Multiple sequence alignment - TraesCS2D01G382700

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 TraesCS2D01G382700 chr2D 100.000 4100 0 0 1 4100 486958665 486954566 0.000000e+00 7572.0
1 TraesCS2D01G382700 chr2D 87.805 779 38 21 2067 2817 643637237 643636488 0.000000e+00 859.0
2 TraesCS2D01G382700 chr2A 89.539 3556 155 66 1 3454 631970475 631967035 0.000000e+00 4305.0
3 TraesCS2D01G382700 chr2A 85.500 200 21 4 3680 3875 631963067 631962872 6.950000e-48 202.0
4 TraesCS2D01G382700 chr2B 90.962 2401 87 40 1153 3454 571533529 571531160 0.000000e+00 3112.0
5 TraesCS2D01G382700 chr2B 90.607 1054 41 17 1 1033 571534917 571533901 0.000000e+00 1345.0
6 TraesCS2D01G382700 chr2B 86.755 302 18 10 3570 3857 571530843 571530550 2.380000e-82 316.0
7 TraesCS2D01G382700 chr2B 90.816 196 14 3 3903 4098 571530554 571530363 4.070000e-65 259.0
8 TraesCS2D01G382700 chr5D 88.716 771 39 17 2068 2817 365088058 365088801 0.000000e+00 898.0
9 TraesCS2D01G382700 chr7A 88.586 771 45 18 2068 2817 176279531 176278783 0.000000e+00 896.0
10 TraesCS2D01G382700 chr7A 88.586 771 45 18 2068 2817 670564404 670563656 0.000000e+00 896.0
11 TraesCS2D01G382700 chr3A 87.938 771 47 20 2068 2817 693453535 693452790 0.000000e+00 867.0
12 TraesCS2D01G382700 chrUn 87.902 777 40 26 2068 2812 116830638 116831392 0.000000e+00 865.0
13 TraesCS2D01G382700 chr3B 87.712 236 20 4 2048 2275 32282286 32282052 2.430000e-67 267.0
14 TraesCS2D01G382700 chr3B 83.590 195 16 8 2311 2504 32280458 32280279 7.050000e-38 169.0
15 TraesCS2D01G382700 chr6D 88.785 107 12 0 1417 1523 310523083 310522977 9.250000e-27 132.0
16 TraesCS2D01G382700 chr6B 88.679 106 11 1 1414 1519 478753293 478753397 1.200000e-25 128.0
17 TraesCS2D01G382700 chr7B 93.333 45 3 0 3470 3514 171992403 171992359 2.640000e-07 67.6
18 TraesCS2D01G382700 chr7B 94.872 39 2 0 3476 3514 587915622 587915660 1.230000e-05 62.1
19 TraesCS2D01G382700 chr4D 93.333 45 3 0 3470 3514 148697332 148697288 2.640000e-07 67.6
20 TraesCS2D01G382700 chr4D 95.000 40 1 1 3477 3516 336801475 336801513 1.230000e-05 62.1
21 TraesCS2D01G382700 chr4D 92.683 41 2 1 3476 3516 431411372 431411333 1.590000e-04 58.4
22 TraesCS2D01G382700 chr4A 93.182 44 3 0 3470 3513 381220582 381220539 9.510000e-07 65.8
23 TraesCS2D01G382700 chr4B 92.683 41 2 1 3476 3516 579295383 579295422 1.590000e-04 58.4
24 TraesCS2D01G382700 chr1D 92.683 41 2 1 3476 3516 449529900 449529861 1.590000e-04 58.4
25 TraesCS2D01G382700 chr1A 92.683 41 2 1 3476 3516 354689342 354689381 1.590000e-04 58.4


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 TraesCS2D01G382700 chr2D 486954566 486958665 4099 True 7572.0 7572 100.0000 1 4100 1 chr2D.!!$R1 4099
1 TraesCS2D01G382700 chr2D 643636488 643637237 749 True 859.0 859 87.8050 2067 2817 1 chr2D.!!$R2 750
2 TraesCS2D01G382700 chr2A 631962872 631970475 7603 True 2253.5 4305 87.5195 1 3875 2 chr2A.!!$R1 3874
3 TraesCS2D01G382700 chr2B 571530363 571534917 4554 True 1258.0 3112 89.7850 1 4098 4 chr2B.!!$R1 4097
4 TraesCS2D01G382700 chr5D 365088058 365088801 743 False 898.0 898 88.7160 2068 2817 1 chr5D.!!$F1 749
5 TraesCS2D01G382700 chr7A 176278783 176279531 748 True 896.0 896 88.5860 2068 2817 1 chr7A.!!$R1 749
6 TraesCS2D01G382700 chr7A 670563656 670564404 748 True 896.0 896 88.5860 2068 2817 1 chr7A.!!$R2 749
7 TraesCS2D01G382700 chr3A 693452790 693453535 745 True 867.0 867 87.9380 2068 2817 1 chr3A.!!$R1 749
8 TraesCS2D01G382700 chrUn 116830638 116831392 754 False 865.0 865 87.9020 2068 2812 1 chrUn.!!$F1 744
9 TraesCS2D01G382700 chr3B 32280279 32282286 2007 True 218.0 267 85.6510 2048 2504 2 chr3B.!!$R1 456

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
891 939 0.036010 CAAATCGCCTCACCTCACCT 60.036 55.000 0.00 0.00 0.00 4.00 F
1013 1080 0.035630 ACTGCTCACTCCCAAGCATC 60.036 55.000 0.00 0.00 46.69 3.91 F
1903 2245 0.237498 GACCAAGCGTAAGTGCCAAC 59.763 55.000 0.00 0.00 41.68 3.77 F
1958 2300 1.273887 CGGTCGTACGTACTAGCCG 59.726 63.158 25.89 25.89 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2380 1.148310 CGTGCTACCAAGAACAGTGG 58.852 55.000 0.00 0.0 42.28 4.00 R
2950 4957 0.179171 CCGTCCTACGTACACAGCAG 60.179 60.000 0.00 0.0 40.58 4.24 R
2970 4977 2.443390 AGCATGCAATCCCCAGCC 60.443 61.111 21.98 0.0 0.00 4.85 R
3191 5202 2.868899 AGGGCAAAAGACAGGAAGAAG 58.131 47.619 0.00 0.0 0.00 2.85 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
60 61 2.203070 CCATGTAGCCTGCGGGTC 60.203 66.667 14.55 5.61 34.28 4.46
100 101 4.520846 CGACGCTGCGATTTGGCC 62.521 66.667 30.47 0.00 0.00 5.36
194 195 5.106673 ACAAAAACCGAAGCTAGATAACTGC 60.107 40.000 0.00 0.00 0.00 4.40
241 245 1.083489 TAAAAATGCGTCGCCTCTGG 58.917 50.000 15.88 0.00 0.00 3.86
271 275 2.817396 GACAGAAGCGCTCCAGCC 60.817 66.667 12.06 0.00 37.91 4.85
332 336 5.334414 GGATCACAAAGATTCACACAGTGAC 60.334 44.000 7.81 0.00 42.60 3.67
375 379 3.016474 GAGCGCGAAACAGGACTGC 62.016 63.158 12.10 0.00 0.00 4.40
385 389 3.560251 AGGACTGCGGGCACTGTT 61.560 61.111 0.00 0.00 36.83 3.16
546 568 2.694760 CCTGCCCGCTTTTCAGAGC 61.695 63.158 0.00 0.00 39.29 4.09
602 624 2.358737 GCCACTGTTCCCTGTCCG 60.359 66.667 0.00 0.00 0.00 4.79
762 797 4.527583 GAGCGAGCAGGAGCAGGG 62.528 72.222 0.00 0.00 45.49 4.45
835 883 2.302478 GAGGCTTTCTCGAATCGGC 58.698 57.895 1.76 0.00 32.18 5.54
889 937 2.029838 ATCAAATCGCCTCACCTCAC 57.970 50.000 0.00 0.00 0.00 3.51
890 938 0.036388 TCAAATCGCCTCACCTCACC 60.036 55.000 0.00 0.00 0.00 4.02
891 939 0.036010 CAAATCGCCTCACCTCACCT 60.036 55.000 0.00 0.00 0.00 4.00
892 940 0.250513 AAATCGCCTCACCTCACCTC 59.749 55.000 0.00 0.00 0.00 3.85
893 941 0.904865 AATCGCCTCACCTCACCTCA 60.905 55.000 0.00 0.00 0.00 3.86
937 989 3.375610 AGACTAGAGTATATGCGCATCCG 59.624 47.826 29.11 9.54 37.57 4.18
946 998 1.439353 ATGCGCATCCGTTCATCCAC 61.439 55.000 19.28 0.00 36.67 4.02
979 1031 4.103627 CGTTTCCCCCACTATATAAACCCT 59.896 45.833 0.00 0.00 0.00 4.34
1003 1070 1.539869 ATCCCCACCACTGCTCACT 60.540 57.895 0.00 0.00 0.00 3.41
1006 1073 2.348998 CCACCACTGCTCACTCCC 59.651 66.667 0.00 0.00 0.00 4.30
1007 1074 2.519622 CCACCACTGCTCACTCCCA 61.520 63.158 0.00 0.00 0.00 4.37
1008 1075 1.451504 CACCACTGCTCACTCCCAA 59.548 57.895 0.00 0.00 0.00 4.12
1009 1076 0.604780 CACCACTGCTCACTCCCAAG 60.605 60.000 0.00 0.00 0.00 3.61
1011 1078 1.071987 CACTGCTCACTCCCAAGCA 59.928 57.895 0.00 0.00 45.83 3.91
1012 1079 0.322277 CACTGCTCACTCCCAAGCAT 60.322 55.000 0.00 0.00 46.69 3.79
1013 1080 0.035630 ACTGCTCACTCCCAAGCATC 60.036 55.000 0.00 0.00 46.69 3.91
1015 1082 1.300963 GCTCACTCCCAAGCATCCA 59.699 57.895 0.00 0.00 38.42 3.41
1018 1085 0.548031 TCACTCCCAAGCATCCATCC 59.452 55.000 0.00 0.00 0.00 3.51
1079 1146 1.574526 CCCCTCCCCTGATCAAAGCA 61.575 60.000 0.00 0.00 0.00 3.91
1081 1148 0.745845 CCTCCCCTGATCAAAGCACG 60.746 60.000 0.00 0.00 0.00 5.34
1099 1166 2.413351 CGCCGAGCAAGCTAGCTA 59.587 61.111 19.70 0.00 46.75 3.32
1100 1167 1.659954 CGCCGAGCAAGCTAGCTAG 60.660 63.158 19.70 16.84 46.75 3.42
1101 1168 1.953642 GCCGAGCAAGCTAGCTAGC 60.954 63.158 33.96 33.96 46.75 3.42
1132 1199 4.562425 CGCAGGTGGTGGTGTGGT 62.562 66.667 0.00 0.00 0.00 4.16
1134 1201 2.203337 CAGGTGGTGGTGTGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
1148 1215 1.068417 GGTGGGCGCATACATACGA 59.932 57.895 10.83 0.00 0.00 3.43
1157 1468 4.322804 GGCGCATACATACGATTACTGTAC 59.677 45.833 10.83 0.00 0.00 2.90
1197 1508 2.475466 CGCCAGCACCATGATGTCC 61.475 63.158 0.00 0.00 30.62 4.02
1392 1730 2.291282 ACCCTCTCGTCTCACAATCTCT 60.291 50.000 0.00 0.00 0.00 3.10
1395 1733 3.192422 CCTCTCGTCTCACAATCTCTTGT 59.808 47.826 0.00 0.00 46.54 3.16
1661 2003 2.146342 CAGCGTCTTTGAACTGATGGT 58.854 47.619 0.00 0.00 31.67 3.55
1663 2005 3.745975 CAGCGTCTTTGAACTGATGGTAA 59.254 43.478 0.00 0.00 31.67 2.85
1722 2064 2.348666 GGATGAAATGTCGTCGTTCCAG 59.651 50.000 0.00 0.00 40.25 3.86
1903 2245 0.237498 GACCAAGCGTAAGTGCCAAC 59.763 55.000 0.00 0.00 41.68 3.77
1912 2254 2.548067 CGTAAGTGCCAACCTCAGTTCT 60.548 50.000 0.00 0.00 32.45 3.01
1957 2299 1.643832 CCGGTCGTACGTACTAGCC 59.356 63.158 22.55 18.52 0.00 3.93
1958 2300 1.273887 CGGTCGTACGTACTAGCCG 59.726 63.158 25.89 25.89 0.00 5.52
1996 2345 3.787001 CCCTGGGCCGGAGAACTC 61.787 72.222 15.75 0.00 0.00 3.01
1997 2346 3.787001 CCTGGGCCGGAGAACTCC 61.787 72.222 15.75 10.51 46.18 3.85
2156 2506 3.942115 GGAAGAGGCCTGTTGAATAGTTC 59.058 47.826 21.75 2.33 0.00 3.01
2220 2582 5.656213 TTTTCCCAAACTCCAACGTTAAA 57.344 34.783 0.00 0.00 0.00 1.52
2233 2598 4.323336 CCAACGTTAAAATATGCACAGTGC 59.677 41.667 19.37 19.37 45.29 4.40
2315 4239 9.862371 ACATAATCAGTTCTGTAAGTTCTGTAG 57.138 33.333 0.00 0.00 37.18 2.74
2316 4240 9.307121 CATAATCAGTTCTGTAAGTTCTGTAGG 57.693 37.037 0.00 0.00 37.18 3.18
2317 4241 5.723672 TCAGTTCTGTAAGTTCTGTAGGG 57.276 43.478 0.00 0.00 37.18 3.53
2318 4242 4.527038 TCAGTTCTGTAAGTTCTGTAGGGG 59.473 45.833 0.00 0.00 37.18 4.79
2319 4243 4.283722 CAGTTCTGTAAGTTCTGTAGGGGT 59.716 45.833 0.00 0.00 33.67 4.95
2320 4244 5.479375 CAGTTCTGTAAGTTCTGTAGGGGTA 59.521 44.000 0.00 0.00 33.67 3.69
2321 4245 5.479724 AGTTCTGTAAGTTCTGTAGGGGTAC 59.520 44.000 0.00 0.00 33.76 3.34
2322 4246 4.347607 TCTGTAAGTTCTGTAGGGGTACC 58.652 47.826 2.17 2.17 42.44 3.34
2579 4550 4.595762 GCATGATGCATGGTTTCCTAAT 57.404 40.909 13.36 0.00 44.26 1.73
2580 4551 4.553323 GCATGATGCATGGTTTCCTAATC 58.447 43.478 13.36 0.00 44.26 1.75
2707 4680 7.845037 TCTTCTCTATTTCTCATTCTCAGCAA 58.155 34.615 0.00 0.00 0.00 3.91
2745 4718 5.239351 TCGGGTTCGATCTTTGATTTGTTA 58.761 37.500 0.00 0.00 40.88 2.41
2772 4745 8.613060 ATGCTTTGTGTATTTATCATCGATCT 57.387 30.769 0.00 0.00 0.00 2.75
2897 4875 6.070136 GGAGGCCCTAAAACCTAATCCTATAG 60.070 46.154 0.00 0.00 36.05 1.31
2898 4876 5.791141 AGGCCCTAAAACCTAATCCTATAGG 59.209 44.000 13.07 13.07 46.62 2.57
2920 4903 2.159043 ACTATGTCCGTGCAGAATCAGG 60.159 50.000 0.00 0.00 0.00 3.86
2950 4957 5.293079 CAGCTAGCACTTATGTTCTCCTTTC 59.707 44.000 18.83 0.00 0.00 2.62
3075 5083 0.989890 CTCCGTTTTAGCGTCTTCCG 59.010 55.000 0.00 0.00 40.40 4.30
3125 5133 0.338467 TTCTAGCTAGGGTGCTGGGA 59.662 55.000 20.58 0.00 43.87 4.37
3131 5142 1.500474 CTAGGGTGCTGGGAGATCAA 58.500 55.000 0.00 0.00 0.00 2.57
3160 5171 6.990546 TCTTGAGATGTATCGTATCGTATCG 58.009 40.000 0.00 0.00 0.00 2.92
3161 5172 6.589139 TCTTGAGATGTATCGTATCGTATCGT 59.411 38.462 0.00 0.00 0.00 3.73
3162 5173 7.756722 TCTTGAGATGTATCGTATCGTATCGTA 59.243 37.037 0.00 0.00 0.00 3.43
3163 5174 7.998753 TGAGATGTATCGTATCGTATCGTAT 57.001 36.000 0.00 0.00 0.00 3.06
3164 5175 8.058916 TGAGATGTATCGTATCGTATCGTATC 57.941 38.462 0.00 0.00 0.00 2.24
3191 5202 5.059465 CGAGTACTCTTCTAGTTTTCGTTGC 59.941 44.000 20.34 0.00 39.80 4.17
3225 5236 1.875488 TGCCCTTTCCCTAGTCCTAC 58.125 55.000 0.00 0.00 0.00 3.18
3265 5276 0.675633 GAGGTTGCTGTGTTTGCCAT 59.324 50.000 0.00 0.00 0.00 4.40
3357 5379 4.205587 TCCTAACTCCGGCTTTCTACTAG 58.794 47.826 0.00 0.00 0.00 2.57
3364 5386 6.125029 ACTCCGGCTTTCTACTAGTTACATA 58.875 40.000 0.00 0.00 0.00 2.29
3388 5410 6.822667 TCTGCTGAATAATTGAACATGTGT 57.177 33.333 0.00 0.00 0.00 3.72
3435 5457 7.710907 TCCTCAAATTACTAGTGACATGTATGC 59.289 37.037 5.39 0.00 0.00 3.14
3458 5480 8.195165 TGCTACTATAGGATTTTAGATGCACT 57.805 34.615 4.43 0.00 0.00 4.40
3459 5481 8.651389 TGCTACTATAGGATTTTAGATGCACTT 58.349 33.333 4.43 0.00 0.00 3.16
3460 5482 9.495572 GCTACTATAGGATTTTAGATGCACTTT 57.504 33.333 4.43 0.00 0.00 2.66
3479 5538 6.695713 GCACTTTTTATCTCGAAAAGGTTGTT 59.304 34.615 10.42 0.00 44.44 2.83
3491 5774 7.763356 TCGAAAAGGTTGTTTTAGATTTGTCA 58.237 30.769 0.00 0.00 0.00 3.58
3520 5803 4.948004 CGGATGTATCTATACACTAGGCCA 59.052 45.833 5.01 0.00 45.11 5.36
3656 6114 4.206375 TGGATGTTTCTCAAGCAGTTTCA 58.794 39.130 0.00 0.00 0.00 2.69
3685 6145 7.883217 TGTACAACAACTTAACCAAACAAGAA 58.117 30.769 0.00 0.00 0.00 2.52
3696 6156 9.626045 CTTAACCAAACAAGAAAATCATAGTCC 57.374 33.333 0.00 0.00 0.00 3.85
3710 9475 5.204409 TCATAGTCCGCGTAACCAAATAT 57.796 39.130 4.92 0.00 0.00 1.28
3716 9481 6.154445 AGTCCGCGTAACCAAATATATGTAG 58.846 40.000 4.92 0.00 0.00 2.74
3932 9700 8.731275 AAAAGAAATGATACACGGACATATCA 57.269 30.769 0.00 0.00 41.00 2.15
4061 9829 9.599866 CACCAAGATACTAATCATGTAACAAGA 57.400 33.333 0.00 0.00 34.28 3.02
4080 9848 8.991243 AACAAGAACATTATCCATGTCAAATG 57.009 30.769 8.70 8.70 46.23 2.32
4085 9853 3.395054 TTATCCATGTCAAATGGGGCA 57.605 42.857 0.00 0.00 39.60 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.679082 CTACATGGGCTACTACCTGGT 58.321 52.381 4.05 4.05 0.00 4.00
194 195 6.847956 TTTTGATTGATTGACTGGCTTTTG 57.152 33.333 0.00 0.00 0.00 2.44
225 226 2.436646 CCCAGAGGCGACGCATTT 60.437 61.111 23.09 7.00 0.00 2.32
260 264 2.188994 GATTCAGGCTGGAGCGCT 59.811 61.111 11.27 11.27 43.26 5.92
308 312 4.756642 TCACTGTGTGAATCTTTGTGATCC 59.243 41.667 7.79 0.00 39.78 3.36
364 368 2.594592 GTGCCCGCAGTCCTGTTT 60.595 61.111 0.00 0.00 0.00 2.83
524 546 3.752339 GAAAAGCGGGCAGGGCAG 61.752 66.667 0.00 0.00 0.00 4.85
525 547 4.594854 TGAAAAGCGGGCAGGGCA 62.595 61.111 0.00 0.00 0.00 5.36
526 548 3.752339 CTGAAAAGCGGGCAGGGC 61.752 66.667 0.00 0.00 0.00 5.19
527 549 2.034066 TCTGAAAAGCGGGCAGGG 59.966 61.111 0.00 0.00 0.00 4.45
528 550 2.694760 GCTCTGAAAAGCGGGCAGG 61.695 63.158 0.00 0.00 31.56 4.85
529 551 2.873288 GCTCTGAAAAGCGGGCAG 59.127 61.111 0.00 0.00 31.56 4.85
546 568 2.544685 CTAGCATCTTGGGACTGTTCG 58.455 52.381 0.00 0.00 0.00 3.95
602 624 0.468029 CTCTCTCCTCTCCTCTGCCC 60.468 65.000 0.00 0.00 0.00 5.36
604 626 1.447317 CGCTCTCTCCTCTCCTCTGC 61.447 65.000 0.00 0.00 0.00 4.26
605 627 0.819259 CCGCTCTCTCCTCTCCTCTG 60.819 65.000 0.00 0.00 0.00 3.35
606 628 1.531748 CCGCTCTCTCCTCTCCTCT 59.468 63.158 0.00 0.00 0.00 3.69
835 883 3.635373 CCTGATGGATTTGATTGACCTGG 59.365 47.826 0.00 0.00 34.57 4.45
889 937 1.200252 ACGAGACGTGATGAGTTGAGG 59.800 52.381 0.00 0.00 39.18 3.86
890 938 2.510874 GACGAGACGTGATGAGTTGAG 58.489 52.381 0.00 0.00 41.37 3.02
891 939 1.136057 CGACGAGACGTGATGAGTTGA 60.136 52.381 0.00 0.00 41.37 3.18
892 940 1.136057 TCGACGAGACGTGATGAGTTG 60.136 52.381 0.00 0.00 41.37 3.16
893 941 1.136029 GTCGACGAGACGTGATGAGTT 60.136 52.381 0.00 0.00 41.37 3.01
937 989 1.678970 GCAGTGGGGGTGGATGAAC 60.679 63.158 0.00 0.00 0.00 3.18
979 1031 1.616327 CAGTGGTGGGGATGGGAGA 60.616 63.158 0.00 0.00 0.00 3.71
1003 1070 1.309013 AGGGGATGGATGCTTGGGA 60.309 57.895 0.00 0.00 0.00 4.37
1006 1073 0.110104 GGAGAGGGGATGGATGCTTG 59.890 60.000 0.00 0.00 0.00 4.01
1007 1074 0.029267 AGGAGAGGGGATGGATGCTT 60.029 55.000 0.00 0.00 0.00 3.91
1008 1075 0.473501 GAGGAGAGGGGATGGATGCT 60.474 60.000 0.00 0.00 0.00 3.79
1009 1076 0.473501 AGAGGAGAGGGGATGGATGC 60.474 60.000 0.00 0.00 0.00 3.91
1011 1078 0.491371 GGAGAGGAGAGGGGATGGAT 59.509 60.000 0.00 0.00 0.00 3.41
1012 1079 0.631998 AGGAGAGGAGAGGGGATGGA 60.632 60.000 0.00 0.00 0.00 3.41
1013 1080 0.178935 GAGGAGAGGAGAGGGGATGG 60.179 65.000 0.00 0.00 0.00 3.51
1015 1082 1.725169 CGGAGGAGAGGAGAGGGGAT 61.725 65.000 0.00 0.00 0.00 3.85
1055 1122 4.455137 ATCAGGGGAGGGGGTGGG 62.455 72.222 0.00 0.00 0.00 4.61
1056 1123 2.774351 GATCAGGGGAGGGGGTGG 60.774 72.222 0.00 0.00 0.00 4.61
1057 1124 1.214305 TTTGATCAGGGGAGGGGGTG 61.214 60.000 0.00 0.00 0.00 4.61
1066 1133 2.787249 CGCGTGCTTTGATCAGGG 59.213 61.111 0.00 0.00 0.00 4.45
1081 1148 3.774959 TAGCTAGCTTGCTCGGCGC 62.775 63.158 25.94 0.00 42.97 6.53
1115 1182 4.562425 ACCACACCACCACCTGCG 62.562 66.667 0.00 0.00 0.00 5.18
1116 1183 2.906897 CACCACACCACCACCTGC 60.907 66.667 0.00 0.00 0.00 4.85
1117 1184 2.203337 CCACCACACCACCACCTG 60.203 66.667 0.00 0.00 0.00 4.00
1129 1196 1.227409 CGTATGTATGCGCCCACCA 60.227 57.895 4.18 0.00 0.00 4.17
1130 1197 0.320421 ATCGTATGTATGCGCCCACC 60.320 55.000 4.18 0.00 35.83 4.61
1132 1199 2.297880 AGTAATCGTATGTATGCGCCCA 59.702 45.455 4.18 0.00 35.83 5.36
1134 1201 3.314553 ACAGTAATCGTATGTATGCGCC 58.685 45.455 4.18 0.00 35.83 6.53
1138 1205 4.028757 GCGCGTACAGTAATCGTATGTATG 59.971 45.833 8.43 0.00 38.75 2.39
1140 1207 3.544651 GCGCGTACAGTAATCGTATGTA 58.455 45.455 8.43 0.00 0.00 2.29
1148 1215 2.219562 GCGTCGCGCGTACAGTAAT 61.220 57.895 30.98 0.00 44.55 1.89
1274 1585 4.756458 ACAGCTGCTCCTGCTCGC 62.756 66.667 15.27 0.00 36.55 5.03
1342 1678 2.509336 AACTGAGGCGCGAATCGG 60.509 61.111 12.10 14.48 38.94 4.18
1351 1687 1.627550 GGAAACGAGCGAACTGAGGC 61.628 60.000 0.00 0.00 0.00 4.70
1392 1730 2.962786 CGCCACACGGACGAACAA 60.963 61.111 0.00 0.00 38.44 2.83
1680 2022 4.225942 TCCTGCAGGAGTCAAGTAATCAAT 59.774 41.667 32.00 0.00 39.78 2.57
1681 2023 3.582647 TCCTGCAGGAGTCAAGTAATCAA 59.417 43.478 32.00 3.90 39.78 2.57
1682 2024 3.173151 TCCTGCAGGAGTCAAGTAATCA 58.827 45.455 32.00 4.40 39.78 2.57
1683 2025 3.895232 TCCTGCAGGAGTCAAGTAATC 57.105 47.619 32.00 0.00 39.78 1.75
1731 2073 3.955291 CTGATCCGTCAGTAGGCTG 57.045 57.895 0.00 0.00 45.51 4.85
1743 2085 3.743017 TTGGGGCTGGCCTGATCC 61.743 66.667 20.47 13.46 36.10 3.36
1957 2299 1.795768 TCAAGGTGCTTTGACTAGCG 58.204 50.000 0.00 0.00 44.18 4.26
1958 2300 2.159462 GCATCAAGGTGCTTTGACTAGC 60.159 50.000 0.00 1.69 39.68 3.42
2031 2380 1.148310 CGTGCTACCAAGAACAGTGG 58.852 55.000 0.00 0.00 42.28 4.00
2156 2506 2.023414 TACTATTGGGCCGGTGAGCG 62.023 60.000 1.90 0.00 0.00 5.03
2201 2557 6.570764 GCATATTTTAACGTTGGAGTTTGGGA 60.571 38.462 11.99 0.00 35.70 4.37
2220 2582 4.327982 AGTATCTCGCACTGTGCATATT 57.672 40.909 29.86 15.12 45.36 1.28
2317 4241 4.434354 TGGCGGCCCATTGGTACC 62.434 66.667 17.97 4.43 35.79 3.34
2318 4242 2.828549 CTGGCGGCCCATTGGTAC 60.829 66.667 17.97 0.00 41.21 3.34
2319 4243 4.122149 CCTGGCGGCCCATTGGTA 62.122 66.667 17.97 0.00 41.21 3.25
2322 4246 3.762247 CAACCTGGCGGCCCATTG 61.762 66.667 17.97 13.90 41.21 2.82
2578 4549 2.809119 CTCGTCTCTGCGTACATAGGAT 59.191 50.000 0.00 0.00 0.00 3.24
2579 4550 2.159000 TCTCGTCTCTGCGTACATAGGA 60.159 50.000 0.00 0.00 0.00 2.94
2580 4551 2.210961 TCTCGTCTCTGCGTACATAGG 58.789 52.381 0.00 0.00 0.00 2.57
2704 4677 3.108144 CCGATCCGATCAAAATGTTTGC 58.892 45.455 9.07 0.00 0.00 3.68
2707 4680 2.999331 ACCCGATCCGATCAAAATGTT 58.001 42.857 9.07 0.00 0.00 2.71
2745 4718 9.669353 GATCGATGATAAATACACAAAGCATTT 57.331 29.630 0.54 0.00 40.26 2.32
2772 4745 1.879737 GCCCACTGATGCATGCACAA 61.880 55.000 25.37 13.38 0.00 3.33
2898 4876 3.119291 CTGATTCTGCACGGACATAGTC 58.881 50.000 0.00 0.00 0.00 2.59
2920 4903 3.265791 ACATAAGTGCTAGCTGCTCAAC 58.734 45.455 17.23 4.28 43.37 3.18
2950 4957 0.179171 CCGTCCTACGTACACAGCAG 60.179 60.000 0.00 0.00 40.58 4.24
2970 4977 2.443390 AGCATGCAATCCCCAGCC 60.443 61.111 21.98 0.00 0.00 4.85
3131 5142 6.876789 ACGATACGATACATCTCAAGATCTCT 59.123 38.462 0.00 0.00 31.21 3.10
3161 5172 9.029243 CGAAAACTAGAAGAGTACTCGTAGATA 57.971 37.037 24.90 13.56 37.44 1.98
3162 5173 7.548780 ACGAAAACTAGAAGAGTACTCGTAGAT 59.451 37.037 24.90 16.32 46.14 1.98
3163 5174 6.870965 ACGAAAACTAGAAGAGTACTCGTAGA 59.129 38.462 24.90 12.07 46.14 2.59
3164 5175 7.059448 ACGAAAACTAGAAGAGTACTCGTAG 57.941 40.000 17.07 18.88 46.14 3.51
3191 5202 2.868899 AGGGCAAAAGACAGGAAGAAG 58.131 47.619 0.00 0.00 0.00 2.85
3225 5236 4.309933 TCATTAGCTGATAGGCGAACATG 58.690 43.478 0.00 0.00 37.29 3.21
3302 5313 6.768515 AATTTAAAACGATAATGTGCGACG 57.231 33.333 0.00 0.00 0.00 5.12
3304 5315 9.480538 GAACTAATTTAAAACGATAATGTGCGA 57.519 29.630 0.00 0.00 0.00 5.10
3364 5386 7.255569 CACACATGTTCAATTATTCAGCAGAT 58.744 34.615 0.00 0.00 0.00 2.90
3388 5410 6.431722 AGGAATTCGAAGGATAAAAATCCCA 58.568 36.000 3.35 0.00 41.65 4.37
3454 5476 6.206498 ACAACCTTTTCGAGATAAAAAGTGC 58.794 36.000 5.95 0.00 40.50 4.40
3455 5477 8.628882 AAACAACCTTTTCGAGATAAAAAGTG 57.371 30.769 5.95 2.17 40.50 3.16
3463 5485 8.630037 ACAAATCTAAAACAACCTTTTCGAGAT 58.370 29.630 0.00 0.00 0.00 2.75
3464 5486 7.992008 ACAAATCTAAAACAACCTTTTCGAGA 58.008 30.769 0.00 0.00 0.00 4.04
3465 5487 7.913297 TGACAAATCTAAAACAACCTTTTCGAG 59.087 33.333 0.00 0.00 0.00 4.04
3466 5488 7.763356 TGACAAATCTAAAACAACCTTTTCGA 58.237 30.769 0.00 0.00 0.00 3.71
3509 5792 3.700863 ATACTCCCTTGGCCTAGTGTA 57.299 47.619 13.38 12.42 0.00 2.90
3517 5800 5.891551 TCCTCAAATTTTATACTCCCTTGGC 59.108 40.000 0.00 0.00 0.00 4.52
3520 5803 8.950007 TTGTTCCTCAAATTTTATACTCCCTT 57.050 30.769 0.00 0.00 32.64 3.95
3630 6088 4.660168 ACTGCTTGAGAAACATCCAATCT 58.340 39.130 0.00 0.00 0.00 2.40
3656 6114 7.659186 TGTTTGGTTAAGTTGTTGTACAGTTT 58.341 30.769 0.00 0.00 0.00 2.66
3685 6145 3.530265 TGGTTACGCGGACTATGATTT 57.470 42.857 12.47 0.00 0.00 2.17
3693 6153 5.164022 GCTACATATATTTGGTTACGCGGAC 60.164 44.000 12.47 8.87 0.00 4.79
3694 6154 4.925054 GCTACATATATTTGGTTACGCGGA 59.075 41.667 12.47 0.00 0.00 5.54
3696 6156 5.832568 TGCTACATATATTTGGTTACGCG 57.167 39.130 3.53 3.53 0.00 6.01
3710 9475 9.542462 ACGAGATTAGCTTTAATTTGCTACATA 57.458 29.630 0.00 0.00 40.89 2.29
3755 9520 9.826574 GGTCCTACAATGTGATTAACTACATAA 57.173 33.333 0.00 0.00 36.56 1.90
3773 9538 5.728937 ACTAGATGTCTTAGGGTCCTACA 57.271 43.478 0.00 0.00 0.00 2.74
3777 9542 6.295719 TCAAAACTAGATGTCTTAGGGTCC 57.704 41.667 0.00 0.00 0.00 4.46
3906 9674 9.825109 TGATATGTCCGTGTATCATTTCTTTTA 57.175 29.630 0.00 0.00 33.60 1.52
4065 9833 3.395054 TGCCCCATTTGACATGGATAA 57.605 42.857 0.00 0.00 41.64 1.75


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

AutoCloner maintained by Alex Coulton.