Multiple sequence alignment - TraesCS4D01G343900

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 TraesCS4D01G343900 chr4D 100.000 2258 0 0 1 2258 499500586 499502843 0.000000e+00 4170
1 TraesCS4D01G343900 chr4B 86.902 2321 111 81 65 2258 642454677 642456931 0.000000e+00 2423
2 TraesCS4D01G343900 chr5A 82.292 1265 102 56 65 1268 680501254 680502457 0.000000e+00 983
3 TraesCS4D01G343900 chr5A 94.611 167 9 0 2092 2258 680502765 680502931 2.220000e-65 259


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 TraesCS4D01G343900 chr4D 499500586 499502843 2257 False 4170 4170 100.0000 1 2258 1 chr4D.!!$F1 2257
1 TraesCS4D01G343900 chr4B 642454677 642456931 2254 False 2423 2423 86.9020 65 2258 1 chr4B.!!$F1 2193
2 TraesCS4D01G343900 chr5A 680501254 680502931 1677 False 621 983 88.4515 65 2258 2 chr5A.!!$F1 2193

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
967 1069 0.162294 CAAACCCTAACGCGAACGAC 59.838 55.0 15.93 0.0 43.93 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2260 0.777631 CAATCGTTTTGCCGCTGTTG 59.222 50.0 0.0 0.0 0.0 3.33 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 7.674471 AAACTGCTTAGTTCCTCTGAATTAC 57.326 36.000 0.00 0.00 31.98 1.89
25 26 5.735766 ACTGCTTAGTTCCTCTGAATTACC 58.264 41.667 0.00 0.00 31.98 2.85
26 27 5.248477 ACTGCTTAGTTCCTCTGAATTACCA 59.752 40.000 0.00 0.00 31.98 3.25
27 28 6.069963 ACTGCTTAGTTCCTCTGAATTACCAT 60.070 38.462 0.00 0.00 31.98 3.55
28 29 7.125811 ACTGCTTAGTTCCTCTGAATTACCATA 59.874 37.037 0.00 0.00 31.98 2.74
29 30 8.034313 TGCTTAGTTCCTCTGAATTACCATAT 57.966 34.615 0.00 0.00 31.98 1.78
30 31 9.154632 TGCTTAGTTCCTCTGAATTACCATATA 57.845 33.333 0.00 0.00 31.98 0.86
31 32 9.998106 GCTTAGTTCCTCTGAATTACCATATAA 57.002 33.333 0.00 0.00 31.98 0.98
35 36 8.778059 AGTTCCTCTGAATTACCATATAAACCA 58.222 33.333 0.00 0.00 31.98 3.67
36 37 9.574516 GTTCCTCTGAATTACCATATAAACCAT 57.425 33.333 0.00 0.00 31.98 3.55
37 38 9.793259 TTCCTCTGAATTACCATATAAACCATC 57.207 33.333 0.00 0.00 0.00 3.51
38 39 8.383175 TCCTCTGAATTACCATATAAACCATCC 58.617 37.037 0.00 0.00 0.00 3.51
39 40 7.611855 CCTCTGAATTACCATATAAACCATCCC 59.388 40.741 0.00 0.00 0.00 3.85
40 41 8.287904 TCTGAATTACCATATAAACCATCCCT 57.712 34.615 0.00 0.00 0.00 4.20
41 42 9.400208 TCTGAATTACCATATAAACCATCCCTA 57.600 33.333 0.00 0.00 0.00 3.53
57 58 8.007405 ACCATCCCTAAATAAAATTGTACAGC 57.993 34.615 0.00 0.00 0.00 4.40
58 59 7.839200 ACCATCCCTAAATAAAATTGTACAGCT 59.161 33.333 0.00 0.00 0.00 4.24
59 60 8.352942 CCATCCCTAAATAAAATTGTACAGCTC 58.647 37.037 0.00 0.00 0.00 4.09
60 61 8.902806 CATCCCTAAATAAAATTGTACAGCTCA 58.097 33.333 0.00 0.00 0.00 4.26
61 62 9.646522 ATCCCTAAATAAAATTGTACAGCTCAT 57.353 29.630 0.00 0.00 0.00 2.90
82 83 3.482156 AGCTGAGAGAAAAGTCAAGCA 57.518 42.857 0.00 0.00 33.16 3.91
113 114 5.413499 TCTAACGAAATAACTTTCCTCCGG 58.587 41.667 0.00 0.00 37.99 5.14
165 166 3.782244 GAGCACGACAGGCTTGCG 61.782 66.667 0.00 10.21 45.59 4.85
166 167 4.299547 AGCACGACAGGCTTGCGA 62.300 61.111 16.78 0.00 45.59 5.10
177 178 2.359107 CTTGCGAGGAAGCTGGCA 60.359 61.111 0.00 0.00 36.32 4.92
303 304 3.471680 GCACATACCTTCCTCAATCTCC 58.528 50.000 0.00 0.00 0.00 3.71
331 338 3.503748 GTGCTGGTGCCTATGATAAATCC 59.496 47.826 0.00 0.00 38.71 3.01
456 477 1.207089 TCGTCCTCTCGAATTTGCCAT 59.793 47.619 0.00 0.00 36.89 4.40
475 508 5.300792 TGCCATATCGGATAATATCTGCGTA 59.699 40.000 4.24 1.38 36.56 4.42
510 543 1.982913 CGCGAATTAAAACCTTGCCAC 59.017 47.619 0.00 0.00 0.00 5.01
516 549 0.179051 TAAAACCTTGCCACGACCGT 60.179 50.000 0.00 0.00 0.00 4.83
632 679 9.612066 TGCATATAAAAAGGAAAATGAAATCCC 57.388 29.630 0.00 0.00 36.31 3.85
641 688 7.441903 AGGAAAATGAAATCCCTTGCATAAT 57.558 32.000 0.00 0.00 36.31 1.28
642 689 7.277396 AGGAAAATGAAATCCCTTGCATAATG 58.723 34.615 0.00 0.00 36.31 1.90
662 718 9.730420 CATAATGGTAAAAATTGTACTACCAGC 57.270 33.333 13.11 0.00 45.22 4.85
665 721 5.179742 TGGTAAAAATTGTACTACCAGCACG 59.820 40.000 5.55 0.00 39.06 5.34
672 728 4.524316 TGTACTACCAGCACGTTAATGT 57.476 40.909 0.00 0.00 0.00 2.71
717 775 4.697352 CCATTAATTTCCTAGGCGGATCTG 59.303 45.833 2.96 0.00 42.70 2.90
738 802 8.814038 ATCTGGATAATAATGGTGGAATTAGC 57.186 34.615 0.00 0.00 0.00 3.09
768 841 4.617520 ATGCCACGTGCGTCCACA 62.618 61.111 10.91 1.08 45.60 4.17
791 864 4.889856 CGTGCGATGCCGGATCCA 62.890 66.667 13.41 0.00 38.66 3.41
805 878 1.153168 ATCCAACGGCTGGGAATCG 60.153 57.895 6.02 0.00 46.44 3.34
847 929 3.953712 ATCCAAAAACATTCCCGTTCC 57.046 42.857 0.00 0.00 0.00 3.62
851 933 1.858372 AAAACATTCCCGTTCCGGCG 61.858 55.000 0.00 0.00 46.86 6.46
854 936 4.807039 ATTCCCGTTCCGGCGTCG 62.807 66.667 0.29 0.29 46.86 5.12
860 942 4.651008 GTTCCGGCGTCGTCCACA 62.651 66.667 9.28 0.00 33.95 4.17
861 943 4.651008 TTCCGGCGTCGTCCACAC 62.651 66.667 9.28 0.00 33.95 3.82
869 951 3.608662 TCGTCCACACGGGGTGTC 61.609 66.667 9.90 1.37 43.92 3.67
870 952 4.675029 CGTCCACACGGGGTGTCC 62.675 72.222 9.90 0.00 43.92 4.02
873 955 3.238497 CCACACGGGGTGTCCTGA 61.238 66.667 9.90 0.00 43.92 3.86
874 956 2.592993 CCACACGGGGTGTCCTGAT 61.593 63.158 9.90 0.00 43.92 2.90
875 957 1.079127 CACACGGGGTGTCCTGATC 60.079 63.158 1.21 0.00 43.92 2.92
877 959 3.075005 ACGGGGTGTCCTGATCCG 61.075 66.667 0.00 0.00 42.08 4.18
878 960 2.758327 CGGGGTGTCCTGATCCGA 60.758 66.667 0.00 0.00 42.94 4.55
879 961 2.134287 CGGGGTGTCCTGATCCGAT 61.134 63.158 0.00 0.00 42.94 4.18
880 962 1.749033 GGGGTGTCCTGATCCGATC 59.251 63.158 1.01 1.01 0.00 3.69
881 963 1.749033 GGGTGTCCTGATCCGATCC 59.251 63.158 5.91 0.00 0.00 3.36
882 964 1.048724 GGGTGTCCTGATCCGATCCA 61.049 60.000 5.91 0.00 0.00 3.41
900 982 6.017934 CCGATCCAAAGTGTCCTGTATAAATG 60.018 42.308 0.00 0.00 0.00 2.32
939 1031 0.373370 CTCGCTGACTCTGTCTCTCG 59.627 60.000 0.00 1.22 33.15 4.04
941 1033 1.138671 GCTGACTCTGTCTCTCGCC 59.861 63.158 0.00 0.00 33.15 5.54
942 1034 1.590610 GCTGACTCTGTCTCTCGCCA 61.591 60.000 0.00 0.00 33.15 5.69
946 1048 0.678366 ACTCTGTCTCTCGCCACGAT 60.678 55.000 0.00 0.00 34.61 3.73
967 1069 0.162294 CAAACCCTAACGCGAACGAC 59.838 55.000 15.93 0.00 43.93 4.34
1271 1381 2.123077 CTGATCCTCCGCCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
1296 1406 3.957535 GGGCGATCGCTTGGCATG 61.958 66.667 36.25 0.00 41.60 4.06
1297 1407 4.619140 GGCGATCGCTTGGCATGC 62.619 66.667 36.25 15.82 41.60 4.06
1298 1408 4.619140 GCGATCGCTTGGCATGCC 62.619 66.667 31.94 30.54 38.26 4.40
1299 1409 4.303603 CGATCGCTTGGCATGCCG 62.304 66.667 30.87 19.06 39.42 5.69
1300 1410 3.957535 GATCGCTTGGCATGCCGG 61.958 66.667 30.87 25.31 39.42 6.13
1321 1431 4.183686 GCGCATGCATCTTGCCGT 62.184 61.111 19.57 0.00 44.23 5.68
1474 1612 6.369065 AGCCGCGGATTCTAATAAGAAATAAG 59.631 38.462 33.48 0.00 44.75 1.73
1476 1614 7.095355 GCCGCGGATTCTAATAAGAAATAAGAA 60.095 37.037 33.48 0.00 44.75 2.52
1500 1673 6.506538 ACTGTAATAGGCCAGATGATTTCT 57.493 37.500 5.01 0.00 33.90 2.52
1571 1749 4.795970 AAAAGTGTGCTAACTTCGACTG 57.204 40.909 5.27 0.00 39.48 3.51
1653 1857 0.106268 TTTGCCTGAGCCCAGTTTCA 60.106 50.000 0.00 0.00 38.74 2.69
1654 1858 0.106268 TTGCCTGAGCCCAGTTTCAA 60.106 50.000 0.00 0.00 38.74 2.69
1656 1860 1.260544 GCCTGAGCCCAGTTTCAATT 58.739 50.000 0.00 0.00 38.74 2.32
1657 1861 1.620323 GCCTGAGCCCAGTTTCAATTT 59.380 47.619 0.00 0.00 38.74 1.82
1658 1862 2.037641 GCCTGAGCCCAGTTTCAATTTT 59.962 45.455 0.00 0.00 38.74 1.82
1659 1863 3.494924 GCCTGAGCCCAGTTTCAATTTTT 60.495 43.478 0.00 0.00 38.74 1.94
1710 1918 0.328258 TTCTGCCTTTGCTAGTCCCC 59.672 55.000 0.00 0.00 38.71 4.81
1721 1929 4.178956 TGCTAGTCCCCTTTTTGTCTTT 57.821 40.909 0.00 0.00 0.00 2.52
1736 1944 9.437045 CTTTTTGTCTTTGCAAATTGGATTAAC 57.563 29.630 13.23 2.47 38.05 2.01
1748 1956 8.277713 GCAAATTGGATTAACATGACATAATGC 58.722 33.333 0.00 7.36 32.42 3.56
1755 1963 8.132362 GGATTAACATGACATAATGCGGTTTAA 58.868 33.333 0.00 0.00 0.00 1.52
1978 2190 0.747283 CAGGAGAGCAAGGCACCATC 60.747 60.000 0.00 0.00 0.00 3.51
1979 2191 1.452833 GGAGAGCAAGGCACCATCC 60.453 63.158 0.00 0.00 0.00 3.51
1980 2192 1.817099 GAGAGCAAGGCACCATCCG 60.817 63.158 0.00 0.00 0.00 4.18
1981 2193 2.244117 GAGAGCAAGGCACCATCCGA 62.244 60.000 0.00 0.00 0.00 4.55
2024 2236 2.224066 ACAGACAGAACACACTGCTACC 60.224 50.000 0.00 0.00 41.06 3.18
2048 2260 1.348036 ACCAGGCACCAGAACTTACTC 59.652 52.381 0.00 0.00 0.00 2.59
2074 2286 0.040425 GGCAAAACGATTGCACGACT 60.040 50.000 24.34 0.00 46.58 4.18
2076 2288 2.230864 GCAAAACGATTGCACGACTAC 58.769 47.619 20.35 0.00 44.34 2.73
2078 2290 2.157834 AAACGATTGCACGACTACCA 57.842 45.000 3.48 0.00 37.03 3.25
2080 2292 2.157834 ACGATTGCACGACTACCAAA 57.842 45.000 3.48 0.00 37.03 3.28
2082 2294 1.393539 CGATTGCACGACTACCAAAGG 59.606 52.381 0.00 0.00 35.09 3.11
2083 2295 1.130561 GATTGCACGACTACCAAAGGC 59.869 52.381 0.00 0.00 0.00 4.35
2084 2296 0.887387 TTGCACGACTACCAAAGGCC 60.887 55.000 0.00 0.00 0.00 5.19
2085 2297 1.302192 GCACGACTACCAAAGGCCA 60.302 57.895 5.01 0.00 0.00 5.36
2086 2298 1.298859 GCACGACTACCAAAGGCCAG 61.299 60.000 5.01 0.00 0.00 4.85
2089 2301 1.549170 ACGACTACCAAAGGCCAGTAG 59.451 52.381 5.01 12.72 39.50 2.57
2090 2302 1.822990 CGACTACCAAAGGCCAGTAGA 59.177 52.381 21.90 0.00 37.50 2.59
2091 2303 2.431057 CGACTACCAAAGGCCAGTAGAT 59.569 50.000 21.90 10.92 37.50 1.98
2142 2380 7.218228 ACATTTGCTGACAAGATTGTATTCA 57.782 32.000 0.00 0.00 42.43 2.57
2234 2472 0.179100 ACCTGATCGTTGATCCTGCG 60.179 55.000 4.47 0.00 38.20 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.655425 GGTAATTCAGAGGAACTAAGCAGTTT 59.345 38.462 0.00 0.00 45.18 2.66
2 3 5.248477 TGGTAATTCAGAGGAACTAAGCAGT 59.752 40.000 0.00 0.00 41.55 4.40
3 4 5.734720 TGGTAATTCAGAGGAACTAAGCAG 58.265 41.667 0.00 0.00 41.55 4.24
4 5 5.755409 TGGTAATTCAGAGGAACTAAGCA 57.245 39.130 0.00 0.00 41.55 3.91
5 6 9.998106 TTATATGGTAATTCAGAGGAACTAAGC 57.002 33.333 0.00 0.00 41.55 3.09
10 11 8.974060 TGGTTTATATGGTAATTCAGAGGAAC 57.026 34.615 0.00 0.00 35.46 3.62
11 12 9.793259 GATGGTTTATATGGTAATTCAGAGGAA 57.207 33.333 0.00 0.00 37.45 3.36
12 13 8.383175 GGATGGTTTATATGGTAATTCAGAGGA 58.617 37.037 0.00 0.00 0.00 3.71
13 14 7.611855 GGGATGGTTTATATGGTAATTCAGAGG 59.388 40.741 0.00 0.00 0.00 3.69
14 15 8.386264 AGGGATGGTTTATATGGTAATTCAGAG 58.614 37.037 0.00 0.00 0.00 3.35
15 16 8.287904 AGGGATGGTTTATATGGTAATTCAGA 57.712 34.615 0.00 0.00 0.00 3.27
31 32 8.474831 GCTGTACAATTTTATTTAGGGATGGTT 58.525 33.333 0.00 0.00 0.00 3.67
32 33 7.839200 AGCTGTACAATTTTATTTAGGGATGGT 59.161 33.333 0.00 0.00 0.00 3.55
33 34 8.237811 AGCTGTACAATTTTATTTAGGGATGG 57.762 34.615 0.00 0.00 0.00 3.51
34 35 8.902806 TGAGCTGTACAATTTTATTTAGGGATG 58.097 33.333 0.00 0.00 0.00 3.51
35 36 9.646522 ATGAGCTGTACAATTTTATTTAGGGAT 57.353 29.630 0.00 0.00 0.00 3.85
38 39 9.884465 GCTATGAGCTGTACAATTTTATTTAGG 57.116 33.333 0.00 0.00 38.45 2.69
58 59 5.174395 GCTTGACTTTTCTCTCAGCTATGA 58.826 41.667 0.00 0.00 0.00 2.15
59 60 4.934001 TGCTTGACTTTTCTCTCAGCTATG 59.066 41.667 0.00 0.00 0.00 2.23
60 61 5.157940 TGCTTGACTTTTCTCTCAGCTAT 57.842 39.130 0.00 0.00 0.00 2.97
61 62 4.607293 TGCTTGACTTTTCTCTCAGCTA 57.393 40.909 0.00 0.00 0.00 3.32
62 63 3.482156 TGCTTGACTTTTCTCTCAGCT 57.518 42.857 0.00 0.00 0.00 4.24
63 64 4.214971 TGAATGCTTGACTTTTCTCTCAGC 59.785 41.667 0.00 0.00 0.00 4.26
82 83 8.398665 GGAAAGTTATTTCGTTAGATGCTGAAT 58.601 33.333 0.00 0.00 44.87 2.57
177 178 2.018727 CTGCTCTGCTCCTCGCTGAT 62.019 60.000 0.00 0.00 44.19 2.90
187 188 1.947597 CTCTTCGCCTCTGCTCTGCT 61.948 60.000 0.00 0.00 34.43 4.24
303 304 2.547640 ATAGGCACCAGCACCAGCAG 62.548 60.000 0.00 0.00 45.49 4.24
456 477 8.846211 TGATGAATACGCAGATATTATCCGATA 58.154 33.333 8.66 0.00 0.00 2.92
475 508 9.729023 TTTTAATTCGCGATGTAAATGATGAAT 57.271 25.926 10.88 0.00 0.00 2.57
510 543 2.758770 TTCCTCGCCAAAGACGGTCG 62.759 60.000 1.89 0.00 0.00 4.79
516 549 2.073816 GTCGAATTTCCTCGCCAAAGA 58.926 47.619 0.00 0.00 38.73 2.52
545 578 8.603304 ACTGGATTTCCTACGGCTATAATAAAT 58.397 33.333 0.00 0.00 36.82 1.40
546 579 7.970102 ACTGGATTTCCTACGGCTATAATAAA 58.030 34.615 0.00 0.00 36.82 1.40
547 580 7.549147 ACTGGATTTCCTACGGCTATAATAA 57.451 36.000 0.00 0.00 36.82 1.40
548 581 7.549147 AACTGGATTTCCTACGGCTATAATA 57.451 36.000 0.00 0.00 36.82 0.98
549 582 6.435292 AACTGGATTTCCTACGGCTATAAT 57.565 37.500 0.00 0.00 36.82 1.28
558 591 8.225777 CGTGTTAACTAAAACTGGATTTCCTAC 58.774 37.037 7.22 0.00 36.82 3.18
607 650 9.836864 AGGGATTTCATTTTCCTTTTTATATGC 57.163 29.630 0.00 0.00 32.34 3.14
624 667 7.487822 TTTTACCATTATGCAAGGGATTTCA 57.512 32.000 0.00 0.00 37.84 2.69
625 668 8.962884 ATTTTTACCATTATGCAAGGGATTTC 57.037 30.769 0.00 0.00 37.84 2.17
641 688 5.179742 CGTGCTGGTAGTACAATTTTTACCA 59.820 40.000 8.63 8.63 42.31 3.25
642 689 5.179929 ACGTGCTGGTAGTACAATTTTTACC 59.820 40.000 2.06 0.00 36.84 2.85
717 775 6.183360 GCTCGCTAATTCCACCATTATTATCC 60.183 42.308 0.00 0.00 0.00 2.59
774 847 4.889856 TGGATCCGGCATCGCACG 62.890 66.667 7.39 0.00 34.56 5.34
775 848 2.513666 TTGGATCCGGCATCGCAC 60.514 61.111 7.39 0.00 34.56 5.34
776 849 2.513666 GTTGGATCCGGCATCGCA 60.514 61.111 7.39 0.00 34.56 5.10
777 850 3.640000 CGTTGGATCCGGCATCGC 61.640 66.667 7.39 0.00 34.56 4.58
778 851 2.967076 CCGTTGGATCCGGCATCG 60.967 66.667 7.39 7.02 38.85 3.84
790 863 2.436646 AGCGATTCCCAGCCGTTG 60.437 61.111 0.00 0.00 0.00 4.10
791 864 2.125106 GAGCGATTCCCAGCCGTT 60.125 61.111 0.00 0.00 0.00 4.44
860 942 2.873557 ATCGGATCAGGACACCCCGT 62.874 60.000 0.00 0.00 40.87 5.28
861 943 2.088674 GATCGGATCAGGACACCCCG 62.089 65.000 13.02 0.00 40.87 5.73
862 944 1.749033 GATCGGATCAGGACACCCC 59.251 63.158 13.02 0.00 0.00 4.95
866 948 2.093500 CACTTTGGATCGGATCAGGACA 60.093 50.000 18.99 5.56 0.00 4.02
868 950 2.168521 GACACTTTGGATCGGATCAGGA 59.831 50.000 18.99 2.18 0.00 3.86
869 951 2.555199 GACACTTTGGATCGGATCAGG 58.445 52.381 18.99 8.32 0.00 3.86
870 952 2.169352 AGGACACTTTGGATCGGATCAG 59.831 50.000 18.99 10.61 0.00 2.90
873 955 1.909302 ACAGGACACTTTGGATCGGAT 59.091 47.619 0.00 0.00 0.00 4.18
874 956 1.348064 ACAGGACACTTTGGATCGGA 58.652 50.000 0.00 0.00 0.00 4.55
875 957 3.543680 ATACAGGACACTTTGGATCGG 57.456 47.619 0.00 0.00 0.00 4.18
877 959 8.506168 TTCATTTATACAGGACACTTTGGATC 57.494 34.615 0.00 0.00 0.00 3.36
878 960 8.739972 GTTTCATTTATACAGGACACTTTGGAT 58.260 33.333 0.00 0.00 0.00 3.41
879 961 7.094975 CGTTTCATTTATACAGGACACTTTGGA 60.095 37.037 0.00 0.00 0.00 3.53
880 962 7.021196 CGTTTCATTTATACAGGACACTTTGG 58.979 38.462 0.00 0.00 0.00 3.28
881 963 7.021196 CCGTTTCATTTATACAGGACACTTTG 58.979 38.462 0.00 0.00 0.00 2.77
882 964 6.349033 GCCGTTTCATTTATACAGGACACTTT 60.349 38.462 0.00 0.00 0.00 2.66
923 1005 1.138671 GGCGAGAGACAGAGTCAGC 59.861 63.158 0.00 0.21 40.66 4.26
939 1031 1.092348 GTTAGGGTTTGGATCGTGGC 58.908 55.000 0.00 0.00 0.00 5.01
941 1033 0.725117 GCGTTAGGGTTTGGATCGTG 59.275 55.000 0.00 0.00 0.00 4.35
942 1034 0.738412 CGCGTTAGGGTTTGGATCGT 60.738 55.000 0.00 0.00 0.00 3.73
946 1048 0.945265 CGTTCGCGTTAGGGTTTGGA 60.945 55.000 5.77 0.00 35.57 3.53
977 1079 3.222855 CCCTGCCTCGCTCGATCT 61.223 66.667 0.00 0.00 0.00 2.75
1152 1262 2.868566 TTGGCCAGGAACCCCCAT 60.869 61.111 5.11 0.00 37.41 4.00
1280 1390 4.619140 GCATGCCAAGCGATCGCC 62.619 66.667 34.89 20.58 43.17 5.54
1281 1391 4.619140 GGCATGCCAAGCGATCGC 62.619 66.667 32.15 32.15 37.45 4.58
1282 1392 4.303603 CGGCATGCCAAGCGATCG 62.304 66.667 34.93 15.41 35.37 3.69
1283 1393 3.957535 CCGGCATGCCAAGCGATC 61.958 66.667 34.93 6.89 35.37 3.69
1389 1499 4.490319 GCACGTCATTAATCACACACTACG 60.490 45.833 0.00 0.00 0.00 3.51
1474 1612 7.500559 AGAAATCATCTGGCCTATTACAGTTTC 59.499 37.037 3.32 5.72 36.88 2.78
1476 1614 6.904626 AGAAATCATCTGGCCTATTACAGTT 58.095 36.000 3.32 0.00 36.88 3.16
1565 1743 1.028130 CAGCATAGAGAGCCAGTCGA 58.972 55.000 0.00 0.00 0.00 4.20
1566 1744 0.031857 CCAGCATAGAGAGCCAGTCG 59.968 60.000 0.00 0.00 0.00 4.18
1567 1745 0.392336 CCCAGCATAGAGAGCCAGTC 59.608 60.000 0.00 0.00 0.00 3.51
1568 1746 0.031716 TCCCAGCATAGAGAGCCAGT 60.032 55.000 0.00 0.00 0.00 4.00
1569 1747 1.126488 TTCCCAGCATAGAGAGCCAG 58.874 55.000 0.00 0.00 0.00 4.85
1570 1748 1.487976 CTTTCCCAGCATAGAGAGCCA 59.512 52.381 0.00 0.00 0.00 4.75
1571 1749 1.202746 CCTTTCCCAGCATAGAGAGCC 60.203 57.143 0.00 0.00 0.00 4.70
1710 1918 9.437045 GTTAATCCAATTTGCAAAGACAAAAAG 57.563 29.630 18.19 0.87 42.45 2.27
1721 1929 9.315525 CATTATGTCATGTTAATCCAATTTGCA 57.684 29.630 0.00 0.00 0.00 4.08
1736 1944 8.655092 ACAAAAATTAAACCGCATTATGTCATG 58.345 29.630 0.00 0.00 0.00 3.07
1855 2065 1.814169 GGATGGAAGACGGAACCGC 60.814 63.158 13.32 6.39 44.19 5.68
1921 2133 6.017109 TGTCCAGTCTGCTTGAAAAACTTATC 60.017 38.462 0.00 0.00 0.00 1.75
1923 2135 5.189928 TGTCCAGTCTGCTTGAAAAACTTA 58.810 37.500 0.00 0.00 0.00 2.24
1978 2190 1.604604 AATTTGACAGTGGTGGTCGG 58.395 50.000 0.00 0.00 38.10 4.79
1979 2191 3.135225 TGTAATTTGACAGTGGTGGTCG 58.865 45.455 0.00 0.00 38.10 4.79
1980 2192 3.502211 CCTGTAATTTGACAGTGGTGGTC 59.498 47.826 7.43 0.00 44.54 4.02
1981 2193 3.137544 TCCTGTAATTTGACAGTGGTGGT 59.862 43.478 7.43 0.00 44.54 4.16
2024 2236 1.898574 GTTCTGGTGCCTGGTGGTG 60.899 63.158 0.00 0.00 35.27 4.17
2048 2260 0.777631 CAATCGTTTTGCCGCTGTTG 59.222 50.000 0.00 0.00 0.00 3.33
2074 2286 6.354130 GTCAATTATCTACTGGCCTTTGGTA 58.646 40.000 3.32 1.38 0.00 3.25
2076 2288 4.273480 CGTCAATTATCTACTGGCCTTTGG 59.727 45.833 3.32 0.00 0.00 3.28
2078 2290 5.353394 TCGTCAATTATCTACTGGCCTTT 57.647 39.130 3.32 0.00 0.00 3.11
2080 2292 5.353394 TTTCGTCAATTATCTACTGGCCT 57.647 39.130 3.32 0.00 0.00 5.19
2082 2294 6.200286 TCGAATTTCGTCAATTATCTACTGGC 59.800 38.462 17.61 0.00 41.35 4.85
2083 2295 7.096023 CCTCGAATTTCGTCAATTATCTACTGG 60.096 40.741 17.61 0.00 41.35 4.00
2084 2296 7.096023 CCCTCGAATTTCGTCAATTATCTACTG 60.096 40.741 17.61 0.00 41.35 2.74
2085 2297 6.924060 CCCTCGAATTTCGTCAATTATCTACT 59.076 38.462 17.61 0.00 41.35 2.57
2086 2298 6.700520 ACCCTCGAATTTCGTCAATTATCTAC 59.299 38.462 17.61 0.00 41.35 2.59
2089 2301 5.522460 TCACCCTCGAATTTCGTCAATTATC 59.478 40.000 17.61 0.00 41.35 1.75
2090 2302 5.424757 TCACCCTCGAATTTCGTCAATTAT 58.575 37.500 17.61 0.00 41.35 1.28
2091 2303 4.823157 TCACCCTCGAATTTCGTCAATTA 58.177 39.130 17.61 0.00 41.35 1.40
2142 2380 3.121030 GATTCGTGCACCGCTGCT 61.121 61.111 12.15 0.00 44.57 4.24
2223 2461 1.421485 CGTCAAGCGCAGGATCAAC 59.579 57.895 11.47 0.00 0.00 3.18
2234 2472 2.268076 ACCATTGCCACCGTCAAGC 61.268 57.895 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.