Multiple sequence alignment - TraesCS3B01G214300

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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 TraesCS3B01G214300 chr3B 100.000 3038 0 0 1 3038 254767459 254770496 0.000000e+00 5611.0
1 TraesCS3B01G214300 chr3B 97.727 1012 17 1 2027 3038 78622068 78621063 0.000000e+00 1736.0
2 TraesCS3B01G214300 chr3B 95.366 971 37 5 2070 3038 765984045 765985009 0.000000e+00 1537.0
3 TraesCS3B01G214300 chr3B 95.057 971 40 5 2070 3038 819513542 819514506 0.000000e+00 1520.0
4 TraesCS3B01G214300 chr3B 76.410 195 36 8 37 224 91149002 91148811 2.490000e-16 97.1
5 TraesCS3B01G214300 chr3D 96.088 1866 49 12 180 2027 175400687 175402546 0.000000e+00 3020.0
6 TraesCS3B01G214300 chr3D 80.142 141 25 3 37 176 457000447 457000585 5.360000e-18 102.0
7 TraesCS3B01G214300 chr3A 95.972 1862 49 11 180 2027 215471089 215472938 0.000000e+00 3000.0
8 TraesCS3B01G214300 chr6B 98.714 1011 13 0 2028 3038 29246787 29247797 0.000000e+00 1796.0
9 TraesCS3B01G214300 chr7B 96.910 971 23 4 2070 3038 636941682 636942647 0.000000e+00 1620.0
10 TraesCS3B01G214300 chr7B 96.704 971 25 4 2070 3038 641029523 641030488 0.000000e+00 1609.0
11 TraesCS3B01G214300 chr4B 96.292 971 29 4 2070 3038 518672534 518673499 0.000000e+00 1587.0
12 TraesCS3B01G214300 chr5B 95.263 971 38 5 2070 3038 617241609 617242573 0.000000e+00 1531.0
13 TraesCS3B01G214300 chr5B 80.000 140 25 2 37 176 327077868 327078004 1.930000e-17 100.0
14 TraesCS3B01G214300 chr5B 78.195 133 28 1 44 176 271151514 271151383 1.940000e-12 84.2
15 TraesCS3B01G214300 chr2A 94.342 972 46 6 2070 3038 768726745 768725780 0.000000e+00 1482.0
16 TraesCS3B01G214300 chr7D 80.537 149 27 2 37 184 465568239 465568386 2.480000e-21 113.0
17 TraesCS3B01G214300 chr5D 81.295 139 26 0 38 176 529087958 529087820 2.480000e-21 113.0
18 TraesCS3B01G214300 chr5D 80.851 141 25 2 43 182 242581820 242581681 3.200000e-20 110.0
19 TraesCS3B01G214300 chr5D 80.714 140 25 2 37 176 262833070 262832933 1.150000e-19 108.0
20 TraesCS3B01G214300 chr4D 78.912 147 31 0 37 183 489448461 489448607 1.930000e-17 100.0
21 TraesCS3B01G214300 chr2D 91.489 47 4 0 1600 1646 599287941 599287895 7.030000e-07 65.8
22 TraesCS3B01G214300 chr2B 91.489 47 4 0 1600 1646 728752319 728752273 7.030000e-07 65.8


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 TraesCS3B01G214300 chr3B 254767459 254770496 3037 False 5611 5611 100.000 1 3038 1 chr3B.!!$F1 3037
1 TraesCS3B01G214300 chr3B 78621063 78622068 1005 True 1736 1736 97.727 2027 3038 1 chr3B.!!$R1 1011
2 TraesCS3B01G214300 chr3B 765984045 765985009 964 False 1537 1537 95.366 2070 3038 1 chr3B.!!$F2 968
3 TraesCS3B01G214300 chr3B 819513542 819514506 964 False 1520 1520 95.057 2070 3038 1 chr3B.!!$F3 968
4 TraesCS3B01G214300 chr3D 175400687 175402546 1859 False 3020 3020 96.088 180 2027 1 chr3D.!!$F1 1847
5 TraesCS3B01G214300 chr3A 215471089 215472938 1849 False 3000 3000 95.972 180 2027 1 chr3A.!!$F1 1847
6 TraesCS3B01G214300 chr6B 29246787 29247797 1010 False 1796 1796 98.714 2028 3038 1 chr6B.!!$F1 1010
7 TraesCS3B01G214300 chr7B 636941682 636942647 965 False 1620 1620 96.910 2070 3038 1 chr7B.!!$F1 968
8 TraesCS3B01G214300 chr7B 641029523 641030488 965 False 1609 1609 96.704 2070 3038 1 chr7B.!!$F2 968
9 TraesCS3B01G214300 chr4B 518672534 518673499 965 False 1587 1587 96.292 2070 3038 1 chr4B.!!$F1 968
10 TraesCS3B01G214300 chr5B 617241609 617242573 964 False 1531 1531 95.263 2070 3038 1 chr5B.!!$F2 968
11 TraesCS3B01G214300 chr2A 768725780 768726745 965 True 1482 1482 94.342 2070 3038 1 chr2A.!!$R1 968

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
56 57 0.114364 AAAAGGGGCCGAGAATTGGT 59.886 50.0 0.00 0.00 43.65 3.67 F
151 152 0.179192 CAAACGGACACATGCGGATG 60.179 55.0 16.07 16.07 45.25 3.51 F
161 162 0.308684 CATGCGGATGAAATGGGTCG 59.691 55.0 12.09 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1969 1.152963 GCGCACTTGTATCCCCCAT 60.153 57.895 0.30 0.0 0.00 4.00 R
1978 2003 2.811317 GCACTCGACCTTGCTCCG 60.811 66.667 2.36 0.0 35.74 4.63 R
2316 2343 1.676006 CGTGAAAAAGTGGCTCTTGGT 59.324 47.619 2.09 0.0 36.40 3.67 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
20 21 3.806949 TGGAGTTGGCCTTAAGACATT 57.193 42.857 3.32 0.00 0.00 2.71
21 22 4.112634 TGGAGTTGGCCTTAAGACATTT 57.887 40.909 3.32 0.00 0.00 2.32
22 23 3.826157 TGGAGTTGGCCTTAAGACATTTG 59.174 43.478 3.32 0.00 0.00 2.32
23 24 3.367395 GGAGTTGGCCTTAAGACATTTGC 60.367 47.826 3.32 0.00 0.00 3.68
24 25 3.500343 AGTTGGCCTTAAGACATTTGCT 58.500 40.909 3.32 0.00 0.00 3.91
25 26 3.897505 AGTTGGCCTTAAGACATTTGCTT 59.102 39.130 3.32 0.00 0.00 3.91
26 27 3.940209 TGGCCTTAAGACATTTGCTTG 57.060 42.857 3.32 0.00 0.00 4.01
27 28 2.562298 TGGCCTTAAGACATTTGCTTGG 59.438 45.455 3.32 0.00 0.00 3.61
28 29 2.562738 GGCCTTAAGACATTTGCTTGGT 59.437 45.455 3.36 0.00 0.00 3.67
29 30 3.761752 GGCCTTAAGACATTTGCTTGGTA 59.238 43.478 3.36 0.00 0.00 3.25
30 31 4.219725 GGCCTTAAGACATTTGCTTGGTAA 59.780 41.667 3.36 0.00 0.00 2.85
31 32 5.105351 GGCCTTAAGACATTTGCTTGGTAAT 60.105 40.000 3.36 0.00 0.00 1.89
32 33 6.096282 GGCCTTAAGACATTTGCTTGGTAATA 59.904 38.462 3.36 0.00 0.00 0.98
33 34 7.363443 GGCCTTAAGACATTTGCTTGGTAATAA 60.363 37.037 3.36 0.00 0.00 1.40
34 35 8.197439 GCCTTAAGACATTTGCTTGGTAATAAT 58.803 33.333 3.36 0.00 0.00 1.28
55 56 1.266178 AAAAAGGGGCCGAGAATTGG 58.734 50.000 0.00 0.00 45.02 3.16
56 57 0.114364 AAAAGGGGCCGAGAATTGGT 59.886 50.000 0.00 0.00 43.65 3.67
57 58 0.323451 AAAGGGGCCGAGAATTGGTC 60.323 55.000 0.00 0.00 46.28 4.02
63 64 4.201951 CGAGAATTGGTCGGTGGG 57.798 61.111 0.00 0.00 33.66 4.61
64 65 2.106683 CGAGAATTGGTCGGTGGGC 61.107 63.158 0.00 0.00 33.66 5.36
65 66 2.046314 AGAATTGGTCGGTGGGCG 60.046 61.111 0.00 0.00 0.00 6.13
66 67 3.131478 GAATTGGTCGGTGGGCGG 61.131 66.667 0.00 0.00 0.00 6.13
67 68 3.615509 GAATTGGTCGGTGGGCGGA 62.616 63.158 0.00 0.00 0.00 5.54
68 69 3.912745 AATTGGTCGGTGGGCGGAC 62.913 63.158 0.00 0.00 42.15 4.79
71 72 4.629523 GGTCGGTGGGCGGACAAA 62.630 66.667 7.42 0.00 43.90 2.83
72 73 2.592287 GTCGGTGGGCGGACAAAA 60.592 61.111 0.00 0.00 42.35 2.44
73 74 2.188161 GTCGGTGGGCGGACAAAAA 61.188 57.895 0.00 0.00 42.35 1.94
74 75 1.894756 TCGGTGGGCGGACAAAAAG 60.895 57.895 0.00 0.00 0.00 2.27
75 76 2.338620 GGTGGGCGGACAAAAAGC 59.661 61.111 0.00 0.00 0.00 3.51
76 77 2.494530 GGTGGGCGGACAAAAAGCA 61.495 57.895 0.00 0.00 0.00 3.91
77 78 1.665442 GTGGGCGGACAAAAAGCAT 59.335 52.632 0.00 0.00 0.00 3.79
78 79 0.885196 GTGGGCGGACAAAAAGCATA 59.115 50.000 0.00 0.00 0.00 3.14
79 80 1.476488 GTGGGCGGACAAAAAGCATAT 59.524 47.619 0.00 0.00 0.00 1.78
80 81 1.476085 TGGGCGGACAAAAAGCATATG 59.524 47.619 0.00 0.00 0.00 1.78
81 82 1.559831 GGCGGACAAAAAGCATATGC 58.440 50.000 20.36 20.36 42.49 3.14
93 94 0.933097 GCATATGCGTGTCTGTCTGG 59.067 55.000 12.82 0.00 0.00 3.86
94 95 1.575244 CATATGCGTGTCTGTCTGGG 58.425 55.000 0.00 0.00 0.00 4.45
95 96 1.134699 CATATGCGTGTCTGTCTGGGT 60.135 52.381 0.00 0.00 0.00 4.51
96 97 0.530744 TATGCGTGTCTGTCTGGGTC 59.469 55.000 0.00 0.00 0.00 4.46
97 98 2.430921 GCGTGTCTGTCTGGGTCG 60.431 66.667 0.00 0.00 0.00 4.79
98 99 2.258591 CGTGTCTGTCTGGGTCGG 59.741 66.667 0.00 0.00 0.00 4.79
99 100 2.048127 GTGTCTGTCTGGGTCGGC 60.048 66.667 0.00 0.00 0.00 5.54
100 101 2.523168 TGTCTGTCTGGGTCGGCA 60.523 61.111 0.00 0.00 0.00 5.69
101 102 2.048127 GTCTGTCTGGGTCGGCAC 60.048 66.667 0.00 0.00 0.00 5.01
115 116 3.284449 GCACGTTGGGCCGACTTT 61.284 61.111 21.44 5.73 0.00 2.66
116 117 2.841160 GCACGTTGGGCCGACTTTT 61.841 57.895 21.44 3.14 0.00 2.27
117 118 1.281656 CACGTTGGGCCGACTTTTC 59.718 57.895 21.44 0.00 0.00 2.29
118 119 1.147600 ACGTTGGGCCGACTTTTCT 59.852 52.632 21.44 0.00 0.00 2.52
119 120 1.164041 ACGTTGGGCCGACTTTTCTG 61.164 55.000 21.44 7.46 0.00 3.02
120 121 1.164041 CGTTGGGCCGACTTTTCTGT 61.164 55.000 21.44 0.00 0.00 3.41
121 122 0.591659 GTTGGGCCGACTTTTCTGTC 59.408 55.000 17.07 0.00 0.00 3.51
122 123 0.536460 TTGGGCCGACTTTTCTGTCC 60.536 55.000 0.00 0.00 31.49 4.02
123 124 2.033194 GGGCCGACTTTTCTGTCCG 61.033 63.158 0.00 0.00 33.70 4.79
124 125 2.677979 GGCCGACTTTTCTGTCCGC 61.678 63.158 0.00 0.00 39.33 5.54
125 126 2.677979 GCCGACTTTTCTGTCCGCC 61.678 63.158 0.00 0.00 35.97 6.13
126 127 2.380410 CCGACTTTTCTGTCCGCCG 61.380 63.158 0.00 0.00 33.70 6.46
127 128 2.861006 GACTTTTCTGTCCGCCGC 59.139 61.111 0.00 0.00 0.00 6.53
128 129 3.011760 GACTTTTCTGTCCGCCGCG 62.012 63.158 5.59 5.59 0.00 6.46
142 143 4.072088 CGCGGCTCAAACGGACAC 62.072 66.667 0.00 0.00 0.00 3.67
143 144 2.970324 GCGGCTCAAACGGACACA 60.970 61.111 0.00 0.00 0.00 3.72
144 145 2.325082 GCGGCTCAAACGGACACAT 61.325 57.895 0.00 0.00 0.00 3.21
145 146 1.497278 CGGCTCAAACGGACACATG 59.503 57.895 0.00 0.00 0.00 3.21
146 147 1.210155 GGCTCAAACGGACACATGC 59.790 57.895 0.00 0.00 0.00 4.06
147 148 1.154413 GCTCAAACGGACACATGCG 60.154 57.895 0.00 0.00 46.59 4.73
148 149 1.497278 CTCAAACGGACACATGCGG 59.503 57.895 0.00 0.00 45.25 5.69
149 150 0.948623 CTCAAACGGACACATGCGGA 60.949 55.000 0.00 0.00 45.25 5.54
150 151 0.321210 TCAAACGGACACATGCGGAT 60.321 50.000 0.00 0.00 45.25 4.18
151 152 0.179192 CAAACGGACACATGCGGATG 60.179 55.000 16.07 16.07 45.25 3.51
152 153 0.321210 AAACGGACACATGCGGATGA 60.321 50.000 24.66 0.00 45.25 2.92
153 154 0.321210 AACGGACACATGCGGATGAA 60.321 50.000 24.66 0.00 45.25 2.57
154 155 0.321210 ACGGACACATGCGGATGAAA 60.321 50.000 24.66 0.00 45.25 2.69
155 156 1.016627 CGGACACATGCGGATGAAAT 58.983 50.000 24.66 7.94 35.75 2.17
156 157 1.268184 CGGACACATGCGGATGAAATG 60.268 52.381 24.66 13.77 35.75 2.32
157 158 1.066002 GGACACATGCGGATGAAATGG 59.934 52.381 24.66 9.39 33.36 3.16
158 159 1.066002 GACACATGCGGATGAAATGGG 59.934 52.381 24.66 0.00 33.36 4.00
159 160 1.105457 CACATGCGGATGAAATGGGT 58.895 50.000 24.66 0.00 33.36 4.51
160 161 1.066002 CACATGCGGATGAAATGGGTC 59.934 52.381 24.66 0.00 33.36 4.46
161 162 0.308684 CATGCGGATGAAATGGGTCG 59.691 55.000 12.09 0.00 0.00 4.79
162 163 0.819259 ATGCGGATGAAATGGGTCGG 60.819 55.000 0.00 0.00 0.00 4.79
163 164 2.834618 GCGGATGAAATGGGTCGGC 61.835 63.158 0.00 0.00 0.00 5.54
164 165 2.534019 CGGATGAAATGGGTCGGCG 61.534 63.158 0.00 0.00 0.00 6.46
165 166 2.715624 GATGAAATGGGTCGGCGC 59.284 61.111 0.00 0.00 0.00 6.53
166 167 3.168237 GATGAAATGGGTCGGCGCG 62.168 63.158 0.00 0.00 0.00 6.86
189 190 2.289565 GGAGTTGGCCTAAGCACATAC 58.710 52.381 3.32 0.00 42.56 2.39
190 191 1.933853 GAGTTGGCCTAAGCACATACG 59.066 52.381 3.32 0.00 42.56 3.06
191 192 0.377203 GTTGGCCTAAGCACATACGC 59.623 55.000 3.32 0.00 42.56 4.42
219 221 0.960364 GGGTGCCAACATGTCACGAT 60.960 55.000 0.00 0.00 0.00 3.73
351 357 5.736951 AGCTAGTCAGTCAATCAGTTCTT 57.263 39.130 0.00 0.00 0.00 2.52
362 368 1.374252 CAGTTCTTCCCCCGTCACG 60.374 63.158 0.00 0.00 0.00 4.35
509 519 2.093500 TGTTGCTGCGAGGATCTTGTAT 60.093 45.455 0.00 0.00 0.00 2.29
687 697 6.869388 TGTTGTTTTGTTTTCTCCTTGTTACC 59.131 34.615 0.00 0.00 0.00 2.85
1028 1047 4.372656 GAGTTTTCCTACCATGAGATCGG 58.627 47.826 0.00 0.00 0.00 4.18
1629 1651 3.883744 CTTCGGCGTGGTGCTCCTT 62.884 63.158 6.85 0.00 45.43 3.36
1805 1828 3.625897 CAGGTCCTGTCCGTGGCA 61.626 66.667 11.09 0.00 0.00 4.92
1957 1982 1.484653 TCGTGTCATGGGGGATACAAG 59.515 52.381 0.00 0.00 39.74 3.16
2316 2343 0.320683 CATGAAGCACACGGACCTCA 60.321 55.000 0.00 0.00 0.00 3.86
2630 2657 4.930405 GGATGTAGATCGTCGAGTATCTGA 59.070 45.833 16.22 6.40 34.36 3.27
2638 2665 1.476891 GTCGAGTATCTGAGCAACCCA 59.523 52.381 0.00 0.00 0.00 4.51
2691 2718 5.940470 GCTTGTTGGAGAGGAAGAATTAAGA 59.060 40.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.806949 AATGTCTTAAGGCCAACTCCA 57.193 42.857 5.01 0.00 0.00 3.86
3 4 3.500343 AGCAAATGTCTTAAGGCCAACT 58.500 40.909 5.01 0.00 0.00 3.16
4 5 3.942130 AGCAAATGTCTTAAGGCCAAC 57.058 42.857 5.01 0.00 0.00 3.77
7 8 2.562738 ACCAAGCAAATGTCTTAAGGCC 59.437 45.455 4.27 0.00 0.00 5.19
8 9 3.942130 ACCAAGCAAATGTCTTAAGGC 57.058 42.857 0.00 0.00 0.00 4.35
36 37 1.266178 CCAATTCTCGGCCCCTTTTT 58.734 50.000 0.00 0.00 0.00 1.94
37 38 0.114364 ACCAATTCTCGGCCCCTTTT 59.886 50.000 0.00 0.00 0.00 2.27
38 39 0.323451 GACCAATTCTCGGCCCCTTT 60.323 55.000 0.00 0.00 0.00 3.11
39 40 1.303282 GACCAATTCTCGGCCCCTT 59.697 57.895 0.00 0.00 0.00 3.95
40 41 2.998949 GACCAATTCTCGGCCCCT 59.001 61.111 0.00 0.00 0.00 4.79
41 42 2.513897 CGACCAATTCTCGGCCCC 60.514 66.667 0.00 0.00 0.00 5.80
42 43 2.513897 CCGACCAATTCTCGGCCC 60.514 66.667 7.92 0.00 44.04 5.80
46 47 2.106683 GCCCACCGACCAATTCTCG 61.107 63.158 0.00 0.00 0.00 4.04
47 48 2.106683 CGCCCACCGACCAATTCTC 61.107 63.158 0.00 0.00 40.02 2.87
48 49 2.046314 CGCCCACCGACCAATTCT 60.046 61.111 0.00 0.00 40.02 2.40
49 50 3.131478 CCGCCCACCGACCAATTC 61.131 66.667 0.00 0.00 40.02 2.17
50 51 3.642503 TCCGCCCACCGACCAATT 61.643 61.111 0.00 0.00 40.02 2.32
51 52 4.404098 GTCCGCCCACCGACCAAT 62.404 66.667 0.00 0.00 40.02 3.16
54 55 4.629523 TTTGTCCGCCCACCGACC 62.630 66.667 0.00 0.00 40.02 4.79
55 56 2.125202 CTTTTTGTCCGCCCACCGAC 62.125 60.000 0.00 0.00 40.02 4.79
56 57 1.894756 CTTTTTGTCCGCCCACCGA 60.895 57.895 0.00 0.00 40.02 4.69
57 58 2.642700 CTTTTTGTCCGCCCACCG 59.357 61.111 0.00 0.00 0.00 4.94
58 59 1.815817 ATGCTTTTTGTCCGCCCACC 61.816 55.000 0.00 0.00 0.00 4.61
59 60 0.885196 TATGCTTTTTGTCCGCCCAC 59.115 50.000 0.00 0.00 0.00 4.61
60 61 1.476085 CATATGCTTTTTGTCCGCCCA 59.524 47.619 0.00 0.00 0.00 5.36
61 62 1.802508 GCATATGCTTTTTGTCCGCCC 60.803 52.381 20.64 0.00 38.21 6.13
62 63 1.559831 GCATATGCTTTTTGTCCGCC 58.440 50.000 20.64 0.00 38.21 6.13
63 64 1.191096 CGCATATGCTTTTTGTCCGC 58.809 50.000 24.56 0.00 39.32 5.54
64 65 2.176369 CACGCATATGCTTTTTGTCCG 58.824 47.619 24.56 8.79 39.32 4.79
65 66 3.119849 AGACACGCATATGCTTTTTGTCC 60.120 43.478 27.50 17.82 36.11 4.02
66 67 3.848019 CAGACACGCATATGCTTTTTGTC 59.152 43.478 25.71 25.71 39.32 3.18
67 68 3.253188 ACAGACACGCATATGCTTTTTGT 59.747 39.130 24.56 19.90 39.32 2.83
68 69 3.825308 ACAGACACGCATATGCTTTTTG 58.175 40.909 24.56 17.20 39.32 2.44
69 70 3.753272 AGACAGACACGCATATGCTTTTT 59.247 39.130 24.56 5.50 39.32 1.94
70 71 3.125829 CAGACAGACACGCATATGCTTTT 59.874 43.478 24.56 9.40 39.32 2.27
71 72 2.674852 CAGACAGACACGCATATGCTTT 59.325 45.455 24.56 9.37 39.32 3.51
72 73 2.274437 CAGACAGACACGCATATGCTT 58.726 47.619 24.56 13.70 39.32 3.91
73 74 1.472201 CCAGACAGACACGCATATGCT 60.472 52.381 24.56 6.90 39.32 3.79
74 75 0.933097 CCAGACAGACACGCATATGC 59.067 55.000 18.08 18.08 37.78 3.14
75 76 1.134699 ACCCAGACAGACACGCATATG 60.135 52.381 0.00 0.00 0.00 1.78
76 77 1.137086 GACCCAGACAGACACGCATAT 59.863 52.381 0.00 0.00 0.00 1.78
77 78 0.530744 GACCCAGACAGACACGCATA 59.469 55.000 0.00 0.00 0.00 3.14
78 79 1.293498 GACCCAGACAGACACGCAT 59.707 57.895 0.00 0.00 0.00 4.73
79 80 2.734591 GACCCAGACAGACACGCA 59.265 61.111 0.00 0.00 0.00 5.24
80 81 2.430921 CGACCCAGACAGACACGC 60.431 66.667 0.00 0.00 0.00 5.34
81 82 2.258591 CCGACCCAGACAGACACG 59.741 66.667 0.00 0.00 0.00 4.49
82 83 2.048127 GCCGACCCAGACAGACAC 60.048 66.667 0.00 0.00 0.00 3.67
83 84 2.523168 TGCCGACCCAGACAGACA 60.523 61.111 0.00 0.00 0.00 3.41
84 85 2.048127 GTGCCGACCCAGACAGAC 60.048 66.667 0.00 0.00 0.00 3.51
85 86 3.680786 CGTGCCGACCCAGACAGA 61.681 66.667 0.00 0.00 0.00 3.41
86 87 3.515316 AACGTGCCGACCCAGACAG 62.515 63.158 0.00 0.00 0.00 3.51
87 88 3.542676 AACGTGCCGACCCAGACA 61.543 61.111 0.00 0.00 0.00 3.41
88 89 3.041940 CAACGTGCCGACCCAGAC 61.042 66.667 0.00 0.00 0.00 3.51
89 90 4.308458 CCAACGTGCCGACCCAGA 62.308 66.667 0.00 0.00 0.00 3.86
98 99 2.726850 GAAAAGTCGGCCCAACGTGC 62.727 60.000 0.00 0.00 34.94 5.34
99 100 1.164041 AGAAAAGTCGGCCCAACGTG 61.164 55.000 0.00 0.00 34.94 4.49
100 101 1.147600 AGAAAAGTCGGCCCAACGT 59.852 52.632 0.00 0.00 34.94 3.99
101 102 1.164041 ACAGAAAAGTCGGCCCAACG 61.164 55.000 0.00 0.00 0.00 4.10
102 103 0.591659 GACAGAAAAGTCGGCCCAAC 59.408 55.000 0.00 0.00 0.00 3.77
103 104 0.536460 GGACAGAAAAGTCGGCCCAA 60.536 55.000 0.00 0.00 39.42 4.12
104 105 1.072505 GGACAGAAAAGTCGGCCCA 59.927 57.895 0.00 0.00 39.42 5.36
105 106 2.033194 CGGACAGAAAAGTCGGCCC 61.033 63.158 0.00 0.00 39.42 5.80
106 107 3.562635 CGGACAGAAAAGTCGGCC 58.437 61.111 0.00 0.00 39.42 6.13
108 109 2.380410 CGGCGGACAGAAAAGTCGG 61.380 63.158 0.00 0.00 39.42 4.79
109 110 3.011760 GCGGCGGACAGAAAAGTCG 62.012 63.158 9.78 0.00 39.42 4.18
110 111 2.861006 GCGGCGGACAGAAAAGTC 59.139 61.111 9.78 0.00 37.80 3.01
111 112 3.041940 CGCGGCGGACAGAAAAGT 61.042 61.111 15.84 0.00 0.00 2.66
125 126 4.072088 GTGTCCGTTTGAGCCGCG 62.072 66.667 0.00 0.00 0.00 6.46
126 127 2.325082 ATGTGTCCGTTTGAGCCGC 61.325 57.895 0.00 0.00 0.00 6.53
127 128 1.497278 CATGTGTCCGTTTGAGCCG 59.503 57.895 0.00 0.00 0.00 5.52
128 129 1.210155 GCATGTGTCCGTTTGAGCC 59.790 57.895 0.00 0.00 0.00 4.70
129 130 1.154413 CGCATGTGTCCGTTTGAGC 60.154 57.895 0.00 0.00 0.00 4.26
130 131 0.948623 TCCGCATGTGTCCGTTTGAG 60.949 55.000 5.38 0.00 0.00 3.02
131 132 0.321210 ATCCGCATGTGTCCGTTTGA 60.321 50.000 5.38 0.00 0.00 2.69
132 133 0.179192 CATCCGCATGTGTCCGTTTG 60.179 55.000 5.38 0.00 0.00 2.93
133 134 0.321210 TCATCCGCATGTGTCCGTTT 60.321 50.000 5.38 0.00 0.00 3.60
134 135 0.321210 TTCATCCGCATGTGTCCGTT 60.321 50.000 5.38 0.00 0.00 4.44
135 136 0.321210 TTTCATCCGCATGTGTCCGT 60.321 50.000 5.38 0.00 0.00 4.69
136 137 1.016627 ATTTCATCCGCATGTGTCCG 58.983 50.000 5.38 0.00 0.00 4.79
137 138 1.066002 CCATTTCATCCGCATGTGTCC 59.934 52.381 5.38 0.00 0.00 4.02
138 139 1.066002 CCCATTTCATCCGCATGTGTC 59.934 52.381 5.38 0.00 0.00 3.67
139 140 1.105457 CCCATTTCATCCGCATGTGT 58.895 50.000 5.38 0.00 0.00 3.72
140 141 1.066002 GACCCATTTCATCCGCATGTG 59.934 52.381 0.00 0.00 0.00 3.21
141 142 1.392589 GACCCATTTCATCCGCATGT 58.607 50.000 0.00 0.00 0.00 3.21
142 143 0.308684 CGACCCATTTCATCCGCATG 59.691 55.000 0.00 0.00 0.00 4.06
143 144 0.819259 CCGACCCATTTCATCCGCAT 60.819 55.000 0.00 0.00 0.00 4.73
144 145 1.451207 CCGACCCATTTCATCCGCA 60.451 57.895 0.00 0.00 0.00 5.69
145 146 2.834618 GCCGACCCATTTCATCCGC 61.835 63.158 0.00 0.00 0.00 5.54
146 147 2.534019 CGCCGACCCATTTCATCCG 61.534 63.158 0.00 0.00 0.00 4.18
147 148 2.834618 GCGCCGACCCATTTCATCC 61.835 63.158 0.00 0.00 0.00 3.51
148 149 2.715624 GCGCCGACCCATTTCATC 59.284 61.111 0.00 0.00 0.00 2.92
149 150 3.202001 CGCGCCGACCCATTTCAT 61.202 61.111 0.00 0.00 0.00 2.57
163 164 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
164 165 1.745489 CTTAGGCCAACTCCACCGC 60.745 63.158 5.01 0.00 0.00 5.68
165 166 1.745489 GCTTAGGCCAACTCCACCG 60.745 63.158 5.01 0.00 0.00 4.94
166 167 0.960861 GTGCTTAGGCCAACTCCACC 60.961 60.000 5.01 0.00 37.74 4.61
167 168 0.250727 TGTGCTTAGGCCAACTCCAC 60.251 55.000 5.01 6.06 37.74 4.02
168 169 0.698238 ATGTGCTTAGGCCAACTCCA 59.302 50.000 5.01 0.00 37.74 3.86
169 170 2.289565 GTATGTGCTTAGGCCAACTCC 58.710 52.381 5.01 0.00 37.74 3.85
170 171 1.933853 CGTATGTGCTTAGGCCAACTC 59.066 52.381 5.01 0.00 37.74 3.01
171 172 2.012051 GCGTATGTGCTTAGGCCAACT 61.012 52.381 5.01 0.00 37.74 3.16
172 173 0.377203 GCGTATGTGCTTAGGCCAAC 59.623 55.000 5.01 0.00 37.74 3.77
173 174 2.775351 GCGTATGTGCTTAGGCCAA 58.225 52.632 5.01 0.00 37.74 4.52
174 175 4.532490 GCGTATGTGCTTAGGCCA 57.468 55.556 5.01 0.00 37.74 5.36
175 176 3.732470 GGCGTATGTGCTTAGGCC 58.268 61.111 0.00 0.00 43.52 5.19
176 177 1.379527 AAAGGCGTATGTGCTTAGGC 58.620 50.000 0.00 0.00 39.26 3.93
177 178 3.190535 ACAAAAAGGCGTATGTGCTTAGG 59.809 43.478 0.00 0.00 34.52 2.69
178 179 4.158384 CACAAAAAGGCGTATGTGCTTAG 58.842 43.478 6.40 0.00 37.03 2.18
189 190 2.028925 GGCACCCACAAAAAGGCG 59.971 61.111 0.00 0.00 0.00 5.52
190 191 0.813610 GTTGGCACCCACAAAAAGGC 60.814 55.000 0.00 0.00 30.78 4.35
191 192 0.539051 TGTTGGCACCCACAAAAAGG 59.461 50.000 0.00 0.00 30.78 3.11
219 221 6.605594 AGACTGTTTTGTTCCAGGTCAAATAA 59.394 34.615 11.35 5.02 34.30 1.40
256 258 5.755409 AACCTCAATCACCATGTACTACA 57.245 39.130 0.00 0.00 0.00 2.74
362 368 4.489771 CCCCCACCTGATCACGCC 62.490 72.222 0.00 0.00 0.00 5.68
509 519 1.596934 GAGGAGTGGTTGCGATGGA 59.403 57.895 0.00 0.00 0.00 3.41
687 697 8.742777 TCCTAAAGGATGATGAAATTTGTCTTG 58.257 33.333 0.00 0.00 39.78 3.02
774 784 4.067192 GGTAAAGGTTGGTGATTACGTGT 58.933 43.478 0.00 0.00 0.00 4.49
908 924 3.406361 CGTGTGTGAGCGGAGTGC 61.406 66.667 0.00 0.00 46.98 4.40
1539 1561 3.087906 AGGTACCCCATCGTGCCC 61.088 66.667 8.74 0.00 39.17 5.36
1629 1651 4.519437 CGCCCGCTGATGAGCTCA 62.519 66.667 20.79 20.79 43.77 4.26
1944 1969 1.152963 GCGCACTTGTATCCCCCAT 60.153 57.895 0.30 0.00 0.00 4.00
1957 1982 4.104633 CGTCGTCTTCACGCGCAC 62.105 66.667 5.73 0.00 46.28 5.34
1978 2003 2.811317 GCACTCGACCTTGCTCCG 60.811 66.667 2.36 0.00 35.74 4.63
2316 2343 1.676006 CGTGAAAAAGTGGCTCTTGGT 59.324 47.619 2.09 0.00 36.40 3.67
2485 2512 3.984193 ATTCAGTGGCCGAGGCAGC 62.984 63.158 16.65 7.68 44.11 5.25
2499 2526 2.936919 ACAGGTCTGTTGCTCATTCA 57.063 45.000 0.00 0.00 41.83 2.57
2630 2657 2.839098 CAGACTGGGTGGGTTGCT 59.161 61.111 0.00 0.00 0.00 3.91
2638 2665 4.018960 AGTTTATTCTGATGCAGACTGGGT 60.019 41.667 4.26 0.00 40.46 4.51
2691 2718 7.682787 AGGTACTATTGATCATGGTCTTCTT 57.317 36.000 7.64 0.00 36.02 2.52
2712 2739 6.608002 AGAGAATACTTCGGTATCTCAAAGGT 59.392 38.462 0.00 0.00 39.94 3.50


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

AutoCloner maintained by Alex Coulton.