Multiple sequence alignment - TraesCS4B01G097200

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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 TraesCS4B01G097200 chr4B 100.000 3149 0 0 2592 5740 101776358 101779506 0.000000e+00 5816.0
1 TraesCS4B01G097200 chr4B 100.000 2251 0 0 1 2251 101773767 101776017 0.000000e+00 4157.0
2 TraesCS4B01G097200 chr4D 92.954 3165 159 26 2592 5740 69128084 69131200 0.000000e+00 4551.0
3 TraesCS4B01G097200 chr4D 95.727 1568 47 14 698 2251 69126484 69128045 0.000000e+00 2507.0
4 TraesCS4B01G097200 chr4D 86.525 705 81 10 1 696 67232014 67232713 0.000000e+00 763.0
5 TraesCS4B01G097200 chr4D 85.155 485 64 6 200 677 348419410 348418927 1.860000e-134 490.0
6 TraesCS4B01G097200 chr4A 92.019 3195 155 44 2592 5740 520126228 520129368 0.000000e+00 4396.0
7 TraesCS4B01G097200 chr4A 95.933 1549 45 9 715 2251 520124650 520126192 0.000000e+00 2495.0
8 TraesCS4B01G097200 chr4A 83.921 709 85 18 1 702 727755469 727756155 0.000000e+00 651.0
9 TraesCS4B01G097200 chr7A 86.846 707 76 13 1 694 6530402 6531104 0.000000e+00 774.0
10 TraesCS4B01G097200 chr1A 86.234 632 68 13 1 617 104923151 104923778 0.000000e+00 667.0
11 TraesCS4B01G097200 chr1A 86.184 152 20 1 3788 3938 395177600 395177449 4.600000e-36 163.0
12 TraesCS4B01G097200 chr1D 84.438 694 89 11 16 694 467856830 467856141 0.000000e+00 665.0
13 TraesCS4B01G097200 chr1D 85.526 152 21 1 3788 3938 314705757 314705606 2.140000e-34 158.0
14 TraesCS4B01G097200 chr2A 84.294 694 94 12 7 690 289736585 289737273 0.000000e+00 664.0
15 TraesCS4B01G097200 chr3A 83.784 703 97 10 1 691 423972321 423973018 0.000000e+00 651.0
16 TraesCS4B01G097200 chr2B 86.433 457 50 8 4 454 800996256 800995806 1.860000e-134 490.0
17 TraesCS4B01G097200 chr3B 76.374 364 78 7 345 702 746857133 746857494 7.590000e-44 189.0
18 TraesCS4B01G097200 chr3B 76.177 361 78 8 348 702 744589825 744589467 3.530000e-42 183.0
19 TraesCS4B01G097200 chr5D 86.842 152 19 1 3788 3938 347443876 347443725 9.890000e-38 169.0
20 TraesCS4B01G097200 chr5B 86.452 155 20 1 3785 3938 403708577 403708731 9.890000e-38 169.0
21 TraesCS4B01G097200 chr3D 87.248 149 17 2 3788 3935 76230994 76231141 9.890000e-38 169.0
22 TraesCS4B01G097200 chr3D 86.184 152 19 2 3788 3938 73853238 73853088 4.600000e-36 163.0
23 TraesCS4B01G097200 chr7D 85.526 152 21 1 3788 3938 575593985 575594136 2.140000e-34 158.0
24 TraesCS4B01G097200 chr7D 97.222 36 0 1 2032 2066 205553560 205553595 6.210000e-05 60.2


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 TraesCS4B01G097200 chr4B 101773767 101779506 5739 False 4986.5 5816 100.0000 1 5740 2 chr4B.!!$F1 5739
1 TraesCS4B01G097200 chr4D 69126484 69131200 4716 False 3529.0 4551 94.3405 698 5740 2 chr4D.!!$F2 5042
2 TraesCS4B01G097200 chr4D 67232014 67232713 699 False 763.0 763 86.5250 1 696 1 chr4D.!!$F1 695
3 TraesCS4B01G097200 chr4A 520124650 520129368 4718 False 3445.5 4396 93.9760 715 5740 2 chr4A.!!$F2 5025
4 TraesCS4B01G097200 chr4A 727755469 727756155 686 False 651.0 651 83.9210 1 702 1 chr4A.!!$F1 701
5 TraesCS4B01G097200 chr7A 6530402 6531104 702 False 774.0 774 86.8460 1 694 1 chr7A.!!$F1 693
6 TraesCS4B01G097200 chr1A 104923151 104923778 627 False 667.0 667 86.2340 1 617 1 chr1A.!!$F1 616
7 TraesCS4B01G097200 chr1D 467856141 467856830 689 True 665.0 665 84.4380 16 694 1 chr1D.!!$R2 678
8 TraesCS4B01G097200 chr2A 289736585 289737273 688 False 664.0 664 84.2940 7 690 1 chr2A.!!$F1 683
9 TraesCS4B01G097200 chr3A 423972321 423973018 697 False 651.0 651 83.7840 1 691 1 chr3A.!!$F1 690

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
635 667 1.270358 GGCTAACAGCTTAGGGATCCG 60.270 57.143 5.45 0.0 41.99 4.18 F
1162 1209 0.108424 CGGCCTCCTCTTCAACTGAG 60.108 60.000 0.00 0.0 0.00 3.35 F
2787 2840 0.394565 ACTATTGGCTCCATCGGCTC 59.605 55.000 0.00 0.0 0.00 4.70 F
2844 2897 0.396435 TTCACCATGAGTTCACGGCT 59.604 50.000 0.00 0.0 31.24 5.52 F
2947 3000 0.679640 CCCATGCCATGTTACCACGT 60.680 55.000 3.63 0.0 0.00 4.49 F
2970 3023 1.154150 GATCTGGTTTGCTGCACGC 60.154 57.895 0.00 0.0 39.77 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1584 0.902984 TAGCAGCGGAAGAAGGTGGA 60.903 55.000 0.00 0.00 37.55 4.02 R
2925 2978 0.701147 TGGTAACATGGCATGGGACA 59.299 50.000 29.49 19.28 46.17 4.02 R
3771 3854 0.108585 GAGTCCTTCCCAGCAACACA 59.891 55.000 0.00 0.00 0.00 3.72 R
3772 3855 0.606673 GGAGTCCTTCCCAGCAACAC 60.607 60.000 0.41 0.00 40.37 3.32 R
4358 4443 1.143183 ACGAGCCACTCAACGTTGT 59.857 52.632 26.47 7.37 35.47 3.32 R
4936 5023 1.473258 TGGTCTATGTTTGCATGGCC 58.527 50.000 0.00 0.00 36.58 5.36 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
192 204 1.354031 TGCTTCAGAAACATAGCCCCA 59.646 47.619 0.00 0.00 32.73 4.96
213 225 4.065110 GCAGAAAGCGTTGGAGGT 57.935 55.556 0.00 0.00 0.00 3.85
237 249 4.521010 CGCACGATATTAGAGTGTACGAA 58.479 43.478 0.00 0.00 38.10 3.85
242 254 5.147865 CGATATTAGAGTGTACGAAGCCAG 58.852 45.833 0.00 0.00 0.00 4.85
266 278 2.575694 TGCAACAAGACGCATGTTTT 57.424 40.000 0.00 0.00 38.90 2.43
267 279 2.191802 TGCAACAAGACGCATGTTTTG 58.808 42.857 0.00 0.00 43.75 2.44
285 297 7.575414 TGTTTTGGAAACATAGCTTCAGTTA 57.425 32.000 0.00 0.00 42.32 2.24
301 313 8.035394 AGCTTCAGTTATAGAAATCGTCAAAGA 58.965 33.333 0.00 0.00 0.00 2.52
424 439 1.588932 CTGACGCGCGATATGGTGT 60.589 57.895 39.36 11.73 0.00 4.16
440 455 3.755628 GTGCCATGGTGCTGCAGG 61.756 66.667 17.12 1.22 35.33 4.85
522 543 2.506957 TTGGGTGCAGCTCTGTCGA 61.507 57.895 16.65 0.00 0.00 4.20
635 667 1.270358 GGCTAACAGCTTAGGGATCCG 60.270 57.143 5.45 0.00 41.99 4.18
648 680 2.362503 ATCCGACGGCTGTCCAGA 60.363 61.111 19.98 16.57 42.37 3.86
754 787 8.429641 TGTGAACCAATTAGACTTTAGACTCTT 58.570 33.333 0.00 0.00 0.00 2.85
755 788 9.274206 GTGAACCAATTAGACTTTAGACTCTTT 57.726 33.333 0.00 0.00 0.00 2.52
756 789 9.847224 TGAACCAATTAGACTTTAGACTCTTTT 57.153 29.630 0.00 0.00 0.00 2.27
806 847 3.955887 GACGATCTTTTGTCACGTCTC 57.044 47.619 0.00 0.00 46.00 3.36
851 896 2.501316 ACATGTGATCGAAGATGGGACA 59.499 45.455 0.00 0.00 45.12 4.02
889 934 2.678836 GTGCTAGCTTAGACGTGAGAGA 59.321 50.000 17.23 0.00 0.00 3.10
914 959 8.767478 AAATCATCCACAACAGAAAAATCATC 57.233 30.769 0.00 0.00 0.00 2.92
944 991 9.832445 TGGTCCTTATCATTATCTAACAAAGAC 57.168 33.333 0.00 0.00 36.93 3.01
984 1031 9.570488 CTAATCTTAGTAGTGCTACTTTTTCGT 57.430 33.333 15.91 2.94 43.35 3.85
1083 1130 6.262944 TCCACTATAAATAAGCCAACATGCAG 59.737 38.462 0.00 0.00 0.00 4.41
1114 1161 2.987547 TCACTCCGTCACGTCCCC 60.988 66.667 0.00 0.00 0.00 4.81
1162 1209 0.108424 CGGCCTCCTCTTCAACTGAG 60.108 60.000 0.00 0.00 0.00 3.35
1266 1313 3.198853 AGCAACAGATAGAACCCTTCCTC 59.801 47.826 0.00 0.00 0.00 3.71
1581 1628 2.126031 GCCGTTCGTGTCTCCCTC 60.126 66.667 0.00 0.00 0.00 4.30
1599 1646 3.102972 CCTCCTCATCATCGGACCATAT 58.897 50.000 0.00 0.00 0.00 1.78
1664 1711 5.878332 TGCATTGTGACTTACTGGTTATG 57.122 39.130 0.00 0.00 0.00 1.90
1749 1796 7.451732 TGACTTAGATCTCGCCTACTATTACT 58.548 38.462 0.00 0.00 0.00 2.24
1774 1821 5.899299 AGTTAGAAGATGGAAATTGCATGC 58.101 37.500 11.82 11.82 0.00 4.06
1917 1969 3.392882 TGCTCTATATGGCGTTGATGTG 58.607 45.455 0.00 0.00 0.00 3.21
2084 2137 5.395768 CCTCGTTGGATAAAGGTTCAGAGAT 60.396 44.000 0.00 0.00 38.35 2.75
2089 2142 7.495934 CGTTGGATAAAGGTTCAGAGATGTAAT 59.504 37.037 0.00 0.00 0.00 1.89
2114 2167 9.668497 ATTTAGGTCTTTTATCTGGACAAGTAC 57.332 33.333 0.00 0.00 0.00 2.73
2127 2180 6.602406 TCTGGACAAGTACTAGCTACCTAAAG 59.398 42.308 0.00 0.00 0.00 1.85
2772 2825 6.897966 TCTTGGTGGAAGACTATCTGAACTAT 59.102 38.462 0.00 0.00 35.64 2.12
2787 2840 0.394565 ACTATTGGCTCCATCGGCTC 59.605 55.000 0.00 0.00 0.00 4.70
2796 2849 1.376424 CCATCGGCTCTTGCACACT 60.376 57.895 0.00 0.00 41.91 3.55
2808 2861 3.053693 TCTTGCACACTAAATGGGGCTAT 60.054 43.478 0.00 0.00 34.71 2.97
2844 2897 0.396435 TTCACCATGAGTTCACGGCT 59.604 50.000 0.00 0.00 31.24 5.52
2847 2900 1.450312 CCATGAGTTCACGGCTCCC 60.450 63.158 0.00 0.00 32.31 4.30
2853 2906 3.645660 TTCACGGCTCCCATGGCA 61.646 61.111 6.09 0.00 0.00 4.92
2859 2912 1.076192 GGCTCCCATGGCATATGCT 59.924 57.895 26.12 5.59 41.70 3.79
2898 2951 1.218763 CTGAGATGCTCATCCTTGCG 58.781 55.000 6.27 0.00 39.92 4.85
2925 2978 3.580604 CTTGGCTGGCCCTGCTCTT 62.581 63.158 12.66 0.00 34.56 2.85
2947 3000 0.679640 CCCATGCCATGTTACCACGT 60.680 55.000 3.63 0.00 0.00 4.49
2970 3023 1.154150 GATCTGGTTTGCTGCACGC 60.154 57.895 0.00 0.00 39.77 5.34
3025 3078 4.910195 ACATCACTTGCACTCCATCTAAA 58.090 39.130 0.00 0.00 0.00 1.85
3134 3188 5.816919 TGTTCTTTTGTGATCGGAGAAAAC 58.183 37.500 0.00 0.00 43.58 2.43
3136 3190 6.039270 TGTTCTTTTGTGATCGGAGAAAACAT 59.961 34.615 0.00 0.00 43.58 2.71
3254 3310 3.969976 AGCACCATGACTACCATCACTAT 59.030 43.478 0.00 0.00 31.94 2.12
3331 3387 7.979444 ATATTTATGGAACGGACAAGGTATG 57.021 36.000 0.00 0.00 0.00 2.39
3351 3407 7.780745 AGGTATGTAGTGTTCTGCTATCTTACT 59.219 37.037 0.00 0.00 0.00 2.24
3466 3522 2.481289 ACTCTGGCAAAGGTAAGCTC 57.519 50.000 0.00 0.00 0.00 4.09
3599 3655 5.774690 TGATATGTTGGCTCTTTTTCCTTGT 59.225 36.000 0.00 0.00 0.00 3.16
3632 3709 1.224592 CCTAGGGCGTGGCATCTTT 59.775 57.895 0.00 0.00 0.00 2.52
3654 3736 6.757897 TTGGTTCTCTGCTACATTATTTGG 57.242 37.500 0.00 0.00 0.00 3.28
3735 3818 3.686726 CCTGCACTAGTGAACAATTCCTC 59.313 47.826 27.08 5.03 0.00 3.71
3784 3867 8.831550 GTTTAAAAATATTTGTGTTGCTGGGAA 58.168 29.630 0.39 0.00 0.00 3.97
3916 3999 8.954350 CCATATTGAGATATCCAAACCATCTTC 58.046 37.037 9.69 0.00 0.00 2.87
4283 4368 7.982252 ACTCATGGTCATACAAATCCTATCAT 58.018 34.615 0.00 0.00 0.00 2.45
4500 4585 5.359756 TGCTTAGTTCGTGATATGCTTGAT 58.640 37.500 0.00 0.00 0.00 2.57
4557 4642 1.153524 AAGCAGGCATGTGGGAACA 59.846 52.632 0.00 0.00 38.70 3.18
4559 4644 1.303561 GCAGGCATGTGGGAACAGA 60.304 57.895 0.00 0.00 44.46 3.41
4612 4698 5.880332 TGCCTTTGTACTTCCAATATCAGAC 59.120 40.000 0.00 0.00 0.00 3.51
4815 4902 7.012610 GTGTTTGGTTTTAGCCTAACTTCTACA 59.987 37.037 10.19 0.00 42.15 2.74
4867 4954 4.183101 TGAAACTTTTGCTTGCCTTTGAG 58.817 39.130 0.00 0.00 0.00 3.02
4870 4957 4.206477 ACTTTTGCTTGCCTTTGAGTTT 57.794 36.364 0.00 0.00 0.00 2.66
4873 4960 3.608316 TTGCTTGCCTTTGAGTTTGTT 57.392 38.095 0.00 0.00 0.00 2.83
4881 4968 4.336993 TGCCTTTGAGTTTGTTAACATCGT 59.663 37.500 9.56 0.00 36.70 3.73
4924 5011 3.397482 GGTACAAAAACATTGGCATGCA 58.603 40.909 21.36 0.00 33.05 3.96
4934 5021 3.007074 ACATTGGCATGCAAAGACATTGA 59.993 39.130 21.36 0.00 40.95 2.57
4936 5023 3.239587 TGGCATGCAAAGACATTGATG 57.760 42.857 21.36 0.00 41.85 3.07
4942 5029 2.093921 TGCAAAGACATTGATGGCCATG 60.094 45.455 26.56 13.44 41.85 3.66
4957 5044 2.417243 GGCCATGCAAACATAGACCAAC 60.417 50.000 0.00 0.00 33.67 3.77
4994 5081 5.538053 TCATGAACAAAAAGTTGATAGGGCA 59.462 36.000 0.00 0.00 41.51 5.36
4995 5082 6.211184 TCATGAACAAAAAGTTGATAGGGCAT 59.789 34.615 0.00 0.00 41.51 4.40
5008 5095 0.921896 AGGGCATATGAGTGTTGGCT 59.078 50.000 6.97 0.00 36.30 4.75
5052 5139 9.574516 AAAGTGTTCTCACAAGTATTATTCCTT 57.425 29.630 1.36 0.00 46.01 3.36
5132 5219 1.671845 CTACGGGCTCCTATCTATCGC 59.328 57.143 0.00 0.00 0.00 4.58
5135 5222 0.889306 GGGCTCCTATCTATCGCGTT 59.111 55.000 5.77 0.00 0.00 4.84
5184 5272 7.974504 AGGTGATAACCCATTTCGTATCTATT 58.025 34.615 0.00 0.00 0.00 1.73
5239 5327 5.012561 AGAGAGAGCAAATCACTACAAGGTT 59.987 40.000 0.00 0.00 0.00 3.50
5342 5431 1.873270 GCCCGGGAATTGTCGCTTTT 61.873 55.000 29.31 0.00 34.59 2.27
5343 5432 0.109319 CCCGGGAATTGTCGCTTTTG 60.109 55.000 18.48 0.00 34.59 2.44
5344 5433 0.596082 CCGGGAATTGTCGCTTTTGT 59.404 50.000 0.00 0.00 34.59 2.83
5345 5434 1.807742 CCGGGAATTGTCGCTTTTGTA 59.192 47.619 0.00 0.00 34.59 2.41
5346 5435 2.413634 CCGGGAATTGTCGCTTTTGTAC 60.414 50.000 0.00 0.00 34.59 2.90
5348 5437 2.413634 GGGAATTGTCGCTTTTGTACGG 60.414 50.000 0.00 0.00 33.96 4.02
5349 5438 2.224784 GGAATTGTCGCTTTTGTACGGT 59.775 45.455 0.00 0.00 0.00 4.83
5351 5440 4.083908 GGAATTGTCGCTTTTGTACGGTAA 60.084 41.667 0.00 0.00 0.00 2.85
5353 5442 4.455917 TTGTCGCTTTTGTACGGTAAAG 57.544 40.909 9.38 9.38 35.09 1.85
5354 5443 3.456280 TGTCGCTTTTGTACGGTAAAGT 58.544 40.909 13.23 0.00 34.59 2.66
5360 5449 5.120519 CGCTTTTGTACGGTAAAGTTATCCA 59.879 40.000 13.23 0.00 34.59 3.41
5448 5537 3.361158 TGCGCGGAACCCATGTTG 61.361 61.111 8.83 0.00 33.97 3.33
5489 5578 2.664916 GTGACATCGCATTGCAAACTT 58.335 42.857 1.71 0.00 0.00 2.66
5530 5619 5.813080 AAACGACAACTCAAAAGTTAGCT 57.187 34.783 0.00 0.00 43.99 3.32
5531 5620 5.813080 AACGACAACTCAAAAGTTAGCTT 57.187 34.783 0.00 0.00 43.99 3.74
5641 5730 8.595362 TCATATTCATAGGGATAGACGATGTT 57.405 34.615 0.00 0.00 0.00 2.71
5687 5776 2.654749 TCTAGTGCAGTTCATCCACG 57.345 50.000 0.00 0.00 34.79 4.94
5701 5796 4.196193 TCATCCACGAGTGTTCTTTTTGT 58.804 39.130 2.36 0.00 0.00 2.83
5723 5818 6.698380 TGTTAACTTCTAGAGATGTTCCACC 58.302 40.000 12.58 3.28 41.04 4.61
5727 5822 5.799213 ACTTCTAGAGATGTTCCACCTTTG 58.201 41.667 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.263842 TGAAACAAGATCTCTGTTGCAGAAAT 59.736 34.615 19.37 7.48 40.18 2.17
153 165 0.896940 AAGACCCCTGTTGCATGCAG 60.897 55.000 21.50 10.66 0.00 4.41
154 166 1.153524 AAGACCCCTGTTGCATGCA 59.846 52.632 18.46 18.46 0.00 3.96
155 167 1.588082 CAAGACCCCTGTTGCATGC 59.412 57.895 11.82 11.82 0.00 4.06
156 168 1.588082 GCAAGACCCCTGTTGCATG 59.412 57.895 2.26 0.00 46.83 4.06
157 169 4.102113 GCAAGACCCCTGTTGCAT 57.898 55.556 2.26 0.00 46.83 3.96
192 204 0.947244 CTCCAACGCTTTCTGCAACT 59.053 50.000 0.00 0.00 43.06 3.16
213 225 2.863401 ACACTCTAATATCGTGCGCA 57.137 45.000 5.66 5.66 32.07 6.09
237 249 0.828762 TCTTGTTGCAATGCCTGGCT 60.829 50.000 21.03 2.27 0.00 4.75
242 254 0.388907 ATGCGTCTTGTTGCAATGCC 60.389 50.000 0.59 0.00 45.45 4.40
266 278 9.905713 ATTTCTATAACTGAAGCTATGTTTCCA 57.094 29.630 4.62 0.00 0.00 3.53
285 297 4.636206 GGGCACTTCTTTGACGATTTCTAT 59.364 41.667 0.00 0.00 0.00 1.98
434 449 3.350833 AGCTAAATTGAACTCCCTGCAG 58.649 45.455 6.78 6.78 0.00 4.41
440 455 5.105997 ACATGCAGAAGCTAAATTGAACTCC 60.106 40.000 0.00 0.00 42.74 3.85
477 493 2.272447 CGCCGTCAACCCCCAAATT 61.272 57.895 0.00 0.00 0.00 1.82
509 530 4.074526 GGCCTCGACAGAGCTGCA 62.075 66.667 1.02 0.00 43.05 4.41
522 543 0.538746 CAACAAACTTACCCCGGCCT 60.539 55.000 0.00 0.00 0.00 5.19
531 553 6.260870 TGCAGAAACAAGACAACAAACTTA 57.739 33.333 0.00 0.00 0.00 2.24
648 680 5.179368 CAGATGTATTGAAATTATCCGCCGT 59.821 40.000 0.00 0.00 0.00 5.68
754 787 3.018149 ACCGCGGATGCCTTAATAAAAA 58.982 40.909 35.90 0.00 38.08 1.94
755 788 2.356382 CACCGCGGATGCCTTAATAAAA 59.644 45.455 35.90 0.00 38.08 1.52
756 789 1.944024 CACCGCGGATGCCTTAATAAA 59.056 47.619 35.90 0.00 38.08 1.40
806 847 5.753744 TCACTAAATAAAACAGGTGCAACG 58.246 37.500 0.00 0.00 38.12 4.10
866 911 3.017442 TCTCACGTCTAAGCTAGCACAT 58.983 45.455 18.83 5.17 0.00 3.21
867 912 2.420372 CTCTCACGTCTAAGCTAGCACA 59.580 50.000 18.83 2.50 0.00 4.57
889 934 8.591072 AGATGATTTTTCTGTTGTGGATGATTT 58.409 29.630 0.00 0.00 0.00 2.17
960 1007 8.709646 CAACGAAAAAGTAGCACTACTAAGATT 58.290 33.333 10.63 4.42 44.96 2.40
984 1031 0.611618 ATTGCCGTTGATGAGCCCAA 60.612 50.000 0.00 0.00 0.00 4.12
1073 1120 2.757099 GGAGGGCCTGCATGTTGG 60.757 66.667 21.34 0.00 0.00 3.77
1083 1130 2.514824 GTGAGCAATCGGAGGGCC 60.515 66.667 0.00 0.00 0.00 5.80
1114 1161 2.490148 TAGATGCGCTCTGACCCGG 61.490 63.158 9.73 0.00 35.28 5.73
1537 1584 0.902984 TAGCAGCGGAAGAAGGTGGA 60.903 55.000 0.00 0.00 37.55 4.02
1572 1619 1.697284 CGATGATGAGGAGGGAGACA 58.303 55.000 0.00 0.00 0.00 3.41
1578 1625 1.346062 ATGGTCCGATGATGAGGAGG 58.654 55.000 0.00 0.00 37.18 4.30
1581 1628 3.678252 GCTGATATGGTCCGATGATGAGG 60.678 52.174 0.00 0.00 0.00 3.86
1599 1646 1.611006 GCAGGATACGAGATGAGCTGA 59.389 52.381 0.00 0.00 46.39 4.26
1701 1748 7.589954 GTCATTACTGCAGTTTCATTTTTACGT 59.410 33.333 27.06 0.00 0.00 3.57
1702 1749 7.803189 AGTCATTACTGCAGTTTCATTTTTACG 59.197 33.333 27.06 2.74 33.57 3.18
1703 1750 9.463443 AAGTCATTACTGCAGTTTCATTTTTAC 57.537 29.630 27.06 10.87 35.62 2.01
1718 1765 5.446143 AGGCGAGATCTAAGTCATTACTG 57.554 43.478 0.00 0.00 35.62 2.74
1749 1796 6.405065 GCATGCAATTTCCATCTTCTAACTCA 60.405 38.462 14.21 0.00 0.00 3.41
1774 1821 4.323868 GTCTACTCAAGATTCCAACGTTCG 59.676 45.833 0.00 0.00 36.36 3.95
1917 1969 9.130312 GTCAGTCACACGAGATTATAATAATCC 57.870 37.037 0.00 0.00 0.00 3.01
2089 2142 8.877195 AGTACTTGTCCAGATAAAAGACCTAAA 58.123 33.333 0.00 0.00 0.00 1.85
2108 2161 9.953697 CTATCAACTTTAGGTAGCTAGTACTTG 57.046 37.037 0.00 0.00 0.00 3.16
2109 2162 9.917887 TCTATCAACTTTAGGTAGCTAGTACTT 57.082 33.333 0.00 0.00 0.00 2.24
2194 2247 8.968242 GTGTTTTTCTGTCATTGGATTTCTAAC 58.032 33.333 0.00 0.00 0.00 2.34
2211 2264 9.832445 TCATGTTCTTACTCTTAGTGTTTTTCT 57.168 29.630 0.00 0.00 0.00 2.52
2664 2717 8.661257 CGTATGTCCATTATCTAACAAACACAA 58.339 33.333 0.00 0.00 0.00 3.33
2772 2825 1.078214 CAAGAGCCGATGGAGCCAA 60.078 57.895 0.00 0.00 0.00 4.52
2787 2840 1.549203 AGCCCCATTTAGTGTGCAAG 58.451 50.000 0.00 0.00 0.00 4.01
2796 2849 5.833131 GTGGATCTTTTCATAGCCCCATTTA 59.167 40.000 0.00 0.00 0.00 1.40
2808 2861 3.826157 GGTGAACATGGTGGATCTTTTCA 59.174 43.478 0.00 0.00 0.00 2.69
2853 2906 1.416030 TGTCCGTACCATGCAGCATAT 59.584 47.619 7.82 1.82 0.00 1.78
2859 2912 1.295101 CCAGTGTCCGTACCATGCA 59.705 57.895 0.00 0.00 0.00 3.96
2868 2921 1.153489 CATCTCAGCCCAGTGTCCG 60.153 63.158 0.00 0.00 0.00 4.79
2925 2978 0.701147 TGGTAACATGGCATGGGACA 59.299 50.000 29.49 19.28 46.17 4.02
2947 3000 0.961019 GCAGCAAACCAGATCCACAA 59.039 50.000 0.00 0.00 0.00 3.33
3124 3177 5.992829 TGTTACAAAGCTATGTTTTCTCCGA 59.007 36.000 0.00 0.00 34.75 4.55
3254 3310 3.226777 GCTCTTGCTCTGTCCTCCTATA 58.773 50.000 0.00 0.00 36.03 1.31
3331 3387 7.763356 TCAAGAGTAAGATAGCAGAACACTAC 58.237 38.462 0.00 0.00 0.00 2.73
3386 3442 2.768253 TGACTTAGTGACCTGCCATG 57.232 50.000 0.00 0.00 0.00 3.66
3599 3655 3.008704 GCCCTAGGAAGTGGACAAGTTTA 59.991 47.826 11.48 0.00 0.00 2.01
3632 3709 4.640201 GCCAAATAATGTAGCAGAGAACCA 59.360 41.667 0.00 0.00 0.00 3.67
3654 3736 0.331616 AACCTATGGTTGGTGGGAGC 59.668 55.000 0.71 0.00 45.07 4.70
3766 3849 3.763897 GTCCTTCCCAGCAACACAAATAT 59.236 43.478 0.00 0.00 0.00 1.28
3771 3854 0.108585 GAGTCCTTCCCAGCAACACA 59.891 55.000 0.00 0.00 0.00 3.72
3772 3855 0.606673 GGAGTCCTTCCCAGCAACAC 60.607 60.000 0.41 0.00 40.37 3.32
3848 3931 6.502136 TGAATGAACACACACACTAAAACA 57.498 33.333 0.00 0.00 0.00 2.83
4028 4111 5.285845 CCGTTTGTACGTGTCATATTACGAA 59.714 40.000 0.00 0.00 46.20 3.85
4048 4131 9.990360 ATAAATACCTTCATTTTTGTTTCCGTT 57.010 25.926 0.00 0.00 30.84 4.44
4140 4225 7.172654 TGTTCGATCCAATGATACAATAACG 57.827 36.000 0.00 0.00 0.00 3.18
4144 4229 5.237996 CAGCTGTTCGATCCAATGATACAAT 59.762 40.000 5.25 0.00 0.00 2.71
4283 4368 4.837093 ATCCGGAGACCACTTGAATTAA 57.163 40.909 11.34 0.00 0.00 1.40
4358 4443 1.143183 ACGAGCCACTCAACGTTGT 59.857 52.632 26.47 7.37 35.47 3.32
4557 4642 6.773200 TCTCGACTATGTCTCCATATTTGTCT 59.227 38.462 0.00 0.00 33.18 3.41
4559 4644 6.515862 GCTCTCGACTATGTCTCCATATTTGT 60.516 42.308 0.00 0.00 33.18 2.83
4612 4698 9.261180 AGATAGATTGTCCAATTATGTACAACG 57.739 33.333 0.00 0.00 34.89 4.10
4716 4803 7.603180 AGTCTCATACTGGTATTGCTCATAA 57.397 36.000 0.00 0.00 36.93 1.90
4717 4804 7.724061 TGTAGTCTCATACTGGTATTGCTCATA 59.276 37.037 0.00 0.00 39.39 2.15
4924 5011 2.181125 TGCATGGCCATCAATGTCTTT 58.819 42.857 17.61 0.00 0.00 2.52
4934 5021 2.034124 GGTCTATGTTTGCATGGCCAT 58.966 47.619 14.09 14.09 36.58 4.40
4936 5023 1.473258 TGGTCTATGTTTGCATGGCC 58.527 50.000 0.00 0.00 36.58 5.36
4976 5063 6.891908 ACTCATATGCCCTATCAACTTTTTGT 59.108 34.615 0.00 0.00 34.02 2.83
4994 5081 3.716353 TGGATGGTAGCCAACACTCATAT 59.284 43.478 0.00 0.00 36.95 1.78
4995 5082 3.111484 TGGATGGTAGCCAACACTCATA 58.889 45.455 0.00 0.00 36.95 2.15
5008 5095 3.226777 CTTTGGGTGTGTTTGGATGGTA 58.773 45.455 0.00 0.00 0.00 3.25
5033 5120 6.701841 GCGATCAAGGAATAATACTTGTGAGA 59.298 38.462 2.64 0.00 43.40 3.27
5035 5122 5.758296 GGCGATCAAGGAATAATACTTGTGA 59.242 40.000 2.64 0.00 43.40 3.58
5052 5139 0.389391 GGAGATTTCTCGGGCGATCA 59.611 55.000 1.67 0.00 43.76 2.92
5099 5186 1.133790 GCCCGTAGAACGAAGAAGCTA 59.866 52.381 0.15 0.00 46.05 3.32
5132 5219 7.883073 CTTTATAGATAAAGCACAAGCAACG 57.117 36.000 8.66 0.00 45.49 4.10
5167 5254 5.815740 GTGACACAATAGATACGAAATGGGT 59.184 40.000 0.00 0.00 0.00 4.51
5239 5327 1.372375 TTTGCAGTCGCGATCGTGA 60.372 52.632 26.46 26.46 42.97 4.35
5342 5431 5.395546 GGTCCATGGATAACTTTACCGTACA 60.396 44.000 19.62 0.00 0.00 2.90
5343 5432 5.052481 GGTCCATGGATAACTTTACCGTAC 58.948 45.833 19.62 0.00 0.00 3.67
5344 5433 4.202141 CGGTCCATGGATAACTTTACCGTA 60.202 45.833 19.62 0.00 42.68 4.02
5345 5434 3.431207 CGGTCCATGGATAACTTTACCGT 60.431 47.826 19.62 0.00 42.68 4.83
5346 5435 3.128349 CGGTCCATGGATAACTTTACCG 58.872 50.000 19.62 19.38 42.12 4.02
5348 5437 4.377897 CTCCGGTCCATGGATAACTTTAC 58.622 47.826 19.62 2.19 34.32 2.01
5349 5438 3.389983 CCTCCGGTCCATGGATAACTTTA 59.610 47.826 19.62 0.00 34.32 1.85
5351 5440 1.768870 CCTCCGGTCCATGGATAACTT 59.231 52.381 19.62 0.00 34.32 2.66
5353 5442 0.396811 CCCTCCGGTCCATGGATAAC 59.603 60.000 19.62 10.68 34.32 1.89
5354 5443 0.766674 CCCCTCCGGTCCATGGATAA 60.767 60.000 19.62 2.97 34.32 1.75
5360 5449 0.793617 ATCTATCCCCTCCGGTCCAT 59.206 55.000 0.00 0.00 0.00 3.41
5448 5537 7.433131 TGTCACGTTCACGATAAGAAATATACC 59.567 37.037 6.30 0.00 43.02 2.73
5489 5578 0.762418 TTCCCCAGCTTTCGTCTTCA 59.238 50.000 0.00 0.00 0.00 3.02
5530 5619 2.627945 CACGATACTTGCTAAGGCCAA 58.372 47.619 5.01 0.00 37.74 4.52
5531 5620 1.134521 CCACGATACTTGCTAAGGCCA 60.135 52.381 5.01 0.00 37.74 5.36
5588 5677 2.922740 TTCTGTTAGGAACGGCAACT 57.077 45.000 0.00 0.00 37.69 3.16
5641 5730 2.922740 ACCACCTTGCGTAAGAGAAA 57.077 45.000 15.38 0.00 43.02 2.52


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

AutoCloner maintained by Alex Coulton.