Multiple sequence alignment - TraesCS4D01G350900

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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 TraesCS4D01G350900 chr4D 100.000 3017 0 0 1 3017 502867135 502870151 0.000000e+00 5572.0
1 TraesCS4D01G350900 chr4D 95.223 2784 107 19 199 2974 507114494 507111729 0.000000e+00 4381.0
2 TraesCS4D01G350900 chr4D 94.672 2759 103 18 195 2934 428529855 428532588 0.000000e+00 4241.0
3 TraesCS4D01G350900 chr4D 92.500 200 15 0 1 200 300247579 300247380 1.370000e-73 287.0
4 TraesCS4D01G350900 chr4D 100.000 45 0 0 2973 3017 507111670 507111626 1.930000e-12 84.2
5 TraesCS4D01G350900 chr1D 97.908 2820 57 2 198 3017 420011141 420008324 0.000000e+00 4879.0
6 TraesCS4D01G350900 chr1D 95.760 2783 95 16 199 2974 475528296 475525530 0.000000e+00 4464.0
7 TraesCS4D01G350900 chr1D 100.000 46 0 0 2972 3017 110901430 110901385 5.360000e-13 86.1
8 TraesCS4D01G350900 chr3D 97.765 2819 52 7 199 3017 359622499 359625306 0.000000e+00 4846.0
9 TraesCS4D01G350900 chr3D 95.332 2785 104 18 199 2974 85226134 85228901 0.000000e+00 4399.0
10 TraesCS4D01G350900 chr3D 95.902 244 9 1 199 442 85233472 85233230 7.840000e-106 394.0
11 TraesCS4D01G350900 chr3D 92.500 200 11 4 1 198 87548428 87548625 1.770000e-72 283.0
12 TraesCS4D01G350900 chr2D 96.779 2825 69 4 197 3017 382702780 382699974 0.000000e+00 4693.0
13 TraesCS4D01G350900 chr2D 96.391 2826 70 8 196 3017 182632460 182629663 0.000000e+00 4625.0
14 TraesCS4D01G350900 chr2D 95.855 2847 61 7 199 3017 74953112 74955929 0.000000e+00 4551.0
15 TraesCS4D01G350900 chr2D 94.530 2724 105 18 198 2915 547563444 547566129 0.000000e+00 4165.0
16 TraesCS4D01G350900 chr2D 96.889 2379 70 2 600 2974 605551640 605549262 0.000000e+00 3980.0
17 TraesCS4D01G350900 chr2D 92.424 198 15 0 1 198 301655704 301655507 1.770000e-72 283.0
18 TraesCS4D01G350900 chr6D 93.766 2727 109 22 193 2915 156246484 156249153 0.000000e+00 4037.0
19 TraesCS4D01G350900 chr7B 88.013 2411 157 60 199 2545 592365044 592367386 0.000000e+00 2730.0
20 TraesCS4D01G350900 chr3B 92.850 951 33 9 199 1134 766032546 766033476 0.000000e+00 1347.0
21 TraesCS4D01G350900 chr3B 93.299 194 12 1 1 194 500276548 500276356 4.920000e-73 285.0
22 TraesCS4D01G350900 chr7D 93.798 258 15 1 185 442 10888780 10889036 1.310000e-103 387.0
23 TraesCS4D01G350900 chr7D 92.929 198 13 1 1 198 215313183 215312987 1.370000e-73 287.0
24 TraesCS4D01G350900 chr7D 100.000 46 0 0 2972 3017 36172934 36172889 5.360000e-13 86.1
25 TraesCS4D01G350900 chr5D 93.434 198 13 0 1 198 447801442 447801639 8.180000e-76 294.0
26 TraesCS4D01G350900 chr5D 92.965 199 11 3 1 198 62050713 62050517 1.370000e-73 287.0
27 TraesCS4D01G350900 chr5B 93.467 199 12 1 1 198 546740796 546740994 8.180000e-76 294.0
28 TraesCS4D01G350900 chr1B 92.929 198 13 1 1 198 583379764 583379960 1.370000e-73 287.0


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 TraesCS4D01G350900 chr4D 502867135 502870151 3016 False 5572.0 5572 100.0000 1 3017 1 chr4D.!!$F2 3016
1 TraesCS4D01G350900 chr4D 428529855 428532588 2733 False 4241.0 4241 94.6720 195 2934 1 chr4D.!!$F1 2739
2 TraesCS4D01G350900 chr4D 507111626 507114494 2868 True 2232.6 4381 97.6115 199 3017 2 chr4D.!!$R2 2818
3 TraesCS4D01G350900 chr1D 420008324 420011141 2817 True 4879.0 4879 97.9080 198 3017 1 chr1D.!!$R2 2819
4 TraesCS4D01G350900 chr1D 475525530 475528296 2766 True 4464.0 4464 95.7600 199 2974 1 chr1D.!!$R3 2775
5 TraesCS4D01G350900 chr3D 359622499 359625306 2807 False 4846.0 4846 97.7650 199 3017 1 chr3D.!!$F3 2818
6 TraesCS4D01G350900 chr3D 85226134 85228901 2767 False 4399.0 4399 95.3320 199 2974 1 chr3D.!!$F1 2775
7 TraesCS4D01G350900 chr2D 382699974 382702780 2806 True 4693.0 4693 96.7790 197 3017 1 chr2D.!!$R3 2820
8 TraesCS4D01G350900 chr2D 182629663 182632460 2797 True 4625.0 4625 96.3910 196 3017 1 chr2D.!!$R1 2821
9 TraesCS4D01G350900 chr2D 74953112 74955929 2817 False 4551.0 4551 95.8550 199 3017 1 chr2D.!!$F1 2818
10 TraesCS4D01G350900 chr2D 547563444 547566129 2685 False 4165.0 4165 94.5300 198 2915 1 chr2D.!!$F2 2717
11 TraesCS4D01G350900 chr2D 605549262 605551640 2378 True 3980.0 3980 96.8890 600 2974 1 chr2D.!!$R4 2374
12 TraesCS4D01G350900 chr6D 156246484 156249153 2669 False 4037.0 4037 93.7660 193 2915 1 chr6D.!!$F1 2722
13 TraesCS4D01G350900 chr7B 592365044 592367386 2342 False 2730.0 2730 88.0130 199 2545 1 chr7B.!!$F1 2346
14 TraesCS4D01G350900 chr3B 766032546 766033476 930 False 1347.0 1347 92.8500 199 1134 1 chr3B.!!$F1 935

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
137 138 0.112412 TCTGGGGGCTTCTTTTGGTC 59.888 55.0 0.0 0.0 0.0 4.02 F
565 644 0.251653 ACTCCTACTCTTGGACGCCA 60.252 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 1635 0.529378 CAGCCTGGACAAGCAATTCC 59.471 55.00 0.0 0.0 0.00 3.01 R
2094 2216 4.474394 TCACATTCCCCAAAATGTACACA 58.526 39.13 0.0 0.0 45.68 3.72 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
33 34 4.522971 GGTCTTCGAGCCATCCAC 57.477 61.111 0.00 0.00 0.00 4.02
34 35 1.519455 GGTCTTCGAGCCATCCACG 60.519 63.158 0.00 0.00 0.00 4.94
35 36 1.511305 GTCTTCGAGCCATCCACGA 59.489 57.895 0.00 0.00 0.00 4.35
36 37 0.526524 GTCTTCGAGCCATCCACGAG 60.527 60.000 0.00 0.00 37.36 4.18
37 38 0.679960 TCTTCGAGCCATCCACGAGA 60.680 55.000 0.00 0.00 37.36 4.04
38 39 0.387202 CTTCGAGCCATCCACGAGAT 59.613 55.000 0.00 0.00 37.36 2.75
39 40 1.609072 CTTCGAGCCATCCACGAGATA 59.391 52.381 0.00 0.00 37.36 1.98
40 41 1.239347 TCGAGCCATCCACGAGATAG 58.761 55.000 0.00 0.00 32.37 2.08
41 42 0.242286 CGAGCCATCCACGAGATAGG 59.758 60.000 0.00 0.00 32.37 2.57
42 43 0.605589 GAGCCATCCACGAGATAGGG 59.394 60.000 0.00 0.00 32.37 3.53
43 44 0.833834 AGCCATCCACGAGATAGGGG 60.834 60.000 0.00 0.00 32.37 4.79
44 45 1.831652 GCCATCCACGAGATAGGGGG 61.832 65.000 0.00 0.00 34.80 5.40
99 100 3.394836 GGGCAGCCCGAGACTCTT 61.395 66.667 17.05 0.00 32.13 2.85
100 101 2.185608 GGCAGCCCGAGACTCTTC 59.814 66.667 0.00 0.00 0.00 2.87
101 102 2.355193 GGCAGCCCGAGACTCTTCT 61.355 63.158 0.00 0.00 33.37 2.85
102 103 1.153667 GCAGCCCGAGACTCTTCTG 60.154 63.158 0.03 6.09 29.47 3.02
103 104 1.515020 CAGCCCGAGACTCTTCTGG 59.485 63.158 0.03 0.00 29.47 3.86
104 105 0.967887 CAGCCCGAGACTCTTCTGGA 60.968 60.000 0.03 0.00 29.11 3.86
105 106 0.968393 AGCCCGAGACTCTTCTGGAC 60.968 60.000 0.03 0.00 29.11 4.02
106 107 1.950973 GCCCGAGACTCTTCTGGACC 61.951 65.000 0.03 0.00 29.11 4.46
107 108 0.612174 CCCGAGACTCTTCTGGACCA 60.612 60.000 0.03 0.00 29.11 4.02
108 109 1.257743 CCGAGACTCTTCTGGACCAA 58.742 55.000 0.03 0.00 29.11 3.67
109 110 1.067495 CCGAGACTCTTCTGGACCAAC 60.067 57.143 0.03 0.00 29.11 3.77
110 111 1.889829 CGAGACTCTTCTGGACCAACT 59.110 52.381 0.03 0.00 29.11 3.16
111 112 2.094957 CGAGACTCTTCTGGACCAACTC 60.095 54.545 0.03 0.00 29.11 3.01
112 113 3.161866 GAGACTCTTCTGGACCAACTCT 58.838 50.000 0.00 0.00 29.47 3.24
113 114 3.576550 GAGACTCTTCTGGACCAACTCTT 59.423 47.826 0.00 0.00 29.47 2.85
114 115 3.970640 AGACTCTTCTGGACCAACTCTTT 59.029 43.478 0.00 0.00 0.00 2.52
115 116 4.410555 AGACTCTTCTGGACCAACTCTTTT 59.589 41.667 0.00 0.00 0.00 2.27
116 117 5.602978 AGACTCTTCTGGACCAACTCTTTTA 59.397 40.000 0.00 0.00 0.00 1.52
117 118 5.612351 ACTCTTCTGGACCAACTCTTTTAC 58.388 41.667 0.00 0.00 0.00 2.01
118 119 5.367060 ACTCTTCTGGACCAACTCTTTTACT 59.633 40.000 0.00 0.00 0.00 2.24
119 120 5.855045 TCTTCTGGACCAACTCTTTTACTC 58.145 41.667 0.00 0.00 0.00 2.59
120 121 5.602978 TCTTCTGGACCAACTCTTTTACTCT 59.397 40.000 0.00 0.00 0.00 3.24
121 122 5.215252 TCTGGACCAACTCTTTTACTCTG 57.785 43.478 0.00 0.00 0.00 3.35
122 123 4.040461 TCTGGACCAACTCTTTTACTCTGG 59.960 45.833 0.00 0.00 0.00 3.86
123 124 3.072476 TGGACCAACTCTTTTACTCTGGG 59.928 47.826 0.00 0.00 0.00 4.45
124 125 3.559384 GGACCAACTCTTTTACTCTGGGG 60.559 52.174 0.00 0.00 0.00 4.96
125 126 2.375509 ACCAACTCTTTTACTCTGGGGG 59.624 50.000 0.00 0.00 0.00 5.40
126 127 2.437413 CAACTCTTTTACTCTGGGGGC 58.563 52.381 0.00 0.00 0.00 5.80
127 128 2.040412 CAACTCTTTTACTCTGGGGGCT 59.960 50.000 0.00 0.00 0.00 5.19
128 129 2.349445 ACTCTTTTACTCTGGGGGCTT 58.651 47.619 0.00 0.00 0.00 4.35
129 130 2.306219 ACTCTTTTACTCTGGGGGCTTC 59.694 50.000 0.00 0.00 0.00 3.86
130 131 2.573915 CTCTTTTACTCTGGGGGCTTCT 59.426 50.000 0.00 0.00 0.00 2.85
131 132 2.986728 TCTTTTACTCTGGGGGCTTCTT 59.013 45.455 0.00 0.00 0.00 2.52
132 133 3.397955 TCTTTTACTCTGGGGGCTTCTTT 59.602 43.478 0.00 0.00 0.00 2.52
133 134 3.895704 TTTACTCTGGGGGCTTCTTTT 57.104 42.857 0.00 0.00 0.00 2.27
134 135 2.879103 TACTCTGGGGGCTTCTTTTG 57.121 50.000 0.00 0.00 0.00 2.44
135 136 0.113190 ACTCTGGGGGCTTCTTTTGG 59.887 55.000 0.00 0.00 0.00 3.28
136 137 0.113190 CTCTGGGGGCTTCTTTTGGT 59.887 55.000 0.00 0.00 0.00 3.67
137 138 0.112412 TCTGGGGGCTTCTTTTGGTC 59.888 55.000 0.00 0.00 0.00 4.02
138 139 0.900182 CTGGGGGCTTCTTTTGGTCC 60.900 60.000 0.00 0.00 0.00 4.46
139 140 1.155155 GGGGGCTTCTTTTGGTCCA 59.845 57.895 0.00 0.00 0.00 4.02
140 141 0.252239 GGGGGCTTCTTTTGGTCCAT 60.252 55.000 0.00 0.00 0.00 3.41
141 142 1.006639 GGGGGCTTCTTTTGGTCCATA 59.993 52.381 0.00 0.00 0.00 2.74
142 143 2.558800 GGGGGCTTCTTTTGGTCCATAA 60.559 50.000 0.00 0.00 0.00 1.90
143 144 3.169908 GGGGCTTCTTTTGGTCCATAAA 58.830 45.455 0.00 0.00 0.00 1.40
144 145 3.580895 GGGGCTTCTTTTGGTCCATAAAA 59.419 43.478 0.00 0.00 0.00 1.52
145 146 4.041075 GGGGCTTCTTTTGGTCCATAAAAA 59.959 41.667 0.00 0.00 0.00 1.94
175 176 5.705609 AAAATTAGCACGTCAATTGGACT 57.294 34.783 5.42 0.00 44.68 3.85
176 177 4.946784 AATTAGCACGTCAATTGGACTC 57.053 40.909 5.42 0.00 44.68 3.36
177 178 2.380084 TAGCACGTCAATTGGACTCC 57.620 50.000 5.42 0.00 44.68 3.85
178 179 0.396435 AGCACGTCAATTGGACTCCA 59.604 50.000 5.42 0.00 44.68 3.86
179 180 1.003580 AGCACGTCAATTGGACTCCAT 59.996 47.619 5.42 0.00 44.68 3.41
180 181 1.812571 GCACGTCAATTGGACTCCATT 59.187 47.619 5.42 0.00 44.68 3.16
181 182 2.228822 GCACGTCAATTGGACTCCATTT 59.771 45.455 5.42 0.00 44.68 2.32
182 183 3.825308 CACGTCAATTGGACTCCATTTG 58.175 45.455 20.17 20.17 44.68 2.32
183 184 2.819608 ACGTCAATTGGACTCCATTTGG 59.180 45.455 23.53 15.21 44.68 3.28
184 185 2.819608 CGTCAATTGGACTCCATTTGGT 59.180 45.455 23.53 0.00 44.68 3.67
185 186 4.006989 CGTCAATTGGACTCCATTTGGTA 58.993 43.478 23.53 9.95 44.68 3.25
186 187 4.640201 CGTCAATTGGACTCCATTTGGTAT 59.360 41.667 23.53 3.12 44.68 2.73
187 188 5.125417 CGTCAATTGGACTCCATTTGGTATT 59.875 40.000 23.53 8.22 44.68 1.89
188 189 6.564328 GTCAATTGGACTCCATTTGGTATTC 58.436 40.000 23.53 11.52 42.02 1.75
189 190 5.656416 TCAATTGGACTCCATTTGGTATTCC 59.344 40.000 23.53 2.39 42.02 3.01
190 191 4.946160 TTGGACTCCATTTGGTATTCCT 57.054 40.909 0.00 0.00 36.34 3.36
191 192 4.946160 TGGACTCCATTTGGTATTCCTT 57.054 40.909 0.00 0.00 36.34 3.36
192 193 5.269554 TGGACTCCATTTGGTATTCCTTT 57.730 39.130 0.00 0.00 36.34 3.11
193 194 5.650283 TGGACTCCATTTGGTATTCCTTTT 58.350 37.500 0.00 0.00 36.34 2.27
194 195 6.081356 TGGACTCCATTTGGTATTCCTTTTT 58.919 36.000 0.00 0.00 36.34 1.94
326 337 1.714899 CCAAATCGCCCGTTGCTAGG 61.715 60.000 0.00 0.00 38.05 3.02
481 535 2.170166 CCTCTCACTCTGCTCTCACTT 58.830 52.381 0.00 0.00 0.00 3.16
544 623 2.026641 CTCTCCTCTCTGCTCTTGGAG 58.973 57.143 0.00 0.00 44.00 3.86
545 624 1.357420 TCTCCTCTCTGCTCTTGGAGT 59.643 52.381 0.00 0.00 43.34 3.85
546 625 2.578480 TCTCCTCTCTGCTCTTGGAGTA 59.422 50.000 0.00 0.00 43.34 2.59
547 626 2.687935 CTCCTCTCTGCTCTTGGAGTAC 59.312 54.545 0.00 0.00 39.39 2.73
548 627 2.310349 TCCTCTCTGCTCTTGGAGTACT 59.690 50.000 0.00 0.00 33.13 2.73
549 628 2.687935 CCTCTCTGCTCTTGGAGTACTC 59.312 54.545 14.87 14.87 33.13 2.59
565 644 0.251653 ACTCCTACTCTTGGACGCCA 60.252 55.000 0.00 0.00 0.00 5.69
627 706 1.128200 CCTGGAATGACGGGGATACA 58.872 55.000 0.00 0.00 39.74 2.29
927 1017 5.301551 AGGTGATTTTGTTGCTGTGTTCATA 59.698 36.000 0.00 0.00 0.00 2.15
1124 1214 5.376854 AATCATTTTCTTCTGAACCCACG 57.623 39.130 0.00 0.00 31.02 4.94
1143 1233 4.335315 CCACGCATGTATTTACAAGGATGT 59.665 41.667 0.00 0.00 43.74 3.06
1526 1635 1.027357 CCCTGGCATCCAATTCTTCG 58.973 55.000 0.00 0.00 30.80 3.79
1696 1805 3.765381 TCCAAGATGTTTGATTGGCAGA 58.235 40.909 0.00 0.00 42.65 4.26
1697 1806 4.346730 TCCAAGATGTTTGATTGGCAGAT 58.653 39.130 0.00 0.00 42.65 2.90
2093 2215 7.658982 GCCTAACAATCTGATGTGAAGATATGA 59.341 37.037 0.00 0.00 33.17 2.15
2094 2216 9.722184 CCTAACAATCTGATGTGAAGATATGAT 57.278 33.333 0.00 0.00 33.17 2.45
2146 2268 8.427902 AATCTAGTCTATGTCTATGCCAATGA 57.572 34.615 0.00 0.00 0.00 2.57
2160 2282 8.486210 TCTATGCCAATGATAAGAACTGTAGTT 58.514 33.333 0.00 0.00 41.64 2.24
2165 2289 8.893727 GCCAATGATAAGAACTGTAGTTTATGT 58.106 33.333 0.00 0.00 38.56 2.29
2388 2529 1.080354 CTCCACCCACCCTCCACTA 59.920 63.158 0.00 0.00 0.00 2.74
2458 2601 1.203050 CCACACCCCACCTCTTGAAAT 60.203 52.381 0.00 0.00 0.00 2.17
2710 2853 1.386485 ATCAGGTGGGCTAGGGCAT 60.386 57.895 0.00 0.00 40.87 4.40
2714 2857 1.461461 GGTGGGCTAGGGCATAGGA 60.461 63.158 8.42 0.00 40.87 2.94
2722 2865 3.583086 GGCTAGGGCATAGGAAGTAATCA 59.417 47.826 8.42 0.00 40.87 2.57
2736 2879 3.108376 AGTAATCACTCCTCACCCTTCC 58.892 50.000 0.00 0.00 0.00 3.46
2879 3025 2.373540 CAGAATGTTTGCATGGTGGG 57.626 50.000 0.00 0.00 35.15 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.506472 GATGGCTCGAAGACCCCC 59.494 66.667 0.00 0.00 29.35 5.40
14 15 2.367202 TGGATGGCTCGAAGACCCC 61.367 63.158 0.00 0.00 29.35 4.95
15 16 1.153349 GTGGATGGCTCGAAGACCC 60.153 63.158 0.00 0.00 31.64 4.46
16 17 1.519455 CGTGGATGGCTCGAAGACC 60.519 63.158 0.00 0.00 0.00 3.85
17 18 0.526524 CTCGTGGATGGCTCGAAGAC 60.527 60.000 0.00 0.00 33.32 3.01
18 19 0.679960 TCTCGTGGATGGCTCGAAGA 60.680 55.000 0.00 0.00 33.32 2.87
19 20 0.387202 ATCTCGTGGATGGCTCGAAG 59.613 55.000 0.00 0.00 32.69 3.79
20 21 1.609072 CTATCTCGTGGATGGCTCGAA 59.391 52.381 0.00 0.00 35.98 3.71
21 22 1.239347 CTATCTCGTGGATGGCTCGA 58.761 55.000 4.44 0.00 35.98 4.04
22 23 0.242286 CCTATCTCGTGGATGGCTCG 59.758 60.000 4.44 0.00 35.98 5.03
23 24 0.605589 CCCTATCTCGTGGATGGCTC 59.394 60.000 4.44 0.00 35.98 4.70
24 25 0.833834 CCCCTATCTCGTGGATGGCT 60.834 60.000 4.44 0.00 35.98 4.75
25 26 1.674057 CCCCTATCTCGTGGATGGC 59.326 63.158 4.44 0.00 35.98 4.40
26 27 2.366469 CCCCCTATCTCGTGGATGG 58.634 63.158 4.44 1.99 35.98 3.51
80 81 4.459089 GAGTCTCGGGCTGCCCAC 62.459 72.222 35.22 25.66 45.83 4.61
81 82 4.704103 AGAGTCTCGGGCTGCCCA 62.704 66.667 35.22 21.50 45.83 5.36
82 83 3.378399 GAAGAGTCTCGGGCTGCCC 62.378 68.421 28.17 28.17 41.09 5.36
83 84 2.185608 GAAGAGTCTCGGGCTGCC 59.814 66.667 11.05 11.05 0.00 4.85
84 85 1.153667 CAGAAGAGTCTCGGGCTGC 60.154 63.158 0.00 0.00 28.78 5.25
85 86 0.967887 TCCAGAAGAGTCTCGGGCTG 60.968 60.000 0.00 10.75 31.34 4.85
86 87 0.968393 GTCCAGAAGAGTCTCGGGCT 60.968 60.000 0.00 0.00 31.34 5.19
87 88 1.513622 GTCCAGAAGAGTCTCGGGC 59.486 63.158 0.00 0.00 31.34 6.13
88 89 0.612174 TGGTCCAGAAGAGTCTCGGG 60.612 60.000 0.00 0.00 32.43 5.14
89 90 1.067495 GTTGGTCCAGAAGAGTCTCGG 60.067 57.143 0.00 0.00 28.78 4.63
90 91 1.889829 AGTTGGTCCAGAAGAGTCTCG 59.110 52.381 0.00 0.00 28.78 4.04
91 92 3.161866 AGAGTTGGTCCAGAAGAGTCTC 58.838 50.000 0.00 0.00 28.78 3.36
92 93 3.252554 AGAGTTGGTCCAGAAGAGTCT 57.747 47.619 0.00 0.00 32.85 3.24
93 94 4.344359 AAAGAGTTGGTCCAGAAGAGTC 57.656 45.455 0.00 0.00 0.00 3.36
94 95 4.779993 AAAAGAGTTGGTCCAGAAGAGT 57.220 40.909 0.00 0.00 0.00 3.24
95 96 5.859495 AGTAAAAGAGTTGGTCCAGAAGAG 58.141 41.667 0.00 0.00 0.00 2.85
96 97 5.602978 AGAGTAAAAGAGTTGGTCCAGAAGA 59.397 40.000 0.00 0.00 0.00 2.87
97 98 5.698545 CAGAGTAAAAGAGTTGGTCCAGAAG 59.301 44.000 0.00 0.00 0.00 2.85
98 99 5.454755 CCAGAGTAAAAGAGTTGGTCCAGAA 60.455 44.000 0.00 0.00 0.00 3.02
99 100 4.040461 CCAGAGTAAAAGAGTTGGTCCAGA 59.960 45.833 0.00 0.00 0.00 3.86
100 101 4.319177 CCAGAGTAAAAGAGTTGGTCCAG 58.681 47.826 0.00 0.00 0.00 3.86
101 102 3.072476 CCCAGAGTAAAAGAGTTGGTCCA 59.928 47.826 0.00 0.00 0.00 4.02
102 103 3.559384 CCCCAGAGTAAAAGAGTTGGTCC 60.559 52.174 0.00 0.00 0.00 4.46
103 104 3.559384 CCCCCAGAGTAAAAGAGTTGGTC 60.559 52.174 0.00 0.00 0.00 4.02
104 105 2.375509 CCCCCAGAGTAAAAGAGTTGGT 59.624 50.000 0.00 0.00 0.00 3.67
105 106 2.880167 GCCCCCAGAGTAAAAGAGTTGG 60.880 54.545 0.00 0.00 0.00 3.77
106 107 2.040412 AGCCCCCAGAGTAAAAGAGTTG 59.960 50.000 0.00 0.00 0.00 3.16
107 108 2.349445 AGCCCCCAGAGTAAAAGAGTT 58.651 47.619 0.00 0.00 0.00 3.01
108 109 2.046280 AGCCCCCAGAGTAAAAGAGT 57.954 50.000 0.00 0.00 0.00 3.24
109 110 2.573915 AGAAGCCCCCAGAGTAAAAGAG 59.426 50.000 0.00 0.00 0.00 2.85
110 111 2.632537 AGAAGCCCCCAGAGTAAAAGA 58.367 47.619 0.00 0.00 0.00 2.52
111 112 3.441500 AAGAAGCCCCCAGAGTAAAAG 57.558 47.619 0.00 0.00 0.00 2.27
112 113 3.895041 CAAAAGAAGCCCCCAGAGTAAAA 59.105 43.478 0.00 0.00 0.00 1.52
113 114 3.496331 CAAAAGAAGCCCCCAGAGTAAA 58.504 45.455 0.00 0.00 0.00 2.01
114 115 2.225017 CCAAAAGAAGCCCCCAGAGTAA 60.225 50.000 0.00 0.00 0.00 2.24
115 116 1.354368 CCAAAAGAAGCCCCCAGAGTA 59.646 52.381 0.00 0.00 0.00 2.59
116 117 0.113190 CCAAAAGAAGCCCCCAGAGT 59.887 55.000 0.00 0.00 0.00 3.24
117 118 0.113190 ACCAAAAGAAGCCCCCAGAG 59.887 55.000 0.00 0.00 0.00 3.35
118 119 0.112412 GACCAAAAGAAGCCCCCAGA 59.888 55.000 0.00 0.00 0.00 3.86
119 120 0.900182 GGACCAAAAGAAGCCCCCAG 60.900 60.000 0.00 0.00 0.00 4.45
120 121 1.155155 GGACCAAAAGAAGCCCCCA 59.845 57.895 0.00 0.00 0.00 4.96
121 122 0.252239 ATGGACCAAAAGAAGCCCCC 60.252 55.000 0.00 0.00 0.00 5.40
122 123 2.525105 TATGGACCAAAAGAAGCCCC 57.475 50.000 0.00 0.00 0.00 5.80
123 124 4.882842 TTTTATGGACCAAAAGAAGCCC 57.117 40.909 0.00 0.00 0.00 5.19
156 157 9.436751 CAAATGGAGTCCAATTGACGTGCTAAT 62.437 40.741 29.01 0.26 44.56 1.73
157 158 8.220917 CAAATGGAGTCCAATTGACGTGCTAA 62.221 42.308 29.01 0.00 44.56 3.09
158 159 6.823407 CAAATGGAGTCCAATTGACGTGCTA 61.823 44.000 29.01 0.00 44.56 3.49
159 160 6.105156 CAAATGGAGTCCAATTGACGTGCT 62.105 45.833 29.01 1.45 44.56 4.40
160 161 3.914514 CAAATGGAGTCCAATTGACGTGC 60.915 47.826 29.01 0.00 44.56 5.34
161 162 3.366273 CCAAATGGAGTCCAATTGACGTG 60.366 47.826 32.77 17.23 44.56 4.49
162 163 2.819608 CCAAATGGAGTCCAATTGACGT 59.180 45.455 32.77 7.41 44.56 4.34
163 164 2.819608 ACCAAATGGAGTCCAATTGACG 59.180 45.455 32.77 22.19 44.56 4.35
164 165 6.405842 GGAATACCAAATGGAGTCCAATTGAC 60.406 42.308 32.77 19.83 44.56 3.18
165 166 5.656416 GGAATACCAAATGGAGTCCAATTGA 59.344 40.000 32.77 19.15 44.56 2.57
166 167 5.658190 AGGAATACCAAATGGAGTCCAATTG 59.342 40.000 26.87 26.87 42.28 2.32
167 168 5.842339 AGGAATACCAAATGGAGTCCAATT 58.158 37.500 17.71 11.88 36.32 2.32
168 169 5.472301 AGGAATACCAAATGGAGTCCAAT 57.528 39.130 17.71 4.50 36.32 3.16
169 170 4.946160 AGGAATACCAAATGGAGTCCAA 57.054 40.909 17.71 0.00 36.32 3.53
170 171 4.946160 AAGGAATACCAAATGGAGTCCA 57.054 40.909 15.88 15.88 38.94 4.02
171 172 6.605471 AAAAAGGAATACCAAATGGAGTCC 57.395 37.500 6.42 0.73 38.94 3.85
194 195 9.727859 TGGTAGTTTAATGCTATTTACTCACAA 57.272 29.630 0.00 0.00 0.00 3.33
195 196 9.158233 GTGGTAGTTTAATGCTATTTACTCACA 57.842 33.333 0.00 0.00 0.00 3.58
544 623 1.404748 GGCGTCCAAGAGTAGGAGTAC 59.595 57.143 0.00 0.00 35.42 2.73
545 624 1.005097 TGGCGTCCAAGAGTAGGAGTA 59.995 52.381 0.00 0.00 35.42 2.59
546 625 0.251653 TGGCGTCCAAGAGTAGGAGT 60.252 55.000 0.00 0.00 35.42 3.85
547 626 0.457851 CTGGCGTCCAAGAGTAGGAG 59.542 60.000 0.35 0.00 35.42 3.69
548 627 1.605058 GCTGGCGTCCAAGAGTAGGA 61.605 60.000 0.35 0.00 30.80 2.94
549 628 1.153549 GCTGGCGTCCAAGAGTAGG 60.154 63.158 0.35 0.00 30.80 3.18
550 629 1.517257 CGCTGGCGTCCAAGAGTAG 60.517 63.158 6.83 0.00 30.80 2.57
551 630 2.571757 CGCTGGCGTCCAAGAGTA 59.428 61.111 6.83 0.00 30.80 2.59
552 631 4.379243 CCGCTGGCGTCCAAGAGT 62.379 66.667 13.84 0.00 37.81 3.24
1124 1214 5.590259 ACCTGACATCCTTGTAAATACATGC 59.410 40.000 0.00 0.00 35.79 4.06
1143 1233 2.306847 GGGTTCAGAAAAGCAACCTGA 58.693 47.619 0.00 0.00 39.73 3.86
1424 1533 7.710907 TGAAATATACATCACTAAGTGCACTCC 59.289 37.037 21.95 0.00 32.98 3.85
1526 1635 0.529378 CAGCCTGGACAAGCAATTCC 59.471 55.000 0.00 0.00 0.00 3.01
2093 2215 5.083122 TCACATTCCCCAAAATGTACACAT 58.917 37.500 0.00 0.00 45.68 3.21
2094 2216 4.474394 TCACATTCCCCAAAATGTACACA 58.526 39.130 0.00 0.00 45.68 3.72
2160 2282 7.938140 AGCATTAAAGGTTCTAGCAACATAA 57.062 32.000 7.18 4.67 0.00 1.90
2165 2289 7.996098 AACTTAGCATTAAAGGTTCTAGCAA 57.004 32.000 0.00 0.00 0.00 3.91
2388 2529 4.593634 GGGTGGAGTAGGCTATTTATGAGT 59.406 45.833 0.00 0.00 0.00 3.41
2710 2853 4.016479 AGGGTGAGGAGTGATTACTTCCTA 60.016 45.833 8.09 0.00 37.25 2.94
2714 2857 3.519913 GGAAGGGTGAGGAGTGATTACTT 59.480 47.826 0.00 0.00 37.25 2.24
2722 2865 0.838122 CTGGTGGAAGGGTGAGGAGT 60.838 60.000 0.00 0.00 0.00 3.85
2736 2879 2.949106 CGCCACTTTGCTCTGGTG 59.051 61.111 0.00 0.00 0.00 4.17
2829 2975 5.871396 AGAGTTGTACAGAAAGTGGAAGA 57.129 39.130 0.00 0.00 0.00 2.87
2860 3006 1.894466 TCCCACCATGCAAACATTCTG 59.106 47.619 0.00 0.00 32.87 3.02


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

AutoCloner maintained by Alex Coulton.