Multiple sequence alignment - TraesCS2A01G391200

Loading Multiple Alignment...

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 TraesCS2A01G391200 chr2A 100.000 2606 0 0 1 2606 640863725 640861120 0.000000e+00 4813.0
1 TraesCS2A01G391200 chr2A 87.273 110 13 1 1930 2039 707795587 707795479 9.790000e-25 124.0
2 TraesCS2A01G391200 chr2A 86.087 115 13 3 1929 2042 565200952 565200840 1.270000e-23 121.0
3 TraesCS2A01G391200 chr2D 91.919 1980 80 29 1 1934 492899440 492901385 0.000000e+00 2697.0
4 TraesCS2A01G391200 chr2D 89.221 603 36 9 2031 2606 492901376 492901976 0.000000e+00 726.0
5 TraesCS2A01G391200 chr2B 91.355 1897 89 30 74 1934 579523884 579525741 0.000000e+00 2525.0
6 TraesCS2A01G391200 chr2B 88.827 537 30 6 2085 2594 579525764 579526297 1.320000e-177 632.0
7 TraesCS2A01G391200 chr6D 89.381 113 10 2 1930 2042 299167834 299167944 9.720000e-30 141.0
8 TraesCS2A01G391200 chr5D 88.182 110 11 2 1930 2039 382294595 382294702 2.100000e-26 130.0
9 TraesCS2A01G391200 chr5A 87.069 116 12 3 1929 2044 650507381 650507493 7.570000e-26 128.0
10 TraesCS2A01G391200 chr4D 86.486 111 13 2 1931 2041 39211020 39210912 1.270000e-23 121.0
11 TraesCS2A01G391200 chr3D 86.916 107 12 2 1932 2038 575494541 575494437 4.560000e-23 119.0
12 TraesCS2A01G391200 chr6B 87.129 101 13 0 2134 2234 704874634 704874534 5.890000e-22 115.0
13 TraesCS2A01G391200 chr4A 83.465 127 17 4 1929 2053 738935580 738935456 5.890000e-22 115.0
14 TraesCS2A01G391200 chrUn 83.200 125 17 4 1916 2038 32898328 32898450 7.620000e-21 111.0
15 TraesCS2A01G391200 chr7A 85.294 102 14 1 2133 2234 638491339 638491439 1.280000e-18 104.0
16 TraesCS2A01G391200 chr7B 83.333 108 12 6 2128 2232 382521381 382521485 7.680000e-16 95.3
17 TraesCS2A01G391200 chr7B 83.654 104 12 4 2133 2234 644184270 644184370 2.760000e-15 93.5
18 TraesCS2A01G391200 chr1B 79.091 110 19 3 2134 2241 57435385 57435492 3.600000e-09 73.1
19 TraesCS2A01G391200 chr5B 76.577 111 19 6 2134 2240 670806505 670806612 1.000000e-03 54.7


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 TraesCS2A01G391200 chr2A 640861120 640863725 2605 True 4813.0 4813 100.000 1 2606 1 chr2A.!!$R2 2605
1 TraesCS2A01G391200 chr2D 492899440 492901976 2536 False 1711.5 2697 90.570 1 2606 2 chr2D.!!$F1 2605
2 TraesCS2A01G391200 chr2B 579523884 579526297 2413 False 1578.5 2525 90.091 74 2594 2 chr2B.!!$F1 2520

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
316 325 0.034616 CCTTCTCATCCATCTCGCCC 59.965 60.0 0.0 0.0 0.00 6.13 F
617 629 1.606606 GCGGTCGCTTCTTTTTGATG 58.393 50.0 8.2 0.0 38.26 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1504 1.512926 GCACCATGAGTTCGTTGTCT 58.487 50.000 0.00 0.00 0.0 3.41 R
2195 2260 2.080693 ACGTTTTGAACAGCTGACACA 58.919 42.857 23.35 13.88 0.0 3.72 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
39 41 0.541863 ACATCCGGCCAAAGTAGGAG 59.458 55.000 2.24 0.00 36.08 3.69
66 68 5.457140 GCATAATTTTCTTGTGGAACGTCA 58.543 37.500 0.00 0.00 42.39 4.35
67 69 5.569059 GCATAATTTTCTTGTGGAACGTCAG 59.431 40.000 0.00 0.00 42.39 3.51
68 70 6.668323 CATAATTTTCTTGTGGAACGTCAGT 58.332 36.000 0.00 0.00 42.39 3.41
75 77 3.648339 TGTGGAACGTCAGTAGTAACC 57.352 47.619 0.00 0.00 42.39 2.85
162 170 1.903139 CTTACGTACGCACTCACTTCG 59.097 52.381 16.72 0.00 0.00 3.79
164 172 0.520404 ACGTACGCACTCACTTCGAT 59.480 50.000 16.72 0.00 0.00 3.59
207 215 3.689649 ACAATTCCGTATGCTCCAAACTC 59.310 43.478 0.00 0.00 0.00 3.01
208 216 3.914426 ATTCCGTATGCTCCAAACTCT 57.086 42.857 0.00 0.00 0.00 3.24
231 239 3.492068 GGGAAACGGAACCCCTCT 58.508 61.111 0.00 0.00 40.19 3.69
232 240 1.002502 GGGAAACGGAACCCCTCTG 60.003 63.158 0.00 0.00 40.19 3.35
233 241 1.002502 GGAAACGGAACCCCTCTGG 60.003 63.158 0.00 0.00 41.37 3.86
234 242 1.674651 GAAACGGAACCCCTCTGGC 60.675 63.158 0.00 0.00 37.83 4.85
235 243 3.205851 AAACGGAACCCCTCTGGCC 62.206 63.158 0.00 0.00 37.83 5.36
236 244 4.658786 ACGGAACCCCTCTGGCCT 62.659 66.667 3.32 0.00 37.83 5.19
237 245 3.787001 CGGAACCCCTCTGGCCTC 61.787 72.222 3.32 0.00 37.83 4.70
238 246 3.412408 GGAACCCCTCTGGCCTCC 61.412 72.222 3.32 0.00 37.83 4.30
239 247 2.285743 GAACCCCTCTGGCCTCCT 60.286 66.667 3.32 0.00 37.83 3.69
240 248 2.285743 AACCCCTCTGGCCTCCTC 60.286 66.667 3.32 0.00 37.83 3.71
241 249 2.831394 GAACCCCTCTGGCCTCCTCT 62.831 65.000 3.32 0.00 37.83 3.69
316 325 0.034616 CCTTCTCATCCATCTCGCCC 59.965 60.000 0.00 0.00 0.00 6.13
375 384 1.751437 GGTAGGTGCCCTGTCAATTC 58.249 55.000 4.16 0.00 34.61 2.17
427 436 2.043248 ACGTAGCCTGGGATCGGT 60.043 61.111 0.00 0.00 0.00 4.69
439 448 4.334481 CCTGGGATCGGTTATACAACAAAC 59.666 45.833 0.00 0.00 36.29 2.93
449 458 3.636282 ATACAACAAACAAACCGGAGC 57.364 42.857 9.46 0.00 0.00 4.70
520 529 3.248602 CCCGATCCTCGATCATTTTGTTC 59.751 47.826 0.00 0.00 43.74 3.18
521 530 3.060272 CCGATCCTCGATCATTTTGTTCG 60.060 47.826 0.00 2.41 43.74 3.95
560 572 4.236935 GTGTTGGTTGCTGTATGGATTTG 58.763 43.478 0.00 0.00 0.00 2.32
563 575 5.714333 TGTTGGTTGCTGTATGGATTTGTAT 59.286 36.000 0.00 0.00 0.00 2.29
617 629 1.606606 GCGGTCGCTTCTTTTTGATG 58.393 50.000 8.20 0.00 38.26 3.07
680 692 2.586357 GCGCCAGATCTCCGGTTC 60.586 66.667 0.00 0.00 0.00 3.62
708 737 2.734723 CACGAGCACCACAGACCG 60.735 66.667 0.00 0.00 0.00 4.79
709 738 4.664677 ACGAGCACCACAGACCGC 62.665 66.667 0.00 0.00 0.00 5.68
710 739 4.662961 CGAGCACCACAGACCGCA 62.663 66.667 0.00 0.00 0.00 5.69
711 740 2.740055 GAGCACCACAGACCGCAG 60.740 66.667 0.00 0.00 0.00 5.18
712 741 4.996434 AGCACCACAGACCGCAGC 62.996 66.667 0.00 0.00 0.00 5.25
867 907 1.918293 CCACCACCAGTAGAGGGCA 60.918 63.158 0.00 0.00 0.00 5.36
922 962 2.639286 CCAGCGCTGAAACACACC 59.361 61.111 38.06 0.00 0.00 4.16
929 969 2.512745 TGAAACACACCGCACGCT 60.513 55.556 0.00 0.00 0.00 5.07
930 970 2.052237 GAAACACACCGCACGCTG 60.052 61.111 0.00 0.00 0.00 5.18
931 971 3.521308 GAAACACACCGCACGCTGG 62.521 63.158 0.00 0.00 0.00 4.85
932 972 4.849310 AACACACCGCACGCTGGT 62.849 61.111 0.62 0.62 41.47 4.00
1449 1504 0.677098 CTGACGAGGAGGACGAGGAA 60.677 60.000 0.00 0.00 34.70 3.36
1453 1508 0.677098 CGAGGAGGACGAGGAAGACA 60.677 60.000 0.00 0.00 0.00 3.41
1656 1711 0.605319 TGCCCACGTCACTCCAATTC 60.605 55.000 0.00 0.00 0.00 2.17
1801 1864 3.070076 TGCTGATCACGGAGCAATC 57.930 52.632 4.98 0.00 42.22 2.67
1823 1886 6.073447 TCAAATAAGGTCTAAATGGCTGGA 57.927 37.500 0.00 0.00 0.00 3.86
1921 1986 7.797121 AGATATTTCCTTTGTCCCAAAATGT 57.203 32.000 0.00 0.00 0.00 2.71
1922 1987 7.614494 AGATATTTCCTTTGTCCCAAAATGTG 58.386 34.615 0.00 0.00 0.00 3.21
1923 1988 5.885449 ATTTCCTTTGTCCCAAAATGTGA 57.115 34.783 0.00 0.00 0.00 3.58
1924 1989 5.683876 TTTCCTTTGTCCCAAAATGTGAA 57.316 34.783 0.00 0.00 0.00 3.18
1926 1991 3.640967 TCCTTTGTCCCAAAATGTGAAGG 59.359 43.478 0.00 0.00 35.01 3.46
1927 1992 3.244181 CCTTTGTCCCAAAATGTGAAGGG 60.244 47.826 0.00 0.00 42.86 3.95
1932 1997 4.028993 TCCCAAAATGTGAAGGGAGTAC 57.971 45.455 0.00 0.00 45.15 2.73
1933 1998 3.655777 TCCCAAAATGTGAAGGGAGTACT 59.344 43.478 0.00 0.00 45.15 2.73
1934 1999 4.847512 TCCCAAAATGTGAAGGGAGTACTA 59.152 41.667 0.00 0.00 45.15 1.82
1935 2000 5.491078 TCCCAAAATGTGAAGGGAGTACTAT 59.509 40.000 0.00 0.00 45.15 2.12
1936 2001 5.823045 CCCAAAATGTGAAGGGAGTACTATC 59.177 44.000 0.00 0.00 44.30 2.08
1937 2002 6.353082 CCCAAAATGTGAAGGGAGTACTATCT 60.353 42.308 0.00 0.00 44.30 1.98
1938 2003 6.763610 CCAAAATGTGAAGGGAGTACTATCTC 59.236 42.308 0.00 0.00 0.00 2.75
1939 2004 7.365117 CCAAAATGTGAAGGGAGTACTATCTCT 60.365 40.741 0.00 0.00 35.11 3.10
1940 2005 8.696374 CAAAATGTGAAGGGAGTACTATCTCTA 58.304 37.037 0.00 0.00 35.11 2.43
1941 2006 9.440761 AAAATGTGAAGGGAGTACTATCTCTAT 57.559 33.333 0.00 0.00 35.11 1.98
1942 2007 9.440761 AAATGTGAAGGGAGTACTATCTCTATT 57.559 33.333 0.00 0.00 35.11 1.73
1943 2008 8.644374 ATGTGAAGGGAGTACTATCTCTATTC 57.356 38.462 0.00 0.00 35.11 1.75
1944 2009 7.583625 TGTGAAGGGAGTACTATCTCTATTCA 58.416 38.462 0.00 0.00 36.99 2.57
1945 2010 8.228206 TGTGAAGGGAGTACTATCTCTATTCAT 58.772 37.037 0.00 0.00 39.01 2.57
1946 2011 9.084533 GTGAAGGGAGTACTATCTCTATTCATT 57.915 37.037 0.00 0.00 39.01 2.57
1947 2012 9.661954 TGAAGGGAGTACTATCTCTATTCATTT 57.338 33.333 0.00 0.00 35.83 2.32
1974 2039 9.970395 TTATAAGACGTTTTAGACTTTCAGACA 57.030 29.630 4.75 0.00 0.00 3.41
1975 2040 6.585389 AAGACGTTTTAGACTTTCAGACAC 57.415 37.500 0.00 0.00 0.00 3.67
1976 2041 5.903810 AGACGTTTTAGACTTTCAGACACT 58.096 37.500 0.00 0.00 0.00 3.55
1977 2042 7.035840 AGACGTTTTAGACTTTCAGACACTA 57.964 36.000 0.00 0.00 0.00 2.74
1978 2043 7.659186 AGACGTTTTAGACTTTCAGACACTAT 58.341 34.615 0.00 0.00 0.00 2.12
1979 2044 8.142551 AGACGTTTTAGACTTTCAGACACTATT 58.857 33.333 0.00 0.00 0.00 1.73
1980 2045 8.658499 ACGTTTTAGACTTTCAGACACTATTT 57.342 30.769 0.00 0.00 0.00 1.40
1981 2046 9.754382 ACGTTTTAGACTTTCAGACACTATTTA 57.246 29.630 0.00 0.00 0.00 1.40
2011 2076 8.856490 AGTACAAAGCAAAACTGTCTAAAATG 57.144 30.769 0.00 0.00 0.00 2.32
2012 2077 8.466798 AGTACAAAGCAAAACTGTCTAAAATGT 58.533 29.630 0.00 0.00 0.00 2.71
2013 2078 7.755582 ACAAAGCAAAACTGTCTAAAATGTC 57.244 32.000 0.00 0.00 0.00 3.06
2014 2079 7.547227 ACAAAGCAAAACTGTCTAAAATGTCT 58.453 30.769 0.00 0.00 0.00 3.41
2015 2080 8.034804 ACAAAGCAAAACTGTCTAAAATGTCTT 58.965 29.630 0.00 0.00 0.00 3.01
2016 2081 9.515020 CAAAGCAAAACTGTCTAAAATGTCTTA 57.485 29.630 0.00 0.00 0.00 2.10
2032 2097 9.471084 AAAATGTCTTATAAAAACAAACGGAGG 57.529 29.630 4.87 0.00 0.00 4.30
2033 2098 7.989416 ATGTCTTATAAAAACAAACGGAGGA 57.011 32.000 4.87 0.00 0.00 3.71
2046 2111 5.047731 ACAAACGGAGGAAGTACTTACTACC 60.048 44.000 22.36 20.44 32.95 3.18
2047 2112 4.307032 ACGGAGGAAGTACTTACTACCA 57.693 45.455 22.36 0.00 32.95 3.25
2147 2212 6.485648 GTGTAAATGTTGTACTCCCTCTGTTT 59.514 38.462 0.00 0.00 0.00 2.83
2149 2214 8.380099 TGTAAATGTTGTACTCCCTCTGTTTAT 58.620 33.333 0.00 0.00 0.00 1.40
2195 2260 3.055530 CAGACAGCCCACAGAATAGTTCT 60.056 47.826 0.00 0.00 41.70 3.01
2207 2272 5.220710 AGAATAGTTCTGTGTCAGCTGTT 57.779 39.130 14.67 0.00 38.91 3.16
2234 2299 7.481275 AAACGTCTTATAAAAGTGAACGGAA 57.519 32.000 0.00 0.00 35.75 4.30
2235 2300 7.481275 AACGTCTTATAAAAGTGAACGGAAA 57.519 32.000 0.00 0.00 35.75 3.13
2330 2418 5.123502 AGAGTGCTTTTATCTGATGTTGCAG 59.876 40.000 0.00 0.00 37.24 4.41
2377 2465 1.612462 CCAGCTGCAGGTGAAGAATCA 60.612 52.381 40.03 0.00 45.66 2.57
2386 2474 4.940046 GCAGGTGAAGAATCATCTTTCTCA 59.060 41.667 0.00 0.00 44.83 3.27
2454 2545 9.827411 CTAGTTTTGATCCTTTTACTGCTAAAC 57.173 33.333 0.00 0.00 0.00 2.01
2550 2642 3.751698 AGATGGAACCGAAGTTAAACTGC 59.248 43.478 0.00 0.00 35.94 4.40
2561 2653 5.790495 CGAAGTTAAACTGCTATCTTGTTGC 59.210 40.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.906720 TGTTAATGTGGAGCCTAGTCC 57.093 47.619 0.00 0.00 37.10 3.85
39 41 4.695217 TCCACAAGAAAATTATGCGGTC 57.305 40.909 0.00 0.00 0.00 4.79
66 68 3.259876 TGCGGTGATGAAAGGTTACTACT 59.740 43.478 0.00 0.00 0.00 2.57
67 69 3.592059 TGCGGTGATGAAAGGTTACTAC 58.408 45.455 0.00 0.00 0.00 2.73
68 70 3.965379 TGCGGTGATGAAAGGTTACTA 57.035 42.857 0.00 0.00 0.00 1.82
75 77 2.399396 AAACGTTGCGGTGATGAAAG 57.601 45.000 0.00 0.00 0.00 2.62
162 170 4.277672 TGTGGAGGTGTATAGCTTACGATC 59.722 45.833 0.00 0.00 34.13 3.69
164 172 3.379372 GTGTGGAGGTGTATAGCTTACGA 59.621 47.826 0.00 0.00 34.13 3.43
207 215 0.669625 GGTTCCGTTTCCCTGTCGAG 60.670 60.000 0.00 0.00 0.00 4.04
208 216 1.368579 GGTTCCGTTTCCCTGTCGA 59.631 57.895 0.00 0.00 0.00 4.20
234 242 3.086600 GGTCTGGGCCAGAGGAGG 61.087 72.222 35.81 9.39 41.46 4.30
235 243 1.277580 AATGGTCTGGGCCAGAGGAG 61.278 60.000 35.81 10.22 41.46 3.69
236 244 0.846427 AAATGGTCTGGGCCAGAGGA 60.846 55.000 35.81 24.56 41.46 3.71
237 245 0.040204 AAAATGGTCTGGGCCAGAGG 59.960 55.000 35.81 11.08 41.46 3.69
238 246 1.928868 AAAAATGGTCTGGGCCAGAG 58.071 50.000 35.81 11.92 41.46 3.35
296 305 1.043816 GGCGAGATGGATGAGAAGGA 58.956 55.000 0.00 0.00 0.00 3.36
407 416 2.728817 GATCCCAGGCTACGTCCG 59.271 66.667 0.00 0.00 0.00 4.79
427 436 4.319622 CGCTCCGGTTTGTTTGTTGTATAA 60.320 41.667 0.00 0.00 0.00 0.98
439 448 2.377310 CCGTGTACGCTCCGGTTTG 61.377 63.158 0.00 0.00 37.00 2.93
449 458 2.948323 GGGTTTTGGCCGTGTACG 59.052 61.111 0.00 0.00 39.44 3.67
520 529 2.279517 GTCCTCGGCCATACAGCG 60.280 66.667 2.24 0.00 0.00 5.18
521 530 2.279517 CGTCCTCGGCCATACAGC 60.280 66.667 2.24 0.00 0.00 4.40
560 572 5.357257 ACGACATTTCCCATCTGTACATAC 58.643 41.667 0.00 0.00 0.00 2.39
563 575 3.973206 ACGACATTTCCCATCTGTACA 57.027 42.857 0.00 0.00 0.00 2.90
669 681 2.506472 GGCCTGGAACCGGAGATC 59.494 66.667 9.46 2.88 0.00 2.75
730 759 4.589700 CGTGTGTGTGCCGTGTGC 62.590 66.667 0.00 0.00 41.77 4.57
789 829 0.468585 TGGGGCAATGATGATGGCTC 60.469 55.000 0.00 0.00 43.69 4.70
842 882 2.748058 CTACTGGTGGTGGTGGTGGC 62.748 65.000 0.00 0.00 0.00 5.01
852 892 2.579201 CGTGCCCTCTACTGGTGG 59.421 66.667 0.00 0.00 0.00 4.61
853 893 2.125512 GCGTGCCCTCTACTGGTG 60.126 66.667 0.00 0.00 0.00 4.17
854 894 3.391382 GGCGTGCCCTCTACTGGT 61.391 66.667 0.00 0.00 0.00 4.00
855 895 4.514577 CGGCGTGCCCTCTACTGG 62.515 72.222 5.08 0.00 0.00 4.00
922 962 3.716006 CTGACCAACCAGCGTGCG 61.716 66.667 0.00 0.00 0.00 5.34
929 969 2.194597 GTGGCCACTGACCAACCA 59.805 61.111 29.12 0.00 39.39 3.67
930 970 2.515901 AGTGGCCACTGACCAACC 59.484 61.111 37.39 6.87 40.75 3.77
997 1037 3.630148 GTCGCGCATGGACATCGG 61.630 66.667 8.75 0.00 34.56 4.18
1449 1504 1.512926 GCACCATGAGTTCGTTGTCT 58.487 50.000 0.00 0.00 0.00 3.41
1453 1508 2.325082 GCGGCACCATGAGTTCGTT 61.325 57.895 0.00 0.00 0.00 3.85
1801 1864 6.966534 ATCCAGCCATTTAGACCTTATTTG 57.033 37.500 0.00 0.00 0.00 2.32
1823 1886 5.590530 TTGTGGTTAGTTGCAAGTTCAAT 57.409 34.783 12.95 0.00 0.00 2.57
1909 1972 2.176798 ACTCCCTTCACATTTTGGGACA 59.823 45.455 0.00 0.00 43.20 4.02
1918 1983 8.228206 TGAATAGAGATAGTACTCCCTTCACAT 58.772 37.037 0.00 0.00 35.22 3.21
1921 1986 9.661954 AAATGAATAGAGATAGTACTCCCTTCA 57.338 33.333 0.00 0.00 39.61 3.02
1948 2013 9.970395 TGTCTGAAAGTCTAAAACGTCTTATAA 57.030 29.630 0.00 0.00 33.76 0.98
1949 2014 9.403110 GTGTCTGAAAGTCTAAAACGTCTTATA 57.597 33.333 0.00 0.00 33.76 0.98
1950 2015 8.142551 AGTGTCTGAAAGTCTAAAACGTCTTAT 58.857 33.333 0.00 0.00 33.76 1.73
1951 2016 7.486647 AGTGTCTGAAAGTCTAAAACGTCTTA 58.513 34.615 0.00 0.00 33.76 2.10
1952 2017 6.338937 AGTGTCTGAAAGTCTAAAACGTCTT 58.661 36.000 0.00 0.00 33.76 3.01
1953 2018 5.903810 AGTGTCTGAAAGTCTAAAACGTCT 58.096 37.500 0.00 0.00 33.76 4.18
1954 2019 7.870588 ATAGTGTCTGAAAGTCTAAAACGTC 57.129 36.000 0.00 0.00 33.76 4.34
1955 2020 8.658499 AAATAGTGTCTGAAAGTCTAAAACGT 57.342 30.769 0.00 0.00 33.76 3.99
1985 2050 9.944663 CATTTTAGACAGTTTTGCTTTGTACTA 57.055 29.630 0.00 0.00 0.00 1.82
1986 2051 8.466798 ACATTTTAGACAGTTTTGCTTTGTACT 58.533 29.630 0.00 0.00 0.00 2.73
1987 2052 8.628882 ACATTTTAGACAGTTTTGCTTTGTAC 57.371 30.769 0.00 0.00 0.00 2.90
1988 2053 8.682710 AGACATTTTAGACAGTTTTGCTTTGTA 58.317 29.630 0.00 0.00 0.00 2.41
1989 2054 7.547227 AGACATTTTAGACAGTTTTGCTTTGT 58.453 30.769 0.00 0.00 0.00 2.83
1990 2055 7.992180 AGACATTTTAGACAGTTTTGCTTTG 57.008 32.000 0.00 0.00 0.00 2.77
2006 2071 9.471084 CCTCCGTTTGTTTTTATAAGACATTTT 57.529 29.630 5.05 0.00 0.00 1.82
2007 2072 8.852135 TCCTCCGTTTGTTTTTATAAGACATTT 58.148 29.630 5.05 0.00 0.00 2.32
2008 2073 8.398878 TCCTCCGTTTGTTTTTATAAGACATT 57.601 30.769 5.05 0.00 0.00 2.71
2009 2074 7.989416 TCCTCCGTTTGTTTTTATAAGACAT 57.011 32.000 5.05 0.00 0.00 3.06
2010 2075 7.499895 ACTTCCTCCGTTTGTTTTTATAAGACA 59.500 33.333 0.00 1.00 0.00 3.41
2011 2076 7.868775 ACTTCCTCCGTTTGTTTTTATAAGAC 58.131 34.615 0.00 0.00 0.00 3.01
2012 2077 8.992073 GTACTTCCTCCGTTTGTTTTTATAAGA 58.008 33.333 0.00 0.00 0.00 2.10
2013 2078 8.996271 AGTACTTCCTCCGTTTGTTTTTATAAG 58.004 33.333 0.00 0.00 0.00 1.73
2014 2079 8.907222 AGTACTTCCTCCGTTTGTTTTTATAA 57.093 30.769 0.00 0.00 0.00 0.98
2015 2080 8.907222 AAGTACTTCCTCCGTTTGTTTTTATA 57.093 30.769 1.12 0.00 0.00 0.98
2016 2081 7.812690 AAGTACTTCCTCCGTTTGTTTTTAT 57.187 32.000 1.12 0.00 0.00 1.40
2017 2082 7.986889 AGTAAGTACTTCCTCCGTTTGTTTTTA 59.013 33.333 12.39 0.00 31.13 1.52
2018 2083 6.825213 AGTAAGTACTTCCTCCGTTTGTTTTT 59.175 34.615 12.39 0.00 31.13 1.94
2019 2084 6.351711 AGTAAGTACTTCCTCCGTTTGTTTT 58.648 36.000 12.39 0.00 31.13 2.43
2020 2085 5.922053 AGTAAGTACTTCCTCCGTTTGTTT 58.078 37.500 12.39 0.00 31.13 2.83
2021 2086 5.541953 AGTAAGTACTTCCTCCGTTTGTT 57.458 39.130 12.39 0.00 31.13 2.83
2022 2087 5.047731 GGTAGTAAGTACTTCCTCCGTTTGT 60.048 44.000 12.39 0.00 39.72 2.83
2023 2088 5.047802 TGGTAGTAAGTACTTCCTCCGTTTG 60.048 44.000 12.39 0.00 42.30 2.93
2024 2089 5.079643 TGGTAGTAAGTACTTCCTCCGTTT 58.920 41.667 12.39 0.00 42.30 3.60
2025 2090 4.666512 TGGTAGTAAGTACTTCCTCCGTT 58.333 43.478 12.39 0.00 42.30 4.44
2026 2091 4.307032 TGGTAGTAAGTACTTCCTCCGT 57.693 45.455 12.39 0.00 42.30 4.69
2027 2092 4.439837 GCTTGGTAGTAAGTACTTCCTCCG 60.440 50.000 12.39 1.78 42.30 4.63
2028 2093 4.710865 AGCTTGGTAGTAAGTACTTCCTCC 59.289 45.833 12.39 10.00 42.30 4.30
2029 2094 5.918426 AGCTTGGTAGTAAGTACTTCCTC 57.082 43.478 12.39 4.45 42.30 3.71
2030 2095 5.778750 TGAAGCTTGGTAGTAAGTACTTCCT 59.221 40.000 12.39 8.83 42.30 3.36
2031 2096 6.034161 TGAAGCTTGGTAGTAAGTACTTCC 57.966 41.667 12.39 7.76 42.20 3.46
2032 2097 8.549338 AAATGAAGCTTGGTAGTAAGTACTTC 57.451 34.615 12.39 4.24 37.73 3.01
2033 2098 9.654663 CTAAATGAAGCTTGGTAGTAAGTACTT 57.345 33.333 13.68 13.68 37.73 2.24
2098 2163 4.697828 TCATACGTGTTTGTACCATGCAAT 59.302 37.500 0.00 0.00 0.00 3.56
2119 2184 5.542635 AGAGGGAGTACAACATTTACACTCA 59.457 40.000 0.00 0.00 37.87 3.41
2128 2193 8.706322 AAAAATAAACAGAGGGAGTACAACAT 57.294 30.769 0.00 0.00 0.00 2.71
2195 2260 2.080693 ACGTTTTGAACAGCTGACACA 58.919 42.857 23.35 13.88 0.00 3.72
2196 2261 2.351726 AGACGTTTTGAACAGCTGACAC 59.648 45.455 23.35 11.36 0.00 3.67
2202 2267 7.853929 TCACTTTTATAAGACGTTTTGAACAGC 59.146 33.333 0.83 0.00 35.30 4.40
2207 2272 7.224362 TCCGTTCACTTTTATAAGACGTTTTGA 59.776 33.333 0.83 0.00 35.30 2.69
2257 2323 5.897050 TGGTAAAATGTGTTGTGGTCTTTC 58.103 37.500 0.00 0.00 0.00 2.62
2330 2418 4.654915 GGAGACCCTGGATAGAGTACTAC 58.345 52.174 0.00 0.00 0.00 2.73
2377 2465 4.298103 AGAGTGTGCCAATGAGAAAGAT 57.702 40.909 0.00 0.00 0.00 2.40
2386 2474 4.403432 CCAAATCCATTAGAGTGTGCCAAT 59.597 41.667 0.00 0.00 0.00 3.16
2454 2545 3.181497 CGAATGATAGCACCAAAACAGGG 60.181 47.826 0.00 0.00 0.00 4.45
2550 2642 4.695396 AGAGATGCTCTGCAACAAGATAG 58.305 43.478 0.00 0.00 43.62 2.08


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

AutoCloner maintained by Alex Coulton.