Multiple sequence alignment - TraesCS1B01G192000

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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 TraesCS1B01G192000 chr1B 100.000 4211 0 0 1 4211 343658979 343663189 0.000000e+00 7777
1 TraesCS1B01G192000 chr1B 94.898 98 4 1 1888 1984 112863574 112863671 7.290000e-33 152
2 TraesCS1B01G192000 chr1A 96.469 2209 66 8 1974 4180 343616943 343619141 0.000000e+00 3637
3 TraesCS1B01G192000 chr1A 94.275 1904 73 14 6 1889 343615057 343616944 0.000000e+00 2880
4 TraesCS1B01G192000 chr1D 94.462 1896 72 12 1 1889 270018327 270020196 0.000000e+00 2889
5 TraesCS1B01G192000 chr1D 96.564 1426 45 4 1974 3397 270020195 270021618 0.000000e+00 2359
6 TraesCS1B01G192000 chr1D 95.455 770 32 2 3436 4205 270021617 270022383 0.000000e+00 1225
7 TraesCS1B01G192000 chr5A 94.774 574 29 1 3638 4211 430642518 430641946 0.000000e+00 893
8 TraesCS1B01G192000 chr5D 94.425 574 28 4 3638 4211 325956363 325956932 0.000000e+00 880
9 TraesCS1B01G192000 chr7B 93.229 576 32 4 3638 4211 5917113 5917683 0.000000e+00 841
10 TraesCS1B01G192000 chr6B 95.050 101 3 2 1881 1979 154545059 154545159 1.570000e-34 158
11 TraesCS1B01G192000 chr6B 89.831 118 7 5 1889 2003 679569169 679569284 3.390000e-31 147
12 TraesCS1B01G192000 chr3B 95.050 101 3 2 1881 1979 512457410 512457510 1.570000e-34 158
13 TraesCS1B01G192000 chr5B 94.175 103 5 1 1875 1976 135750632 135750734 5.640000e-34 156
14 TraesCS1B01G192000 chr5B 93.269 104 5 2 1881 1982 345770303 345770200 7.290000e-33 152
15 TraesCS1B01G192000 chr4A 95.876 97 3 1 1881 1976 723335662 723335566 5.640000e-34 156
16 TraesCS1B01G192000 chr4B 93.269 104 5 2 1881 1982 189189381 189189278 7.290000e-33 152
17 TraesCS1B01G192000 chr2A 92.453 106 8 0 1879 1984 407739278 407739173 7.290000e-33 152


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 TraesCS1B01G192000 chr1B 343658979 343663189 4210 False 7777.000000 7777 100.000000 1 4211 1 chr1B.!!$F2 4210
1 TraesCS1B01G192000 chr1A 343615057 343619141 4084 False 3258.500000 3637 95.372000 6 4180 2 chr1A.!!$F1 4174
2 TraesCS1B01G192000 chr1D 270018327 270022383 4056 False 2157.666667 2889 95.493667 1 4205 3 chr1D.!!$F1 4204
3 TraesCS1B01G192000 chr5A 430641946 430642518 572 True 893.000000 893 94.774000 3638 4211 1 chr5A.!!$R1 573
4 TraesCS1B01G192000 chr5D 325956363 325956932 569 False 880.000000 880 94.425000 3638 4211 1 chr5D.!!$F1 573
5 TraesCS1B01G192000 chr7B 5917113 5917683 570 False 841.000000 841 93.229000 3638 4211 1 chr7B.!!$F1 573

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
456 463 0.034337 AGTGGAATTGCGTGTACCGT 59.966 50.000 5.79 0.0 39.32 4.83 F
1410 1434 1.066430 GGGTTCGGAACAGTCATAGCA 60.066 52.381 21.36 0.0 0.00 3.49 F
2330 2355 1.825090 CACACTATGCAAGCTGGGAA 58.175 50.000 0.00 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1542 2.149973 AGGCCATCCTGAATTCCAAC 57.850 50.000 5.01 0.0 42.34 3.77 R
3099 3124 0.741221 GGTCATGGCGAGTGAACTCC 60.741 60.000 4.90 0.0 39.79 3.85 R
3792 3851 1.271102 TGCCGTGGTTTAATTGCTTCC 59.729 47.619 0.00 0.0 0.00 3.46 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
32 33 2.749044 AATCACCGCAGCTGGCAG 60.749 61.111 17.12 10.94 45.17 4.85
304 308 2.104111 TCAGCGTCAGGAAAAGGAGAAA 59.896 45.455 0.00 0.00 0.00 2.52
379 383 3.257127 CGTCCTCTCCCTTCCTGATATTC 59.743 52.174 0.00 0.00 0.00 1.75
382 386 3.501349 CTCTCCCTTCCTGATATTCGGA 58.499 50.000 0.00 0.00 0.00 4.55
390 394 5.509840 CCTTCCTGATATTCGGAACACCTAG 60.510 48.000 0.00 0.00 35.55 3.02
391 395 4.800023 TCCTGATATTCGGAACACCTAGA 58.200 43.478 0.00 0.00 0.00 2.43
392 396 4.583489 TCCTGATATTCGGAACACCTAGAC 59.417 45.833 0.00 0.00 0.00 2.59
393 397 4.537965 CTGATATTCGGAACACCTAGACG 58.462 47.826 0.00 0.00 0.00 4.18
394 398 3.317149 TGATATTCGGAACACCTAGACGG 59.683 47.826 0.00 0.00 39.35 4.79
395 399 0.175073 ATTCGGAACACCTAGACGGC 59.825 55.000 0.00 0.00 35.61 5.68
396 400 2.202570 CGGAACACCTAGACGGCG 60.203 66.667 4.80 4.80 35.61 6.46
397 401 2.968206 GGAACACCTAGACGGCGT 59.032 61.111 14.65 14.65 35.61 5.68
398 402 1.291272 GGAACACCTAGACGGCGTT 59.709 57.895 16.19 6.99 40.65 4.84
431 438 3.128349 GGACGAACAGCTGTTTAGTCAA 58.872 45.455 39.19 0.00 42.35 3.18
452 459 5.877564 TCAAATATCAGTGGAATTGCGTGTA 59.122 36.000 0.00 0.00 0.00 2.90
453 460 5.734855 AATATCAGTGGAATTGCGTGTAC 57.265 39.130 0.00 0.00 0.00 2.90
454 461 1.803334 TCAGTGGAATTGCGTGTACC 58.197 50.000 0.00 0.00 0.00 3.34
455 462 0.442310 CAGTGGAATTGCGTGTACCG 59.558 55.000 0.00 0.00 40.40 4.02
456 463 0.034337 AGTGGAATTGCGTGTACCGT 59.966 50.000 5.79 0.00 39.32 4.83
457 464 1.273048 AGTGGAATTGCGTGTACCGTA 59.727 47.619 5.79 0.00 39.32 4.02
458 465 1.657094 GTGGAATTGCGTGTACCGTAG 59.343 52.381 5.79 0.00 39.32 3.51
481 488 1.324736 CAATCTACGACGGAAAGCAGC 59.675 52.381 0.00 0.00 0.00 5.25
591 600 5.163301 GCTGTGAGGAGAATAGGGATAACAA 60.163 44.000 0.00 0.00 0.00 2.83
823 835 1.604604 ACATTCCAGAAACCACACGG 58.395 50.000 0.00 0.00 38.77 4.94
878 890 9.709495 ACGAAATTTAGTATGTGTAAGGTTACA 57.291 29.630 1.71 0.00 41.06 2.41
919 931 7.256475 CCAGACCTTATATAAAGAGCTGATGGT 60.256 40.741 14.62 7.99 0.00 3.55
1200 1224 6.654161 TCTCGCTCTTGTATATACTAGAACCC 59.346 42.308 22.01 14.45 37.55 4.11
1293 1317 6.030849 CGCAGGTAATCTACTAGCATCATAC 58.969 44.000 0.00 0.00 0.00 2.39
1310 1334 9.334947 AGCATCATACTGATTATAATATGTGCC 57.665 33.333 18.02 3.07 34.28 5.01
1324 1348 5.772825 ATATGTGCCATTTGTGGATGTAC 57.227 39.130 0.00 0.00 0.00 2.90
1410 1434 1.066430 GGGTTCGGAACAGTCATAGCA 60.066 52.381 21.36 0.00 0.00 3.49
1473 1497 4.221041 TCTGGAAAAGTTTTCCGTGGTTTT 59.779 37.500 32.25 0.00 41.43 2.43
1511 1535 5.635280 CAGTATTTCTGATAGGTATGCACCG 59.365 44.000 0.00 0.00 46.98 4.94
1583 1607 4.460382 AGCATTTTCAATGACAGGATTCGT 59.540 37.500 0.49 0.00 0.00 3.85
1609 1633 5.106317 GCAACGTATTTGAGATTCTTCCCAA 60.106 40.000 0.00 0.00 37.39 4.12
1776 1800 6.516860 GCCTCTTTATGAGCCTCTTCGTATTA 60.517 42.308 0.00 0.00 41.35 0.98
1895 1919 9.064706 TGATGCTAACATACTAACTAGTACTCC 57.935 37.037 0.00 0.00 41.18 3.85
1896 1920 7.814264 TGCTAACATACTAACTAGTACTCCC 57.186 40.000 0.00 0.00 41.18 4.30
1897 1921 7.580910 TGCTAACATACTAACTAGTACTCCCT 58.419 38.462 0.00 0.00 41.18 4.20
1898 1922 7.718753 TGCTAACATACTAACTAGTACTCCCTC 59.281 40.741 0.00 0.00 41.18 4.30
1899 1923 7.174772 GCTAACATACTAACTAGTACTCCCTCC 59.825 44.444 0.00 0.00 41.18 4.30
1900 1924 5.619220 ACATACTAACTAGTACTCCCTCCG 58.381 45.833 0.00 0.00 41.18 4.63
1901 1925 5.131809 ACATACTAACTAGTACTCCCTCCGT 59.868 44.000 0.00 0.00 41.18 4.69
1902 1926 6.327626 ACATACTAACTAGTACTCCCTCCGTA 59.672 42.308 0.00 0.00 41.18 4.02
1903 1927 5.700402 ACTAACTAGTACTCCCTCCGTAA 57.300 43.478 0.00 0.00 34.13 3.18
1904 1928 6.067217 ACTAACTAGTACTCCCTCCGTAAA 57.933 41.667 0.00 0.00 34.13 2.01
1905 1929 5.883115 ACTAACTAGTACTCCCTCCGTAAAC 59.117 44.000 0.00 0.00 34.13 2.01
1906 1930 4.582973 ACTAGTACTCCCTCCGTAAACT 57.417 45.455 0.00 0.00 0.00 2.66
1907 1931 5.700402 ACTAGTACTCCCTCCGTAAACTA 57.300 43.478 0.00 0.00 0.00 2.24
1908 1932 6.067217 ACTAGTACTCCCTCCGTAAACTAA 57.933 41.667 0.00 0.00 0.00 2.24
1909 1933 6.667661 ACTAGTACTCCCTCCGTAAACTAAT 58.332 40.000 0.00 0.00 0.00 1.73
1910 1934 7.806180 ACTAGTACTCCCTCCGTAAACTAATA 58.194 38.462 0.00 0.00 0.00 0.98
1911 1935 8.443979 ACTAGTACTCCCTCCGTAAACTAATAT 58.556 37.037 0.00 0.00 0.00 1.28
1912 1936 9.950496 CTAGTACTCCCTCCGTAAACTAATATA 57.050 37.037 0.00 0.00 0.00 0.86
1914 1938 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1915 1939 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1916 1940 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1917 1941 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1918 1942 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1919 1943 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
1920 1944 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1921 1945 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1922 1946 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1923 1947 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1924 1948 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1936 1960 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1937 1961 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1938 1962 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
1939 1963 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
1940 1964 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
1951 1975 9.918630 TCACTACTTTAGTAATTTAAACGCTCT 57.081 29.630 0.00 0.00 37.23 4.09
1970 1994 9.490379 AACGCTCTTATATTATTTTACAGAGGG 57.510 33.333 8.36 8.36 42.53 4.30
1971 1995 8.867097 ACGCTCTTATATTATTTTACAGAGGGA 58.133 33.333 14.96 0.00 40.49 4.20
1972 1996 9.360093 CGCTCTTATATTATTTTACAGAGGGAG 57.640 37.037 4.76 0.00 40.49 4.30
2053 2077 5.296748 TCTTACCAAAGAAAAATTGCAGGC 58.703 37.500 0.00 0.00 38.81 4.85
2060 2084 2.137523 GAAAAATTGCAGGCTGTGTGG 58.862 47.619 17.16 0.00 0.00 4.17
2071 2095 4.012374 CAGGCTGTGTGGATGAGTATTTT 58.988 43.478 6.28 0.00 0.00 1.82
2330 2355 1.825090 CACACTATGCAAGCTGGGAA 58.175 50.000 0.00 0.00 0.00 3.97
2378 2403 5.650266 CAGTTACCCATGGCAAAAGTATGTA 59.350 40.000 6.09 0.00 0.00 2.29
2546 2571 8.637986 AGCAAAACCATCTTTCTGTAAATAACA 58.362 29.630 0.00 0.00 36.42 2.41
2880 2905 4.125703 CCTCATTCAAGACTGATACAGCC 58.874 47.826 0.00 0.00 34.37 4.85
2883 2908 4.467438 TCATTCAAGACTGATACAGCCTCA 59.533 41.667 0.00 0.00 34.37 3.86
2917 2942 5.537674 AGGAAGAACACAAAAGCAGATCAAT 59.462 36.000 0.00 0.00 0.00 2.57
3099 3124 4.640364 TGGAAAGGGCTGCAAATTTTAAG 58.360 39.130 0.50 0.00 0.00 1.85
3249 3274 5.111989 TCAAAGCAGCAGTGTATAGATCAC 58.888 41.667 0.00 0.00 36.22 3.06
3294 3319 5.689383 TCTTTGGTTCGAAAAAGATGAGG 57.311 39.130 17.16 0.00 37.46 3.86
3303 3328 3.375299 CGAAAAAGATGAGGGGTGTGATC 59.625 47.826 0.00 0.00 0.00 2.92
3326 3352 8.879342 ATCTCAATAACTACTGTTAGCATGAC 57.121 34.615 0.00 0.00 41.33 3.06
3340 3366 7.109501 TGTTAGCATGACATACATTTAGGTGT 58.890 34.615 0.00 0.00 37.07 4.16
3341 3367 7.609918 TGTTAGCATGACATACATTTAGGTGTT 59.390 33.333 0.00 0.00 37.07 3.32
3385 3411 1.069978 TGAGTCGTTTGCAGATGTCCA 59.930 47.619 0.00 0.00 0.00 4.02
3388 3414 2.143122 GTCGTTTGCAGATGTCCAAGA 58.857 47.619 0.00 0.00 0.00 3.02
3396 3422 3.118847 TGCAGATGTCCAAGAGATCAGAC 60.119 47.826 4.76 0.00 35.21 3.51
3397 3423 3.132646 GCAGATGTCCAAGAGATCAGACT 59.867 47.826 4.76 0.00 35.21 3.24
3398 3424 4.382901 GCAGATGTCCAAGAGATCAGACTT 60.383 45.833 4.76 0.00 35.21 3.01
3399 3425 5.110598 CAGATGTCCAAGAGATCAGACTTG 58.889 45.833 15.50 15.50 41.85 3.16
3405 3431 4.815533 CAAGAGATCAGACTTGGAAGGA 57.184 45.455 14.97 0.00 39.52 3.36
3406 3432 5.356291 CAAGAGATCAGACTTGGAAGGAT 57.644 43.478 14.97 0.00 39.52 3.24
3407 3433 5.117584 CAAGAGATCAGACTTGGAAGGATG 58.882 45.833 14.97 0.00 39.52 3.51
3408 3434 4.360889 AGAGATCAGACTTGGAAGGATGT 58.639 43.478 0.00 0.00 0.00 3.06
3409 3435 4.782156 AGAGATCAGACTTGGAAGGATGTT 59.218 41.667 0.00 0.00 0.00 2.71
3410 3436 5.250313 AGAGATCAGACTTGGAAGGATGTTT 59.750 40.000 0.00 0.00 0.00 2.83
3411 3437 6.441924 AGAGATCAGACTTGGAAGGATGTTTA 59.558 38.462 0.00 0.00 0.00 2.01
3412 3438 7.020827 AGATCAGACTTGGAAGGATGTTTAA 57.979 36.000 0.00 0.00 0.00 1.52
3413 3439 7.637511 AGATCAGACTTGGAAGGATGTTTAAT 58.362 34.615 0.00 0.00 0.00 1.40
3414 3440 7.772757 AGATCAGACTTGGAAGGATGTTTAATC 59.227 37.037 0.00 0.00 0.00 1.75
3415 3441 7.020827 TCAGACTTGGAAGGATGTTTAATCT 57.979 36.000 0.00 0.00 0.00 2.40
3416 3442 8.146053 TCAGACTTGGAAGGATGTTTAATCTA 57.854 34.615 0.00 0.00 0.00 1.98
3417 3443 8.772250 TCAGACTTGGAAGGATGTTTAATCTAT 58.228 33.333 0.00 0.00 0.00 1.98
3418 3444 9.401058 CAGACTTGGAAGGATGTTTAATCTATT 57.599 33.333 0.00 0.00 0.00 1.73
3451 3509 7.074653 AGTAATTCACCTGTTTTCCAGACTA 57.925 36.000 0.00 0.00 44.49 2.59
3499 3557 0.966920 TCCTTCTCTGACCCGTGTTC 59.033 55.000 0.00 0.00 0.00 3.18
3792 3851 7.220683 CGATAAAATCCTGCACACAAATAAAGG 59.779 37.037 0.00 0.00 0.00 3.11
3805 3864 8.495148 CACACAAATAAAGGGAAGCAATTAAAC 58.505 33.333 0.00 0.00 0.00 2.01
3817 3876 2.731027 GCAATTAAACCACGGCAGCTAC 60.731 50.000 0.00 0.00 0.00 3.58
3848 3907 5.733620 ATGCATGTCAGAACCAAGAATTT 57.266 34.783 0.00 0.00 0.00 1.82
3854 3913 4.161333 GTCAGAACCAAGAATTTGATGCG 58.839 43.478 0.00 0.00 36.36 4.73
4016 4075 1.603739 GGCAACTCCTGGTGGGAAC 60.604 63.158 0.33 0.00 44.58 3.62
4044 4103 7.415989 GCATCAGCAAAAGAAGATTTATCTCCA 60.416 37.037 0.00 0.00 41.58 3.86
4170 4230 1.600957 CCTGAAATAGAGGTGCATGCG 59.399 52.381 14.09 0.00 0.00 4.73
4174 4234 2.401583 AATAGAGGTGCATGCGTCAA 57.598 45.000 14.09 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.215382 CGGTGATTCTCTGCCGTCA 59.785 57.895 0.00 0.00 39.41 4.35
304 308 3.642901 GTCACAGGACGATACGCAT 57.357 52.632 0.00 0.00 33.68 4.73
353 357 0.335361 AGGAAGGGAGAGGACGCTAA 59.665 55.000 0.00 0.00 32.90 3.09
355 359 1.684049 CAGGAAGGGAGAGGACGCT 60.684 63.158 0.00 0.00 34.62 5.07
379 383 2.202570 CGCCGTCTAGGTGTTCCG 60.203 66.667 0.00 0.00 45.30 4.30
409 413 2.067013 GACTAAACAGCTGTTCGTCCC 58.933 52.381 31.72 19.53 37.25 4.46
420 424 9.778993 CAATTCCACTGATATTTGACTAAACAG 57.221 33.333 0.00 0.00 0.00 3.16
431 438 4.574828 GGTACACGCAATTCCACTGATATT 59.425 41.667 0.00 0.00 0.00 1.28
455 462 1.027357 TCCGTCGTAGATTGGCCTAC 58.973 55.000 3.32 0.00 40.67 3.18
456 463 1.766494 TTCCGTCGTAGATTGGCCTA 58.234 50.000 3.32 0.00 40.67 3.93
457 464 0.899720 TTTCCGTCGTAGATTGGCCT 59.100 50.000 3.32 0.00 40.67 5.19
458 465 1.287425 CTTTCCGTCGTAGATTGGCC 58.713 55.000 0.00 0.00 40.67 5.36
459 466 0.651031 GCTTTCCGTCGTAGATTGGC 59.349 55.000 0.00 0.00 40.67 4.52
481 488 1.410517 ACCTACAGAGCATGACCATCG 59.589 52.381 0.00 0.00 0.00 3.84
793 805 2.905075 TCTGGAATGTTGCTATCGTGG 58.095 47.619 0.00 0.00 0.00 4.94
823 835 2.290641 ACGATGTTGTGAAAAGTGGCTC 59.709 45.455 0.00 0.00 0.00 4.70
878 890 2.017049 GTCTGGGCTTCAATAATGCGT 58.983 47.619 0.00 0.00 0.00 5.24
919 931 2.906389 ACAGTAAGTGATGCTCCTTCCA 59.094 45.455 0.00 0.00 0.00 3.53
1089 1113 2.744318 CATGCGTACGCCCACCAA 60.744 61.111 35.11 17.66 41.09 3.67
1200 1224 4.207165 TCTTTCCCACTCCTTTGAACAAG 58.793 43.478 0.00 0.00 0.00 3.16
1310 1334 4.695455 ACCGAAGAAGTACATCCACAAATG 59.305 41.667 0.00 0.00 0.00 2.32
1324 1348 4.119862 TCACTTGTCAGAAACCGAAGAAG 58.880 43.478 0.00 0.00 0.00 2.85
1410 1434 7.937942 AGTTCAATGATAAATGCTAGAGATGCT 59.062 33.333 0.00 0.00 0.00 3.79
1473 1497 5.245531 AGAAATACTGAAGATGCCACGAAA 58.754 37.500 0.00 0.00 0.00 3.46
1507 1531 4.320202 CCTGAATTCCAACTTTACACGGTG 60.320 45.833 6.58 6.58 0.00 4.94
1511 1535 5.622233 GCCATCCTGAATTCCAACTTTACAC 60.622 44.000 2.27 0.00 0.00 2.90
1518 1542 2.149973 AGGCCATCCTGAATTCCAAC 57.850 50.000 5.01 0.00 42.34 3.77
1583 1607 4.394920 GGAAGAATCTCAAATACGTTGCCA 59.605 41.667 0.00 0.00 37.13 4.92
1874 1898 7.387397 CGGAGGGAGTACTAGTTAGTATGTTAG 59.613 44.444 0.00 0.00 40.55 2.34
1889 1913 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1892 1916 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
1893 1917 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
1894 1918 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1895 1919 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1896 1920 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1897 1921 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1898 1922 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1910 1934 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1911 1935 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1912 1936 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1913 1937 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1914 1938 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
1925 1949 9.918630 AGAGCGTTTAAATTACTAAAGTAGTGA 57.081 29.630 0.00 0.00 39.81 3.41
1944 1968 9.490379 CCCTCTGTAAAATAATATAAGAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
1945 1969 8.867097 TCCCTCTGTAAAATAATATAAGAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
1946 1970 9.360093 CTCCCTCTGTAAAATAATATAAGAGCG 57.640 37.037 0.00 0.00 0.00 5.03
1963 1987 9.689501 GCTATTAGTAGATAATACTCCCTCTGT 57.310 37.037 0.00 0.00 35.63 3.41
1964 1988 9.914834 AGCTATTAGTAGATAATACTCCCTCTG 57.085 37.037 0.00 0.00 35.63 3.35
2023 2047 9.274065 GCAATTTTTCTTTGGTAAGATACTACG 57.726 33.333 0.00 0.00 40.01 3.51
2053 2077 5.410924 TCTCGAAAATACTCATCCACACAG 58.589 41.667 0.00 0.00 0.00 3.66
2060 2084 8.864069 TTCTCTTGATCTCGAAAATACTCATC 57.136 34.615 0.00 0.00 0.00 2.92
2071 2095 4.933505 ATCATGCTTCTCTTGATCTCGA 57.066 40.909 0.00 0.00 35.41 4.04
2112 2136 5.426504 CAGTATGAATGGAAGCTCTTGACT 58.573 41.667 0.00 0.00 39.69 3.41
2330 2355 2.224606 CACTGCATTGAGTGTCTTGGT 58.775 47.619 0.00 0.00 38.88 3.67
2378 2403 4.006319 GTCTAAGCACAGATCCAAGCTTT 58.994 43.478 17.67 6.27 44.22 3.51
2546 2571 9.325198 TCGATAAATATAACTTTGTGAGCACAT 57.675 29.630 3.90 0.00 41.52 3.21
2883 2908 9.914131 GCTTTTGTGTTCTTCCTTTCTAATATT 57.086 29.630 0.00 0.00 0.00 1.28
2917 2942 1.203287 CCTCTCACTGCGTTCTGATGA 59.797 52.381 0.00 0.00 0.00 2.92
3099 3124 0.741221 GGTCATGGCGAGTGAACTCC 60.741 60.000 4.90 0.00 39.79 3.85
3267 3292 9.334693 CTCATCTTTTTCGAACCAAAGAATAAG 57.665 33.333 22.34 16.82 41.28 1.73
3281 3306 2.778299 TCACACCCCTCATCTTTTTCG 58.222 47.619 0.00 0.00 0.00 3.46
3294 3319 5.978814 ACAGTAGTTATTGAGATCACACCC 58.021 41.667 0.00 0.00 0.00 4.61
3303 3328 8.654230 ATGTCATGCTAACAGTAGTTATTGAG 57.346 34.615 0.00 0.00 39.36 3.02
3357 3383 4.183865 TCTGCAAACGACTCATTGATAGG 58.816 43.478 0.00 0.00 0.00 2.57
3366 3392 1.795768 TGGACATCTGCAAACGACTC 58.204 50.000 0.00 0.00 0.00 3.36
3385 3411 4.782156 ACATCCTTCCAAGTCTGATCTCTT 59.218 41.667 0.00 0.00 0.00 2.85
3388 3414 5.511386 AAACATCCTTCCAAGTCTGATCT 57.489 39.130 0.00 0.00 0.00 2.75
3422 3448 8.335532 CTGGAAAACAGGTGAATTACTATTCA 57.664 34.615 0.00 0.00 43.83 2.57
3499 3557 3.572682 AGCTGCATAATCATCCAATGTGG 59.427 43.478 1.02 0.00 39.43 4.17
3792 3851 1.271102 TGCCGTGGTTTAATTGCTTCC 59.729 47.619 0.00 0.00 0.00 3.46
3805 3864 1.687123 ACTATTAGGTAGCTGCCGTGG 59.313 52.381 15.76 10.02 33.47 4.94
3817 3876 6.524734 TGGTTCTGACATGCATACTATTAGG 58.475 40.000 0.00 0.00 0.00 2.69
3943 4002 7.974504 ACCCAGGTAAATATCGATGAGTATTT 58.025 34.615 8.54 8.51 35.39 1.40
4016 4075 7.481642 AGATAAATCTTCTTTTGCTGATGCAG 58.518 34.615 0.00 0.00 41.66 4.41
4044 4103 4.889780 AGTGGGAGAACCTGAATCTAGAT 58.110 43.478 0.00 0.00 41.11 1.98


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

AutoCloner maintained by Alex Coulton.