Multiple sequence alignment - TraesCS1A01G264400

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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 TraesCS1A01G264400 chr1A 100.000 3923 0 0 1 3923 459951951 459948029 0.000000e+00 7245
1 TraesCS1A01G264400 chr1B 94.474 3384 133 23 579 3923 482455526 482452158 0.000000e+00 5164
2 TraesCS1A01G264400 chr1B 84.192 582 70 11 6 582 482456434 482455870 2.670000e-151 545
3 TraesCS1A01G264400 chr1D 95.028 3258 127 16 546 3786 360391628 360388389 0.000000e+00 5086
4 TraesCS1A01G264400 chr1D 97.857 140 3 0 3784 3923 360388078 360387939 3.920000e-60 243
5 TraesCS1A01G264400 chr3A 76.836 967 199 16 1871 2820 651588867 651587909 4.490000e-144 521
6 TraesCS1A01G264400 chr3A 88.194 144 9 3 375 518 534181996 534181861 8.720000e-37 165
7 TraesCS1A01G264400 chr3D 76.701 970 201 18 1868 2820 516385913 516384952 2.090000e-142 516
8 TraesCS1A01G264400 chr6A 88.158 152 14 3 368 518 409093032 409093180 1.120000e-40 178
9 TraesCS1A01G264400 chr7D 88.079 151 14 3 368 517 525768109 525767962 4.030000e-40 176
10 TraesCS1A01G264400 chr7D 86.093 151 13 3 368 518 397554936 397555078 5.250000e-34 156
11 TraesCS1A01G264400 chr7A 87.013 154 12 3 368 521 451519952 451519807 2.420000e-37 167
12 TraesCS1A01G264400 chr2A 87.417 151 11 3 368 518 758586597 758586739 2.420000e-37 167
13 TraesCS1A01G264400 chr2B 85.366 164 16 3 368 531 521975016 521974861 3.140000e-36 163
14 TraesCS1A01G264400 chr6B 85.714 154 13 4 368 520 615991081 615991226 1.890000e-33 154


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 TraesCS1A01G264400 chr1A 459948029 459951951 3922 True 7245.0 7245 100.0000 1 3923 1 chr1A.!!$R1 3922
1 TraesCS1A01G264400 chr1B 482452158 482456434 4276 True 2854.5 5164 89.3330 6 3923 2 chr1B.!!$R1 3917
2 TraesCS1A01G264400 chr1D 360387939 360391628 3689 True 2664.5 5086 96.4425 546 3923 2 chr1D.!!$R1 3377
3 TraesCS1A01G264400 chr3A 651587909 651588867 958 True 521.0 521 76.8360 1871 2820 1 chr3A.!!$R2 949
4 TraesCS1A01G264400 chr3D 516384952 516385913 961 True 516.0 516 76.7010 1868 2820 1 chr3D.!!$R1 952

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
175 177 0.685458 GATGGGGCAGTTGAGGCAAT 60.685 55.0 0.00 0.0 35.46 3.56 F
253 257 0.869730 GGTAAAAGCCGCGACAGAAA 59.130 50.0 8.23 0.0 0.00 2.52 F
1753 2146 0.882042 CCCAATCGCCTTCATCCTCG 60.882 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2562 0.036765 TGGGCATGAAGTCGTACACC 60.037 55.000 0.00 0.0 0.00 4.16 R
2256 2658 4.082787 GCCACATCCATTATTATGTTCCGG 60.083 45.833 0.00 0.0 34.12 5.14 R
3161 3571 1.021390 CAGCGCTAGTTGGTTCCCAG 61.021 60.000 10.99 0.0 33.81 4.45 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
26 27 7.966204 ACACGTAATTATTGTGATTTACTTGCC 59.034 33.333 20.99 0.00 37.08 4.52
42 44 5.883503 ACTTGCCATTTTTATTGCCAATG 57.116 34.783 0.00 0.00 0.00 2.82
43 45 4.156373 ACTTGCCATTTTTATTGCCAATGC 59.844 37.500 0.00 0.00 38.26 3.56
79 81 2.761559 TCGGATTGTATATGCCAACCG 58.238 47.619 7.15 7.15 37.59 4.44
81 83 3.135225 CGGATTGTATATGCCAACCGAA 58.865 45.455 7.61 0.00 38.03 4.30
84 86 4.142902 GGATTGTATATGCCAACCGAATCG 60.143 45.833 0.00 0.00 0.00 3.34
94 96 4.936411 TGCCAACCGAATCGAAACTTATTA 59.064 37.500 3.36 0.00 0.00 0.98
97 99 5.813672 CCAACCGAATCGAAACTTATTAGGA 59.186 40.000 3.36 0.00 33.53 2.94
166 168 3.525800 ACTGTTAAAAGATGGGGCAGT 57.474 42.857 0.00 0.00 0.00 4.40
175 177 0.685458 GATGGGGCAGTTGAGGCAAT 60.685 55.000 0.00 0.00 35.46 3.56
210 213 7.538303 AAAATGCTGAAAAATCGACAAAACT 57.462 28.000 0.00 0.00 0.00 2.66
216 219 9.092876 TGCTGAAAAATCGACAAAACTAAAAAT 57.907 25.926 0.00 0.00 0.00 1.82
225 229 5.637809 GACAAAACTAAAAATAGAGGCGGG 58.362 41.667 0.00 0.00 0.00 6.13
228 232 4.311520 AACTAAAAATAGAGGCGGGGTT 57.688 40.909 0.00 0.00 0.00 4.11
235 239 2.308118 TAGAGGCGGGGTTAGGAGGG 62.308 65.000 0.00 0.00 0.00 4.30
237 241 2.041612 GGCGGGGTTAGGAGGGTA 60.042 66.667 0.00 0.00 0.00 3.69
243 247 1.064166 GGGGTTAGGAGGGTAAAAGCC 60.064 57.143 0.00 0.00 38.48 4.35
245 249 1.376543 GTTAGGAGGGTAAAAGCCGC 58.623 55.000 0.00 0.00 41.56 6.53
253 257 0.869730 GGTAAAAGCCGCGACAGAAA 59.130 50.000 8.23 0.00 0.00 2.52
262 266 3.627577 AGCCGCGACAGAAATTTATGAAT 59.372 39.130 19.19 0.00 0.00 2.57
287 291 7.054124 TGTTGTTGAAGTAGGAGAGAATTTGT 58.946 34.615 0.00 0.00 0.00 2.83
293 297 7.386851 TGAAGTAGGAGAGAATTTGTGTTAGG 58.613 38.462 0.00 0.00 0.00 2.69
298 302 3.753272 GAGAGAATTTGTGTTAGGCTGCA 59.247 43.478 0.50 0.00 0.00 4.41
313 317 2.353109 GGCTGCAAAGGGAGTTCAAATC 60.353 50.000 0.50 0.00 34.49 2.17
320 324 5.699839 CAAAGGGAGTTCAAATCCGTAAAG 58.300 41.667 0.00 0.00 37.75 1.85
326 330 5.294552 GGAGTTCAAATCCGTAAAGATCCTG 59.705 44.000 0.00 0.00 0.00 3.86
330 334 5.661458 TCAAATCCGTAAAGATCCTGAGAC 58.339 41.667 0.00 0.00 0.00 3.36
332 336 3.095912 TCCGTAAAGATCCTGAGACCA 57.904 47.619 0.00 0.00 0.00 4.02
374 378 3.181434 TGGTTCCTGGTTGCAATAGAGTT 60.181 43.478 0.59 0.00 0.00 3.01
376 380 4.280929 GGTTCCTGGTTGCAATAGAGTTTT 59.719 41.667 0.59 0.00 0.00 2.43
378 382 6.015772 GGTTCCTGGTTGCAATAGAGTTTTTA 60.016 38.462 0.59 0.00 0.00 1.52
380 384 8.736244 GTTCCTGGTTGCAATAGAGTTTTTATA 58.264 33.333 0.59 0.00 0.00 0.98
381 385 8.506168 TCCTGGTTGCAATAGAGTTTTTATAG 57.494 34.615 0.59 0.00 0.00 1.31
415 420 9.935682 AATATGAACTACATACGAAGCAAAATG 57.064 29.630 0.00 0.00 43.12 2.32
420 425 4.685169 ACATACGAAGCAAAATGAGTGG 57.315 40.909 0.00 0.00 0.00 4.00
427 432 4.259970 CGAAGCAAAATGAGTGGATCTACG 60.260 45.833 3.29 0.00 0.00 3.51
469 474 5.499004 ACATCCGTATGTAGGCCATATTT 57.501 39.130 5.01 0.00 44.66 1.40
470 475 5.876357 ACATCCGTATGTAGGCCATATTTT 58.124 37.500 5.01 0.00 44.66 1.82
471 476 5.705441 ACATCCGTATGTAGGCCATATTTTG 59.295 40.000 5.01 0.00 44.66 2.44
476 481 8.158132 TCCGTATGTAGGCCATATTTTGAAATA 58.842 33.333 5.01 0.00 38.29 1.40
533 538 7.230309 AGAGGGAGTATTAACGTACTGTAATCC 59.770 40.741 0.00 0.00 35.14 3.01
534 539 7.065504 AGGGAGTATTAACGTACTGTAATCCT 58.934 38.462 12.94 1.26 35.14 3.24
538 543 9.875675 GAGTATTAACGTACTGTAATCCTACTG 57.124 37.037 0.00 0.00 35.14 2.74
564 569 8.757789 GTTTTGAAATAAAACTTCCTTTACCCG 58.242 33.333 7.74 0.00 37.22 5.28
565 570 7.585579 TTGAAATAAAACTTCCTTTACCCGT 57.414 32.000 0.00 0.00 0.00 5.28
566 571 8.688747 TTGAAATAAAACTTCCTTTACCCGTA 57.311 30.769 0.00 0.00 0.00 4.02
567 572 8.688747 TGAAATAAAACTTCCTTTACCCGTAA 57.311 30.769 0.00 0.00 0.00 3.18
608 961 2.362736 TCAAACAGATGAGCCAGATGC 58.637 47.619 0.00 0.00 41.71 3.91
628 981 2.692041 GCCTGGATTAGCAGAAGCATTT 59.308 45.455 0.00 0.00 45.49 2.32
630 983 4.261363 GCCTGGATTAGCAGAAGCATTTAC 60.261 45.833 0.00 0.00 45.49 2.01
690 1043 3.537206 GAAGTCGCAGCCACCACCT 62.537 63.158 0.00 0.00 0.00 4.00
700 1056 1.986413 CCACCACCTCCTCCTCTTG 59.014 63.158 0.00 0.00 0.00 3.02
747 1103 3.391382 CAGACCCCTCCCACGTCC 61.391 72.222 0.00 0.00 0.00 4.79
759 1115 4.746309 ACGTCCCCATCGGTCCGA 62.746 66.667 18.01 18.01 41.13 4.55
889 1261 5.280215 CCATTTTACTCCAACCACTCTCTCT 60.280 44.000 0.00 0.00 0.00 3.10
909 1281 2.049618 CCCGCTATCTGCTCGAGC 60.050 66.667 30.42 30.42 40.11 5.03
948 1320 1.447314 CTCCCAACGTAAGCCGACC 60.447 63.158 0.00 0.00 45.62 4.79
1122 1515 2.264794 CTGACCTACGTGCCCACC 59.735 66.667 0.00 0.00 0.00 4.61
1488 1881 2.579738 GACCTCTCGTCCTTGCCC 59.420 66.667 0.00 0.00 35.23 5.36
1753 2146 0.882042 CCCAATCGCCTTCATCCTCG 60.882 60.000 0.00 0.00 0.00 4.63
1754 2147 1.502163 CCAATCGCCTTCATCCTCGC 61.502 60.000 0.00 0.00 0.00 5.03
1761 2154 1.227089 CTTCATCCTCGCCCTGTCG 60.227 63.158 0.00 0.00 0.00 4.35
1887 2280 1.369625 CCAACACCGGCTCAATACTC 58.630 55.000 0.00 0.00 0.00 2.59
2004 2397 1.380302 GGATGGGTCTGTGGTTGCT 59.620 57.895 0.00 0.00 0.00 3.91
2160 2562 2.363683 GAAGGGAAGCAGATGTTCCTG 58.636 52.381 11.43 0.00 42.84 3.86
2256 2658 0.733566 CATTGACATGGGCACAACGC 60.734 55.000 0.00 0.00 41.28 4.84
2685 3093 2.206635 CGAGAGCCCAAGAGGTGAT 58.793 57.895 0.00 0.00 38.26 3.06
2736 3144 1.020861 TGTGCGCTCATGTGATGGTC 61.021 55.000 9.73 0.00 0.00 4.02
2874 3282 0.952984 GGAGCAACTTCAGCGCTTCT 60.953 55.000 7.50 0.00 35.75 2.85
2886 3294 1.663074 CGCTTCTCCGGCTATCAGC 60.663 63.158 0.00 0.00 41.46 4.26
2957 3365 4.764823 TGTTTGTTCTGGTCAACTGAAGTT 59.235 37.500 0.00 0.00 37.65 2.66
2972 3380 2.168313 TGAAGTTCAGAGCTGTGTGTCA 59.832 45.455 11.09 7.45 0.00 3.58
2973 3381 3.181462 TGAAGTTCAGAGCTGTGTGTCAT 60.181 43.478 11.09 0.00 0.00 3.06
2977 3385 3.319137 TCAGAGCTGTGTGTCATTACC 57.681 47.619 11.09 0.00 0.00 2.85
2986 3395 5.391310 GCTGTGTGTCATTACCTCTTGATTG 60.391 44.000 0.00 0.00 0.00 2.67
3052 3461 8.057742 GCATTCACATCAAACTTTGTTACTTTG 58.942 33.333 1.44 0.00 0.00 2.77
3075 3484 2.684881 CACCTTGGCCATCATCACTAAC 59.315 50.000 6.09 0.00 0.00 2.34
3076 3485 2.308570 ACCTTGGCCATCATCACTAACA 59.691 45.455 6.09 0.00 0.00 2.41
3077 3486 3.053395 ACCTTGGCCATCATCACTAACAT 60.053 43.478 6.09 0.00 0.00 2.71
3078 3487 3.956199 CCTTGGCCATCATCACTAACATT 59.044 43.478 6.09 0.00 0.00 2.71
3083 3492 4.498682 GGCCATCATCACTAACATTCAAGC 60.499 45.833 0.00 0.00 0.00 4.01
3094 3503 4.568152 AACATTCAAGCCACACTGTAAC 57.432 40.909 0.00 0.00 0.00 2.50
3221 3631 8.526147 CCAGACATGAAAAGGAAGATACATTTT 58.474 33.333 0.00 0.00 36.67 1.82
3222 3632 9.918630 CAGACATGAAAAGGAAGATACATTTTT 57.081 29.630 0.00 0.00 34.68 1.94
3248 3658 3.374220 TGCACAAGGAAATTGAAGCTG 57.626 42.857 0.00 0.00 41.83 4.24
3283 3693 2.676463 GCAGGTAGAGGAGCTTCAGTTG 60.676 54.545 0.00 0.00 31.94 3.16
3455 3865 2.417978 CTGCTGGTGCTGGAAACAA 58.582 52.632 0.00 0.00 42.06 2.83
3471 3881 2.447244 ACAAGAGGAGAACTTCAGCG 57.553 50.000 0.00 0.00 0.00 5.18
3495 3905 6.148811 CGATTTCTCAGCTTTTGGGTTACTTA 59.851 38.462 0.00 0.00 0.00 2.24
3500 3910 5.876357 TCAGCTTTTGGGTTACTTATCAGT 58.124 37.500 0.00 0.00 36.99 3.41
3602 4013 1.409427 GGACTGGGTAGAGGTGATTCG 59.591 57.143 0.00 0.00 0.00 3.34
3660 4071 7.839907 TGAAAAATAATGCAGCAAGGAACTAT 58.160 30.769 0.00 0.00 38.49 2.12
3766 4177 6.770785 AGCAACACTTTACTGAAACCAAGATA 59.229 34.615 0.00 0.00 0.00 1.98
3815 4539 5.136828 TCCATTTCACTAGTTGGCAAAAGA 58.863 37.500 15.54 1.94 0.00 2.52
3896 4620 4.574013 GTGCTCAAGAATTACCATCCTCAG 59.426 45.833 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.965655 TGGCAAGTAAATCACAATAATTACGTG 59.034 33.333 0.00 9.58 39.28 4.49
2 3 8.046294 TGGCAAGTAAATCACAATAATTACGT 57.954 30.769 0.00 0.00 34.32 3.57
3 4 9.515020 AATGGCAAGTAAATCACAATAATTACG 57.485 29.630 0.00 0.00 34.32 3.18
12 13 7.118971 GGCAATAAAAATGGCAAGTAAATCACA 59.881 33.333 0.00 0.00 42.45 3.58
13 14 7.463544 GGCAATAAAAATGGCAAGTAAATCAC 58.536 34.615 0.00 0.00 42.45 3.06
60 62 2.761559 TCGGTTGGCATATACAATCCG 58.238 47.619 17.36 17.36 40.49 4.18
67 69 4.699637 AGTTTCGATTCGGTTGGCATATA 58.300 39.130 6.18 0.00 0.00 0.86
149 151 3.193479 CCTCAACTGCCCCATCTTTTAAC 59.807 47.826 0.00 0.00 0.00 2.01
150 152 3.430453 CCTCAACTGCCCCATCTTTTAA 58.570 45.455 0.00 0.00 0.00 1.52
156 158 0.685458 ATTGCCTCAACTGCCCCATC 60.685 55.000 0.00 0.00 0.00 3.51
161 163 2.818130 TGAAAATTGCCTCAACTGCC 57.182 45.000 0.00 0.00 0.00 4.85
210 213 4.039339 TCCTAACCCCGCCTCTATTTTTA 58.961 43.478 0.00 0.00 0.00 1.52
216 219 1.232216 CCTCCTAACCCCGCCTCTA 59.768 63.158 0.00 0.00 0.00 2.43
221 225 0.620030 TTTTACCCTCCTAACCCCGC 59.380 55.000 0.00 0.00 0.00 6.13
225 229 2.015588 GCGGCTTTTACCCTCCTAACC 61.016 57.143 0.00 0.00 0.00 2.85
228 232 0.971959 TCGCGGCTTTTACCCTCCTA 60.972 55.000 6.13 0.00 0.00 2.94
235 239 2.894307 ATTTCTGTCGCGGCTTTTAC 57.106 45.000 13.81 0.00 0.00 2.01
237 241 2.793278 AAATTTCTGTCGCGGCTTTT 57.207 40.000 13.81 1.33 0.00 2.27
243 247 5.794945 ACAACATTCATAAATTTCTGTCGCG 59.205 36.000 0.00 0.00 0.00 5.87
245 249 8.726650 TCAACAACATTCATAAATTTCTGTCG 57.273 30.769 0.00 0.00 0.00 4.35
253 257 9.739276 TCTCCTACTTCAACAACATTCATAAAT 57.261 29.630 0.00 0.00 0.00 1.40
262 266 7.012327 CACAAATTCTCTCCTACTTCAACAACA 59.988 37.037 0.00 0.00 0.00 3.33
277 281 3.754965 TGCAGCCTAACACAAATTCTCT 58.245 40.909 0.00 0.00 0.00 3.10
287 291 0.771127 ACTCCCTTTGCAGCCTAACA 59.229 50.000 0.00 0.00 0.00 2.41
293 297 2.353109 GGATTTGAACTCCCTTTGCAGC 60.353 50.000 0.00 0.00 0.00 5.25
298 302 5.627135 TCTTTACGGATTTGAACTCCCTTT 58.373 37.500 0.00 0.00 0.00 3.11
313 317 3.444703 CTGGTCTCAGGATCTTTACGG 57.555 52.381 0.00 0.00 37.36 4.02
326 330 1.139947 GTGCTACGAGCCTGGTCTC 59.860 63.158 7.74 7.74 41.51 3.36
351 355 3.012518 CTCTATTGCAACCAGGAACCAG 58.987 50.000 0.00 0.00 0.00 4.00
352 356 2.375174 ACTCTATTGCAACCAGGAACCA 59.625 45.455 0.00 0.00 0.00 3.67
353 357 3.073274 ACTCTATTGCAACCAGGAACC 57.927 47.619 0.00 0.00 0.00 3.62
354 358 5.453567 AAAACTCTATTGCAACCAGGAAC 57.546 39.130 0.00 0.00 0.00 3.62
355 359 7.775053 ATAAAAACTCTATTGCAACCAGGAA 57.225 32.000 0.00 0.00 0.00 3.36
356 360 8.325787 TCTATAAAAACTCTATTGCAACCAGGA 58.674 33.333 0.00 0.00 0.00 3.86
357 361 8.506168 TCTATAAAAACTCTATTGCAACCAGG 57.494 34.615 0.00 0.00 0.00 4.45
358 362 9.383519 TCTCTATAAAAACTCTATTGCAACCAG 57.616 33.333 0.00 1.91 0.00 4.00
392 397 7.334421 ACTCATTTTGCTTCGTATGTAGTTCAT 59.666 33.333 0.00 0.00 40.25 2.57
395 400 6.128282 CCACTCATTTTGCTTCGTATGTAGTT 60.128 38.462 0.00 0.00 0.00 2.24
401 406 5.431765 AGATCCACTCATTTTGCTTCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
403 408 3.679389 AGATCCACTCATTTTGCTTCGT 58.321 40.909 0.00 0.00 0.00 3.85
406 411 3.375299 GCGTAGATCCACTCATTTTGCTT 59.625 43.478 0.00 0.00 0.00 3.91
409 414 4.785669 GAGCGTAGATCCACTCATTTTG 57.214 45.455 0.00 0.00 36.66 2.44
415 420 7.884600 ACGTAGTTTAGAGCGTAGATCCACTC 61.885 46.154 0.00 0.00 42.27 3.51
494 499 9.725206 TTAATACTCCCTCTGTTCCTAAATACT 57.275 33.333 0.00 0.00 0.00 2.12
495 500 9.761504 GTTAATACTCCCTCTGTTCCTAAATAC 57.238 37.037 0.00 0.00 0.00 1.89
496 501 8.636213 CGTTAATACTCCCTCTGTTCCTAAATA 58.364 37.037 0.00 0.00 0.00 1.40
497 502 7.125356 ACGTTAATACTCCCTCTGTTCCTAAAT 59.875 37.037 0.00 0.00 0.00 1.40
498 503 6.438425 ACGTTAATACTCCCTCTGTTCCTAAA 59.562 38.462 0.00 0.00 0.00 1.85
503 508 6.127786 ACAGTACGTTAATACTCCCTCTGTTC 60.128 42.308 0.00 0.00 32.92 3.18
508 513 7.230309 AGGATTACAGTACGTTAATACTCCCTC 59.770 40.741 0.00 0.00 32.92 4.30
517 522 9.195411 CAAAACAGTAGGATTACAGTACGTTAA 57.805 33.333 0.00 0.00 30.34 2.01
538 543 8.757789 CGGGTAAAGGAAGTTTTATTTCAAAAC 58.242 33.333 4.79 4.79 39.67 2.43
572 577 9.599322 CATCTGTTTGAACACTACATAAACTTC 57.401 33.333 0.00 0.00 34.70 3.01
586 939 3.427233 GCATCTGGCTCATCTGTTTGAAC 60.427 47.826 0.00 0.00 40.25 3.18
608 961 4.883585 TGTAAATGCTTCTGCTAATCCAGG 59.116 41.667 0.00 0.00 40.48 4.45
628 981 5.564063 CGTGAACTGTGGATTAGTGAGTGTA 60.564 44.000 0.00 0.00 0.00 2.90
630 983 3.675225 CGTGAACTGTGGATTAGTGAGTG 59.325 47.826 0.00 0.00 0.00 3.51
690 1043 1.990060 CCGGAAGCCAAGAGGAGGA 60.990 63.158 0.00 0.00 36.89 3.71
720 1076 4.410400 GGGGTCTGGCTGGTTCGG 62.410 72.222 0.00 0.00 0.00 4.30
777 1133 3.087906 GTATGACGGGTGGGGCCT 61.088 66.667 0.84 0.00 37.43 5.19
778 1134 3.087906 AGTATGACGGGTGGGGCC 61.088 66.667 0.00 0.00 0.00 5.80
909 1281 1.139947 GAGCGAGAGAGGGGAAACG 59.860 63.158 0.00 0.00 0.00 3.60
910 1282 0.458260 GAGAGCGAGAGAGGGGAAAC 59.542 60.000 0.00 0.00 0.00 2.78
957 1329 2.603652 GGAGGGTGGAACAGGGGTC 61.604 68.421 0.00 0.00 41.80 4.46
958 1330 2.531942 GGAGGGTGGAACAGGGGT 60.532 66.667 0.00 0.00 41.80 4.95
959 1331 3.339093 GGGAGGGTGGAACAGGGG 61.339 72.222 0.00 0.00 41.80 4.79
960 1332 3.339093 GGGGAGGGTGGAACAGGG 61.339 72.222 0.00 0.00 41.80 4.45
1109 1502 2.267961 GGAAGGTGGGCACGTAGG 59.732 66.667 0.00 0.00 0.00 3.18
1341 1734 4.821589 GGCGACGGGAAGCAGGAG 62.822 72.222 0.00 0.00 34.54 3.69
1574 1967 1.404315 CGGTGAGGTAGAAGCAGTTCC 60.404 57.143 0.00 0.00 32.48 3.62
1761 2154 0.678048 AGACAAAGAATGCGAGGGCC 60.678 55.000 0.00 0.00 38.85 5.80
1763 2156 1.089920 CCAGACAAAGAATGCGAGGG 58.910 55.000 0.00 0.00 0.00 4.30
1887 2280 2.103143 AGCTCGGCGATGTCGAAG 59.897 61.111 11.27 0.00 39.77 3.79
2004 2397 2.106338 TGGGTTGAGCATCTTCTTGACA 59.894 45.455 0.00 0.00 34.92 3.58
2160 2562 0.036765 TGGGCATGAAGTCGTACACC 60.037 55.000 0.00 0.00 0.00 4.16
2256 2658 4.082787 GCCACATCCATTATTATGTTCCGG 60.083 45.833 0.00 0.00 34.12 5.14
2685 3093 2.582052 AGAACAAACCTTTCGATGGCA 58.418 42.857 5.06 0.00 0.00 4.92
2886 3294 2.825532 CCCATTATCCATTAAAGGGCCG 59.174 50.000 0.00 0.00 40.85 6.13
2957 3365 2.899900 AGGTAATGACACACAGCTCTGA 59.100 45.455 3.60 0.00 0.00 3.27
2963 3371 5.702670 ACAATCAAGAGGTAATGACACACAG 59.297 40.000 0.00 0.00 0.00 3.66
2972 3380 9.965902 AGAAAGTCAATACAATCAAGAGGTAAT 57.034 29.630 0.00 0.00 0.00 1.89
2973 3381 9.219603 CAGAAAGTCAATACAATCAAGAGGTAA 57.780 33.333 0.00 0.00 0.00 2.85
2977 3385 9.770503 CATTCAGAAAGTCAATACAATCAAGAG 57.229 33.333 0.00 0.00 0.00 2.85
2986 3395 6.690194 ATGCCTCATTCAGAAAGTCAATAC 57.310 37.500 0.00 0.00 0.00 1.89
3017 3426 5.470777 AGTTTGATGTGAATGCCATTTTTGG 59.529 36.000 0.00 0.00 0.00 3.28
3019 3428 7.067251 ACAAAGTTTGATGTGAATGCCATTTTT 59.933 29.630 22.23 0.00 0.00 1.94
3075 3484 2.884012 TGGTTACAGTGTGGCTTGAATG 59.116 45.455 5.88 0.00 0.00 2.67
3076 3485 3.149196 CTGGTTACAGTGTGGCTTGAAT 58.851 45.455 5.88 0.00 39.92 2.57
3077 3486 2.571212 CTGGTTACAGTGTGGCTTGAA 58.429 47.619 5.88 0.00 39.92 2.69
3078 3487 1.202758 CCTGGTTACAGTGTGGCTTGA 60.203 52.381 5.88 0.00 43.36 3.02
3083 3492 2.420129 GCCTATCCTGGTTACAGTGTGG 60.420 54.545 5.88 0.00 43.36 4.17
3094 3503 4.910195 TGTATAATTGCTGCCTATCCTGG 58.090 43.478 0.00 0.00 0.00 4.45
3161 3571 1.021390 CAGCGCTAGTTGGTTCCCAG 61.021 60.000 10.99 0.00 33.81 4.45
3221 3631 5.860941 TCAATTTCCTTGTGCAACCTTAA 57.139 34.783 0.00 0.00 36.20 1.85
3222 3632 5.738783 GCTTCAATTTCCTTGTGCAACCTTA 60.739 40.000 0.00 0.00 36.32 2.69
3306 3716 1.946283 GCAGGAAGACAAGTAGGCCAC 60.946 57.143 5.01 0.54 0.00 5.01
3455 3865 3.513515 AGAAATCGCTGAAGTTCTCCTCT 59.486 43.478 4.17 0.00 0.00 3.69
3471 3881 5.966742 AGTAACCCAAAAGCTGAGAAATC 57.033 39.130 0.00 0.00 0.00 2.17
3495 3905 2.744202 CCGCACTTTCTGCTTTACTGAT 59.256 45.455 0.00 0.00 44.64 2.90
3500 3910 2.809696 GGTAACCGCACTTTCTGCTTTA 59.190 45.455 0.00 0.00 44.64 1.85
3570 3981 6.353082 CCTCTACCCAGTCCAATTGAATAACT 60.353 42.308 7.12 2.18 0.00 2.24
3602 4013 2.749621 CTGTCTTCATACCCTGCAAACC 59.250 50.000 0.00 0.00 0.00 3.27
3660 4071 4.010667 ACCAAATAACTCGCCACTACAA 57.989 40.909 0.00 0.00 0.00 2.41
3750 4161 5.826643 AGGGCATTATCTTGGTTTCAGTAA 58.173 37.500 0.00 0.00 0.00 2.24
3766 4177 4.754411 AATCATATCCTCCAAGGGCATT 57.246 40.909 0.00 0.00 35.59 3.56
3841 4565 9.155975 TGCTTTCTTCAGTCTAGAATTAATCAC 57.844 33.333 0.00 0.00 32.09 3.06


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

AutoCloner maintained by Alex Coulton.