Multiple sequence alignment - TraesCS3A01G029100

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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 TraesCS3A01G029100 chr3A 100.000 5306 0 0 1 5306 15450497 15455802 0.000000e+00 9799.0
1 TraesCS3A01G029100 chr3A 89.172 471 19 7 1068 1530 12150378 12149932 4.640000e-155 558.0
2 TraesCS3A01G029100 chr3A 93.697 238 15 0 1574 1811 12149935 12149698 1.820000e-94 357.0
3 TraesCS3A01G029100 chr3A 84.751 341 34 9 473 807 12151767 12151439 5.120000e-85 326.0
4 TraesCS3A01G029100 chr3A 82.979 188 18 10 823 1001 12150556 12150374 1.980000e-34 158.0
5 TraesCS3A01G029100 chr3A 89.796 49 1 4 2188 2234 32225225 32225179 5.740000e-05 60.2
6 TraesCS3A01G029100 chr3D 92.247 2902 144 45 823 3668 5761272 5758396 0.000000e+00 4037.0
7 TraesCS3A01G029100 chr3D 91.118 1655 106 17 3663 5306 5758328 5756704 0.000000e+00 2204.0
8 TraesCS3A01G029100 chr3D 81.443 291 40 10 25 309 5795956 5795674 5.350000e-55 226.0
9 TraesCS3A01G029100 chr3D 95.455 44 2 0 419 462 5795363 5795320 2.650000e-08 71.3
10 TraesCS3A01G029100 chr3D 86.207 58 4 4 2188 2243 23148855 23148800 5.740000e-05 60.2
11 TraesCS3A01G029100 chr3B 92.189 2586 125 38 443 2967 12104840 12102271 0.000000e+00 3585.0
12 TraesCS3A01G029100 chr3B 88.713 1391 108 25 3923 5306 12100758 12099410 0.000000e+00 1653.0
13 TraesCS3A01G029100 chr3B 87.482 703 47 19 2971 3668 12102085 12101419 0.000000e+00 773.0
14 TraesCS3A01G029100 chr3B 92.233 412 32 0 8 419 12105324 12104913 7.660000e-163 584.0
15 TraesCS3A01G029100 chr3B 81.864 397 59 10 26 418 11965511 11965898 6.630000e-84 322.0
16 TraesCS3A01G029100 chr3B 93.659 205 10 3 3663 3865 12101349 12101146 2.400000e-78 303.0
17 TraesCS3A01G029100 chr3B 92.157 51 4 0 419 469 11946623 11946573 7.370000e-09 73.1
18 TraesCS3A01G029100 chr3B 89.796 49 1 4 2188 2234 40849984 40849938 5.740000e-05 60.2
19 TraesCS3A01G029100 chr7D 91.123 2129 85 31 443 2503 42166103 42164011 0.000000e+00 2789.0
20 TraesCS3A01G029100 chr7D 91.905 1606 101 13 3663 5259 42162817 42161232 0.000000e+00 2218.0
21 TraesCS3A01G029100 chr7D 89.335 1022 61 19 2656 3668 42163868 42162886 0.000000e+00 1240.0
22 TraesCS3A01G029100 chr7D 92.010 413 32 1 8 419 42173965 42173553 3.560000e-161 579.0
23 TraesCS3A01G029100 chrUn 92.297 1467 65 19 443 1893 35213542 35214976 0.000000e+00 2039.0
24 TraesCS3A01G029100 chrUn 88.822 1655 116 30 3663 5306 35216994 35218590 0.000000e+00 1967.0
25 TraesCS3A01G029100 chrUn 88.914 1353 62 38 1927 3215 35215059 35216387 0.000000e+00 1587.0
26 TraesCS3A01G029100 chrUn 91.250 720 41 13 1927 2628 36385724 36386439 0.000000e+00 961.0
27 TraesCS3A01G029100 chrUn 91.904 457 33 3 3215 3668 35216467 35216922 2.080000e-178 636.0
28 TraesCS3A01G029100 chrUn 89.639 415 28 3 8 419 35213067 35213469 1.020000e-141 514.0
29 TraesCS3A01G029100 chrUn 85.500 200 25 4 102 299 32303098 32302901 6.970000e-49 206.0
30 TraesCS3A01G029100 chr1B 79.224 722 119 24 1333 2037 599514415 599513708 1.730000e-129 473.0
31 TraesCS3A01G029100 chr1D 78.453 724 131 20 1333 2037 441308941 441308224 2.910000e-122 449.0
32 TraesCS3A01G029100 chr1A 78.303 719 127 21 1340 2037 536652745 536653455 2.270000e-118 436.0
33 TraesCS3A01G029100 chr5D 85.556 90 11 2 1142 1230 476673903 476673815 5.660000e-15 93.5
34 TraesCS3A01G029100 chr7A 89.796 49 1 4 2188 2234 200600647 200600601 5.740000e-05 60.2


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 TraesCS3A01G029100 chr3A 15450497 15455802 5305 False 9799.000000 9799 100.000000 1 5306 1 chr3A.!!$F1 5305
1 TraesCS3A01G029100 chr3A 12149698 12151767 2069 True 349.750000 558 87.649750 473 1811 4 chr3A.!!$R2 1338
2 TraesCS3A01G029100 chr3D 5756704 5761272 4568 True 3120.500000 4037 91.682500 823 5306 2 chr3D.!!$R2 4483
3 TraesCS3A01G029100 chr3B 12099410 12105324 5914 True 1379.600000 3585 90.855200 8 5306 5 chr3B.!!$R3 5298
4 TraesCS3A01G029100 chr7D 42161232 42166103 4871 True 2082.333333 2789 90.787667 443 5259 3 chr7D.!!$R2 4816
5 TraesCS3A01G029100 chrUn 35213067 35218590 5523 False 1348.600000 2039 90.315200 8 5306 5 chrUn.!!$F2 5298
6 TraesCS3A01G029100 chrUn 36385724 36386439 715 False 961.000000 961 91.250000 1927 2628 1 chrUn.!!$F1 701
7 TraesCS3A01G029100 chr1B 599513708 599514415 707 True 473.000000 473 79.224000 1333 2037 1 chr1B.!!$R1 704
8 TraesCS3A01G029100 chr1D 441308224 441308941 717 True 449.000000 449 78.453000 1333 2037 1 chr1D.!!$R1 704
9 TraesCS3A01G029100 chr1A 536652745 536653455 710 False 436.000000 436 78.303000 1340 2037 1 chr1A.!!$F1 697

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
378 382 0.469917 AACCACGCAGGCTATATGCT 59.530 50.0 0.00 0.0 43.14 3.79 F
1324 2319 0.948678 TGCGCTTACCTTGTTGAACC 59.051 50.0 9.73 0.0 0.00 3.62 F
2975 4312 0.775542 TAGTATCCTCCAGCGGGCTA 59.224 55.0 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 3222 0.040958 GAGTTGGTGTTCAAGCTGCG 60.041 55.0 0.00 0.00 35.80 5.18 R
3142 4486 0.316841 TTCCAAATGGCGCCAAAGAC 59.683 50.0 36.33 1.76 34.44 3.01 R
4326 6208 0.109086 ATGCACGAGAAGTCTCACCG 60.109 55.0 8.95 0.00 43.00 4.94 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
30 31 2.045926 GTTCCAGGCATCGGCACT 60.046 61.111 0.00 0.00 43.71 4.40
37 38 4.465512 GCATCGGCACTGGCAACG 62.466 66.667 3.16 0.00 43.71 4.10
98 99 3.882102 TGAATCCTATTCCATGGTGGG 57.118 47.619 12.58 4.91 38.32 4.61
122 123 1.753073 CCTTGTGCCTCCCAAATGATC 59.247 52.381 0.00 0.00 0.00 2.92
172 173 8.958119 TTATCTGAACCTGTAATATTGTGTCC 57.042 34.615 0.00 0.00 0.00 4.02
235 239 2.890945 TCTGATTGACGACCAGAACTCA 59.109 45.455 0.00 0.00 34.38 3.41
254 258 8.139989 AGAACTCATCTCTTTTTGTTTGATTGG 58.860 33.333 0.00 0.00 30.46 3.16
277 281 5.931146 GGCTATCAGTACTCATCTTGATTGG 59.069 44.000 0.00 0.00 0.00 3.16
284 288 3.341823 ACTCATCTTGATTGGTCTGTGC 58.658 45.455 0.00 0.00 0.00 4.57
288 292 2.497138 TCTTGATTGGTCTGTGCACAG 58.503 47.619 36.07 36.07 45.08 3.66
305 309 3.242543 GCACAGTGCTATGGATTTTCGAG 60.243 47.826 18.92 0.00 40.96 4.04
322 326 6.817765 TTTCGAGGAAACTTGCATCTTTAT 57.182 33.333 0.00 0.00 44.43 1.40
333 337 2.167487 TGCATCTTTATTTTTCGGGGGC 59.833 45.455 0.00 0.00 0.00 5.80
342 346 7.342284 TCTTTATTTTTCGGGGGCATATTTGTA 59.658 33.333 0.00 0.00 0.00 2.41
368 372 1.007387 GCCAAGGAAAACCACGCAG 60.007 57.895 0.00 0.00 0.00 5.18
378 382 0.469917 AACCACGCAGGCTATATGCT 59.530 50.000 0.00 0.00 43.14 3.79
434 459 5.831525 TCATGCATCTATCCAGCAATCTTTT 59.168 36.000 0.00 0.00 42.15 2.27
435 460 5.762825 TGCATCTATCCAGCAATCTTTTC 57.237 39.130 0.00 0.00 34.97 2.29
448 501 7.147312 CAGCAATCTTTTCTTTTCCATGTGTA 58.853 34.615 0.00 0.00 0.00 2.90
466 519 4.957684 CGCTCATCTCGGGCGCAT 62.958 66.667 10.83 0.00 42.28 4.73
635 694 2.061773 CGTTCGCTGTTCAGAGTGAAT 58.938 47.619 3.84 0.00 42.78 2.57
843 1779 0.976641 TCCGTTGGTGAATCTCAGCT 59.023 50.000 7.31 0.00 44.58 4.24
864 1809 6.703607 CAGCTGTCCGTTTTCTAATAGATCAT 59.296 38.462 5.25 0.00 0.00 2.45
865 1810 7.225538 CAGCTGTCCGTTTTCTAATAGATCATT 59.774 37.037 5.25 0.00 0.00 2.57
910 1882 4.081406 TGTGGCATCAGCAATCTTTTACT 58.919 39.130 0.00 0.00 44.61 2.24
911 1883 5.123820 GTGTGGCATCAGCAATCTTTTACTA 59.876 40.000 0.00 0.00 44.61 1.82
912 1884 5.123820 TGTGGCATCAGCAATCTTTTACTAC 59.876 40.000 0.00 0.00 44.61 2.73
921 1896 8.908903 TCAGCAATCTTTTACTACCTTCAAAAA 58.091 29.630 0.00 0.00 0.00 1.94
930 1908 8.974060 TTTACTACCTTCAAAAACAGAGACAT 57.026 30.769 0.00 0.00 0.00 3.06
951 1929 4.056125 CGCTGACCGAGTGAGCCA 62.056 66.667 9.19 0.00 39.50 4.75
1244 2232 1.135083 CAGCTTCCTGGTACGGTACTG 60.135 57.143 17.14 0.00 35.38 2.74
1308 2303 3.558505 CATGTTCTTCTTCCACTTTGCG 58.441 45.455 0.00 0.00 0.00 4.85
1322 2317 2.685897 ACTTTGCGCTTACCTTGTTGAA 59.314 40.909 9.73 0.00 0.00 2.69
1324 2319 0.948678 TGCGCTTACCTTGTTGAACC 59.051 50.000 9.73 0.00 0.00 3.62
1326 2321 1.539827 GCGCTTACCTTGTTGAACCAT 59.460 47.619 0.00 0.00 0.00 3.55
1327 2322 2.668279 GCGCTTACCTTGTTGAACCATG 60.668 50.000 0.00 0.00 0.00 3.66
1581 2578 1.135333 CTCTTCTTCTACGGGTGGCTC 59.865 57.143 0.00 0.00 0.00 4.70
1680 2677 4.648626 GTGCTGGTCTGCTGGGCA 62.649 66.667 1.84 0.00 36.92 5.36
1698 2695 2.343758 CTGGTGTACAGGCTGCGT 59.656 61.111 15.89 0.00 43.70 5.24
2042 3106 3.702792 CCGTCCTCTCCATCTGGTATAT 58.297 50.000 0.00 0.00 36.34 0.86
2043 3107 4.856509 CCGTCCTCTCCATCTGGTATATA 58.143 47.826 0.00 0.00 36.34 0.86
2046 3110 6.487331 CCGTCCTCTCCATCTGGTATATATAC 59.513 46.154 13.60 13.60 36.34 1.47
2077 3143 5.738909 TCTTCCTTCTCTTTGTGATGGATC 58.261 41.667 0.00 0.00 37.52 3.36
2080 3146 4.222810 TCCTTCTCTTTGTGATGGATCGAA 59.777 41.667 0.00 0.00 34.27 3.71
2102 3187 1.043816 ATCTCCATGGACGATCGCTT 58.956 50.000 16.60 0.00 0.00 4.68
2127 3222 2.597805 TATCTCTCTCCGGCCGGC 60.598 66.667 39.89 21.18 34.68 6.13
2507 3629 9.781834 TTGACTTGTAAACAAAAATCTACACTG 57.218 29.630 0.00 0.00 35.15 3.66
2536 3660 6.127619 ACCAGTGTATACGTACTTTACTTCCC 60.128 42.308 0.00 0.00 0.00 3.97
2540 3664 5.360714 TGTATACGTACTTTACTTCCCTGGG 59.639 44.000 6.33 6.33 0.00 4.45
2578 3705 2.402564 TCATTTTGACTGGGGGCAAAA 58.597 42.857 11.38 11.38 44.92 2.44
2579 3706 2.774234 TCATTTTGACTGGGGGCAAAAA 59.226 40.909 12.71 0.00 44.28 1.94
2616 3747 6.519679 TCGTGGTTAGCTTAGTTAGAATGA 57.480 37.500 0.00 0.00 0.00 2.57
2716 3851 1.202371 ACAAGTTGAGACGTCGAAGCA 60.202 47.619 10.54 4.68 0.00 3.91
2937 4091 2.711311 CATGATGCCACCTTCGCG 59.289 61.111 0.00 0.00 0.00 5.87
2975 4312 0.775542 TAGTATCCTCCAGCGGGCTA 59.224 55.000 0.00 0.00 0.00 3.93
2983 4320 2.213499 CTCCAGCGGGCTAAGTAATTG 58.787 52.381 0.00 0.00 0.00 2.32
3163 4507 0.033228 CTTTGGCGCCATTTGGAACA 59.967 50.000 33.25 10.05 37.39 3.18
3283 4710 2.810274 TGCTCTCTTTGTGACTGCAATC 59.190 45.455 0.00 0.00 0.00 2.67
3297 4724 4.853007 ACTGCAATCTCTAGATTTTGCCT 58.147 39.130 25.29 14.47 42.41 4.75
3318 4745 1.551883 GCATGGCATCAAAAAGAGGGT 59.448 47.619 0.00 0.00 0.00 4.34
3357 4784 6.856426 CGTGGTTTTAGTTTCTCTTGGAATTC 59.144 38.462 0.00 0.00 33.53 2.17
3366 4793 7.108847 AGTTTCTCTTGGAATTCCTGATACAG 58.891 38.462 24.73 11.79 36.82 2.74
3367 4794 6.874278 TTCTCTTGGAATTCCTGATACAGA 57.126 37.500 24.73 13.65 36.82 3.41
3389 4816 8.859090 ACAGACCATCTCAATTTCAATGTTTTA 58.141 29.630 0.00 0.00 0.00 1.52
3443 4870 3.895704 ATGGGGACTAAAGTTTGGTGT 57.104 42.857 9.59 0.11 0.00 4.16
3463 4890 5.174579 GGTGTGTTTTCTAGTTCGTGTAGTC 59.825 44.000 0.00 0.00 0.00 2.59
3468 4895 4.928661 TTCTAGTTCGTGTAGTCGTACC 57.071 45.455 0.00 0.00 32.99 3.34
3478 4907 4.612712 CGTGTAGTCGTACCTTTTTACCGA 60.613 45.833 0.00 0.00 0.00 4.69
3628 5057 1.578897 TGGTATCCCTGCAGCACTAA 58.421 50.000 8.66 0.00 0.00 2.24
3690 5196 6.117975 ACTTCCTTTCCGGTTTATTAGTCA 57.882 37.500 0.00 0.00 0.00 3.41
3838 5350 9.040939 TGTATTACATCGGTCTAATTGTCAATG 57.959 33.333 0.00 0.00 0.00 2.82
3883 5395 0.179073 CCGGAATGGAGGCAGTAGTG 60.179 60.000 0.00 0.00 42.00 2.74
3887 5399 2.706190 GGAATGGAGGCAGTAGTGGTAT 59.294 50.000 0.00 0.00 0.00 2.73
3990 5865 0.827507 AATTGGTGGTGCTGGTGGTC 60.828 55.000 0.00 0.00 0.00 4.02
4326 6208 6.232139 TGATCAATGACATCGCATAACATC 57.768 37.500 0.00 0.00 0.00 3.06
4338 6220 3.735208 CGCATAACATCGGTGAGACTTCT 60.735 47.826 0.65 0.00 0.00 2.85
4382 6264 8.227791 TGCTACTTAAACGATGTCTCAAAATTC 58.772 33.333 0.00 0.00 0.00 2.17
4383 6265 7.692705 GCTACTTAAACGATGTCTCAAAATTCC 59.307 37.037 0.00 0.00 0.00 3.01
4497 6379 9.864034 GGTGTAAAATTTATGATGATGTACTCG 57.136 33.333 0.00 0.00 0.00 4.18
4504 6386 9.823647 AATTTATGATGATGTACTCGTTCTTCT 57.176 29.630 0.00 0.00 0.00 2.85
4512 6394 5.859521 TGTACTCGTTCTTCTACTCTGTC 57.140 43.478 0.00 0.00 0.00 3.51
4653 6535 7.602644 GTGTACTTTGAGAAGTCATCCACAATA 59.397 37.037 0.00 0.00 44.75 1.90
4658 6540 8.812513 TTTGAGAAGTCATCCACAATATCAAT 57.187 30.769 0.00 0.00 29.61 2.57
4660 6542 9.904198 TTGAGAAGTCATCCACAATATCAATAA 57.096 29.630 0.00 0.00 30.85 1.40
4689 6572 1.508632 TTATTCGCCAAGGCTATCGC 58.491 50.000 9.73 0.00 39.32 4.58
4700 6583 1.212935 AGGCTATCGCATTTTGGAGGT 59.787 47.619 0.00 0.00 38.10 3.85
4717 6600 4.977739 TGGAGGTCCAAAGAGATCCATATT 59.022 41.667 0.00 0.00 44.35 1.28
4731 6614 6.842676 AGATCCATATTAAGGAGGTCCAAAC 58.157 40.000 0.00 0.00 38.83 2.93
4734 6617 4.574828 CCATATTAAGGAGGTCCAAACGTG 59.425 45.833 0.00 0.00 38.89 4.49
4758 6644 4.569943 AGTTGTGATCACGCTCTTAACAT 58.430 39.130 20.54 6.13 0.00 2.71
4771 6657 9.088512 CACGCTCTTAACATAATACTTCTTTCT 57.911 33.333 0.00 0.00 0.00 2.52
4774 6660 9.601217 GCTCTTAACATAATACTTCTTTCTGGA 57.399 33.333 0.00 0.00 0.00 3.86
4836 6722 8.458573 AACACAATTAGTCCAAGAATGTGTTA 57.541 30.769 16.90 0.00 43.30 2.41
4898 6784 1.228793 CCACAACCACCCCAAGTCA 59.771 57.895 0.00 0.00 0.00 3.41
4914 6800 1.701847 AGTCAGCTATGGCCATTAGGG 59.298 52.381 26.37 11.97 39.73 3.53
5000 6886 5.316987 CCCACAAAGACCTATTTGAGACTT 58.683 41.667 6.22 0.00 41.71 3.01
5094 6980 9.905713 AGCAAGTTATAATGAAAGGATTAGACA 57.094 29.630 0.00 0.00 0.00 3.41
5158 7044 3.806949 TGCCCAGTCAATTACCTTTCT 57.193 42.857 0.00 0.00 0.00 2.52
5197 7085 7.745620 AAAAGACAACATTTGAGGTAGTAGG 57.254 36.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.605232 CCTGGAACCCGTTTAACACAC 59.395 52.381 0.00 0.00 0.00 3.82
1 2 1.970092 CCTGGAACCCGTTTAACACA 58.030 50.000 0.00 0.00 0.00 3.72
2 3 0.594602 GCCTGGAACCCGTTTAACAC 59.405 55.000 0.00 0.00 0.00 3.32
3 4 0.183014 TGCCTGGAACCCGTTTAACA 59.817 50.000 0.00 0.00 0.00 2.41
4 5 1.471287 GATGCCTGGAACCCGTTTAAC 59.529 52.381 0.00 0.00 0.00 2.01
5 6 1.828979 GATGCCTGGAACCCGTTTAA 58.171 50.000 0.00 0.00 0.00 1.52
6 7 0.391927 CGATGCCTGGAACCCGTTTA 60.392 55.000 0.00 0.00 0.00 2.01
14 15 2.046023 CAGTGCCGATGCCTGGAA 60.046 61.111 0.00 0.00 34.24 3.53
37 38 4.072088 CCACGAACACGAAGGCGC 62.072 66.667 0.00 0.00 42.48 6.53
98 99 0.111639 TTTGGGAGGCACAAGGGTAC 59.888 55.000 0.00 0.00 0.00 3.34
172 173 5.924475 AATTGTACAGTTTCCGTCTGAAG 57.076 39.130 0.00 0.00 36.81 3.02
213 217 3.246619 GAGTTCTGGTCGTCAATCAGAC 58.753 50.000 0.00 0.00 44.02 3.51
215 219 3.303881 TGAGTTCTGGTCGTCAATCAG 57.696 47.619 0.00 0.00 0.00 2.90
235 239 8.125978 TGATAGCCAATCAAACAAAAAGAGAT 57.874 30.769 0.00 0.00 41.75 2.75
254 258 6.520272 ACCAATCAAGATGAGTACTGATAGC 58.480 40.000 0.00 0.00 0.00 2.97
284 288 3.310774 CCTCGAAAATCCATAGCACTGTG 59.689 47.826 2.76 2.76 0.00 3.66
288 292 4.636206 AGTTTCCTCGAAAATCCATAGCAC 59.364 41.667 0.00 0.00 33.14 4.40
305 309 6.090763 CCCGAAAAATAAAGATGCAAGTTTCC 59.909 38.462 0.00 0.00 0.00 3.13
322 326 5.422331 TGAATACAAATATGCCCCCGAAAAA 59.578 36.000 0.00 0.00 0.00 1.94
342 346 4.142182 CGTGGTTTTCCTTGGCATATGAAT 60.142 41.667 6.97 0.00 41.38 2.57
434 459 3.394674 TGAGCGTACACATGGAAAAGA 57.605 42.857 0.00 0.00 0.00 2.52
435 460 3.935203 AGATGAGCGTACACATGGAAAAG 59.065 43.478 0.00 0.00 0.00 2.27
530 584 1.753649 AGCGATCTATGTGCACTCACT 59.246 47.619 19.41 3.00 43.49 3.41
547 601 1.030488 TGGAGGGAGTCGAACTAGCG 61.030 60.000 0.00 0.00 0.00 4.26
591 650 4.261072 GGTGGACGTTCCTTCTTTTTCTTC 60.261 45.833 0.00 0.00 37.46 2.87
635 694 1.299648 CGTCAATTCCCTGGAGGCA 59.700 57.895 0.00 0.00 34.51 4.75
910 1882 6.866770 CGTCTATGTCTCTGTTTTTGAAGGTA 59.133 38.462 0.00 0.00 0.00 3.08
911 1883 5.696724 CGTCTATGTCTCTGTTTTTGAAGGT 59.303 40.000 0.00 0.00 0.00 3.50
912 1884 5.389935 GCGTCTATGTCTCTGTTTTTGAAGG 60.390 44.000 0.00 0.00 0.00 3.46
921 1896 1.746220 GGTCAGCGTCTATGTCTCTGT 59.254 52.381 0.00 0.00 0.00 3.41
930 1908 1.645704 GCTCACTCGGTCAGCGTCTA 61.646 60.000 0.00 0.00 0.00 2.59
951 1929 3.083997 CCGCTGGGGAGCTACCTT 61.084 66.667 16.60 0.00 38.47 3.50
980 1958 2.115427 TGCTTAACTCCATGGATCCGA 58.885 47.619 16.63 1.33 0.00 4.55
1308 2303 2.295909 TGCATGGTTCAACAAGGTAAGC 59.704 45.455 0.00 0.00 0.00 3.09
1324 2319 3.896133 GCCCGTCTGCCATGCATG 61.896 66.667 20.19 20.19 38.13 4.06
1326 2321 4.429522 ATGCCCGTCTGCCATGCA 62.430 61.111 0.00 0.00 36.92 3.96
1327 2322 3.896133 CATGCCCGTCTGCCATGC 61.896 66.667 0.00 0.00 0.00 4.06
1398 2393 1.339055 TGCTTGTACACTCCCAGCATC 60.339 52.381 13.80 0.00 0.00 3.91
1464 2461 4.579384 CCGGTGTTGGCCCACACT 62.579 66.667 32.26 0.00 45.56 3.55
1581 2578 4.619227 AACCGGACGTGGCACTGG 62.619 66.667 16.72 13.83 38.40 4.00
1680 2677 2.343758 CGCAGCCTGTACACCAGT 59.656 61.111 0.00 0.00 39.74 4.00
1731 2728 0.677288 CGTTGGTGAGGTAGGACACA 59.323 55.000 0.00 0.00 38.57 3.72
1791 2788 0.252103 ACCCCGTCCAGCTCTTCTTA 60.252 55.000 0.00 0.00 0.00 2.10
2042 3106 9.658799 CAAAGAGAAGGAAGATGAACTTGTATA 57.341 33.333 0.00 0.00 39.13 1.47
2043 3107 8.160106 ACAAAGAGAAGGAAGATGAACTTGTAT 58.840 33.333 0.00 0.00 39.13 2.29
2046 3110 6.484643 TCACAAAGAGAAGGAAGATGAACTTG 59.515 38.462 0.00 0.00 39.13 3.16
2052 3116 5.494724 TCCATCACAAAGAGAAGGAAGATG 58.505 41.667 0.00 0.00 33.32 2.90
2077 3143 2.800881 TCGTCCATGGAGATGATTCG 57.199 50.000 16.81 13.50 0.00 3.34
2080 3146 1.067283 GCGATCGTCCATGGAGATGAT 60.067 52.381 23.34 21.30 43.62 2.45
2102 3187 2.887783 GCCGGAGAGAGATACATCAAGA 59.112 50.000 5.05 0.00 0.00 3.02
2127 3222 0.040958 GAGTTGGTGTTCAAGCTGCG 60.041 55.000 0.00 0.00 35.80 5.18
2517 3639 5.360999 ACCCAGGGAAGTAAAGTACGTATAC 59.639 44.000 14.54 0.00 0.00 1.47
2536 3660 0.463116 GGGCGGTACATACAACCCAG 60.463 60.000 11.79 0.00 40.59 4.45
2540 3664 1.134340 TGATGGGGCGGTACATACAAC 60.134 52.381 0.00 0.00 0.00 3.32
2578 3705 7.339466 AGCTAACCACGAATTCCATAGATTTTT 59.661 33.333 0.00 0.00 0.00 1.94
2579 3706 6.828785 AGCTAACCACGAATTCCATAGATTTT 59.171 34.615 0.00 0.00 0.00 1.82
2616 3747 6.665992 TGCTAGGTTACGGATAATTGATCT 57.334 37.500 0.00 0.00 34.66 2.75
2716 3851 1.684049 CGGAAGGCCTGAGAGACCT 60.684 63.158 5.69 0.00 34.45 3.85
2975 4312 8.506437 CACGTATGCATCCATAATCAATTACTT 58.494 33.333 0.19 0.00 35.79 2.24
3005 4342 3.454375 TCACTTTGAACGAGTCCAACTC 58.546 45.455 0.00 0.00 41.71 3.01
3006 4343 3.132289 TCTCACTTTGAACGAGTCCAACT 59.868 43.478 0.00 0.00 0.00 3.16
3122 4462 9.859427 CAAAGACATATTTCTTGCAGGAATAAA 57.141 29.630 12.50 0.00 35.92 1.40
3142 4486 0.316841 TTCCAAATGGCGCCAAAGAC 59.683 50.000 36.33 1.76 34.44 3.01
3163 4507 8.565896 AAAAGAAAGCAGGAAACAATTCTTTT 57.434 26.923 14.76 14.76 45.20 2.27
3263 4689 3.072944 AGATTGCAGTCACAAAGAGAGC 58.927 45.455 12.16 0.00 32.27 4.09
3283 4710 3.984508 CCATGCAGGCAAAATCTAGAG 57.015 47.619 0.00 0.00 0.00 2.43
3297 4724 1.551430 CCCTCTTTTTGATGCCATGCA 59.449 47.619 0.00 0.00 44.86 3.96
3318 4745 7.609960 ACTAAAACCACGAAAAACCCTAAAAA 58.390 30.769 0.00 0.00 0.00 1.94
3357 4784 6.351711 TGAAATTGAGATGGTCTGTATCAGG 58.648 40.000 0.00 0.00 31.51 3.86
3366 4793 9.696917 AAGTAAAACATTGAAATTGAGATGGTC 57.303 29.630 0.00 0.00 0.00 4.02
3389 4816 6.371809 TGAACTTGAAACTTGCGAATAAGT 57.628 33.333 0.00 0.00 42.43 2.24
3400 4827 5.913137 TTGGAACACATGAACTTGAAACT 57.087 34.783 0.00 0.00 39.29 2.66
3443 4870 5.173774 ACGACTACACGAACTAGAAAACA 57.826 39.130 0.00 0.00 37.03 2.83
3463 4890 5.809464 ACAGTTTTTCGGTAAAAAGGTACG 58.191 37.500 0.00 0.00 43.42 3.67
3468 4895 8.996271 ACCTATAGACAGTTTTTCGGTAAAAAG 58.004 33.333 0.00 0.00 43.42 2.27
3478 4907 4.760204 GTGCCACACCTATAGACAGTTTTT 59.240 41.667 0.00 0.00 0.00 1.94
3628 5057 4.154942 AGATGGCACTTGAAGGTGAAAAT 58.845 39.130 0.00 0.00 39.34 1.82
3721 5227 7.612065 TGGCCTATACAAGTCATATTGTACT 57.388 36.000 3.32 0.00 45.68 2.73
3722 5228 8.671384 TTTGGCCTATACAAGTCATATTGTAC 57.329 34.615 3.32 0.00 45.68 2.90
3820 5332 5.365605 TCCCTACATTGACAATTAGACCGAT 59.634 40.000 14.11 0.00 0.00 4.18
3829 5341 5.693961 TGCATGTATCCCTACATTGACAAT 58.306 37.500 0.00 0.00 44.42 2.71
3838 5350 8.565416 GTTTATTAGGTTTGCATGTATCCCTAC 58.435 37.037 8.04 0.00 0.00 3.18
3960 5835 9.600432 ACCAGCACCACCAATTATTATTATTAT 57.400 29.630 0.00 0.00 0.00 1.28
3961 5836 8.855110 CACCAGCACCACCAATTATTATTATTA 58.145 33.333 0.00 0.00 0.00 0.98
3982 5857 3.625764 CCCAAATATAACACGACCACCAG 59.374 47.826 0.00 0.00 0.00 4.00
3990 5865 6.018751 CAGAGTGATCACCCAAATATAACACG 60.019 42.308 22.21 0.00 0.00 4.49
4184 6061 6.045955 CCCAAAAATCGAAAGGAACAAGAAA 58.954 36.000 0.00 0.00 0.00 2.52
4197 6074 1.302913 TCAGGCGCCCAAAAATCGA 60.303 52.632 26.15 4.00 0.00 3.59
4198 6075 1.154035 GTCAGGCGCCCAAAAATCG 60.154 57.895 26.15 1.34 0.00 3.34
4295 6177 3.186613 CGATGTCATTGATCATGGCTCTG 59.813 47.826 0.00 0.00 38.45 3.35
4326 6208 0.109086 ATGCACGAGAAGTCTCACCG 60.109 55.000 8.95 0.00 43.00 4.94
4382 6264 5.622346 AGCCTCTATTTTCTAGAAGTGGG 57.378 43.478 5.12 5.24 0.00 4.61
4383 6265 9.050601 CATAAAGCCTCTATTTTCTAGAAGTGG 57.949 37.037 5.12 5.68 0.00 4.00
4494 6376 5.811399 ATGAGACAGAGTAGAAGAACGAG 57.189 43.478 0.00 0.00 0.00 4.18
4580 6462 7.277319 CCATGGATGATACTCAAGATACATTCG 59.723 40.741 5.56 0.00 0.00 3.34
4663 6545 8.142994 CGATAGCCTTGGCGAATAATAATAAT 57.857 34.615 5.95 0.00 0.00 1.28
4664 6546 7.534085 CGATAGCCTTGGCGAATAATAATAA 57.466 36.000 5.95 0.00 0.00 1.40
4700 6583 6.851836 ACCTCCTTAATATGGATCTCTTTGGA 59.148 38.462 0.00 0.00 32.56 3.53
4717 6600 3.233507 ACTACACGTTTGGACCTCCTTA 58.766 45.455 0.00 0.00 36.82 2.69
4734 6617 4.921515 TGTTAAGAGCGTGATCACAACTAC 59.078 41.667 24.93 15.35 0.00 2.73
4808 6694 7.285401 ACACATTCTTGGACTAATTGTGTTTCT 59.715 33.333 8.36 0.00 34.84 2.52
4836 6722 7.329226 CGTTGGTTTGAGAAATCTGCAAATATT 59.671 33.333 0.00 0.00 34.47 1.28
4844 6730 5.696724 AGTCTACGTTGGTTTGAGAAATCTG 59.303 40.000 0.00 0.00 0.00 2.90
4855 6741 3.554337 CCACAAGCTAGTCTACGTTGGTT 60.554 47.826 0.00 0.00 0.00 3.67
4898 6784 2.843113 GAGATCCCTAATGGCCATAGCT 59.157 50.000 21.15 11.22 39.73 3.32
4961 6847 0.111446 TGGGGCATGTCGAAGGAAAA 59.889 50.000 0.00 0.00 0.00 2.29
4964 6850 1.773856 TTGTGGGGCATGTCGAAGGA 61.774 55.000 0.00 0.00 0.00 3.36
5000 6886 7.387948 GTGTGTGAAAGCTTTTAGGAGAGATAA 59.612 37.037 14.05 0.00 0.00 1.75
5176 7062 7.735326 ATACCTACTACCTCAAATGTTGTCT 57.265 36.000 0.00 0.00 0.00 3.41
5177 7063 9.694137 GATATACCTACTACCTCAAATGTTGTC 57.306 37.037 0.00 0.00 0.00 3.18
5197 7085 9.352784 TGCTTTACAAATTTGTGCAAGATATAC 57.647 29.630 30.62 20.09 42.31 1.47
5274 7162 0.960364 ATTACCGCTGGTGGCAAGTG 60.960 55.000 10.01 0.00 41.91 3.16


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

AutoCloner maintained by Alex Coulton.