Multiple sequence alignment - TraesCS3B01G549700

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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 TraesCS3B01G549700 chr3B 100.000 2764 0 0 1 2764 784871603 784868840 0.000000e+00 5105
1 TraesCS3B01G549700 chr3B 86.260 393 45 6 1366 1749 784900559 784900167 4.260000e-113 418
2 TraesCS3B01G549700 chr3B 77.051 780 128 25 1008 1750 785043159 785042394 4.290000e-108 401
3 TraesCS3B01G549700 chr3B 83.171 410 41 13 924 1318 784900955 784900559 1.580000e-92 350
4 TraesCS3B01G549700 chr3B 93.939 99 4 2 1827 1924 574905936 574905839 6.170000e-32 148
5 TraesCS3B01G549700 chr3A 90.880 1864 124 17 1 1860 716949236 716947415 0.000000e+00 2459
6 TraesCS3B01G549700 chr3A 81.477 826 94 29 1005 1815 716966944 716966163 8.410000e-175 623
7 TraesCS3B01G549700 chr3A 87.838 518 51 7 1 513 716949884 716949374 5.100000e-167 597
8 TraesCS3B01G549700 chr3A 85.507 345 26 9 1909 2238 716947324 716946989 3.410000e-89 339
9 TraesCS3B01G549700 chr3A 82.451 359 47 9 1411 1754 717010587 717010230 1.610000e-77 300
10 TraesCS3B01G549700 chr3A 87.795 254 30 1 2150 2403 716946990 716946738 2.080000e-76 296
11 TraesCS3B01G549700 chr3D 94.109 1290 50 7 489 1778 587587085 587585822 0.000000e+00 1938
12 TraesCS3B01G549700 chr3D 81.884 828 87 30 1005 1815 587596507 587595726 8.350000e-180 640
13 TraesCS3B01G549700 chr3D 88.791 455 44 5 1 453 587587536 587587087 4.020000e-153 551
14 TraesCS3B01G549700 chr3D 79.161 787 96 26 1008 1750 587648487 587647725 1.490000e-132 483
15 TraesCS3B01G549700 chr3D 84.538 498 32 18 1927 2403 587585713 587585240 4.200000e-123 451
16 TraesCS3B01G549700 chr3D 89.080 348 33 2 2415 2761 587583305 587582962 7.070000e-116 427
17 TraesCS3B01G549700 chr3D 83.262 466 55 15 1365 1812 587746038 587746498 9.220000e-110 407
18 TraesCS3B01G549700 chr6B 97.778 90 2 0 1838 1927 4185989 4185900 3.690000e-34 156
19 TraesCS3B01G549700 chr4D 96.739 92 3 0 1833 1924 26146514 26146605 1.330000e-33 154
20 TraesCS3B01G549700 chr7D 94.845 97 5 0 1831 1927 131620231 131620135 4.770000e-33 152
21 TraesCS3B01G549700 chr4B 96.739 92 2 1 1834 1924 402243786 402243695 4.770000e-33 152
22 TraesCS3B01G549700 chr1D 96.739 92 2 1 1834 1924 186375632 186375723 4.770000e-33 152
23 TraesCS3B01G549700 chr1D 96.739 92 2 1 1834 1924 469447386 469447295 4.770000e-33 152
24 TraesCS3B01G549700 chr1D 92.308 104 5 3 1838 1939 268929834 268929936 7.980000e-31 145
25 TraesCS3B01G549700 chr4A 93.939 99 5 1 1834 1931 241153029 241152931 6.170000e-32 148


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 TraesCS3B01G549700 chr3B 784868840 784871603 2763 True 5105.00 5105 100.0000 1 2764 1 chr3B.!!$R2 2763
1 TraesCS3B01G549700 chr3B 785042394 785043159 765 True 401.00 401 77.0510 1008 1750 1 chr3B.!!$R3 742
2 TraesCS3B01G549700 chr3B 784900167 784900955 788 True 384.00 418 84.7155 924 1749 2 chr3B.!!$R4 825
3 TraesCS3B01G549700 chr3A 716946738 716949884 3146 True 922.75 2459 88.0050 1 2403 4 chr3A.!!$R3 2402
4 TraesCS3B01G549700 chr3A 716966163 716966944 781 True 623.00 623 81.4770 1005 1815 1 chr3A.!!$R1 810
5 TraesCS3B01G549700 chr3D 587582962 587587536 4574 True 841.75 1938 89.1295 1 2761 4 chr3D.!!$R3 2760
6 TraesCS3B01G549700 chr3D 587595726 587596507 781 True 640.00 640 81.8840 1005 1815 1 chr3D.!!$R1 810
7 TraesCS3B01G549700 chr3D 587647725 587648487 762 True 483.00 483 79.1610 1008 1750 1 chr3D.!!$R2 742

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
851 1505 0.458669 GCTCAACCTGATTGCATGGG 59.541 55.0 0.0 0.0 38.29 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 3273 0.107165 GAGGGCACATGTAACCTCCC 60.107 60.0 26.36 18.41 42.87 4.3 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
43 44 8.862325 AACATATGGTGAAACTCTATGAAACA 57.138 30.769 7.80 0.00 35.87 2.83
44 45 9.466497 AACATATGGTGAAACTCTATGAAACAT 57.534 29.630 7.80 0.00 35.87 2.71
95 744 8.700439 AAAACCTAGTAAAACCTGATAAGCAA 57.300 30.769 0.00 0.00 0.00 3.91
308 958 7.567771 GCGTACTAGAATGCATCACTATGTTTC 60.568 40.741 0.00 0.00 35.38 2.78
389 1040 6.533730 TGGAAGTGATATTGTTTCAGTGTCT 58.466 36.000 0.00 0.00 0.00 3.41
407 1058 5.934625 AGTGTCTTAGTTGCAAGGAACATAG 59.065 40.000 0.00 3.91 0.00 2.23
442 1093 9.270640 TCATAAATTGGATTTGTGGTTCAAAAG 57.729 29.630 9.31 0.00 46.97 2.27
492 1143 9.932207 ATCATACAAAAATCATGAACATGTGTT 57.068 25.926 13.35 0.00 41.64 3.32
557 1208 1.077501 AATCCCGGTCACTGCATGG 60.078 57.895 0.00 0.00 0.00 3.66
575 1226 2.883574 TGGCATAAAGGTAACGTCGAG 58.116 47.619 0.00 0.00 46.39 4.04
590 1241 3.052745 CGTCGAGGATGTCACATAATGG 58.947 50.000 0.00 0.00 0.00 3.16
591 1242 3.243401 CGTCGAGGATGTCACATAATGGA 60.243 47.826 0.00 0.00 0.00 3.41
676 1327 2.420372 GCTGAGCCATGCATGAGATATG 59.580 50.000 28.31 10.97 0.00 1.78
752 1406 6.156949 TCTCTGGAGTATGCCTTTTAGACATT 59.843 38.462 0.00 0.00 0.00 2.71
851 1505 0.458669 GCTCAACCTGATTGCATGGG 59.541 55.000 0.00 0.00 38.29 4.00
905 1559 7.650903 GCTGATCAATCTGGATAAAATTCAACC 59.349 37.037 0.00 0.00 0.00 3.77
908 1562 8.599624 ATCAATCTGGATAAAATTCAACCAGT 57.400 30.769 0.00 0.00 45.50 4.00
933 1587 1.077429 CAAGCAGGCTAGGTTCCCC 60.077 63.158 0.00 0.00 0.00 4.81
980 1636 0.677288 TCCACACGAACGAGACCAAT 59.323 50.000 0.14 0.00 0.00 3.16
983 1639 1.455786 CACACGAACGAGACCAATCAC 59.544 52.381 0.14 0.00 0.00 3.06
1074 1749 1.320344 CGGACATCTTCTCCGGTGGA 61.320 60.000 0.00 0.00 45.90 4.02
1116 1791 2.125106 CAGTTGCCGGGCCTAGAC 60.125 66.667 17.97 9.95 0.00 2.59
1117 1792 3.400054 AGTTGCCGGGCCTAGACC 61.400 66.667 17.97 0.00 0.00 3.85
1118 1793 3.400054 GTTGCCGGGCCTAGACCT 61.400 66.667 17.97 0.00 0.00 3.85
1119 1794 2.062177 GTTGCCGGGCCTAGACCTA 61.062 63.158 17.97 0.00 0.00 3.08
1120 1795 1.760875 TTGCCGGGCCTAGACCTAG 60.761 63.158 17.97 0.00 0.00 3.02
1321 2014 4.685628 CGCTTAACTAAACCCAACTCGTTA 59.314 41.667 0.00 0.00 0.00 3.18
1338 2031 4.021229 TCGTTAATCTTCTCTGGGCTACA 58.979 43.478 0.00 0.00 0.00 2.74
1339 2032 4.113354 CGTTAATCTTCTCTGGGCTACAC 58.887 47.826 0.00 0.00 0.00 2.90
1340 2033 4.381612 CGTTAATCTTCTCTGGGCTACACA 60.382 45.833 0.00 0.00 0.00 3.72
1341 2034 3.618690 AATCTTCTCTGGGCTACACAC 57.381 47.619 0.00 0.00 0.00 3.82
1342 2035 2.009681 TCTTCTCTGGGCTACACACA 57.990 50.000 0.00 0.00 0.00 3.72
1343 2036 2.540383 TCTTCTCTGGGCTACACACAT 58.460 47.619 0.00 0.00 0.00 3.21
1344 2037 2.234661 TCTTCTCTGGGCTACACACATG 59.765 50.000 0.00 0.00 0.00 3.21
1346 2039 2.470990 TCTCTGGGCTACACACATGAT 58.529 47.619 0.00 0.00 0.00 2.45
1347 2040 3.642141 TCTCTGGGCTACACACATGATA 58.358 45.455 0.00 0.00 0.00 2.15
1348 2041 4.226384 TCTCTGGGCTACACACATGATAT 58.774 43.478 0.00 0.00 0.00 1.63
1349 2042 4.655649 TCTCTGGGCTACACACATGATATT 59.344 41.667 0.00 0.00 0.00 1.28
1350 2043 5.130975 TCTCTGGGCTACACACATGATATTT 59.869 40.000 0.00 0.00 0.00 1.40
1351 2044 5.754782 TCTGGGCTACACACATGATATTTT 58.245 37.500 0.00 0.00 0.00 1.82
1362 2055 6.478673 CACACATGATATTTTCCTACGCTACA 59.521 38.462 0.00 0.00 0.00 2.74
1549 2269 4.559063 CTGCAGGCCGGGAGATGG 62.559 72.222 19.60 0.00 0.00 3.51
1559 2279 3.474570 GGAGATGGCACGGCTCCT 61.475 66.667 19.85 0.00 44.44 3.69
1580 2300 4.021925 GTCTCCGCCACCTGCCTT 62.022 66.667 0.00 0.00 36.24 4.35
1631 2351 2.034066 CTGAACACCATGGCCGGT 59.966 61.111 13.04 0.60 41.07 5.28
1703 2423 2.103143 ATCAGCTCGTCCGCTTCG 59.897 61.111 0.00 0.00 38.41 3.79
1773 2535 7.884877 ACACATGGATCTTCTGACTTAAATTCA 59.115 33.333 0.00 0.00 0.00 2.57
1779 2541 7.699812 GGATCTTCTGACTTAAATTCATGTTGC 59.300 37.037 0.00 0.00 0.00 4.17
1780 2542 7.509141 TCTTCTGACTTAAATTCATGTTGCA 57.491 32.000 0.00 0.00 0.00 4.08
1795 2558 1.726791 GTTGCAGTCGTGTCATCGATT 59.273 47.619 0.00 0.00 41.78 3.34
1800 2563 3.240861 GCAGTCGTGTCATCGATTCTTAC 59.759 47.826 0.00 0.00 41.78 2.34
1848 2611 9.978336 GTTCCAGTATTATATAGTACTCCCTCT 57.022 37.037 13.44 0.00 0.00 3.69
1853 2616 9.354108 AGTATTATATAGTACTCCCTCTGTCCT 57.646 37.037 11.15 0.00 0.00 3.85
1882 2645 9.908152 AATATAAGAAAGTTTTTGGCACTACAC 57.092 29.630 0.00 0.00 0.00 2.90
1885 2648 6.619801 AGAAAGTTTTTGGCACTACACTAG 57.380 37.500 0.00 0.00 0.00 2.57
1899 2662 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
1900 2663 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
1901 2664 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
1902 2665 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
1904 2667 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
1986 2795 2.457366 ACGTTGACTGAGGTGGATTC 57.543 50.000 0.00 0.00 0.00 2.52
1999 2808 3.542648 GGTGGATTCAGCTAAAGGGTAC 58.457 50.000 0.00 0.00 38.29 3.34
2010 2819 6.759827 TCAGCTAAAGGGTACATACGAATTTC 59.240 38.462 0.00 0.00 0.00 2.17
2148 2970 7.035004 TCAATTAGTTTATTGTGCATGCTTCC 58.965 34.615 20.33 7.42 36.95 3.46
2159 2981 0.323633 CATGCTTCCATCCCACCACA 60.324 55.000 0.00 0.00 0.00 4.17
2169 2991 2.188207 CCACCACACCACACGACA 59.812 61.111 0.00 0.00 0.00 4.35
2170 2992 1.227823 CCACCACACCACACGACAT 60.228 57.895 0.00 0.00 0.00 3.06
2204 3113 7.391148 AAAAGGTAACATAGCACGATGAAAT 57.609 32.000 0.00 0.00 41.41 2.17
2247 3159 6.238022 GCTTACCTTGACCGATAACATGTAAC 60.238 42.308 0.00 0.00 0.00 2.50
2265 3177 5.865085 TGTAACTAAGGTTCTGATGCAAGT 58.135 37.500 0.00 0.00 36.92 3.16
2283 3195 8.824159 ATGCAAGTCATCTGTATAATGTAGTC 57.176 34.615 0.00 0.00 0.00 2.59
2325 3237 4.318831 CGACAAGTTTCTCCTACTGCAAAC 60.319 45.833 0.00 0.00 0.00 2.93
2326 3238 3.560068 ACAAGTTTCTCCTACTGCAAACG 59.440 43.478 0.00 0.00 34.54 3.60
2361 3273 4.162040 AGCATTGGAGTTGGAGGATAAG 57.838 45.455 0.00 0.00 0.00 1.73
2362 3274 3.117738 AGCATTGGAGTTGGAGGATAAGG 60.118 47.826 0.00 0.00 0.00 2.69
2393 3305 3.313791 TGTGCCCTCTAGCCATATGTAA 58.686 45.455 1.24 0.00 0.00 2.41
2403 3315 6.398095 TCTAGCCATATGTAACATGGATTCG 58.602 40.000 5.55 0.00 44.95 3.34
2404 3316 4.326826 AGCCATATGTAACATGGATTCGG 58.673 43.478 5.55 0.00 44.95 4.30
2405 3317 4.072131 GCCATATGTAACATGGATTCGGT 58.928 43.478 5.55 0.00 44.95 4.69
2407 3319 4.083324 CCATATGTAACATGGATTCGGTGC 60.083 45.833 1.24 0.00 44.95 5.01
2410 3322 2.746904 TGTAACATGGATTCGGTGCAAG 59.253 45.455 0.00 0.00 0.00 4.01
2412 3324 0.608856 ACATGGATTCGGTGCAAGCA 60.609 50.000 0.00 0.00 0.00 3.91
2419 5254 0.392461 TTCGGTGCAAGCATAGTCCC 60.392 55.000 0.00 0.00 0.00 4.46
2421 5256 1.819632 GGTGCAAGCATAGTCCCCG 60.820 63.158 0.00 0.00 0.00 5.73
2477 5312 1.577922 CTGCGAACAGTGCAAGCAT 59.422 52.632 0.00 0.00 42.70 3.79
2488 5323 1.078709 TGCAAGCATAGTCTTGTCGC 58.921 50.000 5.55 0.00 43.92 5.19
2496 5331 2.724977 TAGTCTTGTCGCAGAAGGTG 57.275 50.000 0.00 0.00 39.69 4.00
2534 5369 1.360820 TCGAACAGTTTGCAACGACA 58.639 45.000 0.00 0.00 36.23 4.35
2540 5375 2.223479 ACAGTTTGCAACGACATTGGTC 60.223 45.455 0.00 0.00 38.88 4.02
2551 5386 1.952296 GACATTGGTCCATGGAGATGC 59.048 52.381 16.81 11.65 38.12 3.91
2592 5427 4.720902 CCCGTGCTGGATGTGGCA 62.721 66.667 0.00 0.00 42.00 4.92
2601 5436 2.808202 GCTGGATGTGGCAGTATACTGG 60.808 54.545 29.45 14.51 43.94 4.00
2604 5439 2.545952 GGATGTGGCAGTATACTGGTCG 60.546 54.545 29.45 9.02 43.94 4.79
2620 5455 1.132643 GGTCGAGTTCACTAGCATCGT 59.867 52.381 0.00 0.00 35.05 3.73
2635 5470 2.837498 CATCGTATCTGCCATTGGTGA 58.163 47.619 4.26 3.91 0.00 4.02
2643 5478 3.229293 TCTGCCATTGGTGAAACATTGA 58.771 40.909 4.26 0.00 39.98 2.57
2656 5492 7.986320 TGGTGAAACATTGATCTTGACAATTTT 59.014 29.630 0.00 0.00 39.98 1.82
2665 5501 6.554419 TGATCTTGACAATTTTAATGAGGCG 58.446 36.000 0.00 0.00 0.00 5.52
2666 5502 5.309323 TCTTGACAATTTTAATGAGGCGG 57.691 39.130 0.00 0.00 0.00 6.13
2667 5503 4.157656 TCTTGACAATTTTAATGAGGCGGG 59.842 41.667 0.00 0.00 0.00 6.13
2668 5504 2.165437 TGACAATTTTAATGAGGCGGGC 59.835 45.455 0.00 0.00 0.00 6.13
2687 5523 1.017177 CATGCCATTGCCAACACAGC 61.017 55.000 0.00 0.00 36.33 4.40
2688 5524 2.047939 GCCATTGCCAACACAGCC 60.048 61.111 0.00 0.00 0.00 4.85
2693 5529 1.047596 ATTGCCAACACAGCCCACAA 61.048 50.000 0.00 0.00 0.00 3.33
2700 5536 2.203394 ACAGCCCACAACAGCCTG 60.203 61.111 0.00 0.00 0.00 4.85
2701 5537 3.677648 CAGCCCACAACAGCCTGC 61.678 66.667 0.00 0.00 0.00 4.85
2712 5548 2.999648 AGCCTGCTGCCGAAGAGA 61.000 61.111 0.00 0.00 42.71 3.10
2714 5550 2.507992 CCTGCTGCCGAAGAGACG 60.508 66.667 0.00 0.00 0.00 4.18
2738 5574 3.825611 GCGGCCGCCATGAACAAT 61.826 61.111 39.89 0.00 34.56 2.71
2748 5584 1.019673 CATGAACAATGGAGGAGGCG 58.980 55.000 0.00 0.00 32.10 5.52
2761 5597 1.006571 GAGGCGAGGAACAACGACA 60.007 57.895 0.00 0.00 40.37 4.35
2762 5598 0.389948 GAGGCGAGGAACAACGACAT 60.390 55.000 0.00 0.00 40.37 3.06
2763 5599 0.034896 AGGCGAGGAACAACGACATT 59.965 50.000 0.00 0.00 40.37 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.039870 GTTTCACCATATGTTTCACAATTTGAA 57.960 29.630 2.79 0.68 42.83 2.69
14 15 8.492673 TCATAGAGTTTCACCATATGTTTCAC 57.507 34.615 1.24 0.00 0.00 3.18
43 44 8.775527 CACGTGTTCTAGAGTGTATCACTATAT 58.224 37.037 7.58 0.00 45.44 0.86
44 45 7.983484 TCACGTGTTCTAGAGTGTATCACTATA 59.017 37.037 16.51 3.58 45.44 1.31
127 777 7.636259 ATGTTTGTTTTCGTGGAACATAATG 57.364 32.000 0.00 0.00 44.52 1.90
208 858 8.458052 TGTAGTATTATGTTTGAAGCATGTTGG 58.542 33.333 4.71 0.00 0.00 3.77
365 1016 6.533730 AGACACTGAAACAATATCACTTCCA 58.466 36.000 0.00 0.00 0.00 3.53
367 1018 9.209175 ACTAAGACACTGAAACAATATCACTTC 57.791 33.333 0.00 0.00 0.00 3.01
389 1040 5.300539 TGTTTGCTATGTTCCTTGCAACTAA 59.699 36.000 0.00 0.00 43.74 2.24
485 1136 4.012374 ACTCCCAAGCAATAGAACACATG 58.988 43.478 0.00 0.00 0.00 3.21
486 1137 4.012374 CACTCCCAAGCAATAGAACACAT 58.988 43.478 0.00 0.00 0.00 3.21
487 1138 3.181445 ACACTCCCAAGCAATAGAACACA 60.181 43.478 0.00 0.00 0.00 3.72
492 1143 3.173151 TCTCACACTCCCAAGCAATAGA 58.827 45.455 0.00 0.00 0.00 1.98
557 1208 3.155093 TCCTCGACGTTACCTTTATGC 57.845 47.619 0.00 0.00 0.00 3.14
575 1226 9.337396 TGTTTATTAGTCCATTATGTGACATCC 57.663 33.333 0.00 0.00 0.00 3.51
676 1327 1.067516 AGCAATTCTGTTGTGCACACC 59.932 47.619 21.56 14.35 40.83 4.16
752 1406 0.984230 AGAGAACTGATTTGGCCCGA 59.016 50.000 0.00 0.00 0.00 5.14
851 1505 2.508526 ACTTCTCATGGCTGGTTTGAC 58.491 47.619 0.00 0.00 0.00 3.18
905 1559 2.687700 AGCCTGCTTGATCTACACTG 57.312 50.000 0.00 0.00 0.00 3.66
908 1562 2.752030 ACCTAGCCTGCTTGATCTACA 58.248 47.619 0.00 0.00 0.00 2.74
933 1587 3.899980 TGTAGAGATGATGGTGGATGAGG 59.100 47.826 0.00 0.00 0.00 3.86
980 1636 1.446792 GCTCGCAGCTAGCTTGTGA 60.447 57.895 16.46 19.68 42.61 3.58
983 1639 0.027716 CATTGCTCGCAGCTAGCTTG 59.972 55.000 16.46 11.10 42.97 4.01
1103 1778 2.123425 CTAGGTCTAGGCCCGGCA 60.123 66.667 10.56 0.00 0.00 5.69
1116 1791 1.734137 CGGGATGTCGTGGTCTAGG 59.266 63.158 0.00 0.00 0.00 3.02
1117 1792 1.734137 CCGGGATGTCGTGGTCTAG 59.266 63.158 0.00 0.00 0.00 2.43
1118 1793 2.420568 GCCGGGATGTCGTGGTCTA 61.421 63.158 2.18 0.00 0.00 2.59
1119 1794 3.771160 GCCGGGATGTCGTGGTCT 61.771 66.667 2.18 0.00 0.00 3.85
1321 2014 2.906389 TGTGTGTAGCCCAGAGAAGATT 59.094 45.455 0.00 0.00 0.00 2.40
1338 2031 6.479001 GTGTAGCGTAGGAAAATATCATGTGT 59.521 38.462 0.00 0.00 0.00 3.72
1339 2032 6.478673 TGTGTAGCGTAGGAAAATATCATGTG 59.521 38.462 0.00 0.00 0.00 3.21
1340 2033 6.479001 GTGTGTAGCGTAGGAAAATATCATGT 59.521 38.462 0.00 0.00 0.00 3.21
1341 2034 6.478673 TGTGTGTAGCGTAGGAAAATATCATG 59.521 38.462 0.00 0.00 0.00 3.07
1342 2035 6.578944 TGTGTGTAGCGTAGGAAAATATCAT 58.421 36.000 0.00 0.00 0.00 2.45
1343 2036 5.968254 TGTGTGTAGCGTAGGAAAATATCA 58.032 37.500 0.00 0.00 0.00 2.15
1344 2037 6.479001 ACATGTGTGTAGCGTAGGAAAATATC 59.521 38.462 0.00 0.00 36.63 1.63
1346 2039 5.579119 CACATGTGTGTAGCGTAGGAAAATA 59.421 40.000 18.03 0.00 40.96 1.40
1347 2040 4.391830 CACATGTGTGTAGCGTAGGAAAAT 59.608 41.667 18.03 0.00 40.96 1.82
1348 2041 3.743911 CACATGTGTGTAGCGTAGGAAAA 59.256 43.478 18.03 0.00 40.96 2.29
1349 2042 3.322369 CACATGTGTGTAGCGTAGGAAA 58.678 45.455 18.03 0.00 40.96 3.13
1350 2043 2.954316 CACATGTGTGTAGCGTAGGAA 58.046 47.619 18.03 0.00 40.96 3.36
1351 2044 2.647529 CACATGTGTGTAGCGTAGGA 57.352 50.000 18.03 0.00 40.96 2.94
1362 2055 0.037326 ACGGAATCTCGCACATGTGT 60.037 50.000 26.01 5.88 0.00 3.72
1379 2072 3.550950 ATCGATCAGATGCTCAGTACG 57.449 47.619 0.00 0.00 38.36 3.67
1549 2269 1.008309 GAGACGATAGGAGCCGTGC 60.008 63.158 0.00 0.00 39.30 5.34
1580 2300 1.628340 ACCATGATTTCCCTGTCGTCA 59.372 47.619 0.00 0.00 0.00 4.35
1631 2351 4.657408 TTGGACATGGGCAGCGCA 62.657 61.111 15.49 15.49 0.00 6.09
1703 2423 2.278332 AGGTCCTGTTCTGAAAAGCC 57.722 50.000 1.85 0.00 0.00 4.35
1773 2535 1.070821 CGATGACACGACTGCAACAT 58.929 50.000 0.00 0.00 35.09 2.71
1779 2541 3.478874 CGTAAGAATCGATGACACGACTG 59.521 47.826 13.64 0.00 42.50 3.51
1780 2542 3.681855 CGTAAGAATCGATGACACGACT 58.318 45.455 13.64 0.00 42.50 4.18
1800 2563 4.090930 ACGTCAACGGTTAAGATCAAATCG 59.909 41.667 10.81 10.81 44.95 3.34
1860 2623 7.771826 ACTAGTGTAGTGCCAAAAACTTTCTTA 59.228 33.333 0.00 0.00 37.69 2.10
1861 2624 5.914898 AGTGTAGTGCCAAAAACTTTCTT 57.085 34.783 0.00 0.00 0.00 2.52
1862 2625 6.120220 ACTAGTGTAGTGCCAAAAACTTTCT 58.880 36.000 0.00 0.00 37.69 2.52
1885 2648 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
1887 2650 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
1888 2651 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
1889 2652 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
1890 2653 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
1891 2654 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
1892 2655 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
1894 2657 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
1895 2658 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
1896 2659 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
1897 2660 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
1898 2661 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1899 2662 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1900 2663 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1901 2664 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1902 2665 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1904 2667 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
1907 2712 3.562108 ATATTACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
1965 2774 2.169832 ATCCACCTCAGTCAACGTTG 57.830 50.000 22.35 22.35 0.00 4.10
1966 2775 2.104111 TGAATCCACCTCAGTCAACGTT 59.896 45.455 0.00 0.00 0.00 3.99
1974 2783 3.539604 CCTTTAGCTGAATCCACCTCAG 58.460 50.000 0.00 0.00 42.73 3.35
1986 2795 6.761714 AGAAATTCGTATGTACCCTTTAGCTG 59.238 38.462 0.00 0.00 0.00 4.24
2031 2840 6.245408 TGGTGGATATTTGATAACCCATAGC 58.755 40.000 0.00 0.00 0.00 2.97
2124 2933 6.812656 TGGAAGCATGCACAATAAACTAATTG 59.187 34.615 21.98 0.00 41.65 2.32
2148 2970 1.965930 CGTGTGGTGTGGTGGGATG 60.966 63.158 0.00 0.00 0.00 3.51
2183 3005 4.816385 CCATTTCATCGTGCTATGTTACCT 59.184 41.667 0.00 0.00 0.00 3.08
2194 3103 3.761657 CACCATTCACCATTTCATCGTG 58.238 45.455 0.00 0.00 0.00 4.35
2204 3113 0.388659 GCAAAGTGCACCATTCACCA 59.611 50.000 14.63 0.00 44.26 4.17
2281 3193 3.364023 CGTGATCCGTTTGACACTTAGAC 59.636 47.826 0.00 0.00 0.00 2.59
2283 3195 3.364023 GTCGTGATCCGTTTGACACTTAG 59.636 47.826 0.00 0.00 37.94 2.18
2325 3237 3.247648 CCAATGCTATAACCGAGAAACCG 59.752 47.826 0.00 0.00 0.00 4.44
2326 3238 4.448210 TCCAATGCTATAACCGAGAAACC 58.552 43.478 0.00 0.00 0.00 3.27
2361 3273 0.107165 GAGGGCACATGTAACCTCCC 60.107 60.000 26.36 18.41 42.87 4.30
2362 3274 3.478540 GAGGGCACATGTAACCTCC 57.521 57.895 26.36 14.75 42.87 4.30
2393 3305 0.608856 TGCTTGCACCGAATCCATGT 60.609 50.000 0.00 0.00 0.00 3.21
2403 3315 1.819632 CGGGGACTATGCTTGCACC 60.820 63.158 0.00 0.00 0.00 5.01
2404 3316 2.472909 GCGGGGACTATGCTTGCAC 61.473 63.158 0.00 0.00 0.00 4.57
2405 3317 2.124736 GCGGGGACTATGCTTGCA 60.125 61.111 0.00 0.00 0.00 4.08
2407 3319 2.588877 CGGCGGGGACTATGCTTG 60.589 66.667 0.00 0.00 0.00 4.01
2426 5261 1.501741 CAAGTTCACATTCGGGGCG 59.498 57.895 0.00 0.00 0.00 6.13
2430 5265 2.185004 AGACCCAAGTTCACATTCGG 57.815 50.000 0.00 0.00 0.00 4.30
2477 5312 1.272490 CCACCTTCTGCGACAAGACTA 59.728 52.381 0.00 0.00 0.00 2.59
2488 5323 1.333619 CACACCGAAAACCACCTTCTG 59.666 52.381 0.00 0.00 0.00 3.02
2496 5331 1.467342 GATAGCACCACACCGAAAACC 59.533 52.381 0.00 0.00 0.00 3.27
2534 5369 0.179009 CCGCATCTCCATGGACCAAT 60.179 55.000 11.44 1.81 0.00 3.16
2540 5375 1.300465 CTCGACCGCATCTCCATGG 60.300 63.158 4.97 4.97 0.00 3.66
2576 5411 2.520465 TACTGCCACATCCAGCACGG 62.520 60.000 0.00 0.00 34.68 4.94
2592 5427 4.575645 GCTAGTGAACTCGACCAGTATACT 59.424 45.833 0.00 0.00 36.15 2.12
2601 5436 2.546195 ACGATGCTAGTGAACTCGAC 57.454 50.000 0.00 0.00 33.74 4.20
2604 5439 3.978217 GCAGATACGATGCTAGTGAACTC 59.022 47.826 0.00 0.00 40.59 3.01
2620 5455 5.015515 TCAATGTTTCACCAATGGCAGATA 58.984 37.500 0.00 0.00 0.00 1.98
2643 5478 5.163519 CCCGCCTCATTAAAATTGTCAAGAT 60.164 40.000 0.00 0.00 0.00 2.40
2667 5503 1.004799 TGTGTTGGCAATGGCATGC 60.005 52.632 11.08 9.90 45.67 4.06
2668 5504 1.017177 GCTGTGTTGGCAATGGCATG 61.017 55.000 11.08 0.00 43.71 4.06
2679 5515 1.066257 GCTGTTGTGGGCTGTGTTG 59.934 57.895 0.00 0.00 0.00 3.33
2681 5517 2.519302 GGCTGTTGTGGGCTGTGT 60.519 61.111 0.00 0.00 0.00 3.72
2687 5523 3.677648 GCAGCAGGCTGTTGTGGG 61.678 66.667 28.32 7.54 45.24 4.61
2688 5524 3.677648 GGCAGCAGGCTGTTGTGG 61.678 66.667 28.32 7.89 45.24 4.17
2700 5536 0.388649 TTCTTCGTCTCTTCGGCAGC 60.389 55.000 0.00 0.00 0.00 5.25
2701 5537 1.989165 CTTTCTTCGTCTCTTCGGCAG 59.011 52.381 0.00 0.00 0.00 4.85
2704 5540 0.985549 CGCTTTCTTCGTCTCTTCGG 59.014 55.000 0.00 0.00 0.00 4.30
2714 5550 3.134127 ATGGCGGCCGCTTTCTTC 61.134 61.111 45.23 29.60 41.60 2.87
2738 5574 1.535444 TTGTTCCTCGCCTCCTCCA 60.535 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.