Multiple sequence alignment - TraesCS1A01G266700

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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 TraesCS1A01G266700 chr1A 100.000 2716 0 0 1 2716 462122915 462125630 0.000000e+00 5016.0
1 TraesCS1A01G266700 chr1A 82.262 451 59 14 2266 2698 66710123 66710570 1.190000e-98 370.0
2 TraesCS1A01G266700 chr1B 88.164 2788 195 48 1 2716 485804234 485806958 0.000000e+00 3195.0
3 TraesCS1A01G266700 chr1B 80.068 587 91 16 2156 2716 427598273 427598859 1.950000e-111 412.0
4 TraesCS1A01G266700 chr1D 91.439 1904 90 23 1 1879 362780374 362782229 0.000000e+00 2545.0
5 TraesCS1A01G266700 chr1D 85.991 464 49 9 2266 2713 479132948 479132485 1.460000e-132 483.0
6 TraesCS1A01G266700 chr1D 89.759 166 4 3 1876 2041 362782367 362782519 1.650000e-47 200.0
7 TraesCS1A01G266700 chr3B 83.646 587 66 11 2156 2714 585028817 585029401 2.400000e-145 525.0
8 TraesCS1A01G266700 chr3B 81.525 590 80 15 2156 2716 106064166 106063577 2.460000e-125 459.0
9 TraesCS1A01G266700 chr3B 84.382 461 60 6 2268 2716 410066128 410065668 2.480000e-120 442.0
10 TraesCS1A01G266700 chr3B 77.826 230 36 7 2156 2370 203697874 203698103 7.890000e-26 128.0
11 TraesCS1A01G266700 chr5D 83.217 572 79 7 2161 2715 475386858 475386287 2.410000e-140 508.0
12 TraesCS1A01G266700 chr5D 80.889 450 61 9 2266 2702 445066945 445066508 5.610000e-87 331.0
13 TraesCS1A01G266700 chr5D 80.998 421 51 13 2266 2671 326780057 326779651 9.450000e-80 307.0
14 TraesCS1A01G266700 chr3A 84.881 463 56 6 2266 2716 421127447 421126987 3.190000e-124 455.0
15 TraesCS1A01G266700 chr3A 94.118 85 5 0 1093 1177 637290458 637290542 2.190000e-26 130.0
16 TraesCS1A01G266700 chr5A 84.978 446 54 6 2266 2698 621865518 621865073 8.930000e-120 440.0
17 TraesCS1A01G266700 chr3D 83.864 471 56 7 2266 2716 458325730 458326200 5.370000e-117 431.0
18 TraesCS1A01G266700 chr3D 94.118 85 5 0 1093 1177 497373287 497373203 2.190000e-26 130.0
19 TraesCS1A01G266700 chr4A 87.977 341 36 3 2374 2713 678203101 678202765 5.450000e-107 398.0
20 TraesCS1A01G266700 chr7D 81.169 462 70 8 2266 2713 506030548 506031006 3.330000e-94 355.0
21 TraesCS1A01G266700 chr7D 78.261 230 35 7 2156 2370 401775560 401775331 1.700000e-27 134.0
22 TraesCS1A01G266700 chr4B 82.043 323 37 13 2266 2572 41204700 41205017 3.470000e-64 255.0
23 TraesCS1A01G266700 chr2B 100.000 31 0 0 1141 1171 31730844 31730814 1.050000e-04 58.4


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 TraesCS1A01G266700 chr1A 462122915 462125630 2715 False 5016.0 5016 100.000 1 2716 1 chr1A.!!$F2 2715
1 TraesCS1A01G266700 chr1B 485804234 485806958 2724 False 3195.0 3195 88.164 1 2716 1 chr1B.!!$F2 2715
2 TraesCS1A01G266700 chr1B 427598273 427598859 586 False 412.0 412 80.068 2156 2716 1 chr1B.!!$F1 560
3 TraesCS1A01G266700 chr1D 362780374 362782519 2145 False 1372.5 2545 90.599 1 2041 2 chr1D.!!$F1 2040
4 TraesCS1A01G266700 chr3B 585028817 585029401 584 False 525.0 525 83.646 2156 2714 1 chr3B.!!$F2 558
5 TraesCS1A01G266700 chr3B 106063577 106064166 589 True 459.0 459 81.525 2156 2716 1 chr3B.!!$R1 560
6 TraesCS1A01G266700 chr5D 475386287 475386858 571 True 508.0 508 83.217 2161 2715 1 chr5D.!!$R3 554

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
52 53 0.399454 TTCTCTCTTGCAGCAGCCTT 59.601 50.0 0.0 0.0 41.13 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1773 0.866061 CACGTATCCGCCTGAAGACG 60.866 60.0 0.0 0.0 40.39 4.18 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
52 53 0.399454 TTCTCTCTTGCAGCAGCCTT 59.601 50.000 0.00 0.00 41.13 4.35
63 64 2.581354 CAGCCTTCCCTCTCACCG 59.419 66.667 0.00 0.00 0.00 4.94
69 70 1.658686 CTTCCCTCTCACCGGTCTCG 61.659 65.000 2.59 0.00 0.00 4.04
200 201 4.825679 CCACTCCTCCCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
219 220 3.061848 CCACCACCATTGCCCGAC 61.062 66.667 0.00 0.00 0.00 4.79
246 253 7.945664 TGAGATCTCCTCCCTTTAAGTAGATAC 59.054 40.741 20.03 0.00 41.25 2.24
257 264 7.254863 CCCTTTAAGTAGATACAGAGAGACGTC 60.255 44.444 7.70 7.70 0.00 4.34
263 270 8.370266 AGTAGATACAGAGAGACGTCCTATAT 57.630 38.462 13.01 1.17 0.00 0.86
264 271 8.472413 AGTAGATACAGAGAGACGTCCTATATC 58.528 40.741 13.01 10.71 0.00 1.63
265 272 6.646267 AGATACAGAGAGACGTCCTATATCC 58.354 44.000 13.01 0.00 0.00 2.59
266 273 4.708576 ACAGAGAGACGTCCTATATCCA 57.291 45.455 13.01 0.00 0.00 3.41
267 274 5.050126 ACAGAGAGACGTCCTATATCCAA 57.950 43.478 13.01 0.00 0.00 3.53
268 275 5.636123 ACAGAGAGACGTCCTATATCCAAT 58.364 41.667 13.01 0.00 0.00 3.16
303 310 1.477295 CTCCTCCGTCTTGTAGGGTTC 59.523 57.143 0.00 0.00 34.56 3.62
304 311 1.076677 TCCTCCGTCTTGTAGGGTTCT 59.923 52.381 0.00 0.00 34.56 3.01
312 324 4.023193 CGTCTTGTAGGGTTCTTGCATTTT 60.023 41.667 0.00 0.00 0.00 1.82
320 332 2.226437 GGTTCTTGCATTTTGCTCGAGA 59.774 45.455 18.75 0.00 45.31 4.04
327 339 2.413371 GCATTTTGCTCGAGAACTGGAC 60.413 50.000 18.75 0.00 40.96 4.02
328 340 1.497991 TTTTGCTCGAGAACTGGACG 58.502 50.000 18.75 0.00 0.00 4.79
329 341 0.944311 TTTGCTCGAGAACTGGACGC 60.944 55.000 18.75 0.00 0.00 5.19
330 342 2.082629 TTGCTCGAGAACTGGACGCA 62.083 55.000 18.75 0.52 0.00 5.24
331 343 1.803519 GCTCGAGAACTGGACGCAG 60.804 63.158 18.75 0.00 0.00 5.18
367 379 3.008813 TGATGCTTCTTCTCTTCTTGGCT 59.991 43.478 0.88 0.00 0.00 4.75
381 393 4.039092 GGCTGCTGCAGGGAGGAA 62.039 66.667 29.05 0.00 41.91 3.36
386 398 1.222113 GCTGCAGGGAGGAAGTACC 59.778 63.158 17.12 0.00 39.35 3.34
387 399 1.517832 CTGCAGGGAGGAAGTACCG 59.482 63.158 5.57 0.00 44.74 4.02
393 405 2.108970 AGGGAGGAAGTACCGCTAAAG 58.891 52.381 0.00 0.00 44.74 1.85
479 492 4.589908 CAACTATACTTGGGTTTCAGCCT 58.410 43.478 0.00 0.00 36.53 4.58
480 493 4.489306 ACTATACTTGGGTTTCAGCCTC 57.511 45.455 0.00 0.00 36.53 4.70
481 494 3.844211 ACTATACTTGGGTTTCAGCCTCA 59.156 43.478 0.00 0.00 36.53 3.86
482 495 2.859165 TACTTGGGTTTCAGCCTCAG 57.141 50.000 0.00 0.00 36.53 3.35
483 496 0.538287 ACTTGGGTTTCAGCCTCAGC 60.538 55.000 0.00 0.00 36.53 4.26
484 497 1.228552 TTGGGTTTCAGCCTCAGCC 60.229 57.895 0.00 0.00 41.25 4.85
619 632 3.242091 GCAGTGTGATTAGTATGCGTGTG 60.242 47.826 0.00 0.00 0.00 3.82
643 656 1.818060 GGTGTGATGGCATTGCAGTTA 59.182 47.619 11.39 0.00 0.00 2.24
651 664 2.233431 TGGCATTGCAGTTACCAATTCC 59.767 45.455 11.39 0.00 36.78 3.01
743 756 0.543749 ATAGAGTGGAAGGTGCCAGC 59.456 55.000 0.00 0.00 38.95 4.85
764 777 2.030457 CCGTGCCGCAAGTTTCTTATAG 59.970 50.000 5.56 0.00 0.00 1.31
837 855 1.233285 GCATGGCGAGCAGATAAGGG 61.233 60.000 0.00 0.00 0.00 3.95
922 951 1.227089 CCGAGCCAAGATCACGGAG 60.227 63.158 0.00 0.00 45.31 4.63
927 956 1.144936 CCAAGATCACGGAGGAGCC 59.855 63.158 0.00 0.00 0.00 4.70
960 989 2.452295 ATCGGTCGTCTAGCTCGATA 57.548 50.000 11.63 3.86 38.55 2.92
1069 1098 1.617018 CGCCTCCTCCATGAAGGACA 61.617 60.000 0.00 0.00 43.07 4.02
1179 1208 2.989639 CACCTCATCAAGCCCGGA 59.010 61.111 0.73 0.00 0.00 5.14
1300 1344 4.882396 GCTCGCCGGAGAAGCTCC 62.882 72.222 9.83 3.36 46.44 4.70
1337 1382 4.396478 GGTGAGTAAAGAAAGATTCTGGCC 59.604 45.833 0.00 0.00 40.59 5.36
1353 1398 3.494336 CCTCCGCGAGCTGCTTTG 61.494 66.667 8.23 0.51 43.27 2.77
1357 1411 2.501222 CGCGAGCTGCTTTGCTTG 60.501 61.111 20.54 8.97 44.17 4.01
1358 1412 2.641559 GCGAGCTGCTTTGCTTGT 59.358 55.556 17.27 0.00 44.17 3.16
1359 1413 1.728426 GCGAGCTGCTTTGCTTGTG 60.728 57.895 17.27 4.31 44.17 3.33
1360 1414 1.728426 CGAGCTGCTTTGCTTGTGC 60.728 57.895 2.53 0.00 44.17 4.57
1361 1415 1.658673 GAGCTGCTTTGCTTGTGCT 59.341 52.632 2.53 0.00 44.17 4.40
1423 1477 2.432628 GCGGTGACAAGAGGACGG 60.433 66.667 0.00 0.00 0.00 4.79
1424 1478 2.927580 GCGGTGACAAGAGGACGGA 61.928 63.158 0.00 0.00 0.00 4.69
1425 1479 1.080705 CGGTGACAAGAGGACGGAC 60.081 63.158 0.00 0.00 0.00 4.79
1426 1480 1.080705 GGTGACAAGAGGACGGACG 60.081 63.158 0.00 0.00 0.00 4.79
1528 1584 6.520021 ACCTGAATCAATCCCTGATGATTA 57.480 37.500 1.34 0.00 44.43 1.75
1717 1773 2.409870 CCTTTCTGCCGCCATGACC 61.410 63.158 0.00 0.00 0.00 4.02
1724 1780 2.264480 CCGCCATGACCGTCTTCA 59.736 61.111 0.00 0.00 0.00 3.02
1747 1804 1.132199 GGATACGTGCGTGTCTGTCG 61.132 60.000 18.00 0.00 36.64 4.35
1756 1813 1.647084 GTGTCTGTCGTGTTTGCCC 59.353 57.895 0.00 0.00 0.00 5.36
1759 1816 1.885388 TCTGTCGTGTTTGCCCGTG 60.885 57.895 0.00 0.00 0.00 4.94
1858 1915 2.294512 TGATGGTAGTAGATGAGCAGCG 59.705 50.000 0.00 0.00 32.33 5.18
1863 1920 2.575694 AGTAGATGAGCAGCGTTCAG 57.424 50.000 0.00 0.00 0.00 3.02
1992 2200 7.672983 TTTTGCGAGTTCTTCTAATCTGATT 57.327 32.000 8.14 8.14 0.00 2.57
2052 2260 7.724061 AGGAATTAAAGAAAAGTGGAGCTAACA 59.276 33.333 0.00 0.00 0.00 2.41
2080 2288 3.686016 TCAAACTTAGGGCATCTCCAAC 58.314 45.455 0.00 0.00 36.21 3.77
2081 2289 3.073798 TCAAACTTAGGGCATCTCCAACA 59.926 43.478 0.00 0.00 36.21 3.33
2082 2290 3.356529 AACTTAGGGCATCTCCAACAG 57.643 47.619 0.00 0.00 36.21 3.16
2083 2291 1.065126 ACTTAGGGCATCTCCAACAGC 60.065 52.381 0.00 0.00 36.21 4.40
2089 2298 1.376424 CATCTCCAACAGCAGCCGT 60.376 57.895 0.00 0.00 0.00 5.68
2092 2301 0.613260 TCTCCAACAGCAGCCGTAAT 59.387 50.000 0.00 0.00 0.00 1.89
2102 2311 3.057596 CAGCAGCCGTAATTTTTCTTCCA 60.058 43.478 0.00 0.00 0.00 3.53
2104 2313 3.057526 GCAGCCGTAATTTTTCTTCCACT 60.058 43.478 0.00 0.00 0.00 4.00
2108 2317 4.719040 CCGTAATTTTTCTTCCACTTCCG 58.281 43.478 0.00 0.00 0.00 4.30
2112 2321 5.845391 AATTTTTCTTCCACTTCCGTCAA 57.155 34.783 0.00 0.00 0.00 3.18
2113 2322 4.625972 TTTTTCTTCCACTTCCGTCAAC 57.374 40.909 0.00 0.00 0.00 3.18
2114 2323 1.860676 TTCTTCCACTTCCGTCAACG 58.139 50.000 0.00 0.00 39.44 4.10
2124 2333 2.978824 CGTCAACGGACAGGGGAT 59.021 61.111 0.00 0.00 44.54 3.85
2125 2334 1.153628 CGTCAACGGACAGGGGATC 60.154 63.158 0.00 0.00 44.54 3.36
2144 2353 3.188786 GTCCGTGGACGCAGATGC 61.189 66.667 2.78 0.00 38.18 3.91
2149 2358 1.812922 GTGGACGCAGATGCAGGAG 60.813 63.158 5.55 0.00 42.21 3.69
2153 2362 2.584418 CGCAGATGCAGGAGGACG 60.584 66.667 5.55 0.00 42.21 4.79
2154 2363 2.894387 GCAGATGCAGGAGGACGC 60.894 66.667 0.00 0.00 41.59 5.19
2159 2368 0.322975 GATGCAGGAGGACGCCATAT 59.677 55.000 0.00 0.00 0.00 1.78
2171 2382 3.058501 GGACGCCATATATTTCAAACCGG 60.059 47.826 0.00 0.00 0.00 5.28
2203 2414 2.149578 CCGGGCAAAATTCATGCAAAA 58.850 42.857 15.56 0.00 45.60 2.44
2204 2415 2.748532 CCGGGCAAAATTCATGCAAAAT 59.251 40.909 15.56 0.00 45.60 1.82
2207 2418 3.119424 GGGCAAAATTCATGCAAAATGGG 60.119 43.478 15.56 0.00 45.60 4.00
2217 2428 6.219417 TCATGCAAAATGGGTGGTATTTAG 57.781 37.500 0.00 0.00 0.00 1.85
2222 2433 5.703130 GCAAAATGGGTGGTATTTAGCAAAA 59.297 36.000 0.00 0.00 35.24 2.44
2243 2454 8.998377 GCAAAATTTGGGTAGAAAATAACACAT 58.002 29.630 7.89 0.00 0.00 3.21
2247 2458 6.988622 TTGGGTAGAAAATAACACATACCG 57.011 37.500 0.00 0.00 34.73 4.02
2276 2502 4.142315 ACATAGCATGCAAACAATGTCTCC 60.142 41.667 21.98 0.00 0.00 3.71
2315 2541 6.015519 CCCAGATGTCCAACAAGTTTTTCATA 60.016 38.462 0.00 0.00 0.00 2.15
2341 2567 4.507756 CGGATCATGACGTTTCACACATAT 59.492 41.667 0.00 0.00 33.38 1.78
2356 2582 4.772100 CACACATATTCCCCCTTCAACTTT 59.228 41.667 0.00 0.00 0.00 2.66
2373 2612 4.634012 ACTTTATCCAACAGTGTGGCTA 57.366 40.909 0.00 0.00 38.68 3.93
2382 2621 0.179062 CAGTGTGGCTATCCCTCTGC 60.179 60.000 0.00 0.00 0.00 4.26
2491 2730 6.127980 GCAAGAGGAAGTAAAACTTACCATCC 60.128 42.308 0.00 9.42 39.92 3.51
2492 2731 6.697641 AGAGGAAGTAAAACTTACCATCCA 57.302 37.500 15.74 0.00 39.92 3.41
2503 2742 2.568546 TACCATCCAGTCCATGTCCT 57.431 50.000 0.00 0.00 0.00 3.85
2513 2752 0.612744 TCCATGTCCTCGTGCAATGA 59.387 50.000 0.00 0.00 0.00 2.57
2529 2768 0.904865 ATGACCACCTTGCCTCGAGA 60.905 55.000 15.71 0.00 0.00 4.04
2572 2811 3.650070 TGATGACGCTGATCTGGATAC 57.350 47.619 1.46 0.00 0.00 2.24
2586 2825 3.748083 CTGGATACTGTGCCAGCAATAT 58.252 45.455 15.49 0.00 44.53 1.28
2589 2828 4.202493 TGGATACTGTGCCAGCAATATGAT 60.202 41.667 0.00 0.00 34.37 2.45
2590 2829 4.155462 GGATACTGTGCCAGCAATATGATG 59.845 45.833 0.00 0.00 34.37 3.07
2643 2882 1.740296 GTCGTAGGGCGCAATGTGT 60.740 57.895 10.83 0.00 41.07 3.72
2677 2916 4.373156 AACCTTTCATGCACTTACTCCT 57.627 40.909 0.00 0.00 0.00 3.69
2703 2946 1.096386 GCTTCCCTCTGCTCATGCTG 61.096 60.000 0.00 0.00 40.48 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.045242 CGAGACCGGTGAGAGGGA 60.045 66.667 14.63 0.00 0.00 4.20
63 64 1.156645 GCCTGATGATGCACGAGACC 61.157 60.000 0.00 0.00 0.00 3.85
69 70 1.456296 TCAACAGCCTGATGATGCAC 58.544 50.000 0.00 0.00 0.00 4.57
201 202 4.358841 TCGGGCAATGGTGGTGGG 62.359 66.667 0.00 0.00 0.00 4.61
219 220 6.369629 TCTACTTAAAGGGAGGAGATCTCAG 58.630 44.000 23.85 11.50 44.19 3.35
246 253 6.349777 GGAATTGGATATAGGACGTCTCTCTG 60.350 46.154 16.46 0.00 0.00 3.35
257 264 8.844244 GCAATATAGCTTGGAATTGGATATAGG 58.156 37.037 0.00 0.00 31.46 2.57
263 270 5.072741 GGAGCAATATAGCTTGGAATTGGA 58.927 41.667 0.00 0.00 46.75 3.53
264 271 5.075493 AGGAGCAATATAGCTTGGAATTGG 58.925 41.667 0.00 0.00 46.75 3.16
265 272 5.182760 GGAGGAGCAATATAGCTTGGAATTG 59.817 44.000 0.00 0.00 46.75 2.32
266 273 5.320277 GGAGGAGCAATATAGCTTGGAATT 58.680 41.667 0.00 0.00 46.75 2.17
267 274 4.564406 CGGAGGAGCAATATAGCTTGGAAT 60.564 45.833 0.00 0.00 46.75 3.01
268 275 3.244215 CGGAGGAGCAATATAGCTTGGAA 60.244 47.826 0.00 0.00 46.75 3.53
312 324 2.258591 GCGTCCAGTTCTCGAGCA 59.741 61.111 7.81 0.00 0.00 4.26
320 332 1.447317 CTGTTTGCCTGCGTCCAGTT 61.447 55.000 0.00 0.00 37.38 3.16
327 339 2.848858 AACTGCCTGTTTGCCTGCG 61.849 57.895 0.00 0.00 34.84 5.18
328 340 1.300388 CAACTGCCTGTTTGCCTGC 60.300 57.895 0.00 0.00 36.63 4.85
329 341 0.963962 ATCAACTGCCTGTTTGCCTG 59.036 50.000 0.00 0.00 36.63 4.85
330 342 0.963962 CATCAACTGCCTGTTTGCCT 59.036 50.000 0.00 0.00 36.63 4.75
331 343 0.668401 GCATCAACTGCCTGTTTGCC 60.668 55.000 1.03 0.00 45.66 4.52
356 368 1.306642 CCTGCAGCAGCCAAGAAGAG 61.307 60.000 17.81 0.00 41.13 2.85
357 369 1.303074 CCTGCAGCAGCCAAGAAGA 60.303 57.895 17.81 0.00 41.13 2.87
358 370 2.341101 CCCTGCAGCAGCCAAGAAG 61.341 63.158 17.81 1.08 41.13 2.85
359 371 2.282674 CCCTGCAGCAGCCAAGAA 60.283 61.111 17.81 0.00 41.13 2.52
360 372 3.251509 TCCCTGCAGCAGCCAAGA 61.252 61.111 17.81 7.65 41.13 3.02
361 373 2.750637 CTCCCTGCAGCAGCCAAG 60.751 66.667 17.81 9.45 41.13 3.61
362 374 4.355720 CCTCCCTGCAGCAGCCAA 62.356 66.667 17.81 3.25 41.13 4.52
367 379 1.553690 GGTACTTCCTCCCTGCAGCA 61.554 60.000 8.66 0.00 0.00 4.41
380 392 1.900486 AGCTCACCTTTAGCGGTACTT 59.100 47.619 0.00 0.00 44.87 2.24
381 393 1.558233 AGCTCACCTTTAGCGGTACT 58.442 50.000 0.00 0.00 44.87 2.73
386 398 3.814945 CAAAAGAAGCTCACCTTTAGCG 58.185 45.455 8.51 0.00 44.87 4.26
387 399 3.569548 GCAAAAGAAGCTCACCTTTAGC 58.430 45.455 8.51 0.00 40.40 3.09
393 405 0.038801 GCAGGCAAAAGAAGCTCACC 60.039 55.000 0.00 0.00 0.00 4.02
479 492 2.172483 GAAGCAGAAGGACGGGCTGA 62.172 60.000 0.00 0.00 35.10 4.26
480 493 1.743252 GAAGCAGAAGGACGGGCTG 60.743 63.158 0.00 0.00 35.10 4.85
481 494 2.665603 GAAGCAGAAGGACGGGCT 59.334 61.111 0.00 0.00 36.06 5.19
482 495 2.436824 GGAAGCAGAAGGACGGGC 60.437 66.667 0.00 0.00 0.00 6.13
483 496 2.269241 GGGAAGCAGAAGGACGGG 59.731 66.667 0.00 0.00 0.00 5.28
484 497 1.078848 CAGGGAAGCAGAAGGACGG 60.079 63.158 0.00 0.00 0.00 4.79
585 598 6.820656 ACTAATCACACTGCTATGGAAGAAAG 59.179 38.462 0.00 0.00 0.00 2.62
619 632 1.153978 CAATGCCATCACACCACGC 60.154 57.895 0.00 0.00 0.00 5.34
643 656 1.378762 CCAGGTGTCCGGAATTGGT 59.621 57.895 5.23 0.00 0.00 3.67
651 664 1.019278 CAATCCGAACCAGGTGTCCG 61.019 60.000 0.00 0.00 0.00 4.79
722 735 1.833630 CTGGCACCTTCCACTCTATGA 59.166 52.381 0.00 0.00 31.74 2.15
837 855 1.374758 CTGAGTTCACCGTGCCCTC 60.375 63.158 9.24 9.24 0.00 4.30
927 956 4.257376 CGATTGCTCGCTCGCACG 62.257 66.667 0.00 0.00 40.09 5.34
940 969 1.595466 ATCGAGCTAGACGACCGATT 58.405 50.000 13.04 0.00 42.37 3.34
1069 1098 2.990479 GTTGGTGGAGGAGCCGAT 59.010 61.111 0.00 0.00 40.66 4.18
1353 1398 1.136984 GCATGAGCAGAGCACAAGC 59.863 57.895 0.00 1.43 36.83 4.01
1357 1411 2.747822 CCACGCATGAGCAGAGCAC 61.748 63.158 0.00 0.00 42.27 4.40
1358 1412 2.435410 CCACGCATGAGCAGAGCA 60.435 61.111 0.00 0.00 42.27 4.26
1359 1413 3.873883 GCCACGCATGAGCAGAGC 61.874 66.667 0.00 0.00 42.27 4.09
1360 1414 3.200593 GGCCACGCATGAGCAGAG 61.201 66.667 0.00 0.00 42.27 3.35
1407 1461 1.080705 GTCCGTCCTCTTGTCACCG 60.081 63.158 0.00 0.00 0.00 4.94
1444 1498 4.175599 CAGCTACTGCAGACACGG 57.824 61.111 23.35 5.56 42.74 4.94
1528 1584 4.726416 CAAACGCAGTGCAAAAGATAGAT 58.274 39.130 16.83 0.00 45.00 1.98
1717 1773 0.866061 CACGTATCCGCCTGAAGACG 60.866 60.000 0.00 0.00 40.39 4.18
1724 1780 3.695022 GACACGCACGTATCCGCCT 62.695 63.158 0.00 0.00 37.70 5.52
1747 1804 1.803334 TACAGATCACGGGCAAACAC 58.197 50.000 0.00 0.00 0.00 3.32
1756 1813 4.201676 CGCTCTAGCTCTATACAGATCACG 60.202 50.000 0.00 0.00 39.32 4.35
1759 1816 5.063438 CACTCGCTCTAGCTCTATACAGATC 59.937 48.000 0.00 0.00 39.32 2.75
1858 1915 6.743627 CGAGACTAACTAGACATGAACTGAAC 59.256 42.308 0.00 0.00 0.00 3.18
1863 1920 4.096682 AGGCGAGACTAACTAGACATGAAC 59.903 45.833 0.00 0.00 31.50 3.18
1992 2200 3.135167 AGGAACCTTTTGAGACACCGTTA 59.865 43.478 0.00 0.00 0.00 3.18
2052 2260 4.476479 AGATGCCCTAAGTTTGAGGATTCT 59.524 41.667 0.00 0.00 35.99 2.40
2080 2288 3.057596 TGGAAGAAAAATTACGGCTGCTG 60.058 43.478 6.98 6.98 0.00 4.41
2081 2289 3.057526 GTGGAAGAAAAATTACGGCTGCT 60.058 43.478 0.00 0.00 0.00 4.24
2082 2290 3.057526 AGTGGAAGAAAAATTACGGCTGC 60.058 43.478 0.00 0.00 0.00 5.25
2083 2291 4.766404 AGTGGAAGAAAAATTACGGCTG 57.234 40.909 0.00 0.00 0.00 4.85
2108 2317 0.108138 CTGATCCCCTGTCCGTTGAC 60.108 60.000 0.00 0.00 42.12 3.18
2112 2321 4.035843 GACTGATCCCCTGTCCGT 57.964 61.111 0.00 0.00 37.65 4.69
2124 2333 1.977009 ATCTGCGTCCACGGACTGA 60.977 57.895 14.12 9.58 42.54 3.41
2125 2334 1.807165 CATCTGCGTCCACGGACTG 60.807 63.158 14.12 8.77 42.54 3.51
2137 2346 2.894387 GCGTCCTCCTGCATCTGC 60.894 66.667 0.00 0.00 42.50 4.26
2142 2351 1.644509 ATATATGGCGTCCTCCTGCA 58.355 50.000 0.00 0.00 0.00 4.41
2144 2353 4.271696 TGAAATATATGGCGTCCTCCTG 57.728 45.455 0.00 0.00 0.00 3.86
2149 2358 3.058501 CCGGTTTGAAATATATGGCGTCC 60.059 47.826 0.00 0.00 0.00 4.79
2153 2362 8.974408 GTTAAAATCCGGTTTGAAATATATGGC 58.026 33.333 0.00 0.00 0.00 4.40
2159 2368 8.235905 CGGTTAGTTAAAATCCGGTTTGAAATA 58.764 33.333 0.00 2.31 37.92 1.40
2171 2382 6.869388 TGAATTTTGCCCGGTTAGTTAAAATC 59.131 34.615 0.00 0.00 30.16 2.17
2187 2398 4.477780 CACCCATTTTGCATGAATTTTGC 58.522 39.130 0.00 7.23 40.55 3.68
2203 2414 6.413892 CCAAATTTTGCTAAATACCACCCAT 58.586 36.000 6.55 0.00 32.85 4.00
2204 2415 5.280215 CCCAAATTTTGCTAAATACCACCCA 60.280 40.000 6.55 0.00 32.85 4.51
2207 2418 7.832769 TCTACCCAAATTTTGCTAAATACCAC 58.167 34.615 6.55 0.00 32.85 4.16
2217 2428 8.371770 TGTGTTATTTTCTACCCAAATTTTGC 57.628 30.769 3.50 0.00 0.00 3.68
2222 2433 7.612633 ACGGTATGTGTTATTTTCTACCCAAAT 59.387 33.333 0.00 0.00 0.00 2.32
2238 2449 3.639561 TGCTATGTATGGACGGTATGTGT 59.360 43.478 0.00 0.00 0.00 3.72
2243 2454 2.630580 TGCATGCTATGTATGGACGGTA 59.369 45.455 20.33 0.00 0.00 4.02
2245 2456 2.168326 TGCATGCTATGTATGGACGG 57.832 50.000 20.33 0.00 0.00 4.79
2247 2458 4.898829 TGTTTGCATGCTATGTATGGAC 57.101 40.909 20.33 5.12 0.00 4.02
2276 2502 5.207110 ACATCTGGGATCTAGTCGAATTG 57.793 43.478 0.00 0.00 0.00 2.32
2332 2558 3.591527 AGTTGAAGGGGGAATATGTGTGA 59.408 43.478 0.00 0.00 0.00 3.58
2341 2567 4.140900 TGTTGGATAAAGTTGAAGGGGGAA 60.141 41.667 0.00 0.00 0.00 3.97
2356 2582 2.438021 GGGATAGCCACACTGTTGGATA 59.562 50.000 0.00 10.04 41.69 2.59
2373 2612 0.983378 GTACCACAGGGCAGAGGGAT 60.983 60.000 0.00 0.00 37.90 3.85
2491 2730 0.320683 TTGCACGAGGACATGGACTG 60.321 55.000 0.00 0.00 0.00 3.51
2492 2731 0.615331 ATTGCACGAGGACATGGACT 59.385 50.000 0.00 0.00 0.00 3.85
2503 2742 2.627791 CAAGGTGGTCATTGCACGA 58.372 52.632 0.00 0.00 0.00 4.35
2513 2752 0.904865 TCATCTCGAGGCAAGGTGGT 60.905 55.000 13.56 0.00 0.00 4.16
2529 2768 5.852282 AGTTTTGCAACTTGGTTAGTCAT 57.148 34.783 0.00 0.00 40.66 3.06
2586 2825 0.666274 GCAACGTGAGGTCGTCATCA 60.666 55.000 0.00 0.00 43.38 3.07
2589 2828 2.354188 CGCAACGTGAGGTCGTCA 60.354 61.111 0.00 0.00 43.38 4.35
2590 2829 2.354305 ACGCAACGTGAGGTCGTC 60.354 61.111 0.00 0.00 43.38 4.20
2609 2848 5.991606 CCCTACGACATGTACATCATTCAAT 59.008 40.000 5.07 0.00 34.09 2.57
2643 2882 2.161808 TGAAAGGTTTCACGCACGAAAA 59.838 40.909 0.87 0.00 41.88 2.29
2672 2911 3.325994 GGGAAGCCCTTCTAGGAGT 57.674 57.895 7.85 0.00 41.34 3.85


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

AutoCloner maintained by Alex Coulton.