Multiple sequence alignment - TraesCS7D01G351000

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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 TraesCS7D01G351000 chr7D 100.000 4642 0 0 1 4642 451965701 451970342 0.000000e+00 8573
1 TraesCS7D01G351000 chr7B 94.881 2559 93 20 297 2833 474402255 474404797 0.000000e+00 3965
2 TraesCS7D01G351000 chr7B 89.723 1586 101 35 2841 4402 474405062 474406609 0.000000e+00 1969
3 TraesCS7D01G351000 chr7B 95.341 279 10 3 4366 4642 474406611 474406888 1.530000e-119 440
4 TraesCS7D01G351000 chr7B 84.861 251 22 6 2 250 474400415 474400651 6.000000e-59 239
5 TraesCS7D01G351000 chr7A 87.958 2782 183 63 161 2839 545549480 545546748 0.000000e+00 3142
6 TraesCS7D01G351000 chr7A 88.795 830 47 20 2840 3654 545546373 545545575 0.000000e+00 976
7 TraesCS7D01G351000 chr7A 84.140 372 32 17 3804 4164 545545500 545545145 7.440000e-88 335
8 TraesCS7D01G351000 chr7A 94.149 188 10 1 4180 4367 545545162 545544976 7.600000e-73 285
9 TraesCS7D01G351000 chr7A 80.964 394 43 13 2204 2577 706477344 706477725 2.730000e-72 283
10 TraesCS7D01G351000 chr7A 87.634 186 15 6 2656 2839 706477749 706477928 4.710000e-50 209
11 TraesCS7D01G351000 chr5B 88.172 186 13 7 2655 2839 54112488 54112311 3.640000e-51 213
12 TraesCS7D01G351000 chr4A 87.634 186 15 6 2656 2839 38749000 38749179 4.710000e-50 209


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 TraesCS7D01G351000 chr7D 451965701 451970342 4641 False 8573.00 8573 100.0000 1 4642 1 chr7D.!!$F1 4641
1 TraesCS7D01G351000 chr7B 474400415 474406888 6473 False 1653.25 3965 91.2015 2 4642 4 chr7B.!!$F1 4640
2 TraesCS7D01G351000 chr7A 545544976 545549480 4504 True 1184.50 3142 88.7605 161 4367 4 chr7A.!!$R1 4206
3 TraesCS7D01G351000 chr7A 706477344 706477928 584 False 246.00 283 84.2990 2204 2839 2 chr7A.!!$F1 635

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
81 84 0.034863 TTAATCCCACGGCCTTGGTC 60.035 55.0 25.56 0.00 34.44 4.02 F
721 2307 0.747852 CTCGAGCTTAGGAGGGGTTC 59.252 60.0 0.00 0.00 0.00 3.62 F
1632 3242 0.110486 ATGTGAAGGTCGTTGGGCTT 59.890 50.0 0.00 0.00 0.00 4.35 F
1656 3266 0.591659 GAGACGGTTTTGGCTCAACC 59.408 55.0 8.01 8.01 40.46 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 3194 0.883833 CAGTTTCCTGCATCACACCC 59.116 55.0 0.00 0.0 0.00 4.61 R
2137 3759 0.676466 CATGAGCGCCAACCCAAGTA 60.676 55.0 2.29 0.0 0.00 2.24 R
3245 5314 0.805711 ACTTGTTTGCGGTTTGCTGC 60.806 50.0 0.00 0.0 46.63 5.25 R
3654 5734 0.038618 CTGGGCTTTTACCAAACCGC 60.039 55.0 0.00 0.0 37.59 5.68 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
25 26 8.918202 TCCAAAAGAGACTTTAGAATGCTTTA 57.082 30.769 0.00 0.00 0.00 1.85
81 84 0.034863 TTAATCCCACGGCCTTGGTC 60.035 55.000 25.56 0.00 34.44 4.02
103 106 1.577922 CCACATGCATGCTATCCGC 59.422 57.895 26.53 0.00 39.77 5.54
107 110 1.232119 CATGCATGCTATCCGCTTGA 58.768 50.000 20.33 0.00 44.19 3.02
117 120 7.484140 CATGCTATCCGCTTGATCTTACTATA 58.516 38.462 0.00 0.00 44.19 1.31
118 121 7.646548 TGCTATCCGCTTGATCTTACTATAT 57.353 36.000 0.00 0.00 40.11 0.86
119 122 8.067751 TGCTATCCGCTTGATCTTACTATATT 57.932 34.615 0.00 0.00 40.11 1.28
120 123 8.531982 TGCTATCCGCTTGATCTTACTATATTT 58.468 33.333 0.00 0.00 40.11 1.40
121 124 9.026074 GCTATCCGCTTGATCTTACTATATTTC 57.974 37.037 0.00 0.00 34.76 2.17
122 125 9.522804 CTATCCGCTTGATCTTACTATATTTCC 57.477 37.037 0.00 0.00 34.76 3.13
123 126 6.698380 TCCGCTTGATCTTACTATATTTCCC 58.302 40.000 0.00 0.00 0.00 3.97
124 127 6.269077 TCCGCTTGATCTTACTATATTTCCCA 59.731 38.462 0.00 0.00 0.00 4.37
125 128 6.934645 CCGCTTGATCTTACTATATTTCCCAA 59.065 38.462 0.00 0.00 0.00 4.12
126 129 7.607991 CCGCTTGATCTTACTATATTTCCCAAT 59.392 37.037 0.00 0.00 0.00 3.16
127 130 9.003658 CGCTTGATCTTACTATATTTCCCAATT 57.996 33.333 0.00 0.00 0.00 2.32
179 182 3.289834 CACAGCACCAGCCACCAC 61.290 66.667 0.00 0.00 43.56 4.16
186 189 3.357079 CCAGCCACCACAGCGTTC 61.357 66.667 0.00 0.00 34.64 3.95
201 204 2.159366 AGCGTTCATTACTCGAGGAGTG 60.159 50.000 18.41 15.99 43.30 3.51
203 206 2.422479 CGTTCATTACTCGAGGAGTGGA 59.578 50.000 19.08 8.77 43.30 4.02
260 772 2.266627 ATCCTATCCGTCCGTCCGC 61.267 63.158 0.00 0.00 0.00 5.54
272 803 3.462678 GTCCGCCCTCCAGACTCC 61.463 72.222 0.00 0.00 0.00 3.85
293 1844 2.671682 GAGTCCAGGGGCAGAACC 59.328 66.667 0.00 0.00 37.93 3.62
530 2112 0.976590 AAAGGTAGGTCTCCTCGCCC 60.977 60.000 0.00 0.00 34.61 6.13
533 2115 3.352748 TAGGTCTCCTCGCCCCCA 61.353 66.667 0.00 0.00 34.61 4.96
551 2133 1.671054 ACCGCACTCGTTCATTGGG 60.671 57.895 0.00 0.00 0.00 4.12
644 2226 4.410743 GGCGCTGCTTGGCTGTTC 62.411 66.667 7.64 0.00 0.00 3.18
645 2227 4.410743 GCGCTGCTTGGCTGTTCC 62.411 66.667 0.00 0.00 0.00 3.62
646 2228 4.093952 CGCTGCTTGGCTGTTCCG 62.094 66.667 0.00 0.00 37.80 4.30
721 2307 0.747852 CTCGAGCTTAGGAGGGGTTC 59.252 60.000 0.00 0.00 0.00 3.62
815 2401 2.920912 TTCGCCTTCACCCTCGGT 60.921 61.111 0.00 0.00 35.62 4.69
890 2478 3.242870 GCACTGCGCTTATGCTATTTCTT 60.243 43.478 19.44 0.00 36.40 2.52
1461 3064 1.446366 GTCCTACGAGATTGGGGCC 59.554 63.158 0.00 0.00 0.00 5.80
1511 3114 2.158623 TGAACCATCTGCAGGTGAGTTT 60.159 45.455 28.75 17.08 39.86 2.66
1512 3115 2.191128 ACCATCTGCAGGTGAGTTTC 57.809 50.000 28.75 0.00 38.13 2.78
1513 3116 1.701847 ACCATCTGCAGGTGAGTTTCT 59.298 47.619 28.75 0.00 38.13 2.52
1535 3140 2.774126 GCGGTTTCGAGGCGTAAC 59.226 61.111 0.00 0.00 36.64 2.50
1574 3184 5.719085 TGGTTATTGGGCACTGACATATTTT 59.281 36.000 0.00 0.00 0.00 1.82
1576 3186 6.756542 GGTTATTGGGCACTGACATATTTTTC 59.243 38.462 0.00 0.00 0.00 2.29
1577 3187 7.363793 GGTTATTGGGCACTGACATATTTTTCT 60.364 37.037 0.00 0.00 0.00 2.52
1578 3188 8.682710 GTTATTGGGCACTGACATATTTTTCTA 58.317 33.333 0.00 0.00 0.00 2.10
1582 3192 8.133024 TGGGCACTGACATATTTTTCTATTTT 57.867 30.769 0.00 0.00 0.00 1.82
1584 3194 8.872845 GGGCACTGACATATTTTTCTATTTTTG 58.127 33.333 0.00 0.00 0.00 2.44
1585 3195 8.872845 GGCACTGACATATTTTTCTATTTTTGG 58.127 33.333 0.00 0.00 0.00 3.28
1586 3196 8.872845 GCACTGACATATTTTTCTATTTTTGGG 58.127 33.333 0.00 0.00 0.00 4.12
1587 3197 9.927668 CACTGACATATTTTTCTATTTTTGGGT 57.072 29.630 0.00 0.00 0.00 4.51
1588 3198 9.927668 ACTGACATATTTTTCTATTTTTGGGTG 57.072 29.630 0.00 0.00 0.00 4.61
1632 3242 0.110486 ATGTGAAGGTCGTTGGGCTT 59.890 50.000 0.00 0.00 0.00 4.35
1641 3251 1.135053 GTCGTTGGGCTTCTAGGAGAC 60.135 57.143 0.77 0.00 0.00 3.36
1650 3260 2.347731 CTTCTAGGAGACGGTTTTGGC 58.652 52.381 0.00 0.00 0.00 4.52
1653 3263 1.275291 CTAGGAGACGGTTTTGGCTCA 59.725 52.381 0.00 0.00 0.00 4.26
1656 3266 0.591659 GAGACGGTTTTGGCTCAACC 59.408 55.000 8.01 8.01 40.46 3.77
1760 3370 4.469657 TCACACACTAGCATTTCCCTTTT 58.530 39.130 0.00 0.00 0.00 2.27
1886 3496 7.741027 ATGTGAAAGTGATGCTCCATAATAG 57.259 36.000 0.00 0.00 0.00 1.73
1887 3497 5.528690 TGTGAAAGTGATGCTCCATAATAGC 59.471 40.000 0.00 0.00 40.50 2.97
1996 3611 5.988287 AGAGGCCTTCTTTGAATCTCTTAG 58.012 41.667 6.77 0.00 29.61 2.18
2026 3641 6.851609 TGTGTTACATTTATTGGCAGATGTC 58.148 36.000 9.93 1.43 34.76 3.06
2032 3647 7.656707 ACATTTATTGGCAGATGTCAAAAAC 57.343 32.000 3.68 0.00 43.42 2.43
2083 3700 3.057526 GTCGCCATAAGGAGTTGCTTTTT 60.058 43.478 0.00 0.00 36.89 1.94
2137 3759 2.487265 GGGTGACACTGTTGAGGTGAAT 60.487 50.000 5.39 0.00 38.01 2.57
2402 4044 4.947388 TGGGTTATGATGAACAAGCTTACC 59.053 41.667 0.00 0.00 0.00 2.85
2436 4078 4.408182 AGAATTCCAGATGAAGTACGGG 57.592 45.455 0.65 0.00 36.14 5.28
2471 4113 3.181516 CGTTCTTTTCTGAGTATGCTGCC 60.182 47.826 0.00 0.00 0.00 4.85
2501 4143 2.029380 CCAAGACCACCGAAAATTTCCC 60.029 50.000 0.00 0.00 0.00 3.97
2514 4156 2.683211 ATTTCCCAAACTGCCAGAGT 57.317 45.000 0.00 0.00 35.94 3.24
2595 4237 6.073058 ACACACATACAGTACAAGATTGCAAG 60.073 38.462 4.94 0.00 0.00 4.01
2596 4238 5.997746 ACACATACAGTACAAGATTGCAAGT 59.002 36.000 4.94 0.00 0.00 3.16
2835 4894 9.635520 CAGAAGCTGTTTTGATTTAATCTTCAT 57.364 29.630 6.50 0.00 32.29 2.57
2838 4897 9.635520 AAGCTGTTTTGATTTAATCTTCATCTG 57.364 29.630 6.50 0.33 0.00 2.90
2856 4915 2.051334 TGGCCAAATATCCCAGAACG 57.949 50.000 0.61 0.00 0.00 3.95
3074 5140 7.764443 CGTAAAAGATCTTGACTGGAATCCTTA 59.236 37.037 9.17 0.00 0.00 2.69
3075 5141 9.620259 GTAAAAGATCTTGACTGGAATCCTTAT 57.380 33.333 9.17 0.00 0.00 1.73
3102 5168 5.706833 ACATAACTTGTCTGCATGTCATTCA 59.293 36.000 0.00 0.00 30.89 2.57
3245 5314 9.889128 ACAAAGAATAATCATTTGGTAAATGGG 57.111 29.630 12.72 0.00 46.40 4.00
3247 5316 7.673641 AGAATAATCATTTGGTAAATGGGCA 57.326 32.000 12.72 0.00 46.40 5.36
3257 5326 1.181741 TAAATGGGCAGCAAACCGCA 61.182 50.000 0.00 0.00 46.13 5.69
3271 5340 3.305398 AACCGCAAACAAGTGAAACAA 57.695 38.095 0.00 0.00 41.43 2.83
3281 5350 6.937886 AACAAGTGAAACAAACCTAAAACG 57.062 33.333 0.00 0.00 41.43 3.60
3321 5396 9.499479 AATTGACATTTAATTGGTGCATGTTAA 57.501 25.926 0.00 0.00 30.64 2.01
3322 5397 9.669887 ATTGACATTTAATTGGTGCATGTTAAT 57.330 25.926 0.00 0.00 32.28 1.40
3325 5400 8.940768 ACATTTAATTGGTGCATGTTAATACC 57.059 30.769 0.00 0.00 0.00 2.73
3326 5401 7.704472 ACATTTAATTGGTGCATGTTAATACCG 59.296 33.333 0.00 0.00 35.98 4.02
3333 5409 7.575414 TGGTGCATGTTAATACCGAAATATT 57.425 32.000 0.00 0.00 35.98 1.28
3348 5424 5.340403 CCGAAATATTGATACATTTGCAGCG 59.660 40.000 0.00 0.00 0.00 5.18
3404 5484 2.124570 AGCGCGCCAATCTCCATT 60.125 55.556 30.33 0.79 0.00 3.16
3643 5723 0.530744 GTGGCTCTGTCGTGGTGATA 59.469 55.000 0.00 0.00 0.00 2.15
3654 5734 1.869754 CGTGGTGATATTCGGCAGGAG 60.870 57.143 0.00 0.00 0.00 3.69
3672 5752 0.468400 AGCGGTTTGGTAAAAGCCCA 60.468 50.000 0.00 0.00 40.03 5.36
3700 5782 0.251077 ACCCGGACGTGTTCTCTACT 60.251 55.000 0.73 0.00 0.00 2.57
3757 5844 5.551189 TGGATGTGTATAATCCCATCATGGA 59.449 40.000 4.75 0.00 42.63 3.41
3764 5852 7.120285 GTGTATAATCCCATCATGGAATCACAG 59.880 40.741 4.75 0.00 40.96 3.66
3765 5853 4.531357 AATCCCATCATGGAATCACAGT 57.469 40.909 4.75 0.00 40.96 3.55
3773 5861 4.040047 TCATGGAATCACAGTGGGATACT 58.960 43.478 8.67 0.00 41.36 2.12
3775 5863 2.771943 TGGAATCACAGTGGGATACTCC 59.228 50.000 16.39 16.39 37.60 3.85
3778 5866 4.446371 GAATCACAGTGGGATACTCCAAG 58.554 47.826 8.67 0.00 38.64 3.61
3780 5868 3.248024 TCACAGTGGGATACTCCAAGTT 58.752 45.455 0.00 0.00 38.64 2.66
3781 5869 4.422057 TCACAGTGGGATACTCCAAGTTA 58.578 43.478 0.00 0.00 38.64 2.24
3782 5870 5.030147 TCACAGTGGGATACTCCAAGTTAT 58.970 41.667 0.00 0.00 38.64 1.89
3783 5871 6.199376 TCACAGTGGGATACTCCAAGTTATA 58.801 40.000 0.00 0.00 38.64 0.98
3784 5872 6.844388 TCACAGTGGGATACTCCAAGTTATAT 59.156 38.462 0.00 0.00 38.64 0.86
3785 5873 6.931281 CACAGTGGGATACTCCAAGTTATATG 59.069 42.308 0.00 0.00 38.64 1.78
3786 5874 5.934625 CAGTGGGATACTCCAAGTTATATGC 59.065 44.000 0.00 0.00 38.64 3.14
3787 5875 5.606749 AGTGGGATACTCCAAGTTATATGCA 59.393 40.000 0.00 0.00 38.64 3.96
3788 5876 6.273260 AGTGGGATACTCCAAGTTATATGCAT 59.727 38.462 3.79 3.79 38.64 3.96
3789 5877 7.457852 AGTGGGATACTCCAAGTTATATGCATA 59.542 37.037 9.27 9.27 38.64 3.14
3790 5878 7.549488 GTGGGATACTCCAAGTTATATGCATAC 59.451 40.741 8.99 0.00 38.64 2.39
3791 5879 7.236640 TGGGATACTCCAAGTTATATGCATACA 59.763 37.037 8.99 0.00 38.64 2.29
3792 5880 8.267894 GGGATACTCCAAGTTATATGCATACAT 58.732 37.037 8.99 0.00 38.64 2.29
3842 5930 2.771943 AGAAAGTGTGTGAAGGTGGAGA 59.228 45.455 0.00 0.00 0.00 3.71
3843 5931 3.199946 AGAAAGTGTGTGAAGGTGGAGAA 59.800 43.478 0.00 0.00 0.00 2.87
3848 5936 4.021016 AGTGTGTGAAGGTGGAGAAGATAC 60.021 45.833 0.00 0.00 0.00 2.24
3855 5943 1.202545 GGTGGAGAAGATACGAAGGGC 60.203 57.143 0.00 0.00 0.00 5.19
3863 5951 3.246416 AGATACGAAGGGCATAGGAGT 57.754 47.619 0.00 0.00 0.00 3.85
3881 5969 1.134753 AGTGCGATGAGAAGCAGAGAG 59.865 52.381 0.00 0.00 44.70 3.20
3885 5973 1.747924 CGATGAGAAGCAGAGAGGACA 59.252 52.381 0.00 0.00 0.00 4.02
3929 6018 7.993101 TCGAGTTTGTAGCTATATTACTGTGT 58.007 34.615 9.52 0.00 0.00 3.72
3930 6019 7.913821 TCGAGTTTGTAGCTATATTACTGTGTG 59.086 37.037 9.52 0.78 0.00 3.82
3931 6020 7.913821 CGAGTTTGTAGCTATATTACTGTGTGA 59.086 37.037 9.52 0.00 0.00 3.58
3970 6064 1.375908 CCACACACACCTGGGATCG 60.376 63.158 0.00 0.00 0.00 3.69
3971 6065 1.671166 CACACACACCTGGGATCGA 59.329 57.895 0.00 0.00 0.00 3.59
4028 6126 3.128242 CCTTGAGAGCAGCCTGTTTTATG 59.872 47.826 0.00 0.00 0.00 1.90
4105 6203 2.576615 GCTTCTTCTTGTCCTGGTTGT 58.423 47.619 0.00 0.00 0.00 3.32
4110 6208 3.945285 TCTTCTTGTCCTGGTTGTTTGTC 59.055 43.478 0.00 0.00 0.00 3.18
4146 6244 3.652869 TGAAACTTGAGATCCTGGGTCTT 59.347 43.478 11.53 0.00 0.00 3.01
4163 6261 0.318441 CTTGAGCTGTCCGACCTTGA 59.682 55.000 0.00 0.00 0.00 3.02
4168 6266 2.814336 GAGCTGTCCGACCTTGATTTTT 59.186 45.455 0.00 0.00 0.00 1.94
4221 6319 0.456653 CGCGGCTGCTAAATGCTTTT 60.457 50.000 17.03 2.86 43.37 2.27
4329 6427 2.493278 GGGGTTGACACATCAAATCTGG 59.507 50.000 0.00 0.00 46.40 3.86
4336 6434 4.768448 TGACACATCAAATCTGGAAAGCAT 59.232 37.500 0.00 0.00 0.00 3.79
4370 6468 5.234466 AGAACATGCAGACTCCTAACTTT 57.766 39.130 0.00 0.00 0.00 2.66
4511 6648 5.885449 TTCCTGTGTTTTCCAATTCCAAT 57.115 34.783 0.00 0.00 0.00 3.16
4522 6659 7.928307 TTTCCAATTCCAATGAAACAAACAA 57.072 28.000 0.00 0.00 33.32 2.83
4528 6665 4.681744 TCCAATGAAACAAACAACAGAGC 58.318 39.130 0.00 0.00 0.00 4.09
4533 6670 3.181511 TGAAACAAACAACAGAGCTGACG 60.182 43.478 4.21 0.00 0.00 4.35
4549 6686 3.694566 GCTGACGGAATCCCTATGTTTTT 59.305 43.478 0.00 0.00 0.00 1.94
4551 6688 4.266714 TGACGGAATCCCTATGTTTTTCC 58.733 43.478 0.00 0.00 33.93 3.13
4553 6690 4.270008 ACGGAATCCCTATGTTTTTCCAG 58.730 43.478 0.00 0.00 36.47 3.86
4577 6714 2.475487 GACGTGTGTTTCTGGCTACTTC 59.525 50.000 0.00 0.00 0.00 3.01
4634 6771 4.053295 CAACTTTTTGGCAGTCCATGAAG 58.947 43.478 0.00 0.00 43.05 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.823745 AAAGCATTCTAAAGTCTCTTTTGGA 57.176 32.000 0.15 0.00 0.00 3.53
64 67 2.355115 GACCAAGGCCGTGGGATT 59.645 61.111 36.48 19.78 43.56 3.01
107 110 9.588096 GTGGGAAATTGGGAAATATAGTAAGAT 57.412 33.333 0.00 0.00 0.00 2.40
117 120 3.901222 AGAAACGTGGGAAATTGGGAAAT 59.099 39.130 0.00 0.00 0.00 2.17
118 121 3.301274 AGAAACGTGGGAAATTGGGAAA 58.699 40.909 0.00 0.00 0.00 3.13
119 122 2.888414 GAGAAACGTGGGAAATTGGGAA 59.112 45.455 0.00 0.00 0.00 3.97
120 123 2.107552 AGAGAAACGTGGGAAATTGGGA 59.892 45.455 0.00 0.00 0.00 4.37
121 124 2.488153 GAGAGAAACGTGGGAAATTGGG 59.512 50.000 0.00 0.00 0.00 4.12
122 125 2.488153 GGAGAGAAACGTGGGAAATTGG 59.512 50.000 0.00 0.00 0.00 3.16
123 126 2.488153 GGGAGAGAAACGTGGGAAATTG 59.512 50.000 0.00 0.00 0.00 2.32
124 127 2.791655 GGGAGAGAAACGTGGGAAATT 58.208 47.619 0.00 0.00 0.00 1.82
125 128 1.338769 CGGGAGAGAAACGTGGGAAAT 60.339 52.381 0.00 0.00 0.00 2.17
126 129 0.034337 CGGGAGAGAAACGTGGGAAA 59.966 55.000 0.00 0.00 0.00 3.13
127 130 1.117142 ACGGGAGAGAAACGTGGGAA 61.117 55.000 0.00 0.00 39.64 3.97
128 131 1.532316 ACGGGAGAGAAACGTGGGA 60.532 57.895 0.00 0.00 39.64 4.37
165 168 4.962836 GCTGTGGTGGCTGGTGCT 62.963 66.667 0.00 0.00 39.59 4.40
179 182 2.159366 ACTCCTCGAGTAATGAACGCTG 60.159 50.000 12.31 0.00 41.51 5.18
186 189 2.099921 CCTGTCCACTCCTCGAGTAATG 59.900 54.545 12.31 5.91 41.37 1.90
201 204 3.197766 TGTTGATGTGATCCTACCTGTCC 59.802 47.826 0.00 0.00 0.00 4.02
203 206 4.718774 AGATGTTGATGTGATCCTACCTGT 59.281 41.667 0.00 0.00 0.00 4.00
272 803 3.406200 CTGCCCCTGGACTCCCTG 61.406 72.222 0.00 0.00 0.00 4.45
344 1907 1.125093 TGTCACAGGGGTAGGGTGTG 61.125 60.000 0.00 0.00 42.48 3.82
345 1908 0.836400 CTGTCACAGGGGTAGGGTGT 60.836 60.000 0.00 0.00 0.00 4.16
410 1975 1.135402 GGTTTGTATTCTGGCGGCTTG 60.135 52.381 11.43 3.13 0.00 4.01
481 2061 4.176851 GGAGACGACGACGGAGGC 62.177 72.222 12.58 0.00 44.46 4.70
530 2112 1.671054 AATGAACGAGTGCGGTGGG 60.671 57.895 0.00 0.00 37.73 4.61
533 2115 1.671054 CCCAATGAACGAGTGCGGT 60.671 57.895 0.00 0.00 42.43 5.68
551 2133 2.046217 GACCAAGAACCGCCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
674 2259 1.069978 GAGGGCAGCAGAGATCCTAAC 59.930 57.143 0.00 0.00 0.00 2.34
761 2347 4.556302 GCAACCAGAGCAAAAGAGAAGAAG 60.556 45.833 0.00 0.00 0.00 2.85
806 2392 4.410400 GGGCAGGAACCGAGGGTG 62.410 72.222 0.00 0.00 35.34 4.61
815 2401 2.124736 GCAGCATACGGGCAGGAA 60.125 61.111 0.00 0.00 35.83 3.36
1511 3114 2.736995 CTCGAAACCGCGGCAAGA 60.737 61.111 28.58 18.39 0.00 3.02
1512 3115 3.788766 CCTCGAAACCGCGGCAAG 61.789 66.667 28.58 14.79 0.00 4.01
1535 3140 5.757320 CCAATAACCAGATAGAGCAGTCTTG 59.243 44.000 0.00 0.00 33.84 3.02
1574 3184 4.220382 CCTGCATCACACCCAAAAATAGAA 59.780 41.667 0.00 0.00 0.00 2.10
1576 3186 3.763360 TCCTGCATCACACCCAAAAATAG 59.237 43.478 0.00 0.00 0.00 1.73
1577 3187 3.772387 TCCTGCATCACACCCAAAAATA 58.228 40.909 0.00 0.00 0.00 1.40
1578 3188 2.607499 TCCTGCATCACACCCAAAAAT 58.393 42.857 0.00 0.00 0.00 1.82
1582 3192 1.133513 AGTTTCCTGCATCACACCCAA 60.134 47.619 0.00 0.00 0.00 4.12
1584 3194 0.883833 CAGTTTCCTGCATCACACCC 59.116 55.000 0.00 0.00 0.00 4.61
1632 3242 1.549170 GAGCCAAAACCGTCTCCTAGA 59.451 52.381 0.00 0.00 0.00 2.43
1641 3251 2.914908 CGGGGTTGAGCCAAAACCG 61.915 63.158 13.17 13.17 46.77 4.44
1650 3260 1.776662 TACTCATCTCCGGGGTTGAG 58.223 55.000 32.10 32.10 41.06 3.02
1653 3263 1.206371 CGTTTACTCATCTCCGGGGTT 59.794 52.381 0.00 0.00 0.00 4.11
1656 3266 1.108776 TCCGTTTACTCATCTCCGGG 58.891 55.000 0.00 0.00 36.19 5.73
1886 3496 9.746711 CTAATAATTATGACATAAAGCAGACGC 57.253 33.333 11.80 0.00 38.99 5.19
1996 3611 6.385843 TGCCAATAAATGTAACACATGACAC 58.614 36.000 0.00 0.00 37.97 3.67
2026 3641 9.959775 TTCAGCTAACAAAATTAAACGTTTTTG 57.040 25.926 20.19 18.50 44.50 2.44
2032 3647 8.803799 ACAACTTTCAGCTAACAAAATTAAACG 58.196 29.630 0.00 0.00 0.00 3.60
2137 3759 0.676466 CATGAGCGCCAACCCAAGTA 60.676 55.000 2.29 0.00 0.00 2.24
2402 4044 4.022589 TCTGGAATTCTTGCAAGCTTTCTG 60.023 41.667 26.47 20.88 0.00 3.02
2436 4078 3.831715 AAAGAACGGCACTATTTCAGC 57.168 42.857 0.00 0.00 0.00 4.26
2471 4113 1.806542 CGGTGGTCTTGGTCTTCAATG 59.193 52.381 0.00 0.00 34.45 2.82
2501 4143 2.002586 CGGTCATACTCTGGCAGTTTG 58.997 52.381 15.27 8.69 36.43 2.93
2650 4293 1.788229 TATCAAGATCAGCCCACCGA 58.212 50.000 0.00 0.00 0.00 4.69
2835 4894 2.421388 CGTTCTGGGATATTTGGCCAGA 60.421 50.000 5.11 0.08 36.01 3.86
2838 4897 2.341846 TCGTTCTGGGATATTTGGCC 57.658 50.000 0.00 0.00 0.00 5.36
3074 5140 9.565090 AATGACATGCAGACAAGTTATGTATAT 57.435 29.630 0.00 0.00 44.12 0.86
3075 5141 8.962884 AATGACATGCAGACAAGTTATGTATA 57.037 30.769 0.00 0.00 44.12 1.47
3081 5147 6.656270 AGAATGAATGACATGCAGACAAGTTA 59.344 34.615 1.81 0.00 39.39 2.24
3082 5148 5.475909 AGAATGAATGACATGCAGACAAGTT 59.524 36.000 1.81 0.00 39.39 2.66
3193 5262 4.658063 TGAATTTGTAATCCTCCAACGGT 58.342 39.130 0.00 0.00 0.00 4.83
3241 5310 2.506061 TTTGCGGTTTGCTGCCCAT 61.506 52.632 0.00 0.00 46.11 4.00
3245 5314 0.805711 ACTTGTTTGCGGTTTGCTGC 60.806 50.000 0.00 0.00 46.63 5.25
3247 5316 0.814457 TCACTTGTTTGCGGTTTGCT 59.186 45.000 0.00 0.00 46.63 3.91
3257 5326 6.366604 CCGTTTTAGGTTTGTTTCACTTGTTT 59.633 34.615 0.00 0.00 0.00 2.83
3271 5340 5.585820 TTTCTTTTCTGCCGTTTTAGGTT 57.414 34.783 0.00 0.00 0.00 3.50
3310 5385 7.644490 TCAATATTTCGGTATTAACATGCACC 58.356 34.615 0.00 0.00 0.00 5.01
3321 5396 8.023128 GCTGCAAATGTATCAATATTTCGGTAT 58.977 33.333 0.00 0.00 0.00 2.73
3322 5397 7.359595 GCTGCAAATGTATCAATATTTCGGTA 58.640 34.615 0.00 0.00 0.00 4.02
3323 5398 6.208644 GCTGCAAATGTATCAATATTTCGGT 58.791 36.000 0.00 0.00 0.00 4.69
3325 5400 5.164254 GCGCTGCAAATGTATCAATATTTCG 60.164 40.000 0.00 0.00 0.00 3.46
3326 5401 5.117592 GGCGCTGCAAATGTATCAATATTTC 59.882 40.000 7.64 0.00 0.00 2.17
3333 5409 1.720894 CGGCGCTGCAAATGTATCA 59.279 52.632 7.64 0.00 0.00 2.15
3348 5424 1.032114 AATCAGGGTTAAGCTGCGGC 61.032 55.000 10.33 10.33 39.06 6.53
3376 5456 4.760047 GCGCGCTCTGAAAGGGGA 62.760 66.667 26.67 0.00 38.35 4.81
3382 5462 1.811266 GAGATTGGCGCGCTCTGAA 60.811 57.895 32.29 18.26 0.00 3.02
3620 5700 2.430921 CACGACAGAGCCACCGTC 60.431 66.667 0.00 0.00 32.50 4.79
3643 5723 2.040544 CAAACCGCTCCTGCCGAAT 61.041 57.895 0.00 0.00 35.36 3.34
3654 5734 0.038618 CTGGGCTTTTACCAAACCGC 60.039 55.000 0.00 0.00 37.59 5.68
3686 5768 3.255149 TCCTTTCCAGTAGAGAACACGTC 59.745 47.826 0.00 0.00 0.00 4.34
3690 5772 6.183361 TGTGATTTCCTTTCCAGTAGAGAACA 60.183 38.462 0.00 0.00 0.00 3.18
3700 5782 3.640498 TGCAATGTGTGATTTCCTTTCCA 59.360 39.130 0.00 0.00 0.00 3.53
3810 5898 8.820933 CCTTCACACACTTTCTATGTATGTATG 58.179 37.037 0.00 0.00 0.00 2.39
3820 5908 3.964688 TCTCCACCTTCACACACTTTCTA 59.035 43.478 0.00 0.00 0.00 2.10
3842 5930 3.322254 CACTCCTATGCCCTTCGTATCTT 59.678 47.826 0.00 0.00 0.00 2.40
3843 5931 2.894126 CACTCCTATGCCCTTCGTATCT 59.106 50.000 0.00 0.00 0.00 1.98
3848 5936 1.592669 CGCACTCCTATGCCCTTCG 60.593 63.158 0.00 0.00 42.99 3.79
3855 5943 2.223900 TGCTTCTCATCGCACTCCTATG 60.224 50.000 0.00 0.00 0.00 2.23
3863 5951 0.459078 CCTCTCTGCTTCTCATCGCA 59.541 55.000 0.00 0.00 34.54 5.10
3881 5969 8.024285 TCGATAATTACAACACCAATTTTGTCC 58.976 33.333 0.00 0.00 37.19 4.02
3885 5973 9.974980 AAACTCGATAATTACAACACCAATTTT 57.025 25.926 0.00 0.00 0.00 1.82
3925 6014 3.786368 TTCACTTCCCATCATCACACA 57.214 42.857 0.00 0.00 0.00 3.72
3929 6018 3.657398 AGCATTCACTTCCCATCATCA 57.343 42.857 0.00 0.00 0.00 3.07
3930 6019 4.564940 GAAGCATTCACTTCCCATCATC 57.435 45.455 0.00 0.00 46.62 2.92
3967 6061 1.407936 CCCCAGACAGACAGATCGAT 58.592 55.000 0.00 0.00 0.00 3.59
3970 6064 0.177604 CAGCCCCAGACAGACAGATC 59.822 60.000 0.00 0.00 0.00 2.75
3971 6065 0.546267 ACAGCCCCAGACAGACAGAT 60.546 55.000 0.00 0.00 0.00 2.90
4105 6203 1.092921 AGCACGTTTCGGCAGACAAA 61.093 50.000 0.00 0.00 0.00 2.83
4110 6208 0.657368 GTTTCAGCACGTTTCGGCAG 60.657 55.000 0.00 0.00 0.00 4.85
4146 6244 0.976641 AATCAAGGTCGGACAGCTCA 59.023 50.000 10.76 0.00 30.18 4.26
4329 6427 5.291614 TGTTCTTGCACAGAAAAATGCTTTC 59.708 36.000 11.33 0.00 43.52 2.62
4397 6532 3.010472 TCCTCCATTTTTCATCTGCCTCA 59.990 43.478 0.00 0.00 0.00 3.86
4398 6533 3.624777 TCCTCCATTTTTCATCTGCCTC 58.375 45.455 0.00 0.00 0.00 4.70
4399 6534 3.744940 TCCTCCATTTTTCATCTGCCT 57.255 42.857 0.00 0.00 0.00 4.75
4511 6648 3.181511 CGTCAGCTCTGTTGTTTGTTTCA 60.182 43.478 0.00 0.00 0.00 2.69
4522 6659 0.616111 AGGGATTCCGTCAGCTCTGT 60.616 55.000 0.00 0.00 38.33 3.41
4528 6665 4.335594 GGAAAAACATAGGGATTCCGTCAG 59.664 45.833 0.14 0.00 38.33 3.51
4533 6670 4.098501 CAGCTGGAAAAACATAGGGATTCC 59.901 45.833 5.57 0.00 39.96 3.01
4549 6686 0.464036 AGAAACACACGTCAGCTGGA 59.536 50.000 15.13 0.00 0.00 3.86
4551 6688 0.583438 CCAGAAACACACGTCAGCTG 59.417 55.000 7.63 7.63 0.00 4.24
4553 6690 1.160329 AGCCAGAAACACACGTCAGC 61.160 55.000 0.00 0.00 0.00 4.26
4577 6714 3.927758 CAGTCTCAGAGAAACTGCATCTG 59.072 47.826 0.20 7.77 45.38 2.90


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

AutoCloner maintained by Alex Coulton.