Multiple sequence alignment - TraesCS5A01G228400

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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 TraesCS5A01G228400 chr5A 100.000 4205 0 0 1 4205 444563500 444559296 0.000000e+00 7766.0
1 TraesCS5A01G228400 chr5A 100.000 196 0 0 4380 4575 444559121 444558926 3.360000e-96 363.0
2 TraesCS5A01G228400 chr5A 87.571 177 18 3 3214 3389 672417370 672417197 7.760000e-48 202.0
3 TraesCS5A01G228400 chr5D 96.248 2905 93 13 493 3389 347362733 347365629 0.000000e+00 4747.0
4 TraesCS5A01G228400 chr5D 95.633 664 22 5 3398 4059 347365828 347366486 0.000000e+00 1059.0
5 TraesCS5A01G228400 chr5D 93.839 211 12 1 158 367 347362500 347362710 2.660000e-82 316.0
6 TraesCS5A01G228400 chr5D 92.638 163 9 1 4415 4574 347367972 347368134 9.900000e-57 231.0
7 TraesCS5A01G228400 chr5D 97.561 41 1 0 4535 4575 430917963 430918003 2.280000e-08 71.3
8 TraesCS5A01G228400 chr5B 94.712 1456 68 6 449 1900 403783623 403782173 0.000000e+00 2254.0
9 TraesCS5A01G228400 chr5B 94.942 1206 37 6 2185 3389 403781775 403780593 0.000000e+00 1868.0
10 TraesCS5A01G228400 chr5B 89.562 776 34 11 3385 4158 403780400 403779670 0.000000e+00 941.0
11 TraesCS5A01G228400 chr5B 92.674 273 13 2 1885 2150 403782045 403781773 2.000000e-103 387.0
12 TraesCS5A01G228400 chr5B 94.340 212 10 2 158 367 403783833 403783622 1.590000e-84 324.0
13 TraesCS5A01G228400 chr5B 89.308 159 15 1 1 157 403784022 403783864 1.000000e-46 198.0
14 TraesCS5A01G228400 chr5B 93.617 94 5 1 2556 2648 706306970 706306877 6.170000e-29 139.0
15 TraesCS5A01G228400 chr5B 95.349 43 2 0 4533 4575 551796809 551796767 8.210000e-08 69.4
16 TraesCS5A01G228400 chr4D 87.634 186 20 2 3205 3389 491692003 491692186 3.590000e-51 213.0
17 TraesCS5A01G228400 chr4D 86.631 187 20 4 3205 3389 490602601 490602784 7.760000e-48 202.0
18 TraesCS5A01G228400 chr2A 87.821 156 16 2 4382 4535 52478539 52478693 3.640000e-41 180.0
19 TraesCS5A01G228400 chr2A 100.000 86 0 0 366 451 516432488 516432403 4.740000e-35 159.0
20 TraesCS5A01G228400 chr3A 98.876 89 1 0 366 454 638068161 638068073 4.740000e-35 159.0
21 TraesCS5A01G228400 chr3A 98.851 87 1 0 366 452 709065584 709065498 6.130000e-34 156.0
22 TraesCS5A01G228400 chr3A 89.189 111 12 0 356 466 15606451 15606561 6.170000e-29 139.0
23 TraesCS5A01G228400 chr3A 91.667 48 4 0 4525 4572 654061672 654061719 2.950000e-07 67.6
24 TraesCS5A01G228400 chr4B 98.876 89 0 1 366 453 629939750 629939838 1.700000e-34 158.0
25 TraesCS5A01G228400 chr1A 97.778 90 2 0 362 451 514886271 514886360 6.130000e-34 156.0
26 TraesCS5A01G228400 chr1A 97.778 90 2 0 362 451 515142537 515142626 6.130000e-34 156.0
27 TraesCS5A01G228400 chr7B 95.789 95 2 1 359 453 622831034 622831126 7.930000e-33 152.0
28 TraesCS5A01G228400 chr7B 93.000 100 7 0 358 457 414314546 414314447 3.690000e-31 147.0
29 TraesCS5A01G228400 chr1B 93.750 96 5 1 2556 2651 493871969 493871875 4.770000e-30 143.0
30 TraesCS5A01G228400 chr1B 91.837 98 7 1 2555 2651 493871873 493871970 7.980000e-28 135.0
31 TraesCS5A01G228400 chr2D 94.186 86 4 1 2561 2646 459300641 459300557 3.710000e-26 130.0
32 TraesCS5A01G228400 chr6D 92.222 90 7 0 2561 2650 292073457 292073368 1.340000e-25 128.0
33 TraesCS5A01G228400 chr6D 89.286 56 5 1 4519 4574 451799300 451799354 8.210000e-08 69.4
34 TraesCS5A01G228400 chr2B 92.222 90 7 0 2561 2650 764537697 764537608 1.340000e-25 128.0
35 TraesCS5A01G228400 chr3D 87.387 111 10 4 2557 2666 7258124 7258017 1.730000e-24 124.0
36 TraesCS5A01G228400 chr3D 92.157 51 2 2 4525 4574 113460759 113460808 2.280000e-08 71.3
37 TraesCS5A01G228400 chr1D 95.775 71 3 0 4430 4500 470945275 470945205 1.040000e-21 115.0
38 TraesCS5A01G228400 chr7D 90.385 52 4 1 4524 4574 586386841 586386892 2.950000e-07 67.6
39 TraesCS5A01G228400 chr7A 95.238 42 2 0 4534 4575 463012483 463012442 2.950000e-07 67.6
40 TraesCS5A01G228400 chrUn 93.333 45 2 1 4532 4575 22043185 22043229 1.060000e-06 65.8


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 TraesCS5A01G228400 chr5A 444558926 444563500 4574 True 4064.500000 7766 100.000000 1 4575 2 chr5A.!!$R2 4574
1 TraesCS5A01G228400 chr5D 347362500 347368134 5634 False 1588.250000 4747 94.589500 158 4574 4 chr5D.!!$F2 4416
2 TraesCS5A01G228400 chr5B 403779670 403784022 4352 True 995.333333 2254 92.589667 1 4158 6 chr5B.!!$R3 4157

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
462 497 0.247736 GGGAGTATATGCGAGGCCAG 59.752 60.0 5.01 0.0 0.00 4.85 F
468 503 0.533755 ATATGCGAGGCCAGCTTGAC 60.534 55.0 21.29 0.0 35.28 3.18 F
1998 2187 0.620556 TTTGTGATCTCCCTCCCAGC 59.379 55.0 0.00 0.0 0.00 4.85 F
2370 2567 1.035932 CCGTCCCACCAGATACGACT 61.036 60.0 0.00 0.0 37.53 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2167 1.004745 GCTGGGAGGGAGATCACAAAA 59.995 52.381 0.00 0.0 30.63 2.44 R
2353 2550 1.405821 CAGAGTCGTATCTGGTGGGAC 59.594 57.143 10.56 0.0 42.52 4.46 R
2820 3019 0.605083 TCACGACAAGAGCAGCAGAT 59.395 50.000 0.00 0.0 0.00 2.90 R
4017 4623 0.521242 CGCCGCTACATTTTGCAGTC 60.521 55.000 0.00 0.0 0.00 3.51 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
48 51 4.548669 AGATAGTGTTTCCCTAGGGAGAC 58.451 47.826 34.67 34.67 46.06 3.36
60 63 4.566488 CCCTAGGGAGACATGATTATTGGC 60.566 50.000 24.99 0.00 37.50 4.52
66 69 4.814234 GGAGACATGATTATTGGCGTGTTA 59.186 41.667 0.00 0.00 34.61 2.41
73 76 7.551262 ACATGATTATTGGCGTGTTAGTCTTTA 59.449 33.333 0.00 0.00 30.50 1.85
74 77 7.298507 TGATTATTGGCGTGTTAGTCTTTAC 57.701 36.000 0.00 0.00 0.00 2.01
85 88 4.159135 TGTTAGTCTTTACATCCCTCGTCC 59.841 45.833 0.00 0.00 0.00 4.79
103 106 5.972935 TCGTCCTGCATACTCTAAAATTGA 58.027 37.500 0.00 0.00 0.00 2.57
120 123 2.284625 AGGACGATGGTGGGAGCA 60.285 61.111 0.00 0.00 0.00 4.26
200 234 7.138692 GCCATAGTAATTTGATAGGCTTCAG 57.861 40.000 0.00 0.00 37.89 3.02
257 291 7.594386 TGATACATTTGTACAATTGTTGTGCTG 59.406 33.333 30.43 11.64 45.05 4.41
265 299 3.243839 ACAATTGTTGTGCTGGGAATGTC 60.244 43.478 4.92 0.00 43.48 3.06
281 315 5.292101 GGGAATGTCGTTCTGTGATTAGAAG 59.708 44.000 4.81 0.00 37.36 2.85
292 326 6.202331 TCTGTGATTAGAAGTTGGGAGGATA 58.798 40.000 0.00 0.00 0.00 2.59
367 402 4.947388 TGGTTTCCACTGCCTATGATTTAC 59.053 41.667 0.00 0.00 0.00 2.01
368 403 5.193679 GGTTTCCACTGCCTATGATTTACT 58.806 41.667 0.00 0.00 0.00 2.24
369 404 5.297029 GGTTTCCACTGCCTATGATTTACTC 59.703 44.000 0.00 0.00 0.00 2.59
370 405 4.689612 TCCACTGCCTATGATTTACTCC 57.310 45.455 0.00 0.00 0.00 3.85
371 406 3.391296 TCCACTGCCTATGATTTACTCCC 59.609 47.826 0.00 0.00 0.00 4.30
372 407 3.392616 CCACTGCCTATGATTTACTCCCT 59.607 47.826 0.00 0.00 0.00 4.20
373 408 4.503991 CCACTGCCTATGATTTACTCCCTC 60.504 50.000 0.00 0.00 0.00 4.30
374 409 4.346418 CACTGCCTATGATTTACTCCCTCT 59.654 45.833 0.00 0.00 0.00 3.69
375 410 4.346418 ACTGCCTATGATTTACTCCCTCTG 59.654 45.833 0.00 0.00 0.00 3.35
376 411 4.298626 TGCCTATGATTTACTCCCTCTGT 58.701 43.478 0.00 0.00 0.00 3.41
377 412 5.464069 TGCCTATGATTTACTCCCTCTGTA 58.536 41.667 0.00 0.00 0.00 2.74
378 413 5.903010 TGCCTATGATTTACTCCCTCTGTAA 59.097 40.000 0.00 0.00 0.00 2.41
379 414 6.385759 TGCCTATGATTTACTCCCTCTGTAAA 59.614 38.462 0.00 0.00 41.94 2.01
380 415 6.706716 GCCTATGATTTACTCCCTCTGTAAAC 59.293 42.308 0.00 0.00 40.98 2.01
381 416 7.419172 GCCTATGATTTACTCCCTCTGTAAACT 60.419 40.741 0.00 0.00 40.98 2.66
382 417 9.144298 CCTATGATTTACTCCCTCTGTAAACTA 57.856 37.037 0.00 0.00 40.98 2.24
392 427 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
394 429 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
441 476 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
442 477 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
443 478 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
444 479 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
445 480 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
446 481 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
447 482 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
448 483 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
449 484 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
462 497 0.247736 GGGAGTATATGCGAGGCCAG 59.752 60.000 5.01 0.00 0.00 4.85
468 503 0.533755 ATATGCGAGGCCAGCTTGAC 60.534 55.000 21.29 0.00 35.28 3.18
477 512 2.084546 GGCCAGCTTGACGAAAACTAT 58.915 47.619 0.00 0.00 0.00 2.12
501 536 8.753497 ATCAAAGTTTAGTCTTCCAGTCTTTT 57.247 30.769 0.00 0.00 0.00 2.27
555 590 3.616956 TGGACACTGCTATTTGGAGAG 57.383 47.619 0.00 0.00 37.57 3.20
824 859 5.607119 ATTGTAGGTTTTCAGCTGTTACG 57.393 39.130 14.67 0.00 31.45 3.18
837 872 3.933332 AGCTGTTACGTGCCTATTCTTTC 59.067 43.478 0.00 0.00 0.00 2.62
1023 1061 4.711399 TGGTGAAGGATCATCTAATGCTG 58.289 43.478 0.00 0.00 37.58 4.41
1272 1310 6.605849 CAGTGTAAAGGTTCACATCATTCAG 58.394 40.000 0.00 0.00 37.07 3.02
1391 1429 5.360429 TGTCGCACCAGTGTTTACCTATATA 59.640 40.000 0.00 0.00 0.00 0.86
1436 1479 8.863872 AGAGCATTTGTTTGGTAGTTTATACT 57.136 30.769 0.00 0.00 38.44 2.12
1437 1480 9.953565 AGAGCATTTGTTTGGTAGTTTATACTA 57.046 29.630 0.00 0.00 35.78 1.82
1501 1544 5.130477 TGATTAGGGGTCAACACTATCCTTC 59.870 44.000 0.00 0.00 0.00 3.46
1652 1698 6.151691 TCTCATTGTTTGCAGCTTTATCAAC 58.848 36.000 0.00 0.00 0.00 3.18
1769 1815 7.447374 TTGTTGTACTGTTTATCCTTCATGG 57.553 36.000 0.00 0.00 37.10 3.66
1998 2187 0.620556 TTTGTGATCTCCCTCCCAGC 59.379 55.000 0.00 0.00 0.00 4.85
2085 2280 1.090052 GTCCACGCCAGTCCTTATGC 61.090 60.000 0.00 0.00 0.00 3.14
2122 2318 4.144297 TCTCCAAGTTGATTCTTGTTGGG 58.856 43.478 3.87 0.00 42.01 4.12
2209 2406 3.710724 GGTCTCTCCCTAGGTAAAGTGT 58.289 50.000 8.29 0.00 0.00 3.55
2332 2529 8.811017 TCTGCCATGAGGTGAATTTATTTTTAA 58.189 29.630 0.00 0.00 37.19 1.52
2358 2555 3.578978 TCTATAAAGTATGCCCGTCCCA 58.421 45.455 0.00 0.00 0.00 4.37
2370 2567 1.035932 CCGTCCCACCAGATACGACT 61.036 60.000 0.00 0.00 37.53 4.18
2379 2576 3.440522 CACCAGATACGACTCTGAACTGA 59.559 47.826 16.88 0.00 44.48 3.41
2447 2644 1.306997 TCCCAGACCCCATCCTGAC 60.307 63.158 0.00 0.00 32.37 3.51
2459 2656 3.370527 CCCATCCTGACGAAACTACCATT 60.371 47.826 0.00 0.00 0.00 3.16
2482 2679 9.309516 CATTGATATAAGGCATGGCATAATTTC 57.690 33.333 22.64 14.72 0.00 2.17
2486 2683 4.836125 AAGGCATGGCATAATTTCGTAG 57.164 40.909 22.64 0.00 0.00 3.51
2574 2771 9.958234 CATGTTTATATATACTCCCTCTGATCG 57.042 37.037 5.15 0.00 0.00 3.69
2584 2781 6.301169 ACTCCCTCTGATCGAAAATAAGTT 57.699 37.500 0.00 0.00 0.00 2.66
2659 2856 6.608405 TCGGAGGGAGTAGTATTCAATTGTTA 59.392 38.462 5.13 0.00 0.00 2.41
2820 3019 2.203337 ACTGCTGCCTTTTGCCGA 60.203 55.556 0.00 0.00 40.16 5.54
3019 3218 3.058293 TCAGCAATGTTTTCAGTAAGCGG 60.058 43.478 0.00 0.00 0.00 5.52
3040 3240 6.366332 AGCGGAATACTCTTTTAAGATATGCG 59.634 38.462 0.00 0.00 33.93 4.73
3042 3242 7.410942 GCGGAATACTCTTTTAAGATATGCGAG 60.411 40.741 0.00 0.00 33.93 5.03
3094 3294 8.667076 TCAGTATTCATATCTGTGGTTCATTG 57.333 34.615 0.00 0.00 0.00 2.82
3308 3509 6.155910 TCCTTGAGCTCTGAATTCAGTTAGAT 59.844 38.462 29.80 21.47 44.12 1.98
3396 3794 4.629200 TGTGTTCCTTGTCAAAATTTGCAC 59.371 37.500 0.00 1.93 0.00 4.57
3400 3798 5.336150 TCCTTGTCAAAATTTGCACTTGA 57.664 34.783 0.00 0.00 0.00 3.02
3405 3994 4.340666 TGTCAAAATTTGCACTTGAGCCTA 59.659 37.500 0.00 0.00 30.00 3.93
3582 4171 2.494059 ACCACAACCTTGAAGATGTCG 58.506 47.619 0.00 0.00 0.00 4.35
3583 4172 2.158813 ACCACAACCTTGAAGATGTCGT 60.159 45.455 0.00 0.00 0.00 4.34
3587 4176 0.670546 ACCTTGAAGATGTCGTGCCG 60.671 55.000 0.00 0.00 0.00 5.69
3589 4178 1.645034 CTTGAAGATGTCGTGCCGAT 58.355 50.000 0.67 0.00 38.42 4.18
3659 4248 4.332819 CGAATCACCAAAGGAGTTATGGTC 59.667 45.833 0.00 0.00 45.45 4.02
3708 4297 2.339418 CGTACTTTACGTCATTGCCCA 58.661 47.619 0.00 0.00 46.41 5.36
3971 4561 9.214957 TGCTAGAATTGTATTATTAATGTCCCG 57.785 33.333 0.00 0.00 0.00 5.14
3972 4562 9.431887 GCTAGAATTGTATTATTAATGTCCCGA 57.568 33.333 0.00 0.00 0.00 5.14
4008 4614 3.164026 TGCTTCTGCGCATGATCTT 57.836 47.368 12.24 0.00 43.34 2.40
4011 4617 1.376543 CTTCTGCGCATGATCTTGGT 58.623 50.000 12.24 0.00 0.00 3.67
4017 4623 0.933097 CGCATGATCTTGGTTCCTCG 59.067 55.000 10.35 1.10 0.00 4.63
4028 4634 1.879380 TGGTTCCTCGACTGCAAAATG 59.121 47.619 0.00 0.00 0.00 2.32
4077 4694 4.463186 GGTAGACAGTGTTAGTGGATCAGT 59.537 45.833 0.00 0.00 0.00 3.41
4106 6020 6.315393 GTGCTTATACTCTCCCGAAATGAAAA 59.685 38.462 0.00 0.00 0.00 2.29
4119 6033 3.760580 AATGAAAATTTTGCGACCCCA 57.239 38.095 8.47 0.00 0.00 4.96
4120 6034 3.979101 ATGAAAATTTTGCGACCCCAT 57.021 38.095 8.47 0.81 0.00 4.00
4160 6075 1.004628 TGCTGGCACTTATGTGGTGAT 59.995 47.619 10.47 0.00 43.97 3.06
4161 6076 1.672881 GCTGGCACTTATGTGGTGATC 59.327 52.381 10.47 0.00 43.97 2.92
4184 6099 1.887198 CTCCTGTGACGTTAGTGACCT 59.113 52.381 0.00 0.00 33.40 3.85
4192 6107 6.282167 TGTGACGTTAGTGACCTTATTTTGA 58.718 36.000 0.00 0.00 33.40 2.69
4203 6118 8.383175 AGTGACCTTATTTTGAGTATTCCTGAA 58.617 33.333 0.00 0.00 0.00 3.02
4204 6119 8.669243 GTGACCTTATTTTGAGTATTCCTGAAG 58.331 37.037 0.00 0.00 0.00 3.02
4400 6315 3.508762 GAAGCTTGACAAGAATGCATGG 58.491 45.455 19.51 0.00 0.00 3.66
4439 6354 4.281898 ACCACCGCAATAAACTAGAACT 57.718 40.909 0.00 0.00 0.00 3.01
4489 6404 8.862325 TCATATTACCTATATTGGTGGCAAAG 57.138 34.615 17.84 5.04 41.05 2.77
4533 6451 9.574516 AAAGAACTAGACCAAAACATACATCTT 57.425 29.630 0.00 0.00 0.00 2.40
4540 6458 3.500982 CAAAACATACATCTTGGGCGTG 58.499 45.455 0.00 0.00 0.00 5.34
4566 6484 1.377994 GCCTGCATATGGCCTAGCT 59.622 57.895 3.32 0.00 44.32 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.287552 TGTCTCCCTAGGGAAACACTATC 58.712 47.826 29.92 14.53 40.02 2.08
37 40 4.566488 GCCAATAATCATGTCTCCCTAGGG 60.566 50.000 23.22 23.22 0.00 3.53
41 44 2.439507 ACGCCAATAATCATGTCTCCCT 59.560 45.455 0.00 0.00 0.00 4.20
48 51 5.991328 AGACTAACACGCCAATAATCATG 57.009 39.130 0.00 0.00 0.00 3.07
60 63 4.103357 CGAGGGATGTAAAGACTAACACG 58.897 47.826 0.00 0.00 0.00 4.49
66 69 2.761208 CAGGACGAGGGATGTAAAGACT 59.239 50.000 0.00 0.00 0.00 3.24
73 76 0.753262 GTATGCAGGACGAGGGATGT 59.247 55.000 0.00 0.00 0.00 3.06
74 77 1.000283 GAGTATGCAGGACGAGGGATG 60.000 57.143 0.00 0.00 0.00 3.51
85 88 6.042777 TCGTCCTCAATTTTAGAGTATGCAG 58.957 40.000 0.00 0.00 0.00 4.41
103 106 1.690219 GATGCTCCCACCATCGTCCT 61.690 60.000 0.00 0.00 30.88 3.85
120 123 5.488919 TCTGGGTTGATGAGAACTTAAGGAT 59.511 40.000 7.53 0.00 0.00 3.24
157 160 6.973229 ATGGCTAAAAACTGATGAAAATGC 57.027 33.333 0.00 0.00 0.00 3.56
200 234 2.829741 TGTGCCAATAAAAACCAGCC 57.170 45.000 0.00 0.00 0.00 4.85
205 239 2.474735 CACCGCTTGTGCCAATAAAAAC 59.525 45.455 0.00 0.00 38.34 2.43
257 291 4.755411 TCTAATCACAGAACGACATTCCC 58.245 43.478 0.00 0.00 38.16 3.97
265 299 4.566004 TCCCAACTTCTAATCACAGAACG 58.434 43.478 0.00 0.00 31.34 3.95
281 315 4.457257 GCATAGCATTTCTATCCTCCCAAC 59.543 45.833 0.00 0.00 35.86 3.77
368 403 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
415 450 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
416 451 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
417 452 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
418 453 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
419 454 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
420 455 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
421 456 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
422 457 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
423 458 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
428 463 8.693625 GCATATACTCCCTCCGTAAACTAATAT 58.306 37.037 0.00 0.00 0.00 1.28
429 464 7.148188 CGCATATACTCCCTCCGTAAACTAATA 60.148 40.741 0.00 0.00 0.00 0.98
430 465 6.349944 CGCATATACTCCCTCCGTAAACTAAT 60.350 42.308 0.00 0.00 0.00 1.73
431 466 5.048504 CGCATATACTCCCTCCGTAAACTAA 60.049 44.000 0.00 0.00 0.00 2.24
432 467 4.456911 CGCATATACTCCCTCCGTAAACTA 59.543 45.833 0.00 0.00 0.00 2.24
433 468 3.255149 CGCATATACTCCCTCCGTAAACT 59.745 47.826 0.00 0.00 0.00 2.66
434 469 3.254166 TCGCATATACTCCCTCCGTAAAC 59.746 47.826 0.00 0.00 0.00 2.01
435 470 3.489355 TCGCATATACTCCCTCCGTAAA 58.511 45.455 0.00 0.00 0.00 2.01
436 471 3.079578 CTCGCATATACTCCCTCCGTAA 58.920 50.000 0.00 0.00 0.00 3.18
437 472 2.617276 CCTCGCATATACTCCCTCCGTA 60.617 54.545 0.00 0.00 0.00 4.02
438 473 1.535833 CTCGCATATACTCCCTCCGT 58.464 55.000 0.00 0.00 0.00 4.69
439 474 0.811915 CCTCGCATATACTCCCTCCG 59.188 60.000 0.00 0.00 0.00 4.63
440 475 0.533032 GCCTCGCATATACTCCCTCC 59.467 60.000 0.00 0.00 0.00 4.30
441 476 0.533032 GGCCTCGCATATACTCCCTC 59.467 60.000 0.00 0.00 0.00 4.30
442 477 0.178932 TGGCCTCGCATATACTCCCT 60.179 55.000 3.32 0.00 0.00 4.20
443 478 0.247736 CTGGCCTCGCATATACTCCC 59.752 60.000 3.32 0.00 0.00 4.30
444 479 0.390472 GCTGGCCTCGCATATACTCC 60.390 60.000 3.32 0.00 0.00 3.85
445 480 0.605589 AGCTGGCCTCGCATATACTC 59.394 55.000 17.81 0.00 0.00 2.59
446 481 1.051812 AAGCTGGCCTCGCATATACT 58.948 50.000 17.81 0.00 0.00 2.12
447 482 1.151668 CAAGCTGGCCTCGCATATAC 58.848 55.000 17.81 0.00 0.00 1.47
448 483 1.047801 TCAAGCTGGCCTCGCATATA 58.952 50.000 17.81 0.51 0.00 0.86
449 484 0.533755 GTCAAGCTGGCCTCGCATAT 60.534 55.000 17.81 3.31 0.00 1.78
477 512 8.458843 CAAAAAGACTGGAAGACTAAACTTTGA 58.541 33.333 0.00 0.00 38.20 2.69
491 526 6.279513 ACACATGTTTTCAAAAAGACTGGA 57.720 33.333 0.00 0.00 0.00 3.86
521 556 1.630878 GTGTCCATCCCAACCTTCTCT 59.369 52.381 0.00 0.00 0.00 3.10
522 557 1.630878 AGTGTCCATCCCAACCTTCTC 59.369 52.381 0.00 0.00 0.00 2.87
524 559 1.826385 CAGTGTCCATCCCAACCTTC 58.174 55.000 0.00 0.00 0.00 3.46
555 590 8.995906 CGCTTACTATATGTAAAACAACTTTGC 58.004 33.333 0.00 0.00 40.24 3.68
587 622 6.431198 TGTTTCTACTTTCCACAAACACTC 57.569 37.500 0.00 0.00 33.17 3.51
712 747 8.150945 GTGAGAGATAAGAGGCACCAAATATTA 58.849 37.037 0.00 0.00 0.00 0.98
824 859 3.326747 ACACTCACGAAAGAATAGGCAC 58.673 45.455 0.00 0.00 0.00 5.01
837 872 9.825972 ACATGATTTCTTATAAAAACACTCACG 57.174 29.630 0.00 0.00 0.00 4.35
896 933 6.229561 GCTAAATAAATCTTAGCGTCCTGG 57.770 41.667 0.00 0.00 41.23 4.45
1023 1061 3.548818 GCACCATTAGGCGATCAACATTC 60.549 47.826 0.00 0.00 39.06 2.67
1272 1310 9.285770 CTTCAAGTAACAAAAACCAGAGTTTAC 57.714 33.333 0.00 0.00 45.54 2.01
1317 1355 6.982141 GCTTCCAGATAAATTGATCAAATGCA 59.018 34.615 13.09 0.00 0.00 3.96
1318 1356 6.982141 TGCTTCCAGATAAATTGATCAAATGC 59.018 34.615 13.09 7.01 0.00 3.56
1435 1478 7.490725 CAGATTGACTAACAGAGAACCACATAG 59.509 40.741 0.00 0.00 0.00 2.23
1436 1479 7.323420 CAGATTGACTAACAGAGAACCACATA 58.677 38.462 0.00 0.00 0.00 2.29
1437 1480 6.169094 CAGATTGACTAACAGAGAACCACAT 58.831 40.000 0.00 0.00 0.00 3.21
1501 1544 4.035208 GTCCCAAGTAATAGCCGACATTTG 59.965 45.833 0.00 0.00 0.00 2.32
1706 1752 7.624549 TGAACTAAGCTCTGACATAGGAAAAT 58.375 34.615 0.00 0.00 0.00 1.82
1716 1762 2.996621 ACGCAATGAACTAAGCTCTGAC 59.003 45.455 0.00 0.00 0.00 3.51
1769 1815 1.291132 GGACGCCAAGAGAACTATGC 58.709 55.000 0.00 0.00 0.00 3.14
1978 2167 1.004745 GCTGGGAGGGAGATCACAAAA 59.995 52.381 0.00 0.00 30.63 2.44
2034 2223 5.176741 ACAGAGAGAAAGCTTGATTCCAT 57.823 39.130 0.00 0.00 0.00 3.41
2085 2280 8.705594 TCAACTTGGAGATCTATTAGTTAAGGG 58.294 37.037 12.75 4.74 0.00 3.95
2332 2529 5.995897 GGACGGGCATACTTTATAGAACATT 59.004 40.000 0.00 0.00 0.00 2.71
2338 2535 3.556423 GGTGGGACGGGCATACTTTATAG 60.556 52.174 0.00 0.00 0.00 1.31
2353 2550 1.405821 CAGAGTCGTATCTGGTGGGAC 59.594 57.143 10.56 0.00 42.52 4.46
2358 2555 3.687125 TCAGTTCAGAGTCGTATCTGGT 58.313 45.455 16.08 3.34 45.60 4.00
2370 2567 6.542821 AGGTAATTTCCAACATCAGTTCAGA 58.457 36.000 3.73 0.00 35.28 3.27
2379 2576 5.105756 GCTGCAGTAAGGTAATTTCCAACAT 60.106 40.000 16.64 0.00 0.00 2.71
2447 2644 7.361201 CCATGCCTTATATCAATGGTAGTTTCG 60.361 40.741 0.00 0.00 0.00 3.46
2459 2656 6.658816 ACGAAATTATGCCATGCCTTATATCA 59.341 34.615 0.00 0.00 0.00 2.15
2482 2679 7.862873 TCAAGTATCTATGTCTTGAATGCTACG 59.137 37.037 4.68 0.00 42.61 3.51
2486 2683 9.270640 AGAATCAAGTATCTATGTCTTGAATGC 57.729 33.333 10.14 4.41 46.41 3.56
2574 2771 9.934190 TGTACTAAAACCACGAAACTTATTTTC 57.066 29.630 0.00 0.00 40.40 2.29
2584 2781 8.460428 AGTTCAAATTTGTACTAAAACCACGAA 58.540 29.630 24.00 2.55 37.09 3.85
2675 2872 2.516930 AGCCACCACTGCACACAC 60.517 61.111 0.00 0.00 0.00 3.82
2676 2873 2.516695 CAGCCACCACTGCACACA 60.517 61.111 0.00 0.00 0.00 3.72
2820 3019 0.605083 TCACGACAAGAGCAGCAGAT 59.395 50.000 0.00 0.00 0.00 2.90
2899 3098 7.676468 AGGGGAAAACATAAATAAGTAGGCAAA 59.324 33.333 0.00 0.00 0.00 3.68
3019 3218 9.134734 CCTCTCGCATATCTTAAAAGAGTATTC 57.865 37.037 0.00 0.00 38.66 1.75
3042 3242 2.107953 GCGGAGAGATGGTGCCTC 59.892 66.667 0.00 0.00 0.00 4.70
3094 3294 3.052745 GCAGTAAGAAAAGCTGCCAAAC 58.947 45.455 4.60 0.00 46.93 2.93
3308 3509 8.486210 ACAACTCATATAGGATAACAAAGCAGA 58.514 33.333 0.00 0.00 0.00 4.26
3340 3541 8.697507 AGAAAGACAAGATTTGGTAACTCAAT 57.302 30.769 0.00 0.00 34.12 2.57
3396 3794 5.978814 AGTTAGTGGTTACATAGGCTCAAG 58.021 41.667 0.00 0.00 0.00 3.02
3400 3798 4.225267 AGCAAGTTAGTGGTTACATAGGCT 59.775 41.667 0.00 0.00 0.00 4.58
3405 3994 3.000727 GCGAGCAAGTTAGTGGTTACAT 58.999 45.455 0.00 0.00 0.00 2.29
3614 4203 1.477700 GCAAGCCAGCAATCCAATGTA 59.522 47.619 0.00 0.00 0.00 2.29
3708 4297 3.539431 CGTCTCAGAACGTTACACTCT 57.461 47.619 0.00 0.00 37.86 3.24
3869 4458 2.268076 TGGCCTTCAGAAAAGCCGC 61.268 57.895 15.86 0.05 43.80 6.53
3955 4545 9.701098 TCATGTTACTCGGGACATTAATAATAC 57.299 33.333 0.00 0.00 34.42 1.89
3957 4547 9.793259 ATTCATGTTACTCGGGACATTAATAAT 57.207 29.630 0.00 0.00 34.42 1.28
3958 4548 9.621629 AATTCATGTTACTCGGGACATTAATAA 57.378 29.630 0.00 0.00 34.42 1.40
3959 4549 9.051679 CAATTCATGTTACTCGGGACATTAATA 57.948 33.333 0.00 0.00 34.42 0.98
3960 4550 7.013274 CCAATTCATGTTACTCGGGACATTAAT 59.987 37.037 0.00 0.00 34.42 1.40
3961 4551 6.317642 CCAATTCATGTTACTCGGGACATTAA 59.682 38.462 0.00 0.00 34.42 1.40
3962 4552 5.820423 CCAATTCATGTTACTCGGGACATTA 59.180 40.000 0.00 0.00 34.42 1.90
3963 4553 4.640201 CCAATTCATGTTACTCGGGACATT 59.360 41.667 0.00 0.00 34.42 2.71
3964 4554 4.199310 CCAATTCATGTTACTCGGGACAT 58.801 43.478 0.00 0.00 36.97 3.06
3965 4555 3.008594 ACCAATTCATGTTACTCGGGACA 59.991 43.478 0.00 0.00 0.00 4.02
3966 4556 3.606687 ACCAATTCATGTTACTCGGGAC 58.393 45.455 0.00 0.00 0.00 4.46
3967 4557 3.992943 ACCAATTCATGTTACTCGGGA 57.007 42.857 0.00 0.00 0.00 5.14
3968 4558 4.570772 CACTACCAATTCATGTTACTCGGG 59.429 45.833 0.00 0.00 0.00 5.14
3969 4559 4.034048 GCACTACCAATTCATGTTACTCGG 59.966 45.833 0.00 0.00 0.00 4.63
3970 4560 4.870426 AGCACTACCAATTCATGTTACTCG 59.130 41.667 0.00 0.00 0.00 4.18
3971 4561 6.595716 AGAAGCACTACCAATTCATGTTACTC 59.404 38.462 0.00 0.00 0.00 2.59
3972 4562 6.372659 CAGAAGCACTACCAATTCATGTTACT 59.627 38.462 0.00 0.00 0.00 2.24
4008 4614 1.879380 CATTTTGCAGTCGAGGAACCA 59.121 47.619 0.00 0.00 0.00 3.67
4011 4617 2.742053 GCTACATTTTGCAGTCGAGGAA 59.258 45.455 0.00 0.00 0.00 3.36
4017 4623 0.521242 CGCCGCTACATTTTGCAGTC 60.521 55.000 0.00 0.00 0.00 3.51
4028 4634 0.668706 ATGAGATCATGCGCCGCTAC 60.669 55.000 11.67 0.00 34.83 3.58
4077 4694 2.158769 TCGGGAGAGTATAAGCACCGTA 60.159 50.000 0.00 0.00 40.60 4.02
4106 6020 1.774110 TGCATATGGGGTCGCAAAAT 58.226 45.000 4.56 0.00 0.00 1.82
4119 6033 1.457823 CGCATGGCCCAGTTGCATAT 61.458 55.000 9.82 0.00 36.15 1.78
4120 6034 2.120282 CGCATGGCCCAGTTGCATA 61.120 57.895 9.82 0.00 36.15 3.14
4160 6075 1.611977 CACTAACGTCACAGGAGTGGA 59.388 52.381 0.00 0.00 45.91 4.02
4161 6076 1.611977 TCACTAACGTCACAGGAGTGG 59.388 52.381 0.00 0.00 45.91 4.00
4379 6294 3.508762 CCATGCATTCTTGTCAAGCTTC 58.491 45.455 7.78 0.00 0.00 3.86
4380 6295 2.232941 CCCATGCATTCTTGTCAAGCTT 59.767 45.455 7.78 0.00 0.00 3.74
4412 6327 7.507733 TCTAGTTTATTGCGGTGGTTAAAAA 57.492 32.000 0.00 0.00 0.00 1.94
4413 6328 7.229106 AGTTCTAGTTTATTGCGGTGGTTAAAA 59.771 33.333 0.00 0.00 0.00 1.52
4423 6338 4.270325 GGCTACCAGTTCTAGTTTATTGCG 59.730 45.833 0.00 0.00 0.00 4.85
4518 6436 2.491693 ACGCCCAAGATGTATGTTTTGG 59.508 45.455 0.00 0.00 39.77 3.28
4533 6451 3.532155 GGCAACCAAACACGCCCA 61.532 61.111 0.00 0.00 38.67 5.36
4540 6458 2.298411 CCATATGCAGGCAACCAAAC 57.702 50.000 0.00 0.00 37.17 2.93


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

AutoCloner maintained by Alex Coulton.