Multiple sequence alignment - TraesCS5A01G168800

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 TraesCS5A01G168800 chr5A 100.000 3977 0 0 1 3977 359733840 359737816 0.000000e+00 7345
1 TraesCS5A01G168800 chr5D 97.590 2365 42 9 855 3204 270250980 270253344 0.000000e+00 4037
2 TraesCS5A01G168800 chr5D 94.825 657 23 3 3332 3977 270253337 270253993 0.000000e+00 1014
3 TraesCS5A01G168800 chr5D 86.398 794 68 17 1 758 270249373 270250162 0.000000e+00 832
4 TraesCS5A01G168800 chr5B 95.718 2429 77 17 795 3204 307268858 307271278 0.000000e+00 3884
5 TraesCS5A01G168800 chr5B 94.360 656 19 7 3332 3977 307271271 307271918 0.000000e+00 990
6 TraesCS5A01G168800 chr4D 96.324 136 4 1 3197 3331 98932989 98932854 5.170000e-54 222
7 TraesCS5A01G168800 chr4D 96.241 133 5 0 3199 3331 455759737 455759605 6.690000e-53 219
8 TraesCS5A01G168800 chr6A 89.313 131 14 0 3201 3331 28665193 28665323 8.840000e-37 165


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 TraesCS5A01G168800 chr5A 359733840 359737816 3976 False 7345 7345 100.000000 1 3977 1 chr5A.!!$F1 3976
1 TraesCS5A01G168800 chr5D 270249373 270253993 4620 False 1961 4037 92.937667 1 3977 3 chr5D.!!$F1 3976
2 TraesCS5A01G168800 chr5B 307268858 307271918 3060 False 2437 3884 95.039000 795 3977 2 chr5B.!!$F1 3182

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
847 1613 0.318120 AAAGCAAGCAAACCCATCGG 59.682 50.0 0.0 0.0 0.0 4.18 F
1231 2033 0.178897 TCTCCCGTTTCCCCCTAACA 60.179 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 3273 0.108138 CTAAGGTTGACCGAGGGCTG 60.108 60.000 0.0 0.0 42.08 4.85 R
3228 4032 1.227497 GCTCCGCTCCCTGATGAAG 60.227 63.158 0.0 0.0 0.00 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
35 36 5.105635 TGACTCAACACTACTAATTACGGGG 60.106 44.000 0.00 0.00 0.00 5.73
41 42 7.287466 TCAACACTACTAATTACGGGGCTATTA 59.713 37.037 0.00 0.00 0.00 0.98
54 56 3.134623 GGGGCTATTATTTTGGCAAGCTT 59.865 43.478 0.00 0.00 0.00 3.74
63 65 2.095604 TTGGCAAGCTTAAACCCCTT 57.904 45.000 0.00 0.00 0.00 3.95
72 74 2.419713 GCTTAAACCCCTTCGTAGGAGG 60.420 54.545 10.07 11.32 45.05 4.30
94 96 2.295349 GCCTCCATGCATTCATTACCAG 59.705 50.000 0.00 0.00 0.00 4.00
103 105 7.039574 CCATGCATTCATTACCAGAATTATGGA 60.040 37.037 25.55 4.44 42.79 3.41
139 141 9.843334 TTTATTACTAAAACAAAACCATAGCCG 57.157 29.630 0.00 0.00 0.00 5.52
173 175 3.790089 TGGATATAGGCAGAGACGAGA 57.210 47.619 0.00 0.00 0.00 4.04
191 193 3.003689 CGAGAGTGGATTTTGTGTGCTTT 59.996 43.478 0.00 0.00 0.00 3.51
206 208 3.634910 TGTGCTTTGTAAAGAAAGGGTCC 59.365 43.478 8.47 0.00 38.28 4.46
207 209 2.882137 TGCTTTGTAAAGAAAGGGTCCG 59.118 45.455 8.47 0.00 38.28 4.79
223 225 2.384203 CCGAATTCTTGTCCTCGGC 58.616 57.895 3.52 0.00 43.83 5.54
237 239 1.407437 CCTCGGCCATCTTTGCTTAGT 60.407 52.381 2.24 0.00 0.00 2.24
239 241 3.495100 CCTCGGCCATCTTTGCTTAGTAT 60.495 47.826 2.24 0.00 0.00 2.12
278 301 7.460296 CACGATTGTGCTTTGTGTGTATATAA 58.540 34.615 0.00 0.00 39.67 0.98
324 347 5.855395 TGTTTTGCTCATTTGTTTTTGTTGC 59.145 32.000 0.00 0.00 0.00 4.17
360 383 9.436957 TTTTTGGTGCAACTGAAATTACTTTTA 57.563 25.926 2.04 0.00 36.74 1.52
422 467 5.407995 CGGGATTGCAATTTTTGTGTGTAAT 59.592 36.000 14.33 0.00 31.39 1.89
423 468 6.073331 CGGGATTGCAATTTTTGTGTGTAATT 60.073 34.615 14.33 0.00 29.27 1.40
424 469 7.076983 GGGATTGCAATTTTTGTGTGTAATTG 58.923 34.615 14.33 0.00 40.49 2.32
429 474 6.601741 CAATTTTTGTGTGTAATTGCACCT 57.398 33.333 21.81 0.00 38.52 4.00
430 475 7.014092 CAATTTTTGTGTGTAATTGCACCTT 57.986 32.000 21.81 3.43 38.52 3.50
431 476 7.470900 CAATTTTTGTGTGTAATTGCACCTTT 58.529 30.769 21.81 4.65 38.52 3.11
432 477 7.622893 ATTTTTGTGTGTAATTGCACCTTTT 57.377 28.000 21.81 0.57 38.52 2.27
513 558 9.333724 TGTGTAACTTTAGGGTTAGAAGAAAAG 57.666 33.333 0.00 0.00 38.04 2.27
556 601 5.423886 GTTCACATTTTCTTGGAACCCAAA 58.576 37.500 0.00 0.00 43.44 3.28
620 666 8.462016 AGCCTTAATACATGAAAGTGTTCAATC 58.538 33.333 0.00 0.00 46.66 2.67
631 677 5.529581 AAGTGTTCAATCGGGACAAAAAT 57.470 34.783 0.00 0.00 0.00 1.82
640 686 7.158021 TCAATCGGGACAAAAATTAAGCAAAT 58.842 30.769 0.00 0.00 0.00 2.32
658 704 2.010145 ATGAAGGATCGACCGTGTTG 57.990 50.000 0.00 0.00 44.74 3.33
670 716 4.023963 TCGACCGTGTTGCATTTATTTTCA 60.024 37.500 0.00 0.00 0.00 2.69
777 847 8.984482 TTTGAATGCGTAAACATCAAAATTTG 57.016 26.923 0.00 0.00 30.87 2.32
791 861 3.760580 AAATTTGGGAACGGCATTCAA 57.239 38.095 0.00 0.00 39.30 2.69
792 862 3.979101 AATTTGGGAACGGCATTCAAT 57.021 38.095 0.00 0.00 39.30 2.57
793 863 3.525268 ATTTGGGAACGGCATTCAATC 57.475 42.857 0.00 0.00 39.30 2.67
847 1613 0.318120 AAAGCAAGCAAACCCATCGG 59.682 50.000 0.00 0.00 0.00 4.18
850 1616 1.664873 CAAGCAAACCCATCGGCAA 59.335 52.632 0.00 0.00 0.00 4.52
894 1674 3.212906 TTGCGCGCTCTCACTGTCT 62.213 57.895 33.29 0.00 0.00 3.41
1017 1819 1.277580 CCATGGCTCCAAGACCTCCT 61.278 60.000 0.00 0.00 0.00 3.69
1227 2029 2.285442 CCTCTCCCGTTTCCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
1231 2033 0.178897 TCTCCCGTTTCCCCCTAACA 60.179 55.000 0.00 0.00 0.00 2.41
1369 2171 2.752238 CTCTCCCGCTCGAGGTGT 60.752 66.667 15.58 0.00 0.00 4.16
1626 2430 2.636412 CGTCGGCTTCCAGGTCTCA 61.636 63.158 0.00 0.00 0.00 3.27
1910 2714 0.900647 AAGTGGAGGTCTCGTCCTGG 60.901 60.000 9.36 0.00 38.97 4.45
1917 2721 1.605971 GGTCTCGTCCTGGAGGGTTC 61.606 65.000 15.78 6.77 34.74 3.62
2285 3089 0.544697 GGTGTCCACCGTTATCCCAT 59.455 55.000 0.00 0.00 42.29 4.00
2469 3273 4.683671 GCAAGGTTGAAGGATCCTAGTACC 60.684 50.000 16.55 20.48 0.00 3.34
2752 3556 0.242017 GCAAATGACGAGGCTGCTTT 59.758 50.000 0.00 0.00 0.00 3.51
3166 3970 3.743521 TCAGCACTTCAGCATGTTTAGT 58.256 40.909 0.00 0.00 37.40 2.24
3193 3997 9.952030 TTGTCAGTTAGTATTGTGGATGATTTA 57.048 29.630 0.00 0.00 0.00 1.40
3204 4008 8.915057 ATTGTGGATGATTTATGAGACTAAGG 57.085 34.615 0.00 0.00 0.00 2.69
3205 4009 6.291377 TGTGGATGATTTATGAGACTAAGGC 58.709 40.000 0.00 0.00 0.00 4.35
3206 4010 6.100279 TGTGGATGATTTATGAGACTAAGGCT 59.900 38.462 0.00 0.00 0.00 4.58
3207 4011 6.426328 GTGGATGATTTATGAGACTAAGGCTG 59.574 42.308 0.00 0.00 0.00 4.85
3208 4012 6.100279 TGGATGATTTATGAGACTAAGGCTGT 59.900 38.462 0.00 0.00 0.00 4.40
3209 4013 6.426328 GGATGATTTATGAGACTAAGGCTGTG 59.574 42.308 0.00 0.00 0.00 3.66
3210 4014 6.299805 TGATTTATGAGACTAAGGCTGTGT 57.700 37.500 0.00 0.00 0.00 3.72
3211 4015 6.711277 TGATTTATGAGACTAAGGCTGTGTT 58.289 36.000 0.00 0.00 0.00 3.32
3212 4016 6.818644 TGATTTATGAGACTAAGGCTGTGTTC 59.181 38.462 0.00 0.00 0.00 3.18
3213 4017 2.724977 TGAGACTAAGGCTGTGTTCG 57.275 50.000 0.00 0.00 0.00 3.95
3214 4018 1.272490 TGAGACTAAGGCTGTGTTCGG 59.728 52.381 0.00 0.00 0.00 4.30
3215 4019 0.037232 AGACTAAGGCTGTGTTCGGC 60.037 55.000 0.00 0.00 44.51 5.54
3216 4020 0.320421 GACTAAGGCTGTGTTCGGCA 60.320 55.000 0.00 0.00 46.81 5.69
3217 4021 0.107831 ACTAAGGCTGTGTTCGGCAA 59.892 50.000 0.00 0.00 46.81 4.52
3218 4022 1.271379 ACTAAGGCTGTGTTCGGCAAT 60.271 47.619 0.00 0.00 46.81 3.56
3219 4023 1.398390 CTAAGGCTGTGTTCGGCAATC 59.602 52.381 0.00 0.00 46.81 2.67
3220 4024 1.577328 AAGGCTGTGTTCGGCAATCG 61.577 55.000 0.00 0.00 46.81 3.34
3221 4025 2.202349 GCTGTGTTCGGCAATCGC 60.202 61.111 0.00 0.00 44.61 4.58
3231 4035 3.577313 GCAATCGCCCGCTCCTTC 61.577 66.667 0.00 0.00 0.00 3.46
3232 4036 2.125147 CAATCGCCCGCTCCTTCA 60.125 61.111 0.00 0.00 0.00 3.02
3233 4037 1.524621 CAATCGCCCGCTCCTTCAT 60.525 57.895 0.00 0.00 0.00 2.57
3234 4038 1.227674 AATCGCCCGCTCCTTCATC 60.228 57.895 0.00 0.00 0.00 2.92
3235 4039 1.971505 AATCGCCCGCTCCTTCATCA 61.972 55.000 0.00 0.00 0.00 3.07
3236 4040 2.374830 ATCGCCCGCTCCTTCATCAG 62.375 60.000 0.00 0.00 0.00 2.90
3237 4041 2.203126 GCCCGCTCCTTCATCAGG 60.203 66.667 0.00 0.00 45.64 3.86
3238 4042 2.507944 CCCGCTCCTTCATCAGGG 59.492 66.667 0.00 0.00 44.12 4.45
3239 4043 2.066393 CCCGCTCCTTCATCAGGGA 61.066 63.158 0.00 0.00 44.12 4.20
3243 4047 1.445095 CTCCTTCATCAGGGAGCGG 59.555 63.158 0.00 0.00 44.12 5.52
3244 4048 1.001631 TCCTTCATCAGGGAGCGGA 59.998 57.895 0.00 0.00 44.12 5.54
3245 4049 1.045350 TCCTTCATCAGGGAGCGGAG 61.045 60.000 0.00 0.00 44.12 4.63
3267 4071 4.338327 CGGAGCTACGTATTGGCC 57.662 61.111 11.15 0.00 0.00 5.36
3268 4072 1.660575 CGGAGCTACGTATTGGCCG 60.661 63.158 11.15 0.00 0.00 6.13
3269 4073 1.954651 GGAGCTACGTATTGGCCGC 60.955 63.158 0.00 0.00 0.00 6.53
3270 4074 1.067582 GAGCTACGTATTGGCCGCT 59.932 57.895 4.60 4.60 0.00 5.52
3271 4075 0.940047 GAGCTACGTATTGGCCGCTC 60.940 60.000 14.16 14.16 37.35 5.03
3272 4076 1.954651 GCTACGTATTGGCCGCTCC 60.955 63.158 0.00 0.00 0.00 4.70
3273 4077 1.300697 CTACGTATTGGCCGCTCCC 60.301 63.158 0.00 0.00 0.00 4.30
3274 4078 2.710724 CTACGTATTGGCCGCTCCCC 62.711 65.000 0.00 0.00 0.00 4.81
3275 4079 4.169696 CGTATTGGCCGCTCCCCA 62.170 66.667 0.00 0.00 0.00 4.96
3276 4080 2.274104 GTATTGGCCGCTCCCCAA 59.726 61.111 0.00 2.67 45.63 4.12
3277 4081 1.379309 GTATTGGCCGCTCCCCAAA 60.379 57.895 0.00 0.00 44.80 3.28
3278 4082 0.755327 GTATTGGCCGCTCCCCAAAT 60.755 55.000 0.00 0.00 44.80 2.32
3279 4083 0.032615 TATTGGCCGCTCCCCAAATT 60.033 50.000 0.00 0.00 44.80 1.82
3280 4084 0.909133 ATTGGCCGCTCCCCAAATTT 60.909 50.000 0.00 0.00 44.80 1.82
3281 4085 1.540435 TTGGCCGCTCCCCAAATTTC 61.540 55.000 0.00 0.00 39.29 2.17
3282 4086 1.682344 GGCCGCTCCCCAAATTTCT 60.682 57.895 0.00 0.00 0.00 2.52
3283 4087 0.395173 GGCCGCTCCCCAAATTTCTA 60.395 55.000 0.00 0.00 0.00 2.10
3284 4088 0.738975 GCCGCTCCCCAAATTTCTAC 59.261 55.000 0.00 0.00 0.00 2.59
3285 4089 1.682087 GCCGCTCCCCAAATTTCTACT 60.682 52.381 0.00 0.00 0.00 2.57
3286 4090 2.017049 CCGCTCCCCAAATTTCTACTG 58.983 52.381 0.00 0.00 0.00 2.74
3287 4091 2.355716 CCGCTCCCCAAATTTCTACTGA 60.356 50.000 0.00 0.00 0.00 3.41
3288 4092 3.343617 CGCTCCCCAAATTTCTACTGAA 58.656 45.455 0.00 0.00 0.00 3.02
3289 4093 3.947834 CGCTCCCCAAATTTCTACTGAAT 59.052 43.478 0.00 0.00 31.56 2.57
3290 4094 4.201950 CGCTCCCCAAATTTCTACTGAATG 60.202 45.833 0.00 0.00 31.56 2.67
3291 4095 4.440663 GCTCCCCAAATTTCTACTGAATGC 60.441 45.833 0.00 0.00 31.56 3.56
3292 4096 4.023291 TCCCCAAATTTCTACTGAATGCC 58.977 43.478 0.00 0.00 31.56 4.40
3293 4097 3.768757 CCCCAAATTTCTACTGAATGCCA 59.231 43.478 0.00 0.00 31.56 4.92
3294 4098 4.381932 CCCCAAATTTCTACTGAATGCCAC 60.382 45.833 0.00 0.00 31.56 5.01
3295 4099 4.463891 CCCAAATTTCTACTGAATGCCACT 59.536 41.667 0.00 0.00 31.56 4.00
3296 4100 5.393461 CCCAAATTTCTACTGAATGCCACTC 60.393 44.000 0.00 0.00 31.56 3.51
3297 4101 5.393461 CCAAATTTCTACTGAATGCCACTCC 60.393 44.000 0.00 0.00 31.56 3.85
3298 4102 2.672961 TTCTACTGAATGCCACTCCG 57.327 50.000 0.00 0.00 0.00 4.63
3299 4103 0.175760 TCTACTGAATGCCACTCCGC 59.824 55.000 0.00 0.00 0.00 5.54
3300 4104 0.176680 CTACTGAATGCCACTCCGCT 59.823 55.000 0.00 0.00 0.00 5.52
3301 4105 0.175760 TACTGAATGCCACTCCGCTC 59.824 55.000 0.00 0.00 0.00 5.03
3302 4106 1.817099 CTGAATGCCACTCCGCTCC 60.817 63.158 0.00 0.00 0.00 4.70
3303 4107 2.892425 GAATGCCACTCCGCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
3304 4108 3.665675 GAATGCCACTCCGCTCCGT 62.666 63.158 0.00 0.00 0.00 4.69
3305 4109 3.958147 AATGCCACTCCGCTCCGTG 62.958 63.158 0.00 0.00 0.00 4.94
3319 4123 1.776662 TCCGTGGAGGAGTTATGGAG 58.223 55.000 0.00 0.00 45.98 3.86
3320 4124 0.105039 CCGTGGAGGAGTTATGGAGC 59.895 60.000 0.00 0.00 45.00 4.70
3321 4125 0.249073 CGTGGAGGAGTTATGGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
3322 4126 0.105039 GTGGAGGAGTTATGGAGCGG 59.895 60.000 0.00 0.00 0.00 5.52
3323 4127 0.032515 TGGAGGAGTTATGGAGCGGA 60.033 55.000 0.00 0.00 0.00 5.54
3324 4128 0.676736 GGAGGAGTTATGGAGCGGAG 59.323 60.000 0.00 0.00 0.00 4.63
3325 4129 0.676736 GAGGAGTTATGGAGCGGAGG 59.323 60.000 0.00 0.00 0.00 4.30
3326 4130 0.760945 AGGAGTTATGGAGCGGAGGG 60.761 60.000 0.00 0.00 0.00 4.30
3327 4131 0.759436 GGAGTTATGGAGCGGAGGGA 60.759 60.000 0.00 0.00 0.00 4.20
3328 4132 1.343069 GAGTTATGGAGCGGAGGGAT 58.657 55.000 0.00 0.00 0.00 3.85
3329 4133 1.694696 GAGTTATGGAGCGGAGGGATT 59.305 52.381 0.00 0.00 0.00 3.01
3330 4134 1.694696 AGTTATGGAGCGGAGGGATTC 59.305 52.381 0.00 0.00 0.00 2.52
3331 4135 1.416401 GTTATGGAGCGGAGGGATTCA 59.584 52.381 0.00 0.00 0.00 2.57
3332 4136 1.342074 TATGGAGCGGAGGGATTCAG 58.658 55.000 0.00 0.00 0.00 3.02
3333 4137 2.049627 ATGGAGCGGAGGGATTCAGC 62.050 60.000 0.00 0.00 45.91 4.26
3350 4154 0.117340 AGCCTAAGTGTCCCTGAGGT 59.883 55.000 0.00 0.00 43.32 3.85
3356 4160 1.059913 AGTGTCCCTGAGGTTGAAGG 58.940 55.000 0.00 0.00 0.00 3.46
3586 4391 3.629398 GGAGCCCAAGATTGTACAAGATG 59.371 47.826 14.65 11.79 0.00 2.90
3787 4601 1.300697 GGCTCGGTGAGTTCGTGTT 60.301 57.895 0.00 0.00 31.39 3.32
3790 4604 1.847818 CTCGGTGAGTTCGTGTTGAA 58.152 50.000 0.00 0.00 0.00 2.69
3799 4613 6.430451 GTGAGTTCGTGTTGAATTCTTTCAT 58.570 36.000 7.05 0.00 42.21 2.57
3828 4642 0.620556 ATGAATTCCAGAGGCCGTGT 59.379 50.000 2.27 0.00 0.00 4.49
3958 4773 6.346919 CCTCATCTCTTGACAACGTTGTAAAG 60.347 42.308 37.31 37.31 46.57 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.117685 GCCCCGTAATTAGTAGTGTTGAG 58.882 47.826 0.00 0.00 0.00 3.02
35 36 6.257849 GGGTTTAAGCTTGCCAAAATAATAGC 59.742 38.462 9.86 0.00 0.00 2.97
41 42 2.978978 AGGGGTTTAAGCTTGCCAAAAT 59.021 40.909 9.86 0.00 0.00 1.82
72 74 1.615392 GGTAATGAATGCATGGAGGCC 59.385 52.381 0.00 0.00 34.26 5.19
114 116 8.460428 CCGGCTATGGTTTTGTTTTAGTAATAA 58.540 33.333 0.00 0.00 0.00 1.40
115 117 7.415429 GCCGGCTATGGTTTTGTTTTAGTAATA 60.415 37.037 22.15 0.00 0.00 0.98
139 141 5.509670 GCCTATATCCATTGGTTGAAAAGCC 60.510 44.000 1.86 0.00 45.42 4.35
173 175 5.590530 TTACAAAGCACACAAAATCCACT 57.409 34.783 0.00 0.00 0.00 4.00
191 193 5.237236 AGAATTCGGACCCTTTCTTTACA 57.763 39.130 0.00 0.00 0.00 2.41
206 208 0.391130 TGGCCGAGGACAAGAATTCG 60.391 55.000 0.00 0.00 0.00 3.34
207 209 1.943340 GATGGCCGAGGACAAGAATTC 59.057 52.381 0.01 0.00 36.35 2.17
239 241 8.487313 AGCACAATCGTGTTTCAATAATAGTA 57.513 30.769 0.00 0.00 45.50 1.82
248 250 3.119673 ACACAAAGCACAATCGTGTTTCA 60.120 39.130 0.00 0.00 44.73 2.69
289 312 7.548780 ACAAATGAGCAAAACACTTACAAACAT 59.451 29.630 0.00 0.00 0.00 2.71
431 476 9.377312 CTAAAACCCAAGAAATTCACAGAAAAA 57.623 29.630 0.00 0.00 0.00 1.94
432 477 8.754080 TCTAAAACCCAAGAAATTCACAGAAAA 58.246 29.630 0.00 0.00 0.00 2.29
437 482 7.654022 AGTTCTAAAACCCAAGAAATTCACA 57.346 32.000 0.00 0.00 35.92 3.58
491 536 8.983702 TTGCTTTTCTTCTAACCCTAAAGTTA 57.016 30.769 0.00 0.00 0.00 2.24
494 539 9.764363 ATTTTTGCTTTTCTTCTAACCCTAAAG 57.236 29.630 0.00 0.00 0.00 1.85
537 582 6.100424 TGGTTATTTGGGTTCCAAGAAAATGT 59.900 34.615 0.00 0.00 44.84 2.71
620 666 6.128580 CCTTCATTTGCTTAATTTTTGTCCCG 60.129 38.462 0.00 0.00 0.00 5.14
631 677 3.621268 CGGTCGATCCTTCATTTGCTTAA 59.379 43.478 0.00 0.00 0.00 1.85
640 686 0.669318 GCAACACGGTCGATCCTTCA 60.669 55.000 0.00 0.00 0.00 3.02
658 704 7.244192 AGAAGCGAGTTACTGAAAATAAATGC 58.756 34.615 0.00 0.00 0.00 3.56
670 716 9.880064 GAAAATAAGAAAAAGAAGCGAGTTACT 57.120 29.630 0.00 0.00 0.00 2.24
758 828 5.201713 TCCCAAATTTTGATGTTTACGCA 57.798 34.783 10.72 0.00 0.00 5.24
760 830 5.117897 CCGTTCCCAAATTTTGATGTTTACG 59.882 40.000 10.72 10.13 0.00 3.18
761 831 5.107259 GCCGTTCCCAAATTTTGATGTTTAC 60.107 40.000 10.72 0.30 0.00 2.01
764 834 3.181461 TGCCGTTCCCAAATTTTGATGTT 60.181 39.130 10.72 0.00 0.00 2.71
777 847 2.426738 TGAATGATTGAATGCCGTTCCC 59.573 45.455 0.00 0.00 35.91 3.97
792 862 9.958234 TTATTTTCTGTTTTTCACGATGAATGA 57.042 25.926 0.00 0.00 36.11 2.57
847 1613 1.153997 GACGGAGAGAGACGGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
850 1616 0.253610 AGATGACGGAGAGAGACGGT 59.746 55.000 0.00 0.00 0.00 4.83
853 1619 2.793237 GCGAAAGATGACGGAGAGAGAC 60.793 54.545 0.00 0.00 0.00 3.36
894 1674 1.347707 GTGTGGGGTCAATCTGTCAGA 59.652 52.381 4.68 4.68 0.00 3.27
1017 1819 1.076192 GGCGAGGAGGTAGAAGGGA 60.076 63.158 0.00 0.00 0.00 4.20
1086 1888 2.126031 GAGAAGGCGACGGTGGTC 60.126 66.667 0.00 0.00 39.89 4.02
1227 2029 2.537143 GAGGTGGAGAAGGAGGTGTTA 58.463 52.381 0.00 0.00 0.00 2.41
1231 2033 0.494095 AAGGAGGTGGAGAAGGAGGT 59.506 55.000 0.00 0.00 0.00 3.85
2007 2811 0.606401 CACCACTGCCAACCACTAGG 60.606 60.000 0.00 0.00 42.21 3.02
2217 3021 2.229543 GCTGCCATTTGACATGAACTCA 59.770 45.455 0.00 0.00 0.00 3.41
2285 3089 2.347490 GCCGAGCCCAGTTGAGAA 59.653 61.111 0.00 0.00 0.00 2.87
2304 3108 0.673333 TGCCGACTGCCACATTGTAG 60.673 55.000 0.00 0.00 40.16 2.74
2469 3273 0.108138 CTAAGGTTGACCGAGGGCTG 60.108 60.000 0.00 0.00 42.08 4.85
2752 3556 4.415881 TCACACAGCTCAAACCTAGAAA 57.584 40.909 0.00 0.00 0.00 2.52
2878 3682 6.608405 TCAAGATCCATAGGTGCATTTGAAAT 59.392 34.615 0.00 0.00 0.00 2.17
3059 3863 7.442364 GGACTAGAACATAATTGAGCAGCAATA 59.558 37.037 0.00 0.00 46.25 1.90
3166 3970 8.862325 AATCATCCACAATACTAACTGACAAA 57.138 30.769 0.00 0.00 0.00 2.83
3193 3997 2.093973 CCGAACACAGCCTTAGTCTCAT 60.094 50.000 0.00 0.00 0.00 2.90
3199 4003 1.398390 GATTGCCGAACACAGCCTTAG 59.602 52.381 0.00 0.00 0.00 2.18
3200 4004 1.448985 GATTGCCGAACACAGCCTTA 58.551 50.000 0.00 0.00 0.00 2.69
3201 4005 1.577328 CGATTGCCGAACACAGCCTT 61.577 55.000 0.00 0.00 41.76 4.35
3202 4006 2.034879 CGATTGCCGAACACAGCCT 61.035 57.895 0.00 0.00 41.76 4.58
3203 4007 2.480555 CGATTGCCGAACACAGCC 59.519 61.111 0.00 0.00 41.76 4.85
3204 4008 2.202349 GCGATTGCCGAACACAGC 60.202 61.111 0.00 0.00 41.76 4.40
3214 4018 3.577313 GAAGGAGCGGGCGATTGC 61.577 66.667 0.00 0.00 41.71 3.56
3215 4019 1.502163 GATGAAGGAGCGGGCGATTG 61.502 60.000 0.00 0.00 0.00 2.67
3216 4020 1.227674 GATGAAGGAGCGGGCGATT 60.228 57.895 0.00 0.00 0.00 3.34
3217 4021 2.374830 CTGATGAAGGAGCGGGCGAT 62.375 60.000 0.00 0.00 0.00 4.58
3218 4022 3.074369 TGATGAAGGAGCGGGCGA 61.074 61.111 0.00 0.00 0.00 5.54
3219 4023 2.587194 CTGATGAAGGAGCGGGCG 60.587 66.667 0.00 0.00 0.00 6.13
3227 4031 1.445095 CTCCGCTCCCTGATGAAGG 59.555 63.158 0.00 0.00 46.94 3.46
3228 4032 1.227497 GCTCCGCTCCCTGATGAAG 60.227 63.158 0.00 0.00 0.00 3.02
3229 4033 2.903357 GCTCCGCTCCCTGATGAA 59.097 61.111 0.00 0.00 0.00 2.57
3230 4034 3.531207 CGCTCCGCTCCCTGATGA 61.531 66.667 0.00 0.00 0.00 2.92
3245 4049 4.977126 ATACGTAGCTCCGCGCGC 62.977 66.667 27.36 23.91 45.59 6.86
3246 4050 2.353145 AATACGTAGCTCCGCGCG 60.353 61.111 25.67 25.67 45.59 6.86
3247 4051 2.300787 CCAATACGTAGCTCCGCGC 61.301 63.158 0.00 0.00 39.57 6.86
3248 4052 2.300787 GCCAATACGTAGCTCCGCG 61.301 63.158 0.00 0.00 0.00 6.46
3249 4053 1.954651 GGCCAATACGTAGCTCCGC 60.955 63.158 0.00 0.00 0.00 5.54
3250 4054 1.660575 CGGCCAATACGTAGCTCCG 60.661 63.158 2.24 7.60 0.00 4.63
3251 4055 1.954651 GCGGCCAATACGTAGCTCC 60.955 63.158 2.24 0.00 0.00 4.70
3252 4056 0.940047 GAGCGGCCAATACGTAGCTC 60.940 60.000 14.16 14.16 43.11 4.09
3253 4057 1.067582 GAGCGGCCAATACGTAGCT 59.932 57.895 2.24 2.67 37.69 3.32
3254 4058 1.954651 GGAGCGGCCAATACGTAGC 60.955 63.158 2.24 0.00 36.34 3.58
3255 4059 1.300697 GGGAGCGGCCAATACGTAG 60.301 63.158 2.24 0.00 38.95 3.51
3256 4060 2.799452 GGGGAGCGGCCAATACGTA 61.799 63.158 2.24 0.00 38.95 3.57
3257 4061 4.171103 GGGGAGCGGCCAATACGT 62.171 66.667 2.24 0.00 38.95 3.57
3258 4062 3.690685 TTGGGGAGCGGCCAATACG 62.691 63.158 2.24 0.00 38.95 3.06
3259 4063 0.755327 ATTTGGGGAGCGGCCAATAC 60.755 55.000 2.24 0.00 38.95 1.89
3260 4064 0.032615 AATTTGGGGAGCGGCCAATA 60.033 50.000 2.24 0.00 38.95 1.90
3261 4065 0.909133 AAATTTGGGGAGCGGCCAAT 60.909 50.000 2.24 0.00 38.95 3.16
3262 4066 1.535202 AAATTTGGGGAGCGGCCAA 60.535 52.632 2.24 0.00 38.95 4.52
3263 4067 1.981853 GAAATTTGGGGAGCGGCCA 60.982 57.895 2.24 0.00 38.95 5.36
3264 4068 0.395173 TAGAAATTTGGGGAGCGGCC 60.395 55.000 0.00 0.00 0.00 6.13
3265 4069 0.738975 GTAGAAATTTGGGGAGCGGC 59.261 55.000 0.00 0.00 0.00 6.53
3266 4070 2.017049 CAGTAGAAATTTGGGGAGCGG 58.983 52.381 0.00 0.00 0.00 5.52
3267 4071 2.985896 TCAGTAGAAATTTGGGGAGCG 58.014 47.619 0.00 0.00 0.00 5.03
3268 4072 4.440663 GCATTCAGTAGAAATTTGGGGAGC 60.441 45.833 0.00 0.00 37.29 4.70
3269 4073 4.098501 GGCATTCAGTAGAAATTTGGGGAG 59.901 45.833 0.00 0.00 37.29 4.30
3270 4074 4.023291 GGCATTCAGTAGAAATTTGGGGA 58.977 43.478 0.00 0.00 37.29 4.81
3271 4075 3.768757 TGGCATTCAGTAGAAATTTGGGG 59.231 43.478 0.00 0.00 37.29 4.96
3272 4076 4.463891 AGTGGCATTCAGTAGAAATTTGGG 59.536 41.667 0.00 0.00 37.29 4.12
3273 4077 5.393461 GGAGTGGCATTCAGTAGAAATTTGG 60.393 44.000 12.30 0.00 37.29 3.28
3274 4078 5.644644 GGAGTGGCATTCAGTAGAAATTTG 58.355 41.667 12.30 0.00 37.29 2.32
3275 4079 4.396166 CGGAGTGGCATTCAGTAGAAATTT 59.604 41.667 12.30 0.00 37.29 1.82
3276 4080 3.941483 CGGAGTGGCATTCAGTAGAAATT 59.059 43.478 12.30 0.00 37.29 1.82
3277 4081 3.535561 CGGAGTGGCATTCAGTAGAAAT 58.464 45.455 12.30 0.00 37.29 2.17
3278 4082 2.935238 GCGGAGTGGCATTCAGTAGAAA 60.935 50.000 12.30 0.00 37.29 2.52
3279 4083 1.405526 GCGGAGTGGCATTCAGTAGAA 60.406 52.381 12.30 0.00 38.31 2.10
3280 4084 0.175760 GCGGAGTGGCATTCAGTAGA 59.824 55.000 12.30 0.00 0.00 2.59
3281 4085 0.176680 AGCGGAGTGGCATTCAGTAG 59.823 55.000 12.30 1.62 34.64 2.57
3282 4086 0.175760 GAGCGGAGTGGCATTCAGTA 59.824 55.000 12.30 0.00 34.64 2.74
3283 4087 1.078848 GAGCGGAGTGGCATTCAGT 60.079 57.895 12.30 0.00 34.64 3.41
3284 4088 1.817099 GGAGCGGAGTGGCATTCAG 60.817 63.158 12.30 9.01 34.64 3.02
3285 4089 2.268920 GGAGCGGAGTGGCATTCA 59.731 61.111 12.30 0.00 34.64 2.57
3286 4090 2.892425 CGGAGCGGAGTGGCATTC 60.892 66.667 0.66 0.66 34.64 2.67
3287 4091 3.706373 ACGGAGCGGAGTGGCATT 61.706 61.111 0.00 0.00 34.64 3.56
3288 4092 4.457496 CACGGAGCGGAGTGGCAT 62.457 66.667 0.00 0.00 34.93 4.40
3300 4104 1.776662 CTCCATAACTCCTCCACGGA 58.223 55.000 0.00 0.00 40.30 4.69
3301 4105 0.105039 GCTCCATAACTCCTCCACGG 59.895 60.000 0.00 0.00 0.00 4.94
3302 4106 0.249073 CGCTCCATAACTCCTCCACG 60.249 60.000 0.00 0.00 0.00 4.94
3303 4107 0.105039 CCGCTCCATAACTCCTCCAC 59.895 60.000 0.00 0.00 0.00 4.02
3304 4108 0.032515 TCCGCTCCATAACTCCTCCA 60.033 55.000 0.00 0.00 0.00 3.86
3305 4109 0.676736 CTCCGCTCCATAACTCCTCC 59.323 60.000 0.00 0.00 0.00 4.30
3306 4110 0.676736 CCTCCGCTCCATAACTCCTC 59.323 60.000 0.00 0.00 0.00 3.71
3307 4111 0.760945 CCCTCCGCTCCATAACTCCT 60.761 60.000 0.00 0.00 0.00 3.69
3308 4112 0.759436 TCCCTCCGCTCCATAACTCC 60.759 60.000 0.00 0.00 0.00 3.85
3309 4113 1.343069 ATCCCTCCGCTCCATAACTC 58.657 55.000 0.00 0.00 0.00 3.01
3310 4114 1.694696 GAATCCCTCCGCTCCATAACT 59.305 52.381 0.00 0.00 0.00 2.24
3311 4115 1.416401 TGAATCCCTCCGCTCCATAAC 59.584 52.381 0.00 0.00 0.00 1.89
3312 4116 1.694150 CTGAATCCCTCCGCTCCATAA 59.306 52.381 0.00 0.00 0.00 1.90
3313 4117 1.342074 CTGAATCCCTCCGCTCCATA 58.658 55.000 0.00 0.00 0.00 2.74
3314 4118 2.049627 GCTGAATCCCTCCGCTCCAT 62.050 60.000 0.00 0.00 31.90 3.41
3315 4119 2.735772 GCTGAATCCCTCCGCTCCA 61.736 63.158 0.00 0.00 31.90 3.86
3316 4120 2.110006 GCTGAATCCCTCCGCTCC 59.890 66.667 0.00 0.00 31.90 4.70
3317 4121 1.115930 TAGGCTGAATCCCTCCGCTC 61.116 60.000 0.00 0.00 34.84 5.03
3318 4122 0.691078 TTAGGCTGAATCCCTCCGCT 60.691 55.000 0.00 0.00 34.84 5.52
3319 4123 0.250081 CTTAGGCTGAATCCCTCCGC 60.250 60.000 0.00 0.00 33.88 5.54
3320 4124 1.123928 ACTTAGGCTGAATCCCTCCG 58.876 55.000 0.00 0.00 33.88 4.63
3321 4125 1.840635 ACACTTAGGCTGAATCCCTCC 59.159 52.381 0.00 0.00 33.88 4.30
3322 4126 2.158885 GGACACTTAGGCTGAATCCCTC 60.159 54.545 0.00 0.00 33.88 4.30
3323 4127 1.840635 GGACACTTAGGCTGAATCCCT 59.159 52.381 0.00 0.00 36.47 4.20
3324 4128 1.134068 GGGACACTTAGGCTGAATCCC 60.134 57.143 0.00 2.06 37.74 3.85
3325 4129 1.840635 AGGGACACTTAGGCTGAATCC 59.159 52.381 0.00 0.00 0.00 3.01
3326 4130 2.501723 TCAGGGACACTTAGGCTGAATC 59.498 50.000 0.00 0.00 0.00 2.52
3327 4131 2.503356 CTCAGGGACACTTAGGCTGAAT 59.497 50.000 0.00 0.00 0.00 2.57
3328 4132 1.902508 CTCAGGGACACTTAGGCTGAA 59.097 52.381 0.00 0.00 0.00 3.02
3329 4133 1.561643 CTCAGGGACACTTAGGCTGA 58.438 55.000 0.00 0.00 0.00 4.26
3330 4134 0.539051 CCTCAGGGACACTTAGGCTG 59.461 60.000 0.00 0.00 33.99 4.85
3331 4135 0.117340 ACCTCAGGGACACTTAGGCT 59.883 55.000 4.75 0.00 43.20 4.58
3332 4136 0.984995 AACCTCAGGGACACTTAGGC 59.015 55.000 4.75 0.00 43.20 3.93
3333 4137 2.257207 TCAACCTCAGGGACACTTAGG 58.743 52.381 3.20 3.20 44.65 2.69
3350 4154 3.328931 AGAAGCTGGATCTGTTCCTTCAA 59.671 43.478 6.35 0.00 45.68 2.69
3356 4160 5.466058 CACATATGAGAAGCTGGATCTGTTC 59.534 44.000 10.38 0.00 0.00 3.18
3548 4353 6.634889 TGGGCTCCTGCATGTTATAATATA 57.365 37.500 0.00 0.00 41.91 0.86
3586 4391 7.602517 AATCACAGTATAGAGCAGTTTGTTC 57.397 36.000 0.00 0.00 0.00 3.18
3787 4601 7.170277 TCATGAGTTCTCCATGAAAGAATTCA 58.830 34.615 24.52 24.52 46.67 2.57
3799 4613 4.080695 CCTCTGGAATTCATGAGTTCTCCA 60.081 45.833 24.83 17.63 0.00 3.86
3828 4642 4.513692 CAGTGTATTTTCCACCGAGTTCAA 59.486 41.667 0.00 0.00 33.20 2.69


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

AutoCloner maintained by Alex Coulton.