Multiple sequence alignment - TraesCS2B01G483500

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 TraesCS2B01G483500 chr2B 100.000 2605 0 0 1 2605 680755916 680753312 0.000000e+00 4811.0
1 TraesCS2B01G483500 chr2B 88.351 1674 165 15 841 2492 680668397 680666732 0.000000e+00 1984.0
2 TraesCS2B01G483500 chr2B 100.000 718 0 0 2867 3584 680753050 680752333 0.000000e+00 1327.0
3 TraesCS2B01G483500 chr2B 89.873 79 3 1 760 838 680668497 680668424 2.950000e-16 97.1
4 TraesCS2B01G483500 chr2A 90.373 2545 175 16 1 2511 707738723 707736215 0.000000e+00 3278.0
5 TraesCS2B01G483500 chr2A 88.737 1678 162 9 841 2497 707634229 707632558 0.000000e+00 2026.0
6 TraesCS2B01G483500 chr2A 90.155 579 45 7 3009 3582 707668782 707668211 0.000000e+00 743.0
7 TraesCS2B01G483500 chr2D 93.977 1710 87 1 815 2524 568194089 568192396 0.000000e+00 2573.0
8 TraesCS2B01G483500 chr2D 89.222 1670 158 10 841 2492 568130046 568128381 0.000000e+00 2067.0
9 TraesCS2B01G483500 chr2D 85.810 747 68 24 2867 3583 568189532 568188794 0.000000e+00 758.0
10 TraesCS2B01G483500 chr2D 92.262 336 24 2 478 812 568197623 568197289 3.240000e-130 475.0
11 TraesCS2B01G483500 chr3D 75.458 546 96 15 75 603 498946892 498946368 7.740000e-57 231.0
12 TraesCS2B01G483500 chr3B 85.827 127 18 0 115 241 674272525 674272651 6.240000e-28 135.0


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 TraesCS2B01G483500 chr2B 680752333 680755916 3583 True 3069.000000 4811 100.000 1 3584 2 chr2B.!!$R2 3583
1 TraesCS2B01G483500 chr2B 680666732 680668497 1765 True 1040.550000 1984 89.112 760 2492 2 chr2B.!!$R1 1732
2 TraesCS2B01G483500 chr2A 707736215 707738723 2508 True 3278.000000 3278 90.373 1 2511 1 chr2A.!!$R3 2510
3 TraesCS2B01G483500 chr2A 707632558 707634229 1671 True 2026.000000 2026 88.737 841 2497 1 chr2A.!!$R1 1656
4 TraesCS2B01G483500 chr2A 707668211 707668782 571 True 743.000000 743 90.155 3009 3582 1 chr2A.!!$R2 573
5 TraesCS2B01G483500 chr2D 568128381 568130046 1665 True 2067.000000 2067 89.222 841 2492 1 chr2D.!!$R1 1651
6 TraesCS2B01G483500 chr2D 568188794 568197623 8829 True 1268.666667 2573 90.683 478 3583 3 chr2D.!!$R2 3105
7 TraesCS2B01G483500 chr3D 498946368 498946892 524 True 231.000000 231 75.458 75 603 1 chr3D.!!$R1 528

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
474 489 0.250989 TTAGGCCGGAAACAGGTTGG 60.251 55.0 5.05 0.0 0.00 3.77 F
1065 4347 0.323302 TCGCACTAGAAATGGTGGCA 59.677 50.0 0.00 0.0 34.41 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 4770 0.241213 CGAAGCTGTTCTCGGTGAGA 59.759 55.0 0.0 0.0 36.86 3.27 R
2915 9014 0.394352 TCGGTCCTACGGGGTCTTAC 60.394 60.0 0.0 0.0 36.25 2.34 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
17 18 2.501610 GTAGAGCAAGGCCTCCCG 59.498 66.667 5.23 0.00 35.76 5.14
60 61 1.300963 GGATTCCTCCTGCTGTGCA 59.699 57.895 0.00 0.00 38.65 4.57
61 62 0.322816 GGATTCCTCCTGCTGTGCAA 60.323 55.000 0.00 0.00 38.41 4.08
102 103 2.606961 CGCACCTTCGAGCTTTGCA 61.607 57.895 9.96 0.00 32.51 4.08
107 108 1.555075 ACCTTCGAGCTTTGCATCCTA 59.445 47.619 0.00 0.00 0.00 2.94
113 114 2.483876 GAGCTTTGCATCCTACGCATA 58.516 47.619 0.00 0.00 39.58 3.14
143 144 0.392193 CTTCTCTTGGCCGACTGCAT 60.392 55.000 0.00 0.00 43.89 3.96
185 186 1.600916 GCTTCTTCTTGGGCGGTGT 60.601 57.895 0.00 0.00 0.00 4.16
253 268 2.035155 TGAGGTCGAAGGAGGCGA 59.965 61.111 0.00 0.00 35.08 5.54
291 306 3.998672 GCGTCAAGGGTCGGGACA 61.999 66.667 0.75 0.00 0.00 4.02
307 322 0.309922 GACATCATCCATGGCAAGCG 59.690 55.000 6.96 0.00 40.85 4.68
308 323 1.105167 ACATCATCCATGGCAAGCGG 61.105 55.000 6.96 0.00 36.72 5.52
309 324 2.198287 ATCATCCATGGCAAGCGGC 61.198 57.895 6.96 0.00 43.74 6.53
380 395 1.751563 TGGTTGTGCCATCGACTGA 59.248 52.632 0.00 0.00 43.61 3.41
384 399 1.811645 TTGTGCCATCGACTGACGGA 61.812 55.000 0.00 0.00 42.82 4.69
405 420 2.365237 GGGAAGGAGTAGGCGGGT 60.365 66.667 0.00 0.00 0.00 5.28
424 439 2.955391 TCGCGCGTGTTCGTTTCA 60.955 55.556 30.98 2.41 39.49 2.69
453 468 1.068333 CCAACGCAAATGAGACCCAAG 60.068 52.381 0.00 0.00 0.00 3.61
457 472 3.482436 ACGCAAATGAGACCCAAGTTTA 58.518 40.909 0.00 0.00 0.00 2.01
467 482 0.885879 CCCAAGTTTAGGCCGGAAAC 59.114 55.000 22.06 22.06 37.11 2.78
468 483 1.611519 CCAAGTTTAGGCCGGAAACA 58.388 50.000 27.73 0.95 38.91 2.83
472 487 1.144298 AGTTTAGGCCGGAAACAGGTT 59.856 47.619 27.73 12.21 38.91 3.50
474 489 0.250989 TTAGGCCGGAAACAGGTTGG 60.251 55.000 5.05 0.00 0.00 3.77
476 491 2.909965 GCCGGAAACAGGTTGGCA 60.910 61.111 5.05 0.00 45.06 4.92
479 494 2.919494 CGGAAACAGGTTGGCAGGC 61.919 63.158 0.00 0.00 0.00 4.85
480 495 2.644992 GAAACAGGTTGGCAGGCG 59.355 61.111 0.00 0.00 0.00 5.52
482 497 3.429372 AAACAGGTTGGCAGGCGGA 62.429 57.895 0.00 0.00 0.00 5.54
483 498 4.643387 ACAGGTTGGCAGGCGGAC 62.643 66.667 0.00 0.00 0.00 4.79
484 499 4.641645 CAGGTTGGCAGGCGGACA 62.642 66.667 0.00 0.00 0.00 4.02
489 504 2.435418 TTGGCAGGCGGACAAAAAT 58.565 47.368 2.56 0.00 43.07 1.82
502 517 1.369930 AAAAATGTGGACGCGCGTG 60.370 52.632 42.90 19.78 0.00 5.34
548 563 5.275494 CGATTTTTGTGTCCGTTTTAACCT 58.725 37.500 0.00 0.00 0.00 3.50
551 566 7.112426 CGATTTTTGTGTCCGTTTTAACCTAAG 59.888 37.037 0.00 0.00 0.00 2.18
559 574 3.248125 CCGTTTTAACCTAAGCGAACACA 59.752 43.478 0.00 0.00 0.00 3.72
573 588 2.284150 CGAACACACGCGGATGAAATAT 59.716 45.455 17.48 0.17 0.00 1.28
592 607 4.287781 TCGGCGCGTTGGAGTTGA 62.288 61.111 8.43 0.00 0.00 3.18
600 615 2.599082 CGCGTTGGAGTTGATCTAAGTC 59.401 50.000 0.00 0.00 37.89 3.01
642 657 2.101750 TGAACCAGCGAGACAAGTACAA 59.898 45.455 0.00 0.00 0.00 2.41
643 658 2.902705 ACCAGCGAGACAAGTACAAA 57.097 45.000 0.00 0.00 0.00 2.83
644 659 3.188159 ACCAGCGAGACAAGTACAAAA 57.812 42.857 0.00 0.00 0.00 2.44
645 660 2.870411 ACCAGCGAGACAAGTACAAAAC 59.130 45.455 0.00 0.00 0.00 2.43
647 662 2.869801 CAGCGAGACAAGTACAAAACCA 59.130 45.455 0.00 0.00 0.00 3.67
648 663 2.870411 AGCGAGACAAGTACAAAACCAC 59.130 45.455 0.00 0.00 0.00 4.16
650 665 2.220133 CGAGACAAGTACAAAACCACCG 59.780 50.000 0.00 0.00 0.00 4.94
668 684 4.320935 CCACCGGTGAATTTTACTCCTTTG 60.321 45.833 36.07 9.05 0.00 2.77
812 853 9.872684 AACCATCATCCATTTTCTGTTATCTAT 57.127 29.630 0.00 0.00 0.00 1.98
813 854 9.872684 ACCATCATCCATTTTCTGTTATCTATT 57.127 29.630 0.00 0.00 0.00 1.73
882 4149 3.426787 TCAAACTTCCCGCCAGATTTA 57.573 42.857 0.00 0.00 0.00 1.40
937 4209 1.372997 CCTCGGGTTGACACTCACG 60.373 63.158 0.00 0.00 0.00 4.35
977 4252 3.907894 TGGTCCGATGTTGCTTAAAAC 57.092 42.857 0.00 0.00 0.00 2.43
1065 4347 0.323302 TCGCACTAGAAATGGTGGCA 59.677 50.000 0.00 0.00 34.41 4.92
1272 4584 2.281070 CGGCACTGCAACTGGACT 60.281 61.111 2.82 0.00 0.00 3.85
1326 4638 1.521010 CATCCAGCTGCTCCAGACG 60.521 63.158 8.66 0.00 32.44 4.18
1538 4850 1.979693 AGCTCCTCGACCTCACCAC 60.980 63.158 0.00 0.00 0.00 4.16
1587 4899 1.302033 CCTCTGCAACTGTTCGGCT 60.302 57.895 4.75 0.00 0.00 5.52
1882 5194 1.302033 CGCTGCAAGAACCTCACCT 60.302 57.895 0.00 0.00 34.07 4.00
1905 5217 2.936498 GCTCAACATATACAGCAACCGT 59.064 45.455 0.00 0.00 0.00 4.83
1955 5267 2.435059 GCTCGTCAACCTGGAGGC 60.435 66.667 0.00 0.00 39.32 4.70
1957 5269 4.373116 TCGTCAACCTGGAGGCGC 62.373 66.667 0.00 0.00 39.32 6.53
2204 5516 2.069165 AACAACTCCCTGTCTGGCCC 62.069 60.000 0.00 0.00 0.00 5.80
2239 5551 4.951963 GGGCGCTCCGGAATCTCG 62.952 72.222 5.23 8.14 0.00 4.04
2293 5605 0.817634 CCCAATTCCGGCGAGCATAA 60.818 55.000 9.30 0.00 0.00 1.90
2448 5760 2.807045 GACCTGCTCGACTGCGTG 60.807 66.667 0.00 0.00 38.98 5.34
2541 5853 6.766084 TGTTTTATTTGTGGAAAAACTTGCG 58.234 32.000 10.25 0.00 0.00 4.85
2549 8648 6.325919 TGTGGAAAAACTTGCGATCTATTT 57.674 33.333 0.00 0.00 0.00 1.40
2561 8660 3.363378 GCGATCTATTTTCTGTCATGGCG 60.363 47.826 0.00 0.00 0.00 5.69
2563 8662 3.627395 TCTATTTTCTGTCATGGCGGT 57.373 42.857 5.94 0.00 0.00 5.68
2582 8681 4.023021 GCGGTACAAGGAACACCAAAATAA 60.023 41.667 0.00 0.00 32.32 1.40
2583 8682 5.336134 GCGGTACAAGGAACACCAAAATAAT 60.336 40.000 0.00 0.00 32.32 1.28
2584 8683 6.319399 CGGTACAAGGAACACCAAAATAATC 58.681 40.000 0.00 0.00 32.32 1.75
2588 8687 9.535878 GTACAAGGAACACCAAAATAATCAAAA 57.464 29.630 0.00 0.00 0.00 2.44
2590 8689 9.625747 ACAAGGAACACCAAAATAATCAAAATT 57.374 25.926 0.00 0.00 0.00 1.82
2593 8692 9.844257 AGGAACACCAAAATAATCAAAATTTCA 57.156 25.926 0.00 0.00 0.00 2.69
2901 9000 6.467723 AAAACTTTATGCAGTAGACAGTCG 57.532 37.500 0.00 0.00 0.00 4.18
2903 9002 3.762288 ACTTTATGCAGTAGACAGTCGGA 59.238 43.478 0.00 0.00 0.00 4.55
2907 9006 3.678056 TGCAGTAGACAGTCGGAAATT 57.322 42.857 0.00 0.00 0.00 1.82
2908 9007 3.585862 TGCAGTAGACAGTCGGAAATTC 58.414 45.455 0.00 0.00 0.00 2.17
2909 9008 2.599082 GCAGTAGACAGTCGGAAATTCG 59.401 50.000 0.00 0.00 0.00 3.34
2915 9014 2.346803 ACAGTCGGAAATTCGTCATGG 58.653 47.619 0.00 0.00 0.00 3.66
2948 9047 0.949105 GACCGACGCACCAGAACAAT 60.949 55.000 0.00 0.00 0.00 2.71
2953 9052 2.670905 CGACGCACCAGAACAATAATCA 59.329 45.455 0.00 0.00 0.00 2.57
2954 9053 3.483574 CGACGCACCAGAACAATAATCAC 60.484 47.826 0.00 0.00 0.00 3.06
2955 9054 2.747446 ACGCACCAGAACAATAATCACC 59.253 45.455 0.00 0.00 0.00 4.02
2966 9065 3.555956 ACAATAATCACCGTCGATGAAGC 59.444 43.478 6.11 0.00 0.00 3.86
2990 9089 7.936950 CGAAGCATATGTCAGAAGAATCTAA 57.063 36.000 4.29 0.00 33.50 2.10
2993 9092 7.129457 AGCATATGTCAGAAGAATCTAACCA 57.871 36.000 4.29 0.00 33.50 3.67
2996 9095 8.677300 GCATATGTCAGAAGAATCTAACCAAAA 58.323 33.333 4.29 0.00 33.50 2.44
2999 9098 7.730364 TGTCAGAAGAATCTAACCAAAAGAC 57.270 36.000 0.00 0.00 33.50 3.01
3000 9099 7.279615 TGTCAGAAGAATCTAACCAAAAGACA 58.720 34.615 0.00 0.00 33.50 3.41
3001 9100 7.226720 TGTCAGAAGAATCTAACCAAAAGACAC 59.773 37.037 0.00 0.00 33.50 3.67
3050 9158 2.436646 CCAAGATCAACGCCGCCT 60.437 61.111 0.00 0.00 0.00 5.52
3075 9183 1.615883 CCCATGAGATTCGTCGGAGAT 59.384 52.381 0.00 0.00 40.67 2.75
3136 9245 7.889469 AGACGTTCCTAGTATTTGTGTTAGAA 58.111 34.615 0.00 0.00 0.00 2.10
3305 9419 9.702253 TTATTGTCTCTAGAATCTAGACCAACT 57.298 33.333 20.72 15.15 39.10 3.16
3342 9456 0.109597 CACTCACCATTTTCGCAGGC 60.110 55.000 0.00 0.00 0.00 4.85
3359 9473 1.227674 GCCGCCACTCCTAAGATGG 60.228 63.158 0.00 0.00 36.51 3.51
3394 9512 1.722852 GGAGACGCGACATCGATCG 60.723 63.158 15.93 9.36 45.09 3.69
3400 9518 0.989315 CGCGACATCGATCGAGACAG 60.989 60.000 23.84 15.10 45.13 3.51
3453 9571 3.416156 CTTCCATCATTAAGGCCCTAGC 58.584 50.000 0.00 0.00 38.76 3.42
3479 9597 0.505655 GTACGAATTATGCCGACGCC 59.494 55.000 0.00 0.00 0.00 5.68
3481 9599 0.741574 ACGAATTATGCCGACGCCAA 60.742 50.000 0.00 0.00 0.00 4.52
3490 9608 1.226030 GCCGACGCCAACACTACTTT 61.226 55.000 0.00 0.00 0.00 2.66
3495 9613 4.260702 CCGACGCCAACACTACTTTAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
3527 9655 3.417101 TGGTATTGACTGAAAATGGCGT 58.583 40.909 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.316651 GAGGAATCCAATGGCTGAGC 58.683 55.000 0.61 0.00 0.00 4.26
33 34 1.213678 CAGGAGGAATCCAATGGCTGA 59.786 52.381 0.61 0.00 0.00 4.26
35 36 0.106318 GCAGGAGGAATCCAATGGCT 60.106 55.000 0.61 0.00 0.00 4.75
37 38 1.064166 ACAGCAGGAGGAATCCAATGG 60.064 52.381 0.61 0.00 0.00 3.16
44 45 0.957395 CGTTGCACAGCAGGAGGAAT 60.957 55.000 0.00 0.00 40.61 3.01
82 83 1.961277 CAAAGCTCGAAGGTGCGGT 60.961 57.895 0.00 0.00 33.30 5.68
87 88 0.326264 AGGATGCAAAGCTCGAAGGT 59.674 50.000 0.00 0.00 0.00 3.50
88 89 1.936547 GTAGGATGCAAAGCTCGAAGG 59.063 52.381 0.00 0.00 0.00 3.46
124 125 0.392193 ATGCAGTCGGCCAAGAGAAG 60.392 55.000 2.24 0.00 43.89 2.85
222 223 2.182030 CTCACCTTCGTCGCCTCC 59.818 66.667 0.00 0.00 0.00 4.30
230 231 0.171455 CTCCTTCGACCTCACCTTCG 59.829 60.000 0.00 0.00 36.55 3.79
279 294 2.221918 GGATGATGTCCCGACCCTT 58.778 57.895 0.00 0.00 41.50 3.95
291 306 2.198287 GCCGCTTGCCATGGATGAT 61.198 57.895 18.40 0.00 0.00 2.45
317 332 4.699522 AAACTCCCGCCCGCTCAC 62.700 66.667 0.00 0.00 0.00 3.51
318 333 3.485346 AAAAACTCCCGCCCGCTCA 62.485 57.895 0.00 0.00 0.00 4.26
338 353 1.077005 CCATTTCTCCCCACTTTCCCA 59.923 52.381 0.00 0.00 0.00 4.37
341 356 2.171003 CCACCATTTCTCCCCACTTTC 58.829 52.381 0.00 0.00 0.00 2.62
344 359 0.405585 CACCACCATTTCTCCCCACT 59.594 55.000 0.00 0.00 0.00 4.00
351 366 1.039856 GCACAACCACCACCATTTCT 58.960 50.000 0.00 0.00 0.00 2.52
373 388 2.675423 CCCTGGTCCGTCAGTCGA 60.675 66.667 0.00 0.00 42.86 4.20
380 395 0.324460 CTACTCCTTCCCTGGTCCGT 60.324 60.000 0.00 0.00 0.00 4.69
384 399 1.686110 CGCCTACTCCTTCCCTGGT 60.686 63.158 0.00 0.00 0.00 4.00
405 420 3.200126 GAAACGAACACGCGCGACA 62.200 57.895 39.36 0.00 33.86 4.35
414 429 0.584396 GCGTGGACATGAAACGAACA 59.416 50.000 18.77 0.00 39.64 3.18
424 439 1.523154 ATTTGCGTTGGCGTGGACAT 61.523 50.000 0.00 0.00 44.10 3.06
453 468 1.268625 CAACCTGTTTCCGGCCTAAAC 59.731 52.381 18.75 18.75 37.35 2.01
457 472 2.115266 CCAACCTGTTTCCGGCCT 59.885 61.111 0.00 0.00 0.00 5.19
467 482 4.641645 TGTCCGCCTGCCAACCTG 62.642 66.667 0.00 0.00 0.00 4.00
468 483 2.920076 TTTTGTCCGCCTGCCAACCT 62.920 55.000 0.00 0.00 0.00 3.50
472 487 1.112315 ACATTTTTGTCCGCCTGCCA 61.112 50.000 0.00 0.00 0.00 4.92
474 489 0.667184 CCACATTTTTGTCCGCCTGC 60.667 55.000 0.00 0.00 0.00 4.85
476 491 0.958822 GTCCACATTTTTGTCCGCCT 59.041 50.000 0.00 0.00 0.00 5.52
479 494 0.724453 CGCGTCCACATTTTTGTCCG 60.724 55.000 0.00 0.00 0.00 4.79
480 495 1.001745 GCGCGTCCACATTTTTGTCC 61.002 55.000 8.43 0.00 0.00 4.02
482 497 1.369930 CGCGCGTCCACATTTTTGT 60.370 52.632 24.19 0.00 0.00 2.83
483 498 1.369930 ACGCGCGTCCACATTTTTG 60.370 52.632 32.73 0.00 0.00 2.44
484 499 1.369930 CACGCGCGTCCACATTTTT 60.370 52.632 35.61 3.97 0.00 1.94
513 528 2.400896 AAAAATCGGCACAACGCGCT 62.401 50.000 5.73 0.00 43.84 5.92
559 574 1.497991 CCGACATATTTCATCCGCGT 58.502 50.000 4.92 0.00 0.00 6.01
567 582 0.315869 CCAACGCGCCGACATATTTC 60.316 55.000 5.73 0.00 0.00 2.17
573 588 4.595538 AACTCCAACGCGCCGACA 62.596 61.111 5.73 0.00 0.00 4.35
600 615 2.233922 ACTTCGGTCCATGTACTCAAGG 59.766 50.000 0.00 0.00 34.16 3.61
642 657 3.570975 GGAGTAAAATTCACCGGTGGTTT 59.429 43.478 33.40 27.95 31.02 3.27
643 658 3.151554 GGAGTAAAATTCACCGGTGGTT 58.848 45.455 33.40 24.31 31.02 3.67
644 659 2.374170 AGGAGTAAAATTCACCGGTGGT 59.626 45.455 33.40 20.02 35.62 4.16
645 660 3.067684 AGGAGTAAAATTCACCGGTGG 57.932 47.619 33.40 15.70 0.00 4.61
647 662 4.466827 ACAAAGGAGTAAAATTCACCGGT 58.533 39.130 0.00 0.00 0.00 5.28
648 663 6.563222 TTACAAAGGAGTAAAATTCACCGG 57.437 37.500 0.00 0.00 31.45 5.28
650 665 7.658261 AGCTTTACAAAGGAGTAAAATTCACC 58.342 34.615 4.01 0.00 41.78 4.02
668 684 3.110593 GCTCTTTTCAGCGAGCTTTAC 57.889 47.619 4.17 0.00 46.87 2.01
694 710 1.866015 TGATGGTCCACGGAGAAGAT 58.134 50.000 0.00 0.00 0.00 2.40
882 4149 2.234908 CGAAAGGGACCAGATTGACTCT 59.765 50.000 0.00 0.00 33.14 3.24
937 4209 3.036084 CCGTCCACGTCTGTGTGC 61.036 66.667 0.00 0.00 44.92 4.57
1006 4281 9.029243 CAGACTTCAATCTCATGTGAATACTAC 57.971 37.037 0.90 0.00 33.45 2.73
1065 4347 1.889105 CAGCAGCCAAGTGTGACGT 60.889 57.895 0.00 0.00 0.00 4.34
1356 4668 2.045926 AGCGTGGAGATGTTGCCC 60.046 61.111 0.00 0.00 0.00 5.36
1458 4770 0.241213 CGAAGCTGTTCTCGGTGAGA 59.759 55.000 0.00 0.00 36.86 3.27
1514 4826 3.386237 GGTCGAGGAGCTGCAGGT 61.386 66.667 20.31 20.31 0.00 4.00
1538 4850 2.738521 CTCCGGTGAGCGTGTTGG 60.739 66.667 0.00 0.00 0.00 3.77
1581 4893 3.733344 GAGCGCCCACATAGCCGAA 62.733 63.158 2.29 0.00 0.00 4.30
1636 4948 3.567797 GAGGTCGCCGATGCAAGC 61.568 66.667 0.00 0.00 37.32 4.01
1753 5065 2.594592 GCCGGACAGCTTGTTGGT 60.595 61.111 5.05 0.00 31.37 3.67
1860 5172 4.269523 AGGTTCTTGCAGCGGCCA 62.270 61.111 6.32 0.00 40.13 5.36
1882 5194 3.373748 CGGTTGCTGTATATGTTGAGCAA 59.626 43.478 0.00 0.00 46.49 3.91
1955 5267 2.304401 TTGTCGTACAACCGCAGCG 61.304 57.895 8.18 8.18 32.34 5.18
1963 5275 1.542272 GACAGCGCGTTGTCGTACAA 61.542 55.000 34.51 0.00 38.23 2.41
2023 5335 1.987213 TGGACAGCCCAAGCGATAA 59.013 52.632 0.00 0.00 46.67 1.75
2140 5452 4.584327 TGACAAGATTCGTCAGAGACAA 57.416 40.909 0.00 0.00 38.45 3.18
2141 5453 4.299155 GTTGACAAGATTCGTCAGAGACA 58.701 43.478 0.00 0.00 43.85 3.41
2204 5516 3.257561 CGATGTTCTCCGGCAGCG 61.258 66.667 0.00 0.00 38.12 5.18
2239 5551 1.964552 CTGTGGATGATGAGCTTCCC 58.035 55.000 0.00 0.00 39.48 3.97
2448 5760 1.079750 GACCAGAGTGCGGAGGTTC 60.080 63.158 0.00 0.00 33.77 3.62
2524 5836 4.647424 AGATCGCAAGTTTTTCCACAAA 57.353 36.364 0.00 0.00 39.48 2.83
2526 5838 5.957842 AATAGATCGCAAGTTTTTCCACA 57.042 34.783 0.00 0.00 39.48 4.17
2528 5840 7.083858 CAGAAAATAGATCGCAAGTTTTTCCA 58.916 34.615 0.00 0.00 34.97 3.53
2529 5841 7.084486 ACAGAAAATAGATCGCAAGTTTTTCC 58.916 34.615 0.00 0.00 34.97 3.13
2532 5844 7.202016 TGACAGAAAATAGATCGCAAGTTTT 57.798 32.000 0.00 0.00 39.48 2.43
2533 5845 6.801539 TGACAGAAAATAGATCGCAAGTTT 57.198 33.333 0.00 0.00 39.48 2.66
2534 5846 6.183360 CCATGACAGAAAATAGATCGCAAGTT 60.183 38.462 0.00 0.00 39.48 2.66
2535 5847 5.295292 CCATGACAGAAAATAGATCGCAAGT 59.705 40.000 0.00 0.00 39.48 3.16
2537 5849 4.035558 GCCATGACAGAAAATAGATCGCAA 59.964 41.667 0.00 0.00 0.00 4.85
2538 5850 3.561310 GCCATGACAGAAAATAGATCGCA 59.439 43.478 0.00 0.00 0.00 5.10
2539 5851 3.363378 CGCCATGACAGAAAATAGATCGC 60.363 47.826 0.00 0.00 0.00 4.58
2540 5852 3.185188 CCGCCATGACAGAAAATAGATCG 59.815 47.826 0.00 0.00 0.00 3.69
2541 5853 4.130118 ACCGCCATGACAGAAAATAGATC 58.870 43.478 0.00 0.00 0.00 2.75
2549 8648 1.338674 CCTTGTACCGCCATGACAGAA 60.339 52.381 0.00 0.00 0.00 3.02
2561 8660 7.222000 TGATTATTTTGGTGTTCCTTGTACC 57.778 36.000 0.00 0.00 35.05 3.34
2877 8976 6.073222 CCGACTGTCTACTGCATAAAGTTTTT 60.073 38.462 6.21 0.00 0.00 1.94
2884 8983 4.794278 TTTCCGACTGTCTACTGCATAA 57.206 40.909 6.21 0.00 0.00 1.90
2901 9000 3.626217 GGGTCTTACCATGACGAATTTCC 59.374 47.826 0.00 0.00 41.02 3.13
2903 9002 3.617284 GGGGTCTTACCATGACGAATTT 58.383 45.455 0.00 0.00 41.02 1.82
2907 9006 0.612732 ACGGGGTCTTACCATGACGA 60.613 55.000 0.00 0.00 41.02 4.20
2908 9007 1.066605 CTACGGGGTCTTACCATGACG 59.933 57.143 0.00 0.13 41.02 4.35
2909 9008 1.411612 CCTACGGGGTCTTACCATGAC 59.588 57.143 0.00 0.00 41.02 3.06
2915 9014 0.394352 TCGGTCCTACGGGGTCTTAC 60.394 60.000 0.00 0.00 36.25 2.34
2933 9032 3.181510 GGTGATTATTGTTCTGGTGCGTC 60.182 47.826 0.00 0.00 0.00 5.19
2934 9033 2.747446 GGTGATTATTGTTCTGGTGCGT 59.253 45.455 0.00 0.00 0.00 5.24
2940 9039 4.803613 TCATCGACGGTGATTATTGTTCTG 59.196 41.667 6.73 0.00 0.00 3.02
2948 9047 1.402613 TCGCTTCATCGACGGTGATTA 59.597 47.619 12.35 0.00 33.02 1.75
2953 9052 1.805945 GCTTCGCTTCATCGACGGT 60.806 57.895 0.00 0.00 38.30 4.83
2954 9053 1.148157 ATGCTTCGCTTCATCGACGG 61.148 55.000 0.00 0.00 38.30 4.79
2955 9054 1.477105 TATGCTTCGCTTCATCGACG 58.523 50.000 0.00 0.00 38.30 5.12
2966 9065 7.095857 GGTTAGATTCTTCTGACATATGCTTCG 60.096 40.741 1.58 0.00 39.59 3.79
2987 9086 5.666969 TCGTTCATGTGTCTTTTGGTTAG 57.333 39.130 0.00 0.00 0.00 2.34
2988 9087 5.818336 TCTTCGTTCATGTGTCTTTTGGTTA 59.182 36.000 0.00 0.00 0.00 2.85
2990 9089 4.035208 GTCTTCGTTCATGTGTCTTTTGGT 59.965 41.667 0.00 0.00 0.00 3.67
2993 9092 4.273480 CCAGTCTTCGTTCATGTGTCTTTT 59.727 41.667 0.00 0.00 0.00 2.27
2996 9095 2.289072 CCCAGTCTTCGTTCATGTGTCT 60.289 50.000 0.00 0.00 0.00 3.41
2997 9096 2.069273 CCCAGTCTTCGTTCATGTGTC 58.931 52.381 0.00 0.00 0.00 3.67
2998 9097 1.416401 ACCCAGTCTTCGTTCATGTGT 59.584 47.619 0.00 0.00 0.00 3.72
2999 9098 2.069273 GACCCAGTCTTCGTTCATGTG 58.931 52.381 0.00 0.00 0.00 3.21
3000 9099 1.002087 GGACCCAGTCTTCGTTCATGT 59.998 52.381 0.00 0.00 32.47 3.21
3001 9100 1.726853 GGACCCAGTCTTCGTTCATG 58.273 55.000 0.00 0.00 32.47 3.07
3050 9158 2.224042 CCGACGAATCTCATGGGATTCA 60.224 50.000 35.92 1.49 46.94 2.57
3075 9183 2.700371 TCTGAGGACGTACGGAGGTATA 59.300 50.000 21.06 0.00 0.00 1.47
3111 9219 7.458409 TCTAACACAAATACTAGGAACGTCT 57.542 36.000 0.00 0.00 0.00 4.18
3136 9245 7.397476 TCATAAGAATGCCGACCTATCTCTAAT 59.603 37.037 0.00 0.00 32.76 1.73
3293 9407 6.472686 AAATCTAGCGAAGTTGGTCTAGAT 57.527 37.500 17.72 17.72 45.58 1.98
3305 9419 4.464951 TGAGTGGACCTAAAATCTAGCGAA 59.535 41.667 0.00 0.00 0.00 4.70
3342 9456 0.541863 AACCATCTTAGGAGTGGCGG 59.458 55.000 0.00 0.00 36.47 6.13
3359 9473 4.326548 CGTCTCCGAGAAGTGGAAATTAAC 59.673 45.833 0.00 0.00 34.44 2.01
3394 9512 3.118956 CCACTTGTATGGAGGTCTGTCTC 60.119 52.174 0.00 0.00 43.02 3.36
3400 9518 1.679032 GGCACCACTTGTATGGAGGTC 60.679 57.143 0.00 0.00 43.02 3.85
3453 9571 2.088512 CGGCATAATTCGTACGTCATCG 59.911 50.000 16.05 6.25 43.34 3.84
3495 9613 6.299805 TCAGTCAATACCAGCACTATCTTT 57.700 37.500 0.00 0.00 0.00 2.52
3496 9614 5.939764 TCAGTCAATACCAGCACTATCTT 57.060 39.130 0.00 0.00 0.00 2.40
3497 9615 5.939764 TTCAGTCAATACCAGCACTATCT 57.060 39.130 0.00 0.00 0.00 1.98
3498 9616 6.985188 TTTTCAGTCAATACCAGCACTATC 57.015 37.500 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.