Multiple sequence alignment - TraesCS2D01G288800

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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 TraesCS2D01G288800 chr2D 100.000 6568 0 0 1 6568 370236575 370243142 0.000000e+00 12129.0
1 TraesCS2D01G288800 chr2D 100.000 325 0 0 6910 7234 370243484 370243808 1.040000e-167 601.0
2 TraesCS2D01G288800 chr2A 95.284 6065 167 40 494 6462 501316984 501323025 0.000000e+00 9505.0
3 TraesCS2D01G288800 chr2A 89.034 383 39 3 111 491 501316537 501316918 8.490000e-129 472.0
4 TraesCS2D01G288800 chr2A 80.669 269 12 11 6967 7234 501323149 501323378 9.650000e-39 172.0
5 TraesCS2D01G288800 chr2A 94.792 96 5 0 6460 6555 501323054 501323149 4.520000e-32 150.0
6 TraesCS2D01G288800 chr2B 92.695 2902 120 27 1 2834 439766609 439769486 0.000000e+00 4100.0
7 TraesCS2D01G288800 chr2B 92.255 1885 102 21 2833 4680 439769564 439771441 0.000000e+00 2632.0
8 TraesCS2D01G288800 chr2B 90.347 1730 82 33 4775 6462 439771814 439773500 0.000000e+00 2191.0
9 TraesCS2D01G288800 chr2B 89.046 283 23 3 6953 7234 439773690 439773965 1.930000e-90 344.0
10 TraesCS2D01G288800 chr2B 95.000 60 3 0 6460 6519 439773529 439773588 2.150000e-15 95.3
11 TraesCS2D01G288800 chr2B 78.400 125 20 7 224 344 699214341 699214220 2.800000e-09 75.0
12 TraesCS2D01G288800 chr6B 72.688 919 190 51 4635 5519 699005527 699004636 4.330000e-62 250.0
13 TraesCS2D01G288800 chr6B 79.636 275 42 10 3505 3770 699007326 699007057 1.240000e-42 185.0
14 TraesCS2D01G288800 chr6B 83.721 86 9 5 254 335 76485014 76484930 7.780000e-10 76.8
15 TraesCS2D01G288800 chr6D 80.147 272 44 8 3506 3770 459697802 459697534 2.060000e-45 195.0
16 TraesCS2D01G288800 chr6A 79.422 277 37 14 3505 3770 605379651 605379384 2.070000e-40 178.0
17 TraesCS2D01G288800 chr4B 82.692 104 15 3 234 335 59225241 59225343 1.000000e-13 89.8
18 TraesCS2D01G288800 chr4A 82.178 101 13 5 236 333 728854111 728854209 1.670000e-11 82.4
19 TraesCS2D01G288800 chr1D 85.000 80 10 2 254 331 457775844 457775923 6.020000e-11 80.5
20 TraesCS2D01G288800 chr1A 79.130 115 22 2 248 360 552204087 552204201 2.160000e-10 78.7
21 TraesCS2D01G288800 chr1B 85.938 64 8 1 275 338 682026643 682026581 4.680000e-07 67.6


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 TraesCS2D01G288800 chr2D 370236575 370243808 7233 False 6365.00 12129 100.00000 1 7234 2 chr2D.!!$F1 7233
1 TraesCS2D01G288800 chr2A 501316537 501323378 6841 False 2574.75 9505 89.94475 111 7234 4 chr2A.!!$F1 7123
2 TraesCS2D01G288800 chr2B 439766609 439773965 7356 False 1872.46 4100 91.86860 1 7234 5 chr2B.!!$F1 7233
3 TraesCS2D01G288800 chr6B 699004636 699007326 2690 True 217.50 250 76.16200 3505 5519 2 chr6B.!!$R2 2014

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
678 773 0.604780 CCTCACAGACACCTGGCTTG 60.605 60.000 0.00 0.0 44.60 4.01 F
1029 1166 0.830648 ACATATACGCCACCACAGCT 59.169 50.000 0.00 0.0 0.00 4.24 F
1501 1647 0.893727 GGTTGGTGAATTGGGAGCGT 60.894 55.000 0.00 0.0 0.00 5.07 F
1558 1704 1.028330 TACTGAGTACTGACCGCCGG 61.028 60.000 0.00 0.0 0.00 6.13 F
1738 1884 1.377856 GAAGCAGAAGTGGAGCCCC 60.378 63.158 0.00 0.0 0.00 5.80 F
2995 3256 1.678101 GCACAGAGCAAAAACACTCCT 59.322 47.619 0.00 0.0 44.79 3.69 F
3602 3864 1.271054 ACTAGTGGCAGCACAGGAAAG 60.271 52.381 0.00 0.0 0.00 2.62 F
5477 6985 3.379240 TGTTTCACATCCAAAATGTGCG 58.621 40.909 12.22 0.0 46.49 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1968 2.340210 TCACAAACAAGCTAGCACCA 57.660 45.000 18.83 0.0 0.00 4.17 R
2665 2813 2.355132 TGTACACCGTTGCAATTTTCGT 59.645 40.909 0.59 0.0 0.00 3.85 R
2995 3256 2.554344 GGCCACCACCAAAGTATCTGAA 60.554 50.000 0.00 0.0 0.00 3.02 R
3071 3332 2.753452 AGGCATCAATGAAGAACAGCAG 59.247 45.455 0.00 0.0 0.00 4.24 R
3117 3378 6.013898 ACATCCATGATCAAGAGTATACTGGG 60.014 42.308 10.90 0.0 0.00 4.45 R
4010 4289 0.606673 AGCCTCAAAAGCGAAGGGTC 60.607 55.000 0.00 0.0 34.64 4.46 R
5564 7073 0.868406 CTCAGTTTGGACGAAGCCAC 59.132 55.000 0.00 0.0 37.75 5.01 R
7015 8587 0.808060 TGCTCGTGTCTTTCGCAACA 60.808 50.000 0.00 0.0 0.00 3.33 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
163 165 3.257375 ACCTTACAAATCGGAAAAAGGGC 59.743 43.478 0.00 0.00 38.22 5.19
174 176 1.954382 GAAAAAGGGCGAGTGTTTCCT 59.046 47.619 0.00 0.00 0.00 3.36
212 215 5.473846 AGCATGGCTTAGATGATTTGATCTG 59.526 40.000 0.00 0.00 33.89 2.90
214 217 5.635278 TGGCTTAGATGATTTGATCTGGA 57.365 39.130 0.00 0.00 34.42 3.86
262 265 6.631016 TCTAAACTTAGACATTGATGCTCGT 58.369 36.000 0.00 0.00 34.99 4.18
349 352 5.277345 CGACTATGAGACGTGTGTGATGATA 60.277 44.000 0.00 0.00 0.00 2.15
426 429 8.588472 ACTGTATATGTGTATGTGAGCATATGT 58.412 33.333 4.29 0.00 39.49 2.29
465 471 5.240121 CCCAAAAATGAGAAATTGGTGAGG 58.760 41.667 0.00 0.00 40.55 3.86
610 705 0.666577 GTCCGTCCGTTCTGTTCCAG 60.667 60.000 0.00 0.00 0.00 3.86
633 728 4.755507 GACCCCGACCCCGAGAGT 62.756 72.222 0.00 0.00 38.22 3.24
678 773 0.604780 CCTCACAGACACCTGGCTTG 60.605 60.000 0.00 0.00 44.60 4.01
796 913 1.067000 AGCAGCAAGAGCACTCTACAG 60.067 52.381 0.00 0.00 45.49 2.74
931 1054 5.508994 CGCCCCAAAAGTCAGAAATAGTTTT 60.509 40.000 0.00 0.00 31.26 2.43
1011 1148 4.218722 CCGTCAATGGCCCAGTAC 57.781 61.111 0.00 0.00 0.00 2.73
1029 1166 0.830648 ACATATACGCCACCACAGCT 59.169 50.000 0.00 0.00 0.00 4.24
1321 1467 3.873910 TCTCCACTTCCCATTTCGATTC 58.126 45.455 0.00 0.00 0.00 2.52
1501 1647 0.893727 GGTTGGTGAATTGGGAGCGT 60.894 55.000 0.00 0.00 0.00 5.07
1558 1704 1.028330 TACTGAGTACTGACCGCCGG 61.028 60.000 0.00 0.00 0.00 6.13
1738 1884 1.377856 GAAGCAGAAGTGGAGCCCC 60.378 63.158 0.00 0.00 0.00 5.80
1822 1968 2.095919 GTGCCTAAGCGTGTTCGATTTT 60.096 45.455 0.00 0.00 43.12 1.82
2056 2202 5.828299 TTGCCAGGTAAATATGCTGTTAC 57.172 39.130 0.00 0.00 0.00 2.50
2630 2778 4.081697 TCACCTACATATGTCCACACTGTG 60.082 45.833 12.68 6.19 0.00 3.66
2649 2797 8.673711 ACACTGTGCATACAAATATTTATCGTT 58.326 29.630 7.90 0.00 36.14 3.85
2967 3219 2.431454 TGAAATTACCAGATGTGCGCA 58.569 42.857 5.66 5.66 0.00 6.09
2995 3256 1.678101 GCACAGAGCAAAAACACTCCT 59.322 47.619 0.00 0.00 44.79 3.69
3115 3376 7.362056 GCCTTATGCAATGTCTGAACTCTAAAA 60.362 37.037 0.00 0.00 40.77 1.52
3117 3378 9.713740 CTTATGCAATGTCTGAACTCTAAAATC 57.286 33.333 0.00 0.00 0.00 2.17
3118 3379 6.500684 TGCAATGTCTGAACTCTAAAATCC 57.499 37.500 0.00 0.00 0.00 3.01
3157 3418 4.826274 TGGATGTTACTTCTTCTGGGAG 57.174 45.455 0.00 0.00 0.00 4.30
3196 3457 8.291191 TGATCATATGCACAGAATTGGTTTAA 57.709 30.769 0.00 0.00 0.00 1.52
3360 3621 9.301153 GCAGGTATATCCAAATTAAACAAGTTG 57.699 33.333 0.00 0.00 39.02 3.16
3602 3864 1.271054 ACTAGTGGCAGCACAGGAAAG 60.271 52.381 0.00 0.00 0.00 2.62
3818 4085 3.551551 GCATAAATTTGGTCGCGGTATC 58.448 45.455 6.13 0.00 0.00 2.24
4074 4521 8.699749 GTTGTAACTTATTTCTTGAATGCAACC 58.300 33.333 0.00 0.00 0.00 3.77
4239 5408 7.308529 CCTGTGTGCTCATTTGAACATTTAGTA 60.309 37.037 0.00 0.00 0.00 1.82
4327 5496 3.626217 CCGGGAAGCTTTTTCTACCATAC 59.374 47.826 0.00 0.00 0.00 2.39
4372 5541 4.540359 AATGGTGCAACAACATATGCTT 57.460 36.364 9.38 0.00 41.31 3.91
4394 5563 6.146347 GCTTCCGAGCGAAATCTCTAATAATT 59.854 38.462 0.00 0.00 39.48 1.40
4402 5571 9.817809 AGCGAAATCTCTAATAATTTCTGTACA 57.182 29.630 0.00 0.00 38.93 2.90
4735 5922 8.246430 TGGTGGTTTTATGGTAATTGTGTTTA 57.754 30.769 0.00 0.00 0.00 2.01
4781 6246 3.993081 AGCTCTCAAAGTGAGTTTCATCG 59.007 43.478 5.23 0.00 44.58 3.84
4959 6424 7.172532 CCTCTTACTTTGTAATTACTGTGCACA 59.827 37.037 20.37 20.37 0.00 4.57
4960 6425 8.615878 TCTTACTTTGTAATTACTGTGCACAT 57.384 30.769 22.00 13.04 0.00 3.21
5227 6723 8.485392 TGTGATCCAGAATTACATGTTCATAGA 58.515 33.333 2.30 0.00 29.52 1.98
5257 6753 4.822036 TTAAATTTGTGTGTCAGGGACG 57.178 40.909 0.00 0.00 34.95 4.79
5306 6802 6.293845 GGAAGAGTGGATGATGTTATCAATGC 60.294 42.308 0.00 0.00 43.50 3.56
5361 6857 6.611381 TCACGCTTCCTTGAATTGAAATTAG 58.389 36.000 0.00 0.00 0.00 1.73
5362 6858 6.429692 TCACGCTTCCTTGAATTGAAATTAGA 59.570 34.615 0.00 0.00 0.00 2.10
5365 6861 6.694411 CGCTTCCTTGAATTGAAATTAGATGG 59.306 38.462 0.00 0.00 0.00 3.51
5366 6862 6.478016 GCTTCCTTGAATTGAAATTAGATGGC 59.522 38.462 0.00 0.00 0.00 4.40
5367 6863 7.632245 GCTTCCTTGAATTGAAATTAGATGGCT 60.632 37.037 0.00 0.00 0.00 4.75
5369 6865 8.137745 TCCTTGAATTGAAATTAGATGGCTTT 57.862 30.769 0.00 0.00 0.00 3.51
5477 6985 3.379240 TGTTTCACATCCAAAATGTGCG 58.621 40.909 12.22 0.00 46.49 5.34
5564 7073 0.036732 CCATATCATGACCCCCACCG 59.963 60.000 0.00 0.00 0.00 4.94
5721 7230 2.359900 CGCAGCCAGGTATTTTCTTCT 58.640 47.619 0.00 0.00 0.00 2.85
5752 7262 4.274950 TCTTAAAGTGTTGGTTGCTACTGC 59.725 41.667 0.00 0.00 40.20 4.40
5775 7285 4.134379 ACTGCAAGAGATCTATGTGTGG 57.866 45.455 0.00 0.00 37.43 4.17
5809 7319 1.718757 CTAACAATGGCTCCGCTGGC 61.719 60.000 0.00 0.00 0.00 4.85
5824 7334 4.344865 GGCGCTGGGGAAGTTGGA 62.345 66.667 7.64 0.00 0.00 3.53
5838 7348 5.279006 GGGAAGTTGGAACCTGATTTTTCTC 60.279 44.000 0.00 0.00 0.00 2.87
5853 7363 1.964608 TTCTCGCCCTGCTGATCTGG 61.965 60.000 1.46 0.00 0.00 3.86
5892 7402 5.047377 TGCTTTTTCAATGATGGAACCTACC 60.047 40.000 0.00 0.00 0.00 3.18
5908 7418 5.138125 ACCTACCATTTCAACATGCTTTG 57.862 39.130 0.00 0.00 0.00 2.77
5944 7454 5.728637 ACCTTTTGAGATTGAATGGAACC 57.271 39.130 0.00 0.00 0.00 3.62
5948 7458 6.870439 CCTTTTGAGATTGAATGGAACCTTTC 59.130 38.462 11.06 11.06 0.00 2.62
6053 7563 2.964464 TGTCATTTTGTGGCAGATTGGT 59.036 40.909 0.00 0.00 37.56 3.67
6313 7823 2.158957 TCTTGCCTCGGGTGCTAAATAG 60.159 50.000 0.00 0.00 0.00 1.73
6314 7824 1.200519 TGCCTCGGGTGCTAAATAGT 58.799 50.000 0.00 0.00 0.00 2.12
6315 7825 2.390696 TGCCTCGGGTGCTAAATAGTA 58.609 47.619 0.00 0.00 0.00 1.82
6321 7831 4.275810 TCGGGTGCTAAATAGTACAGAGT 58.724 43.478 10.22 0.00 40.15 3.24
6325 7835 6.380190 GGGTGCTAAATAGTACAGAGTATCG 58.620 44.000 10.22 0.00 40.15 2.92
6457 7967 6.599244 GGATCACATCACAGAAAAATACTCCA 59.401 38.462 0.00 0.00 0.00 3.86
6458 7968 6.801539 TCACATCACAGAAAAATACTCCAC 57.198 37.500 0.00 0.00 0.00 4.02
6494 8036 6.912203 TTAATGTGAGACGAACACTTGAAA 57.088 33.333 0.00 0.00 38.81 2.69
6519 8061 3.535561 ACTTGAGCGGATATTGAGGTTG 58.464 45.455 0.00 0.00 0.00 3.77
6955 8505 2.349755 GCACGGCAACCTCCCTAA 59.650 61.111 0.00 0.00 0.00 2.69
6956 8506 1.302993 GCACGGCAACCTCCCTAAA 60.303 57.895 0.00 0.00 0.00 1.85
6957 8507 1.305930 GCACGGCAACCTCCCTAAAG 61.306 60.000 0.00 0.00 0.00 1.85
6958 8508 0.676782 CACGGCAACCTCCCTAAAGG 60.677 60.000 0.00 0.00 42.55 3.11
6960 8510 1.379977 GGCAACCTCCCTAAAGGCC 60.380 63.158 0.00 0.00 40.34 5.19
6961 8511 1.379977 GCAACCTCCCTAAAGGCCC 60.380 63.158 0.00 0.00 40.34 5.80
6962 8512 2.083715 CAACCTCCCTAAAGGCCCA 58.916 57.895 0.00 0.00 40.34 5.36
6963 8513 0.407918 CAACCTCCCTAAAGGCCCAA 59.592 55.000 0.00 0.00 40.34 4.12
6964 8514 1.163408 AACCTCCCTAAAGGCCCAAA 58.837 50.000 0.00 0.00 40.34 3.28
6965 8515 0.704664 ACCTCCCTAAAGGCCCAAAG 59.295 55.000 0.00 0.00 40.34 2.77
6966 8516 0.704664 CCTCCCTAAAGGCCCAAAGT 59.295 55.000 0.00 0.00 34.51 2.66
6984 8555 7.147915 GCCCAAAGTGTAAAATCCAAGATGATA 60.148 37.037 0.00 0.00 0.00 2.15
7015 8587 2.473576 ATCTAGGGGGAACGTAGCTT 57.526 50.000 0.00 0.00 37.45 3.74
7020 8592 1.583495 GGGGGAACGTAGCTTGTTGC 61.583 60.000 12.62 12.62 43.29 4.17
7046 8618 0.534412 CACGAGCATTCCTGGAGTCT 59.466 55.000 0.00 0.00 0.00 3.24
7090 8662 1.349234 GCGATTGTTGGCCAAATGTC 58.651 50.000 22.47 16.41 36.44 3.06
7122 8694 4.452733 CCGGCGTTGGAGTCTCCC 62.453 72.222 16.60 0.67 35.03 4.30
7154 8726 0.764369 TGGAGTGAGGGAGTTGCAGT 60.764 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 110 3.246226 CCTTAGATCGGCAATTTGACTCG 59.754 47.826 0.00 1.16 0.00 4.18
203 205 3.011595 TGGTTCCACCATCCAGATCAAAT 59.988 43.478 0.00 0.00 44.79 2.32
204 206 2.378208 TGGTTCCACCATCCAGATCAAA 59.622 45.455 0.00 0.00 44.79 2.69
288 291 7.282585 TCCTCCCACTGAATAAATATTGTCAG 58.717 38.462 16.74 16.74 0.00 3.51
289 292 7.127186 TCTCCTCCCACTGAATAAATATTGTCA 59.873 37.037 0.00 0.00 0.00 3.58
369 372 0.526739 ACGCACGCATCTACGCATAA 60.527 50.000 0.00 0.00 36.19 1.90
371 374 1.358725 AAACGCACGCATCTACGCAT 61.359 50.000 0.00 0.00 36.19 4.73
377 380 3.159353 TCACTATAAACGCACGCATCT 57.841 42.857 0.00 0.00 0.00 2.90
426 429 8.553153 TCATTTTTGGGGAACATAGTATAGTCA 58.447 33.333 0.00 0.00 0.00 3.41
506 575 8.785329 TTCTTGCCAAAAGAACAGTTTAAAAT 57.215 26.923 0.00 0.00 31.86 1.82
523 592 2.103432 TGGTTTCGACTAGTTCTTGCCA 59.897 45.455 0.00 1.07 0.00 4.92
633 728 6.049149 AGAATCGACACTCTTTTTGTTCTGA 58.951 36.000 0.00 0.00 0.00 3.27
743 860 7.445707 CAGCTACTACTACTGTCTATGGATTCA 59.554 40.741 0.00 0.00 0.00 2.57
796 913 1.452145 TTTTTCTGGTGGCACGGAGC 61.452 55.000 12.17 0.00 44.65 4.70
1011 1148 1.502231 GAGCTGTGGTGGCGTATATG 58.498 55.000 0.00 0.00 34.52 1.78
1079 1225 2.124403 GAGACGACGAGGGGGCTA 60.124 66.667 0.00 0.00 0.00 3.93
1086 1232 2.052941 GGCGATCGAGACGACGAG 60.053 66.667 21.57 4.87 45.22 4.18
1321 1467 1.026718 GTCTGGGGCCGAATCAACAG 61.027 60.000 0.00 0.00 0.00 3.16
1423 1569 4.776837 CAGTCCCTATCTGCCTTATCTGAT 59.223 45.833 0.00 0.00 0.00 2.90
1558 1704 3.573967 ACACAATCAGGGAATGTTCAACC 59.426 43.478 0.00 0.00 0.00 3.77
1738 1884 3.119779 GGTTCTCAGTACAGACTTCCTCG 60.120 52.174 0.00 0.00 31.73 4.63
1822 1968 2.340210 TCACAAACAAGCTAGCACCA 57.660 45.000 18.83 0.00 0.00 4.17
2056 2202 6.421501 ACATGTTACATGCAATTGTTTCACTG 59.578 34.615 23.43 0.00 0.00 3.66
2247 2393 4.657039 ACTGGGGTAAAACTTACAGAGTGA 59.343 41.667 0.00 0.00 39.00 3.41
2603 2751 6.092670 CAGTGTGGACATATGTAGGTGAAAAG 59.907 42.308 8.71 0.00 0.00 2.27
2630 2778 9.417284 GCGGTATAACGATAAATATTTGTATGC 57.583 33.333 15.85 0.00 35.47 3.14
2649 2797 7.799447 GCAATTTTCGTATACAAATGCGGTATA 59.201 33.333 3.32 0.00 41.03 1.47
2665 2813 2.355132 TGTACACCGTTGCAATTTTCGT 59.645 40.909 0.59 0.00 0.00 3.85
2977 3229 3.620488 TGAAGGAGTGTTTTTGCTCTGT 58.380 40.909 0.00 0.00 32.67 3.41
2995 3256 2.554344 GGCCACCACCAAAGTATCTGAA 60.554 50.000 0.00 0.00 0.00 3.02
3071 3332 2.753452 AGGCATCAATGAAGAACAGCAG 59.247 45.455 0.00 0.00 0.00 4.24
3115 3376 6.326161 TCCATGATCAAGAGTATACTGGGAT 58.674 40.000 10.90 9.84 0.00 3.85
3117 3378 6.013898 ACATCCATGATCAAGAGTATACTGGG 60.014 42.308 10.90 0.00 0.00 4.45
3118 3379 7.002250 ACATCCATGATCAAGAGTATACTGG 57.998 40.000 10.90 2.87 0.00 4.00
3196 3457 9.579932 AACTTCAGACTTTGGATTAGATTTCTT 57.420 29.630 0.00 0.00 0.00 2.52
3368 3629 8.830580 TCTGTGCTTAAAAATCAGATACATAGC 58.169 33.333 0.00 0.00 31.51 2.97
3818 4085 4.516698 ACAGTAAGAAACACAGCTTCCATG 59.483 41.667 0.00 0.00 0.00 3.66
4010 4289 0.606673 AGCCTCAAAAGCGAAGGGTC 60.607 55.000 0.00 0.00 34.64 4.46
4017 4464 5.973565 CCAATCTAAATAAGCCTCAAAAGCG 59.026 40.000 0.00 0.00 34.64 4.68
4074 4521 2.093447 CAGGGTAGTTTGGAGCCTACAG 60.093 54.545 0.00 0.00 42.97 2.74
4239 5408 3.262420 GCACCACTTAACTGATGACGAT 58.738 45.455 0.00 0.00 0.00 3.73
4372 5541 7.382488 CAGAAATTATTAGAGATTTCGCTCGGA 59.618 37.037 0.00 0.00 43.56 4.55
4735 5922 4.813697 CCGAAATTTCCCACACACAATTTT 59.186 37.500 12.54 0.00 30.66 1.82
4781 6246 6.736853 GCATTACAGTTCGATTCAACAAGTAC 59.263 38.462 0.00 0.00 0.00 2.73
5257 6753 3.378427 GTCAGCCAATGGTAACCATCTTC 59.622 47.826 0.00 0.00 44.40 2.87
5361 6857 3.928992 GCTTCAAAGCCTTTAAAGCCATC 59.071 43.478 13.18 0.00 46.20 3.51
5362 6858 3.930336 GCTTCAAAGCCTTTAAAGCCAT 58.070 40.909 13.18 0.00 46.20 4.40
5413 6921 1.301623 CCAATCCGGTGCCCACTAA 59.698 57.895 0.00 0.00 0.00 2.24
5564 7073 0.868406 CTCAGTTTGGACGAAGCCAC 59.132 55.000 0.00 0.00 37.75 5.01
5721 7230 7.284489 AGCAACCAACACTTTAAGAAACTATCA 59.716 33.333 0.00 0.00 0.00 2.15
5752 7262 4.331992 CCACACATAGATCTCTTGCAGTTG 59.668 45.833 0.00 0.00 0.00 3.16
5753 7263 4.019860 ACCACACATAGATCTCTTGCAGTT 60.020 41.667 0.00 0.00 0.00 3.16
5754 7264 3.517100 ACCACACATAGATCTCTTGCAGT 59.483 43.478 0.00 0.00 0.00 4.40
5755 7265 3.869832 CACCACACATAGATCTCTTGCAG 59.130 47.826 0.00 0.00 0.00 4.41
5756 7266 3.369787 CCACCACACATAGATCTCTTGCA 60.370 47.826 0.00 0.00 0.00 4.08
5757 7267 3.118629 TCCACCACACATAGATCTCTTGC 60.119 47.826 0.00 0.00 0.00 4.01
5767 7277 2.616765 CGGGTTCATTCCACCACACATA 60.617 50.000 0.00 0.00 35.80 2.29
5775 7285 1.092348 GTTAGCCGGGTTCATTCCAC 58.908 55.000 13.43 0.00 0.00 4.02
5809 7319 1.971695 GGTTCCAACTTCCCCAGCG 60.972 63.158 0.00 0.00 0.00 5.18
5810 7320 0.895559 CAGGTTCCAACTTCCCCAGC 60.896 60.000 0.00 0.00 0.00 4.85
5815 7325 5.562890 CGAGAAAAATCAGGTTCCAACTTCC 60.563 44.000 0.00 0.00 0.00 3.46
5824 7334 2.162681 CAGGGCGAGAAAAATCAGGTT 58.837 47.619 0.00 0.00 0.00 3.50
5838 7348 0.677731 TTTTCCAGATCAGCAGGGCG 60.678 55.000 0.00 0.00 0.00 6.13
5853 7363 9.667989 ATTGAAAAAGCACAAGCATTATTTTTC 57.332 25.926 11.89 11.89 43.79 2.29
5892 7402 6.774354 AAACTAGCAAAGCATGTTGAAATG 57.226 33.333 0.45 0.00 0.00 2.32
5923 7433 5.990120 AGGTTCCATTCAATCTCAAAAGG 57.010 39.130 0.00 0.00 0.00 3.11
6002 7512 8.832521 TGTATGTCTTTACACTCGTTTCAAAAT 58.167 29.630 0.00 0.00 38.78 1.82
6053 7563 2.515757 TCAGGTGCTGCAAACGCA 60.516 55.556 2.77 0.00 37.92 5.24
6089 7599 3.382832 CGTGTCTTCGGGAGCCCT 61.383 66.667 3.70 0.00 0.00 5.19
6227 7737 1.204704 TCCATCCTCACACGCTAACTG 59.795 52.381 0.00 0.00 0.00 3.16
6313 7823 6.585322 GGCACATATAAACCGATACTCTGTAC 59.415 42.308 0.00 0.00 0.00 2.90
6314 7824 6.265876 TGGCACATATAAACCGATACTCTGTA 59.734 38.462 0.00 0.00 0.00 2.74
6315 7825 5.069914 TGGCACATATAAACCGATACTCTGT 59.930 40.000 0.00 0.00 0.00 3.41
6321 7831 3.061322 GCGTGGCACATATAAACCGATA 58.939 45.455 19.09 0.00 44.52 2.92
6325 7835 2.287547 CCATGCGTGGCACATATAAACC 60.288 50.000 19.09 0.00 43.04 3.27
6412 7922 7.812191 GTGATCCAACAATTTACATTTACAGCA 59.188 33.333 0.00 0.00 0.00 4.41
6414 7924 9.859427 ATGTGATCCAACAATTTACATTTACAG 57.141 29.630 0.00 0.00 32.81 2.74
6457 7967 6.201044 GTCTCACATTAATGCAGCTAATACGT 59.799 38.462 15.48 0.00 0.00 3.57
6458 7968 6.584954 GTCTCACATTAATGCAGCTAATACG 58.415 40.000 15.48 0.00 0.00 3.06
6494 8036 3.181471 CCTCAATATCCGCTCAAGTCACT 60.181 47.826 0.00 0.00 0.00 3.41
6519 8061 5.862678 AGGAGACTACTTAATGAAGAGGC 57.137 43.478 0.00 0.00 40.61 4.70
6915 8457 4.466370 CCTGTACCTCTGTAACCATTGAGA 59.534 45.833 0.00 0.00 0.00 3.27
6921 8463 1.621814 GTGCCTGTACCTCTGTAACCA 59.378 52.381 0.00 0.00 0.00 3.67
6931 8473 3.053896 GGTTGCCGTGCCTGTACC 61.054 66.667 0.00 0.00 0.00 3.34
6955 8505 3.582164 TGGATTTTACACTTTGGGCCTT 58.418 40.909 4.53 0.00 0.00 4.35
6956 8506 3.252554 TGGATTTTACACTTTGGGCCT 57.747 42.857 4.53 0.00 0.00 5.19
6957 8507 3.576550 TCTTGGATTTTACACTTTGGGCC 59.423 43.478 0.00 0.00 0.00 5.80
6958 8508 4.864704 TCTTGGATTTTACACTTTGGGC 57.135 40.909 0.00 0.00 0.00 5.36
6962 8512 9.807649 GCAATATCATCTTGGATTTTACACTTT 57.192 29.630 0.00 0.00 0.00 2.66
6963 8513 8.131100 CGCAATATCATCTTGGATTTTACACTT 58.869 33.333 0.00 0.00 0.00 3.16
6964 8514 7.498900 TCGCAATATCATCTTGGATTTTACACT 59.501 33.333 0.00 0.00 0.00 3.55
6965 8515 7.639039 TCGCAATATCATCTTGGATTTTACAC 58.361 34.615 0.00 0.00 0.00 2.90
6966 8516 7.800155 TCGCAATATCATCTTGGATTTTACA 57.200 32.000 0.00 0.00 0.00 2.41
6984 8555 2.900546 CCCCCTAGATACTCTTCGCAAT 59.099 50.000 0.00 0.00 0.00 3.56
7015 8587 0.808060 TGCTCGTGTCTTTCGCAACA 60.808 50.000 0.00 0.00 0.00 3.33
7020 8592 1.391485 CAGGAATGCTCGTGTCTTTCG 59.609 52.381 0.00 0.00 33.61 3.46
7090 8662 2.278206 CGGTCAGCCTCGACATCG 60.278 66.667 0.00 0.00 37.66 3.84
7122 8694 1.550524 TCACTCCATCGACCTCCTTTG 59.449 52.381 0.00 0.00 0.00 2.77
7183 8755 2.441901 TCGCCATTCATTGCCCCC 60.442 61.111 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.