Multiple sequence alignment - TraesCS7B01G039200

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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 TraesCS7B01G039200 chr7B 100.000 2327 0 0 1 2327 38632598 38630272 0.000000e+00 4298.0
1 TraesCS7B01G039200 chr7B 81.653 496 50 16 1736 2214 38624274 38623803 7.850000e-100 374.0
2 TraesCS7B01G039200 chr1B 91.488 1680 135 8 1 1677 613010076 613008402 0.000000e+00 2303.0
3 TraesCS7B01G039200 chr1B 85.205 1683 229 17 1 1674 592573602 592571931 0.000000e+00 1711.0
4 TraesCS7B01G039200 chr6B 90.621 1674 145 12 1 1669 232073939 232075605 0.000000e+00 2211.0
5 TraesCS7B01G039200 chr6B 89.556 1599 154 11 74 1669 79247719 79246131 0.000000e+00 2015.0
6 TraesCS7B01G039200 chr6B 87.261 1672 191 11 1 1669 695921031 695922683 0.000000e+00 1888.0
7 TraesCS7B01G039200 chr6B 85.062 1687 225 22 1 1673 544397827 544396154 0.000000e+00 1694.0
8 TraesCS7B01G039200 chr6B 82.400 1625 269 17 56 1673 715763175 715761561 0.000000e+00 1400.0
9 TraesCS7B01G039200 chr5B 87.821 1675 185 15 1 1669 548384008 548382347 0.000000e+00 1945.0
10 TraesCS7B01G039200 chr3B 85.621 1676 218 22 2 1669 106936258 106937918 0.000000e+00 1738.0
11 TraesCS7B01G039200 chr2B 84.286 1610 236 15 68 1669 748211383 748212983 0.000000e+00 1555.0
12 TraesCS7B01G039200 chr2B 84.358 179 23 5 1494 1669 298008768 298008944 1.110000e-38 171.0
13 TraesCS7B01G039200 chr2A 83.838 495 54 16 1736 2215 50441108 50440625 4.560000e-122 448.0
14 TraesCS7B01G039200 chr7D 81.538 585 46 21 1670 2215 88369202 88368641 2.140000e-115 425.0
15 TraesCS7B01G039200 chr7A 81.462 561 62 18 1670 2214 89963640 89963106 2.760000e-114 422.0
16 TraesCS7B01G039200 chr7A 90.909 154 11 3 1759 1910 89946935 89946783 1.090000e-48 204.0
17 TraesCS7B01G039200 chr7A 81.735 219 21 6 2005 2211 89932745 89932534 5.140000e-37 165.0
18 TraesCS7B01G039200 chr7A 88.462 104 11 1 2225 2327 89932548 89932445 8.730000e-25 124.0
19 TraesCS7B01G039200 chr6A 94.231 52 3 0 1760 1811 124911553 124911502 1.920000e-11 80.5
20 TraesCS7B01G039200 chr5A 90.476 42 4 0 2133 2174 563176448 563176489 3.230000e-04 56.5


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 TraesCS7B01G039200 chr7B 38630272 38632598 2326 True 4298 4298 100.000 1 2327 1 chr7B.!!$R2 2326
1 TraesCS7B01G039200 chr1B 613008402 613010076 1674 True 2303 2303 91.488 1 1677 1 chr1B.!!$R2 1676
2 TraesCS7B01G039200 chr1B 592571931 592573602 1671 True 1711 1711 85.205 1 1674 1 chr1B.!!$R1 1673
3 TraesCS7B01G039200 chr6B 232073939 232075605 1666 False 2211 2211 90.621 1 1669 1 chr6B.!!$F1 1668
4 TraesCS7B01G039200 chr6B 79246131 79247719 1588 True 2015 2015 89.556 74 1669 1 chr6B.!!$R1 1595
5 TraesCS7B01G039200 chr6B 695921031 695922683 1652 False 1888 1888 87.261 1 1669 1 chr6B.!!$F2 1668
6 TraesCS7B01G039200 chr6B 544396154 544397827 1673 True 1694 1694 85.062 1 1673 1 chr6B.!!$R2 1672
7 TraesCS7B01G039200 chr6B 715761561 715763175 1614 True 1400 1400 82.400 56 1673 1 chr6B.!!$R3 1617
8 TraesCS7B01G039200 chr5B 548382347 548384008 1661 True 1945 1945 87.821 1 1669 1 chr5B.!!$R1 1668
9 TraesCS7B01G039200 chr3B 106936258 106937918 1660 False 1738 1738 85.621 2 1669 1 chr3B.!!$F1 1667
10 TraesCS7B01G039200 chr2B 748211383 748212983 1600 False 1555 1555 84.286 68 1669 1 chr2B.!!$F2 1601
11 TraesCS7B01G039200 chr7D 88368641 88369202 561 True 425 425 81.538 1670 2215 1 chr7D.!!$R1 545
12 TraesCS7B01G039200 chr7A 89963106 89963640 534 True 422 422 81.462 1670 2214 1 chr7A.!!$R2 544

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
976 985 0.320374 CACTTGTCCGGTGGCTAGAA 59.68 55.0 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2186 0.107993 ACATGTGTCATCTCCTGGCG 60.108 55.0 0.0 0.0 29.52 5.69 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
33 34 1.065491 TGTTGTGAATCCTGGATCGGG 60.065 52.381 10.14 0.00 0.00 5.14
46 47 1.070758 GGATCGGGAATGCAGCTTCTA 59.929 52.381 0.00 0.00 0.00 2.10
48 49 3.406764 GATCGGGAATGCAGCTTCTATT 58.593 45.455 0.00 0.00 0.00 1.73
50 51 4.623932 TCGGGAATGCAGCTTCTATTAT 57.376 40.909 0.00 0.00 0.00 1.28
51 52 5.738619 TCGGGAATGCAGCTTCTATTATA 57.261 39.130 0.00 0.00 0.00 0.98
52 53 6.299805 TCGGGAATGCAGCTTCTATTATAT 57.700 37.500 0.00 0.00 0.00 0.86
198 200 2.678336 GCATGAGGGTCGAAAAAGGTAG 59.322 50.000 0.00 0.00 0.00 3.18
228 230 5.182380 GGTAAAATGGTCCAGAATTTGTCGA 59.818 40.000 0.00 0.00 0.00 4.20
237 239 4.080356 TCCAGAATTTGTCGATCCAAGGAT 60.080 41.667 0.16 0.16 37.59 3.24
249 251 1.583611 TCCAAGGATAAGGGAGGCCTA 59.416 52.381 4.42 0.00 0.00 3.93
256 258 1.533808 TAAGGGAGGCCTAGGGGTGT 61.534 60.000 4.42 0.00 34.45 4.16
411 414 0.541764 TTGGTGACTCCCCCATTTGC 60.542 55.000 0.00 0.00 34.77 3.68
424 427 2.485835 CCCATTTGCAAGGCCATTATGG 60.486 50.000 14.53 14.53 41.55 2.74
430 433 1.683385 GCAAGGCCATTATGGAAGTCC 59.317 52.381 16.46 6.47 40.96 3.85
446 449 4.396478 GGAAGTCCAAGAATTCTACCTTGC 59.604 45.833 8.75 9.61 36.93 4.01
579 583 1.976132 ATCAGGGGATCACTGTGGCG 61.976 60.000 8.11 0.00 37.25 5.69
581 585 1.918293 AGGGGATCACTGTGGCGAA 60.918 57.895 8.11 0.00 0.00 4.70
717 723 2.290260 TGATCAAGTAGTGTGGGCCTTG 60.290 50.000 4.53 0.00 36.49 3.61
770 776 8.893727 CCAAATCAGTTTATAAGTACCAGGAAG 58.106 37.037 0.00 0.00 0.00 3.46
890 896 4.484026 ACTAGGGATGTGATGAGGAGAT 57.516 45.455 0.00 0.00 0.00 2.75
934 942 5.551233 TCTTGTTCCTTCTGTGATAACAGG 58.449 41.667 10.50 0.00 38.23 4.00
976 985 0.320374 CACTTGTCCGGTGGCTAGAA 59.680 55.000 0.00 0.00 0.00 2.10
1003 1012 0.611714 GAGGACGGTTGGGTGTATGT 59.388 55.000 0.00 0.00 0.00 2.29
1014 1023 1.064979 GGGTGTATGTTGGGAACGGAT 60.065 52.381 0.00 0.00 0.00 4.18
1054 1063 1.604604 GCAGTACTTTTCCTGGTGCA 58.395 50.000 0.00 0.00 0.00 4.57
1176 1185 8.103948 TCAAAAAGATGAGATCTCCTTTTGAC 57.896 34.615 26.79 11.22 43.77 3.18
1278 1287 1.093159 CCAAGATGCTGAGAGGCAAC 58.907 55.000 0.00 0.00 45.68 4.17
1339 1370 6.602406 AGGGATCAACTGAAGATCAAAATGAG 59.398 38.462 13.17 0.00 42.84 2.90
1340 1371 6.600822 GGGATCAACTGAAGATCAAAATGAGA 59.399 38.462 13.17 0.00 42.84 3.27
1375 1416 1.432270 CTTCGCTTCGCCTGGGATTC 61.432 60.000 0.00 0.00 0.00 2.52
1385 1426 1.373570 CCTGGGATTCGCTGTCTTTC 58.626 55.000 2.19 0.00 0.00 2.62
1405 1446 1.607148 CGTTCCTGGTCCTTTTGGTTC 59.393 52.381 0.00 0.00 41.38 3.62
1421 1462 0.243907 GTTCTGCTAGTCTGGTGCGA 59.756 55.000 0.00 0.00 0.00 5.10
1445 1486 2.056223 GGTGGTAGGCTCCTGCGTA 61.056 63.158 0.00 0.00 40.82 4.42
1489 1531 4.425180 TGGTGCTGGTAGTTTAACTTGA 57.575 40.909 1.94 0.00 0.00 3.02
1707 1753 9.605955 TGTTAATTTCACTGTATCAATTTGTCG 57.394 29.630 0.00 0.00 0.00 4.35
1725 1771 5.427036 TGTCGTTTGAATTGGAACTAACC 57.573 39.130 0.00 0.00 0.00 2.85
1730 1776 6.072728 TCGTTTGAATTGGAACTAACCATGAG 60.073 38.462 0.00 0.00 39.82 2.90
1734 1780 1.295020 TGGAACTAACCATGAGGGGG 58.705 55.000 0.00 0.00 42.91 5.40
1774 1841 3.490348 AGTTTGGGACATGGAGTTTCTG 58.510 45.455 0.00 0.00 39.30 3.02
1790 1857 4.651045 AGTTTCTGCTCCCAAACTCAAATT 59.349 37.500 0.00 0.00 38.22 1.82
1807 1874 7.918076 ACTCAAATTCTCCCTCATAAACAGTA 58.082 34.615 0.00 0.00 0.00 2.74
1875 1942 8.662141 ACAAACATTAATGAACCGTCTACATAC 58.338 33.333 22.16 0.00 0.00 2.39
1876 1943 8.661257 CAAACATTAATGAACCGTCTACATACA 58.339 33.333 22.16 0.00 0.00 2.29
1877 1944 8.958119 AACATTAATGAACCGTCTACATACAT 57.042 30.769 22.16 0.00 0.00 2.29
1878 1945 8.365399 ACATTAATGAACCGTCTACATACATG 57.635 34.615 22.16 0.00 0.00 3.21
1879 1946 8.201464 ACATTAATGAACCGTCTACATACATGA 58.799 33.333 22.16 0.00 0.00 3.07
1880 1947 9.040939 CATTAATGAACCGTCTACATACATGAA 57.959 33.333 10.04 0.00 0.00 2.57
1881 1948 9.778741 ATTAATGAACCGTCTACATACATGAAT 57.221 29.630 0.00 0.00 0.00 2.57
1884 1951 9.778741 AATGAACCGTCTACATACATGAATATT 57.221 29.630 0.00 0.00 0.00 1.28
1885 1952 9.778741 ATGAACCGTCTACATACATGAATATTT 57.221 29.630 0.00 0.00 0.00 1.40
1886 1953 9.607988 TGAACCGTCTACATACATGAATATTTT 57.392 29.630 0.00 0.00 0.00 1.82
1887 1954 9.864034 GAACCGTCTACATACATGAATATTTTG 57.136 33.333 0.00 0.00 0.00 2.44
1888 1955 8.378172 ACCGTCTACATACATGAATATTTTGG 57.622 34.615 0.00 0.00 0.00 3.28
1889 1956 7.990886 ACCGTCTACATACATGAATATTTTGGT 59.009 33.333 0.00 0.00 0.00 3.67
1890 1957 8.282592 CCGTCTACATACATGAATATTTTGGTG 58.717 37.037 0.00 0.00 0.00 4.17
1891 1958 9.040939 CGTCTACATACATGAATATTTTGGTGA 57.959 33.333 0.00 0.00 0.00 4.02
1943 2010 4.574599 AGTCAATGCTCCAAAAACACTC 57.425 40.909 0.00 0.00 0.00 3.51
1950 2017 5.398603 TGCTCCAAAAACACTCTTTTTCA 57.601 34.783 0.00 0.00 30.00 2.69
1952 2019 5.868801 TGCTCCAAAAACACTCTTTTTCAAG 59.131 36.000 0.00 0.00 30.00 3.02
1954 2021 6.597832 TCCAAAAACACTCTTTTTCAAGGA 57.402 33.333 0.00 0.00 30.00 3.36
1955 2022 7.181569 TCCAAAAACACTCTTTTTCAAGGAT 57.818 32.000 0.00 0.00 30.00 3.24
1958 2025 8.177013 CCAAAAACACTCTTTTTCAAGGATTTG 58.823 33.333 0.00 0.00 35.57 2.32
1959 2026 7.848223 AAAACACTCTTTTTCAAGGATTTGG 57.152 32.000 0.00 0.00 34.97 3.28
1975 2045 5.369404 AGGATTTGGGAAATGGTTGTTTTCT 59.631 36.000 0.00 0.00 34.29 2.52
1979 2049 7.425224 TTTGGGAAATGGTTGTTTTCTAGAA 57.575 32.000 0.00 0.00 34.29 2.10
1982 2052 6.553100 TGGGAAATGGTTGTTTTCTAGAACAT 59.447 34.615 4.18 1.43 39.12 2.71
2022 2092 5.124617 TCAGCGGAAATTTGCATGTATGTAA 59.875 36.000 10.49 0.00 0.00 2.41
2120 2192 1.748122 AGCATTTGAGCTCGCCAGG 60.748 57.895 9.64 0.00 42.18 4.45
2121 2193 1.746615 GCATTTGAGCTCGCCAGGA 60.747 57.895 9.64 0.00 0.00 3.86
2124 2196 0.835941 ATTTGAGCTCGCCAGGAGAT 59.164 50.000 9.64 0.00 45.98 2.75
2125 2197 0.107993 TTTGAGCTCGCCAGGAGATG 60.108 55.000 9.64 0.00 42.62 2.90
2126 2198 0.972471 TTGAGCTCGCCAGGAGATGA 60.972 55.000 9.64 0.00 42.62 2.92
2127 2199 1.067250 GAGCTCGCCAGGAGATGAC 59.933 63.158 0.00 0.00 42.62 3.06
2128 2200 1.670949 GAGCTCGCCAGGAGATGACA 61.671 60.000 0.00 0.00 42.62 3.58
2129 2201 1.520342 GCTCGCCAGGAGATGACAC 60.520 63.158 0.00 0.00 46.23 3.67
2130 2202 1.893062 CTCGCCAGGAGATGACACA 59.107 57.895 0.00 0.00 46.23 3.72
2168 2249 3.753797 GGACTCCACTTGGATTTTCAGAC 59.246 47.826 0.00 0.00 44.46 3.51
2200 2283 9.766277 GAGTCTCAAAATTCTACATTTAGCTTG 57.234 33.333 0.00 0.00 0.00 4.01
2207 2290 7.793927 AATTCTACATTTAGCTTGCTACTCC 57.206 36.000 1.37 0.00 0.00 3.85
2209 2292 4.962995 TCTACATTTAGCTTGCTACTCCCT 59.037 41.667 1.37 0.00 0.00 4.20
2234 2317 6.555463 TTTTCGGGGACATCTTATTACTCT 57.445 37.500 0.00 0.00 0.00 3.24
2235 2318 5.786264 TTCGGGGACATCTTATTACTCTC 57.214 43.478 0.00 0.00 0.00 3.20
2236 2319 3.819337 TCGGGGACATCTTATTACTCTCG 59.181 47.826 0.00 0.00 0.00 4.04
2237 2320 3.568853 CGGGGACATCTTATTACTCTCGT 59.431 47.826 0.00 0.00 0.00 4.18
2238 2321 4.037684 CGGGGACATCTTATTACTCTCGTT 59.962 45.833 0.00 0.00 0.00 3.85
2239 2322 5.451520 CGGGGACATCTTATTACTCTCGTTT 60.452 44.000 0.00 0.00 0.00 3.60
2240 2323 6.346896 GGGGACATCTTATTACTCTCGTTTT 58.653 40.000 0.00 0.00 0.00 2.43
2241 2324 7.495055 GGGGACATCTTATTACTCTCGTTTTA 58.505 38.462 0.00 0.00 0.00 1.52
2242 2325 7.983484 GGGGACATCTTATTACTCTCGTTTTAA 59.017 37.037 0.00 0.00 0.00 1.52
2243 2326 9.374838 GGGACATCTTATTACTCTCGTTTTAAA 57.625 33.333 0.00 0.00 0.00 1.52
2252 2335 8.626093 ATTACTCTCGTTTTAAAGTATCGGTC 57.374 34.615 0.00 0.00 0.00 4.79
2253 2336 6.264841 ACTCTCGTTTTAAAGTATCGGTCT 57.735 37.500 0.00 0.00 0.00 3.85
2254 2337 7.383102 ACTCTCGTTTTAAAGTATCGGTCTA 57.617 36.000 0.00 0.00 0.00 2.59
2255 2338 7.994194 ACTCTCGTTTTAAAGTATCGGTCTAT 58.006 34.615 0.00 0.00 0.00 1.98
2256 2339 7.914346 ACTCTCGTTTTAAAGTATCGGTCTATG 59.086 37.037 0.00 0.00 0.00 2.23
2257 2340 6.694411 TCTCGTTTTAAAGTATCGGTCTATGC 59.306 38.462 0.00 0.00 0.00 3.14
2258 2341 6.331845 TCGTTTTAAAGTATCGGTCTATGCA 58.668 36.000 0.00 0.00 0.00 3.96
2259 2342 6.982141 TCGTTTTAAAGTATCGGTCTATGCAT 59.018 34.615 3.79 3.79 0.00 3.96
2260 2343 7.168637 TCGTTTTAAAGTATCGGTCTATGCATC 59.831 37.037 0.19 0.00 0.00 3.91
2261 2344 7.042992 CGTTTTAAAGTATCGGTCTATGCATCA 60.043 37.037 0.19 0.00 0.00 3.07
2262 2345 8.609176 GTTTTAAAGTATCGGTCTATGCATCAA 58.391 33.333 0.19 0.00 0.00 2.57
2263 2346 8.902540 TTTAAAGTATCGGTCTATGCATCAAT 57.097 30.769 0.19 0.00 0.00 2.57
2264 2347 8.902540 TTAAAGTATCGGTCTATGCATCAATT 57.097 30.769 0.19 0.00 0.00 2.32
2265 2348 7.807977 AAAGTATCGGTCTATGCATCAATTT 57.192 32.000 0.19 0.00 0.00 1.82
2266 2349 7.426929 AAGTATCGGTCTATGCATCAATTTC 57.573 36.000 0.19 0.00 0.00 2.17
2267 2350 6.524734 AGTATCGGTCTATGCATCAATTTCA 58.475 36.000 0.19 0.00 0.00 2.69
2268 2351 5.936686 ATCGGTCTATGCATCAATTTCAG 57.063 39.130 0.19 0.00 0.00 3.02
2269 2352 4.769688 TCGGTCTATGCATCAATTTCAGT 58.230 39.130 0.19 0.00 0.00 3.41
2270 2353 4.811024 TCGGTCTATGCATCAATTTCAGTC 59.189 41.667 0.19 0.00 0.00 3.51
2271 2354 4.813161 CGGTCTATGCATCAATTTCAGTCT 59.187 41.667 0.19 0.00 0.00 3.24
2272 2355 5.295292 CGGTCTATGCATCAATTTCAGTCTT 59.705 40.000 0.19 0.00 0.00 3.01
2273 2356 6.479990 CGGTCTATGCATCAATTTCAGTCTTA 59.520 38.462 0.19 0.00 0.00 2.10
2274 2357 7.172190 CGGTCTATGCATCAATTTCAGTCTTAT 59.828 37.037 0.19 0.00 0.00 1.73
2275 2358 8.844244 GGTCTATGCATCAATTTCAGTCTTATT 58.156 33.333 0.19 0.00 0.00 1.40
2280 2363 9.932207 ATGCATCAATTTCAGTCTTATTTTTCA 57.068 25.926 0.00 0.00 0.00 2.69
2281 2364 9.932207 TGCATCAATTTCAGTCTTATTTTTCAT 57.068 25.926 0.00 0.00 0.00 2.57
2310 2393 9.541143 TGGACATTTTTCCAAAATTCTTTACTC 57.459 29.630 0.00 0.00 43.04 2.59
2311 2394 9.541143 GGACATTTTTCCAAAATTCTTTACTCA 57.459 29.630 0.00 0.00 35.49 3.41
2318 2401 9.762933 TTTCCAAAATTCTTTACTCAAATGAGG 57.237 29.630 14.50 0.00 46.13 3.86
2319 2402 7.895759 TCCAAAATTCTTTACTCAAATGAGGG 58.104 34.615 14.50 2.30 46.13 4.30
2320 2403 7.728083 TCCAAAATTCTTTACTCAAATGAGGGA 59.272 33.333 14.50 4.41 46.13 4.20
2321 2404 8.031277 CCAAAATTCTTTACTCAAATGAGGGAG 58.969 37.037 14.50 8.87 46.13 4.30
2322 2405 6.765915 AATTCTTTACTCAAATGAGGGAGC 57.234 37.500 14.50 0.00 46.13 4.70
2323 2406 4.908601 TCTTTACTCAAATGAGGGAGCA 57.091 40.909 14.50 0.00 46.13 4.26
2324 2407 5.241403 TCTTTACTCAAATGAGGGAGCAA 57.759 39.130 14.50 0.18 46.13 3.91
2325 2408 5.248640 TCTTTACTCAAATGAGGGAGCAAG 58.751 41.667 14.50 8.50 46.13 4.01
2326 2409 2.503895 ACTCAAATGAGGGAGCAAGG 57.496 50.000 14.50 0.00 46.13 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.157289 CCAGGATTCACAACATTTGAGGAG 59.843 45.833 0.00 0.00 0.00 3.69
33 34 7.588143 ACGACATATAATAGAAGCTGCATTC 57.412 36.000 1.02 3.15 0.00 2.67
48 49 9.745880 GAGTTAAGAAGGATCAAACGACATATA 57.254 33.333 0.00 0.00 32.17 0.86
50 51 7.608153 TGAGTTAAGAAGGATCAAACGACATA 58.392 34.615 0.00 0.00 32.17 2.29
51 52 6.464222 TGAGTTAAGAAGGATCAAACGACAT 58.536 36.000 0.00 0.00 32.17 3.06
52 53 5.849510 TGAGTTAAGAAGGATCAAACGACA 58.150 37.500 0.00 0.00 32.17 4.35
132 134 0.823356 GCTTGTCCAGCTTCCCAACA 60.823 55.000 0.00 0.00 46.27 3.33
189 191 7.513856 ACCATTTTACCAAATGCTACCTTTTT 58.486 30.769 2.66 0.00 45.63 1.94
198 200 4.799564 TCTGGACCATTTTACCAAATGC 57.200 40.909 0.00 0.00 45.63 3.56
228 230 1.060244 AGGCCTCCCTTATCCTTGGAT 60.060 52.381 0.00 7.37 38.74 3.41
237 239 1.316969 CACCCCTAGGCCTCCCTTA 59.683 63.158 9.68 0.00 42.87 2.69
249 251 4.202524 TGTTTATGCAAGTCTTACACCCCT 60.203 41.667 0.00 0.00 0.00 4.79
378 381 7.396339 GGGGAGTCACCAAATTTAGATTTAACT 59.604 37.037 6.53 0.00 41.20 2.24
402 405 1.202330 TAATGGCCTTGCAAATGGGG 58.798 50.000 3.32 0.00 0.00 4.96
411 414 3.017048 TGGACTTCCATAATGGCCTTG 57.983 47.619 3.32 0.00 42.01 3.61
424 427 4.093556 CGCAAGGTAGAATTCTTGGACTTC 59.906 45.833 14.36 6.81 40.31 3.01
446 449 0.908180 AAGTAACACCCTCCTCCCCG 60.908 60.000 0.00 0.00 0.00 5.73
579 583 5.908341 TCACCCACACCATTTTTAAAGTTC 58.092 37.500 0.00 0.00 0.00 3.01
581 585 7.604657 TTATCACCCACACCATTTTTAAAGT 57.395 32.000 0.00 0.00 0.00 2.66
934 942 0.178990 ACAGGTGCTGGGAAGTTTCC 60.179 55.000 2.17 2.17 46.82 3.13
976 985 1.211949 CCCAACCGTCCTCCACATAAT 59.788 52.381 0.00 0.00 0.00 1.28
1003 1012 2.194201 GGACAAAGATCCGTTCCCAA 57.806 50.000 0.00 0.00 0.00 4.12
1054 1063 2.444766 CCCCATCAGGAAGGAAGCTATT 59.555 50.000 0.00 0.00 38.24 1.73
1278 1287 2.350425 CGCATCATGTTCGCAGCG 60.350 61.111 9.06 9.06 39.17 5.18
1339 1370 2.481104 CGAAGCTGGAGAGACAATCCTC 60.481 54.545 0.00 0.00 37.74 3.71
1340 1371 1.480137 CGAAGCTGGAGAGACAATCCT 59.520 52.381 0.00 0.00 37.74 3.24
1375 1416 0.600255 ACCAGGAACGAAAGACAGCG 60.600 55.000 0.00 0.00 0.00 5.18
1385 1426 1.607148 GAACCAAAAGGACCAGGAACG 59.393 52.381 0.00 0.00 0.00 3.95
1405 1446 0.174389 ACATCGCACCAGACTAGCAG 59.826 55.000 0.00 0.00 0.00 4.24
1421 1462 1.004745 CAGGAGCCTACCACCAAACAT 59.995 52.381 0.00 0.00 0.00 2.71
1445 1486 2.821969 CAGGCTAACCAAAGTCATGCTT 59.178 45.455 0.00 0.00 39.06 3.91
1489 1531 6.463755 GGAAAACCCAGTGACACCAAAATATT 60.464 38.462 0.84 0.00 34.14 1.28
1691 1737 7.594758 CCAATTCAAACGACAAATTGATACAGT 59.405 33.333 0.00 0.00 40.97 3.55
1693 1739 7.652727 TCCAATTCAAACGACAAATTGATACA 58.347 30.769 0.00 0.00 40.97 2.29
1696 1742 7.209475 AGTTCCAATTCAAACGACAAATTGAT 58.791 30.769 0.00 0.00 40.97 2.57
1703 1749 4.882427 TGGTTAGTTCCAATTCAAACGACA 59.118 37.500 0.00 0.00 34.24 4.35
1707 1753 6.389906 CCTCATGGTTAGTTCCAATTCAAAC 58.610 40.000 0.00 0.00 41.09 2.93
1725 1771 3.766051 CCTTCTTTTCTTTCCCCCTCATG 59.234 47.826 0.00 0.00 0.00 3.07
1730 1776 4.678256 AGAATCCTTCTTTTCTTTCCCCC 58.322 43.478 0.00 0.00 36.36 5.40
1734 1780 8.300286 CCCAAACTAGAATCCTTCTTTTCTTTC 58.700 37.037 0.00 0.00 41.14 2.62
1774 1841 2.493675 GGGAGAATTTGAGTTTGGGAGC 59.506 50.000 0.00 0.00 0.00 4.70
1778 1845 7.039784 TGTTTATGAGGGAGAATTTGAGTTTGG 60.040 37.037 0.00 0.00 0.00 3.28
1783 1850 8.792830 TTACTGTTTATGAGGGAGAATTTGAG 57.207 34.615 0.00 0.00 0.00 3.02
1830 1897 9.985730 ATGTTTGTTGACAAAACATATCAGATT 57.014 25.926 13.97 0.00 46.08 2.40
1858 1925 9.778741 AATATTCATGTATGTAGACGGTTCATT 57.221 29.630 0.00 0.00 0.00 2.57
1879 1946 9.541143 ACGAATGTTTTTCTTCACCAAAATATT 57.459 25.926 0.00 0.00 36.78 1.28
1882 1949 8.934507 TTACGAATGTTTTTCTTCACCAAAAT 57.065 26.923 0.00 0.00 0.00 1.82
1883 1950 8.758633 TTTACGAATGTTTTTCTTCACCAAAA 57.241 26.923 0.00 0.00 0.00 2.44
1884 1951 8.934507 ATTTACGAATGTTTTTCTTCACCAAA 57.065 26.923 0.00 0.00 0.00 3.28
1885 1952 9.453325 GTATTTACGAATGTTTTTCTTCACCAA 57.547 29.630 0.00 0.00 0.00 3.67
1886 1953 8.842280 AGTATTTACGAATGTTTTTCTTCACCA 58.158 29.630 0.00 0.00 0.00 4.17
1887 1954 9.326339 GAGTATTTACGAATGTTTTTCTTCACC 57.674 33.333 0.00 0.00 0.00 4.02
1890 1957 9.543018 CCAGAGTATTTACGAATGTTTTTCTTC 57.457 33.333 0.00 0.00 0.00 2.87
1891 1958 9.280174 TCCAGAGTATTTACGAATGTTTTTCTT 57.720 29.630 0.00 0.00 0.00 2.52
1892 1959 8.842358 TCCAGAGTATTTACGAATGTTTTTCT 57.158 30.769 0.00 0.00 0.00 2.52
1893 1960 9.887406 TTTCCAGAGTATTTACGAATGTTTTTC 57.113 29.630 0.00 0.00 0.00 2.29
1943 2010 6.298361 ACCATTTCCCAAATCCTTGAAAAAG 58.702 36.000 0.00 0.00 34.14 2.27
1950 2017 5.645056 AAACAACCATTTCCCAAATCCTT 57.355 34.783 0.00 0.00 0.00 3.36
1952 2019 5.620206 AGAAAACAACCATTTCCCAAATCC 58.380 37.500 0.00 0.00 37.47 3.01
1954 2021 7.610580 TCTAGAAAACAACCATTTCCCAAAT 57.389 32.000 0.00 0.00 37.47 2.32
1955 2022 7.093289 TGTTCTAGAAAACAACCATTTCCCAAA 60.093 33.333 6.78 0.00 37.47 3.28
1958 2025 6.399639 TGTTCTAGAAAACAACCATTTCCC 57.600 37.500 6.78 0.00 37.47 3.97
1959 2026 9.626045 CTAATGTTCTAGAAAACAACCATTTCC 57.374 33.333 17.06 0.00 42.10 3.13
1999 2069 3.772932 ACATACATGCAAATTTCCGCTG 58.227 40.909 0.00 1.82 0.00 5.18
2000 2070 5.574891 TTACATACATGCAAATTTCCGCT 57.425 34.783 0.00 0.00 0.00 5.52
2001 2071 6.639671 TTTTACATACATGCAAATTTCCGC 57.360 33.333 0.00 0.00 0.00 5.54
2022 2092 9.971922 TTTTGTCCAAAACATTCACAAATTTTT 57.028 22.222 1.18 0.00 36.95 1.94
2077 2149 9.413734 CTCCCTCCTGAATAGTAAAATCAAAAT 57.586 33.333 0.00 0.00 0.00 1.82
2078 2150 7.339466 GCTCCCTCCTGAATAGTAAAATCAAAA 59.661 37.037 0.00 0.00 0.00 2.44
2114 2186 0.107993 ACATGTGTCATCTCCTGGCG 60.108 55.000 0.00 0.00 29.52 5.69
2120 2192 2.816087 AGTGGCAAACATGTGTCATCTC 59.184 45.455 0.00 0.00 35.16 2.75
2121 2193 2.867624 AGTGGCAAACATGTGTCATCT 58.132 42.857 0.00 0.00 35.16 2.90
2124 2196 3.207265 AGTAGTGGCAAACATGTGTCA 57.793 42.857 0.00 0.00 0.00 3.58
2125 2197 3.304659 CCAAGTAGTGGCAAACATGTGTC 60.305 47.826 0.00 0.00 41.72 3.67
2126 2198 2.622942 CCAAGTAGTGGCAAACATGTGT 59.377 45.455 0.00 0.00 41.72 3.72
2127 2199 3.287312 CCAAGTAGTGGCAAACATGTG 57.713 47.619 0.00 0.00 41.72 3.21
2215 2298 3.568853 ACGAGAGTAATAAGATGTCCCCG 59.431 47.826 0.00 0.00 46.88 5.73
2231 2314 7.096558 GCATAGACCGATACTTTAAAACGAGAG 60.097 40.741 0.00 0.00 0.00 3.20
2232 2315 6.694411 GCATAGACCGATACTTTAAAACGAGA 59.306 38.462 0.00 0.00 0.00 4.04
2233 2316 6.474427 TGCATAGACCGATACTTTAAAACGAG 59.526 38.462 0.00 0.00 0.00 4.18
2234 2317 6.331845 TGCATAGACCGATACTTTAAAACGA 58.668 36.000 0.00 0.00 0.00 3.85
2235 2318 6.578020 TGCATAGACCGATACTTTAAAACG 57.422 37.500 0.00 0.00 0.00 3.60
2236 2319 8.138365 TGATGCATAGACCGATACTTTAAAAC 57.862 34.615 0.00 0.00 0.00 2.43
2237 2320 8.725405 TTGATGCATAGACCGATACTTTAAAA 57.275 30.769 0.00 0.00 0.00 1.52
2238 2321 8.902540 ATTGATGCATAGACCGATACTTTAAA 57.097 30.769 0.00 0.00 0.00 1.52
2239 2322 8.902540 AATTGATGCATAGACCGATACTTTAA 57.097 30.769 0.00 0.00 0.00 1.52
2240 2323 8.902540 AAATTGATGCATAGACCGATACTTTA 57.097 30.769 0.00 0.00 0.00 1.85
2241 2324 7.498900 TGAAATTGATGCATAGACCGATACTTT 59.501 33.333 0.00 0.00 0.00 2.66
2242 2325 6.992123 TGAAATTGATGCATAGACCGATACTT 59.008 34.615 0.00 0.00 0.00 2.24
2243 2326 6.524734 TGAAATTGATGCATAGACCGATACT 58.475 36.000 0.00 0.00 0.00 2.12
2244 2327 6.425114 ACTGAAATTGATGCATAGACCGATAC 59.575 38.462 0.00 0.00 0.00 2.24
2245 2328 6.524734 ACTGAAATTGATGCATAGACCGATA 58.475 36.000 0.00 0.00 0.00 2.92
2246 2329 5.371526 ACTGAAATTGATGCATAGACCGAT 58.628 37.500 0.00 0.00 0.00 4.18
2247 2330 4.769688 ACTGAAATTGATGCATAGACCGA 58.230 39.130 0.00 0.00 0.00 4.69
2248 2331 4.813161 AGACTGAAATTGATGCATAGACCG 59.187 41.667 0.00 0.00 0.00 4.79
2249 2332 6.690194 AAGACTGAAATTGATGCATAGACC 57.310 37.500 0.00 0.00 0.00 3.85
2254 2337 9.932207 TGAAAAATAAGACTGAAATTGATGCAT 57.068 25.926 0.00 0.00 0.00 3.96
2255 2338 9.932207 ATGAAAAATAAGACTGAAATTGATGCA 57.068 25.926 0.00 0.00 0.00 3.96
2284 2367 9.541143 GAGTAAAGAATTTTGGAAAAATGTCCA 57.459 29.630 0.00 0.00 46.24 4.02
2285 2368 9.541143 TGAGTAAAGAATTTTGGAAAAATGTCC 57.459 29.630 0.00 0.00 40.09 4.02
2292 2375 9.762933 CCTCATTTGAGTAAAGAATTTTGGAAA 57.237 29.630 6.81 0.00 40.48 3.13
2293 2376 8.367156 CCCTCATTTGAGTAAAGAATTTTGGAA 58.633 33.333 6.81 0.00 40.48 3.53
2294 2377 7.728083 TCCCTCATTTGAGTAAAGAATTTTGGA 59.272 33.333 6.81 0.00 40.48 3.53
2295 2378 7.895759 TCCCTCATTTGAGTAAAGAATTTTGG 58.104 34.615 6.81 0.00 40.48 3.28
2296 2379 7.543520 GCTCCCTCATTTGAGTAAAGAATTTTG 59.456 37.037 6.81 0.00 40.48 2.44
2297 2380 7.233348 TGCTCCCTCATTTGAGTAAAGAATTTT 59.767 33.333 6.81 0.00 40.48 1.82
2298 2381 6.721208 TGCTCCCTCATTTGAGTAAAGAATTT 59.279 34.615 6.81 0.00 40.48 1.82
2299 2382 6.248433 TGCTCCCTCATTTGAGTAAAGAATT 58.752 36.000 6.81 0.00 40.48 2.17
2300 2383 5.819991 TGCTCCCTCATTTGAGTAAAGAAT 58.180 37.500 6.81 0.00 40.48 2.40
2301 2384 5.241403 TGCTCCCTCATTTGAGTAAAGAA 57.759 39.130 6.81 0.00 40.48 2.52
2302 2385 4.908601 TGCTCCCTCATTTGAGTAAAGA 57.091 40.909 6.81 0.00 40.48 2.52
2303 2386 4.397417 CCTTGCTCCCTCATTTGAGTAAAG 59.603 45.833 6.81 2.73 40.48 1.85
2304 2387 4.335416 CCTTGCTCCCTCATTTGAGTAAA 58.665 43.478 6.81 0.00 40.48 2.01
2305 2388 3.955471 CCTTGCTCCCTCATTTGAGTAA 58.045 45.455 6.81 0.00 40.48 2.24
2306 2389 3.634397 CCTTGCTCCCTCATTTGAGTA 57.366 47.619 6.81 0.00 40.48 2.59
2307 2390 2.503895 CCTTGCTCCCTCATTTGAGT 57.496 50.000 6.81 0.00 40.48 3.41


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

AutoCloner maintained by Alex Coulton.