Multiple sequence alignment - TraesCS1D01G426100

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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 TraesCS1D01G426100 chr1D 100.000 2990 0 0 1 2990 479518529 479521518 0.000000e+00 5522.0
1 TraesCS1D01G426100 chr1D 82.090 134 14 5 762 889 479518946 479519075 4.080000e-19 106.0
2 TraesCS1D01G426100 chr1D 82.090 134 14 5 418 547 479519290 479519417 4.080000e-19 106.0
3 TraesCS1D01G426100 chr1B 93.328 2443 108 26 587 2990 667715577 667718003 0.000000e+00 3557.0
4 TraesCS1D01G426100 chr1B 80.567 247 38 9 1928 2169 667724838 667725079 6.580000e-42 182.0
5 TraesCS1D01G426100 chr1B 84.828 145 20 2 28 172 589979808 589979666 8.640000e-31 145.0
6 TraesCS1D01G426100 chr1B 80.000 195 32 7 40 231 497475904 497475714 1.450000e-28 137.0
7 TraesCS1D01G426100 chr1A 94.840 1686 44 11 762 2409 575776427 575778107 0.000000e+00 2591.0
8 TraesCS1D01G426100 chr1A 91.082 527 26 9 2466 2990 575778103 575778610 0.000000e+00 693.0
9 TraesCS1D01G426100 chr1A 83.811 593 51 20 16 577 575776027 575776605 3.420000e-144 521.0
10 TraesCS1D01G426100 chr1A 82.114 246 34 10 1928 2169 575779454 575779693 5.050000e-48 202.0
11 TraesCS1D01G426100 chr3D 81.553 206 36 2 34 239 17703115 17702912 5.130000e-38 169.0
12 TraesCS1D01G426100 chr3D 76.440 191 42 2 46 236 523341151 523341338 1.900000e-17 100.0
13 TraesCS1D01G426100 chr7B 79.812 213 39 4 25 236 106277638 106277847 5.160000e-33 152.0
14 TraesCS1D01G426100 chrUn 83.217 143 22 2 34 176 37701450 37701310 2.420000e-26 130.0
15 TraesCS1D01G426100 chr3A 76.974 152 25 7 587 737 724933474 724933616 8.890000e-11 78.7
16 TraesCS1D01G426100 chr3A 76.316 152 26 7 587 737 724892371 724892513 4.130000e-09 73.1


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 TraesCS1D01G426100 chr1D 479518529 479521518 2989 False 1911.333333 5522 88.06000 1 2990 3 chr1D.!!$F1 2989
1 TraesCS1D01G426100 chr1B 667715577 667718003 2426 False 3557.000000 3557 93.32800 587 2990 1 chr1B.!!$F1 2403
2 TraesCS1D01G426100 chr1A 575776027 575779693 3666 False 1001.750000 2591 87.96175 16 2990 4 chr1A.!!$F1 2974

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
580 594 0.178973 GCCAACCCCACCTTAACAGT 60.179 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2478 0.468226 TGCTAATAGCTTCCCACCCG 59.532 55.0 13.88 0.0 42.97 5.28 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
30 31 4.629092 TGCATAGTCTTGAGCTCATCATC 58.371 43.478 19.04 8.74 37.89 2.92
35 36 0.529337 CTTGAGCTCATCATCGCCGT 60.529 55.000 19.04 0.00 37.89 5.68
79 80 2.899044 CGCCCGGAGCAAAACGAAA 61.899 57.895 0.73 0.00 44.04 3.46
83 84 1.472990 CCGGAGCAAAACGAAACAAC 58.527 50.000 0.00 0.00 0.00 3.32
84 85 1.064952 CCGGAGCAAAACGAAACAACT 59.935 47.619 0.00 0.00 0.00 3.16
85 86 2.108700 CGGAGCAAAACGAAACAACTG 58.891 47.619 0.00 0.00 0.00 3.16
90 91 4.905269 AGCAAAACGAAACAACTGTAGAC 58.095 39.130 0.00 0.00 0.00 2.59
100 101 4.162690 CTGTAGACAGGGGCCGGC 62.163 72.222 21.18 21.18 40.20 6.13
102 103 4.162690 GTAGACAGGGGCCGGCAG 62.163 72.222 30.85 17.05 0.00 4.85
104 105 3.305619 TAGACAGGGGCCGGCAGTA 62.306 63.158 30.85 5.14 0.00 2.74
156 157 0.827368 GGCTTAGGCAGTAGCAGACT 59.173 55.000 0.00 0.00 44.61 3.24
164 165 2.510238 GTAGCAGACTGGGCGCAG 60.510 66.667 27.57 27.57 36.08 5.18
179 180 2.663796 CAGCAGCAGGAGCAGACT 59.336 61.111 0.00 0.00 45.49 3.24
183 184 1.821936 CAGCAGGAGCAGACTAGGG 59.178 63.158 0.00 0.00 45.49 3.53
186 187 1.903877 GCAGGAGCAGACTAGGGCAA 61.904 60.000 0.00 0.00 41.58 4.52
190 191 0.742635 GAGCAGACTAGGGCAAGTGC 60.743 60.000 0.00 0.00 41.14 4.40
244 245 2.508439 CGCCACGCTACAACGGAT 60.508 61.111 0.00 0.00 37.37 4.18
245 246 2.798501 CGCCACGCTACAACGGATG 61.799 63.158 0.00 0.00 37.37 3.51
247 248 2.461110 CCACGCTACAACGGATGCC 61.461 63.158 0.00 0.00 37.37 4.40
287 297 4.463879 CCTCGGCAGACCAGCTGG 62.464 72.222 31.60 31.60 45.03 4.85
292 302 2.587247 GGCAGACCAGCTGGAGACA 61.587 63.158 39.19 0.00 45.03 3.41
324 334 2.364579 TAACCGGCCCGTCCTGAT 60.365 61.111 0.00 0.00 0.00 2.90
354 364 4.454504 CGGGTTGCTTAATGTAAGAGTTGT 59.545 41.667 0.00 0.00 38.02 3.32
409 421 1.614413 AGTTTCAGACCTCACCGTCTC 59.386 52.381 0.00 0.00 41.23 3.36
415 427 1.978580 AGACCTCACCGTCTCCAAAAT 59.021 47.619 0.00 0.00 38.83 1.82
429 441 7.275560 CCGTCTCCAAAATTCCATAATCAAAAC 59.724 37.037 0.00 0.00 0.00 2.43
538 552 9.657419 AATTGATTTTGGAAAGTGATAATGGTC 57.343 29.630 0.00 0.00 0.00 4.02
539 553 7.773489 TGATTTTGGAAAGTGATAATGGTCA 57.227 32.000 0.00 0.00 0.00 4.02
540 554 8.365060 TGATTTTGGAAAGTGATAATGGTCAT 57.635 30.769 0.00 0.00 0.00 3.06
541 555 8.469200 TGATTTTGGAAAGTGATAATGGTCATC 58.531 33.333 0.00 0.00 0.00 2.92
542 556 6.435430 TTTGGAAAGTGATAATGGTCATCG 57.565 37.500 0.00 0.00 0.00 3.84
543 557 5.351948 TGGAAAGTGATAATGGTCATCGA 57.648 39.130 0.00 0.00 0.00 3.59
544 558 5.928976 TGGAAAGTGATAATGGTCATCGAT 58.071 37.500 0.00 0.00 0.00 3.59
545 559 5.991606 TGGAAAGTGATAATGGTCATCGATC 59.008 40.000 0.00 0.00 0.00 3.69
546 560 5.119279 GGAAAGTGATAATGGTCATCGATCG 59.881 44.000 9.36 9.36 0.00 3.69
547 561 3.579709 AGTGATAATGGTCATCGATCGC 58.420 45.455 11.09 0.00 0.00 4.58
548 562 2.668457 GTGATAATGGTCATCGATCGCC 59.332 50.000 11.09 6.38 0.00 5.54
549 563 2.298729 TGATAATGGTCATCGATCGCCA 59.701 45.455 16.87 16.87 35.28 5.69
550 564 2.438868 TAATGGTCATCGATCGCCAG 57.561 50.000 18.68 2.44 34.18 4.85
551 565 0.250038 AATGGTCATCGATCGCCAGG 60.250 55.000 18.68 0.00 34.18 4.45
552 566 2.663188 GGTCATCGATCGCCAGGC 60.663 66.667 11.09 0.00 0.00 4.85
553 567 2.663188 GTCATCGATCGCCAGGCC 60.663 66.667 11.09 0.00 0.00 5.19
554 568 4.284860 TCATCGATCGCCAGGCCG 62.285 66.667 11.09 3.74 0.00 6.13
577 591 4.107029 GGCCAACCCCACCTTAAC 57.893 61.111 0.00 0.00 0.00 2.01
578 592 1.154221 GGCCAACCCCACCTTAACA 59.846 57.895 0.00 0.00 0.00 2.41
579 593 0.898326 GGCCAACCCCACCTTAACAG 60.898 60.000 0.00 0.00 0.00 3.16
580 594 0.178973 GCCAACCCCACCTTAACAGT 60.179 55.000 0.00 0.00 0.00 3.55
581 595 1.905637 CCAACCCCACCTTAACAGTC 58.094 55.000 0.00 0.00 0.00 3.51
582 596 1.144093 CCAACCCCACCTTAACAGTCA 59.856 52.381 0.00 0.00 0.00 3.41
583 597 2.225017 CCAACCCCACCTTAACAGTCAT 60.225 50.000 0.00 0.00 0.00 3.06
584 598 3.009695 CCAACCCCACCTTAACAGTCATA 59.990 47.826 0.00 0.00 0.00 2.15
585 599 4.507691 CCAACCCCACCTTAACAGTCATAA 60.508 45.833 0.00 0.00 0.00 1.90
586 600 5.261216 CAACCCCACCTTAACAGTCATAAT 58.739 41.667 0.00 0.00 0.00 1.28
587 601 5.530176 ACCCCACCTTAACAGTCATAATT 57.470 39.130 0.00 0.00 0.00 1.40
588 602 5.261216 ACCCCACCTTAACAGTCATAATTG 58.739 41.667 0.00 0.00 0.00 2.32
589 603 5.222254 ACCCCACCTTAACAGTCATAATTGT 60.222 40.000 0.00 0.00 0.00 2.71
590 604 5.714806 CCCCACCTTAACAGTCATAATTGTT 59.285 40.000 0.00 0.00 38.66 2.83
591 605 6.350110 CCCCACCTTAACAGTCATAATTGTTG 60.350 42.308 0.48 0.00 36.19 3.33
596 610 9.295825 ACCTTAACAGTCATAATTGTTGAATGA 57.704 29.630 20.48 5.88 40.61 2.57
599 613 9.986833 TTAACAGTCATAATTGTTGAATGATCG 57.013 29.630 20.48 6.50 40.61 3.69
600 614 7.615582 ACAGTCATAATTGTTGAATGATCGT 57.384 32.000 20.48 6.97 40.61 3.73
612 626 4.494484 TGAATGATCGTCGATGTGTTTCT 58.506 39.130 13.54 0.00 0.00 2.52
679 701 8.353423 ACAATATTCTTGTTGCAAAGAGGTAT 57.647 30.769 0.00 2.05 37.48 2.73
680 702 8.246180 ACAATATTCTTGTTGCAAAGAGGTATG 58.754 33.333 0.00 3.13 37.48 2.39
684 706 2.806434 TGTTGCAAAGAGGTATGGCAT 58.194 42.857 4.88 4.88 34.03 4.40
708 730 2.103771 TGAGCAACCTAGATCAGATGGC 59.896 50.000 0.00 0.00 29.40 4.40
716 738 0.821301 AGATCAGATGGCTCGCGAGA 60.821 55.000 38.74 20.29 39.12 4.04
730 752 0.526954 GCGAGACGGCGGATCTTTTA 60.527 55.000 13.24 0.00 0.00 1.52
731 753 1.478137 CGAGACGGCGGATCTTTTAG 58.522 55.000 13.24 0.00 0.00 1.85
735 757 3.522553 AGACGGCGGATCTTTTAGAAAG 58.477 45.455 13.24 0.00 0.00 2.62
736 758 3.194968 AGACGGCGGATCTTTTAGAAAGA 59.805 43.478 13.24 5.67 0.00 2.52
737 759 3.259902 ACGGCGGATCTTTTAGAAAGAC 58.740 45.455 13.24 1.31 0.00 3.01
738 760 2.608090 CGGCGGATCTTTTAGAAAGACC 59.392 50.000 0.00 8.08 0.00 3.85
741 763 2.608090 CGGATCTTTTAGAAAGACCGCC 59.392 50.000 20.41 14.52 35.71 6.13
742 764 2.608090 GGATCTTTTAGAAAGACCGCCG 59.392 50.000 5.34 0.00 0.00 6.46
778 801 2.755655 TGCCCCATAACCAAAACATACG 59.244 45.455 0.00 0.00 0.00 3.06
780 803 3.181494 GCCCCATAACCAAAACATACGTC 60.181 47.826 0.00 0.00 0.00 4.34
790 813 6.158598 ACCAAAACATACGTCGTAGTACAAT 58.841 36.000 11.31 0.00 0.00 2.71
905 929 3.001514 GGCTTCAGATCCAGGCCA 58.998 61.111 5.01 0.00 42.08 5.36
906 930 1.304282 GGCTTCAGATCCAGGCCAA 59.696 57.895 5.01 0.00 42.08 4.52
1641 1689 4.815308 CACATGTTCATGATCTTCTCCCTC 59.185 45.833 17.96 0.00 0.00 4.30
1910 1961 4.960866 CCAGCAGCAGCACCACCA 62.961 66.667 3.17 0.00 45.49 4.17
1911 1962 3.667282 CAGCAGCAGCACCACCAC 61.667 66.667 3.17 0.00 45.49 4.16
1912 1963 4.962836 AGCAGCAGCACCACCACC 62.963 66.667 3.17 0.00 45.49 4.61
1929 1980 0.748367 ACCATCAGCATCAGCAGCAG 60.748 55.000 0.00 0.00 45.49 4.24
2123 2174 2.461300 TTGGACAGGAGGATCTCGAT 57.539 50.000 0.00 0.00 33.73 3.59
2219 2275 5.279306 GCCCTAGACATATTTGTATCCGACA 60.279 44.000 0.00 0.00 35.79 4.35
2333 2390 5.009310 TCCATGCATTGTCAAAGATATCTGC 59.991 40.000 5.86 4.23 0.00 4.26
2476 2542 1.799916 CGTGTAGACATGCGCGTGA 60.800 57.895 34.95 11.20 39.74 4.35
2551 2617 1.065998 TGCTGCATCATACAGTCTGCA 60.066 47.619 0.00 0.00 41.98 4.41
2552 2618 2.219458 GCTGCATCATACAGTCTGCAT 58.781 47.619 0.00 0.00 43.12 3.96
2553 2619 2.223611 GCTGCATCATACAGTCTGCATC 59.776 50.000 0.00 0.00 43.12 3.91
2554 2620 3.463944 CTGCATCATACAGTCTGCATCA 58.536 45.455 0.00 0.00 43.12 3.07
2581 2647 3.525537 CGTGATGGTATCTGAAGCAGTT 58.474 45.455 0.00 0.00 32.61 3.16
2598 2664 8.585881 TGAAGCAGTTAAGTCTGTTAGAGTATT 58.414 33.333 0.00 0.00 37.70 1.89
2624 2690 5.814188 TCACAAAGATCATCACATAGCTCAC 59.186 40.000 0.00 0.00 0.00 3.51
2783 2850 1.207488 AGGGCTGGTATGTTGCCTGA 61.207 55.000 0.00 0.00 45.45 3.86
2862 2929 1.251527 ACGCAAGACATCCTCGGAGT 61.252 55.000 4.02 0.00 43.62 3.85
2907 2978 2.099756 GTGATGCCTTGGGTTTCATAGC 59.900 50.000 0.00 0.00 0.00 2.97
2941 3012 5.824904 AGTGTGTTGCTCATCCATAATTC 57.175 39.130 0.00 0.00 0.00 2.17
2971 3042 3.098377 TCATCCATGATTTTGGTGGTGG 58.902 45.455 0.00 0.00 38.01 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.156645 GCTCAAGACTATGCAGGCGG 61.157 60.000 0.00 0.00 33.60 6.13
4 5 0.179089 AGCTCAAGACTATGCAGGCG 60.179 55.000 0.00 0.00 33.60 5.52
7 8 4.056092 TGATGAGCTCAAGACTATGCAG 57.944 45.455 22.50 0.00 0.00 4.41
8 9 4.629092 GATGATGAGCTCAAGACTATGCA 58.371 43.478 22.50 9.07 37.44 3.96
9 10 3.674281 CGATGATGAGCTCAAGACTATGC 59.326 47.826 22.50 4.31 37.44 3.14
10 11 3.674281 GCGATGATGAGCTCAAGACTATG 59.326 47.826 22.50 8.77 37.44 2.23
11 12 3.305950 GGCGATGATGAGCTCAAGACTAT 60.306 47.826 22.50 10.52 37.44 2.12
12 13 2.035193 GGCGATGATGAGCTCAAGACTA 59.965 50.000 22.50 5.87 37.44 2.59
13 14 1.202510 GGCGATGATGAGCTCAAGACT 60.203 52.381 22.50 3.33 37.44 3.24
14 15 1.216122 GGCGATGATGAGCTCAAGAC 58.784 55.000 22.50 15.26 37.44 3.01
35 36 1.529226 CGGTGTTTGCCATGGTAAGA 58.471 50.000 15.25 5.05 0.00 2.10
64 65 1.064952 AGTTGTTTCGTTTTGCTCCGG 59.935 47.619 0.00 0.00 0.00 5.14
68 69 4.393680 TGTCTACAGTTGTTTCGTTTTGCT 59.606 37.500 0.00 0.00 0.00 3.91
69 70 4.654015 TGTCTACAGTTGTTTCGTTTTGC 58.346 39.130 0.00 0.00 0.00 3.68
75 76 2.413837 CCCCTGTCTACAGTTGTTTCG 58.586 52.381 9.17 0.00 42.27 3.46
79 80 1.827399 CGGCCCCTGTCTACAGTTGT 61.827 60.000 9.17 0.00 42.27 3.32
83 84 4.162690 GCCGGCCCCTGTCTACAG 62.163 72.222 18.11 3.02 43.40 2.74
85 86 4.162690 CTGCCGGCCCCTGTCTAC 62.163 72.222 26.77 0.00 0.00 2.59
100 101 3.112075 CACGTGGCTGCGGTACTG 61.112 66.667 7.95 0.00 35.98 2.74
101 102 4.373116 CCACGTGGCTGCGGTACT 62.373 66.667 24.02 0.00 35.98 2.73
108 109 3.636231 TTCCCTCCCACGTGGCTG 61.636 66.667 29.75 21.51 0.00 4.85
110 111 3.268103 ATGTTCCCTCCCACGTGGC 62.268 63.158 29.75 13.91 0.00 5.01
111 112 1.078426 GATGTTCCCTCCCACGTGG 60.078 63.158 28.26 28.26 0.00 4.94
112 113 1.078426 GGATGTTCCCTCCCACGTG 60.078 63.158 9.08 9.08 0.00 4.49
160 161 4.754667 TCTGCTCCTGCTGCTGCG 62.755 66.667 11.21 5.84 43.34 5.18
161 162 2.236223 TAGTCTGCTCCTGCTGCTGC 62.236 60.000 8.89 8.89 40.48 5.25
164 165 1.143620 CCTAGTCTGCTCCTGCTGC 59.856 63.158 0.00 0.00 40.48 5.25
223 224 3.788766 GTTGTAGCGTGGCGGCTG 61.789 66.667 11.43 3.72 44.50 4.85
275 285 0.952984 GTTGTCTCCAGCTGGTCTGC 60.953 60.000 31.58 19.58 41.50 4.26
285 295 1.285950 CTGCGACGAGTTGTCTCCA 59.714 57.895 8.89 5.04 45.87 3.86
287 297 2.089349 GGCTGCGACGAGTTGTCTC 61.089 63.158 8.89 1.13 45.87 3.36
292 302 1.080025 GTTAGGGCTGCGACGAGTT 60.080 57.895 0.00 0.00 0.00 3.01
313 323 1.369321 GATCTGGATCAGGACGGGC 59.631 63.158 5.79 0.00 37.74 6.13
318 328 1.123077 CAACCCGATCTGGATCAGGA 58.877 55.000 16.91 0.00 42.00 3.86
324 334 2.238646 ACATTAAGCAACCCGATCTGGA 59.761 45.455 10.54 0.00 42.00 3.86
409 421 9.889128 AGGTATGTTTTGATTATGGAATTTTGG 57.111 29.630 0.00 0.00 0.00 3.28
512 526 9.657419 GACCATTATCACTTTCCAAAATCAATT 57.343 29.630 0.00 0.00 0.00 2.32
513 527 8.814931 TGACCATTATCACTTTCCAAAATCAAT 58.185 29.630 0.00 0.00 0.00 2.57
514 528 8.187913 TGACCATTATCACTTTCCAAAATCAA 57.812 30.769 0.00 0.00 0.00 2.57
515 529 7.773489 TGACCATTATCACTTTCCAAAATCA 57.227 32.000 0.00 0.00 0.00 2.57
516 530 7.645340 CGATGACCATTATCACTTTCCAAAATC 59.355 37.037 0.00 0.00 0.00 2.17
517 531 7.339212 TCGATGACCATTATCACTTTCCAAAAT 59.661 33.333 0.00 0.00 0.00 1.82
518 532 6.657117 TCGATGACCATTATCACTTTCCAAAA 59.343 34.615 0.00 0.00 0.00 2.44
519 533 6.176896 TCGATGACCATTATCACTTTCCAAA 58.823 36.000 0.00 0.00 0.00 3.28
520 534 5.739959 TCGATGACCATTATCACTTTCCAA 58.260 37.500 0.00 0.00 0.00 3.53
521 535 5.351948 TCGATGACCATTATCACTTTCCA 57.648 39.130 0.00 0.00 0.00 3.53
522 536 5.119279 CGATCGATGACCATTATCACTTTCC 59.881 44.000 10.26 0.00 0.00 3.13
523 537 5.388890 GCGATCGATGACCATTATCACTTTC 60.389 44.000 21.57 0.00 0.00 2.62
524 538 4.449068 GCGATCGATGACCATTATCACTTT 59.551 41.667 21.57 0.00 0.00 2.66
525 539 3.990469 GCGATCGATGACCATTATCACTT 59.010 43.478 21.57 0.00 0.00 3.16
526 540 3.579709 GCGATCGATGACCATTATCACT 58.420 45.455 21.57 0.00 0.00 3.41
527 541 2.668457 GGCGATCGATGACCATTATCAC 59.332 50.000 21.57 0.00 0.00 3.06
528 542 2.298729 TGGCGATCGATGACCATTATCA 59.701 45.455 21.57 0.00 0.00 2.15
529 543 2.926200 CTGGCGATCGATGACCATTATC 59.074 50.000 21.57 0.00 0.00 1.75
530 544 2.354103 CCTGGCGATCGATGACCATTAT 60.354 50.000 21.57 0.00 0.00 1.28
531 545 1.000843 CCTGGCGATCGATGACCATTA 59.999 52.381 21.57 0.00 0.00 1.90
532 546 0.250038 CCTGGCGATCGATGACCATT 60.250 55.000 21.57 0.00 0.00 3.16
533 547 1.368950 CCTGGCGATCGATGACCAT 59.631 57.895 21.57 0.00 0.00 3.55
534 548 2.814604 CCTGGCGATCGATGACCA 59.185 61.111 21.57 15.39 0.00 4.02
535 549 2.663188 GCCTGGCGATCGATGACC 60.663 66.667 21.57 11.08 0.00 4.02
536 550 2.663188 GGCCTGGCGATCGATGAC 60.663 66.667 21.57 5.94 0.00 3.06
537 551 4.284860 CGGCCTGGCGATCGATGA 62.285 66.667 21.57 0.00 0.00 2.92
560 574 0.898326 CTGTTAAGGTGGGGTTGGCC 60.898 60.000 0.00 0.00 0.00 5.36
561 575 0.178973 ACTGTTAAGGTGGGGTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
562 576 1.144093 TGACTGTTAAGGTGGGGTTGG 59.856 52.381 0.00 0.00 0.00 3.77
563 577 2.649531 TGACTGTTAAGGTGGGGTTG 57.350 50.000 0.00 0.00 0.00 3.77
564 578 5.530176 ATTATGACTGTTAAGGTGGGGTT 57.470 39.130 0.00 0.00 0.00 4.11
565 579 5.222254 ACAATTATGACTGTTAAGGTGGGGT 60.222 40.000 0.00 0.00 0.00 4.95
566 580 5.261216 ACAATTATGACTGTTAAGGTGGGG 58.739 41.667 0.00 0.00 0.00 4.96
567 581 6.432783 TCAACAATTATGACTGTTAAGGTGGG 59.567 38.462 0.00 0.00 34.04 4.61
568 582 7.447374 TCAACAATTATGACTGTTAAGGTGG 57.553 36.000 0.00 0.00 34.04 4.61
569 583 9.345517 CATTCAACAATTATGACTGTTAAGGTG 57.654 33.333 0.00 0.00 34.04 4.00
570 584 9.295825 TCATTCAACAATTATGACTGTTAAGGT 57.704 29.630 9.26 0.00 34.04 3.50
573 587 9.986833 CGATCATTCAACAATTATGACTGTTAA 57.013 29.630 9.26 0.00 34.04 2.01
574 588 9.161629 ACGATCATTCAACAATTATGACTGTTA 57.838 29.630 0.00 0.00 34.04 2.41
575 589 8.044060 ACGATCATTCAACAATTATGACTGTT 57.956 30.769 0.00 3.74 36.19 3.16
576 590 7.464577 CGACGATCATTCAACAATTATGACTGT 60.465 37.037 0.00 3.59 31.66 3.55
577 591 6.842780 CGACGATCATTCAACAATTATGACTG 59.157 38.462 0.00 5.07 31.66 3.51
578 592 6.756542 TCGACGATCATTCAACAATTATGACT 59.243 34.615 0.00 0.00 31.66 3.41
579 593 6.933130 TCGACGATCATTCAACAATTATGAC 58.067 36.000 0.00 0.00 31.66 3.06
580 594 7.224557 ACATCGACGATCATTCAACAATTATGA 59.775 33.333 7.54 0.00 33.25 2.15
581 595 7.319615 CACATCGACGATCATTCAACAATTATG 59.680 37.037 7.54 0.00 0.00 1.90
582 596 7.011389 ACACATCGACGATCATTCAACAATTAT 59.989 33.333 7.54 0.00 0.00 1.28
583 597 6.312672 ACACATCGACGATCATTCAACAATTA 59.687 34.615 7.54 0.00 0.00 1.40
584 598 5.122239 ACACATCGACGATCATTCAACAATT 59.878 36.000 7.54 0.00 0.00 2.32
585 599 4.631377 ACACATCGACGATCATTCAACAAT 59.369 37.500 7.54 0.00 0.00 2.71
586 600 3.993736 ACACATCGACGATCATTCAACAA 59.006 39.130 7.54 0.00 0.00 2.83
587 601 3.584834 ACACATCGACGATCATTCAACA 58.415 40.909 7.54 0.00 0.00 3.33
588 602 4.584029 AACACATCGACGATCATTCAAC 57.416 40.909 7.54 0.00 0.00 3.18
589 603 4.929211 AGAAACACATCGACGATCATTCAA 59.071 37.500 7.54 0.00 0.00 2.69
590 604 4.327087 CAGAAACACATCGACGATCATTCA 59.673 41.667 7.54 0.00 0.00 2.57
591 605 4.562789 TCAGAAACACATCGACGATCATTC 59.437 41.667 7.54 9.74 0.00 2.67
596 610 4.055360 TGTTTCAGAAACACATCGACGAT 58.945 39.130 22.53 4.05 45.79 3.73
645 659 9.545105 TTGCAACAAGAATATTGTTTCAGAAAT 57.455 25.926 2.95 0.00 40.30 2.17
660 674 3.255642 GCCATACCTCTTTGCAACAAGAA 59.744 43.478 0.00 0.00 0.00 2.52
669 683 2.617308 CTCAGCATGCCATACCTCTTTG 59.383 50.000 15.66 1.63 34.76 2.77
679 701 0.393402 CTAGGTTGCTCAGCATGCCA 60.393 55.000 15.66 1.49 38.76 4.92
680 702 0.107508 TCTAGGTTGCTCAGCATGCC 60.108 55.000 15.66 6.40 38.76 4.40
684 706 2.460669 TCTGATCTAGGTTGCTCAGCA 58.539 47.619 0.00 0.00 36.04 4.41
716 738 3.259902 GTCTTTCTAAAAGATCCGCCGT 58.740 45.455 5.50 0.00 0.00 5.68
720 742 2.608090 GGCGGTCTTTCTAAAAGATCCG 59.392 50.000 23.72 23.72 40.51 4.18
721 743 2.608090 CGGCGGTCTTTCTAAAAGATCC 59.392 50.000 0.00 7.77 0.00 3.36
757 780 2.755655 CGTATGTTTTGGTTATGGGGCA 59.244 45.455 0.00 0.00 0.00 5.36
759 782 3.064271 CGACGTATGTTTTGGTTATGGGG 59.936 47.826 0.00 0.00 0.00 4.96
905 929 3.606687 CTGCGACTTATTAAGGTGGGTT 58.393 45.455 8.26 0.00 0.00 4.11
906 930 2.679930 GCTGCGACTTATTAAGGTGGGT 60.680 50.000 8.26 0.00 0.00 4.51
983 1019 3.026694 CCCATGGATGAGGAGGAAAAAC 58.973 50.000 15.22 0.00 0.00 2.43
1266 1314 3.396911 ATCGTGCGCGTCGATGACT 62.397 57.895 29.37 13.80 44.57 3.41
1284 1332 3.307906 CAGTGGAACGACGGGGGA 61.308 66.667 0.00 0.00 45.86 4.81
1910 1961 0.748367 CTGCTGCTGATGCTGATGGT 60.748 55.000 0.00 0.00 40.01 3.55
1911 1962 2.025719 CTGCTGCTGATGCTGATGG 58.974 57.895 0.00 0.00 40.01 3.51
1912 1963 1.356979 GCTGCTGCTGATGCTGATG 59.643 57.895 10.92 0.00 40.01 3.07
2123 2174 8.892723 CCAACTATAACTGATAATGAAGTTGCA 58.107 33.333 6.40 0.00 40.60 4.08
2333 2390 7.028962 TGTATCTTCGATCAAAAGCAATTTGG 58.971 34.615 13.11 1.02 46.85 3.28
2421 2478 0.468226 TGCTAATAGCTTCCCACCCG 59.532 55.000 13.88 0.00 42.97 5.28
2551 2617 3.196469 CAGATACCATCACGGCCTATGAT 59.804 47.826 12.42 12.42 39.03 2.45
2552 2618 2.562738 CAGATACCATCACGGCCTATGA 59.437 50.000 8.85 8.85 39.03 2.15
2553 2619 2.562738 TCAGATACCATCACGGCCTATG 59.437 50.000 0.00 0.00 39.03 2.23
2554 2620 2.889512 TCAGATACCATCACGGCCTAT 58.110 47.619 0.00 0.00 39.03 2.57
2598 2664 6.127253 TGAGCTATGTGATGATCTTTGTGAGA 60.127 38.462 0.00 0.00 39.13 3.27
2624 2690 6.726258 TGTGCAGTTTTACATGAGTATCTG 57.274 37.500 0.00 3.82 34.92 2.90
2709 2776 1.003580 GCCATGTCCAGGAGTTTCTGA 59.996 52.381 0.00 0.00 36.93 3.27
2774 2841 1.967535 CCTCGACTCTCAGGCAACA 59.032 57.895 0.00 0.00 41.41 3.33
2783 2850 1.153549 GCGGAATTGCCTCGACTCT 60.154 57.895 0.00 0.00 0.00 3.24
2907 2978 5.186996 AGCAACACACTTGTTTAGATTGG 57.813 39.130 0.00 0.00 43.89 3.16
2941 3012 5.473846 CCAAAATCATGGATGATCTCCTCAG 59.526 44.000 2.59 3.65 46.22 3.35
2971 3042 3.334054 AAGGGGGAGAGCCAGCAC 61.334 66.667 0.00 0.00 35.15 4.40


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

AutoCloner maintained by Alex Coulton.