Multiple sequence alignment - TraesCS3B01G243000

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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 TraesCS3B01G243000 chr3B 100.000 4430 0 0 1 4430 384309340 384313769 0.000000e+00 8181.0
1 TraesCS3B01G243000 chr3D 96.005 2303 60 10 1380 3667 291225151 291227436 0.000000e+00 3714.0
2 TraesCS3B01G243000 chr3D 97.101 759 22 0 3672 4430 380838011 380838769 0.000000e+00 1280.0
3 TraesCS3B01G243000 chr3D 93.591 749 27 6 11 758 291223027 291223755 0.000000e+00 1098.0
4 TraesCS3B01G243000 chr3D 94.674 582 20 7 758 1337 291224209 291224781 0.000000e+00 893.0
5 TraesCS3B01G243000 chr3D 92.481 133 5 3 1895 2026 520636855 520636983 7.570000e-43 185.0
6 TraesCS3B01G243000 chr3D 100.000 28 0 0 1867 1894 63168893 63168866 8.000000e-03 52.8
7 TraesCS3B01G243000 chr3A 96.650 1642 46 7 2030 3667 384195336 384196972 0.000000e+00 2719.0
8 TraesCS3B01G243000 chr3A 88.318 1070 59 28 830 1878 384194310 384195334 0.000000e+00 1223.0
9 TraesCS3B01G243000 chr3A 93.872 359 12 3 463 820 384193824 384194173 2.350000e-147 532.0
10 TraesCS3B01G243000 chr3A 89.965 289 12 3 179 467 384193281 384193552 1.520000e-94 357.0
11 TraesCS3B01G243000 chr7D 97.139 769 21 1 3663 4430 191502149 191501381 0.000000e+00 1297.0
12 TraesCS3B01G243000 chr2D 97.739 752 17 0 3679 4430 118326803 118326052 0.000000e+00 1295.0
13 TraesCS3B01G243000 chr2D 97.337 751 20 0 3680 4430 432083291 432082541 0.000000e+00 1277.0
14 TraesCS3B01G243000 chr2B 96.719 762 25 0 3669 4430 302910193 302910954 0.000000e+00 1269.0
15 TraesCS3B01G243000 chr2B 96.719 762 23 2 3670 4430 715028259 715027499 0.000000e+00 1267.0
16 TraesCS3B01G243000 chr2B 96.438 758 27 0 3673 4430 548527040 548526283 0.000000e+00 1251.0
17 TraesCS3B01G243000 chr1B 96.583 761 26 0 3670 4430 444941892 444941132 0.000000e+00 1262.0
18 TraesCS3B01G243000 chr7A 96.443 759 27 0 3672 4430 174843539 174842781 0.000000e+00 1253.0
19 TraesCS3B01G243000 chr6B 92.647 136 6 2 1895 2029 526105175 526105043 4.520000e-45 193.0
20 TraesCS3B01G243000 chr2A 92.086 139 7 2 1894 2031 270497810 270497945 4.520000e-45 193.0
21 TraesCS3B01G243000 chr6D 92.593 135 6 2 1895 2028 204160147 204160016 1.630000e-44 191.0
22 TraesCS3B01G243000 chr6D 90.845 142 8 3 1895 2035 196767425 196767288 7.570000e-43 185.0
23 TraesCS3B01G243000 chr6A 91.971 137 7 2 1894 2029 555975412 555975279 5.850000e-44 189.0
24 TraesCS3B01G243000 chr5B 92.537 134 6 2 1894 2026 144588373 144588503 5.850000e-44 189.0
25 TraesCS3B01G243000 chr5B 96.875 32 0 1 1871 1902 584999583 584999553 8.000000e-03 52.8
26 TraesCS3B01G243000 chr1D 93.130 131 5 2 1897 2026 299262892 299262765 5.850000e-44 189.0
27 TraesCS3B01G243000 chr7B 91.304 46 4 0 92 137 532269961 532270006 3.700000e-06 63.9


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 TraesCS3B01G243000 chr3B 384309340 384313769 4429 False 8181.000000 8181 100.000000 1 4430 1 chr3B.!!$F1 4429
1 TraesCS3B01G243000 chr3D 291223027 291227436 4409 False 1901.666667 3714 94.756667 11 3667 3 chr3D.!!$F3 3656
2 TraesCS3B01G243000 chr3D 380838011 380838769 758 False 1280.000000 1280 97.101000 3672 4430 1 chr3D.!!$F1 758
3 TraesCS3B01G243000 chr3A 384193281 384196972 3691 False 1207.750000 2719 92.201250 179 3667 4 chr3A.!!$F1 3488
4 TraesCS3B01G243000 chr7D 191501381 191502149 768 True 1297.000000 1297 97.139000 3663 4430 1 chr7D.!!$R1 767
5 TraesCS3B01G243000 chr2D 118326052 118326803 751 True 1295.000000 1295 97.739000 3679 4430 1 chr2D.!!$R1 751
6 TraesCS3B01G243000 chr2D 432082541 432083291 750 True 1277.000000 1277 97.337000 3680 4430 1 chr2D.!!$R2 750
7 TraesCS3B01G243000 chr2B 302910193 302910954 761 False 1269.000000 1269 96.719000 3669 4430 1 chr2B.!!$F1 761
8 TraesCS3B01G243000 chr2B 715027499 715028259 760 True 1267.000000 1267 96.719000 3670 4430 1 chr2B.!!$R2 760
9 TraesCS3B01G243000 chr2B 548526283 548527040 757 True 1251.000000 1251 96.438000 3673 4430 1 chr2B.!!$R1 757
10 TraesCS3B01G243000 chr1B 444941132 444941892 760 True 1262.000000 1262 96.583000 3670 4430 1 chr1B.!!$R1 760
11 TraesCS3B01G243000 chr7A 174842781 174843539 758 True 1253.000000 1253 96.443000 3672 4430 1 chr7A.!!$R1 758

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
422 425 0.688087 GGGTAGTGGAGGAGTGGAGG 60.688 65.0 0.00 0.0 0.0 4.30 F
1284 2156 0.651031 GGGAACAGATTAGAACGCGC 59.349 55.0 5.73 0.0 0.0 6.86 F
2275 3503 0.036732 TTCACAGGCCTTGCTACCAG 59.963 55.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 2217 0.518195 AAATAAACGCGGAACCACGG 59.482 50.0 12.47 0.0 0.00 4.94 R
2924 4153 0.107017 CCATGAAGTTCTCCCGGCAT 60.107 55.0 4.17 0.0 0.00 4.40 R
3915 5146 0.970937 AGGAATGCGAGGGTCTTCGA 60.971 55.0 6.67 0.0 43.03 3.71 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
26 27 1.955080 ACCGCGTTTGGTTCCAATTTA 59.045 42.857 4.92 0.00 39.99 1.40
50 51 2.931325 CGAAAAACATAATCCGGACCGA 59.069 45.455 17.49 1.45 0.00 4.69
56 57 1.183030 ATAATCCGGACCGATCGGCA 61.183 55.000 33.62 13.04 46.43 5.69
123 125 2.029964 GCGGTTTGAGGGTCGACA 59.970 61.111 18.91 0.00 0.00 4.35
137 139 1.133025 GTCGACATTGGAAATGCCCTG 59.867 52.381 11.55 0.00 34.97 4.45
217 219 3.917329 TCACTAGGAACGTTGTGAGAG 57.083 47.619 5.00 0.00 34.94 3.20
370 373 6.166984 TCGTACGTATATAGATAGAGGGGG 57.833 45.833 16.05 0.00 0.00 5.40
374 377 7.226325 CGTACGTATATAGATAGAGGGGGAAAG 59.774 44.444 7.22 0.00 0.00 2.62
398 401 4.207891 AGATTGTAGCTGTACCTTGTGG 57.792 45.455 0.00 0.00 39.83 4.17
415 418 1.684734 GGAAGCGGGTAGTGGAGGA 60.685 63.158 0.00 0.00 0.00 3.71
416 419 1.677637 GGAAGCGGGTAGTGGAGGAG 61.678 65.000 0.00 0.00 0.00 3.69
417 420 0.971447 GAAGCGGGTAGTGGAGGAGT 60.971 60.000 0.00 0.00 0.00 3.85
418 421 1.258445 AAGCGGGTAGTGGAGGAGTG 61.258 60.000 0.00 0.00 0.00 3.51
419 422 2.722201 GCGGGTAGTGGAGGAGTGG 61.722 68.421 0.00 0.00 0.00 4.00
420 423 1.000019 CGGGTAGTGGAGGAGTGGA 60.000 63.158 0.00 0.00 0.00 4.02
421 424 1.038130 CGGGTAGTGGAGGAGTGGAG 61.038 65.000 0.00 0.00 0.00 3.86
422 425 0.688087 GGGTAGTGGAGGAGTGGAGG 60.688 65.000 0.00 0.00 0.00 4.30
531 810 2.564947 AGCTGATTCGACAGAGGACTTT 59.435 45.455 7.19 0.00 39.94 2.66
630 910 2.290464 AGCGGAGTACTACTACTGCTG 58.710 52.381 13.32 0.00 38.79 4.41
631 911 1.268640 GCGGAGTACTACTACTGCTGC 60.269 57.143 2.99 0.00 38.79 5.25
632 912 2.290464 CGGAGTACTACTACTGCTGCT 58.710 52.381 2.99 0.00 38.79 4.24
633 913 3.464907 CGGAGTACTACTACTGCTGCTA 58.535 50.000 2.99 0.00 38.79 3.49
634 914 3.495377 CGGAGTACTACTACTGCTGCTAG 59.505 52.174 2.99 0.00 38.79 3.42
635 915 4.453751 GGAGTACTACTACTGCTGCTAGT 58.546 47.826 0.00 4.00 38.11 2.57
686 966 4.376223 TCCTCTTTCTCTCTCCTCTCCTA 58.624 47.826 0.00 0.00 0.00 2.94
722 1002 0.823460 CTCTCCCTCTCTTGCTGACC 59.177 60.000 0.00 0.00 0.00 4.02
961 1825 7.503492 AGAGAGCCCTAGAAAAAGAAAGTAT 57.497 36.000 0.00 0.00 0.00 2.12
963 1827 9.219715 AGAGAGCCCTAGAAAAAGAAAGTATAT 57.780 33.333 0.00 0.00 0.00 0.86
1090 1957 9.844257 CCCTATTTCTTCTTATCTTTCTGTCAT 57.156 33.333 0.00 0.00 0.00 3.06
1096 1963 7.840931 TCTTCTTATCTTTCTGTCATACTGCA 58.159 34.615 0.00 0.00 0.00 4.41
1101 1968 2.680312 TTCTGTCATACTGCAGCCTC 57.320 50.000 15.27 0.79 33.09 4.70
1128 1995 4.214327 CGCCTCCGCTCTTCCTCC 62.214 72.222 0.00 0.00 0.00 4.30
1129 1996 4.214327 GCCTCCGCTCTTCCTCCG 62.214 72.222 0.00 0.00 0.00 4.63
1130 1997 4.214327 CCTCCGCTCTTCCTCCGC 62.214 72.222 0.00 0.00 0.00 5.54
1131 1998 4.214327 CTCCGCTCTTCCTCCGCC 62.214 72.222 0.00 0.00 0.00 6.13
1226 2098 1.829222 TCCTCGCCGATTTTACCTTCT 59.171 47.619 0.00 0.00 0.00 2.85
1232 2104 1.664151 CCGATTTTACCTTCTGGCGTC 59.336 52.381 0.00 0.00 36.63 5.19
1284 2156 0.651031 GGGAACAGATTAGAACGCGC 59.349 55.000 5.73 0.00 0.00 6.86
1350 2222 2.716244 CTCTCCGATCGTCCGTGG 59.284 66.667 15.09 0.00 0.00 4.94
1361 2233 1.664333 GTCCGTGGTTCCGCGTTTA 60.664 57.895 20.61 5.99 38.14 2.01
1370 2242 2.229543 GGTTCCGCGTTTATTTTTCCCT 59.770 45.455 4.92 0.00 0.00 4.20
1376 2248 4.542735 CGCGTTTATTTTTCCCTCACTTT 58.457 39.130 0.00 0.00 0.00 2.66
1431 2642 6.258899 GCTCCTTTTTCGAGGATAAATCAAC 58.741 40.000 0.00 0.00 44.56 3.18
1460 2671 2.473984 CGTGGTTTTCAACGACTACTCC 59.526 50.000 0.00 0.00 37.89 3.85
1510 2721 3.874392 ATTTTTCAGGAGATTTGCCGG 57.126 42.857 0.00 0.00 0.00 6.13
1511 2722 2.286365 TTTTCAGGAGATTTGCCGGT 57.714 45.000 1.90 0.00 0.00 5.28
1512 2723 2.286365 TTTCAGGAGATTTGCCGGTT 57.714 45.000 1.90 0.00 0.00 4.44
1564 2781 3.550842 GCTGCGAGGAAACAAAACAATCT 60.551 43.478 0.00 0.00 0.00 2.40
1566 2783 3.004315 TGCGAGGAAACAAAACAATCTCC 59.996 43.478 0.00 0.00 0.00 3.71
1697 2914 9.288576 CTTTCCTGATGCTTTAATCCATGTATA 57.711 33.333 0.00 0.00 0.00 1.47
1769 2986 0.463620 TTTGGCTCTTGGTTGGTTGC 59.536 50.000 0.00 0.00 0.00 4.17
1819 3042 4.511454 CGTGGAGTGATTCTTCTGTTTTGA 59.489 41.667 0.00 0.00 0.00 2.69
1826 3049 6.429385 AGTGATTCTTCTGTTTTGACTCCATC 59.571 38.462 0.00 0.00 0.00 3.51
1887 3112 8.639761 TCTTCTAAATAAATTCTACTCCCTCCG 58.360 37.037 0.00 0.00 0.00 4.63
1888 3113 7.909485 TCTAAATAAATTCTACTCCCTCCGT 57.091 36.000 0.00 0.00 0.00 4.69
1889 3114 8.315220 TCTAAATAAATTCTACTCCCTCCGTT 57.685 34.615 0.00 0.00 0.00 4.44
1890 3115 8.419442 TCTAAATAAATTCTACTCCCTCCGTTC 58.581 37.037 0.00 0.00 0.00 3.95
1891 3116 3.908643 AAATTCTACTCCCTCCGTTCC 57.091 47.619 0.00 0.00 0.00 3.62
1892 3117 2.544844 ATTCTACTCCCTCCGTTCCA 57.455 50.000 0.00 0.00 0.00 3.53
1893 3118 2.544844 TTCTACTCCCTCCGTTCCAT 57.455 50.000 0.00 0.00 0.00 3.41
1894 3119 3.675348 TTCTACTCCCTCCGTTCCATA 57.325 47.619 0.00 0.00 0.00 2.74
1895 3120 3.225177 TCTACTCCCTCCGTTCCATAG 57.775 52.381 0.00 0.00 0.00 2.23
1942 3167 6.766944 CAGAGGAGCAAAATGAGTGAATCTAT 59.233 38.462 0.00 0.00 0.00 1.98
1980 3205 5.949952 TCTATATACATGCGTATGTGGTCCT 59.050 40.000 26.72 10.72 46.63 3.85
1985 3210 3.702548 ACATGCGTATGTGGTCCTTAGTA 59.297 43.478 18.78 0.00 45.54 1.82
1992 3217 6.200475 GCGTATGTGGTCCTTAGTAAAATCTC 59.800 42.308 0.00 0.00 0.00 2.75
1995 3220 9.747293 GTATGTGGTCCTTAGTAAAATCTCTAC 57.253 37.037 0.00 0.00 0.00 2.59
2023 3248 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2034 3259 5.593502 AGAAACGGAGGGAGTAGTACTATTG 59.406 44.000 5.75 0.00 0.00 1.90
2275 3503 0.036732 TTCACAGGCCTTGCTACCAG 59.963 55.000 0.00 0.00 0.00 4.00
2489 3717 1.307097 CTGCTCCTAATCAAGCTGGC 58.693 55.000 0.00 0.00 39.31 4.85
2582 3810 4.333926 GTCAATTCAGAGGATTACACCTGC 59.666 45.833 0.00 0.00 40.73 4.85
2600 3828 1.069427 CGTTGTTACCCGTGGTCCA 59.931 57.895 0.00 0.00 37.09 4.02
2822 4051 2.627945 TGCACCATCGTTATGTTCTCC 58.372 47.619 0.00 0.00 0.00 3.71
2924 4153 0.251474 AAGCCTTCTGCAGCATGGAA 60.251 50.000 19.03 5.38 44.83 3.53
2996 4225 4.804420 TCTGATCCCAGCGGCCCT 62.804 66.667 0.00 0.00 40.20 5.19
3012 4241 1.886542 GCCCTTCCTTTGACAATCGTT 59.113 47.619 0.00 0.00 0.00 3.85
3170 4400 1.978712 CTGCTGCGGCACTGATGAAG 61.979 60.000 18.37 0.00 44.28 3.02
3333 4563 5.506686 TTCAATTGGACGTCATTTTGTCA 57.493 34.783 18.91 0.65 36.83 3.58
3347 4577 4.481930 TTTTGTCAACGCCTATTGAGTG 57.518 40.909 0.00 0.00 39.25 3.51
3435 4665 9.031537 TGAGTATACTATCTTGTTCACCTTTCA 57.968 33.333 5.09 0.00 0.00 2.69
3442 4672 8.375506 ACTATCTTGTTCACCTTTCATTCTGTA 58.624 33.333 0.00 0.00 0.00 2.74
3606 4836 5.070770 TGCATTTGTTTGAGTGAACTTGT 57.929 34.783 0.00 0.00 0.00 3.16
3655 4885 6.345298 TGATCATTGAATTAGCCGACAAGTA 58.655 36.000 0.00 0.00 0.00 2.24
3667 4897 3.487209 GCCGACAAGTAGCTACTACTGTC 60.487 52.174 31.51 31.51 45.28 3.51
3885 5116 9.025041 TCAACTCATCAAAGATAGAGTCTACAA 57.975 33.333 0.85 0.00 40.22 2.41
3915 5146 2.006888 CGTTCTTGATTATGCCCGTGT 58.993 47.619 0.00 0.00 0.00 4.49
4141 5372 2.366266 ACTGCAGCAAAATGTGGTCAAT 59.634 40.909 15.27 0.00 35.13 2.57
4196 5427 1.820519 GATGCTTGGTCTTGCAATCCA 59.179 47.619 16.28 16.28 42.74 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.231160 GAGTAAATTGGAACCAAACGCG 58.769 45.455 3.53 3.53 39.55 6.01
9 10 3.058777 TCGAGTAAATTGGAACCAAACGC 60.059 43.478 10.36 5.65 39.55 4.84
20 21 8.178964 TCCGGATTATGTTTTTCGAGTAAATTG 58.821 33.333 0.00 0.00 0.00 2.32
22 23 7.201670 GGTCCGGATTATGTTTTTCGAGTAAAT 60.202 37.037 7.81 0.00 0.00 1.40
26 27 3.937079 GGTCCGGATTATGTTTTTCGAGT 59.063 43.478 7.81 0.00 0.00 4.18
50 51 1.470979 GGTCGTGTATTGTCTGCCGAT 60.471 52.381 0.00 0.00 0.00 4.18
54 55 1.011968 TGCGGTCGTGTATTGTCTGC 61.012 55.000 0.00 0.00 0.00 4.26
56 57 1.999735 CAATGCGGTCGTGTATTGTCT 59.000 47.619 7.36 0.00 0.00 3.41
105 107 2.741211 GTCGACCCTCAAACCGCC 60.741 66.667 3.51 0.00 0.00 6.13
106 108 0.953960 AATGTCGACCCTCAAACCGC 60.954 55.000 14.12 0.00 0.00 5.68
123 125 2.023695 AGGACATCAGGGCATTTCCAAT 60.024 45.455 0.00 0.00 36.21 3.16
137 139 7.715249 TGTGCCTACAAAATAGATAAGGACATC 59.285 37.037 0.00 0.00 32.88 3.06
326 328 6.837312 ACGATTGGGGATTATGTCATTCTAA 58.163 36.000 0.00 0.00 0.00 2.10
329 331 5.120208 CGTACGATTGGGGATTATGTCATTC 59.880 44.000 10.44 0.00 0.00 2.67
370 373 7.173390 ACAAGGTACAGCTACAATCTTTCTTTC 59.827 37.037 0.00 0.00 0.00 2.62
374 377 5.122396 CCACAAGGTACAGCTACAATCTTTC 59.878 44.000 0.00 0.00 0.00 2.62
398 401 0.971447 ACTCCTCCACTACCCGCTTC 60.971 60.000 0.00 0.00 0.00 3.86
415 418 1.963515 GCCACAAATGTTTCCTCCACT 59.036 47.619 0.00 0.00 0.00 4.00
416 419 1.686052 TGCCACAAATGTTTCCTCCAC 59.314 47.619 0.00 0.00 0.00 4.02
417 420 2.079170 TGCCACAAATGTTTCCTCCA 57.921 45.000 0.00 0.00 0.00 3.86
418 421 2.365293 ACTTGCCACAAATGTTTCCTCC 59.635 45.455 0.00 0.00 0.00 4.30
419 422 3.383761 CACTTGCCACAAATGTTTCCTC 58.616 45.455 0.00 0.00 0.00 3.71
420 423 2.102925 CCACTTGCCACAAATGTTTCCT 59.897 45.455 0.00 0.00 0.00 3.36
421 424 2.102252 TCCACTTGCCACAAATGTTTCC 59.898 45.455 0.00 0.00 0.00 3.13
422 425 3.123050 GTCCACTTGCCACAAATGTTTC 58.877 45.455 0.00 0.00 0.00 2.78
686 966 4.331108 GGAGAGAGGTTTGAAAAGAGCAT 58.669 43.478 0.00 0.00 0.00 3.79
722 1002 2.967459 TGCTTGTCATGTTGTTAGCG 57.033 45.000 0.00 0.00 0.00 4.26
822 1556 9.774413 GTTGTTGGCTAATTAGTACTGGTATAT 57.226 33.333 13.91 0.00 0.00 0.86
961 1825 8.561769 CCAACCCCTTCTCTCTCTCTATATATA 58.438 40.741 0.00 0.00 0.00 0.86
963 1827 6.240615 CCCAACCCCTTCTCTCTCTCTATATA 60.241 46.154 0.00 0.00 0.00 0.86
965 1829 4.140900 CCCAACCCCTTCTCTCTCTCTATA 60.141 50.000 0.00 0.00 0.00 1.31
967 1831 2.023888 CCCAACCCCTTCTCTCTCTCTA 60.024 54.545 0.00 0.00 0.00 2.43
1090 1957 2.759973 CGAGGGGAGGCTGCAGTA 60.760 66.667 16.64 0.00 0.00 2.74
1113 1980 4.214327 GCGGAGGAAGAGCGGAGG 62.214 72.222 0.00 0.00 0.00 4.30
1226 2098 2.585698 GGTAAATCCCCGACGCCA 59.414 61.111 0.00 0.00 0.00 5.69
1232 2104 1.145377 CAGGTCCGGTAAATCCCCG 59.855 63.158 0.00 0.00 45.07 5.73
1284 2156 2.148558 GATTAGGAGCCCCTCGCGAG 62.149 65.000 29.06 29.06 43.14 5.03
1343 2215 1.015607 ATAAACGCGGAACCACGGAC 61.016 55.000 12.47 0.00 0.00 4.79
1345 2217 0.518195 AAATAAACGCGGAACCACGG 59.482 50.000 12.47 0.00 0.00 4.94
1350 2222 3.058085 TGAGGGAAAAATAAACGCGGAAC 60.058 43.478 12.47 0.00 0.00 3.62
1431 2642 2.221055 CGTTGAAAACCACGAGAAGAGG 59.779 50.000 0.00 0.00 46.28 3.69
1460 2671 2.731572 ACCAAGATGAAAGGCCATGAG 58.268 47.619 5.01 0.00 0.00 2.90
1564 2781 1.841556 AACCGTCCTTGCCTCAGGA 60.842 57.895 0.00 0.00 41.00 3.86
1566 2783 1.071471 ACAACCGTCCTTGCCTCAG 59.929 57.895 0.00 0.00 0.00 3.35
1884 3109 6.496911 TCCATATGAAATCTCTATGGAACGGA 59.503 38.462 16.34 0.00 44.89 4.69
1885 3110 6.701340 TCCATATGAAATCTCTATGGAACGG 58.299 40.000 16.34 0.00 44.89 4.44
1889 3114 8.956446 TGTAGTCCATATGAAATCTCTATGGA 57.044 34.615 3.65 15.41 45.39 3.41
1894 3119 9.593565 TCTGTATGTAGTCCATATGAAATCTCT 57.406 33.333 3.65 0.00 38.29 3.10
1895 3120 9.853555 CTCTGTATGTAGTCCATATGAAATCTC 57.146 37.037 3.65 0.00 38.29 2.75
1913 3138 5.181009 TCACTCATTTTGCTCCTCTGTATG 58.819 41.667 0.00 0.00 0.00 2.39
1917 3142 4.942483 AGATTCACTCATTTTGCTCCTCTG 59.058 41.667 0.00 0.00 0.00 3.35
1918 3143 5.176741 AGATTCACTCATTTTGCTCCTCT 57.823 39.130 0.00 0.00 0.00 3.69
1967 3192 6.047231 AGATTTTACTAAGGACCACATACGC 58.953 40.000 0.00 0.00 0.00 4.42
1969 3194 9.747293 GTAGAGATTTTACTAAGGACCACATAC 57.253 37.037 0.00 0.00 0.00 2.39
1995 3220 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
2180 3408 2.033299 ACATTTGGTGCTCAGTTTGACG 59.967 45.455 0.00 0.00 0.00 4.35
2275 3503 1.069358 GGAAGGACGATCTGGGTGATC 59.931 57.143 0.00 0.00 46.07 2.92
2354 3582 1.484240 CTGAGAGAATCCACCAGTCCC 59.516 57.143 0.00 0.00 33.66 4.46
2489 3717 4.321718 TCTCATCTTTCTGTTCAAGCAGG 58.678 43.478 0.00 0.00 37.12 4.85
2582 3810 0.532417 TTGGACCACGGGTAACAACG 60.532 55.000 0.00 0.00 35.25 4.10
2600 3828 5.594199 AAATGTGGGTAGTTCTAGGGTTT 57.406 39.130 0.00 0.00 0.00 3.27
2822 4051 6.470235 CGCAGATCTATTAAACCAGCAAAAAG 59.530 38.462 0.00 0.00 0.00 2.27
2924 4153 0.107017 CCATGAAGTTCTCCCGGCAT 60.107 55.000 4.17 0.00 0.00 4.40
2928 4157 3.118629 TCATCTTCCATGAAGTTCTCCCG 60.119 47.826 4.17 0.00 40.24 5.14
2996 4225 4.582701 AATGCAACGATTGTCAAAGGAA 57.417 36.364 0.00 0.00 0.00 3.36
3012 4241 3.256383 CACTGGATCAGTTGGAAAATGCA 59.744 43.478 0.00 0.00 42.59 3.96
3204 4434 5.018809 CCTCCAAAAATTTGAGGATCCAGA 58.981 41.667 15.82 0.00 40.55 3.86
3333 4563 2.806244 GACACAACACTCAATAGGCGTT 59.194 45.455 0.00 0.00 0.00 4.84
3347 4577 6.183360 GCTTAGGTTCAGATACATGACACAAC 60.183 42.308 0.00 0.00 0.00 3.32
3435 4665 7.835682 TCATCAAATGAAGACCCAATACAGAAT 59.164 33.333 0.00 0.00 36.11 2.40
3442 4672 8.057623 ACTCTAATCATCAAATGAAGACCCAAT 58.942 33.333 0.00 0.00 43.50 3.16
3489 4719 3.327757 ACACTACTCCTGCCAAGAATCAA 59.672 43.478 0.00 0.00 0.00 2.57
3606 4836 3.804036 ACTGATCACAACCAAGTTTCGA 58.196 40.909 0.00 0.00 0.00 3.71
3885 5116 5.934625 GCATAATCAAGAACGAGTGGGATAT 59.065 40.000 0.00 0.00 0.00 1.63
3915 5146 0.970937 AGGAATGCGAGGGTCTTCGA 60.971 55.000 6.67 0.00 43.03 3.71
4141 5372 2.225522 TGTGACCAGGAGGAGGATACAA 60.226 50.000 0.00 0.00 38.69 2.41
4196 5427 1.112315 CGGACAGGAGAGCTAGGCAT 61.112 60.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.