Multiple sequence alignment - TraesCS2A01G358800

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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 TraesCS2A01G358800 chr2A 100.000 8506 0 0 1 8506 602783725 602775220 0.000000e+00 15708.0
1 TraesCS2A01G358800 chr2A 88.549 2716 282 20 930 3626 277166316 277163611 0.000000e+00 3265.0
2 TraesCS2A01G358800 chr2A 85.036 695 77 8 3090 3769 9349829 9350511 0.000000e+00 682.0
3 TraesCS2A01G358800 chr6B 94.211 4958 224 27 915 5835 658236133 658241064 0.000000e+00 7507.0
4 TraesCS2A01G358800 chr6B 84.387 538 49 19 925 1430 63169523 63170057 5.930000e-136 496.0
5 TraesCS2A01G358800 chr2D 97.791 2671 33 8 5836 8504 459823877 459821231 0.000000e+00 4582.0
6 TraesCS2A01G358800 chr2D 84.541 925 138 3 5838 6758 459814289 459813366 0.000000e+00 911.0
7 TraesCS2A01G358800 chr3B 92.262 2688 190 6 1095 3776 803416074 803418749 0.000000e+00 3795.0
8 TraesCS2A01G358800 chr3B 91.735 2686 199 9 1095 3776 803462940 803465606 0.000000e+00 3709.0
9 TraesCS2A01G358800 chr3B 87.431 2705 314 17 931 3626 132612352 132609665 0.000000e+00 3088.0
10 TraesCS2A01G358800 chr3B 93.712 1829 112 3 4010 5836 470501788 470499961 0.000000e+00 2737.0
11 TraesCS2A01G358800 chr3B 98.072 830 14 2 1 830 145707092 145706265 0.000000e+00 1443.0
12 TraesCS2A01G358800 chr7B 91.468 2602 211 7 1100 3698 721903838 721901245 0.000000e+00 3565.0
13 TraesCS2A01G358800 chr7B 98.075 831 15 1 1 831 256499260 256498431 0.000000e+00 1445.0
14 TraesCS2A01G358800 chr7D 88.849 2807 276 18 974 3762 370132331 370135118 0.000000e+00 3415.0
15 TraesCS2A01G358800 chr7D 88.648 2625 277 17 1019 3631 31044379 31041764 0.000000e+00 3177.0
16 TraesCS2A01G358800 chr5A 88.476 2716 284 20 930 3626 692673218 692670513 0.000000e+00 3254.0
17 TraesCS2A01G358800 chr4B 88.524 2710 282 20 927 3617 251475767 251478466 0.000000e+00 3254.0
18 TraesCS2A01G358800 chr3D 88.506 2697 276 25 962 3631 12710096 12707407 0.000000e+00 3232.0
19 TraesCS2A01G358800 chr3D 83.065 124 19 2 927 1049 262687887 262688009 2.510000e-20 111.0
20 TraesCS2A01G358800 chr3D 97.368 38 1 0 3706 3743 220963681 220963718 1.980000e-06 65.8
21 TraesCS2A01G358800 chr5D 94.031 1843 108 2 3994 5835 473411989 473413830 0.000000e+00 2793.0
22 TraesCS2A01G358800 chr6A 93.676 1850 114 3 3989 5836 599251390 599249542 0.000000e+00 2765.0
23 TraesCS2A01G358800 chr6A 93.804 1840 111 3 3999 5836 607387205 607385367 0.000000e+00 2763.0
24 TraesCS2A01G358800 chr6A 93.638 1839 114 3 3999 5835 1788332 1790169 0.000000e+00 2745.0
25 TraesCS2A01G358800 chr6A 98.315 831 11 3 1 830 116668303 116669131 0.000000e+00 1454.0
26 TraesCS2A01G358800 chr3A 93.395 1847 119 3 3989 5833 19332690 19334535 0.000000e+00 2732.0
27 TraesCS2A01G358800 chr5B 87.595 2362 266 17 930 3272 355960577 355958224 0.000000e+00 2713.0
28 TraesCS2A01G358800 chr5B 93.186 1849 120 6 3989 5835 461585901 461584057 0.000000e+00 2712.0
29 TraesCS2A01G358800 chr5B 97.867 844 15 3 1 844 617212007 617211167 0.000000e+00 1456.0
30 TraesCS2A01G358800 chr7A 93.046 1855 125 4 3980 5833 37141039 37142890 0.000000e+00 2708.0
31 TraesCS2A01G358800 chr7A 92.025 163 13 0 3500 3662 37140597 37140759 6.640000e-56 230.0
32 TraesCS2A01G358800 chr1D 85.380 2647 340 30 1141 3759 160523874 160521247 0.000000e+00 2700.0
33 TraesCS2A01G358800 chr4A 85.789 1710 212 12 930 2609 712494807 712493099 0.000000e+00 1783.0
34 TraesCS2A01G358800 chr4A 98.319 833 13 1 1 833 96043069 96043900 0.000000e+00 1459.0
35 TraesCS2A01G358800 chr4A 98.072 830 14 2 2 831 632803001 632802174 0.000000e+00 1443.0
36 TraesCS2A01G358800 chr1B 98.795 830 8 2 1 830 510844709 510843882 0.000000e+00 1476.0
37 TraesCS2A01G358800 chr1A 98.075 831 15 1 1 831 564067434 564066605 0.000000e+00 1445.0
38 TraesCS2A01G358800 chr2B 97.844 835 14 4 1 835 465771333 465770503 0.000000e+00 1439.0
39 TraesCS2A01G358800 chr2B 88.736 1092 103 6 5836 6923 541092948 541091873 0.000000e+00 1317.0
40 TraesCS2A01G358800 chr2B 81.608 1169 123 53 6921 8069 541091845 541090749 0.000000e+00 883.0
41 TraesCS2A01G358800 chr2B 82.119 755 127 7 6008 6758 541018974 541018224 2.590000e-179 640.0
42 TraesCS2A01G358800 chr2B 80.871 528 77 12 6931 7443 541018082 541017564 2.230000e-105 394.0
43 TraesCS2A01G358800 chr2B 79.518 332 36 19 7746 8045 541017078 541016747 3.110000e-49 207.0
44 TraesCS2A01G358800 chr2B 95.868 121 4 1 8364 8483 541090339 541090219 2.420000e-45 195.0
45 TraesCS2A01G358800 chrUn 90.765 823 60 5 2958 3776 325197000 325197810 0.000000e+00 1085.0
46 TraesCS2A01G358800 chrUn 88.525 793 62 9 2990 3779 451885751 451884985 0.000000e+00 933.0


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 TraesCS2A01G358800 chr2A 602775220 602783725 8505 True 15708.000000 15708 100.000000 1 8506 1 chr2A.!!$R2 8505
1 TraesCS2A01G358800 chr2A 277163611 277166316 2705 True 3265.000000 3265 88.549000 930 3626 1 chr2A.!!$R1 2696
2 TraesCS2A01G358800 chr2A 9349829 9350511 682 False 682.000000 682 85.036000 3090 3769 1 chr2A.!!$F1 679
3 TraesCS2A01G358800 chr6B 658236133 658241064 4931 False 7507.000000 7507 94.211000 915 5835 1 chr6B.!!$F2 4920
4 TraesCS2A01G358800 chr6B 63169523 63170057 534 False 496.000000 496 84.387000 925 1430 1 chr6B.!!$F1 505
5 TraesCS2A01G358800 chr2D 459821231 459823877 2646 True 4582.000000 4582 97.791000 5836 8504 1 chr2D.!!$R2 2668
6 TraesCS2A01G358800 chr2D 459813366 459814289 923 True 911.000000 911 84.541000 5838 6758 1 chr2D.!!$R1 920
7 TraesCS2A01G358800 chr3B 803416074 803418749 2675 False 3795.000000 3795 92.262000 1095 3776 1 chr3B.!!$F1 2681
8 TraesCS2A01G358800 chr3B 803462940 803465606 2666 False 3709.000000 3709 91.735000 1095 3776 1 chr3B.!!$F2 2681
9 TraesCS2A01G358800 chr3B 132609665 132612352 2687 True 3088.000000 3088 87.431000 931 3626 1 chr3B.!!$R1 2695
10 TraesCS2A01G358800 chr3B 470499961 470501788 1827 True 2737.000000 2737 93.712000 4010 5836 1 chr3B.!!$R3 1826
11 TraesCS2A01G358800 chr3B 145706265 145707092 827 True 1443.000000 1443 98.072000 1 830 1 chr3B.!!$R2 829
12 TraesCS2A01G358800 chr7B 721901245 721903838 2593 True 3565.000000 3565 91.468000 1100 3698 1 chr7B.!!$R2 2598
13 TraesCS2A01G358800 chr7B 256498431 256499260 829 True 1445.000000 1445 98.075000 1 831 1 chr7B.!!$R1 830
14 TraesCS2A01G358800 chr7D 370132331 370135118 2787 False 3415.000000 3415 88.849000 974 3762 1 chr7D.!!$F1 2788
15 TraesCS2A01G358800 chr7D 31041764 31044379 2615 True 3177.000000 3177 88.648000 1019 3631 1 chr7D.!!$R1 2612
16 TraesCS2A01G358800 chr5A 692670513 692673218 2705 True 3254.000000 3254 88.476000 930 3626 1 chr5A.!!$R1 2696
17 TraesCS2A01G358800 chr4B 251475767 251478466 2699 False 3254.000000 3254 88.524000 927 3617 1 chr4B.!!$F1 2690
18 TraesCS2A01G358800 chr3D 12707407 12710096 2689 True 3232.000000 3232 88.506000 962 3631 1 chr3D.!!$R1 2669
19 TraesCS2A01G358800 chr5D 473411989 473413830 1841 False 2793.000000 2793 94.031000 3994 5835 1 chr5D.!!$F1 1841
20 TraesCS2A01G358800 chr6A 599249542 599251390 1848 True 2765.000000 2765 93.676000 3989 5836 1 chr6A.!!$R1 1847
21 TraesCS2A01G358800 chr6A 607385367 607387205 1838 True 2763.000000 2763 93.804000 3999 5836 1 chr6A.!!$R2 1837
22 TraesCS2A01G358800 chr6A 1788332 1790169 1837 False 2745.000000 2745 93.638000 3999 5835 1 chr6A.!!$F1 1836
23 TraesCS2A01G358800 chr6A 116668303 116669131 828 False 1454.000000 1454 98.315000 1 830 1 chr6A.!!$F2 829
24 TraesCS2A01G358800 chr3A 19332690 19334535 1845 False 2732.000000 2732 93.395000 3989 5833 1 chr3A.!!$F1 1844
25 TraesCS2A01G358800 chr5B 355958224 355960577 2353 True 2713.000000 2713 87.595000 930 3272 1 chr5B.!!$R1 2342
26 TraesCS2A01G358800 chr5B 461584057 461585901 1844 True 2712.000000 2712 93.186000 3989 5835 1 chr5B.!!$R2 1846
27 TraesCS2A01G358800 chr5B 617211167 617212007 840 True 1456.000000 1456 97.867000 1 844 1 chr5B.!!$R3 843
28 TraesCS2A01G358800 chr7A 37140597 37142890 2293 False 1469.000000 2708 92.535500 3500 5833 2 chr7A.!!$F1 2333
29 TraesCS2A01G358800 chr1D 160521247 160523874 2627 True 2700.000000 2700 85.380000 1141 3759 1 chr1D.!!$R1 2618
30 TraesCS2A01G358800 chr4A 712493099 712494807 1708 True 1783.000000 1783 85.789000 930 2609 1 chr4A.!!$R2 1679
31 TraesCS2A01G358800 chr4A 96043069 96043900 831 False 1459.000000 1459 98.319000 1 833 1 chr4A.!!$F1 832
32 TraesCS2A01G358800 chr4A 632802174 632803001 827 True 1443.000000 1443 98.072000 2 831 1 chr4A.!!$R1 829
33 TraesCS2A01G358800 chr1B 510843882 510844709 827 True 1476.000000 1476 98.795000 1 830 1 chr1B.!!$R1 829
34 TraesCS2A01G358800 chr1A 564066605 564067434 829 True 1445.000000 1445 98.075000 1 831 1 chr1A.!!$R1 830
35 TraesCS2A01G358800 chr2B 465770503 465771333 830 True 1439.000000 1439 97.844000 1 835 1 chr2B.!!$R1 834
36 TraesCS2A01G358800 chr2B 541090219 541092948 2729 True 798.333333 1317 88.737333 5836 8483 3 chr2B.!!$R3 2647
37 TraesCS2A01G358800 chr2B 541016747 541018974 2227 True 413.666667 640 80.836000 6008 8045 3 chr2B.!!$R2 2037
38 TraesCS2A01G358800 chrUn 325197000 325197810 810 False 1085.000000 1085 90.765000 2958 3776 1 chrUn.!!$F1 818
39 TraesCS2A01G358800 chrUn 451884985 451885751 766 True 933.000000 933 88.525000 2990 3779 1 chrUn.!!$R1 789

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
865 867 0.179034 AATCTGCTTCCCCTCGATGC 60.179 55.000 0.00 0.00 41.06 3.91 F
1217 1290 0.249489 CATACAGTGCTCCGCCTACC 60.249 60.000 0.00 0.00 0.00 3.18 F
2234 2319 0.749091 CATGGACATCGGTGCCACAT 60.749 55.000 13.02 4.49 35.40 3.21 F
3586 3718 0.403655 TTGCCTAACCATGGTGCAGA 59.596 50.000 23.01 14.22 32.88 4.26 F
4019 4271 0.250295 CTTCTCCAACACCTTCGCCA 60.250 55.000 0.00 0.00 0.00 5.69 F
5159 5413 0.041839 GCATTCTGCGCTATGTTCGG 60.042 55.000 9.73 0.00 31.71 4.30 F
5192 5446 0.685458 ATGGTCTCCATTTGCAGCCC 60.685 55.000 0.00 0.00 42.23 5.19 F
5793 6050 1.134699 ACATGACAGCCGTATCCAGTG 60.135 52.381 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2247 0.473886 AACCCAGGCTCCTGTGTAGT 60.474 55.000 14.27 4.23 42.15 2.73 R
3069 3187 0.608130 ACTGCACCGTTCTGCTGATA 59.392 50.000 9.76 0.00 38.94 2.15 R
3967 4177 0.249868 CGAGTCCACAAACTCTGCCA 60.250 55.000 2.89 0.00 42.90 4.92 R
4514 4766 0.396435 CTGGGGGCTGACGCATATAA 59.604 55.000 0.00 0.00 38.10 0.98 R
5192 5446 1.021390 AGATCAAACCAGAAGCCGCG 61.021 55.000 0.00 0.00 0.00 6.46 R
6091 6348 0.409092 TAGACCACACGGAAGGGGTA 59.591 55.000 0.00 0.00 40.46 3.69 R
6432 6692 2.279120 GCGTCAGCCTCCATCGAG 60.279 66.667 0.00 0.00 37.42 4.04 R
7582 7890 1.279271 CAGTTAGCCTTACCACAGCCT 59.721 52.381 0.00 0.00 0.00 4.58 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
833 835 0.532862 GTACATGACCCCATCAGGCG 60.533 60.000 0.00 0.00 43.13 5.52
834 836 2.324014 TACATGACCCCATCAGGCGC 62.324 60.000 0.00 0.00 43.13 6.53
835 837 3.092511 ATGACCCCATCAGGCGCT 61.093 61.111 7.64 0.00 41.91 5.92
836 838 3.112205 ATGACCCCATCAGGCGCTC 62.112 63.158 7.64 0.00 41.91 5.03
837 839 3.474570 GACCCCATCAGGCGCTCT 61.475 66.667 7.64 0.00 0.00 4.09
838 840 2.041922 ACCCCATCAGGCGCTCTA 60.042 61.111 7.64 0.00 0.00 2.43
839 841 2.370647 GACCCCATCAGGCGCTCTAC 62.371 65.000 7.64 0.00 0.00 2.59
840 842 2.434843 CCCCATCAGGCGCTCTACA 61.435 63.158 7.64 0.00 0.00 2.74
841 843 1.227380 CCCATCAGGCGCTCTACAC 60.227 63.158 7.64 0.00 0.00 2.90
842 844 1.227380 CCATCAGGCGCTCTACACC 60.227 63.158 7.64 0.00 0.00 4.16
843 845 1.589993 CATCAGGCGCTCTACACCG 60.590 63.158 7.64 0.00 0.00 4.94
844 846 2.786495 ATCAGGCGCTCTACACCGG 61.786 63.158 7.64 0.00 0.00 5.28
845 847 4.514577 CAGGCGCTCTACACCGGG 62.515 72.222 7.64 0.00 0.00 5.73
846 848 4.753662 AGGCGCTCTACACCGGGA 62.754 66.667 7.64 0.00 0.00 5.14
847 849 3.766691 GGCGCTCTACACCGGGAA 61.767 66.667 7.64 0.00 0.00 3.97
848 850 2.499685 GCGCTCTACACCGGGAAT 59.500 61.111 6.32 0.00 0.00 3.01
849 851 1.591863 GCGCTCTACACCGGGAATC 60.592 63.158 6.32 0.00 0.00 2.52
850 852 2.017559 GCGCTCTACACCGGGAATCT 62.018 60.000 6.32 0.00 0.00 2.40
851 853 0.249073 CGCTCTACACCGGGAATCTG 60.249 60.000 6.32 0.00 0.00 2.90
852 854 0.530870 GCTCTACACCGGGAATCTGC 60.531 60.000 6.32 0.00 0.00 4.26
853 855 1.115467 CTCTACACCGGGAATCTGCT 58.885 55.000 6.32 0.00 0.00 4.24
854 856 1.482593 CTCTACACCGGGAATCTGCTT 59.517 52.381 6.32 0.00 0.00 3.91
855 857 1.480954 TCTACACCGGGAATCTGCTTC 59.519 52.381 6.32 0.00 0.00 3.86
861 863 4.865865 GGAATCTGCTTCCCCTCG 57.134 61.111 0.00 0.00 46.81 4.63
862 864 2.212327 GGAATCTGCTTCCCCTCGA 58.788 57.895 0.00 0.00 46.81 4.04
863 865 0.761802 GGAATCTGCTTCCCCTCGAT 59.238 55.000 0.00 0.00 46.81 3.59
864 866 1.542108 GGAATCTGCTTCCCCTCGATG 60.542 57.143 0.00 0.00 46.81 3.84
865 867 0.179034 AATCTGCTTCCCCTCGATGC 60.179 55.000 0.00 0.00 41.06 3.91
866 868 1.340399 ATCTGCTTCCCCTCGATGCA 61.340 55.000 0.00 0.00 46.33 3.96
867 869 1.147824 CTGCTTCCCCTCGATGCAT 59.852 57.895 0.00 0.00 46.98 3.96
868 870 0.883814 CTGCTTCCCCTCGATGCATC 60.884 60.000 17.10 17.10 46.98 3.91
869 871 1.340399 TGCTTCCCCTCGATGCATCT 61.340 55.000 23.73 0.00 44.35 2.90
870 872 0.883814 GCTTCCCCTCGATGCATCTG 60.884 60.000 23.73 16.77 40.52 2.90
871 873 0.250209 CTTCCCCTCGATGCATCTGG 60.250 60.000 23.73 22.50 0.00 3.86
872 874 2.281345 CCCCTCGATGCATCTGGC 60.281 66.667 23.73 0.00 45.13 4.85
873 875 2.815945 CCCCTCGATGCATCTGGCT 61.816 63.158 23.73 0.00 45.15 4.75
874 876 1.475169 CCCCTCGATGCATCTGGCTA 61.475 60.000 23.73 4.12 45.15 3.93
875 877 0.320247 CCCTCGATGCATCTGGCTAC 60.320 60.000 23.73 0.00 45.15 3.58
876 878 0.665670 CCTCGATGCATCTGGCTACG 60.666 60.000 23.73 10.04 45.15 3.51
877 879 1.280886 CTCGATGCATCTGGCTACGC 61.281 60.000 23.73 0.00 45.15 4.42
878 880 1.300465 CGATGCATCTGGCTACGCT 60.300 57.895 23.73 0.00 45.15 5.07
879 881 1.554891 CGATGCATCTGGCTACGCTG 61.555 60.000 23.73 0.98 45.15 5.18
880 882 1.226686 GATGCATCTGGCTACGCTGG 61.227 60.000 19.70 0.00 45.15 4.85
881 883 2.590007 GCATCTGGCTACGCTGGG 60.590 66.667 0.00 0.00 40.25 4.45
882 884 3.094062 GCATCTGGCTACGCTGGGA 62.094 63.158 0.00 0.00 40.25 4.37
883 885 1.227380 CATCTGGCTACGCTGGGAC 60.227 63.158 0.00 0.00 0.00 4.46
884 886 1.381872 ATCTGGCTACGCTGGGACT 60.382 57.895 0.00 0.00 0.00 3.85
885 887 1.395826 ATCTGGCTACGCTGGGACTC 61.396 60.000 0.00 0.00 0.00 3.36
886 888 2.283604 TGGCTACGCTGGGACTCA 60.284 61.111 0.00 0.00 0.00 3.41
887 889 2.290122 CTGGCTACGCTGGGACTCAG 62.290 65.000 0.00 0.00 46.03 3.35
894 896 4.220413 CTGGGACTCAGCTGCATG 57.780 61.111 9.47 4.21 36.60 4.06
895 897 2.045634 TGGGACTCAGCTGCATGC 60.046 61.111 11.82 11.82 43.29 4.06
919 921 0.889186 GCACCTCCGTCAAACCATGT 60.889 55.000 0.00 0.00 0.00 3.21
921 923 2.346803 CACCTCCGTCAAACCATGTAG 58.653 52.381 0.00 0.00 0.00 2.74
1105 1161 2.541120 CCTACGAGGCTCCGTACGG 61.541 68.421 28.66 28.66 43.20 4.02
1139 1212 2.361483 TACGGCGCACCTCCTACA 60.361 61.111 10.83 0.00 0.00 2.74
1146 1219 4.162690 CACCTCCTACAGCGCCCC 62.163 72.222 2.29 0.00 0.00 5.80
1214 1287 1.264749 TTCCATACAGTGCTCCGCCT 61.265 55.000 0.00 0.00 0.00 5.52
1217 1290 0.249489 CATACAGTGCTCCGCCTACC 60.249 60.000 0.00 0.00 0.00 3.18
1237 1310 3.805307 CGACTCGCAGCTCTCCGT 61.805 66.667 0.00 0.00 0.00 4.69
1505 1579 1.160137 GTGCCATTCAGTCTTCGCTT 58.840 50.000 0.00 0.00 0.00 4.68
1512 1586 1.183549 TCAGTCTTCGCTTACTCCCC 58.816 55.000 0.00 0.00 0.00 4.81
1513 1587 1.187087 CAGTCTTCGCTTACTCCCCT 58.813 55.000 0.00 0.00 0.00 4.79
1539 1613 3.776158 GCATGGTGGTCTTTGCCA 58.224 55.556 0.00 0.00 36.64 4.92
1540 1614 2.279842 GCATGGTGGTCTTTGCCAT 58.720 52.632 0.00 0.00 43.14 4.40
1948 2023 1.529244 GTGGTGCCAAGCAGAAGGT 60.529 57.895 0.00 0.00 40.08 3.50
1995 2073 3.382832 CGTCGGCTCCACCTCCTT 61.383 66.667 0.00 0.00 35.61 3.36
2042 2126 0.877649 GCGAGTCATGCGGTGATGAT 60.878 55.000 0.00 0.00 39.48 2.45
2163 2247 2.916702 TGAGAAACAAGCTGCTCTCA 57.083 45.000 12.76 12.76 37.33 3.27
2234 2319 0.749091 CATGGACATCGGTGCCACAT 60.749 55.000 13.02 4.49 35.40 3.21
2242 2327 3.578282 ACATCGGTGCCACATATCATCTA 59.422 43.478 0.00 0.00 0.00 1.98
2401 2486 3.675698 GTCTCCTTGATGTTCTTCGTGTC 59.324 47.826 0.00 0.00 0.00 3.67
2414 2499 1.116308 TCGTGTCCCTTCAGTCACAA 58.884 50.000 0.00 0.00 0.00 3.33
2425 2510 4.576463 CCTTCAGTCACAAGTAGTTTGCTT 59.424 41.667 0.00 0.00 40.59 3.91
2567 2682 1.153369 GCTCTTGATGTGCCGCCTA 60.153 57.895 0.00 0.00 0.00 3.93
2872 2987 6.204688 TCAGTTTCATTGATGCTTTTAGTCGT 59.795 34.615 0.00 0.00 0.00 4.34
3069 3187 5.682234 TCATGTGTCTTGTCCTCATACAT 57.318 39.130 0.00 0.00 0.00 2.29
3244 3362 2.708325 ACATGAAATCTCCCCTAGAGGC 59.292 50.000 0.00 0.00 43.44 4.70
3339 3457 5.332355 CCGTACAATAAGCATAAACTCGAGC 60.332 44.000 13.61 0.00 0.00 5.03
3489 3607 0.758734 CACACTCTCACCTTCCACCA 59.241 55.000 0.00 0.00 0.00 4.17
3497 3615 4.684724 TCTCACCTTCCACCAATACTACT 58.315 43.478 0.00 0.00 0.00 2.57
3507 3625 3.630769 CACCAATACTACTGCTACCGAGA 59.369 47.826 0.00 0.00 0.00 4.04
3520 3638 1.270907 ACCGAGATGCACTCCTTTCT 58.729 50.000 9.71 0.00 42.18 2.52
3586 3718 0.403655 TTGCCTAACCATGGTGCAGA 59.596 50.000 23.01 14.22 32.88 4.26
3676 3835 3.838271 GCCAGATGGGTCGCTCGA 61.838 66.667 0.12 0.00 39.65 4.04
3678 3837 2.278206 CAGATGGGTCGCTCGACG 60.278 66.667 15.07 0.00 45.41 5.12
3679 3838 2.750637 AGATGGGTCGCTCGACGT 60.751 61.111 15.07 0.00 45.41 4.34
3680 3839 2.579787 GATGGGTCGCTCGACGTG 60.580 66.667 15.07 0.00 45.41 4.49
3681 3840 4.129737 ATGGGTCGCTCGACGTGG 62.130 66.667 15.07 0.00 45.41 4.94
3689 3848 3.470567 CTCGACGTGGCGCTTGAC 61.471 66.667 7.64 0.51 0.00 3.18
3813 4014 3.774528 CCGAGCTGGCTGCCACTA 61.775 66.667 19.30 0.00 44.23 2.74
3814 4015 2.503061 CGAGCTGGCTGCCACTAT 59.497 61.111 19.30 6.23 44.23 2.12
3910 4111 4.431131 CACTCCGGGCCCAGCATT 62.431 66.667 24.92 0.00 0.00 3.56
3946 4147 3.622514 GGTCTCTCCGGAGCATGT 58.377 61.111 27.39 0.00 39.31 3.21
3967 4177 2.273619 AGAGCCTGTGGAATCTCCTTT 58.726 47.619 0.00 0.00 37.46 3.11
3976 4186 2.376518 TGGAATCTCCTTTGGCAGAGTT 59.623 45.455 4.18 0.00 37.46 3.01
4019 4271 0.250295 CTTCTCCAACACCTTCGCCA 60.250 55.000 0.00 0.00 0.00 5.69
4029 4281 1.255667 ACCTTCGCCACCTGTCGTAT 61.256 55.000 0.00 0.00 0.00 3.06
4157 4409 2.178273 GTGGAACCGCGGCATTTC 59.822 61.111 28.58 21.41 0.00 2.17
4214 4466 0.548031 TGGAACAGGAGATCCATGCC 59.452 55.000 0.92 0.00 41.27 4.40
4251 4503 0.543410 TTGGCGTCTGGTTCCTCCTA 60.543 55.000 0.00 0.00 37.07 2.94
4285 4537 6.258507 GTCAATGTTATTGATTCCAAATGGGC 59.741 38.462 7.42 0.00 35.67 5.36
4352 4604 2.113139 CGACTGGTGGCCAAAGGT 59.887 61.111 7.24 6.17 30.80 3.50
4396 4648 9.529325 CCTTGATTATGAAGATACGTTTAGTCA 57.471 33.333 0.00 0.00 0.00 3.41
4449 4701 0.530744 TTCGCTGGCTGTTACTCGAT 59.469 50.000 0.00 0.00 0.00 3.59
4552 4804 0.310854 GGTTTTGTTGACCCTGCTCG 59.689 55.000 0.00 0.00 0.00 5.03
4668 4921 3.071312 ACATGGGTTTGTACCGTCTACAA 59.929 43.478 0.00 0.03 46.04 2.41
4958 5211 2.024369 TGCTACCACTCCTATGTCCTCA 60.024 50.000 0.00 0.00 0.00 3.86
5159 5413 0.041839 GCATTCTGCGCTATGTTCGG 60.042 55.000 9.73 0.00 31.71 4.30
5165 5419 3.089784 CGCTATGTTCGGCACACC 58.910 61.111 0.00 0.00 38.61 4.16
5192 5446 0.685458 ATGGTCTCCATTTGCAGCCC 60.685 55.000 0.00 0.00 42.23 5.19
5392 5648 2.701951 TGCCACAGCTGAGATCATATGA 59.298 45.455 23.35 8.10 40.80 2.15
5489 5745 6.166279 GCTACATATCTTTCATCCAATCCGA 58.834 40.000 0.00 0.00 0.00 4.55
5610 5866 4.142227 GGATCAGCTTGCTGACATTTTCAT 60.142 41.667 25.00 8.86 36.05 2.57
5616 5872 6.643770 CAGCTTGCTGACATTTTCATTAAACT 59.356 34.615 16.78 0.00 32.17 2.66
5718 5974 7.299036 AGGGAGGGTGTTAGACTAGGTATATTA 59.701 40.741 0.00 0.00 0.00 0.98
5790 6047 8.528044 TTATATATACATGACAGCCGTATCCA 57.472 34.615 0.00 0.00 0.00 3.41
5791 6048 3.667497 ATACATGACAGCCGTATCCAG 57.333 47.619 0.00 0.00 0.00 3.86
5793 6050 1.134699 ACATGACAGCCGTATCCAGTG 60.135 52.381 0.00 0.00 0.00 3.66
5827 6084 5.836358 AGCATTGTTCCAAACCCTAGTTTTA 59.164 36.000 0.00 0.00 43.82 1.52
6091 6348 1.304713 CACCTCAATTGCCCTGGCT 60.305 57.895 9.97 0.00 42.51 4.75
6383 6643 2.867109 ATCCTTATGCGAATGGAGGG 57.133 50.000 7.56 0.00 31.59 4.30
6432 6692 0.461961 AGTCCAGGCTCGAACTATGC 59.538 55.000 0.00 0.00 0.00 3.14
6542 6802 1.206849 TGTGATTAGCTGCACCGATGA 59.793 47.619 1.02 0.00 34.19 2.92
6600 6860 6.514048 GCACTTTCACAGTTGAGCTTAATTCT 60.514 38.462 0.00 0.00 30.92 2.40
7027 7317 1.255033 AGAGGAGTGGGGATGGGATA 58.745 55.000 0.00 0.00 0.00 2.59
7582 7890 7.332557 TCTTAAACTAAGTGACACTTTGGACA 58.667 34.615 25.10 6.85 39.51 4.02
7728 8241 6.740110 AGACAAACAGAGGATATAGTTAGCG 58.260 40.000 0.00 0.00 0.00 4.26
7759 8284 4.340894 TGAGCGTAGTTTTGATTGATGC 57.659 40.909 0.00 0.00 0.00 3.91
7988 8543 3.036819 AGCAGAGATGATACTGGAAGCA 58.963 45.455 0.00 0.00 37.60 3.91
8084 8639 8.955002 CCGTACAATCATATACGCAAGATATAC 58.045 37.037 0.00 0.00 42.20 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 0.388649 GCTCCACTCGACGTTGATGT 60.389 55.000 5.82 4.13 0.00 3.06
833 835 0.530870 GCAGATTCCCGGTGTAGAGC 60.531 60.000 0.00 0.00 0.00 4.09
834 836 1.115467 AGCAGATTCCCGGTGTAGAG 58.885 55.000 0.00 0.00 0.00 2.43
835 837 1.480954 GAAGCAGATTCCCGGTGTAGA 59.519 52.381 0.00 0.00 31.14 2.59
836 838 1.941325 GAAGCAGATTCCCGGTGTAG 58.059 55.000 0.00 0.00 31.14 2.74
845 847 1.876322 CATCGAGGGGAAGCAGATTC 58.124 55.000 0.00 0.00 37.17 2.52
846 848 0.179034 GCATCGAGGGGAAGCAGATT 60.179 55.000 0.00 0.00 39.15 2.40
847 849 1.340399 TGCATCGAGGGGAAGCAGAT 61.340 55.000 0.00 0.00 43.83 2.90
848 850 1.989508 TGCATCGAGGGGAAGCAGA 60.990 57.895 0.00 0.00 43.83 4.26
849 851 2.586245 TGCATCGAGGGGAAGCAG 59.414 61.111 0.00 0.00 43.83 4.24
851 853 0.883814 CAGATGCATCGAGGGGAAGC 60.884 60.000 20.67 0.00 39.75 3.86
852 854 0.250209 CCAGATGCATCGAGGGGAAG 60.250 60.000 25.09 9.65 0.00 3.46
853 855 1.832219 CCAGATGCATCGAGGGGAA 59.168 57.895 25.09 0.00 0.00 3.97
854 856 2.811514 GCCAGATGCATCGAGGGGA 61.812 63.158 30.09 0.00 40.77 4.81
855 857 1.475169 TAGCCAGATGCATCGAGGGG 61.475 60.000 30.09 24.73 44.83 4.79
856 858 0.320247 GTAGCCAGATGCATCGAGGG 60.320 60.000 30.09 26.60 44.83 4.30
857 859 0.665670 CGTAGCCAGATGCATCGAGG 60.666 60.000 27.19 27.19 44.83 4.63
858 860 2.806577 CGTAGCCAGATGCATCGAG 58.193 57.895 20.67 16.44 44.83 4.04
877 879 2.113433 GCATGCAGCTGAGTCCCAG 61.113 63.158 20.43 0.00 45.67 4.45
878 880 2.045634 GCATGCAGCTGAGTCCCA 60.046 61.111 20.43 5.55 41.15 4.37
899 901 1.303317 ATGGTTTGACGGAGGTGCC 60.303 57.895 0.00 0.00 0.00 5.01
900 902 0.889186 ACATGGTTTGACGGAGGTGC 60.889 55.000 0.00 0.00 0.00 5.01
901 903 2.346803 CTACATGGTTTGACGGAGGTG 58.653 52.381 0.00 0.00 0.00 4.00
902 904 1.338769 GCTACATGGTTTGACGGAGGT 60.339 52.381 0.00 0.00 0.00 3.85
903 905 1.338674 TGCTACATGGTTTGACGGAGG 60.339 52.381 0.00 0.00 0.00 4.30
904 906 2.093306 TGCTACATGGTTTGACGGAG 57.907 50.000 0.00 0.00 0.00 4.63
905 907 2.627945 GATGCTACATGGTTTGACGGA 58.372 47.619 0.00 0.00 0.00 4.69
906 908 1.327460 CGATGCTACATGGTTTGACGG 59.673 52.381 0.00 0.00 0.00 4.79
907 909 1.267532 GCGATGCTACATGGTTTGACG 60.268 52.381 0.00 0.00 0.00 4.35
908 910 2.009774 AGCGATGCTACATGGTTTGAC 58.990 47.619 0.00 0.00 36.99 3.18
909 911 2.093500 AGAGCGATGCTACATGGTTTGA 60.093 45.455 0.00 0.00 39.88 2.69
910 912 2.283298 AGAGCGATGCTACATGGTTTG 58.717 47.619 0.00 0.00 39.88 2.93
911 913 2.698855 AGAGCGATGCTACATGGTTT 57.301 45.000 0.00 0.00 39.88 3.27
912 914 2.543861 CGTAGAGCGATGCTACATGGTT 60.544 50.000 0.00 0.00 44.77 3.67
913 915 1.001268 CGTAGAGCGATGCTACATGGT 60.001 52.381 0.00 0.00 44.77 3.55
1114 1173 3.181967 GTGCGCCGTAGAGCTGTG 61.182 66.667 4.18 0.00 32.71 3.66
1115 1174 4.436998 GGTGCGCCGTAGAGCTGT 62.437 66.667 4.18 0.00 32.71 4.40
1120 1179 2.117156 GTAGGAGGTGCGCCGTAGA 61.117 63.158 11.42 0.00 40.50 2.59
1129 1188 4.162690 GGGGCGCTGTAGGAGGTG 62.163 72.222 7.64 0.00 0.00 4.00
1146 1219 2.066262 GTAGTGTTGGTGATGACCGTG 58.934 52.381 0.00 0.00 46.62 4.94
1186 1259 2.096496 GCACTGTATGGAATCAGCACAC 59.904 50.000 0.00 0.00 35.37 3.82
1214 1287 4.631773 AGCTGCGAGTCGTAGGTA 57.368 55.556 29.70 4.75 46.75 3.08
1217 1290 1.353804 GGAGAGCTGCGAGTCGTAG 59.646 63.158 24.21 24.21 42.13 3.51
1237 1310 2.589157 CCTGGTTCAGCCACCGGTA 61.589 63.158 6.87 0.00 43.61 4.02
1539 1613 0.249615 CATGCATCCCTCGACGTCAT 60.250 55.000 17.16 0.00 0.00 3.06
1540 1614 1.141665 CATGCATCCCTCGACGTCA 59.858 57.895 17.16 1.87 0.00 4.35
1878 1953 3.450115 GCCCTCCGTGTAGACGCT 61.450 66.667 6.94 0.00 44.68 5.07
2019 2102 4.377708 ACCGCATGACTCGCAGCA 62.378 61.111 0.00 0.00 0.00 4.41
2163 2247 0.473886 AACCCAGGCTCCTGTGTAGT 60.474 55.000 14.27 4.23 42.15 2.73
2223 2308 3.552068 CGTTAGATGATATGTGGCACCGA 60.552 47.826 16.26 2.74 0.00 4.69
2401 2486 3.251004 GCAAACTACTTGTGACTGAAGGG 59.749 47.826 0.00 0.00 37.36 3.95
2414 2499 3.487120 AGGAACCGAAAGCAAACTACT 57.513 42.857 0.00 0.00 0.00 2.57
2425 2510 5.634859 GTCACGAGTTAATTTAGGAACCGAA 59.365 40.000 0.00 0.00 0.00 4.30
2591 2706 2.122797 ACTGTGACGACGACACCCA 61.123 57.895 23.80 8.80 37.45 4.51
2730 2845 3.380004 AGAGAAAGGTAGCTGATGACTCG 59.620 47.826 0.00 0.00 0.00 4.18
3069 3187 0.608130 ACTGCACCGTTCTGCTGATA 59.392 50.000 9.76 0.00 38.94 2.15
3202 3320 0.830444 AAGGAGTCGTGTGGGTAGCA 60.830 55.000 0.00 0.00 0.00 3.49
3244 3362 9.442047 AGTAATTTGGAGTCTCATGAAGTAAAG 57.558 33.333 1.47 0.00 0.00 1.85
3339 3457 6.587990 AGAAACACACACTTCTTAGATCGATG 59.412 38.462 0.54 0.00 0.00 3.84
3489 3607 3.889538 TGCATCTCGGTAGCAGTAGTATT 59.110 43.478 0.00 0.00 33.75 1.89
3497 3615 0.684479 AGGAGTGCATCTCGGTAGCA 60.684 55.000 9.29 0.00 43.60 3.49
3507 3625 3.507622 GGCAAAACTAGAAAGGAGTGCAT 59.492 43.478 0.00 0.00 31.72 3.96
3520 3638 6.065374 TCTACAAATTGGTCAGGCAAAACTA 58.935 36.000 0.00 0.00 0.00 2.24
3586 3718 2.430367 GAGCACCCCGTCCAGTTT 59.570 61.111 0.00 0.00 0.00 2.66
3648 3795 0.603707 CCATCTGGCGTCACAACTGT 60.604 55.000 0.00 0.00 0.00 3.55
3662 3809 2.750637 ACGTCGAGCGACCCATCT 60.751 61.111 16.35 0.00 44.77 2.90
3678 3837 3.764049 GTCGTCGTCAAGCGCCAC 61.764 66.667 2.29 0.00 41.07 5.01
3684 3843 3.164011 GTCGCGGTCGTCGTCAAG 61.164 66.667 6.13 0.00 41.72 3.02
3690 3849 4.831307 ATCAGCGTCGCGGTCGTC 62.831 66.667 16.84 14.73 34.62 4.20
3691 3850 4.831307 GATCAGCGTCGCGGTCGT 62.831 66.667 16.84 4.99 34.62 4.34
3779 3977 1.966451 GGGTTGCCGAACTGGAGTG 60.966 63.158 0.00 0.00 42.00 3.51
3780 3978 2.430367 GGGTTGCCGAACTGGAGT 59.570 61.111 0.00 0.00 42.00 3.85
3802 4003 0.464036 CCGAACTATAGTGGCAGCCA 59.536 55.000 11.22 11.22 0.00 4.75
3809 4010 1.300697 GGGCGGCCGAACTATAGTG 60.301 63.158 33.48 0.00 0.00 2.74
3812 4013 2.519063 TCGGGCGGCCGAACTATA 60.519 61.111 45.79 26.04 39.34 1.31
3813 4014 3.912907 CTCGGGCGGCCGAACTAT 61.913 66.667 45.47 0.00 41.77 2.12
3940 4141 1.279496 TTCCACAGGCTCTACATGCT 58.721 50.000 0.00 0.00 0.00 3.79
3946 4147 2.856760 AGGAGATTCCACAGGCTCTA 57.143 50.000 0.00 0.00 39.61 2.43
3967 4177 0.249868 CGAGTCCACAAACTCTGCCA 60.250 55.000 2.89 0.00 42.90 4.92
3976 4186 2.031012 CAGCAGGCGAGTCCACAA 59.969 61.111 0.00 0.00 37.29 3.33
4151 4403 2.998279 AAGCGCTGCCTGGAAATGC 61.998 57.895 12.58 0.00 0.00 3.56
4228 4480 0.320697 AGGAACCAGACGCCAAGTAC 59.679 55.000 0.00 0.00 0.00 2.73
4285 4537 3.003689 AGCATGTTTCTTCACCTTGAACG 59.996 43.478 0.00 0.00 32.21 3.95
4396 4648 4.689612 ATAGTCGTGGGCTTGATAACAT 57.310 40.909 0.00 0.00 0.00 2.71
4449 4701 1.446099 GCTGACGAAGCGACCATCA 60.446 57.895 0.00 0.00 43.45 3.07
4514 4766 0.396435 CTGGGGGCTGACGCATATAA 59.604 55.000 0.00 0.00 38.10 0.98
4958 5211 7.816031 CCATCAAAAGCTGATAATTTGTCTGTT 59.184 33.333 7.50 0.00 43.28 3.16
5065 5319 6.305399 CACACGGTTAACTGCAAATGAAATAG 59.695 38.462 14.52 0.00 0.00 1.73
5159 5413 1.693083 GACCATACGAAGCGGTGTGC 61.693 60.000 0.00 0.00 46.98 4.57
5165 5419 2.225068 AATGGAGACCATACGAAGCG 57.775 50.000 3.64 0.00 44.40 4.68
5192 5446 1.021390 AGATCAAACCAGAAGCCGCG 61.021 55.000 0.00 0.00 0.00 6.46
5392 5648 3.006323 ACTCTCGAAGCAATGACTGAACT 59.994 43.478 0.00 0.00 0.00 3.01
5489 5745 3.692101 TGTTTCGTTCGGGCATGAAATAT 59.308 39.130 0.00 0.00 34.83 1.28
5610 5866 8.899771 CAAAAGAAGGTAAGGACAAGAGTTTAA 58.100 33.333 0.00 0.00 0.00 1.52
5616 5872 6.062095 CCTTCAAAAGAAGGTAAGGACAAGA 58.938 40.000 14.57 0.00 44.99 3.02
5790 6047 2.111384 ACAATGCTCGATACCCTCACT 58.889 47.619 0.00 0.00 0.00 3.41
5791 6048 2.604046 ACAATGCTCGATACCCTCAC 57.396 50.000 0.00 0.00 0.00 3.51
5793 6050 2.158957 TGGAACAATGCTCGATACCCTC 60.159 50.000 0.00 0.00 31.92 4.30
5827 6084 1.625508 GGAGGTGGGGGACTGTTAGAT 60.626 57.143 0.00 0.00 0.00 1.98
6091 6348 0.409092 TAGACCACACGGAAGGGGTA 59.591 55.000 0.00 0.00 40.46 3.69
6383 6643 2.901292 GCACAGCCCAGCATATCGC 61.901 63.158 0.00 0.00 42.91 4.58
6432 6692 2.279120 GCGTCAGCCTCCATCGAG 60.279 66.667 0.00 0.00 37.42 4.04
6600 6860 2.433239 GGATACCTTCTTAACTCGGCCA 59.567 50.000 2.24 0.00 0.00 5.36
7027 7317 2.444421 CTCATTTGCAGCTTTCTCCCT 58.556 47.619 0.00 0.00 0.00 4.20
7098 7388 3.060895 GGACATCGTCGAAACAGTGAATC 59.939 47.826 0.00 0.00 32.65 2.52
7215 7505 9.265901 CAATACAGATAACAGGACTAATTGGAG 57.734 37.037 0.00 0.00 0.00 3.86
7582 7890 1.279271 CAGTTAGCCTTACCACAGCCT 59.721 52.381 0.00 0.00 0.00 4.58
7728 8241 2.301577 ACTACGCTCATCAGAAAGGC 57.698 50.000 0.00 0.00 0.00 4.35
7938 8475 5.888982 ACCCTTCACTAAGTCTTCTCAAA 57.111 39.130 0.00 0.00 0.00 2.69
7940 8477 5.391256 TGTACCCTTCACTAAGTCTTCTCA 58.609 41.667 0.00 0.00 0.00 3.27
7988 8543 3.828451 ACATTGCTACAAGATGCCTTTGT 59.172 39.130 3.56 3.56 0.00 2.83
8117 8672 9.020731 ACTACGTATACATAATGATGATGACCA 57.979 33.333 3.32 0.00 36.48 4.02
8118 8673 9.856488 AACTACGTATACATAATGATGATGACC 57.144 33.333 3.32 0.00 36.48 4.02
8183 8738 4.201980 CCATGGCATGTATGAACAGACAAG 60.202 45.833 24.80 3.72 39.49 3.16
8315 8911 8.190784 AGTACTTTGAAAACCACTTTGATGAAG 58.809 33.333 0.00 0.00 41.32 3.02


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

AutoCloner maintained by Alex Coulton.