.462 0.00 0.00 0.00 3.51
3533 3645 2.452823 TCCCCCATTTCTTCCTTTCCAA 59.547 45.455 0.00 0.00 0.00 3.53
3540 3652 2.621668 CCAGTCTTCCCCCATTTCTTCC 60.622 54.545 0.00 0.00 0.00 3.46
3615 3776 4.438744 GGTTTGCAGCCATCTATACAACAC 60.439 45.833 4.72 0.00 0.00 3.32
3616 3777 3.694072 GGTTTGCAGCCATCTATACAACA 59.306 43.478 4.72 0.00 0.00 3.33
3617 3778 3.947834 AGGTTTGCAGCCATCTATACAAC 59.052 43.478 11.27 0.00 0.00 3.32
3618 3779 3.947196 CAGGTTTGCAGCCATCTATACAA 59.053 43.478 11.27 0.00 0.00 2.41
3619 3780 3.199727 TCAGGTTTGCAGCCATCTATACA 59.800 43.478 11.27 0.00 0.00 2.29
3620 3781 3.808728 TCAGGTTTGCAGCCATCTATAC 58.191 45.455 11.27 0.00 0.00 1.47
3621 3782 4.712051 ATCAGGTTTGCAGCCATCTATA 57.288 40.909 11.27 0.00 0.00 1.31
3622 3783 3.589951 ATCAGGTTTGCAGCCATCTAT 57.410 42.857 11.27 0.00 0.00 1.98
3623 3784 3.018856 CAATCAGGTTTGCAGCCATCTA 58.981 45.455 11.27 0.00 0.00 1.98
3624 3785 1.822990 CAATCAGGTTTGCAGCCATCT 59.177 47.619 11.27 0.00 0.00 2.90
3625 3786 1.820519 TCAATCAGGTTTGCAGCCATC 59.179 47.619 11.27 0.00 0.00 3.51
3728 3900 2.197819 GATTCTCAATCTCCGCGGAGC 61.198 57.143 43.44 25.53 42.12 4.70
3729 3901 1.339610 AGATTCTCAATCTCCGCGGAG 59.660 52.381 42.89 42.89 44.79 4.63
3730 3902 1.403814 AGATTCTCAATCTCCGCGGA 58.596 50.000 29.03 29.03 44.79 5.54
3731 3903 3.976339 AGATTCTCAATCTCCGCGG 57.024 52.632 22.12 22.12 44.79 6.46
3738 3910 4.245845 GGTACTCCCGAGATTCTCAATC 57.754 50.000 13.88 0.00 38.20 2.67
3751 3923 1.583495 GCCAGCAAAACGGTACTCCC 61.583 60.000 0.00 0.00 0.00 4.30
3752 3924 0.605589 AGCCAGCAAAACGGTACTCC 60.606 55.000 0.00 0.00 0.00 3.85
3753 3925 0.796927 GAGCCAGCAAAACGGTACTC 59.203 55.000 0.00 0.00 0.00 2.59
3754 3926 0.396811 AGAGCCAGCAAAACGGTACT 59.603 50.000 0.00 0.00 0.00 2.73
3755 3927 0.517316 CAGAGCCAGCAAAACGGTAC 59.483 55.000 0.00 0.00 0.00 3.34
3756 3928 1.234615 GCAGAGCCAGCAAAACGGTA 61.235 55.000 0.00 0.00 0.00 4.02
3757 3929 2.555547 GCAGAGCCAGCAAAACGGT 61.556 57.895 0.00 0.00 0.00 4.83
3758 3930 2.256461 GCAGAGCCAGCAAAACGG 59.744 61.111 0.00 0.00 0.00 4.44
3759 3931 1.370900 GTGCAGAGCCAGCAAAACG 60.371 57.895 0.00 0.00 44.64 3.60
3760 3932 0.386838 AAGTGCAGAGCCAGCAAAAC 59.613 50.000 0.00 0.00 44.64 2.43
3761 3933 1.067516 GAAAGTGCAGAGCCAGCAAAA 59.932 47.619 0.00 0.00 44.64 2.44
3762 3934 0.670162 GAAAGTGCAGAGCCAGCAAA 59.330 50.000 0.00 0.00 44.64 3.68
3763 3935 1.509644 CGAAAGTGCAGAGCCAGCAA 61.510 55.000 0.00 0.00 44.64 3.91
3764 3936 1.962822 CGAAAGTGCAGAGCCAGCA 60.963 57.895 0.00 0.00 40.19 4.41
3765 3937 1.230635 TTCGAAAGTGCAGAGCCAGC 61.231 55.000 0.00 0.00 0.00 4.85
3766 3938 0.514691 GTTCGAAAGTGCAGAGCCAG 59.485 55.000 0.00 0.00 0.00 4.85
3767 3939 0.106708 AGTTCGAAAGTGCAGAGCCA 59.893 50.000 0.00 0.00 0.00 4.75
3768 3940 2.080286 TAGTTCGAAAGTGCAGAGCC 57.920 50.000 0.00 0.00 0.00 4.70
3769 3941 4.024809 AGTTTTAGTTCGAAAGTGCAGAGC 60.025 41.667 0.00 0.00 0.00 4.09
3770 3942 5.610552 CGAGTTTTAGTTCGAAAGTGCAGAG 60.611 44.000 0.00 0.00 39.06 3.35
3771 3943 4.208460 CGAGTTTTAGTTCGAAAGTGCAGA 59.792 41.667 0.00 0.00 39.06 4.26
3772 3944 4.446234 CGAGTTTTAGTTCGAAAGTGCAG 58.554 43.478 0.00 0.00 39.06 4.41
3773 3945 3.246699 CCGAGTTTTAGTTCGAAAGTGCA 59.753 43.478 0.00 0.00 39.06 4.57
3774 3946 3.246936 ACCGAGTTTTAGTTCGAAAGTGC 59.753 43.478 0.00 0.00 39.06 4.40
3775 3947 4.505191 TGACCGAGTTTTAGTTCGAAAGTG 59.495 41.667 0.00 0.00 39.06 3.16
3776 3948 4.685924 TGACCGAGTTTTAGTTCGAAAGT 58.314 39.130 0.00 0.00 39.06 2.66
3777 3949 4.376109 GCTGACCGAGTTTTAGTTCGAAAG 60.376 45.833 0.00 0.00 39.06 2.62
3778 3950 3.492011 GCTGACCGAGTTTTAGTTCGAAA 59.508 43.478 0.00 0.00 39.06 3.46
3779 3951 3.054878 GCTGACCGAGTTTTAGTTCGAA 58.945 45.455 0.00 0.00 39.06 3.71
3780 3952 2.669364 GCTGACCGAGTTTTAGTTCGA 58.331 47.619 0.00 0.00 39.06 3.71
3781 3953 1.385743 CGCTGACCGAGTTTTAGTTCG 59.614 52.381 0.00 0.00 40.02 3.95
3782 3954 1.725164 CCGCTGACCGAGTTTTAGTTC 59.275 52.381 0.00 0.00 40.02 3.01
3783 3955 1.792006 CCGCTGACCGAGTTTTAGTT 58.208 50.000 0.00 0.00 40.02 2.24
3784 3956 0.669625 GCCGCTGACCGAGTTTTAGT 60.670 55.000 0.00 0.00 40.02 2.24
3785 3957 1.359459 GGCCGCTGACCGAGTTTTAG 61.359 60.000 0.00 0.00 40.02 1.85
3786 3958 1.375013 GGCCGCTGACCGAGTTTTA 60.375 57.895 0.00 0.00 40.02 1.52
3787 3959 2.668550 GGCCGCTGACCGAGTTTT 60.669 61.111 0.00 0.00 40.02 2.43
3788 3960 3.591254 GAGGCCGCTGACCGAGTTT 62.591 63.158 0.00 0.00 40.02 2.66
3789 3961 4.070552 GAGGCCGCTGACCGAGTT 62.071 66.667 0.00 0.00 40.02 3.01
3811 3983 3.394836 GTTCGGAGCCCCTCTGCT 61.395 66.667 0.00 0.00 46.37 4.24
3812 3984 3.672295 CTGTTCGGAGCCCCTCTGC 62.672 68.421 0.00 0.00 36.85 4.26
3813 3985 2.581354 CTGTTCGGAGCCCCTCTG 59.419 66.667 0.00 0.00 38.15 3.35
3814 3986 2.685380 CCTGTTCGGAGCCCCTCT 60.685 66.667 0.00 0.00 33.16 3.69
3815 3987 4.475135 GCCTGTTCGGAGCCCCTC 62.475 72.222 0.00 0.00 33.16 4.30
3819 3991 2.193087 TTAAGGGCCTGTTCGGAGCC 62.193 60.000 6.92 0.00 46.37 4.70
3820 3992 1.025113 GTTAAGGGCCTGTTCGGAGC 61.025 60.000 6.92 0.00 33.16 4.70
3821 3993 0.392595 GGTTAAGGGCCTGTTCGGAG 60.393 60.000 6.92 0.00 33.16 4.63
3822 3994 0.838987 AGGTTAAGGGCCTGTTCGGA 60.839 55.000 6.92 0.00 34.56 4.55
3823 3995 0.392595 GAGGTTAAGGGCCTGTTCGG 60.393 60.000 6.92 0.00 36.29 4.30
3824 3996 0.613777 AGAGGTTAAGGGCCTGTTCG 59.386 55.000 6.92 0.00 36.29 3.95
3825 3997 3.492829 CGATAGAGGTTAAGGGCCTGTTC 60.493 52.174 6.92 0.00 36.29 3.18
3826 3998 2.434702 CGATAGAGGTTAAGGGCCTGTT 59.565 50.000 6.92 0.00 36.29 3.16
3827 3999 2.040178 CGATAGAGGTTAAGGGCCTGT 58.960 52.381 6.92 0.00 36.29 4.00
3828 4000 1.344763 CCGATAGAGGTTAAGGGCCTG 59.655 57.143 6.92 0.00 36.29 4.85
3829 4001 1.219724 TCCGATAGAGGTTAAGGGCCT 59.780 52.381 0.00 0.00 39.42 5.19
3830 4002 1.713297 TCCGATAGAGGTTAAGGGCC 58.287 55.000 0.00 0.00 39.76 5.80
3831 4003 2.224233 GGTTCCGATAGAGGTTAAGGGC 60.224 54.545 0.00 0.00 39.76 5.19
3832 4004 3.069729 CAGGTTCCGATAGAGGTTAAGGG 59.930 52.174 0.00 0.00 39.76 3.95
3833 4005 3.492829 GCAGGTTCCGATAGAGGTTAAGG 60.493 52.174 0.00 0.00 39.76 2.69
3834 4006 3.385111 AGCAGGTTCCGATAGAGGTTAAG 59.615 47.826 0.00 0.00 39.76 1.85
3835 4007 3.371965 AGCAGGTTCCGATAGAGGTTAA 58.628 45.455 0.00 0.00 39.76 2.01
3836 4008 2.957006 GAGCAGGTTCCGATAGAGGTTA 59.043 50.000 0.00 0.00 39.76 2.85
3842 4014 1.996798 TAGGGAGCAGGTTCCGATAG 58.003 55.000 0.00 0.00 38.17 2.08
3843 4015 2.526432 GATAGGGAGCAGGTTCCGATA 58.474 52.381 0.00 0.00 38.17 2.92
3849 4021 1.840635 GTGAAGGATAGGGAGCAGGTT 59.159 52.381 0.00 0.00 0.00 3.50
3911 4083 3.433314 CCATGAGCTTCAGATTAGCCACT 60.433 47.826 0.00 0.00 39.47 4.00
3915 4087 1.878734 GGCCATGAGCTTCAGATTAGC 59.121 52.381 0.00 0.00 43.05 3.09
3935 4107 2.290514 TGGAGTGGAATCTGCCAAGAAG 60.291 50.000 0.00 0.00 40.20 2.85
3941 4113 0.908198 AGAGTGGAGTGGAATCTGCC 59.092 55.000 0.00 0.00 0.00 4.85
3942 4114 2.021355 CAGAGTGGAGTGGAATCTGC 57.979 55.000 0.00 0.00 31.83 4.26
3943 4115 1.554160 AGCAGAGTGGAGTGGAATCTG 59.446 52.381 0.00 0.00 40.26 2.90
3944 4116 1.830477 GAGCAGAGTGGAGTGGAATCT 59.170 52.381 0.00 0.00 0.00 2.40
3945 4117 1.830477 AGAGCAGAGTGGAGTGGAATC 59.170 52.381 0.00 0.00 0.00 2.52
3946 4118 1.554160 CAGAGCAGAGTGGAGTGGAAT 59.446 52.381 0.00 0.00 0.00 3.01
3947 4119 0.972134 CAGAGCAGAGTGGAGTGGAA 59.028 55.000 0.00 0.00 0.00 3.53
3948 4120 1.539560 GCAGAGCAGAGTGGAGTGGA 61.540 60.000 0.00 0.00 0.00 4.02
3949 4121 1.079266 GCAGAGCAGAGTGGAGTGG 60.079 63.158 0.00 0.00 0.00 4.00
3950 4122 0.108709 GAGCAGAGCAGAGTGGAGTG 60.109 60.000 0.00 0.00 0.00 3.51
3951 4123 1.257055 GGAGCAGAGCAGAGTGGAGT 61.257 60.000 0.00 0.00 0.00 3.85
3973 4632 3.275338 GCCTACTGATGCTGCGGC 61.275 66.667 11.65 11.65 39.26 6.53
3990 4649 4.908687 TGAATCCCGGCGCGATGG 62.909 66.667 12.10 10.71 0.00 3.51
4009 4668 4.671880 ATAATGTTGCGCGAGTGTTTAA 57.328 36.364 12.10 0.00 0.00 1.52
4027 4686 6.127675 TGCAATGCAGCAAAGTTCAGATATAA 60.128 34.615 2.72 0.00 42.46 0.98
4052 4711 3.502211 ACAAGCAACTAATAAGCAAGCGT 59.498 39.130 0.00 0.00 0.00 5.07
4067 4726 0.746204 TGCTCCGTGACAACAAGCAA 60.746 50.000 4.83 0.00 40.11 3.91
4075 4734 0.529773 GTGTGTTCTGCTCCGTGACA 60.530 55.000 0.00 0.00 0.00 3.58
4083 4742 1.123077 TCAGGAGTGTGTGTTCTGCT 58.877 50.000 0.00 0.00 32.85 4.24
4084 4743 2.175878 ATCAGGAGTGTGTGTTCTGC 57.824 50.000 0.00 0.00 0.00 4.26
4095 4754 5.422214 AAAGTATCGACCAAATCAGGAGT 57.578 39.130 0.00 0.00 0.00 3.85
4113 4772 5.766670 TGTTCATTCATCAGCAGAGAAAAGT 59.233 36.000 0.00 0.00 0.00 2.66
4167 4826 0.329261 ATGTATGGTGCTGCTGTGGT 59.671 50.000 0.00 0.00 0.00 4.16
4173 4832 5.541845 TCTTCTATGTATGTATGGTGCTGC 58.458 41.667 0.00 0.00 0.00 5.25
4205 4864 3.722728 CATCATCACACTCTCGATGGA 57.277 47.619 0.00 0.00 39.60 3.41


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

AutoCloner maintained by Alex Coulton.