Multiple sequence alignment - TraesCS5D01G203100

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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 TraesCS5D01G203100 chr5D 100.000 3623 0 0 1 3623 308231277 308227655 0.000000e+00 6691.0
1 TraesCS5D01G203100 chr5A 95.692 3203 103 13 441 3623 389713392 389716579 0.000000e+00 5118.0
2 TraesCS5D01G203100 chr5A 89.569 441 33 5 1 441 389712935 389713362 6.840000e-152 547.0
3 TraesCS5D01G203100 chr5A 82.857 105 14 4 3377 3478 365256974 365256871 1.390000e-14 91.6
4 TraesCS5D01G203100 chr5B 94.531 2304 70 16 695 2993 353040836 353038584 0.000000e+00 3506.0
5 TraesCS5D01G203100 chr5B 89.600 500 28 9 3136 3623 353038586 353038099 6.650000e-172 614.0
6 TraesCS5D01G203100 chr6B 94.161 137 7 1 2991 3126 226361518 226361654 1.320000e-49 207.0
7 TraesCS5D01G203100 chr2B 94.161 137 7 1 2991 3126 608226725 608226861 1.320000e-49 207.0
8 TraesCS5D01G203100 chr2B 85.165 182 25 2 3368 3548 63837492 63837312 6.180000e-43 185.0
9 TraesCS5D01G203100 chr2B 89.474 76 8 0 480 555 653264913 653264838 2.980000e-16 97.1
10 TraesCS5D01G203100 chr6A 93.431 137 8 1 2991 3126 151467131 151466995 6.130000e-48 202.0
11 TraesCS5D01G203100 chr6A 84.663 163 22 3 3378 3538 77799171 77799010 3.740000e-35 159.0
12 TraesCS5D01G203100 chr4A 93.431 137 8 1 2991 3126 137966979 137967115 6.130000e-48 202.0
13 TraesCS5D01G203100 chr4A 93.431 137 8 1 2991 3126 137972830 137972694 6.130000e-48 202.0
14 TraesCS5D01G203100 chr3A 93.431 137 8 1 2991 3126 585500349 585500213 6.130000e-48 202.0
15 TraesCS5D01G203100 chr3A 85.714 105 15 0 3378 3482 25992064 25991960 1.060000e-20 111.0
16 TraesCS5D01G203100 chr2D 93.431 137 8 1 2991 3126 134301488 134301624 6.130000e-48 202.0
17 TraesCS5D01G203100 chr2D 85.714 182 24 2 3368 3548 37044390 37044570 1.330000e-44 191.0
18 TraesCS5D01G203100 chr1B 92.199 141 9 2 2986 3125 53067516 53067377 7.930000e-47 198.0
19 TraesCS5D01G203100 chr7D 85.256 156 15 8 3215 3369 387333756 387333608 1.740000e-33 154.0
20 TraesCS5D01G203100 chr7D 94.118 51 2 1 3254 3303 469530192 469530242 3.880000e-10 76.8
21 TraesCS5D01G203100 chr2A 89.474 76 8 0 480 555 448562431 448562356 2.980000e-16 97.1


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 TraesCS5D01G203100 chr5D 308227655 308231277 3622 True 6691.0 6691 100.0000 1 3623 1 chr5D.!!$R1 3622
1 TraesCS5D01G203100 chr5A 389712935 389716579 3644 False 2832.5 5118 92.6305 1 3623 2 chr5A.!!$F1 3622
2 TraesCS5D01G203100 chr5B 353038099 353040836 2737 True 2060.0 3506 92.0655 695 3623 2 chr5B.!!$R1 2928

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
421 422 0.107643 GCCCTCCAAGTATGAGAGGC 59.892 60.0 0.00 0.00 40.18 4.70 F
782 821 0.178973 TGACTCGTCTCACTTCCCCA 60.179 55.0 0.00 0.00 0.00 4.96 F
1771 1818 0.103572 GCCTGCCTACAATGCATTGG 59.896 55.0 35.85 23.24 41.96 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1448 0.747255 GGAGGTCAGATAGCAGCGAA 59.253 55.0 0.0 0.0 0.00 4.70 R
2548 2595 0.606673 GGGAGTTCTTGGTCACTGCC 60.607 60.0 0.0 0.0 43.41 4.85 R
3333 3385 0.535797 GAGGTAGGGTCGGTTTGGAG 59.464 60.0 0.0 0.0 0.00 3.86 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
18 19 1.471540 AGGCCTCAAGGGAGAGACA 59.528 57.895 0.00 0.00 44.26 3.41
55 56 1.295423 GGCCGAGTTGGACTAAGCA 59.705 57.895 0.00 0.00 45.46 3.91
116 117 2.601367 CAACCAAGGCCACCCTGG 60.601 66.667 5.01 8.66 41.90 4.45
155 156 2.426522 TGAAGGAAGCCATGAAGAACG 58.573 47.619 0.00 0.00 0.00 3.95
156 157 2.224523 TGAAGGAAGCCATGAAGAACGT 60.225 45.455 0.00 0.00 0.00 3.99
158 159 0.721718 GGAAGCCATGAAGAACGTCG 59.278 55.000 0.00 0.00 0.00 5.12
159 160 1.429463 GAAGCCATGAAGAACGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
186 187 3.041940 GTCCCGTCGCACACCAAG 61.042 66.667 0.00 0.00 0.00 3.61
190 191 2.317609 CCGTCGCACACCAAGGAAG 61.318 63.158 0.00 0.00 0.00 3.46
205 206 1.017177 GGAAGAACGTGCATGCGGTA 61.017 55.000 14.09 0.00 35.98 4.02
235 236 1.815421 CGCCAGGATCAAGTTCCCG 60.815 63.158 0.00 0.00 36.35 5.14
255 256 2.336667 GGCCAAACACACATACAATGC 58.663 47.619 0.00 0.00 0.00 3.56
258 259 3.995705 GCCAAACACACATACAATGCAAT 59.004 39.130 0.00 0.00 0.00 3.56
285 286 2.479566 TCAAGAAGGTCATGGAGTGC 57.520 50.000 0.00 0.00 0.00 4.40
295 296 1.346395 TCATGGAGTGCCTAAACACGT 59.654 47.619 0.00 0.00 45.45 4.49
317 318 6.037098 CGTTCAAACTCTTGAGGGTATCTAG 58.963 44.000 2.55 0.00 42.48 2.43
319 320 4.962995 TCAAACTCTTGAGGGTATCTAGGG 59.037 45.833 2.55 0.00 36.62 3.53
357 358 4.491676 TGTACTTGCACCGTCTCTAATTC 58.508 43.478 0.00 0.00 0.00 2.17
358 359 3.963428 ACTTGCACCGTCTCTAATTCT 57.037 42.857 0.00 0.00 0.00 2.40
359 360 3.851098 ACTTGCACCGTCTCTAATTCTC 58.149 45.455 0.00 0.00 0.00 2.87
360 361 2.961526 TGCACCGTCTCTAATTCTCC 57.038 50.000 0.00 0.00 0.00 3.71
361 362 2.457598 TGCACCGTCTCTAATTCTCCT 58.542 47.619 0.00 0.00 0.00 3.69
362 363 2.166459 TGCACCGTCTCTAATTCTCCTG 59.834 50.000 0.00 0.00 0.00 3.86
363 364 2.427453 GCACCGTCTCTAATTCTCCTGA 59.573 50.000 0.00 0.00 0.00 3.86
364 365 3.068873 GCACCGTCTCTAATTCTCCTGAT 59.931 47.826 0.00 0.00 0.00 2.90
365 366 4.794655 GCACCGTCTCTAATTCTCCTGATC 60.795 50.000 0.00 0.00 0.00 2.92
366 367 4.339530 CACCGTCTCTAATTCTCCTGATCA 59.660 45.833 0.00 0.00 0.00 2.92
367 368 4.956700 ACCGTCTCTAATTCTCCTGATCAA 59.043 41.667 0.00 0.00 0.00 2.57
368 369 5.600484 ACCGTCTCTAATTCTCCTGATCAAT 59.400 40.000 0.00 0.00 0.00 2.57
369 370 6.155827 CCGTCTCTAATTCTCCTGATCAATC 58.844 44.000 0.00 0.00 0.00 2.67
372 373 7.083858 GTCTCTAATTCTCCTGATCAATCTCG 58.916 42.308 0.00 0.00 0.00 4.04
384 385 4.867047 TGATCAATCTCGAGTTCAAAGCTC 59.133 41.667 13.13 1.81 0.00 4.09
388 389 4.527509 ATCTCGAGTTCAAAGCTCTTCA 57.472 40.909 13.13 0.00 0.00 3.02
421 422 0.107643 GCCCTCCAAGTATGAGAGGC 59.892 60.000 0.00 0.00 40.18 4.70
433 434 7.122650 CCAAGTATGAGAGGCATTCCTTTTTAA 59.877 37.037 0.00 0.00 44.46 1.52
436 437 8.523658 AGTATGAGAGGCATTCCTTTTTAAAAC 58.476 33.333 0.00 0.00 44.46 2.43
457 488 8.607441 AAAACCAATTCCTTTCAAAATCTAGC 57.393 30.769 0.00 0.00 0.00 3.42
458 489 6.916360 ACCAATTCCTTTCAAAATCTAGCA 57.084 33.333 0.00 0.00 0.00 3.49
460 491 5.801947 CCAATTCCTTTCAAAATCTAGCACG 59.198 40.000 0.00 0.00 0.00 5.34
489 522 5.880341 ACTCCAACTTATAAAATCAAGCGC 58.120 37.500 0.00 0.00 0.00 5.92
501 534 2.985847 AAGCGCCACCCTTGCTTC 60.986 61.111 2.29 0.00 45.24 3.86
543 576 5.095145 AGAGTACGAAATCCTTAAACCCC 57.905 43.478 0.00 0.00 0.00 4.95
584 617 4.605183 TCTCTCCCTCTCTTCCTACAAAG 58.395 47.826 0.00 0.00 0.00 2.77
589 622 4.528596 TCCCTCTCTTCCTACAAAGACTTG 59.471 45.833 0.00 0.00 38.61 3.16
666 701 2.597903 GGTGGATGGAGCCCTTCC 59.402 66.667 15.25 15.25 44.98 3.46
669 704 1.213296 GTGGATGGAGCCCTTCCTTA 58.787 55.000 19.93 5.43 46.92 2.69
679 714 5.422012 TGGAGCCCTTCCTTATTCAAAATTC 59.578 40.000 0.00 0.00 46.92 2.17
738 776 1.585521 GTCTCACCGTCGCCGTATG 60.586 63.158 0.00 0.00 0.00 2.39
746 784 1.227176 GTCGCCGTATGGTCCTTCC 60.227 63.158 2.17 0.00 37.67 3.46
781 820 0.528470 CTGACTCGTCTCACTTCCCC 59.472 60.000 0.00 0.00 0.00 4.81
782 821 0.178973 TGACTCGTCTCACTTCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
783 822 1.187087 GACTCGTCTCACTTCCCCAT 58.813 55.000 0.00 0.00 0.00 4.00
784 823 1.550976 GACTCGTCTCACTTCCCCATT 59.449 52.381 0.00 0.00 0.00 3.16
785 824 1.550976 ACTCGTCTCACTTCCCCATTC 59.449 52.381 0.00 0.00 0.00 2.67
786 825 1.550524 CTCGTCTCACTTCCCCATTCA 59.449 52.381 0.00 0.00 0.00 2.57
787 826 1.275291 TCGTCTCACTTCCCCATTCAC 59.725 52.381 0.00 0.00 0.00 3.18
788 827 1.276421 CGTCTCACTTCCCCATTCACT 59.724 52.381 0.00 0.00 0.00 3.41
868 908 1.682684 GCGACCTCCTCTTCCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
904 944 3.095332 GACCCTAACTTCCTCGGTAAGT 58.905 50.000 0.00 0.00 38.82 2.24
1374 1421 3.880846 CTGGCCAATTCGCTCGCC 61.881 66.667 7.01 0.00 41.99 5.54
1506 1553 4.545706 GATGATGCGGTCCGGGCA 62.546 66.667 14.38 7.49 45.71 5.36
1771 1818 0.103572 GCCTGCCTACAATGCATTGG 59.896 55.000 35.85 23.24 41.96 3.16
1819 1866 2.945984 CACGTGCGCAGGAACATT 59.054 55.556 34.34 10.72 0.00 2.71
2247 2294 1.668826 AGGCTGTTGAGGTATGGGAA 58.331 50.000 0.00 0.00 0.00 3.97
2422 2469 3.010420 GTTTTGAGGGATAGGCTGACAC 58.990 50.000 0.00 0.00 0.00 3.67
2538 2585 4.777896 AGTAGTAAGAGGGCTGATGAAACA 59.222 41.667 0.00 0.00 0.00 2.83
2548 2595 0.516877 TGATGAAACAAGAAGCGCGG 59.483 50.000 8.83 0.00 0.00 6.46
2570 2617 1.417890 CAGTGACCAAGAACTCCCAGT 59.582 52.381 0.00 0.00 0.00 4.00
2734 2781 9.933723 TTTAAGGTAGTAAAATGTCCAGTCTAC 57.066 33.333 0.00 0.00 0.00 2.59
3001 3051 4.270834 TCATACTATCATACTCCCTCCGC 58.729 47.826 0.00 0.00 0.00 5.54
3044 3095 8.893219 TTAGAGATTGCAATAAGGACTACATG 57.107 34.615 12.97 0.00 0.00 3.21
3083 3134 8.804688 ACATATTTTAGAGTGTAGATTCGCTC 57.195 34.615 0.00 0.00 42.95 5.03
3098 3149 3.656651 TCGCTCATTTTGCTTCGTATG 57.343 42.857 0.00 0.00 0.00 2.39
3112 3163 1.067974 TCGTATGTAGTCCGCATTGGG 59.932 52.381 0.00 0.00 38.76 4.12
3115 3166 2.550830 ATGTAGTCCGCATTGGGATC 57.449 50.000 1.69 0.00 38.61 3.36
3131 3182 5.636903 TGGGATCTCTAAAAAGATGGAGG 57.363 43.478 0.00 0.00 36.13 4.30
3138 3189 6.261435 TCTCTAAAAAGATGGAGGGAGTACA 58.739 40.000 0.00 0.00 0.00 2.90
3246 3297 7.654022 ATTAAAGGAGAGTTTGTTGGTTTCA 57.346 32.000 0.00 0.00 0.00 2.69
3330 3382 6.523840 ACCACGCGATAACCCTAATTAATTA 58.476 36.000 15.93 7.66 0.00 1.40
3333 3385 8.173130 CCACGCGATAACCCTAATTAATTATTC 58.827 37.037 15.93 0.30 0.00 1.75
3433 3486 3.662759 TTCCTTACCTTTGCCTATGGG 57.337 47.619 0.00 0.00 0.00 4.00
3441 3494 2.379005 CTTTGCCTATGGGTTCCCTTC 58.621 52.381 9.43 0.00 34.45 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.795110 GCTCTGCGCTCCAGGAGAT 61.795 63.158 21.89 0.00 42.05 2.75
36 37 1.810030 GCTTAGTCCAACTCGGCCG 60.810 63.158 22.12 22.12 33.14 6.13
46 47 4.273318 AGAATTGTTCCCATGCTTAGTCC 58.727 43.478 0.00 0.00 0.00 3.85
55 56 2.505819 AGCGACCTAGAATTGTTCCCAT 59.494 45.455 0.00 0.00 0.00 4.00
72 73 1.670949 GATGGTCTCCTGCTCAGCGA 61.671 60.000 0.00 0.00 0.00 4.93
74 75 1.145819 GGATGGTCTCCTGCTCAGC 59.854 63.158 0.00 0.00 41.29 4.26
129 130 1.562942 TCATGGCTTCCTTCATCTGCT 59.437 47.619 0.00 0.00 0.00 4.24
155 156 4.773117 GGACGGCGACTCCACGAC 62.773 72.222 16.62 0.00 38.00 4.34
174 175 0.586802 GTTCTTCCTTGGTGTGCGAC 59.413 55.000 0.00 0.00 0.00 5.19
177 178 0.307760 CACGTTCTTCCTTGGTGTGC 59.692 55.000 0.00 0.00 0.00 4.57
186 187 1.017177 TACCGCATGCACGTTCTTCC 61.017 55.000 19.57 0.00 0.00 3.46
190 191 1.708027 GACTACCGCATGCACGTTC 59.292 57.895 19.57 4.80 0.00 3.95
235 236 2.288702 TGCATTGTATGTGTGTTTGGCC 60.289 45.455 0.00 0.00 0.00 5.36
255 256 2.154462 ACCTTCTTGAACCGCTCATTG 58.846 47.619 0.00 0.00 32.78 2.82
258 259 0.756294 TGACCTTCTTGAACCGCTCA 59.244 50.000 0.00 0.00 0.00 4.26
268 269 1.366319 AGGCACTCCATGACCTTCTT 58.634 50.000 0.00 0.00 36.75 2.52
285 286 5.277345 CCTCAAGAGTTTGAACGTGTTTAGG 60.277 44.000 0.00 0.00 42.48 2.69
295 296 5.425539 CCCTAGATACCCTCAAGAGTTTGAA 59.574 44.000 0.00 0.00 42.48 2.69
319 320 4.828072 AGTACAAGAGTTTGGGAGGATC 57.172 45.455 0.00 0.00 38.66 3.36
357 358 4.645762 TGAACTCGAGATTGATCAGGAG 57.354 45.455 21.68 2.33 35.68 3.69
358 359 5.405935 TTTGAACTCGAGATTGATCAGGA 57.594 39.130 21.68 5.50 0.00 3.86
359 360 4.033817 GCTTTGAACTCGAGATTGATCAGG 59.966 45.833 21.68 11.58 0.00 3.86
360 361 4.869297 AGCTTTGAACTCGAGATTGATCAG 59.131 41.667 21.68 6.91 0.00 2.90
361 362 4.825422 AGCTTTGAACTCGAGATTGATCA 58.175 39.130 21.68 11.78 0.00 2.92
362 363 5.108517 AGAGCTTTGAACTCGAGATTGATC 58.891 41.667 21.68 10.46 39.23 2.92
363 364 5.083533 AGAGCTTTGAACTCGAGATTGAT 57.916 39.130 21.68 1.29 39.23 2.57
364 365 4.527509 AGAGCTTTGAACTCGAGATTGA 57.472 40.909 21.68 0.86 39.23 2.57
365 366 4.687948 TGAAGAGCTTTGAACTCGAGATTG 59.312 41.667 21.68 4.03 39.23 2.67
366 367 4.887748 TGAAGAGCTTTGAACTCGAGATT 58.112 39.130 21.68 9.73 39.23 2.40
367 368 4.527509 TGAAGAGCTTTGAACTCGAGAT 57.472 40.909 21.68 7.33 39.23 2.75
368 369 4.489810 GATGAAGAGCTTTGAACTCGAGA 58.510 43.478 21.68 0.00 39.23 4.04
369 370 3.616379 GGATGAAGAGCTTTGAACTCGAG 59.384 47.826 11.84 11.84 39.23 4.04
372 373 2.675348 CGGGATGAAGAGCTTTGAACTC 59.325 50.000 0.00 0.00 0.00 3.01
384 385 3.261897 AGGGCTATTATGTCGGGATGAAG 59.738 47.826 0.00 0.00 0.00 3.02
388 389 2.188817 GGAGGGCTATTATGTCGGGAT 58.811 52.381 0.00 0.00 0.00 3.85
433 434 7.657354 GTGCTAGATTTTGAAAGGAATTGGTTT 59.343 33.333 0.00 0.00 0.00 3.27
436 437 5.801947 CGTGCTAGATTTTGAAAGGAATTGG 59.198 40.000 0.00 0.00 0.00 3.16
451 482 2.100197 TGGAGTTGCTACGTGCTAGAT 58.900 47.619 0.00 0.00 43.37 1.98
456 487 1.226746 AAGTTGGAGTTGCTACGTGC 58.773 50.000 0.00 0.00 43.25 5.34
457 488 6.715344 TTTATAAGTTGGAGTTGCTACGTG 57.285 37.500 0.00 0.00 0.00 4.49
458 489 7.604927 TGATTTTATAAGTTGGAGTTGCTACGT 59.395 33.333 0.00 0.00 0.00 3.57
460 491 9.774742 CTTGATTTTATAAGTTGGAGTTGCTAC 57.225 33.333 0.00 0.00 0.00 3.58
465 498 6.322491 GCGCTTGATTTTATAAGTTGGAGTT 58.678 36.000 0.00 0.00 0.00 3.01
472 505 3.380320 GGGTGGCGCTTGATTTTATAAGT 59.620 43.478 7.64 0.00 0.00 2.24
515 548 7.983484 GGTTTAAGGATTTCGTACTCTTCCATA 59.017 37.037 0.00 0.00 0.00 2.74
543 576 0.806868 AGAAAGCATGTGTCGGCATG 59.193 50.000 0.00 1.88 46.50 4.06
625 658 1.241315 GCTAGTGGGCCGCTCAAAAA 61.241 55.000 25.40 4.35 0.00 1.94
649 684 2.597903 GGAAGGGCTCCATCCACC 59.402 66.667 9.75 0.00 44.67 4.61
669 704 9.264719 CTCTTTGTAAGGCTTTGAATTTTGAAT 57.735 29.630 4.45 0.00 0.00 2.57
714 749 1.300697 GCGACGGTGAGACAAGGTT 60.301 57.895 0.00 0.00 0.00 3.50
738 776 0.895559 CTTGGGCTTGTGGAAGGACC 60.896 60.000 0.00 0.00 39.54 4.46
746 784 1.338020 GTCAGGAAACTTGGGCTTGTG 59.662 52.381 0.00 0.00 40.21 3.33
781 820 2.295885 GAGGGCCTGAATGAGTGAATG 58.704 52.381 12.95 0.00 0.00 2.67
782 821 1.213926 GGAGGGCCTGAATGAGTGAAT 59.786 52.381 12.95 0.00 0.00 2.57
783 822 0.620556 GGAGGGCCTGAATGAGTGAA 59.379 55.000 12.95 0.00 0.00 3.18
784 823 0.252881 AGGAGGGCCTGAATGAGTGA 60.253 55.000 12.95 0.00 44.90 3.41
785 824 2.305095 AGGAGGGCCTGAATGAGTG 58.695 57.895 12.95 0.00 44.90 3.51
786 825 4.928981 AGGAGGGCCTGAATGAGT 57.071 55.556 12.95 0.00 44.90 3.41
1078 1119 4.388499 GGGCGAGGCGGTGAAGAA 62.388 66.667 0.00 0.00 0.00 2.52
1124 1171 3.827898 CTCGGTCGACCTCTGGGC 61.828 72.222 30.92 4.32 35.63 5.36
1126 1173 3.141488 CCCTCGGTCGACCTCTGG 61.141 72.222 30.92 26.05 0.00 3.86
1127 1174 3.827898 GCCCTCGGTCGACCTCTG 61.828 72.222 30.92 19.56 0.00 3.35
1128 1175 3.999297 GAGCCCTCGGTCGACCTCT 62.999 68.421 30.92 18.75 0.00 3.69
1129 1176 3.519930 GAGCCCTCGGTCGACCTC 61.520 72.222 30.92 17.30 0.00 3.85
1401 1448 0.747255 GGAGGTCAGATAGCAGCGAA 59.253 55.000 0.00 0.00 0.00 4.70
1410 1457 3.083997 GCCGGTGGGAGGTCAGAT 61.084 66.667 1.90 0.00 34.06 2.90
1479 1526 1.742146 CGCATCATCCGGGAGAAGA 59.258 57.895 0.00 0.79 0.00 2.87
1498 1545 1.700042 ATGGAGGAGAATGCCCGGAC 61.700 60.000 0.73 0.00 0.00 4.79
1506 1553 2.455565 CCCCGCCATGGAGGAGAAT 61.456 63.158 33.93 0.00 40.01 2.40
1819 1866 3.374988 CGGCTCTGTTGCATATCTTTCAA 59.625 43.478 0.00 0.00 34.04 2.69
2206 2253 5.823045 CCTTATCAATCCTTCCTACACCAAC 59.177 44.000 0.00 0.00 0.00 3.77
2247 2294 1.303317 GCCACGTGTTTCCATCCCT 60.303 57.895 15.65 0.00 0.00 4.20
2538 2585 4.314440 TCACTGCCCGCGCTTCTT 62.314 61.111 5.56 0.00 35.36 2.52
2548 2595 0.606673 GGGAGTTCTTGGTCACTGCC 60.607 60.000 0.00 0.00 43.41 4.85
2570 2617 4.595762 TCATTCTCATCGAGATCATGCA 57.404 40.909 0.00 0.00 38.56 3.96
2734 2781 6.926826 TGTATTAGTACAACTTCCATATGGCG 59.073 38.462 17.58 12.49 37.86 5.69
2927 2975 8.114331 AGTTCATATCAGCAAATGAGAAACAA 57.886 30.769 0.00 0.00 42.53 2.83
3028 3079 2.833794 TCCGCATGTAGTCCTTATTGC 58.166 47.619 0.00 0.00 0.00 3.56
3080 3131 5.470845 ACTACATACGAAGCAAAATGAGC 57.529 39.130 0.00 0.00 0.00 4.26
3083 3134 4.782195 GCGGACTACATACGAAGCAAAATG 60.782 45.833 0.00 0.00 0.00 2.32
3098 3149 1.689273 AGAGATCCCAATGCGGACTAC 59.311 52.381 0.00 0.00 36.56 2.73
3112 3163 6.493189 ACTCCCTCCATCTTTTTAGAGATC 57.507 41.667 0.00 0.00 34.20 2.75
3115 3166 6.546428 TGTACTCCCTCCATCTTTTTAGAG 57.454 41.667 0.00 0.00 0.00 2.43
3131 3182 4.959596 TCTTGACAGACGTATGTACTCC 57.040 45.455 17.01 4.23 32.25 3.85
3138 3189 4.456280 TGAAGCATCTTGACAGACGTAT 57.544 40.909 0.00 0.00 0.00 3.06
3246 3297 1.079323 AGGGGTGGAAGCAATGGAAAT 59.921 47.619 0.00 0.00 34.77 2.17
3330 3382 1.558294 GGTAGGGTCGGTTTGGAGAAT 59.442 52.381 0.00 0.00 0.00 2.40
3333 3385 0.535797 GAGGTAGGGTCGGTTTGGAG 59.464 60.000 0.00 0.00 0.00 3.86
3433 3486 4.200092 GAGATATGTTGTGGGAAGGGAAC 58.800 47.826 0.00 0.00 0.00 3.62
3441 3494 5.297776 GGTTGAGATTGAGATATGTTGTGGG 59.702 44.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.