Multiple sequence alignment - TraesCS4B01G124500

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 TraesCS4B01G124500 chr4B 100.000 6847 0 0 1 6847 149733247 149726401 0.000000e+00 12645
1 TraesCS4B01G124500 chr4B 98.245 6724 95 12 1 6710 261499260 261492546 0.000000e+00 11742
2 TraesCS4B01G124500 chr4B 98.202 6728 87 16 1 6710 14719145 14712434 0.000000e+00 11723
3 TraesCS4B01G124500 chr4B 99.315 146 0 1 6702 6847 261475790 261475646 5.270000e-66 263
4 TraesCS4B01G124500 chr4B 98.639 147 0 2 6702 6847 417550566 417550711 6.810000e-65 259
5 TraesCS4B01G124500 chr2A 98.410 6730 81 13 1 6710 687279601 687272878 0.000000e+00 11812
6 TraesCS4B01G124500 chr2A 99.315 146 0 1 6702 6847 687266554 687266410 5.270000e-66 263
7 TraesCS4B01G124500 chr2A 98.639 147 0 2 6702 6847 389203673 389203528 6.810000e-65 259
8 TraesCS4B01G124500 chr5A 98.394 6725 79 15 1 6710 294227000 294233710 0.000000e+00 11793
9 TraesCS4B01G124500 chr5A 98.202 6731 94 14 1 6710 9618907 9625631 0.000000e+00 11734
10 TraesCS4B01G124500 chr5A 99.315 146 0 1 6702 6847 294240033 294240177 5.270000e-66 263
11 TraesCS4B01G124500 chr5A 98.649 148 0 2 6702 6847 9632598 9632745 1.890000e-65 261
12 TraesCS4B01G124500 chr5A 98.649 148 0 2 6702 6847 9637281 9637428 1.890000e-65 261
13 TraesCS4B01G124500 chr5A 99.310 145 0 1 6702 6846 17471134 17471277 1.890000e-65 261
14 TraesCS4B01G124500 chr2B 98.172 6730 91 17 1 6710 741902557 741909274 0.000000e+00 11718
15 TraesCS4B01G124500 chr2B 97.963 6726 82 18 1 6710 608467354 608460668 0.000000e+00 11611
16 TraesCS4B01G124500 chr2B 98.223 6640 84 10 83 6710 99558154 99564771 0.000000e+00 11577
17 TraesCS4B01G124500 chr7A 98.144 6734 90 19 1 6710 23298660 23291938 0.000000e+00 11710
18 TraesCS4B01G124500 chr7A 95.097 1591 74 2 5121 6707 675349167 675350757 0.000000e+00 2503
19 TraesCS4B01G124500 chr1A 98.054 6732 100 15 1 6710 127080742 127087464 0.000000e+00 11677
20 TraesCS4B01G124500 chr1A 98.009 6729 106 15 1 6710 255464230 255470949 0.000000e+00 11659
21 TraesCS4B01G124500 chr1A 98.639 147 0 2 6702 6847 255477275 255477420 6.810000e-65 259
22 TraesCS4B01G124500 chr1B 98.138 4725 69 7 2000 6710 637609065 637613784 0.000000e+00 8220
23 TraesCS4B01G124500 chr1D 94.694 1093 50 5 5620 6710 58460923 58462009 0.000000e+00 1690
24 TraesCS4B01G124500 chr5D 93.956 1092 57 5 5620 6710 526640642 526639559 0.000000e+00 1642
25 TraesCS4B01G124500 chr4D 93.681 1092 64 4 5620 6710 19166394 19167481 0.000000e+00 1629


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 TraesCS4B01G124500 chr4B 149726401 149733247 6846 True 12645 12645 100.000 1 6847 1 chr4B.!!$R2 6846
1 TraesCS4B01G124500 chr4B 261492546 261499260 6714 True 11742 11742 98.245 1 6710 1 chr4B.!!$R4 6709
2 TraesCS4B01G124500 chr4B 14712434 14719145 6711 True 11723 11723 98.202 1 6710 1 chr4B.!!$R1 6709
3 TraesCS4B01G124500 chr2A 687272878 687279601 6723 True 11812 11812 98.410 1 6710 1 chr2A.!!$R3 6709
4 TraesCS4B01G124500 chr5A 294227000 294233710 6710 False 11793 11793 98.394 1 6710 1 chr5A.!!$F5 6709
5 TraesCS4B01G124500 chr5A 9618907 9625631 6724 False 11734 11734 98.202 1 6710 1 chr5A.!!$F1 6709
6 TraesCS4B01G124500 chr2B 741902557 741909274 6717 False 11718 11718 98.172 1 6710 1 chr2B.!!$F2 6709
7 TraesCS4B01G124500 chr2B 608460668 608467354 6686 True 11611 11611 97.963 1 6710 1 chr2B.!!$R1 6709
8 TraesCS4B01G124500 chr2B 99558154 99564771 6617 False 11577 11577 98.223 83 6710 1 chr2B.!!$F1 6627
9 TraesCS4B01G124500 chr7A 23291938 23298660 6722 True 11710 11710 98.144 1 6710 1 chr7A.!!$R1 6709
10 TraesCS4B01G124500 chr7A 675349167 675350757 1590 False 2503 2503 95.097 5121 6707 1 chr7A.!!$F1 1586
11 TraesCS4B01G124500 chr1A 127080742 127087464 6722 False 11677 11677 98.054 1 6710 1 chr1A.!!$F1 6709
12 TraesCS4B01G124500 chr1A 255464230 255470949 6719 False 11659 11659 98.009 1 6710 1 chr1A.!!$F2 6709
13 TraesCS4B01G124500 chr1B 637609065 637613784 4719 False 8220 8220 98.138 2000 6710 1 chr1B.!!$F1 4710
14 TraesCS4B01G124500 chr1D 58460923 58462009 1086 False 1690 1690 94.694 5620 6710 1 chr1D.!!$F1 1090
15 TraesCS4B01G124500 chr5D 526639559 526640642 1083 True 1642 1642 93.956 5620 6710 1 chr5D.!!$R1 1090
16 TraesCS4B01G124500 chr4D 19166394 19167481 1087 False 1629 1629 93.681 5620 6710 1 chr4D.!!$F1 1090

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
519 525 1.620819 CTGTGTGCAACTAGGGACTCT 59.379 52.381 0.00 0.0 38.04 3.24 F
1203 1215 3.941836 GCTAATCGCCAGCCACGC 61.942 66.667 0.00 0.0 32.68 5.34 F
2553 2573 0.610509 TTTTATGGCCTGGCTTGCGA 60.611 50.000 19.68 0.0 0.00 5.10 F
3477 3507 1.964448 CACGGAGCAGACACCACTA 59.036 57.895 0.00 0.0 0.00 2.74 F
5032 5126 0.338120 AGCTCCCAGACCTAAGCTCT 59.662 55.000 0.00 0.0 41.05 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1469 8.152898 ACTGCTGCATAATTTCATCACTATCTA 58.847 33.333 1.31 0.0 0.00 1.98 R
3136 3158 4.099266 TGTGCAGATTGCCAAACTTAAAGT 59.901 37.500 0.00 0.0 44.23 2.66 R
3833 3867 2.921754 ACGACTAATACGCACTTTCTGC 59.078 45.455 0.00 0.0 43.21 4.26 R
5346 5440 0.677098 TCTCTCGTCTCTGAACCCCG 60.677 60.000 0.00 0.0 0.00 5.73 R
5988 6095 1.004277 GGGTGTGGCAATTCTCTGGTA 59.996 52.381 0.00 0.0 0.00 3.25 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
43 44 3.998341 GGCTGATTTCGTAGTTGGTGTTA 59.002 43.478 0.00 0.00 0.00 2.41
47 48 6.617953 GCTGATTTCGTAGTTGGTGTTAAGAC 60.618 42.308 0.00 0.00 0.00 3.01
334 338 6.887013 TCACTGTTTTTGTACTAGGTGGTTA 58.113 36.000 0.00 0.00 0.00 2.85
519 525 1.620819 CTGTGTGCAACTAGGGACTCT 59.379 52.381 0.00 0.00 38.04 3.24
1203 1215 3.941836 GCTAATCGCCAGCCACGC 61.942 66.667 0.00 0.00 32.68 5.34
2553 2573 0.610509 TTTTATGGCCTGGCTTGCGA 60.611 50.000 19.68 0.00 0.00 5.10
3184 3206 6.991531 ACATGTTCATTTTAAATTGGCACACT 59.008 30.769 13.59 5.00 39.29 3.55
3477 3507 1.964448 CACGGAGCAGACACCACTA 59.036 57.895 0.00 0.00 0.00 2.74
4476 4568 1.621672 GGCAGTGAGAGGGGAGAAGG 61.622 65.000 0.00 0.00 0.00 3.46
4922 5015 6.014584 TGACAAGAGCCTGTTCTTATCAACTA 60.015 38.462 2.74 0.00 37.59 2.24
5032 5126 0.338120 AGCTCCCAGACCTAAGCTCT 59.662 55.000 0.00 0.00 41.05 4.09
5048 5142 2.105006 CTCTAGCAAGAGCAAGGCAA 57.895 50.000 0.00 0.00 42.79 4.52
5069 5163 0.916086 ATCCACGGCAAACCCTCATA 59.084 50.000 0.00 0.00 0.00 2.15
5346 5440 2.029020 GGGAACAGGCCACAAAAGATTC 60.029 50.000 5.01 0.00 0.00 2.52
5618 5713 3.576982 TCCAACTATCAAAGTGTCGTCCT 59.423 43.478 0.00 0.00 38.88 3.85
5715 5810 2.482336 CGCCAACTACAACACTATTGCA 59.518 45.455 0.00 0.00 0.00 4.08
5809 5904 9.205719 CGAAGATCAAACTCTTATCATGATGAT 57.794 33.333 18.72 13.10 40.72 2.45
5988 6095 5.625150 AGCTCAAGAACTAGATGTTGGTTT 58.375 37.500 9.56 0.00 39.30 3.27
6327 6434 3.769739 AGTATGTTGCACAGAACAGGA 57.230 42.857 0.00 0.00 39.18 3.86
6710 6832 5.712152 AGGAGTTTTGAGCCATGTTTTAG 57.288 39.130 0.00 0.00 0.00 1.85
6711 6833 5.140454 AGGAGTTTTGAGCCATGTTTTAGT 58.860 37.500 0.00 0.00 0.00 2.24
6712 6834 5.598417 AGGAGTTTTGAGCCATGTTTTAGTT 59.402 36.000 0.00 0.00 0.00 2.24
6713 6835 5.691754 GGAGTTTTGAGCCATGTTTTAGTTG 59.308 40.000 0.00 0.00 0.00 3.16
6714 6836 5.049828 AGTTTTGAGCCATGTTTTAGTTGC 58.950 37.500 0.00 0.00 0.00 4.17
6715 6837 4.662468 TTTGAGCCATGTTTTAGTTGCA 57.338 36.364 0.00 0.00 0.00 4.08
6716 6838 3.641437 TGAGCCATGTTTTAGTTGCAC 57.359 42.857 0.00 0.00 0.00 4.57
6717 6839 2.954989 TGAGCCATGTTTTAGTTGCACA 59.045 40.909 0.00 0.00 0.00 4.57
6718 6840 3.573538 TGAGCCATGTTTTAGTTGCACAT 59.426 39.130 0.00 0.00 0.00 3.21
6719 6841 4.039004 TGAGCCATGTTTTAGTTGCACATT 59.961 37.500 0.00 0.00 0.00 2.71
6720 6842 4.959723 AGCCATGTTTTAGTTGCACATTT 58.040 34.783 0.00 0.00 0.00 2.32
6721 6843 6.095432 AGCCATGTTTTAGTTGCACATTTA 57.905 33.333 0.00 0.00 0.00 1.40
6722 6844 6.700352 AGCCATGTTTTAGTTGCACATTTAT 58.300 32.000 0.00 0.00 0.00 1.40
6723 6845 6.591062 AGCCATGTTTTAGTTGCACATTTATG 59.409 34.615 0.00 0.00 0.00 1.90
6724 6846 6.589523 GCCATGTTTTAGTTGCACATTTATGA 59.410 34.615 0.00 0.00 0.00 2.15
6725 6847 7.117523 GCCATGTTTTAGTTGCACATTTATGAA 59.882 33.333 0.00 0.00 0.00 2.57
6726 6848 9.153721 CCATGTTTTAGTTGCACATTTATGAAT 57.846 29.630 0.00 0.00 0.00 2.57
6733 6855 7.945033 AGTTGCACATTTATGAATTTTTCGT 57.055 28.000 0.00 0.00 0.00 3.85
6734 6856 8.364129 AGTTGCACATTTATGAATTTTTCGTT 57.636 26.923 0.00 0.00 0.00 3.85
6735 6857 8.274939 AGTTGCACATTTATGAATTTTTCGTTG 58.725 29.630 0.00 0.00 0.00 4.10
6736 6858 6.588552 TGCACATTTATGAATTTTTCGTTGC 58.411 32.000 0.00 0.00 31.40 4.17
6737 6859 6.201615 TGCACATTTATGAATTTTTCGTTGCA 59.798 30.769 0.00 0.00 35.95 4.08
6738 6860 6.516017 GCACATTTATGAATTTTTCGTTGCAC 59.484 34.615 0.00 0.00 31.21 4.57
6739 6861 7.562412 CACATTTATGAATTTTTCGTTGCACA 58.438 30.769 0.00 0.00 0.00 4.57
6740 6862 8.222433 CACATTTATGAATTTTTCGTTGCACAT 58.778 29.630 0.00 0.00 0.00 3.21
6741 6863 8.222433 ACATTTATGAATTTTTCGTTGCACATG 58.778 29.630 0.00 0.00 0.00 3.21
6742 6864 7.706281 TTTATGAATTTTTCGTTGCACATGT 57.294 28.000 0.00 0.00 0.00 3.21
6743 6865 7.706281 TTATGAATTTTTCGTTGCACATGTT 57.294 28.000 0.00 0.00 0.00 2.71
6744 6866 5.633996 TGAATTTTTCGTTGCACATGTTC 57.366 34.783 0.00 0.00 0.00 3.18
6745 6867 5.105063 TGAATTTTTCGTTGCACATGTTCA 58.895 33.333 0.00 0.00 0.00 3.18
6746 6868 5.578336 TGAATTTTTCGTTGCACATGTTCAA 59.422 32.000 6.83 6.83 0.00 2.69
6747 6869 4.831741 TTTTTCGTTGCACATGTTCAAC 57.168 36.364 25.57 25.57 39.20 3.18
6748 6870 3.494045 TTTCGTTGCACATGTTCAACA 57.506 38.095 31.27 19.87 41.80 3.33
6749 6871 3.494045 TTCGTTGCACATGTTCAACAA 57.506 38.095 31.27 23.17 41.80 2.83
6750 6872 3.494045 TCGTTGCACATGTTCAACAAA 57.506 38.095 31.27 20.31 41.80 2.83
6751 6873 3.433709 TCGTTGCACATGTTCAACAAAG 58.566 40.909 31.27 19.83 41.80 2.77
6752 6874 2.034675 CGTTGCACATGTTCAACAAAGC 60.035 45.455 31.27 15.68 41.80 3.51
6753 6875 2.928757 GTTGCACATGTTCAACAAAGCA 59.071 40.909 28.89 15.91 41.46 3.91
6754 6876 3.455990 TGCACATGTTCAACAAAGCAT 57.544 38.095 9.94 0.00 31.56 3.79
6755 6877 3.794717 TGCACATGTTCAACAAAGCATT 58.205 36.364 9.94 0.00 31.56 3.56
6756 6878 3.556365 TGCACATGTTCAACAAAGCATTG 59.444 39.130 9.94 0.00 42.46 2.82
6757 6879 3.059461 GCACATGTTCAACAAAGCATTGG 60.059 43.478 6.62 0.00 41.01 3.16
6758 6880 3.495377 CACATGTTCAACAAAGCATTGGG 59.505 43.478 6.62 0.00 41.01 4.12
6759 6881 2.237393 TGTTCAACAAAGCATTGGGC 57.763 45.000 6.62 0.00 41.01 5.36
6803 6925 8.980143 TTTGCAAATAATAACTAGAAGTTGGC 57.020 30.769 8.05 0.00 39.11 4.52
6804 6926 7.938140 TGCAAATAATAACTAGAAGTTGGCT 57.062 32.000 0.00 0.00 39.11 4.75
6805 6927 8.348285 TGCAAATAATAACTAGAAGTTGGCTT 57.652 30.769 0.00 0.00 39.11 4.35
6806 6928 8.802267 TGCAAATAATAACTAGAAGTTGGCTTT 58.198 29.630 0.00 0.00 39.11 3.51
6814 6936 9.686683 ATAACTAGAAGTTGGCTTTAATCATGT 57.313 29.630 0.00 0.00 39.11 3.21
6815 6937 8.409358 AACTAGAAGTTGGCTTTAATCATGTT 57.591 30.769 0.00 0.00 37.00 2.71
6816 6938 8.409358 ACTAGAAGTTGGCTTTAATCATGTTT 57.591 30.769 0.00 0.00 34.61 2.83
6817 6939 8.860088 ACTAGAAGTTGGCTTTAATCATGTTTT 58.140 29.630 0.00 0.00 34.61 2.43
6823 6945 9.218440 AGTTGGCTTTAATCATGTTTTAATTGG 57.782 29.630 0.00 0.00 0.00 3.16
6824 6946 7.608308 TGGCTTTAATCATGTTTTAATTGGC 57.392 32.000 0.00 7.86 0.00 4.52
6825 6947 6.597280 TGGCTTTAATCATGTTTTAATTGGCC 59.403 34.615 19.95 19.95 34.00 5.36
6826 6948 6.597280 GGCTTTAATCATGTTTTAATTGGCCA 59.403 34.615 0.00 0.00 33.82 5.36
6827 6949 7.201635 GGCTTTAATCATGTTTTAATTGGCCAG 60.202 37.037 5.11 0.00 33.82 4.85
6828 6950 7.548780 GCTTTAATCATGTTTTAATTGGCCAGA 59.451 33.333 5.11 0.00 0.00 3.86
6829 6951 9.603921 CTTTAATCATGTTTTAATTGGCCAGAT 57.396 29.630 5.11 0.75 0.00 2.90
6832 6954 8.947055 AATCATGTTTTAATTGGCCAGATAAC 57.053 30.769 5.11 8.29 0.00 1.89
6833 6955 7.716799 TCATGTTTTAATTGGCCAGATAACT 57.283 32.000 5.11 0.00 0.00 2.24
6834 6956 7.771183 TCATGTTTTAATTGGCCAGATAACTC 58.229 34.615 5.11 6.02 0.00 3.01
6835 6957 6.189677 TGTTTTAATTGGCCAGATAACTCG 57.810 37.500 5.11 0.00 0.00 4.18
6836 6958 5.708230 TGTTTTAATTGGCCAGATAACTCGT 59.292 36.000 5.11 0.00 0.00 4.18
6837 6959 6.207810 TGTTTTAATTGGCCAGATAACTCGTT 59.792 34.615 5.11 0.00 0.00 3.85
6838 6960 6.827586 TTTAATTGGCCAGATAACTCGTTT 57.172 33.333 5.11 0.00 0.00 3.60
6839 6961 6.827586 TTAATTGGCCAGATAACTCGTTTT 57.172 33.333 5.11 0.00 0.00 2.43
6840 6962 5.722021 AATTGGCCAGATAACTCGTTTTT 57.278 34.783 5.11 0.00 0.00 1.94
6841 6963 6.827586 AATTGGCCAGATAACTCGTTTTTA 57.172 33.333 5.11 0.00 0.00 1.52
6842 6964 5.873179 TTGGCCAGATAACTCGTTTTTAG 57.127 39.130 5.11 0.00 0.00 1.85
6843 6965 4.901868 TGGCCAGATAACTCGTTTTTAGT 58.098 39.130 0.00 0.00 0.00 2.24
6844 6966 5.310451 TGGCCAGATAACTCGTTTTTAGTT 58.690 37.500 0.00 0.00 40.25 2.24
6845 6967 5.180492 TGGCCAGATAACTCGTTTTTAGTTG 59.820 40.000 0.00 0.00 37.71 3.16
6846 6968 5.391629 GGCCAGATAACTCGTTTTTAGTTGG 60.392 44.000 0.00 0.00 37.71 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.320164 TGTGCAACTAACCACTTAAATGTCTT 59.680 34.615 0.00 0.00 38.04 3.01
47 48 7.763172 TTTTGTGCAACTAACCACTTAAATG 57.237 32.000 0.00 0.00 38.04 2.32
243 247 3.386726 AGCCAAGTACTATATGGACGCAA 59.613 43.478 15.03 0.00 36.27 4.85
334 338 5.793817 TGTGCAACTGAACACAGTATAGAT 58.206 37.500 3.33 0.00 43.00 1.98
699 707 2.923020 CCACAACAAAAGACTTGCACAC 59.077 45.455 0.00 0.00 0.00 3.82
822 830 7.556844 CCAACTGTGACAAGTAATACCTAGAT 58.443 38.462 0.00 0.00 0.00 1.98
1203 1215 2.031012 TCAACACTCTGCGCAGGG 59.969 61.111 35.18 35.18 34.32 4.45
1454 1469 8.152898 ACTGCTGCATAATTTCATCACTATCTA 58.847 33.333 1.31 0.00 0.00 1.98
1504 1519 8.514330 ACAAAAAGGTTGTTATTGACAGACTA 57.486 30.769 0.00 0.00 39.94 2.59
2553 2573 5.412904 GTGCTAGAAAAGTACTGAAGGCAAT 59.587 40.000 0.00 0.00 37.79 3.56
2827 2847 7.358830 CAAACAAAAGAAAAAGCCAAGTTCAA 58.641 30.769 0.00 0.00 0.00 2.69
3136 3158 4.099266 TGTGCAGATTGCCAAACTTAAAGT 59.901 37.500 0.00 0.00 44.23 2.66
3477 3507 3.816523 CAGCTTGCAAAATTCCACCAAAT 59.183 39.130 0.00 0.00 0.00 2.32
3598 3628 6.320434 TGTCCAACTGAATATACATCCCAA 57.680 37.500 0.00 0.00 0.00 4.12
3609 3639 9.077885 ACAAAAGTTATACATGTCCAACTGAAT 57.922 29.630 20.00 10.69 31.80 2.57
3833 3867 2.921754 ACGACTAATACGCACTTTCTGC 59.078 45.455 0.00 0.00 43.21 4.26
3843 3877 7.449827 TGTGATAAGCAAAAACGACTAATACG 58.550 34.615 0.00 0.00 0.00 3.06
4922 5015 8.770828 CATGTCAATTTGATTCTTTTCAGCTTT 58.229 29.630 1.78 0.00 0.00 3.51
5032 5126 2.086869 GATGTTGCCTTGCTCTTGCTA 58.913 47.619 0.00 0.00 40.48 3.49
5048 5142 1.303317 GAGGGTTTGCCGTGGATGT 60.303 57.895 0.00 0.00 34.97 3.06
5069 5163 3.073062 ACTGCTTTACACTTCTGGACCAT 59.927 43.478 0.00 0.00 0.00 3.55
5346 5440 0.677098 TCTCTCGTCTCTGAACCCCG 60.677 60.000 0.00 0.00 0.00 5.73
5483 5578 3.252458 GTGGTTTTGACTGTGACCATACC 59.748 47.826 0.00 0.00 43.44 2.73
5618 5713 3.627577 GGTTGCTGAAAGACAACTCTTGA 59.372 43.478 5.91 0.00 44.62 3.02
5715 5810 3.890756 TGCATCATTCACTGACTTGGTTT 59.109 39.130 0.00 0.00 36.48 3.27
5809 5904 2.359850 GGTGCATCGCAGAACCCA 60.360 61.111 0.00 0.00 43.58 4.51
5988 6095 1.004277 GGGTGTGGCAATTCTCTGGTA 59.996 52.381 0.00 0.00 0.00 3.25
6327 6434 5.897377 AAGAACAGTGTGCAACTAAAAGT 57.103 34.783 3.49 0.00 36.83 2.66
6710 6832 7.058241 GCAACGAAAAATTCATAAATGTGCAAC 59.942 33.333 0.00 0.00 37.35 4.17
6711 6833 7.068341 GCAACGAAAAATTCATAAATGTGCAA 58.932 30.769 0.00 0.00 0.00 4.08
6712 6834 6.201615 TGCAACGAAAAATTCATAAATGTGCA 59.798 30.769 0.00 0.00 0.00 4.57
6713 6835 6.516017 GTGCAACGAAAAATTCATAAATGTGC 59.484 34.615 0.00 0.00 0.00 4.57
6714 6836 7.562412 TGTGCAACGAAAAATTCATAAATGTG 58.438 30.769 0.00 0.00 42.39 3.21
6715 6837 7.706281 TGTGCAACGAAAAATTCATAAATGT 57.294 28.000 0.00 0.00 42.39 2.71
6716 6838 8.222433 ACATGTGCAACGAAAAATTCATAAATG 58.778 29.630 0.00 0.00 42.39 2.32
6717 6839 8.309163 ACATGTGCAACGAAAAATTCATAAAT 57.691 26.923 0.00 0.00 42.39 1.40
6718 6840 7.706281 ACATGTGCAACGAAAAATTCATAAA 57.294 28.000 0.00 0.00 42.39 1.40
6719 6841 7.436376 TGAACATGTGCAACGAAAAATTCATAA 59.564 29.630 3.25 0.00 42.39 1.90
6720 6842 6.920210 TGAACATGTGCAACGAAAAATTCATA 59.080 30.769 3.25 0.00 42.39 2.15
6721 6843 5.752472 TGAACATGTGCAACGAAAAATTCAT 59.248 32.000 3.25 0.00 42.39 2.57
6722 6844 5.105063 TGAACATGTGCAACGAAAAATTCA 58.895 33.333 3.25 0.00 42.39 2.57
6723 6845 5.633996 TGAACATGTGCAACGAAAAATTC 57.366 34.783 3.25 0.00 42.39 2.17
6724 6846 5.349817 TGTTGAACATGTGCAACGAAAAATT 59.650 32.000 34.11 1.45 45.47 1.82
6725 6847 4.867047 TGTTGAACATGTGCAACGAAAAAT 59.133 33.333 34.11 1.66 45.47 1.82
6726 6848 4.237724 TGTTGAACATGTGCAACGAAAAA 58.762 34.783 34.11 20.00 45.47 1.94
6727 6849 3.838120 TGTTGAACATGTGCAACGAAAA 58.162 36.364 34.11 20.32 45.47 2.29
6728 6850 3.494045 TGTTGAACATGTGCAACGAAA 57.506 38.095 34.11 20.63 45.47 3.46
6729 6851 3.494045 TTGTTGAACATGTGCAACGAA 57.506 38.095 34.11 27.13 45.47 3.85
6730 6852 3.433709 CTTTGTTGAACATGTGCAACGA 58.566 40.909 34.11 31.68 45.47 3.85
6731 6853 2.034675 GCTTTGTTGAACATGTGCAACG 60.035 45.455 34.11 24.65 45.47 4.10
6732 6854 2.928757 TGCTTTGTTGAACATGTGCAAC 59.071 40.909 34.08 34.08 43.45 4.17
6733 6855 3.242549 TGCTTTGTTGAACATGTGCAA 57.757 38.095 15.66 15.66 29.82 4.08
6734 6856 2.955477 TGCTTTGTTGAACATGTGCA 57.045 40.000 1.03 1.03 0.00 4.57
6735 6857 3.059461 CCAATGCTTTGTTGAACATGTGC 60.059 43.478 0.00 0.00 0.00 4.57
6736 6858 3.495377 CCCAATGCTTTGTTGAACATGTG 59.505 43.478 0.00 0.00 0.00 3.21
6737 6859 3.731089 CCCAATGCTTTGTTGAACATGT 58.269 40.909 11.03 0.00 0.00 3.21
6738 6860 2.481185 GCCCAATGCTTTGTTGAACATG 59.519 45.455 11.03 0.00 36.87 3.21
6739 6861 2.104451 TGCCCAATGCTTTGTTGAACAT 59.896 40.909 11.03 0.00 42.00 2.71
6740 6862 1.483827 TGCCCAATGCTTTGTTGAACA 59.516 42.857 11.03 0.00 42.00 3.18
6741 6863 2.137523 CTGCCCAATGCTTTGTTGAAC 58.862 47.619 11.03 0.00 42.00 3.18
6742 6864 1.761784 ACTGCCCAATGCTTTGTTGAA 59.238 42.857 11.03 0.00 42.00 2.69
6743 6865 1.340889 GACTGCCCAATGCTTTGTTGA 59.659 47.619 11.03 0.00 42.00 3.18
6744 6866 1.068895 TGACTGCCCAATGCTTTGTTG 59.931 47.619 11.03 3.71 42.00 3.33
6745 6867 1.412079 TGACTGCCCAATGCTTTGTT 58.588 45.000 11.03 0.00 42.00 2.83
6746 6868 1.412079 TTGACTGCCCAATGCTTTGT 58.588 45.000 11.03 0.00 42.00 2.83
6747 6869 2.754946 ATTGACTGCCCAATGCTTTG 57.245 45.000 5.37 5.37 42.00 2.77
6748 6870 3.775261 AAATTGACTGCCCAATGCTTT 57.225 38.095 0.00 0.00 42.00 3.51
6749 6871 3.775261 AAAATTGACTGCCCAATGCTT 57.225 38.095 0.00 0.00 42.00 3.91
6750 6872 3.775261 AAAAATTGACTGCCCAATGCT 57.225 38.095 0.00 0.00 42.00 3.79
6777 6899 9.418045 GCCAACTTCTAGTTATTATTTGCAAAA 57.582 29.630 17.19 0.11 36.03 2.44
6778 6900 8.802267 AGCCAACTTCTAGTTATTATTTGCAAA 58.198 29.630 15.44 15.44 36.03 3.68
6779 6901 8.348285 AGCCAACTTCTAGTTATTATTTGCAA 57.652 30.769 0.00 0.00 36.03 4.08
6780 6902 7.938140 AGCCAACTTCTAGTTATTATTTGCA 57.062 32.000 0.00 0.00 36.03 4.08
6788 6910 9.686683 ACATGATTAAAGCCAACTTCTAGTTAT 57.313 29.630 0.00 0.00 36.03 1.89
6789 6911 9.515226 AACATGATTAAAGCCAACTTCTAGTTA 57.485 29.630 0.00 0.00 36.03 2.24
6790 6912 8.409358 AACATGATTAAAGCCAACTTCTAGTT 57.591 30.769 0.00 0.00 39.39 2.24
6791 6913 8.409358 AAACATGATTAAAGCCAACTTCTAGT 57.591 30.769 0.00 0.00 34.05 2.57
6797 6919 9.218440 CCAATTAAAACATGATTAAAGCCAACT 57.782 29.630 0.00 0.00 0.00 3.16
6798 6920 7.962373 GCCAATTAAAACATGATTAAAGCCAAC 59.038 33.333 0.00 0.00 0.00 3.77
6799 6921 7.120432 GGCCAATTAAAACATGATTAAAGCCAA 59.880 33.333 23.44 6.26 37.17 4.52
6800 6922 6.597280 GGCCAATTAAAACATGATTAAAGCCA 59.403 34.615 23.44 5.58 37.17 4.75
6801 6923 6.597280 TGGCCAATTAAAACATGATTAAAGCC 59.403 34.615 22.65 22.65 37.43 4.35
6802 6924 7.548780 TCTGGCCAATTAAAACATGATTAAAGC 59.451 33.333 7.01 9.22 0.00 3.51
6803 6925 9.603921 ATCTGGCCAATTAAAACATGATTAAAG 57.396 29.630 7.01 2.90 0.00 1.85
6807 6929 8.761689 AGTTATCTGGCCAATTAAAACATGATT 58.238 29.630 7.01 0.00 0.00 2.57
6808 6930 8.310122 AGTTATCTGGCCAATTAAAACATGAT 57.690 30.769 7.01 4.37 0.00 2.45
6809 6931 7.415095 CGAGTTATCTGGCCAATTAAAACATGA 60.415 37.037 7.01 0.00 0.00 3.07
6810 6932 6.692681 CGAGTTATCTGGCCAATTAAAACATG 59.307 38.462 7.01 0.00 0.00 3.21
6811 6933 6.377146 ACGAGTTATCTGGCCAATTAAAACAT 59.623 34.615 7.01 0.00 0.00 2.71
6812 6934 5.708230 ACGAGTTATCTGGCCAATTAAAACA 59.292 36.000 7.01 0.00 0.00 2.83
6813 6935 6.190954 ACGAGTTATCTGGCCAATTAAAAC 57.809 37.500 7.01 7.41 0.00 2.43
6814 6936 6.827586 AACGAGTTATCTGGCCAATTAAAA 57.172 33.333 7.01 0.00 0.00 1.52
6815 6937 6.827586 AAACGAGTTATCTGGCCAATTAAA 57.172 33.333 7.01 0.00 0.00 1.52
6816 6938 6.827586 AAAACGAGTTATCTGGCCAATTAA 57.172 33.333 7.01 4.82 0.00 1.40
6817 6939 6.827586 AAAAACGAGTTATCTGGCCAATTA 57.172 33.333 7.01 0.00 0.00 1.40
6818 6940 5.722021 AAAAACGAGTTATCTGGCCAATT 57.278 34.783 7.01 0.00 0.00 2.32
6819 6941 5.944007 ACTAAAAACGAGTTATCTGGCCAAT 59.056 36.000 7.01 6.27 0.00 3.16
6820 6942 5.310451 ACTAAAAACGAGTTATCTGGCCAA 58.690 37.500 7.01 0.00 0.00 4.52
6821 6943 4.901868 ACTAAAAACGAGTTATCTGGCCA 58.098 39.130 4.71 4.71 0.00 5.36
6822 6944 5.391629 CCAACTAAAAACGAGTTATCTGGCC 60.392 44.000 0.00 0.00 35.36 5.36
6823 6945 5.628134 CCAACTAAAAACGAGTTATCTGGC 58.372 41.667 0.00 0.00 35.36 4.85


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

AutoCloner maintained by Alex Coulton.