Multiple sequence alignment - TraesCS4B01G337200

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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 TraesCS4B01G337200 chr4B 100.000 3210 0 0 1 3210 629907175 629910384 0.000000e+00 5928
1 TraesCS4B01G337200 chr4B 96.059 3070 86 19 154 3210 665900182 665903229 0.000000e+00 4966
2 TraesCS4B01G337200 chr3B 97.778 3060 61 6 154 3210 452563153 452560098 0.000000e+00 5267
3 TraesCS4B01G337200 chr3B 97.387 3062 72 5 154 3210 73031280 73034338 0.000000e+00 5204
4 TraesCS4B01G337200 chr3B 92.550 349 16 3 502 840 792749690 792749342 2.880000e-135 492
5 TraesCS4B01G337200 chr2B 97.129 3065 84 4 150 3210 553880192 553883256 0.000000e+00 5169
6 TraesCS4B01G337200 chr1A 96.446 3067 95 7 155 3208 444169075 444166010 0.000000e+00 5048
7 TraesCS4B01G337200 chr4A 96.025 3069 108 9 155 3210 36004230 36001163 0.000000e+00 4979
8 TraesCS4B01G337200 chr5A 95.526 1967 58 15 154 2111 705867910 705869855 0.000000e+00 3118
9 TraesCS4B01G337200 chr5A 97.011 1104 33 0 2107 3210 705883335 705884438 0.000000e+00 1857
10 TraesCS4B01G337200 chr5A 97.327 1085 29 0 1129 2213 262471612 262470528 0.000000e+00 1844
11 TraesCS4B01G337200 chr5A 89.917 724 36 8 154 840 310728836 310728113 0.000000e+00 898
12 TraesCS4B01G337200 chr2A 96.866 1085 34 0 1129 2213 694743563 694742479 0.000000e+00 1816
13 TraesCS4B01G337200 chr2A 96.113 283 11 0 849 1131 694743887 694743605 2.260000e-126 462
14 TraesCS4B01G337200 chr6D 97.363 986 24 2 2225 3210 75301815 75300832 0.000000e+00 1676
15 TraesCS4B01G337200 chr5D 97.262 986 26 1 2225 3210 309068221 309067237 0.000000e+00 1670
16 TraesCS4B01G337200 chr7A 92.264 698 42 5 155 840 699627689 699626992 0.000000e+00 979
17 TraesCS4B01G337200 chr7A 96.140 285 11 0 847 1131 709138064 709137780 1.740000e-127 466
18 TraesCS4B01G337200 chr5B 84.416 154 24 0 2 155 231839533 231839686 5.550000e-33 152
19 TraesCS4B01G337200 chr2D 83.117 154 21 4 2 151 566282007 566282159 5.590000e-28 135


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 TraesCS4B01G337200 chr4B 629907175 629910384 3209 False 5928 5928 100.0000 1 3210 1 chr4B.!!$F1 3209
1 TraesCS4B01G337200 chr4B 665900182 665903229 3047 False 4966 4966 96.0590 154 3210 1 chr4B.!!$F2 3056
2 TraesCS4B01G337200 chr3B 452560098 452563153 3055 True 5267 5267 97.7780 154 3210 1 chr3B.!!$R1 3056
3 TraesCS4B01G337200 chr3B 73031280 73034338 3058 False 5204 5204 97.3870 154 3210 1 chr3B.!!$F1 3056
4 TraesCS4B01G337200 chr2B 553880192 553883256 3064 False 5169 5169 97.1290 150 3210 1 chr2B.!!$F1 3060
5 TraesCS4B01G337200 chr1A 444166010 444169075 3065 True 5048 5048 96.4460 155 3208 1 chr1A.!!$R1 3053
6 TraesCS4B01G337200 chr4A 36001163 36004230 3067 True 4979 4979 96.0250 155 3210 1 chr4A.!!$R1 3055
7 TraesCS4B01G337200 chr5A 705867910 705869855 1945 False 3118 3118 95.5260 154 2111 1 chr5A.!!$F1 1957
8 TraesCS4B01G337200 chr5A 705883335 705884438 1103 False 1857 1857 97.0110 2107 3210 1 chr5A.!!$F2 1103
9 TraesCS4B01G337200 chr5A 262470528 262471612 1084 True 1844 1844 97.3270 1129 2213 1 chr5A.!!$R1 1084
10 TraesCS4B01G337200 chr5A 310728113 310728836 723 True 898 898 89.9170 154 840 1 chr5A.!!$R2 686
11 TraesCS4B01G337200 chr2A 694742479 694743887 1408 True 1139 1816 96.4895 849 2213 2 chr2A.!!$R1 1364
12 TraesCS4B01G337200 chr6D 75300832 75301815 983 True 1676 1676 97.3630 2225 3210 1 chr6D.!!$R1 985
13 TraesCS4B01G337200 chr5D 309067237 309068221 984 True 1670 1670 97.2620 2225 3210 1 chr5D.!!$R1 985
14 TraesCS4B01G337200 chr7A 699626992 699627689 697 True 979 979 92.2640 155 840 1 chr7A.!!$R1 685

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
30 31 0.108804 GACGAGCAGATCCGGTTCAA 60.109 55.0 14.83 0.00 0.00 2.69 F
660 718 0.181114 CCGCCTTCTTGGATCCATCA 59.819 55.0 17.06 1.59 38.35 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1719 1.071385 CTTCAACTGCAGTGAGTCCCT 59.929 52.381 22.49 0.0 0.0 4.20 R
2318 2433 0.251564 TGCGTCCATCCCCAAACAAT 60.252 50.000 0.00 0.0 0.0 2.71 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
27 28 2.490217 CGACGAGCAGATCCGGTT 59.510 61.111 0.00 0.00 0.00 4.44
28 29 1.586564 CGACGAGCAGATCCGGTTC 60.587 63.158 0.00 1.92 0.00 3.62
29 30 1.511305 GACGAGCAGATCCGGTTCA 59.489 57.895 14.83 0.00 0.00 3.18
30 31 0.108804 GACGAGCAGATCCGGTTCAA 60.109 55.000 14.83 0.00 0.00 2.69
31 32 0.537188 ACGAGCAGATCCGGTTCAAT 59.463 50.000 14.83 0.00 0.00 2.57
32 33 1.212616 CGAGCAGATCCGGTTCAATC 58.787 55.000 14.83 4.05 0.00 2.67
33 34 1.587547 GAGCAGATCCGGTTCAATCC 58.412 55.000 14.83 0.38 0.00 3.01
34 35 0.181350 AGCAGATCCGGTTCAATCCC 59.819 55.000 14.83 0.00 0.00 3.85
35 36 0.181350 GCAGATCCGGTTCAATCCCT 59.819 55.000 14.83 0.00 0.00 4.20
36 37 1.416401 GCAGATCCGGTTCAATCCCTA 59.584 52.381 14.83 0.00 0.00 3.53
37 38 2.807108 GCAGATCCGGTTCAATCCCTAC 60.807 54.545 14.83 0.00 0.00 3.18
38 39 2.700897 CAGATCCGGTTCAATCCCTACT 59.299 50.000 14.83 0.00 0.00 2.57
39 40 3.134804 CAGATCCGGTTCAATCCCTACTT 59.865 47.826 14.83 0.00 0.00 2.24
40 41 3.388350 AGATCCGGTTCAATCCCTACTTC 59.612 47.826 14.83 0.00 0.00 3.01
41 42 1.479323 TCCGGTTCAATCCCTACTTCG 59.521 52.381 0.00 0.00 0.00 3.79
42 43 1.206371 CCGGTTCAATCCCTACTTCGT 59.794 52.381 0.00 0.00 0.00 3.85
43 44 2.537401 CGGTTCAATCCCTACTTCGTC 58.463 52.381 0.00 0.00 0.00 4.20
44 45 2.165845 CGGTTCAATCCCTACTTCGTCT 59.834 50.000 0.00 0.00 0.00 4.18
45 46 3.368116 CGGTTCAATCCCTACTTCGTCTT 60.368 47.826 0.00 0.00 0.00 3.01
46 47 4.576879 GGTTCAATCCCTACTTCGTCTTT 58.423 43.478 0.00 0.00 0.00 2.52
47 48 4.392138 GGTTCAATCCCTACTTCGTCTTTG 59.608 45.833 0.00 0.00 0.00 2.77
48 49 4.884668 TCAATCCCTACTTCGTCTTTGT 57.115 40.909 0.00 0.00 0.00 2.83
49 50 4.817517 TCAATCCCTACTTCGTCTTTGTC 58.182 43.478 0.00 0.00 0.00 3.18
50 51 4.527038 TCAATCCCTACTTCGTCTTTGTCT 59.473 41.667 0.00 0.00 0.00 3.41
51 52 5.713389 TCAATCCCTACTTCGTCTTTGTCTA 59.287 40.000 0.00 0.00 0.00 2.59
52 53 5.838531 ATCCCTACTTCGTCTTTGTCTAG 57.161 43.478 0.00 0.00 0.00 2.43
53 54 4.660168 TCCCTACTTCGTCTTTGTCTAGT 58.340 43.478 0.00 0.00 0.00 2.57
54 55 5.809001 TCCCTACTTCGTCTTTGTCTAGTA 58.191 41.667 0.00 0.00 0.00 1.82
55 56 5.645497 TCCCTACTTCGTCTTTGTCTAGTAC 59.355 44.000 0.00 0.00 0.00 2.73
56 57 5.647225 CCCTACTTCGTCTTTGTCTAGTACT 59.353 44.000 0.00 0.00 0.00 2.73
57 58 6.150809 CCCTACTTCGTCTTTGTCTAGTACTT 59.849 42.308 0.00 0.00 0.00 2.24
58 59 7.242783 CCTACTTCGTCTTTGTCTAGTACTTC 58.757 42.308 0.00 0.00 0.00 3.01
59 60 6.011476 ACTTCGTCTTTGTCTAGTACTTCC 57.989 41.667 0.00 0.00 0.00 3.46
60 61 4.675190 TCGTCTTTGTCTAGTACTTCCG 57.325 45.455 0.00 0.00 0.00 4.30
61 62 3.120060 TCGTCTTTGTCTAGTACTTCCGC 60.120 47.826 0.00 0.00 0.00 5.54
62 63 3.169733 GTCTTTGTCTAGTACTTCCGCG 58.830 50.000 0.00 0.00 0.00 6.46
63 64 3.076621 TCTTTGTCTAGTACTTCCGCGA 58.923 45.455 8.23 0.00 0.00 5.87
64 65 3.126514 TCTTTGTCTAGTACTTCCGCGAG 59.873 47.826 8.23 0.00 0.00 5.03
65 66 2.391616 TGTCTAGTACTTCCGCGAGA 57.608 50.000 8.23 0.00 0.00 4.04
66 67 2.703416 TGTCTAGTACTTCCGCGAGAA 58.297 47.619 8.23 8.88 0.00 2.87
73 74 2.358247 TTCCGCGAGAAGGGTTGC 60.358 61.111 8.23 0.00 0.00 4.17
74 75 3.171828 TTCCGCGAGAAGGGTTGCA 62.172 57.895 8.23 0.00 0.00 4.08
75 76 2.668185 TTCCGCGAGAAGGGTTGCAA 62.668 55.000 8.23 0.00 0.00 4.08
76 77 2.680913 CCGCGAGAAGGGTTGCAAG 61.681 63.158 8.23 0.00 0.00 4.01
77 78 2.680913 CGCGAGAAGGGTTGCAAGG 61.681 63.158 0.00 0.00 0.00 3.61
78 79 2.335712 GCGAGAAGGGTTGCAAGGG 61.336 63.158 0.00 0.00 0.00 3.95
79 80 1.073199 CGAGAAGGGTTGCAAGGGT 59.927 57.895 0.00 0.00 0.00 4.34
80 81 1.237285 CGAGAAGGGTTGCAAGGGTG 61.237 60.000 0.00 0.00 0.00 4.61
90 91 4.740822 CAAGGGTGCCGGGAAGGG 62.741 72.222 2.18 0.00 41.48 3.95
107 108 3.818787 GCAAGGCAGCCGTGGATG 61.819 66.667 26.50 13.26 33.72 3.51
108 109 2.046023 CAAGGCAGCCGTGGATGA 60.046 61.111 19.07 0.00 32.62 2.92
109 110 1.452651 CAAGGCAGCCGTGGATGAT 60.453 57.895 19.07 0.00 32.62 2.45
110 111 1.153086 AAGGCAGCCGTGGATGATC 60.153 57.895 8.61 0.00 32.62 2.92
111 112 1.630126 AAGGCAGCCGTGGATGATCT 61.630 55.000 8.61 1.55 32.62 2.75
112 113 1.596477 GGCAGCCGTGGATGATCTC 60.596 63.158 8.61 0.00 32.62 2.75
113 114 1.596477 GCAGCCGTGGATGATCTCC 60.596 63.158 8.61 0.00 45.19 3.71
114 115 1.070445 CAGCCGTGGATGATCTCCC 59.930 63.158 0.00 3.52 44.23 4.30
115 116 2.143419 AGCCGTGGATGATCTCCCC 61.143 63.158 8.25 1.35 44.23 4.81
116 117 3.151906 CCGTGGATGATCTCCCCC 58.848 66.667 8.25 0.00 44.23 5.40
117 118 1.766059 CCGTGGATGATCTCCCCCA 60.766 63.158 8.25 1.51 44.23 4.96
118 119 1.130054 CCGTGGATGATCTCCCCCAT 61.130 60.000 8.25 0.00 44.23 4.00
119 120 1.644509 CGTGGATGATCTCCCCCATA 58.355 55.000 8.25 0.00 44.23 2.74
120 121 1.552337 CGTGGATGATCTCCCCCATAG 59.448 57.143 8.25 0.58 44.23 2.23
121 122 1.280421 GTGGATGATCTCCCCCATAGC 59.720 57.143 8.25 0.00 44.23 2.97
122 123 0.915364 GGATGATCTCCCCCATAGCC 59.085 60.000 0.00 0.00 38.19 3.93
123 124 1.661463 GATGATCTCCCCCATAGCCA 58.339 55.000 0.00 0.00 0.00 4.75
124 125 2.203584 GATGATCTCCCCCATAGCCAT 58.796 52.381 0.00 0.00 0.00 4.40
125 126 3.387962 GATGATCTCCCCCATAGCCATA 58.612 50.000 0.00 0.00 0.00 2.74
126 127 3.290039 TGATCTCCCCCATAGCCATAA 57.710 47.619 0.00 0.00 0.00 1.90
127 128 3.608067 TGATCTCCCCCATAGCCATAAA 58.392 45.455 0.00 0.00 0.00 1.40
128 129 4.186320 TGATCTCCCCCATAGCCATAAAT 58.814 43.478 0.00 0.00 0.00 1.40
129 130 4.018141 TGATCTCCCCCATAGCCATAAATG 60.018 45.833 0.00 0.00 0.00 2.32
130 131 3.335748 TCTCCCCCATAGCCATAAATGT 58.664 45.455 0.00 0.00 0.00 2.71
131 132 3.330701 TCTCCCCCATAGCCATAAATGTC 59.669 47.826 0.00 0.00 0.00 3.06
132 133 3.059853 TCCCCCATAGCCATAAATGTCA 58.940 45.455 0.00 0.00 0.00 3.58
133 134 3.465210 TCCCCCATAGCCATAAATGTCAA 59.535 43.478 0.00 0.00 0.00 3.18
134 135 3.828451 CCCCCATAGCCATAAATGTCAAG 59.172 47.826 0.00 0.00 0.00 3.02
135 136 4.473444 CCCCATAGCCATAAATGTCAAGT 58.527 43.478 0.00 0.00 0.00 3.16
136 137 4.895297 CCCCATAGCCATAAATGTCAAGTT 59.105 41.667 0.00 0.00 0.00 2.66
137 138 5.363580 CCCCATAGCCATAAATGTCAAGTTT 59.636 40.000 0.00 0.00 0.00 2.66
138 139 6.127083 CCCCATAGCCATAAATGTCAAGTTTT 60.127 38.462 0.00 0.00 0.00 2.43
139 140 6.757947 CCCATAGCCATAAATGTCAAGTTTTG 59.242 38.462 0.00 0.00 0.00 2.44
140 141 6.757947 CCATAGCCATAAATGTCAAGTTTTGG 59.242 38.462 5.32 5.32 0.00 3.28
141 142 5.806654 AGCCATAAATGTCAAGTTTTGGT 57.193 34.783 9.40 0.00 0.00 3.67
142 143 6.909550 AGCCATAAATGTCAAGTTTTGGTA 57.090 33.333 9.40 0.00 0.00 3.25
143 144 6.924111 AGCCATAAATGTCAAGTTTTGGTAG 58.076 36.000 9.40 0.00 0.00 3.18
144 145 6.493458 AGCCATAAATGTCAAGTTTTGGTAGT 59.507 34.615 9.40 0.00 0.00 2.73
145 146 6.806739 GCCATAAATGTCAAGTTTTGGTAGTC 59.193 38.462 9.40 0.00 0.00 2.59
146 147 7.312899 CCATAAATGTCAAGTTTTGGTAGTCC 58.687 38.462 2.68 0.00 0.00 3.85
147 148 5.432885 AAATGTCAAGTTTTGGTAGTCCG 57.567 39.130 0.00 0.00 36.30 4.79
148 149 3.823281 TGTCAAGTTTTGGTAGTCCGA 57.177 42.857 0.00 0.00 36.30 4.55
152 153 4.151867 GTCAAGTTTTGGTAGTCCGATGAC 59.848 45.833 0.00 0.00 42.09 3.06
202 203 2.160219 GGTCGTGTTCCGGGTTTTATTC 59.840 50.000 0.00 0.00 37.11 1.75
287 290 0.727970 CACGAACCGACAAAACCACA 59.272 50.000 0.00 0.00 0.00 4.17
499 509 4.421479 CTGCCCTCGTTCGTCGCT 62.421 66.667 0.00 0.00 39.67 4.93
535 572 4.161295 CCGCCGCTCATCCCTTCA 62.161 66.667 0.00 0.00 0.00 3.02
660 718 0.181114 CCGCCTTCTTGGATCCATCA 59.819 55.000 17.06 1.59 38.35 3.07
674 739 1.218047 CATCACGTGGATCCACCGT 59.782 57.895 34.05 29.79 43.49 4.83
677 742 2.987547 ACGTGGATCCACCGTCGT 60.988 61.111 34.05 26.51 43.49 4.34
1019 1084 3.483869 GCTGGATCCCGGGAAGCT 61.484 66.667 30.44 16.12 0.00 3.74
1117 1182 4.319549 CCTCGGTTACTTGCTCTGTTTTTC 60.320 45.833 0.00 0.00 0.00 2.29
1122 1188 3.692791 ACTTGCTCTGTTTTTCGTTCC 57.307 42.857 0.00 0.00 0.00 3.62
1284 1396 7.626842 CAAGCAAAATTGAATGGTCCAAACCA 61.627 38.462 0.00 0.00 45.12 3.67
1498 1610 6.101588 TCTCAATTCTGTATTGGGATGGATGA 59.898 38.462 5.58 0.00 46.44 2.92
1742 1854 5.882557 ACGAATTGGACTGAGAAATGCTAAT 59.117 36.000 0.00 0.00 0.00 1.73
2386 2501 0.036671 AACGGATCCTTGGTTCGGAC 60.037 55.000 10.75 0.00 32.41 4.79
2692 2808 3.499338 TCAATTGAGGGCACTGTGATTT 58.501 40.909 12.86 0.00 0.00 2.17
3037 3153 5.111989 GCTACATAGTCTGTTCATCTTGCA 58.888 41.667 0.00 0.00 39.39 4.08
3139 3255 4.446234 CGATTTGCGTCGGAAATATTCTC 58.554 43.478 22.42 11.26 37.94 2.87
3144 3260 4.607955 TGCGTCGGAAATATTCTCACTAG 58.392 43.478 0.00 0.00 0.00 2.57
3165 3281 5.649782 AGTTGCATGAATTTTAGACCCTG 57.350 39.130 0.00 0.00 0.00 4.45
3203 3319 5.049167 TGCATTTTGTGTTGAGAAACATCC 58.951 37.500 0.00 0.00 34.86 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.815569 GATCTGCTCGTCGCCGGAG 62.816 68.421 5.05 0.00 38.05 4.63
5 6 3.889044 GATCTGCTCGTCGCCGGA 61.889 66.667 5.05 0.00 38.05 5.14
6 7 4.933064 GGATCTGCTCGTCGCCGG 62.933 72.222 0.00 0.00 38.05 6.13
8 9 4.933064 CCGGATCTGCTCGTCGCC 62.933 72.222 0.00 0.00 38.05 5.54
9 10 3.701604 AACCGGATCTGCTCGTCGC 62.702 63.158 9.46 0.00 39.77 5.19
10 11 1.586564 GAACCGGATCTGCTCGTCG 60.587 63.158 9.46 0.00 0.00 5.12
11 12 0.108804 TTGAACCGGATCTGCTCGTC 60.109 55.000 9.46 0.00 0.00 4.20
12 13 0.537188 ATTGAACCGGATCTGCTCGT 59.463 50.000 9.46 0.00 0.00 4.18
13 14 1.212616 GATTGAACCGGATCTGCTCG 58.787 55.000 9.46 0.00 0.00 5.03
14 15 1.587547 GGATTGAACCGGATCTGCTC 58.412 55.000 9.46 4.32 0.00 4.26
15 16 0.181350 GGGATTGAACCGGATCTGCT 59.819 55.000 9.46 0.00 0.00 4.24
16 17 0.181350 AGGGATTGAACCGGATCTGC 59.819 55.000 9.46 0.00 0.00 4.26
17 18 2.700897 AGTAGGGATTGAACCGGATCTG 59.299 50.000 9.46 0.00 0.00 2.90
18 19 3.047695 AGTAGGGATTGAACCGGATCT 57.952 47.619 9.46 0.00 0.00 2.75
19 20 3.729966 GAAGTAGGGATTGAACCGGATC 58.270 50.000 9.46 6.62 0.00 3.36
20 21 2.102588 CGAAGTAGGGATTGAACCGGAT 59.897 50.000 9.46 0.00 0.00 4.18
21 22 1.479323 CGAAGTAGGGATTGAACCGGA 59.521 52.381 9.46 0.00 0.00 5.14
22 23 1.206371 ACGAAGTAGGGATTGAACCGG 59.794 52.381 0.00 0.00 41.94 5.28
23 24 2.667473 ACGAAGTAGGGATTGAACCG 57.333 50.000 0.00 0.00 41.94 4.44
37 38 5.087397 CGGAAGTACTAGACAAAGACGAAG 58.913 45.833 0.00 0.00 0.00 3.79
38 39 4.614535 GCGGAAGTACTAGACAAAGACGAA 60.615 45.833 0.00 0.00 0.00 3.85
39 40 3.120060 GCGGAAGTACTAGACAAAGACGA 60.120 47.826 0.00 0.00 0.00 4.20
40 41 3.169733 GCGGAAGTACTAGACAAAGACG 58.830 50.000 0.00 0.00 0.00 4.18
41 42 3.120060 TCGCGGAAGTACTAGACAAAGAC 60.120 47.826 6.13 0.00 0.00 3.01
42 43 3.076621 TCGCGGAAGTACTAGACAAAGA 58.923 45.455 6.13 0.00 0.00 2.52
43 44 3.126514 TCTCGCGGAAGTACTAGACAAAG 59.873 47.826 6.13 0.00 0.00 2.77
44 45 3.076621 TCTCGCGGAAGTACTAGACAAA 58.923 45.455 6.13 0.00 0.00 2.83
45 46 2.703416 TCTCGCGGAAGTACTAGACAA 58.297 47.619 6.13 0.00 0.00 3.18
46 47 2.391616 TCTCGCGGAAGTACTAGACA 57.608 50.000 6.13 0.00 0.00 3.41
47 48 3.322230 CTTCTCGCGGAAGTACTAGAC 57.678 52.381 21.80 0.00 44.59 2.59
56 57 2.358247 GCAACCCTTCTCGCGGAA 60.358 61.111 6.13 8.10 0.00 4.30
57 58 3.171828 TTGCAACCCTTCTCGCGGA 62.172 57.895 6.13 0.00 0.00 5.54
58 59 2.668212 TTGCAACCCTTCTCGCGG 60.668 61.111 6.13 0.00 0.00 6.46
59 60 2.680913 CCTTGCAACCCTTCTCGCG 61.681 63.158 0.00 0.00 0.00 5.87
60 61 2.335712 CCCTTGCAACCCTTCTCGC 61.336 63.158 0.00 0.00 0.00 5.03
61 62 1.073199 ACCCTTGCAACCCTTCTCG 59.927 57.895 0.00 0.00 0.00 4.04
62 63 2.646121 CACCCTTGCAACCCTTCTC 58.354 57.895 0.00 0.00 0.00 2.87
63 64 4.929807 CACCCTTGCAACCCTTCT 57.070 55.556 0.00 0.00 0.00 2.85
73 74 4.740822 CCCTTCCCGGCACCCTTG 62.741 72.222 0.00 0.00 0.00 3.61
90 91 3.818787 CATCCACGGCTGCCTTGC 61.819 66.667 18.89 0.00 0.00 4.01
91 92 1.442526 GATCATCCACGGCTGCCTTG 61.443 60.000 17.52 17.52 0.00 3.61
92 93 1.153086 GATCATCCACGGCTGCCTT 60.153 57.895 17.92 4.00 0.00 4.35
93 94 2.037620 GAGATCATCCACGGCTGCCT 62.038 60.000 17.92 0.55 0.00 4.75
94 95 1.596477 GAGATCATCCACGGCTGCC 60.596 63.158 9.11 9.11 0.00 4.85
95 96 4.040068 GAGATCATCCACGGCTGC 57.960 61.111 0.00 0.00 0.00 5.25
104 105 1.661463 TGGCTATGGGGGAGATCATC 58.339 55.000 0.00 0.00 0.00 2.92
105 106 2.373117 ATGGCTATGGGGGAGATCAT 57.627 50.000 0.00 0.00 0.00 2.45
106 107 3.290039 TTATGGCTATGGGGGAGATCA 57.710 47.619 0.00 0.00 0.00 2.92
107 108 4.018050 ACATTTATGGCTATGGGGGAGATC 60.018 45.833 0.00 0.00 0.00 2.75
108 109 3.925370 ACATTTATGGCTATGGGGGAGAT 59.075 43.478 0.00 0.00 0.00 2.75
109 110 3.330701 GACATTTATGGCTATGGGGGAGA 59.669 47.826 0.00 0.00 31.49 3.71
110 111 3.074390 TGACATTTATGGCTATGGGGGAG 59.926 47.826 0.00 0.00 36.54 4.30
111 112 3.059853 TGACATTTATGGCTATGGGGGA 58.940 45.455 0.00 0.00 36.54 4.81
112 113 3.524095 TGACATTTATGGCTATGGGGG 57.476 47.619 0.00 0.00 36.54 5.40
113 114 4.473444 ACTTGACATTTATGGCTATGGGG 58.527 43.478 0.00 0.00 36.54 4.96
114 115 6.469782 AAACTTGACATTTATGGCTATGGG 57.530 37.500 0.00 0.00 36.54 4.00
115 116 6.757947 CCAAAACTTGACATTTATGGCTATGG 59.242 38.462 0.00 0.00 36.54 2.74
116 117 7.322664 ACCAAAACTTGACATTTATGGCTATG 58.677 34.615 0.00 0.00 36.54 2.23
117 118 7.480760 ACCAAAACTTGACATTTATGGCTAT 57.519 32.000 0.00 0.00 36.54 2.97
118 119 6.909550 ACCAAAACTTGACATTTATGGCTA 57.090 33.333 0.00 0.00 36.54 3.93
119 120 5.806654 ACCAAAACTTGACATTTATGGCT 57.193 34.783 0.00 0.00 36.54 4.75
120 121 6.687604 ACTACCAAAACTTGACATTTATGGC 58.312 36.000 0.00 0.00 35.98 4.40
121 122 7.312899 GGACTACCAAAACTTGACATTTATGG 58.687 38.462 0.00 0.00 35.97 2.74
122 123 7.021196 CGGACTACCAAAACTTGACATTTATG 58.979 38.462 0.00 0.00 35.59 1.90
123 124 6.938030 TCGGACTACCAAAACTTGACATTTAT 59.062 34.615 0.00 0.00 35.59 1.40
124 125 6.289834 TCGGACTACCAAAACTTGACATTTA 58.710 36.000 0.00 0.00 35.59 1.40
125 126 5.127491 TCGGACTACCAAAACTTGACATTT 58.873 37.500 0.00 0.00 35.59 2.32
126 127 4.710324 TCGGACTACCAAAACTTGACATT 58.290 39.130 0.00 0.00 35.59 2.71
127 128 4.345859 TCGGACTACCAAAACTTGACAT 57.654 40.909 0.00 0.00 35.59 3.06
128 129 3.823281 TCGGACTACCAAAACTTGACA 57.177 42.857 0.00 0.00 35.59 3.58
129 130 4.151867 GTCATCGGACTACCAAAACTTGAC 59.848 45.833 0.00 0.00 40.99 3.18
130 131 4.202274 TGTCATCGGACTACCAAAACTTGA 60.202 41.667 0.00 0.00 44.61 3.02
131 132 4.062293 TGTCATCGGACTACCAAAACTTG 58.938 43.478 0.00 0.00 44.61 3.16
132 133 4.345859 TGTCATCGGACTACCAAAACTT 57.654 40.909 0.00 0.00 44.61 2.66
133 134 4.223032 AGATGTCATCGGACTACCAAAACT 59.777 41.667 7.18 0.00 44.61 2.66
134 135 4.504858 AGATGTCATCGGACTACCAAAAC 58.495 43.478 7.18 0.00 44.61 2.43
135 136 4.466370 AGAGATGTCATCGGACTACCAAAA 59.534 41.667 7.18 0.00 44.61 2.44
136 137 4.023980 AGAGATGTCATCGGACTACCAAA 58.976 43.478 7.18 0.00 44.61 3.28
137 138 3.632333 AGAGATGTCATCGGACTACCAA 58.368 45.455 7.18 0.00 44.61 3.67
138 139 3.298686 AGAGATGTCATCGGACTACCA 57.701 47.619 7.18 0.00 44.61 3.25
139 140 4.391155 AGTAGAGATGTCATCGGACTACC 58.609 47.826 25.66 16.68 44.61 3.18
140 141 4.453136 GGAGTAGAGATGTCATCGGACTAC 59.547 50.000 23.94 23.94 44.61 2.73
141 142 4.348461 AGGAGTAGAGATGTCATCGGACTA 59.652 45.833 13.85 12.32 44.61 2.59
142 143 3.137544 AGGAGTAGAGATGTCATCGGACT 59.862 47.826 13.79 13.79 44.61 3.85
143 144 3.482436 AGGAGTAGAGATGTCATCGGAC 58.518 50.000 7.18 6.88 44.57 4.79
144 145 3.866703 AGGAGTAGAGATGTCATCGGA 57.133 47.619 7.18 0.00 0.00 4.55
145 146 5.475220 ACATTAGGAGTAGAGATGTCATCGG 59.525 44.000 7.18 0.00 0.00 4.18
146 147 6.429692 AGACATTAGGAGTAGAGATGTCATCG 59.570 42.308 14.80 0.00 45.51 3.84
147 148 7.446931 TGAGACATTAGGAGTAGAGATGTCATC 59.553 40.741 14.80 4.52 45.51 2.92
148 149 7.293828 TGAGACATTAGGAGTAGAGATGTCAT 58.706 38.462 14.80 0.00 45.51 3.06
152 153 7.424803 CAACTGAGACATTAGGAGTAGAGATG 58.575 42.308 0.00 0.00 0.00 2.90
202 203 2.718073 CCGGGTAAGGTGGGACGAG 61.718 68.421 0.00 0.00 0.00 4.18
241 242 1.684734 GCGGGAGGTGGGAGAAGTA 60.685 63.158 0.00 0.00 0.00 2.24
242 243 3.003763 GCGGGAGGTGGGAGAAGT 61.004 66.667 0.00 0.00 0.00 3.01
243 244 2.685380 AGCGGGAGGTGGGAGAAG 60.685 66.667 0.00 0.00 40.33 2.85
287 290 1.043673 GCTGGTGGAGGACTCGGTAT 61.044 60.000 0.00 0.00 0.00 2.73
499 509 2.272146 GGCGAAGGGATGAAGGCA 59.728 61.111 0.00 0.00 0.00 4.75
781 846 1.825341 CTGGATGAGGTCGATGCCA 59.175 57.895 0.00 0.00 0.00 4.92
832 897 4.082523 CACGACCAGGTGGCGGAT 62.083 66.667 0.00 0.00 38.43 4.18
928 993 3.509137 AACCTCTCGCGCAACCGAA 62.509 57.895 8.75 0.00 36.72 4.30
933 998 2.390599 GCATCAACCTCTCGCGCAA 61.391 57.895 8.75 0.00 0.00 4.85
1019 1084 2.080336 CTTCTTGGGGGTGAAGGCCA 62.080 60.000 5.01 0.00 36.84 5.36
1117 1182 7.041721 AGTGGTACATATATATGCATGGAACG 58.958 38.462 20.46 0.00 44.52 3.95
1122 1188 8.037166 ACACAGAGTGGTACATATATATGCATG 58.963 37.037 20.46 9.77 44.52 4.06
1498 1610 6.932400 TCGACAAAACAATGTATCTACCTTGT 59.068 34.615 5.51 5.51 43.59 3.16
1572 1684 3.342627 CCTTTGGTCGCGACGCAA 61.343 61.111 30.99 29.17 0.00 4.85
1603 1715 2.527624 TGCAGTGAGTCCCTGGCT 60.528 61.111 4.71 0.00 0.00 4.75
1607 1719 1.071385 CTTCAACTGCAGTGAGTCCCT 59.929 52.381 22.49 0.00 0.00 4.20
1742 1854 2.023984 TGCATGGTCTTCTCCTCCTCTA 60.024 50.000 0.00 0.00 0.00 2.43
2223 2338 2.449137 CTCCAAATCAGGGGAGCATT 57.551 50.000 0.00 0.00 43.80 3.56
2318 2433 0.251564 TGCGTCCATCCCCAAACAAT 60.252 50.000 0.00 0.00 0.00 2.71
2692 2808 9.131791 TCACTTACATGATACATGTAGCTAGAA 57.868 33.333 20.91 9.57 36.09 2.10
3037 3153 4.657814 TTGGTTTCTCCTAAGAAGGCAT 57.342 40.909 0.00 0.00 42.36 4.40
3139 3255 6.375455 AGGGTCTAAAATTCATGCAACTAGTG 59.625 38.462 0.00 0.00 0.00 2.74
3144 3260 4.082026 AGCAGGGTCTAAAATTCATGCAAC 60.082 41.667 0.00 0.00 34.93 4.17


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

AutoCloner maintained by Alex Coulton.