Multiple sequence alignment - TraesCS5D01G129600

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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 TraesCS5D01G129600 chr5D 100.000 6446 0 0 1 6446 204073732 204080177 0.000000e+00 11904.0
1 TraesCS5D01G129600 chr5D 87.736 742 82 8 5 741 362087145 362086408 0.000000e+00 857.0
2 TraesCS5D01G129600 chr5D 75.418 598 129 15 1481 2069 318442168 318442756 2.290000e-69 274.0
3 TraesCS5D01G129600 chr5D 96.923 65 2 0 5829 5893 204079495 204079559 6.830000e-20 110.0
4 TraesCS5D01G129600 chr5D 96.923 65 2 0 5764 5828 204079560 204079624 6.830000e-20 110.0
5 TraesCS5D01G129600 chr5A 97.942 3159 41 9 760 3909 238694181 238697324 0.000000e+00 5452.0
6 TraesCS5D01G129600 chr5A 97.460 1929 34 6 3904 5828 238697362 238699279 0.000000e+00 3277.0
7 TraesCS5D01G129600 chr5A 91.186 624 30 11 5829 6444 238699215 238699821 0.000000e+00 824.0
8 TraesCS5D01G129600 chr5A 75.251 598 130 15 1481 2069 413041601 413042189 1.070000e-67 268.0
9 TraesCS5D01G129600 chr5A 94.595 37 2 0 6144 6180 238699463 238699499 2.510000e-04 58.4
10 TraesCS5D01G129600 chr5B 97.645 3142 61 4 771 3909 208257545 208260676 0.000000e+00 5380.0
11 TraesCS5D01G129600 chr5B 97.466 1934 31 4 3909 5828 208260719 208262648 0.000000e+00 3284.0
12 TraesCS5D01G129600 chr5B 85.826 642 38 25 5829 6444 208262584 208263198 3.280000e-177 632.0
13 TraesCS5D01G129600 chr5B 75.084 598 131 15 1481 2069 368486467 368487055 4.960000e-66 263.0
14 TraesCS5D01G129600 chr3D 90.679 751 54 11 1 741 217534176 217533432 0.000000e+00 985.0
15 TraesCS5D01G129600 chr3D 89.382 744 74 4 1 741 385131723 385132464 0.000000e+00 931.0
16 TraesCS5D01G129600 chr3D 88.369 748 77 8 1 741 257855768 257855024 0.000000e+00 891.0
17 TraesCS5D01G129600 chr3D 84.409 186 25 4 6261 6444 62073887 62073704 5.130000e-41 180.0
18 TraesCS5D01G129600 chr2D 89.879 741 71 4 1 737 346817794 346817054 0.000000e+00 950.0
19 TraesCS5D01G129600 chr2D 89.229 752 66 11 1 741 114473491 114472744 0.000000e+00 926.0
20 TraesCS5D01G129600 chr2D 94.737 38 1 1 6266 6303 609868400 609868364 2.510000e-04 58.4
21 TraesCS5D01G129600 chr6D 89.023 747 75 5 1 741 94431041 94430296 0.000000e+00 918.0
22 TraesCS5D01G129600 chr6B 88.664 741 75 8 5 741 258356905 258357640 0.000000e+00 894.0
23 TraesCS5D01G129600 chr1D 88.086 747 78 10 1 741 191553212 191552471 0.000000e+00 876.0
24 TraesCS5D01G129600 chr1D 79.585 289 56 3 4311 4597 430413539 430413826 3.050000e-48 204.0
25 TraesCS5D01G129600 chr3A 88.172 186 19 3 6261 6444 503024762 503024578 1.090000e-52 219.0
26 TraesCS5D01G129600 chr3A 85.484 186 25 2 6261 6444 700743675 700743490 6.600000e-45 193.0
27 TraesCS5D01G129600 chr1B 81.818 176 18 11 6265 6428 638894300 638894127 1.130000e-27 135.0
28 TraesCS5D01G129600 chr4A 78.836 189 25 12 6262 6445 46050612 46050790 5.280000e-21 113.0
29 TraesCS5D01G129600 chr3B 96.078 51 1 1 6262 6311 172315696 172315746 1.490000e-11 82.4


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 TraesCS5D01G129600 chr5D 204073732 204080177 6445 False 4041.333333 11904 97.948667 1 6446 3 chr5D.!!$F2 6445
1 TraesCS5D01G129600 chr5D 362086408 362087145 737 True 857.000000 857 87.736000 5 741 1 chr5D.!!$R1 736
2 TraesCS5D01G129600 chr5D 318442168 318442756 588 False 274.000000 274 75.418000 1481 2069 1 chr5D.!!$F1 588
3 TraesCS5D01G129600 chr5A 238694181 238699821 5640 False 2402.850000 5452 95.295750 760 6444 4 chr5A.!!$F2 5684
4 TraesCS5D01G129600 chr5A 413041601 413042189 588 False 268.000000 268 75.251000 1481 2069 1 chr5A.!!$F1 588
5 TraesCS5D01G129600 chr5B 208257545 208263198 5653 False 3098.666667 5380 93.645667 771 6444 3 chr5B.!!$F2 5673
6 TraesCS5D01G129600 chr5B 368486467 368487055 588 False 263.000000 263 75.084000 1481 2069 1 chr5B.!!$F1 588
7 TraesCS5D01G129600 chr3D 217533432 217534176 744 True 985.000000 985 90.679000 1 741 1 chr3D.!!$R2 740
8 TraesCS5D01G129600 chr3D 385131723 385132464 741 False 931.000000 931 89.382000 1 741 1 chr3D.!!$F1 740
9 TraesCS5D01G129600 chr3D 257855024 257855768 744 True 891.000000 891 88.369000 1 741 1 chr3D.!!$R3 740
10 TraesCS5D01G129600 chr2D 346817054 346817794 740 True 950.000000 950 89.879000 1 737 1 chr2D.!!$R2 736
11 TraesCS5D01G129600 chr2D 114472744 114473491 747 True 926.000000 926 89.229000 1 741 1 chr2D.!!$R1 740
12 TraesCS5D01G129600 chr6D 94430296 94431041 745 True 918.000000 918 89.023000 1 741 1 chr6D.!!$R1 740
13 TraesCS5D01G129600 chr6B 258356905 258357640 735 False 894.000000 894 88.664000 5 741 1 chr6B.!!$F1 736
14 TraesCS5D01G129600 chr1D 191552471 191553212 741 True 876.000000 876 88.086000 1 741 1 chr1D.!!$R1 740

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
547 557 0.038310 AGGCAAGTTCAAGGGCTACC 59.962 55.000 0.00 0.00 35.48 3.18 F
890 903 0.321996 ACGGACTTGCCTCTCCTTTC 59.678 55.000 0.00 0.00 0.00 2.62 F
1676 1699 0.548682 ACATGCTCCCCTTCACCTCT 60.549 55.000 0.00 0.00 0.00 3.69 F
1886 1909 1.152368 CAGCCCCTTCCCATCATCC 59.848 63.158 0.00 0.00 0.00 3.51 F
2471 2494 2.051334 TGGCATATTACACTGTGGCC 57.949 50.000 13.09 13.72 40.29 5.36 F
3955 4024 5.535783 TGAACATTCATGTGTCAACCTCATT 59.464 36.000 0.00 0.00 41.61 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1443 1.533033 TCGTCCCAGCAGAAGGTCA 60.533 57.895 0.00 0.0 0.00 4.02 R
2795 2818 1.221293 CCTGCAGCTTCTCTCCAGG 59.779 63.158 8.66 0.0 37.35 4.45 R
3363 3388 3.070878 TGTCACCACGTCATATGCCATAT 59.929 43.478 0.00 0.0 0.00 1.78 R
3403 3428 9.918630 AAGATCTGAGAAATTAAATGGTTGTTG 57.081 29.630 0.00 0.0 0.00 3.33 R
4109 4179 1.639722 TACTGCTTGACTGGGCTACA 58.360 50.000 0.00 0.0 0.00 2.74 R
5818 5905 0.250124 TTTGTGTACTGAGGGTGCGG 60.250 55.000 0.00 0.0 33.14 5.69 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
54 55 1.623311 GTTGGGGTTGGGGAAATTCTG 59.377 52.381 0.00 0.00 0.00 3.02
57 58 1.077169 GGGGTTGGGGAAATTCTGAGT 59.923 52.381 0.00 0.00 0.00 3.41
96 97 2.981350 GGCCAAACCCGCTCGAAA 60.981 61.111 0.00 0.00 0.00 3.46
150 151 1.740297 GTCTGGAGTCGACTCAGCTA 58.260 55.000 38.52 23.38 44.60 3.32
237 238 2.124570 AGCGCTAGCCATGTTGGG 60.125 61.111 8.99 0.00 46.67 4.12
315 321 5.952347 TTTGGGGATCTAAGTCTCCTTAC 57.048 43.478 0.00 0.00 39.63 2.34
390 398 1.157257 ATGTATTCATTCGGCGCGCA 61.157 50.000 34.42 13.69 0.00 6.09
424 433 5.126067 CGACCACAGGAAGGAATCATAAAT 58.874 41.667 0.00 0.00 0.00 1.40
426 435 6.078456 ACCACAGGAAGGAATCATAAATGA 57.922 37.500 0.00 0.00 41.70 2.57
440 449 5.125356 TCATAAATGATGCACATCGAGGTT 58.875 37.500 0.00 0.00 40.63 3.50
450 459 2.363680 CACATCGAGGTTAGAGCCAGAT 59.636 50.000 0.00 0.00 0.00 2.90
507 517 1.468520 GCAAAGCCGAAGACATAAGCA 59.531 47.619 0.00 0.00 0.00 3.91
547 557 0.038310 AGGCAAGTTCAAGGGCTACC 59.962 55.000 0.00 0.00 35.48 3.18
560 570 1.076923 GCTACCGAGGGAGTCCTGA 60.077 63.158 9.58 0.00 45.05 3.86
654 666 2.363975 CCTTTCCCCGTCCGGATGA 61.364 63.158 25.65 8.48 37.50 2.92
672 684 1.280133 TGAGACTCTCCTTTGCATGGG 59.720 52.381 3.68 3.14 0.00 4.00
675 687 1.003580 GACTCTCCTTTGCATGGGTGA 59.996 52.381 6.44 7.88 0.00 4.02
683 696 3.763360 CCTTTGCATGGGTGACAAGATTA 59.237 43.478 0.00 0.00 0.00 1.75
686 699 2.290832 TGCATGGGTGACAAGATTAGCA 60.291 45.455 0.00 0.00 0.00 3.49
703 716 3.350219 AGCATCCGGATGTGTAGTTTT 57.650 42.857 37.88 15.68 40.80 2.43
706 719 3.309954 GCATCCGGATGTGTAGTTTTCTC 59.690 47.826 37.88 17.94 40.80 2.87
711 724 3.933332 CGGATGTGTAGTTTTCTCCTTCC 59.067 47.826 0.00 0.00 0.00 3.46
741 754 0.974010 TCTGTACAACCCTAGGCCCG 60.974 60.000 2.05 0.00 0.00 6.13
742 755 1.968050 CTGTACAACCCTAGGCCCGG 61.968 65.000 2.05 0.00 0.00 5.73
743 756 1.991722 GTACAACCCTAGGCCCGGT 60.992 63.158 2.05 0.00 0.00 5.28
744 757 1.991167 TACAACCCTAGGCCCGGTG 60.991 63.158 2.05 1.07 30.96 4.94
745 758 4.109675 CAACCCTAGGCCCGGTGG 62.110 72.222 2.05 0.99 30.96 4.61
750 763 4.096003 CTAGGCCCGGTGGGTGTG 62.096 72.222 0.00 0.00 46.51 3.82
847 860 1.804326 GAACACCGTCCGTCCGATG 60.804 63.158 0.00 0.00 0.00 3.84
890 903 0.321996 ACGGACTTGCCTCTCCTTTC 59.678 55.000 0.00 0.00 0.00 2.62
969 986 2.040278 CTCCCTGGGCTCTCACCT 59.960 66.667 8.22 0.00 0.00 4.00
970 987 1.311403 CTCCCTGGGCTCTCACCTA 59.689 63.158 8.22 0.00 0.00 3.08
971 988 0.758685 CTCCCTGGGCTCTCACCTAG 60.759 65.000 8.22 0.00 38.01 3.02
972 989 2.439104 CCCTGGGCTCTCACCTAGC 61.439 68.421 0.00 0.00 36.99 3.42
1169 1192 0.742505 CGCGATCCTACACCAACCTA 59.257 55.000 0.00 0.00 0.00 3.08
1463 1486 2.681778 CTCCTGCTCCACCTCCGT 60.682 66.667 0.00 0.00 0.00 4.69
1676 1699 0.548682 ACATGCTCCCCTTCACCTCT 60.549 55.000 0.00 0.00 0.00 3.69
1886 1909 1.152368 CAGCCCCTTCCCATCATCC 59.848 63.158 0.00 0.00 0.00 3.51
2327 2350 4.243550 CCAAGGGGTGGTAGTGGA 57.756 61.111 0.00 0.00 43.20 4.02
2471 2494 2.051334 TGGCATATTACACTGTGGCC 57.949 50.000 13.09 13.72 40.29 5.36
2913 2936 9.733556 TCAAAAAGCTTACTGTGGATTCTATTA 57.266 29.630 0.00 0.00 0.00 0.98
3170 3193 7.721402 ACTTTATGAGGTATGCTCTCACTTAG 58.279 38.462 4.59 5.21 43.07 2.18
3403 3428 6.479990 TGGTGACATCATAGAACGATCATTTC 59.520 38.462 0.00 0.00 33.40 2.17
3955 4024 5.535783 TGAACATTCATGTGTCAACCTCATT 59.464 36.000 0.00 0.00 41.61 2.57
4040 4109 7.991084 ATGCAACTATACAACATGCTGATAT 57.009 32.000 2.44 0.62 37.86 1.63
4504 4577 1.666888 GGTTTTGGATCTGCACAAGCG 60.667 52.381 0.00 0.00 46.23 4.68
4814 4887 4.853196 CCACTTGTGATAGTGAATTTTGCG 59.147 41.667 5.39 0.00 46.72 4.85
5031 5104 3.567585 TCCTATCGATGCTGACAGAGAAG 59.432 47.826 8.54 0.00 0.00 2.85
5283 5356 5.163395 ACCAGAAGAATCGGAGATACTTTCC 60.163 44.000 0.00 0.00 45.12 3.13
5378 5464 6.061441 TGTCTAAATTGAAGCCAAGTTCAGA 58.939 36.000 0.00 0.00 39.47 3.27
5466 5552 6.145209 GTCTAGTTTTGGTCTCTTTTACCGTC 59.855 42.308 0.00 0.00 40.08 4.79
5567 5653 8.919145 CATGGTAGGTATCTTTTCTAGACTTCT 58.081 37.037 0.00 0.00 35.19 2.85
5603 5690 7.942990 AGTAGCAGGTAGTGTATGTAAGATTC 58.057 38.462 0.00 0.00 0.00 2.52
5615 5702 5.786401 ATGTAAGATTCGAGTGTTTCTGC 57.214 39.130 0.00 0.00 0.00 4.26
5732 5819 5.160386 ACCCATATTTTACTCCCTCCGTAT 58.840 41.667 0.00 0.00 0.00 3.06
5745 5832 6.057321 TCCCTCCGTATCAAATTACTTGTT 57.943 37.500 0.00 0.00 36.34 2.83
5773 5860 9.019764 CCAACAGACAAAAATTAGTACACAAAG 57.980 33.333 0.00 0.00 0.00 2.77
5774 5861 9.567848 CAACAGACAAAAATTAGTACACAAAGT 57.432 29.630 0.00 0.00 0.00 2.66
5792 5879 8.403236 ACACAAAGTTAACTTTACATTCAGACC 58.597 33.333 28.43 0.00 43.72 3.85
5793 5880 7.586300 CACAAAGTTAACTTTACATTCAGACCG 59.414 37.037 28.43 16.04 43.72 4.79
5794 5881 7.281549 ACAAAGTTAACTTTACATTCAGACCGT 59.718 33.333 28.43 16.58 43.72 4.83
5795 5882 7.417496 AAGTTAACTTTACATTCAGACCGTC 57.583 36.000 15.22 0.00 30.82 4.79
5796 5883 5.930569 AGTTAACTTTACATTCAGACCGTCC 59.069 40.000 1.12 0.00 0.00 4.79
5797 5884 4.345859 AACTTTACATTCAGACCGTCCA 57.654 40.909 0.00 0.00 0.00 4.02
5798 5885 3.926616 ACTTTACATTCAGACCGTCCAG 58.073 45.455 0.00 0.00 0.00 3.86
5799 5886 3.576982 ACTTTACATTCAGACCGTCCAGA 59.423 43.478 0.00 0.00 0.00 3.86
5800 5887 4.223032 ACTTTACATTCAGACCGTCCAGAT 59.777 41.667 0.00 0.00 0.00 2.90
5801 5888 4.819105 TTACATTCAGACCGTCCAGATT 57.181 40.909 0.00 0.00 0.00 2.40
5802 5889 3.703001 ACATTCAGACCGTCCAGATTT 57.297 42.857 0.00 0.00 0.00 2.17
5803 5890 3.600388 ACATTCAGACCGTCCAGATTTC 58.400 45.455 0.00 0.00 0.00 2.17
5804 5891 3.007940 ACATTCAGACCGTCCAGATTTCA 59.992 43.478 0.00 0.00 0.00 2.69
5805 5892 3.762407 TTCAGACCGTCCAGATTTCAA 57.238 42.857 0.00 0.00 0.00 2.69
5806 5893 3.762407 TCAGACCGTCCAGATTTCAAA 57.238 42.857 0.00 0.00 0.00 2.69
5807 5894 4.079980 TCAGACCGTCCAGATTTCAAAA 57.920 40.909 0.00 0.00 0.00 2.44
5808 5895 4.456535 TCAGACCGTCCAGATTTCAAAAA 58.543 39.130 0.00 0.00 0.00 1.94
5809 5896 4.515191 TCAGACCGTCCAGATTTCAAAAAG 59.485 41.667 0.00 0.00 0.00 2.27
5810 5897 4.275936 CAGACCGTCCAGATTTCAAAAAGT 59.724 41.667 0.00 0.00 0.00 2.66
5811 5898 4.887655 AGACCGTCCAGATTTCAAAAAGTT 59.112 37.500 0.00 0.00 0.00 2.66
5812 5899 5.008712 AGACCGTCCAGATTTCAAAAAGTTC 59.991 40.000 0.00 0.00 0.00 3.01
5813 5900 4.887655 ACCGTCCAGATTTCAAAAAGTTCT 59.112 37.500 0.00 0.00 0.00 3.01
5814 5901 5.008712 ACCGTCCAGATTTCAAAAAGTTCTC 59.991 40.000 0.00 0.00 0.00 2.87
5815 5902 5.008613 CCGTCCAGATTTCAAAAAGTTCTCA 59.991 40.000 0.00 0.00 0.00 3.27
5816 5903 6.138761 CGTCCAGATTTCAAAAAGTTCTCAG 58.861 40.000 0.00 0.00 0.00 3.35
5817 5904 6.442112 GTCCAGATTTCAAAAAGTTCTCAGG 58.558 40.000 0.00 0.00 0.00 3.86
5818 5905 5.010012 TCCAGATTTCAAAAAGTTCTCAGGC 59.990 40.000 0.00 0.00 0.00 4.85
5819 5906 5.225642 CAGATTTCAAAAAGTTCTCAGGCC 58.774 41.667 0.00 0.00 0.00 5.19
5820 5907 3.708563 TTTCAAAAAGTTCTCAGGCCG 57.291 42.857 0.00 0.00 0.00 6.13
5821 5908 0.951558 TCAAAAAGTTCTCAGGCCGC 59.048 50.000 0.00 0.00 0.00 6.53
5822 5909 0.667993 CAAAAAGTTCTCAGGCCGCA 59.332 50.000 0.00 0.00 0.00 5.69
5823 5910 0.668535 AAAAAGTTCTCAGGCCGCAC 59.331 50.000 0.00 0.00 0.00 5.34
5824 5911 1.172812 AAAAGTTCTCAGGCCGCACC 61.173 55.000 0.00 0.00 39.61 5.01
5825 5912 3.553095 AAGTTCTCAGGCCGCACCC 62.553 63.158 0.00 0.00 40.58 4.61
5826 5913 4.021925 GTTCTCAGGCCGCACCCT 62.022 66.667 0.00 0.00 40.58 4.34
5827 5914 3.706373 TTCTCAGGCCGCACCCTC 61.706 66.667 0.00 0.00 40.58 4.30
5829 5916 4.463879 CTCAGGCCGCACCCTCAG 62.464 72.222 0.00 0.00 40.58 3.35
5831 5918 3.390521 CAGGCCGCACCCTCAGTA 61.391 66.667 0.00 0.00 40.58 2.74
5832 5919 3.391382 AGGCCGCACCCTCAGTAC 61.391 66.667 0.00 0.00 40.58 2.73
5833 5920 3.702048 GGCCGCACCCTCAGTACA 61.702 66.667 0.00 0.00 0.00 2.90
5834 5921 2.434359 GCCGCACCCTCAGTACAC 60.434 66.667 0.00 0.00 0.00 2.90
5835 5922 3.056458 CCGCACCCTCAGTACACA 58.944 61.111 0.00 0.00 0.00 3.72
5836 5923 1.369692 CCGCACCCTCAGTACACAA 59.630 57.895 0.00 0.00 0.00 3.33
5837 5924 0.250124 CCGCACCCTCAGTACACAAA 60.250 55.000 0.00 0.00 0.00 2.83
5963 6050 3.077907 GGGGGCTGTTGCACTCTA 58.922 61.111 0.00 0.00 40.68 2.43
5964 6051 1.078143 GGGGGCTGTTGCACTCTAG 60.078 63.158 0.00 0.00 40.68 2.43
5993 6093 2.809174 CGTGATCCAGCGCGACAA 60.809 61.111 12.10 0.00 43.93 3.18
6050 6150 2.920645 CGATAGATCCACGCCGGCT 61.921 63.158 26.68 8.92 39.76 5.52
6306 6428 9.859427 CAGTTATCCTGCATTCATTAAGAAAAA 57.141 29.630 0.00 0.00 35.45 1.94
6335 6457 4.479158 TGCTCAGTTAATTGGGGAAAACT 58.521 39.130 0.00 0.00 32.52 2.66
6337 6459 4.809673 CTCAGTTAATTGGGGAAAACTGC 58.190 43.478 10.40 0.00 45.34 4.40
6416 6539 1.762957 AGCGGCACACATAAGATACCT 59.237 47.619 1.45 0.00 0.00 3.08
6444 6567 0.040351 CCACTCCAGAGAGGGTCTCA 59.960 60.000 6.70 0.00 45.73 3.27
6445 6568 1.342874 CCACTCCAGAGAGGGTCTCAT 60.343 57.143 6.70 0.00 45.73 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.554142 TCGGCAATGATGTGATGACTC 58.446 47.619 0.00 0.00 0.00 3.36
57 58 3.543665 TCAATCGGCAATGATGTGATGA 58.456 40.909 0.00 0.00 0.00 2.92
96 97 2.640826 CCCCTCGTAGATCTAGTCTCCT 59.359 54.545 1.64 0.00 38.42 3.69
150 151 1.448540 CGCTCCGTGCCTCATCTTT 60.449 57.895 0.00 0.00 38.78 2.52
168 169 0.107459 GGAGGGTGATTGGCAGAGTC 60.107 60.000 0.00 0.00 0.00 3.36
258 261 1.586154 CGCAGAGGAAAAACCGCCAT 61.586 55.000 0.00 0.00 44.74 4.40
315 321 1.730902 CGCTCGGACGGCATCTATG 60.731 63.158 0.00 0.00 0.00 2.23
371 377 1.157257 TGCGCGCCGAATGAATACAT 61.157 50.000 30.77 0.00 38.50 2.29
390 398 1.673033 CCTGTGGTCGCTTCGATTTCT 60.673 52.381 0.00 0.00 38.42 2.52
424 433 2.481969 GCTCTAACCTCGATGTGCATCA 60.482 50.000 12.03 0.00 37.69 3.07
426 435 1.202580 GGCTCTAACCTCGATGTGCAT 60.203 52.381 0.00 0.00 0.00 3.96
440 449 4.499188 CGGATTAACGACAATCTGGCTCTA 60.499 45.833 12.08 0.00 37.56 2.43
547 557 2.103263 CCCTTAATTCAGGACTCCCTCG 59.897 54.545 7.28 0.00 42.02 4.63
560 570 1.920532 GCCCGAGGACCCCTTAATT 59.079 57.895 0.00 0.00 31.76 1.40
654 666 1.004044 CACCCATGCAAAGGAGAGTCT 59.996 52.381 12.08 0.00 0.00 3.24
672 684 3.179443 TCCGGATGCTAATCTTGTCAC 57.821 47.619 0.00 0.00 32.95 3.67
675 687 3.118261 ACACATCCGGATGCTAATCTTGT 60.118 43.478 38.44 29.58 42.39 3.16
683 696 3.055094 AGAAAACTACACATCCGGATGCT 60.055 43.478 38.44 27.23 42.39 3.79
686 699 3.775316 AGGAGAAAACTACACATCCGGAT 59.225 43.478 12.38 12.38 31.97 4.18
703 716 1.815003 GAGTCGGTTTACGGAAGGAGA 59.185 52.381 0.00 0.00 44.45 3.71
706 719 1.271656 ACAGAGTCGGTTTACGGAAGG 59.728 52.381 0.00 0.00 44.45 3.46
711 724 2.982470 GGTTGTACAGAGTCGGTTTACG 59.018 50.000 0.00 0.00 46.11 3.18
751 764 3.161450 TACCAGGGAGATGCCGCC 61.161 66.667 0.00 0.00 37.63 6.13
752 765 2.423446 CTACCAGGGAGATGCCGC 59.577 66.667 0.00 0.00 37.63 6.53
753 766 3.142393 CCTACCAGGGAGATGCCG 58.858 66.667 0.00 0.00 37.63 5.69
754 767 1.422161 ATGCCTACCAGGGAGATGCC 61.422 60.000 0.00 0.00 39.79 4.40
755 768 0.475906 AATGCCTACCAGGGAGATGC 59.524 55.000 0.00 0.00 39.79 3.91
756 769 1.072965 GGAATGCCTACCAGGGAGATG 59.927 57.143 0.00 0.00 39.79 2.90
757 770 1.439543 GGAATGCCTACCAGGGAGAT 58.560 55.000 0.00 0.00 39.79 2.75
758 771 0.694444 GGGAATGCCTACCAGGGAGA 60.694 60.000 0.00 0.00 39.79 3.71
890 903 2.159707 CGGGGCAGATATTTTATTCGCG 60.160 50.000 0.00 0.00 0.00 5.87
934 947 4.791069 GAGGGCACGGGGGAGGTA 62.791 72.222 0.00 0.00 0.00 3.08
969 986 1.379977 CAGGAGGTGACGAGGGCTA 60.380 63.158 0.00 0.00 0.00 3.93
970 987 2.681778 CAGGAGGTGACGAGGGCT 60.682 66.667 0.00 0.00 0.00 5.19
971 988 4.459089 GCAGGAGGTGACGAGGGC 62.459 72.222 0.00 0.00 0.00 5.19
972 989 2.997315 TGCAGGAGGTGACGAGGG 60.997 66.667 0.00 0.00 0.00 4.30
1169 1192 1.043116 TCCCATTGGCGAGATCGAGT 61.043 55.000 6.39 0.00 43.02 4.18
1420 1443 1.533033 TCGTCCCAGCAGAAGGTCA 60.533 57.895 0.00 0.00 0.00 4.02
1886 1909 1.649815 CAGGCTACGGTAGAGCTCG 59.350 63.158 19.02 0.00 39.98 5.03
2327 2350 3.506067 CCTTTAATCCTTGCACGTCCTTT 59.494 43.478 0.00 0.00 0.00 3.11
2554 2577 1.826720 GTGCATCACCACCATCCAAAT 59.173 47.619 0.00 0.00 0.00 2.32
2795 2818 1.221293 CCTGCAGCTTCTCTCCAGG 59.779 63.158 8.66 0.00 37.35 4.45
2913 2936 5.700832 TGTTCGACTTCTTGTAATCAGCAAT 59.299 36.000 0.00 0.00 0.00 3.56
3363 3388 3.070878 TGTCACCACGTCATATGCCATAT 59.929 43.478 0.00 0.00 0.00 1.78
3403 3428 9.918630 AAGATCTGAGAAATTAAATGGTTGTTG 57.081 29.630 0.00 0.00 0.00 3.33
3955 4024 2.853430 TCCCTATCCAAGTTTAGCCCA 58.147 47.619 0.00 0.00 0.00 5.36
4109 4179 1.639722 TACTGCTTGACTGGGCTACA 58.360 50.000 0.00 0.00 0.00 2.74
4110 4180 2.762535 TTACTGCTTGACTGGGCTAC 57.237 50.000 0.00 0.00 0.00 3.58
4286 4359 2.666619 GCTGTTGAGATGAAACTTGCCG 60.667 50.000 0.00 0.00 0.00 5.69
4814 4887 0.960861 GGCCCCTCACAAGTTAGCAC 60.961 60.000 0.00 0.00 0.00 4.40
4879 4952 6.789268 TCCAGAAAGAATCCAGGATTTGTTA 58.211 36.000 16.33 0.00 31.89 2.41
5294 5367 1.009829 GACACGACTTCATCATGCCC 58.990 55.000 0.00 0.00 0.00 5.36
5378 5464 4.272489 TGCTAAAGTTGCATTCCAGCTAT 58.728 39.130 8.63 0.00 33.49 2.97
5466 5552 4.003648 ACTCCAAAATTACGAGAAGGCAG 58.996 43.478 0.00 0.00 0.00 4.85
5603 5690 7.898309 GTGTATATAAACTTGCAGAAACACTCG 59.102 37.037 0.00 0.00 32.75 4.18
5745 5832 6.095580 TGTGTACTAATTTTTGTCTGTTGGCA 59.904 34.615 0.00 0.00 0.00 4.92
5773 5860 5.697633 TGGACGGTCTGAATGTAAAGTTAAC 59.302 40.000 8.23 0.00 0.00 2.01
5774 5861 5.856156 TGGACGGTCTGAATGTAAAGTTAA 58.144 37.500 8.23 0.00 0.00 2.01
5775 5862 5.244402 TCTGGACGGTCTGAATGTAAAGTTA 59.756 40.000 8.23 0.00 0.00 2.24
5776 5863 4.039973 TCTGGACGGTCTGAATGTAAAGTT 59.960 41.667 8.23 0.00 0.00 2.66
5777 5864 3.576982 TCTGGACGGTCTGAATGTAAAGT 59.423 43.478 8.23 0.00 0.00 2.66
5778 5865 4.188247 TCTGGACGGTCTGAATGTAAAG 57.812 45.455 8.23 0.00 0.00 1.85
5779 5866 4.819105 ATCTGGACGGTCTGAATGTAAA 57.181 40.909 8.23 0.00 0.00 2.01
5780 5867 4.819105 AATCTGGACGGTCTGAATGTAA 57.181 40.909 8.23 0.00 0.00 2.41
5781 5868 4.221924 TGAAATCTGGACGGTCTGAATGTA 59.778 41.667 8.23 0.00 0.00 2.29
5782 5869 3.007940 TGAAATCTGGACGGTCTGAATGT 59.992 43.478 8.23 0.00 0.00 2.71
5783 5870 3.599343 TGAAATCTGGACGGTCTGAATG 58.401 45.455 8.23 0.00 0.00 2.67
5784 5871 3.981071 TGAAATCTGGACGGTCTGAAT 57.019 42.857 8.23 0.00 0.00 2.57
5785 5872 3.762407 TTGAAATCTGGACGGTCTGAA 57.238 42.857 8.23 0.00 0.00 3.02
5786 5873 3.762407 TTTGAAATCTGGACGGTCTGA 57.238 42.857 8.23 7.39 0.00 3.27
5787 5874 4.275936 ACTTTTTGAAATCTGGACGGTCTG 59.724 41.667 8.23 1.98 0.00 3.51
5788 5875 4.461198 ACTTTTTGAAATCTGGACGGTCT 58.539 39.130 8.23 0.00 0.00 3.85
5789 5876 4.830826 ACTTTTTGAAATCTGGACGGTC 57.169 40.909 0.00 0.00 0.00 4.79
5790 5877 4.887655 AGAACTTTTTGAAATCTGGACGGT 59.112 37.500 0.00 0.00 0.00 4.83
5791 5878 5.008613 TGAGAACTTTTTGAAATCTGGACGG 59.991 40.000 0.00 0.00 0.00 4.79
5792 5879 6.060028 TGAGAACTTTTTGAAATCTGGACG 57.940 37.500 0.00 0.00 0.00 4.79
5793 5880 6.442112 CCTGAGAACTTTTTGAAATCTGGAC 58.558 40.000 0.00 0.00 0.00 4.02
5794 5881 5.010012 GCCTGAGAACTTTTTGAAATCTGGA 59.990 40.000 4.67 0.00 0.00 3.86
5795 5882 5.225642 GCCTGAGAACTTTTTGAAATCTGG 58.774 41.667 0.00 0.00 0.00 3.86
5796 5883 5.225642 GGCCTGAGAACTTTTTGAAATCTG 58.774 41.667 0.00 0.00 0.00 2.90
5797 5884 4.022849 CGGCCTGAGAACTTTTTGAAATCT 60.023 41.667 0.00 0.00 0.00 2.40
5798 5885 4.229876 CGGCCTGAGAACTTTTTGAAATC 58.770 43.478 0.00 0.00 0.00 2.17
5799 5886 3.552890 GCGGCCTGAGAACTTTTTGAAAT 60.553 43.478 0.00 0.00 0.00 2.17
5800 5887 2.223711 GCGGCCTGAGAACTTTTTGAAA 60.224 45.455 0.00 0.00 0.00 2.69
5801 5888 1.336755 GCGGCCTGAGAACTTTTTGAA 59.663 47.619 0.00 0.00 0.00 2.69
5802 5889 0.951558 GCGGCCTGAGAACTTTTTGA 59.048 50.000 0.00 0.00 0.00 2.69
5803 5890 0.667993 TGCGGCCTGAGAACTTTTTG 59.332 50.000 0.00 0.00 0.00 2.44
5804 5891 0.668535 GTGCGGCCTGAGAACTTTTT 59.331 50.000 0.00 0.00 0.00 1.94
5805 5892 1.172812 GGTGCGGCCTGAGAACTTTT 61.173 55.000 0.00 0.00 0.00 2.27
5806 5893 1.600916 GGTGCGGCCTGAGAACTTT 60.601 57.895 0.00 0.00 0.00 2.66
5807 5894 2.032681 GGTGCGGCCTGAGAACTT 59.967 61.111 0.00 0.00 0.00 2.66
5808 5895 4.021925 GGGTGCGGCCTGAGAACT 62.022 66.667 0.00 0.00 37.43 3.01
5809 5896 3.959991 GAGGGTGCGGCCTGAGAAC 62.960 68.421 0.00 0.00 37.43 3.01
5810 5897 3.706373 GAGGGTGCGGCCTGAGAA 61.706 66.667 0.00 0.00 37.43 2.87
5812 5899 4.463879 CTGAGGGTGCGGCCTGAG 62.464 72.222 0.00 0.00 37.43 3.35
5813 5900 3.897681 TACTGAGGGTGCGGCCTGA 62.898 63.158 0.00 0.00 37.43 3.86
5814 5901 3.390521 TACTGAGGGTGCGGCCTG 61.391 66.667 0.00 0.00 37.43 4.85
5815 5902 3.391382 GTACTGAGGGTGCGGCCT 61.391 66.667 0.00 0.00 37.43 5.19
5816 5903 3.702048 TGTACTGAGGGTGCGGCC 61.702 66.667 0.00 0.00 33.14 6.13
5817 5904 2.434359 GTGTACTGAGGGTGCGGC 60.434 66.667 0.00 0.00 33.14 6.53
5818 5905 0.250124 TTTGTGTACTGAGGGTGCGG 60.250 55.000 0.00 0.00 33.14 5.69
5819 5906 1.148310 CTTTGTGTACTGAGGGTGCG 58.852 55.000 0.00 0.00 33.14 5.34
5820 5907 2.256117 ACTTTGTGTACTGAGGGTGC 57.744 50.000 0.00 0.00 0.00 5.01
5821 5908 6.877611 AATTAACTTTGTGTACTGAGGGTG 57.122 37.500 0.00 0.00 0.00 4.61
5822 5909 7.891498 AAAATTAACTTTGTGTACTGAGGGT 57.109 32.000 0.00 0.00 0.00 4.34
5823 5910 8.842280 TGTAAAATTAACTTTGTGTACTGAGGG 58.158 33.333 0.00 0.00 0.00 4.30
5831 5918 9.744468 GGTCTGAATGTAAAATTAACTTTGTGT 57.256 29.630 0.00 0.00 0.00 3.72
5832 5919 9.191995 GGGTCTGAATGTAAAATTAACTTTGTG 57.808 33.333 0.00 0.00 0.00 3.33
5833 5920 9.143155 AGGGTCTGAATGTAAAATTAACTTTGT 57.857 29.630 0.00 0.00 0.00 2.83
5834 5921 9.626045 GAGGGTCTGAATGTAAAATTAACTTTG 57.374 33.333 0.00 0.00 0.00 2.77
5835 5922 8.803235 GGAGGGTCTGAATGTAAAATTAACTTT 58.197 33.333 0.00 0.00 0.00 2.66
5836 5923 7.947890 TGGAGGGTCTGAATGTAAAATTAACTT 59.052 33.333 0.00 0.00 0.00 2.66
5837 5924 7.466804 TGGAGGGTCTGAATGTAAAATTAACT 58.533 34.615 0.00 0.00 0.00 2.24
5904 5991 2.146061 GCTATGGGGAGGCAGAGCT 61.146 63.158 0.00 0.00 33.37 4.09
5948 6035 1.746991 GCCTAGAGTGCAACAGCCC 60.747 63.158 0.00 0.00 41.43 5.19
5949 6036 2.103042 CGCCTAGAGTGCAACAGCC 61.103 63.158 0.00 0.00 41.43 4.85
5957 6044 2.811101 CCTGGAGCGCCTAGAGTG 59.189 66.667 8.34 0.00 34.31 3.51
5958 6045 3.151022 GCCTGGAGCGCCTAGAGT 61.151 66.667 8.34 0.00 34.31 3.24
5959 6046 3.922640 GGCCTGGAGCGCCTAGAG 61.923 72.222 8.34 0.00 45.17 2.43
5988 6075 3.864686 CGGCGCCTGGATTTGTCG 61.865 66.667 26.68 2.46 0.00 4.35
6061 6161 2.091112 CAGAAGAGTGCGGTCGCTG 61.091 63.158 16.36 0.84 42.51 5.18
6071 6171 2.109774 CATCCTCCTCAGCAGAAGAGT 58.890 52.381 4.27 0.00 31.62 3.24
6279 6398 8.579850 TTTCTTAATGAATGCAGGATAACTGT 57.420 30.769 0.00 0.00 40.81 3.55
6306 6428 4.524328 CCCCAATTAACTGAGCAACTCTTT 59.476 41.667 0.00 0.00 0.00 2.52
6307 6429 4.082125 CCCCAATTAACTGAGCAACTCTT 58.918 43.478 0.00 0.00 0.00 2.85
6308 6430 3.330701 TCCCCAATTAACTGAGCAACTCT 59.669 43.478 0.00 0.00 0.00 3.24
6335 6457 2.897780 GCAATCTGGTTTTTGCGCA 58.102 47.368 5.66 5.66 38.88 6.09
6416 6539 0.752658 CTCTGGAGTGGTGTGTGTGA 59.247 55.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.