Multiple sequence alignment - TraesCS4D01G126200

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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 TraesCS4D01G126200 chr4D 100.000 5051 0 0 478 5528 110116222 110111172 0.000000e+00 9328.0
1 TraesCS4D01G126200 chr4D 100.000 181 0 0 1 181 110116699 110116519 8.870000e-88 335.0
2 TraesCS4D01G126200 chr4D 92.727 110 8 0 1333 1442 360762930 360763039 5.730000e-35 159.0
3 TraesCS4D01G126200 chr4A 93.198 4337 169 53 846 5124 466571717 466575985 0.000000e+00 6259.0
4 TraesCS4D01G126200 chr4A 92.339 248 4 7 5124 5371 466575949 466576181 6.860000e-89 339.0
5 TraesCS4D01G126200 chr4A 92.818 181 11 2 1 179 466570930 466571110 1.530000e-65 261.0
6 TraesCS4D01G126200 chr4A 92.899 169 3 2 5360 5528 466578380 466578539 2.570000e-58 237.0
7 TraesCS4D01G126200 chr4A 87.952 166 18 2 665 830 466571483 466571646 1.570000e-45 195.0
8 TraesCS4D01G126200 chr4A 93.519 108 7 0 1335 1442 539752683 539752576 1.590000e-35 161.0
9 TraesCS4D01G126200 chr4B 93.748 3711 157 31 1444 5124 171610070 171613735 0.000000e+00 5498.0
10 TraesCS4D01G126200 chr4B 95.062 648 15 8 651 1285 171609412 171610055 0.000000e+00 1003.0
11 TraesCS4D01G126200 chr4B 90.909 275 7 7 5258 5528 171613981 171614241 2.450000e-93 353.0
12 TraesCS4D01G126200 chr4B 96.992 133 1 1 1 133 171608982 171609111 2.590000e-53 220.0
13 TraesCS4D01G126200 chr4B 83.523 176 18 9 484 653 171609200 171609370 2.670000e-33 154.0
14 TraesCS4D01G126200 chr4B 92.157 102 4 2 5126 5227 171613701 171613798 2.080000e-29 141.0
15 TraesCS4D01G126200 chr4B 95.349 43 2 0 5229 5271 171613920 171613962 9.940000e-08 69.4
16 TraesCS4D01G126200 chr6B 93.496 123 6 1 1328 1448 138590613 138590735 1.220000e-41 182.0
17 TraesCS4D01G126200 chr6B 88.618 123 12 2 1330 1452 506127978 506128098 1.240000e-31 148.0
18 TraesCS4D01G126200 chrUn 94.444 108 6 0 1335 1442 288604690 288604583 3.430000e-37 167.0
19 TraesCS4D01G126200 chr7B 94.444 108 6 0 1335 1442 709475548 709475655 3.430000e-37 167.0
20 TraesCS4D01G126200 chr2A 93.578 109 7 0 1334 1442 90419433 90419325 4.430000e-36 163.0
21 TraesCS4D01G126200 chr5A 92.105 114 9 0 1335 1448 700359350 700359463 1.590000e-35 161.0


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 TraesCS4D01G126200 chr4D 110111172 110116699 5527 True 4831.500000 9328 100.000000 1 5528 2 chr4D.!!$R1 5527
1 TraesCS4D01G126200 chr4A 466570930 466578539 7609 False 1458.200000 6259 91.841200 1 5528 5 chr4A.!!$F1 5527
2 TraesCS4D01G126200 chr4B 171608982 171614241 5259 False 1062.628571 5498 92.534286 1 5528 7 chr4B.!!$F1 5527

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
534 541 2.781681 TTCCTTTTGACCTCCGATCC 57.218 50.000 0.00 0.00 0.00 3.36 F
1916 2184 0.387622 TCGTAAGTGGTGCGCTACAC 60.388 55.000 21.89 21.89 43.79 2.90 F
2171 2439 0.393537 CCATCTCCGCTGCCTCTTTT 60.394 55.000 0.00 0.00 0.00 2.27 F
3260 3544 2.025605 ACTGGATGATGTGGATGCTGTT 60.026 45.455 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2427 0.519077 GACAGGAAAAAGAGGCAGCG 59.481 55.000 0.00 0.0 0.00 5.18 R
3868 4179 1.242076 GAGGCTTTGCAGCTTCTTCA 58.758 50.000 3.18 0.0 46.38 3.02 R
3978 4289 8.811994 TGAGGGTCATATACAATATCAATCGAA 58.188 33.333 0.00 0.0 0.00 3.71 R
5116 5438 0.105039 GTGAGATGGTAGGGCGGAAG 59.895 60.000 0.00 0.0 0.00 3.46 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
25 27 8.546597 TCTTCCAAAGTTTCTTTTTCCAAAAG 57.453 30.769 3.02 3.02 0.00 2.27
148 151 8.679288 AATATTCAAATGCTCTGTTTCTTTCG 57.321 30.769 0.00 0.00 0.00 3.46
153 156 7.202526 TCAAATGCTCTGTTTCTTTCGAAAAT 58.797 30.769 12.41 0.00 40.57 1.82
530 537 3.939592 GGTCTTATTCCTTTTGACCTCCG 59.060 47.826 0.00 0.00 42.63 4.63
531 538 4.323257 GGTCTTATTCCTTTTGACCTCCGA 60.323 45.833 0.00 0.00 42.63 4.55
532 539 5.429130 GTCTTATTCCTTTTGACCTCCGAT 58.571 41.667 0.00 0.00 0.00 4.18
533 540 5.524281 GTCTTATTCCTTTTGACCTCCGATC 59.476 44.000 0.00 0.00 0.00 3.69
534 541 2.781681 TTCCTTTTGACCTCCGATCC 57.218 50.000 0.00 0.00 0.00 3.36
548 555 4.202357 CCTCCGATCCAGTTGATTATTCCA 60.202 45.833 0.00 0.00 32.41 3.53
613 689 7.450634 ACTCCACTAGTGTACTGATTGACTTAA 59.549 37.037 21.18 0.00 36.93 1.85
727 904 4.497473 TTGCCTACACAACTTAATGCAC 57.503 40.909 0.00 0.00 0.00 4.57
1047 1290 0.469917 TGGGCAAGTATGAGCTAGGC 59.530 55.000 0.00 0.00 0.00 3.93
1297 1542 1.663695 CCCCATCGCTGTATTTTCGT 58.336 50.000 0.00 0.00 0.00 3.85
1308 1553 5.329493 GCTGTATTTTCGTGGTACAAATCC 58.671 41.667 0.00 0.00 44.16 3.01
1311 1556 2.547299 TTTCGTGGTACAAATCCGGT 57.453 45.000 0.00 0.00 44.16 5.28
1331 1576 2.802247 GTTGCCACTTTTGCCTGAATTC 59.198 45.455 0.00 0.00 0.00 2.17
1343 1588 2.769095 GCCTGAATTCAGTACTCCCTCT 59.231 50.000 29.03 0.00 42.27 3.69
1344 1589 3.181470 GCCTGAATTCAGTACTCCCTCTC 60.181 52.174 29.03 5.96 42.27 3.20
1361 1606 4.811557 CCCTCTCTTCACTTTTATAAGGCG 59.188 45.833 0.00 0.00 35.61 5.52
1362 1607 4.271291 CCTCTCTTCACTTTTATAAGGCGC 59.729 45.833 0.00 0.00 35.61 6.53
1381 1626 3.579709 CGCTGTAGACATTTCAGACAGT 58.420 45.455 12.75 0.00 38.96 3.55
1391 1636 2.823196 TTCAGACAGTGTGCAAAACG 57.177 45.000 0.00 0.00 0.00 3.60
1396 1641 1.369209 CAGTGTGCAAAACGGCTCG 60.369 57.895 0.00 0.00 34.04 5.03
1403 1648 1.069296 TGCAAAACGGCTCGATTTCAG 60.069 47.619 1.50 0.00 30.05 3.02
1409 1654 1.000955 ACGGCTCGATTTCAGTTGTCT 59.999 47.619 1.50 0.00 0.00 3.41
1431 1676 9.268268 TGTCTGAAACGACTTATAAAAGTGAAT 57.732 29.630 0.00 0.00 46.09 2.57
1439 1684 6.480320 CGACTTATAAAAGTGAATGGAGGGAG 59.520 42.308 0.00 0.00 46.09 4.30
1448 1710 8.950007 AAAGTGAATGGAGGGAGTAATTTTTA 57.050 30.769 0.00 0.00 0.00 1.52
1657 1921 1.563879 TGTTATGTCTGGGGTCCATGG 59.436 52.381 4.97 4.97 30.82 3.66
1658 1922 1.843851 GTTATGTCTGGGGTCCATGGA 59.156 52.381 11.44 11.44 30.82 3.41
1856 2124 7.957002 TGGGAAGCAAAACAAAAATCTACATA 58.043 30.769 0.00 0.00 0.00 2.29
1898 2166 1.129437 GGCGAGCTCTTTGACACAATC 59.871 52.381 12.85 0.00 0.00 2.67
1906 2174 4.377431 GCTCTTTGACACAATCGTAAGTGG 60.377 45.833 0.00 0.00 39.99 4.00
1909 2177 2.139917 TGACACAATCGTAAGTGGTGC 58.860 47.619 0.00 0.00 39.99 5.01
1916 2184 0.387622 TCGTAAGTGGTGCGCTACAC 60.388 55.000 21.89 21.89 43.79 2.90
1959 2227 4.673580 CGCTGATGCAGTTTGCTTATCTTT 60.674 41.667 2.48 0.00 45.31 2.52
1960 2228 4.561606 GCTGATGCAGTTTGCTTATCTTTG 59.438 41.667 2.48 0.00 45.31 2.77
1970 2238 3.976169 TGCTTATCTTTGGCAAACACAC 58.024 40.909 8.93 0.00 32.79 3.82
2159 2427 1.039856 GTGAGCTCCTCTCCATCTCC 58.960 60.000 12.15 0.00 41.18 3.71
2167 2435 2.086251 CTCTCCATCTCCGCTGCCTC 62.086 65.000 0.00 0.00 0.00 4.70
2171 2439 0.393537 CCATCTCCGCTGCCTCTTTT 60.394 55.000 0.00 0.00 0.00 2.27
2184 2452 2.560105 GCCTCTTTTTCCTGTCAATGCT 59.440 45.455 0.00 0.00 0.00 3.79
2198 2466 6.149308 CCTGTCAATGCTAAATGTACTCACAA 59.851 38.462 0.00 0.00 38.42 3.33
2326 2594 7.277319 GCTCAAGGTACGGGTTTATTATATAGC 59.723 40.741 0.00 0.00 0.00 2.97
2327 2595 8.426569 TCAAGGTACGGGTTTATTATATAGCT 57.573 34.615 0.00 0.00 0.00 3.32
2328 2596 8.873144 TCAAGGTACGGGTTTATTATATAGCTT 58.127 33.333 0.00 0.00 31.08 3.74
2407 2675 7.572523 TTAGCAGATAATCATGTTCCTTTGG 57.427 36.000 0.00 0.00 0.00 3.28
3118 3402 8.378565 ACTAATAATCCCACATCTTACTCCATG 58.621 37.037 0.00 0.00 0.00 3.66
3124 3408 6.084060 TCCCACATCTTACTCCATGATATCA 58.916 40.000 8.10 8.10 0.00 2.15
3140 3424 9.011095 CCATGATATCAAAGCTAATGTCTTGAT 57.989 33.333 9.99 12.40 0.00 2.57
3174 3458 6.525976 GCAGAGAATAACAGTTCAAGAAATGC 59.474 38.462 9.85 0.00 39.72 3.56
3179 3463 9.507329 AGAATAACAGTTCAAGAAATGCTAGAA 57.493 29.630 9.85 0.00 39.72 2.10
3260 3544 2.025605 ACTGGATGATGTGGATGCTGTT 60.026 45.455 0.00 0.00 0.00 3.16
3456 3740 7.223260 TCTGAATGCATTTGAACTGATTTCT 57.777 32.000 14.33 0.00 34.97 2.52
3667 3977 4.951715 TGAATCATGAAAGCCAGCAGTTAT 59.048 37.500 0.00 0.00 0.00 1.89
3740 4051 8.668353 CACTTAGAGCTTTATGCACATTTTCTA 58.332 33.333 0.00 0.00 45.94 2.10
3774 4085 9.840427 TTTATGATTTCGAAACTTCATTCTTCC 57.160 29.630 24.48 0.00 31.59 3.46
3868 4179 5.163612 GCCTAAAGAAATTCTCCGCAAGATT 60.164 40.000 0.00 0.00 43.02 2.40
4003 4314 9.088512 GTTCGATTGATATTGTATATGACCCTC 57.911 37.037 0.00 0.00 0.00 4.30
4143 4454 7.395489 AGAATATGCTGAACTGAATCCACTTTT 59.605 33.333 0.00 0.00 0.00 2.27
4242 4553 2.165437 TGAAGTTCGCAAAGCAAAAGGT 59.835 40.909 0.00 0.00 0.00 3.50
4576 4888 5.710567 GGGTAAACTATTAGCATCCCATTCC 59.289 44.000 0.00 0.00 40.49 3.01
4613 4925 2.825223 TCTCAGGAGCTGGATCAAGAA 58.175 47.619 0.00 0.00 31.51 2.52
4614 4926 3.176411 TCTCAGGAGCTGGATCAAGAAA 58.824 45.455 0.00 0.00 31.51 2.52
4644 4956 2.737783 CACCGCATTTTGTAAGTACCGA 59.262 45.455 0.00 0.00 0.00 4.69
4873 5188 0.815213 CACATCGGCCGGTCATCATT 60.815 55.000 27.83 0.00 0.00 2.57
4874 5189 0.107214 ACATCGGCCGGTCATCATTT 60.107 50.000 27.83 0.00 0.00 2.32
4875 5190 0.588252 CATCGGCCGGTCATCATTTC 59.412 55.000 27.83 0.00 0.00 2.17
4876 5191 0.880278 ATCGGCCGGTCATCATTTCG 60.880 55.000 27.83 0.00 0.00 3.46
4951 5267 6.668323 CCTTGTTACATACACTTGTTCCTTG 58.332 40.000 0.00 0.00 36.21 3.61
5089 5411 2.756283 CCGCCGGTCTTCTCTCCT 60.756 66.667 1.90 0.00 0.00 3.69
5090 5412 1.453379 CCGCCGGTCTTCTCTCCTA 60.453 63.158 1.90 0.00 0.00 2.94
5091 5413 1.726533 CCGCCGGTCTTCTCTCCTAC 61.727 65.000 1.90 0.00 0.00 3.18
5092 5414 1.726533 CGCCGGTCTTCTCTCCTACC 61.727 65.000 1.90 0.00 0.00 3.18
5093 5415 0.683504 GCCGGTCTTCTCTCCTACCA 60.684 60.000 1.90 0.00 32.04 3.25
5094 5416 2.030045 GCCGGTCTTCTCTCCTACCAT 61.030 57.143 1.90 0.00 32.04 3.55
5095 5417 1.957877 CCGGTCTTCTCTCCTACCATC 59.042 57.143 0.00 0.00 32.04 3.51
5096 5418 2.423660 CCGGTCTTCTCTCCTACCATCT 60.424 54.545 0.00 0.00 32.04 2.90
5097 5419 2.882137 CGGTCTTCTCTCCTACCATCTC 59.118 54.545 0.00 0.00 32.04 2.75
5098 5420 3.685835 CGGTCTTCTCTCCTACCATCTCA 60.686 52.174 0.00 0.00 32.04 3.27
5099 5421 3.634910 GGTCTTCTCTCCTACCATCTCAC 59.365 52.174 0.00 0.00 32.04 3.51
5100 5422 3.314080 GTCTTCTCTCCTACCATCTCACG 59.686 52.174 0.00 0.00 0.00 4.35
5101 5423 3.200165 TCTTCTCTCCTACCATCTCACGA 59.800 47.826 0.00 0.00 0.00 4.35
5102 5424 2.920524 TCTCTCCTACCATCTCACGAC 58.079 52.381 0.00 0.00 0.00 4.34
5103 5425 2.506231 TCTCTCCTACCATCTCACGACT 59.494 50.000 0.00 0.00 0.00 4.18
5104 5426 2.616376 CTCTCCTACCATCTCACGACTG 59.384 54.545 0.00 0.00 0.00 3.51
5105 5427 2.026169 TCTCCTACCATCTCACGACTGT 60.026 50.000 0.00 0.00 0.00 3.55
5106 5428 2.755655 CTCCTACCATCTCACGACTGTT 59.244 50.000 0.00 0.00 0.00 3.16
5107 5429 3.162666 TCCTACCATCTCACGACTGTTT 58.837 45.455 0.00 0.00 0.00 2.83
5108 5430 3.576982 TCCTACCATCTCACGACTGTTTT 59.423 43.478 0.00 0.00 0.00 2.43
5109 5431 3.679980 CCTACCATCTCACGACTGTTTTG 59.320 47.826 0.00 0.00 0.00 2.44
5110 5432 1.873591 ACCATCTCACGACTGTTTTGC 59.126 47.619 0.00 0.00 0.00 3.68
5111 5433 2.146342 CCATCTCACGACTGTTTTGCT 58.854 47.619 0.00 0.00 0.00 3.91
5112 5434 2.096069 CCATCTCACGACTGTTTTGCTG 60.096 50.000 0.00 0.00 0.00 4.41
5113 5435 2.309528 TCTCACGACTGTTTTGCTGT 57.690 45.000 0.00 0.00 0.00 4.40
5114 5436 1.933181 TCTCACGACTGTTTTGCTGTG 59.067 47.619 0.00 0.00 0.00 3.66
5115 5437 1.933181 CTCACGACTGTTTTGCTGTGA 59.067 47.619 0.00 0.00 35.31 3.58
5116 5438 1.663643 TCACGACTGTTTTGCTGTGAC 59.336 47.619 0.00 0.00 31.93 3.67
5117 5439 1.665679 CACGACTGTTTTGCTGTGACT 59.334 47.619 0.00 0.00 0.00 3.41
5118 5440 2.095853 CACGACTGTTTTGCTGTGACTT 59.904 45.455 0.00 0.00 0.00 3.01
5119 5441 2.351726 ACGACTGTTTTGCTGTGACTTC 59.648 45.455 0.00 0.00 0.00 3.01
5120 5442 2.286418 CGACTGTTTTGCTGTGACTTCC 60.286 50.000 0.00 0.00 0.00 3.46
5121 5443 1.670811 ACTGTTTTGCTGTGACTTCCG 59.329 47.619 0.00 0.00 0.00 4.30
5122 5444 0.380378 TGTTTTGCTGTGACTTCCGC 59.620 50.000 0.00 0.00 0.00 5.54
5123 5445 0.317854 GTTTTGCTGTGACTTCCGCC 60.318 55.000 0.00 0.00 0.00 6.13
5124 5446 1.452145 TTTTGCTGTGACTTCCGCCC 61.452 55.000 0.00 0.00 0.00 6.13
5205 5527 2.223203 GCAACATGCACTGTGAGATAGC 60.223 50.000 12.86 4.04 44.26 2.97
5206 5528 3.268330 CAACATGCACTGTGAGATAGCT 58.732 45.455 12.86 0.00 38.39 3.32
5207 5529 4.436332 CAACATGCACTGTGAGATAGCTA 58.564 43.478 12.86 0.00 38.39 3.32
5208 5530 4.319139 ACATGCACTGTGAGATAGCTAG 57.681 45.455 12.86 0.00 36.48 3.42
5209 5531 2.879002 TGCACTGTGAGATAGCTAGC 57.121 50.000 12.86 6.62 0.00 3.42
5271 5713 0.250124 TGCTCATCGTGGTTTCGGTT 60.250 50.000 0.00 0.00 0.00 4.44
5272 5714 1.001068 TGCTCATCGTGGTTTCGGTTA 59.999 47.619 0.00 0.00 0.00 2.85
5273 5715 2.070783 GCTCATCGTGGTTTCGGTTAA 58.929 47.619 0.00 0.00 0.00 2.01
5274 5716 2.481185 GCTCATCGTGGTTTCGGTTAAA 59.519 45.455 0.00 0.00 0.00 1.52
5275 5717 3.424433 GCTCATCGTGGTTTCGGTTAAAG 60.424 47.826 0.00 0.00 0.00 1.85
5276 5718 3.991773 CTCATCGTGGTTTCGGTTAAAGA 59.008 43.478 0.00 0.00 0.00 2.52
5278 5720 4.390603 TCATCGTGGTTTCGGTTAAAGATG 59.609 41.667 0.00 0.00 31.82 2.90
5279 5721 2.481185 TCGTGGTTTCGGTTAAAGATGC 59.519 45.455 0.00 0.00 0.00 3.91
5387 8074 2.498885 GGTGGAGTGTACCCTCGTTTAT 59.501 50.000 0.00 0.00 31.98 1.40
5481 8168 1.064134 GCGCCGATGGTTTTGATCC 59.936 57.895 0.00 0.00 0.00 3.36
5482 8169 1.727467 CGCCGATGGTTTTGATCCC 59.273 57.895 0.00 0.00 0.00 3.85
5483 8170 1.727467 GCCGATGGTTTTGATCCCG 59.273 57.895 0.00 0.00 0.00 5.14
5484 8171 1.029947 GCCGATGGTTTTGATCCCGT 61.030 55.000 0.00 0.00 0.00 5.28
5485 8172 1.014352 CCGATGGTTTTGATCCCGTC 58.986 55.000 0.00 0.00 34.09 4.79
5500 8187 2.181021 GTCGCCGTCGAGTCCATT 59.819 61.111 0.00 0.00 46.46 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
481 484 4.081406 TGTTTTTGGATCTGGACAGGATG 58.919 43.478 0.00 0.00 46.00 3.51
482 485 4.082125 GTGTTTTTGGATCTGGACAGGAT 58.918 43.478 0.00 0.00 0.00 3.24
486 489 2.226330 CCGTGTTTTTGGATCTGGACA 58.774 47.619 0.00 0.00 0.00 4.02
530 537 9.178758 AGTTAAACTGGAATAATCAACTGGATC 57.821 33.333 0.00 0.00 34.28 3.36
531 538 9.533831 AAGTTAAACTGGAATAATCAACTGGAT 57.466 29.630 0.00 0.00 38.05 3.41
532 539 8.792633 CAAGTTAAACTGGAATAATCAACTGGA 58.207 33.333 0.00 0.00 0.00 3.86
533 540 8.028938 CCAAGTTAAACTGGAATAATCAACTGG 58.971 37.037 0.00 0.00 0.00 4.00
534 541 7.542130 GCCAAGTTAAACTGGAATAATCAACTG 59.458 37.037 8.03 0.00 0.00 3.16
579 655 5.634020 CAGTACACTAGTGGAGTTGTTTAGC 59.366 44.000 26.12 3.22 35.64 3.09
613 689 8.109634 ACTGAACCCATAAATAAGTTGTCTGAT 58.890 33.333 0.00 0.00 0.00 2.90
617 695 8.106247 TGAACTGAACCCATAAATAAGTTGTC 57.894 34.615 0.00 0.00 0.00 3.18
710 887 3.994392 AGACCGTGCATTAAGTTGTGTAG 59.006 43.478 0.00 0.00 0.00 2.74
727 904 2.202492 CGAGGAACGAGCAGACCG 60.202 66.667 0.00 0.00 45.77 4.79
987 1230 2.551856 TACTCATCCCCTGCCTGCCT 62.552 60.000 0.00 0.00 0.00 4.75
988 1231 2.072487 TACTCATCCCCTGCCTGCC 61.072 63.158 0.00 0.00 0.00 4.85
989 1232 1.147153 GTACTCATCCCCTGCCTGC 59.853 63.158 0.00 0.00 0.00 4.85
990 1233 0.911769 TTGTACTCATCCCCTGCCTG 59.088 55.000 0.00 0.00 0.00 4.85
1297 1542 0.110678 TGGCAACCGGATTTGTACCA 59.889 50.000 9.46 4.17 0.00 3.25
1331 1576 5.476091 AAAAGTGAAGAGAGGGAGTACTG 57.524 43.478 0.00 0.00 0.00 2.74
1343 1588 4.575885 ACAGCGCCTTATAAAAGTGAAGA 58.424 39.130 2.29 0.00 0.00 2.87
1344 1589 4.946784 ACAGCGCCTTATAAAAGTGAAG 57.053 40.909 2.29 0.00 0.00 3.02
1361 1606 4.151335 CACACTGTCTGAAATGTCTACAGC 59.849 45.833 15.11 0.00 39.84 4.40
1362 1607 4.151335 GCACACTGTCTGAAATGTCTACAG 59.849 45.833 14.10 14.10 40.97 2.74
1381 1626 0.665835 AAATCGAGCCGTTTTGCACA 59.334 45.000 0.00 0.00 29.48 4.57
1403 1648 8.545420 TCACTTTTATAAGTCGTTTCAGACAAC 58.455 33.333 0.00 0.00 42.67 3.32
1409 1654 8.610248 TCCATTCACTTTTATAAGTCGTTTCA 57.390 30.769 0.00 0.00 42.67 2.69
1412 1657 6.598064 CCCTCCATTCACTTTTATAAGTCGTT 59.402 38.462 0.00 0.00 42.67 3.85
1621 1885 7.542824 CAGACATAACATGATGCACATTTCAAA 59.457 33.333 0.00 0.00 37.07 2.69
1622 1886 7.030768 CAGACATAACATGATGCACATTTCAA 58.969 34.615 0.00 0.00 37.07 2.69
1623 1887 6.404954 CCAGACATAACATGATGCACATTTCA 60.405 38.462 0.00 0.00 37.07 2.69
1657 1921 4.137116 TGAGTAGTATTGTGGCATGGTC 57.863 45.455 0.00 0.00 0.00 4.02
1658 1922 4.568072 TTGAGTAGTATTGTGGCATGGT 57.432 40.909 0.00 0.00 0.00 3.55
1898 2166 2.067616 GTGTAGCGCACCACTTACG 58.932 57.895 18.71 0.00 42.10 3.18
1906 2174 1.128692 GAAACATCTGGTGTAGCGCAC 59.871 52.381 11.47 6.60 46.97 5.34
1909 2177 2.002586 CAGGAAACATCTGGTGTAGCG 58.997 52.381 0.00 0.00 41.14 4.26
1916 2184 2.032550 CGCATAAGCAGGAAACATCTGG 59.967 50.000 0.00 0.00 42.27 3.86
1918 2186 1.672881 GCGCATAAGCAGGAAACATCT 59.327 47.619 0.30 0.00 42.27 2.90
1919 2187 1.672881 AGCGCATAAGCAGGAAACATC 59.327 47.619 11.47 0.00 42.27 3.06
1959 2227 2.683362 TGTTGTAATCGTGTGTTTGCCA 59.317 40.909 0.00 0.00 0.00 4.92
1960 2228 3.040099 GTGTTGTAATCGTGTGTTTGCC 58.960 45.455 0.00 0.00 0.00 4.52
2015 2283 4.379652 GTTAACCTTTACGACAAGGGACA 58.620 43.478 17.91 4.02 46.98 4.02
2159 2427 0.519077 GACAGGAAAAAGAGGCAGCG 59.481 55.000 0.00 0.00 0.00 5.18
2167 2435 8.299570 AGTACATTTAGCATTGACAGGAAAAAG 58.700 33.333 0.00 0.00 0.00 2.27
2171 2439 6.371548 GTGAGTACATTTAGCATTGACAGGAA 59.628 38.462 0.00 0.00 0.00 3.36
2198 2466 9.515226 TGCAAGTAGTTTGGTTTAGATAGATTT 57.485 29.630 0.00 0.00 37.26 2.17
2326 2594 7.044181 TGATAACTTAGGAGTGCATGAAGAAG 58.956 38.462 0.00 0.00 35.91 2.85
2327 2595 6.946340 TGATAACTTAGGAGTGCATGAAGAA 58.054 36.000 0.00 0.00 35.91 2.52
2328 2596 6.544928 TGATAACTTAGGAGTGCATGAAGA 57.455 37.500 0.00 0.00 35.91 2.87
2929 3210 1.881973 TGGTTCAATGAGCTCTTGTGC 59.118 47.619 16.19 12.40 0.00 4.57
2975 3257 4.568072 ACAACCTACTGGATGCATTGTA 57.432 40.909 0.00 4.45 39.43 2.41
3111 3395 7.743749 AGACATTAGCTTTGATATCATGGAGT 58.256 34.615 6.17 0.00 0.00 3.85
3124 3408 7.761249 GCCACAATTTATCAAGACATTAGCTTT 59.239 33.333 0.00 0.00 0.00 3.51
3140 3424 7.446931 TGAACTGTTATTCTCTGCCACAATTTA 59.553 33.333 0.00 0.00 0.00 1.40
3174 3458 6.593382 CCTTTCTTGAACCACTCATCTTCTAG 59.407 42.308 0.00 0.00 32.78 2.43
3179 3463 4.713792 ACCTTTCTTGAACCACTCATCT 57.286 40.909 0.00 0.00 32.78 2.90
3260 3544 6.009589 TGGGCTTACTTCTGAATCATTGAAA 58.990 36.000 0.00 0.00 0.00 2.69
3456 3740 2.121948 AGATTGAGGCCTGCTGACATA 58.878 47.619 12.00 0.00 0.00 2.29
3740 4051 9.221775 GAAGTTTCGAAATCATAAATGCGTAAT 57.778 29.630 14.69 0.00 0.00 1.89
3868 4179 1.242076 GAGGCTTTGCAGCTTCTTCA 58.758 50.000 3.18 0.00 46.38 3.02
3978 4289 8.811994 TGAGGGTCATATACAATATCAATCGAA 58.188 33.333 0.00 0.00 0.00 3.71
3981 4292 9.950496 ACTTGAGGGTCATATACAATATCAATC 57.050 33.333 0.00 0.00 0.00 2.67
4242 4553 6.174720 ACCTTGTGAAATTCTAGAGTGTCA 57.825 37.500 4.05 4.05 0.00 3.58
4298 4609 1.606737 GCACCTCTCAGTTGACAGACC 60.607 57.143 0.00 0.00 0.00 3.85
4576 4888 4.695396 CTGAGAATGGATCAACTCAGGAG 58.305 47.826 20.03 0.00 46.93 3.69
4613 4925 5.809719 ACAAAATGCGGTGAACAATTTTT 57.190 30.435 0.00 0.00 0.00 1.94
4614 4926 6.536941 ACTTACAAAATGCGGTGAACAATTTT 59.463 30.769 0.00 0.00 0.00 1.82
4644 4956 1.133976 GCTGACAACAGGGCTATCCAT 60.134 52.381 0.00 0.00 43.62 3.41
4873 5188 5.008811 ACAATTTACAATGGGAACGAACGAA 59.991 36.000 0.14 0.00 0.00 3.85
4874 5189 4.515944 ACAATTTACAATGGGAACGAACGA 59.484 37.500 0.14 0.00 0.00 3.85
4875 5190 4.615121 CACAATTTACAATGGGAACGAACG 59.385 41.667 0.00 0.00 0.00 3.95
4876 5191 5.764131 TCACAATTTACAATGGGAACGAAC 58.236 37.500 0.00 0.00 0.00 3.95
4951 5267 4.633565 CCCTTCAGTTCTGATTTACAGCTC 59.366 45.833 3.28 0.00 45.38 4.09
4993 5309 5.303971 CCCTCATGTATCATCCTCTGAAAC 58.696 45.833 0.00 0.00 37.44 2.78
5089 5411 3.064207 GCAAAACAGTCGTGAGATGGTA 58.936 45.455 0.00 0.00 45.19 3.25
5090 5412 1.873591 GCAAAACAGTCGTGAGATGGT 59.126 47.619 0.00 0.00 45.19 3.55
5091 5413 2.096069 CAGCAAAACAGTCGTGAGATGG 60.096 50.000 0.00 0.00 45.19 3.51
5092 5414 2.545526 ACAGCAAAACAGTCGTGAGATG 59.454 45.455 0.00 0.00 45.19 2.90
5093 5415 2.545526 CACAGCAAAACAGTCGTGAGAT 59.454 45.455 0.00 0.00 45.19 2.75
5094 5416 1.933181 CACAGCAAAACAGTCGTGAGA 59.067 47.619 0.00 0.00 38.16 3.27
5095 5417 1.933181 TCACAGCAAAACAGTCGTGAG 59.067 47.619 0.00 0.00 0.00 3.51
5096 5418 1.663643 GTCACAGCAAAACAGTCGTGA 59.336 47.619 0.00 0.00 0.00 4.35
5097 5419 1.665679 AGTCACAGCAAAACAGTCGTG 59.334 47.619 0.00 0.00 0.00 4.35
5098 5420 2.024176 AGTCACAGCAAAACAGTCGT 57.976 45.000 0.00 0.00 0.00 4.34
5099 5421 2.286418 GGAAGTCACAGCAAAACAGTCG 60.286 50.000 0.00 0.00 0.00 4.18
5100 5422 2.286418 CGGAAGTCACAGCAAAACAGTC 60.286 50.000 0.00 0.00 0.00 3.51
5101 5423 1.670811 CGGAAGTCACAGCAAAACAGT 59.329 47.619 0.00 0.00 0.00 3.55
5102 5424 1.597937 GCGGAAGTCACAGCAAAACAG 60.598 52.381 0.00 0.00 0.00 3.16
5103 5425 0.380378 GCGGAAGTCACAGCAAAACA 59.620 50.000 0.00 0.00 0.00 2.83
5104 5426 0.317854 GGCGGAAGTCACAGCAAAAC 60.318 55.000 0.00 0.00 34.40 2.43
5105 5427 1.452145 GGGCGGAAGTCACAGCAAAA 61.452 55.000 0.00 0.00 37.54 2.44
5106 5428 1.896660 GGGCGGAAGTCACAGCAAA 60.897 57.895 0.00 0.00 37.54 3.68
5107 5429 1.476845 TAGGGCGGAAGTCACAGCAA 61.477 55.000 0.00 0.00 37.54 3.91
5108 5430 1.911269 TAGGGCGGAAGTCACAGCA 60.911 57.895 0.00 0.00 37.54 4.41
5109 5431 1.448013 GTAGGGCGGAAGTCACAGC 60.448 63.158 0.00 0.00 37.54 4.40
5110 5432 1.218316 GGTAGGGCGGAAGTCACAG 59.782 63.158 0.00 0.00 37.54 3.66
5111 5433 0.907704 ATGGTAGGGCGGAAGTCACA 60.908 55.000 0.00 0.00 37.54 3.58
5112 5434 0.179081 GATGGTAGGGCGGAAGTCAC 60.179 60.000 0.00 0.00 37.54 3.67
5113 5435 0.325296 AGATGGTAGGGCGGAAGTCA 60.325 55.000 0.00 0.00 37.54 3.41
5114 5436 0.389757 GAGATGGTAGGGCGGAAGTC 59.610 60.000 0.00 0.00 0.00 3.01
5115 5437 0.325296 TGAGATGGTAGGGCGGAAGT 60.325 55.000 0.00 0.00 0.00 3.01
5116 5438 0.105039 GTGAGATGGTAGGGCGGAAG 59.895 60.000 0.00 0.00 0.00 3.46
5117 5439 1.672854 CGTGAGATGGTAGGGCGGAA 61.673 60.000 0.00 0.00 0.00 4.30
5118 5440 2.125326 CGTGAGATGGTAGGGCGGA 61.125 63.158 0.00 0.00 0.00 5.54
5119 5441 2.417516 CGTGAGATGGTAGGGCGG 59.582 66.667 0.00 0.00 0.00 6.13
5120 5442 2.417516 CCGTGAGATGGTAGGGCG 59.582 66.667 0.00 0.00 0.00 6.13
5121 5443 2.109181 GCCGTGAGATGGTAGGGC 59.891 66.667 0.00 0.00 40.17 5.19
5122 5444 1.330655 ACAGCCGTGAGATGGTAGGG 61.331 60.000 0.00 0.00 0.00 3.53
5123 5445 0.537188 AACAGCCGTGAGATGGTAGG 59.463 55.000 0.00 0.00 0.00 3.18
5124 5446 2.386661 AAACAGCCGTGAGATGGTAG 57.613 50.000 0.00 0.00 0.00 3.18
5205 5527 7.429633 ACTACTAGAATGCTATGTGTTGCTAG 58.570 38.462 0.00 0.00 0.00 3.42
5206 5528 7.348080 ACTACTAGAATGCTATGTGTTGCTA 57.652 36.000 0.00 0.00 0.00 3.49
5207 5529 6.227298 ACTACTAGAATGCTATGTGTTGCT 57.773 37.500 0.00 0.00 0.00 3.91
5208 5530 7.867909 TGATACTACTAGAATGCTATGTGTTGC 59.132 37.037 0.00 0.00 0.00 4.17
5209 5531 9.920133 ATGATACTACTAGAATGCTATGTGTTG 57.080 33.333 0.00 0.00 0.00 3.33
5279 5721 1.736645 GCACTTGCAAGGCAGCATG 60.737 57.895 29.18 17.96 45.19 4.06
5336 5813 5.009811 ACTTGCGTTAACTAGTCTTCACTCT 59.990 40.000 3.71 0.00 33.62 3.24
5337 5814 5.221130 ACTTGCGTTAACTAGTCTTCACTC 58.779 41.667 3.71 0.00 33.62 3.51
5338 5815 5.197682 ACTTGCGTTAACTAGTCTTCACT 57.802 39.130 3.71 0.00 36.55 3.41
5339 5816 5.667175 CAACTTGCGTTAACTAGTCTTCAC 58.333 41.667 3.71 0.00 0.00 3.18
5340 5817 4.210537 GCAACTTGCGTTAACTAGTCTTCA 59.789 41.667 3.71 0.00 31.71 3.02
5341 5818 4.699303 GCAACTTGCGTTAACTAGTCTTC 58.301 43.478 3.71 0.00 31.71 2.87
5342 5819 4.727235 GCAACTTGCGTTAACTAGTCTT 57.273 40.909 3.71 0.00 31.71 3.01
5387 8074 1.399744 ATGCAGATCGGCCGGAGTAA 61.400 55.000 27.83 5.39 0.00 2.24
5483 8170 1.872679 GAATGGACTCGACGGCGAC 60.873 63.158 10.67 6.59 42.51 5.19
5484 8171 2.044555 AGAATGGACTCGACGGCGA 61.045 57.895 15.22 15.22 45.71 5.54
5485 8172 1.874019 CAGAATGGACTCGACGGCG 60.874 63.158 2.87 2.87 39.35 6.46
5486 8173 2.167861 GCAGAATGGACTCGACGGC 61.168 63.158 0.00 0.00 35.86 5.68
5500 8187 7.582667 ATCAATGAATCAATCAATCTGCAGA 57.417 32.000 20.79 20.79 42.54 4.26


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

AutoCloner maintained by Alex Coulton.