Multiple sequence alignment - TraesCS5A01G491400

Loading Multiple Alignment...

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 TraesCS5A01G491400 chr5A 100.000 5073 0 0 1 5073 660401112 660396040 0.000000e+00 9369.0
1 TraesCS5A01G491400 chr4D 95.330 4454 137 28 635 5073 482232552 482236949 0.000000e+00 7007.0
2 TraesCS5A01G491400 chr4D 81.281 609 36 35 23 581 482231971 482232551 6.070000e-114 422.0
3 TraesCS5A01G491400 chr4B 94.533 4463 157 38 635 5073 612024242 612028641 0.000000e+00 6809.0
4 TraesCS5A01G491400 chr4B 87.295 244 11 9 18 249 612023754 612023989 1.400000e-65 261.0
5 TraesCS5A01G491400 chr4B 88.095 168 5 5 377 541 612024060 612024215 8.670000e-43 185.0
6 TraesCS5A01G491400 chr3A 94.131 426 25 0 1321 1746 209601544 209601969 0.000000e+00 649.0
7 TraesCS5A01G491400 chr2A 92.771 166 12 0 1321 1486 617819469 617819634 1.830000e-59 241.0
8 TraesCS5A01G491400 chr2A 98.077 52 1 0 1764 1815 617819632 617819683 1.950000e-14 91.6


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 TraesCS5A01G491400 chr5A 660396040 660401112 5072 True 9369.000000 9369 100.000000 1 5073 1 chr5A.!!$R1 5072
1 TraesCS5A01G491400 chr4D 482231971 482236949 4978 False 3714.500000 7007 88.305500 23 5073 2 chr4D.!!$F1 5050
2 TraesCS5A01G491400 chr4B 612023754 612028641 4887 False 2418.333333 6809 89.974333 18 5073 3 chr4B.!!$F1 5055

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
252 273 0.102300 TCGTCATACCGAGGCATGTG 59.898 55.0 2.57 0.0 32.18 3.21 F
805 867 0.112801 TTTTCCCAGGTAAACCCCCG 59.887 55.0 0.00 0.0 36.42 5.73 F
2117 2205 0.175760 CCGGAGACATACCACCAGTG 59.824 60.0 0.00 0.0 0.00 3.66 F
2614 2705 0.031721 ACGTGTCCTTCAACGGTCTC 59.968 55.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2199 0.392998 GCAATGTCCCGATCACTGGT 60.393 55.000 0.00 0.00 0.00 4.00 R
2609 2700 0.318762 GGTATGATGCCGGAGAGACC 59.681 60.000 5.05 0.00 0.00 3.85 R
3274 3365 1.126846 CTGCTACTTCTGGAAAACGCG 59.873 52.381 3.53 3.53 0.00 6.01 R
4437 4533 1.562008 TCCTCGGCCATTTGGAATGTA 59.438 47.619 2.24 0.00 37.39 2.29 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
64 65 3.764658 CGGTTAAACTATCCGGCCA 57.235 52.632 2.24 0.00 40.49 5.36
66 67 1.671979 GGTTAAACTATCCGGCCACC 58.328 55.000 2.24 0.00 0.00 4.61
69 70 2.632136 TAAACTATCCGGCCACCGCG 62.632 60.000 2.24 0.00 46.86 6.46
151 163 3.258872 TGGGCACTTATACGTTACACACT 59.741 43.478 0.00 0.00 0.00 3.55
200 212 2.877582 GTACGTGCGCGGTACTGG 60.878 66.667 25.20 4.85 43.45 4.00
209 221 4.789075 CGGTACTGGCACGACGGG 62.789 72.222 0.00 0.00 0.00 5.28
235 256 1.670811 GCAACCACCACCTAATCATCG 59.329 52.381 0.00 0.00 0.00 3.84
252 273 0.102300 TCGTCATACCGAGGCATGTG 59.898 55.000 2.57 0.00 32.18 3.21
253 274 0.179111 CGTCATACCGAGGCATGTGT 60.179 55.000 2.57 0.00 0.00 3.72
270 291 2.126773 TACCAGCACGTACACGCG 60.127 61.111 3.53 3.53 44.43 6.01
322 350 4.393155 TACCCACGCCTGCTGCTG 62.393 66.667 0.00 0.00 38.05 4.41
339 391 0.370273 CTGCATGCTTAACGACGGAC 59.630 55.000 20.33 0.00 0.00 4.79
383 435 2.736995 CGCTCCGCTCCAACGAAA 60.737 61.111 0.00 0.00 34.06 3.46
476 531 3.878358 CGGAGGAGGAGATTCCCC 58.122 66.667 0.00 0.00 37.19 4.81
487 542 3.272847 ATTCCCCCACACCCACCC 61.273 66.667 0.00 0.00 0.00 4.61
488 543 4.865228 TTCCCCCACACCCACCCA 62.865 66.667 0.00 0.00 0.00 4.51
492 547 3.966543 CCCACACCCACCCACCTC 61.967 72.222 0.00 0.00 0.00 3.85
494 549 2.854032 CACACCCACCCACCTCCT 60.854 66.667 0.00 0.00 0.00 3.69
495 550 1.537889 CACACCCACCCACCTCCTA 60.538 63.158 0.00 0.00 0.00 2.94
496 551 0.914417 CACACCCACCCACCTCCTAT 60.914 60.000 0.00 0.00 0.00 2.57
497 552 0.620700 ACACCCACCCACCTCCTATC 60.621 60.000 0.00 0.00 0.00 2.08
498 553 0.326618 CACCCACCCACCTCCTATCT 60.327 60.000 0.00 0.00 0.00 1.98
499 554 0.326618 ACCCACCCACCTCCTATCTG 60.327 60.000 0.00 0.00 0.00 2.90
500 555 1.700042 CCCACCCACCTCCTATCTGC 61.700 65.000 0.00 0.00 0.00 4.26
501 556 0.692419 CCACCCACCTCCTATCTGCT 60.692 60.000 0.00 0.00 0.00 4.24
502 557 0.467384 CACCCACCTCCTATCTGCTG 59.533 60.000 0.00 0.00 0.00 4.41
503 558 1.341156 ACCCACCTCCTATCTGCTGC 61.341 60.000 0.00 0.00 0.00 5.25
504 559 1.053264 CCCACCTCCTATCTGCTGCT 61.053 60.000 0.00 0.00 0.00 4.24
505 560 1.709578 CCACCTCCTATCTGCTGCTA 58.290 55.000 0.00 0.00 0.00 3.49
509 564 1.066286 CCTCCTATCTGCTGCTATGCC 60.066 57.143 0.00 0.00 0.00 4.40
521 576 4.584518 TATGCCCTGCCGCCCATG 62.585 66.667 0.00 0.00 0.00 3.66
544 599 4.096003 CCAGCGATCCACCCGGTT 62.096 66.667 0.00 0.00 35.43 4.44
546 601 3.782443 AGCGATCCACCCGGTTCC 61.782 66.667 0.00 0.00 33.72 3.62
547 602 4.851179 GCGATCCACCCGGTTCCC 62.851 72.222 0.00 0.00 0.00 3.97
549 604 3.012722 GATCCACCCGGTTCCCCA 61.013 66.667 0.00 0.00 0.00 4.96
550 605 3.335729 ATCCACCCGGTTCCCCAC 61.336 66.667 0.00 0.00 0.00 4.61
555 610 3.904617 CCCGGTTCCCCACCCAAA 61.905 66.667 0.00 0.00 43.83 3.28
556 611 2.599281 CCGGTTCCCCACCCAAAC 60.599 66.667 0.00 0.00 43.83 2.93
583 638 4.430423 GCCTTTGCAGTCGCGACG 62.430 66.667 31.56 25.80 42.97 5.12
596 651 3.554692 CGACGCGCCTGGATGAAC 61.555 66.667 5.73 0.00 0.00 3.18
597 652 2.434185 GACGCGCCTGGATGAACA 60.434 61.111 5.73 0.00 0.00 3.18
598 653 2.031919 ACGCGCCTGGATGAACAA 59.968 55.556 5.73 0.00 0.00 2.83
599 654 1.369091 GACGCGCCTGGATGAACAAT 61.369 55.000 5.73 0.00 0.00 2.71
600 655 1.353103 CGCGCCTGGATGAACAATC 59.647 57.895 0.00 0.00 34.19 2.67
610 665 1.936547 GATGAACAATCCTCGTCTGCC 59.063 52.381 0.00 0.00 0.00 4.85
611 666 0.976641 TGAACAATCCTCGTCTGCCT 59.023 50.000 0.00 0.00 0.00 4.75
612 667 1.347707 TGAACAATCCTCGTCTGCCTT 59.652 47.619 0.00 0.00 0.00 4.35
613 668 2.224523 TGAACAATCCTCGTCTGCCTTT 60.225 45.455 0.00 0.00 0.00 3.11
614 669 2.100605 ACAATCCTCGTCTGCCTTTC 57.899 50.000 0.00 0.00 0.00 2.62
615 670 1.347707 ACAATCCTCGTCTGCCTTTCA 59.652 47.619 0.00 0.00 0.00 2.69
616 671 2.224523 ACAATCCTCGTCTGCCTTTCAA 60.225 45.455 0.00 0.00 0.00 2.69
617 672 2.813754 CAATCCTCGTCTGCCTTTCAAA 59.186 45.455 0.00 0.00 0.00 2.69
618 673 2.631160 TCCTCGTCTGCCTTTCAAAA 57.369 45.000 0.00 0.00 0.00 2.44
619 674 2.925724 TCCTCGTCTGCCTTTCAAAAA 58.074 42.857 0.00 0.00 0.00 1.94
691 746 0.330267 TTTTCCCAACCCGATCTCCC 59.670 55.000 0.00 0.00 0.00 4.30
705 760 2.801282 TCTCCCCCATCATCATCTCA 57.199 50.000 0.00 0.00 0.00 3.27
714 774 2.094100 TCATCATCTCACCTCCCCTC 57.906 55.000 0.00 0.00 0.00 4.30
746 806 1.900545 GAGGTTTGACCCCTCCCTCG 61.901 65.000 0.00 0.00 42.29 4.63
805 867 0.112801 TTTTCCCAGGTAAACCCCCG 59.887 55.000 0.00 0.00 36.42 5.73
806 868 2.429235 TTTCCCAGGTAAACCCCCGC 62.429 60.000 0.00 0.00 36.42 6.13
807 869 4.789123 CCCAGGTAAACCCCCGCG 62.789 72.222 0.00 0.00 36.42 6.46
808 870 4.024545 CCAGGTAAACCCCCGCGT 62.025 66.667 4.92 0.00 36.42 6.01
809 871 2.658064 CCAGGTAAACCCCCGCGTA 61.658 63.158 4.92 0.00 36.42 4.42
810 872 1.448365 CAGGTAAACCCCCGCGTAC 60.448 63.158 4.92 0.00 36.42 3.67
811 873 2.125147 GGTAAACCCCCGCGTACC 60.125 66.667 4.92 5.39 0.00 3.34
854 921 4.383861 GGACCAACCCGACCGGAC 62.384 72.222 9.46 0.00 37.50 4.79
855 922 4.383861 GACCAACCCGACCGGACC 62.384 72.222 9.46 0.00 37.50 4.46
864 931 2.126580 GACCGGACCGACGTCAAG 60.127 66.667 17.49 8.75 41.13 3.02
1019 1095 6.999272 TGGACTATACTTAGACCTCATCACTC 59.001 42.308 3.80 0.00 39.92 3.51
1025 1101 1.566211 AGACCTCATCACTCCCACTG 58.434 55.000 0.00 0.00 0.00 3.66
1796 1884 2.118313 TGAACTACATCTCCGTCCGA 57.882 50.000 0.00 0.00 0.00 4.55
1805 1893 1.801913 CTCCGTCCGAAGCAACGAG 60.802 63.158 4.23 0.00 41.29 4.18
2111 2199 0.824109 CTCTTGCCGGAGACATACCA 59.176 55.000 5.05 0.00 35.52 3.25
2117 2205 0.175760 CCGGAGACATACCACCAGTG 59.824 60.000 0.00 0.00 0.00 3.66
2255 2343 2.546795 CCTTATGCTCACCGGAGACATC 60.547 54.545 9.46 0.00 44.26 3.06
2267 2355 2.584608 GACATCCCGGTGTCCCTG 59.415 66.667 13.00 0.00 42.04 4.45
2322 2410 6.706270 AGTGTTCGTTCAGTACTCAATTTCAT 59.294 34.615 0.00 0.00 0.00 2.57
2330 2418 7.307493 TCAGTACTCAATTTCATCCAATTCG 57.693 36.000 0.00 0.00 0.00 3.34
2346 2437 2.634982 TTCGTCCAATGCTTTGATGC 57.365 45.000 13.58 3.05 34.60 3.91
2358 2449 5.239359 TGCTTTGATGCATGATGACTAAC 57.761 39.130 2.46 0.00 38.12 2.34
2359 2450 4.945543 TGCTTTGATGCATGATGACTAACT 59.054 37.500 2.46 0.00 38.12 2.24
2360 2451 5.163693 TGCTTTGATGCATGATGACTAACTG 60.164 40.000 2.46 0.00 38.12 3.16
2361 2452 5.065602 GCTTTGATGCATGATGACTAACTGA 59.934 40.000 2.46 0.00 0.00 3.41
2363 2454 6.426980 TTGATGCATGATGACTAACTGAAC 57.573 37.500 2.46 0.00 0.00 3.18
2364 2455 5.737860 TGATGCATGATGACTAACTGAACT 58.262 37.500 2.46 0.00 0.00 3.01
2365 2456 5.583457 TGATGCATGATGACTAACTGAACTG 59.417 40.000 2.46 0.00 0.00 3.16
2366 2457 5.151297 TGCATGATGACTAACTGAACTGA 57.849 39.130 0.00 0.00 0.00 3.41
2367 2458 5.550290 TGCATGATGACTAACTGAACTGAA 58.450 37.500 0.00 0.00 0.00 3.02
2368 2459 6.175471 TGCATGATGACTAACTGAACTGAAT 58.825 36.000 0.00 0.00 0.00 2.57
2369 2460 6.314648 TGCATGATGACTAACTGAACTGAATC 59.685 38.462 0.00 0.00 0.00 2.52
2373 2464 8.260270 TGATGACTAACTGAACTGAATCATTG 57.740 34.615 0.00 0.00 0.00 2.82
2419 2510 2.732619 GGGAGTGATCCCGGACACC 61.733 68.421 0.73 0.00 40.59 4.16
2449 2540 3.451141 CTGACTTACCTCAGGATGCTC 57.549 52.381 0.00 0.00 35.00 4.26
2530 2621 3.295093 CCTTGATCTGCTAGACCTCTCA 58.705 50.000 0.00 0.00 0.00 3.27
2537 2628 5.638530 TCTGCTAGACCTCTCAGAGAATA 57.361 43.478 2.09 0.00 32.43 1.75
2609 2700 3.242608 ACATTTCAACGTGTCCTTCAACG 60.243 43.478 0.00 0.00 0.00 4.10
2614 2705 0.031721 ACGTGTCCTTCAACGGTCTC 59.968 55.000 0.00 0.00 0.00 3.36
2800 2891 3.356290 ACTTATTGGGGTCTGCATTGTC 58.644 45.455 0.00 0.00 0.00 3.18
2829 2920 7.112779 GCTATGAACATTAGGGCCTATACAAT 58.887 38.462 15.37 3.48 0.00 2.71
2913 3004 0.744771 GTCGGATCTCCAGGCCAAAC 60.745 60.000 5.01 0.00 35.14 2.93
2986 3077 2.308866 TGAAGATTGGGAGGAAGGAACC 59.691 50.000 0.00 0.00 0.00 3.62
3525 3616 0.106708 TCTTATGCTGCCATCGGGTC 59.893 55.000 0.00 0.00 36.17 4.46
3565 3656 1.115467 CCCCGAGCTTGAGATACAGT 58.885 55.000 1.22 0.00 0.00 3.55
3870 3961 7.800092 AGGACTAATTCTTGATGTTCTGCTAT 58.200 34.615 0.00 0.00 0.00 2.97
4076 4172 8.134895 TGAATAAATGGCTATTTTGGTCGAATC 58.865 33.333 13.63 0.00 37.64 2.52
4080 4176 5.092554 TGGCTATTTTGGTCGAATCACTA 57.907 39.130 0.00 0.00 0.00 2.74
4086 4182 7.012421 GCTATTTTGGTCGAATCACTAATTCCT 59.988 37.037 0.00 0.00 40.69 3.36
4191 4287 1.027357 CGCTCTGATTGGGAAATGGG 58.973 55.000 0.00 0.00 0.00 4.00
4230 4326 4.165372 TGGTCAGACCTAAACACTCCTTTT 59.835 41.667 20.82 0.00 39.58 2.27
4241 4337 6.994421 AAACACTCCTTTTATTTGTGGGAT 57.006 33.333 0.00 0.00 33.44 3.85
4371 4467 5.370880 AGCTCATCTAACCCACAATATCCTT 59.629 40.000 0.00 0.00 0.00 3.36
4372 4468 5.703130 GCTCATCTAACCCACAATATCCTTC 59.297 44.000 0.00 0.00 0.00 3.46
4434 4530 1.007118 AGATTTCATCCCCAACCCACC 59.993 52.381 0.00 0.00 0.00 4.61
4435 4531 0.789687 ATTTCATCCCCAACCCACCA 59.210 50.000 0.00 0.00 0.00 4.17
4436 4532 0.563173 TTTCATCCCCAACCCACCAA 59.437 50.000 0.00 0.00 0.00 3.67
4437 4533 0.789687 TTCATCCCCAACCCACCAAT 59.210 50.000 0.00 0.00 0.00 3.16
4575 4671 2.268920 GCGATCTCCACCAAGCCA 59.731 61.111 0.00 0.00 0.00 4.75
4576 4672 1.153086 GCGATCTCCACCAAGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
4578 4674 0.178767 CGATCTCCACCAAGCCATCA 59.821 55.000 0.00 0.00 0.00 3.07
4623 4719 1.006922 GGCCAAGCTTGTTGTCAGC 60.007 57.895 24.35 18.17 0.00 4.26
4680 4776 2.668457 CCTACAAGACATGTCACGCTTC 59.332 50.000 27.02 0.00 42.70 3.86
4902 5001 0.179161 CGGAGGACTACAGCAACTCG 60.179 60.000 0.00 0.00 0.00 4.18
4994 5093 2.133553 CGATGATGACCATGAGCTGAC 58.866 52.381 0.00 0.00 35.17 3.51
4995 5094 2.492012 GATGATGACCATGAGCTGACC 58.508 52.381 0.00 0.00 35.17 4.02
4996 5095 1.278537 TGATGACCATGAGCTGACCA 58.721 50.000 0.00 0.00 0.00 4.02
5001 5100 0.250901 ACCATGAGCTGACCACCAAC 60.251 55.000 0.00 0.00 0.00 3.77
5003 5102 1.003355 ATGAGCTGACCACCAACCG 60.003 57.895 0.00 0.00 0.00 4.44
5006 5105 4.947147 GCTGACCACCAACCGGCA 62.947 66.667 0.00 0.00 34.57 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.394712 GGTGGCGTGGACCAGAGG 62.395 72.222 0.00 0.00 41.46 3.69
6 7 3.625897 TGGTGGCGTGGACCAGAG 61.626 66.667 0.00 0.00 41.46 3.35
7 8 3.936203 GTGGTGGCGTGGACCAGA 61.936 66.667 0.00 0.00 44.30 3.86
8 9 3.883744 GAGTGGTGGCGTGGACCAG 62.884 68.421 0.00 0.00 44.30 4.00
9 10 3.936203 GAGTGGTGGCGTGGACCA 61.936 66.667 0.00 0.00 41.37 4.02
10 11 4.699522 GGAGTGGTGGCGTGGACC 62.700 72.222 0.00 0.00 0.00 4.46
19 20 4.767255 GAGGCAGCCGGAGTGGTG 62.767 72.222 5.05 0.00 41.21 4.17
40 41 1.808891 CGGATAGTTTAACCGGCAGGG 60.809 57.143 8.08 0.00 43.47 4.45
69 70 1.010574 TTTATTATGCACGGCGCGC 60.011 52.632 25.94 25.94 46.97 6.86
83 95 2.026822 CCAGTCTCCAGTGGCTGTTTAT 60.027 50.000 3.51 0.00 36.25 1.40
113 125 2.493030 CACGCCGATCGGTAACCT 59.507 61.111 33.33 10.30 43.86 3.50
151 163 3.141398 GCCGATCCAGCAATTATCAAGA 58.859 45.455 0.00 0.00 0.00 3.02
235 256 2.470821 GTACACATGCCTCGGTATGAC 58.529 52.381 18.91 5.11 39.96 3.06
252 273 2.430942 CGCGTGTACGTGCTGGTAC 61.431 63.158 4.97 9.92 43.06 3.34
253 274 2.126773 CGCGTGTACGTGCTGGTA 60.127 61.111 4.97 0.00 43.06 3.25
283 304 3.035251 CGGTACATTACATTGCATTGCG 58.965 45.455 8.48 0.00 0.00 4.85
285 306 5.504994 GGGTACGGTACATTACATTGCATTG 60.505 44.000 19.14 7.04 0.00 2.82
290 318 3.552699 CGTGGGTACGGTACATTACATTG 59.447 47.826 19.14 6.52 46.23 2.82
322 350 1.343821 CGTCCGTCGTTAAGCATGC 59.656 57.895 10.51 10.51 34.52 4.06
330 382 2.355481 GTTGCTCCGTCCGTCGTT 60.355 61.111 0.00 0.00 37.94 3.85
368 420 0.942410 TTCGTTTCGTTGGAGCGGAG 60.942 55.000 0.00 0.00 0.00 4.63
370 422 1.491563 CTTCGTTTCGTTGGAGCGG 59.508 57.895 0.00 0.00 0.00 5.52
476 531 3.966543 GGAGGTGGGTGGGTGTGG 61.967 72.222 0.00 0.00 0.00 4.17
487 542 2.612471 GCATAGCAGCAGATAGGAGGTG 60.612 54.545 0.00 0.00 36.39 4.00
488 543 1.622811 GCATAGCAGCAGATAGGAGGT 59.377 52.381 0.00 0.00 0.00 3.85
491 546 0.979665 GGGCATAGCAGCAGATAGGA 59.020 55.000 0.00 0.00 35.83 2.94
492 547 0.982704 AGGGCATAGCAGCAGATAGG 59.017 55.000 0.00 0.00 35.83 2.57
494 549 0.035881 GCAGGGCATAGCAGCAGATA 59.964 55.000 0.00 0.00 35.83 1.98
495 550 1.228184 GCAGGGCATAGCAGCAGAT 60.228 57.895 0.00 0.00 35.83 2.90
496 551 2.191375 GCAGGGCATAGCAGCAGA 59.809 61.111 0.00 0.00 35.83 4.26
497 552 2.905880 GGCAGGGCATAGCAGCAG 60.906 66.667 0.00 0.00 35.83 4.24
498 553 4.862447 CGGCAGGGCATAGCAGCA 62.862 66.667 0.00 0.00 35.83 4.41
503 558 4.275508 ATGGGCGGCAGGGCATAG 62.276 66.667 12.47 0.00 44.56 2.23
504 559 4.584518 CATGGGCGGCAGGGCATA 62.585 66.667 12.47 0.00 44.56 3.14
543 598 2.200092 GCAGGTTTGGGTGGGGAA 59.800 61.111 0.00 0.00 0.00 3.97
544 599 4.278513 CGCAGGTTTGGGTGGGGA 62.279 66.667 0.00 0.00 32.93 4.81
546 601 4.974721 AGCGCAGGTTTGGGTGGG 62.975 66.667 11.47 0.00 39.31 4.61
555 610 2.730094 CAAAGGCAAAGCGCAGGT 59.270 55.556 11.47 0.00 45.17 4.00
556 611 2.735857 GCAAAGGCAAAGCGCAGG 60.736 61.111 11.47 0.00 45.17 4.85
581 636 1.369091 GATTGTTCATCCAGGCGCGT 61.369 55.000 8.43 0.00 0.00 6.01
590 645 1.936547 GGCAGACGAGGATTGTTCATC 59.063 52.381 0.00 0.00 28.27 2.92
591 646 1.556911 AGGCAGACGAGGATTGTTCAT 59.443 47.619 0.00 0.00 28.27 2.57
592 647 0.976641 AGGCAGACGAGGATTGTTCA 59.023 50.000 0.00 0.00 28.27 3.18
593 648 2.100605 AAGGCAGACGAGGATTGTTC 57.899 50.000 0.00 0.00 28.27 3.18
594 649 2.224523 TGAAAGGCAGACGAGGATTGTT 60.225 45.455 0.00 0.00 28.27 2.83
595 650 1.347707 TGAAAGGCAGACGAGGATTGT 59.652 47.619 0.00 0.00 33.40 2.71
596 651 2.099141 TGAAAGGCAGACGAGGATTG 57.901 50.000 0.00 0.00 0.00 2.67
597 652 2.859165 TTGAAAGGCAGACGAGGATT 57.141 45.000 0.00 0.00 0.00 3.01
598 653 2.859165 TTTGAAAGGCAGACGAGGAT 57.141 45.000 0.00 0.00 0.00 3.24
599 654 2.631160 TTTTGAAAGGCAGACGAGGA 57.369 45.000 0.00 0.00 0.00 3.71
625 680 1.886542 GCCCAGACGAGGATTGTTTTT 59.113 47.619 0.00 0.00 28.27 1.94
626 681 1.534729 GCCCAGACGAGGATTGTTTT 58.465 50.000 0.00 0.00 28.27 2.43
627 682 0.322546 GGCCCAGACGAGGATTGTTT 60.323 55.000 0.00 0.00 28.27 2.83
628 683 1.299976 GGCCCAGACGAGGATTGTT 59.700 57.895 0.00 0.00 28.27 2.83
629 684 1.918293 TGGCCCAGACGAGGATTGT 60.918 57.895 0.00 0.00 33.40 2.71
630 685 1.450312 GTGGCCCAGACGAGGATTG 60.450 63.158 0.00 0.00 0.00 2.67
631 686 1.918293 TGTGGCCCAGACGAGGATT 60.918 57.895 0.00 0.00 0.00 3.01
632 687 2.284625 TGTGGCCCAGACGAGGAT 60.285 61.111 0.00 0.00 0.00 3.24
633 688 3.311110 GTGTGGCCCAGACGAGGA 61.311 66.667 0.00 0.00 0.00 3.71
663 718 4.272511 TTGGGAAAAGGGCGGCGA 62.273 61.111 12.98 0.00 0.00 5.54
665 720 3.691342 GGTTGGGAAAAGGGCGGC 61.691 66.667 0.00 0.00 0.00 6.53
691 746 1.350351 GGGAGGTGAGATGATGATGGG 59.650 57.143 0.00 0.00 0.00 4.00
705 760 3.120191 CCTAGGGTGAGGGGAGGT 58.880 66.667 0.00 0.00 32.39 3.85
714 774 0.698818 AAACCTCCAAGCCTAGGGTG 59.301 55.000 15.71 8.73 37.18 4.61
746 806 1.179174 AACTGCTTTCTTTCCGGGGC 61.179 55.000 0.00 0.00 0.00 5.80
898 965 1.943730 AACCAACTGCCACTTCCCCA 61.944 55.000 0.00 0.00 0.00 4.96
899 966 1.152546 AACCAACTGCCACTTCCCC 60.153 57.895 0.00 0.00 0.00 4.81
901 968 1.949257 CGAACCAACTGCCACTTCC 59.051 57.895 0.00 0.00 0.00 3.46
1019 1095 4.394712 GCTCCGGTGGACAGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
1025 1101 4.222847 GGATCGGCTCCGGTGGAC 62.223 72.222 8.59 0.00 40.25 4.02
1050 1126 2.584873 TTAGCTCCTCCTCCGGGGTC 62.585 65.000 0.00 0.00 36.25 4.46
1966 2054 3.353600 CGCAGGTGGCAATGTTGA 58.646 55.556 0.00 0.00 45.17 3.18
2073 2161 2.019897 GCATTCGCCCCCAAATCCAG 62.020 60.000 0.00 0.00 0.00 3.86
2111 2199 0.392998 GCAATGTCCCGATCACTGGT 60.393 55.000 0.00 0.00 0.00 4.00
2117 2205 2.237751 CGACCGCAATGTCCCGATC 61.238 63.158 0.00 0.00 31.35 3.69
2255 2343 2.484287 ATTTGCTCAGGGACACCGGG 62.484 60.000 6.32 0.00 43.47 5.73
2322 2410 3.153130 TCAAAGCATTGGACGAATTGGA 58.847 40.909 1.24 0.00 37.15 3.53
2346 2437 7.838771 TGATTCAGTTCAGTTAGTCATCATG 57.161 36.000 0.00 0.00 0.00 3.07
2347 2438 8.890718 CAATGATTCAGTTCAGTTAGTCATCAT 58.109 33.333 0.00 0.00 31.62 2.45
2351 2442 5.997129 TGCAATGATTCAGTTCAGTTAGTCA 59.003 36.000 0.00 0.00 0.00 3.41
2352 2443 6.402983 CCTGCAATGATTCAGTTCAGTTAGTC 60.403 42.308 11.69 0.00 0.00 2.59
2354 2445 5.645067 TCCTGCAATGATTCAGTTCAGTTAG 59.355 40.000 11.69 0.00 0.00 2.34
2355 2446 5.559770 TCCTGCAATGATTCAGTTCAGTTA 58.440 37.500 11.69 0.00 0.00 2.24
2356 2447 4.401022 TCCTGCAATGATTCAGTTCAGTT 58.599 39.130 11.69 0.00 0.00 3.16
2358 2449 5.578005 ATTCCTGCAATGATTCAGTTCAG 57.422 39.130 6.76 6.76 0.00 3.02
2359 2450 5.988310 AATTCCTGCAATGATTCAGTTCA 57.012 34.783 0.00 0.00 0.00 3.18
2360 2451 6.161381 ACAAATTCCTGCAATGATTCAGTTC 58.839 36.000 0.00 0.00 0.00 3.01
2361 2452 6.014840 AGACAAATTCCTGCAATGATTCAGTT 60.015 34.615 0.00 0.00 0.00 3.16
2363 2454 5.805486 CAGACAAATTCCTGCAATGATTCAG 59.195 40.000 0.00 0.00 0.00 3.02
2364 2455 5.336929 CCAGACAAATTCCTGCAATGATTCA 60.337 40.000 0.00 0.00 0.00 2.57
2365 2456 5.107133 CCAGACAAATTCCTGCAATGATTC 58.893 41.667 0.00 0.00 0.00 2.52
2366 2457 4.622220 GCCAGACAAATTCCTGCAATGATT 60.622 41.667 0.00 0.00 0.00 2.57
2367 2458 3.118884 GCCAGACAAATTCCTGCAATGAT 60.119 43.478 0.00 0.00 0.00 2.45
2368 2459 2.231964 GCCAGACAAATTCCTGCAATGA 59.768 45.455 0.00 0.00 0.00 2.57
2369 2460 2.028839 TGCCAGACAAATTCCTGCAATG 60.029 45.455 0.00 0.00 0.00 2.82
2373 2464 1.340889 TGTTGCCAGACAAATTCCTGC 59.659 47.619 0.00 0.00 40.82 4.85
2419 2510 3.071023 TGAGGTAAGTCAGGTTGTTGAGG 59.929 47.826 0.00 0.00 0.00 3.86
2449 2540 3.121944 CGAGTTGGTTCTTGTGAAGATCG 59.878 47.826 0.00 0.00 37.38 3.69
2530 2621 2.292521 TGGCCCAGTCAGTCTATTCTCT 60.293 50.000 0.00 0.00 0.00 3.10
2537 2628 1.994463 GGATTGGCCCAGTCAGTCT 59.006 57.895 8.63 0.00 0.00 3.24
2609 2700 0.318762 GGTATGATGCCGGAGAGACC 59.681 60.000 5.05 0.00 0.00 3.85
2614 2705 1.875576 GCAGAAGGTATGATGCCGGAG 60.876 57.143 5.05 0.00 32.49 4.63
2740 2831 5.773575 ACAATGACGATTATGATAGCGACT 58.226 37.500 0.00 0.00 0.00 4.18
2776 2867 4.889409 ACAATGCAGACCCCAATAAGTATG 59.111 41.667 0.00 0.00 0.00 2.39
2800 2891 2.880890 GGCCCTAATGTTCATAGCACAG 59.119 50.000 0.00 0.00 0.00 3.66
2829 2920 1.342474 CCTGCTCCTCCTTACTCCTCA 60.342 57.143 0.00 0.00 0.00 3.86
2986 3077 2.023673 TCTTTGTCAACCAGTGCCTTG 58.976 47.619 0.00 0.00 0.00 3.61
3274 3365 1.126846 CTGCTACTTCTGGAAAACGCG 59.873 52.381 3.53 3.53 0.00 6.01
3525 3616 2.111878 CTAGCTCCGGGGCAATGG 59.888 66.667 31.81 6.85 34.17 3.16
3565 3656 7.171508 CCAAAGCTAAATACATCGCTCTTATCA 59.828 37.037 0.00 0.00 31.30 2.15
3684 3775 4.501571 CCGATTTAGTACCATCCTCCAGTG 60.502 50.000 0.00 0.00 0.00 3.66
3870 3961 6.373759 TCCTATTCTGCTACTATGTTCCAGA 58.626 40.000 0.00 0.00 0.00 3.86
3962 4058 7.672239 GGACTGGGGCCACAATAATAATAATAA 59.328 37.037 10.16 0.00 0.00 1.40
3963 4059 7.019153 AGGACTGGGGCCACAATAATAATAATA 59.981 37.037 10.16 0.00 0.00 0.98
3964 4060 6.016555 GGACTGGGGCCACAATAATAATAAT 58.983 40.000 10.16 0.00 0.00 1.28
4191 4287 6.094186 GGTCTGACCATGAAGATAAAAGGTTC 59.906 42.308 21.70 0.00 38.42 3.62
4230 4326 4.540099 ACTCCTCTTTGGATCCCACAAATA 59.460 41.667 9.90 0.00 45.16 1.40
4241 4337 5.163141 TGGACAATAACAACTCCTCTTTGGA 60.163 40.000 0.00 0.00 43.86 3.53
4259 4355 6.723298 AAAAGTTGATACACCATTGGACAA 57.277 33.333 10.37 5.07 0.00 3.18
4371 4467 7.731235 TGTATTTAGTGCTGGTATATGTAGGGA 59.269 37.037 0.00 0.00 0.00 4.20
4372 4468 7.903145 TGTATTTAGTGCTGGTATATGTAGGG 58.097 38.462 0.00 0.00 0.00 3.53
4434 4530 3.243501 CCTCGGCCATTTGGAATGTATTG 60.244 47.826 2.24 0.00 37.39 1.90
4435 4531 2.958355 CCTCGGCCATTTGGAATGTATT 59.042 45.455 2.24 0.00 37.39 1.89
4436 4532 2.174639 TCCTCGGCCATTTGGAATGTAT 59.825 45.455 2.24 0.00 37.39 2.29
4437 4533 1.562008 TCCTCGGCCATTTGGAATGTA 59.438 47.619 2.24 0.00 37.39 2.29
4575 4671 2.909006 ACATGAGAAGACTGTGGGTGAT 59.091 45.455 0.00 0.00 0.00 3.06
4576 4672 2.300152 GACATGAGAAGACTGTGGGTGA 59.700 50.000 0.00 0.00 0.00 4.02
4578 4674 1.625818 GGACATGAGAAGACTGTGGGT 59.374 52.381 0.00 0.00 0.00 4.51
4623 4719 1.303236 TTCCCACTGGAATGGCACG 60.303 57.895 0.00 0.00 45.88 5.34
4680 4776 2.961721 CGATCGGACGGTGCATGG 60.962 66.667 7.38 0.00 0.00 3.66
4902 5001 2.435059 GCAGAGGTGTTCCCGCTC 60.435 66.667 0.00 0.00 42.14 5.03
5006 5105 2.441901 CGCTCCTCAGAGGGCTCT 60.442 66.667 17.10 0.00 44.96 4.09


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

AutoCloner maintained by Alex Coulton.