Multiple sequence alignment - TraesCS4A01G136100

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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 TraesCS4A01G136100 chr4A 100.000 2837 0 0 1 2837 189671796 189668960 0.000000e+00 5240.0
1 TraesCS4A01G136100 chr4D 93.076 1531 45 16 328 1805 297832304 297833826 0.000000e+00 2183.0
2 TraesCS4A01G136100 chr4D 92.683 492 21 6 1968 2452 297834003 297834486 0.000000e+00 695.0
3 TraesCS4A01G136100 chr4D 90.938 320 21 5 14 332 297831155 297831467 9.400000e-115 424.0
4 TraesCS4A01G136100 chr4D 83.333 228 29 6 2476 2701 297840498 297840718 4.790000e-48 202.0
5 TraesCS4A01G136100 chr4D 95.000 100 5 0 1847 1946 297833916 297834015 1.050000e-34 158.0
6 TraesCS4A01G136100 chr4D 82.803 157 16 6 2689 2836 297840859 297841013 2.290000e-26 130.0
7 TraesCS4A01G136100 chr4B 92.906 1015 42 13 826 1834 369147777 369148767 0.000000e+00 1448.0
8 TraesCS4A01G136100 chr4B 86.169 911 71 22 1970 2837 369148905 369149803 0.000000e+00 933.0
9 TraesCS4A01G136100 chr4B 89.245 437 20 14 372 791 369147355 369147781 3.240000e-144 521.0
10 TraesCS4A01G136100 chr4B 92.163 319 20 2 14 332 369146401 369146714 2.010000e-121 446.0
11 TraesCS4A01G136100 chr4B 87.755 98 5 4 1847 1944 369148823 369148913 1.070000e-19 108.0
12 TraesCS4A01G136100 chr1A 100.000 34 0 0 2151 2184 376473278 376473311 2.360000e-06 63.9


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 TraesCS4A01G136100 chr4A 189668960 189671796 2836 True 5240.0 5240 100.00000 1 2837 1 chr4A.!!$R1 2836
1 TraesCS4A01G136100 chr4D 297831155 297834486 3331 False 865.0 2183 92.92425 14 2452 4 chr4D.!!$F1 2438
2 TraesCS4A01G136100 chr4B 369146401 369149803 3402 False 691.2 1448 89.64760 14 2837 5 chr4B.!!$F1 2823

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
692 1620 0.89553 CACGGACAGGACACCAGTAT 59.104 55.0 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2950 0.179227 CACACACACACACACACACG 60.179 55.0 0.0 0.0 0.0 4.49 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
63 64 4.338879 ACATTGAGTCTTGGGGAGAAATG 58.661 43.478 0.00 0.00 36.69 2.32
67 68 1.428912 AGTCTTGGGGAGAAATGCCAA 59.571 47.619 0.00 0.00 35.79 4.52
142 143 5.043737 TGTAGAGGTTTGGCTGTAAACTT 57.956 39.130 10.13 4.62 39.78 2.66
171 172 1.993370 GATCAACTCTTTGGTCGGTCG 59.007 52.381 0.00 0.00 33.14 4.79
230 231 7.869429 AGTTTTTCTTCTCTTTTATGTGCCATG 59.131 33.333 0.00 0.00 0.00 3.66
259 260 4.767409 GGAATACCTTGCCTTTTCTTCACT 59.233 41.667 0.00 0.00 0.00 3.41
260 261 5.243954 GGAATACCTTGCCTTTTCTTCACTT 59.756 40.000 0.00 0.00 0.00 3.16
261 262 6.433093 GGAATACCTTGCCTTTTCTTCACTTA 59.567 38.462 0.00 0.00 0.00 2.24
265 266 9.700831 ATACCTTGCCTTTTCTTCACTTATTAT 57.299 29.630 0.00 0.00 0.00 1.28
272 273 7.910683 GCCTTTTCTTCACTTATTATGTGCTAC 59.089 37.037 5.13 0.00 35.58 3.58
277 278 7.489160 TCTTCACTTATTATGTGCTACATCGT 58.511 34.615 5.25 0.36 39.88 3.73
299 300 3.262151 TCATATCCAACCAACGAGGAACA 59.738 43.478 5.70 0.00 41.22 3.18
300 301 2.879103 ATCCAACCAACGAGGAACAT 57.121 45.000 5.70 0.00 41.22 2.71
474 1373 2.037649 CACTCGATCGACTGTTATCGC 58.962 52.381 15.15 0.00 43.57 4.58
521 1420 1.081648 ACCCACCTACACCTACCCC 59.918 63.158 0.00 0.00 0.00 4.95
555 1454 2.151202 GGTGCTGGAGTTCAATTTCGA 58.849 47.619 0.00 0.00 0.00 3.71
692 1620 0.895530 CACGGACAGGACACCAGTAT 59.104 55.000 0.00 0.00 0.00 2.12
693 1621 1.135083 CACGGACAGGACACCAGTATC 60.135 57.143 0.00 0.00 0.00 2.24
694 1622 1.272536 ACGGACAGGACACCAGTATCT 60.273 52.381 0.00 0.00 0.00 1.98
695 1623 1.405821 CGGACAGGACACCAGTATCTC 59.594 57.143 0.00 0.00 0.00 2.75
719 1647 3.309388 TCTATCTCGCGTACGTACTACC 58.691 50.000 22.55 10.30 41.18 3.18
722 1650 1.002366 CTCGCGTACGTACTACCAGT 58.998 55.000 22.55 0.00 41.18 4.00
724 1652 2.193447 TCGCGTACGTACTACCAGTAG 58.807 52.381 22.55 6.40 41.18 2.57
747 1682 2.017049 AGATGAATGTAAAGTGCGCCC 58.983 47.619 4.18 0.00 0.00 6.13
871 1806 4.516092 GCCACATTCGCGATATATAACC 57.484 45.455 10.88 0.00 0.00 2.85
1055 2002 1.676967 GGAGCACAAGGAAGGGCAG 60.677 63.158 0.00 0.00 0.00 4.85
1063 2010 4.918201 GGAAGGGCAGGCGATCGG 62.918 72.222 18.30 0.83 0.00 4.18
1401 2363 3.554692 CTTCGGCGCATCGTCACC 61.555 66.667 10.83 0.00 0.00 4.02
1453 2415 4.371590 TCGCCGTTAGCAGCAGCA 62.372 61.111 3.17 0.00 45.49 4.41
1641 2606 1.301716 CCTGGTGGTGGTGAAGACG 60.302 63.158 0.00 0.00 0.00 4.18
1687 2652 1.744639 GAGAGCATGGCGGAGATGA 59.255 57.895 0.00 0.00 0.00 2.92
1827 2800 0.107410 ACATCGCCGGCCAAAGAATA 60.107 50.000 23.46 0.00 0.00 1.75
1834 2807 1.024579 CGGCCAAAGAATACGCCACT 61.025 55.000 2.24 0.00 41.71 4.00
1835 2808 1.741055 CGGCCAAAGAATACGCCACTA 60.741 52.381 2.24 0.00 41.71 2.74
1837 2810 2.629051 GCCAAAGAATACGCCACTAGT 58.371 47.619 0.00 0.00 0.00 2.57
1838 2811 3.431207 GGCCAAAGAATACGCCACTAGTA 60.431 47.826 0.00 0.00 41.25 1.82
1840 2813 3.795101 CCAAAGAATACGCCACTAGTACG 59.205 47.826 14.12 14.12 0.00 3.67
1842 2815 4.548991 AAGAATACGCCACTAGTACGAG 57.451 45.455 20.63 0.91 0.00 4.18
1843 2816 2.877168 AGAATACGCCACTAGTACGAGG 59.123 50.000 20.63 8.33 0.00 4.63
1844 2817 0.950116 ATACGCCACTAGTACGAGGC 59.050 55.000 20.63 16.07 43.61 4.70
1845 2818 1.097547 TACGCCACTAGTACGAGGCC 61.098 60.000 20.63 0.00 44.18 5.19
1893 2909 6.392354 AGGAATTACATCACAATGCACTTTG 58.608 36.000 0.00 0.00 36.26 2.77
1899 2915 1.333308 TCACAATGCACTTTGGTGTCG 59.667 47.619 5.11 0.00 44.65 4.35
1942 2958 0.954938 TGCATGCATAGCGTGTGTGT 60.955 50.000 18.46 0.00 46.10 3.72
1943 2959 0.521867 GCATGCATAGCGTGTGTGTG 60.522 55.000 14.21 0.00 46.10 3.82
1944 2960 0.798159 CATGCATAGCGTGTGTGTGT 59.202 50.000 0.00 0.00 40.30 3.72
1945 2961 0.798159 ATGCATAGCGTGTGTGTGTG 59.202 50.000 0.00 0.00 0.00 3.82
1946 2962 0.531753 TGCATAGCGTGTGTGTGTGT 60.532 50.000 0.00 0.00 0.00 3.72
1947 2963 0.110688 GCATAGCGTGTGTGTGTGTG 60.111 55.000 0.00 0.00 0.00 3.82
1948 2964 1.217001 CATAGCGTGTGTGTGTGTGT 58.783 50.000 0.00 0.00 0.00 3.72
1949 2965 1.070643 CATAGCGTGTGTGTGTGTGTG 60.071 52.381 0.00 0.00 0.00 3.82
1950 2966 0.108567 TAGCGTGTGTGTGTGTGTGT 60.109 50.000 0.00 0.00 0.00 3.72
1951 2967 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
1952 2968 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
1953 2969 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
1954 2970 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1955 2971 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1956 2972 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1957 2973 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1958 2974 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1959 2975 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1960 2976 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1961 2977 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1962 2978 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1963 2979 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1964 2980 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1965 2981 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1966 2982 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1992 3008 7.278424 TGTGTGTGTGTGTGATCATAATCATAG 59.722 37.037 0.00 0.00 43.62 2.23
2001 3017 7.173735 GTGTGATCATAATCATAGCATTGACCA 59.826 37.037 0.00 0.00 43.62 4.02
2031 3053 2.617308 GCTCATGGTCATGATCCAAGTG 59.383 50.000 17.35 14.88 45.74 3.16
2119 3153 5.347635 ACAAGTTTCTTTCTTTTGCGTTTCC 59.652 36.000 0.00 0.00 0.00 3.13
2141 3175 4.061570 CGAACTTTCATCGGTTGGTAAC 57.938 45.455 0.00 0.00 36.68 2.50
2158 3195 4.463879 CCGCTCTGGTCCTGGCAG 62.464 72.222 7.75 7.75 0.00 4.85
2345 3386 7.777440 TGTGATTACCCAATAATGATAGTTGCA 59.223 33.333 0.00 0.00 33.37 4.08
2388 3429 2.574195 ATCAGCACCCTCCATCCCCT 62.574 60.000 0.00 0.00 0.00 4.79
2395 3436 2.907042 CACCCTCCATCCCCTATTAGTC 59.093 54.545 0.00 0.00 0.00 2.59
2402 3443 5.708544 TCCATCCCCTATTAGTCGACTTAA 58.291 41.667 25.44 15.53 0.00 1.85
2407 3448 8.774586 CATCCCCTATTAGTCGACTTAAATTTG 58.225 37.037 25.44 13.32 0.00 2.32
2457 3498 9.527566 CAAAAATAAAATGTCATTTTACAGCGG 57.472 29.630 25.81 15.28 44.66 5.52
2458 3499 7.826260 AAATAAAATGTCATTTTACAGCGGG 57.174 32.000 25.81 0.00 44.66 6.13
2459 3500 4.864704 AAAATGTCATTTTACAGCGGGT 57.135 36.364 19.69 0.00 40.44 5.28
2460 3501 4.434713 AAATGTCATTTTACAGCGGGTC 57.565 40.909 4.91 0.00 31.70 4.46
2461 3502 1.816074 TGTCATTTTACAGCGGGTCC 58.184 50.000 0.00 0.00 0.00 4.46
2475 3527 1.202463 CGGGTCCTATGCTTCACTCAG 60.202 57.143 0.00 0.00 0.00 3.35
2504 3556 8.192774 AGATACTATTCGAAAATTACACCGTCA 58.807 33.333 0.00 0.00 0.00 4.35
2505 3557 8.706492 ATACTATTCGAAAATTACACCGTCAA 57.294 30.769 0.00 0.00 0.00 3.18
2506 3558 7.605410 ACTATTCGAAAATTACACCGTCAAT 57.395 32.000 0.00 0.00 0.00 2.57
2532 3584 3.053831 TGGGAGAAAACCTTTCTAGCG 57.946 47.619 1.73 0.00 0.00 4.26
2571 3623 1.561542 GTCATGTCCTCCAACCTCCAT 59.438 52.381 0.00 0.00 0.00 3.41
2573 3625 1.842562 CATGTCCTCCAACCTCCATCT 59.157 52.381 0.00 0.00 0.00 2.90
2595 3647 5.290493 TGGTACAGGATAGGCAAAGTATG 57.710 43.478 0.00 0.00 0.00 2.39
2597 3649 5.427157 TGGTACAGGATAGGCAAAGTATGAA 59.573 40.000 0.00 0.00 0.00 2.57
2616 3668 8.996271 AGTATGAAGTCATTGTATACATGCATG 58.004 33.333 25.09 25.09 37.76 4.06
2630 3682 4.380531 ACATGCATGAATAACCTACCGAG 58.619 43.478 32.75 0.59 0.00 4.63
2643 3695 3.868757 CTACCGAGGAGATGAAACACA 57.131 47.619 0.00 0.00 0.00 3.72
2681 3733 3.355378 TGCAACATAACTGGCAAGCTAT 58.645 40.909 0.00 0.00 32.54 2.97
2761 3819 4.974591 GGCAATCAATAGCCGAATGTATC 58.025 43.478 0.00 0.00 41.70 2.24
2764 3822 5.611919 CAATCAATAGCCGAATGTATCACG 58.388 41.667 0.00 0.00 0.00 4.35
2773 3831 2.190161 GAATGTATCACGCGCACTACA 58.810 47.619 5.73 11.84 0.00 2.74
2775 3833 0.806241 TGTATCACGCGCACTACAGA 59.194 50.000 5.73 0.00 0.00 3.41
2779 3837 2.088763 CACGCGCACTACAGACCTG 61.089 63.158 5.73 0.00 0.00 4.00
2789 3847 5.544650 GCACTACAGACCTGTAAAGGTTTA 58.455 41.667 5.92 0.00 44.47 2.01
2792 3850 7.012610 GCACTACAGACCTGTAAAGGTTTAAAA 59.987 37.037 5.92 0.00 44.47 1.52
2812 3870 6.663944 AAAACTACTTGAACTATGATCGGC 57.336 37.500 0.00 0.00 0.00 5.54
2819 3877 2.135139 GAACTATGATCGGCATCGCAA 58.865 47.619 0.00 0.00 38.44 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.894784 TCTCTTCGCCAAAATTAGTGACT 58.105 39.130 0.00 0.00 0.00 3.41
1 2 5.803020 ATCTCTTCGCCAAAATTAGTGAC 57.197 39.130 0.00 0.00 0.00 3.67
2 3 6.876789 TGTTATCTCTTCGCCAAAATTAGTGA 59.123 34.615 0.00 0.00 0.00 3.41
3 4 6.961554 GTGTTATCTCTTCGCCAAAATTAGTG 59.038 38.462 0.00 0.00 0.00 2.74
4 5 6.653320 TGTGTTATCTCTTCGCCAAAATTAGT 59.347 34.615 0.00 0.00 0.00 2.24
5 6 6.961554 GTGTGTTATCTCTTCGCCAAAATTAG 59.038 38.462 0.00 0.00 0.00 1.73
6 7 6.128117 GGTGTGTTATCTCTTCGCCAAAATTA 60.128 38.462 0.00 0.00 0.00 1.40
7 8 5.335661 GGTGTGTTATCTCTTCGCCAAAATT 60.336 40.000 0.00 0.00 0.00 1.82
8 9 4.156008 GGTGTGTTATCTCTTCGCCAAAAT 59.844 41.667 0.00 0.00 0.00 1.82
9 10 3.500680 GGTGTGTTATCTCTTCGCCAAAA 59.499 43.478 0.00 0.00 0.00 2.44
10 11 3.071479 GGTGTGTTATCTCTTCGCCAAA 58.929 45.455 0.00 0.00 0.00 3.28
11 12 2.301870 AGGTGTGTTATCTCTTCGCCAA 59.698 45.455 0.00 0.00 0.00 4.52
12 13 1.899814 AGGTGTGTTATCTCTTCGCCA 59.100 47.619 0.00 0.00 0.00 5.69
142 143 5.200483 ACCAAAGAGTTGATCAAAGAACCA 58.800 37.500 10.35 0.00 36.83 3.67
171 172 8.437360 TCAGTACCATATGTTCACATTGAATC 57.563 34.615 1.24 0.00 38.79 2.52
230 231 5.595952 AGAAAAGGCAAGGTATTCCATGATC 59.404 40.000 0.00 0.00 34.72 2.92
246 247 6.856895 AGCACATAATAAGTGAAGAAAAGGC 58.143 36.000 0.00 0.00 39.30 4.35
259 260 8.527810 TGGATATGACGATGTAGCACATAATAA 58.472 33.333 0.00 0.00 39.27 1.40
260 261 8.062065 TGGATATGACGATGTAGCACATAATA 57.938 34.615 0.00 1.26 39.27 0.98
261 262 6.935167 TGGATATGACGATGTAGCACATAAT 58.065 36.000 0.00 0.00 39.27 1.28
265 266 4.368315 GTTGGATATGACGATGTAGCACA 58.632 43.478 0.00 0.00 0.00 4.57
272 273 3.453424 TCGTTGGTTGGATATGACGATG 58.547 45.455 0.00 0.00 34.98 3.84
275 276 2.159156 TCCTCGTTGGTTGGATATGACG 60.159 50.000 0.00 0.00 37.07 4.35
277 278 3.262151 TGTTCCTCGTTGGTTGGATATGA 59.738 43.478 0.00 0.00 37.07 2.15
299 300 7.234166 GTGGTATTGGTGTAGGTGGTACTATAT 59.766 40.741 0.00 0.00 32.19 0.86
300 301 6.550854 GTGGTATTGGTGTAGGTGGTACTATA 59.449 42.308 0.00 0.00 32.19 1.31
414 1310 1.412606 GAGCGTGCGTTTCTTCTCG 59.587 57.895 0.00 0.00 0.00 4.04
692 1620 2.034432 ACGTACGCGAGATAGAGAGAGA 59.966 50.000 15.93 0.00 42.00 3.10
693 1621 2.396601 ACGTACGCGAGATAGAGAGAG 58.603 52.381 15.93 0.00 42.00 3.20
694 1622 2.505628 ACGTACGCGAGATAGAGAGA 57.494 50.000 15.93 0.00 42.00 3.10
695 1623 3.307674 AGTACGTACGCGAGATAGAGAG 58.692 50.000 15.93 0.00 42.00 3.20
719 1647 7.358765 GCGCACTTTACATTCATCTATCTACTG 60.359 40.741 0.30 0.00 0.00 2.74
722 1650 5.926542 GGCGCACTTTACATTCATCTATCTA 59.073 40.000 10.83 0.00 0.00 1.98
724 1652 4.083802 GGGCGCACTTTACATTCATCTATC 60.084 45.833 10.83 0.00 0.00 2.08
747 1682 3.081804 GTGAACTGGTCCTGGTATTTGG 58.918 50.000 0.33 0.00 0.00 3.28
871 1806 2.185350 CCCAGCTAGCTCACGGTG 59.815 66.667 16.15 3.01 0.00 4.94
937 1883 2.959357 GCCAAGACAGAGCGTGTGC 61.959 63.158 0.00 0.00 40.56 4.57
1341 2303 3.593794 GCGTCTATCCCGCCGAGT 61.594 66.667 0.00 0.00 45.20 4.18
1641 2606 3.507009 CTCTCCGGGTCCGACGAC 61.507 72.222 11.39 0.00 42.83 4.34
1662 2627 2.976903 GCCATGCTCTCCGCCATC 60.977 66.667 0.00 0.00 38.05 3.51
1827 2800 3.194719 GCCTCGTACTAGTGGCGT 58.805 61.111 17.18 0.00 40.34 5.68
1834 2807 3.019564 GTGTTTAGGAGGCCTCGTACTA 58.980 50.000 30.13 20.84 34.61 1.82
1835 2808 1.823610 GTGTTTAGGAGGCCTCGTACT 59.176 52.381 30.13 21.82 34.61 2.73
1837 2810 1.188863 GGTGTTTAGGAGGCCTCGTA 58.811 55.000 27.37 27.37 34.61 3.43
1838 2811 0.544595 AGGTGTTTAGGAGGCCTCGT 60.545 55.000 29.49 29.49 34.61 4.18
1840 2813 1.208293 CAGAGGTGTTTAGGAGGCCTC 59.792 57.143 25.59 25.59 44.37 4.70
1842 2815 1.276622 TCAGAGGTGTTTAGGAGGCC 58.723 55.000 0.00 0.00 0.00 5.19
1843 2816 3.636153 ATTCAGAGGTGTTTAGGAGGC 57.364 47.619 0.00 0.00 0.00 4.70
1844 2817 5.188751 AGAGAATTCAGAGGTGTTTAGGAGG 59.811 44.000 8.44 0.00 0.00 4.30
1845 2818 6.293004 AGAGAATTCAGAGGTGTTTAGGAG 57.707 41.667 8.44 0.00 0.00 3.69
1875 2891 4.502171 CACCAAAGTGCATTGTGATGTA 57.498 40.909 0.00 0.00 37.14 2.29
1893 2909 1.096967 TCATCCATGCATGCGACACC 61.097 55.000 21.69 0.00 0.00 4.16
1899 2915 0.243907 GCATCCTCATCCATGCATGC 59.756 55.000 21.69 11.82 44.18 4.06
1934 2950 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1942 2958 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1943 2959 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1944 2960 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1945 2961 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1946 2962 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1947 2963 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1948 2964 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1949 2965 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1950 2966 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1951 2967 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1952 2968 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1953 2969 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1954 2970 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1955 2971 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1956 2972 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1957 2973 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1958 2974 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1959 2975 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1960 2976 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1961 2977 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
1962 2978 2.006169 GATCACACACACACACACACA 58.994 47.619 0.00 0.00 0.00 3.72
1963 2979 2.006169 TGATCACACACACACACACAC 58.994 47.619 0.00 0.00 0.00 3.82
1964 2980 2.393271 TGATCACACACACACACACA 57.607 45.000 0.00 0.00 0.00 3.72
1965 2981 5.179182 TGATTATGATCACACACACACACAC 59.821 40.000 0.00 0.00 37.37 3.82
1966 2982 5.303971 TGATTATGATCACACACACACACA 58.696 37.500 0.00 0.00 37.37 3.72
1992 3008 1.406539 AGCCGATCAATTGGTCAATGC 59.593 47.619 18.55 16.00 33.62 3.56
2001 3017 2.715749 TGACCATGAGCCGATCAATT 57.284 45.000 0.00 0.00 42.53 2.32
2031 3053 7.349711 TCAAGACTAAAACGCAACAAGAATAC 58.650 34.615 0.00 0.00 0.00 1.89
2141 3175 4.463879 CTGCCAGGACCAGAGCGG 62.464 72.222 0.00 0.00 42.50 5.52
2142 3176 4.463879 CCTGCCAGGACCAGAGCG 62.464 72.222 4.15 0.00 37.67 5.03
2143 3177 4.106925 CCCTGCCAGGACCAGAGC 62.107 72.222 13.74 0.00 37.67 4.09
2158 3195 2.281484 TTCAGCCTCACAACGCCC 60.281 61.111 0.00 0.00 0.00 6.13
2407 3448 8.932945 TGTTTGTGATGAATCTGTATCTAGAC 57.067 34.615 0.00 0.00 0.00 2.59
2444 3485 3.804036 CATAGGACCCGCTGTAAAATGA 58.196 45.455 0.00 0.00 0.00 2.57
2456 3497 1.139853 CCTGAGTGAAGCATAGGACCC 59.860 57.143 0.00 0.00 0.00 4.46
2457 3498 1.834263 ACCTGAGTGAAGCATAGGACC 59.166 52.381 0.00 0.00 32.86 4.46
2458 3499 3.954904 TCTACCTGAGTGAAGCATAGGAC 59.045 47.826 0.00 0.00 32.86 3.85
2459 3500 4.251103 TCTACCTGAGTGAAGCATAGGA 57.749 45.455 0.00 0.00 32.86 2.94
2460 3501 5.772672 AGTATCTACCTGAGTGAAGCATAGG 59.227 44.000 0.00 0.00 34.70 2.57
2461 3502 6.892658 AGTATCTACCTGAGTGAAGCATAG 57.107 41.667 0.00 0.00 0.00 2.23
2475 3527 8.909671 CGGTGTAATTTTCGAATAGTATCTACC 58.090 37.037 0.00 7.63 0.00 3.18
2504 3556 9.413734 CTAGAAAGGTTTTCTCCCATCATAATT 57.586 33.333 7.29 0.00 0.00 1.40
2505 3557 7.503902 GCTAGAAAGGTTTTCTCCCATCATAAT 59.496 37.037 7.29 0.00 0.00 1.28
2506 3558 6.828785 GCTAGAAAGGTTTTCTCCCATCATAA 59.171 38.462 7.29 0.00 0.00 1.90
2514 3566 3.055209 ACCGCTAGAAAGGTTTTCTCC 57.945 47.619 7.29 1.05 37.49 3.71
2550 3602 1.280457 GGAGGTTGGAGGACATGACT 58.720 55.000 0.00 0.00 0.00 3.41
2563 3615 2.642171 TCCTGTACCAGATGGAGGTT 57.358 50.000 5.72 0.00 40.54 3.50
2571 3623 3.450904 ACTTTGCCTATCCTGTACCAGA 58.549 45.455 0.00 0.00 32.44 3.86
2573 3625 4.966168 TCATACTTTGCCTATCCTGTACCA 59.034 41.667 0.00 0.00 0.00 3.25
2586 3638 9.655769 CATGTATACAATGACTTCATACTTTGC 57.344 33.333 10.14 0.00 35.10 3.68
2588 3640 9.394767 TGCATGTATACAATGACTTCATACTTT 57.605 29.630 10.14 0.00 35.10 2.66
2594 3646 7.862512 TTCATGCATGTATACAATGACTTCA 57.137 32.000 25.43 0.00 0.00 3.02
2597 3649 8.786898 GGTTATTCATGCATGTATACAATGACT 58.213 33.333 25.43 13.20 0.00 3.41
2616 3668 5.786264 TTCATCTCCTCGGTAGGTTATTC 57.214 43.478 0.00 0.00 44.09 1.75
2660 3712 1.619654 AGCTTGCCAGTTATGTTGCA 58.380 45.000 0.00 0.00 0.00 4.08
2668 3720 4.301072 TTGGTTCTATAGCTTGCCAGTT 57.699 40.909 0.00 0.00 0.00 3.16
2672 3724 6.238759 CCTTATGTTTGGTTCTATAGCTTGCC 60.239 42.308 0.00 0.00 0.00 4.52
2681 3733 5.941647 GCCTGTAACCTTATGTTTGGTTCTA 59.058 40.000 0.34 0.00 44.47 2.10
2737 3789 2.620115 ACATTCGGCTATTGATTGCCTG 59.380 45.455 13.19 8.22 44.78 4.85
2739 3791 4.455533 TGATACATTCGGCTATTGATTGCC 59.544 41.667 6.40 6.40 43.76 4.52
2752 3810 1.187271 GTAGTGCGCGTGATACATTCG 59.813 52.381 8.43 0.00 0.00 3.34
2754 3812 2.159296 TCTGTAGTGCGCGTGATACATT 60.159 45.455 8.43 0.00 0.00 2.71
2757 3815 1.189403 GTCTGTAGTGCGCGTGATAC 58.811 55.000 8.43 8.80 0.00 2.24
2761 3819 2.088763 CAGGTCTGTAGTGCGCGTG 61.089 63.158 8.43 0.00 0.00 5.34
2764 3822 1.993370 CTTTACAGGTCTGTAGTGCGC 59.007 52.381 0.00 0.00 45.57 6.09
2789 3847 6.170506 TGCCGATCATAGTTCAAGTAGTTTT 58.829 36.000 0.00 0.00 0.00 2.43
2792 3850 5.533482 GATGCCGATCATAGTTCAAGTAGT 58.467 41.667 0.00 0.00 35.05 2.73


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

AutoCloner maintained by Alex Coulton.