Multiple sequence alignment - TraesCS3A01G077700

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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 TraesCS3A01G077700 chr3A 100.000 5690 0 0 1 5690 49985774 49980085 0.000000e+00 10508.0
1 TraesCS3A01G077700 chr3D 94.364 5784 171 69 1 5690 38753569 38747847 0.000000e+00 8732.0
2 TraesCS3A01G077700 chr3B 92.823 5504 186 77 6 5391 61565550 61560138 0.000000e+00 7782.0
3 TraesCS3A01G077700 chr3B 93.578 218 8 2 5455 5671 61560135 61559923 2.560000e-83 320.0
4 TraesCS3A01G077700 chr1B 100.000 33 0 0 467 499 661058058 661058026 1.710000e-05 62.1


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 TraesCS3A01G077700 chr3A 49980085 49985774 5689 True 10508 10508 100.0000 1 5690 1 chr3A.!!$R1 5689
1 TraesCS3A01G077700 chr3D 38747847 38753569 5722 True 8732 8732 94.3640 1 5690 1 chr3D.!!$R1 5689
2 TraesCS3A01G077700 chr3B 61559923 61565550 5627 True 4051 7782 93.2005 6 5671 2 chr3B.!!$R1 5665

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
952 971 1.339151 CCCCTCTTGGAAGTAGCACAC 60.339 57.143 0.00 0.00 35.39 3.82 F
1867 1893 0.107508 TCCAATGGAGTAGCAGCTGC 60.108 55.000 31.53 31.53 42.49 5.25 F
2986 3060 0.940126 GCATGCTTACTGTCCGGATG 59.060 55.000 7.81 6.66 0.00 3.51 F
3546 3684 1.101331 AGGTACGTACTGCTACTGGC 58.899 55.000 24.07 5.30 42.22 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1934 0.035458 CTTGGCGTCCTCTTTGACCT 59.965 55.0 0.0 0.00 31.35 3.85 R
3065 3139 0.470833 CCTCCTGATGATCTCCCCGT 60.471 60.0 0.0 0.00 0.00 5.28 R
4270 4430 0.538584 TGGTCAGGATGCAGTGCTAG 59.461 55.0 17.6 1.75 34.76 3.42 R
5488 5663 0.742281 CTCGGTGGGTGCATTCTCAG 60.742 60.0 0.0 0.00 0.00 3.35 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
121 124 3.684413 CGAATAGTGTGGGGCCTTGTATT 60.684 47.826 0.84 0.30 0.00 1.89
241 248 6.552932 AGGACATATGTATAGCTACTCCACA 58.447 40.000 8.71 0.00 0.00 4.17
339 347 3.072211 GGACCTTTTCTACTTTCACCCG 58.928 50.000 0.00 0.00 0.00 5.28
544 552 8.423349 ACGTACAGCTTATGGGTAATAATACAA 58.577 33.333 0.00 0.00 33.45 2.41
553 561 3.723154 GGGTAATAATACAACCCCAGGGA 59.277 47.826 7.25 0.00 46.12 4.20
666 674 2.265367 TCACCTGTAATTGGCAGAGGA 58.735 47.619 11.82 7.13 36.12 3.71
702 714 3.290710 GTGCAAGAGAGAGAGGAGAGAT 58.709 50.000 0.00 0.00 0.00 2.75
830 848 1.700955 GCTCATGGGCATCTCCATTT 58.299 50.000 14.19 0.00 44.55 2.32
851 869 6.509418 TTTTTCAAACTCAACAGTAGCAGT 57.491 33.333 0.00 0.00 30.14 4.40
853 871 6.598753 TTTCAAACTCAACAGTAGCAGTAC 57.401 37.500 0.00 0.00 30.14 2.73
893 911 4.096984 AGGTTGTGTTCTTGAGAAAGCTTG 59.903 41.667 0.00 0.00 35.58 4.01
907 925 3.665544 GCTTGGAGAGAGCTAGCTG 57.334 57.895 24.99 5.97 37.18 4.24
952 971 1.339151 CCCCTCTTGGAAGTAGCACAC 60.339 57.143 0.00 0.00 35.39 3.82
1035 1054 0.323908 CTTCCTCCTCCGACCTCAGT 60.324 60.000 0.00 0.00 0.00 3.41
1076 1095 0.179006 GATGACCTCCCATGGCCTTC 60.179 60.000 6.09 0.00 0.00 3.46
1077 1096 0.625683 ATGACCTCCCATGGCCTTCT 60.626 55.000 6.09 0.00 0.00 2.85
1078 1097 1.274703 TGACCTCCCATGGCCTTCTC 61.275 60.000 6.09 0.00 0.00 2.87
1087 1106 1.283029 CATGGCCTTCTCCTTCTTCCA 59.717 52.381 3.32 0.00 0.00 3.53
1095 1114 2.830370 CCTTCTTCCATGCCGCCC 60.830 66.667 0.00 0.00 0.00 6.13
1155 1174 2.757099 CACCAATGGAGCCAGCCC 60.757 66.667 6.16 0.00 0.00 5.19
1185 1204 6.998258 CTGTAAGCACCTTCTTCAATTTTG 57.002 37.500 0.00 0.00 0.00 2.44
1186 1205 5.288804 TGTAAGCACCTTCTTCAATTTTGC 58.711 37.500 0.00 0.00 0.00 3.68
1187 1206 3.391506 AGCACCTTCTTCAATTTTGCC 57.608 42.857 0.00 0.00 0.00 4.52
1188 1207 2.967887 AGCACCTTCTTCAATTTTGCCT 59.032 40.909 0.00 0.00 0.00 4.75
1189 1208 4.151883 AGCACCTTCTTCAATTTTGCCTA 58.848 39.130 0.00 0.00 0.00 3.93
1190 1209 4.774200 AGCACCTTCTTCAATTTTGCCTAT 59.226 37.500 0.00 0.00 0.00 2.57
1191 1210 5.951747 AGCACCTTCTTCAATTTTGCCTATA 59.048 36.000 0.00 0.00 0.00 1.31
1192 1211 6.608808 AGCACCTTCTTCAATTTTGCCTATAT 59.391 34.615 0.00 0.00 0.00 0.86
1220 1239 3.149196 TCAGCAGTTTTCATCTTCACCC 58.851 45.455 0.00 0.00 0.00 4.61
1229 1248 6.040955 AGTTTTCATCTTCACCCCTCTTTTTC 59.959 38.462 0.00 0.00 0.00 2.29
1231 1250 5.324832 TCATCTTCACCCCTCTTTTTCTT 57.675 39.130 0.00 0.00 0.00 2.52
1232 1251 5.705400 TCATCTTCACCCCTCTTTTTCTTT 58.295 37.500 0.00 0.00 0.00 2.52
1233 1252 6.136155 TCATCTTCACCCCTCTTTTTCTTTT 58.864 36.000 0.00 0.00 0.00 2.27
1234 1253 6.265422 TCATCTTCACCCCTCTTTTTCTTTTC 59.735 38.462 0.00 0.00 0.00 2.29
1235 1254 5.766590 TCTTCACCCCTCTTTTTCTTTTCT 58.233 37.500 0.00 0.00 0.00 2.52
1236 1255 6.194967 TCTTCACCCCTCTTTTTCTTTTCTT 58.805 36.000 0.00 0.00 0.00 2.52
1237 1256 6.667848 TCTTCACCCCTCTTTTTCTTTTCTTT 59.332 34.615 0.00 0.00 0.00 2.52
1238 1257 6.867519 TCACCCCTCTTTTTCTTTTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
1239 1258 6.873997 TCACCCCTCTTTTTCTTTTCTTTTC 58.126 36.000 0.00 0.00 0.00 2.29
1240 1259 6.667848 TCACCCCTCTTTTTCTTTTCTTTTCT 59.332 34.615 0.00 0.00 0.00 2.52
1241 1260 7.180229 TCACCCCTCTTTTTCTTTTCTTTTCTT 59.820 33.333 0.00 0.00 0.00 2.52
1242 1261 7.824289 CACCCCTCTTTTTCTTTTCTTTTCTTT 59.176 33.333 0.00 0.00 0.00 2.52
1243 1262 8.383175 ACCCCTCTTTTTCTTTTCTTTTCTTTT 58.617 29.630 0.00 0.00 0.00 2.27
1244 1263 9.231297 CCCCTCTTTTTCTTTTCTTTTCTTTTT 57.769 29.630 0.00 0.00 0.00 1.94
1464 1483 0.737019 GTGCATTGGGAATTGTGGCG 60.737 55.000 0.00 0.00 0.00 5.69
1573 1592 5.845391 TTTTGTTGGTTTCCTACAAGAGG 57.155 39.130 13.29 0.00 46.10 3.69
1574 1593 2.858745 TGTTGGTTTCCTACAAGAGGC 58.141 47.619 1.10 0.00 46.25 4.70
1676 1695 4.927978 AGCAGACCACATCTATCTACAC 57.072 45.455 0.00 0.00 35.15 2.90
1677 1696 4.281657 AGCAGACCACATCTATCTACACA 58.718 43.478 0.00 0.00 35.15 3.72
1678 1697 4.098654 AGCAGACCACATCTATCTACACAC 59.901 45.833 0.00 0.00 35.15 3.82
1796 1822 0.170561 GCTTGCTGCTCCATTGACAG 59.829 55.000 0.00 0.00 38.95 3.51
1867 1893 0.107508 TCCAATGGAGTAGCAGCTGC 60.108 55.000 31.53 31.53 42.49 5.25
1888 1914 4.933064 GCCGCCGATGGAGACTCG 62.933 72.222 0.00 0.00 35.92 4.18
1925 1951 1.118965 TGAGGTCAAAGAGGACGCCA 61.119 55.000 0.00 0.00 38.70 5.69
1933 1959 1.192146 AAGAGGACGCCAAGCTACCA 61.192 55.000 0.00 0.00 0.00 3.25
2110 2145 1.663074 CGAGATGCTAGCTTCGGCC 60.663 63.158 21.13 14.53 43.01 6.13
2132 2167 2.350134 TCTGCAAGAGCCTGCTGG 59.650 61.111 5.03 5.03 38.67 4.85
2248 2283 1.135915 CCTCCTCCTGTTCATCGTCTG 59.864 57.143 0.00 0.00 0.00 3.51
2302 2337 3.005897 ACAAGGTCAGTGCTACTACTGTG 59.994 47.826 5.89 0.51 46.32 3.66
2303 2338 2.877866 AGGTCAGTGCTACTACTGTGT 58.122 47.619 5.89 0.00 46.32 3.72
2315 2350 2.224967 ACTACTGTGTACCGTCCTCCTT 60.225 50.000 0.00 0.00 0.00 3.36
2318 2353 0.963962 TGTGTACCGTCCTCCTTGAC 59.036 55.000 0.00 0.00 0.00 3.18
2319 2354 1.254954 GTGTACCGTCCTCCTTGACT 58.745 55.000 0.00 0.00 32.97 3.41
2338 2373 8.001292 CCTTGACTTAATTAAAGAGATGGGGAT 58.999 37.037 0.00 0.00 38.67 3.85
2442 2477 5.612351 TGGCACAACAGTTGTATAAGTACA 58.388 37.500 18.74 7.53 43.23 2.90
2443 2478 6.234920 TGGCACAACAGTTGTATAAGTACAT 58.765 36.000 18.74 0.00 43.23 2.29
2473 2508 5.632034 AATACTGACCCAGGGATCTAAAC 57.368 43.478 14.54 0.00 35.51 2.01
2474 2509 3.207044 ACTGACCCAGGGATCTAAACT 57.793 47.619 14.54 0.00 35.51 2.66
2579 2622 3.575965 AAGCTTAATTTTGCTGACCCG 57.424 42.857 0.00 0.00 39.71 5.28
2718 2770 1.066143 GGGTCATCTTTTCTCTCGCCA 60.066 52.381 0.00 0.00 0.00 5.69
2857 2914 7.914110 GCAATTGCATACATGTCGTCCAGAC 62.914 48.000 25.36 0.00 44.64 3.51
2878 2935 1.869754 CGATCCAGTTCGGCGATCAAT 60.870 52.381 19.04 9.76 35.50 2.57
2907 2977 8.848474 ATTATTACAATGTAGCCAGTATCCAC 57.152 34.615 0.00 0.00 0.00 4.02
2914 2984 5.435686 TGTAGCCAGTATCCACTCATTTT 57.564 39.130 0.00 0.00 30.46 1.82
2958 3030 5.922739 TGCAAATGTGTGTACAAGACTAG 57.077 39.130 0.00 0.00 40.84 2.57
2968 3042 3.751175 TGTACAAGACTAGCCAATTGTGC 59.249 43.478 4.43 7.69 38.32 4.57
2969 3043 2.862541 ACAAGACTAGCCAATTGTGCA 58.137 42.857 17.54 0.00 34.71 4.57
2981 3055 3.504863 CAATTGTGCATGCTTACTGTCC 58.495 45.455 20.33 0.00 0.00 4.02
2986 3060 0.940126 GCATGCTTACTGTCCGGATG 59.060 55.000 7.81 6.66 0.00 3.51
3037 3111 1.815003 GTGCCTGCTGCTTTATTGAGT 59.185 47.619 0.00 0.00 42.00 3.41
3049 3123 4.723248 CTTTATTGAGTGGAAACGGAAGC 58.277 43.478 0.00 0.00 0.00 3.86
3340 3452 5.163332 TGTTATGTTGGGTAGTGTGTGTGTA 60.163 40.000 0.00 0.00 0.00 2.90
3358 3474 5.694458 GTGTGTATGTGTTGTACTGATCACA 59.306 40.000 12.40 12.40 43.30 3.58
3397 3513 6.368791 TCATGTGTTACTGAGCATGAGTTTAC 59.631 38.462 0.00 0.00 41.60 2.01
3545 3683 2.734492 GCAAGGTACGTACTGCTACTGG 60.734 54.545 24.77 13.51 0.00 4.00
3546 3684 1.101331 AGGTACGTACTGCTACTGGC 58.899 55.000 24.07 5.30 42.22 4.85
3780 3923 6.838612 ACAATACATGGCCTTATGGTAATTGT 59.161 34.615 18.18 18.18 36.41 2.71
3827 3970 4.694037 GCATGGTTTAGTCCTTTTCGTACT 59.306 41.667 0.00 0.00 0.00 2.73
3900 4053 5.750067 CCCAAAGAACAATGTTTTCAGACTG 59.250 40.000 0.00 0.00 0.00 3.51
3921 4074 6.293698 ACTGAAACGGTATTTAAGGTCAACT 58.706 36.000 0.00 0.00 0.00 3.16
3930 4083 7.551617 CGGTATTTAAGGTCAACTTGTCCTATT 59.448 37.037 7.86 0.00 40.37 1.73
3978 4131 5.123979 GCTGAATTTACTCTTTGGGGTACAG 59.876 44.000 0.00 0.00 0.00 2.74
3979 4132 6.442541 TGAATTTACTCTTTGGGGTACAGA 57.557 37.500 0.00 0.00 0.00 3.41
3980 4133 6.235664 TGAATTTACTCTTTGGGGTACAGAC 58.764 40.000 0.00 0.00 0.00 3.51
3981 4134 6.043938 TGAATTTACTCTTTGGGGTACAGACT 59.956 38.462 0.00 0.00 0.00 3.24
3982 4135 7.236019 TGAATTTACTCTTTGGGGTACAGACTA 59.764 37.037 0.00 0.00 0.00 2.59
3983 4136 5.990120 TTACTCTTTGGGGTACAGACTAC 57.010 43.478 0.00 0.00 0.00 2.73
3984 4137 3.853207 ACTCTTTGGGGTACAGACTACA 58.147 45.455 0.00 0.00 0.00 2.74
4012 4165 7.872483 AGTACAGTTGGGCAAAAGATAAATTTG 59.128 33.333 0.00 0.00 40.04 2.32
4268 4428 9.705103 AATAATTAATGCCTCTATGTGCCATAT 57.295 29.630 0.00 0.00 0.00 1.78
4270 4430 8.511604 AATTAATGCCTCTATGTGCCATATAC 57.488 34.615 0.00 0.00 0.00 1.47
4304 4464 4.129380 CCTGACCATCATCGCTCATTTAA 58.871 43.478 0.00 0.00 0.00 1.52
4319 4479 6.020916 CGCTCATTTAATTCATGCAGACTTTG 60.021 38.462 0.00 0.00 0.00 2.77
4381 4541 1.155424 ACAACACAACAGCGGGTACG 61.155 55.000 0.00 0.00 44.63 3.67
4520 4682 3.354948 ACTTGCCTGATGATGCTTACA 57.645 42.857 0.00 0.00 0.00 2.41
4525 4687 3.379057 TGCCTGATGATGCTTACACATTG 59.621 43.478 0.00 0.00 0.00 2.82
4536 4698 6.641169 TGCTTACACATTGATGTTGGTTTA 57.359 33.333 0.00 0.00 39.39 2.01
4596 4758 2.814336 GGAAGCAAAGGTTGATCTTCGT 59.186 45.455 0.00 0.00 33.36 3.85
4802 4964 9.665719 AGAAAAATATGTTCTCTTTCTCTCTCC 57.334 33.333 0.00 0.00 32.25 3.71
4809 4971 1.219393 CTTTCTCTCTCCCGGGCAC 59.781 63.158 18.49 0.00 0.00 5.01
4884 5046 3.726557 AGCCAAGTGAATCATCTGGAA 57.273 42.857 15.19 0.00 0.00 3.53
4915 5078 7.602517 AAGAACTAGTCATGTGAAACTATGC 57.397 36.000 0.00 0.00 38.04 3.14
4938 5110 1.029681 TGCAGATCATGGAAGCATGC 58.970 50.000 10.51 10.51 32.87 4.06
4974 5146 3.452264 AGATGTCATGCTGCTGGTTACTA 59.548 43.478 0.00 0.00 0.00 1.82
5061 5233 5.948162 AGCACTGTTCACCTATCATGAATTT 59.052 36.000 0.00 0.00 38.31 1.82
5411 5586 7.087409 TCATTAAGTTGCTCATGTATTGGTG 57.913 36.000 0.00 0.00 0.00 4.17
5415 5590 4.005650 AGTTGCTCATGTATTGGTGACAG 58.994 43.478 0.00 0.00 44.54 3.51
5482 5657 3.876914 CACTACCTGAAGTTCAAACAGCA 59.123 43.478 7.06 0.00 0.00 4.41
5488 5663 4.346129 CTGAAGTTCAAACAGCAGAACAC 58.654 43.478 7.06 2.90 44.94 3.32
5492 5667 3.624861 AGTTCAAACAGCAGAACACTGAG 59.375 43.478 7.88 0.00 44.94 3.35
5571 5746 6.417635 CACATTGCGAATACAACAAGAACTTT 59.582 34.615 0.00 0.00 31.03 2.66
5600 5775 6.327104 AGAATATTCAGATGCAGGAGTTCTCT 59.673 38.462 17.56 0.00 0.00 3.10
5638 5813 8.812972 TCAGTGTCCTGAATAACTAAATAGTGT 58.187 33.333 0.00 0.00 44.67 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 9.959775 GAGTCTAACTTTGATCAACGATTTAAG 57.040 33.333 17.97 8.93 0.00 1.85
82 85 8.304596 ACACTATTCGAGTCTAACTTTGATCAA 58.695 33.333 3.38 3.38 35.64 2.57
241 248 4.828829 AGCTAATTAGTACGCCAACTGTT 58.171 39.130 13.91 0.00 0.00 3.16
333 340 2.178876 ATCATGTTGCGACCGGGTGA 62.179 55.000 3.30 1.63 0.00 4.02
339 347 5.173774 ACATATCAAATCATGTTGCGACC 57.826 39.130 0.45 0.00 31.32 4.79
553 561 3.825908 AGAGACAGTCTTTCTCTCCCT 57.174 47.619 12.01 0.00 45.63 4.20
666 674 4.339748 TCTTGCACATACACTCTCTCTCT 58.660 43.478 0.00 0.00 0.00 3.10
702 714 3.197766 GTGACTCTCTCTCTCCTCTCTCA 59.802 52.174 0.00 0.00 0.00 3.27
830 848 6.346096 AGTACTGCTACTGTTGAGTTTGAAA 58.654 36.000 0.00 0.00 31.46 2.69
851 869 6.445786 ACAACCTCCAATGGGAAACTATAGTA 59.554 38.462 5.65 0.00 44.38 1.82
853 871 5.590259 CACAACCTCCAATGGGAAACTATAG 59.410 44.000 0.00 0.00 44.38 1.31
893 911 1.032014 CAGTCCAGCTAGCTCTCTCC 58.968 60.000 16.15 1.19 0.00 3.71
907 925 3.129462 GGAAGCTTAGAAAATGCCAGTCC 59.871 47.826 0.00 0.00 0.00 3.85
1046 1065 1.377536 GAGGTCATCTTGCAAGAGCC 58.622 55.000 31.14 28.66 41.13 4.70
1076 1095 1.821332 GGCGGCATGGAAGAAGGAG 60.821 63.158 3.07 0.00 0.00 3.69
1077 1096 2.272146 GGCGGCATGGAAGAAGGA 59.728 61.111 3.07 0.00 0.00 3.36
1078 1097 2.830370 GGGCGGCATGGAAGAAGG 60.830 66.667 12.47 0.00 0.00 3.46
1177 1196 8.352201 GCTGAACACATATATAGGCAAAATTGA 58.648 33.333 0.00 0.00 0.00 2.57
1178 1197 8.136800 TGCTGAACACATATATAGGCAAAATTG 58.863 33.333 0.00 0.00 0.00 2.32
1179 1198 8.236585 TGCTGAACACATATATAGGCAAAATT 57.763 30.769 0.00 0.00 0.00 1.82
1180 1199 7.503566 ACTGCTGAACACATATATAGGCAAAAT 59.496 33.333 0.00 0.00 0.00 1.82
1182 1201 6.356556 ACTGCTGAACACATATATAGGCAAA 58.643 36.000 0.00 0.00 0.00 3.68
1183 1202 5.928976 ACTGCTGAACACATATATAGGCAA 58.071 37.500 0.00 0.00 0.00 4.52
1185 1204 6.867662 AAACTGCTGAACACATATATAGGC 57.132 37.500 0.00 0.00 0.00 3.93
1186 1205 8.437360 TGAAAACTGCTGAACACATATATAGG 57.563 34.615 0.00 0.00 0.00 2.57
1188 1207 9.836864 AGATGAAAACTGCTGAACACATATATA 57.163 29.630 0.00 0.00 0.00 0.86
1189 1208 8.743085 AGATGAAAACTGCTGAACACATATAT 57.257 30.769 0.00 0.00 0.00 0.86
1190 1209 8.565896 AAGATGAAAACTGCTGAACACATATA 57.434 30.769 0.00 0.00 0.00 0.86
1191 1210 7.175467 TGAAGATGAAAACTGCTGAACACATAT 59.825 33.333 0.00 0.00 0.00 1.78
1192 1211 6.486320 TGAAGATGAAAACTGCTGAACACATA 59.514 34.615 0.00 0.00 0.00 2.29
1242 1261 9.703892 TCTCTTTCAACAATTTCTCAACAAAAA 57.296 25.926 0.00 0.00 0.00 1.94
1243 1262 9.357652 CTCTCTTTCAACAATTTCTCAACAAAA 57.642 29.630 0.00 0.00 0.00 2.44
1244 1263 7.975616 CCTCTCTTTCAACAATTTCTCAACAAA 59.024 33.333 0.00 0.00 0.00 2.83
1256 1275 8.043710 GGAAGATTCTATCCTCTCTTTCAACAA 58.956 37.037 7.32 0.00 32.75 2.83
1287 1306 7.442969 TCCTCGCTTAATTTTCTACTTTCAACA 59.557 33.333 0.00 0.00 0.00 3.33
1464 1483 3.968649 TCTGAACTTGTCATTTTGCTGC 58.031 40.909 0.00 0.00 35.07 5.25
1573 1592 0.165944 GAAGCATACACACACCACGC 59.834 55.000 0.00 0.00 0.00 5.34
1574 1593 0.796312 GGAAGCATACACACACCACG 59.204 55.000 0.00 0.00 0.00 4.94
1640 1659 5.008415 GTGGTCTGCTTAATGATTCATCCAG 59.992 44.000 0.00 5.23 0.00 3.86
1796 1822 1.404391 CAGCTGATGATGAGGGTTTGC 59.596 52.381 8.42 0.00 0.00 3.68
1888 1914 0.368227 CATCTTGCGCTGTCTCGTTC 59.632 55.000 9.73 0.00 0.00 3.95
1908 1934 0.035458 CTTGGCGTCCTCTTTGACCT 59.965 55.000 0.00 0.00 31.35 3.85
1925 1951 2.204306 AAGGGGCCCTGGTAGCTT 60.204 61.111 29.60 12.61 32.13 3.74
1933 1959 3.984732 GGAAGCACAAGGGGCCCT 61.985 66.667 22.67 22.67 33.87 5.19
2110 2145 1.544691 AGCAGGCTCTTGCAGAATTTG 59.455 47.619 6.74 0.00 46.47 2.32
2302 2337 4.732672 ATTAAGTCAAGGAGGACGGTAC 57.267 45.455 0.00 0.00 42.62 3.34
2303 2338 6.855763 TTAATTAAGTCAAGGAGGACGGTA 57.144 37.500 0.00 0.00 42.62 4.02
2338 2373 7.479352 TTTTCCATCATGGCTCTCAATTAAA 57.521 32.000 0.00 0.00 37.47 1.52
2399 2434 3.916172 CCAGCAAATTCACAATTCAGTCG 59.084 43.478 0.00 0.00 0.00 4.18
2442 2477 7.947782 TCCCTGGGTCAGTATTAATTTCTAT 57.052 36.000 13.56 0.00 0.00 1.98
2443 2478 7.794683 AGATCCCTGGGTCAGTATTAATTTCTA 59.205 37.037 13.56 0.00 0.00 2.10
2457 2492 2.158885 GCAGAGTTTAGATCCCTGGGTC 60.159 54.545 13.56 9.74 0.00 4.46
2461 2496 3.964031 ACCTAGCAGAGTTTAGATCCCTG 59.036 47.826 0.00 0.00 0.00 4.45
2473 2508 1.406614 CCTTTCAGCCACCTAGCAGAG 60.407 57.143 0.00 0.00 34.23 3.35
2474 2509 0.615331 CCTTTCAGCCACCTAGCAGA 59.385 55.000 0.00 0.00 34.23 4.26
2556 2598 4.749598 CGGGTCAGCAAAATTAAGCTTTTT 59.250 37.500 3.20 0.00 39.50 1.94
2579 2622 3.873952 CCATCTAGCTACCTCTTGCAAAC 59.126 47.826 0.00 0.00 0.00 2.93
2718 2770 6.749036 ATGCTATAGTAGTACTTTTGGGCT 57.251 37.500 8.40 0.00 0.00 5.19
2748 2800 2.041485 TGGATGGATGGAACTGCAAGAA 59.959 45.455 0.00 0.00 37.43 2.52
2878 2935 8.690203 ATACTGGCTACATTGTAATAATTGCA 57.310 30.769 0.00 0.00 0.00 4.08
2924 2994 9.357652 GTACACACATTTGCATATTTTCAAGAT 57.642 29.630 0.00 0.00 0.00 2.40
2925 2995 8.355913 TGTACACACATTTGCATATTTTCAAGA 58.644 29.630 0.00 0.00 0.00 3.02
2934 3004 6.092122 GCTAGTCTTGTACACACATTTGCATA 59.908 38.462 0.00 0.00 33.76 3.14
2958 3030 2.264813 CAGTAAGCATGCACAATTGGC 58.735 47.619 21.98 10.82 0.00 4.52
2968 3042 0.940126 GCATCCGGACAGTAAGCATG 59.060 55.000 6.12 0.00 0.00 4.06
2969 3043 0.541392 TGCATCCGGACAGTAAGCAT 59.459 50.000 6.12 0.00 0.00 3.79
2981 3055 3.362596 CGTCGTACCAAATTATGCATCCG 60.363 47.826 0.19 0.00 0.00 4.18
2986 3060 3.666001 CACACGTCGTACCAAATTATGC 58.334 45.455 0.00 0.00 0.00 3.14
3037 3111 4.980805 AGCGCGCTTCCGTTTCCA 62.981 61.111 31.32 0.00 36.67 3.53
3065 3139 0.470833 CCTCCTGATGATCTCCCCGT 60.471 60.000 0.00 0.00 0.00 5.28
3119 3193 6.256686 GCTTCTTCTTCGACGATACTTCTAA 58.743 40.000 0.00 0.00 0.00 2.10
3123 3197 3.444388 AGGCTTCTTCTTCGACGATACTT 59.556 43.478 0.00 0.00 0.00 2.24
3340 3452 7.229306 AGTGAATTTGTGATCAGTACAACACAT 59.771 33.333 16.49 0.60 41.67 3.21
3358 3474 6.936900 AGTAACACATGAGCAGTAGTGAATTT 59.063 34.615 0.00 0.00 35.97 1.82
3391 3507 5.782893 TTAACAAGCAATGCAGGTAAACT 57.217 34.783 8.35 0.00 0.00 2.66
3397 3513 7.009815 CACTCATTAATTAACAAGCAATGCAGG 59.990 37.037 8.35 0.70 0.00 4.85
3565 3703 7.497925 TTTTTGGTGGTAAATGGTAATTTGC 57.502 32.000 0.00 0.00 36.65 3.68
3763 3906 5.427157 TGAGAGTACAATTACCATAAGGCCA 59.573 40.000 5.01 0.00 39.06 5.36
3780 3923 4.763279 TGGTCATGTACTTTCGTGAGAGTA 59.237 41.667 0.00 0.00 43.69 2.59
3900 4053 6.962686 ACAAGTTGACCTTAAATACCGTTTC 58.037 36.000 10.54 0.00 0.00 2.78
3921 4074 6.765989 GGTCTGTGCATACATAAATAGGACAA 59.234 38.462 0.00 0.00 35.97 3.18
3930 4083 4.225042 ACAAGAGGGTCTGTGCATACATAA 59.775 41.667 0.00 0.00 35.97 1.90
3978 4131 2.561419 TGCCCAACTGTACTCTGTAGTC 59.439 50.000 0.00 0.00 37.15 2.59
3979 4132 2.605257 TGCCCAACTGTACTCTGTAGT 58.395 47.619 0.00 0.00 39.91 2.73
3980 4133 3.678056 TTGCCCAACTGTACTCTGTAG 57.322 47.619 0.00 0.00 0.00 2.74
3981 4134 4.101898 TCTTTTGCCCAACTGTACTCTGTA 59.898 41.667 0.00 0.00 0.00 2.74
3982 4135 3.118038 TCTTTTGCCCAACTGTACTCTGT 60.118 43.478 0.00 0.00 0.00 3.41
3983 4136 3.476552 TCTTTTGCCCAACTGTACTCTG 58.523 45.455 0.00 0.00 0.00 3.35
3984 4137 3.857157 TCTTTTGCCCAACTGTACTCT 57.143 42.857 0.00 0.00 0.00 3.24
4012 4165 7.845617 TGCGTCGAAATATTATTTATTTGCC 57.154 32.000 0.00 0.00 0.00 4.52
4089 4245 8.619546 GGATTCTCCTTTTCATGAAGATTACTG 58.380 37.037 8.41 0.00 32.53 2.74
4090 4246 7.777440 GGGATTCTCCTTTTCATGAAGATTACT 59.223 37.037 8.41 0.00 36.57 2.24
4091 4247 7.777440 AGGGATTCTCCTTTTCATGAAGATTAC 59.223 37.037 8.41 0.00 36.57 1.89
4092 4248 7.876371 AGGGATTCTCCTTTTCATGAAGATTA 58.124 34.615 8.41 0.00 36.57 1.75
4102 4261 4.593956 ACATGTGAGGGATTCTCCTTTTC 58.406 43.478 0.00 0.00 41.76 2.29
4240 4400 8.932434 TGGCACATAGAGGCATTAATTATTTA 57.068 30.769 0.00 0.00 36.56 1.40
4268 4428 1.757118 GGTCAGGATGCAGTGCTAGTA 59.243 52.381 17.60 0.00 34.76 1.82
4269 4429 0.539051 GGTCAGGATGCAGTGCTAGT 59.461 55.000 17.60 2.04 34.76 2.57
4270 4430 0.538584 TGGTCAGGATGCAGTGCTAG 59.461 55.000 17.60 1.75 34.76 3.42
4304 4464 1.741706 CCGCTCAAAGTCTGCATGAAT 59.258 47.619 0.00 0.00 0.00 2.57
4319 4479 2.088674 ATCTCATGTACGGCCCGCTC 62.089 60.000 1.23 0.00 0.00 5.03
4429 4591 6.697395 ACCCATTGCTTATTAACAGGTTTTC 58.303 36.000 0.00 0.00 0.00 2.29
4520 4682 5.471797 TGTCGACATAAACCAACATCAATGT 59.528 36.000 15.76 0.00 44.20 2.71
4525 4687 3.374058 CCCTGTCGACATAAACCAACATC 59.626 47.826 20.40 0.00 0.00 3.06
4536 4698 3.771160 GACGGCCCCTGTCGACAT 61.771 66.667 20.40 1.19 43.95 3.06
4596 4758 1.195115 CCAAGCACAGCCCTCTACTA 58.805 55.000 0.00 0.00 0.00 1.82
4812 4974 5.470047 AAGGAGATATGTACATCCCGTTC 57.530 43.478 12.68 4.65 31.86 3.95
4915 5078 3.793797 TGCTTCCATGATCTGCAATTG 57.206 42.857 0.00 0.00 0.00 2.32
4942 5114 2.237893 AGCATGACATCTCCATGACACA 59.762 45.455 0.00 0.00 42.89 3.72
4943 5115 2.612672 CAGCATGACATCTCCATGACAC 59.387 50.000 0.00 0.00 42.89 3.67
4999 5171 7.892609 ACTAATTTTATGGGTTGACACTTTCC 58.107 34.615 0.00 0.00 0.00 3.13
5001 5173 7.655732 GCAACTAATTTTATGGGTTGACACTTT 59.344 33.333 8.08 0.00 39.39 2.66
5061 5233 5.818678 TCTGTTTTCCTGCCTAGTCTTTA 57.181 39.130 0.00 0.00 0.00 1.85
5406 5581 3.282885 TGTTGTGTATTGCTGTCACCAA 58.717 40.909 0.00 0.00 0.00 3.67
5411 5586 7.133891 AGAGTATTTGTTGTGTATTGCTGTC 57.866 36.000 0.00 0.00 0.00 3.51
5453 5628 3.745975 TGAACTTCAGGTAGTGATTTGCG 59.254 43.478 0.00 0.00 34.17 4.85
5482 5657 1.421268 TGGGTGCATTCTCAGTGTTCT 59.579 47.619 0.00 0.00 0.00 3.01
5488 5663 0.742281 CTCGGTGGGTGCATTCTCAG 60.742 60.000 0.00 0.00 0.00 3.35
5492 5667 1.648467 GAAGCTCGGTGGGTGCATTC 61.648 60.000 0.00 0.00 37.60 2.67
5571 5746 6.656902 ACTCCTGCATCTGAATATTCTTCAA 58.343 36.000 16.24 0.39 0.00 2.69
5600 5775 4.371624 AGGACACTGATCCATCAACAAA 57.628 40.909 5.70 0.00 41.73 2.83
5635 5810 6.475402 GGTTGCATAGCACCAAAATAATACAC 59.525 38.462 0.21 0.00 38.71 2.90
5636 5811 6.406400 GGGTTGCATAGCACCAAAATAATACA 60.406 38.462 7.57 0.00 38.71 2.29
5637 5812 5.983118 GGGTTGCATAGCACCAAAATAATAC 59.017 40.000 7.57 0.00 38.71 1.89
5638 5813 5.658634 TGGGTTGCATAGCACCAAAATAATA 59.341 36.000 7.57 0.00 38.71 0.98
5639 5814 4.469227 TGGGTTGCATAGCACCAAAATAAT 59.531 37.500 7.57 0.00 38.71 1.28


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

AutoCloner maintained by Alex Coulton.