Multiple sequence alignment - TraesCS5D01G370200

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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 TraesCS5D01G370200 chr5D 100.000 6712 0 0 1 6712 445197950 445204661 0.000000e+00 12395
1 TraesCS5D01G370200 chr5A 97.775 4765 89 9 1954 6712 562536873 562541626 0.000000e+00 8196
2 TraesCS5D01G370200 chr5A 95.302 1192 24 15 752 1932 562535713 562536883 0.000000e+00 1862
3 TraesCS5D01G370200 chr5A 89.609 818 50 16 1 809 562534941 562535732 0.000000e+00 1007
4 TraesCS5D01G370200 chr5B 96.708 4313 108 11 1954 6257 542927823 542932110 0.000000e+00 7147
5 TraesCS5D01G370200 chr5B 92.456 1710 78 32 244 1932 542926154 542927833 0.000000e+00 2396
6 TraesCS5D01G370200 chr5B 95.588 68 3 0 6338 6405 542932279 542932346 7.120000e-20 110
7 TraesCS5D01G370200 chr5B 96.610 59 2 0 6403 6461 542932439 542932497 1.540000e-16 99
8 TraesCS5D01G370200 chr3B 83.400 3476 544 27 2169 5629 80167902 80164445 0.000000e+00 3192
9 TraesCS5D01G370200 chr3B 86.194 536 64 7 1211 1738 80168871 80168338 7.550000e-159 571
10 TraesCS5D01G370200 chr3A 84.054 1988 301 12 2169 4151 63563411 63561435 0.000000e+00 1901
11 TraesCS5D01G370200 chr3A 83.844 1436 224 7 4201 5630 63561416 63559983 0.000000e+00 1360
12 TraesCS5D01G370200 chr3A 85.448 536 68 8 1211 1738 63564319 63563786 3.540000e-152 549
13 TraesCS5D01G370200 chr3D 82.339 1274 218 6 4362 5630 50552479 50551208 0.000000e+00 1099
14 TraesCS5D01G370200 chr3D 83.453 417 59 8 1211 1619 50552889 50552475 4.910000e-101 379


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 TraesCS5D01G370200 chr5D 445197950 445204661 6711 False 12395.000000 12395 100.000000 1 6712 1 chr5D.!!$F1 6711
1 TraesCS5D01G370200 chr5A 562534941 562541626 6685 False 3688.333333 8196 94.228667 1 6712 3 chr5A.!!$F1 6711
2 TraesCS5D01G370200 chr5B 542926154 542932497 6343 False 2438.000000 7147 95.340500 244 6461 4 chr5B.!!$F1 6217
3 TraesCS5D01G370200 chr3B 80164445 80168871 4426 True 1881.500000 3192 84.797000 1211 5629 2 chr3B.!!$R1 4418
4 TraesCS5D01G370200 chr3A 63559983 63564319 4336 True 1270.000000 1901 84.448667 1211 5630 3 chr3A.!!$R1 4419
5 TraesCS5D01G370200 chr3D 50551208 50552889 1681 True 739.000000 1099 82.896000 1211 5630 2 chr3D.!!$R1 4419

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
723 727 0.251341 ACCTTCTTCTGGGCGCAAAT 60.251 50.000 10.83 0.0 0.00 2.32 F
729 745 0.455410 TTCTGGGCGCAAATGTATGC 59.545 50.000 10.83 0.0 42.94 3.14 F
1942 2023 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1944 2025 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1950 2031 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1956 2037 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1958 2039 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1964 2045 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
2846 3006 1.737793 GCATTCCCTGTAAACAGTCCG 59.262 52.381 9.17 0.0 42.27 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2014 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.0 3.72 R
1939 2020 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.0 3.72 R
2846 3006 4.232221 CAAGGACATTCAATGCAGACAAC 58.768 43.478 0.00 0.0 0.0 3.32 R
3926 4086 5.486775 AGCTATTACAGGGTCATCAGCATAT 59.513 40.000 0.00 0.0 0.0 1.78 R
3959 4119 2.224281 TGCCATTCTAGCCTTGGTATCG 60.224 50.000 7.12 0.0 32.9 2.92 R
5061 5230 0.798776 GCGATGCCTTCCAATATCCG 59.201 55.000 0.00 0.0 0.0 4.18 R
5201 5370 2.775911 TCAACCATGCAGAAGAGGAG 57.224 50.000 0.00 0.0 0.0 3.69 R
5285 5454 5.012893 ACCTCCATGTTTCTGAAATCCTTC 58.987 41.667 6.06 0.0 0.0 3.46 R
5713 5885 0.878523 TCGACGTTCAGCAGTTTGGG 60.879 55.000 0.00 0.0 0.0 4.12 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
41 42 2.264480 CGGACCCACATGCTTCGA 59.736 61.111 0.00 0.00 0.00 3.71
79 80 5.434408 TCTCATGTGGATTCCTTCATCAAG 58.566 41.667 3.95 8.44 0.00 3.02
231 232 1.468908 GCACACTCTCCATCTCACTCG 60.469 57.143 0.00 0.00 0.00 4.18
234 235 1.358402 CTCTCCATCTCACTCGCGG 59.642 63.158 6.13 0.00 0.00 6.46
339 340 9.485206 TCTACATAAGTACAAGAAACCTGAAAC 57.515 33.333 0.00 0.00 0.00 2.78
356 357 6.001460 CCTGAAACTTAGTATTTGACCACCA 58.999 40.000 0.00 0.00 0.00 4.17
357 358 6.149474 CCTGAAACTTAGTATTTGACCACCAG 59.851 42.308 0.00 0.00 0.00 4.00
358 359 6.597562 TGAAACTTAGTATTTGACCACCAGT 58.402 36.000 0.00 0.00 0.00 4.00
361 363 6.877611 ACTTAGTATTTGACCACCAGTTTG 57.122 37.500 0.00 0.00 0.00 2.93
451 453 5.906113 AGGCTATCGATATGTGGTAGAAG 57.094 43.478 5.40 0.00 0.00 2.85
541 543 3.929610 GCTGTCTTCTTCTGTCATACCAC 59.070 47.826 0.00 0.00 0.00 4.16
591 593 2.210116 CGATTCAAACCCTATCCCACG 58.790 52.381 0.00 0.00 0.00 4.94
640 643 7.665974 TCCAGTCACATACATAACTCGATCTAT 59.334 37.037 0.00 0.00 0.00 1.98
700 704 4.095782 TCTCGACACATATGATGTTCGTGA 59.904 41.667 10.38 13.23 42.70 4.35
714 718 6.368791 TGATGTTCGTGATAAACCTTCTTCTG 59.631 38.462 0.00 0.00 0.00 3.02
716 720 4.202245 TCGTGATAAACCTTCTTCTGGG 57.798 45.455 0.00 0.00 0.00 4.45
719 723 1.671328 GATAAACCTTCTTCTGGGCGC 59.329 52.381 0.00 0.00 0.00 6.53
720 724 0.398696 TAAACCTTCTTCTGGGCGCA 59.601 50.000 10.83 2.47 0.00 6.09
722 726 0.467290 AACCTTCTTCTGGGCGCAAA 60.467 50.000 10.83 1.83 0.00 3.68
723 727 0.251341 ACCTTCTTCTGGGCGCAAAT 60.251 50.000 10.83 0.00 0.00 2.32
729 745 0.455410 TTCTGGGCGCAAATGTATGC 59.545 50.000 10.83 0.00 42.94 3.14
748 764 7.924940 TGTATGCGCTACATAAATCAATTCAA 58.075 30.769 9.73 0.00 42.88 2.69
749 765 8.069574 TGTATGCGCTACATAAATCAATTCAAG 58.930 33.333 9.73 0.00 42.88 3.02
759 775 5.911378 AAATCAATTCAAGAGGCCTCTTC 57.089 39.130 39.60 13.95 46.13 2.87
760 776 4.581309 ATCAATTCAAGAGGCCTCTTCA 57.419 40.909 39.60 29.48 46.13 3.02
763 779 6.065976 TCAATTCAAGAGGCCTCTTCAATA 57.934 37.500 36.01 23.34 46.13 1.90
764 780 6.666678 TCAATTCAAGAGGCCTCTTCAATAT 58.333 36.000 36.01 25.04 46.13 1.28
767 783 5.287674 TCAAGAGGCCTCTTCAATATGAG 57.712 43.478 39.60 26.70 46.13 2.90
881 941 1.604604 CACCAAACTCATTCGGTGGT 58.395 50.000 0.00 0.00 44.26 4.16
882 942 2.773487 CACCAAACTCATTCGGTGGTA 58.227 47.619 0.00 0.00 44.26 3.25
883 943 2.482721 CACCAAACTCATTCGGTGGTAC 59.517 50.000 0.00 0.00 44.26 3.34
914 974 2.614229 GGAGTTGAGCTTTGGTCTCTCC 60.614 54.545 17.45 17.45 40.74 3.71
987 1053 1.370437 CGCCCAGATCAGATCCCAG 59.630 63.158 6.80 0.00 0.00 4.45
1729 1808 1.651240 CCCGCCTTGCTGACATTGAG 61.651 60.000 0.00 0.00 0.00 3.02
1806 1885 9.260002 CCCACCAATTACATTTTTATATTGCTC 57.740 33.333 0.00 0.00 0.00 4.26
1852 1933 5.560724 TGCTGCTCTGTTCCTTTATTACTT 58.439 37.500 0.00 0.00 0.00 2.24
1878 1959 8.268850 AGTATTGTGATAGTTTAACTTGCAGG 57.731 34.615 1.94 0.00 0.00 4.85
1932 2013 8.479313 ACTATACTTATTCATGTGTGTGTGTG 57.521 34.615 0.00 0.00 0.00 3.82
1933 2014 8.094548 ACTATACTTATTCATGTGTGTGTGTGT 58.905 33.333 0.00 0.00 0.00 3.72
1934 2015 5.422666 ACTTATTCATGTGTGTGTGTGTG 57.577 39.130 0.00 0.00 0.00 3.82
1935 2016 4.881273 ACTTATTCATGTGTGTGTGTGTGT 59.119 37.500 0.00 0.00 0.00 3.72
1936 2017 3.696281 ATTCATGTGTGTGTGTGTGTG 57.304 42.857 0.00 0.00 0.00 3.82
1937 2018 2.106477 TCATGTGTGTGTGTGTGTGT 57.894 45.000 0.00 0.00 0.00 3.72
1938 2019 1.736681 TCATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
1939 2020 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
1940 2021 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1941 2022 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1942 2023 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1943 2024 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1944 2025 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1945 2026 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1946 2027 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1947 2028 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1948 2029 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1949 2030 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1950 2031 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1951 2032 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1952 2033 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1953 2034 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1954 2035 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1955 2036 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1956 2037 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1957 2038 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1958 2039 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1959 2040 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1960 2041 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1961 2042 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1962 2043 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1963 2044 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1964 2045 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2037 2118 2.052891 CAATTTGACCGTGTGCACATG 58.947 47.619 28.62 28.62 0.00 3.21
2075 2192 2.550830 ACTTGCCTTGAGTACCTGTG 57.449 50.000 0.00 0.00 0.00 3.66
2183 2343 4.154918 CCACAGATTAGCAAGAACCAAGAC 59.845 45.833 0.00 0.00 0.00 3.01
2303 2463 2.839632 ATGATGGAGCCGCTCGGA 60.840 61.111 14.21 3.82 37.50 4.55
2357 2517 2.093235 GTGCTCCCTCTTGAACATAGCT 60.093 50.000 0.00 0.00 0.00 3.32
2846 3006 1.737793 GCATTCCCTGTAAACAGTCCG 59.262 52.381 9.17 0.00 42.27 4.79
3926 4086 5.651387 TCACCACTTTGTTGAACAATTCA 57.349 34.783 11.97 0.00 38.00 2.57
3959 4119 3.288092 CCCTGTAATAGCTTTTGGGGTC 58.712 50.000 0.00 0.00 0.00 4.46
5003 5172 2.672961 TGAACCTAATGGCTGACTCG 57.327 50.000 0.00 0.00 36.63 4.18
5061 5230 4.767255 CTGGTGGCGAGGCAGACC 62.767 72.222 0.00 0.00 34.47 3.85
5075 5244 1.884235 CAGACCGGATATTGGAAGGC 58.116 55.000 9.46 0.00 0.00 4.35
5201 5370 9.494271 TGCTTAATAGTTGATGGAATATCAGTC 57.506 33.333 0.00 0.00 0.00 3.51
5285 5454 2.724977 TTGCTCAGAGTTACTCACCG 57.275 50.000 15.23 2.84 32.06 4.94
5372 5541 5.023533 TGCAGTCACTTAAAGACTTGTCT 57.976 39.130 7.34 0.00 43.47 3.41
5543 5715 4.481368 TGGTGTACTGTCAAAGACAAGT 57.519 40.909 1.19 4.83 42.26 3.16
5597 5769 2.023673 TGGCTTCAAGTCAACAAGGTG 58.976 47.619 0.00 0.00 0.00 4.00
5633 5805 2.230660 CCAGAGGTTTTCCCTGACAAC 58.769 52.381 0.00 0.00 46.51 3.32
5728 5900 0.605319 TAGGCCCAAACTGCTGAACG 60.605 55.000 0.00 0.00 0.00 3.95
6019 6191 2.644798 AGGTGGATGAGGTAGCAAAACT 59.355 45.455 0.00 0.00 0.00 2.66
6022 6194 2.026262 TGGATGAGGTAGCAAAACTCCC 60.026 50.000 2.06 0.00 0.00 4.30
6023 6195 2.026262 GGATGAGGTAGCAAAACTCCCA 60.026 50.000 2.06 0.00 0.00 4.37
6024 6196 3.372025 GGATGAGGTAGCAAAACTCCCAT 60.372 47.826 2.06 0.00 0.00 4.00
6026 6198 2.290896 TGAGGTAGCAAAACTCCCATGG 60.291 50.000 4.14 4.14 0.00 3.66
6027 6199 1.992557 AGGTAGCAAAACTCCCATGGA 59.007 47.619 15.22 0.00 0.00 3.41
6028 6200 2.582636 AGGTAGCAAAACTCCCATGGAT 59.417 45.455 15.22 0.00 0.00 3.41
6040 6212 6.341408 ACTCCCATGGATTTTTACCATACT 57.659 37.500 15.22 0.00 45.00 2.12
6187 6360 4.488879 GTTGAACATGGCTTGAGGATTTC 58.511 43.478 7.45 1.12 0.00 2.17
6227 6402 2.817258 TGGTAACCTTTTCGCCTTGATG 59.183 45.455 0.00 0.00 0.00 3.07
6235 6410 1.822114 TTCGCCTTGATGGGTCGACA 61.822 55.000 18.91 0.00 35.75 4.35
6261 6479 5.659440 ATGGTTGTAGGCCTATTTGTTTG 57.341 39.130 17.38 0.00 0.00 2.93
6468 6826 5.886960 ATTCTGGTAATCAACAGACTTGC 57.113 39.130 0.00 0.00 42.91 4.01
6469 6827 4.350368 TCTGGTAATCAACAGACTTGCA 57.650 40.909 0.00 0.00 38.71 4.08
6479 6837 4.811024 TCAACAGACTTGCAGAAGTAGTTG 59.189 41.667 20.06 20.06 46.83 3.16
6493 6851 7.810759 GCAGAAGTAGTTGTATTCTAGCTATCC 59.189 40.741 0.00 0.00 32.16 2.59
6578 6936 5.791666 TGCAATTTTCATGATAAAGGTGCA 58.208 33.333 22.80 22.80 37.49 4.57
6594 6952 5.589367 AGGTGCATAAATAGATGGGTCAT 57.411 39.130 0.00 0.00 0.00 3.06
6620 6978 8.461222 TCATTTTTATGTGACCATGATTCTCAC 58.539 33.333 0.00 0.17 35.79 3.51
6632 6990 3.731089 TGATTCTCACGCATGCATGATA 58.269 40.909 30.64 7.40 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.370051 CGCGCATGATCAAGCCATG 60.370 57.895 16.72 4.79 43.06 3.66
41 42 3.579586 ACATGAGAAATGGGTTGCATTGT 59.420 39.130 0.00 0.00 0.00 2.71
177 178 4.202326 CCGCCTATGGGTATTCTAAGTTGT 60.202 45.833 0.00 0.00 34.45 3.32
180 181 2.904434 CCCGCCTATGGGTATTCTAAGT 59.096 50.000 0.00 0.00 44.76 2.24
208 209 2.103373 GTGAGATGGAGAGTGTGCCTA 58.897 52.381 0.00 0.00 0.00 3.93
210 211 0.901124 AGTGAGATGGAGAGTGTGCC 59.099 55.000 0.00 0.00 0.00 5.01
231 232 1.001378 ACAATTCTTGCTTGTCACCGC 60.001 47.619 0.00 0.00 31.29 5.68
234 235 6.645700 TGAAAAACAATTCTTGCTTGTCAC 57.354 33.333 0.00 0.00 35.84 3.67
339 340 5.240623 TGCAAACTGGTGGTCAAATACTAAG 59.759 40.000 0.00 0.00 0.00 2.18
356 357 6.815089 TGACCATTTTTAGTTCATGCAAACT 58.185 32.000 8.74 8.74 42.10 2.66
357 358 7.599998 AGATGACCATTTTTAGTTCATGCAAAC 59.400 33.333 0.00 0.00 0.00 2.93
358 359 7.669427 AGATGACCATTTTTAGTTCATGCAAA 58.331 30.769 0.00 0.00 0.00 3.68
361 363 8.623903 TCATAGATGACCATTTTTAGTTCATGC 58.376 33.333 0.00 0.00 0.00 4.06
451 453 1.154225 CATTGCGGCGAAGGTGTTC 60.154 57.895 12.98 0.00 0.00 3.18
541 543 7.837202 TGACTCGGTATTTAACTTAACCATG 57.163 36.000 0.00 0.00 32.04 3.66
551 553 2.667481 CGCGGTTTGACTCGGTATTTAA 59.333 45.455 0.00 0.00 0.00 1.52
558 560 1.011968 TGAATCGCGGTTTGACTCGG 61.012 55.000 5.86 0.00 0.00 4.63
591 593 6.238076 GGATGTGTTGAAAATTGTGGTTTGTC 60.238 38.462 0.00 0.00 0.00 3.18
640 643 2.169769 CGGAGCCTTTACCATTCCACTA 59.830 50.000 0.00 0.00 0.00 2.74
700 704 1.004277 TGCGCCCAGAAGAAGGTTTAT 59.996 47.619 4.18 0.00 0.00 1.40
729 745 6.138761 GCCTCTTGAATTGATTTATGTAGCG 58.861 40.000 0.00 0.00 0.00 4.26
835 895 6.581171 TTTTGCCTTTGTTTGGTTTGAAAT 57.419 29.167 0.00 0.00 0.00 2.17
880 940 5.115480 AGCTCAACTCCTAGTACTACGTAC 58.885 45.833 0.00 0.00 39.10 3.67
881 941 5.350504 AGCTCAACTCCTAGTACTACGTA 57.649 43.478 0.00 0.00 0.00 3.57
882 942 4.219264 AGCTCAACTCCTAGTACTACGT 57.781 45.455 0.00 0.00 0.00 3.57
883 943 5.333513 CAAAGCTCAACTCCTAGTACTACG 58.666 45.833 0.00 0.00 0.00 3.51
1806 1885 1.596260 GTCTCCATGATCATGTGTGCG 59.404 52.381 29.23 16.42 37.11 5.34
1852 1933 9.378551 CCTGCAAGTTAAACTATCACAATACTA 57.621 33.333 0.00 0.00 0.00 1.82
1878 1959 6.453092 TCAGTACACTAACCTAAAAGAGCAC 58.547 40.000 0.00 0.00 0.00 4.40
1932 2013 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1933 2014 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1934 2015 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1935 2016 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1936 2017 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1937 2018 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1938 2019 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1939 2020 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1940 2021 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1941 2022 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1942 2023 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1943 2024 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1944 2025 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1945 2026 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1946 2027 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1947 2028 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1948 2029 2.287308 ACAAACACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
1949 2030 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
1950 2031 2.697431 ACAAACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
1951 2032 3.127721 CCATACAAACACACACACACACA 59.872 43.478 0.00 0.00 0.00 3.72
1952 2033 3.375610 TCCATACAAACACACACACACAC 59.624 43.478 0.00 0.00 0.00 3.82
1953 2034 3.610911 TCCATACAAACACACACACACA 58.389 40.909 0.00 0.00 0.00 3.72
1954 2035 3.003275 CCTCCATACAAACACACACACAC 59.997 47.826 0.00 0.00 0.00 3.82
1955 2036 3.210227 CCTCCATACAAACACACACACA 58.790 45.455 0.00 0.00 0.00 3.72
1956 2037 2.552315 CCCTCCATACAAACACACACAC 59.448 50.000 0.00 0.00 0.00 3.82
1957 2038 2.173782 ACCCTCCATACAAACACACACA 59.826 45.455 0.00 0.00 0.00 3.72
1958 2039 2.858745 ACCCTCCATACAAACACACAC 58.141 47.619 0.00 0.00 0.00 3.82
1959 2040 3.586470 AACCCTCCATACAAACACACA 57.414 42.857 0.00 0.00 0.00 3.72
1960 2041 6.386654 CAATTAACCCTCCATACAAACACAC 58.613 40.000 0.00 0.00 0.00 3.82
1961 2042 5.478679 CCAATTAACCCTCCATACAAACACA 59.521 40.000 0.00 0.00 0.00 3.72
1962 2043 5.712917 TCCAATTAACCCTCCATACAAACAC 59.287 40.000 0.00 0.00 0.00 3.32
1963 2044 5.893500 TCCAATTAACCCTCCATACAAACA 58.106 37.500 0.00 0.00 0.00 2.83
1964 2045 5.949952 ACTCCAATTAACCCTCCATACAAAC 59.050 40.000 0.00 0.00 0.00 2.93
2037 2118 5.458015 CAAGTAAAAATGGAGTCGGTTTCC 58.542 41.667 0.00 0.00 35.20 3.13
2075 2192 5.991606 TCCAAACTAGCATGATACATAGTGC 59.008 40.000 0.00 0.00 37.84 4.40
2357 2517 1.629861 TGGCTCACATCCATGTCTTCA 59.370 47.619 0.00 0.00 39.39 3.02
2846 3006 4.232221 CAAGGACATTCAATGCAGACAAC 58.768 43.478 0.00 0.00 0.00 3.32
3926 4086 5.486775 AGCTATTACAGGGTCATCAGCATAT 59.513 40.000 0.00 0.00 0.00 1.78
3959 4119 2.224281 TGCCATTCTAGCCTTGGTATCG 60.224 50.000 7.12 0.00 32.90 2.92
5061 5230 0.798776 GCGATGCCTTCCAATATCCG 59.201 55.000 0.00 0.00 0.00 4.18
5201 5370 2.775911 TCAACCATGCAGAAGAGGAG 57.224 50.000 0.00 0.00 0.00 3.69
5285 5454 5.012893 ACCTCCATGTTTCTGAAATCCTTC 58.987 41.667 6.06 0.00 0.00 3.46
5543 5715 2.343758 GTGTTCTCCTCGCTGGCA 59.656 61.111 0.00 0.00 35.26 4.92
5713 5885 0.878523 TCGACGTTCAGCAGTTTGGG 60.879 55.000 0.00 0.00 0.00 4.12
6019 6191 5.890985 CACAGTATGGTAAAAATCCATGGGA 59.109 40.000 13.02 0.00 44.26 4.37
6022 6194 6.206395 TGCACAGTATGGTAAAAATCCATG 57.794 37.500 7.58 0.00 44.26 3.66
6023 6195 6.437162 ACTTGCACAGTATGGTAAAAATCCAT 59.563 34.615 3.02 3.02 46.00 3.41
6024 6196 5.772672 ACTTGCACAGTATGGTAAAAATCCA 59.227 36.000 0.00 0.00 43.62 3.41
6026 6198 5.572896 GCACTTGCACAGTATGGTAAAAATC 59.427 40.000 0.00 0.00 43.62 2.17
6027 6199 5.243730 AGCACTTGCACAGTATGGTAAAAAT 59.756 36.000 3.62 0.00 45.16 1.82
6028 6200 4.582656 AGCACTTGCACAGTATGGTAAAAA 59.417 37.500 3.62 0.00 45.16 1.94
6040 6212 3.357919 GCATCCAGCACTTGCACA 58.642 55.556 3.62 0.00 45.16 4.57
6141 6313 4.641541 CCAATTCACTCAATATGCACTGGA 59.358 41.667 0.00 0.00 0.00 3.86
6187 6360 5.815233 ACCATGTATTCCAGATCCTACAG 57.185 43.478 0.00 0.00 0.00 2.74
6227 6402 4.817517 CCTACAACCATATATGTCGACCC 58.182 47.826 14.12 0.00 0.00 4.46
6235 6410 9.077885 CAAACAAATAGGCCTACAACCATATAT 57.922 33.333 16.61 0.00 0.00 0.86
6261 6479 7.737744 CGCTGTAGAATTTTCGATATGATTGTC 59.262 37.037 0.00 0.00 0.00 3.18
6284 6502 2.094026 TCATCAGCTACACATTCACGCT 60.094 45.455 0.00 0.00 0.00 5.07
6468 6826 8.301002 GGGATAGCTAGAATACAACTACTTCTG 58.699 40.741 0.00 0.00 31.89 3.02
6469 6827 7.175293 CGGGATAGCTAGAATACAACTACTTCT 59.825 40.741 0.00 0.00 33.91 2.85
6479 6837 5.725325 ACCTTTCGGGATAGCTAGAATAC 57.275 43.478 0.00 0.00 38.76 1.89
6493 6851 5.438761 ACTTCTCATTCAAAACCTTTCGG 57.561 39.130 0.00 0.00 0.00 4.30
6594 6952 8.578448 TGAGAATCATGGTCACATAAAAATGA 57.422 30.769 0.00 0.00 42.56 2.57
6611 6969 4.758165 ATTATCATGCATGCGTGAGAATCA 59.242 37.500 38.53 25.62 45.21 2.57


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

AutoCloner maintained by Alex Coulton.