Multiple sequence alignment - TraesCS5A01G209000

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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 TraesCS5A01G209000 chr5A 100.000 3454 0 0 1 3454 422075615 422072162 0.000000e+00 6379
1 TraesCS5A01G209000 chr5A 99.359 312 2 0 620 931 547620678 547620367 1.800000e-157 566
2 TraesCS5A01G209000 chr4B 98.595 3273 20 4 207 3454 439195476 439198747 0.000000e+00 5766
3 TraesCS5A01G209000 chr4A 98.594 3272 19 4 208 3454 548526247 548522978 0.000000e+00 5762
4 TraesCS5A01G209000 chr6A 98.533 3272 23 3 208 3454 466092189 466095460 0.000000e+00 5753
5 TraesCS5A01G209000 chr6B 97.254 3278 59 7 205 3454 698114880 698118154 0.000000e+00 5526
6 TraesCS5A01G209000 chr6B 96.548 3273 73 6 208 3454 458495685 458498943 0.000000e+00 5382
7 TraesCS5A01G209000 chr6B 99.010 2526 17 2 936 3454 325035064 325037588 0.000000e+00 4519
8 TraesCS5A01G209000 chr6B 93.411 774 15 6 208 947 325034348 325035119 0.000000e+00 1114
9 TraesCS5A01G209000 chr1A 99.179 2558 14 1 904 3454 80308210 80305653 0.000000e+00 4601
10 TraesCS5A01G209000 chr7A 99.248 2526 12 1 936 3454 176257263 176259788 0.000000e+00 4553
11 TraesCS5A01G209000 chr7A 96.179 759 10 3 207 947 176256561 176257318 0.000000e+00 1223
12 TraesCS5A01G209000 chr2A 99.169 2526 14 1 936 3454 642923998 642921473 0.000000e+00 4542
13 TraesCS5A01G209000 chr2A 95.151 763 16 5 207 950 642924700 642923940 0.000000e+00 1184
14 TraesCS5A01G209000 chr2A 92.931 778 19 6 204 947 351419575 351420350 0.000000e+00 1099
15 TraesCS5A01G209000 chr2A 98.196 388 7 0 208 595 351178741 351178354 0.000000e+00 678
16 TraesCS5A01G209000 chr2B 99.010 2526 17 2 936 3454 669227501 669230025 0.000000e+00 4519
17 TraesCS5A01G209000 chr5B 96.452 761 8 3 205 947 161074843 161075602 0.000000e+00 1238
18 TraesCS5A01G209000 chr5B 93.839 211 9 2 1 207 376335918 376335708 7.200000e-82 315
19 TraesCS5A01G209000 chr5D 93.333 210 8 3 2 207 324588363 324588156 4.330000e-79 305


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 TraesCS5A01G209000 chr5A 422072162 422075615 3453 True 6379.0 6379 100.0000 1 3454 1 chr5A.!!$R1 3453
1 TraesCS5A01G209000 chr4B 439195476 439198747 3271 False 5766.0 5766 98.5950 207 3454 1 chr4B.!!$F1 3247
2 TraesCS5A01G209000 chr4A 548522978 548526247 3269 True 5762.0 5762 98.5940 208 3454 1 chr4A.!!$R1 3246
3 TraesCS5A01G209000 chr6A 466092189 466095460 3271 False 5753.0 5753 98.5330 208 3454 1 chr6A.!!$F1 3246
4 TraesCS5A01G209000 chr6B 698114880 698118154 3274 False 5526.0 5526 97.2540 205 3454 1 chr6B.!!$F2 3249
5 TraesCS5A01G209000 chr6B 458495685 458498943 3258 False 5382.0 5382 96.5480 208 3454 1 chr6B.!!$F1 3246
6 TraesCS5A01G209000 chr6B 325034348 325037588 3240 False 2816.5 4519 96.2105 208 3454 2 chr6B.!!$F3 3246
7 TraesCS5A01G209000 chr1A 80305653 80308210 2557 True 4601.0 4601 99.1790 904 3454 1 chr1A.!!$R1 2550
8 TraesCS5A01G209000 chr7A 176256561 176259788 3227 False 2888.0 4553 97.7135 207 3454 2 chr7A.!!$F1 3247
9 TraesCS5A01G209000 chr2A 642921473 642924700 3227 True 2863.0 4542 97.1600 207 3454 2 chr2A.!!$R2 3247
10 TraesCS5A01G209000 chr2A 351419575 351420350 775 False 1099.0 1099 92.9310 204 947 1 chr2A.!!$F1 743
11 TraesCS5A01G209000 chr2B 669227501 669230025 2524 False 4519.0 4519 99.0100 936 3454 1 chr2B.!!$F1 2518
12 TraesCS5A01G209000 chr5B 161074843 161075602 759 False 1238.0 1238 96.4520 205 947 1 chr5B.!!$F1 742

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
133 134 0.106268 TGTTGACCCACAAGCCATGT 60.106 50.0 0.0 0.0 45.34 3.21 F
134 135 0.598065 GTTGACCCACAAGCCATGTC 59.402 55.0 0.0 0.0 41.46 3.06 F
1724 1872 0.107456 CGCCTATCCCTTGAGCATGT 59.893 55.0 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1872 2.875672 GCTGGCACAACCTTCATGTCTA 60.876 50.000 0.0 0.0 38.7 2.59 R
2399 2547 1.344438 TCTGTCGCACCTGAATCAAGT 59.656 47.619 0.0 0.0 0.0 3.16 R
2934 3083 0.686224 CAGCCATGAAAGCCCCAAAA 59.314 50.000 0.0 0.0 0.0 2.44 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
29 30 3.411351 GTCGTCAACGGCGCACAT 61.411 61.111 10.83 0.00 40.29 3.21
30 31 3.109547 TCGTCAACGGCGCACATC 61.110 61.111 10.83 0.00 40.29 3.06
31 32 3.112075 CGTCAACGGCGCACATCT 61.112 61.111 10.83 0.00 35.37 2.90
32 33 2.778679 GTCAACGGCGCACATCTC 59.221 61.111 10.83 0.00 0.00 2.75
33 34 2.434185 TCAACGGCGCACATCTCC 60.434 61.111 10.83 0.00 0.00 3.71
34 35 3.499737 CAACGGCGCACATCTCCC 61.500 66.667 10.83 0.00 0.00 4.30
35 36 3.706373 AACGGCGCACATCTCCCT 61.706 61.111 10.83 0.00 0.00 4.20
36 37 3.958147 AACGGCGCACATCTCCCTG 62.958 63.158 10.83 0.00 0.00 4.45
37 38 4.147449 CGGCGCACATCTCCCTGA 62.147 66.667 10.83 0.00 0.00 3.86
38 39 2.507944 GGCGCACATCTCCCTGAT 59.492 61.111 10.83 0.00 35.40 2.90
45 46 2.704108 CATCTCCCTGATGCTGTGC 58.296 57.895 0.00 0.00 44.96 4.57
46 47 0.107361 CATCTCCCTGATGCTGTGCA 60.107 55.000 0.00 0.00 44.96 4.57
58 59 3.835378 TGCTGTGCATAGACAATTGTG 57.165 42.857 17.58 2.29 31.71 3.33
59 60 2.488937 TGCTGTGCATAGACAATTGTGG 59.511 45.455 17.58 3.87 31.71 4.17
60 61 2.489329 GCTGTGCATAGACAATTGTGGT 59.511 45.455 17.58 5.52 0.00 4.16
61 62 3.671433 GCTGTGCATAGACAATTGTGGTG 60.671 47.826 17.58 12.28 0.00 4.17
62 63 2.228582 TGTGCATAGACAATTGTGGTGC 59.771 45.455 17.58 20.95 0.00 5.01
63 64 2.489329 GTGCATAGACAATTGTGGTGCT 59.511 45.455 26.44 17.07 31.63 4.40
64 65 2.749076 TGCATAGACAATTGTGGTGCTC 59.251 45.455 26.44 11.16 31.63 4.26
65 66 2.098117 GCATAGACAATTGTGGTGCTCC 59.902 50.000 17.58 0.00 0.00 4.70
66 67 3.346315 CATAGACAATTGTGGTGCTCCA 58.654 45.455 17.58 2.64 42.05 3.86
67 68 2.363306 AGACAATTGTGGTGCTCCAA 57.637 45.000 17.58 0.00 46.15 3.53
68 69 2.880443 AGACAATTGTGGTGCTCCAAT 58.120 42.857 17.58 0.00 46.15 3.16
69 70 4.032960 AGACAATTGTGGTGCTCCAATA 57.967 40.909 17.58 0.63 46.15 1.90
70 71 4.603131 AGACAATTGTGGTGCTCCAATAT 58.397 39.130 17.58 3.17 46.15 1.28
71 72 4.641989 AGACAATTGTGGTGCTCCAATATC 59.358 41.667 17.58 2.91 46.15 1.63
72 73 3.701040 ACAATTGTGGTGCTCCAATATCC 59.299 43.478 11.07 0.00 46.15 2.59
73 74 3.668141 ATTGTGGTGCTCCAATATCCA 57.332 42.857 9.53 0.00 46.15 3.41
74 75 2.418368 TGTGGTGCTCCAATATCCAC 57.582 50.000 9.53 5.80 46.15 4.02
75 76 2.418368 GTGGTGCTCCAATATCCACA 57.582 50.000 9.53 0.00 46.15 4.17
76 77 2.292267 GTGGTGCTCCAATATCCACAG 58.708 52.381 9.53 0.00 46.15 3.66
77 78 1.915489 TGGTGCTCCAATATCCACAGT 59.085 47.619 4.68 0.00 41.25 3.55
78 79 3.111484 TGGTGCTCCAATATCCACAGTA 58.889 45.455 4.68 0.00 41.25 2.74
79 80 3.118408 TGGTGCTCCAATATCCACAGTAC 60.118 47.826 4.68 0.00 41.25 2.73
80 81 3.123804 GTGCTCCAATATCCACAGTACG 58.876 50.000 0.00 0.00 0.00 3.67
81 82 3.028130 TGCTCCAATATCCACAGTACGA 58.972 45.455 0.00 0.00 0.00 3.43
82 83 3.449377 TGCTCCAATATCCACAGTACGAA 59.551 43.478 0.00 0.00 0.00 3.85
83 84 4.100963 TGCTCCAATATCCACAGTACGAAT 59.899 41.667 0.00 0.00 0.00 3.34
84 85 5.303333 TGCTCCAATATCCACAGTACGAATA 59.697 40.000 0.00 0.00 0.00 1.75
85 86 5.634020 GCTCCAATATCCACAGTACGAATAC 59.366 44.000 0.00 0.00 0.00 1.89
86 87 6.092955 TCCAATATCCACAGTACGAATACC 57.907 41.667 0.00 0.00 30.88 2.73
87 88 5.599242 TCCAATATCCACAGTACGAATACCA 59.401 40.000 0.00 0.00 30.88 3.25
88 89 6.098552 TCCAATATCCACAGTACGAATACCAA 59.901 38.462 0.00 0.00 30.88 3.67
89 90 6.202188 CCAATATCCACAGTACGAATACCAAC 59.798 42.308 0.00 0.00 30.88 3.77
90 91 4.811969 ATCCACAGTACGAATACCAACA 57.188 40.909 0.00 0.00 30.88 3.33
91 92 3.916761 TCCACAGTACGAATACCAACAC 58.083 45.455 0.00 0.00 30.88 3.32
92 93 2.997986 CCACAGTACGAATACCAACACC 59.002 50.000 0.00 0.00 30.88 4.16
93 94 2.664568 CACAGTACGAATACCAACACCG 59.335 50.000 0.00 0.00 30.88 4.94
94 95 1.657094 CAGTACGAATACCAACACCGC 59.343 52.381 0.00 0.00 30.88 5.68
95 96 1.547372 AGTACGAATACCAACACCGCT 59.453 47.619 0.00 0.00 30.88 5.52
96 97 1.657094 GTACGAATACCAACACCGCTG 59.343 52.381 0.00 0.00 0.00 5.18
97 98 0.672401 ACGAATACCAACACCGCTGG 60.672 55.000 0.00 0.00 40.05 4.85
98 99 1.800681 GAATACCAACACCGCTGGC 59.199 57.895 0.00 0.00 37.48 4.85
99 100 1.977594 GAATACCAACACCGCTGGCG 61.978 60.000 8.08 8.08 37.48 5.69
100 101 2.457743 AATACCAACACCGCTGGCGA 62.458 55.000 16.79 0.00 42.83 5.54
101 102 2.852495 ATACCAACACCGCTGGCGAG 62.852 60.000 16.79 10.66 42.83 5.03
102 103 4.988598 CCAACACCGCTGGCGAGT 62.989 66.667 16.79 11.28 42.83 4.18
103 104 2.048597 CAACACCGCTGGCGAGTA 60.049 61.111 16.79 0.00 42.83 2.59
104 105 1.447838 CAACACCGCTGGCGAGTAT 60.448 57.895 16.79 0.00 42.83 2.12
105 106 1.019278 CAACACCGCTGGCGAGTATT 61.019 55.000 16.79 5.55 42.83 1.89
106 107 1.019278 AACACCGCTGGCGAGTATTG 61.019 55.000 16.79 7.54 42.83 1.90
107 108 2.173669 CACCGCTGGCGAGTATTGG 61.174 63.158 16.79 0.28 42.83 3.16
109 110 3.272334 CGCTGGCGAGTATTGGCC 61.272 66.667 9.51 4.19 46.21 5.36
110 111 2.902343 GCTGGCGAGTATTGGCCC 60.902 66.667 8.78 0.00 46.70 5.80
111 112 2.588877 CTGGCGAGTATTGGCCCG 60.589 66.667 8.78 0.00 46.70 6.13
112 113 3.078196 TGGCGAGTATTGGCCCGA 61.078 61.111 8.78 0.00 46.70 5.14
113 114 2.383245 CTGGCGAGTATTGGCCCGAT 62.383 60.000 8.78 0.00 46.70 4.18
114 115 1.227853 GGCGAGTATTGGCCCGATT 60.228 57.895 0.00 0.00 41.92 3.34
115 116 1.507141 GGCGAGTATTGGCCCGATTG 61.507 60.000 0.00 0.00 41.92 2.67
116 117 0.814010 GCGAGTATTGGCCCGATTGT 60.814 55.000 0.00 0.00 0.00 2.71
117 118 1.663695 CGAGTATTGGCCCGATTGTT 58.336 50.000 0.00 0.00 0.00 2.83
118 119 1.330521 CGAGTATTGGCCCGATTGTTG 59.669 52.381 0.00 0.00 0.00 3.33
119 120 2.639065 GAGTATTGGCCCGATTGTTGA 58.361 47.619 0.00 0.00 0.00 3.18
120 121 2.354821 GAGTATTGGCCCGATTGTTGAC 59.645 50.000 0.00 0.00 0.00 3.18
121 122 1.404035 GTATTGGCCCGATTGTTGACC 59.596 52.381 0.00 0.00 0.00 4.02
122 123 0.970427 ATTGGCCCGATTGTTGACCC 60.970 55.000 0.00 0.00 0.00 4.46
123 124 2.034999 GGCCCGATTGTTGACCCA 59.965 61.111 0.00 0.00 0.00 4.51
124 125 2.340328 GGCCCGATTGTTGACCCAC 61.340 63.158 0.00 0.00 0.00 4.61
125 126 1.602323 GCCCGATTGTTGACCCACA 60.602 57.895 0.00 0.00 0.00 4.17
126 127 1.175983 GCCCGATTGTTGACCCACAA 61.176 55.000 0.00 0.00 40.92 3.33
127 128 0.881118 CCCGATTGTTGACCCACAAG 59.119 55.000 0.00 0.00 40.01 3.16
128 129 0.240945 CCGATTGTTGACCCACAAGC 59.759 55.000 0.00 0.00 40.01 4.01
129 130 0.240945 CGATTGTTGACCCACAAGCC 59.759 55.000 0.00 0.00 39.44 4.35
130 131 1.327303 GATTGTTGACCCACAAGCCA 58.673 50.000 0.00 0.00 40.01 4.75
131 132 1.895131 GATTGTTGACCCACAAGCCAT 59.105 47.619 0.00 0.00 40.01 4.40
132 133 1.039068 TTGTTGACCCACAAGCCATG 58.961 50.000 0.00 0.00 39.30 3.66
133 134 0.106268 TGTTGACCCACAAGCCATGT 60.106 50.000 0.00 0.00 45.34 3.21
134 135 0.598065 GTTGACCCACAAGCCATGTC 59.402 55.000 0.00 0.00 41.46 3.06
135 136 0.888736 TTGACCCACAAGCCATGTCG 60.889 55.000 0.00 0.00 41.46 4.35
136 137 1.302511 GACCCACAAGCCATGTCGT 60.303 57.895 0.00 0.00 41.46 4.34
137 138 0.889186 GACCCACAAGCCATGTCGTT 60.889 55.000 0.00 0.00 41.46 3.85
138 139 1.172180 ACCCACAAGCCATGTCGTTG 61.172 55.000 0.00 0.00 41.46 4.10
139 140 1.081242 CCACAAGCCATGTCGTTGC 60.081 57.895 0.00 0.00 41.46 4.17
140 141 1.440850 CACAAGCCATGTCGTTGCG 60.441 57.895 0.00 0.00 41.46 4.85
141 142 1.596752 ACAAGCCATGTCGTTGCGA 60.597 52.632 0.00 0.00 37.96 5.10
142 143 1.163420 ACAAGCCATGTCGTTGCGAA 61.163 50.000 0.00 0.00 37.96 4.70
143 144 0.725784 CAAGCCATGTCGTTGCGAAC 60.726 55.000 0.00 0.00 37.72 3.95
144 145 1.163420 AAGCCATGTCGTTGCGAACA 61.163 50.000 0.00 0.00 37.72 3.18
145 146 1.163420 AGCCATGTCGTTGCGAACAA 61.163 50.000 0.00 0.00 37.72 2.83
156 157 2.132740 TGCGAACAACAAAATCCTGC 57.867 45.000 0.00 0.00 0.00 4.85
157 158 1.406898 TGCGAACAACAAAATCCTGCA 59.593 42.857 0.00 0.00 0.00 4.41
158 159 2.159184 TGCGAACAACAAAATCCTGCAA 60.159 40.909 0.00 0.00 0.00 4.08
159 160 2.863137 GCGAACAACAAAATCCTGCAAA 59.137 40.909 0.00 0.00 0.00 3.68
160 161 3.308323 GCGAACAACAAAATCCTGCAAAA 59.692 39.130 0.00 0.00 0.00 2.44
161 162 4.201763 GCGAACAACAAAATCCTGCAAAAA 60.202 37.500 0.00 0.00 0.00 1.94
162 163 5.503846 GCGAACAACAAAATCCTGCAAAAAT 60.504 36.000 0.00 0.00 0.00 1.82
163 164 6.292596 GCGAACAACAAAATCCTGCAAAAATA 60.293 34.615 0.00 0.00 0.00 1.40
164 165 7.625553 CGAACAACAAAATCCTGCAAAAATAA 58.374 30.769 0.00 0.00 0.00 1.40
165 166 8.119226 CGAACAACAAAATCCTGCAAAAATAAA 58.881 29.630 0.00 0.00 0.00 1.40
166 167 9.437045 GAACAACAAAATCCTGCAAAAATAAAG 57.563 29.630 0.00 0.00 0.00 1.85
167 168 8.504812 ACAACAAAATCCTGCAAAAATAAAGT 57.495 26.923 0.00 0.00 0.00 2.66
168 169 8.611757 ACAACAAAATCCTGCAAAAATAAAGTC 58.388 29.630 0.00 0.00 0.00 3.01
169 170 7.406799 ACAAAATCCTGCAAAAATAAAGTCG 57.593 32.000 0.00 0.00 0.00 4.18
170 171 6.983890 ACAAAATCCTGCAAAAATAAAGTCGT 59.016 30.769 0.00 0.00 0.00 4.34
171 172 7.494298 ACAAAATCCTGCAAAAATAAAGTCGTT 59.506 29.630 0.00 0.00 0.00 3.85
172 173 8.334632 CAAAATCCTGCAAAAATAAAGTCGTTT 58.665 29.630 0.00 0.00 0.00 3.60
173 174 8.432110 AAATCCTGCAAAAATAAAGTCGTTTT 57.568 26.923 0.00 0.00 0.00 2.43
174 175 7.637709 ATCCTGCAAAAATAAAGTCGTTTTC 57.362 32.000 0.00 0.00 0.00 2.29
175 176 6.565234 TCCTGCAAAAATAAAGTCGTTTTCA 58.435 32.000 0.00 0.00 0.00 2.69
176 177 7.206687 TCCTGCAAAAATAAAGTCGTTTTCAT 58.793 30.769 0.00 0.00 0.00 2.57
177 178 8.353684 TCCTGCAAAAATAAAGTCGTTTTCATA 58.646 29.630 0.00 0.00 0.00 2.15
178 179 8.638565 CCTGCAAAAATAAAGTCGTTTTCATAG 58.361 33.333 0.00 0.00 0.00 2.23
179 180 9.393249 CTGCAAAAATAAAGTCGTTTTCATAGA 57.607 29.630 0.00 0.00 0.00 1.98
180 181 9.906660 TGCAAAAATAAAGTCGTTTTCATAGAT 57.093 25.926 0.00 0.00 0.00 1.98
1724 1872 0.107456 CGCCTATCCCTTGAGCATGT 59.893 55.000 0.00 0.00 0.00 3.21
1980 2128 1.127567 CAGGACACTCAGGGGGTCAA 61.128 60.000 4.67 0.00 33.26 3.18
2399 2547 4.202274 TGTGATCCTTGACAAGTTCGGTTA 60.202 41.667 14.03 0.00 0.00 2.85
2840 2988 4.530553 TCACAAGGATGAGGTGTTTAGCTA 59.469 41.667 0.00 0.00 34.13 3.32
2934 3083 4.454504 GGAACGGAGTATGTGAACAACATT 59.545 41.667 0.00 0.00 44.87 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.305252 TTGACGACGTCAACTACTCG 57.695 50.000 33.39 4.45 45.88 4.18
12 13 3.348967 GATGTGCGCCGTTGACGAC 62.349 63.158 4.18 0.00 43.02 4.34
13 14 3.109547 GATGTGCGCCGTTGACGA 61.110 61.111 4.18 0.00 43.02 4.20
14 15 3.071459 GAGATGTGCGCCGTTGACG 62.071 63.158 4.18 0.00 39.44 4.35
15 16 2.740714 GGAGATGTGCGCCGTTGAC 61.741 63.158 4.18 0.00 0.00 3.18
16 17 2.434185 GGAGATGTGCGCCGTTGA 60.434 61.111 4.18 0.00 0.00 3.18
17 18 3.499737 GGGAGATGTGCGCCGTTG 61.500 66.667 4.18 0.00 37.33 4.10
18 19 3.706373 AGGGAGATGTGCGCCGTT 61.706 61.111 4.18 0.00 37.33 4.44
19 20 4.457496 CAGGGAGATGTGCGCCGT 62.457 66.667 4.18 0.00 37.33 5.68
20 21 3.451556 ATCAGGGAGATGTGCGCCG 62.452 63.158 4.18 0.00 37.33 6.46
21 22 2.507944 ATCAGGGAGATGTGCGCC 59.492 61.111 4.18 0.00 35.06 6.53
28 29 2.304069 TGCACAGCATCAGGGAGAT 58.696 52.632 0.00 0.00 37.48 2.75
29 30 3.810255 TGCACAGCATCAGGGAGA 58.190 55.556 0.00 0.00 31.71 3.71
38 39 2.488937 CCACAATTGTCTATGCACAGCA 59.511 45.455 8.48 0.00 44.86 4.41
39 40 2.489329 ACCACAATTGTCTATGCACAGC 59.511 45.455 8.48 0.00 0.00 4.40
40 41 3.671433 GCACCACAATTGTCTATGCACAG 60.671 47.826 23.64 6.58 31.29 3.66
41 42 2.228582 GCACCACAATTGTCTATGCACA 59.771 45.455 23.64 0.00 31.29 4.57
42 43 2.489329 AGCACCACAATTGTCTATGCAC 59.511 45.455 27.39 9.83 32.58 4.57
43 44 2.749076 GAGCACCACAATTGTCTATGCA 59.251 45.455 27.39 0.00 32.58 3.96
44 45 2.098117 GGAGCACCACAATTGTCTATGC 59.902 50.000 22.13 22.13 35.97 3.14
45 46 3.346315 TGGAGCACCACAATTGTCTATG 58.654 45.455 8.48 8.37 41.77 2.23
46 47 3.719268 TGGAGCACCACAATTGTCTAT 57.281 42.857 8.48 0.00 41.77 1.98
47 48 3.500448 TTGGAGCACCACAATTGTCTA 57.500 42.857 8.48 0.00 46.80 2.59
48 49 2.363306 TTGGAGCACCACAATTGTCT 57.637 45.000 8.48 2.31 46.80 3.41
49 50 4.202050 GGATATTGGAGCACCACAATTGTC 60.202 45.833 8.48 0.00 46.80 3.18
50 51 3.701040 GGATATTGGAGCACCACAATTGT 59.299 43.478 4.92 4.92 46.80 2.71
51 52 3.700539 TGGATATTGGAGCACCACAATTG 59.299 43.478 0.85 3.24 46.80 2.32
52 53 3.701040 GTGGATATTGGAGCACCACAATT 59.299 43.478 0.85 0.00 46.80 2.32
53 54 3.290710 GTGGATATTGGAGCACCACAAT 58.709 45.455 0.85 0.00 46.80 2.71
54 55 2.722094 GTGGATATTGGAGCACCACAA 58.278 47.619 0.85 0.00 46.80 3.33
55 56 2.418368 GTGGATATTGGAGCACCACA 57.582 50.000 0.85 0.00 46.80 4.17
56 57 2.292267 CTGTGGATATTGGAGCACCAC 58.708 52.381 0.85 0.00 46.80 4.16
57 58 1.915489 ACTGTGGATATTGGAGCACCA 59.085 47.619 0.00 0.00 45.34 4.17
58 59 2.717639 ACTGTGGATATTGGAGCACC 57.282 50.000 0.00 0.00 0.00 5.01
59 60 3.123804 CGTACTGTGGATATTGGAGCAC 58.876 50.000 0.00 0.00 0.00 4.40
60 61 3.028130 TCGTACTGTGGATATTGGAGCA 58.972 45.455 0.00 0.00 0.00 4.26
61 62 3.728076 TCGTACTGTGGATATTGGAGC 57.272 47.619 0.00 0.00 0.00 4.70
62 63 6.157211 GGTATTCGTACTGTGGATATTGGAG 58.843 44.000 0.00 0.00 0.00 3.86
63 64 5.599242 TGGTATTCGTACTGTGGATATTGGA 59.401 40.000 0.00 0.00 0.00 3.53
64 65 5.849510 TGGTATTCGTACTGTGGATATTGG 58.150 41.667 0.00 0.00 0.00 3.16
65 66 6.759356 TGTTGGTATTCGTACTGTGGATATTG 59.241 38.462 0.00 0.00 0.00 1.90
66 67 6.759827 GTGTTGGTATTCGTACTGTGGATATT 59.240 38.462 0.00 0.00 0.00 1.28
67 68 6.278363 GTGTTGGTATTCGTACTGTGGATAT 58.722 40.000 0.00 0.00 0.00 1.63
68 69 5.394443 GGTGTTGGTATTCGTACTGTGGATA 60.394 44.000 0.00 0.00 0.00 2.59
69 70 4.501071 GTGTTGGTATTCGTACTGTGGAT 58.499 43.478 0.00 0.00 0.00 3.41
70 71 3.306225 GGTGTTGGTATTCGTACTGTGGA 60.306 47.826 0.00 0.00 0.00 4.02
71 72 2.997986 GGTGTTGGTATTCGTACTGTGG 59.002 50.000 0.00 0.00 0.00 4.17
72 73 2.664568 CGGTGTTGGTATTCGTACTGTG 59.335 50.000 0.00 0.00 0.00 3.66
73 74 2.927871 GCGGTGTTGGTATTCGTACTGT 60.928 50.000 0.00 0.00 0.00 3.55
74 75 1.657094 GCGGTGTTGGTATTCGTACTG 59.343 52.381 0.00 0.00 0.00 2.74
75 76 1.547372 AGCGGTGTTGGTATTCGTACT 59.453 47.619 0.00 0.00 0.00 2.73
76 77 1.657094 CAGCGGTGTTGGTATTCGTAC 59.343 52.381 6.41 0.00 0.00 3.67
77 78 1.404449 CCAGCGGTGTTGGTATTCGTA 60.404 52.381 14.40 0.00 0.00 3.43
78 79 0.672401 CCAGCGGTGTTGGTATTCGT 60.672 55.000 14.40 0.00 0.00 3.85
79 80 1.977594 GCCAGCGGTGTTGGTATTCG 61.978 60.000 14.40 0.00 36.29 3.34
80 81 1.800681 GCCAGCGGTGTTGGTATTC 59.199 57.895 14.40 0.00 36.29 1.75
81 82 2.038269 CGCCAGCGGTGTTGGTATT 61.038 57.895 14.40 0.00 36.29 1.89
82 83 2.435938 CGCCAGCGGTGTTGGTAT 60.436 61.111 14.40 0.00 36.29 2.73
83 84 3.583276 CTCGCCAGCGGTGTTGGTA 62.583 63.158 14.40 0.00 36.29 3.25
84 85 4.988598 CTCGCCAGCGGTGTTGGT 62.989 66.667 14.40 0.00 36.29 3.67
85 86 2.852495 ATACTCGCCAGCGGTGTTGG 62.852 60.000 14.40 0.00 40.25 3.77
86 87 1.019278 AATACTCGCCAGCGGTGTTG 61.019 55.000 14.40 5.42 40.25 3.33
87 88 1.019278 CAATACTCGCCAGCGGTGTT 61.019 55.000 14.40 10.36 40.25 3.32
88 89 1.447838 CAATACTCGCCAGCGGTGT 60.448 57.895 14.40 13.40 40.25 4.16
89 90 2.173669 CCAATACTCGCCAGCGGTG 61.174 63.158 12.71 7.86 40.25 4.94
90 91 2.186903 CCAATACTCGCCAGCGGT 59.813 61.111 12.71 11.25 40.25 5.68
91 92 3.272334 GCCAATACTCGCCAGCGG 61.272 66.667 12.71 5.62 40.25 5.52
92 93 3.272334 GGCCAATACTCGCCAGCG 61.272 66.667 5.50 5.50 45.01 5.18
96 97 1.227853 AATCGGGCCAATACTCGCC 60.228 57.895 4.39 0.00 44.92 5.54
97 98 0.814010 ACAATCGGGCCAATACTCGC 60.814 55.000 4.39 0.00 0.00 5.03
98 99 1.330521 CAACAATCGGGCCAATACTCG 59.669 52.381 4.39 0.00 0.00 4.18
99 100 2.354821 GTCAACAATCGGGCCAATACTC 59.645 50.000 4.39 0.00 0.00 2.59
100 101 2.365582 GTCAACAATCGGGCCAATACT 58.634 47.619 4.39 0.00 0.00 2.12
101 102 1.404035 GGTCAACAATCGGGCCAATAC 59.596 52.381 4.39 0.00 0.00 1.89
102 103 1.683629 GGGTCAACAATCGGGCCAATA 60.684 52.381 4.39 0.00 0.00 1.90
103 104 0.970427 GGGTCAACAATCGGGCCAAT 60.970 55.000 4.39 0.00 0.00 3.16
104 105 1.605165 GGGTCAACAATCGGGCCAA 60.605 57.895 4.39 0.00 0.00 4.52
105 106 2.034999 GGGTCAACAATCGGGCCA 59.965 61.111 4.39 0.00 0.00 5.36
106 107 2.034999 TGGGTCAACAATCGGGCC 59.965 61.111 0.00 0.00 0.00 5.80
107 108 1.175983 TTGTGGGTCAACAATCGGGC 61.176 55.000 0.00 0.00 35.16 6.13
108 109 0.881118 CTTGTGGGTCAACAATCGGG 59.119 55.000 0.00 0.00 39.25 5.14
109 110 0.240945 GCTTGTGGGTCAACAATCGG 59.759 55.000 0.00 0.00 39.25 4.18
110 111 0.240945 GGCTTGTGGGTCAACAATCG 59.759 55.000 0.00 0.00 39.25 3.34
111 112 1.327303 TGGCTTGTGGGTCAACAATC 58.673 50.000 0.00 0.00 39.25 2.67
112 113 1.619827 CATGGCTTGTGGGTCAACAAT 59.380 47.619 0.00 0.00 39.25 2.71
113 114 1.039068 CATGGCTTGTGGGTCAACAA 58.961 50.000 0.00 0.00 37.71 2.83
114 115 0.106268 ACATGGCTTGTGGGTCAACA 60.106 50.000 5.09 0.00 37.11 3.33
115 116 0.598065 GACATGGCTTGTGGGTCAAC 59.402 55.000 11.09 0.00 39.18 3.18
116 117 0.888736 CGACATGGCTTGTGGGTCAA 60.889 55.000 11.09 0.00 39.18 3.18
117 118 1.302431 CGACATGGCTTGTGGGTCA 60.302 57.895 11.09 0.00 39.18 4.02
118 119 0.889186 AACGACATGGCTTGTGGGTC 60.889 55.000 17.42 1.15 39.18 4.46
119 120 1.150536 AACGACATGGCTTGTGGGT 59.849 52.632 17.42 9.93 39.18 4.51
120 121 1.580942 CAACGACATGGCTTGTGGG 59.419 57.895 17.42 9.29 39.18 4.61
121 122 1.081242 GCAACGACATGGCTTGTGG 60.081 57.895 11.09 12.06 39.18 4.17
122 123 1.440850 CGCAACGACATGGCTTGTG 60.441 57.895 11.09 10.04 39.18 3.33
123 124 1.163420 TTCGCAACGACATGGCTTGT 61.163 50.000 5.63 5.63 42.79 3.16
124 125 0.725784 GTTCGCAACGACATGGCTTG 60.726 55.000 0.00 1.52 34.89 4.01
125 126 1.163420 TGTTCGCAACGACATGGCTT 61.163 50.000 0.00 0.00 34.89 4.35
126 127 1.163420 TTGTTCGCAACGACATGGCT 61.163 50.000 0.00 0.00 34.89 4.75
127 128 0.996727 GTTGTTCGCAACGACATGGC 60.997 55.000 12.02 0.00 46.47 4.40
128 129 3.071495 GTTGTTCGCAACGACATGG 57.929 52.632 12.02 0.00 46.47 3.66
136 137 2.159184 TGCAGGATTTTGTTGTTCGCAA 60.159 40.909 0.00 0.00 34.21 4.85
137 138 1.406898 TGCAGGATTTTGTTGTTCGCA 59.593 42.857 0.00 0.00 0.00 5.10
138 139 2.132740 TGCAGGATTTTGTTGTTCGC 57.867 45.000 0.00 0.00 0.00 4.70
139 140 5.462034 TTTTTGCAGGATTTTGTTGTTCG 57.538 34.783 0.00 0.00 0.00 3.95
140 141 9.437045 CTTTATTTTTGCAGGATTTTGTTGTTC 57.563 29.630 0.00 0.00 0.00 3.18
141 142 8.955388 ACTTTATTTTTGCAGGATTTTGTTGTT 58.045 25.926 0.00 0.00 0.00 2.83
142 143 8.504812 ACTTTATTTTTGCAGGATTTTGTTGT 57.495 26.923 0.00 0.00 0.00 3.32
143 144 7.793427 CGACTTTATTTTTGCAGGATTTTGTTG 59.207 33.333 0.00 0.00 0.00 3.33
144 145 7.494298 ACGACTTTATTTTTGCAGGATTTTGTT 59.506 29.630 0.00 0.00 0.00 2.83
145 146 6.983890 ACGACTTTATTTTTGCAGGATTTTGT 59.016 30.769 0.00 0.00 0.00 2.83
146 147 7.406799 ACGACTTTATTTTTGCAGGATTTTG 57.593 32.000 0.00 0.00 0.00 2.44
147 148 8.432110 AAACGACTTTATTTTTGCAGGATTTT 57.568 26.923 0.00 0.00 0.00 1.82
148 149 8.432110 AAAACGACTTTATTTTTGCAGGATTT 57.568 26.923 0.00 0.00 0.00 2.17
149 150 7.708752 TGAAAACGACTTTATTTTTGCAGGATT 59.291 29.630 0.00 0.00 0.00 3.01
150 151 7.206687 TGAAAACGACTTTATTTTTGCAGGAT 58.793 30.769 0.00 0.00 0.00 3.24
151 152 6.565234 TGAAAACGACTTTATTTTTGCAGGA 58.435 32.000 0.00 0.00 0.00 3.86
152 153 6.820470 TGAAAACGACTTTATTTTTGCAGG 57.180 33.333 0.00 0.00 0.00 4.85
153 154 9.393249 TCTATGAAAACGACTTTATTTTTGCAG 57.607 29.630 0.00 0.00 0.00 4.41
154 155 9.906660 ATCTATGAAAACGACTTTATTTTTGCA 57.093 25.926 0.00 0.00 0.00 4.08
185 186 9.436957 CAACAGTACCTGATTACATCTTACTTT 57.563 33.333 0.00 0.00 35.18 2.66
186 187 8.812972 TCAACAGTACCTGATTACATCTTACTT 58.187 33.333 0.00 0.00 35.18 2.24
187 188 8.362464 TCAACAGTACCTGATTACATCTTACT 57.638 34.615 0.00 0.00 35.18 2.24
188 189 8.870879 GTTCAACAGTACCTGATTACATCTTAC 58.129 37.037 0.00 0.00 35.18 2.34
189 190 8.038944 GGTTCAACAGTACCTGATTACATCTTA 58.961 37.037 0.00 0.00 35.18 2.10
190 191 6.879458 GGTTCAACAGTACCTGATTACATCTT 59.121 38.462 0.00 0.00 35.18 2.40
191 192 6.407202 GGTTCAACAGTACCTGATTACATCT 58.593 40.000 0.00 0.00 35.18 2.90
192 193 5.291128 CGGTTCAACAGTACCTGATTACATC 59.709 44.000 0.00 0.00 35.18 3.06
193 194 5.175859 CGGTTCAACAGTACCTGATTACAT 58.824 41.667 0.00 0.00 35.18 2.29
194 195 4.561938 CCGGTTCAACAGTACCTGATTACA 60.562 45.833 0.00 0.00 35.18 2.41
195 196 3.930848 CCGGTTCAACAGTACCTGATTAC 59.069 47.826 0.00 0.00 35.18 1.89
196 197 3.579586 ACCGGTTCAACAGTACCTGATTA 59.420 43.478 0.00 0.00 35.18 1.75
197 198 2.370849 ACCGGTTCAACAGTACCTGATT 59.629 45.455 0.00 0.00 35.18 2.57
198 199 1.975680 ACCGGTTCAACAGTACCTGAT 59.024 47.619 0.00 0.00 35.18 2.90
199 200 1.416243 ACCGGTTCAACAGTACCTGA 58.584 50.000 0.00 0.00 35.18 3.86
200 201 3.259064 CATACCGGTTCAACAGTACCTG 58.741 50.000 15.04 0.00 37.52 4.00
201 202 2.235402 CCATACCGGTTCAACAGTACCT 59.765 50.000 15.04 0.00 32.08 3.08
202 203 2.624636 CCATACCGGTTCAACAGTACC 58.375 52.381 15.04 0.00 0.00 3.34
203 204 2.624636 CCCATACCGGTTCAACAGTAC 58.375 52.381 15.04 0.00 0.00 2.73
1724 1872 2.875672 GCTGGCACAACCTTCATGTCTA 60.876 50.000 0.00 0.00 38.70 2.59
2399 2547 1.344438 TCTGTCGCACCTGAATCAAGT 59.656 47.619 0.00 0.00 0.00 3.16
2840 2988 5.537674 ACAAGAGCATGGAAGTTCTGAAAAT 59.462 36.000 2.25 0.00 0.00 1.82
2934 3083 0.686224 CAGCCATGAAAGCCCCAAAA 59.314 50.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.