Multiple sequence alignment - TraesCS3D01G155200

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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 TraesCS3D01G155200 chr3D 100.000 2267 0 0 1 2267 121976412 121978678 0.000000e+00 4187
1 TraesCS3D01G155200 chr3B 91.382 1172 60 18 479 1625 173557983 173559138 0.000000e+00 1567
2 TraesCS3D01G155200 chr3B 90.641 577 42 6 1692 2267 173559145 173559710 0.000000e+00 756
3 TraesCS3D01G155200 chr3B 89.006 473 29 12 1 461 173557537 173557998 4.230000e-157 564
4 TraesCS3D01G155200 chr3B 90.959 365 27 4 950 1313 175953207 175952848 9.410000e-134 486
5 TraesCS3D01G155200 chr3B 89.583 96 8 2 745 838 175953374 175953279 1.100000e-23 121
6 TraesCS3D01G155200 chr3A 89.890 1088 39 21 479 1537 128164466 128165511 0.000000e+00 1334
7 TraesCS3D01G155200 chr3A 94.030 335 13 2 134 461 128164147 128164481 3.360000e-138 501
8 TraesCS3D01G155200 chr3A 85.451 488 22 16 950 1421 130896642 130896188 1.590000e-126 462
9 TraesCS3D01G155200 chr3A 96.403 139 5 0 4 142 128163826 128163964 1.750000e-56 230
10 TraesCS3D01G155200 chr3A 84.783 138 8 5 583 711 130897009 130896876 2.360000e-25 126
11 TraesCS3D01G155200 chr7D 77.286 339 62 12 1937 2267 555165689 555165358 3.850000e-43 185
12 TraesCS3D01G155200 chr6D 79.608 255 45 6 2017 2267 398172044 398171793 2.310000e-40 176
13 TraesCS3D01G155200 chr5B 77.592 299 58 8 1968 2262 446995091 446995384 2.990000e-39 172
14 TraesCS3D01G155200 chr6B 76.261 337 69 9 1937 2267 591510191 591509860 3.870000e-38 169
15 TraesCS3D01G155200 chr6B 76.261 337 69 9 1937 2267 591514953 591514622 3.870000e-38 169
16 TraesCS3D01G155200 chr6B 76.261 337 69 9 1937 2267 591517259 591516928 3.870000e-38 169
17 TraesCS3D01G155200 chr2B 76.974 304 62 7 1968 2267 610592623 610592922 1.390000e-37 167
18 TraesCS3D01G155200 chrUn 75.510 343 73 9 1931 2267 398717071 398717408 8.380000e-35 158


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 TraesCS3D01G155200 chr3D 121976412 121978678 2266 False 4187.000000 4187 100.000 1 2267 1 chr3D.!!$F1 2266
1 TraesCS3D01G155200 chr3B 173557537 173559710 2173 False 962.333333 1567 90.343 1 2267 3 chr3B.!!$F1 2266
2 TraesCS3D01G155200 chr3B 175952848 175953374 526 True 303.500000 486 90.271 745 1313 2 chr3B.!!$R1 568
3 TraesCS3D01G155200 chr3A 128163826 128165511 1685 False 688.333333 1334 93.441 4 1537 3 chr3A.!!$F1 1533
4 TraesCS3D01G155200 chr3A 130896188 130897009 821 True 294.000000 462 85.117 583 1421 2 chr3A.!!$R1 838

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
916 1177 0.107945 GCGAGCTCAGACCTTGGATT 60.108 55.0 15.4 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2272 0.868602 ATCGCGCTTCATGCAATTGC 60.869 50.0 23.69 23.69 43.06 3.56 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
132 138 1.328279 TGTTTCTCTCTCACGGCTCA 58.672 50.000 0.00 0.00 0.00 4.26
150 347 3.508762 CTCAGCAAAATTGACATCAGCC 58.491 45.455 0.00 0.00 0.00 4.85
166 363 0.606401 AGCCACACCTTCAATCCACG 60.606 55.000 0.00 0.00 0.00 4.94
168 365 1.609580 GCCACACCTTCAATCCACGTA 60.610 52.381 0.00 0.00 0.00 3.57
172 369 5.123227 CCACACCTTCAATCCACGTAATAT 58.877 41.667 0.00 0.00 0.00 1.28
287 484 2.438951 TACTGCACGTTTCCGTCCCC 62.439 60.000 0.00 0.00 46.28 4.81
409 620 1.820010 AACCCTCGTAACACCCGTCC 61.820 60.000 0.00 0.00 0.00 4.79
462 673 2.282462 CCTGGCCGGCTCAACTTT 60.282 61.111 28.56 0.00 0.00 2.66
463 674 1.903404 CCTGGCCGGCTCAACTTTT 60.903 57.895 28.56 0.00 0.00 2.27
464 675 1.463553 CCTGGCCGGCTCAACTTTTT 61.464 55.000 28.56 0.00 0.00 1.94
707 955 3.670377 GCCACAACTGCCCGTTCC 61.670 66.667 0.00 0.00 32.27 3.62
719 967 0.462937 CCCGTTCCAACACACACTGA 60.463 55.000 0.00 0.00 0.00 3.41
728 976 2.203800 ACACACACTGACACACGTAG 57.796 50.000 0.00 0.00 0.00 3.51
729 977 0.852777 CACACACTGACACACGTAGC 59.147 55.000 0.00 0.00 0.00 3.58
730 978 0.458260 ACACACTGACACACGTAGCA 59.542 50.000 0.00 0.00 0.00 3.49
731 979 0.852777 CACACTGACACACGTAGCAC 59.147 55.000 0.00 0.00 0.00 4.40
732 980 0.458260 ACACTGACACACGTAGCACA 59.542 50.000 0.00 0.00 0.00 4.57
912 1173 1.447489 CCAGCGAGCTCAGACCTTG 60.447 63.158 15.40 2.19 0.00 3.61
916 1177 0.107945 GCGAGCTCAGACCTTGGATT 60.108 55.000 15.40 0.00 0.00 3.01
917 1178 1.933247 CGAGCTCAGACCTTGGATTC 58.067 55.000 15.40 0.00 0.00 2.52
918 1179 1.800655 CGAGCTCAGACCTTGGATTCG 60.801 57.143 15.40 0.00 0.00 3.34
919 1180 1.478510 GAGCTCAGACCTTGGATTCGA 59.521 52.381 9.40 0.00 0.00 3.71
920 1181 1.205893 AGCTCAGACCTTGGATTCGAC 59.794 52.381 0.00 0.00 0.00 4.20
976 1241 3.244770 CCACCACCTACAAAGCTTCCTAA 60.245 47.826 0.00 0.00 0.00 2.69
990 1255 0.683504 TCCTAACCTGGTCTCGAGGC 60.684 60.000 13.56 11.38 33.39 4.70
1349 1645 6.280643 TCATTCATGACTAACTTACGATGGG 58.719 40.000 0.00 0.00 0.00 4.00
1362 1658 2.285368 ATGGGCCTGGGAGACGAA 60.285 61.111 4.53 0.00 0.00 3.85
1461 1762 6.671614 ATTTGCTTGTTATGAAATGGCATG 57.328 33.333 0.00 0.00 0.00 4.06
1497 1812 3.263261 TGCTAATTTGGACGCGTTGATA 58.737 40.909 15.53 0.00 0.00 2.15
1547 1872 1.873591 GTGTGAAACTGAGGATTGCGT 59.126 47.619 0.00 0.00 38.04 5.24
1553 1878 3.895232 AACTGAGGATTGCGTATGTCT 57.105 42.857 0.00 0.00 0.00 3.41
1554 1879 3.895232 ACTGAGGATTGCGTATGTCTT 57.105 42.857 0.00 0.00 0.00 3.01
1555 1880 5.339008 AACTGAGGATTGCGTATGTCTTA 57.661 39.130 0.00 0.00 0.00 2.10
1556 1881 5.339008 ACTGAGGATTGCGTATGTCTTAA 57.661 39.130 0.00 0.00 0.00 1.85
1615 1940 6.878923 TGCATGTATAATATTGCTCTGGGTAC 59.121 38.462 0.00 0.00 36.10 3.34
1618 1943 7.612065 TGTATAATATTGCTCTGGGTACAGT 57.388 36.000 0.00 0.00 45.14 3.55
1625 1950 2.301870 TGCTCTGGGTACAGTTAGTTGG 59.698 50.000 0.00 0.00 45.14 3.77
1626 1951 2.565834 GCTCTGGGTACAGTTAGTTGGA 59.434 50.000 0.00 0.00 45.14 3.53
1627 1952 3.368531 GCTCTGGGTACAGTTAGTTGGAG 60.369 52.174 0.00 0.00 45.14 3.86
1628 1953 4.087182 CTCTGGGTACAGTTAGTTGGAGA 58.913 47.826 0.00 0.00 45.14 3.71
1629 1954 3.830755 TCTGGGTACAGTTAGTTGGAGAC 59.169 47.826 0.00 0.00 45.14 3.36
1630 1955 3.576982 CTGGGTACAGTTAGTTGGAGACA 59.423 47.826 0.00 0.00 39.92 3.41
1631 1956 4.164981 TGGGTACAGTTAGTTGGAGACAT 58.835 43.478 0.00 0.00 42.32 3.06
1632 1957 4.020573 TGGGTACAGTTAGTTGGAGACATG 60.021 45.833 0.00 0.00 42.32 3.21
1633 1958 4.020485 GGGTACAGTTAGTTGGAGACATGT 60.020 45.833 0.00 0.00 42.32 3.21
1637 1962 4.100963 ACAGTTAGTTGGAGACATGTGTGA 59.899 41.667 1.15 0.00 42.32 3.58
1638 1963 4.449068 CAGTTAGTTGGAGACATGTGTGAC 59.551 45.833 1.15 0.00 42.32 3.67
1639 1964 2.550830 AGTTGGAGACATGTGTGACC 57.449 50.000 1.15 0.00 42.32 4.02
1640 1965 2.050144 AGTTGGAGACATGTGTGACCT 58.950 47.619 1.15 0.00 42.32 3.85
1642 1967 3.840666 AGTTGGAGACATGTGTGACCTAT 59.159 43.478 1.15 0.00 42.32 2.57
1643 1968 4.081420 AGTTGGAGACATGTGTGACCTATC 60.081 45.833 1.15 0.00 42.32 2.08
1644 1969 3.713003 TGGAGACATGTGTGACCTATCT 58.287 45.455 1.15 0.00 33.40 1.98
1645 1970 4.867086 TGGAGACATGTGTGACCTATCTA 58.133 43.478 1.15 0.00 33.40 1.98
1646 1971 5.458595 TGGAGACATGTGTGACCTATCTAT 58.541 41.667 1.15 0.00 33.40 1.98
1647 1972 6.610830 TGGAGACATGTGTGACCTATCTATA 58.389 40.000 1.15 0.00 33.40 1.31
1648 1973 6.490381 TGGAGACATGTGTGACCTATCTATAC 59.510 42.308 1.15 0.00 33.40 1.47
1649 1974 6.717540 GGAGACATGTGTGACCTATCTATACT 59.282 42.308 1.15 0.00 0.00 2.12
1650 1975 7.883833 GGAGACATGTGTGACCTATCTATACTA 59.116 40.741 1.15 0.00 0.00 1.82
1651 1976 8.856153 AGACATGTGTGACCTATCTATACTAG 57.144 38.462 1.15 0.00 0.00 2.57
1652 1977 8.441572 AGACATGTGTGACCTATCTATACTAGT 58.558 37.037 1.15 0.00 0.00 2.57
1653 1978 9.722184 GACATGTGTGACCTATCTATACTAGTA 57.278 37.037 1.15 4.77 0.00 1.82
1699 2024 9.626045 AATTAAGCTTCTTAATGTAAACTGCAC 57.374 29.630 0.00 0.00 0.00 4.57
1700 2025 6.633500 AAGCTTCTTAATGTAAACTGCACA 57.367 33.333 0.00 0.00 0.00 4.57
1701 2026 6.633500 AGCTTCTTAATGTAAACTGCACAA 57.367 33.333 0.00 0.00 0.00 3.33
1702 2027 7.038154 AGCTTCTTAATGTAAACTGCACAAA 57.962 32.000 0.00 0.00 0.00 2.83
1703 2028 7.488322 AGCTTCTTAATGTAAACTGCACAAAA 58.512 30.769 0.00 0.00 0.00 2.44
1704 2029 7.435192 AGCTTCTTAATGTAAACTGCACAAAAC 59.565 33.333 0.00 0.00 0.00 2.43
1705 2030 7.221838 GCTTCTTAATGTAAACTGCACAAAACA 59.778 33.333 0.00 0.00 0.00 2.83
1706 2031 9.248291 CTTCTTAATGTAAACTGCACAAAACAT 57.752 29.630 0.00 0.00 0.00 2.71
1707 2032 8.572828 TCTTAATGTAAACTGCACAAAACATG 57.427 30.769 0.00 0.00 0.00 3.21
1725 2050 7.476540 AAACATGTGTGACCTATCTGTACTA 57.523 36.000 0.00 0.00 0.00 1.82
1787 2112 1.151677 AGCCAAACCCCCTACTCCA 60.152 57.895 0.00 0.00 0.00 3.86
1788 2113 1.001269 GCCAAACCCCCTACTCCAC 60.001 63.158 0.00 0.00 0.00 4.02
1789 2114 1.498176 GCCAAACCCCCTACTCCACT 61.498 60.000 0.00 0.00 0.00 4.00
1790 2115 0.618981 CCAAACCCCCTACTCCACTC 59.381 60.000 0.00 0.00 0.00 3.51
1791 2116 1.358152 CAAACCCCCTACTCCACTCA 58.642 55.000 0.00 0.00 0.00 3.41
1792 2117 1.916181 CAAACCCCCTACTCCACTCAT 59.084 52.381 0.00 0.00 0.00 2.90
1793 2118 3.112263 CAAACCCCCTACTCCACTCATA 58.888 50.000 0.00 0.00 0.00 2.15
1797 2122 3.469771 ACCCCCTACTCCACTCATATGTA 59.530 47.826 1.90 0.00 0.00 2.29
1798 2123 4.109765 ACCCCCTACTCCACTCATATGTAT 59.890 45.833 1.90 0.00 0.00 2.29
1800 2125 4.467795 CCCCTACTCCACTCATATGTATGG 59.532 50.000 17.16 17.16 34.50 2.74
1804 2129 2.300152 CTCCACTCATATGTATGGGCGT 59.700 50.000 20.77 1.48 37.70 5.68
1806 2131 4.093743 TCCACTCATATGTATGGGCGTAT 58.906 43.478 20.77 0.00 37.70 3.06
1808 2133 5.359860 TCCACTCATATGTATGGGCGTATAG 59.640 44.000 20.77 3.90 37.70 1.31
1821 2146 2.273557 GCGTATAGCCCGAACAGAAAA 58.726 47.619 0.00 0.00 40.81 2.29
1863 2188 5.949354 CCCCAAACTCAACCTATATGTTTGA 59.051 40.000 15.55 5.22 45.75 2.69
1864 2189 6.435904 CCCCAAACTCAACCTATATGTTTGAA 59.564 38.462 15.55 0.00 45.75 2.69
1880 2205 2.254546 TGAATTGTCTCGCACACCTT 57.745 45.000 0.00 0.00 33.41 3.50
1918 2243 3.001939 GTGGGGCGTGTTAGAATATTTCG 59.998 47.826 0.00 0.00 34.02 3.46
1924 2249 5.276254 GGCGTGTTAGAATATTTCGAGACAC 60.276 44.000 0.00 10.79 37.78 3.67
1928 2253 7.174082 GTGTTAGAATATTTCGAGACACAAGC 58.826 38.462 13.66 0.00 39.30 4.01
1938 2263 2.792890 CGAGACACAAGCTGATCTACCG 60.793 54.545 0.00 0.00 0.00 4.02
1940 2265 2.425312 AGACACAAGCTGATCTACCGAG 59.575 50.000 0.00 0.00 0.00 4.63
1947 2272 5.221342 ACAAGCTGATCTACCGAGGATTAAG 60.221 44.000 0.00 0.00 0.00 1.85
1980 2305 3.123804 AGCGCGATCGAGATTTGTTAAT 58.876 40.909 23.47 0.00 38.10 1.40
1989 2314 9.784824 CGATCGAGATTTGTTAATGAGATTTAC 57.215 33.333 10.26 0.00 0.00 2.01
2001 2326 6.839124 AATGAGATTTACCAAACATCAGCA 57.161 33.333 0.00 0.00 0.00 4.41
2002 2327 6.839124 ATGAGATTTACCAAACATCAGCAA 57.161 33.333 0.00 0.00 0.00 3.91
2036 2361 1.044611 GACTATGGGTGCTCCTCTCC 58.955 60.000 4.53 0.00 36.20 3.71
2038 2363 0.757188 CTATGGGTGCTCCTCTCCGT 60.757 60.000 4.53 0.00 36.20 4.69
2044 2369 1.202428 GGTGCTCCTCTCCGTTGATAC 60.202 57.143 0.00 0.00 0.00 2.24
2045 2370 1.112113 TGCTCCTCTCCGTTGATACC 58.888 55.000 0.00 0.00 0.00 2.73
2047 2372 0.030908 CTCCTCTCCGTTGATACCGC 59.969 60.000 0.00 0.00 0.00 5.68
2073 2398 3.947132 CTGCACACCGGCCTCTCAG 62.947 68.421 0.00 0.00 0.00 3.35
2088 2413 2.821366 CAGGAGCCGACACATGCC 60.821 66.667 0.00 0.00 0.00 4.40
2113 2438 1.682854 CTTCCCTTGTGCACATGTGTT 59.317 47.619 26.01 0.00 0.00 3.32
2114 2439 1.031235 TCCCTTGTGCACATGTGTTG 58.969 50.000 26.01 9.77 0.00 3.33
2115 2440 0.746063 CCCTTGTGCACATGTGTTGT 59.254 50.000 26.01 0.00 39.91 3.32
2116 2441 1.136695 CCCTTGTGCACATGTGTTGTT 59.863 47.619 26.01 0.00 36.00 2.83
2133 2458 8.518430 TGTGTTGTTATGTTGGCATAGATTAT 57.482 30.769 0.00 0.00 38.64 1.28
2212 2537 3.131755 ACACGGCTCTATACCCTGTTTAC 59.868 47.826 0.00 0.00 0.00 2.01
2214 2539 2.752121 GGCTCTATACCCTGTTTACGC 58.248 52.381 0.00 0.00 0.00 4.42
2222 2547 2.070783 ACCCTGTTTACGCACAATACG 58.929 47.619 0.00 0.00 0.00 3.06
2229 2554 5.459768 TGTTTACGCACAATACGACTCTAA 58.540 37.500 0.00 0.00 0.00 2.10
2242 2567 9.411801 CAATACGACTCTAAGTGCATATGTAAT 57.588 33.333 4.29 0.00 0.00 1.89
2246 2571 9.015367 ACGACTCTAAGTGCATATGTAATCTAT 57.985 33.333 4.29 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 26 1.035923 TAATGGCCGAGAGAGCTCAG 58.964 55.000 17.77 4.03 41.36 3.35
132 138 2.629137 TGTGGCTGATGTCAATTTTGCT 59.371 40.909 0.00 0.00 0.00 3.91
150 347 5.815222 TCATATTACGTGGATTGAAGGTGTG 59.185 40.000 0.00 0.00 0.00 3.82
166 363 2.076863 GCATGGACCGGCTCATATTAC 58.923 52.381 0.00 0.00 0.00 1.89
168 365 0.473755 TGCATGGACCGGCTCATATT 59.526 50.000 0.00 0.00 0.00 1.28
172 369 2.124612 CATGCATGGACCGGCTCA 60.125 61.111 19.40 0.00 0.00 4.26
287 484 3.551890 CGGATATTGTCGAGGACTTTGTG 59.448 47.826 0.00 0.00 33.15 3.33
409 620 1.190984 CTCGCACCAAATGATCGATCG 59.809 52.381 20.03 9.36 0.00 3.69
474 685 2.597217 TTGAGCCGGCCAGGTTTG 60.597 61.111 26.15 0.00 43.70 2.93
475 686 1.774894 TAGTTGAGCCGGCCAGGTTT 61.775 55.000 26.15 1.92 43.70 3.27
476 687 1.774894 TTAGTTGAGCCGGCCAGGTT 61.775 55.000 26.15 2.91 43.70 3.50
477 688 1.774894 TTTAGTTGAGCCGGCCAGGT 61.775 55.000 26.15 3.43 43.70 4.00
478 689 1.002624 TTTAGTTGAGCCGGCCAGG 60.003 57.895 26.15 6.38 44.97 4.45
479 690 0.605319 TGTTTAGTTGAGCCGGCCAG 60.605 55.000 26.15 0.00 0.00 4.85
480 691 0.179015 TTGTTTAGTTGAGCCGGCCA 60.179 50.000 26.15 18.56 0.00 5.36
481 692 0.521735 CTTGTTTAGTTGAGCCGGCC 59.478 55.000 26.15 15.80 0.00 6.13
482 693 0.109735 GCTTGTTTAGTTGAGCCGGC 60.110 55.000 21.89 21.89 0.00 6.13
483 694 1.069227 GTGCTTGTTTAGTTGAGCCGG 60.069 52.381 0.00 0.00 34.30 6.13
484 695 1.398451 CGTGCTTGTTTAGTTGAGCCG 60.398 52.381 0.00 0.00 34.30 5.52
485 696 1.663161 GCGTGCTTGTTTAGTTGAGCC 60.663 52.381 0.00 0.00 34.30 4.70
486 697 1.663161 GGCGTGCTTGTTTAGTTGAGC 60.663 52.381 0.00 0.00 35.74 4.26
487 698 1.069227 GGGCGTGCTTGTTTAGTTGAG 60.069 52.381 0.00 0.00 0.00 3.02
488 699 0.948678 GGGCGTGCTTGTTTAGTTGA 59.051 50.000 0.00 0.00 0.00 3.18
610 821 1.512522 CGTGCATGCATGTCAACGG 60.513 57.895 28.25 17.61 0.00 4.44
707 955 1.075542 ACGTGTGTCAGTGTGTGTTG 58.924 50.000 0.00 0.00 0.00 3.33
719 967 1.113517 AGACCCTGTGCTACGTGTGT 61.114 55.000 0.00 0.00 0.00 3.72
728 976 2.032681 GGTGTGGAGACCCTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
729 977 2.343758 CGGTGTGGAGACCCTGTG 59.656 66.667 0.00 0.00 31.57 3.66
730 978 2.923035 CCGGTGTGGAGACCCTGT 60.923 66.667 0.00 0.00 42.00 4.00
731 979 4.394712 GCCGGTGTGGAGACCCTG 62.395 72.222 1.90 0.00 42.00 4.45
873 1134 3.530910 AACGAAGCGGACCAGGTGG 62.531 63.158 0.00 0.00 42.17 4.61
875 1136 2.030562 CAACGAAGCGGACCAGGT 59.969 61.111 0.00 0.00 0.00 4.00
912 1173 0.672401 TGCCGTCTTTGGTCGAATCC 60.672 55.000 0.00 0.00 0.00 3.01
916 1177 2.342279 CCTGCCGTCTTTGGTCGA 59.658 61.111 0.00 0.00 0.00 4.20
917 1178 2.742372 CCCTGCCGTCTTTGGTCG 60.742 66.667 0.00 0.00 0.00 4.79
918 1179 3.056328 GCCCTGCCGTCTTTGGTC 61.056 66.667 0.00 0.00 0.00 4.02
920 1181 4.697756 TCGCCCTGCCGTCTTTGG 62.698 66.667 0.00 0.00 0.00 3.28
945 1206 0.676782 GTAGGTGGTGGTGGTGATGC 60.677 60.000 0.00 0.00 0.00 3.91
976 1241 2.681778 CCTGCCTCGAGACCAGGT 60.682 66.667 29.26 0.00 40.92 4.00
990 1255 1.092348 TCGTCTCCATGTACGTCCTG 58.908 55.000 10.92 0.00 39.99 3.86
1349 1645 1.605058 TAGCACTTCGTCTCCCAGGC 61.605 60.000 0.00 0.00 0.00 4.85
1447 1748 8.785946 CAGACACATATACATGCCATTTCATAA 58.214 33.333 0.00 0.00 35.39 1.90
1461 1762 9.489084 TCCAAATTAGCATACAGACACATATAC 57.511 33.333 0.00 0.00 0.00 1.47
1497 1812 6.705825 GCCACCACTAACTTGAAATTCAAAAT 59.294 34.615 9.85 4.32 35.73 1.82
1591 1916 6.878923 TGTACCCAGAGCAATATTATACATGC 59.121 38.462 0.00 4.31 39.06 4.06
1615 1940 4.449068 GTCACACATGTCTCCAACTAACTG 59.551 45.833 0.00 0.00 0.00 3.16
1618 1943 3.646162 AGGTCACACATGTCTCCAACTAA 59.354 43.478 0.00 0.00 0.00 2.24
1625 1950 7.753309 AGTATAGATAGGTCACACATGTCTC 57.247 40.000 0.00 0.00 32.77 3.36
1626 1951 8.441572 ACTAGTATAGATAGGTCACACATGTCT 58.558 37.037 0.00 0.00 42.77 3.41
1627 1952 8.624367 ACTAGTATAGATAGGTCACACATGTC 57.376 38.462 0.00 0.00 42.77 3.06
1673 1998 9.626045 GTGCAGTTTACATTAAGAAGCTTAATT 57.374 29.630 0.00 0.00 0.00 1.40
1674 1999 8.792633 TGTGCAGTTTACATTAAGAAGCTTAAT 58.207 29.630 0.00 6.61 0.00 1.40
1675 2000 8.160521 TGTGCAGTTTACATTAAGAAGCTTAA 57.839 30.769 0.00 2.49 0.00 1.85
1676 2001 7.737972 TGTGCAGTTTACATTAAGAAGCTTA 57.262 32.000 0.00 0.00 0.00 3.09
1677 2002 6.633500 TGTGCAGTTTACATTAAGAAGCTT 57.367 33.333 0.00 0.00 0.00 3.74
1678 2003 6.633500 TTGTGCAGTTTACATTAAGAAGCT 57.367 33.333 0.00 0.00 0.00 3.74
1679 2004 7.221838 TGTTTTGTGCAGTTTACATTAAGAAGC 59.778 33.333 0.00 0.00 0.00 3.86
1680 2005 8.627487 TGTTTTGTGCAGTTTACATTAAGAAG 57.373 30.769 0.00 0.00 0.00 2.85
1681 2006 9.029243 CATGTTTTGTGCAGTTTACATTAAGAA 57.971 29.630 0.00 0.00 0.00 2.52
1682 2007 8.194104 ACATGTTTTGTGCAGTTTACATTAAGA 58.806 29.630 0.00 0.00 37.11 2.10
1683 2008 8.351495 ACATGTTTTGTGCAGTTTACATTAAG 57.649 30.769 0.00 0.00 37.11 1.85
1698 2023 5.376625 ACAGATAGGTCACACATGTTTTGT 58.623 37.500 0.00 0.00 39.91 2.83
1699 2024 5.947228 ACAGATAGGTCACACATGTTTTG 57.053 39.130 0.00 0.00 0.00 2.44
1700 2025 6.769512 AGTACAGATAGGTCACACATGTTTT 58.230 36.000 0.00 0.00 0.00 2.43
1701 2026 6.360370 AGTACAGATAGGTCACACATGTTT 57.640 37.500 0.00 0.00 0.00 2.83
1702 2027 6.663953 ACTAGTACAGATAGGTCACACATGTT 59.336 38.462 0.00 0.00 0.00 2.71
1703 2028 6.188407 ACTAGTACAGATAGGTCACACATGT 58.812 40.000 0.00 0.00 0.00 3.21
1704 2029 6.701145 ACTAGTACAGATAGGTCACACATG 57.299 41.667 0.00 0.00 0.00 3.21
1705 2030 8.998277 AATACTAGTACAGATAGGTCACACAT 57.002 34.615 4.31 0.00 0.00 3.21
1706 2031 8.050930 TGAATACTAGTACAGATAGGTCACACA 58.949 37.037 4.31 0.00 0.00 3.72
1707 2032 8.447924 TGAATACTAGTACAGATAGGTCACAC 57.552 38.462 4.31 0.00 0.00 3.82
1768 2093 1.303282 GGAGTAGGGGGTTTGGCTG 59.697 63.158 0.00 0.00 0.00 4.85
1774 2099 3.311402 ACATATGAGTGGAGTAGGGGGTT 60.311 47.826 10.38 0.00 0.00 4.11
1787 2112 5.263968 GCTATACGCCCATACATATGAGT 57.736 43.478 10.38 0.00 35.75 3.41
1821 2146 1.003928 GGGTCCGGTTAGGTGATGTTT 59.996 52.381 0.00 0.00 41.99 2.83
1863 2188 3.252458 GGTTTAAGGTGTGCGAGACAATT 59.748 43.478 0.00 0.00 35.91 2.32
1864 2189 2.812011 GGTTTAAGGTGTGCGAGACAAT 59.188 45.455 0.00 0.00 35.91 2.71
1880 2205 2.174639 CCCCACATATGAGCTGGGTTTA 59.825 50.000 22.21 0.00 43.01 2.01
1918 2243 2.423892 TCGGTAGATCAGCTTGTGTCTC 59.576 50.000 0.00 0.00 0.00 3.36
1924 2249 3.742433 AATCCTCGGTAGATCAGCTTG 57.258 47.619 0.00 0.00 0.00 4.01
1928 2253 4.855715 TGCTTAATCCTCGGTAGATCAG 57.144 45.455 0.00 0.00 0.00 2.90
1938 2263 4.743644 GCTTCATGCAATTGCTTAATCCTC 59.256 41.667 29.37 9.57 42.66 3.71
1940 2265 3.488310 CGCTTCATGCAATTGCTTAATCC 59.512 43.478 29.37 13.65 43.06 3.01
1947 2272 0.868602 ATCGCGCTTCATGCAATTGC 60.869 50.000 23.69 23.69 43.06 3.56
1980 2305 6.647334 TTTGCTGATGTTTGGTAAATCTCA 57.353 33.333 0.00 0.00 0.00 3.27
1989 2314 5.600908 CCAAAGATTTTGCTGATGTTTGG 57.399 39.130 15.94 15.94 45.49 3.28
2001 2326 6.725834 ACCCATAGTCATGTTCCAAAGATTTT 59.274 34.615 0.00 0.00 0.00 1.82
2002 2327 6.153340 CACCCATAGTCATGTTCCAAAGATTT 59.847 38.462 0.00 0.00 0.00 2.17
2036 2361 2.215587 CAGTATTGTCGCGGTATCAACG 59.784 50.000 6.13 0.00 0.00 4.10
2038 2363 2.198406 GCAGTATTGTCGCGGTATCAA 58.802 47.619 6.13 7.79 0.00 2.57
2044 2369 1.419922 GTGTGCAGTATTGTCGCGG 59.580 57.895 6.13 0.00 0.00 6.46
2045 2370 1.419922 GGTGTGCAGTATTGTCGCG 59.580 57.895 0.00 0.00 0.00 5.87
2047 2372 1.966493 GCCGGTGTGCAGTATTGTCG 61.966 60.000 1.90 0.00 0.00 4.35
2099 2424 4.645762 ACATAACAACACATGTGCACAA 57.354 36.364 25.72 7.59 42.99 3.33
2154 2479 7.036059 ACACTTGTATCCTAGGCCTCCTATATA 60.036 40.741 9.68 0.71 35.36 0.86
2212 2537 2.279136 GCACTTAGAGTCGTATTGTGCG 59.721 50.000 11.59 0.00 39.54 5.34
2214 2539 6.697455 ACATATGCACTTAGAGTCGTATTGTG 59.303 38.462 1.58 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.