Multiple sequence alignment - TraesCS4A01G138900

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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 TraesCS4A01G138900 chr4A 100.000 4937 0 0 1 4937 207379491 207384427 0.000000e+00 9118.0
1 TraesCS4A01G138900 chr4A 100.000 3082 0 0 5272 8353 207384762 207387843 0.000000e+00 5692.0
2 TraesCS4A01G138900 chr4A 95.067 750 32 5 6240 6986 353123433 353122686 0.000000e+00 1175.0
3 TraesCS4A01G138900 chr4A 94.291 508 25 4 7378 7882 353110057 353109551 0.000000e+00 774.0
4 TraesCS4A01G138900 chr4A 87.066 317 18 3 7073 7388 353122678 353122384 3.740000e-88 337.0
5 TraesCS4A01G138900 chr4A 89.640 222 20 2 3556 3775 687398144 687397924 6.380000e-71 279.0
6 TraesCS4A01G138900 chr4A 85.448 268 37 2 3104 3370 584546743 584546477 2.300000e-70 278.0
7 TraesCS4A01G138900 chr4A 95.000 60 3 0 15 74 705328387 705328328 2.480000e-15 95.3
8 TraesCS4A01G138900 chr4A 96.875 32 1 0 4242 4273 207383609 207383640 4.000000e-03 54.7
9 TraesCS4A01G138900 chr4A 96.875 32 1 0 4119 4150 207383732 207383763 4.000000e-03 54.7
10 TraesCS4A01G138900 chr6A 97.815 3569 39 6 1388 4937 599240113 599236565 0.000000e+00 6122.0
11 TraesCS4A01G138900 chr6A 97.537 1624 39 1 6730 8353 599217668 599216046 0.000000e+00 2776.0
12 TraesCS4A01G138900 chr6A 98.426 1461 21 2 5272 6731 599236517 599235058 0.000000e+00 2569.0
13 TraesCS4A01G138900 chr6A 98.094 1102 12 6 69 1168 599241532 599240438 0.000000e+00 1910.0
14 TraesCS4A01G138900 chr6A 91.057 123 10 1 855 977 447842648 447842769 1.870000e-36 165.0
15 TraesCS4A01G138900 chr6A 90.400 125 11 1 855 979 601155792 601155669 6.710000e-36 163.0
16 TraesCS4A01G138900 chr6A 96.875 32 1 0 4119 4150 599237262 599237231 4.000000e-03 54.7
17 TraesCS4A01G138900 chr2B 86.349 1238 83 24 980 2151 9122880 9121663 0.000000e+00 1271.0
18 TraesCS4A01G138900 chr2B 88.300 547 45 2 1862 2389 8999572 9000118 9.140000e-179 638.0
19 TraesCS4A01G138900 chr2B 89.542 459 43 2 7890 8348 789011524 789011977 2.020000e-160 577.0
20 TraesCS4A01G138900 chr2B 83.716 479 40 8 1928 2389 9091588 9091131 1.300000e-112 418.0
21 TraesCS4A01G138900 chr2B 86.364 352 29 10 1420 1769 8999087 8999421 4.760000e-97 366.0
22 TraesCS4A01G138900 chr2B 75.871 804 99 48 1507 2250 8538233 8539001 1.050000e-83 322.0
23 TraesCS4A01G138900 chr2B 90.323 217 18 3 3563 3777 105837332 105837547 1.780000e-71 281.0
24 TraesCS4A01G138900 chr2B 96.970 33 1 0 2234 2266 8539155 8539187 1.000000e-03 56.5
25 TraesCS4A01G138900 chr2B 100.000 28 0 0 984 1011 8998933 8998960 1.500000e-02 52.8
26 TraesCS4A01G138900 chrUn 85.450 1299 92 22 1110 2359 418518220 418519470 0.000000e+00 1262.0
27 TraesCS4A01G138900 chrUn 82.915 1434 119 42 1027 2389 15914708 15913330 0.000000e+00 1175.0
28 TraesCS4A01G138900 chrUn 85.133 1056 70 23 1036 2059 364735908 364736908 0.000000e+00 1000.0
29 TraesCS4A01G138900 chrUn 100.000 404 0 0 3184 3587 478307493 478307090 0.000000e+00 747.0
30 TraesCS4A01G138900 chrUn 90.233 215 18 3 3563 3775 350282178 350281965 2.300000e-70 278.0
31 TraesCS4A01G138900 chrUn 87.821 156 17 2 1107 1261 15490891 15490737 1.850000e-41 182.0
32 TraesCS4A01G138900 chrUn 90.400 125 11 1 855 979 33216781 33216658 6.710000e-36 163.0
33 TraesCS4A01G138900 chrUn 95.789 95 3 1 855 949 49949792 49949885 1.450000e-32 152.0
34 TraesCS4A01G138900 chr7A 96.486 740 20 6 6244 6980 269089629 269088893 0.000000e+00 1218.0
35 TraesCS4A01G138900 chr7A 92.506 814 36 5 7072 7882 269088891 269088100 0.000000e+00 1142.0
36 TraesCS4A01G138900 chr7A 83.276 580 56 13 308 852 33510936 33511509 5.820000e-136 496.0
37 TraesCS4A01G138900 chr7A 92.308 273 17 2 3960 4232 665667283 665667015 1.320000e-102 385.0
38 TraesCS4A01G138900 chr7A 90.610 213 18 1 4269 4481 665667009 665666799 1.780000e-71 281.0
39 TraesCS4A01G138900 chr7A 81.938 227 19 3 6485 6701 634394615 634394829 1.110000e-38 172.0
40 TraesCS4A01G138900 chr7A 96.491 57 2 0 15 71 304764966 304764910 2.480000e-15 95.3
41 TraesCS4A01G138900 chr7A 80.583 103 14 4 6712 6812 12404375 12404473 3.230000e-09 75.0
42 TraesCS4A01G138900 chr7A 96.875 32 1 0 4242 4273 665667124 665667093 4.000000e-03 54.7
43 TraesCS4A01G138900 chr1D 92.140 687 34 6 4269 4937 364490986 364491670 0.000000e+00 952.0
44 TraesCS4A01G138900 chr1D 93.112 421 28 1 3781 4201 364473648 364474067 4.280000e-172 616.0
45 TraesCS4A01G138900 chr1D 88.337 463 48 2 7890 8348 421660529 421660989 1.230000e-152 551.0
46 TraesCS4A01G138900 chr1D 91.941 273 19 1 3960 4232 12979788 12979519 6.120000e-101 379.0
47 TraesCS4A01G138900 chr1D 90.187 214 18 2 4269 4481 12979513 12979302 8.260000e-70 276.0
48 TraesCS4A01G138900 chr1D 88.889 216 21 3 7669 7882 421660111 421660325 6.430000e-66 263.0
49 TraesCS4A01G138900 chr1D 96.875 32 1 0 4242 4273 364473985 364474016 4.000000e-03 54.7
50 TraesCS4A01G138900 chr2A 79.606 1319 137 58 1027 2249 2325755 2327037 0.000000e+00 824.0
51 TraesCS4A01G138900 chr2A 86.629 703 43 14 1592 2247 2383022 2383720 0.000000e+00 730.0
52 TraesCS4A01G138900 chr2A 85.988 678 45 5 1522 2151 2490023 2489348 0.000000e+00 680.0
53 TraesCS4A01G138900 chr2A 89.648 454 45 1 7889 8342 197558855 197559306 2.020000e-160 577.0
54 TraesCS4A01G138900 chr2A 86.866 434 28 10 1027 1457 2490442 2490035 7.640000e-125 459.0
55 TraesCS4A01G138900 chr2A 82.143 448 65 8 189 633 58956406 58956841 3.680000e-98 370.0
56 TraesCS4A01G138900 chr2A 91.406 256 17 3 1035 1288 2382585 2382837 6.210000e-91 346.0
57 TraesCS4A01G138900 chr2A 94.222 225 12 1 2165 2389 2920065 2920288 8.030000e-90 342.0
58 TraesCS4A01G138900 chr2A 81.250 208 15 8 1367 1558 2382828 2383027 6.760000e-31 147.0
59 TraesCS4A01G138900 chr2A 95.385 65 3 0 2325 2389 2383759 2383823 4.120000e-18 104.0
60 TraesCS4A01G138900 chr2D 86.259 735 50 6 1493 2177 2537742 2537009 0.000000e+00 750.0
61 TraesCS4A01G138900 chr2D 86.254 582 37 12 1825 2389 2466798 2467353 7.220000e-165 592.0
62 TraesCS4A01G138900 chr2D 89.205 352 27 5 1127 1477 22566608 22566267 5.990000e-116 429.0
63 TraesCS4A01G138900 chr2D 89.286 56 6 0 135 190 565857539 565857594 4.180000e-08 71.3
64 TraesCS4A01G138900 chr2D 96.774 31 1 0 984 1014 22566789 22566759 1.500000e-02 52.8
65 TraesCS4A01G138900 chr6D 90.733 464 38 2 7885 8348 336836142 336835684 1.540000e-171 614.0
66 TraesCS4A01G138900 chr3A 90.414 459 41 2 7890 8347 46216175 46215719 1.200000e-167 601.0
67 TraesCS4A01G138900 chr6B 89.849 463 39 5 7889 8348 42818857 42818400 9.340000e-164 588.0
68 TraesCS4A01G138900 chr6B 88.196 449 48 4 7901 8348 101740109 101739665 1.600000e-146 531.0
69 TraesCS4A01G138900 chr6B 90.233 215 18 3 3563 3775 19942454 19942667 2.300000e-70 278.0
70 TraesCS4A01G138900 chr6B 90.233 215 18 3 3563 3775 19960577 19960790 2.300000e-70 278.0
71 TraesCS4A01G138900 chr6B 90.187 214 19 1 7669 7882 101740445 101740234 2.300000e-70 278.0
72 TraesCS4A01G138900 chr6B 96.491 57 2 0 15 71 100072739 100072683 2.480000e-15 95.3
73 TraesCS4A01G138900 chr5A 88.913 460 49 1 7889 8348 671547362 671547819 4.380000e-157 566.0
74 TraesCS4A01G138900 chr5A 91.200 125 10 1 855 979 433727039 433726916 1.440000e-37 169.0
75 TraesCS4A01G138900 chr5A 100.000 51 0 0 15 65 597892542 597892592 2.480000e-15 95.3
76 TraesCS4A01G138900 chr5A 100.000 35 0 0 3784 3818 602965051 602965017 1.950000e-06 65.8
77 TraesCS4A01G138900 chr1B 94.100 339 20 0 3781 4119 487774231 487774569 4.470000e-142 516.0
78 TraesCS4A01G138900 chr1B 100.000 51 0 0 15 65 473499471 473499521 2.480000e-15 95.3
79 TraesCS4A01G138900 chr3B 89.514 391 37 3 2392 2782 328600217 328600603 7.530000e-135 492.0
80 TraesCS4A01G138900 chr3B 82.173 359 53 9 7143 7495 73252771 73252418 1.760000e-76 298.0
81 TraesCS4A01G138900 chr3B 89.474 133 12 2 848 979 328599897 328600028 5.190000e-37 167.0
82 TraesCS4A01G138900 chr3B 96.491 57 2 0 15 71 754953590 754953534 2.480000e-15 95.3
83 TraesCS4A01G138900 chr5B 84.980 506 41 13 5779 6284 430290035 430289565 1.630000e-131 481.0
84 TraesCS4A01G138900 chr5B 81.229 602 66 26 283 852 123405553 123406139 7.690000e-120 442.0
85 TraesCS4A01G138900 chr5B 81.399 586 61 23 300 852 123205234 123205804 1.290000e-117 435.0
86 TraesCS4A01G138900 chr5B 92.391 276 18 2 5501 5776 430290420 430290148 2.830000e-104 390.0
87 TraesCS4A01G138900 chr5B 96.842 95 2 1 855 949 49501636 49501729 3.120000e-34 158.0
88 TraesCS4A01G138900 chr5B 98.182 55 1 0 15 69 137673772 137673826 6.900000e-16 97.1
89 TraesCS4A01G138900 chr5B 91.111 45 4 0 3781 3825 278795932 278795976 2.520000e-05 62.1
90 TraesCS4A01G138900 chr4B 75.885 904 148 42 1501 2361 634317960 634318836 1.690000e-106 398.0
91 TraesCS4A01G138900 chr4B 85.766 274 37 2 3098 3370 27645102 27645374 1.060000e-73 289.0
92 TraesCS4A01G138900 chr5D 92.164 268 18 2 3960 4227 404406089 404406353 7.920000e-100 375.0
93 TraesCS4A01G138900 chr5D 90.654 214 18 1 7669 7882 298137223 298137434 4.940000e-72 283.0
94 TraesCS4A01G138900 chr5D 90.821 207 17 1 4269 4475 404406364 404406568 8.260000e-70 276.0
95 TraesCS4A01G138900 chr3D 85.761 309 38 6 3464 3771 601882460 601882763 1.050000e-83 322.0
96 TraesCS4A01G138900 chr3D 85.305 279 39 2 3466 3744 55102914 55102638 3.820000e-73 287.0
97 TraesCS4A01G138900 chr3D 97.297 37 1 0 3781 3817 560157398 560157434 7.000000e-06 63.9
98 TraesCS4A01G138900 chr7D 84.946 279 38 4 3466 3744 497575910 497576184 6.380000e-71 279.0
99 TraesCS4A01G138900 chr7D 96.629 89 2 1 855 943 477107272 477107359 6.760000e-31 147.0
100 TraesCS4A01G138900 chr7D 96.667 60 1 1 15 74 489245832 489245890 1.920000e-16 99.0
101 TraesCS4A01G138900 chr7D 80.583 103 14 4 6712 6812 13003907 13004005 3.230000e-09 75.0
102 TraesCS4A01G138900 chr4D 85.448 268 37 2 3104 3370 16056010 16055744 2.300000e-70 278.0
103 TraesCS4A01G138900 chr7B 79.255 376 48 12 188 561 592674751 592674404 1.400000e-57 235.0
104 TraesCS4A01G138900 chr7B 86.547 223 15 3 6482 6701 592517290 592517500 1.810000e-56 231.0
105 TraesCS4A01G138900 chr1A 100.000 50 0 0 16 65 546267832 546267783 8.930000e-15 93.5


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 TraesCS4A01G138900 chr4A 207379491 207387843 8352 False 3729.850000 9118 98.437500 1 8353 4 chr4A.!!$F1 8352
1 TraesCS4A01G138900 chr4A 353109551 353110057 506 True 774.000000 774 94.291000 7378 7882 1 chr4A.!!$R1 504
2 TraesCS4A01G138900 chr4A 353122384 353123433 1049 True 756.000000 1175 91.066500 6240 7388 2 chr4A.!!$R5 1148
3 TraesCS4A01G138900 chr6A 599216046 599217668 1622 True 2776.000000 2776 97.537000 6730 8353 1 chr6A.!!$R1 1623
4 TraesCS4A01G138900 chr6A 599235058 599241532 6474 True 2663.925000 6122 97.802500 69 6731 4 chr6A.!!$R3 6662
5 TraesCS4A01G138900 chr2B 9121663 9122880 1217 True 1271.000000 1271 86.349000 980 2151 1 chr2B.!!$R2 1171
6 TraesCS4A01G138900 chr2B 8998933 9000118 1185 False 352.266667 638 91.554667 984 2389 3 chr2B.!!$F4 1405
7 TraesCS4A01G138900 chrUn 418518220 418519470 1250 False 1262.000000 1262 85.450000 1110 2359 1 chrUn.!!$F3 1249
8 TraesCS4A01G138900 chrUn 15913330 15914708 1378 True 1175.000000 1175 82.915000 1027 2389 1 chrUn.!!$R2 1362
9 TraesCS4A01G138900 chrUn 364735908 364736908 1000 False 1000.000000 1000 85.133000 1036 2059 1 chrUn.!!$F2 1023
10 TraesCS4A01G138900 chr7A 269088100 269089629 1529 True 1180.000000 1218 94.496000 6244 7882 2 chr7A.!!$R2 1638
11 TraesCS4A01G138900 chr7A 33510936 33511509 573 False 496.000000 496 83.276000 308 852 1 chr7A.!!$F2 544
12 TraesCS4A01G138900 chr1D 364490986 364491670 684 False 952.000000 952 92.140000 4269 4937 1 chr1D.!!$F1 668
13 TraesCS4A01G138900 chr1D 421660111 421660989 878 False 407.000000 551 88.613000 7669 8348 2 chr1D.!!$F3 679
14 TraesCS4A01G138900 chr2A 2325755 2327037 1282 False 824.000000 824 79.606000 1027 2249 1 chr2A.!!$F1 1222
15 TraesCS4A01G138900 chr2A 2489348 2490442 1094 True 569.500000 680 86.427000 1027 2151 2 chr2A.!!$R1 1124
16 TraesCS4A01G138900 chr2A 2382585 2383823 1238 False 331.750000 730 88.667500 1035 2389 4 chr2A.!!$F5 1354
17 TraesCS4A01G138900 chr2D 2537009 2537742 733 True 750.000000 750 86.259000 1493 2177 1 chr2D.!!$R1 684
18 TraesCS4A01G138900 chr2D 2466798 2467353 555 False 592.000000 592 86.254000 1825 2389 1 chr2D.!!$F1 564
19 TraesCS4A01G138900 chr2D 22566267 22566789 522 True 240.900000 429 92.989500 984 1477 2 chr2D.!!$R2 493
20 TraesCS4A01G138900 chr6B 101739665 101740445 780 True 404.500000 531 89.191500 7669 8348 2 chr6B.!!$R3 679
21 TraesCS4A01G138900 chr3B 328599897 328600603 706 False 329.500000 492 89.494000 848 2782 2 chr3B.!!$F1 1934
22 TraesCS4A01G138900 chr5B 123405553 123406139 586 False 442.000000 442 81.229000 283 852 1 chr5B.!!$F3 569
23 TraesCS4A01G138900 chr5B 430289565 430290420 855 True 435.500000 481 88.685500 5501 6284 2 chr5B.!!$R1 783
24 TraesCS4A01G138900 chr5B 123205234 123205804 570 False 435.000000 435 81.399000 300 852 1 chr5B.!!$F2 552
25 TraesCS4A01G138900 chr4B 634317960 634318836 876 False 398.000000 398 75.885000 1501 2361 1 chr4B.!!$F2 860

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
43 44 0.042731 AGGGGGTCAATTCTCGGAGA 59.957 55.000 2.97 2.97 0.00 3.71 F
63 64 0.686789 ATTGCCCAAAAGAACTGGCC 59.313 50.000 0.00 0.00 43.35 5.36 F
67 68 1.228429 CCAAAAGAACTGGCCCCGA 60.228 57.895 0.00 0.00 0.00 5.14 F
1366 1520 1.536766 TCAGCACCTTTCTTTGATGCG 59.463 47.619 0.00 0.00 41.23 4.73 F
3895 4378 0.478072 TGGGTTGTGGAAGACTGCAT 59.522 50.000 0.00 0.00 0.00 3.96 F
4016 4499 0.755698 TATCGCCTCTGTCTCCACCC 60.756 60.000 0.00 0.00 0.00 4.61 F
5685 6185 1.287815 CTGCCATTGCCATATGCCG 59.712 57.895 0.00 0.00 40.16 5.69 F
7009 7624 0.968405 TCCATTGTTGCCTGCCTTTC 59.032 50.000 0.00 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2297 0.820891 ACACCTGAACAGCAAGCCAG 60.821 55.000 0.00 0.00 0.00 4.85 R
2966 3449 7.166473 GCCTTTGAAAATATATTTCAGAGCACG 59.834 37.037 11.08 5.43 38.53 5.34 R
3053 3536 3.531262 ACCGTGCGACAAACTAAAATC 57.469 42.857 0.00 0.00 0.00 2.17 R
4119 4602 1.073722 CAAGCAGAAGCCACCCTCA 59.926 57.895 0.00 0.00 43.56 3.86 R
6245 6856 0.320771 AGACCTGTTACCTTGCTGCG 60.321 55.000 0.00 0.00 0.00 5.18 R
6993 7608 1.648116 ATGGAAAGGCAGGCAACAAT 58.352 45.000 0.00 0.00 41.41 2.71 R
7267 7882 1.301244 ATGATGTCGATGAGCCCGC 60.301 57.895 0.00 0.00 0.00 6.13 R
7963 8779 6.430864 TGAGGACCCAAATTTATGAATGCTA 58.569 36.000 0.00 0.00 0.00 3.49 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
17 18 3.404773 GGGTGGGAGGGACTGAAG 58.595 66.667 0.00 0.00 41.55 3.02
18 19 2.671682 GGTGGGAGGGACTGAAGC 59.328 66.667 0.00 0.00 41.55 3.86
19 20 1.920835 GGTGGGAGGGACTGAAGCT 60.921 63.158 0.00 0.00 41.55 3.74
20 21 1.298014 GTGGGAGGGACTGAAGCTG 59.702 63.158 0.00 0.00 41.55 4.24
21 22 1.920325 TGGGAGGGACTGAAGCTGG 60.920 63.158 0.00 0.00 41.55 4.85
22 23 2.674220 GGGAGGGACTGAAGCTGGG 61.674 68.421 0.00 0.00 41.55 4.45
23 24 2.674220 GGAGGGACTGAAGCTGGGG 61.674 68.421 0.00 0.00 41.55 4.96
24 25 1.613630 GAGGGACTGAAGCTGGGGA 60.614 63.158 0.00 0.00 41.55 4.81
25 26 1.614824 AGGGACTGAAGCTGGGGAG 60.615 63.158 0.00 0.00 37.18 4.30
26 27 2.674220 GGGACTGAAGCTGGGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
27 28 2.674220 GGACTGAAGCTGGGGAGGG 61.674 68.421 0.00 0.00 0.00 4.30
28 29 2.612115 ACTGAAGCTGGGGAGGGG 60.612 66.667 0.00 0.00 0.00 4.79
29 30 3.415087 CTGAAGCTGGGGAGGGGG 61.415 72.222 0.00 0.00 0.00 5.40
30 31 4.285790 TGAAGCTGGGGAGGGGGT 62.286 66.667 0.00 0.00 0.00 4.95
31 32 3.412408 GAAGCTGGGGAGGGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
32 33 4.285790 AAGCTGGGGAGGGGGTCA 62.286 66.667 0.00 0.00 0.00 4.02
33 34 3.829311 AAGCTGGGGAGGGGGTCAA 62.829 63.158 0.00 0.00 0.00 3.18
34 35 3.023735 GCTGGGGAGGGGGTCAAT 61.024 66.667 0.00 0.00 0.00 2.57
35 36 2.626467 GCTGGGGAGGGGGTCAATT 61.626 63.158 0.00 0.00 0.00 2.32
36 37 1.615262 CTGGGGAGGGGGTCAATTC 59.385 63.158 0.00 0.00 0.00 2.17
37 38 0.921256 CTGGGGAGGGGGTCAATTCT 60.921 60.000 0.00 0.00 0.00 2.40
38 39 0.919289 TGGGGAGGGGGTCAATTCTC 60.919 60.000 0.00 0.00 0.00 2.87
39 40 1.527370 GGGAGGGGGTCAATTCTCG 59.473 63.158 0.00 0.00 0.00 4.04
40 41 1.527370 GGAGGGGGTCAATTCTCGG 59.473 63.158 0.00 0.00 0.00 4.63
41 42 0.981277 GGAGGGGGTCAATTCTCGGA 60.981 60.000 0.00 0.00 0.00 4.55
42 43 0.466124 GAGGGGGTCAATTCTCGGAG 59.534 60.000 0.00 0.00 0.00 4.63
43 44 0.042731 AGGGGGTCAATTCTCGGAGA 59.957 55.000 2.97 2.97 0.00 3.71
44 45 0.909623 GGGGGTCAATTCTCGGAGAA 59.090 55.000 21.69 21.69 38.78 2.87
45 46 1.490910 GGGGGTCAATTCTCGGAGAAT 59.509 52.381 24.03 24.03 46.22 2.40
52 53 2.806945 ATTCTCGGAGAATTGCCCAA 57.193 45.000 24.03 1.04 41.90 4.12
53 54 2.577606 TTCTCGGAGAATTGCCCAAA 57.422 45.000 16.19 0.00 34.09 3.28
54 55 2.577606 TCTCGGAGAATTGCCCAAAA 57.422 45.000 4.96 0.00 34.09 2.44
55 56 2.436417 TCTCGGAGAATTGCCCAAAAG 58.564 47.619 4.96 0.00 34.09 2.27
56 57 2.039746 TCTCGGAGAATTGCCCAAAAGA 59.960 45.455 4.96 0.00 34.09 2.52
57 58 2.819608 CTCGGAGAATTGCCCAAAAGAA 59.180 45.455 0.00 0.00 34.09 2.52
58 59 2.556622 TCGGAGAATTGCCCAAAAGAAC 59.443 45.455 0.00 0.00 0.00 3.01
59 60 2.558359 CGGAGAATTGCCCAAAAGAACT 59.442 45.455 0.00 0.00 0.00 3.01
60 61 3.612479 CGGAGAATTGCCCAAAAGAACTG 60.612 47.826 0.00 0.00 0.00 3.16
61 62 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
62 63 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
63 64 0.686789 ATTGCCCAAAAGAACTGGCC 59.313 50.000 0.00 0.00 43.35 5.36
64 65 1.406860 TTGCCCAAAAGAACTGGCCC 61.407 55.000 0.00 0.00 43.35 5.80
65 66 2.583441 GCCCAAAAGAACTGGCCCC 61.583 63.158 0.00 0.00 37.94 5.80
66 67 2.275380 CCCAAAAGAACTGGCCCCG 61.275 63.158 0.00 0.00 32.10 5.73
67 68 1.228429 CCAAAAGAACTGGCCCCGA 60.228 57.895 0.00 0.00 0.00 5.14
1288 1439 3.393089 TGTGAGAGGAGAAGCAGAAAC 57.607 47.619 0.00 0.00 0.00 2.78
1289 1440 2.037772 TGTGAGAGGAGAAGCAGAAACC 59.962 50.000 0.00 0.00 0.00 3.27
1335 1488 2.233676 GGCACCCAAAATACTTTCCTGG 59.766 50.000 0.00 0.00 0.00 4.45
1336 1489 2.353704 GCACCCAAAATACTTTCCTGGC 60.354 50.000 0.00 0.00 0.00 4.85
1366 1520 1.536766 TCAGCACCTTTCTTTGATGCG 59.463 47.619 0.00 0.00 41.23 4.73
1386 1540 4.749245 CGAAGCAGGAACAACATACTTT 57.251 40.909 0.00 0.00 0.00 2.66
1628 1866 4.473196 ACACCCCTTTTCTTTCCACAAATT 59.527 37.500 0.00 0.00 0.00 1.82
1632 1871 6.556874 ACCCCTTTTCTTTCCACAAATTGATA 59.443 34.615 0.00 0.00 0.00 2.15
1938 2297 6.187125 TGTTCTTGCATCTCTAATTTCTGC 57.813 37.500 0.00 0.00 0.00 4.26
2876 3359 4.274459 GCTGGTTGTTCATATCCTTAGCTG 59.726 45.833 0.00 0.00 0.00 4.24
2965 3448 5.793675 CATGCGATGCTACTTCTATATTGC 58.206 41.667 0.00 0.00 0.00 3.56
2966 3449 4.245660 TGCGATGCTACTTCTATATTGCC 58.754 43.478 0.00 0.00 0.00 4.52
3182 3665 2.728839 CAGAACACTCTTGAGAAGCGAC 59.271 50.000 4.49 0.00 0.00 5.19
3867 4350 2.969238 CATCGCTGGATCGGTGGC 60.969 66.667 0.00 0.00 36.96 5.01
3895 4378 0.478072 TGGGTTGTGGAAGACTGCAT 59.522 50.000 0.00 0.00 0.00 3.96
4016 4499 0.755698 TATCGCCTCTGTCTCCACCC 60.756 60.000 0.00 0.00 0.00 4.61
4119 4602 1.967319 ATGAACTGCAGGACGTGTTT 58.033 45.000 19.93 0.18 0.00 2.83
4620 5103 8.239038 TGATTTTAAGGTCTGAGTCGATCTAT 57.761 34.615 0.00 0.00 0.00 1.98
4856 5356 1.885887 GCCCAGATTAGTTGTTGTGCA 59.114 47.619 0.00 0.00 0.00 4.57
5366 5866 3.787001 GGTGGCGGAGGAGGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
5367 5867 3.787001 GTGGCGGAGGAGGAAGGG 61.787 72.222 0.00 0.00 0.00 3.95
5539 6039 8.997621 AGCTTAATCTGAAACTAATTACACGA 57.002 30.769 0.00 0.00 0.00 4.35
5568 6068 5.677178 GTGCTTTAATTTGCTAGATGTACGC 59.323 40.000 0.00 0.00 0.00 4.42
5685 6185 1.287815 CTGCCATTGCCATATGCCG 59.712 57.895 0.00 0.00 40.16 5.69
5848 6458 2.296190 TCTCTGCTGCACGAGAACTTAA 59.704 45.455 21.38 5.91 33.62 1.85
6174 6785 2.040009 CTGTCCGGTGGGTCAGTTGT 62.040 60.000 0.00 0.00 42.39 3.32
6240 6851 2.656069 CCCTCACCCACTACCACGG 61.656 68.421 0.00 0.00 0.00 4.94
6245 6856 3.782443 CCCACTACCACGGCTCCC 61.782 72.222 0.00 0.00 0.00 4.30
6993 7608 2.942752 GCACATCTGGAGCATCTTTCCA 60.943 50.000 0.00 0.00 42.30 3.53
7009 7624 0.968405 TCCATTGTTGCCTGCCTTTC 59.032 50.000 0.00 0.00 0.00 2.62
7025 7640 4.082081 TGCCTTTCCATTGTTAAGATGCTG 60.082 41.667 0.00 0.00 0.00 4.41
7041 7656 1.005097 TGCTGGAGGAGACTAACCGTA 59.995 52.381 0.00 0.00 44.43 4.02
7140 7755 3.932545 TTATTGCTGCCAAATGTCGTT 57.067 38.095 0.00 0.00 34.05 3.85
7154 7769 6.403200 CCAAATGTCGTTGGTACTAATTCTGG 60.403 42.308 0.00 0.00 42.74 3.86
7635 8252 8.173542 TCCATCTCATATTTTTCATCCATGTG 57.826 34.615 0.00 0.00 0.00 3.21
7963 8779 6.015180 TGCTCTTTCATCAGCCATTTTACTTT 60.015 34.615 0.00 0.00 34.47 2.66
8163 8979 8.095452 AGAGAACCTATTGGACTACATTGATT 57.905 34.615 0.00 0.00 37.04 2.57
8337 9157 8.408043 TGTGTATTTCATTTCAGGATCACTTT 57.592 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.674220 CCCAGCTTCAGTCCCTCCC 61.674 68.421 0.00 0.00 0.00 4.30
5 6 2.674220 CCCCAGCTTCAGTCCCTCC 61.674 68.421 0.00 0.00 0.00 4.30
6 7 1.613630 TCCCCAGCTTCAGTCCCTC 60.614 63.158 0.00 0.00 0.00 4.30
8 9 2.674220 CCTCCCCAGCTTCAGTCCC 61.674 68.421 0.00 0.00 0.00 4.46
9 10 2.674220 CCCTCCCCAGCTTCAGTCC 61.674 68.421 0.00 0.00 0.00 3.85
10 11 2.674220 CCCCTCCCCAGCTTCAGTC 61.674 68.421 0.00 0.00 0.00 3.51
11 12 2.612115 CCCCTCCCCAGCTTCAGT 60.612 66.667 0.00 0.00 0.00 3.41
12 13 3.415087 CCCCCTCCCCAGCTTCAG 61.415 72.222 0.00 0.00 0.00 3.02
13 14 4.285790 ACCCCCTCCCCAGCTTCA 62.286 66.667 0.00 0.00 0.00 3.02
14 15 3.412408 GACCCCCTCCCCAGCTTC 61.412 72.222 0.00 0.00 0.00 3.86
15 16 3.829311 TTGACCCCCTCCCCAGCTT 62.829 63.158 0.00 0.00 0.00 3.74
16 17 3.603330 ATTGACCCCCTCCCCAGCT 62.603 63.158 0.00 0.00 0.00 4.24
17 18 2.573893 GAATTGACCCCCTCCCCAGC 62.574 65.000 0.00 0.00 0.00 4.85
18 19 0.921256 AGAATTGACCCCCTCCCCAG 60.921 60.000 0.00 0.00 0.00 4.45
19 20 0.919289 GAGAATTGACCCCCTCCCCA 60.919 60.000 0.00 0.00 0.00 4.96
20 21 1.923586 GAGAATTGACCCCCTCCCC 59.076 63.158 0.00 0.00 0.00 4.81
21 22 1.527370 CGAGAATTGACCCCCTCCC 59.473 63.158 0.00 0.00 0.00 4.30
22 23 0.981277 TCCGAGAATTGACCCCCTCC 60.981 60.000 0.00 0.00 0.00 4.30
23 24 0.466124 CTCCGAGAATTGACCCCCTC 59.534 60.000 0.00 0.00 0.00 4.30
24 25 0.042731 TCTCCGAGAATTGACCCCCT 59.957 55.000 0.00 0.00 0.00 4.79
25 26 0.909623 TTCTCCGAGAATTGACCCCC 59.090 55.000 6.75 0.00 0.00 5.40
33 34 2.806945 TTGGGCAATTCTCCGAGAAT 57.193 45.000 16.56 16.56 46.22 2.40
34 35 2.577606 TTTGGGCAATTCTCCGAGAA 57.422 45.000 13.22 13.22 38.78 2.87
35 36 2.039746 TCTTTTGGGCAATTCTCCGAGA 59.960 45.455 0.00 0.00 0.00 4.04
36 37 2.436417 TCTTTTGGGCAATTCTCCGAG 58.564 47.619 0.00 0.00 0.00 4.63
37 38 2.556622 GTTCTTTTGGGCAATTCTCCGA 59.443 45.455 0.00 0.00 0.00 4.55
38 39 2.558359 AGTTCTTTTGGGCAATTCTCCG 59.442 45.455 0.00 0.00 0.00 4.63
39 40 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
40 41 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
41 42 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
42 43 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
43 44 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
48 49 2.275380 CGGGGCCAGTTCTTTTGGG 61.275 63.158 4.39 0.00 36.19 4.12
49 50 1.228429 TCGGGGCCAGTTCTTTTGG 60.228 57.895 4.39 0.00 38.78 3.28
50 51 0.537371 ACTCGGGGCCAGTTCTTTTG 60.537 55.000 4.39 0.00 0.00 2.44
51 52 0.250770 GACTCGGGGCCAGTTCTTTT 60.251 55.000 4.39 0.00 0.00 2.27
52 53 1.375326 GACTCGGGGCCAGTTCTTT 59.625 57.895 4.39 0.00 0.00 2.52
53 54 2.943978 CGACTCGGGGCCAGTTCTT 61.944 63.158 4.39 0.00 0.00 2.52
54 55 3.382832 CGACTCGGGGCCAGTTCT 61.383 66.667 4.39 0.00 0.00 3.01
66 67 4.732106 CCAATACGGGAGCGACTC 57.268 61.111 0.00 0.00 0.00 3.36
105 106 2.554032 CAAGACGCTTGGAACCTGATTT 59.446 45.455 10.56 0.00 0.00 2.17
106 107 2.154462 CAAGACGCTTGGAACCTGATT 58.846 47.619 10.56 0.00 0.00 2.57
107 108 1.072331 ACAAGACGCTTGGAACCTGAT 59.928 47.619 19.13 0.00 0.00 2.90
228 229 2.386935 CCCCCTTGACTCCCATCCC 61.387 68.421 0.00 0.00 0.00 3.85
981 1031 0.036765 TTGTCCTGCACGGTGGATAC 60.037 55.000 10.60 9.00 34.58 2.24
1288 1439 3.017048 TGTGCTTAATCCCCATCTTGG 57.983 47.619 0.00 0.00 37.25 3.61
1289 1440 3.319972 CCATGTGCTTAATCCCCATCTTG 59.680 47.826 0.00 0.00 0.00 3.02
1315 1466 2.353704 GCCAGGAAAGTATTTTGGGTGC 60.354 50.000 0.00 0.00 39.27 5.01
1316 1467 3.056607 CAGCCAGGAAAGTATTTTGGGTG 60.057 47.826 6.62 6.62 39.27 4.61
1317 1468 3.165071 CAGCCAGGAAAGTATTTTGGGT 58.835 45.455 0.00 0.00 39.27 4.51
1318 1469 3.430453 TCAGCCAGGAAAGTATTTTGGG 58.570 45.455 0.00 0.00 39.27 4.12
1321 1472 6.950619 AGAAATCTCAGCCAGGAAAGTATTTT 59.049 34.615 0.00 0.00 39.27 1.82
1366 1520 6.072112 TCAAAAGTATGTTGTTCCTGCTTC 57.928 37.500 0.00 0.00 34.08 3.86
1386 1540 5.488341 GAGCCCAGTTATAGTTCAGTTCAA 58.512 41.667 0.00 0.00 0.00 2.69
1607 1845 4.719273 TCAATTTGTGGAAAGAAAAGGGGT 59.281 37.500 0.00 0.00 0.00 4.95
1628 1866 8.081633 GGTTGATAATGATGCCGATTTTTATCA 58.918 33.333 0.00 0.00 35.43 2.15
1632 1871 6.219417 TGGTTGATAATGATGCCGATTTTT 57.781 33.333 0.00 0.00 0.00 1.94
1938 2297 0.820891 ACACCTGAACAGCAAGCCAG 60.821 55.000 0.00 0.00 0.00 4.85
2965 3448 7.645340 CCTTTGAAAATATATTTCAGAGCACGG 59.355 37.037 11.08 2.37 38.53 4.94
2966 3449 7.166473 GCCTTTGAAAATATATTTCAGAGCACG 59.834 37.037 11.08 5.43 38.53 5.34
3053 3536 3.531262 ACCGTGCGACAAACTAAAATC 57.469 42.857 0.00 0.00 0.00 2.17
3084 3567 9.860650 TCCTTGCCTTGATAGCTAATATTTAAA 57.139 29.630 0.00 0.00 0.00 1.52
3089 3572 9.051259 TCTTATCCTTGCCTTGATAGCTAATAT 57.949 33.333 0.00 0.00 0.00 1.28
3182 3665 4.701765 AGCATGAAGATGTTACCTAGCTG 58.298 43.478 0.00 0.00 31.50 4.24
3587 4070 7.859377 AGTTGCTTAGAAAAATCATATGCATCG 59.141 33.333 0.19 0.00 31.96 3.84
3817 4300 3.471244 CGAAGCCGAGCCGTAGGAG 62.471 68.421 0.00 0.00 46.40 3.69
4016 4499 2.559998 AACCTGCAAACTGAAACGTG 57.440 45.000 0.00 0.00 0.00 4.49
4119 4602 1.073722 CAAGCAGAAGCCACCCTCA 59.926 57.895 0.00 0.00 43.56 3.86
4620 5103 5.604758 ACAGAGCTATCAACTGAGCAATA 57.395 39.130 6.38 0.00 41.36 1.90
4661 5144 9.167311 GCGATGGAGTCCTAATTCATATATTTT 57.833 33.333 11.33 0.00 0.00 1.82
4856 5356 1.608025 CCAGTAGCACGAACACCACAT 60.608 52.381 0.00 0.00 0.00 3.21
5539 6039 6.149474 ACATCTAGCAAATTAAAGCACTCGTT 59.851 34.615 0.00 0.00 0.00 3.85
5568 6068 3.510388 TCATCTCCTACAACTGAAGCG 57.490 47.619 0.00 0.00 0.00 4.68
5787 6397 3.575256 AGCAAACCAAATCTGCTGAATCA 59.425 39.130 0.00 0.00 44.56 2.57
5848 6458 4.706476 CCCACCACATTGATGTTACATCTT 59.294 41.667 23.48 10.45 39.39 2.40
6174 6785 2.433145 CGAAGGCGCTGAAGAGCA 60.433 61.111 7.64 0.00 46.62 4.26
6245 6856 0.320771 AGACCTGTTACCTTGCTGCG 60.321 55.000 0.00 0.00 0.00 5.18
6993 7608 1.648116 ATGGAAAGGCAGGCAACAAT 58.352 45.000 0.00 0.00 41.41 2.71
7009 7624 3.881688 CTCCTCCAGCATCTTAACAATGG 59.118 47.826 0.00 0.00 0.00 3.16
7025 7640 3.210227 GGTAGTACGGTTAGTCTCCTCC 58.790 54.545 0.00 0.00 0.00 4.30
7041 7656 3.380637 AGAAGCGTGTTATCATCGGTAGT 59.619 43.478 0.00 0.00 34.95 2.73
7140 7755 9.832445 GACTGAAATAATCCAGAATTAGTACCA 57.168 33.333 0.00 0.00 33.38 3.25
7154 7769 4.271291 GCCTCGAACTGGACTGAAATAATC 59.729 45.833 0.00 0.00 0.00 1.75
7265 7880 3.445518 GATGTCGATGAGCCCGCCA 62.446 63.158 0.00 0.00 0.00 5.69
7267 7882 1.301244 ATGATGTCGATGAGCCCGC 60.301 57.895 0.00 0.00 0.00 6.13
7635 8252 8.122330 TCTTTATCATGTGCATTTGTTCGTATC 58.878 33.333 0.00 0.00 0.00 2.24
7963 8779 6.430864 TGAGGACCCAAATTTATGAATGCTA 58.569 36.000 0.00 0.00 0.00 3.49
7997 8813 7.549134 TGGTGATAGCAAAGTACTGTTATTGAG 59.451 37.037 8.83 0.00 0.00 3.02
8148 8964 8.175925 TCATTGTTTGAATCAATGTAGTCCAA 57.824 30.769 21.61 5.09 46.76 3.53
8163 8979 8.046107 TGACCATGAGTGTATATCATTGTTTGA 58.954 33.333 0.00 0.00 34.28 2.69
8309 9129 8.859090 AGTGATCCTGAAATGAAATACACAAAA 58.141 29.630 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.