Multiple sequence alignment - TraesCS3D01G099300

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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 TraesCS3D01G099300 chr3D 100.000 5890 0 0 1 5890 51038388 51044277 0.000000e+00 10877.0
1 TraesCS3D01G099300 chr3D 80.660 212 31 7 5684 5890 388330252 388330046 7.900000e-34 156.0
2 TraesCS3D01G099300 chr3A 95.069 5516 189 22 6 5477 63904809 63910285 0.000000e+00 8602.0
3 TraesCS3D01G099300 chr3A 96.804 219 7 0 5471 5689 63911723 63911941 3.350000e-97 366.0
4 TraesCS3D01G099300 chr3A 94.554 202 7 3 5685 5884 63912201 63912400 5.730000e-80 309.0
5 TraesCS3D01G099300 chr3A 83.226 155 19 5 5684 5832 509380486 509380333 1.030000e-27 135.0
6 TraesCS3D01G099300 chr3B 95.239 4285 115 21 35 4270 81812964 81817208 0.000000e+00 6700.0
7 TraesCS3D01G099300 chr3B 89.084 1310 65 22 4385 5689 81817504 81818740 0.000000e+00 1555.0
8 TraesCS3D01G099300 chr1D 72.561 492 110 20 2993 3469 108832553 108832072 2.860000e-28 137.0
9 TraesCS3D01G099300 chr1B 72.617 493 105 24 2993 3469 164711460 164710982 1.030000e-27 135.0
10 TraesCS3D01G099300 chr1A 72.358 492 111 20 2993 3469 112038384 112037903 1.330000e-26 132.0
11 TraesCS3D01G099300 chr2D 80.137 146 25 4 5745 5890 177355587 177355446 8.070000e-19 106.0
12 TraesCS3D01G099300 chr7B 86.667 75 9 1 5747 5821 530017519 530017592 1.360000e-11 82.4


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 TraesCS3D01G099300 chr3D 51038388 51044277 5889 False 10877.000000 10877 100.000000 1 5890 1 chr3D.!!$F1 5889
1 TraesCS3D01G099300 chr3A 63904809 63912400 7591 False 3092.333333 8602 95.475667 6 5884 3 chr3A.!!$F1 5878
2 TraesCS3D01G099300 chr3B 81812964 81818740 5776 False 4127.500000 6700 92.161500 35 5689 2 chr3B.!!$F1 5654

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
483 493 0.548989 TGGCTTGTAGGTGTGGTGTT 59.451 50.000 0.00 0.00 0.00 3.32 F
1137 1177 0.598065 ACCAATCTTTTCCTGCACGC 59.402 50.000 0.00 0.00 0.00 5.34 F
1931 1989 0.979709 TGGACCTCTGCCATCTCCAG 60.980 60.000 0.00 0.00 0.00 3.86 F
1954 2012 1.153168 AGCACAGCTTGTTCGTGGT 60.153 52.632 0.38 0.38 33.89 4.16 F
3504 3562 2.632028 TCTCATGCTCCCTCTAATGCTC 59.368 50.000 0.00 0.00 0.00 4.26 F
4325 4396 1.287739 CCCTCTCCCTCTGTCTCTCTT 59.712 57.143 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2012 1.154197 CAGACTCGGTCGACACTACA 58.846 55.000 18.91 0.00 37.67 2.74 R
3041 3099 1.077429 GAGGGATGGCAACCAGGTC 60.077 63.158 16.20 5.31 36.75 3.85 R
3437 3495 3.142174 GCTGTATATCCAACTCCCAAGC 58.858 50.000 0.00 0.00 0.00 4.01 R
3624 3683 4.141251 TGAGGTTTTAAAACAGCCTCCTCT 60.141 41.667 27.56 15.19 43.64 3.69 R
4642 4885 1.209128 CATTATCGTCCGCTGTCACC 58.791 55.000 0.00 0.00 0.00 4.02 R
5580 7272 0.252375 ACAGTTAGGCGGGGTTAGGA 60.252 55.000 0.00 0.00 0.00 2.94 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
107 108 1.616159 TTTCTAAGCAACTGGTGGGC 58.384 50.000 0.00 0.00 0.00 5.36
163 164 2.978010 CGTTTTCCCCGTGCTGCT 60.978 61.111 0.00 0.00 0.00 4.24
188 189 1.209261 TGGTCGCTGCCATTTCTGATA 59.791 47.619 0.00 0.00 32.81 2.15
235 236 4.441217 GGGATCTACGAAGTCAGGGTTTAC 60.441 50.000 0.00 0.00 43.93 2.01
369 371 1.220529 TTGTGAAGCAACTCGAGCTG 58.779 50.000 13.61 12.47 42.53 4.24
377 379 1.284657 CAACTCGAGCTGGTAGCATG 58.715 55.000 13.61 0.00 45.56 4.06
399 401 7.042523 GCATGACTTGTTCTAATTTTGCAGTTT 60.043 33.333 0.00 0.00 0.00 2.66
431 433 1.808411 TTTCCTGTAGCGAGCCTTTG 58.192 50.000 0.00 0.00 0.00 2.77
439 441 1.598130 GCGAGCCTTTGGTGACTGT 60.598 57.895 0.00 0.00 0.00 3.55
440 442 1.166531 GCGAGCCTTTGGTGACTGTT 61.167 55.000 0.00 0.00 0.00 3.16
445 447 2.092323 GCCTTTGGTGACTGTTATCCC 58.908 52.381 0.00 0.00 0.00 3.85
454 456 3.683340 GTGACTGTTATCCCCGAGTTTTC 59.317 47.826 0.00 0.00 0.00 2.29
468 470 2.893489 GAGTTTTCAGGTGGAAATGGCT 59.107 45.455 0.00 0.00 44.59 4.75
483 493 0.548989 TGGCTTGTAGGTGTGGTGTT 59.451 50.000 0.00 0.00 0.00 3.32
500 510 3.431766 GGTGTTCTACTGTTGTGTGTCCT 60.432 47.826 0.00 0.00 0.00 3.85
504 514 5.116882 GTTCTACTGTTGTGTGTCCTTTCT 58.883 41.667 0.00 0.00 0.00 2.52
528 538 2.434884 ATTGCCGACTGCGAGGTG 60.435 61.111 0.00 0.00 45.60 4.00
541 551 1.927895 CGAGGTGGCTCACTGTAATC 58.072 55.000 5.48 0.00 34.40 1.75
656 688 3.004734 GGCAGTGCTTGTATCAAACAGTT 59.995 43.478 16.11 0.00 39.87 3.16
680 712 4.156008 GGTGTTTGGCGTCAGAAATAGAAT 59.844 41.667 0.00 0.00 0.00 2.40
682 714 4.092821 TGTTTGGCGTCAGAAATAGAATCG 59.907 41.667 0.00 0.00 0.00 3.34
731 763 5.880901 ACAGTCTTCTACATTCCCATTGTT 58.119 37.500 0.00 0.00 0.00 2.83
732 764 6.306987 ACAGTCTTCTACATTCCCATTGTTT 58.693 36.000 0.00 0.00 0.00 2.83
733 765 6.777580 ACAGTCTTCTACATTCCCATTGTTTT 59.222 34.615 0.00 0.00 0.00 2.43
734 766 7.287696 ACAGTCTTCTACATTCCCATTGTTTTT 59.712 33.333 0.00 0.00 0.00 1.94
763 795 3.007182 AGCATTCCCATTGTTCTGGTTTG 59.993 43.478 0.00 0.00 34.23 2.93
784 816 1.192146 AGGTACTTGGCAAGCTCGGA 61.192 55.000 26.45 4.83 27.25 4.55
789 821 3.004752 ACTTGGCAAGCTCGGATTTAT 57.995 42.857 26.45 0.28 0.00 1.40
822 854 6.883744 TGATGTTTTTAAGGAGCCACTTTTT 58.116 32.000 0.00 0.00 32.02 1.94
877 909 7.825761 TGCTGTCAGATATAATATGATGTTGGG 59.174 37.037 3.32 0.00 32.55 4.12
911 943 7.954788 ACTCTTTTGATCACTAGTTTCAGAC 57.045 36.000 0.00 0.00 0.00 3.51
1071 1111 1.134965 CGGAAGGCAGAGACCTACAAG 60.135 57.143 0.00 0.00 39.93 3.16
1072 1112 2.180276 GGAAGGCAGAGACCTACAAGA 58.820 52.381 0.00 0.00 39.93 3.02
1137 1177 0.598065 ACCAATCTTTTCCTGCACGC 59.402 50.000 0.00 0.00 0.00 5.34
1228 1268 6.258947 CCTCTCTAAACAGCTATTTGGTTAGC 59.741 42.308 0.00 0.00 44.37 3.09
1245 1285 7.048629 TGGTTAGCACATTTCTTTTGATTCA 57.951 32.000 0.00 0.00 0.00 2.57
1314 1354 4.829064 TCTTGGTTGATTTTCGGAACAG 57.171 40.909 0.00 0.00 0.00 3.16
1723 1781 2.237392 GTGCCTACCACTTCCAGAGAAT 59.763 50.000 0.00 0.00 41.35 2.40
1774 1832 1.002468 CACAAGTTTCGCCACTTCCAG 60.002 52.381 0.00 0.00 34.60 3.86
1931 1989 0.979709 TGGACCTCTGCCATCTCCAG 60.980 60.000 0.00 0.00 0.00 3.86
1954 2012 1.153168 AGCACAGCTTGTTCGTGGT 60.153 52.632 0.38 0.38 33.89 4.16
2060 2118 4.470462 CAGTGCAAGTAGAACATCAAAGC 58.530 43.478 0.00 0.00 0.00 3.51
2437 2495 8.178313 GCTATTCTGTTTTCTTGATTACCTGTC 58.822 37.037 0.00 0.00 0.00 3.51
2652 2710 4.497674 GCAAATCATCATCTGCTGGAGAAC 60.498 45.833 2.14 0.00 33.12 3.01
2906 2964 3.806949 TTGAGGGCAACTGTAAAGGAT 57.193 42.857 0.00 0.00 0.00 3.24
3437 3495 5.704515 AGAAGTTGAGATGTTTGATCCAGTG 59.295 40.000 0.00 0.00 0.00 3.66
3500 3558 3.051940 TGGTCTCATGCTCCCTCTAAT 57.948 47.619 0.00 0.00 0.00 1.73
3504 3562 2.632028 TCTCATGCTCCCTCTAATGCTC 59.368 50.000 0.00 0.00 0.00 4.26
3620 3679 6.434018 AGAGCAGACAAAAGAAATGCTATC 57.566 37.500 0.00 0.00 46.67 2.08
3624 3683 6.432162 AGCAGACAAAAGAAATGCTATCAAGA 59.568 34.615 0.00 0.00 44.97 3.02
3644 3703 4.399219 AGAGAGGAGGCTGTTTTAAAACC 58.601 43.478 24.55 12.25 38.11 3.27
3741 3801 8.303876 CCTGGCATTATTGTATTATGGTTTACC 58.696 37.037 0.00 0.00 0.00 2.85
3978 4038 2.514205 ATGCATTTTTCCCGCTATGC 57.486 45.000 0.00 0.00 42.75 3.14
3983 4043 1.757682 TTTTTCCCGCTATGCCGATT 58.242 45.000 0.00 0.00 0.00 3.34
4292 4354 1.916181 CTGTTACTGTCCTGGGGGAAT 59.084 52.381 0.00 0.00 44.15 3.01
4294 4356 2.197465 GTTACTGTCCTGGGGGAATCT 58.803 52.381 0.00 0.00 44.15 2.40
4325 4396 1.287739 CCCTCTCCCTCTGTCTCTCTT 59.712 57.143 0.00 0.00 0.00 2.85
4361 4432 5.539574 TGTGATCATCAAGTTCCCAAAATGT 59.460 36.000 0.00 0.00 0.00 2.71
4376 4447 7.213678 TCCCAAAATGTCAACAAATTACCTTC 58.786 34.615 0.00 0.00 0.00 3.46
4377 4448 6.989169 CCCAAAATGTCAACAAATTACCTTCA 59.011 34.615 0.00 0.00 0.00 3.02
4642 4885 1.586422 CAAGAGGATATGGGTGTGCG 58.414 55.000 0.00 0.00 0.00 5.34
5219 5465 1.002792 GCGTGGTTCCTTGTTTCTGTC 60.003 52.381 0.00 0.00 0.00 3.51
5221 5467 2.544267 CGTGGTTCCTTGTTTCTGTCTC 59.456 50.000 0.00 0.00 0.00 3.36
5298 5544 3.596214 GAGTGGCTACTCGGAAATTTGA 58.404 45.455 14.93 0.00 43.49 2.69
5415 5663 4.159879 TCTGTTCTTGTACCTAGCTTAGCC 59.840 45.833 0.00 0.00 0.00 3.93
5460 5708 3.181458 GCCCGTGGAGATAAATAGTTCCA 60.181 47.826 0.00 0.00 37.38 3.53
5461 5709 4.505039 GCCCGTGGAGATAAATAGTTCCAT 60.505 45.833 0.00 0.00 41.41 3.41
5516 7208 2.107950 TGGACTATTCTGGCGGTTTG 57.892 50.000 0.00 0.00 0.00 2.93
5574 7266 4.950050 AGCGAAGAATATGGTCCTAACTG 58.050 43.478 0.00 0.00 0.00 3.16
5580 7272 4.965532 AGAATATGGTCCTAACTGACAGCT 59.034 41.667 1.25 0.00 36.97 4.24
5673 7365 1.471684 CTTGAGAGATTGCCAACCAGC 59.528 52.381 0.00 0.00 0.00 4.85
5689 7381 0.758734 CAGCGGATAGTTCCCATGGA 59.241 55.000 15.22 0.00 39.01 3.41
5690 7382 0.759346 AGCGGATAGTTCCCATGGAC 59.241 55.000 15.22 4.04 39.01 4.02
5691 7383 0.600255 GCGGATAGTTCCCATGGACG 60.600 60.000 15.22 0.00 39.01 4.79
5726 7682 1.610038 CATGTGCTGAAAAGCCACAGA 59.390 47.619 0.00 0.00 36.38 3.41
5764 7720 2.164219 TCCCTCATTTCAAGCGCATTTC 59.836 45.455 11.47 0.00 0.00 2.17
5766 7722 2.179589 CTCATTTCAAGCGCATTTCGG 58.820 47.619 11.47 0.00 38.94 4.30
5814 7770 9.321532 ACATTATGCCTCTAGGTATATGTGTAA 57.678 33.333 16.72 3.38 41.36 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.267806 CACCTGAACCATCAAGTGCAC 59.732 52.381 9.40 9.40 40.19 4.57
1 2 1.608055 CACCTGAACCATCAAGTGCA 58.392 50.000 0.00 0.00 40.19 4.57
3 4 0.518636 CGCACCTGAACCATCAAGTG 59.481 55.000 3.74 3.74 46.38 3.16
4 5 1.237285 GCGCACCTGAACCATCAAGT 61.237 55.000 0.30 0.00 34.49 3.16
7 8 2.741985 CGCGCACCTGAACCATCA 60.742 61.111 8.75 0.00 0.00 3.07
163 164 0.036164 AAATGGCAGCGACCAGTGTA 59.964 50.000 6.87 0.00 44.71 2.90
188 189 0.246360 GGTTGCTAGGCGCCAAAAAT 59.754 50.000 31.54 10.27 38.05 1.82
235 236 1.431496 ACACGTAAAATTCGTCCCCG 58.569 50.000 0.00 0.00 39.55 5.73
369 371 6.528072 GCAAAATTAGAACAAGTCATGCTACC 59.472 38.462 0.00 0.00 0.00 3.18
377 379 8.406172 TCAAAACTGCAAAATTAGAACAAGTC 57.594 30.769 0.00 0.00 0.00 3.01
431 433 1.192428 ACTCGGGGATAACAGTCACC 58.808 55.000 0.00 0.00 38.37 4.02
439 441 2.026636 CCACCTGAAAACTCGGGGATAA 60.027 50.000 5.04 0.00 40.42 1.75
440 442 1.557832 CCACCTGAAAACTCGGGGATA 59.442 52.381 5.04 0.00 40.42 2.59
445 447 2.228822 CCATTTCCACCTGAAAACTCGG 59.771 50.000 0.00 0.00 45.67 4.63
454 456 2.094675 CCTACAAGCCATTTCCACCTG 58.905 52.381 0.00 0.00 0.00 4.00
468 470 3.707611 ACAGTAGAACACCACACCTACAA 59.292 43.478 0.00 0.00 35.26 2.41
483 493 5.597182 ACTAGAAAGGACACACAACAGTAGA 59.403 40.000 0.00 0.00 0.00 2.59
500 510 2.483877 CAGTCGGCAATGCAACTAGAAA 59.516 45.455 7.79 0.00 0.00 2.52
504 514 1.634757 CGCAGTCGGCAATGCAACTA 61.635 55.000 7.79 0.00 45.17 2.24
528 538 1.009829 CGGCAAGATTACAGTGAGCC 58.990 55.000 0.00 0.00 37.32 4.70
541 551 3.114616 CACGAGCTCCACGGCAAG 61.115 66.667 8.47 0.00 34.93 4.01
617 630 2.338140 GCCTGCAGCAACTAAGAAAC 57.662 50.000 8.66 0.00 42.97 2.78
656 688 1.686355 ATTTCTGACGCCAAACACCA 58.314 45.000 0.00 0.00 0.00 4.17
680 712 5.293814 TGTGTTTCCGTCAAAAGATTTACGA 59.706 36.000 0.00 0.00 38.17 3.43
682 714 6.970613 AGTTGTGTTTCCGTCAAAAGATTTAC 59.029 34.615 0.00 0.00 0.00 2.01
733 765 7.153985 CAGAACAATGGGAATGCTTCTAAAAA 58.846 34.615 0.00 0.00 0.00 1.94
734 766 6.295236 CCAGAACAATGGGAATGCTTCTAAAA 60.295 38.462 0.00 0.00 36.64 1.52
735 767 5.185635 CCAGAACAATGGGAATGCTTCTAAA 59.814 40.000 0.00 0.00 36.64 1.85
736 768 4.706476 CCAGAACAATGGGAATGCTTCTAA 59.294 41.667 0.00 0.00 36.64 2.10
737 769 4.263905 ACCAGAACAATGGGAATGCTTCTA 60.264 41.667 0.00 0.00 45.25 2.10
738 770 3.094572 CCAGAACAATGGGAATGCTTCT 58.905 45.455 0.00 0.00 36.64 2.85
739 771 2.827921 ACCAGAACAATGGGAATGCTTC 59.172 45.455 0.00 0.00 45.25 3.86
740 772 2.893424 ACCAGAACAATGGGAATGCTT 58.107 42.857 0.00 0.00 45.25 3.91
741 773 2.610438 ACCAGAACAATGGGAATGCT 57.390 45.000 0.00 0.00 45.25 3.79
742 774 3.328505 CAAACCAGAACAATGGGAATGC 58.671 45.455 0.00 0.00 45.25 3.56
743 775 3.577848 TCCAAACCAGAACAATGGGAATG 59.422 43.478 0.00 0.00 45.25 2.67
744 776 3.834231 CTCCAAACCAGAACAATGGGAAT 59.166 43.478 0.00 0.00 45.25 3.01
745 777 3.230134 CTCCAAACCAGAACAATGGGAA 58.770 45.455 0.00 0.00 45.25 3.97
746 778 2.490718 CCTCCAAACCAGAACAATGGGA 60.491 50.000 0.00 0.00 45.25 4.37
747 779 1.895131 CCTCCAAACCAGAACAATGGG 59.105 52.381 0.00 0.00 45.25 4.00
748 780 2.597455 ACCTCCAAACCAGAACAATGG 58.403 47.619 0.00 0.00 46.47 3.16
749 781 4.398319 AGTACCTCCAAACCAGAACAATG 58.602 43.478 0.00 0.00 0.00 2.82
750 782 4.724279 AGTACCTCCAAACCAGAACAAT 57.276 40.909 0.00 0.00 0.00 2.71
751 783 4.204012 CAAGTACCTCCAAACCAGAACAA 58.796 43.478 0.00 0.00 0.00 2.83
752 784 3.434453 CCAAGTACCTCCAAACCAGAACA 60.434 47.826 0.00 0.00 0.00 3.18
753 785 3.146847 CCAAGTACCTCCAAACCAGAAC 58.853 50.000 0.00 0.00 0.00 3.01
754 786 2.488347 GCCAAGTACCTCCAAACCAGAA 60.488 50.000 0.00 0.00 0.00 3.02
763 795 0.741221 CGAGCTTGCCAAGTACCTCC 60.741 60.000 6.28 0.00 0.00 4.30
784 816 9.787532 CTTAAAAACATCATGACGTCCATAAAT 57.212 29.630 14.12 0.00 33.31 1.40
789 821 5.309638 TCCTTAAAAACATCATGACGTCCA 58.690 37.500 14.12 1.26 0.00 4.02
877 909 5.986135 AGTGATCAAAAGAGTACTGACACAC 59.014 40.000 0.00 6.61 33.64 3.82
1071 1111 2.238521 TCTTGTTTTGGTGCTGGGATC 58.761 47.619 0.00 0.00 0.00 3.36
1072 1112 2.380064 TCTTGTTTTGGTGCTGGGAT 57.620 45.000 0.00 0.00 0.00 3.85
1137 1177 0.383231 GCGCATCTTCCCCAAGATTG 59.617 55.000 0.30 0.00 45.68 2.67
1245 1285 8.458052 TCACTGTAACGAAATTGCAAATGATAT 58.542 29.630 1.71 0.00 31.94 1.63
1314 1354 3.702045 AGTACTGATGAGGAACAGGCTAC 59.298 47.826 0.00 0.00 38.30 3.58
1610 1650 8.677148 ACAAAGTACATACAAACTGAAGTGAT 57.323 30.769 0.00 0.00 0.00 3.06
1630 1670 7.416817 TCACACATCACAATCAGTTTACAAAG 58.583 34.615 0.00 0.00 0.00 2.77
1723 1781 5.929992 GCCACTAATCACGCCTTTGTATATA 59.070 40.000 0.00 0.00 0.00 0.86
1774 1832 2.426522 TGTGCATGGTCTAGCTCAAAC 58.573 47.619 0.00 0.00 32.10 2.93
1931 1989 1.578423 GAACAAGCTGTGCTCCTGC 59.422 57.895 0.00 0.00 38.25 4.85
1954 2012 1.154197 CAGACTCGGTCGACACTACA 58.846 55.000 18.91 0.00 37.67 2.74
2060 2118 4.450419 AGAAGACTCTTCATCAAAGTTGCG 59.550 41.667 19.00 0.00 36.31 4.85
2317 2375 3.013921 GGTGGCGTTTGATGGATCTTTA 58.986 45.455 0.00 0.00 0.00 1.85
2437 2495 7.867403 AGCATAATGTGAAAATAATTAAGGGCG 59.133 33.333 0.00 0.00 0.00 6.13
2652 2710 7.976135 AGCAGCTCCATCTATTTATACTTTG 57.024 36.000 0.00 0.00 0.00 2.77
2906 2964 7.015098 TGCAGTTCCTGAATTTTTCTTTCCATA 59.985 33.333 0.00 0.00 32.44 2.74
3041 3099 1.077429 GAGGGATGGCAACCAGGTC 60.077 63.158 16.20 5.31 36.75 3.85
3247 3305 5.909621 AAGCAATGCAGATAGTCAAACAT 57.090 34.783 8.35 0.00 0.00 2.71
3437 3495 3.142174 GCTGTATATCCAACTCCCAAGC 58.858 50.000 0.00 0.00 0.00 4.01
3500 3558 5.748402 AGAACATTCCACTGAATATGAGCA 58.252 37.500 0.00 0.00 39.20 4.26
3504 3562 8.511604 AGGTTTAGAACATTCCACTGAATATG 57.488 34.615 0.00 0.00 39.20 1.78
3620 3679 5.278512 GGTTTTAAAACAGCCTCCTCTCTTG 60.279 44.000 27.56 0.00 40.63 3.02
3624 3683 4.141251 TGAGGTTTTAAAACAGCCTCCTCT 60.141 41.667 27.56 15.19 43.64 3.69
3644 3703 9.844790 TTAAGAACATCAAATATGCAGTTTGAG 57.155 29.630 25.00 20.24 45.54 3.02
3741 3801 8.837788 TTCCTATTGATCATATGCAACTACAG 57.162 34.615 0.00 0.00 0.00 2.74
3983 4043 8.038944 AGCGGAATGAATAACTGTAGTTCTAAA 58.961 33.333 0.00 0.00 39.31 1.85
4060 4121 2.879103 ACCACCAACAACATAGAGGG 57.121 50.000 0.00 0.00 0.00 4.30
4308 4370 3.591527 AGAGAAAGAGAGACAGAGGGAGA 59.408 47.826 0.00 0.00 0.00 3.71
4309 4371 3.968265 AGAGAAAGAGAGACAGAGGGAG 58.032 50.000 0.00 0.00 0.00 4.30
4310 4372 4.085733 CAAGAGAAAGAGAGACAGAGGGA 58.914 47.826 0.00 0.00 0.00 4.20
4311 4373 4.082245 GTCAAGAGAAAGAGAGACAGAGGG 60.082 50.000 0.00 0.00 0.00 4.30
4314 4376 3.829601 GGGTCAAGAGAAAGAGAGACAGA 59.170 47.826 0.00 0.00 0.00 3.41
4315 4377 3.831911 AGGGTCAAGAGAAAGAGAGACAG 59.168 47.826 0.00 0.00 0.00 3.51
4316 4378 3.576118 CAGGGTCAAGAGAAAGAGAGACA 59.424 47.826 0.00 0.00 0.00 3.41
4317 4379 3.576550 ACAGGGTCAAGAGAAAGAGAGAC 59.423 47.826 0.00 0.00 0.00 3.36
4325 4396 3.840078 TGATGATCACAGGGTCAAGAGAA 59.160 43.478 0.00 0.00 0.00 2.87
4642 4885 1.209128 CATTATCGTCCGCTGTCACC 58.791 55.000 0.00 0.00 0.00 4.02
5243 5489 1.680735 AGTTCAATTTGTTCAGGCGCA 59.319 42.857 10.83 0.00 0.00 6.09
5289 5535 5.830457 TGGGGTTTTTCCATTTCAAATTTCC 59.170 36.000 0.00 0.00 38.11 3.13
5298 5544 4.853468 AACAGTTGGGGTTTTTCCATTT 57.147 36.364 0.00 0.00 38.11 2.32
5384 5632 8.154856 AGCTAGGTACAAGAACAGAACAAATAA 58.845 33.333 0.00 0.00 0.00 1.40
5386 5634 6.534634 AGCTAGGTACAAGAACAGAACAAAT 58.465 36.000 0.00 0.00 0.00 2.32
5441 5689 5.333339 CGCAATGGAACTATTTATCTCCACG 60.333 44.000 0.00 0.00 40.69 4.94
5460 5708 1.442769 CTTACAGCCACAGACGCAAT 58.557 50.000 0.00 0.00 0.00 3.56
5461 5709 1.227999 GCTTACAGCCACAGACGCAA 61.228 55.000 0.00 0.00 34.48 4.85
5516 7208 1.266178 CATCCCAAACTTTCCCACCC 58.734 55.000 0.00 0.00 0.00 4.61
5574 7266 2.187163 GCGGGGTTAGGAGCTGTC 59.813 66.667 0.00 0.00 0.00 3.51
5580 7272 0.252375 ACAGTTAGGCGGGGTTAGGA 60.252 55.000 0.00 0.00 0.00 2.94
5689 7381 0.955428 ATGCACGGTTCATTGCTCGT 60.955 50.000 0.00 0.00 39.62 4.18
5690 7382 0.521867 CATGCACGGTTCATTGCTCG 60.522 55.000 0.00 0.00 39.62 5.03
5691 7383 0.523072 ACATGCACGGTTCATTGCTC 59.477 50.000 0.00 0.00 39.62 4.26
5726 7682 4.887071 TGAGGGATGCGCAATAAAATAACT 59.113 37.500 17.11 2.40 0.00 2.24
5764 7720 4.448395 ACATGTTTGTGAATTTTCATGCCG 59.552 37.500 0.00 0.00 39.73 5.69
5766 7722 7.405469 TGTACATGTTTGTGAATTTTCATGC 57.595 32.000 2.30 0.00 39.73 4.06
5856 7814 4.532834 AGCTCCATAAAGGCCGAATTTTA 58.467 39.130 0.00 0.00 37.29 1.52


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

AutoCloner maintained by Alex Coulton.