Multiple sequence alignment - TraesCS3B01G097500

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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 TraesCS3B01G097500 chr3B 100.000 2663 0 0 1 2663 65270447 65267785 0.000000e+00 4918.0
1 TraesCS3B01G097500 chr3B 99.170 723 6 0 1927 2649 148433643 148434365 0.000000e+00 1303.0
2 TraesCS3B01G097500 chr3A 91.607 1120 50 18 791 1888 53257551 53256454 0.000000e+00 1507.0
3 TraesCS3B01G097500 chr3A 87.732 701 72 9 1 695 60069884 60070576 0.000000e+00 806.0
4 TraesCS3B01G097500 chr3D 90.269 1151 65 20 815 1927 41746819 41745678 0.000000e+00 1461.0
5 TraesCS3B01G097500 chr3D 89.631 704 55 10 1 690 30976448 30975749 0.000000e+00 880.0
6 TraesCS3B01G097500 chr6B 97.376 724 17 1 1927 2650 561263518 561264239 0.000000e+00 1230.0
7 TraesCS3B01G097500 chr6B 97.103 725 19 1 1927 2649 91148380 91149104 0.000000e+00 1221.0
8 TraesCS3B01G097500 chr6B 87.874 701 68 11 1 690 671467843 671467149 0.000000e+00 808.0
9 TraesCS3B01G097500 chr5A 97.107 726 21 0 1927 2652 595424957 595424232 0.000000e+00 1225.0
10 TraesCS3B01G097500 chr5A 94.545 55 3 0 734 788 640712632 640712578 4.720000e-13 86.1
11 TraesCS3B01G097500 chr5A 92.727 55 4 0 734 788 540056785 540056839 2.200000e-11 80.5
12 TraesCS3B01G097500 chr4B 97.234 723 19 1 1927 2649 39510313 39509592 0.000000e+00 1223.0
13 TraesCS3B01G097500 chr4B 97.357 719 17 1 1930 2646 124921865 124922583 0.000000e+00 1221.0
14 TraesCS3B01G097500 chr4B 88.952 706 61 10 1 690 574230984 574230280 0.000000e+00 856.0
15 TraesCS3B01G097500 chrUn 97.103 725 19 1 1927 2649 77422107 77421383 0.000000e+00 1221.0
16 TraesCS3B01G097500 chrUn 97.103 725 19 1 1927 2649 352588555 352589279 0.000000e+00 1221.0
17 TraesCS3B01G097500 chrUn 95.652 46 2 0 741 786 362824252 362824207 1.020000e-09 75.0
18 TraesCS3B01G097500 chrUn 95.652 46 2 0 741 786 406646455 406646410 1.020000e-09 75.0
19 TraesCS3B01G097500 chr1B 96.966 725 21 1 1926 2649 347841592 347840868 0.000000e+00 1216.0
20 TraesCS3B01G097500 chr1B 88.842 708 63 9 1 692 589776513 589775806 0.000000e+00 856.0
21 TraesCS3B01G097500 chr1B 95.455 44 2 0 741 784 626146982 626146939 1.320000e-08 71.3
22 TraesCS3B01G097500 chr2B 89.675 707 53 12 1 692 505509558 505508857 0.000000e+00 883.0
23 TraesCS3B01G097500 chr2B 89.941 676 64 3 993 1666 705348858 705348185 0.000000e+00 869.0
24 TraesCS3B01G097500 chr2B 88.499 713 60 13 1 692 731714719 731714008 0.000000e+00 843.0
25 TraesCS3B01G097500 chr2B 88.352 704 69 7 1 692 530269006 530268304 0.000000e+00 833.0
26 TraesCS3B01G097500 chr2B 87.286 700 82 4 972 1666 705357398 705358095 0.000000e+00 793.0
27 TraesCS3B01G097500 chr6A 89.528 678 55 11 20 694 29156077 29155413 0.000000e+00 845.0
28 TraesCS3B01G097500 chr6A 88.365 679 66 10 20 694 29164423 29163754 0.000000e+00 804.0
29 TraesCS3B01G097500 chr2A 89.333 675 66 5 993 1664 718965666 718964995 0.000000e+00 843.0
30 TraesCS3B01G097500 chr2A 88.376 671 76 2 997 1666 718975861 718976530 0.000000e+00 806.0
31 TraesCS3B01G097500 chr2D 89.069 677 68 5 993 1666 584858573 584857900 0.000000e+00 835.0
32 TraesCS3B01G097500 chr2D 87.714 700 76 7 972 1664 584867281 584867977 0.000000e+00 808.0
33 TraesCS3B01G097500 chr2D 80.978 184 28 6 1454 1635 568229377 568229555 3.570000e-29 139.0
34 TraesCS3B01G097500 chr2D 95.833 48 2 0 741 788 425414456 425414503 7.900000e-11 78.7
35 TraesCS3B01G097500 chr4A 95.652 46 2 0 741 786 714814361 714814316 1.020000e-09 75.0
36 TraesCS3B01G097500 chr1A 92.157 51 4 0 740 790 1143922 1143972 3.680000e-09 73.1
37 TraesCS3B01G097500 chr1A 88.333 60 7 0 734 793 1144081 1144022 3.680000e-09 73.1


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 TraesCS3B01G097500 chr3B 65267785 65270447 2662 True 4918 4918 100.000 1 2663 1 chr3B.!!$R1 2662
1 TraesCS3B01G097500 chr3B 148433643 148434365 722 False 1303 1303 99.170 1927 2649 1 chr3B.!!$F1 722
2 TraesCS3B01G097500 chr3A 53256454 53257551 1097 True 1507 1507 91.607 791 1888 1 chr3A.!!$R1 1097
3 TraesCS3B01G097500 chr3A 60069884 60070576 692 False 806 806 87.732 1 695 1 chr3A.!!$F1 694
4 TraesCS3B01G097500 chr3D 41745678 41746819 1141 True 1461 1461 90.269 815 1927 1 chr3D.!!$R2 1112
5 TraesCS3B01G097500 chr3D 30975749 30976448 699 True 880 880 89.631 1 690 1 chr3D.!!$R1 689
6 TraesCS3B01G097500 chr6B 561263518 561264239 721 False 1230 1230 97.376 1927 2650 1 chr6B.!!$F2 723
7 TraesCS3B01G097500 chr6B 91148380 91149104 724 False 1221 1221 97.103 1927 2649 1 chr6B.!!$F1 722
8 TraesCS3B01G097500 chr6B 671467149 671467843 694 True 808 808 87.874 1 690 1 chr6B.!!$R1 689
9 TraesCS3B01G097500 chr5A 595424232 595424957 725 True 1225 1225 97.107 1927 2652 1 chr5A.!!$R1 725
10 TraesCS3B01G097500 chr4B 39509592 39510313 721 True 1223 1223 97.234 1927 2649 1 chr4B.!!$R1 722
11 TraesCS3B01G097500 chr4B 124921865 124922583 718 False 1221 1221 97.357 1930 2646 1 chr4B.!!$F1 716
12 TraesCS3B01G097500 chr4B 574230280 574230984 704 True 856 856 88.952 1 690 1 chr4B.!!$R2 689
13 TraesCS3B01G097500 chrUn 77421383 77422107 724 True 1221 1221 97.103 1927 2649 1 chrUn.!!$R1 722
14 TraesCS3B01G097500 chrUn 352588555 352589279 724 False 1221 1221 97.103 1927 2649 1 chrUn.!!$F1 722
15 TraesCS3B01G097500 chr1B 347840868 347841592 724 True 1216 1216 96.966 1926 2649 1 chr1B.!!$R1 723
16 TraesCS3B01G097500 chr1B 589775806 589776513 707 True 856 856 88.842 1 692 1 chr1B.!!$R2 691
17 TraesCS3B01G097500 chr2B 505508857 505509558 701 True 883 883 89.675 1 692 1 chr2B.!!$R1 691
18 TraesCS3B01G097500 chr2B 705348185 705348858 673 True 869 869 89.941 993 1666 1 chr2B.!!$R3 673
19 TraesCS3B01G097500 chr2B 731714008 731714719 711 True 843 843 88.499 1 692 1 chr2B.!!$R4 691
20 TraesCS3B01G097500 chr2B 530268304 530269006 702 True 833 833 88.352 1 692 1 chr2B.!!$R2 691
21 TraesCS3B01G097500 chr2B 705357398 705358095 697 False 793 793 87.286 972 1666 1 chr2B.!!$F1 694
22 TraesCS3B01G097500 chr6A 29155413 29156077 664 True 845 845 89.528 20 694 1 chr6A.!!$R1 674
23 TraesCS3B01G097500 chr6A 29163754 29164423 669 True 804 804 88.365 20 694 1 chr6A.!!$R2 674
24 TraesCS3B01G097500 chr2A 718964995 718965666 671 True 843 843 89.333 993 1664 1 chr2A.!!$R1 671
25 TraesCS3B01G097500 chr2A 718975861 718976530 669 False 806 806 88.376 997 1666 1 chr2A.!!$F1 669
26 TraesCS3B01G097500 chr2D 584857900 584858573 673 True 835 835 89.069 993 1666 1 chr2D.!!$R1 673
27 TraesCS3B01G097500 chr2D 584867281 584867977 696 False 808 808 87.714 972 1664 1 chr2D.!!$F3 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
447 475 0.04796 AGGGAAGCCTAGGGGGAAAT 59.952 55.0 11.72 0.0 37.23 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2007 0.619255 TATGAAGGCGGGTGGGAAGA 60.619 55.0 0.0 0.0 0.0 2.87 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
184 201 2.319096 CGTGCGCCGTTTTTCCCTA 61.319 57.895 4.18 0.00 0.00 3.53
219 236 4.760047 GCGCCTGTCGGTGGTGAT 62.760 66.667 0.00 0.00 41.23 3.06
444 472 1.947254 AGAGGGAAGCCTAGGGGGA 60.947 63.158 11.72 0.00 37.23 4.81
447 475 0.047960 AGGGAAGCCTAGGGGGAAAT 59.952 55.000 11.72 0.00 37.23 2.17
459 495 1.203250 GGGGGAAATGGGAGGAAACAA 60.203 52.381 0.00 0.00 0.00 2.83
655 693 2.740447 ACCGACACTAAAAATTCGCCTC 59.260 45.455 0.00 0.00 0.00 4.70
671 714 0.999712 CCTCAAGGGCCTTTTAGGGA 59.000 55.000 26.79 16.64 35.37 4.20
696 739 1.484240 GCTGGAGATGCTCTTACCAGT 59.516 52.381 0.00 0.00 46.55 4.00
697 740 2.093235 GCTGGAGATGCTCTTACCAGTT 60.093 50.000 0.00 0.00 46.55 3.16
698 741 3.529533 CTGGAGATGCTCTTACCAGTTG 58.470 50.000 0.00 0.00 41.91 3.16
699 742 2.237143 TGGAGATGCTCTTACCAGTTGG 59.763 50.000 0.00 0.00 42.17 3.77
700 743 2.284190 GAGATGCTCTTACCAGTTGGC 58.716 52.381 0.00 0.00 39.32 4.52
701 744 1.065126 AGATGCTCTTACCAGTTGGCC 60.065 52.381 0.00 0.00 39.32 5.36
702 745 0.392998 ATGCTCTTACCAGTTGGCCG 60.393 55.000 0.00 0.00 39.32 6.13
703 746 1.745489 GCTCTTACCAGTTGGCCGG 60.745 63.158 0.00 0.00 39.32 6.13
704 747 1.745489 CTCTTACCAGTTGGCCGGC 60.745 63.158 21.18 21.18 39.32 6.13
705 748 2.750237 CTTACCAGTTGGCCGGCC 60.750 66.667 39.40 39.40 39.32 6.13
706 749 4.708386 TTACCAGTTGGCCGGCCG 62.708 66.667 39.00 26.78 39.32 6.13
711 754 4.572571 AGTTGGCCGGCCGAACAA 62.573 61.111 38.65 28.80 39.42 2.83
712 755 3.370231 GTTGGCCGGCCGAACAAT 61.370 61.111 35.74 0.00 39.42 2.71
713 756 3.369400 TTGGCCGGCCGAACAATG 61.369 61.111 39.00 10.02 39.42 2.82
716 759 3.810896 GCCGGCCGAACAATGGTC 61.811 66.667 30.73 0.21 0.00 4.02
719 762 3.174788 GGCCGAACAATGGTCGTC 58.825 61.111 19.82 6.55 0.00 4.20
720 763 2.396157 GGCCGAACAATGGTCGTCC 61.396 63.158 19.82 13.05 0.00 4.79
729 772 2.028484 TGGTCGTCCACTCGTTGC 59.972 61.111 0.00 0.00 39.03 4.17
730 773 2.338984 GGTCGTCCACTCGTTGCT 59.661 61.111 0.00 0.00 0.00 3.91
731 774 1.174078 TGGTCGTCCACTCGTTGCTA 61.174 55.000 0.00 0.00 39.03 3.49
732 775 0.172803 GGTCGTCCACTCGTTGCTAT 59.827 55.000 0.00 0.00 0.00 2.97
733 776 1.269166 GTCGTCCACTCGTTGCTATG 58.731 55.000 0.00 0.00 0.00 2.23
734 777 0.172578 TCGTCCACTCGTTGCTATGG 59.827 55.000 0.00 0.00 0.00 2.74
735 778 0.172578 CGTCCACTCGTTGCTATGGA 59.827 55.000 0.00 0.00 38.94 3.41
737 780 0.172578 TCCACTCGTTGCTATGGACG 59.827 55.000 0.00 0.00 36.30 4.79
738 781 1.421410 CCACTCGTTGCTATGGACGC 61.421 60.000 0.00 0.00 39.03 5.19
739 782 0.735978 CACTCGTTGCTATGGACGCA 60.736 55.000 0.00 0.00 39.03 5.24
740 783 0.458543 ACTCGTTGCTATGGACGCAG 60.459 55.000 0.00 0.00 38.80 5.18
741 784 1.756375 CTCGTTGCTATGGACGCAGC 61.756 60.000 0.00 0.00 38.80 5.25
742 785 1.811266 CGTTGCTATGGACGCAGCT 60.811 57.895 0.00 0.00 38.80 4.24
743 786 1.361668 CGTTGCTATGGACGCAGCTT 61.362 55.000 0.00 0.00 38.80 3.74
744 787 0.375106 GTTGCTATGGACGCAGCTTC 59.625 55.000 0.00 0.00 38.80 3.86
745 788 1.083806 TTGCTATGGACGCAGCTTCG 61.084 55.000 3.63 3.63 38.80 3.79
746 789 2.240500 GCTATGGACGCAGCTTCGG 61.241 63.158 11.19 0.00 34.86 4.30
747 790 1.141881 CTATGGACGCAGCTTCGGT 59.858 57.895 11.19 0.00 0.00 4.69
748 791 1.148157 CTATGGACGCAGCTTCGGTG 61.148 60.000 11.19 0.00 0.00 4.94
757 800 0.169009 CAGCTTCGGTGCCTTAAAGC 59.831 55.000 10.07 10.07 43.44 3.51
758 801 0.250727 AGCTTCGGTGCCTTAAAGCA 60.251 50.000 16.48 0.00 45.08 3.91
767 810 3.518992 TGCCTTAAAGCACCTACCTTT 57.481 42.857 0.00 0.00 38.00 3.11
768 811 4.644163 TGCCTTAAAGCACCTACCTTTA 57.356 40.909 0.00 0.00 38.00 1.85
769 812 5.187621 TGCCTTAAAGCACCTACCTTTAT 57.812 39.130 0.00 0.00 38.00 1.40
770 813 4.947388 TGCCTTAAAGCACCTACCTTTATG 59.053 41.667 0.00 0.00 38.00 1.90
771 814 4.948004 GCCTTAAAGCACCTACCTTTATGT 59.052 41.667 0.00 0.00 35.42 2.29
772 815 5.066117 GCCTTAAAGCACCTACCTTTATGTC 59.934 44.000 0.00 0.00 35.42 3.06
773 816 6.415573 CCTTAAAGCACCTACCTTTATGTCT 58.584 40.000 0.00 0.00 35.42 3.41
774 817 7.562135 CCTTAAAGCACCTACCTTTATGTCTA 58.438 38.462 0.00 0.00 35.42 2.59
775 818 8.211629 CCTTAAAGCACCTACCTTTATGTCTAT 58.788 37.037 0.00 0.00 35.42 1.98
776 819 8.958119 TTAAAGCACCTACCTTTATGTCTATG 57.042 34.615 0.00 0.00 35.42 2.23
777 820 6.808321 AAGCACCTACCTTTATGTCTATGA 57.192 37.500 0.00 0.00 0.00 2.15
778 821 6.163135 AGCACCTACCTTTATGTCTATGAC 57.837 41.667 0.00 0.00 0.00 3.06
779 822 5.661312 AGCACCTACCTTTATGTCTATGACA 59.339 40.000 2.77 2.77 46.90 3.58
788 831 1.583556 TGTCTATGACATGTGGGCCT 58.416 50.000 1.15 0.00 37.67 5.19
789 832 2.758130 TGTCTATGACATGTGGGCCTA 58.242 47.619 1.15 0.00 37.67 3.93
1308 1366 1.949257 CGTCAAGAACACCAAGCCC 59.051 57.895 0.00 0.00 0.00 5.19
1339 1397 1.934220 CTACAGCTTCGACGGCCAGA 61.934 60.000 2.24 0.00 0.00 3.86
1388 1446 2.112297 GTTCACGCAACCCCCTGA 59.888 61.111 0.00 0.00 0.00 3.86
1681 1739 5.112686 GCTAGTGAATTTAGGAGTGACTGG 58.887 45.833 0.00 0.00 0.00 4.00
1696 1754 6.599244 GGAGTGACTGGTTGATTGATTGATTA 59.401 38.462 0.00 0.00 0.00 1.75
1824 1912 2.033424 GTGGAGTTGCTTTTCACTGTCC 59.967 50.000 0.00 0.00 0.00 4.02
1831 1919 5.539955 AGTTGCTTTTCACTGTCCCATAAAT 59.460 36.000 0.00 0.00 0.00 1.40
1869 1968 9.121658 GGAGGACAAATTTCTACTATTAAAGGG 57.878 37.037 0.00 0.00 0.00 3.95
1879 1978 3.964411 ACTATTAAAGGGGAGTTGGTGC 58.036 45.455 0.00 0.00 0.00 5.01
1889 1988 0.602638 GAGTTGGTGCATCACGTCCA 60.603 55.000 0.00 0.00 34.83 4.02
1891 1990 1.147153 TTGGTGCATCACGTCCACA 59.853 52.632 0.00 0.00 34.83 4.17
1897 1996 1.276138 TGCATCACGTCCACATTCTCT 59.724 47.619 0.00 0.00 0.00 3.10
1900 1999 3.189287 GCATCACGTCCACATTCTCTTTT 59.811 43.478 0.00 0.00 0.00 2.27
1901 2000 4.715896 CATCACGTCCACATTCTCTTTTG 58.284 43.478 0.00 0.00 0.00 2.44
2018 2117 9.771534 TTTGAAGAAATGGAAACCGAATTAATT 57.228 25.926 0.00 0.00 0.00 1.40
2308 2412 4.281898 AGTTACTTCCATAACCAAGCGT 57.718 40.909 0.00 0.00 35.95 5.07
2410 2514 3.049206 CACAACCAACAAGTATTTGCCG 58.951 45.455 0.00 0.00 37.85 5.69
2472 2576 3.119245 GCATGGGGTATCGTACATATCGT 60.119 47.826 0.00 0.00 0.00 3.73
2655 2759 4.484872 GCCCACCCCTACGCCTTC 62.485 72.222 0.00 0.00 0.00 3.46
2656 2760 3.006728 CCCACCCCTACGCCTTCA 61.007 66.667 0.00 0.00 0.00 3.02
2657 2761 2.375345 CCCACCCCTACGCCTTCAT 61.375 63.158 0.00 0.00 0.00 2.57
2658 2762 1.607612 CCACCCCTACGCCTTCATT 59.392 57.895 0.00 0.00 0.00 2.57
2659 2763 0.463833 CCACCCCTACGCCTTCATTC 60.464 60.000 0.00 0.00 0.00 2.67
2660 2764 0.541863 CACCCCTACGCCTTCATTCT 59.458 55.000 0.00 0.00 0.00 2.40
2661 2765 1.065418 CACCCCTACGCCTTCATTCTT 60.065 52.381 0.00 0.00 0.00 2.52
2662 2766 1.633945 ACCCCTACGCCTTCATTCTTT 59.366 47.619 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
444 472 1.146152 TCCCGTTGTTTCCTCCCATTT 59.854 47.619 0.00 0.00 0.00 2.32
447 475 0.551879 TTTCCCGTTGTTTCCTCCCA 59.448 50.000 0.00 0.00 0.00 4.37
459 495 1.074951 CAGGAAGCCCTTTTCCCGT 59.925 57.895 1.35 0.00 46.38 5.28
573 609 2.654289 GCCGGTTTGGGCGAAATT 59.346 55.556 1.90 0.00 44.40 1.82
605 641 2.278013 GGTCTAGTCGCGCCTTCG 60.278 66.667 0.00 0.00 39.07 3.79
606 642 2.061182 ATCGGTCTAGTCGCGCCTTC 62.061 60.000 0.00 0.00 0.00 3.46
655 693 1.313091 GCGTCCCTAAAAGGCCCTTG 61.313 60.000 0.00 0.00 32.73 3.61
664 707 2.998480 TCCAGCCGCGTCCCTAAA 60.998 61.111 4.92 0.00 0.00 1.85
671 714 4.521062 GAGCATCTCCAGCCGCGT 62.521 66.667 4.92 0.00 0.00 6.01
695 738 3.370231 ATTGTTCGGCCGGCCAAC 61.370 61.111 42.78 38.02 35.37 3.77
696 739 3.369400 CATTGTTCGGCCGGCCAA 61.369 61.111 42.78 31.37 35.37 4.52
699 742 3.810896 GACCATTGTTCGGCCGGC 61.811 66.667 27.83 21.18 0.00 6.13
700 743 3.496131 CGACCATTGTTCGGCCGG 61.496 66.667 27.83 9.81 0.00 6.13
701 744 2.736682 GACGACCATTGTTCGGCCG 61.737 63.158 22.12 22.12 0.00 6.13
702 745 3.174788 GACGACCATTGTTCGGCC 58.825 61.111 8.50 0.00 0.00 6.13
703 746 1.669760 TGGACGACCATTGTTCGGC 60.670 57.895 8.50 4.63 41.77 5.54
704 747 4.685447 TGGACGACCATTGTTCGG 57.315 55.556 8.50 0.00 41.77 4.30
712 755 1.174078 TAGCAACGAGTGGACGACCA 61.174 55.000 1.37 1.37 44.76 4.02
713 756 0.172803 ATAGCAACGAGTGGACGACC 59.827 55.000 0.00 0.00 37.03 4.79
714 757 1.269166 CATAGCAACGAGTGGACGAC 58.731 55.000 0.00 0.00 37.03 4.34
715 758 0.172578 CCATAGCAACGAGTGGACGA 59.827 55.000 0.00 0.00 37.03 4.20
716 759 0.172578 TCCATAGCAACGAGTGGACG 59.827 55.000 0.00 0.00 35.91 4.79
718 761 0.172578 CGTCCATAGCAACGAGTGGA 59.827 55.000 0.00 0.00 41.29 4.02
719 762 1.421410 GCGTCCATAGCAACGAGTGG 61.421 60.000 0.00 0.00 41.29 4.00
720 763 0.735978 TGCGTCCATAGCAACGAGTG 60.736 55.000 0.00 0.00 42.18 3.51
721 764 0.458543 CTGCGTCCATAGCAACGAGT 60.459 55.000 0.00 0.00 44.67 4.18
722 765 1.756375 GCTGCGTCCATAGCAACGAG 61.756 60.000 0.00 0.00 44.67 4.18
723 766 1.809619 GCTGCGTCCATAGCAACGA 60.810 57.895 0.00 0.00 44.67 3.85
724 767 1.361668 AAGCTGCGTCCATAGCAACG 61.362 55.000 0.00 0.00 44.67 4.10
725 768 0.375106 GAAGCTGCGTCCATAGCAAC 59.625 55.000 4.11 0.00 44.67 4.17
726 769 1.083806 CGAAGCTGCGTCCATAGCAA 61.084 55.000 5.73 0.00 44.67 3.91
727 770 1.519234 CGAAGCTGCGTCCATAGCA 60.519 57.895 5.73 0.00 42.29 3.49
728 771 2.240500 CCGAAGCTGCGTCCATAGC 61.241 63.158 14.34 0.00 40.18 2.97
729 772 1.141881 ACCGAAGCTGCGTCCATAG 59.858 57.895 14.34 0.00 0.00 2.23
730 773 1.153647 CACCGAAGCTGCGTCCATA 60.154 57.895 14.34 0.00 0.00 2.74
731 774 2.434884 CACCGAAGCTGCGTCCAT 60.435 61.111 14.34 0.00 0.00 3.41
735 778 2.725203 TTAAGGCACCGAAGCTGCGT 62.725 55.000 14.34 0.00 35.31 5.24
736 779 1.573829 TTTAAGGCACCGAAGCTGCG 61.574 55.000 7.28 7.28 35.31 5.18
737 780 0.169009 CTTTAAGGCACCGAAGCTGC 59.831 55.000 0.00 0.00 34.17 5.25
738 781 0.169009 GCTTTAAGGCACCGAAGCTG 59.831 55.000 4.44 0.00 40.87 4.24
739 782 0.250727 TGCTTTAAGGCACCGAAGCT 60.251 50.000 8.37 0.00 43.60 3.74
740 783 2.253513 TGCTTTAAGGCACCGAAGC 58.746 52.632 8.37 14.53 43.54 3.86
747 790 3.518992 AAAGGTAGGTGCTTTAAGGCA 57.481 42.857 8.37 8.37 40.15 4.75
748 791 4.948004 ACATAAAGGTAGGTGCTTTAAGGC 59.052 41.667 1.97 1.97 0.00 4.35
749 792 6.415573 AGACATAAAGGTAGGTGCTTTAAGG 58.584 40.000 0.00 0.00 0.00 2.69
750 793 9.046296 CATAGACATAAAGGTAGGTGCTTTAAG 57.954 37.037 0.00 0.00 0.00 1.85
751 794 8.764558 TCATAGACATAAAGGTAGGTGCTTTAA 58.235 33.333 0.00 0.00 0.00 1.52
752 795 8.202137 GTCATAGACATAAAGGTAGGTGCTTTA 58.798 37.037 0.00 0.00 32.09 1.85
753 796 7.048512 GTCATAGACATAAAGGTAGGTGCTTT 58.951 38.462 0.00 0.00 32.09 3.51
754 797 6.156256 TGTCATAGACATAAAGGTAGGTGCTT 59.844 38.462 0.00 0.00 37.67 3.91
755 798 5.661312 TGTCATAGACATAAAGGTAGGTGCT 59.339 40.000 0.00 0.00 37.67 4.40
756 799 5.914033 TGTCATAGACATAAAGGTAGGTGC 58.086 41.667 0.00 0.00 37.67 5.01
769 812 1.583556 AGGCCCACATGTCATAGACA 58.416 50.000 0.00 1.95 46.90 3.41
770 813 2.548920 GCTAGGCCCACATGTCATAGAC 60.549 54.545 0.00 0.00 0.00 2.59
771 814 1.694150 GCTAGGCCCACATGTCATAGA 59.306 52.381 0.00 0.00 0.00 1.98
772 815 1.417517 TGCTAGGCCCACATGTCATAG 59.582 52.381 0.00 0.00 0.00 2.23
773 816 1.506025 TGCTAGGCCCACATGTCATA 58.494 50.000 0.00 0.00 0.00 2.15
774 817 0.848735 ATGCTAGGCCCACATGTCAT 59.151 50.000 0.00 0.00 0.00 3.06
775 818 0.181114 GATGCTAGGCCCACATGTCA 59.819 55.000 0.00 0.00 0.00 3.58
776 819 0.882042 CGATGCTAGGCCCACATGTC 60.882 60.000 0.00 0.00 0.00 3.06
777 820 1.146930 CGATGCTAGGCCCACATGT 59.853 57.895 0.00 0.00 0.00 3.21
778 821 0.882042 GACGATGCTAGGCCCACATG 60.882 60.000 0.00 0.00 0.00 3.21
779 822 1.447643 GACGATGCTAGGCCCACAT 59.552 57.895 0.00 0.00 0.00 3.21
780 823 2.731571 GGACGATGCTAGGCCCACA 61.732 63.158 0.00 0.00 0.00 4.17
781 824 2.109181 GGACGATGCTAGGCCCAC 59.891 66.667 0.00 0.00 0.00 4.61
959 1013 0.251354 TGAGCTGGCTGGATCTTGTC 59.749 55.000 0.00 0.00 0.00 3.18
1308 1366 2.103143 CTGTAGTGCGCCTCGAGG 59.897 66.667 27.83 27.83 38.53 4.63
1317 1375 2.445438 GCCGTCGAAGCTGTAGTGC 61.445 63.158 0.00 0.00 0.00 4.40
1339 1397 2.811101 CCTGATCCGCTCGAAGCT 59.189 61.111 5.53 0.00 39.60 3.74
1362 1420 2.144078 TTGCGTGAACCCCTCCTCA 61.144 57.895 0.00 0.00 0.00 3.86
1622 1680 3.365265 CGGGCTTGCACTTGACCC 61.365 66.667 0.00 0.00 37.19 4.46
1696 1754 4.675510 TTCACTACTGAAAACGACGAAGT 58.324 39.130 0.00 0.00 37.06 3.01
1751 1839 4.538490 AGTGGGGACAATCTACCAACAATA 59.462 41.667 0.00 0.00 46.06 1.90
1780 1868 3.641437 TGATGTAAGTGCAAAAGCACC 57.359 42.857 16.13 3.11 41.19 5.01
1789 1877 4.726416 CAACTCCACAATGATGTAAGTGC 58.274 43.478 0.00 0.00 37.82 4.40
1796 1884 4.682860 GTGAAAAGCAACTCCACAATGATG 59.317 41.667 0.00 0.00 0.00 3.07
1804 1892 2.297701 GGACAGTGAAAAGCAACTCCA 58.702 47.619 0.00 0.00 0.00 3.86
1831 1919 9.320295 AGAAATTTGTCCTCCACCATAATAAAA 57.680 29.630 0.00 0.00 0.00 1.52
1840 1928 9.457436 TTTAATAGTAGAAATTTGTCCTCCACC 57.543 33.333 0.00 0.00 0.00 4.61
1846 1945 9.121658 CTCCCCTTTAATAGTAGAAATTTGTCC 57.878 37.037 0.00 0.00 0.00 4.02
1869 1968 1.298859 GGACGTGATGCACCAACTCC 61.299 60.000 0.00 0.00 0.00 3.85
1879 1978 4.715896 CAAAAGAGAATGTGGACGTGATG 58.284 43.478 0.00 0.00 0.00 3.07
1908 2007 0.619255 TATGAAGGCGGGTGGGAAGA 60.619 55.000 0.00 0.00 0.00 2.87
2018 2117 8.795842 ATGGTTCGGTTTCTAAATATTGTGTA 57.204 30.769 0.00 0.00 0.00 2.90
2060 2160 3.750652 GGTTAACCGAATAAACCGAACCA 59.249 43.478 9.34 0.00 33.98 3.67
2308 2412 1.001974 GGAGTATGTATGCATGCCCGA 59.998 52.381 16.68 0.00 38.28 5.14


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

AutoCloner maintained by Alex Coulton.