Multiple sequence alignment - TraesCS6D01G123400

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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 TraesCS6D01G123400 chr6D 100.000 4190 0 0 1 4190 88675555 88679744 0.000000e+00 7738.0
1 TraesCS6D01G123400 chr6D 82.560 711 118 6 3482 4190 70783932 70783226 4.600000e-174 621.0
2 TraesCS6D01G123400 chr6B 93.535 3434 164 31 1 3409 169027232 169030632 0.000000e+00 5059.0
3 TraesCS6D01G123400 chr6A 94.598 2536 97 19 783 3284 106477941 106480470 0.000000e+00 3888.0
4 TraesCS6D01G123400 chr6A 88.202 712 81 3 3481 4190 575190265 575189555 0.000000e+00 846.0
5 TraesCS6D01G123400 chr6A 86.942 605 41 15 207 787 106476167 106476757 0.000000e+00 645.0
6 TraesCS6D01G123400 chr5D 91.842 711 56 2 3481 4190 545818265 545818974 0.000000e+00 990.0
7 TraesCS6D01G123400 chr5D 87.658 713 84 4 3480 4190 538557326 538558036 0.000000e+00 826.0
8 TraesCS6D01G123400 chr4D 91.854 712 55 3 3481 4190 428112282 428111572 0.000000e+00 990.0
9 TraesCS6D01G123400 chr7A 89.592 711 72 2 3481 4190 701672231 701671522 0.000000e+00 902.0
10 TraesCS6D01G123400 chr7A 96.970 33 1 0 3101 3133 25131163 25131131 5.850000e-04 56.5
11 TraesCS6D01G123400 chr5A 89.787 705 68 4 3488 4190 400063838 400063136 0.000000e+00 900.0
12 TraesCS6D01G123400 chr5A 80.040 506 95 6 3481 3983 537255063 537254561 1.840000e-98 370.0
13 TraesCS6D01G123400 chr2B 92.605 622 42 3 3485 4106 631444627 631444010 0.000000e+00 891.0
14 TraesCS6D01G123400 chr4A 96.970 33 1 0 3101 3133 708649027 708648995 5.850000e-04 56.5
15 TraesCS6D01G123400 chr1D 97.059 34 0 1 3101 3133 20401422 20401455 5.850000e-04 56.5


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 TraesCS6D01G123400 chr6D 88675555 88679744 4189 False 7738.0 7738 100.000 1 4190 1 chr6D.!!$F1 4189
1 TraesCS6D01G123400 chr6D 70783226 70783932 706 True 621.0 621 82.560 3482 4190 1 chr6D.!!$R1 708
2 TraesCS6D01G123400 chr6B 169027232 169030632 3400 False 5059.0 5059 93.535 1 3409 1 chr6B.!!$F1 3408
3 TraesCS6D01G123400 chr6A 106476167 106480470 4303 False 2266.5 3888 90.770 207 3284 2 chr6A.!!$F1 3077
4 TraesCS6D01G123400 chr6A 575189555 575190265 710 True 846.0 846 88.202 3481 4190 1 chr6A.!!$R1 709
5 TraesCS6D01G123400 chr5D 545818265 545818974 709 False 990.0 990 91.842 3481 4190 1 chr5D.!!$F2 709
6 TraesCS6D01G123400 chr5D 538557326 538558036 710 False 826.0 826 87.658 3480 4190 1 chr5D.!!$F1 710
7 TraesCS6D01G123400 chr4D 428111572 428112282 710 True 990.0 990 91.854 3481 4190 1 chr4D.!!$R1 709
8 TraesCS6D01G123400 chr7A 701671522 701672231 709 True 902.0 902 89.592 3481 4190 1 chr7A.!!$R2 709
9 TraesCS6D01G123400 chr5A 400063136 400063838 702 True 900.0 900 89.787 3488 4190 1 chr5A.!!$R1 702
10 TraesCS6D01G123400 chr5A 537254561 537255063 502 True 370.0 370 80.040 3481 3983 1 chr5A.!!$R2 502
11 TraesCS6D01G123400 chr2B 631444010 631444627 617 True 891.0 891 92.605 3485 4106 1 chr2B.!!$R1 621

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
579 597 0.176910 AAACAAACGGGGGTTTGCTG 59.823 50.0 16.99 0.0 45.33 4.41 F
1300 2580 0.320683 CCTCACCATCGACAGCAACA 60.321 55.0 0.00 0.0 0.00 3.33 F
2457 3737 0.323087 TCGACCGGATCTCCAAGACA 60.323 55.0 9.46 0.0 35.14 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 2840 0.179089 CGCTGTCTTCTCCTGGATGG 60.179 60.000 0.0 0.0 37.10 3.51 R
2562 3842 0.250553 CCCAGGTAAACTTGTCGGCA 60.251 55.000 0.0 0.0 0.00 5.69 R
3360 4658 1.733041 CTGATATACCGCGCCACCG 60.733 63.158 0.0 0.0 37.57 4.94 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
23 24 6.477669 GATATGACGTATACACTCGAAGGA 57.522 41.667 3.32 0.00 0.00 3.36
33 34 9.544314 CGTATACACTCGAAGGAAATTATAGAG 57.456 37.037 3.32 0.00 0.00 2.43
55 56 7.129425 AGAGTTATCAGATATTAGCCCCCTAG 58.871 42.308 0.00 0.00 0.00 3.02
64 65 6.608002 AGATATTAGCCCCCTAGAGATAAACG 59.392 42.308 0.00 0.00 0.00 3.60
67 68 1.540580 GCCCCCTAGAGATAAACGCAC 60.541 57.143 0.00 0.00 0.00 5.34
95 96 6.162079 TGTTCTCTGAAATAAGCTCACTGAG 58.838 40.000 1.21 1.21 0.00 3.35
103 104 2.998316 AAGCTCACTGAGATAAGGCC 57.002 50.000 10.45 0.00 0.00 5.19
105 106 3.320610 AGCTCACTGAGATAAGGCCTA 57.679 47.619 5.16 0.00 0.00 3.93
116 117 5.203060 AGATAAGGCCTAAGACGATTCAC 57.797 43.478 5.16 0.00 0.00 3.18
132 133 1.282817 TCACCAAACACTTCGACACG 58.717 50.000 0.00 0.00 0.00 4.49
165 166 3.071479 CACGTTACACAAGCTAATGGGT 58.929 45.455 0.00 0.00 40.76 4.51
166 167 3.071479 ACGTTACACAAGCTAATGGGTG 58.929 45.455 3.46 2.72 37.55 4.61
168 169 3.120338 CGTTACACAAGCTAATGGGTGTG 60.120 47.826 11.50 11.50 43.69 3.82
172 173 4.151883 ACACAAGCTAATGGGTGTGAAAT 58.848 39.130 18.37 0.00 42.43 2.17
173 174 4.218417 ACACAAGCTAATGGGTGTGAAATC 59.782 41.667 18.37 0.00 42.43 2.17
199 200 7.572523 TTCAATTCTTTGGATATAGCACCTG 57.427 36.000 0.00 0.00 33.44 4.00
242 244 3.179443 TCGTTAACTCCATCAGGCATC 57.821 47.619 3.71 0.00 33.74 3.91
257 260 5.674525 TCAGGCATCAGACCAGTATAAAAG 58.325 41.667 0.00 0.00 0.00 2.27
310 313 7.040961 TGTTTTAAGAATTAACCGGTTCCTCTG 60.041 37.037 26.16 0.00 40.86 3.35
363 381 5.047377 GGTCCCATTTGAAACAAAGCATCTA 60.047 40.000 0.00 0.00 0.00 1.98
368 386 7.442062 CCCATTTGAAACAAAGCATCTAAAACT 59.558 33.333 0.00 0.00 0.00 2.66
400 418 0.879090 GAAAACGGCCTACACAAGGG 59.121 55.000 0.00 0.00 46.65 3.95
432 450 4.437682 TTCTCTGTCACCCTTGTTTCAT 57.562 40.909 0.00 0.00 0.00 2.57
433 451 4.008074 TCTCTGTCACCCTTGTTTCATC 57.992 45.455 0.00 0.00 0.00 2.92
434 452 3.390967 TCTCTGTCACCCTTGTTTCATCA 59.609 43.478 0.00 0.00 0.00 3.07
435 453 4.136796 CTCTGTCACCCTTGTTTCATCAA 58.863 43.478 0.00 0.00 0.00 2.57
436 454 4.531854 TCTGTCACCCTTGTTTCATCAAA 58.468 39.130 0.00 0.00 0.00 2.69
437 455 4.952957 TCTGTCACCCTTGTTTCATCAAAA 59.047 37.500 0.00 0.00 0.00 2.44
455 473 2.052782 AAAAACTCAAGCACCCTCGT 57.947 45.000 0.00 0.00 0.00 4.18
529 547 9.745880 ATGATCATCTTTATCATTGAAGCAAAC 57.254 29.630 1.18 0.00 40.37 2.93
573 591 1.855295 AAACTGAAACAAACGGGGGT 58.145 45.000 0.00 0.00 0.00 4.95
579 597 0.176910 AAACAAACGGGGGTTTGCTG 59.823 50.000 16.99 0.00 45.33 4.41
598 616 3.871594 GCTGTCCTTGTATGTATGTGTCC 59.128 47.826 0.00 0.00 0.00 4.02
603 621 6.127451 TGTCCTTGTATGTATGTGTCCTGTAG 60.127 42.308 0.00 0.00 0.00 2.74
604 622 6.096423 GTCCTTGTATGTATGTGTCCTGTAGA 59.904 42.308 0.00 0.00 0.00 2.59
605 623 6.096423 TCCTTGTATGTATGTGTCCTGTAGAC 59.904 42.308 0.00 0.00 46.51 2.59
606 624 5.847111 TGTATGTATGTGTCCTGTAGACC 57.153 43.478 0.00 0.00 45.68 3.85
607 625 5.516044 TGTATGTATGTGTCCTGTAGACCT 58.484 41.667 0.00 0.00 45.68 3.85
608 626 5.359860 TGTATGTATGTGTCCTGTAGACCTG 59.640 44.000 0.00 0.00 45.68 4.00
609 627 3.774734 TGTATGTGTCCTGTAGACCTGT 58.225 45.455 0.00 0.00 45.68 4.00
610 628 4.925836 TGTATGTGTCCTGTAGACCTGTA 58.074 43.478 0.00 0.00 45.68 2.74
611 629 4.703575 TGTATGTGTCCTGTAGACCTGTAC 59.296 45.833 0.00 0.00 45.68 2.90
612 630 3.520691 TGTGTCCTGTAGACCTGTACT 57.479 47.619 0.00 0.00 45.68 2.73
622 640 7.039923 TCCTGTAGACCTGTACTAAGAAAGTTG 60.040 40.741 0.00 0.00 39.80 3.16
663 683 7.278875 GTCTGATCTATCTTTTCCCTCACAAT 58.721 38.462 0.00 0.00 0.00 2.71
680 700 9.415544 CCCTCACAATAGAAATTTTCTTTTGAG 57.584 33.333 31.51 26.65 45.59 3.02
682 702 9.971922 CTCACAATAGAAATTTTCTTTTGAGGT 57.028 29.630 31.51 17.21 45.59 3.85
735 762 1.275657 GTGTGCGAACGTGTCAAGG 59.724 57.895 0.00 0.00 0.00 3.61
791 2010 2.572290 GTGCAACCTGGTAAGACTTGT 58.428 47.619 0.00 0.00 0.00 3.16
914 2138 2.435372 TCTGACAAGCAAAACCCAGT 57.565 45.000 0.00 0.00 0.00 4.00
975 2250 1.912110 GAAGTTCGAACATCGGTCGAG 59.088 52.381 28.78 0.00 40.88 4.04
976 2251 0.456312 AGTTCGAACATCGGTCGAGC 60.456 55.000 28.78 9.85 40.88 5.03
979 2254 2.508891 CGAACATCGGTCGAGCTGC 61.509 63.158 13.48 0.00 36.00 5.25
1300 2580 0.320683 CCTCACCATCGACAGCAACA 60.321 55.000 0.00 0.00 0.00 3.33
1546 2826 3.308053 CGACTACATGAAGCAACTCCATG 59.692 47.826 0.00 0.00 42.32 3.66
1560 2840 1.817099 CCATGGCCGAGAGCAAGAC 60.817 63.158 0.00 0.00 46.50 3.01
1799 3079 1.138661 GGATCTCTGCCTGTCCTTCTG 59.861 57.143 0.00 0.00 0.00 3.02
2018 3298 2.358737 CCCGGTGCTCAACTCCAC 60.359 66.667 0.00 0.00 31.85 4.02
2457 3737 0.323087 TCGACCGGATCTCCAAGACA 60.323 55.000 9.46 0.00 35.14 3.41
2461 3741 1.482593 ACCGGATCTCCAAGACATCAC 59.517 52.381 9.46 0.00 35.14 3.06
2664 3944 0.884704 ATGTCGCCACGAGTTTGCTT 60.885 50.000 0.00 0.00 36.23 3.91
2705 3988 4.819761 GGCTCATGGCAGCGACGA 62.820 66.667 0.00 0.00 44.01 4.20
2706 3989 3.558411 GCTCATGGCAGCGACGAC 61.558 66.667 0.00 0.00 41.35 4.34
3096 4379 2.240500 GCATGCTAAGTCGCTCCGG 61.241 63.158 11.37 0.00 0.00 5.14
3293 4591 6.760770 TGAATATTGTATGCAACTCATCACGA 59.239 34.615 0.00 0.00 37.44 4.35
3313 4611 4.202284 ACGAACACACACCCACTTATACTT 60.202 41.667 0.00 0.00 0.00 2.24
3317 4615 3.924686 CACACACCCACTTATACTTCGTC 59.075 47.826 0.00 0.00 0.00 4.20
3329 4627 1.227089 CTTCGTCCATCCTGAGGCG 60.227 63.158 0.00 0.00 0.00 5.52
3387 4685 0.667487 CGGTATATCAGCGCCCTGTG 60.667 60.000 2.29 0.00 41.87 3.66
3430 4728 8.992835 TTTTTCTAGACGGAAAATACTCCTAC 57.007 34.615 0.00 0.00 42.38 3.18
3431 4729 7.707624 TTTCTAGACGGAAAATACTCCTACA 57.292 36.000 0.00 0.00 33.04 2.74
3432 4730 7.893124 TTCTAGACGGAAAATACTCCTACAT 57.107 36.000 0.00 0.00 32.82 2.29
3433 4731 8.985315 TTCTAGACGGAAAATACTCCTACATA 57.015 34.615 0.00 0.00 32.82 2.29
3434 4732 9.584008 TTCTAGACGGAAAATACTCCTACATAT 57.416 33.333 0.00 0.00 32.82 1.78
3435 4733 9.228949 TCTAGACGGAAAATACTCCTACATATC 57.771 37.037 0.00 0.00 32.82 1.63
3436 4734 9.233649 CTAGACGGAAAATACTCCTACATATCT 57.766 37.037 0.00 0.00 32.82 1.98
3437 4735 8.113173 AGACGGAAAATACTCCTACATATCTC 57.887 38.462 0.00 0.00 32.82 2.75
3438 4736 7.724506 AGACGGAAAATACTCCTACATATCTCA 59.275 37.037 0.00 0.00 32.82 3.27
3439 4737 8.423906 ACGGAAAATACTCCTACATATCTCAT 57.576 34.615 0.00 0.00 32.82 2.90
3440 4738 9.529823 ACGGAAAATACTCCTACATATCTCATA 57.470 33.333 0.00 0.00 32.82 2.15
3511 4810 7.678207 AGGGGTAAAACCAAGTTTTATTCAA 57.322 32.000 13.93 0.00 45.51 2.69
3756 5055 4.695993 TGGCTGCAATCCGACGCA 62.696 61.111 0.50 0.00 36.52 5.24
3901 5200 0.249120 CCACTCGTCCCTGCATACAA 59.751 55.000 0.00 0.00 0.00 2.41
3908 5207 1.078497 CCCTGCATACAACCGCTGA 60.078 57.895 0.00 0.00 0.00 4.26
3957 5256 4.802039 CCAGCATCTACATGAATTTTGCAC 59.198 41.667 0.00 0.00 31.41 4.57
4078 5378 5.066634 TCAGCAATGAACCTAACAACGAAAA 59.933 36.000 0.00 0.00 0.00 2.29
4113 5413 1.407989 GGGGCTCTGAAAGATGGACTG 60.408 57.143 0.00 0.00 45.62 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.544314 CTCTATAATTTCCTTCGAGTGTATACG 57.456 37.037 0.00 0.00 0.00 3.06
33 34 7.126733 TCTCTAGGGGGCTAATATCTGATAAC 58.873 42.308 0.81 0.00 0.00 1.89
37 38 5.822774 ATCTCTAGGGGGCTAATATCTGA 57.177 43.478 0.00 0.00 0.00 3.27
50 51 4.142138 ACAAGAGTGCGTTTATCTCTAGGG 60.142 45.833 0.00 0.00 37.54 3.53
55 56 5.061560 CAGAGAACAAGAGTGCGTTTATCTC 59.938 44.000 0.00 0.00 0.00 2.75
64 65 5.411053 AGCTTATTTCAGAGAACAAGAGTGC 59.589 40.000 0.00 0.00 0.00 4.40
67 68 6.873076 AGTGAGCTTATTTCAGAGAACAAGAG 59.127 38.462 0.00 0.00 0.00 2.85
95 96 4.202223 TGGTGAATCGTCTTAGGCCTTATC 60.202 45.833 12.58 0.00 0.00 1.75
103 104 5.388475 CGAAGTGTTTGGTGAATCGTCTTAG 60.388 44.000 0.00 0.00 0.00 2.18
105 106 3.247648 CGAAGTGTTTGGTGAATCGTCTT 59.752 43.478 0.00 0.00 0.00 3.01
116 117 2.404215 AGATCGTGTCGAAGTGTTTGG 58.596 47.619 0.00 0.00 39.99 3.28
132 133 7.863375 AGCTTGTGTAACGTGATCTATAAGATC 59.137 37.037 9.50 9.50 45.53 2.75
148 149 4.359434 TCACACCCATTAGCTTGTGTAA 57.641 40.909 12.42 0.00 39.78 2.41
172 173 8.055181 AGGTGCTATATCCAAAGAATTGAAAGA 58.945 33.333 0.00 0.00 38.94 2.52
173 174 8.133627 CAGGTGCTATATCCAAAGAATTGAAAG 58.866 37.037 0.00 0.00 38.94 2.62
192 193 3.788227 TGTGTTTATTCCTCAGGTGCT 57.212 42.857 0.00 0.00 0.00 4.40
199 200 9.962783 ACGATACTACTATTGTGTTTATTCCTC 57.037 33.333 0.00 0.00 0.00 3.71
227 228 1.211457 GGTCTGATGCCTGATGGAGTT 59.789 52.381 0.00 0.00 34.57 3.01
242 244 9.665264 GTTTTGAAGTTCTTTTATACTGGTCTG 57.335 33.333 4.17 0.00 0.00 3.51
283 286 7.668469 AGAGGAACCGGTTAATTCTTAAAACAT 59.332 33.333 22.33 0.00 0.00 2.71
375 393 2.875933 TGTGTAGGCCGTTTTCAGAAAG 59.124 45.455 0.00 0.00 0.00 2.62
400 418 3.799420 GGTGACAGAGAATATGAACGAGC 59.201 47.826 0.00 0.00 0.00 5.03
436 454 1.947456 GACGAGGGTGCTTGAGTTTTT 59.053 47.619 0.00 0.00 0.00 1.94
437 455 1.594331 GACGAGGGTGCTTGAGTTTT 58.406 50.000 0.00 0.00 0.00 2.43
451 469 2.022195 TCCCACTATTTCTCCGACGAG 58.978 52.381 0.00 0.00 37.48 4.18
455 473 5.897824 ACTAAAGATCCCACTATTTCTCCGA 59.102 40.000 0.00 0.00 0.00 4.55
503 521 9.745880 GTTTGCTTCAATGATAAAGATGATCAT 57.254 29.630 8.25 8.25 44.21 2.45
504 522 8.192774 GGTTTGCTTCAATGATAAAGATGATCA 58.807 33.333 0.00 0.00 37.70 2.92
505 523 7.377928 CGGTTTGCTTCAATGATAAAGATGATC 59.622 37.037 0.00 0.00 0.00 2.92
529 547 3.201290 CTGGATTCAAATCACCTCTCGG 58.799 50.000 5.19 0.00 37.15 4.63
550 568 3.183754 CCCCGTTTGTTTCAGTTTTGAC 58.816 45.455 0.00 0.00 31.71 3.18
573 591 5.312895 ACACATACATACAAGGACAGCAAA 58.687 37.500 0.00 0.00 0.00 3.68
579 597 5.086104 ACAGGACACATACATACAAGGAC 57.914 43.478 0.00 0.00 0.00 3.85
598 616 7.039923 TCCAACTTTCTTAGTACAGGTCTACAG 60.040 40.741 0.00 0.00 35.54 2.74
603 621 4.930405 GCTCCAACTTTCTTAGTACAGGTC 59.070 45.833 0.00 0.00 35.54 3.85
604 622 4.560919 CGCTCCAACTTTCTTAGTACAGGT 60.561 45.833 0.00 0.00 35.54 4.00
605 623 3.927142 CGCTCCAACTTTCTTAGTACAGG 59.073 47.826 0.00 0.00 35.54 4.00
606 624 3.368236 GCGCTCCAACTTTCTTAGTACAG 59.632 47.826 0.00 0.00 35.54 2.74
607 625 3.243941 TGCGCTCCAACTTTCTTAGTACA 60.244 43.478 9.73 0.00 35.54 2.90
608 626 3.323243 TGCGCTCCAACTTTCTTAGTAC 58.677 45.455 9.73 0.00 35.54 2.73
609 627 3.671008 TGCGCTCCAACTTTCTTAGTA 57.329 42.857 9.73 0.00 35.54 1.82
610 628 2.543777 TGCGCTCCAACTTTCTTAGT 57.456 45.000 9.73 0.00 39.32 2.24
611 629 2.096496 CCATGCGCTCCAACTTTCTTAG 59.904 50.000 9.73 0.00 0.00 2.18
612 630 2.083774 CCATGCGCTCCAACTTTCTTA 58.916 47.619 9.73 0.00 0.00 2.10
722 749 1.557443 GCTCACCCTTGACACGTTCG 61.557 60.000 0.00 0.00 0.00 3.95
789 2008 2.265367 AGTCACCCCATCACATGTACA 58.735 47.619 0.00 0.00 0.00 2.90
790 2009 3.350219 AAGTCACCCCATCACATGTAC 57.650 47.619 0.00 0.00 0.00 2.90
791 2010 3.308117 GGAAAGTCACCCCATCACATGTA 60.308 47.826 0.00 0.00 0.00 2.29
946 2171 2.070783 TGTTCGAACTTCGTATTGGCC 58.929 47.619 27.32 0.00 41.35 5.36
975 2250 3.567797 GATCGCTGGGTTCGCAGC 61.568 66.667 24.95 24.95 40.75 5.25
976 2251 3.257561 CGATCGCTGGGTTCGCAG 61.258 66.667 0.26 11.62 31.79 5.18
979 2254 2.956964 GCTCGATCGCTGGGTTCG 60.957 66.667 11.09 16.22 38.82 3.95
1546 2826 1.522580 GATGGTCTTGCTCTCGGCC 60.523 63.158 0.00 0.00 40.92 6.13
1560 2840 0.179089 CGCTGTCTTCTCCTGGATGG 60.179 60.000 0.00 0.00 37.10 3.51
1799 3079 2.257676 GCTGCAGCTTGAACAGGC 59.742 61.111 31.33 0.78 38.21 4.85
1869 3149 2.189499 GCCATCCTGGACGAATGCC 61.189 63.158 0.00 0.00 40.96 4.40
1939 3219 2.647158 GGAAGTCGGCGAGGAAGGT 61.647 63.158 11.20 0.00 0.00 3.50
2103 3383 0.893727 TGAGCTGCTCGTAGTCCACA 60.894 55.000 23.35 1.53 32.35 4.17
2562 3842 0.250553 CCCAGGTAAACTTGTCGGCA 60.251 55.000 0.00 0.00 0.00 5.69
2568 3848 0.603065 GGCAAGCCCAGGTAAACTTG 59.397 55.000 0.00 0.00 41.89 3.16
2605 3885 1.134551 GGAGATGCTTCTCTCACCACC 60.135 57.143 24.20 7.37 46.46 4.61
2664 3944 1.435105 CTCCGAGCGCTTGATCTCA 59.565 57.895 26.61 3.39 0.00 3.27
2704 3987 4.127726 GTCCTCGACGTCGTTGTC 57.872 61.111 34.40 20.60 40.80 3.18
3293 4591 4.202284 ACGAAGTATAAGTGGGTGTGTGTT 60.202 41.667 0.00 0.00 41.94 3.32
3313 4611 2.044352 TCGCCTCAGGATGGACGA 60.044 61.111 0.00 0.00 36.16 4.20
3317 4615 3.160047 AGGCTCGCCTCAGGATGG 61.160 66.667 4.23 0.00 44.43 3.51
3329 4627 4.121669 TCTCGCAGTCGCAGGCTC 62.122 66.667 0.00 0.00 40.46 4.70
3360 4658 1.733041 CTGATATACCGCGCCACCG 60.733 63.158 0.00 0.00 37.57 4.94
3361 4659 2.027625 GCTGATATACCGCGCCACC 61.028 63.158 0.00 0.00 0.00 4.61
3362 4660 2.372690 CGCTGATATACCGCGCCAC 61.373 63.158 0.00 0.00 43.98 5.01
3363 4661 2.049526 CGCTGATATACCGCGCCA 60.050 61.111 0.00 0.00 43.98 5.69
3387 4685 2.772102 AAAAAGGGTGGGGCATTCC 58.228 52.632 0.00 0.00 0.00 3.01
3409 4707 9.228949 GATATGTAGGAGTATTTTCCGTCTAGA 57.771 37.037 0.00 0.00 42.29 2.43
3410 4708 9.233649 AGATATGTAGGAGTATTTTCCGTCTAG 57.766 37.037 0.00 0.00 42.29 2.43
3411 4709 9.228949 GAGATATGTAGGAGTATTTTCCGTCTA 57.771 37.037 0.00 0.00 42.29 2.59
3412 4710 7.724506 TGAGATATGTAGGAGTATTTTCCGTCT 59.275 37.037 0.00 0.00 42.29 4.18
3413 4711 7.883217 TGAGATATGTAGGAGTATTTTCCGTC 58.117 38.462 0.00 0.00 42.29 4.79
3414 4712 7.834881 TGAGATATGTAGGAGTATTTTCCGT 57.165 36.000 0.00 0.00 42.29 4.69
3455 4753 9.642327 AATTTGTTTGTAAAAAGAACTAACCGT 57.358 25.926 0.00 0.00 33.46 4.83
3756 5055 2.036346 GGGCATTCAGAGCTTTGTTGTT 59.964 45.455 3.90 0.00 0.00 2.83
3901 5200 2.435418 GAGGAGGATCATCAGCGGT 58.565 57.895 9.94 0.00 46.84 5.68
3908 5207 5.972327 ATTGACAAGAAGAGGAGGATCAT 57.028 39.130 0.00 0.00 36.25 2.45
4078 5378 2.375345 CCCCCAAGCTACCCACGAT 61.375 63.158 0.00 0.00 0.00 3.73
4113 5413 2.052157 GCACGACGTAAGCTATCCATC 58.948 52.381 0.00 0.00 45.62 3.51


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

AutoCloner maintained by Alex Coulton.