Multiple sequence alignment - TraesCS7D01G175400

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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 TraesCS7D01G175400 chr7D 100.000 2414 0 0 1 2414 127419980 127422393 0.000000e+00 4458.0
1 TraesCS7D01G175400 chr7D 93.455 382 23 2 643 1022 127281189 127280808 1.250000e-157 566.0
2 TraesCS7D01G175400 chr7D 89.082 403 30 7 254 652 127282877 127282485 2.790000e-134 488.0
3 TraesCS7D01G175400 chr7D 80.106 568 81 14 1033 1600 24427822 24428357 6.260000e-106 394.0
4 TraesCS7D01G175400 chr7D 91.469 211 13 2 459 667 127278791 127278584 3.930000e-73 285.0
5 TraesCS7D01G175400 chr7B 91.085 1806 98 32 627 2414 89208326 89210086 0.000000e+00 2385.0
6 TraesCS7D01G175400 chr7B 92.904 916 49 8 951 1865 88880538 88879638 0.000000e+00 1317.0
7 TraesCS7D01G175400 chr7B 90.187 907 72 7 44 944 88970994 88970099 0.000000e+00 1166.0
8 TraesCS7D01G175400 chr7B 91.667 192 12 4 441 631 89208106 89208294 1.840000e-66 263.0
9 TraesCS7D01G175400 chr7B 84.746 177 7 5 242 417 89207953 89208110 2.480000e-35 159.0
10 TraesCS7D01G175400 chr7A 89.692 1038 63 19 851 1865 127907525 127906509 0.000000e+00 1284.0
11 TraesCS7D01G175400 chr7A 89.326 890 53 14 928 1794 128153884 128154754 0.000000e+00 1079.0
12 TraesCS7D01G175400 chr7A 91.700 759 47 7 158 914 128151939 128152683 0.000000e+00 1038.0
13 TraesCS7D01G175400 chr7A 80.591 541 70 16 1033 1573 24928081 24928586 3.760000e-103 385.0
14 TraesCS7D01G175400 chr4A 91.667 48 4 0 1870 1917 668932502 668932455 1.550000e-07 67.6
15 TraesCS7D01G175400 chr1B 95.238 42 2 0 1880 1921 292341691 292341650 1.550000e-07 67.6
16 TraesCS7D01G175400 chr1B 95.238 42 2 0 1880 1921 292413178 292413137 1.550000e-07 67.6
17 TraesCS7D01G175400 chr5D 97.297 37 1 0 1882 1918 396448861 396448825 2.000000e-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 TraesCS7D01G175400 chr7D 127419980 127422393 2413 False 4458.000000 4458 100.000000 1 2414 1 chr7D.!!$F2 2413
1 TraesCS7D01G175400 chr7D 127278584 127282877 4293 True 446.333333 566 91.335333 254 1022 3 chr7D.!!$R1 768
2 TraesCS7D01G175400 chr7D 24427822 24428357 535 False 394.000000 394 80.106000 1033 1600 1 chr7D.!!$F1 567
3 TraesCS7D01G175400 chr7B 88879638 88880538 900 True 1317.000000 1317 92.904000 951 1865 1 chr7B.!!$R1 914
4 TraesCS7D01G175400 chr7B 88970099 88970994 895 True 1166.000000 1166 90.187000 44 944 1 chr7B.!!$R2 900
5 TraesCS7D01G175400 chr7B 89207953 89210086 2133 False 935.666667 2385 89.166000 242 2414 3 chr7B.!!$F1 2172
6 TraesCS7D01G175400 chr7A 127906509 127907525 1016 True 1284.000000 1284 89.692000 851 1865 1 chr7A.!!$R1 1014
7 TraesCS7D01G175400 chr7A 128151939 128154754 2815 False 1058.500000 1079 90.513000 158 1794 2 chr7A.!!$F2 1636
8 TraesCS7D01G175400 chr7A 24928081 24928586 505 False 385.000000 385 80.591000 1033 1573 1 chr7A.!!$F1 540

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
22 23 0.665298 GCTTTGGCTCGAATCCCATC 59.335 55.0 0.57 0.0 35.22 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 6045 0.673644 ATTCTCCTCACCCGTTTGCG 60.674 55.0 0.0 0.0 37.95 4.85 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
18 19 2.101700 CTGGCTTTGGCTCGAATCC 58.898 57.895 0.00 0.00 38.73 3.01
19 20 1.378514 TGGCTTTGGCTCGAATCCC 60.379 57.895 1.40 0.00 38.73 3.85
20 21 1.378514 GGCTTTGGCTCGAATCCCA 60.379 57.895 1.40 0.00 38.73 4.37
21 22 0.753111 GGCTTTGGCTCGAATCCCAT 60.753 55.000 0.57 0.00 38.73 4.00
22 23 0.665298 GCTTTGGCTCGAATCCCATC 59.335 55.000 0.57 0.00 35.22 3.51
23 24 1.748591 GCTTTGGCTCGAATCCCATCT 60.749 52.381 0.57 0.00 35.22 2.90
24 25 2.216898 CTTTGGCTCGAATCCCATCTC 58.783 52.381 0.57 0.00 0.00 2.75
25 26 1.203237 TTGGCTCGAATCCCATCTCA 58.797 50.000 0.57 0.00 0.00 3.27
26 27 1.427809 TGGCTCGAATCCCATCTCAT 58.572 50.000 1.40 0.00 0.00 2.90
27 28 1.345741 TGGCTCGAATCCCATCTCATC 59.654 52.381 1.40 0.00 0.00 2.92
28 29 1.622811 GGCTCGAATCCCATCTCATCT 59.377 52.381 0.00 0.00 0.00 2.90
29 30 2.353605 GGCTCGAATCCCATCTCATCTC 60.354 54.545 0.00 0.00 0.00 2.75
30 31 2.353605 GCTCGAATCCCATCTCATCTCC 60.354 54.545 0.00 0.00 0.00 3.71
31 32 2.896044 CTCGAATCCCATCTCATCTCCA 59.104 50.000 0.00 0.00 0.00 3.86
32 33 2.630098 TCGAATCCCATCTCATCTCCAC 59.370 50.000 0.00 0.00 0.00 4.02
33 34 2.366590 CGAATCCCATCTCATCTCCACA 59.633 50.000 0.00 0.00 0.00 4.17
34 35 3.007723 CGAATCCCATCTCATCTCCACAT 59.992 47.826 0.00 0.00 0.00 3.21
35 36 4.325119 GAATCCCATCTCATCTCCACATG 58.675 47.826 0.00 0.00 0.00 3.21
36 37 2.767972 TCCCATCTCATCTCCACATGT 58.232 47.619 0.00 0.00 0.00 3.21
37 38 2.436911 TCCCATCTCATCTCCACATGTG 59.563 50.000 19.31 19.31 0.00 3.21
38 39 2.436911 CCCATCTCATCTCCACATGTGA 59.563 50.000 27.46 12.04 32.34 3.58
39 40 3.072622 CCCATCTCATCTCCACATGTGAT 59.927 47.826 27.46 10.04 37.44 3.06
40 41 4.065789 CCATCTCATCTCCACATGTGATG 58.934 47.826 27.46 20.98 45.81 3.07
41 42 4.444449 CCATCTCATCTCCACATGTGATGT 60.444 45.833 27.46 7.25 45.29 3.06
42 43 4.831674 TCTCATCTCCACATGTGATGTT 57.168 40.909 27.46 10.90 42.70 2.71
51 52 5.988287 TCCACATGTGATGTTGCTTCTATA 58.012 37.500 27.46 0.00 42.70 1.31
58 59 4.058124 TGATGTTGCTTCTATATCGCCAC 58.942 43.478 0.00 0.00 0.00 5.01
101 102 3.704566 TCTAGTATTCACCCAATGTCGCT 59.295 43.478 0.00 0.00 0.00 4.93
107 108 4.955811 TTCACCCAATGTCGCTATATCT 57.044 40.909 0.00 0.00 0.00 1.98
118 119 6.024552 TGTCGCTATATCTACATCATTGCA 57.975 37.500 0.00 0.00 0.00 4.08
119 120 6.633856 TGTCGCTATATCTACATCATTGCAT 58.366 36.000 0.00 0.00 0.00 3.96
136 139 1.002134 ATGCATATACCTGGGCCGC 60.002 57.895 0.00 0.00 0.00 6.53
155 158 2.325082 GCCGCTTCCGTGTTGTCAT 61.325 57.895 0.00 0.00 0.00 3.06
162 165 2.390599 CCGTGTTGTCATGGGCTCG 61.391 63.158 0.00 0.00 44.55 5.03
185 188 5.484715 GGGATCGGGTTAATCATAATCGAA 58.515 41.667 0.00 0.00 35.13 3.71
205 208 6.390721 TCGAAGAAGTTGAGACATAAAGAGG 58.609 40.000 0.00 0.00 0.00 3.69
213 216 8.324191 AGTTGAGACATAAAGAGGATATTCCA 57.676 34.615 0.00 0.00 39.61 3.53
269 272 5.126222 TGTCAACTAGAAATTGGCAAACACA 59.874 36.000 3.01 0.00 38.67 3.72
325 330 1.098050 ATGGCCTCACGAGCATTTTC 58.902 50.000 3.32 0.00 0.00 2.29
371 376 3.667497 GAGACACACTCCACAATCTCA 57.333 47.619 0.00 0.00 39.53 3.27
423 428 7.315142 GTGAAACTCCATATGAAATTTGAGCA 58.685 34.615 3.65 0.00 0.00 4.26
450 455 6.334989 ACTAATCGAACACGGAAATACATGA 58.665 36.000 0.00 0.00 0.00 3.07
471 476 1.747745 GCGCGGGAGGGTTTACAAT 60.748 57.895 8.83 0.00 45.69 2.71
585 591 4.035091 TGCATGGAATATACGTTTCTGTGC 59.965 41.667 15.36 15.36 35.73 4.57
605 611 3.684305 TGCTCATTTACTTCATCCGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
612 619 5.821516 TTACTTCATCCGTGTGTGTTTTT 57.178 34.783 0.00 0.00 0.00 1.94
645 689 7.307042 GCAATGTAGTACTATGCTCATCAACAG 60.307 40.741 16.34 1.74 34.29 3.16
707 2056 2.472695 TGCTCATTTTCTAGCACCGT 57.527 45.000 0.00 0.00 43.56 4.83
1173 5037 1.002868 CTCCACCAACCAGCTCCAG 60.003 63.158 0.00 0.00 0.00 3.86
1174 5038 2.674380 CCACCAACCAGCTCCAGC 60.674 66.667 0.00 0.00 42.49 4.85
1175 5039 2.674380 CACCAACCAGCTCCAGCC 60.674 66.667 0.00 0.00 43.38 4.85
1176 5040 2.856000 ACCAACCAGCTCCAGCCT 60.856 61.111 0.00 0.00 43.38 4.58
1177 5041 2.045536 CCAACCAGCTCCAGCCTC 60.046 66.667 0.00 0.00 43.38 4.70
1178 5042 2.045536 CAACCAGCTCCAGCCTCC 60.046 66.667 0.00 0.00 43.38 4.30
1179 5043 2.530151 AACCAGCTCCAGCCTCCA 60.530 61.111 0.00 0.00 43.38 3.86
1267 5131 2.037367 TACAGCTCCCTCACGGCT 59.963 61.111 0.00 0.00 36.70 5.52
1395 5266 2.654877 GTCGGCCTTCTTCGACCA 59.345 61.111 0.00 0.00 46.79 4.02
1403 5274 2.329379 CCTTCTTCGACCAGAGTTTCG 58.671 52.381 0.00 0.00 36.55 3.46
1429 5300 1.003112 TAACTCCGGCGGCAACAAT 60.003 52.632 23.83 6.39 0.00 2.71
1469 5340 3.200593 CTCCCATGAGCGTGCTGC 61.201 66.667 0.00 0.00 46.98 5.25
1490 5361 3.961414 GGGCCCAAGTCCGGTTCA 61.961 66.667 19.95 0.00 0.00 3.18
1769 5822 5.843019 TTCTTCTGGTTTCCCTACATCTT 57.157 39.130 0.00 0.00 0.00 2.40
1867 5921 2.079925 AGAAATGCAGAGAGTTTCGGC 58.920 47.619 0.00 0.00 45.79 5.54
1868 5922 1.131315 GAAATGCAGAGAGTTTCGGCC 59.869 52.381 3.42 0.00 45.10 6.13
1872 5926 1.446272 CAGAGAGTTTCGGCCCGTC 60.446 63.158 1.63 0.00 0.00 4.79
1887 5941 2.082231 CCCGTCTAGAAGTCAGTCGAA 58.918 52.381 4.93 0.00 0.00 3.71
1941 5995 1.536284 CGGACCTCCTATTTGACGCTC 60.536 57.143 0.00 0.00 0.00 5.03
1947 6001 3.002791 CTCCTATTTGACGCTCTTTGCA 58.997 45.455 0.00 0.00 43.06 4.08
1949 6003 4.009675 TCCTATTTGACGCTCTTTGCATT 58.990 39.130 0.00 0.00 43.06 3.56
1954 6008 1.946081 TGACGCTCTTTGCATTGAACA 59.054 42.857 0.00 0.00 43.06 3.18
1955 6009 2.031769 TGACGCTCTTTGCATTGAACAG 60.032 45.455 0.00 0.00 43.06 3.16
1956 6010 2.221169 ACGCTCTTTGCATTGAACAGA 58.779 42.857 0.00 0.00 43.06 3.41
1957 6011 2.618241 ACGCTCTTTGCATTGAACAGAA 59.382 40.909 0.00 0.00 43.06 3.02
1958 6012 3.231965 CGCTCTTTGCATTGAACAGAAG 58.768 45.455 0.00 0.00 43.06 2.85
1959 6013 3.572584 GCTCTTTGCATTGAACAGAAGG 58.427 45.455 0.00 0.00 42.31 3.46
1960 6014 3.613432 GCTCTTTGCATTGAACAGAAGGG 60.613 47.826 0.00 0.00 42.31 3.95
1961 6015 3.565307 TCTTTGCATTGAACAGAAGGGT 58.435 40.909 0.00 0.00 0.00 4.34
1962 6016 3.960102 TCTTTGCATTGAACAGAAGGGTT 59.040 39.130 0.00 0.00 0.00 4.11
1963 6017 3.731652 TTGCATTGAACAGAAGGGTTG 57.268 42.857 0.00 0.00 0.00 3.77
1964 6018 1.340889 TGCATTGAACAGAAGGGTTGC 59.659 47.619 0.00 0.00 0.00 4.17
1965 6019 1.337167 GCATTGAACAGAAGGGTTGCC 60.337 52.381 0.00 0.00 0.00 4.52
1966 6020 1.068333 CATTGAACAGAAGGGTTGCCG 60.068 52.381 0.00 0.00 0.00 5.69
1967 6021 1.452145 TTGAACAGAAGGGTTGCCGC 61.452 55.000 0.00 0.00 0.00 6.53
1968 6022 1.896660 GAACAGAAGGGTTGCCGCA 60.897 57.895 0.00 0.00 0.00 5.69
1969 6023 2.130073 GAACAGAAGGGTTGCCGCAC 62.130 60.000 0.00 0.00 0.00 5.34
1970 6024 2.594303 CAGAAGGGTTGCCGCACA 60.594 61.111 0.00 0.00 0.00 4.57
1971 6025 2.281761 AGAAGGGTTGCCGCACAG 60.282 61.111 0.00 0.00 0.00 3.66
1972 6026 3.365265 GAAGGGTTGCCGCACAGG 61.365 66.667 0.00 0.00 44.97 4.00
1973 6027 4.974721 AAGGGTTGCCGCACAGGG 62.975 66.667 0.00 0.00 41.48 4.45
2011 6068 1.534729 GCAAACGGGTGAGGAGAATT 58.465 50.000 0.00 0.00 0.00 2.17
2048 6105 6.287107 AGCCGAATGTATTTTATCAAGTCG 57.713 37.500 0.00 0.00 0.00 4.18
2234 6291 7.428826 ACAATTGCAAAAACTTTTTGAAACCA 58.571 26.923 24.91 13.43 30.39 3.67
2235 6292 8.087136 ACAATTGCAAAAACTTTTTGAAACCAT 58.913 25.926 24.91 11.76 30.39 3.55
2236 6293 8.373992 CAATTGCAAAAACTTTTTGAAACCATG 58.626 29.630 24.91 17.45 30.39 3.66
2237 6294 6.808008 TGCAAAAACTTTTTGAAACCATGA 57.192 29.167 24.91 1.67 0.00 3.07
2239 6296 7.080724 TGCAAAAACTTTTTGAAACCATGAAC 58.919 30.769 24.91 8.38 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.379642 GGGATTCGAGCCAAAGCCAG 61.380 60.000 8.43 0.00 41.25 4.85
1 2 1.378514 GGGATTCGAGCCAAAGCCA 60.379 57.895 8.43 0.00 41.25 4.75
2 3 0.753111 ATGGGATTCGAGCCAAAGCC 60.753 55.000 8.43 0.00 41.25 4.35
3 4 0.665298 GATGGGATTCGAGCCAAAGC 59.335 55.000 8.43 0.00 40.32 3.51
4 5 2.216898 GAGATGGGATTCGAGCCAAAG 58.783 52.381 8.43 0.00 0.00 2.77
5 6 1.559219 TGAGATGGGATTCGAGCCAAA 59.441 47.619 8.43 0.00 0.00 3.28
6 7 1.203237 TGAGATGGGATTCGAGCCAA 58.797 50.000 8.43 0.00 0.00 4.52
7 8 1.345741 GATGAGATGGGATTCGAGCCA 59.654 52.381 8.43 0.00 0.00 4.75
8 9 1.622811 AGATGAGATGGGATTCGAGCC 59.377 52.381 0.00 0.00 0.00 4.70
9 10 2.353605 GGAGATGAGATGGGATTCGAGC 60.354 54.545 0.00 0.00 0.00 5.03
10 11 2.896044 TGGAGATGAGATGGGATTCGAG 59.104 50.000 0.00 0.00 0.00 4.04
11 12 2.630098 GTGGAGATGAGATGGGATTCGA 59.370 50.000 0.00 0.00 0.00 3.71
12 13 2.366590 TGTGGAGATGAGATGGGATTCG 59.633 50.000 0.00 0.00 0.00 3.34
13 14 4.202440 ACATGTGGAGATGAGATGGGATTC 60.202 45.833 0.00 0.00 0.00 2.52
14 15 3.720526 ACATGTGGAGATGAGATGGGATT 59.279 43.478 0.00 0.00 0.00 3.01
15 16 3.072622 CACATGTGGAGATGAGATGGGAT 59.927 47.826 18.51 0.00 0.00 3.85
16 17 2.436911 CACATGTGGAGATGAGATGGGA 59.563 50.000 18.51 0.00 0.00 4.37
17 18 2.436911 TCACATGTGGAGATGAGATGGG 59.563 50.000 25.16 0.00 0.00 4.00
18 19 3.832615 TCACATGTGGAGATGAGATGG 57.167 47.619 25.16 0.00 0.00 3.51
20 21 5.123936 CAACATCACATGTGGAGATGAGAT 58.876 41.667 24.89 9.18 44.07 2.75
21 22 4.510571 CAACATCACATGTGGAGATGAGA 58.489 43.478 24.89 7.39 44.07 3.27
22 23 3.064958 GCAACATCACATGTGGAGATGAG 59.935 47.826 24.89 18.64 44.07 2.90
23 24 3.011818 GCAACATCACATGTGGAGATGA 58.988 45.455 24.89 8.70 44.07 2.92
24 25 3.014623 AGCAACATCACATGTGGAGATG 58.985 45.455 25.16 21.77 44.07 2.90
25 26 3.361281 AGCAACATCACATGTGGAGAT 57.639 42.857 25.16 9.27 44.07 2.75
26 27 2.865119 AGCAACATCACATGTGGAGA 57.135 45.000 25.16 7.10 44.07 3.71
27 28 3.079578 AGAAGCAACATCACATGTGGAG 58.920 45.455 25.16 19.09 44.07 3.86
28 29 3.144657 AGAAGCAACATCACATGTGGA 57.855 42.857 25.16 12.59 44.07 4.02
29 30 6.347160 CGATATAGAAGCAACATCACATGTGG 60.347 42.308 25.16 12.86 44.07 4.17
30 31 6.587651 CGATATAGAAGCAACATCACATGTG 58.412 40.000 20.18 20.18 44.07 3.21
32 33 5.390251 GGCGATATAGAAGCAACATCACATG 60.390 44.000 0.00 0.00 0.00 3.21
33 34 4.692625 GGCGATATAGAAGCAACATCACAT 59.307 41.667 0.00 0.00 0.00 3.21
34 35 4.058124 GGCGATATAGAAGCAACATCACA 58.942 43.478 0.00 0.00 0.00 3.58
35 36 4.058124 TGGCGATATAGAAGCAACATCAC 58.942 43.478 0.00 0.00 0.00 3.06
36 37 4.058124 GTGGCGATATAGAAGCAACATCA 58.942 43.478 0.00 0.00 35.06 3.07
37 38 3.433615 GGTGGCGATATAGAAGCAACATC 59.566 47.826 6.69 0.00 36.59 3.06
38 39 3.403038 GGTGGCGATATAGAAGCAACAT 58.597 45.455 6.69 0.00 36.59 2.71
39 40 2.801699 CGGTGGCGATATAGAAGCAACA 60.802 50.000 6.69 0.00 36.59 3.33
40 41 1.792949 CGGTGGCGATATAGAAGCAAC 59.207 52.381 0.00 0.00 34.24 4.17
41 42 1.270094 CCGGTGGCGATATAGAAGCAA 60.270 52.381 0.00 0.00 0.00 3.91
42 43 0.317160 CCGGTGGCGATATAGAAGCA 59.683 55.000 0.00 0.00 0.00 3.91
58 59 0.108138 AAGATTCAAGTCGGAGCCGG 60.108 55.000 9.29 0.00 40.25 6.13
68 69 7.331026 TGGGTGAATACTAGACAAGATTCAAG 58.669 38.462 0.00 0.00 39.37 3.02
118 119 1.002134 GCGGCCCAGGTATATGCAT 60.002 57.895 3.79 3.79 0.00 3.96
119 120 2.429930 GCGGCCCAGGTATATGCA 59.570 61.111 0.00 0.00 0.00 3.96
136 139 4.072088 GACAACACGGAAGCGGCG 62.072 66.667 0.51 0.51 0.00 6.46
140 143 1.875963 CCCATGACAACACGGAAGC 59.124 57.895 0.00 0.00 30.08 3.86
147 150 1.561769 ATCCCGAGCCCATGACAACA 61.562 55.000 0.00 0.00 0.00 3.33
155 158 3.682644 TAACCCGATCCCGAGCCCA 62.683 63.158 0.00 0.00 38.22 5.36
162 165 5.080969 TCGATTATGATTAACCCGATCCC 57.919 43.478 0.00 0.00 0.00 3.85
269 272 5.220662 CGCATCCACTCGTTTCATTTTAGAT 60.221 40.000 0.00 0.00 0.00 1.98
371 376 6.937436 AAAAACACTTATCGAGAAGGTTGT 57.063 33.333 22.72 15.78 0.00 3.32
395 400 8.634335 TCAAATTTCATATGGAGTTTCACTCA 57.366 30.769 1.60 0.00 46.79 3.41
423 428 7.424227 TGTATTTCCGTGTTCGATTAGTTTT 57.576 32.000 0.00 0.00 39.71 2.43
450 455 1.747745 GTAAACCCTCCCGCGCATT 60.748 57.895 8.75 0.00 0.00 3.56
471 476 5.151297 TGAGCTGATGATGTGTTGTAAGA 57.849 39.130 0.00 0.00 0.00 2.10
512 517 5.818136 TGTAGAAGCTTGCAAATACATCC 57.182 39.130 2.10 0.00 0.00 3.51
585 591 4.690748 ACACACACGGATGAAGTAAATGAG 59.309 41.667 0.00 0.00 0.00 2.90
612 619 6.582636 AGCATAGTACTACATTGCAGCTTAA 58.417 36.000 22.63 0.00 32.77 1.85
624 631 6.150396 ACCTGTTGATGAGCATAGTACTAC 57.850 41.667 4.31 0.00 0.00 2.73
645 689 6.686630 TCAAACATTCCACAACATCATAACC 58.313 36.000 0.00 0.00 0.00 2.85
707 2056 5.265191 AGCTCAGAACAACCATCTACTCTA 58.735 41.667 0.00 0.00 0.00 2.43
752 2102 4.429212 TGCGATCACCGTCCCGTG 62.429 66.667 0.00 0.00 41.15 4.94
767 2117 1.101635 GGAGTAATTTCCCCCGCTGC 61.102 60.000 0.00 0.00 0.00 5.25
776 2126 2.349886 CACAGCAGAGCGGAGTAATTTC 59.650 50.000 0.00 0.00 0.00 2.17
900 2258 0.321830 ATGGTAACGGGGTGAAACGG 60.322 55.000 0.00 0.00 37.13 4.44
1267 5131 4.063967 CTGTACACCCGCAGCCGA 62.064 66.667 0.00 0.00 36.29 5.54
1395 5266 3.509184 GGAGTTACCTACCACGAAACTCT 59.491 47.826 11.88 0.00 43.48 3.24
1403 5274 1.140375 CGCCGGAGTTACCTACCAC 59.860 63.158 5.05 0.00 36.31 4.16
1408 5279 3.315949 TTGCCGCCGGAGTTACCT 61.316 61.111 7.68 0.00 36.31 3.08
1409 5280 3.122971 GTTGCCGCCGGAGTTACC 61.123 66.667 7.68 0.00 0.00 2.85
1469 5340 4.101448 CCGGACTTGGGCCCTCAG 62.101 72.222 25.70 21.02 0.00 3.35
1490 5361 2.609610 TAGGCCAGCCCGACCTTT 60.610 61.111 5.01 0.00 39.21 3.11
1832 5886 5.001232 TGCATTTCTTGGTGGAGTAAGTAC 58.999 41.667 0.00 0.00 0.00 2.73
1867 5921 1.735386 TCGACTGACTTCTAGACGGG 58.265 55.000 0.86 0.00 34.86 5.28
1868 5922 3.374367 TCATTCGACTGACTTCTAGACGG 59.626 47.826 0.65 0.00 34.86 4.79
1872 5926 5.811399 AGTCTCATTCGACTGACTTCTAG 57.189 43.478 0.65 0.00 42.39 2.43
1922 5976 1.757699 AGAGCGTCAAATAGGAGGTCC 59.242 52.381 0.00 0.00 0.00 4.46
1941 5995 4.053295 CAACCCTTCTGTTCAATGCAAAG 58.947 43.478 0.00 0.00 0.00 2.77
1947 6001 1.247567 CGGCAACCCTTCTGTTCAAT 58.752 50.000 0.00 0.00 0.00 2.57
1949 6003 1.896660 GCGGCAACCCTTCTGTTCA 60.897 57.895 0.00 0.00 0.00 3.18
1954 6008 2.281761 CTGTGCGGCAACCCTTCT 60.282 61.111 3.23 0.00 0.00 2.85
1955 6009 3.365265 CCTGTGCGGCAACCCTTC 61.365 66.667 3.23 0.00 0.00 3.46
1956 6010 4.974721 CCCTGTGCGGCAACCCTT 62.975 66.667 3.23 0.00 0.00 3.95
1977 6031 3.186106 TGCGGACGCATCCAAATG 58.814 55.556 16.11 0.00 46.67 2.32
1991 6045 0.673644 ATTCTCCTCACCCGTTTGCG 60.674 55.000 0.00 0.00 37.95 4.85
2005 6059 5.404096 GGCTCGCTAGATTACCTAATTCTC 58.596 45.833 0.00 0.00 0.00 2.87
2011 6068 2.556144 TCGGCTCGCTAGATTACCTA 57.444 50.000 0.00 0.00 0.00 3.08
2092 6149 1.063027 CGCTGTAGTACATCGGTTCGA 59.937 52.381 16.77 0.00 41.13 3.71
2210 6267 7.864307 TGGTTTCAAAAAGTTTTTGCAATTG 57.136 28.000 28.56 11.52 0.00 2.32
2215 6272 7.304735 AGTTCATGGTTTCAAAAAGTTTTTGC 58.695 30.769 28.56 18.24 0.00 3.68
2260 6319 5.699915 TCCAAAATATGTTTGTGTTGCCATG 59.300 36.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.