Multiple sequence alignment - TraesCS4D01G120500

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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 TraesCS4D01G120500 chr4D 100.000 4319 0 0 1 4319 101507705 101503387 0.000000e+00 7976.0
1 TraesCS4D01G120500 chr4D 82.386 176 26 5 8 180 55274287 55274114 9.680000e-32 148.0
2 TraesCS4D01G120500 chr4B 95.351 4173 142 26 170 4319 145532915 145528772 0.000000e+00 6584.0
3 TraesCS4D01G120500 chr4A 95.427 3914 124 26 437 4319 473764546 473768435 0.000000e+00 6185.0
4 TraesCS4D01G120500 chr5D 82.555 963 153 10 1559 2509 232849555 232848596 0.000000e+00 833.0
5 TraesCS4D01G120500 chr5A 82.227 979 153 16 1544 2504 322478806 322479781 0.000000e+00 824.0
6 TraesCS4D01G120500 chr5A 86.667 90 12 0 38 127 537958509 537958420 2.750000e-17 100.0
7 TraesCS4D01G120500 chr5B 81.231 991 173 11 1529 2509 272166987 272167974 0.000000e+00 787.0
8 TraesCS4D01G120500 chr2A 80.645 124 21 3 1 124 62376866 62376746 4.600000e-15 93.5
9 TraesCS4D01G120500 chr7A 100.000 28 0 0 8 35 39777569 39777596 8.000000e-03 52.8
10 TraesCS4D01G120500 chr7A 100.000 28 0 0 8 35 39793843 39793870 8.000000e-03 52.8
11 TraesCS4D01G120500 chr7A 100.000 28 0 0 8 35 39809431 39809458 8.000000e-03 52.8


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 TraesCS4D01G120500 chr4D 101503387 101507705 4318 True 7976 7976 100.000 1 4319 1 chr4D.!!$R2 4318
1 TraesCS4D01G120500 chr4B 145528772 145532915 4143 True 6584 6584 95.351 170 4319 1 chr4B.!!$R1 4149
2 TraesCS4D01G120500 chr4A 473764546 473768435 3889 False 6185 6185 95.427 437 4319 1 chr4A.!!$F1 3882
3 TraesCS4D01G120500 chr5D 232848596 232849555 959 True 833 833 82.555 1559 2509 1 chr5D.!!$R1 950
4 TraesCS4D01G120500 chr5A 322478806 322479781 975 False 824 824 82.227 1544 2504 1 chr5A.!!$F1 960
5 TraesCS4D01G120500 chr5B 272166987 272167974 987 False 787 787 81.231 1529 2509 1 chr5B.!!$F1 980

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
794 812 0.038709 GCAGCACCGCCATTTTACAA 60.039 50.0 0.0 0.0 0.0 2.41 F
964 984 0.178947 ATTGCGGGAAAAACCAGGGA 60.179 50.0 0.0 0.0 41.2 4.20 F
967 987 0.538746 GCGGGAAAAACCAGGGAGAA 60.539 55.0 0.0 0.0 41.2 2.87 F
1968 2010 0.817634 CCAACTTGTCAGCAACGGGA 60.818 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2010 0.529337 CGATGCTCAGCTCGGACAAT 60.529 55.000 9.8 0.0 0.00 2.71 R
2472 2520 3.980775 CACCAAAAATCAACTAGGCAACG 59.019 43.478 0.0 0.0 46.39 4.10 R
2478 2526 5.830912 TGCAGAACACCAAAAATCAACTAG 58.169 37.500 0.0 0.0 0.00 2.57 R
3643 3706 0.107703 GTCCATCGTCCAATGCCTCA 60.108 55.000 0.0 0.0 0.00 3.86 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
25 26 8.375608 CATCTCTATGTGCTTTAAGTATTGCT 57.624 34.615 0.00 0.00 0.00 3.91
26 27 8.494347 CATCTCTATGTGCTTTAAGTATTGCTC 58.506 37.037 0.00 0.00 0.00 4.26
27 28 7.555965 TCTCTATGTGCTTTAAGTATTGCTCA 58.444 34.615 0.00 0.00 34.29 4.26
28 29 8.206867 TCTCTATGTGCTTTAAGTATTGCTCAT 58.793 33.333 0.00 0.00 40.87 2.90
29 30 8.370493 TCTATGTGCTTTAAGTATTGCTCATC 57.630 34.615 0.00 0.00 39.37 2.92
30 31 8.206867 TCTATGTGCTTTAAGTATTGCTCATCT 58.793 33.333 0.00 0.00 39.37 2.90
31 32 9.481340 CTATGTGCTTTAAGTATTGCTCATCTA 57.519 33.333 0.00 0.00 39.37 1.98
32 33 8.737168 ATGTGCTTTAAGTATTGCTCATCTAA 57.263 30.769 0.00 0.00 35.60 2.10
33 34 8.201554 TGTGCTTTAAGTATTGCTCATCTAAG 57.798 34.615 0.00 0.00 0.00 2.18
34 35 7.824289 TGTGCTTTAAGTATTGCTCATCTAAGT 59.176 33.333 0.00 0.00 0.00 2.24
35 36 8.331742 GTGCTTTAAGTATTGCTCATCTAAGTC 58.668 37.037 0.00 0.00 0.00 3.01
36 37 8.260818 TGCTTTAAGTATTGCTCATCTAAGTCT 58.739 33.333 0.00 0.00 0.00 3.24
37 38 9.103861 GCTTTAAGTATTGCTCATCTAAGTCTT 57.896 33.333 0.00 0.00 0.00 3.01
42 43 9.757227 AAGTATTGCTCATCTAAGTCTTATGTC 57.243 33.333 0.00 0.00 0.00 3.06
43 44 8.918116 AGTATTGCTCATCTAAGTCTTATGTCA 58.082 33.333 0.00 0.00 0.00 3.58
44 45 9.703892 GTATTGCTCATCTAAGTCTTATGTCAT 57.296 33.333 0.00 0.00 0.00 3.06
67 68 9.663904 TCATTAATTTTACGCTAAGATTCATGC 57.336 29.630 0.00 0.00 30.29 4.06
68 69 9.449550 CATTAATTTTACGCTAAGATTCATGCA 57.550 29.630 0.00 0.00 0.00 3.96
70 71 9.847706 TTAATTTTACGCTAAGATTCATGCAAA 57.152 25.926 0.00 0.00 0.00 3.68
71 72 7.740519 ATTTTACGCTAAGATTCATGCAAAC 57.259 32.000 0.00 0.00 0.00 2.93
72 73 5.871465 TTACGCTAAGATTCATGCAAACA 57.129 34.783 0.00 0.00 0.00 2.83
73 74 4.970662 ACGCTAAGATTCATGCAAACAT 57.029 36.364 0.00 0.00 36.79 2.71
74 75 5.314923 ACGCTAAGATTCATGCAAACATT 57.685 34.783 0.00 0.00 32.87 2.71
75 76 5.713025 ACGCTAAGATTCATGCAAACATTT 58.287 33.333 0.00 0.00 32.87 2.32
76 77 6.158598 ACGCTAAGATTCATGCAAACATTTT 58.841 32.000 0.00 0.00 32.87 1.82
77 78 6.308766 ACGCTAAGATTCATGCAAACATTTTC 59.691 34.615 0.00 0.00 32.87 2.29
78 79 6.529125 CGCTAAGATTCATGCAAACATTTTCT 59.471 34.615 0.00 0.00 32.87 2.52
79 80 7.062605 CGCTAAGATTCATGCAAACATTTTCTT 59.937 33.333 0.00 0.00 32.87 2.52
80 81 8.715088 GCTAAGATTCATGCAAACATTTTCTTT 58.285 29.630 0.00 0.00 32.87 2.52
83 84 8.441312 AGATTCATGCAAACATTTTCTTTTGT 57.559 26.923 0.00 0.00 35.51 2.83
84 85 8.553696 AGATTCATGCAAACATTTTCTTTTGTC 58.446 29.630 0.00 0.00 35.51 3.18
85 86 7.846644 TTCATGCAAACATTTTCTTTTGTCT 57.153 28.000 0.00 0.00 35.51 3.41
86 87 7.846644 TCATGCAAACATTTTCTTTTGTCTT 57.153 28.000 0.00 0.00 35.51 3.01
87 88 8.266392 TCATGCAAACATTTTCTTTTGTCTTT 57.734 26.923 0.00 0.00 35.51 2.52
88 89 8.728833 TCATGCAAACATTTTCTTTTGTCTTTT 58.271 25.926 0.00 0.00 35.51 2.27
89 90 9.002080 CATGCAAACATTTTCTTTTGTCTTTTC 57.998 29.630 0.00 0.00 35.51 2.29
90 91 8.321650 TGCAAACATTTTCTTTTGTCTTTTCT 57.678 26.923 0.00 0.00 35.51 2.52
91 92 8.442384 TGCAAACATTTTCTTTTGTCTTTTCTC 58.558 29.630 0.00 0.00 35.51 2.87
92 93 7.904977 GCAAACATTTTCTTTTGTCTTTTCTCC 59.095 33.333 0.00 0.00 35.51 3.71
93 94 9.154847 CAAACATTTTCTTTTGTCTTTTCTCCT 57.845 29.630 0.00 0.00 0.00 3.69
94 95 9.725019 AAACATTTTCTTTTGTCTTTTCTCCTT 57.275 25.926 0.00 0.00 0.00 3.36
95 96 8.932945 ACATTTTCTTTTGTCTTTTCTCCTTC 57.067 30.769 0.00 0.00 0.00 3.46
96 97 8.753133 ACATTTTCTTTTGTCTTTTCTCCTTCT 58.247 29.630 0.00 0.00 0.00 2.85
102 103 9.853177 TCTTTTGTCTTTTCTCCTTCTATTTCT 57.147 29.630 0.00 0.00 0.00 2.52
140 141 9.360093 GTGACATAGATGTATAATAACCAGAGC 57.640 37.037 0.00 0.00 41.95 4.09
141 142 9.088987 TGACATAGATGTATAATAACCAGAGCA 57.911 33.333 0.00 0.00 41.95 4.26
162 163 4.627467 GCATATCTAGATGTGCCCTAAACG 59.373 45.833 32.93 7.93 46.14 3.60
163 164 5.566826 GCATATCTAGATGTGCCCTAAACGA 60.567 44.000 32.93 4.56 46.14 3.85
164 165 6.455647 CATATCTAGATGTGCCCTAAACGAA 58.544 40.000 15.51 0.00 0.00 3.85
165 166 4.119442 TCTAGATGTGCCCTAAACGAAC 57.881 45.455 0.00 0.00 0.00 3.95
166 167 2.109425 AGATGTGCCCTAAACGAACC 57.891 50.000 0.00 0.00 0.00 3.62
167 168 1.628846 AGATGTGCCCTAAACGAACCT 59.371 47.619 0.00 0.00 0.00 3.50
168 169 1.737793 GATGTGCCCTAAACGAACCTG 59.262 52.381 0.00 0.00 0.00 4.00
172 173 1.418637 TGCCCTAAACGAACCTGAGTT 59.581 47.619 0.00 0.00 39.54 3.01
204 205 5.922739 AAAGAATTTGTCCAAAAATCCGC 57.077 34.783 0.00 0.00 36.60 5.54
232 233 1.004440 GAGAACGCTTGTCCTGCCT 60.004 57.895 0.00 0.00 0.00 4.75
237 238 0.385390 ACGCTTGTCCTGCCTTTTTG 59.615 50.000 0.00 0.00 0.00 2.44
240 250 2.669391 CGCTTGTCCTGCCTTTTTGATC 60.669 50.000 0.00 0.00 0.00 2.92
252 262 7.148407 CCTGCCTTTTTGATCGATATGGTATAC 60.148 40.741 0.00 0.00 0.00 1.47
271 281 9.379770 TGGTATACAATTAGATTCCATCTCTCA 57.620 33.333 5.01 0.00 40.76 3.27
275 285 7.295322 ACAATTAGATTCCATCTCTCATCGA 57.705 36.000 0.00 0.00 40.76 3.59
276 286 7.730084 ACAATTAGATTCCATCTCTCATCGAA 58.270 34.615 0.00 0.00 40.76 3.71
277 287 7.871973 ACAATTAGATTCCATCTCTCATCGAAG 59.128 37.037 0.00 0.00 40.76 3.79
278 288 7.773489 ATTAGATTCCATCTCTCATCGAAGA 57.227 36.000 0.00 0.00 40.76 2.87
282 292 5.667539 TTCCATCTCTCATCGAAGAACTT 57.332 39.130 0.00 0.00 43.58 2.66
290 300 8.657074 TCTCTCATCGAAGAACTTTACAAAAA 57.343 30.769 0.00 0.00 43.58 1.94
339 351 3.554692 CGCCACGACGATGAAGCC 61.555 66.667 0.00 0.00 34.06 4.35
374 386 2.105477 CACCCCATCCATCTTCTTCGAT 59.895 50.000 0.00 0.00 0.00 3.59
378 390 1.797046 CATCCATCTTCTTCGATGCCG 59.203 52.381 0.00 0.00 39.51 5.69
648 662 1.270147 ACCTCAGCGACCTACAAACAC 60.270 52.381 0.00 0.00 0.00 3.32
650 664 1.792949 CTCAGCGACCTACAAACACAC 59.207 52.381 0.00 0.00 0.00 3.82
689 706 2.208431 CACCTCGCAAATCATCTCTCC 58.792 52.381 0.00 0.00 0.00 3.71
794 812 0.038709 GCAGCACCGCCATTTTACAA 60.039 50.000 0.00 0.00 0.00 2.41
795 813 1.404047 GCAGCACCGCCATTTTACAAT 60.404 47.619 0.00 0.00 0.00 2.71
804 823 3.132111 CGCCATTTTACAATAAAGCCCCT 59.868 43.478 0.00 0.00 0.00 4.79
818 837 2.034048 GCCCCTTCTGATCTCCCGTC 62.034 65.000 0.00 0.00 0.00 4.79
838 857 0.661020 CACAAACGAACCCCTCACAC 59.339 55.000 0.00 0.00 0.00 3.82
876 895 1.795507 GAGCAGAAGCAGCAGAAGC 59.204 57.895 0.00 0.00 45.49 3.86
964 984 0.178947 ATTGCGGGAAAAACCAGGGA 60.179 50.000 0.00 0.00 41.20 4.20
966 986 1.074248 GCGGGAAAAACCAGGGAGA 59.926 57.895 0.00 0.00 41.20 3.71
967 987 0.538746 GCGGGAAAAACCAGGGAGAA 60.539 55.000 0.00 0.00 41.20 2.87
1968 2010 0.817634 CCAACTTGTCAGCAACGGGA 60.818 55.000 0.00 0.00 0.00 5.14
2085 2133 2.632028 TGTGTGGTTTGATTTGGATGGG 59.368 45.455 0.00 0.00 0.00 4.00
2130 2178 0.988439 CAAACAACGTGTGTGCAACC 59.012 50.000 0.00 0.00 40.60 3.77
2472 2520 4.792521 ACCTGTGATTGAGAGTGAGTAC 57.207 45.455 0.00 0.00 0.00 2.73
2478 2526 2.433868 TTGAGAGTGAGTACGTTGCC 57.566 50.000 0.00 0.00 0.00 4.52
2898 2946 5.711506 TGTGCTGTTCCAGTGAAATTCATAT 59.288 36.000 0.00 0.00 33.43 1.78
3072 3121 3.631250 TGCAGTGAGAACCTTCCTTTTT 58.369 40.909 0.00 0.00 0.00 1.94
3276 3337 7.641020 GTGCAATGAAAATTTTCCTTTGTCTTG 59.359 33.333 27.25 19.32 36.36 3.02
3288 3349 9.793259 TTTTCCTTTGTCTTGTTAGAGATGTAT 57.207 29.630 0.00 0.00 0.00 2.29
3323 3384 4.862574 TGTACTTTCTTGATGATCGAACCG 59.137 41.667 0.00 0.00 0.00 4.44
3390 3452 6.478512 AGGGTGTCATTGTTATTGTTTGTT 57.521 33.333 0.00 0.00 0.00 2.83
3488 3550 8.506168 AGAATGTATAATTGGTGTAAGTGTGG 57.494 34.615 0.00 0.00 0.00 4.17
3492 3554 6.876789 TGTATAATTGGTGTAAGTGTGGTCAG 59.123 38.462 0.00 0.00 0.00 3.51
3643 3706 2.831685 TCCAGCATAGTGTTGTTCGT 57.168 45.000 0.00 0.00 0.00 3.85
3764 3827 1.907255 ACCTTTACCTAGGCTGGTCAC 59.093 52.381 9.30 0.00 41.22 3.67
3776 3839 0.393077 CTGGTCACGGAACTGTCCTT 59.607 55.000 0.00 0.00 42.44 3.36
3870 3934 5.222027 TGGAGATACTTGTCACAAAATCCCA 60.222 40.000 13.35 13.35 0.00 4.37
3993 4057 1.167851 CATGGGTGCACGTTCATCTT 58.832 50.000 11.45 0.00 0.00 2.40
4097 4162 5.283294 TGTCACTTTGCTGATCATGTTTTG 58.717 37.500 0.00 0.00 0.00 2.44
4192 4264 5.003804 AGAATACGGTGCTGAAGTTGAAAT 58.996 37.500 0.00 0.00 0.00 2.17
4251 4323 1.331756 GTGAGTGGTGCTGAAGTGTTG 59.668 52.381 0.00 0.00 0.00 3.33
4271 4343 2.251600 GCAGAAGCAACCCTGAGTG 58.748 57.895 0.00 0.00 41.58 3.51
4282 4354 5.606749 AGCAACCCTGAGTGGTATAATGATA 59.393 40.000 0.00 0.00 37.76 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.375608 AGCAATACTTAAAGCACATAGAGATG 57.624 34.615 0.00 0.00 39.16 2.90
1 2 8.206867 TGAGCAATACTTAAAGCACATAGAGAT 58.793 33.333 0.00 0.00 0.00 2.75
2 3 7.555965 TGAGCAATACTTAAAGCACATAGAGA 58.444 34.615 0.00 0.00 0.00 3.10
3 4 7.776933 TGAGCAATACTTAAAGCACATAGAG 57.223 36.000 0.00 0.00 0.00 2.43
4 5 8.206867 AGATGAGCAATACTTAAAGCACATAGA 58.793 33.333 0.00 0.00 38.17 1.98
5 6 8.375608 AGATGAGCAATACTTAAAGCACATAG 57.624 34.615 0.00 0.00 38.17 2.23
6 7 9.830975 TTAGATGAGCAATACTTAAAGCACATA 57.169 29.630 0.00 0.00 38.17 2.29
7 8 8.737168 TTAGATGAGCAATACTTAAAGCACAT 57.263 30.769 0.00 0.00 40.17 3.21
8 9 7.824289 ACTTAGATGAGCAATACTTAAAGCACA 59.176 33.333 0.00 0.00 32.51 4.57
9 10 8.202745 ACTTAGATGAGCAATACTTAAAGCAC 57.797 34.615 0.00 0.00 0.00 4.40
10 11 8.260818 AGACTTAGATGAGCAATACTTAAAGCA 58.739 33.333 0.00 0.00 0.00 3.91
11 12 8.655651 AGACTTAGATGAGCAATACTTAAAGC 57.344 34.615 0.00 0.00 0.00 3.51
16 17 9.757227 GACATAAGACTTAGATGAGCAATACTT 57.243 33.333 5.19 0.00 0.00 2.24
17 18 8.918116 TGACATAAGACTTAGATGAGCAATACT 58.082 33.333 5.19 0.00 0.00 2.12
18 19 9.703892 ATGACATAAGACTTAGATGAGCAATAC 57.296 33.333 5.19 0.00 0.00 1.89
41 42 9.663904 GCATGAATCTTAGCGTAAAATTAATGA 57.336 29.630 0.00 0.00 0.00 2.57
42 43 9.449550 TGCATGAATCTTAGCGTAAAATTAATG 57.550 29.630 0.00 0.00 0.00 1.90
44 45 9.847706 TTTGCATGAATCTTAGCGTAAAATTAA 57.152 25.926 0.00 0.00 0.00 1.40
45 46 9.284594 GTTTGCATGAATCTTAGCGTAAAATTA 57.715 29.630 0.00 0.00 0.00 1.40
46 47 7.812191 TGTTTGCATGAATCTTAGCGTAAAATT 59.188 29.630 0.00 0.00 0.00 1.82
47 48 7.312154 TGTTTGCATGAATCTTAGCGTAAAAT 58.688 30.769 0.00 0.00 0.00 1.82
48 49 6.673106 TGTTTGCATGAATCTTAGCGTAAAA 58.327 32.000 0.00 0.00 0.00 1.52
49 50 6.247727 TGTTTGCATGAATCTTAGCGTAAA 57.752 33.333 0.00 0.00 0.00 2.01
50 51 5.871465 TGTTTGCATGAATCTTAGCGTAA 57.129 34.783 0.00 0.00 0.00 3.18
51 52 6.435430 AATGTTTGCATGAATCTTAGCGTA 57.565 33.333 0.00 0.00 35.15 4.42
52 53 4.970662 ATGTTTGCATGAATCTTAGCGT 57.029 36.364 0.00 0.00 33.37 5.07
53 54 6.529125 AGAAAATGTTTGCATGAATCTTAGCG 59.471 34.615 0.00 0.00 35.15 4.26
54 55 7.823149 AGAAAATGTTTGCATGAATCTTAGC 57.177 32.000 0.00 0.00 35.15 3.09
57 58 8.895737 ACAAAAGAAAATGTTTGCATGAATCTT 58.104 25.926 0.00 0.00 38.10 2.40
58 59 8.441312 ACAAAAGAAAATGTTTGCATGAATCT 57.559 26.923 0.00 0.00 38.10 2.40
59 60 8.553696 AGACAAAAGAAAATGTTTGCATGAATC 58.446 29.630 0.00 0.00 38.10 2.52
60 61 8.441312 AGACAAAAGAAAATGTTTGCATGAAT 57.559 26.923 0.00 0.00 38.10 2.57
61 62 7.846644 AGACAAAAGAAAATGTTTGCATGAA 57.153 28.000 0.00 0.00 38.10 2.57
62 63 7.846644 AAGACAAAAGAAAATGTTTGCATGA 57.153 28.000 0.00 0.00 38.10 3.07
63 64 8.898983 AAAAGACAAAAGAAAATGTTTGCATG 57.101 26.923 0.00 0.00 38.10 4.06
64 65 8.949177 AGAAAAGACAAAAGAAAATGTTTGCAT 58.051 25.926 0.00 0.00 38.10 3.96
65 66 8.321650 AGAAAAGACAAAAGAAAATGTTTGCA 57.678 26.923 0.00 0.00 38.10 4.08
66 67 7.904977 GGAGAAAAGACAAAAGAAAATGTTTGC 59.095 33.333 0.00 0.00 38.10 3.68
67 68 9.154847 AGGAGAAAAGACAAAAGAAAATGTTTG 57.845 29.630 0.00 0.00 39.98 2.93
68 69 9.725019 AAGGAGAAAAGACAAAAGAAAATGTTT 57.275 25.926 0.00 0.00 0.00 2.83
69 70 9.371136 GAAGGAGAAAAGACAAAAGAAAATGTT 57.629 29.630 0.00 0.00 0.00 2.71
70 71 8.753133 AGAAGGAGAAAAGACAAAAGAAAATGT 58.247 29.630 0.00 0.00 0.00 2.71
76 77 9.853177 AGAAATAGAAGGAGAAAAGACAAAAGA 57.147 29.630 0.00 0.00 0.00 2.52
114 115 9.360093 GCTCTGGTTATTATACATCTATGTCAC 57.640 37.037 0.00 0.00 41.97 3.67
115 116 9.088987 TGCTCTGGTTATTATACATCTATGTCA 57.911 33.333 0.00 0.00 41.97 3.58
128 129 8.253810 GCACATCTAGATATGCTCTGGTTATTA 58.746 37.037 25.39 0.00 38.16 0.98
129 130 7.102346 GCACATCTAGATATGCTCTGGTTATT 58.898 38.462 25.39 0.00 38.16 1.40
130 131 6.351711 GGCACATCTAGATATGCTCTGGTTAT 60.352 42.308 29.70 0.00 40.81 1.89
131 132 5.047021 GGCACATCTAGATATGCTCTGGTTA 60.047 44.000 29.70 0.00 40.81 2.85
132 133 4.262808 GGCACATCTAGATATGCTCTGGTT 60.263 45.833 29.70 0.00 40.81 3.67
133 134 3.260380 GGCACATCTAGATATGCTCTGGT 59.740 47.826 29.70 8.79 40.81 4.00
134 135 3.369261 GGGCACATCTAGATATGCTCTGG 60.369 52.174 29.70 8.18 38.61 3.86
135 136 3.859443 GGGCACATCTAGATATGCTCTG 58.141 50.000 29.70 10.35 38.61 3.35
136 137 3.788933 AGGGCACATCTAGATATGCTCT 58.211 45.455 28.95 28.95 46.41 4.09
137 138 5.667539 TTAGGGCACATCTAGATATGCTC 57.332 43.478 29.70 27.72 41.84 4.26
138 139 5.567623 CGTTTAGGGCACATCTAGATATGCT 60.568 44.000 29.70 17.06 40.81 3.79
139 140 4.627467 CGTTTAGGGCACATCTAGATATGC 59.373 45.833 24.83 24.83 40.32 3.14
140 141 6.025749 TCGTTTAGGGCACATCTAGATATG 57.974 41.667 6.64 6.64 0.00 1.78
141 142 6.456501 GTTCGTTTAGGGCACATCTAGATAT 58.543 40.000 4.54 0.00 0.00 1.63
142 143 5.221382 GGTTCGTTTAGGGCACATCTAGATA 60.221 44.000 4.54 0.00 0.00 1.98
143 144 4.443034 GGTTCGTTTAGGGCACATCTAGAT 60.443 45.833 0.00 0.00 0.00 1.98
144 145 3.118884 GGTTCGTTTAGGGCACATCTAGA 60.119 47.826 0.00 0.00 0.00 2.43
145 146 3.118738 AGGTTCGTTTAGGGCACATCTAG 60.119 47.826 0.00 0.00 0.00 2.43
146 147 2.835764 AGGTTCGTTTAGGGCACATCTA 59.164 45.455 0.00 0.00 0.00 1.98
147 148 1.628846 AGGTTCGTTTAGGGCACATCT 59.371 47.619 0.00 0.00 0.00 2.90
148 149 1.737793 CAGGTTCGTTTAGGGCACATC 59.262 52.381 0.00 0.00 0.00 3.06
149 150 1.349688 TCAGGTTCGTTTAGGGCACAT 59.650 47.619 0.00 0.00 0.00 3.21
150 151 0.759959 TCAGGTTCGTTTAGGGCACA 59.240 50.000 0.00 0.00 0.00 4.57
151 152 1.270678 ACTCAGGTTCGTTTAGGGCAC 60.271 52.381 0.00 0.00 0.00 5.01
152 153 1.053424 ACTCAGGTTCGTTTAGGGCA 58.947 50.000 0.00 0.00 0.00 5.36
153 154 2.180432 AACTCAGGTTCGTTTAGGGC 57.820 50.000 0.00 0.00 0.00 5.19
199 200 2.859165 TTCTCTTTGAACTGGCGGAT 57.141 45.000 0.00 0.00 0.00 4.18
219 220 0.667993 TCAAAAAGGCAGGACAAGCG 59.332 50.000 0.00 0.00 0.00 4.68
258 268 5.841810 AGTTCTTCGATGAGAGATGGAATC 58.158 41.667 0.94 0.00 46.04 2.52
260 270 5.667539 AAGTTCTTCGATGAGAGATGGAA 57.332 39.130 0.94 0.00 0.00 3.53
262 272 6.333416 TGTAAAGTTCTTCGATGAGAGATGG 58.667 40.000 0.94 0.00 0.00 3.51
263 273 7.818493 TTGTAAAGTTCTTCGATGAGAGATG 57.182 36.000 0.94 0.00 0.00 2.90
264 274 8.833231 TTTTGTAAAGTTCTTCGATGAGAGAT 57.167 30.769 0.94 0.00 0.00 2.75
265 275 8.657074 TTTTTGTAAAGTTCTTCGATGAGAGA 57.343 30.769 0.94 0.00 0.00 3.10
290 300 7.011295 CGCCCATGCTATAATTGTTCAATTTTT 59.989 33.333 14.54 7.17 34.43 1.94
293 303 5.301551 TCGCCCATGCTATAATTGTTCAATT 59.698 36.000 13.93 13.93 34.43 2.32
294 304 4.826733 TCGCCCATGCTATAATTGTTCAAT 59.173 37.500 0.00 0.00 34.43 2.57
322 334 3.554692 GGCTTCATCGTCGTGGCG 61.555 66.667 0.00 0.00 0.00 5.69
374 386 4.776322 CAGGGATGGTTCGCGGCA 62.776 66.667 6.13 0.00 39.67 5.69
378 390 3.499737 CGTGCAGGGATGGTTCGC 61.500 66.667 0.00 0.00 35.12 4.70
648 662 2.287970 GGGGTCTTTTTGTAAAGCCGTG 60.288 50.000 0.00 0.00 40.47 4.94
650 664 1.957877 TGGGGTCTTTTTGTAAAGCCG 59.042 47.619 0.00 0.00 40.47 5.52
689 706 0.329261 TTTGGATGCTCCTGTCCTGG 59.671 55.000 4.21 0.00 37.46 4.45
794 812 2.713708 GGGAGATCAGAAGGGGCTTTAT 59.286 50.000 0.00 0.00 0.00 1.40
795 813 2.127708 GGGAGATCAGAAGGGGCTTTA 58.872 52.381 0.00 0.00 0.00 1.85
804 823 1.639722 TTGTGGACGGGAGATCAGAA 58.360 50.000 0.00 0.00 0.00 3.02
818 837 0.464735 TGTGAGGGGTTCGTTTGTGG 60.465 55.000 0.00 0.00 0.00 4.17
838 857 2.122729 TGGAGAGTGGGGTCCAGG 59.877 66.667 0.00 0.00 37.96 4.45
964 984 4.584743 GGGCTCGGATGGAAATAAATTTCT 59.415 41.667 13.57 0.00 44.21 2.52
966 986 3.641436 GGGGCTCGGATGGAAATAAATTT 59.359 43.478 0.00 0.00 0.00 1.82
967 987 3.117131 AGGGGCTCGGATGGAAATAAATT 60.117 43.478 0.00 0.00 0.00 1.82
1968 2010 0.529337 CGATGCTCAGCTCGGACAAT 60.529 55.000 9.80 0.00 0.00 2.71
2472 2520 3.980775 CACCAAAAATCAACTAGGCAACG 59.019 43.478 0.00 0.00 46.39 4.10
2478 2526 5.830912 TGCAGAACACCAAAAATCAACTAG 58.169 37.500 0.00 0.00 0.00 2.57
2898 2946 6.014669 CCAAAATGGAATTGAGTTGGAACCTA 60.015 38.462 0.00 0.00 41.87 3.08
3089 3139 4.851639 AGAAGGTACAGCCAGAAATGAT 57.148 40.909 0.00 0.00 40.61 2.45
3203 3264 4.747108 GGTTCGATCATCAATCAGGTACAG 59.253 45.833 0.00 0.00 33.65 2.74
3276 3337 7.655328 ACAGCTAGAAATGCATACATCTCTAAC 59.345 37.037 11.55 4.70 35.82 2.34
3288 3349 6.230472 TCAAGAAAGTACAGCTAGAAATGCA 58.770 36.000 0.00 0.00 0.00 3.96
3357 3419 4.142038 ACAATGACACCCTTGTAAGTTCC 58.858 43.478 0.00 0.00 35.47 3.62
3488 3550 7.600375 TGTTCTATCTTCAGTTTGATGTCTGAC 59.400 37.037 0.00 0.00 39.87 3.51
3492 3554 8.602328 CATCTGTTCTATCTTCAGTTTGATGTC 58.398 37.037 0.00 0.00 0.00 3.06
3643 3706 0.107703 GTCCATCGTCCAATGCCTCA 60.108 55.000 0.00 0.00 0.00 3.86
3708 3771 2.983229 AGACAGGAGCTTATGCAACAG 58.017 47.619 3.16 0.00 42.74 3.16
3709 3772 3.423539 AAGACAGGAGCTTATGCAACA 57.576 42.857 3.16 0.00 42.74 3.33
3776 3839 6.470877 GTCAATTGTTAAAGTGCGAGAAACAA 59.529 34.615 5.13 0.00 42.35 2.83
3870 3934 0.915872 TGCTCATGACCTCCACCCAT 60.916 55.000 0.00 0.00 0.00 4.00
4097 4162 3.380004 TGTGACAGAAACATTTGACCACC 59.620 43.478 0.00 0.00 0.00 4.61
4165 4230 5.992829 TCAACTTCAGCACCGTATTCTTTAA 59.007 36.000 0.00 0.00 0.00 1.52
4166 4231 5.543714 TCAACTTCAGCACCGTATTCTTTA 58.456 37.500 0.00 0.00 0.00 1.85
4225 4297 1.644509 TCAGCACCACTCACCACTAT 58.355 50.000 0.00 0.00 0.00 2.12
4271 4343 6.702329 ACCAGCTTAGCACTATCATTATACC 58.298 40.000 7.07 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.