Multiple sequence alignment - TraesCS5B01G198600

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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 TraesCS5B01G198600 chr5B 100.000 4236 0 0 1 4236 358383249 358379014 0.000000e+00 7823
1 TraesCS5B01G198600 chr5B 76.232 568 118 17 1601 2161 358637871 358637314 6.930000e-73 285
2 TraesCS5B01G198600 chr5D 94.094 3962 171 20 308 4236 312063770 312059839 0.000000e+00 5962
3 TraesCS5B01G198600 chr5D 95.975 323 8 5 1 321 312064104 312063785 1.750000e-143 520
4 TraesCS5B01G198600 chr5D 74.395 703 151 28 1514 2202 312370049 312369362 1.500000e-69 274
5 TraesCS5B01G198600 chr5A 94.208 3436 153 21 809 4235 405019469 405016071 0.000000e+00 5201
6 TraesCS5B01G198600 chr5A 93.625 502 31 1 131 631 405020343 405019842 0.000000e+00 749
7 TraesCS5B01G198600 chr5A 73.965 749 169 26 1466 2202 406483510 406482776 3.230000e-71 279
8 TraesCS5B01G198600 chr5A 90.789 76 7 0 732 807 405019630 405019555 7.490000e-18 102


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 TraesCS5B01G198600 chr5B 358379014 358383249 4235 True 7823.000000 7823 100.0000 1 4236 1 chr5B.!!$R1 4235
1 TraesCS5B01G198600 chr5B 358637314 358637871 557 True 285.000000 285 76.2320 1601 2161 1 chr5B.!!$R2 560
2 TraesCS5B01G198600 chr5D 312059839 312064104 4265 True 3241.000000 5962 95.0345 1 4236 2 chr5D.!!$R2 4235
3 TraesCS5B01G198600 chr5D 312369362 312370049 687 True 274.000000 274 74.3950 1514 2202 1 chr5D.!!$R1 688
4 TraesCS5B01G198600 chr5A 405016071 405020343 4272 True 2017.333333 5201 92.8740 131 4235 3 chr5A.!!$R2 4104
5 TraesCS5B01G198600 chr5A 406482776 406483510 734 True 279.000000 279 73.9650 1466 2202 1 chr5A.!!$R1 736

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
355 390 1.066858 TCAATCCGCTCTTGGTCTCAC 60.067 52.381 0.00 0.0 0.00 3.51 F
1107 1341 0.105039 GATCGAAGGCGTGGGAAGAT 59.895 55.000 0.00 0.0 38.98 2.40 F
1454 1688 0.462759 GAGGAACTTGGATCGCCTGG 60.463 60.000 0.00 0.0 41.55 4.45 F
2194 2428 0.752658 AACCTTTGCAAACCAGAGCC 59.247 50.000 8.05 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1702 0.038166 GTGGGAACATCAGGCAAGGA 59.962 55.0 0.00 0.00 46.14 3.36 R
2373 2607 0.526211 TCTCACACATCTTACGCGCT 59.474 50.0 5.73 0.00 0.00 5.92 R
2745 2987 0.610174 TAGACCCAGAAGTGCAGCTG 59.390 55.0 10.11 10.11 0.00 4.24 R
3790 4043 0.105224 TGCTCAAAAAGGTCGGTCGA 59.895 50.0 0.00 0.00 0.00 4.20 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
41 42 6.055231 TGTTTGGAGTGATTTGTACTTTCG 57.945 37.500 0.00 0.00 0.00 3.46
46 47 5.175859 GGAGTGATTTGTACTTTCGGATCA 58.824 41.667 0.00 0.00 0.00 2.92
57 58 4.950050 ACTTTCGGATCATCCTCATACAC 58.050 43.478 1.10 0.00 33.30 2.90
68 69 8.816640 ATCATCCTCATACACAAAAACAAAAC 57.183 30.769 0.00 0.00 0.00 2.43
75 76 3.123804 ACACAAAAACAAAACGTGTGCA 58.876 36.364 0.00 0.00 42.63 4.57
76 77 3.743396 ACACAAAAACAAAACGTGTGCAT 59.257 34.783 0.00 0.00 42.63 3.96
81 82 7.321271 CACAAAAACAAAACGTGTGCATTTTTA 59.679 29.630 10.58 0.00 40.60 1.52
342 373 4.178545 AGGCAACAAAAATCTCAATCCG 57.821 40.909 0.00 0.00 41.41 4.18
355 390 1.066858 TCAATCCGCTCTTGGTCTCAC 60.067 52.381 0.00 0.00 0.00 3.51
393 428 3.702334 GAAACACGGCAGCGATCGC 62.702 63.158 32.15 32.15 42.33 4.58
470 505 2.457366 TCTTGCTCCGTTTCTTCTCC 57.543 50.000 0.00 0.00 0.00 3.71
478 513 4.555116 GCTCCGTTTCTTCTCCGTAGATAG 60.555 50.000 0.00 0.00 0.00 2.08
496 531 1.070445 GTGCTGTCAGCCTGTCACT 59.930 57.895 21.99 0.00 41.51 3.41
516 551 3.885297 ACTCATGACTGGTTTTCTTGGTG 59.115 43.478 0.00 0.00 0.00 4.17
525 560 3.198635 TGGTTTTCTTGGTGGATTTTGCA 59.801 39.130 0.00 0.00 0.00 4.08
574 613 3.005554 AGATCTGATTGGTCAACTTGCG 58.994 45.455 0.00 0.00 33.05 4.85
575 614 2.254546 TCTGATTGGTCAACTTGCGT 57.745 45.000 0.00 0.00 33.05 5.24
596 635 4.137543 GTCGGATAAAATTGCATCTCCCT 58.862 43.478 0.00 0.00 0.00 4.20
598 637 5.763204 GTCGGATAAAATTGCATCTCCCTAA 59.237 40.000 0.00 0.00 0.00 2.69
607 646 2.165641 TGCATCTCCCTAACTGTGTACG 59.834 50.000 0.00 0.00 0.00 3.67
617 656 5.507482 CCCTAACTGTGTACGTATGGATCAG 60.507 48.000 0.00 6.27 0.00 2.90
618 657 5.067413 CCTAACTGTGTACGTATGGATCAGT 59.933 44.000 0.00 6.87 36.45 3.41
648 687 2.670934 GCATATGGCTCGGCAGGG 60.671 66.667 4.56 0.00 40.25 4.45
679 732 3.699538 GGGGTGAAAAATGGTACCATCTC 59.300 47.826 27.49 21.96 35.31 2.75
683 736 4.956075 GTGAAAAATGGTACCATCTCCCAT 59.044 41.667 27.49 8.30 40.68 4.00
684 737 6.126409 GTGAAAAATGGTACCATCTCCCATA 58.874 40.000 27.49 8.69 38.00 2.74
686 739 4.724279 AAATGGTACCATCTCCCATACC 57.276 45.455 27.49 0.00 38.00 2.73
688 741 3.138123 TGGTACCATCTCCCATACCAA 57.862 47.619 11.60 0.00 43.18 3.67
689 742 3.675613 TGGTACCATCTCCCATACCAAT 58.324 45.455 11.60 0.00 43.18 3.16
690 743 3.650942 TGGTACCATCTCCCATACCAATC 59.349 47.826 11.60 0.00 43.18 2.67
691 744 3.910627 GGTACCATCTCCCATACCAATCT 59.089 47.826 7.15 0.00 37.59 2.40
692 745 5.091552 GGTACCATCTCCCATACCAATCTA 58.908 45.833 7.15 0.00 37.59 1.98
693 746 5.726793 GGTACCATCTCCCATACCAATCTAT 59.273 44.000 7.15 0.00 37.59 1.98
694 747 6.901300 GGTACCATCTCCCATACCAATCTATA 59.099 42.308 7.15 0.00 37.59 1.31
695 748 7.402071 GGTACCATCTCCCATACCAATCTATAA 59.598 40.741 7.15 0.00 37.59 0.98
696 749 8.993424 GTACCATCTCCCATACCAATCTATAAT 58.007 37.037 0.00 0.00 0.00 1.28
697 750 8.095452 ACCATCTCCCATACCAATCTATAATC 57.905 38.462 0.00 0.00 0.00 1.75
720 773 6.888105 TCTATGTAGTTTGAATGGCATCAGA 58.112 36.000 0.00 0.00 0.00 3.27
737 887 5.298777 GCATCAGAACCATTAATCAGAAGCT 59.701 40.000 0.00 0.00 0.00 3.74
745 895 4.036027 CCATTAATCAGAAGCTGCAACGAT 59.964 41.667 1.02 0.00 0.00 3.73
759 909 5.094429 TGCAACGATATTCCATTTGATCG 57.906 39.130 0.00 1.83 45.15 3.69
760 910 4.813697 TGCAACGATATTCCATTTGATCGA 59.186 37.500 9.84 0.00 42.94 3.59
770 920 6.528537 TTCCATTTGATCGATTTGAATGGT 57.471 33.333 28.48 0.00 44.40 3.55
777 927 6.091718 TGATCGATTTGAATGGTATCGGTA 57.908 37.500 0.00 0.00 40.99 4.02
778 928 6.697395 TGATCGATTTGAATGGTATCGGTAT 58.303 36.000 0.00 0.00 40.99 2.73
807 1041 1.936547 GCGCTCCCATTGTTCTTCTAG 59.063 52.381 0.00 0.00 0.00 2.43
814 1048 5.488341 TCCCATTGTTCTTCTAGCTGTTAC 58.512 41.667 0.00 0.00 0.00 2.50
818 1052 6.402222 CATTGTTCTTCTAGCTGTTACTCCT 58.598 40.000 0.00 0.00 0.00 3.69
823 1057 7.094291 TGTTCTTCTAGCTGTTACTCCTCTAAC 60.094 40.741 0.00 0.00 0.00 2.34
827 1061 3.367321 AGCTGTTACTCCTCTAACTCCC 58.633 50.000 0.00 0.00 0.00 4.30
830 1064 4.162509 GCTGTTACTCCTCTAACTCCCAAT 59.837 45.833 0.00 0.00 0.00 3.16
911 1145 5.332707 GTTCCACAGAGAACTTGTTCAAAC 58.667 41.667 14.80 6.73 42.37 2.93
943 1177 8.028938 AGGAAATGCTGAAATATTAACACACAC 58.971 33.333 0.00 0.00 0.00 3.82
980 1214 4.331968 TGGCTACATTTTTACTGGTCCTG 58.668 43.478 0.00 0.00 0.00 3.86
1068 1302 3.011517 AATGGCAGCCTCTCCCGT 61.012 61.111 14.15 0.00 0.00 5.28
1107 1341 0.105039 GATCGAAGGCGTGGGAAGAT 59.895 55.000 0.00 0.00 38.98 2.40
1293 1527 1.683707 AGCTGGCTCTGATCCGACA 60.684 57.895 0.00 0.00 0.00 4.35
1303 1537 3.157881 TCTGATCCGACACAGAAGAAGT 58.842 45.455 0.00 0.00 39.68 3.01
1388 1622 2.227388 AGGATCTTGTTTTGCTTCGCAG 59.773 45.455 0.00 0.00 40.61 5.18
1403 1637 1.749063 TCGCAGTGACACTAATCGGAT 59.251 47.619 8.02 0.00 0.00 4.18
1454 1688 0.462759 GAGGAACTTGGATCGCCTGG 60.463 60.000 0.00 0.00 41.55 4.45
1468 1702 1.772836 GCCTGGGCAGAATGATCTTT 58.227 50.000 6.75 0.00 39.69 2.52
1689 1923 3.054802 AGAATCAGGATGTTGGTCAGGAC 60.055 47.826 0.00 0.00 37.40 3.85
1742 1976 2.033602 GCACGGTTACCTGCCCTT 59.966 61.111 12.60 0.00 0.00 3.95
1850 2084 7.359595 TCTACATTTTTGGATTTGTTCGACAG 58.640 34.615 0.00 0.00 0.00 3.51
1999 2233 1.740025 GGGAGAGGCAACAAAAGATCG 59.260 52.381 0.00 0.00 41.41 3.69
2169 2403 4.077108 TCAAAGCACAGCTCATGAAAGAT 58.923 39.130 0.00 0.00 38.25 2.40
2194 2428 0.752658 AACCTTTGCAAACCAGAGCC 59.247 50.000 8.05 0.00 0.00 4.70
2372 2606 1.984570 CTCAGGAAGACTGGGGCGA 60.985 63.158 0.00 0.00 44.34 5.54
2373 2607 1.544825 CTCAGGAAGACTGGGGCGAA 61.545 60.000 0.00 0.00 44.34 4.70
2374 2608 1.078848 CAGGAAGACTGGGGCGAAG 60.079 63.158 0.00 0.00 43.70 3.79
2789 3031 6.803154 AACTAGCAAGGAAACTGTTATCAC 57.197 37.500 0.00 0.00 42.68 3.06
2817 3059 6.540083 AGATGGTATGAATGAAGATGATGCA 58.460 36.000 0.00 0.00 0.00 3.96
2976 3218 3.958147 TGACCTATCCTACAATTGCTCGA 59.042 43.478 5.05 0.00 0.00 4.04
3015 3257 1.409412 CTATGCCGTACAGATGCGAC 58.591 55.000 0.00 0.00 35.74 5.19
3018 3260 0.099968 TGCCGTACAGATGCGACTAC 59.900 55.000 0.00 0.00 35.74 2.73
3032 3274 2.516923 CGACTACGAGGTAGCAACAAG 58.483 52.381 2.82 0.00 39.51 3.16
3054 3296 1.006337 TGCCGGACTTGCAATTTGC 60.006 52.632 14.49 14.49 45.29 3.68
3186 3428 6.838198 TCTCGTATTAACCATACATTGTGC 57.162 37.500 0.00 0.00 38.17 4.57
3215 3457 0.892358 TTCTGCAAGCAAGGCCTCAG 60.892 55.000 5.23 8.30 0.00 3.35
3283 3525 9.320295 TCCATGTAAGACCCTTTTCAAATTTAT 57.680 29.630 0.00 0.00 0.00 1.40
3380 3622 2.930826 TCTTTTTGGAAGGAGACGCT 57.069 45.000 0.00 0.00 0.00 5.07
3386 3628 0.984230 TGGAAGGAGACGCTGGATTT 59.016 50.000 0.00 0.00 0.00 2.17
3434 3676 5.277154 CGACATTTGTTCAGACGGTTTTAGT 60.277 40.000 0.00 0.00 0.00 2.24
3447 3689 3.514645 GGTTTTAGTGAATGCATGCTGG 58.485 45.455 20.33 0.00 0.00 4.85
3702 3955 0.116143 AGTCCTCTTCTGGTGCTCCT 59.884 55.000 6.34 0.00 34.23 3.69
3790 4043 3.073798 TCAACAATGATACACCACCACCT 59.926 43.478 0.00 0.00 0.00 4.00
3791 4044 3.350219 ACAATGATACACCACCACCTC 57.650 47.619 0.00 0.00 0.00 3.85
3792 4045 2.279741 CAATGATACACCACCACCTCG 58.720 52.381 0.00 0.00 0.00 4.63
3793 4046 1.860641 ATGATACACCACCACCTCGA 58.139 50.000 0.00 0.00 0.00 4.04
3797 4050 2.695520 TACACCACCACCTCGACCGA 62.696 60.000 0.00 0.00 0.00 4.69
3879 4134 1.133884 CAGGATGCATGGGATCACAGT 60.134 52.381 2.46 0.00 0.00 3.55
3886 4141 2.843701 CATGGGATCACAGTTCTAGCC 58.156 52.381 2.98 0.00 0.00 3.93
3892 4147 3.551863 GGATCACAGTTCTAGCCAGATCG 60.552 52.174 0.00 0.00 33.14 3.69
3904 4159 2.107204 AGCCAGATCGCCAATTAATCCT 59.893 45.455 0.00 0.00 0.00 3.24
3968 4223 1.909302 GGAACATCTCAAGGGACCAGA 59.091 52.381 0.00 0.00 0.00 3.86
4015 4270 3.717400 ACAGATATCTTCATGCGTCGT 57.283 42.857 1.33 0.00 0.00 4.34
4065 4320 0.883833 GACTGGCACAAATGTCCTGG 59.116 55.000 10.93 0.00 38.70 4.45
4067 4322 1.423541 ACTGGCACAAATGTCCTGGTA 59.576 47.619 0.00 0.00 38.70 3.25
4069 4324 2.228822 CTGGCACAAATGTCCTGGTAAC 59.771 50.000 0.00 0.00 38.70 2.50
4074 4329 4.258543 CACAAATGTCCTGGTAACCGTAT 58.741 43.478 0.00 0.00 0.00 3.06
4075 4330 5.421277 CACAAATGTCCTGGTAACCGTATA 58.579 41.667 0.00 0.00 0.00 1.47
4076 4331 5.292589 CACAAATGTCCTGGTAACCGTATAC 59.707 44.000 0.00 0.00 0.00 1.47
4092 4347 8.687292 AACCGTATACTAGATAACATGTCTGA 57.313 34.615 0.00 0.00 0.00 3.27
4125 4380 4.547367 GGTCGGGATTGGCCTCCG 62.547 72.222 17.10 17.10 44.59 4.63
4226 4481 5.523188 CCAGTTCTTTATTAGCTCAGCTCAG 59.477 44.000 0.00 0.00 40.44 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.018669 GGATGATCCGAAAGTACAAATCACTC 60.019 42.308 0.00 0.00 0.00 3.51
41 42 6.757897 TGTTTTTGTGTATGAGGATGATCC 57.242 37.500 2.46 2.46 36.58 3.36
46 47 6.695278 CACGTTTTGTTTTTGTGTATGAGGAT 59.305 34.615 0.00 0.00 0.00 3.24
57 58 6.666479 AAAAATGCACACGTTTTGTTTTTG 57.334 29.167 0.00 0.00 42.77 2.44
68 69 7.370317 CACAAGTTCAAAATAAAAATGCACACG 59.630 33.333 0.00 0.00 0.00 4.49
106 107 3.664107 TGCACACAGTTTCTGTCCTATC 58.336 45.455 0.00 0.00 43.43 2.08
342 373 1.599576 GGAGGGTGAGACCAAGAGC 59.400 63.158 0.00 0.00 41.02 4.09
393 428 3.030291 AGGTCAGAGTAGAGCTGGATTG 58.970 50.000 0.00 0.00 44.08 2.67
470 505 1.678627 AGGCTGACAGCACTATCTACG 59.321 52.381 27.87 0.00 44.75 3.51
478 513 0.948141 GAGTGACAGGCTGACAGCAC 60.948 60.000 27.87 20.67 44.75 4.40
496 531 3.117701 TCCACCAAGAAAACCAGTCATGA 60.118 43.478 0.00 0.00 0.00 3.07
512 547 2.364970 CAGGAAAGTGCAAAATCCACCA 59.635 45.455 13.57 0.00 34.30 4.17
516 551 3.243401 ACGAACAGGAAAGTGCAAAATCC 60.243 43.478 5.06 5.06 0.00 3.01
525 560 5.334879 GCACATATCAAACGAACAGGAAAGT 60.335 40.000 0.00 0.00 0.00 2.66
574 613 4.137543 AGGGAGATGCAATTTTATCCGAC 58.862 43.478 0.00 0.00 0.00 4.79
575 614 4.437682 AGGGAGATGCAATTTTATCCGA 57.562 40.909 0.00 0.00 0.00 4.55
596 635 7.628769 TTACTGATCCATACGTACACAGTTA 57.371 36.000 19.09 12.16 38.01 2.24
598 637 6.096423 ACATTACTGATCCATACGTACACAGT 59.904 38.462 18.41 18.41 39.74 3.55
607 646 6.090088 GCGAGAATCACATTACTGATCCATAC 59.910 42.308 0.00 0.00 33.17 2.39
617 656 4.962693 GCCATATGCGAGAATCACATTAC 58.037 43.478 0.00 0.00 38.98 1.89
648 687 0.411848 TTTTTCACCCCCATCCCCTC 59.588 55.000 0.00 0.00 0.00 4.30
654 707 2.112691 TGGTACCATTTTTCACCCCCAT 59.887 45.455 11.60 0.00 0.00 4.00
655 708 1.503784 TGGTACCATTTTTCACCCCCA 59.496 47.619 11.60 0.00 0.00 4.96
660 713 4.340617 TGGGAGATGGTACCATTTTTCAC 58.659 43.478 27.97 23.98 36.70 3.18
692 745 9.797642 TGATGCCATTCAAACTACATAGATTAT 57.202 29.630 0.00 0.00 0.00 1.28
693 746 9.276590 CTGATGCCATTCAAACTACATAGATTA 57.723 33.333 0.00 0.00 0.00 1.75
694 747 7.994911 TCTGATGCCATTCAAACTACATAGATT 59.005 33.333 0.00 0.00 0.00 2.40
695 748 7.512130 TCTGATGCCATTCAAACTACATAGAT 58.488 34.615 0.00 0.00 0.00 1.98
696 749 6.888105 TCTGATGCCATTCAAACTACATAGA 58.112 36.000 0.00 0.00 0.00 1.98
697 750 7.412853 GTTCTGATGCCATTCAAACTACATAG 58.587 38.462 0.00 0.00 0.00 2.23
720 773 4.379813 CGTTGCAGCTTCTGATTAATGGTT 60.380 41.667 0.00 0.00 32.44 3.67
730 880 2.938451 TGGAATATCGTTGCAGCTTCTG 59.062 45.455 0.00 0.00 34.12 3.02
737 887 4.813697 TCGATCAAATGGAATATCGTTGCA 59.186 37.500 0.00 0.00 41.41 4.08
745 895 8.236585 ACCATTCAAATCGATCAAATGGAATA 57.763 30.769 32.15 1.32 46.00 1.75
759 909 8.621286 ACAGAAAATACCGATACCATTCAAATC 58.379 33.333 0.00 0.00 0.00 2.17
760 910 8.519799 ACAGAAAATACCGATACCATTCAAAT 57.480 30.769 0.00 0.00 0.00 2.32
770 920 3.527533 AGCGCAACAGAAAATACCGATA 58.472 40.909 11.47 0.00 0.00 2.92
777 927 1.549203 ATGGGAGCGCAACAGAAAAT 58.451 45.000 11.47 0.00 0.00 1.82
778 928 1.000385 CAATGGGAGCGCAACAGAAAA 60.000 47.619 11.47 0.00 0.00 2.29
807 1041 3.097614 TGGGAGTTAGAGGAGTAACAGC 58.902 50.000 0.00 0.00 35.65 4.40
814 1048 2.766828 ACCGAATTGGGAGTTAGAGGAG 59.233 50.000 14.12 0.00 44.64 3.69
818 1052 3.700038 GAGAGACCGAATTGGGAGTTAGA 59.300 47.826 14.12 0.00 44.64 2.10
823 1057 1.103803 TCGAGAGACCGAATTGGGAG 58.896 55.000 14.12 0.00 44.64 4.30
827 1061 2.871182 TGGATCGAGAGACCGAATTG 57.129 50.000 0.00 0.00 46.97 2.32
830 1064 3.887621 AAAATGGATCGAGAGACCGAA 57.112 42.857 0.00 0.00 46.97 4.30
964 1198 4.871933 AAAGGCAGGACCAGTAAAAATG 57.128 40.909 0.00 0.00 43.14 2.32
1068 1302 1.460273 GGAGCCTTTTCGGGTTTGCA 61.460 55.000 0.00 0.00 45.40 4.08
1116 1350 0.107848 CCTTCCCGCCAACGTAGATT 60.108 55.000 0.00 0.00 37.70 2.40
1253 1487 0.391228 TGCTGTACTCTTCCGTTGCA 59.609 50.000 0.00 0.00 0.00 4.08
1293 1527 5.932883 GGGAAAGAACGATAACTTCTTCTGT 59.067 40.000 0.00 0.00 37.04 3.41
1303 1537 2.617021 GGCTGGTGGGAAAGAACGATAA 60.617 50.000 0.00 0.00 0.00 1.75
1388 1622 2.159099 TGGCTCATCCGATTAGTGTCAC 60.159 50.000 0.00 0.00 37.80 3.67
1403 1637 2.265367 TGTGATTACCCTCTTGGCTCA 58.735 47.619 0.00 0.00 37.83 4.26
1422 1656 1.276421 AGTTCCTCGTGAGACCCATTG 59.724 52.381 0.00 0.00 35.39 2.82
1454 1688 2.100418 GGCAAGGAAAGATCATTCTGCC 59.900 50.000 21.14 21.14 40.92 4.85
1468 1702 0.038166 GTGGGAACATCAGGCAAGGA 59.962 55.000 0.00 0.00 46.14 3.36
1689 1923 3.466791 AAGCTCGCCATGGGATCCG 62.467 63.158 15.13 8.60 0.00 4.18
1742 1976 1.770658 GTCCTCCATGGTCCATCATCA 59.229 52.381 12.58 0.00 37.07 3.07
1850 2084 1.000171 CCTTCAGCTTGGCCTTTTCAC 60.000 52.381 3.32 0.00 0.00 3.18
2169 2403 4.274147 TCTGGTTTGCAAAGGTTGAGTTA 58.726 39.130 13.26 0.00 0.00 2.24
2194 2428 1.011242 CACGACGCACCACAAACAG 60.011 57.895 0.00 0.00 0.00 3.16
2372 2606 1.067846 TCTCACACATCTTACGCGCTT 60.068 47.619 5.73 0.00 0.00 4.68
2373 2607 0.526211 TCTCACACATCTTACGCGCT 59.474 50.000 5.73 0.00 0.00 5.92
2374 2608 0.640768 GTCTCACACATCTTACGCGC 59.359 55.000 5.73 0.00 0.00 6.86
2375 2609 1.135373 AGGTCTCACACATCTTACGCG 60.135 52.381 3.53 3.53 0.00 6.01
2376 2610 2.656560 AGGTCTCACACATCTTACGC 57.343 50.000 0.00 0.00 0.00 4.42
2377 2611 3.056821 TCCAAGGTCTCACACATCTTACG 60.057 47.826 0.00 0.00 0.00 3.18
2378 2612 4.537135 TCCAAGGTCTCACACATCTTAC 57.463 45.455 0.00 0.00 0.00 2.34
2379 2613 4.838423 TCTTCCAAGGTCTCACACATCTTA 59.162 41.667 0.00 0.00 0.00 2.10
2454 2696 6.684613 GCTTCACATCCCTAATTGCATCAAAT 60.685 38.462 0.00 0.00 0.00 2.32
2490 2732 1.065928 ATCGCTCTTAACTCCGCGG 59.934 57.895 22.12 22.12 45.11 6.46
2493 2735 1.209275 CCGCATCGCTCTTAACTCCG 61.209 60.000 0.00 0.00 0.00 4.63
2506 2748 2.886523 TGGAAAATGATCCATCCGCATC 59.113 45.455 0.00 0.00 44.52 3.91
2745 2987 0.610174 TAGACCCAGAAGTGCAGCTG 59.390 55.000 10.11 10.11 0.00 4.24
2789 3031 8.722394 CATCATCTTCATTCATACCATCTTCAG 58.278 37.037 0.00 0.00 0.00 3.02
2817 3059 1.294138 GCCACAGCATGCAAATGGT 59.706 52.632 26.38 12.86 42.53 3.55
2976 3218 3.754965 AGCCAATATATCACGTGCCATT 58.245 40.909 11.67 4.43 0.00 3.16
3003 3245 1.669779 ACCTCGTAGTCGCATCTGTAC 59.330 52.381 0.00 0.00 36.96 2.90
3015 3257 2.492484 AGTCCTTGTTGCTACCTCGTAG 59.508 50.000 0.00 0.00 38.97 3.51
3018 3260 1.714794 CAGTCCTTGTTGCTACCTCG 58.285 55.000 0.00 0.00 0.00 4.63
3032 3274 1.244019 AATTGCAAGTCCGGCAGTCC 61.244 55.000 4.94 0.00 43.05 3.85
3054 3296 2.534298 CAGTGCTTATGACCTGACTCG 58.466 52.381 0.00 0.00 0.00 4.18
3186 3428 1.168714 GCTTGCAGAACCTAGGGTTG 58.831 55.000 14.81 9.04 46.95 3.77
3215 3457 2.611292 CTCAGTCGGAAAGATCATTGGC 59.389 50.000 0.00 0.00 0.00 4.52
3219 3461 5.394663 CCAAGTACTCAGTCGGAAAGATCAT 60.395 44.000 0.00 0.00 0.00 2.45
3301 3543 7.507733 GCCATAGCTTAGTACTACTAGTTCA 57.492 40.000 0.00 0.00 31.47 3.18
3380 3622 5.390461 CGCACATTTCTCGTCTTTAAATCCA 60.390 40.000 0.00 0.00 0.00 3.41
3386 3628 3.678072 CCTTCGCACATTTCTCGTCTTTA 59.322 43.478 0.00 0.00 0.00 1.85
3434 3676 3.286329 AGTGATACCAGCATGCATTCA 57.714 42.857 21.98 11.67 31.97 2.57
3447 3689 9.299963 CTCATAATCATAGCTGCTAAGTGATAC 57.700 37.037 20.32 0.00 0.00 2.24
3548 3798 8.974060 AAACTAGAAGTGGAAATTACTGACAA 57.026 30.769 0.00 0.00 0.00 3.18
3581 3831 6.897706 TCATTGGATGAGATGTTGACAAAA 57.102 33.333 0.00 0.00 33.59 2.44
3754 4007 3.297134 TTGTTGAGACAAAAGCCTCCT 57.703 42.857 0.00 0.00 42.54 3.69
3790 4043 0.105224 TGCTCAAAAAGGTCGGTCGA 59.895 50.000 0.00 0.00 0.00 4.20
3791 4044 0.941542 TTGCTCAAAAAGGTCGGTCG 59.058 50.000 0.00 0.00 0.00 4.79
3792 4045 1.333791 CGTTGCTCAAAAAGGTCGGTC 60.334 52.381 0.00 0.00 0.00 4.79
3793 4046 0.661020 CGTTGCTCAAAAAGGTCGGT 59.339 50.000 0.00 0.00 0.00 4.69
3797 4050 0.248458 CGTGCGTTGCTCAAAAAGGT 60.248 50.000 0.00 0.00 0.00 3.50
3879 4134 4.415881 TTAATTGGCGATCTGGCTAGAA 57.584 40.909 3.02 0.00 45.14 2.10
3886 4141 3.077359 GGGAGGATTAATTGGCGATCTG 58.923 50.000 0.00 0.00 0.00 2.90
3892 4147 1.063266 TGGGTGGGAGGATTAATTGGC 60.063 52.381 0.00 0.00 0.00 4.52
3904 4159 1.621072 GCATTGGGTATTTGGGTGGGA 60.621 52.381 0.00 0.00 0.00 4.37
3968 4223 1.865865 CTGGTAACTTCTGTGCGTGT 58.134 50.000 0.00 0.00 37.61 4.49
4000 4255 0.459899 AGCCACGACGCATGAAGATA 59.540 50.000 0.00 0.00 0.00 1.98
4065 4320 9.823098 CAGACATGTTATCTAGTATACGGTTAC 57.177 37.037 0.00 0.00 0.00 2.50
4067 4322 8.687292 TCAGACATGTTATCTAGTATACGGTT 57.313 34.615 0.00 0.00 0.00 4.44
4092 4347 6.555463 TCCCGACCTCTGAAAATAGTATTT 57.445 37.500 2.10 2.10 0.00 1.40
4125 4380 0.741927 TCGCGCTTAGTTTTAGCCCC 60.742 55.000 5.56 0.00 35.18 5.80


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

AutoCloner maintained by Alex Coulton.