Multiple sequence alignment - TraesCS7D01G109400

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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 TraesCS7D01G109400 chr7D 100.000 2950 0 0 1 2950 65904121 65901172 0.000000e+00 5448.0
1 TraesCS7D01G109400 chr7D 94.728 607 26 5 287 888 626953328 626953933 0.000000e+00 939.0
2 TraesCS7D01G109400 chr7D 97.667 300 6 1 1 300 214344335 214344037 5.640000e-142 514.0
3 TraesCS7D01G109400 chr7D 97.667 300 6 1 1 300 521897620 521897322 5.640000e-142 514.0
4 TraesCS7D01G109400 chr7D 97.667 300 6 1 1 300 626952304 626952602 5.640000e-142 514.0
5 TraesCS7D01G109400 chr7D 97.333 300 7 1 1 300 208793741 208793443 2.620000e-140 508.0
6 TraesCS7D01G109400 chr7D 83.416 404 40 14 2350 2751 69043548 69043926 1.680000e-92 350.0
7 TraesCS7D01G109400 chr7D 78.240 625 74 26 2153 2750 66346297 66345708 7.830000e-91 344.0
8 TraesCS7D01G109400 chr7D 82.353 408 40 23 2348 2750 66546488 66546108 2.840000e-85 326.0
9 TraesCS7D01G109400 chr7D 79.959 489 59 18 2270 2750 548817205 548816748 1.020000e-84 324.0
10 TraesCS7D01G109400 chr7D 79.600 500 55 29 2270 2751 68909379 68909849 6.140000e-82 315.0
11 TraesCS7D01G109400 chr7D 81.463 410 44 18 2349 2750 83600652 83600267 1.030000e-79 307.0
12 TraesCS7D01G109400 chr7D 79.098 488 61 22 2270 2750 85346865 85347318 6.180000e-77 298.0
13 TraesCS7D01G109400 chr7D 80.292 411 52 10 2348 2751 548811290 548810902 1.730000e-72 283.0
14 TraesCS7D01G109400 chr7D 81.266 379 36 21 889 1246 69041579 69041943 1.040000e-69 274.0
15 TraesCS7D01G109400 chr7D 79.506 405 50 12 2348 2746 85283074 85283451 1.050000e-64 257.0
16 TraesCS7D01G109400 chr7D 80.054 371 50 17 891 1246 548812919 548812558 1.360000e-63 254.0
17 TraesCS7D01G109400 chr7D 81.416 339 35 14 886 1214 68901839 68902159 4.880000e-63 252.0
18 TraesCS7D01G109400 chr7D 86.087 230 27 5 986 1214 66348240 66348015 2.940000e-60 243.0
19 TraesCS7D01G109400 chr7D 85.398 226 24 6 994 1213 66548034 66547812 2.960000e-55 226.0
20 TraesCS7D01G109400 chr7D 78.811 387 39 24 889 1246 66105551 66105179 1.380000e-53 220.0
21 TraesCS7D01G109400 chr7D 87.209 172 19 2 966 1137 548818638 548818470 3.000000e-45 193.0
22 TraesCS7D01G109400 chr7D 75.219 456 65 33 989 1426 41693161 41693586 3.910000e-39 172.0
23 TraesCS7D01G109400 chr7D 74.702 336 63 17 913 1230 82449345 82449014 2.390000e-26 130.0
24 TraesCS7D01G109400 chr7D 76.824 233 50 4 989 1219 73218149 73218379 8.580000e-26 128.0
25 TraesCS7D01G109400 chr7D 74.678 233 52 5 989 1219 73178211 73178438 2.420000e-16 97.1
26 TraesCS7D01G109400 chr7D 97.959 49 1 0 903 951 548818742 548818694 5.240000e-13 86.1
27 TraesCS7D01G109400 chr7D 88.679 53 4 2 2153 2204 548817355 548817304 2.450000e-06 63.9
28 TraesCS7D01G109400 chr7A 95.582 679 20 3 886 1554 70267985 70267307 0.000000e+00 1079.0
29 TraesCS7D01G109400 chr7A 88.342 549 28 18 1613 2151 70267086 70266564 6.940000e-176 627.0
30 TraesCS7D01G109400 chr7A 79.422 588 71 33 964 1548 74741758 74742298 1.290000e-98 370.0
31 TraesCS7D01G109400 chr7A 78.628 627 73 24 2153 2750 70765688 70765094 2.800000e-95 359.0
32 TraesCS7D01G109400 chr7A 80.855 491 41 22 1695 2147 74742446 74742921 1.310000e-88 337.0
33 TraesCS7D01G109400 chr7A 82.266 406 55 7 2351 2751 47050992 47051385 4.710000e-88 335.0
34 TraesCS7D01G109400 chr7A 82.673 404 44 11 2350 2751 74686827 74687206 4.710000e-88 335.0
35 TraesCS7D01G109400 chr7A 82.396 409 37 17 2348 2750 85197327 85196948 1.020000e-84 324.0
36 TraesCS7D01G109400 chr7A 82.178 404 45 12 2350 2750 70734716 70734337 3.670000e-84 322.0
37 TraesCS7D01G109400 chr7A 96.392 194 7 0 2391 2584 70266300 70266107 1.320000e-83 320.0
38 TraesCS7D01G109400 chr7A 81.454 399 44 15 2356 2751 74594186 74594557 1.720000e-77 300.0
39 TraesCS7D01G109400 chr7A 83.183 333 47 2 2420 2751 47021281 47020957 2.220000e-76 296.0
40 TraesCS7D01G109400 chr7A 80.353 397 59 16 886 1272 70767350 70766963 1.730000e-72 283.0
41 TraesCS7D01G109400 chr7A 94.886 176 6 2 2778 2950 70265861 70265686 3.750000e-69 272.0
42 TraesCS7D01G109400 chr7A 80.049 411 47 12 2348 2750 86467956 86468339 3.750000e-69 272.0
43 TraesCS7D01G109400 chr7A 82.090 335 38 17 889 1213 74642510 74642832 1.740000e-67 267.0
44 TraesCS7D01G109400 chr7A 79.899 398 46 14 2361 2750 86424489 86424860 8.110000e-66 261.0
45 TraesCS7D01G109400 chr7A 76.684 579 65 35 2153 2693 634361941 634361395 1.050000e-64 257.0
46 TraesCS7D01G109400 chr7A 89.372 207 11 2 2153 2348 70266505 70266299 1.760000e-62 250.0
47 TraesCS7D01G109400 chr7A 96.622 148 4 1 2153 2299 625755385 625755532 8.170000e-61 244.0
48 TraesCS7D01G109400 chr7A 90.643 171 6 4 1983 2152 625755168 625755329 4.950000e-53 219.0
49 TraesCS7D01G109400 chr7A 77.644 416 52 25 889 1272 70754324 70753918 6.400000e-52 215.0
50 TraesCS7D01G109400 chr7A 95.455 132 6 0 2620 2751 70266100 70265969 8.280000e-51 211.0
51 TraesCS7D01G109400 chr7A 81.091 275 37 9 972 1246 634349306 634349047 3.850000e-49 206.0
52 TraesCS7D01G109400 chr7A 86.628 172 20 2 966 1137 634363195 634363027 1.400000e-43 187.0
53 TraesCS7D01G109400 chr7A 75.676 333 67 10 1626 1954 70897800 70897478 1.420000e-33 154.0
54 TraesCS7D01G109400 chr7A 92.929 99 7 0 2234 2332 74743070 74743168 8.520000e-31 145.0
55 TraesCS7D01G109400 chr7A 77.186 263 43 15 989 1244 78080678 78080426 1.430000e-28 137.0
56 TraesCS7D01G109400 chr7A 95.455 66 3 0 886 951 634363316 634363251 4.020000e-19 106.0
57 TraesCS7D01G109400 chr7A 100.000 37 0 0 2746 2782 70265939 70265903 5.280000e-08 69.4
58 TraesCS7D01G109400 chr3D 95.146 618 24 6 287 899 26668980 26668364 0.000000e+00 970.0
59 TraesCS7D01G109400 chr3D 94.745 609 28 4 287 891 157350174 157349566 0.000000e+00 944.0
60 TraesCS7D01G109400 chr3D 97.667 300 6 1 1 300 26670013 26669715 5.640000e-142 514.0
61 TraesCS7D01G109400 chr3D 85.185 270 10 8 1901 2151 28389222 28389480 1.760000e-62 250.0
62 TraesCS7D01G109400 chr3D 95.238 147 7 0 2153 2299 28389541 28389687 1.770000e-57 233.0
63 TraesCS7D01G109400 chr3D 87.179 78 8 2 2153 2229 208625676 208625600 1.460000e-13 87.9
64 TraesCS7D01G109400 chr5D 95.545 606 22 4 287 890 459963506 459962904 0.000000e+00 965.0
65 TraesCS7D01G109400 chr5D 95.545 606 21 5 286 888 545959019 545959621 0.000000e+00 965.0
66 TraesCS7D01G109400 chr5D 95.082 610 23 7 287 892 344410671 344411277 0.000000e+00 953.0
67 TraesCS7D01G109400 chr5D 95.041 605 25 5 287 888 277478758 277478156 0.000000e+00 946.0
68 TraesCS7D01G109400 chr4D 95.537 605 23 4 287 888 508428284 508428887 0.000000e+00 965.0
69 TraesCS7D01G109400 chr4D 95.364 604 26 2 287 888 450521812 450522415 0.000000e+00 959.0
70 TraesCS7D01G109400 chr4D 98.000 300 5 1 1 300 26141588 26141886 1.210000e-143 520.0
71 TraesCS7D01G109400 chr4D 97.333 300 7 1 1 300 8007407 8007109 2.620000e-140 508.0
72 TraesCS7D01G109400 chr7B 78.596 1168 138 53 1027 2156 10916956 10918049 0.000000e+00 669.0
73 TraesCS7D01G109400 chr7B 97.333 300 7 1 1 300 668383207 668382909 2.620000e-140 508.0
74 TraesCS7D01G109400 chr7B 82.673 404 44 11 2350 2751 10895277 10895656 4.710000e-88 335.0
75 TraesCS7D01G109400 chr7B 81.265 411 45 18 2348 2750 32896334 32895948 1.330000e-78 303.0
76 TraesCS7D01G109400 chr7B 81.283 374 43 17 886 1246 10880976 10881335 8.050000e-71 278.0
77 TraesCS7D01G109400 chr7B 80.097 412 46 15 2348 2750 34890672 34891056 1.040000e-69 274.0
78 TraesCS7D01G109400 chr7B 79.412 408 55 15 2348 2750 592425833 592425450 8.110000e-66 261.0
79 TraesCS7D01G109400 chr7B 81.791 335 37 13 886 1214 10067563 10067879 2.920000e-65 259.0
80 TraesCS7D01G109400 chr7B 81.571 331 44 12 886 1209 10892017 10892337 1.050000e-64 257.0
81 TraesCS7D01G109400 chr7B 75.666 563 82 35 994 1533 34889115 34889645 2.290000e-56 230.0
82 TraesCS7D01G109400 chr7B 77.228 404 47 23 2350 2751 10883032 10883392 8.340000e-46 195.0
83 TraesCS7D01G109400 chr7B 88.125 160 19 0 2423 2582 10918510 10918669 1.080000e-44 191.0
84 TraesCS7D01G109400 chr7B 76.762 383 53 22 904 1266 10639328 10639694 6.490000e-42 182.0
85 TraesCS7D01G109400 chr7B 80.702 228 34 6 989 1214 10946579 10946798 5.060000e-38 169.0
86 TraesCS7D01G109400 chr7B 75.964 337 56 16 913 1230 30766223 30765893 1.830000e-32 150.0
87 TraesCS7D01G109400 chr7B 78.541 233 40 8 989 1219 16524397 16524621 8.520000e-31 145.0
88 TraesCS7D01G109400 chr7B 75.281 356 57 17 889 1213 8448695 8448340 1.100000e-29 141.0
89 TraesCS7D01G109400 chr7B 75.542 323 60 11 913 1219 29830057 29829738 1.100000e-29 141.0
90 TraesCS7D01G109400 chr7B 74.438 356 74 12 1626 1976 7731638 7731295 1.430000e-28 137.0
91 TraesCS7D01G109400 chr7B 78.112 233 40 6 989 1214 674144316 674144544 1.430000e-28 137.0
92 TraesCS7D01G109400 chr7B 75.627 279 61 5 942 1219 16732305 16732577 6.630000e-27 132.0
93 TraesCS7D01G109400 chr7B 84.173 139 8 5 1983 2121 10918234 10918358 3.990000e-24 122.0
94 TraesCS7D01G109400 chr7B 90.217 92 9 0 2422 2513 10062658 10062749 1.440000e-23 121.0
95 TraesCS7D01G109400 chr7B 72.470 494 95 27 997 1477 15935427 15935892 1.440000e-23 121.0
96 TraesCS7D01G109400 chr7B 89.286 84 6 2 889 969 10558914 10558997 5.200000e-18 102.0
97 TraesCS7D01G109400 chr7B 97.561 41 1 0 2153 2193 10918105 10918145 1.470000e-08 71.3
98 TraesCS7D01G109400 chr7B 87.273 55 2 4 916 969 16950899 16950949 1.140000e-04 58.4
99 TraesCS7D01G109400 chr6D 97.667 300 6 1 1 300 38872322 38872024 5.640000e-142 514.0
100 TraesCS7D01G109400 chr1D 87.696 382 33 5 1569 1950 398992771 398992404 1.620000e-117 433.0
101 TraesCS7D01G109400 chr1A 88.064 377 30 5 1574 1950 495745065 495744704 1.620000e-117 433.0
102 TraesCS7D01G109400 chr1A 90.476 147 5 6 1983 2129 42201494 42201357 5.020000e-43 185.0
103 TraesCS7D01G109400 chrUn 81.016 374 44 17 886 1246 305654346 305654705 3.750000e-69 272.0
104 TraesCS7D01G109400 chrUn 82.463 268 32 8 986 1246 308151873 308151614 1.380000e-53 220.0
105 TraesCS7D01G109400 chrUn 82.463 268 32 8 986 1246 308155981 308155722 1.380000e-53 220.0
106 TraesCS7D01G109400 chrUn 77.228 404 47 23 2350 2751 305656402 305656762 8.340000e-46 195.0
107 TraesCS7D01G109400 chrUn 77.228 404 47 23 2350 2751 308149917 308149557 8.340000e-46 195.0
108 TraesCS7D01G109400 chrUn 77.228 404 47 23 2350 2751 308154025 308153665 8.340000e-46 195.0
109 TraesCS7D01G109400 chr4A 95.918 147 6 0 2153 2299 49209970 49210116 3.800000e-59 239.0
110 TraesCS7D01G109400 chr4A 91.228 171 5 4 1983 2152 49209751 49209912 1.060000e-54 224.0
111 TraesCS7D01G109400 chr4A 74.670 454 73 28 988 1426 648880733 648881159 2.350000e-36 163.0
112 TraesCS7D01G109400 chr4A 95.238 84 4 0 2328 2411 49210103 49210186 1.840000e-27 134.0
113 TraesCS7D01G109400 chr4A 87.273 55 7 0 2170 2224 656743549 656743603 2.450000e-06 63.9
114 TraesCS7D01G109400 chr3A 90.476 147 5 2 1983 2129 662402326 662402463 5.020000e-43 185.0
115 TraesCS7D01G109400 chr2A 90.476 147 5 2 1983 2129 39318507 39318370 5.020000e-43 185.0
116 TraesCS7D01G109400 chr2A 79.817 218 27 13 889 1090 51388523 51388307 3.060000e-30 143.0
117 TraesCS7D01G109400 chr2A 92.727 55 4 0 2170 2224 51387794 51387740 2.440000e-11 80.5
118 TraesCS7D01G109400 chr6B 90.345 145 5 5 1983 2127 658277180 658277315 6.490000e-42 182.0
119 TraesCS7D01G109400 chr6B 75.749 367 62 16 2170 2516 360921984 360921625 3.040000e-35 159.0
120 TraesCS7D01G109400 chr2D 71.973 603 97 44 923 1477 33374207 33373629 8.640000e-21 111.0


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 TraesCS7D01G109400 chr7D 65901172 65904121 2949 True 5448.000000 5448 100.000000 1 2950 1 chr7D.!!$R1 2949
1 TraesCS7D01G109400 chr7D 626952304 626953933 1629 False 726.500000 939 96.197500 1 888 2 chr7D.!!$F9 887
2 TraesCS7D01G109400 chr7D 69041579 69043926 2347 False 312.000000 350 82.341000 889 2751 2 chr7D.!!$F8 1862
3 TraesCS7D01G109400 chr7D 66345708 66348240 2532 True 293.500000 344 82.163500 986 2750 2 chr7D.!!$R8 1764
4 TraesCS7D01G109400 chr7D 66546108 66548034 1926 True 276.000000 326 83.875500 994 2750 2 chr7D.!!$R9 1756
5 TraesCS7D01G109400 chr7D 548810902 548818742 7840 True 200.666667 324 85.692000 891 2751 6 chr7D.!!$R10 1860
6 TraesCS7D01G109400 chr7A 70265686 70267985 2299 True 404.057143 1079 94.289857 886 2950 7 chr7A.!!$R8 2064
7 TraesCS7D01G109400 chr7A 70765094 70767350 2256 True 321.000000 359 79.490500 886 2750 2 chr7A.!!$R9 1864
8 TraesCS7D01G109400 chr7A 74741758 74743168 1410 False 284.000000 370 84.402000 964 2332 3 chr7A.!!$F7 1368
9 TraesCS7D01G109400 chr3D 157349566 157350174 608 True 944.000000 944 94.745000 287 891 1 chr3D.!!$R1 604
10 TraesCS7D01G109400 chr3D 26668364 26670013 1649 True 742.000000 970 96.406500 1 899 2 chr3D.!!$R3 898
11 TraesCS7D01G109400 chr5D 459962904 459963506 602 True 965.000000 965 95.545000 287 890 1 chr5D.!!$R2 603
12 TraesCS7D01G109400 chr5D 545959019 545959621 602 False 965.000000 965 95.545000 286 888 1 chr5D.!!$F2 602
13 TraesCS7D01G109400 chr5D 344410671 344411277 606 False 953.000000 953 95.082000 287 892 1 chr5D.!!$F1 605
14 TraesCS7D01G109400 chr5D 277478156 277478758 602 True 946.000000 946 95.041000 287 888 1 chr5D.!!$R1 601
15 TraesCS7D01G109400 chr4D 508428284 508428887 603 False 965.000000 965 95.537000 287 888 1 chr4D.!!$F3 601
16 TraesCS7D01G109400 chr4D 450521812 450522415 603 False 959.000000 959 95.364000 287 888 1 chr4D.!!$F2 601
17 TraesCS7D01G109400 chr7B 10892017 10895656 3639 False 296.000000 335 82.122000 886 2751 2 chr7B.!!$F12 1865
18 TraesCS7D01G109400 chr7B 10916956 10918669 1713 False 263.325000 669 87.113750 1027 2582 4 chr7B.!!$F13 1555
19 TraesCS7D01G109400 chr7B 34889115 34891056 1941 False 252.000000 274 77.881500 994 2750 2 chr7B.!!$F14 1756
20 TraesCS7D01G109400 chr7B 10880976 10883392 2416 False 236.500000 278 79.255500 886 2751 2 chr7B.!!$F11 1865
21 TraesCS7D01G109400 chrUn 305654346 305656762 2416 False 233.500000 272 79.122000 886 2751 2 chrUn.!!$F1 1865
22 TraesCS7D01G109400 chrUn 308149557 308155981 6424 True 207.500000 220 79.845500 986 2751 4 chrUn.!!$R1 1765

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
373 1121 0.107945 ATGCTCTTCTTCCTGGACGC 60.108 55.0 0.00 0.00 0.00 5.19 F
1154 1967 0.590732 CACGTGTACGATCCCTACGC 60.591 60.0 11.79 3.48 43.02 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 4105 0.043637 ATACGGACCTCCCCCTGAAA 59.956 55.0 0.0 0.0 0.00 2.69 R
2516 15935 0.178873 TTGTAGGGGTCCTGGCTCTT 60.179 55.0 0.0 0.0 34.61 2.85 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
85 86 1.068895 CCTGCTCGCTCTCAATGATCT 59.931 52.381 0.00 0.00 0.00 2.75
123 124 2.848694 ACAACAGGTCATGATCTCCCAT 59.151 45.455 5.21 0.00 0.00 4.00
373 1121 0.107945 ATGCTCTTCTTCCTGGACGC 60.108 55.000 0.00 0.00 0.00 5.19
492 1242 3.131478 GTGCACCCGCCGCTAAAT 61.131 61.111 5.22 0.00 37.32 1.40
627 1380 1.615116 CGGGATATACCTAGTGGCGGA 60.615 57.143 1.51 0.00 38.98 5.54
662 1415 3.387947 GGAGGCGAGTCGGGGAAA 61.388 66.667 15.52 0.00 0.00 3.13
807 1564 1.206831 GCTTTTCGTCGTCTTGGGC 59.793 57.895 0.00 0.00 0.00 5.36
824 1582 4.764336 CGCGCGACTGGACCGTTA 62.764 66.667 28.94 0.00 0.00 3.18
858 1616 0.887387 CGAAAAAGTCGCCTTGGGGA 60.887 55.000 2.10 2.10 44.14 4.81
1154 1967 0.590732 CACGTGTACGATCCCTACGC 60.591 60.000 11.79 3.48 43.02 4.42
1275 3309 1.451387 CAACCACTACCATCCGGGC 60.451 63.158 0.00 0.00 42.05 6.13
1402 3452 0.683504 GAGGTACCTCCGCTGGAAGA 60.684 60.000 28.87 0.00 41.99 2.87
1551 3663 3.056313 GCCATGCCCGCTTCTTGAC 62.056 63.158 0.00 0.00 0.00 3.18
1556 3756 0.881118 TGCCCGCTTCTTGACATTTC 59.119 50.000 0.00 0.00 0.00 2.17
1559 3759 1.135972 CCCGCTTCTTGACATTTCACG 60.136 52.381 0.00 0.00 0.00 4.35
1608 3935 6.974048 TCTTGATGGCATTTTCGTATTTGATG 59.026 34.615 0.00 0.00 0.00 3.07
1609 3936 6.448207 TGATGGCATTTTCGTATTTGATGA 57.552 33.333 0.00 0.00 0.00 2.92
1610 3937 7.041635 TGATGGCATTTTCGTATTTGATGAT 57.958 32.000 0.00 0.00 0.00 2.45
1611 3938 7.490840 TGATGGCATTTTCGTATTTGATGATT 58.509 30.769 0.00 0.00 0.00 2.57
1645 3972 3.433343 TGGCATCATGATGGTTCTTTGT 58.567 40.909 31.62 0.00 39.16 2.83
1683 4022 2.203938 TCCCCGGAAGCCTGACTT 60.204 61.111 0.73 0.00 42.98 3.01
1684 4023 2.045926 CCCCGGAAGCCTGACTTG 60.046 66.667 0.73 0.00 39.29 3.16
1685 4024 2.045926 CCCGGAAGCCTGACTTGG 60.046 66.667 0.73 0.00 39.29 3.61
1686 4025 2.592993 CCCGGAAGCCTGACTTGGA 61.593 63.158 0.73 0.00 39.29 3.53
1687 4026 1.376037 CCGGAAGCCTGACTTGGAC 60.376 63.158 0.00 0.00 39.29 4.02
1688 4027 1.674057 CGGAAGCCTGACTTGGACT 59.326 57.895 0.00 0.00 39.29 3.85
1838 4231 0.949105 GTGTCGCCAACCTCGTCATT 60.949 55.000 0.00 0.00 0.00 2.57
1928 4321 1.081708 CCACATCGTCGTCGTCACA 60.082 57.895 1.33 0.00 38.33 3.58
1955 4348 1.541310 CGCCTGGTGAGTGACCCTAA 61.541 60.000 0.00 0.00 45.45 2.69
1958 4351 1.978580 CCTGGTGAGTGACCCTAAACT 59.021 52.381 0.00 0.00 45.45 2.66
1959 4352 2.028020 CCTGGTGAGTGACCCTAAACTC 60.028 54.545 0.00 0.00 45.45 3.01
1960 4353 1.975680 TGGTGAGTGACCCTAAACTCC 59.024 52.381 0.00 0.00 45.45 3.85
1991 4412 8.367156 ACTCTTCTCCTCATATTTGCTAATCTC 58.633 37.037 0.00 0.00 0.00 2.75
2050 4533 9.747293 GTACTAGTCTGAAGAACAGTTTACTTT 57.253 33.333 0.00 0.00 45.86 2.66
2052 4535 9.747293 ACTAGTCTGAAGAACAGTTTACTTTAC 57.253 33.333 0.00 0.00 45.86 2.01
2054 4537 8.649973 AGTCTGAAGAACAGTTTACTTTACTG 57.350 34.615 0.00 0.00 46.56 2.74
2055 4538 8.475639 AGTCTGAAGAACAGTTTACTTTACTGA 58.524 33.333 9.74 0.00 44.52 3.41
2056 4539 9.095065 GTCTGAAGAACAGTTTACTTTACTGAA 57.905 33.333 9.74 0.00 44.52 3.02
2057 4540 9.661563 TCTGAAGAACAGTTTACTTTACTGAAA 57.338 29.630 9.74 0.00 44.52 2.69
2063 4546 9.582223 GAACAGTTTACTTTACTGAAATTCTCG 57.418 33.333 9.74 0.00 44.52 4.04
2064 4547 7.573627 ACAGTTTACTTTACTGAAATTCTCGC 58.426 34.615 9.74 0.00 44.52 5.03
2065 4548 7.441458 ACAGTTTACTTTACTGAAATTCTCGCT 59.559 33.333 9.74 0.00 44.52 4.93
2151 15064 8.758633 ACATCAGTAAGAGTTGTTGTACATAC 57.241 34.615 0.00 0.00 0.00 2.39
2162 15184 9.494479 GAGTTGTTGTACATACATCATTTCATG 57.506 33.333 0.00 0.00 36.24 3.07
2166 15188 8.882736 TGTTGTACATACATCATTTCATGAGTC 58.117 33.333 0.00 0.00 43.53 3.36
2354 15443 6.377327 ACACTGTTTTGAACCTCATTACAG 57.623 37.500 13.09 13.09 40.72 2.74
2380 15469 3.138884 TGAGGTTTTGCACATCAGCTA 57.861 42.857 0.00 0.00 41.31 3.32
2385 15796 4.397417 AGGTTTTGCACATCAGCTATCTTC 59.603 41.667 0.00 0.00 34.99 2.87
2386 15797 4.439289 GGTTTTGCACATCAGCTATCTTCC 60.439 45.833 0.00 0.00 34.99 3.46
2413 15825 6.349243 TCTTCTCATTAACCCGTTTCTGTA 57.651 37.500 0.00 0.00 0.00 2.74
2516 15935 2.294512 CGATGCCTAGTACAGAGATGCA 59.705 50.000 0.00 0.00 0.00 3.96
2564 16013 3.405831 TGCTGTTCACATCTTCAGAAGG 58.594 45.455 10.42 0.00 0.00 3.46
2589 16038 1.626654 CGCCTCGGACACAATCACAC 61.627 60.000 0.00 0.00 0.00 3.82
2590 16039 0.602638 GCCTCGGACACAATCACACA 60.603 55.000 0.00 0.00 0.00 3.72
2591 16040 1.877637 CCTCGGACACAATCACACAA 58.122 50.000 0.00 0.00 0.00 3.33
2592 16041 1.531149 CCTCGGACACAATCACACAAC 59.469 52.381 0.00 0.00 0.00 3.32
2593 16042 1.192312 CTCGGACACAATCACACAACG 59.808 52.381 0.00 0.00 0.00 4.10
2594 16043 1.202428 TCGGACACAATCACACAACGA 60.202 47.619 0.00 0.00 0.00 3.85
2595 16044 1.070843 CGGACACAATCACACAACGAC 60.071 52.381 0.00 0.00 0.00 4.34
2596 16045 1.937223 GGACACAATCACACAACGACA 59.063 47.619 0.00 0.00 0.00 4.35
2598 16047 3.544651 GACACAATCACACAACGACATG 58.455 45.455 0.00 0.00 0.00 3.21
2605 16054 0.681733 ACACAACGACATGAGAGCCT 59.318 50.000 0.00 0.00 0.00 4.58
2615 16064 4.187694 GACATGAGAGCCTAGTTCCTTTG 58.812 47.826 0.00 0.00 0.00 2.77
2729 16188 4.433186 TTGCCATCACGGTTCTAAAATG 57.567 40.909 0.00 0.00 36.97 2.32
2810 16350 1.321474 ACATGGTTCCTGCTGTGTTG 58.679 50.000 0.00 0.00 0.00 3.33
2928 16471 5.684704 AGATCAAAGTTCTGAACAAGGTGA 58.315 37.500 21.50 17.04 0.00 4.02
2937 16480 4.072131 TCTGAACAAGGTGAGGTTAATGC 58.928 43.478 0.00 0.00 0.00 3.56
2941 16484 0.679960 AAGGTGAGGTTAATGCGCCC 60.680 55.000 4.18 0.00 32.71 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 2.012673 GGAGATCATGACCTGTTGTGC 58.987 52.381 0.00 0.00 0.00 4.57
105 106 5.370584 TCAAATATGGGAGATCATGACCTGT 59.629 40.000 0.00 0.00 0.00 4.00
662 1415 6.265577 CGTCAGGTGAAAAGTCAAGATTTTT 58.734 36.000 3.38 3.38 34.87 1.94
807 1564 4.764336 TAACGGTCCAGTCGCGCG 62.764 66.667 26.76 26.76 0.00 6.86
818 1575 1.694955 CGCCGGCGTAAAATAACGGT 61.695 55.000 39.71 0.00 45.85 4.83
880 1639 1.467734 GAGCTGTTGGTTGAGAGCATG 59.532 52.381 0.00 0.00 38.32 4.06
1275 3309 4.210331 CCTCCCAAATAATCTCCACCAAG 58.790 47.826 0.00 0.00 0.00 3.61
1402 3452 2.742372 GACGCTGACGCCATTGGT 60.742 61.111 4.26 0.00 45.53 3.67
1551 3663 1.433064 CAATCCCCGCCGTGAAATG 59.567 57.895 0.00 0.00 0.00 2.32
1608 3935 2.923121 TGCCAGCCAGTAGATCAAATC 58.077 47.619 0.00 0.00 0.00 2.17
1609 3936 3.117776 TGATGCCAGCCAGTAGATCAAAT 60.118 43.478 0.00 0.00 0.00 2.32
1610 3937 2.239402 TGATGCCAGCCAGTAGATCAAA 59.761 45.455 0.00 0.00 0.00 2.69
1611 3938 1.839354 TGATGCCAGCCAGTAGATCAA 59.161 47.619 0.00 0.00 0.00 2.57
1645 3972 1.372683 GGGAGCTGCAAGTGAGTCA 59.627 57.895 7.79 0.00 35.30 3.41
1683 4022 0.601558 GACCGCAACAGTCTAGTCCA 59.398 55.000 0.00 0.00 0.00 4.02
1684 4023 0.456312 CGACCGCAACAGTCTAGTCC 60.456 60.000 0.00 0.00 31.83 3.85
1685 4024 1.071567 GCGACCGCAACAGTCTAGTC 61.072 60.000 9.73 0.00 41.49 2.59
1686 4025 1.080705 GCGACCGCAACAGTCTAGT 60.081 57.895 9.73 0.00 41.49 2.57
1687 4026 2.152699 CGCGACCGCAACAGTCTAG 61.153 63.158 14.91 0.00 42.06 2.43
1688 4027 2.126618 CGCGACCGCAACAGTCTA 60.127 61.111 14.91 0.00 42.06 2.59
1766 4105 0.043637 ATACGGACCTCCCCCTGAAA 59.956 55.000 0.00 0.00 0.00 2.69
1838 4231 0.888736 CATCACGTGTGGGGAAGCAA 60.889 55.000 16.51 0.00 0.00 3.91
1903 4296 0.109272 GACGACGATGTGGAAGAGCA 60.109 55.000 0.00 0.00 0.00 4.26
1947 4340 3.596956 AGAGTAGGAGGAGTTTAGGGTCA 59.403 47.826 0.00 0.00 0.00 4.02
1955 4348 3.594232 TGAGGAGAAGAGTAGGAGGAGTT 59.406 47.826 0.00 0.00 0.00 3.01
1958 4351 6.538209 AATATGAGGAGAAGAGTAGGAGGA 57.462 41.667 0.00 0.00 0.00 3.71
1959 4352 6.518200 GCAAATATGAGGAGAAGAGTAGGAGG 60.518 46.154 0.00 0.00 0.00 4.30
1960 4353 6.267471 AGCAAATATGAGGAGAAGAGTAGGAG 59.733 42.308 0.00 0.00 0.00 3.69
1991 4412 4.853924 ACACTATTTTCCAAGCACAAGG 57.146 40.909 0.00 0.00 0.00 3.61
2050 4533 7.489160 TGATTTAGCTAGCGAGAATTTCAGTA 58.511 34.615 9.55 0.00 0.00 2.74
2052 4535 6.834959 TGATTTAGCTAGCGAGAATTTCAG 57.165 37.500 9.55 0.00 0.00 3.02
2054 4537 9.163903 GAAAATGATTTAGCTAGCGAGAATTTC 57.836 33.333 9.55 10.00 0.00 2.17
2055 4538 8.677300 TGAAAATGATTTAGCTAGCGAGAATTT 58.323 29.630 9.55 9.24 0.00 1.82
2056 4539 8.213518 TGAAAATGATTTAGCTAGCGAGAATT 57.786 30.769 9.55 3.57 0.00 2.17
2057 4540 7.497249 ACTGAAAATGATTTAGCTAGCGAGAAT 59.503 33.333 9.55 10.67 0.00 2.40
2058 4541 6.818644 ACTGAAAATGATTTAGCTAGCGAGAA 59.181 34.615 9.55 6.01 0.00 2.87
2061 4544 6.985188 AACTGAAAATGATTTAGCTAGCGA 57.015 33.333 9.55 0.00 0.00 4.93
2062 4545 7.224753 TCCTAACTGAAAATGATTTAGCTAGCG 59.775 37.037 9.55 0.00 0.00 4.26
2063 4546 8.338986 GTCCTAACTGAAAATGATTTAGCTAGC 58.661 37.037 6.62 6.62 0.00 3.42
2064 4547 9.383519 TGTCCTAACTGAAAATGATTTAGCTAG 57.616 33.333 0.00 0.00 0.00 3.42
2065 4548 9.905713 ATGTCCTAACTGAAAATGATTTAGCTA 57.094 29.630 0.00 0.00 0.00 3.32
2122 15029 8.080417 TGTACAACAACTCTTACTGATGTCTAC 58.920 37.037 0.00 0.00 31.81 2.59
2354 15443 4.180057 TGATGTGCAAAACCTCAAAACAC 58.820 39.130 0.00 0.00 0.00 3.32
2380 15469 6.463614 CGGGTTAATGAGAAGATCAGGAAGAT 60.464 42.308 0.00 0.00 42.53 2.40
2385 15796 4.408182 ACGGGTTAATGAGAAGATCAGG 57.592 45.455 0.00 0.00 42.53 3.86
2386 15797 6.036517 CAGAAACGGGTTAATGAGAAGATCAG 59.963 42.308 0.00 0.00 42.53 2.90
2413 15825 3.268330 GCATCATGTGTCACAGACAGAT 58.732 45.455 12.03 9.02 45.31 2.90
2516 15935 0.178873 TTGTAGGGGTCCTGGCTCTT 60.179 55.000 0.00 0.00 34.61 2.85
2585 16034 0.792640 GGCTCTCATGTCGTTGTGTG 59.207 55.000 0.00 0.00 0.00 3.82
2589 16038 2.949451 ACTAGGCTCTCATGTCGTTG 57.051 50.000 0.00 0.00 0.00 4.10
2590 16039 2.166664 GGAACTAGGCTCTCATGTCGTT 59.833 50.000 0.00 0.00 0.00 3.85
2591 16040 1.751924 GGAACTAGGCTCTCATGTCGT 59.248 52.381 0.00 0.00 0.00 4.34
2592 16041 2.028130 AGGAACTAGGCTCTCATGTCG 58.972 52.381 0.00 0.00 36.02 4.35
2593 16042 4.187694 CAAAGGAACTAGGCTCTCATGTC 58.812 47.826 0.00 0.00 38.49 3.06
2594 16043 3.054802 CCAAAGGAACTAGGCTCTCATGT 60.055 47.826 0.00 0.00 38.49 3.21
2595 16044 3.054802 ACCAAAGGAACTAGGCTCTCATG 60.055 47.826 0.00 0.00 38.49 3.07
2596 16045 3.185455 ACCAAAGGAACTAGGCTCTCAT 58.815 45.455 0.00 0.00 38.49 2.90
2598 16047 3.008049 TCAACCAAAGGAACTAGGCTCTC 59.992 47.826 0.00 0.00 38.49 3.20
2605 16054 5.491078 ACCCATATCTCAACCAAAGGAACTA 59.509 40.000 0.00 0.00 38.49 2.24
2615 16064 4.503714 TTCCTGAACCCATATCTCAACC 57.496 45.455 0.00 0.00 0.00 3.77
2729 16188 3.245990 GCCATTGTTCAAACAGTTTCAGC 59.754 43.478 0.00 0.00 40.50 4.26
2810 16350 3.930634 AAGAGAAATGCAGCAAGAACC 57.069 42.857 0.00 0.00 0.00 3.62
2848 16391 8.801882 TGGACTGAAACTTTAATCGGAATAAT 57.198 30.769 0.00 0.00 0.00 1.28
2856 16399 6.372659 TCTGCTGATGGACTGAAACTTTAATC 59.627 38.462 0.00 0.00 0.00 1.75
2862 16405 3.777106 TTCTGCTGATGGACTGAAACT 57.223 42.857 0.00 0.00 0.00 2.66
2928 16471 2.124860 GTCCGGGCGCATTAACCT 60.125 61.111 10.83 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.