Multiple sequence alignment - TraesCS7A01G317200

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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 TraesCS7A01G317200 chr7A 100.000 4285 0 0 1 4285 456205700 456201416 0.000000e+00 7914.0
1 TraesCS7A01G317200 chr7A 82.137 627 89 17 3665 4285 96286743 96287352 2.280000e-142 516.0
2 TraesCS7A01G317200 chr7A 82.051 117 19 2 32 147 109103963 109104078 9.810000e-17 99.0
3 TraesCS7A01G317200 chr7A 82.353 119 15 5 32 147 608965400 608965515 9.810000e-17 99.0
4 TraesCS7A01G317200 chr2A 97.699 2347 33 8 1941 4285 505213102 505215429 0.000000e+00 4015.0
5 TraesCS7A01G317200 chr2A 91.771 1118 36 7 865 1942 505211949 505213050 0.000000e+00 1504.0
6 TraesCS7A01G317200 chr2A 87.242 1019 98 18 3195 4210 613519897 613520886 0.000000e+00 1133.0
7 TraesCS7A01G317200 chr2A 86.341 410 52 3 3671 4077 690332532 690332940 1.090000e-120 444.0
8 TraesCS7A01G317200 chr2A 82.724 492 51 16 1182 1656 613478424 613478898 1.430000e-109 407.0
9 TraesCS7A01G317200 chr2A 91.057 123 9 2 1660 1781 613478971 613479092 9.530000e-37 165.0
10 TraesCS7A01G317200 chr3B 96.726 1619 18 12 1941 3558 829810146 829811730 0.000000e+00 2663.0
11 TraesCS7A01G317200 chr3B 91.390 1115 46 8 865 1942 829808993 829810094 0.000000e+00 1482.0
12 TraesCS7A01G317200 chr3B 91.211 1115 48 8 865 1942 829805227 829806328 0.000000e+00 1471.0
13 TraesCS7A01G317200 chr3B 99.012 405 4 0 1941 2345 829806380 829806784 0.000000e+00 726.0
14 TraesCS7A01G317200 chr3B 92.593 108 4 2 1432 1539 259144639 259144536 7.420000e-33 152.0
15 TraesCS7A01G317200 chrUn 96.418 1619 23 12 1941 3558 184606627 184608211 0.000000e+00 2636.0
16 TraesCS7A01G317200 chrUn 91.778 523 13 2 1449 1942 184606054 184606575 0.000000e+00 701.0
17 TraesCS7A01G317200 chrUn 91.429 105 5 2 1432 1536 22082778 22082878 1.610000e-29 141.0
18 TraesCS7A01G317200 chrUn 88.889 99 11 0 2354 2452 22083219 22083317 5.820000e-24 122.0
19 TraesCS7A01G317200 chr7B 91.921 1510 77 15 2343 3837 633234117 633235596 0.000000e+00 2071.0
20 TraesCS7A01G317200 chr7B 88.399 1224 100 19 3071 4285 542882511 542883701 0.000000e+00 1435.0
21 TraesCS7A01G317200 chr7B 91.839 870 36 15 32 867 483529173 483530041 0.000000e+00 1181.0
22 TraesCS7A01G317200 chr7B 93.995 383 21 1 3834 4214 633235688 633236070 2.870000e-161 579.0
23 TraesCS7A01G317200 chr7B 87.062 371 25 10 1996 2343 542882018 542882388 8.630000e-107 398.0
24 TraesCS7A01G317200 chr7B 85.603 257 32 5 611 864 483529427 483529173 9.140000e-67 265.0
25 TraesCS7A01G317200 chr7B 83.755 277 35 7 597 864 531822180 531821905 1.980000e-63 254.0
26 TraesCS7A01G317200 chr7B 83.203 256 37 2 612 866 531823952 531824202 3.330000e-56 230.0
27 TraesCS7A01G317200 chr5A 88.480 1224 99 19 3071 4285 489105674 489106864 0.000000e+00 1441.0
28 TraesCS7A01G317200 chr5A 86.792 371 26 10 1996 2343 489105133 489105503 4.020000e-105 392.0
29 TraesCS7A01G317200 chr5A 84.539 401 47 8 2478 2865 519566034 519566432 2.420000e-102 383.0
30 TraesCS7A01G317200 chr5A 84.289 401 48 8 2478 2865 575085859 575086257 1.120000e-100 377.0
31 TraesCS7A01G317200 chr5A 83.651 367 42 12 2478 2831 220902515 220902154 3.190000e-86 329.0
32 TraesCS7A01G317200 chr5A 88.596 114 12 1 1541 1653 163504378 163504491 2.080000e-28 137.0
33 TraesCS7A01G317200 chr5A 91.000 100 8 1 2354 2452 163504650 163504749 2.690000e-27 134.0
34 TraesCS7A01G317200 chr5A 81.897 116 15 5 35 147 76132597 76132485 4.560000e-15 93.5
35 TraesCS7A01G317200 chr6B 94.712 851 25 7 32 864 664492649 664493497 0.000000e+00 1304.0
36 TraesCS7A01G317200 chr6B 94.249 852 29 7 29 862 288045880 288046729 0.000000e+00 1284.0
37 TraesCS7A01G317200 chr6B 89.885 870 72 6 3418 4285 49313385 49312530 0.000000e+00 1105.0
38 TraesCS7A01G317200 chr6B 85.539 733 72 15 2877 3605 559466845 559467547 0.000000e+00 736.0
39 TraesCS7A01G317200 chr6B 86.151 621 55 12 3671 4285 559467753 559468348 3.610000e-180 641.0
40 TraesCS7A01G317200 chr6B 92.593 108 4 2 1432 1539 507882031 507881928 7.420000e-33 152.0
41 TraesCS7A01G317200 chr6B 88.889 99 11 0 2354 2452 507881590 507881492 5.820000e-24 122.0
42 TraesCS7A01G317200 chr6B 82.114 123 15 6 29 147 696292804 696292923 9.810000e-17 99.0
43 TraesCS7A01G317200 chr4B 94.124 868 30 8 17 864 568604559 568605425 0.000000e+00 1301.0
44 TraesCS7A01G317200 chr4B 82.759 261 38 7 605 861 88422105 88422362 4.310000e-55 226.0
45 TraesCS7A01G317200 chr2D 89.595 913 58 19 2348 3245 562220851 562219961 0.000000e+00 1125.0
46 TraesCS7A01G317200 chr2D 86.290 620 58 15 1043 1656 562223237 562222639 0.000000e+00 649.0
47 TraesCS7A01G317200 chr2D 88.808 411 22 9 1956 2343 562222163 562221754 2.320000e-132 483.0
48 TraesCS7A01G317200 chr1B 88.489 695 56 17 2348 3037 621990848 621990173 0.000000e+00 819.0
49 TraesCS7A01G317200 chr5B 85.294 748 68 22 2877 3614 15141070 15140355 0.000000e+00 734.0
50 TraesCS7A01G317200 chr5B 87.419 620 65 9 3672 4285 10491580 10490968 0.000000e+00 701.0
51 TraesCS7A01G317200 chr5B 84.824 738 67 21 2877 3605 469970329 469971030 0.000000e+00 701.0
52 TraesCS7A01G317200 chr3A 84.750 741 79 17 2877 3614 65818401 65817692 0.000000e+00 712.0
53 TraesCS7A01G317200 chr3A 85.644 613 58 10 3679 4285 65817296 65816708 6.090000e-173 617.0
54 TraesCS7A01G317200 chr3A 85.657 251 35 1 612 861 587561359 587561609 3.290000e-66 263.0
55 TraesCS7A01G317200 chr3A 90.741 108 6 2 1432 1539 275644421 275644318 1.610000e-29 141.0
56 TraesCS7A01G317200 chr3A 92.000 100 7 1 2354 2452 275643981 275643882 5.780000e-29 139.0
57 TraesCS7A01G317200 chr2B 84.337 747 77 20 2877 3614 658919752 658919037 0.000000e+00 695.0
58 TraesCS7A01G317200 chr2B 87.719 114 12 2 35 147 796928183 796928071 9.670000e-27 132.0
59 TraesCS7A01G317200 chr1A 85.971 613 55 11 3679 4285 532453559 532452972 1.010000e-175 627.0
60 TraesCS7A01G317200 chr4D 84.026 626 68 15 3666 4285 252696733 252696134 1.340000e-159 573.0
61 TraesCS7A01G317200 chr7D 87.073 410 48 4 3671 4077 622371769 622372176 3.900000e-125 459.0
62 TraesCS7A01G317200 chr6A 89.815 108 7 2 1432 1539 467921926 467921823 7.470000e-28 135.0
63 TraesCS7A01G317200 chr1D 87.069 116 14 1 1541 1656 249059442 249059556 3.480000e-26 130.0


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 TraesCS7A01G317200 chr7A 456201416 456205700 4284 True 7914.000000 7914 100.00000 1 4285 1 chr7A.!!$R1 4284
1 TraesCS7A01G317200 chr7A 96286743 96287352 609 False 516.000000 516 82.13700 3665 4285 1 chr7A.!!$F1 620
2 TraesCS7A01G317200 chr2A 505211949 505215429 3480 False 2759.500000 4015 94.73500 865 4285 2 chr2A.!!$F3 3420
3 TraesCS7A01G317200 chr2A 613519897 613520886 989 False 1133.000000 1133 87.24200 3195 4210 1 chr2A.!!$F1 1015
4 TraesCS7A01G317200 chr2A 613478424 613479092 668 False 286.000000 407 86.89050 1182 1781 2 chr2A.!!$F4 599
5 TraesCS7A01G317200 chr3B 829805227 829811730 6503 False 1585.500000 2663 94.58475 865 3558 4 chr3B.!!$F1 2693
6 TraesCS7A01G317200 chrUn 184606054 184608211 2157 False 1668.500000 2636 94.09800 1449 3558 2 chrUn.!!$F2 2109
7 TraesCS7A01G317200 chr7B 633234117 633236070 1953 False 1325.000000 2071 92.95800 2343 4214 2 chr7B.!!$F4 1871
8 TraesCS7A01G317200 chr7B 483529173 483530041 868 False 1181.000000 1181 91.83900 32 867 1 chr7B.!!$F1 835
9 TraesCS7A01G317200 chr7B 542882018 542883701 1683 False 916.500000 1435 87.73050 1996 4285 2 chr7B.!!$F3 2289
10 TraesCS7A01G317200 chr5A 489105133 489106864 1731 False 916.500000 1441 87.63600 1996 4285 2 chr5A.!!$F4 2289
11 TraesCS7A01G317200 chr6B 664492649 664493497 848 False 1304.000000 1304 94.71200 32 864 1 chr6B.!!$F2 832
12 TraesCS7A01G317200 chr6B 288045880 288046729 849 False 1284.000000 1284 94.24900 29 862 1 chr6B.!!$F1 833
13 TraesCS7A01G317200 chr6B 49312530 49313385 855 True 1105.000000 1105 89.88500 3418 4285 1 chr6B.!!$R1 867
14 TraesCS7A01G317200 chr6B 559466845 559468348 1503 False 688.500000 736 85.84500 2877 4285 2 chr6B.!!$F4 1408
15 TraesCS7A01G317200 chr4B 568604559 568605425 866 False 1301.000000 1301 94.12400 17 864 1 chr4B.!!$F2 847
16 TraesCS7A01G317200 chr2D 562219961 562223237 3276 True 752.333333 1125 88.23100 1043 3245 3 chr2D.!!$R1 2202
17 TraesCS7A01G317200 chr1B 621990173 621990848 675 True 819.000000 819 88.48900 2348 3037 1 chr1B.!!$R1 689
18 TraesCS7A01G317200 chr5B 15140355 15141070 715 True 734.000000 734 85.29400 2877 3614 1 chr5B.!!$R2 737
19 TraesCS7A01G317200 chr5B 10490968 10491580 612 True 701.000000 701 87.41900 3672 4285 1 chr5B.!!$R1 613
20 TraesCS7A01G317200 chr5B 469970329 469971030 701 False 701.000000 701 84.82400 2877 3605 1 chr5B.!!$F1 728
21 TraesCS7A01G317200 chr3A 65816708 65818401 1693 True 664.500000 712 85.19700 2877 4285 2 chr3A.!!$R1 1408
22 TraesCS7A01G317200 chr2B 658919037 658919752 715 True 695.000000 695 84.33700 2877 3614 1 chr2B.!!$R1 737
23 TraesCS7A01G317200 chr1A 532452972 532453559 587 True 627.000000 627 85.97100 3679 4285 1 chr1A.!!$R1 606
24 TraesCS7A01G317200 chr4D 252696134 252696733 599 True 573.000000 573 84.02600 3666 4285 1 chr4D.!!$R1 619

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
923 4725 0.034337 GTTACTCCCGCACAACCTCA 59.966 55.0 0.00 0.00 0.00 3.86 F
991 4799 0.169009 GAGCAAACATCACCGCTTCC 59.831 55.0 0.00 0.00 34.12 3.46 F
1214 5022 0.327924 TGGCCTTGATGTCACCGATT 59.672 50.0 3.32 0.00 0.00 3.34 F
1717 5625 0.537143 TTTGCGGAATCTGGCAGTGT 60.537 50.0 15.27 3.17 40.75 3.55 F
2606 7566 1.068352 AAGCCAGGGTGGAAGAAGGT 61.068 55.0 0.00 0.00 40.96 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 7848 0.465460 TGACCCCACAAGACACAAGC 60.465 55.000 0.0 0.0 0.0 4.01 R
2880 7849 1.597742 CTGACCCCACAAGACACAAG 58.402 55.000 0.0 0.0 0.0 3.16 R
2881 7850 0.465460 GCTGACCCCACAAGACACAA 60.465 55.000 0.0 0.0 0.0 3.33 R
2886 7855 3.636231 CCGGCTGACCCCACAAGA 61.636 66.667 0.0 0.0 0.0 3.02 R
4245 9738 4.319177 AGTGGAATTACAGTTCAGACAGC 58.681 43.478 0.0 0.0 0.0 4.40 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
20 21 3.337301 TCGCTAAAACAAAACGTTCCC 57.663 42.857 0.00 0.00 36.59 3.97
21 22 2.681848 TCGCTAAAACAAAACGTTCCCA 59.318 40.909 0.00 0.00 36.59 4.37
22 23 2.784928 CGCTAAAACAAAACGTTCCCAC 59.215 45.455 0.00 0.00 36.59 4.61
199 219 2.831742 CGGCATGCTGGGCAGAAT 60.832 61.111 19.33 0.00 43.65 2.40
239 259 2.355837 GAACGGCAGCGACTGTGA 60.356 61.111 8.32 0.00 33.43 3.58
555 591 1.677576 ACGAACGGACTGCGGATATTA 59.322 47.619 0.00 0.00 0.00 0.98
758 794 2.050985 GCTGCCACGTGTTGCTTC 60.051 61.111 15.65 4.25 0.00 3.86
813 849 5.726980 TTTGTCATTTCATTTCAGAGGGG 57.273 39.130 0.00 0.00 0.00 4.79
814 850 3.700538 TGTCATTTCATTTCAGAGGGGG 58.299 45.455 0.00 0.00 0.00 5.40
815 851 3.075882 TGTCATTTCATTTCAGAGGGGGT 59.924 43.478 0.00 0.00 0.00 4.95
816 852 3.696548 GTCATTTCATTTCAGAGGGGGTC 59.303 47.826 0.00 0.00 0.00 4.46
817 853 3.593328 TCATTTCATTTCAGAGGGGGTCT 59.407 43.478 0.00 0.00 35.00 3.85
818 854 4.044571 TCATTTCATTTCAGAGGGGGTCTT 59.955 41.667 0.00 0.00 30.64 3.01
819 855 4.469469 TTTCATTTCAGAGGGGGTCTTT 57.531 40.909 0.00 0.00 30.64 2.52
820 856 4.469469 TTCATTTCAGAGGGGGTCTTTT 57.531 40.909 0.00 0.00 30.64 2.27
821 857 4.469469 TCATTTCAGAGGGGGTCTTTTT 57.531 40.909 0.00 0.00 30.64 1.94
840 876 5.688348 TTTTTGACAATTTTGTTCGACGG 57.312 34.783 0.00 0.00 42.43 4.79
841 877 4.617808 TTTGACAATTTTGTTCGACGGA 57.382 36.364 0.00 0.00 42.43 4.69
842 878 4.822036 TTGACAATTTTGTTCGACGGAT 57.178 36.364 0.00 0.00 42.43 4.18
843 879 4.140518 TGACAATTTTGTTCGACGGATG 57.859 40.909 0.00 0.00 42.43 3.51
844 880 3.058570 TGACAATTTTGTTCGACGGATGG 60.059 43.478 0.00 0.00 42.43 3.51
845 881 2.882137 ACAATTTTGTTCGACGGATGGT 59.118 40.909 0.00 0.00 38.47 3.55
846 882 3.058501 ACAATTTTGTTCGACGGATGGTC 60.059 43.478 0.00 0.00 38.47 4.02
847 883 2.536761 TTTTGTTCGACGGATGGTCT 57.463 45.000 0.00 0.00 43.79 3.85
848 884 2.074547 TTTGTTCGACGGATGGTCTC 57.925 50.000 0.00 0.00 43.79 3.36
849 885 1.254026 TTGTTCGACGGATGGTCTCT 58.746 50.000 0.00 0.00 43.79 3.10
850 886 1.254026 TGTTCGACGGATGGTCTCTT 58.746 50.000 0.00 0.00 43.79 2.85
851 887 1.616865 TGTTCGACGGATGGTCTCTTT 59.383 47.619 0.00 0.00 43.79 2.52
852 888 2.036733 TGTTCGACGGATGGTCTCTTTT 59.963 45.455 0.00 0.00 43.79 2.27
853 889 3.256383 TGTTCGACGGATGGTCTCTTTTA 59.744 43.478 0.00 0.00 43.79 1.52
854 890 4.240096 GTTCGACGGATGGTCTCTTTTAA 58.760 43.478 0.00 0.00 43.79 1.52
855 891 3.841643 TCGACGGATGGTCTCTTTTAAC 58.158 45.455 0.00 0.00 43.79 2.01
856 892 3.256383 TCGACGGATGGTCTCTTTTAACA 59.744 43.478 0.00 0.00 43.79 2.41
857 893 3.991773 CGACGGATGGTCTCTTTTAACAA 59.008 43.478 0.00 0.00 43.79 2.83
858 894 4.449743 CGACGGATGGTCTCTTTTAACAAA 59.550 41.667 0.00 0.00 43.79 2.83
859 895 5.049954 CGACGGATGGTCTCTTTTAACAAAA 60.050 40.000 0.00 0.00 43.79 2.44
860 896 6.512091 CGACGGATGGTCTCTTTTAACAAAAA 60.512 38.462 0.00 0.00 43.79 1.94
923 4725 0.034337 GTTACTCCCGCACAACCTCA 59.966 55.000 0.00 0.00 0.00 3.86
978 4786 7.925622 AGAAGGATGGATATATCATGAGCAAA 58.074 34.615 14.60 0.00 0.00 3.68
986 4794 6.183360 GGATATATCATGAGCAAACATCACCG 60.183 42.308 14.60 0.00 0.00 4.94
991 4799 0.169009 GAGCAAACATCACCGCTTCC 59.831 55.000 0.00 0.00 34.12 3.46
1214 5022 0.327924 TGGCCTTGATGTCACCGATT 59.672 50.000 3.32 0.00 0.00 3.34
1216 5024 1.818674 GGCCTTGATGTCACCGATTTT 59.181 47.619 0.00 0.00 0.00 1.82
1264 5081 3.798511 TGTGGGTGGTTCGTGCCA 61.799 61.111 0.00 0.00 35.93 4.92
1288 5110 1.002659 CCGTACCACCAACAAGGATGA 59.997 52.381 0.00 0.00 41.22 2.92
1293 5115 1.478471 CCACCAACAAGGATGACACCA 60.478 52.381 0.00 0.00 41.22 4.17
1294 5116 1.881973 CACCAACAAGGATGACACCAG 59.118 52.381 0.00 0.00 41.22 4.00
1295 5117 1.774254 ACCAACAAGGATGACACCAGA 59.226 47.619 0.00 0.00 41.22 3.86
1296 5118 2.154462 CCAACAAGGATGACACCAGAC 58.846 52.381 0.00 0.00 41.22 3.51
1297 5119 2.487086 CCAACAAGGATGACACCAGACA 60.487 50.000 0.00 0.00 41.22 3.41
1298 5120 2.549754 CAACAAGGATGACACCAGACAC 59.450 50.000 0.00 0.00 0.00 3.67
1299 5121 1.072331 ACAAGGATGACACCAGACACC 59.928 52.381 0.00 0.00 0.00 4.16
1300 5122 1.349026 CAAGGATGACACCAGACACCT 59.651 52.381 0.00 0.00 0.00 4.00
1361 5183 2.990967 CCACCTGCGCCCAATGTT 60.991 61.111 4.18 0.00 0.00 2.71
1362 5184 2.259204 CACCTGCGCCCAATGTTG 59.741 61.111 4.18 0.00 0.00 3.33
1363 5185 2.115052 ACCTGCGCCCAATGTTGA 59.885 55.556 4.18 0.00 0.00 3.18
1364 5186 1.973281 ACCTGCGCCCAATGTTGAG 60.973 57.895 4.18 0.00 0.00 3.02
1365 5187 2.703798 CCTGCGCCCAATGTTGAGG 61.704 63.158 4.18 0.00 0.00 3.86
1366 5188 1.973281 CTGCGCCCAATGTTGAGGT 60.973 57.895 4.18 0.00 0.00 3.85
1367 5189 1.926511 CTGCGCCCAATGTTGAGGTC 61.927 60.000 4.18 0.00 0.00 3.85
1384 5206 1.630878 GGTCTTGAGGGTGTGATTCCT 59.369 52.381 0.00 0.00 35.82 3.36
1578 5416 5.171147 CTGAGATTCAGTCATGGCATTTC 57.829 43.478 0.00 0.00 39.58 2.17
1589 5427 5.587844 AGTCATGGCATTTCTTGTCAGTATC 59.412 40.000 0.00 0.00 44.71 2.24
1717 5625 0.537143 TTTGCGGAATCTGGCAGTGT 60.537 50.000 15.27 3.17 40.75 3.55
1839 5798 3.507233 GCTCTTGACATGTTCCATTTGGA 59.493 43.478 0.00 0.00 43.73 3.53
2262 6301 4.749245 ACTTTCTTGTGATTTGCCTACG 57.251 40.909 0.00 0.00 0.00 3.51
2606 7566 1.068352 AAGCCAGGGTGGAAGAAGGT 61.068 55.000 0.00 0.00 40.96 3.50
2867 7836 5.163405 TGAGATAACAAGGTGCAGAGGATAC 60.163 44.000 0.00 0.00 0.00 2.24
2875 7844 2.420129 GGTGCAGAGGATACGAATGGTT 60.420 50.000 0.00 0.00 46.39 3.67
2876 7845 3.181469 GGTGCAGAGGATACGAATGGTTA 60.181 47.826 0.00 0.00 46.39 2.85
2877 7846 4.503296 GGTGCAGAGGATACGAATGGTTAT 60.503 45.833 0.00 0.00 46.39 1.89
2878 7847 4.449068 GTGCAGAGGATACGAATGGTTATG 59.551 45.833 0.00 0.00 46.39 1.90
2879 7848 3.997021 GCAGAGGATACGAATGGTTATGG 59.003 47.826 0.00 0.00 46.39 2.74
2880 7849 3.997021 CAGAGGATACGAATGGTTATGGC 59.003 47.826 0.00 0.00 46.39 4.40
2881 7850 3.904339 AGAGGATACGAATGGTTATGGCT 59.096 43.478 0.00 0.00 46.39 4.75
2886 7855 2.790433 ACGAATGGTTATGGCTTGTGT 58.210 42.857 0.00 0.00 0.00 3.72
3326 8352 3.743521 ACGGATGCATATATGTGTGCTT 58.256 40.909 14.14 6.06 42.33 3.91
3637 8880 4.741928 AACCTGGGTCCTTTACATTCTT 57.258 40.909 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.784928 CGTGGGAACGTTTTGTTTTAGC 59.215 45.455 0.46 0.00 42.09 3.09
3 4 4.030366 GTCGTGGGAACGTTTTGTTTTAG 58.970 43.478 0.46 0.00 42.09 1.85
4 5 3.181502 GGTCGTGGGAACGTTTTGTTTTA 60.182 43.478 0.46 0.00 42.09 1.52
8 9 0.107557 AGGTCGTGGGAACGTTTTGT 60.108 50.000 0.46 0.00 34.09 2.83
10 11 0.466963 AGAGGTCGTGGGAACGTTTT 59.533 50.000 0.46 0.00 34.09 2.43
12 13 0.886563 CTAGAGGTCGTGGGAACGTT 59.113 55.000 0.00 0.00 34.09 3.99
13 14 0.037303 TCTAGAGGTCGTGGGAACGT 59.963 55.000 0.00 0.00 34.09 3.99
14 15 1.171308 TTCTAGAGGTCGTGGGAACG 58.829 55.000 0.00 0.00 34.09 3.95
15 16 3.889520 AATTCTAGAGGTCGTGGGAAC 57.110 47.619 0.00 0.00 0.00 3.62
16 17 4.903045 AAAATTCTAGAGGTCGTGGGAA 57.097 40.909 0.00 0.00 0.00 3.97
17 18 4.041198 ACAAAAATTCTAGAGGTCGTGGGA 59.959 41.667 0.00 0.00 0.00 4.37
18 19 4.324267 ACAAAAATTCTAGAGGTCGTGGG 58.676 43.478 0.00 0.00 0.00 4.61
19 20 4.994852 TGACAAAAATTCTAGAGGTCGTGG 59.005 41.667 0.00 0.00 0.00 4.94
20 21 6.539649 TTGACAAAAATTCTAGAGGTCGTG 57.460 37.500 0.00 0.00 0.00 4.35
21 22 7.497909 TCTTTTGACAAAAATTCTAGAGGTCGT 59.502 33.333 14.04 0.00 34.81 4.34
22 23 7.861630 TCTTTTGACAAAAATTCTAGAGGTCG 58.138 34.615 14.04 0.00 34.81 4.79
23 24 9.057089 TCTCTTTTGACAAAAATTCTAGAGGTC 57.943 33.333 18.38 0.00 34.81 3.85
24 25 8.980481 TCTCTTTTGACAAAAATTCTAGAGGT 57.020 30.769 18.38 0.00 34.81 3.85
555 591 4.164294 GTTTCGTACACGCTGATTACTCT 58.836 43.478 0.00 0.00 39.60 3.24
798 834 4.469469 AAAGACCCCCTCTGAAATGAAA 57.531 40.909 0.00 0.00 0.00 2.69
799 835 4.469469 AAAAGACCCCCTCTGAAATGAA 57.531 40.909 0.00 0.00 0.00 2.57
800 836 4.469469 AAAAAGACCCCCTCTGAAATGA 57.531 40.909 0.00 0.00 0.00 2.57
818 854 5.399858 TCCGTCGAACAAAATTGTCAAAAA 58.600 33.333 0.00 0.00 41.31 1.94
819 855 4.982999 TCCGTCGAACAAAATTGTCAAAA 58.017 34.783 0.00 0.00 41.31 2.44
820 856 4.617808 TCCGTCGAACAAAATTGTCAAA 57.382 36.364 0.00 0.00 41.31 2.69
821 857 4.532276 CATCCGTCGAACAAAATTGTCAA 58.468 39.130 0.00 0.00 41.31 3.18
822 858 3.058570 CCATCCGTCGAACAAAATTGTCA 60.059 43.478 0.00 0.00 41.31 3.58
823 859 3.058501 ACCATCCGTCGAACAAAATTGTC 60.059 43.478 0.00 0.00 41.31 3.18
824 860 2.882137 ACCATCCGTCGAACAAAATTGT 59.118 40.909 0.00 0.00 44.72 2.71
825 861 3.188460 AGACCATCCGTCGAACAAAATTG 59.812 43.478 0.00 0.00 46.92 2.32
826 862 3.408634 AGACCATCCGTCGAACAAAATT 58.591 40.909 0.00 0.00 46.92 1.82
827 863 3.000727 GAGACCATCCGTCGAACAAAAT 58.999 45.455 0.00 0.00 46.92 1.82
828 864 2.036733 AGAGACCATCCGTCGAACAAAA 59.963 45.455 0.00 0.00 46.92 2.44
829 865 1.616865 AGAGACCATCCGTCGAACAAA 59.383 47.619 0.00 0.00 46.92 2.83
830 866 1.254026 AGAGACCATCCGTCGAACAA 58.746 50.000 0.00 0.00 46.92 2.83
831 867 1.254026 AAGAGACCATCCGTCGAACA 58.746 50.000 0.00 0.00 46.92 3.18
832 868 2.365408 AAAGAGACCATCCGTCGAAC 57.635 50.000 0.00 0.00 46.92 3.95
833 869 4.240096 GTTAAAAGAGACCATCCGTCGAA 58.760 43.478 0.00 0.00 46.92 3.71
834 870 3.256383 TGTTAAAAGAGACCATCCGTCGA 59.744 43.478 0.00 0.00 46.92 4.20
835 871 3.581755 TGTTAAAAGAGACCATCCGTCG 58.418 45.455 0.00 0.00 46.92 5.12
836 872 5.934935 TTTGTTAAAAGAGACCATCCGTC 57.065 39.130 0.00 0.00 42.32 4.79
837 873 6.702716 TTTTTGTTAAAAGAGACCATCCGT 57.297 33.333 0.00 0.00 0.00 4.69
857 893 1.212195 GGGGCTAGAGGTCGGATTTTT 59.788 52.381 0.00 0.00 0.00 1.94
858 894 0.837940 GGGGCTAGAGGTCGGATTTT 59.162 55.000 0.00 0.00 0.00 1.82
859 895 1.400530 CGGGGCTAGAGGTCGGATTT 61.401 60.000 0.00 0.00 0.00 2.17
860 896 1.833049 CGGGGCTAGAGGTCGGATT 60.833 63.158 0.00 0.00 0.00 3.01
861 897 2.203509 CGGGGCTAGAGGTCGGAT 60.204 66.667 0.00 0.00 0.00 4.18
902 938 2.030958 GGTTGTGCGGGAGTAACGG 61.031 63.158 0.00 0.00 0.00 4.44
936 4738 1.107114 TCTCGATCTGCAGGAGGAAC 58.893 55.000 15.13 0.00 0.00 3.62
945 4753 4.734398 ATATCCATCCTTCTCGATCTGC 57.266 45.455 0.00 0.00 0.00 4.26
978 4786 1.201429 AGGAAGGGAAGCGGTGATGT 61.201 55.000 0.00 0.00 0.00 3.06
986 4794 1.821332 CGCATGGAGGAAGGGAAGC 60.821 63.158 0.00 0.00 0.00 3.86
1214 5022 2.589442 GACACCGCCCACGTCAAA 60.589 61.111 0.00 0.00 37.70 2.69
1216 5024 3.542676 AAGACACCGCCCACGTCA 61.543 61.111 0.00 0.00 37.70 4.35
1250 5059 2.033448 TGATGGCACGAACCACCC 59.967 61.111 3.30 0.68 44.17 4.61
1264 5081 1.271163 CCTTGTTGGTGGTACGGTGAT 60.271 52.381 0.00 0.00 0.00 3.06
1293 5115 0.980231 GGAGAGGCCATCAGGTGTCT 60.980 60.000 5.01 0.00 37.19 3.41
1294 5116 1.524482 GGAGAGGCCATCAGGTGTC 59.476 63.158 5.01 0.00 37.19 3.67
1295 5117 1.997874 GGGAGAGGCCATCAGGTGT 60.998 63.158 5.01 0.00 38.95 4.16
1296 5118 1.692042 AGGGAGAGGCCATCAGGTG 60.692 63.158 5.01 0.00 38.95 4.00
1297 5119 1.692042 CAGGGAGAGGCCATCAGGT 60.692 63.158 5.01 0.00 38.95 4.00
1298 5120 1.383664 TCAGGGAGAGGCCATCAGG 60.384 63.158 5.01 0.00 38.95 3.86
1299 5121 0.398239 TCTCAGGGAGAGGCCATCAG 60.398 60.000 5.01 0.00 44.81 2.90
1300 5122 0.043183 TTCTCAGGGAGAGGCCATCA 59.957 55.000 5.01 0.00 44.81 3.07
1360 5182 1.801242 TCACACCCTCAAGACCTCAA 58.199 50.000 0.00 0.00 0.00 3.02
1361 5183 2.030027 ATCACACCCTCAAGACCTCA 57.970 50.000 0.00 0.00 0.00 3.86
1362 5184 2.355209 GGAATCACACCCTCAAGACCTC 60.355 54.545 0.00 0.00 0.00 3.85
1363 5185 1.630878 GGAATCACACCCTCAAGACCT 59.369 52.381 0.00 0.00 0.00 3.85
1364 5186 1.630878 AGGAATCACACCCTCAAGACC 59.369 52.381 0.00 0.00 0.00 3.85
1365 5187 3.515901 ACTAGGAATCACACCCTCAAGAC 59.484 47.826 0.00 0.00 34.11 3.01
1366 5188 3.515502 CACTAGGAATCACACCCTCAAGA 59.484 47.826 0.00 0.00 34.11 3.02
1367 5189 3.515502 TCACTAGGAATCACACCCTCAAG 59.484 47.826 0.00 0.00 34.11 3.02
1384 5206 1.303888 ACGGCGGTCCTTCTCACTA 60.304 57.895 13.24 0.00 0.00 2.74
1409 5231 1.073923 GGGAGGTGTGAAGTCCATTGT 59.926 52.381 0.00 0.00 31.31 2.71
1578 5416 4.567959 TCATGTTCATGCGATACTGACAAG 59.432 41.667 7.80 0.00 0.00 3.16
1589 5427 4.614946 TCAGTCTCTATCATGTTCATGCG 58.385 43.478 7.80 0.57 0.00 4.73
1717 5625 6.944290 ACATGATTCTCATTCTTGGACTGAAA 59.056 34.615 0.00 0.00 34.28 2.69
2092 6111 2.299993 TCAGCAATAGACTTCCAGCG 57.700 50.000 0.00 0.00 0.00 5.18
2139 6158 2.236395 TCCCGGCTCCTTAAGAAGAAAG 59.764 50.000 3.36 0.00 0.00 2.62
2140 6159 2.262637 TCCCGGCTCCTTAAGAAGAAA 58.737 47.619 3.36 0.00 0.00 2.52
2141 6160 1.946984 TCCCGGCTCCTTAAGAAGAA 58.053 50.000 3.36 0.00 0.00 2.52
2142 6161 1.831736 CTTCCCGGCTCCTTAAGAAGA 59.168 52.381 3.36 0.00 34.07 2.87
2867 7836 3.009723 AGACACAAGCCATAACCATTCG 58.990 45.455 0.00 0.00 0.00 3.34
2875 7844 1.271871 CCCCACAAGACACAAGCCATA 60.272 52.381 0.00 0.00 0.00 2.74
2876 7845 0.540365 CCCCACAAGACACAAGCCAT 60.540 55.000 0.00 0.00 0.00 4.40
2877 7846 1.152777 CCCCACAAGACACAAGCCA 60.153 57.895 0.00 0.00 0.00 4.75
2878 7847 1.152756 ACCCCACAAGACACAAGCC 60.153 57.895 0.00 0.00 0.00 4.35
2879 7848 0.465460 TGACCCCACAAGACACAAGC 60.465 55.000 0.00 0.00 0.00 4.01
2880 7849 1.597742 CTGACCCCACAAGACACAAG 58.402 55.000 0.00 0.00 0.00 3.16
2881 7850 0.465460 GCTGACCCCACAAGACACAA 60.465 55.000 0.00 0.00 0.00 3.33
2886 7855 3.636231 CCGGCTGACCCCACAAGA 61.636 66.667 0.00 0.00 0.00 3.02
3839 9308 9.383519 GATGAATATACACTCAGGACAAGAAAA 57.616 33.333 0.00 0.00 0.00 2.29
4136 9629 5.755861 GGAGAGGGAATTCTACAATTTCTCG 59.244 44.000 5.23 0.00 35.74 4.04
4245 9738 4.319177 AGTGGAATTACAGTTCAGACAGC 58.681 43.478 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.