Multiple sequence alignment - TraesCS2A01G304000

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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 TraesCS2A01G304000 chr2A 100.000 3443 0 0 1 3443 522490338 522486896 0.000000e+00 6359.0
1 TraesCS2A01G304000 chr2B 92.519 3275 132 39 1 3231 457338212 457335007 0.000000e+00 4586.0
2 TraesCS2A01G304000 chr2B 89.706 68 6 1 3376 3443 782545434 782545368 6.120000e-13 86.1
3 TraesCS2A01G304000 chr2D 94.455 2759 94 18 575 3287 386482029 386479284 0.000000e+00 4193.0
4 TraesCS2A01G304000 chr2D 95.085 590 20 5 1 587 386483843 386483260 0.000000e+00 920.0
5 TraesCS2A01G304000 chr7D 92.958 71 5 0 3373 3443 633233919 633233989 1.690000e-18 104.0
6 TraesCS2A01G304000 chr1D 92.188 64 5 0 3380 3443 469789659 469789596 1.320000e-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 TraesCS2A01G304000 chr2A 522486896 522490338 3442 True 6359.0 6359 100.000 1 3443 1 chr2A.!!$R1 3442
1 TraesCS2A01G304000 chr2B 457335007 457338212 3205 True 4586.0 4586 92.519 1 3231 1 chr2B.!!$R1 3230
2 TraesCS2A01G304000 chr2D 386479284 386483843 4559 True 2556.5 4193 94.770 1 3287 2 chr2D.!!$R1 3286

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
403 413 0.696501 ACCTCCGTTTGGTTAGCCAT 59.303 50.0 0.0 0.0 45.56 4.40 F
1121 2388 0.877649 GATCGCGCCACTGTCATGAT 60.878 55.0 0.0 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 3202 1.003718 GACCAAGGACGGGTTCAGG 60.004 63.158 0.00 0.00 39.19 3.86 R
2446 3725 0.936297 GAATGAATGAATGGGCGCGC 60.936 55.000 25.94 25.94 0.00 6.86 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
57 59 3.294493 CAACCAGGCAACCACCCG 61.294 66.667 0.00 0.00 37.17 5.28
108 110 7.122353 ACATTTTCTTGAGGGAATGAGATTCTG 59.878 37.037 11.49 0.00 39.24 3.02
170 172 0.956902 AACGTATGCCCCAAACCGTC 60.957 55.000 0.00 0.00 0.00 4.79
171 173 2.110352 CGTATGCCCCAAACCGTCC 61.110 63.158 0.00 0.00 0.00 4.79
172 174 1.301954 GTATGCCCCAAACCGTCCT 59.698 57.895 0.00 0.00 0.00 3.85
173 175 0.746923 GTATGCCCCAAACCGTCCTC 60.747 60.000 0.00 0.00 0.00 3.71
174 176 2.246761 TATGCCCCAAACCGTCCTCG 62.247 60.000 0.00 0.00 0.00 4.63
175 177 4.324991 GCCCCAAACCGTCCTCGT 62.325 66.667 0.00 0.00 35.01 4.18
296 304 5.649831 ACCTCAACTTAGGCATCAATCTTTC 59.350 40.000 0.00 0.00 40.62 2.62
390 400 2.665089 TATGTGTGCCCCACCTCCG 61.665 63.158 1.61 0.00 43.85 4.63
403 413 0.696501 ACCTCCGTTTGGTTAGCCAT 59.303 50.000 0.00 0.00 45.56 4.40
411 421 4.819630 CCGTTTGGTTAGCCATACATACAT 59.180 41.667 16.99 0.00 45.56 2.29
412 422 5.992829 CCGTTTGGTTAGCCATACATACATA 59.007 40.000 16.99 0.00 45.56 2.29
413 423 6.073440 CCGTTTGGTTAGCCATACATACATAC 60.073 42.308 16.99 0.00 45.56 2.39
437 447 1.732259 AGTGTAAAAGCGGATCTTGCG 59.268 47.619 5.11 0.00 34.67 4.85
450 460 1.557099 TCTTGCGGTGTGGACTAGAT 58.443 50.000 0.00 0.00 0.00 1.98
451 461 1.204704 TCTTGCGGTGTGGACTAGATG 59.795 52.381 0.00 0.00 0.00 2.90
509 519 2.494073 ACAAGCTACTAGTCCACTCTGC 59.506 50.000 0.00 0.00 0.00 4.26
522 532 1.473677 CACTCTGCTCTCCTCTGTCAG 59.526 57.143 0.00 0.00 0.00 3.51
548 561 6.183360 ACACACACATTGTTAACTAACACCAG 60.183 38.462 7.22 0.00 45.01 4.00
603 1859 1.956629 TAGCGGTGGAGCTTGGTAGC 61.957 60.000 0.00 0.00 46.80 3.58
921 2177 2.304180 CCTCGCCCATCTCCATTAATCT 59.696 50.000 0.00 0.00 0.00 2.40
1121 2388 0.877649 GATCGCGCCACTGTCATGAT 60.878 55.000 0.00 0.00 0.00 2.45
1170 2437 2.376808 AGGTTGAGCTTGATCACGAG 57.623 50.000 2.89 0.00 0.00 4.18
1187 2454 1.961180 GAGGACGGGGATGTGAGTGG 61.961 65.000 0.00 0.00 0.00 4.00
1189 2456 2.607750 ACGGGGATGTGAGTGGCT 60.608 61.111 0.00 0.00 0.00 4.75
1190 2457 2.187946 CGGGGATGTGAGTGGCTC 59.812 66.667 0.00 0.00 0.00 4.70
1195 2462 1.153549 GATGTGAGTGGCTCCGGAC 60.154 63.158 0.00 0.00 0.00 4.79
1197 2464 4.436998 GTGAGTGGCTCCGGACCG 62.437 72.222 6.99 6.99 0.00 4.79
1809 3088 2.192979 GAGGATGGCCGCCATGAA 59.807 61.111 29.86 0.00 45.26 2.57
1923 3202 1.097547 CATTGGCTCACATCCGGTCC 61.098 60.000 0.00 0.00 0.00 4.46
2446 3725 0.512952 CAAGAACGAGCCCTGAAACG 59.487 55.000 0.00 0.00 0.00 3.60
2524 3806 6.490040 TCCGATTCTTCTTGGTTTCTTCATTT 59.510 34.615 0.00 0.00 0.00 2.32
2726 4019 2.575262 GCATCACGAGCTTTGCGC 60.575 61.111 0.00 0.00 39.57 6.09
2727 4020 2.862436 CATCACGAGCTTTGCGCA 59.138 55.556 5.66 5.66 42.61 6.09
2839 4157 1.002888 TCGAGTCTAGTCCCGACTGTT 59.997 52.381 7.63 0.00 41.53 3.16
2861 4179 3.003275 TCAACTGACATTTTGCTTCGACC 59.997 43.478 0.00 0.00 0.00 4.79
2898 4221 3.906846 AGCATATCCCTTCCTTCCTAGTG 59.093 47.826 0.00 0.00 0.00 2.74
2943 4266 3.198068 CACTGGAAAGGTCGGATATGTG 58.802 50.000 0.00 0.00 0.00 3.21
3019 4342 6.918569 CGGTCAGTCTACACCTAATAAAGATG 59.081 42.308 0.00 0.00 0.00 2.90
3094 4417 0.320374 CCGGTACTCAAGCACAAGGA 59.680 55.000 0.00 0.00 0.00 3.36
3132 4455 8.940952 TCAGATATAATCGTCATCTACAGTGAG 58.059 37.037 0.00 0.00 0.00 3.51
3133 4456 8.940952 CAGATATAATCGTCATCTACAGTGAGA 58.059 37.037 0.00 0.00 0.00 3.27
3175 4503 1.548269 CCGAGATAAGATGGAGAGGCC 59.452 57.143 0.00 0.00 37.10 5.19
3222 4550 6.642540 GGTTTGACTTTCCAATCATCTTTCAC 59.357 38.462 0.00 0.00 0.00 3.18
3242 4570 0.103572 GCATGCTAGTGGCCATTTGG 59.896 55.000 9.72 3.66 40.92 3.28
3247 4575 1.755179 CTAGTGGCCATTTGGTCCTG 58.245 55.000 9.72 0.00 39.61 3.86
3250 4578 1.228831 TGGCCATTTGGTCCTGTGG 60.229 57.895 0.00 4.06 39.61 4.17
3282 4610 5.396548 ACGTAGTACTCCTCAGAGCATCTAA 60.397 44.000 0.00 0.00 43.31 2.10
3294 4622 3.931578 GAGCATCTAAAGCCGGATATGT 58.068 45.455 5.05 0.00 0.00 2.29
3295 4623 3.929610 GAGCATCTAAAGCCGGATATGTC 59.070 47.826 5.05 0.00 0.00 3.06
3296 4624 3.003480 GCATCTAAAGCCGGATATGTCC 58.997 50.000 5.05 0.00 41.40 4.02
3297 4625 3.600388 CATCTAAAGCCGGATATGTCCC 58.400 50.000 5.05 0.00 41.83 4.46
3298 4626 2.972348 TCTAAAGCCGGATATGTCCCT 58.028 47.619 5.05 0.00 41.83 4.20
3299 4627 3.314693 TCTAAAGCCGGATATGTCCCTT 58.685 45.455 5.05 0.00 41.83 3.95
3300 4628 4.485875 TCTAAAGCCGGATATGTCCCTTA 58.514 43.478 5.05 0.00 41.83 2.69
3301 4629 3.771577 AAAGCCGGATATGTCCCTTAG 57.228 47.619 5.05 0.00 41.83 2.18
3302 4630 2.696526 AGCCGGATATGTCCCTTAGA 57.303 50.000 5.05 0.00 41.83 2.10
3303 4631 2.530701 AGCCGGATATGTCCCTTAGAG 58.469 52.381 5.05 0.00 41.83 2.43
3304 4632 1.066787 GCCGGATATGTCCCTTAGAGC 60.067 57.143 5.05 0.00 41.83 4.09
3305 4633 2.248248 CCGGATATGTCCCTTAGAGCA 58.752 52.381 0.00 0.00 41.83 4.26
3306 4634 2.834549 CCGGATATGTCCCTTAGAGCAT 59.165 50.000 0.00 0.00 41.83 3.79
3307 4635 3.118956 CCGGATATGTCCCTTAGAGCATC 60.119 52.174 0.00 0.00 41.83 3.91
3308 4636 3.766591 CGGATATGTCCCTTAGAGCATCT 59.233 47.826 2.45 0.00 45.39 2.90
3309 4637 4.950475 CGGATATGTCCCTTAGAGCATCTA 59.050 45.833 2.45 0.00 42.77 1.98
3310 4638 6.859112 GGATATGTCCCTTAGAGCATCTAA 57.141 41.667 0.00 0.00 45.76 2.10
3324 4652 6.701145 GAGCATCTAAGGTCGGATATATCA 57.299 41.667 14.60 0.00 0.00 2.15
3325 4653 7.101652 GAGCATCTAAGGTCGGATATATCAA 57.898 40.000 14.60 0.00 0.00 2.57
3326 4654 7.482169 AGCATCTAAGGTCGGATATATCAAA 57.518 36.000 14.60 0.00 0.00 2.69
3327 4655 8.083828 AGCATCTAAGGTCGGATATATCAAAT 57.916 34.615 14.60 0.00 0.00 2.32
3328 4656 7.984050 AGCATCTAAGGTCGGATATATCAAATG 59.016 37.037 14.60 1.77 0.00 2.32
3329 4657 7.766278 GCATCTAAGGTCGGATATATCAAATGT 59.234 37.037 14.60 0.00 0.00 2.71
3330 4658 9.091784 CATCTAAGGTCGGATATATCAAATGTG 57.908 37.037 14.60 0.00 0.00 3.21
3331 4659 7.611770 TCTAAGGTCGGATATATCAAATGTGG 58.388 38.462 14.60 0.00 0.00 4.17
3332 4660 4.579869 AGGTCGGATATATCAAATGTGGC 58.420 43.478 14.60 0.00 0.00 5.01
3333 4661 3.689649 GGTCGGATATATCAAATGTGGCC 59.310 47.826 14.60 0.00 0.00 5.36
3334 4662 3.689649 GTCGGATATATCAAATGTGGCCC 59.310 47.826 14.60 0.00 0.00 5.80
3335 4663 3.587061 TCGGATATATCAAATGTGGCCCT 59.413 43.478 14.60 0.00 0.00 5.19
3336 4664 4.042809 TCGGATATATCAAATGTGGCCCTT 59.957 41.667 14.60 0.00 0.00 3.95
3337 4665 4.396166 CGGATATATCAAATGTGGCCCTTC 59.604 45.833 14.60 0.00 0.00 3.46
3338 4666 5.324409 GGATATATCAAATGTGGCCCTTCA 58.676 41.667 14.60 0.00 0.00 3.02
3339 4667 5.774690 GGATATATCAAATGTGGCCCTTCAA 59.225 40.000 14.60 0.00 0.00 2.69
3340 4668 6.267471 GGATATATCAAATGTGGCCCTTCAAA 59.733 38.462 14.60 0.00 0.00 2.69
3341 4669 7.038799 GGATATATCAAATGTGGCCCTTCAAAT 60.039 37.037 14.60 0.00 0.00 2.32
3342 4670 3.681593 TCAAATGTGGCCCTTCAAATG 57.318 42.857 0.00 1.49 0.00 2.32
3343 4671 2.078392 CAAATGTGGCCCTTCAAATGC 58.922 47.619 0.00 0.00 0.00 3.56
3344 4672 0.614812 AATGTGGCCCTTCAAATGCC 59.385 50.000 0.00 0.00 45.56 4.40
3345 4673 1.266867 ATGTGGCCCTTCAAATGCCC 61.267 55.000 0.00 0.00 44.72 5.36
3346 4674 2.679642 TGGCCCTTCAAATGCCCG 60.680 61.111 0.00 0.00 44.72 6.13
3347 4675 4.147449 GGCCCTTCAAATGCCCGC 62.147 66.667 0.00 0.00 39.30 6.13
3348 4676 4.496927 GCCCTTCAAATGCCCGCG 62.497 66.667 0.00 0.00 0.00 6.46
3349 4677 3.825611 CCCTTCAAATGCCCGCGG 61.826 66.667 21.04 21.04 0.00 6.46
3350 4678 2.749839 CCTTCAAATGCCCGCGGA 60.750 61.111 30.73 8.21 0.00 5.54
3351 4679 2.485122 CTTCAAATGCCCGCGGAC 59.515 61.111 30.73 18.13 0.00 4.79
3352 4680 3.381169 CTTCAAATGCCCGCGGACG 62.381 63.158 30.73 12.70 39.67 4.79
3363 4691 4.729856 GCGGACGCGTTGGGTACT 62.730 66.667 15.53 0.00 0.00 2.73
3364 4692 2.807895 CGGACGCGTTGGGTACTG 60.808 66.667 15.53 0.00 0.00 2.74
3365 4693 2.652530 GGACGCGTTGGGTACTGA 59.347 61.111 15.53 0.00 0.00 3.41
3366 4694 1.735559 GGACGCGTTGGGTACTGAC 60.736 63.158 15.53 0.00 0.00 3.51
3367 4695 1.288127 GACGCGTTGGGTACTGACT 59.712 57.895 15.53 0.00 0.00 3.41
3368 4696 1.006571 ACGCGTTGGGTACTGACTG 60.007 57.895 5.58 0.00 0.00 3.51
3369 4697 1.287815 CGCGTTGGGTACTGACTGA 59.712 57.895 0.00 0.00 0.00 3.41
3370 4698 0.732880 CGCGTTGGGTACTGACTGAG 60.733 60.000 0.00 0.00 0.00 3.35
3371 4699 0.389948 GCGTTGGGTACTGACTGAGG 60.390 60.000 0.00 0.00 0.00 3.86
3372 4700 1.254026 CGTTGGGTACTGACTGAGGA 58.746 55.000 0.00 0.00 0.00 3.71
3373 4701 1.202582 CGTTGGGTACTGACTGAGGAG 59.797 57.143 0.00 0.00 0.00 3.69
3374 4702 1.550976 GTTGGGTACTGACTGAGGAGG 59.449 57.143 0.00 0.00 0.00 4.30
3375 4703 0.614979 TGGGTACTGACTGAGGAGGC 60.615 60.000 0.00 0.00 0.00 4.70
3376 4704 1.331399 GGGTACTGACTGAGGAGGCC 61.331 65.000 0.00 0.00 0.00 5.19
3377 4705 0.324830 GGTACTGACTGAGGAGGCCT 60.325 60.000 3.86 3.86 36.03 5.19
3389 4717 3.532641 AGGAGGCCTCAAATTTCACTT 57.467 42.857 33.29 0.00 0.00 3.16
3390 4718 3.160269 AGGAGGCCTCAAATTTCACTTG 58.840 45.455 33.29 0.00 0.00 3.16
3391 4719 2.893489 GGAGGCCTCAAATTTCACTTGT 59.107 45.455 33.29 0.00 0.00 3.16
3392 4720 3.321968 GGAGGCCTCAAATTTCACTTGTT 59.678 43.478 33.29 0.00 0.00 2.83
3393 4721 4.522789 GGAGGCCTCAAATTTCACTTGTTA 59.477 41.667 33.29 0.00 0.00 2.41
3394 4722 5.453567 AGGCCTCAAATTTCACTTGTTAC 57.546 39.130 0.00 0.00 0.00 2.50
3395 4723 4.892934 AGGCCTCAAATTTCACTTGTTACA 59.107 37.500 0.00 0.00 0.00 2.41
3396 4724 5.539955 AGGCCTCAAATTTCACTTGTTACAT 59.460 36.000 0.00 0.00 0.00 2.29
3397 4725 5.863935 GGCCTCAAATTTCACTTGTTACATC 59.136 40.000 0.00 0.00 0.00 3.06
3398 4726 5.863935 GCCTCAAATTTCACTTGTTACATCC 59.136 40.000 0.00 0.00 0.00 3.51
3399 4727 6.086222 CCTCAAATTTCACTTGTTACATCCG 58.914 40.000 0.00 0.00 0.00 4.18
3400 4728 6.007936 TCAAATTTCACTTGTTACATCCGG 57.992 37.500 0.00 0.00 0.00 5.14
3401 4729 5.765677 TCAAATTTCACTTGTTACATCCGGA 59.234 36.000 6.61 6.61 0.00 5.14
3402 4730 5.622770 AATTTCACTTGTTACATCCGGAC 57.377 39.130 6.12 0.00 0.00 4.79
3403 4731 3.755112 TTCACTTGTTACATCCGGACA 57.245 42.857 6.12 0.00 0.00 4.02
3404 4732 3.973206 TCACTTGTTACATCCGGACAT 57.027 42.857 6.12 0.00 0.00 3.06
3405 4733 3.857052 TCACTTGTTACATCCGGACATC 58.143 45.455 6.12 0.00 0.00 3.06
3406 4734 3.513912 TCACTTGTTACATCCGGACATCT 59.486 43.478 6.12 0.00 0.00 2.90
3407 4735 3.865745 CACTTGTTACATCCGGACATCTC 59.134 47.826 6.12 0.00 0.00 2.75
3408 4736 3.513912 ACTTGTTACATCCGGACATCTCA 59.486 43.478 6.12 0.72 0.00 3.27
3409 4737 4.162320 ACTTGTTACATCCGGACATCTCAT 59.838 41.667 6.12 0.00 0.00 2.90
3410 4738 5.362717 ACTTGTTACATCCGGACATCTCATA 59.637 40.000 6.12 0.00 0.00 2.15
3411 4739 5.196341 TGTTACATCCGGACATCTCATAC 57.804 43.478 6.12 0.00 0.00 2.39
3412 4740 4.893524 TGTTACATCCGGACATCTCATACT 59.106 41.667 6.12 0.00 0.00 2.12
3413 4741 6.066032 TGTTACATCCGGACATCTCATACTA 58.934 40.000 6.12 0.00 0.00 1.82
3414 4742 6.719829 TGTTACATCCGGACATCTCATACTAT 59.280 38.462 6.12 0.00 0.00 2.12
3415 4743 7.886446 TGTTACATCCGGACATCTCATACTATA 59.114 37.037 6.12 0.00 0.00 1.31
3416 4744 8.904834 GTTACATCCGGACATCTCATACTATAT 58.095 37.037 6.12 0.00 0.00 0.86
3417 4745 7.962995 ACATCCGGACATCTCATACTATATT 57.037 36.000 6.12 0.00 0.00 1.28
3418 4746 8.001881 ACATCCGGACATCTCATACTATATTC 57.998 38.462 6.12 0.00 0.00 1.75
3419 4747 7.836685 ACATCCGGACATCTCATACTATATTCT 59.163 37.037 6.12 0.00 0.00 2.40
3420 4748 8.690884 CATCCGGACATCTCATACTATATTCTT 58.309 37.037 6.12 0.00 0.00 2.52
3421 4749 9.922477 ATCCGGACATCTCATACTATATTCTTA 57.078 33.333 6.12 0.00 0.00 2.10
3422 4750 9.749340 TCCGGACATCTCATACTATATTCTTAA 57.251 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 0.396435 GGGCAAAGGTGAAAAAGGGG 59.604 55.000 0.00 0.00 0.00 4.79
108 110 4.201822 GGACATGGAATCAGTAAAAGTCGC 60.202 45.833 0.00 0.00 0.00 5.19
172 174 8.670922 GAGCATCATCGTATACGTCAAGACGA 62.671 46.154 27.09 10.26 46.70 4.20
174 176 4.537965 AGCATCATCGTATACGTCAAGAC 58.462 43.478 23.67 11.48 40.80 3.01
175 177 4.610680 CGAGCATCATCGTATACGTCAAGA 60.611 45.833 23.67 16.72 37.91 3.02
282 290 3.011032 AGGTGGAAGAAAGATTGATGCCT 59.989 43.478 0.00 0.00 0.00 4.75
296 304 6.040504 GCCAATTTAATAGGGTTAGGTGGAAG 59.959 42.308 0.00 0.00 0.00 3.46
403 413 7.916977 CCGCTTTTACACTGTAGTATGTATGTA 59.083 37.037 0.00 0.00 31.55 2.29
411 421 5.909621 AGATCCGCTTTTACACTGTAGTA 57.090 39.130 0.00 0.00 0.00 1.82
412 422 4.803098 AGATCCGCTTTTACACTGTAGT 57.197 40.909 0.00 0.00 0.00 2.73
413 423 4.201724 GCAAGATCCGCTTTTACACTGTAG 60.202 45.833 0.00 0.00 33.60 2.74
437 447 0.103208 CTCGCCATCTAGTCCACACC 59.897 60.000 0.00 0.00 0.00 4.16
450 460 2.639065 GGTTTCAATGGTATCTCGCCA 58.361 47.619 0.00 0.00 40.68 5.69
451 461 1.597663 CGGTTTCAATGGTATCTCGCC 59.402 52.381 0.00 0.00 0.00 5.54
509 519 2.030363 GTGTGTGTCTGACAGAGGAGAG 60.030 54.545 11.41 0.00 34.28 3.20
522 532 6.183360 TGGTGTTAGTTAACAATGTGTGTGTC 60.183 38.462 8.61 0.00 46.54 3.67
548 561 5.164061 CGCTGAATTAAGCATTGTTCAAACC 60.164 40.000 15.31 0.00 43.73 3.27
603 1859 1.032794 TCATCTACCGGCTGCTAGTG 58.967 55.000 0.00 0.00 0.00 2.74
604 1860 2.002505 ATCATCTACCGGCTGCTAGT 57.997 50.000 0.00 0.00 0.00 2.57
605 1861 2.425312 CCTATCATCTACCGGCTGCTAG 59.575 54.545 0.00 0.00 0.00 3.42
606 1862 2.225041 ACCTATCATCTACCGGCTGCTA 60.225 50.000 0.00 0.00 0.00 3.49
607 1863 1.261480 CCTATCATCTACCGGCTGCT 58.739 55.000 0.00 0.00 0.00 4.24
608 1864 0.969894 ACCTATCATCTACCGGCTGC 59.030 55.000 0.00 0.00 0.00 5.25
921 2177 2.880879 CAGAAGCTAGCGCGCGAA 60.881 61.111 37.18 19.95 42.32 4.70
1121 2388 2.542409 ATCTCTGGCCTGGAGGAGCA 62.542 60.000 20.54 7.03 37.39 4.26
1170 2437 2.584608 CCACTCACATCCCCGTCC 59.415 66.667 0.00 0.00 0.00 4.79
1809 3088 2.264794 GGGTCGGTCTTGATGCGT 59.735 61.111 0.00 0.00 0.00 5.24
1879 3158 2.356793 CGGATCCCATGAGCTCGC 60.357 66.667 9.64 0.00 0.00 5.03
1923 3202 1.003718 GACCAAGGACGGGTTCAGG 60.004 63.158 0.00 0.00 39.19 3.86
1979 3258 3.134127 ATCTTCCGGCGCCTTTGC 61.134 61.111 26.68 0.00 0.00 3.68
2446 3725 0.936297 GAATGAATGAATGGGCGCGC 60.936 55.000 25.94 25.94 0.00 6.86
2524 3806 4.947883 TCTCTCTCTCCCAATAAGGAACA 58.052 43.478 0.00 0.00 41.22 3.18
2765 4083 7.663493 TGTTTATGGATGATTAGTCAACACACA 59.337 33.333 0.00 0.00 38.01 3.72
2782 4100 4.233789 GCTTGCACGATTTTGTTTATGGA 58.766 39.130 0.00 0.00 0.00 3.41
2787 4105 4.024977 GGAAATGCTTGCACGATTTTGTTT 60.025 37.500 0.00 0.00 0.00 2.83
2839 4157 3.003275 GGTCGAAGCAAAATGTCAGTTGA 59.997 43.478 3.74 0.00 0.00 3.18
2874 4192 4.595350 ACTAGGAAGGAAGGGATATGCTTC 59.405 45.833 0.00 0.00 42.49 3.86
2898 4221 5.725864 GCAGATCCGTTCGTTGTTTTATACC 60.726 44.000 0.00 0.00 0.00 2.73
2943 4266 2.481952 GTCTTCTGATTGTCCTGTGCAC 59.518 50.000 10.75 10.75 0.00 4.57
3019 4342 2.185494 GCTATCTGCCCAGCTGCAC 61.185 63.158 8.66 2.32 36.04 4.57
3132 4455 4.165036 CGATGATCTCTGTCGATCCATTC 58.835 47.826 0.00 0.00 39.20 2.67
3133 4456 3.613671 GCGATGATCTCTGTCGATCCATT 60.614 47.826 12.27 0.00 39.20 3.16
3175 4503 3.896133 GCATGCCGTGGCCATCTG 61.896 66.667 9.72 1.43 41.09 2.90
3222 4550 0.248743 CAAATGGCCACTAGCATGCG 60.249 55.000 8.16 0.84 46.50 4.73
3242 4570 1.081376 CGTCTCACGACCACAGGAC 60.081 63.158 0.00 0.00 46.05 3.85
3247 4575 2.072298 AGTACTACGTCTCACGACCAC 58.928 52.381 2.48 0.00 46.05 4.16
3250 4578 2.602660 GAGGAGTACTACGTCTCACGAC 59.397 54.545 0.00 0.00 46.05 4.34
3259 4587 3.472652 AGATGCTCTGAGGAGTACTACG 58.527 50.000 6.83 0.00 41.38 3.51
3271 4599 2.540265 ATCCGGCTTTAGATGCTCTG 57.460 50.000 0.00 0.00 0.00 3.35
3287 4615 6.859112 TTAGATGCTCTAAGGGACATATCC 57.141 41.667 2.63 0.00 37.88 2.59
3298 4626 8.053355 TGATATATCCGACCTTAGATGCTCTAA 58.947 37.037 10.25 5.78 36.68 2.10
3299 4627 7.574607 TGATATATCCGACCTTAGATGCTCTA 58.425 38.462 10.25 0.00 0.00 2.43
3300 4628 6.427441 TGATATATCCGACCTTAGATGCTCT 58.573 40.000 10.25 0.00 0.00 4.09
3301 4629 6.701145 TGATATATCCGACCTTAGATGCTC 57.299 41.667 10.25 0.00 0.00 4.26
3302 4630 7.482169 TTTGATATATCCGACCTTAGATGCT 57.518 36.000 10.25 0.00 0.00 3.79
3303 4631 7.766278 ACATTTGATATATCCGACCTTAGATGC 59.234 37.037 10.25 0.00 0.00 3.91
3304 4632 9.091784 CACATTTGATATATCCGACCTTAGATG 57.908 37.037 10.25 3.74 0.00 2.90
3305 4633 8.260818 CCACATTTGATATATCCGACCTTAGAT 58.739 37.037 10.25 0.00 0.00 1.98
3306 4634 7.611770 CCACATTTGATATATCCGACCTTAGA 58.388 38.462 10.25 0.00 0.00 2.10
3307 4635 6.313905 GCCACATTTGATATATCCGACCTTAG 59.686 42.308 10.25 0.00 0.00 2.18
3308 4636 6.170506 GCCACATTTGATATATCCGACCTTA 58.829 40.000 10.25 0.00 0.00 2.69
3309 4637 5.003804 GCCACATTTGATATATCCGACCTT 58.996 41.667 10.25 0.00 0.00 3.50
3310 4638 4.565652 GGCCACATTTGATATATCCGACCT 60.566 45.833 10.25 0.00 0.00 3.85
3311 4639 3.689649 GGCCACATTTGATATATCCGACC 59.310 47.826 10.25 0.00 0.00 4.79
3312 4640 3.689649 GGGCCACATTTGATATATCCGAC 59.310 47.826 4.39 0.00 0.00 4.79
3313 4641 3.587061 AGGGCCACATTTGATATATCCGA 59.413 43.478 6.18 0.00 0.00 4.55
3314 4642 3.955471 AGGGCCACATTTGATATATCCG 58.045 45.455 6.18 0.00 0.00 4.18
3315 4643 5.324409 TGAAGGGCCACATTTGATATATCC 58.676 41.667 6.18 0.00 0.00 2.59
3316 4644 6.899393 TTGAAGGGCCACATTTGATATATC 57.101 37.500 6.18 5.73 0.00 1.63
3317 4645 7.673180 CATTTGAAGGGCCACATTTGATATAT 58.327 34.615 6.18 0.00 0.00 0.86
3318 4646 6.462768 GCATTTGAAGGGCCACATTTGATATA 60.463 38.462 6.18 0.00 0.00 0.86
3319 4647 5.685599 GCATTTGAAGGGCCACATTTGATAT 60.686 40.000 6.18 0.00 0.00 1.63
3320 4648 4.382901 GCATTTGAAGGGCCACATTTGATA 60.383 41.667 6.18 0.00 0.00 2.15
3321 4649 3.620472 GCATTTGAAGGGCCACATTTGAT 60.620 43.478 6.18 0.00 0.00 2.57
3322 4650 2.289569 GCATTTGAAGGGCCACATTTGA 60.290 45.455 6.18 0.00 0.00 2.69
3323 4651 2.078392 GCATTTGAAGGGCCACATTTG 58.922 47.619 6.18 7.54 0.00 2.32
3324 4652 1.003464 GGCATTTGAAGGGCCACATTT 59.997 47.619 6.18 0.00 46.92 2.32
3325 4653 0.614812 GGCATTTGAAGGGCCACATT 59.385 50.000 6.18 0.00 46.92 2.71
3326 4654 2.289840 GGCATTTGAAGGGCCACAT 58.710 52.632 6.18 0.00 46.92 3.21
3327 4655 3.790223 GGCATTTGAAGGGCCACA 58.210 55.556 6.18 2.21 46.92 4.17
3331 4659 4.496927 CGCGGGCATTTGAAGGGC 62.497 66.667 0.00 0.00 34.24 5.19
3332 4660 3.825611 CCGCGGGCATTTGAAGGG 61.826 66.667 20.10 0.00 0.00 3.95
3333 4661 2.749839 TCCGCGGGCATTTGAAGG 60.750 61.111 27.83 0.00 0.00 3.46
3334 4662 2.485122 GTCCGCGGGCATTTGAAG 59.515 61.111 27.96 0.00 0.00 3.02
3335 4663 3.427425 CGTCCGCGGGCATTTGAA 61.427 61.111 31.65 1.84 0.00 2.69
3346 4674 4.729856 AGTACCCAACGCGTCCGC 62.730 66.667 14.44 0.68 38.22 5.54
3347 4675 2.807895 CAGTACCCAACGCGTCCG 60.808 66.667 14.44 6.98 41.14 4.79
3348 4676 1.735559 GTCAGTACCCAACGCGTCC 60.736 63.158 14.44 0.00 0.00 4.79
3349 4677 1.007336 CAGTCAGTACCCAACGCGTC 61.007 60.000 14.44 0.00 0.00 5.19
3350 4678 1.006571 CAGTCAGTACCCAACGCGT 60.007 57.895 5.58 5.58 0.00 6.01
3351 4679 0.732880 CTCAGTCAGTACCCAACGCG 60.733 60.000 3.53 3.53 0.00 6.01
3352 4680 0.389948 CCTCAGTCAGTACCCAACGC 60.390 60.000 0.00 0.00 0.00 4.84
3353 4681 1.202582 CTCCTCAGTCAGTACCCAACG 59.797 57.143 0.00 0.00 0.00 4.10
3354 4682 1.550976 CCTCCTCAGTCAGTACCCAAC 59.449 57.143 0.00 0.00 0.00 3.77
3355 4683 1.938585 CCTCCTCAGTCAGTACCCAA 58.061 55.000 0.00 0.00 0.00 4.12
3356 4684 0.614979 GCCTCCTCAGTCAGTACCCA 60.615 60.000 0.00 0.00 0.00 4.51
3357 4685 1.331399 GGCCTCCTCAGTCAGTACCC 61.331 65.000 0.00 0.00 0.00 3.69
3358 4686 0.324830 AGGCCTCCTCAGTCAGTACC 60.325 60.000 0.00 0.00 0.00 3.34
3359 4687 3.291497 AGGCCTCCTCAGTCAGTAC 57.709 57.895 0.00 0.00 0.00 2.73
3369 4697 3.160269 CAAGTGAAATTTGAGGCCTCCT 58.840 45.455 29.95 13.87 35.27 3.69
3370 4698 2.893489 ACAAGTGAAATTTGAGGCCTCC 59.107 45.455 29.95 13.66 35.27 4.30
3371 4699 4.590850 AACAAGTGAAATTTGAGGCCTC 57.409 40.909 26.78 26.78 35.27 4.70
3372 4700 4.892934 TGTAACAAGTGAAATTTGAGGCCT 59.107 37.500 3.86 3.86 35.27 5.19
3373 4701 5.195001 TGTAACAAGTGAAATTTGAGGCC 57.805 39.130 0.00 0.00 35.27 5.19
3374 4702 5.863935 GGATGTAACAAGTGAAATTTGAGGC 59.136 40.000 0.00 0.00 35.27 4.70
3375 4703 6.086222 CGGATGTAACAAGTGAAATTTGAGG 58.914 40.000 0.00 0.00 35.27 3.86
3376 4704 6.072728 TCCGGATGTAACAAGTGAAATTTGAG 60.073 38.462 0.00 0.00 35.27 3.02
3377 4705 5.765677 TCCGGATGTAACAAGTGAAATTTGA 59.234 36.000 0.00 0.00 35.27 2.69
3378 4706 5.856455 GTCCGGATGTAACAAGTGAAATTTG 59.144 40.000 7.81 0.00 39.72 2.32
3379 4707 5.533154 TGTCCGGATGTAACAAGTGAAATTT 59.467 36.000 7.81 0.00 0.00 1.82
3380 4708 5.067273 TGTCCGGATGTAACAAGTGAAATT 58.933 37.500 7.81 0.00 0.00 1.82
3381 4709 4.647611 TGTCCGGATGTAACAAGTGAAAT 58.352 39.130 7.81 0.00 0.00 2.17
3382 4710 4.074627 TGTCCGGATGTAACAAGTGAAA 57.925 40.909 7.81 0.00 0.00 2.69
3383 4711 3.755112 TGTCCGGATGTAACAAGTGAA 57.245 42.857 7.81 0.00 0.00 3.18
3384 4712 3.513912 AGATGTCCGGATGTAACAAGTGA 59.486 43.478 7.81 0.00 0.00 3.41
3385 4713 3.861840 AGATGTCCGGATGTAACAAGTG 58.138 45.455 7.81 0.00 0.00 3.16
3386 4714 3.513912 TGAGATGTCCGGATGTAACAAGT 59.486 43.478 7.81 0.00 0.00 3.16
3387 4715 4.123497 TGAGATGTCCGGATGTAACAAG 57.877 45.455 7.81 0.00 0.00 3.16
3388 4716 4.753516 ATGAGATGTCCGGATGTAACAA 57.246 40.909 7.81 0.00 0.00 2.83
3389 4717 4.893524 AGTATGAGATGTCCGGATGTAACA 59.106 41.667 7.81 0.07 0.00 2.41
3390 4718 5.455056 AGTATGAGATGTCCGGATGTAAC 57.545 43.478 7.81 0.00 0.00 2.50
3391 4719 9.475620 AATATAGTATGAGATGTCCGGATGTAA 57.524 33.333 7.81 0.00 0.00 2.41
3392 4720 9.121658 GAATATAGTATGAGATGTCCGGATGTA 57.878 37.037 7.81 0.00 0.00 2.29
3393 4721 7.836685 AGAATATAGTATGAGATGTCCGGATGT 59.163 37.037 7.81 0.00 0.00 3.06
3394 4722 8.231692 AGAATATAGTATGAGATGTCCGGATG 57.768 38.462 7.81 0.00 0.00 3.51
3395 4723 8.830915 AAGAATATAGTATGAGATGTCCGGAT 57.169 34.615 7.81 0.00 0.00 4.18
3396 4724 9.749340 TTAAGAATATAGTATGAGATGTCCGGA 57.251 33.333 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.