Multiple sequence alignment - TraesCS6A01G221900

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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 TraesCS6A01G221900 chr6A 100.000 4531 0 0 1 4531 413731630 413736160 0.000000e+00 8368.0
1 TraesCS6A01G221900 chr6B 93.657 4036 161 36 394 4395 468012302 468008328 0.000000e+00 5947.0
2 TraesCS6A01G221900 chr6B 86.286 175 6 4 211 367 468013792 468013618 1.680000e-39 174.0
3 TraesCS6A01G221900 chr6B 92.727 110 8 0 21 130 468013905 468013796 4.690000e-35 159.0
4 TraesCS6A01G221900 chr6D 94.793 1863 61 14 1889 3724 302250139 302248286 0.000000e+00 2870.0
5 TraesCS6A01G221900 chr6D 92.280 1697 46 30 211 1885 302251952 302250319 0.000000e+00 2329.0
6 TraesCS6A01G221900 chr6D 83.038 790 91 26 3732 4482 302247872 302247087 0.000000e+00 676.0
7 TraesCS6A01G221900 chr6D 89.583 96 7 2 21 116 302252092 302252000 7.960000e-23 119.0
8 TraesCS6A01G221900 chr2B 81.105 344 50 12 2297 2628 562218608 562218948 1.250000e-65 261.0
9 TraesCS6A01G221900 chr2B 100.000 29 0 0 1241 1269 41381512 41381540 2.000000e-03 54.7
10 TraesCS6A01G221900 chr2A 80.580 345 50 14 2297 2628 621921830 621922170 2.710000e-62 250.0
11 TraesCS6A01G221900 chr2A 80.169 237 46 1 4136 4372 734592014 734591779 4.660000e-40 176.0
12 TraesCS6A01G221900 chr2D 80.233 344 53 12 2297 2628 479180479 479180819 1.260000e-60 244.0
13 TraesCS6A01G221900 chr4B 79.822 337 60 7 2297 2626 548767358 548767693 5.860000e-59 239.0
14 TraesCS6A01G221900 chr4B 83.857 223 36 0 2406 2628 659689013 659688791 3.550000e-51 213.0
15 TraesCS6A01G221900 chr4B 78.571 266 55 2 1187 1450 548766961 548767226 1.680000e-39 174.0
16 TraesCS6A01G221900 chr4B 79.646 226 46 0 3299 3524 660092222 660092447 3.630000e-36 163.0
17 TraesCS6A01G221900 chr4A 85.153 229 34 0 2398 2626 25497114 25496886 7.580000e-58 235.0
18 TraesCS6A01G221900 chr4A 78.486 251 52 2 1201 1450 25497607 25497358 3.630000e-36 163.0
19 TraesCS6A01G221900 chr4D 84.279 229 36 0 2398 2626 441901561 441901789 1.640000e-54 224.0
20 TraesCS6A01G221900 chr5A 80.228 263 51 1 4129 4391 123707033 123707294 3.580000e-46 196.0
21 TraesCS6A01G221900 chrUn 100.000 30 0 0 1240 1269 24657905 24657876 6.330000e-04 56.5
22 TraesCS6A01G221900 chr1D 100.000 30 0 0 1240 1269 72498133 72498162 6.330000e-04 56.5
23 TraesCS6A01G221900 chr1B 100.000 30 0 0 1240 1269 113564144 113564173 6.330000e-04 56.5


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 TraesCS6A01G221900 chr6A 413731630 413736160 4530 False 8368.000000 8368 100.0000 1 4531 1 chr6A.!!$F1 4530
1 TraesCS6A01G221900 chr6B 468008328 468013905 5577 True 2093.333333 5947 90.8900 21 4395 3 chr6B.!!$R1 4374
2 TraesCS6A01G221900 chr6D 302247087 302252092 5005 True 1498.500000 2870 89.9235 21 4482 4 chr6D.!!$R1 4461
3 TraesCS6A01G221900 chr4B 548766961 548767693 732 False 206.500000 239 79.1965 1187 2626 2 chr4B.!!$F2 1439

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
257 288 0.039978 TACCGCCGTGCAATGTTTTG 60.040 50.0 0.00 0.0 35.85 2.44 F
1783 3131 0.463833 GGGCGAATAAGGACCCAGTG 60.464 60.0 0.00 0.0 42.33 3.66 F
1800 3149 0.591659 GTGGAAAAGAAGGGACGTGC 59.408 55.0 0.00 0.0 0.00 5.34 F
1871 3220 0.593128 GGTGCAGCAACATCGTCTTT 59.407 50.0 11.86 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 3583 1.022982 AGGCGTCACGATCGTGTAGA 61.023 55.000 38.72 23.14 45.55 2.59 R
3380 4944 0.320946 CGTAGGACGGGCAAAGGAAA 60.321 55.000 0.00 0.00 38.08 3.13 R
3493 5057 1.005924 GAAGGCCAATCTTCTTCCCCA 59.994 52.381 5.01 0.00 39.84 4.96 R
3785 5770 2.607187 ACTAGTACATTCGTGCACAGC 58.393 47.619 18.64 0.00 0.00 4.40 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 3.430374 CCTGACCTATTTAGTCCACCACG 60.430 52.174 0.00 0.00 33.09 4.94
52 53 1.919654 TGGTGCTAATCCAGGCCTTTA 59.080 47.619 0.00 0.00 0.00 1.85
57 58 3.244215 TGCTAATCCAGGCCTTTATCTCG 60.244 47.826 0.00 0.00 0.00 4.04
130 161 7.956508 TTCATGTAAAAATAATACGCAACGG 57.043 32.000 0.00 0.00 0.00 4.44
131 162 7.074507 TCATGTAAAAATAATACGCAACGGT 57.925 32.000 0.00 0.00 0.00 4.83
132 163 8.194433 TCATGTAAAAATAATACGCAACGGTA 57.806 30.769 0.00 0.00 0.00 4.02
133 164 8.828644 TCATGTAAAAATAATACGCAACGGTAT 58.171 29.630 0.00 0.00 34.65 2.73
134 165 9.440784 CATGTAAAAATAATACGCAACGGTATT 57.559 29.630 3.75 3.75 43.52 1.89
136 167 9.837525 TGTAAAAATAATACGCAACGGTATTTT 57.162 25.926 3.59 10.11 41.83 1.82
142 173 9.533253 AATAATACGCAACGGTATTTTAGTACT 57.467 29.630 0.00 0.00 41.83 2.73
143 174 7.455331 AATACGCAACGGTATTTTAGTACTC 57.545 36.000 0.00 0.00 39.44 2.59
144 175 5.064441 ACGCAACGGTATTTTAGTACTCT 57.936 39.130 0.00 0.00 0.00 3.24
145 176 5.473039 ACGCAACGGTATTTTAGTACTCTT 58.527 37.500 0.00 0.00 0.00 2.85
146 177 6.620678 ACGCAACGGTATTTTAGTACTCTTA 58.379 36.000 0.00 0.00 0.00 2.10
147 178 7.260603 ACGCAACGGTATTTTAGTACTCTTAT 58.739 34.615 0.00 0.00 0.00 1.73
148 179 8.405531 ACGCAACGGTATTTTAGTACTCTTATA 58.594 33.333 0.00 0.00 0.00 0.98
149 180 9.236691 CGCAACGGTATTTTAGTACTCTTATAA 57.763 33.333 0.00 0.00 0.00 0.98
180 211 3.756933 TTTGCGGGTGACTACTTAAGT 57.243 42.857 13.68 13.68 42.80 2.24
181 212 4.870123 TTTGCGGGTGACTACTTAAGTA 57.130 40.909 14.52 14.52 39.07 2.24
182 213 4.870123 TTGCGGGTGACTACTTAAGTAA 57.130 40.909 15.95 0.00 39.07 2.24
183 214 4.870123 TGCGGGTGACTACTTAAGTAAA 57.130 40.909 15.95 2.99 39.07 2.01
184 215 4.559153 TGCGGGTGACTACTTAAGTAAAC 58.441 43.478 15.95 13.43 39.07 2.01
185 216 4.039004 TGCGGGTGACTACTTAAGTAAACA 59.961 41.667 15.95 14.68 39.07 2.83
186 217 5.173664 GCGGGTGACTACTTAAGTAAACAT 58.826 41.667 15.95 2.94 39.07 2.71
187 218 5.063060 GCGGGTGACTACTTAAGTAAACATG 59.937 44.000 15.95 6.98 39.07 3.21
188 219 5.063060 CGGGTGACTACTTAAGTAAACATGC 59.937 44.000 15.95 8.19 39.07 4.06
189 220 5.935789 GGGTGACTACTTAAGTAAACATGCA 59.064 40.000 15.95 0.00 39.07 3.96
190 221 6.428771 GGGTGACTACTTAAGTAAACATGCAA 59.571 38.462 15.95 0.00 39.07 4.08
191 222 7.040961 GGGTGACTACTTAAGTAAACATGCAAA 60.041 37.037 15.95 0.00 39.07 3.68
192 223 8.015658 GGTGACTACTTAAGTAAACATGCAAAG 58.984 37.037 15.95 5.17 39.07 2.77
193 224 8.557029 GTGACTACTTAAGTAAACATGCAAAGT 58.443 33.333 15.95 8.20 39.07 2.66
194 225 9.116067 TGACTACTTAAGTAAACATGCAAAGTT 57.884 29.630 15.95 0.00 39.07 2.66
195 226 9.382244 GACTACTTAAGTAAACATGCAAAGTTG 57.618 33.333 15.95 5.59 39.07 3.16
196 227 9.116067 ACTACTTAAGTAAACATGCAAAGTTGA 57.884 29.630 15.95 0.00 36.36 3.18
197 228 9.599322 CTACTTAAGTAAACATGCAAAGTTGAG 57.401 33.333 15.95 0.00 0.00 3.02
198 229 8.220755 ACTTAAGTAAACATGCAAAGTTGAGA 57.779 30.769 6.26 0.00 0.00 3.27
199 230 8.345565 ACTTAAGTAAACATGCAAAGTTGAGAG 58.654 33.333 6.26 5.00 0.00 3.20
200 231 6.942532 AAGTAAACATGCAAAGTTGAGAGA 57.057 33.333 8.45 0.00 0.00 3.10
201 232 6.305693 AGTAAACATGCAAAGTTGAGAGAC 57.694 37.500 8.45 3.72 0.00 3.36
202 233 5.822519 AGTAAACATGCAAAGTTGAGAGACA 59.177 36.000 8.45 0.00 0.00 3.41
203 234 5.581126 AAACATGCAAAGTTGAGAGACAA 57.419 34.783 8.45 0.00 36.02 3.18
204 235 4.825546 ACATGCAAAGTTGAGAGACAAG 57.174 40.909 0.00 0.00 39.30 3.16
205 236 3.004106 ACATGCAAAGTTGAGAGACAAGC 59.996 43.478 0.00 0.00 39.30 4.01
206 237 2.642427 TGCAAAGTTGAGAGACAAGCA 58.358 42.857 0.00 0.00 39.30 3.91
209 240 3.979495 GCAAAGTTGAGAGACAAGCAATG 59.021 43.478 0.00 0.00 39.30 2.82
257 288 0.039978 TACCGCCGTGCAATGTTTTG 60.040 50.000 0.00 0.00 35.85 2.44
382 431 2.894763 TAAGTAACCGCGGCATACAT 57.105 45.000 31.39 25.45 0.00 2.29
383 432 2.894763 AAGTAACCGCGGCATACATA 57.105 45.000 31.39 13.60 0.00 2.29
384 433 3.396260 AAGTAACCGCGGCATACATAT 57.604 42.857 31.39 19.76 0.00 1.78
385 434 4.524316 AAGTAACCGCGGCATACATATA 57.476 40.909 31.39 10.97 0.00 0.86
464 1802 3.505464 ACAGTTGTGGCGAGATACTAC 57.495 47.619 0.00 0.00 0.00 2.73
480 1818 8.744011 CGAGATACTACAGAAAAACGGATTTAG 58.256 37.037 0.00 0.00 0.00 1.85
629 1967 1.371558 GCCTCCAAGTGTCGTCCTT 59.628 57.895 0.00 0.00 0.00 3.36
817 2156 2.915463 CGGACGCGCCTTCTATATAAAG 59.085 50.000 5.73 0.00 0.00 1.85
818 2157 3.611057 CGGACGCGCCTTCTATATAAAGT 60.611 47.826 5.73 0.00 0.00 2.66
859 2198 2.413453 GACATCCAAGAACAAGCTCGAC 59.587 50.000 0.00 0.00 0.00 4.20
860 2199 2.224281 ACATCCAAGAACAAGCTCGACA 60.224 45.455 0.00 0.00 0.00 4.35
870 2209 1.145759 AAGCTCGACACACACACACG 61.146 55.000 0.00 0.00 0.00 4.49
889 2228 2.587753 ACGCACACACGGGAACAG 60.588 61.111 0.00 0.00 37.37 3.16
890 2229 4.012895 CGCACACACGGGAACAGC 62.013 66.667 0.00 0.00 0.00 4.40
891 2230 2.591715 GCACACACGGGAACAGCT 60.592 61.111 0.00 0.00 0.00 4.24
892 2231 2.186826 GCACACACGGGAACAGCTT 61.187 57.895 0.00 0.00 0.00 3.74
1437 2776 2.044946 GCCTTCCATGTCCCGCTT 60.045 61.111 0.00 0.00 0.00 4.68
1528 2872 1.138069 ACAGTGTGTGGTTCATCGACA 59.862 47.619 0.00 0.00 32.61 4.35
1568 2915 9.506018 GTAGGAGTTACTAGCTAGCTTATTAGT 57.494 37.037 24.88 21.44 0.00 2.24
1730 3078 1.139654 CCATCATGTGAGGACCGTCAT 59.860 52.381 0.00 0.00 0.00 3.06
1780 3128 2.904905 CGGGCGAATAAGGACCCA 59.095 61.111 0.00 0.00 42.97 4.51
1783 3131 0.463833 GGGCGAATAAGGACCCAGTG 60.464 60.000 0.00 0.00 42.33 3.66
1800 3149 0.591659 GTGGAAAAGAAGGGACGTGC 59.408 55.000 0.00 0.00 0.00 5.34
1809 3158 4.546829 AGAAGGGACGTGCTAATTACAA 57.453 40.909 7.11 0.00 0.00 2.41
1871 3220 0.593128 GGTGCAGCAACATCGTCTTT 59.407 50.000 11.86 0.00 0.00 2.52
1906 3431 5.288952 GGCGTAGTCAAGAAGTAGATCAAAC 59.711 44.000 0.00 0.00 0.00 2.93
1971 3496 4.200838 TCAGTGCGGTGAATATTTCTCA 57.799 40.909 0.00 0.00 0.00 3.27
2058 3583 5.104277 TCCCCTATCGTGGTGAAAACAATAT 60.104 40.000 0.00 0.00 0.00 1.28
2134 3659 7.468357 GCTCTAGAAATTCATTTGGTCCTGATG 60.468 40.741 0.00 0.00 0.00 3.07
2563 4106 1.617536 AGCTGATGAAGGGCTCCCA 60.618 57.895 7.82 0.00 38.92 4.37
2651 4194 1.676006 GCATACCTTACCCACATGCAC 59.324 52.381 0.00 0.00 41.25 4.57
2703 4246 5.015515 ACACACTTTCCCTAGTAGAGTACC 58.984 45.833 0.00 0.00 0.00 3.34
2986 4541 2.165319 ACAAAAGCGAGACCTGTACC 57.835 50.000 0.00 0.00 0.00 3.34
3132 4687 2.159282 AGCCGTAGATTCGTCATCGTTT 60.159 45.455 0.00 0.00 36.93 3.60
3141 4696 7.274442 AGATTCGTCATCGTTTAACTTGTAC 57.726 36.000 0.00 0.00 36.93 2.90
3285 4845 9.802039 GTTCATAATGTCCCCTTTATATGGTTA 57.198 33.333 0.00 0.00 0.00 2.85
3344 4908 0.882927 GCGTGGAGCACAAAGTGGTA 60.883 55.000 1.45 0.00 44.55 3.25
3395 4959 1.067060 GCATATTTCCTTTGCCCGTCC 59.933 52.381 0.00 0.00 0.00 4.79
3493 5057 2.300152 TGCAGGAAGACGTCAAGAAGAT 59.700 45.455 19.50 0.00 0.00 2.40
3685 5262 5.223382 TCTCTTTCTGAAACTAAGAGTGCG 58.777 41.667 13.63 0.00 43.32 5.34
3729 5307 5.102953 TCCCCTGTCTCAAAATGATAGTG 57.897 43.478 0.00 0.00 0.00 2.74
3757 5742 9.846248 CAAAAACTCCTTATATTTTGAGACAGG 57.154 33.333 4.30 0.00 42.48 4.00
3785 5770 9.722056 GGAGTAATAATTTGTGCTTGTAGAATG 57.278 33.333 0.00 0.00 0.00 2.67
3786 5771 9.226345 GAGTAATAATTTGTGCTTGTAGAATGC 57.774 33.333 0.00 0.00 0.00 3.56
3941 5930 0.320697 GCACCTACAACCGAAGTCCT 59.679 55.000 0.00 0.00 0.00 3.85
4022 6015 0.898789 CCGGGCTATCCATAGTCGGT 60.899 60.000 15.97 0.00 40.67 4.69
4030 6023 1.548081 TCCATAGTCGGTCCAAACGA 58.452 50.000 0.00 0.00 38.13 3.85
4140 6134 2.583593 GCCGATGGTCTGACGAGC 60.584 66.667 1.07 0.00 38.14 5.03
4142 6136 2.951745 CGATGGTCTGACGAGCGC 60.952 66.667 16.73 0.00 40.48 5.92
4148 6160 2.676822 TCTGACGAGCGCCTCCTT 60.677 61.111 2.29 0.00 0.00 3.36
4263 6275 1.276622 TTTCCCCTTTCTCCTCTCCG 58.723 55.000 0.00 0.00 0.00 4.63
4266 6278 2.496817 CCTTTCTCCTCTCCGCCG 59.503 66.667 0.00 0.00 0.00 6.46
4267 6279 2.352032 CCTTTCTCCTCTCCGCCGT 61.352 63.158 0.00 0.00 0.00 5.68
4307 6319 2.438434 GCTACCATGCCAAGGCGT 60.438 61.111 6.60 2.79 45.51 5.68
4309 6321 1.221840 CTACCATGCCAAGGCGTCT 59.778 57.895 2.09 0.00 45.51 4.18
4321 6333 0.537188 AGGCGTCTAATCACCACCTG 59.463 55.000 0.00 0.00 0.00 4.00
4338 6350 2.202987 GAGGCATGCTCACTCCGG 60.203 66.667 18.92 0.00 0.00 5.14
4378 6390 3.474570 GCAGATCCGGGTGAGGCT 61.475 66.667 0.00 0.00 0.00 4.58
4399 6411 2.006772 CTACTCATTTCGCCACCGC 58.993 57.895 0.00 0.00 0.00 5.68
4401 6413 1.895020 TACTCATTTCGCCACCGCCT 61.895 55.000 0.00 0.00 0.00 5.52
4403 6415 1.982073 CTCATTTCGCCACCGCCTTC 61.982 60.000 0.00 0.00 0.00 3.46
4428 6448 1.101635 TGGAGCCGTCGTAGGATGAG 61.102 60.000 6.21 0.00 0.00 2.90
4431 6451 0.820074 AGCCGTCGTAGGATGAGGAG 60.820 60.000 6.21 0.00 0.00 3.69
4434 6454 1.231221 CGTCGTAGGATGAGGAGGAG 58.769 60.000 0.00 0.00 0.00 3.69
4442 6462 0.831711 GATGAGGAGGAGGAGGAGGC 60.832 65.000 0.00 0.00 0.00 4.70
4452 6475 3.157949 GAGGAGGCGGGGAAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
4460 6483 3.010226 CGGGGAAGGAGGAGGAGGA 62.010 68.421 0.00 0.00 0.00 3.71
4463 6486 1.595058 GGGAAGGAGGAGGAGGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
4465 6488 0.105709 GAAGGAGGAGGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
4466 6489 0.556380 AAGGAGGAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
4482 6505 2.445654 GAGGAGGAGGGGGAGCAG 60.446 72.222 0.00 0.00 0.00 4.24
4483 6506 4.814041 AGGAGGAGGGGGAGCAGC 62.814 72.222 0.00 0.00 0.00 5.25
4501 6524 4.168291 CGCTGGAAGAGGAGCCCC 62.168 72.222 0.00 0.00 34.07 5.80
4502 6525 3.011517 GCTGGAAGAGGAGCCCCA 61.012 66.667 0.00 0.00 34.07 4.96
4503 6526 2.606587 GCTGGAAGAGGAGCCCCAA 61.607 63.158 0.00 0.00 34.07 4.12
4504 6527 1.301293 CTGGAAGAGGAGCCCCAAC 59.699 63.158 0.00 0.00 34.07 3.77
4505 6528 2.203549 CTGGAAGAGGAGCCCCAACC 62.204 65.000 0.00 0.00 34.07 3.77
4506 6529 1.925972 GGAAGAGGAGCCCCAACCT 60.926 63.158 0.00 0.00 39.41 3.50
4507 6530 0.620700 GGAAGAGGAGCCCCAACCTA 60.621 60.000 0.00 0.00 36.57 3.08
4508 6531 1.512735 GAAGAGGAGCCCCAACCTAT 58.487 55.000 0.00 0.00 36.57 2.57
4509 6532 2.690840 GAAGAGGAGCCCCAACCTATA 58.309 52.381 0.00 0.00 36.57 1.31
4510 6533 2.407340 AGAGGAGCCCCAACCTATAG 57.593 55.000 0.00 0.00 36.57 1.31
4511 6534 1.866943 AGAGGAGCCCCAACCTATAGA 59.133 52.381 0.00 0.00 36.57 1.98
4512 6535 2.158234 AGAGGAGCCCCAACCTATAGAG 60.158 54.545 0.00 0.00 36.57 2.43
4513 6536 1.132689 AGGAGCCCCAACCTATAGAGG 60.133 57.143 0.61 0.61 41.30 3.69
4514 6537 3.524958 AGGAGCCCCAACCTATAGAGGA 61.525 54.545 11.21 0.00 39.13 3.71
4515 6538 5.376929 AGGAGCCCCAACCTATAGAGGAG 62.377 56.522 11.21 1.94 39.13 3.69
4523 6546 2.573920 CTATAGAGGAGGAGGCGGC 58.426 63.158 0.00 0.00 0.00 6.53
4524 6547 1.303398 TATAGAGGAGGAGGCGGCG 60.303 63.158 0.51 0.51 0.00 6.46
4525 6548 2.766306 TATAGAGGAGGAGGCGGCGG 62.766 65.000 9.78 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.280317 GGTGGACTAAATAGGTCAGGTTTGA 60.280 44.000 0.00 0.00 35.61 2.69
4 5 4.600111 TGGTGGACTAAATAGGTCAGGTTT 59.400 41.667 0.00 0.00 35.61 3.27
6 7 3.518303 GTGGTGGACTAAATAGGTCAGGT 59.482 47.826 0.00 0.00 35.61 4.00
7 8 3.430374 CGTGGTGGACTAAATAGGTCAGG 60.430 52.174 0.00 0.00 35.61 3.86
8 9 3.194968 ACGTGGTGGACTAAATAGGTCAG 59.805 47.826 0.00 0.00 35.61 3.51
9 10 3.056393 CACGTGGTGGACTAAATAGGTCA 60.056 47.826 7.95 0.00 35.61 4.02
10 11 3.056322 ACACGTGGTGGACTAAATAGGTC 60.056 47.826 21.57 0.00 37.94 3.85
11 12 2.901839 ACACGTGGTGGACTAAATAGGT 59.098 45.455 21.57 0.00 37.94 3.08
12 13 3.259064 CACACGTGGTGGACTAAATAGG 58.741 50.000 21.57 0.00 44.04 2.57
29 30 1.032114 GGCCTGGATTAGCACCACAC 61.032 60.000 0.00 0.00 33.57 3.82
36 37 3.006967 TCGAGATAAAGGCCTGGATTAGC 59.993 47.826 5.69 4.11 0.00 3.09
52 53 9.314321 CAAAATAGTACTGGTGTTATTCGAGAT 57.686 33.333 5.39 0.00 0.00 2.75
57 58 9.983804 GTTAGCAAAATAGTACTGGTGTTATTC 57.016 33.333 5.39 0.00 0.00 1.75
106 107 7.528307 ACCGTTGCGTATTATTTTTACATGAA 58.472 30.769 0.00 0.00 0.00 2.57
123 154 7.689953 ATAAGAGTACTAAAATACCGTTGCG 57.310 36.000 0.00 0.00 0.00 4.85
158 189 4.453751 ACTTAAGTAGTCACCCGCAAAAA 58.546 39.130 6.26 0.00 28.23 1.94
159 190 4.075963 ACTTAAGTAGTCACCCGCAAAA 57.924 40.909 6.26 0.00 28.23 2.44
160 191 3.756933 ACTTAAGTAGTCACCCGCAAA 57.243 42.857 6.26 0.00 28.23 3.68
161 192 4.870123 TTACTTAAGTAGTCACCCGCAA 57.130 40.909 14.73 0.00 38.33 4.85
162 193 4.039004 TGTTTACTTAAGTAGTCACCCGCA 59.961 41.667 14.73 4.97 38.33 5.69
163 194 4.559153 TGTTTACTTAAGTAGTCACCCGC 58.441 43.478 14.73 2.85 38.33 6.13
164 195 5.063060 GCATGTTTACTTAAGTAGTCACCCG 59.937 44.000 14.73 10.92 38.33 5.28
165 196 5.935789 TGCATGTTTACTTAAGTAGTCACCC 59.064 40.000 14.73 11.96 38.33 4.61
166 197 7.429636 TTGCATGTTTACTTAAGTAGTCACC 57.570 36.000 14.73 12.22 38.33 4.02
167 198 8.557029 ACTTTGCATGTTTACTTAAGTAGTCAC 58.443 33.333 14.73 13.05 38.33 3.67
168 199 8.671384 ACTTTGCATGTTTACTTAAGTAGTCA 57.329 30.769 14.73 16.51 38.33 3.41
169 200 9.382244 CAACTTTGCATGTTTACTTAAGTAGTC 57.618 33.333 14.73 12.17 38.33 2.59
170 201 9.116067 TCAACTTTGCATGTTTACTTAAGTAGT 57.884 29.630 14.73 5.17 41.04 2.73
171 202 9.599322 CTCAACTTTGCATGTTTACTTAAGTAG 57.401 33.333 14.73 5.15 0.00 2.57
172 203 9.332502 TCTCAACTTTGCATGTTTACTTAAGTA 57.667 29.630 11.38 11.38 0.00 2.24
173 204 8.220755 TCTCAACTTTGCATGTTTACTTAAGT 57.779 30.769 13.68 13.68 0.00 2.24
174 205 8.559536 TCTCTCAACTTTGCATGTTTACTTAAG 58.440 33.333 0.00 0.00 0.00 1.85
175 206 8.342634 GTCTCTCAACTTTGCATGTTTACTTAA 58.657 33.333 3.28 0.00 0.00 1.85
176 207 7.497579 TGTCTCTCAACTTTGCATGTTTACTTA 59.502 33.333 3.28 0.00 0.00 2.24
177 208 6.318648 TGTCTCTCAACTTTGCATGTTTACTT 59.681 34.615 3.28 0.00 0.00 2.24
178 209 5.822519 TGTCTCTCAACTTTGCATGTTTACT 59.177 36.000 3.28 0.00 0.00 2.24
179 210 6.060028 TGTCTCTCAACTTTGCATGTTTAC 57.940 37.500 3.28 0.24 0.00 2.01
180 211 6.691754 TTGTCTCTCAACTTTGCATGTTTA 57.308 33.333 3.28 0.00 0.00 2.01
181 212 5.581126 TTGTCTCTCAACTTTGCATGTTT 57.419 34.783 3.28 0.00 0.00 2.83
182 213 4.498682 GCTTGTCTCTCAACTTTGCATGTT 60.499 41.667 0.00 0.00 32.18 2.71
183 214 3.004106 GCTTGTCTCTCAACTTTGCATGT 59.996 43.478 0.00 0.00 32.18 3.21
184 215 3.004002 TGCTTGTCTCTCAACTTTGCATG 59.996 43.478 0.00 0.00 31.67 4.06
185 216 3.216800 TGCTTGTCTCTCAACTTTGCAT 58.783 40.909 0.00 0.00 31.67 3.96
186 217 2.642427 TGCTTGTCTCTCAACTTTGCA 58.358 42.857 0.00 0.00 33.32 4.08
187 218 3.698029 TTGCTTGTCTCTCAACTTTGC 57.302 42.857 0.00 0.00 32.18 3.68
188 219 5.179045 ACATTGCTTGTCTCTCAACTTTG 57.821 39.130 0.00 0.00 30.89 2.77
205 236 3.730715 GTCAAACTCGGCAAAAGACATTG 59.269 43.478 0.00 0.00 0.00 2.82
206 237 3.243401 GGTCAAACTCGGCAAAAGACATT 60.243 43.478 0.00 0.00 0.00 2.71
209 240 1.333791 CGGTCAAACTCGGCAAAAGAC 60.334 52.381 0.00 0.00 0.00 3.01
270 319 1.959899 GCGTCACAACCATCTGCTCG 61.960 60.000 0.00 0.00 0.00 5.03
384 433 9.817809 GAGATTTTCTGGAAGTGTGTATGTATA 57.182 33.333 0.00 0.00 33.76 1.47
385 434 8.321353 TGAGATTTTCTGGAAGTGTGTATGTAT 58.679 33.333 0.00 0.00 33.76 2.29
486 1824 1.710013 CGATGCGGACGGCTATATTT 58.290 50.000 6.55 0.00 44.05 1.40
487 1825 0.736325 GCGATGCGGACGGCTATATT 60.736 55.000 6.55 0.00 44.05 1.28
488 1826 1.153823 GCGATGCGGACGGCTATAT 60.154 57.895 6.55 0.00 44.05 0.86
731 2070 4.994471 CACTCGTGGGCAGCAGCA 62.994 66.667 2.65 0.00 44.61 4.41
817 2156 0.677731 TGTGAGCATGGGCAAGCTAC 60.678 55.000 0.00 0.00 42.04 3.58
818 2157 0.256752 ATGTGAGCATGGGCAAGCTA 59.743 50.000 0.00 0.00 42.04 3.32
859 2198 3.858989 TGCGTGCGTGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
860 2199 3.860125 GTGCGTGCGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
870 2209 4.307908 GTTCCCGTGTGTGCGTGC 62.308 66.667 0.00 0.00 0.00 5.34
1032 2371 2.037367 TAGCTGTCCGCCAGAGGT 59.963 61.111 0.00 0.00 44.49 3.85
1452 2791 2.821366 CCGTAGCTGCAAGGGCTG 60.821 66.667 9.07 0.00 40.52 4.85
1568 2915 7.421087 TCGAGCTAGCTCTATATTAGGAGTA 57.579 40.000 35.36 5.99 40.69 2.59
1578 2925 3.000041 CACTCGATCGAGCTAGCTCTAT 59.000 50.000 38.12 31.17 45.54 1.98
1687 3034 8.372877 TGGGAAAGCTTTCAAATATTATTCCA 57.627 30.769 33.88 24.94 38.92 3.53
1737 3085 8.504815 GCACTACTACTAAATGTCTCGATCATA 58.495 37.037 4.15 0.00 0.00 2.15
1780 3128 1.814248 GCACGTCCCTTCTTTTCCACT 60.814 52.381 0.00 0.00 0.00 4.00
1783 3131 2.467566 TAGCACGTCCCTTCTTTTCC 57.532 50.000 0.00 0.00 0.00 3.13
1800 3149 7.772332 AGACCAGCTTAATCGTTGTAATTAG 57.228 36.000 0.00 0.00 0.00 1.73
1834 3183 5.049167 TGCACCAGCTTTTTATTTTGACAG 58.951 37.500 0.00 0.00 42.74 3.51
1871 3220 1.070914 TGACTACGCCACAACATTCCA 59.929 47.619 0.00 0.00 0.00 3.53
1906 3431 4.082523 ACATCAGACACCCGCGGG 62.083 66.667 42.17 42.17 42.03 6.13
2058 3583 1.022982 AGGCGTCACGATCGTGTAGA 61.023 55.000 38.72 23.14 45.55 2.59
2128 3653 1.563410 AGCTTCCTTTCCTCCATCAGG 59.437 52.381 0.00 0.00 45.15 3.86
2134 3659 7.969004 AGATTAACTATAGCTTCCTTTCCTCC 58.031 38.462 0.00 0.00 0.00 4.30
2256 3787 9.392259 ACAAGCTTTTCTTAAGTTACTGTTAGT 57.608 29.630 0.00 0.00 32.74 2.24
2257 3788 9.651718 CACAAGCTTTTCTTAAGTTACTGTTAG 57.348 33.333 0.00 0.00 32.74 2.34
2258 3789 9.169592 ACACAAGCTTTTCTTAAGTTACTGTTA 57.830 29.630 0.00 0.00 32.74 2.41
2261 3792 7.429340 CACACACAAGCTTTTCTTAAGTTACTG 59.571 37.037 0.00 0.00 32.74 2.74
2367 3904 3.311110 GGTGTGTCCCAGGCTCGA 61.311 66.667 0.00 0.00 0.00 4.04
2368 3905 4.742201 CGGTGTGTCCCAGGCTCG 62.742 72.222 0.00 0.00 0.00 5.03
2563 4106 4.643387 GCTTGACGGCCACCCACT 62.643 66.667 2.24 0.00 0.00 4.00
2651 4194 3.093717 AGGAGTATCGGTTAACATGCG 57.906 47.619 8.10 2.10 34.37 4.73
2703 4246 2.486918 TCATGAGCTGACAAGTGTGTG 58.513 47.619 0.00 0.00 38.41 3.82
2986 4541 0.750546 CCATGTGAGCACCATGGAGG 60.751 60.000 21.47 11.40 46.46 4.30
3030 4585 4.994471 CGCTGTGCTGTGCCTGGA 62.994 66.667 0.00 0.00 0.00 3.86
3132 4687 5.840149 TCTGTTAACTCCCTGGTACAAGTTA 59.160 40.000 7.22 0.00 37.91 2.24
3141 4696 4.470602 AGGTTTTTCTGTTAACTCCCTGG 58.529 43.478 7.22 0.00 0.00 4.45
3285 4845 9.347240 GTTGCTCCATGCCTTCAATATATATAT 57.653 33.333 0.00 0.00 42.00 0.86
3293 4853 1.927487 TGTTGCTCCATGCCTTCAAT 58.073 45.000 0.00 0.00 42.00 2.57
3344 4908 4.268939 TCCGTCGTCGCGTTGGTT 62.269 61.111 5.77 0.00 35.54 3.67
3380 4944 0.320946 CGTAGGACGGGCAAAGGAAA 60.321 55.000 0.00 0.00 38.08 3.13
3395 4959 2.331805 CCGATGGGCGAGTCGTAG 59.668 66.667 15.08 0.00 44.57 3.51
3493 5057 1.005924 GAAGGCCAATCTTCTTCCCCA 59.994 52.381 5.01 0.00 39.84 4.96
3518 5082 3.622163 CAGGAGCAATCTACAGCAGAAAG 59.378 47.826 0.00 0.00 36.67 2.62
3657 5224 7.495934 CACTCTTAGTTTCAGAAAGAGAACCAA 59.504 37.037 16.01 0.00 45.94 3.67
3685 5262 7.081976 GGGAGTAACAAATTACAATGACACAC 58.918 38.462 0.00 0.00 42.83 3.82
3757 5742 5.914898 ACAAGCACAAATTATTACTCCCC 57.085 39.130 0.00 0.00 0.00 4.81
3785 5770 2.607187 ACTAGTACATTCGTGCACAGC 58.393 47.619 18.64 0.00 0.00 4.40
3786 5771 4.095932 TCCTACTAGTACATTCGTGCACAG 59.904 45.833 18.64 9.95 0.00 3.66
3821 5806 4.598036 ATCCCCCATTCTTATATGCCTG 57.402 45.455 0.00 0.00 0.00 4.85
3860 5845 8.093307 GGTAAATACAATAGAACCTAGCCCTAC 58.907 40.741 0.00 0.00 0.00 3.18
3925 5914 3.181478 GGTATGAGGACTTCGGTTGTAGG 60.181 52.174 0.00 0.00 0.00 3.18
3941 5930 1.448893 GCGTTTGAGGCGGGTATGA 60.449 57.895 0.00 0.00 0.00 2.15
3976 5965 1.610363 GGCAAAATTTTGTCCGGGCAT 60.610 47.619 27.13 0.00 40.24 4.40
3979 5968 1.507562 GTGGCAAAATTTTGTCCGGG 58.492 50.000 27.82 6.24 41.89 5.73
4022 6015 2.738480 CCAGTCCGGTCGTTTGGA 59.262 61.111 0.00 0.00 0.00 3.53
4043 6036 1.674057 GGCCGGATATGAGGAGTGG 59.326 63.158 5.05 0.00 0.00 4.00
4050 6043 2.038952 CTCAGATTTGGGCCGGATATGA 59.961 50.000 5.05 13.42 0.00 2.15
4099 6093 2.893398 GGTCAGAGCCTACGTGGG 59.107 66.667 14.62 14.62 36.00 4.61
4129 6123 4.500116 GGAGGCGCTCGTCAGACC 62.500 72.222 7.64 0.00 0.00 3.85
4140 6134 4.069232 TGTGGAGCGAAGGAGGCG 62.069 66.667 0.00 0.00 35.00 5.52
4142 6136 2.266055 GGTGTGGAGCGAAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
4227 6239 0.634465 AAATGGGGCGGATAGGGTTT 59.366 50.000 0.00 0.00 0.00 3.27
4263 6275 0.442699 GGATTTGAAGTGACGACGGC 59.557 55.000 0.00 0.00 0.00 5.68
4266 6278 0.442699 GGCGGATTTGAAGTGACGAC 59.557 55.000 0.00 0.00 0.00 4.34
4267 6279 0.672401 GGGCGGATTTGAAGTGACGA 60.672 55.000 0.00 0.00 0.00 4.20
4301 6313 1.066143 CAGGTGGTGATTAGACGCCTT 60.066 52.381 0.00 0.00 42.84 4.35
4307 6319 1.951209 TGCCTCAGGTGGTGATTAGA 58.049 50.000 0.00 0.00 33.51 2.10
4309 6321 1.408683 GCATGCCTCAGGTGGTGATTA 60.409 52.381 6.36 0.00 33.51 1.75
4321 6333 2.202987 CCGGAGTGAGCATGCCTC 60.203 66.667 15.66 13.77 41.15 4.70
4338 6350 3.842923 TAGCTGCAGCCTCCGCTC 61.843 66.667 34.39 5.26 43.95 5.03
4372 6384 1.134699 CGAAATGAGTAGCCAGCCTCA 60.135 52.381 1.82 1.82 41.61 3.86
4408 6428 1.101635 TCATCCTACGACGGCTCCAG 61.102 60.000 0.00 0.00 0.00 3.86
4409 6429 1.077285 TCATCCTACGACGGCTCCA 60.077 57.895 0.00 0.00 0.00 3.86
4420 6440 2.069775 CTCCTCCTCCTCCTCATCCTA 58.930 57.143 0.00 0.00 0.00 2.94
4431 6451 4.798682 TTCCCCGCCTCCTCCTCC 62.799 72.222 0.00 0.00 0.00 4.30
4434 6454 4.798682 TCCTTCCCCGCCTCCTCC 62.799 72.222 0.00 0.00 0.00 4.30
4442 6462 2.444895 CCTCCTCCTCCTTCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
4452 6475 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
4460 6483 3.039526 CCCCCTCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
4463 6486 3.773154 GCTCCCCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
4465 6488 2.445654 CTGCTCCCCCTCCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
4466 6489 4.814041 GCTGCTCCCCCTCCTCCT 62.814 72.222 0.00 0.00 0.00 3.69
4482 6505 4.847444 GGCTCCTCTTCCAGCGGC 62.847 72.222 0.00 0.00 36.41 6.53
4483 6506 4.168291 GGGCTCCTCTTCCAGCGG 62.168 72.222 0.00 0.00 36.41 5.52
4484 6507 4.168291 GGGGCTCCTCTTCCAGCG 62.168 72.222 0.00 0.00 36.41 5.18
4485 6508 2.606587 TTGGGGCTCCTCTTCCAGC 61.607 63.158 3.07 0.00 34.65 4.85
4486 6509 1.301293 GTTGGGGCTCCTCTTCCAG 59.699 63.158 3.07 0.00 0.00 3.86
4487 6510 2.231380 GGTTGGGGCTCCTCTTCCA 61.231 63.158 3.07 0.00 0.00 3.53
4488 6511 0.620700 TAGGTTGGGGCTCCTCTTCC 60.621 60.000 3.07 0.57 35.51 3.46
4489 6512 1.512735 ATAGGTTGGGGCTCCTCTTC 58.487 55.000 3.07 0.00 35.51 2.87
4490 6513 2.250273 TCTATAGGTTGGGGCTCCTCTT 59.750 50.000 3.07 0.00 35.51 2.85
4491 6514 1.866943 TCTATAGGTTGGGGCTCCTCT 59.133 52.381 3.07 1.07 35.51 3.69
4492 6515 2.252714 CTCTATAGGTTGGGGCTCCTC 58.747 57.143 3.07 0.00 35.51 3.71
4493 6516 1.132689 CCTCTATAGGTTGGGGCTCCT 60.133 57.143 3.07 0.00 38.19 3.69
4494 6517 1.132817 TCCTCTATAGGTTGGGGCTCC 60.133 57.143 0.00 0.00 44.09 4.70
4495 6518 2.252714 CTCCTCTATAGGTTGGGGCTC 58.747 57.143 0.00 0.00 44.09 4.70
4496 6519 1.132689 CCTCCTCTATAGGTTGGGGCT 60.133 57.143 0.00 0.00 44.09 5.19
4497 6520 1.132817 TCCTCCTCTATAGGTTGGGGC 60.133 57.143 0.00 0.00 44.09 5.80
4498 6521 2.493687 CCTCCTCCTCTATAGGTTGGGG 60.494 59.091 0.00 0.46 44.09 4.96
4499 6522 2.896039 CCTCCTCCTCTATAGGTTGGG 58.104 57.143 0.00 0.00 44.09 4.12
4500 6523 2.252714 GCCTCCTCCTCTATAGGTTGG 58.747 57.143 0.00 0.82 44.09 3.77
4501 6524 1.889829 CGCCTCCTCCTCTATAGGTTG 59.110 57.143 0.00 0.00 44.09 3.77
4502 6525 1.203075 CCGCCTCCTCCTCTATAGGTT 60.203 57.143 0.00 0.00 44.09 3.50
4503 6526 0.406361 CCGCCTCCTCCTCTATAGGT 59.594 60.000 0.00 0.00 44.09 3.08
4504 6527 0.968393 GCCGCCTCCTCCTCTATAGG 60.968 65.000 0.00 0.00 45.21 2.57
4505 6528 1.309499 CGCCGCCTCCTCCTCTATAG 61.309 65.000 0.00 0.00 0.00 1.31
4506 6529 1.303398 CGCCGCCTCCTCCTCTATA 60.303 63.158 0.00 0.00 0.00 1.31
4507 6530 2.598985 CGCCGCCTCCTCCTCTAT 60.599 66.667 0.00 0.00 0.00 1.98
4508 6531 4.896829 CCGCCGCCTCCTCCTCTA 62.897 72.222 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.