Multiple sequence alignment - TraesCS1D01G231600

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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 TraesCS1D01G231600 chr1D 100.000 5376 0 0 1 5376 319936983 319931608 0.000000e+00 9928.0
1 TraesCS1D01G231600 chr1D 100.000 30 0 0 2054 2083 59876072 59876043 7.520000e-04 56.5
2 TraesCS1D01G231600 chr1A 94.375 4818 170 48 610 5376 403022766 403027533 0.000000e+00 7302.0
3 TraesCS1D01G231600 chr1A 85.256 624 58 17 1 614 403022013 403022612 3.560000e-171 612.0
4 TraesCS1D01G231600 chr1B 94.085 3432 126 34 1985 5376 432823822 432820428 0.000000e+00 5142.0
5 TraesCS1D01G231600 chr1B 91.014 1391 39 20 621 1987 432825177 432823849 0.000000e+00 1797.0
6 TraesCS1D01G231600 chr1B 83.279 610 47 25 2 600 432825824 432825259 1.340000e-140 510.0
7 TraesCS1D01G231600 chr2A 88.852 305 34 0 5000 5304 621265122 621265426 5.080000e-100 375.0
8 TraesCS1D01G231600 chr2D 88.525 305 35 0 5000 5304 478118173 478118477 2.370000e-98 370.0
9 TraesCS1D01G231600 chr2B 88.525 305 35 0 5000 5304 560458447 560458751 2.370000e-98 370.0
10 TraesCS1D01G231600 chr3D 86.667 270 34 2 1373 1641 460497245 460497513 1.130000e-76 298.0
11 TraesCS1D01G231600 chr3A 86.296 270 35 2 1373 1641 602917576 602917844 5.270000e-75 292.0
12 TraesCS1D01G231600 chr4A 85.766 274 37 2 1382 1655 114592031 114591760 6.810000e-74 289.0
13 TraesCS1D01G231600 chr4D 85.252 278 40 1 1370 1646 350492634 350492911 8.810000e-73 285.0
14 TraesCS1D01G231600 chr4B 84.643 280 43 0 1370 1649 433641730 433642009 4.100000e-71 279.0
15 TraesCS1D01G231600 chr6A 96.970 33 0 1 2055 2087 469430128 469430097 3.000000e-03 54.7


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 TraesCS1D01G231600 chr1D 319931608 319936983 5375 True 9928 9928 100.000000 1 5376 1 chr1D.!!$R2 5375
1 TraesCS1D01G231600 chr1A 403022013 403027533 5520 False 3957 7302 89.815500 1 5376 2 chr1A.!!$F1 5375
2 TraesCS1D01G231600 chr1B 432820428 432825824 5396 True 2483 5142 89.459333 2 5376 3 chr1B.!!$R1 5374

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
69 70 0.038526 ATGACAACGTGACCTCGGTC 60.039 55.000 9.15 9.15 44.77 4.79 F
743 939 0.253020 TAGTCAAACCCCTCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30 F
1958 2174 1.134250 GGAAGACCAGAGCTTGATCCC 60.134 57.143 0.00 0.00 35.97 3.85 F
1960 2176 1.890552 AGACCAGAGCTTGATCCCAT 58.109 50.000 0.00 0.00 0.00 4.00 F
2137 2385 2.103373 TGTGGCATCTCTAGACCAGTC 58.897 52.381 0.14 0.00 31.46 3.51 F
3541 3815 1.669211 GGTGTCAGGAGTTGCTACGAC 60.669 57.143 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2152 2.419851 GGATCAAGCTCTGGTCTTCCTG 60.420 54.545 8.44 0.00 35.28 3.86 R
2443 2699 1.139853 GCCATCTCGAAGGTCAAGGAT 59.860 52.381 0.00 0.00 0.00 3.24 R
3247 3508 0.967662 CCATGTGGCACATTTCACCA 59.032 50.000 29.57 0.95 44.52 4.17 R
3293 3554 1.501604 AGTTTTGCCCCCACCTTCTTA 59.498 47.619 0.00 0.00 0.00 2.10 R
3717 3991 2.093658 TCCGAGCAATCCTAACCTGAAC 60.094 50.000 0.00 0.00 0.00 3.18 R
4444 4729 0.467384 CATAGCTCTGTCAGTGGGGG 59.533 60.000 0.00 0.00 0.00 5.40 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
31 32 1.406069 CCAAGGTTGTCCATCTCGAGG 60.406 57.143 13.56 0.00 35.89 4.63
38 39 2.278857 CCATCTCGAGGTTCGCCG 60.279 66.667 13.56 0.00 43.66 6.46
57 58 1.127951 CGCGAGGTTAACCATGACAAC 59.872 52.381 26.26 7.45 38.89 3.32
58 59 1.127951 GCGAGGTTAACCATGACAACG 59.872 52.381 26.26 17.80 38.89 4.10
61 62 3.395639 GAGGTTAACCATGACAACGTGA 58.604 45.455 26.26 0.00 38.89 4.35
62 63 3.135994 AGGTTAACCATGACAACGTGAC 58.864 45.455 26.26 0.00 38.89 3.67
63 64 2.224784 GGTTAACCATGACAACGTGACC 59.775 50.000 20.12 0.00 35.25 4.02
64 65 3.135994 GTTAACCATGACAACGTGACCT 58.864 45.455 0.00 0.00 35.25 3.85
65 66 1.878953 AACCATGACAACGTGACCTC 58.121 50.000 0.00 0.00 35.25 3.85
66 67 0.319555 ACCATGACAACGTGACCTCG 60.320 55.000 0.00 0.00 35.25 4.63
67 68 1.014044 CCATGACAACGTGACCTCGG 61.014 60.000 0.00 0.00 35.25 4.63
68 69 0.319555 CATGACAACGTGACCTCGGT 60.320 55.000 0.00 0.00 35.25 4.69
69 70 0.038526 ATGACAACGTGACCTCGGTC 60.039 55.000 9.15 9.15 44.77 4.79
108 110 8.913487 ACAATATGTTGAGCTCATTCATATGA 57.087 30.769 32.08 20.50 38.71 2.15
117 119 7.738847 TGAGCTCATTCATATGATTGGAGTTA 58.261 34.615 21.56 6.72 39.94 2.24
153 155 8.097791 TGAGTTAACCCCTACTATAAATGCTT 57.902 34.615 0.88 0.00 0.00 3.91
154 156 9.216148 TGAGTTAACCCCTACTATAAATGCTTA 57.784 33.333 0.88 0.00 0.00 3.09
155 157 9.708092 GAGTTAACCCCTACTATAAATGCTTAG 57.292 37.037 0.88 0.00 0.00 2.18
176 178 5.084818 AGCCATGCTTAATAAAACCCAAC 57.915 39.130 0.00 0.00 33.89 3.77
177 179 3.862845 GCCATGCTTAATAAAACCCAACG 59.137 43.478 0.00 0.00 0.00 4.10
179 181 5.339990 CCATGCTTAATAAAACCCAACGAG 58.660 41.667 0.00 0.00 0.00 4.18
238 240 1.100510 ACTTAGGTCTGATACGCGCA 58.899 50.000 5.73 0.00 0.00 6.09
250 252 1.511318 TACGCGCAAAACATGGCAGT 61.511 50.000 5.73 0.00 0.00 4.40
366 371 4.302067 AGGTATGATAGCCCCAGATATGG 58.698 47.826 0.00 0.00 0.00 2.74
424 429 6.942886 AACAATGCAAATGTACATTTACCG 57.057 33.333 28.64 19.32 38.84 4.02
527 535 2.742589 GACATTGAAAACGGACCCTCTC 59.257 50.000 0.00 0.00 0.00 3.20
537 551 1.872773 GGACCCTCTCTGAGACCATT 58.127 55.000 2.58 0.00 0.00 3.16
538 552 1.760029 GGACCCTCTCTGAGACCATTC 59.240 57.143 2.58 0.00 0.00 2.67
614 644 8.757982 AAACGGATGAAGTACTATAGAGGTTA 57.242 34.615 6.78 0.00 0.00 2.85
615 645 8.757982 AACGGATGAAGTACTATAGAGGTTAA 57.242 34.615 6.78 0.00 0.00 2.01
616 646 8.937207 ACGGATGAAGTACTATAGAGGTTAAT 57.063 34.615 6.78 0.00 0.00 1.40
637 825 2.508663 GTAGAACCGGTCGGCAGC 60.509 66.667 8.04 0.00 39.32 5.25
736 932 1.838073 CTGCCCGTAGTCAAACCCCT 61.838 60.000 0.00 0.00 0.00 4.79
737 933 1.078637 GCCCGTAGTCAAACCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
738 934 1.600638 CCCGTAGTCAAACCCCTCC 59.399 63.158 0.00 0.00 0.00 4.30
739 935 1.600638 CCGTAGTCAAACCCCTCCC 59.399 63.158 0.00 0.00 0.00 4.30
740 936 0.908180 CCGTAGTCAAACCCCTCCCT 60.908 60.000 0.00 0.00 0.00 4.20
741 937 0.535797 CGTAGTCAAACCCCTCCCTC 59.464 60.000 0.00 0.00 0.00 4.30
742 938 0.910338 GTAGTCAAACCCCTCCCTCC 59.090 60.000 0.00 0.00 0.00 4.30
743 939 0.253020 TAGTCAAACCCCTCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
813 1013 4.717313 GGGTCCCACGAGGCAACC 62.717 72.222 1.78 11.60 38.07 3.77
815 1015 2.358737 GTCCCACGAGGCAACCAG 60.359 66.667 0.00 0.00 34.51 4.00
816 1016 3.636231 TCCCACGAGGCAACCAGG 61.636 66.667 0.00 0.00 34.51 4.45
1023 1229 2.359107 TCCGAGCTCACGTACCGT 60.359 61.111 15.40 0.00 42.36 4.83
1177 1386 3.842923 CCCTCGTCGGCATGCTCT 61.843 66.667 18.92 0.00 0.00 4.09
1587 1802 1.959985 CAGATCTACCATCTCGCCTGT 59.040 52.381 0.00 0.00 0.00 4.00
1685 1900 1.938577 CAACTGCTTGGATCTCGATGG 59.061 52.381 0.00 0.00 0.00 3.51
1936 2152 1.565156 TTCTGCGCATCGTGGTGTTC 61.565 55.000 12.24 0.00 0.00 3.18
1958 2174 1.134250 GGAAGACCAGAGCTTGATCCC 60.134 57.143 0.00 0.00 35.97 3.85
1960 2176 1.890552 AGACCAGAGCTTGATCCCAT 58.109 50.000 0.00 0.00 0.00 4.00
1970 2186 4.086457 AGCTTGATCCCATTTACCGTTTT 58.914 39.130 0.00 0.00 0.00 2.43
1976 2192 3.768878 TCCCATTTACCGTTTTCACCAT 58.231 40.909 0.00 0.00 0.00 3.55
1981 2200 7.038941 TCCCATTTACCGTTTTCACCATAAAAT 60.039 33.333 0.00 0.00 31.43 1.82
1990 2238 8.024285 CCGTTTTCACCATAAAATTTACTAGCA 58.976 33.333 0.00 0.00 31.43 3.49
2008 2256 7.935338 ACTAGCATTTTGTTCAATCAAACAG 57.065 32.000 0.00 0.00 40.08 3.16
2009 2257 5.662211 AGCATTTTGTTCAATCAAACAGC 57.338 34.783 0.00 0.00 40.08 4.40
2020 2268 5.626142 TCAATCAAACAGCTGGGTTAGTAA 58.374 37.500 19.93 0.00 0.00 2.24
2094 2342 2.297033 ACACAGCCATAGCAAAAGTTGG 59.703 45.455 0.00 0.00 43.56 3.77
2096 2344 2.558359 ACAGCCATAGCAAAAGTTGGTC 59.442 45.455 0.00 0.00 43.56 4.02
2137 2385 2.103373 TGTGGCATCTCTAGACCAGTC 58.897 52.381 0.14 0.00 31.46 3.51
2138 2386 2.291865 TGTGGCATCTCTAGACCAGTCT 60.292 50.000 5.50 5.50 43.40 3.24
2139 2387 3.053619 TGTGGCATCTCTAGACCAGTCTA 60.054 47.826 7.29 7.29 40.93 2.59
2140 2388 3.316868 GTGGCATCTCTAGACCAGTCTAC 59.683 52.174 3.36 0.00 40.93 2.59
2141 2389 3.203263 TGGCATCTCTAGACCAGTCTACT 59.797 47.826 3.36 0.00 40.93 2.57
2438 2694 5.076182 TCCTTTGGAAATGCTATGTGTGAA 58.924 37.500 0.00 0.00 0.00 3.18
2439 2695 5.716228 TCCTTTGGAAATGCTATGTGTGAAT 59.284 36.000 0.00 0.00 0.00 2.57
2440 2696 5.808540 CCTTTGGAAATGCTATGTGTGAATG 59.191 40.000 0.00 0.00 0.00 2.67
2441 2697 5.981088 TTGGAAATGCTATGTGTGAATGT 57.019 34.783 0.00 0.00 0.00 2.71
2442 2698 5.313520 TGGAAATGCTATGTGTGAATGTG 57.686 39.130 0.00 0.00 0.00 3.21
2443 2699 5.008980 TGGAAATGCTATGTGTGAATGTGA 58.991 37.500 0.00 0.00 0.00 3.58
2655 2911 3.640498 CTCATACTCCTCCAGCTCATTCA 59.360 47.826 0.00 0.00 0.00 2.57
2676 2932 6.121776 TCATAAGTGTGATGGTGTTAGGTT 57.878 37.500 0.00 0.00 0.00 3.50
2686 2942 6.879458 GTGATGGTGTTAGGTTTCTCATTAGT 59.121 38.462 0.00 0.00 0.00 2.24
2739 2995 2.937591 TGTTACACGAGGTTAGCGAAG 58.062 47.619 0.00 0.00 0.00 3.79
2869 3125 3.491639 TCATTACGTTTCACACTTCCGTG 59.508 43.478 0.00 0.00 46.63 4.94
2880 3136 3.260475 CACTTCCGTGTGATATTGGGA 57.740 47.619 0.00 0.00 40.12 4.37
2925 3181 3.007182 TGGGGTTGTCCTAGTTTTACTCG 59.993 47.826 0.00 0.00 35.33 4.18
2989 3246 7.146960 TGGGGGTGGATTGAGAATAGAAAATAT 60.147 37.037 0.00 0.00 0.00 1.28
3051 3311 3.567478 ACAGAAGAAGGAAGCACAAGT 57.433 42.857 0.00 0.00 0.00 3.16
3066 3326 2.928757 CACAAGTAGAGCAGTGATGAGC 59.071 50.000 0.00 0.00 33.99 4.26
3306 3567 1.985895 AGTGAAGTAAGAAGGTGGGGG 59.014 52.381 0.00 0.00 0.00 5.40
3541 3815 1.669211 GGTGTCAGGAGTTGCTACGAC 60.669 57.143 0.00 0.00 0.00 4.34
3622 3896 6.908825 TGAGGTATTTTGTCATTTGTGCTAC 58.091 36.000 0.00 0.00 0.00 3.58
3626 3900 6.582295 GGTATTTTGTCATTTGTGCTACACTG 59.418 38.462 0.00 0.00 35.11 3.66
3632 3906 7.770801 TGTCATTTGTGCTACACTGATATAC 57.229 36.000 0.00 0.00 35.11 1.47
3664 3938 4.675510 CACTGAAATTTCCATTCCATCCG 58.324 43.478 15.48 0.00 0.00 4.18
3717 3991 9.128107 GATTGGTGTATTTTGTTGTATTCACTG 57.872 33.333 0.00 0.00 0.00 3.66
3870 4144 7.246171 ACTGTAAGCTTCCTCTTATTCTCAA 57.754 36.000 0.00 0.00 37.60 3.02
3871 4145 7.327214 ACTGTAAGCTTCCTCTTATTCTCAAG 58.673 38.462 0.00 0.00 37.60 3.02
3872 4146 7.038658 ACTGTAAGCTTCCTCTTATTCTCAAGT 60.039 37.037 0.00 0.00 37.60 3.16
3873 4147 8.362464 TGTAAGCTTCCTCTTATTCTCAAGTA 57.638 34.615 0.00 0.00 31.92 2.24
3874 4148 8.812972 TGTAAGCTTCCTCTTATTCTCAAGTAA 58.187 33.333 0.00 0.00 31.92 2.24
3987 4266 4.618920 ACGTTTCTGATTTGGTAGGTCT 57.381 40.909 0.00 0.00 0.00 3.85
3999 4278 5.934402 TTGGTAGGTCTTCTCTAACCATC 57.066 43.478 0.00 0.00 38.06 3.51
4347 4632 2.223971 GGATCTTCGGCGACCAAGATAA 60.224 50.000 19.32 0.00 39.09 1.75
4444 4729 3.092301 AGCTTGCTTCTTGGTTAATCCC 58.908 45.455 0.00 0.00 34.77 3.85
4549 4835 0.810823 TTTGTCGTCGCCTTTTCCGT 60.811 50.000 0.00 0.00 0.00 4.69
4682 4974 5.259832 TGTTGTTTCAGAAATGTGCATCA 57.740 34.783 0.00 0.00 0.00 3.07
4683 4975 5.283294 TGTTGTTTCAGAAATGTGCATCAG 58.717 37.500 0.00 0.00 0.00 2.90
4684 4976 5.163530 TGTTGTTTCAGAAATGTGCATCAGT 60.164 36.000 0.00 0.00 0.00 3.41
4694 4986 1.078637 TGCATCAGTCCAGCTGCTC 60.079 57.895 8.66 3.04 44.66 4.26
4707 4999 1.307097 GCTGCTCCAGGAAGCTAATG 58.693 55.000 5.94 0.00 43.24 1.90
4712 5004 2.801342 GCTCCAGGAAGCTAATGTCTCG 60.801 54.545 0.00 0.00 39.27 4.04
4713 5005 2.428890 CTCCAGGAAGCTAATGTCTCGT 59.571 50.000 0.00 0.00 0.00 4.18
4714 5006 2.427453 TCCAGGAAGCTAATGTCTCGTC 59.573 50.000 0.00 0.00 0.00 4.20
4747 5039 4.723309 AGAACTTCAGAGTGGAGCAAAAT 58.277 39.130 0.00 0.00 35.91 1.82
4821 5113 5.316167 TCATCTGCTGCTTCTTTTTCCTTA 58.684 37.500 0.00 0.00 0.00 2.69
4824 5116 4.887071 TCTGCTGCTTCTTTTTCCTTACAA 59.113 37.500 0.00 0.00 0.00 2.41
4833 5125 8.168626 GCTTCTTTTTCCTTACAAAAACAGTTG 58.831 33.333 0.00 0.00 32.88 3.16
5055 5347 0.036952 CCAGCTCCACATTGTCGTCT 60.037 55.000 0.00 0.00 0.00 4.18
5103 5395 0.326238 TCCCCGGGTAGAGCTTGATT 60.326 55.000 21.85 0.00 0.00 2.57
5114 5406 2.037772 AGAGCTTGATTGTCTTGTCGGT 59.962 45.455 0.00 0.00 0.00 4.69
5200 5492 1.688772 CAGGATGAAGAAGGGCATGG 58.311 55.000 0.00 0.00 39.69 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.490348 AGATGGACAACCTTGGTTTGAG 58.510 45.455 1.76 0.00 37.04 3.02
31 32 2.733671 GGTTAACCTCGCGGCGAAC 61.734 63.158 26.28 19.57 34.74 3.95
38 39 1.127951 CGTTGTCATGGTTAACCTCGC 59.872 52.381 24.78 12.78 36.82 5.03
57 58 0.598158 TTTTTCCGACCGAGGTCACG 60.598 55.000 20.75 10.77 44.77 4.35
58 59 3.294079 TTTTTCCGACCGAGGTCAC 57.706 52.632 20.75 0.00 44.77 3.67
88 89 7.002276 TCCAATCATATGAATGAGCTCAACAT 58.998 34.615 29.13 29.13 45.17 2.71
89 90 6.358991 TCCAATCATATGAATGAGCTCAACA 58.641 36.000 22.50 22.61 45.17 3.33
108 110 8.697507 AACTCAGAGACAAAAATAACTCCAAT 57.302 30.769 3.79 0.00 0.00 3.16
111 113 8.504815 GGTTAACTCAGAGACAAAAATAACTCC 58.495 37.037 3.79 0.00 0.00 3.85
117 119 5.953571 AGGGGTTAACTCAGAGACAAAAAT 58.046 37.500 7.98 0.00 0.00 1.82
129 131 9.708092 CTAAGCATTTATAGTAGGGGTTAACTC 57.292 37.037 5.42 0.00 0.00 3.01
153 155 5.163602 CGTTGGGTTTTATTAAGCATGGCTA 60.164 40.000 0.00 0.00 38.25 3.93
154 156 4.381505 CGTTGGGTTTTATTAAGCATGGCT 60.382 41.667 0.00 0.00 42.56 4.75
155 157 3.862845 CGTTGGGTTTTATTAAGCATGGC 59.137 43.478 0.00 0.00 0.00 4.40
228 230 0.179176 GCCATGTTTTGCGCGTATCA 60.179 50.000 8.43 3.77 0.00 2.15
366 371 9.374838 AGGATTTGAAATGTCTTGAATTATTGC 57.625 29.630 0.00 0.00 0.00 3.56
406 411 7.618502 ATTAGACGGTAAATGTACATTTGCA 57.381 32.000 35.06 21.95 42.61 4.08
500 508 5.046159 AGGGTCCGTTTTCAATGTCATAGTA 60.046 40.000 0.00 0.00 0.00 1.82
501 509 4.007659 GGGTCCGTTTTCAATGTCATAGT 58.992 43.478 0.00 0.00 0.00 2.12
502 510 4.261801 AGGGTCCGTTTTCAATGTCATAG 58.738 43.478 0.00 0.00 0.00 2.23
512 520 1.893801 TCTCAGAGAGGGTCCGTTTTC 59.106 52.381 0.00 0.00 0.00 2.29
537 551 8.783660 AGATACTCAGAAATTACCACCATAGA 57.216 34.615 0.00 0.00 0.00 1.98
569 583 8.761689 TCCGTTTCTTTAGGTATACATAGGTTT 58.238 33.333 5.01 0.00 0.00 3.27
570 584 8.310122 TCCGTTTCTTTAGGTATACATAGGTT 57.690 34.615 5.01 0.00 0.00 3.50
582 604 9.680315 CTATAGTACTTCATCCGTTTCTTTAGG 57.320 37.037 0.00 0.00 0.00 2.69
609 639 4.692155 CGACCGGTTCTACAAAATTAACCT 59.308 41.667 9.42 0.00 39.39 3.50
614 644 1.808343 GCCGACCGGTTCTACAAAATT 59.192 47.619 9.42 0.00 37.65 1.82
615 645 1.270947 TGCCGACCGGTTCTACAAAAT 60.271 47.619 9.42 0.00 37.65 1.82
616 646 0.106335 TGCCGACCGGTTCTACAAAA 59.894 50.000 9.42 0.00 37.65 2.44
619 649 2.967397 CTGCCGACCGGTTCTACA 59.033 61.111 9.42 4.33 37.65 2.74
783 979 4.754667 GACCCGACCCGTTGGAGC 62.755 72.222 2.40 0.00 36.15 4.70
1662 1877 2.964740 TCGAGATCCAAGCAGTTGAAG 58.035 47.619 0.00 0.00 35.46 3.02
1663 1878 3.264947 CATCGAGATCCAAGCAGTTGAA 58.735 45.455 0.00 0.00 35.46 2.69
1685 1900 3.304057 CGAGAAGCCAGGAAAAGTCAAAC 60.304 47.826 0.00 0.00 0.00 2.93
1901 2116 2.982470 GCAGAAAGCTCCAAAATTGACG 59.018 45.455 0.00 0.00 41.15 4.35
1936 2152 2.419851 GGATCAAGCTCTGGTCTTCCTG 60.420 54.545 8.44 0.00 35.28 3.86
1981 2200 9.809096 TGTTTGATTGAACAAAATGCTAGTAAA 57.191 25.926 0.00 0.00 40.62 2.01
1990 2238 5.058490 CCCAGCTGTTTGATTGAACAAAAT 58.942 37.500 13.81 0.00 40.62 1.82
1994 2242 2.665165 ACCCAGCTGTTTGATTGAACA 58.335 42.857 13.81 0.00 37.87 3.18
2008 2256 3.352648 TGGCAGATTTTACTAACCCAGC 58.647 45.455 0.00 0.00 0.00 4.85
2009 2257 5.888161 AGATTGGCAGATTTTACTAACCCAG 59.112 40.000 0.00 0.00 0.00 4.45
2020 2268 6.257994 TCTCCTATCAAGATTGGCAGATTT 57.742 37.500 5.78 0.00 34.38 2.17
2094 2342 9.421806 CACATCTAGAAAATCTGATGATAGGAC 57.578 37.037 18.22 0.00 36.47 3.85
2096 2344 7.333921 GCCACATCTAGAAAATCTGATGATAGG 59.666 40.741 18.22 16.60 36.47 2.57
2438 2694 3.099905 TCTCGAAGGTCAAGGATCACAT 58.900 45.455 0.00 0.00 0.00 3.21
2439 2695 2.525368 TCTCGAAGGTCAAGGATCACA 58.475 47.619 0.00 0.00 0.00 3.58
2440 2696 3.452474 CATCTCGAAGGTCAAGGATCAC 58.548 50.000 0.00 0.00 0.00 3.06
2441 2697 2.432146 CCATCTCGAAGGTCAAGGATCA 59.568 50.000 0.00 0.00 0.00 2.92
2442 2698 2.804933 GCCATCTCGAAGGTCAAGGATC 60.805 54.545 0.00 0.00 0.00 3.36
2443 2699 1.139853 GCCATCTCGAAGGTCAAGGAT 59.860 52.381 0.00 0.00 0.00 3.24
2655 2911 6.779860 AGAAACCTAACACCATCACACTTAT 58.220 36.000 0.00 0.00 0.00 1.73
2676 2932 9.421399 TGATAGATCTGGTACAACTAATGAGAA 57.579 33.333 5.18 0.00 38.70 2.87
2766 3022 4.538746 AAGACTGGGCAACTTCTACTAC 57.461 45.455 0.00 0.00 0.00 2.73
2817 3073 4.633565 GTCCAGAAGACCAGAAACATCATC 59.366 45.833 0.00 0.00 39.84 2.92
2869 3125 5.246203 TCAGCATACCTACTCCCAATATCAC 59.754 44.000 0.00 0.00 0.00 3.06
2880 3136 5.636903 AATCCATGTTCAGCATACCTACT 57.363 39.130 0.00 0.00 35.74 2.57
2925 3181 6.218746 TCGAAACTACTTCCAAAACTACTCC 58.781 40.000 0.00 0.00 0.00 3.85
2989 3246 7.617723 AGATATAACCCAACTGGCAAAATGTTA 59.382 33.333 0.00 0.00 37.83 2.41
2995 3252 5.044772 TGGTAGATATAACCCAACTGGCAAA 60.045 40.000 4.64 0.00 37.83 3.68
3030 3290 3.891049 ACTTGTGCTTCCTTCTTCTGTT 58.109 40.909 0.00 0.00 0.00 3.16
3051 3311 4.541973 TCAAAAGCTCATCACTGCTCTA 57.458 40.909 0.00 0.00 38.75 2.43
3247 3508 0.967662 CCATGTGGCACATTTCACCA 59.032 50.000 29.57 0.95 44.52 4.17
3293 3554 1.501604 AGTTTTGCCCCCACCTTCTTA 59.498 47.619 0.00 0.00 0.00 2.10
3415 3676 7.546667 ACATGACAAATGCATTCATAGAAAACC 59.453 33.333 13.38 0.00 31.46 3.27
3541 3815 3.188786 GCTGTACGCTTGCCCTCG 61.189 66.667 2.99 0.00 35.14 4.63
3622 3896 4.633126 AGTGCTTGCAACAGTATATCAGTG 59.367 41.667 0.00 0.00 0.00 3.66
3626 3900 5.801350 TTCAGTGCTTGCAACAGTATATC 57.199 39.130 0.00 0.00 0.00 1.63
3632 3906 3.492011 GGAAATTTCAGTGCTTGCAACAG 59.508 43.478 19.49 0.00 0.00 3.16
3664 3938 8.639761 ACTACACATACAGACCTATTTCCATAC 58.360 37.037 0.00 0.00 0.00 2.39
3669 3943 9.035607 CAATCACTACACATACAGACCTATTTC 57.964 37.037 0.00 0.00 0.00 2.17
3717 3991 2.093658 TCCGAGCAATCCTAACCTGAAC 60.094 50.000 0.00 0.00 0.00 3.18
3987 4266 9.739276 AATTATTGTTCACTGATGGTTAGAGAA 57.261 29.630 0.00 0.00 0.00 2.87
3999 4278 6.982141 AGCATTGCCATAATTATTGTTCACTG 59.018 34.615 4.70 0.00 0.00 3.66
4444 4729 0.467384 CATAGCTCTGTCAGTGGGGG 59.533 60.000 0.00 0.00 0.00 5.40
4549 4835 3.118371 TCTGTCCGTATAGCTGAGACTGA 60.118 47.826 0.00 3.00 34.38 3.41
4682 4974 1.537397 TTCCTGGAGCAGCTGGACT 60.537 57.895 17.12 4.45 0.00 3.85
4683 4975 1.078567 CTTCCTGGAGCAGCTGGAC 60.079 63.158 17.12 0.00 0.00 4.02
4684 4976 2.964310 GCTTCCTGGAGCAGCTGGA 61.964 63.158 17.12 0.00 42.25 3.86
4694 4986 2.166459 TGACGAGACATTAGCTTCCTGG 59.834 50.000 0.00 0.00 0.00 4.45
4703 4995 5.240844 TCTCTTGTGTTCTGACGAGACATTA 59.759 40.000 0.00 0.00 33.53 1.90
4707 4999 3.627732 TCTCTTGTGTTCTGACGAGAC 57.372 47.619 0.00 0.00 33.53 3.36
4712 5004 5.352284 TCTGAAGTTCTCTTGTGTTCTGAC 58.648 41.667 4.17 0.00 33.64 3.51
4713 5005 5.127845 ACTCTGAAGTTCTCTTGTGTTCTGA 59.872 40.000 4.17 0.00 33.64 3.27
4714 5006 5.233902 CACTCTGAAGTTCTCTTGTGTTCTG 59.766 44.000 4.17 0.00 31.71 3.02
4821 5113 7.548780 AGAATGTAAACATGCAACTGTTTTTGT 59.451 29.630 20.28 7.81 44.76 2.83
4824 5116 8.194104 TGTAGAATGTAAACATGCAACTGTTTT 58.806 29.630 20.28 5.81 44.76 2.43
4833 5125 5.043248 GGGCAATGTAGAATGTAAACATGC 58.957 41.667 0.00 0.00 36.56 4.06
5103 5395 2.280797 GCCAGCACCGACAAGACA 60.281 61.111 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.