Multiple sequence alignment - TraesCS7D01G312800

Loading Multiple Alignment...

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 TraesCS7D01G312800 chr7D 100.000 4475 0 0 1 4475 396437770 396442244 0.000000e+00 8264.0
1 TraesCS7D01G312800 chr7D 96.515 746 15 8 1 740 175915171 175915911 0.000000e+00 1223.0
2 TraesCS7D01G312800 chr7D 80.392 153 28 2 2817 2967 598724563 598724715 1.020000e-21 115.0
3 TraesCS7D01G312800 chr7D 79.452 146 30 0 2822 2967 599066896 599067041 2.200000e-18 104.0
4 TraesCS7D01G312800 chr7D 83.333 90 14 1 650 739 65639397 65639485 1.030000e-11 82.4
5 TraesCS7D01G312800 chr7D 75.460 163 38 2 2810 2970 396389645 396389807 1.330000e-10 78.7
6 TraesCS7D01G312800 chr7B 97.297 1739 43 2 909 2643 399795985 399797723 0.000000e+00 2948.0
7 TraesCS7D01G312800 chr7B 91.162 1403 74 17 2680 4058 399797718 399799094 0.000000e+00 1858.0
8 TraesCS7D01G312800 chr7B 94.634 205 11 0 4055 4259 399799252 399799456 7.220000e-83 318.0
9 TraesCS7D01G312800 chr7B 90.826 218 18 2 4259 4475 399799497 399799713 1.570000e-74 291.0
10 TraesCS7D01G312800 chr7B 94.776 134 6 1 776 908 668203187 668203320 1.630000e-49 207.0
11 TraesCS7D01G312800 chr7B 95.385 130 5 1 785 913 461475692 461475563 5.870000e-49 206.0
12 TraesCS7D01G312800 chr7B 81.938 227 32 8 518 739 585460469 585460691 2.750000e-42 183.0
13 TraesCS7D01G312800 chr7B 80.822 146 28 0 2822 2967 678338580 678338725 1.020000e-21 115.0
14 TraesCS7D01G312800 chr7B 96.000 50 1 1 739 788 399795937 399795985 3.710000e-11 80.5
15 TraesCS7D01G312800 chr7A 91.119 2162 122 33 2345 4475 450009094 450011216 0.000000e+00 2865.0
16 TraesCS7D01G312800 chr7A 92.087 1466 94 12 909 2358 450007577 450009036 0.000000e+00 2045.0
17 TraesCS7D01G312800 chr7A 79.739 153 29 2 2817 2967 691272572 691272724 4.730000e-20 110.0
18 TraesCS7D01G312800 chr7A 79.085 153 30 2 2817 2967 691277633 691277785 2.200000e-18 104.0
19 TraesCS7D01G312800 chr3D 96.110 437 10 5 1 434 22123953 22124385 0.000000e+00 706.0
20 TraesCS7D01G312800 chr3D 90.260 308 13 3 434 740 22124448 22124739 1.950000e-103 387.0
21 TraesCS7D01G312800 chr3D 92.593 54 4 0 3971 4024 538338688 538338741 1.330000e-10 78.7
22 TraesCS7D01G312800 chr2B 94.761 439 18 3 1 434 16774824 16774386 0.000000e+00 678.0
23 TraesCS7D01G312800 chr2B 93.396 318 19 2 434 749 16774323 16774006 1.880000e-128 470.0
24 TraesCS7D01G312800 chr2B 91.573 178 15 0 1020 1197 367775826 367775649 3.460000e-61 246.0
25 TraesCS7D01G312800 chr3A 91.304 437 18 6 1 434 617012131 617011712 3.000000e-161 579.0
26 TraesCS7D01G312800 chr3A 94.839 310 13 2 434 740 617011650 617011341 8.710000e-132 481.0
27 TraesCS7D01G312800 chr5B 95.489 133 4 2 779 910 640272736 640272867 1.260000e-50 211.0
28 TraesCS7D01G312800 chr5B 93.617 141 7 2 776 915 660586826 660586965 4.540000e-50 209.0
29 TraesCS7D01G312800 chr5B 88.571 70 8 0 671 740 700310327 700310258 7.980000e-13 86.1
30 TraesCS7D01G312800 chr5A 94.853 136 5 2 780 914 135538708 135538574 1.260000e-50 211.0
31 TraesCS7D01G312800 chr2D 94.203 138 7 1 777 913 62390414 62390551 4.540000e-50 209.0
32 TraesCS7D01G312800 chr2A 94.815 135 5 2 781 914 413337858 413337991 4.540000e-50 209.0
33 TraesCS7D01G312800 chr4B 93.007 143 8 2 769 910 399133485 399133626 1.630000e-49 207.0
34 TraesCS7D01G312800 chr6B 89.809 157 10 6 760 910 542584712 542584868 3.530000e-46 196.0
35 TraesCS7D01G312800 chr4D 81.283 187 20 11 557 739 386761384 386761559 2.170000e-28 137.0
36 TraesCS7D01G312800 chr5D 78.000 150 32 1 2822 2970 446098880 446098731 4.770000e-15 93.5
37 TraesCS7D01G312800 chr3B 88.235 68 8 0 672 739 205691492 205691559 1.030000e-11 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 TraesCS7D01G312800 chr7D 396437770 396442244 4474 False 8264.0 8264 100.0000 1 4475 1 chr7D.!!$F4 4474
1 TraesCS7D01G312800 chr7D 175915171 175915911 740 False 1223.0 1223 96.5150 1 740 1 chr7D.!!$F2 739
2 TraesCS7D01G312800 chr7B 399795937 399799713 3776 False 1099.1 2948 93.9838 739 4475 5 chr7B.!!$F4 3736
3 TraesCS7D01G312800 chr7A 450007577 450011216 3639 False 2455.0 2865 91.6030 909 4475 2 chr7A.!!$F3 3566
4 TraesCS7D01G312800 chr3D 22123953 22124739 786 False 546.5 706 93.1850 1 740 2 chr3D.!!$F2 739
5 TraesCS7D01G312800 chr2B 16774006 16774824 818 True 574.0 678 94.0785 1 749 2 chr2B.!!$R2 748
6 TraesCS7D01G312800 chr3A 617011341 617012131 790 True 530.0 579 93.0715 1 740 2 chr3A.!!$R1 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
801 878 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.0 0.0 0.0 3.28 F
1199 1276 0.614812 TACCCAGAGCCCCGTAAAAC 59.385 55.000 0.0 0.0 0.0 2.43 F
1546 1623 1.719709 GTTGCCTTATTCGTCGCCC 59.280 57.895 0.0 0.0 0.0 6.13 F
3201 3419 0.944386 CAATAAATCTCCCCGTGGCG 59.056 55.000 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 2935 3.242316 GCAGTTTAACGTGCATACCTAGC 60.242 47.826 12.25 0.0 39.62 3.42 R
2890 3095 0.863799 GTTTGACCCCGTTCGAGTTC 59.136 55.000 0.00 0.0 0.00 3.01 R
3227 3445 0.036875 GTTGAGCCTTGCCACTACCT 59.963 55.000 0.00 0.0 0.00 3.08 R
4068 4466 1.541588 GTGAAGGAAGAATTGCGCCTT 59.458 47.619 4.18 0.0 43.33 4.35 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
530 602 4.762251 CCCAAAACAAACAACCCAAAAAGA 59.238 37.500 0.00 0.00 0.00 2.52
591 664 4.039124 CCAGAAGTTACAACAAAATGGGCT 59.961 41.667 0.00 0.00 0.00 5.19
672 749 0.250124 TCCGACAAACAACCAGCGAT 60.250 50.000 0.00 0.00 0.00 4.58
754 831 1.014352 CCCTTCCTTTTATGTCCGCG 58.986 55.000 0.00 0.00 0.00 6.46
792 869 9.790344 TCTGTTGTACTTATATACTACTCCCTC 57.210 37.037 0.00 0.00 33.57 4.30
793 870 8.930846 TGTTGTACTTATATACTACTCCCTCC 57.069 38.462 0.00 0.00 33.57 4.30
794 871 7.663081 TGTTGTACTTATATACTACTCCCTCCG 59.337 40.741 0.00 0.00 33.57 4.63
795 872 7.321717 TGTACTTATATACTACTCCCTCCGT 57.678 40.000 0.00 0.00 0.00 4.69
796 873 7.390027 TGTACTTATATACTACTCCCTCCGTC 58.610 42.308 0.00 0.00 0.00 4.79
797 874 5.814481 ACTTATATACTACTCCCTCCGTCC 58.186 45.833 0.00 0.00 0.00 4.79
798 875 3.735720 ATATACTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
799 876 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
800 877 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
801 878 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
802 879 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
803 880 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
804 881 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
805 882 1.427753 ACTCCCTCCGTCCCAAAATTT 59.572 47.619 0.00 0.00 0.00 1.82
806 883 2.158370 ACTCCCTCCGTCCCAAAATTTT 60.158 45.455 0.00 0.00 0.00 1.82
807 884 2.897326 CTCCCTCCGTCCCAAAATTTTT 59.103 45.455 0.00 0.00 0.00 1.94
808 885 2.630580 TCCCTCCGTCCCAAAATTTTTG 59.369 45.455 13.76 13.76 0.00 2.44
809 886 2.367241 CCCTCCGTCCCAAAATTTTTGT 59.633 45.455 18.05 0.00 0.00 2.83
810 887 3.554129 CCCTCCGTCCCAAAATTTTTGTC 60.554 47.826 18.05 9.04 0.00 3.18
811 888 3.320826 CCTCCGTCCCAAAATTTTTGTCT 59.679 43.478 18.05 0.00 0.00 3.41
812 889 4.202212 CCTCCGTCCCAAAATTTTTGTCTT 60.202 41.667 18.05 0.00 0.00 3.01
813 890 5.010213 CCTCCGTCCCAAAATTTTTGTCTTA 59.990 40.000 18.05 1.26 0.00 2.10
814 891 6.461788 CCTCCGTCCCAAAATTTTTGTCTTAA 60.462 38.462 18.05 2.01 0.00 1.85
815 892 7.056844 TCCGTCCCAAAATTTTTGTCTTAAT 57.943 32.000 18.05 0.00 0.00 1.40
816 893 7.501844 TCCGTCCCAAAATTTTTGTCTTAATT 58.498 30.769 18.05 0.00 0.00 1.40
817 894 7.988028 TCCGTCCCAAAATTTTTGTCTTAATTT 59.012 29.630 18.05 0.00 35.95 1.82
818 895 8.616942 CCGTCCCAAAATTTTTGTCTTAATTTT 58.383 29.630 18.05 0.00 41.91 1.82
819 896 9.995957 CGTCCCAAAATTTTTGTCTTAATTTTT 57.004 25.926 18.05 0.00 40.23 1.94
842 919 9.878667 TTTTCTAAATACGGATGTATCAAGTCA 57.121 29.630 0.00 0.00 40.42 3.41
843 920 8.867112 TTCTAAATACGGATGTATCAAGTCAC 57.133 34.615 0.00 0.00 40.42 3.67
844 921 7.136772 TCTAAATACGGATGTATCAAGTCACG 58.863 38.462 0.00 0.00 40.42 4.35
845 922 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
846 923 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
847 924 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
848 925 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
849 926 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
850 927 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
851 928 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
852 929 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
853 930 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
854 931 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
857 934 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
858 935 9.578439 GTATCAAGTCACGTTTTAGTATTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
860 937 8.970691 TCAAGTCACGTTTTAGTATTAGGTAC 57.029 34.615 0.00 0.00 0.00 3.34
861 938 8.575589 TCAAGTCACGTTTTAGTATTAGGTACA 58.424 33.333 0.00 0.00 35.67 2.90
862 939 9.362539 CAAGTCACGTTTTAGTATTAGGTACAT 57.637 33.333 0.00 0.00 35.67 2.29
863 940 9.578439 AAGTCACGTTTTAGTATTAGGTACATC 57.422 33.333 0.00 0.00 35.67 3.06
864 941 8.193438 AGTCACGTTTTAGTATTAGGTACATCC 58.807 37.037 0.00 0.00 35.67 3.51
865 942 7.166473 GTCACGTTTTAGTATTAGGTACATCCG 59.834 40.741 0.00 0.00 41.99 4.18
866 943 6.974622 CACGTTTTAGTATTAGGTACATCCGT 59.025 38.462 0.00 0.00 41.99 4.69
867 944 8.128582 CACGTTTTAGTATTAGGTACATCCGTA 58.871 37.037 0.00 0.00 41.99 4.02
868 945 8.850156 ACGTTTTAGTATTAGGTACATCCGTAT 58.150 33.333 0.00 0.00 41.99 3.06
869 946 9.334693 CGTTTTAGTATTAGGTACATCCGTATC 57.665 37.037 0.00 0.00 41.99 2.24
901 978 7.651027 ATCTAAGACAAGAATTTTGGGATGG 57.349 36.000 5.68 0.00 0.00 3.51
902 979 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
903 980 5.990120 AAGACAAGAATTTTGGGATGGAG 57.010 39.130 5.68 0.00 0.00 3.86
904 981 4.347607 AGACAAGAATTTTGGGATGGAGG 58.652 43.478 5.68 0.00 0.00 4.30
905 982 3.444029 ACAAGAATTTTGGGATGGAGGG 58.556 45.455 5.68 0.00 0.00 4.30
906 983 3.077391 ACAAGAATTTTGGGATGGAGGGA 59.923 43.478 5.68 0.00 0.00 4.20
907 984 3.677156 AGAATTTTGGGATGGAGGGAG 57.323 47.619 0.00 0.00 0.00 4.30
920 997 2.304761 TGGAGGGAGTAGTTGCGATTTT 59.695 45.455 0.00 0.00 0.00 1.82
948 1025 4.732285 ATTGCGCGGACTTTATATTCTG 57.268 40.909 8.83 0.00 0.00 3.02
949 1026 2.479837 TGCGCGGACTTTATATTCTGG 58.520 47.619 8.83 0.00 0.00 3.86
1185 1262 1.075525 CGACCCCATCTCCTACCCA 60.076 63.158 0.00 0.00 0.00 4.51
1197 1274 0.979187 CCTACCCAGAGCCCCGTAAA 60.979 60.000 0.00 0.00 0.00 2.01
1199 1276 0.614812 TACCCAGAGCCCCGTAAAAC 59.385 55.000 0.00 0.00 0.00 2.43
1546 1623 1.719709 GTTGCCTTATTCGTCGCCC 59.280 57.895 0.00 0.00 0.00 6.13
2298 2391 9.680315 ATGTCATTTAAAAATTGCCAAATGTTG 57.320 25.926 13.97 0.00 38.75 3.33
2350 2443 6.875972 TTCAGAATAAGGGATATAGGAGGC 57.124 41.667 0.00 0.00 0.00 4.70
2400 2564 4.423732 ACACAAATGTTGTTCAAGCACTC 58.576 39.130 0.00 0.00 43.23 3.51
2730 2935 6.467047 GCTTCTTGTTGTGATGACGATTTATG 59.533 38.462 0.00 0.00 0.00 1.90
2745 2950 4.447724 CGATTTATGCTAGGTATGCACGTT 59.552 41.667 0.00 0.00 43.59 3.99
2781 2986 5.713389 TGAATCACTGAATCCTGCAATTTCT 59.287 36.000 0.00 0.00 0.00 2.52
2792 2997 7.992754 ATCCTGCAATTTCTATTCCATCTAC 57.007 36.000 0.00 0.00 0.00 2.59
2806 3011 6.428083 TTCCATCTACTTTAGGTTGTCACA 57.572 37.500 0.00 0.00 0.00 3.58
2890 3095 7.043192 AGCAAATTTGATGAAGAAACACTTTCG 60.043 33.333 22.31 0.00 44.29 3.46
2970 3175 7.544566 CAGAAACGAGTACATAGTGGTATGTTT 59.455 37.037 3.50 0.00 45.99 2.83
3043 3250 2.571212 GTCTGTCACATGTTGGTTCCA 58.429 47.619 0.00 0.00 0.00 3.53
3082 3289 6.935167 TGAAGCTTTCCTTTTTCTTTTCTGT 58.065 32.000 0.00 0.00 32.78 3.41
3083 3290 7.035612 TGAAGCTTTCCTTTTTCTTTTCTGTC 58.964 34.615 0.00 0.00 32.78 3.51
3084 3291 6.782082 AGCTTTCCTTTTTCTTTTCTGTCT 57.218 33.333 0.00 0.00 0.00 3.41
3096 3306 6.500684 TCTTTTCTGTCTAAACATGGATGC 57.499 37.500 0.00 0.00 34.13 3.91
3097 3307 5.415701 TCTTTTCTGTCTAAACATGGATGCC 59.584 40.000 0.00 0.00 34.13 4.40
3110 3320 3.266510 TGGATGCCTCACACTATTGTC 57.733 47.619 0.00 0.00 31.66 3.18
3201 3419 0.944386 CAATAAATCTCCCCGTGGCG 59.056 55.000 0.00 0.00 0.00 5.69
3291 3509 1.544246 GTATGCAGGCCGTTTCCTTTT 59.456 47.619 0.00 0.00 33.25 2.27
3314 3532 7.962934 TTTGTTCAATAAATTAGCGAATCGG 57.037 32.000 4.35 0.00 0.00 4.18
3353 3573 8.405531 TCTGATGTTATATTTTAGTTTGCTGCC 58.594 33.333 0.00 0.00 0.00 4.85
3359 3579 3.817709 TTTTAGTTTGCTGCCTTGCTT 57.182 38.095 0.00 0.00 0.00 3.91
3426 3646 0.817654 ATGCGGATGACGTTCTCTCA 59.182 50.000 0.00 0.00 46.52 3.27
3466 3686 1.974028 TTACCCATACCTGAAGCCCA 58.026 50.000 0.00 0.00 0.00 5.36
3522 3742 2.445155 GTGCCTTTGGATGGGGGT 59.555 61.111 0.00 0.00 0.00 4.95
3543 3763 0.392060 GACGGTCACCATGTAACCCC 60.392 60.000 2.62 0.00 0.00 4.95
3585 3805 5.865085 AGAACACAAGCAAGTGATAGGTTA 58.135 37.500 14.45 0.00 42.05 2.85
3594 3814 5.823045 AGCAAGTGATAGGTTAAACATAGGC 59.177 40.000 0.00 0.00 0.00 3.93
3636 3867 2.159156 TGCTACCGATCGCAATGTTAGT 60.159 45.455 10.32 1.92 32.40 2.24
3689 3921 3.625853 CTTCTGAAAAGGATTCTCCCCC 58.374 50.000 0.00 0.00 37.19 5.40
3775 4007 4.142609 TGACACTGAGAGCATATTTCCC 57.857 45.455 0.00 0.00 0.00 3.97
3813 4045 8.218441 GCAAAACGTATCTTTTATCCCAAAAAC 58.782 33.333 0.00 0.00 0.00 2.43
3814 4046 9.250624 CAAAACGTATCTTTTATCCCAAAAACA 57.749 29.630 0.00 0.00 0.00 2.83
3947 4184 5.130145 TCATCTTCCTCATTCTTCCTCCTTC 59.870 44.000 0.00 0.00 0.00 3.46
3948 4185 4.693420 TCTTCCTCATTCTTCCTCCTTCT 58.307 43.478 0.00 0.00 0.00 2.85
3949 4186 5.097234 TCTTCCTCATTCTTCCTCCTTCTT 58.903 41.667 0.00 0.00 0.00 2.52
3951 4188 5.428184 TCCTCATTCTTCCTCCTTCTTTC 57.572 43.478 0.00 0.00 0.00 2.62
3952 4189 4.846367 TCCTCATTCTTCCTCCTTCTTTCA 59.154 41.667 0.00 0.00 0.00 2.69
3953 4190 5.490357 TCCTCATTCTTCCTCCTTCTTTCAT 59.510 40.000 0.00 0.00 0.00 2.57
3954 4191 6.012157 TCCTCATTCTTCCTCCTTCTTTCATT 60.012 38.462 0.00 0.00 0.00 2.57
3955 4192 6.318396 CCTCATTCTTCCTCCTTCTTTCATTC 59.682 42.308 0.00 0.00 0.00 2.67
3956 4193 6.782986 TCATTCTTCCTCCTTCTTTCATTCA 58.217 36.000 0.00 0.00 0.00 2.57
3957 4194 7.408543 TCATTCTTCCTCCTTCTTTCATTCAT 58.591 34.615 0.00 0.00 0.00 2.57
3958 4195 7.338703 TCATTCTTCCTCCTTCTTTCATTCATG 59.661 37.037 0.00 0.00 0.00 3.07
4068 4466 3.849911 CATGCGAAGTAGTCAAGAAGGA 58.150 45.455 0.00 0.00 0.00 3.36
4074 4472 1.066787 AGTAGTCAAGAAGGAAGGCGC 60.067 52.381 0.00 0.00 0.00 6.53
4120 4518 1.704628 TGGGCACTTCTTCTGAATGGA 59.295 47.619 0.00 0.00 0.00 3.41
4123 4521 4.018506 TGGGCACTTCTTCTGAATGGATTA 60.019 41.667 0.00 0.00 0.00 1.75
4162 4560 0.183492 AGTGACATGCTGGTGTGGTT 59.817 50.000 0.00 0.00 31.16 3.67
4169 4567 1.550327 TGCTGGTGTGGTTTGAAACA 58.450 45.000 10.53 0.00 0.00 2.83
4322 4762 4.508461 TCGTAAACGACAAGGAAGATGA 57.492 40.909 0.14 0.00 44.22 2.92
4373 4813 0.748367 CTCGTCGGAGATGGTGAGGA 60.748 60.000 0.00 0.00 45.05 3.71
4384 4824 1.682684 GGTGAGGAGAAGGAGGCGA 60.683 63.158 0.00 0.00 0.00 5.54
4451 4891 0.613260 CAGCAAGGTGGGCAGTAGTA 59.387 55.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
359 368 6.586344 TGCCATAGACTTGAGGATAAAGAAG 58.414 40.000 0.00 0.00 0.00 2.85
530 602 1.760480 GGGCCTTTGTGTTGTGGGT 60.760 57.895 0.84 0.00 0.00 4.51
591 664 2.288273 CCCCGCACGGAACAAATAAAAA 60.288 45.455 11.42 0.00 37.50 1.94
654 731 0.110238 CATCGCTGGTTGTTTGTCGG 60.110 55.000 0.00 0.00 0.00 4.79
672 749 6.630071 TCAGTCGAATGAAGTATTGATGACA 58.370 36.000 14.01 0.00 30.37 3.58
783 860 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
784 861 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
785 862 1.073098 AATTTTGGGACGGAGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85
786 863 2.215942 AAATTTTGGGACGGAGGGAG 57.784 50.000 0.00 0.00 0.00 4.30
787 864 2.630580 CAAAAATTTTGGGACGGAGGGA 59.369 45.455 10.41 0.00 0.00 4.20
788 865 2.367241 ACAAAAATTTTGGGACGGAGGG 59.633 45.455 20.79 0.00 0.00 4.30
789 866 3.320826 AGACAAAAATTTTGGGACGGAGG 59.679 43.478 20.79 0.00 0.00 4.30
790 867 4.584327 AGACAAAAATTTTGGGACGGAG 57.416 40.909 20.79 0.00 0.00 4.63
791 868 6.466885 TTAAGACAAAAATTTTGGGACGGA 57.533 33.333 20.79 1.94 0.00 4.69
792 869 7.722795 AATTAAGACAAAAATTTTGGGACGG 57.277 32.000 20.79 0.00 0.00 4.79
793 870 9.995957 AAAAATTAAGACAAAAATTTTGGGACG 57.004 25.926 20.79 0.00 41.86 4.79
816 893 9.878667 TGACTTGATACATCCGTATTTAGAAAA 57.121 29.630 0.00 0.00 38.48 2.29
817 894 9.309516 GTGACTTGATACATCCGTATTTAGAAA 57.690 33.333 0.00 0.00 38.48 2.52
818 895 7.646526 CGTGACTTGATACATCCGTATTTAGAA 59.353 37.037 0.00 0.00 38.48 2.10
819 896 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
820 897 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
821 898 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
822 899 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
823 900 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
824 901 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
825 902 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
826 903 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
827 904 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
828 905 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
831 908 9.577110 CCTAATACTAAAACGTGACTTGATACA 57.423 33.333 0.00 0.00 0.00 2.29
832 909 9.578439 ACCTAATACTAAAACGTGACTTGATAC 57.422 33.333 0.00 0.00 0.00 2.24
834 911 9.578439 GTACCTAATACTAAAACGTGACTTGAT 57.422 33.333 0.00 0.00 0.00 2.57
835 912 8.575589 TGTACCTAATACTAAAACGTGACTTGA 58.424 33.333 0.00 0.00 34.56 3.02
836 913 8.746922 TGTACCTAATACTAAAACGTGACTTG 57.253 34.615 0.00 0.00 34.56 3.16
837 914 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
838 915 8.193438 GGATGTACCTAATACTAAAACGTGACT 58.807 37.037 0.00 0.00 34.56 3.41
839 916 7.166473 CGGATGTACCTAATACTAAAACGTGAC 59.834 40.741 0.00 0.00 34.56 3.67
840 917 7.148086 ACGGATGTACCTAATACTAAAACGTGA 60.148 37.037 0.00 0.00 34.56 4.35
841 918 6.974622 ACGGATGTACCTAATACTAAAACGTG 59.025 38.462 0.00 0.00 34.56 4.49
842 919 7.100458 ACGGATGTACCTAATACTAAAACGT 57.900 36.000 0.00 0.00 34.56 3.99
843 920 9.334693 GATACGGATGTACCTAATACTAAAACG 57.665 37.037 0.00 0.00 34.56 3.60
875 952 8.534496 CCATCCCAAAATTCTTGTCTTAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
876 953 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
877 954 7.413446 TCCATCCCAAAATTCTTGTCTTAGAT 58.587 34.615 0.00 0.00 0.00 1.98
878 955 6.789268 TCCATCCCAAAATTCTTGTCTTAGA 58.211 36.000 0.00 0.00 0.00 2.10
879 956 6.096001 CCTCCATCCCAAAATTCTTGTCTTAG 59.904 42.308 0.00 0.00 0.00 2.18
880 957 5.951747 CCTCCATCCCAAAATTCTTGTCTTA 59.048 40.000 0.00 0.00 0.00 2.10
881 958 4.774200 CCTCCATCCCAAAATTCTTGTCTT 59.226 41.667 0.00 0.00 0.00 3.01
882 959 4.347607 CCTCCATCCCAAAATTCTTGTCT 58.652 43.478 0.00 0.00 0.00 3.41
883 960 3.448660 CCCTCCATCCCAAAATTCTTGTC 59.551 47.826 0.00 0.00 0.00 3.18
884 961 3.077391 TCCCTCCATCCCAAAATTCTTGT 59.923 43.478 0.00 0.00 0.00 3.16
885 962 3.703052 CTCCCTCCATCCCAAAATTCTTG 59.297 47.826 0.00 0.00 0.00 3.02
886 963 3.337909 ACTCCCTCCATCCCAAAATTCTT 59.662 43.478 0.00 0.00 0.00 2.52
887 964 2.929043 ACTCCCTCCATCCCAAAATTCT 59.071 45.455 0.00 0.00 0.00 2.40
888 965 3.388552 ACTCCCTCCATCCCAAAATTC 57.611 47.619 0.00 0.00 0.00 2.17
889 966 3.858638 ACTACTCCCTCCATCCCAAAATT 59.141 43.478 0.00 0.00 0.00 1.82
890 967 3.474920 ACTACTCCCTCCATCCCAAAAT 58.525 45.455 0.00 0.00 0.00 1.82
891 968 2.929301 ACTACTCCCTCCATCCCAAAA 58.071 47.619 0.00 0.00 0.00 2.44
892 969 2.576191 CAACTACTCCCTCCATCCCAAA 59.424 50.000 0.00 0.00 0.00 3.28
893 970 2.196595 CAACTACTCCCTCCATCCCAA 58.803 52.381 0.00 0.00 0.00 4.12
894 971 1.879575 CAACTACTCCCTCCATCCCA 58.120 55.000 0.00 0.00 0.00 4.37
895 972 0.470341 GCAACTACTCCCTCCATCCC 59.530 60.000 0.00 0.00 0.00 3.85
896 973 0.105039 CGCAACTACTCCCTCCATCC 59.895 60.000 0.00 0.00 0.00 3.51
897 974 1.112113 TCGCAACTACTCCCTCCATC 58.888 55.000 0.00 0.00 0.00 3.51
898 975 1.794714 ATCGCAACTACTCCCTCCAT 58.205 50.000 0.00 0.00 0.00 3.41
899 976 1.568504 AATCGCAACTACTCCCTCCA 58.431 50.000 0.00 0.00 0.00 3.86
900 977 2.693267 AAATCGCAACTACTCCCTCC 57.307 50.000 0.00 0.00 0.00 4.30
901 978 3.863041 AGAAAATCGCAACTACTCCCTC 58.137 45.455 0.00 0.00 0.00 4.30
902 979 3.983044 AGAAAATCGCAACTACTCCCT 57.017 42.857 0.00 0.00 0.00 4.20
903 980 5.372547 AAAAGAAAATCGCAACTACTCCC 57.627 39.130 0.00 0.00 0.00 4.30
904 981 8.850452 CAATAAAAAGAAAATCGCAACTACTCC 58.150 33.333 0.00 0.00 0.00 3.85
905 982 8.365938 GCAATAAAAAGAAAATCGCAACTACTC 58.634 33.333 0.00 0.00 0.00 2.59
906 983 7.060633 CGCAATAAAAAGAAAATCGCAACTACT 59.939 33.333 0.00 0.00 0.00 2.57
907 984 7.157699 CGCAATAAAAAGAAAATCGCAACTAC 58.842 34.615 0.00 0.00 0.00 2.73
920 997 3.907894 AAAGTCCGCGCAATAAAAAGA 57.092 38.095 8.75 0.00 0.00 2.52
949 1026 2.637947 GAGGGCTTTGGAGATCAACTC 58.362 52.381 0.00 0.00 44.24 3.01
1156 1233 2.280592 GGGGTCGTCGTTGTTGCT 60.281 61.111 0.00 0.00 0.00 3.91
1161 1238 1.153628 GGAGATGGGGTCGTCGTTG 60.154 63.158 0.00 0.00 34.23 4.10
1162 1239 0.033796 TAGGAGATGGGGTCGTCGTT 60.034 55.000 0.00 0.00 34.23 3.85
1164 1241 1.453762 GGTAGGAGATGGGGTCGTCG 61.454 65.000 0.00 0.00 34.23 5.12
1185 1262 1.595357 CGAGGTTTTACGGGGCTCT 59.405 57.895 0.00 0.00 0.00 4.09
1197 1274 2.047443 GGAGAGACCGAGCGAGGTT 61.047 63.158 7.56 0.00 46.09 3.50
1199 1276 3.213402 GGGAGAGACCGAGCGAGG 61.213 72.222 0.00 0.00 40.11 4.63
1910 1993 6.183360 ACGAACCTTAGAGATCAATAGCATGT 60.183 38.462 0.00 0.00 0.00 3.21
2083 2172 5.473504 ACTGGTTACATTGCTACTTTTCCTG 59.526 40.000 0.00 0.00 0.00 3.86
2174 2263 7.702348 GCAAATTAAGTACACATCCAGATTTCC 59.298 37.037 0.00 0.00 0.00 3.13
2298 2391 4.773323 AAGCTTAGTTTCAGTGAATGCC 57.227 40.909 6.36 0.00 0.00 4.40
2350 2443 8.661257 CACTAATCGGTATCTAGACACTCTATG 58.339 40.741 0.34 0.00 0.00 2.23
2400 2564 9.347934 GTTCTGATATCCATTACTATGTCTTCG 57.652 37.037 0.00 0.00 0.00 3.79
2516 2680 5.869888 GTGAATCGTCAGAATAGACCAAACT 59.130 40.000 0.00 0.00 35.07 2.66
2678 2882 7.067008 AGCCCATGTATATAAAAGTGTCAACAC 59.933 37.037 5.11 5.11 46.77 3.32
2679 2883 7.066887 CAGCCCATGTATATAAAAGTGTCAACA 59.933 37.037 0.00 0.00 0.00 3.33
2730 2935 3.242316 GCAGTTTAACGTGCATACCTAGC 60.242 47.826 12.25 0.00 39.62 3.42
2745 2950 5.213891 TCAGTGATTCACTCTGCAGTTTA 57.786 39.130 16.39 0.00 43.43 2.01
2781 2986 8.141298 TGTGACAACCTAAAGTAGATGGAATA 57.859 34.615 0.00 0.00 0.00 1.75
2792 2997 7.925993 TCTATGTTTGTTGTGACAACCTAAAG 58.074 34.615 24.05 13.95 45.01 1.85
2806 3011 5.319043 TCCAAGAACCCTCTATGTTTGTT 57.681 39.130 0.00 0.00 0.00 2.83
2890 3095 0.863799 GTTTGACCCCGTTCGAGTTC 59.136 55.000 0.00 0.00 0.00 3.01
3023 3230 2.571212 TGGAACCAACATGTGACAGAC 58.429 47.619 0.00 0.00 0.00 3.51
3082 3289 3.264193 AGTGTGAGGCATCCATGTTTAGA 59.736 43.478 0.00 0.00 0.00 2.10
3083 3290 3.614092 AGTGTGAGGCATCCATGTTTAG 58.386 45.455 0.00 0.00 0.00 1.85
3084 3291 3.719268 AGTGTGAGGCATCCATGTTTA 57.281 42.857 0.00 0.00 0.00 2.01
3096 3306 5.910614 TCAGATCATGACAATAGTGTGAGG 58.089 41.667 0.00 0.00 38.41 3.86
3097 3307 6.803642 TCTCAGATCATGACAATAGTGTGAG 58.196 40.000 0.00 10.96 38.41 3.51
3201 3419 2.358267 CAGATCTGCAGGGCTTTTGATC 59.642 50.000 15.13 7.03 0.00 2.92
3227 3445 0.036875 GTTGAGCCTTGCCACTACCT 59.963 55.000 0.00 0.00 0.00 3.08
3228 3446 0.036875 AGTTGAGCCTTGCCACTACC 59.963 55.000 0.00 0.00 0.00 3.18
3291 3509 7.079182 ACCGATTCGCTAATTTATTGAACAA 57.921 32.000 0.00 0.00 0.00 2.83
3340 3560 5.229423 CAATAAGCAAGGCAGCAAACTAAA 58.771 37.500 4.78 0.00 36.85 1.85
3353 3573 4.836125 AACAGTGTGACCAATAAGCAAG 57.164 40.909 0.00 0.00 0.00 4.01
3359 3579 3.137544 ACCCTGAAACAGTGTGACCAATA 59.862 43.478 0.00 0.00 0.00 1.90
3426 3646 1.118838 CCTTCCGCATCCTCTCTTCT 58.881 55.000 0.00 0.00 0.00 2.85
3466 3686 0.108662 TCTGCTCGTCATCACGCAAT 60.109 50.000 0.00 0.00 46.28 3.56
3522 3742 1.270947 GGGTTACATGGTGACCGTCAA 60.271 52.381 1.88 0.00 42.17 3.18
3543 3763 6.036844 GTGTTCTTATAACTAGAAAAGGGCCG 59.963 42.308 0.00 0.00 33.71 6.13
3585 3805 1.141053 GACCCTCCATCGCCTATGTTT 59.859 52.381 0.00 0.00 33.34 2.83
3594 3814 0.531532 GAGTGCATGACCCTCCATCG 60.532 60.000 0.00 0.00 0.00 3.84
3644 3875 6.654582 AGGGCATCATTGTTAAAAATGGAAAC 59.345 34.615 16.67 6.91 37.98 2.78
3647 3878 6.213195 AGAAGGGCATCATTGTTAAAAATGGA 59.787 34.615 16.67 5.91 37.98 3.41
3648 3879 6.314400 CAGAAGGGCATCATTGTTAAAAATGG 59.686 38.462 16.67 4.75 37.98 3.16
3649 3880 7.098477 TCAGAAGGGCATCATTGTTAAAAATG 58.902 34.615 11.58 11.58 38.63 2.32
3650 3881 7.243604 TCAGAAGGGCATCATTGTTAAAAAT 57.756 32.000 0.00 0.00 0.00 1.82
3689 3921 1.543802 TCGCTAGGTGCCCAAAATTTG 59.456 47.619 0.00 0.00 38.78 2.32
3707 3939 4.036852 TGACTAGCCAACTCATAGACATCG 59.963 45.833 0.00 0.00 0.00 3.84
3775 4007 7.672983 AGATACGTTTTGCCATTATAGGATG 57.327 36.000 0.00 0.00 0.00 3.51
3866 4100 7.184862 AGGTCAAGTTGATTTGAGGGATTAAT 58.815 34.615 9.18 0.00 37.72 1.40
3947 4184 3.663995 TTGGCCACACATGAATGAAAG 57.336 42.857 3.88 0.00 0.00 2.62
3948 4185 5.187381 ACATATTGGCCACACATGAATGAAA 59.813 36.000 21.49 0.00 0.00 2.69
3949 4186 4.710865 ACATATTGGCCACACATGAATGAA 59.289 37.500 21.49 0.00 0.00 2.57
3951 4188 4.613944 GACATATTGGCCACACATGAATG 58.386 43.478 21.49 10.80 0.00 2.67
3952 4189 4.924305 GACATATTGGCCACACATGAAT 57.076 40.909 21.49 8.00 0.00 2.57
4024 4261 4.857871 GCATGTGCGTTCAATAAGACTA 57.142 40.909 0.00 0.00 0.00 2.59
4068 4466 1.541588 GTGAAGGAAGAATTGCGCCTT 59.458 47.619 4.18 0.00 43.33 4.35
4074 4472 3.187227 CGTGACTGGTGAAGGAAGAATTG 59.813 47.826 0.00 0.00 0.00 2.32
4120 4518 8.869109 CACTAGGAGAAGGAAGATGAGAATAAT 58.131 37.037 0.00 0.00 0.00 1.28
4123 4521 6.323739 GTCACTAGGAGAAGGAAGATGAGAAT 59.676 42.308 0.00 0.00 0.00 2.40
4162 4560 3.810386 TCCGATGATTCGTTGTGTTTCAA 59.190 39.130 0.00 0.00 43.97 2.69
4169 4567 2.201732 CCGATTCCGATGATTCGTTGT 58.798 47.619 6.24 0.00 43.97 3.32
4272 4670 3.391382 CTTCTCCCCGGCGTTCCT 61.391 66.667 6.01 0.00 0.00 3.36
4373 4813 1.684386 CCTCAGCATCGCCTCCTTCT 61.684 60.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.