Multiple sequence alignment - TraesCS1B01G227900

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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 TraesCS1B01G227900 chr1B 100.000 4205 0 0 1 4205 409608675 409604471 0.000000e+00 7766.0
1 TraesCS1B01G227900 chr1A 94.912 3734 132 24 505 4205 377216781 377213073 0.000000e+00 5790.0
2 TraesCS1B01G227900 chr1A 91.234 308 12 5 199 506 377217127 377216835 5.060000e-109 405.0
3 TraesCS1B01G227900 chr1A 92.611 203 15 0 1 203 377220089 377219887 4.110000e-75 292.0
4 TraesCS1B01G227900 chr1D 96.612 3394 100 9 816 4205 302699452 302696070 0.000000e+00 5616.0
5 TraesCS1B01G227900 chr5B 76.557 273 45 13 509 772 31233291 31233029 9.490000e-27 132.0
6 TraesCS1B01G227900 chr6D 90.588 85 4 2 3767 3849 16604155 16604073 4.440000e-20 110.0
7 TraesCS1B01G227900 chr7D 89.888 89 2 5 3767 3851 622233892 622233977 1.600000e-19 108.0
8 TraesCS1B01G227900 chr4A 89.412 85 8 1 3767 3850 99009814 99009730 5.750000e-19 106.0
9 TraesCS1B01G227900 chr4A 84.706 85 10 2 3767 3849 99009731 99009814 9.690000e-12 82.4
10 TraesCS1B01G227900 chr3D 87.500 88 5 4 3766 3849 486153998 486153913 3.460000e-16 97.1
11 TraesCS1B01G227900 chr7B 87.059 85 9 2 3767 3849 490685098 490685182 1.240000e-15 95.3
12 TraesCS1B01G227900 chr4B 87.059 85 7 3 3767 3849 450478140 450478058 4.480000e-15 93.5
13 TraesCS1B01G227900 chr2B 85.075 67 7 1 519 582 184466142 184466208 9.760000e-07 65.8


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 TraesCS1B01G227900 chr1B 409604471 409608675 4204 True 7766.000000 7766 100.000 1 4205 1 chr1B.!!$R1 4204
1 TraesCS1B01G227900 chr1A 377213073 377220089 7016 True 2162.333333 5790 92.919 1 4205 3 chr1A.!!$R1 4204
2 TraesCS1B01G227900 chr1D 302696070 302699452 3382 True 5616.000000 5616 96.612 816 4205 1 chr1D.!!$R1 3389

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
413 3178 0.02970 CATGCAGGTGTGTGTGTGTG 59.970 55.0 0.0 0.0 0.0 3.82 F
1641 4486 0.25077 GGTTCTCGCCCAAGTCCTTT 60.251 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 4696 1.753141 GCATCATCATCACCAGGCCTT 60.753 52.381 0.0 0.0 0.0 4.35 R
3408 6253 0.901827 TTCAAGGATAGAGCCGCACA 59.098 50.000 0.0 0.0 0.0 4.57 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 6.019318 CACGGCAACCACATTTAGTACTATAC 60.019 42.308 2.79 0.00 0.00 1.47
29 30 6.704493 CGGCAACCACATTTAGTACTATACAT 59.296 38.462 2.79 0.00 0.00 2.29
31 32 7.041372 GGCAACCACATTTAGTACTATACATGG 60.041 40.741 16.76 16.76 0.00 3.66
65 66 1.647084 GCGTCGCTCAAGTTTGGTT 59.353 52.632 10.68 0.00 0.00 3.67
66 67 0.657368 GCGTCGCTCAAGTTTGGTTG 60.657 55.000 10.68 0.00 0.00 3.77
107 108 2.174349 CGCTCGCTGCCTTTTCAC 59.826 61.111 0.00 0.00 38.78 3.18
116 117 1.273327 CTGCCTTTTCACCATTGTCCC 59.727 52.381 0.00 0.00 0.00 4.46
118 119 1.546029 GCCTTTTCACCATTGTCCCTC 59.454 52.381 0.00 0.00 0.00 4.30
145 146 0.103208 GCCTCGACGATGTCATTCCT 59.897 55.000 0.00 0.00 32.09 3.36
149 150 3.797256 CCTCGACGATGTCATTCCTTAAC 59.203 47.826 0.00 0.00 32.09 2.01
157 158 5.994054 CGATGTCATTCCTTAACTGGATCAT 59.006 40.000 0.00 0.00 35.83 2.45
170 171 1.634973 TGGATCATGCCCAAGAAGACA 59.365 47.619 4.45 0.00 0.00 3.41
190 191 0.947180 CATGGTGCTTGCAAGTTGGC 60.947 55.000 26.55 14.39 0.00 4.52
214 2979 1.287425 GTCCCTTTCGTATCGCCTTG 58.713 55.000 0.00 0.00 0.00 3.61
262 3027 0.938192 CCTCTAACCCTCTCCCCTCT 59.062 60.000 0.00 0.00 0.00 3.69
268 3033 1.687493 CCCTCTCCCCTCTGACACC 60.687 68.421 0.00 0.00 0.00 4.16
287 3052 1.296715 GGTGACCTGAACCGCTCAT 59.703 57.895 0.00 0.00 32.14 2.90
288 3053 0.535335 GGTGACCTGAACCGCTCATA 59.465 55.000 0.00 0.00 32.14 2.15
289 3054 1.139058 GGTGACCTGAACCGCTCATAT 59.861 52.381 0.00 0.00 32.14 1.78
386 3151 1.618837 GCCGCTAGGTCCATGAAGATA 59.381 52.381 0.00 0.00 40.50 1.98
399 3164 3.002038 TGAAGATACATGGTGCATGCA 57.998 42.857 18.46 18.46 44.80 3.96
400 3165 2.946990 TGAAGATACATGGTGCATGCAG 59.053 45.455 23.41 12.18 44.80 4.41
407 3172 1.529152 ATGGTGCATGCAGGTGTGTG 61.529 55.000 23.41 0.00 0.00 3.82
408 3173 2.195567 GGTGCATGCAGGTGTGTGT 61.196 57.895 23.41 0.00 0.00 3.72
409 3174 1.008194 GTGCATGCAGGTGTGTGTG 60.008 57.895 23.41 0.00 0.00 3.82
410 3175 1.453562 TGCATGCAGGTGTGTGTGT 60.454 52.632 18.46 0.00 0.00 3.72
411 3176 1.008194 GCATGCAGGTGTGTGTGTG 60.008 57.895 14.21 0.00 0.00 3.82
412 3177 1.727511 GCATGCAGGTGTGTGTGTGT 61.728 55.000 14.21 0.00 0.00 3.72
413 3178 0.029700 CATGCAGGTGTGTGTGTGTG 59.970 55.000 0.00 0.00 0.00 3.82
414 3179 0.394216 ATGCAGGTGTGTGTGTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
415 3180 1.304509 TGCAGGTGTGTGTGTGTGTG 61.305 55.000 0.00 0.00 0.00 3.82
416 3181 1.429021 CAGGTGTGTGTGTGTGTGC 59.571 57.895 0.00 0.00 0.00 4.57
438 3203 1.743623 CGCTGTTCCGCCCATAACA 60.744 57.895 0.00 0.00 34.57 2.41
456 3221 7.936847 CCCATAACATGTAGAATTTGCCTACTA 59.063 37.037 0.00 0.00 37.84 1.82
498 3263 3.651803 TTTGCCGAAAATACACCTTGG 57.348 42.857 0.00 0.00 0.00 3.61
521 3341 8.207350 TGGGACATGGGTAAAATATTTTTGAA 57.793 30.769 18.14 0.00 0.00 2.69
522 3342 8.097662 TGGGACATGGGTAAAATATTTTTGAAC 58.902 33.333 18.14 10.58 0.00 3.18
542 3362 3.074412 ACCTTTGTCGGAACAAGCATAG 58.926 45.455 0.00 0.00 45.72 2.23
567 3387 8.462811 AGTCTAGTGTATCACTCACATGTAAAG 58.537 37.037 0.00 1.58 41.21 1.85
573 3393 8.009974 GTGTATCACTCACATGTAAAGTTTCAC 58.990 37.037 9.70 11.50 36.05 3.18
599 3419 4.685169 AAATGACTTGCGTGGTATTCTG 57.315 40.909 0.00 0.00 0.00 3.02
604 3424 3.932710 GACTTGCGTGGTATTCTGAATGA 59.067 43.478 13.01 0.00 0.00 2.57
622 3442 9.371136 TCTGAATGAATACAAACTGACTGATAC 57.629 33.333 0.00 0.00 0.00 2.24
641 3461 9.540538 ACTGATACTATATCAAGTGGAGCTTAT 57.459 33.333 0.00 0.00 35.27 1.73
648 3468 7.976135 ATATCAAGTGGAGCTTATCATTCAC 57.024 36.000 0.00 0.00 35.27 3.18
650 3470 4.937620 TCAAGTGGAGCTTATCATTCACAC 59.062 41.667 0.00 0.00 35.27 3.82
651 3471 3.525537 AGTGGAGCTTATCATTCACACG 58.474 45.455 0.00 0.00 33.18 4.49
663 3483 4.193090 TCATTCACACGGTTTGTAGTTGT 58.807 39.130 0.00 0.00 35.67 3.32
682 3502 7.749539 AGTTGTAATTTTGTCGTTTTTCCAG 57.250 32.000 0.00 0.00 0.00 3.86
692 3512 6.932901 TGTCGTTTTTCCAGTAATACTACG 57.067 37.500 5.16 5.16 32.87 3.51
799 3632 0.666274 TGCGCTTACACTCAGGTTCG 60.666 55.000 9.73 0.00 0.00 3.95
807 3640 5.179555 GCTTACACTCAGGTTCGAAAAATCT 59.820 40.000 0.00 0.00 0.00 2.40
818 3651 3.787785 TCGAAAAATCTGCACCGCTATA 58.212 40.909 0.00 0.00 0.00 1.31
821 3654 3.904136 AAAATCTGCACCGCTATATGC 57.096 42.857 0.00 0.00 42.40 3.14
1042 3887 4.382541 TCTGCTCCCTCCTCCGCA 62.383 66.667 0.00 0.00 0.00 5.69
1073 3918 4.722700 CTCCCTTGCCCACCACCG 62.723 72.222 0.00 0.00 0.00 4.94
1371 4216 2.281429 GGCTCCTACCTACCCCGT 59.719 66.667 0.00 0.00 0.00 5.28
1410 4255 1.142748 GCTCACCTCCATCCTCACG 59.857 63.158 0.00 0.00 0.00 4.35
1479 4324 2.181773 ACCCTACCTCCACTCCCCA 61.182 63.158 0.00 0.00 0.00 4.96
1587 4432 2.504026 CGCGTCGTGCAAGAGCTA 60.504 61.111 1.39 0.00 46.97 3.32
1641 4486 0.250770 GGTTCTCGCCCAAGTCCTTT 60.251 55.000 0.00 0.00 0.00 3.11
1821 4666 3.190118 AGAAAGTCGTCGATTTAGTCCGT 59.810 43.478 3.21 0.00 0.00 4.69
1851 4696 1.116536 TTACTCCAGTGGTGACCGCA 61.117 55.000 18.51 0.00 36.32 5.69
2020 4865 4.315264 GGGGGCATTGTGGGGTGT 62.315 66.667 0.00 0.00 0.00 4.16
2046 4891 1.154150 GTTGCTCGCCAATGTCTGC 60.154 57.895 0.00 0.00 35.55 4.26
2064 4909 4.574013 GTCTGCCTGGATGAGTTTGATAAG 59.426 45.833 0.00 0.00 0.00 1.73
2082 4927 3.810310 AAGTGGATGGACGAGAAGATC 57.190 47.619 0.00 0.00 0.00 2.75
2136 4981 2.533463 GGGAGGGGAGGATGGCATC 61.533 68.421 19.23 19.23 0.00 3.91
2461 5306 0.981943 CGAGAAGGGGGTTGGTACTT 59.018 55.000 0.00 0.00 0.00 2.24
2469 5314 1.351350 GGGGTTGGTACTTTGCTCTCT 59.649 52.381 0.00 0.00 0.00 3.10
2487 5332 4.776349 TCTCTGTTACAGCCAGTTTGAAA 58.224 39.130 7.61 0.00 0.00 2.69
2577 5422 1.378382 CCGGATGTTCCATGCCACA 60.378 57.895 0.00 0.00 35.91 4.17
2676 5521 3.801114 AAGGTTGTCAACTTTTGCTCC 57.199 42.857 15.17 0.00 0.00 4.70
2856 5701 5.184096 TCTTGTAGACTCAGTTGATGGACTC 59.816 44.000 0.00 0.00 0.00 3.36
2943 5788 3.065371 CAGACCACGAGAAGTTTTTGCTT 59.935 43.478 0.00 0.00 0.00 3.91
3024 5869 2.025699 GGAGGGGCTTATAACACCACAA 60.026 50.000 8.47 0.00 0.00 3.33
3105 5950 6.119240 TCAAAAGAGAGTGATGTCCAAGAT 57.881 37.500 0.00 0.00 0.00 2.40
3129 5974 4.223032 TCCATAGAAGACCTTGGTTCAGAC 59.777 45.833 0.00 0.00 0.00 3.51
3153 5998 8.408043 ACACAGATGAATTGAATAACAAGGAA 57.592 30.769 0.00 0.00 42.02 3.36
3222 6067 9.725019 ATGTCTTGAGTGTCAATAATTTCTGTA 57.275 29.630 0.00 0.00 35.59 2.74
3235 6080 8.872845 CAATAATTTCTGTAAAATCACCAAGGC 58.127 33.333 0.00 0.00 0.00 4.35
3243 6088 9.474313 TCTGTAAAATCACCAAGGCTTAATTAT 57.526 29.630 0.00 0.00 0.00 1.28
3264 6109 1.885887 GATAACAGTTGGTTGCTGCCA 59.114 47.619 0.00 0.00 40.73 4.92
3300 6145 2.232941 GACCAACTCACCGATGGACTAA 59.767 50.000 0.00 0.00 37.76 2.24
3302 6147 3.000727 CCAACTCACCGATGGACTAAAC 58.999 50.000 0.00 0.00 37.76 2.01
3327 6172 9.021807 ACAGACTATGTAAATGTGTACTACTGT 57.978 33.333 0.00 0.00 41.60 3.55
3425 6270 1.959042 ATTGTGCGGCTCTATCCTTG 58.041 50.000 0.00 0.00 0.00 3.61
3473 6330 3.286353 TGGTGCAAGAACATGAACTTCA 58.714 40.909 0.00 0.00 0.00 3.02
3474 6331 3.698539 TGGTGCAAGAACATGAACTTCAA 59.301 39.130 0.00 0.00 0.00 2.69
3475 6332 4.341806 TGGTGCAAGAACATGAACTTCAAT 59.658 37.500 0.00 0.00 0.00 2.57
3476 6333 5.534278 TGGTGCAAGAACATGAACTTCAATA 59.466 36.000 0.00 0.00 0.00 1.90
3477 6334 6.040278 TGGTGCAAGAACATGAACTTCAATAA 59.960 34.615 0.00 0.00 0.00 1.40
3478 6335 7.092716 GGTGCAAGAACATGAACTTCAATAAT 58.907 34.615 0.00 0.00 0.00 1.28
3479 6336 7.062605 GGTGCAAGAACATGAACTTCAATAATG 59.937 37.037 0.00 0.00 0.00 1.90
3480 6337 6.587226 TGCAAGAACATGAACTTCAATAATGC 59.413 34.615 0.00 4.00 0.00 3.56
3481 6338 6.587226 GCAAGAACATGAACTTCAATAATGCA 59.413 34.615 0.00 0.00 0.00 3.96
3482 6339 7.116662 GCAAGAACATGAACTTCAATAATGCAA 59.883 33.333 0.00 0.00 0.00 4.08
3483 6340 8.430063 CAAGAACATGAACTTCAATAATGCAAC 58.570 33.333 0.00 0.00 0.00 4.17
3484 6341 7.889469 AGAACATGAACTTCAATAATGCAACT 58.111 30.769 0.00 0.00 0.00 3.16
3637 6497 8.216423 AGATTCTATGACAGCATATCCTGTTTT 58.784 33.333 0.00 0.00 45.55 2.43
3739 6599 2.233271 CTTGTGGAAGGTTGCTCATGT 58.767 47.619 0.00 0.00 0.00 3.21
3741 6601 3.500448 TGTGGAAGGTTGCTCATGTTA 57.500 42.857 0.00 0.00 0.00 2.41
3776 6636 5.529289 TGATATGGTGAAGTACTCCCTCTT 58.471 41.667 0.00 0.00 0.00 2.85
3793 6653 9.765795 ACTCCCTCTTTATCAAAATATAAGACG 57.234 33.333 0.00 0.00 0.00 4.18
3855 6718 3.231207 TGATAGAGGGAGTAGCTCACC 57.769 52.381 0.00 0.00 33.78 4.02
3866 6729 0.106708 TAGCTCACCGGATGCCAATC 59.893 55.000 9.46 0.00 0.00 2.67
3910 6773 0.897863 TGCGGAAACCCCTGAATTGG 60.898 55.000 0.00 0.00 0.00 3.16
4095 6959 8.408043 TTCAACCATATTTTTGTGACTGATCT 57.592 30.769 0.00 0.00 0.00 2.75
4155 7019 5.816955 TTTTCTATTTGTTTTCCCCTGGG 57.183 39.130 5.50 5.50 0.00 4.45
4202 7066 6.631016 ACCTTCAAGGAAAAGAAAAACAGTC 58.369 36.000 11.59 0.00 37.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.352323 GCGGGTTACCAACTTTTCCATG 60.352 50.000 2.98 0.00 36.13 3.66
29 30 1.320507 GCGGGTTACCAACTTTTCCA 58.679 50.000 2.98 0.00 36.13 3.53
31 32 0.946528 ACGCGGGTTACCAACTTTTC 59.053 50.000 12.47 0.00 36.13 2.29
38 39 4.424566 GAGCGACGCGGGTTACCA 62.425 66.667 15.18 0.00 36.13 3.25
101 102 2.593026 GTGGAGGGACAATGGTGAAAA 58.407 47.619 0.00 0.00 0.00 2.29
107 108 2.683475 GGGGTGGAGGGACAATGG 59.317 66.667 0.00 0.00 0.00 3.16
145 146 4.018506 TCTTCTTGGGCATGATCCAGTTAA 60.019 41.667 0.00 0.00 35.48 2.01
149 150 2.295885 GTCTTCTTGGGCATGATCCAG 58.704 52.381 0.00 0.00 35.48 3.86
157 158 0.478072 ACCATGTGTCTTCTTGGGCA 59.522 50.000 0.00 0.00 37.08 5.36
170 171 0.390124 CCAACTTGCAAGCACCATGT 59.610 50.000 26.27 2.62 0.00 3.21
190 191 1.823828 CGATACGAAAGGGACGTCAG 58.176 55.000 18.91 3.56 43.62 3.51
231 2996 0.106894 GTTAGAGGGAAGGCCGGATG 59.893 60.000 5.05 0.00 33.83 3.51
232 2997 1.054978 GGTTAGAGGGAAGGCCGGAT 61.055 60.000 5.05 0.00 33.83 4.18
233 2998 1.688187 GGTTAGAGGGAAGGCCGGA 60.688 63.158 5.05 0.00 33.83 5.14
234 2999 2.743179 GGGTTAGAGGGAAGGCCGG 61.743 68.421 0.00 0.00 33.83 6.13
235 3000 1.687297 GAGGGTTAGAGGGAAGGCCG 61.687 65.000 0.00 0.00 33.83 6.13
236 3001 0.326713 AGAGGGTTAGAGGGAAGGCC 60.327 60.000 0.00 0.00 0.00 5.19
237 3002 1.124780 GAGAGGGTTAGAGGGAAGGC 58.875 60.000 0.00 0.00 0.00 4.35
262 3027 1.444250 GTTCAGGTCACCGGTGTCA 59.556 57.895 32.74 13.54 0.00 3.58
287 3052 1.517694 GAGCCGCGACGACCAAATA 60.518 57.895 8.23 0.00 0.00 1.40
288 3053 2.813908 GAGCCGCGACGACCAAAT 60.814 61.111 8.23 0.00 0.00 2.32
289 3054 3.793775 TTGAGCCGCGACGACCAAA 62.794 57.895 8.23 0.00 0.00 3.28
335 3100 4.538283 AGCGACGATGGCGAGACG 62.538 66.667 0.00 0.00 41.64 4.18
386 3151 1.228644 ACACCTGCATGCACCATGT 60.229 52.632 18.46 17.57 43.10 3.21
399 3164 2.106074 CGCACACACACACACACCT 61.106 57.895 0.00 0.00 0.00 4.00
400 3165 2.403186 CGCACACACACACACACC 59.597 61.111 0.00 0.00 0.00 4.16
407 3172 4.360027 CAGCGAGCGCACACACAC 62.360 66.667 17.68 0.00 44.88 3.82
408 3173 4.889856 ACAGCGAGCGCACACACA 62.890 61.111 17.68 0.00 44.88 3.72
409 3174 3.564342 GAACAGCGAGCGCACACAC 62.564 63.158 17.68 0.00 44.88 3.82
410 3175 3.337889 GAACAGCGAGCGCACACA 61.338 61.111 17.68 0.00 44.88 3.72
411 3176 4.077188 GGAACAGCGAGCGCACAC 62.077 66.667 17.68 0.00 44.88 3.82
498 3263 8.318412 AGGTTCAAAAATATTTTACCCATGTCC 58.682 33.333 20.50 16.17 33.84 4.02
521 3341 1.981256 ATGCTTGTTCCGACAAAGGT 58.019 45.000 0.00 0.00 44.65 3.50
522 3342 3.074412 ACTATGCTTGTTCCGACAAAGG 58.926 45.455 0.00 0.00 44.65 3.11
542 3362 8.244802 ACTTTACATGTGAGTGATACACTAGAC 58.755 37.037 9.11 5.70 45.44 2.59
567 3387 3.177643 CGCAAGTCATTTTGTCGTGAAAC 59.822 43.478 0.00 0.00 0.00 2.78
614 3434 7.461182 AGCTCCACTTGATATAGTATCAGTC 57.539 40.000 0.56 0.00 0.00 3.51
622 3442 9.149225 GTGAATGATAAGCTCCACTTGATATAG 57.851 37.037 0.00 0.00 39.58 1.31
632 3452 2.236146 ACCGTGTGAATGATAAGCTCCA 59.764 45.455 0.00 0.00 0.00 3.86
641 3461 4.193090 ACAACTACAAACCGTGTGAATGA 58.807 39.130 0.00 0.00 41.89 2.57
642 3462 4.545823 ACAACTACAAACCGTGTGAATG 57.454 40.909 0.00 0.00 41.89 2.67
648 3468 6.139482 CGACAAAATTACAACTACAAACCGTG 59.861 38.462 0.00 0.00 0.00 4.94
650 3470 6.193761 ACGACAAAATTACAACTACAAACCG 58.806 36.000 0.00 0.00 0.00 4.44
651 3471 7.974243 AACGACAAAATTACAACTACAAACC 57.026 32.000 0.00 0.00 0.00 3.27
708 3528 4.966850 ATCACTCACGTGTAAAGTTTCG 57.033 40.909 16.51 0.74 41.89 3.46
768 3590 1.877443 GTAAGCGCACCCTGAGAAAAA 59.123 47.619 11.47 0.00 0.00 1.94
772 3594 1.185618 AGTGTAAGCGCACCCTGAGA 61.186 55.000 11.47 0.00 40.04 3.27
773 3595 0.737715 GAGTGTAAGCGCACCCTGAG 60.738 60.000 11.47 0.00 40.04 3.35
775 3597 1.005037 TGAGTGTAAGCGCACCCTG 60.005 57.895 11.47 0.00 40.04 4.45
776 3598 1.293498 CTGAGTGTAAGCGCACCCT 59.707 57.895 11.47 0.00 40.04 4.34
799 3632 4.222114 GCATATAGCGGTGCAGATTTTTC 58.778 43.478 0.00 0.00 40.94 2.29
818 3651 0.322322 CATTGGGCTTTGTGGTGCAT 59.678 50.000 0.00 0.00 0.00 3.96
821 3654 1.672898 CCCATTGGGCTTTGTGGTG 59.327 57.895 9.28 0.00 35.35 4.17
822 3655 4.213630 CCCATTGGGCTTTGTGGT 57.786 55.556 9.28 0.00 35.35 4.16
901 3734 0.035056 GGGAAGTGAGATGGTGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
902 3735 0.035056 GGGGAAGTGAGATGGTGGTG 60.035 60.000 0.00 0.00 0.00 4.17
903 3736 0.475632 TGGGGAAGTGAGATGGTGGT 60.476 55.000 0.00 0.00 0.00 4.16
1028 3873 3.934962 GGATGCGGAGGAGGGAGC 61.935 72.222 0.00 0.00 0.00 4.70
1049 3894 4.811364 GGGCAAGGGAGGAGCAGC 62.811 72.222 0.00 0.00 0.00 5.25
1164 4009 2.785776 GGTGGGGTCCAAGGGGTTT 61.786 63.158 0.00 0.00 34.18 3.27
1371 4216 2.768344 GAGGCGGGGATGGAGGAA 60.768 66.667 0.00 0.00 0.00 3.36
1587 4432 2.993840 TCGAGCAGCAGCAGGAGT 60.994 61.111 3.17 0.00 45.49 3.85
1608 4453 2.508439 AACCGCGCCTCATACACG 60.508 61.111 0.00 0.00 0.00 4.49
1672 4517 2.494918 GCGGATGCTACGGAGTGT 59.505 61.111 0.00 0.00 45.73 3.55
1773 4618 3.469970 ACATCCCGGATGAGCGCA 61.470 61.111 30.51 0.00 42.09 6.09
1785 4630 1.873591 ACTTTCTTGTCACGCACATCC 59.126 47.619 0.00 0.00 33.90 3.51
1821 4666 2.125673 GGAGTAAGCAGCGCCGAA 60.126 61.111 2.29 0.00 0.00 4.30
1851 4696 1.753141 GCATCATCATCACCAGGCCTT 60.753 52.381 0.00 0.00 0.00 4.35
2046 4891 5.102953 TCCACTTATCAAACTCATCCAGG 57.897 43.478 0.00 0.00 0.00 4.45
2064 4909 3.452474 CTTGATCTTCTCGTCCATCCAC 58.548 50.000 0.00 0.00 0.00 4.02
2082 4927 2.338500 GACGGCTTGTAGAACTCCTTG 58.662 52.381 0.00 0.00 0.00 3.61
2136 4981 2.420642 CATGATGTATTCCCCTGCTCG 58.579 52.381 0.00 0.00 0.00 5.03
2461 5306 1.694150 ACTGGCTGTAACAGAGAGCAA 59.306 47.619 0.00 0.00 46.39 3.91
2469 5314 4.013728 ACTGTTTCAAACTGGCTGTAACA 58.986 39.130 11.44 9.33 34.29 2.41
2577 5422 2.874701 CTGCAAGTTAGTGTGAGCTTGT 59.125 45.455 0.00 0.00 40.09 3.16
2856 5701 5.684704 ACCATTGACATCCTTGTATACTGG 58.315 41.667 4.17 6.77 35.79 4.00
2922 5767 2.919228 AGCAAAAACTTCTCGTGGTCT 58.081 42.857 0.00 0.00 0.00 3.85
3105 5950 4.844085 TCTGAACCAAGGTCTTCTATGGAA 59.156 41.667 0.00 0.00 36.75 3.53
3129 5974 8.517878 AGTTCCTTGTTATTCAATTCATCTGTG 58.482 33.333 0.00 0.00 35.35 3.66
3235 6080 9.507280 CAGCAACCAACTGTTATCATAATTAAG 57.493 33.333 0.00 0.00 34.69 1.85
3243 6088 1.885887 GGCAGCAACCAACTGTTATCA 59.114 47.619 0.00 0.00 37.47 2.15
3264 6109 6.483640 GTGAGTTGGTCTCTTGTAAATTCAGT 59.516 38.462 0.00 0.00 43.13 3.41
3300 6145 9.856488 CAGTAGTACACATTTACATAGTCTGTT 57.144 33.333 2.52 0.00 39.39 3.16
3302 6147 9.504710 GACAGTAGTACACATTTACATAGTCTG 57.495 37.037 2.52 0.00 0.00 3.51
3327 6172 4.990257 GCAAAATGCTAGAATCTGCTTGA 58.010 39.130 9.56 0.00 40.96 3.02
3408 6253 0.901827 TTCAAGGATAGAGCCGCACA 59.098 50.000 0.00 0.00 0.00 4.57
3473 6330 6.759827 GCAAAATGATCCTGAGTTGCATTATT 59.240 34.615 10.17 0.00 40.74 1.40
3474 6331 6.097839 AGCAAAATGATCCTGAGTTGCATTAT 59.902 34.615 14.92 0.00 42.90 1.28
3475 6332 5.419788 AGCAAAATGATCCTGAGTTGCATTA 59.580 36.000 14.92 0.00 42.90 1.90
3476 6333 4.222145 AGCAAAATGATCCTGAGTTGCATT 59.778 37.500 14.92 0.00 42.90 3.56
3477 6334 3.767673 AGCAAAATGATCCTGAGTTGCAT 59.232 39.130 14.92 0.00 42.90 3.96
3478 6335 3.159472 AGCAAAATGATCCTGAGTTGCA 58.841 40.909 14.92 0.00 42.90 4.08
3479 6336 3.863142 AGCAAAATGATCCTGAGTTGC 57.137 42.857 8.01 8.01 41.23 4.17
3480 6337 4.219070 TGGAAGCAAAATGATCCTGAGTTG 59.781 41.667 0.00 0.00 33.02 3.16
3481 6338 4.410099 TGGAAGCAAAATGATCCTGAGTT 58.590 39.130 0.00 0.00 33.02 3.01
3482 6339 4.038271 TGGAAGCAAAATGATCCTGAGT 57.962 40.909 0.00 0.00 33.02 3.41
3483 6340 5.166398 GTTTGGAAGCAAAATGATCCTGAG 58.834 41.667 0.00 0.00 33.02 3.35
3484 6341 4.588106 TGTTTGGAAGCAAAATGATCCTGA 59.412 37.500 0.00 0.00 33.02 3.86
3612 6472 7.976135 AAACAGGATATGCTGTCATAGAATC 57.024 36.000 27.50 0.00 38.46 2.52
3637 6497 8.408043 AAGATTGTACAGATGACCATTTGAAA 57.592 30.769 7.42 0.92 0.00 2.69
3739 6599 5.935206 TCACCATATCAGCGAAACAAGTTAA 59.065 36.000 0.00 0.00 0.00 2.01
3741 6601 4.323417 TCACCATATCAGCGAAACAAGTT 58.677 39.130 0.00 0.00 0.00 2.66
3824 6685 9.863845 GCTACTCCCTCTATCAAAATATAAGTC 57.136 37.037 0.00 0.00 0.00 3.01
3825 6686 9.608718 AGCTACTCCCTCTATCAAAATATAAGT 57.391 33.333 0.00 0.00 0.00 2.24
3840 6701 0.468400 ATCCGGTGAGCTACTCCCTC 60.468 60.000 0.00 0.00 0.00 4.30
3843 6704 1.068250 GCATCCGGTGAGCTACTCC 59.932 63.158 0.00 0.00 0.00 3.85
3866 6729 0.723414 CTTATGGCTCACACACTGCG 59.277 55.000 0.00 0.00 0.00 5.18
4086 6950 7.293828 ACAGATTCTAGGACATAGATCAGTCA 58.706 38.462 12.89 0.00 40.27 3.41
4095 6959 9.201989 ACTGAAACATACAGATTCTAGGACATA 57.798 33.333 0.00 0.00 38.55 2.29
4171 7035 2.673775 TTTCCTTGAAGGTCATGCCA 57.326 45.000 11.60 0.00 40.61 4.92
4179 7043 5.743872 CGACTGTTTTTCTTTTCCTTGAAGG 59.256 40.000 4.45 4.45 36.46 3.46


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

AutoCloner maintained by Alex Coulton.