Multiple sequence alignment - TraesCS3D01G093000

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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 TraesCS3D01G093000 chr3D 100.000 1981 0 0 416 2396 47094276 47092296 0.000000e+00 3659.0
1 TraesCS3D01G093000 chr3D 82.143 336 22 19 2038 2348 47086277 47086599 1.100000e-63 254.0
2 TraesCS3D01G093000 chr3D 100.000 55 0 0 1 55 47094691 47094637 4.210000e-18 102.0
3 TraesCS3D01G093000 chr3D 95.652 46 2 0 1781 1826 47085828 47085873 9.190000e-10 75.0
4 TraesCS3D01G093000 chr3D 100.000 33 0 0 2328 2360 47086609 47086641 7.150000e-06 62.1
5 TraesCS3D01G093000 chr5A 94.592 980 51 2 416 1394 582094957 582093979 0.000000e+00 1515.0
6 TraesCS3D01G093000 chr2D 96.954 591 18 0 804 1394 467996079 467996669 0.000000e+00 992.0
7 TraesCS3D01G093000 chr2D 96.961 362 11 0 447 808 467990833 467991194 2.040000e-170 608.0
8 TraesCS3D01G093000 chr2D 98.182 55 1 0 1 55 467990532 467990586 1.960000e-16 97.1
9 TraesCS3D01G093000 chr3B 83.555 602 59 24 1431 2004 73604714 73605303 5.870000e-146 527.0
10 TraesCS3D01G093000 chr3B 83.978 181 11 11 2144 2321 73626746 73626911 8.870000e-35 158.0
11 TraesCS3D01G093000 chr3A 91.404 349 27 3 1431 1777 58844550 58844203 2.160000e-130 475.0
12 TraesCS3D01G093000 chr3A 82.661 248 20 16 2144 2373 58835440 58835682 5.220000e-47 198.0
13 TraesCS3D01G093000 chr3A 100.000 107 0 0 2038 2144 58843711 58843605 5.220000e-47 198.0
14 TraesCS3D01G093000 chr3A 97.143 105 3 0 2038 2142 58835302 58835406 6.810000e-41 178.0
15 TraesCS3D01G093000 chr3A 81.028 253 15 7 1782 2033 58844163 58843943 1.140000e-38 171.0
16 TraesCS3D01G093000 chr3A 80.753 239 23 15 2144 2376 58840706 58840485 5.300000e-37 165.0
17 TraesCS3D01G093000 chr3A 95.745 47 2 0 1780 1826 58834898 58834944 2.550000e-10 76.8
18 TraesCS3D01G093000 chr7A 72.967 984 234 24 429 1394 711304709 711305678 4.970000e-82 315.0


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 TraesCS3D01G093000 chr3D 47092296 47094691 2395 True 1880.50 3659 100.00000 1 2396 2 chr3D.!!$R1 2395
1 TraesCS3D01G093000 chr5A 582093979 582094957 978 True 1515.00 1515 94.59200 416 1394 1 chr5A.!!$R1 978
2 TraesCS3D01G093000 chr2D 467996079 467996669 590 False 992.00 992 96.95400 804 1394 1 chr2D.!!$F1 590
3 TraesCS3D01G093000 chr2D 467990532 467991194 662 False 352.55 608 97.57150 1 808 2 chr2D.!!$F2 807
4 TraesCS3D01G093000 chr3B 73604714 73605303 589 False 527.00 527 83.55500 1431 2004 1 chr3B.!!$F1 573
5 TraesCS3D01G093000 chr3A 58840485 58844550 4065 True 252.25 475 88.29625 1431 2376 4 chr3A.!!$R1 945
6 TraesCS3D01G093000 chr7A 711304709 711305678 969 False 315.00 315 72.96700 429 1394 1 chr7A.!!$F1 965

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
845 846 1.134946 CATCACGAAGGGGAAAATGGC 59.865 52.381 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 5536 0.45395 CAACGTACCAGTCGGAGTCG 60.454 60.0 0.0 0.0 35.59 4.18 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
664 665 6.166984 TGTTACTTTTGAATGATTGCCCAA 57.833 33.333 0.00 0.00 0.00 4.12
753 754 1.606313 CAAACCGGCTCCCACCATT 60.606 57.895 0.00 0.00 0.00 3.16
799 800 1.135632 GCTATATCGACAGCCTCCGAC 60.136 57.143 4.54 0.00 37.64 4.79
817 818 2.362120 GCATTGAGCAGCACCCCT 60.362 61.111 0.00 0.00 44.79 4.79
845 846 1.134946 CATCACGAAGGGGAAAATGGC 59.865 52.381 0.00 0.00 0.00 4.40
858 859 1.497309 AAATGGCGGTCTCCCTGGAA 61.497 55.000 0.00 0.00 0.00 3.53
971 972 1.804151 GCTGAACGTTGATGGTGCTTA 59.196 47.619 5.00 0.00 0.00 3.09
1394 1399 2.747467 GCAATCTCTGCCAGCAGGATTA 60.747 50.000 23.77 9.83 46.13 1.75
1395 1400 3.548770 CAATCTCTGCCAGCAGGATTAA 58.451 45.455 23.77 6.84 43.75 1.40
1396 1401 4.142790 CAATCTCTGCCAGCAGGATTAAT 58.857 43.478 23.77 10.02 43.75 1.40
1397 1402 5.311265 CAATCTCTGCCAGCAGGATTAATA 58.689 41.667 23.77 5.71 43.75 0.98
1398 1403 4.342862 TCTCTGCCAGCAGGATTAATAC 57.657 45.455 19.04 0.00 43.75 1.89
1399 1404 3.711190 TCTCTGCCAGCAGGATTAATACA 59.289 43.478 19.04 0.00 43.75 2.29
1400 1405 4.164030 TCTCTGCCAGCAGGATTAATACAA 59.836 41.667 19.04 0.00 43.75 2.41
1401 1406 5.052693 TCTGCCAGCAGGATTAATACAAT 57.947 39.130 19.04 0.00 43.75 2.71
1402 1407 5.065914 TCTGCCAGCAGGATTAATACAATC 58.934 41.667 19.04 0.00 43.75 2.67
1403 1408 4.144297 TGCCAGCAGGATTAATACAATCC 58.856 43.478 0.00 7.77 45.08 3.01
1404 1409 4.144297 GCCAGCAGGATTAATACAATCCA 58.856 43.478 16.26 0.00 46.70 3.41
1405 1410 4.768968 GCCAGCAGGATTAATACAATCCAT 59.231 41.667 16.26 1.88 46.70 3.41
1406 1411 5.945784 GCCAGCAGGATTAATACAATCCATA 59.054 40.000 16.26 0.00 46.70 2.74
1407 1412 6.604795 GCCAGCAGGATTAATACAATCCATAT 59.395 38.462 16.26 1.28 46.70 1.78
1408 1413 7.201767 GCCAGCAGGATTAATACAATCCATATC 60.202 40.741 16.26 4.52 46.70 1.63
1409 1414 7.011763 CCAGCAGGATTAATACAATCCATATCG 59.988 40.741 16.26 3.29 46.70 2.92
1410 1415 7.550551 CAGCAGGATTAATACAATCCATATCGT 59.449 37.037 16.26 0.00 46.70 3.73
1411 1416 8.103305 AGCAGGATTAATACAATCCATATCGTT 58.897 33.333 16.26 0.00 46.70 3.85
1412 1417 8.730680 GCAGGATTAATACAATCCATATCGTTT 58.269 33.333 16.26 0.00 46.70 3.60
1414 1419 9.151471 AGGATTAATACAATCCATATCGTTTCG 57.849 33.333 16.26 0.00 46.70 3.46
1415 1420 7.903431 GGATTAATACAATCCATATCGTTTCGC 59.097 37.037 10.46 0.00 44.33 4.70
1416 1421 7.716768 TTAATACAATCCATATCGTTTCGCA 57.283 32.000 0.00 0.00 0.00 5.10
1417 1422 6.612247 AATACAATCCATATCGTTTCGCAA 57.388 33.333 0.00 0.00 0.00 4.85
1418 1423 4.273005 ACAATCCATATCGTTTCGCAAC 57.727 40.909 0.00 0.00 0.00 4.17
1419 1424 3.687212 ACAATCCATATCGTTTCGCAACA 59.313 39.130 0.00 0.00 32.54 3.33
1420 1425 4.155099 ACAATCCATATCGTTTCGCAACAA 59.845 37.500 0.00 0.00 32.54 2.83
1421 1426 4.955925 ATCCATATCGTTTCGCAACAAA 57.044 36.364 0.00 0.00 32.54 2.83
1422 1427 4.750952 TCCATATCGTTTCGCAACAAAA 57.249 36.364 0.00 0.00 32.54 2.44
1423 1428 5.109662 TCCATATCGTTTCGCAACAAAAA 57.890 34.783 0.00 0.00 32.54 1.94
1447 1452 8.831715 AAAAAGTCAACTTCTGTTCATTTTGT 57.168 26.923 0.00 0.00 34.61 2.83
1506 1511 3.119637 CCGTGTAACCATCCAACCATTTC 60.120 47.826 0.00 0.00 0.00 2.17
1555 1560 1.921982 ATGTGTTTGCACTATGGGCA 58.078 45.000 0.00 0.00 45.44 5.36
1563 1568 1.230635 GCACTATGGGCATGTAGGCG 61.231 60.000 0.00 0.00 45.36 5.52
1657 1662 7.698836 ATTTCTTGGTTTCGATTTGAAGTTG 57.301 32.000 0.00 0.00 37.99 3.16
1661 1666 3.629855 TGGTTTCGATTTGAAGTTGAGCA 59.370 39.130 0.00 0.00 37.99 4.26
1695 1703 5.410746 TCTTGAGATGAGTTCAGCAACATTC 59.589 40.000 0.00 0.00 34.60 2.67
1759 1767 9.693157 GATCTTTGATTTGAAAGTTTGTGTTTG 57.307 29.630 0.00 0.00 34.95 2.93
1762 1770 9.875675 CTTTGATTTGAAAGTTTGTGTTTGAAA 57.124 25.926 0.00 0.00 0.00 2.69
1777 1785 9.959749 TTGTGTTTGAAATTTAGTCCATTCTAC 57.040 29.630 0.00 0.00 0.00 2.59
1778 1786 9.349713 TGTGTTTGAAATTTAGTCCATTCTACT 57.650 29.630 0.00 0.00 0.00 2.57
1787 1830 4.457834 AGTCCATTCTACTCCGTTTCTG 57.542 45.455 0.00 0.00 0.00 3.02
1794 1837 3.340928 TCTACTCCGTTTCTGTCGATGA 58.659 45.455 0.00 0.00 0.00 2.92
1830 1873 3.208884 GACGTCACGTGGCTCTGGT 62.209 63.158 19.37 8.45 41.37 4.00
1849 1893 7.306866 GCTCTGGTCATCGACTTATAAATTCAC 60.307 40.741 0.00 0.00 32.47 3.18
1857 1901 7.655236 TCGACTTATAAATTCACGAAAACCA 57.345 32.000 0.00 0.00 0.00 3.67
1873 1917 7.852945 CACGAAAACCATTTATAATCTCTCTGC 59.147 37.037 0.00 0.00 0.00 4.26
1880 1924 2.540265 ATAATCTCTCTGCTTGGCGG 57.460 50.000 0.00 0.00 36.06 6.13
1881 1925 1.485124 TAATCTCTCTGCTTGGCGGA 58.515 50.000 1.03 1.03 42.08 5.54
1882 1926 0.107945 AATCTCTCTGCTTGGCGGAC 60.108 55.000 0.00 0.00 39.19 4.79
1883 1927 0.975040 ATCTCTCTGCTTGGCGGACT 60.975 55.000 0.00 0.00 39.19 3.85
1884 1928 1.153667 CTCTCTGCTTGGCGGACTC 60.154 63.158 0.00 0.00 39.19 3.36
1885 1929 1.603236 CTCTCTGCTTGGCGGACTCT 61.603 60.000 0.00 0.00 39.19 3.24
1886 1930 1.188219 TCTCTGCTTGGCGGACTCTT 61.188 55.000 0.00 0.00 39.19 2.85
1887 1931 0.532573 CTCTGCTTGGCGGACTCTTA 59.467 55.000 0.00 0.00 39.19 2.10
1888 1932 0.973632 TCTGCTTGGCGGACTCTTAA 59.026 50.000 0.00 0.00 39.19 1.85
1889 1933 1.346395 TCTGCTTGGCGGACTCTTAAA 59.654 47.619 0.00 0.00 39.19 1.52
1890 1934 2.151202 CTGCTTGGCGGACTCTTAAAA 58.849 47.619 0.00 0.00 37.02 1.52
1891 1935 2.151202 TGCTTGGCGGACTCTTAAAAG 58.849 47.619 0.00 0.00 0.00 2.27
1892 1936 2.224426 TGCTTGGCGGACTCTTAAAAGA 60.224 45.455 0.00 0.00 0.00 2.52
1893 1937 3.010420 GCTTGGCGGACTCTTAAAAGAT 58.990 45.455 0.00 0.00 33.93 2.40
1894 1938 3.440522 GCTTGGCGGACTCTTAAAAGATT 59.559 43.478 0.00 0.00 33.93 2.40
1918 1962 0.306533 GTGGTACGTGGTGCAACAAG 59.693 55.000 16.53 16.53 39.98 3.16
1923 1967 2.177580 CGTGGTGCAACAAGTCCGT 61.178 57.895 5.70 0.00 39.98 4.69
1932 1976 0.324943 AACAAGTCCGTCCATCCAGG 59.675 55.000 0.00 0.00 39.47 4.45
1981 2026 3.214328 ACGAATGCTCAAGGTCAAAGTT 58.786 40.909 0.00 0.00 0.00 2.66
2010 2055 1.544982 GGCATGCATGATCCTAGCACT 60.545 52.381 30.64 0.00 41.60 4.40
2012 2057 2.152016 CATGCATGATCCTAGCACTGG 58.848 52.381 22.59 0.00 41.60 4.00
2025 2070 2.132996 CACTGGGCAACTGGGCAAA 61.133 57.895 0.00 0.00 45.66 3.68
2190 5361 0.802607 GTCTGAATCCTGCGACGACC 60.803 60.000 0.00 0.00 0.00 4.79
2192 5363 0.803768 CTGAATCCTGCGACGACCAG 60.804 60.000 0.00 0.00 0.00 4.00
2196 5367 4.436998 CCTGCGACGACCAGGTCC 62.437 72.222 14.46 0.10 43.86 4.46
2197 5368 3.680786 CTGCGACGACCAGGTCCA 61.681 66.667 14.46 5.10 33.30 4.02
2198 5369 3.633094 CTGCGACGACCAGGTCCAG 62.633 68.421 14.46 11.15 33.30 3.86
2199 5370 4.436998 GCGACGACCAGGTCCAGG 62.437 72.222 14.46 2.63 33.30 4.45
2200 5371 2.675423 CGACGACCAGGTCCAGGA 60.675 66.667 14.46 0.00 33.30 3.86
2201 5372 2.971452 GACGACCAGGTCCAGGAC 59.029 66.667 14.46 11.70 0.00 3.85
2209 5380 2.187946 GGTCCAGGACCGCATGAG 59.812 66.667 23.67 0.00 43.14 2.90
2210 5381 2.512515 GTCCAGGACCGCATGAGC 60.513 66.667 8.65 0.00 37.42 4.26
2211 5382 3.002583 TCCAGGACCGCATGAGCA 61.003 61.111 0.00 0.00 42.27 4.26
2212 5383 2.191375 CCAGGACCGCATGAGCAT 59.809 61.111 0.00 0.00 42.27 3.79
2215 5386 3.589881 GGACCGCATGAGCATGGC 61.590 66.667 12.00 4.22 42.27 4.40
2258 5435 1.898574 CCACAGCCCACAAGTGTCC 60.899 63.158 0.00 0.00 0.00 4.02
2261 5438 1.601759 CAGCCCACAAGTGTCCAGG 60.602 63.158 0.00 0.00 0.00 4.45
2283 5460 4.815973 ACCCGGGCCCTGCTCATA 62.816 66.667 24.08 0.00 0.00 2.15
2285 5462 2.348998 CCGGGCCCTGCTCATATC 59.651 66.667 22.43 0.00 0.00 1.63
2287 5464 1.757306 CGGGCCCTGCTCATATCTT 59.243 57.895 22.43 0.00 0.00 2.40
2289 5466 1.613836 GGGCCCTGCTCATATCTTTG 58.386 55.000 17.04 0.00 0.00 2.77
2290 5467 1.143684 GGGCCCTGCTCATATCTTTGA 59.856 52.381 17.04 0.00 0.00 2.69
2291 5468 2.225467 GGCCCTGCTCATATCTTTGAC 58.775 52.381 0.00 0.00 0.00 3.18
2355 5536 1.827969 ACACATGGTCTCAGCTACTCC 59.172 52.381 0.00 0.00 0.00 3.85
2373 5554 1.580845 CCGACTCCGACTGGTACGTT 61.581 60.000 0.00 0.00 38.22 3.99
2376 5557 0.595095 ACTCCGACTGGTACGTTGTC 59.405 55.000 0.00 0.00 36.30 3.18
2394 5575 3.039588 GACGAGGTCGGCGCAAAA 61.040 61.111 10.83 0.00 44.95 2.44
2395 5576 3.011760 GACGAGGTCGGCGCAAAAG 62.012 63.158 10.83 0.00 44.95 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.544650 CACATATGAGTGCTGGATATGTCA 58.455 41.667 10.38 0.00 39.97 3.58
426 427 4.152938 GCGAGGGAGTTTGTAATTAAACGT 59.847 41.667 0.00 0.00 43.51 3.99
753 754 1.896220 AAAACCTGCGAGATGCTTCA 58.104 45.000 2.07 0.00 46.63 3.02
799 800 2.874648 TAGGGGTGCTGCTCAATGCG 62.875 60.000 0.00 0.00 46.63 4.73
817 818 1.407618 CCCCTTCGTGATGTCGTCATA 59.592 52.381 0.00 0.00 39.48 2.15
858 859 4.065281 GTGTGGCTCCTACGCGGT 62.065 66.667 12.47 0.00 0.00 5.68
1386 1391 7.849804 ACGATATGGATTGTATTAATCCTGC 57.150 36.000 16.93 5.77 45.01 4.85
1394 1399 6.037720 TGTTGCGAAACGATATGGATTGTATT 59.962 34.615 0.88 0.00 0.00 1.89
1395 1400 5.525745 TGTTGCGAAACGATATGGATTGTAT 59.474 36.000 0.88 0.00 0.00 2.29
1396 1401 4.870991 TGTTGCGAAACGATATGGATTGTA 59.129 37.500 0.88 0.00 0.00 2.41
1397 1402 3.687212 TGTTGCGAAACGATATGGATTGT 59.313 39.130 0.88 0.00 0.00 2.71
1398 1403 4.271590 TGTTGCGAAACGATATGGATTG 57.728 40.909 0.88 0.00 0.00 2.67
1399 1404 4.955925 TTGTTGCGAAACGATATGGATT 57.044 36.364 0.88 0.00 0.00 3.01
1400 1405 4.955925 TTTGTTGCGAAACGATATGGAT 57.044 36.364 0.88 0.00 0.00 3.41
1401 1406 4.750952 TTTTGTTGCGAAACGATATGGA 57.249 36.364 0.88 0.00 0.00 3.41
1422 1427 8.831715 ACAAAATGAACAGAAGTTGACTTTTT 57.168 26.923 0.00 0.00 38.30 1.94
1423 1428 9.921637 TTACAAAATGAACAGAAGTTGACTTTT 57.078 25.926 0.00 0.00 38.30 2.27
1424 1429 9.353999 GTTACAAAATGAACAGAAGTTGACTTT 57.646 29.630 0.00 0.00 38.30 2.66
1425 1430 8.519526 TGTTACAAAATGAACAGAAGTTGACTT 58.480 29.630 0.00 0.00 38.30 3.01
1426 1431 8.050778 TGTTACAAAATGAACAGAAGTTGACT 57.949 30.769 0.00 0.00 38.30 3.41
1427 1432 8.682128 TTGTTACAAAATGAACAGAAGTTGAC 57.318 30.769 0.00 0.00 38.30 3.18
1428 1433 8.519526 ACTTGTTACAAAATGAACAGAAGTTGA 58.480 29.630 0.00 0.00 38.30 3.18
1429 1434 8.687824 ACTTGTTACAAAATGAACAGAAGTTG 57.312 30.769 0.00 0.00 38.30 3.16
1435 1440 7.424803 TGGATGACTTGTTACAAAATGAACAG 58.575 34.615 0.00 0.00 36.92 3.16
1521 1526 9.949174 GTGCAAACACATATATGTATTGAATGA 57.051 29.630 29.65 16.41 46.61 2.57
1563 1568 1.278238 CAAGTCGAGGCGGACAATAC 58.722 55.000 12.98 0.00 39.42 1.89
1591 1596 2.889512 TGGCTTCTAGTGAACCTCTGA 58.110 47.619 0.00 0.00 0.00 3.27
1682 1690 5.673337 TGTTGACTAGAATGTTGCTGAAC 57.327 39.130 0.00 0.00 0.00 3.18
1725 1733 5.371115 TTCAAATCAAAGATCCCAACGTC 57.629 39.130 0.00 0.00 0.00 4.34
1759 1767 7.845066 AACGGAGTAGAATGGACTAAATTTC 57.155 36.000 0.00 0.00 45.00 2.17
1762 1770 7.042335 CAGAAACGGAGTAGAATGGACTAAAT 58.958 38.462 0.00 0.00 45.00 1.40
1777 1785 2.672714 TGTTCATCGACAGAAACGGAG 58.327 47.619 3.92 0.00 0.00 4.63
1778 1786 2.804697 TGTTCATCGACAGAAACGGA 57.195 45.000 3.92 0.00 0.00 4.69
1787 1830 3.181540 CGTGTTGTGATCTGTTCATCGAC 60.182 47.826 0.00 0.00 36.54 4.20
1794 1837 2.755650 GTCTCCGTGTTGTGATCTGTT 58.244 47.619 0.00 0.00 0.00 3.16
1830 1873 8.385111 GGTTTTCGTGAATTTATAAGTCGATGA 58.615 33.333 0.00 0.00 0.00 2.92
1849 1893 8.147642 AGCAGAGAGATTATAAATGGTTTTCG 57.852 34.615 0.00 0.00 0.00 3.46
1857 1901 4.999950 CCGCCAAGCAGAGAGATTATAAAT 59.000 41.667 0.00 0.00 0.00 1.40
1873 1917 6.927294 ATAATCTTTTAAGAGTCCGCCAAG 57.073 37.500 0.00 0.00 38.66 3.61
1883 1927 9.590451 CCACGTACCACTAATAATCTTTTAAGA 57.410 33.333 0.00 0.00 39.78 2.10
1884 1928 9.374838 ACCACGTACCACTAATAATCTTTTAAG 57.625 33.333 0.00 0.00 0.00 1.85
1885 1929 9.153721 CACCACGTACCACTAATAATCTTTTAA 57.846 33.333 0.00 0.00 0.00 1.52
1886 1930 7.278424 GCACCACGTACCACTAATAATCTTTTA 59.722 37.037 0.00 0.00 0.00 1.52
1887 1931 6.093082 GCACCACGTACCACTAATAATCTTTT 59.907 38.462 0.00 0.00 0.00 2.27
1888 1932 5.583457 GCACCACGTACCACTAATAATCTTT 59.417 40.000 0.00 0.00 0.00 2.52
1889 1933 5.114081 GCACCACGTACCACTAATAATCTT 58.886 41.667 0.00 0.00 0.00 2.40
1890 1934 4.160814 TGCACCACGTACCACTAATAATCT 59.839 41.667 0.00 0.00 0.00 2.40
1891 1935 4.435425 TGCACCACGTACCACTAATAATC 58.565 43.478 0.00 0.00 0.00 1.75
1892 1936 4.475051 TGCACCACGTACCACTAATAAT 57.525 40.909 0.00 0.00 0.00 1.28
1893 1937 3.957591 TGCACCACGTACCACTAATAA 57.042 42.857 0.00 0.00 0.00 1.40
1894 1938 3.006644 TGTTGCACCACGTACCACTAATA 59.993 43.478 0.00 0.00 0.00 0.98
1918 1962 3.399181 TGCCCTGGATGGACGGAC 61.399 66.667 0.00 0.00 38.35 4.79
1923 1967 2.622977 GGTTATTTGTGCCCTGGATGGA 60.623 50.000 0.00 0.00 38.35 3.41
1932 1976 3.001939 CGAAGATACGGGTTATTTGTGCC 59.998 47.826 0.00 0.00 0.00 5.01
1981 2026 4.467082 AGGATCATGCATGCCTTGTTTAAA 59.533 37.500 22.25 0.53 0.00 1.52
2010 2055 2.215625 CCATTTGCCCAGTTGCCCA 61.216 57.895 0.00 0.00 0.00 5.36
2012 2057 2.046988 GCCATTTGCCCAGTTGCC 60.047 61.111 0.00 0.00 0.00 4.52
2033 2078 1.388065 CCCTCGATCCTGAGCGTCTT 61.388 60.000 4.63 0.00 41.48 3.01
2034 2079 1.826054 CCCTCGATCCTGAGCGTCT 60.826 63.158 4.63 0.00 41.48 4.18
2035 2080 2.122167 ACCCTCGATCCTGAGCGTC 61.122 63.158 4.63 0.00 41.48 5.19
2036 2081 2.043852 ACCCTCGATCCTGAGCGT 60.044 61.111 4.63 0.00 41.48 5.07
2161 5332 1.639298 GGATTCAGACTGCGTGTGCC 61.639 60.000 0.00 0.00 41.78 5.01
2162 5333 0.671781 AGGATTCAGACTGCGTGTGC 60.672 55.000 0.00 0.00 43.20 4.57
2172 5343 1.248101 TGGTCGTCGCAGGATTCAGA 61.248 55.000 0.00 0.00 0.00 3.27
2193 5364 2.512515 GCTCATGCGGTCCTGGAC 60.513 66.667 18.65 18.65 0.00 4.02
2194 5365 2.369633 ATGCTCATGCGGTCCTGGA 61.370 57.895 0.00 0.00 43.34 3.86
2195 5366 2.184830 CATGCTCATGCGGTCCTGG 61.185 63.158 0.00 0.00 43.34 4.45
2196 5367 2.184830 CCATGCTCATGCGGTCCTG 61.185 63.158 4.40 0.00 43.34 3.86
2197 5368 2.191375 CCATGCTCATGCGGTCCT 59.809 61.111 4.40 0.00 43.34 3.85
2198 5369 3.589881 GCCATGCTCATGCGGTCC 61.590 66.667 4.40 0.00 43.34 4.46
2199 5370 2.515523 AGCCATGCTCATGCGGTC 60.516 61.111 4.40 0.00 43.34 4.79
2239 5410 2.519302 ACACTTGTGGGCTGTGGC 60.519 61.111 5.72 0.00 36.16 5.01
2241 5412 1.152984 TGGACACTTGTGGGCTGTG 60.153 57.895 5.72 0.00 37.67 3.66
2244 5415 2.839098 CCTGGACACTTGTGGGCT 59.161 61.111 5.72 0.00 0.00 5.19
2246 5417 1.302832 GAGCCTGGACACTTGTGGG 60.303 63.158 0.00 0.00 0.00 4.61
2248 5419 0.886490 GTGGAGCCTGGACACTTGTG 60.886 60.000 0.00 0.00 32.58 3.33
2249 5420 1.451936 GTGGAGCCTGGACACTTGT 59.548 57.895 0.00 0.00 32.58 3.16
2250 5421 1.302832 GGTGGAGCCTGGACACTTG 60.303 63.158 13.66 0.00 35.53 3.16
2251 5422 2.529744 GGGTGGAGCCTGGACACTT 61.530 63.158 13.66 0.00 37.43 3.16
2252 5423 2.930562 GGGTGGAGCCTGGACACT 60.931 66.667 13.66 0.00 37.43 3.55
2253 5424 4.394712 CGGGTGGAGCCTGGACAC 62.395 72.222 0.00 2.83 40.02 3.67
2273 5450 2.103094 TCCGTCAAAGATATGAGCAGGG 59.897 50.000 0.00 0.00 0.00 4.45
2276 5453 3.198068 GCTTCCGTCAAAGATATGAGCA 58.802 45.455 0.00 0.00 0.00 4.26
2281 5458 3.462021 GAGCTGCTTCCGTCAAAGATAT 58.538 45.455 2.53 0.00 0.00 1.63
2282 5459 2.735444 CGAGCTGCTTCCGTCAAAGATA 60.735 50.000 2.53 0.00 0.00 1.98
2283 5460 1.731720 GAGCTGCTTCCGTCAAAGAT 58.268 50.000 2.53 0.00 0.00 2.40
2285 5462 0.667487 TCGAGCTGCTTCCGTCAAAG 60.667 55.000 2.53 0.00 0.00 2.77
2287 5464 0.458543 GATCGAGCTGCTTCCGTCAA 60.459 55.000 2.53 0.00 0.00 3.18
2289 5466 1.139734 TGATCGAGCTGCTTCCGTC 59.860 57.895 2.53 5.22 0.00 4.79
2290 5467 1.153745 GTGATCGAGCTGCTTCCGT 60.154 57.895 2.53 0.00 0.00 4.69
2291 5468 2.226896 CGTGATCGAGCTGCTTCCG 61.227 63.158 2.53 3.72 39.71 4.30
2333 5514 2.232452 GAGTAGCTGAGACCATGTGTGT 59.768 50.000 0.00 0.00 0.00 3.72
2355 5536 0.453950 CAACGTACCAGTCGGAGTCG 60.454 60.000 0.00 0.00 35.59 4.18
2377 5558 3.011760 CTTTTGCGCCGACCTCGTC 62.012 63.158 4.18 0.00 37.74 4.20
2378 5559 3.041940 CTTTTGCGCCGACCTCGT 61.042 61.111 4.18 0.00 37.74 4.18


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

AutoCloner maintained by Alex Coulton.