Multiple sequence alignment - TraesCS6A01G102300

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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 TraesCS6A01G102300 chr6A 100.000 5713 0 0 1 5713 71446225 71451937 0.000000e+00 10551
1 TraesCS6A01G102300 chr6D 94.690 5706 249 35 46 5713 56845159 56850848 0.000000e+00 8809
2 TraesCS6A01G102300 chr6B 93.464 2953 182 9 2765 5713 127323879 127326824 0.000000e+00 4373
3 TraesCS6A01G102300 chr6B 88.769 2413 190 42 3 2370 127321107 127323483 0.000000e+00 2880
4 TraesCS6A01G102300 chr6B 93.684 380 21 3 2404 2781 127323486 127323864 2.990000e-157 566


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 TraesCS6A01G102300 chr6A 71446225 71451937 5712 False 10551.000000 10551 100.000000 1 5713 1 chr6A.!!$F1 5712
1 TraesCS6A01G102300 chr6D 56845159 56850848 5689 False 8809.000000 8809 94.690000 46 5713 1 chr6D.!!$F1 5667
2 TraesCS6A01G102300 chr6B 127321107 127326824 5717 False 2606.333333 4373 91.972333 3 5713 3 chr6B.!!$F1 5710

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
870 906 0.179062 CTGAGGCCGGGATTCTCAAG 60.179 60.000 2.18 6.91 37.13 3.02 F
1051 1093 0.326927 GTAGGCCCTGCTGTTGGTTA 59.673 55.000 0.00 0.00 0.00 2.85 F
1417 1461 0.467384 ATCGTCTTCATCAGGGCAGG 59.533 55.000 0.00 0.00 0.00 4.85 F
1604 1655 1.213296 GGGGGCTAGAATTGTCCTCA 58.787 55.000 0.00 0.00 28.30 3.86 F
2106 2161 2.054799 ACCACTGACCTGCTCCTTTAA 58.945 47.619 0.00 0.00 0.00 1.52 F
3999 4091 0.883833 ATGTGCTTAGCAGTGCCAAC 59.116 50.000 12.58 3.97 40.08 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2188 4.096231 CCTACATCGCAATTCACAAATCCA 59.904 41.667 0.00 0.0 0.00 3.41 R
2902 2988 2.500229 ACATCAAAGGTGGTGGTTACG 58.500 47.619 0.00 0.0 40.49 3.18 R
3297 3383 4.079269 TCCAATGGATTGTACATGGACCAT 60.079 41.667 5.38 0.0 39.38 3.55 R
3676 3762 6.322491 TCATAACATGACAGTGAGAACTACG 58.678 40.000 0.00 0.0 33.59 3.51 R
4112 4204 0.951558 AGCCGATTTCGCACAAAGTT 59.048 45.000 0.00 0.0 38.18 2.66 R
5177 5272 0.837272 TAATGGTGCAGGAGGTAGCC 59.163 55.000 0.00 0.0 0.00 3.93 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
32 34 9.326413 ACATCTACAGAAAAATTAATCGGTAGG 57.674 33.333 20.34 13.06 41.60 3.18
33 35 7.781548 TCTACAGAAAAATTAATCGGTAGGC 57.218 36.000 20.34 0.00 41.60 3.93
72 74 5.228665 AGTAGTCGGAACAAAAGCTAGAAC 58.771 41.667 0.00 0.00 0.00 3.01
107 109 7.925043 TTGAAAAAGGAGTGTGTTACAAGTA 57.075 32.000 0.00 0.00 0.00 2.24
130 132 3.895232 ATAGGAGCAACTGTCGACAAT 57.105 42.857 20.49 6.72 0.00 2.71
137 139 3.120546 AGCAACTGTCGACAATTTGATCG 60.121 43.478 30.18 16.45 39.72 3.69
140 143 1.062587 CTGTCGACAATTTGATCGCCC 59.937 52.381 20.49 4.38 38.24 6.13
146 149 3.501950 GACAATTTGATCGCCCAAAGAC 58.498 45.455 2.79 0.00 39.13 3.01
160 163 3.696051 CCCAAAGACGATCATTTCATGGT 59.304 43.478 0.00 0.00 0.00 3.55
166 169 4.881850 AGACGATCATTTCATGGTTTACCC 59.118 41.667 0.00 0.00 34.29 3.69
207 210 8.553085 TCAAATCAGATAGTCCTATTTCTCCA 57.447 34.615 0.00 0.00 0.00 3.86
214 217 4.429854 AGTCCTATTTCTCCATCTTGCC 57.570 45.455 0.00 0.00 0.00 4.52
219 222 2.386661 TTTCTCCATCTTGCCGACTC 57.613 50.000 0.00 0.00 0.00 3.36
220 223 1.561643 TTCTCCATCTTGCCGACTCT 58.438 50.000 0.00 0.00 0.00 3.24
253 257 3.503748 AGCCAAGTTCGAAAGGATTGAAG 59.496 43.478 14.66 2.65 0.00 3.02
279 283 9.584839 GATTGTAGCACATTGTTTTTCATTTTC 57.415 29.630 0.00 0.00 0.00 2.29
281 285 8.129161 TGTAGCACATTGTTTTTCATTTTCAG 57.871 30.769 0.00 0.00 0.00 3.02
282 286 7.763528 TGTAGCACATTGTTTTTCATTTTCAGT 59.236 29.630 0.00 0.00 0.00 3.41
283 287 7.007313 AGCACATTGTTTTTCATTTTCAGTG 57.993 32.000 0.00 0.00 0.00 3.66
285 299 6.193761 CACATTGTTTTTCATTTTCAGTGCC 58.806 36.000 0.00 0.00 0.00 5.01
291 305 1.927487 TCATTTTCAGTGCCATGGCT 58.073 45.000 35.53 15.87 42.51 4.75
302 317 1.202114 TGCCATGGCTTGAAAATCGAC 59.798 47.619 35.53 4.22 42.51 4.20
339 354 3.495806 GGCTGGGACCTCATCTTGAATAG 60.496 52.174 0.00 0.00 0.00 1.73
342 357 3.711704 TGGGACCTCATCTTGAATAGGAC 59.288 47.826 8.13 3.30 33.16 3.85
349 364 6.041865 ACCTCATCTTGAATAGGACATCTGAG 59.958 42.308 8.13 0.00 33.16 3.35
404 419 9.679596 CAAAAATAAAGCGCAAAAGATGAATAG 57.320 29.630 11.47 0.00 0.00 1.73
500 516 1.522569 CCACTCCACTCCGATTCCC 59.477 63.158 0.00 0.00 0.00 3.97
527 543 4.335584 CCGCCTCCGCTCGATCTC 62.336 72.222 0.00 0.00 0.00 2.75
528 544 4.335584 CGCCTCCGCTCGATCTCC 62.336 72.222 0.00 0.00 0.00 3.71
529 545 4.335584 GCCTCCGCTCGATCTCCG 62.336 72.222 0.00 0.00 40.25 4.63
530 546 3.665226 CCTCCGCTCGATCTCCGG 61.665 72.222 0.00 0.00 43.21 5.14
531 547 4.335584 CTCCGCTCGATCTCCGGC 62.336 72.222 0.00 0.00 41.68 6.13
588 604 0.531200 CGAGGTTCGTTTCTAGGCCT 59.469 55.000 11.78 11.78 34.72 5.19
695 725 2.437895 GCGTTTGGGGGTAGGAGC 60.438 66.667 0.00 0.00 0.00 4.70
749 779 3.239449 GGGTTTCCCTTGAAATGGACTT 58.761 45.455 0.00 0.00 42.20 3.01
751 781 3.258372 GGTTTCCCTTGAAATGGACTTCC 59.742 47.826 0.00 0.00 42.20 3.46
752 782 4.152647 GTTTCCCTTGAAATGGACTTCCT 58.847 43.478 0.00 0.00 42.20 3.36
755 785 3.054361 TCCCTTGAAATGGACTTCCTAGC 60.054 47.826 0.00 0.00 36.82 3.42
770 800 0.533755 CTAGCCAGCCCACAGTATGC 60.534 60.000 0.00 0.00 42.53 3.14
806 842 2.287915 CAGTGAGGTTTTTCCGTCAGTG 59.712 50.000 0.00 0.00 41.99 3.66
817 853 2.352805 GTCAGTGGGGCAAGGAGG 59.647 66.667 0.00 0.00 0.00 4.30
846 882 3.258372 TCCTTGCAGTTTCGTCAGTCTAT 59.742 43.478 0.00 0.00 0.00 1.98
860 896 0.671251 GTCTATGAGTCTGAGGCCGG 59.329 60.000 0.00 0.00 0.00 6.13
862 898 0.468214 CTATGAGTCTGAGGCCGGGA 60.468 60.000 2.18 0.00 0.00 5.14
868 904 1.001631 TCTGAGGCCGGGATTCTCA 59.998 57.895 2.18 6.61 36.30 3.27
870 906 0.179062 CTGAGGCCGGGATTCTCAAG 60.179 60.000 2.18 6.91 37.13 3.02
873 909 2.115291 GGCCGGGATTCTCAAGTGC 61.115 63.158 2.18 0.00 0.00 4.40
916 958 1.134788 CCGCCGGAGATTTGTACTTCT 60.135 52.381 5.05 0.00 0.00 2.85
956 998 9.255304 GAGTGGAAGATATACTGAATTTGACTC 57.745 37.037 0.00 0.00 0.00 3.36
1051 1093 0.326927 GTAGGCCCTGCTGTTGGTTA 59.673 55.000 0.00 0.00 0.00 2.85
1064 1106 4.726416 CTGTTGGTTATGCACACATCTTC 58.274 43.478 0.00 0.00 37.74 2.87
1066 1108 4.826733 TGTTGGTTATGCACACATCTTCTT 59.173 37.500 0.00 0.00 37.74 2.52
1115 1157 2.793278 GACAAAATGTGGCGGTTTCT 57.207 45.000 0.00 0.00 0.00 2.52
1174 1218 3.214328 ACTTTCTTGACAAGGAATGCGT 58.786 40.909 15.13 4.74 0.00 5.24
1178 1222 3.937814 TCTTGACAAGGAATGCGTGTAT 58.062 40.909 15.13 0.00 0.00 2.29
1188 1232 6.169557 AGGAATGCGTGTATGGAGTATAAA 57.830 37.500 0.00 0.00 0.00 1.40
1209 1253 0.754217 TCGTATGCCCGAGTAAGCCT 60.754 55.000 0.00 0.00 32.18 4.58
1276 1320 4.336889 ACAGCTTACACAAACTCTAGCA 57.663 40.909 0.00 0.00 0.00 3.49
1279 1323 4.387256 CAGCTTACACAAACTCTAGCAGAC 59.613 45.833 0.00 0.00 0.00 3.51
1304 1348 2.912025 GGTTGCCACTGGGGTGTG 60.912 66.667 0.00 0.00 41.53 3.82
1417 1461 0.467384 ATCGTCTTCATCAGGGCAGG 59.533 55.000 0.00 0.00 0.00 4.85
1460 1504 3.118884 GCCGAGGTATTAGTCAAACTCCA 60.119 47.826 0.00 0.00 0.00 3.86
1523 1574 4.216257 ACATGTGCCACTTACTCATGAAAC 59.784 41.667 0.00 0.00 39.98 2.78
1545 1596 4.130118 CCAGCTGTTCTTCTGTGTTTACT 58.870 43.478 13.81 0.00 0.00 2.24
1578 1629 6.989759 TGCAAGTTGTCATACTCTGTCTAAAA 59.010 34.615 4.48 0.00 0.00 1.52
1579 1630 7.661437 TGCAAGTTGTCATACTCTGTCTAAAAT 59.339 33.333 4.48 0.00 0.00 1.82
1580 1631 7.959651 GCAAGTTGTCATACTCTGTCTAAAATG 59.040 37.037 4.48 0.00 0.00 2.32
1583 1634 9.778741 AGTTGTCATACTCTGTCTAAAATGAAA 57.221 29.630 0.00 0.00 0.00 2.69
1600 1651 3.631250 TGAAATGGGGGCTAGAATTGTC 58.369 45.455 0.00 0.00 0.00 3.18
1604 1655 1.213296 GGGGGCTAGAATTGTCCTCA 58.787 55.000 0.00 0.00 28.30 3.86
1627 1678 8.190326 TCATACCTCTCGAAATGGTTATACAT 57.810 34.615 8.60 0.00 35.48 2.29
1766 1821 9.605275 CAGTGGTGATTTATAAATCTTCTCTCA 57.395 33.333 29.37 18.32 43.97 3.27
1913 1968 9.787532 AAACCATACATCGAATTTACTTGATTG 57.212 29.630 0.00 0.00 0.00 2.67
2106 2161 2.054799 ACCACTGACCTGCTCCTTTAA 58.945 47.619 0.00 0.00 0.00 1.52
2902 2988 7.234187 TCAATATCGTCTTTTGCTCATGTAC 57.766 36.000 0.00 0.00 0.00 2.90
3297 3383 7.526142 AGACAGTACTTGAGTTGATTAGTCA 57.474 36.000 0.00 0.00 34.36 3.41
3676 3762 8.837389 GGTGACTATCCTTTGTCATTTATAACC 58.163 37.037 0.00 0.00 43.75 2.85
3697 3783 4.521639 ACCGTAGTTCTCACTGTCATGTTA 59.478 41.667 0.00 0.00 34.06 2.41
3937 4025 4.372656 AGCAGTCTTTAGTGTGTTCTCAC 58.627 43.478 0.00 0.00 44.08 3.51
3941 4029 2.370849 TCTTTAGTGTGTTCTCACCCCC 59.629 50.000 2.11 0.00 43.26 5.40
3999 4091 0.883833 ATGTGCTTAGCAGTGCCAAC 59.116 50.000 12.58 3.97 40.08 3.77
4023 4115 6.128035 ACTGCGAACAAATGCTTGTAATATCA 60.128 34.615 0.00 0.00 45.25 2.15
4118 4210 6.086765 CGTGCAATGCTCTAAGTTAAACTTTG 59.913 38.462 6.82 0.00 39.51 2.77
4121 4213 6.129088 GCAATGCTCTAAGTTAAACTTTGTGC 60.129 38.462 2.36 2.36 44.48 4.57
4142 4234 3.363378 GCGAAATCGGCTGACTGATAATG 60.363 47.826 0.00 0.00 41.23 1.90
4223 4315 5.630661 TGAGTCTTTAAGACCTCGAGAAG 57.369 43.478 20.05 8.48 46.18 2.85
4264 4356 3.514645 CATGGCTGAGGTAAACAAATGC 58.485 45.455 0.00 0.00 0.00 3.56
4316 4409 6.714810 ACTTCTTGCACTGTTATATTTGTCCA 59.285 34.615 0.00 0.00 0.00 4.02
4374 4468 7.523293 TTTTGTCCTCATTCTCATTTTGCTA 57.477 32.000 0.00 0.00 0.00 3.49
4375 4469 7.707624 TTTGTCCTCATTCTCATTTTGCTAT 57.292 32.000 0.00 0.00 0.00 2.97
4434 4528 2.166254 CGTGCAAATTATGGGCTCCTTT 59.834 45.455 0.00 0.00 0.00 3.11
4553 4648 2.816958 AGTTCTGCGATGCTGCCG 60.817 61.111 0.00 0.00 0.00 5.69
4700 4795 6.777580 AGGGATTGACACAGAACAATAAACTT 59.222 34.615 0.00 0.00 36.94 2.66
4702 4797 6.363357 GGATTGACACAGAACAATAAACTTGC 59.637 38.462 0.00 0.00 36.94 4.01
4716 4811 0.392998 ACTTGCCGTGGAATAGCAGG 60.393 55.000 0.00 0.00 37.89 4.85
4746 4841 3.714798 TGCCCCTTAGAACTGTATTAGGG 59.285 47.826 9.09 9.09 41.63 3.53
4773 4868 3.454812 ACCAGATTACTACCATGGGTGTC 59.545 47.826 18.09 8.20 36.19 3.67
4776 4871 3.711704 AGATTACTACCATGGGTGTCCTG 59.288 47.826 18.09 0.26 36.19 3.86
4778 4873 0.840288 ACTACCATGGGTGTCCTGCA 60.840 55.000 18.09 0.00 36.19 4.41
4786 4881 1.648467 GGGTGTCCTGCAGCGAAATC 61.648 60.000 8.66 2.56 45.88 2.17
4912 5007 3.067742 CCTTCTTCCATGAATCCATGTGC 59.932 47.826 0.00 0.00 46.68 4.57
4919 5014 2.627515 TGAATCCATGTGCTAGGAGC 57.372 50.000 0.00 0.00 42.82 4.70
4928 5023 2.977914 TGTGCTAGGAGCTGATCAAAC 58.022 47.619 0.00 0.00 42.97 2.93
5131 5226 2.092212 AGCTGTATGGTTAAGGCATGCT 60.092 45.455 18.92 0.24 0.00 3.79
5132 5227 2.689983 GCTGTATGGTTAAGGCATGCTT 59.310 45.455 18.92 7.19 0.00 3.91
5133 5228 3.131046 GCTGTATGGTTAAGGCATGCTTT 59.869 43.478 19.67 19.67 0.00 3.51
5159 5254 2.697751 AGGCTAATCTGAGCTACCACAG 59.302 50.000 0.00 0.00 42.43 3.66
5177 5272 2.894126 ACAGGAGCTCCTATGGTTATCG 59.106 50.000 34.67 20.56 46.65 2.92
5207 5305 1.202867 TGCACCATTAGCCTGACAACA 60.203 47.619 0.00 0.00 0.00 3.33
5305 5403 2.512515 GGCATCGCAGGACAGGAC 60.513 66.667 0.00 0.00 0.00 3.85
5393 5491 1.280457 CCACCTCCTCCTTTACTGCT 58.720 55.000 0.00 0.00 0.00 4.24
5584 5682 3.761218 TCTTCTCCTAGAGCACTTGACAG 59.239 47.826 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.283291 GCCTACCGATTAATTTTTCTGTAGATG 58.717 37.037 14.82 6.05 33.83 2.90
43 45 6.465084 AGCTTTTGTTCCGACTACTCTATTT 58.535 36.000 0.00 0.00 0.00 1.40
45 47 5.662674 AGCTTTTGTTCCGACTACTCTAT 57.337 39.130 0.00 0.00 0.00 1.98
46 48 5.942236 TCTAGCTTTTGTTCCGACTACTCTA 59.058 40.000 0.00 0.00 0.00 2.43
47 49 4.765856 TCTAGCTTTTGTTCCGACTACTCT 59.234 41.667 0.00 0.00 0.00 3.24
49 51 5.010820 AGTTCTAGCTTTTGTTCCGACTACT 59.989 40.000 0.00 0.00 0.00 2.57
50 52 5.228665 AGTTCTAGCTTTTGTTCCGACTAC 58.771 41.667 0.00 0.00 0.00 2.73
51 53 5.464030 AGTTCTAGCTTTTGTTCCGACTA 57.536 39.130 0.00 0.00 0.00 2.59
52 54 4.338379 AGTTCTAGCTTTTGTTCCGACT 57.662 40.909 0.00 0.00 0.00 4.18
53 55 4.510340 TGAAGTTCTAGCTTTTGTTCCGAC 59.490 41.667 4.17 0.00 0.00 4.79
72 74 9.403110 CACACTCCTTTTTCAAATTATCTGAAG 57.597 33.333 0.00 0.00 34.41 3.02
107 109 5.339008 TTGTCGACAGTTGCTCCTATTAT 57.661 39.130 19.11 0.00 0.00 1.28
130 132 2.107950 ATCGTCTTTGGGCGATCAAA 57.892 45.000 0.00 0.00 43.27 2.69
160 163 8.848474 TTGATTTGTCTTTGTTTTTGGGTAAA 57.152 26.923 0.00 0.00 0.00 2.01
171 174 8.734386 GGACTATCTGATTTGATTTGTCTTTGT 58.266 33.333 0.00 0.00 33.50 2.83
172 175 8.954350 AGGACTATCTGATTTGATTTGTCTTTG 58.046 33.333 0.00 0.00 33.50 2.77
207 210 0.107945 GGAAGCAGAGTCGGCAAGAT 60.108 55.000 17.72 0.56 0.00 2.40
214 217 1.153939 CTCGGTGGAAGCAGAGTCG 60.154 63.158 0.00 0.00 32.91 4.18
219 222 2.032528 TTGGCTCGGTGGAAGCAG 59.967 61.111 0.00 0.00 0.00 4.24
220 223 2.032528 CTTGGCTCGGTGGAAGCA 59.967 61.111 0.00 0.00 0.00 3.91
253 257 9.584839 GAAAATGAAAAACAATGTGCTACAATC 57.415 29.630 0.00 0.00 0.00 2.67
279 283 2.613691 GATTTTCAAGCCATGGCACTG 58.386 47.619 37.18 30.67 44.88 3.66
281 285 1.202114 TCGATTTTCAAGCCATGGCAC 59.798 47.619 37.18 10.61 44.88 5.01
282 286 1.202114 GTCGATTTTCAAGCCATGGCA 59.798 47.619 37.18 17.20 44.88 4.92
283 287 1.202114 TGTCGATTTTCAAGCCATGGC 59.798 47.619 30.12 30.12 42.33 4.40
285 299 4.263677 CGATTTGTCGATTTTCAAGCCATG 59.736 41.667 0.00 0.00 34.64 3.66
291 305 2.817258 AGGCCGATTTGTCGATTTTCAA 59.183 40.909 0.00 0.00 34.64 2.69
339 354 0.985490 AAGGCCCTCCTCAGATGTCC 60.985 60.000 0.00 0.00 43.40 4.02
342 357 0.758123 GAGAAGGCCCTCCTCAGATG 59.242 60.000 0.00 0.00 43.40 2.90
349 364 3.254024 TTGTGCGAGAAGGCCCTCC 62.254 63.158 0.00 0.00 0.00 4.30
404 419 4.778143 AGGTTGCGGCCACGGATC 62.778 66.667 2.24 0.00 41.08 3.36
447 462 2.231721 AGGAGCTCGTAGTTCTGTTTCC 59.768 50.000 7.25 0.00 0.00 3.13
546 562 4.447342 AATGCCGGGAGCTTGGGG 62.447 66.667 2.18 0.00 44.23 4.96
588 604 2.606751 TTGGGGGAAATTAAGCGGAA 57.393 45.000 0.00 0.00 0.00 4.30
668 685 2.724358 CCAAACGCACGCGGAAAC 60.724 61.111 16.70 0.00 44.69 2.78
688 718 0.755698 TCCCACGGATCAGCTCCTAC 60.756 60.000 0.00 0.00 42.47 3.18
695 725 4.899239 GCGCCTCCCACGGATCAG 62.899 72.222 0.00 0.00 0.00 2.90
749 779 0.031111 ATACTGTGGGCTGGCTAGGA 60.031 55.000 0.00 0.00 0.00 2.94
751 781 0.533755 GCATACTGTGGGCTGGCTAG 60.534 60.000 0.00 0.00 0.00 3.42
752 782 1.526887 GCATACTGTGGGCTGGCTA 59.473 57.895 0.00 0.00 0.00 3.93
755 785 2.514592 CCGCATACTGTGGGCTGG 60.515 66.667 0.00 0.00 44.04 4.85
770 800 1.006102 ACTGTTCGTTCTGAGCCCG 60.006 57.895 0.00 0.00 0.00 6.13
817 853 0.591659 GAAACTGCAAGGAACCGACC 59.408 55.000 0.00 0.00 39.30 4.79
846 882 1.306141 AATCCCGGCCTCAGACTCA 60.306 57.895 0.00 0.00 0.00 3.41
860 896 0.179215 CGCAACGCACTTGAGAATCC 60.179 55.000 0.00 0.00 31.56 3.01
862 898 1.726791 CTACGCAACGCACTTGAGAAT 59.273 47.619 2.42 0.00 34.02 2.40
868 904 1.726791 CTTCATCTACGCAACGCACTT 59.273 47.619 0.00 0.00 0.00 3.16
870 906 1.068474 ACTTCATCTACGCAACGCAC 58.932 50.000 0.00 0.00 0.00 5.34
873 909 2.278094 CGGTAACTTCATCTACGCAACG 59.722 50.000 0.00 0.00 0.00 4.10
916 958 5.007034 TCTTCCACTCAAAACTGTGAACAA 58.993 37.500 0.00 0.00 36.38 2.83
956 998 9.838339 AACAATAATAAGAGACATCCTGTTAGG 57.162 33.333 0.00 0.00 34.61 2.69
1038 1080 1.068333 GTGTGCATAACCAACAGCAGG 60.068 52.381 0.00 0.00 37.72 4.85
1051 1093 6.883217 AGTATCTGAAAAGAAGATGTGTGCAT 59.117 34.615 0.00 0.00 35.92 3.96
1115 1157 7.768582 TGTCAAATTAACTCAAGAGAGACAACA 59.231 33.333 3.73 0.00 44.98 3.33
1151 1193 3.250762 CGCATTCCTTGTCAAGAAAGTCA 59.749 43.478 14.42 0.00 0.00 3.41
1152 1194 3.251004 ACGCATTCCTTGTCAAGAAAGTC 59.749 43.478 14.42 0.00 0.00 3.01
1153 1195 3.003689 CACGCATTCCTTGTCAAGAAAGT 59.996 43.478 14.42 2.85 0.00 2.66
1154 1196 3.003689 ACACGCATTCCTTGTCAAGAAAG 59.996 43.478 14.42 5.20 0.00 2.62
1174 1218 7.101054 GGGCATACGAATTTATACTCCATACA 58.899 38.462 0.00 0.00 0.00 2.29
1178 1222 4.281435 TCGGGCATACGAATTTATACTCCA 59.719 41.667 0.00 0.00 40.34 3.86
1188 1232 1.270147 GGCTTACTCGGGCATACGAAT 60.270 52.381 0.00 0.00 42.98 3.34
1233 1277 4.657814 AAAATAGCAGAGAACCCTTCCA 57.342 40.909 0.00 0.00 0.00 3.53
1304 1348 2.358737 CAACTGGGCTGACGGGAC 60.359 66.667 0.00 0.00 0.00 4.46
1309 1353 3.042560 GCCAACAACTGGGCTGAC 58.957 61.111 0.00 0.00 46.54 3.51
1417 1461 4.662569 CTGAGGTCAGCTGCTCACTAGC 62.663 59.091 17.14 6.02 42.21 3.42
1523 1574 4.130118 AGTAAACACAGAAGAACAGCTGG 58.870 43.478 19.93 0.00 36.47 4.85
1545 1596 7.171508 CAGAGTATGACAACTTGCAGTTCTTTA 59.828 37.037 0.00 0.00 36.03 1.85
1562 1613 7.775093 CCCCATTTCATTTTAGACAGAGTATGA 59.225 37.037 0.00 0.00 0.00 2.15
1565 1616 6.423182 CCCCCATTTCATTTTAGACAGAGTA 58.577 40.000 0.00 0.00 0.00 2.59
1578 1629 4.218312 GACAATTCTAGCCCCCATTTCAT 58.782 43.478 0.00 0.00 0.00 2.57
1579 1630 3.627237 GGACAATTCTAGCCCCCATTTCA 60.627 47.826 0.00 0.00 0.00 2.69
1580 1631 2.959030 GGACAATTCTAGCCCCCATTTC 59.041 50.000 0.00 0.00 0.00 2.17
1583 1634 1.777272 GAGGACAATTCTAGCCCCCAT 59.223 52.381 0.00 0.00 0.00 4.00
1584 1635 1.213296 GAGGACAATTCTAGCCCCCA 58.787 55.000 0.00 0.00 0.00 4.96
1585 1636 1.213296 TGAGGACAATTCTAGCCCCC 58.787 55.000 0.00 0.00 0.00 5.40
1600 1651 4.408182 AACCATTTCGAGAGGTATGAGG 57.592 45.455 6.02 0.00 34.63 3.86
1913 1968 7.817962 AGTCATACAACACCACACTTTACTATC 59.182 37.037 0.00 0.00 0.00 2.08
2106 2161 6.263168 CCTGGATAGACGGCTAATTTTGAATT 59.737 38.462 0.00 0.00 0.00 2.17
2133 2188 4.096231 CCTACATCGCAATTCACAAATCCA 59.904 41.667 0.00 0.00 0.00 3.41
2318 2373 6.716934 TTAAGTTGGAAAACAGTTATGCCA 57.283 33.333 0.00 0.00 0.00 4.92
2465 2520 7.067129 TGCGACTGTAGAACATAAGATCTAGTT 59.933 37.037 0.00 1.46 30.82 2.24
2902 2988 2.500229 ACATCAAAGGTGGTGGTTACG 58.500 47.619 0.00 0.00 40.49 3.18
3120 3206 9.241919 AGGTAACAATGACAAATGTAATGATGA 57.758 29.630 0.00 0.00 41.41 2.92
3297 3383 4.079269 TCCAATGGATTGTACATGGACCAT 60.079 41.667 5.38 0.00 39.38 3.55
3676 3762 6.322491 TCATAACATGACAGTGAGAACTACG 58.678 40.000 0.00 0.00 33.59 3.51
3941 4029 3.320541 TGCCAATTGTACTTCACCAAAGG 59.679 43.478 4.43 0.00 39.47 3.11
3975 4067 2.749621 GGCACTGCTAAGCACATTTAGT 59.250 45.455 0.00 0.00 33.79 2.24
3999 4091 6.257423 TGATATTACAAGCATTTGTTCGCAG 58.743 36.000 0.00 0.00 45.01 5.18
4112 4204 0.951558 AGCCGATTTCGCACAAAGTT 59.048 45.000 0.00 0.00 38.18 2.66
4118 4210 1.014044 TCAGTCAGCCGATTTCGCAC 61.014 55.000 0.00 0.00 38.18 5.34
4121 4213 3.363378 GCATTATCAGTCAGCCGATTTCG 60.363 47.826 0.00 0.00 39.44 3.46
4142 4234 1.608590 TGCAGGAAAGCAAACACTAGC 59.391 47.619 0.00 0.00 42.46 3.42
4201 4293 5.071370 ACTTCTCGAGGTCTTAAAGACTCA 58.929 41.667 13.56 0.00 44.46 3.41
4223 4315 1.586154 CCAACCCAATGGACAGCGAC 61.586 60.000 0.00 0.00 43.54 5.19
4288 4381 9.543018 GACAAATATAACAGTGCAAGAAGTTAC 57.457 33.333 0.00 0.00 30.19 2.50
4293 4386 7.701539 ATGGACAAATATAACAGTGCAAGAA 57.298 32.000 0.00 0.00 35.97 2.52
4342 4436 3.328931 AGAATGAGGACAAAAGCAGAGGA 59.671 43.478 0.00 0.00 0.00 3.71
4374 4468 7.847096 TGTATACACATGGTGAGTAAGAACAT 58.153 34.615 0.08 0.00 36.96 2.71
4375 4469 7.234661 TGTATACACATGGTGAGTAAGAACA 57.765 36.000 0.08 0.00 36.96 3.18
4434 4528 0.322726 CACCATGTGACCAGCCATCA 60.323 55.000 0.00 0.00 35.23 3.07
4553 4648 1.491670 TAATGAATCAGAGCGAGCGC 58.508 50.000 6.78 6.78 42.33 5.92
4585 4680 7.922278 AGCTTTATTATGCACACAAACATATGG 59.078 33.333 7.80 0.00 0.00 2.74
4700 4795 0.037590 AAACCTGCTATTCCACGGCA 59.962 50.000 0.00 0.00 34.66 5.69
4702 4797 2.671070 GCAAAAACCTGCTATTCCACGG 60.671 50.000 0.00 0.00 39.34 4.94
4716 4811 2.628178 AGTTCTAAGGGGCAGCAAAAAC 59.372 45.455 0.00 0.00 0.00 2.43
4746 4841 6.918473 ACCCATGGTAGTAATCTGGTACAGC 61.918 48.000 11.73 0.00 46.24 4.40
4773 4868 1.577328 AACACGGATTTCGCTGCAGG 61.577 55.000 17.12 5.82 43.89 4.85
4776 4871 0.793861 TACAACACGGATTTCGCTGC 59.206 50.000 0.00 0.00 43.89 5.25
4778 4873 2.967362 TCATACAACACGGATTTCGCT 58.033 42.857 0.00 0.00 43.89 4.93
4786 4881 3.364621 GCTTTGCATTTCATACAACACGG 59.635 43.478 0.00 0.00 0.00 4.94
4928 5023 6.959361 ACATGCAGTAACAGTTTCAAACTAG 58.041 36.000 1.43 0.50 40.46 2.57
4977 5072 5.582950 TGAATAATGATAGAAGGGGTGGG 57.417 43.478 0.00 0.00 0.00 4.61
4981 5076 8.917088 ACATTGTTTGAATAATGATAGAAGGGG 58.083 33.333 16.72 0.00 39.11 4.79
5131 5226 6.610020 TGGTAGCTCAGATTAGCCTTACTAAA 59.390 38.462 0.00 0.00 43.99 1.85
5132 5227 6.040616 GTGGTAGCTCAGATTAGCCTTACTAA 59.959 42.308 0.00 0.00 44.87 2.24
5133 5228 5.535406 GTGGTAGCTCAGATTAGCCTTACTA 59.465 44.000 0.00 0.00 43.86 1.82
5159 5254 1.066787 GCCGATAACCATAGGAGCTCC 60.067 57.143 26.22 26.22 0.00 4.70
5177 5272 0.837272 TAATGGTGCAGGAGGTAGCC 59.163 55.000 0.00 0.00 0.00 3.93
5320 5418 2.156917 ACATCAAGTACCTCGACGACA 58.843 47.619 0.00 0.00 0.00 4.35
5411 5509 1.133181 TCATCAGGTTCAGGGTGCCA 61.133 55.000 0.00 0.00 0.00 4.92
5584 5682 2.203451 CCCCTCATCTGCCATGCC 60.203 66.667 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.