Multiple sequence alignment - TraesCS3A01G513500

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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 TraesCS3A01G513500 chr3A 100.000 5367 0 0 1 5367 732664245 732669611 0.000000e+00 9912.0
1 TraesCS3A01G513500 chr3A 97.222 36 1 0 2738 2773 732666845 732666880 1.610000e-05 62.1
2 TraesCS3A01G513500 chr3A 97.222 36 1 0 2601 2636 732666982 732667017 1.610000e-05 62.1
3 TraesCS3A01G513500 chr3B 91.599 3845 190 47 854 4627 810325563 810329345 0.000000e+00 5188.0
4 TraesCS3A01G513500 chr3B 89.085 284 21 6 4627 4903 740507760 740507480 1.430000e-90 344.0
5 TraesCS3A01G513500 chr3B 80.652 460 64 17 4918 5355 168970916 168971372 3.100000e-87 333.0
6 TraesCS3A01G513500 chr3B 86.861 274 27 5 4628 4894 168970544 168970815 1.130000e-76 298.0
7 TraesCS3A01G513500 chr3B 92.727 110 7 1 776 885 810325457 810325565 2.000000e-34 158.0
8 TraesCS3A01G513500 chr3D 94.793 1978 70 14 1644 3592 603418646 603416673 0.000000e+00 3051.0
9 TraesCS3A01G513500 chr3D 90.593 1669 92 28 1 1646 603420558 603418932 0.000000e+00 2152.0
10 TraesCS3A01G513500 chr3D 96.875 1024 30 2 3606 4627 603415241 603414218 0.000000e+00 1712.0
11 TraesCS3A01G513500 chr3D 78.846 156 24 8 2497 2644 603417638 603417484 4.420000e-16 97.1
12 TraesCS3A01G513500 chr3D 75.839 149 23 9 2636 2773 603417791 603417645 4.490000e-06 63.9
13 TraesCS3A01G513500 chr1A 93.342 751 40 5 4627 5367 588202736 588201986 0.000000e+00 1101.0
14 TraesCS3A01G513500 chr1A 93.342 751 40 5 4627 5367 588219060 588218310 0.000000e+00 1101.0
15 TraesCS3A01G513500 chr1A 93.209 751 41 5 4627 5367 588166605 588165855 0.000000e+00 1096.0
16 TraesCS3A01G513500 chr6A 93.209 751 36 8 4628 5367 61682230 61682976 0.000000e+00 1090.0
17 TraesCS3A01G513500 chr2B 88.028 284 24 5 4627 4903 535017021 535017301 1.440000e-85 327.0
18 TraesCS3A01G513500 chr1D 84.507 284 31 7 4626 4900 1356840 1356561 8.860000e-68 268.0
19 TraesCS3A01G513500 chr7A 85.496 262 24 9 4652 4903 441805502 441805759 1.480000e-65 261.0


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 TraesCS3A01G513500 chr3A 732664245 732669611 5366 False 3345.4 9912 98.1480 1 5367 3 chr3A.!!$F1 5366
1 TraesCS3A01G513500 chr3B 810325457 810329345 3888 False 2673.0 5188 92.1630 776 4627 2 chr3B.!!$F2 3851
2 TraesCS3A01G513500 chr3B 168970544 168971372 828 False 315.5 333 83.7565 4628 5355 2 chr3B.!!$F1 727
3 TraesCS3A01G513500 chr3D 603414218 603420558 6340 True 1415.2 3051 87.3892 1 4627 5 chr3D.!!$R1 4626
4 TraesCS3A01G513500 chr1A 588201986 588202736 750 True 1101.0 1101 93.3420 4627 5367 1 chr1A.!!$R2 740
5 TraesCS3A01G513500 chr1A 588218310 588219060 750 True 1101.0 1101 93.3420 4627 5367 1 chr1A.!!$R3 740
6 TraesCS3A01G513500 chr1A 588165855 588166605 750 True 1096.0 1096 93.2090 4627 5367 1 chr1A.!!$R1 740
7 TraesCS3A01G513500 chr6A 61682230 61682976 746 False 1090.0 1090 93.2090 4628 5367 1 chr6A.!!$F1 739

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
990 1031 1.231751 TCCCATCCTCCTCACTCCCT 61.232 60.0 0.00 0.00 0.00 4.20 F
1814 2177 0.249447 CGCTTGCCGGAGATCATACA 60.249 55.0 5.05 0.00 0.00 2.29 F
2696 3071 0.539518 CATGGTCACCGTACCCATCA 59.460 55.0 0.00 0.00 36.85 3.07 F
3763 5572 0.897863 TGCTAACCCATGGGCAACAC 60.898 55.0 31.73 16.78 39.32 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2620 0.182537 CCCCACGGAAGATATTGCCA 59.817 55.0 0.00 0.00 0.00 4.92 R
2934 3323 0.383949 GCAGGAAAAAGGTTGCACGA 59.616 50.0 0.00 0.00 36.59 4.35 R
4237 6049 0.587242 CGATGGCTTTCGCGATGTTG 60.587 55.0 10.88 1.41 34.53 3.33 R
4864 6693 0.459489 GTGCTTGCACACCAAAGGAA 59.541 50.0 19.36 0.00 34.35 3.36 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
34 35 6.465439 TGATATCTGACCGTTGACTATTGT 57.535 37.500 3.98 0.00 0.00 2.71
45 46 5.924254 CCGTTGACTATTGTCTGTTGACTTA 59.076 40.000 8.74 0.00 43.29 2.24
192 193 7.815840 TGTTCATGAGTTGGAAAGTATTCAA 57.184 32.000 0.00 0.00 37.29 2.69
292 293 8.640651 TCTTGGATTTGAGAATTGTTCATGAAA 58.359 29.630 10.35 0.00 0.00 2.69
295 296 9.781633 TGGATTTGAGAATTGTTCATGAAATTT 57.218 25.926 10.35 4.16 0.00 1.82
318 319 9.980780 ATTTTAAAAACGTTCATGGTTTGAAAG 57.019 25.926 0.00 0.72 45.71 2.62
513 514 6.997239 AAAAACCGATGGAACCTATTAGAC 57.003 37.500 0.00 0.00 0.00 2.59
515 516 2.626743 ACCGATGGAACCTATTAGACGG 59.373 50.000 0.00 0.00 42.78 4.79
516 517 2.609737 CCGATGGAACCTATTAGACGGC 60.610 54.545 0.00 0.00 0.00 5.68
517 518 2.296471 CGATGGAACCTATTAGACGGCT 59.704 50.000 0.00 0.00 0.00 5.52
519 520 2.037144 TGGAACCTATTAGACGGCTCC 58.963 52.381 0.00 0.00 36.34 4.70
520 521 1.343789 GGAACCTATTAGACGGCTCCC 59.656 57.143 0.00 0.00 30.85 4.30
538 539 4.262292 GCTCCCAAAACCGGTTAGAAAAAT 60.262 41.667 22.60 0.00 0.00 1.82
540 541 4.281435 TCCCAAAACCGGTTAGAAAAATCC 59.719 41.667 22.60 0.00 0.00 3.01
545 546 7.371936 CAAAACCGGTTAGAAAAATCCACATA 58.628 34.615 22.60 0.00 0.00 2.29
546 547 7.527568 AAACCGGTTAGAAAAATCCACATAA 57.472 32.000 22.60 0.00 0.00 1.90
549 550 5.449999 CCGGTTAGAAAAATCCACATAAGCC 60.450 44.000 0.00 0.00 0.00 4.35
560 561 4.101114 TCCACATAAGCCGGTCCATATAT 58.899 43.478 1.90 0.00 0.00 0.86
596 597 4.161565 TGGGAGATGTGAGTGTGTTATACC 59.838 45.833 0.00 0.00 0.00 2.73
602 603 5.731957 TGTGAGTGTGTTATACCTTAGCA 57.268 39.130 0.00 0.00 0.00 3.49
613 614 4.765813 ATACCTTAGCATGTTAACCGGT 57.234 40.909 14.77 14.77 0.00 5.28
617 618 1.444836 TAGCATGTTAACCGGTGTGC 58.555 50.000 8.52 14.08 0.00 4.57
647 648 6.136541 CCAGATAGGAACTGGCATAAAAAC 57.863 41.667 0.00 0.00 46.30 2.43
659 660 5.636123 TGGCATAAAAACCAGTAGAGGAAA 58.364 37.500 0.00 0.00 0.00 3.13
667 668 2.436173 ACCAGTAGAGGAAATAGCTGCC 59.564 50.000 0.00 0.00 0.00 4.85
695 696 4.083431 CCGTCGAGGAAGAATCACGTATAT 60.083 45.833 6.70 0.00 45.00 0.86
721 722 6.839124 ATTTCAAGCATAACTTCCATGACA 57.161 33.333 0.00 0.00 36.04 3.58
726 727 7.669427 TCAAGCATAACTTCCATGACAAAAAT 58.331 30.769 0.00 0.00 36.04 1.82
841 844 4.069232 CGCTCTCTTGGCCCGTCA 62.069 66.667 0.00 0.00 0.00 4.35
990 1031 1.231751 TCCCATCCTCCTCACTCCCT 61.232 60.000 0.00 0.00 0.00 4.20
1257 1305 1.586564 CGCGCGGTTTGTTTTTCCA 60.587 52.632 24.84 0.00 0.00 3.53
1266 1314 5.564768 CGGTTTGTTTTTCCATTGTTTTCC 58.435 37.500 0.00 0.00 0.00 3.13
1406 1459 0.963856 TAGCGGACGGTGTCACTGAT 60.964 55.000 18.86 2.84 33.68 2.90
1419 1473 5.928839 GGTGTCACTGATAGGCTACATATTG 59.071 44.000 2.35 0.00 0.00 1.90
1420 1474 6.463049 GGTGTCACTGATAGGCTACATATTGT 60.463 42.308 2.35 0.00 0.00 2.71
1536 1596 4.516698 GGCCTCCTACACACATATCAATTG 59.483 45.833 0.00 0.00 0.00 2.32
1624 1698 2.789092 GCTTGCCTGTCGATTTCATTCG 60.789 50.000 0.00 0.00 40.46 3.34
1646 1720 5.066634 TCGGTTGAAGCACTTTCATGTTTAA 59.933 36.000 0.00 0.00 44.90 1.52
1647 1721 5.173131 CGGTTGAAGCACTTTCATGTTTAAC 59.827 40.000 0.00 0.00 44.90 2.01
1648 1722 6.039616 GGTTGAAGCACTTTCATGTTTAACA 58.960 36.000 0.00 0.00 44.90 2.41
1650 1724 6.449635 TGAAGCACTTTCATGTTTAACACT 57.550 33.333 0.00 0.00 40.82 3.55
1652 1726 7.319646 TGAAGCACTTTCATGTTTAACACTTT 58.680 30.769 0.00 0.00 40.82 2.66
1681 2044 1.428912 ACCCTGCCCTCTTTCATTTGA 59.571 47.619 0.00 0.00 0.00 2.69
1754 2117 0.328258 GCTCCAGGTCTAAAAGGCCA 59.672 55.000 5.01 0.00 44.17 5.36
1814 2177 0.249447 CGCTTGCCGGAGATCATACA 60.249 55.000 5.05 0.00 0.00 2.29
1852 2215 1.269778 GGTGAGGCTTCTTTTTGGTGC 60.270 52.381 0.00 0.00 0.00 5.01
1858 2221 3.256631 AGGCTTCTTTTTGGTGCTGTATG 59.743 43.478 0.00 0.00 0.00 2.39
1862 2225 5.175673 GCTTCTTTTTGGTGCTGTATGTTTC 59.824 40.000 0.00 0.00 0.00 2.78
1874 2237 6.639279 GTGCTGTATGTTTCAATTTAAACGGT 59.361 34.615 9.95 4.99 41.33 4.83
2045 2417 8.007716 ACGTTTATGAACAATGAAACTACTTCG 58.992 33.333 0.95 0.00 34.65 3.79
2120 2492 8.398665 GGTCTGATGGTATTAATTCAACACTTC 58.601 37.037 0.00 0.00 0.00 3.01
2192 2564 9.567848 GTTTCTCTTGTCTTCTCTAGTAGAATG 57.432 37.037 0.64 0.00 43.32 2.67
2193 2565 8.871629 TTCTCTTGTCTTCTCTAGTAGAATGT 57.128 34.615 0.64 0.00 43.32 2.71
2194 2566 8.275015 TCTCTTGTCTTCTCTAGTAGAATGTG 57.725 38.462 0.64 0.00 43.32 3.21
2195 2567 6.857956 TCTTGTCTTCTCTAGTAGAATGTGC 58.142 40.000 0.64 0.00 43.32 4.57
2198 2570 5.712446 TGTCTTCTCTAGTAGAATGTGCTGT 59.288 40.000 0.64 0.00 43.32 4.40
2199 2571 6.884836 TGTCTTCTCTAGTAGAATGTGCTGTA 59.115 38.462 0.64 0.00 43.32 2.74
2200 2572 7.558081 TGTCTTCTCTAGTAGAATGTGCTGTAT 59.442 37.037 0.64 0.00 43.32 2.29
2201 2573 9.058174 GTCTTCTCTAGTAGAATGTGCTGTATA 57.942 37.037 0.64 0.00 43.32 1.47
2202 2574 9.058174 TCTTCTCTAGTAGAATGTGCTGTATAC 57.942 37.037 0.64 0.00 43.32 1.47
2203 2575 8.747538 TTCTCTAGTAGAATGTGCTGTATACA 57.252 34.615 5.25 5.25 39.36 2.29
2204 2576 8.926092 TCTCTAGTAGAATGTGCTGTATACAT 57.074 34.615 5.91 0.00 40.30 2.29
2246 2620 2.364002 GGTTGCTATTGTTGTTGGTGGT 59.636 45.455 0.00 0.00 0.00 4.16
2306 2680 1.908299 TCTTGACCGCTCCTCTGCA 60.908 57.895 0.00 0.00 0.00 4.41
2337 2711 4.838423 TCGGGTATGAATCATACTCCATGT 59.162 41.667 26.61 0.00 42.87 3.21
2477 2851 2.040278 ACATTTTGGTAGGAGCAGAGCA 59.960 45.455 0.00 0.00 0.00 4.26
2526 2900 7.505258 ACTATTTGGCCAGTTTAATGTTTGTT 58.495 30.769 5.11 0.00 0.00 2.83
2552 2926 6.999705 ATTATGGTTCATTGTGCCCATTAT 57.000 33.333 8.88 4.67 38.58 1.28
2554 2928 2.765135 TGGTTCATTGTGCCCATTATGG 59.235 45.455 3.85 3.85 37.25 2.74
2696 3071 0.539518 CATGGTCACCGTACCCATCA 59.460 55.000 0.00 0.00 36.85 3.07
2714 3102 2.453521 TCACGTAAGCACATCCTAGGT 58.546 47.619 9.08 0.00 45.62 3.08
3203 3592 2.097466 CCGTTGTGCAGAAAGTGAGTTT 59.903 45.455 8.60 0.00 0.00 2.66
3272 3661 8.652810 AAAGTTGGAGAAATTTCTTTCACATG 57.347 30.769 21.33 0.00 42.71 3.21
3319 3708 5.651387 TCTTGATAGTCCAGTGTCTTCTG 57.349 43.478 0.00 0.00 35.45 3.02
3429 3819 4.044308 TGTGGGTAATGGGACTACATGAT 58.956 43.478 0.00 0.00 0.00 2.45
3541 3931 8.558973 AAAATGAAAAATGACAGTCCAACAAA 57.441 26.923 0.00 0.00 0.00 2.83
3581 3971 7.651027 ATGCATCTATTTAAGCTGGTTTCTT 57.349 32.000 0.00 0.00 0.00 2.52
3592 3982 4.068599 AGCTGGTTTCTTGTTCTAGCTTC 58.931 43.478 0.00 0.00 41.79 3.86
3593 3983 3.815401 GCTGGTTTCTTGTTCTAGCTTCA 59.185 43.478 0.00 0.00 33.91 3.02
3741 5550 5.415077 ACCACACAGTACAGATCTACAGTAC 59.585 44.000 11.93 11.93 40.30 2.73
3749 5558 7.317842 GTACAGATCTACAGTACTGTGCTAA 57.682 40.000 33.77 16.18 44.63 3.09
3763 5572 0.897863 TGCTAACCCATGGGCAACAC 60.898 55.000 31.73 16.78 39.32 3.32
3936 5748 5.226396 TGTTTATTTTGCCTTGACCATTCG 58.774 37.500 0.00 0.00 0.00 3.34
4041 5853 0.904394 ACCCAAATGCCCGCATTCTT 60.904 50.000 14.91 0.00 44.86 2.52
4083 5895 4.274950 GAGGTTATCTCAAGAGACCTCTCG 59.725 50.000 24.37 0.00 46.65 4.04
4139 5951 2.370849 AGAACAACATTCCTGGTACGGT 59.629 45.455 0.00 0.00 0.00 4.83
4159 5971 1.416401 TGGATATCGGTTTCTGAGGCC 59.584 52.381 0.00 0.00 0.00 5.19
4237 6049 1.398692 TCAACCTCCAAAACACTGGC 58.601 50.000 0.00 0.00 36.32 4.85
4330 6142 0.182775 AAAGCACGGAGGGTTCACTT 59.817 50.000 0.00 0.00 0.00 3.16
4346 6158 5.049129 GGTTCACTTGATCAAGAAGACAAGG 60.049 44.000 36.15 16.59 40.79 3.61
4387 6199 2.300956 TCCAAGAGCTGTCTGTCTCT 57.699 50.000 0.00 0.00 41.10 3.10
4464 6276 3.983741 ACTCGAAGAAGAGAAACCACTG 58.016 45.455 0.62 0.00 40.57 3.66
4583 6404 7.618019 AATACTTCTATTGCTCCTGATGGTA 57.382 36.000 0.00 0.00 34.23 3.25
4615 6436 2.303311 ACAGAAGGTGAGGGTTTCTAGC 59.697 50.000 0.00 0.00 30.43 3.42
4705 6526 2.289320 GCTTCGTGATCAGGCCATAGAT 60.289 50.000 5.01 5.12 0.00 1.98
4801 6626 3.318017 CACTTCTACAAGTACGCAAGCT 58.682 45.455 0.00 0.00 41.24 3.74
4850 6678 0.657312 CATATGCGTCACGTGCCAAT 59.343 50.000 11.67 4.47 0.00 3.16
4864 6693 2.108514 CCAATCAGTGCGGCGATGT 61.109 57.895 12.98 0.00 0.00 3.06
4865 6694 1.647545 CCAATCAGTGCGGCGATGTT 61.648 55.000 12.98 0.00 0.00 2.71
4929 6841 5.363939 AGCTCTACATATGCACTTTCCTTC 58.636 41.667 1.58 0.00 0.00 3.46
5041 6962 9.322776 CTGCATAGAAAATACGAAATAATCAGC 57.677 33.333 0.00 0.00 0.00 4.26
5076 6998 9.722056 GAAAATATAGTGTTTTCATGAGCGAAT 57.278 29.630 0.00 0.00 42.35 3.34
5238 7160 4.422073 TCCATGCATCGGAAAGTATCTT 57.578 40.909 13.44 0.00 0.00 2.40
5270 7192 1.134401 AGATTTGATGCCGTCGGTGAT 60.134 47.619 13.94 5.35 0.00 3.06
5276 7206 4.760047 GCCGTCGGTGATGCCACT 62.760 66.667 13.94 0.00 42.77 4.00
5298 7229 8.818057 CCACTTAAATTATCGTCCTCTAACAAG 58.182 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.211573 TCGTGGAGTTTTAATAAGTCAACAGA 58.788 34.615 10.64 7.56 0.00 3.41
136 137 9.364989 TCAACTTTTTGTGAATTCTTTTCGAAT 57.635 25.926 7.05 0.00 37.69 3.34
137 138 8.749841 TCAACTTTTTGTGAATTCTTTTCGAA 57.250 26.923 7.05 0.00 34.02 3.71
138 139 8.749841 TTCAACTTTTTGTGAATTCTTTTCGA 57.250 26.923 7.05 0.00 34.02 3.71
139 140 9.804547 TTTTCAACTTTTTGTGAATTCTTTTCG 57.195 25.926 7.05 0.00 34.02 3.46
167 168 8.299570 GTTGAATACTTTCCAACTCATGAACAT 58.700 33.333 0.00 0.00 0.00 2.71
172 173 9.480053 AAAATGTTGAATACTTTCCAACTCATG 57.520 29.630 0.00 0.00 30.67 3.07
340 341 9.502145 GTGAACATCTATGAAAATTGCGAAATA 57.498 29.630 0.00 0.00 0.00 1.40
468 469 7.847711 TTTTCTTGGGATGGATTTTACTTGA 57.152 32.000 0.00 0.00 0.00 3.02
513 514 1.302671 TAACCGGTTTTGGGAGCCG 60.303 57.895 27.64 0.00 44.55 5.52
515 516 1.900245 TTCTAACCGGTTTTGGGAGC 58.100 50.000 27.64 0.00 0.00 4.70
516 517 4.922471 TTTTTCTAACCGGTTTTGGGAG 57.078 40.909 27.64 16.46 0.00 4.30
517 518 4.281435 GGATTTTTCTAACCGGTTTTGGGA 59.719 41.667 27.64 15.42 0.00 4.37
519 520 4.986034 GTGGATTTTTCTAACCGGTTTTGG 59.014 41.667 27.64 15.86 0.00 3.28
520 521 5.593010 TGTGGATTTTTCTAACCGGTTTTG 58.407 37.500 27.64 18.51 0.00 2.44
538 539 1.796017 TATGGACCGGCTTATGTGGA 58.204 50.000 0.00 0.00 0.00 4.02
540 541 7.103641 AGTTTATATATGGACCGGCTTATGTG 58.896 38.462 0.00 0.00 0.00 3.21
545 546 6.461640 GTGTAGTTTATATATGGACCGGCTT 58.538 40.000 0.00 0.00 0.00 4.35
546 547 5.336213 CGTGTAGTTTATATATGGACCGGCT 60.336 44.000 0.00 0.00 0.00 5.52
549 550 7.274904 CCATTCGTGTAGTTTATATATGGACCG 59.725 40.741 0.00 0.00 33.51 4.79
560 561 5.186215 TCACATCTCCCATTCGTGTAGTTTA 59.814 40.000 0.00 0.00 0.00 2.01
596 597 2.159572 GCACACCGGTTAACATGCTAAG 60.160 50.000 2.97 0.00 0.00 2.18
602 603 1.243902 CTTGGCACACCGGTTAACAT 58.756 50.000 2.97 0.00 39.29 2.71
613 614 1.450134 CTATCTGGCGCTTGGCACA 60.450 57.895 7.64 0.00 44.19 4.57
617 618 0.179000 AGTTCCTATCTGGCGCTTGG 59.821 55.000 7.64 0.00 35.26 3.61
627 628 6.136541 CTGGTTTTTATGCCAGTTCCTATC 57.863 41.667 2.66 0.00 45.28 2.08
640 641 7.283354 GCAGCTATTTCCTCTACTGGTTTTTAT 59.717 37.037 0.00 0.00 0.00 1.40
647 648 2.546795 CGGCAGCTATTTCCTCTACTGG 60.547 54.545 0.00 0.00 0.00 4.00
653 654 1.440145 GGCACGGCAGCTATTTCCTC 61.440 60.000 0.00 0.00 34.17 3.71
695 696 8.801299 TGTCATGGAAGTTATGCTTGAAATTTA 58.199 29.630 0.00 0.00 35.74 1.40
713 714 9.995003 ACAGCTAAAAATAATTTTTGTCATGGA 57.005 25.926 7.28 0.00 42.41 3.41
1242 1290 4.608073 AAACAATGGAAAAACAAACCGC 57.392 36.364 0.00 0.00 0.00 5.68
1257 1305 1.671166 GCCTTGCCGGGAAAACAAT 59.329 52.632 10.50 0.00 0.00 2.71
1356 1409 2.438614 CGGCCTCGACTCTCCAGA 60.439 66.667 0.00 0.00 39.00 3.86
1397 1450 6.731292 ACAATATGTAGCCTATCAGTGACA 57.269 37.500 0.00 0.00 0.00 3.58
1419 1473 8.489990 TGACCGCTACTGATATTATCTAGTAC 57.510 38.462 5.33 0.00 0.00 2.73
1420 1474 7.769507 CCTGACCGCTACTGATATTATCTAGTA 59.230 40.741 5.33 9.38 0.00 1.82
1428 1482 1.344763 GGCCTGACCGCTACTGATATT 59.655 52.381 0.00 0.00 0.00 1.28
1536 1596 4.734854 CCATATTGACAACAAATACAGCGC 59.265 41.667 0.00 0.00 39.54 5.92
1646 1720 2.165167 CAGGGTGCATCATGAAAGTGT 58.835 47.619 5.49 0.00 0.00 3.55
1647 1721 1.135199 GCAGGGTGCATCATGAAAGTG 60.135 52.381 17.26 0.00 44.26 3.16
1648 1722 1.180029 GCAGGGTGCATCATGAAAGT 58.820 50.000 17.26 0.00 44.26 2.66
1681 2044 1.973515 TCAGTGATGCCTGACTTCTGT 59.026 47.619 0.00 0.00 36.57 3.41
1814 2177 4.285863 TCACCTTTGGGTCAATGTTTTCT 58.714 39.130 0.00 0.00 45.41 2.52
1841 2204 5.843673 TGAAACATACAGCACCAAAAAGA 57.156 34.783 0.00 0.00 0.00 2.52
1852 2215 8.789881 TGAACCGTTTAAATTGAAACATACAG 57.210 30.769 16.94 2.15 38.92 2.74
1858 2221 7.009723 ACACACATGAACCGTTTAAATTGAAAC 59.990 33.333 8.22 8.22 36.21 2.78
1862 2225 5.746245 ACACACACATGAACCGTTTAAATTG 59.254 36.000 0.00 0.00 0.00 2.32
1874 2237 7.920160 ATTACATGATGTACACACACATGAA 57.080 32.000 26.04 19.35 41.57 2.57
2041 2413 8.596380 GTTTCAGTCTATCTATTTGGAACGAAG 58.404 37.037 0.00 0.00 0.00 3.79
2045 2417 8.561738 TTGGTTTCAGTCTATCTATTTGGAAC 57.438 34.615 0.00 0.00 0.00 3.62
2120 2492 2.096819 GGCTTGGAATGCATTGCAATTG 59.903 45.455 36.41 28.43 44.99 2.32
2188 2560 9.722056 CTCCTTTTAAATGTATACAGCACATTC 57.278 33.333 11.91 0.00 43.94 2.67
2192 2564 8.494016 ACTCTCCTTTTAAATGTATACAGCAC 57.506 34.615 11.91 0.00 0.00 4.40
2200 2572 8.956426 CCTGCAATTACTCTCCTTTTAAATGTA 58.044 33.333 0.00 0.00 0.00 2.29
2201 2573 7.451566 ACCTGCAATTACTCTCCTTTTAAATGT 59.548 33.333 0.00 0.00 0.00 2.71
2202 2574 7.830739 ACCTGCAATTACTCTCCTTTTAAATG 58.169 34.615 0.00 0.00 0.00 2.32
2203 2575 8.306761 CAACCTGCAATTACTCTCCTTTTAAAT 58.693 33.333 0.00 0.00 0.00 1.40
2204 2576 7.657336 CAACCTGCAATTACTCTCCTTTTAAA 58.343 34.615 0.00 0.00 0.00 1.52
2246 2620 0.182537 CCCCACGGAAGATATTGCCA 59.817 55.000 0.00 0.00 0.00 4.92
2306 2680 8.367660 AGTATGATTCATACCCGATGTAATCT 57.632 34.615 26.00 6.97 45.37 2.40
2477 2851 5.960113 TGGCACGAATTAAATAACAAGCAT 58.040 33.333 0.00 0.00 0.00 3.79
2526 2900 5.122707 TGGGCACAATGAACCATAATAGA 57.877 39.130 0.00 0.00 0.00 1.98
2674 3048 0.539518 TGGGTACGGTGACCATGATG 59.460 55.000 1.11 0.00 41.73 3.07
2696 3071 5.452917 GGAAATACCTAGGATGTGCTTACGT 60.453 44.000 17.98 0.00 35.41 3.57
2877 3266 8.020819 CGACAAATCATGTGGTTACTTAACAAT 58.979 33.333 1.72 0.00 44.12 2.71
2930 3319 2.955660 AGGAAAAAGGTTGCACGATCAA 59.044 40.909 0.00 0.00 0.00 2.57
2934 3323 0.383949 GCAGGAAAAAGGTTGCACGA 59.616 50.000 0.00 0.00 36.59 4.35
3203 3592 4.141937 ACTGCATAGCGAAGATTAAGGACA 60.142 41.667 0.00 0.00 0.00 4.02
3270 3659 6.400568 CATTCATAAGCACCAGTTTTTCCAT 58.599 36.000 0.00 0.00 0.00 3.41
3272 3661 5.170748 CCATTCATAAGCACCAGTTTTTCC 58.829 41.667 0.00 0.00 0.00 3.13
3319 3708 3.553828 TGTAGCTAAACCTATGGCACC 57.446 47.619 0.00 0.00 0.00 5.01
3320 3709 8.041323 ACATATATGTAGCTAAACCTATGGCAC 58.959 37.037 16.85 0.00 39.68 5.01
3376 3765 7.211966 AGGAGCATGACAATTAATAAGATGC 57.788 36.000 0.00 11.13 35.93 3.91
3429 3819 2.910319 AGTGGAGTGCTTATGTGGGTAA 59.090 45.455 0.00 0.00 0.00 2.85
3581 3971 6.016276 GTCCCAGAAAAATTGAAGCTAGAACA 60.016 38.462 0.00 0.00 0.00 3.18
3592 3982 6.183360 ACACTGTAACTGTCCCAGAAAAATTG 60.183 38.462 12.05 3.62 35.18 2.32
3593 3983 5.891551 ACACTGTAACTGTCCCAGAAAAATT 59.108 36.000 12.05 0.00 35.18 1.82
3741 5550 0.611618 TTGCCCATGGGTTAGCACAG 60.612 55.000 31.58 3.44 34.37 3.66
3749 5558 1.114722 CAACAGTGTTGCCCATGGGT 61.115 55.000 31.58 8.20 37.65 4.51
3763 5572 5.105310 ACACACTATAACTAGAGGCCAACAG 60.105 44.000 5.01 0.00 0.00 3.16
3865 5674 8.629158 ACAGTACTGTTCATTTCAAAAATAGCA 58.371 29.630 22.95 0.00 41.83 3.49
3908 5717 6.045955 TGGTCAAGGCAAAATAAACAAAGAC 58.954 36.000 0.00 0.00 0.00 3.01
4041 5853 3.628032 CCTCGTTATAGCTCACTGTCTCA 59.372 47.826 0.00 0.00 0.00 3.27
4083 5895 1.299541 CGGCAGTCATGTCCATTACC 58.700 55.000 0.00 0.00 0.00 2.85
4139 5951 1.416401 GGCCTCAGAAACCGATATCCA 59.584 52.381 0.00 0.00 0.00 3.41
4159 5971 3.099362 CGACGATCGGAAACAGTAAGAG 58.901 50.000 20.98 0.00 36.00 2.85
4237 6049 0.587242 CGATGGCTTTCGCGATGTTG 60.587 55.000 10.88 1.41 34.53 3.33
4346 6158 1.412710 TCACCACTCACTGACCAAGAC 59.587 52.381 0.00 0.00 0.00 3.01
4464 6276 6.640907 AGTTTTCTGCGAATTTTTATGTCCAC 59.359 34.615 0.00 0.00 0.00 4.02
4583 6404 2.158623 TCACCTTCTGTTGCTCACCAAT 60.159 45.455 0.00 0.00 35.55 3.16
4750 6571 1.977188 CACACTGTCGCTGAATACGA 58.023 50.000 0.00 0.00 37.17 3.43
4801 6626 1.067295 ACAGCAAGGACTTGGGATGA 58.933 50.000 13.41 0.00 40.74 2.92
4850 6678 2.434185 GGAACATCGCCGCACTGA 60.434 61.111 0.00 0.00 0.00 3.41
4864 6693 0.459489 GTGCTTGCACACCAAAGGAA 59.541 50.000 19.36 0.00 34.35 3.36
4865 6694 0.682532 TGTGCTTGCACACCAAAGGA 60.683 50.000 22.47 0.00 39.93 3.36
4940 6853 8.668934 CGAACAAATTTTAAAAGAAAATTGCGG 58.331 29.630 6.79 5.24 39.13 5.69
4951 6868 7.705752 GTCCAACTACCCGAACAAATTTTAAAA 59.294 33.333 2.51 2.51 0.00 1.52
5041 6962 8.015087 TGAAAACACTATATTTTCTGTGCTTCG 58.985 33.333 10.56 0.00 43.47 3.79
5049 6970 8.492673 TCGCTCATGAAAACACTATATTTTCT 57.507 30.769 10.56 0.00 43.47 2.52
5270 7192 5.353394 AGAGGACGATAATTTAAGTGGCA 57.647 39.130 0.00 0.00 0.00 4.92
5276 7206 7.494625 CCTGCTTGTTAGAGGACGATAATTTAA 59.505 37.037 0.00 0.00 0.00 1.52
5321 7252 4.081142 TGGCGAGTCCTATCTGAATTTCAA 60.081 41.667 0.01 0.00 35.26 2.69
5328 7259 2.073252 ATGTGGCGAGTCCTATCTGA 57.927 50.000 0.00 0.00 35.26 3.27
5332 7263 6.246919 AGTATAGTTATGTGGCGAGTCCTAT 58.753 40.000 0.00 0.00 35.26 2.57


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

AutoCloner maintained by Alex Coulton.