Multiple sequence alignment - TraesCS3B01G418800

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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 TraesCS3B01G418800 chr3B 100.000 3065 0 0 1 3065 655481284 655478220 0.000000e+00 5661
1 TraesCS3B01G418800 chr3D 89.253 2475 158 58 1 2405 496586192 496583756 0.000000e+00 2998
2 TraesCS3B01G418800 chr3D 89.555 651 58 10 2422 3065 496583615 496582968 0.000000e+00 817
3 TraesCS3B01G418800 chr3A 92.130 1690 82 19 789 2453 638291600 638293263 0.000000e+00 2337
4 TraesCS3B01G418800 chr3A 84.450 746 68 28 1 729 638290888 638291602 0.000000e+00 691
5 TraesCS3B01G418800 chr3A 89.600 125 10 2 2484 2605 638293652 638293776 4.090000e-34 156
6 TraesCS3B01G418800 chr5B 76.804 388 60 15 2699 3064 219092385 219092006 1.120000e-44 191
7 TraesCS3B01G418800 chr5A 75.959 391 63 18 2696 3064 264589760 264589379 4.060000e-39 172


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 TraesCS3B01G418800 chr3B 655478220 655481284 3064 True 5661.000000 5661 100.000000 1 3065 1 chr3B.!!$R1 3064
1 TraesCS3B01G418800 chr3D 496582968 496586192 3224 True 1907.500000 2998 89.404000 1 3065 2 chr3D.!!$R1 3064
2 TraesCS3B01G418800 chr3A 638290888 638293776 2888 False 1061.333333 2337 88.726667 1 2605 3 chr3A.!!$F1 2604

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
774 834 0.038159 AGCACGACTGCCACTTACTC 60.038 55.0 0.0 0.0 45.53 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2195 0.248565 GTCACATCCTCAGCTGCTCA 59.751 55.0 9.47 0.0 0.0 4.26 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
37 38 3.181480 GGGTTAAGCATACCCGTACGTTA 60.181 47.826 15.21 5.41 45.42 3.18
38 39 4.429108 GGTTAAGCATACCCGTACGTTAA 58.571 43.478 15.21 7.61 0.00 2.01
39 40 4.267690 GGTTAAGCATACCCGTACGTTAAC 59.732 45.833 19.18 19.18 0.00 2.01
40 41 2.584492 AGCATACCCGTACGTTAACC 57.416 50.000 15.21 0.00 0.00 2.85
51 52 3.549070 CGTACGTTAACCAGCTTACATCC 59.451 47.826 7.22 0.00 0.00 3.51
81 82 4.787135 TCTGCTTATCTGAGAGAGGAGA 57.213 45.455 13.27 13.27 34.78 3.71
82 83 4.717877 TCTGCTTATCTGAGAGAGGAGAG 58.282 47.826 13.27 0.00 32.66 3.20
180 188 0.233848 CAACTTGTTACGTGGACGCC 59.766 55.000 0.00 0.00 44.43 5.68
247 255 0.951040 CAAGCGGAAAGGAGCTCGTT 60.951 55.000 15.73 15.73 43.78 3.85
248 256 0.250338 AAGCGGAAAGGAGCTCGTTT 60.250 50.000 29.16 29.16 43.78 3.60
280 288 5.106634 CCGGTGTCGTGTGGATTAATTTTAA 60.107 40.000 0.00 0.00 33.95 1.52
281 289 6.403855 CCGGTGTCGTGTGGATTAATTTTAAT 60.404 38.462 0.00 0.00 33.82 1.40
282 290 7.024768 CGGTGTCGTGTGGATTAATTTTAATT 58.975 34.615 0.00 0.00 33.72 1.40
283 291 7.539366 CGGTGTCGTGTGGATTAATTTTAATTT 59.461 33.333 0.00 0.00 33.72 1.82
284 292 9.198837 GGTGTCGTGTGGATTAATTTTAATTTT 57.801 29.630 0.00 0.00 33.72 1.82
298 306 5.459110 TTTAATTTTATCGCGCGACTTCT 57.541 34.783 37.37 22.26 0.00 2.85
300 308 2.273370 TTTTATCGCGCGACTTCTCT 57.727 45.000 37.37 21.01 0.00 3.10
328 336 0.582005 GACAAATCTATCGCACCGCC 59.418 55.000 0.00 0.00 0.00 6.13
329 337 0.178068 ACAAATCTATCGCACCGCCT 59.822 50.000 0.00 0.00 0.00 5.52
373 382 0.249741 AGCACGTACGCAAAGTCCTT 60.250 50.000 16.72 0.00 0.00 3.36
411 423 5.622378 CAAGAAGATTAACGGTGAGCTTTC 58.378 41.667 0.00 0.00 0.00 2.62
442 457 4.918810 ACCCAAAGCAACAAACTAGAAG 57.081 40.909 0.00 0.00 0.00 2.85
454 469 0.533032 ACTAGAAGCGGAACTGAGGC 59.467 55.000 0.00 0.00 0.00 4.70
458 473 3.883744 AAGCGGAACTGAGGCACCG 62.884 63.158 9.17 9.17 46.74 4.94
487 508 1.732259 CGTCAGTCATCTTTTTCCCCG 59.268 52.381 0.00 0.00 0.00 5.73
488 509 2.779506 GTCAGTCATCTTTTTCCCCGT 58.220 47.619 0.00 0.00 0.00 5.28
489 510 2.742589 GTCAGTCATCTTTTTCCCCGTC 59.257 50.000 0.00 0.00 0.00 4.79
490 511 2.370519 TCAGTCATCTTTTTCCCCGTCA 59.629 45.455 0.00 0.00 0.00 4.35
491 512 2.744202 CAGTCATCTTTTTCCCCGTCAG 59.256 50.000 0.00 0.00 0.00 3.51
493 514 2.742589 GTCATCTTTTTCCCCGTCAGAC 59.257 50.000 0.00 0.00 0.00 3.51
494 515 2.370519 TCATCTTTTTCCCCGTCAGACA 59.629 45.455 0.41 0.00 0.00 3.41
496 517 2.778299 TCTTTTTCCCCGTCAGACATG 58.222 47.619 0.41 0.00 0.00 3.21
498 519 3.325425 TCTTTTTCCCCGTCAGACATGTA 59.675 43.478 0.00 0.00 0.00 2.29
499 520 3.773418 TTTTCCCCGTCAGACATGTAA 57.227 42.857 0.00 0.00 0.00 2.41
502 523 1.972075 TCCCCGTCAGACATGTAACAA 59.028 47.619 0.00 0.00 0.00 2.83
505 526 3.369471 CCCCGTCAGACATGTAACAATCT 60.369 47.826 0.00 0.00 0.00 2.40
507 528 5.416083 CCCGTCAGACATGTAACAATCTTA 58.584 41.667 0.00 0.00 0.00 2.10
508 529 5.520288 CCCGTCAGACATGTAACAATCTTAG 59.480 44.000 0.00 0.00 0.00 2.18
509 530 6.100004 CCGTCAGACATGTAACAATCTTAGT 58.900 40.000 0.00 0.00 0.00 2.24
526 551 9.899226 CAATCTTAGTATGTTGATCGTAGATCA 57.101 33.333 8.48 8.48 45.12 2.92
531 556 6.304624 AGTATGTTGATCGTAGATCACCCTA 58.695 40.000 11.75 1.26 45.12 3.53
533 558 5.707242 TGTTGATCGTAGATCACCCTATC 57.293 43.478 11.75 0.00 45.12 2.08
535 560 3.698289 TGATCGTAGATCACCCTATCCC 58.302 50.000 8.48 0.00 45.12 3.85
540 565 1.428869 AGATCACCCTATCCCTGTGC 58.571 55.000 0.00 0.00 0.00 4.57
586 624 3.135530 AGATGTGTGGATAAGCCTTCCTC 59.864 47.826 0.00 0.00 37.63 3.71
592 630 4.202567 TGTGGATAAGCCTTCCTCTTTTGT 60.203 41.667 0.00 0.00 37.63 2.83
606 655 6.108687 TCCTCTTTTGTAGTGCTACATCATG 58.891 40.000 12.18 5.98 44.54 3.07
607 656 5.295292 CCTCTTTTGTAGTGCTACATCATGG 59.705 44.000 12.18 8.12 44.54 3.66
615 664 5.263968 AGTGCTACATCATGGTACTGTAC 57.736 43.478 9.46 9.46 33.39 2.90
638 687 0.320374 AACCTCGCGTCCAAGATTCA 59.680 50.000 5.77 0.00 0.00 2.57
679 728 1.569479 GCAGTGAACCGAGGAGTTGC 61.569 60.000 0.00 0.00 0.00 4.17
700 749 1.454276 CACGCAGAAACGTCACGTAAT 59.546 47.619 1.57 0.00 46.34 1.89
734 794 5.291128 GTGTATTGTATATATCCAGTGCGCC 59.709 44.000 4.18 0.00 0.00 6.53
748 808 3.505184 CGCCGCGCCCATAAGTTT 61.505 61.111 0.00 0.00 0.00 2.66
749 809 2.102161 GCCGCGCCCATAAGTTTG 59.898 61.111 0.00 0.00 0.00 2.93
765 825 0.525242 TTTGTTGCAAGCACGACTGC 60.525 50.000 0.00 0.00 44.63 4.40
766 826 2.050985 GTTGCAAGCACGACTGCC 60.051 61.111 0.00 0.00 45.53 4.85
767 827 2.515757 TTGCAAGCACGACTGCCA 60.516 55.556 0.00 0.00 45.53 4.92
769 829 2.974698 GCAAGCACGACTGCCACT 60.975 61.111 0.00 0.00 45.53 4.00
770 830 2.546494 GCAAGCACGACTGCCACTT 61.546 57.895 0.00 0.00 45.53 3.16
774 834 0.038159 AGCACGACTGCCACTTACTC 60.038 55.000 0.00 0.00 45.53 2.59
787 847 3.181530 CCACTTACTCGCTGAATTCGTTG 60.182 47.826 0.04 0.00 0.00 4.10
849 914 2.680339 GAGAATCTCTTTCAAAGGCGGG 59.320 50.000 2.45 0.00 36.75 6.13
884 951 4.685924 TGGCCGCTACAACTTATAAGTAC 58.314 43.478 18.31 5.69 38.57 2.73
913 987 3.793144 GCTTTCGCGTGCTCCTGG 61.793 66.667 5.77 0.00 0.00 4.45
965 1039 4.629115 GTGCGTGGTGGTTGCAGC 62.629 66.667 0.00 0.00 39.67 5.25
1024 1113 4.933064 GCGAGATGGGCGAGGACG 62.933 72.222 0.00 0.00 42.93 4.79
1045 1134 2.044352 TGGCGGAGATCCTCGTCA 60.044 61.111 8.25 8.25 38.73 4.35
1440 1535 0.965866 TCTCCGTGCTGTCCTTCGAT 60.966 55.000 0.00 0.00 0.00 3.59
1566 1661 3.111939 CTCGACTTCGGCCTCGAT 58.888 61.111 14.41 0.00 45.51 3.59
1581 1676 1.099295 TCGATACCGACGCCATGTCT 61.099 55.000 0.00 0.00 45.87 3.41
1601 1696 2.693762 CCACCATGCACTGCTTCGG 61.694 63.158 1.98 2.75 0.00 4.30
1794 1889 3.283684 CTTGTGGACGCGGGCAAA 61.284 61.111 12.47 0.00 0.00 3.68
1830 1925 3.314331 CACGAGCTGGGGGTCTGT 61.314 66.667 0.00 0.00 37.77 3.41
2031 2126 3.689161 TCATACAAATCTGGCTGTTTCCG 59.311 43.478 0.00 0.00 0.00 4.30
2089 2184 3.950794 ATACCGCACGCCACACTGG 62.951 63.158 0.00 0.00 41.55 4.00
2119 2214 0.248565 TGAGCAGCTGAGGATGTGAC 59.751 55.000 20.43 0.00 0.00 3.67
2148 2243 3.053831 AGAATGTGGGTCCGTTTACTG 57.946 47.619 0.00 0.00 0.00 2.74
2214 2311 7.101054 AGATACGTACAGCAAAGTCCAAATAA 58.899 34.615 0.00 0.00 0.00 1.40
2237 2334 3.612860 GGGATGCACGATACGATTATCAC 59.387 47.826 0.00 0.00 34.72 3.06
2407 2505 6.785191 TCTCGATTTCTTATCATTTGTTGCC 58.215 36.000 0.00 0.00 0.00 4.52
2409 2507 6.918626 TCGATTTCTTATCATTTGTTGCCAA 58.081 32.000 0.00 0.00 0.00 4.52
2412 2510 7.329226 CGATTTCTTATCATTTGTTGCCAAAGT 59.671 33.333 0.00 0.00 43.45 2.66
2416 2514 7.771183 TCTTATCATTTGTTGCCAAAGTATCC 58.229 34.615 0.00 0.00 43.45 2.59
2417 2515 4.799564 TCATTTGTTGCCAAAGTATCCC 57.200 40.909 0.00 0.00 43.45 3.85
2418 2516 3.192422 TCATTTGTTGCCAAAGTATCCCG 59.808 43.478 0.00 0.00 43.45 5.14
2420 2518 1.529226 TGTTGCCAAAGTATCCCGTG 58.471 50.000 0.00 0.00 0.00 4.94
2561 3142 4.927978 AGTCATCCTTATCTCACTTCCG 57.072 45.455 0.00 0.00 0.00 4.30
2565 3146 6.207810 AGTCATCCTTATCTCACTTCCGTATC 59.792 42.308 0.00 0.00 0.00 2.24
2568 3151 6.978674 TCCTTATCTCACTTCCGTATCAAT 57.021 37.500 0.00 0.00 0.00 2.57
2622 3206 7.525158 TCAGATCCCTTAAAACTTAATCCCT 57.475 36.000 0.00 0.00 0.00 4.20
2623 3207 7.574607 TCAGATCCCTTAAAACTTAATCCCTC 58.425 38.462 0.00 0.00 0.00 4.30
2628 3214 8.785184 TCCCTTAAAACTTAATCCCTCAAAAA 57.215 30.769 0.00 0.00 0.00 1.94
2629 3215 8.866093 TCCCTTAAAACTTAATCCCTCAAAAAG 58.134 33.333 0.00 0.00 0.00 2.27
2640 3226 9.898152 TTAATCCCTCAAAAAGAATTTGTTGTT 57.102 25.926 1.35 0.00 39.02 2.83
2642 3228 9.546428 AATCCCTCAAAAAGAATTTGTTGTTAG 57.454 29.630 1.35 0.00 39.02 2.34
2654 3240 8.527810 AGAATTTGTTGTTAGTTCTTCCAAACA 58.472 29.630 0.00 0.00 0.00 2.83
2741 3328 9.627395 GCATAACATCATAATAGAACTACGAGT 57.373 33.333 0.00 0.00 0.00 4.18
2760 3347 9.888878 CTACGAGTATAAATAAAGTTCATCGGA 57.111 33.333 0.00 0.00 0.00 4.55
2792 3379 9.737427 CAAACAACTAAACATAACCACAATGTA 57.263 29.630 0.00 0.00 36.56 2.29
2804 3391 5.195001 ACCACAATGTATCAAAACACACC 57.805 39.130 0.00 0.00 30.75 4.16
2859 3447 2.685106 TGGTGGACCAAAAGCCATTA 57.315 45.000 0.00 0.00 44.35 1.90
2874 3462 2.623416 GCCATTATAGTTCACAAGGGCC 59.377 50.000 0.00 0.00 41.93 5.80
2878 3466 2.789409 ATAGTTCACAAGGGCCTCAC 57.211 50.000 6.46 0.00 0.00 3.51
2879 3467 0.320374 TAGTTCACAAGGGCCTCACG 59.680 55.000 6.46 0.40 0.00 4.35
2890 3478 4.662961 CCTCACGCACTCGCACCA 62.663 66.667 0.00 0.00 39.84 4.17
2898 3486 1.667830 CACTCGCACCATCACCGTT 60.668 57.895 0.00 0.00 0.00 4.44
2903 3491 1.574428 GCACCATCACCGTTGACAC 59.426 57.895 0.00 0.00 33.38 3.67
2912 3500 0.106918 ACCGTTGACACCACCATTGT 60.107 50.000 0.00 0.00 0.00 2.71
2916 3504 1.408702 GTTGACACCACCATTGTTGCT 59.591 47.619 0.00 0.00 0.00 3.91
2926 3514 1.457267 ATTGTTGCTGCCACCACCA 60.457 52.632 1.07 0.00 0.00 4.17
2939 3527 0.616111 ACCACCACCAAACTTTGCCA 60.616 50.000 0.00 0.00 0.00 4.92
2964 3552 1.217244 CCCCACGAGTTAACTCCCG 59.783 63.158 26.12 19.66 39.79 5.14
3024 3612 4.077300 TCCACATGATAGCACATTCCTC 57.923 45.455 0.00 0.00 0.00 3.71
3052 3640 3.560882 CCCTCTTGTTCATTTGCTCCTCT 60.561 47.826 0.00 0.00 0.00 3.69
3056 3644 1.202915 TGTTCATTTGCTCCTCTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
3057 3645 1.200948 GTTCATTTGCTCCTCTGCCAC 59.799 52.381 0.00 0.00 0.00 5.01
3059 3647 0.609957 CATTTGCTCCTCTGCCACCA 60.610 55.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 7.095910 TCTCTCAGATAAGCAGAAAGAAACAG 58.904 38.462 0.00 0.00 0.00 3.16
81 82 4.053983 CAAGCATACATACGCATGTCTCT 58.946 43.478 4.09 0.00 44.42 3.10
82 83 3.804325 ACAAGCATACATACGCATGTCTC 59.196 43.478 4.09 0.00 44.42 3.36
123 127 2.970974 GAAGCTGCCACTTGGACGC 61.971 63.158 0.00 0.18 37.39 5.19
159 167 0.233848 CGTCCACGTAACAAGTTGGC 59.766 55.000 7.96 0.00 34.11 4.52
280 288 2.535984 CAGAGAAGTCGCGCGATAAAAT 59.464 45.455 37.03 20.59 0.00 1.82
281 289 1.917955 CAGAGAAGTCGCGCGATAAAA 59.082 47.619 37.03 10.53 0.00 1.52
282 290 1.545759 CAGAGAAGTCGCGCGATAAA 58.454 50.000 37.03 11.00 0.00 1.40
283 291 0.866061 GCAGAGAAGTCGCGCGATAA 60.866 55.000 37.03 11.46 0.00 1.75
284 292 1.298413 GCAGAGAAGTCGCGCGATA 60.298 57.895 37.03 12.39 0.00 2.92
298 306 5.391950 GCGATAGATTTGTCAAAAAGGCAGA 60.392 40.000 1.31 0.00 39.76 4.26
300 308 4.217334 TGCGATAGATTTGTCAAAAAGGCA 59.783 37.500 1.31 4.32 39.76 4.75
328 336 6.020916 GTGAAATGCAATCATGAATCAACGAG 60.021 38.462 0.00 0.00 32.23 4.18
329 337 5.801444 GTGAAATGCAATCATGAATCAACGA 59.199 36.000 0.00 0.00 32.23 3.85
454 469 4.337060 TGACGGAGACACGCGGTG 62.337 66.667 12.47 9.20 39.75 4.94
458 473 0.798771 GATGACTGACGGAGACACGC 60.799 60.000 0.00 0.00 37.37 5.34
487 508 9.587772 ACATACTAAGATTGTTACATGTCTGAC 57.412 33.333 0.00 0.00 0.00 3.51
494 515 9.817809 ACGATCAACATACTAAGATTGTTACAT 57.182 29.630 0.00 0.00 32.58 2.29
499 520 9.900710 GATCTACGATCAACATACTAAGATTGT 57.099 33.333 0.00 0.00 38.36 2.71
502 523 8.516234 GGTGATCTACGATCAACATACTAAGAT 58.484 37.037 15.06 0.00 35.87 2.40
505 526 6.776116 AGGGTGATCTACGATCAACATACTAA 59.224 38.462 19.91 0.00 37.47 2.24
507 528 5.141182 AGGGTGATCTACGATCAACATACT 58.859 41.667 19.91 8.25 37.47 2.12
508 529 5.455056 AGGGTGATCTACGATCAACATAC 57.545 43.478 19.91 6.43 37.47 2.39
509 530 6.377429 GGATAGGGTGATCTACGATCAACATA 59.623 42.308 19.91 17.82 37.47 2.29
526 551 2.367202 CCACGCACAGGGATAGGGT 61.367 63.158 0.00 0.00 0.00 4.34
531 556 1.441729 CGTATCCACGCACAGGGAT 59.558 57.895 0.00 0.00 45.60 3.85
561 599 4.706962 GGAAGGCTTATCCACACATCTTTT 59.293 41.667 0.00 0.00 36.92 2.27
592 630 5.008316 CGTACAGTACCATGATGTAGCACTA 59.992 44.000 5.07 0.00 30.43 2.74
606 655 1.730446 GCGAGGTTCACGTACAGTACC 60.730 57.143 5.07 0.00 32.78 3.34
607 656 1.611043 GCGAGGTTCACGTACAGTAC 58.389 55.000 0.00 0.00 0.00 2.73
615 664 2.355363 TTGGACGCGAGGTTCACG 60.355 61.111 15.93 0.00 32.45 4.35
638 687 3.687321 ATTCGCTGCGTGGCCAGAT 62.687 57.895 22.48 3.51 34.77 2.90
679 728 0.935831 TACGTGACGTTTCTGCGTGG 60.936 55.000 18.28 0.00 45.79 4.94
700 749 2.570442 TACAATACACGCATGCTCGA 57.430 45.000 17.13 0.00 0.00 4.04
734 794 1.070471 GCAACAAACTTATGGGCGCG 61.070 55.000 0.00 0.00 0.00 6.86
738 798 3.059166 GTGCTTGCAACAAACTTATGGG 58.941 45.455 0.00 0.00 0.00 4.00
739 799 2.725723 CGTGCTTGCAACAAACTTATGG 59.274 45.455 0.00 0.00 0.00 2.74
742 802 2.680841 AGTCGTGCTTGCAACAAACTTA 59.319 40.909 0.00 0.00 0.00 2.24
744 804 1.094785 AGTCGTGCTTGCAACAAACT 58.905 45.000 0.00 4.15 0.00 2.66
765 825 2.607187 ACGAATTCAGCGAGTAAGTGG 58.393 47.619 6.22 0.00 0.00 4.00
766 826 3.722082 GCAACGAATTCAGCGAGTAAGTG 60.722 47.826 6.22 0.00 0.00 3.16
767 827 2.412089 GCAACGAATTCAGCGAGTAAGT 59.588 45.455 6.22 0.00 0.00 2.24
769 829 2.409012 TGCAACGAATTCAGCGAGTAA 58.591 42.857 6.22 0.00 0.00 2.24
770 830 1.992667 CTGCAACGAATTCAGCGAGTA 59.007 47.619 6.22 0.00 0.00 2.59
774 834 0.792640 ACTCTGCAACGAATTCAGCG 59.207 50.000 6.22 0.00 0.00 5.18
798 858 5.349543 GCTTCAAACCTGAATTAAATGCCTG 59.650 40.000 0.00 0.00 40.78 4.85
800 860 5.237048 TGCTTCAAACCTGAATTAAATGCC 58.763 37.500 0.00 0.00 40.78 4.40
913 987 4.395583 GAGTGCAACAGCAGCGGC 62.396 66.667 0.00 0.00 41.43 6.53
1024 1113 2.107953 GAGGATCTCCGCCAGCAC 59.892 66.667 0.00 0.00 42.08 4.40
1581 1676 2.203523 AAGCAGTGCATGGTGGCA 60.204 55.556 19.20 0.00 40.26 4.92
1770 1865 2.045926 GCGTCCACAAGCTCCCAT 60.046 61.111 0.00 0.00 0.00 4.00
1779 1874 3.053291 GATTTGCCCGCGTCCACA 61.053 61.111 4.92 0.00 0.00 4.17
1794 1889 3.000819 TTCGCCACCCACTCGGAT 61.001 61.111 0.00 0.00 34.64 4.18
2099 2194 0.535797 TCACATCCTCAGCTGCTCAG 59.464 55.000 9.47 0.00 0.00 3.35
2100 2195 0.248565 GTCACATCCTCAGCTGCTCA 59.751 55.000 9.47 0.00 0.00 4.26
2101 2196 0.461693 GGTCACATCCTCAGCTGCTC 60.462 60.000 9.47 0.00 0.00 4.26
2119 2214 1.750399 CCCACATTCTTGGAGGCGG 60.750 63.158 0.00 0.00 39.24 6.13
2189 2284 4.530710 TTGGACTTTGCTGTACGTATCT 57.469 40.909 0.00 0.00 0.00 1.98
2190 2285 5.796350 ATTTGGACTTTGCTGTACGTATC 57.204 39.130 0.00 0.00 0.00 2.24
2191 2286 6.315393 CCTTATTTGGACTTTGCTGTACGTAT 59.685 38.462 0.00 0.00 0.00 3.06
2192 2287 5.640357 CCTTATTTGGACTTTGCTGTACGTA 59.360 40.000 0.00 0.00 0.00 3.57
2193 2288 4.454504 CCTTATTTGGACTTTGCTGTACGT 59.545 41.667 0.00 0.00 0.00 3.57
2194 2289 4.142687 CCCTTATTTGGACTTTGCTGTACG 60.143 45.833 0.00 0.00 0.00 3.67
2195 2290 5.007682 TCCCTTATTTGGACTTTGCTGTAC 58.992 41.667 0.00 0.00 0.00 2.90
2214 2311 3.509967 TGATAATCGTATCGTGCATCCCT 59.490 43.478 0.00 0.00 39.29 4.20
2237 2334 9.692749 AGCATTGCATCAATCAAATATAGAAAG 57.307 29.630 11.91 0.00 31.05 2.62
2270 2368 9.799106 CAGAATACAAATAGATTCCCCTACAAT 57.201 33.333 0.00 0.00 33.34 2.71
2362 2460 9.778741 TCGAGATTAGTCAAATAGGCAAATTAT 57.221 29.630 0.00 0.00 0.00 1.28
2363 2461 9.778741 ATCGAGATTAGTCAAATAGGCAAATTA 57.221 29.630 0.00 0.00 0.00 1.40
2364 2462 8.682936 ATCGAGATTAGTCAAATAGGCAAATT 57.317 30.769 0.00 0.00 0.00 1.82
2407 2505 2.997986 GGTACACACACGGGATACTTTG 59.002 50.000 0.00 0.00 0.00 2.77
2409 2507 1.551883 GGGTACACACACGGGATACTT 59.448 52.381 0.00 0.00 0.00 2.24
2412 2510 1.272592 TGAGGGTACACACACGGGATA 60.273 52.381 0.00 0.00 31.29 2.59
2416 2514 1.822990 AGTATGAGGGTACACACACGG 59.177 52.381 0.00 0.00 31.29 4.94
2417 2515 3.587797 AAGTATGAGGGTACACACACG 57.412 47.619 0.00 0.00 31.29 4.49
2418 2516 4.251268 GGAAAGTATGAGGGTACACACAC 58.749 47.826 0.00 0.00 0.00 3.82
2420 2518 3.677976 CGGGAAAGTATGAGGGTACACAC 60.678 52.174 0.00 0.00 0.00 3.82
2470 3005 6.952773 ACACCAGTGCATTTTCTTTAAGTA 57.047 33.333 0.00 0.00 0.00 2.24
2472 3007 6.198966 GTCAACACCAGTGCATTTTCTTTAAG 59.801 38.462 0.00 0.00 0.00 1.85
2618 3202 8.073467 ACTAACAACAAATTCTTTTTGAGGGA 57.927 30.769 5.17 0.00 33.83 4.20
2628 3214 8.527810 TGTTTGGAAGAACTAACAACAAATTCT 58.472 29.630 0.00 0.00 0.00 2.40
2629 3215 8.696410 TGTTTGGAAGAACTAACAACAAATTC 57.304 30.769 0.00 0.00 0.00 2.17
2631 3217 9.665719 AAATGTTTGGAAGAACTAACAACAAAT 57.334 25.926 0.00 0.00 34.54 2.32
2754 3341 6.128035 TGTTTAGTTGTTTGATGGATCCGATG 60.128 38.462 7.39 0.00 0.00 3.84
2758 3345 7.973944 GGTTATGTTTAGTTGTTTGATGGATCC 59.026 37.037 4.20 4.20 0.00 3.36
2760 3347 8.303876 GTGGTTATGTTTAGTTGTTTGATGGAT 58.696 33.333 0.00 0.00 0.00 3.41
2761 3348 7.285629 TGTGGTTATGTTTAGTTGTTTGATGGA 59.714 33.333 0.00 0.00 0.00 3.41
2792 3379 4.909696 TGTTCATTCGGTGTGTTTTGAT 57.090 36.364 0.00 0.00 0.00 2.57
2799 3386 2.217750 TGGACTTGTTCATTCGGTGTG 58.782 47.619 0.00 0.00 0.00 3.82
2804 3391 8.690840 GTTTCTTTTAATGGACTTGTTCATTCG 58.309 33.333 10.24 0.47 35.50 3.34
2859 3447 1.066143 CGTGAGGCCCTTGTGAACTAT 60.066 52.381 0.00 0.00 0.00 2.12
2879 3467 3.490759 CGGTGATGGTGCGAGTGC 61.491 66.667 0.00 0.00 43.20 4.40
2884 3472 1.958715 TGTCAACGGTGATGGTGCG 60.959 57.895 6.36 0.00 35.80 5.34
2890 3478 0.400213 ATGGTGGTGTCAACGGTGAT 59.600 50.000 6.36 0.00 35.80 3.06
2898 3486 3.511362 AGCAACAATGGTGGTGTCA 57.489 47.368 0.73 0.00 44.95 3.58
2912 3500 3.668922 TTGGTGGTGGTGGCAGCAA 62.669 57.895 22.39 3.58 34.15 3.91
2916 3504 0.616111 AAAGTTTGGTGGTGGTGGCA 60.616 50.000 0.00 0.00 0.00 4.92
2926 3514 2.365293 GGACATCTTGGCAAAGTTTGGT 59.635 45.455 17.11 4.59 34.78 3.67
2939 3527 2.904434 AGTTAACTCGTGGGGACATCTT 59.096 45.455 1.12 0.00 46.14 2.40
2964 3552 7.655328 AGATGGACGAGAATGAAAGACAATATC 59.345 37.037 0.00 0.00 0.00 1.63
3024 3612 2.185004 AATGAACAAGAGGGTGGTCG 57.815 50.000 0.00 0.00 38.11 4.79


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

AutoCloner maintained by Alex Coulton.