Multiple sequence alignment - TraesCS2A01G215000

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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 TraesCS2A01G215000 chr2A 100.000 2913 0 0 1 2913 202044461 202041549 0.000000e+00 5380
1 TraesCS2A01G215000 chr2B 94.949 1881 66 16 167 2037 244537441 244535580 0.000000e+00 2920
2 TraesCS2A01G215000 chr2B 91.756 837 37 11 2101 2913 244535400 244534572 0.000000e+00 1134
3 TraesCS2A01G215000 chr2B 88.690 168 19 0 1 168 244564326 244564159 3.810000e-49 206
4 TraesCS2A01G215000 chr2B 95.455 66 3 0 2036 2101 244535555 244535490 3.970000e-19 106
5 TraesCS2A01G215000 chr2D 91.244 1439 74 23 269 1697 188434346 188432950 0.000000e+00 1912
6 TraesCS2A01G215000 chr2D 98.482 461 5 2 2454 2913 188432083 188431624 0.000000e+00 811
7 TraesCS2A01G215000 chr2D 85.976 763 42 36 1736 2455 188432948 188432208 0.000000e+00 756


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 TraesCS2A01G215000 chr2A 202041549 202044461 2912 True 5380.000000 5380 100.000000 1 2913 1 chr2A.!!$R1 2912
1 TraesCS2A01G215000 chr2B 244534572 244537441 2869 True 1386.666667 2920 94.053333 167 2913 3 chr2B.!!$R2 2746
2 TraesCS2A01G215000 chr2D 188431624 188434346 2722 True 1159.666667 1912 91.900667 269 2913 3 chr2D.!!$R1 2644

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
750 758 0.318699 CACCGTCGACACATGTCTGT 60.319 55.0 17.16 0.0 42.66 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2254 0.747852 TGTGTACTCGTGGCTGTTGA 59.252 50.0 0.0 0.0 0.0 3.18 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 4.725790 AAAAACCATGCTCTTGATAGCC 57.274 40.909 0.00 0.00 42.05 3.93
28 29 3.370840 AAACCATGCTCTTGATAGCCA 57.629 42.857 0.00 0.00 42.05 4.75
29 30 2.338577 ACCATGCTCTTGATAGCCAC 57.661 50.000 0.00 0.00 42.05 5.01
30 31 1.133976 ACCATGCTCTTGATAGCCACC 60.134 52.381 0.00 0.00 42.05 4.61
31 32 1.224075 CATGCTCTTGATAGCCACCG 58.776 55.000 0.00 0.00 42.05 4.94
32 33 0.533755 ATGCTCTTGATAGCCACCGC 60.534 55.000 0.00 0.00 42.05 5.68
40 41 3.207354 TAGCCACCGCTAGTCTGC 58.793 61.111 0.00 0.00 46.08 4.26
41 42 1.379977 TAGCCACCGCTAGTCTGCT 60.380 57.895 0.00 0.00 46.08 4.24
42 43 1.384989 TAGCCACCGCTAGTCTGCTC 61.385 60.000 0.00 0.00 46.08 4.26
43 44 2.716017 GCCACCGCTAGTCTGCTCT 61.716 63.158 0.00 0.00 0.00 4.09
44 45 1.140589 CCACCGCTAGTCTGCTCTG 59.859 63.158 0.00 0.00 0.00 3.35
45 46 1.518133 CACCGCTAGTCTGCTCTGC 60.518 63.158 0.00 0.00 0.00 4.26
46 47 1.680651 ACCGCTAGTCTGCTCTGCT 60.681 57.895 0.00 0.00 0.00 4.24
47 48 1.254284 ACCGCTAGTCTGCTCTGCTT 61.254 55.000 0.00 0.00 0.00 3.91
48 49 0.527385 CCGCTAGTCTGCTCTGCTTC 60.527 60.000 0.00 0.00 0.00 3.86
49 50 0.527385 CGCTAGTCTGCTCTGCTTCC 60.527 60.000 0.00 0.00 0.00 3.46
50 51 0.534412 GCTAGTCTGCTCTGCTTCCA 59.466 55.000 0.00 0.00 0.00 3.53
51 52 1.066573 GCTAGTCTGCTCTGCTTCCAA 60.067 52.381 0.00 0.00 0.00 3.53
52 53 2.419851 GCTAGTCTGCTCTGCTTCCAAT 60.420 50.000 0.00 0.00 0.00 3.16
53 54 2.875094 AGTCTGCTCTGCTTCCAATT 57.125 45.000 0.00 0.00 0.00 2.32
54 55 2.434428 AGTCTGCTCTGCTTCCAATTG 58.566 47.619 0.00 0.00 0.00 2.32
55 56 2.157738 GTCTGCTCTGCTTCCAATTGT 58.842 47.619 4.43 0.00 0.00 2.71
56 57 2.095364 GTCTGCTCTGCTTCCAATTGTG 60.095 50.000 4.43 0.00 0.00 3.33
57 58 1.884579 CTGCTCTGCTTCCAATTGTGT 59.115 47.619 4.43 0.00 0.00 3.72
58 59 1.610038 TGCTCTGCTTCCAATTGTGTG 59.390 47.619 4.43 0.00 0.00 3.82
59 60 1.881973 GCTCTGCTTCCAATTGTGTGA 59.118 47.619 4.43 0.00 0.00 3.58
60 61 2.351157 GCTCTGCTTCCAATTGTGTGAC 60.351 50.000 4.43 0.00 0.00 3.67
61 62 3.144506 CTCTGCTTCCAATTGTGTGACT 58.855 45.455 4.43 0.00 0.00 3.41
62 63 4.318332 CTCTGCTTCCAATTGTGTGACTA 58.682 43.478 4.43 0.00 0.00 2.59
63 64 4.713553 TCTGCTTCCAATTGTGTGACTAA 58.286 39.130 4.43 0.00 0.00 2.24
64 65 4.515191 TCTGCTTCCAATTGTGTGACTAAC 59.485 41.667 4.43 0.00 0.00 2.34
65 66 4.203226 TGCTTCCAATTGTGTGACTAACA 58.797 39.130 4.43 0.00 36.04 2.41
77 78 3.968649 GTGACTAACACTGTACCGAACA 58.031 45.455 0.00 0.00 45.13 3.18
78 79 4.553323 GTGACTAACACTGTACCGAACAT 58.447 43.478 0.00 0.00 45.13 2.71
79 80 4.986659 GTGACTAACACTGTACCGAACATT 59.013 41.667 0.00 0.00 45.13 2.71
80 81 5.464389 GTGACTAACACTGTACCGAACATTT 59.536 40.000 0.00 0.00 45.13 2.32
81 82 5.693104 TGACTAACACTGTACCGAACATTTC 59.307 40.000 0.00 0.00 37.50 2.17
122 123 8.102800 TCACATATTGCATATTCATTCACTCC 57.897 34.615 0.00 0.00 0.00 3.85
123 124 7.940688 TCACATATTGCATATTCATTCACTCCT 59.059 33.333 0.00 0.00 0.00 3.69
124 125 8.573885 CACATATTGCATATTCATTCACTCCTT 58.426 33.333 0.00 0.00 0.00 3.36
125 126 8.790718 ACATATTGCATATTCATTCACTCCTTC 58.209 33.333 0.00 0.00 0.00 3.46
126 127 6.645790 ATTGCATATTCATTCACTCCTTCC 57.354 37.500 0.00 0.00 0.00 3.46
127 128 5.378230 TGCATATTCATTCACTCCTTCCT 57.622 39.130 0.00 0.00 0.00 3.36
128 129 5.128205 TGCATATTCATTCACTCCTTCCTG 58.872 41.667 0.00 0.00 0.00 3.86
129 130 4.023365 GCATATTCATTCACTCCTTCCTGC 60.023 45.833 0.00 0.00 0.00 4.85
130 131 2.496899 TTCATTCACTCCTTCCTGCC 57.503 50.000 0.00 0.00 0.00 4.85
131 132 1.361204 TCATTCACTCCTTCCTGCCA 58.639 50.000 0.00 0.00 0.00 4.92
132 133 1.704628 TCATTCACTCCTTCCTGCCAA 59.295 47.619 0.00 0.00 0.00 4.52
133 134 2.309755 TCATTCACTCCTTCCTGCCAAT 59.690 45.455 0.00 0.00 0.00 3.16
134 135 2.205022 TTCACTCCTTCCTGCCAATG 57.795 50.000 0.00 0.00 0.00 2.82
135 136 1.067295 TCACTCCTTCCTGCCAATGT 58.933 50.000 0.00 0.00 0.00 2.71
136 137 1.425066 TCACTCCTTCCTGCCAATGTT 59.575 47.619 0.00 0.00 0.00 2.71
137 138 1.542915 CACTCCTTCCTGCCAATGTTG 59.457 52.381 0.00 0.00 0.00 3.33
138 139 1.425066 ACTCCTTCCTGCCAATGTTGA 59.575 47.619 0.00 0.00 0.00 3.18
139 140 2.042162 ACTCCTTCCTGCCAATGTTGAT 59.958 45.455 0.00 0.00 0.00 2.57
140 141 2.686915 CTCCTTCCTGCCAATGTTGATC 59.313 50.000 0.00 0.00 0.00 2.92
141 142 1.402968 CCTTCCTGCCAATGTTGATCG 59.597 52.381 0.00 0.00 0.00 3.69
142 143 1.402968 CTTCCTGCCAATGTTGATCGG 59.597 52.381 0.00 0.00 0.00 4.18
143 144 0.394216 TCCTGCCAATGTTGATCGGG 60.394 55.000 0.00 1.24 0.00 5.14
144 145 0.680921 CCTGCCAATGTTGATCGGGT 60.681 55.000 0.00 0.00 0.00 5.28
145 146 1.176527 CTGCCAATGTTGATCGGGTT 58.823 50.000 0.00 0.00 0.00 4.11
146 147 0.887247 TGCCAATGTTGATCGGGTTG 59.113 50.000 0.00 0.00 0.00 3.77
147 148 1.173043 GCCAATGTTGATCGGGTTGA 58.827 50.000 0.00 0.00 0.00 3.18
148 149 1.135402 GCCAATGTTGATCGGGTTGAC 60.135 52.381 0.00 0.00 0.00 3.18
149 150 2.158559 CCAATGTTGATCGGGTTGACA 58.841 47.619 0.00 0.00 0.00 3.58
150 151 2.556189 CCAATGTTGATCGGGTTGACAA 59.444 45.455 0.00 0.00 0.00 3.18
151 152 3.005261 CCAATGTTGATCGGGTTGACAAA 59.995 43.478 0.00 0.00 0.00 2.83
152 153 4.321899 CCAATGTTGATCGGGTTGACAAAT 60.322 41.667 0.00 0.00 0.00 2.32
153 154 4.701956 ATGTTGATCGGGTTGACAAATC 57.298 40.909 0.00 0.00 0.00 2.17
154 155 3.750371 TGTTGATCGGGTTGACAAATCT 58.250 40.909 0.00 0.00 0.00 2.40
155 156 3.751175 TGTTGATCGGGTTGACAAATCTC 59.249 43.478 0.00 0.00 0.00 2.75
156 157 3.981071 TGATCGGGTTGACAAATCTCT 57.019 42.857 0.00 0.00 0.00 3.10
157 158 4.286297 TGATCGGGTTGACAAATCTCTT 57.714 40.909 0.00 0.00 0.00 2.85
158 159 5.414789 TGATCGGGTTGACAAATCTCTTA 57.585 39.130 0.00 0.00 0.00 2.10
159 160 5.175859 TGATCGGGTTGACAAATCTCTTAC 58.824 41.667 0.00 0.00 0.00 2.34
160 161 3.934068 TCGGGTTGACAAATCTCTTACC 58.066 45.455 0.00 0.00 0.00 2.85
161 162 3.581332 TCGGGTTGACAAATCTCTTACCT 59.419 43.478 0.00 0.00 0.00 3.08
162 163 4.041198 TCGGGTTGACAAATCTCTTACCTT 59.959 41.667 0.00 0.00 0.00 3.50
163 164 5.246656 TCGGGTTGACAAATCTCTTACCTTA 59.753 40.000 0.00 0.00 0.00 2.69
164 165 5.350640 CGGGTTGACAAATCTCTTACCTTAC 59.649 44.000 0.00 0.00 0.00 2.34
165 166 6.473758 GGGTTGACAAATCTCTTACCTTACT 58.526 40.000 0.00 0.00 0.00 2.24
174 175 2.429610 CTCTTACCTTACTGCGCCCTAA 59.570 50.000 4.18 0.00 0.00 2.69
194 195 6.240002 CCCTAATAGGCCATAACTTCATGACT 60.240 42.308 5.01 0.00 32.73 3.41
199 200 5.216622 AGGCCATAACTTCATGACTACCTA 58.783 41.667 5.01 0.00 0.00 3.08
205 206 7.707035 CCATAACTTCATGACTACCTAGACAAC 59.293 40.741 0.00 0.00 32.27 3.32
212 213 4.737578 TGACTACCTAGACAACTGAGGTT 58.262 43.478 0.00 0.00 40.85 3.50
232 233 3.663995 TGGTGTTGAATCCATTGCAAG 57.336 42.857 4.94 0.00 0.00 4.01
251 252 2.563406 AGCCCTAAGACCCTAAGCTTT 58.437 47.619 3.20 0.00 0.00 3.51
253 254 2.421670 GCCCTAAGACCCTAAGCTTTCC 60.422 54.545 3.20 0.00 0.00 3.13
263 264 3.416156 CCTAAGCTTTCCCATAGGATGC 58.584 50.000 3.20 0.00 43.54 3.91
313 318 1.665442 GGTGTTGGCGCCAATCTTT 59.335 52.632 41.80 0.00 44.43 2.52
356 361 6.774656 TGATCTCTCTAGCTCACATTGTGATA 59.225 38.462 19.29 9.49 41.94 2.15
414 419 5.991606 TGAAATAGGGCGAGAAACATAGATG 59.008 40.000 0.00 0.00 0.00 2.90
417 422 3.300388 AGGGCGAGAAACATAGATGAGA 58.700 45.455 0.00 0.00 0.00 3.27
432 437 1.280982 TGAGATCGACGCAAATCTGC 58.719 50.000 2.56 0.00 45.75 4.26
633 641 6.927416 AGTGAAATTTCAAATGCTATGCTGA 58.073 32.000 22.07 0.00 39.21 4.26
750 758 0.318699 CACCGTCGACACATGTCTGT 60.319 55.000 17.16 0.00 42.66 3.41
792 800 1.026718 CCAAATGGAGGTCAGGCGAC 61.027 60.000 0.00 0.00 38.31 5.19
874 882 1.772063 GATAAGGTTTCGCGCCGCAT 61.772 55.000 10.75 0.00 0.00 4.73
889 897 1.425428 GCATAGGACAGCAACACGC 59.575 57.895 0.00 0.00 42.91 5.34
915 923 6.055588 ACACGTCCTCCTCATATATTTTTGG 58.944 40.000 0.00 0.00 0.00 3.28
1262 1270 4.767255 CCGTGAGTGCCTCCAGCC 62.767 72.222 0.50 0.00 42.71 4.85
1290 1306 7.516481 TCGTACATCATCTATACTCGCTTTAC 58.484 38.462 0.00 0.00 0.00 2.01
1291 1307 7.172019 TCGTACATCATCTATACTCGCTTTACA 59.828 37.037 0.00 0.00 0.00 2.41
1292 1308 7.268659 CGTACATCATCTATACTCGCTTTACAC 59.731 40.741 0.00 0.00 0.00 2.90
1293 1309 7.039313 ACATCATCTATACTCGCTTTACACA 57.961 36.000 0.00 0.00 0.00 3.72
1295 1311 8.144478 ACATCATCTATACTCGCTTTACACAAT 58.856 33.333 0.00 0.00 0.00 2.71
1296 1312 9.626045 CATCATCTATACTCGCTTTACACAATA 57.374 33.333 0.00 0.00 0.00 1.90
1360 1377 2.237643 TGGATGATTTGGGTGTGTGTG 58.762 47.619 0.00 0.00 0.00 3.82
1361 1378 2.238521 GGATGATTTGGGTGTGTGTGT 58.761 47.619 0.00 0.00 0.00 3.72
1695 1712 2.119801 ACCATCTCGCAATTTCAGCT 57.880 45.000 0.00 0.00 0.00 4.24
1696 1713 3.266510 ACCATCTCGCAATTTCAGCTA 57.733 42.857 0.00 0.00 0.00 3.32
1697 1714 3.813443 ACCATCTCGCAATTTCAGCTAT 58.187 40.909 0.00 0.00 0.00 2.97
1801 1821 1.131638 AACAGGTGTGAGCTTCTCCA 58.868 50.000 11.55 0.00 0.00 3.86
2092 2138 1.129624 TGCGCACAAATCCGATGTAAC 59.870 47.619 5.66 0.00 0.00 2.50
2108 2154 7.274033 TCCGATGTAACAACGAATAGTAACTTG 59.726 37.037 0.00 0.00 31.46 3.16
2119 2254 6.037098 CGAATAGTAACTTGCAGTTAGAGCT 58.963 40.000 8.44 0.00 40.95 4.09
2134 2269 4.988065 GCTCAACAGCCACGAGTA 57.012 55.556 0.00 0.00 40.14 2.59
2135 2270 2.446341 GCTCAACAGCCACGAGTAC 58.554 57.895 0.00 0.00 40.14 2.73
2226 2368 1.671845 GTCAGTAAACACCGTGCCAAA 59.328 47.619 0.00 0.00 0.00 3.28
2266 2415 6.902771 TTCCCCACGATTTTCATTAAGAAA 57.097 33.333 0.00 0.00 44.21 2.52
2305 2454 2.158842 ACAAGCATCAGCCTAGTCATCC 60.159 50.000 0.00 0.00 43.56 3.51
2365 2522 4.367039 AAGACCAGCTAAACAGGCTTAA 57.633 40.909 0.00 0.00 38.03 1.85
2371 2528 6.116126 ACCAGCTAAACAGGCTTAAATCTAG 58.884 40.000 0.00 0.00 38.03 2.43
2426 2583 5.451242 GCTACAAGTTCCAAACCAATGACAA 60.451 40.000 0.00 0.00 0.00 3.18
2440 2597 0.943673 TGACAACAATGACGTGCCAG 59.056 50.000 0.00 0.00 0.00 4.85
2452 2609 2.866762 GACGTGCCAGGTATTTGAGATC 59.133 50.000 0.00 0.00 0.00 2.75
2471 2754 6.168270 AGATCTAACAGAAATCAGCTACCC 57.832 41.667 0.00 0.00 0.00 3.69
2510 2793 6.036517 CAGCTGATAAGTGTTTATCCTGTCAC 59.963 42.308 8.42 0.00 42.93 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.082026 GTGGCTATCAAGAGCATGGTTTTT 60.082 41.667 0.00 0.00 44.76 1.94
7 8 3.445096 GTGGCTATCAAGAGCATGGTTTT 59.555 43.478 0.00 0.00 44.76 2.43
8 9 3.019564 GTGGCTATCAAGAGCATGGTTT 58.980 45.455 0.00 0.00 44.76 3.27
9 10 2.648059 GTGGCTATCAAGAGCATGGTT 58.352 47.619 0.00 0.00 44.76 3.67
10 11 1.133976 GGTGGCTATCAAGAGCATGGT 60.134 52.381 0.00 0.00 44.76 3.55
11 12 1.602311 GGTGGCTATCAAGAGCATGG 58.398 55.000 0.00 0.00 44.76 3.66
12 13 1.224075 CGGTGGCTATCAAGAGCATG 58.776 55.000 0.00 0.00 44.76 4.06
13 14 0.533755 GCGGTGGCTATCAAGAGCAT 60.534 55.000 0.00 0.00 44.76 3.79
14 15 1.153369 GCGGTGGCTATCAAGAGCA 60.153 57.895 0.00 0.00 44.76 4.26
15 16 3.724494 GCGGTGGCTATCAAGAGC 58.276 61.111 0.00 0.00 42.05 4.09
25 26 2.202810 GAGCAGACTAGCGGTGGC 60.203 66.667 0.00 0.00 40.15 5.01
26 27 1.140589 CAGAGCAGACTAGCGGTGG 59.859 63.158 0.00 0.00 40.15 4.61
27 28 1.518133 GCAGAGCAGACTAGCGGTG 60.518 63.158 0.00 0.00 40.15 4.94
28 29 1.254284 AAGCAGAGCAGACTAGCGGT 61.254 55.000 0.00 0.00 40.15 5.68
29 30 0.527385 GAAGCAGAGCAGACTAGCGG 60.527 60.000 0.00 0.00 40.15 5.52
30 31 0.527385 GGAAGCAGAGCAGACTAGCG 60.527 60.000 0.00 0.00 40.15 4.26
31 32 0.534412 TGGAAGCAGAGCAGACTAGC 59.466 55.000 0.00 0.00 0.00 3.42
32 33 3.540314 ATTGGAAGCAGAGCAGACTAG 57.460 47.619 0.00 0.00 0.00 2.57
33 34 3.008375 ACAATTGGAAGCAGAGCAGACTA 59.992 43.478 10.83 0.00 0.00 2.59
34 35 2.224719 ACAATTGGAAGCAGAGCAGACT 60.225 45.455 10.83 0.00 0.00 3.24
35 36 2.095364 CACAATTGGAAGCAGAGCAGAC 60.095 50.000 10.83 0.00 0.00 3.51
36 37 2.156917 CACAATTGGAAGCAGAGCAGA 58.843 47.619 10.83 0.00 0.00 4.26
37 38 1.884579 ACACAATTGGAAGCAGAGCAG 59.115 47.619 10.83 0.00 0.00 4.24
38 39 1.610038 CACACAATTGGAAGCAGAGCA 59.390 47.619 10.83 0.00 0.00 4.26
39 40 1.881973 TCACACAATTGGAAGCAGAGC 59.118 47.619 10.83 0.00 0.00 4.09
40 41 3.144506 AGTCACACAATTGGAAGCAGAG 58.855 45.455 10.83 0.00 0.00 3.35
41 42 3.213206 AGTCACACAATTGGAAGCAGA 57.787 42.857 10.83 0.00 0.00 4.26
42 43 4.275689 TGTTAGTCACACAATTGGAAGCAG 59.724 41.667 10.83 0.00 0.00 4.24
43 44 4.203226 TGTTAGTCACACAATTGGAAGCA 58.797 39.130 10.83 0.00 0.00 3.91
44 45 4.829064 TGTTAGTCACACAATTGGAAGC 57.171 40.909 10.83 0.00 0.00 3.86
56 57 3.968649 TGTTCGGTACAGTGTTAGTCAC 58.031 45.455 0.00 0.00 46.46 3.67
57 58 4.859304 ATGTTCGGTACAGTGTTAGTCA 57.141 40.909 0.00 0.00 40.83 3.41
58 59 6.149504 GAAATGTTCGGTACAGTGTTAGTC 57.850 41.667 0.00 0.00 40.83 2.59
96 97 8.737175 GGAGTGAATGAATATGCAATATGTGAT 58.263 33.333 0.00 0.00 38.94 3.06
97 98 7.940688 AGGAGTGAATGAATATGCAATATGTGA 59.059 33.333 0.00 0.00 38.94 3.58
98 99 8.107399 AGGAGTGAATGAATATGCAATATGTG 57.893 34.615 0.00 0.00 38.94 3.21
99 100 8.701908 AAGGAGTGAATGAATATGCAATATGT 57.298 30.769 0.00 0.00 38.94 2.29
100 101 8.242053 GGAAGGAGTGAATGAATATGCAATATG 58.758 37.037 0.00 0.00 38.94 1.78
101 102 8.168725 AGGAAGGAGTGAATGAATATGCAATAT 58.831 33.333 0.00 0.00 42.49 1.28
102 103 7.446319 CAGGAAGGAGTGAATGAATATGCAATA 59.554 37.037 0.00 0.00 0.00 1.90
103 104 6.264744 CAGGAAGGAGTGAATGAATATGCAAT 59.735 38.462 0.00 0.00 0.00 3.56
104 105 5.591472 CAGGAAGGAGTGAATGAATATGCAA 59.409 40.000 0.00 0.00 0.00 4.08
105 106 5.128205 CAGGAAGGAGTGAATGAATATGCA 58.872 41.667 0.00 0.00 0.00 3.96
106 107 4.023365 GCAGGAAGGAGTGAATGAATATGC 60.023 45.833 0.00 0.00 0.00 3.14
107 108 4.518211 GGCAGGAAGGAGTGAATGAATATG 59.482 45.833 0.00 0.00 0.00 1.78
108 109 4.166725 TGGCAGGAAGGAGTGAATGAATAT 59.833 41.667 0.00 0.00 0.00 1.28
109 110 3.523157 TGGCAGGAAGGAGTGAATGAATA 59.477 43.478 0.00 0.00 0.00 1.75
110 111 2.309755 TGGCAGGAAGGAGTGAATGAAT 59.690 45.455 0.00 0.00 0.00 2.57
111 112 1.704628 TGGCAGGAAGGAGTGAATGAA 59.295 47.619 0.00 0.00 0.00 2.57
112 113 1.361204 TGGCAGGAAGGAGTGAATGA 58.639 50.000 0.00 0.00 0.00 2.57
113 114 2.205022 TTGGCAGGAAGGAGTGAATG 57.795 50.000 0.00 0.00 0.00 2.67
114 115 2.042162 ACATTGGCAGGAAGGAGTGAAT 59.958 45.455 0.00 0.00 0.00 2.57
115 116 1.425066 ACATTGGCAGGAAGGAGTGAA 59.575 47.619 0.00 0.00 0.00 3.18
116 117 1.067295 ACATTGGCAGGAAGGAGTGA 58.933 50.000 0.00 0.00 0.00 3.41
117 118 1.542915 CAACATTGGCAGGAAGGAGTG 59.457 52.381 0.00 0.00 0.00 3.51
118 119 1.425066 TCAACATTGGCAGGAAGGAGT 59.575 47.619 0.00 0.00 0.00 3.85
119 120 2.205022 TCAACATTGGCAGGAAGGAG 57.795 50.000 0.00 0.00 0.00 3.69
120 121 2.726821 GATCAACATTGGCAGGAAGGA 58.273 47.619 0.00 0.00 0.00 3.36
121 122 1.402968 CGATCAACATTGGCAGGAAGG 59.597 52.381 0.00 0.00 0.00 3.46
122 123 1.402968 CCGATCAACATTGGCAGGAAG 59.597 52.381 0.00 0.00 0.00 3.46
123 124 1.462616 CCGATCAACATTGGCAGGAA 58.537 50.000 0.00 0.00 0.00 3.36
124 125 0.394216 CCCGATCAACATTGGCAGGA 60.394 55.000 0.00 0.00 32.39 3.86
125 126 0.680921 ACCCGATCAACATTGGCAGG 60.681 55.000 0.00 0.00 32.39 4.85
126 127 1.135315 CAACCCGATCAACATTGGCAG 60.135 52.381 0.00 0.00 32.39 4.85
127 128 0.887247 CAACCCGATCAACATTGGCA 59.113 50.000 0.00 0.00 32.39 4.92
128 129 1.135402 GTCAACCCGATCAACATTGGC 60.135 52.381 0.00 0.00 32.39 4.52
129 130 2.158559 TGTCAACCCGATCAACATTGG 58.841 47.619 0.00 0.00 33.49 3.16
130 131 3.913548 TTGTCAACCCGATCAACATTG 57.086 42.857 0.00 0.00 0.00 2.82
131 132 4.766891 AGATTTGTCAACCCGATCAACATT 59.233 37.500 0.00 0.00 0.00 2.71
132 133 4.335416 AGATTTGTCAACCCGATCAACAT 58.665 39.130 0.00 0.00 0.00 2.71
133 134 3.750371 AGATTTGTCAACCCGATCAACA 58.250 40.909 0.00 0.00 0.00 3.33
134 135 4.003648 AGAGATTTGTCAACCCGATCAAC 58.996 43.478 0.00 0.00 0.00 3.18
135 136 4.286297 AGAGATTTGTCAACCCGATCAA 57.714 40.909 0.00 0.00 0.00 2.57
136 137 3.981071 AGAGATTTGTCAACCCGATCA 57.019 42.857 0.00 0.00 0.00 2.92
137 138 4.571176 GGTAAGAGATTTGTCAACCCGATC 59.429 45.833 0.00 0.00 0.00 3.69
138 139 4.225267 AGGTAAGAGATTTGTCAACCCGAT 59.775 41.667 0.00 0.00 0.00 4.18
139 140 3.581332 AGGTAAGAGATTTGTCAACCCGA 59.419 43.478 0.00 0.00 0.00 5.14
140 141 3.939066 AGGTAAGAGATTTGTCAACCCG 58.061 45.455 0.00 0.00 0.00 5.28
141 142 6.371825 CAGTAAGGTAAGAGATTTGTCAACCC 59.628 42.308 0.00 0.00 0.00 4.11
142 143 6.128254 GCAGTAAGGTAAGAGATTTGTCAACC 60.128 42.308 0.00 0.00 0.00 3.77
143 144 6.401153 CGCAGTAAGGTAAGAGATTTGTCAAC 60.401 42.308 0.00 0.00 0.00 3.18
144 145 5.637810 CGCAGTAAGGTAAGAGATTTGTCAA 59.362 40.000 0.00 0.00 0.00 3.18
145 146 5.168569 CGCAGTAAGGTAAGAGATTTGTCA 58.831 41.667 0.00 0.00 0.00 3.58
146 147 4.033014 GCGCAGTAAGGTAAGAGATTTGTC 59.967 45.833 0.30 0.00 0.00 3.18
147 148 3.933332 GCGCAGTAAGGTAAGAGATTTGT 59.067 43.478 0.30 0.00 0.00 2.83
148 149 3.309954 GGCGCAGTAAGGTAAGAGATTTG 59.690 47.826 10.83 0.00 0.00 2.32
149 150 3.532542 GGCGCAGTAAGGTAAGAGATTT 58.467 45.455 10.83 0.00 0.00 2.17
150 151 2.158943 GGGCGCAGTAAGGTAAGAGATT 60.159 50.000 10.83 0.00 0.00 2.40
151 152 1.413077 GGGCGCAGTAAGGTAAGAGAT 59.587 52.381 10.83 0.00 0.00 2.75
152 153 0.822164 GGGCGCAGTAAGGTAAGAGA 59.178 55.000 10.83 0.00 0.00 3.10
153 154 0.824759 AGGGCGCAGTAAGGTAAGAG 59.175 55.000 10.83 0.00 0.00 2.85
154 155 2.148446 TAGGGCGCAGTAAGGTAAGA 57.852 50.000 10.83 0.00 0.00 2.10
155 156 2.973694 TTAGGGCGCAGTAAGGTAAG 57.026 50.000 10.83 0.00 0.00 2.34
156 157 3.322828 CCTATTAGGGCGCAGTAAGGTAA 59.677 47.826 10.83 0.00 0.00 2.85
157 158 2.895404 CCTATTAGGGCGCAGTAAGGTA 59.105 50.000 10.83 0.00 0.00 3.08
158 159 1.692519 CCTATTAGGGCGCAGTAAGGT 59.307 52.381 10.83 0.00 0.00 3.50
159 160 1.608283 GCCTATTAGGGCGCAGTAAGG 60.608 57.143 10.83 9.04 42.82 2.69
160 161 1.797025 GCCTATTAGGGCGCAGTAAG 58.203 55.000 10.83 0.00 42.82 2.34
174 175 5.846714 AGGTAGTCATGAAGTTATGGCCTAT 59.153 40.000 3.32 0.00 33.18 2.57
182 183 7.668469 TCAGTTGTCTAGGTAGTCATGAAGTTA 59.332 37.037 0.00 0.00 0.00 2.24
190 191 4.383931 ACCTCAGTTGTCTAGGTAGTCA 57.616 45.455 0.00 0.00 41.86 3.41
205 206 2.862541 TGGATTCAACACCAACCTCAG 58.137 47.619 0.00 0.00 32.93 3.35
212 213 2.288948 GCTTGCAATGGATTCAACACCA 60.289 45.455 0.00 0.00 40.57 4.17
213 214 2.340337 GCTTGCAATGGATTCAACACC 58.660 47.619 0.00 0.00 0.00 4.16
215 216 1.275856 GGGCTTGCAATGGATTCAACA 59.724 47.619 0.00 0.00 0.00 3.33
232 233 2.421670 GGAAAGCTTAGGGTCTTAGGGC 60.422 54.545 0.00 0.00 0.00 5.19
251 252 1.053835 TTCGCCAGCATCCTATGGGA 61.054 55.000 0.00 0.00 46.81 4.37
253 254 1.605710 CTTTTCGCCAGCATCCTATGG 59.394 52.381 0.00 0.00 39.73 2.74
263 264 4.155826 TGTCATTGGTATTCTTTTCGCCAG 59.844 41.667 0.00 0.00 0.00 4.85
264 265 4.075682 TGTCATTGGTATTCTTTTCGCCA 58.924 39.130 0.00 0.00 0.00 5.69
292 297 2.203480 ATTGGCGCCAACACCTGT 60.203 55.556 42.32 24.04 38.88 4.00
293 298 1.526575 AAGATTGGCGCCAACACCTG 61.527 55.000 42.32 0.00 38.88 4.00
313 318 0.613260 CATTCCTCACCCGACTTCCA 59.387 55.000 0.00 0.00 0.00 3.53
356 361 5.308014 TGCGGACTTGCATCAATCTAATAT 58.692 37.500 0.00 0.00 40.62 1.28
364 369 1.199789 GATGTTGCGGACTTGCATCAA 59.800 47.619 3.90 0.00 44.89 2.57
365 370 0.804364 GATGTTGCGGACTTGCATCA 59.196 50.000 2.41 2.41 45.78 3.07
451 456 6.412214 AGTAAGTTTACCACAACACAACTCT 58.588 36.000 0.00 0.00 34.19 3.24
585 592 6.762702 TCACATCACTGCATTAATCATTGT 57.237 33.333 0.00 0.00 0.00 2.71
633 641 3.631250 ACACCATGGCCGATTTCTTTAT 58.369 40.909 13.04 0.00 0.00 1.40
750 758 2.356278 GCCCTGGCCAATGAGTGA 59.644 61.111 7.01 0.00 34.56 3.41
792 800 4.789075 GGCTTGTGGCATGCTGCG 62.789 66.667 18.92 3.30 46.21 5.18
889 897 7.385205 CCAAAAATATATGAGGAGGACGTGTAG 59.615 40.741 0.00 0.00 0.00 2.74
1262 1270 4.569981 CGAGTATAGATGATGTACGAGCG 58.430 47.826 0.00 0.00 31.17 5.03
1304 1320 7.652507 GCGTAAAATTCTACTCCTTGCTATACT 59.347 37.037 0.00 0.00 0.00 2.12
1305 1321 7.095732 GGCGTAAAATTCTACTCCTTGCTATAC 60.096 40.741 0.00 0.00 0.00 1.47
1308 1324 5.105064 AGGCGTAAAATTCTACTCCTTGCTA 60.105 40.000 0.00 0.00 34.04 3.49
1309 1325 3.939592 GGCGTAAAATTCTACTCCTTGCT 59.060 43.478 0.00 0.00 0.00 3.91
1311 1327 5.175859 TCAGGCGTAAAATTCTACTCCTTG 58.824 41.667 0.00 0.00 35.29 3.61
1312 1328 5.416271 TCAGGCGTAAAATTCTACTCCTT 57.584 39.130 0.00 0.00 35.29 3.36
1313 1329 5.364157 AGATCAGGCGTAAAATTCTACTCCT 59.636 40.000 0.00 0.00 37.46 3.69
1314 1330 5.463724 CAGATCAGGCGTAAAATTCTACTCC 59.536 44.000 0.00 0.00 0.00 3.85
1315 1331 6.273825 TCAGATCAGGCGTAAAATTCTACTC 58.726 40.000 0.00 0.00 0.00 2.59
1316 1332 6.222038 TCAGATCAGGCGTAAAATTCTACT 57.778 37.500 0.00 0.00 0.00 2.57
1317 1333 6.073548 CCATCAGATCAGGCGTAAAATTCTAC 60.074 42.308 0.00 0.00 0.00 2.59
1318 1334 5.991606 CCATCAGATCAGGCGTAAAATTCTA 59.008 40.000 0.00 0.00 0.00 2.10
1319 1335 4.818546 CCATCAGATCAGGCGTAAAATTCT 59.181 41.667 0.00 0.00 0.00 2.40
1320 1336 4.816385 TCCATCAGATCAGGCGTAAAATTC 59.184 41.667 0.00 0.00 0.00 2.17
1321 1337 4.780815 TCCATCAGATCAGGCGTAAAATT 58.219 39.130 0.00 0.00 0.00 1.82
1382 1399 1.079057 GAAGTCCCTTGCCTCGTCC 60.079 63.158 0.00 0.00 0.00 4.79
1696 1713 9.388506 CATGTTTCTGAAGAGACATAAGGTAAT 57.611 33.333 14.18 0.00 44.77 1.89
1697 1714 7.824289 CCATGTTTCTGAAGAGACATAAGGTAA 59.176 37.037 14.18 0.00 44.77 2.85
1801 1821 3.540314 TGGTCAAGCTGCAAACAAAAT 57.460 38.095 1.02 0.00 0.00 1.82
2108 2154 1.082690 GGCTGTTGAGCTCTAACTGC 58.917 55.000 30.25 30.25 45.44 4.40
2119 2254 0.747852 TGTGTACTCGTGGCTGTTGA 59.252 50.000 0.00 0.00 0.00 3.18
2129 2264 3.985925 GGTTGGACTAAACTGTGTACTCG 59.014 47.826 0.00 0.00 0.00 4.18
2134 2269 3.547054 TTCGGTTGGACTAAACTGTGT 57.453 42.857 0.00 0.00 37.62 3.72
2135 2270 6.737254 ATTATTCGGTTGGACTAAACTGTG 57.263 37.500 0.00 0.00 37.62 3.66
2266 2415 9.277783 GATGCTTGTATGAACTTCTATATGGTT 57.722 33.333 0.00 0.00 0.00 3.67
2326 2475 1.879380 CTTTGCTGTTCCCGTTGATCA 59.121 47.619 0.00 0.00 0.00 2.92
2365 2522 4.286032 TGTTGGTAGCTGTGGTTCTAGATT 59.714 41.667 0.00 0.00 0.00 2.40
2371 2528 3.003480 GAGATGTTGGTAGCTGTGGTTC 58.997 50.000 0.00 0.00 0.00 3.62
2426 2583 2.487762 CAAATACCTGGCACGTCATTGT 59.512 45.455 0.00 0.00 0.00 2.71
2440 2597 8.555361 GCTGATTTCTGTTAGATCTCAAATACC 58.445 37.037 0.00 0.00 0.00 2.73
2452 2609 5.220931 GCATTGGGTAGCTGATTTCTGTTAG 60.221 44.000 0.00 0.00 0.00 2.34
2471 2754 2.703416 TCAGCTGGAGTTGTAGCATTG 58.297 47.619 15.13 0.00 42.29 2.82


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

AutoCloner maintained by Alex Coulton.