Multiple sequence alignment - TraesCS4D01G322400

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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 TraesCS4D01G322400 chr4D 100.000 5903 0 0 1 5903 484407232 484401330 0 10901
1 TraesCS4D01G322400 chr5A 92.574 5979 248 73 1 5902 664813995 664808136 0 8401
2 TraesCS4D01G322400 chr4B 91.548 3431 156 51 54 3401 616310643 616307264 0 4606
3 TraesCS4D01G322400 chr4B 91.167 1268 85 21 3415 4669 616307206 616305953 0 1696
4 TraesCS4D01G322400 chr4B 87.931 986 64 36 4733 5704 616305872 616304928 0 1110


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 TraesCS4D01G322400 chr4D 484401330 484407232 5902 True 10901.000000 10901 100.000000 1 5903 1 chr4D.!!$R1 5902
1 TraesCS4D01G322400 chr5A 664808136 664813995 5859 True 8401.000000 8401 92.574000 1 5902 1 chr5A.!!$R1 5901
2 TraesCS4D01G322400 chr4B 616304928 616310643 5715 True 2470.666667 4606 90.215333 54 5704 3 chr4B.!!$R1 5650

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
554 631 0.112412 AGCTAGGAGCCTAGGAGAGC 59.888 60.0 21.70 12.32 43.77 4.09 F
2021 2131 0.541863 TCGCCCCTCTTTCCTTGATC 59.458 55.0 0.00 0.00 0.00 2.92 F
2197 2311 0.299895 CATACGCTCTGCTTGCTTCG 59.700 55.0 0.00 0.00 0.00 3.79 F
3455 3613 0.250209 ATCTTGCTATGCAGAGCCCG 60.250 55.0 29.15 19.62 42.11 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2306 0.307760 CCACCTGACAACAACGAAGC 59.692 55.000 0.00 0.00 0.00 3.86 R
3422 3580 0.674581 CAAGATGCTCACAGCCCGAA 60.675 55.000 0.00 0.00 41.51 4.30 R
3466 3624 2.533266 GAGGCAATACAACTGCAATGC 58.467 47.619 0.00 0.00 41.78 3.56 R
5020 5229 0.522626 TTCAATCACACAGCGCATGG 59.477 50.000 11.47 0.14 0.00 3.66 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
194 234 0.323725 GTACGTACCCTCCCCACTCA 60.324 60.000 15.00 0.00 0.00 3.41
195 235 0.409092 TACGTACCCTCCCCACTCAA 59.591 55.000 0.00 0.00 0.00 3.02
308 373 2.543802 CGGAGCCGCTCATCGACTA 61.544 63.158 21.76 0.00 41.67 2.59
386 455 4.047059 GCTGGGTTCGTCGACCGA 62.047 66.667 10.58 7.98 45.66 4.69
441 515 3.548214 GCTCTGGTTTCCTTGTCGTTTTC 60.548 47.826 0.00 0.00 0.00 2.29
442 516 3.877508 CTCTGGTTTCCTTGTCGTTTTCT 59.122 43.478 0.00 0.00 0.00 2.52
443 517 4.266714 TCTGGTTTCCTTGTCGTTTTCTT 58.733 39.130 0.00 0.00 0.00 2.52
444 518 4.334481 TCTGGTTTCCTTGTCGTTTTCTTC 59.666 41.667 0.00 0.00 0.00 2.87
445 519 3.064271 TGGTTTCCTTGTCGTTTTCTTCG 59.936 43.478 0.00 0.00 0.00 3.79
446 520 3.064408 GGTTTCCTTGTCGTTTTCTTCGT 59.936 43.478 0.00 0.00 0.00 3.85
447 521 4.269312 GTTTCCTTGTCGTTTTCTTCGTC 58.731 43.478 0.00 0.00 0.00 4.20
448 522 3.447918 TCCTTGTCGTTTTCTTCGTCT 57.552 42.857 0.00 0.00 0.00 4.18
449 523 3.378339 TCCTTGTCGTTTTCTTCGTCTC 58.622 45.455 0.00 0.00 0.00 3.36
457 531 2.327081 TTTCTTCGTCTCCTTCGTCG 57.673 50.000 0.00 0.00 0.00 5.12
461 535 2.196382 TTCGTCTCCTTCGTCGGCAG 62.196 60.000 0.00 0.00 0.00 4.85
462 536 2.507324 GTCTCCTTCGTCGGCAGC 60.507 66.667 0.00 0.00 0.00 5.25
487 561 2.590645 CTCCTCCTCCGTCTCCGA 59.409 66.667 0.00 0.00 35.63 4.55
488 562 1.820481 CTCCTCCTCCGTCTCCGAC 60.820 68.421 0.00 0.00 35.63 4.79
489 563 2.260088 CTCCTCCTCCGTCTCCGACT 62.260 65.000 0.00 0.00 35.63 4.18
490 564 1.820481 CCTCCTCCGTCTCCGACTC 60.820 68.421 0.00 0.00 35.63 3.36
491 565 1.222387 CTCCTCCGTCTCCGACTCT 59.778 63.158 0.00 0.00 35.63 3.24
492 566 0.812412 CTCCTCCGTCTCCGACTCTC 60.812 65.000 0.00 0.00 35.63 3.20
493 567 1.820481 CCTCCGTCTCCGACTCTCC 60.820 68.421 0.00 0.00 35.63 3.71
494 568 2.125229 TCCGTCTCCGACTCTCCG 60.125 66.667 0.00 0.00 35.63 4.63
504 578 1.658686 CGACTCTCCGTGGGGAAGAG 61.659 65.000 2.46 2.46 43.27 2.85
507 581 0.614979 CTCTCCGTGGGGAAGAGGAA 60.615 60.000 0.00 0.00 43.27 3.36
518 592 1.657751 GAAGAGGAAACGCCATGGCC 61.658 60.000 30.79 16.40 40.02 5.36
520 597 1.754234 GAGGAAACGCCATGGCCAT 60.754 57.895 30.79 14.09 40.02 4.40
550 627 5.313280 GCTATATAGCTAGGAGCCTAGGA 57.687 47.826 24.63 0.00 43.77 2.94
552 629 5.072600 GCTATATAGCTAGGAGCCTAGGAGA 59.927 48.000 24.63 0.00 43.77 3.71
553 630 5.646692 ATATAGCTAGGAGCCTAGGAGAG 57.353 47.826 21.70 2.21 43.77 3.20
554 631 0.112412 AGCTAGGAGCCTAGGAGAGC 59.888 60.000 21.70 12.32 43.77 4.09
667 747 1.136695 TCTACCGTCTCGTCTCTCTCC 59.863 57.143 0.00 0.00 0.00 3.71
684 767 3.260205 TCTCCCTTCACTTTCTTCCCAT 58.740 45.455 0.00 0.00 0.00 4.00
872 960 0.596600 CAGCCATGCGCATCAAATCC 60.597 55.000 22.51 5.19 41.38 3.01
1268 1363 4.758251 TCGGCAGCACCATCACCG 62.758 66.667 0.00 0.00 45.15 4.94
1318 1416 4.112341 GACGACGACGGGGGTGAG 62.112 72.222 12.58 0.00 44.46 3.51
1319 1417 4.962836 ACGACGACGGGGGTGAGT 62.963 66.667 12.58 0.00 44.46 3.41
1320 1418 4.112341 CGACGACGGGGGTGAGTC 62.112 72.222 0.00 0.00 35.72 3.36
1321 1419 3.756727 GACGACGGGGGTGAGTCC 61.757 72.222 0.00 0.00 34.10 3.85
1379 1489 3.423154 CGGTGAAGGAACGGCTGC 61.423 66.667 0.00 0.00 0.00 5.25
1380 1490 2.281484 GGTGAAGGAACGGCTGCA 60.281 61.111 0.50 0.00 0.00 4.41
1843 1953 3.677424 GCAACGCTCTCAAGGTAGAGATT 60.677 47.826 5.09 0.00 44.93 2.40
1844 1954 3.791973 ACGCTCTCAAGGTAGAGATTG 57.208 47.619 5.09 0.00 44.93 2.67
1856 1966 1.376543 AGAGATTGTGGCTCATTGCG 58.623 50.000 0.00 0.00 44.05 4.85
1868 1978 1.863454 CTCATTGCGAATCCCTTCTCG 59.137 52.381 0.00 0.00 38.11 4.04
1891 2001 2.448961 TCCTTTCCATTCTCCAAACCCA 59.551 45.455 0.00 0.00 0.00 4.51
1895 2005 4.666412 TTCCATTCTCCAAACCCATGTA 57.334 40.909 0.00 0.00 0.00 2.29
1898 2008 4.017591 TCCATTCTCCAAACCCATGTATGT 60.018 41.667 0.00 0.00 0.00 2.29
2021 2131 0.541863 TCGCCCCTCTTTCCTTGATC 59.458 55.000 0.00 0.00 0.00 2.92
2025 2135 3.369175 GCCCCTCTTTCCTTGATCATTT 58.631 45.455 0.00 0.00 0.00 2.32
2075 2185 5.813513 AAATTTTGCAGGAGGTTGATCTT 57.186 34.783 0.00 0.00 0.00 2.40
2090 2200 6.045955 GGTTGATCTTAGAGGTTCTGATGTC 58.954 44.000 0.00 0.00 0.00 3.06
2125 2235 1.951510 CACAGGTGCGCTGAAACAT 59.048 52.632 9.73 0.00 0.00 2.71
2182 2296 2.427232 TGCCGGTATCGCTAACATAC 57.573 50.000 1.90 0.00 34.56 2.39
2192 2306 1.256376 CGCTAACATACGCTCTGCTTG 59.744 52.381 0.00 0.00 0.00 4.01
2193 2307 1.004504 GCTAACATACGCTCTGCTTGC 60.005 52.381 0.00 0.00 0.00 4.01
2195 2309 1.813513 AACATACGCTCTGCTTGCTT 58.186 45.000 0.00 0.00 0.00 3.91
2196 2310 1.363744 ACATACGCTCTGCTTGCTTC 58.636 50.000 0.00 0.00 0.00 3.86
2197 2311 0.299895 CATACGCTCTGCTTGCTTCG 59.700 55.000 0.00 0.00 0.00 3.79
2222 2336 1.471287 TGTCAGGTGGTCGATACTTCG 59.529 52.381 0.00 0.00 46.87 3.79
2600 2714 2.690778 GGCAATTCGGCTGCGAAGT 61.691 57.895 11.30 7.07 40.88 3.01
2609 2723 0.601311 GGCTGCGAAGTGTCAAGACT 60.601 55.000 1.53 0.00 0.00 3.24
2633 2747 5.782331 TGGGAGTATGGATCTTATCTTGGAG 59.218 44.000 0.00 0.00 0.00 3.86
2850 2964 5.555017 AGCTCCATACTAGTGGCATTAATG 58.445 41.667 11.27 11.27 39.19 1.90
2935 3049 4.017591 TGTGGATGTTCAGAATAATGGGGT 60.018 41.667 0.00 0.00 0.00 4.95
2936 3050 5.192722 TGTGGATGTTCAGAATAATGGGGTA 59.807 40.000 0.00 0.00 0.00 3.69
3337 3451 5.652518 GGTTTGGATGAGTAGTCAGTAGAC 58.347 45.833 6.39 1.70 45.31 2.59
3364 3478 4.729868 ACAACTCTCTAAAAACCTGGCAT 58.270 39.130 0.00 0.00 0.00 4.40
3366 3480 3.600388 ACTCTCTAAAAACCTGGCATCG 58.400 45.455 0.00 0.00 0.00 3.84
3401 3515 6.867293 CCTAATACCCGTATCTTTACTTGAGC 59.133 42.308 0.00 0.00 0.00 4.26
3419 3577 1.009829 GCGGCTCAAATAGGAGTGTG 58.990 55.000 0.00 0.00 37.24 3.82
3422 3580 3.741388 GCGGCTCAAATAGGAGTGTGTAT 60.741 47.826 0.00 0.00 37.24 2.29
3424 3582 4.508124 CGGCTCAAATAGGAGTGTGTATTC 59.492 45.833 0.00 0.00 37.24 1.75
3432 3590 1.359848 GAGTGTGTATTCGGGCTGTG 58.640 55.000 0.00 0.00 0.00 3.66
3433 3591 0.973632 AGTGTGTATTCGGGCTGTGA 59.026 50.000 0.00 0.00 0.00 3.58
3455 3613 0.250209 ATCTTGCTATGCAGAGCCCG 60.250 55.000 29.15 19.62 42.11 6.13
3466 3624 1.006832 CAGAGCCCGGATTTTGTACG 58.993 55.000 0.73 0.00 0.00 3.67
3492 3650 1.004610 CAGTTGTATTGCCTCGATGCG 60.005 52.381 8.19 0.00 0.00 4.73
3572 3735 2.303311 GGCAGGGACTCTTAAACAGACT 59.697 50.000 0.00 0.00 34.60 3.24
3692 3857 4.462132 TGTTTGCATACATACAACTGCCAT 59.538 37.500 5.83 0.00 35.21 4.40
3825 3990 1.981256 TCAAGAAAGTTGGGCACTCC 58.019 50.000 0.00 0.00 32.94 3.85
4028 4193 0.869454 GAGAGCAGATTCAGTCCGCG 60.869 60.000 0.00 0.00 35.35 6.46
4251 4416 1.609072 GAGAAACCTGTCACCCTTTGC 59.391 52.381 0.00 0.00 0.00 3.68
4295 4460 3.625853 TCAGTGAACACAAACCAATGGA 58.374 40.909 6.16 0.00 0.00 3.41
4441 4606 0.958822 AAAGCGGTTCGGCATTTCTT 59.041 45.000 0.00 0.00 34.64 2.52
4566 4731 5.411781 AGTGCTAAAACAGTTAGGATCTCG 58.588 41.667 0.00 0.00 0.00 4.04
4743 4950 4.469586 TCCAGTAGTCATATGCTTGGTGAA 59.530 41.667 13.19 0.00 0.00 3.18
4881 5088 9.326413 GAATAGGAAAGAATAGGAATTTGTCGA 57.674 33.333 0.00 0.00 0.00 4.20
5020 5229 4.510038 TGAAAGCTTTCTTGAAGGCATC 57.490 40.909 33.03 14.75 38.02 3.91
5022 5231 2.592102 AGCTTTCTTGAAGGCATCCA 57.408 45.000 17.40 0.00 35.82 3.41
5023 5232 3.097342 AGCTTTCTTGAAGGCATCCAT 57.903 42.857 17.40 0.00 35.82 3.41
5024 5233 2.758979 AGCTTTCTTGAAGGCATCCATG 59.241 45.455 17.40 0.00 35.82 3.66
5025 5234 7.810771 AAAGCTTTCTTGAAGGCATCCATGC 62.811 44.000 17.40 2.68 41.76 4.06
5035 5244 1.721664 GCATCCATGCGCTGTGTGAT 61.722 55.000 9.73 9.66 44.67 3.06
5036 5245 0.736636 CATCCATGCGCTGTGTGATT 59.263 50.000 9.73 0.00 0.00 2.57
5038 5247 0.321475 TCCATGCGCTGTGTGATTGA 60.321 50.000 9.73 0.00 0.00 2.57
5039 5248 0.522626 CCATGCGCTGTGTGATTGAA 59.477 50.000 9.73 0.00 0.00 2.69
5040 5249 1.609932 CATGCGCTGTGTGATTGAAC 58.390 50.000 9.73 0.00 0.00 3.18
5070 5279 2.029288 ATGCCTTCACGCGTCAGTG 61.029 57.895 9.86 0.00 43.11 3.66
5194 5411 4.277476 TCCCTTGTAAAATTCGATGGCAT 58.723 39.130 0.00 0.00 0.00 4.40
5279 5496 5.179368 TGTTTAGCTGACAGTAAGAATGCAC 59.821 40.000 3.99 0.00 0.00 4.57
5291 5508 6.036408 CAGTAAGAATGCACTCATCGATCAAA 59.964 38.462 0.00 0.00 31.27 2.69
5350 5568 3.822735 CCAGATCAGTGAAGGCTTTTTCA 59.177 43.478 0.00 0.00 34.83 2.69
5376 5595 0.327924 TGGTCATGTGTAAGGCAGGG 59.672 55.000 0.00 0.00 0.00 4.45
5403 5624 3.389866 TCTAGACTCCTAGACAGCCTCT 58.610 50.000 0.00 0.00 44.69 3.69
5598 5822 3.722147 ACAGTCTGCGATTGCTTATAGG 58.278 45.455 6.47 0.00 43.34 2.57
5641 5869 7.465353 TTTTCTCTGAATGTGCATTGGAATA 57.535 32.000 1.77 0.00 0.00 1.75
5642 5870 7.649533 TTTCTCTGAATGTGCATTGGAATAT 57.350 32.000 1.77 0.00 0.00 1.28
5655 5883 5.407387 GCATTGGAATATGCCTGCTATTTTG 59.593 40.000 6.70 0.00 44.01 2.44
5707 5941 1.889105 CACAAGTGCGGCAGTGACT 60.889 57.895 11.71 0.00 33.99 3.41
5720 5954 5.334569 GCGGCAGTGACTTAGTAATTCAAAA 60.335 40.000 4.64 0.00 0.00 2.44
5721 5955 6.622896 GCGGCAGTGACTTAGTAATTCAAAAT 60.623 38.462 4.64 0.00 0.00 1.82
5749 5983 8.797266 AGTAGTATAAAGCAAAACAAAACTGC 57.203 30.769 0.00 0.00 36.29 4.40
5753 5987 8.417884 AGTATAAAGCAAAACAAAACTGCCTAA 58.582 29.630 0.00 0.00 36.73 2.69
5755 5989 4.736126 AGCAAAACAAAACTGCCTAACT 57.264 36.364 0.00 0.00 36.73 2.24
5756 5990 4.432712 AGCAAAACAAAACTGCCTAACTG 58.567 39.130 0.00 0.00 36.73 3.16
5767 6001 6.715347 AACTGCCTAACTGACAAAGAAATT 57.285 33.333 0.00 0.00 0.00 1.82
5768 6002 6.319141 ACTGCCTAACTGACAAAGAAATTC 57.681 37.500 0.00 0.00 0.00 2.17
5774 6008 7.379797 GCCTAACTGACAAAGAAATTCAGAAAC 59.620 37.037 4.88 0.00 39.36 2.78
5779 6013 9.956720 ACTGACAAAGAAATTCAGAAACTAATG 57.043 29.630 4.88 0.00 39.36 1.90
5797 6034 6.218746 ACTAATGAAAGACCGTTCGTTAACT 58.781 36.000 3.71 0.00 38.11 2.24
5840 6077 2.747855 GCCGGCTTGGAGTTGGAG 60.748 66.667 22.15 0.00 42.00 3.86
5866 6103 2.674084 GGTACGGCGACCTTTGTGC 61.674 63.158 16.62 0.00 36.47 4.57
5869 6106 4.389576 CGGCGACCTTTGTGCTGC 62.390 66.667 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.954904 TCTCAATTTCTACTCCTCCTCCG 59.045 47.826 0.00 0.00 0.00 4.63
90 94 0.177604 CAAGTAGCCTCTGCCTCTGG 59.822 60.000 0.00 0.00 38.69 3.86
200 240 1.003866 CAGGAATAAAGTTAGCCGCGC 60.004 52.381 0.00 0.00 0.00 6.86
282 347 3.781770 GAGCGGCTCCGGATCACTG 62.782 68.421 19.20 3.97 40.19 3.66
308 373 1.562672 ATAGGGCCCGACAAGCAGTT 61.563 55.000 18.44 0.00 0.00 3.16
396 465 3.620785 AGATCAGATCGGGGCGCC 61.621 66.667 21.18 21.18 0.00 6.53
397 466 2.356793 CAGATCAGATCGGGGCGC 60.357 66.667 0.00 0.00 0.00 6.53
398 467 1.288439 CTCAGATCAGATCGGGGCG 59.712 63.158 10.32 0.00 0.00 6.13
399 468 1.005156 GCTCAGATCAGATCGGGGC 60.005 63.158 18.29 18.29 43.36 5.80
400 469 0.317799 CAGCTCAGATCAGATCGGGG 59.682 60.000 10.32 8.28 0.00 5.73
441 515 1.514443 GCCGACGAAGGAGACGAAG 60.514 63.158 0.00 0.00 34.70 3.79
442 516 2.196382 CTGCCGACGAAGGAGACGAA 62.196 60.000 0.00 0.00 34.70 3.85
443 517 2.670592 TGCCGACGAAGGAGACGA 60.671 61.111 0.00 0.00 34.70 4.20
444 518 2.202492 CTGCCGACGAAGGAGACG 60.202 66.667 0.00 0.00 0.00 4.18
445 519 2.507324 GCTGCCGACGAAGGAGAC 60.507 66.667 0.00 0.00 0.00 3.36
446 520 4.116328 CGCTGCCGACGAAGGAGA 62.116 66.667 0.00 0.00 36.29 3.71
468 542 2.684735 GGAGACGGAGGAGGAGGT 59.315 66.667 0.00 0.00 0.00 3.85
487 561 1.305381 CCTCTTCCCCACGGAGAGT 60.305 63.158 0.00 0.00 40.10 3.24
488 562 0.614979 TTCCTCTTCCCCACGGAGAG 60.615 60.000 0.00 0.00 40.10 3.20
489 563 0.178915 TTTCCTCTTCCCCACGGAGA 60.179 55.000 0.00 0.00 40.10 3.71
490 564 0.036294 GTTTCCTCTTCCCCACGGAG 60.036 60.000 0.00 0.00 40.10 4.63
491 565 1.823169 CGTTTCCTCTTCCCCACGGA 61.823 60.000 0.00 0.00 35.88 4.69
492 566 1.375523 CGTTTCCTCTTCCCCACGG 60.376 63.158 0.00 0.00 0.00 4.94
493 567 2.033194 GCGTTTCCTCTTCCCCACG 61.033 63.158 0.00 0.00 0.00 4.94
494 568 1.674651 GGCGTTTCCTCTTCCCCAC 60.675 63.158 0.00 0.00 0.00 4.61
504 578 2.495866 CATGGCCATGGCGTTTCC 59.504 61.111 34.31 16.34 43.06 3.13
544 621 1.657556 GCGCTAGTGCTCTCCTAGG 59.342 63.158 20.99 0.82 36.97 3.02
545 622 1.281353 CGCGCTAGTGCTCTCCTAG 59.719 63.158 24.83 4.78 36.97 3.02
546 623 3.422061 CGCGCTAGTGCTCTCCTA 58.578 61.111 24.83 0.00 36.97 2.94
589 668 2.927618 CGTTGTCGTGGTCGTGCAG 61.928 63.158 0.00 0.00 38.33 4.41
644 724 1.928503 GAGAGACGAGACGGTAGACAG 59.071 57.143 0.00 0.00 0.00 3.51
667 747 1.821136 GCCATGGGAAGAAAGTGAAGG 59.179 52.381 15.13 0.00 0.00 3.46
872 960 3.117372 GCAGCAGGCAGGCAATAG 58.883 61.111 0.00 0.00 43.97 1.73
1182 1277 2.430382 GAACTCGGGGAAGTCGTGCA 62.430 60.000 0.00 0.00 0.00 4.57
1185 1280 1.228800 AGGAACTCGGGGAAGTCGT 60.229 57.895 0.00 0.00 0.00 4.34
1528 1638 3.450115 ACGGTGCGGTAGCTCTCC 61.450 66.667 0.00 0.00 45.42 3.71
1660 1770 2.505557 CGCGGGTACTCGTTGTCC 60.506 66.667 17.95 0.00 0.00 4.02
1843 1953 1.031571 GGGATTCGCAATGAGCCACA 61.032 55.000 0.00 0.00 41.38 4.17
1844 1954 0.749454 AGGGATTCGCAATGAGCCAC 60.749 55.000 3.36 0.00 41.38 5.01
1856 1966 3.271729 GGAAAGGAACGAGAAGGGATTC 58.728 50.000 0.00 0.00 0.00 2.52
1868 1978 3.258372 GGGTTTGGAGAATGGAAAGGAAC 59.742 47.826 0.00 0.00 0.00 3.62
1891 2001 3.994204 TGATACGCACGGTACATACAT 57.006 42.857 0.00 0.00 32.95 2.29
1895 2005 2.882927 ACATGATACGCACGGTACAT 57.117 45.000 0.00 0.00 32.95 2.29
1898 2008 3.054166 GCATAACATGATACGCACGGTA 58.946 45.455 0.00 0.00 35.11 4.02
2021 2131 9.612620 GATGTAGTTTTAGAACACAAGGAAATG 57.387 33.333 0.00 0.00 38.26 2.32
2025 2135 7.441157 CACAGATGTAGTTTTAGAACACAAGGA 59.559 37.037 0.00 0.00 38.26 3.36
2075 2185 2.946329 GCTCGAGACATCAGAACCTCTA 59.054 50.000 18.75 0.00 0.00 2.43
2115 2225 4.406069 CATGAACTTGGTATGTTTCAGCG 58.594 43.478 0.00 0.00 0.00 5.18
2141 2255 3.604130 CGGCATTCTACCGCAAAAG 57.396 52.632 0.00 0.00 44.90 2.27
2165 2279 1.068748 AGCGTATGTTAGCGATACCGG 60.069 52.381 0.00 0.00 38.61 5.28
2166 2280 2.095869 AGAGCGTATGTTAGCGATACCG 60.096 50.000 0.00 0.00 38.61 4.02
2182 2296 1.154525 CAACGAAGCAAGCAGAGCG 60.155 57.895 0.00 0.00 37.01 5.03
2192 2306 0.307760 CCACCTGACAACAACGAAGC 59.692 55.000 0.00 0.00 0.00 3.86
2193 2307 1.597663 GACCACCTGACAACAACGAAG 59.402 52.381 0.00 0.00 0.00 3.79
2195 2309 0.528901 CGACCACCTGACAACAACGA 60.529 55.000 0.00 0.00 0.00 3.85
2196 2310 0.528901 TCGACCACCTGACAACAACG 60.529 55.000 0.00 0.00 0.00 4.10
2197 2311 1.878953 ATCGACCACCTGACAACAAC 58.121 50.000 0.00 0.00 0.00 3.32
2222 2336 3.119245 TCTCTGGTACAATTGCTCGGTAC 60.119 47.826 5.05 0.00 38.70 3.34
2600 2714 3.184382 TCCATACTCCCAGTCTTGACA 57.816 47.619 3.49 0.00 0.00 3.58
2609 2723 5.726560 TCCAAGATAAGATCCATACTCCCA 58.273 41.667 0.00 0.00 0.00 4.37
2633 2747 3.434984 TGCAGTTGTTTGGCAAGAAAAAC 59.565 39.130 0.00 0.00 37.83 2.43
2935 3049 3.559171 GCCACAATCTGTTTCTCCCTGTA 60.559 47.826 0.00 0.00 0.00 2.74
2936 3050 2.815589 GCCACAATCTGTTTCTCCCTGT 60.816 50.000 0.00 0.00 0.00 4.00
2969 3083 4.699257 CCTTCATCCTCTTGTTTCCTGAAG 59.301 45.833 0.00 0.00 38.41 3.02
3337 3451 6.147985 GCCAGGTTTTTAGAGAGTTGTCTAAG 59.852 42.308 0.00 0.00 39.61 2.18
3348 3462 2.359900 AGCGATGCCAGGTTTTTAGAG 58.640 47.619 0.00 0.00 0.00 2.43
3349 3463 2.489938 AGCGATGCCAGGTTTTTAGA 57.510 45.000 0.00 0.00 0.00 2.10
3364 3478 3.508793 CGGGTATTAGGAAGGAATAGCGA 59.491 47.826 0.00 0.00 37.88 4.93
3366 3480 4.886496 ACGGGTATTAGGAAGGAATAGC 57.114 45.455 0.00 0.00 36.81 2.97
3401 3515 2.386661 ACACACTCCTATTTGAGCCG 57.613 50.000 0.00 0.00 35.72 5.52
3419 3577 1.202580 AGATGCTCACAGCCCGAATAC 60.203 52.381 0.00 0.00 41.51 1.89
3422 3580 0.674581 CAAGATGCTCACAGCCCGAA 60.675 55.000 0.00 0.00 41.51 4.30
3424 3582 2.758089 GCAAGATGCTCACAGCCCG 61.758 63.158 0.00 0.00 41.51 6.13
3455 3613 3.216147 ACTGCAATGCGTACAAAATCC 57.784 42.857 0.00 0.00 0.00 3.01
3466 3624 2.533266 GAGGCAATACAACTGCAATGC 58.467 47.619 0.00 0.00 41.78 3.56
3492 3650 9.543783 AAAGGGAATAATATTTACTCAGACGTC 57.456 33.333 7.70 7.70 0.00 4.34
3552 3713 3.686916 AGTCTGTTTAAGAGTCCCTGC 57.313 47.619 0.00 0.00 32.78 4.85
3622 3785 6.529829 GTGTGTCTTTCAGTTGCAAATTGTTA 59.470 34.615 0.00 0.00 34.82 2.41
3825 3990 7.603404 TCAATGACCATTTGCAATTTCTTTAGG 59.397 33.333 0.00 0.00 0.00 2.69
4251 4416 1.549620 AGCATGTGACTCTGAGACCTG 59.450 52.381 12.44 4.73 0.00 4.00
4356 4521 3.077359 CCGGAATATGCATCTTTCCTCC 58.923 50.000 26.59 12.65 37.38 4.30
4441 4606 4.993705 ACTTGAGGTCATAAACTTCCCA 57.006 40.909 0.00 0.00 33.14 4.37
4566 4731 1.541588 GGTTGAACTGCAGGATTCACC 59.458 52.381 19.93 17.27 34.61 4.02
4602 4767 3.071479 GCAGTGTCAGGATTAACCGAAA 58.929 45.455 0.00 0.00 44.74 3.46
4743 4950 3.110705 ACAGACCAGGCTGACAGATAAT 58.889 45.455 17.94 0.00 39.20 1.28
4996 5203 4.624015 TGCCTTCAAGAAAGCTTTCAATG 58.376 39.130 34.39 30.10 39.61 2.82
4997 5204 4.942761 TGCCTTCAAGAAAGCTTTCAAT 57.057 36.364 34.39 22.65 39.61 2.57
4998 5205 4.262164 GGATGCCTTCAAGAAAGCTTTCAA 60.262 41.667 34.39 21.63 39.61 2.69
5020 5229 0.522626 TTCAATCACACAGCGCATGG 59.477 50.000 11.47 0.14 0.00 3.66
5022 5231 1.237533 TGTTCAATCACACAGCGCAT 58.762 45.000 11.47 0.00 0.00 4.73
5023 5232 1.020437 TTGTTCAATCACACAGCGCA 58.980 45.000 11.47 0.00 0.00 6.09
5024 5233 2.336554 ATTGTTCAATCACACAGCGC 57.663 45.000 0.00 0.00 0.00 5.92
5025 5234 5.393124 ACATAATTGTTCAATCACACAGCG 58.607 37.500 0.00 0.00 29.55 5.18
5026 5235 7.381948 TGAAACATAATTGTTCAATCACACAGC 59.618 33.333 0.00 0.00 45.30 4.40
5027 5236 8.800231 TGAAACATAATTGTTCAATCACACAG 57.200 30.769 0.00 0.00 45.30 3.66
5028 5237 9.194271 CATGAAACATAATTGTTCAATCACACA 57.806 29.630 0.00 0.00 45.30 3.72
5029 5238 8.164153 GCATGAAACATAATTGTTCAATCACAC 58.836 33.333 0.00 0.00 45.30 3.82
5030 5239 7.331440 GGCATGAAACATAATTGTTCAATCACA 59.669 33.333 0.00 0.00 45.30 3.58
5031 5240 7.546667 AGGCATGAAACATAATTGTTCAATCAC 59.453 33.333 0.00 0.00 45.30 3.06
5035 5244 7.384660 GTGAAGGCATGAAACATAATTGTTCAA 59.615 33.333 0.00 0.00 45.30 2.69
5036 5245 6.867816 GTGAAGGCATGAAACATAATTGTTCA 59.132 34.615 0.00 0.00 45.30 3.18
5039 5248 5.401550 CGTGAAGGCATGAAACATAATTGT 58.598 37.500 0.00 0.00 33.26 2.71
5040 5249 4.266029 GCGTGAAGGCATGAAACATAATTG 59.734 41.667 0.00 0.00 32.63 2.32
5049 5258 1.291184 CTGACGCGTGAAGGCATGAA 61.291 55.000 20.70 0.00 32.63 2.57
5052 5261 2.029288 CACTGACGCGTGAAGGCAT 61.029 57.895 20.70 0.00 37.06 4.40
5070 5279 2.273370 TTCATCTTCGTACCGCTCAC 57.727 50.000 0.00 0.00 0.00 3.51
5077 5286 5.231568 CACCGTAAAGGATTCATCTTCGTAC 59.768 44.000 0.00 0.00 45.00 3.67
5078 5287 5.345702 CACCGTAAAGGATTCATCTTCGTA 58.654 41.667 0.00 0.00 45.00 3.43
5088 5305 3.119495 GCATTTCAGCACCGTAAAGGATT 60.119 43.478 0.00 0.00 45.00 3.01
5194 5411 5.880332 GGATGCAAGTAAGATCAGTTAACCA 59.120 40.000 0.88 0.00 0.00 3.67
5279 5496 5.829829 TGAGAGATGAGTTTGATCGATGAG 58.170 41.667 0.54 0.00 0.00 2.90
5291 5508 4.569966 GCATTTTCGACATGAGAGATGAGT 59.430 41.667 0.00 0.00 0.00 3.41
5350 5568 2.143122 CTTACACATGACCAACGCTGT 58.857 47.619 0.00 0.00 0.00 4.40
5376 5595 2.914695 TCTAGGAGTCTAGACGGCTC 57.085 55.000 17.07 9.40 44.99 4.70
5408 5629 6.109156 TCCTATTATGTATGCACCATCGTT 57.891 37.500 4.08 0.00 0.00 3.85
5529 5752 4.969359 AGCAAGGTATACAGGTGTAATCCT 59.031 41.667 5.01 9.35 38.40 3.24
5544 5767 5.885912 GGTTATGGATTTCTGAAGCAAGGTA 59.114 40.000 0.00 0.00 0.00 3.08
5585 5808 5.468072 AGAAACATCAGCCTATAAGCAATCG 59.532 40.000 0.00 0.00 34.23 3.34
5635 5863 4.955450 ACACAAAATAGCAGGCATATTCCA 59.045 37.500 0.00 0.00 0.00 3.53
5637 5865 7.707104 AGTAACACAAAATAGCAGGCATATTC 58.293 34.615 0.00 0.00 0.00 1.75
5641 5869 6.316390 GTCTAGTAACACAAAATAGCAGGCAT 59.684 38.462 0.00 0.00 0.00 4.40
5642 5870 5.642063 GTCTAGTAACACAAAATAGCAGGCA 59.358 40.000 0.00 0.00 0.00 4.75
5655 5883 8.638685 TTCTTGTGTACTTTGTCTAGTAACAC 57.361 34.615 0.00 0.00 35.53 3.32
5728 5962 8.484799 GTTAGGCAGTTTTGTTTTGCTTTATAC 58.515 33.333 0.00 0.00 37.93 1.47
5732 5966 5.351189 CAGTTAGGCAGTTTTGTTTTGCTTT 59.649 36.000 0.00 0.00 37.93 3.51
5737 5971 5.652994 TGTCAGTTAGGCAGTTTTGTTTT 57.347 34.783 0.00 0.00 0.00 2.43
5749 5983 8.624776 AGTTTCTGAATTTCTTTGTCAGTTAGG 58.375 33.333 0.00 0.00 39.82 2.69
5753 5987 9.956720 CATTAGTTTCTGAATTTCTTTGTCAGT 57.043 29.630 0.00 0.00 39.82 3.41
5767 6001 5.404366 CGAACGGTCTTTCATTAGTTTCTGA 59.596 40.000 0.00 0.00 0.00 3.27
5768 6002 5.176958 ACGAACGGTCTTTCATTAGTTTCTG 59.823 40.000 0.00 0.00 0.00 3.02
5774 6008 6.364165 TCAGTTAACGAACGGTCTTTCATTAG 59.636 38.462 0.00 0.00 40.76 1.73
5779 6013 4.143179 CCATCAGTTAACGAACGGTCTTTC 60.143 45.833 0.00 0.00 40.76 2.62
5781 6015 3.006110 TCCATCAGTTAACGAACGGTCTT 59.994 43.478 0.00 0.00 40.76 3.01
5782 6016 2.559668 TCCATCAGTTAACGAACGGTCT 59.440 45.455 0.00 0.00 40.76 3.85
5783 6017 2.950433 TCCATCAGTTAACGAACGGTC 58.050 47.619 0.00 0.00 40.76 4.79
5785 6019 4.939509 AATTCCATCAGTTAACGAACGG 57.060 40.909 0.00 6.48 40.76 4.44
5786 6020 7.229228 TGATAATTCCATCAGTTAACGAACG 57.771 36.000 0.00 0.00 40.76 3.95
5797 6034 5.006153 ACGACGAACTGATAATTCCATCA 57.994 39.130 0.00 0.00 33.88 3.07
5829 6066 1.072505 GCGGTTCCTCCAACTCCAA 59.927 57.895 0.00 0.00 35.06 3.53
5830 6067 2.747686 GCGGTTCCTCCAACTCCA 59.252 61.111 0.00 0.00 35.06 3.86
5831 6068 2.434359 CGCGGTTCCTCCAACTCC 60.434 66.667 0.00 0.00 35.06 3.85
5832 6069 1.880819 TACCGCGGTTCCTCCAACTC 61.881 60.000 38.94 0.00 35.06 3.01
5833 6070 1.909781 TACCGCGGTTCCTCCAACT 60.910 57.895 38.94 9.80 35.06 3.16
5834 6071 1.739196 GTACCGCGGTTCCTCCAAC 60.739 63.158 38.94 22.83 35.57 3.77


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

AutoCloner maintained by Alex Coulton.