Multiple sequence alignment - TraesCS2D01G416200

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 TraesCS2D01G416200 chr2D 100.000 5401 0 0 1 5401 529679543 529684943 0.000000e+00 9974
1 TraesCS2D01G416200 chr2D 79.174 533 95 12 4598 5125 537338598 537339119 6.650000e-94 355
2 TraesCS2D01G416200 chr2A 93.801 2807 127 28 960 3743 674529120 674531902 0.000000e+00 4176
3 TraesCS2D01G416200 chr2A 94.754 1220 48 9 4198 5401 674532510 674533729 0.000000e+00 1884
4 TraesCS2D01G416200 chr2A 91.264 435 31 7 3744 4175 674532020 674532450 2.170000e-163 586
5 TraesCS2D01G416200 chr2A 78.571 560 95 20 4598 5147 679964625 679965169 4.000000e-91 346
6 TraesCS2D01G416200 chr2B 92.365 2842 154 36 934 3743 629811374 629814184 0.000000e+00 3988
7 TraesCS2D01G416200 chr2B 93.545 1673 86 14 3744 5401 629814302 629815967 0.000000e+00 2471
8 TraesCS2D01G416200 chr3D 95.657 944 24 5 1 933 424619386 424618449 0.000000e+00 1500
9 TraesCS2D01G416200 chr6B 94.603 945 33 8 1 933 415032963 415033901 0.000000e+00 1447
10 TraesCS2D01G416200 chr4D 79.370 349 60 8 1 338 108901104 108900757 9.040000e-58 235
11 TraesCS2D01G416200 chr5B 76.062 259 48 9 1 248 44055069 44055324 7.350000e-24 122
12 TraesCS2D01G416200 chr7D 74.899 247 55 5 9 248 123876578 123876824 7.400000e-19 106
13 TraesCS2D01G416200 chr7D 74.899 247 55 5 9 248 123961992 123962238 7.400000e-19 106


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 TraesCS2D01G416200 chr2D 529679543 529684943 5400 False 9974.000000 9974 100.000 1 5401 1 chr2D.!!$F1 5400
1 TraesCS2D01G416200 chr2D 537338598 537339119 521 False 355.000000 355 79.174 4598 5125 1 chr2D.!!$F2 527
2 TraesCS2D01G416200 chr2A 674529120 674533729 4609 False 2215.333333 4176 93.273 960 5401 3 chr2A.!!$F2 4441
3 TraesCS2D01G416200 chr2A 679964625 679965169 544 False 346.000000 346 78.571 4598 5147 1 chr2A.!!$F1 549
4 TraesCS2D01G416200 chr2B 629811374 629815967 4593 False 3229.500000 3988 92.955 934 5401 2 chr2B.!!$F1 4467
5 TraesCS2D01G416200 chr3D 424618449 424619386 937 True 1500.000000 1500 95.657 1 933 1 chr3D.!!$R1 932
6 TraesCS2D01G416200 chr6B 415032963 415033901 938 False 1447.000000 1447 94.603 1 933 1 chr6B.!!$F1 932

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
165 177 1.977293 GCCAGGGGTTGTGCCAAAAA 61.977 55.0 0.00 0.0 39.65 1.94 F
1925 1955 2.036475 CACTGCTGACTGTACTTCCACT 59.964 50.0 0.00 0.0 0.00 4.00 F
3432 3484 0.108804 CACATACCAGGACGCGACTT 60.109 55.0 15.93 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2178 1.134670 GTCTACCAGCCACATCACCTC 60.135 57.143 0.0 0.0 0.00 3.85 R
3682 3734 0.250124 AGGTTCACGATTGGTTGCGA 60.250 50.000 0.0 0.0 0.00 5.10 R
4714 4941 0.251354 GCTTGGTGCTCTCCATCTGA 59.749 55.000 0.0 0.0 37.33 3.27 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
162 174 4.149019 TGCCAGGGGTTGTGCCAA 62.149 61.111 0.00 0.00 39.65 4.52
163 175 2.841988 GCCAGGGGTTGTGCCAAA 60.842 61.111 0.00 0.00 39.65 3.28
164 176 2.439104 GCCAGGGGTTGTGCCAAAA 61.439 57.895 0.00 0.00 39.65 2.44
165 177 1.977293 GCCAGGGGTTGTGCCAAAAA 61.977 55.000 0.00 0.00 39.65 1.94
224 236 2.548920 GGGATAGAAGGCCATCAACGAG 60.549 54.545 11.19 0.00 0.00 4.18
263 275 3.328931 ACTGGGTGTTGATGAGAACTGAT 59.671 43.478 0.00 0.00 0.00 2.90
348 360 2.358003 AGCACTGCTCCACGCTTC 60.358 61.111 0.00 0.00 40.11 3.86
434 446 7.428282 TGTTTGAACTATGTTCGATTAGCAA 57.572 32.000 6.05 0.00 0.00 3.91
480 492 2.923605 GCAGCGCTTGAACATGACAAAT 60.924 45.455 7.50 0.00 0.00 2.32
714 726 4.007940 CGTGGACGCCGTTTGTGG 62.008 66.667 0.00 0.00 0.00 4.17
832 844 4.831155 CCTCTGGCATGGACAAATTATCAT 59.169 41.667 0.00 0.00 0.00 2.45
878 890 3.576356 GCATGGATCCACACGCCG 61.576 66.667 18.99 2.69 0.00 6.46
879 891 2.125147 CATGGATCCACACGCCGT 60.125 61.111 18.99 0.00 0.00 5.68
936 949 4.083324 GGCTCACAAACAGATTTTCGATGA 60.083 41.667 0.00 0.00 0.00 2.92
947 960 6.017770 ACAGATTTTCGATGAAAACCGTGTTA 60.018 34.615 6.84 0.00 42.98 2.41
949 962 7.537306 CAGATTTTCGATGAAAACCGTGTTATT 59.463 33.333 6.84 0.00 42.98 1.40
1041 1056 9.184523 CATCCCAAAAACAAATATACTCCTACA 57.815 33.333 0.00 0.00 0.00 2.74
1089 1105 5.617252 TCGTTAGAAAATTTCCAGTCCTGT 58.383 37.500 1.57 0.00 0.00 4.00
1669 1688 5.757808 GGGATTTCTCTGATTTCTCACTAGC 59.242 44.000 0.00 0.00 0.00 3.42
1725 1750 9.362151 TGGAACCTGTTAATTTTGATTAGAAGT 57.638 29.630 0.00 0.00 0.00 3.01
1811 1839 7.961325 AGTTTAATTTGCCTGTTTATGGTTG 57.039 32.000 0.00 0.00 0.00 3.77
1841 1869 3.788937 CTTCCAATGCCCATGATTGTTC 58.211 45.455 0.00 0.00 0.00 3.18
1842 1870 2.109774 TCCAATGCCCATGATTGTTCC 58.890 47.619 0.00 0.00 0.00 3.62
1881 1910 3.189287 AGTTGAACACTCCGCATTTCATC 59.811 43.478 0.00 0.00 0.00 2.92
1916 1946 2.988010 TGTCTTTCACTGCTGACTGT 57.012 45.000 0.00 0.00 0.00 3.55
1925 1955 2.036475 CACTGCTGACTGTACTTCCACT 59.964 50.000 0.00 0.00 0.00 4.00
1940 1970 7.656137 TGTACTTCCACTAATTTCTGTGAGTTC 59.344 37.037 0.00 3.97 36.38 3.01
1952 1998 6.954487 TTCTGTGAGTTCTAGTGTTACAGA 57.046 37.500 12.24 12.24 40.65 3.41
1990 2039 7.852971 ATCAAGGTTGCATAATGGAAATTTG 57.147 32.000 0.00 0.00 30.34 2.32
2107 2156 3.261981 ACTTGTATAGGGGCTTCAACG 57.738 47.619 0.00 0.00 0.00 4.10
2129 2178 3.457610 AAAATGGGCCATTAAGCGATG 57.542 42.857 30.89 0.00 32.43 3.84
2187 2236 2.028112 TGCTCATAGTGAACCCTGTGAC 60.028 50.000 0.00 0.00 30.59 3.67
2192 2241 1.227853 GTGAACCCTGTGACGGCTT 60.228 57.895 0.00 0.00 0.00 4.35
2314 2364 5.297278 TGCTTTACTGTCGGTTACACAAATT 59.703 36.000 0.00 0.00 33.45 1.82
2656 2706 2.035066 ACAGCAATTGTCAGAAACAGGC 59.965 45.455 7.40 0.00 39.58 4.85
2743 2793 4.499399 GCTCAACCTCAAAAGTTCGAAAAC 59.501 41.667 0.00 0.00 35.50 2.43
2757 2807 4.795970 TCGAAAACTTCTTCTGTTGAGC 57.204 40.909 0.00 0.00 0.00 4.26
2791 2841 9.912634 TGTGTCTTTTCCTTGATTTCATATTTC 57.087 29.630 0.00 0.00 0.00 2.17
2824 2874 3.251729 TGACAGATGAAGTTTCAAGCAGC 59.748 43.478 0.00 0.00 41.13 5.25
2845 2895 4.072131 GCCACACCTCTTCAAATACTTCA 58.928 43.478 0.00 0.00 0.00 3.02
2857 2907 4.631377 TCAAATACTTCAAGCAGATCCACG 59.369 41.667 0.00 0.00 0.00 4.94
2863 2913 1.827344 TCAAGCAGATCCACGATCACT 59.173 47.619 4.56 0.00 41.12 3.41
2894 2944 4.941873 CCCAAGGTGTCATTAGTTAACTCC 59.058 45.833 12.39 5.25 0.00 3.85
2952 3003 6.424509 ACATGTTATTTTTCGACCGTCAGTTA 59.575 34.615 0.00 0.00 0.00 2.24
2961 3012 6.500684 TTCGACCGTCAGTTACTTACTATT 57.499 37.500 0.00 0.00 34.56 1.73
3010 3061 0.843309 CACACCATATGTAGCCCCCA 59.157 55.000 1.24 0.00 40.64 4.96
3011 3062 1.140312 ACACCATATGTAGCCCCCAG 58.860 55.000 1.24 0.00 40.88 4.45
3012 3063 0.401738 CACCATATGTAGCCCCCAGG 59.598 60.000 1.24 0.00 0.00 4.45
3049 3100 7.395190 TCAACACCAATTATTTCATCCTCTG 57.605 36.000 0.00 0.00 0.00 3.35
3061 3112 0.253820 ATCCTCTGGTGGTTCCCCAT 60.254 55.000 0.00 0.00 44.35 4.00
3111 3162 3.612860 CGAAGTTCTATTCTGGTCCAACG 59.387 47.826 0.56 0.00 0.00 4.10
3126 3177 1.135083 CCAACGTCGCCTACAAGATCT 60.135 52.381 0.00 0.00 0.00 2.75
3144 3195 4.464244 AGATCTCGTTCTGAAGACCAATCA 59.536 41.667 0.00 0.00 0.00 2.57
3189 3240 1.771255 AGTCATCAGTATTCAGCCCCC 59.229 52.381 0.00 0.00 0.00 5.40
3220 3271 0.321298 ACGCCGCTCATTTACAGGTT 60.321 50.000 0.00 0.00 0.00 3.50
3222 3273 0.733150 GCCGCTCATTTACAGGTTCC 59.267 55.000 0.00 0.00 0.00 3.62
3229 3280 3.146066 TCATTTACAGGTTCCACACAGC 58.854 45.455 0.00 0.00 0.00 4.40
3244 3295 2.172505 ACACAGCGGATTATCAATGGGA 59.827 45.455 0.00 0.00 0.00 4.37
3273 3325 7.065085 CGCTATATTCATTTGGGATAGTTCCTG 59.935 40.741 0.00 0.00 42.20 3.86
3288 3340 7.040409 GGATAGTTCCTGAACATGTTTGTTCTT 60.040 37.037 13.36 0.00 45.95 2.52
3363 3415 1.464608 CGGTTGGTCACTATGCTGTTG 59.535 52.381 0.00 0.00 0.00 3.33
3369 3421 3.324846 TGGTCACTATGCTGTTGACTCTT 59.675 43.478 0.00 0.00 0.00 2.85
3372 3424 5.106908 GGTCACTATGCTGTTGACTCTTTTC 60.107 44.000 0.00 0.00 0.00 2.29
3410 3462 3.343941 TCACCCTATAACACTTGTGGC 57.656 47.619 5.72 0.00 0.00 5.01
3411 3463 2.026636 TCACCCTATAACACTTGTGGCC 60.027 50.000 0.00 0.00 0.00 5.36
3426 3478 1.449601 GGCCACACATACCAGGACG 60.450 63.158 0.00 0.00 0.00 4.79
3432 3484 0.108804 CACATACCAGGACGCGACTT 60.109 55.000 15.93 0.00 0.00 3.01
3468 3520 4.924305 TGGAGCATTCTTGGCAAATATC 57.076 40.909 0.00 0.00 0.00 1.63
3483 3535 6.700960 TGGCAAATATCAAGGAATTTAATGCG 59.299 34.615 0.00 0.00 0.00 4.73
3521 3573 0.179119 GTAGCGCGGTTCACCAGTAT 60.179 55.000 19.09 0.00 35.14 2.12
3584 3636 8.552865 ACAAAAATCATGTGATGTGATGTTTTG 58.447 29.630 17.89 17.89 40.04 2.44
3592 3644 6.724263 TGTGATGTGATGTTTTGTACTTGAC 58.276 36.000 0.00 0.00 0.00 3.18
3611 3663 3.244770 TGACCAATTTCTACAGGACACCC 60.245 47.826 0.00 0.00 0.00 4.61
3613 3665 4.172807 ACCAATTTCTACAGGACACCCTA 58.827 43.478 0.00 0.00 42.02 3.53
3652 3704 5.596836 TTTTTGGAACAGAGCACAAAGAT 57.403 34.783 0.00 0.00 42.39 2.40
3653 3705 4.836125 TTTGGAACAGAGCACAAAGATC 57.164 40.909 0.00 0.00 42.39 2.75
3750 3919 3.250762 TGAACAAGCTGGTTTCAAGATCG 59.749 43.478 8.18 0.00 0.00 3.69
3787 3956 3.694072 TGTGCATAGGCCATTGTAGTTTC 59.306 43.478 5.01 0.00 40.13 2.78
3790 3959 2.032680 TAGGCCATTGTAGTTTCGGC 57.967 50.000 5.01 0.00 42.21 5.54
3795 3964 1.375013 ATTGTAGTTTCGGCGCGGT 60.375 52.632 15.06 0.00 0.00 5.68
3796 3965 0.952010 ATTGTAGTTTCGGCGCGGTT 60.952 50.000 15.06 2.57 0.00 4.44
3802 3971 1.812093 TTTCGGCGCGGTTATCCTG 60.812 57.895 15.06 0.00 0.00 3.86
3806 3975 1.831389 CGGCGCGGTTATCCTGAATG 61.831 60.000 8.83 0.00 0.00 2.67
3822 3991 6.661777 TCCTGAATGACATGATGTAAATGGA 58.338 36.000 0.00 0.00 0.00 3.41
3839 4008 2.946785 TGGATATGGTCATGCATGCAA 58.053 42.857 26.68 8.17 0.00 4.08
3849 4018 3.991773 GTCATGCATGCAATTCAACAAGT 59.008 39.130 26.68 0.00 0.00 3.16
3850 4019 3.991121 TCATGCATGCAATTCAACAAGTG 59.009 39.130 26.68 14.13 0.00 3.16
3904 4076 6.520272 AGTTGAGACTGTCAGATATATTGGC 58.480 40.000 10.88 0.00 36.21 4.52
3922 4094 4.359434 TGGCCTGTGTAATTGACTTGTA 57.641 40.909 3.32 0.00 0.00 2.41
3933 4105 9.463443 GTGTAATTGACTTGTAAATTGAAGCTT 57.537 29.630 0.00 0.00 0.00 3.74
4053 4225 9.865321 ATGTTAATCATGGATCAAAAGTTGAAG 57.135 29.630 0.00 0.00 38.08 3.02
4085 4257 1.276415 GTTGTGTTGCATTGCACGTT 58.724 45.000 11.66 0.00 38.71 3.99
4127 4308 5.187772 TCCTCTATACATTATGCAATCCGCT 59.812 40.000 0.00 0.00 43.06 5.52
4136 4317 8.284945 ACATTATGCAATCCGCTTATTATGAT 57.715 30.769 0.00 0.00 43.06 2.45
4139 4320 4.650734 TGCAATCCGCTTATTATGATCCA 58.349 39.130 0.00 0.00 43.06 3.41
4143 4324 6.127925 GCAATCCGCTTATTATGATCCATGAA 60.128 38.462 0.00 0.00 37.77 2.57
4148 4329 8.708378 TCCGCTTATTATGATCCATGAATAGAT 58.292 33.333 0.00 0.00 0.00 1.98
4162 4343 9.699410 TCCATGAATAGATCTGTTATTTTTGGT 57.301 29.630 5.18 0.00 31.52 3.67
4163 4344 9.956720 CCATGAATAGATCTGTTATTTTTGGTC 57.043 33.333 5.18 0.00 0.00 4.02
4180 4361 2.433239 TGGTCTATAAAAGAGGGGCGAC 59.567 50.000 0.00 0.00 33.88 5.19
4187 4368 0.253327 AAAGAGGGGCGACATCTTCC 59.747 55.000 8.29 0.00 37.04 3.46
4237 4456 4.565022 CTTCTCAACTCCTGTTCTTCTCC 58.435 47.826 0.00 0.00 33.52 3.71
4289 4513 6.316890 TGTGTTTGTTAGTTTCCAGTAGTTCC 59.683 38.462 0.00 0.00 0.00 3.62
4501 4725 3.138798 CAGCAGCTGGCCATGGTC 61.139 66.667 17.12 10.20 46.50 4.02
4645 4872 3.005539 AGCATGGTGGACCTCGCT 61.006 61.111 0.00 6.70 38.69 4.93
4839 5066 3.506096 CGGCTGCTACGACGAGGA 61.506 66.667 0.00 0.00 37.71 3.71
4840 5067 2.882876 GGCTGCTACGACGAGGAA 59.117 61.111 0.00 0.00 0.00 3.36
4926 5153 4.068302 GTACCTGCTGTACGCGTC 57.932 61.111 18.63 8.55 40.44 5.19
5166 5397 0.966370 CCCTCGACGAGAAACCTCCT 60.966 60.000 26.11 0.00 0.00 3.69
5169 5400 0.894184 TCGACGAGAAACCTCCTGCT 60.894 55.000 0.00 0.00 0.00 4.24
5211 5442 2.759973 CACCTGCTCGGCCTCCTA 60.760 66.667 0.00 0.00 35.61 2.94
5235 5466 0.677731 ACTACATCGTCGGAACCGGA 60.678 55.000 9.46 4.20 40.25 5.14
5381 5615 0.179089 CTGAAGGAGATGGGCGTCAG 60.179 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 236 1.945394 CAGTGGCCTCTTGCATGTATC 59.055 52.381 4.10 0.00 43.89 2.24
263 275 8.511321 ACGCATTACAAACTGAAAATTCATAGA 58.489 29.630 0.00 0.00 36.46 1.98
348 360 0.179034 GCCCCTGCAGATTGAGGTAG 60.179 60.000 17.39 0.00 37.47 3.18
413 425 9.340695 CAAATTTGCTAATCGAACATAGTTCAA 57.659 29.630 5.01 0.00 0.00 2.69
434 446 9.592720 GCAAACAAAACGATATTTAAGCAAATT 57.407 25.926 0.00 0.00 35.88 1.82
668 680 3.157087 CCATAAATGCCTACCCACCATC 58.843 50.000 0.00 0.00 0.00 3.51
714 726 1.838568 GCCGTGTTGTTCCTTCGTCC 61.839 60.000 0.00 0.00 0.00 4.79
832 844 4.219070 CCTGTATTTCCCGTCCGTATATCA 59.781 45.833 0.00 0.00 0.00 2.15
878 890 2.168521 TCCTGAAATCCAGACCGATGAC 59.831 50.000 0.00 0.00 45.78 3.06
879 891 2.466846 TCCTGAAATCCAGACCGATGA 58.533 47.619 0.00 0.00 45.78 2.92
919 932 5.685511 ACGGTTTTCATCGAAAATCTGTTTG 59.314 36.000 9.95 0.00 42.31 2.93
936 949 6.708949 TGCTCTCTCTAAAATAACACGGTTTT 59.291 34.615 0.00 0.00 0.00 2.43
947 960 4.767578 TCCATGCTGCTCTCTCTAAAAT 57.232 40.909 0.00 0.00 0.00 1.82
949 962 4.558226 TTTCCATGCTGCTCTCTCTAAA 57.442 40.909 0.00 0.00 0.00 1.85
1062 1078 5.106317 GGACTGGAAATTTTCTAACGATGCA 60.106 40.000 8.93 0.00 0.00 3.96
1168 1184 4.827087 CATCGCTGCCTCTGCCGT 62.827 66.667 0.00 0.00 36.33 5.68
1173 1192 4.218578 CTCGCCATCGCTGCCTCT 62.219 66.667 0.00 0.00 35.26 3.69
1236 1255 3.518998 ACGGCCAGGATCTCGTCG 61.519 66.667 2.24 0.00 0.00 5.12
1811 1839 3.727419 GCATTGGAAGCCACATCAC 57.273 52.632 0.00 0.00 30.78 3.06
1841 1869 2.755469 CCACCTTCGCCAATGGGG 60.755 66.667 10.38 10.38 40.85 4.96
1842 1870 1.750399 CTCCACCTTCGCCAATGGG 60.750 63.158 0.00 0.00 32.73 4.00
1916 1946 7.963532 AGAACTCACAGAAATTAGTGGAAGTA 58.036 34.615 5.96 0.00 36.43 2.24
1925 1955 9.692749 CTGTAACACTAGAACTCACAGAAATTA 57.307 33.333 0.00 0.00 35.12 1.40
1952 1998 7.271511 TGCAACCTTGATAAGTCAAACAAAAT 58.728 30.769 0.00 0.00 43.39 1.82
2107 2156 3.518634 TCGCTTAATGGCCCATTTTTC 57.481 42.857 15.41 3.11 35.54 2.29
2129 2178 1.134670 GTCTACCAGCCACATCACCTC 60.135 57.143 0.00 0.00 0.00 3.85
2221 2271 6.183360 CCACAAATCTGGTTTAGTAGCTTAGC 60.183 42.308 0.00 0.00 0.00 3.09
2277 2327 6.402442 CGACAGTAAAGCATTCATCAATCACA 60.402 38.462 0.00 0.00 0.00 3.58
2282 2332 4.323417 ACCGACAGTAAAGCATTCATCAA 58.677 39.130 0.00 0.00 0.00 2.57
2399 2449 9.590451 AATCATGTTGATGTTGATTTGGATAAC 57.410 29.630 0.00 0.00 37.15 1.89
2656 2706 3.632189 TGCATCTACATCACGATCTTCG 58.368 45.455 0.00 0.00 46.93 3.79
2718 2768 3.275143 TCGAACTTTTGAGGTTGAGCAA 58.725 40.909 0.00 0.00 0.00 3.91
2743 2793 4.907879 AACTTTGGCTCAACAGAAGAAG 57.092 40.909 0.00 0.00 0.00 2.85
2744 2794 4.462483 ACAAACTTTGGCTCAACAGAAGAA 59.538 37.500 6.47 0.00 34.12 2.52
2745 2795 4.016444 ACAAACTTTGGCTCAACAGAAGA 58.984 39.130 6.47 0.00 34.12 2.87
2754 2804 4.112634 GGAAAAGACACAAACTTTGGCTC 58.887 43.478 6.47 0.52 37.59 4.70
2757 2807 5.719173 TCAAGGAAAAGACACAAACTTTGG 58.281 37.500 6.47 0.00 37.59 3.28
2798 2848 7.509141 TGCTTGAAACTTCATCTGTCAATTA 57.491 32.000 0.00 0.00 37.00 1.40
2824 2874 5.335191 GCTTGAAGTATTTGAAGAGGTGTGG 60.335 44.000 1.39 0.00 0.00 4.17
2845 2895 1.827344 TCAGTGATCGTGGATCTGCTT 59.173 47.619 7.10 0.00 39.56 3.91
2857 2907 2.295885 CCTTGGGCTGATTCAGTGATC 58.704 52.381 14.90 0.00 33.43 2.92
2863 2913 0.770499 TGACACCTTGGGCTGATTCA 59.230 50.000 0.00 0.00 0.00 2.57
2931 2981 6.457851 AGTAACTGACGGTCGAAAAATAAC 57.542 37.500 3.34 0.00 0.00 1.89
2933 2983 7.370383 AGTAAGTAACTGACGGTCGAAAAATA 58.630 34.615 3.34 0.00 36.93 1.40
2934 2984 6.218746 AGTAAGTAACTGACGGTCGAAAAAT 58.781 36.000 3.34 0.00 36.93 1.82
2939 2990 5.643348 TCAATAGTAAGTAACTGACGGTCGA 59.357 40.000 3.34 0.00 39.39 4.20
2961 3012 6.440647 AGAACTGGTATCCTGTGAATACTTCA 59.559 38.462 0.00 0.00 35.88 3.02
3061 3112 5.104151 TGGATGGACCAGTTGAATATGCTAA 60.104 40.000 0.00 0.00 44.64 3.09
3111 3162 2.097791 AGAACGAGATCTTGTAGGCGAC 59.902 50.000 16.19 4.96 0.00 5.19
3126 3177 2.037121 TGCTGATTGGTCTTCAGAACGA 59.963 45.455 4.93 0.00 42.63 3.85
3144 3195 5.600898 TGATCCATTCCATGATGAAAATGCT 59.399 36.000 12.26 5.06 0.00 3.79
3189 3240 2.202492 CGGCGTTGAGGAGAGACG 60.202 66.667 0.00 0.00 39.61 4.18
3220 3271 3.205338 CATTGATAATCCGCTGTGTGGA 58.795 45.455 2.17 2.17 46.70 4.02
3222 3273 2.291465 CCCATTGATAATCCGCTGTGTG 59.709 50.000 0.00 0.00 0.00 3.82
3229 3280 2.069273 GCGACTCCCATTGATAATCCG 58.931 52.381 0.00 0.00 0.00 4.18
3244 3295 7.246171 ACTATCCCAAATGAATATAGCGACT 57.754 36.000 0.00 0.00 0.00 4.18
3288 3340 4.500887 CGAGGTCGCCCTAGAAATATCAAA 60.501 45.833 0.00 0.00 42.86 2.69
3291 3343 2.557490 ACGAGGTCGCCCTAGAAATATC 59.443 50.000 0.00 0.00 42.86 1.63
3299 3351 2.617276 CCATCTATACGAGGTCGCCCTA 60.617 54.545 0.00 0.00 42.86 3.53
3393 3445 2.290641 TGTGGCCACAAGTGTTATAGGG 60.291 50.000 36.10 0.00 38.56 3.53
3394 3446 2.747446 GTGTGGCCACAAGTGTTATAGG 59.253 50.000 39.23 0.00 43.77 2.57
3410 3462 1.809619 CGCGTCCTGGTATGTGTGG 60.810 63.158 0.00 0.00 0.00 4.17
3411 3463 1.076533 GTCGCGTCCTGGTATGTGTG 61.077 60.000 5.77 0.00 0.00 3.82
3415 3467 1.135083 AGAAAGTCGCGTCCTGGTATG 60.135 52.381 5.77 0.00 0.00 2.39
3426 3478 4.795278 CCAAATTGCTCATAAGAAAGTCGC 59.205 41.667 0.00 0.00 0.00 5.19
3432 3484 6.379133 AGAATGCTCCAAATTGCTCATAAGAA 59.621 34.615 0.00 0.00 0.00 2.52
3468 3520 4.922692 TGTTTCTGCGCATTAAATTCCTTG 59.077 37.500 12.24 0.00 0.00 3.61
3483 3535 0.371645 CCTCTCGCGATTGTTTCTGC 59.628 55.000 10.36 0.00 0.00 4.26
3507 3559 5.587443 AGGTTATAAAATACTGGTGAACCGC 59.413 40.000 0.00 0.00 40.03 5.68
3546 3598 9.460019 TCACATGATTTTTGTGGATACTAATGA 57.540 29.630 0.00 0.00 43.67 2.57
3549 3601 9.241919 ACATCACATGATTTTTGTGGATACTAA 57.758 29.630 0.00 0.00 43.67 2.24
3550 3602 8.676401 CACATCACATGATTTTTGTGGATACTA 58.324 33.333 0.00 0.00 43.67 1.82
3551 3603 7.394077 TCACATCACATGATTTTTGTGGATACT 59.606 33.333 0.00 0.00 43.67 2.12
3552 3604 7.537715 TCACATCACATGATTTTTGTGGATAC 58.462 34.615 0.00 0.00 43.67 2.24
3565 3617 7.228308 TCAAGTACAAAACATCACATCACATGA 59.772 33.333 0.00 0.00 0.00 3.07
3571 3623 6.312399 TGGTCAAGTACAAAACATCACATC 57.688 37.500 0.00 0.00 0.00 3.06
3580 3632 7.776030 TCCTGTAGAAATTGGTCAAGTACAAAA 59.224 33.333 0.00 0.00 0.00 2.44
3584 3636 6.147328 GTGTCCTGTAGAAATTGGTCAAGTAC 59.853 42.308 0.00 0.00 0.00 2.73
3592 3644 3.721087 AGGGTGTCCTGTAGAAATTGG 57.279 47.619 0.00 0.00 42.98 3.16
3611 3663 6.238320 CCAAAAATCTCCTCTGCTTTCGATAG 60.238 42.308 0.00 0.00 0.00 2.08
3613 3665 4.397417 CCAAAAATCTCCTCTGCTTTCGAT 59.603 41.667 0.00 0.00 0.00 3.59
3682 3734 0.250124 AGGTTCACGATTGGTTGCGA 60.250 50.000 0.00 0.00 0.00 5.10
3750 3919 6.370166 GCCTATGCACAGATTTCTAAGGATAC 59.630 42.308 0.00 0.00 37.47 2.24
3787 3956 1.594293 ATTCAGGATAACCGCGCCG 60.594 57.895 0.00 0.00 41.83 6.46
3790 3959 1.934589 TGTCATTCAGGATAACCGCG 58.065 50.000 0.00 0.00 41.83 6.46
3795 3964 9.070179 CCATTTACATCATGTCATTCAGGATAA 57.930 33.333 0.00 0.00 44.25 1.75
3796 3965 8.439172 TCCATTTACATCATGTCATTCAGGATA 58.561 33.333 0.00 0.00 44.25 2.59
3802 3971 9.017509 ACCATATCCATTTACATCATGTCATTC 57.982 33.333 0.00 0.00 0.00 2.67
3806 3975 7.984422 TGACCATATCCATTTACATCATGTC 57.016 36.000 0.00 0.00 0.00 3.06
3822 3991 5.163395 TGTTGAATTGCATGCATGACCATAT 60.163 36.000 30.64 7.12 0.00 1.78
3863 4032 6.757010 GTCTCAACTCTCACTTGTTACAGAAA 59.243 38.462 0.00 0.00 0.00 2.52
3866 4035 5.689514 CAGTCTCAACTCTCACTTGTTACAG 59.310 44.000 0.00 0.00 31.71 2.74
3868 4037 5.593010 ACAGTCTCAACTCTCACTTGTTAC 58.407 41.667 0.00 0.00 31.71 2.50
3869 4038 5.359860 TGACAGTCTCAACTCTCACTTGTTA 59.640 40.000 1.31 0.00 31.71 2.41
3878 4049 7.471260 GCCAATATATCTGACAGTCTCAACTCT 60.471 40.741 1.59 0.00 31.71 3.24
3879 4050 6.644592 GCCAATATATCTGACAGTCTCAACTC 59.355 42.308 1.59 0.00 31.71 3.01
3904 4076 9.398170 CTTCAATTTACAAGTCAATTACACAGG 57.602 33.333 0.00 0.00 0.00 4.00
3922 4094 4.571984 GGTGCTGAAAACAAGCTTCAATTT 59.428 37.500 0.00 0.00 41.42 1.82
3933 4105 1.490490 AGACAGGAGGTGCTGAAAACA 59.510 47.619 5.40 0.00 0.00 2.83
4053 4225 0.765510 ACACAACCTGGAGGAACCTC 59.234 55.000 11.97 11.97 42.04 3.85
4085 4257 5.190677 AGAGGAAACCTTTCGACTTTTTCA 58.809 37.500 9.13 0.00 38.06 2.69
4136 4317 9.699410 ACCAAAAATAACAGATCTATTCATGGA 57.301 29.630 18.55 0.00 33.18 3.41
4154 4335 5.359860 CGCCCCTCTTTTATAGACCAAAAAT 59.640 40.000 0.00 0.00 0.00 1.82
4157 4338 3.520317 TCGCCCCTCTTTTATAGACCAAA 59.480 43.478 0.00 0.00 0.00 3.28
4158 4339 3.109151 TCGCCCCTCTTTTATAGACCAA 58.891 45.455 0.00 0.00 0.00 3.67
4160 4341 2.433239 TGTCGCCCCTCTTTTATAGACC 59.567 50.000 0.00 0.00 0.00 3.85
4161 4342 3.814005 TGTCGCCCCTCTTTTATAGAC 57.186 47.619 0.00 0.00 0.00 2.59
4162 4343 4.223953 AGATGTCGCCCCTCTTTTATAGA 58.776 43.478 0.00 0.00 0.00 1.98
4163 4344 4.608948 AGATGTCGCCCCTCTTTTATAG 57.391 45.455 0.00 0.00 0.00 1.31
4164 4345 4.202326 GGAAGATGTCGCCCCTCTTTTATA 60.202 45.833 0.00 0.00 29.64 0.98
4165 4346 3.433740 GGAAGATGTCGCCCCTCTTTTAT 60.434 47.826 0.00 0.00 29.64 1.40
4166 4347 2.093128 GGAAGATGTCGCCCCTCTTTTA 60.093 50.000 0.00 0.00 29.64 1.52
4167 4348 1.340114 GGAAGATGTCGCCCCTCTTTT 60.340 52.381 0.00 0.00 29.64 2.27
4187 4368 1.009829 GCAACAGTTATCCTCCAGCG 58.990 55.000 0.00 0.00 0.00 5.18
4191 4372 3.618690 AGACTGCAACAGTTATCCTCC 57.381 47.619 1.15 0.00 45.44 4.30
4237 4456 3.878778 CCTAACCACCAGAGAATGAAGG 58.121 50.000 0.00 0.00 0.00 3.46
4289 4513 1.741706 CTGCATGTCAGCAACCTAAGG 59.258 52.381 4.55 0.00 45.13 2.69
4486 4710 4.783621 TCGACCATGGCCAGCTGC 62.784 66.667 13.05 3.68 40.16 5.25
4494 4718 1.448540 GTGGTGCTCTCGACCATGG 60.449 63.158 11.19 11.19 45.27 3.66
4501 4725 2.890847 GATGGTCGGTGGTGCTCTCG 62.891 65.000 0.00 0.00 0.00 4.04
4552 4779 3.418068 GCTGCTTGCTCGAACGCT 61.418 61.111 0.00 0.00 38.95 5.07
4562 4789 3.793144 GAACTCCCGCGCTGCTTG 61.793 66.667 5.56 0.00 0.00 4.01
4704 4931 1.949847 CTCCATCTGAAGGACGGCGT 61.950 60.000 14.65 14.65 0.00 5.68
4714 4941 0.251354 GCTTGGTGCTCTCCATCTGA 59.749 55.000 0.00 0.00 37.33 3.27
4839 5066 4.016706 CGAGACCCCGCACCCTTT 62.017 66.667 0.00 0.00 0.00 3.11
5169 5400 1.005037 CGTGTAGCTGCTGTCCCAA 60.005 57.895 13.43 0.00 0.00 4.12
5211 5442 1.398390 GTTCCGACGATGTAGTACCGT 59.602 52.381 4.54 4.54 39.41 4.83
5235 5466 1.179814 ACTCGGACGAGAGCTTGGTT 61.180 55.000 26.41 0.23 44.53 3.67
5381 5615 4.168291 CGGAGAGCAGCCCCTTCC 62.168 72.222 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.