Multiple sequence alignment - TraesCS5A01G032600

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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 TraesCS5A01G032600 chr5A 100.000 3707 0 0 508 4214 29886505 29890211 0.000000e+00 6846.0
1 TraesCS5A01G032600 chr5A 100.000 206 0 0 1 206 29885998 29886203 8.550000e-102 381.0
2 TraesCS5A01G032600 chr5D 94.036 3756 148 36 508 4214 41540547 41544275 0.000000e+00 5626.0
3 TraesCS5A01G032600 chr5D 93.689 206 13 0 1 206 41540259 41540464 4.090000e-80 309.0
4 TraesCS5A01G032600 chr5D 95.902 122 5 0 3126 3247 41600446 41600567 9.240000e-47 198.0
5 TraesCS5A01G032600 chr5B 93.530 3014 141 28 508 3495 36072296 36075281 0.000000e+00 4436.0
6 TraesCS5A01G032600 chr7D 86.957 667 77 8 1393 2055 404391015 404390355 0.000000e+00 741.0
7 TraesCS5A01G032600 chr7D 89.048 210 20 2 1076 1282 404391220 404391011 1.500000e-64 257.0
8 TraesCS5A01G032600 chr7D 90.761 184 13 1 2096 2279 404390350 404390171 4.210000e-60 243.0
9 TraesCS5A01G032600 chrUn 90.625 448 36 4 1835 2280 38373542 38373985 1.300000e-164 590.0
10 TraesCS5A01G032600 chr2B 78.571 140 19 7 572 709 488197848 488197978 9.710000e-12 82.4


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 TraesCS5A01G032600 chr5A 29885998 29890211 4213 False 3613.500000 6846 100.0000 1 4214 2 chr5A.!!$F1 4213
1 TraesCS5A01G032600 chr5D 41540259 41544275 4016 False 2967.500000 5626 93.8625 1 4214 2 chr5D.!!$F2 4213
2 TraesCS5A01G032600 chr5B 36072296 36075281 2985 False 4436.000000 4436 93.5300 508 3495 1 chr5B.!!$F1 2987
3 TraesCS5A01G032600 chr7D 404390171 404391220 1049 True 413.666667 741 88.9220 1076 2279 3 chr7D.!!$R1 1203

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
63 64 0.250945 TTCCGTGCAACATTAGCCCA 60.251 50.0 0.00 0.0 35.74 5.36 F
167 168 0.453950 CGATGTGAGCAGCAACAAGC 60.454 55.0 5.14 1.1 46.19 4.01 F
1788 1857 0.039437 TGTCGGTTGAGAACTCGCTC 60.039 55.0 0.00 0.0 35.46 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1800 0.540365 CCTTCACAGCCAACCCATGT 60.540 55.0 0.00 0.00 0.0 3.21 R
1945 2014 1.104577 GTTGGTGAAAACCCCGCAGA 61.105 55.0 0.00 0.00 0.0 4.26 R
3697 3774 0.956633 ACCAAGTTGATGTGCTGCAG 59.043 50.0 10.11 10.11 0.0 4.41 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
49 50 2.380410 GCGCGTCAGTCAATTCCGT 61.380 57.895 8.43 0.00 0.00 4.69
56 57 2.226437 GTCAGTCAATTCCGTGCAACAT 59.774 45.455 0.00 0.00 35.74 2.71
57 58 2.884012 TCAGTCAATTCCGTGCAACATT 59.116 40.909 0.00 0.00 35.74 2.71
63 64 0.250945 TTCCGTGCAACATTAGCCCA 60.251 50.000 0.00 0.00 35.74 5.36
82 83 2.484287 AAAGGTGGGGATGGCGTGAG 62.484 60.000 0.00 0.00 0.00 3.51
95 96 1.291877 GCGTGAGGAACAACAGCGAT 61.292 55.000 0.00 0.00 0.00 4.58
133 134 1.437986 GCCGAGCTAGGACATCGTT 59.562 57.895 18.16 0.00 34.71 3.85
139 140 1.827969 AGCTAGGACATCGTTGAAGCT 59.172 47.619 0.00 6.13 34.15 3.74
158 159 1.003839 GGGGACAACGATGTGAGCA 60.004 57.895 1.86 0.00 40.74 4.26
167 168 0.453950 CGATGTGAGCAGCAACAAGC 60.454 55.000 5.14 1.10 46.19 4.01
184 185 1.444383 GCTGCGACGTCTCATGTGA 60.444 57.895 14.70 0.00 0.00 3.58
530 531 2.683933 GAGGTCGAGGGAAGGGCA 60.684 66.667 0.00 0.00 0.00 5.36
536 537 3.732849 GAGGGAAGGGCAGGGTGG 61.733 72.222 0.00 0.00 0.00 4.61
537 538 4.617595 AGGGAAGGGCAGGGTGGT 62.618 66.667 0.00 0.00 0.00 4.16
547 548 4.988716 AGGGTGGTGAGGCGACGA 62.989 66.667 0.00 0.00 0.00 4.20
548 549 4.736896 GGGTGGTGAGGCGACGAC 62.737 72.222 0.00 0.00 0.00 4.34
622 623 3.129813 TGCTACGCGAGAAAGAAGGATAA 59.870 43.478 15.93 0.00 0.00 1.75
670 671 0.676736 GTTTTGGGCCGTTGGATGAA 59.323 50.000 0.00 0.00 0.00 2.57
678 679 2.139118 GCCGTTGGATGAAGATCTAGC 58.861 52.381 0.00 0.00 0.00 3.42
683 684 2.950781 TGGATGAAGATCTAGCGGTCT 58.049 47.619 0.00 0.00 0.00 3.85
731 732 4.227300 ACTTTTCCAGGTGCCTGATGTATA 59.773 41.667 19.04 0.00 46.30 1.47
732 733 4.422073 TTTCCAGGTGCCTGATGTATAG 57.578 45.455 19.04 1.41 46.30 1.31
733 734 2.329267 TCCAGGTGCCTGATGTATAGG 58.671 52.381 19.04 0.54 46.30 2.57
750 751 2.143876 AGGCGCTCCCATGTAAAAAT 57.856 45.000 7.64 0.00 35.39 1.82
751 752 2.456577 AGGCGCTCCCATGTAAAAATT 58.543 42.857 7.64 0.00 35.39 1.82
753 754 2.481276 GGCGCTCCCATGTAAAAATTCC 60.481 50.000 7.64 0.00 0.00 3.01
754 755 2.165437 GCGCTCCCATGTAAAAATTCCA 59.835 45.455 0.00 0.00 0.00 3.53
838 839 3.165875 CCAGAAAGGAGAGACTACACCA 58.834 50.000 0.00 0.00 41.22 4.17
857 858 5.990996 ACACCATTTGCACCTCTTTTATTTG 59.009 36.000 0.00 0.00 0.00 2.32
862 863 9.050601 CCATTTGCACCTCTTTTATTTGTTTTA 57.949 29.630 0.00 0.00 0.00 1.52
1010 1074 4.465512 CACGTGAATGGCAGGCGC 62.466 66.667 10.90 0.00 35.84 6.53
1313 1380 4.069232 CGCGCTCTCCCACTTCCA 62.069 66.667 5.56 0.00 0.00 3.53
1314 1381 2.347490 GCGCTCTCCCACTTCCAA 59.653 61.111 0.00 0.00 0.00 3.53
1321 1388 1.064463 TCTCCCACTTCCAATCCATGC 60.064 52.381 0.00 0.00 0.00 4.06
1323 1390 1.064463 TCCCACTTCCAATCCATGCTC 60.064 52.381 0.00 0.00 0.00 4.26
1329 1396 3.212685 CTTCCAATCCATGCTCTTCTCC 58.787 50.000 0.00 0.00 0.00 3.71
1359 1426 4.880426 ATCCTCCCGTCCCCGCAT 62.880 66.667 0.00 0.00 0.00 4.73
1365 1432 2.513897 CCGTCCCCGCATTCCTTC 60.514 66.667 0.00 0.00 0.00 3.46
1453 1520 4.785453 GCAAGGTCCCCTCGGCTG 62.785 72.222 0.00 0.00 33.11 4.85
1497 1564 3.056250 CCTCTCTGCTCAACATGTACTGT 60.056 47.826 0.00 0.00 40.84 3.55
1505 1572 3.935203 CTCAACATGTACTGTAAGCTGGG 59.065 47.826 0.00 0.00 36.98 4.45
1630 1698 1.064832 AGGCCTTTGAGATCTTCCAGC 60.065 52.381 0.00 0.00 0.00 4.85
1662 1730 3.544615 GTGCCCGTCACAGAAAAAC 57.455 52.632 0.82 0.00 44.98 2.43
1731 1800 3.479203 CCGATGGGGGTGCAGCTA 61.479 66.667 16.65 3.18 0.00 3.32
1779 1848 1.063469 GTGGTGTTTGTGTCGGTTGAG 59.937 52.381 0.00 0.00 0.00 3.02
1788 1857 0.039437 TGTCGGTTGAGAACTCGCTC 60.039 55.000 0.00 0.00 35.46 5.03
1794 1863 0.666374 TTGAGAACTCGCTCGTCACA 59.334 50.000 0.00 0.00 37.73 3.58
1945 2014 6.579666 TTAGAATGTTCTTGCAGATGCTTT 57.420 33.333 6.35 0.00 39.14 3.51
1995 2064 2.568090 GTTGGGGTGCTCAATGCG 59.432 61.111 0.00 0.00 46.63 4.73
2205 2274 4.120331 GCCGGGCATGTGCAGAAC 62.120 66.667 15.62 0.00 44.36 3.01
2229 2298 1.209019 GAGCATGAGGAAGCCTTGAGA 59.791 52.381 0.00 0.00 31.76 3.27
2361 2430 1.270625 ACGCAAATCCTCAAGTTCGGA 60.271 47.619 0.00 0.00 0.00 4.55
2544 2613 2.092429 AGCACTTGACCTGTTTGAGGAA 60.092 45.455 0.00 0.00 46.33 3.36
2677 2746 6.986904 CCAAAGACTATGGTTTAACTCCTC 57.013 41.667 0.00 0.00 33.08 3.71
2962 3031 2.019984 GGGTGAGGCATTTGATGAGAC 58.980 52.381 0.00 0.00 0.00 3.36
2963 3032 2.618816 GGGTGAGGCATTTGATGAGACA 60.619 50.000 0.00 0.00 0.00 3.41
2965 3034 3.314635 GGTGAGGCATTTGATGAGACATC 59.685 47.826 4.98 4.98 0.00 3.06
3244 3313 7.552687 TCAAATGACAAGAACAGTGAGTACTTT 59.447 33.333 0.00 0.00 34.07 2.66
3273 3342 9.447157 TTGTTTCTTCTTGAATTTGGAAAATGT 57.553 25.926 0.00 0.00 34.24 2.71
3289 3358 9.738832 TTGGAAAATGTAACTAACAAAAGCTAC 57.261 29.630 0.00 0.00 42.70 3.58
3329 3398 6.538742 TGGCAGTATTTATGCTGAACTTACTC 59.461 38.462 11.34 0.00 42.19 2.59
3330 3399 6.017852 GGCAGTATTTATGCTGAACTTACTCC 60.018 42.308 11.34 0.00 42.19 3.85
3331 3400 6.538742 GCAGTATTTATGCTGAACTTACTCCA 59.461 38.462 11.34 0.00 42.19 3.86
3373 3450 8.109705 TGTTTCTATGCATCATTGTTAAGTGT 57.890 30.769 0.19 0.00 0.00 3.55
3401 3478 2.678336 AGTTGGCGTTCATTAGCTTAGC 59.322 45.455 0.00 0.00 0.00 3.09
3477 3554 7.432252 CCAGTTTTATGAATAAAATCGTCCTGC 59.568 37.037 10.54 0.00 42.26 4.85
3519 3596 5.358160 GCTAGCTTGATATTGTTTTCCCAGT 59.642 40.000 7.70 0.00 0.00 4.00
3521 3598 7.229506 GCTAGCTTGATATTGTTTTCCCAGTAT 59.770 37.037 7.70 0.00 0.00 2.12
3547 3624 1.588674 TTTTGGCTCTACACCACGTG 58.411 50.000 9.08 9.08 36.76 4.49
3572 3649 5.808366 AATCCCCTTTTCCAGAGTTTTTC 57.192 39.130 0.00 0.00 0.00 2.29
3632 3709 6.116806 TCACTCTTAAGCAAACCAAGTAACA 58.883 36.000 0.00 0.00 0.00 2.41
3697 3774 9.783256 AGATAATTAAACTTTGTAAATGACGCC 57.217 29.630 0.00 0.00 0.00 5.68
3746 3823 3.053842 AGCACTCATCATCTCCCAAACAT 60.054 43.478 0.00 0.00 0.00 2.71
3771 3848 1.899142 GTAAATGCACCCACCATGGTT 59.101 47.619 16.84 0.00 36.12 3.67
3780 3857 2.712087 ACCCACCATGGTTACACTGTTA 59.288 45.455 16.84 0.00 33.91 2.41
3784 3861 4.059511 CACCATGGTTACACTGTTAACGA 58.940 43.478 16.84 4.53 0.00 3.85
3803 3880 9.148104 GTTAACGAAAGGTTTGTGATATACTCT 57.852 33.333 0.00 0.00 40.09 3.24
3806 3883 8.928270 ACGAAAGGTTTGTGATATACTCTAAG 57.072 34.615 0.00 0.00 0.00 2.18
3807 3884 7.980099 ACGAAAGGTTTGTGATATACTCTAAGG 59.020 37.037 0.00 0.00 0.00 2.69
3808 3885 7.042658 CGAAAGGTTTGTGATATACTCTAAGGC 60.043 40.741 0.00 0.00 0.00 4.35
3809 3886 6.808321 AGGTTTGTGATATACTCTAAGGCA 57.192 37.500 0.00 0.00 0.00 4.75
3810 3887 6.821388 AGGTTTGTGATATACTCTAAGGCAG 58.179 40.000 0.00 0.00 0.00 4.85
3811 3888 5.467063 GGTTTGTGATATACTCTAAGGCAGC 59.533 44.000 0.00 0.00 0.00 5.25
3812 3889 5.869649 TTGTGATATACTCTAAGGCAGCA 57.130 39.130 0.00 0.00 0.00 4.41
3813 3890 5.869649 TGTGATATACTCTAAGGCAGCAA 57.130 39.130 0.00 0.00 0.00 3.91
3853 3930 5.118286 ACAAATTTCTCAAGGCCTTGTTTG 58.882 37.500 34.57 34.57 41.16 2.93
3867 3944 5.262588 CCTTGTTTGGCACTAGAGTTTTT 57.737 39.130 0.00 0.00 30.28 1.94
3882 3967 8.583296 ACTAGAGTTTTTGGAGAGTATTTACGT 58.417 33.333 0.00 0.00 0.00 3.57
3907 3992 2.655073 CCCGGCCCATCCCAAAAAC 61.655 63.158 0.00 0.00 0.00 2.43
3910 3995 1.229496 GGCCCATCCCAAAAACCCT 60.229 57.895 0.00 0.00 0.00 4.34
3913 3998 1.266178 CCCATCCCAAAAACCCTGTC 58.734 55.000 0.00 0.00 0.00 3.51
3923 4008 1.963172 AAACCCTGTCGAACCTCAAC 58.037 50.000 0.00 0.00 0.00 3.18
3999 4084 1.201424 CCTACCCCTCCCTGTGTAAC 58.799 60.000 0.00 0.00 37.35 2.50
4007 4092 3.021695 CCTCCCTGTGTAACTCGATACA 58.978 50.000 0.00 0.00 38.04 2.29
4020 4105 1.143277 TCGATACACTCCTCTCCCCTC 59.857 57.143 0.00 0.00 0.00 4.30
4042 4128 9.843334 CCCTCGTGTATCTTCTATATTTTCTAC 57.157 37.037 0.00 0.00 0.00 2.59
4075 4161 6.536582 TGTCACTCTTTTTCTTCTGTCTCTTG 59.463 38.462 0.00 0.00 0.00 3.02
4079 4165 7.065085 CACTCTTTTTCTTCTGTCTCTTGTGAA 59.935 37.037 0.00 0.00 0.00 3.18
4087 4173 8.370493 TCTTCTGTCTCTTGTGAATTTAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4089 4175 7.715265 TCTGTCTCTTGTGAATTTAAGTGAC 57.285 36.000 17.27 17.27 42.90 3.67
4098 4184 3.501828 TGAATTTAAGTGACGCTGCACAT 59.498 39.130 0.00 0.00 41.19 3.21
4099 4185 4.023279 TGAATTTAAGTGACGCTGCACATT 60.023 37.500 0.00 0.00 41.19 2.71
4100 4186 3.980646 TTTAAGTGACGCTGCACATTT 57.019 38.095 0.00 5.27 41.19 2.32
4134 4220 0.370273 GCTGATGTGACCGTAAAGCG 59.630 55.000 0.00 0.00 40.95 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.617850 CACCTTTGGGCTAATGTTGCA 59.382 47.619 0.00 0.00 35.63 4.08
63 64 2.035626 CACGCCATCCCCACCTTT 59.964 61.111 0.00 0.00 0.00 3.11
82 83 1.089920 ATGCTCATCGCTGTTGTTCC 58.910 50.000 0.00 0.00 40.11 3.62
133 134 0.321564 CATCGTTGTCCCCAGCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
139 140 1.003839 GCTCACATCGTTGTCCCCA 60.004 57.895 0.00 0.00 32.34 4.96
167 168 0.987715 CTTCACATGAGACGTCGCAG 59.012 55.000 25.74 19.10 0.00 5.18
530 531 4.988716 TCGTCGCCTCACCACCCT 62.989 66.667 0.00 0.00 0.00 4.34
582 583 0.469331 CACGGGCCTATCCAGACCTA 60.469 60.000 0.84 0.00 36.21 3.08
644 645 1.339610 CAACGGCCCAAAACAGATTGA 59.660 47.619 0.00 0.00 31.84 2.57
670 671 7.502895 TCACTTTTATCTTAGACCGCTAGATCT 59.497 37.037 0.00 0.00 0.00 2.75
678 679 7.710907 TCCATCAATCACTTTTATCTTAGACCG 59.289 37.037 0.00 0.00 0.00 4.79
709 710 1.915141 ACATCAGGCACCTGGAAAAG 58.085 50.000 16.52 5.29 43.75 2.27
731 732 2.143876 ATTTTTACATGGGAGCGCCT 57.856 45.000 2.29 0.00 0.00 5.52
732 733 2.481276 GGAATTTTTACATGGGAGCGCC 60.481 50.000 2.29 0.00 0.00 6.53
733 734 2.165437 TGGAATTTTTACATGGGAGCGC 59.835 45.455 0.00 0.00 0.00 5.92
734 735 4.654091 ATGGAATTTTTACATGGGAGCG 57.346 40.909 0.00 0.00 0.00 5.03
813 814 5.245526 GGTGTAGTCTCTCCTTTCTGGTTAA 59.754 44.000 0.00 0.00 37.07 2.01
814 815 4.771054 GGTGTAGTCTCTCCTTTCTGGTTA 59.229 45.833 0.00 0.00 37.07 2.85
815 816 3.579151 GGTGTAGTCTCTCCTTTCTGGTT 59.421 47.826 0.00 0.00 37.07 3.67
816 817 3.166679 GGTGTAGTCTCTCCTTTCTGGT 58.833 50.000 0.00 0.00 37.07 4.00
817 818 3.165875 TGGTGTAGTCTCTCCTTTCTGG 58.834 50.000 0.00 0.00 37.10 3.86
818 819 5.413309 AATGGTGTAGTCTCTCCTTTCTG 57.587 43.478 0.00 0.00 0.00 3.02
820 821 4.393371 GCAAATGGTGTAGTCTCTCCTTTC 59.607 45.833 0.00 0.00 0.00 2.62
831 832 4.853924 AAAAGAGGTGCAAATGGTGTAG 57.146 40.909 0.00 0.00 0.00 2.74
857 858 6.691388 CGGCAGCTATAACCTGAAAATAAAAC 59.309 38.462 4.66 0.00 32.03 2.43
862 863 2.618709 GCGGCAGCTATAACCTGAAAAT 59.381 45.455 0.00 0.00 41.01 1.82
1243 1310 2.066999 GGGAGTTCCAGGAGGCGAT 61.067 63.158 0.00 0.00 37.91 4.58
1313 1380 2.705127 GAGGAGGAGAAGAGCATGGATT 59.295 50.000 0.00 0.00 0.00 3.01
1314 1381 2.328319 GAGGAGGAGAAGAGCATGGAT 58.672 52.381 0.00 0.00 0.00 3.41
1321 1388 2.485795 CGGGCGAGGAGGAGAAGAG 61.486 68.421 0.00 0.00 0.00 2.85
1323 1390 4.214327 GCGGGCGAGGAGGAGAAG 62.214 72.222 0.00 0.00 0.00 2.85
1359 1426 3.927163 GAAGACGGCGGCGAAGGAA 62.927 63.158 38.93 0.00 0.00 3.36
1453 1520 1.828331 GACACGAACACGTTGGAGCC 61.828 60.000 0.00 0.00 38.21 4.70
1581 1649 2.440409 CACTTTGTGGAAGCATAGCCT 58.560 47.619 0.00 0.00 39.04 4.58
1630 1698 2.758089 GGCACTCCGCAAGCATCAG 61.758 63.158 0.00 0.00 45.17 2.90
1662 1730 4.025401 GCCGTGGCCACAAACTCG 62.025 66.667 34.16 19.58 34.56 4.18
1731 1800 0.540365 CCTTCACAGCCAACCCATGT 60.540 55.000 0.00 0.00 0.00 3.21
1779 1848 1.419374 ACATTGTGACGAGCGAGTTC 58.581 50.000 0.00 0.00 0.00 3.01
1788 1857 2.162208 AGCCTTTGCATACATTGTGACG 59.838 45.455 0.00 0.00 41.13 4.35
1794 1863 1.826720 CACCCAGCCTTTGCATACATT 59.173 47.619 0.00 0.00 41.13 2.71
1945 2014 1.104577 GTTGGTGAAAACCCCGCAGA 61.105 55.000 0.00 0.00 0.00 4.26
1950 2019 2.067365 ACTCAGTTGGTGAAAACCCC 57.933 50.000 0.00 0.00 33.60 4.95
1995 2064 2.679837 CAATGCTCCCACATCACTACAC 59.320 50.000 0.00 0.00 0.00 2.90
2181 2250 3.069946 ACATGCCCGGCAACCATG 61.070 61.111 18.00 12.73 43.62 3.66
2205 2274 2.203126 GCTTCCTCATGCTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
2229 2298 3.559069 CTTGTCCATCCTGGCATACAAT 58.441 45.455 0.00 0.00 37.47 2.71
2361 2430 3.230976 GACAGAAGACCCCAAACCAAAT 58.769 45.455 0.00 0.00 0.00 2.32
2544 2613 1.407989 GCAGTGCCCTCTAGCTTCATT 60.408 52.381 2.85 0.00 0.00 2.57
2677 2746 1.068748 GCAAGCATAATGATCCAGCCG 60.069 52.381 0.00 0.00 0.00 5.52
2844 2913 1.196766 ACTCCATCAGCTGCTCACCA 61.197 55.000 9.47 0.00 0.00 4.17
2962 3031 2.691409 TCTTTGCTAACTCCCCGATG 57.309 50.000 0.00 0.00 0.00 3.84
2963 3032 2.104963 GGATCTTTGCTAACTCCCCGAT 59.895 50.000 0.00 0.00 0.00 4.18
2965 3034 1.209504 TGGATCTTTGCTAACTCCCCG 59.790 52.381 0.00 0.00 0.00 5.73
3014 3083 4.511082 CCCCAACAACAAACACATGAATTC 59.489 41.667 0.00 0.00 0.00 2.17
3164 3233 7.652909 ACTCGAATTGATCTTCTTCATGAGATC 59.347 37.037 13.24 13.24 38.05 2.75
3289 3358 1.788308 CTGCCACAAAATTTCACAGCG 59.212 47.619 0.00 0.00 0.00 5.18
3329 3398 3.641648 ACAGTGAATTCGTTTTGCATGG 58.358 40.909 0.00 0.00 0.00 3.66
3330 3399 5.459762 AGAAACAGTGAATTCGTTTTGCATG 59.540 36.000 10.15 0.00 33.18 4.06
3331 3400 5.591099 AGAAACAGTGAATTCGTTTTGCAT 58.409 33.333 10.15 0.00 33.18 3.96
3373 3450 5.414454 AGCTAATGAACGCCAACTAAAATGA 59.586 36.000 0.00 0.00 0.00 2.57
3401 3478 6.039829 TGAGTTACACAGTAGGAGCATATCAG 59.960 42.308 0.00 0.00 0.00 2.90
3477 3554 1.884579 AGCACTTCTGCAATTCCACAG 59.115 47.619 0.00 0.00 46.97 3.66
3490 3567 6.969473 GGAAAACAATATCAAGCTAGCACTTC 59.031 38.462 18.83 2.73 0.00 3.01
3519 3596 8.832521 CGTGGTGTAGAGCCAAAAATAATTATA 58.167 33.333 0.00 0.00 37.81 0.98
3521 3598 6.655848 ACGTGGTGTAGAGCCAAAAATAATTA 59.344 34.615 0.00 0.00 37.81 1.40
3547 3624 6.665992 AAAACTCTGGAAAAGGGGATTTAC 57.334 37.500 0.00 0.00 0.00 2.01
3572 3649 6.128363 GGATACTGAACGAAGTACCCAAAAAG 60.128 42.308 0.00 0.00 45.00 2.27
3697 3774 0.956633 ACCAAGTTGATGTGCTGCAG 59.043 50.000 10.11 10.11 0.00 4.41
3762 3839 4.059511 TCGTTAACAGTGTAACCATGGTG 58.940 43.478 20.60 7.24 37.80 4.17
3763 3840 4.339872 TCGTTAACAGTGTAACCATGGT 57.660 40.909 13.00 13.00 37.80 3.55
3764 3841 5.334569 CCTTTCGTTAACAGTGTAACCATGG 60.335 44.000 11.19 11.19 37.80 3.66
3771 3848 5.873712 TCACAAACCTTTCGTTAACAGTGTA 59.126 36.000 6.39 0.00 33.05 2.90
3780 3857 9.367444 CTTAGAGTATATCACAAACCTTTCGTT 57.633 33.333 0.00 0.00 35.70 3.85
3784 3861 7.630082 TGCCTTAGAGTATATCACAAACCTTT 58.370 34.615 0.00 0.00 0.00 3.11
3803 3880 1.350684 TCACCATCACTTGCTGCCTTA 59.649 47.619 0.00 0.00 0.00 2.69
3804 3881 0.111061 TCACCATCACTTGCTGCCTT 59.889 50.000 0.00 0.00 0.00 4.35
3805 3882 0.111061 TTCACCATCACTTGCTGCCT 59.889 50.000 0.00 0.00 0.00 4.75
3806 3883 1.135199 CATTCACCATCACTTGCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
3807 3884 1.734707 GCATTCACCATCACTTGCTGC 60.735 52.381 0.00 0.00 0.00 5.25
3808 3885 1.135199 GGCATTCACCATCACTTGCTG 60.135 52.381 0.00 0.00 0.00 4.41
3809 3886 1.180029 GGCATTCACCATCACTTGCT 58.820 50.000 0.00 0.00 0.00 3.91
3810 3887 0.889994 TGGCATTCACCATCACTTGC 59.110 50.000 0.00 0.00 33.75 4.01
3811 3888 2.296752 TGTTGGCATTCACCATCACTTG 59.703 45.455 0.00 0.00 40.13 3.16
3812 3889 2.596346 TGTTGGCATTCACCATCACTT 58.404 42.857 0.00 0.00 40.13 3.16
3813 3890 2.291209 TGTTGGCATTCACCATCACT 57.709 45.000 0.00 0.00 40.13 3.41
3853 3930 4.009370 ACTCTCCAAAAACTCTAGTGCC 57.991 45.455 0.00 0.00 0.00 5.01
3867 3944 6.294342 CGGGATAATCACGTAAATACTCTCCA 60.294 42.308 0.00 0.00 38.72 3.86
3882 3967 1.497309 GGGATGGGCCGGGATAATCA 61.497 60.000 2.18 0.00 37.63 2.57
3907 3992 1.374252 CCGTTGAGGTTCGACAGGG 60.374 63.158 0.00 0.00 30.06 4.45
3910 3995 1.364901 GGTCCGTTGAGGTTCGACA 59.635 57.895 0.00 0.00 41.99 4.35
3913 3998 2.337532 ACGGTCCGTTGAGGTTCG 59.662 61.111 12.23 0.00 36.35 3.95
3941 4026 1.332686 GGACTGAACCCGTGTGAAAAC 59.667 52.381 0.00 0.00 0.00 2.43
3999 4084 1.144093 AGGGGAGAGGAGTGTATCGAG 59.856 57.143 0.00 0.00 0.00 4.04
4007 4092 0.927767 ATACACGAGGGGAGAGGAGT 59.072 55.000 0.00 0.00 0.00 3.85
4012 4097 4.726035 ATAGAAGATACACGAGGGGAGA 57.274 45.455 0.00 0.00 0.00 3.71
4020 4105 7.806487 TGGCGTAGAAAATATAGAAGATACACG 59.194 37.037 0.00 0.00 0.00 4.49
4042 4128 5.551760 AGAAAAAGAGTGACAATATGGCG 57.448 39.130 0.00 0.00 0.00 5.69
4052 4138 6.536582 CACAAGAGACAGAAGAAAAAGAGTGA 59.463 38.462 0.00 0.00 0.00 3.41
4075 4161 3.226347 GTGCAGCGTCACTTAAATTCAC 58.774 45.455 0.00 0.00 34.29 3.18
4079 4165 4.503741 AAATGTGCAGCGTCACTTAAAT 57.496 36.364 11.59 0.00 37.81 1.40
4134 4220 5.790593 TGTCCATCTTTAGTTACAGGTGTC 58.209 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.