Multiple sequence alignment - TraesCS3D01G199100

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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 TraesCS3D01G199100 chr3D 100.000 4939 0 0 1 4939 219241130 219236192 0.000000e+00 9121.0
1 TraesCS3D01G199100 chr3D 100.000 29 0 0 1252 1280 456095941 456095969 2.000000e-03 54.7
2 TraesCS3D01G199100 chr3B 93.639 2704 141 19 2242 4939 324259139 324256461 0.000000e+00 4012.0
3 TraesCS3D01G199100 chr3B 92.354 1321 55 10 824 2139 324260631 324259352 0.000000e+00 1838.0
4 TraesCS3D01G199100 chr3B 93.437 838 32 10 2 820 324261757 324260924 0.000000e+00 1221.0
5 TraesCS3D01G199100 chr3A 94.064 2645 143 11 1731 4371 293062990 293060356 0.000000e+00 4002.0
6 TraesCS3D01G199100 chr3A 91.110 1451 70 34 11 1458 293069121 293067727 0.000000e+00 1910.0
7 TraesCS3D01G199100 chr3A 99.251 267 2 0 1453 1719 293063585 293063319 2.670000e-132 483.0
8 TraesCS3D01G199100 chr3A 94.089 203 12 0 4737 4939 293060355 293060153 4.800000e-80 309.0
9 TraesCS3D01G199100 chr7A 76.923 273 52 9 2876 3138 708436078 708436349 1.430000e-30 145.0
10 TraesCS3D01G199100 chr2A 88.406 69 1 6 2073 2134 18004771 18004703 5.300000e-10 76.8
11 TraesCS3D01G199100 chr1B 100.000 32 0 0 3703 3734 41557398 41557367 5.340000e-05 60.2
12 TraesCS3D01G199100 chr1B 100.000 30 0 0 1253 1282 141771904 141771875 6.910000e-04 56.5
13 TraesCS3D01G199100 chr1B 96.875 32 1 0 1247 1278 683586919 683586888 2.000000e-03 54.7
14 TraesCS3D01G199100 chr2B 100.000 29 0 0 1252 1280 499260139 499260111 2.000000e-03 54.7
15 TraesCS3D01G199100 chr2B 100.000 28 0 0 1252 1279 481913507 481913534 9.000000e-03 52.8


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 TraesCS3D01G199100 chr3D 219236192 219241130 4938 True 9121 9121 100.000000 1 4939 1 chr3D.!!$R1 4938
1 TraesCS3D01G199100 chr3B 324256461 324261757 5296 True 2357 4012 93.143333 2 4939 3 chr3B.!!$R1 4937
2 TraesCS3D01G199100 chr3A 293067727 293069121 1394 True 1910 1910 91.110000 11 1458 1 chr3A.!!$R1 1447
3 TraesCS3D01G199100 chr3A 293060153 293063585 3432 True 1598 4002 95.801333 1453 4939 3 chr3A.!!$R2 3486

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
231 235 0.675522 GGGCAAGTAAGCTTACCGCA 60.676 55.0 32.87 6.39 38.71 5.69 F
466 471 1.734163 ACCGCCTAAACAAGAATCCG 58.266 50.0 0.00 0.00 0.00 4.18 F
2109 2755 0.474184 CAAGTCCCCGGCTCCATTAT 59.526 55.0 0.00 0.00 0.00 1.28 F
2800 3557 0.034337 TGTACTTCGTGGGGCTCAAC 59.966 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1528 0.531200 GACGGAAGGAGTAGGTGTGG 59.469 60.0 0.00 0.0 0.0 4.17 R
2216 2889 1.583556 TAATCTTCCTCCTGGCAGCA 58.416 50.0 9.56 0.0 0.0 4.41 R
3625 4382 0.808125 GTGTCTGTGTGTGGTTTGCA 59.192 50.0 0.00 0.0 0.0 4.08 R
4260 5021 0.322546 GTGAGAGGTGGGGCGAAATT 60.323 55.0 0.00 0.0 0.0 1.82 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
91 92 9.620259 TGACAATTATGTTGCACCACTTATATA 57.380 29.630 0.00 0.00 40.74 0.86
190 194 1.219935 GTTTAGGATGGACGGGCGT 59.780 57.895 0.00 0.00 0.00 5.68
207 211 2.268298 GCGTGTGGTCTAGTGTAATGG 58.732 52.381 0.00 0.00 0.00 3.16
231 235 0.675522 GGGCAAGTAAGCTTACCGCA 60.676 55.000 32.87 6.39 38.71 5.69
262 266 5.363979 TGGATTTTTGCGCGCATAATATA 57.636 34.783 36.83 21.10 0.00 0.86
266 270 6.032460 GGATTTTTGCGCGCATAATATAGAAC 59.968 38.462 36.83 20.64 0.00 3.01
400 405 3.866883 TGAACTCTGACGCATCATACA 57.133 42.857 0.00 0.00 33.22 2.29
466 471 1.734163 ACCGCCTAAACAAGAATCCG 58.266 50.000 0.00 0.00 0.00 4.18
505 513 9.449719 AAGAACGGACAACAAAATATATCTTCT 57.550 29.630 0.00 0.00 0.00 2.85
619 628 7.094508 TGAGTTCACAAATTTAACTGCAGAA 57.905 32.000 23.35 4.48 33.72 3.02
718 727 2.162408 GTGTCTGCTTGCCTCCATTAAC 59.838 50.000 0.00 0.00 0.00 2.01
820 855 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
821 856 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
822 857 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
828 1152 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
832 1156 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
837 1161 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
864 1190 7.966753 CGCTACCTATATATACACACGAACATT 59.033 37.037 0.00 0.00 0.00 2.71
894 1220 6.650807 TCCATTCAATCCTTCGTAGCATAATC 59.349 38.462 0.00 0.00 0.00 1.75
947 1273 9.765795 GTAGCTTGTATCAGTATTAGGAATTGT 57.234 33.333 0.00 0.00 0.00 2.71
998 1324 6.127479 GGGATCGATCTCTAATAATCTGCAGT 60.127 42.308 23.96 0.00 0.00 4.40
1174 1500 2.277084 CCGGCGCTTACTACTTTGAAT 58.723 47.619 7.64 0.00 0.00 2.57
1202 1528 5.005779 GCGTGTATGCATACTTATATGGCTC 59.994 44.000 31.35 6.95 38.97 4.70
1207 1533 4.641396 TGCATACTTATATGGCTCCACAC 58.359 43.478 0.00 0.00 38.97 3.82
1230 1556 5.769162 ACCTACTCCTTCCGTCTCATAATAC 59.231 44.000 0.00 0.00 0.00 1.89
1382 1710 7.873719 TTCTGTTTTCATTTACCTTCTCACA 57.126 32.000 0.00 0.00 0.00 3.58
1384 1712 9.567776 TTCTGTTTTCATTTACCTTCTCACATA 57.432 29.630 0.00 0.00 0.00 2.29
1408 1736 6.888105 ACAAAGAATTGAGGATGGTTTGTTT 58.112 32.000 0.00 0.00 38.94 2.83
1704 2032 5.007034 TCCTTCAAACAAACAACAGACAGA 58.993 37.500 0.00 0.00 0.00 3.41
1805 2450 2.827322 TGTCATCAAAGGAGCCCAATTG 59.173 45.455 0.00 0.00 0.00 2.32
1930 2576 6.682746 TGCTTTCTGTTGCCGATAATAAAAA 58.317 32.000 0.00 0.00 0.00 1.94
2109 2755 0.474184 CAAGTCCCCGGCTCCATTAT 59.526 55.000 0.00 0.00 0.00 1.28
2110 2756 1.697432 CAAGTCCCCGGCTCCATTATA 59.303 52.381 0.00 0.00 0.00 0.98
2111 2757 1.349067 AGTCCCCGGCTCCATTATAC 58.651 55.000 0.00 0.00 0.00 1.47
2168 2841 3.707156 CTGATGCCTTTCGCGTGCG 62.707 63.158 5.77 8.14 42.08 5.34
2169 2842 4.520846 GATGCCTTTCGCGTGCGG 62.521 66.667 14.89 5.96 42.08 5.69
2185 2858 1.067565 TGCGGAAGTGCAACAAAAACA 60.068 42.857 0.00 0.00 43.02 2.83
2216 2889 2.463589 TTTTCATCTCGCGGCCCAGT 62.464 55.000 6.13 0.00 0.00 4.00
2233 2906 0.913451 AGTGCTGCCAGGAGGAAGAT 60.913 55.000 0.00 0.00 44.27 2.40
2260 3017 8.567285 AAATGTTACAAAGGATCTCTACCTTG 57.433 34.615 0.00 0.00 45.55 3.61
2463 3220 1.349357 TGGAAACATGATCGTGGGACA 59.651 47.619 18.97 9.31 33.40 4.02
2649 3406 5.927281 AACCAGACATATGTAACGTAGGT 57.073 39.130 8.71 7.77 0.00 3.08
2800 3557 0.034337 TGTACTTCGTGGGGCTCAAC 59.966 55.000 0.00 0.00 0.00 3.18
2872 3629 3.709880 CTTCGTCATGGCGGCCGTA 62.710 63.158 28.70 17.12 0.00 4.02
3159 3916 2.697751 CCACCATTTCACCAAGACCAAA 59.302 45.455 0.00 0.00 0.00 3.28
3223 3980 6.410942 AGTGATTGATAATGGTCGATCTGA 57.589 37.500 0.00 0.00 39.01 3.27
3279 4036 0.458370 CCAGCACGACGATCATGTCA 60.458 55.000 0.00 0.00 38.84 3.58
3280 4037 1.564207 CAGCACGACGATCATGTCAT 58.436 50.000 0.00 0.00 38.84 3.06
3369 4126 5.380043 CTTGGGTTTGACATCAGGCTATAT 58.620 41.667 0.00 0.00 0.00 0.86
3413 4170 0.455815 TCCATCCATCGTGTCGTGAG 59.544 55.000 0.00 0.00 0.00 3.51
3445 4202 5.085920 TGATCCAACCATGTTTTCCTGATT 58.914 37.500 0.00 0.00 0.00 2.57
3448 4205 5.016173 TCCAACCATGTTTTCCTGATTAGG 58.984 41.667 0.00 0.00 46.06 2.69
3625 4382 1.904865 TCGGAAGGTACCACTGCGT 60.905 57.895 21.60 0.00 0.00 5.24
3676 4433 1.000843 CCCCAGTTAACTTTTGGCTGC 59.999 52.381 5.07 0.00 0.00 5.25
3851 4608 2.253758 GCTCAACTGCAAGGACGCA 61.254 57.895 0.00 0.00 39.30 5.24
3858 4615 1.153066 TGCAAGGACGCAAGGAACA 60.153 52.632 0.00 0.00 46.39 3.18
3943 4700 3.325870 CAAACGGCACTGACTGATAGAA 58.674 45.455 0.00 0.00 0.00 2.10
4010 4767 2.168326 ATGTCATCGTCAGTTGCACA 57.832 45.000 0.00 0.00 0.00 4.57
4040 4797 1.140852 AGTTGTGCTACAGCTCACCAA 59.859 47.619 5.52 0.08 43.16 3.67
4045 4802 0.517316 GCTACAGCTCACCAAAACGG 59.483 55.000 0.00 0.00 38.40 4.44
4049 4806 4.038080 GCTCACCAAAACGGGCCG 62.038 66.667 27.06 27.06 40.22 6.13
4050 4807 2.593436 CTCACCAAAACGGGCCGT 60.593 61.111 28.83 28.83 43.97 5.68
4072 4830 3.006940 ACACACGCAACAAAAGAGAGAA 58.993 40.909 0.00 0.00 0.00 2.87
4096 4857 6.380079 AAGTTAGAGCATCCCCTATAATGG 57.620 41.667 0.00 0.00 33.66 3.16
4164 4925 6.780706 TTTTAAGAGACGCTTCTACTTTGG 57.219 37.500 9.16 0.00 38.05 3.28
4194 4955 5.066505 GCCCCTAAACACATCAACATAGAAG 59.933 44.000 0.00 0.00 0.00 2.85
4208 4969 6.207614 TCAACATAGAAGATCTCTCCATACGG 59.792 42.308 0.00 0.00 35.41 4.02
4218 4979 7.607250 AGATCTCTCCATACGGTTTCATAATC 58.393 38.462 0.00 0.00 0.00 1.75
4226 4987 6.802348 CCATACGGTTTCATAATCTCTACTCG 59.198 42.308 0.00 0.00 0.00 4.18
4241 5002 4.174009 TCTACTCGTAATGAAGCAGTTGC 58.826 43.478 0.00 0.00 42.49 4.17
4253 5014 1.351153 GCAGTTGCTAGTCTCCGTTC 58.649 55.000 0.00 0.00 38.21 3.95
4257 5018 2.367567 AGTTGCTAGTCTCCGTTCCAAA 59.632 45.455 0.00 0.00 0.00 3.28
4258 5019 3.135994 GTTGCTAGTCTCCGTTCCAAAA 58.864 45.455 0.00 0.00 0.00 2.44
4259 5020 3.478857 TGCTAGTCTCCGTTCCAAAAA 57.521 42.857 0.00 0.00 0.00 1.94
4276 5037 2.009681 AAAAATTTCGCCCCACCTCT 57.990 45.000 0.00 0.00 0.00 3.69
4283 5044 2.671682 GCCCCACCTCTCACCTTC 59.328 66.667 0.00 0.00 0.00 3.46
4284 5045 2.982130 CCCCACCTCTCACCTTCG 59.018 66.667 0.00 0.00 0.00 3.79
4285 5046 1.913762 CCCCACCTCTCACCTTCGT 60.914 63.158 0.00 0.00 0.00 3.85
4286 5047 1.592223 CCCACCTCTCACCTTCGTC 59.408 63.158 0.00 0.00 0.00 4.20
4287 5048 0.900647 CCCACCTCTCACCTTCGTCT 60.901 60.000 0.00 0.00 0.00 4.18
4288 5049 0.244994 CCACCTCTCACCTTCGTCTG 59.755 60.000 0.00 0.00 0.00 3.51
4289 5050 1.248486 CACCTCTCACCTTCGTCTGA 58.752 55.000 0.00 0.00 0.00 3.27
4290 5051 1.821753 CACCTCTCACCTTCGTCTGAT 59.178 52.381 0.00 0.00 0.00 2.90
4291 5052 2.232452 CACCTCTCACCTTCGTCTGATT 59.768 50.000 0.00 0.00 0.00 2.57
4292 5053 2.900546 ACCTCTCACCTTCGTCTGATTT 59.099 45.455 0.00 0.00 0.00 2.17
4293 5054 3.325135 ACCTCTCACCTTCGTCTGATTTT 59.675 43.478 0.00 0.00 0.00 1.82
4294 5055 4.527038 ACCTCTCACCTTCGTCTGATTTTA 59.473 41.667 0.00 0.00 0.00 1.52
4295 5056 5.187967 ACCTCTCACCTTCGTCTGATTTTAT 59.812 40.000 0.00 0.00 0.00 1.40
4296 5057 6.109359 CCTCTCACCTTCGTCTGATTTTATT 58.891 40.000 0.00 0.00 0.00 1.40
4297 5058 6.595716 CCTCTCACCTTCGTCTGATTTTATTT 59.404 38.462 0.00 0.00 0.00 1.40
4318 5094 9.567848 TTATTTCGTCTGCTTATTTTCATTTCC 57.432 29.630 0.00 0.00 0.00 3.13
4326 5102 4.469586 GCTTATTTTCATTTCCCCTCCCAA 59.530 41.667 0.00 0.00 0.00 4.12
4338 5114 2.225117 CCCCTCCCAACAACATCTTCTT 60.225 50.000 0.00 0.00 0.00 2.52
4411 5188 3.834489 TTCCCTAACCACACACGTTAA 57.166 42.857 0.00 0.00 0.00 2.01
4434 5212 3.473113 AAGGGCAGGATACCAAACAAT 57.527 42.857 0.00 0.00 37.17 2.71
4468 5246 8.801882 ATTTCATGGCAATCAATTTCAAATCT 57.198 26.923 0.00 0.00 0.00 2.40
4501 5279 1.772836 GCATTGATCCCTGCCTTTCT 58.227 50.000 5.51 0.00 32.15 2.52
4506 5284 4.380843 TTGATCCCTGCCTTTCTTAACA 57.619 40.909 0.00 0.00 0.00 2.41
4508 5286 4.934356 TGATCCCTGCCTTTCTTAACAAT 58.066 39.130 0.00 0.00 0.00 2.71
4544 5322 6.831868 ACTCCTGTAATCTTCTCTTACTCCTC 59.168 42.308 0.00 0.00 31.71 3.71
4574 5352 6.925718 AGTACCTAAGTTGTTTAGTTCGTTCC 59.074 38.462 0.00 0.00 37.62 3.62
4587 5365 1.868713 TCGTTCCTTACCCCATGCTA 58.131 50.000 0.00 0.00 0.00 3.49
4592 5370 3.344535 TCCTTACCCCATGCTAGATCA 57.655 47.619 0.00 0.00 0.00 2.92
4612 5390 2.917971 CAATCGACACTCCTTTCGTCTC 59.082 50.000 0.00 0.00 36.60 3.36
4613 5391 0.879765 TCGACACTCCTTTCGTCTCC 59.120 55.000 0.00 0.00 36.60 3.71
4625 5403 3.505464 TTCGTCTCCCGATTTTCTCTC 57.495 47.619 0.00 0.00 46.75 3.20
4626 5404 2.724454 TCGTCTCCCGATTTTCTCTCT 58.276 47.619 0.00 0.00 41.60 3.10
4687 5465 1.227089 CACGCCATCTCTCCTTCCG 60.227 63.158 0.00 0.00 0.00 4.30
4749 5527 5.383476 CAATCAGATTTAGGAGAGGGCAAT 58.617 41.667 0.00 0.00 0.00 3.56
4877 5655 1.381327 CCGGCCCTTCTCTACTCCA 60.381 63.158 0.00 0.00 0.00 3.86
4886 5664 1.982395 CTCTACTCCACCGCCACCA 60.982 63.158 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.454504 GTGTTCACGTTTTCCCTACATCAT 59.545 41.667 0.00 0.00 0.00 2.45
5 6 4.619437 TTTGTGTTCACGTTTTCCCTAC 57.381 40.909 0.00 0.00 0.00 3.18
91 92 9.921637 TTGAACAACTCAATTTACAAAGTTTCT 57.078 25.926 0.00 0.00 39.20 2.52
190 194 4.082081 CCGTTACCATTACACTAGACCACA 60.082 45.833 0.00 0.00 0.00 4.17
231 235 3.303001 CGCGCAAAAATCCAACACAAAAT 60.303 39.130 8.75 0.00 0.00 1.82
262 266 2.489329 CCGCATTCATGTCCTTTGTTCT 59.511 45.455 0.00 0.00 0.00 3.01
266 270 2.030007 ACAACCGCATTCATGTCCTTTG 60.030 45.455 0.00 0.00 0.00 2.77
400 405 1.656263 CGTCCATACATACGCGCGT 60.656 57.895 39.05 39.05 31.66 6.01
406 411 1.068417 TGCCCGCGTCCATACATAC 59.932 57.895 4.92 0.00 0.00 2.39
466 471 1.462791 CGTTCTTTTCCGTGTTGCAC 58.537 50.000 0.00 0.00 0.00 4.57
718 727 3.097877 TGAGCGATACAAGGCATACAG 57.902 47.619 0.00 0.00 0.00 2.74
820 855 2.766263 AGCGAAGAGAGAGAGAGAGAGA 59.234 50.000 0.00 0.00 0.00 3.10
821 856 3.185246 AGCGAAGAGAGAGAGAGAGAG 57.815 52.381 0.00 0.00 0.00 3.20
822 857 3.181469 GGTAGCGAAGAGAGAGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
828 1152 8.979534 TGTATATATAGGTAGCGAAGAGAGAGA 58.020 37.037 0.00 0.00 0.00 3.10
832 1156 7.277319 CGTGTGTATATATAGGTAGCGAAGAGA 59.723 40.741 0.00 0.00 0.00 3.10
837 1161 6.650390 TGTTCGTGTGTATATATAGGTAGCGA 59.350 38.462 0.00 0.00 0.00 4.93
864 1190 4.235079 ACGAAGGATTGAATGGAATGGA 57.765 40.909 0.00 0.00 0.00 3.41
894 1220 0.461693 GCTGGCTAGACTGCAGGAAG 60.462 60.000 21.58 12.81 35.65 3.46
938 1264 4.959210 CCTCCTCTTCTCTCACAATTCCTA 59.041 45.833 0.00 0.00 0.00 2.94
947 1273 0.260230 ATCGGCCTCCTCTTCTCTCA 59.740 55.000 0.00 0.00 0.00 3.27
998 1324 0.918983 CAGGCACTCCTTCCCCATAA 59.081 55.000 0.00 0.00 41.93 1.90
1174 1500 2.394930 AAGTATGCATACACGCACCA 57.605 45.000 32.69 0.00 46.56 4.17
1190 1516 4.557705 AGTAGGTGTGGAGCCATATAAGT 58.442 43.478 0.00 0.00 0.00 2.24
1202 1528 0.531200 GACGGAAGGAGTAGGTGTGG 59.469 60.000 0.00 0.00 0.00 4.17
1207 1533 5.768662 TGTATTATGAGACGGAAGGAGTAGG 59.231 44.000 0.00 0.00 0.00 3.18
1248 1574 5.163499 CCTCCGTCCCATAATATAAGAGAGC 60.163 48.000 0.00 0.00 0.00 4.09
1249 1575 5.361285 CCCTCCGTCCCATAATATAAGAGAG 59.639 48.000 0.00 0.00 0.00 3.20
1250 1576 5.015924 TCCCTCCGTCCCATAATATAAGAGA 59.984 44.000 0.00 0.00 0.00 3.10
1382 1710 7.781324 ACAAACCATCCTCAATTCTTTGTAT 57.219 32.000 0.00 0.00 34.32 2.29
1384 1712 6.484364 AACAAACCATCCTCAATTCTTTGT 57.516 33.333 0.00 0.00 33.00 2.83
1973 2619 6.649557 ACTCTTTGGTTAATACTTTCTCCGTG 59.350 38.462 0.00 0.00 0.00 4.94
2026 2672 4.759516 TCTCAAAAACGATTTGGTAGCC 57.240 40.909 15.02 0.00 0.00 3.93
2216 2889 1.583556 TAATCTTCCTCCTGGCAGCA 58.416 50.000 9.56 0.00 0.00 4.41
2219 2892 4.591321 ACATTTAATCTTCCTCCTGGCA 57.409 40.909 0.00 0.00 0.00 4.92
2260 3017 7.910683 CGTTTATCAGAGAAAAATAAAGGGAGC 59.089 37.037 0.00 0.00 31.76 4.70
2422 3179 1.903404 GGTTTGTGGCTGTCCCAGG 60.903 63.158 0.00 0.00 46.54 4.45
2649 3406 5.650703 TGGAACTATATCACGTCAACTCTGA 59.349 40.000 0.00 0.00 0.00 3.27
2727 3484 4.076394 ACACACACCACGCCTAATAAATT 58.924 39.130 0.00 0.00 0.00 1.82
2800 3557 4.657824 ACGGTCGGCGTTGTGGAG 62.658 66.667 6.85 0.00 0.00 3.86
2872 3629 2.830923 CCTCACTGTCTCCATCTTGAGT 59.169 50.000 0.00 0.00 33.93 3.41
3034 3791 2.654912 GGGAAGTGTTGTCGCGTCG 61.655 63.158 5.77 0.00 34.39 5.12
3044 3801 2.594592 GTTGCCGCTGGGAAGTGT 60.595 61.111 2.07 0.00 32.69 3.55
3159 3916 2.353406 GCATGATTGCTGGAAACAAGCT 60.353 45.455 11.01 0.00 45.77 3.74
3223 3980 1.480137 CCTCTCCGACATCTTGCTCTT 59.520 52.381 0.00 0.00 0.00 2.85
3279 4036 4.059304 TGCACCCCGGCCATCAAT 62.059 61.111 2.24 0.00 0.00 2.57
3280 4037 4.738998 CTGCACCCCGGCCATCAA 62.739 66.667 2.24 0.00 0.00 2.57
3307 4064 4.941609 GTCCATGACCACGCTGAT 57.058 55.556 0.00 0.00 0.00 2.90
3413 4170 2.806945 TGGTTGGATCAATCAGGTCC 57.193 50.000 0.00 0.00 28.74 4.46
3445 4202 2.856231 ACCCCCTGCATAATTCAACCTA 59.144 45.455 0.00 0.00 0.00 3.08
3448 4205 1.756538 CCACCCCCTGCATAATTCAAC 59.243 52.381 0.00 0.00 0.00 3.18
3533 4290 1.452651 CAGCGGGCTGAACATGGAT 60.453 57.895 15.38 0.00 46.30 3.41
3625 4382 0.808125 GTGTCTGTGTGTGGTTTGCA 59.192 50.000 0.00 0.00 0.00 4.08
3660 4417 2.362077 CCACAGCAGCCAAAAGTTAACT 59.638 45.455 1.12 1.12 0.00 2.24
3676 4433 2.169832 AGGACATCAAACGACCACAG 57.830 50.000 0.00 0.00 0.00 3.66
3799 4556 2.685017 TCTCTGGAGCCGTGCCAT 60.685 61.111 0.00 0.00 34.33 4.40
3800 4557 3.695606 GTCTCTGGAGCCGTGCCA 61.696 66.667 0.00 0.00 0.00 4.92
3851 4608 2.668550 GCGGCGTTCCTGTTCCTT 60.669 61.111 9.37 0.00 0.00 3.36
3943 4700 2.203394 CTTGTGTGGCCACCAGCT 60.203 61.111 32.62 0.00 41.09 4.24
3970 4727 6.114767 ACATATGTATGATGCGCAATCCATA 58.885 36.000 17.11 18.86 37.15 2.74
4025 4782 1.225855 CGTTTTGGTGAGCTGTAGCA 58.774 50.000 6.65 0.00 45.16 3.49
4040 4797 2.662527 CGTGTGTACGGCCCGTTT 60.663 61.111 16.82 0.00 46.23 3.60
4049 4806 3.554324 TCTCTCTTTTGTTGCGTGTGTAC 59.446 43.478 0.00 0.00 0.00 2.90
4050 4807 3.787785 TCTCTCTTTTGTTGCGTGTGTA 58.212 40.909 0.00 0.00 0.00 2.90
4072 4830 6.562608 TCCATTATAGGGGATGCTCTAACTTT 59.437 38.462 0.00 0.00 0.00 2.66
4148 4909 4.557205 CTTGTACCAAAGTAGAAGCGTCT 58.443 43.478 7.47 7.47 41.36 4.18
4164 4925 3.681593 TGATGTGTTTAGGGGCTTGTAC 58.318 45.455 0.00 0.00 0.00 2.90
4194 4955 7.607250 AGATTATGAAACCGTATGGAGAGATC 58.393 38.462 8.33 2.32 39.21 2.75
4218 4979 4.266502 GCAACTGCTTCATTACGAGTAGAG 59.733 45.833 0.00 0.00 38.21 2.43
4257 5018 1.893137 GAGAGGTGGGGCGAAATTTTT 59.107 47.619 0.00 0.00 0.00 1.94
4258 5019 1.203001 TGAGAGGTGGGGCGAAATTTT 60.203 47.619 0.00 0.00 0.00 1.82
4259 5020 0.404040 TGAGAGGTGGGGCGAAATTT 59.596 50.000 0.00 0.00 0.00 1.82
4260 5021 0.322546 GTGAGAGGTGGGGCGAAATT 60.323 55.000 0.00 0.00 0.00 1.82
4261 5022 1.299976 GTGAGAGGTGGGGCGAAAT 59.700 57.895 0.00 0.00 0.00 2.17
4267 5028 1.889530 GACGAAGGTGAGAGGTGGGG 61.890 65.000 0.00 0.00 0.00 4.96
4270 5031 1.248486 TCAGACGAAGGTGAGAGGTG 58.752 55.000 0.00 0.00 0.00 4.00
4276 5037 5.929992 ACGAAATAAAATCAGACGAAGGTGA 59.070 36.000 0.00 0.00 0.00 4.02
4283 5044 5.456192 AGCAGACGAAATAAAATCAGACG 57.544 39.130 0.00 0.00 0.00 4.18
4284 5045 9.774742 AAATAAGCAGACGAAATAAAATCAGAC 57.225 29.630 0.00 0.00 0.00 3.51
4292 5053 9.567848 GGAAATGAAAATAAGCAGACGAAATAA 57.432 29.630 0.00 0.00 0.00 1.40
4293 5054 8.188139 GGGAAATGAAAATAAGCAGACGAAATA 58.812 33.333 0.00 0.00 0.00 1.40
4294 5055 7.035612 GGGAAATGAAAATAAGCAGACGAAAT 58.964 34.615 0.00 0.00 0.00 2.17
4295 5056 6.386654 GGGAAATGAAAATAAGCAGACGAAA 58.613 36.000 0.00 0.00 0.00 3.46
4296 5057 5.105917 GGGGAAATGAAAATAAGCAGACGAA 60.106 40.000 0.00 0.00 0.00 3.85
4297 5058 4.398044 GGGGAAATGAAAATAAGCAGACGA 59.602 41.667 0.00 0.00 0.00 4.20
4313 5089 2.383338 AGATGTTGTTGGGAGGGGAAAT 59.617 45.455 0.00 0.00 0.00 2.17
4318 5094 2.821969 CAAGAAGATGTTGTTGGGAGGG 59.178 50.000 4.69 0.00 34.10 4.30
4326 5102 2.297701 ACCAACGCAAGAAGATGTTGT 58.702 42.857 3.62 0.00 39.95 3.32
4391 5168 3.834489 TTAACGTGTGTGGTTAGGGAA 57.166 42.857 0.00 0.00 32.01 3.97
4411 5188 3.582164 TGTTTGGTATCCTGCCCTTTTT 58.418 40.909 0.00 0.00 0.00 1.94
4415 5193 4.601406 TTATTGTTTGGTATCCTGCCCT 57.399 40.909 0.00 0.00 0.00 5.19
4449 5227 9.558396 AAAGTTAAGATTTGAAATTGATTGCCA 57.442 25.926 0.00 0.00 0.00 4.92
4468 5246 5.355910 GGGATCAATGCGTTAGGAAAGTTAA 59.644 40.000 0.00 0.00 0.00 2.01
4482 5260 1.772836 AGAAAGGCAGGGATCAATGC 58.227 50.000 11.80 11.80 41.80 3.56
4522 5300 6.040391 CCTGAGGAGTAAGAGAAGATTACAGG 59.960 46.154 0.00 0.00 35.92 4.00
4523 5301 6.040391 CCCTGAGGAGTAAGAGAAGATTACAG 59.960 46.154 0.00 0.00 35.92 2.74
4544 5322 6.356186 ACTAAACAACTTAGGTACTCCCTG 57.644 41.667 0.00 0.00 45.81 4.45
4565 5343 1.339727 GCATGGGGTAAGGAACGAACT 60.340 52.381 0.00 0.00 0.00 3.01
4574 5352 4.021104 TCGATTGATCTAGCATGGGGTAAG 60.021 45.833 0.00 0.00 0.00 2.34
4587 5365 3.193691 ACGAAAGGAGTGTCGATTGATCT 59.806 43.478 0.00 0.00 39.64 2.75
4592 5370 2.094649 GGAGACGAAAGGAGTGTCGATT 60.095 50.000 0.00 0.00 39.64 3.34
4612 5390 5.106515 GGAAAGTGAAAGAGAGAAAATCGGG 60.107 44.000 0.00 0.00 0.00 5.14
4613 5391 5.703130 AGGAAAGTGAAAGAGAGAAAATCGG 59.297 40.000 0.00 0.00 0.00 4.18
4660 5438 2.749621 GAGAGATGGCGTGTGGATTTTT 59.250 45.455 0.00 0.00 0.00 1.94
4669 5447 1.227089 CGGAAGGAGAGATGGCGTG 60.227 63.158 0.00 0.00 0.00 5.34
4687 5465 6.412362 TTCAAGAGAGATATGCCTTACTCC 57.588 41.667 0.00 0.00 0.00 3.85
4715 5493 9.129532 CTCCTAAATCTGATTGCCTTTCTATTT 57.870 33.333 3.22 0.00 0.00 1.40
4716 5494 8.497745 TCTCCTAAATCTGATTGCCTTTCTATT 58.502 33.333 3.22 0.00 0.00 1.73
4717 5495 8.038862 TCTCCTAAATCTGATTGCCTTTCTAT 57.961 34.615 3.22 0.00 0.00 1.98
4749 5527 4.373116 GTCTCGCGGGAGGCAACA 62.373 66.667 27.10 6.47 44.47 3.33
4856 5634 4.893601 GTAGAGAAGGGCCGGCGC 62.894 72.222 34.39 34.39 0.00 6.53
4886 5664 2.738521 GTGCCTCGACATGCGTGT 60.739 61.111 12.38 12.38 42.49 4.49


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

AutoCloner maintained by Alex Coulton.