Multiple sequence alignment - TraesCS3A01G366000

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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 TraesCS3A01G366000 chr3A 100.000 2813 0 0 1 2813 615050174 615052986 0.000000e+00 5195
1 TraesCS3A01G366000 chr3A 88.669 759 68 10 2072 2813 610560523 610561280 0.000000e+00 909
2 TraesCS3A01G366000 chr3A 87.483 751 72 10 2074 2813 35094429 35095168 0.000000e+00 846
3 TraesCS3A01G366000 chr3D 92.099 1696 82 21 379 2054 472941496 472943159 0.000000e+00 2342
4 TraesCS3A01G366000 chr3D 90.327 765 58 9 2061 2813 64695861 64696621 0.000000e+00 989
5 TraesCS3A01G366000 chr3D 84.975 406 29 14 1 385 472941078 472941472 1.580000e-102 383
6 TraesCS3A01G366000 chr3B 90.616 1705 75 25 381 2025 628101176 628102855 0.000000e+00 2183
7 TraesCS3A01G366000 chr6D 88.975 771 69 10 2058 2813 381526467 381527236 0.000000e+00 939
8 TraesCS3A01G366000 chr5A 89.005 764 72 7 2061 2813 398188427 398187665 0.000000e+00 935
9 TraesCS3A01G366000 chr2D 89.005 764 70 9 2061 2813 411346098 411346858 0.000000e+00 933
10 TraesCS3A01G366000 chr2D 88.073 763 80 6 2061 2813 293069139 293069900 0.000000e+00 894
11 TraesCS3A01G366000 chr7A 89.488 742 66 8 2072 2803 605144933 605144194 0.000000e+00 928
12 TraesCS3A01G366000 chr2A 89.081 751 69 7 2072 2813 41991572 41990826 0.000000e+00 920
13 TraesCS3A01G366000 chr1D 88.166 769 70 13 2061 2813 62697923 62697160 0.000000e+00 896


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 TraesCS3A01G366000 chr3A 615050174 615052986 2812 False 5195.0 5195 100.000 1 2813 1 chr3A.!!$F3 2812
1 TraesCS3A01G366000 chr3A 610560523 610561280 757 False 909.0 909 88.669 2072 2813 1 chr3A.!!$F2 741
2 TraesCS3A01G366000 chr3A 35094429 35095168 739 False 846.0 846 87.483 2074 2813 1 chr3A.!!$F1 739
3 TraesCS3A01G366000 chr3D 472941078 472943159 2081 False 1362.5 2342 88.537 1 2054 2 chr3D.!!$F2 2053
4 TraesCS3A01G366000 chr3D 64695861 64696621 760 False 989.0 989 90.327 2061 2813 1 chr3D.!!$F1 752
5 TraesCS3A01G366000 chr3B 628101176 628102855 1679 False 2183.0 2183 90.616 381 2025 1 chr3B.!!$F1 1644
6 TraesCS3A01G366000 chr6D 381526467 381527236 769 False 939.0 939 88.975 2058 2813 1 chr6D.!!$F1 755
7 TraesCS3A01G366000 chr5A 398187665 398188427 762 True 935.0 935 89.005 2061 2813 1 chr5A.!!$R1 752
8 TraesCS3A01G366000 chr2D 411346098 411346858 760 False 933.0 933 89.005 2061 2813 1 chr2D.!!$F2 752
9 TraesCS3A01G366000 chr2D 293069139 293069900 761 False 894.0 894 88.073 2061 2813 1 chr2D.!!$F1 752
10 TraesCS3A01G366000 chr7A 605144194 605144933 739 True 928.0 928 89.488 2072 2803 1 chr7A.!!$R1 731
11 TraesCS3A01G366000 chr2A 41990826 41991572 746 True 920.0 920 89.081 2072 2813 1 chr2A.!!$R1 741
12 TraesCS3A01G366000 chr1D 62697160 62697923 763 True 896.0 896 88.166 2061 2813 1 chr1D.!!$R1 752

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
103 105 0.040067 CTTTCTTTGGGCGTGAGTGC 60.04 55.0 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
1891 2012 0.184451 ATCACAGGCAGCCATTAGGG 59.816 55.0 15.8 1.23 40.85 3.53 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
24 25 2.599082 CGTGTGTCGCTTATCTTCTTCC 59.401 50.000 0.00 0.00 0.00 3.46
38 39 1.289160 TCTTCCTAGGGCTGCATGTT 58.711 50.000 9.46 0.00 0.00 2.71
103 105 0.040067 CTTTCTTTGGGCGTGAGTGC 60.040 55.000 0.00 0.00 0.00 4.40
108 110 0.821301 TTTGGGCGTGAGTGCATTGA 60.821 50.000 0.00 0.00 36.28 2.57
110 112 1.307355 TGGGCGTGAGTGCATTGATG 61.307 55.000 0.00 0.00 36.28 3.07
131 133 1.202758 CCCCAGCCATCGTATTTGCTA 60.203 52.381 0.00 0.00 31.69 3.49
133 135 2.485426 CCCAGCCATCGTATTTGCTATG 59.515 50.000 0.00 0.00 31.69 2.23
134 136 3.402110 CCAGCCATCGTATTTGCTATGA 58.598 45.455 0.00 0.00 31.69 2.15
140 142 5.626543 GCCATCGTATTTGCTATGACATTTG 59.373 40.000 0.00 0.00 0.00 2.32
189 203 7.387643 AGTAGGGTGAAAGACTATTTTGAGAC 58.612 38.462 0.00 0.00 0.00 3.36
204 218 5.567037 TTTGAGACAATCTTCTTCCTCCA 57.433 39.130 0.00 0.00 0.00 3.86
205 219 4.815533 TGAGACAATCTTCTTCCTCCAG 57.184 45.455 0.00 0.00 0.00 3.86
206 220 4.420206 TGAGACAATCTTCTTCCTCCAGA 58.580 43.478 0.00 0.00 0.00 3.86
224 238 1.700186 AGACACCAGTTCTTTCTCCCC 59.300 52.381 0.00 0.00 0.00 4.81
295 316 1.126488 CCATCTCTCTAAGGCCTGCA 58.874 55.000 5.69 0.00 0.00 4.41
296 317 1.202627 CCATCTCTCTAAGGCCTGCAC 60.203 57.143 5.69 0.00 0.00 4.57
297 318 1.127343 ATCTCTCTAAGGCCTGCACC 58.873 55.000 5.69 0.00 0.00 5.01
298 319 0.978146 TCTCTCTAAGGCCTGCACCC 60.978 60.000 5.69 0.00 0.00 4.61
299 320 0.980231 CTCTCTAAGGCCTGCACCCT 60.980 60.000 5.69 0.00 0.00 4.34
300 321 1.222936 CTCTAAGGCCTGCACCCTG 59.777 63.158 5.69 0.00 31.73 4.45
301 322 2.439156 CTAAGGCCTGCACCCTGC 60.439 66.667 5.69 0.00 45.29 4.85
327 348 6.326583 ACCACCGGAGAAAAGATAGATAATGA 59.673 38.462 9.46 0.00 0.00 2.57
342 363 5.092968 AGATAATGAGGCTATGGCTTCTCT 58.907 41.667 14.20 5.88 43.69 3.10
344 365 1.126488 TGAGGCTATGGCTTCTCTGG 58.874 55.000 14.20 0.00 43.69 3.86
351 372 0.394080 ATGGCTTCTCTGGCAAGCTC 60.394 55.000 8.64 0.78 44.87 4.09
375 396 5.568023 CGGGGTGAACTAGAAAATGTGACTA 60.568 44.000 0.00 0.00 0.00 2.59
378 399 6.708949 GGGTGAACTAGAAAATGTGACTAACA 59.291 38.462 0.00 0.00 44.79 2.41
494 545 2.822255 GGCCGGCGATGCTAAACA 60.822 61.111 22.54 0.00 0.00 2.83
498 553 1.333791 GCCGGCGATGCTAAACAATAC 60.334 52.381 12.58 0.00 0.00 1.89
506 561 4.328983 CGATGCTAAACAATACGGACAACT 59.671 41.667 0.00 0.00 0.00 3.16
516 571 1.157870 ACGGACAACTCAACTTGCGG 61.158 55.000 0.00 0.00 0.00 5.69
520 575 1.008538 CAACTCAACTTGCGGTGGC 60.009 57.895 0.00 0.00 40.52 5.01
545 600 1.360192 GGTGCTTGCTGTTCACACC 59.640 57.895 0.00 0.00 43.57 4.16
570 625 6.414109 CGAGTCCAAACATCATTACGTACTAG 59.586 42.308 0.00 0.00 0.00 2.57
571 626 7.400599 AGTCCAAACATCATTACGTACTAGA 57.599 36.000 0.00 0.00 0.00 2.43
572 627 7.481642 AGTCCAAACATCATTACGTACTAGAG 58.518 38.462 0.00 0.00 0.00 2.43
573 628 7.122353 AGTCCAAACATCATTACGTACTAGAGT 59.878 37.037 0.00 0.00 0.00 3.24
574 629 8.400947 GTCCAAACATCATTACGTACTAGAGTA 58.599 37.037 0.00 0.00 0.00 2.59
575 630 8.400947 TCCAAACATCATTACGTACTAGAGTAC 58.599 37.037 9.40 9.40 45.47 2.73
576 631 8.404000 CCAAACATCATTACGTACTAGAGTACT 58.596 37.037 15.88 0.00 46.43 2.73
626 687 1.324736 GATCAAATCTCACGGCGTGTC 59.675 52.381 35.65 21.13 34.79 3.67
642 705 2.090041 CGTGTCCTCAACAACGATAACG 59.910 50.000 0.00 0.00 40.31 3.18
644 707 3.364023 GTGTCCTCAACAACGATAACGAG 59.636 47.826 0.00 0.00 40.31 4.18
694 763 0.684805 ACGCTCCCTTCCCACTCTAG 60.685 60.000 0.00 0.00 0.00 2.43
699 768 2.166664 CTCCCTTCCCACTCTAGTTTCG 59.833 54.545 0.00 0.00 0.00 3.46
705 774 0.460311 CCACTCTAGTTTCGGCCGAT 59.540 55.000 31.56 17.61 0.00 4.18
739 831 2.983136 CGTTGACAGCGATATCCATCTC 59.017 50.000 5.70 0.00 0.00 2.75
745 837 0.179124 GCGATATCCATCTCTCGGGC 60.179 60.000 0.00 0.00 0.00 6.13
831 923 1.093159 ACCGTACAAACCAAACGCAA 58.907 45.000 0.00 0.00 35.36 4.85
834 926 2.312348 CGTACAAACCAAACGCAATCC 58.688 47.619 0.00 0.00 0.00 3.01
839 931 2.504681 CCAAACGCAATCCGCAGC 60.505 61.111 0.00 0.00 42.60 5.25
883 996 0.611896 CCCGAGCAAACCCCAAATCT 60.612 55.000 0.00 0.00 0.00 2.40
940 1054 2.760477 CCGTTTCCATCCCACCCA 59.240 61.111 0.00 0.00 0.00 4.51
992 1106 2.604686 AGACCCAAGAGCGAGCCA 60.605 61.111 0.00 0.00 0.00 4.75
993 1107 2.125350 GACCCAAGAGCGAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
1007 1121 2.892425 CCAGCCGAAGATGTCCGC 60.892 66.667 0.00 0.00 0.00 5.54
1012 1126 1.815421 CCGAAGATGTCCGCCCAAG 60.815 63.158 0.00 0.00 0.00 3.61
1013 1127 1.218047 CGAAGATGTCCGCCCAAGA 59.782 57.895 0.00 0.00 0.00 3.02
1014 1128 0.391130 CGAAGATGTCCGCCCAAGAA 60.391 55.000 0.00 0.00 0.00 2.52
1306 1426 1.716826 GCTCTACGCGCTCCACTACT 61.717 60.000 5.73 0.00 0.00 2.57
1802 1922 2.819595 CAAGGCCGTCATCCCGTG 60.820 66.667 0.00 0.00 0.00 4.94
1833 1953 1.517242 CTCTGCAACTTCTGTCACCC 58.483 55.000 0.00 0.00 0.00 4.61
1845 1965 2.056223 GTCACCCGGGATCGAAGGA 61.056 63.158 32.02 9.57 39.00 3.36
1850 1971 1.283905 ACCCGGGATCGAAGGAAAAAT 59.716 47.619 32.02 0.00 39.00 1.82
1866 1987 1.620822 AAATTGGTGTGGCTGAGGAC 58.379 50.000 0.00 0.00 0.00 3.85
1891 2012 8.414003 ACAACTGTAATTCCTTTTCTTCCTTTC 58.586 33.333 0.00 0.00 0.00 2.62
1904 2025 0.258774 TCCTTTCCCTAATGGCTGCC 59.741 55.000 12.87 12.87 31.44 4.85
1957 2078 6.147656 CCTTTGGAAAACTGAATATGGTTTGC 59.852 38.462 0.00 0.00 36.06 3.68
1961 2082 6.095377 GGAAAACTGAATATGGTTTGCAGAG 58.905 40.000 0.00 0.00 36.06 3.35
1975 2096 6.127366 TGGTTTGCAGAGAATGAACTTTTCTT 60.127 34.615 0.00 0.00 33.65 2.52
1978 2099 9.468532 GTTTGCAGAGAATGAACTTTTCTTAAT 57.531 29.630 0.00 0.00 33.65 1.40
1997 2118 7.004086 TCTTAATCCTCAACCACATTGTTCTT 58.996 34.615 0.00 0.00 39.54 2.52
2008 2129 5.305128 ACCACATTGTTCTTTGGATCAACAT 59.695 36.000 0.00 0.00 35.03 2.71
2009 2130 5.865552 CCACATTGTTCTTTGGATCAACATC 59.134 40.000 0.00 0.00 35.03 3.06
2025 2146 2.928334 ACATCCAACCATGCTCATCTC 58.072 47.619 0.00 0.00 0.00 2.75
2026 2147 2.240414 ACATCCAACCATGCTCATCTCA 59.760 45.455 0.00 0.00 0.00 3.27
2027 2148 2.408271 TCCAACCATGCTCATCTCAC 57.592 50.000 0.00 0.00 0.00 3.51
2028 2149 1.012086 CCAACCATGCTCATCTCACG 58.988 55.000 0.00 0.00 0.00 4.35
2029 2150 1.676916 CCAACCATGCTCATCTCACGT 60.677 52.381 0.00 0.00 0.00 4.49
2030 2151 2.418609 CCAACCATGCTCATCTCACGTA 60.419 50.000 0.00 0.00 0.00 3.57
2031 2152 3.461061 CAACCATGCTCATCTCACGTAT 58.539 45.455 0.00 0.00 0.00 3.06
2034 2155 6.389906 CAACCATGCTCATCTCACGTATATA 58.610 40.000 0.00 0.00 0.00 0.86
2035 2156 6.590234 ACCATGCTCATCTCACGTATATAA 57.410 37.500 0.00 0.00 0.00 0.98
2054 2184 3.297830 AACCCGCAGACTAAAAATTGC 57.702 42.857 0.00 0.00 0.00 3.56
2055 2185 2.235016 ACCCGCAGACTAAAAATTGCA 58.765 42.857 0.00 0.00 36.37 4.08
2056 2186 2.625790 ACCCGCAGACTAAAAATTGCAA 59.374 40.909 0.00 0.00 36.37 4.08
2057 2187 3.244976 CCCGCAGACTAAAAATTGCAAG 58.755 45.455 4.94 0.00 36.37 4.01
2058 2188 3.057596 CCCGCAGACTAAAAATTGCAAGA 60.058 43.478 4.94 0.00 36.37 3.02
2059 2189 4.380867 CCCGCAGACTAAAAATTGCAAGAT 60.381 41.667 4.94 0.00 36.37 2.40
2091 2221 6.367969 ACGTATAATGTCTGAGTTGGTTGAAC 59.632 38.462 0.00 0.00 34.40 3.18
2110 2240 9.274065 GGTTGAACAGTATTCACGATTTATTTC 57.726 33.333 0.00 0.00 0.00 2.17
2125 2255 5.682943 TTTATTTCCGTCTCACCACTTTG 57.317 39.130 0.00 0.00 0.00 2.77
2170 2302 4.953781 TTTTCATTCCCTTCCTCATCCT 57.046 40.909 0.00 0.00 0.00 3.24
2175 2307 5.226803 TCATTCCCTTCCTCATCCTATCAA 58.773 41.667 0.00 0.00 0.00 2.57
2241 2374 6.644347 ACGGATCAGAACTTTTCATACTGAT 58.356 36.000 0.00 0.00 46.42 2.90
2538 2674 0.325296 TCCTGCCCTACCACTCGAAT 60.325 55.000 0.00 0.00 0.00 3.34
2580 2716 1.757340 GTAGCCTCGTGCCCTACCT 60.757 63.158 0.00 0.00 42.71 3.08
2581 2717 1.001248 TAGCCTCGTGCCCTACCTT 59.999 57.895 0.00 0.00 42.71 3.50
2596 2732 2.797285 ACCTTATCCCGGATTCCTCT 57.203 50.000 0.73 0.00 0.00 3.69
2609 2745 3.629796 GGATTCCTCTCTCTCCCTCACTT 60.630 52.174 0.00 0.00 0.00 3.16
2611 2747 3.551635 TCCTCTCTCTCCCTCACTTTT 57.448 47.619 0.00 0.00 0.00 2.27
2657 2819 3.733507 ATGGGCCGCTCCTCGTAGA 62.734 63.158 0.00 0.00 36.19 2.59
2693 2855 1.811266 GGCATCGTGTCGTCAGCAT 60.811 57.895 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.637229 CCCTAGGAAGAAGATAAGCGACA 59.363 47.826 11.48 0.00 0.00 4.35
24 25 2.475466 CGCCAACATGCAGCCCTAG 61.475 63.158 0.00 0.00 0.00 3.02
80 82 3.020984 ACTCACGCCCAAAGAAAGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
88 90 0.387622 CAATGCACTCACGCCCAAAG 60.388 55.000 0.00 0.00 0.00 2.77
103 105 4.288234 ATGGCTGGGGCATCAATG 57.712 55.556 0.70 0.00 45.69 2.82
110 112 2.032981 CAAATACGATGGCTGGGGC 58.967 57.895 0.00 0.00 37.82 5.80
113 115 3.187227 GTCATAGCAAATACGATGGCTGG 59.813 47.826 0.00 0.00 37.17 4.85
115 117 4.071961 TGTCATAGCAAATACGATGGCT 57.928 40.909 0.00 0.00 40.26 4.75
119 121 7.229306 ACATCCAAATGTCATAGCAAATACGAT 59.771 33.333 0.00 0.00 42.59 3.73
131 133 3.903090 ACCAACCAACATCCAAATGTCAT 59.097 39.130 0.00 0.00 45.48 3.06
133 135 4.335400 AACCAACCAACATCCAAATGTC 57.665 40.909 0.00 0.00 45.48 3.06
166 180 7.311092 TGTCTCAAAATAGTCTTTCACCCTA 57.689 36.000 0.00 0.00 0.00 3.53
177 191 7.826744 GGAGGAAGAAGATTGTCTCAAAATAGT 59.173 37.037 0.00 0.00 0.00 2.12
189 203 3.008375 TGGTGTCTGGAGGAAGAAGATTG 59.992 47.826 0.00 0.00 0.00 2.67
204 218 1.700186 GGGGAGAAAGAACTGGTGTCT 59.300 52.381 0.00 0.00 0.00 3.41
205 219 1.271434 GGGGGAGAAAGAACTGGTGTC 60.271 57.143 0.00 0.00 0.00 3.67
206 220 0.771755 GGGGGAGAAAGAACTGGTGT 59.228 55.000 0.00 0.00 0.00 4.16
267 288 1.361176 TAGAGAGATGGGAGGGGCGA 61.361 60.000 0.00 0.00 0.00 5.54
295 316 4.954118 TCTCCGGTGGTGCAGGGT 62.954 66.667 0.00 0.00 33.01 4.34
296 317 2.690653 TTTTCTCCGGTGGTGCAGGG 62.691 60.000 0.00 0.00 33.01 4.45
297 318 1.228124 TTTTCTCCGGTGGTGCAGG 60.228 57.895 0.00 0.00 0.00 4.85
298 319 0.250295 TCTTTTCTCCGGTGGTGCAG 60.250 55.000 0.00 0.00 0.00 4.41
299 320 0.400213 ATCTTTTCTCCGGTGGTGCA 59.600 50.000 0.00 0.00 0.00 4.57
300 321 2.093658 TCTATCTTTTCTCCGGTGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
301 322 3.887621 TCTATCTTTTCTCCGGTGGTG 57.112 47.619 0.00 0.00 0.00 4.17
327 348 0.984961 TGCCAGAGAAGCCATAGCCT 60.985 55.000 0.00 0.00 41.25 4.58
342 363 3.565214 TTCACCCCGAGCTTGCCA 61.565 61.111 0.00 0.00 0.00 4.92
344 365 0.741221 CTAGTTCACCCCGAGCTTGC 60.741 60.000 0.00 0.00 36.46 4.01
351 372 3.435671 GTCACATTTTCTAGTTCACCCCG 59.564 47.826 0.00 0.00 0.00 5.73
494 545 2.478894 CGCAAGTTGAGTTGTCCGTATT 59.521 45.455 7.16 0.00 0.00 1.89
498 553 1.157870 ACCGCAAGTTGAGTTGTCCG 61.158 55.000 7.16 0.00 0.00 4.79
516 571 0.738412 GCAAGCACCAATGATGCCAC 60.738 55.000 0.00 0.00 44.53 5.01
520 575 2.029739 TGAACAGCAAGCACCAATGATG 60.030 45.455 0.00 0.00 38.82 3.07
521 576 2.029649 GTGAACAGCAAGCACCAATGAT 60.030 45.455 0.00 0.00 0.00 2.45
522 577 1.337703 GTGAACAGCAAGCACCAATGA 59.662 47.619 0.00 0.00 0.00 2.57
545 600 5.100259 AGTACGTAATGATGTTTGGACTCG 58.900 41.667 0.00 0.00 0.00 4.18
589 644 9.028284 AGATTTGATCTTTGCTAATTGGAAGAA 57.972 29.630 0.00 0.00 35.76 2.52
626 687 5.404366 TCTTTTCTCGTTATCGTTGTTGAGG 59.596 40.000 0.00 0.00 38.33 3.86
642 705 5.467063 ACGATCCTCAAACAGTTCTTTTCTC 59.533 40.000 0.00 0.00 0.00 2.87
644 707 5.674933 ACGATCCTCAAACAGTTCTTTTC 57.325 39.130 0.00 0.00 0.00 2.29
785 877 4.286320 CGAGAGGGGAATCGGGCG 62.286 72.222 0.00 0.00 35.33 6.13
883 996 4.830600 TGATATATACTGTTCAGCGGTGGA 59.169 41.667 15.67 2.03 37.27 4.02
1509 1629 3.727258 TTGACCCGCATCCCCCAG 61.727 66.667 0.00 0.00 0.00 4.45
1791 1911 0.385751 AGTAGATGCACGGGATGACG 59.614 55.000 0.00 0.00 40.31 4.35
1802 1922 2.102252 AGTTGCAGAGGCTAGTAGATGC 59.898 50.000 0.00 5.84 41.91 3.91
1833 1953 2.752903 ACCAATTTTTCCTTCGATCCCG 59.247 45.455 0.00 0.00 37.07 5.14
1845 1965 2.365293 GTCCTCAGCCACACCAATTTTT 59.635 45.455 0.00 0.00 0.00 1.94
1850 1971 0.465460 GTTGTCCTCAGCCACACCAA 60.465 55.000 0.00 0.00 0.00 3.67
1866 1987 7.867909 GGAAAGGAAGAAAAGGAATTACAGTTG 59.132 37.037 0.00 0.00 0.00 3.16
1891 2012 0.184451 ATCACAGGCAGCCATTAGGG 59.816 55.000 15.80 1.23 40.85 3.53
1904 2025 2.995283 TCAGGCAATCCTCAATCACAG 58.005 47.619 0.00 0.00 41.93 3.66
1929 2050 7.797121 ACCATATTCAGTTTTCCAAAGGAAT 57.203 32.000 0.00 0.00 41.71 3.01
1942 2063 6.182627 TCATTCTCTGCAAACCATATTCAGT 58.817 36.000 0.00 0.00 0.00 3.41
1943 2064 6.688637 TCATTCTCTGCAAACCATATTCAG 57.311 37.500 0.00 0.00 0.00 3.02
1957 2078 9.224267 TGAGGATTAAGAAAAGTTCATTCTCTG 57.776 33.333 0.00 0.00 36.14 3.35
1961 2082 8.576442 TGGTTGAGGATTAAGAAAAGTTCATTC 58.424 33.333 0.00 0.00 0.00 2.67
1975 2096 6.015519 CCAAAGAACAATGTGGTTGAGGATTA 60.016 38.462 5.77 0.00 40.37 1.75
1978 2099 3.636300 CCAAAGAACAATGTGGTTGAGGA 59.364 43.478 5.77 0.00 40.37 3.71
2008 2129 1.405933 CGTGAGATGAGCATGGTTGGA 60.406 52.381 0.00 0.00 0.00 3.53
2009 2130 1.012086 CGTGAGATGAGCATGGTTGG 58.988 55.000 0.00 0.00 0.00 3.77
2010 2131 1.730501 ACGTGAGATGAGCATGGTTG 58.269 50.000 0.00 0.00 0.00 3.77
2025 2146 3.637998 AGTCTGCGGGTTATATACGTG 57.362 47.619 0.00 0.00 0.00 4.49
2026 2147 5.772825 TTTAGTCTGCGGGTTATATACGT 57.227 39.130 0.00 0.00 0.00 3.57
2027 2148 7.647907 ATTTTTAGTCTGCGGGTTATATACG 57.352 36.000 0.00 0.00 0.00 3.06
2028 2149 7.801783 GCAATTTTTAGTCTGCGGGTTATATAC 59.198 37.037 0.00 0.00 0.00 1.47
2029 2150 7.499563 TGCAATTTTTAGTCTGCGGGTTATATA 59.500 33.333 0.00 0.00 37.62 0.86
2030 2151 6.320164 TGCAATTTTTAGTCTGCGGGTTATAT 59.680 34.615 0.00 0.00 37.62 0.86
2031 2152 5.648526 TGCAATTTTTAGTCTGCGGGTTATA 59.351 36.000 0.00 0.00 37.62 0.98
2034 2155 2.625790 TGCAATTTTTAGTCTGCGGGTT 59.374 40.909 0.00 0.00 37.62 4.11
2035 2156 2.235016 TGCAATTTTTAGTCTGCGGGT 58.765 42.857 0.00 0.00 37.62 5.28
2059 2189 9.000486 CCAACTCAGACATTATACGTAGAGATA 58.000 37.037 10.19 0.00 0.00 1.98
2068 2198 7.387948 ACTGTTCAACCAACTCAGACATTATAC 59.612 37.037 0.00 0.00 35.79 1.47
2070 2200 6.299141 ACTGTTCAACCAACTCAGACATTAT 58.701 36.000 0.00 0.00 35.79 1.28
2091 2221 7.222031 TGAGACGGAAATAAATCGTGAATACTG 59.778 37.037 0.00 0.00 37.25 2.74
2110 2240 1.784525 GACTCAAAGTGGTGAGACGG 58.215 55.000 9.10 0.00 46.76 4.79
2125 2255 6.822073 AAAACCAGCAAAATAAAACGACTC 57.178 33.333 0.00 0.00 0.00 3.36
2156 2288 6.851836 ACTAAATTGATAGGATGAGGAAGGGA 59.148 38.462 0.00 0.00 0.00 4.20
2161 2293 6.706270 GCGAAACTAAATTGATAGGATGAGGA 59.294 38.462 0.00 0.00 0.00 3.71
2164 2296 7.714813 TGATGCGAAACTAAATTGATAGGATGA 59.285 33.333 0.00 0.00 0.00 2.92
2170 2302 6.119536 AGGGTGATGCGAAACTAAATTGATA 58.880 36.000 0.00 0.00 0.00 2.15
2175 2307 4.192317 GAGAGGGTGATGCGAAACTAAAT 58.808 43.478 0.00 0.00 0.00 1.40
2580 2716 3.500654 GGAGAGAGAGGAATCCGGGATAA 60.501 52.174 10.54 0.00 0.00 1.75
2581 2717 2.041891 GGAGAGAGAGGAATCCGGGATA 59.958 54.545 10.54 0.00 0.00 2.59
2596 2732 4.227197 AGAGACAAAAAGTGAGGGAGAGA 58.773 43.478 0.00 0.00 0.00 3.10
2609 2745 0.529773 AGCGTGCACGAGAGACAAAA 60.530 50.000 41.19 0.00 43.02 2.44
2611 2747 1.371758 GAGCGTGCACGAGAGACAA 60.372 57.895 41.19 0.00 43.02 3.18
2657 2819 1.687612 CAAGGAGGATGGTGGCAGT 59.312 57.895 0.00 0.00 0.00 4.40
2693 2855 1.142465 ACCCTCGATACCTAGCGAAGA 59.858 52.381 0.00 0.00 43.89 2.87


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

AutoCloner maintained by Alex Coulton.