Multiple sequence alignment - TraesCS5B01G097100

Loading Multiple Alignment...

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 TraesCS5B01G097100 chr5B 100.000 5170 0 0 1 5170 128220081 128214912 0.000000e+00 9548
1 TraesCS5B01G097100 chr5D 95.498 4909 172 23 136 5033 116175789 116170919 0.000000e+00 7795
2 TraesCS5B01G097100 chr5D 94.161 137 8 0 1 137 116176076 116175940 5.250000e-50 209
3 TraesCS5B01G097100 chr5D 89.583 144 7 6 5031 5170 116170879 116170740 5.320000e-40 176
4 TraesCS5B01G097100 chr5A 95.019 4477 180 26 579 5033 123713294 123708839 0.000000e+00 6992
5 TraesCS5B01G097100 chr5A 89.041 146 6 7 5031 5170 123708799 123708658 6.880000e-39 172
6 TraesCS5B01G097100 chr4B 80.122 327 50 6 3159 3484 53449631 53449319 4.030000e-56 230
7 TraesCS5B01G097100 chr4B 80.000 330 48 8 3159 3484 53474648 53474333 1.450000e-55 228
8 TraesCS5B01G097100 chr4B 83.628 226 37 0 1437 1662 195464293 195464068 4.060000e-51 213
9 TraesCS5B01G097100 chr4B 83.621 116 19 0 2581 2696 195463262 195463147 5.470000e-20 110
10 TraesCS5B01G097100 chr4D 83.628 226 37 0 1437 1662 136187128 136186903 4.060000e-51 213
11 TraesCS5B01G097100 chr4D 83.621 116 19 0 2581 2696 136186098 136185983 5.470000e-20 110
12 TraesCS5B01G097100 chr4A 83.628 226 37 0 1437 1662 423155672 423155897 4.060000e-51 213
13 TraesCS5B01G097100 chr4A 82.759 116 20 0 2581 2696 423156566 423156681 2.550000e-18 104


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 TraesCS5B01G097100 chr5B 128214912 128220081 5169 True 9548.000000 9548 100.000000 1 5170 1 chr5B.!!$R1 5169
1 TraesCS5B01G097100 chr5D 116170740 116176076 5336 True 2726.666667 7795 93.080667 1 5170 3 chr5D.!!$R1 5169
2 TraesCS5B01G097100 chr5A 123708658 123713294 4636 True 3582.000000 6992 92.030000 579 5170 2 chr5A.!!$R1 4591

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
405 558 0.040692 TTCGTCAGACCTTGTCGTCG 60.041 55.0 0.00 0.0 39.02 5.12 F
420 573 0.100682 CGTCGACCTCATCCGATGTT 59.899 55.0 10.58 0.0 37.13 2.71 F
624 777 0.321671 GCTAGCTGGTCACTGGTCAA 59.678 55.0 7.70 0.0 0.00 3.18 F
2376 2548 0.320247 GCATATCGCAGAGTGGAGGG 60.320 60.0 0.00 0.0 43.63 4.30 F
2846 3018 1.566018 GGTGGAACTGGTTTCGCTCG 61.566 60.0 5.46 0.0 36.74 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1896 0.749454 AATCCGTGGAATCAGCAGCC 60.749 55.000 0.0 0.0 0.00 4.85 R
2369 2541 0.951040 CTCAACAAGACGCCCTCCAC 60.951 60.000 0.0 0.0 0.00 4.02 R
2431 2603 2.691409 TGCTGCCTATGTTGTCCTAC 57.309 50.000 0.0 0.0 0.00 3.18 R
3743 3916 0.036577 CTGGTGCTGTCCTGAAGGAG 60.037 60.000 0.0 0.0 46.49 3.69 R
4645 4818 1.888826 CGGCCTAACAACCCCATTGAA 60.889 52.381 0.0 0.0 41.23 2.69 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
21 22 0.408309 TCTTCCTCTGGTTCTCCGGA 59.592 55.000 2.93 2.93 45.86 5.14
37 38 2.035442 GGAGTTGGAGAAGCGTGGC 61.035 63.158 0.00 0.00 0.00 5.01
67 68 1.379146 GACCCCAAGTGGTTCCTCC 59.621 63.158 0.00 0.00 39.24 4.30
71 72 2.351276 CAAGTGGTTCCTCCCCGG 59.649 66.667 0.00 0.00 34.77 5.73
89 90 3.025619 CGATGGCCGGAGCAAATC 58.974 61.111 5.05 0.00 42.56 2.17
117 118 8.466617 AGTAGAAGTTGATATTACGATCCAGT 57.533 34.615 0.00 0.00 0.00 4.00
123 124 6.767902 AGTTGATATTACGATCCAGTTGCAAT 59.232 34.615 0.59 0.00 0.00 3.56
137 138 5.051106 CCAGTTGCAATTTTACTTTTCGGTG 60.051 40.000 0.59 0.00 0.00 4.94
139 140 6.035542 CAGTTGCAATTTTACTTTTCGGTGTT 59.964 34.615 0.59 0.00 0.00 3.32
140 141 7.221067 CAGTTGCAATTTTACTTTTCGGTGTTA 59.779 33.333 0.59 0.00 0.00 2.41
141 142 7.760340 AGTTGCAATTTTACTTTTCGGTGTTAA 59.240 29.630 0.59 0.00 0.00 2.01
142 143 8.544597 GTTGCAATTTTACTTTTCGGTGTTAAT 58.455 29.630 0.59 0.00 0.00 1.40
143 144 8.649973 TGCAATTTTACTTTTCGGTGTTAATT 57.350 26.923 0.00 0.00 0.00 1.40
144 145 9.099454 TGCAATTTTACTTTTCGGTGTTAATTT 57.901 25.926 0.00 0.00 0.00 1.82
145 146 9.923786 GCAATTTTACTTTTCGGTGTTAATTTT 57.076 25.926 0.00 0.00 0.00 1.82
165 318 4.655762 TTAGCTCGAGCATTATGTGACT 57.344 40.909 36.87 16.14 45.16 3.41
170 323 4.559502 GCTCGAGCATTATGTGACTGGATA 60.560 45.833 31.91 0.00 41.59 2.59
183 336 4.040952 GTGACTGGATATTGGCTCACCTAT 59.959 45.833 0.00 0.00 36.63 2.57
218 371 7.016361 AGTTTATTATTGAGGACGATGTTGC 57.984 36.000 0.00 0.00 0.00 4.17
220 373 2.951457 TATTGAGGACGATGTTGCGA 57.049 45.000 0.00 0.00 34.83 5.10
226 379 0.438830 GGACGATGTTGCGACAAGAC 59.561 55.000 11.67 8.63 39.66 3.01
229 382 0.091344 CGATGTTGCGACAAGACGAC 59.909 55.000 11.67 0.00 39.66 4.34
269 422 1.743394 CAAACCGCCTTGTTCCTATCC 59.257 52.381 0.00 0.00 0.00 2.59
271 424 1.262640 ACCGCCTTGTTCCTATCCGT 61.263 55.000 0.00 0.00 0.00 4.69
284 437 4.611367 TCCTATCCGTCTTTCTTTCTCCT 58.389 43.478 0.00 0.00 0.00 3.69
320 473 4.003648 TCCCGCAATCTTCTTCTTTCTTC 58.996 43.478 0.00 0.00 0.00 2.87
325 478 5.180117 CGCAATCTTCTTCTTTCTTCCTTCA 59.820 40.000 0.00 0.00 0.00 3.02
364 517 4.544968 TCTTCTCCTCTCTTACTACCCCTT 59.455 45.833 0.00 0.00 0.00 3.95
405 558 0.040692 TTCGTCAGACCTTGTCGTCG 60.041 55.000 0.00 0.00 39.02 5.12
419 572 0.746923 TCGTCGACCTCATCCGATGT 60.747 55.000 10.58 0.00 41.18 3.06
420 573 0.100682 CGTCGACCTCATCCGATGTT 59.899 55.000 10.58 0.00 37.13 2.71
422 575 0.380733 TCGACCTCATCCGATGTTCG 59.619 55.000 16.84 16.84 40.07 3.95
459 612 0.865218 GAGATCGAGCGCTGACACTG 60.865 60.000 18.48 0.00 0.00 3.66
467 620 1.409227 GCGCTGACACTGATCGTCTG 61.409 60.000 0.00 2.36 35.94 3.51
495 648 2.675317 CGAGAGAGAATGTGAACCCACC 60.675 54.545 0.00 0.00 42.53 4.61
533 686 3.306917 TTTAAAGAGCATGTCGTCGGA 57.693 42.857 0.00 0.00 0.00 4.55
608 761 3.641436 CACTACCACCACCATATGAGCTA 59.359 47.826 3.65 0.00 0.00 3.32
624 777 0.321671 GCTAGCTGGTCACTGGTCAA 59.678 55.000 7.70 0.00 0.00 3.18
650 803 7.342026 ACCTCTCCTCTTCTTTCTTCTAAGATC 59.658 40.741 0.00 0.00 34.33 2.75
664 817 7.831955 TCTTCTAAGATCTATTCCTCCCTCTT 58.168 38.462 0.00 0.00 0.00 2.85
725 884 6.757237 TGCATTTTTCTTTCATGCCTAAAGA 58.243 32.000 4.42 4.42 42.31 2.52
731 890 8.918202 TTTTCTTTCATGCCTAAAGACTAGAA 57.082 30.769 7.40 0.00 41.43 2.10
1095 1267 4.697756 CACGGCGCTTCCTTCCCA 62.698 66.667 6.90 0.00 0.00 4.37
1246 1418 3.426525 GGTTTCTTGCTTCTTGCGAATTG 59.573 43.478 0.00 0.00 46.63 2.32
1251 1423 3.940209 TGCTTCTTGCGAATTGGATTT 57.060 38.095 0.00 0.00 46.63 2.17
1696 1868 2.876550 AGTGACTTGTTAAACGCCTTCC 59.123 45.455 0.00 0.00 0.00 3.46
1780 1952 2.423231 CCAGGATTGATGTGGCATACCA 60.423 50.000 0.00 0.00 46.51 3.25
1791 1963 3.485463 TGGCATACCATTACCTACTGC 57.515 47.619 0.00 0.00 42.67 4.40
1793 1965 3.458118 TGGCATACCATTACCTACTGCTT 59.542 43.478 0.00 0.00 42.67 3.91
1794 1966 4.080015 TGGCATACCATTACCTACTGCTTT 60.080 41.667 0.00 0.00 42.67 3.51
1795 1967 4.887655 GGCATACCATTACCTACTGCTTTT 59.112 41.667 0.00 0.00 35.26 2.27
1796 1968 5.359860 GGCATACCATTACCTACTGCTTTTT 59.640 40.000 0.00 0.00 35.26 1.94
1827 1999 4.402793 TGACAGTAGGAGCTTAGGATGTTC 59.597 45.833 0.00 0.00 0.00 3.18
1852 2024 9.170734 TCTCTTGATATCAATTGACTTTTCAGG 57.829 33.333 18.26 11.33 35.02 3.86
1935 2107 9.167311 CTGTTAGGAACTTGCAATATTCTTAGT 57.833 33.333 18.14 1.28 41.75 2.24
2040 2212 8.730680 GTCATATGTGATGTTTACCTTGAAAGT 58.269 33.333 1.90 0.00 36.60 2.66
2059 2231 6.864685 TGAAAGTCGTTTTCGTGTGAGTATAT 59.135 34.615 9.44 0.00 46.65 0.86
2089 2261 5.888691 TTTGGTCTTGCGCATATTTAGAA 57.111 34.783 12.75 0.00 0.00 2.10
2135 2307 4.521146 TGGGGTTTCCGCGTATATAAAAA 58.479 39.130 4.92 0.00 39.47 1.94
2184 2356 2.872858 GACTATCTGCCCATCGGTTTTC 59.127 50.000 0.00 0.00 0.00 2.29
2197 2369 6.826741 CCCATCGGTTTTCTCTTTCCTAATAA 59.173 38.462 0.00 0.00 0.00 1.40
2235 2407 3.338249 GTGACACATAGCTGTCCATGTT 58.662 45.455 0.00 0.00 40.02 2.71
2310 2482 4.110482 CTGCTTTCTTTAATCATGCCTGC 58.890 43.478 0.00 0.00 0.00 4.85
2337 2509 1.206371 GCTGATTTTGATTGCCTGCCT 59.794 47.619 0.00 0.00 0.00 4.75
2376 2548 0.320247 GCATATCGCAGAGTGGAGGG 60.320 60.000 0.00 0.00 43.63 4.30
2395 2567 3.502211 AGGGCGTCTTGTTGAGTTTTATG 59.498 43.478 0.00 0.00 0.00 1.90
2460 2632 7.264373 ACAACATAGGCAGCATAAATTAGTC 57.736 36.000 0.00 0.00 0.00 2.59
2834 3006 3.023832 CCAGGGTTTGATATGGTGGAAC 58.976 50.000 0.00 0.00 0.00 3.62
2846 3018 1.566018 GGTGGAACTGGTTTCGCTCG 61.566 60.000 5.46 0.00 36.74 5.03
2858 3030 6.128007 ACTGGTTTCGCTCGAATAAATTGAAT 60.128 34.615 5.50 0.00 33.79 2.57
2889 3061 3.808618 GCCTCATCTTGTGGAGTTTGAGT 60.809 47.826 0.00 0.00 36.16 3.41
2924 3096 7.858052 AATTGTGATTTCGAACTTGACATTC 57.142 32.000 0.00 0.00 0.00 2.67
2933 3105 7.596749 TTCGAACTTGACATTCTTAGATTCC 57.403 36.000 0.00 0.00 0.00 3.01
3028 3201 8.616076 CCCATTCTTAATGTTTGAGAGATGTAC 58.384 37.037 0.00 0.00 37.18 2.90
3036 3209 6.101650 TGTTTGAGAGATGTACTGACATGT 57.898 37.500 0.00 0.00 46.64 3.21
3160 3333 4.007659 GCTGCTACTTTAGTAAAAGCCCA 58.992 43.478 14.04 2.63 45.06 5.36
3162 3335 5.449177 GCTGCTACTTTAGTAAAAGCCCATG 60.449 44.000 14.04 5.95 45.06 3.66
3175 3348 9.981114 AGTAAAAGCCCATGCATTATATTTAAC 57.019 29.630 0.00 0.00 41.13 2.01
3182 3355 9.942850 GCCCATGCATTATATTTAACCTAAATT 57.057 29.630 0.00 0.00 37.23 1.82
3330 3503 6.922407 GGAGCTAGTAAAAATAACCTACTCGG 59.078 42.308 0.00 0.00 39.35 4.63
3447 3620 6.801539 TTCTTTGCGAACATTGATCTACTT 57.198 33.333 0.00 0.00 0.00 2.24
3464 3637 3.641434 ACTTCAGTAGCATGGCTGAAT 57.359 42.857 7.33 0.00 46.52 2.57
3532 3705 3.656457 TGTGCATTGAGGACAGCAT 57.344 47.368 0.00 0.00 44.19 3.79
3539 3712 5.297776 GTGCATTGAGGACAGCATAATTAGT 59.702 40.000 0.00 0.00 39.43 2.24
3717 3890 4.156556 CGGATGTTCATGTTGATCACCTTT 59.843 41.667 0.00 0.00 29.90 3.11
3928 4101 6.074648 TCACCTTAAAAGACATGGTTGGAAT 58.925 36.000 0.00 0.00 0.00 3.01
4053 4226 1.151668 CTCTTGGTCTTGCTCCAACG 58.848 55.000 0.00 0.00 39.62 4.10
4094 4267 2.355818 GGTATTTCCCGAGGCTTGTTCT 60.356 50.000 0.12 0.00 0.00 3.01
4145 4318 1.500474 TCTGCTCATCCACCCTTAGG 58.500 55.000 0.00 0.00 40.04 2.69
4157 4330 0.765510 CCCTTAGGTACCATGCCCTC 59.234 60.000 15.94 0.00 32.08 4.30
4232 4405 4.716287 TCCATGTACAATCTGGAGACATCA 59.284 41.667 11.83 0.00 41.51 3.07
4237 4410 3.607741 ACAATCTGGAGACATCAAGCTG 58.392 45.455 0.00 0.00 41.51 4.24
4438 4611 3.782656 ATTTTGTCCGGTAGGTTGTCT 57.217 42.857 0.00 0.00 39.05 3.41
4559 4732 6.358991 TCATCATCTTGTGAGCATCCAATAA 58.641 36.000 0.00 0.00 40.92 1.40
4645 4818 4.837860 TCCTGGCTGTCAAATAAATTGGTT 59.162 37.500 0.00 0.00 39.62 3.67
4689 4862 5.456265 GTTTTGATGGCTTCTTTGTCTCTC 58.544 41.667 1.86 0.00 0.00 3.20
4909 5086 1.457267 ATGTGCAACCAACCTGCCA 60.457 52.632 0.00 0.00 39.13 4.92
5033 5210 1.477105 GCCGTTTTCACTTGCTGAAC 58.523 50.000 0.00 0.00 38.70 3.18
5038 5256 3.447742 GTTTTCACTTGCTGAACCAAGG 58.552 45.455 6.82 0.00 44.98 3.61
5060 5278 5.998363 AGGCAGTAGAAGGTTCTGTAAAAAG 59.002 40.000 2.32 0.00 38.19 2.27
5095 5318 1.134220 GCATCGGATCCTGGTTGGTTA 60.134 52.381 10.75 0.00 37.07 2.85
5096 5319 2.838736 CATCGGATCCTGGTTGGTTAG 58.161 52.381 10.75 0.00 37.07 2.34
5097 5320 2.241281 TCGGATCCTGGTTGGTTAGA 57.759 50.000 10.75 0.00 37.07 2.10
5099 5322 3.112263 TCGGATCCTGGTTGGTTAGAAT 58.888 45.455 10.75 0.00 37.07 2.40
5103 5326 5.883673 CGGATCCTGGTTGGTTAGAATAAAA 59.116 40.000 10.75 0.00 37.07 1.52
5126 5349 2.713967 GGTGGCCATGTGGTGCATC 61.714 63.158 9.72 0.00 35.19 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.357517 CGCCACGCTTCTCCAACT 60.358 61.111 0.00 0.00 0.00 3.16
37 38 2.125269 GGGGTCATCGAACCACCG 60.125 66.667 8.50 0.00 42.10 4.94
71 72 3.186390 GATTTGCTCCGGCCATCGC 62.186 63.158 2.24 1.20 37.74 4.58
89 90 8.568794 TGGATCGTAATATCAACTTCTACTCAG 58.431 37.037 0.00 0.00 0.00 3.35
112 113 5.163499 ACCGAAAAGTAAAATTGCAACTGGA 60.163 36.000 0.00 0.00 0.00 3.86
117 118 8.649973 ATTAACACCGAAAAGTAAAATTGCAA 57.350 26.923 0.00 0.00 0.00 4.08
137 138 8.335356 TCACATAATGCTCGAGCTAAAATTAAC 58.665 33.333 35.27 5.71 42.66 2.01
139 140 7.710907 AGTCACATAATGCTCGAGCTAAAATTA 59.289 33.333 35.27 28.09 42.66 1.40
140 141 6.540189 AGTCACATAATGCTCGAGCTAAAATT 59.460 34.615 35.27 27.02 42.66 1.82
141 142 6.018425 CAGTCACATAATGCTCGAGCTAAAAT 60.018 38.462 35.27 19.47 42.66 1.82
142 143 5.291858 CAGTCACATAATGCTCGAGCTAAAA 59.708 40.000 35.27 17.99 42.66 1.52
143 144 4.805719 CAGTCACATAATGCTCGAGCTAAA 59.194 41.667 35.27 21.28 42.66 1.85
144 145 4.363138 CAGTCACATAATGCTCGAGCTAA 58.637 43.478 35.27 21.62 42.66 3.09
145 146 3.243535 CCAGTCACATAATGCTCGAGCTA 60.244 47.826 35.27 22.10 42.66 3.32
146 147 2.482664 CCAGTCACATAATGCTCGAGCT 60.483 50.000 35.27 20.62 42.66 4.09
147 148 1.863454 CCAGTCACATAATGCTCGAGC 59.137 52.381 30.42 30.42 42.50 5.03
165 318 5.848286 AATCATAGGTGAGCCAATATCCA 57.152 39.130 0.00 0.00 37.87 3.41
170 323 6.506538 ACTAGAAATCATAGGTGAGCCAAT 57.493 37.500 0.00 0.00 37.87 3.16
205 358 0.716108 CTTGTCGCAACATCGTCCTC 59.284 55.000 0.00 0.00 34.73 3.71
213 366 1.593209 GGGTCGTCTTGTCGCAACA 60.593 57.895 0.00 0.00 0.00 3.33
218 371 1.374252 CCAAGGGGTCGTCTTGTCG 60.374 63.158 0.00 0.00 39.78 4.35
220 373 2.430367 GCCAAGGGGTCGTCTTGT 59.570 61.111 0.00 0.00 39.78 3.16
269 422 4.393371 GGGATTGAAGGAGAAAGAAAGACG 59.607 45.833 0.00 0.00 0.00 4.18
271 424 5.850046 AGGGATTGAAGGAGAAAGAAAGA 57.150 39.130 0.00 0.00 0.00 2.52
304 457 9.585369 AGAAATGAAGGAAGAAAGAAGAAGATT 57.415 29.630 0.00 0.00 0.00 2.40
306 459 8.986929 AAGAAATGAAGGAAGAAAGAAGAAGA 57.013 30.769 0.00 0.00 0.00 2.87
307 460 9.676195 GAAAGAAATGAAGGAAGAAAGAAGAAG 57.324 33.333 0.00 0.00 0.00 2.85
308 461 8.633561 GGAAAGAAATGAAGGAAGAAAGAAGAA 58.366 33.333 0.00 0.00 0.00 2.52
320 473 3.935828 GAGAGTCGGGAAAGAAATGAAGG 59.064 47.826 0.00 0.00 0.00 3.46
325 478 4.081365 GGAGAAGAGAGTCGGGAAAGAAAT 60.081 45.833 0.00 0.00 0.00 2.17
364 517 1.584724 GGATGGGAGAAGGAAGGTGA 58.415 55.000 0.00 0.00 0.00 4.02
405 558 1.134367 TGACGAACATCGGATGAGGTC 59.866 52.381 23.98 22.69 45.59 3.85
440 593 0.865218 CAGTGTCAGCGCTCGATCTC 60.865 60.000 7.13 5.43 32.31 2.75
459 612 1.003972 CTCTCGAGCTCACAGACGATC 60.004 57.143 15.40 0.00 34.41 3.69
467 620 2.421775 TCACATTCTCTCTCGAGCTCAC 59.578 50.000 15.40 0.00 37.19 3.51
502 655 1.393883 GCTCTTTAAAAGGCTCGTCGG 59.606 52.381 0.00 0.00 0.00 4.79
505 658 3.412386 ACATGCTCTTTAAAAGGCTCGT 58.588 40.909 11.57 7.11 0.00 4.18
584 737 2.771943 CTCATATGGTGGTGGTAGTGGT 59.228 50.000 2.13 0.00 0.00 4.16
608 761 1.056700 AGGTTGACCAGTGACCAGCT 61.057 55.000 2.56 0.00 38.89 4.24
624 777 6.557568 TCTTAGAAGAAAGAAGAGGAGAGGT 58.442 40.000 0.00 0.00 32.59 3.85
650 803 6.183361 GGGACTAAAGAAAGAGGGAGGAATAG 60.183 46.154 0.00 0.00 0.00 1.73
655 808 3.182152 TGGGACTAAAGAAAGAGGGAGG 58.818 50.000 0.00 0.00 0.00 4.30
664 817 5.416271 AATCTACGCTTGGGACTAAAGAA 57.584 39.130 0.00 0.00 0.00 2.52
731 890 8.591072 TGGCTTGTACTAGTATTTGTTTAGTCT 58.409 33.333 5.75 0.00 0.00 3.24
856 1027 1.217916 TCGGACTGAGAGAGGAGGAT 58.782 55.000 0.00 0.00 0.00 3.24
1079 1251 4.394712 CTGGGAAGGAAGCGCCGT 62.395 66.667 2.29 0.00 43.43 5.68
1095 1267 4.680440 GCAACAACCAAACTGAACCAATCT 60.680 41.667 0.00 0.00 0.00 2.40
1251 1423 7.670979 TCAAAAAGATTTCCAGATCAATCAGGA 59.329 33.333 0.33 0.33 40.23 3.86
1266 1438 5.519927 CCAACACGAAGCTTCAAAAAGATTT 59.480 36.000 25.47 4.58 41.04 2.17
1270 1442 4.027572 TCCAACACGAAGCTTCAAAAAG 57.972 40.909 25.47 11.54 35.47 2.27
1381 1553 2.510691 CGCGAGCCCAATTACGGT 60.511 61.111 0.00 0.00 0.00 4.83
1696 1868 6.641314 GCAGAATTCTCATGCTGATAAAATGG 59.359 38.462 4.57 0.00 38.28 3.16
1723 1895 1.630126 ATCCGTGGAATCAGCAGCCT 61.630 55.000 0.00 0.00 0.00 4.58
1724 1896 0.749454 AATCCGTGGAATCAGCAGCC 60.749 55.000 0.00 0.00 0.00 4.85
1794 1966 4.127171 GCTCCTACTGTCAGTGTGAAAAA 58.873 43.478 16.03 0.00 0.00 1.94
1795 1967 3.388024 AGCTCCTACTGTCAGTGTGAAAA 59.612 43.478 16.03 0.00 0.00 2.29
1796 1968 2.965831 AGCTCCTACTGTCAGTGTGAAA 59.034 45.455 16.03 0.00 0.00 2.69
1797 1969 2.598565 AGCTCCTACTGTCAGTGTGAA 58.401 47.619 16.03 0.00 0.00 3.18
1798 1970 2.294449 AGCTCCTACTGTCAGTGTGA 57.706 50.000 16.03 10.35 0.00 3.58
1827 1999 7.914346 GCCTGAAAAGTCAATTGATATCAAGAG 59.086 37.037 21.97 16.39 39.47 2.85
1935 2107 7.644490 ACATAAACGAACAAATAAGCTGACAA 58.356 30.769 0.00 0.00 0.00 3.18
1949 2121 5.866335 TCACCAACCATACATAAACGAAC 57.134 39.130 0.00 0.00 0.00 3.95
2040 2212 7.821595 AATGAATATACTCACACGAAAACGA 57.178 32.000 0.00 0.00 0.00 3.85
2059 2231 4.511617 TGCGCAAGACCAAAATAATGAA 57.488 36.364 8.16 0.00 43.02 2.57
2135 2307 6.664428 ATTGGGCCGCTAATGTTTATAAAT 57.336 33.333 0.31 0.00 0.00 1.40
2184 2356 8.784043 CCGATACCCATTTTTATTAGGAAAGAG 58.216 37.037 0.00 0.00 0.00 2.85
2197 2369 3.053991 TGTCACCATCCGATACCCATTTT 60.054 43.478 0.00 0.00 0.00 1.82
2205 2377 3.005791 CAGCTATGTGTCACCATCCGATA 59.994 47.826 0.00 0.00 0.00 2.92
2235 2407 2.373335 TTTCCTTGTTTGCTGGCCTA 57.627 45.000 3.32 0.00 0.00 3.93
2310 2482 5.429957 GGCAATCAAAATCAGCCTACTAG 57.570 43.478 0.00 0.00 42.01 2.57
2319 2491 2.250031 ACAGGCAGGCAATCAAAATCA 58.750 42.857 0.00 0.00 0.00 2.57
2360 2532 3.538614 GCCCTCCACTCTGCGATA 58.461 61.111 0.00 0.00 0.00 2.92
2364 2536 2.948720 AAGACGCCCTCCACTCTGC 61.949 63.158 0.00 0.00 0.00 4.26
2366 2538 1.122019 AACAAGACGCCCTCCACTCT 61.122 55.000 0.00 0.00 0.00 3.24
2369 2541 0.951040 CTCAACAAGACGCCCTCCAC 60.951 60.000 0.00 0.00 0.00 4.02
2374 2546 3.821841 CATAAAACTCAACAAGACGCCC 58.178 45.455 0.00 0.00 0.00 6.13
2376 2548 4.147219 AGCATAAAACTCAACAAGACGC 57.853 40.909 0.00 0.00 0.00 5.19
2395 2567 8.850454 TTCAAACTTCAAAACAATGTAGTAGC 57.150 30.769 0.00 0.00 31.65 3.58
2431 2603 2.691409 TGCTGCCTATGTTGTCCTAC 57.309 50.000 0.00 0.00 0.00 3.18
2437 2609 7.502120 AGACTAATTTATGCTGCCTATGTTG 57.498 36.000 0.00 0.00 0.00 3.33
2708 2880 8.585471 AACCACATTAAATTCTGATGTCTGAT 57.415 30.769 0.00 0.00 32.01 2.90
2779 2951 7.282224 CGATTCCATTGTTCCCTGTAGAAAATA 59.718 37.037 0.00 0.00 0.00 1.40
2781 2953 5.414454 CGATTCCATTGTTCCCTGTAGAAAA 59.586 40.000 0.00 0.00 0.00 2.29
2834 3006 5.216566 TCAATTTATTCGAGCGAAACCAG 57.783 39.130 9.52 0.00 37.69 4.00
2846 3018 7.094377 TGAGGCCGGCTATAATTCAATTTATTC 60.094 37.037 28.56 2.03 0.00 1.75
2858 3030 2.047061 ACAAGATGAGGCCGGCTATAA 58.953 47.619 28.56 9.27 0.00 0.98
2889 3061 7.603963 TCGAAATCACAATTTCTTCCGAATA 57.396 32.000 8.70 0.00 45.72 1.75
3012 3185 6.705302 ACATGTCAGTACATCTCTCAAACAT 58.295 36.000 0.00 0.00 44.70 2.71
3061 3234 5.644977 TCAGTCTCGATTGTGACATTACT 57.355 39.130 15.73 0.00 40.28 2.24
3247 3420 8.129840 TCAAATTAAGTAGCAAAACACGCTTAA 58.870 29.630 0.00 0.00 40.96 1.85
3251 3424 5.912955 ACTCAAATTAAGTAGCAAAACACGC 59.087 36.000 0.00 0.00 0.00 5.34
3361 3534 7.526142 AGATTTATCTTGCGGTGAGTAGATA 57.474 36.000 0.00 0.00 31.97 1.98
3369 3542 6.912591 GGAAACAATAGATTTATCTTGCGGTG 59.087 38.462 0.00 0.00 38.32 4.94
3447 3620 4.818005 CACAATATTCAGCCATGCTACTGA 59.182 41.667 7.10 7.10 41.06 3.41
3486 3659 5.761726 TCGAGCATGAATCTGCATAGAAAAT 59.238 36.000 0.00 0.00 44.77 1.82
3513 3686 1.460504 ATGCTGTCCTCAATGCACAG 58.539 50.000 0.00 0.00 40.53 3.66
3532 3705 4.141824 TGGCATCATGACCGACACTAATTA 60.142 41.667 0.00 0.00 0.00 1.40
3539 3712 0.832626 AGATGGCATCATGACCGACA 59.167 50.000 27.93 5.02 32.98 4.35
3743 3916 0.036577 CTGGTGCTGTCCTGAAGGAG 60.037 60.000 0.00 0.00 46.49 3.69
3798 3971 4.162040 GGACATCTTCCATCTGGACATT 57.838 45.455 0.00 0.00 45.39 2.71
3815 3988 2.183478 ACTCGATTGCAACATGGACA 57.817 45.000 0.00 0.00 0.00 4.02
4094 4267 2.905736 TGATGATTGACTGTGGAGGTCA 59.094 45.455 0.00 0.00 41.23 4.02
4145 4318 2.585247 GTCGCGAGGGCATGGTAC 60.585 66.667 10.24 0.00 39.92 3.34
4237 4410 3.879892 GGGAAAGATGGTGATGAAGCTAC 59.120 47.826 0.00 0.00 0.00 3.58
4559 4732 4.012374 CAGGATAACATGTGAGGCTGTTT 58.988 43.478 0.00 0.00 36.92 2.83
4645 4818 1.888826 CGGCCTAACAACCCCATTGAA 60.889 52.381 0.00 0.00 41.23 2.69
4909 5086 2.552315 CGTGTACAATCTTGGCAAAGGT 59.448 45.455 0.00 0.00 33.90 3.50
5007 5184 1.034838 AAGTGAAAACGGCCACTGCA 61.035 50.000 2.24 0.00 42.25 4.41
5033 5210 2.039084 ACAGAACCTTCTACTGCCTTGG 59.961 50.000 0.00 0.00 35.34 3.61
5038 5256 7.492352 TTCTTTTTACAGAACCTTCTACTGC 57.508 36.000 0.00 0.00 35.34 4.40
5095 5318 3.252554 TGGCCACCTTGGTTTTATTCT 57.747 42.857 0.00 0.00 40.46 2.40
5096 5319 3.260632 ACATGGCCACCTTGGTTTTATTC 59.739 43.478 8.16 0.00 40.46 1.75
5097 5320 3.007831 CACATGGCCACCTTGGTTTTATT 59.992 43.478 8.16 0.00 40.46 1.40
5099 5322 1.967066 CACATGGCCACCTTGGTTTTA 59.033 47.619 8.16 0.00 40.46 1.52
5103 5326 2.118076 CCACATGGCCACCTTGGT 59.882 61.111 8.16 0.00 40.46 3.67
5106 5329 2.601367 GCACCACATGGCCACCTT 60.601 61.111 8.16 0.00 39.32 3.50


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

AutoCloner maintained by Alex Coulton.