Multiple sequence alignment - TraesCS7A01G218100

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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 TraesCS7A01G218100 chr7A 100.000 5423 0 0 1 5423 184937944 184932522 0.000000e+00 10015.0
1 TraesCS7A01G218100 chr7A 90.625 64 4 2 482 544 456115416 456115354 3.480000e-12 84.2
2 TraesCS7A01G218100 chr7D 96.725 3053 83 11 587 3632 180418107 180415065 0.000000e+00 5068.0
3 TraesCS7A01G218100 chr7D 91.376 1206 62 18 3632 4802 180414980 180413782 0.000000e+00 1613.0
4 TraesCS7A01G218100 chr7D 93.466 551 27 7 4882 5423 180413103 180412553 0.000000e+00 809.0
5 TraesCS7A01G218100 chr7D 91.089 202 18 0 4981 5182 180089182 180088981 1.920000e-69 274.0
6 TraesCS7A01G218100 chr7B 95.200 3000 122 15 647 3632 146144136 146141145 0.000000e+00 4723.0
7 TraesCS7A01G218100 chr7B 92.118 1015 62 11 3803 4805 146141106 146140098 0.000000e+00 1415.0
8 TraesCS7A01G218100 chr7B 92.674 546 18 8 1 545 544151182 544151706 0.000000e+00 767.0
9 TraesCS7A01G218100 chr7B 94.722 360 11 6 5068 5423 146139512 146139157 2.210000e-153 553.0
10 TraesCS7A01G218100 chr7B 88.462 156 13 3 4625 4779 145978398 145978247 3.340000e-42 183.0
11 TraesCS7A01G218100 chr7B 97.143 35 1 0 5389 5423 113143129 113143095 5.870000e-05 60.2
12 TraesCS7A01G218100 chr3D 89.837 551 19 5 1 545 433962969 433962450 0.000000e+00 673.0
13 TraesCS7A01G218100 chr1D 92.506 427 16 4 89 515 96168633 96168223 1.010000e-166 597.0
14 TraesCS7A01G218100 chr1D 88.544 419 37 9 145 556 46926022 46926436 1.050000e-136 497.0
15 TraesCS7A01G218100 chr1D 81.818 275 49 1 1 274 160453796 160454070 4.230000e-56 230.0
16 TraesCS7A01G218100 chr1D 100.000 95 0 0 1 95 96174617 96174523 5.580000e-40 176.0
17 TraesCS7A01G218100 chr5B 85.654 237 33 1 1 237 174598556 174598791 1.170000e-61 248.0
18 TraesCS7A01G218100 chr1A 88.235 119 9 5 431 545 106773881 106773764 2.630000e-28 137.0
19 TraesCS7A01G218100 chr6A 92.188 64 3 2 483 545 142943510 142943448 7.480000e-14 89.8
20 TraesCS7A01G218100 chrUn 88.406 69 6 2 482 549 343067105 343067038 1.250000e-11 82.4
21 TraesCS7A01G218100 chr1B 85.000 80 10 2 477 555 449049110 449049032 4.500000e-11 80.5
22 TraesCS7A01G218100 chr4B 97.143 35 1 0 5389 5423 403055407 403055373 5.870000e-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 TraesCS7A01G218100 chr7A 184932522 184937944 5422 True 10015.000000 10015 100.000000 1 5423 1 chr7A.!!$R1 5422
1 TraesCS7A01G218100 chr7D 180412553 180418107 5554 True 2496.666667 5068 93.855667 587 5423 3 chr7D.!!$R2 4836
2 TraesCS7A01G218100 chr7B 146139157 146144136 4979 True 2230.333333 4723 94.013333 647 5423 3 chr7B.!!$R3 4776
3 TraesCS7A01G218100 chr7B 544151182 544151706 524 False 767.000000 767 92.674000 1 545 1 chr7B.!!$F1 544
4 TraesCS7A01G218100 chr3D 433962450 433962969 519 True 673.000000 673 89.837000 1 545 1 chr3D.!!$R1 544

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
194 195 0.613572 TGGTCTACATCCCTGCGACA 60.614 55.0 0.00 0.00 31.32 4.35 F
325 326 0.664466 GCCGGCTGTGCTTTCTTTTC 60.664 55.0 22.15 0.00 0.00 2.29 F
2037 2058 0.323178 CAGCTCTTCATTGGCCACCT 60.323 55.0 3.88 0.00 0.00 4.00 F
2428 2450 0.106519 AGCAGCAGAGGTTTTGTGGT 60.107 50.0 0.00 0.00 0.00 4.16 F
2885 2907 0.525761 CCTTAATGTTGTGGCCACCG 59.474 55.0 32.62 10.34 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1687 1.425066 AGAGAATGAACCAACTGGGCA 59.575 47.619 0.0 0.0 42.05 5.36 R
2176 2197 1.545651 GGGCAATAGGGGACATAGCAC 60.546 57.143 0.0 0.0 0.00 4.40 R
3174 3198 1.209019 TGCCACACAAGCACCAAAAAT 59.791 42.857 0.0 0.0 34.69 1.82 R
3882 4003 1.237533 TGCATACCAGCAACAGTGTG 58.762 50.000 0.0 0.0 42.46 3.82 R
4848 5260 0.385390 CACACCCAAAGAGCAACACC 59.615 55.000 0.0 0.0 0.00 4.16 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
150 151 0.965866 AGCTCGATGACGTTGGGAGA 60.966 55.000 9.96 0.00 40.69 3.71
181 182 1.446907 GGAGAGACGACGTTGGTCTA 58.553 55.000 19.28 0.00 44.41 2.59
194 195 0.613572 TGGTCTACATCCCTGCGACA 60.614 55.000 0.00 0.00 31.32 4.35
198 199 1.064685 TCTACATCCCTGCGACAGAGA 60.065 52.381 8.20 1.55 32.44 3.10
200 201 1.198713 ACATCCCTGCGACAGAGATT 58.801 50.000 8.20 0.00 26.43 2.40
256 257 4.994201 GCAGCGACGTCGGACACA 62.994 66.667 36.13 0.00 40.23 3.72
325 326 0.664466 GCCGGCTGTGCTTTCTTTTC 60.664 55.000 22.15 0.00 0.00 2.29
366 367 0.741915 TTCACGGGAGGCACAAAAAC 59.258 50.000 0.00 0.00 0.00 2.43
399 406 2.728007 GGCCTGGCCCAATAGATATTC 58.272 52.381 27.77 0.00 44.06 1.75
426 433 1.070843 CCCAATAACGAACATAGCGCG 60.071 52.381 0.00 0.00 0.00 6.86
442 449 1.785518 GCGCGGCCGAATAATATTTCG 60.786 52.381 33.48 19.61 46.14 3.46
524 531 6.128688 CGGATTAAAAATTTGGTGAAACGCAT 60.129 34.615 0.00 0.00 38.12 4.73
537 544 6.127758 TGGTGAAACGCATCTTGCTTTATTAT 60.128 34.615 0.00 0.00 42.25 1.28
538 545 7.066404 TGGTGAAACGCATCTTGCTTTATTATA 59.934 33.333 0.00 0.00 42.25 0.98
539 546 7.587757 GGTGAAACGCATCTTGCTTTATTATAG 59.412 37.037 0.00 0.00 42.25 1.31
540 547 8.122952 GTGAAACGCATCTTGCTTTATTATAGT 58.877 33.333 0.00 0.00 42.25 2.12
545 552 8.712363 ACGCATCTTGCTTTATTATAGTGTATG 58.288 33.333 0.00 0.00 42.25 2.39
546 553 8.712363 CGCATCTTGCTTTATTATAGTGTATGT 58.288 33.333 0.00 0.00 42.25 2.29
730 739 8.290325 GGAGCCAAAAATCCGAGTAATAATAAG 58.710 37.037 0.00 0.00 0.00 1.73
739 748 4.522022 CCGAGTAATAATAAGTCCCCTCGT 59.478 45.833 0.00 0.00 39.00 4.18
792 801 6.087820 CGTAAAAGAAGACCTCGTTGAACTAG 59.912 42.308 0.00 0.00 0.00 2.57
830 839 1.154016 ACATCTCGTGAACTCGCCG 60.154 57.895 0.00 0.00 0.00 6.46
1150 1160 3.551496 CTGTGCGCCTTTGGGGAGA 62.551 63.158 4.18 0.00 37.91 3.71
1287 1299 3.244700 ACTGTTCTGCATCTTTACAGCCT 60.245 43.478 11.39 0.00 39.77 4.58
1482 1494 1.595093 CCGGCCATTTCCAGTTGGTC 61.595 60.000 2.24 0.00 35.34 4.02
1484 1496 0.890683 GGCCATTTCCAGTTGGTCAG 59.109 55.000 0.00 0.00 37.56 3.51
1513 1525 3.354948 TGGCAGATAGCAAACTGACAT 57.645 42.857 8.18 0.00 45.57 3.06
1514 1526 3.689347 TGGCAGATAGCAAACTGACATT 58.311 40.909 8.18 0.00 45.57 2.71
1551 1563 1.740025 GCTCACCAGGTGCTGATTTAC 59.260 52.381 15.64 0.00 32.44 2.01
1673 1686 1.026718 ACAGCATGCTTACGGCCTTC 61.027 55.000 19.98 0.00 42.53 3.46
1674 1687 0.745845 CAGCATGCTTACGGCCTTCT 60.746 55.000 19.98 0.00 40.92 2.85
1850 1871 3.505680 TGTGAGTTGTGGTGATTTATGCC 59.494 43.478 0.00 0.00 0.00 4.40
1851 1872 3.088532 TGAGTTGTGGTGATTTATGCCC 58.911 45.455 0.00 0.00 0.00 5.36
1911 1932 3.194968 TGGCAAGGACACTAGCTTAGTAC 59.805 47.826 0.00 0.00 37.23 2.73
2037 2058 0.323178 CAGCTCTTCATTGGCCACCT 60.323 55.000 3.88 0.00 0.00 4.00
2042 2063 1.985159 TCTTCATTGGCCACCTGTAGT 59.015 47.619 3.88 0.00 0.00 2.73
2058 2079 8.076178 CCACCTGTAGTAAAAGTTGAATTCTTG 58.924 37.037 7.05 0.00 0.00 3.02
2176 2197 2.492881 TGCCACTTGCCATGTTTGATAG 59.507 45.455 0.00 0.00 40.16 2.08
2428 2450 0.106519 AGCAGCAGAGGTTTTGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
2704 2726 2.307098 GGCTGTCCTGAGGGCATTATAT 59.693 50.000 6.11 0.00 0.00 0.86
2883 2905 3.681593 TCTACCTTAATGTTGTGGCCAC 58.318 45.455 29.67 29.67 0.00 5.01
2885 2907 0.525761 CCTTAATGTTGTGGCCACCG 59.474 55.000 32.62 10.34 0.00 4.94
2996 3020 6.432607 TGCAGCAGAATTTATTCTTCTCAG 57.567 37.500 2.27 0.00 44.28 3.35
3174 3198 6.119536 ACTGTTACTGATTTGGAGTTCAACA 58.880 36.000 0.00 0.00 34.67 3.33
3191 3215 3.931468 TCAACATTTTTGGTGCTTGTGTG 59.069 39.130 0.00 0.00 0.00 3.82
3300 3324 9.569167 CGTAAGTTGTGATTTATGTCTCTTCTA 57.431 33.333 0.00 0.00 0.00 2.10
3380 3404 3.117474 TGTGGAAGACAACCCCAATTACA 60.117 43.478 0.00 0.00 0.00 2.41
3457 3481 7.759433 GTCTTTCAACTGGAATTTCAAGAACAA 59.241 33.333 7.82 0.00 34.91 2.83
3573 3597 8.099537 TCTCTTGCATGATTATCCTTCTATTCC 58.900 37.037 2.33 0.00 0.00 3.01
3614 3638 7.147312 TCTCCTGAAACAAAAGCATGTATTTG 58.853 34.615 18.06 18.06 32.02 2.32
3619 3643 5.655893 AACAAAAGCATGTATTTGTGTGC 57.344 34.783 22.91 0.00 37.84 4.57
3660 3769 9.331282 ACTAGATTATGTTTTAGGCTTCATGAC 57.669 33.333 0.00 0.00 0.00 3.06
3684 3793 7.875971 ACTTCCTTCACATGATCTTTTGTAAC 58.124 34.615 0.00 0.00 0.00 2.50
3689 3798 7.066284 CCTTCACATGATCTTTTGTAACTAGGG 59.934 40.741 0.00 0.00 0.00 3.53
3760 3869 5.242171 TGAATGCCATATCCACATGCTTAAG 59.758 40.000 0.00 0.00 0.00 1.85
3834 3955 7.681304 GAGCTGACTCAAACATTGATATGCAAT 60.681 37.037 0.00 0.00 44.07 3.56
3882 4003 9.991906 TTCTACTTGCACCTATAATGTATAACC 57.008 33.333 0.00 0.00 0.00 2.85
3883 4004 9.150028 TCTACTTGCACCTATAATGTATAACCA 57.850 33.333 0.00 0.00 0.00 3.67
3884 4005 9.204570 CTACTTGCACCTATAATGTATAACCAC 57.795 37.037 0.00 0.00 0.00 4.16
3906 4045 3.691118 CACTGTTGCTGGTATGCACTATT 59.309 43.478 0.00 0.00 43.20 1.73
3955 4094 9.797642 ACCATTATGCTGATAAATGACAAGATA 57.202 29.630 0.00 0.00 0.00 1.98
4009 4150 6.763610 CACTATCCATTACTTTGTTCCTCCTC 59.236 42.308 0.00 0.00 0.00 3.71
4010 4151 4.202245 TCCATTACTTTGTTCCTCCTCG 57.798 45.455 0.00 0.00 0.00 4.63
4026 4167 1.869767 CCTCGAAGCATAGCATTCACC 59.130 52.381 0.00 0.00 0.00 4.02
4048 4189 4.940046 CCTGTCTTGTGTATTCATGCTTCT 59.060 41.667 0.00 0.00 0.00 2.85
4078 4219 9.770097 TCATACATTCTTCCTATTCTGTCATTC 57.230 33.333 0.00 0.00 0.00 2.67
4079 4220 9.775854 CATACATTCTTCCTATTCTGTCATTCT 57.224 33.333 0.00 0.00 0.00 2.40
4125 4266 1.535028 CAACTGATGTTTGCGCTGGTA 59.465 47.619 9.73 0.00 33.52 3.25
4132 4273 1.059942 GTTTGCGCTGGTATTTGCAC 58.940 50.000 9.73 0.00 37.01 4.57
4314 4455 2.711547 AGGGCTAAAAGAGTCAACCACT 59.288 45.455 0.00 0.00 38.45 4.00
4317 4458 2.226674 GCTAAAAGAGTCAACCACTGGC 59.773 50.000 0.00 0.00 34.41 4.85
4338 4479 2.797156 CGGTAAGAGAATTCCATCAGCG 59.203 50.000 0.65 3.60 0.00 5.18
4407 4548 3.631250 AGAAAAGCCAGAAACAAGACCA 58.369 40.909 0.00 0.00 0.00 4.02
4482 4626 0.546122 TGCACCAACTTCACCTGAGT 59.454 50.000 0.00 0.00 0.00 3.41
4544 4688 3.622627 GCATTCTTAAGAGCATGCTCC 57.377 47.619 37.79 22.90 45.38 4.70
4549 4693 3.878778 TCTTAAGAGCATGCTCCCTTTC 58.121 45.455 37.79 18.03 43.70 2.62
4779 4923 3.740115 TCTTGTTGGACTTCTTGTAGGC 58.260 45.455 0.00 0.00 0.00 3.93
4815 5227 6.573664 ATTGTTCTTAGCAGTTGTTATGCA 57.426 33.333 0.00 0.00 46.31 3.96
4863 5275 1.733402 TTGCGGTGTTGCTCTTTGGG 61.733 55.000 0.00 0.00 35.36 4.12
4864 5276 2.193536 GCGGTGTTGCTCTTTGGGT 61.194 57.895 0.00 0.00 0.00 4.51
4865 5277 1.654220 CGGTGTTGCTCTTTGGGTG 59.346 57.895 0.00 0.00 0.00 4.61
4866 5278 1.101049 CGGTGTTGCTCTTTGGGTGT 61.101 55.000 0.00 0.00 0.00 4.16
4867 5279 0.385390 GGTGTTGCTCTTTGGGTGTG 59.615 55.000 0.00 0.00 0.00 3.82
4868 5280 1.102978 GTGTTGCTCTTTGGGTGTGT 58.897 50.000 0.00 0.00 0.00 3.72
4869 5281 1.476488 GTGTTGCTCTTTGGGTGTGTT 59.524 47.619 0.00 0.00 0.00 3.32
4870 5282 1.476085 TGTTGCTCTTTGGGTGTGTTG 59.524 47.619 0.00 0.00 0.00 3.33
4871 5283 0.459489 TTGCTCTTTGGGTGTGTTGC 59.541 50.000 0.00 0.00 0.00 4.17
4872 5284 1.008538 GCTCTTTGGGTGTGTTGCG 60.009 57.895 0.00 0.00 0.00 4.85
4873 5285 1.654220 CTCTTTGGGTGTGTTGCGG 59.346 57.895 0.00 0.00 0.00 5.69
4874 5286 1.795170 CTCTTTGGGTGTGTTGCGGG 61.795 60.000 0.00 0.00 0.00 6.13
4875 5287 2.835431 TTTGGGTGTGTTGCGGGG 60.835 61.111 0.00 0.00 0.00 5.73
4876 5288 3.360423 TTTGGGTGTGTTGCGGGGA 62.360 57.895 0.00 0.00 0.00 4.81
4877 5289 3.783362 TTGGGTGTGTTGCGGGGAG 62.783 63.158 0.00 0.00 0.00 4.30
4927 5926 3.206150 CCACAACATTATTCTCGAGGGG 58.794 50.000 13.56 0.00 0.00 4.79
4928 5927 3.206150 CACAACATTATTCTCGAGGGGG 58.794 50.000 13.56 0.00 0.00 5.40
4931 5931 4.018779 ACAACATTATTCTCGAGGGGGAAA 60.019 41.667 13.56 0.00 0.00 3.13
4970 5970 7.308408 CCACTGTGAATGGAATGCTAATATGAG 60.308 40.741 9.86 0.00 39.87 2.90
5011 6012 5.529060 GTGTTCTTTCCTCCTGCTATAATGG 59.471 44.000 0.00 0.00 0.00 3.16
5056 6057 0.545309 ACACCTGAAGCCTAGCCAGA 60.545 55.000 0.00 0.00 0.00 3.86
5070 6071 2.893424 AGCCAGACCAACCATTTCAAT 58.107 42.857 0.00 0.00 0.00 2.57
5100 6101 5.376625 TGTATGACAAGAGCTCTTTTGGTT 58.623 37.500 26.44 12.54 33.11 3.67
5278 6283 8.349983 GCCAAAAACTATCACTTTGAGACTAAA 58.650 33.333 0.00 0.00 32.87 1.85
5352 6357 5.506730 TGGTACCCACAAATGAACTGATA 57.493 39.130 10.07 0.00 0.00 2.15
5387 6392 3.004734 ACCTTCCTTGCACTTGATTTTCG 59.995 43.478 0.00 0.00 0.00 3.46
5416 6421 1.138069 CGTTTGGCAAGGGAGGTTTTT 59.862 47.619 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 2.685380 CTCTCCCCAACCTCGCCT 60.685 66.667 0.00 0.00 0.00 5.52
181 182 4.442038 TCTCTGTCGCAGGGATGT 57.558 55.556 5.46 0.00 35.88 3.06
194 195 2.815308 CCCGCCGTAGCAATCTCT 59.185 61.111 0.00 0.00 39.83 3.10
239 240 4.994201 TGTGTCCGACGTCGCTGC 62.994 66.667 31.73 21.89 38.18 5.25
240 241 3.097728 GTGTGTCCGACGTCGCTG 61.098 66.667 31.73 19.35 38.18 5.18
241 242 3.538028 CTGTGTGTCCGACGTCGCT 62.538 63.158 31.73 0.00 38.18 4.93
242 243 3.097728 CTGTGTGTCCGACGTCGC 61.098 66.667 31.73 19.56 38.18 5.19
243 244 1.440518 CTCTGTGTGTCCGACGTCG 60.441 63.158 30.33 30.33 39.44 5.12
256 257 4.262420 GGTCTGCTCTTTCTTCTTCTCTGT 60.262 45.833 0.00 0.00 0.00 3.41
366 367 1.663695 CCAGGCCATGTTTAGTACGG 58.336 55.000 5.01 0.00 0.00 4.02
399 406 1.339631 TGTTCGTTATTGGGCTCCTGG 60.340 52.381 0.00 0.00 0.00 4.45
442 449 6.301861 CGAGGTGGTACTAAATTTTTCGTTC 58.698 40.000 0.00 0.00 0.00 3.95
628 635 8.090250 TGCGTTACAGTATAAGACAACAAAAT 57.910 30.769 0.00 0.00 0.00 1.82
696 704 1.259840 ATTTTTGGCTCCGGCTGCAT 61.260 50.000 18.39 3.21 38.73 3.96
730 739 3.064931 CAGTCAGTTTAAACGAGGGGAC 58.935 50.000 12.54 14.50 0.00 4.46
739 748 5.543714 TGGTAAGATCGCAGTCAGTTTAAA 58.456 37.500 0.00 0.00 0.00 1.52
792 801 2.668550 AACCTGGGAAAGCGACGC 60.669 61.111 13.03 13.03 0.00 5.19
873 882 1.605992 CAAGCTGCAGAGGGATGGA 59.394 57.895 20.43 0.00 0.00 3.41
1150 1160 3.704545 ACCTTCCCTCTCTGATCTCAT 57.295 47.619 0.00 0.00 0.00 2.90
1261 1271 4.910195 TGTAAAGATGCAGAACAGTGGAT 58.090 39.130 0.00 0.00 0.00 3.41
1265 1275 3.077359 GGCTGTAAAGATGCAGAACAGT 58.923 45.455 14.33 0.00 41.33 3.55
1298 1310 7.559533 TGCCATTTATACCAATGAAGAAGCTTA 59.440 33.333 0.00 0.00 36.39 3.09
1482 1494 3.943381 TGCTATCTGCCAAAATGAGACTG 59.057 43.478 0.00 0.00 42.00 3.51
1484 1496 4.970662 TTGCTATCTGCCAAAATGAGAC 57.029 40.909 0.00 0.00 42.00 3.36
1589 1602 7.120051 AGCCTGTTAGAGTCTAATGAAGTCTA 58.880 38.462 15.53 0.00 0.00 2.59
1673 1686 1.815003 GAGAATGAACCAACTGGGCAG 59.185 52.381 0.00 0.00 42.05 4.85
1674 1687 1.425066 AGAGAATGAACCAACTGGGCA 59.575 47.619 0.00 0.00 42.05 5.36
1850 1871 1.813513 AGACGAAAGCACCATTCAGG 58.186 50.000 0.00 0.00 45.67 3.86
1851 1872 2.549754 ACAAGACGAAAGCACCATTCAG 59.450 45.455 0.00 0.00 0.00 3.02
1911 1932 5.914635 AGATAAACAAAAGTGTGCACAATCG 59.085 36.000 23.59 14.83 38.27 3.34
1973 1994 3.753272 GAGCTGAACTAACTGATTTGCCA 59.247 43.478 0.00 0.00 0.00 4.92
2037 2058 8.410141 CCAACCAAGAATTCAACTTTTACTACA 58.590 33.333 8.44 0.00 0.00 2.74
2042 2063 6.227298 TGCCAACCAAGAATTCAACTTTTA 57.773 33.333 8.44 0.00 0.00 1.52
2058 2079 2.229792 TCAACACTCTTCATGCCAACC 58.770 47.619 0.00 0.00 0.00 3.77
2176 2197 1.545651 GGGCAATAGGGGACATAGCAC 60.546 57.143 0.00 0.00 0.00 4.40
2428 2450 4.424566 GTTAGCGCGACACCCGGA 62.425 66.667 12.10 0.00 39.04 5.14
2716 2738 2.376518 AGTGGATTTTGAAGGAGGAGCA 59.623 45.455 0.00 0.00 0.00 4.26
3174 3198 1.209019 TGCCACACAAGCACCAAAAAT 59.791 42.857 0.00 0.00 34.69 1.82
3191 3215 2.225467 GGAATGATCCAAGCTACTGCC 58.775 52.381 0.00 0.00 45.79 4.85
3380 3404 8.037166 GGCATCAGGACAAGAAAGAAAAATATT 58.963 33.333 0.00 0.00 0.00 1.28
3457 3481 7.423199 CAAAGCAGATATCATAATTGCACAGT 58.577 34.615 14.25 0.00 37.24 3.55
3561 3585 4.130118 GCACATTGACGGAATAGAAGGAT 58.870 43.478 0.00 0.00 0.00 3.24
3573 3597 2.485426 AGGAGAAACATGCACATTGACG 59.515 45.455 0.00 0.00 0.00 4.35
3608 3632 4.053469 ACAAACTTGGGCACACAAATAC 57.947 40.909 0.00 0.00 0.00 1.89
3614 3638 3.881089 AGTACTAACAAACTTGGGCACAC 59.119 43.478 0.00 0.00 0.00 3.82
3619 3643 9.886132 ACATAATCTAGTACTAACAAACTTGGG 57.114 33.333 3.76 0.00 0.00 4.12
3660 3769 8.103948 AGTTACAAAAGATCATGTGAAGGAAG 57.896 34.615 8.55 0.00 0.00 3.46
3716 3825 9.341899 GCATTCATACGAACACTTCTTTATTTT 57.658 29.630 0.00 0.00 32.81 1.82
3717 3826 7.968405 GGCATTCATACGAACACTTCTTTATTT 59.032 33.333 0.00 0.00 32.81 1.40
3718 3827 7.120579 TGGCATTCATACGAACACTTCTTTATT 59.879 33.333 0.00 0.00 32.81 1.40
3724 3833 4.882671 ATGGCATTCATACGAACACTTC 57.117 40.909 0.00 0.00 33.61 3.01
3732 3841 4.437794 GCATGTGGATATGGCATTCATACG 60.438 45.833 4.78 0.00 40.75 3.06
3738 3847 4.021719 GCTTAAGCATGTGGATATGGCATT 60.022 41.667 22.59 0.00 41.59 3.56
3760 3869 6.870439 AGAGGTGCTTTCTTTTATCAAAATGC 59.130 34.615 0.00 0.00 0.00 3.56
3779 3888 2.989840 CACTTCTACGAGCAAAGAGGTG 59.010 50.000 0.00 1.02 41.51 4.00
3795 3916 3.594134 AGTCAGCTCATAAGTGCACTTC 58.406 45.455 34.29 19.82 37.40 3.01
3875 3996 3.408634 ACCAGCAACAGTGTGGTTATAC 58.591 45.455 0.00 0.00 42.10 1.47
3877 3998 2.656947 ACCAGCAACAGTGTGGTTAT 57.343 45.000 0.00 0.00 42.10 1.89
3879 4000 2.229792 CATACCAGCAACAGTGTGGTT 58.770 47.619 8.32 0.00 42.10 3.67
3880 4001 1.896220 CATACCAGCAACAGTGTGGT 58.104 50.000 8.12 8.12 46.54 4.16
3882 4003 1.237533 TGCATACCAGCAACAGTGTG 58.762 50.000 0.00 0.00 42.46 3.82
3883 4004 3.723772 TGCATACCAGCAACAGTGT 57.276 47.368 0.00 0.00 42.46 3.55
3906 4045 9.137459 TGGTGAAAAAGGTATGTTATTCTCAAA 57.863 29.630 0.00 0.00 0.00 2.69
3955 4094 7.495606 CAGGCTTTCTATTGTTTTGGAAACTTT 59.504 33.333 5.30 0.00 0.00 2.66
3956 4095 6.986231 CAGGCTTTCTATTGTTTTGGAAACTT 59.014 34.615 5.30 0.00 0.00 2.66
3966 4105 2.171003 GTGGGCAGGCTTTCTATTGTT 58.829 47.619 0.00 0.00 0.00 2.83
4009 4150 2.283298 ACAGGTGAATGCTATGCTTCG 58.717 47.619 0.00 0.00 0.00 3.79
4010 4151 3.539604 AGACAGGTGAATGCTATGCTTC 58.460 45.455 0.00 0.00 0.00 3.86
4026 4167 6.492007 AAGAAGCATGAATACACAAGACAG 57.508 37.500 0.00 0.00 0.00 3.51
4064 4205 7.492020 CACAAAGAGAGAGAATGACAGAATAGG 59.508 40.741 0.00 0.00 0.00 2.57
4078 4219 3.070159 TCACAGGTTCCACAAAGAGAGAG 59.930 47.826 0.00 0.00 0.00 3.20
4079 4220 3.038280 TCACAGGTTCCACAAAGAGAGA 58.962 45.455 0.00 0.00 0.00 3.10
4132 4273 2.743752 CCGAGGTTGCACTGCATCG 61.744 63.158 15.53 15.53 38.76 3.84
4314 4455 2.503765 TGATGGAATTCTCTTACCGCCA 59.496 45.455 5.23 0.00 0.00 5.69
4317 4458 2.797156 CGCTGATGGAATTCTCTTACCG 59.203 50.000 5.23 0.00 0.00 4.02
4407 4548 5.141182 TCTTCAACTTAGACAGAGTCCACT 58.859 41.667 0.00 0.00 32.18 4.00
4482 4626 5.013391 ACCGTCTTCCCTCAATAAGGTTAAA 59.987 40.000 0.00 0.00 44.56 1.52
4498 4642 3.521560 TGCATACAGATTGACCGTCTTC 58.478 45.455 0.00 0.00 0.00 2.87
4544 4688 2.555448 GGAAGAACAAGAGGGGGAAAGG 60.555 54.545 0.00 0.00 0.00 3.11
4549 4693 2.834113 TCTAGGAAGAACAAGAGGGGG 58.166 52.381 0.00 0.00 0.00 5.40
4815 5227 7.262048 CCAACAATTTGGTGTGTAAAAGTACT 58.738 34.615 13.18 0.00 46.63 2.73
4848 5260 0.385390 CACACCCAAAGAGCAACACC 59.615 55.000 0.00 0.00 0.00 4.16
4903 5902 5.050490 CCCTCGAGAATAATGTTGTGGTAG 58.950 45.833 15.71 0.00 0.00 3.18
4906 5905 3.206150 CCCCTCGAGAATAATGTTGTGG 58.794 50.000 15.71 1.19 0.00 4.17
5034 6035 1.555075 TGGCTAGGCTTCAGGTGTTAG 59.445 52.381 18.18 0.00 0.00 2.34
5043 6044 0.393132 GGTTGGTCTGGCTAGGCTTC 60.393 60.000 18.18 7.52 0.00 3.86
5056 6057 4.898861 ACAGGTACAATTGAAATGGTTGGT 59.101 37.500 13.59 0.00 0.00 3.67
5070 6071 4.772624 AGAGCTCTTGTCATACAGGTACAA 59.227 41.667 11.45 0.00 0.00 2.41
5100 6101 2.642311 TCCCATTTGCTCAGGTCTTGTA 59.358 45.455 0.00 0.00 0.00 2.41
5278 6283 3.782992 AGGATCTGGAAGTTGCCAAAAT 58.217 40.909 0.00 0.00 37.52 1.82
5352 6357 4.502087 GCAAGGAAGGTTTGCTCTTTCAAT 60.502 41.667 2.93 0.00 45.64 2.57
5387 6392 1.068541 CCTTGCCAAACGAAGCCTAAC 60.069 52.381 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.