Multiple sequence alignment - TraesCS1B01G128700

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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 TraesCS1B01G128700 chr1B 100.000 5388 0 0 1 5388 158314089 158308702 0.000000e+00 9950
1 TraesCS1B01G128700 chr1D 97.005 4074 74 11 446 4485 102777900 102773841 0.000000e+00 6804
2 TraesCS1B01G128700 chr1D 88.191 923 46 22 4501 5388 102773856 102772962 0.000000e+00 1042
3 TraesCS1B01G128700 chr1D 95.904 415 15 2 1 413 102778316 102777902 0.000000e+00 671
4 TraesCS1B01G128700 chr1A 96.019 2939 92 19 1 2927 102163804 102166729 0.000000e+00 4756
5 TraesCS1B01G128700 chr1A 91.958 2487 105 28 2918 5388 102168852 102171259 0.000000e+00 3397
6 TraesCS1B01G128700 chr1A 82.488 217 13 12 265 472 102164412 102164612 3.340000e-37 167
7 TraesCS1B01G128700 chr5D 94.531 128 5 1 5159 5286 477298169 477298294 4.260000e-46 196
8 TraesCS1B01G128700 chr5B 78.967 271 34 15 3202 3462 278011328 278011585 4.320000e-36 163
9 TraesCS1B01G128700 chr2D 90.426 94 6 3 3362 3453 543186295 543186387 2.640000e-23 121
10 TraesCS1B01G128700 chr2B 88.298 94 8 3 3362 3453 648070377 648070469 5.710000e-20 110
11 TraesCS1B01G128700 chr7A 88.710 62 5 2 3362 3422 70830399 70830339 2.080000e-09 75


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 TraesCS1B01G128700 chr1B 158308702 158314089 5387 True 9950.0 9950 100.0000 1 5388 1 chr1B.!!$R1 5387
1 TraesCS1B01G128700 chr1D 102772962 102778316 5354 True 2839.0 6804 93.7000 1 5388 3 chr1D.!!$R1 5387
2 TraesCS1B01G128700 chr1A 102168852 102171259 2407 False 3397.0 3397 91.9580 2918 5388 1 chr1A.!!$F1 2470
3 TraesCS1B01G128700 chr1A 102163804 102166729 2925 False 2461.5 4756 89.2535 1 2927 2 chr1A.!!$F2 2926

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
519 522 0.034186 TAGGCAAATGGGGCTGTCAG 60.034 55.0 0.00 0.00 44.27 3.51 F
1062 1070 1.014044 TCTGCTTTCCTGCTAACGCG 61.014 55.0 3.53 3.53 39.65 6.01 F
2100 2125 0.108945 GCAGAGGAAATGCACTTGCC 60.109 55.0 0.00 0.00 43.31 4.52 F
2906 2932 0.242017 GTGTTGCTGAGATGGTTGGC 59.758 55.0 0.00 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2111 0.037975 CCAGTGGCAAGTGCATTTCC 60.038 55.000 5.52 0.0 44.36 3.13 R
2963 2989 0.257328 TGTGCCACCTCACAGGAAAA 59.743 50.000 0.00 0.0 41.57 2.29 R
3103 3129 1.202336 ACAGCTGTTTTCTGTGCAAGC 60.202 47.619 15.25 0.0 42.63 4.01 R
4852 4943 0.381801 GCACACACAACCCAACAGAG 59.618 55.000 0.00 0.0 0.00 3.35 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
94 96 1.662044 CTTTGCTGGTTGGCTGGTC 59.338 57.895 0.00 0.00 0.00 4.02
95 97 0.825010 CTTTGCTGGTTGGCTGGTCT 60.825 55.000 0.00 0.00 0.00 3.85
125 127 2.613133 CGTTCGTTCTTGGGGTTTGTAA 59.387 45.455 0.00 0.00 0.00 2.41
171 173 4.729227 GAGTTTAGCTCTGAGTAGGCTT 57.271 45.455 6.53 0.00 40.98 4.35
379 382 5.512232 GGATTTTGCCCTATGTTTGTTTGGA 60.512 40.000 0.00 0.00 0.00 3.53
464 467 9.529325 GGAGCAAGTTCTGTTTTACTTTTAATT 57.471 29.630 0.00 0.00 32.50 1.40
519 522 0.034186 TAGGCAAATGGGGCTGTCAG 60.034 55.000 0.00 0.00 44.27 3.51
682 685 2.128035 GTATTTCTGCTATCGCGCTGT 58.872 47.619 5.56 0.00 39.65 4.40
773 780 5.858581 CAGCATTAGCAGGTTTTGAGTTAAC 59.141 40.000 0.00 0.00 45.49 2.01
871 878 7.253917 CGATGCTAATAGATGATTCGGAATGTC 60.254 40.741 8.18 6.31 0.00 3.06
929 936 7.408756 TCAGAAGCCATTTTGCTAATTATGT 57.591 32.000 0.00 0.00 41.80 2.29
1008 1016 2.877168 GTGACTGCATTCCATGGATCTC 59.123 50.000 17.06 6.19 0.00 2.75
1062 1070 1.014044 TCTGCTTTCCTGCTAACGCG 61.014 55.000 3.53 3.53 39.65 6.01
1155 1163 5.106197 TGCTGGTTGAGTTGCATAGTTAATG 60.106 40.000 0.00 0.00 38.74 1.90
1185 1193 5.784177 TGTGTCACCTGACTTTATTCTCTC 58.216 41.667 6.97 0.00 44.99 3.20
1274 1282 7.827701 TCAAGATCTACACTACTTGGTTAGTG 58.172 38.462 8.43 8.43 46.59 2.74
1447 1462 1.303282 GTGGCCCTTACCCTTCAGG 59.697 63.158 0.00 0.00 43.78 3.86
1818 1836 5.585047 GGAACTATGGTACCTGCTAAACTTG 59.415 44.000 14.36 0.00 0.00 3.16
1847 1865 2.299013 TCTACAGGTATGCCTAATGCCG 59.701 50.000 0.43 0.00 45.31 5.69
2100 2125 0.108945 GCAGAGGAAATGCACTTGCC 60.109 55.000 0.00 0.00 43.31 4.52
2438 2464 0.464036 TTGAGTTCAGTGTGTCGGCT 59.536 50.000 0.00 0.00 0.00 5.52
2516 2542 2.820059 TCCTATACATCAAGGCTGCG 57.180 50.000 0.00 0.00 32.55 5.18
2773 2799 4.798387 CAGTTTTTCTGTTCTTTTCGGTGG 59.202 41.667 0.00 0.00 39.17 4.61
2906 2932 0.242017 GTGTTGCTGAGATGGTTGGC 59.758 55.000 0.00 0.00 0.00 4.52
2951 2977 3.523157 TGGACTTTTGGAGCATGGATAGA 59.477 43.478 0.00 0.00 0.00 1.98
2963 2989 3.435601 GCATGGATAGATGGGTTGGAAGT 60.436 47.826 0.00 0.00 0.00 3.01
3095 3121 3.046390 GGCACGTTTCTGAGATATCTCG 58.954 50.000 24.27 19.01 45.72 4.04
3103 3129 6.141527 CGTTTCTGAGATATCTCGCTAGTTTG 59.858 42.308 24.27 9.06 45.72 2.93
3174 3212 4.334203 TGTCTGTACATGTTTGTGTTGGTC 59.666 41.667 2.30 0.00 36.53 4.02
3175 3213 4.574828 GTCTGTACATGTTTGTGTTGGTCT 59.425 41.667 2.30 0.00 36.53 3.85
3176 3214 5.756347 GTCTGTACATGTTTGTGTTGGTCTA 59.244 40.000 2.30 0.00 36.53 2.59
3177 3215 6.259167 GTCTGTACATGTTTGTGTTGGTCTAA 59.741 38.462 2.30 0.00 36.53 2.10
3178 3216 6.995686 TCTGTACATGTTTGTGTTGGTCTAAT 59.004 34.615 2.30 0.00 36.53 1.73
3179 3217 6.964908 TGTACATGTTTGTGTTGGTCTAATG 58.035 36.000 2.30 0.00 36.53 1.90
3180 3218 6.544197 TGTACATGTTTGTGTTGGTCTAATGT 59.456 34.615 2.30 0.00 36.53 2.71
3181 3219 7.715686 TGTACATGTTTGTGTTGGTCTAATGTA 59.284 33.333 2.30 0.00 36.53 2.29
3182 3220 6.966021 ACATGTTTGTGTTGGTCTAATGTAC 58.034 36.000 0.00 0.00 33.85 2.90
3183 3221 6.544197 ACATGTTTGTGTTGGTCTAATGTACA 59.456 34.615 0.00 0.00 33.85 2.90
3184 3222 6.612247 TGTTTGTGTTGGTCTAATGTACAG 57.388 37.500 0.33 0.00 0.00 2.74
3185 3223 6.116806 TGTTTGTGTTGGTCTAATGTACAGT 58.883 36.000 0.33 0.07 0.00 3.55
3218 3256 0.459078 GCTACTCCCTCCGTACCAAC 59.541 60.000 0.00 0.00 0.00 3.77
3374 3412 8.909708 AATTCGGTGTTGTAAATGTTGATATG 57.090 30.769 0.00 0.00 0.00 1.78
3460 3499 1.374572 TGGAACGGAGGGGGTATTTT 58.625 50.000 0.00 0.00 0.00 1.82
3461 3500 2.560080 TGGAACGGAGGGGGTATTTTA 58.440 47.619 0.00 0.00 0.00 1.52
3475 3514 4.449131 GGTATTTTAGTACTGACCCTGCC 58.551 47.826 5.39 0.00 0.00 4.85
3542 3581 6.814506 ATCAATATGACTGGATAGCTTTGC 57.185 37.500 0.00 0.00 0.00 3.68
3583 3636 4.577693 TCATCAATGACTGGATAGCTTTGC 59.422 41.667 0.00 0.00 0.00 3.68
3598 3651 1.344114 CTTTGCTTTAAGCTTGGGGCA 59.656 47.619 18.20 12.99 42.97 5.36
3642 3695 0.616111 ATCTCACTCGGCAACCTCCT 60.616 55.000 0.00 0.00 0.00 3.69
3738 3791 3.380637 GGATGTCTGCTTGATTGCTTCAT 59.619 43.478 0.00 0.00 33.34 2.57
3740 3793 3.151554 TGTCTGCTTGATTGCTTCATGT 58.848 40.909 0.00 0.00 33.34 3.21
3908 3961 3.034635 AGAATTATCAGGGAGACGCACT 58.965 45.455 0.00 0.00 0.00 4.40
4191 4244 2.732412 TCGAAAGCACCTGAAGAGAG 57.268 50.000 0.00 0.00 0.00 3.20
4379 4435 0.179000 GCTGGTCCCGATGAAGATGT 59.821 55.000 0.00 0.00 0.00 3.06
4401 4457 9.750125 GATGTCCAACTAAAAGATTCAAAAACT 57.250 29.630 0.00 0.00 0.00 2.66
4447 4503 2.166664 GTCTTGCTCGTTGATAGGAGGT 59.833 50.000 0.00 0.00 36.90 3.85
4488 4545 1.349688 TGCTTGATAACCGTGGGAGTT 59.650 47.619 0.00 0.00 0.00 3.01
4569 4628 1.836166 CAGGGAGAGAGGCTTTCATGA 59.164 52.381 7.87 0.00 0.00 3.07
4570 4629 2.438763 CAGGGAGAGAGGCTTTCATGAT 59.561 50.000 7.87 0.00 0.00 2.45
4571 4630 3.117963 CAGGGAGAGAGGCTTTCATGATT 60.118 47.826 7.87 0.00 0.00 2.57
4572 4631 3.526841 AGGGAGAGAGGCTTTCATGATTT 59.473 43.478 7.87 0.00 0.00 2.17
4573 4632 4.017683 AGGGAGAGAGGCTTTCATGATTTT 60.018 41.667 7.87 0.00 0.00 1.82
4574 4633 4.337836 GGGAGAGAGGCTTTCATGATTTTC 59.662 45.833 7.87 0.00 0.00 2.29
4575 4634 4.946157 GGAGAGAGGCTTTCATGATTTTCA 59.054 41.667 7.87 0.00 0.00 2.69
4612 4671 1.568504 TTGGGCCTACAGTCTACCAG 58.431 55.000 4.53 0.00 0.00 4.00
4637 4696 4.641989 TCTCTGGAAAGGAATTATGCAAGC 59.358 41.667 0.00 0.00 0.00 4.01
4675 4734 2.380084 ACGTCTTGGTAACGATGCAT 57.620 45.000 0.00 0.00 42.62 3.96
4714 4773 8.747666 GCTCGTTTGTTGTGTTAAATTAAATGA 58.252 29.630 0.00 0.00 0.00 2.57
4772 4857 6.664428 TGAGGTTTTTCCCAGGAAATTTAG 57.336 37.500 12.50 0.00 42.71 1.85
4785 4870 9.025041 CCCAGGAAATTTAGTTCAACTTTATCT 57.975 33.333 0.00 0.00 0.00 1.98
4796 4881 7.645402 AGTTCAACTTTATCTAACCCGTTTTG 58.355 34.615 0.00 0.00 0.00 2.44
4808 4893 3.999046 ACCCGTTTTGTCTACTCGATTT 58.001 40.909 0.00 0.00 0.00 2.17
4840 4931 6.552445 ATCTACTTCAGTATGCATATCCCC 57.448 41.667 10.16 0.00 34.76 4.81
4841 4932 5.655394 TCTACTTCAGTATGCATATCCCCT 58.345 41.667 10.16 0.00 34.76 4.79
4842 4933 4.630644 ACTTCAGTATGCATATCCCCTG 57.369 45.455 10.16 12.10 34.76 4.45
4843 4934 4.234550 ACTTCAGTATGCATATCCCCTGA 58.765 43.478 16.66 16.66 34.76 3.86
4844 4935 4.848660 ACTTCAGTATGCATATCCCCTGAT 59.151 41.667 19.67 8.28 34.76 2.90
4845 4936 5.046014 ACTTCAGTATGCATATCCCCTGATC 60.046 44.000 19.67 2.29 34.76 2.92
4846 4937 3.776969 TCAGTATGCATATCCCCTGATCC 59.223 47.826 16.66 0.00 34.76 3.36
4847 4938 3.779183 CAGTATGCATATCCCCTGATCCT 59.221 47.826 10.16 0.00 32.18 3.24
4848 4939 4.226846 CAGTATGCATATCCCCTGATCCTT 59.773 45.833 10.16 0.00 32.18 3.36
4849 4940 3.733883 ATGCATATCCCCTGATCCTTG 57.266 47.619 0.00 0.00 32.18 3.61
4850 4941 2.705148 TGCATATCCCCTGATCCTTGA 58.295 47.619 0.00 0.00 32.18 3.02
4851 4942 3.055328 TGCATATCCCCTGATCCTTGAA 58.945 45.455 0.00 0.00 32.18 2.69
4852 4943 3.181440 TGCATATCCCCTGATCCTTGAAC 60.181 47.826 0.00 0.00 32.18 3.18
4902 4993 3.218453 GGAGCTAGCTGTCAGTGAGATA 58.782 50.000 24.99 0.00 0.00 1.98
4970 5061 4.466370 TGCATGCTCTAGTAAGGTAGTGTT 59.534 41.667 20.33 0.00 0.00 3.32
4972 5063 6.183360 TGCATGCTCTAGTAAGGTAGTGTTAG 60.183 42.308 20.33 0.00 0.00 2.34
5089 5180 2.613691 GCATCTGGCAGGTTTTCATTG 58.386 47.619 15.73 0.00 43.97 2.82
5224 5316 2.957474 AGCACCAATTACCAAACCTGT 58.043 42.857 0.00 0.00 0.00 4.00
5225 5317 2.627699 AGCACCAATTACCAAACCTGTG 59.372 45.455 0.00 0.00 0.00 3.66
5246 5338 0.825425 TTCCCATTTGCAGGCACGAA 60.825 50.000 0.00 0.00 0.00 3.85
5247 5339 1.080569 CCCATTTGCAGGCACGAAC 60.081 57.895 0.00 0.00 0.00 3.95
5248 5340 1.659233 CCATTTGCAGGCACGAACA 59.341 52.632 0.00 0.00 0.00 3.18
5289 5389 4.096532 TGCTAACGAACTGGACTGAGATAG 59.903 45.833 0.00 0.00 0.00 2.08
5290 5390 4.335874 GCTAACGAACTGGACTGAGATAGA 59.664 45.833 0.00 0.00 0.00 1.98
5291 5391 5.009210 GCTAACGAACTGGACTGAGATAGAT 59.991 44.000 0.00 0.00 0.00 1.98
5292 5392 4.909696 ACGAACTGGACTGAGATAGATG 57.090 45.455 0.00 0.00 0.00 2.90
5322 5422 2.514592 ATCCATCCGGCAAGCACG 60.515 61.111 0.00 0.00 0.00 5.34
5363 5465 4.612033 GCGACGTTGCTTTACAGGTTAATT 60.612 41.667 20.81 0.00 0.00 1.40
5364 5466 5.445845 CGACGTTGCTTTACAGGTTAATTT 58.554 37.500 0.00 0.00 0.00 1.82
5367 5469 7.424452 CGACGTTGCTTTACAGGTTAATTTATC 59.576 37.037 0.00 0.00 0.00 1.75
5368 5470 7.238571 ACGTTGCTTTACAGGTTAATTTATCG 58.761 34.615 0.00 0.00 0.00 2.92
5369 5471 6.685403 CGTTGCTTTACAGGTTAATTTATCGG 59.315 38.462 0.00 0.00 0.00 4.18
5371 5475 6.181908 TGCTTTACAGGTTAATTTATCGGGT 58.818 36.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 2.019897 GCCAACCAGCAAAGCACAGT 62.020 55.000 0.00 0.00 0.00 3.55
94 96 0.723414 AGAACGAACGCATGCATCAG 59.277 50.000 19.57 13.04 0.00 2.90
95 97 1.136000 CAAGAACGAACGCATGCATCA 60.136 47.619 19.57 0.00 0.00 3.07
125 127 3.203040 CACACCCCCATTTCCTCTATTCT 59.797 47.826 0.00 0.00 0.00 2.40
171 173 6.830912 AGCTAAACCACATGCTATCAATCTA 58.169 36.000 0.00 0.00 33.64 1.98
379 382 5.222048 TGGGAAACAAGTGAAAGGCTATACT 60.222 40.000 0.00 0.00 0.00 2.12
519 522 7.545265 TCAGCTATGAATTGGTAATTGCAAAAC 59.455 33.333 1.71 4.88 30.61 2.43
552 555 2.019897 GCCAACCAGCAAAGCACACT 62.020 55.000 0.00 0.00 0.00 3.55
682 685 1.638529 CATAGGCACAACCCCCAAAA 58.361 50.000 0.00 0.00 40.58 2.44
822 829 7.087639 TCGCTTGGTAATAAAAATTGACCTTG 58.912 34.615 0.00 0.00 0.00 3.61
871 878 0.039256 CCATGCAACCAACAGTTCCG 60.039 55.000 0.00 0.00 36.18 4.30
929 936 5.077134 ACATCTCACGATCAGTTCATCAA 57.923 39.130 0.00 0.00 0.00 2.57
1008 1016 0.037882 TGAGCTCAGAGTTTGCCTCG 60.038 55.000 13.74 0.00 45.44 4.63
1062 1070 5.711036 ACCATATGGAGTCGGATAGTAAGTC 59.289 44.000 28.77 0.00 38.94 3.01
1447 1462 3.188048 GCCATCAGCTATAGCACAATGTC 59.812 47.826 26.07 12.22 45.16 3.06
1818 1836 0.249489 CATACCTGTAGAGCACGGCC 60.249 60.000 0.00 0.00 31.51 6.13
1840 1858 4.757657 ACAATTACAAGTGTGACGGCATTA 59.242 37.500 0.00 0.00 35.69 1.90
1847 1865 8.015658 GGATAACTCAACAATTACAAGTGTGAC 58.984 37.037 0.00 0.00 37.29 3.67
2086 2111 0.037975 CCAGTGGCAAGTGCATTTCC 60.038 55.000 5.52 0.00 44.36 3.13
2098 2123 2.428171 ACAAATACATGCATCCAGTGGC 59.572 45.455 3.51 0.00 0.00 5.01
2100 2125 5.585844 TGAGTACAAATACATGCATCCAGTG 59.414 40.000 0.00 0.00 33.30 3.66
2438 2464 8.057536 TGGCTGTTTTTCTTTACTTAAGTTCA 57.942 30.769 14.49 0.00 35.28 3.18
2516 2542 1.494721 TCCCCTCTGGATTGCCAATAC 59.505 52.381 0.00 0.00 45.41 1.89
2568 2594 1.080705 CACCACCTCGAAGTCGTCC 60.081 63.158 0.00 0.00 40.80 4.79
2773 2799 9.524106 GCCATACACCTTAAATTAACATAAACC 57.476 33.333 0.00 0.00 0.00 3.27
2963 2989 0.257328 TGTGCCACCTCACAGGAAAA 59.743 50.000 0.00 0.00 41.57 2.29
3002 3028 3.126858 GCAAGATACATTTCAAGGCGACA 59.873 43.478 0.00 0.00 0.00 4.35
3095 3121 3.354089 TTTCTGTGCAAGCAAACTAGC 57.646 42.857 0.00 0.00 0.00 3.42
3103 3129 1.202336 ACAGCTGTTTTCTGTGCAAGC 60.202 47.619 15.25 0.00 42.63 4.01
3174 3212 7.515059 GCAAGCAAACAACAAACTGTACATTAG 60.515 37.037 0.00 0.00 0.00 1.73
3175 3213 6.254589 GCAAGCAAACAACAAACTGTACATTA 59.745 34.615 0.00 0.00 0.00 1.90
3176 3214 5.063312 GCAAGCAAACAACAAACTGTACATT 59.937 36.000 0.00 0.00 0.00 2.71
3177 3215 4.566360 GCAAGCAAACAACAAACTGTACAT 59.434 37.500 0.00 0.00 0.00 2.29
3178 3216 3.923461 GCAAGCAAACAACAAACTGTACA 59.077 39.130 0.00 0.00 0.00 2.90
3179 3217 4.173256 AGCAAGCAAACAACAAACTGTAC 58.827 39.130 0.00 0.00 0.00 2.90
3180 3218 4.448537 AGCAAGCAAACAACAAACTGTA 57.551 36.364 0.00 0.00 0.00 2.74
3181 3219 3.317603 AGCAAGCAAACAACAAACTGT 57.682 38.095 0.00 0.00 0.00 3.55
3182 3220 4.423732 AGTAGCAAGCAAACAACAAACTG 58.576 39.130 0.00 0.00 0.00 3.16
3183 3221 4.440112 GGAGTAGCAAGCAAACAACAAACT 60.440 41.667 0.00 0.00 0.00 2.66
3184 3222 3.796717 GGAGTAGCAAGCAAACAACAAAC 59.203 43.478 0.00 0.00 0.00 2.93
3185 3223 3.181480 GGGAGTAGCAAGCAAACAACAAA 60.181 43.478 0.00 0.00 0.00 2.83
3329 3367 9.173939 CCGAATTTGCTTCATTAGATTCATTAC 57.826 33.333 0.00 0.00 33.10 1.89
3460 3499 2.056223 GCGGGCAGGGTCAGTACTA 61.056 63.158 0.00 0.00 0.00 1.82
3461 3500 3.391382 GCGGGCAGGGTCAGTACT 61.391 66.667 0.00 0.00 0.00 2.73
3475 3514 1.587946 GTTTGTTTGTGAAAGCAGCGG 59.412 47.619 0.00 0.00 0.00 5.52
3542 3581 6.688637 TGATGATAACAGCATCCAAAGAAG 57.311 37.500 2.27 0.00 41.05 2.85
3583 3636 5.859205 AAAGATATGCCCCAAGCTTAAAG 57.141 39.130 0.00 0.00 44.23 1.85
3598 3651 7.125391 TCAAGGGAAATGGCAGTAAAAGATAT 58.875 34.615 0.00 0.00 0.00 1.63
3642 3695 5.063204 AGTGTATCTGCAAGTAAAACAGCA 58.937 37.500 0.00 0.00 33.76 4.41
3738 3791 2.935238 GCTTCTTCCGCCTCATACAACA 60.935 50.000 0.00 0.00 0.00 3.33
3740 3793 1.277842 TGCTTCTTCCGCCTCATACAA 59.722 47.619 0.00 0.00 0.00 2.41
3908 3961 2.124736 GCCGTTGCCTGCCAGATA 60.125 61.111 0.00 0.00 0.00 1.98
4191 4244 4.762251 AGGCATTCTTAACTTCAGTTGGAC 59.238 41.667 2.26 0.00 38.90 4.02
4379 4435 9.594478 GGAAAGTTTTTGAATCTTTTAGTTGGA 57.406 29.630 0.00 0.00 32.59 3.53
4401 4457 1.139058 GCTCCGGCTGATAAGAGGAAA 59.861 52.381 0.00 0.00 35.22 3.13
4447 4503 4.708177 CAAGTCAGAACCCAAAAGAGAGA 58.292 43.478 0.00 0.00 0.00 3.10
4488 4545 7.977853 CCCTACTTATTAAGCTGAAGAACGTTA 59.022 37.037 0.00 0.00 0.00 3.18
4612 4671 4.202441 TGCATAATTCCTTTCCAGAGAGC 58.798 43.478 0.00 0.00 0.00 4.09
4628 4687 1.452110 ACGCATCACTGCTTGCATAA 58.548 45.000 0.00 0.00 46.65 1.90
4658 4717 2.030946 GCTCATGCATCGTTACCAAGAC 59.969 50.000 0.00 0.00 39.41 3.01
4738 4797 4.442753 GGGAAAAACCTCAATGAGCAACAA 60.443 41.667 4.40 0.00 38.98 2.83
4772 4857 7.420002 ACAAAACGGGTTAGATAAAGTTGAAC 58.580 34.615 0.00 0.00 0.00 3.18
4785 4870 4.789012 ATCGAGTAGACAAAACGGGTTA 57.211 40.909 0.00 0.00 0.00 2.85
4822 4913 4.897509 TCAGGGGATATGCATACTGAAG 57.102 45.455 17.76 5.32 32.60 3.02
4824 4915 3.776969 GGATCAGGGGATATGCATACTGA 59.223 47.826 20.71 20.71 39.05 3.41
4825 4916 3.779183 AGGATCAGGGGATATGCATACTG 59.221 47.826 8.99 11.70 32.67 2.74
4826 4917 4.085854 AGGATCAGGGGATATGCATACT 57.914 45.455 8.99 0.00 32.67 2.12
4827 4918 4.225942 TCAAGGATCAGGGGATATGCATAC 59.774 45.833 8.99 3.26 32.67 2.39
4829 4920 3.262842 TCAAGGATCAGGGGATATGCAT 58.737 45.455 3.79 3.79 32.67 3.96
4830 4921 2.705148 TCAAGGATCAGGGGATATGCA 58.295 47.619 0.00 0.00 32.67 3.96
4831 4922 3.073650 AGTTCAAGGATCAGGGGATATGC 59.926 47.826 0.00 0.00 32.67 3.14
4832 4923 4.596643 AGAGTTCAAGGATCAGGGGATATG 59.403 45.833 0.00 0.00 32.67 1.78
4833 4924 4.596643 CAGAGTTCAAGGATCAGGGGATAT 59.403 45.833 0.00 0.00 32.67 1.63
4834 4925 3.969976 CAGAGTTCAAGGATCAGGGGATA 59.030 47.826 0.00 0.00 32.67 2.59
4835 4926 2.776536 CAGAGTTCAAGGATCAGGGGAT 59.223 50.000 0.00 0.00 36.13 3.85
4836 4927 2.191400 CAGAGTTCAAGGATCAGGGGA 58.809 52.381 0.00 0.00 0.00 4.81
4837 4928 1.912043 ACAGAGTTCAAGGATCAGGGG 59.088 52.381 0.00 0.00 0.00 4.79
4838 4929 3.341823 CAACAGAGTTCAAGGATCAGGG 58.658 50.000 0.00 0.00 0.00 4.45
4839 4930 3.341823 CCAACAGAGTTCAAGGATCAGG 58.658 50.000 0.00 0.00 0.00 3.86
4840 4931 3.244700 ACCCAACAGAGTTCAAGGATCAG 60.245 47.826 0.00 0.00 0.00 2.90
4841 4932 2.711009 ACCCAACAGAGTTCAAGGATCA 59.289 45.455 0.00 0.00 0.00 2.92
4842 4933 3.425162 ACCCAACAGAGTTCAAGGATC 57.575 47.619 0.00 0.00 0.00 3.36
4843 4934 3.117512 ACAACCCAACAGAGTTCAAGGAT 60.118 43.478 0.00 0.00 0.00 3.24
4844 4935 2.241176 ACAACCCAACAGAGTTCAAGGA 59.759 45.455 0.00 0.00 0.00 3.36
4845 4936 2.358898 CACAACCCAACAGAGTTCAAGG 59.641 50.000 0.00 0.00 0.00 3.61
4846 4937 3.016736 ACACAACCCAACAGAGTTCAAG 58.983 45.455 0.00 0.00 0.00 3.02
4847 4938 2.752354 CACACAACCCAACAGAGTTCAA 59.248 45.455 0.00 0.00 0.00 2.69
4848 4939 2.290641 ACACACAACCCAACAGAGTTCA 60.291 45.455 0.00 0.00 0.00 3.18
4849 4940 2.097466 CACACACAACCCAACAGAGTTC 59.903 50.000 0.00 0.00 0.00 3.01
4850 4941 2.091541 CACACACAACCCAACAGAGTT 58.908 47.619 0.00 0.00 0.00 3.01
4851 4942 1.750193 CACACACAACCCAACAGAGT 58.250 50.000 0.00 0.00 0.00 3.24
4852 4943 0.381801 GCACACACAACCCAACAGAG 59.618 55.000 0.00 0.00 0.00 3.35
4902 4993 3.181412 ACCACCAACCAACCTAATCCAAT 60.181 43.478 0.00 0.00 0.00 3.16
4970 5061 3.778075 TGCATCTTTAGGTTAGGTGGCTA 59.222 43.478 0.00 0.00 0.00 3.93
4972 5063 2.945668 CTGCATCTTTAGGTTAGGTGGC 59.054 50.000 0.00 0.00 0.00 5.01
5124 5215 7.039504 CCAGGTTAAGTAGTAGTACAAGGTTGA 60.040 40.741 10.33 0.00 0.00 3.18
5246 5338 3.067106 CACCTAATGAACGCTCTGTTGT 58.933 45.455 0.00 0.00 42.09 3.32
5247 5339 2.159653 GCACCTAATGAACGCTCTGTTG 60.160 50.000 0.00 0.00 42.09 3.33
5248 5340 2.076863 GCACCTAATGAACGCTCTGTT 58.923 47.619 0.00 0.00 45.61 3.16
5341 5441 4.657075 ATTAACCTGTAAAGCAACGTCG 57.343 40.909 0.00 0.00 0.00 5.12
5363 5465 4.041198 ACAAAGAGAACCTGAACCCGATAA 59.959 41.667 0.00 0.00 0.00 1.75
5364 5466 3.581332 ACAAAGAGAACCTGAACCCGATA 59.419 43.478 0.00 0.00 0.00 2.92
5367 5469 2.256117 ACAAAGAGAACCTGAACCCG 57.744 50.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.