Multiple sequence alignment - TraesCS2A01G297400

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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 TraesCS2A01G297400 chr2A 100.000 6227 0 0 1 6227 511122687 511116461 0.000000e+00 11500.0
1 TraesCS2A01G297400 chr2A 92.437 119 8 1 1966 2084 767958563 767958680 1.070000e-37 169.0
2 TraesCS2A01G297400 chr2D 95.426 5750 171 27 516 6227 377163698 377158003 0.000000e+00 9077.0
3 TraesCS2A01G297400 chr2B 95.291 5713 188 35 512 6179 448879378 448873702 0.000000e+00 8985.0
4 TraesCS2A01G297400 chr2B 79.608 255 30 4 5837 6075 13814050 13813802 4.990000e-36 163.0
5 TraesCS2A01G297400 chr2B 97.917 48 1 0 6180 6227 448873682 448873635 4.000000e-12 84.2
6 TraesCS2A01G297400 chr3B 96.950 918 26 1 3300 4217 1272376 1271461 0.000000e+00 1539.0
7 TraesCS2A01G297400 chr3B 88.377 499 58 0 1 499 687746887 687747385 8.930000e-168 601.0
8 TraesCS2A01G297400 chr3B 87.302 504 64 0 1 504 466641409 466640906 1.510000e-160 577.0
9 TraesCS2A01G297400 chr3B 91.257 183 15 1 1 183 186649902 186650083 1.340000e-61 248.0
10 TraesCS2A01G297400 chr7A 96.875 512 14 1 1 510 395551363 395551874 0.000000e+00 856.0
11 TraesCS2A01G297400 chr7A 80.276 507 94 5 1 504 646100309 646100812 1.640000e-100 377.0
12 TraesCS2A01G297400 chr7A 78.125 352 69 7 1 348 733734103 733733756 3.780000e-52 217.0
13 TraesCS2A01G297400 chr7A 81.048 248 45 2 1 247 733742013 733741767 4.920000e-46 196.0
14 TraesCS2A01G297400 chr5A 93.151 511 32 3 1 510 17718144 17718652 0.000000e+00 747.0
15 TraesCS2A01G297400 chr3A 81.609 435 76 3 72 504 121470861 121471293 2.130000e-94 357.0
16 TraesCS2A01G297400 chr1A 100.000 34 0 0 318 351 555070444 555070477 5.210000e-06 63.9


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 TraesCS2A01G297400 chr2A 511116461 511122687 6226 True 11500.0 11500 100.000 1 6227 1 chr2A.!!$R1 6226
1 TraesCS2A01G297400 chr2D 377158003 377163698 5695 True 9077.0 9077 95.426 516 6227 1 chr2D.!!$R1 5711
2 TraesCS2A01G297400 chr2B 448873635 448879378 5743 True 4534.6 8985 96.604 512 6227 2 chr2B.!!$R2 5715
3 TraesCS2A01G297400 chr3B 1271461 1272376 915 True 1539.0 1539 96.950 3300 4217 1 chr3B.!!$R1 917
4 TraesCS2A01G297400 chr3B 466640906 466641409 503 True 577.0 577 87.302 1 504 1 chr3B.!!$R2 503
5 TraesCS2A01G297400 chr7A 395551363 395551874 511 False 856.0 856 96.875 1 510 1 chr7A.!!$F1 509
6 TraesCS2A01G297400 chr7A 646100309 646100812 503 False 377.0 377 80.276 1 504 1 chr7A.!!$F2 503
7 TraesCS2A01G297400 chr5A 17718144 17718652 508 False 747.0 747 93.151 1 510 1 chr5A.!!$F1 509

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
140 141 0.389817 CACCGCAACGAAGGATCTCA 60.390 55.000 0.00 0.00 0.00 3.27 F
510 515 0.468226 GGGAAGGCCACGATATCACA 59.532 55.000 5.01 0.00 35.15 3.58 F
1302 1314 0.736053 TTCGGTGAGGTTTTGTGCAC 59.264 50.000 10.75 10.75 0.00 4.57 F
1862 1877 1.085091 CTGCAGTTCTCATGCCTGAC 58.915 55.000 5.25 0.00 43.18 3.51 F
2242 2260 1.206610 CTGACACTGGTGCTATCTGCT 59.793 52.381 0.17 0.00 43.37 4.24 F
3344 3376 4.032900 CGTTGGAGGTAATCATTGTCTTCG 59.967 45.833 0.00 0.00 0.00 3.79 F
4432 4478 0.108585 GGAAGAGCTGGTTGGTGTCA 59.891 55.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1554 0.617535 CCCCAAACCCCAAATCTCCC 60.618 60.000 0.00 0.0 0.00 4.30 R
2265 2283 1.402968 AGCAATCCGCATGATCACAAC 59.597 47.619 0.00 0.0 46.13 3.32 R
3135 3167 9.363763 CTATACCACTAATATCTCTGCAACATG 57.636 37.037 0.00 0.0 0.00 3.21 R
3482 3514 3.044986 CTGTGACAATTTCAAGGTTGCG 58.955 45.455 0.00 0.0 35.39 4.85 R
3564 3596 3.128349 GTTCTGTCTGCGACAAGGTTAA 58.872 45.455 11.49 1.6 42.26 2.01 R
4576 4622 1.118356 TTTGCCATCCCGCCAAAGTT 61.118 50.000 0.00 0.0 0.00 2.66 R
6122 6201 0.458260 ACGGGGTTTGTGCTTTGTTC 59.542 50.000 0.00 0.0 0.00 3.18 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
140 141 0.389817 CACCGCAACGAAGGATCTCA 60.390 55.000 0.00 0.00 0.00 3.27
510 515 0.468226 GGGAAGGCCACGATATCACA 59.532 55.000 5.01 0.00 35.15 3.58
511 516 1.072331 GGGAAGGCCACGATATCACAT 59.928 52.381 5.01 0.00 35.15 3.21
512 517 2.301870 GGGAAGGCCACGATATCACATA 59.698 50.000 5.01 0.00 35.15 2.29
513 518 3.244422 GGGAAGGCCACGATATCACATAA 60.244 47.826 5.01 0.00 35.15 1.90
514 519 4.385825 GGAAGGCCACGATATCACATAAA 58.614 43.478 5.01 0.00 0.00 1.40
520 525 3.997021 CCACGATATCACATAAAGCTCCC 59.003 47.826 3.12 0.00 0.00 4.30
534 539 3.959495 AGCTCCCAATTACCACATGAT 57.041 42.857 0.00 0.00 0.00 2.45
583 589 8.412456 CCAAACAAAAATAAAGCTCCCAATTTT 58.588 29.630 0.00 0.00 34.00 1.82
584 590 9.235537 CAAACAAAAATAAAGCTCCCAATTTTG 57.764 29.630 16.54 16.54 40.35 2.44
589 595 7.910441 AAATAAAGCTCCCAATTTTGTGATG 57.090 32.000 0.00 0.00 0.00 3.07
590 596 4.961438 AAAGCTCCCAATTTTGTGATGT 57.039 36.364 0.00 0.00 0.00 3.06
593 599 6.418057 AAGCTCCCAATTTTGTGATGTTTA 57.582 33.333 0.00 0.00 0.00 2.01
594 600 6.418057 AGCTCCCAATTTTGTGATGTTTAA 57.582 33.333 0.00 0.00 0.00 1.52
595 601 6.825610 AGCTCCCAATTTTGTGATGTTTAAA 58.174 32.000 0.00 0.00 0.00 1.52
596 602 7.278875 AGCTCCCAATTTTGTGATGTTTAAAA 58.721 30.769 0.00 0.00 0.00 1.52
597 603 7.442062 AGCTCCCAATTTTGTGATGTTTAAAAG 59.558 33.333 0.00 0.00 0.00 2.27
598 604 7.440856 GCTCCCAATTTTGTGATGTTTAAAAGA 59.559 33.333 0.00 0.00 0.00 2.52
599 605 9.323985 CTCCCAATTTTGTGATGTTTAAAAGAA 57.676 29.630 0.00 0.00 0.00 2.52
713 725 6.537660 AGACCCTCGAAGAAATAAAATAACCG 59.462 38.462 0.00 0.00 34.09 4.44
830 842 1.000955 TCTTCTCTCCTCGCGCTTTTT 59.999 47.619 5.56 0.00 0.00 1.94
1202 1214 1.638529 GAGGGGATCGTCATCAGGAT 58.361 55.000 0.00 0.00 0.00 3.24
1285 1297 2.030096 GGAGGGATCTTCGTACGGATTC 60.030 54.545 16.52 9.68 0.00 2.52
1302 1314 0.736053 TTCGGTGAGGTTTTGTGCAC 59.264 50.000 10.75 10.75 0.00 4.57
1325 1337 2.159099 TCGAGCTGTCATTTAGCGGAAT 60.159 45.455 0.00 0.00 45.61 3.01
1387 1402 2.906354 AGAATCGTCGGCAGCTTATTT 58.094 42.857 0.00 0.00 0.00 1.40
1394 1409 2.945668 GTCGGCAGCTTATTTCCATTCT 59.054 45.455 0.00 0.00 0.00 2.40
1485 1500 9.194972 TGGTATCAATTGCAAATTGGAGTAATA 57.805 29.630 1.71 0.69 0.00 0.98
1644 1659 2.874701 GCTTGAGAGTTGCTTCTTGTCA 59.125 45.455 0.00 0.00 0.00 3.58
1717 1732 9.031360 GTAGCATTTGATACTTTGTAGAATCGA 57.969 33.333 0.00 0.00 34.37 3.59
1768 1783 3.853831 TGTTGCAACTATGATTGGCAG 57.146 42.857 28.61 0.00 0.00 4.85
1862 1877 1.085091 CTGCAGTTCTCATGCCTGAC 58.915 55.000 5.25 0.00 43.18 3.51
2091 2108 3.665323 CGACTTTTCACATTGAAGCTCCG 60.665 47.826 0.00 0.00 37.70 4.63
2108 2125 4.332819 AGCTCCGCAAATATAGTTGTGTTC 59.667 41.667 21.13 11.69 37.31 3.18
2127 2145 7.374272 TGTGTTCTTTAGAGAGATTCTGAGTG 58.626 38.462 0.00 0.00 36.61 3.51
2242 2260 1.206610 CTGACACTGGTGCTATCTGCT 59.793 52.381 0.17 0.00 43.37 4.24
2265 2283 9.383519 TGCTCTAGGTTTTCTTATATCTTTGTG 57.616 33.333 0.00 0.00 0.00 3.33
2302 2320 6.397272 GGATTGCTGTCCATTTTCATTGTTA 58.603 36.000 3.45 0.00 38.20 2.41
2473 2498 7.386848 CACTGAATGATGCATTTTCTCCTTTTT 59.613 33.333 18.54 0.00 33.90 1.94
2690 2715 4.553323 GCACGTAGAAACCTCTTGTTCTA 58.447 43.478 0.00 0.00 35.67 2.10
2788 2815 4.597404 TTTGAATGCATGCACCTTTGTA 57.403 36.364 25.37 2.46 0.00 2.41
2954 2981 9.875691 TTATATCGTCATGCTTGATATTAGCTT 57.124 29.630 14.98 3.74 39.38 3.74
2955 2982 8.783833 ATATCGTCATGCTTGATATTAGCTTT 57.216 30.769 5.49 0.00 39.38 3.51
2956 2983 6.925610 TCGTCATGCTTGATATTAGCTTTT 57.074 33.333 5.49 0.00 39.38 2.27
2957 2984 8.607441 ATCGTCATGCTTGATATTAGCTTTTA 57.393 30.769 5.49 0.00 39.38 1.52
2958 2985 7.851508 TCGTCATGCTTGATATTAGCTTTTAC 58.148 34.615 5.49 5.96 39.38 2.01
3035 3067 7.684529 AGAGAATTGCCTGGTTAGATATTAGG 58.315 38.462 0.00 0.00 0.00 2.69
3135 3167 9.245962 CTGAAGATGGCATTTTAGATTTGAATC 57.754 33.333 0.00 0.00 35.64 2.52
3222 3254 6.617784 TGGTCCCTATTGATACAAGATTACCA 59.382 38.462 0.00 0.00 0.00 3.25
3344 3376 4.032900 CGTTGGAGGTAATCATTGTCTTCG 59.967 45.833 0.00 0.00 0.00 3.79
3482 3514 8.870879 ACGTATTGCTGTAATTTTCTAGTTCTC 58.129 33.333 0.00 0.00 0.00 2.87
3564 3596 8.150296 ACATTTTAATCTAAGCAGCCTTTTGTT 58.850 29.630 0.00 0.00 32.47 2.83
3688 3721 7.876068 TGACTGTAATTTGTCTGGTACCTAAAG 59.124 37.037 14.36 2.04 34.57 1.85
3763 3796 4.232091 AGGTGAGGGAGTTAACTGAAGAA 58.768 43.478 14.14 0.00 0.00 2.52
3952 3990 9.844790 TCTGTTTTACTGAGAAATGCAATATTG 57.155 29.630 11.27 11.27 0.00 1.90
3991 4029 7.750903 GGTCACTTTATTGCTAATTGTTCAGAC 59.249 37.037 0.00 0.00 0.00 3.51
4150 4188 5.734720 TCCTGATGAGGTAATGAAACAGTC 58.265 41.667 0.00 0.00 40.76 3.51
4164 4202 8.450578 AATGAAACAGTCAAAGTGATGAGTTA 57.549 30.769 0.00 0.00 40.50 2.24
4220 4266 5.148651 ACTAACTATTTTGCGACCTCTGT 57.851 39.130 0.00 0.00 0.00 3.41
4221 4267 4.929808 ACTAACTATTTTGCGACCTCTGTG 59.070 41.667 0.00 0.00 0.00 3.66
4222 4268 3.678056 ACTATTTTGCGACCTCTGTGA 57.322 42.857 0.00 0.00 0.00 3.58
4223 4269 4.002906 ACTATTTTGCGACCTCTGTGAA 57.997 40.909 0.00 0.00 0.00 3.18
4224 4270 4.579869 ACTATTTTGCGACCTCTGTGAAT 58.420 39.130 0.00 0.00 0.00 2.57
4225 4271 4.631813 ACTATTTTGCGACCTCTGTGAATC 59.368 41.667 0.00 0.00 0.00 2.52
4226 4272 2.839486 TTTGCGACCTCTGTGAATCT 57.161 45.000 0.00 0.00 0.00 2.40
4227 4273 2.084610 TTGCGACCTCTGTGAATCTG 57.915 50.000 0.00 0.00 0.00 2.90
4252 4298 5.624159 TCCTTAATCAGGCTGGTGATTATG 58.376 41.667 15.73 12.70 44.88 1.90
4432 4478 0.108585 GGAAGAGCTGGTTGGTGTCA 59.891 55.000 0.00 0.00 0.00 3.58
4461 4507 1.022451 CAAGGCATGCAAATGTGGCC 61.022 55.000 21.36 0.00 44.92 5.36
4553 4599 4.455533 GCCGAATATTCAGCATATCCACAA 59.544 41.667 17.04 0.00 31.08 3.33
4576 4622 7.231317 ACAAAACTCCAGATCTAAATGCTCAAA 59.769 33.333 0.00 0.00 0.00 2.69
4584 4630 6.309737 CAGATCTAAATGCTCAAAACTTTGGC 59.690 38.462 0.00 5.74 38.66 4.52
4782 4832 2.687370 TGTCCATGACATCTGTGAACG 58.313 47.619 0.00 0.00 37.67 3.95
5052 5130 8.674607 ACGTATCCTTTAAGAAATGAATTCACC 58.325 33.333 11.07 3.31 40.72 4.02
5058 5136 7.485913 CCTTTAAGAAATGAATTCACCGTGATG 59.514 37.037 11.07 1.79 40.72 3.07
5079 5157 4.254492 TGTTGTTTAAAAAGGCACAACCC 58.746 39.130 13.36 0.00 45.60 4.11
5191 5269 1.727511 GCAACAGCCAGCAGTTGTCA 61.728 55.000 23.32 0.00 42.74 3.58
5193 5271 1.450531 AACAGCCAGCAGTTGTCAGC 61.451 55.000 0.00 0.00 39.27 4.26
5261 5339 6.825213 TGATGATTAGGACATTCTGGAACAAG 59.175 38.462 0.00 0.00 38.70 3.16
5311 5389 2.701551 TCTTCCTGGGACTCTTTGGAA 58.298 47.619 0.00 0.00 35.74 3.53
5353 5432 2.328099 GCGTCCTTTCTGGCAGTGG 61.328 63.158 15.27 14.76 35.26 4.00
5354 5433 2.328099 CGTCCTTTCTGGCAGTGGC 61.328 63.158 15.27 10.30 40.13 5.01
5422 5501 1.645710 TTCACCTCCTCCTTCCAGTC 58.354 55.000 0.00 0.00 0.00 3.51
5458 5537 5.386958 TGAGTCGCTAGTATTTTGTGTCT 57.613 39.130 0.00 0.00 0.00 3.41
5570 5649 6.530019 AAAACCTGTAAATATTCTGGCAGG 57.470 37.500 15.73 18.15 46.32 4.85
5590 5669 3.068560 GGCGTGTACAAAGTACAATGGA 58.931 45.455 11.19 0.00 0.00 3.41
5592 5671 4.871557 GGCGTGTACAAAGTACAATGGATA 59.128 41.667 11.19 0.00 0.00 2.59
5629 5708 1.668419 AGGGCATATGTCGAGCAAAC 58.332 50.000 4.29 0.00 0.00 2.93
5657 5736 6.335777 GCAAATTCCATGCAGAAGAGTTTAT 58.664 36.000 0.00 0.00 43.29 1.40
5694 5773 3.181516 GCATTGACGATTTCTGGACTCAC 60.182 47.826 0.00 0.00 0.00 3.51
5709 5788 5.814481 TGGACTCACCATTCATTGTTATCA 58.186 37.500 0.00 0.00 44.64 2.15
5710 5789 6.425735 TGGACTCACCATTCATTGTTATCAT 58.574 36.000 0.00 0.00 44.64 2.45
5795 5874 8.144155 GGATTACTATCCTGTTTTACAAGAGC 57.856 38.462 0.00 0.00 45.88 4.09
5900 5979 2.315925 TGCATAGACTACCAGCAAGC 57.684 50.000 4.20 0.00 31.42 4.01
5923 6002 2.728318 CACATCGATCGAAGTGCCTATG 59.272 50.000 32.49 21.12 37.10 2.23
5927 6006 1.789464 CGATCGAAGTGCCTATGCTTC 59.211 52.381 10.26 0.00 38.71 3.86
6118 6197 4.866508 ATCCCAATCTGCAGCATTTATG 57.133 40.909 9.47 1.31 0.00 1.90
6122 6201 5.300034 TCCCAATCTGCAGCATTTATGTTAG 59.700 40.000 9.47 0.00 0.00 2.34
6135 6214 7.925483 AGCATTTATGTTAGAACAAAGCACAAA 59.075 29.630 0.00 0.00 43.03 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 1.460699 GCAAGGTTGGGGGAGACTT 59.539 57.895 0.00 0.00 0.00 3.01
510 515 5.765510 TCATGTGGTAATTGGGAGCTTTAT 58.234 37.500 0.00 0.00 0.00 1.40
511 516 5.186256 TCATGTGGTAATTGGGAGCTTTA 57.814 39.130 0.00 0.00 0.00 1.85
512 517 4.046286 TCATGTGGTAATTGGGAGCTTT 57.954 40.909 0.00 0.00 0.00 3.51
513 518 3.737559 TCATGTGGTAATTGGGAGCTT 57.262 42.857 0.00 0.00 0.00 3.74
514 519 3.959495 ATCATGTGGTAATTGGGAGCT 57.041 42.857 0.00 0.00 0.00 4.09
557 563 7.509141 AATTGGGAGCTTTATTTTTGTTTGG 57.491 32.000 0.00 0.00 0.00 3.28
595 601 8.437742 CGTGTAACACTATTCCGTAATTTTCTT 58.562 33.333 0.00 0.00 35.74 2.52
596 602 7.063780 CCGTGTAACACTATTCCGTAATTTTCT 59.936 37.037 0.00 0.00 35.74 2.52
597 603 7.063308 TCCGTGTAACACTATTCCGTAATTTTC 59.937 37.037 0.00 0.00 35.74 2.29
598 604 6.873076 TCCGTGTAACACTATTCCGTAATTTT 59.127 34.615 0.00 0.00 35.74 1.82
599 605 6.311200 GTCCGTGTAACACTATTCCGTAATTT 59.689 38.462 0.00 0.00 35.74 1.82
602 608 4.671508 CGTCCGTGTAACACTATTCCGTAA 60.672 45.833 0.00 0.00 35.74 3.18
612 618 1.152989 TTGTGCCGTCCGTGTAACAC 61.153 55.000 0.00 0.00 35.74 3.32
677 689 4.099573 TCTTCGAGGGTCTGGATGTAAATC 59.900 45.833 0.00 0.00 0.00 2.17
713 725 2.665185 AGGGTTGTTCTGCGACGC 60.665 61.111 14.19 14.19 42.77 5.19
830 842 2.123180 TGCGAGGGGTTAAGGGGA 59.877 61.111 0.00 0.00 0.00 4.81
953 965 3.822192 CGAGTCCGGCGATCACCA 61.822 66.667 9.30 0.00 0.00 4.17
1285 1297 0.738389 AAGTGCACAAAACCTCACCG 59.262 50.000 21.04 0.00 0.00 4.94
1302 1314 1.590238 CCGCTAAATGACAGCTCGAAG 59.410 52.381 0.00 0.00 36.86 3.79
1387 1402 5.226803 TCCCCAGATTATTCAGAGAATGGA 58.773 41.667 2.65 0.00 0.00 3.41
1394 1409 6.730447 TCAATGTTTCCCCAGATTATTCAGA 58.270 36.000 0.00 0.00 0.00 3.27
1539 1554 0.617535 CCCCAAACCCCAAATCTCCC 60.618 60.000 0.00 0.00 0.00 4.30
1588 1603 6.868339 GGATTAAGGAAAACAACCTGAATGTG 59.132 38.462 0.00 0.00 38.36 3.21
1644 1659 1.646977 ACTCTAGTACCCTCCCAAGCT 59.353 52.381 0.00 0.00 0.00 3.74
1717 1732 5.277345 GGCGACAGCGAATTTACATCTAAAT 60.277 40.000 0.00 0.00 46.35 1.40
1768 1783 2.805099 CAGAAGCACCAGAACTGAGAAC 59.195 50.000 3.19 0.00 0.00 3.01
2108 2125 7.659390 ACCAAAACACTCAGAATCTCTCTAAAG 59.341 37.037 0.00 0.00 31.12 1.85
2127 2145 7.408910 CAAATGACAATTTCCTTCACCAAAAC 58.591 34.615 0.00 0.00 33.59 2.43
2216 2234 5.069119 CAGATAGCACCAGTGTCAGGTATAA 59.931 44.000 0.00 0.00 37.23 0.98
2265 2283 1.402968 AGCAATCCGCATGATCACAAC 59.597 47.619 0.00 0.00 46.13 3.32
3135 3167 9.363763 CTATACCACTAATATCTCTGCAACATG 57.636 37.037 0.00 0.00 0.00 3.21
3482 3514 3.044986 CTGTGACAATTTCAAGGTTGCG 58.955 45.455 0.00 0.00 35.39 4.85
3564 3596 3.128349 GTTCTGTCTGCGACAAGGTTAA 58.872 45.455 11.49 1.60 42.26 2.01
3924 3962 5.342806 TGCATTTCTCAGTAAAACAGACG 57.657 39.130 0.00 0.00 0.00 4.18
3952 3990 7.095649 GCAATAAAGTGACCTTTGGAAATGAAC 60.096 37.037 0.00 0.00 41.03 3.18
4150 4188 8.954950 AAGTAGATGGATAACTCATCACTTTG 57.045 34.615 6.80 0.00 42.38 2.77
4252 4298 4.504858 ACGATTGTGTATCTCCTTTGGAC 58.495 43.478 0.00 0.00 0.00 4.02
4449 4495 1.530419 AGGTTCGGCCACATTTGCA 60.530 52.632 2.24 0.00 40.61 4.08
4461 4507 1.374758 GTCTGTGGAGGCAGGTTCG 60.375 63.158 0.00 0.00 37.12 3.95
4553 4599 7.449704 AGTTTTGAGCATTTAGATCTGGAGTTT 59.550 33.333 5.18 0.00 32.67 2.66
4576 4622 1.118356 TTTGCCATCCCGCCAAAGTT 61.118 50.000 0.00 0.00 0.00 2.66
4584 4630 2.222027 GGAGTTATCTTTGCCATCCCG 58.778 52.381 0.00 0.00 0.00 5.14
4747 4797 6.430925 TGTCATGGACAAAGAAGTTATGAAGG 59.569 38.462 0.00 0.00 39.78 3.46
4756 4806 4.999311 TCACAGATGTCATGGACAAAGAAG 59.001 41.667 2.87 0.00 45.96 2.85
4759 4809 4.377738 CGTTCACAGATGTCATGGACAAAG 60.378 45.833 2.87 0.00 45.96 2.77
5052 5130 4.800993 TGTGCCTTTTTAAACAACATCACG 59.199 37.500 0.00 0.00 0.00 4.35
5079 5157 5.047847 TCAAGTACTTCAAAGTTGAGGTCG 58.952 41.667 11.59 1.69 42.93 4.79
5228 5306 8.557864 CAGAATGTCCTAATCATCATCTTGTTC 58.442 37.037 0.00 0.00 0.00 3.18
5261 5339 2.833631 TCCCCAAGAAACGAACTCTC 57.166 50.000 0.00 0.00 0.00 3.20
5311 5389 6.458210 CAAAATTTGGTAGAAATCACCAGCT 58.542 36.000 0.00 0.00 46.44 4.24
5353 5432 1.915614 CTGAACACACATCGCCAGGC 61.916 60.000 0.00 0.00 0.00 4.85
5354 5433 0.603707 ACTGAACACACATCGCCAGG 60.604 55.000 0.00 0.00 0.00 4.45
5363 5442 6.142320 GCAAAGCAATAAGTTACTGAACACAC 59.858 38.462 0.00 0.00 38.10 3.82
5422 5501 2.216488 GCGACTCAATGTACATACGCTG 59.784 50.000 23.33 14.37 41.25 5.18
5458 5537 1.669115 GCTCAAGCGGCAGACTGAA 60.669 57.895 6.65 0.00 0.00 3.02
5533 5612 3.633986 ACAGGTTTTTGCAGAGGAAGAAG 59.366 43.478 0.00 0.00 0.00 2.85
5570 5649 4.939509 ATCCATTGTACTTTGTACACGC 57.060 40.909 9.70 0.00 0.00 5.34
5613 5692 3.043635 CACAGTTTGCTCGACATATGC 57.956 47.619 1.58 0.00 0.00 3.14
5629 5708 3.057104 TCTTCTGCATGGAATTTGCACAG 60.057 43.478 0.00 0.00 44.73 3.66
5657 5736 4.016444 GTCAATGCTTGGGAAATGACCTA 58.984 43.478 0.00 0.00 32.96 3.08
5745 5824 8.424918 CCCAATGTATCAGAGACAAACTAGTAT 58.575 37.037 1.07 0.00 0.00 2.12
5793 5872 3.181477 TGTTTTGTATGTTTGCTGCTGCT 60.181 39.130 17.00 0.00 40.48 4.24
5794 5873 3.122297 TGTTTTGTATGTTTGCTGCTGC 58.878 40.909 8.89 8.89 40.20 5.25
5795 5874 4.805192 ACTTGTTTTGTATGTTTGCTGCTG 59.195 37.500 0.00 0.00 0.00 4.41
5873 5952 1.605712 GGTAGTCTATGCATCACGCCC 60.606 57.143 0.19 3.43 41.33 6.13
5886 5965 1.374758 GTGCGCTTGCTGGTAGTCT 60.375 57.895 9.73 0.00 40.12 3.24
5887 5966 1.021390 ATGTGCGCTTGCTGGTAGTC 61.021 55.000 9.73 0.00 40.12 2.59
5923 6002 2.552802 ACTGATGCAGCAGTGAAGC 58.447 52.632 34.99 0.00 46.72 3.86
6096 6175 5.387788 ACATAAATGCTGCAGATTGGGATA 58.612 37.500 20.43 4.53 0.00 2.59
6118 6197 3.713288 GGGGTTTGTGCTTTGTTCTAAC 58.287 45.455 0.00 0.00 0.00 2.34
6122 6201 0.458260 ACGGGGTTTGTGCTTTGTTC 59.542 50.000 0.00 0.00 0.00 3.18
6135 6214 2.904434 ACTTCTTAATCACAGACGGGGT 59.096 45.455 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.