Multiple sequence alignment - TraesCS3A01G535300

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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 TraesCS3A01G535300 chr3A 100.000 2868 0 0 1 2868 746919375 746916508 0.000000e+00 5297.0
1 TraesCS3A01G535300 chr3D 88.875 2463 122 44 490 2863 612273928 612271529 0.000000e+00 2891.0
2 TraesCS3A01G535300 chr3D 91.274 424 37 0 1 424 612274383 612273960 1.920000e-161 579.0
3 TraesCS3A01G535300 chr3B 89.873 1975 86 41 621 2546 826724679 826726588 0.000000e+00 2435.0
4 TraesCS3A01G535300 chr3B 85.302 1075 82 27 1846 2862 826736390 826737446 0.000000e+00 1040.0
5 TraesCS3A01G535300 chr3B 89.836 305 25 5 2562 2863 826727441 826727742 1.250000e-103 387.0
6 TraesCS3A01G535300 chr4D 81.260 635 108 9 1234 1866 476875915 476875290 1.190000e-138 503.0
7 TraesCS3A01G535300 chr4B 81.102 635 109 9 1234 1866 601099543 601098918 5.520000e-137 497.0
8 TraesCS3A01G535300 chr4A 80.854 632 111 8 1239 1868 683617603 683616980 3.320000e-134 488.0
9 TraesCS3A01G535300 chr7D 79.392 296 55 5 1519 1811 433876553 433876845 1.350000e-48 204.0
10 TraesCS3A01G535300 chr7D 81.897 116 20 1 343 458 208212122 208212008 2.350000e-16 97.1
11 TraesCS3A01G535300 chr7B 78.912 294 60 2 1519 1811 451289895 451290187 6.270000e-47 198.0
12 TraesCS3A01G535300 chr7B 81.897 116 20 1 343 458 193330807 193330921 2.350000e-16 97.1
13 TraesCS3A01G535300 chr7A 78.912 294 60 2 1519 1811 484525260 484525552 6.270000e-47 198.0
14 TraesCS3A01G535300 chr1B 82.328 232 36 4 248 478 638953434 638953661 2.250000e-46 196.0
15 TraesCS3A01G535300 chr1B 91.837 49 2 2 2142 2189 546687619 546687666 1.840000e-07 67.6
16 TraesCS3A01G535300 chr6A 81.624 234 43 0 1541 1774 464538529 464538762 8.110000e-46 195.0
17 TraesCS3A01G535300 chr2A 80.172 232 38 7 246 473 765756672 765756445 1.770000e-37 167.0
18 TraesCS3A01G535300 chr6B 80.000 195 25 13 270 458 559064096 559063910 6.450000e-27 132.0
19 TraesCS3A01G535300 chr5B 80.921 152 24 5 331 479 252299638 252299787 6.490000e-22 115.0
20 TraesCS3A01G535300 chr1D 79.817 109 11 8 2091 2189 406666080 406666187 5.130000e-08 69.4


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 TraesCS3A01G535300 chr3A 746916508 746919375 2867 True 5297 5297 100.0000 1 2868 1 chr3A.!!$R1 2867
1 TraesCS3A01G535300 chr3D 612271529 612274383 2854 True 1735 2891 90.0745 1 2863 2 chr3D.!!$R1 2862
2 TraesCS3A01G535300 chr3B 826724679 826727742 3063 False 1411 2435 89.8545 621 2863 2 chr3B.!!$F2 2242
3 TraesCS3A01G535300 chr3B 826736390 826737446 1056 False 1040 1040 85.3020 1846 2862 1 chr3B.!!$F1 1016
4 TraesCS3A01G535300 chr4D 476875290 476875915 625 True 503 503 81.2600 1234 1866 1 chr4D.!!$R1 632
5 TraesCS3A01G535300 chr4B 601098918 601099543 625 True 497 497 81.1020 1234 1866 1 chr4B.!!$R1 632
6 TraesCS3A01G535300 chr4A 683616980 683617603 623 True 488 488 80.8540 1239 1868 1 chr4A.!!$R1 629

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
145 146 0.462581 CCATCCGGTCATGTCACAGG 60.463 60.0 0.0 0.0 33.19 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2115 0.598562 TTCCTGACTGACTGACTCGC 59.401 55.0 0.0 0.0 0.0 5.03 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
42 43 3.000727 CCTAACCTTGTCGATGACAACC 58.999 50.000 8.21 0.00 45.88 3.77
45 46 2.426522 ACCTTGTCGATGACAACCATG 58.573 47.619 8.21 0.00 45.88 3.66
77 78 0.995024 ATGTGCTTCTAAGGGCCAGT 59.005 50.000 6.18 0.00 0.00 4.00
108 109 3.195661 GGTAGTCATCATCGTTGAACCC 58.804 50.000 0.00 0.00 34.96 4.11
139 140 3.644966 ATGTTTACCATCCGGTCATGT 57.355 42.857 0.00 0.00 44.71 3.21
140 141 2.980568 TGTTTACCATCCGGTCATGTC 58.019 47.619 0.00 0.00 44.71 3.06
145 146 0.462581 CCATCCGGTCATGTCACAGG 60.463 60.000 0.00 0.00 33.19 4.00
151 152 3.770388 TCCGGTCATGTCACAGGTAATAA 59.230 43.478 0.00 0.00 33.61 1.40
153 154 4.119862 CGGTCATGTCACAGGTAATAAGG 58.880 47.826 0.00 0.00 0.00 2.69
219 220 3.609409 GCGTCCATCTTCTTTGTTTCCAC 60.609 47.826 0.00 0.00 0.00 4.02
224 225 4.262164 CCATCTTCTTTGTTTCCACTTGGG 60.262 45.833 0.00 0.00 35.41 4.12
228 229 3.037549 TCTTTGTTTCCACTTGGGCAAT 58.962 40.909 0.00 0.00 36.21 3.56
229 230 3.069443 TCTTTGTTTCCACTTGGGCAATC 59.931 43.478 0.00 0.00 36.21 2.67
235 236 3.534357 TCCACTTGGGCAATCCTTAAA 57.466 42.857 0.00 0.00 36.21 1.52
241 242 3.825908 TGGGCAATCCTTAAACTTCCT 57.174 42.857 0.00 0.00 36.20 3.36
250 251 5.836024 TCCTTAAACTTCCTTTCAGGCTA 57.164 39.130 0.00 0.00 34.35 3.93
251 252 5.805728 TCCTTAAACTTCCTTTCAGGCTAG 58.194 41.667 0.00 0.00 34.35 3.42
268 269 3.495100 GGCTAGTCACAATGGGAGGTATG 60.495 52.174 0.00 0.00 0.00 2.39
329 330 8.899427 ATGATATTATATCCACAGTGCATAGC 57.101 34.615 9.45 0.00 0.00 2.97
332 333 8.899427 ATATTATATCCACAGTGCATAGCATC 57.101 34.615 0.00 0.00 41.91 3.91
333 334 1.875009 ATCCACAGTGCATAGCATCG 58.125 50.000 0.00 0.00 41.91 3.84
336 337 2.167487 TCCACAGTGCATAGCATCGTAA 59.833 45.455 0.00 0.00 41.91 3.18
345 346 6.201044 AGTGCATAGCATCGTAACTTGTTATC 59.799 38.462 0.00 0.00 41.91 1.75
349 350 8.376203 GCATAGCATCGTAACTTGTTATCATAG 58.624 37.037 0.00 0.00 0.00 2.23
352 353 7.489160 AGCATCGTAACTTGTTATCATAGTGA 58.511 34.615 0.00 0.00 0.00 3.41
373 374 5.975344 GTGACCTCATTTATTGTCATGCATG 59.025 40.000 21.07 21.07 39.66 4.06
402 403 8.159447 ACATGCTACTACATCATTTACCATGAT 58.841 33.333 0.00 0.00 39.16 2.45
440 441 9.770097 TCATGATACTTAATCCTCACATTTCTC 57.230 33.333 0.00 0.00 33.22 2.87
441 442 9.551734 CATGATACTTAATCCTCACATTTCTCA 57.448 33.333 0.00 0.00 33.22 3.27
451 452 9.865321 AATCCTCACATTTCTCATTTAATTGTG 57.135 29.630 0.00 0.00 38.57 3.33
452 453 8.408043 TCCTCACATTTCTCATTTAATTGTGT 57.592 30.769 0.00 0.00 38.45 3.72
453 454 8.298854 TCCTCACATTTCTCATTTAATTGTGTG 58.701 33.333 9.85 9.85 38.45 3.82
454 455 7.062605 CCTCACATTTCTCATTTAATTGTGTGC 59.937 37.037 10.72 0.00 38.45 4.57
455 456 6.867816 TCACATTTCTCATTTAATTGTGTGCC 59.132 34.615 10.72 0.00 38.45 5.01
456 457 6.645827 CACATTTCTCATTTAATTGTGTGCCA 59.354 34.615 5.59 0.00 35.23 4.92
457 458 6.646240 ACATTTCTCATTTAATTGTGTGCCAC 59.354 34.615 0.00 0.00 34.56 5.01
458 459 4.782019 TCTCATTTAATTGTGTGCCACC 57.218 40.909 0.00 0.00 32.73 4.61
461 462 4.148079 TCATTTAATTGTGTGCCACCTCA 58.852 39.130 0.00 0.00 32.73 3.86
462 463 4.218200 TCATTTAATTGTGTGCCACCTCAG 59.782 41.667 0.00 0.00 32.73 3.35
464 465 2.949177 AATTGTGTGCCACCTCAGTA 57.051 45.000 0.00 0.00 32.73 2.74
466 467 2.719531 TTGTGTGCCACCTCAGTAAA 57.280 45.000 0.00 0.00 32.73 2.01
468 469 3.006112 TGTGTGCCACCTCAGTAAAAA 57.994 42.857 0.00 0.00 32.73 1.94
470 471 3.317711 TGTGTGCCACCTCAGTAAAAATG 59.682 43.478 0.00 0.00 32.73 2.32
474 475 2.298729 GCCACCTCAGTAAAAATGCCAA 59.701 45.455 0.00 0.00 0.00 4.52
475 476 3.614870 GCCACCTCAGTAAAAATGCCAAG 60.615 47.826 0.00 0.00 0.00 3.61
476 477 3.573967 CCACCTCAGTAAAAATGCCAAGT 59.426 43.478 0.00 0.00 0.00 3.16
481 482 5.010012 CCTCAGTAAAAATGCCAAGTTGACT 59.990 40.000 3.87 0.00 0.00 3.41
482 483 6.206634 CCTCAGTAAAAATGCCAAGTTGACTA 59.793 38.462 3.87 0.00 0.00 2.59
485 486 3.942130 AAAATGCCAAGTTGACTAGCC 57.058 42.857 3.87 0.00 0.00 3.93
488 489 1.055849 TGCCAAGTTGACTAGCCTCA 58.944 50.000 3.87 0.00 0.00 3.86
492 493 3.274288 CCAAGTTGACTAGCCTCATTCC 58.726 50.000 3.87 0.00 0.00 3.01
501 502 1.138568 AGCCTCATTCCTCCTCATGG 58.861 55.000 0.00 0.00 0.00 3.66
504 505 1.072015 CCTCATTCCTCCTCATGGCTC 59.928 57.143 0.00 0.00 0.00 4.70
505 506 1.072015 CTCATTCCTCCTCATGGCTCC 59.928 57.143 0.00 0.00 0.00 4.70
521 522 1.228552 TCCCCTGCTTGAGTTTGCC 60.229 57.895 0.00 0.00 0.00 4.52
533 534 2.044848 TTTGCCGGTGTGGTGTGT 60.045 55.556 1.90 0.00 41.21 3.72
540 541 2.606065 GCCGGTGTGGTGTGTTTATTTC 60.606 50.000 1.90 0.00 41.21 2.17
548 549 8.021396 GGTGTGGTGTGTTTATTTCTCTATTTC 58.979 37.037 0.00 0.00 0.00 2.17
594 597 7.312657 TGATTTTGGAAGATCGATTTGAGAG 57.687 36.000 0.00 0.00 0.00 3.20
602 605 7.042335 GGAAGATCGATTTGAGAGGTAAAAGA 58.958 38.462 0.00 0.00 0.00 2.52
603 606 7.223777 GGAAGATCGATTTGAGAGGTAAAAGAG 59.776 40.741 0.00 0.00 0.00 2.85
607 610 7.891183 TCGATTTGAGAGGTAAAAGAGAAAG 57.109 36.000 0.00 0.00 0.00 2.62
614 617 8.221965 TGAGAGGTAAAAGAGAAAGAAAAACC 57.778 34.615 0.00 0.00 0.00 3.27
617 620 9.256228 AGAGGTAAAAGAGAAAGAAAAACCTTT 57.744 29.630 0.00 0.00 38.92 3.11
618 621 9.871238 GAGGTAAAAGAGAAAGAAAAACCTTTT 57.129 29.630 0.00 0.00 36.58 2.27
708 735 1.815613 TGGATCTAGATAGCTCAGCGC 59.184 52.381 4.89 0.00 39.57 5.92
801 829 2.242965 TGTGCAATCTGATCCCAATCCT 59.757 45.455 0.00 0.00 0.00 3.24
880 921 2.189499 GCCGGCCTCACATCCATTC 61.189 63.158 18.11 0.00 0.00 2.67
897 939 5.535029 TCCATTCCCGGGCTATATATAACT 58.465 41.667 18.49 0.00 0.00 2.24
942 1001 4.452114 CACACAATTCAACACTGCTAGCTA 59.548 41.667 17.23 1.31 0.00 3.32
975 1034 2.126882 ACCGATCCATCCATCCAGAAA 58.873 47.619 0.00 0.00 0.00 2.52
976 1035 2.509548 ACCGATCCATCCATCCAGAAAA 59.490 45.455 0.00 0.00 0.00 2.29
977 1036 3.053693 ACCGATCCATCCATCCAGAAAAA 60.054 43.478 0.00 0.00 0.00 1.94
1138 1197 1.077716 GGCATGGCCTTCGGTAAGT 60.078 57.895 8.35 0.00 46.69 2.24
1141 1200 0.541863 CATGGCCTTCGGTAAGTCCT 59.458 55.000 3.32 0.00 31.73 3.85
1143 1202 2.170012 TGGCCTTCGGTAAGTCCTAT 57.830 50.000 3.32 0.00 31.73 2.57
1164 1223 4.485653 TCCCCATTTCTTTCTCCCTTTT 57.514 40.909 0.00 0.00 0.00 2.27
1168 1227 4.322273 CCCATTTCTTTCTCCCTTTTCTGC 60.322 45.833 0.00 0.00 0.00 4.26
1194 1253 2.622942 TCGACCGATCATCATGTCATCA 59.377 45.455 5.43 0.00 0.00 3.07
1195 1254 2.728318 CGACCGATCATCATGTCATCAC 59.272 50.000 5.43 0.00 0.00 3.06
1202 1261 5.694910 CGATCATCATGTCATCACTCATCAA 59.305 40.000 0.00 0.00 0.00 2.57
1222 1286 3.138798 ACGCCGTACTGATCGCCT 61.139 61.111 0.00 0.00 0.00 5.52
1886 1965 5.174395 ACTGAAAACCTCAATCTCATCTCG 58.826 41.667 0.00 0.00 32.17 4.04
1951 2031 1.728426 AGCAAGTGTACGTCGTCGC 60.728 57.895 0.00 0.55 41.18 5.19
1984 2064 5.858581 CAGTAAGCCAGTTTAGTTTCATTGC 59.141 40.000 0.00 0.00 0.00 3.56
1985 2065 3.559238 AGCCAGTTTAGTTTCATTGCG 57.441 42.857 0.00 0.00 0.00 4.85
1988 2071 3.119990 GCCAGTTTAGTTTCATTGCGCTA 60.120 43.478 9.73 0.00 0.00 4.26
1996 2087 3.375299 AGTTTCATTGCGCTATCTTGTCC 59.625 43.478 9.73 0.00 0.00 4.02
2024 2115 5.299279 AGAAATTCAGGGTAAACAGTGTGTG 59.701 40.000 0.00 0.00 0.00 3.82
2025 2116 1.961793 TCAGGGTAAACAGTGTGTGC 58.038 50.000 0.00 0.00 0.00 4.57
2054 2145 6.041409 TCAGTCAGTCAGGAATAATCTCATCC 59.959 42.308 0.00 0.00 0.00 3.51
2069 2160 7.688918 AATCTCATCCTTCTCTTATCTTGGT 57.311 36.000 0.00 0.00 0.00 3.67
2070 2161 6.477053 TCTCATCCTTCTCTTATCTTGGTG 57.523 41.667 0.00 0.00 0.00 4.17
2071 2162 5.960811 TCTCATCCTTCTCTTATCTTGGTGT 59.039 40.000 0.00 0.00 0.00 4.16
2072 2163 7.126061 TCTCATCCTTCTCTTATCTTGGTGTA 58.874 38.462 0.00 0.00 0.00 2.90
2073 2164 7.786943 TCTCATCCTTCTCTTATCTTGGTGTAT 59.213 37.037 0.00 0.00 0.00 2.29
2183 2278 2.821969 GTCTTGCCAATCTTGTGTCCAT 59.178 45.455 0.00 0.00 0.00 3.41
2259 2391 4.749976 CATTGTTGATTGTGATGGATGCA 58.250 39.130 0.00 0.00 0.00 3.96
2270 2402 6.288941 TGTGATGGATGCAAAGAAATTGAT 57.711 33.333 0.00 0.00 41.85 2.57
2285 2417 7.715265 AGAAATTGATAGTTCGATTGCGTAT 57.285 32.000 0.00 0.00 36.65 3.06
2286 2418 8.812147 AGAAATTGATAGTTCGATTGCGTATA 57.188 30.769 0.00 0.00 36.65 1.47
2354 2496 6.003234 TGAATGATTGCAAAATGCCAAAAG 57.997 33.333 1.71 0.00 44.23 2.27
2369 2511 4.161189 TGCCAAAAGGAAAAGACAATGACA 59.839 37.500 0.00 0.00 0.00 3.58
2370 2512 4.746611 GCCAAAAGGAAAAGACAATGACAG 59.253 41.667 0.00 0.00 0.00 3.51
2372 2514 6.739565 GCCAAAAGGAAAAGACAATGACAGAT 60.740 38.462 0.00 0.00 0.00 2.90
2373 2515 6.643770 CCAAAAGGAAAAGACAATGACAGATG 59.356 38.462 0.00 0.00 0.00 2.90
2398 2540 0.774491 TTCCCAACTAGGCCAGGGTT 60.774 55.000 5.01 3.61 42.12 4.11
2408 2550 1.064685 AGGCCAGGGTTTATAGCACAC 60.065 52.381 5.01 0.00 0.00 3.82
2409 2551 1.389555 GCCAGGGTTTATAGCACACC 58.610 55.000 0.00 0.00 0.00 4.16
2425 2567 3.616317 GCACACCCACCCAAAATATGTTC 60.616 47.826 0.00 0.00 0.00 3.18
2485 2627 1.621814 CCCTCTAAACGGGACTCACAA 59.378 52.381 0.00 0.00 44.90 3.33
2498 2640 4.505039 GGGACTCACAACTCACACCTTAAT 60.505 45.833 0.00 0.00 0.00 1.40
2715 3702 0.969894 AACTGGCTTCACTAGAGCGT 59.030 50.000 0.00 0.00 0.00 5.07
2717 3704 0.528017 CTGGCTTCACTAGAGCGTGA 59.472 55.000 0.00 0.00 41.82 4.35
2761 3748 0.575390 CAACGTGTCAAGTCGGTGAC 59.425 55.000 0.00 7.58 45.89 3.67
2790 3777 1.671054 ATGGTTTGACCGGAGTGCG 60.671 57.895 9.46 0.00 42.58 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.668867 GCCCCTCCGATAAGAGAGC 59.331 63.158 0.00 0.00 35.82 4.09
13 14 2.253403 GACAAGGTTAGGCCCCTCCG 62.253 65.000 0.00 0.00 40.77 4.63
45 46 3.682858 AGAAGCACATGCATGAAAAATGC 59.317 39.130 32.75 27.87 45.16 3.56
77 78 1.195115 GATGACTACCACTCTGGGCA 58.805 55.000 0.00 0.00 43.37 5.36
170 171 1.849829 GCGCAATGCCCGTAAAATAAC 59.150 47.619 0.30 0.00 37.76 1.89
199 200 5.507985 CCAAGTGGAAACAAAGAAGATGGAC 60.508 44.000 0.00 0.00 46.06 4.02
219 220 4.089361 AGGAAGTTTAAGGATTGCCCAAG 58.911 43.478 0.00 0.00 37.41 3.61
241 242 2.642311 TCCCATTGTGACTAGCCTGAAA 59.358 45.455 0.00 0.00 0.00 2.69
250 251 7.019388 AGTATATCATACCTCCCATTGTGACT 58.981 38.462 0.00 0.00 0.00 3.41
251 252 7.246171 AGTATATCATACCTCCCATTGTGAC 57.754 40.000 0.00 0.00 0.00 3.67
319 320 3.618594 ACAAGTTACGATGCTATGCACTG 59.381 43.478 0.00 0.00 43.04 3.66
328 329 7.306632 GGTCACTATGATAACAAGTTACGATGC 60.307 40.741 0.00 0.00 0.00 3.91
329 330 7.921214 AGGTCACTATGATAACAAGTTACGATG 59.079 37.037 0.00 0.00 0.00 3.84
332 333 7.255569 TGAGGTCACTATGATAACAAGTTACG 58.744 38.462 0.00 0.00 0.00 3.18
333 334 9.601217 AATGAGGTCACTATGATAACAAGTTAC 57.399 33.333 0.00 0.00 0.00 2.50
345 346 7.012610 TGCATGACAATAAATGAGGTCACTATG 59.987 37.037 0.00 0.00 42.43 2.23
349 350 5.565592 TGCATGACAATAAATGAGGTCAC 57.434 39.130 0.00 0.00 42.43 3.67
366 367 3.872771 TGTAGTAGCATGTGTCATGCATG 59.127 43.478 28.18 21.07 46.77 4.06
373 374 6.761242 TGGTAAATGATGTAGTAGCATGTGTC 59.239 38.462 0.00 0.00 35.16 3.67
380 381 9.875691 TCATATCATGGTAAATGATGTAGTAGC 57.124 33.333 10.38 0.00 38.98 3.58
425 426 9.865321 CACAATTAAATGAGAAATGTGAGGATT 57.135 29.630 0.00 0.00 0.00 3.01
426 427 9.028284 ACACAATTAAATGAGAAATGTGAGGAT 57.972 29.630 9.82 0.00 0.00 3.24
427 428 8.298854 CACACAATTAAATGAGAAATGTGAGGA 58.701 33.333 9.82 0.00 37.67 3.71
428 429 7.062605 GCACACAATTAAATGAGAAATGTGAGG 59.937 37.037 12.80 4.09 37.67 3.86
429 430 7.062605 GGCACACAATTAAATGAGAAATGTGAG 59.937 37.037 12.80 4.24 37.67 3.51
430 431 6.867816 GGCACACAATTAAATGAGAAATGTGA 59.132 34.615 12.80 0.00 37.67 3.58
431 432 6.645827 TGGCACACAATTAAATGAGAAATGTG 59.354 34.615 0.00 2.59 38.32 3.21
432 433 6.757237 TGGCACACAATTAAATGAGAAATGT 58.243 32.000 0.00 0.00 0.00 2.71
450 451 2.295909 GCATTTTTACTGAGGTGGCACA 59.704 45.455 20.82 0.00 0.00 4.57
451 452 2.352715 GGCATTTTTACTGAGGTGGCAC 60.353 50.000 9.70 9.70 33.04 5.01
452 453 1.892474 GGCATTTTTACTGAGGTGGCA 59.108 47.619 0.00 0.00 33.04 4.92
453 454 1.892474 TGGCATTTTTACTGAGGTGGC 59.108 47.619 0.00 0.00 0.00 5.01
454 455 3.573967 ACTTGGCATTTTTACTGAGGTGG 59.426 43.478 0.00 0.00 0.00 4.61
455 456 4.853924 ACTTGGCATTTTTACTGAGGTG 57.146 40.909 0.00 0.00 0.00 4.00
456 457 4.892934 TCAACTTGGCATTTTTACTGAGGT 59.107 37.500 0.00 0.00 0.00 3.85
457 458 5.010012 AGTCAACTTGGCATTTTTACTGAGG 59.990 40.000 0.00 0.00 0.00 3.86
458 459 6.076981 AGTCAACTTGGCATTTTTACTGAG 57.923 37.500 0.00 0.00 0.00 3.35
461 462 5.048013 GGCTAGTCAACTTGGCATTTTTACT 60.048 40.000 12.02 0.00 42.11 2.24
462 463 5.048013 AGGCTAGTCAACTTGGCATTTTTAC 60.048 40.000 17.48 0.00 44.19 2.01
464 465 3.897505 AGGCTAGTCAACTTGGCATTTTT 59.102 39.130 17.48 0.00 44.19 1.94
466 467 3.084786 GAGGCTAGTCAACTTGGCATTT 58.915 45.455 17.48 0.69 44.19 2.32
468 469 1.630369 TGAGGCTAGTCAACTTGGCAT 59.370 47.619 17.48 7.55 44.19 4.40
470 471 2.409948 ATGAGGCTAGTCAACTTGGC 57.590 50.000 9.53 9.53 42.66 4.52
474 475 2.769095 GGAGGAATGAGGCTAGTCAACT 59.231 50.000 0.00 0.00 0.00 3.16
475 476 2.769095 AGGAGGAATGAGGCTAGTCAAC 59.231 50.000 0.00 0.00 0.00 3.18
476 477 3.034635 GAGGAGGAATGAGGCTAGTCAA 58.965 50.000 0.00 0.00 0.00 3.18
481 482 2.333069 CCATGAGGAGGAATGAGGCTA 58.667 52.381 0.00 0.00 36.89 3.93
482 483 1.138568 CCATGAGGAGGAATGAGGCT 58.861 55.000 0.00 0.00 36.89 4.58
485 486 1.072015 GGAGCCATGAGGAGGAATGAG 59.928 57.143 0.00 0.00 36.89 2.90
488 489 1.064824 GGGGAGCCATGAGGAGGAAT 61.065 60.000 0.00 0.00 36.89 3.01
492 493 3.117452 GCAGGGGAGCCATGAGGAG 62.117 68.421 0.00 0.00 37.52 3.69
501 502 1.871126 GCAAACTCAAGCAGGGGAGC 61.871 60.000 0.00 0.00 34.48 4.70
504 505 2.629656 CGGCAAACTCAAGCAGGGG 61.630 63.158 0.00 0.00 0.00 4.79
505 506 2.629656 CCGGCAAACTCAAGCAGGG 61.630 63.158 0.00 0.00 41.54 4.45
521 522 3.813166 AGAGAAATAAACACACCACACCG 59.187 43.478 0.00 0.00 0.00 4.94
540 541 7.814264 ATGGCACCTTTAGATTGAAATAGAG 57.186 36.000 0.00 0.00 0.00 2.43
570 571 6.317140 CCTCTCAAATCGATCTTCCAAAATCA 59.683 38.462 0.00 0.00 0.00 2.57
571 572 6.317391 ACCTCTCAAATCGATCTTCCAAAATC 59.683 38.462 0.00 0.00 0.00 2.17
582 584 8.314751 TCTTTCTCTTTTACCTCTCAAATCGAT 58.685 33.333 0.00 0.00 0.00 3.59
656 683 2.807967 GGTTTCTTTTGGGCAGCAAATC 59.192 45.455 0.00 0.00 0.00 2.17
801 829 0.184692 TGCCATCGCCATTGGGATTA 59.815 50.000 4.53 0.00 41.79 1.75
880 921 6.570692 CAGTGTTAGTTATATATAGCCCGGG 58.429 44.000 19.09 19.09 0.00 5.73
897 939 2.993220 GTGTGTCGATCATGCAGTGTTA 59.007 45.455 0.00 0.00 0.00 2.41
942 1001 0.944311 GATCGGTTCGTGTGCTGTGT 60.944 55.000 0.00 0.00 0.00 3.72
948 1007 0.108377 TGGATGGATCGGTTCGTGTG 60.108 55.000 0.00 0.00 0.00 3.82
955 1014 1.806496 TTCTGGATGGATGGATCGGT 58.194 50.000 0.00 0.00 0.00 4.69
976 1035 1.602377 CGACGGGCACTCTTTCTTTTT 59.398 47.619 0.00 0.00 0.00 1.94
977 1036 1.202604 TCGACGGGCACTCTTTCTTTT 60.203 47.619 0.00 0.00 0.00 2.27
981 1040 1.223187 TTTTCGACGGGCACTCTTTC 58.777 50.000 0.00 0.00 0.00 2.62
1138 1197 3.722101 GGGAGAAAGAAATGGGGATAGGA 59.278 47.826 0.00 0.00 0.00 2.94
1141 1200 5.813965 AAAGGGAGAAAGAAATGGGGATA 57.186 39.130 0.00 0.00 0.00 2.59
1143 1202 4.107961 AGAAAAGGGAGAAAGAAATGGGGA 59.892 41.667 0.00 0.00 0.00 4.81
1164 1223 1.066422 GATCGGTCGATGCAGCAGA 59.934 57.895 10.77 0.00 34.60 4.26
1168 1227 1.725164 CATGATGATCGGTCGATGCAG 59.275 52.381 10.77 0.00 34.60 4.41
1194 1253 1.476891 AGTACGGCGTGATTGATGAGT 59.523 47.619 24.86 0.00 0.00 3.41
1195 1254 1.854743 CAGTACGGCGTGATTGATGAG 59.145 52.381 24.86 0.00 0.00 2.90
1202 1261 1.299165 GCGATCAGTACGGCGTGAT 60.299 57.895 24.86 17.02 36.07 3.06
1222 1286 3.976000 GCCACGCCATGCACAACA 61.976 61.111 0.00 0.00 0.00 3.33
1886 1965 1.069765 ATGGCGATGACGGATGGAC 59.930 57.895 0.00 0.00 40.15 4.02
1951 2031 3.170791 ACTGGCTTACTGATGATGACG 57.829 47.619 0.00 0.00 0.00 4.35
1984 2064 5.582269 TGAATTTCTCAAGGACAAGATAGCG 59.418 40.000 0.00 0.00 0.00 4.26
1985 2065 6.038050 CCTGAATTTCTCAAGGACAAGATAGC 59.962 42.308 0.00 0.00 32.17 2.97
1988 2071 5.222213 ACCCTGAATTTCTCAAGGACAAGAT 60.222 40.000 3.44 0.00 37.82 2.40
1996 2087 6.263168 ACACTGTTTACCCTGAATTTCTCAAG 59.737 38.462 0.00 0.00 32.17 3.02
2024 2115 0.598562 TTCCTGACTGACTGACTCGC 59.401 55.000 0.00 0.00 0.00 5.03
2025 2116 4.703645 TTATTCCTGACTGACTGACTCG 57.296 45.455 0.00 0.00 0.00 4.18
2069 2160 8.852135 TCATAATTGAGGACGTACATACATACA 58.148 33.333 0.00 0.00 0.00 2.29
2070 2161 9.687210 TTCATAATTGAGGACGTACATACATAC 57.313 33.333 0.00 0.00 32.27 2.39
2072 2163 9.208022 CATTCATAATTGAGGACGTACATACAT 57.792 33.333 0.00 0.00 32.27 2.29
2073 2164 7.170828 GCATTCATAATTGAGGACGTACATACA 59.829 37.037 0.00 0.00 32.27 2.29
2141 2236 3.834813 ACATCAAGTTGCTAGGAGAGACA 59.165 43.478 0.00 0.00 0.00 3.41
2259 2391 6.842163 ACGCAATCGAACTATCAATTTCTTT 58.158 32.000 0.00 0.00 39.41 2.52
2270 2402 4.150451 TCGATCGTATACGCAATCGAACTA 59.850 41.667 32.44 19.51 45.41 2.24
2285 2417 9.093970 ACAATCTGTGAAATTAATTCGATCGTA 57.906 29.630 15.94 5.83 41.18 3.43
2286 2418 7.974675 ACAATCTGTGAAATTAATTCGATCGT 58.025 30.769 15.94 0.00 41.18 3.73
2354 2496 5.702670 TCTCACATCTGTCATTGTCTTTTCC 59.297 40.000 0.00 0.00 0.00 3.13
2369 2511 3.135530 GCCTAGTTGGGAATCTCACATCT 59.864 47.826 0.00 0.00 34.49 2.90
2370 2512 3.471680 GCCTAGTTGGGAATCTCACATC 58.528 50.000 0.00 0.00 36.00 3.06
2372 2514 1.559682 GGCCTAGTTGGGAATCTCACA 59.440 52.381 0.00 0.00 36.00 3.58
2373 2515 1.559682 TGGCCTAGTTGGGAATCTCAC 59.440 52.381 3.32 0.00 36.00 3.51
2398 2540 3.527507 TTTTGGGTGGGTGTGCTATAA 57.472 42.857 0.00 0.00 0.00 0.98
2408 2550 5.674052 TGATTGAACATATTTTGGGTGGG 57.326 39.130 0.00 0.00 0.00 4.61
2409 2551 7.160726 ACTTTGATTGAACATATTTTGGGTGG 58.839 34.615 0.00 0.00 0.00 4.61
2485 2627 3.863400 GCGTGGTGTATTAAGGTGTGAGT 60.863 47.826 0.00 0.00 0.00 3.41
2498 2640 3.943691 GGGTGGGTGCGTGGTGTA 61.944 66.667 0.00 0.00 0.00 2.90
2585 3566 9.055248 CATCGATGAAGACAAATAACAAGTTTC 57.945 33.333 21.02 0.00 0.00 2.78
2761 3748 2.035626 AAACCATGGCCCTCACCG 59.964 61.111 13.04 0.00 0.00 4.94
2790 3777 2.030946 GGCATGACGCTTCAAGACATAC 59.969 50.000 0.00 0.00 41.91 2.39


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

AutoCloner maintained by Alex Coulton.