Multiple sequence alignment - TraesCS4A01G341600

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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 TraesCS4A01G341600 chr4A 100.000 4515 0 0 1 4515 621820172 621815658 0.000000e+00 8338
1 TraesCS4A01G341600 chr5D 91.747 2690 133 45 34 2659 546917696 546920360 0.000000e+00 3655
2 TraesCS4A01G341600 chr5D 93.552 1861 97 14 2661 4515 546920441 546922284 0.000000e+00 2750
3 TraesCS4A01G341600 chr5D 88.723 470 40 5 1821 2290 388394945 388394489 3.050000e-156 562
4 TraesCS4A01G341600 chr5D 88.298 470 42 5 1821 2290 462802523 462802979 6.600000e-153 551
5 TraesCS4A01G341600 chr5B 91.197 2681 155 35 44 2659 690089753 690092417 0.000000e+00 3568
6 TraesCS4A01G341600 chr5B 93.408 1866 83 21 2661 4515 690092498 690094334 0.000000e+00 2728
7 TraesCS4A01G341600 chr5B 80.170 353 58 10 4169 4515 576252521 576252175 2.080000e-63 254
8 TraesCS4A01G341600 chr1B 88.486 469 41 5 1822 2290 629472376 629471921 5.100000e-154 555
9 TraesCS4A01G341600 chr3D 85.319 470 43 12 1821 2290 22231091 22231534 3.180000e-126 462
10 TraesCS4A01G341600 chr4B 88.889 297 20 5 1994 2290 626627889 626627606 2.000000e-93 353
11 TraesCS4A01G341600 chr5A 80.690 435 51 22 4096 4515 589384137 589383721 1.580000e-79 307


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 TraesCS4A01G341600 chr4A 621815658 621820172 4514 True 8338.0 8338 100.0000 1 4515 1 chr4A.!!$R1 4514
1 TraesCS4A01G341600 chr5D 546917696 546922284 4588 False 3202.5 3655 92.6495 34 4515 2 chr5D.!!$F2 4481
2 TraesCS4A01G341600 chr5B 690089753 690094334 4581 False 3148.0 3568 92.3025 44 4515 2 chr5B.!!$F1 4471

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
35 36 0.248289 TTAACGGAAGGAAGGGAGCG 59.752 55.000 0.00 0.0 0.00 5.03 F
964 1047 1.352056 GCAGCTTAATTCGGCGTCC 59.648 57.895 6.85 0.0 0.00 4.79 F
2163 2252 0.376852 TTGCACGTTGTCTGAACAGC 59.623 50.000 0.00 0.0 36.57 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 1281 0.109532 TTGCCATTGTTGACCCTCGA 59.890 50.0 0.0 0.0 0.00 4.04 R
2835 3008 0.327924 TGTCAGGTGCCCATTGTAGG 59.672 55.0 0.0 0.0 0.00 3.18 R
3626 3801 0.688087 ACGAATCTCTGGAGGACCCC 60.688 60.0 0.0 0.0 34.81 4.95 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
30 31 2.763651 CGGCTTAACGGAAGGAAGG 58.236 57.895 2.03 0.00 35.49 3.46
31 32 0.743345 CGGCTTAACGGAAGGAAGGG 60.743 60.000 2.03 0.00 35.49 3.95
32 33 0.616891 GGCTTAACGGAAGGAAGGGA 59.383 55.000 2.03 0.00 35.49 4.20
33 34 1.407025 GGCTTAACGGAAGGAAGGGAG 60.407 57.143 2.03 0.00 35.49 4.30
34 35 2.012554 GCTTAACGGAAGGAAGGGAGC 61.013 57.143 2.03 0.00 35.49 4.70
35 36 0.248289 TTAACGGAAGGAAGGGAGCG 59.752 55.000 0.00 0.00 0.00 5.03
36 37 1.610554 TAACGGAAGGAAGGGAGCGG 61.611 60.000 0.00 0.00 0.00 5.52
37 38 4.162690 CGGAAGGAAGGGAGCGGG 62.163 72.222 0.00 0.00 0.00 6.13
38 39 4.491409 GGAAGGAAGGGAGCGGGC 62.491 72.222 0.00 0.00 0.00 6.13
39 40 3.717294 GAAGGAAGGGAGCGGGCA 61.717 66.667 0.00 0.00 0.00 5.36
40 41 3.689002 GAAGGAAGGGAGCGGGCAG 62.689 68.421 0.00 0.00 0.00 4.85
189 201 1.606313 CCCCAACAAACTCCGCCAT 60.606 57.895 0.00 0.00 0.00 4.40
216 238 3.594603 TTGCGGAGGAAAAGTAGAGAG 57.405 47.619 0.00 0.00 32.59 3.20
217 239 2.803956 TGCGGAGGAAAAGTAGAGAGA 58.196 47.619 0.00 0.00 0.00 3.10
464 522 4.569023 CGCGCGGCCTCTGATGTA 62.569 66.667 24.84 0.00 0.00 2.29
488 560 2.255172 CCGGTGGTTTGTTGCGCTA 61.255 57.895 9.73 0.00 0.00 4.26
491 563 1.515081 GGTGGTTTGTTGCGCTAGTA 58.485 50.000 9.73 0.00 0.00 1.82
548 620 4.398598 CCGCCGCCTTTTTGGTCG 62.399 66.667 0.00 0.00 38.35 4.79
580 652 2.040412 AGTGGGGGATTTGTCAGAGTTC 59.960 50.000 0.00 0.00 0.00 3.01
620 692 4.654262 TCTGTATGGGTGGGATTTACTCTC 59.346 45.833 0.00 0.00 0.00 3.20
837 909 3.252284 AGCTCTGGGTGTGGGTGG 61.252 66.667 0.00 0.00 0.00 4.61
838 910 3.249189 GCTCTGGGTGTGGGTGGA 61.249 66.667 0.00 0.00 0.00 4.02
839 911 3.072476 CTCTGGGTGTGGGTGGAG 58.928 66.667 0.00 0.00 0.00 3.86
894 977 3.368116 CGGACCTAGGGTTTACTGTTCAG 60.368 52.174 14.81 0.00 35.25 3.02
916 999 3.958860 AGCAGGGTGAGGTGGCAC 61.959 66.667 9.70 9.70 38.05 5.01
958 1041 1.436983 GGACGGGGCAGCTTAATTCG 61.437 60.000 0.00 0.00 0.00 3.34
964 1047 1.352056 GCAGCTTAATTCGGCGTCC 59.648 57.895 6.85 0.00 0.00 4.79
993 1076 2.507471 GGAGATTTGGACTGATCTGGGT 59.493 50.000 4.49 0.00 32.96 4.51
1095 1178 4.717313 GCCTCCGTGTCCAACCCC 62.717 72.222 0.00 0.00 0.00 4.95
1162 1248 4.880537 CTGGGCTCAGCTACGGCG 62.881 72.222 0.00 4.80 44.37 6.46
1203 1292 1.871676 GGAAACAACTCGAGGGTCAAC 59.128 52.381 18.41 9.04 0.00 3.18
1233 1322 4.135153 TCGGCCTTCGAGCTGCTC 62.135 66.667 19.53 19.53 43.74 4.26
1248 1337 1.279025 TGCTCCCGGGCTTTAAGGAT 61.279 55.000 18.49 0.00 0.00 3.24
1251 1340 0.544697 TCCCGGGCTTTAAGGATGTC 59.455 55.000 18.49 0.00 0.00 3.06
1485 1574 3.011517 CTGACCACCCCTCCCAGG 61.012 72.222 0.00 0.00 34.30 4.45
1536 1625 3.393472 GGATGAGCCTGTGATGGAC 57.607 57.895 0.00 0.00 0.00 4.02
1542 1631 2.976490 GCCTGTGATGGACCCTGCT 61.976 63.158 0.00 0.00 0.00 4.24
1638 1727 5.179555 GGCTAAAAGGTACATCGATCATTCC 59.820 44.000 0.00 0.00 0.00 3.01
1791 1880 5.662674 ACACCTTCTACCAGTTCATCTAC 57.337 43.478 0.00 0.00 0.00 2.59
1878 1967 1.464997 GCGTTGCCACTTAAGGAAGAG 59.535 52.381 7.53 0.00 36.45 2.85
1881 1970 3.084786 GTTGCCACTTAAGGAAGAGCAT 58.915 45.455 7.53 0.00 41.65 3.79
1914 2003 1.965414 TCAGGGCCTTGATTCCACTA 58.035 50.000 14.61 0.00 0.00 2.74
2048 2137 0.758310 TGGCCCATCACAAACAGCAA 60.758 50.000 0.00 0.00 0.00 3.91
2163 2252 0.376852 TTGCACGTTGTCTGAACAGC 59.623 50.000 0.00 0.00 36.57 4.40
2247 2339 4.325028 TTGTGTTGCTTGATGCTTCATT 57.675 36.364 2.75 0.00 43.37 2.57
2308 2400 6.894735 TTGTCCCTGGATAGGTAACAAATA 57.105 37.500 0.00 0.00 41.27 1.40
2529 2623 9.379791 CTCTATTCCATACTTTTCCGTTTACTT 57.620 33.333 0.00 0.00 0.00 2.24
2535 2629 6.349033 CCATACTTTTCCGTTTACTTTCAGGG 60.349 42.308 0.00 0.00 0.00 4.45
2536 2630 3.317149 ACTTTTCCGTTTACTTTCAGGGC 59.683 43.478 0.00 0.00 0.00 5.19
2537 2631 1.900245 TTCCGTTTACTTTCAGGGCC 58.100 50.000 0.00 0.00 0.00 5.80
2572 2666 3.428862 GCGCCCTGTTATTTTGTGCTAAT 60.429 43.478 0.00 0.00 0.00 1.73
2617 2711 3.063725 GCAATCTCTGACATCACAGCTTC 59.936 47.826 0.00 0.00 37.75 3.86
2621 2715 0.671472 CTGACATCACAGCTTCGCCA 60.671 55.000 0.00 0.00 0.00 5.69
2671 2844 7.253422 AGACATAAATGCTGCATGTTTAAGTC 58.747 34.615 23.25 23.25 36.79 3.01
2674 2847 3.747099 ATGCTGCATGTTTAAGTCGTC 57.253 42.857 15.44 0.00 0.00 4.20
2678 2851 3.728864 GCTGCATGTTTAAGTCGTCATGG 60.729 47.826 0.00 0.00 38.32 3.66
2684 2857 2.380084 TTAAGTCGTCATGGAGCACC 57.620 50.000 0.00 0.00 0.00 5.01
2716 2889 2.353889 CAGCACTATGACTGGAACATGC 59.646 50.000 0.00 0.00 38.20 4.06
2717 2890 2.238144 AGCACTATGACTGGAACATGCT 59.762 45.455 0.00 0.00 38.20 3.79
2718 2891 3.452264 AGCACTATGACTGGAACATGCTA 59.548 43.478 0.00 0.00 38.20 3.49
2719 2892 3.806521 GCACTATGACTGGAACATGCTAG 59.193 47.826 0.00 0.00 38.20 3.42
2720 2893 3.806521 CACTATGACTGGAACATGCTAGC 59.193 47.826 8.10 8.10 38.20 3.42
2721 2894 3.452264 ACTATGACTGGAACATGCTAGCA 59.548 43.478 21.85 21.85 38.20 3.49
2722 2895 2.391616 TGACTGGAACATGCTAGCAG 57.608 50.000 23.89 16.67 38.20 4.24
2724 2897 2.302733 TGACTGGAACATGCTAGCAGAA 59.697 45.455 23.89 0.00 38.20 3.02
2725 2898 3.054875 TGACTGGAACATGCTAGCAGAAT 60.055 43.478 23.89 11.00 38.20 2.40
2728 2901 5.500234 ACTGGAACATGCTAGCAGAATAAA 58.500 37.500 23.89 6.64 38.20 1.40
2729 2902 6.125029 ACTGGAACATGCTAGCAGAATAAAT 58.875 36.000 23.89 0.56 38.20 1.40
2730 2903 7.282585 ACTGGAACATGCTAGCAGAATAAATA 58.717 34.615 23.89 4.57 38.20 1.40
2734 2907 6.506500 ACATGCTAGCAGAATAAATATGCC 57.493 37.500 23.89 0.00 40.89 4.40
2740 2913 7.719193 TGCTAGCAGAATAAATATGCCAAAGTA 59.281 33.333 14.93 0.00 40.89 2.24
2793 2966 2.037251 GGCAGTTCTCTGGTTAGTGACA 59.963 50.000 0.00 0.00 41.57 3.58
2794 2967 3.307059 GGCAGTTCTCTGGTTAGTGACAT 60.307 47.826 0.00 0.00 41.57 3.06
2816 2989 7.533426 ACATTGTCACAGAAGCAAATTCTATC 58.467 34.615 0.00 0.00 46.91 2.08
2835 3008 3.302365 TCAGCTGTTTATGGCTTTTGC 57.698 42.857 14.67 0.00 46.64 3.68
2890 3063 0.889186 ATGTCTGTTTCGTGTGGGCC 60.889 55.000 0.00 0.00 0.00 5.80
2893 3066 0.179004 TCTGTTTCGTGTGGGCCATT 60.179 50.000 10.70 0.00 0.00 3.16
2895 3068 2.091541 CTGTTTCGTGTGGGCCATTAT 58.908 47.619 10.70 0.00 0.00 1.28
2902 3075 2.795329 GTGTGGGCCATTATCCTATGG 58.205 52.381 10.70 0.00 46.46 2.74
2978 3151 7.061905 GCACATCTTGAATCTGTCAGAATTTTG 59.938 37.037 6.64 1.97 37.61 2.44
3092 3265 3.335786 CATGCTAGCATGCTTGAAGTC 57.664 47.619 37.34 15.60 45.71 3.01
3146 3321 3.476552 TGTAGCTAATGGTGCTTATGCC 58.523 45.455 0.00 0.00 41.46 4.40
3397 3572 4.085009 CCAAAGCCAAAGAGAAGGAGAAT 58.915 43.478 0.00 0.00 0.00 2.40
3401 3576 7.093596 CCAAAGCCAAAGAGAAGGAGAATAAAT 60.094 37.037 0.00 0.00 0.00 1.40
3460 3635 1.800805 CGTCATCAAGAGCAACCAGT 58.199 50.000 0.00 0.00 0.00 4.00
3613 3788 9.409312 TGCAATTGTGTCTAATGTAAGAATTTG 57.591 29.630 7.40 0.00 0.00 2.32
3703 3879 0.035152 ATCAGGCAGGCAAATCGACA 60.035 50.000 0.00 0.00 0.00 4.35
3834 4011 7.819415 TCATTGCTATATCCTTTATCCTTGTCG 59.181 37.037 0.00 0.00 0.00 4.35
3844 4021 3.826637 TCCTTGTCGGAATTCGGTC 57.173 52.632 12.22 7.91 39.40 4.79
3863 4043 2.039084 GTCACAGTCTGTTCCTCCCATT 59.961 50.000 1.67 0.00 0.00 3.16
3901 4081 0.309612 GCAAATGGTCGGTCGTTGTT 59.690 50.000 0.00 0.00 0.00 2.83
3976 4156 4.272504 TCAAAACGAGTCATGGTTGTTCTC 59.727 41.667 0.00 0.00 0.00 2.87
4109 4292 1.810412 GCGTTCTGTCTTGTTGGAGGT 60.810 52.381 0.00 0.00 0.00 3.85
4133 4316 4.817318 TCTGAATTGGCCATTTTAACCC 57.183 40.909 6.09 0.00 0.00 4.11
4134 4317 3.194542 TCTGAATTGGCCATTTTAACCCG 59.805 43.478 6.09 0.00 0.00 5.28
4135 4318 3.165875 TGAATTGGCCATTTTAACCCGA 58.834 40.909 6.09 0.00 0.00 5.14
4232 4419 2.227388 CACTGGATTCAGAACAAGGTGC 59.773 50.000 8.39 0.00 43.49 5.01
4273 4460 0.255890 ACAACAGCCACCACAAGACT 59.744 50.000 0.00 0.00 0.00 3.24
4274 4461 0.664761 CAACAGCCACCACAAGACTG 59.335 55.000 0.00 0.00 0.00 3.51
4275 4462 1.103398 AACAGCCACCACAAGACTGC 61.103 55.000 0.00 0.00 31.46 4.40
4276 4463 1.228063 CAGCCACCACAAGACTGCT 60.228 57.895 0.00 0.00 0.00 4.24
4277 4464 1.228063 AGCCACCACAAGACTGCTG 60.228 57.895 0.00 0.00 0.00 4.41
4306 4493 2.949644 TGAATGCTGAAGATGATGCTGG 59.050 45.455 0.00 0.00 0.00 4.85
4376 4565 1.281925 AAGGATGGGCGGATGAAGGT 61.282 55.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.743345 CCCTTCCTTCCGTTAAGCCG 60.743 60.000 0.00 0.00 33.49 5.52
13 14 0.616891 TCCCTTCCTTCCGTTAAGCC 59.383 55.000 0.00 0.00 33.49 4.35
14 15 2.012554 GCTCCCTTCCTTCCGTTAAGC 61.013 57.143 0.00 0.00 33.49 3.09
15 16 1.739371 CGCTCCCTTCCTTCCGTTAAG 60.739 57.143 0.00 0.00 34.73 1.85
16 17 0.248289 CGCTCCCTTCCTTCCGTTAA 59.752 55.000 0.00 0.00 0.00 2.01
17 18 1.610554 CCGCTCCCTTCCTTCCGTTA 61.611 60.000 0.00 0.00 0.00 3.18
18 19 2.663196 CGCTCCCTTCCTTCCGTT 59.337 61.111 0.00 0.00 0.00 4.44
19 20 3.391382 CCGCTCCCTTCCTTCCGT 61.391 66.667 0.00 0.00 0.00 4.69
20 21 4.162690 CCCGCTCCCTTCCTTCCG 62.163 72.222 0.00 0.00 0.00 4.30
21 22 4.491409 GCCCGCTCCCTTCCTTCC 62.491 72.222 0.00 0.00 0.00 3.46
22 23 3.689002 CTGCCCGCTCCCTTCCTTC 62.689 68.421 0.00 0.00 0.00 3.46
23 24 3.721706 CTGCCCGCTCCCTTCCTT 61.722 66.667 0.00 0.00 0.00 3.36
40 41 4.552365 TGCGATGCTAGGCTGGCC 62.552 66.667 20.71 5.13 0.00 5.36
41 42 3.275338 GTGCGATGCTAGGCTGGC 61.275 66.667 16.77 16.77 0.00 4.85
42 43 1.434622 CTTGTGCGATGCTAGGCTGG 61.435 60.000 0.00 0.00 0.00 4.85
90 94 2.131972 GAAAAACAAATCCGTGGGCAC 58.868 47.619 0.00 0.00 0.00 5.01
139 151 2.389143 CGTAACGCGTCGCTTTCC 59.611 61.111 14.44 1.99 35.54 3.13
189 201 4.729227 ACTTTTCCTCCGCAAAAGAAAA 57.271 36.364 11.83 7.19 41.52 2.29
213 235 1.896465 CGGAACTTGGACCTTCTCTCT 59.104 52.381 0.00 0.00 0.00 3.10
214 236 1.893801 TCGGAACTTGGACCTTCTCTC 59.106 52.381 0.00 0.00 0.00 3.20
215 237 1.896465 CTCGGAACTTGGACCTTCTCT 59.104 52.381 0.00 0.00 0.00 3.10
216 238 1.619332 ACTCGGAACTTGGACCTTCTC 59.381 52.381 0.00 0.00 0.00 2.87
217 239 1.619332 GACTCGGAACTTGGACCTTCT 59.381 52.381 0.00 0.00 0.00 2.85
253 288 1.684049 AGTCGCTGGAGGAGGAAGG 60.684 63.158 0.00 0.00 0.00 3.46
449 507 1.373497 GGATACATCAGAGGCCGCG 60.373 63.158 0.00 0.00 0.00 6.46
450 508 1.373497 CGGATACATCAGAGGCCGC 60.373 63.158 0.00 0.00 31.80 6.53
451 509 1.290324 CCGGATACATCAGAGGCCG 59.710 63.158 0.00 0.00 38.54 6.13
453 511 1.004440 GGCCGGATACATCAGAGGC 60.004 63.158 5.05 11.69 40.33 4.70
454 512 1.290324 CGGCCGGATACATCAGAGG 59.710 63.158 20.10 0.00 0.00 3.69
455 513 1.290324 CCGGCCGGATACATCAGAG 59.710 63.158 41.82 6.81 37.50 3.35
456 514 3.455152 CCGGCCGGATACATCAGA 58.545 61.111 41.82 0.00 37.50 3.27
678 750 1.853319 CGCGGCTAATCAATCGACC 59.147 57.895 0.00 0.00 0.00 4.79
681 753 1.956170 AGGCGCGGCTAATCAATCG 60.956 57.895 35.57 0.00 0.00 3.34
820 892 3.252284 CCACCCACACCCAGAGCT 61.252 66.667 0.00 0.00 0.00 4.09
830 902 3.909086 GAGCTGTGCCTCCACCCAC 62.909 68.421 0.00 0.00 41.35 4.61
832 904 4.767255 CGAGCTGTGCCTCCACCC 62.767 72.222 0.00 0.00 41.35 4.61
837 909 4.828925 GGAGCCGAGCTGTGCCTC 62.829 72.222 2.98 0.00 39.88 4.70
859 931 4.961511 GTCCGTCGCAGCACCACA 62.962 66.667 0.00 0.00 0.00 4.17
867 950 0.611618 TAAACCCTAGGTCCGTCGCA 60.612 55.000 8.29 0.00 33.12 5.10
870 953 2.174360 ACAGTAAACCCTAGGTCCGTC 58.826 52.381 8.29 0.00 33.12 4.79
894 977 4.341783 ACCTCACCCTGCTGCTGC 62.342 66.667 8.89 8.89 40.20 5.25
944 1027 2.048312 GACGCCGAATTAAGCTGCCC 62.048 60.000 0.00 0.00 0.00 5.36
946 1029 1.352056 GGACGCCGAATTAAGCTGC 59.648 57.895 0.00 0.00 0.00 5.25
964 1047 0.739813 GTCCAAATCTCCCCGACACG 60.740 60.000 0.00 0.00 0.00 4.49
974 1057 2.240667 CCACCCAGATCAGTCCAAATCT 59.759 50.000 0.00 0.00 32.44 2.40
1192 1281 0.109532 TTGCCATTGTTGACCCTCGA 59.890 50.000 0.00 0.00 0.00 4.04
1203 1292 3.277652 GGCCGATGAATTGCCATTG 57.722 52.632 0.00 0.00 44.70 2.82
1233 1322 0.465642 GGACATCCTTAAAGCCCGGG 60.466 60.000 19.09 19.09 0.00 5.73
1248 1337 3.234630 CTTCTCGGCGTTGGGGACA 62.235 63.158 6.85 0.00 39.83 4.02
1251 1340 0.177141 TATTCTTCTCGGCGTTGGGG 59.823 55.000 6.85 0.00 0.00 4.96
1485 1574 4.943705 TCATAGGCTGAAATGTTGTTCTCC 59.056 41.667 0.00 0.00 0.00 3.71
1542 1631 0.592637 CAATCTGCAAGTGCGACCAA 59.407 50.000 0.00 0.00 45.83 3.67
1638 1727 3.685139 TCAAGTAGCCTGAGGACAAAG 57.315 47.619 0.65 0.00 0.00 2.77
1791 1880 3.963665 TCCATTGTGCTTTTCAGTTTCG 58.036 40.909 0.00 0.00 0.00 3.46
1825 1914 3.237746 TGATGCTCCCTAAGATCTCCAG 58.762 50.000 0.00 0.00 0.00 3.86
1878 1967 5.509670 GGCCCTGATAAGGAACAATTTATGC 60.510 44.000 0.00 0.00 0.00 3.14
1881 1970 5.466127 AGGCCCTGATAAGGAACAATTTA 57.534 39.130 0.00 0.00 0.00 1.40
1914 2003 1.807377 GCAATGCACTTTGGCTTGTGT 60.807 47.619 0.00 0.00 36.63 3.72
1968 2057 7.220108 AGTTTACAATCTTTTTCAACGAACTGC 59.780 33.333 0.00 0.00 0.00 4.40
1974 2063 9.284594 TCTGAAAGTTTACAATCTTTTTCAACG 57.715 29.630 0.00 0.00 35.06 4.10
2048 2137 2.965147 CCCAAAAACATCACCTCCTTGT 59.035 45.455 0.00 0.00 0.00 3.16
2163 2252 7.042658 GCGGTTAATATTACCTGAAAGTGAGAG 60.043 40.741 3.18 0.00 33.35 3.20
2211 2302 9.708222 CAAGCAACACAAATAGATGTATACTTC 57.292 33.333 10.10 10.10 30.84 3.01
2247 2339 9.883142 AAAATTACACAACAGAAGAAATGGAAA 57.117 25.926 0.00 0.00 0.00 3.13
2339 2431 6.371548 GCACTACCATGTCTTGAATAGAAACA 59.628 38.462 0.00 0.00 33.81 2.83
2353 2445 7.829211 ACAAATACTAAATCTGCACTACCATGT 59.171 33.333 0.00 0.00 0.00 3.21
2477 2571 6.671614 AACTATCACAAAAGTGTCGTTTCA 57.328 33.333 0.00 0.00 35.07 2.69
2511 2605 6.608610 CCCTGAAAGTAAACGGAAAAGTATG 58.391 40.000 0.00 0.00 0.00 2.39
2516 2610 2.624364 GGCCCTGAAAGTAAACGGAAAA 59.376 45.455 0.00 0.00 0.00 2.29
2572 2666 3.271586 GCACTGCACTGCGTGTCA 61.272 61.111 19.92 5.91 36.23 3.58
2640 2734 9.439500 AAACATGCAGCATTTATGTCTAAAATT 57.561 25.926 4.69 0.00 34.18 1.82
2646 2740 7.161773 ACTTAAACATGCAGCATTTATGTCT 57.838 32.000 4.69 0.00 34.18 3.41
2659 2753 3.485877 GCTCCATGACGACTTAAACATGC 60.486 47.826 0.00 0.00 38.79 4.06
2671 2844 3.190849 CAGCGGTGCTCCATGACG 61.191 66.667 0.00 0.00 36.40 4.35
2695 2868 2.353889 GCATGTTCCAGTCATAGTGCTG 59.646 50.000 0.00 0.00 0.00 4.41
2702 2875 2.502947 TCTGCTAGCATGTTCCAGTCAT 59.497 45.455 19.72 0.00 0.00 3.06
2703 2876 1.901833 TCTGCTAGCATGTTCCAGTCA 59.098 47.619 19.72 0.00 0.00 3.41
2709 2882 7.025963 GGCATATTTATTCTGCTAGCATGTTC 58.974 38.462 19.72 3.80 36.18 3.18
2710 2883 6.491062 TGGCATATTTATTCTGCTAGCATGTT 59.509 34.615 19.72 8.21 36.18 2.71
2712 2885 6.505044 TGGCATATTTATTCTGCTAGCATG 57.495 37.500 19.72 11.24 36.18 4.06
2713 2886 7.232127 ACTTTGGCATATTTATTCTGCTAGCAT 59.768 33.333 19.72 6.17 36.18 3.79
2714 2887 6.547141 ACTTTGGCATATTTATTCTGCTAGCA 59.453 34.615 18.22 18.22 36.18 3.49
2715 2888 6.974965 ACTTTGGCATATTTATTCTGCTAGC 58.025 36.000 8.10 8.10 36.18 3.42
2718 2891 9.586435 GTTTTACTTTGGCATATTTATTCTGCT 57.414 29.630 0.00 0.00 36.18 4.24
2719 2892 9.586435 AGTTTTACTTTGGCATATTTATTCTGC 57.414 29.630 0.00 0.00 35.16 4.26
2768 2941 3.251004 CACTAACCAGAGAACTGCCAAAC 59.749 47.826 0.00 0.00 42.25 2.93
2771 2944 2.037251 GTCACTAACCAGAGAACTGCCA 59.963 50.000 0.00 0.00 42.25 4.92
2772 2945 2.037251 TGTCACTAACCAGAGAACTGCC 59.963 50.000 0.00 0.00 42.25 4.85
2793 2966 7.627939 GCTGATAGAATTTGCTTCTGTGACAAT 60.628 37.037 0.00 0.00 44.12 2.71
2794 2967 6.348786 GCTGATAGAATTTGCTTCTGTGACAA 60.349 38.462 0.00 0.00 44.12 3.18
2816 2989 2.028748 AGGCAAAAGCCATAAACAGCTG 60.029 45.455 13.48 13.48 0.00 4.24
2835 3008 0.327924 TGTCAGGTGCCCATTGTAGG 59.672 55.000 0.00 0.00 0.00 3.18
2890 3063 6.069440 TCCCTGAATTAGGCCATAGGATAATG 60.069 42.308 5.01 0.00 45.89 1.90
2893 3066 4.783227 GTCCCTGAATTAGGCCATAGGATA 59.217 45.833 5.01 0.00 45.89 2.59
2895 3068 2.979678 GTCCCTGAATTAGGCCATAGGA 59.020 50.000 5.01 0.00 45.89 2.94
2902 3075 3.636153 AGTGAAGTCCCTGAATTAGGC 57.364 47.619 0.00 0.00 45.89 3.93
2953 3126 8.294577 TCAAAATTCTGACAGATTCAAGATGTG 58.705 33.333 5.87 0.00 32.21 3.21
2993 3166 9.170734 TCATGAAGAATGAGAATAAAGAACCAG 57.829 33.333 0.00 0.00 40.50 4.00
3034 3207 5.736207 GCCTTCTCCAACAACAAAGTAAAGG 60.736 44.000 0.00 0.00 34.13 3.11
3086 3259 1.040646 ACTCTGGTTCTGCGACTTCA 58.959 50.000 0.00 0.00 0.00 3.02
3092 3265 7.115520 CAGTTAATGATATACTCTGGTTCTGCG 59.884 40.741 0.00 0.00 0.00 5.18
3146 3321 1.345741 TCTCTCAGCAACCTGGAAGTG 59.654 52.381 0.00 0.00 39.61 3.16
3214 3389 3.019564 AGGCAATATCACCTTGCTGTTC 58.980 45.455 7.82 0.00 46.41 3.18
3397 3572 5.472148 CATGTGGCTTCTTGCTTCAATTTA 58.528 37.500 0.00 0.00 42.39 1.40
3401 3576 1.614903 CCATGTGGCTTCTTGCTTCAA 59.385 47.619 0.00 0.00 42.39 2.69
3460 3635 2.601666 ACGAGCACAGCCTCTCCA 60.602 61.111 0.00 0.00 0.00 3.86
3542 3717 8.935844 GCAGAAAAAGAAAAGAAAAGAAAAGGA 58.064 29.630 0.00 0.00 0.00 3.36
3613 3788 2.170817 GAGGACCCCCTACTGATTCAAC 59.829 54.545 0.00 0.00 44.53 3.18
3626 3801 0.688087 ACGAATCTCTGGAGGACCCC 60.688 60.000 0.00 0.00 34.81 4.95
3686 3862 1.651240 CCTGTCGATTTGCCTGCCTG 61.651 60.000 0.00 0.00 0.00 4.85
3691 3867 2.114616 AGATCTCCTGTCGATTTGCCT 58.885 47.619 0.00 0.00 0.00 4.75
3703 3879 1.008206 ACCTGGCTTCTCAGATCTCCT 59.992 52.381 0.00 0.00 36.93 3.69
3741 3917 2.947652 CAAGAAATGATGATGCTCCCGT 59.052 45.455 0.00 0.00 0.00 5.28
3834 4011 2.457366 ACAGACTGTGACCGAATTCC 57.543 50.000 7.47 0.00 0.00 3.01
3844 4021 2.038952 TCAATGGGAGGAACAGACTGTG 59.961 50.000 9.33 0.00 0.00 3.66
3863 4043 1.754226 GCTTCCACAACAAACCCTTCA 59.246 47.619 0.00 0.00 0.00 3.02
3901 4081 2.508716 ACTAGAGATCTACCCACCGACA 59.491 50.000 0.00 0.00 0.00 4.35
3976 4156 1.434555 TTTACAACCATGCCGACTCG 58.565 50.000 0.00 0.00 0.00 4.18
4109 4292 6.406400 CGGGTTAAAATGGCCAATTCAGAATA 60.406 38.462 10.96 0.00 0.00 1.75
4167 4350 3.102097 GCTATGGCGACCAACAGC 58.898 61.111 15.02 15.02 36.95 4.40
4232 4419 5.527214 TGTAATTCAGTTGAACTGTGACCAG 59.473 40.000 23.17 0.00 46.03 4.00
4273 4460 2.989881 GCATTCAGCAGCAGCAGCA 61.990 57.895 12.92 0.00 45.49 4.41
4274 4461 2.202623 GCATTCAGCAGCAGCAGC 60.203 61.111 3.17 0.46 45.49 5.25
4354 4543 2.281070 CATCCGCCCATCCTTCGG 60.281 66.667 0.00 0.00 44.16 4.30


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

AutoCloner maintained by Alex Coulton.