Multiple sequence alignment - TraesCS5B01G156800

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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 TraesCS5B01G156800 chr5B 100.000 3110 0 0 1 3110 289260107 289256998 0.000000e+00 5744.0
1 TraesCS5B01G156800 chr5A 95.772 1916 64 12 811 2718 338925954 338924048 0.000000e+00 3073.0
2 TraesCS5B01G156800 chr5A 82.745 736 117 6 1 732 673036546 673037275 0.000000e+00 647.0
3 TraesCS5B01G156800 chr5A 94.344 389 18 3 2717 3103 338923190 338922804 7.430000e-166 593.0
4 TraesCS5B01G156800 chr5D 94.459 1534 66 11 811 2331 255596949 255595422 0.000000e+00 2344.0
5 TraesCS5B01G156800 chr5D 95.204 417 16 2 2372 2788 255595423 255595011 0.000000e+00 656.0
6 TraesCS5B01G156800 chr5D 97.203 286 7 1 2825 3110 255595016 255594732 1.680000e-132 483.0
7 TraesCS5B01G156800 chr4D 87.636 736 82 3 1 732 479341677 479340947 0.000000e+00 846.0
8 TraesCS5B01G156800 chr3B 86.141 736 91 5 1 732 551527372 551526644 0.000000e+00 784.0
9 TraesCS5B01G156800 chr7D 83.832 736 108 5 1 732 419777262 419777990 0.000000e+00 689.0
10 TraesCS5B01G156800 chr7D 85.185 54 8 0 106 159 126054818 126054765 4.330000e-04 56.5
11 TraesCS5B01G156800 chr7B 83.243 740 107 11 1 732 680657417 680658147 0.000000e+00 664.0
12 TraesCS5B01G156800 chr2A 82.542 716 72 28 975 1683 713367032 713366363 5.780000e-162 580.0
13 TraesCS5B01G156800 chr3A 87.049 471 58 1 1 468 425986032 425986502 2.120000e-146 529.0
14 TraesCS5B01G156800 chr3D 72.624 705 167 24 2 694 602648036 602648726 3.140000e-50 209.0
15 TraesCS5B01G156800 chr3D 74.874 199 47 1 32 227 181091149 181091347 1.540000e-13 87.9
16 TraesCS5B01G156800 chr6D 81.290 155 26 2 1 152 111297335 111297489 4.210000e-24 122.0


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 TraesCS5B01G156800 chr5B 289256998 289260107 3109 True 5744 5744 100.000 1 3110 1 chr5B.!!$R1 3109
1 TraesCS5B01G156800 chr5A 338922804 338925954 3150 True 1833 3073 95.058 811 3103 2 chr5A.!!$R1 2292
2 TraesCS5B01G156800 chr5A 673036546 673037275 729 False 647 647 82.745 1 732 1 chr5A.!!$F1 731
3 TraesCS5B01G156800 chr5D 255594732 255596949 2217 True 1161 2344 95.622 811 3110 3 chr5D.!!$R1 2299
4 TraesCS5B01G156800 chr4D 479340947 479341677 730 True 846 846 87.636 1 732 1 chr4D.!!$R1 731
5 TraesCS5B01G156800 chr3B 551526644 551527372 728 True 784 784 86.141 1 732 1 chr3B.!!$R1 731
6 TraesCS5B01G156800 chr7D 419777262 419777990 728 False 689 689 83.832 1 732 1 chr7D.!!$F1 731
7 TraesCS5B01G156800 chr7B 680657417 680658147 730 False 664 664 83.243 1 732 1 chr7B.!!$F1 731
8 TraesCS5B01G156800 chr2A 713366363 713367032 669 True 580 580 82.542 975 1683 1 chr2A.!!$R1 708
9 TraesCS5B01G156800 chr3D 602648036 602648726 690 False 209 209 72.624 2 694 1 chr3D.!!$F2 692

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
749 757 0.319405 CCCTAAACGTGGTCGGAGTT 59.681 55.0 0.0 0.0 41.85 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2299 0.607489 ACTGATTTCAAGGCAGCGCT 60.607 50.0 2.64 2.64 33.03 5.92 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
75 76 1.167851 CAAAGGCGGATTGCTCTTCA 58.832 50.000 0.00 0.00 45.43 3.02
84 85 5.473931 GCGGATTGCTCTTCAGAGATTATA 58.526 41.667 8.09 0.00 44.74 0.98
212 217 9.816787 TTTTACCTTAGGTATCAAAACCAAGAT 57.183 29.630 12.36 0.00 42.40 2.40
232 237 6.012658 AGATTGTTTCGTTAATGCATGTGT 57.987 33.333 0.00 0.00 0.00 3.72
251 256 1.553704 GTCCGACTTTGTACCCTCCAT 59.446 52.381 0.00 0.00 0.00 3.41
252 257 1.553248 TCCGACTTTGTACCCTCCATG 59.447 52.381 0.00 0.00 0.00 3.66
293 298 9.781425 ATTAGTGATCTCCTCCTCACATATATT 57.219 33.333 5.58 0.00 43.35 1.28
300 305 6.214208 TCTCCTCCTCACATATATTCCAATGG 59.786 42.308 0.00 0.00 0.00 3.16
302 307 4.922206 TCCTCACATATATTCCAATGGCC 58.078 43.478 0.00 0.00 0.00 5.36
339 344 4.700448 TAACCGTCGGGGCCTGGA 62.700 66.667 17.28 2.77 40.62 3.86
362 367 3.803368 GCCTTTGTTGGGAACATTTGGAG 60.803 47.826 0.00 0.00 41.79 3.86
382 388 3.514309 GAGTAAGGCAACCTTCACCTCTA 59.486 47.826 1.28 0.00 43.57 2.43
393 399 5.381757 ACCTTCACCTCTACTCTGCTATAG 58.618 45.833 0.00 0.00 0.00 1.31
404 410 1.957177 TCTGCTATAGGGAGCGTTCAG 59.043 52.381 0.53 0.00 45.99 3.02
405 411 1.000283 CTGCTATAGGGAGCGTTCAGG 60.000 57.143 0.53 0.00 45.99 3.86
438 444 2.486982 CTCTTGAGTGACTTTGCATGGG 59.513 50.000 0.00 0.00 0.00 4.00
447 453 0.888736 CTTTGCATGGGACGGTGTCA 60.889 55.000 0.00 0.00 33.68 3.58
515 521 4.563337 TGTAGAAGGTCGTTATCATCGG 57.437 45.455 0.00 0.00 0.00 4.18
518 524 2.431057 AGAAGGTCGTTATCATCGGCTT 59.569 45.455 0.00 0.00 33.27 4.35
524 530 4.051922 GTCGTTATCATCGGCTTCATCTT 58.948 43.478 0.00 0.00 0.00 2.40
527 533 6.366332 GTCGTTATCATCGGCTTCATCTTATT 59.634 38.462 0.00 0.00 0.00 1.40
530 536 7.307396 CGTTATCATCGGCTTCATCTTATTTGT 60.307 37.037 0.00 0.00 0.00 2.83
531 537 8.988934 GTTATCATCGGCTTCATCTTATTTGTA 58.011 33.333 0.00 0.00 0.00 2.41
532 538 9.725019 TTATCATCGGCTTCATCTTATTTGTAT 57.275 29.630 0.00 0.00 0.00 2.29
533 539 8.627208 ATCATCGGCTTCATCTTATTTGTATT 57.373 30.769 0.00 0.00 0.00 1.89
534 540 9.725019 ATCATCGGCTTCATCTTATTTGTATTA 57.275 29.630 0.00 0.00 0.00 0.98
568 574 2.654749 TGTCCATCTAGTCGTTGCAG 57.345 50.000 0.00 0.00 0.00 4.41
569 575 2.167662 TGTCCATCTAGTCGTTGCAGA 58.832 47.619 0.00 0.00 0.00 4.26
580 586 3.948473 AGTCGTTGCAGAGCTCTAATCTA 59.052 43.478 17.75 3.00 0.00 1.98
610 616 1.377366 CTCCTCCGACTAGCTCGCAA 61.377 60.000 0.00 0.81 41.46 4.85
611 617 0.963856 TCCTCCGACTAGCTCGCAAA 60.964 55.000 0.00 0.00 41.46 3.68
616 623 1.999735 CCGACTAGCTCGCAAATGAAA 59.000 47.619 0.00 0.00 41.46 2.69
630 637 8.858003 TCGCAAATGAAAAAGTATGTGTTTTA 57.142 26.923 0.00 0.00 0.00 1.52
631 638 9.469807 TCGCAAATGAAAAAGTATGTGTTTTAT 57.530 25.926 0.00 0.00 0.00 1.40
646 653 6.607689 TGTGTTTTATTCGCCATGAAGTAAG 58.392 36.000 0.00 0.00 40.65 2.34
651 658 3.763097 TTCGCCATGAAGTAAGCATTG 57.237 42.857 0.00 0.00 31.44 2.82
652 659 2.710377 TCGCCATGAAGTAAGCATTGT 58.290 42.857 0.00 0.00 0.00 2.71
664 671 2.751166 AGCATTGTACTCTTGCTCGT 57.249 45.000 10.64 0.00 42.88 4.18
694 702 3.071023 ACAGAATCTCCTCACGGTGAAAA 59.929 43.478 12.54 2.34 36.48 2.29
705 713 4.059511 TCACGGTGAAAAAGCTCGATTAA 58.940 39.130 8.68 0.00 0.00 1.40
724 732 9.811655 TCGATTAAGCGATCATTAATTTTGATC 57.188 29.630 12.49 15.85 43.89 2.92
732 740 6.860023 CGATCATTAATTTTGATCTCTTGCCC 59.140 38.462 20.21 2.85 44.72 5.36
733 741 7.255381 CGATCATTAATTTTGATCTCTTGCCCT 60.255 37.037 20.21 0.00 44.72 5.19
734 742 9.071276 GATCATTAATTTTGATCTCTTGCCCTA 57.929 33.333 17.48 0.00 43.94 3.53
735 743 8.821686 TCATTAATTTTGATCTCTTGCCCTAA 57.178 30.769 0.00 0.00 0.00 2.69
736 744 9.253832 TCATTAATTTTGATCTCTTGCCCTAAA 57.746 29.630 0.00 0.00 0.00 1.85
737 745 9.305925 CATTAATTTTGATCTCTTGCCCTAAAC 57.694 33.333 0.00 0.00 0.00 2.01
738 746 5.567138 ATTTTGATCTCTTGCCCTAAACG 57.433 39.130 0.00 0.00 0.00 3.60
739 747 3.695830 TTGATCTCTTGCCCTAAACGT 57.304 42.857 0.00 0.00 0.00 3.99
740 748 2.972625 TGATCTCTTGCCCTAAACGTG 58.027 47.619 0.00 0.00 0.00 4.49
741 749 2.280628 GATCTCTTGCCCTAAACGTGG 58.719 52.381 0.00 0.00 0.00 4.94
742 750 1.053424 TCTCTTGCCCTAAACGTGGT 58.947 50.000 0.00 0.00 0.00 4.16
743 751 1.001633 TCTCTTGCCCTAAACGTGGTC 59.998 52.381 0.00 0.00 0.00 4.02
744 752 0.320073 TCTTGCCCTAAACGTGGTCG 60.320 55.000 0.00 0.00 43.34 4.79
745 753 1.296056 CTTGCCCTAAACGTGGTCGG 61.296 60.000 0.00 0.00 41.85 4.79
746 754 1.756408 TTGCCCTAAACGTGGTCGGA 61.756 55.000 0.00 0.00 41.85 4.55
747 755 1.447314 GCCCTAAACGTGGTCGGAG 60.447 63.158 0.00 0.00 41.85 4.63
748 756 1.969862 CCCTAAACGTGGTCGGAGT 59.030 57.895 0.00 0.00 41.85 3.85
749 757 0.319405 CCCTAAACGTGGTCGGAGTT 59.681 55.000 0.00 0.00 41.85 3.01
750 758 1.270465 CCCTAAACGTGGTCGGAGTTT 60.270 52.381 0.00 0.00 41.85 2.66
751 759 2.029110 CCCTAAACGTGGTCGGAGTTTA 60.029 50.000 0.00 1.02 41.85 2.01
752 760 3.554752 CCCTAAACGTGGTCGGAGTTTAA 60.555 47.826 0.00 0.00 39.08 1.52
753 761 3.429881 CCTAAACGTGGTCGGAGTTTAAC 59.570 47.826 0.00 0.00 39.08 2.01
754 762 1.869774 AACGTGGTCGGAGTTTAACC 58.130 50.000 0.00 0.00 41.85 2.85
762 770 2.875080 CGGAGTTTAACCGCAAAGAG 57.125 50.000 0.00 0.00 43.74 2.85
763 771 1.136057 CGGAGTTTAACCGCAAAGAGC 60.136 52.381 0.00 0.00 43.74 4.09
772 780 3.111038 GCAAAGAGCGGTATGGCC 58.889 61.111 0.00 0.00 0.00 5.36
781 789 3.713963 GGTATGGCCGCACGTTAG 58.286 61.111 0.00 0.00 0.00 2.34
782 790 1.885850 GGTATGGCCGCACGTTAGG 60.886 63.158 0.00 1.84 0.00 2.69
791 799 4.807039 CACGTTAGGCCCGACCGG 62.807 72.222 0.00 0.00 46.52 5.28
802 810 4.728102 CGACCGGGTACAAGCGCA 62.728 66.667 11.47 0.00 0.00 6.09
803 811 2.813908 GACCGGGTACAAGCGCAG 60.814 66.667 11.47 3.78 0.00 5.18
823 831 1.953311 GCGGGACATAGAAGCCCAAAA 60.953 52.381 0.00 0.00 42.14 2.44
830 838 6.295859 GGGACATAGAAGCCCAAAAAGAATTT 60.296 38.462 0.00 0.00 40.20 1.82
831 839 6.813649 GGACATAGAAGCCCAAAAAGAATTTC 59.186 38.462 0.00 0.00 37.28 2.17
833 841 4.257267 AGAAGCCCAAAAAGAATTTCGG 57.743 40.909 0.00 0.00 37.28 4.30
835 843 1.001974 AGCCCAAAAAGAATTTCGGCC 59.998 47.619 6.03 0.00 41.47 6.13
836 844 1.001974 GCCCAAAAAGAATTTCGGCCT 59.998 47.619 0.00 0.00 37.28 5.19
837 845 2.232696 GCCCAAAAAGAATTTCGGCCTA 59.767 45.455 0.00 0.00 37.28 3.93
838 846 3.306433 GCCCAAAAAGAATTTCGGCCTAA 60.306 43.478 0.00 0.00 37.28 2.69
859 867 3.770040 CTCCACGTCGGCCCATCA 61.770 66.667 0.00 0.00 33.14 3.07
863 871 4.760047 ACGTCGGCCCATCAGCAC 62.760 66.667 0.00 0.00 0.00 4.40
871 879 2.738139 CCATCAGCACGTGACGCA 60.738 61.111 22.23 0.00 38.28 5.24
896 904 9.599866 CATATAGATCTGTCCAGAGAGTAGTAG 57.400 40.741 5.18 0.00 41.33 2.57
902 910 2.867975 GTCCAGAGAGTAGTAGACGAGC 59.132 54.545 0.00 0.00 0.00 5.03
904 912 2.420269 CCAGAGAGTAGTAGACGAGCCA 60.420 54.545 0.00 0.00 0.00 4.75
906 914 2.767394 AGAGAGTAGTAGACGAGCCAGA 59.233 50.000 0.00 0.00 0.00 3.86
915 923 1.939769 GACGAGCCAGACACTCCTCC 61.940 65.000 0.00 0.00 0.00 4.30
916 924 2.716017 CGAGCCAGACACTCCTCCC 61.716 68.421 0.00 0.00 0.00 4.30
918 926 1.305718 AGCCAGACACTCCTCCCTC 60.306 63.158 0.00 0.00 0.00 4.30
925 933 1.390125 CACTCCTCCCTCACCTCCT 59.610 63.158 0.00 0.00 0.00 3.69
927 935 0.853586 ACTCCTCCCTCACCTCCTCT 60.854 60.000 0.00 0.00 0.00 3.69
929 937 1.075600 CCTCCCTCACCTCCTCTCC 60.076 68.421 0.00 0.00 0.00 3.71
930 938 1.075600 CTCCCTCACCTCCTCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
931 939 2.443016 CCCTCACCTCCTCTCCCG 60.443 72.222 0.00 0.00 0.00 5.14
932 940 2.684104 CCTCACCTCCTCTCCCGA 59.316 66.667 0.00 0.00 0.00 5.14
933 941 1.231641 CCTCACCTCCTCTCCCGAT 59.768 63.158 0.00 0.00 0.00 4.18
943 951 1.231221 CTCTCCCGATTCGTCGATCT 58.769 55.000 5.20 0.00 34.64 2.75
944 952 1.195900 CTCTCCCGATTCGTCGATCTC 59.804 57.143 5.20 0.00 34.64 2.75
947 955 1.065102 TCCCGATTCGTCGATCTCAAC 59.935 52.381 5.20 0.00 34.64 3.18
952 964 0.901114 TTCGTCGATCTCAACCCCCA 60.901 55.000 0.00 0.00 0.00 4.96
963 975 3.232497 AACCCCCAATTCCCCACCG 62.232 63.158 0.00 0.00 0.00 4.94
970 982 2.157452 AATTCCCCACCGACCCACA 61.157 57.895 0.00 0.00 0.00 4.17
1621 1637 4.475135 GGAAGCGGTCAGGGGAGC 62.475 72.222 0.00 0.00 38.17 4.70
1668 1687 0.254178 GCAAGAGCAGGGGAAGATCA 59.746 55.000 0.00 0.00 41.58 2.92
1704 1723 2.830923 CAGGAAGAGTGACAGTGAGGAT 59.169 50.000 0.00 0.00 0.00 3.24
1869 1888 2.223688 CCAGACGGATGACTCATCAGAC 60.224 54.545 21.70 16.52 42.13 3.51
1988 2007 0.039618 TCCCCACATGAAAGGAAGCC 59.960 55.000 0.00 0.00 0.00 4.35
2058 2077 0.904649 AGGATGAGCGACATTGTCCA 59.095 50.000 11.12 4.17 39.56 4.02
2124 2144 1.557371 GGCTAAAGAGGAGGCTGAAGT 59.443 52.381 0.00 0.00 36.58 3.01
2138 2158 3.005791 GGCTGAAGTGGTAAATTGCACTT 59.994 43.478 0.00 0.00 40.16 3.16
2158 2178 4.754618 ACTTATCGATGTTTGCAACAGTGA 59.245 37.500 8.54 3.87 45.95 3.41
2160 2180 3.811722 TCGATGTTTGCAACAGTGATC 57.188 42.857 0.00 0.00 45.95 2.92
2167 2187 1.511850 TGCAACAGTGATCGTCCTTG 58.488 50.000 0.00 0.00 0.00 3.61
2188 2208 7.286546 TCCTTGGTTATTTGTCTTGTCAAATGA 59.713 33.333 13.26 5.35 44.40 2.57
2283 2303 8.539770 ACTATCCATATATGCATAAATAGCGC 57.460 34.615 11.13 0.00 33.85 5.92
2509 2531 6.095680 AGGCTATTGGGTGGGATAACTTATA 58.904 40.000 0.00 0.00 0.00 0.98
2582 2604 3.181497 GCAAATTCATGTGCCGTAGACAT 60.181 43.478 0.00 0.00 34.58 3.06
2615 2637 5.294356 TCGGTACTGACACATATATTTGGC 58.706 41.667 0.00 0.79 0.00 4.52
2812 3693 7.558161 TGAATACATCTCTTACATGCCTTTG 57.442 36.000 0.00 0.00 0.00 2.77
2852 3733 2.828877 TGGAGAACCTGTTACAACACG 58.171 47.619 0.00 0.00 34.70 4.49
2905 3788 7.069877 AGGATTTGGTATATGTTACGGCTAA 57.930 36.000 0.00 0.00 0.00 3.09
2996 3879 4.262463 CCTTGGTAGTGACTTTAGTCTGCA 60.262 45.833 10.92 0.00 44.99 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.685224 CTTTGTCCCAGGCAGGCTA 59.315 57.895 0.00 0.00 35.39 3.93
44 45 2.677875 CCTTTGTCCCAGGCAGGC 60.678 66.667 0.00 0.00 35.39 4.85
75 76 8.891985 TGAAGCTGATACCTGATATAATCTCT 57.108 34.615 0.00 0.00 0.00 3.10
84 85 2.158900 CCGGTTGAAGCTGATACCTGAT 60.159 50.000 0.00 0.00 0.00 2.90
156 160 1.545841 GGTTGTCCCAATTCTGACCC 58.454 55.000 2.32 0.00 0.00 4.46
195 199 6.264518 ACGAAACAATCTTGGTTTTGATACCT 59.735 34.615 11.14 0.00 38.41 3.08
204 208 5.837437 TGCATTAACGAAACAATCTTGGTT 58.163 33.333 0.00 0.00 41.61 3.67
212 217 4.541779 GGACACATGCATTAACGAAACAA 58.458 39.130 0.00 0.00 0.00 2.83
232 237 1.553248 CATGGAGGGTACAAAGTCGGA 59.447 52.381 0.00 0.00 0.00 4.55
251 256 8.708378 AGATCACTAATGTGGTAATCAAGATCA 58.292 33.333 0.00 0.00 43.94 2.92
252 257 9.202273 GAGATCACTAATGTGGTAATCAAGATC 57.798 37.037 0.00 0.00 43.94 2.75
283 288 4.353489 TCAGGGCCATTGGAATATATGTGA 59.647 41.667 6.18 0.00 0.00 3.58
336 341 0.260230 TGTTCCCAACAAAGGCTCCA 59.740 50.000 0.00 0.00 38.72 3.86
339 344 2.104622 CCAAATGTTCCCAACAAAGGCT 59.895 45.455 0.00 0.00 45.86 4.58
362 367 2.861147 AGAGGTGAAGGTTGCCTTAC 57.139 50.000 0.00 0.89 44.82 2.34
382 388 1.957877 GAACGCTCCCTATAGCAGAGT 59.042 52.381 15.55 9.20 42.91 3.24
393 399 4.021925 ACAGCCCTGAACGCTCCC 62.022 66.667 1.69 0.00 33.17 4.30
404 410 2.289945 ACTCAAGAGATGAACACAGCCC 60.290 50.000 3.73 0.00 37.67 5.19
405 411 2.740981 CACTCAAGAGATGAACACAGCC 59.259 50.000 3.73 0.00 37.67 4.85
438 444 1.865340 GAACAAGTCCTTGACACCGTC 59.135 52.381 13.69 0.00 42.93 4.79
504 510 6.712241 AATAAGATGAAGCCGATGATAACG 57.288 37.500 0.00 0.00 0.00 3.18
508 514 8.627208 AATACAAATAAGATGAAGCCGATGAT 57.373 30.769 0.00 0.00 0.00 2.45
534 540 9.373450 ACTAGATGGACAACTCACTGATAATAT 57.627 33.333 0.00 0.00 0.00 1.28
568 574 8.088365 GGAGAAGGAAGAATTAGATTAGAGCTC 58.912 40.741 5.27 5.27 0.00 4.09
569 575 7.789349 AGGAGAAGGAAGAATTAGATTAGAGCT 59.211 37.037 0.00 0.00 0.00 4.09
580 586 3.445987 AGTCGGAGGAGAAGGAAGAATT 58.554 45.455 0.00 0.00 0.00 2.17
610 616 8.921670 GGCGAATAAAACACATACTTTTTCATT 58.078 29.630 0.00 0.00 0.00 2.57
611 617 8.085296 TGGCGAATAAAACACATACTTTTTCAT 58.915 29.630 0.00 0.00 0.00 2.57
616 623 7.151999 TCATGGCGAATAAAACACATACTTT 57.848 32.000 0.00 0.00 0.00 2.66
630 637 3.696051 ACAATGCTTACTTCATGGCGAAT 59.304 39.130 0.00 0.00 31.69 3.34
631 638 3.081061 ACAATGCTTACTTCATGGCGAA 58.919 40.909 0.00 0.00 0.00 4.70
646 653 2.726066 GCAACGAGCAAGAGTACAATGC 60.726 50.000 8.89 8.89 44.79 3.56
664 671 1.556911 GAGGAGATTCTGTGGAGGCAA 59.443 52.381 0.00 0.00 0.00 4.52
694 702 7.426929 AATTAATGATCGCTTAATCGAGCTT 57.573 32.000 16.67 8.72 44.24 3.74
715 723 5.476945 ACGTTTAGGGCAAGAGATCAAAATT 59.523 36.000 0.00 0.00 0.00 1.82
718 726 3.751175 CACGTTTAGGGCAAGAGATCAAA 59.249 43.478 0.00 0.00 0.00 2.69
724 732 1.439679 GACCACGTTTAGGGCAAGAG 58.560 55.000 0.00 0.00 33.02 2.85
732 740 3.429881 GGTTAAACTCCGACCACGTTTAG 59.570 47.826 0.00 0.00 35.36 1.85
733 741 3.389221 GGTTAAACTCCGACCACGTTTA 58.611 45.455 0.00 0.00 37.88 2.01
734 742 2.212652 GGTTAAACTCCGACCACGTTT 58.787 47.619 0.00 0.00 37.88 3.60
735 743 1.869774 GGTTAAACTCCGACCACGTT 58.130 50.000 0.00 0.00 37.88 3.99
736 744 3.593834 GGTTAAACTCCGACCACGT 57.406 52.632 0.00 0.00 37.88 4.49
744 752 2.613730 GCTCTTTGCGGTTAAACTCC 57.386 50.000 0.00 0.00 0.00 3.85
755 763 3.111038 GGCCATACCGCTCTTTGC 58.889 61.111 0.00 0.00 38.57 3.68
764 772 1.885850 CCTAACGTGCGGCCATACC 60.886 63.158 2.24 0.00 0.00 2.73
765 773 2.531376 GCCTAACGTGCGGCCATAC 61.531 63.158 15.48 0.00 40.43 2.39
766 774 2.202960 GCCTAACGTGCGGCCATA 60.203 61.111 15.48 0.00 40.43 2.74
774 782 4.807039 CCGGTCGGGCCTAACGTG 62.807 72.222 14.82 2.27 34.25 4.49
785 793 4.728102 TGCGCTTGTACCCGGTCG 62.728 66.667 9.73 0.00 0.00 4.79
786 794 2.813908 CTGCGCTTGTACCCGGTC 60.814 66.667 9.73 0.00 0.00 4.79
791 799 4.752879 TCCCGCTGCGCTTGTACC 62.753 66.667 18.00 0.00 0.00 3.34
792 800 3.488090 GTCCCGCTGCGCTTGTAC 61.488 66.667 18.00 5.67 0.00 2.90
793 801 1.950973 TATGTCCCGCTGCGCTTGTA 61.951 55.000 18.00 1.52 0.00 2.41
794 802 3.309436 TATGTCCCGCTGCGCTTGT 62.309 57.895 18.00 3.56 0.00 3.16
795 803 2.511373 TATGTCCCGCTGCGCTTG 60.511 61.111 18.00 7.32 0.00 4.01
796 804 2.202932 CTATGTCCCGCTGCGCTT 60.203 61.111 18.00 4.23 0.00 4.68
797 805 2.635229 CTTCTATGTCCCGCTGCGCT 62.635 60.000 18.00 0.66 0.00 5.92
798 806 2.202878 TTCTATGTCCCGCTGCGC 60.203 61.111 18.00 0.00 0.00 6.09
799 807 2.240500 GCTTCTATGTCCCGCTGCG 61.241 63.158 16.34 16.34 0.00 5.18
800 808 1.889573 GGCTTCTATGTCCCGCTGC 60.890 63.158 0.00 0.00 0.00 5.25
801 809 1.227674 GGGCTTCTATGTCCCGCTG 60.228 63.158 0.00 0.00 0.00 5.18
802 810 1.271840 TTGGGCTTCTATGTCCCGCT 61.272 55.000 0.00 0.00 42.98 5.52
803 811 0.393808 TTTGGGCTTCTATGTCCCGC 60.394 55.000 0.00 0.00 42.98 6.13
804 812 2.122783 TTTTGGGCTTCTATGTCCCG 57.877 50.000 0.00 0.00 42.98 5.14
805 813 3.697166 TCTTTTTGGGCTTCTATGTCCC 58.303 45.455 0.00 0.00 40.47 4.46
806 814 5.921962 ATTCTTTTTGGGCTTCTATGTCC 57.078 39.130 0.00 0.00 0.00 4.02
807 815 6.528072 CGAAATTCTTTTTGGGCTTCTATGTC 59.472 38.462 0.00 0.00 0.00 3.06
808 816 6.389906 CGAAATTCTTTTTGGGCTTCTATGT 58.610 36.000 0.00 0.00 0.00 2.29
809 817 5.807011 CCGAAATTCTTTTTGGGCTTCTATG 59.193 40.000 0.00 0.00 41.17 2.23
813 821 2.736721 GCCGAAATTCTTTTTGGGCTTC 59.263 45.455 14.44 0.00 43.93 3.86
823 831 5.589050 GTGGAGTTATTAGGCCGAAATTCTT 59.411 40.000 11.07 0.00 0.00 2.52
830 838 1.406539 GACGTGGAGTTATTAGGCCGA 59.593 52.381 0.00 0.00 0.00 5.54
831 839 1.849097 GACGTGGAGTTATTAGGCCG 58.151 55.000 0.00 0.00 0.00 6.13
833 841 1.849097 CCGACGTGGAGTTATTAGGC 58.151 55.000 0.00 0.00 42.00 3.93
835 843 1.537562 GGGCCGACGTGGAGTTATTAG 60.538 57.143 0.00 0.00 42.00 1.73
836 844 0.461135 GGGCCGACGTGGAGTTATTA 59.539 55.000 0.00 0.00 42.00 0.98
837 845 1.219935 GGGCCGACGTGGAGTTATT 59.780 57.895 0.00 0.00 42.00 1.40
838 846 1.335132 ATGGGCCGACGTGGAGTTAT 61.335 55.000 0.00 0.00 42.00 1.89
859 867 2.554462 AGATCTATATGCGTCACGTGCT 59.446 45.455 11.67 0.00 0.00 4.40
863 871 3.058224 TGGACAGATCTATATGCGTCACG 60.058 47.826 9.93 0.00 0.00 4.35
864 872 4.216472 TCTGGACAGATCTATATGCGTCAC 59.784 45.833 9.93 2.26 31.41 3.67
871 879 9.555411 TCTACTACTCTCTGGACAGATCTATAT 57.445 37.037 2.00 0.00 36.76 0.86
896 904 1.509004 GAGGAGTGTCTGGCTCGTC 59.491 63.158 0.00 0.00 39.56 4.20
902 910 1.261238 GGTGAGGGAGGAGTGTCTGG 61.261 65.000 0.00 0.00 0.00 3.86
904 912 0.040499 GAGGTGAGGGAGGAGTGTCT 59.960 60.000 0.00 0.00 0.00 3.41
906 914 1.079438 GGAGGTGAGGGAGGAGTGT 59.921 63.158 0.00 0.00 0.00 3.55
915 923 0.397816 AATCGGGAGAGGAGGTGAGG 60.398 60.000 0.00 0.00 45.48 3.86
916 924 1.036707 GAATCGGGAGAGGAGGTGAG 58.963 60.000 0.00 0.00 45.48 3.51
918 926 1.038130 ACGAATCGGGAGAGGAGGTG 61.038 60.000 7.80 0.00 45.48 4.00
931 939 1.538419 GGGGGTTGAGATCGACGAATC 60.538 57.143 0.00 3.97 0.00 2.52
932 940 0.464452 GGGGGTTGAGATCGACGAAT 59.536 55.000 0.00 0.00 0.00 3.34
933 941 0.901114 TGGGGGTTGAGATCGACGAA 60.901 55.000 0.00 0.00 0.00 3.85
943 951 1.467432 GTGGGGAATTGGGGGTTGA 59.533 57.895 0.00 0.00 0.00 3.18
944 952 1.612146 GGTGGGGAATTGGGGGTTG 60.612 63.158 0.00 0.00 0.00 3.77
947 955 3.343326 TCGGTGGGGAATTGGGGG 61.343 66.667 0.00 0.00 0.00 5.40
952 964 2.137177 CTGTGGGTCGGTGGGGAATT 62.137 60.000 0.00 0.00 0.00 2.17
963 975 1.602771 GGTTAGGGCTCTGTGGGTC 59.397 63.158 0.00 0.00 0.00 4.46
970 982 0.690077 CGGGTTAGGGTTAGGGCTCT 60.690 60.000 0.00 0.00 0.00 4.09
1428 1444 1.172180 CCTCGAACTTGGCCTTTGCA 61.172 55.000 3.32 0.00 40.13 4.08
1431 1447 1.056660 TCTCCTCGAACTTGGCCTTT 58.943 50.000 3.32 0.00 0.00 3.11
1621 1637 1.151668 CGGCTTGTCTTCTTGTCCTG 58.848 55.000 0.00 0.00 0.00 3.86
1668 1687 1.130054 TCCTGCTCCTCCTGTGCTTT 61.130 55.000 0.00 0.00 34.56 3.51
1704 1723 2.024846 AGTTCTCTCCTCCTCCGAATCA 60.025 50.000 0.00 0.00 0.00 2.57
1850 1869 1.673400 CGTCTGATGAGTCATCCGTCT 59.327 52.381 26.58 0.00 39.87 4.18
1869 1888 1.973515 TCCCCTCCAGATTCATCATCG 59.026 52.381 0.00 0.00 36.93 3.84
1988 2007 2.093288 TGGCTCTTCTGCTTACTGGATG 60.093 50.000 0.00 0.00 0.00 3.51
2124 2144 6.751514 AACATCGATAAGTGCAATTTACCA 57.248 33.333 4.05 0.00 0.00 3.25
2158 2178 5.313712 ACAAGACAAATAACCAAGGACGAT 58.686 37.500 0.00 0.00 0.00 3.73
2160 2180 4.513692 TGACAAGACAAATAACCAAGGACG 59.486 41.667 0.00 0.00 0.00 4.79
2167 2187 8.816640 ACAATCATTTGACAAGACAAATAACC 57.183 30.769 9.47 0.00 45.00 2.85
2188 2208 8.556213 AAGAATCATGCTTAAAATGCAACAAT 57.444 26.923 0.00 0.00 44.01 2.71
2279 2299 0.607489 ACTGATTTCAAGGCAGCGCT 60.607 50.000 2.64 2.64 33.03 5.92
2281 2301 4.361451 AATTACTGATTTCAAGGCAGCG 57.639 40.909 0.00 0.00 33.03 5.18
2283 2303 5.346822 GCACAAATTACTGATTTCAAGGCAG 59.653 40.000 0.00 0.00 35.79 4.85
2330 2352 9.686683 AAATGACAAAAGCCTGAGTAATACTAT 57.313 29.630 0.00 0.00 0.00 2.12
2457 2479 5.248477 ACCACCTGATTACTGAAGAGCTTTA 59.752 40.000 0.00 0.00 0.00 1.85
2458 2480 4.042187 ACCACCTGATTACTGAAGAGCTTT 59.958 41.667 0.00 0.00 0.00 3.51
2509 2531 4.623932 TCTGAGTTCTGCATAAACCTGT 57.376 40.909 8.14 0.00 0.00 4.00
2582 2604 6.330004 TGTGTCAGTACCGATTTTAGTACA 57.670 37.500 0.00 0.00 41.07 2.90
2615 2637 9.918630 ATCAAATCAGACTTTTAGAAATGTTGG 57.081 29.630 0.00 0.00 0.00 3.77
2812 3693 3.262420 CAACTCACCCTAGTGTATGCAC 58.738 50.000 5.71 5.71 44.83 4.57
2819 3700 2.028020 GGTTCTCCAACTCACCCTAGTG 60.028 54.545 0.00 0.00 46.00 2.74
2905 3788 6.949352 AGAGAATTCACAGTTTGATGTTGT 57.051 33.333 8.44 0.00 32.84 3.32
2996 3879 8.762481 AGTAACTTTCCATGGAAGTTAAACTT 57.238 30.769 30.36 20.87 41.95 2.66


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

AutoCloner maintained by Alex Coulton.