Multiple sequence alignment - TraesCS2A01G128800

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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 TraesCS2A01G128800 chr2A 100.000 1680 0 0 933 2612 77194803 77196482 0.000000e+00 3103.0
1 TraesCS2A01G128800 chr2A 100.000 636 0 0 1 636 77193871 77194506 0.000000e+00 1175.0
2 TraesCS2A01G128800 chr2A 83.631 336 29 17 2267 2601 766085681 766085991 2.540000e-75 292.0
3 TraesCS2A01G128800 chr2A 86.713 143 10 4 1680 1821 766084207 766084341 1.620000e-32 150.0
4 TraesCS2A01G128800 chr2A 84.076 157 20 3 2028 2183 766084349 766084501 2.090000e-31 147.0
5 TraesCS2A01G128800 chr2A 81.928 83 9 5 2531 2610 77259617 77259696 6.030000e-07 65.8
6 TraesCS2A01G128800 chr2D 91.774 1714 72 32 933 2612 76652153 76653831 0.000000e+00 2320.0
7 TraesCS2A01G128800 chr2D 83.276 580 60 22 2028 2601 74527174 74527722 1.400000e-137 499.0
8 TraesCS2A01G128800 chr2D 81.944 576 63 26 2028 2601 634168033 634167497 1.430000e-122 449.0
9 TraesCS2A01G128800 chr2D 87.192 406 19 15 258 636 76651692 76652091 5.160000e-117 431.0
10 TraesCS2A01G128800 chr2D 91.667 132 10 1 132 262 452294090 452294221 5.740000e-42 182.0
11 TraesCS2A01G128800 chr2D 90.909 132 11 1 132 262 426844809 426844940 2.670000e-40 176.0
12 TraesCS2A01G128800 chr2D 87.324 142 10 3 1680 1821 74527033 74527166 3.480000e-34 156.0
13 TraesCS2A01G128800 chr2D 81.928 83 10 4 2531 2610 76758022 76758102 6.030000e-07 65.8
14 TraesCS2A01G128800 chr2D 97.297 37 1 0 1680 1716 634170724 634170688 2.170000e-06 63.9
15 TraesCS2A01G128800 chr2B 90.306 1702 95 28 933 2612 117931630 117933283 0.000000e+00 2165.0
16 TraesCS2A01G128800 chr2B 84.029 407 25 13 258 636 117931175 117931569 3.200000e-94 355.0
17 TraesCS2A01G128800 chr2B 92.913 127 8 1 136 261 92026351 92026477 1.600000e-42 183.0
18 TraesCS2A01G128800 chr2B 92.126 127 9 1 136 261 699177664 699177538 7.430000e-41 178.0
19 TraesCS2A01G128800 chr2B 87.591 137 10 3 1 137 117931049 117931178 4.500000e-33 152.0
20 TraesCS2A01G128800 chr6A 87.069 232 27 3 2384 2612 5278027 5277796 2.580000e-65 259.0
21 TraesCS2A01G128800 chr1B 92.424 132 8 2 136 266 113565747 113565877 1.230000e-43 187.0
22 TraesCS2A01G128800 chr5A 91.176 136 11 1 127 261 504767968 504767833 1.600000e-42 183.0
23 TraesCS2A01G128800 chr4B 90.977 133 9 3 134 264 143430855 143430724 2.670000e-40 176.0
24 TraesCS2A01G128800 chr4B 90.299 134 12 1 131 263 611854470 611854603 9.610000e-40 174.0
25 TraesCS2A01G128800 chr3D 89.130 138 14 1 132 268 70929851 70929714 1.240000e-38 171.0


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 TraesCS2A01G128800 chr2A 77193871 77196482 2611 False 2139.000000 3103 100.000000 1 2612 2 chr2A.!!$F2 2611
1 TraesCS2A01G128800 chr2D 76651692 76653831 2139 False 1375.500000 2320 89.483000 258 2612 2 chr2D.!!$F5 2354
2 TraesCS2A01G128800 chr2D 74527033 74527722 689 False 327.500000 499 85.300000 1680 2601 2 chr2D.!!$F4 921
3 TraesCS2A01G128800 chr2D 634167497 634170724 3227 True 256.450000 449 89.620500 1680 2601 2 chr2D.!!$R1 921
4 TraesCS2A01G128800 chr2B 117931049 117933283 2234 False 890.666667 2165 87.308667 1 2612 3 chr2B.!!$F2 2611

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
149 150 0.099082 GCAAGTACTCTCTCCGTCCG 59.901 60.0 0.0 0.0 0.00 4.79 F
993 1030 0.491823 TCCCTGAGGACCAAGAGGAA 59.508 55.0 0.0 0.0 37.19 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1617 2.37269 CCGTTCTCGTTGCAGTCGG 61.373 63.158 12.11 5.13 35.01 4.79 R
2476 5113 0.03467 AAGAGGAGGTGGCTGCAATC 60.035 55.000 0.50 0.00 0.00 2.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.118038 TGCAAAAGAGTACCACAAGTCCT 60.118 43.478 0.00 0.00 0.00 3.85
66 67 3.883489 GCAAAAGAGTACCACAAGTCCTT 59.117 43.478 0.00 0.00 0.00 3.36
67 68 4.338400 GCAAAAGAGTACCACAAGTCCTTT 59.662 41.667 0.00 0.00 0.00 3.11
68 69 5.505819 GCAAAAGAGTACCACAAGTCCTTTC 60.506 44.000 0.00 0.00 0.00 2.62
69 70 4.353383 AAGAGTACCACAAGTCCTTTCC 57.647 45.455 0.00 0.00 0.00 3.13
70 71 2.638363 AGAGTACCACAAGTCCTTTCCC 59.362 50.000 0.00 0.00 0.00 3.97
79 80 1.455822 AGTCCTTTCCCATTCCCACA 58.544 50.000 0.00 0.00 0.00 4.17
89 90 3.118186 TCCCATTCCCACAGGTAATAACG 60.118 47.826 0.00 0.00 0.00 3.18
95 96 1.339247 CCACAGGTAATAACGGCCACA 60.339 52.381 2.24 0.00 0.00 4.17
108 109 3.706373 CCACACCCAGCTAGCCGT 61.706 66.667 12.13 2.11 0.00 5.68
113 114 1.913762 ACCCAGCTAGCCGTTCAGT 60.914 57.895 12.13 0.00 0.00 3.41
120 121 1.268133 GCTAGCCGTTCAGTCTACTCG 60.268 57.143 2.29 0.00 0.00 4.18
133 134 5.124936 TCAGTCTACTCGCAAAGTATAGCAA 59.875 40.000 0.00 0.00 39.73 3.91
134 135 5.457148 CAGTCTACTCGCAAAGTATAGCAAG 59.543 44.000 0.00 0.00 39.73 4.01
135 136 5.125739 AGTCTACTCGCAAAGTATAGCAAGT 59.874 40.000 0.00 0.00 39.73 3.16
136 137 6.318144 AGTCTACTCGCAAAGTATAGCAAGTA 59.682 38.462 0.00 0.00 39.73 2.24
137 138 6.414402 GTCTACTCGCAAAGTATAGCAAGTAC 59.586 42.308 0.00 0.00 39.73 2.73
138 139 5.326200 ACTCGCAAAGTATAGCAAGTACT 57.674 39.130 0.00 0.00 36.07 2.73
139 140 5.341617 ACTCGCAAAGTATAGCAAGTACTC 58.658 41.667 0.00 0.00 36.07 2.59
140 141 5.125739 ACTCGCAAAGTATAGCAAGTACTCT 59.874 40.000 0.00 0.00 36.07 3.24
141 142 5.579718 TCGCAAAGTATAGCAAGTACTCTC 58.420 41.667 0.00 0.00 31.44 3.20
142 143 5.357314 TCGCAAAGTATAGCAAGTACTCTCT 59.643 40.000 0.00 0.00 31.44 3.10
143 144 5.683743 CGCAAAGTATAGCAAGTACTCTCTC 59.316 44.000 0.00 0.00 31.44 3.20
144 145 5.980715 GCAAAGTATAGCAAGTACTCTCTCC 59.019 44.000 0.00 0.00 31.44 3.71
145 146 6.202937 CAAAGTATAGCAAGTACTCTCTCCG 58.797 44.000 0.00 0.00 31.44 4.63
146 147 5.038651 AGTATAGCAAGTACTCTCTCCGT 57.961 43.478 0.00 0.00 0.00 4.69
147 148 5.058490 AGTATAGCAAGTACTCTCTCCGTC 58.942 45.833 0.00 0.00 0.00 4.79
148 149 1.465794 AGCAAGTACTCTCTCCGTCC 58.534 55.000 0.00 0.00 0.00 4.79
149 150 0.099082 GCAAGTACTCTCTCCGTCCG 59.901 60.000 0.00 0.00 0.00 4.79
150 151 0.733729 CAAGTACTCTCTCCGTCCGG 59.266 60.000 0.00 0.00 0.00 5.14
151 152 0.617413 AAGTACTCTCTCCGTCCGGA 59.383 55.000 0.00 0.00 42.90 5.14
152 153 0.617413 AGTACTCTCTCCGTCCGGAA 59.383 55.000 5.23 0.00 44.66 4.30
153 154 1.004044 AGTACTCTCTCCGTCCGGAAA 59.996 52.381 5.23 0.00 44.66 3.13
154 155 2.022934 GTACTCTCTCCGTCCGGAAAT 58.977 52.381 5.23 0.00 44.66 2.17
155 156 2.431954 ACTCTCTCCGTCCGGAAATA 57.568 50.000 5.23 0.00 44.66 1.40
156 157 2.022934 ACTCTCTCCGTCCGGAAATAC 58.977 52.381 5.23 0.00 44.66 1.89
157 158 2.299521 CTCTCTCCGTCCGGAAATACT 58.700 52.381 5.23 0.00 44.66 2.12
158 159 2.688958 CTCTCTCCGTCCGGAAATACTT 59.311 50.000 5.23 0.00 44.66 2.24
159 160 3.881688 CTCTCTCCGTCCGGAAATACTTA 59.118 47.826 5.23 0.00 44.66 2.24
160 161 4.467769 TCTCTCCGTCCGGAAATACTTAT 58.532 43.478 5.23 0.00 44.66 1.73
161 162 4.518211 TCTCTCCGTCCGGAAATACTTATC 59.482 45.833 5.23 0.00 44.66 1.75
162 163 4.209538 TCTCCGTCCGGAAATACTTATCA 58.790 43.478 5.23 0.00 44.66 2.15
163 164 4.831155 TCTCCGTCCGGAAATACTTATCAT 59.169 41.667 5.23 0.00 44.66 2.45
164 165 5.048224 TCTCCGTCCGGAAATACTTATCATC 60.048 44.000 5.23 0.00 44.66 2.92
165 166 4.585581 TCCGTCCGGAAATACTTATCATCA 59.414 41.667 5.23 0.00 42.05 3.07
166 167 5.069383 TCCGTCCGGAAATACTTATCATCAA 59.931 40.000 5.23 0.00 42.05 2.57
167 168 5.756347 CCGTCCGGAAATACTTATCATCAAA 59.244 40.000 5.23 0.00 37.50 2.69
168 169 6.259167 CCGTCCGGAAATACTTATCATCAAAA 59.741 38.462 5.23 0.00 37.50 2.44
169 170 7.041372 CCGTCCGGAAATACTTATCATCAAAAT 60.041 37.037 5.23 0.00 37.50 1.82
170 171 8.984764 CGTCCGGAAATACTTATCATCAAAATA 58.015 33.333 5.23 0.00 0.00 1.40
214 215 8.739649 AGACGTATTTTAATTCTAGATACGCC 57.260 34.615 15.97 8.31 45.51 5.68
215 216 8.574737 AGACGTATTTTAATTCTAGATACGCCT 58.425 33.333 15.97 10.06 45.51 5.52
216 217 9.189723 GACGTATTTTAATTCTAGATACGCCTT 57.810 33.333 15.97 1.93 45.51 4.35
217 218 9.538508 ACGTATTTTAATTCTAGATACGCCTTT 57.461 29.630 15.97 0.00 45.51 3.11
248 249 8.741101 TTCATTTTGATGACAACTATTTTCGG 57.259 30.769 0.00 0.00 35.63 4.30
249 250 8.105097 TCATTTTGATGACAACTATTTTCGGA 57.895 30.769 0.00 0.00 35.63 4.55
250 251 8.020819 TCATTTTGATGACAACTATTTTCGGAC 58.979 33.333 0.00 0.00 35.63 4.79
251 252 5.524511 TTGATGACAACTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
252 253 3.930229 TGATGACAACTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
253 254 3.663995 TGACAACTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
254 255 3.581755 TGACAACTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
255 256 2.928116 GACAACTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
256 257 2.277084 CAACTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
305 309 9.824534 CAAATAAACATAAATTGCTTCCAAACC 57.175 29.630 0.00 0.00 34.05 3.27
309 313 6.418057 ACATAAATTGCTTCCAAACCAAGA 57.582 33.333 0.00 0.00 34.05 3.02
316 320 5.612725 TGCTTCCAAACCAAGAAAAGAAT 57.387 34.783 0.00 0.00 0.00 2.40
318 322 4.991056 GCTTCCAAACCAAGAAAAGAATCC 59.009 41.667 0.00 0.00 0.00 3.01
320 324 4.551671 TCCAAACCAAGAAAAGAATCCCA 58.448 39.130 0.00 0.00 0.00 4.37
326 330 6.499106 ACCAAGAAAAGAATCCCACAAAAT 57.501 33.333 0.00 0.00 0.00 1.82
333 337 7.874528 AGAAAAGAATCCCACAAAATTGCTTAG 59.125 33.333 0.00 0.00 0.00 2.18
338 342 7.992608 AGAATCCCACAAAATTGCTTAGTTTTT 59.007 29.630 0.00 0.00 0.00 1.94
402 414 7.435068 TCTCAATTAGTTGCTGGTTTTAGTC 57.565 36.000 0.00 0.00 35.26 2.59
405 417 6.653320 TCAATTAGTTGCTGGTTTTAGTCGAT 59.347 34.615 0.00 0.00 35.26 3.59
446 458 0.597118 GTGCGTGCCATTTTTGCTCA 60.597 50.000 0.00 0.00 0.00 4.26
455 467 4.512198 TGCCATTTTTGCTCACAAGATTTG 59.488 37.500 0.00 0.00 37.04 2.32
482 517 4.556942 TTTTGACACACTCAGCATCAAG 57.443 40.909 0.00 0.00 31.34 3.02
483 518 3.473923 TTGACACACTCAGCATCAAGA 57.526 42.857 0.00 0.00 0.00 3.02
484 519 3.473923 TGACACACTCAGCATCAAGAA 57.526 42.857 0.00 0.00 0.00 2.52
485 520 3.396560 TGACACACTCAGCATCAAGAAG 58.603 45.455 0.00 0.00 0.00 2.85
486 521 3.070015 TGACACACTCAGCATCAAGAAGA 59.930 43.478 0.00 0.00 0.00 2.87
487 522 3.661944 ACACACTCAGCATCAAGAAGAG 58.338 45.455 0.00 0.00 0.00 2.85
962 999 2.095461 GAGGAATCAAGAACCTTGCCC 58.905 52.381 2.04 3.95 33.89 5.36
991 1028 4.896979 TCCCTGAGGACCAAGAGG 57.103 61.111 0.00 0.00 37.19 3.69
992 1029 2.183445 TCCCTGAGGACCAAGAGGA 58.817 57.895 0.00 3.62 37.19 3.71
993 1030 0.491823 TCCCTGAGGACCAAGAGGAA 59.508 55.000 0.00 0.00 37.19 3.36
1055 1101 4.456253 CAAGAAGCAGCAGCCGCG 62.456 66.667 0.00 0.00 45.49 6.46
1540 1595 1.009389 CAAGGTGTTCGACGAGGAGC 61.009 60.000 0.00 0.00 0.00 4.70
1618 1684 2.393646 ACTGCTCCTCCTGATCCTAAC 58.606 52.381 0.00 0.00 0.00 2.34
1674 1740 0.030638 GTCAGATCAGAGAGAGGCGC 59.969 60.000 0.00 0.00 0.00 6.53
1675 1741 0.394899 TCAGATCAGAGAGAGGCGCA 60.395 55.000 10.83 0.00 0.00 6.09
1676 1742 0.675083 CAGATCAGAGAGAGGCGCAT 59.325 55.000 10.83 0.00 0.00 4.73
1677 1743 1.068895 CAGATCAGAGAGAGGCGCATT 59.931 52.381 10.83 0.00 0.00 3.56
1678 1744 1.340889 AGATCAGAGAGAGGCGCATTC 59.659 52.381 10.83 6.36 0.00 2.67
1740 4357 6.218746 TGTGTATCCTGAATCGATCAATCAG 58.781 40.000 15.68 15.68 37.67 2.90
1782 4399 0.108186 TGTTAGCTGCTCATGGACGG 60.108 55.000 4.91 0.00 0.00 4.79
1783 4400 0.175760 GTTAGCTGCTCATGGACGGA 59.824 55.000 4.91 0.00 0.00 4.69
1784 4401 0.901827 TTAGCTGCTCATGGACGGAA 59.098 50.000 4.91 0.00 0.00 4.30
1899 4516 7.543868 GCTTGTATATGTGTGTAAAATTTGGCA 59.456 33.333 0.00 0.00 0.00 4.92
2026 4644 4.945543 TGGTCAAATCTCTTCATGGATGTG 59.054 41.667 0.00 0.00 0.00 3.21
2091 4710 5.511545 CCAACTGTACTAGCAGGAAGTCTTT 60.512 44.000 0.00 0.00 40.59 2.52
2145 4766 3.891977 ACTCAGTCAGAAGCTGTACTCAA 59.108 43.478 0.00 0.00 35.60 3.02
2185 4806 6.810182 GTGTTCTAAATTAGAGCCACGTCTTA 59.190 38.462 13.08 0.00 35.45 2.10
2198 4819 7.390718 AGAGCCACGTCTTATGTTCTTTAATTT 59.609 33.333 0.00 0.00 0.00 1.82
2199 4820 8.556213 AGCCACGTCTTATGTTCTTTAATTTA 57.444 30.769 0.00 0.00 0.00 1.40
2200 4821 9.005777 AGCCACGTCTTATGTTCTTTAATTTAA 57.994 29.630 0.00 0.00 0.00 1.52
2201 4822 9.783256 GCCACGTCTTATGTTCTTTAATTTAAT 57.217 29.630 0.00 0.00 0.00 1.40
2296 4923 8.535335 TCTGATCTCTTTATCTGTACTTGCTTT 58.465 33.333 0.00 0.00 0.00 3.51
2297 4924 8.484641 TGATCTCTTTATCTGTACTTGCTTTG 57.515 34.615 0.00 0.00 0.00 2.77
2298 4925 8.314021 TGATCTCTTTATCTGTACTTGCTTTGA 58.686 33.333 0.00 0.00 0.00 2.69
2322 4952 5.779922 TGATCCATCTTATAAGTACACGGC 58.220 41.667 12.19 0.02 0.00 5.68
2370 5007 6.294899 GCATTCCATGGATGCACAGTTATATT 60.295 38.462 29.16 0.00 40.72 1.28
2371 5008 7.094248 GCATTCCATGGATGCACAGTTATATTA 60.094 37.037 29.16 8.64 40.72 0.98
2372 5009 8.963725 CATTCCATGGATGCACAGTTATATTAT 58.036 33.333 17.06 0.00 0.00 1.28
2376 5013 9.102757 CCATGGATGCACAGTTATATTATACTC 57.897 37.037 5.56 0.00 0.00 2.59
2379 5016 9.875691 TGGATGCACAGTTATATTATACTCATC 57.124 33.333 0.00 0.00 0.00 2.92
2380 5017 9.319143 GGATGCACAGTTATATTATACTCATCC 57.681 37.037 0.00 0.00 36.74 3.51
2382 5019 7.320399 TGCACAGTTATATTATACTCATCCGG 58.680 38.462 0.00 0.00 0.00 5.14
2476 5113 7.754069 TGTTGCATTCAAGTTGTTTTCTAAG 57.246 32.000 2.11 0.00 31.93 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.840890 TCTTGAACGTTTTGTTGTGCT 57.159 38.095 0.46 0.00 42.09 4.40
13 14 4.461431 AGGAAGGTTCTTGAACGTTTTGTT 59.539 37.500 18.33 1.28 45.61 2.83
14 15 4.014406 AGGAAGGTTCTTGAACGTTTTGT 58.986 39.130 18.33 7.46 31.76 2.83
15 16 4.632538 AGGAAGGTTCTTGAACGTTTTG 57.367 40.909 18.33 0.00 31.76 2.44
65 66 5.265989 GTTATTACCTGTGGGAATGGGAAA 58.734 41.667 4.41 0.00 36.25 3.13
66 67 4.626771 CGTTATTACCTGTGGGAATGGGAA 60.627 45.833 4.41 0.00 36.25 3.97
67 68 3.118186 CGTTATTACCTGTGGGAATGGGA 60.118 47.826 4.41 0.00 36.25 4.37
68 69 3.211045 CGTTATTACCTGTGGGAATGGG 58.789 50.000 4.41 0.00 36.25 4.00
69 70 3.211045 CCGTTATTACCTGTGGGAATGG 58.789 50.000 4.41 0.00 36.25 3.16
70 71 2.616842 GCCGTTATTACCTGTGGGAATG 59.383 50.000 4.41 0.00 36.25 2.67
79 80 0.253894 GGGTGTGGCCGTTATTACCT 59.746 55.000 0.00 0.00 38.44 3.08
89 90 4.803908 GGCTAGCTGGGTGTGGCC 62.804 72.222 15.72 0.00 0.00 5.36
95 96 1.889530 GACTGAACGGCTAGCTGGGT 61.890 60.000 26.90 18.27 0.00 4.51
107 108 5.456173 GCTATACTTTGCGAGTAGACTGAAC 59.544 44.000 6.04 0.00 43.79 3.18
108 109 5.124936 TGCTATACTTTGCGAGTAGACTGAA 59.875 40.000 6.04 0.00 43.79 3.02
120 121 5.980715 GGAGAGAGTACTTGCTATACTTTGC 59.019 44.000 0.00 0.00 32.93 3.68
133 134 0.617413 TTCCGGACGGAGAGAGTACT 59.383 55.000 13.64 0.00 46.06 2.73
134 135 1.457346 TTTCCGGACGGAGAGAGTAC 58.543 55.000 13.64 0.00 46.06 2.73
135 136 2.431954 ATTTCCGGACGGAGAGAGTA 57.568 50.000 13.64 0.00 46.06 2.59
136 137 2.022934 GTATTTCCGGACGGAGAGAGT 58.977 52.381 13.64 0.00 46.06 3.24
137 138 2.299521 AGTATTTCCGGACGGAGAGAG 58.700 52.381 13.64 0.00 46.06 3.20
138 139 2.431954 AGTATTTCCGGACGGAGAGA 57.568 50.000 13.64 3.93 46.06 3.10
139 140 4.277672 TGATAAGTATTTCCGGACGGAGAG 59.722 45.833 13.64 0.00 46.06 3.20
140 141 4.209538 TGATAAGTATTTCCGGACGGAGA 58.790 43.478 13.64 10.06 46.06 3.71
141 142 4.579454 TGATAAGTATTTCCGGACGGAG 57.421 45.455 13.64 0.00 46.06 4.63
142 143 4.585581 TGATGATAAGTATTTCCGGACGGA 59.414 41.667 1.83 9.76 43.52 4.69
143 144 4.878439 TGATGATAAGTATTTCCGGACGG 58.122 43.478 1.83 3.96 0.00 4.79
144 145 6.838198 TTTGATGATAAGTATTTCCGGACG 57.162 37.500 1.83 0.00 0.00 4.79
188 189 9.831737 GGCGTATCTAGAATTAAAATACGTCTA 57.168 33.333 16.76 0.00 43.70 2.59
189 190 8.739649 GGCGTATCTAGAATTAAAATACGTCT 57.260 34.615 16.76 0.00 43.70 4.18
190 191 8.739649 AGGCGTATCTAGAATTAAAATACGTC 57.260 34.615 13.73 13.73 46.00 4.34
191 192 9.538508 AAAGGCGTATCTAGAATTAAAATACGT 57.461 29.630 16.76 0.00 44.18 3.57
222 223 9.357652 CCGAAAATAGTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
223 224 8.572185 TCCGAAAATAGTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
224 225 8.020819 GTCCGAAAATAGTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
225 226 7.007367 CGTCCGAAAATAGTTGTCATCAAAATG 59.993 37.037 0.00 0.00 35.20 2.32
226 227 7.021196 CGTCCGAAAATAGTTGTCATCAAAAT 58.979 34.615 0.00 0.00 35.20 1.82
227 228 6.367421 CGTCCGAAAATAGTTGTCATCAAAA 58.633 36.000 0.00 0.00 35.20 2.44
228 229 5.106869 CCGTCCGAAAATAGTTGTCATCAAA 60.107 40.000 0.00 0.00 35.20 2.69
229 230 4.390603 CCGTCCGAAAATAGTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
230 231 3.930229 CCGTCCGAAAATAGTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
231 232 4.178540 TCCGTCCGAAAATAGTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
232 233 4.181578 CTCCGTCCGAAAATAGTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
233 234 3.581755 CTCCGTCCGAAAATAGTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
234 235 2.928116 CCTCCGTCCGAAAATAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
235 236 2.354403 CCCTCCGTCCGAAAATAGTTGT 60.354 50.000 0.00 0.00 0.00 3.32
236 237 2.093869 TCCCTCCGTCCGAAAATAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
237 238 2.167900 CTCCCTCCGTCCGAAAATAGTT 59.832 50.000 0.00 0.00 0.00 2.24
238 239 1.755380 CTCCCTCCGTCCGAAAATAGT 59.245 52.381 0.00 0.00 0.00 2.12
239 240 1.755380 ACTCCCTCCGTCCGAAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
240 241 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
241 242 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
242 243 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
243 244 1.318158 GCTACTCCCTCCGTCCGAAA 61.318 60.000 0.00 0.00 0.00 3.46
244 245 1.751927 GCTACTCCCTCCGTCCGAA 60.752 63.158 0.00 0.00 0.00 4.30
245 246 2.124403 GCTACTCCCTCCGTCCGA 60.124 66.667 0.00 0.00 0.00 4.55
246 247 2.050350 TTGCTACTCCCTCCGTCCG 61.050 63.158 0.00 0.00 0.00 4.79
247 248 1.516423 GTTGCTACTCCCTCCGTCC 59.484 63.158 0.00 0.00 0.00 4.79
248 249 1.255667 TGGTTGCTACTCCCTCCGTC 61.256 60.000 0.00 0.00 0.00 4.79
249 250 1.229082 TGGTTGCTACTCCCTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
250 251 1.218316 GTGGTTGCTACTCCCTCCG 59.782 63.158 0.00 0.00 0.00 4.63
251 252 0.690762 TTGTGGTTGCTACTCCCTCC 59.309 55.000 0.00 0.00 0.00 4.30
252 253 2.561478 TTTGTGGTTGCTACTCCCTC 57.439 50.000 0.00 0.00 0.00 4.30
253 254 2.956333 GTTTTTGTGGTTGCTACTCCCT 59.044 45.455 0.00 0.00 0.00 4.20
254 255 2.956333 AGTTTTTGTGGTTGCTACTCCC 59.044 45.455 0.00 0.00 0.00 4.30
255 256 5.506815 GGTTAGTTTTTGTGGTTGCTACTCC 60.507 44.000 0.00 0.00 0.00 3.85
256 257 5.066764 TGGTTAGTTTTTGTGGTTGCTACTC 59.933 40.000 0.00 0.00 0.00 2.59
293 297 5.413309 TTCTTTTCTTGGTTTGGAAGCAA 57.587 34.783 5.35 5.35 45.65 3.91
305 309 6.484308 AGCAATTTTGTGGGATTCTTTTCTTG 59.516 34.615 0.00 0.00 0.00 3.02
309 313 7.508687 ACTAAGCAATTTTGTGGGATTCTTTT 58.491 30.769 0.00 0.00 0.00 2.27
316 320 6.917217 CAAAAACTAAGCAATTTTGTGGGA 57.083 33.333 0.00 0.00 38.56 4.37
326 330 2.223618 GGCGGTGACAAAAACTAAGCAA 60.224 45.455 0.00 0.00 0.00 3.91
333 337 2.354188 GCGGGCGGTGACAAAAAC 60.354 61.111 0.00 0.00 0.00 2.43
377 389 7.307751 CGACTAAAACCAGCAACTAATTGAGAA 60.308 37.037 0.00 0.00 38.15 2.87
402 414 6.792250 CAGCCGATTTAGCAACTAATTTATCG 59.208 38.462 10.69 10.69 35.63 2.92
405 417 6.676943 GCACAGCCGATTTAGCAACTAATTTA 60.677 38.462 0.00 0.00 0.00 1.40
446 458 6.147000 GTGTGTCAAAAACAACCAAATCTTGT 59.853 34.615 0.00 0.00 40.31 3.16
455 467 3.179048 GCTGAGTGTGTCAAAAACAACC 58.821 45.455 0.00 0.00 40.31 3.77
482 517 2.239681 TGGTTCTCCTCCTCCTCTTC 57.760 55.000 0.00 0.00 34.23 2.87
483 518 2.723530 TTGGTTCTCCTCCTCCTCTT 57.276 50.000 0.00 0.00 34.23 2.85
484 519 2.158081 ACTTTGGTTCTCCTCCTCCTCT 60.158 50.000 0.00 0.00 34.23 3.69
485 520 2.261729 ACTTTGGTTCTCCTCCTCCTC 58.738 52.381 0.00 0.00 34.23 3.71
486 521 2.424684 ACTTTGGTTCTCCTCCTCCT 57.575 50.000 0.00 0.00 34.23 3.69
487 522 4.635699 TTTACTTTGGTTCTCCTCCTCC 57.364 45.455 0.00 0.00 34.23 4.30
527 562 3.146847 TCTTTTCTTTTCTTCTCCCGGC 58.853 45.455 0.00 0.00 0.00 6.13
566 603 2.708051 GAGGTGGGGTTTACTTAGTGC 58.292 52.381 0.00 0.00 0.00 4.40
986 1023 2.383855 CCTCCATCGTCTCTTCCTCTT 58.616 52.381 0.00 0.00 0.00 2.85
991 1028 1.066587 CGCCCTCCATCGTCTCTTC 59.933 63.158 0.00 0.00 0.00 2.87
992 1029 2.427245 CCGCCCTCCATCGTCTCTT 61.427 63.158 0.00 0.00 0.00 2.85
993 1030 2.835431 CCGCCCTCCATCGTCTCT 60.835 66.667 0.00 0.00 0.00 3.10
1349 1404 4.570874 GGCCCCCGATGAAGAGCC 62.571 72.222 0.00 0.00 0.00 4.70
1402 1457 4.803426 GAGCTGGCCGGACTCGTG 62.803 72.222 18.31 0.00 33.95 4.35
1562 1617 2.372690 CCGTTCTCGTTGCAGTCGG 61.373 63.158 12.11 5.13 35.01 4.79
1618 1684 4.263506 ACCAACTCTAACCCTTGGATTCAG 60.264 45.833 2.69 0.00 38.29 3.02
1674 1740 5.132897 TCCAAGAAACCGAAAATGGAATG 57.867 39.130 0.00 0.00 34.21 2.67
1675 1741 4.832823 ACTCCAAGAAACCGAAAATGGAAT 59.167 37.500 0.00 0.00 36.59 3.01
1676 1742 4.211920 ACTCCAAGAAACCGAAAATGGAA 58.788 39.130 0.00 0.00 36.59 3.53
1677 1743 3.827722 ACTCCAAGAAACCGAAAATGGA 58.172 40.909 0.00 0.00 35.74 3.41
1678 1744 4.278419 AGAACTCCAAGAAACCGAAAATGG 59.722 41.667 0.00 0.00 0.00 3.16
1719 4336 5.866633 GGACTGATTGATCGATTCAGGATAC 59.133 44.000 23.04 13.85 40.92 2.24
1720 4337 5.335976 CGGACTGATTGATCGATTCAGGATA 60.336 44.000 23.04 1.52 40.92 2.59
1731 4348 3.246226 CCAAACGATCGGACTGATTGATC 59.754 47.826 20.98 0.00 40.46 2.92
1740 4357 2.987752 GATCCCCAAACGATCGGAC 58.012 57.895 20.98 0.00 0.00 4.79
1845 4462 4.435253 GCTCTTATTCATCATCAATCGCCG 60.435 45.833 0.00 0.00 0.00 6.46
2026 4644 4.391216 TCTCGAACTGTACTGCTACTGTAC 59.609 45.833 7.57 7.57 38.61 2.90
2232 4859 3.979501 ATTAATCACCCCAGGCTCAAT 57.020 42.857 0.00 0.00 0.00 2.57
2286 4913 6.690194 AAGATGGATCATCAAAGCAAGTAC 57.310 37.500 10.08 0.00 42.72 2.73
2296 4923 7.602753 CCGTGTACTTATAAGATGGATCATCA 58.397 38.462 19.38 2.46 42.72 3.07
2297 4924 6.531948 GCCGTGTACTTATAAGATGGATCATC 59.468 42.308 19.38 0.00 40.80 2.92
2298 4925 6.211584 AGCCGTGTACTTATAAGATGGATCAT 59.788 38.462 19.38 0.00 0.00 2.45
2322 4952 5.340803 CCATCTGTGCATGAAGAAATCAAG 58.659 41.667 0.00 0.00 42.54 3.02
2370 5007 6.228616 TCACATTGTTTCCGGATGAGTATA 57.771 37.500 4.15 0.00 0.00 1.47
2371 5008 5.097742 TCACATTGTTTCCGGATGAGTAT 57.902 39.130 4.15 0.00 0.00 2.12
2372 5009 4.545208 TCACATTGTTTCCGGATGAGTA 57.455 40.909 4.15 0.00 0.00 2.59
2373 5010 3.417069 TCACATTGTTTCCGGATGAGT 57.583 42.857 4.15 0.00 0.00 3.41
2376 5013 2.935849 TCGATCACATTGTTTCCGGATG 59.064 45.455 4.15 1.88 0.00 3.51
2378 5015 2.753055 TCGATCACATTGTTTCCGGA 57.247 45.000 0.00 0.00 0.00 5.14
2379 5016 2.033747 CGATCGATCACATTGTTTCCGG 60.034 50.000 24.40 0.00 0.00 5.14
2380 5017 2.603110 ACGATCGATCACATTGTTTCCG 59.397 45.455 24.34 9.39 0.00 4.30
2382 5019 4.840401 TGACGATCGATCACATTGTTTC 57.160 40.909 24.34 4.50 0.00 2.78
2476 5113 0.034670 AAGAGGAGGTGGCTGCAATC 60.035 55.000 0.50 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.