Multiple sequence alignment - TraesCS5D01G413400

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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 TraesCS5D01G413400 chr5D 100.000 4866 0 0 1 4866 476459439 476464304 0.000000e+00 8986.0
1 TraesCS5D01G413400 chr5D 85.227 176 24 2 3081 3255 458632622 458632796 3.870000e-41 180.0
2 TraesCS5D01G413400 chr5B 93.966 4939 191 52 1 4866 583910225 583915129 0.000000e+00 7371.0
3 TraesCS5D01G413400 chr5B 85.795 176 23 2 3081 3255 562048319 562048493 8.320000e-43 185.0
4 TraesCS5D01G413400 chr5A 91.627 4861 212 80 87 4866 595893195 595897941 0.000000e+00 6541.0
5 TraesCS5D01G413400 chr1B 82.143 280 48 2 3973 4251 678259509 678259787 6.290000e-59 239.0
6 TraesCS5D01G413400 chr1D 81.786 280 49 2 3973 4251 487168521 487168799 2.930000e-57 233.0
7 TraesCS5D01G413400 chr1A 81.786 280 49 2 3973 4251 584676043 584676321 2.930000e-57 233.0
8 TraesCS5D01G413400 chr4A 84.659 176 25 2 3081 3255 532161998 532162172 1.800000e-39 174.0
9 TraesCS5D01G413400 chr7D 84.091 176 26 2 3081 3255 332692750 332692924 8.380000e-38 169.0
10 TraesCS5D01G413400 chr7D 80.137 146 17 7 4348 4493 153314285 153314418 1.110000e-16 99.0
11 TraesCS5D01G413400 chr2D 84.393 173 25 2 3084 3255 601056257 601056086 8.380000e-38 169.0
12 TraesCS5D01G413400 chr2D 83.893 149 22 2 3099 3246 616635060 616634913 1.830000e-29 141.0
13 TraesCS5D01G413400 chr2A 83.893 149 22 2 3099 3246 746852160 746852013 1.830000e-29 141.0
14 TraesCS5D01G413400 chr2A 91.228 57 4 1 1854 1910 199274353 199274298 5.220000e-10 76.8
15 TraesCS5D01G413400 chr2B 91.228 57 4 1 1854 1910 239928643 239928588 5.220000e-10 76.8


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 TraesCS5D01G413400 chr5D 476459439 476464304 4865 False 8986 8986 100.000 1 4866 1 chr5D.!!$F2 4865
1 TraesCS5D01G413400 chr5B 583910225 583915129 4904 False 7371 7371 93.966 1 4866 1 chr5B.!!$F2 4865
2 TraesCS5D01G413400 chr5A 595893195 595897941 4746 False 6541 6541 91.627 87 4866 1 chr5A.!!$F1 4779

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
477 515 0.174389 CCCGTGATCCAGACAGACAG 59.826 60.0 0.0 0.0 0.0 3.51 F
485 523 0.179116 CCAGACAGACAGCGATCCAG 60.179 60.0 0.0 0.0 0.0 3.86 F
488 526 0.528017 GACAGACAGCGATCCAGACA 59.472 55.0 0.0 0.0 0.0 3.41 F
492 530 0.528017 GACAGCGATCCAGACAGACA 59.472 55.0 0.0 0.0 0.0 3.41 F
493 531 0.529833 ACAGCGATCCAGACAGACAG 59.470 55.0 0.0 0.0 0.0 3.51 F
1300 1407 0.664224 GATCCTCGTCGTCTCTTCCC 59.336 60.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2335 0.037419 CATTTTTCTTGTGGCGGGGG 60.037 55.000 0.00 0.00 0.00 5.40 R
2451 2572 3.376935 CTTCTGGTCGCCATCCGCT 62.377 63.158 0.00 0.00 36.73 5.52 R
2700 2821 1.428620 GTCGTAGAGCGTCTCCACC 59.571 63.158 3.66 0.00 42.13 4.61 R
3317 3441 4.854924 CATGTCCGGCCGCCATCA 62.855 66.667 22.85 15.45 0.00 3.07 R
3708 3838 4.162888 TCCTAGGAAAACCCCTCGTATTTC 59.837 45.833 9.71 0.00 37.74 2.17 R
4284 4425 0.041386 AGGAGGCCTACGAGAAGGTT 59.959 55.000 10.07 0.00 39.02 3.50 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 1.590147 GTACCTGGGTCGGTCACTG 59.410 63.158 0.00 0.00 38.49 3.66
83 84 3.618690 ACCTGCACCTTTCTCTGTATC 57.381 47.619 0.00 0.00 0.00 2.24
84 85 2.237392 ACCTGCACCTTTCTCTGTATCC 59.763 50.000 0.00 0.00 0.00 2.59
170 171 0.916086 ACGCCTCCCCATTTATCACA 59.084 50.000 0.00 0.00 0.00 3.58
317 340 3.815962 CAGAGAAAGATGGCTGGATCATG 59.184 47.826 0.00 0.00 0.00 3.07
398 424 1.202580 CCGCGAGATTCCCTTCATTCT 60.203 52.381 8.23 0.00 0.00 2.40
419 445 4.927425 TCTTCTCGTTGTTAGCGCTTAATT 59.073 37.500 18.68 0.00 0.00 1.40
421 447 6.587226 TCTTCTCGTTGTTAGCGCTTAATTAA 59.413 34.615 18.68 0.00 0.00 1.40
424 461 4.017271 CGTTGTTAGCGCTTAATTAACCG 58.983 43.478 18.68 9.61 0.00 4.44
474 512 0.251608 TGTCCCGTGATCCAGACAGA 60.252 55.000 0.00 0.00 34.44 3.41
476 514 0.251608 TCCCGTGATCCAGACAGACA 60.252 55.000 0.00 0.00 0.00 3.41
477 515 0.174389 CCCGTGATCCAGACAGACAG 59.826 60.000 0.00 0.00 0.00 3.51
478 516 0.459237 CCGTGATCCAGACAGACAGC 60.459 60.000 0.00 0.00 0.00 4.40
479 517 0.799917 CGTGATCCAGACAGACAGCG 60.800 60.000 0.00 0.00 0.00 5.18
480 518 0.528017 GTGATCCAGACAGACAGCGA 59.472 55.000 0.00 0.00 0.00 4.93
481 519 1.135915 GTGATCCAGACAGACAGCGAT 59.864 52.381 0.00 0.00 0.00 4.58
482 520 1.406898 TGATCCAGACAGACAGCGATC 59.593 52.381 0.00 0.00 0.00 3.69
483 521 0.749649 ATCCAGACAGACAGCGATCC 59.250 55.000 0.00 0.00 0.00 3.36
484 522 0.611896 TCCAGACAGACAGCGATCCA 60.612 55.000 0.00 0.00 0.00 3.41
485 523 0.179116 CCAGACAGACAGCGATCCAG 60.179 60.000 0.00 0.00 0.00 3.86
486 524 0.813821 CAGACAGACAGCGATCCAGA 59.186 55.000 0.00 0.00 0.00 3.86
487 525 0.814457 AGACAGACAGCGATCCAGAC 59.186 55.000 0.00 0.00 0.00 3.51
488 526 0.528017 GACAGACAGCGATCCAGACA 59.472 55.000 0.00 0.00 0.00 3.41
489 527 0.529833 ACAGACAGCGATCCAGACAG 59.470 55.000 0.00 0.00 0.00 3.51
490 528 0.813821 CAGACAGCGATCCAGACAGA 59.186 55.000 0.00 0.00 0.00 3.41
491 529 0.814457 AGACAGCGATCCAGACAGAC 59.186 55.000 0.00 0.00 0.00 3.51
492 530 0.528017 GACAGCGATCCAGACAGACA 59.472 55.000 0.00 0.00 0.00 3.41
493 531 0.529833 ACAGCGATCCAGACAGACAG 59.470 55.000 0.00 0.00 0.00 3.51
494 532 0.805322 CAGCGATCCAGACAGACAGC 60.805 60.000 0.00 0.00 0.00 4.40
495 533 1.520342 GCGATCCAGACAGACAGCC 60.520 63.158 0.00 0.00 0.00 4.85
496 534 1.954362 GCGATCCAGACAGACAGCCT 61.954 60.000 0.00 0.00 0.00 4.58
512 550 2.045524 AGCCTCTGGATCACTACCATG 58.954 52.381 0.00 0.00 36.79 3.66
531 569 4.142600 CCATGCTAGAGCTGGTTTACAAAC 60.143 45.833 2.72 0.00 42.66 2.93
532 570 4.351874 TGCTAGAGCTGGTTTACAAACT 57.648 40.909 2.72 0.00 42.66 2.66
535 573 4.755123 GCTAGAGCTGGTTTACAAACTGAA 59.245 41.667 0.00 0.00 37.28 3.02
536 574 5.106908 GCTAGAGCTGGTTTACAAACTGAAG 60.107 44.000 0.00 2.70 37.28 3.02
539 577 5.297029 AGAGCTGGTTTACAAACTGAAGAAC 59.703 40.000 0.00 0.00 38.89 3.01
541 579 5.297029 AGCTGGTTTACAAACTGAAGAACTC 59.703 40.000 4.93 0.00 38.89 3.01
542 580 5.505819 GCTGGTTTACAAACTGAAGAACTCC 60.506 44.000 4.93 0.00 38.89 3.85
543 581 5.502079 TGGTTTACAAACTGAAGAACTCCA 58.498 37.500 4.93 0.00 38.89 3.86
544 582 5.588648 TGGTTTACAAACTGAAGAACTCCAG 59.411 40.000 4.93 0.00 38.89 3.86
545 583 5.820947 GGTTTACAAACTGAAGAACTCCAGA 59.179 40.000 4.93 0.00 38.89 3.86
546 584 6.486993 GGTTTACAAACTGAAGAACTCCAGAT 59.513 38.462 4.93 0.00 38.89 2.90
547 585 7.355778 GTTTACAAACTGAAGAACTCCAGATG 58.644 38.462 0.00 0.00 36.03 2.90
548 586 5.296151 ACAAACTGAAGAACTCCAGATGA 57.704 39.130 0.00 0.00 34.65 2.92
564 627 7.905604 TCCAGATGAGTACACTGTAAAAATG 57.094 36.000 0.00 0.00 0.00 2.32
565 628 7.450074 TCCAGATGAGTACACTGTAAAAATGT 58.550 34.615 0.00 0.00 0.00 2.71
597 660 3.970205 GGAATTCCCGGGAAACTGA 57.030 52.632 38.52 17.88 39.98 3.41
598 661 2.437085 GGAATTCCCGGGAAACTGAT 57.563 50.000 38.52 20.25 39.98 2.90
599 662 2.735151 GGAATTCCCGGGAAACTGATT 58.265 47.619 38.52 27.24 39.98 2.57
602 665 4.384868 GGAATTCCCGGGAAACTGATTCTA 60.385 45.833 38.52 13.70 39.98 2.10
617 680 3.500680 TGATTCTACGTTTGGAAACTGCC 59.499 43.478 0.00 0.00 36.77 4.85
783 847 3.510531 TGTCTGTCAGTAGAGTGGACT 57.489 47.619 0.00 0.00 32.84 3.85
846 923 2.570442 GGAGAAAGCGAGTACTCCTG 57.430 55.000 17.23 5.39 43.64 3.86
848 925 1.202582 GAGAAAGCGAGTACTCCTGCA 59.797 52.381 20.47 0.00 0.00 4.41
849 926 1.203523 AGAAAGCGAGTACTCCTGCAG 59.796 52.381 20.47 6.78 0.00 4.41
881 964 9.862585 CTGGTTGAATAAACAAATTAACAAAGC 57.137 29.630 0.00 0.00 40.86 3.51
917 1004 3.309954 GTGATGGAGGATACGTGCTTTTC 59.690 47.826 0.00 0.00 46.39 2.29
944 1031 4.341783 GCAGAGCAGGGTGGCACT 62.342 66.667 18.45 0.00 34.98 4.40
980 1067 3.645268 AAACGCCATCCTGCCTCCC 62.645 63.158 0.00 0.00 0.00 4.30
1051 1138 2.505167 GCGCCGGAATACTAGGGGT 61.505 63.158 5.05 0.00 39.76 4.95
1151 1246 1.048601 CTCCCCGAATGCCTTAGCTA 58.951 55.000 0.00 0.00 40.80 3.32
1160 1255 4.558496 CGAATGCCTTAGCTAGAAGAGAGG 60.558 50.000 2.95 2.95 40.80 3.69
1300 1407 0.664224 GATCCTCGTCGTCTCTTCCC 59.336 60.000 0.00 0.00 0.00 3.97
1319 1426 2.413963 CCGGGCGATTGCATTTGGA 61.414 57.895 7.38 0.00 45.35 3.53
1449 1557 4.759693 CACAAGGTTAGTTGGTGCTGAATA 59.240 41.667 0.00 0.00 0.00 1.75
1498 1606 1.303282 GCTTTTCCCCATCCCTCGT 59.697 57.895 0.00 0.00 0.00 4.18
1552 1668 1.412710 TGTTTGTCTTGCTCTCCGTCT 59.587 47.619 0.00 0.00 0.00 4.18
1725 1846 4.935205 CACGACCTGATTATGAACAAGGAA 59.065 41.667 0.00 0.00 0.00 3.36
1989 2110 3.676605 ATGTCCGACGACCACGCA 61.677 61.111 0.00 0.00 43.96 5.24
2310 2431 1.579429 GTTCACCCGTGTCATTGCC 59.421 57.895 0.00 0.00 0.00 4.52
2361 2482 1.764054 CCTCGAGGGGGCTCTCATT 60.764 63.158 24.62 0.00 33.59 2.57
2412 2533 4.662961 CGCTCTGACCGGCACACA 62.663 66.667 0.00 0.00 0.00 3.72
3317 3441 1.587933 GAGAGGAAGACGGCGACAGT 61.588 60.000 16.62 0.00 0.00 3.55
3708 3838 4.797471 TGATTCTTTGCTTCGATTTGTGG 58.203 39.130 0.00 0.00 0.00 4.17
3790 3920 1.800586 CGTTGTAGCAGTGCACAATCT 59.199 47.619 25.38 14.40 34.33 2.40
3791 3921 2.224079 CGTTGTAGCAGTGCACAATCTT 59.776 45.455 25.38 6.27 34.33 2.40
3797 3927 2.417933 AGCAGTGCACAATCTTTCGATC 59.582 45.455 21.04 0.00 0.00 3.69
3798 3928 2.160219 GCAGTGCACAATCTTTCGATCA 59.840 45.455 21.04 0.00 0.00 2.92
3801 3931 3.434641 AGTGCACAATCTTTCGATCAGTG 59.565 43.478 21.04 0.00 38.02 3.66
3802 3932 3.187227 GTGCACAATCTTTCGATCAGTGT 59.813 43.478 13.17 0.00 37.64 3.55
3803 3933 3.433274 TGCACAATCTTTCGATCAGTGTC 59.567 43.478 0.00 0.00 37.64 3.67
3804 3934 3.433274 GCACAATCTTTCGATCAGTGTCA 59.567 43.478 0.00 0.00 37.64 3.58
3934 4074 4.336993 CGAGACACTGAACTAGGCTAAGAT 59.663 45.833 0.00 0.00 0.00 2.40
4158 4299 2.743928 GTGCTCACCAGCCCGAAG 60.744 66.667 0.00 0.00 46.26 3.79
4533 4674 2.037367 TAGCACTGGAGGACCGCT 59.963 61.111 0.00 0.00 39.42 5.52
4643 4784 4.432741 GGGCTCTTGGCAGACCCC 62.433 72.222 5.21 3.94 44.01 4.95
4681 4822 3.044305 GGCCGCACTGAGTGTCAC 61.044 66.667 14.82 3.54 35.75 3.67
4703 4844 3.925238 CGATACGCTGCCCGCAAC 61.925 66.667 0.00 0.00 41.76 4.17
4709 4850 2.980233 GCTGCCCGCAACAGAAGT 60.980 61.111 2.03 0.00 37.32 3.01
4846 4987 3.976701 CTGGCGGCGGTGAGGAAAT 62.977 63.158 9.78 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.548904 AGTGGTAGATAGATCACGACGC 59.451 50.000 0.00 0.00 35.50 5.19
83 84 1.705450 TAGAGGGAGGGAGGGAGGG 60.705 68.421 0.00 0.00 0.00 4.30
84 85 1.544703 GTAGAGGGAGGGAGGGAGG 59.455 68.421 0.00 0.00 0.00 4.30
238 239 1.314730 TTGAACTTTGAACTCGGGCC 58.685 50.000 0.00 0.00 0.00 5.80
317 340 1.102978 GTCCATGCCACCATTACCAC 58.897 55.000 0.00 0.00 0.00 4.16
398 424 6.401367 GGTTAATTAAGCGCTAACAACGAGAA 60.401 38.462 12.05 0.00 0.00 2.87
419 445 5.818857 GCATTAGATTAACCCAACTCGGTTA 59.181 40.000 0.00 0.00 44.50 2.85
421 447 4.196971 GCATTAGATTAACCCAACTCGGT 58.803 43.478 0.00 0.00 37.93 4.69
424 461 3.003378 GCGGCATTAGATTAACCCAACTC 59.997 47.826 0.00 0.00 0.00 3.01
459 497 0.459237 GCTGTCTGTCTGGATCACGG 60.459 60.000 0.00 0.00 0.00 4.94
474 512 0.529833 CTGTCTGTCTGGATCGCTGT 59.470 55.000 0.00 0.00 0.00 4.40
476 514 1.515020 GCTGTCTGTCTGGATCGCT 59.485 57.895 0.00 0.00 0.00 4.93
477 515 1.520342 GGCTGTCTGTCTGGATCGC 60.520 63.158 0.00 0.00 0.00 4.58
478 516 0.102120 GAGGCTGTCTGTCTGGATCG 59.898 60.000 0.00 0.00 0.00 3.69
479 517 1.136695 CAGAGGCTGTCTGTCTGGATC 59.863 57.143 0.00 0.00 46.89 3.36
480 518 1.193323 CAGAGGCTGTCTGTCTGGAT 58.807 55.000 0.00 0.00 46.89 3.41
481 519 2.663566 CAGAGGCTGTCTGTCTGGA 58.336 57.895 0.00 0.00 46.89 3.86
488 526 2.383855 GTAGTGATCCAGAGGCTGTCT 58.616 52.381 0.00 0.00 35.00 3.41
489 527 1.410882 GGTAGTGATCCAGAGGCTGTC 59.589 57.143 0.00 0.00 0.00 3.51
490 528 1.273267 TGGTAGTGATCCAGAGGCTGT 60.273 52.381 0.00 0.00 0.00 4.40
491 529 1.489481 TGGTAGTGATCCAGAGGCTG 58.511 55.000 0.00 0.00 0.00 4.85
492 530 2.045524 CATGGTAGTGATCCAGAGGCT 58.954 52.381 0.00 0.00 38.42 4.58
493 531 1.542108 GCATGGTAGTGATCCAGAGGC 60.542 57.143 0.00 0.00 38.42 4.70
494 532 2.045524 AGCATGGTAGTGATCCAGAGG 58.954 52.381 0.00 0.00 38.42 3.69
495 533 4.148079 TCTAGCATGGTAGTGATCCAGAG 58.852 47.826 26.66 4.93 38.42 3.35
496 534 4.148079 CTCTAGCATGGTAGTGATCCAGA 58.852 47.826 26.66 10.07 38.42 3.86
512 550 4.315803 TCAGTTTGTAAACCAGCTCTAGC 58.684 43.478 4.00 0.00 39.71 3.42
541 579 7.672983 ACATTTTTACAGTGTACTCATCTGG 57.327 36.000 1.43 0.00 34.02 3.86
542 580 9.385902 CAAACATTTTTACAGTGTACTCATCTG 57.614 33.333 1.43 0.00 35.60 2.90
543 581 8.567948 CCAAACATTTTTACAGTGTACTCATCT 58.432 33.333 1.43 0.00 0.00 2.90
544 582 7.326063 GCCAAACATTTTTACAGTGTACTCATC 59.674 37.037 1.43 0.00 0.00 2.92
545 583 7.145323 GCCAAACATTTTTACAGTGTACTCAT 58.855 34.615 1.43 0.00 0.00 2.90
546 584 6.500041 GCCAAACATTTTTACAGTGTACTCA 58.500 36.000 1.43 0.00 0.00 3.41
547 585 5.623673 CGCCAAACATTTTTACAGTGTACTC 59.376 40.000 1.43 0.00 0.00 2.59
548 586 5.066764 ACGCCAAACATTTTTACAGTGTACT 59.933 36.000 1.43 0.00 0.00 2.73
549 587 5.275494 ACGCCAAACATTTTTACAGTGTAC 58.725 37.500 1.43 0.00 0.00 2.90
597 660 2.817844 GGGCAGTTTCCAAACGTAGAAT 59.182 45.455 0.00 0.00 43.51 2.40
598 661 2.223745 GGGCAGTTTCCAAACGTAGAA 58.776 47.619 0.00 0.00 43.51 2.10
599 662 1.543871 GGGGCAGTTTCCAAACGTAGA 60.544 52.381 0.00 0.00 43.51 2.59
602 665 2.190841 CGGGGCAGTTTCCAAACGT 61.191 57.895 0.00 0.00 43.51 3.99
617 680 1.063469 CATAAAACTTGTAGCGCCGGG 59.937 52.381 2.29 0.00 0.00 5.73
808 872 6.169557 TCTCCTAAACTACAGTTTGAGCAA 57.830 37.500 15.87 0.42 46.56 3.91
846 923 6.572848 TGTTTATTCAACCAGCAGCACTGC 62.573 45.833 14.79 14.79 45.78 4.40
848 925 3.221771 TGTTTATTCAACCAGCAGCACT 58.778 40.909 0.00 0.00 33.97 4.40
849 926 3.641437 TGTTTATTCAACCAGCAGCAC 57.359 42.857 0.00 0.00 33.97 4.40
917 1004 1.306642 CCTGCTCTGCTCTTTGCCTG 61.307 60.000 0.00 0.00 42.00 4.85
929 1016 3.699894 CGAGTGCCACCCTGCTCT 61.700 66.667 0.00 0.00 37.76 4.09
944 1031 3.263261 GTTTTTGGTTTTCTTTGGGCGA 58.737 40.909 0.00 0.00 0.00 5.54
980 1067 1.466858 ATAGGAGGGAGGAGGGAGAG 58.533 60.000 0.00 0.00 0.00 3.20
1089 1180 0.687354 GTGGAAGGAGCAGGAGAACA 59.313 55.000 0.00 0.00 0.00 3.18
1117 1212 2.158959 GGAGTGACGAACGGATGCG 61.159 63.158 4.58 4.58 0.00 4.73
1151 1246 1.254284 CCGCAGACACCCTCTCTTCT 61.254 60.000 0.00 0.00 0.00 2.85
1160 1255 3.718210 GACGATCCCCGCAGACACC 62.718 68.421 0.00 0.00 43.32 4.16
1300 1407 2.104729 CAAATGCAATCGCCCGGG 59.895 61.111 19.09 19.09 37.32 5.73
1449 1557 4.223700 TCATGGCAGAGTAGAGACAACAAT 59.776 41.667 0.00 0.00 0.00 2.71
1498 1606 1.347707 CTGGAACTGTTGCTACCAGGA 59.652 52.381 13.23 0.00 42.77 3.86
1552 1668 1.944234 TACGAGCGAGATTGGCAGCA 61.944 55.000 0.00 0.00 0.00 4.41
2214 2335 0.037419 CATTTTTCTTGTGGCGGGGG 60.037 55.000 0.00 0.00 0.00 5.40
2284 2405 4.619227 ACGGGTGAACGTGGCCAG 62.619 66.667 5.11 2.58 46.64 4.85
2451 2572 3.376935 CTTCTGGTCGCCATCCGCT 62.377 63.158 0.00 0.00 36.73 5.52
2700 2821 1.428620 GTCGTAGAGCGTCTCCACC 59.571 63.158 3.66 0.00 42.13 4.61
3317 3441 4.854924 CATGTCCGGCCGCCATCA 62.855 66.667 22.85 15.45 0.00 3.07
3708 3838 4.162888 TCCTAGGAAAACCCCTCGTATTTC 59.837 45.833 9.71 0.00 37.74 2.17
3790 3920 3.681417 CAGCAAGATGACACTGATCGAAA 59.319 43.478 0.00 0.00 31.67 3.46
3791 3921 3.256558 CAGCAAGATGACACTGATCGAA 58.743 45.455 0.00 0.00 31.67 3.71
3797 3927 2.768253 TACCCAGCAAGATGACACTG 57.232 50.000 0.00 0.00 0.00 3.66
3798 3928 3.614092 CATTACCCAGCAAGATGACACT 58.386 45.455 0.00 0.00 0.00 3.55
3801 3931 2.368439 TGCATTACCCAGCAAGATGAC 58.632 47.619 0.00 0.00 37.90 3.06
3802 3932 2.804986 TGCATTACCCAGCAAGATGA 57.195 45.000 0.00 0.00 37.90 2.92
3803 3933 2.953648 TGATGCATTACCCAGCAAGATG 59.046 45.455 0.00 0.00 44.88 2.90
3804 3934 3.301794 TGATGCATTACCCAGCAAGAT 57.698 42.857 0.00 0.00 44.88 2.40
3909 4039 2.088423 AGCCTAGTTCAGTGTCTCGAG 58.912 52.381 5.93 5.93 0.00 4.04
3997 4138 1.674322 ACCATTTCAAGGACGGCGG 60.674 57.895 13.24 0.00 0.00 6.13
4284 4425 0.041386 AGGAGGCCTACGAGAAGGTT 59.959 55.000 10.07 0.00 39.02 3.50
4433 4574 3.974757 GGTACTCCGGGATCGCCG 61.975 72.222 13.78 13.78 33.83 6.46
4667 4808 0.941463 GACCAGTGACACTCAGTGCG 60.941 60.000 4.13 0.00 44.38 5.34
4681 4822 2.279517 GGGCAGCGTATCGACCAG 60.280 66.667 0.00 0.00 0.00 4.00
4756 4897 1.517257 CGAAGACCCGCTGCTACAG 60.517 63.158 0.00 0.00 34.12 2.74


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

AutoCloner maintained by Alex Coulton.