Multiple sequence alignment - TraesCS3D01G501900

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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 TraesCS3D01G501900 chr3D 100.000 3512 0 0 1 3512 590526827 590523316 0.000000e+00 6486.0
1 TraesCS3D01G501900 chr3D 87.478 1741 148 28 958 2651 590678105 590676388 0.000000e+00 1943.0
2 TraesCS3D01G501900 chr3D 93.898 295 18 0 2124 2418 360589894 360590188 2.490000e-121 446.0
3 TraesCS3D01G501900 chr3D 83.117 77 12 1 2116 2191 7229200 7229276 6.290000e-08 69.4
4 TraesCS3D01G501900 chr3A 90.856 2220 107 38 646 2804 721085521 721087705 0.000000e+00 2887.0
5 TraesCS3D01G501900 chr3A 87.922 1598 143 23 958 2512 721223520 721221930 0.000000e+00 1836.0
6 TraesCS3D01G501900 chr3A 83.226 465 40 13 3068 3512 721087876 721088322 3.290000e-105 392.0
7 TraesCS3D01G501900 chr3A 89.157 249 20 5 3 244 721084838 721085086 1.580000e-78 303.0
8 TraesCS3D01G501900 chr3A 87.764 237 15 5 353 578 721085261 721085494 7.470000e-67 265.0
9 TraesCS3D01G501900 chr3A 91.071 112 9 1 240 350 721085111 721085222 2.180000e-32 150.0
10 TraesCS3D01G501900 chr3A 84.043 94 15 0 3 96 707629897 707629990 1.340000e-14 91.6
11 TraesCS3D01G501900 chr3B 90.622 2186 119 42 642 2772 790520954 790523108 0.000000e+00 2822.0
12 TraesCS3D01G501900 chr3B 88.071 1643 134 31 905 2499 790542822 790541194 0.000000e+00 1892.0
13 TraesCS3D01G501900 chr3B 85.221 521 39 15 3001 3512 790523473 790523964 5.230000e-138 501.0
14 TraesCS3D01G501900 chr3B 98.214 112 2 0 241 352 790520553 790520664 2.770000e-46 196.0
15 TraesCS3D01G501900 chr3B 94.643 112 6 0 241 352 790519303 790519414 1.300000e-39 174.0
16 TraesCS3D01G501900 chr4D 80.769 104 20 0 3 106 427205224 427205327 8.080000e-12 82.4
17 TraesCS3D01G501900 chr6B 84.058 69 11 0 2121 2189 718344381 718344313 2.260000e-07 67.6
18 TraesCS3D01G501900 chr6A 95.238 42 2 0 2121 2162 616832948 616832989 2.260000e-07 67.6


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 TraesCS3D01G501900 chr3D 590523316 590526827 3511 True 6486.00 6486 100.0000 1 3512 1 chr3D.!!$R1 3511
1 TraesCS3D01G501900 chr3D 590676388 590678105 1717 True 1943.00 1943 87.4780 958 2651 1 chr3D.!!$R2 1693
2 TraesCS3D01G501900 chr3A 721221930 721223520 1590 True 1836.00 1836 87.9220 958 2512 1 chr3A.!!$R1 1554
3 TraesCS3D01G501900 chr3A 721084838 721088322 3484 False 799.40 2887 88.4148 3 3512 5 chr3A.!!$F2 3509
4 TraesCS3D01G501900 chr3B 790541194 790542822 1628 True 1892.00 1892 88.0710 905 2499 1 chr3B.!!$R1 1594
5 TraesCS3D01G501900 chr3B 790519303 790523964 4661 False 923.25 2822 92.1750 241 3512 4 chr3B.!!$F1 3271

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
237 245 0.110373 GAACGCGTAAAACCAGCTGG 60.11 55.0 31.6 31.6 42.17 4.85 F
697 1760 0.249868 TGACGCAGAGGAAACTGGTG 60.25 55.0 0.0 0.0 44.43 4.17 F
1414 2525 0.800300 GCTCTCGTTCCTGCTCTTCG 60.80 60.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 2160 0.036875 GGTCACCTTCTTCCCACCAG 59.963 60.0 0.00 0.0 0.00 4.00 R
1952 3105 0.255318 CCTTGGCTTCTCCTGATGCT 59.745 55.0 0.00 0.0 41.41 3.79 R
3117 4477 0.575859 CTTCTGCACGATGATCTGCG 59.424 55.0 10.65 6.3 36.08 5.18 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
26 28 4.332828 AGCCCAATACACTAGAACCAAAC 58.667 43.478 0.00 0.00 0.00 2.93
44 46 8.525290 AACCAAACATGATTCTAGGAATAAGG 57.475 34.615 0.00 0.00 0.00 2.69
45 47 6.547510 ACCAAACATGATTCTAGGAATAAGGC 59.452 38.462 0.00 0.00 0.00 4.35
46 48 6.015940 CCAAACATGATTCTAGGAATAAGGCC 60.016 42.308 0.00 0.00 0.00 5.19
55 57 1.064017 AGGAATAAGGCCCGATTTGCA 60.064 47.619 0.00 0.00 0.00 4.08
62 64 1.368345 GGCCCGATTTGCATTTTGGC 61.368 55.000 0.00 6.30 36.68 4.52
73 75 2.699846 TGCATTTTGGCAGGGATAATCC 59.300 45.455 0.00 0.00 39.25 3.01
96 98 6.045106 TCCCTATAAATCCCTGGAAATACACC 59.955 42.308 0.00 0.00 0.00 4.16
97 99 6.045577 CCCTATAAATCCCTGGAAATACACCT 59.954 42.308 0.00 0.00 0.00 4.00
134 141 2.810274 CAGAAATGTGTGTGTGAGGGAG 59.190 50.000 0.00 0.00 0.00 4.30
139 146 1.040646 GTGTGTGTGAGGGAGAGTCA 58.959 55.000 0.00 0.00 0.00 3.41
141 148 1.412710 TGTGTGTGAGGGAGAGTCAAC 59.587 52.381 0.00 0.00 0.00 3.18
164 172 5.070313 ACTTCCAGCACCAAATTAATGTTGT 59.930 36.000 0.00 0.00 0.00 3.32
208 216 7.657354 CCTCGATCAATTTCCAATCACATACTA 59.343 37.037 0.00 0.00 0.00 1.82
209 217 9.212641 CTCGATCAATTTCCAATCACATACTAT 57.787 33.333 0.00 0.00 0.00 2.12
210 218 9.559732 TCGATCAATTTCCAATCACATACTATT 57.440 29.630 0.00 0.00 0.00 1.73
211 219 9.817365 CGATCAATTTCCAATCACATACTATTC 57.183 33.333 0.00 0.00 0.00 1.75
212 220 9.817365 GATCAATTTCCAATCACATACTATTCG 57.183 33.333 0.00 0.00 0.00 3.34
213 221 8.956533 TCAATTTCCAATCACATACTATTCGA 57.043 30.769 0.00 0.00 0.00 3.71
214 222 9.045223 TCAATTTCCAATCACATACTATTCGAG 57.955 33.333 0.00 0.00 0.00 4.04
215 223 7.969536 ATTTCCAATCACATACTATTCGAGG 57.030 36.000 0.00 0.00 0.00 4.63
218 226 6.749139 TCCAATCACATACTATTCGAGGAAG 58.251 40.000 0.00 0.00 0.00 3.46
221 229 7.169982 CCAATCACATACTATTCGAGGAAGAAC 59.830 40.741 0.00 0.00 32.39 3.01
222 230 5.817988 TCACATACTATTCGAGGAAGAACG 58.182 41.667 0.00 0.00 32.39 3.95
223 231 4.441415 CACATACTATTCGAGGAAGAACGC 59.559 45.833 0.00 0.00 32.39 4.84
226 234 2.679837 ACTATTCGAGGAAGAACGCGTA 59.320 45.455 14.46 0.00 32.39 4.42
228 236 2.420628 TTCGAGGAAGAACGCGTAAA 57.579 45.000 14.46 0.00 0.00 2.01
229 237 2.420628 TCGAGGAAGAACGCGTAAAA 57.579 45.000 14.46 0.00 0.00 1.52
230 238 2.053627 TCGAGGAAGAACGCGTAAAAC 58.946 47.619 14.46 4.94 0.00 2.43
231 239 1.125566 CGAGGAAGAACGCGTAAAACC 59.874 52.381 14.46 14.51 0.00 3.27
232 240 2.137523 GAGGAAGAACGCGTAAAACCA 58.862 47.619 14.46 0.00 0.00 3.67
233 241 2.140717 AGGAAGAACGCGTAAAACCAG 58.859 47.619 14.46 0.00 0.00 4.00
234 242 1.399343 GGAAGAACGCGTAAAACCAGC 60.399 52.381 14.46 0.00 0.00 4.85
235 243 1.529865 GAAGAACGCGTAAAACCAGCT 59.470 47.619 14.46 0.00 0.00 4.24
237 245 0.110373 GAACGCGTAAAACCAGCTGG 60.110 55.000 31.60 31.60 42.17 4.85
364 1412 2.618241 GCATGGACAGTTCACACTCAAA 59.382 45.455 0.00 0.00 0.00 2.69
407 1462 4.125703 CTCCATAGTTAGCAAGCTTCCAG 58.874 47.826 0.00 0.00 0.00 3.86
436 1491 8.441311 TCCTCTATACTACTCCGTATCCTTTA 57.559 38.462 0.00 0.00 32.63 1.85
517 1576 4.344102 TGCCATTGTATCCTAGTGGTAGTC 59.656 45.833 0.00 0.00 32.56 2.59
627 1690 2.148916 ATACACACACACACACGAGG 57.851 50.000 0.00 0.00 0.00 4.63
628 1691 0.818938 TACACACACACACACGAGGT 59.181 50.000 0.00 0.00 0.00 3.85
663 1726 1.444895 GTGTGGTACGTGTAGGCGG 60.445 63.158 0.00 0.00 35.98 6.13
674 1737 4.715130 TAGGCGGCTGGGTGGAGT 62.715 66.667 23.55 0.00 0.00 3.85
697 1760 0.249868 TGACGCAGAGGAAACTGGTG 60.250 55.000 0.00 0.00 44.43 4.17
718 1781 4.442375 GTCTGAAGACGAGATGGAAGAA 57.558 45.455 0.00 0.00 35.12 2.52
719 1782 4.420168 GTCTGAAGACGAGATGGAAGAAG 58.580 47.826 0.00 0.00 35.12 2.85
720 1783 4.156922 GTCTGAAGACGAGATGGAAGAAGA 59.843 45.833 0.00 0.00 35.12 2.87
765 1828 1.539124 AGGCCGGGGACTTCTTCTT 60.539 57.895 2.18 0.00 0.00 2.52
773 1836 1.619332 GGGACTTCTTCTTCGGACTGT 59.381 52.381 0.00 0.00 0.00 3.55
778 1841 2.814280 TCTTCTTCGGACTGTGGAAC 57.186 50.000 0.00 0.00 37.35 3.62
903 1966 4.436998 CGTCTCTCGCCGGCCTTT 62.437 66.667 23.46 0.00 0.00 3.11
1096 2177 1.761174 GCTGGTGGGAAGAAGGTGA 59.239 57.895 0.00 0.00 0.00 4.02
1149 2230 2.733593 GTGCTCACCGTCGTCACC 60.734 66.667 0.00 0.00 0.00 4.02
1171 2252 4.124351 CGCTCGTCTACGCCCCAA 62.124 66.667 0.00 0.00 39.60 4.12
1258 2342 1.448013 GCAGTACAAGGACGGAGCC 60.448 63.158 0.00 0.00 0.00 4.70
1414 2525 0.800300 GCTCTCGTTCCTGCTCTTCG 60.800 60.000 0.00 0.00 0.00 3.79
1941 3067 2.879462 GGCGCGTACAAGGACGAG 60.879 66.667 9.36 6.61 45.82 4.18
1958 3111 4.819761 GAGCACGCCGGAGCATCA 62.820 66.667 5.05 0.00 39.83 3.07
1959 3112 4.827087 AGCACGCCGGAGCATCAG 62.827 66.667 5.05 0.00 39.83 2.90
2175 3349 2.507324 GCGGACCTGACGAAGCTC 60.507 66.667 0.00 0.00 0.00 4.09
2289 3463 3.493176 CCATGATGGAGATGCACTACGAA 60.493 47.826 5.27 0.00 40.96 3.85
2464 3638 4.754667 GGTTCGGCGACACCCTCC 62.755 72.222 22.41 10.75 33.26 4.30
2526 3703 1.746991 GTAGCTGGCTGGCTGGTTC 60.747 63.158 17.04 9.28 43.01 3.62
2548 3725 1.720694 TATGTGCGTCGCCGATCAGA 61.721 55.000 15.88 3.59 35.63 3.27
2568 3745 2.434884 CCGACGAGCTGGTGCATT 60.435 61.111 5.94 0.00 42.74 3.56
2574 3751 2.283298 ACGAGCTGGTGCATTCTAATG 58.717 47.619 0.00 0.00 42.74 1.90
2675 3853 0.861837 CTTGTTCGACAGCACAGACC 59.138 55.000 0.00 0.00 0.00 3.85
2692 3870 4.021544 ACAGACCACACAATGTGTTTTGTT 60.022 37.500 17.31 0.00 45.08 2.83
2715 3893 8.958043 TGTTTATTTGTTTTGTTTTGTTTGTGC 58.042 25.926 0.00 0.00 0.00 4.57
2720 3898 5.879237 TGTTTTGTTTTGTTTGTGCACAAA 58.121 29.167 35.10 35.10 43.42 2.83
2725 3903 4.999751 TTTTGTTTGTGCACAAAAGACC 57.000 36.364 38.81 28.10 46.77 3.85
2728 3906 4.991153 TGTTTGTGCACAAAAGACCATA 57.009 36.364 38.81 18.00 46.08 2.74
2729 3907 5.528043 TGTTTGTGCACAAAAGACCATAT 57.472 34.783 38.81 0.00 46.08 1.78
2732 3910 8.341892 TGTTTGTGCACAAAAGACCATATATA 57.658 30.769 38.81 15.90 46.08 0.86
2733 3911 8.797438 TGTTTGTGCACAAAAGACCATATATAA 58.203 29.630 38.81 15.48 46.08 0.98
2734 3912 9.801873 GTTTGTGCACAAAAGACCATATATAAT 57.198 29.630 38.81 0.00 46.08 1.28
2748 3927 8.749026 ACCATATATAATCCGTCGAATACTCT 57.251 34.615 0.00 0.00 0.00 3.24
2754 3933 3.965292 TCCGTCGAATACTCTGATGAC 57.035 47.619 0.00 0.00 0.00 3.06
2757 3936 4.038361 CCGTCGAATACTCTGATGACAAG 58.962 47.826 0.00 0.00 0.00 3.16
2760 3939 5.447954 CGTCGAATACTCTGATGACAAGACT 60.448 44.000 0.00 0.00 0.00 3.24
2821 4172 7.609097 AATATAGACAGTCTGGTGATGACAT 57.391 36.000 13.84 0.00 36.94 3.06
2824 4175 4.089361 AGACAGTCTGGTGATGACATACA 58.911 43.478 0.91 0.00 36.94 2.29
2925 4276 2.203252 CAGGCACCAGCGGCATAT 60.203 61.111 1.45 0.00 43.41 1.78
2926 4277 1.071299 CAGGCACCAGCGGCATATA 59.929 57.895 1.45 0.00 43.41 0.86
2927 4278 1.071471 AGGCACCAGCGGCATATAC 59.929 57.895 1.45 0.00 43.41 1.47
2928 4279 1.071471 GGCACCAGCGGCATATACT 59.929 57.895 1.45 0.00 43.41 2.12
2932 4283 2.612972 GCACCAGCGGCATATACTACAT 60.613 50.000 1.45 0.00 0.00 2.29
2964 4316 2.057137 ATGTTCCATGCGTTATGCCT 57.943 45.000 0.00 0.00 45.60 4.75
2968 4320 0.541392 TCCATGCGTTATGCCTCTGT 59.459 50.000 0.00 0.00 45.60 3.41
2974 4326 1.929836 GCGTTATGCCTCTGTCTTGAG 59.070 52.381 0.00 0.00 37.76 3.02
2975 4327 2.675317 GCGTTATGCCTCTGTCTTGAGT 60.675 50.000 0.00 0.00 37.76 3.41
2976 4328 3.182967 CGTTATGCCTCTGTCTTGAGTC 58.817 50.000 0.00 0.00 32.50 3.36
2977 4329 3.119316 CGTTATGCCTCTGTCTTGAGTCT 60.119 47.826 0.00 0.00 32.50 3.24
2978 4330 4.619394 CGTTATGCCTCTGTCTTGAGTCTT 60.619 45.833 0.00 0.00 32.50 3.01
2979 4331 2.827800 TGCCTCTGTCTTGAGTCTTG 57.172 50.000 0.00 0.00 32.50 3.02
2980 4332 2.319844 TGCCTCTGTCTTGAGTCTTGA 58.680 47.619 0.00 0.00 32.50 3.02
3064 4416 1.135717 CAATTGATTCACGCGCTGGAA 60.136 47.619 5.73 8.63 0.00 3.53
3065 4417 1.164411 ATTGATTCACGCGCTGGAAA 58.836 45.000 5.73 0.00 0.00 3.13
3068 4420 1.327507 GATTCACGCGCTGGAAAAAC 58.672 50.000 5.73 6.18 0.00 2.43
3075 4427 2.486203 ACGCGCTGGAAAAACAATGATA 59.514 40.909 5.73 0.00 0.00 2.15
3076 4428 3.128589 ACGCGCTGGAAAAACAATGATAT 59.871 39.130 5.73 0.00 0.00 1.63
3083 4438 6.707440 TGGAAAAACAATGATATGCCGTAT 57.293 33.333 0.00 0.00 0.00 3.06
3084 4439 7.106439 TGGAAAAACAATGATATGCCGTATT 57.894 32.000 0.00 0.00 0.00 1.89
3093 4448 2.979814 TATGCCGTATTGTGCAGAGT 57.020 45.000 0.00 0.00 41.46 3.24
3097 4452 1.128692 GCCGTATTGTGCAGAGTTGTC 59.871 52.381 0.00 0.00 0.00 3.18
3117 4477 2.156891 TCGCTGCAAACAAGTATCGTTC 59.843 45.455 0.00 0.00 0.00 3.95
3148 4508 1.930100 GCAGAAGCATCGTCCATCG 59.070 57.895 0.00 0.00 41.58 3.84
3197 4569 0.034337 TCGCTGTACAAACCCAGACC 59.966 55.000 0.00 0.00 0.00 3.85
3198 4570 0.250124 CGCTGTACAAACCCAGACCA 60.250 55.000 0.00 0.00 0.00 4.02
3199 4571 1.812324 CGCTGTACAAACCCAGACCAA 60.812 52.381 0.00 0.00 0.00 3.67
3200 4572 1.607148 GCTGTACAAACCCAGACCAAC 59.393 52.381 0.00 0.00 0.00 3.77
3201 4573 2.748465 GCTGTACAAACCCAGACCAACT 60.748 50.000 0.00 0.00 0.00 3.16
3202 4574 3.551846 CTGTACAAACCCAGACCAACTT 58.448 45.455 0.00 0.00 0.00 2.66
3203 4575 3.547746 TGTACAAACCCAGACCAACTTC 58.452 45.455 0.00 0.00 0.00 3.01
3204 4576 3.201266 TGTACAAACCCAGACCAACTTCT 59.799 43.478 0.00 0.00 0.00 2.85
3205 4577 2.654863 ACAAACCCAGACCAACTTCTG 58.345 47.619 0.00 0.00 42.46 3.02
3206 4578 2.241176 ACAAACCCAGACCAACTTCTGA 59.759 45.455 1.60 0.00 45.19 3.27
3207 4579 3.287222 CAAACCCAGACCAACTTCTGAA 58.713 45.455 1.60 0.00 45.19 3.02
3208 4580 3.662759 AACCCAGACCAACTTCTGAAA 57.337 42.857 1.60 0.00 45.19 2.69
3209 4581 3.662759 ACCCAGACCAACTTCTGAAAA 57.337 42.857 1.60 0.00 45.19 2.29
3210 4582 3.976015 ACCCAGACCAACTTCTGAAAAA 58.024 40.909 1.60 0.00 45.19 1.94
3232 4608 2.986728 ACCCAGACCAAAGGAACATACT 59.013 45.455 0.00 0.00 0.00 2.12
3238 4614 5.065218 CAGACCAAAGGAACATACTATGTGC 59.935 44.000 2.31 0.49 44.07 4.57
3256 4632 3.165606 CAGGAAGTGGACCTGCATC 57.834 57.895 0.00 0.00 46.30 3.91
3300 4681 1.597027 ACGGAGTTTGAACAGCGGG 60.597 57.895 0.00 0.00 37.78 6.13
3418 4807 3.369471 CCCTGTGGTACGAGAATGACATT 60.369 47.826 0.00 0.00 0.00 2.71
3429 4818 4.470462 GAGAATGACATTGAACTGTGCAC 58.530 43.478 10.75 10.75 0.00 4.57
3455 4844 3.414700 GACAACGCAGCCACGGAG 61.415 66.667 0.77 0.00 37.37 4.63
3494 4886 0.616111 TCTGCCTTCCTCTGTCCCTC 60.616 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.216622 TGGTTCTAGTGTATTGGGCTAGAT 58.783 41.667 0.00 0.00 40.29 1.98
26 28 4.020218 TCGGGCCTTATTCCTAGAATCATG 60.020 45.833 0.84 0.00 0.00 3.07
44 46 0.673022 TGCCAAAATGCAAATCGGGC 60.673 50.000 11.46 11.46 38.56 6.13
45 47 1.361793 CTGCCAAAATGCAAATCGGG 58.638 50.000 0.00 0.00 41.51 5.14
46 48 1.361793 CCTGCCAAAATGCAAATCGG 58.638 50.000 0.00 0.00 41.51 4.18
73 75 6.942576 CAGGTGTATTTCCAGGGATTTATAGG 59.057 42.308 0.00 0.00 0.00 2.57
74 76 7.518188 ACAGGTGTATTTCCAGGGATTTATAG 58.482 38.462 0.00 0.00 0.00 1.31
109 116 3.136763 CTCACACACACATTTCTGAGCT 58.863 45.455 0.00 0.00 0.00 4.09
110 117 2.225019 CCTCACACACACATTTCTGAGC 59.775 50.000 0.00 0.00 0.00 4.26
112 119 2.437651 TCCCTCACACACACATTTCTGA 59.562 45.455 0.00 0.00 0.00 3.27
134 141 1.967319 TTGGTGCTGGAAGTTGACTC 58.033 50.000 0.00 0.00 35.30 3.36
139 146 5.806654 ACATTAATTTGGTGCTGGAAGTT 57.193 34.783 0.00 0.00 35.30 2.66
141 148 5.540911 ACAACATTAATTTGGTGCTGGAAG 58.459 37.500 12.13 0.00 37.86 3.46
186 194 9.817365 CGAATAGTATGTGATTGGAAATTGATC 57.183 33.333 0.00 0.00 0.00 2.92
208 216 2.642139 TTACGCGTTCTTCCTCGAAT 57.358 45.000 20.78 0.00 0.00 3.34
209 217 2.420628 TTTACGCGTTCTTCCTCGAA 57.579 45.000 20.78 0.00 0.00 3.71
210 218 2.053627 GTTTTACGCGTTCTTCCTCGA 58.946 47.619 20.78 0.00 0.00 4.04
211 219 1.125566 GGTTTTACGCGTTCTTCCTCG 59.874 52.381 20.78 0.00 0.00 4.63
212 220 2.137523 TGGTTTTACGCGTTCTTCCTC 58.862 47.619 20.78 2.29 0.00 3.71
213 221 2.140717 CTGGTTTTACGCGTTCTTCCT 58.859 47.619 20.78 0.00 0.00 3.36
214 222 1.399343 GCTGGTTTTACGCGTTCTTCC 60.399 52.381 20.78 16.03 0.00 3.46
215 223 1.529865 AGCTGGTTTTACGCGTTCTTC 59.470 47.619 20.78 6.35 0.00 2.87
218 226 0.110373 CCAGCTGGTTTTACGCGTTC 60.110 55.000 25.53 5.95 0.00 3.95
230 238 2.086869 CCTATTGTGACAACCAGCTGG 58.913 52.381 31.60 31.60 42.17 4.85
231 239 2.744202 GTCCTATTGTGACAACCAGCTG 59.256 50.000 6.78 6.78 32.91 4.24
232 240 2.639839 AGTCCTATTGTGACAACCAGCT 59.360 45.455 0.00 0.00 35.15 4.24
233 241 3.003480 GAGTCCTATTGTGACAACCAGC 58.997 50.000 0.00 0.00 35.15 4.85
234 242 3.600388 GGAGTCCTATTGTGACAACCAG 58.400 50.000 0.00 0.74 35.15 4.00
235 243 2.304761 GGGAGTCCTATTGTGACAACCA 59.695 50.000 9.58 0.00 35.02 3.67
237 245 2.304761 TGGGGAGTCCTATTGTGACAAC 59.695 50.000 9.58 0.00 35.15 3.32
238 246 2.626785 TGGGGAGTCCTATTGTGACAA 58.373 47.619 9.58 0.00 35.15 3.18
239 247 2.335681 TGGGGAGTCCTATTGTGACA 57.664 50.000 9.58 0.00 35.15 3.58
240 248 3.933861 ATTGGGGAGTCCTATTGTGAC 57.066 47.619 9.58 0.00 36.20 3.67
241 249 4.235079 CAATTGGGGAGTCCTATTGTGA 57.765 45.455 9.58 0.00 46.51 3.58
249 1260 1.177401 GCTGTTCAATTGGGGAGTCC 58.823 55.000 5.42 0.00 0.00 3.85
436 1491 8.807948 AGGCAATTAAACTTGTGTGTATCTAT 57.192 30.769 0.00 0.00 0.00 1.98
517 1576 6.633668 ATTCAGAGAAACAATTCTACGTCG 57.366 37.500 0.00 0.00 45.91 5.12
602 1665 7.013942 ACCTCGTGTGTGTGTGTGTATATATAT 59.986 37.037 0.00 0.00 0.00 0.86
604 1667 5.126545 ACCTCGTGTGTGTGTGTGTATATAT 59.873 40.000 0.00 0.00 0.00 0.86
606 1669 3.257375 ACCTCGTGTGTGTGTGTGTATAT 59.743 43.478 0.00 0.00 0.00 0.86
607 1670 2.624364 ACCTCGTGTGTGTGTGTGTATA 59.376 45.455 0.00 0.00 0.00 1.47
608 1671 1.411246 ACCTCGTGTGTGTGTGTGTAT 59.589 47.619 0.00 0.00 0.00 2.29
609 1672 0.818938 ACCTCGTGTGTGTGTGTGTA 59.181 50.000 0.00 0.00 0.00 2.90
610 1673 0.739462 CACCTCGTGTGTGTGTGTGT 60.739 55.000 0.57 0.00 40.26 3.72
611 1674 2.005995 CACCTCGTGTGTGTGTGTG 58.994 57.895 0.57 0.00 40.26 3.82
612 1675 4.513519 CACCTCGTGTGTGTGTGT 57.486 55.556 0.57 0.00 40.26 3.72
632 1695 3.349006 CACACTCACTGGCCACGC 61.349 66.667 0.00 0.00 0.00 5.34
633 1696 2.094757 TACCACACTCACTGGCCACG 62.095 60.000 0.00 0.00 31.13 4.94
634 1697 0.602905 GTACCACACTCACTGGCCAC 60.603 60.000 0.00 0.00 31.13 5.01
635 1698 1.752198 GTACCACACTCACTGGCCA 59.248 57.895 4.71 4.71 31.13 5.36
636 1699 1.374252 CGTACCACACTCACTGGCC 60.374 63.158 0.00 0.00 31.13 5.36
637 1700 0.944311 CACGTACCACACTCACTGGC 60.944 60.000 0.00 0.00 31.13 4.85
638 1701 0.387929 ACACGTACCACACTCACTGG 59.612 55.000 0.00 0.00 34.62 4.00
639 1702 2.351447 CCTACACGTACCACACTCACTG 60.351 54.545 0.00 0.00 0.00 3.66
640 1703 1.884579 CCTACACGTACCACACTCACT 59.115 52.381 0.00 0.00 0.00 3.41
646 1709 2.964174 CCGCCTACACGTACCACA 59.036 61.111 0.00 0.00 0.00 4.17
663 1726 1.598130 GTCACACACTCCACCCAGC 60.598 63.158 0.00 0.00 0.00 4.85
674 1737 0.464036 AGTTTCCTCTGCGTCACACA 59.536 50.000 0.00 0.00 0.00 3.72
697 1760 4.156922 TCTTCTTCCATCTCGTCTTCAGAC 59.843 45.833 0.00 0.00 41.47 3.51
718 1781 1.264749 TTCGGCACCTGCACCTATCT 61.265 55.000 0.00 0.00 44.36 1.98
719 1782 0.179045 ATTCGGCACCTGCACCTATC 60.179 55.000 0.00 0.00 44.36 2.08
720 1783 0.179045 GATTCGGCACCTGCACCTAT 60.179 55.000 0.00 0.00 44.36 2.57
751 1814 0.108756 GTCCGAAGAAGAAGTCCCCG 60.109 60.000 0.00 0.00 0.00 5.73
765 1828 0.959553 GTCTCTGTTCCACAGTCCGA 59.040 55.000 3.87 0.00 46.03 4.55
773 1836 1.343465 GTTTCCTCGGTCTCTGTTCCA 59.657 52.381 0.00 0.00 0.00 3.53
778 1841 1.401670 CGTCAGTTTCCTCGGTCTCTG 60.402 57.143 0.00 0.00 0.00 3.35
784 1847 1.801913 CTCGCGTCAGTTTCCTCGG 60.802 63.158 5.77 0.00 0.00 4.63
902 1965 2.742348 TCAGGTCGGCTTATGTAGGAA 58.258 47.619 0.00 0.00 0.00 3.36
903 1966 2.447408 TCAGGTCGGCTTATGTAGGA 57.553 50.000 0.00 0.00 0.00 2.94
1079 2160 0.036875 GGTCACCTTCTTCCCACCAG 59.963 60.000 0.00 0.00 0.00 4.00
1086 2167 1.376037 CCTGCCGGTCACCTTCTTC 60.376 63.158 1.90 0.00 0.00 2.87
1116 2197 4.024893 GTGAGCACGAAGAAGAAATGAACA 60.025 41.667 0.00 0.00 0.00 3.18
1170 2251 2.593956 GGTGGGCGAGAGGAACCTT 61.594 63.158 0.00 0.00 0.00 3.50
1171 2252 3.003763 GGTGGGCGAGAGGAACCT 61.004 66.667 0.00 0.00 0.00 3.50
1503 2626 0.469705 TGTTGGCCATCAGGTGCTTT 60.470 50.000 12.62 0.00 37.19 3.51
1746 2872 2.654877 GACACGAGCTCCCGGAAA 59.345 61.111 8.47 0.00 0.00 3.13
1941 3067 4.819761 TGATGCTCCGGCGTGCTC 62.820 66.667 19.57 14.99 42.25 4.26
1951 3104 1.666054 CTTGGCTTCTCCTGATGCTC 58.334 55.000 0.00 0.00 41.41 4.26
1952 3105 0.255318 CCTTGGCTTCTCCTGATGCT 59.745 55.000 0.00 0.00 41.41 3.79
1954 3107 1.094073 CGCCTTGGCTTCTCCTGATG 61.094 60.000 10.12 0.00 35.26 3.07
2409 3583 1.218316 GTTCTGGCCACCGAGGTAG 59.782 63.158 0.00 0.00 40.61 3.18
2418 3592 3.240134 GAGGCTCACGTTCTGGCCA 62.240 63.158 10.25 4.71 46.23 5.36
2562 3739 3.136626 ACCTACCCTCCATTAGAATGCAC 59.863 47.826 0.00 0.00 35.08 4.57
2568 3745 1.133262 CCGGACCTACCCTCCATTAGA 60.133 57.143 0.00 0.00 34.64 2.10
2692 3870 8.128582 TGTGCACAAACAAAACAAAACAAATAA 58.871 25.926 19.28 0.00 0.00 1.40
2715 3893 7.597369 TCGACGGATTATATATGGTCTTTTGTG 59.403 37.037 0.00 0.00 0.00 3.33
2720 3898 9.186837 AGTATTCGACGGATTATATATGGTCTT 57.813 33.333 0.00 0.00 0.00 3.01
2721 3899 8.749026 AGTATTCGACGGATTATATATGGTCT 57.251 34.615 0.00 0.00 0.00 3.85
2722 3900 8.838365 AGAGTATTCGACGGATTATATATGGTC 58.162 37.037 0.00 0.00 0.00 4.02
2724 3902 8.837389 TCAGAGTATTCGACGGATTATATATGG 58.163 37.037 0.00 0.00 0.00 2.74
2728 3906 8.399425 GTCATCAGAGTATTCGACGGATTATAT 58.601 37.037 0.00 0.00 0.00 0.86
2729 3907 7.389607 TGTCATCAGAGTATTCGACGGATTATA 59.610 37.037 0.00 0.00 0.00 0.98
2732 3910 4.338400 TGTCATCAGAGTATTCGACGGATT 59.662 41.667 0.00 0.00 0.00 3.01
2733 3911 3.883489 TGTCATCAGAGTATTCGACGGAT 59.117 43.478 0.00 0.00 0.00 4.18
2734 3912 3.275999 TGTCATCAGAGTATTCGACGGA 58.724 45.455 0.00 0.00 0.00 4.69
2811 4160 1.396996 GCCGTTGTGTATGTCATCACC 59.603 52.381 10.82 0.41 34.14 4.02
2821 4172 2.243056 CAGTGCATGCCGTTGTGTA 58.757 52.632 16.68 0.00 0.00 2.90
2914 4265 6.015434 TCCATATATGTAGTATATGCCGCTGG 60.015 42.308 11.73 0.00 45.98 4.85
2916 4267 7.287927 AGTTCCATATATGTAGTATATGCCGCT 59.712 37.037 11.73 4.67 45.98 5.52
2945 4296 1.949525 GAGGCATAACGCATGGAACAT 59.050 47.619 0.00 0.00 45.17 2.71
2947 4298 1.331756 CAGAGGCATAACGCATGGAAC 59.668 52.381 0.00 0.00 45.17 3.62
2950 4302 0.940126 GACAGAGGCATAACGCATGG 59.060 55.000 0.00 0.00 45.17 3.66
2964 4316 3.493350 GCCTTGTCAAGACTCAAGACAGA 60.493 47.826 14.42 0.00 42.54 3.41
2968 4320 1.768275 TGGCCTTGTCAAGACTCAAGA 59.232 47.619 14.42 0.00 42.22 3.02
2974 4326 1.973812 GCCCTGGCCTTGTCAAGAC 60.974 63.158 14.42 1.77 34.56 3.01
2975 4327 2.436109 GCCCTGGCCTTGTCAAGA 59.564 61.111 14.42 0.00 34.56 3.02
2976 4328 3.058160 CGCCCTGGCCTTGTCAAG 61.058 66.667 3.32 5.53 37.98 3.02
2977 4329 4.659172 CCGCCCTGGCCTTGTCAA 62.659 66.667 3.32 0.00 37.98 3.18
3036 4388 4.109766 CGCGTGAATCAATTGTACTCCTA 58.890 43.478 5.13 0.00 0.00 2.94
3038 4390 2.536928 GCGCGTGAATCAATTGTACTCC 60.537 50.000 8.43 0.00 0.00 3.85
3039 4391 2.348666 AGCGCGTGAATCAATTGTACTC 59.651 45.455 8.43 1.70 0.00 2.59
3040 4392 2.094258 CAGCGCGTGAATCAATTGTACT 59.906 45.455 8.43 0.00 0.00 2.73
3041 4393 2.430956 CAGCGCGTGAATCAATTGTAC 58.569 47.619 8.43 0.74 0.00 2.90
3052 4404 0.665835 ATTGTTTTTCCAGCGCGTGA 59.334 45.000 8.43 0.00 0.00 4.35
3064 4416 5.748152 GCACAATACGGCATATCATTGTTTT 59.252 36.000 0.00 0.00 39.06 2.43
3065 4417 5.163571 TGCACAATACGGCATATCATTGTTT 60.164 36.000 0.00 0.00 39.06 2.83
3068 4420 4.213906 TCTGCACAATACGGCATATCATTG 59.786 41.667 0.00 0.00 39.65 2.82
3075 4427 1.739466 CAACTCTGCACAATACGGCAT 59.261 47.619 0.00 0.00 39.65 4.40
3076 4428 1.155889 CAACTCTGCACAATACGGCA 58.844 50.000 0.00 0.00 38.52 5.69
3083 4438 2.310309 CAGCGACAACTCTGCACAA 58.690 52.632 0.00 0.00 0.00 3.33
3084 4439 4.032356 CAGCGACAACTCTGCACA 57.968 55.556 0.00 0.00 0.00 4.57
3093 4448 2.096466 CGATACTTGTTTGCAGCGACAA 60.096 45.455 12.16 12.16 34.80 3.18
3097 4452 2.495939 GAACGATACTTGTTTGCAGCG 58.504 47.619 0.00 0.00 0.00 5.18
3117 4477 0.575859 CTTCTGCACGATGATCTGCG 59.424 55.000 10.65 6.30 36.08 5.18
3148 4508 5.578776 ACTCTTCGTTCAATCAAACAAACC 58.421 37.500 0.00 0.00 0.00 3.27
3207 4579 3.445987 TGTTCCTTTGGTCTGGGTTTTT 58.554 40.909 0.00 0.00 0.00 1.94
3208 4580 3.108847 TGTTCCTTTGGTCTGGGTTTT 57.891 42.857 0.00 0.00 0.00 2.43
3209 4581 2.838637 TGTTCCTTTGGTCTGGGTTT 57.161 45.000 0.00 0.00 0.00 3.27
3210 4582 3.397955 AGTATGTTCCTTTGGTCTGGGTT 59.602 43.478 0.00 0.00 0.00 4.11
3211 4583 2.986728 AGTATGTTCCTTTGGTCTGGGT 59.013 45.455 0.00 0.00 0.00 4.51
3212 4584 3.721087 AGTATGTTCCTTTGGTCTGGG 57.279 47.619 0.00 0.00 0.00 4.45
3213 4585 5.586243 CACATAGTATGTTCCTTTGGTCTGG 59.414 44.000 13.25 0.00 42.70 3.86
3214 4586 5.065218 GCACATAGTATGTTCCTTTGGTCTG 59.935 44.000 13.25 0.00 42.70 3.51
3215 4587 5.186198 GCACATAGTATGTTCCTTTGGTCT 58.814 41.667 13.25 0.00 42.70 3.85
3232 4608 1.278985 CAGGTCCACTTCCTGCACATA 59.721 52.381 0.00 0.00 44.46 2.29
3254 4630 3.369471 CCGGCCGACTATATCAAATGGAT 60.369 47.826 30.73 0.00 40.14 3.41
3256 4632 2.346803 CCGGCCGACTATATCAAATGG 58.653 52.381 30.73 0.00 0.00 3.16
3300 4681 3.339141 CTGCCTAAGAAACTTCTCCCAC 58.661 50.000 0.00 0.00 36.28 4.61
3398 4787 4.494484 TCAATGTCATTCTCGTACCACAG 58.506 43.478 0.00 0.00 0.00 3.66
3418 4807 2.279851 CGTCGGGTGCACAGTTCA 60.280 61.111 20.43 0.00 0.00 3.18
3452 4841 1.374758 CTCGTCAACAGGTGGCTCC 60.375 63.158 0.00 0.00 0.00 4.70
3453 4842 1.374758 CCTCGTCAACAGGTGGCTC 60.375 63.158 0.00 0.00 0.00 4.70
3454 4843 2.743718 CCTCGTCAACAGGTGGCT 59.256 61.111 0.00 0.00 0.00 4.75
3455 4844 2.358737 CCCTCGTCAACAGGTGGC 60.359 66.667 0.00 0.00 0.00 5.01
3456 4845 2.358737 GCCCTCGTCAACAGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
3457 4846 1.003355 ATGCCCTCGTCAACAGGTG 60.003 57.895 0.00 0.00 0.00 4.00
3458 4847 1.194781 AGATGCCCTCGTCAACAGGT 61.195 55.000 0.00 0.00 0.00 4.00
3459 4848 0.742281 CAGATGCCCTCGTCAACAGG 60.742 60.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.