Multiple sequence alignment - TraesCS1D01G341500

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 TraesCS1D01G341500 chr1D 100.000 4493 0 0 1 4493 431517335 431521827 0.000000e+00 8298.0
1 TraesCS1D01G341500 chr1B 92.090 3780 258 31 707 4465 582688359 582692118 0.000000e+00 5286.0
2 TraesCS1D01G341500 chr1B 89.916 3709 322 32 788 4465 582708912 582712599 0.000000e+00 4730.0
3 TraesCS1D01G341500 chr1B 92.703 3289 220 6 1155 4436 582720755 582724030 0.000000e+00 4726.0
4 TraesCS1D01G341500 chr1B 83.871 744 68 23 10 715 582687565 582688294 0.000000e+00 662.0
5 TraesCS1D01G341500 chr1B 95.652 276 11 1 885 1159 582715112 582715387 4.120000e-120 442.0
6 TraesCS1D01G341500 chr1A 91.076 2174 185 3 2266 4436 529787459 529789626 0.000000e+00 2931.0
7 TraesCS1D01G341500 chr1A 92.635 1412 59 19 707 2091 529786069 529787462 0.000000e+00 1989.0
8 TraesCS1D01G341500 chr1A 91.560 391 21 6 3 382 529785324 529785713 3.080000e-146 529.0
9 TraesCS1D01G341500 chr1A 97.203 286 8 0 430 715 529785720 529786005 6.760000e-133 484.0
10 TraesCS1D01G341500 chr2A 76.118 2035 411 47 1017 3024 762884014 762886000 0.000000e+00 996.0
11 TraesCS1D01G341500 chr2A 71.865 327 83 8 3992 4315 762739018 762739338 8.010000e-13 86.1
12 TraesCS1D01G341500 chr2D 76.186 1940 402 39 1136 3050 636775783 636773879 0.000000e+00 968.0
13 TraesCS1D01G341500 chr2D 73.574 333 73 10 3992 4314 636928125 636927798 3.670000e-21 113.0
14 TraesCS1D01G341500 chr6B 75.346 2093 443 58 1019 3067 88320570 88318507 0.000000e+00 939.0
15 TraesCS1D01G341500 chr6A 75.312 2086 447 57 1019 3067 49105580 49103526 0.000000e+00 937.0
16 TraesCS1D01G341500 chr6D 75.915 1420 300 37 1666 3067 37673307 37671912 0.000000e+00 689.0
17 TraesCS1D01G341500 chr6D 77.143 560 122 6 1020 1576 37673928 37673372 2.020000e-83 320.0
18 TraesCS1D01G341500 chr7B 72.373 847 187 43 3495 4322 746154781 746153963 1.630000e-54 224.0
19 TraesCS1D01G341500 chr2B 73.193 332 72 16 3991 4315 794426055 794425734 2.210000e-18 104.0
20 TraesCS1D01G341500 chr2B 82.474 97 15 2 4226 4321 794795261 794795166 2.880000e-12 84.2
21 TraesCS1D01G341500 chr5B 78.082 146 28 4 3687 3830 691479655 691479798 6.190000e-14 89.8


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 TraesCS1D01G341500 chr1D 431517335 431521827 4492 False 8298.00 8298 100.0000 1 4493 1 chr1D.!!$F1 4492
1 TraesCS1D01G341500 chr1B 582720755 582724030 3275 False 4726.00 4726 92.7030 1155 4436 1 chr1B.!!$F1 3281
2 TraesCS1D01G341500 chr1B 582687565 582692118 4553 False 2974.00 5286 87.9805 10 4465 2 chr1B.!!$F2 4455
3 TraesCS1D01G341500 chr1B 582708912 582715387 6475 False 2586.00 4730 92.7840 788 4465 2 chr1B.!!$F3 3677
4 TraesCS1D01G341500 chr1A 529785324 529789626 4302 False 1483.25 2931 93.1185 3 4436 4 chr1A.!!$F1 4433
5 TraesCS1D01G341500 chr2A 762884014 762886000 1986 False 996.00 996 76.1180 1017 3024 1 chr2A.!!$F2 2007
6 TraesCS1D01G341500 chr2D 636773879 636775783 1904 True 968.00 968 76.1860 1136 3050 1 chr2D.!!$R1 1914
7 TraesCS1D01G341500 chr6B 88318507 88320570 2063 True 939.00 939 75.3460 1019 3067 1 chr6B.!!$R1 2048
8 TraesCS1D01G341500 chr6A 49103526 49105580 2054 True 937.00 937 75.3120 1019 3067 1 chr6A.!!$R1 2048
9 TraesCS1D01G341500 chr6D 37671912 37673928 2016 True 504.50 689 76.5290 1020 3067 2 chr6D.!!$R1 2047
10 TraesCS1D01G341500 chr7B 746153963 746154781 818 True 224.00 224 72.3730 3495 4322 1 chr7B.!!$R1 827

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
412 449 0.541998 ATGGGCATCCGAGACCGATA 60.542 55.0 0.0 0.0 38.22 2.92 F
1655 1804 1.172175 TCAACAAGCACAACAGCACA 58.828 45.0 0.0 0.0 36.85 4.57 F
2166 2349 0.756294 TTGGGTCTGAGAGTTGCGAA 59.244 50.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2150 0.597568 CCAACGCTGCTCATTTTCCA 59.402 50.0 0.00 0.0 0.00 3.53 R
3266 3455 0.582005 AAGCACTTCTTTCGCGACAC 59.418 50.0 9.15 0.0 0.00 3.67 R
3905 4097 0.249657 CGCTAGGAGACCATCAAGGC 60.250 60.0 0.00 0.0 43.14 4.35 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
102 103 2.493278 CAATGGTTTAGCAGGAACCCAG 59.507 50.000 11.77 1.21 44.73 4.45
124 125 6.299922 CAGAGGTGTCTACATCATCCTAGTA 58.700 44.000 0.00 0.00 39.96 1.82
137 144 8.497745 ACATCATCCTAGTAAAATCCAGTCAAT 58.502 33.333 0.00 0.00 0.00 2.57
152 161 4.263243 CCAGTCAATCAGTTCCCTCTTTCT 60.263 45.833 0.00 0.00 0.00 2.52
180 189 1.203928 CATCTCGAGTCGCCAATCAC 58.796 55.000 13.13 0.00 0.00 3.06
202 211 1.208535 TGCCTGGTACTGAAATACGGG 59.791 52.381 0.00 0.00 0.00 5.28
203 212 1.483415 GCCTGGTACTGAAATACGGGA 59.517 52.381 0.00 0.00 0.00 5.14
210 219 5.644636 TGGTACTGAAATACGGGATTTGAAC 59.355 40.000 2.18 0.00 37.90 3.18
232 241 3.708563 TTTTGGCTTCACTTTCCTTCG 57.291 42.857 0.00 0.00 0.00 3.79
235 244 2.925724 TGGCTTCACTTTCCTTCGAAA 58.074 42.857 0.00 0.00 36.55 3.46
382 419 1.134159 CAGCAGAAAGGGATAGCAGCT 60.134 52.381 0.00 0.00 0.00 4.24
387 424 4.268359 CAGAAAGGGATAGCAGCTTTTCT 58.732 43.478 11.70 11.70 35.82 2.52
389 426 5.184671 CAGAAAGGGATAGCAGCTTTTCTTT 59.815 40.000 14.02 12.85 33.86 2.52
409 446 2.104572 ATCATGGGCATCCGAGACCG 62.105 60.000 0.00 0.00 35.24 4.79
412 449 0.541998 ATGGGCATCCGAGACCGATA 60.542 55.000 0.00 0.00 38.22 2.92
451 488 1.513586 CGTTCACCGTACCTCGAGC 60.514 63.158 6.99 0.00 42.86 5.03
500 537 6.069331 TCCCTCTTCTACTCTATTTATGCGT 58.931 40.000 0.00 0.00 0.00 5.24
557 598 1.755179 GCTGCCAAGCTTCATAAGGA 58.245 50.000 0.00 0.00 46.60 3.36
675 721 8.367911 AGACAACACATGTTTCAGTCTTATCTA 58.632 33.333 11.97 0.00 44.12 1.98
676 722 8.311650 ACAACACATGTTTCAGTCTTATCTAC 57.688 34.615 0.00 0.00 40.06 2.59
750 869 9.515226 AACTCTATTTAATTAGTTGCAAGGACA 57.485 29.630 0.00 0.00 31.20 4.02
751 870 9.686683 ACTCTATTTAATTAGTTGCAAGGACAT 57.313 29.630 0.00 0.00 0.00 3.06
762 881 4.935352 TGCAAGGACATGCTTAAACTTT 57.065 36.364 0.00 0.00 46.54 2.66
853 974 9.739276 ACTTCCTTTTGATAGAAACATATGTGA 57.261 29.630 9.63 0.00 0.00 3.58
868 989 7.881775 ACATATGTGAAGAAAAGGATTACCC 57.118 36.000 7.78 0.00 36.73 3.69
875 996 2.993863 AGAAAAGGATTACCCCACCAGT 59.006 45.455 0.00 0.00 36.73 4.00
878 999 2.899303 AGGATTACCCCACCAGTTTG 57.101 50.000 0.00 0.00 36.73 2.93
886 1007 1.463553 CCCACCAGTTTGGCTTGTCC 61.464 60.000 0.00 0.00 42.67 4.02
942 1064 4.338879 ACAAGTATGCTTCCAGAATGCTT 58.661 39.130 0.00 0.00 36.74 3.91
1248 1374 2.202544 CGTGTCGCTGAGCTCCTC 60.203 66.667 12.15 1.47 0.00 3.71
1350 1476 1.636988 GCAATGCAAGTCATTCTGCC 58.363 50.000 0.00 0.00 43.21 4.85
1648 1797 3.068448 AGTCAATGCATCAACAAGCACAA 59.932 39.130 0.00 0.00 44.49 3.33
1655 1804 1.172175 TCAACAAGCACAACAGCACA 58.828 45.000 0.00 0.00 36.85 4.57
1762 1917 7.027760 GGCTCAACATATATGCAATCATCAAG 58.972 38.462 12.79 0.01 34.22 3.02
1773 1934 4.698780 TGCAATCATCAAGAGGTGAAAGAG 59.301 41.667 0.00 0.00 40.50 2.85
1967 2150 1.748244 CGTGTGGGATGATGCCTTGAT 60.748 52.381 4.19 0.00 0.00 2.57
2125 2308 2.238521 TGAAGGAGGATGTGTTTTGGC 58.761 47.619 0.00 0.00 0.00 4.52
2126 2309 1.200020 GAAGGAGGATGTGTTTTGGCG 59.800 52.381 0.00 0.00 0.00 5.69
2162 2345 2.227388 GTGCATTTGGGTCTGAGAGTTG 59.773 50.000 0.00 0.00 0.00 3.16
2166 2349 0.756294 TTGGGTCTGAGAGTTGCGAA 59.244 50.000 0.00 0.00 0.00 4.70
2183 2366 4.832248 TGCGAAAATGATCCTGAGTTAGT 58.168 39.130 0.00 0.00 0.00 2.24
2193 2376 2.501723 TCCTGAGTTAGTGAGGATTGGC 59.498 50.000 0.00 0.00 30.58 4.52
2337 2520 8.770438 AGTTGAAACAAGAGAAGACTGATATC 57.230 34.615 0.00 0.00 0.00 1.63
2616 2799 5.008613 TGACATGGCAAAACTAGTTTCAGAC 59.991 40.000 20.78 18.03 31.45 3.51
2639 2822 5.047802 ACCATGACTGCTTCACCATAAAAAG 60.048 40.000 0.00 0.00 36.92 2.27
2691 2874 6.975197 AGAATGTTCGTCATCTGTACATACTG 59.025 38.462 0.00 0.00 35.48 2.74
2736 2919 3.256631 CCAACTTGTTGAGCCTAAGCAAT 59.743 43.478 14.30 0.00 43.56 3.56
2786 2972 4.584325 TGACAAGTCTTTTGGGAATCAAGG 59.416 41.667 1.53 0.00 36.62 3.61
2989 3178 3.966154 AGATTATACGTGAAGGAGTGCG 58.034 45.455 0.00 0.00 0.00 5.34
3024 3213 5.811796 TGCCCTGTGACTTTAGTAAGTTA 57.188 39.130 0.00 0.00 44.51 2.24
3157 3346 8.632679 ACCAATTTGATGGACATATGAACATAC 58.367 33.333 10.38 7.88 43.54 2.39
3177 3366 2.289694 ACGGAATCTTGGTTCTGTGAGG 60.290 50.000 7.24 0.00 43.99 3.86
3191 3380 5.164620 TCTGTGAGGAATTGTTATGCAGA 57.835 39.130 0.00 0.00 0.00 4.26
3235 3424 1.759445 AGTATCTTCGCAGACTGGCAT 59.241 47.619 4.26 0.00 34.32 4.40
3250 3439 2.559668 CTGGCATTGACATGGTCTTTGT 59.440 45.455 0.00 0.00 33.15 2.83
3266 3455 1.835494 TTGTCGTACTCTCCTGAGGG 58.165 55.000 0.00 0.00 44.29 4.30
3267 3456 0.697079 TGTCGTACTCTCCTGAGGGT 59.303 55.000 4.86 4.86 45.65 4.34
3270 3459 1.096416 CGTACTCTCCTGAGGGTGTC 58.904 60.000 9.95 2.67 43.16 3.67
3272 3461 0.680280 TACTCTCCTGAGGGTGTCGC 60.680 60.000 9.95 0.00 43.16 5.19
3327 3516 2.093764 CGGTCTTGAATCTCTGCTCCTT 60.094 50.000 0.00 0.00 0.00 3.36
3368 3557 1.494721 TCTCCCAAACTGGTTTCAGCT 59.505 47.619 0.00 0.00 44.59 4.24
3400 3589 2.502142 AAATGAGATGCCTGCTGTGA 57.498 45.000 0.00 0.00 0.00 3.58
3444 3633 4.969484 AGATTGGTACTTTGTCGTCCTTT 58.031 39.130 0.00 0.00 0.00 3.11
3490 3679 2.858344 CGAAATCTACGAAGCGTCCAAT 59.142 45.455 0.00 0.00 41.54 3.16
3535 3724 3.181472 GCCTGCCATCAAGAAATTAAGGG 60.181 47.826 0.00 0.00 0.00 3.95
3575 3764 8.454106 CCAGTTAGAATCATTACCAACTGAAAG 58.546 37.037 15.19 1.70 43.41 2.62
3677 3866 2.948315 CCCTCAAGAAGCTCTTATTGGC 59.052 50.000 14.60 0.00 40.87 4.52
3830 4022 5.757320 ACTGCATATCTCTTACATCTGTTGC 59.243 40.000 0.00 0.00 0.00 4.17
3905 4097 4.576053 TGACAATTGTGAGAACCTGACAAG 59.424 41.667 17.58 0.00 40.44 3.16
3922 4114 2.503356 ACAAGCCTTGATGGTCTCCTAG 59.497 50.000 12.25 0.00 38.35 3.02
3950 4142 0.597568 TGTTTGCCTGCCATTCGAAG 59.402 50.000 3.35 0.00 0.00 3.79
3951 4143 0.598065 GTTTGCCTGCCATTCGAAGT 59.402 50.000 3.35 0.00 0.00 3.01
3952 4144 0.597568 TTTGCCTGCCATTCGAAGTG 59.402 50.000 3.35 2.46 0.00 3.16
4027 4219 5.516768 GGGAGTTTTCCTTACCTGGAAGATT 60.517 44.000 0.00 0.00 45.58 2.40
4031 4223 6.265422 AGTTTTCCTTACCTGGAAGATTTGTG 59.735 38.462 0.00 0.00 45.58 3.33
4071 4263 1.547372 CTCAAATGGCCAAGGGAACTG 59.453 52.381 10.96 0.00 42.68 3.16
4137 4329 4.405680 GGGGATATTTCCTCCTGGTTTTTG 59.594 45.833 1.99 0.00 42.20 2.44
4372 4573 0.907486 TAAGCAGCCTGTGAGCAGAT 59.093 50.000 0.00 0.00 45.28 2.90
4390 4591 4.095334 GCAGATGCACAGATATGTTGTCAA 59.905 41.667 0.00 0.00 41.59 3.18
4426 4627 1.812571 CACCTTCCTGTTCATTTCCGG 59.187 52.381 0.00 0.00 0.00 5.14
4427 4628 1.702957 ACCTTCCTGTTCATTTCCGGA 59.297 47.619 0.00 0.00 0.00 5.14
4440 4641 1.348064 TTCCGGATCAGTTGTGAGGT 58.652 50.000 4.15 0.00 35.66 3.85
4446 4647 1.277557 GATCAGTTGTGAGGTGAGGCT 59.722 52.381 0.00 0.00 35.66 4.58
4453 4654 2.125350 GAGGTGAGGCTGCTTCCG 60.125 66.667 9.40 0.00 0.00 4.30
4456 4657 3.123620 GTGAGGCTGCTTCCGCTG 61.124 66.667 9.40 0.00 38.05 5.18
4465 4666 3.393800 GCTGCTTCCGCTGATCTTATAA 58.606 45.455 0.00 0.00 37.28 0.98
4466 4667 3.431572 GCTGCTTCCGCTGATCTTATAAG 59.568 47.826 6.11 6.11 37.28 1.73
4467 4668 4.797604 GCTGCTTCCGCTGATCTTATAAGA 60.798 45.833 17.32 17.32 37.28 2.10
4468 4669 4.876125 TGCTTCCGCTGATCTTATAAGAG 58.124 43.478 19.51 8.32 36.29 2.85
4470 4671 5.160641 GCTTCCGCTGATCTTATAAGAGAG 58.839 45.833 19.51 17.23 38.66 3.20
4471 4672 5.278758 GCTTCCGCTGATCTTATAAGAGAGT 60.279 44.000 19.51 4.17 38.66 3.24
4472 4673 5.697473 TCCGCTGATCTTATAAGAGAGTG 57.303 43.478 19.51 20.35 38.66 3.51
4475 4676 4.321601 CGCTGATCTTATAAGAGAGTGGGG 60.322 50.000 19.51 11.79 38.66 4.96
4476 4677 4.591072 GCTGATCTTATAAGAGAGTGGGGT 59.409 45.833 19.51 1.30 38.66 4.95
4477 4678 5.775701 GCTGATCTTATAAGAGAGTGGGGTA 59.224 44.000 19.51 0.00 38.66 3.69
4478 4679 6.439058 GCTGATCTTATAAGAGAGTGGGGTAT 59.561 42.308 19.51 0.00 38.66 2.73
4479 4680 7.363443 GCTGATCTTATAAGAGAGTGGGGTATC 60.363 44.444 19.51 9.25 38.66 2.24
4480 4681 7.770662 TGATCTTATAAGAGAGTGGGGTATCT 58.229 38.462 19.51 0.00 38.66 1.98
4481 4682 7.891183 TGATCTTATAAGAGAGTGGGGTATCTC 59.109 40.741 19.51 8.64 41.90 2.75
4487 4688 3.375699 GAGAGTGGGGTATCTCTTTCCA 58.624 50.000 0.00 0.00 40.53 3.53
4488 4689 3.108376 AGAGTGGGGTATCTCTTTCCAC 58.892 50.000 0.00 0.00 45.86 4.02
4490 4691 3.933861 GTGGGGTATCTCTTTCCACAT 57.066 47.619 0.00 0.00 45.11 3.21
4491 4692 3.545703 GTGGGGTATCTCTTTCCACATG 58.454 50.000 0.00 0.00 45.11 3.21
4492 4693 2.509548 TGGGGTATCTCTTTCCACATGG 59.490 50.000 0.00 0.00 28.93 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.704725 TCAATCTTTTTGCTCGGCAC 57.295 45.000 0.00 0.00 38.71 5.01
102 103 7.584122 TTTACTAGGATGATGTAGACACCTC 57.416 40.000 0.00 0.00 0.00 3.85
124 125 5.003096 AGGGAACTGATTGACTGGATTTT 57.997 39.130 0.00 0.00 41.13 1.82
137 144 3.587498 TGGAAGAGAAAGAGGGAACTGA 58.413 45.455 0.00 0.00 44.43 3.41
152 161 1.950216 CGACTCGAGATGGATGGAAGA 59.050 52.381 21.68 0.00 0.00 2.87
180 189 2.936498 CCGTATTTCAGTACCAGGCAAG 59.064 50.000 0.00 0.00 0.00 4.01
202 211 6.849588 AAGTGAAGCCAAAATGTTCAAATC 57.150 33.333 0.00 0.00 32.15 2.17
203 212 6.260714 GGAAAGTGAAGCCAAAATGTTCAAAT 59.739 34.615 0.00 0.00 32.15 2.32
210 219 3.983344 CGAAGGAAAGTGAAGCCAAAATG 59.017 43.478 0.00 0.00 0.00 2.32
235 244 8.535335 AGGTCAATGATATTTACTCGCAGATAT 58.465 33.333 0.00 0.00 33.89 1.63
274 284 7.148052 ACAGTCACCAGTATGTAGATTGTAGAC 60.148 40.741 0.00 0.00 36.62 2.59
327 348 5.587443 TCATTTGCAGATCAATCGACTGAAT 59.413 36.000 0.00 0.00 34.12 2.57
366 403 4.582973 AGAAAAGCTGCTATCCCTTTCT 57.417 40.909 16.53 16.53 0.00 2.52
382 419 4.531854 TCGGATGCCCATGATAAAGAAAA 58.468 39.130 0.00 0.00 0.00 2.29
387 424 2.224523 GGTCTCGGATGCCCATGATAAA 60.225 50.000 0.00 0.00 0.00 1.40
389 426 0.976641 GGTCTCGGATGCCCATGATA 59.023 55.000 0.00 0.00 0.00 2.15
409 446 5.510520 GGTGATGTCCAAGATCACTCCTATC 60.511 48.000 14.49 0.00 46.08 2.08
412 449 2.503356 GGTGATGTCCAAGATCACTCCT 59.497 50.000 14.49 0.00 46.08 3.69
451 488 1.602851 CCGACATACGTGGAGGTAGAG 59.397 57.143 0.00 0.00 40.78 2.43
557 598 6.378280 AGTTTGAATCTTTGTGTGTTCTCCTT 59.622 34.615 0.00 0.00 0.00 3.36
650 696 7.426929 AGATAAGACTGAAACATGTGTTGTC 57.573 36.000 0.00 7.04 37.68 3.18
794 914 9.132521 GAAGTTGTTTTCATGGATAGTTTCATG 57.867 33.333 0.00 0.00 41.35 3.07
853 974 3.401342 ACTGGTGGGGTAATCCTTTTCTT 59.599 43.478 0.00 0.00 35.33 2.52
860 981 1.847328 CCAAACTGGTGGGGTAATCC 58.153 55.000 0.00 0.00 34.77 3.01
868 989 0.468029 AGGACAAGCCAAACTGGTGG 60.468 55.000 0.00 0.00 40.46 4.61
875 996 4.301072 AGCAAGTATAGGACAAGCCAAA 57.699 40.909 0.00 0.00 40.02 3.28
878 999 4.010349 ACAAAGCAAGTATAGGACAAGCC 58.990 43.478 0.00 0.00 32.27 4.35
913 1034 4.528206 TCTGGAAGCATACTTGTTCAGAGA 59.472 41.667 0.00 0.00 35.82 3.10
942 1064 3.010027 TGTGGACAAAGAGGGATGCATTA 59.990 43.478 0.00 0.00 0.00 1.90
980 1106 6.350110 GCTCATAGAGATTGGAGTCTGGATAC 60.350 46.154 0.00 0.00 0.00 2.24
1248 1374 1.180029 CTGCATCTTTGAGGTTGGGG 58.820 55.000 0.00 0.00 0.00 4.96
1350 1476 8.027771 ACGGTAGTCTTGTAGAAGTCAATAAAG 58.972 37.037 0.00 0.00 0.00 1.85
1526 1652 3.753272 CAGATCCTTGTCACGACCAAATT 59.247 43.478 0.00 0.00 0.00 1.82
1527 1653 3.007940 TCAGATCCTTGTCACGACCAAAT 59.992 43.478 0.00 0.00 0.00 2.32
1648 1797 6.952773 TTTATTAACTTGGTTCTGTGCTGT 57.047 33.333 0.00 0.00 0.00 4.40
1762 1917 8.834749 ATTAAGTCAAAGTACTCTTTCACCTC 57.165 34.615 0.00 0.00 41.31 3.85
1967 2150 0.597568 CCAACGCTGCTCATTTTCCA 59.402 50.000 0.00 0.00 0.00 3.53
2125 2308 5.701029 AATGCACAAAGTTTGAAGAAACG 57.299 34.783 22.23 2.93 45.34 3.60
2126 2309 6.250089 CCAAATGCACAAAGTTTGAAGAAAC 58.750 36.000 22.23 5.25 41.69 2.78
2162 2345 4.870426 TCACTAACTCAGGATCATTTTCGC 59.130 41.667 0.00 0.00 0.00 4.70
2166 2349 6.821616 ATCCTCACTAACTCAGGATCATTT 57.178 37.500 0.00 0.00 42.46 2.32
2183 2366 3.700538 ACTATGCTTTTGCCAATCCTCA 58.299 40.909 0.00 0.00 46.87 3.86
2193 2376 6.421801 CCTTCAACTTTGGAACTATGCTTTTG 59.578 38.462 0.00 0.00 0.00 2.44
2616 2799 5.047802 ACTTTTTATGGTGAAGCAGTCATGG 60.048 40.000 0.00 0.00 38.90 3.66
2639 2822 4.236527 ACCATTTGGAAGTCCCTCATAC 57.763 45.455 3.01 0.00 38.94 2.39
2691 2874 0.604780 TGCTCAAGTCTCTGCTTGGC 60.605 55.000 6.06 8.48 44.26 4.52
2736 2919 1.827315 GCGTACGCAGCTTTGTGTGA 61.827 55.000 33.90 0.00 41.49 3.58
2786 2972 2.240493 ACGGTCCATTATAGCTGCAC 57.760 50.000 1.02 0.00 0.00 4.57
2989 3178 4.023963 GTCACAGGGCAAACTTTCTAACTC 60.024 45.833 0.00 0.00 0.00 3.01
3081 3270 6.753279 CGAACTGATTGGTTGCATCAATATTT 59.247 34.615 13.53 8.54 35.26 1.40
3157 3346 2.028112 TCCTCACAGAACCAAGATTCCG 60.028 50.000 0.00 0.00 0.00 4.30
3235 3424 4.038763 AGAGTACGACAAAGACCATGTCAA 59.961 41.667 7.36 0.00 45.90 3.18
3250 3439 0.697079 ACACCCTCAGGAGAGTACGA 59.303 55.000 0.00 0.00 40.40 3.43
3266 3455 0.582005 AAGCACTTCTTTCGCGACAC 59.418 50.000 9.15 0.00 0.00 3.67
3267 3456 0.859232 GAAGCACTTCTTTCGCGACA 59.141 50.000 9.15 0.00 36.69 4.35
3270 3459 1.261619 ACTTGAAGCACTTCTTTCGCG 59.738 47.619 11.44 0.00 40.14 5.87
3272 3461 3.134458 AGGACTTGAAGCACTTCTTTCG 58.866 45.455 11.44 0.97 40.14 3.46
3327 3516 7.015682 GGGAGAGACACATCTGGATAATCTTTA 59.984 40.741 0.00 0.00 34.34 1.85
3368 3557 5.468746 GGCATCTCATTTAGGTTTATACGCA 59.531 40.000 0.00 0.00 0.00 5.24
3400 3589 8.948631 ATCTCGTCATTATTGTTGTCAACTAT 57.051 30.769 16.45 15.89 36.33 2.12
3490 3679 4.877823 CACATAAGCTGGATGCAGAAGTTA 59.122 41.667 19.59 11.77 45.94 2.24
3625 3814 3.988517 ACCAAACTTCTCGAGTCGATTTC 59.011 43.478 16.94 0.00 37.72 2.17
3627 3816 3.318017 CACCAAACTTCTCGAGTCGATT 58.682 45.455 16.94 4.35 37.72 3.34
3631 3820 1.149148 GCCACCAAACTTCTCGAGTC 58.851 55.000 13.13 0.00 37.72 3.36
3632 3821 0.600255 CGCCACCAAACTTCTCGAGT 60.600 55.000 13.13 0.00 41.47 4.18
3677 3866 7.224362 GGATATTGTCTGTGAGATGAGAACTTG 59.776 40.741 0.00 0.00 0.00 3.16
3757 3949 3.582647 GGAAGATTCCACATTTGGGGTTT 59.417 43.478 6.74 0.00 46.76 3.27
3805 3997 6.925718 GCAACAGATGTAAGAGATATGCAGTA 59.074 38.462 0.00 0.00 0.00 2.74
3830 4022 1.247567 GATGGGTGGTTGTCCTTGTG 58.752 55.000 0.00 0.00 34.23 3.33
3905 4097 0.249657 CGCTAGGAGACCATCAAGGC 60.250 60.000 0.00 0.00 43.14 4.35
3922 4114 1.284297 GCAGGCAAACATTGTTCCGC 61.284 55.000 12.97 12.97 0.00 5.54
3950 4142 4.022416 TGCCACAATTCCTAACATCAACAC 60.022 41.667 0.00 0.00 0.00 3.32
3951 4143 4.148079 TGCCACAATTCCTAACATCAACA 58.852 39.130 0.00 0.00 0.00 3.33
3952 4144 4.782019 TGCCACAATTCCTAACATCAAC 57.218 40.909 0.00 0.00 0.00 3.18
4027 4219 1.175983 GGGCAATCACGAACCCACAA 61.176 55.000 0.00 0.00 42.33 3.33
4031 4223 0.252197 ACTAGGGCAATCACGAACCC 59.748 55.000 0.00 0.00 43.17 4.11
4137 4329 2.185004 TGAGGTTTTGTAGGCAGCTC 57.815 50.000 0.00 0.00 35.92 4.09
4197 4389 1.529796 GCCGGGTGGAATGGATGTA 59.470 57.895 2.18 0.00 37.49 2.29
4372 4573 6.654582 AGTGTAATTGACAACATATCTGTGCA 59.345 34.615 0.00 0.00 40.66 4.57
4390 4591 4.562963 GGAAGGTGAAGGTCGAAGTGTAAT 60.563 45.833 0.00 0.00 0.00 1.89
4426 4627 1.277557 AGCCTCACCTCACAACTGATC 59.722 52.381 0.00 0.00 0.00 2.92
4427 4628 1.002888 CAGCCTCACCTCACAACTGAT 59.997 52.381 0.00 0.00 0.00 2.90
4453 4654 4.591072 ACCCCACTCTCTTATAAGATCAGC 59.409 45.833 15.47 0.00 33.93 4.26
4456 4657 8.113462 AGAGATACCCCACTCTCTTATAAGATC 58.887 40.741 15.47 6.48 44.51 2.75
4466 4667 3.133183 GTGGAAAGAGATACCCCACTCTC 59.867 52.174 0.00 0.00 41.77 3.20
4467 4668 3.108376 GTGGAAAGAGATACCCCACTCT 58.892 50.000 0.00 0.00 44.03 3.24
4468 4669 2.838202 TGTGGAAAGAGATACCCCACTC 59.162 50.000 0.00 0.00 45.47 3.51
4470 4671 3.545703 CATGTGGAAAGAGATACCCCAC 58.454 50.000 0.00 0.00 45.47 4.61
4471 4672 2.509548 CCATGTGGAAAGAGATACCCCA 59.490 50.000 0.00 0.00 37.39 4.96
4472 4673 3.214696 CCATGTGGAAAGAGATACCCC 57.785 52.381 0.00 0.00 37.39 4.95


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

AutoCloner maintained by Alex Coulton.