Multiple sequence alignment - TraesCS3D01G315600

Loading Multiple Alignment...

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 TraesCS3D01G315600 chr3D 100.000 2923 0 0 1371 4293 429095150 429098072 0.000000e+00 5398
1 TraesCS3D01G315600 chr3D 100.000 1082 0 0 1 1082 429093780 429094861 0.000000e+00 1999
2 TraesCS3D01G315600 chr3D 90.216 787 58 14 1 776 264140242 264139464 0.000000e+00 1009
3 TraesCS3D01G315600 chr3D 93.878 98 5 1 3728 3824 22679058 22679155 3.460000e-31 147
4 TraesCS3D01G315600 chr3D 93.878 98 5 1 3728 3824 22767900 22767803 3.460000e-31 147
5 TraesCS3D01G315600 chr3D 87.805 123 10 4 3722 3839 12881651 12881773 5.790000e-29 139
6 TraesCS3D01G315600 chr3B 97.168 2366 60 5 1371 3731 561093532 561095895 0.000000e+00 3991
7 TraesCS3D01G315600 chr3B 95.670 485 13 3 3812 4293 561095893 561096372 0.000000e+00 773
8 TraesCS3D01G315600 chr3B 88.055 293 5 5 801 1082 561093253 561093526 1.930000e-83 320
9 TraesCS3D01G315600 chr3A 97.083 2228 59 4 1387 3608 556671113 556668886 0.000000e+00 3749
10 TraesCS3D01G315600 chr3A 96.680 482 15 1 3812 4293 556668685 556668205 0.000000e+00 800
11 TraesCS3D01G315600 chr3A 86.824 296 7 8 801 1082 556671423 556671146 6.980000e-78 302
12 TraesCS3D01G315600 chr3A 95.200 125 5 1 3607 3731 556668806 556668683 3.390000e-46 196
13 TraesCS3D01G315600 chr5B 92.640 788 47 7 1 777 429308042 429308829 0.000000e+00 1123
14 TraesCS3D01G315600 chr5D 92.122 787 51 7 1 776 506942327 506943113 0.000000e+00 1099
15 TraesCS3D01G315600 chr5D 90.506 790 55 14 1 776 503735041 503735824 0.000000e+00 1026
16 TraesCS3D01G315600 chr5D 89.975 788 62 11 1 776 428663666 428664448 0.000000e+00 1002
17 TraesCS3D01G315600 chr5D 90.826 109 5 4 3708 3814 528145979 528145874 1.610000e-29 141
18 TraesCS3D01G315600 chr4D 92.132 788 47 8 1 776 72715331 72716115 0.000000e+00 1098
19 TraesCS3D01G315600 chr4D 95.604 91 3 1 3729 3819 16652517 16652428 1.240000e-30 145
20 TraesCS3D01G315600 chr7D 91.868 787 51 8 1 776 521898894 521898110 0.000000e+00 1086
21 TraesCS3D01G315600 chr7D 88.780 820 70 15 1 801 229765368 229766184 0.000000e+00 985
22 TraesCS3D01G315600 chr6D 89.721 788 65 10 1 776 23078958 23078175 0.000000e+00 992
23 TraesCS3D01G315600 chr7B 94.845 97 4 1 3725 3821 680211517 680211612 2.670000e-32 150
24 TraesCS3D01G315600 chr7A 94.792 96 4 1 3726 3821 692919185 692919279 9.620000e-32 148
25 TraesCS3D01G315600 chr2A 93.814 97 6 0 3728 3824 722077290 722077194 3.460000e-31 147
26 TraesCS3D01G315600 chr2D 91.509 106 6 2 3729 3831 382456025 382455920 4.470000e-30 143


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 TraesCS3D01G315600 chr3D 429093780 429098072 4292 False 3698.500000 5398 100.00000 1 4293 2 chr3D.!!$F3 4292
1 TraesCS3D01G315600 chr3D 264139464 264140242 778 True 1009.000000 1009 90.21600 1 776 1 chr3D.!!$R2 775
2 TraesCS3D01G315600 chr3B 561093253 561096372 3119 False 1694.666667 3991 93.63100 801 4293 3 chr3B.!!$F1 3492
3 TraesCS3D01G315600 chr3A 556668205 556671423 3218 True 1261.750000 3749 93.94675 801 4293 4 chr3A.!!$R1 3492
4 TraesCS3D01G315600 chr5B 429308042 429308829 787 False 1123.000000 1123 92.64000 1 777 1 chr5B.!!$F1 776
5 TraesCS3D01G315600 chr5D 506942327 506943113 786 False 1099.000000 1099 92.12200 1 776 1 chr5D.!!$F3 775
6 TraesCS3D01G315600 chr5D 503735041 503735824 783 False 1026.000000 1026 90.50600 1 776 1 chr5D.!!$F2 775
7 TraesCS3D01G315600 chr5D 428663666 428664448 782 False 1002.000000 1002 89.97500 1 776 1 chr5D.!!$F1 775
8 TraesCS3D01G315600 chr4D 72715331 72716115 784 False 1098.000000 1098 92.13200 1 776 1 chr4D.!!$F1 775
9 TraesCS3D01G315600 chr7D 521898110 521898894 784 True 1086.000000 1086 91.86800 1 776 1 chr7D.!!$R1 775
10 TraesCS3D01G315600 chr7D 229765368 229766184 816 False 985.000000 985 88.78000 1 801 1 chr7D.!!$F1 800
11 TraesCS3D01G315600 chr6D 23078175 23078958 783 True 992.000000 992 89.72100 1 776 1 chr6D.!!$R1 775

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
693 710 0.608130 TATGCGTCTGTGCTTGGACT 59.392 50.000 0.0 0.0 35.36 3.85 F
699 716 1.069765 CTGTGCTTGGACTCACGGT 59.930 57.895 0.0 0.0 35.45 4.83 F
1982 2033 1.369321 GACGATGCCAGGGAGATCC 59.631 63.158 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2033 1.592400 TAGGACGACAGCCGGTTCAG 61.592 60.000 1.9 0.00 43.93 3.02 R
2291 2342 1.963515 GCCCATGTTGTCCAAGAAGTT 59.036 47.619 0.0 0.00 0.00 2.66 R
3390 3445 0.547471 TGAGGCCCATGGAGACTCAA 60.547 55.000 27.3 15.77 35.45 3.02 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
185 188 2.151202 TGTGCTCTTTTTAGCTTCGGG 58.849 47.619 0.00 0.00 43.19 5.14
188 191 3.749609 GTGCTCTTTTTAGCTTCGGGTTA 59.250 43.478 0.00 0.00 43.19 2.85
214 217 5.518487 GCTCTAGATTTGACTAGTTGTGCTC 59.482 44.000 0.00 0.00 40.26 4.26
219 222 6.058183 AGATTTGACTAGTTGTGCTCACTTT 58.942 36.000 0.00 0.00 0.00 2.66
259 262 5.999205 ATGGATGCAAGTTTTGGTATTGA 57.001 34.783 0.00 0.00 0.00 2.57
423 426 6.739008 GCAACCTCTACTTATTTAGGCTCGAT 60.739 42.308 0.00 0.00 31.98 3.59
500 503 2.432146 TGCATCGAGAAGGCACTAATCT 59.568 45.455 0.00 0.00 38.49 2.40
691 708 1.802508 CGATATGCGTCTGTGCTTGGA 60.803 52.381 0.00 0.00 35.36 3.53
693 710 0.608130 TATGCGTCTGTGCTTGGACT 59.392 50.000 0.00 0.00 35.36 3.85
699 716 1.069765 CTGTGCTTGGACTCACGGT 59.930 57.895 0.00 0.00 35.45 4.83
730 748 2.404215 CAGAAACTGTCCGAACACGAT 58.596 47.619 0.00 0.00 0.00 3.73
752 770 3.201266 TCCATTGCCCTACCTAAACGAAT 59.799 43.478 0.00 0.00 0.00 3.34
777 796 2.087009 CGGACAAAGCGGACGTCTC 61.087 63.158 16.46 7.85 0.00 3.36
778 797 2.087009 GGACAAAGCGGACGTCTCG 61.087 63.158 16.46 17.55 0.00 4.04
819 844 1.735559 GTCAACGGGTGAGGTACGC 60.736 63.158 0.00 0.00 36.74 4.42
1065 1104 1.843376 CCACCTCCACCACCACTCT 60.843 63.158 0.00 0.00 0.00 3.24
1067 1106 1.908793 ACCTCCACCACCACTCTCG 60.909 63.158 0.00 0.00 0.00 4.04
1633 1684 1.800315 CTACAACACCCTCGTCGCG 60.800 63.158 0.00 0.00 0.00 5.87
1948 1999 1.739466 GTCATCATCAACGGCATGTGT 59.261 47.619 0.00 0.00 0.00 3.72
1957 2008 2.367202 CGGCATGTGTAGGGAGGGT 61.367 63.158 0.00 0.00 0.00 4.34
1982 2033 1.369321 GACGATGCCAGGGAGATCC 59.631 63.158 0.00 0.00 0.00 3.36
1999 2050 2.432628 CTGAACCGGCTGTCGTCC 60.433 66.667 0.00 0.00 37.11 4.79
2291 2342 2.299013 GGTCGTGTGGATGATGCCTATA 59.701 50.000 0.00 0.00 0.00 1.31
2300 2351 5.471456 GTGGATGATGCCTATAACTTCTTGG 59.529 44.000 0.00 0.00 0.00 3.61
2314 2365 3.245229 ACTTCTTGGACAACATGGGCATA 60.245 43.478 0.00 0.00 0.00 3.14
2493 2544 2.100418 GCCAGAAAGGATTGATTGAGCC 59.900 50.000 0.00 0.00 41.22 4.70
2758 2809 5.416952 CCCTCTAAATGCAGTGACTTTCAAT 59.583 40.000 0.00 0.00 0.00 2.57
2836 2887 3.570975 TGTATCAAATGATGGAGCATGGC 59.429 43.478 6.17 0.00 36.05 4.40
3086 3137 8.319057 TGGGATGTATAACAAGATACTGTTCT 57.681 34.615 0.00 0.00 40.08 3.01
3124 3175 5.748402 TGTGAAACAGATCAGGCTATTGAT 58.252 37.500 0.00 0.00 45.67 2.57
3167 3218 1.429423 GGTTGCATGCCTAACGAGC 59.571 57.895 16.68 0.00 0.00 5.03
3324 3377 6.072286 GCTTCACACTGCATATGCCTTATTAT 60.072 38.462 24.54 1.42 41.18 1.28
3325 3378 7.439157 TTCACACTGCATATGCCTTATTATC 57.561 36.000 24.54 0.00 41.18 1.75
3368 3423 3.746751 GCATATGCCTTGAGTCATGAGGT 60.747 47.826 17.26 0.00 33.03 3.85
3390 3445 7.962441 AGGTTTTGGTGCTTATTAAATTCTGT 58.038 30.769 0.00 0.00 0.00 3.41
3421 3476 1.075374 TGGGCCTCATTTACAGCAAGT 59.925 47.619 4.53 0.00 0.00 3.16
3437 3492 0.893727 AAGTTGGAATCGGGTGGCAC 60.894 55.000 9.70 9.70 0.00 5.01
3444 3499 1.303091 AATCGGGTGGCACGCTTTAC 61.303 55.000 28.62 6.93 39.78 2.01
3464 3519 1.193203 CGTGTGTGCTTCAAGCTACAG 59.807 52.381 17.00 9.81 42.97 2.74
3509 3564 5.221048 GGTGAGCAGTACAAACACAGAAATT 60.221 40.000 0.00 0.00 33.82 1.82
3574 3630 1.741401 CGCGGGATTGCAGACAGAA 60.741 57.895 0.00 0.00 34.15 3.02
3677 3814 7.289084 AGCTACCTTTCAAAAATAAGAACCCAA 59.711 33.333 0.00 0.00 0.00 4.12
3731 3868 6.995511 TCAAATTACCCTGTTAGCATGTAC 57.004 37.500 0.00 0.00 0.00 2.90
3732 3869 6.717289 TCAAATTACCCTGTTAGCATGTACT 58.283 36.000 0.00 0.00 0.00 2.73
3733 3870 6.821665 TCAAATTACCCTGTTAGCATGTACTC 59.178 38.462 0.00 0.00 0.00 2.59
3734 3871 4.748277 TTACCCTGTTAGCATGTACTCC 57.252 45.455 0.00 0.00 0.00 3.85
3735 3872 1.838077 ACCCTGTTAGCATGTACTCCC 59.162 52.381 0.00 0.00 0.00 4.30
3736 3873 2.119495 CCCTGTTAGCATGTACTCCCT 58.881 52.381 0.00 0.00 0.00 4.20
3737 3874 2.103263 CCCTGTTAGCATGTACTCCCTC 59.897 54.545 0.00 0.00 0.00 4.30
3738 3875 3.034635 CCTGTTAGCATGTACTCCCTCT 58.965 50.000 0.00 0.00 0.00 3.69
3739 3876 3.181471 CCTGTTAGCATGTACTCCCTCTG 60.181 52.174 0.00 0.00 0.00 3.35
3740 3877 3.441101 TGTTAGCATGTACTCCCTCTGT 58.559 45.455 0.00 0.00 0.00 3.41
3741 3878 4.606210 TGTTAGCATGTACTCCCTCTGTA 58.394 43.478 0.00 0.00 0.00 2.74
3742 3879 4.645136 TGTTAGCATGTACTCCCTCTGTAG 59.355 45.833 0.00 0.00 0.00 2.74
3743 3880 3.671740 AGCATGTACTCCCTCTGTAGA 57.328 47.619 0.00 0.00 0.00 2.59
3744 3881 3.561143 AGCATGTACTCCCTCTGTAGAG 58.439 50.000 1.86 1.86 41.71 2.43
3745 3882 3.203263 AGCATGTACTCCCTCTGTAGAGA 59.797 47.826 10.40 0.00 44.74 3.10
3746 3883 3.954904 GCATGTACTCCCTCTGTAGAGAA 59.045 47.826 10.40 0.00 44.74 2.87
3747 3884 4.402793 GCATGTACTCCCTCTGTAGAGAAA 59.597 45.833 10.40 0.00 44.74 2.52
3748 3885 5.069781 GCATGTACTCCCTCTGTAGAGAAAT 59.930 44.000 10.40 0.00 44.74 2.17
3749 3886 6.265649 GCATGTACTCCCTCTGTAGAGAAATA 59.734 42.308 10.40 0.00 44.74 1.40
3750 3887 7.039363 GCATGTACTCCCTCTGTAGAGAAATAT 60.039 40.741 10.40 0.00 44.74 1.28
3751 3888 9.521841 CATGTACTCCCTCTGTAGAGAAATATA 57.478 37.037 10.40 0.00 44.74 0.86
3753 3890 9.575868 TGTACTCCCTCTGTAGAGAAATATAAG 57.424 37.037 10.40 0.73 44.74 1.73
3754 3891 9.796180 GTACTCCCTCTGTAGAGAAATATAAGA 57.204 37.037 10.40 0.00 44.74 2.10
3755 3892 8.934023 ACTCCCTCTGTAGAGAAATATAAGAG 57.066 38.462 10.40 5.85 44.74 2.85
3756 3893 7.450323 ACTCCCTCTGTAGAGAAATATAAGAGC 59.550 40.741 10.40 0.00 44.74 4.09
3757 3894 6.431543 TCCCTCTGTAGAGAAATATAAGAGCG 59.568 42.308 10.40 0.00 44.74 5.03
3758 3895 6.207810 CCCTCTGTAGAGAAATATAAGAGCGT 59.792 42.308 10.40 0.00 44.74 5.07
3759 3896 7.255660 CCCTCTGTAGAGAAATATAAGAGCGTT 60.256 40.741 10.40 0.00 44.74 4.84
3760 3897 8.138712 CCTCTGTAGAGAAATATAAGAGCGTTT 58.861 37.037 10.40 0.00 44.74 3.60
3767 3904 9.685828 AGAGAAATATAAGAGCGTTTAGATCAC 57.314 33.333 0.00 0.00 37.82 3.06
3768 3905 9.685828 GAGAAATATAAGAGCGTTTAGATCACT 57.314 33.333 0.00 0.00 37.82 3.41
3775 3912 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
3776 3913 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3808 3945 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
3809 3946 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
3810 3947 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
3811 3948 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3812 3949 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3813 3950 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3814 3951 9.075678 TCTTATATTTCTTTACGGAGGGAGTAG 57.924 37.037 0.00 0.00 0.00 2.57
3815 3952 6.667558 ATATTTCTTTACGGAGGGAGTAGG 57.332 41.667 0.00 0.00 0.00 3.18
4068 4205 8.141268 CAGGCCAATAAAGTTTCTTAGAAACAA 58.859 33.333 31.29 19.97 32.81 2.83
4175 4312 2.086094 TGAGCAATGGTATGTGCACAG 58.914 47.619 25.84 10.59 43.42 3.66
4218 4355 8.244113 GCCTTGTTAACTATGCTTTTCTTGTAT 58.756 33.333 7.22 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 146 3.706600 ACCCCATCGTTTAAGCACTTA 57.293 42.857 0.00 0.00 0.00 2.24
185 188 8.812329 CACAACTAGTCAAATCTAGAGCATAAC 58.188 37.037 0.00 0.00 39.57 1.89
188 191 5.814705 GCACAACTAGTCAAATCTAGAGCAT 59.185 40.000 0.00 0.00 39.57 3.79
411 414 6.644347 TCTTTCTTCTTCATCGAGCCTAAAT 58.356 36.000 0.00 0.00 0.00 1.40
423 426 4.634004 TCTTGCGTGTTTCTTTCTTCTTCA 59.366 37.500 0.00 0.00 0.00 3.02
464 467 6.282930 TCTCGATGCATTCATTGTTGATCTA 58.717 36.000 0.00 0.00 35.89 1.98
500 503 7.676947 ACTTTCATAACTGCTCCTGTAAGTTA 58.323 34.615 0.00 0.00 39.87 2.24
682 698 1.069090 GACCGTGAGTCCAAGCACA 59.931 57.895 0.00 0.00 39.84 4.57
699 716 0.321564 CAGTTTCTGGGATGCGGTGA 60.322 55.000 0.00 0.00 0.00 4.02
730 748 2.189676 TCGTTTAGGTAGGGCAATGGA 58.810 47.619 0.00 0.00 0.00 3.41
781 800 3.901797 GAGGCCAACTCCACCACCG 62.902 68.421 5.01 0.00 40.49 4.94
782 801 2.034221 GAGGCCAACTCCACCACC 59.966 66.667 5.01 0.00 40.49 4.61
784 803 1.768684 GACTGAGGCCAACTCCACCA 61.769 60.000 5.01 0.00 46.01 4.17
819 844 2.550978 ACGATTGGAGCGGTAAATCTG 58.449 47.619 16.17 12.90 0.00 2.90
975 1011 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
976 1012 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
977 1013 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
978 1014 4.596585 GGGTGGTGGTGGTGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
979 1015 4.947147 CGGGTGGTGGTGGTGGTG 62.947 72.222 0.00 0.00 0.00 4.17
1633 1684 2.338984 CCGTAGCGGCAGTATCCC 59.661 66.667 1.45 0.00 41.17 3.85
1927 1978 1.738908 CACATGCCGTTGATGATGACA 59.261 47.619 0.00 0.00 0.00 3.58
1948 1999 4.100084 TCGACGCGACCCTCCCTA 62.100 66.667 15.93 0.00 0.00 3.53
1957 2008 4.829518 CTGGCATCGTCGACGCGA 62.830 66.667 32.19 17.51 45.32 5.87
1982 2033 1.592400 TAGGACGACAGCCGGTTCAG 61.592 60.000 1.90 0.00 43.93 3.02
2291 2342 1.963515 GCCCATGTTGTCCAAGAAGTT 59.036 47.619 0.00 0.00 0.00 2.66
2300 2351 3.507233 CACCCATATATGCCCATGTTGTC 59.493 47.826 7.24 0.00 0.00 3.18
2314 2365 3.657239 TGGTATCAGGATTGCACCCATAT 59.343 43.478 7.04 2.88 31.63 1.78
2758 2809 5.972935 TGACAGAAGAAACTCACAAGTACA 58.027 37.500 0.00 0.00 33.48 2.90
2836 2887 0.911769 TGATCAGGTTAGGGGTGCAG 59.088 55.000 0.00 0.00 0.00 4.41
2872 2923 3.053019 TGCAATCCTTGGTAATCCCATCA 60.053 43.478 0.00 0.00 44.74 3.07
2881 2932 4.041567 TCTTCTGAGTTGCAATCCTTGGTA 59.958 41.667 0.59 0.00 0.00 3.25
3086 3137 5.935945 TGTTTCACATCTTTTACAGAGGGA 58.064 37.500 0.00 0.00 37.65 4.20
3167 3218 6.868864 CCTTCAATGAGTATAATGTAGGTCGG 59.131 42.308 0.00 0.00 0.00 4.79
3300 3351 5.762825 AATAAGGCATATGCAGTGTGAAG 57.237 39.130 28.07 0.00 44.36 3.02
3324 3377 4.449068 GCACATTTCTTTCTCACTCTTCGA 59.551 41.667 0.00 0.00 0.00 3.71
3325 3378 4.212004 TGCACATTTCTTTCTCACTCTTCG 59.788 41.667 0.00 0.00 0.00 3.79
3368 3423 9.474920 CTCAACAGAATTTAATAAGCACCAAAA 57.525 29.630 0.00 0.00 0.00 2.44
3390 3445 0.547471 TGAGGCCCATGGAGACTCAA 60.547 55.000 27.30 15.77 35.45 3.02
3421 3476 2.359354 CGTGCCACCCGATTCCAA 60.359 61.111 0.00 0.00 0.00 3.53
3444 3499 1.193203 CTGTAGCTTGAAGCACACACG 59.807 52.381 20.45 11.83 45.56 4.49
3509 3564 6.443849 ACCTGGAAGAAAGTTACATCCTCATA 59.556 38.462 0.00 0.00 34.07 2.15
3633 3770 6.952358 AGGTAGCTCAAATATATAACGAGGGA 59.048 38.462 0.00 0.00 0.00 4.20
3655 3792 7.189079 TGTTGGGTTCTTATTTTTGAAAGGT 57.811 32.000 0.00 0.00 0.00 3.50
3731 3868 7.361713 CGCTCTTATATTTCTCTACAGAGGGAG 60.362 44.444 6.41 0.00 40.49 4.30
3732 3869 6.431543 CGCTCTTATATTTCTCTACAGAGGGA 59.568 42.308 6.41 0.00 40.49 4.20
3733 3870 6.207810 ACGCTCTTATATTTCTCTACAGAGGG 59.792 42.308 6.41 8.36 42.53 4.30
3734 3871 7.209471 ACGCTCTTATATTTCTCTACAGAGG 57.791 40.000 6.41 0.00 42.30 3.69
3741 3878 9.685828 GTGATCTAAACGCTCTTATATTTCTCT 57.314 33.333 0.00 0.00 0.00 3.10
3742 3879 9.685828 AGTGATCTAAACGCTCTTATATTTCTC 57.314 33.333 0.00 0.00 0.00 2.87
3749 3886 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3750 3887 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
3751 3888 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
3752 3889 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
3782 3919 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
3783 3920 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
3784 3921 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
3785 3922 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
3786 3923 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3787 3924 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3788 3925 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3789 3926 8.305317 CCTACTCCCTCCGTAAAGAAATATAAG 58.695 40.741 0.00 0.00 0.00 1.73
3790 3927 7.786464 ACCTACTCCCTCCGTAAAGAAATATAA 59.214 37.037 0.00 0.00 0.00 0.98
3791 3928 7.300658 ACCTACTCCCTCCGTAAAGAAATATA 58.699 38.462 0.00 0.00 0.00 0.86
3792 3929 6.141790 ACCTACTCCCTCCGTAAAGAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
3793 3930 5.522641 ACCTACTCCCTCCGTAAAGAAATA 58.477 41.667 0.00 0.00 0.00 1.40
3794 3931 4.359996 ACCTACTCCCTCCGTAAAGAAAT 58.640 43.478 0.00 0.00 0.00 2.17
3795 3932 3.782992 ACCTACTCCCTCCGTAAAGAAA 58.217 45.455 0.00 0.00 0.00 2.52
3796 3933 3.463048 ACCTACTCCCTCCGTAAAGAA 57.537 47.619 0.00 0.00 0.00 2.52
3797 3934 3.463048 AACCTACTCCCTCCGTAAAGA 57.537 47.619 0.00 0.00 0.00 2.52
3798 3935 5.866159 ATAAACCTACTCCCTCCGTAAAG 57.134 43.478 0.00 0.00 0.00 1.85
3799 3936 6.625532 AAATAAACCTACTCCCTCCGTAAA 57.374 37.500 0.00 0.00 0.00 2.01
3800 3937 6.625532 AAAATAAACCTACTCCCTCCGTAA 57.374 37.500 0.00 0.00 0.00 3.18
3801 3938 7.125391 TCTAAAATAAACCTACTCCCTCCGTA 58.875 38.462 0.00 0.00 0.00 4.02
3802 3939 5.960202 TCTAAAATAAACCTACTCCCTCCGT 59.040 40.000 0.00 0.00 0.00 4.69
3803 3940 6.475596 TCTAAAATAAACCTACTCCCTCCG 57.524 41.667 0.00 0.00 0.00 4.63
4068 4205 5.238214 GTCTCAAACTGCTGAAACTGAGAAT 59.762 40.000 14.78 0.00 40.55 2.40


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

AutoCloner maintained by Alex Coulton.