Multiple sequence alignment - TraesCS1A01G287300

Loading Multiple Alignment...

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 TraesCS1A01G287300 chr1A 100.000 3203 0 0 1 3203 484302847 484299645 0.000000e+00 5915
1 TraesCS1A01G287300 chr1A 94.170 446 24 2 1 446 543065384 543065827 0.000000e+00 678
2 TraesCS1A01G287300 chr1A 93.289 447 26 4 1 446 2060840 2060397 0.000000e+00 656
3 TraesCS1A01G287300 chr1A 90.807 446 30 4 1 446 57309617 57310051 1.280000e-163 586
4 TraesCS1A01G287300 chr1A 91.729 133 11 0 436 568 543065781 543065913 5.460000e-43 185
5 TraesCS1A01G287300 chr1A 91.111 135 12 0 439 573 2060440 2060306 1.960000e-42 183
6 TraesCS1A01G287300 chr1A 88.742 151 16 1 418 568 484325563 484325712 1.960000e-42 183
7 TraesCS1A01G287300 chr1A 86.928 153 15 5 418 568 9447232 9447381 1.980000e-37 167
8 TraesCS1A01G287300 chr1D 89.484 2539 110 50 576 3004 384475732 384473241 0.000000e+00 3064
9 TraesCS1A01G287300 chr1D 93.125 160 10 1 3028 3186 384472909 384472750 1.920000e-57 233
10 TraesCS1A01G287300 chr1B 88.034 2131 114 62 602 2643 515914558 515912480 0.000000e+00 2392
11 TraesCS1A01G287300 chr1B 86.500 600 26 16 2641 3203 515910036 515909455 2.730000e-170 608
12 TraesCS1A01G287300 chr1B 79.235 183 26 12 395 571 603219817 603219641 2.020000e-22 117
13 TraesCS1A01G287300 chr5A 94.395 446 21 3 1 446 653565089 653564648 0.000000e+00 682
14 TraesCS1A01G287300 chr5A 93.946 446 25 2 1 446 487753021 487752578 0.000000e+00 673
15 TraesCS1A01G287300 chr5A 93.394 439 23 5 1 437 662390555 662390121 0.000000e+00 645
16 TraesCS1A01G287300 chr5A 91.971 411 25 5 1 410 664481238 664480835 1.290000e-158 569
17 TraesCS1A01G287300 chr5A 88.535 157 14 4 418 573 671350234 671350081 1.520000e-43 187
18 TraesCS1A01G287300 chr5A 89.855 138 14 0 440 577 653564690 653564553 9.130000e-41 178
19 TraesCS1A01G287300 chr6A 93.049 446 28 2 1 446 60165223 60164781 0.000000e+00 649
20 TraesCS1A01G287300 chr6A 95.294 340 15 1 1175 1514 389756381 389756719 3.640000e-149 538
21 TraesCS1A01G287300 chr6A 95.035 141 7 0 1541 1681 389756716 389756856 4.160000e-54 222
22 TraesCS1A01G287300 chr7D 90.187 428 38 3 1 428 176129742 176129319 3.610000e-154 555
23 TraesCS1A01G287300 chr7D 87.500 152 16 3 418 568 138089716 138089567 4.250000e-39 172
24 TraesCS1A01G287300 chr7D 78.771 179 28 10 395 568 576172250 576172077 9.390000e-21 111
25 TraesCS1A01G287300 chr3B 88.304 171 19 1 399 569 181680668 181680499 1.510000e-48 204
26 TraesCS1A01G287300 chr3B 86.928 153 18 2 418 569 23791606 23791757 1.530000e-38 171
27 TraesCS1A01G287300 chr3B 78.723 188 29 10 385 568 412423846 412424026 7.260000e-22 115
28 TraesCS1A01G287300 chr5B 82.353 170 19 11 404 568 474746276 474746113 1.550000e-28 137
29 TraesCS1A01G287300 chr2B 79.167 192 32 8 386 574 596102248 596102434 3.350000e-25 126
30 TraesCS1A01G287300 chr4A 79.670 182 25 12 395 570 641361262 641361087 1.560000e-23 121
31 TraesCS1A01G287300 chr3D 80.000 180 23 13 395 568 491639608 491639780 1.560000e-23 121
32 TraesCS1A01G287300 chr3A 78.689 183 27 12 395 571 688600283 688600107 9.390000e-21 111


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 TraesCS1A01G287300 chr1A 484299645 484302847 3202 True 5915.0 5915 100.0000 1 3203 1 chr1A.!!$R1 3202
1 TraesCS1A01G287300 chr1A 543065384 543065913 529 False 431.5 678 92.9495 1 568 2 chr1A.!!$F4 567
2 TraesCS1A01G287300 chr1A 2060306 2060840 534 True 419.5 656 92.2000 1 573 2 chr1A.!!$R2 572
3 TraesCS1A01G287300 chr1D 384472750 384475732 2982 True 1648.5 3064 91.3045 576 3186 2 chr1D.!!$R1 2610
4 TraesCS1A01G287300 chr1B 515909455 515914558 5103 True 1500.0 2392 87.2670 602 3203 2 chr1B.!!$R2 2601
5 TraesCS1A01G287300 chr5A 653564553 653565089 536 True 430.0 682 92.1250 1 577 2 chr5A.!!$R5 576

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
462 464 0.040794 AGGCTGTCTAACCCTACCGT 59.959 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2362 0.039617 TCAGCGCCACAAAATTTCCG 60.04 50.0 2.29 0.0 0.0 4.3 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
102 103 2.094762 TCGAAGGAGCTTACTTTGCC 57.905 50.000 12.27 0.00 30.91 4.52
198 200 1.003573 AGGGGGCGAGAGGAAGAAT 59.996 57.895 0.00 0.00 0.00 2.40
274 276 1.414919 CCACGGCTTATAACTGCCCTA 59.585 52.381 9.51 0.00 45.90 3.53
366 368 3.436001 CGGAGACCGTTAATGCTGT 57.564 52.632 1.80 0.00 42.73 4.40
384 386 4.159693 TGCTGTTGACGTGGATAAGTATCT 59.840 41.667 0.00 0.00 33.28 1.98
434 436 0.544833 TAACCCTACCGCCAGAACCA 60.545 55.000 0.00 0.00 0.00 3.67
435 437 2.120737 AACCCTACCGCCAGAACCAC 62.121 60.000 0.00 0.00 0.00 4.16
436 438 2.291043 CCCTACCGCCAGAACCACT 61.291 63.158 0.00 0.00 0.00 4.00
437 439 1.677552 CCTACCGCCAGAACCACTT 59.322 57.895 0.00 0.00 0.00 3.16
438 440 0.673644 CCTACCGCCAGAACCACTTG 60.674 60.000 0.00 0.00 0.00 3.16
439 441 1.298859 CTACCGCCAGAACCACTTGC 61.299 60.000 0.00 0.00 34.47 4.01
442 444 2.594592 GCCAGAACCACTTGCGGT 60.595 61.111 0.00 0.00 42.71 5.68
443 445 1.302192 GCCAGAACCACTTGCGGTA 60.302 57.895 0.00 0.00 38.76 4.02
444 446 1.298859 GCCAGAACCACTTGCGGTAG 61.299 60.000 0.00 0.00 38.76 3.18
445 447 0.673644 CCAGAACCACTTGCGGTAGG 60.674 60.000 0.00 0.00 38.76 3.18
446 448 1.003718 AGAACCACTTGCGGTAGGC 60.004 57.895 0.00 0.00 38.76 3.93
447 449 1.003718 GAACCACTTGCGGTAGGCT 60.004 57.895 0.00 0.00 44.05 4.58
448 450 1.298859 GAACCACTTGCGGTAGGCTG 61.299 60.000 0.00 0.00 44.05 4.85
449 451 2.052047 AACCACTTGCGGTAGGCTGT 62.052 55.000 0.00 0.00 44.05 4.40
450 452 1.741770 CCACTTGCGGTAGGCTGTC 60.742 63.158 0.00 0.00 44.05 3.51
451 453 1.293498 CACTTGCGGTAGGCTGTCT 59.707 57.895 0.00 0.00 44.05 3.41
452 454 0.530744 CACTTGCGGTAGGCTGTCTA 59.469 55.000 0.00 0.00 44.05 2.59
453 455 1.067142 CACTTGCGGTAGGCTGTCTAA 60.067 52.381 0.00 0.00 44.05 2.10
454 456 1.067071 ACTTGCGGTAGGCTGTCTAAC 60.067 52.381 0.00 0.00 44.05 2.34
455 457 0.248289 TTGCGGTAGGCTGTCTAACC 59.752 55.000 0.00 0.00 44.05 2.85
456 458 1.143401 GCGGTAGGCTGTCTAACCC 59.857 63.158 0.00 0.00 39.11 4.11
457 459 1.328430 GCGGTAGGCTGTCTAACCCT 61.328 60.000 0.00 0.00 39.11 4.34
458 460 2.025863 GCGGTAGGCTGTCTAACCCTA 61.026 57.143 0.00 0.00 39.11 3.53
459 461 1.680207 CGGTAGGCTGTCTAACCCTAC 59.320 57.143 0.00 7.39 46.60 3.18
461 463 1.680207 GTAGGCTGTCTAACCCTACCG 59.320 57.143 0.00 0.00 43.31 4.02
462 464 0.040794 AGGCTGTCTAACCCTACCGT 59.959 55.000 0.00 0.00 0.00 4.83
463 465 0.459078 GGCTGTCTAACCCTACCGTC 59.541 60.000 0.00 0.00 0.00 4.79
464 466 1.180029 GCTGTCTAACCCTACCGTCA 58.820 55.000 0.00 0.00 0.00 4.35
465 467 1.134560 GCTGTCTAACCCTACCGTCAG 59.865 57.143 0.00 0.00 0.00 3.51
466 468 2.719739 CTGTCTAACCCTACCGTCAGA 58.280 52.381 0.00 0.00 0.00 3.27
467 469 3.087031 CTGTCTAACCCTACCGTCAGAA 58.913 50.000 0.00 0.00 0.00 3.02
468 470 2.821969 TGTCTAACCCTACCGTCAGAAC 59.178 50.000 0.00 0.00 0.00 3.01
469 471 2.165234 GTCTAACCCTACCGTCAGAACC 59.835 54.545 0.00 0.00 0.00 3.62
470 472 2.173519 CTAACCCTACCGTCAGAACCA 58.826 52.381 0.00 0.00 0.00 3.67
473 475 0.974383 CCCTACCGTCAGAACCACTT 59.026 55.000 0.00 0.00 0.00 3.16
577 579 3.194116 ACGAAATTTAGCCTCGACTGGTA 59.806 43.478 3.62 0.00 36.45 3.25
578 580 3.550678 CGAAATTTAGCCTCGACTGGTAC 59.449 47.826 0.00 0.00 34.52 3.34
579 581 4.501071 GAAATTTAGCCTCGACTGGTACA 58.499 43.478 0.00 0.00 0.00 2.90
583 585 1.853963 AGCCTCGACTGGTACAAGAT 58.146 50.000 3.64 0.00 38.70 2.40
595 597 3.388024 TGGTACAAGATGGCTAGATGGAC 59.612 47.826 0.00 0.00 31.92 4.02
660 662 4.851214 AGGAGCGGAGAGAGGGGC 62.851 72.222 0.00 0.00 0.00 5.80
713 717 3.253677 AGCCCTAATCGAGTAATCAGTCG 59.746 47.826 0.00 0.00 46.85 4.18
780 797 0.591236 GAAAAGAGCAACGCAACGCA 60.591 50.000 0.00 0.00 0.00 5.24
785 802 2.800746 GCAACGCAACGCATGGAC 60.801 61.111 0.00 0.00 0.00 4.02
786 803 2.499520 CAACGCAACGCATGGACG 60.500 61.111 0.00 0.00 39.50 4.79
823 840 2.029290 ACGACACGAATAAAGCCAGAGT 60.029 45.455 0.00 0.00 0.00 3.24
940 977 2.351726 CGGACAGCAATGGTAGTTTAGC 59.648 50.000 0.00 0.00 0.00 3.09
1080 1133 1.598130 GCGAGGCAAAGACACCAGT 60.598 57.895 0.00 0.00 0.00 4.00
1084 1137 0.109342 AGGCAAAGACACCAGTGAGG 59.891 55.000 4.48 0.00 45.67 3.86
1131 1203 1.542679 GGAGGAGGTCTACGGGGAT 59.457 63.158 0.00 0.00 0.00 3.85
1135 1207 1.232216 GAGGTCTACGGGGATGGGA 59.768 63.158 0.00 0.00 0.00 4.37
1169 1241 1.690219 ATCGACATGGACCTGAGCCC 61.690 60.000 0.00 0.00 0.00 5.19
1170 1242 2.592308 GACATGGACCTGAGCCCC 59.408 66.667 0.00 0.00 0.00 5.80
1171 1243 3.017581 ACATGGACCTGAGCCCCC 61.018 66.667 0.00 0.00 0.00 5.40
1287 1359 0.036010 TCTACAAGGGCAAGCTGCTC 60.036 55.000 1.00 4.31 46.33 4.26
1567 1639 1.604915 GAGAAGAAGCCCTGGTCCC 59.395 63.158 0.00 0.00 0.00 4.46
1585 1657 4.144703 GGAGGCTCCGGTTCGTCC 62.145 72.222 19.53 17.00 0.00 4.79
1758 1848 0.320421 AGAACCCGTTCGGACACATG 60.320 55.000 13.08 0.00 43.97 3.21
1789 1879 2.125391 GCATCACCGAGCAGAGCA 60.125 61.111 0.00 0.00 0.00 4.26
1902 1992 4.477975 CCAGCGTCGTCCTCGTCC 62.478 72.222 0.00 0.00 38.33 4.79
1914 2004 2.033602 TCGTCCTGCTCCTCGACA 59.966 61.111 0.00 0.00 0.00 4.35
1971 2061 3.800863 TGCTCGAGCGACTCCGAC 61.801 66.667 30.75 3.44 45.83 4.79
1972 2062 4.872485 GCTCGAGCGACTCCGACG 62.872 72.222 23.61 0.00 38.22 5.12
1973 2063 4.225340 CTCGAGCGACTCCGACGG 62.225 72.222 7.84 7.84 37.56 4.79
2253 2346 3.181534 CGTCGAATGTGTACAATGGTGTC 60.182 47.826 0.00 0.00 39.30 3.67
2269 2362 3.444742 TGGTGTCTGAAATGATGCATTCC 59.555 43.478 0.00 0.00 32.43 3.01
2311 2404 0.660488 TTGTGTTGGTGTCACGATGC 59.340 50.000 0.00 0.00 38.48 3.91
2339 2432 5.766670 TGCTCAAATCAACTGACTCTGAATT 59.233 36.000 0.00 0.00 0.00 2.17
2340 2433 6.936335 TGCTCAAATCAACTGACTCTGAATTA 59.064 34.615 0.00 0.00 0.00 1.40
2341 2434 7.095060 TGCTCAAATCAACTGACTCTGAATTAC 60.095 37.037 0.00 0.00 0.00 1.89
2342 2435 7.118971 GCTCAAATCAACTGACTCTGAATTACT 59.881 37.037 0.00 0.00 0.00 2.24
2343 2436 9.645059 CTCAAATCAACTGACTCTGAATTACTA 57.355 33.333 0.00 0.00 0.00 1.82
2369 2479 6.475727 CACTAAACCACATCTGATTAGTACGG 59.524 42.308 0.00 0.00 35.62 4.02
2394 2504 9.503399 GGGTAGATTCTTTTTCTGACTCTTAAA 57.497 33.333 0.00 0.00 0.00 1.52
2419 2540 2.017049 GCCTTGCAGTATGGTAACCAG 58.983 52.381 0.00 0.00 36.75 4.00
2422 2543 4.442706 CCTTGCAGTATGGTAACCAGTAG 58.557 47.826 0.00 0.00 36.75 2.57
2426 2547 4.159693 TGCAGTATGGTAACCAGTAGACAG 59.840 45.833 0.00 0.00 36.75 3.51
2427 2548 4.159879 GCAGTATGGTAACCAGTAGACAGT 59.840 45.833 0.00 0.00 36.75 3.55
2430 2551 7.417570 GCAGTATGGTAACCAGTAGACAGTATT 60.418 40.741 0.00 0.00 36.75 1.89
2433 2554 6.045072 TGGTAACCAGTAGACAGTATTTGG 57.955 41.667 0.00 0.00 0.00 3.28
2566 2714 1.601419 TAGCAGTCGTTCCTTCCCCG 61.601 60.000 0.00 0.00 0.00 5.73
2600 2748 5.235186 CGAGTGTGAAAATGACCTCCATATC 59.765 44.000 0.00 0.00 34.45 1.63
2613 2766 0.609131 CCATATCATTCCCCACCGCC 60.609 60.000 0.00 0.00 0.00 6.13
2633 2786 4.260538 CGCCTGCATTTCTTCAGAGATTAC 60.261 45.833 0.00 0.00 32.26 1.89
2634 2787 4.260538 GCCTGCATTTCTTCAGAGATTACG 60.261 45.833 0.00 0.00 32.26 3.18
2740 5339 7.704271 TGAAGGTACGATCAAAGATACTACTG 58.296 38.462 0.00 0.00 0.00 2.74
2741 5340 7.338703 TGAAGGTACGATCAAAGATACTACTGT 59.661 37.037 0.00 0.00 0.00 3.55
2742 5341 8.743085 AAGGTACGATCAAAGATACTACTGTA 57.257 34.615 0.00 0.00 0.00 2.74
2743 5342 8.152309 AGGTACGATCAAAGATACTACTGTAC 57.848 38.462 0.00 0.00 0.00 2.90
2744 5343 7.992033 AGGTACGATCAAAGATACTACTGTACT 59.008 37.037 0.00 0.00 31.61 2.73
2748 5347 9.044150 ACGATCAAAGATACTACTGTACTACTC 57.956 37.037 0.00 0.00 0.00 2.59
2760 5359 6.310764 ACTGTACTACTCCTACTAGCAAGA 57.689 41.667 0.00 0.00 0.00 3.02
2792 5394 2.296190 CCATCAATCCACCATCATGCAG 59.704 50.000 0.00 0.00 0.00 4.41
2793 5395 1.395635 TCAATCCACCATCATGCAGC 58.604 50.000 0.00 0.00 0.00 5.25
2794 5396 1.064240 TCAATCCACCATCATGCAGCT 60.064 47.619 0.00 0.00 0.00 4.24
2795 5397 1.067060 CAATCCACCATCATGCAGCTG 59.933 52.381 10.11 10.11 0.00 4.24
2796 5398 1.107538 ATCCACCATCATGCAGCTGC 61.108 55.000 31.89 31.89 42.50 5.25
2822 5424 0.184451 ACAAGGGCATCATAGGCAGG 59.816 55.000 0.00 0.00 35.46 4.85
2884 5502 6.240894 TCATGCCATTAGTTAATCTGGATCC 58.759 40.000 4.20 4.20 0.00 3.36
2942 5571 6.854496 TCGAAAGCAAAACAATACACTACT 57.146 33.333 0.00 0.00 0.00 2.57
2947 5576 7.907214 AAGCAAAACAATACACTACTAGAGG 57.093 36.000 0.00 0.00 0.00 3.69
2952 5581 6.702716 AACAATACACTACTAGAGGAGAGC 57.297 41.667 0.00 0.00 0.00 4.09
3008 5651 2.705154 GACACACAAAACTTGCTCGAC 58.295 47.619 0.00 0.00 0.00 4.20
3024 5667 4.051922 GCTCGACTTAATCCCACTACATG 58.948 47.826 0.00 0.00 0.00 3.21
3046 5983 8.428852 ACATGAGTATATGTATTAGTGGTTGCA 58.571 33.333 0.00 0.00 39.40 4.08
3055 5992 7.710676 TGTATTAGTGGTTGCAAATACCAAT 57.289 32.000 13.08 13.08 46.62 3.16
3057 5994 9.415008 TGTATTAGTGGTTGCAAATACCAATAT 57.585 29.630 14.96 9.42 46.62 1.28
3067 6004 5.149273 GCAAATACCAATATCATGCTCGTG 58.851 41.667 0.00 0.00 33.69 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 1.227380 CGAGATGGCCCCGAAGAAG 60.227 63.158 0.00 0.00 0.00 2.85
198 200 0.902531 CCGCCCTAAGAACAGAGGAA 59.097 55.000 0.00 0.00 34.46 3.36
230 232 2.692741 CCACCCCTCCCCCTTCTC 60.693 72.222 0.00 0.00 0.00 2.87
252 254 0.179468 GGCAGTTATAAGCCGTGGGA 59.821 55.000 0.36 0.00 41.70 4.37
292 294 3.151710 CGACCCTACCGCCATGGA 61.152 66.667 18.40 0.00 42.00 3.41
295 297 3.152400 GTCCGACCCTACCGCCAT 61.152 66.667 0.00 0.00 0.00 4.40
361 363 2.831685 ACTTATCCACGTCAACAGCA 57.168 45.000 0.00 0.00 0.00 4.41
366 368 5.734220 GCGGTAAGATACTTATCCACGTCAA 60.734 44.000 0.00 0.00 33.17 3.18
384 386 2.047655 CAGAACCTGCGGCGGTAA 60.048 61.111 9.78 0.00 35.89 2.85
434 436 1.067071 GTTAGACAGCCTACCGCAAGT 60.067 52.381 0.00 0.00 41.38 3.16
435 437 1.641577 GTTAGACAGCCTACCGCAAG 58.358 55.000 0.00 0.00 41.38 4.01
436 438 0.248289 GGTTAGACAGCCTACCGCAA 59.752 55.000 0.00 0.00 41.38 4.85
437 439 1.610554 GGGTTAGACAGCCTACCGCA 61.611 60.000 0.00 0.00 40.32 5.69
438 440 1.143401 GGGTTAGACAGCCTACCGC 59.857 63.158 0.00 0.00 40.32 5.68
444 446 0.459078 GACGGTAGGGTTAGACAGCC 59.541 60.000 0.00 0.00 44.40 4.85
445 447 1.134560 CTGACGGTAGGGTTAGACAGC 59.865 57.143 0.00 0.00 0.00 4.40
446 448 2.719739 TCTGACGGTAGGGTTAGACAG 58.280 52.381 0.00 0.00 28.77 3.51
447 449 2.821969 GTTCTGACGGTAGGGTTAGACA 59.178 50.000 0.00 0.00 32.95 3.41
448 450 2.165234 GGTTCTGACGGTAGGGTTAGAC 59.835 54.545 0.00 0.00 32.95 2.59
449 451 2.225091 TGGTTCTGACGGTAGGGTTAGA 60.225 50.000 0.00 0.00 31.53 2.10
450 452 2.094338 GTGGTTCTGACGGTAGGGTTAG 60.094 54.545 0.00 0.00 0.00 2.34
451 453 1.895131 GTGGTTCTGACGGTAGGGTTA 59.105 52.381 0.00 0.00 0.00 2.85
452 454 0.683412 GTGGTTCTGACGGTAGGGTT 59.317 55.000 0.00 0.00 0.00 4.11
453 455 0.178941 AGTGGTTCTGACGGTAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
454 456 0.974383 AAGTGGTTCTGACGGTAGGG 59.026 55.000 0.00 0.00 0.00 3.53
455 457 1.939838 GCAAGTGGTTCTGACGGTAGG 60.940 57.143 0.00 0.00 0.00 3.18
456 458 1.429463 GCAAGTGGTTCTGACGGTAG 58.571 55.000 0.00 0.00 0.00 3.18
457 459 0.319211 CGCAAGTGGTTCTGACGGTA 60.319 55.000 0.00 0.00 0.00 4.02
458 460 1.594293 CGCAAGTGGTTCTGACGGT 60.594 57.895 0.00 0.00 0.00 4.83
459 461 2.317609 CCGCAAGTGGTTCTGACGG 61.318 63.158 0.00 0.00 38.47 4.79
460 462 0.319211 TACCGCAAGTGGTTCTGACG 60.319 55.000 10.96 0.00 43.56 4.35
461 463 1.429463 CTACCGCAAGTGGTTCTGAC 58.571 55.000 10.96 0.00 43.56 3.51
462 464 0.320374 CCTACCGCAAGTGGTTCTGA 59.680 55.000 10.96 0.00 43.56 3.27
463 465 0.320374 TCCTACCGCAAGTGGTTCTG 59.680 55.000 10.96 2.44 43.56 3.02
464 466 1.053424 TTCCTACCGCAAGTGGTTCT 58.947 50.000 10.96 0.00 43.56 3.01
465 467 1.886886 TTTCCTACCGCAAGTGGTTC 58.113 50.000 10.96 0.00 43.56 3.62
466 468 2.351706 TTTTCCTACCGCAAGTGGTT 57.648 45.000 10.96 0.00 43.56 3.67
467 469 2.227194 CTTTTTCCTACCGCAAGTGGT 58.773 47.619 10.50 10.50 46.26 4.16
468 470 1.539827 CCTTTTTCCTACCGCAAGTGG 59.460 52.381 0.00 0.00 0.00 4.00
469 471 2.500229 TCCTTTTTCCTACCGCAAGTG 58.500 47.619 0.00 0.00 0.00 3.16
470 472 2.943036 TCCTTTTTCCTACCGCAAGT 57.057 45.000 0.00 0.00 0.00 3.16
473 475 2.569853 TCTGATCCTTTTTCCTACCGCA 59.430 45.455 0.00 0.00 0.00 5.69
505 507 2.225017 GGATCTGACCCCTGTTGGAAAA 60.225 50.000 0.00 0.00 35.39 2.29
577 579 3.900601 CCTAGTCCATCTAGCCATCTTGT 59.099 47.826 0.00 0.00 43.36 3.16
578 580 4.155709 TCCTAGTCCATCTAGCCATCTTG 58.844 47.826 0.00 0.00 43.36 3.02
579 581 4.477536 TCCTAGTCCATCTAGCCATCTT 57.522 45.455 0.00 0.00 43.36 2.40
583 585 5.805208 ATCTATCCTAGTCCATCTAGCCA 57.195 43.478 0.00 0.00 43.36 4.75
595 597 4.076394 GGCTATCGGGCTATCTATCCTAG 58.924 52.174 0.00 0.00 37.53 3.02
662 664 2.414840 TTTTGCTTTCGCCTTCCGCC 62.415 55.000 0.00 0.00 36.73 6.13
664 666 0.591170 TCTTTTGCTTTCGCCTTCCG 59.409 50.000 0.00 0.00 38.61 4.30
713 717 0.459759 GGACAAGTACCGCCACTAGC 60.460 60.000 0.00 0.00 38.52 3.42
810 827 1.555075 TGCTCGGACTCTGGCTTTATT 59.445 47.619 0.00 0.00 0.00 1.40
842 859 2.351418 CTCACTGTCTGTCTCGCTCTAG 59.649 54.545 0.00 0.00 0.00 2.43
843 860 2.351455 CTCACTGTCTGTCTCGCTCTA 58.649 52.381 0.00 0.00 0.00 2.43
844 861 1.164411 CTCACTGTCTGTCTCGCTCT 58.836 55.000 0.00 0.00 0.00 4.09
845 862 0.455972 GCTCACTGTCTGTCTCGCTC 60.456 60.000 0.00 0.00 0.00 5.03
846 863 1.175347 TGCTCACTGTCTGTCTCGCT 61.175 55.000 0.00 0.00 0.00 4.93
847 864 0.319040 TTGCTCACTGTCTGTCTCGC 60.319 55.000 0.00 0.00 0.00 5.03
1055 1108 2.029288 TCTTTGCCTCGCTTCGCTG 61.029 57.895 0.00 0.00 0.00 5.18
1063 1116 0.249868 TCACTGGTGTCTTTGCCTCG 60.250 55.000 0.53 0.00 0.00 4.63
1080 1133 2.416296 CGCCATCGTTGTAGTAACCTCA 60.416 50.000 0.00 0.00 0.00 3.86
1084 1137 1.587034 GCTCGCCATCGTTGTAGTAAC 59.413 52.381 0.00 0.00 36.96 2.50
1089 1142 1.153647 CCTGCTCGCCATCGTTGTA 60.154 57.895 0.00 0.00 36.96 2.41
1091 1144 3.869272 GCCTGCTCGCCATCGTTG 61.869 66.667 0.00 0.00 36.96 4.10
1131 1203 1.015609 TGTACTCCTCCTCCATCCCA 58.984 55.000 0.00 0.00 0.00 4.37
1135 1207 2.091830 TGTCGATGTACTCCTCCTCCAT 60.092 50.000 0.00 0.00 0.00 3.41
1308 1380 1.323271 GCTCCTCGACCATCTGGACA 61.323 60.000 2.55 0.00 38.94 4.02
1626 1698 2.271800 GCGAACATGGTCTTGAGGTAG 58.728 52.381 9.52 0.00 0.00 3.18
1686 1758 1.674651 GAGGTCCTTTCCGCCCAAC 60.675 63.158 0.00 0.00 0.00 3.77
1887 1977 3.432588 CAGGACGAGGACGACGCT 61.433 66.667 0.00 0.00 42.66 5.07
1889 1979 3.384014 GAGCAGGACGAGGACGACG 62.384 68.421 0.00 0.00 42.66 5.12
1902 1992 0.754957 AGGAGGATGTCGAGGAGCAG 60.755 60.000 0.00 0.00 0.00 4.24
1914 2004 0.336737 AGGACTTGGACGAGGAGGAT 59.663 55.000 0.00 0.00 0.00 3.24
2211 2304 2.779951 TTCATCACGGCACCGACAGG 62.780 60.000 17.40 3.25 42.83 4.00
2253 2346 4.374843 TTTCCGGAATGCATCATTTCAG 57.625 40.909 19.62 0.00 33.90 3.02
2269 2362 0.039617 TCAGCGCCACAAAATTTCCG 60.040 50.000 2.29 0.00 0.00 4.30
2311 2404 4.514441 AGAGTCAGTTGATTTGAGCAACAG 59.486 41.667 11.08 3.87 46.05 3.16
2339 2432 9.251440 ACTAATCAGATGTGGTTTAGTGTAGTA 57.749 33.333 14.21 0.00 34.44 1.82
2340 2433 8.135382 ACTAATCAGATGTGGTTTAGTGTAGT 57.865 34.615 14.21 1.11 34.44 2.73
2341 2434 9.517609 GTACTAATCAGATGTGGTTTAGTGTAG 57.482 37.037 19.92 5.03 35.52 2.74
2342 2435 8.186163 CGTACTAATCAGATGTGGTTTAGTGTA 58.814 37.037 19.92 7.51 35.52 2.90
2343 2436 7.033791 CGTACTAATCAGATGTGGTTTAGTGT 58.966 38.462 19.92 8.20 35.52 3.55
2394 2504 4.081697 GGTTACCATACTGCAAGGCAAAAT 60.082 41.667 0.00 0.00 38.41 1.82
2419 2540 6.649557 ACTTGCACTAACCAAATACTGTCTAC 59.350 38.462 0.00 0.00 0.00 2.59
2422 2543 5.689819 CACTTGCACTAACCAAATACTGTC 58.310 41.667 0.00 0.00 0.00 3.51
2498 2621 1.129437 GCGCTTGACTTTGTGATCTCC 59.871 52.381 0.00 0.00 0.00 3.71
2549 2693 2.434359 CGGGGAAGGAACGACTGC 60.434 66.667 0.00 0.00 0.00 4.40
2566 2714 5.694910 TCATTTTCACACTCGTAAGACTTCC 59.305 40.000 0.00 0.00 45.01 3.46
2600 2748 4.738998 TGCAGGCGGTGGGGAATG 62.739 66.667 0.00 0.00 0.00 2.67
2613 2766 5.006165 GTCCGTAATCTCTGAAGAAATGCAG 59.994 44.000 0.00 0.00 34.49 4.41
2633 2786 4.318121 GCGCTAAGATGAATTTACAGTCCG 60.318 45.833 0.00 0.00 0.00 4.79
2634 2787 4.024809 GGCGCTAAGATGAATTTACAGTCC 60.025 45.833 7.64 0.00 0.00 3.85
2740 5339 6.766944 TCATGTCTTGCTAGTAGGAGTAGTAC 59.233 42.308 0.00 0.00 0.00 2.73
2741 5340 6.896883 TCATGTCTTGCTAGTAGGAGTAGTA 58.103 40.000 0.00 0.00 0.00 1.82
2742 5341 5.756918 TCATGTCTTGCTAGTAGGAGTAGT 58.243 41.667 0.00 0.00 0.00 2.73
2743 5342 6.701145 TTCATGTCTTGCTAGTAGGAGTAG 57.299 41.667 0.00 0.00 0.00 2.57
2744 5343 8.941995 ATATTCATGTCTTGCTAGTAGGAGTA 57.058 34.615 0.00 0.00 0.00 2.59
2748 5347 7.896811 TGGTATATTCATGTCTTGCTAGTAGG 58.103 38.462 0.00 0.00 0.00 3.18
2760 5359 6.851318 TGGTGGATTGATGGTATATTCATGT 58.149 36.000 0.00 0.00 0.00 3.21
2792 5394 3.060615 CCCTTGTCAGGCTGCAGC 61.061 66.667 30.88 30.88 39.20 5.25
2808 5410 2.282745 GGCCCTGCCTATGATGCC 60.283 66.667 0.00 0.00 46.69 4.40
2884 5502 7.364970 TGCATGGTGTATACTTATGTACGTAG 58.635 38.462 4.17 0.00 0.00 3.51
2919 5537 6.854496 AGTAGTGTATTGTTTTGCTTTCGA 57.146 33.333 0.00 0.00 0.00 3.71
2931 5549 6.714810 AGATGCTCTCCTCTAGTAGTGTATTG 59.285 42.308 0.00 0.00 0.00 1.90
2942 5571 5.337894 CCTTGAAACAAGATGCTCTCCTCTA 60.338 44.000 12.25 0.00 0.00 2.43
2947 5576 4.573900 TCTCCTTGAAACAAGATGCTCTC 58.426 43.478 12.25 0.00 0.00 3.20
2952 5581 2.751806 GGCCTCTCCTTGAAACAAGATG 59.248 50.000 12.25 5.54 0.00 2.90
3046 5983 6.942532 AACACGAGCATGATATTGGTATTT 57.057 33.333 0.00 0.00 0.00 1.40
3055 5992 6.238103 GCTTAGCTTTAAACACGAGCATGATA 60.238 38.462 0.00 0.00 38.85 2.15
3057 5994 4.142902 GCTTAGCTTTAAACACGAGCATGA 60.143 41.667 0.00 0.00 38.85 3.07
3067 6004 9.626045 ATTAGTTGATTGTGCTTAGCTTTAAAC 57.374 29.630 5.60 3.27 0.00 2.01


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

AutoCloner maintained by Alex Coulton.