Multiple sequence alignment - TraesCS5D01G176300

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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 TraesCS5D01G176300 chr5D 100.000 3077 0 0 1 3077 276455914 276452838 0.000000e+00 5683.0
1 TraesCS5D01G176300 chr5A 94.651 2262 75 24 782 3025 364959125 364956892 0.000000e+00 3465.0
2 TraesCS5D01G176300 chr5A 89.605 481 44 6 159 635 364960732 364960254 9.440000e-170 606.0
3 TraesCS5D01G176300 chr5A 87.629 97 10 2 702 797 364960151 364960056 9.020000e-21 111.0
4 TraesCS5D01G176300 chr5B 92.109 2357 113 35 690 3025 313210980 313208676 0.000000e+00 3254.0
5 TraesCS5D01G176300 chr5B 87.011 716 73 16 1 705 313211705 313210999 0.000000e+00 789.0
6 TraesCS5D01G176300 chr4D 83.770 191 27 4 1347 1536 480846801 480846988 8.770000e-41 178.0
7 TraesCS5D01G176300 chr2D 88.889 108 11 1 1409 1516 624320867 624320761 6.920000e-27 132.0
8 TraesCS5D01G176300 chr3D 92.000 50 4 0 100 149 104097885 104097934 1.530000e-08 71.3


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 TraesCS5D01G176300 chr5D 276452838 276455914 3076 True 5683.0 5683 100.000000 1 3077 1 chr5D.!!$R1 3076
1 TraesCS5D01G176300 chr5A 364956892 364960732 3840 True 1394.0 3465 90.628333 159 3025 3 chr5A.!!$R1 2866
2 TraesCS5D01G176300 chr5B 313208676 313211705 3029 True 2021.5 3254 89.560000 1 3025 2 chr5B.!!$R1 3024

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
745 807 0.106419 AAAGTTGAGCCCGGTCCAAA 60.106 50.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 3479 1.152383 GATTTCCAGGCTACGGCGTC 61.152 60.0 19.21 2.08 39.81 5.19 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 2.167900 ACGGCCTTACCTTACTAAGCAG 59.832 50.000 0.00 0.00 35.61 4.24
39 40 4.386711 ACCTTACTAAGCAGGACACAAAC 58.613 43.478 0.00 0.00 33.90 2.93
47 48 3.157087 AGCAGGACACAAACCCTAAATG 58.843 45.455 0.00 0.00 0.00 2.32
58 59 8.630037 ACACAAACCCTAAATGAACTTAGAAAG 58.370 33.333 0.00 0.00 31.59 2.62
73 74 7.731882 ACTTAGAAAGACCTAAAAACAGAGC 57.268 36.000 0.00 0.00 0.00 4.09
116 117 3.948719 GGGTCCACCACGCCTCAA 61.949 66.667 0.00 0.00 39.85 3.02
117 118 2.668550 GGTCCACCACGCCTCAAC 60.669 66.667 0.00 0.00 35.64 3.18
139 140 2.494918 CTAGGGCCACCGAAGACG 59.505 66.667 6.18 0.00 43.47 4.18
141 142 2.005960 CTAGGGCCACCGAAGACGAG 62.006 65.000 6.18 0.00 43.47 4.18
142 143 4.452733 GGGCCACCGAAGACGAGG 62.453 72.222 4.39 0.00 42.66 4.63
193 195 3.485463 TTTTCTTTGAAGAGGAGGCGA 57.515 42.857 0.00 0.00 36.22 5.54
199 201 2.044252 AAGAGGAGGCGACGGCTA 60.044 61.111 25.06 0.00 38.98 3.93
223 225 6.212955 ACGTAAAGCAACATGTTAAAAGCAT 58.787 32.000 11.53 0.39 0.00 3.79
331 333 2.378445 TTTGAGTCGATTGATCCGCA 57.622 45.000 0.00 0.00 0.00 5.69
390 392 1.089920 GTCGTAGCGAGTACAGGGAA 58.910 55.000 0.00 0.00 36.23 3.97
424 428 2.278013 GAGGACGCGGACGACATC 60.278 66.667 12.47 0.00 43.93 3.06
432 436 1.516169 CGGACGACATCGCATGTGA 60.516 57.895 12.12 12.12 45.03 3.58
461 466 0.951558 CAAAGGTTGACTGGTTCGGG 59.048 55.000 0.00 0.00 0.00 5.14
467 472 2.284405 GACTGGTTCGGGAGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
504 509 2.162681 CTCCGGAGAAATTTGGTGCTT 58.837 47.619 28.21 0.00 0.00 3.91
510 515 1.970640 AGAAATTTGGTGCTTGGGGAC 59.029 47.619 0.00 0.00 0.00 4.46
534 541 2.508751 GGAGGGATAGTGGGGCGAC 61.509 68.421 0.00 0.00 0.00 5.19
588 597 5.976870 AGGAGAGGGGAAATCAATTAACCTA 59.023 40.000 0.00 0.00 29.84 3.08
645 658 1.307866 GGGAGGGGATGGGTTCTGA 60.308 63.158 0.00 0.00 0.00 3.27
669 682 1.611519 TAGTCGGCCCCAAACAAAAG 58.388 50.000 0.00 0.00 0.00 2.27
675 688 4.583073 GTCGGCCCCAAACAAAAGATATAT 59.417 41.667 0.00 0.00 0.00 0.86
679 692 6.515035 CGGCCCCAAACAAAAGATATATCTTC 60.515 42.308 24.75 10.57 45.83 2.87
680 693 6.551227 GGCCCCAAACAAAAGATATATCTTCT 59.449 38.462 24.75 11.60 45.83 2.85
681 694 7.069950 GGCCCCAAACAAAAGATATATCTTCTT 59.930 37.037 24.75 17.97 45.83 2.52
713 774 6.925610 AAAAATTCTTCTTTTCTGGGCAAC 57.074 33.333 0.00 0.00 0.00 4.17
717 779 0.825840 TTCTTTTCTGGGCAACGGGG 60.826 55.000 0.00 0.00 37.60 5.73
737 799 1.803289 GGCGATCAAAGTTGAGCCC 59.197 57.895 11.46 6.94 40.63 5.19
745 807 0.106419 AAAGTTGAGCCCGGTCCAAA 60.106 50.000 0.00 0.00 0.00 3.28
746 808 0.112412 AAGTTGAGCCCGGTCCAAAT 59.888 50.000 0.00 0.00 0.00 2.32
755 817 0.109319 CCGGTCCAAATGAAAAGGCG 60.109 55.000 0.00 0.00 0.00 5.52
930 1943 1.204786 TGGCCTCTCCAATTTCCGGA 61.205 55.000 0.00 0.00 43.21 5.14
1824 2838 1.419381 GTGGGAGGAAGGAGAGGATC 58.581 60.000 0.00 0.00 0.00 3.36
2215 3230 7.384932 TGGCTTAAAGATACGTCACATATGATG 59.615 37.037 10.38 4.41 45.92 3.07
2245 3260 1.436600 CAGCAGCGGATGATGGTATC 58.563 55.000 3.15 0.00 40.84 2.24
2296 3314 8.627403 AGTGATTAAACTTCCATGATGCTAATG 58.373 33.333 0.00 0.00 0.00 1.90
2329 3347 1.127567 TGGTTCTCCTCACCACCCAG 61.128 60.000 0.00 0.00 39.53 4.45
2444 3479 0.250295 TTGGGTTCAGCTTGTCCTCG 60.250 55.000 0.00 0.00 0.00 4.63
2445 3480 1.118965 TGGGTTCAGCTTGTCCTCGA 61.119 55.000 0.00 0.00 0.00 4.04
2446 3481 0.670854 GGGTTCAGCTTGTCCTCGAC 60.671 60.000 0.00 0.00 0.00 4.20
2505 3543 7.840342 AGCTGTGACAGATTAATCAACTTAG 57.160 36.000 18.18 9.09 32.44 2.18
2593 3634 2.483714 CGGTGGTGGTTATCTGGATCAG 60.484 54.545 0.00 0.00 0.00 2.90
2597 3638 5.253330 GTGGTGGTTATCTGGATCAGAAAA 58.747 41.667 1.53 0.00 44.04 2.29
2636 3677 1.298993 CATGGACACTGCTGCCTCT 59.701 57.895 0.00 0.00 0.00 3.69
2682 3723 2.677836 TGCAGACGCAGAATATGTTTCC 59.322 45.455 0.00 0.00 45.36 3.13
2688 3729 6.260936 CAGACGCAGAATATGTTTCCCTTATT 59.739 38.462 0.00 0.00 0.00 1.40
2705 3746 5.070847 CCCTTATTTGGGCTATGCAGAAATT 59.929 40.000 0.00 0.00 40.84 1.82
2714 3755 9.667107 TTGGGCTATGCAGAAATTATATACTAC 57.333 33.333 0.00 0.00 0.00 2.73
2715 3756 9.046846 TGGGCTATGCAGAAATTATATACTACT 57.953 33.333 0.00 0.00 0.00 2.57
2756 3797 3.396260 TTAAGAACTCAGAACCACCGG 57.604 47.619 0.00 0.00 0.00 5.28
2771 3812 4.035112 ACCACCGGTTCAGATATAAGGAA 58.965 43.478 2.97 0.00 27.29 3.36
2800 3841 2.593436 AGGTTGGTTGCCGGTTCG 60.593 61.111 1.90 0.00 0.00 3.95
2832 3873 7.941795 TGTAGTTTCTAAAGAACTGTGTAGC 57.058 36.000 0.09 0.00 33.13 3.58
2859 3900 4.023291 GTCTTTCTCCTCATGTCCTCTCT 58.977 47.826 0.00 0.00 0.00 3.10
2860 3901 4.097892 GTCTTTCTCCTCATGTCCTCTCTC 59.902 50.000 0.00 0.00 0.00 3.20
2861 3902 2.746279 TCTCCTCATGTCCTCTCTCC 57.254 55.000 0.00 0.00 0.00 3.71
2862 3903 2.213310 TCTCCTCATGTCCTCTCTCCT 58.787 52.381 0.00 0.00 0.00 3.69
2864 3905 3.137544 TCTCCTCATGTCCTCTCTCCTAC 59.862 52.174 0.00 0.00 0.00 3.18
2865 3906 2.853077 TCCTCATGTCCTCTCTCCTACA 59.147 50.000 0.00 0.00 0.00 2.74
2866 3907 3.269643 TCCTCATGTCCTCTCTCCTACAA 59.730 47.826 0.00 0.00 0.00 2.41
2874 3915 4.770010 GTCCTCTCTCCTACAATATCCTGG 59.230 50.000 0.00 0.00 0.00 4.45
2880 3921 4.140447 TCTCCTACAATATCCTGGGACCAT 60.140 45.833 0.00 0.00 0.00 3.55
2889 3930 3.100207 TCCTGGGACCATTTCATTTCC 57.900 47.619 0.00 0.00 0.00 3.13
2891 3932 3.077391 TCCTGGGACCATTTCATTTCCTT 59.923 43.478 0.00 0.00 0.00 3.36
2920 3961 2.369860 CTGCATCCACCTCTGCCTATAA 59.630 50.000 0.00 0.00 37.59 0.98
2940 3982 6.992063 ATAAGACCAAATTAGCTCAGTGTG 57.008 37.500 0.00 0.00 0.00 3.82
2946 3988 4.083643 CCAAATTAGCTCAGTGTGTGTGAG 60.084 45.833 0.00 0.00 43.77 3.51
2948 3990 2.800881 TAGCTCAGTGTGTGTGAGTG 57.199 50.000 0.00 0.00 43.00 3.51
2949 3991 1.114627 AGCTCAGTGTGTGTGAGTGA 58.885 50.000 2.30 0.00 43.00 3.41
2950 3992 1.068281 AGCTCAGTGTGTGTGAGTGAG 59.932 52.381 0.00 0.00 43.00 3.51
2956 3998 2.009774 GTGTGTGTGAGTGAGTTTGCT 58.990 47.619 0.00 0.00 0.00 3.91
2964 4006 3.984633 GTGAGTGAGTTTGCTAGACTGTC 59.015 47.826 0.00 0.00 0.00 3.51
2965 4007 3.891977 TGAGTGAGTTTGCTAGACTGTCT 59.108 43.478 15.57 15.57 0.00 3.41
2992 4034 4.873817 TGATTGCACTTCCACTGAAATTG 58.126 39.130 0.00 0.00 0.00 2.32
3008 4050 5.324409 TGAAATTGTTAGCCAGATGTTCCT 58.676 37.500 0.00 0.00 0.00 3.36
3009 4051 6.480763 TGAAATTGTTAGCCAGATGTTCCTA 58.519 36.000 0.00 0.00 0.00 2.94
3012 4054 7.961326 AATTGTTAGCCAGATGTTCCTATTT 57.039 32.000 0.00 0.00 0.00 1.40
3022 4064 6.546034 CCAGATGTTCCTATTTAAATCGGGTT 59.454 38.462 16.46 2.40 0.00 4.11
3025 4067 9.284968 AGATGTTCCTATTTAAATCGGGTTATG 57.715 33.333 16.46 0.00 0.00 1.90
3026 4068 8.990163 ATGTTCCTATTTAAATCGGGTTATGT 57.010 30.769 16.46 0.00 0.00 2.29
3027 4069 8.215926 TGTTCCTATTTAAATCGGGTTATGTG 57.784 34.615 16.46 0.00 0.00 3.21
3028 4070 7.830201 TGTTCCTATTTAAATCGGGTTATGTGT 59.170 33.333 16.46 0.00 0.00 3.72
3029 4071 8.680001 GTTCCTATTTAAATCGGGTTATGTGTT 58.320 33.333 16.46 0.00 0.00 3.32
3030 4072 9.902684 TTCCTATTTAAATCGGGTTATGTGTTA 57.097 29.630 16.46 0.00 0.00 2.41
3040 4082 7.254227 TCGGGTTATGTGTTATTTCTTATGC 57.746 36.000 0.00 0.00 0.00 3.14
3041 4083 7.051623 TCGGGTTATGTGTTATTTCTTATGCT 58.948 34.615 0.00 0.00 0.00 3.79
3042 4084 7.225931 TCGGGTTATGTGTTATTTCTTATGCTC 59.774 37.037 0.00 0.00 0.00 4.26
3043 4085 7.519970 CGGGTTATGTGTTATTTCTTATGCTCC 60.520 40.741 0.00 0.00 0.00 4.70
3044 4086 7.502561 GGGTTATGTGTTATTTCTTATGCTCCT 59.497 37.037 0.00 0.00 0.00 3.69
3045 4087 8.903820 GGTTATGTGTTATTTCTTATGCTCCTT 58.096 33.333 0.00 0.00 0.00 3.36
3046 4088 9.937175 GTTATGTGTTATTTCTTATGCTCCTTC 57.063 33.333 0.00 0.00 0.00 3.46
3047 4089 9.905713 TTATGTGTTATTTCTTATGCTCCTTCT 57.094 29.630 0.00 0.00 0.00 2.85
3048 4090 7.615582 TGTGTTATTTCTTATGCTCCTTCTG 57.384 36.000 0.00 0.00 0.00 3.02
3049 4091 7.168219 TGTGTTATTTCTTATGCTCCTTCTGT 58.832 34.615 0.00 0.00 0.00 3.41
3050 4092 7.665559 TGTGTTATTTCTTATGCTCCTTCTGTT 59.334 33.333 0.00 0.00 0.00 3.16
3051 4093 8.515414 GTGTTATTTCTTATGCTCCTTCTGTTT 58.485 33.333 0.00 0.00 0.00 2.83
3052 4094 8.730680 TGTTATTTCTTATGCTCCTTCTGTTTC 58.269 33.333 0.00 0.00 0.00 2.78
3053 4095 8.730680 GTTATTTCTTATGCTCCTTCTGTTTCA 58.269 33.333 0.00 0.00 0.00 2.69
3054 4096 6.560253 TTTCTTATGCTCCTTCTGTTTCAC 57.440 37.500 0.00 0.00 0.00 3.18
3055 4097 5.227569 TCTTATGCTCCTTCTGTTTCACA 57.772 39.130 0.00 0.00 0.00 3.58
3056 4098 5.620206 TCTTATGCTCCTTCTGTTTCACAA 58.380 37.500 0.00 0.00 0.00 3.33
3057 4099 6.240894 TCTTATGCTCCTTCTGTTTCACAAT 58.759 36.000 0.00 0.00 0.00 2.71
3058 4100 4.778534 ATGCTCCTTCTGTTTCACAATG 57.221 40.909 0.00 0.00 0.00 2.82
3059 4101 3.554934 TGCTCCTTCTGTTTCACAATGT 58.445 40.909 0.00 0.00 0.00 2.71
3060 4102 4.713553 TGCTCCTTCTGTTTCACAATGTA 58.286 39.130 0.00 0.00 0.00 2.29
3061 4103 4.756642 TGCTCCTTCTGTTTCACAATGTAG 59.243 41.667 0.00 0.00 0.00 2.74
3062 4104 4.757149 GCTCCTTCTGTTTCACAATGTAGT 59.243 41.667 0.00 0.00 0.00 2.73
3063 4105 5.334414 GCTCCTTCTGTTTCACAATGTAGTG 60.334 44.000 0.00 0.00 40.85 2.74
3064 4106 4.515191 TCCTTCTGTTTCACAATGTAGTGC 59.485 41.667 0.00 0.00 39.35 4.40
3065 4107 4.275689 CCTTCTGTTTCACAATGTAGTGCA 59.724 41.667 0.00 0.00 39.35 4.57
3066 4108 5.048504 CCTTCTGTTTCACAATGTAGTGCAT 60.049 40.000 0.00 0.00 39.35 3.96
3067 4109 6.149308 CCTTCTGTTTCACAATGTAGTGCATA 59.851 38.462 0.00 0.00 39.35 3.14
3068 4110 7.148188 CCTTCTGTTTCACAATGTAGTGCATAT 60.148 37.037 0.00 0.00 39.35 1.78
3069 4111 7.686438 TCTGTTTCACAATGTAGTGCATATT 57.314 32.000 0.00 0.00 39.35 1.28
3070 4112 8.785329 TCTGTTTCACAATGTAGTGCATATTA 57.215 30.769 0.00 0.00 39.35 0.98
3071 4113 8.882736 TCTGTTTCACAATGTAGTGCATATTAG 58.117 33.333 0.00 0.00 39.35 1.73
3072 4114 7.984391 TGTTTCACAATGTAGTGCATATTAGG 58.016 34.615 0.00 0.00 39.35 2.69
3073 4115 7.609918 TGTTTCACAATGTAGTGCATATTAGGT 59.390 33.333 0.00 0.00 39.35 3.08
3074 4116 8.458843 GTTTCACAATGTAGTGCATATTAGGTT 58.541 33.333 0.00 0.00 39.35 3.50
3075 4117 8.574251 TTCACAATGTAGTGCATATTAGGTTT 57.426 30.769 0.00 0.00 39.35 3.27
3076 4118 8.574251 TCACAATGTAGTGCATATTAGGTTTT 57.426 30.769 0.00 0.00 39.35 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.188863 GTAAGGTAAGGCCGTGGAGA 58.811 55.000 0.00 0.00 43.70 3.71
16 17 5.511888 GGTTTGTGTCCTGCTTAGTAAGGTA 60.512 44.000 11.84 0.00 34.94 3.08
30 31 5.784578 AAGTTCATTTAGGGTTTGTGTCC 57.215 39.130 0.00 0.00 0.00 4.02
39 40 9.734984 TTTAGGTCTTTCTAAGTTCATTTAGGG 57.265 33.333 0.00 0.00 32.66 3.53
47 48 8.283992 GCTCTGTTTTTAGGTCTTTCTAAGTTC 58.716 37.037 0.00 0.00 31.73 3.01
58 59 4.396478 GGATTCCTGCTCTGTTTTTAGGTC 59.604 45.833 0.00 0.00 0.00 3.85
68 69 0.179936 GTGGGAGGATTCCTGCTCTG 59.820 60.000 21.86 0.00 41.86 3.35
69 70 0.985490 GGTGGGAGGATTCCTGCTCT 60.985 60.000 21.86 0.00 41.86 4.09
70 71 0.985490 AGGTGGGAGGATTCCTGCTC 60.985 60.000 21.86 15.16 41.86 4.26
73 74 1.225704 GCAGGTGGGAGGATTCCTG 59.774 63.158 10.74 5.79 46.96 3.86
133 134 1.216710 CCTGGTCTGCCTCGTCTTC 59.783 63.158 0.00 0.00 35.27 2.87
139 140 0.033011 TCTACCTCCTGGTCTGCCTC 60.033 60.000 0.00 0.00 44.78 4.70
141 142 1.045911 CCTCTACCTCCTGGTCTGCC 61.046 65.000 0.00 0.00 44.78 4.85
142 143 0.033011 TCCTCTACCTCCTGGTCTGC 60.033 60.000 0.00 0.00 44.78 4.26
143 144 2.104170 GTTCCTCTACCTCCTGGTCTG 58.896 57.143 0.00 0.00 44.78 3.51
182 184 2.044252 TAGCCGTCGCCTCCTCTT 60.044 61.111 0.00 0.00 34.57 2.85
199 201 5.583495 TGCTTTTAACATGTTGCTTTACGT 58.417 33.333 21.42 0.00 0.00 3.57
331 333 1.956477 AGGTTGCGCATTGTCTTCTTT 59.044 42.857 12.75 0.00 0.00 2.52
424 428 2.568090 GGTTGCCCTTCACATGCG 59.432 61.111 0.00 0.00 0.00 4.73
461 466 2.766229 GCACCTCCCTCTCCCCTC 60.766 72.222 0.00 0.00 0.00 4.30
485 490 1.885887 CAAGCACCAAATTTCTCCGGA 59.114 47.619 2.93 2.93 0.00 5.14
496 501 2.575455 AAACCGTCCCCAAGCACCAA 62.575 55.000 0.00 0.00 0.00 3.67
504 509 3.253838 CCCTCCAAACCGTCCCCA 61.254 66.667 0.00 0.00 0.00 4.96
510 515 0.180406 CCCACTATCCCTCCAAACCG 59.820 60.000 0.00 0.00 0.00 4.44
548 556 2.191400 CTCCTCTCCACTTCATTCCCA 58.809 52.381 0.00 0.00 0.00 4.37
635 646 2.621998 CCGACTATACGTCAGAACCCAT 59.378 50.000 0.00 0.00 42.98 4.00
636 647 2.019249 CCGACTATACGTCAGAACCCA 58.981 52.381 0.00 0.00 42.98 4.51
645 658 0.176449 GTTTGGGGCCGACTATACGT 59.824 55.000 0.00 0.00 0.00 3.57
698 759 0.825840 CCCCGTTGCCCAGAAAAGAA 60.826 55.000 0.00 0.00 0.00 2.52
717 779 1.226128 GCTCAACTTTGATCGCCGC 60.226 57.895 0.00 0.00 36.46 6.53
737 799 0.109319 CCGCCTTTTCATTTGGACCG 60.109 55.000 0.00 0.00 0.00 4.79
819 1827 0.669318 TCAATCGACGTGGCTGTTCC 60.669 55.000 0.00 0.00 0.00 3.62
930 1943 0.320508 GTTTCTTCTCTTCCCGGCGT 60.321 55.000 6.01 0.00 0.00 5.68
1519 2533 1.964608 CTCTGCCTGATCCCGAGCAA 61.965 60.000 0.00 0.00 34.26 3.91
1628 2642 2.339556 CGGATTTCTTGGCCGCCAA 61.340 57.895 23.46 23.46 41.69 4.52
1824 2838 2.703007 CCCTCTCTCCAAACTATCCCTG 59.297 54.545 0.00 0.00 0.00 4.45
2186 3201 8.559536 CATATGTGACGTATCTTTAAGCCATTT 58.440 33.333 0.00 0.00 0.00 2.32
2215 3230 1.945662 CGCTGCTGGCACAACAAAC 60.946 57.895 0.00 0.00 41.91 2.93
2245 3260 8.271312 TGAAGAAAATTATGTTTAGTACCCGG 57.729 34.615 0.00 0.00 0.00 5.73
2283 3301 6.150474 TGCATTCAGTATCATTAGCATCATGG 59.850 38.462 0.00 0.00 0.00 3.66
2296 3314 5.128919 AGGAGAACCATTGCATTCAGTATC 58.871 41.667 0.94 0.00 38.94 2.24
2300 3318 3.128242 GTGAGGAGAACCATTGCATTCAG 59.872 47.826 0.94 0.00 38.94 3.02
2444 3479 1.152383 GATTTCCAGGCTACGGCGTC 61.152 60.000 19.21 2.08 39.81 5.19
2445 3480 1.153429 GATTTCCAGGCTACGGCGT 60.153 57.895 19.64 19.64 39.81 5.68
2446 3481 1.153449 TGATTTCCAGGCTACGGCG 60.153 57.895 4.80 4.80 39.81 6.46
2608 3649 2.226437 GCAGTGTCCATGGTGTTACAAG 59.774 50.000 12.58 6.19 0.00 3.16
2610 3651 1.419762 AGCAGTGTCCATGGTGTTACA 59.580 47.619 12.58 5.70 0.00 2.41
2611 3652 1.806542 CAGCAGTGTCCATGGTGTTAC 59.193 52.381 12.58 2.66 40.43 2.50
2662 3703 2.032178 GGGAAACATATTCTGCGTCTGC 59.968 50.000 0.00 0.00 43.20 4.26
2682 3723 5.796424 ATTTCTGCATAGCCCAAATAAGG 57.204 39.130 0.00 0.00 0.00 2.69
2688 3729 9.667107 GTAGTATATAATTTCTGCATAGCCCAA 57.333 33.333 0.00 0.00 0.00 4.12
2751 3792 5.277857 ACTTCCTTATATCTGAACCGGTG 57.722 43.478 8.52 0.00 0.00 4.94
2763 3804 7.881232 CCAACCTGTTACTGAAACTTCCTTATA 59.119 37.037 0.00 0.00 38.99 0.98
2771 3812 3.380320 GCAACCAACCTGTTACTGAAACT 59.620 43.478 0.00 0.00 38.99 2.66
2782 3823 2.903547 CGAACCGGCAACCAACCTG 61.904 63.158 0.00 0.00 0.00 4.00
2783 3824 2.593436 CGAACCGGCAACCAACCT 60.593 61.111 0.00 0.00 0.00 3.50
2800 3841 8.669243 CAGTTCTTTAGAAACTACATCCATTCC 58.331 37.037 0.00 0.00 35.58 3.01
2806 3847 8.648968 GCTACACAGTTCTTTAGAAACTACATC 58.351 37.037 0.00 0.00 35.58 3.06
2832 3873 4.006319 GGACATGAGGAGAAAGACAAAGG 58.994 47.826 0.00 0.00 0.00 3.11
2859 3900 3.717507 TGGTCCCAGGATATTGTAGGA 57.282 47.619 0.00 0.00 0.00 2.94
2860 3901 5.163099 TGAAATGGTCCCAGGATATTGTAGG 60.163 44.000 0.00 0.00 0.00 3.18
2861 3902 5.940617 TGAAATGGTCCCAGGATATTGTAG 58.059 41.667 0.00 0.00 0.00 2.74
2862 3903 5.985175 TGAAATGGTCCCAGGATATTGTA 57.015 39.130 0.00 0.00 0.00 2.41
2864 3905 6.239402 GGAAATGAAATGGTCCCAGGATATTG 60.239 42.308 0.00 0.00 0.00 1.90
2865 3906 5.840693 GGAAATGAAATGGTCCCAGGATATT 59.159 40.000 0.00 0.00 0.00 1.28
2866 3907 5.136737 AGGAAATGAAATGGTCCCAGGATAT 59.863 40.000 0.00 0.00 32.97 1.63
2874 3915 5.482163 TTTCCAAGGAAATGAAATGGTCC 57.518 39.130 10.12 0.00 38.95 4.46
2889 3930 1.753073 GGTGGATGCAGGATTTCCAAG 59.247 52.381 7.55 0.00 41.05 3.61
2891 3932 1.002069 AGGTGGATGCAGGATTTCCA 58.998 50.000 1.73 1.73 38.89 3.53
2920 3961 4.067896 CACACACTGAGCTAATTTGGTCT 58.932 43.478 17.66 0.00 35.68 3.85
2940 3982 3.738282 CAGTCTAGCAAACTCACTCACAC 59.262 47.826 0.00 0.00 0.00 3.82
2964 4006 8.008480 TTTCAGTGGAAGTGCAATCATGCTAG 62.008 42.308 2.22 0.00 42.84 3.42
2965 4007 6.266533 TTTCAGTGGAAGTGCAATCATGCTA 61.267 40.000 2.22 0.00 42.84 3.49
2978 4020 4.761739 TCTGGCTAACAATTTCAGTGGAAG 59.238 41.667 0.00 0.00 33.82 3.46
2992 4034 8.283291 CGATTTAAATAGGAACATCTGGCTAAC 58.717 37.037 0.00 0.00 0.00 2.34
3022 4064 9.330063 CAGAAGGAGCATAAGAAATAACACATA 57.670 33.333 0.00 0.00 0.00 2.29
3025 4067 7.617041 ACAGAAGGAGCATAAGAAATAACAC 57.383 36.000 0.00 0.00 0.00 3.32
3026 4068 8.635765 AAACAGAAGGAGCATAAGAAATAACA 57.364 30.769 0.00 0.00 0.00 2.41
3027 4069 8.730680 TGAAACAGAAGGAGCATAAGAAATAAC 58.269 33.333 0.00 0.00 0.00 1.89
3028 4070 8.730680 GTGAAACAGAAGGAGCATAAGAAATAA 58.269 33.333 0.00 0.00 36.32 1.40
3029 4071 7.882791 TGTGAAACAGAAGGAGCATAAGAAATA 59.117 33.333 0.00 0.00 45.67 1.40
3030 4072 6.716628 TGTGAAACAGAAGGAGCATAAGAAAT 59.283 34.615 0.00 0.00 45.67 2.17
3031 4073 6.061441 TGTGAAACAGAAGGAGCATAAGAAA 58.939 36.000 0.00 0.00 45.67 2.52
3032 4074 5.620206 TGTGAAACAGAAGGAGCATAAGAA 58.380 37.500 0.00 0.00 45.67 2.52
3033 4075 5.227569 TGTGAAACAGAAGGAGCATAAGA 57.772 39.130 0.00 0.00 45.67 2.10
3048 4090 7.985476 ACCTAATATGCACTACATTGTGAAAC 58.015 34.615 0.00 0.00 40.38 2.78
3049 4091 8.574251 AACCTAATATGCACTACATTGTGAAA 57.426 30.769 0.00 0.00 40.38 2.69
3050 4092 8.574251 AAACCTAATATGCACTACATTGTGAA 57.426 30.769 0.00 0.00 40.38 3.18
3051 4093 8.574251 AAAACCTAATATGCACTACATTGTGA 57.426 30.769 0.00 0.00 40.38 3.58


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

AutoCloner maintained by Alex Coulton.