Multiple sequence alignment - TraesCS3D01G106000

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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 TraesCS3D01G106000 chr3D 100.000 5391 0 0 1 5391 58113206 58118596 0.000000e+00 9956
1 TraesCS3D01G106000 chr3A 95.065 5167 180 36 265 5391 67151436 67156567 0.000000e+00 8059
2 TraesCS3D01G106000 chr3A 95.833 96 4 0 1 96 67151174 67151269 7.230000e-34 156
3 TraesCS3D01G106000 chr3B 95.103 2675 92 9 2721 5391 91431932 91434571 0.000000e+00 4178
4 TraesCS3D01G106000 chr3B 91.781 1825 99 23 265 2061 91429084 91430885 0.000000e+00 2492
5 TraesCS3D01G106000 chr3B 96.624 622 20 1 2044 2665 91431064 91431684 0.000000e+00 1031
6 TraesCS3D01G106000 chr3B 83.764 271 20 17 1 249 91428764 91429032 9.030000e-58 235


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 TraesCS3D01G106000 chr3D 58113206 58118596 5390 False 9956.0 9956 100.000 1 5391 1 chr3D.!!$F1 5390
1 TraesCS3D01G106000 chr3A 67151174 67156567 5393 False 4107.5 8059 95.449 1 5391 2 chr3A.!!$F1 5390
2 TraesCS3D01G106000 chr3B 91428764 91434571 5807 False 1984.0 4178 91.818 1 5391 4 chr3B.!!$F1 5390

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
682 756 0.692476 ACCTGCCAGTGCACTCATTA 59.308 50.000 18.64 2.85 44.23 1.90 F
1083 1174 0.323629 CTCCGCTCCAAACCCTAACA 59.676 55.000 0.00 0.00 0.00 2.41 F
1452 1550 0.383002 CGTGCGCTACTGTTGTGTTG 60.383 55.000 9.73 0.00 0.00 3.33 F
1862 1963 0.391661 ATCACTGCAGTTACGGCCAG 60.392 55.000 18.94 3.10 0.00 4.85 F
2077 2382 1.066752 GACGCCGGCCTTTGTTTTT 59.933 52.632 23.46 0.00 0.00 1.94 F
2729 3227 1.611491 TCACTCACGTGTGCATGACTA 59.389 47.619 16.51 0.00 41.89 2.59 F
3125 3626 2.292103 TGCCTTTTTGACTTGCACAC 57.708 45.000 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1753 0.107654 GCCCAGTGACATGAGGGTAC 60.108 60.000 0.00 0.00 43.42 3.34 R
2061 2170 0.663269 GAGAAAAACAAAGGCCGGCG 60.663 55.000 22.54 9.21 0.00 6.46 R
2729 3227 2.665165 TCCTTTCAAACAGGCACATGT 58.335 42.857 0.00 0.00 33.96 3.21 R
3719 4223 1.134995 TGTCTGGTGATCTGATCGCAC 60.135 52.381 26.99 18.78 41.46 5.34 R
4024 4528 1.358877 CAGTTCGACCAATGCGATGA 58.641 50.000 0.00 0.00 37.64 2.92 R
4135 4639 2.266055 GGGCTGACCTTCTGTCCG 59.734 66.667 0.00 0.00 43.78 4.79 R
4989 5508 0.981183 TCCTATGTCGGGCAAACAGT 59.019 50.000 0.00 0.00 0.00 3.55 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
55 56 5.120208 GTGCTCTTCTTTGCTAATACGAACA 59.880 40.000 0.00 0.00 0.00 3.18
92 93 9.956720 CAATTGACAGAATTACAAACTTCTCTT 57.043 29.630 0.00 0.00 29.34 2.85
191 220 7.698506 ATGTTCTCATTCTTGATGACACAAT 57.301 32.000 0.00 0.00 39.83 2.71
205 234 5.565592 TGACACAATCATTCTATTGCACC 57.434 39.130 0.00 0.00 39.93 5.01
209 238 4.097437 CACAATCATTCTATTGCACCTGCT 59.903 41.667 0.00 0.00 39.93 4.24
271 341 4.898607 TCCAGTTGTTGTGGAGCC 57.101 55.556 0.00 0.00 39.28 4.70
615 688 4.770874 TAAACAGCCTCCCGCCGC 62.771 66.667 0.00 0.00 38.78 6.53
631 705 1.235724 CCGCGGATATTTCCCCTTTC 58.764 55.000 24.07 0.00 39.01 2.62
641 715 2.133858 TTCCCCTTTCCCTCTGTTCT 57.866 50.000 0.00 0.00 0.00 3.01
642 716 1.362224 TCCCCTTTCCCTCTGTTCTG 58.638 55.000 0.00 0.00 0.00 3.02
643 717 1.068121 CCCCTTTCCCTCTGTTCTGT 58.932 55.000 0.00 0.00 0.00 3.41
644 718 1.425448 CCCCTTTCCCTCTGTTCTGTT 59.575 52.381 0.00 0.00 0.00 3.16
645 719 2.158460 CCCCTTTCCCTCTGTTCTGTTT 60.158 50.000 0.00 0.00 0.00 2.83
646 720 2.887152 CCCTTTCCCTCTGTTCTGTTTG 59.113 50.000 0.00 0.00 0.00 2.93
647 721 3.555966 CCTTTCCCTCTGTTCTGTTTGT 58.444 45.455 0.00 0.00 0.00 2.83
654 728 1.077357 TGTTCTGTTTGTGGCCCGT 60.077 52.632 0.00 0.00 0.00 5.28
682 756 0.692476 ACCTGCCAGTGCACTCATTA 59.308 50.000 18.64 2.85 44.23 1.90
720 794 2.080286 AGACATGGGAAGACGTTTCG 57.920 50.000 0.00 0.00 0.00 3.46
815 889 2.035442 GGAGCTCGCCTGTTGAACC 61.035 63.158 7.83 0.00 0.00 3.62
916 1006 3.564027 GGCCTGCCGAATCGAACG 61.564 66.667 3.36 8.11 0.00 3.95
1082 1173 1.025113 GCTCCGCTCCAAACCCTAAC 61.025 60.000 0.00 0.00 0.00 2.34
1083 1174 0.323629 CTCCGCTCCAAACCCTAACA 59.676 55.000 0.00 0.00 0.00 2.41
1087 1184 2.344025 CGCTCCAAACCCTAACAGTAC 58.656 52.381 0.00 0.00 0.00 2.73
1093 1190 3.588396 CCAAACCCTAACAGTACCCCTAA 59.412 47.826 0.00 0.00 0.00 2.69
1103 1200 3.651423 ACAGTACCCCTAATAATCCTGGC 59.349 47.826 0.00 0.00 0.00 4.85
1115 1212 3.541713 CCTGGCTCTAGGTCCGGC 61.542 72.222 0.00 0.00 32.99 6.13
1128 1226 1.211212 GGTCCGGCTGGTTACCTATTT 59.789 52.381 12.43 0.00 36.30 1.40
1409 1507 1.077716 GGTTAGGCCATGGCGTTCT 60.078 57.895 34.72 25.20 43.06 3.01
1410 1508 0.679960 GGTTAGGCCATGGCGTTCTT 60.680 55.000 34.72 17.42 43.06 2.52
1411 1509 0.733150 GTTAGGCCATGGCGTTCTTC 59.267 55.000 34.72 18.05 43.06 2.87
1412 1510 0.742990 TTAGGCCATGGCGTTCTTCG 60.743 55.000 34.72 0.00 43.06 3.79
1421 1519 1.681025 GGCGTTCTTCGTTCGTAGCC 61.681 60.000 0.00 0.00 42.13 3.93
1452 1550 0.383002 CGTGCGCTACTGTTGTGTTG 60.383 55.000 9.73 0.00 0.00 3.33
1456 1554 0.937304 CGCTACTGTTGTGTTGCAGT 59.063 50.000 0.00 0.00 46.33 4.40
1479 1577 5.687285 GTCTTTCAGACGCACAAATTTGATT 59.313 36.000 24.64 0.00 35.28 2.57
1504 1602 3.300388 TCAGCAGGGAGTAGGATAAGTG 58.700 50.000 0.00 0.00 0.00 3.16
1568 1666 3.304057 GGAACGCCTTCATTTAGCTATGC 60.304 47.826 0.00 0.00 0.00 3.14
1655 1753 8.783833 ATGCACCTATATGTAATTCTAGCAAG 57.216 34.615 0.00 0.00 0.00 4.01
1683 1781 1.968540 GTCACTGGGCTGAGTTGGC 60.969 63.158 0.00 0.00 0.00 4.52
1830 1931 5.246203 CCTAATAGCACTGGTTATCCTGCTA 59.754 44.000 13.37 13.37 45.21 3.49
1835 1936 8.380791 ATAGCACTGGTTATCCTGCTATTGCA 62.381 42.308 15.81 0.99 46.61 4.08
1836 1937 3.313526 CACTGGTTATCCTGCTATTGCAC 59.686 47.826 0.00 0.00 45.31 4.57
1843 1944 1.585267 CCTGCTATTGCACGTGCCAA 61.585 55.000 35.72 27.79 45.31 4.52
1852 1953 1.208358 CACGTGCCAATCACTGCAG 59.792 57.895 13.48 13.48 43.46 4.41
1856 1957 1.135972 CGTGCCAATCACTGCAGTTAC 60.136 52.381 18.94 6.90 43.46 2.50
1857 1958 1.135972 GTGCCAATCACTGCAGTTACG 60.136 52.381 18.94 6.46 42.38 3.18
1862 1963 0.391661 ATCACTGCAGTTACGGCCAG 60.392 55.000 18.94 3.10 0.00 4.85
1916 2020 6.538381 TGAAGATACGTGATGCATATGTGTTT 59.462 34.615 0.00 0.00 0.00 2.83
1917 2021 6.291067 AGATACGTGATGCATATGTGTTTG 57.709 37.500 0.00 0.00 0.00 2.93
1943 2047 9.145865 GATGAACTGAAAACAAAGTGGTAAAAA 57.854 29.630 0.00 0.00 0.00 1.94
1979 2088 2.094100 TTGCCAACTGGGAATTTCCA 57.906 45.000 17.08 5.05 40.75 3.53
1990 2099 2.820197 GGGAATTTCCAAGTCCTCACAC 59.180 50.000 17.08 0.00 44.75 3.82
2061 2170 5.565439 GCACCATATTATGATGCCCTTTGAC 60.565 44.000 11.41 0.00 0.00 3.18
2063 2172 4.379813 CCATATTATGATGCCCTTTGACGC 60.380 45.833 5.21 0.00 0.00 5.19
2064 2173 1.388547 TTATGATGCCCTTTGACGCC 58.611 50.000 0.00 0.00 0.00 5.68
2077 2382 1.066752 GACGCCGGCCTTTGTTTTT 59.933 52.632 23.46 0.00 0.00 1.94
2233 2539 5.554070 TGTTTCCACTTACTTACCTAAGGC 58.446 41.667 0.00 0.00 37.62 4.35
2729 3227 1.611491 TCACTCACGTGTGCATGACTA 59.389 47.619 16.51 0.00 41.89 2.59
2806 3304 6.660887 ACTTGCTATTTGTGTTGGTTTTTG 57.339 33.333 0.00 0.00 0.00 2.44
2835 3333 4.716784 TCTTTACATGGCTGGTGATAGTCT 59.283 41.667 0.00 0.00 0.00 3.24
3026 3524 4.232091 TCAGGTACACCTCTTCCTTTTCT 58.768 43.478 0.00 0.00 46.65 2.52
3034 3532 6.365520 ACACCTCTTCCTTTTCTTACAACAT 58.634 36.000 0.00 0.00 0.00 2.71
3068 3569 9.686683 GCATTATAGGGTAAATCCTGAATGTAT 57.313 33.333 15.05 0.00 40.24 2.29
3125 3626 2.292103 TGCCTTTTTGACTTGCACAC 57.708 45.000 0.00 0.00 0.00 3.82
3168 3669 9.685276 AATTGAGTTATTATGATGAGGTTGTCA 57.315 29.630 0.00 0.00 40.38 3.58
3397 3901 3.547746 ACATTGTACCCACAGTTCGTTT 58.452 40.909 0.00 0.00 35.67 3.60
3421 3925 5.289595 TGCTAGCGGATTTCTTACATACTG 58.710 41.667 10.77 0.00 0.00 2.74
3429 3933 8.242053 GCGGATTTCTTACATACTGCTAGTATA 58.758 37.037 8.03 0.00 39.26 1.47
3516 4020 5.124457 TGAAGAACTGAAAGCTAATCATGCC 59.876 40.000 2.87 0.00 37.60 4.40
3549 4053 7.916977 CAGCATGTAGAGATATTATCTGAGAGC 59.083 40.741 10.93 7.39 40.38 4.09
3719 4223 2.584835 TCATGGACACCAAGAAAGGG 57.415 50.000 0.00 0.00 36.95 3.95
4024 4528 3.049344 GGGGTCTCTGGAGGATTATGTT 58.951 50.000 0.00 0.00 0.00 2.71
4135 4639 9.670719 GATCTTATTAGCATTTTAGTTGAAGCC 57.329 33.333 0.00 0.00 0.00 4.35
4141 4645 3.670627 GCATTTTAGTTGAAGCCGGACAG 60.671 47.826 5.05 0.00 0.00 3.51
4211 4715 6.320418 TCCTTCTTTGGGTAAGTTTTCTGTTC 59.680 38.462 0.00 0.00 35.28 3.18
4222 4726 9.378597 GGTAAGTTTTCTGTTCGATTACTTTTC 57.621 33.333 0.00 0.00 31.83 2.29
4309 4814 5.291971 ACATTGTTGAAAGCCATCTTGTTC 58.708 37.500 0.00 0.00 31.78 3.18
4313 4818 4.036734 TGTTGAAAGCCATCTTGTTCAGTC 59.963 41.667 0.00 0.00 31.78 3.51
4606 5111 7.018235 GCAGTTTCAGTAGAAAATAGTTCAGC 58.982 38.462 0.00 0.00 44.75 4.26
4644 5149 5.931532 AGTCACAGCGAAACTCATATTTTG 58.068 37.500 0.00 0.00 0.00 2.44
4778 5283 5.710099 TCTTCTGTTTGTTTTCCTCTTGTGT 59.290 36.000 0.00 0.00 0.00 3.72
4782 5287 5.956642 TGTTTGTTTTCCTCTTGTGTTACC 58.043 37.500 0.00 0.00 0.00 2.85
4796 5301 2.161609 GTGTTACCAGCACCACTAATGC 59.838 50.000 0.00 0.00 43.74 3.56
4810 5315 4.496341 CCACTAATGCGAAATAGCTGTTGG 60.496 45.833 0.00 0.00 38.13 3.77
4813 5318 0.326595 TGCGAAATAGCTGTTGGGGA 59.673 50.000 0.00 0.00 38.13 4.81
4815 5320 2.024414 GCGAAATAGCTGTTGGGGATT 58.976 47.619 0.00 0.00 0.00 3.01
4832 5337 3.432890 GGGATTTCAGCTGGAACCTAGAG 60.433 52.174 10.35 0.00 34.56 2.43
4851 5356 0.036671 GTGGGGTTTCTTCCGATCGT 60.037 55.000 15.09 0.00 0.00 3.73
4894 5400 3.871006 TCTCACCATGTCACGATAAATGC 59.129 43.478 0.00 0.00 0.00 3.56
4981 5500 4.752063 ACTAGATGGCCATGATAGGTGTA 58.248 43.478 26.56 0.00 0.00 2.90
4982 5501 4.528596 ACTAGATGGCCATGATAGGTGTAC 59.471 45.833 26.56 4.04 0.00 2.90
4983 5502 3.591789 AGATGGCCATGATAGGTGTACT 58.408 45.455 26.56 6.70 0.00 2.73
4984 5503 4.752063 AGATGGCCATGATAGGTGTACTA 58.248 43.478 26.56 0.00 35.80 1.82
4985 5504 5.155161 AGATGGCCATGATAGGTGTACTAA 58.845 41.667 26.56 0.00 34.79 2.24
4986 5505 5.787494 AGATGGCCATGATAGGTGTACTAAT 59.213 40.000 26.56 0.00 34.79 1.73
4987 5506 5.904984 TGGCCATGATAGGTGTACTAATT 57.095 39.130 0.00 0.00 34.79 1.40
4988 5507 6.260700 TGGCCATGATAGGTGTACTAATTT 57.739 37.500 0.00 0.00 34.79 1.82
4989 5508 7.381789 TGGCCATGATAGGTGTACTAATTTA 57.618 36.000 0.00 0.00 34.79 1.40
4990 5509 7.221450 TGGCCATGATAGGTGTACTAATTTAC 58.779 38.462 0.00 0.00 34.79 2.01
4991 5510 7.071950 TGGCCATGATAGGTGTACTAATTTACT 59.928 37.037 0.00 0.00 34.79 2.24
4992 5511 7.387948 GGCCATGATAGGTGTACTAATTTACTG 59.612 40.741 0.00 0.00 34.79 2.74
4993 5512 7.931948 GCCATGATAGGTGTACTAATTTACTGT 59.068 37.037 0.00 0.00 34.79 3.55
5045 5564 7.041098 ACCATAACAGAGTTAAAAGTTCTGCAG 60.041 37.037 7.63 7.63 41.52 4.41
5049 5568 4.058817 AGAGTTAAAAGTTCTGCAGACGG 58.941 43.478 18.03 0.00 0.00 4.79
5191 5711 1.153269 GGCAGTGCTTCCCTCTAGC 60.153 63.158 16.11 0.00 39.10 3.42
5214 5734 2.738846 GTTGCCGCTGATATATCCACAG 59.261 50.000 10.25 3.19 35.14 3.66
5251 5771 0.538057 TCAGCTTCCCACCAGCTTTG 60.538 55.000 0.00 0.00 45.82 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 9.260002 GTAATTCTGTCAATTGATTGTTGGTTT 57.740 29.630 12.12 2.01 38.84 3.27
92 93 2.732412 GCTCTAGTGTTCAGTGAGCA 57.268 50.000 5.45 5.45 46.41 4.26
180 209 6.183360 GGTGCAATAGAATGATTGTGTCATCA 60.183 38.462 0.00 0.00 46.80 3.07
191 220 5.726980 AAAAAGCAGGTGCAATAGAATGA 57.273 34.783 4.48 0.00 45.16 2.57
631 705 0.954452 GCCACAAACAGAACAGAGGG 59.046 55.000 0.00 0.00 0.00 4.30
668 742 2.479566 ACTGGTAATGAGTGCACTGG 57.520 50.000 27.27 6.16 0.00 4.00
676 750 3.306166 CGGAAGCGTAAACTGGTAATGAG 59.694 47.826 0.00 0.00 0.00 2.90
682 756 2.297033 TCTAACGGAAGCGTAAACTGGT 59.703 45.455 0.00 0.00 0.00 4.00
720 794 2.738314 ACAAATACGCAACCCGACTTAC 59.262 45.455 0.00 0.00 41.02 2.34
757 831 3.634910 AGAGCTCGAGAGATTTTACCCTC 59.365 47.826 18.75 8.85 40.84 4.30
960 1050 4.165486 TAGGGTTTAGCGGCGGGC 62.165 66.667 9.78 0.00 44.05 6.13
961 1051 2.108362 CTAGGGTTTAGCGGCGGG 59.892 66.667 9.78 0.00 0.00 6.13
1082 1173 3.910627 AGCCAGGATTATTAGGGGTACTG 59.089 47.826 0.00 0.00 0.00 2.74
1083 1174 4.140423 AGAGCCAGGATTATTAGGGGTACT 60.140 45.833 0.00 0.00 0.00 2.73
1087 1184 3.777522 CCTAGAGCCAGGATTATTAGGGG 59.222 52.174 0.00 0.00 38.00 4.79
1093 1190 2.530701 CGGACCTAGAGCCAGGATTAT 58.469 52.381 3.73 0.00 39.18 1.28
1103 1200 0.745468 GTAACCAGCCGGACCTAGAG 59.255 60.000 5.05 0.00 35.59 2.43
1115 1212 2.422127 CACGGGCAAAATAGGTAACCAG 59.578 50.000 0.00 0.00 37.17 4.00
1409 1507 0.529378 GAGAAGGGGCTACGAACGAA 59.471 55.000 0.14 0.00 0.00 3.85
1410 1508 0.323178 AGAGAAGGGGCTACGAACGA 60.323 55.000 0.14 0.00 0.00 3.85
1411 1509 0.100861 GAGAGAAGGGGCTACGAACG 59.899 60.000 0.00 0.00 0.00 3.95
1412 1510 0.460722 GGAGAGAAGGGGCTACGAAC 59.539 60.000 0.00 0.00 0.00 3.95
1421 1519 4.148825 CGCACGGGGAGAGAAGGG 62.149 72.222 0.00 0.00 0.00 3.95
1456 1554 4.891627 TCAAATTTGTGCGTCTGAAAGA 57.108 36.364 17.47 0.00 43.69 2.52
1479 1577 2.550277 TCCTACTCCCTGCTGATTCA 57.450 50.000 0.00 0.00 0.00 2.57
1568 1666 2.602257 TCATGTGATACAAGGAGGCG 57.398 50.000 0.00 0.00 0.00 5.52
1655 1753 0.107654 GCCCAGTGACATGAGGGTAC 60.108 60.000 0.00 0.00 43.42 3.34
1683 1781 2.806945 TTCCCAATCAGCTAACAGGG 57.193 50.000 7.06 7.06 37.65 4.45
1769 1867 7.969536 ATGTTGATTACTCACATATGTAGGC 57.030 36.000 8.32 0.00 0.00 3.93
1843 1944 0.391661 CTGGCCGTAACTGCAGTGAT 60.392 55.000 22.49 8.39 0.00 3.06
1852 1953 3.323751 TCTAAACTTCCTGGCCGTAAC 57.676 47.619 0.00 0.00 0.00 2.50
1856 1957 4.783764 AAAAATCTAAACTTCCTGGCCG 57.216 40.909 0.00 0.00 0.00 6.13
1857 1958 9.151471 GAAAATAAAAATCTAAACTTCCTGGCC 57.849 33.333 0.00 0.00 0.00 5.36
1900 2001 6.471198 CAGTTCATCAAACACATATGCATCAC 59.529 38.462 0.19 0.00 40.56 3.06
1916 2020 5.913137 ACCACTTTGTTTTCAGTTCATCA 57.087 34.783 0.00 0.00 0.00 3.07
1917 2021 8.696410 TTTTACCACTTTGTTTTCAGTTCATC 57.304 30.769 0.00 0.00 0.00 2.92
1962 2071 1.970640 ACTTGGAAATTCCCAGTTGGC 59.029 47.619 12.44 0.00 39.24 4.52
1969 2078 2.820197 GTGTGAGGACTTGGAAATTCCC 59.180 50.000 9.87 0.00 46.01 3.97
1973 2082 2.158623 TGCAGTGTGAGGACTTGGAAAT 60.159 45.455 0.00 0.00 0.00 2.17
1979 2088 1.417517 TGTGATGCAGTGTGAGGACTT 59.582 47.619 0.00 0.00 0.00 3.01
1990 2099 7.872881 AGCTTTCTGATTATAATGTGATGCAG 58.127 34.615 1.78 3.23 0.00 4.41
2061 2170 0.663269 GAGAAAAACAAAGGCCGGCG 60.663 55.000 22.54 9.21 0.00 6.46
2063 2172 1.036707 TGGAGAAAAACAAAGGCCGG 58.963 50.000 0.00 0.00 0.00 6.13
2064 2173 1.269569 GGTGGAGAAAAACAAAGGCCG 60.270 52.381 0.00 0.00 0.00 6.13
2116 2421 7.575332 TTTTCTTAAACAAACAGCACAGTTC 57.425 32.000 0.00 0.00 0.00 3.01
2177 2483 7.172361 GTGAGATGATAAACCTAAGGAAGCATC 59.828 40.741 0.00 0.00 0.00 3.91
2190 2496 5.886960 ACAAAGGCTGTGAGATGATAAAC 57.113 39.130 12.68 0.00 36.69 2.01
2443 2749 9.722056 AAAGTAAATCAAGAAATATAAGCAGCG 57.278 29.630 0.00 0.00 0.00 5.18
2729 3227 2.665165 TCCTTTCAAACAGGCACATGT 58.335 42.857 0.00 0.00 33.96 3.21
2806 3304 2.890945 ACCAGCCATGTAAAGAACCAAC 59.109 45.455 0.00 0.00 0.00 3.77
2835 3333 5.883115 TCAACACCTAACACAAGAACAATCA 59.117 36.000 0.00 0.00 0.00 2.57
3068 3569 8.853077 AGAAGATCAGAACATTGATTTGTACA 57.147 30.769 0.00 0.00 37.90 2.90
3071 3572 6.944290 TGGAGAAGATCAGAACATTGATTTGT 59.056 34.615 0.00 0.00 37.90 2.83
3397 3901 5.753438 CAGTATGTAAGAAATCCGCTAGCAA 59.247 40.000 16.45 1.90 0.00 3.91
3421 3925 8.365399 TGCAACACATAAAGTCATATACTAGC 57.635 34.615 0.00 0.00 37.50 3.42
3429 3933 5.865552 GCTGAAATGCAACACATAAAGTCAT 59.134 36.000 0.00 0.00 38.34 3.06
3430 3934 5.221204 TGCTGAAATGCAACACATAAAGTCA 60.221 36.000 0.00 0.00 38.34 3.41
3468 3972 6.095300 CAGAACCAATTATAACCTGCATCACA 59.905 38.462 0.00 0.00 0.00 3.58
3549 4053 8.478877 ACAGAATCCTACTTGTTATACTTCTGG 58.521 37.037 11.72 0.00 40.67 3.86
3719 4223 1.134995 TGTCTGGTGATCTGATCGCAC 60.135 52.381 26.99 18.78 41.46 5.34
3839 4343 5.526479 AGCAACATCAGTAGCTGTCATAATG 59.474 40.000 0.00 0.00 35.72 1.90
4024 4528 1.358877 CAGTTCGACCAATGCGATGA 58.641 50.000 0.00 0.00 37.64 2.92
4135 4639 2.266055 GGGCTGACCTTCTGTCCG 59.734 66.667 0.00 0.00 43.78 4.79
4309 4814 5.056480 TGCAATAATAATCAGACCCGACTG 58.944 41.667 0.00 0.00 39.02 3.51
4313 4818 6.144402 GCAAAATGCAATAATAATCAGACCCG 59.856 38.462 0.00 0.00 44.26 5.28
4416 4921 5.796935 CACAAAGAAAGGTCAAATATCGCTG 59.203 40.000 0.00 0.00 0.00 5.18
4624 5129 4.082787 ACCCAAAATATGAGTTTCGCTGTG 60.083 41.667 0.00 0.00 0.00 3.66
4644 5149 3.897239 TGTATTGACATTGATGGGACCC 58.103 45.455 2.45 2.45 0.00 4.46
4778 5283 1.276705 TCGCATTAGTGGTGCTGGTAA 59.723 47.619 0.00 0.00 40.37 2.85
4782 5287 3.546815 GCTATTTCGCATTAGTGGTGCTG 60.547 47.826 0.00 0.00 40.37 4.41
4796 5301 3.694072 TGAAATCCCCAACAGCTATTTCG 59.306 43.478 9.96 0.00 38.69 3.46
4810 5315 2.505819 TCTAGGTTCCAGCTGAAATCCC 59.494 50.000 17.39 0.00 33.94 3.85
4813 5318 3.054802 CCACTCTAGGTTCCAGCTGAAAT 60.055 47.826 17.39 3.16 33.94 2.17
4815 5320 1.902508 CCACTCTAGGTTCCAGCTGAA 59.097 52.381 17.39 4.81 0.00 3.02
4894 5400 4.220602 TGACCATCCATACCATACGATCTG 59.779 45.833 0.00 0.00 0.00 2.90
4981 5500 4.391155 TGTCGGGCAAACAGTAAATTAGT 58.609 39.130 0.00 0.00 0.00 2.24
4982 5501 5.560966 ATGTCGGGCAAACAGTAAATTAG 57.439 39.130 0.00 0.00 0.00 1.73
4983 5502 5.587043 CCTATGTCGGGCAAACAGTAAATTA 59.413 40.000 0.00 0.00 0.00 1.40
4984 5503 4.398044 CCTATGTCGGGCAAACAGTAAATT 59.602 41.667 0.00 0.00 0.00 1.82
4985 5504 3.945285 CCTATGTCGGGCAAACAGTAAAT 59.055 43.478 0.00 0.00 0.00 1.40
4986 5505 3.008157 TCCTATGTCGGGCAAACAGTAAA 59.992 43.478 0.00 0.00 0.00 2.01
4987 5506 2.568062 TCCTATGTCGGGCAAACAGTAA 59.432 45.455 0.00 0.00 0.00 2.24
4988 5507 2.181125 TCCTATGTCGGGCAAACAGTA 58.819 47.619 0.00 0.00 0.00 2.74
4989 5508 0.981183 TCCTATGTCGGGCAAACAGT 59.019 50.000 0.00 0.00 0.00 3.55
4990 5509 2.332063 ATCCTATGTCGGGCAAACAG 57.668 50.000 0.00 0.00 0.00 3.16
4991 5510 2.769663 AGTATCCTATGTCGGGCAAACA 59.230 45.455 0.00 0.00 0.00 2.83
4992 5511 3.470645 AGTATCCTATGTCGGGCAAAC 57.529 47.619 0.00 0.00 0.00 2.93
4993 5512 4.497291 AAAGTATCCTATGTCGGGCAAA 57.503 40.909 0.00 0.00 0.00 3.68
5018 5537 7.934665 TGCAGAACTTTTAACTCTGTTATGGTA 59.065 33.333 0.00 0.00 39.05 3.25
5027 5546 4.058817 CCGTCTGCAGAACTTTTAACTCT 58.941 43.478 20.19 0.00 0.00 3.24
5045 5564 4.557205 ACAGAGATGTTTCTTACACCGTC 58.443 43.478 0.00 0.00 40.19 4.79
5049 5568 7.386299 ACATTCTGACAGAGATGTTTCTTACAC 59.614 37.037 19.20 0.00 40.19 2.90
5121 5641 4.853468 TTCATGTAGGGGCATTGACTTA 57.147 40.909 0.00 0.00 0.00 2.24
5214 5734 3.623510 GCTGAGGATGGTACTAACAAAGC 59.376 47.826 0.00 0.00 0.00 3.51
5251 5771 1.834263 AGATCTTGGACCAGTACAGCC 59.166 52.381 0.00 0.00 0.00 4.85
5338 5858 8.498054 AACTCCAAATGACAGATGTAGTATTG 57.502 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.